# 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/Methanosaeta_harundinacea_6Ac_uid81199/all.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/Methanosaeta_harundinacea_6Ac_uid81199/all.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_harundinacea_6Ac_uid81199/all.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|386003072|ref|YP_005064092.1|  [L=37]
Description: hypothetical protein Mhar_2397 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.1   0.0        0.1   12.5   0.0    1.2  1  LRR_3     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_3  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-06       0.1       2      18 ..       3      19 ..       3      19 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-06
                             LRR_3  2 LVeLnmpySkLeKLWEG 18
                                      L +Lnmp S +++  +G
  gi|386003072|ref|YP_005064092.1|  3 LLHLNMPDSHITTFEKG 19
                                      668********998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.32s 00:00:00.70 Elapsed: 00:00:00.49
# Mc/sec: 228.81
//
Query:       gi|386003073|ref|YP_005064093.1|  [L=46]
Description: hypothetical protein Mhar_2398 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.46
# Mc/sec: 298.70
//
Query:       gi|386003074|ref|YP_005064094.1|  [L=56]
Description: hypothetical protein Mhar_2399 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.1   0.3     0.0048   16.7   0.3    1.2  1  ZZ        Zinc finger, ZZ type


Domain annotation for each model (and alignments):
>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   2.7e-07    0.0048      19      38 ..       4      24 ..       1      28 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-07
                                      EEEESSSSS-EE-HHHHHH.. CS
                                ZZ 19 RyhclrcsdYDLCqsCfst.h 38
                                       y++ r  +YD C++C s+ +
  gi|386003074|ref|YP_005064094.1|  4 SYKSKRRYEYDVCFRCTSEqR 24
                                      599*************99954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 321.85
//
Query:       gi|386003075|ref|YP_005064095.1|  [L=48]
Description: hypothetical protein Mhar_2400 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.47
# Mc/sec: 309.46
//
Query:       gi|386003076|ref|YP_005064096.1|  [L=1124]
Description: hypothetical protein Mhar_2401 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00085   19.7   0.0     0.0025   18.2   0.0    1.7  1  Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal


Domain annotation for each model (and alignments):
>> Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.4e-07    0.0025      46     153 ..      88     200 ..      49     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-07
                          Prim-Pol  46 ranvglatg....psglvvlDvDgke.........agaealarLareeg....plPetvtvttgstgggrhlyfraP 105
                                         n+g+  g     +gl  lD D+               +++    ++g    p+Pe + ++  s   grhl+   P
  gi|386003076|ref|YP_005064096.1|  88 GGNYGIFNGtgpnGAGLATLDADNLPrlaelvdlsLLPPTME-AG-RRGedgePIPERRHFHYLSDLEGRHLLRD-P 161
                                       449999988888888999******985555444442223333.11.12245678888777888888888888877.8 PP

                          Prim-Pol 106 dglalpnsagklapgldlrgeg.gyvvappsvhetgraYrwledpreia 153
                                       +       +g+  +  dlrg+g  +vv p+s h++g  +++le+ r++a
  gi|386003076|ref|YP_005064096.1| 162 E-------TGEVLG--DLRGTGgFQVVGPGSLHPSGAVVEVLEE-RPLA 200
                                       7.......556655..******4456****************88.7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 7877.05
//
Query:       gi|386003077|ref|YP_005064097.1|  [L=54]
Description: hypothetical protein Mhar_2402 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 388.64
//
Query:       gi|386003078|ref|YP_005064098.1|  [L=57]
Description: hypothetical protein Mhar_2403 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 364.05
//
Query:       gi|386003079|ref|YP_005064099.1|  [L=48]
Description: hypothetical protein Mhar_2404 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 326.63
//
Query:       gi|386003080|ref|YP_005064100.1|  [L=63]
Description: hypothetical protein Mhar_2405 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 405.69
//
Query:       gi|386003081|ref|YP_005064101.1|  [L=39]
Description: hypothetical protein Mhar_2406 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 243.89
//
Query:       gi|386003082|ref|YP_005064102.1|  [L=170]
Description: hypothetical protein Mhar_2407 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-06   25.8   0.1    6.9e-06   25.8   0.1    2.4  3  RHH_1           Ribbon-helix-helix protein, copG family
    0.00076   19.3   0.0     0.0018   18.0   0.0    1.7  1  Arc             Arc-like DNA binding domain
     0.0008   19.3   0.0     0.0014   18.5   0.0    1.4  1  RHH_3           Ribbon-helix-helix domain
      0.006   16.4   0.0      0.012   15.5   0.0    1.5  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
     0.0064   16.5   0.0       0.11   12.6   0.0    2.3  2  HTH_29          Winged helix-turn helix
  ------ inclusion threshold ------
      0.018   14.8   0.1       0.15   11.9   0.1    2.3  2  HTH_38          Helix-turn-helix domain
      0.039   14.4   0.2        2.5    8.6   0.0    3.0  3  HTH_40          Helix-turn-helix domain
       0.04   13.3   0.0        0.2   11.1   0.0    2.1  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.047   14.2   1.3       0.38   11.3   0.0    2.8  3  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
       0.11   12.2   0.0       0.23   11.2   0.0    1.5  1  DUF2510         Protein of unknown function (DUF2510)
       0.22   11.4   3.3       0.52   10.2   0.1    3.0  3  HTH_23          Homeodomain-like domain
        1.9    9.0   5.7         14    6.2   0.2    3.5  4  RuvA_C          RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   4.6e-09   6.9e-06       3      36 ..       8      41 ..       8      43 .. 0.96
   2 ?   -2.2   0.2       3.1   4.6e+03      12      21 ..      64      73 ..      63      76 .. 0.59
   3 ?   -0.8   0.1       1.1   1.7e+03      12      31 ..     128     147 ..     119     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.6e-09
                                      EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlrey 36
                                      ++rl+eel+ +L+  a+++gr r el+R+Al++y
  gi|386003082|ref|YP_005064102.1|  8 NVRLPEELIQTLQDVAKETGRDRAELVRDALKRY 41
                                      59*****************************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
                                      HHHHHHHHHH CS
                             RHH_1 12 erLdelarrr 21
                                      e L++++rr+
  gi|386003082|ref|YP_005064102.1| 64 EDLEKRVRRL 73
                                      4466666665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHTSSHHHHHHH CS
                             RHH_1  12 erLdelarrrgrSrSelIRe 31 
                                       e++ ++  +++r+r  + R+
  gi|386003082|ref|YP_005064102.1| 128 EKIKKIWQAGERNRQNIARQ 147
                                       77888888888998887776 PP

>> Arc  Arc-like DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0018       6      28 ..       6      28 ..       1      40 [. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                      EEEEECEHHHHHHHHHHHHHTTS CS
                               Arc  6 kFnlRlPeevrekvkevAeengR 28
                                      ++n+RlPee+   ++ vA+e gR
  gi|386003082|ref|YP_005064102.1|  6 QYNVRLPEELIQTLQDVAKETGR 28
                                      99********************9 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.6e-07    0.0014       5      40 ..       7      42 ..       4      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.6e-07
                             RHH_3  5 ttvsidpelaekLkaLSekTrIprSklldeAiellL 40
                                      + v++++el + L ++ ++T+  r++l++ A++ ++
  gi|386003082|ref|YP_005064102.1|  7 YNVRLPEELIQTLQDVAKETGRDRAELVRDALKRYF 42
                                      5689****************************9875 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.2e-06     0.012       5      35 ..       8      38 ..       8      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-06
                             RHH_5  5 nvtLPeelleeLeewAdeegRsvSnlaafLv 35
                                      nv LPeel   L+  A+e+gR+++ l+   +
  gi|386003082|ref|YP_005064102.1|  8 NVRLPEELIQTLQDVAKETGRDRAELVRDAL 38
                                      788*********************9986555 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.21   3.2e+02      14      35 ..      18      40 ..       9      46 .. 0.68
   2 !   12.6   0.0   7.2e-05      0.11      11      38 ..     137     164 ..     129     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                            HTH_29 14 tvsqiAkllglsrrt.vyrwlkr 35
                                      t +++Ak +g +r   v+++lkr
  gi|386003082|ref|YP_005064102.1| 18 TLQDVAKETGRDRAElVRDALKR 40
                                      56778888888887534555555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.2e-05
                            HTH_29  11 GvstvsqiAkllglsrrtvyrwlkrfee 38 
                                       G+ + ++iA+++g+  rtv+ ++k++  
  gi|386003082|ref|YP_005064102.1| 137 GERNRQNIARQVGYKDRTVQQYIKDCLD 164
                                       444899******************8755 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.6   8.9e+02      22      34 ..      18      30 ..      16      31 .. 0.87
   2 ?   11.9   0.1   9.7e-05      0.15      11      38 ..     128     156 ..     123     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.6
                            HTH_38 22 slreIArrLgrsp 34
                                      +l ++A++ gr++
  gi|386003082|ref|YP_005064102.1| 18 TLQDVAKETGRDR 30
                                      7889*******97 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.7e-05
                            HTH_38  11 eeIerllaeGlslr.eIArrLgrspsTIs 38 
                                       e+I + +++G+ +r  IAr++g++  T++
  gi|386003082|ref|YP_005064102.1| 128 EKIKKIWQAGERNRqNIARQVGYKDRTVQ 156
                                       78************89********99986 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.16   2.4e+02      49      80 ..      11      42 ..       2      48 .. 0.80
   2 ?    0.7   0.1      0.49   7.3e+02      46      59 ..     122     135 ..      65     143 .. 0.67
   3 ?    8.6   0.0    0.0017       2.5      14      41 ..     140     167 ..     126     170 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                            HTH_40 49 vseeeekeIeeaiekvgseklkpikealpeev 80
                                      ++ee +++++++ ++ g+++   +++al+  +
  gi|386003082|ref|YP_005064102.1| 11 LPEELIQTLQDVAKETGRDRAELVRDALKRYF 42
                                      47899999999999999999888888887665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.49
                            HTH_40  46 erlvseeeekeIee 59 
                                       e+l ++e++k+I +
  gi|386003082|ref|YP_005064102.1| 122 EDLATQEKIKKIWQ 135
                                       33444455555544 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0017
                            HTH_40  14 sieeIAkerglkesTIegHLaelieege 41 
                                       + + IA++ g k  T+++++ +++ +ge
  gi|386003082|ref|YP_005064102.1| 140 NRQNIARQVGYKDRTVQQYIKDCLDSGE 167
                                       5689*******************99986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   1.7e+03      28      38 ..      17      27 ..      10      27 .. 0.81
   2 ?   11.1   0.0   0.00014       0.2      21      51 ..     133     162 ..     133     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                      HTH_Tnp_ISL3 28 rsvkavArqlg 38
                                      ++ ++vA+++g
  gi|386003082|ref|YP_005064102.1| 17 QTLQDVAKETG 27
                                      48899999886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
                      HTH_Tnp_ISL3  21 lelllesrsvkavArqlgvSwtTVwrildry 51 
                                       ++++ e+ +++ +Arq+g  ++TV+ +++++
  gi|386003082|ref|YP_005064102.1| 133 IWQAGER-NRQNIARQVGYKDRTVQQYIKDC 162
                                       5899999.******************99986 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.38      45      77 ..       7      39 ..       2      41 .. 0.89
   2 ?   -0.5   0.1       1.3   1.9e+03      36      63 ..      64      89 ..      51      95 .. 0.74
   3 ?   -0.5   0.0       1.2   1.9e+03      64      77 ..     151     164 ..     142     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                    CopG_antitoxin 45 islrlpedlLealkekAnkrdvpyqslikelle 77
                                       ++rlpe+l+++l+  A++ +    +l++++l+
  gi|386003082|ref|YP_005064102.1|  7 YNVRLPEELIQTLQDVAKETGRDRAELVRDALK 39
                                      567*************************99997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                    CopG_antitoxin 36 peLkkktksislrlpedlLealkekAnk 63
                                       +L+k+ +++  ++ +  ++a++ +A++
  gi|386003082|ref|YP_005064102.1| 64 EDLEKRVRRL--EIAQPAIQAIQTTAKR 89
                                      4566666666..8889999999988864 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.2
                    CopG_antitoxin  64 rdvpyqslikelle 77 
                                       +d  +q++ik++l 
  gi|386003082|ref|YP_005064102.1| 151 KDRTVQQYIKDCLD 164
                                       677899****9885 PP

>> DUF2510  Protein of unknown function (DUF2510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.23      13      28 ..      38      53 ..      34      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                           DUF2510 13 llRyWDGarWTehtap 28
                                      l Ry+DG+ W + t+ 
  gi|386003082|ref|YP_005064102.1| 38 LKRYFDGELWRDETTE 53
                                      67********999986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.6     9e+02      19      31 ..      18      30 ..       9      46 .. 0.70
   2 ?   -0.6   0.2      0.82   1.2e+03       3      15 ..      68      80 ..      66      90 .. 0.76
   3 ?   10.2   0.1   0.00035      0.52      19      45 ..     140     166 ..     123     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.6
                            HTH_23 19 svreIAreLgvsr 31
                                      + +++A+e g+ r
  gi|386003082|ref|YP_005064102.1| 18 TLQDVAKETGRDR 30
                                      6667777766654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.82
                            HTH_23  3 sereRlrilllla 15
                                      + ++Rl+i++ + 
  gi|386003082|ref|YP_005064102.1| 68 KRVRRLEIAQPAI 80
                                      6789999998775 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00035
                            HTH_23  19 svreIAreLgvsrrTvyrwlkryreeG 45 
                                       +++ IAr+ g   rTv++++k    +G
  gi|386003082|ref|YP_005064102.1| 140 NRQNIARQVGYKDRTVQQYIKDCLDSG 166
                                       6789*****************986666 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2    0.0094        14      22      44 ..      17      39 ..      12      40 .. 0.85
   2 ?   -2.0   0.1       3.5   5.2e+03      20      29 ..      76      85 ..      74      94 .. 0.68
   3 ?    1.4   0.1      0.31   4.6e+02      18      40 ..     111     131 ..     110     133 .. 0.85
   4 ?    1.8   0.0      0.23   3.4e+02      31      43 ..     151     163 ..     142     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0094
                                      HHHHHHHC-TTS-HHHHHHHHHC CS
                            RuvA_C 22 kAvakvlanpgasveelIraALk 44
                                      ++++ v++++g + +el+r ALk
  gi|386003082|ref|YP_005064102.1| 17 QTLQDVAKETGRDRAELVRDALK 39
                                      6788898899************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                                      HHHHHHHHHC CS
                            RuvA_C 20 aekAvakvla 29
                                      a+ A++++ +
  gi|386003082|ref|YP_005064102.1| 76 AQPAIQAIQT 85
                                      7888888865 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHC-TTS-HHHHHH CS
                            RuvA_C  18 keaekAvakvlanpgasveelIr 40 
                                        ea+ +++++   ++++++e I+
  gi|386003082|ref|YP_005064102.1| 111 PEAKPTIQRL--SEDLATQEKIK 131
                                       599*******..79999999887 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.23
                                       TTS-HHHHHHHHH CS
                            RuvA_C  31 pgasveelIraAL 43 
                                       ++ +v+++I+ +L
  gi|386003082|ref|YP_005064102.1| 151 KDRTVQQYIKDCL 163
                                       6778999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1038.32
//
Query:       gi|386003083|ref|YP_005064103.1|  [L=139]
Description: hypothetical protein Mhar_2408 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.3   0.0       0.21   11.0   0.0    1.1  1  RE_NgoBV  NgoBV restriction endonuclease


Domain annotation for each model (and alignments):
>> RE_NgoBV  NgoBV restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.2e-05      0.21     143     196 ..      30      83 ..      27      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.2e-05
                          RE_NgoBV 143 vweitrrmdgwainlqvkkgvvhkirpgvwysirkknipmfksledfvaaieea 196
                                       vw +t++  g a    v +g +  i+ g+   +  +++p f+ +  f++  +++
  gi|386003083|ref|YP_005064103.1|  30 VWVVTQTQSGLATVTTVYQGNITEIKDGLLCLNCTGDLPGFEWVAKFMTQYDDT 83 
                                       9**********************************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 839.29
//
Query:       gi|386003084|ref|YP_005064104.1|  [L=83]
Description: hypothetical protein Mhar_2409 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 559.39
//
Query:       gi|386003085|ref|YP_005064105.1|  [L=53]
Description: hypothetical protein Mhar_2410 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   21.4   0.0     0.0003   21.4   0.0    1.0  1  RHH_6     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-08    0.0003       4      50 ..       2      47 ..       1      52 [. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-08
                             RHH_6  4 rwnvavspetdqavrafLAsqGggrkGdLSrfieeAVrayllelave 50
                                      + +v++ + t  a+r +++++G g + + S+ ie A + +l+++ ++
  gi|386003085|ref|YP_005064105.1|  2 KTTVTMTDRTAAALRFYIGKEGLGMR-AQSQVIETALKDFLRDRGID 47
                                      569******************75544.47*************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.43
# Mc/sec: 373.53
//
Query:       gi|386003086|ref|YP_005064106.1|  [L=209]
Description: Extracellular nuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-10   39.7   0.0    9.4e-10   38.9   0.0    1.4  1  SNase           Staphylococcal nuclease homologue
    3.4e-06   27.0   0.1    5.8e-06   26.2   0.1    1.4  1  Ada_Zn_binding  Metal binding domain of Ada


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.1e-13   9.4e-10       1      84 [.      42     130 ..      42     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.1e-13
                                       EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S...SBSTTSEEEEEEEET........TEEHH CS
                             SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk...kkDkygrllayvyln........kknin 66 
                                       +vrL+++d+Pe +       p g+ Ak f+ + +l++ v+++++++    +D y+rlla vyl+         + +n
  gi|386003086|ref|YP_005064106.1|  42 RVRLADVDSPEMS------TPEGEPAKVFATDTLLGQRVWLDIDNTsgdGRDPYNRLLAVVYLEdlngtintSHPFN 112
                                       79***********......7779*******************999999999*******************99999** PP

                                       HHHHHTTSSEE---BTTS CS
                             SNase  67 eeLvkeGlArvyevyekn 84 
                                         Lv +G+A+v ++ +++
  gi|386003086|ref|YP_005064106.1| 113 RMLVDAGFAVVKNFTNNE 130
                                       **********98887764 PP

>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   6.5e-10   5.8e-06      14      64 ..     158     208 ..     148     209 .] 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.5e-10
                                       CTTBEEEETTTTEEE-TT-S.SS-S-SCCEEEESSHHHHHHTT-EEETTTTT CS
                    Ada_Zn_binding  14 dgsFvyavkttgiyCrpsCp.arlPkrenveFfdtaaeAeaagfrpCkrcrP 64 
                                       +g+F ++ ++   y  psC+ a +  +en   f++ +eA+aag+ pC  c+P
  gi|386003086|ref|YP_005064106.1| 158 EGQF-VGSTKSDKYHYPSCRwAEKILPENEIWFASSEEARAAGYIPCGVCNP 208
                                       5555.677788889*****9455566************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1372.34
//
Query:       gi|386003087|ref|YP_005064107.1|  [L=203]
Description: hypothetical protein Mhar_2412 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0078   15.4   0.1     0.0097   15.1   0.1    1.1  1  AvrB_AvrC  Avirulence protein
     0.0089   16.0   0.2      0.013   15.4   0.2    1.3  1  PDDEXK_5   PD-(D/E)XK endonuclease


Domain annotation for each model (and alignments):
>> AvrB_AvrC  Avirulence protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.1e-06    0.0097     137     214 ..     101     179 ..      63     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-06
                                       TSCHHHHHHHT-TT-E.EEEEEETTTEEEEEEEEEEEEEETTEEEEEEEEEEE--HHHHHHHHHHHHHHHHHHHHHH CS
                         AvrB_AvrC 137 pYksvkervanrkDae.kekledelllelevkvyritgkisgetiplttisvssDdealrdrlkdlykdlkrrglkd 212
                                        Yk  ++r++n kD++ +++++ +++  l v ++ +t+k +   i    + +++D+ +l + +++ ++++++   kd
  gi|386003087|ref|YP_005064107.1| 101 SYKVEIQRTRNSKDGSnTRSYRADYFDILAVCTFNQTDKWDFMFIRADDLEIVKDNPELLKIMQRVPTKITNPWKKD 177
                                       589999********9625789999********************************998888888887776666655 PP

                                       HH CS
                         AvrB_AvrC 213 ll 214
                                       l+
  gi|386003087|ref|YP_005064107.1| 178 LI 179
                                       54 PP

>> PDDEXK_5  PD-(D/E)XK endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.5e-06     0.013      36      93 ..      73     133 ..      68     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-06
                                       SEEEEETTEEEEEEEEE-...EEETTTSCEEEE-CEEEESSSSEEEEE--CCS-SEEEEEE CS
                          PDDEXK_5  36 DLvadkdgklyriQvKya...wleeksgqlrvknrstktdkngvhrkkYkkedfDflavyl 93 
                                       D+ ++++gk+y+  +K      +++ +  ++v+ ++t+ +k g   ++Y+ + fD+lav +
  gi|386003087|ref|YP_005064107.1|  73 DFAFESKGKSYQMECKNLrneVYKKPEFSYKVEIQRTRNSKDGSNTRSYRADYFDILAVCT 133
                                       999*************9865466777889999999*********************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1446.86
//
Query:       gi|386003088|ref|YP_005064108.1|  [L=64]
Description: hypothetical protein Mhar_2413 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 499.94
//
Query:       gi|386003089|ref|YP_005064109.1|  [L=312]
Description: DNA methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-38  132.2   0.0    2.8e-38  131.9   0.0    1.1  1  N6_N4_Mtase  DNA methylase


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.0   1.6e-42   2.8e-38       2     226 ..      53     300 ..      52     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 1.6e-42
                                       EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHHHHHHH CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk......elkaladei 72 
                                       +livt+pPY ++ +     ++ ++ + ++y++++ ++++e +rvLkddgs++ini+ s  k        +++l+ e 
  gi|386003089|ref|YP_005064109.1|  53 NLIVTSPPYALVFK-----KEYGNVDAQDYVKWFMGFAQEFHRVLKDDGSLVINIGGSWNKGvptrstYHFELIIEL 124
                                       89************.....89999999********************************999******999999999 PP

                                       TT-EEEEEEEEEEESSSTTTSTCC......S-B--EEEEEEEESSTT-..---GGGSSBSS-HHHH.HHHHHH.CHH CS
                       N6_N4_Mtase  73 fggffllnvivwkkpnsmpesnkd......rltsthEyilvfsknkkyllkfnldaikvpyeekdk.lekrga.yts 141
                                       ++ f l++   w +p ++p+++++      r++++ E++l+fsk+     k +   + +py++  + + ++g+ +++
  gi|386003089|ref|YP_005064109.1| 125 AKVFHLAQEFYWYNPAKLPSPAEWvtvrriRVKDSVELVLWFSKSPYP--KADNRSVLQPYSKDMQrIIEKGYvAKK 199
                                       99999**********888888888999999***************999..555555555555444304444449999 PP

                                       HCC-B--BSEE...................E-SCCCTTSTTS-CHH...........----SS---HHHHHHHHHHH CS
                       N6_N4_Mtase 142 kkkgkkiediW...................dlseiqsnekkskgdt...........kkkHpaqkPvallerlIkls 188
                                        + g++i+ ++                                               k Hpa +P +l+++ ++ +
  gi|386003089|ref|YP_005064109.1| 200 RPSGHNITSKFrrdnngaippnvlqvgntdS--------------SspylkkckecgMKPHPARFPKDLPQFFVDFL 262
                                       9**********88777776665555544332..............03334455555689****************** PP

                                       S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                       N6_N4_Mtase 189 tkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                       t++gdiv+DpF+GS  T+ +a++ +rk+i i++ eey+
  gi|386003089|ref|YP_005064109.1| 263 TEPGDIVMDPFCGSNVTGFVAENSKRKWIAIDTVEEYL 300
                                       ************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2093.45
//
Query:       gi|386000718|ref|YP_005919017.1|  [L=1061]
Description: hypothetical protein Mhar_0001 [Methanosaeta harundinacea 6Ac]
Scores for 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   77.3   5.4    1.1e-11   44.8   0.1    4.6  4  DUF11       Domain of unknown function DUF11
    4.4e-05   23.7   0.0    0.00022   21.4   0.0    2.2  2  Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   1.3e-15   1.1e-11       1      80 [.     309     389 ..     309     394 .. 0.94
   2 ?    0.2   0.3       0.1   9.3e+02      18      89 ..     426     496 ..     417     499 .. 0.79
   3 !   18.6   0.0   1.9e-07    0.0017      15      89 ..     787     864 ..     758     866 .. 0.80
   4 !   11.9   0.0   2.4e-05      0.21      15      79 ..     915     981 ..     904     989 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.3e-15
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.qgtasaltsvgsLeagesatlsftv 76 
                                       + K  ++++v+pGd ++yt++ tNtg + +++vv+t   Pag++++s+s +  +  + ++++g+L+  ++ ++ +tv
  gi|386000718|ref|YP_005919017.1| 309 IEKRASSRTVAPGDLLNYTIIYTNTGYNRLTEVVITEKYPAGVEFISSSPApDPGTRNQWTIGDLPVDGTGKIIVTV 385
                                       6799999******************************************9988888899999*************** PP

                             DUF11  77 rvtr 80 
                                       rv++
  gi|386000718|ref|YP_005919017.1| 386 RVSQ 389
                                       9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                             DUF11  18 ytltvtNtgpasa.ngvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasga.ltn 89 
                                       +t+t   t p sa + v+v+D   +g+++  + +++g ++ + +v  L   +s  +   v++t +++++  ++n
  gi|386000718|ref|YP_005919017.1| 426 VTITSAETVPMSAsASVTVED---SGTELDIHEHGSGLYDSEETVLLLTENKSIEMMKDVSATYAPTTLGlYNN 496
                                       788888888888777899999...99999999999999999999888888888888888888877777665555 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.9e-07
                             DUF11  15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsvgsLeagesatlsftvrvtrtaasgal 87 
                                         tyt+   N g+a++  + v+D+ P+g  + + s+         sa+++ + L  g    +++++ vt++  ++ l
  gi|386000718|ref|YP_005919017.1| 787 VATYTIAIENDGNAALGPIYVKDLFPPGAIFKEPSSLrpteLTGTSANWTLTHLGIGDVVEITLQLDVTKRYPQE-L 862
                                       78************************9999887777656663334566777999999999999999999887765.6 PP

                             DUF11  88 tn 89 
                                       tn
  gi|386000718|ref|YP_005919017.1| 863 TN 864
                                       66 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 2.4e-05
                             DUF11  15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvt 79 
                                        v y +  tN  ++++  ++vtD lP+g+ +       ++++ +t +    ++++ e+ t+ ++v+++
  gi|386000718|ref|YP_005919017.1| 915 VVWYRIDITNHDNVAR-VATVTDHLPEGMIFLDTMVPFASYDGRTITwnlIEIAPLETVTIPYRVSAQ 981
                                       56799**********9.9************99999884444444444344888999999999998886 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.5e-08   0.00022      28      89 ..     326     385 ..     315     387 .. 0.87
   2 ?   -2.8   0.0      0.88   7.9e+03      70      87 ..     833     850 ..     814     852 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-08
                        Chlam_OMP6  28 ypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskitvwv 89 
                                       y i  t +g +   +vvit++ p+ vef++s pa  p    +  w+i  l      ki v v
  gi|386000718|ref|YP_005919017.1| 326 YTIIYTNTGYNRLTEVVITEKYPAGVEFISSSPAPDPG--TRNQWTIGDLPVDGTGKIIVTV 385
                                       8888999**************************96665..5677***999988888888877 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.88
                        Chlam_OMP6  70 lvwkidrlgqgekskitv 87 
                                         w++  lg g+   it+
  gi|386000718|ref|YP_005919017.1| 833 ANWTLTHLGIGDVVEITL 850
                                       569999****99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1061 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 7664.38
//
Query:       gi|386000719|ref|YP_005919018.1|  [L=438]
Description: IS66 family element, transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-49  166.7   0.0    7.7e-49  166.7   0.0    1.7  2  DDE_Tnp_IS66    Transposase IS66 family
    6.5e-07   29.6   3.3    1.4e-06   28.5   3.3    1.6  1  zf-IS66         zinc-finger binding domain of transposase IS6
    0.00013   22.2   0.1    0.00047   20.4   0.0    1.9  2  DDE_Tnp_IS240   DDE domain
     0.0035   17.3   0.1     0.0071   16.3   0.1    1.5  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.048   14.0   0.0    2.0  1  DUF5623         Domain of unknown function (DUF5623)
      0.013   15.5   4.6      0.048   13.7   3.0    2.4  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
      0.027   14.8   5.2      0.064   13.6   5.2    1.6  1  DUF737          Protein of unknown function (DUF737)
      0.052   13.6   1.8       0.16   12.0   1.8    1.9  1  MCC-bdg_PDZ     PDZ domain of MCC-2 bdg protein for Usher syn
      0.056   12.9   2.2        5.9    6.4   0.1    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.074   12.8   2.1        3.2    7.6   0.3    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.084   13.1   0.3        1.7    8.9   0.2    2.5  2  MazG            MazG nucleotide pyrophosphohydrolase domain
       0.11   13.0   8.6      0.073   13.5   3.1    3.0  2  ZapB            Cell division protein ZapB
       0.14   12.3   4.1       0.19   11.8   1.9    2.1  2  DivIVA          DivIVA protein
       0.14   12.3   0.5         22    5.3   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.21   11.4   4.0       0.68    9.7   4.0    1.8  1  DivIC           Septum formation initiator
        0.3   10.6   1.8       0.36   10.4   0.6    1.7  2  TMCO5           TMCO5 family
        0.4   10.7   2.9         17    5.5   0.3    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.79    9.1   3.2         15    5.0   0.3    2.5  2  zf-TFIIB        Transcription factor zinc-finger
        1.4    8.5   4.3        1.2    8.7   1.4    2.2  3  Snf7            Snf7
        1.4    9.0   3.8         16    5.7   0.1    2.4  2  UPF0547         Uncharacterised protein family UPF0547
        1.9    7.3   5.8        0.8    8.5   2.0    2.0  2  XRCC4           DNA double-strand break repair and V(D)J reco
        4.9    7.3   9.2       0.96    9.6   1.9    3.1  3  bZIP_1          bZIP transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.5       3.2   2.6e+03     185     223 ..       8      44 ..       2      54 .. 0.66
   2 !  166.7   0.0   9.5e-52   7.7e-49       2     280 ..     149     408 ..     148     410 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.2
                      DDE_Tnp_IS66 185 reareaeaeerlalrqeesrpllaeleawleeqlkkvlp 223
                                       ++++   ++erl++++e +r+ +a+lea l + ++ ++p
  gi|386000719|ref|YP_005919018.1|   8 KQLK--AENERLKRENEFQREQIAKLEARLAKYENAHTP 44 
                                       3333..247888888888888888888877766644444 PP

  == domain 2  score: 166.7 bits;  conditional E-value: 9.5e-52
                      DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtl 77 
                                       +++g++++A++++lky+d lP ++++++l+rl G++++++t+ ++++raa++++  ++a+ + +++++++ +DET++
  gi|386000719|ref|YP_005919018.1| 149 GRFGNNVIAQTTLLKYEDRLPHRKIQNALKRLhGLTICAATVLDLTRRAADAVQSQYDAILNSVRNAPILYVDETSI 225
                                       789************************************************************************** PP

                      DDE_Tnp_IS66  78 rvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaealLag.fkGvlvsDgyagYnklaeeqvthalCwaHl 153
                                       +       +g+++++Wv+ t      ++  + +sRg++v  ++L+  f G++v+Dg+++Y k++    +++ CwaHl
  gi|386000719|ref|YP_005919018.1| 226 K------VQGERHWIWVFTTPS---ETFVVIRKSRGMKVLMEVLTRrFDGIIVCDGWKPYAKFT---KRLQRCWAHL 290
                                       *......89***********88...9*****************9999****************5...899******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakkksqaaaealarigklyaierear.eaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgk 229
                                       +R+ +d+ ++      ++ea+   g+l+++ +e++ + e++   ++r    +   ++l++w+ +       ++k++k
  gi|386000719|ref|YP_005919018.1| 291 LRESKDLADK------IEEAVPLHGDLKDLYEELTdALENDPPPEVRMGLLEMARSKLHQWIMK----EYMSEKVKK 357
                                       *******975......556666666666666666532356777888888888899999999986....468999*** PP

                      DDE_Tnp_IS66 230 airyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                       +i ++ +  e  ++f+ ++ v+++NN+aERa+R  v+ RK+ +++++e+G 
  gi|386000719|ref|YP_005919018.1| 358 LIGKISNGFEYWFTFIIQPAVEPTNNRAERALREHVVLRKIIGTLRNEKGT 408
                                       ************************************************996 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   3.3   1.8e-09   1.4e-06       3      45 ..      91     134 ..      90     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.8e-09
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldip.PakfrViehirpkyaCpcC 45 
                                        Cp+CG+ l +pi ++    + +ip P+ ++V+e+ +  y+Cp+C
  gi|386000719|ref|YP_005919018.1|  91 LCPDCGAkLGDPIRKE-SKIIEEIPePQPIIVTEYKIAHYRCPSC 134
                                       5******888899999.89******9999**************** PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.7e-07   0.00047       6     100 ..     220     302 ..     217     324 .. 0.75
   2 ?   -2.8   0.0       8.1   6.6e+03      95     129 ..     381     421 ..     361     423 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.7e-07
                     DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkreg. 81 
                                       vDET +k++G+ ++++           ++++k R++k    +l++ ++        iv D+ + ya+  k+l+r   
  gi|386000719|ref|YP_005919018.1| 220 VDETSIKVQGERHWIWVFTTPSETF--VVIRKSRGMKVLMEVLTRRFDGI------IVCDGWKPYAKFTKRLQRCWa 288
                                       9***************987665554..578999**999999999988888......****************99543 PP

                     DDE_Tnp_IS240  82 elfdevshvqvkylnnriE 100
                                       +l++     ++k l + iE
  gi|386000719|ref|YP_005919018.1| 289 HLLR-----ESKDLADKIE 302
                                       3333.....3444444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.1
                     DDE_Tnp_IS240  95 lnnriEs...dhrtlKkrl...rptrgfkslksaaktlagf 129
                                        nnr E+   +h  l+k +   r  +g    +++ ++la++
  gi|386000719|ref|YP_005919018.1| 381 TNNRAERalrEHVVLRKIIgtlRNEKGTSIHERIMTVLATW 421
                                       57777752224555665544335555555555555555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.7e-06    0.0071      13      39 ..      90     139 ..      81     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.7e-06
                               DZR  13 rfCseCgtklkavaa.......................edrCpsCgekvd 39 
                                         C++Cg+kl  + +                       ++rCpsC+++v 
  gi|386000719|ref|YP_005919018.1|  90 DLCPDCGAKLGDPIRkeskiieeipepqpiivteykiaHYRCPSCQKEVV 139
                                       58*******9766668899***************************9953 PP

>> DUF5623  Domain of unknown function (DUF5623)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.9e-05     0.048      12      59 ..     306     356 ..     301     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                           DUF5623  12 evHqevgrllkellesvarskg...vssrlsavrstLddWlemEyseeeld 59 
                                        +H ++  l +el+++++++         l+++rs+L++W+ +Ey +e+++
  gi|386000719|ref|YP_005919018.1| 306 PLHGDLKDLYEELTDALENDPPpevRMGLLEMARSKLHQWIMKEYMSEKVK 356
                                       56778888888888888887774423345799*************888766 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.0   5.9e-05     0.048      11      48 ..       4      41 ..       3      49 .. 0.92
   2 ?    0.1   0.0         1   8.2e+02      42      72 ..     287     317 ..     279     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                        TMF_DNA_bd 11 DeqIaqLmeEGekLskkelklnntikkLrkknkeleke 48
                                      +e+I+qL++E e+L+ ++  ++++i kL + +++ e+ 
  gi|386000719|ref|YP_005919018.1|  4 EEIIKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41
                                      699***************************99998875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                        TMF_DNA_bd  42 nkelekeikelkkkleklekeleeleerlke 72 
                                        ++l  e k+l +k+e+ +     l+++++e
  gi|386000719|ref|YP_005919018.1| 287 WAHLLRESKDLADKIEEAVPLHGDLKDLYEE 317
                                       5667788899999999999999988888765 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.2   7.9e-05     0.064     147     180 ..       4      37 ..       1      43 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-05
                            DUF737 147 erkarqLeekekeLkkqdafYkeqlakLeeknae 180
                                       e  ++qL + ++ Lk+ ++f +eq+akLe++ a+
  gi|386000719|ref|YP_005919018.1|   4 EEIIKQLKAENERLKRENEFQREQIAKLEARLAK 37 
                                       5679***************************987 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.8    0.0002      0.16       6      41 ..       7      41 ..       4      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                       MCC-bdg_PDZ  6 IeeLkaqnelLsltleerkqqseeLsldlgkaEsna 41
                                      I +Lka ne+L++  e  ++q ++L  +l k+E na
  gi|386000719|ref|YP_005919018.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKYE-NA 41
                                      899******************************.55 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.012       9.5      19      26 .]      92      99 ..      90      99 .. 0.82
   2 ?    6.4   0.1    0.0073       5.9       2      15 ..     128     142 ..     127     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                       zf-ribbon_3 19 CpyCGtkl 26
                                      Cp CG+kl
  gi|386000719|ref|YP_005919018.1| 92 CPDCGAKL 99
                                      99999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0073
                       zf-ribbon_3   2 tvrCPnCGa.plssd 15 
                                       ++rCP+C + +++sd
  gi|386000719|ref|YP_005919018.1| 128 HYRCPSCQKeVVASD 142
                                       79*****98887776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.004       3.2       2      11 ..      92     101 ..      91     102 .. 0.83
   2 ?    4.6   0.1     0.034        28       1      10 [.     130     139 ..     130     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                     zinc_ribbon_2   2 CpnCGaelqd 11 
                                       Cp CGa+l d
  gi|386000719|ref|YP_005919018.1|  92 CPDCGAKLGD 101
                                       9999999865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.034
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +Cp+C +e+ 
  gi|386000719|ref|YP_005919018.1| 130 RCPSCQKEVV 139
                                       6******986 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.48   3.9e+02      51      73 ..     149     171 ..     142     172 .. 0.85
   2 ?    8.9   0.2    0.0021       1.7       6      37 ..     286     322 ..     281     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                                       H---HHHHHHHHHHHHHHH-GGG CS
                              MazG  51 ggidledvaetileKlerRhphv 73 
                                       g++  + +a+t+l K+e R ph+
  gi|386000719|ref|YP_005919018.1| 149 GRFGNNVIAQTTLLKYEDRLPHR 171
                                       6667777899***********97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHT.....T-HHHHHHHHHHHH CS
                              MazG   6 llaylleEvgEvaeaIkk.....edrdeleeELGDvL 37 
                                         a+ll E + +a++I++     +d ++l eEL D L
  gi|386000719|ref|YP_005919018.1| 286 CWAHLLRESKDLADKIEEavplhGDLKDLYEELTDAL 322
                                       66899*************99*99************87 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.1   8.9e-05     0.073      20      54 ..       7      41 ..       5      48 .. 0.88
   2 ?    1.0   0.3      0.74     6e+02      54      69 ..     347     362 ..     280     364 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                              ZapB 20 itlLqmeieeLkeeneelkeenreleeeneqlkee 54
                                      i++L+ e+e+Lk+ene   e++++le+ + + ++ 
  gi|386000719|ref|YP_005919018.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41
                                      899***********************988887655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.74
                              ZapB  54 ereawqerlkkLLgkl 69 
                                        +e + e++kkL+gk+
  gi|386000719|ref|YP_005919018.1| 347 MKEYMSEKVKKLIGKI 362
                                       3555667777777776 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   0.00024      0.19      25      62 ..       5      42 ..       4      44 .. 0.92
   2 ?   -0.7   0.0       1.7   1.4e+03      35      68 ..     288     321 ..     277     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXX CS
                            DivIVA 25 eFLdqvakdyeallkeneelkekvkeleeklkeykele 62
                                      e+++q+  + e+l +ene ++e++++le +l++y++++
  gi|386000719|ref|YP_005919018.1|  5 EIIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42
                                      67899999**************************9975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXX CS
                            DivIVA  35 eallkeneelkekvkeleeklkeykeleetLkkt 68 
                                         ll+e+++l +k++e+     + k+l e+L ++
  gi|386000719|ref|YP_005919018.1| 288 AHLLRESKDLADKIEEAVPLHGDLKDLYEELTDA 321
                                       5789999999999999877777777777766665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.042        34      27      35 ..      89      98 ..      80     100 .. 0.79
   2 ?    5.3   0.0     0.026        22       6      14 ..     129     137 ..     126     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.042
                       Zn-ribbon_8 27 ta.CPeCgse 35
                                      ++ CP+Cg++
  gi|386000719|ref|YP_005919018.1| 89 IDlCPDCGAK 98
                                      566*****86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.026
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       YrC +C++e
  gi|386000719|ref|YP_005919018.1| 129 YRCPSCQKE 137
                                       888888865 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.0   0.00084      0.68      19      50 ..       7      38 ..       3      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                      +kqlk+e ++l++e++ +++++++Lea+++++
  gi|386000719|ref|YP_005919018.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKY 38
                                      57888888888888888888888888888777 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00044      0.36      61     101 ..       2      42 ..       1      63 [. 0.87
   2 ?   -2.0   0.0       2.6   2.1e+03     164     183 ..     321     344 ..     278     370 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                             TMCO5  61 ekedalkeLeletaklekkneiLlkevveLqkkisrkeskq 101
                                       ++e+  k+L+ e  +l+++ne+  +++++L+ ++ + e+ +
  gi|386000719|ref|YP_005919018.1|   2 HEEEIIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42 
                                       679999****************************9998654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                             TMCO5 164 kmee....eketlllekevsklqs 183
                                        +e+    e  + lle   skl +
  gi|386000719|ref|YP_005919018.1| 321 ALENdpppEVRMGLLEMARSKLHQ 344
                                       222233333333344444444333 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.038        31       2       9 ..      92      99 ..      92     106 .. 0.91
   2 ?    5.5   0.3     0.021        17       1      11 [.     130     140 ..     130     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                    DNA_ligase_ZBD  2 CPvCGsav 9 
                                      CP CG+++
  gi|386000719|ref|YP_005919018.1| 92 CPDCGAKL 99
                                      *****997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+C  +vv 
  gi|386000719|ref|YP_005919018.1| 130 RCPSCQKEVVA 140
                                       5*******995 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.019        15      16      26 ..      86      96 ..      82      96 .. 0.89
   2 ?    3.9   0.2     0.041        33       2      14 ..     131     143 ..     130     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.019
                          zf-TFIIB 16 gveidyCpqCr 26
                                      +v id Cp+C+
  gi|386000719|ref|YP_005919018.1| 86 EVAIDLCPDCG 96
                                      699*******7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                          zf-TFIIB   2 CPkCqdeleeser 14 
                                       CP+Cq e + s++
  gi|386000719|ref|YP_005919018.1| 131 CPSCQKEVVASDH 143
                                       *****99887765 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.4    0.0015       1.2       2      38 ..       6      42 ..       5      62 .. 0.84
   2 ?   -3.0   0.0       5.8   4.7e+03       6      26 ..     283     303 ..     279     323 .. 0.66
   3 ?   -0.9   0.0       1.3   1.1e+03      29      62 ..     353     404 ..     332     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                              Snf7  2 airsLrkaerkldkkqeslekkikkleaelkklakkg 38
                                       i++L+ + ++l+++ e+ +++i+klea l+k+    
  gi|386000719|ref|YP_005919018.1|  6 IIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42
                                      6899****************************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.8
                                       HHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   6 Lrkaerkldkkqeslekkikk 26 
                                       L+++   l ++++ l +ki++
  gi|386000719|ref|YP_005919018.1| 283 LQRCWAHLLRESKDLADKIEE 303
                                       556666666666666666654 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                       HHHHHHHCTT-..................HHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7  29 aelkklakkgn..................kdralllLKqkkryekqldqldn 62 
                                       +++kkl+ k++                  + ra ++L++ + ++k +  l n
  gi|386000719|ref|YP_005919018.1| 353 EKVKKLIGKISngfeywftfiiqpaveptNNRAERALREHVVLRKIIGTLRN 404
                                       4556666665566667777777777777789999999999999998877766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.02        16       7      21 ..      82      96 ..      82      97 .. 0.91
   2 ?    3.8   0.7     0.074        60       2      10 ..     130     138 ..     130     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                           UPF0547  7 eakvPvaaqfCphCG 21
                                      +++v va   Cp+CG
  gi|386000719|ref|YP_005919018.1| 82 DRQVEVAIDLCPDCG 96
                                      68999999******9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.074
                           UPF0547   2 vCPeCeakv 10 
                                       +CP C+ +v
  gi|386000719|ref|YP_005919018.1| 130 RCPSCQKEV 138
                                       6*****998 PP

>> XRCC4  DNA double-strand break repair and V(D)J recombination protein XRCC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.0   0.00098       0.8     137     173 ..       5      41 ..       1      44 [. 0.90
   2 ?   -0.3   0.1      0.47   3.8e+02     147     184 ..     281     317 ..     274     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00098
                             XRCC4 137 dqiaelqakNehLqkENerLlrdwsdvterlekyvka 173
                                       + i++l+a+Ne+L++ENe  +++  ++++rl ky +a
  gi|386000719|ref|YP_005919018.1|   5 EIIKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41 
                                       578899***************************9876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                             XRCC4 147 ehLqkENerLlrdwsdvterlekyvkakEeleadLYkr 184
                                       ++Lq+   +Llr+ +d+ +++e+ v    +l+ dLY+ 
  gi|386000719|ref|YP_005919018.1| 281 KRLQRCWAHLLRESKDLADKIEEAVPLHGDLK-DLYEE 317
                                       679999999***************99999985.88875 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.9    0.0012      0.96      35      61 ..       7      33 ..       4      36 .. 0.89
   2 ?   -1.0   0.1       2.3   1.9e+03      18      27 ..      48      57 ..      46      62 .. 0.82
   3 ?    0.1   0.0       1.1     9e+02      29      51 ..     281     303 ..     278     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 35 vkaLekeNksLkseleelkkevekLks 61
                                       k+L++eN+ Lk e+e  +++++kL+ 
  gi|386000719|ref|YP_005919018.1|  7 IKQLKAENERLKRENEFQREQIAKLEA 33
                                      699********************9975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                      HHHHHHHHHH CS
                            bZIP_1 18 rrsRqRKqae 27
                                      rr R+RK+ +
  gi|386000719|ref|YP_005919018.1| 48 RRGRKRKKGY 57
                                      7889***977 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkselee 51 
                                       ++L+r  + L  e k+L++++ee
  gi|386000719|ref|YP_005919018.1| 281 KRLQRCWAHLLRESKDLADKIEE 303
                                       77888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      871  (0.0485805); expected 358.6 (0.02)
Passed Vit filter:                       147  (0.00819901); 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):              22  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3639.62
//
Query:       gi|386000720|ref|YP_005919019.1|  [L=366]
Description: Tubulin/FtsZ, GTPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-32  113.4   0.0    2.3e-32  112.8   0.0    1.3  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    8.1e-05   22.0   0.0    0.00068   18.9   0.0    2.1  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.0   2.6e-36   2.3e-32       2     195 ..       3     182 ..       2     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 2.6e-36
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       ++++g+GqcGn+i++++ +   +++g     ++l++++s ++  + +  ++ai+t  ++l+e++       +++l++
  gi|386000720|ref|YP_005919019.1|   3 VLMLGIGQCGNRILDAVNR---EAFGG---SSRLSKYYSRQKFPSRV-ETLAINTAVNDLKELRFT---AAKDRLHV 69 
                                       899****************...44343...589******97766666.677****88888888877...77899999 PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                            + +g+g+++ +gk+   e++e+i++e+e+   ++  f+++s +GGTGS+++p++++ l+e+y+k++v+ v+v
  gi|386000720|ref|YP_005919019.1|  70 ----PNLHGVGANRGIGKQGFWENREMIMEEIERRGDFDIAFVMTSASGGTGSSFTPLVVHELRERYKKITVIPVMV 142
                                       ....7789********************************************************************* PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT.-SEEEEEEHHHHHCC CS
                           Tubulin 156 lPsefsevvvepynailalkeliee.sdavividNdaLlki 195
                                       lP+++ e+ ++ +na+++++ ++e  sd +i++dN+ L+++
  gi|386000720|ref|YP_005919019.1| 143 LPFRE-EGSIYLQNAAFSMRDIMEVeSDGIILVDNQYLKRL 182
                                       ***99.******************88************986 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.03   2.7e+02       1      48 [.       4      58 ..       4      69 .. 0.80
   2 !   18.9   0.0   7.6e-08   0.00068     105     226 ..      64     165 ..      59     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.03
                         Tubulin_2  1 lviGLGGtGgkvlaelrrrlreel.......gslelpdkvqFlyiDtdeneknrl 48
                                      l+ G+G  G ++l+++ r  +           +++ p  v+ l+i t +n++++l
  gi|386000720|ref|YP_005919019.1|  4 LMLGIGQCGNRILDAVNREAFGGSsrlskyySRQKFPSRVETLAINTAVNDLKEL 58
                                      67899**********9998877667778887788889999999999999999776 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.6e-08
                         Tubulin_2 105 leelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllr 181
                                       +++l+++++ +G G +R +G+  + +n e i+e+++++ +              fV++S +GGTGS+    v++ lr
  gi|386000720|ref|YP_005919019.1|  64 KDRLHVPNL-HGVGANRGIGKQGFWENREMIMEEIERRGDFDI----------AFVMTSASGGTGSSFTPLVVHELR 129
                                       566666666.999999999999999999999999887644322..........39*************999999999 PP

                         Tubulin_2 182 kilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna 226
                                       + +k+      +i++++lP       e+g  + +Na+ ++ ++  
  gi|386000720|ref|YP_005919019.1| 130 ERYKKIT----VIPVMVLPFR-----EEGSIYLQNAAFSMRDIME 165
                                       9999998....699****985.....5688999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2977.95
//
Query:       gi|386000721|ref|YP_005919020.1|  [L=396]
Description: hypothetical protein Mhar_0004 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-17   61.5   4.0    1.3e-09   38.2   2.1    2.5  2  DUF11        Domain of unknown function DUF11
    7.6e-15   54.8   0.4    7.4e-08   32.0   0.2    2.2  2  TRAP_beta    Translocon-associated protein beta (TRAPB)
    3.7e-10   40.0   0.7    0.00025   21.2   0.0    2.5  2  CARDB        CARDB
      4e-06   25.9   2.8    0.00064   18.7   0.3    2.3  2  BatD         Oxygen tolerance
      2e-05   24.7   0.9       0.19   12.0   0.2    3.7  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
     0.0044   17.2   1.1      0.061   13.5   0.1    2.8  3  bMG10        Bacterial Alpha-2-macroglobulin MG10 domain
  ------ inclusion threshold ------
      0.061   14.2   0.1       0.41   11.6   0.1    2.5  2  DUF756       Domain of unknown function (DUF756)
       0.37   11.0   2.7       0.35   11.1   0.8    1.9  2  Cohesin      Cohesin domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   2.1   5.8e-13   1.3e-09       4      84 ..     149     223 ..     146     264 .. 0.87
   2 !   22.8   0.0   3.7e-08   8.3e-05       8      84 ..     267     339 ..     246     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.8e-13
                             DUF11   4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtlP.aglayvsvsasqgtasaltsv.gsLeagesatlsftvrv 78 
                                       + d++++  Gd+v++t+tvtN g+++a +v v+D +P ++++yv +           ++ +sL+ ges    +++ +
  gi|386000721|ref|YP_005919020.1| 149 SLDRTDLSVGDEVKVTITVTNVGNDTARDVAVQDSPPlPAFRYVAGYPP--------KIkNSLQVGESDLAVYSMVA 217
                                       678999**************************************99999........34467888888888888888 PP

                             DUF11  79 trtaas 84 
                                       +++++ 
  gi|386000721|ref|YP_005919020.1| 218 ATEGEA 223
                                       877765 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.7e-08
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtl...PaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrt 81 
                                        ++  G++ t+t+t +N+g asa++v v+  l    + l+ v++          +s+ +++ag+s   s+t+r +r 
  gi|386000721|ref|YP_005919020.1| 267 GPISYGGEGTFTVTIRNQGDASASRVEVRSNLrsvGSDLEVVEGALD-------QSFFEIPAGGSESYSATLRGSRG 336
                                       48899************************977444466666666666.......555799*************9999 PP

                             DUF11  82 aas 84 
                                       ++ 
  gi|386000721|ref|YP_005919020.1| 337 GNY 339
                                       885 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 !   32.0   0.2   3.3e-11   7.4e-08      32     142 ..     156     262 ..     149     272 .. 0.89
   2 !   21.0   0.0   7.8e-08   0.00018      36     101 ..     274     340 ..     264     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.3e-11
                         TRAP_beta  32 vegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksgsfngtaavvt 108
                                       + g ++ v++t++NvG+ +A+dV ++D s p  aF  v g   +  ++l+ ge+   ++ +++ ++g  ++ a+vv 
  gi|386000721|ref|YP_005919020.1| 156 SVGDEVKVTITVTNVGNDTARDVAVQD-SPPLPAFRYVAGYPPKIKNSLQVGESDLAVYSMVAATEGEAKIPATVVR 231
                                       45899******************9987.66999******************************************** PP

                         TRAP_beta 109 Yresekgaelqlalssepgegdilaerevekkfs 142
                                       Y    ++++++ ++ss+ +   i  +r+++  +s
  gi|386000721|ref|YP_005919020.1| 232 Y---ADSKSAVSSASSKATSVTIKPKRKPDLLLS 262
                                       *...555668999999999999999999876665 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 7.8e-08
                         TRAP_beta  36 dltveytiyNvGssaAldVslvDdsf.peeaFevvsgslsakwerlapgenvshsfvvepkksgsfn 101
                                       + t+++ti N+G+++A  V+++ +     ++ evv+g+l+ ++  +++g + s+s++++    g++ 
  gi|386000721|ref|YP_005919020.1| 274 EGTFTVTIRNQGDASASRVEVRSNLRsVGSDLEVVEGALDQSFFEIPAGGSESYSATLRGSRGGNYT 340
                                       5689******************986636789***************************998888876 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   3.6e-06     0.008       2      82 ..     142     227 ..     141     240 .. 0.75
   2 !   21.2   0.0   1.1e-07   0.00025       1      84 [.     256     345 ..     256     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE........SEE-CTEEEEEEEEEE CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv........psLaagesttvsftwt 70 
                                       p L+v+++l  ++++vg+e+++t+tv+N G+++++++   +  +  l +  +v        +sL+ ges    ++++
  gi|386000721|ref|YP_005919020.1| 142 PKLEVSTSLDRTDLSVGDEVKVTITVTNVGNDTARDVA--VQDSPPLPAFRYVagyppkikNSLQVGESDLAVYSMV 216
                                       889*****************************999865..4555555566666666666667777777777777766 PP

                                       -S-S-CEEEEEE CS
                             CARDB  71 teategevtltv 82 
                                       ++ tege ++ +
  gi|386000721|ref|YP_005919020.1| 217 AA-TEGEAKIPA 227
                                       66.666666555 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.1e-07
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.........SEE-CTEEEEEEEE CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.........psLaagesttvsft 68 
                                       +pDL + + +++++ ++g e t+tvt++NqG+a++  ++v+  l     ++ +v          ++ ag+s++ s+t
  gi|386000721|ref|YP_005919020.1| 256 KPDLLL-SVASAGPISYGGEGTFTVTIRNQGDASASRVEVRSNLRSVG-SDLEVvegaldqsfFEIPAGGSESYSAT 330
                                       599999.888899999999************99998888777666655.7788889999999999************ PP

                                       EE-S-S-CEEEEEEEE CS
                             CARDB  69 wtteategevtltvvv 84 
                                          +   g++t+ +v+
  gi|386000721|ref|YP_005919020.1| 331 LRGS-RGGNYTIDLVA 345
                                       9999.9*****99987 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   2.9e-07   0.00064     270     380 ..     143     252 ..     127     269 .. 0.78
   2 !    7.5   0.0    0.0007       1.6      25      93 ..     275     343 ..     263     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-07
                              BatD 270 sfslsaslskdelkvgepltltvtisGtGN.....lkllqlPelnfpegfevYdpkpedntkktgnglsGsrteeya 341
                                       ++++s sl++++l+vg+ + +t+t++  GN     +     P+l+    +  Y+pk +++ ++ ++ l       y 
  gi|386000721|ref|YP_005919020.1| 143 KLEVSTSLDRTDLSVGDEVKVTITVTNVGNdtardVAVQDSPPLPAFRYVAGYPPKIKNSLQVGESDLA-----VYS 214
                                       678899999999999999999999999998554434445567777777888999999999998886665.....478 PP

                              BatD 342 lvPrkaGkytipaiefsyFDtatkkyetatlpeitikVe 380
                                       +v+ ++G+ +ipa  + y D ++  +  a++++  ++++
  gi|386000721|ref|YP_005919020.1| 215 MVAATEGEAKIPATVVRYADSKS-AVSSASSKATSVTIK 252
                                       89999999999999999999876.456778888888774 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0007
                              BatD  25 etfrLtftvngas..g....epdfsapslekdfevlsg.sqssstqiinGkssssssktwtytLapkkeGtltIpa 93 
                                        tf++t++ +g++  +     ++++  s+ +d+ev++g   +s ++i  G s+s     ++ tL+  + G++tI  
  gi|386000721|ref|YP_005919020.1| 275 GTFTVTIRNQGDAsaSrvevRSNLR--SVGSDLEVVEGaLDQSFFEIPAGGSES-----YSATLRGSRGGNYTIDL 343
                                       5889999988888542444456666..6777*******7667777888887777.....999************74 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 ?    0.2   0.0       0.4   8.9e+02      49      73 ..      31      55 ..      30      57 .. 0.87
   2 !   12.0   0.2   8.7e-05      0.19       3      31 ..     157     185 ..     155     187 .. 0.92
   3 !    8.2   0.1    0.0013         3       3      28 ..     271     296 ..     269     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.4
                       NPCBM_assoc 49 pGetveatvkVtppagaaaGdyevt 73
                                      + +t++ ++ +++++g   Gdy+v+
  gi|386000721|ref|YP_005919020.1| 31 AEDTTSRDFSLRVGEGVRIGDYRVE 55
                                      6678889999*************97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.7e-05
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslP 31 
                                        G++v++t+tvtn g+++a++v ++ s P
  gi|386000721|ref|YP_005919020.1| 157 VGDEVKVTITVTNVGNDTARDVAVQDSPP 185
                                       69**********************98887 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0013
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslsl 28 
                                        G + t+t+t+ n+g+a+a++v+++ 
  gi|386000721|ref|YP_005919020.1| 271 YGGEGTFTVTIRNQGDASASRVEVRS 296
                                       58899******************986 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   2.7e-05     0.061      21      51 ..     151     185 ..     137     188 .. 0.75
   2 ?    0.8   0.0      0.24   5.3e+02     105     123 ..     212     230 ..     201     233 .. 0.85
   3 ?   -2.8   0.0       3.1   6.8e+03      93     118 ..     316     341 ..     314     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                             bMG10  21 a..klkvGdkvrvrltvt.tprdl.eyvaledplP 51 
                                       +   l+vGd+v+v++tvt + +d  ++va++d+ P
  gi|386000721|ref|YP_005919020.1| 151 DrtDLSVGDEVKVTITVTnVGNDTaRDVAVQDSPP 185
                                       1337**************9777555******9644 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                             bMG10 105 eylvravtpGtfsvppaka 123
                                        y + a+t+G+ ++p++ +
  gi|386000721|ref|YP_005919020.1| 212 VYSMVAATEGEAKIPATVV 230
                                       599************9987 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.1
                             bMG10  93 fadylpkgtytfeylvravtpGtfsv 118
                                       f++  + g+ +++ ++r ++ G++++
  gi|386000721|ref|YP_005919020.1| 316 FFEIPAGGSESYSATLRGSRGGNYTI 341
                                       66666778888999999999999986 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.1   4.7e+03      10      10 ..     156     156 ..      95     181 .. 0.60
   2 ?   11.6   0.1   0.00018      0.41      12      65 ..     275     343 ..     142     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                            DUF756  10 a 10 
                                        
  gi|386000721|ref|YP_005919020.1| 156 S 156
                                       1 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00018
                            DUF756  12 gnlrltlrNtgk.aaarftVydnaka.............pwtytveagdqledhwklassg.gwYdltV 65 
                                       g++++t+rN+g+ +a r+ V++n +                 + + ag + +++ +l+ s  g Y +  
  gi|386000721|ref|YP_005919020.1| 275 GTFTVTIRNQGDaSASRVEVRSNLRSvgsdlevvegaldQSFFEIPAGGSESYSATLRGSRgGNYTIDL 343
                                       889********85677*******9889887777777766688888999999999999888878887765 PP

>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00016      0.35       2      28 ..     147     173 ..     146     182 .. 0.84
   2 ?   -2.2   0.0         2   4.6e+03     114     138 ..     199     224 ..     194     251 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       EEEESEEEE-TTSEEEEEEEEESECTT CS
                           Cohesin   2 evkidkvsakvGdtvtvpvtvsnvskk 28 
                                       ++++d+++  vGd+v+v++tv+nv ++
  gi|386000721|ref|YP_005919020.1| 147 STSLDRTDLSVGDEVKVTITVTNVGND 173
                                       678999999***************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                       EEEEEEEEETTSEBE-EEE.ECEEEE CS
                           Cohesin 114 isdtlsfgdgeekeiskvt.vdgtin 138
                                       i+++l +g+++++  s+v+ ++g+ +
  gi|386000721|ref|YP_005919020.1| 199 IKNSLQVGESDLAVYSMVAaTEGEAK 224
                                       55556666666666666655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2760.98
//
Query:       gi|386000722|ref|YP_005919021.1|  [L=279]
Description: nicotinate-nucleotide diphosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-53  181.0   0.0    2.3e-53  180.5   0.0    1.3  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
      3e-20   72.0   0.0    6.9e-20   70.9   0.0    1.6  1  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal
     0.0026   17.1   0.1     0.0084   15.5   0.1    1.8  2  TMP-TENI   Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   0.0   3.8e-57   2.3e-53       1     169 []     109     276 ..     109     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 3.8e-57
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreav 77 
                                       i tlt+ +++ a ++  r++ TRkttPg+r +ek+Av +GGgd hr++Ls+ v+ikdnh+++++ ++ea+ ++r  +
  gi|386000722|ref|YP_005919021.1| 109 ISTLTRDCAALAGRV--RVASTRKTTPGFRSFEKRAVAVGGGDPHRFDLSSSVMIKDNHLKLMS-LEEALAAARRMA 182
                                       667888887777766..9*******************************************998.************ PP

                                       TTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-SEE CS
                         QRPTase_C  78 dkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvdvi 152
                                       ++++kieveve + ++ +++  +adiim+Dn+ ++e++  ve+l +   r  v++e+SGg+t e+v eya +gvdvi
  gi|386000722|ref|YP_005919021.1| 183 SFTKKIEVEVEGVTDAVKAARLGADIIMFDNMRPDEIRAGVELLVREGLRdrVILEASGGITPETVPEYAATGVDVI 259
                                       ******************************************9965555556************************* PP

                                       EECHHCHTB----EEEE CS
                         QRPTase_C 153 svgalthsvkalDislk 169
                                       s+galt s++++D+sl+
  gi|386000722|ref|YP_005919021.1| 260 SLGALTRSSPWIDFSLE 276
                                       ***************95 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.2e-23   6.9e-20      14      89 .]      33     107 ..      28     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.2e-23
                                       TTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  14 eekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                                       +e  aka i+ake +vv+G+++a ++++++ gle + lv++Ge+v++g  ++ei+G+a a+l+aER++Ln++ r+S
  gi|386000722|ref|YP_005919021.1|  33 PEVDAKAAIVAKERCVVSGVAEAFAILNYF-GLEGSGLVPEGEEVAAGRRVMEIRGPAAAILRAERLVLNFMGRMS 107
                                       57789*************************.********************************************9 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.16   9.8e+02     127     163 ..     110     152 ..      89     161 .. 0.66
   2 !   15.5   0.1   1.4e-06    0.0084      67     176 ..     154     260 ..     149     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.16
                          TMP-TENI 127 pTdtKkdaeplgleglkelaeale......iPvvaiGGitlen 163
                                        T t++ a+ +g  +++ +++++       +  va+GG ++++
  gi|386000722|ref|YP_005919021.1| 110 STLTRDCAALAGRVRVASTRKTTPgfrsfeKRAVAVGGGDPHR 152
                                       5666666666666666666666666666668899999988876 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-06
                          TMP-TENI  67 dlalavgadgvHlgqddl..pvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleg 141
                                       dl   v ++  Hl   +l  ++a ar++    + i + v++  +a +a++lgad i++  + p + + + e l  eg
  gi|386000722|ref|YP_005919021.1| 154 DLSSSVMIKDNHLKLMSLeeALAAARRMASFTKKIEVEVEGVTDAVKAARLGADIIMFDNMRPDEIRAGVELLVREG 230
                                       5555566666666654442267788999999999*************************998888887777777777 PP

                          TMP-TENI 142 lkelaealeiPvvaiGGitlenvaevleagadgva 176
                                       l++      + + a GGit+e+v+e +++g+d ++
  gi|386000722|ref|YP_005919021.1| 231 LRDR-----VILEASGGITPETVPEYAATGVDVIS 260
                                       6654.....45789******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1993.15
//
Query:       gi|386000723|ref|YP_005919022.1|  [L=270]
Description: putative L-aspartate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-34  116.4   0.5    1.2e-33  115.3   0.5    1.6  1  DUF108           Domain of unknown function DUF108
    1.3e-21   77.4   0.1    2.6e-21   76.5   0.1    1.5  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    5.8e-07   29.7   0.0      1e-06   28.9   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    2.6e-06   27.9   0.2    4.8e-06   27.1   0.2    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    4.1e-05   23.7   0.1    7.6e-05   22.8   0.1    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00029   21.6   0.0    0.00067   20.5   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00054   20.2   0.2      0.004   17.4   0.1    2.3  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0019   17.6   0.0     0.0033   16.8   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0092   16.2   1.6       0.33   11.2   0.2    3.0  4  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.023   15.1   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.012   15.8   0.0       0.02   15.1   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.069   13.0   1.4       0.16   11.9   0.4    2.1  3  Rossmann-like    Rossmann-like domain


Domain annotation for each model (and alignments):
>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.5   8.2e-37   1.2e-33       2      89 .]     170     256 ..     169     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 8.2e-37
                                       SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEE CS
                            DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenP 78 
                                       ++ptv+FeG+a+ea+ +fP+nvNvaa+l+L a+g  rv+v++vadp+++ nihei +eG+fg+++++ven+psp+nP
  gi|386000723|ref|YP_005919022.1| 170 SKPTVIFEGPAEEAVSAFPANVNVAATLSLTARG-ARVRVRIVADPDIEVNIHEICAEGDFGRITTRVENVPSPRNP 245
                                       789*****************************88.9***************************************** PP

                                       EEEHHHHHHHH CS
                            DUF108  79 ktsalaalsvi 89 
                                       kts laals+i
  gi|386000723|ref|YP_005919022.1| 246 KTSRLAALSAI 256
                                       *********86 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.1   1.7e-24   2.6e-21       1     117 []       9     121 ..       9     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.7e-24
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahldpdvvVEcasseavaelv 76 
                                       G+GaiG +++++++r++   e+elvav dr+ +++++  ++ l+ ++  l+l++l++    d+vVE+as++av e++
  gi|386000723|ref|YP_005919022.1|   9 GCGAIGLEIARAIDRGEV--EAELVAVFDRNgDRARE-LLKGLRGKPRLLELEELVE--GSDIVVEAASQRAVPEVA 80 
                                       9****************8..7**********555555.567999999**********..****************** PP

                                       HHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  77 lkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                        +aL +g d++++++gal d++l+++  e+a+  g+++y++
  gi|386000723|ref|YP_005919022.1|  81 RAALGRGRDLMIMSVGALLDPGLRRTVEELARDRGCRVYLP 121
                                       ***************************************86 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   6.8e-10     1e-06       2     113 ..       4     111 ..       3     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.8e-10
                                       EEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-H CS
                            DapB_N   2 kvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtp 77 
                                       k+++vG+ G +G e+++a+++ + ++elva++dr++      d  + l +g  g +   +lee++e +d++++  + 
  gi|386000723|ref|YP_005919022.1|   4 KIGLVGC-GAIGLEIARAIDRgEVEAELVAVFDRNG------DRARELLKGLRGKPRLLELEELVEGSDIVVEAASQ 73 
                                       89*****.***********996789*********99......5555556678999999******************* PP

                                       HHHHHHHHHHHHTT-EEEE--SS-..-HHHHHHHHHHT CS
                            DapB_N  78 eavlenlklalekgvklViGTTGl..seeelaeleela 113
                                        av e++++al +g +l i + G   ++  + ++eela
  gi|386000723|ref|YP_005919022.1|  74 RAVPEVARAALGRGRDLMIMSVGAllDPGLRRTVEELA 111
                                       *************9999987777544555566666655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   3.2e-09   4.8e-06       1      81 [.       4      83 ..       4      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.2e-09
                                      EEEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78
                                      kig++G+G +g  +a+ ++ +g+ +++ +  + +rn ++a+el + l  k    + ee++e +d+vv a   ++v+ev+
  gi|386000723|ref|YP_005919022.1|  4 KIGLVGCGAIGLEIAR-AIDRGEvEAELVA-VFDRNGDRARELLKGLRGKPRLLELEELVEGSDIVVEAASQRAVPEVA 80
                                      79*************9.6777773555555.66*********************************************9 PP

                                      HHC CS
                     F420_oxidored 79 sel 81
                                      +++
  gi|386000723|ref|YP_005919022.1| 81 RAA 83
                                      886 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   5.1e-08   7.6e-05      14      85 ..       4      73 ..       2     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.1e-08
                                      EEEEES-SHHHHHHHHHHHCC..T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlak..gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85
                                      k+ l+G G ++ ++a+++ +   +++ v+v+ R+ +ra+el + l+g+     +l el+el++ +d+v+ a + 
  gi|386000723|ref|YP_005919022.1|  4 KIGLVGCGAIGLEIARAIDRGevEAELVAVFDRNGDRARELLKGLRGK----PRLLELEELVEGSDIVVEAASQ 73
                                      789***************9883355679*****************999....88999************99875 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.5e-07   0.00067       1      90 [.       3      91 ..       3      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.5e-07
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheel 78
                                      l+++++G+G ig + +r++ + + ++e+va++d++  ra+++ + ++ +    +leel++    d+v+ a   +   e+
  gi|386000723|ref|YP_005919022.1|  3 LKIGLVGCGAIGLEIARAIDRGEVEAELVAVFDRNGDRARELLKGLRGKpRLLELEELVE--GSDIVVEAASQRAVPEV 79
                                      589*******************9999****************888777778889999999..56888878778888888 PP

                                      HHHHHHTT-EEE CS
                      GFO_IDH_MocA 79 akaaleagkhvl 90
                                      a+aal +g +++
  gi|386000723|ref|YP_005919022.1| 80 ARAALGRGRDLM 91
                                      888887777665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.7e-06     0.004       1      97 [.       5      91 ..       5     114 .. 0.84
   2 ?   -3.1   0.0       5.8   8.7e+03      45      71 ..     202     228 ..     192     240 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                                      EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                      + ++G+G++G  +a+ + r +   a  ++v dr+ +++++l+   +g r +++        + L++l+++ d+vv ++ 
  gi|386000723|ref|YP_005919022.1|  5 IGLVGCGAIGLEIARAIDRGEVE-AeLVAVFDRNGDRARELL---KGLRGKPR------LLE-LEELVEGSDIVVEAAS 72
                                      6789***************8765.559**********99998...56665554......456.999************* PP

                                      GGGHHHHHHHHHHHT-EEE CS
                   Sacchrp_dh_NADP 79 pissldvlkaCietgvhyv 97
                                      +    +v++a++ +g + +
  gi|386000723|ref|YP_005919022.1| 73 QRAVPEVARAALGRGRDLM 91
                                      **********998887665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.8
                                       TTTCEEEEE--TTTHHHHHHHHHTTSS CS
                   Sacchrp_dh_NADP  45 lgvrfeaialdaenyeavLaallkegd 71 
                                       +g r+  + +   ++e  + ++++egd
  gi|386000723|ref|YP_005919022.1| 202 RGARVRVRIVADPDIEVNIHEICAEGD 228
                                       444444444444444444555555554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.2e-06    0.0033      38      97 ..       4      69 ..       2      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                                      EEEEES-SHHHHHHHHHHHHTT-E...EEEESSSHHHHH...CHHHHTCEECSHHHHHHH-SEEEE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmk...viaydrskkkee...eeeelgvelvsleellaesDivsl 97
                                      ++G++G+G+IG ++a+ +   +++   v ++dr+ ++ +   +  + + +l +leel++ sDiv+ 
  gi|386000723|ref|YP_005919022.1|  4 KIGLVGCGAIGLEIARAIDRGEVEaelVAVFDRNGDRARellKGLRGKPRLLELEELVEGSDIVVE 69
                                      79****************9655542236677888776665433333334889************85 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   0.00022      0.33       3      38 ..       7      45 ..       5      50 .. 0.90
   2 ?   -3.8   0.0        10   1.5e+04      16      32 ..      59      74 ..      57      82 .. 0.43
   3 ?    2.4   0.0      0.12   1.8e+02      34      72 ..     107     148 ..     103     155 .. 0.77
   4 ?   -1.2   0.0       1.6   2.3e+03      74      96 ..     192     214 ..     178     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      EES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHH CS
                            TrkA_N  3 iiGlGrvGrslaeeLsegg...kdvvvidkdeerveelr 38
                                      ++G+G +G ++a+ + +g+   + v v d++ +r++el 
  gi|386000723|ref|YP_005919022.1|  7 LVGCGAIGLEIARAIDRGEveaELVAVFDRNGDRARELL 45
                                      79***************8889977***********9985 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 10
                                      HHHHTTEEEEEEESSHH CS
                            TrkA_N 16 eLseggkdvvvidkdee 32
                                      eL eg+ d+vv   +++
  gi|386000723|ref|YP_005919022.1| 59 ELVEGS-DIVVEAASQR 74
                                      455544.2333333333 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.12
                                       HHHH.HHTTSEEEE..S-TTSHHHHHHTTGGGESEEEE-SSS CS
                            TrkA_N  34 veel.reeglevvv..gdatdeevLeeagiekadaviaatgd 72 
                                       veel r++g++v+   g  +  + L++ag+ ++d+v  +t +
  gi|386000723|ref|YP_005919022.1| 107 VEELaRDRGCRVYLpsGAISGLDGLKSAGAGRIDIVTLTTTK 148
                                       444426777776665688999999***********9999864 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHTSSSEEEEEE CS
                            TrkA_N  74 eanilavllakelnpkkkiiara 96 
                                        + + ++l+a+  +   +i+a  
  gi|386000723|ref|YP_005919022.1| 192 NVAATLSLTARGARVRVRIVADP 214
                                       34444455555555556666544 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.5e-05     0.023       1      90 [.       4      87 ..       4     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                      EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagv 78
                                      k+++vG  G++G e++r +++ + e+elv+++   r +G + +e+ k l+++  l   +   e +++ div+ a+++ +
  gi|386000723|ref|YP_005919022.1|  4 KIGLVG-CGAIGLEIARAIDRgEVEAELVAVFD--R-NGDRARELLKGLRGKPRLLELE---ELVEGSDIVVEAASQRA 75
                                      799***.9*************888888888776..4.5788888888555554444333...678************** PP

                                      HHHHHHHHHHTT CS
                    Semialdhyde_dh 79 skelapklaeag 90
                                        e+a++++ +g
  gi|386000723|ref|YP_005919022.1| 76 VPEVARAALGRG 87
                                      ****99997766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.3e-05      0.02       1      61 [.       4      69 ..       4     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                                      EEEEE--SHHHHHHHHHHHHTT-E...EEEE-SSHHHHHHHHHT..TEEE-SSHHHHHHHCSEEEE CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagyk...vavynrtkekveelvae..gakaaesieelvasldvvit 61
                                      kig++G G +G ++a+ + + + +   vav++r+ ++++el++   g   + ++eelv++ d+v+ 
  gi|386000723|ref|YP_005919022.1|  4 KIGLVGCGAIGLEIARAIDRGEVEaelVAVFDRNGDRARELLKGlrGKPRLLELEELVEGSDIVVE 69
                                      79****************6655443349**************874347778889999999998864 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00011      0.16      11      86 ..       3      81 ..       1      97 [. 0.80
   2 ?    0.9   0.0      0.26   3.9e+02      51      94 ..      73     116 ..      69     132 .. 0.69
   3 ?   -3.3   0.0       5.2   7.8e+03       9      16 ..     204     211 ..     186     227 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                     Rossmann-like 11 lsvGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdv....pvlevedvaaraellllavPdaelpglv 85
                                      l++G+++ G +G  ++ a++r +     + a+ +   +ra++ l +      +le+e++++ +++++ a     +p++ 
  gi|386000723|ref|YP_005919022.1|  3 LKIGLVGCGAIGLEIARAIDRGEVE-AELVAVFDRNGDRARELLKGLrgkpRLLELEELVEGSDIVVEAASQRAVPEVA 80
                                      89*******************7754.55667778888888887765422225789************999888888876 PP

                     Rossmann-like 86 k 86
                                      +
  gi|386000723|ref|YP_005919022.1| 81 R 81
                                      5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.26
                     Rossmann-like  51 errlPdvpvlevedvaaraellllavP...daelpglvkglaatgav 94 
                                       +r +P+v+++ +    +  +l++++v    d+ l   v++la    +
  gi|386000723|ref|YP_005919022.1|  73 QRAVPEVARAAL---GRGRDLMIMSVGallDPGLRRTVEELARDRGC 116
                                       455777777766...56667777766433399999999999987554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.2
                     Rossmann-like   9 arlsvGii 16 
                                       ar+ v i+
  gi|386000723|ref|YP_005919022.1| 204 ARVRVRIV 211
                                       23333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2074.57
//
Query:       gi|386000724|ref|YP_005919023.1|  [L=462]
Description: Periplasmic copper-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-43  146.4  21.9    6.2e-23   81.3  11.0    2.4  2  NosD             Periplasmic copper-binding protein (NosD)
    9.7e-23   80.8  24.0      2e-15   57.0   0.1    2.3  2  Beta_helix       Right handed beta helix region
     0.0063   16.4  11.5      0.009   15.9   0.0    3.3  2  Pectate_lyase_3  Pectate lyase superfamily protein


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 !   70.2   3.1   2.5e-23   1.5e-19      18     168 ..     124     273 ..     107     277 .. 0.92
   2 !   81.3  11.0     1e-26   6.2e-23     105     240 ..     286     410 ..     282     411 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.5e-23
                              NosD  18 giqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnn 93 
                                       gi +   ++  +++  ++ s++gil++++ n+ti ++ i+ ++ G+ +++ ++ ++ ++t+++++ +G +++ ss+ 
  gi|386000724|ref|YP_005919023.1| 124 GILV-DGNDVLLEDMIVNGSEAGILVKYARNFTILNSSIQRCDIGLLIQEGSGGRVAGSTFQDCKkYGASIEASSGF 199
                                       4444.335556699999**********************************************************99 PP

                              NosD  94 tlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNy 168
                                        le N +++n ++Gi+l+ds+++t++ N + +n +G+fl nss   +++N+ ++n  +G++ ++s+++n+i nN 
  gi|386000724|ref|YP_005919023.1| 200 SLERNQVIGNPGAGIMLKDSTGCTLRWNSFIENWQGLFLWNSSFCDLMENEADRNVYYGMV-IASGSNNSILNNE 273
                                       *************************************************************.************5 PP

  == domain 2  score: 81.3 bits;  conditional E-value: 1e-26
                              NosD 105 nyGill.sdssnntisnNtisnnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFinnsenvkyd 179
                                       ++Gi++ ++s++n +++N+ s+n +G+ l++    n i +N+i++n + Gi  l+++e+n++y+N+F  n ++ +++
  gi|386000724|ref|YP_005919023.1| 286 GFGISIqENSTYNLVAGNVLSENLNGLDLTRGcRFNLIFSNEIYEN-SNGIR-LDKNENNLVYKNNFRRNLITGYDN 360
                                       567854167899******************9989************.*****.**************9999999888 PP

                              NosD 180 gsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgv...iDylplvnp 240
                                       +s  n Wn +              GNy++dy+g+D+dgDG+gD pY i++g+   +D  pl++p
  gi|386000724|ref|YP_005919023.1| 361 AS-HNFWNGSV-------------GNYYDDYRGRDRDGDGVGDDPYWIPKGSscvVDWRPLMTP 410
                                       86.****9999.............**********************9998877889****9998 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 !   57.0   0.1   3.3e-19     2e-15       4     156 ..      79     249 ..      76     251 .. 0.90
   2 !   26.9  19.3   6.2e-10   3.7e-06      37     142 ..     248     358 ..     243     375 .. 0.72

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.3e-19
                                       EE-SS-E.EEESEEEES-.........................SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT- CS
                        Beta_helix   4 singssnvtiknntisns.........................ggyGiylrgssnvvienneiannsgsGiyilgss 55 
                                        i+g ++ +i +++++++                         +++Gi ++g++  ++e+  +++ s+ Gi ++++ 
  gi|386000724|ref|YP_005919023.1|  79 TIRGHGV-QILGFQVDGVpknqedkfrfymdlasrkpqyslnqPNSGILVDGNDV-LLEDMIVNG-SEAGILVKYAR 152
                                       5555555.7888888888888888888888888888888888899*********9.***999999.*********** PP

                                       S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES- CS
                        Beta_helix  56 nntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnN 132
                                       n+ti n++i ++   g+ ++++s+  + ++++ d++++G +++ ss  ++e+N++ +n g+Gi + ds  ++t + N
  gi|386000724|ref|YP_005919023.1| 153 NFTILNSSIQRCD-IGLLIQEGSGGRVAGSTFQDCKKYGASIEASSGFSLERNQVIGNPGAGIMLKDST-GCTLRWN 227
                                       *************.*******************************************************.******* PP

                                       EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix 133 titnnkgaGiavvgsssnvtvrnN 156
                                       ++  n   G+++++ss  + + +N
  gi|386000724|ref|YP_005919023.1| 228 SFIENW-QGLFLWNSSF-CDLMEN 249
                                       ******.*******998.666555 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 6.2e-10
                                       ES-EEES-SS-SEEE-TT-S-EEES-EEE---.......SEEE-TT.--S--EEES-EEES-SS-SEE-T.T-S--E CS
                        Beta_helix  37 enneiannsgsGiyilgssnntisnntisdnn.......gggialf.gasnnlienneitdnggsGiyln.yssnnt 104
                                       e ne   n ++G+ i ++snn i nn+ +  +       g+gi ++ ++ +nl+ +n  ++n + G+ l+ ++  n 
  gi|386000724|ref|YP_005919023.1| 248 E-NEADRNVYYGMVIASGSNNSILNNEARKTGgggygfqGFGISIQeNSTYNLVAGNVLSENLN-GLDLTrGCRFNL 322
                                       4.77777788888888888888888888666666777778888888888888888888888887.888886688888 PP

                                       EES-EEESTT--SEE---TT---EEES-EEES-SSEEE CS
                        Beta_helix 105 ienNiidnnagsGividdsssnvtvtnNtitnnkgaGi 142
                                       i  N i++n+ +Gi +d ++ n+ v +N++  n + G 
  gi|386000724|ref|YP_005919023.1| 323 IFSNEIYENS-NGIRLDKNE-NNLVYKNNFRRNLITGY 358
                                       8888888888.888888888.55555555555543333 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-06     0.009     131     213 ..     101     190 ..      69     192 .. 0.79
   2 ?    0.8   6.3     0.062   3.7e+02     118     205 ..     257     349 ..     227     369 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                                       ES-SSEEE-SSS.......---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E CS
                   Pectate_lyase_3 131 envefemseasg.......tkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg 199
                                       +++ f+m+ as        + ++gi + +g+   l+d++++g ++ gi v    +ft+ n  ++ +  g  +++g+g
  gi|386000724|ref|YP_005919023.1| 101 DKFRFYMDLASRkpqyslnQPNSGI-LVDGNDVLLEDMIVNG-SEAGILVkYARNFTILNSSIQRCDIGLLIQEGSG 175
                                       5667777777763333332222344.445677778*******.*******56************************* PP

                                       EEEEEEEEESSSE.E CS
                   Pectate_lyase_3 200 wtlknvkinnceg.G 213
                                         +++ ++++c++ G
  gi|386000724|ref|YP_005919023.1| 176 GRVAGSTFQDCKKyG 190
                                       9999*******9877 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.062
                                       ES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEE....ES-EEES.-SS-SEEES.-EEEEEES-EEE-S CS
                   Pectate_lyase_3 118 tgihwqtaqatslenvefemseasgtkhqgifiengsggfl....ndlvfsg.lgdigiavg.nqqftvrnitfnna 188
                                       +g+   ++++ s+ n+e + + + g+  qg+ i+ ++++++     ++  ++ +g +  + g + + +++n  ++n 
  gi|386000724|ref|YP_005919023.1| 257 YGMVIASGSNNSILNNEARKTGGGGYGFQGFGISIQENSTYnlvaGNVLSENlNGLDLTR-GcRFNLIFSNEIYEN- 331
                                       555555555555555555555555555554444444444442233344444422222222.123333333333333. PP

                                       --SEEE-TT-E.EEEEEE CS
                   Pectate_lyase_3 189 ttgievlwgwg.wtlknv 205
                                       ++gi+++++++  ++kn+
  gi|386000724|ref|YP_005919023.1| 332 SNGIRLDKNENnLVYKNN 349
                                       577777775555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2666.19
//
Query:       gi|386000725|ref|YP_005919024.1|  [L=458]
Description: phosphoribosylaminoimidazolecarboxamide formyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-87  291.7   0.0    8.6e-87  291.3   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.3   0.0   4.8e-91   8.6e-87      16     296 .]      89     389 ..      77     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: 291.3 bits;  conditional E-value: 4.8e-91
                                       GHHHHHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSE...EEEEEEEEESSSSSTTS-EEEEE-TT CS
                   AICARFT_IMPCHas  16 dYeevleelkk.gevsletrkklaakaFahtaaYDaaiaeylskqlpetlklslekkqkLrYGeNphQkaalyeeee 91 
                                        +  v+e+l + g++s+etr+ la++a     + Da   + l+ + p+ l  ++ek+q+LrYGeN+hQ+a+ly++ +
  gi|386000725|ref|YP_005919024.1|  89 WWGIVMEDLMAeGRLSEETRRLLATEALYFLITRDAEKLSALQGEGPRYLVETYEKVQDLRYGENWHQTASLYSKPD 165
                                       5667888888879*****************************99999999999********************9999 PP

                                       STTHHH-EEEESS---HHHHHHHHHHHHHHCTS..........EEEEEEETTEEEEEEEESSHHHHHHHHHCCSHHH CS
                   AICARFT_IMPCHas  92 eeglakaeqlqGkelsynNllDadaalelvkef..........aavaivKHanpcGvAvgetlaeAyekAlaaDpvS 158
                                         gl++a +l Gke+synN++Da+++le++ ++          a ++ivKHanpcGvA g++  eAy++Ala+Dp S
  gi|386000725|ref|YP_005919024.1| 166 GFGLHRAPKLCGKEMSYNNVVDAETTLEMLMDLleydgvreerALAVIVKHANPCGVAYGSNEIEAYRRALATDPKS 242
                                       99*****************************7666677766554666****************************** PP

                                       HTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EEEE-SS...-........EEEEETTEEEE CS
                   AICARFT_IMPCHas 159 aFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrvlelke...e........elrsvsgglLv 224
                                       aFGg+i ++++vda++aee++++f+ev++Ap++++ealeil++k n r+le++e            + rsv gglLv
  gi|386000725|ref|YP_005919024.1| 243 AFGGVIGFSEPVDADLAEEMRDHFIEVLLAPGYDPEALEILREKPNRRILEISEllsGrsrlyagrQSRSVFGGLLV 319
                                       ****************************************************99665056677888*********** PP

                                       EE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHHHHHHHHHHH CS
                   AICARFT_IMPCHas 225 qerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRvdsarlAvek 296
                                       q+ d+ +i+  ++kvvt++ pt++e+ +l+fawkv k+vkSNa v+++ +qt+giG+Gq+sRvdsar+ +ek
  gi|386000725|ref|YP_005919024.1| 320 QDYDTGDIK--DWKVVTERGPTPAETLALRFAWKVTKFVKSNALVYTTANQTIGIGSGQVSRVDSARFGAEK 389
                                       ****97775..6*******************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2857.22
//
Query:       gi|386000726|ref|YP_005919025.1|  [L=111]
Description: hypothetical protein Mhar_0009 [Methanosaeta harundinacea 6Ac]
Scores for 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-17   61.0   0.0    1.1e-16   60.7   0.0    1.1  1  DUF167           Uncharacterised ACR, YggU family COG1872
     0.0078   15.6   0.0      0.011   15.1   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   1.2e-20   1.1e-16       1      76 [.      17      91 ..      17      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.2e-20
                                      EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                      gv+++ +v Pg+++  ++  +++ +r+al+ ++++ +++G+AN++l + +a+++g+p ++v++ sG+ks +K v +
  gi|386000726|ref|YP_005919025.1| 17 GVLIRFEVAPGSSRLLVP-SGYNPWRKALEAKLTERAERGRANQQLESAVAEIFGIPSHRVQVASGTKSYRKAVIV 91
                                      689***************.8899*************************************************9976 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-06     0.011      18      63 ..      51      97 ..      38     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-06
                                      -SSSSHHHHHHHHHHHHHHT.-SEEEEESSHHHHHHHHHHHTTTTTT CS
                   DegT_DnrJ_EryC1 18 wltsgpeveeFEkafaaylg.vkhaiavssGtaAlhlaLralgvgpg 63
                                         +g+ ++++E+a+a+  g   h + v+sGt++   a  +lgvgp+
  gi|386000726|ref|YP_005919025.1| 51 RAERGRANQQLESAVAEIFGiPSHRVQVASGTKSYRKAVIVLGVGPE 97
                                      3344****************999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 722.87
//
Query:       gi|386000727|ref|YP_005919026.1|  [L=153]
Description: hypothetical protein Mhar_0010 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0004   20.6   0.1     0.0033   17.6   0.1    2.1  1  Toprim    Toprim domain
    0.00076   19.9   0.1     0.0044   17.5   0.1    2.0  1  Toprim_4  Toprim domain
     0.0096   16.3   0.0      0.014   15.8   0.0    1.4  1  Toprim_2  Toprim-like


Domain annotation for each model (and alignments):
>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.4e-07    0.0033      53      88 ..      73     108 ..      42     130 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.4e-07
                                       HHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHT CS
                            Toprim  53 lkalkelakradeiilatDpDreGeaiawellevlk 88 
                                       l++ +     ++e++++tD Dr+G ++a ++  +l+
  gi|386000727|ref|YP_005919026.1|  73 LEVAEDGVMGYEEVVILTDWDRAGDELARRIELHLR 108
                                       33344555899*****************99976655 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.3e-07    0.0044       2      76 ..      42     105 ..      41     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.3e-07
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlae 76 
                                       ++i+VEg+ D  +l + g+++ +     +  +l+ ++   + +          +ev++++d D +G++ a r+  
  gi|386000727|ref|YP_005919026.1|  42 AAIVVEGERDERSLRELGVEGPIVRAARRP-ALEVAEDGVMGY----------EEVVILTDWDRAGDELARRIEL 105
                                       689****************99887666555.556666336666..........9****************99755 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.4e-06     0.014      40      75 ..      81     114 ..      44     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                          Toprim_2  40 erypekkvvlalDnDkaGrkaakrlaellreagvre 75 
                                         y  ++vv+ +D D+aG++ a+r+  +lr  g+r+
  gi|386000727|ref|YP_005919026.1|  81 MGY--EEVVILTDWDRAGDELARRIELHLRGMGARV 114
                                       456..89**********************9888433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 932.57
//
Query:       gi|386000728|ref|YP_005919027.1|  [L=170]
Description: Nucleoside-triphosphatase THEP1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-49  166.6   0.0    5.1e-49  166.4   0.0    1.0  1  NTPase_1     NTPase
    1.6e-06   27.9   0.5    1.9e-06   27.6   0.5    1.1  1  DUF2478      Protein of unknown function (DUF2478)
     0.0001   22.3   1.1      0.019   15.0   0.2    2.4  2  AAA_5        AAA domain (dynein-related subfamily)
    0.00036   21.1   0.0    0.00061   20.3   0.0    1.4  1  AAA_18       AAA domain
    0.00078   19.7   0.5       0.11   12.8   0.2    2.3  2  AAA_22       AAA domain
     0.0013   19.2   1.7     0.0028   18.1   1.7    1.7  1  AAA_16       AAA ATPase domain
     0.0019   18.3   0.3      0.015   15.3   0.3    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
      0.002   18.5   0.9       0.01   16.2   0.9    2.0  1  AAA_19       AAA domain
     0.0021   17.1   0.3     0.0037   16.3   0.3    1.4  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0085   15.8   0.0      0.028   14.1   0.0    1.9  1  AAA_24       AAA domain
  ------ inclusion threshold ------
      0.019   14.7   1.0      0.036   13.8   0.1    1.8  2  AAA_29       P-loop containing region of AAA domain
      0.027   14.2   4.8      0.088   12.5   4.8    1.8  1  AAA_30       AAA domain
      0.028   14.7   1.5      0.055   13.7   1.4    1.8  1  AAA_28       AAA domain
      0.046   13.3   3.1       0.53    9.8   0.1    2.5  2  AAA_25       AAA domain
      0.046   14.1   0.0      0.092   13.2   0.0    1.6  1  AAA          ATPase family associated with various cellular a
      0.051   13.6   0.1        6.2    6.9   0.1    2.1  2  AAA_14       AAA domain
      0.055   13.4   0.1      0.089   12.7   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
      0.065   13.4   0.2       0.11   12.7   0.2    1.7  1  AAA_33       AAA domain
       0.16   11.9   0.2       0.28   11.1   0.2    1.4  1  NACHT        NACHT domain
       0.16   12.4   0.5       0.35   11.3   0.4    1.8  1  AAA_17       AAA domain
       0.17   12.4   0.1       0.24   11.9   0.1    1.4  1  ABC_tran     ABC transporter


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.4   0.0   5.9e-52   5.1e-49       3     167 ..       6     164 ..       4     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.4 bits;  conditional E-value: 5.9e-52
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdve 79 
                                       ++TG pGvGK+Tlv++++ l+   g + gG+ ++evr ggrrigF++ dl +ge g+La+ +   +p+vg+y v++ 
  gi|386000728|ref|YP_005919027.1|   6 AVTGAPGVGKSTLVERAAALI---GGRTGGVSAREVRIGGRRIGFQLSDLLTGEVGTLASLD-GPGPKVGRYRVHLA 78 
                                       79*******************...999***********************************.99************ PP

                                       HHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1  80 sfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevt 156
                                       ++ee++++a+++a++ea+++viDE+G+mEl s++f eave +L+s+kp+lav+h r++++l ++ire   +++f vt
  gi|386000728|ref|YP_005919027.1|  79 DLEEVGARAIERAVREAELVVIDEVGPMELLSEEFVEAVEAALDSDKPILAVVHMRSEHHLAKKIREG--FRLFVVT 153
                                       ******************************************************************87..******* PP

                                       TTTTTTHHHHH CS
                          NTPase_1 157 eenrdalleei 167
                                       +e+rd+l+ e+
  gi|386000728|ref|YP_005919027.1| 154 PESRDRLAGEV 164
                                       *******9987 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.5   2.2e-09   1.9e-06      27     135 ..      27     136 ..       5     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.2e-09
                           DUF2478  27 GlrvaGvvqenaeeaegkkcdmeledlatgeririsqdlgsgsqg..CrLdpeaLaeaaaa.veralaegadlvivn 100
                                       G r +Gv  ++ +   g++   +l dl tge+  +    g+g +    r++ + L+e+ a+ +era+ ++a+lv++ 
  gi|386000728|ref|YP_005919027.1|  27 GGRTGGVSAREVR-IGGRRIGFQLSDLLTGEVGTLASLDGPGPKVgrYRVHLADLEEVGARaIERAV-REAELVVID 101
                                       7778887766666.557889***************99999988762268999****99765166666.9******** PP

                           DUF2478 101 kFGkqEaeGrGlreeiaaalaagiPvltaVsekll 135
                                         G  E   + + e+++aal ++ P+l +V+ + +
  gi|386000728|ref|YP_005919027.1| 102 EVGPMELLSEEFVEAVEAALDSDKPILAVVHMRSE 136
                                       ******************************98765 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 !   15.0   0.2   2.2e-05     0.019       5      26 ..       8      29 ..       6      37 .. 0.87
   2 ?    6.2   0.0     0.011       9.5      50      75 ..      79     104 ..      70     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                      E--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  5 vGppGtgKselaerlaaalnre 26
                                       G+pG+gKs+l+er aa+++ +
  gi|386000728|ref|YP_005919027.1|  8 TGAPGVGKSTLVERAAALIGGR 29
                                      7*****************9544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                                       .......--------G-SEEEEESGG CS
                             AAA_5  50 gttslvdsplvraaregeilvlDEve 75 
                                       + ++    ++ ra+re+e++v+DEv 
  gi|386000728|ref|YP_005919027.1|  79 DLEEVGARAIERAVREAELVVIDEVG 104
                                       555566677889************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.1e-07   0.00061       3     104 ..       7     126 ..       6     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.1e-07
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf................gvnlrdvakenglllevdpe...aldeskrldedkldk 59 
                                       +tG+pGvGK+tl ++ + +  g                 g++l+d+++ +   l   +    ++ ++++   d  ++
  gi|386000728|ref|YP_005919027.1|   7 VTGAPGVGKSTLVERAAALIgGRtggvsarevriggrriGFQLSDLLTGEVGTLASLDGpgpKVGRYRVHLADLEEV 83 
                                       9***************9986455787788888889999999999999877655555555577777777777777666 PP

                            AAA_18  60 lldaleenssaleegknlvidgh.laeleseaakdikkvvLtaspe 104
                                         +a+e++    +e++ +vid + + el+se++++++   L+ ++ 
  gi|386000728|ref|YP_005919027.1|  84 GARAIERA---VREAELVVIDEVgPMELLSEEFVEAVEAALDSDKP 126
                                       66666665...45777888887624556677777766655555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   0.00013      0.11       9      26 ..       6      23 ..       3      31 .. 0.89
   2 ?    5.4   0.0     0.024        20      73     113 ..      78     118 ..      47     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_22  9 vvtGesGtGKTtllrrll 26
                                      +vtG +G+GK+tl++r +
  gi|386000728|ref|YP_005919027.1|  6 AVTGAPGVGKSTLVERAA 23
                                      79************9976 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                            AAA_22  73 lsseell.ealeqalraravielliiDEaqhlr..seealeeLr 113
                                       +++ee+  +a+e+a+r++   el++iDE+  +   see +e + 
  gi|386000728|ref|YP_005919027.1|  78 ADLEEVGaRAIERAVREA---ELVVIDEVGPMEllSEEFVEAVE 118
                                       456666655566666555...57*****8777555666666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.7   3.3e-06    0.0028      28      57 ..       6      34 ..       2     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.3e-06
                            AAA_16 28 llsGesGvGKsslvrellralekdggiflr 57
                                       ++G++GvGKs+lv++++  + ++ g + +
  gi|386000728|ref|YP_005919027.1|  6 AVTGAPGVGKSTLVERAAALIGGRTGGV-S 34
                                      69****************8888884444.2 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   1.8e-05     0.015       2      21 ..       5      24 ..       4     153 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      +a+ G p vGKStL+ +   
  gi|386000728|ref|YP_005919027.1|  5 AAVTGAPGVGKSTLVERAAA 24
                                      799************98763 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.9   1.2e-05      0.01      12     126 ..       4     118 ..       1     131 [. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallv.elggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.........l 78 
                                         +vt+ pG GK+++++ + al+  ++ggv+++e+ +    +r   +l++ l   ++e  T+ +l           +
  gi|386000728|ref|YP_005919027.1|   4 RAAVTGAPGVGKSTLVERAAALIGgRTGGVSAREVRIG--GRRIGFQLSDLL---TGEVGTLASLDGpgpkvgryrV 75 
                                       5789*********9999999887526777877777664..578888999999...99******99668888777666 PP

                            AAA_19  79 dfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLlkall 126
                                       ++ dl++        ++ e+ ++e+el+++DE+  ++ l  ++++a+ 
  gi|386000728|ref|YP_005919027.1|  76 HLADLEEVG-----ARAIERAVREAELVVIDEVGPMELLSEEFVEAVE 118
                                       566655333.....456677897888*******999999999998876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   4.3e-06    0.0037      30      52 ..       3      25 ..       1      38 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                                      EEEEEEE-TTSSHHHHHHHHHHH CS
                              MeaB 30 qvvGltGvPGaGkstlvealgle 52
                                      ++  +tG PG+Gkstlve+ ++ 
  gi|386000728|ref|YP_005919027.1|  3 RRAAVTGAPGVGKSTLVERAAAL 25
                                      57789*************97765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.3e-05     0.028       2      79 ..       2     108 ..       1     144 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfi..........................dtekGlksldadkfpdieswedf 52 
                                       +++ +++G +g+GK+tl+ ++   +l+                             e G+ +  +  +p++  +   
  gi|386000728|ref|YP_005919027.1|   2 SRRAAVTGAPGVGKSTLVERA--AALIGgrtggvsarevriggrrigfqlsdllTGEVGTLASLDGPGPKVGRYRVH 76 
                                       67899***************9..333333334335555555666666666655555556666666666666666666 PP

                            AAA_24  53 ldevvel.....aaeladyktlviDtidelee 79 
                                       l +++e+     +++ ++ + +viD ++ +e 
  gi|386000728|ref|YP_005919027.1|  77 LADLEEVgaraiERAVREAELVVIDEVGPMEL 108
                                       66666667777777777777777777776654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.3e-05     0.036      25      46 ..       5      26 ..       1      33 [. 0.80
   2 ?   -1.6   0.1       2.7   2.3e+03      16      32 ..      44      58 ..      40      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                            AAA_29 25 tlltGpsGsGKSTllDAiqalL 46
                                        +tG+ G+GKSTl+   +al+
  gi|386000728|ref|YP_005919027.1|  5 AAVTGAPGVGKSTLVERAAALI 26
                                      579***********98776665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                            AAA_29 16 tieidlkgatlltGpsG 32
                                      +i ++l++  lltG+ G
  gi|386000728|ref|YP_005919027.1| 44 RIGFQLSD--LLTGEVG 58
                                      56677676..99**988 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.8    0.0001     0.088      21     102 ..       5     108 ..       1     131 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                            AAA_30  21 avltGpAGtGKttalkalreaweaa.g....grviglAptgkaAkvLaeelgieastiakllkrlk........... 81 
                                       a++tG++G GK+t+++ +++++  + g    ++v +     +   +L++ l  e  t+a+l                
  gi|386000728|ref|YP_005919027.1|   5 AAVTGAPGVGKSTLVERAAALIGGRtGgvsaREVRIG--GRRIGFQLSDLLTGEVGTLASLDGPGPkvgryrvhlad 79 
                                       689*****************99988556666333322..22333334444444555555555443355666666668 PP

                            AAA_30  82 .........grarlepgtllivDEagmvdt 102
                                                +  ++++++l+++DE+g +  
  gi|386000728|ref|YP_005919027.1|  80 leevgaraiE-RAVREAELVVIDEVGPMEL 108
                                       8899999753.567778*******998754 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.4   6.4e-05     0.055       2      23 ..       5      27 ..       4     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar.g 23
                                       ++tG+++ GK+tl+e+ aa  g
  gi|386000728|ref|YP_005919027.1|  5 AAVTGAPGVGKSTLVERAAALiG 27
                                      589************99886553 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00062      0.53      35      53 ..       4      22 ..       1      39 [. 0.81
   2 ?    3.4   0.4     0.056        48     131     154 ..      86     106 ..      72     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00062
                            AAA_25 35 lallaGapgtGKttlaldl 53
                                       a+++Gapg+GK+tl+   
  gi|386000728|ref|YP_005919027.1|  4 RAAVTGAPGVGKSTLVERA 22
                                      5789**********97554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.056
                            AAA_25 131 daleaaieevegvrlvviDplsra 154
                                       +a+e+a++e   ++lvviD +  +
  gi|386000728|ref|YP_005919027.1|  86 RAIERAVRE---AELVVIDEVGPM 106
                                       456667666...67*****87655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.092       3      67 ..       7     103 ..       5     125 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SS.............................STTHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsell.sk.............................yvgesekkirel 49 
                                       ++G pG+GK++l++  a  +g +   +s+ e++                                      ++++e+
  gi|386000728|ref|YP_005919027.1|   7 VTGAPGVGKSTLVERAAALIGGRTGGVSAREVRiGGrrigfqlsdlltgevgtlasldgpgpkvgRYRVHLADLEEV 83 
                                       78***************998655444444444411133333344444445666666666666555333344444444 PP

                                       HHHHHHTS..TSEEEEEETG CS
                               AAA  50 fkeakeka..kpsilfiDEi 67 
                                        ++a e a  +   ++iDE+
  gi|386000728|ref|YP_005919027.1|  84 GARAIERAvrEAELVVIDEV 103
                                       44444444433367777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0073       6.2       6      23 ..       6      23 ..       2      31 .. 0.87
   2 ?    4.8   0.0     0.032        27      63     109 ..      93     143 ..      71     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0073
                            AAA_14  6 vitGaRrvGKTtllkqli 23
                                      ++tGa  vGK+tl+++ +
  gi|386000728|ref|YP_005919027.1|  6 AVTGAPGVGKSTLVERAA 23
                                      79***********98765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.032
                            AAA_14  63 ekktylflDEiqev....pewekalkslvdegknldvivtGSnskllskei 109
                                       ++ +++++DE+  +    +e+ +a+   +d++k +  +v   +  +l k+i
  gi|386000728|ref|YP_005919027.1|  93 REAELVVIDEVGPMellsEEFVEAVEAALDSDKPILAVVHMRSEHHLAKKI 143
                                       36789******9887777899999999999886554444433334444445 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1    0.0001     0.089     102     134 ..       5      37 ..       1      45 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                       EEEECSTTSSHHHHHHHHCTT-----S------ CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgevsekl 134
                                       +++ G  GvGKStL+++ +     +tg vs++ 
  gi|386000728|ref|YP_005919027.1|   5 AAVTGAPGVGKSTLVERAAALIGGRTGGVSARE 37 
                                       6789************99999999999999875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00013      0.11       4      20 ..       7      23 ..       5     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      + G+pG+GKstl+er +
  gi|386000728|ref|YP_005919027.1|  7 VTGAPGVGKSTLVERAA 23
                                      57************976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00032      0.28       2      24 ..       4      26 ..       3      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                        +++G++G+GK+tL+++ a ++
  gi|386000728|ref|YP_005919027.1|  4 RAAVTGAPGVGKSTLVERAAALI 26
                                      5689************9977665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00041      0.35       1      17 [.       8      24 ..       8     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                                      EE-TTSSHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklve 17
                                      +G PG+GK+t++e+ + 
  gi|386000728|ref|YP_005919027.1|  8 TGAPGVGKSTLVERAAA 24
                                      7***********99876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00028      0.24      12      42 ..       3      33 ..       1     115 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGei 42
                                      ++ a++G  G GKStL++  a l     G +
  gi|386000728|ref|YP_005919027.1|  3 RRAAVTGAPGVGKSTLVERAAALIGGRTGGV 33
                                      6789************987777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1078.62
//
Query:       gi|386000729|ref|YP_005919028.1|  [L=403]
Description: SufBD protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-46  158.2   0.0      3e-46  157.8   0.0    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
      0.094   13.0   0.0       0.25   11.6   0.0    1.7  1  DUF1428   Protein of unknown function (DUF1428)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.0   3.4e-50     3e-46       2     218 .]     152     374 ..     151     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 3.4e-50
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q +++++++eeg+e++ii   +gc            gv+e++v+++A++++++v+nw+e++ + ++ +  +++  ++
  gi|386000729|ref|YP_005919028.1| 152 QRVHNVVIAEEGSELHII---TGCttpshagrglhlGVSEVYVKRGAHVTFTMVHNWGEEVEVRPRGASLVEAGGSI 225
                                       789***************...888999999999999*****************************998877887788 PP

                           UPF0051  67 elttvslggkltrk.epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgki 142
                                       + ++++l    +++  p++ l+gega a+++++++a+++ ++d++++ ++++p+ts++ +s+ v++ +++++ rg++
  gi|386000729|ref|YP_005919028.1| 226 TENYITLTPVKSLQaFPTATLAGEGAVASFSTIMYARRG-NIDIGNQTILEAPKTSAESISRVVST-GGEIINRGRM 300
                                       88888888776654379********************97.7*************************.599******* PP

                           UPF0051 143 kvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                        v k     +ah+e++ L+l++k+r+++iPel    +   +sH+A+vGki++++l YLm+RGls +eA+++ivrgf
  gi|386000729|ref|YP_005919028.1| 301 -VGK-VPDIRAHVECTGLILTEKGRIYSIPELDGWCGGLDMSHEAAVGKISQQELEYLMARGLSPDEATSVIVRGF 374
                                       .766.9*********************************************************************9 PP

>> DUF1428  Protein of unknown function (DUF1428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05      0.25      39      92 ..     227     280 ..     185     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                           DUF1428  39 ecwgddvpegkltsfpravkakedEtvvfswiewpskatrdaanakvmaDprmk 92 
                                       e+     p ++l+ fp+a+ a e+ +  fs i++  + + d +n+ + + p+++
  gi|386000729|ref|YP_005919028.1| 227 ENYITLTPVKSLQAFPTATLAGEGAVASFSTIMYARRGNIDIGNQTILEAPKTS 280
                                       33333445556679*********************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2847.11
//
Query:       gi|386000730|ref|YP_005919029.1|  [L=258]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-24   86.4   0.0    3.9e-24   85.7   0.0    1.3  1  ABC_tran     ABC transporter
    6.5e-09   36.0   0.0    0.00063   19.6   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0032   16.9   0.2       0.39   10.1   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0036   17.7   0.1     0.0092   16.4   0.1    1.8  1  AAA          ATPase family associated with various cellular a
      0.007   16.9   0.3      0.015   15.8   0.3    1.4  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.021   14.4   0.1    1.3  1  AAA_25       AAA domain
       0.02   14.5   0.1      0.025   14.3   0.1    1.4  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.022   14.5   0.2      0.041   13.6   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.043   13.7   0.8         53    3.6   0.0    3.5  4  CdhC         CO dehydrogenase/acetyl-CoA synthase complex bet
      0.053   12.8   0.0       0.99    8.7   0.0    2.1  2  Zeta_toxin   Zeta toxin
      0.068   13.1   0.0       0.11   12.4   0.0    1.2  1  ATPase_2     ATPase domain predominantly from Archaea
       0.08   12.8   0.0       0.13   12.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.09   13.3   0.1         11    6.6   0.1    2.2  2  AAA_18       AAA domain
        0.1   13.0   0.0       0.11   12.8   0.0    1.4  1  AAA_16       AAA ATPase domain
       0.11   12.4   0.1       0.17   11.8   0.1    1.3  1  NACHT        NACHT domain
       0.11   12.7   0.1       0.17   12.1   0.1    1.3  1  AAA_28       AAA domain
       0.15   11.8   0.0       0.22   11.2   0.0    1.4  1  AAA_24       AAA domain
       0.17   12.2   0.1       0.37   11.1   0.1    1.8  1  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.0   3.9e-27   3.9e-24       1     136 [.      33     172 ..      33     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 3.9e-27
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       lk v++++ +ge++a++G+nG+GK+tLl+++ag  +   + G+i+++g d+++   +e++r  ig+ +q+p   ++l
  gi|386000730|ref|YP_005919029.1|  33 LKGVDMSVGKGETHALFGPNGCGKTTLLSTIAGIPRYvvERGTITFKGVDITHmSMHERARLGIGIAFQHPPTIRGL 109
                                       789******************************988888**************9999******************** PP

                                       BHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +v +     + ++++ k+l+ l+ +e++d+ v    + +SgG+ +r +++++l+++p++++lDEp 
  gi|386000730|ref|YP_005919029.1| 110 KVLDMiklcNPQADAGKILEDLDFTEFADREV---NRGFSGGEVKRSEMVQLLAQEPDFVMLDEPD 172
                                       ****9***9999********************...799**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.3e-07   0.00063       3      39 ..      47      80 ..      46     101 .. 0.76
   2 !   14.5   0.0   2.3e-05     0.023     249     289 ..     157     202 ..     122     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.3e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgg 39
                                      +l GpNg+GK++LL ++ ++    r+v  ++++  +g
  gi|386000730|ref|YP_005919029.1| 47 ALFGPNGCGKTTLLSTIAGI---PRYVVERGTITFKG 80
                                      799**************998...55555555554444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.3e-05
                            AAA_21 249 tallralkkgsllliDEpEngLHPkllrrllellkelsr........ng 289
                                        +l++ +   +++ +DEp++g + + ++ + + +++l++        ++
  gi|386000730|ref|YP_005919029.1| 157 QLLAQEP---DFVMLDEPDSGVDLENIKVIGRAINILTQkdakpsmrTK 202
                                       4455444...9***********************999995555555555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00039      0.39      26      44 ..      45      63 ..      33      70 .. 0.86
   2 ?    4.8   0.0     0.017        17     158     186 ..     162     190 ..     122     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00039
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                        a+ GpNG+GK+ ll  i
  gi|386000730|ref|YP_005919029.1| 45 THALFGPNGCGKTTLLSTI 63
                                      5789**********99887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                                       --SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkek 186
                                          +++lDe d+  D +n+k + + ++  
  gi|386000730|ref|YP_005919029.1| 162 EPDFVMLDEPDSGVDLENIKVIGRAINIL 190
                                       33499*****************9998754 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   9.3e-06    0.0092       3      38 ..      48      87 ..      46     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.3e-06
                                      EESSTTSSHHHHHHHHHHH....HTHEEEEEETTTCSSSS CS
                               AAA  3 lyGppGtGKTllakavake....lgvefleisgsellsky 38
                                      l+Gp G+GKT+l + +a      +++  ++++g +++ + 
  gi|386000730|ref|YP_005919029.1| 48 LFGPNGCGKTTLLSTIAGIpryvVERGTITFKGVDITHMS 87
                                      89***************98544434556666666666443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.5e-05     0.015      23      39 ..      47      63 ..      36      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                      +++GpNG+GKTT+l  i
  gi|386000730|ref|YP_005919029.1| 47 ALFGPNGCGKTTLLSTI 63
                                      689**********9766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.1e-05     0.021      30      54 ..      40      64 ..      20      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                      + +ge+++l+G+ g+GKttl++ +a
  gi|386000730|ref|YP_005919029.1| 40 VGKGETHALFGPNGCGKTTLLSTIA 64
                                      4799****************98766 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.5e-05     0.025      10      36 ..      39      65 ..      33     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                                      -EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 10 pivqGqrtlipgafgvGktvisqslsk 36
                                      ++++G++ +++g +g+Gkt+++++++ 
  gi|386000730|ref|YP_005919029.1| 39 SVGKGETHALFGPNGCGKTTLLSTIAG 65
                                      789*******************99875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.2e-05     0.041      14      40 ..      35      61 ..      27      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllD 40
                                      g ++++   +++ l Gp+G GK+Tll 
  gi|386000730|ref|YP_005919029.1| 35 GVDMSVGKGETHALFGPNGCGKTTLLS 61
                                      566777755599*************95 PP

>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.053        53     105     123 ..      21      39 ..       5      50 .. 0.89
   2 ?    3.6   0.0     0.056        56      40      69 ..      69      98 ..      45     102 .. 0.80
   3 ?    2.6   0.1      0.11   1.1e+02       7      63 ..     143     196 ..     138     214 .. 0.68
   4 ?   -1.0   0.0       1.5   1.5e+03     116     142 ..     201     227 ..     193     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.053
                              CdhC 105 diiwvRiskeavekGlrlk 123
                                       d++wvRi+ ++v kG+ ++
  gi|386000730|ref|YP_005919029.1|  21 DDLWVRIGEKQVLKGVDMS 39 
                                       789************9874 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.056
                              CdhC 40 devedgkieviGpdideveegsrlplailv 69
                                        ve g i+  G di +++  +r  l+i +
  gi|386000730|ref|YP_005919029.1| 69 YVVERGTITFKGVDITHMSMHERARLGIGI 98
                                      56999*************999999888865 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.11
                              CdhC   7 pafeGeriRkedlyvelggkktkafElvkvke.adevedgkieviGpdideveegsrl 63 
                                         f G ++++++++  l ++ ++  ++v+  e  + v+ ++i+viG  i+ ++++++ 
  gi|386000730|ref|YP_005919029.1| 143 RGFSGGEVKRSEMVQ-LLAQ-EP--DFVMLDEpDSGVDLENIKVIGRAINILTQKDAK 196
                                       568888888888854.4444.34..4444444045588899******99988766644 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.5
                              CdhC 116 vekGlrlkhigevlyaklkeefeaivd 142
                                       +++G+ ++h+g++l  + +++ + +++
  gi|386000730|ref|YP_005919029.1| 201 TKSGVIITHFGHILDYMATDKAHVMIE 227
                                       57899999***9999888877766665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   1.1e+02      23      36 ..      50      63 ..      43      71 .. 0.87
   2 ?    8.7   0.0   0.00099      0.99      86     123 ..     212     249 ..     184     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                        Zeta_toxin 23 GqpGAGKselaell 36
                                      G  G+GK++l++ +
  gi|386000730|ref|YP_005919029.1| 50 GPNGCGKTTLLSTI 63
                                      789*******9977 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00099
                        Zeta_toxin  86 kllqeaiengyniivegtlrspdvvkklaealkkaGYe 123
                                        +l++ +  + ++ +egt+     +k++ e++k++GYe
  gi|386000730|ref|YP_005919029.1| 212 HILDYMATDKAHVMIEGTIVCSGSPKEILEQIKANGYE 249
                                       689999*******************************8 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.11      22      41 ..      45      64 ..      36      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                          ATPase_2 22 iyfiYGpegsGKtaLlkeii 41
                                         ++Gp g+GKt+Ll  i+
  gi|386000730|ref|YP_005919029.1| 45 THALFGPNGCGKTTLLSTIA 64
                                      5678************9875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.13      86     121 ..      29      65 ..      16      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +k+ l+ +   + + +t +l G+ G GK+tL+ ++++
  gi|386000730|ref|YP_005919029.1|  29 EKQVLKGVDMSVGKgETHALFGPNGCGKTTLLSTIAG 65 
                                       5555666665555559****************99986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.011        11       3      18 ..      48      63 ..      47      95 .. 0.86
   2 ?    4.8   0.0     0.039        39      25     115 ..     153     248 ..     127     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                            AAA_18  3 ltGtpGvGKttlakeL 18
                                      l G+ G+GKttl   +
  gi|386000730|ref|YP_005919029.1| 48 LFGPNGCGKTTLLSTI 63
                                      78*********98765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.039
                            AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenss..aleegknlvidghlaeleseaakdikk... 96 
                                       ++ ++ +a+e + +  ++p+  +  + +++++  +++++l + ++  +++  +  vi  h ++ ++++a+d+     
  gi|386000730|ref|YP_005919029.1| 153 SEMVQLLAQEPDFVMLDEPD--SGVDLENIKVIGRAINILTQKDAkpSMRTKSG-VIITHFGHILDYMATDKAHvmi 226
                                       56677789999999999999..77788888888888888888888875666666.5556666666666666555588 PP

                            AAA_18  97 ...vvLtaspeelleRlekRgy 115
                                          +v   sp+e le +++ gy
  gi|386000730|ref|YP_005919029.1| 227 egtIVCSGSPKEILEQIKANGY 248
                                       8888888888888888887776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011      0.11      25      46 ..      44      65 ..      30     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                            AAA_16 25 elvllsGesGvGKsslvrellr 46
                                      e   l G+ G+GK++l+ +++ 
  gi|386000730|ref|YP_005919029.1| 44 ETHALFGPNGCGKTTLLSTIAG 65
                                      666789***********88873 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00017      0.17       3      21 ..      46      64 ..      44      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       +l G++G+GKTtLl  +a
  gi|386000730|ref|YP_005919029.1| 46 HALFGPNGCGKTTLLSTIA 64
                                      5788***********9997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00017      0.17       3      21 ..      47      72 ..      45      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                            AAA_28  3 vitGgestGKTtlleaLa.......a 21
                                      +++G+ ++GKTtll+ +a       +
  gi|386000730|ref|YP_005919029.1| 47 ALFGPNGCGKTTLLSTIAgipryvvE 72
                                      799************99944433333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.22       6      27 ..      47      68 ..      42     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                            AAA_24  6 liyGpsgiGKTtlakelgpkpl 27
                                      +++Gp+g GKTtl++++   p 
  gi|386000730|ref|YP_005919029.1| 47 ALFGPNGCGKTTLLSTIAGIPR 68
                                      79*************9944444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00037      0.37       9      26 ..      47      64 ..      42     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                            AAA_22  9 vvtGesGtGKTtllrrll 26
                                      +++G+ G+GKTtll +++
  gi|386000730|ref|YP_005919029.1| 47 ALFGPNGCGKTTLLSTIA 64
                                      699**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1634.66
//
Query:       gi|386000731|ref|YP_005919030.1|  [L=296]
Description: Tungsten formylmethanofuran dehydrogenase, subunit C-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-07   29.1  20.5    3.7e-06   26.7   8.3    2.8  2  GXGXG     GXGXG motif
  ------ inclusion threshold ------
        4.1    5.9   6.4         11    4.6   0.9    2.1  2  FapA      Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   4.0   0.00056       5.1     104     163 ..      53     109 ..      30     122 .. 0.81
   2 !   26.7   8.3   4.2e-10   3.7e-06      99     163 ..     191     256 ..     183     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00056
                                       EEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE CS
                             GXGXG 104 lfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvl 163
                                       + irg++g R +    +  a  +g+g  +    + G++vv g++g  ++ +m +G++yv 
  gi|386000731|ref|YP_005919030.1|  53 VMIRGDVGGRLGSSLGVDLASFGGTGAPI---EATGTIVVDGDVGPRMGISMLRGSIYVS 109
                                       56778888888777777777777766554...478***********************96 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.2e-10
                                       --SEEEEESSB--SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE CS
                             GXGXG  99 atgGklfirgkageRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvl 163
                                       +++G++ i+g+ag  ++v ++g  +v+ g   d+++  m GG + v g+ g  + a m+gG++y  
  gi|386000731|ref|YP_005919030.1| 191 MRSGSIEIKGDAGRNAGVLMKGGRIVIAGKaDDFTAAEMRGGEIFVAGDAGGFICAKMTGGAVYAQ 256
                                       89***************************98999*****************************975 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5    0.0013        12     197     228 ..      81     113 ..      69     119 .. 0.84
   2 ?    4.6   0.9    0.0012        11     184     241 ..     177     237 ..     175     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0013
                              FapA 197 IkfkGsViikGnVeegmkVka.sgditikGvve 228
                                       I+ +G++++ G+V + m ++   g+i ++G v 
  gi|386000731|ref|YP_005919030.1|  81 IEATGTIVVDGDVGPRMGISMlRGSIYVSGSVG 113
                                       777899999999999999985478999999885 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0012
                              FapA 184 leikgdVdlstGnIkfkGsViikGnVeegmkVkas.gditikGvv...esatieAggnItik 241
                                       l+++gd ++s G +   Gs++ikG+   +  V  + g+i i G     ++a+ + gg+I + 
  gi|386000731|ref|YP_005919030.1| 177 LRVEGDAGMSAGILMRSGSIEIKGDAGRNAGVLMKgGRIVIAGKAddfTAAEMR-GGEIFVA 237
                                       789***********************9999998762689999765311344444.5666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 2113.83
//
Query:       gi|386000732|ref|YP_005919031.1|  [L=364]
Description: hypothetical protein Mhar_0015 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-126  420.3   5.9   7.2e-126  420.2   5.9    1.0  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
        8.8    6.1  12.9       0.49   10.2   6.2    2.2  2  DUF2157   Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.2   5.9  8.1e-130  7.2e-126       2     335 .]       3     351 ..       2     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.2 bits;  conditional E-value: 8.1e-130
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvg 78 
                                       +Lvlc+DrDdDlgrkag+++PvvGr+a++ea  +l+ladPeDSDvN+++g+i+vyd+ +++g++ve+a v+Gd++vg
  gi|386000732|ref|YP_005919031.1|   3 ILVLCIDRDDDLGRKAGIESPVVGRAANVEATLSLGLADPEDSDVNTILGGIQVYDDFASQGRTVEIASVAGDPNVG 79 
                                       8**************************************************************************** PP

                            DUF373  79 veadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrk 155
                                       + +d kia+q+d +l+++++++++vVsDGaeDe++lpiiqsrvkv++vkrV+Vkqs+n+Estyyllk++++dp++++
  gi|386000732|ref|YP_005919031.1|  80 LVSDGKIAHQIDYLLERFRPEGVVVVSDGAEDEAILPIIQSRVKVEGVKRVLVKQSHNLESTYYLLKQVFRDPKISH 156
                                       ***************************************************************************** PP

                            DUF373 156 tiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvalllll 232
                                       t+++p+Gl+lliy+ +++lg +++a+++il+++G+yll+rG+gld+ +e++ e++k  l++g++ fvtyv+a++l+l
  gi|386000732|ref|YP_005919031.1| 157 TFFIPIGLALLIYSTFSFLGRSDFAVVAILAAVGVYLLFRGLGLDDFIESTKETFKGNLYRGKVAFVTYVLAAVLVL 233
                                       ***************************************************************************** PP

                            DUF373 233 igiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkre.ekdiarllllpflvlaigl 308
                                       i++i+g + +++++++++++g+++l+++f++++v+w+++a++++ lgki+d yl++  +++ + + ++pf+++a+gl
  gi|386000732|ref|YP_005919031.1| 234 IATIQGSARFWDYYTGDIWYGYIVLVMVFVNYSVWWYVAAAICVNLGKILDLYLEGGrDERSYTYHSYPFFIFATGL 310
                                       ******************************************************877788888999*********** PP

                            DUF373 309 vlygasaylls..............lsilalslvvgivval 335
                                       ++++asa++l               +++la+s +++i++al
  gi|386000732|ref|YP_005919031.1| 311 IFWSASAFILVnsagvafplisgqsTQYLAASAILAIIIAL 351
                                       *********889**************************985 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.5      0.18   1.6e+03      64      79 ..     178     193 ..     157     202 .. 0.46
   2 ?   10.2   6.2   5.5e-05      0.49      35     140 ..     221     352 ..     204     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.18
                           DUF2157  64 lvkfllllvllllsll 79 
                                           +++++++++++l
  gi|386000732|ref|YP_005919031.1| 178 SDFAVVAILAAVGVYL 193
                                       3333333333333332 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.5e-05
                           DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg.avlwrdr...................... 88 
                                       + + +vl+a+l++++ i   A +W+  + ++  + ++++++++++ + +++   +                      
  gi|386000732|ref|YP_005919031.1| 221 AFVTYVLAAVLVLIATIQGSARFWDYYTGDIWYGYIVLVMVFVNYSVwWYVAA-Aicvnlgkildlyleggrdersy 296
                                       557789*****************************************666655.469**************999888 PP

                           DUF2157  89 ...rvpprlgeallllaalllgaaialvgqifq.lsgdaysllllwalllllmayl 140
                                            p ++    l++ +    +++  +g  f  +sg+++++l+++a+l++++a++
  gi|386000732|ref|YP_005919031.1| 297 tyhSYPFFIFATGLIFWSASAFILVNSAGVAFPlISGQSTQYLAASAILAIIIALV 352
                                       88644444455555566666666666667777525888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2208.45
//
Query:       gi|386000733|ref|YP_005919032.1|  [L=152]
Description: hypothetical protein Mhar_0016 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1093.89
//
Query:       gi|386000734|ref|YP_005919033.1|  [L=427]
Description: Thiamine biosynthesis protein ThiC [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.1e-170  568.0   0.3   1.2e-170  567.8   0.3    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.8   0.3  6.7e-175  1.2e-170       3     417 ..       4     420 ..       2     421 .. 0.99

  Alignments for each domain:
  == domain 1  score: 567.8 bits;  conditional E-value: 6.7e-175
                      ThiC_Rad_SAM   3 leaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEve 79 
                                       +e+ar+g+it eme+va++e+v+pef+r+++a G+ivip    ++ + ++iGkgl+tkvna++Gts+d++d+e+Ev+
  gi|386000734|ref|YP_005919033.1|   4 IEDARAGRITAEMEMVAKDEGVTPEFIRRGIAGGTIVIPVSPYRDVRFCGIGKGLKTKVNATVGTSSDIVDVEMEVA 80 
                                       789************************************************************************** PP

                      ThiC_Rad_SAM  80 KlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvd 153
                                       K+++a++agadt+m+Lstggd+ eir++++e+++++vg+vp+Yqa+ e   k+++ +++te++l+++ eeqa+ G +
  gi|386000734|ref|YP_005919033.1|  81 KARAAEEAGADTLMELSTGGDFFEIRKRVVENTSLSVGSVPLYQAFIEairKYGSGVDMTEDDLFQITEEQARLGTN 157
                                       **********************************************99999999*********************** PP

                      ThiC_Rad_SAM 154 fltiHagvtlellellkke.kRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsia 229
                                       f++iH+g+++ ++e++k++ +R+ g++SrgG++++awml+n++enply++f +lleilke++vtlS+g+g+R+G+++
  gi|386000734|ref|YP_005919033.1| 158 FMAIHTGINRICIERIKRQgGRFGGLCSRGGAFMVAWMLHNDQENPLYSDFGYLLEILKEHEVTLSMGNGFRAGAVH 234
                                       ****************99878******************************************************** PP

                      ThiC_Rad_SAM 230 DatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsa 306
                                       Datd+aq++eli+++el+++a++ gvq++veGPGH+p+deieanvk++k+l+ e+Pfy+lGplvtD+apg Dhi++a
  gi|386000734|ref|YP_005919033.1| 235 DATDRAQIQELIINSELADEAHAFGVQTIVEGPGHIPIDEIEANVKVMKRLSGEKPFYMLGPLVTDVAPGRDHIVAA 311
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 307 iGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfela 383
                                       iGa+l++aaGad++CyvtpaEHl+lP++edv+eGv+aa+iaah++d++k+  + r++d a+ +aR+++ w +qf+la
  gi|386000734|ref|YP_005919033.1| 312 IGASLSSAAGADFICYVTPAEHLALPNVEDVREGVMAARIAAHVGDMIKN--GSRDQDLAMGRARRDMLWGEQFRLA 386
                                       *************************************************8..899********************** PP

                      ThiC_Rad_SAM 384 ldpekareireeklpeeeeaCsmCgekCavkive 417
                                       ldp+ a++ir+e++p++ ++C+mCg++Ca kiv+
  gi|386000734|ref|YP_005919033.1| 387 LDPDMAEKIRAERAPADGKVCTMCGDFCAHKIVA 420
                                       *******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2933.18
//
Query:       gi|386000735|ref|YP_005919034.1|  [L=451]
Description: Metalloenzyme domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-10   38.2   0.0    2.8e-09   36.7   0.0    1.6  2  Metalloenzyme    Metalloenzyme superfamily
    1.8e-09   37.7   0.1    3.9e-08   33.3   0.0    2.4  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    3.4e-06   26.7   0.0    6.8e-06   25.7   0.0    1.6  1  Sulfatase        Sulfatase
  ------ inclusion threshold ------
      0.015   14.3   0.0      0.067   12.1   0.0    1.8  2  Alk_phosphatase  Alkaline phosphatase


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.41   1.8e+03       4      14 ..      35      45 ..      33      49 .. 0.86
   2 !   36.7   0.0   6.3e-13   2.8e-09     116     223 ..     197     308 ..     181     326 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.41
                                      EEEEETTBB-- CS
                                      xxxxxxxxxxx RF
                     Metalloenzyme  4 vlvvlDGlGea 14
                                      v++v+DG+G a
  gi|386000735|ref|YP_005919034.1| 35 VVLVVDGMGSA 45
                                      899******86 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 6.3e-13
                                       HHHHHHHHHHHH.CC.-S.EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTT CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 116 avevaekaldailsgkfd.lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedm 191
                                       a + a  ++ a+ +     l++vn+   D++GH+  ++++++ i  +D  ++++++ +e+ + +l++tADHg   + 
  gi|386000735|ref|YP_005919034.1| 197 ALDAASDLVAAMGK--RPfLLIVNVGAVDSAGHNLGPAGYVETISGLDGPLGRLVEGCEAGGVLLLITADHGMSFSS 271
                                       66777888899944..444889**************************************************98776 PP

                                       SS..............-----EEEEEESTT----S--S CS
                                       xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 192 vkrdk......qplTsHtlepVPilivgkglapdkvke 223
                                        +  k      +  +      VP ++vg+g+++ +v++
  gi|386000735|ref|YP_005919034.1| 272 DEG-KgghssaKYSSLAESVMVPAVFVGPGVDEVAVTG 308
                                       653.3466654323333345688889998888755554 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3     0.038   1.7e+02      30      55 ..      72      96 ..      34     114 .. 0.55
   2 !   33.3   0.0   8.7e-12   3.9e-08     158     239 ..     198     272 ..     143     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.038
                                      HSEEESEEE-SSS-SHHHHHHHHHHS CS
                      Phosphodiest 30 egvsapnlrpvfPtlTfpnhaslvTG 55
                                      +g ++ n+ +v  ++T p+h+ lvTG
  gi|386000735|ref|YP_005919034.1| 72 RGARILNV-TVPVPETGPSHSVLVTG 96
                                      44444433.33446788888888888 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 8.7e-12
                                       HCHTHSHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 158 daafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                        +a+ ++v  +++ ++p ll+v++ ++D++gH++Gp      ++++ +D  +g+L+e+ +       + +++++DHG
  gi|386000735|ref|YP_005919034.1| 198 LDAASDLV--AAMgKRPFLLIVNVGAVDSAGHNLGPAG--YVETISGLDGPLGRLVEGCEAG----GVLLLITADHG 266
                                       22322322..2347*********************987..778*****************99....99********* PP

                                       -EEEHT CS
                      Phosphodiest 234 madvsd 239
                                       m+  sd
  gi|386000735|ref|YP_005919034.1| 267 MSFSSD 272
                                       **9874 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.5e-09   6.8e-06     214     308 ..     234     324 ..     168     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG..HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCE CS
                         Sulfatase 214 ylnsveyvDdligrvlaaLeenglldntlvvftSDhgaslee..sngplrggkganayeggtrvPllvwwpgekapr 288
                                       y  +++  D  +gr+++      ++  +l+++t+Dhg s     ++g +   k+ ++ ++++ vP++  +pg  +  
  gi|386000735|ref|YP_005919034.1| 234 YVETISGLDGPLGRLVEGC----EAGGVLLLITADHGMSFSSdeGKGGHSSAKY-SSLAESVMVPAVFVGPGVDEV- 304
                                       889999999999***9999....88889**********9977757777777777.*********************. PP

                                       EECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 289 vseelvshiDlfptildlag 308
                                        + +  s +Dl+pt+ldl+g
  gi|386000735|ref|YP_005919034.1| 305 AVTGNWSEVDLAPTLLDLLG 324
                                       9*****************98 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.1   4.5e+02       5      17 ..      35      47 ..      33      50 .. 0.89
   2 ?   12.1   0.0   1.5e-05     0.067     250     314 ..     210     271 ..     197     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.1
                                      EEEEETT-SHHHH CS
                   Alk_phosphatase  5 illigDGmgvstv 17
                                      ++l+ DGmg ++v
  gi|386000735|ref|YP_005919034.1| 35 VVLVVDGMGSAYV 47
                                      799*******997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.5e-05
                                       TT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEES CS
                   Alk_phosphatase 250 ekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfgg 314
                                       ++ F L+V  + +D a+H+  ++g ++ +  +d  + + +e  +     l++ TaDH     f +
  gi|386000735|ref|YP_005919034.1| 210 KRPFLLIVNVGAVDSAGHNLGPAGYVETISGLDGPLGRLVEGCE-AGGVLLLITADHGMS--FSS 271
                                       6789****************************************.999*********984..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2911.08
//
Query:       gi|386000736|ref|YP_005919035.1|  [L=396]
Description: bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for 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-71  237.3   0.1    1.3e-70  236.5   0.1    1.4  1  Fae             Formaldehyde-activating enzyme (Fae)
    6.6e-21   74.9   0.3    1.4e-20   73.8   0.2    1.6  2  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    3.4e-07   29.9   0.1    6.3e-07   29.0   0.1    1.5  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    0.00097   18.7   0.7       0.12   11.8   0.2    2.2  2  PcrB            PcrB family
     0.0017   17.4   2.5     0.0037   16.4   2.5    1.6  1  FMN_dh          FMN-dependent dehydrogenase
     0.0068   15.5   0.3      0.011   14.7   0.3    1.2  1  IMPDH           IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.013   14.3   0.7      0.027   13.2   0.7    1.4  1  AtuA            Acyclic terpene utilisation family protein At
      0.024   14.4   0.4      0.056   13.2   0.4    1.7  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.5   0.1   5.7e-74   1.3e-70       1     159 []       4     162 ..       4     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 5.7e-74
                               Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfG 77 
                                       +GEal+g+++e+Ah+dl+iG+kdgpvgtAfa+ la+ s+ghtpll+v+rpnl+ kPatl+v+kvt+kn++qa+++fG
  gi|386000736|ref|YP_005919035.1|   4 IGEALIGDEPELAHVDLLIGDKDGPVGTAFASGLAQLSAGHTPLLSVIRPNLPPKPATLIVPKVTVKNMEQAAAIFG 80 
                                       8**************************************************************************** PP

                               Fae  78 paQaavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdka 154
                                       paQ avakavad+v+eg+ipk+e+++lv+i+svfi+p+a+d+++iy+yny AtklA+krA++++P+id+vl ekd++
  gi|386000736|ref|YP_005919035.1|  81 PAQNAVAKAVADSVAEGVIPKAEVENLVVIASVFIHPQARDYDAIYRYNYGATKLAVKRAMEGFPDIDTVLYEKDRS 157
                                       ***************************************************************************** PP

                               Fae 155 khpfv 159
                                       +hp++
  gi|386000736|ref|YP_005919035.1| 158 THPIM 162
                                       **986 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   3.5e+03     115     149 ..      60      95 ..      31     115 .. 0.66
   2 !   73.8   0.2   6.4e-24   1.4e-20       2     224 ..     174     377 ..     173     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                       EEEEEESTSSGGHHHHHH.HSHHHHHHHHHHHHHHH CS
                         OMPdecase 115 gllilaqmsskgnlmlqe.kgytqacveaarehkae 149
                                         li+ +++ k+ ++ +   g +q++v +a +++ +
  gi|386000736|ref|YP_005919035.1|  60 ATLIVPKVTVKNMEQAAAiFGPAQNAVAKAVADSVA 95 
                                       567777777777777777445555555555554433 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 6.4e-24
                                       EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHH CS
                         OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekq 75 
                                        L++alD+ +   + +++ ++ +  ++ ++++++lv+++g     a++++++r       +++D+K+ D Gn + + 
  gi|386000736|ref|YP_005919035.1| 174 YLQVALDLVDLTVVRRVLSQLPDsDHLLIEVGTPLVKKFG-----ASVVKEIRNVRpsSFVVLDLKTLDTGNLEVRL 245
                                       69*********************99***************.....**********9999****************** PP

                                       HHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTT CS
                         OMPdecase  76 atagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedf 151
                                       a      +++ ad+v ++++a +++++ ++++a+k+g     ++++++ ++ l++ ++  +  ++ve  r+  +e  
  gi|386000736|ref|YP_005919035.1| 246 A------ADATADAVVISGLAPQKTLELAIREARKTG--IYSVIDMLNVPDPLEVLRSlAVLPDVVEMHRAIDQE-- 312
                                       *......69***************************9..9*****************557888888888887766.. PP

                                       ESEEECCCHTHHHHHHTTCSCEEEHHHTT.EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 152 vmGfvaqetlnateedaddfihltpgigl.eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                              e++n  e++  +++ +    +     ++++g++ +t+  + + +gadi++ GR+I++++d + +ae+
  gi|386000736|ref|YP_005919035.1| 313 ------AERHN-WEAI-AEIKRMAASSDRkVLVAVAGGIRVDTVASALS-SGADIVVTGRAITGSKDVRDAAEQ 377
                                       ......45555.4555.6777777777766789*********9999988.89********************98 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   2.8e-10   6.3e-07      44     197 ..     212     365 ..     209     366 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.8e-10
                                       B-HHHHHHHGGG...E-S-EEEEEESSSHHHCHHHHHHCT-SEEEEE-S.T-TTHHHHHHHHHHTTSEEEE.EE-TT CS
                    Ribul_P_3_epim  44 igplvvealrkl...telpldvHLmveevdrivpefaeagasiisvHaE.alehlkrtiqeikeaGakagl.vlnpa 115
                                       +g  vv+++r++   + + ld+   ++  +  v   a+a a+ +++      ++l+  i+e +++G+ + +  ln  
  gi|386000736|ref|YP_005919035.1| 212 FGASVVKEIRNVrpsSFVVLDLKT-LDTGNLEVRLAADATADAVVISGLaPQKTLELAIREARKTGIYSVIdMLNVP 287
                                       677777777777322223333331.2223333444555555555444332678889999*******9877747999* PP

                                       --GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEE CS
                    Ribul_P_3_epim 116 tplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklidekeldlkievDGGvkldnieqiaeagadvlV 192
                                        ple+l+ l+   d+v  m    +   Q+   +  e i +++++++++++++ + v GG+++d+++ + + gad++V
  gi|386000736|ref|YP_005919035.1| 288 DPLEVLRSLAVLPDVV-EMHRAID---QEAERHNWEAIAEIKRMAASSDRKVLVAVAGGIRVDTVASALSSGADIVV 360
                                       *****99987766665.4665555...55555667788888999999999*************************** PP

                                       ESHHH CS
                    Ribul_P_3_epim 193 agsav 197
                                       +g+a+
  gi|386000736|ref|YP_005919035.1| 361 TGRAI 365
                                       ***98 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0064        14      23      68 ..     243     289 ..     227     300 .. 0.79
   2 !   11.8   0.2   5.4e-05      0.12     169     216 ..     322     370 ..     309     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0064
                                       HHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-EEEEESSG CS
                              PcrB  23 veiviesgtDavmigGsq.svtldntvrllkkvsriklPivlepsnv 68 
                                       v+ +++  +Dav+i+G   + tl+ ++r  +k   +++  +l + ++
  gi|386000736|ref|YP_005919035.1| 243 VRLAADATADAVVISGLApQKTLELAIREARKTGIYSVIDMLNVPDP 289
                                       56678999********9999999999999999877777666666555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.4e-05
                                       HHHHHHHHHHSSSEEE.EESS--SHHHHHHHHCCSSEEEE-CHHHHHHH CS
                              PcrB 169 eevialkkklekarli.vGGGirsaEkAkevveaADvivvGnvveekde 216
                                        e++++ +  + + l+ v GGir    A      AD++v+G ++  +++
  gi|386000736|ref|YP_005919035.1| 322 AEIKRMAASSDRKVLVaVAGGIRVDTVASALSSGADIVVTGRAITGSKD 370
                                       4444445555554443389*********999999**********98873 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.5   1.6e-06    0.0037     257     329 ..     320     385 ..     217     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                       HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FMN_dh 257 tidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelert 329
                                       +i  + ++++  ++++ v v gGir  + v+ Al  GAd+v+ GR++       G + v+++ e + ael++t
  gi|386000736|ref|YP_005919035.1| 320 AIAEIKRMAASSDRKVLVAVAGGIRVDT-VASALSSGADIVVTGRAI------TGSKDVRDAAEQFLAELKQT 385
                                       333333334444669*********9865.****************99......89999999999999999976 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   5.1e-06     0.011     193     244 ..     318     370 ..     313     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHHHHCTCT..-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTT CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 193 ltAvaevaeaakkag..vpviaDGGikysgdivkAlaaGadavmlGsllagteE 244
                                         A+ae+ ++a++ +  v v   GGi+ +  ++ Al+ Gad+v+ G+ ++g ++
  gi|386000736|ref|YP_005919035.1| 318 WEAIAEIKRMAASSDrkVLVAVAGGIRVD-TVASALSSGADIVVTGRAITGSKD 370
                                       57899998876665433889999***975.79*****************99876 PP

>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   1.2e-05     0.027     139     161 ..     342     364 ..     297     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                              AtuA 139 YlGaegIveALeagAdiVitGRv 161
                                        + ++ +++AL++gAdiV+tGR 
  gi|386000736|ref|YP_005919035.1| 342 GIRVDTVASALSSGADIVVTGRA 364
                                       3556899***************6 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   2.5e-05     0.056     112     162 ..     319     369 ..     265     373 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB- CS
                         QRPTase_C 112 eelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsvk 162
                                       e ++++  +  + +++vl+ v+Gg+  ++v+   +sg d++ +g +++++k
  gi|386000736|ref|YP_005919035.1| 319 EAIAEIKRMAASSDRKVLVAVAGGIRVDTVASALSSGADIVVTGRAITGSK 369
                                       3333333333466677****************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 2163.73
//
Query:       gi|386000737|ref|YP_005919036.1|  [L=380]
Description: Cytochrome c biogenesis protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-13   50.1  13.5    4.8e-13   49.5  13.5    1.3  1  DsbD           Cytochrome C biogenesis protein transmembrane 
    8.3e-10   38.9  23.3    2.3e-08   34.2  22.5    2.3  1  DsbD_2         Cytochrome C biogenesis protein transmembrane 
    4.2e-05   23.7   0.0    8.3e-05   22.7   0.0    1.5  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.029   14.4   0.0       0.05   13.6   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
      0.083   13.3   0.0       0.13   12.7   0.0    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5  13.5   1.4e-16   4.8e-13       1     208 [.     164     372 ..     164     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.4e-16
                              DsbD   1 aflaGllsflsPCilpliPayl.syisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvke 76 
                                       +f aGll+ + PC+l ++     ++is    + ++ +      ++   +F  G+ +++ ++g++     +    +  
  gi|386000737|ref|YP_005919036.1| 164 VFVAGLLAGFNPCLLGILAFLAtAIIS---SSGRRRD--L---VMMVAFFSFGIFVMYYLFGVGLLRTLHAG-AIAA 231
                                       599*************98644313344...3333333..2...456678999**********9987766654.7888 PP

                              DsbD  77 virrvaglivillGlhflgvfk......ievleklkll.........lkikkkaelsvlgalllGltFalgwsPCig 138
                                        +r+  +++ i lGl  ++  +                             + a   +   +llG +F+l+ +PC+g
  gi|386000737|ref|YP_005919036.1| 232 HLRTGLTVLLIALGLVHIEDARrlsaggR--------SlfkaswsqrYVEGALARGRYSSYFLLGALFSLVKAPCVG 300
                                       88888889999999998884445555541........2233333332122334455677889*************** PP

                              DsbD 139 PvlasvlalaaskeslakgallllvyvlGlaipfllvg..lllellkkklkslkk.yskaveiaggvllvllG 208
                                        v  ++l l ++++  ++ga++ll+y lG  +p+ll+g  + +++   ++ s++k +  a++ ++g+ l+ll 
  gi|386000737|ref|YP_005919036.1| 301 AVYIAILGLISEEG-YSSGAVYLLLYNLGVILPILLLGgvIAFGMSPARVDSFRKdHRAAIRLVTGLTLLLLA 372
                                       ************99.99*******************9855557778889999988466789999998887765 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 !   34.2  22.5   6.5e-12   2.3e-08       2     182 ..     164     348 ..     163     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 6.5e-12
                            DsbD_2   2 afllgLlgsl.hClgmCggivlalslskp..kra..lalllynlGRilsYallGalvgllgsvlqlageleglrall 73 
                                       +f++gLl+++ +Cl+   +++++   s++  +r   +  +++++G  + Y l+G+ +     +  + + +++lr  l
  gi|386000737|ref|YP_005919036.1| 164 VFVAGLLAGFnPCLLGILAFLATAIISSSgrRRDlvMMVAFFSFGIFVMYYLFGVGLL--RTLH-AGAIAAHLRTGL 237
                                       89********9**98877766655444431144443369***************6443..3333.33334679**** PP

                            DsbD_2  74 gvllgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnGll..pC.glvysalllalasg 147
                                       +vll++l+l+ + ++ +     +  +  ++ +r+++  +++  +++s +llG+l++l+  pC g vy a+l  ++ +
  gi|386000737|ref|YP_005919036.1| 238 TVLLIALGLVHIEDARRLSAGGRSLFKASWSQRYVEGALAR-GRYSSYFLLGALFSLVkaPCvGAVYIAILGLISEE 313
                                       *********97777765555555556678899999999998.79*************877**99************* PP

                            DsbD_2 148 saleGalvmlaFgLGTlpalllfglllgllskklr 182
                                        +++Ga+++l++ LG ++++ll+g ++++  + +r
  gi|386000737|ref|YP_005919036.1| 314 GYSSGAVYLLLYNLGVILPILLLGGVIAFGMSPAR 348
                                       ****************9999999999988644333 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.3e-08   8.3e-05       1      57 [.      31      91 ..      31      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.3e-08
                                      EEEEESTSSHHHHHHHHHH.....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlL.....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidg 57
                                      vvl ++p+C  C++a r+L     +  gv+ +++dv  + e r++++e   +  vP + +++
  gi|386000737|ref|YP_005919036.1| 31 VVLVSSPGCTKCAAAERTLemilaDHPGVELAVYDVYSE-EGRKAVREHRLRGGVPAIAVGN 91
                                      8999***************99999999***********7.99999999997789***99986 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05      0.05       5      38 ..      34      68 ..      29      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                      EESSSSTTCHHHHHHHHHHCHCC.TCECEEECCTT CS
                     Thioredoxin_3  5 vlgpgCakCpklekavkeaaaek.gikaevekvtd 38
                                      v +pgC+kC ++e+ ++ ++a+  g+++ v++v+ 
  gi|386000737|ref|YP_005919036.1| 34 VSSPGCTKCAAAERTLEMILADHpGVELAVYDVYS 68
                                      4599***************999989***9999843 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05      0.13       2      41 ..      31      71 ..      30     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                      EEEEE-TT-HHHHHHHHHHHH.HCCCTTEEEEEEETTT-CC CS
                            DUF836  2 ltLyskpgChlCeqakekLke.lkleegleleviDIakdee 41
                                      ++L s pgC  C  a+  L+  l+   g+el v D++++e 
  gi|386000737|ref|YP_005919036.1| 31 VVLVSSPGCTKCAAAERTLEMiLADHPGVELAVYDVYSEEG 71
                                      8999****************84455555*********6544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2248.09
//
Query:       gi|386000738|ref|YP_005919037.1|  [L=197]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 1218.50
//
Query:       gi|386000739|ref|YP_005919038.1|  [L=497]
Description: Periplasmic copper-binding protein (NosD) , putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-38  131.8  28.7    7.8e-23   81.0   9.4    2.3  2  NosD             Periplasmic copper-binding protein (NosD)
    1.9e-36  125.3  44.9    6.4e-26   91.1  21.3    2.2  2  Beta_helix       Right handed beta helix region
    8.5e-06   25.3  24.5    0.00053   19.4   8.1    2.9  2  DUF1565          Protein of unknown function (DUF1565)
  ------ inclusion threshold ------
      0.082   12.7  23.0          6    6.7   6.0    3.7  2  Pectate_lyase_3  Pectate lyase superfamily protein


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 !   81.0   9.4   1.7e-26   7.8e-23       3     174 ..      42     222 ..      40     229 .. 0.88
   2 !   54.6  13.5     2e-18     9e-15      90     238 ..     231     377 ..     222     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.7e-26
                              NosD   3 naisgdevlvsa.rgngiqlensegseisnneisnsrdgi.lldnssnntitgntienlryGihlensesntiednt 77 
                                        a+ gd+vl       g+ + +s +    + +i+    +i +   ++++ti+g t+e + yGihl++s ++ti++nt
  gi|386000739|ref|YP_005919038.1|  42 QAVPGDTVLAAPgVYGGVEITKSINLIGDGARIRADDRQIgMKVGADDVTISGFTVEGGFYGIHLVGSRNCTISNNT 118
                                       566677765555634477777776666677778777777767788999***************************** PP

                              NosD  78 lssne.sGialmsssnntlenNtisnnen.....yGillsdssnntisnNtis.nnnkGiflens.ssntitgNrie 146
                                       ++++   Gi l ss +n +enN+++ n       yGi+ls+s+ n i++N++s n ++Gi l  s s+n+i++N  e
  gi|386000739|ref|YP_005919038.1| 119 ITGCVqWGIGLISSDDNRIENNVANYNGLggegwYGIYLSGSHRNLIQDNVASfNGEYGIALFPScSENVIRENVAE 195
                                       ****999******************99878999********************************9*********** PP

                              NosD 147 snqkiGilllsssegntiynNyFinnse 174
                                       +n ++Gi++++++ +n+i +N + +n +
  gi|386000739|ref|YP_005919038.1| 196 RN-DYGIYMFTNCADNLIQKNRLAQNFN 222
                                       **.********************88876 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2e-18
                              NosD  90 ssnntlenNtisnnenyGillsdssn.ntisnNtis.nnnkGiflens..ssntitgNriesnqkiGilllsssegn 162
                                        s+n +  N i +n   Gi+l++ s+ n i++N+i  n++ Gi++++    +nti +N+i+++ + Gi+   +++gn
  gi|386000739|ref|YP_005919038.1| 231 CSKNQILENDIVENGVVGIFLQRGSGyNLIRGNEIAdNSKFGIQIQEGpsGNNTIVENNISAS-QRGIF--VNTDGN 304
                                       34565557777777778**9987655399*******9*********9888*************.*****..67778* PP

                              NosD 163 tiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg.........eDadgDGigDtpYeindg 230
                                       +iy+N  ++  + +++ g   n+W  +             gGN+W dy g         + +  DG++D p  in+ 
  gi|386000739|ref|YP_005919038.1| 305 HIYKNRIFDCVIPAEDRG--VNQWYADY----------PEGGNFWGDYIGtdefggpgqNISGSDGFADLPRIINER 369
                                       ******99********99..89996666..........459*********88888887544789************* PP

                              NosD 231 viDylplv 238
                                         D +p +
  gi|386000739|ref|YP_005919038.1| 370 ARDIYPVM 377
                                       99999987 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 !   91.1  21.3   1.4e-29   6.4e-26       8     158 .]      87     241 ..      80     241 .. 0.97
   2 !   48.3  15.6   2.1e-16   9.4e-13      34     145 ..     210     326 ..     208     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 1.4e-29
                                       S-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---.....SEEE-TT--S- CS
                        Beta_helix   8 ssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn.....gggialfgasn 79 
                                        ++vti+++t+++ g yGi+l gs+n++i+nn+i+++ + Gi++ +s++n i+nn+ + n+      +gi+l+g+++
  gi|386000739|ref|YP_005919038.1|  87 ADDVTISGFTVEG-GFYGIHLVGSRNCTISNNTITGCVQWGIGLISSDDNRIENNVANYNGlggegWYGIYLSGSHR 162
                                       4568*********.9************************************************************** PP

                                       -EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES CS
                        Beta_helix  80 nlienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrn 155
                                       nli++n  + ng++Gi l+ ++s n+i++N+++ n  +Gi++  +++++ +++N++ +n + Gi+ ++++s++++ +
  gi|386000739|ref|YP_005919038.1| 163 NLIQDNVASFNGEYGIALFpSCSENVIRENVAERND-YGIYMFTNCADNLIQKNRLAQNFNSGIKMINGCSKNQILE 238
                                       *******************99***************.*********9999*************************** PP

                                       -E. CS
                        Beta_helix 156 Nti 158
                                       N i
  gi|386000739|ref|YP_005919038.1| 239 NDI 241
                                       976 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2.1e-16
                                       .EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT.--S--EEES-EEES-SS-SEE-TT..-S--EEE CS
                        Beta_helix  34 vvienneiannsgsGiyilgs.snntisnntisdnngggialf.gasnnlienneitdnggsGiylny..ssnntie 106
                                       ++i++n++a+n  sGi + ++ s+n+i +n i +n+ +gi l+ g+++nli++nei dn++ Gi+++   s nnti 
  gi|386000739|ref|YP_005919038.1| 210 NLIQKNRLAQNFNSGIKMINGcSKNQILENDIVENGVVGIFLQrGSGYNLIRGNEIADNSKFGIQIQEgpSGNNTIV 286
                                       49***************99999999999999999999******************************769999**** PP

                                       S-EEESTT--SEE---TT---EEES-EEES-S....SEEEE-T CS
                        Beta_helix 107 nNiidnnagsGividdsssnvtvtnNtitnnk....gaGiavv 145
                                       +N+i++ +  Gi+++  +  + + +N+i++++    + G++++
  gi|386000739|ref|YP_005919038.1| 287 ENNISASQ-RGIFVNTDG--NHIYKNRIFDCVipaeDRGVNQW 326
                                       ****9999.*****9999..55778887777755556777665 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   8.1   1.2e-07   0.00053      88     200 ..      78     208 ..      43     228 .. 0.67
   2 !    8.6  10.7   0.00023         1     124     198 ..     233     302 ..     208     374 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                           DUF1565  88 gvqnvtivlaneatiaGvtitNpnilkgtgvliesa.sakianNtitgniadGiev..........siyeaktgagg 153
                                       + q    v+a+ +ti G+t++       +g+ + ++ + +i+nNtitg+++ Gi            +  +  +g gg
  gi|386000739|ref|YP_005919038.1|  78 DRQIGMKVGADDVTISGFTVEGG----FYGIHLVGSrNCTISNNTITGCVQWGIGLissddnrienNVAN-YNGLGG 149
                                       55555668899**********99....4689988888****************66544444444423333.334333 PP

                           DUF1565 154 .............niisGnsilfekn.GiaisgasaavenkienNiivkNliGvvanalal 200
                                                    n i  n   f+ + Gia   +    en i++N+  +N +G+ + +  +
  gi|386000739|ref|YP_005919038.1| 150 egwygiylsgshrNLIQDNVASFNGEyGIALFPSCS--ENVIRENVAERNDYGIYMFTNCA 208
                                       344443333333344555555566556777665544..5999***********98766554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00023
                           DUF1565 124 sakianNtitgniadGievsiyeaktgaggniisGnsilfekn.Giaisgasaavenki.enNiivkNliGvvanal 198
                                         +i +N i +n+  Gi+     ++ g+g n i Gn+i+++ + Gi+i++   + +n i en  i+  ++G+ +n+ 
  gi|386000739|ref|YP_005919038.1| 233 KNQILENDIVENGVVGIF-----LQRGSGYNLIRGNEIADNSKfGIQIQEGPSG-NNTIvEN-NISASQRGIFVNTD 302
                                       334555555554444443.....3556777888888888887778888877777.5555244.34444555554443 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  12.1    0.0015       6.6      17     214 ..      36     225 ..      28     226 .. 0.75
   2 ?    6.7   6.0    0.0013         6     103     204 ..     208     309 ..     203     319 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0015
                                       -HHHHHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-TTTEEEEE-TT-SS--SEEES-TTT-..-EE CS
                   Pectate_lyase_3  17 dtaaiqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvGdgngrpvlkaaaafvgaglidgdpyvsggseal 93 
                                        +aai++a+        g++V  ++G Y   +++ +++ ++L+Gdg   + ++a ++  g+ +  +d + sg    +
  gi|386000739|ref|YP_005919038.1|  36 LQAAINQAV-------PGDTVLAAPGVY---GGVEITKSINLIGDG---ARIRADDRQIGMKVGADDVTISG----F 95 
                                       455555555.......788888999988...77788999*******...68999999999998888888866....6 PP

                                       EEEEEEEEEGGGG-SS---SSEEEES-E.EE....EEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES CS
                   Pectate_lyase_3  94 iatnnfyrqirnlkiditavapgatgih.wq....taqatslenvefemseasgtkhqgifiengsggflndlvfsg 165
                                       + +  fy  +     + t  +++ tg+  w     ++++  +en++ +++   g+   gi+++ + ++ ++d v+s 
  gi|386000739|ref|YP_005919038.1|  96 TVEGGFYGIHLVGSRNCTISNNTITGCVqWGigliSSDDNRIENNVANYNGLGGEGWYGIYLSGSHRNLIQDNVASF 172
                                       6777788776555555554455667755577777688899999999999998889999***9999999999999999 PP

                                       -SS-SEEE.S..-EEEEEES-EEE-S--SEEE-TT-E.EEEEEEEEESSSE.EE CS
                   Pectate_lyase_3 166 lgdigiav.g..nqqftvrnitfnnattgievlwgwg.wtlknvkinnceg.Gi 214
                                       +g++gia+    +++ ++r+++ + +  gi++ ++ +   ++ +++ +  + Gi
  gi|386000739|ref|YP_005919038.1| 173 NGEYGIALfPscSEN-VIRENVAERNDYGIYMFTNCAdNLIQKNRLAQNFNsGI 225
                                       99*****96355555.55555555559999999988878888887744433376 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0013
                                       GGGG-SS---SSEEEES-E.EEEEEEEEEES-SSEEE-SSS---TT---SS--EEEE..ES-EEES-SS-SEEES.. CS
                   Pectate_lyase_3 103 irnlkiditavapgatgih.wqtaqatslenvefemseasgtkhqgifiengsggfl..ndlvfsglgdigiavg.. 174
                                       + nl+ + + ++++++gi+  + +++ +    ++e++  + +  +gif+++gsg  l   + ++++ +++gi+++  
  gi|386000739|ref|YP_005919038.1| 208 ADNLIQKNRLAQNFNSGIKmINGCSKNQ----ILENDIVE-NGVVGIFLQRGSGYNLirGNEIADN-SKFGIQIQeg 278
                                       5555555444455556655444444444....34444444.4456999999999555577777777.9999999557 PP

                                       ..-EEEEEES-EEE-S--SEEE-TT-EEEEEE CS
                   Pectate_lyase_3 175 ..nqqftvrnitfnnattgievlwgwgwtlkn 204
                                          ++ +v+n+   + ++gi v+++ + ++kn
  gi|386000739|ref|YP_005919038.1| 279 psGNNTIVENNISAS-QRGIFVNTDGNHIYKN 309
                                       865555555544444.7999998866666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3420.34
//
Query:       gi|386000740|ref|YP_005919039.1|  [L=563]
Description: Rhodanese domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-20   72.6   0.0    3.2e-09   37.2   0.0    2.5  2  Rhodanese     Rhodanese-like domain
  ------ inclusion threshold ------
      0.038   13.9   0.1      0.083   12.8   0.1    1.6  1  FlgD_ig       FlgD Ig-like domain
      0.082   10.9   0.0       0.15   10.1   0.0    1.3  1  Peptidase_S6  Immunoglobulin A1 protease
        0.2   11.9   0.0        0.4   10.9   0.0    1.4  1  zf-4CXXC_R1   Zinc-finger domain of monoamine-oxidase A repre
       0.56    9.6   3.6       0.18   11.2   0.3    1.9  2  zf-RanBP      Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   9.1e-13   3.2e-09      15     106 ..     107     203 ..      94     204 .. 0.76
   2 !   32.8   0.0   2.2e-11   7.8e-08      10      96 ..     236     320 ..     232     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 9.1e-13
                         Rhodanese  15 a..llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr.aaaa....aa 84 
                                       a  +lDv +   Y + hI+gA+ + ++ l +++ ++++  e+ e + + gi++++ vv+y+d   +   ++     +
  gi|386000740|ref|YP_005919039.1| 107 AdvILDVGS--HYGTIHIKGAIPLYWEELLDENNNPKSAEEMAEIFGNAGISPEDSVVIYGDCEPCdDISVapfvFW 181
                                       345888877..57789********7777777777777777777777777***********99999955555555455 PP

                         Rhodanese  85 llkklGykn.vsvldGGfkawke 106
                                       ++++lG ++ v+vldGG++aw +
  gi|386000740|ref|YP_005919039.1| 182 AMRYLG-HDsVQVLDGGLDAWTS 203
                                       7779**.777***********87 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2.2e-11
                         Rhodanese  10 ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaall 86 
                                       ++g+ +l+D+R   ++++  I gA+++  d+    +    +  ++++++ + g+d++++vvvy   g raa ++ +l
  gi|386000740|ref|YP_005919039.1| 236 SSGDLQLVDARVLRDFSADKIAGAIHI--DYSEVLTGGRMKGSDDLDRAFS-GLDEERPVVVYSYAGARAAMVWLAL 309
                                       567778*********************..4444444444455555555555.67***************8889**** PP

                         Rhodanese  87 kklGykn.vsv 96 
                                       + +Gy+  v+ 
  gi|386000740|ref|YP_005919039.1| 310 QLMGYESsVYS 320
                                       ****8776764 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.3e-05     0.083      21      78 ..     472     524 ..     454     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                       SSEEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEEEEETT CS
                           FlgD_ig  21 aadevtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkvtatsg 78 
                                       +++++   i+D++G+v  ti+l +    ++  tWd   +  + +++GaY+v+ +a++g
  gi|386000740|ref|YP_005919039.1| 472 PITAAGALIQDSEGRVMATIELVPTLTDEYLGTWD---A--TGAPAGAYNVTLAAATG 524
                                       555666779**************************...4..4569*********9976 PP

>> Peptidase_S6  Immunoglobulin A1 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.2e-05      0.15     699     747 ..     384     432 ..     368     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.2e-05
                                       GG----TT-EE-EEEEEEEEEE-TT-EEEE-TTEEEEEEEEEE-TT-EE CS
                      Peptidase_S6 699 nnevvveddwinrtfkaeniavknsaalvsgrnvsditanitasdnakv 747
                                        +e v+ed  i+    aen++++ + ++vsg ++ di +n t  +   +
  gi|386000740|ref|YP_005919039.1| 384 VEEAVFEDGGIDDIGPAENLSIETNGSIVSGAEIEDIISNATSMEKPTA 432
                                       4799**************************************9876544 PP

>> zf-4CXXC_R1  Zinc-finger domain of monoamine-oxidase A repressor R1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011       0.4      52      72 ..      14      34 ..       7      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                       zf-4CXXC_R1 52 aakkeWvCPkCrgiCncslcr 72
                                      ++  +W CP+C+g  n+sl+ 
  gi|386000740|ref|YP_005919039.1| 14 KHAGKWDCPECKGQSNSSLAI 34
                                      45689***********99754 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3     5e-05      0.18       2      16 ..      16      31 ..      15      34 .. 0.85
   2 ?   -2.0   0.3      0.65   2.3e+03      18      24 ..     434     440 ..     432     440 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                                      SSSEE-SSS-.-EEES CS
                          zf-RanBP  2 egdWdCskCl.vqNfa 16
                                      +g+WdC+ C+  +N++
  gi|386000740|ref|YP_005919039.1| 16 AGKWDCPECKgQSNSS 31
                                      79*******9888887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.65
                                       SSB-TTT CS
                          zf-RanBP  18 stkCvaC 24 
                                       ++ CvaC
  gi|386000740|ref|YP_005919039.1| 434 TMGCVAC 440
                                       667**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 4219.65
//
Query:       gi|386000741|ref|YP_005919040.1|  [L=624]
Description: Peptidase S8 and S53, subtilisin, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-51  174.0   0.1    5.4e-51  173.6   0.1    1.1  1  Peptidase_S8  Subtilase family
     0.0065   17.2   0.1         10    7.0   0.0    3.4  4  Big_7         Bacterial Ig domain
  ------ inclusion threshold ------
       0.16   12.0   0.0         24    5.0   0.0    2.4  2  Y_Y_Y         Y_Y_Y domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.6   0.1   9.1e-55   5.4e-51       2     298 .]     248     514 ..     247     514 .. 0.86

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 9.1e-55
                                       TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   2 kgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanape 78 
                                        gv+va+lDtG dp+h  l        +++d   + ga+++  +     +++  dd+g    HGth+A+++a++   
  gi|386000741|ref|YP_005919040.1| 248 WGVTVAILDTGADPNHRSLD-------DMDDDLFTPGAKIVAFKDFVNGREDVYDDHG----HGTHCASLIAGT--- 310
                                       59******************.......7777777777777776666666677777789....************... PP

                                       SSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHC....T-SEEEE-EESCETTCHHCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  79 egekngvapgakilsvkvldtsggsmetgteliraieeaaed....kvdvinmslgestslpktgrsiealainrav 151
                                        g   g+apga +  +kv+d +g      ++ + a+++++e+    ++dv++ s+g++   +      e  a++r+v
  gi|386000741|ref|YP_005919040.1| 311 -GDGRGIAPGAGLVVIKVMDRDGACY--LSDALTALDWCLENrdslGIDVLSFSVGGEVPSEGATLLDE--ACDRMV 382
                                       .******************9999554..599999******952233466*******5554444444445..****** PP

                                       .CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-..CCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                      Peptidase_S8 152 nkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgn..ivs 226
                                        + g++v ++aGN g      +a+ ++ tp+t++ vitvga+++ g+i   SsrGp+ d ++kpd+va G+n  +++
  gi|386000741|ref|YP_005919040.1| 383 -DAGIVVSVAAGNAG------PATRSIVTPGTAEKVITVGATDPGGMIFQRSSRGPTLDNRVKPDLVAVGVNvtSAK 452
                                       .99************......***************************************************43333 PP

                                       CCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 227 twsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                         + ++         + msGTSmA+P +aga A++l++ p l p+ v+++ll++A+d+   +++ ++ +G+G
  gi|386000741|ref|YP_005919040.1| 453 AGTLRG--------EEDMSGTSMAAPQVAGACAVILEKQPGLDPAGVKRVLLRSADDI--GPSGPDNTFGYG 514
                                       344444........578***************************************99..667********9 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0038        23      18      37 ..      75      94 ..      68     127 .. 0.83
   2 ?   -2.3   0.1       1.3   7.8e+03      27      51 ..     351     397 ..     350     416 .. 0.54
   3 ?   -1.7   0.1      0.89   5.3e+03       8      30 ..     397     421 ..     394     423 .. 0.70
   4 !    7.0   0.0    0.0017        10      13      70 .]     543     605 ..     539     605 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0038
                                      EEEEEEEEE-SS-EEEEEEE CS
                             Big_7 18 tvtisasAsddggvskVefy 37
                                      +v+++a++ dd+gv++V   
  gi|386000741|ref|YP_005919040.1| 75 QVEVRAWVRDDVGVETVYAE 94
                                      699*************9765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                                       -SS-EEEEEEEETTEE.......................EEEE-SSS CS
                             Big_7  27 ddggvskVefyvdgtl.g.....................lgtdtsap 51 
                                       d+ g++   f+v+g++                       +++ +++p
  gi|386000741|ref|YP_005919040.1| 351 DSLGIDVLSFSVGGEVpSegatlldeacdrmvdagivvsVAAGNAGP 397
                                       55667777777777764445555444444444444444444444444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.89
                                       --TT--EB.TS.EEEEEEEEE-SS- CS
                             Big_7   8 Pangatvs.gg.tvtisasAsddgg 30 
                                       Pa  + v+ g+    i++ A+d+gg
  gi|386000741|ref|YP_005919040.1| 397 PATRSIVTpGTaEKVITVGATDPGG 421
                                       7777777743334479999999977 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0017
                                       -EB.TSEEEEEEEEE-SS-EEEEEEEETTEE.......EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  13 tvs.ggtvtisasAsddggvskVefyvdgtl.g.....lgtdtsapysltwtttaltagthtltV 70 
                                       + + g++vti+a +s d   ++Ve+ v g   +      + d ++ y+  w t   + g +++ V
  gi|386000741|ref|YP_005919040.1| 543 AATpGDPVTIEAGVSGD--PATVEVHVIGRDrEiripmGDLDRNGVYTGRWETRFWEPGDYSIAV 605
                                       456699********999..9999999999997799998667899*********9999****9987 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 ?    4.5   0.0    0.0057        34      34      63 ..     117     145 ..     116     148 .. 0.85
   2 ?    5.0   0.0     0.004        24      37      50 ..     597     610 ..     594     620 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0057
                                       ES--SEEEEEEEEEEETTS-B-SS-EEEEE CS
                             Y_Y_Y  34 tnlppGdYtlkVkakdndgqwnyditslsf 63 
                                       +nlppGd  +++ a d+ g+   + ++l +
  gi|386000741|ref|YP_005919040.1| 117 SNLPPGDHPIEIIAVDKAGNAARN-AELVL 145
                                       69******************9999.55555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.004
                                       -SEEEEEEEEEEET CS
                             Y_Y_Y  37 ppGdYtlkVkakdn 50 
                                       +pGdY + V+akd+
  gi|386000741|ref|YP_005919040.1| 597 EPGDYSIAVEAKDP 610
                                       69**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 4679.51
//
Query:       gi|386000742|ref|YP_005919041.1|  [L=182]
Description: Class II aldolase/adducin family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-36  123.7   0.2      9e-36  123.5   0.2    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.2     5e-40     9e-36       4     184 ..       8     175 ..       5     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 5e-40
                                       HHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHH CS
                       Aldolase_II   4 aeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlai 80 
                                        + + ++   gl+ +  GniS+ ++  + +lit +g  ++elt+++++ v  +   +   +e ++ +s et +H+ai
  gi|386000742|ref|YP_005919041.1|   8 SKFGSKIVSSGLTYAHFGNISLLSE--GMILITSTGSILDELTEDEVIAVTPE--APC--PE-DALASCETVVHRAI 77 
                                       56667788899***********955..8888*******************755..444..24.4569********** PP

                                       HHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEET CS
                       Aldolase_II  81 ykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllr 157
                                       y++ ++arav+HtHsp+ava s ++++ +++p++ e+ak+l  + vp+++ ++ g+ el++++++alk  ++a+++r
  gi|386000742|ref|YP_005919041.1|  78 YEK-TTARAVIHTHSPYAVATS-ILEEGPFEPMDGEGAKFL--GAVPIVEGEM-GSRELAKNASAALK-GSRACIVR 148
                                       **7.9*****************.557889**********77..88****9998.*************9.77****** PP

                                       TTEEEEEESSHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 158 nHGlltvGetleeAvalaetleeaaei 184
                                       +HG+++vG tleeA+  a ++e++a i
  gi|386000742|ref|YP_005919041.1| 149 GHGVFAVGSTLEEAYVVACMVEHSAMI 175
                                       ***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 1455.36
//
Query:       gi|386000743|ref|YP_005919042.1|  [L=376]
Description: hypothetical protein Mhar_0026 [Methanosaeta harundinacea 6Ac]
Scores for 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-29   99.7   3.6    3.2e-14   53.1   0.3    2.5  2  CBS             CBS domain
    4.8e-13   49.0  12.1    9.3e-08   31.6   0.6    3.0  3  Peptidase_M50   Peptidase family M50
    0.00011   21.9   4.7    0.00011   21.9   4.7    2.2  2  Peptidase_M50B  Peptidase M50B-like


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.3   4.5e-16   2.7e-12       1      51 [.     255     304 ..     255     309 .. 0.91
   2 !   53.1   0.3   5.4e-18   3.2e-14       1      55 [.     317     370 ..     317     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 4.5e-16
                                       HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDl 51 
                                       V+dim+rd+ tv+pdtt+ e+++l + +++++++PV+ e g+l Givt +D+
  gi|386000743|ref|YP_005919042.1| 255 VRDIMSRDLRTVSPDTTVPEIMNLmF-REKHRGYPVM-EGGRLAGIVTISDV 304
                                       89**********************45.55589*****.89***********8 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 5.4e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       Vgd+m r + ++ p+++ +ea+++m e  ++rlPV+ edg+lvGiv+++Dllra+
  gi|386000743|ref|YP_005919042.1| 317 VGDVMVRAIYVIEPNADAAEAMKKMMEQQIRRLPVM-EDGELVGIVSRSDLLRAI 370
                                       89**********************77888*******.9***************98 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.9   5.8e-09   3.4e-05       1      34 [.      69     102 ..      69     142 .. 0.82
   2 !   31.6   0.6   1.6e-11   9.3e-08     188     246 ..     155     211 ..     127     215 .. 0.78
   3 ?   -0.7   0.1      0.11   6.7e+02      92     109 ..     220     305 ..     216     363 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.8e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsig 34 
                                       af++ll+++v++HElGH +vA + g+k++++ + 
  gi|386000743|ref|YP_005919042.1|  69 AFAILLFLCVALHELGHSFVAMRYGIKIRSITLY 102
                                       599*************************995543 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.6e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglal 246
                                       l+++l++l +i+++L i+NLlP +++DGg++l+a +      p  e ++++a++  ++ 
  gi|386000743|ref|YP_005919042.1| 155 LTTLLWTLGVINIILMIFNLLPAFPMDGGRVLRAWFASRL--PYVEATRRAATIGKFFA 211
                                       45899*****************************988777..66666666555544444 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXX............................................................ CS
                                       xxxxxxxxxxxxxxxxx............................................................ RF
                     Peptidase_M50  92 lAGplanfilailvfvv............................................................ 108
                                       ++G +  +++ai+++++                                                            
  gi|386000743|ref|YP_005919042.1| 220 FGGGILLVVIAIFIYIAandeekataivvplegvkvrdimsrdlrtvspdttvpeimnlmfrekhrgypvmeggrla 296
                                       56666677777777777666666666666666666666666666666666666666666666666666555555555 PP

                                       ........- CS
                                       ........x RF
                     Peptidase_M50 109 ........p 109
                                               +
  gi|386000743|ref|YP_005919042.1| 297 givtisdvQ 305
                                       555543330 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   4.7   1.9e-08   0.00011      21     107 ..      74     169 ..      62     178 .. 0.73
   2 ?   -1.0   0.6      0.19   1.1e+03     114     132 ..     219     237 ..     184     255 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-08
                    Peptidase_M50B  21 kllvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllillsas..... 90 
                                         l v +HElGH ++a+  G ++ +i+l+   +Gv+ ++   +     + +++aG+  + +lG++ ills +     
  gi|386000743|ref|YP_005919042.1|  74 LFLCVALHELGHSFVAMRYGIKIRSITLYI-FGGVASMEDipRDPSMEARMAVAGPGVSGILGAGTILLSLQaasll 149
                                       568899***********************8.589****9994444445889*****************995511222 PP

                    Peptidase_M50B  91 ..gka.rlllvllvllllvl 107
                                         g++ + ll++l ++ ++l
  gi|386000743|ref|YP_005919042.1| 150 ggGHPlTTLLWTLGVINIIL 169
                                       22222344666444443333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.19
                    Peptidase_M50B 114 lfglvlllllgallllvll 132
                                       lfg  +ll+++a+++ ++ 
  gi|386000743|ref|YP_005919042.1| 219 LFGGGILLVVIAIFIYIAA 237
                                       3333444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2620.30
//
Query:       gi|386000744|ref|YP_005919043.1|  [L=411]
Description: TraB family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-32  114.1   0.0    2.5e-32  112.8   0.0    1.6  2  TraB           TraB family
  ------ inclusion threshold ------
      0.057   13.4   1.5        7.1    6.5   0.1    3.2  3  DUF1110        Protein of unknown function (DUF1110)
      0.061   13.4   0.0       0.12   12.4   0.0    1.4  1  Tim44          Tim44-like domain
        3.3    7.5   6.4         15    5.3   1.7    2.3  2  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.0   5.5e-36   2.5e-32      11     253 ..      25     237 ..      18     241 .. 0.86
   2 ?   -2.7   0.0         1   4.5e+03     137     152 ..     351     366 ..     314     368 .. 0.58

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 5.5e-36
                              TraB  11 tsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd...tdeatqkelaklkllpdgktlsdllseelyarl 84 
                                       ++ ++GT+Hvs+ksv+++++++e+   ++d+v+vEl+  ++     e++  e++ + +l+ g++l  ll +  +a +
  gi|386000744|ref|YP_005919043.1|  25 EIVIVGTAHVSEKSVQEVRQAIEDL--RPDVVAVELCRGRYralRGEEETGEIQIKEILS-GGKLYLLLVQWFLAYV 98 
                                       499*********************5..**************7777777777777777887.**************** PP

                              TraB  85 qkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsll.sslpd 160
                                       qk++ +  l++      kP  ++++++++e  +++ag   +lvDr++a t +r + ++++lE++++++s++ +++ +
  gi|386000744|ref|YP_005919043.1|  99 QKKIGS-DLGV------KP--GSEMIAAIEA-AEAAGARVALVDRDIAVTIQRFWTSMSFLEKAKLVFSMIpAAFGK 165
                                       ******.9***......**..9999999997.6888999999*****************************433444 PP

                              TraB 161 eeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsvfv 237
                                        e +  ++  +  +  ++d ++ ++e              e++e +p   evl+deR+++ a+++ + l++ g+v++
  gi|386000744|ref|YP_005919043.1| 166 GEDI-DID-KV--T--EEDVVSAIIE--------------EFREVSPRAAEVLIDERDAYIARNLIR-LARTGRVLA 221
                                       3333.343.22..3..4788999999..............**************************7.5555***** PP

                              TraB 238 aVGagHlaGedgvlal 253
                                       +VGagH  G+  +l++
  gi|386000744|ref|YP_005919043.1| 222 VVGAGHREGIARYLDH 237
                                       ********99998886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1
                              TraB 137 ragkpvgglEtveeql 152
                                       ++ k++++ Et++e++
  gi|386000744|ref|YP_005919043.1| 351 ADMKKLAEAETFKEMM 366
                                       3344444444444444 PP

>> DUF1110  Protein of unknown function (DUF1110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.016        70     109     137 ..      37      65 ..      15      67 .. 0.82
   2 ?    6.5   0.1    0.0016       7.1      40     105 ..     114     179 ..      91     214 .. 0.87
   3 ?    0.6   0.1      0.11   4.7e+02      43      94 ..     357     407 ..     338     410 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                           DUF1110 109 nAlakLreakedaeeAyasvdrCrghLda 137
                                       + +++ r+a ed +    +v+ Crg+ +a
  gi|386000744|ref|YP_005919043.1|  37 KSVQEVRQAIEDLRPDVVAVELCRGRYRA 65 
                                       4678899******************9988 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                           DUF1110  40 rvadeeaaaaardriqlvlgaLedaSrdLalAmslmkaAellalrggavdpstslvdigrlgdqyl 105
                                        +a+ eaa+aa++r+ lv  +++   +   + ms ++ A+l+     a+  + + +di+++ ++++
  gi|386000744|ref|YP_005919043.1| 114 MIAAIEAAEAAGARVALVDRDIAVTIQRFWTSMSFLEKAKLVFSMIPAAFGKGEDIDIDKVTEEDV 179
                                       466779***********************************9988888888888888888888875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.11
                           DUF1110  43 deeaaaaardriqlvlgaLedaSrdLalAmslmkaAellalrggavdpstsl 94 
                                       +e++   +   i l +  L+ a  +L++ ++++ +A l+ lr ++v+p+  +
  gi|386000744|ref|YP_005919043.1| 357 AEAETFKEMMAIPLFRVILVAALANLGSVAGTVLGAYLI-LRMAGVSPEDLV 407
                                       334444455567888889999999************987.568888887655 PP

>> Tim44  Tim44-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05      0.12      18      62 ..     146     190 ..     135     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHH CS
                             Tim44  18 eeFleeakeayepileayakgDletLrkllteevyeefkaeiker 62 
                                        +Fle+ak ++ +i +a+ kg+  ++ k++ e+v++++ +e +e 
  gi|386000744|ref|YP_005919043.1| 146 MSFLEKAKLVFSMIPAAFGKGEDIDIDKVTEEDVVSAIIEEFREV 190
                                       68***********************************99888775 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2    0.0071        32      90     172 ..     200     301 ..     173     312 .. 0.64
   2 ?    5.3   1.7    0.0033        15      89     168 ..     314     396 ..     307     403 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0071
                     FA_desaturase  90 eglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrk...............wrllawlllllawlglw 151
                                       +++ +y++r l +l ++g +la v++  + ++ar+ +++++++ +               +++ a+l+ll+ +++++
  gi|386000744|ref|YP_005919043.1| 200 DERDAYIARNLIRLARTGRVLAVVGAGHREGIARYLDHPERIPPMeemasparrrrisapKVFGALLMLLVLVTIGA 276
                                       55667777778888888877777777788888888888887777777777777777778655555555555443333 PP

                     FA_desaturase 152 lalllllglall....lwlvpllll 172
                                       +++++  +   l    +w+++  +l
  gi|386000744|ref|YP_005919043.1| 277 VLIAGIDSARILaalkIWFLVNGAL 301
                                       3333333333335667777764444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0033
                     FA_desaturase  89 feglfryllrlllgllvlg...wllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglal 162
                                        ++l ++++++l  l  l    w+ + v+++ +++  +  ++ +++++++ ++a+ l++++++++++ l+ ++g +l
  gi|386000744|ref|YP_005919043.1| 314 LSALTAFMIAWLTSLNPLMaagWFAGIVEAWKRKPTMADMKKLAEAETFKEMMAIPLFRVILVAALANLGSVAGTVL 390
                                       4555666555555444444456**************************************99999999999888876 PP

                     FA_desaturase 163 llwlvp 168
                                        ++l+ 
  gi|386000744|ref|YP_005919043.1| 391 GAYLIL 396
                                       655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3294.79
//
Query:       gi|386000745|ref|YP_005919044.1|  [L=234]
Description: NADPH-dependent F420 reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-17   61.6   0.1    1.4e-16   60.8   0.1    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0012   19.3   0.0     0.0019   18.6   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.016   15.4   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.065   13.2   0.0      0.089   12.8   0.0    1.2  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.068   13.1   0.0       0.15   12.0   0.0    1.5  1  OST_P2           Oligosaccharyltransferase Peripheral 2 domai


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.1   3.9e-20   1.4e-16       1      97 []      16     116 ..      16     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 3.9e-20
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvl 67 
                                       ki+++ G+G+ g++++++++ +    heiv++ sr+ +kae++a+el           +++++dn+ a+e +d vvl
  gi|386000745|ref|YP_005919044.1|  16 KIAVVgGTGDCGQGFIKRWAGE----HEIVIG-SRKADKAEAAAAELTrflksrgidSRIKGMDNAAAIEASDLVVL 87 
                                       79***9*************988....9***88.******************************************** PP

                                       -S-HHHHHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  68 avkpedveevlselakdalkgklvisvlag 97 
                                       +v+++ ve++ s+l +++  +++vis +++
  gi|386000745|ref|YP_005919044.1|  88 SVPYNFVESMTSNL-RESYGDQIVISPVVP 116
                                       **************.999********9875 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.3e-07    0.0019       1      89 [.      16     104 ..      16     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-07
                                       EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGCTT-SEEEE-SC CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeelkevdivflalp 75 
                                       k+a+vG+tG  Gq ++++ +  h  v  ++ + +++ a  +l++  k  + g d +++   +++++++ d+v+l++p
  gi|386000745|ref|YP_005919044.1|  16 KIAVVGGTGDCGQGFIKRWAGeHEIVIGSRKADKAEAAAAELTRFLK--SRGIDSRIKGmDNAAAIEASDLVVLSVP 90 
                                       79*****************9944433334433344455555555544..78899999994455666*********** PP

                                       HHHHHHHHHHHHHT CS
                    Semialdhyde_dh  76 agvskelapklaea 89 
                                        +  ++++ +l+e+
  gi|386000745|ref|YP_005919044.1|  91 YNFVESMTSNLRES 104
                                       99999999888765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   4.6e-06     0.016       1      80 [.      17      92 ..      17     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkegdlvvn 75
                                      + ++G+ G  Gq++++  a ++    ei++ +r+ +k+ea+aa++   l    +++ +d   +    aa+++  dlvv 
  gi|386000745|ref|YP_005919044.1| 17 IAVVGGtGDCGQGFIKRWAGEH----EIVIGSRKADKAEAAAAELtrfL----KSRGIDSRIKGMDNAAAIEASDLVVL 87
                                      6789999************998....68***********9999874443....55555555555555567888899884 PP

                                      -SSGG CS
                   Sacchrp_dh_NADP 76 lsppi 80
                                       +p+ 
  gi|386000745|ref|YP_005919044.1| 88 SVPYN 92
                                      44443 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.5e-05     0.089      24      93 ..      39     105 ..      16     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                       -EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC- CS
                    NAD_Gly3P_dh_N  24 evrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqalrevlkklkgll 93 
                                       e+++ +r+++ +e+   + e +++L+   +++ ++   d a+a++ +d++vl vP ++++++  +l +  
  gi|386000745|ref|YP_005919044.1|  39 EIVIGSRKADKAEAA--AAELTRFLKSRGIDSRIKGM-DNAAAIEASDLVVLSVPYNFVESMTSNLRESY 105
                                       566666666666654..44567899999999999875.66889*******************99998765 PP

>> OST_P2  Oligosaccharyltransferase Peripheral 2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.2e-05      0.15      96     123 ..      85     112 ..      59     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                                       EEEE--TTCHHHHHHHHHHHHGGGEEEE CS
                            OST_P2  96 aqaslPedvissyieelkkkyGdkvvvr 123
                                       +  s+P ++++s + +l++ yGd++v+ 
  gi|386000745|ref|YP_005919044.1|  85 VVLSVPYNFVESMTSNLRESYGDQIVIS 112
                                       4579*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1863.48
//
Query:       gi|386000746|ref|YP_005919045.1|  [L=374]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.2e-100  335.6   0.0     5e-100  335.3   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0023   17.5   0.0     0.0044   16.6   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.069   12.9   0.0        0.1   12.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
       0.08   12.7   0.0       0.11   12.2   0.0    1.3  1  Met_10           Met-10+ like-protein
      0.098   12.3   0.0       0.16   11.6   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.13   13.0   0.0        0.3   11.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.3   0.0  1.7e-103    5e-100      17     375 ..      14     356 ..       2     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 335.3 bits;  conditional E-value: 1.7e-103
                                       T--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHH CS
                               TRM  17 keeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeN 93 
                                        e  FYNP+++ nRDl v+++r l +          +ldaL+asG R++R a+E +g+ +v +ND+s++Av+li+eN
  gi|386000746|ref|YP_005919045.1|  14 VEGAFYNPRMRLNRDLGVAMVRALGI---S-----DYLDALAASGARGLRVAKE-AGAAAVALNDVSPRAVALIREN 81 
                                       3678****************665554...4.....589****************.9********************* PP

                                       HHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHH CS
                               TRM  94 vklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrk 170
                                       ++ln      v + ++Anvll  +++rf+++DlDPfGspapfl +a++s+ +  +L +TaTDta+L+Ga+ ++++rk
  gi|386000746|ref|YP_005919045.1|  82 ARLNGLVGCEVLS-SNANVLL--HQRRFEAVDLDPFGSPAPFLAAAARSALD--YLFITATDTAPLCGAHLKSGIRK 153
                                       *****99744444.48*****..89*************************99..*********************** PP

                                       HSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT-- CS
                               TRM 171 YgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgCls 247
                                       Y+av++k e   E++ Rill+a are a+ +k v pll++++d+Yvrv++ + +ga+ +++ le++g++ +C +C  
  gi|386000746|ref|YP_005919045.1| 154 YMAVPVKAEHHREMGARILLGAAARELARVDKGVRPLLTHATDHYVRVYLGIAKGAKSADRALESMGYLEQCRSCGL 230
                                       ***************************************************************************77 PP

                                       EEEE--GGG--.SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EE CS
                               TRM 248 eekvkglakfk.aecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyyd 323
                                        ++v+g+   +  +c++cg + ++aGPlwlgp++d  ++++ l+++e   + + + r  +lL+++ +E +d p+yyd
  gi|386000746|ref|YP_005919045.1| 231 WRTVSGVGCPSsGKCSFCGGRAEVAGPLWLGPIQDPGVIGRALAAMEG--SAARSDRGVRLLQACADE-IDLPMYYD 304
                                       6777777654439**********************************9..4555777788********.******** PP

                                       HHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                               TRM 324 lsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                       +++l+++ k +    +++v++l++lg+ +srtH+++ ++kT+ap+e++ evl
  gi|386000746|ref|YP_005919045.1| 305 HHRLCRRFKATPGTASDLVEELRSLGWSASRTHFSGVGVKTDAPIEVLREVL 356
                                       ************************************************9997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-06    0.0044      36     101 ..      43     109 ..      31     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                       EEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEE CS
                               MTS  36 lDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdli 101
                                       lD  +  G+ g+ +ake   a+v l dv+ rA+++ +en++ n+l  +ev+ s++   +++++f+++
  gi|386000746|ref|YP_005919045.1|  43 LDALAASGARGLRVAKEAGAAAVALNDVSPRAVALIRENARLNGLVgCEVLSSNANVLLHQRRFEAV 109
                                       66667789999**********************************99******99999988888877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.4e-05       0.1       7      76 ..      42     107 ..      40     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfD 76 
                                       +lD+ +++G+ +++ a+e+g  a v + D s++a+ l rena+ +gl  +e+  ++++  l +    ++f 
  gi|386000746|ref|YP_005919045.1|  42 YLDALAASGARGLRVAKEAG-AAAVALNDVSPRAVALIRENARLNGLVGCEVLSSNANVlLHQ----RRFE 107
                                       6898999*********8877.5999*****************************999984443....4444 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05      0.11     105     150 ..      43      88 ..       7     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                                       EETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-T CS
                            Met_10 105 vdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkve 150
                                       +d +A  G   + +ak + a  v  +d+ P++v +++en +lN + 
  gi|386000746|ref|YP_005919045.1|  43 LDALAASGARGLRVAKEAGAAAVALNDVSPRAVALIRENARLNGLV 88 
                                       7889999999999******************************764 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.3e-05      0.16      42     121 ..      39     113 ..      30     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                                       C-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                        + +LD  a sGa gl  A   ga+ + l + +++av++++en +  +l + +++l  +a   l+++     +f+ v
  gi|386000746|ref|YP_005919045.1|  39 ISDYLDALAASGARGLRvAKEAGAAAVALNDVSPRAVALIRENARLNGLVG-CEVLSSNANVLLHQR-----RFEAV 109
                                       56789**********983445699999999******************998.888777777777655.....68888 PP

                                       EE-- CS
                     Cons_hypoth95 118 flDP 121
                                        lDP
  gi|386000746|ref|YP_005919045.1| 110 DLDP 113
                                       8887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001       0.3       3      59 ..      44     101 ..      43     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp 59 
                                       d+ + +G   l++ak+ g+a v   D+s+++++ +re+a+ +gl  +e++  +a+ l 
  gi|386000746|ref|YP_005919045.1|  44 DALAASGARGLRVAKEAGAAAVALNDVSPRAVALIRENARLNGLvGCEVLSSNANVLL 101
                                       6666788888999999999********************9999999999988887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 3051.62
//
Query:       gi|386000747|ref|YP_005919046.1|  [L=65]
Description: hypothetical protein Mhar_0030 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.001   18.8   0.9       0.33   10.8   0.1    2.2  2  Cys_rich_KTR    Cysteine-rich KTR
     0.0026   17.4   6.8       0.02   14.6   1.5    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.003   17.5   2.5      0.003   17.5   2.5    1.7  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0069   16.1   3.5       0.36   10.6   0.2    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0073   15.9   1.7       0.07   12.8   0.4    2.1  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
     0.0086   14.7   1.1     0.0098   14.5   1.1    1.0  1  Terminase_GpA   Phage terminase large subunit (GpA)
  ------ inclusion threshold ------
       0.02   14.9   2.5      0.041   13.9   2.5    1.5  1  DZR             Double zinc ribbon
      0.022   14.7   2.5       0.19   11.7   0.3    2.2  2  Nudix_N_2       Nudix N-terminal
      0.024   14.2   2.1        1.3    8.6   0.0    2.4  2  RecR            RecR protein
      0.036   14.0   4.4        0.2   11.6   4.5    1.9  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.036   14.2   0.4        5.3    7.3   0.1    2.3  2  zf-RING_7       C4-type zinc ribbon domain
       0.05   13.5   3.1        2.4    8.1   0.6    2.4  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.051   13.0   7.6        1.2    8.6   2.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.067   13.5   0.7       0.09   13.1   0.7    1.2  1  DUF3268         zinc-finger-containing domain
      0.078   13.0   0.5      0.091   12.8   0.5    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.082   12.6   6.4       0.12   12.1   1.9    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.15   12.8   4.4        4.5    8.1   0.6    2.1  2  zf-3CxxC_2      Zinc-binding domain
       0.17   12.6   3.4        1.5    9.6   0.4    2.0  2  TniQ            TniQ
       0.24   10.8   7.8          4    6.9   7.8    2.2  1  zf-TFIIB        Transcription factor zinc-finger
       0.32   10.6   3.7         10    5.8   1.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.94    9.7   7.2        4.2    7.6   1.9    2.3  2  Zn-ribbon_8     Zinc ribbon domain
        1.4    8.9   7.0        9.8    6.2   7.0    2.1  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        1.5    8.8   7.4         10    6.1   7.4    2.0  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        1.7    8.7   6.2         12    6.0   6.2    2.1  1  Ogr_Delta       Ogr/Delta-like zinc finger
          5    7.7   6.7        1.9    9.1   0.3    2.3  2  zf-H2C2_2       Zinc-finger double domain
        5.1    7.3   7.3        5.4    7.3   1.5    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        5.4    6.7   9.9          3    7.5   0.3    2.2  2  zf_C2H2_10      C2H2 type zinc-finger


Domain annotation for each model (and alignments):
>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00049      0.33      20      37 ..       5      23 ..       2      30 .. 0.77
   2 !    7.3   0.1    0.0062       4.1      28      34 ..      46      52 ..      37      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                      Cys_rich_KTR 20 dTvLk.nfpLfCPKCkqet 37
                                      d vL+ +f  fCPKC  e+
  gi|386000747|ref|YP_005919046.1|  5 DVVLEaQFVPFCPKCGTEC 23
                                      6667536888*****8875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0062
                      Cys_rich_KTR 28 LfCPKCk 34
                                       +CPKC 
  gi|386000747|ref|YP_005919046.1| 46 YYCPKCD 52
                                      59****5 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.5     3e-05      0.02      15      22 ..      15      22 ..      11      27 .. 0.70
   2 ?    5.7   0.3      0.02        13       1       5 [.      47      51 ..      43      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                     zinc_ribbon_2 15 FCpyCGtp 22
                                      FCp+CGt+
  gi|386000747|ref|YP_005919046.1| 15 FCPKCGTE 22
                                      66666664 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                     zinc_ribbon_2  1 fCpnC 5 
                                      +Cp+C
  gi|386000747|ref|YP_005919046.1| 47 YCPKC 51
                                      56666 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 !   17.5   2.5   4.6e-06     0.003       2      21 ..      16      49 ..      15      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-06
                    DNA_ligase_ZBD  2 CPvCGsavv.Ree.............geaiyRCt 21
                                      CP CG++ + Re               eaiy+C+
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEaRELrraldsenwkkivVEAIYYCP 49
                                      *********666688887765555555******8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00053      0.36      11      29 ..       4      21 ..       3      25 .. 0.86
   2 ?    6.4   0.3     0.011       7.4      20      28 ..      44      52 ..      40      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                     A2L_zn_ribbon 11 gngilnseqgylvCieCga 29
                                      ++++l  +q+  +C++Cg+
  gi|386000747|ref|YP_005919046.1|  4 NDVVL-EAQFVPFCPKCGT 21
                                      57788.999999******7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                     A2L_zn_ribbon 20 gylvCieCg 28
                                      ++++C++C 
  gi|386000747|ref|YP_005919046.1| 44 AIYYCPKCD 52
                                      68******6 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.4    0.0001      0.07      13      23 ..      16      26 ..      13      29 .. 0.86
   2 ?    2.6   0.0      0.15     1e+02      12      16 ..      47      51 ..      37      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                           zf-tcix 13 CpkCGtyNGtR 23
                                      CpkCGt++  R
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEAR 26
                                      *******9776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                           zf-tcix 12 kCpkC 16
                                       CpkC
  gi|386000747|ref|YP_005919046.1| 47 YCPKC 51
                                      6**** PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.1   1.5e-05    0.0098     196     239 ..      11      57 ..       5      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                     Terminase_GpA 196 ryyvpCphCgelqels.fer....lkwpegeaeekaryvCphcgsliee 239
                                       +++  Cp+Cg + e++  +r     +w++     +a y Cp+c+  ++e
  gi|386000747|ref|YP_005919046.1|  11 QFVPFCPKCGTECEAReLRRaldsENWKK--IVVEAIYYCPKCDNYWSE 57 
                                       68888*********775554211133444..6899**********9998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.5   6.2e-05     0.041      14      36 ..      15      53 ..       6      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                               DZR 14 fCseCgtklkavaa.................edrCpsCge 36
                                      fC++Cgt+ +a  +                  + Cp+C+ 
  gi|386000747|ref|YP_005919046.1| 15 FCPKCGTECEAR-ElrraldsenwkkivveaIYYCPKCDN 53
                                      9*******8743.35889999********9999*****86 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00028      0.19       2      13 ..      15      26 ..      14      35 .. 0.88
   2 ?    3.3   0.1      0.12        77       2       6 ..      47      51 ..      46      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                                      B-TTT--B-EEE CS
                         Nudix_N_2  2 FCsqCGtpvelr 13
                                      FC++CGt+ e r
  gi|386000747|ref|YP_005919046.1| 15 FCPKCGTECEAR 26
                                      9******98865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                                      B-TTT CS
                         Nudix_N_2  2 FCsqC 6 
                                      +C++C
  gi|386000747|ref|YP_005919046.1| 47 YCPKC 51
                                      77777 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.8     0.037        24      16      27 ..      13      24 ..      10      28 .. 0.80
   2 ?    8.6   0.0     0.002       1.3      13      25 ..      42      54 ..      39      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                                      -EE-TTT--EES CS
                              RecR 16 vrhCsrCgnlte 27
                                      v +C++Cg+ +e
  gi|386000747|ref|YP_005919046.1| 13 VPFCPKCGTECE 24
                                      679*****8665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                                      HHH-EE-TTT--E CS
                              RecR 13 kekvrhCsrCgnl 25
                                       e + +C++C n+
  gi|386000747|ref|YP_005919046.1| 42 VEAIYYCPKCDNY 54
                                      68899*******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 ?   11.6   4.5   0.00031       0.2      19      43 ..      14      51 ..       5      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt............rglfqCkeC 43
                                      + CP+Cg + +a+++++               + C +C
  gi|386000747|ref|YP_005919046.1| 14 PFCPKCGTEcEARELRRaldsenwkkivvEAIYYCPKC 51
                                      44***************999999999999999999999 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.008       5.3      23      30 ..      13      20 ..       1      21 [. 0.73
   2 ?    5.5   0.0     0.029        19      16      29 ..      27      51 ..      24      52 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.008
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                      v++Cp CG
  gi|386000747|ref|YP_005919046.1| 13 VPFCPKCG 20
                                      8******9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                                      HHCCS.TB..........-EE-TTT CS
                         zf-RING_7 16 elrag.de..........vvtCpeC 29
                                      elr++ d           + +Cp C
  gi|386000747|ref|YP_005919046.1| 27 ELRRAlDSenwkkivveaIYYCPKC 51
                                      5655552234555665669*****9 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.6    0.0037       2.4       3       8 ..      15      20 ..      13      21 .. 0.89
   2 ?    5.6   0.1     0.022        15       3       9 ..      47      53 ..      45      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                                      BESTTT CS
                    RNA_POL_M_15KD  3 FCpkCg 8 
                                      FCpkCg
  gi|386000747|ref|YP_005919046.1| 15 FCPKCG 20
                                      *****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                                      BESTTTS CS
                    RNA_POL_M_15KD  3 FCpkCgN 9 
                                       CpkC N
  gi|386000747|ref|YP_005919046.1| 47 YCPKCDN 53
                                      6****99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.4    0.0019       1.2      17      24 ..      14      21 ..      13      23 .. 0.79
   2 ?    7.3   0.2    0.0047       3.1       3      10 ..      46      53 ..      45      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
                       zf-ribbon_3 17 nvCpyCGt 24
                                      ++Cp+CGt
  gi|386000747|ref|YP_005919046.1| 14 PFCPKCGT 21
                                      68999997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0047
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++CP+C++
  gi|386000747|ref|YP_005919046.1| 46 YYCPKCDN 53
                                      69****87 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   0.00014      0.09       4      39 ..      15      54 ..      12      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                           DUF3268  4 rCpyCGekvilvsaseiYkers....kgkllylCpkCday 39
                                       Cp CG++   ++ +   ++++      + +y CpkCd y
  gi|386000747|ref|YP_005919046.1| 15 FCPKCGTECEARELRRALDSENwkkiVVEAIYYCPKCDNY 54
                                      69*****99998876666444433346678999*****99 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 ?   12.8   0.5   0.00014     0.091      68      95 ..      11      54 ..       2      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                      --EEEETTTS-EEECHH.H.HH..............S-TTTSSS CS
                              HypA 68 pvkvrCreCgkefelee.k.al..............rCpkCgsa 95
                                      + +  C +Cg+e e +e + al               CpkC++ 
  gi|386000747|ref|YP_005919046.1| 11 QFVPFCPKCGTECEARElRrALdsenwkkivveaiyYCPKCDNY 54
                                      45567*********886533338899***************975 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.9   0.00017      0.12       4      15 ..      14      25 ..      14      27 .. 0.84
   2 ?    2.7   0.2      0.15        98      24      27 ..      48      51 ..      46      54 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                     zf-NADH-PPase  4 rFCgrCGaptep 15
                                      +FC++CG+++e 
  gi|386000747|ref|YP_005919046.1| 14 PFCPKCGTECEA 25
                                      5*******9886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                     zf-NADH-PPase 24 CpaC 27
                                      Cp C
  gi|386000747|ref|YP_005919046.1| 48 CPKC 51
                                      5555 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.016        11      30      49 ..      16      35 ..      10      44 .. 0.79
   2 ?    8.1   0.6    0.0068       4.5       8      20 ..      46      58 ..      44      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                        zf-3CxxC_2 30 CkkCkekvepyklrekdkkk 49
                                      C kC++++e  +lr    ++
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEARELRRALDSE 35
                                      9************9854444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0068
                        zf-3CxxC_2  8 fkCekCgkeWsSa 20
                                      + C+kC ++Ws +
  gi|386000747|ref|YP_005919046.1| 46 YYCPKCDNYWSEG 58
                                      88********976 PP

>> TniQ  TniQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4    0.0022       1.5      98     120 ..       8      30 ..       2      35 .. 0.82
   2 ?    5.0   0.3     0.056        37      91     109 ..      33      51 ..      26      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
                              TniQ  98 lrrsgrryCplClaedgepywrl 120
                                       l  +++ +Cp+C +e+++++ r+
  gi|386000747|ref|YP_005919046.1|   8 LEAQFVPFCPKCGTECEARELRR 30 
                                       678899**********9988665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.056
                              TniQ  91 eaisrrglrrsgrryCplC 109
                                          +++++  +   yCp+C
  gi|386000747|ref|YP_005919046.1|  33 DSENWKKIVVEAIYYCPKC 51 
                                       556788899999******* PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.8     0.006         4       2      26 ..      16      52 ..      15      55 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
                          zf-TFIIB  2 CPkCqdele..eser..........ggveidyCpqCr 26
                                      CPkC++e e  e++r              i+yCp+C 
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEarELRRaldsenwkkiVVEAIYYCPKCD 52
                                      ******9885544447777779544233689*****5 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.1     0.016        10       4      14 ..      15      25 ..      14      29 .. 0.79
   2 ?    5.5   0.1      0.02        13       3      11 ..      46      54 ..      44      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C++Cg+e + 
  gi|386000747|ref|YP_005919046.1| 15 FCPKCGTECEA 25
                                      7*****98665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                            zf_UBZ  3 ylCerCgke 11
                                      y C++C+ +
  gi|386000747|ref|YP_005919046.1| 46 YYCPKCDNY 54
                                      89****975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.9    0.0064       4.2      26      37 ..      12      24 ..       3      32 .. 0.74
   2 ?    5.0   7.3     0.039        26       8      33 ..      16      52 ..      11      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0064
                       Zn-ribbon_8 26 lta.CPeCgsevr 37
                                       ++ CP+Cg e++
  gi|386000747|ref|YP_005919046.1| 12 FVPfCPKCGTECE 24
                                      5566999998544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.039
                       Zn-ribbon_8  8 CeeCghefe..vlqsisdap........lta.CPeCg 33
                                      C +Cg+e e  +l+++ d++         +  CP+C 
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEarELRRALDSEnwkkivveAIYyCPKCD 52
                                      9999999998845544444456666666677799995 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.0     0.015       9.8       3      30 .]      14      56 ..       8      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                    PhnA_Zn_Ribbon  3 pkCplCaSeytY...............edgallvCpeCahEwe 30
                                      p Cp+C+ e +                +  a++ Cp+C + w+
  gi|386000747|ref|YP_005919046.1| 14 PFCPKCGTECEArelrraldsenwkkiVVEAIYYCPKCDNYWS 56
                                      77*******998888***********************98775 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.4     0.015        10       7      30 ..      16      51 ..      10      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                    Zn_ribbon_SprT  7 CtgCgreythh..lsi.rrhn.........YrCrrC 30
                                      C+ Cg+e +++  ++  + +n         Y+C++C
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEARelRRAlDSENwkkivveaiYYCPKC 51
                                      999999988764344446666999***********9 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.2     0.018        12       2      18 ..      16      32 ..      15      54 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                         Ogr_Delta  2 CPhCgapaaartsrnls 18
                                      CP+Cg++  ar  r+ +
  gi|386000747|ref|YP_005919046.1| 16 CPKCGTECEARELRRAL 32
                                      ***********987653 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.6      0.77   5.1e+02      17      21 ..      16      20 ..      12      24 .. 0.80
   2 ?    9.1   0.3    0.0029       1.9      12      21 ..      43      52 ..      38      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.77
                         zf-H2C2_2 17 CplCd 21
                                      Cp+C+
  gi|386000747|ref|YP_005919046.1| 16 CPKCG 20
                                      88885 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0029
                         zf-H2C2_2 12 ekpyeCplCd 21
                                      e +y Cp+Cd
  gi|386000747|ref|YP_005919046.1| 43 EAIYYCPKCD 52
                                      668******9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.5    0.0081       5.4      25      32 ..      15      22 ..       7      41 .. 0.85
   2 ?    3.9   0.4      0.09        60      24      31 ..      46      53 ..      37      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0081
                      NOB1_Zn_bind 25 FCpkCGnk 32
                                      FCpkCG +
  gi|386000747|ref|YP_005919046.1| 15 FCPKCGTE 22
                                      ******85 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.09
                      NOB1_Zn_bind 24 kFCpkCGn 31
                                       +CpkC n
  gi|386000747|ref|YP_005919046.1| 46 YYCPKCDN 53
                                      69****98 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   3.9      0.13        83       5       9 ..      16      20 ..      14      23 .. 0.86
   2 ?    7.5   0.3    0.0045         3       3       9 ..      46      52 ..      45      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                        zf_C2H2_10  5 CPKCq 9 
                                      CPKC+
  gi|386000747|ref|YP_005919046.1| 16 CPKCG 20
                                      ****8 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                        zf_C2H2_10  3 fsCPKCq 9 
                                      + CPKC 
  gi|386000747|ref|YP_005919046.1| 46 YYCPKCD 52
                                      67****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 428.24
//
Query:       gi|386000748|ref|YP_005919047.1|  [L=293]
Description: hypothetical protein Mhar_0031 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-77  261.2  14.6    1.4e-77  260.9  14.6    1.1  1  SPP             Signal-peptide peptidase, presenilin aspartyl
    1.5e-07   31.2   4.2    4.6e-07   29.7   4.2    1.7  1  Peptidase_A22B  Signal peptide peptidase
  ------ inclusion threshold ------
        9.4    4.4  12.9         13    4.0  12.9    1.2  1  DUF2070         Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.9  14.6   2.4e-81   1.4e-77       2     282 ..      18     289 ..      17     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: 260.9 bits;  conditional E-value: 2.4e-81
                               SPP   2 alfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvfl 78 
                                       al+v vq+l+l+l  pl ++e++ +edP+ + n   yi l+l ft+f+l++++ +k +i++ v++++v++ ++yv  
  gi|386000748|ref|YP_005919047.1|  18 ALLVAVQLLSLALMPPLSETEVRVFEDPESAANPFSYIFLVLGFTVFILMAMRLKKGWIVTWVVLLAVAMGVYYVIS 94 
                                       899***********************************************************************965 PP

                               SPP  79 vllsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvy 155
                                       +  +          l +l+v+ a++ lly+ypeWyvid +G++++ Gv +lfG+s++ +pa++ll++la ydaisvy
  gi|386000748|ref|YP_005919047.1|  95 AFAP---------PLSALLVSAAVLALLYTYPEWYVIDFVGLLVSAGVGTLFGLSMTPFPAIILLVVLAAYDAISVY 162
                                       4444.........4567888999999*************************************************** PP

                               SPP 156 ktkhmialaegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfleshil..a 230
                                       kt+hm++laegv++++ P+l+v+P++ +ysf+ e++  +e    r ++f+GlGda++P++lv+sa+  l+ + +   
  gi|386000748|ref|YP_005919047.1| 163 KTRHMVTLAEGVMEMRAPLLFVIPRRRGYSFRREGLGSGEA---RGAYFLGLGDAIIPTVLVISANWSLDLPAVevL 236
                                       ***********************************998877...666***********************9987543 PP

                               SPP 231 gl..elavllalaGtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaag 282
                                       g+  +l++l+a+aGt  G+l+ls    r+rp+aGlP+ln+Gai Gfl++vla+g
  gi|386000748|ref|YP_005919047.1| 237 GMaaNLPALGAMAGTAFGFLLLST-TPRDRPQAGLPFLNGGAILGFLLAVLASG 289
                                       44337999***************9.9*************************986 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   4.2   7.7e-11   4.6e-07      84     201 ..      93     222 ..      13     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.7e-11
                                       XXXXXXXXXXXXX------S--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B  84 ielkaaeivalllsiviavlwllkrhwilndilglalailviellrlpslkv.galLLvglflYDifwVFgtdvmve 159
                                       i+  a  + all+s +++ l +  ++w + d +gl ++  v  l  l      + +LLv+l  YD   V+ t  mv+
  gi|386000748|ref|YP_005919047.1|  93 ISAFAPPLSALLVSAAVLALLYTYPEWYVIDFVGLLVSAGVGTLFGLSMTPFpAIILLVVLAAYDAISVYKTRHMVT 169
                                       344445677889999999999999**********9887666555555544431457888999*************** PP

                                       XXX...XXXXXXXXXXXX........XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B 160 vAk...eldiPillklPq........lsneieeaskfsiLGlGDivlPGllia 201
                                       +A+   e+ +P+l+++P+            + ea+    LGlGD ++P +l+ 
  gi|386000748|ref|YP_005919047.1| 170 LAEgvmEMRAPLLFVIPRrrgysfrrEGLGSGEARGAYFLGLGDAIIPTVLVI 222
                                       ***99999**********88866422223456778889***********9985 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  12.9    0.0021        13      80     180 ..      51     167 ..       7     190 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0021
                           DUF2070  80 livviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly........ 148
                                        ++ i+++l+ ++++l++  +   +++++++ +a+ + v++++s   ++ ++l+    ++++++ll+ y        
  gi|386000748|ref|YP_005919047.1|  51 PFSYIFLVLGFTVFILMAMRLKKGWIVTWVVLLAVAMGVYYVISAFAPPLSALL---VSAAVLALLYTYpewyvidf 124
                                       344444444444444444456778888899999999999999998888855544...44555555555556678888 PP

                           DUF2070 149 ..............fspesfllllllslifalavylfivvvdrplk 180
                                                     +   s+ ++ +++l+++la+y  i v + ++ 
  gi|386000748|ref|YP_005919047.1| 125 vgllvsagvgtlfgL---SMTPFPAIILLVVLAAYDAISVYKTRHM 167
                                       888888777775432...3444444445555555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1710.70
//
Query:       gi|386000749|ref|YP_005919048.1|  [L=170]
Description: Adenylyl cyclase CyaB, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-30  105.4   0.1    3.6e-30  105.2   0.1    1.0  1  CYTH      CYTH domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.1     2e-34   3.6e-30       1     179 []       1     163 [.       1     163 [. 0.92

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 2e-34
                                       EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST. CS
                              CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge. 76 
                                       miEvEvK++ +++  e+    +a+l+++  + +   d Y+ +  r +a+tdeaLRiR++ + g++lt+Kgp++d e 
  gi|386000749|ref|YP_005919048.1|   1 MIEVEVKARAPPGIEEK----IAGLGGARTGAEVHLDLYFGSRSRNFAETDEALRIRIK-EAGAFLTYKGPKLDPEt 72 
                                       89********9777676....8999********************************88.99999*********999 PP

                                       ..EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHH CS
                              CYTH  77 ..reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedee 151
                                         r+ev+++v+         d+    ++l++lg+  +a+vkk+R+ky l+ ++++lD+ve+l g ++E+El +++  
  gi|386000749|ref|YP_005919048.1|  73 ksRREVTVQVD---------DPHNLESILESLGFFRAAVVKKRRTKYSLGRATLCLDEVEGL-GSFLEVELSGGEVW 139
                                       999*******9.........******************************************.*********99987 PP

                                       HHHHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 152 evkeaaekllallrelglssaskirrsy 179
                                       e ++  + +l++l +lg+s+   ir+sy
  gi|386000749|ref|YP_005919048.1| 140 EEEK--RAALEVLARLGISE--SIRKSY 163
                                       7333..44578999999999..577777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 1134.62
//
Query:       gi|386000750|ref|YP_005919049.1|  [L=862]
Description: valyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.6e-127  424.1   0.0   2.2e-125  419.3   0.0    2.2  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    1.7e-33  115.8   0.0    3.3e-33  114.8   0.0    1.5  1  Anticodon_1     Anticodon-binding domain of tRNA
    1.3e-22   80.1   0.1    1.3e-13   50.5   0.0    2.6  3  tRNA-synt_1g    tRNA synthetases class I (M)
    1.5e-06   27.8   0.0       0.01   15.2   0.0    2.3  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    0.00026   20.6   0.1    0.00068   19.2   0.1    1.6  1  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
     0.0011   18.9   2.1      0.054   13.5   0.1    3.1  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.13   12.1   0.0        1.5    8.7   0.0    2.4  2  DUF3670         SNF2 Helicase protein
       0.51   10.5   5.3         24    5.1   3.3    3.0  2  Zn-ribbon_8     Zinc ribbon domain
       0.75    9.8   4.8         32    4.5   0.0    3.6  3  Nudix_N_2       Nudix N-terminal
       0.76   10.5   3.5         42    4.9   0.0    3.5  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        1.8    8.3   5.1          3    7.6   0.0    2.8  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        4.1    7.1   4.6         34    4.1   0.0    3.4  3  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.3   0.0  1.5e-128  2.2e-125       3     600 ..      18     561 ..      16     563 .. 0.93

  Alignments for each domain:
  == domain 1  score: 419.3 bits;  conditional E-value: 1.5e-128
                       tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                          W+e+ ++      +  ++++i+  +PPy tG+ HiG+al+    d+v rykrm+G++v +  GwD++Gl++e k
  gi|386000750|ref|YP_005919049.1|  18 VGAWDESIYYFDW---NSGAPQYIIDTPPPYPTGNFHIGNALNWCYIDFVARYKRMRGYNVMFPQGWDCHGLPTEVK 91 
                                       5679998888776...788********************************************************** PP

                       tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgli 156
                                       ve+  g++++    ++ reefr  + e  a+ ++++r ++krlG s D+++ey+T+ +e+   +++ fv++++kg+i
  gi|386000750|ref|YP_005919049.1|  92 VEEIHGITKN----EVPREEFRRLCEELTAKNIAKMRVTMKRLGFSNDWSNEYVTMTPEYYSKTQRSFVQMFEKGMI 164
                                       ***9998886....9************************************************************** PP

                       tRNA-synt_1 157 yrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkekl 233
                                       yr  ++vnw++++ ta++ +Evey   + +l +++f    +    l+iaT +Pe l + +avav+pe          
  gi|386000750|ref|YP_005919049.1| 165 YREDHPVNWCPRCGTAIAFAEVEYDSRTTTLNYLRFGSPLG---DLEIATSRPELLAACVAVAVHPE---------- 228
                                       *************************9999999999975444...679********************.......... PP

                       tRNA-synt_1 234 ilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkyn 310
                                                            de+ ++ +g ev  p+ + ++p+iad+ vd  +GtGvV i    d++D +   ++ 
  gi|386000750|ref|YP_005919049.1| 229 ---------------------DEKKRKYIGTEVSVPVFDYNVPVIADEVVDPAFGTGVVMICTFGDKQDVRWWVEHA 284
                                       .....................8999999************************************************* PP

                       tRNA-synt_1 311 levinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkel 387
                                       l++ +++d  g++te a+ f+g+k+ +++++++ee++ +g++ k+e+ + +v++c+r k+pi+  +  qWfvr+++ 
  gi|386000750|ref|YP_005919049.1| 285 LPLRQAIDRTGRMTEIAGRFSGMKISECKDAIIEEMRSEGTIYKEEPLDQNVGLCWRCKTPIEILSERQWFVRINP- 360
                                       **************************************************************************97. PP

                       tRNA-synt_1 388 adaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekk 463
                                        ++++++  ++++vp+  e r  +w   +  dWciSRqr+  ++ip+++ +  +e  v    +e+          + 
  gi|386000750|ref|YP_005919049.1| 361 -EEIIETSGEIKWVPDHMEIRLLNWTGTMDwDWCISRQRIFATPIPVWYCRGCGEPLVA--EEEWLP-------LDP 427
                                       .99***********************99866***********************99982..222222.......222 PP

                       tRNA-synt_1 464 alekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillsla 540
                                       +l+   +   k++ +e+  ++dvlD+W +S+ +   + g+ +      k ++pa++  +G Diir W    il + a
  gi|386000750|ref|YP_005919049.1| 428 NLTGPPVPCPKCGSEEFDPETDVLDTWMDSSISVLNVTGWLSD----HKPRYPAQLRPQGHDIIRTWAFYTILRARA 500
                                       3333334444899**************************9766....6778************************** PP

                       tRNA-synt_1 541 ltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdin 600
                                       l+g +P+ ++lv+g+v+ e+G+KmSKsl N i+p++v+ kygada R + +   + g+d+ 
  gi|386000750|ref|YP_005919049.1| 501 LVGTRPWDSILVNGMVLGEDGHKMSKSLNNFIAPEEVVAKYGADAFRQWAAvGGSPGSDVM 561
                                       ************************************************9987777777765 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   0.0   2.2e-36   3.3e-33       1     148 [.     600     738 ..     600     744 .. 0.90

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 2.2e-36
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+l el++ ++ vt +++++ f++a++a+ +f w++++d+y+elvk rly+ ++ +kraaq++++e+le+l+ ll
  gi|386000750|ref|YP_005919049.1| 600 DRWLLFELSQMIEAVTGSMDRFAFDEAFRAIRSFAWEEFADNYIELVKARLYGPDGPEKRAAQATIYEALEALTSLL 676
                                       9****************************************************99977777**************** PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpssel 148
                                       aPf+Pfi+Ee+  +        es++ a+wpe ++ l ++     e +l+k++  a+r+++s+ +++ +++l
  gi|386000750|ref|YP_005919049.1| 677 APFTPFIAEEIRMS-----LAGESVHTASWPEPPKVLpQP-----EGSLIKDVAAAVRRYKSDRGMALNAPL 738
                                       ************43.....45689*******866555443.....5689*****************999884 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   8.8e-17   1.3e-13       2     131 ..      38     182 ..      37     191 .. 0.78
   2 ?   -4.2   0.1       3.5   5.3e+03     215     238 ..     382     405 ..     354     410 .. 0.75
   3 !   26.7   0.0   1.4e-09   2.1e-06     306     372 ..     498     568 ..     451     571 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 8.8e-17
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HHH............ CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpee............ 65 
                                       ++ t+ pY++g+ H+G++l+    D +aRykr+rg++v+f  g D hG p+e+k e+ +g+t +e            
  gi|386000750|ref|YP_005919049.1|  38 IIDTPPPYPTGNFHIGNALNWCYIDFVARYKRMRGYNVMFPQGWDCHGLPTEVKVEEiHGITKNEvpreefrrlcee 114
                                       789999************************************************98656666433111122221111 PP

                                       HHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE- CS
                      tRNA-synt_1g  66 lvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflp 131
                                       l++k+ ++++ ++k+l+ s+d  + + t + e ++ +q+ f ++ ekg+iy+++  + +cp++++ ++
  gi|386000750|ref|YP_005919049.1| 115 LTAKNIAKMRVTMKRLGFSNDwsNEYVTMTPEYYSKTQRSFVQMFEKGMIYREDHPVNWCPRCGTAIA 182
                                       455556667778888888888333345778888888999999999*****************998765 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3.5
                                       .HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 215 kewlkegLkdlaisrdldwGipvP 238
                                       ++w  +   d++isr+  ++ p+P
  gi|386000750|ref|YP_005919049.1| 382 LNWTGTMDWDWCISRQRIFATPIP 405
                                       555555556899999999998888 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 1.4e-09
                                       H...TT----S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHH CS
                      tRNA-synt_1g 306 g...aelklpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfv 372
                                       +    + +  +++ +++++   +g+K+SkS ++++ ++e++ ++ ad++R + a+ ++  +D+ f+w+d+v
  gi|386000750|ref|YP_005919049.1| 498 AralVGTRPWDSILVNGMVLgEDGHKMSKSLNNFIAPEEVVAKYGADAFRQWAAVGGSPGSDVMFRWKDVV 568
                                       3335566777889999987615689*******************************************997 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00024      0.36      22      52 ..      49      79 ..      45     176 .. 0.77
   2 !   15.2   0.0   6.7e-06      0.01     231     278 ..     500     548 ..     490     553 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                                      --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                      tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                      + h+G+a +   +D ++r+ +++gY+v+f q
  gi|386000750|ref|YP_005919049.1| 49 NFHIGNALNWCYIDFVARYKRMRGYNVMFPQ 79
                                      57**************************977 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6.7e-06
                                       HHSSS--EEEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHH CS
                      tRNA-synt_1e 231 aafdkqlvkyflhnghlk.iegekmsksLknfitikdvlkkfdprqlRl 278
                                       a+++++     l ng++   +g+kmsksL+nfi  ++v+ k+ + ++R 
  gi|386000750|ref|YP_005919049.1| 500 ALVGTRPWDSILVNGMVLgEDGHKMSKSLNNFIAPEEVVAKYGADAFRQ 548
                                       5556444455566777641679********************9999885 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.6e-07   0.00068      78     147 ..     229     298 ..     222     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-07
                     tRNA-synt_1_2  78 kekeGvftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeek 147
                                        ek+    g+++  P+ + ++p+   + v   +gtg+vm +   d++D +++ ++ lp++q i  +++ +
  gi|386000750|ref|YP_005919049.1| 229 DEKKRKYIGTEVSVPVFDYNVPVIADEVVDPAFGTGVVMICTFGDKQDVRWWVEHALPLRQAIDRTGRMT 298
                                       5666667899999**********9999999*********************************9876544 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.12   1.9e+02      14      22 ..     173     181 ..     165     192 .. 0.75
   2 ?    0.6   0.1       0.4   5.9e+02      28      38 ..     336     346 ..     310     352 .. 0.61
   3 !   13.5   0.1   3.6e-05     0.054      14      41 ..     408     447 ..     401     450 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.12
                               DZR  14 fCseCgtkl 22 
                                        C++Cgt++
  gi|386000750|ref|YP_005919049.1| 173 WCPRCGTAI 181
                                       466666655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.4
                               DZR  28 edrCpsCgekv 38 
                                          C++C++++
  gi|386000750|ref|YP_005919049.1| 336 VGLCWRCKTPI 346
                                       55666666654 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.6e-05
                               DZR  14 fCseCgtklkavaa...........edrCpsCgek.vdpe 41 
                                       +C  Cg++l a+++           +  Cp+Cg++  dpe
  gi|386000750|ref|YP_005919049.1| 408 YCRGCGEPLVAEEEwlpldpnltgpPVPCPKCGSEeFDPE 447
                                       9********98888*******************9867766 PP

>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.48   7.2e+02      25      41 ..      69      86 ..      62     124 .. 0.72
   2 ?    8.7   0.0   0.00097       1.5      81     122 ..     802     843 ..     794     854 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.48
                           DUF3670 25 eaaGvgVllPrwl.kkra 41
                                      +  G++V+ P+++  +  
  gi|386000750|ref|YP_005919049.1| 69 RMRGYNVMFPQGWdCHGL 86
                                      567999999999943333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00097
                           DUF3670  81 eLseeEldrLaeakrpLvrlrgqWvevdpeelrraleflkrr 122
                                       e+++eE++r+aea++ Lv l g+  e+ p +++ a e l++ 
  gi|386000750|ref|YP_005919049.1| 802 EMDPEEVARMAEAGKVLVDLGGEVAELAPGAVEIASETLSAG 843
                                       7899****************************9999998874 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.039        58      23      34 ..     167     179 ..     157     182 .. 0.66
   2 ?    5.1   3.3     0.016        24       8      34 ..     409     441 ..     403     445 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                       Zn-ribbon_8  23 daplta.CPeCgs 34 
                                       ++ ++  CP+Cg 
  gi|386000750|ref|YP_005919049.1| 167 EDHPVNwCPRCGT 179
                                       4445556****97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                       Zn-ribbon_8   8 CeeCghefe......vlqsisdapltaCPeCgs 34 
                                       C+ Cg+         +l +    p+++CP+Cgs
  gi|386000750|ref|YP_005919049.1| 409 CRGCGEPLVaeeewlPLDPNLTGPPVPCPKCGS 441
                                       777776665555555555544666777*****9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.022        32       2      18 ..     173     189 ..     172     192 .. 0.72
   2 ?    4.4   0.1     0.024        36       2      11 ..     408     417 ..     407     421 .. 0.88
   3 ?    0.1   0.4      0.51   7.6e+02       3       8 ..     436     441 ..     436     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                                       B-TTT--B-EEE--TT- CS
                         Nudix_N_2   2 FCsqCGtpvelripdgD 18 
                                        C+ CGt+++ +  + D
  gi|386000750|ref|YP_005919049.1| 173 WCPRCGTAIAFAEVEYD 189
                                       79****99886655555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.024
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       +C+ CG+p+ 
  gi|386000750|ref|YP_005919049.1| 408 YCRGCGEPLV 417
                                       9*******86 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.51
                                       -TTT-- CS
                         Nudix_N_2   3 CsqCGt 8  
                                       C++CG+
  gi|386000750|ref|YP_005919049.1| 436 CPKCGS 441
                                       999997 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.028        42       3      28 ..     172     200 ..     170     202 .. 0.70
   2 ?    0.4   0.2      0.73   1.1e+03      39      47 .]     404     412 ..     387     417 .. 0.67
   3 ?    3.4   0.2     0.084   1.3e+02       2      11 ..     433     442 ..     432     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                           zf-ISL3   3 hrCPnCgsk...tvvkhgkkerrvrhlpi 28 
                                        +CP+Cg       v  ++++++  +l++
  gi|386000750|ref|YP_005919049.1| 172 NWCPRCGTAiafAEVEYDSRTTTLNYLRF 200
                                       69*****9876655777777777666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.73
                           zf-ISL3  39 krRyrCkeC 47 
                                        + ++C+ C
  gi|386000750|ref|YP_005919049.1| 404 IPVWYCRGC 412
                                       556666666 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.084
                           zf-ISL3   2 phrCPnCgsk 11 
                                       p  CP+Cgs 
  gi|386000750|ref|YP_005919049.1| 433 PVPCPKCGSE 442
                                       788*****96 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.002         3       5      17 ..     173     185 ..     172     188 .. 0.82
   2 ?   -3.1   0.1       4.4   6.6e+03       6      15 ..     409     418 ..     408     420 .. 0.68
   3 ?    2.1   0.3       0.1   1.5e+02       6      30 ..     436     442 ..     436     444 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.002
                     zf-NADH-PPase   5 FCgrCGaptepae 17 
                                       +C+rCG++ + ae
  gi|386000750|ref|YP_005919049.1| 173 WCPRCGTAIAFAE 185
                                       7******988776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.4
                     zf-NADH-PPase   6 CgrCGaptep 15 
                                       C  CG p + 
  gi|386000750|ref|YP_005919049.1| 409 CRGCGEPLVA 418
                                       5569998765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.1
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgle 30 
                                       C++CG                   e
  gi|386000750|ref|YP_005919049.1| 436 CPKCG------------------SE 442
                                       55555..................55 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.023        34       5      16 ..     174     185 ..     173     187 .. 0.85
   2 ?    0.6   0.1       0.3   4.5e+02       4      15 ..     338     349 ..     337     353 .. 0.80
   3 ?    1.5   0.2      0.15   2.3e+02       3      10 ..     434     441 ..     433     442 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.023
                            zf_UBZ   5 CerCgkeipese 16 
                                       C+rCg+ i  +e
  gi|386000750|ref|YP_005919049.1| 174 CPRCGTAIAFAE 185
                                       ******998776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.3
                            zf_UBZ   4 lCerCgkeipes 15 
                                       lC rC+++i++ 
  gi|386000750|ref|YP_005919049.1| 338 LCWRCKTPIEIL 349
                                       699******976 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.15
                            zf_UBZ   3 ylCerCgk 10 
                                       ++C++Cg+
  gi|386000750|ref|YP_005919049.1| 434 VPCPKCGS 441
                                       58****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 5430.09
//
Query:       gi|386000751|ref|YP_005919050.1|  [L=167]
Description: hypothetical protein Mhar_0034 [Methanosaeta harundinacea 6Ac]
Scores for 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-46  154.8   0.0      1e-45  154.6   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    7.5e-13   48.1   0.2    1.2e-12   47.4   0.2    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor
  ------ inclusion threshold ------
       0.17   11.6   0.0       0.37   10.5   0.0    1.6  1  DTW            DTW domain


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0   1.7e-49     1e-45       1     127 []      40     163 ..      40     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 1.7e-49
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       +vlsp+++++lspaDr+ v  +g+a++dcsWa++eev   ++   + r+LP+LvAaNpvn+gkp+kLs+vEA+aaal
  gi|386000751|ref|YP_005919050.1|  40 LVLSPFSERALSPADRSEV-GRGLAALDCSWAHAEEVF-GTV-RLKARALPFLVAANPVNFGKPFKLSTVEAFAAAL 113
                                       69*************9886.56************9998.444.3589****************************** PP

                                       HHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  78 yilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       +ilg++ +aee+l+kf+wg+ Fleln+e+l+eYa+++ds+evv++q+eyl
  gi|386000751|ref|YP_005919050.1| 114 VILGERPQAEEILAKFSWGHVFLELNQEPLAEYAAARDSREVVAIQAEYL 163
                                       ***********************************************996 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.2     2e-16   1.2e-12       1      31 [.       1      31 [.       1      36 [. 0.90

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 2e-16
                                      --EEEES---------TTHHHHHTTSEEEES CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvr 31
                                      m l i+ adqCdPK+Ctg+k++rf+++r  +
  gi|386000751|ref|YP_005919050.1|  1 MDLLIYTADQCDPKRCTGRKMVRFGLARTTK 31
                                      7799***********************7644 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.2e-05      0.37     160     188 ..     100     128 ..      46     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.2e-05
                               DTW 160 kgclSTiEaiayaLkeleeekealdnLld 188
                                          lST+Ea a aL  l+e+++a++ L +
  gi|386000751|ref|YP_005919050.1| 100 PFKLSTVEAFAAALVILGERPQAEEILAK 128
                                       5679**************88777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1281.32
//
Query:       gi|386000752|ref|YP_005919051.1|  [L=168]
Description: Heat shock protein Hsp20 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-23   82.9   2.4    1.9e-23   82.5   2.4    1.2  1  HSP20       Hsp20/alpha crystallin family
    1.3e-15   56.7   0.1    1.8e-15   56.2   0.1    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00027   21.9   0.2    0.00042   21.3   0.2    1.3  1  CS          CS domain
  ------ inclusion threshold ------
      0.023   14.9   0.1      0.037   14.2   0.1    1.4  1  DUF1380     Protein of unknown function (DUF1380)
      0.068   13.8   0.0       0.31   11.7   0.0    2.1  1  DUF4404     Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   2.4   5.3e-27   1.9e-23       1     101 [.      68     167 ..      68     168 .] 0.94

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 5.3e-27
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       d+ke+++e  v++d+pg++k +++++v ++ + +k+e++  +ee++e++++kers + ++r++tLP +v+a++ +as
  gi|386000752|ref|YP_005919051.1|  68 DVKETDDEVVVAVDLPGMDKGDVEISVAEDLLEIKAERKveKEEKGEEFYRKERSFSRYERSLTLPAGVKAEEARAS 144
                                       689************************************99999********************************* PP

                                       EETTEEEEEEEBSS--..-------- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerkiqi 101
                                       l+dGvLtv++pk e   +   +k++i
  gi|386000752|ref|YP_005919051.1| 145 LQDGVLTVHLPKVEVTTR---KKVKI 167
                                       ************999855...44444 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.1   5.1e-19   1.8e-15       1      63 []      73     154 ..      73     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 5.1e-19
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedg 57 
                                       dde+v+ +dLP++dk+++++s ++d L Ik++                    ++ R+ tLP  ++++e+ +A+++dg
  gi|386000752|ref|YP_005919051.1|  73 DDEVVVAVDLPGMDKGDVEISVAEDLLEIKAErkvekeekgeefyrkersfsRYERSLTLPAGVKAEEA-RASLQDG 148
                                       79*******************************************************************.******* PP

                        ArsA_HSP20  58 vLeIrF 63 
                                       vL++++
  gi|386000752|ref|YP_005919051.1| 149 VLTVHL 154
                                       ***985 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   1.2e-07   0.00042       6      76 .]      70     156 ..      67     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                       EEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE.................BSS-BETTTEEE CS
                                CS   6 yQtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege.................LfgpIdpeessw 63 
                                        +t+deVvv + ++++  +k dv+++  e+ l++k  +k ek+  +ge                 L + ++ ee++ 
  gi|386000752|ref|YP_005919051.1|  70 KETDDEVVVAVDLPGM--DKGDVEISVAEDLLEIKAeRKvEKEE-KGEefyrkersfsryersltLPAGVKAEEARA 143
                                       589************9..*****************977755554.4447**************************** PP

                                       EEETTEEEEEEEB CS
                                CS  64 tieskkveitLkK 76 
                                       ++++  + ++L K
  gi|386000752|ref|YP_005919051.1| 144 SLQDGVLTVHLPK 156
                                       ***9999999987 PP

>> DUF1380  Protein of unknown function (DUF1380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     1e-05     0.037      46      93 ..      35      82 ..      23     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                           DUF1380 46 qevravlarlddipeeqrlesGissaavmelieqvkenrktvtvpadl 93
                                      +e+r + +r++++ ++  +e  ++++ vm+ +++vke+  +v+v +dl
  gi|386000752|ref|YP_005919051.1| 35 PEIRKIQERMNQLIDDFAVEAPMAAGDVMKPLADVKETDDEVVVAVDL 82
                                      699******************************************998 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.7e-05      0.31      25      69 ..       9      60 ..       6      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.7e-05
                           DUF4404 25 lLeslaedieellaeedaaaeeee.......laerlneaverFeeeHPklag 69
                                      + + l++ +++ll+e +  ++e+        ++er+n++++ F++e P +ag
  gi|386000752|ref|YP_005919051.1|  9 DFKRLQNRMNRLLEEFGISDPEARympeirkIQERMNQLIDDFAVEAPMAAG 60
                                      6678888899999999888888878888999*****************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1207.46
//
Query:       gi|386000753|ref|YP_005919052.1|  [L=405]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-84  282.1   0.6    2.5e-84  281.6   0.6    1.2  1  DHBP_synthase    3,4-dihydroxy-2-butanone 4-phosphate synthas
    2.4e-74  248.4   0.0    5.9e-74  247.1   0.0    1.6  2  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.6   0.6   2.8e-88   2.5e-84       1     191 [.       7     198 ..       7     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 281.6 bits;  conditional E-value: 2.8e-88
                                       HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SSTT-- CS
                     DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveenedkhkt 77 
                                       eeaie+++aG+f++v+Dde renegdL++aAekvtpe+++fm++ha+Glicv+l+ er+ eL Lplm+++n++k++t
  gi|386000753|ref|YP_005919052.1|   7 EEAIEEVRAGRFILVLDDEGRENEGDLVMAAEKVTPEAINFMAKHARGLICVPLSGERVGELSLPLMTQNNTEKMGT 83 
                                       69*************************************************************************** PP

                                       -BB--EEESS.T-SSS-SHHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SB CS
                     DHBP_synthase  78 aftvsvdaae.gttTGIsaaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpa 153
                                       aftvsvda+  g+tTGIsa DRa+T+r+l+dp+a+ +d++ PGh fplra++ggvl+R+ghTEa+vdLar+agl pa
  gi|386000753|ref|YP_005919052.1|  84 AFTVSVDAKGrGVTTGISAFDRAETVRTLIDPAATLNDLVMPGHTFPLRAQDGGVLRRAGHTEASVDLARMAGLYPA 160
                                       ********9768***************************************************************** PP

                                       EEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                     DHBP_synthase 154 avicellnddgtmarrdeleefakkhglkiitiedlie 191
                                       avice++ +dgtmar++ele+fa++hglk++ti+ li+
  gi|386000753|ref|YP_005919052.1| 161 AVICEVMAEDGTMARLPELERFAAEHGLKMLTIDRLIK 198
                                       ************************************96 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       0.8   7.2e+03      65      88 ..       7      28 ..       5      36 .. 0.69
   2 !  247.1   0.0   6.6e-78   5.9e-74       2     163 .]     209     373 ..     208     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.8
                                      HHHHHHHHHH-.EEEEEE--TTTT CS
                   GTP_cyclohydro2 65 dealeliaeegrGvlvylrqegrg 88
                                      +ea+e ++ +gr  ++ l+ egr+
  gi|386000753|ref|YP_005919052.1|  7 EEAIEEVR-AGR-FILVLDDEGRE 28
                                      67888887.664.56666778775 PP

  == domain 2  score: 247.1 bits;  conditional E-value: 6.6e-78
                                       XEEEEEEEETTEEEEEEEE--.....EEEEEE-........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH- CS
                   GTP_cyclohydro2   2 rvaeaklptrfgefrliayedkvdgkehlalvkgdi...pvlvRvHsecltgDvlgslrcdcgeqldealeliaeeg 75 
                                       r+ae++lpt++g+fr+i+ye+ vdg+ hlalv gd+   + lvRvHsecltgDv+gs+rcdcg+ql+ a+++ia++g
  gi|386000753|ref|YP_005919052.1| 209 RIAEVSLPTDYGDFRAIGYESLVDGQCHLALVAGDPssdDALVRVHSECLTGDVFGSRRCDCGDQLHLAMRMIADSG 285
                                       66799*********************************9899*******************************99** PP

                                       .EEEEEE--TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHHC CS
                   GTP_cyclohydro2  76 rGvlvylrqegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaLe 152
                                       +Gvl+y+rqegrgigl+nkl+ayalq++g+DTvean++lg pad+rdyg++aqIL dlg+k++rLlTnnp+k+ +Le
  gi|386000753|ref|YP_005919052.1| 286 NGVLLYMRQEGRGIGLANKLRAYALQERGYDTVEANHRLGYPADLRDYGVGAQILVDLGIKRMRLLTNNPRKIVGLE 362
                                       ***************************************************************************** PP

                                       TT....SEEEE CS
                   GTP_cyclohydro2 153 gfgievvervp 163
                                       g+g+e+v+r p
  gi|386000753|ref|YP_005919052.1| 363 GYGLEIVDRAP 373
                                       *******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2910.46
//
Query:       gi|386000754|ref|YP_005919053.1|  [L=956]
Description: hypothetical protein Mhar_0037 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-24   85.9   1.9    7.2e-24   84.6   1.9    1.4  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   1.9     4e-28   7.2e-24      63     284 ..     541     758 ..     493     774 .. 0.75

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 4e-28
                                       ...HHHHHHHHHH-B..SSSSSB-SST...TSEEE..EEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESC CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxx...xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  63 e..HGthvAGiaaanapeegekngvap...gakil..svkvldtsggsmetgteliraieeaaedkvdvinmslges 132
                                       +  HGt +  i aa  p++g+ +g+a    g k+    ++++++++ +m  +t+    +++a+e++  +i++s+g++
  gi|386000754|ref|YP_005919053.1| 541 AgsHGTGIMNILAAD-PDDGGLVGIASqplGNKLMinLYNIYPPDD-NMSFSTDAFLSLKYALENGSTIISCSWGND 615
                                       144***********9.*********962223343365899996666.66666***********************54 PP

                                       ETTCHHCHHHHHHHHHHHH.CC.T-EEEEE--SS-T-HHEEE-TTCEECTTTST..TCEEEEEESTTSSB-TT--B- CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 133 tslpktgrsiealainravnkk.gvlvviSaGNngktgsslqagspvgtpstsk..nvitvgayttegkiapfSsrG 206
                                          ++  ++  + ++++  n   ++l+v+SaGN g t      +   ++p++ +  n+itvg++ ++   ap S++ 
  gi|386000754|ref|YP_005919053.1| 616 R-ANNALNVAYKKFFKNISNIApERLFVCSAGNGGVTTR---HSDYKHAPGGIEisNMITVGNVMNDRTPAPDSNQN 688
                                       4.444444544556666665555************4444...55556669999888******************888 PP

                                       TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 207 pssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqd 283
                                        +    + + ++apG++  + w+r+++ + +    ++  GTSmA+P++++aaA+++s +p+l++++++++l  t ++
  gi|386000754|ref|YP_005919053.1| 689 IK--DFFEVTLAAPGAQ--AVWGRNDSGDIK----NNSGGTSMAAPHVTAAAAMMRSIYPSLEAKDMKDILRDTGDI 757
                                       76..58***********..889999965543....5789********************************999755 PP

                                       E CS
                                       x RF
                      Peptidase_S8 284 l 284
                                       +
  gi|386000754|ref|YP_005919053.1| 758 T 758
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (956 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 6051.92
//
Query:       gi|386000755|ref|YP_005919054.1|  [L=960]
Description: hypothetical protein Mhar_0038 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-85  284.5 162.0    2.4e-26   92.5  33.5    4.7  5  NosD        Periplasmic copper-binding protein (NosD)
    2.2e-62  209.6 139.8    1.5e-17   63.9  35.0    5.2  5  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 !   55.4  25.0   5.6e-19   5.1e-15      17     149 ..      88     225 ..      74     252 .. 0.75
   2 !   67.1  21.8   1.5e-22   1.3e-18      30     167 ..     253     389 ..     229     389 .. 0.88
   3 !   92.5  33.5   2.7e-30   2.4e-26       4     168 ..     271     436 ..     268     443 .. 0.92
   4 !   59.3  23.2   3.6e-20   3.3e-16      58     175 ..     440     557 ..     433     558 .. 0.82
   5 !   70.3  26.5   1.6e-23   1.4e-19      40     180 ..     535     674 ..     534     695 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 5.6e-19
                              NosD  17 ngiqlensegseisnneisnsrdgilldnssnntitgntienl..ryGihlensesntiedntlssnesGialmsss 91 
                                       +gi++e+      s  +  ++ +g+   +s+nn+i++ ti n    +Gi+l++s +n +e n +s+n+ Gi++ + +
  gi|386000755|ref|YP_005919054.1|  88 DGIVVEGFVSTNYSRGRSPEEAAGV-KIYSNNNKIRNITIYNDgaGTGIVLNGSMNNSVEANNVSHNRFGILILRGQ 163
                                       5555555544444455555555555.678899999999888888888999999999999999999999999999999 PP

                              NosD  92 nntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesn....q 149
                                       +n +++N+++nn   Gi l+ds nnti++N++s n ++Gi+le+s++nt+++N  ++n    +
  gi|386000755|ref|YP_005919054.1| 164 GNYIQGNNATNNGL-GIKLQDSGNNTIEGNNASfNADYGISLERSQYNTLRKNVMNENgrsfE 225
                                       99999999999966.999999999999999999999999999999999999999888833333 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 1.5e-22
                              NosD  30 snneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnen. 105
                                       +  ++s+  + +++ ++sn+ti++ ++ +  yGi+l n+ ++ i dn+l++ ++ i l++s++nt+ +N i++ ++ 
  gi|386000755|ref|YP_005919054.1| 253 TIDSTSEDAAVVYCLSCSNITIKEQVFDETGYGIRLYNTANSMIADNVLNN-KNSIELHESEKNTVGGNHIIGHSDa 328
                                       345666667777***********************************9987.77******************99998 PP

                              NosD 106 yGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynN 167
                                        Gi l++s+nn+i++N+is+ + Gi+l +s++nti++N i +n+k G+  l++s+ nti +N
  gi|386000755|ref|YP_005919054.1| 329 DGIHLNRSRNNSIEGNNISDGSGGISLVRSEGNTIEDNIIVKNEKGGVI-LQESSYNTIKRN 389
                                       9******************************************777777.*********998 PP

  == domain 3  score: 92.5 bits;  conditional E-value: 2.7e-30
                              NosD   4 aisgdevlvsargngiqlensegseisnneisnsrdgilldnssnntitgntienl..ryGihlensesntiedntl 78 
                                       +i+ +e ++++ g+gi+l+n+ +s i +n ++ ++++i l +s++nt+ gn+i     + Gihl+ s +n ie+n +
  gi|386000755|ref|YP_005919054.1| 271 NITIKEQVFDETGYGIRLYNTANSMIADNVLN-NKNSIELHESEKNTVGGNHIIGHsdADGIHLNRSRNNSIEGNNI 346
                                       577778888889**************888776.678899************8777767******************* PP

                              NosD  79 ssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtis..nnnkGiflensssntitgNriesnqkiGi 153
                                       s+ + Gi+l +s++nt+e+N+i +ne+ G++l++ss+nti++N++s  n + G++le+s++nt+t+N+ ++n +iGi
  gi|386000755|ref|YP_005919054.1| 347 SDGSGGISLVRSEGNTIEDNIIVKNEKGGVILQESSYNTIKRNVVSldNGEGGVYLEGSHNNTVTENNASYN-DIGI 422
                                       *********************************************98667779*******************.**** PP

                              NosD 154 lllsssegntiynNy 168
                                       + lsss +n+i +N+
  gi|386000755|ref|YP_005919054.1| 423 H-LSSSLENNISEND 436
                                       *.**********997 PP

  == domain 4  score: 59.3 bits;  conditional E-value: 3.6e-20
                              NosD  58 nlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGifl 132
                                       n  +Gi++e+s++n+i+dn +s+n+ +Gi ++ s +n +e N++s n n G l + s++ntis+N +s n ++Gi+l
  gi|386000755|ref|YP_005919054.1| 440 NHVSGIFIEESNKNIIKDNNASHNDwCGIKIEGSGENRIEANNASYNGN-GLLFESSNGNTISRNIAShNVEYGIRL 515
                                       4478899999999999999999888899999999999999999999988.999999999999999998888999999 PP

                              NosD 133 ensssntitgNriesnqkiGilllsssegntiynNyFinnsen 175
                                       ++s +n i gN  ++n+  Gi  l +s++n i +N + +n +n
  gi|386000755|ref|YP_005919054.1| 516 YASYGNNIAGNDASYNNLAGIK-LVDSQENGIADNFLHGNGVN 557
                                       9999999999999999888888.88888999999988888766 PP

  == domain 5  score: 70.3 bits;  conditional E-value: 1.6e-23
                              NosD  40 gilldnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdss 114
                                       gi l +s++n i +n ++ +  +G+ l+n+ ++ + +n++++n  +Gi+l +s nn l++N +snn++ Gi l dss
  gi|386000755|ref|YP_005919054.1| 535 GIKLVDSQENGIADNFLHGNgVNGLALMNCVRSSVAGNVANNNPaCGITLINSMNNNLTDNGASNNSD-GIALCDSS 610
                                       78899**********999988***********************************************.******** PP

                              NosD 115 nntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydg 180
                                       +n i+nNt+s+n  G++l++s+ n++++N+i++n ++G+  ++sse+nt+ +N   +n+ +v +d+
  gi|386000755|ref|YP_005919054.1| 611 SNLIKNNTASYNRIGVYLYQSNLNELKDNYINKN-EVGVS-FNSSENNTVDDNFTGDNKYDVLIDN 674
                                       **********************************.*****.************9989988888776 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 !   61.1  27.8   1.2e-20   1.1e-16       2     124 ..     111     235 ..     110     245 .. 0.94
   2 !   59.7  23.6   3.2e-20   2.9e-16       3     135 ..     264     392 ..     261     397 .. 0.90
   3 !   48.7  25.4     8e-17   7.2e-13      24     142 ..     374     490 ..     373     491 .. 0.96
   4 !   63.9  35.0   1.7e-21   1.5e-17       1     154 [.     443     593 ..     443     595 .. 0.96
   5 !   29.9  19.7   4.8e-11   4.3e-07      53     138 ..     586     667 ..     584     689 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.2e-20
                                       SEEE-SS-E.EEESEEEES-.SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   2 gisingssnvtiknntisns.ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       g+ i++++n +i+n ti+n   g+Gi l+gs+n+ +e n++++ + +Gi il++++n i++n+ ++n+  gi+l+++
  gi|386000755|ref|YP_005919054.1| 111 GVKIYSNNN-KIRNITIYNDgAGTGIVLNGSMNNSVEANNVSH-NRFGILILRGQGNYIQGNNATNNG-LGIKLQDS 184
                                       899999***.*********9999********************.*********************999.******** PP

                                       S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT....--SEE---TT CS
                        Beta_helix  78 snnlienneitdnggsGiylnyssnntienNiidnna....gsGividdss 124
                                       +nn+ie+n+ + n+++Gi+l+ s+ nt+++N++++n+    ++G+ + d+s
  gi|386000755|ref|YP_005919054.1| 185 GNNTIEGNNASFNADYGISLERSQYNTLRKNVMNENGrsfeAAGLNYIDTS 235
                                       *************************************88888888888777 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 3.2e-20
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---.SEEE-TT--S CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn.gggialfgas 78 
                                       +++ ++sn+tik   +++  gyGi l+++ n  i +n+++n   + i++++s++nt+ +n+i ++  ++gi+l+ + 
  gi|386000755|ref|YP_005919054.1| 264 VYCLSCSNITIKEQVFDE-TGYGIRLYNTANSMIADNVLNN--KNSIELHESEKNTVGGNHIIGHSdADGIHLNRSR 337
                                       688899999999999999.5***********9999999999..999999999********997776789******** PP

                                       --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEE CS
                        Beta_helix  79 nnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtit 135
                                       nn ie+n+i+d +g Gi+l  s+ ntie+Nii  n++ G+ +++ss  +t++ N+++
  gi|386000755|ref|YP_005919054.1| 338 NNSIEGNNISDGSG-GISLVRSEGNTIEDNIIVKNEKGGVILQESS-YNTIKRNVVS 392
                                       ************99.9***99999************9999999999.8889999986 PP

  == domain 3  score: 48.7 bits;  conditional E-value: 8e-17
                                       -SEEE-SSS-.EEES-EEES.-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT CS
                        Beta_helix  24 yGiylrgssnvvienneian.nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylny 99 
                                        G+ l++ss ++i++n+++  n++ G+y++gs nnt+++n+ s n   gi+l+ +  n i+ n+ + n  sGi+++ 
  gi|386000755|ref|YP_005919054.1| 374 GGVILQESSYNTIKRNVVSLdNGEGGVYLEGSHNNTVTENNASYND-IGIHLSSSLENNISENDGSYNHVSGIFIEE 449
                                       599999********99999889************************.****************************** PP

                                       -S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEE CS
                        Beta_helix 100 ssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGi 142
                                       s+ n+i++N++++n  +Gi i+ s+ +++++ N+++ n+ +G+
  gi|386000755|ref|YP_005919054.1| 450 SNKNIIKDNNASHNDWCGIKIEGSG-ENRIEANNASYNG-NGL 490
                                       *************************.**********997.775 PP

  == domain 4  score: 63.9 bits;  conditional E-value: 1.7e-21
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       sgi+i+ s+   ik+n+ s++ ++Gi+++gs+ ++ie n+ ++ +g+G+  ++s++ntis+n  s+n ++gi l+++
  gi|386000755|ref|YP_005919054.1| 443 SGIFIEESNKNIIKDNNASHNDWCGIKIEGSGENRIEANNASY-NGNGLLFESSNGNTISRNIASHNVEYGIRLYAS 518
                                       69********9**************************999999.9******************************** PP

                                       S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEE CS
                        Beta_helix  78 snnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvr 154
                                        +n i +n+ + n+ +Gi l +s+ n i +N +++n+ +G+ +++   +  v +N+++nn  +Gi++++s +n+ ++
  gi|386000755|ref|YP_005919054.1| 519 YGNNIAGNDASYNNLAGIKLVDSQENGIADNFLHGNGVNGLALMNCV-RSSVAGNVANNNPACGITLINSMNNN-LT 593
                                       ***********************************************.8888*******************944.44 PP

  == domain 5  score: 29.9 bits;  conditional E-value: 4.8e-11
                                       TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EE CS
                        Beta_helix  53 gssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtv 129
                                       +s nn++++n  s+n  +gial ++s nli+nn+ + n+  G+yl++s+ n +++N+i+ n+  G+++++s+ n+tv
  gi|386000755|ref|YP_005919054.1| 586 NSMNNNLTDNGASNNS-DGIALCDSSSNLIKNNTASYNRI-GVYLYQSNLNELKDNYINKNE-VGVSFNSSE-NNTV 658
                                       6789999999999999.********************976.9*9999999********9999.******999.9999 PP

                                       ES-EEES-S CS
                        Beta_helix 130 tnNtitnnk 138
                                        +N   +nk
  gi|386000755|ref|YP_005919054.1| 659 DDNFTGDNK 667
                                       999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (960 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 6368.07
//
Query:       gi|386000756|ref|YP_005919055.1|  [L=104]
Description: hypothetical protein Mhar_0039 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 823.51
//
Query:       gi|386000757|ref|YP_005919056.1|  [L=162]
Description: hypothetical protein Mhar_0040 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1343.73
//
Query:       gi|386000758|ref|YP_005919057.1|  [L=97]
Description: hypothetical protein Mhar_0041 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 793.24
//
Query:       gi|386000759|ref|YP_005919058.1|  [L=673]
Description: hypothetical protein Mhar_0042 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-62  207.8  24.7    2.3e-14   53.5   0.4    6.5  6  TPR_12    Tetratricopeptide repeat
    4.3e-37  125.0  16.5    3.4e-05   23.6   0.0   11.3 11  TPR_10    Tetratricopeptide repeat
    1.5e-35  118.4  24.9     0.0033   17.4   0.0   12.2 12  TPR_2     Tetratricopeptide repeat
    8.4e-25   84.9  27.9     0.0011   18.8   0.0   11.1 11  TPR_7     Tetratricopeptide repeat
    2.3e-23   83.1   8.4    4.8e-08   32.7   0.2    4.0  4  TPR_MalT  MalT-like TPR region
    1.2e-21   75.1  24.8      0.018   15.2   0.0   11.3 11  TPR_8     Tetratricopeptide repeat
      8e-20   69.8  17.2       0.12   12.2   0.1   10.8 11  TPR_1     Tetratricopeptide repeat
    7.7e-16   57.0  26.3      0.067   13.9   0.3   10.7 10  TPR_4     Tetratricopeptide repeat
    1.5e-11   44.2   0.5      0.015   15.4   0.0    6.2  7  ANAPC5    Anaphase-promoting complex subunit 5
    6.2e-11   42.1   0.8          6    7.0   0.1    8.4  8  TPR_3     Tetratricopeptide repeat
    1.6e-08   34.5  16.6      0.005   16.9   1.5    8.4  9  MIT       MIT (microtubule interacting and transport) domain
    2.2e-08   33.9   0.8         15    6.2   0.0    9.7 11  TPR_17    Tetratricopeptide repeat
    2.2e-06   27.9  16.3         11    6.9   0.1    9.3  9  TPR_6     Tetratricopeptide repeat
    3.2e-06   26.8   0.0       0.17   11.3   0.0    3.3  3  SNAP      Soluble NSF attachment protein, SNAP
    0.00013   22.6  15.6         16    6.2   0.1    7.9  8  TPR_16    Tetratricopeptide repeat
    0.00041   20.9  23.6         12    7.0   1.2   10.4 10  TPR_14    Tetratricopeptide repeat
     0.0094   16.1   1.0        4.8    7.3   0.0    4.6  5  DUF3151   Protein of unknown function (DUF3151)
  ------ inclusion threshold ------
      0.031   14.2   0.0         22    4.9   0.0    3.9  4  DUF2972   Protein of unknown function (DUF2972)
       0.13   11.8   1.5         19    4.7   0.3    3.1  2  DAO       FAD dependent oxidoreductase
        0.2   11.6   3.6        7.8    6.5   0.1    3.7  3  DUF1876   Domain of unknown function (DUF1876)
       0.67   10.0   6.0         11    6.1   0.1    4.8  5  SRR1      SRR1


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.3   1.8e-10   1.5e-07       4      77 .]     211     282 ..     208     282 .. 0.95
   2 !   53.5   0.4   2.6e-17   2.3e-14       3      76 ..     290     361 ..     287     362 .. 0.94
   3 !   48.4   0.1   9.9e-16   8.5e-13       3      77 .]     370     442 ..     368     442 .. 0.94
   4 !   36.0   0.0   7.2e-12   6.1e-09      16      76 ..     423     481 ..     422     482 .. 0.94
   5 !   36.9   0.5     4e-12   3.4e-09       2      76 ..     489     561 ..     488     562 .. 0.95
   6 !   31.5   0.9   1.9e-10   1.6e-07       5      75 ..     572     640 ..     568     642 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.8e-10
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       ++l +l+++ + lg+yd A ++l++ l + +++  +++ +++++l+ Lg+l   +g+ +e  +l+ ++l+ia++
  gi|386000759|ref|YP_005919058.1| 211 KILDELGEISYNLGDYDNASDYLKHELKLSEEI--DYNRGVLRSLHQLGILAKDRGDIAESCRLHCKSLRIARE 282
                                       56668****************************..999*********************************986 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 2.6e-17
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +++l++l+++ ++ g+ +eA++l+ ++l i + l  +d+ ++a++l+ Lg+l +a+g+  eA++++ee+l+i e
  gi|386000759|ref|YP_005919058.1| 290 SRSLHQLGMLAQATGDITEARRLYGESLKILQDL--GDKSGVARSLHQLGMLAQATGDIVEARRFYEESLKISE 361
                                       67899***************************99..7777*******************************987 PP

  == domain 3  score: 48.4 bits;  conditional E-value: 9.9e-16
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       +++l+nl+a+ ++ g+  eA +++++ l ia++l  +d+ + a++l+ Lg+l + +g+  eA++l+ e+l+i+++
  gi|386000759|ref|YP_005919058.1| 370 SKSLHNLGAIAQATGDIVEAGRFYNEGLKIASEL--GDKSGIASSLHQLGMLAYDTGDISEARRLYGESLKIKRE 442
                                       67899**************************999..7777********************************985 PP

  == domain 4  score: 36.0 bits;  conditional E-value: 7.2e-12
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        g+  eA++l+ ++l i r+l  +d+ + a++l+  g+l +++g++ eA +l++e+l+i e
  gi|386000759|ref|YP_005919058.1| 423 TGDISEARRLYGESLKIKREL--GDKSGIAISLHECGILAQRSGDLTEANRLFNESLKISE 481
                                       58999*************999..7777*******************************987 PP

  == domain 5  score: 36.9 bits;  conditional E-value: 4e-12
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a++l++l+++ +++g+ +eA  l+  +l i + l  +d  + +++l+ Lg l +++g+  eA +l+ e+l+i +
  gi|386000759|ref|YP_005919058.1| 489 IARSLHQLGVLAQARGDIAEAYHLYGDSLKILQDL--GDMSGISRSLHQLGLLAQLSGDIGEAKRLYGESLKISK 561
                                       6899*9***************************99..7777*******************************987 PP

  == domain 6  score: 31.5 bits;  conditional E-value: 1.9e-10
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +l nl+++ +  g++ +Al+l+  +l ia+ l  +d+ + a +l   + l ++ g++e+Al+l +ea a++
  gi|386000759|ref|YP_005919058.1| 572 SLFNLGVLAQNSGELKKALSLYGDSLKIAQDL--DDKTGIAFALAQSALLEEEEGNLEQALDLIREAEALF 640
                                       5669****************************..999******************************9986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.012        10       4      27 ..     212     235 ..     209     243 .. 0.85
   2 !   11.0   0.0   0.00036      0.31       1      35 [.     249     283 ..     249     285 .. 0.95
   3 !   17.0   0.0   4.6e-06    0.0039       3      33 ..     291     321 ..     289     324 .. 0.92
   4 !   22.6   0.0   8.1e-08   6.9e-05       1      35 [.     329     363 ..     329     366 .. 0.96
   5 !    6.5   0.0     0.009       7.7       4      31 ..     372     399 ..     370     404 .. 0.87
   6 !   23.6   0.0   3.9e-08   3.4e-05       2      35 ..     410     443 ..     409     447 .. 0.92
   7 ?    5.7   0.0     0.016        14       2      34 ..     450     482 ..     449     484 .. 0.88
   8 !   11.6   0.1   0.00023      0.19       2      33 ..     490     521 ..     489     523 .. 0.92
   9 !   10.8   0.0   0.00042      0.36       3      35 ..     531     563 ..     529     566 .. 0.95
  10 !    9.2   0.0    0.0013       1.1       7      33 ..     575     601 ..     570     603 .. 0.92
  11 ?   -1.0   0.6         2   1.7e+03      19      35 ..     620     636 ..     609     637 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                            TPR_10   4 slnNLanalrqrgrydeAeallee 27 
                                       +l  L+ + +++g+yd A ++l++
  gi|386000759|ref|YP_005919058.1| 212 ILDELGEISYNLGDYDNASDYLKH 235
                                       7899**************999875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00036
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrl 35 
                                       +++sl+ L+++  +rg+ +e+ +l+ ++l+i r+l
  gi|386000759|ref|YP_005919058.1| 249 VLRSLHQLGILAKDRGDIAESCRLHCKSLRIAREL 283
                                       689****************************9987 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.6e-06
                            TPR_10   3 sslnNLanalrqrgrydeAealleealairr 33 
                                       +sl+ L+++ +++g+ +eA++l+ e+l i +
  gi|386000759|ref|YP_005919058.1| 291 RSLHQLGMLAQATGDITEARRLYGESLKILQ 321
                                       79*************************9977 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 8.1e-08
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrl 35 
                                       +A+sl+ L+++ +++g+  eA++++ee+l i ++l
  gi|386000759|ref|YP_005919058.1| 329 VARSLHQLGMLAQATGDIVEARRFYEESLKISEEL 363
                                       69*****************************9997 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.009
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                       sl+NL+++ +++g+  eA +++ e l i
  gi|386000759|ref|YP_005919058.1| 372 SLHNLGAIAQATGDIVEAGRFYNEGLKI 399
                                       89***************99988887776 PP

  == domain 6  score: 23.6 bits;  conditional E-value: 3.9e-08
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                       Assl+ L+++ +++g+  eA++l+ e+l i r+l
  gi|386000759|ref|YP_005919058.1| 410 ASSLHQLGMLAYDTGDISEARRLYGESLKIKREL 443
                                       9*****************************7775 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.016
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrr 34 
                                       A sl+  +++ ++ g+++eA +l+ e+l i + 
  gi|386000759|ref|YP_005919058.1| 450 AISLHECGILAQRSGDLTEANRLFNESLKISED 482
                                       56788889999******************9885 PP

  == domain 8  score: 11.6 bits;  conditional E-value: 0.00023
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairr 33 
                                       A+sl+ L+++ ++rg+ +eA  l+ ++l i +
  gi|386000759|ref|YP_005919058.1| 490 ARSLHQLGVLAQARGDIAEAYHLYGDSLKILQ 521
                                       99*********************999999876 PP

  == domain 9  score: 10.8 bits;  conditional E-value: 0.00042
                            TPR_10   3 sslnNLanalrqrgrydeAealleealairrrl 35 
                                       +sl+ L+ + +  g+  eA +l+ e+l i ++l
  gi|386000759|ref|YP_005919058.1| 531 RSLHQLGLLAQLSGDIGEAKRLYGESLKISKEL 563
                                       69***************************9997 PP

  == domain 10  score: 9.2 bits;  conditional E-value: 0.0013
                            TPR_10   7 NLanalrqrgrydeAealleealairr 33 
                                       NL+++ ++ g++++A+ l+ ++l i +
  gi|386000759|ref|YP_005919058.1| 575 NLGVLAQNSGELKKALSLYGDSLKIAQ 601
                                       9**********************9987 PP

  == domain 11  score: -1.0 bits;  conditional E-value: 2
                            TPR_10  19 deAealleealairrrl 35 
                                       +e e  le+al++ r++
  gi|386000759|ref|YP_005919058.1| 620 EEEEGNLEQALDLIREA 636
                                       55555566666666654 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.31   2.6e+02       2      16 ..     151     165 ..     150     167 .. 0.89
   2 !   13.2   0.0   8.8e-05     0.075       2      31 ..     211     240 ..     210     243 .. 0.88
   3 ?   -0.6   0.0       2.3     2e+03       4      21 ..     253     270 ..     251     272 .. 0.86
   4 !   13.4   0.0   7.4e-05     0.063       3      30 ..     292     319 ..     290     323 .. 0.91
   5 !   17.4   0.0   3.9e-06    0.0033       1      32 [.     330     361 ..     330     363 .. 0.92
   6 !   11.1   0.0    0.0004      0.34       2      31 ..     371     400 ..     370     403 .. 0.92
   7 !   16.3   0.0   9.1e-06    0.0078       3      31 ..     412     440 ..     410     443 .. 0.91
   8 !   11.1   0.0    0.0004      0.34       2      33 ..     451     482 ..     450     483 .. 0.90
   9 !    9.5   0.2    0.0013       1.1       1      30 [.     490     519 ..     490     523 .. 0.91
  10 !   12.1   0.0   0.00019      0.17       3      32 ..     532     561 ..     530     563 .. 0.91
  11 !   13.1   0.0   9.6e-05     0.082       3      32 ..     572     601 ..     570     603 .. 0.92
  12 ?    5.0   1.1     0.038        32       2      30 ..     611     639 ..     610     642 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.31
                             TPR_2   2 ealynlGlayyklgd 16 
                                       + + ++G+ y+ +g+
  gi|386000759|ref|YP_005919058.1| 151 DFWRYRGNYYELKGR 165
                                       78*********9997 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.8e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       ++l +lG++ y+lgdy+ A ++++  l+l 
  gi|386000759|ref|YP_005919058.1| 211 KILDELGEISYNLGDYDNASDYLKHELKLS 240
                                       57889******************9988886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                             TPR_2   4 lynlGlayyklgdyeeAl 21 
                                       l++lG ++  +gd +e  
  gi|386000759|ref|YP_005919058.1| 253 LHQLGILAKDRGDIAESC 270
                                       899**********99975 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 7.4e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        l++lG+++ + gd  eA++++ ++l++
  gi|386000759|ref|YP_005919058.1| 292 SLHQLGMLAQATGDITEARRLYGESLKI 319
                                       689***********************98 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 3.9e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a+ l++lG+++ + gd  eA++++e++l++ +
  gi|386000759|ref|YP_005919058.1| 330 ARSLHQLGMLAQATGDIVEARRFYEESLKISE 361
                                       6789*************************976 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.0004
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       + l+nlG ++ + gd  eA +++++ l+++
  gi|386000759|ref|YP_005919058.1| 371 KSLHNLGAIAQATGDIVEAGRFYNEGLKIA 400
                                       5799***********************997 PP

  == domain 7  score: 16.3 bits;  conditional E-value: 9.1e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                        l++lG+++y  gd  eA++++ ++l++ 
  gi|386000759|ref|YP_005919058.1| 412 SLHQLGMLAYDTGDISEARRLYGESLKIK 440
                                       699***********************986 PP

  == domain 8  score: 11.1 bits;  conditional E-value: 0.0004
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                         l++ G ++ ++gd+ eA ++f+++l++ ++
  gi|386000759|ref|YP_005919058.1| 451 ISLHECGILAQRSGDLTEANRLFNESLKISED 482
                                       568899**********************9865 PP

  == domain 9  score: 9.5 bits;  conditional E-value: 0.0013
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       a+ l++lG ++ ++gd +eA +++  +l++
  gi|386000759|ref|YP_005919058.1| 490 ARSLHQLGVLAQARGDIAEAYHLYGDSLKI 519
                                       6789********************999987 PP

  == domain 10  score: 12.1 bits;  conditional E-value: 0.00019
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                        l++lGl++  +gd  eA++++ ++l++  
  gi|386000759|ref|YP_005919058.1| 532 SLHQLGLLAQLSGDIGEAKRLYGESLKISK 561
                                       689************************975 PP

  == domain 11  score: 13.1 bits;  conditional E-value: 9.6e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                        l+nlG ++ ++g++++Al ++  +l+++ 
  gi|386000759|ref|YP_005919058.1| 572 SLFNLGVLAQNSGELKKALSLYGDSLKIAQ 601
                                       69**********************999975 PP

  == domain 12  score: 5.0 bits;  conditional E-value: 0.038
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                        al + +l+ ++ g++e+Al++ ++A +l
  gi|386000759|ref|YP_005919058.1| 611 FALAQSALLEEEEGNLEQALDLIREAEAL 639
                                       567777888999**************887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00044      0.37       2      33 ..     213     242 ..     212     245 .. 0.87
   2 ?    5.3   0.0     0.028        24       1      35 [.     252     286 ..     252     287 .. 0.94
   3 !   11.2   0.1   0.00035       0.3       1      35 [.     292     326 ..     292     327 .. 0.95
   4 !   12.3   0.0   0.00016      0.13       1      35 [.     332     366 ..     332     367 .. 0.94
   5 ?    5.4   0.0     0.025        21       1      33 [.     372     404 ..     372     407 .. 0.81
   6 !    9.8   0.1   0.00096      0.82       1      35 [.     412     446 ..     412     447 .. 0.94
   7 ?    4.7   0.0     0.042        36       1      35 [.     452     486 ..     452     487 .. 0.93
   8 !   10.8   0.2   0.00049      0.42       1      35 [.     492     526 ..     492     527 .. 0.95
   9 !    7.3   0.0    0.0063       5.3       1      35 [.     532     566 ..     532     567 .. 0.94
  10 !   18.8   0.0   1.3e-06    0.0011       1      35 [.     572     606 ..     572     607 .. 0.95
  11 ?   -0.9   0.1       2.6   2.2e+03      11      24 ..     622     635 ..     612     642 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       L+ L+++  +lGdy++A ++++   +l  ++e
  gi|386000759|ref|YP_005919058.1| 213 LDELGEISYNLGDYDNASDYLKH--ELKLSEE 242
                                       67899**9***************..8877766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L++L+ l  ++Gd +e  +l+ +sL+++++ +d+
  gi|386000759|ref|YP_005919058.1| 252 SLHQLGILAKDRGDIAESCRLHCKSLRIARELGDK 286
                                       79****************************99987 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00035
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L++L+ l ++ Gd  eA +ly +sL +  d +d+
  gi|386000759|ref|YP_005919058.1| 292 SLHQLGMLAQATGDITEARRLYGESLKILQDLGDK 326
                                       79***************************999987 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00016
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L++L+ l ++ Gd  eA ++ye+sL + ++ +d+
  gi|386000759|ref|YP_005919058.1| 332 SLHQLGMLAQATGDIVEARRFYEESLKISEELGDK 366
                                       79*************************99999887 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.025
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +L+nL+ + ++ Gd  eA ++y + L ++++ +
  gi|386000759|ref|YP_005919058.1| 372 SLHNLGAIAQATGDIVEAGRFYNEGLKIASELG 404
                                       79****************999988555555555 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00096
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L++L+ l  + Gd +eA +ly +sL + ++ +d+
  gi|386000759|ref|YP_005919058.1| 412 SLHQLGMLAYDTGDISEARRLYGESLKIKRELGDK 446
                                       799**************************999987 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.042
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L+  + l +r Gd  eA +l+ +sL + +d +d+
  gi|386000759|ref|YP_005919058.1| 452 SLHECGILAQRSGDLTEANRLFNESLKISEDLGDM 486
                                       68889999***********************9997 PP

  == domain 8  score: 10.8 bits;  conditional E-value: 0.00049
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L++L++l +++Gd +eA  ly  sL +  d +d+
  gi|386000759|ref|YP_005919058.1| 492 SLHQLGVLAQARGDIAEAYHLYGDSLKILQDLGDM 526
                                       79***************************999997 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.0063
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L++L+ l +  Gd  eA +ly +sL + k+ +d+
  gi|386000759|ref|YP_005919058.1| 532 SLHQLGLLAQLSGDIGEAKRLYGESLKISKELGDK 566
                                       79**************************9999987 PP

  == domain 10  score: 18.8 bits;  conditional E-value: 1.3e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +L+nL++l ++ G+ ++A++ly  sL ++ d +d+
  gi|386000759|ref|YP_005919058.1| 572 SLFNLGVLAQNSGELKKALSLYGDSLKIAQDLDDK 606
                                       79*****************************9987 PP

  == domain 11  score: -0.9 bits;  conditional E-value: 2.6
                             TPR_7  11 rlGdyeeAielyeq 24 
                                       ++G+ e+A++l ++
  gi|386000759|ref|YP_005919058.1| 622 EEGNLEQALDLIRE 635
                                       58999999998877 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.2   5.7e-11   4.8e-08      14     185 ..     223     394 ..     217     403 .. 0.84
   2 !   23.3   0.1   4.2e-08   3.6e-05      46     161 ..     336     449 ..     325     462 .. 0.86
   3 !   30.2   0.1   3.3e-10   2.9e-07      45     183 ..     375     512 ..     372     522 .. 0.91
   4 !   24.3   0.1     2e-08   1.7e-05      46     156 ..     536     645 ..     519     655 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.7e-11
                          TPR_MalT  14 sgdaeralelArqALallpeddllariaa.tavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaei 89 
                                        gd + a+++ ++ L+l++e d+   ++  +  lG  +  +Gd +++++ + +  ++ar+ +   ++  +l q++++
  gi|386000759|ref|YP_005919058.1| 223 LGDYDNASDYLKHELKLSEEIDYNRGVLRsLHQLGILAKDRGDIAESCRLHCKSLRIARELGDKSAVSRSLHQLGML 299
                                       5666777777777788888888666644313458999999************************************* PP

                          TPR_MalT  90 lvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayv 165
                                       ++a G+  eA ++y ++l+  ++ g +   ++  l+ +l+ l    +d  eA+++ +e+++++e+l ++ ++ +++ 
  gi|386000759|ref|YP_005919058.1| 300 AQATGDITEARRLYGESLKILQDLGDK-SGVARSLH-QLGMLAQATGDIVEARRFYEESLKISEELgDKSTISKSLH 374
                                       *******************88887776.56666665.55**************************945566668*** PP

                          TPR_MalT 166 llarialaqGdleeAetlle 185
                                        l  ia+a Gd+ eA +  +
  gi|386000759|ref|YP_005919058.1| 375 NLGAIAQATGDIVEAGRFYN 394
                                       ***************88765 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.2e-08
                          TPR_MalT  46 lGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvg 122
                                       lG  ++ +Gd  +A++ ++e  k++ + +   +   +l  ++ i++a G+  eA + y+++l+ a e g +   ++ 
  gi|386000759|ref|YP_005919058.1| 336 LGMLAQATGDIVEARRFYEESLKISEELGDKSTISKSLHNLGAIAQATGDIVEAGRFYNEGLKIASELGDK-SGIAS 411
                                       78889999*****************99999999999999************************88876666.78888 PP

                          TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleqlepeaal 161
                                        l+ l + l y+ +d  eA++   e++++ ++l+ +  +
  gi|386000759|ref|YP_005919058.1| 412 SLHQL-GMLAYDTGDISEARRLYGESLKIKRELGDKSGI 449
                                       88766.*********************999998766555 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 3.3e-10
                          TPR_MalT  45 vlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplv 121
                                       +lG +++ +Gd  +A + ++e  k+a + +     + +l q+++++   G+  eA ++y ++l+ ++++ + +  ++
  gi|386000759|ref|YP_005919058.1| 375 NLGAIAQATGDIVEAGRFYNEGLKIASELGDKSGIASSLHQLGMLAYDTGDISEARRLYGESLK-IKRELGDKSGIA 450
                                       7999************************************************************.666666666666 PP

                          TPR_MalT 122 gfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdleeAetl 183
                                         l  +++ l    +dL+eA +  +e+++++e+l +   +++++  l  +a+a+Gd+ eA++l
  gi|386000759|ref|YP_005919058.1| 451 ISL-HECGILAQRSGDLTEANRLFNESLKISEDLgDMSGIARSLHQLGVLAQARGDIAEAYHL 512
                                       555.677**************************956699999******************998 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 2e-08
                          TPR_MalT  46 lGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvg 122
                                       lG  ++l Gd  +A + + e  k++++ +   + l +l  ++ +++  G+L++Al +y ++l+ a++ + +      
  gi|386000759|ref|YP_005919058.1| 536 LGLLAQLSGDIGEAKRLYGESLKISKELGDKSTFLKSLFNLGVLAQNSGELKKALSLYGDSLKIAQDLDDK--TGIA 610
                                       799999*********************************************************99999988..5888 PP

                          TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleql.e 156
                                       f+l++ a l  E ++Le+A +  +e+ +l  +l +
  gi|386000759|ref|YP_005919058.1| 611 FALAQSALLEEEEGNLEQALDLIREAEALFMKLeS 645
                                       999999*****************999888777644 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   0.00041      0.35       4      32 ..     213     241 ..     210     243 .. 0.84
   2 ?    1.3   0.0      0.59   5.1e+02       2      30 ..     251     279 ..     250     283 .. 0.80
   3 !    9.7   0.0    0.0013       1.1       2      30 ..     291     319 ..     290     321 .. 0.93
   4 !   15.2   0.0   2.1e-05     0.018       1      32 [.     330     361 ..     330     363 .. 0.95
   5 !    7.5   0.0    0.0064       5.5       2      32 ..     371     401 ..     370     403 .. 0.93
   6 !   12.0   0.1   0.00022      0.19       1      32 [.     410     441 ..     410     443 .. 0.94
   7 ?    1.2   0.0      0.65   5.5e+02      11      33 ..     460     482 ..     453     483 .. 0.88
   8 ?    4.2   0.1      0.07        60       1      29 [.     490     518 ..     490     525 .. 0.80
   9 !   10.5   0.1    0.0007       0.6       2      32 ..     531     561 ..     530     563 .. 0.94
  10 !    9.2   0.1    0.0018       1.5       2      33 ..     571     602 ..     570     603 .. 0.93
  11 ?    0.1   0.2       1.5   1.3e+03       5      27 ..     614     636 ..     612     640 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +  lg i  +lgdy++A  y+++ l+l++
  gi|386000759|ref|YP_005919058.1| 213 LDELGEISYNLGDYDNASDYLKHELKLSE 241
                                       6679*****************98777765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.59
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +++++lg + ++ gd+ e+     k l++
  gi|386000759|ref|YP_005919058.1| 251 RSLHQLGILAKDRGDIAESCRLHCKSLRI 279
                                       899*************9987666666655 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0013
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +++++lg++ + +gd+ eA   y + l++
  gi|386000759|ref|YP_005919058.1| 291 RSLHQLGMLAQATGDITEARRLYGESLKI 319
                                       899******************99999986 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.1e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+++++lg++ + +gd+ eA  +ye+ l++++
  gi|386000759|ref|YP_005919058.1| 330 ARSLHQLGMLAQATGDIVEARRFYEESLKISE 361
                                       799***************************97 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0064
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++++nlg i + +gd+ eA  +y++ l+++ 
  gi|386000759|ref|YP_005919058.1| 371 KSLHNLGAIAQATGDIVEAGRFYNEGLKIAS 401
                                       789*************************986 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00022
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+++++lg++  ++gd+ eA   y + l++++
  gi|386000759|ref|YP_005919058.1| 410 ASSLHQLGMLAYDTGDISEARRLYGESLKIKR 441
                                       6789**************************97 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.65
                                       HHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyyekaleldpd 33 
                                        +  gd+ eA   +++ l++++d
  gi|386000759|ref|YP_005919058.1| 460 AQRSGDLTEANRLFNESLKISED 482
                                       5678****************986 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekale 29 
                                       a+++++lg + +  gd+ eA   y   l+
  gi|386000759|ref|YP_005919058.1| 490 ARSLHQLGVLAQARGDIAEAYHLYGDSLK 518
                                       68899999999999999999777766555 PP

  == domain 9  score: 10.5 bits;  conditional E-value: 0.0007
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +++++lg++ +  gd+ eAk  y + l++++
  gi|386000759|ref|YP_005919058.1| 531 RSLHQLGLLAQLSGDIGEAKRLYGESLKISK 561
                                       899**************************97 PP

  == domain 10  score: 9.2 bits;  conditional E-value: 0.0018
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++nlg + ++ g++++A + y   l++++d
  gi|386000759|ref|YP_005919058.1| 571 KSLFNLGVLAQNSGELKKALSLYGDSLKIAQD 602
                                       789***********************999875 PP

  == domain 11  score: 0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyeka 27 
                                        + +++ ++ g++e+A   +++a
  gi|386000759|ref|YP_005919058.1| 614 AQSALLEEEEGNLEQALDLIREA 636
                                       56677889999****99888887 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.8   1.6e+03       2      16 ..     151     165 ..     150     165 .. 0.84
   2 !    6.5   0.1    0.0093         8       7      25 ..     216     234 ..     215     235 .. 0.90
   3 !    6.4   0.0    0.0097       8.3       2      31 ..     291     320 ..     290     323 .. 0.90
   4 !   12.0   0.0   0.00017      0.14       1      32 [.     330     361 ..     330     363 .. 0.93
   5 !   10.1   0.0   0.00065      0.56       2      31 ..     371     400 ..     370     403 .. 0.92
   6 !    8.8   0.0    0.0017       1.4       2      32 ..     411     441 ..     410     443 .. 0.90
   7 ?   -0.9   0.0         2   1.7e+03       7      33 ..     456     482 ..     450     483 .. 0.81
   8 !    6.7   0.1    0.0077       6.6       1      30 [.     490     519 ..     490     523 .. 0.89
   9 ?    5.6   0.0     0.018        15       2      30 ..     531     559 ..     530     562 .. 0.91
  10 !   12.2   0.1   0.00015      0.12       2      32 ..     571     601 ..     570     603 .. 0.91
  11 ?    1.8   0.3      0.28   2.4e+02       8      27 ..     617     636 ..     610     639 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHTT- CS
                             TPR_1   2 kalynlGnayfklgk 16 
                                       + +  +Gn y  +g+
  gi|386000759|ref|YP_005919058.1| 151 DFWRYRGNYYELKGR 165
                                       67999*****99986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0093
                                       HHHHHHHTT-HHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyye 25 
                                       lG + ++lg+yd A +y +
  gi|386000759|ref|YP_005919058.1| 216 LGEISYNLGDYDNASDYLK 234
                                       89999*********99975 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0097
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       ++l +lG++ +  g+  eA   y + L++ 
  gi|386000759|ref|YP_005919058.1| 291 RSLHQLGMLAQATGDITEARRLYGESLKIL 320
                                       57889**********************985 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a++l +lG++ +  g+  eA  +ye+ L++ +
  gi|386000759|ref|YP_005919058.1| 330 ARSLHQLGMLAQATGDIVEARRFYEESLKISE 361
                                       68899************************975 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00065
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       k+l nlG++ +  g+  eA  +y++ L++ 
  gi|386000759|ref|YP_005919058.1| 371 KSLHNLGAIAQATGDIVEAGRFYNEGLKIA 400
                                       7899************************97 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                        +l +lG++ +  g+  eA   y + L++  
  gi|386000759|ref|YP_005919058.1| 411 SSLHQLGMLAYDTGDISEARRLYGESLKIKR 441
                                       57889***********************975 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 2
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                        G + ++ g++ eA   +++ L++ ++
  gi|386000759|ref|YP_005919058.1| 456 CGILAQRSGDLTEANRLFNESLKISED 482
                                       588888999999999999999999765 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.0077
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a++l +lG++ +  g+  eA   y   L++
  gi|386000759|ref|YP_005919058.1| 490 ARSLHQLGVLAQARGDIAEAYHLYGDSLKI 519
                                       68899*****************99888887 PP

  == domain 9  score: 5.6 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       ++l +lG++ +  g+  eA   y + L++
  gi|386000759|ref|YP_005919058.1| 531 RSLHQLGLLAQLSGDIGEAKRLYGESLKI 559
                                       57889**********************98 PP

  == domain 10  score: 12.2 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       k+l+nlG++ ++ g++++Al  y   L++  
  gi|386000759|ref|YP_005919058.1| 571 KSLFNLGVLAQNSGELKKALSLYGDSLKIAQ 601
                                       679********************99999876 PP

  == domain 11  score: 1.8 bits;  conditional E-value: 0.28
                                       HHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   8 GnayfklgkydeAleyyekA 27 
                                       +++  + g++++Al+  ++A
  gi|386000759|ref|YP_005919058.1| 617 ALLEEEEGNLEQALDLIREA 636
                                       6667789********98888 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.069        59       2      23 ..     251     272 ..     250     272 .. 0.90
   2 !   11.5   0.1   0.00045      0.39       2      24 ..     291     313 ..     290     315 .. 0.90
   3 !   13.9   0.3   7.8e-05     0.067       1      26 []     330     355 ..     330     355 .. 0.93
   4 ?    5.9   0.0      0.03        25       4      23 ..     373     392 ..     372     395 .. 0.89
   5 !    9.0   0.0    0.0029       2.5       2      24 ..     411     433 ..     410     435 .. 0.89
   6 ?    1.5   0.0      0.74   6.3e+02       5      23 ..     454     472 ..     450     475 .. 0.82
   7 !    9.2   1.2    0.0025       2.1       1      20 [.     490     509 ..     490     510 .. 0.94
   8 ?    6.3   0.0     0.021        18       2      24 ..     531     553 ..     530     555 .. 0.89
   9 ?    0.8   0.0       1.3   1.1e+03       4      23 ..     573     592 ..     572     594 .. 0.88
  10 ?    2.4   0.7       0.4   3.4e+02      13      26 .]     622     635 ..     610     635 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.069
                             TPR_4   2 rallaLArallalGdldeAral 23 
                                       r l+ L+ ++ ++Gd +e ++l
  gi|386000759|ref|YP_005919058.1| 251 RSLHQLGILAKDRGDIAESCRL 272
                                       78999*************9886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00045
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       r l+ L+++++a+Gd  eAr+l 
  gi|386000759|ref|YP_005919058.1| 291 RSLHQLGMLAQATGDITEARRLY 313
                                       67899****************96 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.8e-05
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       ar l+ L+++++a+Gd  eAr+  e+
  gi|386000759|ref|YP_005919058.1| 330 ARSLHQLGMLAQATGDIVEARRFYEE 355
                                       68999*****************9986 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.03
                             TPR_4   4 llaLArallalGdldeAral 23 
                                       l++L+  ++a+Gd  eA + 
  gi|386000759|ref|YP_005919058.1| 373 LHNLGAIAQATGDIVEAGRF 392
                                       789**************875 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0029
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                         l+ L+++++++Gd  eAr+l 
  gi|386000759|ref|YP_005919058.1| 411 SSLHQLGMLAYDTGDISEARRLY 433
                                       57899****************96 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.74
                             TPR_4   5 laLArallalGdldeAral 23 
                                       +  + ++++ Gdl eA +l
  gi|386000759|ref|YP_005919058.1| 454 HECGILAQRSGDLTEANRL 472
                                       667899*********9776 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.0025
                             TPR_4   1 arallaLArallalGdldeA 20 
                                       ar l+ L+ +++a+Gd +eA
  gi|386000759|ref|YP_005919058.1| 490 ARSLHQLGVLAQARGDIAEA 509
                                       68999**************9 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.021
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       r l+ L+ ++++ Gd  eA +l 
  gi|386000759|ref|YP_005919058.1| 531 RSLHQLGLLAQLSGDIGEAKRLY 553
                                       67899**************9986 PP

  == domain 9  score: 0.8 bits;  conditional E-value: 1.3
                             TPR_4   4 llaLArallalGdldeAral 23 
                                       l +L+ +++  G+l  A+ l
  gi|386000759|ref|YP_005919058.1| 573 LFNLGVLAQNSGELKKALSL 592
                                       689************99976 PP

  == domain 10  score: 2.4 bits;  conditional E-value: 0.4
                             TPR_4  13 alGdldeAraller 26 
                                       + G+l++A++l ++
  gi|386000759|ref|YP_005919058.1| 622 EEGNLEQALDLIRE 635
                                       57*********996 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0074       6.3      12      92 ..     224     301 ..     217     343 .. 0.63
   2 ?    4.6   0.0     0.039        33      45      89 ..     334     378 ..     326     383 .. 0.87
   3 ?    1.3   0.0      0.42   3.6e+02      46      87 ..     375     416 ..     369     420 .. 0.83
   4 !    7.4   0.0    0.0054       4.6      42      91 ..     411     460 ..     400     463 .. 0.87
   5 ?    2.2   0.0      0.22   1.9e+02      49      92 ..     458     501 ..     451     503 .. 0.85
   6 ?    0.5   0.0      0.74   6.3e+02      46      90 ..     495     539 ..     488     543 .. 0.85
   7 !   15.4   0.0   1.7e-05     0.015      37      93 ..     566     622 ..     509     623 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0074
                            ANAPC5  12 kdYqqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlArenkDkscLalalawla 88 
                                        dY++a d+L +    + + + ++       +l +l +l  d g+ +e+++    + r+Are +Dks ++  l+ l 
  gi|386000759|ref|YP_005919058.1| 224 GDYDNASDYLKHELKLSEEIDYNR---GVLRSLHQLGILAKDRGDIAESCRLHCKSLRIARELGDKSAVSRSLHQLG 297
                                       567777777776665444444444...44445556666666667777777777777777777777777666666655 PP

                            ANAPC5  89 rllk 92 
                                        l +
  gi|386000759|ref|YP_005919058.1| 298 MLAQ 301
                                       5443 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.039
                            ANAPC5  45 LnlaslhadfghneeAvkaleeairlArenkDkscLalalawlar 89 
                                        +l +l ++ g+  eA +  ee+ +++ e +Dks+++  l+ l +
  gi|386000759|ref|YP_005919058.1| 334 HQLGMLAQATGDIVEARRFYEESLKISEELGDKSTISKSLHNLGA 378
                                       5789999999**************************999988765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.42
                            ANAPC5  46 nlaslhadfghneeAvkaleeairlArenkDkscLalalawl 87 
                                       nl  + ++ g+  eA +  +e  ++A e +Dks +a  l+ l
  gi|386000759|ref|YP_005919058.1| 375 NLGAIAQATGDIVEAGRFYNEGLKIASELGDKSGIASSLHQL 416
                                       66777777788889999999***************9999876 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0054
                            ANAPC5  42 yalLnlaslhadfghneeAvkaleeairlArenkDkscLalalawlarll 91 
                                       ++l +l +l +d g+  eA +   e+ ++ re +Dks +a+ l+    l 
  gi|386000759|ref|YP_005919058.1| 411 SSLHQLGMLAYDTGDISEARRLYGESLKIKRELGDKSGIAISLHECGILA 460
                                       5677899*********************************9999766665 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.22
                            ANAPC5  49 slhadfghneeAvkaleeairlArenkDkscLalalawlarllk 92 
                                       +l ++ g+  eA + ++e+ +++ + +D+s +a  l+ l  l +
  gi|386000759|ref|YP_005919058.1| 458 ILAQRSGDLTEANRLFNESLKISEDLGDMSGIARSLHQLGVLAQ 501
                                       6777778999***********************99998877765 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.74
                            ANAPC5  46 nlaslhadfghneeAvkaleeairlArenkDkscLalalawlarl 90 
                                       +l +l ++ g+ +eA++   ++ ++ ++ +D+s ++  l+ l  l
  gi|386000759|ref|YP_005919058.1| 495 QLGVLAQARGDIAEAYHLYGDSLKILQDLGDMSGISRSLHQLGLL 539
                                       577888888999*********************999988877655 PP

  == domain 7  score: 15.4 bits;  conditional E-value: 1.7e-05
                            ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleeairlArenkDkscLalalawlarllkk 93 
                                       k ++  +l+nl +l ++ g+ ++A++   ++ ++A++  Dk+ +a+ala  a l+++
  gi|386000759|ref|YP_005919058.1| 566 KSTFLKSLFNLGVLAQNSGELKKALSLYGDSLKIAQDLDDKTGIAFALAQSALLEEE 622
                                       779999******************************************998888765 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.55   4.7e+02      12      23 ..     221     232 ..     217     234 .. 0.90
   2 ?    5.5   0.0      0.02        17       4      27 ..     293     314 ..     292     321 .. 0.84
   3 ?    2.7   0.0      0.15   1.3e+02       4      30 ..     333     357 ..     332     363 .. 0.80
   4 ?    1.2   0.0      0.46     4e+02       1      23 [.     370     392 ..     370     394 .. 0.85
   5 ?    6.2   0.0     0.012        10       4      27 ..     413     434 ..     412     442 .. 0.84
   6 !    7.0   0.1     0.007         6       4      27 ..     493     514 ..     492     520 .. 0.83
   7 ?    0.8   0.0      0.59   5.1e+02       4      35 ..     533     562 ..     532     563 .. 0.82
   8 ?    4.6   0.0      0.04        34       1      27 [.     570     594 ..     570     602 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.55
                                       HHTT-HHHHHHH CS
                             TPR_3  12 ynkkkyqeArel 23 
                                       yn ++y+ A ++
  gi|386000759|ref|YP_005919058.1| 221 YNLGDYDNASDY 232
                                       9********988 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHTT-HHHHHHH..HH CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsYa 27 
                                       l+ ++   +  ++++eAr l  Y+
  gi|386000759|ref|YP_005919058.1| 293 LHQLGMLAQATGDITEARRL--YG 314
                                       677888899***********..75 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHTT-HHHHHHH..HHHHH CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsYalla 30 
                                       l+ ++   +  +++ eAr +  Y+ + 
  gi|386000759|ref|YP_005919058.1| 333 LHQLGMLAQATGDIVEARRF--YEESL 357
                                       677888889***********..76555 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_3   1 ldylysyAaefynkkkyqeArel 23 
                                       +++l+ ++a  +  +++ eA  +
  gi|386000759|ref|YP_005919058.1| 370 SKSLHNLGAIAQATGDIVEAGRF 392
                                       5789999*********9999777 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHTT-HHHHHHH..HH CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsYa 27 
                                       l+ ++   y+ ++++eAr l  Y+
  gi|386000759|ref|YP_005919058.1| 413 LHQLGMLAYDTGDISEARRL--YG 434
                                       67788899************..76 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.007
                                       HHHHHHHHHHTT-HHHHHHH..HH CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsYa 27 
                                       l+ ++   +  +++ eA++l  Y+
  gi|386000759|ref|YP_005919058.1| 493 LHQLGVLAQARGDIAEAYHL--YG 514
                                       66777888999*********..75 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsYallaildke 35 
                                       l+ ++   ++++++ eA  l  Y+ + ++ ke
  gi|386000759|ref|YP_005919058.1| 533 LHQLGLLAQLSGDIGEAKRL--YGESLKISKE 562
                                       77899999*********999..8777777665 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHTT-HHHHHHH..HH CS
                             TPR_3   1 ldylysyAaefynkkkyqeArelfsYa 27 
                                       l++l+ ++   +n++++ +A+ l  Y+
  gi|386000759|ref|YP_005919058.1| 570 LKSLFNLGVLAQNSGELKKALSL--YG 594
                                       5789999****************..76 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       1.5   1.2e+03      29      57 ..     172     199 ..     172     202 .. 0.75
   2 ?    0.0   0.1       1.1   9.1e+02      26      40 ..     225     239 ..     213     252 .. 0.74
   3 ?    3.6   0.0     0.079        68      17      36 ..     303     322 ..     293     336 .. 0.86
   4 ?   -0.4   0.0       1.4   1.2e+03      16      32 ..     342     358 ..     329     363 .. 0.82
   5 ?    0.5   0.0      0.76   6.5e+02      17      32 ..     423     438 ..     410     439 .. 0.84
   6 !    8.3   0.0    0.0028       2.4       9      36 ..     495     522 ..     490     531 .. 0.84
   7 ?   -2.3   0.0       5.6   4.8e+03      18      32 ..     544     558 ..     542     559 .. 0.85
   8 ?    4.7   0.0     0.038        32       7      32 ..     573     598 ..     571     602 .. 0.87
   9 !   16.9   1.5   5.8e-06     0.005       4      53 ..     610     662 ..     609     664 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                               MIT  29 ealelLlqalkekneerrellrekieeYl 57 
                                       ea+++L + l+ ++ +   l r++i+eYl
  gi|386000759|ref|YP_005919058.1| 172 EAIDVLATSLRYQS-KEDLLRRRRINEYL 199
                                       68999999998433.56667788899997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                               MIT  26 lYkealelLlqalke 40 
                                        Y +a ++L++ lk 
  gi|386000759|ref|YP_005919058.1| 225 DYDNASDYLKHELKL 239
                                       599******999883 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.079
                               MIT  17 agnyeeAlelYkealelLlq 36 
                                        g++ eA +lY e+l++L+ 
  gi|386000759|ref|YP_005919058.1| 303 TGDITEARRLYGESLKILQD 322
                                       68999***********9986 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.4
                               MIT  16 nagnyeeAlelYkeale 32 
                                         g++ eA + Y+e+l+
  gi|386000759|ref|YP_005919058.1| 342 ATGDIVEARRFYEESLK 358
                                       568999********986 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.76
                               MIT  17 agnyeeAlelYkeale 32 
                                        g+++eA +lY e+l+
  gi|386000759|ref|YP_005919058.1| 423 TGDISEARRLYGESLK 438
                                       5899********9986 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0028
                               MIT   9 kkAveeDnagnyeeAlelYkealelLlq 36 
                                       +  v +  +g+++eA++lY ++l++L+ 
  gi|386000759|ref|YP_005919058.1| 495 QLGVLAQARGDIAEAYHLYGDSLKILQD 522
                                       666777889***************9985 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 5.6
                               MIT  18 gnyeeAlelYkeale 32 
                                       g++ eA +lY e+l+
  gi|386000759|ref|YP_005919058.1| 544 GDIGEAKRLYGESLK 558
                                       7889******99986 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.038
                               MIT   7 lvkkAveeDnagnyeeAlelYkeale 32 
                                       l++  v + n+g+ ++Al+lY ++l+
  gi|386000759|ref|YP_005919058.1| 573 LFNLGVLAQNSGELKKALSLYGDSLK 598
                                       677789999************99986 PP

  == domain 9  score: 16.9 bits;  conditional E-value: 5.8e-06
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqalk.e.kneer.rellreki 53 
                                       A++l++ A  e+++gn e Al+l +ea  l++++ +   +n++  re l++ki
  gi|386000759|ref|YP_005919058.1| 610 AFALAQSALLEEEEGNLEQALDLIREAEALFMKLESpTaENARYvRERLEKKI 662
                                       89********************************9965544443477777776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.81   6.9e+02      13      28 ..     150     165 ..     149     168 .. 0.87
   2 ?    1.1   0.0      0.78   6.6e+02      18      32 ..     215     229 ..     210     230 .. 0.86
   3 ?   -1.0   0.0       3.6   3.1e+03      15      30 ..     252     267 ..     251     270 .. 0.86
   4 ?   -0.2   0.0         2   1.7e+03      14      33 ..     291     310 ..     289     311 .. 0.88
   5 ?    0.8   0.0      0.96   8.2e+02      13      33 ..     330     350 ..     319     351 .. 0.91
   6 ?    2.8   0.0      0.22   1.9e+02      10      32 ..     367     389 ..     352     391 .. 0.73
   7 ?    0.9   0.0      0.86   7.3e+02      13      33 ..     410     430 ..     405     431 .. 0.89
   8 ?    2.3   0.0      0.31   2.7e+02      13      32 ..     490     509 ..     473     511 .. 0.91
   9 ?    0.5   0.0       1.2     1e+03      13      29 ..     507     523 ..     502     525 .. 0.82
  10 ?    1.0   0.0      0.85   7.3e+02      13      33 ..     530     550 ..     528     551 .. 0.89
  11 ?    6.2   0.0     0.018        15      14      33 ..     571     590 ..     561     591 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.81
                            TPR_17  13 adaynnLAelllknGd 28 
                                       +d++ +++++++ +G+
  gi|386000759|ref|YP_005919058.1| 150 PDFWRYRGNYYELKGR 165
                                       589*********9997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.78
                            TPR_17  18 nLAelllknGdlmtA 32 
                                       +L+e+ +++Gd++ A
  gi|386000759|ref|YP_005919058.1| 215 ELGEISYNLGDYDNA 229
                                       79**********977 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.6
                            TPR_17  15 aynnLAelllknGdlm 30 
                                       ++++L+ l + +Gd +
  gi|386000759|ref|YP_005919058.1| 252 SLHQLGILAKDRGDIA 267
                                       799**********976 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                        ++++L+ l    Gd  +Ar
  gi|386000759|ref|YP_005919058.1| 291 RSLHQLGMLAQATGDITEAR 310
                                       689***********999997 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.96
                            TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                       a ++++L+ l    Gd  +Ar
  gi|386000759|ref|YP_005919058.1| 330 ARSLHQLGMLAQATGDIVEAR 350
                                       6799************99998 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.22
                            TPR_17  10 PnnadaynnLAelllknGdlmtA 32 
                                        + +++++nL+ +    Gd  +A
  gi|386000759|ref|YP_005919058.1| 367 STISKSLHNLGAIAQATGDIVEA 389
                                       45699********9999998776 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.86
                            TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                       a ++++L+ l +  Gd  +Ar
  gi|386000759|ref|YP_005919058.1| 410 ASSLHQLGMLAYDTGDISEAR 430
                                       6799************99997 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.31
                            TPR_17  13 adaynnLAelllknGdlmtA 32 
                                       a ++++L++l   +Gd ++A
  gi|386000759|ref|YP_005919058.1| 490 ARSLHQLGVLAQARGDIAEA 509
                                       7799************9988 PP

  == domain 9  score: 0.5 bits;  conditional E-value: 1.2
                            TPR_17  13 adaynnLAelllknGdl 29 
                                       a+ay++++  l+ + dl
  gi|386000759|ref|YP_005919058.1| 507 AEAYHLYGDSLKILQDL 523
                                       89******999977775 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 0.85
                            TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                       + ++++L+ l    Gd ++A+
  gi|386000759|ref|YP_005919058.1| 530 SRSLHQLGLLAQLSGDIGEAK 550
                                       5689************99996 PP

  == domain 11  score: 6.2 bits;  conditional E-value: 0.018
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                       ++++nL++l  + G+l++A+
  gi|386000759|ref|YP_005919058.1| 571 KSLFNLGVLAQNSGELKKAL 590
                                       699**************996 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.23     2e+02       5      23 ..     215     233 ..     212     234 .. 0.87
   2 ?    6.9   0.1     0.013        11       2      24 ..     292     314 ..     291     319 .. 0.90
   3 ?    5.7   0.0     0.031        26       2      25 ..     332     355 ..     331     359 .. 0.90
   4 ?    6.8   0.0     0.014        12       2      24 ..     412     434 ..     411     438 .. 0.90
   5 ?   -2.1   0.0       9.6   8.2e+03       9      25 ..     460     475 ..     457     478 .. 0.76
   6 ?    0.4   0.1       1.6   1.3e+03       2      23 ..     492     513 ..     489     518 .. 0.72
   7 ?    0.7   0.0       1.2     1e+03       2      24 ..     532     554 ..     531     558 .. 0.83
   8 ?    2.9   0.0      0.25   2.1e+02       2      24 ..     572     594 ..     571     599 .. 0.88
   9 ?    2.3   0.3      0.37   3.1e+02       2      24 ..     612     634 ..     611     638 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAleal 23 
                                        l++  ++lgd+d+A ++l
  gi|386000759|ref|YP_005919058.1| 215 ELGEISYNLGDYDNASDYL 233
                                       5899999999*****9998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleale 24 
                                       +l +l+++ +++gd ++A++++ 
  gi|386000759|ref|YP_005919058.1| 292 SLHQLGMLAQATGDITEARRLYG 314
                                       5889*******99*******996 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                       +l +l+++ +++gd  +A++ +e+
  gi|386000759|ref|YP_005919058.1| 332 SLHQLGMLAQATGDIVEARRFYEE 355
                                       5889*******99*********96 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleale 24 
                                       +l +l+++ + +gd ++A++++ 
  gi|386000759|ref|YP_005919058.1| 412 SLHQLGMLAYDTGDISEARRLYG 434
                                       5889*******99*******996 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 9.6
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealer 25 
                                       ++r++ d ++A +++++
  gi|386000759|ref|YP_005919058.1| 460 AQRSG-DLTEANRLFNE 475
                                       45556.*****999975 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleal 23 
                                       +l +l+ + ++ gd ++A  ++
  gi|386000759|ref|YP_005919058.1| 492 SLHQLGVLAQARGDIAEAYHLY 513
                                       4677887777767888886655 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleale 24 
                                       +l +l+l+ +  gd  +A++++ 
  gi|386000759|ref|YP_005919058.1| 532 SLHQLGLLAQLSGDIGEAKRLYG 554
                                       5789998888866*******996 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleale 24 
                                       +l++l+ + ++ g+  kAl ++ 
  gi|386000759|ref|YP_005919058.1| 572 SLFNLGVLAQNSGELKKALSLYG 594
                                       69****9999977******9996 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAleale 24 
                                       Al + al+ ++ g+ ++Al++ +
  gi|386000759|ref|YP_005919058.1| 612 ALAQSALLEEEEGNLEQALDLIR 634
                                       7888999999989*****99765 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0    0.0002      0.17      56     180 ..     271     395 ..     261     413 .. 0.86
   2 !    8.6   0.0    0.0013       1.1      51     178 ..     426     553 ..     422     562 .. 0.87
   3 ?    3.4   0.1     0.051        43      53     152 ..     548     647 ..     540     656 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--H CS
                              SNAP  56 eaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkeiaelyekelgdl 131
                                       + ++k  ++ ++l++k+  ++++ + +   + + +++eA + + ++ +i+++ g  +  A+   +++ l +   gd+
  gi|386000759|ref|YP_005919058.1| 271 RLHCKSLRIARELGDKSAVSRSLHQLGMLAQATgDITEARRLYGESLKILQDLGDKSGVARSLHQLGMLAQAT-GDI 346
                                       556666667777888888888877776666655599*******************************999988.*** PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP 132 ekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyek 180
                                        +A + Ye+  ++ e+ + k++ +k l ++  ++   ++  +A   y++
  gi|386000759|ref|YP_005919058.1| 347 VEARRFYEESLKISEELGDKSTISKSLHNLGAIAQATGDIVEAGRFYNE 395
                                       *************99999*******999999999999999999888875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                                       THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              SNAP  51 weeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkeiaelyek 126
                                       ++eA + + +  +++++l++k+  a ++ e +   +++ + +eA + ++++ +i  + g ++  A+   +++ l + 
  gi|386000759|ref|YP_005919058.1| 426 ISEARRLYGESLKIKRELGDKSGIAISLHECGILAQRSgDLTEANRLFNESLKISEDLGDMSGIARSLHQLGVLAQA 502
                                       57888899999999****************998888777*********************************99999 PP

                                       TT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              SNAP 127 elgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiy 178
                                         gd+ +A + Y +  ++ ++ +  +  +  l ++  l+   ++  +A  +y
  gi|386000759|ref|YP_005919058.1| 503 R-GDIAEAYHLYGDSLKILQDLGDMSGISRSLHQLGLLAQLSGDIGEAKRLY 553
                                       9.************99999988877777777777777777777777776666 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT CS
                              SNAP  53 eAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkeiaelyekel 128
                                       eA + + +  ++ ++l++k++  +++++ +   +++ + ++A + +  + +i ++ +  +  A    + a l e+e 
  gi|386000759|ref|YP_005919058.1| 548 EAKRLYGESLKISKELGDKSTFLKSLFNLGVLAQNSgELKKALSLYGDSLKIAQDLDDKTGIAFALAQSALLEEEE- 623
                                       4555555555555555555555555555444444443666666666666666666666666666666666555555. PP

                                       --HHHHHHHHHHHHHHHHHTT-HH CS
                              SNAP 129 gdlekAieaYekAaelyeqeeaka 152
                                       g+le+A++  ++A  l+ + e+ +
  gi|386000759|ref|YP_005919058.1| 624 GNLEQALDLIREAEALFMKLESPT 647
                                       777777777777777776655555 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.3     2e+03      25      49 ..     147     165 ..     141     168 .. 0.78
   2 ?    0.5   0.0       1.2     1e+03      24      53 ..     200     229 ..     197     239 .. 0.73
   3 ?    6.2   0.1     0.019        16       3      62 ..     296     358 ..     294     362 .. 0.79
   4 ?   -1.7   0.0       5.6   4.8e+03      40      63 ..     376     399 ..     372     402 .. 0.82
   5 ?    5.1   0.0     0.044        38       3      25 ..     416     438 ..     414     443 .. 0.85
   6 ?    5.9   0.1     0.024        20       5      61 ..     458     510 ..     457     516 .. 0.74
   7 ?    3.9   0.0       0.1        85       7      58 ..     540     595 ..     535     605 .. 0.73
   8 ?    4.9   1.5      0.05        43       2      61 ..     575     637 ..     574     642 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                            TPR_16  25 krdpssPdaaeAllllgdaalrqgr 49 
                                       +r      a++++ ++g+ +  +gr
  gi|386000759|ref|YP_005919058.1| 147 RR------APDFWRYRGNYYELKGR 165
                                       44......455*******9999987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                            TPR_16  24 lkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       l++ +++ +++  l +lg++ + +g+++ A
  gi|386000759|ref|YP_005919058.1| 200 LEKVKDEKETVKILDELGEISYNLGDYDNA 229
                                       555566666666666899999999999988 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.019
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       l+++a + gd ++A++++ + lk      d       a++l  lg +a + g+  eA+ +y++ l+
  gi|386000759|ref|YP_005919058.1| 296 LGMLAQATGDITEARRLYGESLKIL---QDlgdksgVARSLHQLGMLAQATGDIVEARRFYEESLK 358
                                       89999*************9888876...33344666888888888888888999999888888775 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.6
                            TPR_16  40 lgdaalrqgrlaeAaalyraalra 63 
                                       lg +a + g+  eA  +y++ l+ 
  gi|386000759|ref|YP_005919058.1| 376 LGAIAQATGDIVEAGRFYNEGLKI 399
                                       888999999999*99999997665 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.044
                            TPR_16   3 laraalragdyddAaaaleaalk 25 
                                       l+++a++ gd  +A++++ + lk
  gi|386000759|ref|YP_005919058.1| 416 LGMLAYDTGDISEARRLYGESLK 438
                                       89999999999999999977665 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.024
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                        +a r+gd ++A +++++ lk   +  d    + + ++++ ++g la A+  +++a+
  gi|386000759|ref|YP_005919058.1| 458 ILAQRSGDLTEANRLFNESLKISEDLGD----MSGIARSLHQLGVLAQARGDIAEAY 510
                                       5799*****************9966666....5677777777777777774444444 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.1
                            TPR_16   7 alragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAa.alyr 58 
                                       a  +gd  +A +++ + lk  ++  d      +l++lg++a   g+l++A+  + +
  gi|386000759|ref|YP_005919058.1| 540 AQLSGDIGEAKRLYGESLKISKELGDkstFLKSLFNLGVLAQNSGELKKALsLYGD 595
                                       5556777777777777777777776677777899****************955544 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.05
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq...grlaeAaalyraal 61 
                                       +l+ +a ++g+  +A+ ++   lk + +  d    +++l+++al     g+l+ A++l+r+a 
  gi|386000759|ref|YP_005919058.1| 575 NLGVLAQNSGELKKALSLYGDSLKIAQDLDDKTGIAFALAQSALLEeeeGNLEQALDLIREAE 637
                                       6788999999999999999999999999999999999999999988899**********9985 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       1.1   9.4e+02      24      40 ..     142     158 ..     140     192 .. 0.85
   2 ?    2.6   0.0      0.38   3.2e+02       4      25 ..     213     234 ..     210     243 .. 0.86
   3 ?    3.3   0.1      0.22   1.9e+02       4      29 ..     293     318 ..     290     325 .. 0.83
   4 ?    3.1   0.1      0.25   2.2e+02       4      31 ..     333     360 ..     330     364 .. 0.85
   5 ?    2.1   0.0      0.55   4.7e+02       5      29 ..     414     438 ..     410     442 .. 0.85
   6 ?    3.2   0.0      0.23     2e+02       8      32 ..     457     481 ..     452     485 .. 0.84
   7 ?    0.6   0.2       1.6   1.4e+03       4      29 ..     493     518 ..     490     525 .. 0.76
   8 ?    0.4   0.0       1.9   1.6e+03       6      30 ..     535     559 ..     531     564 .. 0.79
   9 ?    2.2   0.0       0.5   4.3e+02      10      42 ..     579     614 ..     573     616 .. 0.67
  10 ?    7.0   1.2     0.015        12       3      32 ..     612     641 ..     609     654 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.1
                            TPR_14  24 lrralalaPddaeawll 40 
                                       l++++++aPd+++++  
  gi|386000759|ref|YP_005919058.1| 142 LDDVIRRAPDFWRYRGN 158
                                       77888999999888754 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.38
                            TPR_14   4 llalaeallalGdpdeAiallr 25 
                                       l +l+e+ ++lGd+d A ++l+
  gi|386000759|ref|YP_005919058.1| 213 LDELGEISYNLGDYDNASDYLK 234
                                       77899999**********9997 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.22
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       l +l+ +  a Gd  eA++l+ + l+
  gi|386000759|ref|YP_005919058.1| 293 LHQLGMLAQATGDITEARRLYGESLK 318
                                       56788888999*********998887 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.25
                            TPR_14   4 llalaeallalGdpdeAiallrralala 31 
                                       l +l+ +  a Gd  eA++ +++ l+  
  gi|386000759|ref|YP_005919058.1| 333 LHQLGMLAQATGDIVEARRFYEESLKIS 360
                                       66888889999************99865 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.55
                            TPR_14   5 lalaeallalGdpdeAiallrrala 29 
                                        +l+ + +  Gd  eA++l+ + l+
  gi|386000759|ref|YP_005919058.1| 414 HQLGMLAYDTGDISEARRLYGESLK 438
                                       6788899999*********988876 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.23
                            TPR_14   8 aeallalGdpdeAiallrralalaP 32 
                                       + +  ++Gd+ eA +l+++ l+   
  gi|386000759|ref|YP_005919058.1| 457 GILAQRSGDLTEANRLFNESLKISE 481
                                       5667899*************99766 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 1.6
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       l +l+ +  a+Gd +eA  l+ + l+
  gi|386000759|ref|YP_005919058.1| 493 LHQLGVLAQARGDIAEAYHLYGDSLK 518
                                       56777778889999999888877776 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.9
                            TPR_14   6 alaeallalGdpdeAiallrralal 30 
                                       +l+ +   +Gd  eA +l+ + l+ 
  gi|386000759|ref|YP_005919058.1| 535 QLGLLAQLSGDIGEAKRLYGESLKI 559
                                       667777778*********9998876 PP

  == domain 9  score: 2.2 bits;  conditional E-value: 0.5
                            TPR_14  10 allalGdpdeAiallrrala..laPdda.eawllla 42 
                                       +  ++G++++A+ l+ + l+  ++ dd   + ++la
  gi|386000759|ref|YP_005919058.1| 579 LAQNSGELKKALSLYGDSLKiaQDLDDKtGIAFALA 614
                                       455789*********999983334455323556666 PP

  == domain 10  score: 7.0 bits;  conditional E-value: 0.015
                            TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                                       al++ a ++++ G++++A++l r+a al+ 
  gi|386000759|ref|YP_005919058.1| 612 ALAQSALLEEEEGNLEQALDLIREAEALFM 641
                                       455667778999*************99875 PP

>> DUF3151  Protein of unknown function (DUF3151)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0056       4.8      86     113 ..     245     272 ..     240     278 .. 0.89
   2 ?    0.6   0.0      0.64   5.5e+02      90     113 ..     289     312 ..     285     327 .. 0.80
   3 ?    1.9   0.0      0.26   2.2e+02      88     113 ..     327     352 ..     319     362 .. 0.89
   4 ?   -2.1   0.0       4.7     4e+03      89     111 ..     488     510 ..     486     524 .. 0.80
   5 ?   -2.6   0.0       6.3   5.4e+03      89     112 ..     528     551 ..     525     553 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0056
                           DUF3151  86 pnrGfLralaaLaraaeaigeedEaerc 113
                                        nrG+Lr+l++L+  a+  g+ +E  r+
  gi|386000759|ref|YP_005919058.1| 245 YNRGVLRSLHQLGILAKDRGDIAESCRL 272
                                       5*****************9999998875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.64
                           DUF3151  90 fLralaaLaraaeaigeedEaerc 113
                                       + r+l++L++ a+a g+  Ea+r+
  gi|386000759|ref|YP_005919058.1| 289 VSRSLHQLGMLAQATGDITEARRL 312
                                       569999999999999999999986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.26
                           DUF3151  88 rGfLralaaLaraaeaigeedEaerc 113
                                        G+ r+l++L++ a+a g+  Ea+r 
  gi|386000759|ref|YP_005919058.1| 327 SGVARSLHQLGMLAQATGDIVEARRF 352
                                       6999***************9999986 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.7
                           DUF3151  89 GfLralaaLaraaeaigeedEae 111
                                       G+ r+l++L+  a+a g+ +Ea 
  gi|386000759|ref|YP_005919058.1| 488 GIARSLHQLGVLAQARGDIAEAY 510
                                       78899999999999988888864 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 6.3
                           DUF3151  89 GfLralaaLaraaeaigeedEaer 112
                                       G+ r+l++L+  a+  g+  Ea+r
  gi|386000759|ref|YP_005919058.1| 528 GISRSLHQLGLLAQLSGDIGEAKR 551
                                       778999999999998888888887 PP

>> DUF2972  Protein of unknown function (DUF2972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.6   1.4e+03     170     189 ..     254     273 ..     185     283 .. 0.70
   2 ?    4.9   0.0     0.026        22     171     199 .]     335     363 ..     329     363 .. 0.92
   3 ?    3.2   0.0     0.084        72     171     199 .]     375     403 ..     367     403 .. 0.89
   4 ?   -0.2   0.0      0.95   8.1e+02     171     194 ..     495     518 ..     493     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                           DUF2972 170 eeLvylkqeRpDiieSWkyY 189
                                       ++L  l++ R Di eS +  
  gi|386000759|ref|YP_005919058.1| 254 HQLGILAKDRGDIAESCRLH 273
                                       36778899999999987765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.026
                           DUF2972 171 eLvylkqeRpDiieSWkyYqeFermCeel 199
                                       +L +l+q   Di+e  ++Y+e +++ eel
  gi|386000759|ref|YP_005919058.1| 335 QLGMLAQATGDIVEARRFYEESLKISEEL 363
                                       68899*******************99986 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.084
                           DUF2972 171 eLvylkqeRpDiieSWkyYqeFermCeel 199
                                       +L  ++q   Di+e  ++Y+e +++  el
  gi|386000759|ref|YP_005919058.1| 375 NLGAIAQATGDIVEAGRFYNEGLKIASEL 403
                                       67889****************99988775 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.95
                           DUF2972 171 eLvylkqeRpDiieSWkyYqeFer 194
                                       +L  l+q R Di e ++ Y + ++
  gi|386000759|ref|YP_005919058.1| 495 QLGVLAQARGDIAEAYHLYGDSLK 518
                                       58899***********99977665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.023        20      39     152 ..     294     396 ..     284     407 .. 0.67
   2 ?    4.7   0.3     0.022        19      35      91 ..     410     463 ..     401     665 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                                       SSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEE CS
                               DAO  39 rnsgllhsglrylpeaselarlslealeelreleeelgididyrrtGllslaadeeelealdkllallleagldael 115
                                       +  g+l+++  +  e     rl+ e+l+ l++l ++ g+   +++ G+l  a+++    + ++ +++   + + +el
  gi|386000759|ref|YP_005919058.1| 294 HQLGMLAQATGDITE---ARRLYGESLKILQDLGDKSGVARSLHQLGMLAQATGD--IVEARRFYEES--LKISEEL 363
                                       556777776654553...349*******************************975..66667888875..3344444 PP

                                       EEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHH CS
                               DAO 116 ldaeevrelepalpgllgalfypdtgqvdpakltaal 152
                                        d++ + +    l + lga+   ++ +v++ ++ +  
  gi|386000759|ref|YP_005919058.1| 364 GDKSTISKS---L-HNLGAIAQATGDIVEAGRFYNEG 396
                                       444412111...1.34566666666666666665554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                                       SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEES CS
                               DAO  35 gaSgrnsgllhsglrylpeaselarlslealeelreleeelgididyrrtGllslaa 91 
                                       ++S +  g+l+    +     e  rl+ e+l+  rel ++ gi i ++++G l   +
  gi|386000759|ref|YP_005919058.1| 410 ASSLHQLGMLAYDTGDIS---EARRLYGESLKIKRELGDKSGIAISLHECGILAQRS 463
                                       455555666655443333...445999999999999999999999999999987744 PP

>> DUF1876  Domain of unknown function (DUF1876)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0092       7.8      47      76 ..     282     309 ..     274     312 .. 0.89
   2 ?    2.5   0.1      0.17   1.4e+02      48      75 ..     323     348 ..     319     352 .. 0.84
   3 ?    0.3   0.1      0.79   6.7e+02      49      78 ..     484     511 ..     478     512 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF1876  47 eiGdElAaaRALsdLaeqLleaaaedieav 76 
                                       e Gd  A++R L++L+  +l++a+ di+++
  gi|386000759|ref|YP_005919058.1| 282 ELGDKSAVSRSLHQLG--MLAQATGDITEA 309
                                       78*************8..79******9986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF1876  48 iGdElAaaRALsdLaeqLleaaaediea 75 
                                        Gd   +aR L++L+  +l++a+ di +
  gi|386000759|ref|YP_005919058.1| 323 LGDKSGVARSLHQLG--MLAQATGDIVE 348
                                       689999********8..79999999866 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                           DUF1876  49 GdElAaaRALsdLaeqLleaaaedieavth 78 
                                       Gd    aR L++L+   l++a  di+++ h
  gi|386000759|ref|YP_005919058.1| 484 GDMSGIARSLHQLG--VLAQARGDIAEAYH 511
                                       6666789******8..79999999998765 PP

>> SRR1  SRR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.46     4e+02       6      24 ..     283     301 ..     283     313 .. 0.77
   2 ?   -0.5   0.0       1.5   1.3e+03       7      23 ..     324     340 ..     323     346 .. 0.80
   3 ?   -1.7   0.0       3.5     3e+03      13      22 ..     410     419 ..     403     421 .. 0.76
   4 ?    0.4   0.0      0.81   6.9e+02       6      23 ..     483     500 ..     483     509 .. 0.84
   5 ?    6.1   0.1     0.013        11       6      33 ..     523     550 ..     523     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.46
                              SRR1   6 LGsfsesssaryQLAllle 24 
                                       LG  s+ s++++QL +l  
  gi|386000759|ref|YP_005919058.1| 283 LGDKSAVSRSLHQLGMLAQ 301
                                       5666778999******975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                              SRR1   7 GsfsesssaryQLAlll 23 
                                       G  s+  ++++QL +l 
  gi|386000759|ref|YP_005919058.1| 324 GDKSGVARSLHQLGMLA 340
                                       5666778999****995 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.5
                              SRR1  13 ssaryQLAll 22 
                                        s+++QL +l
  gi|386000759|ref|YP_005919058.1| 410 ASSLHQLGML 419
                                       6899***998 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.81
                              SRR1   6 LGsfsesssaryQLAlll 23 
                                       LG +s+  ++++QL +l 
  gi|386000759|ref|YP_005919058.1| 483 LGDMSGIARSLHQLGVLA 500
                                       799999999*****9996 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.013
                              SRR1   6 LGsfsesssaryQLAlllelveelkies 33 
                                       LG +s+ s++++QL ll  l  ++++++
  gi|386000759|ref|YP_005919058.1| 523 LGDMSGISRSLHQLGLLAQLSGDIGEAK 550
                                       8999999***********9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 4393.06
//
Query:       gi|386000760|ref|YP_005919059.1|  [L=420]
Description: Signal recognition particle GTPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-07   31.0   0.5    1.1e-06   29.2   0.1    2.1  2  AAA_16         AAA ATPase domain
     0.0018   18.6   0.5       0.28   11.5   0.1    2.7  2  AAA_22         AAA domain
     0.0097   14.9   0.5          3    6.7   0.0    2.5  3  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.034   13.7   0.0       0.28   10.7   0.0    2.1  2  AAA_7          P-loop containing dynein motor region
        0.2   11.4   0.0       0.41   10.4   0.0    1.5  1  AAA_29         P-loop containing region of AAA domain
       0.23   11.9   2.6       0.26   11.7   0.5    2.2  2  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
       0.24   10.6   6.1      0.075   12.3   2.5    1.9  2  KAP_NTPase     KAP family P-loop domain
       0.25   11.3   0.9         27    4.8   0.0    2.6  2  JmjN           jmjN domain
        1.9    9.0   6.9       0.41   11.1   2.5    2.2  2  KELK           KELK-motif containing domain of MRCK Ser/Thr p


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   5.3e-10   1.1e-06      10     149 ..      41     217 ..      38     240 .. 0.63
   2 ?   -1.9   0.0         2   3.9e+03      96     101 ..     347     352 ..     295     390 .. 0.55

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.3e-10
                            AAA_16  10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrql 85 
                                       e+L++ +e   s+r e  l+ G +G+GKs+ +++ll+ +  +++++  +   dql         ++ +++++++  +
  gi|386000760|ref|YP_005919059.1|  41 EELRDRIE--ISDRKEKYLFLGFRGSGKSTELNRLLDMIDPHRFLVvSYSIRDQL--------NVSDFDFRDFFVSM 107
                                       56666666..445557789***********************9666455555555........44445555555555 PP

                            AAA_16  86 lde..............aesaeleawrekleeala...........................avpelagaea..... 116
                                       + +              + + ++ ++ ++++++ +                                          
  gi|386000760|ref|YP_005919059.1| 108 ALMiydraevdgvklnrDIEEDFKDFVKRITKVEEdevsgsraagisltlakvlllklgreaK--------Treyvr 176
                                       555222222222221123333444444444444446666666666666666665555555552........044445 PP

                            AAA_16 117 .......srllellkrll.allsrderplvlvlDdlqwade 149
                                              s+l + l+ l+ +   +++++lv+++Ddl+++  
  gi|386000760|ref|YP_005919059.1| 177 kelemqiSDLIQRLNWLIvDVEDKTDKKLVVIVDDLDKLTR 217
                                       5557888999999999998777777888*********9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                            AAA_16  96 awrekl 101
                                         r++ 
  gi|386000760|ref|YP_005919059.1| 347 KLRRTY 352
                                       222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00014      0.28      11     111 ..      59     223 ..      50     247 .. 0.61
   2 ?   -2.7   0.0       3.2   6.4e+03     108     117 ..     344     353 ..     314     373 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                            AAA_22  11 tGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka................ 70 
                                        G  G+GK+t l+rll+  d +      r  vv++ +  + + +d+ +r+++  + l   +                
  gi|386000760|ref|YP_005919059.1|  59 LGFRGSGKSTELNRLLDMIDPH------RFLVVSYSIRDQLNVSDFdFRDFFVSMALMIYDraevdgvklnrdieed 129
                                       6888999999999999998755......4445544444444444444444444443333333333445555555555 PP

                            AAA_22  71 .................................................erlsseellealeqalrarav....iel 94 
                                                                                         + + ++l+++l+  + +  +    + +
  gi|386000760|ref|YP_005919059.1| 130 fkdfvkritkveedevsgsraagisltlakvlllklgreaktreyvrkeLEMQISDLIQRLNWLIVDVEDktdkKLV 206
                                       55555555555555555666666666666666665555445577766666666666666666666666668888999 PP

                            AAA_22  95 liiDEaqhlrseealee 111
                                       +i+D+ ++l++ e+ ee
  gi|386000760|ref|YP_005919059.1| 207 VIVDDLDKLTRVEQAEE 223
                                       99999999953444333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                            AAA_22 108 aleeLrslln 117
                                       ale+Lr+ ++
  gi|386000760|ref|YP_005919059.1| 344 ALEKLRRTYD 353
                                       3333333333 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0015         3      12      40 ..      50      78 ..      46      87 .. 0.84
   2 !    5.7   0.2    0.0029       5.8     231     264 ..     191     224 ..     161     230 .. 0.76
   3 ?   -3.2   0.1       1.5     3e+03     129     166 ..     326     363 ..     308     366 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0015
                     TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekllrair 40
                                      ++ +++ l++G  GsGK++ l+ ll+ i 
  gi|386000760|ref|YP_005919059.1| 50 SDRKEKYLFLGFRGSGKSTELNRLLDMID 78
                                      556678899****************9885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0029
                     TrwB_AAD_bind 231 ikallslpesrerrlWfflDElpaLgrleelksl 264
                                          +++++++ +++l +++D l++L r+e+ +++
  gi|386000760|ref|YP_005919059.1| 191 NWLIVDVEDKTDKKLVVIVDDLDKLTRVEQAEEF 224
                                       445677999*******************997765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.5
                     TrwB_AAD_bind 129 kksnaallralltadleeLkellagteaaalvaeeaer 166
                                        k  ++  ++++++d+e   e l++t   +l++ ++ r
  gi|386000760|ref|YP_005919059.1| 326 IKAYRNKREKIVNEDVESALEKLRRTYDRTLTEAHKRR 363
                                       33345555666666666666666666666666665555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.28      31      76 ..      51      96 ..      47     100 .. 0.88
   2 ?    0.0   0.1      0.26   5.1e+02      99     110 ..     202     213 ..     199     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsan 76
                                      ++k + l+ G  G+GK++ +++ll+ +d+ ++l+++ ++  q + +
  gi|386000760|ref|YP_005919059.1| 51 DRKEKYLFLGFRGSGKSTELNRLLDMIDPHRFLVVSYSIRDQLNVS 96
                                      678899***************************9999888877665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.26
                             AAA_7  99 gkklvvFvDDln 110
                                        kklvv vDDl+
  gi|386000760|ref|YP_005919059.1| 202 DKKLVVIVDDLD 213
                                       79********97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.41      18      38 ..      48      69 ..      43      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                            AAA_29 18 eidlkg.atlltGpsGsGKSTl 38
                                      ei+ +   +l+ G  GsGKST 
  gi|386000760|ref|YP_005919059.1| 48 EISDRKeKYLFLGFRGSGKSTE 69
                                      55555559*************5 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.6   9.2e+03      13      29 ..     174     190 ..     168     205 .. 0.56
   2 ?   11.7   0.5   0.00013      0.26      23      55 ..     323     354 ..     315     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHHHHH CS
                       GlutR_dimer  13 feawlkslevvptIkal 29 
                                       ++++  +++++++I++l
  gi|386000760|ref|YP_005919059.1| 174 YVRKELEMQISDLIQRL 190
                                       33333444444444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHS-S..----- CS
                       GlutR_dimer  23 vptIkalrekaeeireeeleralkklaldgedr 55 
                                       + tIka+r+k e+i++e +e al+kl+ ++ dr
  gi|386000760|ref|YP_005919059.1| 323 DATIKAYRNKREKIVNEDVESALEKLR-RTYDR 354
                                       679***********************8.44444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.5   3.7e-05     0.075      30     186 ..      63     216 ..      62     225 .. 0.60
   2 ?   -3.5   0.1       2.4   4.7e+03     254     287 ..     339     372 ..     327     389 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                        KAP_NTPase  30 GsGKssllnkledelkefakpvrflfaefnawsf.kggddavaellaaLadaleeeygqlatkllrakk.....lka 100
                                       GsGKs+ ln+l d ++ +    rfl+++++   + + +d  +++++ ++a  ++ ++++  +kl r  +     + +
  gi|386000760|ref|YP_005919059.1|  63 GSGKSTELNRLLDMIDPH----RFLVVSYSIRDQlNVSDFDFRDFFVSMALMIYDRAEVDGVKLNRDIEedfkdFVK 135
                                       788888888888888777....8888888754431444556788888888888888888877777775544444333 PP

                        KAP_NTPase 101 lkikgkiklrkacaiplvlilevalflliegasllavlsraaklkeeaplkklqteveelladmektLda....lqk 173
                                       ++ k+  + ++++ ++   +++ +++ll  g        r ak   e  +k+l ++++ l+++++  + +     +k
  gi|386000760|ref|YP_005919059.1| 136 RITKVEEDEVSGSRAAGISLTLAKVLLLKLG--------REAKT-REYVRKELEMQISDLIQRLNWLIVDvedkTDK 203
                                       3333333322222222222222233333222........22222.23445667777777777777777668888999 PP

                        KAP_NTPase 174 rlVvviDdLDrce 186
                                       +lVv++DdLD ++
  gi|386000760|ref|YP_005919059.1| 204 KLVVIVDDLDKLT 216
                                       **********987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                        KAP_NTPase 254 revkkvlmeaveaseettesesrdetlgnsasks 287
                                       ++v+++l + ++++++t ++  + ++l    sk+
  gi|386000760|ref|YP_005919059.1| 339 EDVESALEKLRRTYDRTLTEAHKRRALAIHESKE 372
                                       4455556666666666655555554444433333 PP

>> JmjN  jmjN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.024        48       6      14 ..      21      29 ..      20      32 .. 0.93
   2 ?    4.8   0.0     0.013        27       7      23 ..     127     146 ..     127     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                                      -HHHHC-HH CS
                              JmjN  6 TeeEFkdpl 14
                                      T eEF+d++
  gi|386000760|ref|YP_005919059.1| 21 TAEEFRDFY 29
                                      89******8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                                       HHHHC-HHHHHHHHHH...H CS
                              JmjN   7 eeEFkdplkYiekiep...l 23 
                                       ee+Fkd+ k i k+e+    
  gi|386000760|ref|YP_005919059.1| 127 EEDFKDFVKRITKVEEdevS 146
                                       79******999999875444 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.1   6.2e+03      17      30 ..     177     190 ..     164     208 .. 0.51
   2 ?   11.1   2.5    0.0002      0.41       8      55 ..     325     374 ..     322     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                              KELK  17 eelqkelaeaqErl 30 
                                       +el+ +++++  rl
  gi|386000760|ref|YP_005919059.1| 177 KELEMQISDLIQRL 190
                                       33444444443333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                              KELK   8 qlrllkqEkeelq.kelaeaqErlk.sqkkeLkdaisqrklamqefsevn 55 
                                       ++++ ++ +e++   +++ a E+l+ + ++ L +a+++r la++e +e+ 
  gi|386000760|ref|YP_005919059.1| 325 TIKAYRNKREKIVnEDVESALEKLRrTYDRTLTEAHKRRALAIHESKEAR 374
                                       678888889987626677789***725699***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2864.52
//
Query:       gi|386000761|ref|YP_005919060.1|  [L=134]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-19   67.9   0.0    8.6e-19   67.5   0.0    1.2  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.014   16.0   0.0      0.022   15.4   0.0    1.3  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   9.6e-23   8.6e-19       1      87 [.       4      90 ..       4      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 9.6e-23
                                      HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEE CS
                    Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieG 79
                                      +++ +r+ l+++k + +AT+d++G+Pnv++v++ +  ++++i +  n   ++++nl+enp+v++l +d e+ ++++i+G
  gi|386000761|ref|YP_005919060.1|  4 MPPDVRATLEKQKPAPVATADASGTPNVVYVGFLKVLDDETIMIGDNFFYKTAANLAENPKVSILCYDTETKKSFQIKG 82
                                      67899***************************99999999*************************************** PP

                                      EEEEESCH CS
                    Putative_PNPOx 80 taelvsdg 87
                                      ta+++++g
  gi|386000761|ref|YP_005919060.1| 83 TATVHKEG 90
                                      *****987 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.5e-06     0.022      19      99 ..      14      87 ..       6      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                                      GGGEEEEEEE-T.TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEE CS
                   Pyridox_oxase_2 19 kstefqlaTvdeeegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkaf 97
                                      k++   +aT d ++g+P+v   v+ gfl+  +  ++   ++ D    K++   ++n++v ++ y +et++ f i+G+a+
  gi|386000761|ref|YP_005919060.1| 14 KQKPAPVATAD-ASGTPNV---VYVGFLKVLD--DE-TIMIGDNFFYKTAANLAENPKVSILCYDTETKKSFQIKGTAT 85
                                      56667778888.5788876...5556777653..33.457788888888777769***********************9 PP

                                      EE CS
                   Pyridox_oxase_2 98 vi 99
                                      v+
  gi|386000761|ref|YP_005919060.1| 86 VH 87
                                      97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 986.56
//
Query:       gi|386000762|ref|YP_005919061.1|  [L=134]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-15   54.8   0.0    1.1e-14   54.4   0.0    1.2  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.037   13.8   0.0      0.038   13.8   0.0    1.2  1  DUF447           Protein of unknown function (DUF447)
      0.057   14.0   0.0      0.081   13.5   0.0    1.2  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
       0.12   11.9   0.0       0.15   11.7   0.0    1.1  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   2.4e-18   1.1e-14       1      87 [.       4      90 ..       4      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.4e-18
                                      HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEE CS
                    Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieG 79
                                      ++ e+re l+++     AT++ +G+Pnv+ ++  +  +++++vfa n   ++++nl+enp ++++ ++++ + +++i+G
  gi|386000762|ref|YP_005919061.1|  4 MPTEVRETLEKQWPIPFATASTEGKPNVVFMGILKVKDDETLVFADNFFNKTAANLAENPWASVVCWSKDPRSSYQIKG 82
                                      56799***************************99999999*************************************** PP

                                      EEEEESCH CS
                    Putative_PNPOx 80 taelvsdg 87
                                      ++++ ++g
  gi|386000762|ref|YP_005919061.1| 83 RVAFAEEG 90
                                      **998876 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.6e-06     0.038       7      56 ..      22      75 ..      20     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-06
                                      EE-TT.-EEEEEEEEEE.SSSE..EEEEEETTSHHHHHHHHHSEEEE.EE---HH CS
                            DUF447  7 Tksek.rpnaaPiGviv.kgdk..vvlrlfkgsrTleNllengelvi.nvtdDpl 56
                                      T s++ +pn+  +G+ + k+d+  v++  f  ++T++Nl+en+++++ +  +Dp+
  gi|386000762|ref|YP_005919061.1| 22 TASTEgKPNVVFMGILKvKDDEtlVFADNFF-NKTAANLAENPWASVvCWSKDPR 75
                                      6666779*********974444567777777.59**********96516667776 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.081      19      98 ..      14      86 ..       4      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                      GGGEEEEEEE-T.TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEE CS
                   Pyridox_oxase_2 19 kstefqlaTvdeeegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkaf 97
                                      k+  + +aT + +egkP+   vvf g l+ k   +++l f +D   +K++   ++n+++ +v + k+ r+ + i+G++ 
  gi|386000762|ref|YP_005919061.1| 14 KQWPIPFATAS-TEGKPN---VVFMGILKVK--DDETLVF-ADNFFNKTAANLAENPWASVVCWSKDPRSSYQIKGRVA 85
                                      55566677877.577886...7999999986..4666666.67777777666669*********************987 PP

                                      E CS
                   Pyridox_oxase_2 98 v 98
                                      +
  gi|386000762|ref|YP_005919061.1| 86 F 86
                                      5 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.3e-05      0.15      19      94 ..      21      96 ..       6     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                     Pyrid_ox_like 19 ttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsGtaevvedrakieel 94
                                      +t +++gk ++  M + kv++d++l f  +  ++ ++++++++ ++++  +++ ++  +++G++++ e+  + ee+
  gi|386000762|ref|YP_005919061.1| 21 ATASTEGKPNVVFMGILKVKDDETLVFADNFFNKTAANLAENPWASVVCWSKDPRSSYQIKGRVAFAEEGPIFEEM 96
                                      5677788899999******************************9888888888888889*****999988777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1035.52
//
Query:       gi|386000763|ref|YP_005919062.1|  [L=463]
Description: Cobyrinic Acid a,c-diamide synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-38  132.9   0.0    1.5e-38  132.4   0.0    1.2  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    6.1e-17   62.1   0.2    1.8e-12   47.5   0.0    2.9  3  AAA_26     AAA domain
    1.1e-15   57.8   0.0    1.7e-15   57.2   0.0    1.3  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.053   13.4   0.0    1.6  1  MobB       Molybdopterin guanine dinucleotide synthesis prote
      0.063   13.1   0.0       0.22   11.4   0.0    1.8  2  SNO        SNO glutamine amidotransferase family
       0.16   11.8   0.0       0.31   10.8   0.0    1.4  1  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.0   5.1e-42   1.5e-38       1     191 [.     255     443 ..     255     447 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 5.1e-42
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       +i+v+ ++a+++y+  +l+++e  +++ v ++p++d+sl+e +d ++++Gg++++ +++l++++++  +i+ a+e+g
  gi|386000763|ref|YP_005919062.1| 255 RIGVALDEAFNFYYrdNLELIELSGAEVVPVSPVHDQSLPE-VDGLYIGGGYPELYAKELSENRSMIGSIRGAHEEG 330
                                       699************************************66.*********************************** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGr 148
                                       +p++++CGGl++L+eei d  g+     + + +gl++++t+ + +++++ +eg+        ++g+ + G+E+H+++
  gi|386000763|ref|YP_005919062.1| 331 VPIFAECGGLMYLCEEI-DWGGE-----SRPAVGLVPAKTRKGGQRIVSYTEGTFLRdcsmGPRGASFLGHEFHHSE 401
                                       ****************7.56787.....99***********************976699999999************ PP

                          GATase_3 149 tilkekakpllkvkv..ggnng.ekdGavkksedgnvlGtYlHglf 191
                                        +l+++a+  ++++   g++++  +dG+v     gn++++Y H++ 
  gi|386000763|ref|YP_005919062.1| 402 LVLDPGAEVEYAIRLrrGTGIDgVRDGIVD----GNLVASYNHFHG 443
                                       *************987555555899***94....6********985 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0     9e-05      0.27       3      34 ..       8      39 ..       7      70 .. 0.86
   2 !   47.5   0.0   6.1e-16   1.8e-12      87     194 ..      72     185 ..      61     188 .. 0.84
   3 ?   -0.9   0.0       0.4   1.2e+03     120     142 ..     271     293 ..     261     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                      ++++g + ++GKT++ +gL++al++++  v+ 
  gi|386000763|ref|YP_005919062.1|  8 VLLAGDRSSSGKTTIVAGLLSALRNRDLTVQS 39
                                      7899999****************988877765 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 6.1e-16
                            AAA_26  87 dlekivkelekdadivvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealr.qknvrvlG 161
                                       ++ ++  + ++ a++ v+EG+ gl ++   +  ++a+iak+l+apvilV+ +++ t  +++l   +   +  v ++G
  gi|386000763|ref|YP_005919062.1|  72 TVREVYAHAAEGAEVAVIEGVRGLYEGYDGDrGSTAQIAKMLKAPVILVVDARSITRSAAALVKGYIDfDPAVDIRG 148
                                       45555345566789***********9988777**********************999999999998876789***** PP

                            AAA_26 162 vilNkvrnp....envetlekksgipvlGvvPylpdl 194
                                       vilNkv       +++ +++ + g++v+Gv+P ++++
  gi|386000763|ref|YP_005919062.1| 149 VILNKVGGGrhadKAISAIRDHAGVEVVGVIPRDDSM 185
                                       *****8666444469*****************98765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.4
                            AAA_26 120 nadiaknlgapvilVargglgti 142
                                       n ++++  ga+v+ V +++++++
  gi|386000763|ref|YP_005919062.1| 271 NLELIELSGAEVVPVSPVHDQSL 293
                                       8899999**********998764 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   5.8e-19   1.7e-15       2     118 ..       9     185 ..       8     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 5.8e-19
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...........HTTEB-HHHH............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxx............. RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...........leglendiep............. 54 
                                       ++a+  + +GKTt++a+L+ al +r l V+ +++  +    ++           l+g  + +e+             
  gi|386000763|ref|YP_005919062.1|   9 LLAGDRSSSGKTTIVAGLLSALRNRDLTVQSYKVALDYIDPSYhtgitgrwcrnLDGHLMPEETvrevyahaaegae 85 
                                       678999***************************9999666665446555555555555555555************* PP

                                       ....................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TT CS
                                       ....................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....................................dlkrllellealgkkkall...lkiagvvlnrvdgeneetl 92 
                                                                           d+ ++ ++++al+k++ ++   ++i gv+ln+v+g ++  +
  gi|386000763|ref|YP_005919062.1|  86 vaviegvrglyegydgdrgstaqiakmlkapvilvvDARSITRSAAALVKGYIDFdpaVDIRGVILNKVGGGRHADK 162
                                       ****************************************************999********************** PP

                                       CHHHHHHHHHHCTS-EEEEEE--CCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  93 lkealeelkqrygvpvlgviprdeav 118
                                        ++a++++    gv+v+gviprd++ 
  gi|386000763|ref|YP_005919062.1| 163 AISAIRDHA---GVEVVGVIPRDDSM 185
                                       *******99...***********986 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.053       7      38 ..      14      45 ..       8      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                              MobB  7 ksgsGKTtLleklipelkarglrvgtiKhahh 38
                                      +s sGKTt++  l+++l++r+l+v   K a +
  gi|386000763|ref|YP_005919062.1| 14 RSSSGKTTIVAGLLSALRNRDLTVQSYKVALD 45
                                      699*********************99887655 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.72   2.2e+03     118     158 ..     134     179 ..     123     191 .. 0.70
   2 ?   11.4   0.0   7.2e-05      0.22      15      87 ..     275     349 ..     263     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
                                       ETTTCSEEEEEESS--EEEEE-.....TTTCEEEEECTT.EEEEEE CS
                               SNO 118 fknliekftavfiraPvieeil....ddeavkvlyeldg.eivvak 158
                                       +k++i+  +av ir  ++++++     d+a+  ++++ g e+v++ 
  gi|386000763|ref|YP_005919062.1| 134 VKGYIDFDPAVDIRGVILNKVGggrhADKAISAIRDHAGvEVVGVI 179
                                       5666766688999999999997322245667788888888898876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.2e-05
                                       HHHTTSEEEEE-..SGGGGCC-SEEEE-SS-HHHHHH.HHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETT CS
                               SNO  15 ikkclaenktvk..rkedlaevdaliiPGGestamsk.liertglyedllefvknsekvvlGtCaGlillskelen 87 
                                       i+ ++ae   v   + + l evd+l i GG     +k l e+  ++ +++  +++   +++  C Gl++l++e++ 
  gi|386000763|ref|YP_005919062.1| 275 IELSGAEVVPVSpvHDQSLPEVDGLYIGGGYPELYAKeLSENRSMIGSIRG-AHEEGVPIFAECGGLMYLCEEIDW 349
                                       56666666555411345699**********877655417777777777766.56666***************9964 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.31      40     110 ..     274     346 ..     251     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                       EEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHH..HHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                         DJ-1_PfpI  40 vkgsrGlkvtvdaslddvkaaeyDalvlpGGrag..perlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                         + +G++v++   + d +  e D l + GG     +++l+en  ++  ++ ++e+g +++a C g + L ++
  gi|386000763|ref|YP_005919062.1| 274 LIELSGAEVVPVSPVHDQSLPEVDGLYIGGGYPElyAKELSENRSMIGSIRGAHEEGVPIFAECGGLMYLCEE 346
                                       5567889999999999999999*********8743399****************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 3240.86
//
Query:       gi|386000764|ref|YP_005919063.1|  [L=264]
Description: Nitrogenase iron protein 1 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-91  304.8   0.2    6.5e-91  304.5   0.2    1.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.2e-11   44.8   0.0    2.2e-11   43.9   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.3e-10   41.2   0.0    6.3e-10   38.9   0.0    2.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    2.8e-08   33.9   0.0    5.3e-08   33.0   0.0    1.4  1  AAA_31       AAA domain
    6.5e-06   25.5   0.9    1.1e-05   24.8   0.5    1.5  2  ArsA_ATPase  Anion-transporting ATPase
     0.0025   17.2   0.2     0.0051   16.1   0.0    1.5  2  MipZ         ATPase MipZ
     0.0032   16.5   0.6     0.0044   16.0   0.6    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0051   16.6   0.0      0.009   15.8   0.0    1.3  1  AAA_24       AAA domain
     0.0065   16.3   0.3        2.2    8.0   0.0    2.2  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.045   13.9   0.0    1.3  1  DUF87        Helicase HerA, central domain
      0.037   14.4   0.0       0.22   11.9   0.0    2.0  2  AAA_16       AAA ATPase domain
       0.05   13.2   0.1       0.11   12.1   0.1    1.4  1  AAA_25       AAA domain
      0.084   12.0   0.0       0.13   11.4   0.0    1.2  1  DUF815       Protein of unknown function (DUF815)
      0.093   12.6   0.1          1    9.3   0.0    2.2  2  NTPase_1     NTPase
       0.13   11.9   0.1        0.2   11.2   0.1    1.3  1  SRP54        SRP54-type protein, GTPase domain
       0.24   10.5   0.1       0.37    9.9   0.1    1.2  1  NB-ARC       NB-ARC domain
       0.29   10.8   0.2       0.42   10.3   0.2    1.2  1  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.5   0.2   6.1e-94   6.5e-91       2     264 ..       6     261 ..       5     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 6.1e-94
                         Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGy 78 
                                       ++aiyGkGGiGks t++n++aa ae+g +vl+vGCDPk+Dst ++l g+ ++t++d++r  g   ++  edvv++Gy
  gi|386000764|ref|YP_005919063.1|   6 HVAIYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDPKSDST-ITLVGRRIPTMMDLIRAGG---EIAEEDVVFEGY 78 
                                       79****************************************.9999************998...599********* PP

                         Fer4_NifH  79 ggvkcvesGGPepGvGCaGrgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelma 154
                                       ggv+c+e GGPepGvGCaGrg+i aie+l + +    ++D+ lyDv GD+vCGGf++Pir++   e yi+tsge m 
  gi|386000764|ref|YP_005919063.1|  79 GGVRCIEVGGPEPGVGCAGRGIIVAIEFLRKVSKVLdEIDLTLYDVPGDIVCGGFSAPIRKGLVTEAYIITSGEYMP 155
                                       *****************************998755517*************************************** PP

                         Fer4_NifH 155 lyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapes 231
                                       +yaanni++g+++ +      l+G+i+nsr+ + ere++ekfa+elg+++++++P+d iv++ e r   vie ap+s
  gi|386000764|ref|YP_005919063.1| 156 IYAANNICRGLRRLN----TPLAGVICNSREAAGEREIVEKFARELGSEMVAFIPKDPIVQRCERRGVSVIEGAPDS 228
                                       ***********9875....579******************************************************* PP

                         Fer4_NifH 232 eqakeyrelarkilenkklviPkplsedeLeel 264
                                       e+a+ yr la++++ ++k   P p+ +d+L el
  gi|386000764|ref|YP_005919063.1| 229 EIAQVYRRLAEHVAGDSKPRHPSPIDDDKLREL 261
                                       ******************************998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   2.1e-14   2.2e-11       3     127 ..       8     220 ..       6     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.1e-14
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       ++ +kGG GK+ +a n a+a a++glrVl+v +Dp + ++    +l++++ p                         
  gi|386000764|ref|YP_005919063.1|   8 AIYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDPKSDSTI---TLVGRRIPtmmdliraggeiaeedvvfegyggv 81 
                                       5789********************************88887...444444445668888888888899********* PP

                                       ............................................................................C CS
                                       ............................................................................x RF
                              CbiA  55 ............................................................................d 55 
                                                                                                                    
  gi|386000764|ref|YP_005919063.1|  82 rcievggpepgvgcagrgiivaieflrkvskvldeidltlydvpgdivcggfsapirkglvteayiitsgeympiyA 158
                                       *************************************************************************9998 PP

                                       CHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  56 lkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                       +  + + l++l ++      +agv+ n  +    e+++ e ++++   +g + +++ip+d  v +++ rg +
  gi|386000764|ref|YP_005919063.1| 159 ANNICRGLRRLNTP------LAGVICNSREAAG-EREIVEKFARE---LGSEMVAFIPKDPIVQRCERRGVS 220
                                       88888888888877......89*****966553.44444444444...4**************999999876 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   5.9e-13   6.3e-10       9     245 ..       9     241 ..       3     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.9e-13
                              ParA   9 lSgKGGVGKStvavnlAlaLakkglkvgllDaD........iyGpsiprllgveeekpeqsekkliPveakgikvmS 77 
                                       + gKGG+GKS +a+n+A+a a+kgl+v ++  D        ++G  ip+++++ ++  e  e+ ++     g++++ 
  gi|386000764|ref|YP_005919063.1|   9 IYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDpksdstitLVGRRIPTMMDLIRAGGEIAEEDVVFEGYGGVRCIE 85 
                                       56***************************98876666776689*********99988888887788777799**999 PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdve..wgelDyLiiDlPPG..tgDeqltvaqklplagaviVttpqeval 150
                                       +g            rG +++  i ++l++v+   +e+D+ + D+P     g  +  + + l +++a i+t+ + + +
  gi|386000764|ref|YP_005919063.1|  86 VGGPE--PGVGCAGRGIIVA--I-EFLRKVSkvLDEIDLTLYDVPGDivCGGFSAPIRKGL-VTEAYIITSGEYMPI 156
                                       99744..4777777777664..4.35555542259**********6522344555555555.89999********** PP

                              ParA 151 advkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvl 227
                                         ++  ++ ++++++++ Gv+ N    +           +++ +ek+a+elg ++++ ip dp ++++  +g ++++
  gi|386000764|ref|YP_005919063.1| 157 YAANNICRGLRRLNTPLAGVICNSREAAG----------EREIVEKFARELGSEMVAFIPKDPIVQRCERRGVSVIE 223
                                       *********************88554433..........3466899******************************* PP

                              ParA 228 kepeseaakaleeiaekv 245
                                        +p+se+a++++++ae+v
  gi|386000764|ref|YP_005919063.1| 224 GAPDSEIAQVYRRLAEHV 241
                                       ***************998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0     5e-11   5.3e-08       9      48 ..      11      50 ..       4      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 5e-11
                            AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattgl 48
                                       KGG+GK+ t+ n+aaa a++g +vL+v +Dp + +t++l
  gi|386000764|ref|YP_005919063.1| 11 GKGGIGKSCTASNVAAACAEKGLRVLMVGCDPKSDSTITL 50
                                      5**********************************99865 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.5   1.1e-08   1.1e-05       2      39 ..       5      42 ..       4      47 .. 0.93
   2 ?   -2.7   0.0       2.5   2.6e+03     210     244 ..     146     180 ..     141     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDP 39
                                      k + + GKGG+GK+  ++ +a+ ++ekg +vl++  DP
  gi|386000764|ref|YP_005919063.1|  5 KHVAIYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDP 42
                                      678899******************************** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                       EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                        +++  E ++++  +  ++ L +++     vi N 
  gi|386000764|ref|YP_005919063.1| 146 YIITSGEYMPIYAANNICRGLRRLNTPLAGVICNS 180
                                       67888999999999999999999999999999985 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.8e-06    0.0051       8      52 ..      11      55 ..       6      63 .. 0.87
   2 ?   -3.0   0.0       3.4   3.5e+03      91     109 ..     108     126 ..     103     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                                      SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHH CS
                              MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenra 52
                                       kGG Gks ta  va a ++kG+rv  +  d +  +    ++ r 
  gi|386000764|ref|YP_005919063.1| 11 GKGGIGKSCTASNVAAACAEKGLRVLMVGCDPKSDSTITLVGRRI 55
                                      59***************************9999988888777776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                                       HHHHHHHHH-SEEEEE--S CS
                              MipZ  91 elvadleaeldfividtPG 109
                                       + v+++  e+d+ + d+PG
  gi|386000764|ref|YP_005919063.1| 108 RKVSKVLDEIDLTLYDVPG 126
                                       5577888899999999999 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.6   4.2e-06    0.0044      30      72 ..       5      47 ..       2     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspft 72
                                      + v + G  G Gks + +++++  +++G rv ++  DP s  t
  gi|386000764|ref|YP_005919063.1|  5 KHVAIYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDPKSDST 47
                                      578899*********************************9876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.5e-06     0.009       4      55 ..       6      64 ..       4      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.5e-06
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedflde 55
                                       ++iyG+ giGK+ +a++        g ++l++ ++  ++s+    + +i+++ d++ +
  gi|386000764|ref|YP_005919063.1|  6 HVAIYGKGGIGKSCTASNVaaacaekGLRVLMVGCDPKSDSTITLVGRRIPTMMDLIRA 64
                                      689****************9***99999*******998888777777777776666655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1     0.007       7.4       1      37 [.       9      45 ..       9      48 .. 0.92
   2 !    8.0   0.0    0.0021       2.2      66     102 ..      98     128 ..      95     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.007
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                      + G  G GK+   ++++  + ++g +v +v  DP ++
  gi|386000764|ref|YP_005919063.1|  9 IYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDPKSD 45
                                      57999*****************************765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                        ATP_bind_1  66 galvvaleflresldwldeelekeeddyllfDtPGQi 102
                                       ++++va+eflr+   ++ +e+     d+ l+D+PG i
  gi|386000764|ref|YP_005919063.1|  98 RGIIVAIEFLRKVS-KVLDEI-----DLTLYDVPGDI 128
                                       589*****999886.9999**.....*********76 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.2e-05     0.045      24      57 ..       5      37 ..       4      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                             DUF87 24 rHlAilgsTGsGKSntvavLleellekkgatili 57
                                      +H+Ai g+ G GKS t++   +  + +kg+++l+
  gi|386000764|ref|YP_005919063.1|  5 KHVAIYGKGGIGKSCTASNVAAACA-EKGLRVLM 37
                                      7*****************9999888.99999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.22      25      63 ..       5      43 ..       1      71 [. 0.80
   2 ?    0.2   0.0      0.83   8.7e+02      47      92 ..     213     248 ..     176     262 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                        v ++G  G+GKs  +  ++ a  ++g  +l   cd  
  gi|386000764|ref|YP_005919063.1|  5 KHVAIYGKGGIGKSCTASNVAAACAEKGLRVLMVGCDPK 43
                                      6899*****************888888888887777766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.83
                            AAA_16  47 alekdggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                       + e++g+ +++g  d+         +aq+  r +l + ++ +++ +
  gi|386000764|ref|YP_005919063.1| 213 RCERRGVSVIEGAPDSE--------IAQVY-R-RLAEHVAGDSKPR 248
                                       22233444455555554........66666.4.5666666555444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0001      0.11      36      76 ..       7      37 ..       4      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                            AAA_25 36 allaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVly 76
                                      ++++G +g GK+  a+++a+a+a +G            +Vl+
  gi|386000764|ref|YP_005919063.1|  7 VAIYGKGGIGKSCTASNVAAACAeKGL-----------RVLM 37
                                      579********************5555...........4444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.13      53      87 ..       4      38 ..       2      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                            DUF815 53 annvLLwGarGtGKSslvkallneyaeegLrliev 87
                                       ++v ++G+ G GKS +   + +++ae+gLr++ v
  gi|386000764|ref|YP_005919063.1|  4 VKHVAIYGKGGIGKSCTASNVAAACAEKGLRVLMV 38
                                      57999**************************9876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00096         1       1      30 [.       6      35 ..       6      63 .. 0.91
   2 ?    0.9   0.0      0.35   3.7e+02      17      44 ..     160     187 ..     158     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00096
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      +v+i G+ G+GK+   ++v+ +++++g++v
  gi|386000764|ref|YP_005919063.1|  6 HVAIYGKGGIGKSCTASNVAAACAEKGLRV 35
                                      78999**********************998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                                       HHHHHHH...GGGEEEEEEEEE------ CS
                          NTPase_1  17 kkvlellkssgvkvgGfyteevreggrr 44 
                                       +++++ l++ + +++G++++     g+r
  gi|386000764|ref|YP_005919063.1| 160 NNICRGLRRLNTPLAGVICNSREAAGER 187
                                       67999999***********998888877 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00019       0.2       4      38 ..       7      41 ..       4      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +++ G  G+GK  t++ +aa + ++g +vl+v +D
  gi|386000764|ref|YP_005919063.1|  7 VAIYGKGGIGKSCTASNVAAACAEKGLRVLMVGCD 41
                                      7789******************************9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00035      0.37      21      42 ..       5      26 ..       1      33 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00035
                                      EEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqiln 42
                                        va++G+gG+GK+  a+++  
  gi|386000764|ref|YP_005919063.1|  5 KHVAIYGKGGIGKSCTASNVAA 26
                                      479*************999976 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0004      0.42      48      81 ..       5      38 ..       1      42 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                         IstB_IS21 48 enivllGpsGvGKshlaialgveavraglsvlfv 81
                                      + +++ G  G+GKs  a  ++ + +++gl+vl v
  gi|386000764|ref|YP_005919063.1|  5 KHVAIYGKGGIGKSCTASNVAAACAEKGLRVLMV 38
                                      6799***************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1865.06
//
Query:       gi|386000765|ref|YP_005919064.1|  [L=988]
Description: S-layer protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.9e-120  398.9   0.0    4.8e-63  212.6   0.2    2.1  2  S-layer    S-layer protein
  ------ inclusion threshold ------
      0.081   12.0   0.0       0.16   11.0   0.0    1.4  1  DUF2625    Protein of unknown function DUF2625


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 !  184.1   0.0   2.8e-58   2.5e-54       9     258 .]      53     293 ..      46     293 .. 0.95
   2 !  212.6   0.2   5.4e-67   4.8e-63       9     258 .]     338     597 ..     332     597 .. 0.93

  Alignments for each domain:
  == domain 1  score: 184.1 bits;  conditional E-value: 2.8e-58
                           S-layer   9 eltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagydn 85 
                                       + +w+a++F  fyyd+d+g++ E+l +e   +++r+i eg l Ys+++ ++ef++  wg+Y+ + fl++kY+agy +
  gi|386000765|ref|YP_005919064.1|  53 NGSWDAESFGWFYYDLDEGVGGERLAAE---AEERRIPEGHLYYSSRVWTEEFDYPGWGRYQAVAFLGKKYLAGYLK 126
                                       668************************9...378*****************************************66 PP

                           S-layer  86 saetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskad 162
                                       s+  +d vs l++++L++vl+d +  +t++s   l Le gY +e+     dg+ ++l L+k+g evd +v+++    
  gi|386000765|ref|YP_005919064.1| 127 SN-FTDAVSALEEGELREVLLDYEGIQTATSKAPLFLEGGYWIEVAGASSDGKMAYLILKKNGVEVDRAVVRV---G 199
                                       65.599*******************************************************************...* PP

                           S-layer 163 styvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddv.leieegdefgkmevksvseneiemenddsi 238
                                       +ty+y+  +gd   ++ii+ +v+ +++gt+  +v i+g+fq+ d + ++ie gd++g mev+ + e +ie+en ++i
  gi|386000765|ref|YP_005919064.1| 200 DTYTYK--VGD-HRLPIIIASVSAAMQGTQMAIVDIDGLFQVRDVPtFKIEVGDQIGAMEVTALAEGRIELENARDI 273
                                       *****8..788.66*****************************98769***************************** PP

                           S-layer 239 tLsrdktieimddlkfkvaD 258
                                        L+r++ti +++ l ++v D
  gi|386000765|ref|YP_005919064.1| 274 ILRRGSTIPLAGGLMLRVRD 293
                                       ***************99976 PP

  == domain 2  score: 212.6 bits;  conditional E-value: 5.4e-67
                           S-layer   9 eltwtasnFsgfyydiddglssEsltlelesksdrtie.........egelvYsttpvekefefeewgsYevigfla 76 
                                        ++w+ +nF gfy+d d++++sEsl+++ +  ++r i+          ++ +Y   + e+efef++wgsY+v+ fl+
  gi|386000765|ref|YP_005919064.1| 338 AARWNDENFTGFYFDDDKKMGSESLIIHRT--DERYIRtparegprlVDGAEYICFVHEVEFEFDPWGSYQVVCFLG 412
                                       567************************955..6777777777777666899************************** PP

                           S-layer  77 ekYfagydnsa.etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqi...DvdgdkvwleLtkdge 149
                                       + +f+gy ++a    + +s+l++e++ +++id+d++ t+ +g+ + L+egY+l+i+++   +v +dk+++eL+k+++
  gi|386000765|ref|YP_005919064.1| 413 DVWFVGYGTTArLDVKPISMLAQEQIGRIIIDTDQRDTAVAGDLYYLGEGYTLSIRDVtkdEVKDDKIFIELRKNNQ 489
                                       *******7776588899***************************************994444668************ PP

                           S-layer 150 evdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqis.ddvleieegdefgkmevksv 225
                                        vd++v+++   +sty+y++d+g+++d++iia hv+++f++ ed++++i+g+fq+s  ++l i+ gde g+m+v  +
  gi|386000765|ref|YP_005919064.1| 490 LVDTAVMRP---NSTYIYKRDVGNVKDLPIIALHVENIFSDGEDQFAIIDGLFQVSdSQFLPIKAGDELGEMTVVLI 563
                                       *********...********************************************5567***************** PP

                           S-layer 226 sen.eiemenddsitLsrdktieimddlkfkvaD 258
                                         +  i m n d i+L+rd+ + i   +++ vaD
  gi|386000765|ref|YP_005919064.1| 564 GPDlGIYMVNMDYINLKRDSVVGILPGMNIAVAD 597
                                       *9989****************************8 PP

>> DUF2625  Protein of unknown function DUF2625
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.8e-05      0.16      56     145 ..     652     755 ..     646     766 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.8e-05
                           DUF2625  56 yetGGlliddGwlrvlGsgseklerslaslnkvkefaevgekaalLlvadDvlGgvfalngg............... 117
                                        ++GG  + +G l+  G g+ +  + l s++ + +++ + + +++Ll   D  Ggv  ln +               
  gi|386000765|ref|YP_005919064.1| 652 VDAGGRRVIQGDLTRSGVGARD--QWLYSWQWNATVP-ALSDDGTLLPESDLQGGVLKLNDTaepvpvsvnfdtsgr 725
                                       5789999999999999999766..8999999888877.888999999*************999**********9999 PP

                           DUF2625 118 ..klgedlGeiyYfapdslewealevgyse 145
                                          + +  GeiyY +p ++e   l+++y+e
  gi|386000765|ref|YP_005919064.1| 726 igLIRDTAGEIYYISPAEYERLGLNATYAE 755
                                       96667889*********9999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (988 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 6831.57
//
Query:       gi|386000766|ref|YP_005919065.1|  [L=302]
Description: proline dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.9   0.0    2.4e-08   33.9   0.0    3.0  2  Pro_dh    Proline dehydrogenase


Domain annotation for each model (and alignments):
>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.3e-12   2.4e-08       8     124 ..      56     162 ..      49     197 .. 0.77
   2 !   19.9   0.0   2.4e-08   0.00043     213     284 ..     223     287 ..     199     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.3e-12
                                       HHHTTEEEEEEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-SEEE-GGG..TT-SGGGHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                            Pro_dh   8 lkkrgvrlsldllgeavlteedadryleayleaiksiekaskalkvleapgvsvklsa..prletaeeeevmeelve 82 
                                       +++rg+r++ld+lge++++ee a+  ++ay+ ++ ++e+++       + ++svkl+        + +    + ++e
  gi|386000766|ref|YP_005919065.1|  56 RNARGIRCTLDVLGENARNEEAAAGSVDAYRSCLTALEEEEG-----LSASISVKLTDlgA----LFD---RRLCLE 120
                                       4557*********************************88887.....4778*****97321....222...35799* PP

                                       HHHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  83 rlrtlakeakelgvrlliDaEeaklqeltlelfrklnkepel 124
                                       +lrtl +ea+++gv++ iD+E   l e tle+  +  +e  l
  gi|386000766|ref|YP_005919065.1| 121 NLRTLSREAAQAGVGFEIDMEGKPLVEFTLEAALECAAEGPL 162
                                       ***************************999998887765555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.4e-08
                                       EEE-S-HHHHHHHHHHHHHT..T--GGGEEEEEETTSSHHHHHHHHHTTS-EEEEEEECEHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 213 avAsHNaesvakalalaeelgqekeksevefqqLlGMadnlsfalakagynvrkYlPvGpveevlpYLvRRl 284
                                        +A+H  e ++ al  ++e+     k+ vef+ L+G++d  +++la +g +v  Y+P+G+ +   +Y  RRl
  gi|386000766|ref|YP_005919065.1| 223 SLATHDPEVIEWALGRLSEE-----KTLVEFGFLMGLSDLTKEKLAGQGWAVSEYVPFGSRRR--AYQARRL 287
                                       389********999999998.....9*********************************9776..4566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2239.50
//
Query:       gi|386000767|ref|YP_005919066.1|  [L=79]
Description: Periplasmic binding protein, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.083   12.4   0.0        0.1   12.1   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.7e-06       0.1     212     237 ..       3      28 ..       1      29 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-06
                                       HHHT-SHHHHTSHHHHTT-EEEE-HH CS
                      Peripla_BP_2 212 eflkenpllaelpAvkngrVyaldss 237
                                       ++++++p+la+++Av+ grV  l+s+
  gi|386000767|ref|YP_005919066.1|   3 DEILSRPELANVKAVRDGRVHVLNSK 28 
                                       899*****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 562.11
//
Query:       gi|386000768|ref|YP_005919067.1|  [L=327]
Description: hypothetical protein Mhar_0051 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.9   0.1        0.2   11.3   0.1    1.2  1  DUF1175   Protein of unknown function (DUF1175)


Domain annotation for each model (and alignments):
>> DUF1175  Protein of unknown function (DUF1175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.1e-05       0.2     117     164 ..     277     325 ..     239     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.1e-05
                           DUF1175 117 kfgafadAktLveentrfvsrdveqA..kpgDllFfdqeddelPyHlmiy 164
                                       + + +  A  L e+ +  v+ + +q   +  Dll+f+q dd  P+H+++y
  gi|386000768|ref|YP_005919067.1| 277 NASGYYYAFVLFEHGAVAVTAEDNQTleRMMDLLYFEQRDDP-PFHILLY 325
                                       4566777888888888888887777622457*********99.****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2318.68
//
Query:       gi|386000769|ref|YP_005919068.1|  [L=284]
Description: Ribose-phosphate pyrophosphokinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-20   73.1   0.3      3e-20   72.3   0.3    1.4  1  Pribosyltran    Phosphoribosyl transferase domain
    3.7e-20   72.0   0.0    3.7e-17   62.3   0.0    2.3  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    3.6e-09   36.9   2.0    5.5e-09   36.3   1.0    1.8  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    1.9e-06   27.5   0.1      3e-06   26.8   0.1    1.4  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.065   12.7   0.0    1.6  2  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.3   8.5e-24     3e-20      14     120 ..     138     236 ..     126     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 8.5e-24
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEE CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkV 90 
                                       ++  l+++ +++ +   +v++ +++g+v +a + a +L+vp++y++k+++++   + a+        +++d ag+ V
  gi|386000769|ref|YP_005919068.1| 138 DATPLLSDEIKKMGLDDPVIISPDKGAVRMARAAAERLGVPYDYLEKTRHSGTEVSMAP--------KEIDAAGRDV 206
                                       56668888888889999*********************************999999888........9********* PP

                                       EEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevri 120
                                       +i DD+++tGgT+  a+ +Lk+kg+++v +
  gi|386000769|ref|YP_005919068.1| 207 VILDDMIATGGTMAQAISILKSKGAKRVYL 236
                                       **************************8754 PP

>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0     1e-20   3.7e-17       3     112 ..       2     106 ..       1     109 [. 0.93
   2 !    7.8   0.0   0.00083         3      10      59 ..     165     215 ..     156     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1e-20
                    Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasa 79 
                                       i+ g ss+ L+ +ia+ l+  l+ ++ s f+dgE++ ++ +++  + ++++qs+ ++   ++++ll ++d +r    
  gi|386000769|ref|YP_005919068.1|   2 IIGGPSSQLLGGRIAAILKEDLALCEYSSFPDGEAYTQVCSDLD-DRIVVVQSTPSD--RDIIQLLQLLDVCR---G 72 
                                       89999**********************************99986.679999*99877..99***********9...8 PP

                    Pribosyltran_N  80 kritaViPylgysrqdrk.ksrepisaklvaklL 112
                                       ++i +ViPy+gy+rqd++ k+ ep+sa+ +a  +
  gi|386000769|ref|YP_005919068.1|  73 RKIDLVIPYFGYARQDKQfKPGEPLSARAMAGAI 106
                                       99***************************99765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00083
                    Pribosyltran_N  10 keLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqslskp 59 
                                         +a++ a+rlgv+    + +r +  E+++  +e +  g+dv+i+ ++ + 
  gi|386000769|ref|YP_005919068.1| 165 VRMARAAAERLGVPYDYLEKTRHSGTEVSMAPKEiDAAGRDVVILDDMIAT 215
                                       56899999**************************99*********998755 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.5   5.3e+03       6      25 ..     156     175 ..     153     179 .. 0.85
   2 !   36.3   1.0   1.5e-12   5.5e-09      80     172 ..     200     284 .]     193     284 .] 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                                       EEEESSGGGHHHHHHHHHHT CS
                    Pribosyl_synth   6 vivakspgsakkatsyaerl 25 
                                       vi++ + g+++ a++ aerl
  gi|386000769|ref|YP_005919068.1| 156 VIISPDKGAVRMARAAAERL 175
                                       88999999999999999998 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1.5e-12
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-TT CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcsk 156
                                       d +Gr  +i+dd+i    ++ +a  +lk +Ga ++y  + h +l+ +a  +l  + ++ ++ t+t+ + +       
  gi|386000769|ref|YP_005919068.1| 200 DAAGRDVVILDDMIATGGTMAQAISILKSKGAKRVYLGSVHPVLTGSAVLKLCRAGVESIIATDTLEKAV------- 269
                                       7899*************************************************************98766....... PP

                                       EEEE--HHHHHHHHHH CS
                    Pribosyl_synth 157 iktvdislllaeairr 172
                                         tv ++ l+aeairr
  gi|386000769|ref|YP_005919068.1| 270 -STVTVAGLVAEAIRR 284
                                       .899***********8 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   8.3e-10     3e-06     114     156 ..     194     236 ..     172     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8.3e-10
                           UPRTase 114 kLPkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlv 156
                                         Pk+i  a r v++lD +iaTGg++a+ai++Lk++g++  ++ +
  gi|386000769|ref|YP_005919068.1| 194 MAPKEIdaAGRDVVILDDMIATGGTMAQAISILKSKGAK--RVYL 236
                                       457888767899***********************9875..4444 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.37   1.3e+03      61      91 ..     161     191 ..     137     197 .. 0.75
   2 ?   12.7   0.0   1.8e-05     0.065     114     153 ..     196     235 ..     168     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.37
                          PRTase_2  61 AEtAtaLghgvadaleeealylhtTRekvag 91 
                                          A+ ++++ a++l   + yl+ TR++ ++
  gi|386000769|ref|YP_005919068.1| 161 DKGAVRMARAAAERLGVPYDYLEKTRHSGTE 191
                                       5567778888888887789999999998755 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.8e-05
                          PRTase_2 114 deellaaakelvLvDDEistGktalnliralqeklprkry 153
                                        +e+ aa + +v+ DD i+tG t+++ i+ l++k  ++ y
  gi|386000769|ref|YP_005919068.1| 196 PKEIDAAGRDVVILDDMIATGGTMAQAISILKSKGAKRVY 235
                                       4455566799*******************99998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1830.37
//
Query:       gi|386000770|ref|YP_005919069.1|  [L=444]
Description: PmbA/TldD family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-51  173.6   0.7    9.7e-51  173.2   0.7    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   0.7   5.4e-55   9.7e-51       1     279 []      23     311 ..      23     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 5.4e-55
                                       EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.. CS
                         PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.. 75 
                                       eaev+    +s  v +++++ve +s+s ++glg+r++  g++gf+st+d+s  +l+ ++e av++a+  ++d+++  
  gi|386000770|ref|YP_005919069.1|  23 EAEVFGLMVRSVDVDLRRDRVEMASESLSRGLGLRAVLRGAVGFSSTSDLS--KLDMVAEGAVRAARARGSDEKWrs 97 
                                       689999999**************************77789******99999..**********************88 PP

                                       ..................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEE.EEEEE......EEE.EEEEEEETTSEEE CS
                         PmbA_TldD  76 ..................eevsaeekielleelekalrsadpkiensk.garisgvsaslsaskeeklianSeGldv 133
                                                         +++ +ee  el++            i+ ++  a++  vs+ +sa+ ++ l++n++Gl++
  gi|386000770|ref|YP_005919069.1|  98 lpvpraaahpegvydpatADLGPEECLELAAT----------LIQGAAtVAGAEPVSGGVSAVSGTELLINTNGLEL 164
                                       77777777775555444433333333333222..........233333344788899999***************** PP

                                       EEEEEEEEEEEEEEE...STCSETEEEEEEEESSHHH.....S..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HH CS
                         PmbA_TldD 134 eqtrtrvslslsvia.d.dggsgdgmgggsgyedlee.....edleeiaeeaaekalasleakplppgkypVvlspe 203
                                        ++ t+++++++ +a d dg    + ++g+++   ++     +d+ e+++ a + a +sl+ ++ + g   V+l+p 
  gi|386000770|ref|YP_005919069.1| 165 WERGTTFTAFIETVArDaDG----SASTGYDF---ANsrsapQDISEVGRSASDLAARSLGGVRGEDGVAQVLLGPI 234
                                       ***************66442....34456655...222335678888****************************** PP

                                       HHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 204 avgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       a++++l +a+ +++ ad v++grS l++++Gekva e l i+dd++  gg+++++fD+EGvp+qrt l+e G+L+ y
  gi|386000770|ref|YP_005919069.1| 235 AFAEILDNAFLPSTFADLVQKGRSSLAGRIGEKVAEESLMIIDDGLFpGGMATSSFDGEGVPSQRTALVEGGILRAY 311
                                       **************************88******************99**************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 3711.41
//
Query:       gi|386000771|ref|YP_005919070.1|  [L=245]
Description: hypothetical protein Mhar_0054 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-54  184.1   0.1    3.8e-54  183.9   0.1    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
       0.17   11.8   0.5        3.3    7.7   0.1    2.9  4  DUF4743   Domain of unknown function (DUF4743)


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.1   4.2e-58   3.8e-54       1     212 [.      10     223 ..      10     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 4.2e-58
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEE. CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqg. 74 
                                       Li+G+pg+G+Vg+l++++Lie+leae   e++s++ lp     p+v+v ++  ++   +++y++  ++rdll+l+g 
  gi|386000771|ref|YP_005919070.1|  10 LIEGLPGVGHVGKLVAEHLIEELEAELMIEVYSPH-LP-----PQVIVLDDgtVKQVRNEIYVHRGENRDLLLLVGd 80 
                                       8**********************************.77.....775555553888888899*997779********7 PP

                                       ...E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.......CT.-C CS
                              PAC2  75 ...repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.......es.ey 140
                                           + +++ye +a a ld++ee+gvk++++Lgg+++g+      ++p +v gaa++ +l+ee++       e+ ++
  gi|386000771|ref|YP_005919070.1|  81 yqsATNEGHYE-LAGAFLDLCEEFGVKRIYTLGGYGTGQFV----DKP-QVLGAANSHDLVEEMKsygvvfqENePG 151
                                       77777777777.************************88775....688.9**************74666654227** PP

                                       EEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 141 ggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       ggivg++glL+++++ r+i+av+l++ +++yl+dPk+a+++l++lsk+l++evd++ Lee+a+e+e+ + +l
  gi|386000771|ref|YP_005919070.1| 152 GGIVGVSGLLVGLSRLRDIDAVCLMGTTSGYLVDPKSAQEVLRVLSKALEIEVDMQALEERAREMERIVGKL 223
                                       *******************************************************************98775 PP

>> DUF4743  Domain of unknown function (DUF4743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.91   8.1e+03      28      40 ..      16      28 ..       7      30 .. 0.73
   2 ?   -0.6   0.0      0.14   1.2e+03      86     100 ..      56      70 ..      51      80 .. 0.73
   3 ?   -0.4   0.0      0.12     1e+03      33      51 ..     131     149 ..     117     169 .. 0.77
   4 ?    7.7   0.1   0.00037       3.3      45      82 ..     191     227 ..     185     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.91
                                      EEEEEEHHHHHHH CS
                           DUF4743 28 qvGlirpdvaekl 40
                                       vG++ + vae+l
  gi|386000771|ref|YP_005919070.1| 16 GVGHVGKLVAEHL 28
                                      5999999999998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.14
                                       SS----S-EEEE-SS CS
                           DUF4743  86 alkgwRdElYeVras 100
                                       ++k++R+E Y  r +
  gi|386000771|ref|YP_005919070.1|  56 TVKQVRNEIYVHRGE 70 
                                       7899*****965555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.12
                                       EHHHHHHHCT-TTTEEE-S CS
                           DUF4743  33 rpdvaeklrkfpdvFevse 51 
                                       ++d++e+++++  vF+ +e
  gi|386000771|ref|YP_005919070.1| 131 SHDLVEEMKSYGVVFQENE 149
                                       35789999******99765 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.00037
                                       TTEEE-SS.EEEE-TT--SHHHHHHHHHHHHHHHHHTT CS
                           DUF4743  45 dvFevsekeaveLapslktyeeRtaaveevleelreeg 82 
                                       +v +v +k a+e++ +++  eeR++++e+++ +lre +
  gi|386000771|ref|YP_005919070.1| 191 EVLRVLSK-ALEIEVDMQALEERAREMERIVGKLREME 227
                                       78888888.99************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1629.46
//
Query:       gi|386000772|ref|YP_005919071.1|  [L=53]
Description: Ribosome biogenesis protein Nop10 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-24   84.5   2.7      4e-24   84.4   2.7    1.0  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family
    8.5e-07   28.4   1.2    1.1e-06   28.1   1.2    1.2  1  RecR      RecR protein
  ------ inclusion threshold ------
      0.014   13.3   0.3      0.014   13.3   0.3    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2
        0.1   11.3   0.4      0.089   11.6   0.4    1.0  1  NRDD      Anaerobic ribonucleoside-triphosphate reductase


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   2.7     9e-28     4e-24       1      51 [.       1      51 [.       1      52 [. 0.98

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 9e-28
                                      .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHHH CS
                            Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralKkr 51
                                      m+s++++c++c+ YTLk++cp cg+ t  ++PaRFSP+D+y++yRral+++
  gi|386000772|ref|YP_005919071.1|  1 MRSKIKRCRTCGLYTLKDICPICGASTSQTKPARFSPEDRYGRYRRALRQE 51
                                      9***********************************************986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   1.2   2.4e-10   1.1e-06      12      35 ..       1      24 [.       1      27 [. 0.92

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.4e-10
                                      HHHH-EE-TTT--EESSSS-CCCC CS
                              RecR 12 akekvrhCsrCgnlteedlCaICs 35
                                      +++k+++C+ Cg +t +d+C+IC 
  gi|386000772|ref|YP_005919071.1|  1 MRSKIKRCRTCGLYTLKDICPICG 24
                                      589********************5 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   3.1e-06     0.014     618     643 ..       5      30 ..       1      51 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-06
                          PolC_DP2 618 rrkCkkCgketlearCeeCgekteek 643
                                        ++C++Cg  tl+  C+ Cg++t+++
  gi|386000772|ref|YP_005919071.1|   5 IKRCRTCGLYTLKDICPICGASTSQT 30 
                                       579*******************9985 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4     2e-05     0.089     506     529 ..       4      27 ..       1      46 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                                       -EEEETT.--EESSSB-TTT--BE CS
                              NRDD 506 kidvCnecgykgeiekCpkCgsee 529
                                       ki++C+ cg   +++ Cp Cg + 
  gi|386000772|ref|YP_005919071.1|   4 KIKRCRTCGLYTLKDICPICGAST 27 
                                       799*******999999*****654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.29u 0.26s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 431.61
//
Query:       gi|386000773|ref|YP_005919072.1|  [L=245]
Description: Translation initiation factor 2, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-22   78.8   0.1    6.2e-22   77.9   0.1    1.5  1  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    8.7e-09   35.6   0.1      2e-08   34.5   0.1    1.6  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.1   6.9e-26   6.2e-22       7     116 .]     109     214 ..     103     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 6.9e-26
                                       HHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHH CS
                       EIF_2_alpha   7 wklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkag 82 
                                         l + y+++y a+ ++a+++ ++l ++++ +e +e++++i ++++k++ v+i++++++t+ ++dGve+I++aLk++
  gi|386000773|ref|YP_005919072.1| 109 GALVKGYESLYVALeDAAVRGIDALAEAGLRPEDAEKVLTISQENVKIPYVEITGYVDITSPAPDGVEQIRKALKKA 185
                                       568899*********************************************************************77 PP

                                       ST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  83 eeasneeeveeeeevkikliapPeYvltvetldk 116
                                       ++ ++     e+++++++++++P+Y+++v+++d+
  gi|386000773|ref|YP_005919072.1| 186 AKTKE-----EDVTLEVRYVGAPRYRIHVTAPDY 214
                                       77444.....56*******************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   2.2e-12     2e-08      12      75 .]       5      69 ..       3      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.2e-12
                                      EEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1 12 VtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      V +v+++GafV l+  ++ +g++++se+++   ++ + +++++G+++  kvl+vd  r  i+ls+k
  gi|386000773|ref|YP_005919072.1|  5 VDQVVDFGAFVILDeyANKRGLIHISEVASG-WIKYIRDHVREGQKIVCKVLNVDPSRHHIDLSLK 69
                                      779***************************9.9999****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 2064.58
//
Query:       gi|386000774|ref|YP_005919073.1|  [L=50]
Description: Ribosomal protein S27 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-23   81.5   1.7    2.7e-23   81.4   1.7    1.0  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.019   14.8   0.7      0.025   14.4   0.7    1.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.034   13.5   1.9        1.5    8.2   0.0    2.1  2  zf-RanBP        Zn-finger in Ran binding protein and others
       0.08   13.5   0.9       0.11   13.1   0.9    1.3  1  Stc1            Stc1 domain
       0.12   11.9   2.4       0.36   10.4   0.0    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.13   12.3   2.9       0.24   11.4   2.9    1.5  1  zinc_ribbon_6   Zinc-ribbon
       0.28   11.2   2.0        2.2    8.4   0.1    2.1  2  zf-BED          BED zinc finger
       0.33   10.8   3.9       0.86    9.5   3.9    1.6  1  ZZ              Zinc finger, ZZ type


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   1.7   1.2e-26   2.7e-23       6      54 ..       1      49 [.       1      50 [] 0.98

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.2e-26
                                      EEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  6 ldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                      ++vkC dCene+v+F+ aatvvkC+ Cg++L+eP GGka++k qile+l
  gi|386000774|ref|YP_005919073.1|  1 MKVKCNDCENEQVIFGNAATVVKCLVCGRTLAEPMGGKAQIKTQILEVL 49
                                      89*********************************************97 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   1.1e-05     0.025      11      37 ..       2      30 ..       1      32 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                      --B-TTT-SB-..-SSSS-EEEETTT--E CS
                              C1_1 11 ptfCkhCgefl..wgkekqglkCswCkll 37
                                      + +C+ C++    +g + + +kC +C+++
  gi|386000774|ref|YP_005919073.1|  2 KVKCNDCENEQviFGNAATVVKCLVCGRT 30
                                      679****87644578***********986 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5    0.0076        17      19      27 ..       3      11 ..       2      12 .. 0.83
   2 ?    8.2   0.0   0.00066       1.5      14      25 ..      17      28 ..      15      28 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0076
                                      SB-TTT--B CS
                          zf-RanBP 19 tkCvaCqap 27
                                      +kC+ C+++
  gi|386000774|ref|YP_005919073.1|  3 VKCNDCENE 11
                                      69****985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00066
                                      EESSSSB-TTT- CS
                          zf-RanBP 14 NfawstkCvaCq 25
                                      N a+ +kC+ C+
  gi|386000774|ref|YP_005919073.1| 17 NAATVVKCLVCG 28
                                      99*********7 PP

>> Stc1  Stc1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   4.9e-05      0.11      39      65 ..       2      34 ..       1      45 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                                      ----TTTS-----E......EE-SSS--EEEST CS
                              Stc1 39 kikCkectakqate......leCsaCqktkpld 65
                                      k+kC++c ++q+        ++C +C++t++  
  gi|386000774|ref|YP_005919073.1|  2 KVKCNDCENEQVIFgnaatvVKCLVCGRTLAEP 34
                                      79******998766777777********98765 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.6      0.11   2.4e+02       4      11 ..       2       9 ..       1      11 [. 0.80
   2 ?   10.4   0.0   0.00016      0.36       3      15 ..      20      32 ..      18      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                                      EEE-TTTS CS
                             Sgf11  4 yvtCpnCg 11
                                       v+C+ C+
  gi|386000774|ref|YP_005919073.1|  2 KVKCNDCE 9 
                                      58999996 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                      -EEE-TTTSSEEE CS
                             Sgf11  3 eyvtCpnCgRqia 15
                                      + v+C+ CgR+ a
  gi|386000774|ref|YP_005919073.1| 20 TVVKCLVCGRTLA 32
                                      679*******987 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.9   0.00011      0.24      29      54 ..       2      28 ..       1      30 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                     zinc_ribbon_6 29 kilCnDCekkse.vkfhvlglkCkeCg 54
                                      k+ CnDCe+++         +kC  Cg
  gi|386000774|ref|YP_005919073.1|  2 KVKCNDCENEQViFGNAATVVKCLVCG 28
                                      799*****9988445556678999996 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.044        98      16      25 ..       2      11 ..       1      17 [. 0.88
   2 ?    8.4   0.1   0.00098       2.2      14      27 ..      19      32 ..      13      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.044
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                      k++C+ C+++
  gi|386000774|ref|YP_005919073.1|  2 KVKCNDCENE 11
                                      79*****985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00098
                                      SS--EETTTTEE-- CS
                            zf-BED 14 eqkavCryCgkils 27
                                       ++++C  Cg++l+
  gi|386000774|ref|YP_005919073.1| 19 ATVVKCLVCGRTLA 32
                                      589********986 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.9   0.00038      0.86       3      25 ..       1      27 [.       1      30 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00038
                                      S-EE-TTT-S..EE....SSEEEESSS CS
                                ZZ  3 kkytCdgCseapli....gvRyhclrc 25
                                      +k++C+ C +  +i     ++++cl+c
  gi|386000774|ref|YP_005919073.1|  1 MKVKCNDCENEQVIfgnaATVVKCLVC 27
                                      689*******88765544789****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.41
# Mc/sec: 368.71
//
Query:       gi|386000775|ref|YP_005919074.1|  [L=93]
Description: 50S ribosomal protein L44e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-23   83.6   4.8    1.3e-23   83.2   4.8    1.1  1  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.014   15.8   7.7        1.7    9.2   0.1    2.4  2  zf-H2C2_2      Zinc-finger double domain
       0.12   12.3   3.2          7    6.6   0.1    2.2  2  zf-C4_ClpX     ClpX C4-type zinc finger
       0.17   12.4   2.1       0.17   12.4   2.1    2.2  2  Ribosomal_L33  Ribosomal protein L33
       0.88    9.5   3.7         13    5.6   0.3    2.1  2  DUF866         Eukaryotic protein of unknown function (DUF866
        1.1    9.0   8.6        5.6    6.8   0.5    2.5  2  Zn_Tnp_IS1     InsA N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   4.8   4.4e-27   1.3e-23       1      76 []      16      91 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 4.4e-27
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      kHt+h ve+++kg+++++a+++R+++r  +g+g  G++++v+++ +K+tK+++lr++C+ Ckk++ ++++++ kf+lv
  gi|386000775|ref|YP_005919074.1| 16 KHTSHVVERVRKGRATSMAHIDRQKQR-AQGIGnsGKFSKVPGG-DKPTKRVNLRYRCSLCKKAHNRKGFKVSKFDLV 91
                                      8**************************.99**************.******************************996 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.7    0.0011       3.4      10      26 .]       4      20 ..       1      20 [. 0.81
   2 ?    9.2   0.1   0.00058       1.7      14      23 ..      68      77 ..      57      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                         zf-H2C2_2 10 tgekpyeCplCdkaFkt 26
                                      ++e++ +Cp+C+k +++
  gi|386000775|ref|YP_005919074.1|  4 PKEFKAHCPFCKKHTSH 20
                                      567788*******9876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00058
                         zf-H2C2_2 14 pyeCplCdka 23
                                      +y C+lC+ka
  gi|386000775|ref|YP_005919074.1| 68 RYRCSLCKKA 77
                                      59*******8 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0023         7       2      13 ..      10      21 ..       9      33 .. 0.88
   2 ?    6.4   0.5    0.0028       8.5       2      12 ..      70      80 ..      69      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                        zf-C4_ClpX  2 rCSFCgksesev 13
                                      +C FC k  s v
  gi|386000775|ref|YP_005919074.1| 10 HCPFCKKHTSHV 21
                                      8******99887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0028
                        zf-C4_ClpX  2 rCSFCgksese 12
                                      rCS C k ++ 
  gi|386000775|ref|YP_005919074.1| 70 RCSLCKKAHNR 80
                                      8******9876 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.1   5.6e-05      0.17      29      43 ..       6      20 ..       4      23 .. 0.90
   2 ?    0.4   0.3      0.31   9.3e+02       7      12 ..      71      76 ..      60      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-05
                                      EEEEEETTTTEEEEE CS
                     Ribosomal_L33 29 elkKYcprcrkhtlh 43
                                      e+k +cp+c+kht h
  gi|386000775|ref|YP_005919074.1|  6 EFKAHCPFCKKHTSH 20
                                      67889********99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.31
                                      ET.... CS
                     Ribosomal_L33  7 Ctecks 12
                                      C+ ck+
  gi|386000775|ref|YP_005919074.1| 71 CSLCKK 76
                                      444444 PP

>> DUF866  Eukaryotic protein of unknown function (DUF866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3    0.0044        13      60      82 ..       6      28 ..       2      55 .. 0.71
   2 ?    5.3   0.3    0.0056        17      58      73 ..      64      79 ..      54      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0044
                                      SEEE--SSSS--EEEEEE-.-TT CS
                            DUF866 60 nfvvkcklckressisikketek 82
                                       f  +c +ck++ s  +++  + 
  gi|386000775|ref|YP_005919074.1|  6 EFKAHCPFCKKHTSHVVERVRKG 28
                                      68899******999988875333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0056
                                      EESEEE--SSSS--EE CS
                            DUF866 58 eanfvvkcklckress 73
                                       +n+ ++c+lck+ ++
  gi|386000775|ref|YP_005919074.1| 64 RVNLRYRCSLCKKAHN 79
                                      57999*******9886 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.4    0.0042        13       7      24 ..      10      32 ..       7      38 .. 0.69
   2 ?    6.8   0.5    0.0019       5.6      28      35 .]      68      75 ..      60      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0042
                        Zn_Tnp_IS1  7 hCPrCsstd..V...yRhGksta 24
                                      hCP C+     V   +R+G+ t+
  gi|386000775|ref|YP_005919074.1| 10 HCPFCKKHTshVverVRKGRATS 32
                                      9****643223524469999886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0019
                        Zn_Tnp_IS1 28 RfrCrdCk 35
                                      R+rC+ Ck
  gi|386000775|ref|YP_005919074.1| 68 RYRCSLCK 75
                                      9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 691.88
//
Query:       gi|386000776|ref|YP_005919075.1|  [L=194]
Description: hypothetical protein Mhar_0059 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.9   0.1      0.051   14.0   0.1    1.4  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.9e-06     0.051      39     108 ..      16     100 ..       3     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-06
                                       TSSSSTTTTTTHHHHHHHHHHHHT...................HCHHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS- CS
                              Sld5  39 kssdlpslpphflelavkllelard..................ldelkrllrdllevRlakirkfaenledaagggg 97 
                                       + + lp    ++ +++++l el+rd                  l+  +  +  l+++R++ki k ++  ++a+   +
  gi|386000776|ref|YP_005919075.1|  16 AAELLPLETGFYEKVGEYLAELERDrsqvkdpysveaqiledeLKAARGSIGRLIDLRIKKISKKVQRAGSAS---K 89 
                                       333455555556668899******98888888888888886666666699*********************99...9 PP

                                       TCCHCCS-HHH CS
                              Sld5  98 gellsglseeE 108
                                        ++ +g+++eE
  gi|386000776|ref|YP_005919075.1|  90 DVAVKGMTPEE 100
                                       99999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1320.44
//
Query:       gi|386000777|ref|YP_005919076.1|  [L=409]
Description: DNA primase small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-21   77.7   0.0    6.1e-21   75.2   0.0    2.2  1  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   3.4e-25   6.1e-21       1     177 []      97     341 ..      97     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 3.4e-25
                                       EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d++ +    ++ e+ ++fv+    +l e+l++dfgf   +i +vfsg+rG+H++v+d ++ +l+++er++iv
  gi|386000777|ref|YP_005919076.1|  97 FDLDADHLRN-APSSYHEM-LDFVKAETTKLLEFLTGDFGFGaeEIQVVFSGGRGYHIHVRDPRVTDLGSGERREIV 171
                                       9********9.44455555.7777777777779********999********************************* PP

                                       HH..........................................HCHHHHCT--------................. CS
                     DNA_primase_S  76 nylnly....rplhpflsrs.mlkivkpvveeiileeqdpf...eikkllrllpdkslre..........kkkw... 131
                                       +yl+      +++ + +s + ++++ k v  ++  e+ + +   + k++l+++     ++          +k +   
  gi|386000777|ref|YP_005919076.1| 172 DYLTGRgldiKKFISKVSVDgDFGVDKAVILKCPPENAPGWgkrFNKSILSSFERLREMDedeainlltsRKGIgkt 248
                                       *6555568887799999999999999999999999999***999666666655555555543333355554444888 PP

                                       ..................................................................----------- CS
                     DNA_primase_S 132 ....................................................eakedivlvllyprldeqvtkgikh 156
                                                                                                   +    ++de+vt+++k+
  gi|386000777|ref|YP_005919076.1| 249 iamhiyrtalrddildkirggesidffrgsegffwnpliedylsgegvqigfS-----LGQEEKGETDEPVTTDVKR 320
                                       888889999999999999*****************************555541.....56678899*********** PP

                                       ------....---------.. CS
                     DNA_primase_S 157 llkapfcihgktgnvcvpldv 177
                                       l++ p ++hg+tg +++pl++
  gi|386000777|ref|YP_005919076.1| 321 LIRFPLSLHGGTGLRVTPLTI 341
                                       ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2676.26
//
Query:       gi|386000778|ref|YP_005919077.1|  [L=248]
Description: nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-42  146.2   0.0    1.3e-42  146.0   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.0   0.0   7.2e-47   1.3e-42       2     261 .]       3     230 ..       2     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 7.2e-47
                                       EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                      CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiav 78 
                                       +A++Ql++  +++e+nl ++l+l+++A+  ga+++v+PElf+tg+ + ++ l  +   + ++l+ l+  a+++g++v
  gi|386000778|ref|YP_005919077.1|   3 AACIQLQIQLCEREENLRRALSLANKAVGGGAEILVFPELFLTGF-CYRRDL--SDRPPYPSLDPLRSFAEEHGCLV 76 
                                       89******99***********************************.444433..346778***************** PP

                                       EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGG CS
                      CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCye 155
                                       v+ l        +l   n++++ld  g   g + K+h f         +e+e f  g++i +++t+ g+iG++iCy+
  gi|386000778|ref|YP_005919077.1|  77 VGSLVDG-----RL---NRGFCLDGAGI--GFQEKIHPF--------GTEKEHFDGGESISPVKTSRGRIGLSICYD 135
                                       ***8886.....45...******77776..9******66........89********999999************** PP

                                       GGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TT CS
                      CN_hydrolase 156 igfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpd 232
                                        +fpe++r lal ga++lv+ +  a++p s+g  + e+l rara+en++  i +n +g       ++ g+S+i dp+
  gi|386000778|ref|YP_005919077.1| 136 LRFPEVARSLALAGADLLVT-I--AQFPPSRGRVW-ETLCRARAIENQIHHIGCNGAGP------EFSGGSVILDPR 202
                                       ********************.5..699***99866.***********************......************ PP

                                       S-EEEECCSSSTEEEEEEEEHHHHHHHHH CS
                      CN_hydrolase 233 Grilaglgeeeegvliaeidladvratrr 261
                                       Gr la++g +ee v+ aeidla+  ++rr
  gi|386000778|ref|YP_005919077.1| 203 GRALAEAGPDEE-VILAEIDLAERDSARR 230
                                       ***********7.*********9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1746.17
//
Query:       gi|386000779|ref|YP_005919078.1|  [L=62]
Description: hypothetical protein Mhar_0061 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00044   19.7   0.3       0.33   10.5   0.0    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00046   19.5   0.9       0.12   11.8   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0012   18.5   0.9       0.23   11.2   0.0    2.3  2  zinc_ribbon_2    zinc-ribbon domain
     0.0012   18.4   1.2        1.3    8.8   0.2    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0013   18.7   0.6       0.53   10.3   0.1    2.3  2  ADK_lid          Adenylate kinase, active site lid
     0.0069   16.3   0.8       0.29   11.1   0.1    2.2  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0092   16.4   0.3        2.7    8.5   0.0    2.1  2  ribosomal_L24    Ribosomal proteins 50S L24/mitochondrial 39S
  ------ inclusion threshold ------
       0.01   15.8   0.2      0.032   14.3   0.2    1.7  1  DZR              Double zinc ribbon
      0.015   15.2   0.1       0.18   11.7   0.0    2.2  2  zinc_ribbon_4    zinc-ribbon domain
      0.016   15.5   2.2      0.076   13.4   0.6    2.0  2  ZF-HD_dimer      ZF-HD protein dimerisation region
      0.018   15.0   1.4       0.34   10.8   1.2    2.0  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.026   14.1   1.0       0.25   11.0   0.1    2.1  2  zf_C2H2_13       Zinc finger domain
      0.031   14.4   0.9        0.1   12.8   0.9    1.9  1  Zn-ribbon_8      Zinc ribbon domain
      0.062   13.1   1.2       0.92    9.3   0.2    2.4  2  zf-HYPF          HypF finger
      0.077   13.0   3.6        3.9    7.5   0.2    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.078   13.1   3.0        2.9    8.1   0.5    2.2  2  UPF0547          Uncharacterised protein family UPF0547
      0.085   13.1   1.2        4.3    7.7   0.2    2.2  2  Ribosomal_L32p   Ribosomal L32p protein family
       0.11   12.5   2.6        8.7    6.4   0.0    2.3  2  Nudix_N_2        Nudix N-terminal
       0.12   12.1   1.0          3    7.7   0.1    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.13   11.7   0.3        3.3    7.2   0.0    2.0  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
       0.14   12.1   0.0       0.14   12.1   0.0    1.0  1  UPF1_Zn_bind     RNA helicase (UPF2 interacting domain)
       0.15   12.5   1.7        4.9    7.6   1.5    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.15   11.8   3.6       0.91    9.3   0.1    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.16   11.7   3.5        5.9    6.7   0.4    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.18   11.6   2.7       0.93    9.3   2.7    1.9  1  zf-RING_4        RING/Ubox like zinc-binding domain
       0.33   10.9   2.8        4.1    7.4   3.3    2.0  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.37   10.7   3.4        2.2    8.3   0.3    2.1  2  zf-HIT           HIT zinc finger
       0.68   10.2   0.0       0.68   10.2   0.0    2.4  3  zf-RING_7        C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0042       2.7      17      27 ..      15      26 ..       3      32 .. 0.79
   2 !   10.5   0.0   0.00051      0.33       2      11 ..      46      55 ..      45      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                                      TTCE.EESSSSB CS
                      TF_Zn_Ribbon 17 rgel.vCtdCGl 27
                                        e+ vC +CG+
  gi|386000779|ref|YP_005919078.1| 15 GEEFrVCAACGY 26
                                      45777******7 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00051
                                      EETTTTCEEC CS
                      TF_Zn_Ribbon  2 kCPnCgstnl 11
                                      +CPnCg +++
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGARYD 55
                                      7*****9885 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0079         5      17      24 ..      19      26 ..      15      27 .. 0.87
   2 !   11.8   0.1   0.00018      0.12       5      10 ..      47      52 ..      44      60 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0079
                       zf-ribbon_3 17 nvCpyCGt 24
                                      +vC+ CG+
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGY 26
                                      69*****8 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                       zf-ribbon_3  5 CPnCGa 10
                                      CPnCGa
  gi|386000779|ref|YP_005919078.1| 47 CPNCGA 52
                                      666666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.016        10      15      22 ..      18      27 ..      12      27 .. 0.70
   2 !   11.2   0.0   0.00036      0.23       2       7 ..      47      52 ..      35      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                     zinc_ribbon_2 15 F..CpyCGtp 22
                                      F  C  CG++
  gi|386000779|ref|YP_005919078.1| 18 FrvCAACGYE 27
                                      4449999986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00036
                     zinc_ribbon_2  2 CpnCGa 7 
                                      CpnCGa
  gi|386000779|ref|YP_005919078.1| 47 CPNCGA 52
                                      666665 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.2     0.002       1.3      22      30 ..      19      27 ..      10      27 .. 0.82
   2 !    8.7   0.1     0.002       1.3      23      31 ..      46      54 ..      43      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                     zf-NADH-PPase 22 rvCpaCgle 30
                                      rvC+aCg+e
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGYE 27
                                      99****986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                     zf-NADH-PPase 23 vCpaCgleh 31
                                       Cp+Cg+++
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGARY 54
                                      699999886 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0      0.01       6.5       2      15 ..      19      34 ..      19      40 .. 0.82
   2 !   10.3   0.1   0.00082      0.53       3      12 ..      46      55 ..      45      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.01
                                      EE-TTT-..-EEETTT CS
                           ADK_lid  2 rvCpkCG..rsYhvvf 15
                                      rvC +CG  r +hv f
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGyeRGFHVSF 34
                                      8*****9667888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00082
                                      E-TTT--EEE CS
                           ADK_lid  3 vCpkCGrsYh 12
                                      +Cp+CG+ Y 
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGARYD 55
                                      9******997 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.08        51      21      28 ..      20      27 ..      14      27 .. 0.89
   2 !   11.1   0.1   0.00045      0.29      18      26 ..      43      51 ..      40      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.08
                    PhnA_Zn_Ribbon 21 vCpeCahE 28
                                      vC  C++E
  gi|386000779|ref|YP_005919078.1| 20 VCAACGYE 27
                                      9*****98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00045
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                       +l+Cp+C+
  gi|386000779|ref|YP_005919078.1| 43 IVLICPNCG 51
                                      79******7 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.018        12      47      64 ..       8      27 ..       2      28 .. 0.73
   2 !    8.5   0.0    0.0042       2.7      31      47 ..      43      59 ..      41      62 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                     ribosomal_L24 47 rlk..edgkkvRvskksgee 64
                                      +++  e g+  Rv+  +g e
  gi|386000779|ref|YP_005919078.1|  8 EIRraEAGEEFRVCAACGYE 27
                                      444447899********975 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0042
                     ribosomal_L24 31 Vmlvdpkcgkptrvgfr 47
                                      + l++p+cg    vg+r
  gi|386000779|ref|YP_005919078.1| 43 IVLICPNCGARYDVGWR 59
                                      679*************6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.9e-05     0.032      10      43 ..      16      59 ..      11      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                               DZR 10 pdarfCseCgtk....lkavaa..........edrCpsCgekvdpear 43
                                      ++ r+C +Cg +    +    +             Cp+Cg+  d ++r
  gi|386000779|ref|YP_005919078.1| 16 EEFRVCAACGYErgfhV----SflrdgadykiVLICPNCGARYDVGWR 59
                                      57899*****9966551....24445667999999*****99998876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.59   3.8e+02      28      32 ..      21      25 ..      18      38 .. 0.76
   2 ?   11.7   0.0   0.00029      0.18       4      14 ..      46      56 ..      44      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.59
                     zinc_ribbon_4 28 CskCg 32
                                      C++Cg
  gi|386000779|ref|YP_005919078.1| 21 CAACG 25
                                      56665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                     zinc_ribbon_4  4 tCpsCkakyei 14
                                       Cp+C+a+y +
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGARYDV 56
                                      6********87 PP

>> ZF-HD_dimer  ZF-HD protein dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   0.00012     0.076      37      50 ..      18      31 ..       6      36 .. 0.80
   2 ?    2.4   0.0      0.33   2.1e+02      26      44 ..      34      51 ..      32      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                       ZF-HD_dimer 37 aLkCaaCgChrnFH 50
                                         CaaCg  r FH
  gi|386000779|ref|YP_005919078.1| 18 FRVCAACGYERGFH 31
                                      446*********** PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.33
                       ZF-HD_dimer 26 FmasgeegtaeaLkCaaCg 44
                                      F+ +g++  +  L C +Cg
  gi|386000779|ref|YP_005919078.1| 34 FLRDGAD-YKIVLICPNCG 51
                                      5666664.567899****9 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.2   0.00053      0.34       6      31 ..      20      51 ..      20      51 .. 0.91
   2 ?    7.5   0.2    0.0057       3.7       6      15 ..      46      55 ..      41      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                    Zn_ribbon_SprT  6 rCtgCgreythhlsi.rrhn.....YrCrrCk 31
                                      +C  Cg e ++h s+ r  +      +C+ C+
  gi|386000779|ref|YP_005919078.1| 20 VCAACGYERGFHVSFlRDGAdykivLICPNCG 51
                                      699************877779*********95 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0057
                    Zn_ribbon_SprT  6 rCtgCgreyt 15
                                       C++Cg +y+
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGARYD 55
                                      6*****9996 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00039      0.25      15      24 ..      16      25 ..       6      26 .. 0.87
   2 ?    2.1   0.1      0.22   1.4e+02      19      24 ..      46      51 ..      32      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                        zf_C2H2_13 15 lnYRvCnkCG 24
                                       ++RvC +CG
  gi|386000779|ref|YP_005919078.1| 16 EEFRVCAACG 25
                                      58*******9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.22
                        zf_C2H2_13 19 vCnkCG 24
                                      +C +CG
  gi|386000779|ref|YP_005919078.1| 46 ICPNCG 51
                                      8****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.9   0.00016       0.1       6      35 ..      18      53 ..       3      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                       Zn-ribbon_8  6 Yr.CeeCghefe....vlqsisdaplta.CPeCgse 35
                                      +r C +Cg e       l+  +d + +  CP+Cg++
  gi|386000779|ref|YP_005919078.1| 18 FRvCAACGYERGfhvsFLRDGADYKIVLiCPNCGAR 53
                                      666*****665554544444445557778*****84 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.22   1.4e+02      21      28 ..      18      25 ..       6      27 .. 0.77
   2 ?    9.3   0.2    0.0014      0.92      24      31 ..      47      54 ..      45      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.22
                                      T---TTTS CS
                           zf-HYPF 21 fisCtnCG 28
                                      f  C  CG
  gi|386000779|ref|YP_005919078.1| 18 FRVCAACG 25
                                      55688887 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                                      -TTTS--E CS
                           zf-HYPF 24 CtnCGPrl 31
                                      C+nCG r+
  gi|386000779|ref|YP_005919078.1| 47 CPNCGARY 54
                                      *******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 ?    7.5   0.2    0.0062       3.9      19      33 ..      19      36 ..       6      42 .. 0.75
   2 ?    7.1   0.4    0.0083       5.3      20      27 ..      46      53 ..      36      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0062
                     Zn_Tnp_IS1595 19 fvCPhCgsr...kayrik 33
                                      +vC +Cg++   ++ +++
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGYErgfHVSFLR 36
                                      78*****99766666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0083
                     Zn_Tnp_IS1595 20 vCPhCgsr 27
                                      +CP+Cg r
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGAR 53
                                      6*****66 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0045       2.9      15      23 ..      19      27 ..      16      27 .. 0.88
   2 ?    5.5   0.1     0.029        19      16      21 ..      46      51 ..      44      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0045
                           UPF0547 15 qfCphCGyv 23
                                      ++C+ CGy+
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGYE 27
                                      79******7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                           UPF0547 16 fCphCG 21
                                      +Cp CG
  gi|386000779|ref|YP_005919078.1| 46 ICPNCG 51
                                      788888 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0067       4.3      40      53 ..      19      32 ..      18      33 .. 0.87
   2 ?    4.3   0.0     0.076        49      28      34 ..      46      52 ..      42      56 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0067
                                      C-BTTTTBSSSBXS CS
                    Ribosomal_L32p 40 rvcpscGyYkgrev 53
                                      rvc +cGy +g +v
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGYERGFHV 32
                                      8********99665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.076
                                      EETTTCC CS
                    Ribosomal_L32p 28 ecpncge 34
                                       cpncg+
  gi|386000779|ref|YP_005919078.1| 46 ICPNCGA 52
                                      4777765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9      0.02        13      23      30 ..      19      26 ..       3      26 .. 0.75
   2 ?    6.4   0.0     0.014       8.7      25      29 ..      47      51 ..      39      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.02
                                      EEETTTTE CS
                         Nudix_N_2 23 lvCpaCgt 30
                                       vC+aCg+
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGY 26
                                      49****97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                                      ETTTT CS
                         Nudix_N_2 25 CpaCg 29
                                      Cp+Cg
  gi|386000779|ref|YP_005919078.1| 47 CPNCG 51
                                      55555 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.11        68      22      30 ..      19      27 ..      15      28 .. 0.84
   2 ?    7.7   0.1    0.0047         3      22      29 ..      45      52 ..      44      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                     A2L_zn_ribbon 22 lvCieCgas 30
                                      +vC  Cg++
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGYE 27
                                      689999985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                     A2L_zn_ribbon 22 lvCieCga 29
                                      l+C++Cga
  gi|386000779|ref|YP_005919078.1| 45 LICPNCGA 52
                                      79*****8 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0052       3.3      19      40 ..       3      25 ..       1      34 [. 0.81
   2 ?    5.2   1.8     0.021        13      11      42 ..      20      53 ..      20      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0052
                       Vps36-NZF-N 19 Nevpsnfdp.nastplPpClaCG 40
                                       +v+ ++   +a +++ +C aCG
  gi|386000779|ref|YP_005919078.1|  3 EKVEEEIRRaEAGEEFRVCAACG 25
                                      56778887778999********* PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                       Vps36-NZF-N 11 vCpICsfsNevpsnfdp..nastplPpClaCGvk 42
                                      vC  C ++  +   f     + + + +C +CG  
  gi|386000779|ref|YP_005919078.1| 20 VCAACGYERGFHVSFLRdgADYKIVLICPNCGAR 53
                                      788899988888888667778888999****966 PP

>> UPF1_Zn_bind  RNA helicase (UPF2 interacting domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.14      54      94 ..      12      51 ..       2      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                      UPF1_Zn_bind 54 splgdtvleCyncgsknvflLgfipaksesvvvllcrepca 94
                                       ++g++   C  cg +  f+++f+   ++ ++vl+c + c 
  gi|386000779|ref|YP_005919078.1| 12 AEAGEEFRVCAACGYERGFHVSFLRDGADYKIVLICPN-CG 51
                                      566777888***************************88.53 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.015       9.8      15      40 ..       5      31 ..       2      42 .. 0.62
   2 ?    7.6   1.5    0.0077       4.9       4      36 ..      19      52 ..      16      61 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                   Lar_restr_allev 15 lersqrvvaeigqcvyCadCga.stpw 40
                                      +e++ r+++ ++++  Ca Cg+  + +
  gi|386000779|ref|YP_005919078.1|  5 VEEEIRRAEAGEEFRVCAACGYeRGFH 31
                                      4455555555555999*****964444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0077
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigq.cvyCadCga 36
                                        C  Cg +   + s +++    + + +C +Cga
  gi|386000779|ref|YP_005919078.1| 19 RVCAACGYERGFHVSFLRDGADYKiVLICPNCGA 52
                                      5677777666666666655544446999999999 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.5     0.095        61      22      28 ..      19      25 ..      18      28 .. 0.68
   2 ?    9.3   0.1    0.0014      0.91       5      17 ..      45      58 ..      43      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.095
                           zf-RRN7 22 yyCrrCh 28
                                      ++C  C+
  gi|386000779|ref|YP_005919078.1| 19 RVCAACG 25
                                      5666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                           zf-RRN7  5 ppCgvCgc.rsftl 17
                                       +C+ Cg+ +++++
  gi|386000779|ref|YP_005919078.1| 45 LICPNCGArYDVGW 58
                                      58******667665 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0091       5.9       2       9 ..      20      27 ..      20      31 .. 0.89
   2 ?    6.1   0.2     0.014       9.2      17      22 ..      47      52 ..      46      55 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0091
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      vC +CG+e
  gi|386000779|ref|YP_005919078.1| 20 VCAACGYE 27
                                      7******8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cg+
  gi|386000779|ref|YP_005919078.1| 47 CPNCGA 52
                                      777764 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.7    0.0015      0.93      10      48 .]      13      55 ..       6      55 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                         zf-RING_4 10 etdkdlkpC.eCgyqiClfCyhrile.....eeegrCPaCreeYk 48
                                      e +++++ C  Cgy+  +  +   l+     +   +CP+C  +Y+
  gi|386000779|ref|YP_005919078.1| 13 EAGEEFRVCaACGYE--RGFHVSFLRdgadyKIVLICPNCGARYD 55
                                      578899999889998..3333344442222334789****99996 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.31     2e+02      21      27 ..      19      25 ..       9      34 .. 0.79
   2 ?    7.4   3.3    0.0063       4.1      20      30 ..      44      54 ..      19      56 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                       Prok-RING_1 21 VvCpeCg 27
                                       vC +Cg
  gi|386000779|ref|YP_005919078.1| 19 RVCAACG 25
                                      5888887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0063
                       Prok-RING_1 20 iVvCpeCgtpy 30
                                      + +Cp+Cg+ y
  gi|386000779|ref|YP_005919078.1| 44 VLICPNCGARY 54
                                      669*****988 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.11        72       4      11 ..      20      27 ..      18      30 .. 0.82
   2 ?    8.3   0.3    0.0034       2.2      16      23 ..      47      54 ..      45      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                                      B-TTT-SB CS
                            zf-HIT  4 lCgvCgfp 11
                                      +C+ Cg++
  gi|386000779|ref|YP_005919078.1| 20 VCAACGYE 27
                                      79***985 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0034
                                      -TTT--EE CS
                            zf-HIT 16 CpkCntry 23
                                      Cp+C++ry
  gi|386000779|ref|YP_005919078.1| 47 CPNCGARY 54
                                      *******9 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.3       3.6   2.3e+03       1       5 [.      20      24 ..       2      25 .. 0.49
   2 ?   -0.5   0.7       2.2   1.4e+03       1       6 [.      20      25 ..      20      27 .. 0.80
   3 ?   10.2   0.0    0.0011      0.68      23      31 ..      44      52 ..      31      52 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                                      EETTT CS
                         zf-RING_7  1 tCgGC 5 
                                      +C +C
  gi|386000779|ref|YP_005919078.1| 20 VCAAC 24
                                      24444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                                      EETTT- CS
                         zf-RING_7  1 tCgGCh 6 
                                      +C +C+
  gi|386000779|ref|YP_005919078.1| 20 VCAACG 25
                                      699997 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0011
                                      -EE-TTT-- CS
                         zf-RING_7 23 vvtCpeCGR 31
                                      v  Cp+CG+
  gi|386000779|ref|YP_005919078.1| 44 VLICPNCGA 52
                                      899*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 433.10
//
Query:       gi|386000780|ref|YP_005919079.1|  [L=63]
Description: PUA domain containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-07   31.0   0.7    1.9e-07   30.9   0.7    1.0  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.098   12.9   0.0        0.1   12.9   0.0    1.1  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.7   2.1e-11   1.9e-07       2      53 ..      11      62 ..      10      63 .] 0.96

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.1e-11
                                      EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEES CS
                               PUA  2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlan 53
                                      ++v+ d Av ++++g  ++   +v+++ d++ g++V +vd++++++  ++a 
  gi|386000780|ref|YP_005919079.1| 11 KMVISDAAVPFVARGGRVFGRQIVSADLDISDGEEVLVVDRNDRIITTARAV 62
                                      89********************************************999986 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05       0.1      14      50 ..      24      60 ..      10      63 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                           UPF0113 14 YGrdvlkesilkitesvkenqvvvVlnengeplGiGk 50
                                       G  v++ +i++ + ++ +++ v+V++ n++++  ++
  gi|386000780|ref|YP_005919079.1| 24 RGGRVFGRQIVSADLDISDGEEVLVVDRNDRIITTAR 60
                                      4899****************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 457.71
//
Query:       gi|386000781|ref|YP_005919080.1|  [L=276]
Description: Phosphoglyceromutase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-34  119.5   1.8    1.1e-24   87.2   1.2    2.0  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   1.2   6.4e-29   1.1e-24       1     115 [.      40     159 ..      40     175 .. 0.93
   2 !   31.3   0.0   8.2e-12   1.5e-07     100     171 ..     169     242 ..     160     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 6.4e-29
                                       EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EE..EE-SSHHHHHHHHHHHHCTT...--EE CS
                        His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidai..ysSplkRarqTaeliaealg...lpve 72 
                                       l+L+RHG++ +n+e+r+ g+ dvpL+++G+++A+++++ l++++++    ++S lkRa++T  l++e+++   ++  
  gi|386000781|ref|YP_005919080.1|  40 LILLRHGQSVYNREKRFTGWADVPLSPTGEAEARRAGRLLRSQGLEYEiaFTSLLKRAIKTLWLVSEEMElewVSAV 116
                                       79****************************************77776667********************8888889 PP

                                       E-GGGS----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-B CS
                        His_Phos_1  73 ldegLrEidfGdweglttaeiaeeypeeleawlrdpadvrppg 115
                                       +  +L+E+++G+++g+t++e+a+   ee  + +r+  ++rpp+
  gi|386000781|ref|YP_005919080.1| 117 KAVELNERHYGALQGRTRDEVAALAGEEQVRLWRRGFSERPPP 159
                                       999**************************99999999999886 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 8.2e-12
                                       SHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHH.HHHHHTTTSE.EEEEE-HHHHHHHHHHHHT--GGGGGGB-- CS
                        His_Phos_1 100 eleawlrdpadvrppggEsledvaaRvaaale.elaarheget.vlvVsHggvirallarllglpleelrrlel 171
                                       +++++ r  a +r p  E l+dv +R+++++  ++a + ++++ vlvVsHg ++ral+++l g++ + +  +e+
  gi|386000781|ref|YP_005919080.1| 169 RFDRRYRFLAADRLPSAEALADVSDRIVPFWTdRIAPEVRSGRrVLVVSHGNALRALVKYLEGISDDGIAAVEI 242
                                       4455555556689999*************998678877777777*******************99887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1891.77
//
Query:       gi|386000782|ref|YP_005919081.1|  [L=168]
Description: hypothetical protein Mhar_0065 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-09   36.2   0.0    6.2e-09   35.6   0.0    1.3  1  dUTPase   dUTPase
  ------ inclusion threshold ------
      0.012   14.4   0.0      0.013   14.3   0.0    1.3  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   6.9e-13   6.2e-09      31     106 ..      78     153 ..      72     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.9e-13
                                       EEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTS..EEEEEEEE-SSS-EEE-TT-EEEEEEEEEBE CS
                           dUTPase  31 tvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrG..evkvvlfnltkkdvkikkgdRiAqLifaril 105
                                        +lv+++ ++ +p+++aal  pRS+l ++g +v++ ++d  yrG  +  +v+fn ++   ++k+++R+ qL f r+ 
  gi|386000782|ref|YP_005919081.1|  78 AYLVTFNEAVSIPKDIAALARPRSSLLRSGATVETALWDPGYRGrsQSLLVVFNPGG--LRLKRNARLIQLAFYRLS 152
                                       5799****************************************5555567777777..**************9887 PP

                                       C CS
                           dUTPase 106 t 106
                                       +
  gi|386000782|ref|YP_005919081.1| 153 A 153
                                       7 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-06     0.013       4     110 ..       3     105 ..       1     157 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-06
                               DCD   4 ilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlek 80 
                                       i++  e+++l+++ga++      e q+q   +DL L ++   + a+  + + ++ ++k+++ +   +d +  + l+ 
  gi|386000782|ref|YP_005919081.1|   3 IIAGIELRDLLDRGAVTDMV-DPEVQVQVCGVDLTLRSVE--LFATPGAVDYDNRERKVSKTEEIPFDESGWVHLDP 76 
                                       56666788888888885443.4567999999999997654..44444444455667777777777777777777887 PP

                               DCD  81 gcvYivplleslaLpadlsaaanpksstGR 110
                                       g+ Y+v ++e++++p+d++a a p+ss  R
  gi|386000782|ref|YP_005919081.1|  77 GA-YLVTFNEAVSIPKDIAALARPRSSLLR 105
                                       75.***********************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1096.37
//
Query:       gi|386000783|ref|YP_005919082.1|  [L=269]
Description: hypothetical protein Mhar_0066 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-46  156.9  14.1    4.8e-46  156.9  14.1    1.8  2  DUF1614   Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4      0.12   2.1e+03      51      68 ..       6      22 ..       5      42 .. 0.52
   2 !  156.9  14.1   2.7e-50   4.8e-46       2     170 .]      55     245 ..      54     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.12
                           DUF1614 51 viPlllslylllrlavsl 68
                                      +iP+ l++ ll+ +a  l
  gi|386000783|ref|YP_005919082.1|  6 LIPISLAILLLILAAP-L 22
                                      5666666665554442.2 PP

  == domain 2  score: 156.9 bits;  conditional E-value: 2.7e-50
                           DUF1614   2 lgslinipvaelkske.elvevkvlgisykvpvleeeekk....tvvavNvGGaviPlllslylllrlavsllaall 73 
                                       lgs++n+p+++ + +e ++  + +  +s+  p l+ +  +    +v+avN+GG++iP+l+sl++l+r++vs+ +a+l
  gi|386000783|ref|YP_005919082.1|  55 LGSSVNFPLHSGTITEyPP--IFLGAASILSPALDLSFPAtfhpVVLAVNLGGCLIPILVSLTILVRCQVSARRAIL 129
                                       79***********977455..566666667777766666666669******************************** PP

                           DUF1614  74 avlivaavvyllarpvpgvGivvpllipplvaalaalllaeeea..aavaYisgvlGtLiGadllnl...kkieklg 145
                                       ++livaa++y++a+pv g Gi +p++++p +aa+++l+la++ +  +a+aYisg++GtL+Gad++nl   + +++l+
  gi|386000783|ref|YP_005919082.1| 130 GTLIVAAITYRMAMPVAGEGILLPVYVAPTLAAISGLVLARRLQaaPALAYISGTMGTLLGADIFNLltpGVLAALA 206
                                       ************************************98888877789********************8876666666 PP

                           DUF1614 146 ap..............vvsIGGaGtFdGifltgilavll 170
                                        p              v+sIGGaG+FdGifltgi+avll
  gi|386000783|ref|YP_005919082.1| 207 PPmvgpgsmgiaprplVLSIGGAGVFDGIFLTGIIAVLL 245
                                       6689999999999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1863.08
//
Query:       gi|386000784|ref|YP_005919083.1|  [L=88]
Description: hypothetical protein Mhar_0067 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.2  15.2    1.8e-10   40.9  15.2    1.1  1  BofA      SigmaK-factor processing regulatory protein BofA
  ------ inclusion threshold ------
        1.2    8.7  11.9        1.5    8.4  11.9    1.0  1  DUF5336   Family of unknown function (DUF5336)


Domain annotation for each model (and alignments):
>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9  15.2     2e-14   1.8e-10       2      75 .]      14      84 ..      13      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2e-14
                              BofA  2 gilllllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillklf 75
                                      g+ll+++++  +   ++ +  l++++++Gl++Lfl+N   av gl+ip++l  +l++++lG pG+i++i+l +f
  gi|386000784|ref|YP_005919083.1| 14 GLLLIFAIYASFSLIMRSVKFLAVHTLVGLLILFLAN---AVGGLAIPYSLPVLLVCALLGAPGAIAVIILDFF 84
                                      899**********************************...899****************************976 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  11.9   0.00017       1.5      77     155 ..       9      82 ..       2      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00017
                           DUF5336  77 lglavvllLlagLlAgvslLPkqksktavaAvlsvlgfLlvlaevinapegvsiawglwvvlvlallqaaaAvaaLL 153
                                        +l + llL+ ++ A  sl+ +      + Av  ++g+L +   + na  g+ i + l v+lv+all a  A+a++ 
  gi|386000784|ref|YP_005919083.1|   9 EILILGLLLIFAIYASFSLIMRSV---KFLAVHTLVGLLIL--FLANAVGGLAIPYSLPVLLVCALLGAPGAIAVII 80 
                                       456788999***********9877...78899999998754..567888899***********************99 PP

                           DUF5336 154 fe 155
                                       ++
  gi|386000784|ref|YP_005919083.1|  81 LD 82 
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 673.27
//
Query:       gi|386000785|ref|YP_005919084.1|  [L=1065]
Description: Na+/solute symporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-46  157.6   0.0      7e-31  106.8   0.0    2.6  2  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
        4.4    7.4   7.0          5    7.3   1.6    3.0  2  TPPK_C    Thiamine pyrophosphokinase C terminal


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.2e-16     1e-12       6     122 ..     643     765 ..     641     772 .. 0.85
   2 !  106.8   0.0   7.8e-35     7e-31       7     136 .]     922    1055 ..     916    1055 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.2e-16
                            DUF835   6 ekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkvee..entvsPtnlekltetivkflkeaekgvv 80 
                                       eka+e+++d++++gv++l+it + p++ir++ + +++++i l+  ++   + + P+nl+ +  ti++f+++ +++++
  gi|386000785|ref|YP_005919084.1| 643 EKAYEVFTDQITHGVEGLCITSSDPEEIRSRWHFTETPIIRLSHQRGrgDRYIAPNNLPLIFITIKSFVEKSKNNII 719
                                       7899******************************************744669************************* PP

                            DUF835  81 liDgleyLvlengF....esvlkflltlkDavllkngtlilvidke 122
                                       l+D+le L+ en       +vl+f+++l        ++li+++ +e
  gi|386000785|ref|YP_005919084.1| 720 LLDSLEELIEENAStvpeAEVLDFVHALEELSSRGRTRLIIQARQE 765
                                       *********9996522224677777777777777777777766655 PP

  == domain 2  score: 106.8 bits;  conditional E-value: 7.8e-35
                            DUF835    7 kakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkvee....entvsPtnlekltetivkflkeaek 77  
                                        ++ +i +dlv +gv++l+i+R +p+ ++e+++++  +viwlt++ +     ++v+Ptn+++l ++i++fl++a +
  gi|386000785|ref|YP_005919084.1|  922 QSLRIYADLVARGVEGLCISRYHPERLMERYGLPPERVIWLTQSAGigpeVRQVDPTNFPRLSGMISDFLSRADE 996 
                                        5678999**************************************8554445*********************** PP

                            DUF835   78 gvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136 
                                         ++l++gl yL++++++esvl+f+++ +D v+lk g+l+++id+ al+ ke + L +e+
  gi|386000785|ref|YP_005919084.1|  997 PLILLEGLGYLITQSNYESVLRFVQSQRDEVALKRGILMIHIDPLALDLKERHRLVSEM 1055
                                        *******************************************************9997 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.6   0.00055         5      20      37 ..     115     132 ..     106     140 .. 0.81
   2 ?    1.6   0.3     0.033   2.9e+02      19      31 ..     159     171 ..     153     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00055
                            TPPK_C  20 vlAaLvAvavallvspag 37 
                                       v++aLvAva+ ++++p +
  gi|386000785|ref|YP_005919084.1| 115 VIGALVAVAILIVITPYV 132
                                       89**************43 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.033
                            TPPK_C  19 lvlAaLvAvaval 31 
                                       l++A+L+Av++++
  gi|386000785|ref|YP_005919084.1| 159 LMVAVLLAVFAII 171
                                       7899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 7682.52
//
Query:       gi|386000786|ref|YP_005919085.1|  [L=471]
Description: Aspartyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-89  300.0   0.0      2e-89  299.8   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    5.3e-11   42.4   0.0    9.9e-11   41.5   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0038   16.7   1.4        1.8    7.9   0.1    3.1  4  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.8   0.0   3.3e-93     2e-89       3     313 ..     156     465 ..     154     466 .. 0.96

  Alignments for each domain:
  == domain 1  score: 299.8 bits;  conditional E-value: 3.3e-93
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                       ++rl+ r++dlr++ v +v+r+ s+v++++r++++engfie+ tP ++ ++te+g  lF +       ++f    +L
  gi|386000786|ref|YP_005919085.1| 156 DTRLDSRFIDLRRPPVLAVFRIESEVLRSFREFFSENGFIEVCTPKVVATATEGGTALFPI-------TYFereaFL 225
                                       89***********************************************************.......44444445* PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                       +qspqly+++l++ag+drvf+i++ FRaE+++t+rhl+E ++i++e+sf++eed+m +le+ + +  ++v ++++kd
  gi|386000786|ref|YP_005919085.1| 226 NQSPQLYKQMLMSAGLDRVFEIGPIFRAEEHDTRRHLNEAISIDVEVSFADEEDVMALLERAMAKAYTDVADRCQKD 302
                                       **************************************************************************999 PP

                                       CCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS.......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrnskdlkkpfkrltykeaieklnei.......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkee 222
                                       +          +k+pfkr+ty+ea++++ne        g+dld++ era     + e +f+t++P ++kp+y++  e
  gi|386000786|ref|YP_005919085.1| 303 LSALGVDLA-APKTPFKRVTYTEALKIANEGreneiewGDDLDTEAERAIGS-AIGEHYFMTEWPTTIKPYYTQPYE 377
                                       988888765.8899*************99889*******************9.999********************* PP

                                       TSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 223 ddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlll 299
                                       d++++++++Dl+ + +El++G++R++dp +l ek++++gld   +e f++yl+a+++G+pph+G+glGl R+v ++l
  gi|386000786|ref|YP_005919085.1| 378 DRPEISRGFDLMHPTMELASGAQRVHDPALLVEKIRRQGLD---PEGFEFYLRAFRFGMPPHAGWGLGLGRVVLTML 451
                                       *****************************************...********************************* PP

                                       T-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxx RF
                       tRNA-synt_2 300 gsesIrdviaFPkl 313
                                       g+e+Ird+++FP+ 
  gi|386000786|ref|YP_005919085.1| 452 GLENIRDAVLFPRD 465
                                       ************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   1.7e-14   9.9e-11       1      75 [.      57     135 ..      57     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.7e-14
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkv 70 
                                       Vt+aG+ + +  r+ g+++f++lrD++g  qv+l      ++  +   +l +++v+ v+Grvk     p+g +e++ 
  gi|386000786|ref|YP_005919085.1|  57 VTLAGWAHEV--RDLGGICFLVLRDREGFAQVTLVAkkvdKDLLERVRRLSRESVLLVRGRVKGEpkaPRG-YEIIP 130
                                       89********..***************999999999878888888888888**************888888.***99 PP

                                       EEEEE CS
                   tRNA_anti-codon  71 eeiel 75 
                                       +ei l
  gi|386000786|ref|YP_005919085.1| 131 SEIDL 135
                                       99976 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.0       1.7     1e+04      81      89 ..      38      46 ..      35      53 .. 0.81
   2 ?   -0.2   0.0     0.098   5.8e+02      20      44 ..     179     203 ..     172     214 .. 0.84
   3 !    5.5   0.0    0.0017        10     102     152 ..     242     288 ..     226     301 .. 0.73
   4 !    7.9   0.1   0.00031       1.8     212     234 ..     437     459 ..     432     468 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 1.7
                                      EEE-SSTHH CS
                      tRNA-synt_2d 81 llLRthtta 89
                                      l+LRth + 
  gi|386000786|ref|YP_005919085.1| 38 LVLRTHYSG 46
                                      79****985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.098
                                       HHHHHHHHHHHHCTTCEESSTTSEE CS
                      tRNA-synt_2d  20 tkvleeikeiflelgfeevegpeve 44 
                                       ++vl+ ++e+f e gf ev  p+v 
  gi|386000786|ref|YP_005919085.1| 179 SEVLRSFREFFSENGFIEVCTPKVV 203
                                       678999***********99988875 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0017
                                       EEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHH CS
                      tRNA-synt_2d 102 ikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkkl 152
                                        +++ ig +fR ++ D ++    h  e + +d +vs+ad   v+  l +++
  gi|386000786|ref|YP_005919085.1| 242 DRVFEIGPIFRAEEHDTRR----HLNEAISIDVEVSFADEEDVMALLERAM 288
                                       589***********66554....5568899999999988877777666666 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.00031
                                       EEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                       +++GlG+ R+ + ++g+e+iR+ 
  gi|386000786|ref|YP_005919085.1| 437 AGWGLGLGRVVLTMLGLENIRDA 459
                                       58*******************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 3472.66
//
Query:       gi|386000787|ref|YP_005919086.1|  [L=235]
Description: hypothetical protein Mhar_0070, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-22   78.3   0.1    6.5e-22   77.5   0.1    1.4  1  DUF333    Domain of unknown function (DUF333)


Domain annotation for each model (and alignments):
>> DUF333  Domain of unknown function (DUF333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.1   3.6e-26   6.5e-22       2      48 .]       1      48 [.       1      48 [. 0.98

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 3.6e-26
                            DUF333  2 maNPAsvyCvkqGGkleiakdad.GgqvgyCqlpdGkrceEwaLyrgd 48
                                      m+NPAs+yC   G++++i++d+  Gg+vgyC++pdG++ceEwa+yrg+
  gi|386000787|ref|YP_005919086.1|  1 MPNPASAYCKALGYTSVIRTDPRtGGEVGYCVFPDGSSCEEWAFYRGS 48
                                      9**********************9**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1892.86
//
Query:       gi|386000788|ref|YP_005919087.1|  [L=216]
Description: hypothetical protein Mhar_0071 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 1785.59
//
Query:       gi|386000789|ref|YP_005919088.1|  [L=68]
Description: hypothetical protein Mhar_0072 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-05   23.3   0.5    8.4e-05   22.9   0.5    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
    0.00015   21.7   0.7     0.0002   21.3   0.7    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00078   19.1   0.1    0.00078   19.1   0.1    1.6  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0063   16.6   0.6        1.2    9.3   0.0    2.2  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.041   13.6   3.0        1.3    8.8   0.0    2.4  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.068   13.5   1.1       0.11   12.9   1.1    1.3  1  C1_2             C1 domain
      0.078   12.8   2.3       0.84    9.5   2.5    2.0  2  PADR1            PADR1 (NUC008) domain
        0.1   12.6   0.0        0.1   12.6   0.0    1.1  1  CRISPR_assoc     CRISPR associated protein
       0.12   12.3   3.0        1.7    8.6   0.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.15   11.8   3.0        4.1    7.2   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.49   10.0   5.0        2.6    7.6   5.0    2.2  1  TF_Zn_Ribbon     TFIIB zinc-binding


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 !   22.9   0.5   5.2e-08   8.4e-05       5      47 ..      11      50 ..       8      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.2e-08
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaede 47
                                       CP Cg+ + + ++++ v +   + +C+dC++++  + +a+de
  gi|386000789|ref|YP_005919088.1| 11 VCPVCGSSEMYLETGGYVGK---VYHCKDCNYMGALVVEADDE 50
                                      6*************999998...9********65555555544 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 !   21.3   0.7   1.2e-07    0.0002      20      45 ..      11      39 ..       3      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt...rglfqCkeCrk 45
                                      vCP Cgs++ y  ++    ++++Ck+C++
  gi|386000789|ref|YP_005919088.1| 11 VCPVCGSSEMYLETGgyvGKVYHCKDCNY 39
                                      8*******99988889999********87 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   4.8e-07   0.00078       2      23 ..       7      28 ..       6      28 .. 0.91
   2 ?   -2.4   0.5       2.6   4.2e+03       7      11 ..      34      38 ..      33      38 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.8e-07
                           zf-RRN7  2 ekgppCgvCgcrsftlddGfyy 23
                                      +++++C+vCg+ + +l+ G y+
  gi|386000789|ref|YP_005919088.1|  7 RMVEVCPVCGSSEMYLETGGYV 28
                                      689**************99986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                           zf-RRN7  7 CgvCg 11
                                      C  C+
  gi|386000789|ref|YP_005919088.1| 34 CKDCN 38
                                      88887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00073       1.2      26      35 ..       8      19 ..       1      21 [. 0.67
   2 !    6.2   0.1     0.007        11       6      13 ..      32      39 ..      31      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00073
                       Zn-ribbon_8 26 lta.CPeCgs.e 35
                                      +++ CP Cgs e
  gi|386000789|ref|YP_005919088.1|  8 MVEvCPVCGSsE 19
                                      4455*****955 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.007
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      Y+C++C+ 
  gi|386000789|ref|YP_005919088.1| 32 YHCKDCNY 39
                                      9*****94 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00081       1.3      22      32 ..      10      20 ..       5      21 .. 0.82
   2 ?    4.5   0.6     0.018        30      22      29 ..      32      39 ..      30      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00081
                     A2L_zn_ribbon 22 lvCieCgasfp 32
                                      +vC+ Cg+s+ 
  gi|386000789|ref|YP_005919088.1| 10 EVCPVCGSSEM 20
                                      8*******985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.018
                     A2L_zn_ribbon 22 lvCieCga 29
                                      + C++C++
  gi|386000789|ref|YP_005919088.1| 32 YHCKDCNY 39
                                      55888876 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.1   6.5e-05      0.11      19      41 ..      10      40 ..       2      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                              C1_2 19 fnCsaCgrk.....idgff....YsCseCdfs 41
                                        C +Cg +     + g +    Y+C+ C+++
  gi|386000789|ref|YP_005919088.1| 10 EVCPVCGSSemyleTGG-YvgkvYHCKDCNYM 40
                                      6799***9988886333.24788*******96 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.5   0.00052      0.84      14      44 ..      10      38 ..       8      41 .. 0.75
   2 ?    3.8   0.4      0.03        48      11      21 ..      29      39 ..      26      48 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00052
                             PADR1 14 ekCpeCkegqlvfdssgYkCtGnmsewtkCt 44
                                      e Cp C++++++++++gY+  G++   + C+
  gi|386000789|ref|YP_005919088.1| 10 EVCPVCGSSEMYLETGGYV--GKVYHCKDCN 38
                                      78************99886..5555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.03
                             PADR1 11 GalekCpeCke 21
                                      G++ +C+ C+ 
  gi|386000789|ref|YP_005919088.1| 29 GKVYHCKDCNY 39
                                      67777777774 PP

>> CRISPR_assoc  CRISPR associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.4e-05       0.1     185     216 ..      32      63 ..       3      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                                       EEEEEEEEECEEEESSHHHHHHHHHH-CSS-G CS
                      CRISPR_assoc 185 vtlssvtfeGlltVtDpelfreaLleGiGraK 216
                                        + ++ ++ G l V+  +++ ea++eG Gr+K
  gi|386000789|ref|YP_005919088.1|  32 YHCKDCNYMGALVVEADDEMVEAIKEGYGREK 63 
                                       5678899***********************98 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1     0.001       1.7       3      13 ..      12      22 ..      10      24 .. 0.88
   2 ?    3.8   0.6     0.032        52      28      36 ..      31      39 ..      30      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                           TFIIS_C  3 CpkCgsreayf 13
                                      Cp Cgs e+y 
  gi|386000789|ref|YP_005919088.1| 12 CPVCGSSEMYL 22
                                      *********95 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.032
                           TFIIS_C 28 fykCtkCgh 36
                                       y C++C++
  gi|386000789|ref|YP_005919088.1| 31 VYHCKDCNY 39
                                      599****96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.013        21      17      23 ..      12      18 ..      11      19 .. 0.79
   2 ?    7.2   0.2    0.0025       4.1       1      10 [.      32      41 ..      32      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
                      Rubredoxin_2 17 CpsCgsW 23
                                      Cp Cgs 
  gi|386000789|ref|YP_005919088.1| 12 CPVCGSS 18
                                      9999985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0025
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y+C++C++  
  gi|386000789|ref|YP_005919088.1| 32 YHCKDCNYMG 41
                                      8999999865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.0    0.0016       2.6       2      14 ..      11      23 ..      10      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
                                      EETTTTCEECHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                      +CP+Cgs++++++
  gi|386000789|ref|YP_005919088.1| 11 VCPVCGSSEMYLE 23
                                      8******995544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 455.13
//
Query:       gi|386000790|ref|YP_005919089.1|  [L=410]
Description: extracellular ligand-binding receptor [Methanosaeta harundinacea 6Ac]
Scores for complete 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-26   92.1   2.2    8.2e-26   91.5   2.2    1.3  1  Peripla_BP_6    Periplasmic binding protein
      8e-24   84.4   0.1    1.1e-23   83.9   0.1    1.2  1  ANF_receptor    Receptor family ligand binding region
    7.4e-09   34.9   0.1    9.9e-09   34.5   0.1    1.1  1  LppC            LppC putative lipoprotein
     0.0063   16.1   0.2       0.01   15.4   0.2    1.4  1  Peripla_BP_4    Periplasmic binding protein domain
  ------ inclusion threshold ------
      0.016   14.2   0.0      0.027   13.5   0.0    1.4  1  Peripla_BP_5    Periplasmic binding protein domain
       0.17   12.2   0.0        1.9    8.8   0.0    2.3  2  preATP-grasp_3  pre ATP-grasp 3 domain


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   2.2   2.7e-29   8.2e-26       3     319 ..      31     359 ..      29     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 2.7e-29
                                       EEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHH.TTEET.TEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   3 kiGlltplsGpyassgksllagaqaafeeiNa.aGGin.GrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       +iG+l p+sG+ as+g+s+  + + a ++iN     +n  ++i++++ D+  dp+ + ea ++l   +g ++++gp 
  gi|386000790|ref|YP_005919089.1|  31 TIGALLPMSGDWASTGISAQIALEHAEADINNfLTDMNkSTRIQIIVKDTRTDPEATFEALKELEA-QGLRIIIGPE 106
                                       8*****************99999999999999546666556***********************66.********** PP

                                       SHHHHHHHHHHHHHHT-EEEESS-HHC..CTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHH CS
                      Peripla_BP_6  78 ssavaaavaevlakdgvpvigpagltg..ekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregi 152
                                        sa  ++v+e++++ g+++i+ +++++      + +f+l+ ++ + a+a+++ l++  g+k v+ ++ ++ +g+++i
  gi|386000790|ref|YP_005919089.1| 107 DSASLSRVREYANESGIILISGGSTAPslAISGDTTFRLASDDTNLANAMAD-LMTRNGAKAVVALARNDVWGNDLI 182
                                       *********************887776346999*******************.56668******************* PP

                                       HHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTT..........T-SEEEEESSHHHHHHHHHHHHHTT-SS.S CS
                      Peripla_BP_6 153 aalkaaakaaGgevvgeepvplgttdfsaqvlqikaa..........gadavllagtgadlaallkaaaeaGlda.k 218
                                       +a+++++ + Gg  + + ++ ++++dfs ++  ++a           ga av+l+++ +++  l++a ++  l   +
  gi|386000790|ref|YP_005919089.1| 183 NATAESLSQMGGVKMTPLRYNPNSDDFSQILGDLRALledardeygdGAVAVYLIAFDESMEILVQASRDPALASaR 259
                                       **********998667********************95555555555555899998888888888888887776413 PP

                                       CEEEECCC-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHC CS
                      Peripla_BP_6 219 rillvswsgseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealka 295
                                        +  + +++   + ++++ + a +v +++p f++ ++  vr+++++++++ + +    ++a++ y+aa+l++     
  gi|386000790|ref|YP_005919089.1| 260 WYGTDPSGVLIREDERAA-QFAIKVGFIYPTFSQGNSSVVRRIAEDIRERQKID--MVSYAMNDYDAAWLITYTYLL 333
                                       344444444444334444.4788999999999999**************99887..899****************** PP

                                       CTHCCHHHHHHHHHHS-..BECCCTC CS
                      Peripla_BP_6 296 agsltreavraaleslg..fdgllgp 319
                                       +gs ++++++ al  +   + g  g+
  gi|386000790|ref|YP_005919089.1| 334 TGSSDPADFMRALPVFArtYRGYSGD 359
                                       **********9997633356666665 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.1   3.8e-27   1.1e-23       3     350 ..      50     378 ..      48     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 3.8e-27
                                       HHHHHHHHHHHHT-TTSSTTE.EEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEE CS
                      ANF_receptor   3 leAmklAveeinsdpnllpgi.klgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvi 78 
                                       + A+++A  +in+  + +++  +++++++dt  d++++ ea  ++ ++   ++iGp  s++++ v ++an+  i++i
  gi|386000790|ref|YP_005919089.1|  50 QIALEHAEADINNFLTDMNKStRIQIIVKDTRTDPEATFEALKELEAQGLRIIIGPEDSASLSRVREYANESGIILI 126
                                       679999******9987777666*************************88**************************** PP

                                       ESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT.-EEEEEE CS
                      ANF_receptor  79 sygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleerg.icvalke 154
                                       s gst+p+l       t +r++ +dt +a A++d++++ g k v++++ +d +g+ +++a  e+l++ g ++++   
  gi|386000790|ref|YP_005919089.1| 127 SGGSTAPSLAISGD--TTFRLASDDTNLANAMADLMTRNGAKAVVALARNDVWGNDLINATAESLSQMGgVKMTPLR 201
                                       ***********888..88***********************************************999999999888 PP

                                       EEST...CHHHCHHHHHHHHHHTT....T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC CS
                      ANF_receptor 155 kipe...ssnddevvrkllkeiks....karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpe 224
                                       + p     s++  ++r+ll+++++     a +++l +  e+++ l++a r+  l++    w ++d  +  +  d++ 
  gi|386000790|ref|YP_005919089.1| 202 YNPNsddFSQILGDLRALLEDARDeygdGAVAVYLIAFDESMEILVQASRDPALAS--ARWYGTDPSGVLIREDER- 275
                                       88853333333344555577777787756666666666666666666666666776..9***99998888888888. PP

                                       ..HHHHHTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSH CS
                      ANF_receptor 225 ltgleaaegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgr 301
                                       +  + +  g+++ +  + ns  ++++    e++++        +  ++sy++   Yda +l+ +    ++       
  gi|386000790|ref|YP_005919089.1| 276 AAQFAIKVGFIYPTFSQGNSSVVRRIA---EDIRE------RQKIDMVSYAMND-YDAAWLITYTYLLTG------- 335
                                       568889999999999999999999999...66655......4456667777766.*******99999998....... PP

                                       CCB-HHHHCCHHHHHHHHHHHT-EEEETTSCEEB-TTSBBE.-EEEEEEE CS
                      ANF_receptor 302 alscntlkpweggqkllrylrnvnfeGltGdvkfdengdrv.ptydilnl 350
                                            +++p +  ++l   +  ++++G +Gd  +++ gdr+ + y  + l
  gi|386000790|ref|YP_005919089.1| 336 -----SSDPADFMRALP--VFARTYRGYSGDAVLNDAGDRAfAFYTFWSL 378
                                       .....334556666665..4568999999999999999999777776665 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   3.3e-12   9.9e-09     221     486 ..      31     318 ..      23     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.3e-12
                                       -EEEEE--SSTTHHHHHHHHHHHHHHH...........TT--S-EEEEETTTS..-HHHHHHHHHHTT--EEE---S CS
                              LppC 221 kvalLLPlsGklakvaetirdGFlaak........daetqsnaqvkvfDtaae..slediyaqakaagidlvVGPLl 287
                                        ++ LLP+sG+ a  +   +   + a+        d ++ +++q+ v Dt +   +  ++ ++++a+g ++++GP  
  gi|386000790|ref|YP_005919089.1|  31 TIGALLPMSGDWASTGISAQIALEHAEadinnfltDMNKSTRIQIIVKDTRTDpeATFEALKELEAQGLRIIIGPED 107
                                       4899**********9999999999888889888777778888888888*88874466677899************** PP

                                       HHHHHHHHHSGG.GTTSEEEES---TT---BTTEEE----HHHH..HHHHHHHHHHTT-SSEEEEEESSHHHHHHHH CS
                              LppC 288 kqnvdkllaqeqlvqsidvLaLNssdnsraiaqlcyfgLspEde..aesaAsklwadgvRnplvlvpqndlGrRvve 362
                                          ++ + + ++   +i +++  s+  s ai++   f L+ +d   a++ A+ +  +g + +++l+ ++ +G+  ++
  gi|386000790|ref|YP_005919089.1| 108 SASLSRVREYANE-SGIILISGGSTAPSLAISGDTTFRLASDDTnlANAMADLMTRNGAKAVVALARNDVWGNDLIN 183
                                       *******999888.8999************************975578899************************** PP

                                       HHHHHHHHHHSS-.-EEEEESSGGGHHHHHH..........HH-.TTTEEEEE---HHHHHHHHHHHHT.T-TTEEE CS
                              LppC 363 AFnerwqqlagtd.aaielvdqpadlaqqlk..........dasrqdidavyivanskelaeikptlanasakdlkl 428
                                       A  e+  q++g +   +++  +  d +q l           d+  + + avy++a  + +  +            + 
  gi|386000790|ref|YP_005919089.1| 184 ATAESLSQMGGVKmTPLRYNPNSDDFSQILGdlralledarDEYGDGAVAVYLIAFDESMEILVQASRDPALASARW 260
                                       ***********995567777667777776667889998777555567889999998877665433222223333445 PP

                                       EE-GGG--H.HT-HHHHHHTTT-EEEE-GGGG-SSSHHHHHHH.HHTTT-HHHHHHHHH CS
                              LppC 429 yasSrsvsg.ntkpeqdedlngiqfsdiPflvdpassikkkvaaklpeaegsllrLyAl 486
                                       y++  s      + +  ++   + f   P + +++ss+ +++a  + e +   +  yA+
  gi|386000790|ref|YP_005919089.1| 261 YGTDPSGVLiREDERAAQFAIKVGFI-YPTFSQGNSSVVRRIAEDIRERQKIDMVSYAM 318
                                       55554433312222222222333333.45666666666666666666666666666666 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   3.5e-06      0.01      17     128 ..      61     170 ..      47     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHHTTCEEEEEECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTT...G CS
                      Peripla_BP_4  17 regleeaakelgaevtvvgdaendaaeQvaqiedaiakgvdgiivapvdstalapalkkakaaGIpVvafdsd...d 90 
                                       ++ l ++ k   ++ +v  d+++d ++  +++  + a+g   ii+ p ds+ l+ + + a++ GI  ++  s     
  gi|386000790|ref|YP_005919089.1|  61 NNFLTDMNKSTRIQIIV-KDTRTDPEATFEALKELEAQGLR-IIIGPEDSASLSRVREYANESGIILISGGSTapsL 135
                                       55666666666666666.7*********************9.***************************88888888 PP

                                       CTTT-CEEEEEC-HHHHHHHHHHHHHHHCTTH.EEEEE CS
                      Peripla_BP_4  91 apsgerlayvgfdneaaGelqaeylaeklggkkgkvvi 128
                                       a sg+ +   + d +  + ++a+++ ++  +    vv+
  gi|386000790|ref|YP_005919089.1| 136 AISGDTTFRLASDDTNLANAMADLMTRNGAKA---VVA 170
                                       99***********************9988753...333 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.1e-06     0.027       2     190 ..      31     221 ..      30     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-06
                      Peripla_BP_5   2 kvGvLhSlsGtmaisekslkdaallaieeina..agGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcw 76 
                                        +G L  +sG  a +  s++ a   a ++in+  ++  ++++i+ +v+d + d+e+  e  ++l e +++++++G  
  gi|386000790|ref|YP_005919089.1|  31 TIGALLPMSGDWASTGISAQIALEHAEADINNflTDMNKSTRIQIIVKDTRTDPEATFEALKEL-EAQGLRIIIGPE 106
                                       588888889988888877777777777777763223346899************9988777776.669********* PP

                      Peripla_BP_5  77 tSasRkavlpvveelnalLfYp.vqYEGeEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnr 152
                                        Sas   v +  +e+  +L+    +     +s +  +  a+ + ++ +a++ l++++gak v+ +  + v+     +
  gi|386000790|ref|YP_005919089.1| 107 DSASLSRVREYANESGIILISGgSTAPSLAISGDTTFRLASDDTNLANAMADLMTRNGAKAVVALARNDVWGNDLIN 183
                                       ***************999987525667899******************************************99888 PP

                      Peripla_BP_5 153 ilkallkakgg.evvgeeYlplgssdvqkivakikkakp 190
                                        +++ l++ gg ++   +Y p +s+d+++i+ ++++   
  gi|386000790|ref|YP_005919089.1| 184 ATAESLSQMGGvKMTPLRYNP-NSDDFSQILGDLRALLE 221
                                       888888888774777778877.78999999999887655 PP

>> preATP-grasp_3  pre ATP-grasp 3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00063       1.9      17      76 ..      70     132 ..      60     132 .. 0.88
   2 ?    0.2   0.0      0.31   9.2e+02      32      47 ..     312     327 ..     295     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00063
                    preATP-grasp_3  17 p.avevlvvdseedvdetfrrl..aaeaDaVlvIAPEtdgiLarltrlveaagkrlLGssskA 76 
                                       + +++++v d++ d+ +tf+ l  +++  +  +I PE    L+r+ + + ++g++l++  s+A
  gi|386000790|ref|YP_005919089.1|  70 StRIQIIVKDTRTDPEATFEALkeLEAQGLRIIIGPEDSASLSRVREYANESGIILISGGSTA 132
                                       357999999999********99889999999*************************9888776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.31
                    preATP-grasp_3  32 etfrrlaaeaDaVlvI 47 
                                       + ++ +++++Da ++I
  gi|386000790|ref|YP_005919089.1| 312 DMVSYAMNDYDAAWLI 327
                                       66778999******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3100.45
//
Query:       gi|386000791|ref|YP_005919090.1|  [L=497]
Description: Efflux pump antibiotic resistance protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.9e-56  189.2  52.4    9.9e-56  189.2  52.4    1.7  2  MFS_1       Major Facilitator Superfamily
    1.3e-06   27.5  19.7      5e-05   22.3   4.1    2.2  2  MFS_1_like  MFS_1 like family
    0.00028   19.6  16.3    0.00028   19.6  16.3    3.7  3  MFS_2       MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.2  52.4   1.6e-59   9.9e-56       3     352 ..      53     440 ..      51     441 .. 0.93
   2 ?    0.1   1.0     0.051     3e+02     222     260 ..     440     486 ..     436     495 .. 0.38

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 1.6e-59
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       +aafl a+a s++++alp  ++ ++g+++  +g+++t   l++av+++plGr +d +Gr+r++ lg+ +fa+++l++
  gi|386000791|ref|YP_005919090.1|  53 VAAFLPAFANSAINVALP-PIGVEFGMDAVLLGWVVTSHLLAMAVFMVPLGRAADIWGRKRFFTLGMGIFAASSLFC 128
                                       689999************.8*****************************************************9999 PP

                             MFS_1  80 lfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       +f +s+  +l+++r++qG++++++f +++al++ +fp+ ergra+g+  +++ lG  lgp lgg+l+s+lgWr++f+
  gi|386000791|ref|YP_005919090.1| 129 AF-PSSGsALIFFRLFQGMASAMIFGTAVALLTSVFPPGERGRALGINVTAVYLGLSLGPFLGGILTSYLGWRSIFL 204
                                       99.888999******************************************************************** PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeee............................................ 188
                                       ++ ++++ +     +ll+ ++ e ++++ + e+                                            
  gi|386000791|ref|YP_005919090.1| 205 VNVPLGAWV-----VLLTLRRLEGEWVEAAGERfdwlgssiyalalistvygltslpsaagagflalgllgllafgl 276
                                       *******99.....555556666666666666667799*************************************** PP

                             MFS_1 189 .kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailalla 264
                                        + + ++p+++  ++++ ++v+ +  +a+l++  +++++ + l+lylq+v gls  l ag++la   +v a+l+++a
  gi|386000791|ref|YP_005919090.1| 277 vELRSRSPVLN-VRLFRDNRVFALSNLAALINYGATFAVAFVLTLYLQTVKGLS-PLAAGFVLASQPAVQAVLSPWA 351
                                       99999999999.********997566777777779999****************.8********************* PP

                             MFS_1 265 grlsdrlgrrrrlllallllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagtasgl 340
                                       grlsdr+ ++     +++++++++l+lal    ++ + +++ vl+l+G+g++f++++ ++++++++ ++  g asg 
  gi|386000791|ref|YP_005919090.1| 352 GRLSDRIEAQVVASAGMGFVAAGLLLLALGLDGETGLGFIVaVLALLGLGFAFFSSPNTNAIMSSVEKRDYGVASGM 428
                                       ******9988888888888888888888888888888888889999******************************* PP

                             MFS_1 341 fntagslggalg 352
                                       ++t++s+g++ +
  gi|386000791|ref|YP_005919090.1| 429 VGTMRSIGMMAS 440
                                       ********9976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.051
                             MFS_1 222 gfsglltllplylqevlgls........glllaglllallalvgail 260
                                        +++++t+l +++  v   +        ++  ++ ++ +l+++g+++
  gi|386000791|ref|YP_005919090.1| 440 SMAIAMTFLSIFMGRVQVTPevypqfleAVTAVLSVFFVLCVLGIFA 486
                                       33334455555433333333555533332222222233333333333 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   4.1   8.4e-09     5e-05     223     383 ..      43     203 ..       8     205 .. 0.85
   2 !   11.0   7.7   2.4e-05      0.14      21     192 ..     317     482 ..     304     494 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.4e-09
                        MFS_1_like 223 knpeviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiall 298
                                       ++ +v+++ +va++l ++ + + n +   +  e g    llG +v+   +a  ++ +   +  ++ G  +  ++++ 
  gi|386000791|ref|YP_005919090.1|  43 SKSSVLFIATVAAFLPAFANSAINVALPPIgVEFGMDAVLLGWVVTSHLLAMAVFMVPLGRAADIWGRKRFFTLGMG 119
                                       555666666666666666665555555555568899999*********9999999999******************* PP

                        MFS_1_like 299 ayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwd 375
                                       ++++  l  a+ ++ + ++++ +++g++ ++++++av     ++p++ +++  g+ +++ + lG  lG ++GG+l  
  gi|386000791|ref|YP_005919090.1| 120 IFAASSLFCAFPSSGSALIFFRLFQGMASAMIFGTAVALLTSVFPPGERGRALGINVTAVY-LGLSLGPFLGGILTS 195
                                       *******************************************************988754.888999999999987 PP

                        MFS_1_like 376 lksaiflF 383
                                       + + + +F
  gi|386000791|ref|YP_005919090.1| 196 YLGWRSIF 203
                                       77777776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.4e-05
                        MFS_1_like  21 Yltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesk 96 
                                        lt+yl+  kgl++   g++++  p+++ + +p  g l+Dr++++  v+++++ + a+ +l ll             
  gi|386000791|ref|YP_005919090.1| 317 VLTLYLQtVKGLSPLAAGFVLASQPAVQAVLSPWAGRLSDRIEAQ-VVASAGMGFVAAGLL-LL------------- 378
                                       589***9779*******************************9876.466666666665555.33............. PP

                        MFS_1_like  97 levsvaqdvdaektfwilfllvvlasfflaa.ilvlldaatlkelgedrkdyGrqrlfGsv.GyaifafitGilidh 171
                                         +   ++++ + ++++l+ll + + ff+++ +++++ ++  ++ g  ++  G  r  G   ++ai++++++i++  
  gi|386000791|ref|YP_005919090.1| 379 -ALGLDGETGLGFIVAVLALLGLGFAFFSSPnTNAIMSSVEKRDYGVASGMVGTMRSIGMMaSMAIAMTFLSIFMGR 454
                                       .2557888899999999****999***99884689999999999***************865899**********99 PP

                        MFS_1_like 172 ysvnllp.........ysallyvlaallvi 192
                                       ++v+  p         + a+l v+ +l v+
  gi|386000791|ref|YP_005919090.1| 455 VQVT--PevypqfleaVTAVLSVFFVLCVL 482
                                       9884..445557644433444444443333 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   9.2    0.0064        38     260     343 ..      82     163 ..      75     201 .. 0.76
   2 ?    0.7   0.6     0.025   1.5e+02      98     181 ..     190     272 ..     171     279 .. 0.70
   3 !   19.6  16.3   4.6e-08   0.00028      13     190 ..     311     488 ..     296     495 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0064
                             MFS_2 260 aasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpw 336
                                          ++ + + ++++++++   ++a  +g+k+ + lg+ + ++ ++++ +   s  +l ++ l+ ++ + ++++ ++ 
  gi|386000791|ref|YP_005919090.1|  82 LLGWVVTSHLLAMAVFMVPLGRAADIWGRKRFFTLGMGIFAASSLFCAFP-SSGSALIFFRLFQGMAS-AMIFGTAV 156
                                       56789999999999*****************************9999999.55555555555555544.55666666 PP

                             MFS_2 337 smladvv 343
                                       ++l+ v+
  gi|386000791|ref|YP_005919090.1| 157 ALLTSVF 163
                                       6666655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.025
                             MFS_2  98 iwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgg.lkserkgyli 173
                                         +l +y+++r  + l+++p +++v+ lt ++ e + + +  + + +lg+ + a+  +  v  l++ ++ +  g+l+
  gi|386000791|ref|YP_005919090.1| 190 GGILTSYLGWRSIF-LVNVPLGAWVVLLTLRRLEGEWVEAAGERFDWLGSSIYALALISTVYGLTSlPSAAGAGFLA 265
                                       55667777787766.89999999999999999999999999999999998887765555555555525555555555 PP

                             MFS_2 174 faliialL 181
                                       ++l+  lL
  gi|386000791|ref|YP_005919090.1| 266 LGLL-GLL 272
                                       5554.444 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 4.6e-08
                             MFS_2  13 svllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsiillftpp 89 
                                       + ++a++l+ ++  v gls+ ++g+vl +   v a+  p +G l+d+  +   +    +++sa +  v+  ll +++
  gi|386000791|ref|YP_005919090.1| 311 TFAVAFVLTLYLQTVKGLSPLAAGFVLASQPAVQAVLSPWAGRLSDRIEA---Q----VVASAGMGFVAAGLLLLAL 380
                                       5688999999*************************************999...3....5666666666666666666 PP

                             MFS_2  90 elsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgg... 163
                                       +l   + + ++++++ ll + +++f+ p++  ++    ++ +   ++++  ++  +g ++ +++a++++ i+ g   
  gi|386000791|ref|YP_005919090.1| 381 GLDGETGLGFIVAVLALLGLGFAFFSSPNTNAIMSS-VEKRDYGVASGMVGTMRSIGMMASMAIAMTFLSIFMGrvq 456
                                       666778888888999999999********9999876.99999999999999****************9999999999 PP

                             MFS_2 164 .....lkserkgylifaliialLmllgviivv 190
                                            + +  ++ +++++++ +L +lg++++ 
  gi|386000791|ref|YP_005919090.1| 457 vtpevYPQFLEAVTAVLSVFFVLCVLGIFASL 488
                                       98555555555555666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3832.29
//
Query:       gi|386000792|ref|YP_005919091.1|  [L=194]
Description: NADPH-dependent FMN reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-33  115.6   0.0    2.2e-33  115.2   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    7.6e-09   35.6   0.0      1e-08   35.2   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.025   14.4   0.3       0.83    9.5   0.1    2.3  2  TetR_N        Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.0   3.6e-37   2.2e-33       1     150 [.       1     154 [.       1     158 [. 0.93

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 3.6e-37
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH- CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaa 73 
                                       mki++i+GS+r ++ t+ ++++a+++l+e+g+ ++ ++++++ i pc   ++c+  +e  +   dd+ +l+  +++a
  gi|386000792|ref|YP_005919091.1|   1 MKIVGICGSPR-EKATDHILKEALRMLEERGFATTSFTVRGKrISPClhcDFCLTNKE--CRIRDDMYQLYPLLQEA 74 
                                       9*********8.778*******************************998877776664..69*************** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSE CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraa 147
                                       d+++++tP+Yng++s++ K+++Dr+++   ++ + +rgK++++vavgg+r gg++++     ++   +g+i+v+++ 
  gi|386000792|ref|YP_005919091.1|  75 DGIVFATPVYNGGVSAQTKAVMDRCRAlvAADFDFFRGKAGMAVAVGGDRMGGQELAITQIIAFYvLNGVIPVGGGS 151
                                       *************************99**9***********************************668999998887 PP

                                       EEE CS
                           FMN_red 148 vav 150
                                       + +
  gi|386000792|ref|YP_005919091.1| 152 FGA 154
                                       765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.7e-12     1e-08       1     107 [.       1     102 [.       1     138 [. 0.79

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.7e-12
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTTC.HHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeekp.adveseq.iek 74 
                                       mki+ i ++pr+  + + ++++++++ le+ g    t + +      p l  +     l+++e + +  ++ q    
  gi|386000792|ref|YP_005919091.1|   1 MKIVGICGSPRE--KATDHILKEALRMLEERG-FATTSFTVRGKrISPCLHCDFC---LTNKE-CrIRDDMYQlYPL 70 
                                       9999*******9..788***************.8889999999744444444333...57777.66888888888** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TT CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDrvltag 107
                                       l++ad iv+++P+++ gv+a+ K+ +Dr  +a 
  gi|386000792|ref|YP_005919091.1|  71 LQEADGIVFATPVYNGGVSAQTKAVMDRC-RAL 102
                                       ***************************94.444 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00014      0.83       1      18 [.      18      35 ..      18      37 .. 0.93
   2 ?    2.8   0.0     0.017     1e+02      17      47 .]      90     120 ..      86     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHHHTTT-- CS
                            TetR_N  1 IldaArelfaerGydatt 18
                                      Il+ A+++++erG++ t+
  gi|386000792|ref|YP_005919091.1| 18 ILKEALRMLEERGFATTS 35
                                      99*************998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.017
                                       --HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                            TetR_N  17 ttvreIAkrAGvskgalYryFpsKeeLleal 47 
                                       ++++++ +r+    +a +  F++K++++ a+
  gi|386000792|ref|YP_005919091.1|  90 AQTKAVMDRCRALVAADFDFFRGKAGMAVAV 120
                                       5688899999999999999*******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1675.14
//
Query:       gi|386000793|ref|YP_005919092.1|  [L=190]
Description: flavoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-16   59.5   0.0    3.9e-16   59.2   0.0    1.3  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   2.2e-20   3.9e-16       1     106 [.       9     133 ..       9     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.2e-20
                                       EEEEEEE-SSCGGGCH.HHHHHHHHH...TTEEEEEEESCHHHHCCHHGGS.....TCSSHHHHHHCT......... CS
                      Flavoprotein   1 kkillgiTGsvaaika.lellekLkk...egievqvvltkaAkkfiskeklklaa.redpilhielrr......... 63 
                                       k++++giTGs + i + + +++++++   +++e++v+++ka+ ++++  ++kl    e++       +         
  gi|386000793|ref|YP_005919092.1|   9 KRVVWGITGSGDRIREtAAVMKEMRRkydDEVEIRVYISKAGDQVVK--YYKLFPeLEEEFD-----Kiwveanana 78 
                                       79************99999*******9999*****************..5555432222333.....2555557788 PP

                                       ..........TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE CS
                      Flavoprotein  64 ..........wadllviaPasantlakianGiadnlltlilra..takkpiliaP 106
                                                 +++l++iaPa+ nt+aki + iad++lt+ + +  +   p +i+P
  gi|386000793|ref|YP_005919092.1|  79 pflagqvqmgRFELILIAPATSNTVAKISLRIADTMLTNAAIMsqKVMLPLYIMP 133
                                       9999999999****************************99955455556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1197.99
//
Query:       gi|386000794|ref|YP_005919093.1|  [L=93]
Description: Transcriptional regulator TrmB, putative, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0079   16.1   0.0      0.011   15.6   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.055   13.7   0.0       0.12   12.6   0.0    1.6  2  HTH_34    Winged helix DNA-binding domain
       0.12   12.3   0.0       0.13   12.2   0.0    1.1  1  MoaF      MoaF N-terminal domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-06     0.011      16      64 ..       3      58 ..       1      68 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYra 64
                                      +L + ++at +ei   +++ ++ v  ++r+L + +++  ++++       +++Y+ 
  gi|386000794|ref|YP_005919093.1|  3 YLACVDEATSREIEMGSDLRQPEVSIAMRELRKLDWISERDEKnpgkgrpYRIYKL 58
                                      5667799******************************9999888999996557775 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05      0.12       6      60 ..       1      57 [.       1      74 [. 0.80
   2 ?   -0.8   0.0       0.3   1.8e+03      42      53 ..      67      78 ..      55      86 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                            HTH_34  6 lsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefk..gkkprtllr 60
                                      ++yLa vdea+ +e+     + + + s+ ++ L k ++i+ + e++  +++p  +++
  gi|386000794|ref|YP_005919093.1|  1 MTYLACVDEATSREIEMGSDLRQPEVSIAMRELRKLDWISERDEKNpgKGRPYRIYK 57
                                      89*************************************876555411444555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                            HTH_34 42 gYievdkefkgk 53
                                      +Y+e +k+ +  
  gi|386000794|ref|YP_005919093.1| 67 DYLETNKKTETD 78
                                      455555544433 PP

>> MoaF  MoaF N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13      38      86 ..      25      76 ..       3      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                      EEE...EETTEEEEEE..TTTTEEEEEE-EEEECCTTEE.EEEEEETTSTTE CS
                              MoaF 38 tieheffdadtlrWte..eekeesgeaeyeatevregiY.fvdflkkereae 86
                                      ++++ + +  +l+W +  +ek+     +y+++++++g+Y ++d+l++++++e
  gi|386000794|ref|YP_005919093.1| 25 EVSIAMRELRKLDWISerDEKNPGKGRPYRIYKLKKGLYdIIDYLETNKKTE 76
                                      5555667778999988644444555689***********7789999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 687.40
//
Query:       gi|386000795|ref|YP_005919094.1|  [L=235]
Description: alanyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   49.8   0.4    5.2e-13   48.9   0.4    1.5  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    5.8e-12   44.9   0.0    8.1e-12   44.4   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
  ------ inclusion threshold ------
      0.084   12.8   0.0        0.2   11.6   0.0    1.7  2  pRN1_helical  Primase helical domain


Domain annotation for each model (and alignments):
>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.4   8.7e-17   5.2e-13       1      44 []     185     228 ..     185     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 8.7e-17
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       vr v+++ i+ ++CgGtHv++TgeIg +k l+ e+++k +rR+y
  gi|386000795|ref|YP_005919094.1| 185 VRGVEVEGIDLQACGGTHVQRTGEIGRIKMLKAENKGKANRRVY 228
                                       899***88***********************************9 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   1.4e-15   8.1e-12     474     552 .]      13      89 ..       8      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.4e-15
                                       EEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXH CS
                      tRNA-synt_2c 474 efveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevde 550
                                       +f+ +v e+ ++ v+Ld+T+fY++sGGq  D+G++   g++f v+ v+ a+g + h++      l  g+ v++e+d+
  gi|386000795|ref|YP_005919094.1|  13 SFEGRVVEVLDDEVILDKTAFYPDSGGQPHDTGTLAMGGESFPVVYVRPADGKIAHRVGRP--GLVAGELVRGEIDW 87 
                                       567778889999*********************************************9996..8999*********9 PP

                                       HH CS
                      tRNA-synt_2c 551 er 552
                                       er
  gi|386000795|ref|YP_005919094.1|  88 ER 89 
                                       86 PP

>> pRN1_helical  Primase helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7     1e+04      20      33 ..      13      26 ..      10      29 .. 0.82
   2 ?   11.6   0.0   3.4e-05       0.2      71     111 ..     116     156 ..      79     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                      pRN1_helical 20 rykgktleaireel 33
                                       + g+ +e + +e+
  gi|386000795|ref|YP_005919094.1| 13 SFEGRVVEVLDDEV 26
                                      58999999999998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.4e-05
                      pRN1_helical  71 tyaeigidrsrgdwallyvllshgatdldvleqllpedskv 111
                                       t  +igidrsr d++l  +  s  a  ++ +++++ +d  v
  gi|386000795|ref|YP_005919094.1| 116 TGNQIGIDRSRVDFSLQDFDRSDLADYVETVNEIIRQDRAV 156
                                       5578******************9999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1437.82
//
Query:       gi|386000796|ref|YP_005919095.1|  [L=280]
Description: Putative methanogenesis marker protein 8 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-106  355.6   0.2   1.5e-106  355.3   0.2    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.3   0.2  8.6e-111  1.5e-106       3     257 .]       4     254 ..       3     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 355.3 bits;  conditional E-value: 8.6e-111
                           DUF2099   3 iealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGasE 79 
                                       +e+lg++rvvvkdg+vve gep +++CPlf+k+rgikeit+ea  +n+efr++e+G+ft+ Rkle++  fv+fGasE
  gi|386000796|ref|YP_005919095.1|   4 MELLGRTRVVVKDGRVVETGEPLLRWCPLFDKVRGIKEITSEAAAANMEFRMREHGMFTPARKLEMD-VFVGFGASE 79 
                                       9******************************************************************.********* PP

                           DUF2099  80 ilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveGvk 156
                                       +++ta ++gli+aav+vcdgaGtv+++np+l+qg+gg+isGlv+T+Pi+ev++ ie +gg+vld++ta+idqv+G+k
  gi|386000796|ref|YP_005919095.1|  80 VMMTATRRGLIEAAVTVCDGAGTVVTANPSLIQGMGGWISGLVTTDPIPEVLAGIEARGGVVLDPATARIDQVAGAK 156
                                       ***************************************************************************** PP

                           DUF2099 157 kAiekgykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkkall 233
                                        A+e+ yk++avtva+ae+a++lr+leke++v+il+++vh+tgi +e ae+l++aaD+vt+cAsk +re v+  +l+
  gi|386000796|ref|YP_005919095.1| 157 IAAER-YKSFAVTVADAETAERLRALEKERDVRILVVGVHLTGIGEEGAERLLAAADIVTSCASKPLREKVR--PLV 230
                                       **998.****************************************************************99..9** PP

                           DUF2099 234 qvgksvpvfaltekGkelilerlk 257
                                       qvg++vp+f+lt +Gke+++er+k
  gi|386000796|ref|YP_005919095.1| 231 QVGTAVPLFGLTAWGKEVLVERAK 254
                                       *********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 2019.11
//
Query:       gi|386000797|ref|YP_005919096.1|  [L=211]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1606.09
//
Query:       gi|386000798|ref|YP_005919097.1|  [L=183]
Description: hypothetical protein Mhar_0081 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1326.73
//
Query:       gi|386000799|ref|YP_005919098.1|  [L=313]
Description: Putative snoRNA binding domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-40  137.2   0.2    8.4e-40  136.7   0.2    1.3  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7   0.2   4.7e-44   8.4e-40      83     229 ..     141     284 ..      95     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 4.7e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHH CS
                               Nop  83 edlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekal 159
                                       e+ + i  ++++vl+l+++r+++++ le+   +  PNls+L G+ +aar+is aGgL +L++mPas iq++Gaek+l
  gi|386000799|ref|YP_005919098.1| 141 EEEEAIGVVARSVLDLADARRSVQRSLETATVQASPNLSSLAGPLLAARIISRAGGLARLSEMPASAIQVMGAEKSL 217
                                       56677888999****************************************************************** PP

                                       CCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                               Nop 160 fralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                       f++l+ k  +pk+G+iy ++ v+  tp++l++++aR+laaK+a+aaRiD f   +g++ ++l+  ++++++
  gi|386000799|ref|YP_005919098.1| 218 FKHLRgKAPSPKHGMIYRHPAVM-GTPRRLRGRAARALAAKLAIAARIDRF---SGEVNDRLKPALDRRID 284
                                       *****5559**************.66***********************99...59999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1985.37
//
Query:       gi|386000800|ref|YP_005919099.1|  [L=519]
Description: Single-stranded DNA-binding replication protein A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00039   20.4   0.3        6.8    6.8   0.0    3.6  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.018   14.9   0.0       0.04   13.8   0.0    1.5  1  RMI1_C           Recq-mediated genome instability protein 1, 
      0.041   13.3   0.2        4.2    6.7   0.1    3.0  3  Gasdermin        Gasdermin pore forming domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0011       6.8      23      71 ..     104     149 ..      85     156 .. 0.86
   2 !    4.4   0.0    0.0062        37      23      48 ..     210     243 ..     189     268 .. 0.77
   3 !    4.9   0.0    0.0043        26      23      72 ..     315     361 ..     295     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                                       EEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEE CS
                   tRNA_anti-codon  23 lrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkve 71 
                                       l D+tg+i+ v +    ++ + +l+ G+ +  +     +++g+ +++k +
  gi|386000800|ref|YP_005919099.1| 104 LGDETGTIKFVKWT---KADLPELEAGKSYLFKnAVTDEFQGK-FSVKLN 149
                                       89************...****************5555555666.999987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0062
                                       EEETTEEEEEEEET........HHHHHHHTTS-T CS
                   tRNA_anti-codon  23 lrDgtgriqvvlfr........eeatklaenlke 48 
                                       + D+tg+i+ v +         e++++l++nl  
  gi|386000800|ref|YP_005919099.1| 210 IGDETGTIKFVKWAksgipdlaEGKSYLFKNLVT 243
                                       78************66666665555555555543 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0043
                                       EEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon  23 lrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                       + D+tg i+ v +    ++   +l eG+ +  +  v+   +g +++k ++
  gi|386000800|ref|YP_005919099.1| 315 IGDETGVIKFVKWA---KSEIPDLAEGKSYLFKNVVTDEFEGRFSVKLNR 361
                                       78************...999999999999999987777755558888775 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.7e-06      0.04      34      88 ..     409     465 ..     394     475 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-06
                            RMI1_C  34 llgkleaskgkwql..kakisDGsaildvdlssevlteligfspaelkeslalkkdq 88 
                                       + g+  +++g+++l  ka+++DG ++ +v +++e  ++l+g+s +e k+++    d+
  gi|386000800|ref|YP_005919099.1| 409 VCGEHGKQEGTYDLriKAVLDDGVKVQEVLINRERTESLMGISMEEAKTMAMEALDH 465
                                       5566677788876522789**************************976665554444 PP

>> Gasdermin  Gasdermin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0007       4.2      68     144 ..     122     195 ..     112     202 .. 0.85
   2 ?    0.9   0.0     0.041   2.5e+02      68     129 ..     228     289 ..     222     307 .. 0.78
   3 ?    1.2   0.0     0.034     2e+02      67     124 ..     332     390 ..     327     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0007
                         Gasdermin  68 pevvesdffkfkdkveqkvegsvevalgvelkvsg.kaavesqsssgslevqevsvqqlkleslqerklldaepsfL 143
                                       pe++  ++  fk++v ++ +g+  v+l  +  v + + +v   + s+s +vqe++v++ k e     + +d++ ++ 
  gi|386000800|ref|YP_005919099.1| 122 PELEAGKSYLFKNAVTDEFQGKFSVKLNRTSGVEElTKVVAAAEPSASSQVQEMKVSEIKEEG----RWIDLRAKVV 194
                                       89999**********************97777765367788999999*********9999887....6667776666 PP

                         Gasdermin 144 q 144
                                       q
  gi|386000800|ref|YP_005919099.1| 195 Q 195
                                       5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.041
                         Gasdermin  68 pevvesdffkfkdkveqkvegsvevalgvelkvsgkaavesqsssgslevqevsvqqlkles 129
                                       p++ e ++  fk+ v ++ +g+  v+l  +  v   +a    s     +vqe++++q   e 
  gi|386000800|ref|YP_005919099.1| 228 PDLAEGKSYLFKNLVTDEFQGRFSVKLNRTSGVEPLEAEVEASDAPGGQVQEMKISQIGEEG 289
                                       88999999******************998888887776666666677788888888876665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.034
                         Gasdermin  67 epevvesdffkfkdkveqkvegsvevalgvelkv.sgkaavesqsssgslevqevsvqq 124
                                        p++ e ++  fk++v ++ eg+  v+l  + ++   ++ ve+  ++++    +v+vq+
  gi|386000800|ref|YP_005919099.1| 332 IPDLAEGKSYLFKNVVTDEFEGRFSVKLNRTSEIlPLEEEVEVSPQEANFTGAIVDVQK 390
                                       5899999*******************999554441456667778888888877777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 4045.75
//
Query:       gi|386000801|ref|YP_005919100.1|  [L=287]
Description: hypothetical protein Mhar_0084 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2070.26
//
Query:       gi|386000802|ref|YP_005919101.1|  [L=76]
Description: AsnC family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-12   45.9   0.6    4.7e-12   45.7   0.6    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    8.5e-05   22.5   0.9    9.7e-05   22.3   0.9    1.1  1  NapD            NapD protein
    0.00017   21.4   0.1    0.00021   21.2   0.1    1.1  1  GYD             GYD domain
     0.0029   18.2   0.1       0.36   11.4   0.1    2.1  2  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.6   1.1e-15   4.7e-12       2      71 ..       7      72 ..       6      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.1e-15
                                      EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                    AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                                      +v++ pg+    +++  al+e++ ++ +y+v G+yd+++   v+ l  l+r++++ ++++ +v+ t+t +
  gi|386000802|ref|YP_005919101.1|  7 MVKVVPGQ---ERSVYNALREIDGIKDVYHVFGEYDFVVVLEVEGLSVLNRLVDT-IREIHNVTATQTVV 72
                                      69999999...*****************************************999.************76 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.9   2.2e-08   9.7e-05       7      70 ..       7      71 ..       1      74 [. 0.93

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-08
                              NapD  7 vVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsaslv 70
                                       V++ p++  +v +al++++g+ +v+++ +e   Vvv+E e    l + +++i+++ +V +++ v
  gi|386000802|ref|YP_005919101.1|  7 MVKVVPGQERSVYNALREIDGIkDVYHVFGEYDFVVVLEVEGLSVLNRLVDTIREIHNVTATQTV 71
                                      799******************879***********************************999876 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   4.6e-08   0.00021      16      78 ..       9      70 ..       4      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.6e-08
                               GYD 16 kdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrt.et 78
                                      k  p +++++  al ++++g ++++y ++GeyD+vv++E++  +   +l  ++++  +v++ +t
  gi|386000802|ref|YP_005919101.1|  9 KVVPGQERSVYNAL-REIDG-IKDVYHVFGEYDFVVVLEVEGLSVLNRLVDTIREIHNVTAtQT 70
                                      55566666677777.66655.689****************998888888888887777776555 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0     0.009        40      64      79 ..      17      32 ..      13      32 .. 0.89
   2 !   11.4   0.1     8e-05      0.36      51      77 ..      41      67 ..      36      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.009
                             ACT_4 64 rviakLraipgVisVe 79
                                      +v ++Lr+i+g+++V+
  gi|386000802|ref|YP_005919101.1| 17 SVYNALREIDGIKDVY 32
                                      7899**********96 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8e-05
                             ACT_4 51 kitveVkdvehLsrviakLraipgVis 77
                                       + +eV+ ++ L+r+++ +r+i++V+ 
  gi|386000802|ref|YP_005919101.1| 41 VVVLEVEGLSVLNRLVDTIREIHNVTA 67
                                      6789*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 592.34
//
Query:       gi|386000803|ref|YP_005919102.1|  [L=611]
Description: type 2 DNA topoisomerase 6 subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-64  216.1   0.0    3.4e-64  215.5   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    2.4e-32  111.5   0.0    4.5e-32  110.6   0.0    1.5  1  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
    3.6e-08   33.9   0.0    7.4e-08   32.9   0.0    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    4.1e-06   26.7   0.0    8.3e-06   25.7   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    7.6e-06   25.0   0.2    5.1e-05   22.2   0.0    2.0  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.0   9.5e-68   3.4e-64       1     159 []     309     472 ..     309     472 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 9.5e-68
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+tdclspigeeli++gl+ke++++f+a+++r+++vy g+pf vEvg+ayGGel+ + k+e+lRfaNrvPLly++g+
  gi|386000803|ref|YP_005919102.1| 309 PPTDCLSPIGEELIRAGLEKEYRVDFIATTKRPVSVYAGNPFQVEVGLAYGGELKGDGKVEVLRFANRVPLLYQQGG 385
                                       99*************************************************************************** PP

                    Topo-VIb_trans  78 dvitkavksinwkrYkleq.....pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylsk 149
                                       ++it+a+++++wk Y+l+q     p +p+++lvh+ast++Pf+se+K+a+adv+ei +e++l l+ev+rkL++y+sk
  gi|386000803|ref|YP_005919102.1| 386 CAITHAIENVSWKIYSLSQpgggvPVGPAALLVHIASTNIPFTSESKDAVADVPEIVAEVELGLKEVGRKLRRYISK 462
                                       ***********************999*************************************************** PP

                    Topo-VIb_trans 150 kekekeekek 159
                                       k++ +e+kek
  gi|386000803|ref|YP_005919102.1| 463 KSALSERKEK 472
                                       ***9999876 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   1.3e-35   4.5e-32       2     113 ..     493     604 ..     492     605 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.3e-35
                                       SS---SHHHHHHHTT-EEEEEEE--SSS-.EEEEEEE---------EEE--EES-----------EEE-SSSEEE-E CS
                           Top6b_C   2 reepdidpvvArimgnvlvereveengdg.vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkW 77 
                                       reepdi+pvvA+imgn+lv+r+v ++ +g + v+l+v N++d ++ f+lhe++++e+e+++p a+v+++++ yd+ W
  gi|386000803|ref|YP_005919102.1| 493 REEPDINPVVAKIMGNLLVKRSVASE-NGlALVTLEVANYGDASKAFKLHETVSVEAEAVEPPARVIALGDGYDHLW 568
                                       89**********************98.898*********************************************** PP

                                       EE---TT-EEEE----SS-GGGS--B---------- CS
                           Top6b_C  78 elsvsageskvleYsvdseaeeelsliveGveeekv 113
                                       ++s+++ge+++++Y+v se     + +veGv++e+v
  gi|386000803|ref|YP_005919102.1| 569 KISLRPGERQQIRYTVPSEGVRFSEPVVEGVASELV 604
                                       *******************999999*********98 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 !   32.9   0.0     2e-11   7.4e-08       4      85 ..      34     124 ..      31     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2e-11
                                       HHHHHHHHHHHHHHHHHHSTTT...EEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCH.....HCSTCHTS CS
                         HATPase_c   4 krLrqiisnlvdNavkfatkag...eieveikaseddlvisveDnGiGipkedlkklfe.kfsq.....ddstkrgg 71 
                                       + L   ++++vdN++++  +a+   +i+v+i ++ + +++ veDnG+Gi   +++++f+          + +++rg+
  gi|386000803|ref|YP_005919102.1|  34 RALITTVKEAVDNSLDACEEADilpDIFVQILRRGEGFRVVVEDNGPGIVGGEVPRVFAkL-LYgsrfhALKQSRGQ 109
                                       678899**********94444444488999997668*******************999953.333688777888888 PP

                                       TSSSHHHHHHHH.HH CS
                         HATPase_c  72 ggtGlGlsivkk.lv 85 
                                       +g G+++ +  + l+
  gi|386000803|ref|YP_005919102.1| 110 QGIGISAGVLYSqLT 124
                                       898887777655444 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 !   25.7   0.0   2.3e-09   8.3e-06       6      86 ..      39     122 ..      35     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.3e-09
                       HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiG 76 
                                        + e vdNsldA  e      + +++ + rg+  ++v+eD+G G+   e+ +++ +l   s+  +  ++s+G+ GiG
  gi|386000803|ref|YP_005919102.1|  39 TVKEAVDNSLDACEEAdilpdIFVQILR-RGEGFRVVVEDNGPGIVGGEVPRVFaKLLYGSRF-HALKQSRGQQGIG 113
                                       589*********9998999886666666.4789*******************77589999988.57899******** PP

                       HATPase_c_3  77 lklAslslgk 86 
                                         +A++  ++
  gi|386000803|ref|YP_005919102.1| 114 -ISAGVLYSQ 122
                                       .555544333 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.4e-08   5.1e-05     178     238 ..     246     304 ..     215     342 .. 0.84
   2 ?    0.1   0.2     0.071   2.5e+02     295     359 ..     463     527 ..     453     552 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                                       HHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHH CS
                              FbpA 178 fkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqel 238
                                       +        +k+l+ +L+ +f+ ++  +++e++ ra+ld+e   ++l+ ++++rl +a++e+
  gi|386000803|ref|YP_005919102.1| 246 MLR---YtDKKKLKSFLAGSFSSVGAIISQEICDRAELDPEMAPQDLTHSEATRLLAAFKEM 304
                                       333...33679************************************************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.071
                                       -SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCGGHHHHHCCHH------------------- CS
                              FbpA 295 drveqkrsdlekrveneleklekklkklekelekaekaenyrligelltaylyaikkgmsevele 359
                                       + + ++r++ e++++++l +  kkl++l ++ e   +    +++g+ll   + a ++g   v+le
  gi|386000803|ref|YP_005919102.1| 463 KSALSERKEKEEIIRKILPRISKKLSELLAREEPDINPVVAKIMGNLLVKRSVASENGLALVTLE 527
                                       44556788888889999999999999998888888888888888888888888888887765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 4759.23
//
Query:       gi|386000804|ref|YP_005919103.1|  [L=360]
Description: Type 2 DNA topoisomerase 6 subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-17   62.4   0.2    6.7e-17   61.2   0.2    1.7  1  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.2   3.7e-21   6.7e-17       2      62 .]      68     133 ..      67     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3.7e-21
                                       HHHHHHHHHHHH.HHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   2 kfaqllkvleli.helleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLnv 62 
                                       ++ ++++++el+ +e+l++++ +T+R+iYY     dv++F++Qaesdrl++d+e l+ ++Re+++v
  gi|386000804|ref|YP_005919103.1|  68 SLLKTTYLIELLiNEHLRQNRGSTLREIYYIsenwDVAKFGEQAESDRLVEDLEILTALLREDFHV 133
                                       56788899987559******************9999*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2169.00
//
Query:       gi|386000805|ref|YP_005919104.1|  [L=266]
Description: amidohydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-29  103.2   1.3    2.8e-29  102.8   1.3    1.2  1  Amidohydro_2  Amidohydrolase
  ------ inclusion threshold ------
      0.045   13.1   0.0       0.23   10.8   0.0    2.2  1  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   1.3   3.1e-33   2.8e-29       1     290 [.       3     264 ..       3     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 3.1e-33
                                       EEEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSS.ECCCEHCHHHHHHHHTSHHCH.....HHHHHHHHHHHH CS
                      Amidohydro_2   1 iDvHaHllppeaairddgepngfdpeerlafmkragvd.pqlaspeallvlnaaagiara.....vivaalcrgann 71 
                                       iD HaH++            +   p     + +r gv+ p l ++++l+ ++a ag++r      + + +++r +n+
  gi|386000805|ref|YP_005919104.1|   3 IDFHAHIYT-----------DDMAPKAIASVKRRMGVRvPGLGTVADLRGSMAKAGVERSiilplAPLPKHVRPTND 68 
                                       788999765...........222233333344444444255566677777777777777744433556666666666 PP

                                       HHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE CS
                      Amidohydro_2  72 rvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdih 148
                                           +aa+  d++v+++a+ p  +++ ++e+  +++ +g++Gv+  p  +  +++++r d ++++a +++g ++ +h
  gi|386000805|ref|YP_005919104.1|  69 F--FLAAADGDGLVPFGAIHP--FQEDLEEELDRLQAAGVRGVKAVPFLQSFYPDDPRCD-RLYQAVADRGMVLLLH 140
                                       4..45566679*****99999..6666666677777************************.**************** PP

                                       ....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHH.HHHHHHHCCEEECCGHHHSSEEE CS
                      Amidohydro_2 149 tGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraale.llarrpnvyvklsglytellyfd 224
                                       +G     ++ + +e      p  ++++a+++P+l +vlaH+Gg  e +  ++e l+  ++nvy+++          +
  gi|386000805|ref|YP_005919104.1| 141 AG----KVPEDLPE--FFGTPDRFARMAERHPDLVVVLAHLGGW-EMWSGVREyLIPAAENVYFDTAY--------I 202
                                       77....33333333..447899999******************9.66666654266799*****9966........7 PP

                                       CCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHCT CS
                      Amidohydro_2 225 spladppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarlyg 290
                                       sp  +      li ++g+dr+lfG+DyP++++ +e  ++  +dl    s  e++ il++NA+rl++
  gi|386000805|ref|YP_005919104.1| 203 SPSLTSAEACDLIVEIGADRVLFGTDYPWTDQAEEICFVEGMDL----SGREKRMILSENAERLLF 264
                                       8899999999999999***************************9....****************95 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.6e-05      0.23     159     211 ..     176     234 ..       3     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.6e-05
                                       S-HHHHHHHHHT......TEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEE CS
                        TatD_DNase 159 gsaeeakkflkl......gyyislsglltfknakelrelvkavpldrlLiETDaPyltp 211
                                       g +e+ + + ++      ++y+  + +++   + e+ +l+ ++  dr+L +TD+P+ ++
  gi|386000805|ref|YP_005919104.1| 176 GGWEMWSGVREYlipaaeNVYFDTAYISPSLTSAEACDLIVEIGADRVLFGTDYPWTDQ 234
                                       5555555555444555557777777777887888999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2033.47
//
Query:       gi|386000806|ref|YP_005919105.1|  [L=64]
Description: hypothetical protein Mhar_0089 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-12   48.2   0.6    1.9e-12   47.5   0.6    1.3  1  Trm112p          Trm112p-like protein
  ------ inclusion threshold ------
      0.018   15.3   0.1      0.023   15.0   0.1    1.2  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.021   15.2   0.2      0.024   15.0   0.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.061   13.3   0.0      0.082   12.9   0.0    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        0.1   12.1   0.3       0.18   11.3   0.3    1.5  1  UBM              Ubiquitin binding region
       0.14   12.2   0.0       0.16   12.0   0.0    1.1  1  Elf1             Transcription elongation factor Elf1 like
       0.16   11.5   3.2       0.85    9.2   3.2    2.0  1  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.6   7.6e-16   1.9e-12       1      68 []       2      49 ..       2      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 7.6e-16
                                      BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                           Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                      k++l++iLaCp+ckg L++ea+ e+ +                    +i++g L C+ cg +YpI+dG
  gi|386000806|ref|YP_005919105.1|  2 KRDLMEILACPLCKGDLELEAFEEKDG--------------------EILDGRLRCKGCGEVYPIEDG 49
                                      789**************99******98....................8*******************9 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   8.9e-06     0.023       5      33 ..      10      41 ..       8      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
                                      --TTTT-TTTEE.ETT.......S-EEETTTTB CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrFr.fddkdgr...GtwfCrqCgg 33
                                      +CP C+G      f++kdg    G   C+ C g
  gi|386000806|ref|YP_005919105.1| 10 ACPLCKGDLELEaFEEKDGEildGRLRCKGC-G 41
                                      7******************************.4 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   9.4e-06     0.024       2      36 ..       7      42 ..       6      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.4e-06
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigq.cvyCadCga 36
                                      e++ CP C+g+ +le  + ++ ei      C+ Cg 
  gi|386000806|ref|YP_005919105.1|  7 EILACPLCKGDLELEAFEEKDGEILDgRLRCKGCGE 42
                                      7899******************99999*******97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.082      20      45 ..      10      42 ..       6      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt......rglfqCkeCrk 45
                                       CP C+++ ++  ++        g+++Ck C++
  gi|386000806|ref|YP_005919105.1| 10 ACPLCKGDlELEAFEEkdgeilDGRLRCKGCGE 42
                                      5********666666667*************85 PP

>> UBM  Ubiquitin binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3     7e-05      0.18      16      24 ..      53      61 ..      52      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                               UBM 16 aLPpdLReE 24
                                      +LPpdLReE
  gi|386000806|ref|YP_005919105.1| 53 MLPPDLREE 61
                                      7*******9 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.4e-05      0.16      18      56 ..       5      45 ..       1      54 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                              Elf1 18 lptkFdCpfCnheksvevkldkkek....iaevsCkvCgesfe 56
                                      l +   Cp C+ +  +e +  ++++     ++++Ck Cge + 
  gi|386000806|ref|YP_005919105.1|  5 LMEILACPLCKGD--LELEAFEEKDgeilDGRLRCKGCGEVYP 45
                                      667889******9..555444433347999*********9876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.2   0.00033      0.85       3      29 ..      11      44 ..       9      52 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00033
                                      ETTTTCEE.C....HEE..TSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  3 CPnCgstn.l....veD..pergelvCtdCGlVl 29
                                      CP C+++  l    + D     g l+C+ CG+V 
  gi|386000806|ref|YP_005919105.1| 11 CPLCKGDLeLeafeEKDgeILDGRLRCKGCGEVY 44
                                      99999986668666333333347899******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 508.89
//
Query:       gi|386000807|ref|YP_005919106.1|  [L=526]
Description: CTP synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.3e-116  386.9   0.2   5.5e-116  386.5   0.2    1.1  1  CTP_synth_N    CTP synthase N-terminus
    1.1e-52  178.6   0.0      3e-52  177.2   0.0    1.8  2  GATase         Glutamine amidotransferase class-I
      9e-07   28.9   0.0    0.00022   21.1   0.0    3.0  2  Peptidase_C26  Peptidase C26
    0.00094   19.2   0.0     0.0017   18.4   0.0    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.072   13.0   0.0       0.11   12.4   0.0    1.3  1  AAA_31         AAA domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.5   0.2  1.5e-119  5.5e-116      10     265 .]       1     254 [.       1     254 [. 0.98

  Alignments for each domain:
  == domain 1  score: 386.5 bits;  conditional E-value: 1.5e-119
                                       STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT----GGGE CS
                       CTP_synth_N  10 vSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikltkenn 86 
                                       +SglGkGi+aas+g++l +rg+kvt+ikiDPY+n+dag +sp++hGEvf+l+dG+e+DlDlGnYeRfld++lt+++n
  gi|386000807|ref|YP_005919106.1|   1 MSGLGKGITAASIGRMLMERGYKVTAIKIDPYINIDAGLMSPFQHGEVFILKDGGEVDLDLGNYERFLDVELTRDHN 77 
                                       69*************************************************************************** PP

                                       EEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH CS
                       CTP_synth_N  87 ittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlklel 163
                                       ittGk+yk+viekerrG+ylGktvq+iph+t+eikeri++vak++  dv+++e+gGtvgdie++pflea+rql++e 
  gi|386000807|ref|YP_005919106.1|  78 ITTGKVYKTVIEKERRGEYLGKTVQIIPHITNEIKERIRTVAKESGCDVCVIEVGGTVGDIEGMPFLEAMRQLRNEE 154
                                       *******************************************999***************************9995 PP

                                       -TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE-- CS
                       CTP_synth_N 164 gkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdv 240
                                          n++++hvtl p+  + ge+ktkptqhsvke+r+lG+qpdi+ +r++k+l+ee+k+ki+lfc+v+ e v+s++dv
  gi|386000807|ref|YP_005919106.1| 155 -MGNIAFVHVTLAPTT-TDGEQKTKPTQHSVKEMRALGLQPDIVSVRCTKPLREETKSKISLFCDVPVEGVVSNHDV 229
                                       .79***********99.69********************************************************** PP

                                       S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 241 esiyevpllleeqglaelileklkl 265
                                       +++y+vpllleeq+   +++++l+l
  gi|386000807|ref|YP_005919106.1| 230 DDVYQVPLLLEEQRTPLYLMKMLRL 254
                                       **************99999999876 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.5   8.9e+03      12      30 ..      12      30 ..      10      37 .. 0.80
   2 !  177.2   0.0   8.3e-56     3e-52       2     189 ..     295     516 ..     294     517 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.5
                                      HHHHHHHHTT-EEEEEETT CS
                            GATase 12 nlvhalvelgvkvevvpid 30
                                      ++ + l+e+g+kv+ ++id
  gi|386000807|ref|YP_005919106.1| 12 SIGRMLMERGYKVTAIKID 30
                                      5678999999999998887 PP

  == domain 2  score: 177.2 bits;  conditional E-value: 8.3e-56
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH...THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile...llknpdgilvsgGpgspgvegkieaikearenkiPiL 75 
                                       + D y s+ e+l+ha++e+g+  ++ +ida+ +e      ll ++dgilv+gG+g++g+ gk++ai++aren+iP+L
  gi|386000807|ref|YP_005919106.1| 295 MEDTYLSIREALKHAGIEAGAWPKISWIDAEELERSPaadLLADFDGILVPGGFGARGTCGKMAAIRYARENGIPYL 371
                                       679***************************999984465469*********************************** PP

                                       EETHHHHHHHHHTTTEEE......................EEECEEEEEEEEEEEETTT........CGGTTTTSEE CS
                            GATase  76 GICLGmQllaiefgrkvv......................kekekehhggtmrlgddet........allyglknev 122
                                       GIC+GmQl++ ef+ +v                       +++  e++g+tmrlgd+e+        +++yg+  ++
  gi|386000807|ref|YP_005919106.1| 372 GICFGMQLAVVEFCCHVLgldgassgefgetphpvitilpEQEGVEDMGATMRLGDYEAilregslaEEIYGS-LRI 447
                                       ***************88888888888888888888899*97777***********************9****9.99* PP

                                       EEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 123 ierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                        erhrHryevnp+   ++e++g+++++k+ +   +mei e +  p f+++QFHPE++s+p++p+++f  +++
  gi|386000807|ref|YP_005919106.1| 448 VERHRHRYEVNPEyipRIEEKGMIFSGKNRN---RMEIAEIPGhPfFFSTQFHPEMKSRPGRPSPPFLAFVR 516
                                       *****************************55...699999999999*********************99987 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.014        49      22      67 ..     299     347 ..     279     352 .. 0.70
   2 !   21.1   0.0   6.1e-08   0.00022      94     216 .]     356     499 ..     350     499 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
                     Peptidase_C26  22 esylaasyveavekagglpvllpiee...deedvkaildkldgllltGg 67 
                                       +  ++++  +a  +ag++p + +i++   +++ ++++l+ +dg+l++Gg
  gi|386000807|ref|YP_005919106.1| 299 YLSIREALKHAGIEAGAWPKISWIDAeelERSPAADLLADFDGILVPGG 347
                                       344555566677789999999999873345677999************9 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 6.1e-08
                     Peptidase_C26  94 elaLiraalergvPilgiCrGlqllnvalGGtly.qdieeqsgltdhrehe...............q..saashavk 152
                                       ++a ir a e+g+P lgiC G+ql  v +  ++   d  + sg+   + h                +       +  
  gi|386000807|ref|YP_005919106.1| 356 KMAAIRYARENGIPYLGICFGMQLAVVEFCCHVLgLDGAS-SGEFGETPHPvitilpeqegvedmgAtmRLGDYEAI 431
                                       5788999******************999887654134333.333333344456677665554433303344455556 PP

                     Peptidase_C26 153 vekgsllaellgseeievnslHhqaike.....laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +++gsl +e++gs +i     H+  ++      ++e+  + +  + + +E  e++ ++ f+++ Q+HPE
  gi|386000807|ref|YP_005919106.1| 432 LREGSLAEEIYGSLRIVERHRHRYEVNPeyiprIEEKGMIFSGKNRNRMEIAEIPGHP-FFFSTQFHPE 499
                                       66**********88888889999888767777799999******************88.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.7e-07    0.0017       8      47 ..       2      38 ..       1     297 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.7e-07
                                      TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileg 47
                                      +G GK  +aa+++r l +rg++V +++ Dp  n +a   g
  gi|386000807|ref|YP_005919106.1|  2 SGLGKGITAASIGRMLMERGYKVTAIKIDPYINIDA---G 38
                                      89****************************998877...3 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.1e-05      0.11      12      47 ..       3      38 ..       2     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattg 47
                                      G GK  t+  ++ +l+++g+kv  + +Dp  n   g
  gi|386000807|ref|YP_005919106.1|  3 GLGKGITAASIGRMLMERGYKVTAIKIDPYINIDAG 38
                                      89***************************9998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3240.60
//
Query:       gi|386000808|ref|YP_005919107.1|  [L=438]
Description: IS66 family element, transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-49  166.7   0.0    7.7e-49  166.7   0.0    1.7  2  DDE_Tnp_IS66    Transposase IS66 family
    6.5e-07   29.6   3.3    1.4e-06   28.5   3.3    1.6  1  zf-IS66         zinc-finger binding domain of transposase IS6
    0.00013   22.2   0.1    0.00047   20.4   0.0    1.9  2  DDE_Tnp_IS240   DDE domain
     0.0035   17.3   0.1     0.0071   16.3   0.1    1.5  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.048   14.0   0.0    2.0  1  DUF5623         Domain of unknown function (DUF5623)
      0.013   15.5   4.6      0.048   13.7   3.0    2.4  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
      0.027   14.8   5.2      0.064   13.6   5.2    1.6  1  DUF737          Protein of unknown function (DUF737)
      0.052   13.6   1.8       0.16   12.0   1.8    1.9  1  MCC-bdg_PDZ     PDZ domain of MCC-2 bdg protein for Usher syn
      0.056   12.9   2.2        5.9    6.4   0.1    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.074   12.8   2.1        3.2    7.6   0.3    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.084   13.1   0.3        1.7    8.9   0.2    2.5  2  MazG            MazG nucleotide pyrophosphohydrolase domain
       0.11   13.0   8.6      0.073   13.5   3.1    3.0  2  ZapB            Cell division protein ZapB
       0.14   12.3   4.1       0.19   11.8   1.9    2.1  2  DivIVA          DivIVA protein
       0.14   12.3   0.5         22    5.3   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.21   11.4   4.0       0.68    9.7   4.0    1.8  1  DivIC           Septum formation initiator
        0.3   10.6   1.8       0.36   10.4   0.6    1.7  2  TMCO5           TMCO5 family
        0.4   10.7   2.9         17    5.5   0.3    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.79    9.1   3.2         15    5.0   0.3    2.5  2  zf-TFIIB        Transcription factor zinc-finger
        1.4    8.5   4.3        1.2    8.7   1.4    2.2  3  Snf7            Snf7
        1.4    9.0   3.8         16    5.7   0.1    2.4  2  UPF0547         Uncharacterised protein family UPF0547
        1.9    7.3   5.8        0.8    8.5   2.0    2.0  2  XRCC4           DNA double-strand break repair and V(D)J reco
        4.9    7.3   9.2       0.96    9.6   1.9    3.1  3  bZIP_1          bZIP transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.5       3.2   2.6e+03     185     223 ..       8      44 ..       2      54 .. 0.66
   2 !  166.7   0.0   9.5e-52   7.7e-49       2     280 ..     149     408 ..     148     410 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.2
                      DDE_Tnp_IS66 185 reareaeaeerlalrqeesrpllaeleawleeqlkkvlp 223
                                       ++++   ++erl++++e +r+ +a+lea l + ++ ++p
  gi|386000808|ref|YP_005919107.1|   8 KQLK--AENERLKRENEFQREQIAKLEARLAKYENAHTP 44 
                                       3333..247888888888888888888877766644444 PP

  == domain 2  score: 166.7 bits;  conditional E-value: 9.5e-52
                      DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtl 77 
                                       +++g++++A++++lky+d lP ++++++l+rl G++++++t+ ++++raa++++  ++a+ + +++++++ +DET++
  gi|386000808|ref|YP_005919107.1| 149 GRFGNNVIAQTTLLKYEDRLPHRKIQNALKRLhGLTICAATVLDLTRRAADAVQSQYDAILNSVRNAPILYVDETSI 225
                                       789************************************************************************** PP

                      DDE_Tnp_IS66  78 rvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaealLag.fkGvlvsDgyagYnklaeeqvthalCwaHl 153
                                       +       +g+++++Wv+ t      ++  + +sRg++v  ++L+  f G++v+Dg+++Y k++    +++ CwaHl
  gi|386000808|ref|YP_005919107.1| 226 K------VQGERHWIWVFTTPS---ETFVVIRKSRGMKVLMEVLTRrFDGIIVCDGWKPYAKFT---KRLQRCWAHL 290
                                       *......89***********88...9*****************9999****************5...899******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakkksqaaaealarigklyaierear.eaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgk 229
                                       +R+ +d+ ++      ++ea+   g+l+++ +e++ + e++   ++r    +   ++l++w+ +       ++k++k
  gi|386000808|ref|YP_005919107.1| 291 LRESKDLADK------IEEAVPLHGDLKDLYEELTdALENDPPPEVRMGLLEMARSKLHQWIMK----EYMSEKVKK 357
                                       *******975......556666666666666666532356777888888888899999999986....468999*** PP

                      DDE_Tnp_IS66 230 airyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                       +i ++ +  e  ++f+ ++ v+++NN+aERa+R  v+ RK+ +++++e+G 
  gi|386000808|ref|YP_005919107.1| 358 LIGKISNGFEYWFTFIIQPAVEPTNNRAERALREHVVLRKIIGTLRNEKGT 408
                                       ************************************************996 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   3.3   1.8e-09   1.4e-06       3      45 ..      91     134 ..      90     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.8e-09
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldip.PakfrViehirpkyaCpcC 45 
                                        Cp+CG+ l +pi ++    + +ip P+ ++V+e+ +  y+Cp+C
  gi|386000808|ref|YP_005919107.1|  91 LCPDCGAkLGDPIRKE-SKIIEEIPePQPIIVTEYKIAHYRCPSC 134
                                       5******888899999.89******9999**************** PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.7e-07   0.00047       6     100 ..     220     302 ..     217     324 .. 0.75
   2 ?   -2.8   0.0       8.1   6.6e+03      95     129 ..     381     421 ..     361     423 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.7e-07
                     DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkreg. 81 
                                       vDET +k++G+ ++++           ++++k R++k    +l++ ++        iv D+ + ya+  k+l+r   
  gi|386000808|ref|YP_005919107.1| 220 VDETSIKVQGERHWIWVFTTPSETF--VVIRKSRGMKVLMEVLTRRFDGI------IVCDGWKPYAKFTKRLQRCWa 288
                                       9***************987665554..578999**999999999988888......****************99543 PP

                     DDE_Tnp_IS240  82 elfdevshvqvkylnnriE 100
                                       +l++     ++k l + iE
  gi|386000808|ref|YP_005919107.1| 289 HLLR-----ESKDLADKIE 302
                                       3333.....3444444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.1
                     DDE_Tnp_IS240  95 lnnriEs...dhrtlKkrl...rptrgfkslksaaktlagf 129
                                        nnr E+   +h  l+k +   r  +g    +++ ++la++
  gi|386000808|ref|YP_005919107.1| 381 TNNRAERalrEHVVLRKIIgtlRNEKGTSIHERIMTVLATW 421
                                       57777752224555665544335555555555555555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.7e-06    0.0071      13      39 ..      90     139 ..      81     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.7e-06
                               DZR  13 rfCseCgtklkavaa.......................edrCpsCgekvd 39 
                                         C++Cg+kl  + +                       ++rCpsC+++v 
  gi|386000808|ref|YP_005919107.1|  90 DLCPDCGAKLGDPIRkeskiieeipepqpiivteykiaHYRCPSCQKEVV 139
                                       58*******9766668899***************************9953 PP

>> DUF5623  Domain of unknown function (DUF5623)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.9e-05     0.048      12      59 ..     306     356 ..     301     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                           DUF5623  12 evHqevgrllkellesvarskg...vssrlsavrstLddWlemEyseeeld 59 
                                        +H ++  l +el+++++++         l+++rs+L++W+ +Ey +e+++
  gi|386000808|ref|YP_005919107.1| 306 PLHGDLKDLYEELTDALENDPPpevRMGLLEMARSKLHQWIMKEYMSEKVK 356
                                       56778888888888888887774423345799*************888766 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.0   5.9e-05     0.048      11      48 ..       4      41 ..       3      49 .. 0.92
   2 ?    0.1   0.0         1   8.2e+02      42      72 ..     287     317 ..     279     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                        TMF_DNA_bd 11 DeqIaqLmeEGekLskkelklnntikkLrkknkeleke 48
                                      +e+I+qL++E e+L+ ++  ++++i kL + +++ e+ 
  gi|386000808|ref|YP_005919107.1|  4 EEIIKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41
                                      699***************************99998875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                        TMF_DNA_bd  42 nkelekeikelkkkleklekeleeleerlke 72 
                                        ++l  e k+l +k+e+ +     l+++++e
  gi|386000808|ref|YP_005919107.1| 287 WAHLLRESKDLADKIEEAVPLHGDLKDLYEE 317
                                       5667788899999999999999988888765 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.2   7.9e-05     0.064     147     180 ..       4      37 ..       1      43 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-05
                            DUF737 147 erkarqLeekekeLkkqdafYkeqlakLeeknae 180
                                       e  ++qL + ++ Lk+ ++f +eq+akLe++ a+
  gi|386000808|ref|YP_005919107.1|   4 EEIIKQLKAENERLKRENEFQREQIAKLEARLAK 37 
                                       5679***************************987 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.8    0.0002      0.16       6      41 ..       7      41 ..       4      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                       MCC-bdg_PDZ  6 IeeLkaqnelLsltleerkqqseeLsldlgkaEsna 41
                                      I +Lka ne+L++  e  ++q ++L  +l k+E na
  gi|386000808|ref|YP_005919107.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKYE-NA 41
                                      899******************************.55 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.012       9.5      19      26 .]      92      99 ..      90      99 .. 0.82
   2 ?    6.4   0.1    0.0073       5.9       2      15 ..     128     142 ..     127     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                       zf-ribbon_3 19 CpyCGtkl 26
                                      Cp CG+kl
  gi|386000808|ref|YP_005919107.1| 92 CPDCGAKL 99
                                      99999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0073
                       zf-ribbon_3   2 tvrCPnCGa.plssd 15 
                                       ++rCP+C + +++sd
  gi|386000808|ref|YP_005919107.1| 128 HYRCPSCQKeVVASD 142
                                       79*****98887776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.004       3.2       2      11 ..      92     101 ..      91     102 .. 0.83
   2 ?    4.6   0.1     0.034        28       1      10 [.     130     139 ..     130     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                     zinc_ribbon_2   2 CpnCGaelqd 11 
                                       Cp CGa+l d
  gi|386000808|ref|YP_005919107.1|  92 CPDCGAKLGD 101
                                       9999999865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.034
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +Cp+C +e+ 
  gi|386000808|ref|YP_005919107.1| 130 RCPSCQKEVV 139
                                       6******986 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.48   3.9e+02      51      73 ..     149     171 ..     142     172 .. 0.85
   2 ?    8.9   0.2    0.0021       1.7       6      37 ..     286     322 ..     281     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                                       H---HHHHHHHHHHHHHHH-GGG CS
                              MazG  51 ggidledvaetileKlerRhphv 73 
                                       g++  + +a+t+l K+e R ph+
  gi|386000808|ref|YP_005919107.1| 149 GRFGNNVIAQTTLLKYEDRLPHR 171
                                       6667777899***********97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHT.....T-HHHHHHHHHHHH CS
                              MazG   6 llaylleEvgEvaeaIkk.....edrdeleeELGDvL 37 
                                         a+ll E + +a++I++     +d ++l eEL D L
  gi|386000808|ref|YP_005919107.1| 286 CWAHLLRESKDLADKIEEavplhGDLKDLYEELTDAL 322
                                       66899*************99*99************87 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.1   8.9e-05     0.073      20      54 ..       7      41 ..       5      48 .. 0.88
   2 ?    1.0   0.3      0.74     6e+02      54      69 ..     347     362 ..     280     364 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                              ZapB 20 itlLqmeieeLkeeneelkeenreleeeneqlkee 54
                                      i++L+ e+e+Lk+ene   e++++le+ + + ++ 
  gi|386000808|ref|YP_005919107.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41
                                      899***********************988887655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.74
                              ZapB  54 ereawqerlkkLLgkl 69 
                                        +e + e++kkL+gk+
  gi|386000808|ref|YP_005919107.1| 347 MKEYMSEKVKKLIGKI 362
                                       3555667777777776 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   0.00024      0.19      25      62 ..       5      42 ..       4      44 .. 0.92
   2 ?   -0.7   0.0       1.7   1.4e+03      35      68 ..     288     321 ..     277     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXX CS
                            DivIVA 25 eFLdqvakdyeallkeneelkekvkeleeklkeykele 62
                                      e+++q+  + e+l +ene ++e++++le +l++y++++
  gi|386000808|ref|YP_005919107.1|  5 EIIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42
                                      67899999**************************9975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXX CS
                            DivIVA  35 eallkeneelkekvkeleeklkeykeleetLkkt 68 
                                         ll+e+++l +k++e+     + k+l e+L ++
  gi|386000808|ref|YP_005919107.1| 288 AHLLRESKDLADKIEEAVPLHGDLKDLYEELTDA 321
                                       5789999999999999877777777777766665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.042        34      27      35 ..      89      98 ..      80     100 .. 0.79
   2 ?    5.3   0.0     0.026        22       6      14 ..     129     137 ..     126     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.042
                       Zn-ribbon_8 27 ta.CPeCgse 35
                                      ++ CP+Cg++
  gi|386000808|ref|YP_005919107.1| 89 IDlCPDCGAK 98
                                      566*****86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.026
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       YrC +C++e
  gi|386000808|ref|YP_005919107.1| 129 YRCPSCQKE 137
                                       888888865 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.0   0.00084      0.68      19      50 ..       7      38 ..       3      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                      +kqlk+e ++l++e++ +++++++Lea+++++
  gi|386000808|ref|YP_005919107.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKY 38
                                      57888888888888888888888888888777 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00044      0.36      61     101 ..       2      42 ..       1      63 [. 0.87
   2 ?   -2.0   0.0       2.6   2.1e+03     164     183 ..     321     344 ..     278     370 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                             TMCO5  61 ekedalkeLeletaklekkneiLlkevveLqkkisrkeskq 101
                                       ++e+  k+L+ e  +l+++ne+  +++++L+ ++ + e+ +
  gi|386000808|ref|YP_005919107.1|   2 HEEEIIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42 
                                       679999****************************9998654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                             TMCO5 164 kmee....eketlllekevsklqs 183
                                        +e+    e  + lle   skl +
  gi|386000808|ref|YP_005919107.1| 321 ALENdpppEVRMGLLEMARSKLHQ 344
                                       222233333333344444444333 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.038        31       2       9 ..      92      99 ..      92     106 .. 0.91
   2 ?    5.5   0.3     0.021        17       1      11 [.     130     140 ..     130     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                    DNA_ligase_ZBD  2 CPvCGsav 9 
                                      CP CG+++
  gi|386000808|ref|YP_005919107.1| 92 CPDCGAKL 99
                                      *****997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+C  +vv 
  gi|386000808|ref|YP_005919107.1| 130 RCPSCQKEVVA 140
                                       5*******995 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.019        15      16      26 ..      86      96 ..      82      96 .. 0.89
   2 ?    3.9   0.2     0.041        33       2      14 ..     131     143 ..     130     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.019
                          zf-TFIIB 16 gveidyCpqCr 26
                                      +v id Cp+C+
  gi|386000808|ref|YP_005919107.1| 86 EVAIDLCPDCG 96
                                      699*******7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                          zf-TFIIB   2 CPkCqdeleeser 14 
                                       CP+Cq e + s++
  gi|386000808|ref|YP_005919107.1| 131 CPSCQKEVVASDH 143
                                       *****99887765 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.4    0.0015       1.2       2      38 ..       6      42 ..       5      62 .. 0.84
   2 ?   -3.0   0.0       5.8   4.7e+03       6      26 ..     283     303 ..     279     323 .. 0.66
   3 ?   -0.9   0.0       1.3   1.1e+03      29      62 ..     353     404 ..     332     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                              Snf7  2 airsLrkaerkldkkqeslekkikkleaelkklakkg 38
                                       i++L+ + ++l+++ e+ +++i+klea l+k+    
  gi|386000808|ref|YP_005919107.1|  6 IIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42
                                      6899****************************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.8
                                       HHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   6 Lrkaerkldkkqeslekkikk 26 
                                       L+++   l ++++ l +ki++
  gi|386000808|ref|YP_005919107.1| 283 LQRCWAHLLRESKDLADKIEE 303
                                       556666666666666666654 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                       HHHHHHHCTT-..................HHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7  29 aelkklakkgn..................kdralllLKqkkryekqldqldn 62 
                                       +++kkl+ k++                  + ra ++L++ + ++k +  l n
  gi|386000808|ref|YP_005919107.1| 353 EKVKKLIGKISngfeywftfiiqpaveptNNRAERALREHVVLRKIIGTLRN 404
                                       4556666665566667777777777777789999999999999998877766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.02        16       7      21 ..      82      96 ..      82      97 .. 0.91
   2 ?    3.8   0.7     0.074        60       2      10 ..     130     138 ..     130     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                           UPF0547  7 eakvPvaaqfCphCG 21
                                      +++v va   Cp+CG
  gi|386000808|ref|YP_005919107.1| 82 DRQVEVAIDLCPDCG 96
                                      68999999******9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.074
                           UPF0547   2 vCPeCeakv 10 
                                       +CP C+ +v
  gi|386000808|ref|YP_005919107.1| 130 RCPSCQKEV 138
                                       6*****998 PP

>> XRCC4  DNA double-strand break repair and V(D)J recombination protein XRCC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.0   0.00098       0.8     137     173 ..       5      41 ..       1      44 [. 0.90
   2 ?   -0.3   0.1      0.47   3.8e+02     147     184 ..     281     317 ..     274     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00098
                             XRCC4 137 dqiaelqakNehLqkENerLlrdwsdvterlekyvka 173
                                       + i++l+a+Ne+L++ENe  +++  ++++rl ky +a
  gi|386000808|ref|YP_005919107.1|   5 EIIKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41 
                                       578899***************************9876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                             XRCC4 147 ehLqkENerLlrdwsdvterlekyvkakEeleadLYkr 184
                                       ++Lq+   +Llr+ +d+ +++e+ v    +l+ dLY+ 
  gi|386000808|ref|YP_005919107.1| 281 KRLQRCWAHLLRESKDLADKIEEAVPLHGDLK-DLYEE 317
                                       679999999***************99999985.88875 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.9    0.0012      0.96      35      61 ..       7      33 ..       4      36 .. 0.89
   2 ?   -1.0   0.1       2.3   1.9e+03      18      27 ..      48      57 ..      46      62 .. 0.82
   3 ?    0.1   0.0       1.1     9e+02      29      51 ..     281     303 ..     278     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 35 vkaLekeNksLkseleelkkevekLks 61
                                       k+L++eN+ Lk e+e  +++++kL+ 
  gi|386000808|ref|YP_005919107.1|  7 IKQLKAENERLKRENEFQREQIAKLEA 33
                                      699********************9975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                      HHHHHHHHHH CS
                            bZIP_1 18 rrsRqRKqae 27
                                      rr R+RK+ +
  gi|386000808|ref|YP_005919107.1| 48 RRGRKRKKGY 57
                                      7889***977 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkselee 51 
                                       ++L+r  + L  e k+L++++ee
  gi|386000808|ref|YP_005919107.1| 281 KRLQRCWAHLLRESKDLADKIEE 303
                                       77888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      871  (0.0485805); expected 358.6 (0.02)
Passed Vit filter:                       147  (0.00819901); 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):              22  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3007.99
//
Query:       gi|386000809|ref|YP_005919108.1|  [L=165]
Description: hypothetical protein Mhar_0092 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.23   11.7   0.0    1.5  1  PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal


Domain annotation for each model (and alignments):
>> 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 ?   11.7   0.0   1.3e-05      0.23      44      61 ..     108     125 ..     107     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                                       ETTCCEEEEEEEESSHHH CS
                        PGM_PMM_IV  44 SGTepllrvyvEaksdee 61 
                                       SGTepl ++ +Ea++  +
  gi|386000809|ref|YP_005919108.1| 108 SGTEPLAVLIAEATDPHR 125
                                       9************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1092.99
//
Query:       gi|386000810|ref|YP_005919109.1|  [L=153]
Description: hypothetical protein Mhar_0093 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-16   60.6   0.2    3.8e-16   60.0   0.2    1.3  1  DUF4065   Protein of unknown function (DUF4065)


Domain annotation for each model (and alignments):
>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.2   2.1e-20   3.8e-16       1     108 [.      26     128 ..      26     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.1e-20
                           DUF4065   1 LqKllYfadflhlkrtgkpitglkyiawkyGPVvpevydeikelgsk.pieekeeeisdeklekkekkeveeleddk 76 
                                       L+Kl+Y++d+ h+ rt+ +i++ k+   ++GP+v ++ d+ ke+ +  + e++++++ d+k+    +       +++
  gi|386000810|ref|YP_005919109.1|  26 LTKLVYLSDWRHCLRTNSQISNIKWFFNNFGPFVWDIKDTAKENPHIfELETTTNMYGDQKTIFILN-------SKD 95 
                                       89*************************************9999988766666666666655544332.......223 PP

                           DUF4065  77 eae.lseeekevidkvikkykdlsaseLselth 108
                                       ++  lseee++ id+vi+++k+l+++++++l++
  gi|386000810|ref|YP_005919109.1|  96 YSPrLSEEEMKSIDHVINETKNLNWDQFIRLVY 128
                                       3334*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1271.68
//
Query:       gi|386000811|ref|YP_005919110.1|  [L=437]
Description: ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-29  103.6   0.1    5.8e-28   98.6   0.1    2.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.4e-23   83.5   0.0    1.2e-10   41.7   0.0    2.1  2  AAA_15    AAA ATPase domain
    6.3e-09   36.6   0.0    8.6e-09   36.2   0.0    1.3  1  AAA_23    AAA domain
    5.5e-07   29.3   0.0    1.6e-05   24.4   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00014   21.5   0.0    0.00026   20.7   0.0    1.3  1  AAA_29    P-loop containing region of AAA domain
     0.0021   18.6   0.0     0.0041   17.6   0.0    1.4  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
       0.12   11.6   0.1        5.7    6.1   0.0    2.1  2  DUF2813   Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.1   2.3e-31   5.8e-28       1     303 []      50     359 ..      50     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 2.3e-31
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       l++l GpNgsGKS+++d + +l+   + + gl    +++g +++   + +++ +ei+ +++ +  ++  + y  ++ 
  gi|386000811|ref|YP_005919110.1|  50 LTALLGPNGSGKSTVFDVFAFLS--ECFSVGLRRAWDKRGRFKELHTRGTTGPIEIELKYRER-GNLPLITYHLSIA 123
                                       69********************9..56666666666677788888888888888888888888.8888888888888 PP

                            AAA_21  78 lersqv...eeklssvetllesgl.lldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsr 150
                                        +  +    ee+l+ +++ +++++ +ld ++ e ++v+  +++++ g v                       +++s+
  gi|386000811|ref|YP_005919110.1| 124 EGLAGPvvaEEWLQWRRKSQGKPFrFLDFKNGEGRVVSGEMPDETEGRVE---------------------EKLDSP 179
                                       88888888777777777777666524444555555555555544444443.....................334444 PP

                            AAA_21 151 awsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer........ 219
                                          +   l  +   ++++ ++ +++++++++  l+ + vr++ ++++  ++++ g++l++ ++ +  +         
  gi|386000811|ref|YP_005919110.1| 180 EMLAVNTLGQFA--KHPRVSALRRFITGWHVSYLTADSVRGVAEAGPQERLSTTGDNLPNVIQYLKEQHperlaeil 254
                                       444444444444..*************************************************999999******** PP

                            AAA_21 220 .......................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                                               + + + ++ +++ a  +SdGt+++l  lt l++ +++  ll i+EpEn+LHP+
  gi|386000811|ref|YP_005919110.1| 255 galsrrvprlervdsefmpdgrlLLEIKDAPFEKPILAKFASDGTLKMLSYLTVLYDPDPP-QLLGIEEPENHLHPR 330
                                       ***********************************************************99.*************** PP

                            AAA_21 274 llrrllellkelsrngaQviltTHSpllld 303
                                       +l++l+e  +++s  ++Q+++tTHSp++++
  gi|386000811|ref|YP_005919110.1| 331 ILPELAEECRNASG-RTQLLVTTHSPFFVN 359
                                       ******99999999.***********9886 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.6e-13     4e-10       3      84 ..      28     119 ..      27     203 .. 0.75
   2 !   41.7   0.0   4.6e-14   1.2e-10     323     369 .]     314     358 ..     296     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.6e-13
                            AAA_15   3 IkkikikNFRslkdveidlsee..ltvliGkNnsGKSsilealdlFlnnkekkn......kkvikiekedleifeni 71 
                                       I++i+ikN+R+l+d  ++l++   lt l G+N+sGKS++ +++  Fl++   ++      +    ++   +++ + +
  gi|386000811|ref|YP_005919110.1|  28 IESIRIKNYRALRD--LELKPLapLTALLGPNGSGKSTVFDVF-AFLSE--CFSvglrraW----DKRGRFKELHTR 95 
                                       99************..55555556*******************.77773..3557755442....677888888888 PP

                            AAA_15  72 seskdikIdvef...........a 84 
                                        +  +i+I++++            
  gi|386000811|ref|YP_005919110.1|  96 GTTGPIEIELKYrergnlplityH 119
                                       888888888888555555555550 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 4.6e-14
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                       ++ +l iEEPE+hLHp    +l++ +++++  +  Q+++tTHSp+++
  gi|386000811|ref|YP_005919110.1| 314 PPQLLGIEEPENHLHPRILPELAEECRNASGRT--QLLVTTHSPFFV 358
                                       7899***************************99..**********97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   3.4e-12   8.6e-09       1      42 [.      30      71 ..      30     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.4e-12
                            AAA_23  1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAikla 42
                                      +++i+n+r +rd e+    +lt++ GpNG+GK+T++d + + 
  gi|386000811|ref|YP_005919110.1| 30 SIRIKNYRALRDLELKPLAPLTALLGPNGSGKSTVFDVFAFL 71
                                      69***********************************98875 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   6.4e-09   1.6e-05       2      47 ..      28      71 ..      27      84 .. 0.84
   2 ?    2.5   0.0     0.032        81     143     200 ..     299     356 ..     287     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.4e-09
                                      EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFv 47
                                      +++++i+n++ ++    +l+    +ta++GpNGSGKs ++d   F+
  gi|386000811|ref|YP_005919110.1| 28 IESIRIKNYRALR--DLELKPLAPLTALLGPNGSGKSTVFDVFAFL 71
                                      899*********5..666666666*****************98874 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 143 tLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislree 200
                                       tL +l+ l  ++  +p  l  + e + +L  +   ++ae  +++s ++Q++v++++  
  gi|386000811|ref|YP_005919110.1| 299 TLKMLSYLTVLYDPDPPQLLGIEEPENHLHPRILPELAEECRNASGRTQLLVTTHSPF 356
                                       677777777788888888999999999***************************9865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     1e-07   0.00026      15      44 ..      40      70 ..      27      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1e-07
                            AAA_29 15 htieidlkg.atlltGpsGsGKSTllDAiqa 44
                                      +++e+++    t l Gp+GsGKST++D +++
  gi|386000811|ref|YP_005919110.1| 40 RDLELKPLApLTALLGPNGSGKSTVFDVFAF 70
                                      445555555589***************7765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.6e-06    0.0041      13      34 ..      50      71 ..      42      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                      EEEEEESTTSSHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagl 34
                                      ++a++G+nG+GKSt++ ++a l
  gi|386000811|ref|YP_005919110.1| 50 LTALLGPNGSGKSTVFDVFAFL 71
                                      689*************998755 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0022       5.7       4      43 ..      29      69 ..      27      77 .. 0.89
   2 ?    3.3   0.1     0.016        41     287     301 ..     318     332 ..     309     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0022
                           DUF2813  4 erieisGFRGinrLSls.leentvLiGENaWGKSSLldALs 43
                                      e+i i+ +R ++ L l+ l ++t+L+G N  GKS  +d   
  gi|386000811|ref|YP_005919110.1| 29 ESIRIKNYRALRDLELKpLAPLTALLGPNGSGKSTVFDVFA 69
                                      7899************879****************999765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                           DUF2813 287 lllEdpearLHPtml 301
                                       l +E+pe++LHP+ l
  gi|386000811|ref|YP_005919110.1| 318 LGIEEPENHLHPRIL 332
                                       559*********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3320.13
//
Query:       gi|386000812|ref|YP_005919111.1|  [L=207]
Description: hypothetical protein Mhar_0095 [Methanosaeta harundinacea 6Ac]
Scores for 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-29  101.1   0.0    9.5e-29  100.9   0.0    1.0  1  DUF4276   Domain of unknown function (DUF4276)


Domain annotation for each model (and alignments):
>> DUF4276  Domain of unknown function (DUF4276)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   5.3e-33   9.5e-29       1     183 [.       7     198 ..       7     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 5.3e-33
                           DUF4276   1 vEGqteeeflkellrrlleskgiylsarvsysk...lkkdikkllkqekd...edtavttliDlyal..dafkr.ve 68 
                                       vE+++ e++l++l++++l s   +  +r  ++    l + ++ llk  ++   +d+++++l+D +++  ++ k  +e
  gi|386000812|ref|YP_005919111.1|   7 VEEPSAEAALRNLVPKILGSGVEFRVIR--FQGkqdLLSRLPGLLKGYRRwitADWRIVVLVDEDRQdcRELKAeLE 81 
                                       8********************6665555..22222355555555555555999**************9944444488 PP

                           DUF4276  69 eleralkedidsk....gderfipyiqlhefEawlladpealkekseslsklkkirkefsnPenindgpktapskrl 141
                                       + + +++ +++s     +++++ ++i ++e+Eaw++ d+eal+ ++++++   + ++++++P++i++g+++a+++ l
  gi|386000812|ref|YP_005919111.1|  82 KAAGDAELSTRSVtrggSAFQVLNRISIEELEAWFFGDVEALHLAYPRIPPSLATSSKYRDPDAIQGGTWEALEREL 158
                                       88888888887779999************************************************************ PP

                           DUF4276 142 eeafpvkgrYeKvedgakiaeeidleklrekcpsfkrwlerL 183
                                       +   +++g+ +K+e +++i +++d++++r+k  sf+ + + L
  gi|386000812|ref|YP_005919111.1| 159 QGKGYFRGGLAKIEAAKAISAHMDPDQNRSK--SFQVFRDGL 198
                                       ******************************5..898887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1462.12
//
Query:       gi|386000813|ref|YP_005919112.1|  [L=63]
Description: hypothetical protein Mhar_0096 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   12.5   1.8      0.063   12.3   1.8    1.0  1  DUF898    Bacterial protein of unknown function (DUF898)
       0.45    9.2   1.4       0.48    9.1   1.4    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF898  Bacterial protein of unknown function (DUF898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8     7e-06     0.063      69     118 ..      12      61 ..       8      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-06
                            DUF898  69 ialvllvlysvasalapllglllllllflllpwaivramrFrlrntswRG 118
                                       +al + +++ +asa+++++ l  +l  +l++ + +v ++ F  +  +wRG
  gi|386000813|ref|YP_005919112.1|  12 FALTIAIAVILASAIGEMMELSPVLTALLAGGICVVANLVFISASGRWRG 61 
                                       35666667779999***********************************9 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.4   5.4e-05      0.48     382     438 ..       6      60 ..       2      63 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 5.4e-05
                           DUF2207 382 klsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrt 438
                                       +l+++ ++l+i++ +++  a++ +       ++++l+ + i++++ l+f +  gr+ 
  gi|386000813|ref|YP_005919112.1|   6 SLRIIRFALTIAIAVILASAIGEMM--ELSPVLTALLAGGICVVANLVFISASGRWR 60 
                                       5555555555555554444444333..899999999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 479.28
//
Query:       gi|386000814|ref|YP_005919113.1|  [L=267]
Description: Phenazine biosynthesis protein PhzF family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.3e-72  241.9   0.0    1.7e-71  241.0   0.0    1.4  1  PhzC-PhzF  Phenazine biosynthesis-like protein


Domain annotation for each model (and alignments):
>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.0   0.0   9.2e-76   1.7e-71       1     283 []       8     262 ..       8     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 241.0 bits;  conditional E-value: 9.2e-76
                                       EEET-SSTTSSEEEEEEESTTCS-HHHHHHHHHHHTSSEEEEEE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHH CS
                         PhzC-PhzF   1 vdaFtespfkGNpaaVvldadelddeelqsiAaelnlseTaFllkpsdekarfrlRyFTPvaEvdlcGHatlasaha 77 
                                       vdaFt++pf GNpaaV+l+++ +dd ++q++Aae+nlseTaF++++      frlR+F P+aEv+lcGHatlasah+
  gi|386000814|ref|YP_005919113.1|   8 VDAFTSEPFSGNPAAVCLLEEPRDDGWMQKVAAEMNLSETAFMTPE---GDGFRLRWFAPKAEVELCGHATLASAHL 81 
                                       8********************************************6...569************************* PP

                                       HHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEEEEEE-HHHHHHHHHHCCTSGG-TTS-BEEEES CS
                         PhzC-PhzF  78 laekglvasaetveletkaGilpvkslkekddgeellielkfPvikteevssedlallakllklaaqkalpiavkst 154
                                       l e+g +a+ e   + tk+G l +       +++  +ie++fP+  ++ ++++    ++++  +a     p      
  gi|386000814|ref|YP_005919113.1|  82 LWEEGVLAEDEIARFATKSGPLFA-------ERRGGFIEMDFPAEPERPIKCSPP--MLEAALGA-----PFSYVGD 144
                                       *******99**************9.......68889*******988887777654..33444444.....4455555 PP

                                       SSEEEEEEBSTCCHHHH----HHHHHHHCT-EEEEEEEETTTSSCCEEEEEEEEGGGTEEEESS-HHHHHHHHHHHH CS
                         PhzC-PhzF 155 glekvivplsseeavaelspdlaeeikkcpkkgvivtaaaeagskkdfhsRmFaPklGivEDpvtGsAsgaLaayls 231
                                          +++v+l  ee++ el p++ + +kk+p +gv+vt a++++ ++df sR+FaP lG++EDpvtGsA++ L+ y++
  gi|386000814|ref|YP_005919113.1| 145 NRFDLLVELDGEETLRELRPNF-DLLKKIPVRGVMVT-AESDSPEYDFVSRFFAPTLGVDEDPVTGSAHCCLGPYWA 219
                                       5789******************.***********776.67899********************************** PP

                                       HCC-SSSEEEEEEEE-GGGT--EEEEEEEE.E-TTCEEEEEEEE-EEEEEEE CS
                         PhzC-PhzF 232 eklnleesakikieqgqalgrsgtlevevevkvdkekervkvtGkAvtvmeg 283
                                       ++l +     ++++ +qa++r g ++    v+ +++  rvk+ G+Avtv +g
  gi|386000814|ref|YP_005919113.1| 220 RRLGK-----FELVGYQASERGGVVR----VRGGEDGDRVKIGGEAVTVLKG 262
                                       *****.....****************....55667789***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1991.86
//
Query:       gi|386000815|ref|YP_005919114.1|  [L=173]
Description: N-acetyltransferase GCN5 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-14   53.4   0.0    2.7e-14   53.2   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.1e-09   37.6   0.0    2.4e-09   37.4   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.1e-08   33.5   0.0    5.9e-08   33.0   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0012   18.9   0.0     0.0035   17.4   0.0    1.8  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.013   16.1   0.0      0.019   15.6   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.021   14.8   0.0      0.033   14.2   0.0    1.3  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   9.2e-18   2.7e-14      33     125 ..      69     163 ..      38     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 9.2e-18
                   Acetyltransf_10  33 llvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFk 107
                                       +++ e  g +vGv++  +g+ + ll ++p ++g+Gig+aLl ++eee++ +g+++ +l++ + +  a +fY+  G++
  gi|386000815|ref|YP_005919114.1|  69 IVGREGVGGVVGVAAA-SGDAVDLLWIHPRHHGRGIGTALLGRLEEEMRAAGNRTgRLSCFSENlRAMRFYQARGWT 144
                                       4444445667777754.4459******************************************************** PP

                   Acetyltransf_10 108 av.geeqeenGirfvpMek 125
                                       a  + + ee+G   ++Mek
  gi|386000815|ref|YP_005919114.1| 145 AAgEGVNEETGAPETRMEK 163
                                       **8899***********98 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   8.1e-13   2.4e-09      63     117 .]      89     143 ..      22     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 8.1e-13
                                       EEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  63 ieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       ++ l+++p ++g+G+G+aLl  lee++r  g +   l +++ n +a+r+Y+  G+
  gi|386000815|ref|YP_005919114.1|  89 VDLLWIHPRHHGRGIGTALLGRLEEEMRAAGNRTGRLSCFSENLRAMRFYQARGW 143
                                       46799*************************88666999************87885 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0     2e-11   5.9e-08      11      75 ..      66     144 ..      49     145 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2e-11
                                       T.........TEEEEEEEEEEESTCTEEEEE-GGGTTSSHHHHHHH.H.TT.......SEEEEEEEEE.THH.HHHH CS
                    Acetyltransf_7  11 d.........gkivGfialslldaeitrlaVdpeyrgkGiGraLle.a.ae.......kgiileqlel.nae.kaik 67 
                                                 g++vG +a+s +      l+++p ++g+GiG+aLl  + +e       +g +l+     +++ +a +
  gi|386000815|ref|YP_005919114.1|  66 AagivgregvGGVVGVAAASGD--AVDLLWIHPRHHGRGIGTALLGrLeEEmraagnrTG-RLS---CfSENlRAMR 136
                                       2444444445667776666665..4666****************9534311344233333.122...23222499** PP

                                       HHHHTTEE CS
                    Acetyltransf_7  68 fYeklGFe 75 
                                       fY+  G++
  gi|386000815|ref|YP_005919114.1| 137 FYQARGWT 144
                                       *****985 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.98   2.9e+03       2      18 ..       6      22 ..       6      31 .. 0.85
   2 !   17.4   0.0   1.2e-06    0.0035      81     126 ..      94     144 ..      75     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.98
                                      EEEE-GGGHHHHHHHHH CS
                    Acetyltransf_9  2 irelteedldevlellk 18
                                      +r++ +ed++++++l  
  gi|386000815|ref|YP_005919114.1|  6 LRRAAKEDVPAIVRLCI 22
                                      5899999***9999865 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.2e-06
                                       E-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                    Acetyltransf_9  81 vapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                        +p h grg+ ++Ll r+ eemr+ g +   l       +++++Y+  G+ 
  gi|386000815|ref|YP_005919114.1|  94 IHPRHHGRGIGTALLGRLEEEMRAAGNRTGRLSCfsenlRAMRFYQARGWT 144
                                       69**************************99999955566567********7 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   6.4e-06     0.019       3     134 ..       5     140 ..       3     144 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.4e-06
                    Acetyltransf_3   3 lLrplteeDlealfelrsdpevmrylpepltleeaeewlera.........waeeseeegygwaivl.......kdt 63 
                                       +Lr++ +eD++a+++l+  +++ + ++   + e  + w+e           w +      +  a+ +       +++
  gi|386000815|ref|YP_005919114.1|   5 VLRRAAKEDVPAIVRLCI-ETIPEVYGSIIPAETLRPWVEGDaveglvevqWPR------MMVAVADsaagivgREG 74 
                                       799999999999987544.44444434444445556666633233322223322......22333331111111555 PP

                    Acetyltransf_3  64 gviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlek 134
                                        v G+vg+  ++++   a   ++++p ++g+G++t  +  l e + +  g ++ +  +  eN +  r ++ 
  gi|386000815|ref|YP_005919114.1|  75 -VGGVVGVAAASGD---AVDLLWIHPRHHGRGIGTALLGRLEEEM-RAAGNRTGRLSCFSENLRAMRFYQA 140
                                       .7788888888777...4444899***9********999999999.6666777888888888888887765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.033      25      79 ..      90     145 ..      68     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  25 galqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfek 79 
                                         l ++p h +rG g+ l   l +e++++g+ t  l    +N ++ r+y++ G+++
  gi|386000815|ref|YP_005919114.1|  90 DLLWIHPRHHGRGIGTALLGRLEEEMRAAGNrTGRLSCFSENLRAMRFYQARGWTA 145
                                       56889***********************7752678999999********9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1273.40
//
Query:       gi|386000816|ref|YP_005919115.1|  [L=106]
Description: hypothetical protein Mhar_0099 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0082   15.6   0.0     0.0087   15.5   0.0    1.1  1  AroM      AroM protein


Domain annotation for each model (and alignments):
>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.9e-07    0.0087     163     208 ..      49      93 ..      21     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.9e-07
                              AroM 163 eelaeaarelaeqgadlivldciGYteemkaavaealgkpVllars 208
                                       e l+eaa+ela qg+  +  dc G+ + +++++a++l++pV l+  
  gi|386000816|ref|YP_005919115.1|  49 EPLREAAEELAGQGVRAVTGDC-GFLALHQRRLAARLEIPVFLSSL 93 
                                       7799*****************9.*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 808.19
//
Query:       gi|386000817|ref|YP_005919116.1|  [L=116]
Description: hypothetical protein Mhar_0100, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 887.95
//
Query:       gi|386000818|ref|YP_005919117.1|  [L=721]
Description: Copper-exporting ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-52  177.7   2.5    1.6e-52  177.7   2.5    2.4  3  E1-E2_ATPase  E1-E2 ATPase
    3.7e-43  148.3   0.7    3.7e-43  148.3   0.7    1.5  2  Hydrolase     haloacid dehalogenase-like hydrolase
    1.8e-06   27.9   0.0     0.0015   18.3   0.1    2.4  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
    6.2e-05   23.5   0.1    0.00021   21.8   0.0    2.0  2  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.027   14.5   0.0      0.069   13.2   0.0    1.6  1  HAD_2         Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.14     5e+02     109     157 ..      72     123 ..      66     126 .. 0.84
   2 ?   -3.9   0.1       2.3   8.1e+03     109     132 ..     146     169 ..     130     179 .. 0.53
   3 !  177.7   2.5   4.4e-56   1.6e-52       2     180 ..     207     385 ..     206     386 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHH CS
                      E1-E2_ATPase 109 tplqkkldklgkvlvpvvlliallvflialllgksla...eallralallva 157
                                       + lq + ++l+  l ++v ++al  ++++++ ++ ++   ++ll+al+ lv 
  gi|386000818|ref|YP_005919117.1|  72 AMLQDFKRRLFVSLLITVPVLALSPMIQTFFGFDLVFpgsFYLLFALSSLVY 123
                                       5678888899999999999999999999999998888999999999999986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.3
                                       -HHHHHHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 109 tplqkkldklgkvlvpvvlliall 132
                                         l   + +++ +++ +v++ ++ 
  gi|386000818|ref|YP_005919117.1| 146 MTLIGVAISVAYFYSSAVVFGLAG 169
                                       344444444444444444444444 PP

  == domain 3  score: 177.7 bits;  conditional E-value: 4.4e-56
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                        +p++a++irdg++ee++++ l+ GD v +++g++vp+Dg ++eg+++v+es+LTGEs+pv k +g++v++G+++ +
  gi|386000818|ref|YP_005919117.1| 207 VMPSEAHLIRDGQVEEVEIASLKKGDRVMVRPGEKVPVDGTVLEGKSSVNESLLTGESKPVGKMEGSRVIGGSMNGE 283
                                       5799************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155
                                       g+++++V +tg++t+l+++++lv +a+++++++q  +++ + +l++++l +++++f++++++g+++++a+ r+++++
  gi|386000818|ref|YP_005919117.1| 284 GSLVVEVGKTGKETYLSTVIALVTSAQESRSKTQDLANRAAFFLTVIALSVGAITFAAWIYYGRDVVFAIERGVTVM 360
                                       ***************************************************************************** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlak 180
                                       v+++P aL+la+pl++a++++ +ak
  gi|386000818|ref|YP_005919117.1| 361 VITCPHALGLAIPLVVAVSTSLAAK 385
                                       ********************99998 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.7   9.7e+03       8      22 ..     244     258 ..     244     262 .. 0.84
   2 !  148.3   0.7     1e-46   3.7e-43       1     210 []     402     624 ..     402     624 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                                       SBTTTBCHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                         Hydrolase   8 kdGTLttgepsvedv 22 
                                       +dGT+++g++sv + 
  gi|386000818|ref|YP_005919117.1| 244 VDGTVLEGKSSVNES 258
                                       59*******999875 PP

  == domain 2  score: 148.3 bits;  conditional E-value: 1e-46
                                       SSEEEEESBTTTBCHHHHHHHHHHHH..............CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa..............alalaaaletgsehpigkalvaaakarsgal...tgf 60 
                                       i++vvfDk+GTLt+ge  v++vi+ +               l laa le +seh i++ +v+ a++r++++   ++f
  gi|386000818|ref|YP_005919117.1| 402 IEAVVFDKTGTLTRGEFGVTEVIPLVgvgevgkegeaemeVLRLAASLEASSEHSIARGVVKGAEDRGISTapaDEF 478
                                       789****************************************************************5555556*** PP

                                       HHETTTE........HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHH CS
                                       xxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  61 atfigrg........ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeav 127
                                       + ++g+g        ++ + +p +l+     +  ++++ +a++ g+tv++l  +   l+ +++ d+  v+pe +eav
  gi|386000818|ref|YP_005919117.1| 479 QSMPGKGvlgvvdgrRLKVVSPGYLEGA-GIELDDERVRAAEEGGKTVVFLleDETPLGALALGDS--VRPESKEAV 552
                                       ***************9999999999999.77777888999999999999999999***********..********* PP

                                       HHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 128 asLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaa 204
                                       ++Lk++g++  +ltgdn+  ae++ + lG           +e +a+++p +k ++ire q++   vamVGDgvnDa+
  gi|386000818|ref|YP_005919117.1| 553 ERLKSMGLKCMMLTGDNRYVAEEVSRDLG----------LDEFFAEVLPHQKAEKIREVQERY-TVAMVGDGVNDAP 618
                                       *****************************..........5555****************8665.7************ PP

                                       HHHHTT CS
                                       xxxxxx RF
                         Hydrolase 205 alaaAg 210
                                       ala+A+
  gi|386000818|ref|YP_005919117.1| 619 ALAQAD 624
                                       *****8 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0012       4.3      15      58 ..     543     586 ..     538     589 .. 0.91
   2 !   18.3   0.1   4.3e-07    0.0015     205     248 ..     606     649 ..     592     656 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0012
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       ++ +++kea+++lk+ g k +  TG + + +++v ++lgld ++
  gi|386000818|ref|YP_005919117.1| 543 SVRPESKEAVERLKSMGLKCMMLTGDNRYVAEEVSRDLGLDEFF 586
                                       6889***********************************99765 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.3e-07
                                       GEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG CS
                       Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne 248
                                        v+ +GDg ND + L +a++g+A+g +++ + + Ad +   n+ 
  gi|386000818|ref|YP_005919117.1| 606 TVAMVGDGVNDAPALAQADVGIAIGAGTDVAVETADIILVRNDP 649
                                       57889********************************9988876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.9     1e+04      71     105 ..     202     235 ..     175     236 .. 0.65
   2 !   21.8   0.0   5.8e-08   0.00021      86     187 ..     544     620 ..     504     621 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.9
                               HAD  71 aelerfvaevirpklldpgalella.ahraaGdrvv 105
                                       +el++ + ++++  l++ g +e ++ a +++Gdrv 
  gi|386000818|ref|YP_005919117.1| 202 EELAKVMPSEAH--LIRDGQVEEVEiASLKKGDRVM 235
                                       344444433333..5667777777778888888875 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 5.8e-08
                               HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewl 162
                                        +p+ +e++++ ++ G ++ +++g +r+++e++ + lg    l++       +++e      p  +++k+++++e  
  gi|386000818|ref|YP_005919117.1| 544 VRPESKEAVERLKSMGLKCMMLTGDNRYVAEEVSRDLG----LDE-------FFAE----VLPHQKAEKIREVQE-- 603
                                       4587788888788*************************....888.......7777....233334445566666.. PP

                               HAD 163 aaegegidleevvayGDspsDlpll 187
                                               + +v  +GD+++D p+l
  gi|386000818|ref|YP_005919117.1| 604 --------RYTVAMVGDGVNDAPAL 620
                                       ........2335555********98 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.069      82     133 ..     546     597 ..     542     628 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                             HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvek 133
                                       ++ ke++e Lk++g+k+   T  +r ++ee  + lg++++F  ++  +++ek
  gi|386000818|ref|YP_005919117.1| 546 PESKEAVERLKSMGLKCMMLTGDNRYVAEEVSRDLGLDEFFAEVLPHQKAEK 597
                                       7899***************************************998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 5228.14
//
Query:       gi|386000819|ref|YP_005919118.1|  [L=561]
Description: hypothetical protein Mhar_0102 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-33  115.9   0.6    2.8e-33  115.9   0.6    2.4  2  DUF262    Protein of unknown function DUF262
    7.2e-30  103.7   0.3    7.2e-30  103.7   0.3    2.0  3  DUF1524   Protein of unknown function (DUF1524)
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.33   11.0   0.0    1.7  2  Cnd1      non-SMC mitotic condensation complex subunit 1


Domain annotation for each model (and alignments):
>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.6   4.7e-37   2.8e-33       1     220 [.      13     233 ..      13     234 .. 0.82
   2 ?   -1.7   2.3      0.45   2.7e+03      67      67 ..     371     371 ..     242     548 .. 0.62

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 4.7e-37
                            DUF262   1 ledllskskrglriPdfQRpyvWeeeqveeLiedlla...........lkgyplGsivlwskaadsageleviDGQQ 66 
                                       +++++s++   + iP +QRpy+W++e++ eL++d+ +            ++y+lGsivl    +d a+  +v+DGQQ
  gi|386000819|ref|YP_005919118.1|  13 ISKIFSDEFV-FTIPLYQRPYAWTTEHAGELLDDIITfrednnedggsVSPYFLGSIVL---IKDYAPDAQVVDGQQ 85 
                                       6789999999.9***********************************************...88889********** PP

                            DUF262  67 RltTltlllaat...keesekriknleaeiekekeeededrlkrreresdkellqkllrseklsleekeelaelnsl 140
                                       Rl Tlt+ll         ++++i  +++e    + +   +r++++ +e+d e++++++++e+  ++ ++  a     
  gi|386000819|ref|YP_005919118.1|  86 RLATLTILLSTLrhlTPTYASDITPFIYEKGS-EIKGTPNRYRLTLKEKDAEFFKEYIQDENGLEKLRNLGA----- 156
                                       ***********334566666666666666665.44556678899999**************98765433333..... PP

                            DUF262 141 tkkdlakeekrneeknlikayevieeilksa.......llsalktklslieieleseddedqayeiFerlNsrGvpL 210
                                                 +++++n+ ++  ++ ++lk++       l +++ +++ ++ +++ + ++   a +iF  lN+rG+ L
  gi|386000819|ref|YP_005919118.1| 157 -------GRLSDSQRNIAENALYFLDKLKDYsekellsLTQFIINHCIIVGVSTPDFNS---AWRIFSILNDRGLDL 223
                                       .......3337788888888888888888876666665555556788888888888777...*************** PP

                            DUF262 211 tasellkall 220
                                       +  +++ka++
  gi|386000819|ref|YP_005919118.1| 224 SITDIIKADV 233
                                       *******986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.45
                            DUF262  67 R 67 
                                       R
  gi|386000819|ref|YP_005919118.1| 371 R 371
                                       0 PP

>> DUF1524  Protein of unknown function (DUF1524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.4   8.4e+03      91     109 ..     164     182 ..     143     194 .. 0.56
   2 ?   -3.3   0.0       1.3   7.7e+03       6      35 ..     261     289 ..     259     302 .. 0.66
   3 !  103.7   0.3   1.2e-33   7.2e-30       5     138 ..     418     553 ..     415     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.4
                           DUF1524  91 lNsslsnkpfleKrdlykk 109
                                        N + +   fl+K + y++
  gi|386000819|ref|YP_005919118.1| 164 RNIAENALYFLDKLKDYSE 182
                                       3333333444444444443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                           DUF1524   6 efrrallnaklysssrkklryilakelesa 35 
                                        fr+ +++ +  ++++k+   il+ e++++
  gi|386000819|ref|YP_005919118.1| 261 TFRDLFAHIRMIHRKTKQKDTILE-EFRQY 289
                                       677778888888888887788888.77644 PP

  == domain 3  score: 103.7 bits;  conditional E-value: 1.2e-33
                           DUF1524   5 eefrrallnaklysssrkklryilakelesalreedeeegeakkltiEHilPqslaekwegag.qedeekreelvnd 80 
                                       +e+ +al+++ + s++  + ry+l  +l+ al++  +  +e++++tiEH++Pq+++e + +++ + d+e+re +v++
  gi|386000819|ref|YP_005919118.1| 418 SEILNALNGNIYLSKN--VPRYVLL-RLDAALSDG-KASYEYPFITIEHVMPQNPSEGSYWTKhFPDKEDREMFVHK 490
                                       6778888888887777..678****.***999966.4455558888***********65455538899********* PP

                           DUF1524  81 lgNLtlltkslNsslsnkpfleKrdlykk.....sslrlnrklaekdewdeeaiearqeaLak 138
                                       lgNL+ll++++Ns++ n +f++K+ +y       s + l++++ +++ew++e+ie+rqe L++
  gi|386000819|ref|YP_005919118.1| 491 LGNLVLLSRKKNSQARNYDFDKKKRQYFAtdkgiSPFVLTTQVMQEQEWTPEVIEKRQEHLIE 553
                                       *************************99999*******************************98 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.6e-05      0.33      55     104 ..     143     196 ..     137     217 .. 0.78
   2 ?   -3.8   0.0         2   1.2e+04     115     140 ..     278     303 ..     265     305 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
                              Cnd1  55 kekgflselakl....leDenprVvanalaalteiseksenaiynllpdiiskl 104
                                       ++++ l++l++l    l+D+++++ +nal++l ++++ se+++++l++ ii++ 
  gi|386000819|ref|YP_005919118.1| 143 QDENGLEKLRNLgagrLSDSQRNIAENALYFLDKLKDYSEKELLSLTQFIINHC 196
                                       55555555555433339**********************9*******9999986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                              Cnd1 115 gqitilefLlsyipkdkqeaeslvek 140
                                       +  tile   +y+ k +++ +s +++
  gi|386000819|ref|YP_005919118.1| 278 QKDTILEEFRQYVVKPTKDSKSFIDN 303
                                       45567777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3941.14
//
Query:       gi|386000820|ref|YP_005919119.1|  [L=54]
Description: hypothetical protein Mhar_0103 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 369.22
//
Query:       gi|386000821|ref|YP_005919120.1|  [L=144]
Description: hypothetical protein Mhar_0105 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1065.25
//
Query:       gi|386000822|ref|YP_005919121.1|  [L=404]
Description: gluconate transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-28   99.6  21.8      2e-16   59.8   0.9    2.0  2  GntP_permease  GntP family permease
      0.005   16.1  23.4     0.0079   15.4  23.4    1.3  1  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> GntP_permease  GntP family permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8  14.0   7.6e-16   6.9e-12       6     181 ..       3     178 ..       1     192 [. 0.90
   2 !   59.8   0.9   2.2e-20     2e-16     260     424 ..     235     386 ..     227     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7.6e-16
                     GntP_permease   6 vligvilllllviklklnafvaLllvsllvglvsGmpldkvvksiekGlGgtlGslaiiiglGamlGklledsGaae 82 
                                        l+++il+ ll+ k+ l +f++L++ +l+ g+++Gm   +++ s++ Gl   +  laii+  Ga++   l  s ++e
  gi|386000822|ref|YP_005919121.1|   3 FLVAIILVALLTAKFGLSPFLSLVVSALAYGVLTGMGP-ELIGSVSGGLARIFSALAIIVFSGAVIAEQLRRSRGVE 78 
                                       6899********************************97.57899********************************* PP

                     GntP_permease  83 rialtlikklgkkkvqwalvlagfivgialFfevg.lvlLiplvfaiakeakisllklgiplvaalavvhgllpPhP 158
                                       r+   l+  lg+ +  +a  l+g++++++    ++  ++L p+v  +++ea+ s   l     a  +    l+ P P
  gi|386000822|ref|YP_005919121.1|  79 RVVADLLGLLGRGRGLLASGLSGYLLALPTMCSITsYLVLEPVVRGMGREAGGSERRLLFTAGAFSVLSFNLVYPSP 155
                                       *****************************999985278899*************99999888777778889999*** PP

                     GntP_permease 159 gplavaellgadiGkvllyGliv 181
                                         +a+ + lg+   + l +Gl +
  gi|386000822|ref|YP_005919121.1| 156 VMVALTGSLGVAPAEALRFGLPL 178
                                       ****9999998766666666655 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 2.2e-20
                     GntP_permease 260 fiGnpvvalliallvaiytlglrrgksikkvldileealksiaiilliigaGGafkqvlvdsgvgkalaellsnlel 336
                                       ++G+p vall   l   +  gl+r+       ++++ a + +++i++ + + Gaf +v+ ++g+g  l  +l   ++
  gi|386000822|ref|YP_005919121.1| 235 LVGSPEVALLAGAL---FSAGLAREGAG----EMIKAATRRAGVIIFDLCGAGAFAAVIAQGGLGPELYAALG-EAF 303
                                       56777777766544...44455555444....456789999***************************88775.579 PP

                     GntP_permease 337 spillaflvaallrialGsatVaaltaaglvapiiaqlpgvnlallvlaigaGslilshvnDagFWlvkeylgltvk 413
                                       +++ll+fl a l+++a+Gs +V+++      ++++  l   ++  +  +i+aG+ +ls + D+ FWl+k+ +g  +k
  gi|386000822|ref|YP_005919121.1| 304 PLLLLPFLTASLIQLAQGSRVVTVVI----ASEMMRDL-PLDPLTILFSISAGAFVLSSLSDPYFWLLKDTTGSDLK 375
                                       9********************98875....56777777.67889999****************************** PP

                     GntP_permease 414 etlktwtvlet 424
                                       etl  +t+  t
  gi|386000822|ref|YP_005919121.1| 376 ETLLGYTLPLT 386
                                       *******9876 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  23.4   8.8e-07    0.0079       6     298 ..      14     349 ..       3     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.8e-07
                                       xxx......xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   6 lek......lrldvvallvlvll......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlagg 70 
                                       + k      l+l v al  +vl+      + +    l+ i s ++++++ + +i++ l ++ +++r++a ll l g+
  gi|386000822|ref|YP_005919121.1|  14 TAKfglspfLSLVVSALAYGVLTgmgpelIGSVSGGLARIFSALAIIVFSGAVIAEQLRRSRGVERVVADLLGLLGR 90 
                                       333555555666666666666665555544444448888888889******************************** PP

                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  71 krdllvllvlltallsafvsn..dgvvlimipivlslakrlkklppl..........lliplalaaniggaltpiGt 135
                                        r  l++ +l   ll a+++    +  l++ p+v  ++++ +++ ++          l  +l++++ ++ alt    
  gi|386000822|ref|YP_005919121.1|  91 GRG-LLASGLSGYLL-ALPTMcsITSYLVLEPVVRGMGREAGGSERRllftagafsvLSFNLVYPSPVMVALT---- 161
                                       999.66666666666.4443323455**************988888864444444444444555555555555.... PP

                                       xxxxxx..............................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 136 pttraa..............................................arpglslpnllllalllvgllplvl 166
                                                                                            r++ ++p  l lal+ +gll+   
  gi|386000822|ref|YP_005919121.1| 162 -----GslgvapaealrfglplslllfvpgllymrrlpagdegaipeggplpPRLRSWAPLALPLALIGAGLLTPRA 233
                                       .....044444566866666666666666666666666666666666666655555555555556777777755555 PP

                                       xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 167 lfmfgvalalpvnap.....kvkkqkaiieaiarsllpvatilllaykkveWsvlllfaGvfllvgaleqtGileal 238
                                        ++ +  +al+  a        +   ++i+a +r++     ++           ++ ++G++ +++++ q G++  l
  gi|386000822|ref|YP_005919121.1| 234 WLVGSPEVALLAGALfsaglAREGAGEMIKAATRRAG----VI-----------IFDLCGAGAFAAVIAQGGLGPEL 295
                                       5544444444444445555456666666666666555....44...........458999999999******99999 PP

                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 239 adllgaggplvalalvlglial.lsafisnvavaalmapialgmapalgllspsplalala 298
                                        ++lg++ pl+   l+ +l+a  + +++++  v+   + ia +m+ +l  l+p  +++ + 
  gi|386000822|ref|YP_005919121.1| 296 YAALGEAFPLL---LLPFLTASlIQLAQGSRVVT---VVIASEMMRDLP-LDPLTILFSIS 349
                                       99996653433...45555555499999999776...777777777766.66666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2986.51
//
Query:       gi|386000823|ref|YP_005919122.1|  [L=1048]
Description: hypothetical protein Mhar_0107 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-16   58.9   0.4     0.0072   16.6   0.3    8.1  6  DUF11        Domain of unknown function DUF11
    1.8e-14   53.8   0.0    0.00072   19.8   0.0    8.0  8  CARDB        CARDB
    5.9e-10   39.3   3.9    0.00088   19.5   0.7    7.2  8  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
      0.001   18.5   0.1         19    4.6   0.0    5.2  6  TRAP_beta    Translocon-associated protein beta (TRAPB)
     0.0077   16.2   0.0         39    4.4   0.0    5.7  7  DUF1573      Protein of unknown function (DUF1573)
     0.0094   14.8   0.3        4.8    5.9   0.0    3.9  5  BatD         Oxygen tolerance
  ------ inclusion threshold ------
      0.019   14.8   0.1        6.4    6.7   0.0    4.0  4  A2M          Alpha-2-macroglobulin family
      0.028   15.2   0.0        1.9    9.3   0.0    3.9  4  N_BRCA1_IG   Ig-like domain from next to BRCA1 gene
       0.23   11.4   0.0         22    5.1   0.0    3.0  3  AGS_C        Adenylyl/Guanylyl and SMODS C-terminal sensor do


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0018       3.5      16      56 ..      40      94 ..      30     142 .. 0.65
   2 !   16.6   0.3   3.6e-06    0.0072       8      44 ..     156     189 ..     139     371 .. 0.81
   3 ?    0.6   0.0      0.36   7.1e+02       5      36 ..     444     475 ..     440     476 .. 0.88
   4 !   13.0   0.1     5e-05     0.099       8      83 ..     642     759 ..     636     765 .. 0.74
   5 ?    3.7   0.1     0.039        79      19      36 ..     751     768 ..     734     791 .. 0.81
   6 !    5.6   0.0    0.0098        20       7      29 ..     838     860 ..     823     864 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                             DUF11 16 vtytltvtNtgpasangvvvtDtl.........Paglayvsvsas.....qgtas 56
                                      ++yt+  +N+g  +++g+ ++D           P+g a+  ++++     ++ ++
  gi|386000823|ref|YP_005919122.1| 40 LNYTIRIKNSGREPLYGISISDNFgqvgfiarlPEGAALDLARTTpalttSAEIR 94
                                      79********************999999999996555555555543233222222 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.6e-06
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPagla 44 
                                       + vrpG+  t+  tvtN+gp ++ gv ++    +g +
  gi|386000823|ref|YP_005919122.1| 156 PSVRPGERATVRMTVTNRGPHPLRGVEISG---PGWT 189
                                       479***********************9987...3333 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.36
                             DUF11   5 vdksevrpGdtvtytltvtNtgpasangvvvt 36 
                                        +k+ v  G+ + +   + N+g++++++v ++
  gi|386000823|ref|YP_005919122.1| 444 ANKTLVHRGERIAFRCAAVNRGQVPLTDVELR 475
                                       57788999*******************99885 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 5e-05
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtl........................Paglayvsvsas......... 51 
                                       +++ pG++v+++ t +Ntg +++  v vt +                         Pag ++v ++a          
  gi|386000823|ref|YP_005919122.1| 642 AAAYPGEAVEVVWTIRNTGEVDL--VDVTMVIdgnssfrlpaiaaggstqvssshqPAGSRGVLARAEgrtaggeti 716
                                       4799*******************..5555555667999999999999999999999899988888888888887766 PP

                             DUF11  52 ..qgtasaltsv.........gsLeagesatlsftvrvtrtaa 83 
                                         +++++ ++ +          ++ea++++ +++t  vt+t++
  gi|386000823|ref|YP_005919122.1| 717 ssEAAFQIRVVSpglslnvkpSEVEASQKKPFNLTFLVTNTGD 759
                                       5533333333335544444445668888888888888888876 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.039
                             DUF11  19 tltvtNtgpasangvvvt 36 
                                       t  vtNtg +++ +v+++
  gi|386000823|ref|YP_005919122.1| 751 TFLVTNTGDDPLRDVTIS 768
                                       5569*********99986 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.0098
                             DUF11   7 ksevrpGdtvtytltvtNtgpas 29 
                                       ++e++pG+ v +t  v N+g ++
  gi|386000823|ref|YP_005919122.1| 838 PAEAAPGGSVHVTFSVENRGEVP 860
                                       4589****************876 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.21   4.1e+02       8      36 ..      27      55 ..      23      66 .. 0.82
   2 !    6.6   0.0    0.0045         9       6      63 ..     151     201 ..     144     225 .. 0.71
   3 ?   -0.4   0.0      0.69   1.4e+03      12      66 ..     250     301 ..     241     320 .. 0.62
   4 ?    0.6   0.0      0.35     7e+02       2      38 ..     436     472 ..     430     489 .. 0.73
   5 !    5.7   0.0    0.0089        18       2      72 ..     533     599 ..     532     616 .. 0.74
   6 !   19.8   0.0   3.6e-07   0.00072       4      72 ..     633     697 ..     630     708 .. 0.85
   7 ?    4.2   0.0     0.025        50       4      81 ..     731     804 ..     728     821 .. 0.70
   8 ?    2.1   0.0      0.11   2.3e+02      10      32 ..     836     858 ..     828     865 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                                      EEEC-SEEETTSEEEEEEEEEE-SSS-EE CS
                             CARDB  8 ntlnpseafvgeentitvtvkNqGtaasg 36
                                        l+++e+++ + ++ t+ +kN+G +  +
  gi|386000823|ref|YP_005919122.1| 27 LDLEETEVEYLSPLNYTIRIKNSGREPLY 55
                                      5677889999999999********98655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0045
                                       E.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEE CS
                             CARDB   6 vtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagest 63 
                                       v   + p ++ +ge  t+++tv+N G    + +++    +g    tv+v  L++ges+
  gi|386000823|ref|YP_005919122.1| 151 V--GAYPPSVRPGERATVRMTVTNRGPHPLRGVEI----SGPG-WTVEVGDLNPGESK 201
                                       3..7788999****************988776653....3444.44555566666655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.69
                                       -SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEE CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvs 66 
                                       p + + g + + ++ +kN G++  + ++++     +l    ++p La+ge+++ +
  gi|386000823|ref|YP_005919122.1| 250 PIPDSSGGAGRTEYRLKNGGEELLTRITLKDARGATL---GILPRLAPGETKNLT 301
                                       5555555555666777777776666666554333333...367999999999876 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.35
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEE CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgat 38 
                                       pD  vt ++n + ++ ge + +++   N G+   +++
  gi|386000823|ref|YP_005919122.1| 436 PDIAVTLQANKTLVHRGERIAFRCAAVNRGQVPLTDV 472
                                       7777777888888888888888888888876555554 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0089
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                       p L v+++++p+  + ge ++i v ++N G++  +++++  y d  + g   vp L +ge +t   + t+e
  gi|386000823|ref|YP_005919122.1| 533 PALRVEVSQEPGRISRGERVSIAVRLENGGDDLLTEISA--YDDLGEIG--RVPTLRPGEVVTLMRNSTVE 599
                                       789999************************987665544..44433333..78888888888887777776 PP

  == domain 6  score: 19.8 bits;  conditional E-value: 3.6e-07
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                       L ++++ + ++a++ge++++  t++N+G+ +   + v++++dg++  ++ +p++aag+st+vs +++++
  gi|386000823|ref|YP_005919122.1| 633 LSLEVEPKDAAAYPGEAVEVVWTIRNTGEVDL--VDVTMVIDGNS--SFRLPAIAAGGSTQVSSSHQPA 697
                                       55666777889*****************9887..5678899**99..89**************999987 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.025
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtl 80 
                                       L ++++ ++ ea++++ +++t+ v+N+G++  ++++++    g+l     +  L++g+ +  s  ++t+ t  +  l
  gi|386000823|ref|YP_005919122.1| 731 LSLNVKPSEVEASQKKPFNLTFLVTNTGDDPLRDVTISERSLGTL---ERIGRLEPGDFRVASHDFFTD-TNTTFRL 803
                                       5555566677889999999999********999988776666666...357888888777777777777.5555555 PP

                                       E CS
                             CARDB  81 t 81 
                                       +
  gi|386000823|ref|YP_005919122.1| 804 E 804
                                       5 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.11
                                       EC-SEEETTSEEEEEEEEEE-SS CS
                             CARDB  10 lnpseafvgeentitvtvkNqGt 32 
                                        +p+ea +g ++ +t++v+N G+
  gi|386000823|ref|YP_005919122.1| 836 PEPAEAAPGGSVHVTFSVENRGE 858
                                       57899999*************97 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   4.3e+03       7      27 ..      40      60 ..      38      61 .. 0.88
   2 ?   -3.9   0.2       8.5   1.7e+04      55      69 ..     109     124 ..     106     127 .. 0.63
   3 !   19.5   0.7   4.4e-07   0.00088       2      66 ..     159     214 ..     158     231 .. 0.91
   4 !    5.9   0.0    0.0077        15       2      27 ..     450     475 ..     449     478 .. 0.92
   5 ?   -2.8   0.0         4     8e+03       2      24 ..     547     569 ..     546     570 .. 0.85
   6 ?    0.6   0.0      0.33   6.7e+02       3      27 ..     646     670 ..     644     673 .. 0.84
   7 ?    5.1   0.0     0.013        27       5      27 ..     746     768 ..     742     770 .. 0.87
   8 ?   -0.8   0.0      0.92   1.8e+03       2      21 ..     842     861 ..     841     863 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                       NPCBM_assoc  7 vtltltvtndgtaaatnvsls 27
                                       ++t+ ++n+g++++ ++s+s
  gi|386000823|ref|YP_005919122.1| 40 LNYTIRIKNSGREPLYGISIS 60
                                      578999**********99986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.5
                       NPCBM_assoc  55 atvkVtppag.aaaGd 69 
                                       a v+V pp+g aaaG+
  gi|386000823|ref|YP_005919122.1| 109 APVEVAPPPGeAAAGE 124
                                       5677777654266665 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 4.4e-07
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaa 66 
                                       +pGe+ t+++tvtn g  ++++v++s  + +GWt       ++ +l pGe+  +t +V + ++a 
  gi|386000823|ref|YP_005919122.1| 159 RPGERATVRMTVTNRGPHPLRGVEIS--G-PGWT------VEVGDLNPGESKAFTREVAVAEEAS 214
                                       79********************9886..4.5***......8899*************99988875 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0077
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsls 27 
                                        +Ge+ +++ +++n g+ ++t+v+l+
  gi|386000823|ref|YP_005919122.1| 450 HRGERIAFRCAAVNRGQVPLTDVELR 475
                                       6899*******************997 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 4
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnv 24 
                                       ++Ge+v++ + + n+g++ +t++
  gi|386000823|ref|YP_005919122.1| 547 SRGERVSIAVRLENGGDDLLTEI 569
                                       78999*********999988776 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.33
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvsls 27 
                                       pGe v++  t+ n+g+  + +v + 
  gi|386000823|ref|YP_005919122.1| 646 PGEAVEVVWTIRNTGEVDLVDVTMV 670
                                       8999999999999999999988765 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.013
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvsls 27 
                                       ++ +lt+ vtn+g++++++v +s
  gi|386000823|ref|YP_005919122.1| 746 KPFNLTFLVTNTGDDPLRDVTIS 768
                                       67889999************987 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 0.92
                       NPCBM_assoc   2 epGetvtltltvtndgtaaa 21 
                                        pG +v +t++v n g+ ++
  gi|386000823|ref|YP_005919122.1| 842 APGGSVHVTFSVENRGEVPI 861
                                       58889999999999998875 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 ?   -0.5   0.0      0.34   6.8e+02      36      59 ..      39      62 ..      31      66 .. 0.90
   2 !    4.6   0.0    0.0096        19      34      93 ..     161     220 ..     153     246 .. 0.88
   3 ?    2.1   0.0     0.054   1.1e+02      15      57 ..     433     475 ..     423     478 .. 0.84
   4 ?   -2.2   0.0       1.2   2.3e+03      33      59 ..     548     574 ..     545     574 .. 0.90
   5 ?    0.3   0.0       0.2   3.9e+02      90     116 ..     635     661 ..     633     686 .. 0.68
   6 ?    2.3   0.0     0.048        95      31      61 ..     742     772 ..     736     776 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                         TRAP_beta 36 dltveytiyNvGssaAldVslvDd 59
                                       l+ ++ i N G ++ + +s++D+
  gi|386000823|ref|YP_005919122.1| 39 PLNYTIRIKNSGREPLYGISISDN 62
                                      6788999***************97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0096
                         TRAP_beta  34 gedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvve 93 
                                       ge+ tv++t++N G  + + V+++  ++  e  ++  g+++a    +a  e+ s  +v +
  gi|386000823|ref|YP_005919122.1| 161 GERATVRMTVTNRGPHPLRGVEISGPGWTVEVGDLNPGESKAFTREVAVAEEASMEIVAT 220
                                       8999*************************9999999999999999999888888877755 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.054
                         TRAP_beta  15 dasarvlvkKkilnrllvegedltveytiyNvGssaAldVslv 57 
                                       +a++ ++v  ++ + l+  ge+++++   +N G+ + +dV+l+
  gi|386000823|ref|YP_005919122.1| 433 EAAPDIAVTLQANKTLVHRGERIAFRCAAVNRGQVPLTDVELR 475
                                       4567778888888899999*********************996 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.2
                         TRAP_beta  33 egedltveytiyNvGssaAldVslvDd 59 
                                        ge++++++ + N G+   +++s++Dd
  gi|386000823|ref|YP_005919122.1| 548 RGERVSIAVRLENGGDDLLTEISAYDD 574
                                       689*************99999999997 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.2
                         TRAP_beta  90 fvvepkksgsfngtaavvtYresekga 116
                                       ++vepk   ++ g+a++v +++ ++g+
  gi|386000823|ref|YP_005919122.1| 635 LEVEPKDAAAYPGEAVEVVWTIRNTGE 661
                                       567777777777777777666655533 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.048
                         TRAP_beta  31 lvegedltveytiyNvGssaAldVslvDdsf 61 
                                       +++++  ++++ ++N G+ + +dV++++ s+
  gi|386000823|ref|YP_005919122.1| 742 ASQKKPFNLTFLVTNTGDDPLRDVTISERSL 772
                                       567888999999***************9987 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.62   1.2e+03      13      33 ..      34      54 ..      26      60 .. 0.84
   2 ?   -1.0   0.0      0.94   1.9e+03      15      33 ..     160     178 ..     156     183 .. 0.74
   3 ?   -2.0   0.0       1.9   3.8e+03      19      58 ..     455     490 ..     445     501 .. 0.70
   4 ?   -1.5   0.0       1.3   2.6e+03       9      32 ..     542     565 ..     535     569 .. 0.72
   5 ?   -0.0   0.0      0.46   9.1e+02      16      34 ..     647     665 ..     642     701 .. 0.88
   6 ?    4.4   0.0      0.02        39      14      33 ..     743     762 ..     736     769 .. 0.88
   7 ?    0.8   0.0      0.26   5.2e+02      16      33 ..     844     861 ..     839     866 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.62
                           DUF1573 13 ieegekvtatFeftNtgkapl 33
                                      +e  ++ ++t++++N g +pl
  gi|386000823|ref|YP_005919122.1| 34 VEYLSPLNYTIRIKNSGREPL 54
                                      577789999**********99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.94
                           DUF1573  15 egekvtatFeftNtgkapl 33 
                                        ge++t++ ++tN g +pl
  gi|386000823|ref|YP_005919122.1| 160 PGERATVRMTVTNRGPHPL 178
                                       4677788888888888776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                           DUF1573  19 vtatFeftNtgkaplvitnvktsCgCttpeypkepiapGe 58 
                                       +  +    N g+ p  +t+v+  Cg  +++   e +apG+
  gi|386000823|ref|YP_005919122.1| 455 IAFRCAAVNRGQVP--LTDVELRCGGEVAS--AELLAPGD 490
                                       45555566777666..58999999988777..45666665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.3
                           DUF1573   9 dfgkieegekvtatFeftNtgkap 32 
                                       + g i++ge+v++  +++N g++ 
  gi|386000823|ref|YP_005919122.1| 542 EPGRISRGERVSIAVRLENGGDDL 565
                                       457777788888888888877765 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 0.46
                           DUF1573  16 gekvtatFeftNtgkaplv 34 
                                       ge v+++ +++Ntg+  lv
  gi|386000823|ref|YP_005919122.1| 647 GEAVEVVWTIRNTGEVDLV 665
                                       6789999*******98886 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.02
                           DUF1573  14 eegekvtatFeftNtgkapl 33 
                                       +++++ + tF +tNtg++pl
  gi|386000823|ref|YP_005919122.1| 743 SQKKPFNLTFLVTNTGDDPL 762
                                       678999*************8 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 0.26
                           DUF1573  16 gekvtatFeftNtgkapl 33 
                                       g++v++tF+++N g+ p+
  gi|386000823|ref|YP_005919122.1| 844 GGSVHVTFSVENRGEVPI 861
                                       68999*********9987 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.012        24     234     258 ..     225     254 ..     200     266 .. 0.72
   2 ?   -3.5   0.0       1.7   3.4e+03      10      38 ..     535     562 ..     530     569 .. 0.80
   3 ?   -2.2   0.0      0.69   1.4e+03     129     160 ..     633     664 ..     621     684 .. 0.71
   4 ?   -1.5   0.0       0.4     8e+02     235     254 ..     718     737 ..     676     760 .. 0.71
   5 !    5.9   0.0    0.0024       4.8     232     272 ..     813     848 ..     786     857 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.012
                              BatD 234 g.....gyrevkkrvsspavtitVkplPae 258
                                       g      +++ k+ ++spa+t+tV p+P++
  gi|386000823|ref|YP_005919122.1| 225 GgeaasARQSLKVSTVSPALTVTVVPIPDS 254
                                       22445678999*****************86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                              BatD  10 aeftasvdknevevgetfrLtftvngasg 38 
                                        ++++s  + +++ ge++++ +++++  g
  gi|386000823|ref|YP_005919122.1| 535 LRVEVSQEPGRISRGERVSIAVRLENG-G 562
                                       578888899999999999999999987.4 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.69
                              BatD 129 lflraevskksvYvqeqvlvtlklytrvnvnl 160
                                       l l++e++   +Y +e+v v+  +    +v+l
  gi|386000823|ref|YP_005919122.1| 633 LSLEVEPKDAAAYPGEAVEVVWTIRNTGEVDL 664
                                       66788888888888888888777765544444 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.4
                              BatD 235 gyrevkkrvsspavtitVkp 254
                                       +    ++rv+sp ++++Vkp
  gi|386000823|ref|YP_005919122.1| 718 SEAAFQIRVVSPGLSLNVKP 737
                                       55667889999999999998 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0024
                              BatD 232 ngg.gyrevkkrvsspavtitVkplPaeglPadFsgavgsfs 272
                                       ng    rev ++++s+++++ ++p Pae++P       gs+ 
  gi|386000823|ref|YP_005919122.1| 813 NGVnDSREVAVKLVSANIELSIRPEPAEAAPG------GSVH 848
                                       2224789*********************9998......5444 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   3.6e+03      20      48 ..      82     110 ..      74     115 .. 0.80
   2 ?    6.7   0.0    0.0032       6.4      61      86 ..     153     178 ..     130     183 .. 0.86
   3 ?    0.7   0.0      0.24   4.9e+02      63      84 ..     543     564 ..     518     569 .. 0.87
   4 ?    1.0   0.0      0.19   3.8e+02      23      52 ..     795     823 ..     787     864 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                       EEEESSSCEEEEEEEEEETTTEEEEEEEE CS
                               A2M  20 ftlPDsiTtWrvtavalsedkglgvaepl 48 
                                        t P   T+ ++ +va s+ + lg a ++
  gi|386000823|ref|YP_005919122.1|  82 RTTPALTTSAEIRVVASSDGEELGRAAAP 110
                                       57788889999********9999998873 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                                       E--SEEETTSEEEEEEEEEE-SSS-E CS
                               A2M  61 nlPysvrrgeqveikavvfNyldkei 86 
                                         P svr ge+ +++++v N  ++++
  gi|386000823|ref|YP_005919122.1| 153 AYPPSVRPGERATVRMTVTNRGPHPL 178
                                       5799****************987765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.24
                                       -SEEETTSEEEEEEEEEE-SSS CS
                               A2M  63 PysvrrgeqveikavvfNyldk 84 
                                       P ++ rge+v+i + + N  d+
  gi|386000823|ref|YP_005919122.1| 543 PGRISRGERVSIAVRLENGGDD 564
                                       8899**********99998766 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.19
                                       ESSSCEEEEEEEEEETTTEEEEEEEEEEEE CS
                               A2M  23 PDsiTtWrvtavalsedkglgvaeplevrv 52 
                                        D+ Tt+r+ a  ++   g gv ++ ev v
  gi|386000823|ref|YP_005919122.1| 795 TDTNTTFRLEATGIDSR-GNGVNDSREVAV 823
                                       699***********999.999999866554 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.93   1.8e+03      60      60 ..     198     198 ..     130     279 .. 0.61
   2 ?    9.3   0.0   0.00094       1.9       8      68 ..     644     693 ..     639     706 .. 0.75
   3 ?   -1.1   0.0       1.6   3.1e+03      10      27 ..     744     761 ..     737     770 .. 0.80
   4 ?   -3.6   0.0         9   1.8e+04       8      26 ..     841     859 ..     836     861 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.93
                        N_BRCA1_IG  60 g 60 
                                       g
  gi|386000823|ref|YP_005919122.1| 198 G 198
                                       1 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00094
                        N_BRCA1_IG   8 vppgteftktWrlrNtGseaWpagtklvfvgGdkmgsasaeessvsvpavapgeevevsve 68 
                                         pg+  + +W++rNtG+++   ++++v++g           ss+  pa+a+g +++vs +
  gi|386000823|ref|YP_005919122.1| 644 AYPGEAVEVVWTIRNTGEVDL-VDVTMVIDGN----------SSFRLPAIAAGGSTQVSSS 693
                                       579999*************97.7777777772..........5566777777777777655 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.6
                        N_BRCA1_IG  10 pgteftktWrlrNtGsea 27 
                                        ++ f+ t+ ++NtG+ +
  gi|386000823|ref|YP_005919122.1| 744 QKKPFNLTFLVTNTGDDP 761
                                       57889**********976 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 9
                        N_BRCA1_IG   8 vppgteftktWrlrNtGse 26 
                                        +pg     t+ ++N G++
  gi|386000823|ref|YP_005919122.1| 841 AAPGGSVHVTFSVENRGEV 859
                                       5677777788888888875 PP

>> AGS_C  Adenylyl/Guanylyl and SMODS C-terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.011        22      42      76 ..     626     661 ..     593     663 .. 0.74
   2 ?    2.5   0.0     0.069   1.4e+02      42      80 ..     724     763 ..     704     787 .. 0.78
   3 ?   -2.4   0.0       2.2   4.4e+03      62      77 ..     843     859 ..     796     868 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                             AGS_C  42 sellekgksLkFkiknttsvp.epykvkWkvrNtGe 76 
                                        +l e+g sL+ + k+ + +p e ++v W++rNtGe
  gi|386000823|ref|YP_005919122.1| 626 LKLSEPGLSLEVEPKDAAAYPgEAVEVVWTIRNTGE 661
                                       4566677777777788888888899**********7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.069
                             AGS_C  42 sellekgksLkFki.knttsvpepykvkWkvrNtGeeAer 80 
                                        +++++g sL+ k  + ++s ++p+++ + v+NtG++  r
  gi|386000823|ref|YP_005919122.1| 724 IRVVSPGLSLNVKPsEVEASQKKPFNLTFLVTNTGDDPLR 763
                                       66777777777777433446679************98765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.2
                             AGS_C  62 p.epykvkWkvrNtGee 77 
                                       p   ++v + v N+Ge 
  gi|386000823|ref|YP_005919122.1| 843 PgGSVHVTFSVENRGEV 859
                                       44667899999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1048 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 6179.29
//
Query:       gi|386000824|ref|YP_005919123.1|  [L=431]
Description: hypothetical protein Mhar_0108 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2762.25
//
Query:       gi|386000825|ref|YP_005919124.1|  [L=122]
Description: hypothetical protein Mhar_0109 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.017   15.8   3.3      0.022   15.4   3.0    1.3  1  YabA           Initiation control protein YabA
       0.17   12.5   2.2       0.23   12.1   1.3    1.6  2  SlyX           SlyX
       0.18   12.2   7.7        1.3    9.4   3.7    2.9  3  kleA_kleC      Uncharacterized KorC regulated protein A
        2.1    8.2   3.9        6.4    6.6   1.1    2.3  3  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   3.0   4.8e-06     0.022       7      73 ..      10      76 ..       4      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  7 fdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenL 73
                                       +++ee+ee++ + ++e e+lk+e aell + +eL+     lr+   e+ ++  +++++l+   +++
  gi|386000825|ref|YP_005919124.1| 10 EKSFEEMEEDMLSHQTESERLKKEAAELLRRSDELRSRSVDLRSADPEAAEEMWQESEDLRGESREM 76
                                      4789****************************************99666666665555554444444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.3   5.1e-05      0.23      14      59 ..       8      53 ..       6      62 .. 0.88
   2 ?   -2.1   0.0       1.4   6.2e+03      29      43 ..      62      76 ..      57      86 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX 14 fqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgasea 59
                                      f e+  ee+ + +  +q + +rl+++ ++l +r  el+++s + ++
  gi|386000825|ref|YP_005919124.1|  8 FVEKSFEEMEEDMLSHQTESERLKKEAAELLRRSDELRSRSVDLRS 53
                                      78999*****************************999999876555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHH CS
                              SlyX 29 qqqqidrlqrqlrll 43
                                       +q+ + l+ + r++
  gi|386000825|ref|YP_005919124.1| 62 MWQESEDLRGESREM 76
                                      455555555555544 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.7   0.00028       1.3      13      63 ..      14      64 ..       9      67 .. 0.85
   2 ?    4.4   0.4      0.01        47      31      50 ..      57      76 ..      50      98 .. 0.75
   3 ?    2.1   0.0     0.055   2.4e+02      23      40 ..      97     114 ..      81     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00028
                         kleA_kleC 13 pevatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaLedrakkrWt 63
                                      +e ++d++++  +   + +eA+eL r+ +eLR +    ++a  + a + W 
  gi|386000825|ref|YP_005919124.1| 14 EEMEEDMLSHQTESERLKKEAAELLRRSDELRSRSVDLRSADPEAAEEMWQ 64
                                      6677788888888888999***************99999999888888885 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                         kleA_kleC 31 aeAeeLvrqaeeLRakvyee 50
                                      + Aee+ ++ e+LR++ +e 
  gi|386000825|ref|YP_005919124.1| 57 EAAEEMWQESEDLRGESREM 76
                                      6899**********998864 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.055
                         kleA_kleC  23 RdkiAaklaeAeeLvrqa 40 
                                        d+i a + +A+e+ + a
  gi|386000825|ref|YP_005919124.1|  97 HDQIVAVVDRADEIWKGA 114
                                       589999999999998866 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.1    0.0014       6.4      24      59 ..      18      53 ..       9      57 .. 0.75
   2 ?    1.5   0.0     0.056   2.5e+02      33      51 ..      59      77 ..      54      86 .. 0.62
   3 ?   -2.5   0.0       1.1   4.7e+03      28      42 ..      95     109 ..      88     114 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                                      HHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHH CS
                     Synaptobrevin 24 dkvlergekldeLvdktenLqssaqqFkkqarklkr 59
                                      +++l+ + + + L++++ +L   +++ ++++ +l+ 
  gi|386000825|ref|YP_005919124.1| 18 EDMLSHQTESERLKKEAAELLRRSDELRSRSVDLRS 53
                                      467777777788888888888888888888888775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.056
                                      HHHHCCCCHHHHHHHHHHH CS
                     Synaptobrevin 33 ldeLvdktenLqssaqqFk 51
                                       +e+ +++e+L+ ++++  
  gi|386000825|ref|YP_005919124.1| 59 AEEMWQESEDLRGESREMM 77
                                      4555566666666665544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                                       CCCCCHHHHCCCCHH CS
                     Synaptobrevin  28 ergekldeLvdkten 42 
                                       e ++++   vd++++
  gi|386000825|ref|YP_005919124.1|  95 EIHDQIVAVVDRADE 109
                                       455555555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 860.82
//
Query:       gi|386000826|ref|YP_005919125.1|  [L=175]
Description: Glutamine amidotransferase subunit pdxT [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-40  139.6   0.0    1.2e-40  139.4   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    1.6e-09   37.6   0.0    2.1e-09   37.3   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00085   19.0   0.1     0.0012   18.5   0.1    1.2  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.018   14.9   0.1    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
      0.031   14.1   0.2       0.28   10.9   0.2    2.0  1  GATase         Glutamine amidotransferase class-I
       0.23   11.2   1.1         18    5.0   0.2    2.9  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.0     4e-44   1.2e-40      26     187 ..      15     173 ..       2     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 4e-44
                                       -SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.SS-SS--CCEEEE CS
                               SNO  26 krkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene.lvktlellkvkvk 101
                                       ++   + ++d++++PGGest++++ + rtg+ +++ +  + +  +++ tCaGli++s e+ +e     l+ll+v+v 
  gi|386000826|ref|YP_005919125.1|  15 RKGGIVPGCDGIVLPGGESTTIARHLARTGVGDEVAAASRSG-VPIMATCAGLIVVSTEIVEEtRFLPLGLLDVRVA 90 
                                       55555679**********************888877665555.*****************99978899********* PP

                                       TTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEE.ETTEEEESS-GGGSTTHCH CS
                               SNO 102 rnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldgeivvak.qkkilatsfhPelaeddir 177
                                       rnafG q +sfe++l++ +++ ++ avfiraP i   +  e v+ l   + e+ va+  +++l+++fhPel+ed  r
  gi|386000826|ref|YP_005919125.1|  91 RNAFGSQRESFEADLEVAGFDSPYRAVFIRAPAIVGWG--EGVEPLARIE-EVAVAArEENLLGLAFHPELTED-DR 163
                                       **********************************8877..8999999999.665555277*************9.7* PP

                                       HHHHHHHHHC CS
                               SNO 178 vhdyfveevv 187
                                       +h++f+++++
  gi|386000826|ref|YP_005919125.1| 164 FHQLFLRMIE 173
                                       *******987 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   6.9e-13   2.1e-09      25     117 ..       7      91 ..       1     112 [. 0.85

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.9e-13
                          GATase_3  25 vrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvege 101
                                        r+ +v++++  + + +d ++lpGg++t+ +  l+r  g+ +++++a+++g+p+++ C+Gl++ ++ei+++      
  gi|386000826|ref|YP_005919125.1|   7 ARGSVVEVRKGGIVPGCDGIVLPGGESTTIARHLART-GVGDEVAAASRSGVPIMATCAGLIVVSTEIVEET----- 77 
                                       5667777778888899************999988888.******************************9865..... PP

                          GATase_3 102 ageveglglLdietef 117
                                         +   lglLd++++ 
  gi|386000826|ref|YP_005919125.1|  78 --RFLPLGLLDVRVAR 91 
                                       ..77889999988765 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.1e-07    0.0012      84     135 ..      24      75 ..      14      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.1e-07
                                       SEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GG CS
                     Peptidase_S51  84 dviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiet 135
                                       d+i++ GG+   +++ l++tg+ +    a ++g++++ + AG iv++++i  
  gi|386000826|ref|YP_005919125.1|  24 DGIVLPGGESTTIARHLARTGVGDEVAAASRSGVPIMATCAGLIVVSTEIVE 75 
                                       99*********************************************99976 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     6e-06     0.018      62     114 ..      23      75 ..      13      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                                       -SEEEE--BHHH..HHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTT CS
                         DJ-1_PfpI  62 yDalvlpGGrag..perlrenekvvelvkefaekgklvaaICagpqlLaaagvlk 114
                                        D +vlpGG++   + +l++ + v++ v  + ++g ++ a Cag ++ +++++++
  gi|386000826|ref|YP_005919125.1|  23 CDGIVLPGGESTtiARHLAR-TGVGDEVAAASRSGVPIMATCAG-LIVVSTEIVE 75 
                                       599******98422445554.599********************.5556666665 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   9.4e-05      0.28      41     178 ..      21     163 ..       5     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.4e-05
                                       HSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE...........EEECEEEE CS
                            GATase  41 knpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvv...........kekekehh 101
                                        ++dgi+++gG  +       ++g  + +  a  +++Pi+  C G+ ++  e+ +++             ++ ++ +
  gi|386000826|ref|YP_005919125.1|  21 PGCDGIVLPGGESTTIarhlaRTGVGDEVAAASRSGVPIMATCAGLIVVSTEIVEETRflplglldvrvARNAFGSQ 97 
                                       578999999998877677788555555555555579*********99999999996666655555544322224555 PP

                                       EEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTT CS
                            GATase 102 ggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpe 178
                                         + + +     ++ g ++++++ +    ++       +g+e +a+ e+    ++++e++  + g+ FHPE t   +
  gi|386000826|ref|YP_005919125.1|  98 RESFEADL----EVAGFDSPYRAVFIRAPAIVG---WGEGVEPLARIEE--VAVAAREEN--LLGLAFHPELTEDDR 163
                                       55555554....788888888888888888888...8888999888844..345555555..699999999987666 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.006        18      99     116 ..      50      67 ..      15      73 .. 0.79
   2 ?    2.9   0.0     0.027        81     195     216 .]     136     157 ..     129     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.006
                     Peptidase_C26  99 raalergvPilgiCrGlq 116
                                       +aa ++gvPi+++C Gl 
  gi|386000826|ref|YP_005919125.1|  50 AAASRSGVPIMATCAGLI 67 
                                       577888999999999975 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.027
                     Peptidase_C26 195 viEaieseeakafvlgvQwHPE 216
                                        iE + + ++++ +lg+ +HPE
  gi|386000826|ref|YP_005919125.1| 136 RIEEVAVAAREENLLGLAFHPE 157
                                       589999999999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1226.95
//
Query:       gi|386000827|ref|YP_005919126.1|  [L=271]
Description: pyridoxal biosynthesis lyase pdxS [Methanosaeta harundinacea 6Ac]
Scores for complete 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-93  310.8   8.2    5.8e-93  310.4   8.2    1.2  1  SOR_SNZ       SOR/SNZ family
    1.5e-08   34.3  10.0    1.5e-07   31.0   0.3    2.5  2  ThiG          Thiazole biosynthesis protein ThiG
    8.5e-07   28.4   0.3     0.0018   17.5   0.0    2.2  2  Dus           Dihydrouridine synthase (Dus)
    0.00062   19.0   2.6      0.015   14.5   0.0    2.8  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0045   16.4   0.1     0.0045   16.4   0.1    1.9  2  NMO           Nitronate monooxygenase
      0.007   15.6   0.3       0.19   10.9   0.0    2.3  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.017   14.3   0.2      0.037   13.2   0.0    1.7  2  IGPS          Indole-3-glycerol phosphate synthase
      0.028   13.9   0.2        0.2   11.1   0.0    2.1  2  His_biosynth  Histidine biosynthesis protein
       0.47    9.8   4.2        2.3    7.5   0.2    2.8  3  TMP-TENI      Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.4   8.2   2.9e-96   5.8e-93      18     207 .]       1     189 [.       1     189 [. 0.99

  Alignments for each domain:
  == domain 1  score: 310.4 bits;  conditional E-value: 2.9e-96
                                       EEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HHHHHHHHHTT-S CS
                           SOR_SNZ  18 mdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfveaqilealgvd 94 
                                       mdv+++eqa iaeeaGavavmal+ vpadirk ggvarm+dpk+i ei+e v+ipvmakvriGhf+eaqilea+gvd
  gi|386000827|ref|YP_005919126.1|   1 MDVTTPEQAVIAEEAGAVAVMALQAVPADIRKMGGVARMADPKIIMEIIEEVTIPVMAKVRIGHFAEAQILEAIGVD 77 
                                       9**************************************************************************** PP

                                       EEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHHHHHHHTT CS
                           SOR_SNZ  95 yiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkikeeirklks 171
                                       +iDesevltpade +h+dk++f+vpfvcGarnlgealrri+eGaamirtkGeagtGdv eavrh+r i  +ir+lk 
  gi|386000827|ref|YP_005919126.1|  78 MIDESEVLTPADE-FHVDKSRFTVPFVCGARNLGEALRRIKEGAAMIRTKGEAGTGDVREAVRHMRLIGGSIRSLKG 153
                                       ************7.8************************************************************** PP

                                       S-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 172 lseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                       + +eel++la+e++a+l lv e+++++rlpvvnfaa
  gi|386000827|ref|YP_005919126.1| 154 MADEELAKLAREIEAELGLVLECRDMQRLPVVNFAA 189
                                       **********************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   3.9    0.0025       4.9     141     200 ..      13      78 ..       3      92 .. 0.79
   2 !   31.0   0.3   7.5e-11   1.5e-07     174     225 ..     180     233 ..     162     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0025
                                       HHTT-SEBEEBSSS......TTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SE CS
                              ThiG 141 eevGcaavmPlaap......iGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGada 200
                                       ee+G+ avm l a       +G    +++++ +  iiee+++Pv+    ig+  +a     +G+d 
  gi|386000827|ref|YP_005919126.1|  13 EEAGAVAVMALQAVpadirkMGGVARMADPKIIMEIIEEVTIPVMAKVRIGHFAEAQILEAIGVDM 78 
                                       799******99763233222466666778899999*****************99998887888886 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 7.5e-11
                                       -SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 174 akvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                        ++Pv+  A  Gi +p da   m++Gad+v++ + + ++++p  mA+a+  av+
  gi|386000827|ref|YP_005919126.1| 180 QRLPVVNFAagGIATPADASLMMQMGADGVFVGSGIFKSQNPELMASAIVEAVN 233
                                       478888544349***************************************997 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00035       0.7      95     134 ..      30      65 ..      26      79 .. 0.80
   2 !   17.5   0.0   8.9e-07    0.0018     180     232 ..     180     234 ..     161     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00035
                                       TTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESS CS
                               Dus  95 trggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigid 134
                                       +r+++G a +++p+ + +i+++    v iPv +k+rig  
  gi|386000827|ref|YP_005919126.1|  30 IRKMGGVARMADPKIIMEIIEE----VTIPVMAKVRIGHF 65 
                                       78999*********99999987....68*********965 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.9e-07
                                       HH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHH..CCSTTHHHH.HHHHHHS CS
                               Dus 180 qavsipviaNGdIkdaedaqaileetGadgvmigrga..lgnPwlfae.stavktg 232
                                       q+++++ +a G+I ++ da+ +++  Gadgv +g g    +nP l+a+   ++ ++
  gi|386000827|ref|YP_005919126.1| 180 QRLPVVNFAAGGIATPADASLMMQM-GADGVFVGSGIfkSQNPELMASaIVEAVNN 234
                                       566778899**************99.**********733589***99544333333 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.1     0.028        56     100     170 ..       4      79 ..       1      92 [. 0.51
   2 !   14.5   0.0   7.4e-06     0.015     144     180 ..     183     219 ..     151     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.028
                                       SSHHHHHHHHHTT-SEEE-TTTTSSTTS-......SS--HHHHHHH.HHTT--EEEES---SHHHHHHHHTT--SEE CS
                              NanE 100 stleeglvakklGvdivGttlsGytkeeek.....aepDfalvkal.seaglkviaeGrintPekakkaieiGvdav 170
                                        t e++++a+++G+  v  +l+    + +k        D +++ ++  e  + v+a  ri   ++a+    iGvd++
  gi|386000827|ref|YP_005919126.1|   4 TTPEQAVIAEEAGAVAVM-ALQAVPADIRKmggvaRMADPKIIMEIiEEVTIPVMAKVRIGHFAEAQILEAIGVDMI 79 
                                       555555555555543332.2222222222222233334444444430444566777777777777777777777665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.4e-06
                                       T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 144 glkviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                        +   a G i tP+ a  ++++G+d v vGs i + +
  gi|386000827|ref|YP_005919126.1| 183 PVVNFAAGGIATPADASLMMQMGADGVFVGSGIFKSQ 219
                                       4556799************************997643 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.38   7.7e+02     122     158 ..      41      77 ..       6      79 .. 0.69
   2 !   16.4   0.1   2.3e-06    0.0045     179     227 ..     167     217 ..     151     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.38
                               NMO 122 glpteevvarlkeagvvliptissvkearkvearGaD 158
                                       +++  + ++++ +  v++ + i+   ea+++ea G D
  gi|386000827|ref|YP_005919126.1|  41 DPKIIMEIIEEVTIPVMAKVRIGHFAEAQILEAIGVD 77 
                                       4444555666666666777777777777777777776 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.3e-06
                               NMO 179 kglfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                       + ++ Lv + +d   +Pv+  AaGGi +  +   ++ +GA gv +g+    
  gi|386000827|ref|YP_005919126.1| 167 EAELGLVLECRDMQRLPVVnfAAGGIATPADASLMMQMGADGVFVGSGIFK 217
                                       466778888899999***877*************************97665 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.032        65      47      85 ..      39      79 ..      18      88 .. 0.67
   2 !   10.9   0.0   9.4e-05      0.19     169     233 ..     164     231 ..     133     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.032
                            DUF561 47 aadpklvkkvksvsniPiCvsaveakllleav...kaGadlv 85
                                       adpk++ ++ + + iP+  + v + +++ea+   + G+d++
  gi|386000827|ref|YP_005919126.1| 39 MADPKIIMEIIEEVTIPVM-AKVRIGHFAEAQileAIGVDMI 79
                                      5788888888888888874.4566666666652222355544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.4e-05
                            DUF561 169 ekslstlastyeiskkvslPvi..casGlsd.vtvplalslgasGiGigsavsklndeeemvallsei 233
                                       +++   l  + e     +lPv+  +a G+++   ++l +++ga G+ +gs + k ++ e m +++ e 
  gi|386000827|ref|YP_005919126.1| 164 REIEAELGLVLECRDMQRLPVVnfAAGGIATpADASLMMQMGADGVFVGSGIFKSQNPELMASAIVEA 231
                                       555556666677777789999755799997626799***********************999988664 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1         1     2e+03     127     140 ..      12      25 ..       2      75 .. 0.53
   2 ?   13.2   0.0   1.8e-05     0.037     197     250 ..     171     224 ..     151     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                                       HHHCT-SEEEEECC CS
                              IGPS 127 aralgadaiLLivk 140
                                       a  +ga a++ + +
  gi|386000827|ref|YP_005919126.1|  12 AEEAGAVAVMALQA 25 
                                       44444444433333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.8e-05
                                       HHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                              IGPS 197 ntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                       + + e +++ +  v+  a  Gi+t++d++ + + g++++ vG+ + ++++ e +
  gi|386000827|ref|YP_005919126.1| 171 GLVLECRDMQRLPVVNFAAGGIATPADASLMMQMGADGVFVGSGIFKSQNPELM 224
                                       4455555555566888899****************************9998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.2   4.1e+02      61      97 ..      41      77 ..      23      84 .. 0.73
   2 ?   11.1   0.0    0.0001       0.2      78     112 ..     188     224 ..     159     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S CS
                      His_biosynth 61 nldlveeiaeevfipvqvGGGIrsledveelleagad 97
                                      + +++ ei+eev+ipv+    I ++ +++ l  +g+d
  gi|386000827|ref|YP_005919126.1| 41 DPKIIMEIIEEVTIPVMAKVRIGHFAEAQILEAIGVD 77
                                      4567888888888888777666666666666555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                                       EESSSSSHHHHHHHHHCT-SEEEESHHHH..H-THHH CS
                      His_biosynth  78 vGGGIrsledveelleagadkviigtaav..knpeli 112
                                         GGI +  d+  ++++gad v +g+  +  +npel+
  gi|386000827|ref|YP_005919126.1| 188 AAGGIATPADASLMMQMGADGVFVGSGIFksQNPELM 224
                                       5677777777777777777777777776522455555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.037        74     104     155 ..       4      58 ..       2      79 .. 0.73
   2 ?   -0.9   0.0      0.45   8.9e+02      88     109 ..     133     154 ..     126     165 .. 0.80
   3 ?    7.5   0.2    0.0012       2.3     145     181 .]     176     215 ..     160     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.037
                          TMP-TENI 104 hsleeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiPvva 155
                                        ++e+a  ae++ga  +++ +  p d +k+    ++++ + + e+ e+++iPv+a
  gi|386000827|ref|YP_005919126.1|   4 TTPEQAVIAEEAGAVAVMALQAVPADIRKMGgvaRMADPKIIMEIIEEVTIPVMA 58 
                                       5778889999999977777677788888876555778889999999999999988 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.45
                          TMP-TENI  88 earellgpdliiGlSvhsleea 109
                                       ++re + +  +iG S+ sl+ +
  gi|386000827|ref|YP_005919126.1| 133 DVREAVRHMRLIGGSIRSLKGM 154
                                       7899999999*****9998764 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0012
                          TMP-TENI 145 laealeiPvv..aiGGi.tlenvaevleagadgvavvsai 181
                                       ++++ ++Pvv  a GGi t++++  +++ gadgv v s+i
  gi|386000827|ref|YP_005919126.1| 176 CRDMQRLPVVnfAAGGIaTPADASLMMQMGADGVFVGSGI 215
                                       455555666433999996789999999*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1584.05
//
Query:       gi|386000828|ref|YP_005919127.1|  [L=1202]
Description: Periplasmic component of the Tol biopolymer transport system-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-09   36.7   2.5     0.0033   16.2   0.1    6.0  7  Pectate_lyase22  Oligogalacturonate lyase
    5.3e-08   32.0  10.9       0.56    8.9   0.1    7.4  8  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    0.00017   21.1   8.8        2.6    7.4   0.1    5.7  7  DUF5046          Domain of unknown function (DUF5046)
  ------ inclusion threshold ------
      0.043   13.8   3.0        8.6    6.4   0.1    4.4  4  phage_tail_N     Prophage tail fibre N-terminal
      0.059   13.3   9.4         53    4.0   0.0    7.5  8  PQQ              PQQ enzyme repeat
       0.32   10.8  15.9        4.6    7.0   0.1    8.1 12  DUF2606          Protein of unknown function (DUF2606)
        3.3    7.9   4.5         85    3.4   0.1    4.1  5  CsgF             Type VIII secretion system (T8SS), CsgF prot


Domain annotation for each model (and alignments):
>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0021       5.3      46      77 ..     127     158 ..     106     165 .. 0.86
   2 ?   -0.6   0.0      0.16   4.2e+02      47      86 ..     170     209 ..     163     242 .. 0.76
   3 !   16.2   0.1   1.3e-06    0.0033      46     127 ..     335     417 ..     303     430 .. 0.80
   4 ?   -1.1   0.0      0.22   5.7e+02      48      81 ..     463     496 ..     459     528 .. 0.85
   5 ?   -3.2   0.0      0.99   2.5e+03      44      81 ..     680     717 ..     675     720 .. 0.86
   6 ?    3.1   0.0     0.012        31      47      82 ..     767     801 ..     760     829 .. 0.82
   7 !    4.5   0.0    0.0044        11      44      83 ..    1092    1131 ..    1085    1174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0021
                   Pectate_lyase22  46 dgskllfggafdgprnyylldlntqqavqlte 77 
                                       dg+++++  + dg++n y+ dl t +  ++t 
  gi|386000828|ref|YP_005919127.1| 127 DGDRVVWMDDRDGNWNVYMHDLATGEERRITT 158
                                       99********************9988777765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.16
                   Pectate_lyase22  47 gskllfggafdgprnyylldlntqqavqltegkgdntfgg 86 
                                       g+ ++++ + +g+ + y+ dl++ +   l+ g g++ f  
  gi|386000828|ref|YP_005919127.1| 170 GDLIVWTDDRNGNSDIYIYDLEAGRESPLSTGPGEQVFPD 209
                                       566778889999***********99999*99999999854 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.3e-06
                   Pectate_lyase22  46 dgskllfggafdgprnyylldlntqqavqltegkgdntfggflssdddalfyvkn...ernlmrvdletleetviyq 119
                                       dg++++++ +  g++n y++dl t q +q+t+ + +++    +s   d + y  n   +++l+  dl t eet + +
  gi|386000828|ref|YP_005919127.1| 335 DGDRVVWTDDRTGKFNVYMIDLSTSQEIQITDSEDEKS-SPSISG--DIILYTDNrsgNLDLFVYDLRTGEETRVTD 408
                                       99*****************************9886655.555554..456666652224678899********9987 PP

                   Pectate_lyase22 120 vd.eewvgy 127
                                        + ++w g 
  gi|386000828|ref|YP_005919127.1| 409 DPsDQWYGM 417
                                       652678774 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.22
                   Pectate_lyase22  48 skllfggafdgprnyylldlntqqavqltegkgd 81 
                                       +++ +  +  g+++ ++ +l t+  vq+t   g 
  gi|386000828|ref|YP_005919127.1| 463 DRVAWMDNRAGNWDIFVYNLSTRSEVQVTTDPGK 496
                                       5666667778******************987665 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 0.99
                   Pectate_lyase22  44 trdgskllfggafdgprnyylldlntqqavqltegkgd 81 
                                       +  g+ l++  + +g+++   l+l + + + +++g+g 
  gi|386000828|ref|YP_005919127.1| 680 AASGDLLVWQDDRNGDWDILALNLTSGEEIVVADGRGA 717
                                       667889999999***************99999999996 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.012
                   Pectate_lyase22  47 gskllfggafdgprnyylldlntqqavqltegkgdn 82 
                                       g+ l++  + +g+++ y+ dl t + ++lt g+gd+
  gi|386000828|ref|YP_005919127.1| 767 GDLLVWQDDRNGEWDVYVCDLATGEETKLT-GEGDQ 801
                                       7788999999*******************9.66664 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.0044
                   Pectate_lyase22   44 trdgskllfggafdgprnyylldlntqqavqltegkgdnt 83  
                                        t dgs +++  + +g+++ y  dl t +  qlt    ++t
  gi|386000828|ref|YP_005919127.1| 1092 TTDGSLVVWQDNRNGNWDLYSHDLATGKVEQLTSDPSNQT 1131
                                        88*******************************8776665 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 !    8.9   0.1   0.00022      0.56      62      86 ..     140     164 ..      91     191 .. 0.75
   2 ?   -1.9   0.0      0.43   1.1e+03      62      85 ..     182     205 ..     166     210 .. 0.65
   3 !    8.9   0.1   0.00022      0.56      24      87 ..     350     415 ..     340     427 .. 0.76
   4 !    5.1   0.0    0.0031       7.8     209     238 ..     390     419 ..     378     467 .. 0.57
   5 !    4.7   0.1    0.0041        10      62      83 ..     474     495 ..     437     504 .. 0.87
   6 ?    2.0   0.0     0.028        72      62      83 ..     779     800 ..     777     810 .. 0.86
   7 ?    0.6   0.2     0.073   1.9e+02      51     102 ..     922     983 ..     897     986 .. 0.75
   8 !    5.1   0.0    0.0032       8.2      62      85 ..    1107    1130 ..    1105    1142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00022
                                       TTEEEEESTTTSEEEECES-STTTE CS
                           DPPIV_N  62 nnnLyvrelatgkeiqlTsdgsagi 86 
                                       n+n+y+++latg+e+++T+d +++i
  gi|386000828|ref|YP_005919127.1| 140 NWNVYMHDLATGEERRITTDPKDQI 164
                                       79******************99887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                                       TTEEEEESTTTSEEEECES-STTT CS
                           DPPIV_N  62 nnnLyvrelatgkeiqlTsdgsag 85 
                                       n+++y+ +l+ g+e  l+++  ++
  gi|386000828|ref|YP_005919127.1| 182 NSDIYIYDLEAGRESPLSTGPGEQ 205
                                       556666666666666666555555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00022
                                       EEEEEETTTEECEEEETTTT.BSEEEEESS..TTEEEEEETT....EEEEESTTTSEEEECES-STTTEE CS
                           DPPIV_N  24 eyyiydletneveelspgeeklqlakwSPa..gdklafvrnn....nLyvrelatgkeiqlTsdgsagif 87 
                                       ++y+ dl+t +  +++++    ++ k SP   gd + ++ n+    +L+v +l tg+e+++T+d s++ +
  gi|386000828|ref|YP_005919127.1| 350 NVYMIDLSTSQEIQITDS----EDEKSSPSisGDIILYTDNRsgnlDLFVYDLRTGEETRVTDDPSDQWY 415
                                       566778888777777777....6666677665888999876555559*****************988766 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0031
                                       EEEEEEEETTTCCEEEEEEEESSS-SSS-S CS
                           DPPIV_N 209 rlkvvlvdaetgravvkleetsdgWvelhd 238
                                       +l+++++d++tg+ ++++++ sd W+    
  gi|386000828|ref|YP_005919127.1| 390 NLDLFVYDLRTGEETRVTDDPSDQWYGMVA 419
                                       345555555555555555555555553333 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0041
                                       TTEEEEESTTTSEEEECES-ST CS
                           DPPIV_N  62 nnnLyvrelatgkeiqlTsdgs 83 
                                       n++++v +l+t++e+q+T+d  
  gi|386000828|ref|YP_005919127.1| 474 NWDIFVYNLSTRSEVQVTTDPG 495
                                       89*****************983 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.028
                                       TTEEEEESTTTSEEEECES-ST CS
                           DPPIV_N  62 nnnLyvrelatgkeiqlTsdgs 83 
                                       ++++yv +latg+e++lT +g+
  gi|386000828|ref|YP_005919127.1| 779 EWDVYVCDLATGEETKLTGEGD 800
                                       79****************8883 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.073
                                       ESS..TTEEEEE....ETTEEEEESTTTSEEEECES-S....TTTEEESB--HHHHHHTSSS CS
                           DPPIV_N  51 SPa..gdklafv....rnnnLyvrelatgkeiqlTsdg....sagifnGvadWvyeEEvlgs 102
                                       SPa  gd+++++    +n ++y+ +l ++ e  l  +       +i+n+v  W y EE ++s
  gi|386000828|ref|YP_005919127.1| 922 SPAvsGDWVVWMdnrtQNPDIYLYNLVENVEWPLAAGKefdmYPDIINDVVVWMYLEEQFNS 983
                                       55555667766511114669*********999999866344467788***********8865 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.0032
                                        TTEEEEESTTTSEEEECES-STTT CS
                           DPPIV_N   62 nnnLyvrelatgkeiqlTsdgsag 85  
                                        n++Ly ++latgk+ qlTsd s++
  gi|386000828|ref|YP_005919127.1| 1107 NWDLYSHDLATGKVEQLTSDPSNQ 1130
                                        89******************9765 PP

>> DUF5046  Domain of unknown function (DUF5046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   2.8e+03      57      83 ..      43      71 ..      34      79 .. 0.75
   2 !    7.4   0.1     0.001       2.6      27      85 ..     137     199 ..     125     226 .. 0.82
   3 ?    1.7   0.0     0.055   1.4e+02      30      84 ..     184     240 ..     174     247 .. 0.81
   4 ?    3.6   0.1     0.015        38       1      92 [.     270     370 ..     270     402 .. 0.63
   5 !    4.6   0.3    0.0072        18      32      87 ..     352     409 ..     345     449 .. 0.77
   6 !    5.2   0.0    0.0048        12      33      79 ..     784     831 ..     764     840 .. 0.83
   7 ?    2.9   0.0     0.024        63      14      85 ..    1050    1124 ..    1035    1174 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                           DUF5046 57 PGavvlwnsge..dsryelidletGektp 83
                                       G +v w  +   ++   ++dletG  + 
  gi|386000828|ref|YP_005919127.1| 43 DGHIVAWADNRsgNFDIFMYDLETGTERG 71
                                      58899997776334455689*****8765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.001
                           DUF5046  27 edgrye..lidlastedsellatfdrsvstyaPGavvlwnsge..dsryelidletGektpvy 85 
                                       +dg+ +  + dla++e++ + +    +++  + G +++w  +   +s   ++dle+G   p+ 
  gi|386000828|ref|YP_005919127.1| 137 RDGNWNvyMHDLATGEERRITTDPKDQIQPKISGDLIVWTDDRngNSDIYIYDLEAGRESPLS 199
                                       5665541157*********99999999999*********9887556778899*****999985 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.055
                           DUF5046  30 ryelidlastedsellatfdrsvstyaPGavvlwnsge..dsryelidletGektpv 84 
                                          ++dl+++ +s l +   ++v   + G +v+w  +   d+   + dl tG+ t +
  gi|386000828|ref|YP_005919127.1| 184 DIYIYDLEAGRESPLSTGPGEQVFPDIDGDLVVWSDNRtgDYDIVILDLPTGQETVI 240
                                       4567999999999977777899999999*999998777557777789*****99987 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.015
                           DUF5046   1 lyntvtGeelt...Gfd....qvcgvGv..aslrtedgryelidlastedsellatfdrsvstyaPGavvlwnsged 68 
                                       lyn+ tGee     G           Gv  +  r+ d+   + d++ t d  + +   +s + ++ G  v+w  +  
  gi|386000828|ref|YP_005919127.1| 270 LYNVDTGEEALvspGSVkmnpALGERGVvwSDHRAPDSDVYIFDFTLTADEVIASGPHNSSNPWIDGDRVVWTDDRT 346
                                       677777776431113333332222234411346678999999999777766666677888999*********99996 PP

                           DUF5046  69 srye..lidletGektpvydvdardk 92 
                                        +++  +idl+t +   + d   +d+
  gi|386000828|ref|YP_005919127.1| 347 GKFNvyMIDLSTSQEIQITDS--EDE 370
                                       666611567777666665544..433 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0072
                           DUF5046  32 elidlastedsellatfdrsvstyaPGavvlwnsge..dsryelidletGektpvydv 87 
                                        +idl+++++ ++    d++ s  + G ++l+  +   +    ++dl tGe t v d 
  gi|386000828|ref|YP_005919127.1| 352 YMIDLSTSQEIQITDSEDEKSSPSISGDIILYTDNRsgNLDLFVYDLRTGEETRVTDD 409
                                       578**999999999999************9998766334555679********99863 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.0048
                           DUF5046  33 lidlastedsellatfdrsvstyaPGavvlwnsge..dsryelidletG 79 
                                       + dla++e+++l +  d +++ ++ G +++w+     d +y l+d + G
  gi|386000828|ref|YP_005919127.1| 784 VCDLATGEETKLTGEGD-QINPHVSGNIIVWEDSTtgDISYYLWDRKWG 831
                                       57*********766665.799*********9865557999*99998766 PP

  == domain 7  score: 2.9 bits;  conditional E-value: 0.024
                           DUF5046   14 dqvcgvGvaslrt.edgryelidlastedsellatfdrsvstyaPGavvlwnsgedsryel..idletGektpvy 85  
                                        +  +g+ +  ++  ++g+ +++  ++t  + + +    +++  + G +v+w+ + + +++l  +dl+tG+ + + 
  gi|386000828|ref|YP_005919127.1| 1050 NPSVGGSLVVYQDnQNGNWDIYVWSGTTRKPVYTGPGDQTHPTTDGSLVVWQDNRNGNWDLysHDLATGKVEQLT 1124
                                        555555566666556777777777777777777777777777788888888877766666633588888776654 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 ?    3.5   0.1     0.026        67      49      91 ..     352     396 ..     334     417 .. 0.73
   2 ?   -0.8   0.0      0.55   1.4e+03      65      92 ..     759     786 ..     757     794 .. 0.84
   3 ?    6.4   0.1    0.0033       8.6      46      90 ..     780     825 ..     770     834 .. 0.79
   4 ?   -0.2   0.0      0.36   9.2e+02      66      86 ..    1048    1068 ..    1045    1077 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.026
                      phage_tail_N  49 ysldvetGky.svilkvd.gfpeshaGditvyedskPGtlndfli 91 
                                       y +d  t +   ++   d   ++s  Gdi +y d + G l+ f+ 
  gi|386000828|ref|YP_005919127.1| 352 YMIDLSTSQEiQITDSEDeKSSPSISGDIILYTDNRSGNLDLFVY 396
                                       55555555531333333414578999**************98875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.55
                      phage_tail_N  65 dgfpeshaGditvyedskPGtlndflia 92 
                                       d  ++s  Gd+ v++d + G  + +++ 
  gi|386000828|ref|YP_005919127.1| 759 DQINPSISGDLLVWQDDRNGEWDVYVCD 786
                                       8899**************9988877775 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0033
                      phage_tail_N  46 aGrysldvetGkys.vilkvdgfpeshaGditvyedskPGtlndfl 90 
                                          y  d  tG+ + ++ + d  +++  G+i v+eds  G +  +l
  gi|386000828|ref|YP_005919127.1| 780 WDVYVCDLATGEETkLTGEGDQINPHVSGNIIVWEDSTTGDISYYL 825
                                       4557788888876525567899*****************9988776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.36
                      phage_tail_N   66 gfpeshaGditvyedskPGtl 86  
                                        g ++s  G++ vy+d + G  
  gi|386000828|ref|YP_005919127.1| 1048 GENPSVGGSLVVYQDNQNGNW 1068
                                        6789999**********9975 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.89   2.3e+03      12      22 ..      59      69 ..      58      70 .. 0.84
   2 ?   -3.6   0.0       5.3   1.4e+04      12      22 ..     185     195 ..     183     195 .. 0.87
   3 ?   -1.1   0.0      0.83   2.1e+03       8      22 ..     223     237 ..     221     237 .. 0.84
   4 ?    1.9   0.0     0.094   2.4e+02      11      22 ..     267     278 ..     266     279 .. 0.90
   5 ?    0.9   0.0      0.19   4.9e+02      12      22 ..     393     403 ..     390     404 .. 0.92
   6 ?   -2.5   0.1       2.4   6.1e+03      18      25 ..     419     426 ..     418     433 .. 0.59
   7 ?    3.3   0.0     0.034        87      12      27 ..     698     713 ..     695     724 .. 0.77
   8 ?    4.0   0.0     0.021        53      12      23 ..    1152    1163 ..    1149    1167 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.89
                                      EEEEETTTCCE CS
                               PQQ 12 lyAlDadTGkv 22
                                      ++ +D++TG++
  gi|386000828|ref|YP_005919127.1| 59 IFMYDLETGTE 69
                                      6779*****98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.3
                                       EEEEETTTCCE CS
                               PQQ  12 lyAlDadTGkv 22 
                                       +y +D++ G++
  gi|386000828|ref|YP_005919127.1| 185 IYIYDLEAGRE 195
                                       89****99975 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.83
                                       TTSEEEEEETTTCCE CS
                               PQQ   8 adGylyAlDadTGkv 22 
                                        d+ ++ lD+ TG++
  gi|386000828|ref|YP_005919127.1| 223 GDYDIVILDLPTGQE 237
                                       578899*******86 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.094
                                       EEEEEETTTCCE CS
                               PQQ  11 ylyAlDadTGkv 22 
                                       ++y +++dTG++
  gi|386000828|ref|YP_005919127.1| 267 QVYLYNVDTGEE 278
                                       79********98 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.19
                                       EEEEETTTCCE CS
                               PQQ  12 lyAlDadTGkv 22 
                                       l+ +D++TG++
  gi|386000828|ref|YP_005919127.1| 393 LFVYDLRTGEE 403
                                       799******97 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 2.4
                                       TTCCEEEE CS
                               PQQ  18 dTGkvlWr 25 
                                       ++G+v+W 
  gi|386000828|ref|YP_005919127.1| 419 ADGRVVWI 426
                                       46666663 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.034
                                       EEEEETTTCCEEEEEE CS
                               PQQ  12 lyAlDadTGkvlWrfk 27 
                                       ++Al++++G+++ + +
  gi|386000828|ref|YP_005919127.1| 698 ILALNLTSGEEIVVAD 713
                                       89*********98766 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.021
                                        EEEEETTTCCEE CS
                               PQQ   12 lyAlDadTGkvl 23  
                                        ++AlD++TG+++
  gi|386000828|ref|YP_005919127.1| 1152 IRALDLATGREM 1163
                                        89*******997 PP

>> DUF2606  Protein of unknown function (DUF2606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.19   4.8e+02      90     113 ..      47      70 ..      37      84 .. 0.80
   2 ?    0.7   0.0      0.16   4.2e+02      87     129 ..     127     168 ..     122     169 .. 0.74
   3 ?    3.8   0.0     0.018        45      85     105 ..     209     230 ..     184     243 .. 0.75
   4 ?    7.0   0.1    0.0018       4.6      89     123 ..     338     372 ..     334     377 .. 0.75
   5 ?   -1.9   0.0         1   2.6e+03      87     105 ..     420     438 ..     418     462 .. 0.73
   6 ?   -0.9   0.0       0.5   1.3e+03      89     115 ..     464     488 ..     439     500 .. 0.76
   7 ?   -2.5   0.0       1.6   4.2e+03      90     104 ..     549     563 ..     546     568 .. 0.86
   8 ?   -3.1   0.0       2.4     6e+03      81     101 ..     632     655 ..     630     657 .. 0.73
   9 ?   -1.7   0.0      0.86   2.2e+03      90     124 ..     686     718 ..     681     724 .. 0.62
  10 ?   -2.6   0.0       1.7   4.4e+03      90     109 ..     770     789 ..     765     800 .. 0.73
  11 ?   -3.6   0.0       3.5   8.8e+03      89     104 ..    1097    1112 ..    1092    1135 .. 0.71
  12 ?   -1.7   0.1      0.91   2.3e+03      87     102 ..    1137    1152 ..    1122    1196 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.19
                           DUF2606  90 vkwdtvrkGdyivaltknetsvth 113
                                       v w + r G++ +++ + et   +
  gi|386000828|ref|YP_005919127.1|  47 VAWADNRSGNFDIFMYDLETGTER 70 
                                       67**************99996655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                           DUF2606  87 eGd.vkwdtvrkGdyivaltknetsvthqivliedkddtkkilv 129
                                       +Gd v+w + r G++ v++ +  t    +  ++ d +d+ ++++
  gi|386000828|ref|YP_005919127.1| 127 DGDrVVWMDDRDGNWNVYMHDLAT--GEERRITTDPKDQIQPKI 168
                                       454499************999888..555556677777666665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.018
                           DUF2606  85 dkeGd.vkwdtvrkGdyivalt 105
                                       d +Gd v+w + r+Gdy +++ 
  gi|386000828|ref|YP_005919127.1| 209 DIDGDlVVWSDNRTGDYDIVIL 230
                                       56677478*********76543 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0018
                           DUF2606  89 dvkwdtvrkGdyivaltknetsvthqivliedkdd 123
                                        v+w + r+G++ v++ +  ts   qi+  ed ++
  gi|386000828|ref|YP_005919127.1| 338 RVVWTDDRTGKFNVYMIDLSTSQEIQITDSEDEKS 372
                                       599***************99976666655555544 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 1
                           DUF2606  87 eGdvkwdtvrkGdyivalt 105
                                       +G v+w + r+Gd  + + 
  gi|386000828|ref|YP_005919127.1| 420 DGRVVWIDDRTGDDQIRVH 438
                                       799*********9877654 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 0.5
                           DUF2606  89 dvkwdtvrkGdyivaltknetsvthqi 115
                                        v w + r G++ +++ +  t    ++
  gi|386000828|ref|YP_005919127.1| 464 RVAWMDNRAGNWDIFVYNLSTRS--EV 488
                                       599************99888743..33 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 1.6
                           DUF2606  90 vkwdtvrkGdyival 104
                                       + w + r+Gdy ++l
  gi|386000828|ref|YP_005919127.1| 549 ISWLDDRNGDYDIYL 563
                                       7899*******9988 PP

  == domain 8  score: -3.1 bits;  conditional E-value: 2.4
                           DUF2606  81 lGktd..keGd.vkwdtvrkGdyi 101
                                       lGk+d   +G  ++w + r Gd+ 
  gi|386000828|ref|YP_005919127.1| 632 LGKADiaTNGSlIVWADNRGGDWD 655
                                       78887445676478*******986 PP

  == domain 9  score: -1.7 bits;  conditional E-value: 0.86
                           DUF2606  90 vkwdtvrkGdyivaltknetsvthqivliedkddt 124
                                       ++w++ r+Gd+ ++ + n t    +iv+ + + ++
  gi|386000828|ref|YP_005919127.1| 686 LVWQDDRNGDWDIL-ALNLT-SGEEIVVADGRGAQ 718
                                       57********9764.33444.24556666666555 PP

  == domain 10  score: -2.6 bits;  conditional E-value: 1.7
                           DUF2606  90 vkwdtvrkGdyivaltknet 109
                                       ++w++ r+G++ v++ +  t
  gi|386000828|ref|YP_005919127.1| 770 LVWQDDRNGEWDVYVCDLAT 789
                                       57*******99988765443 PP

  == domain 11  score: -3.6 bits;  conditional E-value: 3.5
                           DUF2606   89 dvkwdtvrkGdyival 104 
                                         v+w++ r+G++ ++ 
  gi|386000828|ref|YP_005919127.1| 1097 LVVWQDNRNGNWDLYS 1112
                                        489**99*99976654 PP

  == domain 12  score: -1.7 bits;  conditional E-value: 0.91
                           DUF2606   87 eGdvkwdtvrkGdyiv 102 
                                        +G ++w++ r+Gd+ +
  gi|386000828|ref|YP_005919127.1| 1137 DGVLVWQDDRNGDWDI 1152
                                        4445555555555433 PP

>> CsgF  Type VIII secretion system (T8SS), CsgF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.7e+03     104     130 ..     131     157 ..     128     158 .. 0.84
   2 ?    3.0   0.0     0.043   1.1e+02     102     130 ..     213     241 ..     210     243 .. 0.86
   3 ?    3.4   0.1     0.033        85      99     130 ..     376     407 ..     349     407 .. 0.79
   4 ?   -4.0   0.1       6.3   1.6e+04     107     129 ..     426     448 ..     421     450 .. 0.69
   5 ?   -1.9   0.0       1.4   3.5e+03     108     129 ..     774     795 ..     766     796 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                                       EEEEEEETTEEEEEEEESSS--EEEEE CS
                              CsgF 104 qieitnsgsgvsititdtstGesttvt 130
                                        + +++++++ ++ + d  tGe+  +t
  gi|386000828|ref|YP_005919127.1| 131 VVWMDDRDGNWNVYMHDLATGEERRIT 157
                                       677889999*************98875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.043
                                       SEEEEEEEETTEEEEEEEESSS--EEEEE CS
                              CsgF 102 syqieitnsgsgvsititdtstGesttvt 130
                                       ++ +  +n+++ + i i+d  tG++t ++
  gi|386000828|ref|YP_005919127.1| 213 DLVVWSDNRTGDYDIVILDLPTGQETVIE 241
                                       667777899999**************997 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.033
                                       E-SSEEEEEEEETTEEEEEEEESSS--EEEEE CS
                              CsgF  99 tfgsyqieitnsgsgvsititdtstGesttvt 130
                                         g++ +  +n+ +++ + + d +tGe+t vt
  gi|386000828|ref|YP_005919127.1| 376 ISGDIILYTDNRSGNLDLFVYDLRTGEETRVT 407
                                       457778888899999**************996 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 6.3
                                       EEEETTEEEEEEEESSS--EEEE CS
                              CsgF 107 itnsgsgvsititdtstGesttv 129
                                       i+++++  +i++ d s G++ ++
  gi|386000828|ref|YP_005919127.1| 426 IDDRTGDDQIRVHDLSDGSEIQI 448
                                       55666667788888888876665 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 1.4
                                       EEETTEEEEEEEESSS--EEEE CS
                              CsgF 108 tnsgsgvsititdtstGesttv 129
                                       ++++++  + + d  tGe+t++
  gi|386000828|ref|YP_005919127.1| 774 DDRNGEWDVYVCDLATGEETKL 795
                                       5667788899*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.50
# Mc/sec: 7169.97
//
Query:       gi|386000829|ref|YP_005919128.1|  [L=367]
Description: GTP-binding/TGS domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-27   93.9   0.2    1.1e-26   93.0   0.2    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    1.4e-21   76.7   0.0    3.7e-21   75.3   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    1.1e-16   60.6   0.1    3.4e-16   59.0   0.0    1.9  2  TGS           TGS domain
    3.5e-14   52.6   0.0    1.1e-13   51.0   0.0    1.8  2  FeoB_N        Ferrous iron transport protein B
    4.8e-05   23.5   0.6      0.091   12.8   0.0    2.8  3  Dynamin_N     Dynamin family
    0.00016   21.6   0.6       0.03   14.2   0.2    2.6  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.018   14.4   0.0    1.4  1  AIG1          AIG1 family
      0.037   14.5   0.9      0.076   13.5   0.0    1.9  2  ABC_tran      ABC transporter
      0.072   13.5   0.1       0.18   12.2   0.1    1.6  1  AAA_16        AAA ATPase domain
      0.072   12.6   0.1        3.9    7.0   0.0    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.083   12.3   0.0       0.17   11.3   0.0    1.5  1  SRPRB         Signal recognition particle receptor beta subun


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.2   6.5e-30   1.1e-26       1     105 [.     183     289 ..     183     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 6.5e-30
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       kgGi +++t++lt+++e ++ +il+ y+i+n  ++iredv+++ l+d+++gnr Y+p l v+NKiDl  ++  ++++
  gi|386000829|ref|YP_005919128.1| 183 KGGIIVRNTIPLTQMTEVEIAEILRAYGIVNGIITIREDVDTETLVDFLAGNRIYVPQLAVINKIDLEYDDVREDIK 259
                                       69*****************************************************************9999999999 PP

                      MMR_HSR1_Xtn  78 re..pnsvviSaekelnldeLkekiweeLn 105
                                       ++  ++ +++S+ek+++++eLke i+++L+
  gi|386000829|ref|YP_005919128.1| 260 STiaREFIPLSVEKGVGVEELKELIYDTLG 289
                                       965589*********************997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   2.3e-24   3.7e-21       2      96 ..      66     161 ..      65     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.3e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       va+vG+p vGKS+L+n ltg+ a+v+++++tT++++ g +++kg +i+++D+pG+i+gas++kg g+++    + ad
  gi|386000829|ref|YP_005919128.1|  66 VALVGYPSVGKSSLLNLLTGSYAEVGAYHFTTLEVIPGVMEYKGAKIQILDMPGIIKGASKGKGRGREVITAARaAD 142
                                       9**************************************************************9999999888857* PP

                                       EEEEEEETTTTCSHHHHHH CS
                          MMR_HSR1  78 lillvvdaseeklkpldee 96 
                                       +ill+ d+ +  l+ l++e
  gi|386000829|ref|YP_005919128.1| 143 IILLMGDVYNYRLDVLERE 161
                                       ****999664344444444 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.3     1e+04      36      45 ..     209     223 ..     208     226 .. 0.67
   2 !   59.0   0.0   2.1e-19   3.4e-16       1      59 [.     291     363 ..     291     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.3
                                       EEEECS.....EEEE CS
                               TGS  36 yAlVnG.....qrvg 45 
                                       y++VnG     + v+
  gi|386000829|ref|YP_005919128.1| 209 YGIVNGiitirEDVD 223
                                       899999776555555 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 2.1e-19
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       ir+y+ P+  + d      +  g+tv+ ++ ++hr++++ f+yA+V+G       q vgldhvL d+dv++Iv
  gi|386000829|ref|YP_005919128.1| 291 IRIYLkPQRGKADmkdplvILDGSTVRTVCEHLHRDFVRLFRYAKVWGrsakfpgQSVGLDHVLTDEDVLTIV 363
                                       7999977666666899*99999**************************************************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   6.9e-17   1.1e-13       2      90 ..      65     152 ..      64     169 .. 0.82
   2 ?   -1.5   0.0         1   1.6e+03     128     155 ..     256     283 ..     236     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 6.9e-17
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       tvalvG p vGk++l+n ltg++ +vg +  +t e   g +++kg +++i+D+PGi  ++  s+ +   r++++  +
  gi|386000829|ref|YP_005919128.1|  65 TVALVGYPSVGKSSLLNLLTGSYAEVGAYHFTTLEVIPGVMEYKGAKIQILDMPGI--IKGASKGKGRGREVITAAR 139
                                       79*****************************************************9..5677777777777777544 PP

                                       .SSEEEEEEEGGG CS
                            FeoB_N  79 .pdvvvnvvdatn 90 
                                        +d+++ + d  n
  gi|386000829|ref|YP_005919128.1| 140 aADIILLMGDVYN 152
                                       1566666666555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                                       HHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 128 kkLsekLgvpvvktsakkkegieellka 155
                                       + +++++  + +++s +k+ g+eel++ 
  gi|386000829|ref|YP_005919128.1| 256 EDIKSTIAREFIPLSVEKGVGVEELKEL 283
                                       4567778888999999999999999875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       5.7   9.4e+03      53      54 ..      23      24 ..       5      51 .. 0.44
   2 !   12.8   0.0   5.6e-05     0.091       1      21 [.      66      86 ..      66     102 .. 0.87
   3 !    8.1   0.0    0.0015       2.5     101     137 ..     110     149 ..     103     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.7
                                      SS CS
                         Dynamin_N 53 ee 54
                                      ++
  gi|386000829|ref|YP_005919128.1| 23 AT 24
                                      11 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.6e-05
                                      EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                      +a+vG  S GKSS+ln L+g+
  gi|386000829|ref|YP_005919128.1| 66 VALVGYPSVGKSSLLNLLTGS 86
                                      799***************997 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                                       -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                        ++ ++D+PG+++ + + +   + v ++++ adiil++ +
  gi|386000829|ref|YP_005919128.1| 110 AKIQILDMPGIIKGASKGKgrgREVITAARAADIILLMGD 149
                                       6899*********999999899888888999999999855 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   1.8e-05      0.03      95     122 ..      59      86 ..       8     139 .. 0.79
   2 ?    5.3   0.0      0.01        17      46      99 ..     237     286 ..     197     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                                       HHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallpe 122
                                       ++  d t++lvG   vGKS+L+n l+++
  gi|386000829|ref|YP_005919128.1|  59 KKSGDATVALVGYPSVGKSSLLNLLTGS 86 
                                       45567899*****************997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                                       T-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  46 giepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                        ++ + v+nKiDl  ++   e++k+   ++  e++ +s++++ g+eelkel+ d
  gi|386000829|ref|YP_005919128.1| 237 YVPQLAVINKIDLEYDDV-REDIKS---TIAREFIPLSVEKGVGVEELKELIYD 286
                                       4677889******99988.455544...55567899999999*****9998866 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.018       2      96 ..      65     153 ..      64     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       t+ lvG   +GkS+  N + g+ a     + +  t ++   + + +g ki++ D Pg++   ++ +   +e++    
  gi|386000829|ref|YP_005919128.1|  65 TVALVGYPSVGKSSLLNLLTGSYAE--VGAYHFTTLEVIPGVMEYKGAKIQILDMPGIIKGASKGKGRGREVIT--- 136
                                       788**************98887653..3356888999999999********************99999999995... PP

                                       HCTT-ESEEEEEEETTB- CS
                              AIG1  79 lseegihalllvlslgrf 96 
                                        ++   +++ll  +++++
  gi|386000829|ref|YP_005919128.1| 137 -AARAADIILLMGDVYNY 153
                                       .67778888888776643 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       4.1   6.6e+03      38      67 ..      11      41 ..       2      48 .. 0.42
   2 ?   13.5   0.0   4.7e-05     0.076      11      36 ..      63      88 ..      56     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                                      SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS CS
                                      xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 38 teGeilld.gkdlkeqeleslrkeigvlpqe 67
                                       e+ei    +++ +e+ + +l+++i+ l+ +
  gi|386000829|ref|YP_005919128.1| 11 IEEEIFSTqKNKATEHHIGKLKAKIAKLKAQ 41
                                      3334422212233333444444444444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.7e-05
                                      TSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllk 36
                                      + +va+vG    GKS+Ll+ll+g + 
  gi|386000829|ref|YP_005919128.1| 63 DATVALVGYPSVGKSSLLNLLTGSYA 88
                                      5789*******************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.18      25      51 ..      64      90 ..      56     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                        v l+G++ vGKssl++ l  ++ + 
  gi|386000829|ref|YP_005919128.1| 64 ATVALVGYPSVGKSSLLNLLTGSYAEV 90
                                      6899**************998776655 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.05        81      66     100 ..     106     147 ..      87     152 .. 0.68
   2 ?    7.0   0.0    0.0024       3.9     100     149 ..     215     265 ..     199     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.05
                                       TCSSEEEEEEEESSSGG.......GHHHHHHHHHT-SEEEEE CS
                          GTP_EFTU  66 etkkylinliDtPGHvd.......FskevirglrvlDgavlv 100
                                       e+k  +i+++D PG ++         +evi+++r++D+ +l+
  gi|386000829|ref|YP_005919128.1| 106 EYKGAKIQILDMPGIIKgaskgkgRGREVITAARAADIILLM 147
                                       588999999999997762111111346889999999988886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
                                       EEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHH.HHHHHHHH CS
                          GTP_EFTU 100 vvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelke.iveevkqk 149
                                       ++ ++e+v + t   +   ++  vp   +iNK+D   ++++e i++++ ++
  gi|386000829|ref|YP_005919128.1| 215 IITIREDVDTETLVDFLAGNRIYVPQLAVINKIDLEYDDVREdIKSTIARE 265
                                       56667777777777777777777889********97555544133334433 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.17       4      59 ..      64     120 ..      61     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT- CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGh 59 
                                        +v lvG    GK sl+++Lt   ++         ++   v + kg k++++D+PG 
  gi|386000829|ref|YP_005919128.1|  64 ATVALVGYPSVGKSSLLNLLTGSYAEVGAYHFtTLEVIPGVMEYKGAKIQILDMPGI 120
                                       5799***************99884443333332445555556779**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2227.45
//
Query:       gi|386000830|ref|YP_005919129.1|  [L=135]
Description: 30S ribosomal protein S8e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  112.7   2.2    1.7e-32  112.5   2.2    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   2.2   9.4e-37   1.7e-32       3     137 .]      10     133 ..       8     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 9.4e-37
                                       XBXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEE CS
                     Ribosomal_S8e   3 isrdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIl 79 
                                       +++++ +krk tGg+  + r k+k+elgr++ +  + ++r k++r+rgG++k+r+lr++ a+v++p ++++k +kI 
  gi|386000830|ref|YP_005919129.1|  10 MKWQGSSKRKFTGGRLISNRGKQKHELGREAGEPNVDTTRKKQIRTRGGNIKMRLLRCDVASVADPVTGKSKIAKIE 86 
                                       5799************************************************************************* PP

                                       EEECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  80 gVkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       +Vk+n +n +y+r+++++Kgaii++d+++           A+vtsrPgqdG+vna+l+
  gi|386000830|ref|YP_005919129.1|  87 RVKDNSANLNYIRRNIISKGAIIKTDLGD-----------ARVTSRPGQDGVVNAILV 133
                                       *****************************...........***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 854.52
//
Query:       gi|386000831|ref|YP_005919130.1|  [L=69]
Description: hypothetical protein Mhar_0115 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-31  106.8   0.4    5.3e-31  106.7   0.4    1.0  1  DUF1922   Domain of unknown function (DUF1922)
  ------ inclusion threshold ------
       0.32   10.8   1.6       0.61    9.9   0.0    1.9  2  zf-CSL    CSL zinc finger


Domain annotation for each model (and alignments):
>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.4   5.9e-35   5.3e-31       1      66 [.       2      68 ..       2      69 .] 0.99

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 5.9e-35
                                      EEEEEET.TS--EEEETT-SEEEETTTEEEE--SSS-BS--SSHHHHHHHHHHHSS---S-TTSS-T CS
                           DUF1922  1 YlifRCd.CGRvlYakegaktrkCvCGktikvkerrilkkaedaeeAselVrklqeekyGltafkta 66
                                      YlifRC+ CGR+lYa+eg++tr+C+CGk+ik+ ++++l++a+d++eA++lVr+lq e +G+t+f+ a
  gi|386000831|ref|YP_005919130.1|  2 YLIFRCSgCGRHLYAEEGSATRTCPCGKRIKLGQVKVLSRARDEREAGDLVRALQVEGRGMTGFSPA 68
                                      9***************************************************************987 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.058   5.2e+02      43      50 ..       3      10 ..       1      14 [. 0.81
   2 ?    9.9   0.0   6.8e-05      0.61      13      31 ..      17      35 ..      11      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.058
                                      -EEEETTS CS
                            zf-CSL 43 vvvqCssC 50
                                      ++ +Cs+C
  gi|386000831|ref|YP_005919130.1|  3 LIFRCSGC 10
                                      57899999 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.8e-05
                                      TTTEEEEEETTSSEEEEEH CS
                            zf-CSL 13 eeesyyypCRCgdeFelte 31
                                      ee+s +++C+Cg++ +l +
  gi|386000831|ref|YP_005919130.1| 17 EEGSATRTCPCGKRIKLGQ 35
                                      677899*******987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 434.65
//
Query:       gi|386000832|ref|YP_005919131.1|  [L=117]
Description: hypothetical protein Mhar_0116 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 746.03
//
Query:       gi|386000833|ref|YP_005919132.1|  [L=325]
Description: Radical SAM domain family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-15   57.1   0.0    7.4e-15   55.7   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    0.00061   20.3   0.0     0.0014   19.1   0.0    1.6  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.078   12.8   0.0       0.13   12.0   0.0    1.3  1  ChuX_HutX    Haem utilisation ChuX/HutX
       0.16   12.0   0.1        4.3    7.4   0.1    2.4  2  DUF2388      Protein of unknown function (DUF2388)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   1.7e-18   7.4e-15       6     165 ..      32     173 ..      29     175 .. 0.91
   2 ?   -2.8   0.0       1.6   7.4e+03     127     158 ..     211     241 ..     204     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.7e-18
                                       EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                        CnlrC+fC  +     + +g +++ +ei + ++ ++ + g+++      epll+p++  +l+++++l   g+ +++
  gi|386000833|ref|YP_005919132.1|  32 RCNLRCPFCEYW-----RTPGPEMTSDEIFAMLDDAR-SFGIGVYNAWTAEPLLRPELPAILRHAKAL---GMVTSL 99 
                                       7***********.....68*****************6.999***************************...****** PP

                                       EECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  83 etngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       +tng l+     er  +l  +d +s++++ + +      + rg  +e vle+++++r+ag + v +++v+ +  n  
  gi|386000833|ref|YP_005919132.1| 100 ITNGALL----SERVGDLScLDLLSVSVDGIGSY---PEI-RGAPLEPVLEGIRAARRAGHR-VLINCVISR-KNLG 166
                                       ******9....4888888889************9...688.99****************999.999998877.6666 PP

                                       HHHHHHH CS
                                       xxxxxxx RF
                       Radical_SAM 159 eleelle 165
                                       el el++
  gi|386000833|ref|YP_005919132.1| 167 ELAELVR 173
                                       6666665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGende 158
                                       + + +++l  +++ g++ +++ i+ l+ + d+
  gi|386000833|ref|YP_005919132.1| 211 YRRSIDGLIDIKRTGGP-IINSITYLKMVRDQ 241
                                       67788888889999999.88888888776665 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.1e-07    0.0014       1      67 [.     247     300 ..     247     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-07
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqe...frkskkfplielCrnC 67 
                                       C+ap   l ++sdG+V+ C  +    v++  lGn ++  l+++w  ++ ++   +r          C  C
  gi|386000833|ref|YP_005919132.1| 247 CHAPGIVLSVASDGTVHAC--R----VQKEPLGNASQ-GLASVWAASKRRReeiVR---------ECGGC 300
                                       99999**************..2....4569*****75.******776544423222.........25555 PP

>> ChuX_HutX  Haem utilisation ChuX/HutX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.13      23      61 ..      79     116 ..      69     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                       EEGGGHHHHHHHHTTS-EEEEEEEESSEEEEEEEE.... CS
                         ChuX_HutX  23 ldgedfeallealeelgevmalvrnegavhEkkGkyenv 61 
                                       l++ +++a+l+++++lg v+ l+ n +   E++G + ++
  gi|386000833|ref|YP_005919132.1|  79 LRP-ELPAILRHAKALGMVTSLITNGALLSERVGDLSCL 116
                                       677.99****************************98776 PP

>> DUF2388  Protein of unknown function (DUF2388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00097       4.3      32      53 ..     126     147 ..     125     153 .. 0.87
   2 ?    1.6   0.0      0.06   2.7e+02      32      45 ..     256     269 ..     254     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00097
                           DUF2388  32 VASdGairGarLEaaLqelRse 53 
                                       ++S  +irGa LE  L+ +R++
  gi|386000833|ref|YP_005919132.1| 126 IGSYPEIRGAPLEPVLEGIRAA 147
                                       567779**************86 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.06
                           DUF2388  32 VASdGairGarLEa 45 
                                       VASdG++++ r+++
  gi|386000833|ref|YP_005919132.1| 256 VASDGTVHACRVQK 269
                                       9*******998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1952.69
//
Query:       gi|386000834|ref|YP_005919133.1|  [L=427]
Description: diaminopimelate decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-60  204.7   0.0    1.9e-60  204.3   0.0    1.2  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    5.2e-25   87.5   0.0    5.7e-25   87.4   0.0    1.2  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    6.2e-14   52.2   0.1    1.2e-13   51.3   0.1    1.4  1  Ala_racemase_N   Alanine racemase, N-terminal domain


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3   0.0   3.1e-64   1.9e-60       2     247 .]      39     288 ..      38     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 3.1e-64
                                       HHHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHH CS
                     Orn_Arg_deC_N   2 asierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelry 78 
                                       a+++++++++++a+p++ +++avKan +la+l++lae+Glg d+ S +El lv  ag++ e++ f ++ k  eel++
  gi|386000834|ref|YP_005919133.1|  39 ARLRANARAYREAFPEALIYFAVKANGNLALLRILAEEGLGADVFSAGELSLVRMAGIPGEKVLFNGNSKRTEELKM 115
                                       5688999********************************************************************** PP

                                       HHHCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTT CS
                     Orn_Arg_deC_N  79 alekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaaleeavealleaakeen 151
                                       ale gv+ + +d+ +el  la++a+e    a+v  R+++dvsa+t++ i+tg + sKFG+  ++ ve++++a+  e+
  gi|386000834|ref|YP_005919133.1| 116 ALEAGVR-ISADSLDELLALAEVAKEmgeeAEVAFRVNPDVSAKTHPKIATGLKTSKFGIPWQDLVEVYERAMGLEG 191
                                       *******.99*************9999999*********************************************** PP

                                       EEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 152 lqlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeea 228
                                       ++ vG+++H+GS++ d+++fv+a+ ++++l  +++e+G k++++d GGG+g+ y+ e+ +   ++ a+ i++  ee 
  gi|386000834|ref|YP_005919133.1| 192 VKPVGLHCHIGSQILDTAPFVEAAARMMELAGRIVEVGGKIEMMDFGGGLGIPYTPETAAPTPSQLASGIKPVFEEG 268
                                       *******************************************************99988888************** PP

                                       HH.TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 229 fp.gdkevtiiaEpGRalva 247
                                       ++  + ++++i+EpGR++va
  gi|386000834|ref|YP_005919133.1| 269 CRrLGISPRMILEPGRSIVA 288
                                       **96667***********98 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   9.6e-29   5.7e-25       5      98 .]     233     377 ..      33     377 .. 0.69

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 9.6e-29
                                       E.......................................................GGEEEEEEEEEEEEETCEEEE CS
                                       x.......................................................xxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   5 d.......................................................eagvLvtrViavkesekkkfv 26 
                                       +                                                       ++ +++trV+ vk+ +  +fv
  gi|386000834|ref|YP_005919133.1| 233 EmmdfggglgipytpetaaptpsqlasgikpvfeegcrrlgisprmilepgrsivaDSTIFLTRVNVVKRAHV-NFV 308
                                       055555555555555555555555555555555555555555555555566666668899*********9997.8** PP

                                       EES--TTTS-HHHHCTT-S-EESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  27 ivdaGmndllrpalygsfheipvkeeeaekeeeeeeevdvvGptCesgDvlakdrelpelevGdllafedaG 98 
                                        vdaG+n l+rp ly+++h+++v    ++++ ++ee+++vvGp+CesgDvlakdr+lp++e+Gdl+a+ daG
  gi|386000834|ref|YP_005919133.1| 309 GVDAGFNLLARPMLYDAYHHVVVA---NKADGRAEERYTVVGPICESGDVLAKDRNLPRIERGDLIAMLDAG 377
                                       *********************443...2334556789*********************************98 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1     2e-17   1.2e-13       3     171 ..      38     216 ..      36     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2e-17
                                       HHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC..S CS
                    Ala_racemase_N   3 ldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg..f 77 
                                        ++lr+N r+ r+++ p+a ++  vKan+  + +  +a+     gad   v++  E+  +r agi ++ ++++g   
  gi|386000834|ref|YP_005919133.1|  38 EARLRANARAYREAF-PEALIYFAVKANGNLALLRILAEEG--LGAD---VFSAGELSLVRMAGIPGEKVLFNGnsK 108
                                       689************.9999*******77666664444422..3466...88899999*******888889999866 PP

                                       TGGGHHHHHHTTEEEEESSHHHHHHHHHHHHH............TTS-EEEEEEBESSSS..SSSBSCHHHHHHHHH CS
                    Ala_racemase_N  78 speelaalaeydltvtvdsleqlealaaaare............agkplrvhlkidtgmg..RlGftpeeleellea 140
                                       + eel+ ++e+++ +  dsl++l ala++a+e             +  ++ h ki tg+   + G+++++l e++e+
  gi|386000834|ref|YP_005919133.1| 109 RTEELKMALEAGVRISADSLDELLALAEVAKEmgeeaevafrvnPDVSAKTHPKIATGLKtsKFGIPWQDLVEVYER 185
                                       99*****************************************9999***********99***************** PP

                                       HHHTTTEEEEEEE-S-SST..TSTSHHHHHHHH CS
                    Ala_racemase_N 141 laalpglrleglmtHfasa..depdeeteaqla 171
                                       +  l+g++++gl  H +s   d+   ++ +  a
  gi|386000834|ref|YP_005919133.1| 186 AMGLEGVKPVGLHCHIGSQilDTA--PFVEAAA 216
                                       ***************999754543..3333334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2555.73
//
Query:       gi|386000835|ref|YP_005919134.1|  [L=224]
Description: CMP/dCMP deaminase zinc-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-29  100.4   1.6    5.5e-29  100.0   1.6    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.1e-18   67.3   0.1    1.5e-18   66.8   0.1    1.1  1  MafB19-deam      MafB19-like deaminase
     0.0024   17.9   0.2     0.0065   16.5   0.2    1.6  1  Bd3614-deam      Bd3614-like deaminase
  ------ inclusion threshold ------
      0.024   14.5   1.6       0.05   13.5   1.6    1.5  1  APOBEC_N         APOBEC-like N-terminal domain
      0.065   13.4   0.5       0.15   12.2   0.5    1.7  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
        0.1   12.5   1.4        1.3    8.9   1.4    2.6  1  Inv-AAD          Invertebrate-AID/APOBEC-deaminase
       0.13   12.1   2.2       0.21   11.5   1.5    1.7  1  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
       0.18   11.9   1.1       0.47   10.5   1.1    1.7  1  NAD1             Novel AID APOBEC clade 1


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   1.6   2.5e-32   5.5e-29       2     100 ..      75     192 ..      74     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.5e-32
                                       HHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.....................TTB-HHHH CS
                   dCMP_cyt_deam_1   2 ekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.....................ktiHAEvn 57 
                                       + de+++e+a  +a+++ +c + +VGav+v++++i+stgyng p g +                     + +HAE+n
  gi|386000835|ref|YP_005919134.1|  75 SLDEYFMEIASVVATRS-TCLRHQVGAVLVREKRILSTGYNGAPMGLPhclevgcrrenvesgyrhelcRAVHAEQN 150
                                       579**************.*********************************************************** PP

                                       HHHHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  58 AilkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                       Ai++aa   g++  gatly+t++PC  Cak+ii+s+i++vv+g
  gi|386000835|ref|YP_005919134.1| 151 AIIQAAIH-GVSTSGATLYCTHQPCILCAKIIINSQIQRVVYG 192
                                       ******88.88899***************************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   6.8e-22   1.5e-18       4     107 ..      77     201 ..      75     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 6.8e-22
                       MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEiaa 57 
                                       +++f+++++ v  ++ +   ++gav v +k+++ +g+n                       ++e       HaE +a
  gi|386000835|ref|YP_005919134.1|  77 DEYFMEIASVVATRSTCLRHQVGAVLVREKRILSTGYNgapmglphclevgcrrenvesgyRHE--LCRAVHAEQNA 151
                                       689**************************************************99887755444..44567****** PP

                       MafB19-deam  58 lqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks..l 107
                                       + qAa  + s+  ++atly t++pC  Ca++i++++++++vyg  +p+   l
  gi|386000835|ref|YP_005919134.1| 152 IIQAAIHGVST--SGATLYCTHQPCILCAKIIINSQIQRVVYGNPYPDDeaL 201
                                       ****5555555..******************************999986453 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.9e-06    0.0065      76     113 ..     163     193 ..     155     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                       Bd3614-deam  76 egarllvtlqcCkmCAalvvaaadapgrevllkvvYle 113
                                        ga+l+ t+q+C +CA ++++           +vvY++
  gi|386000835|ref|YP_005919134.1| 163 SGATLYCTHQPCILCAKIIINSQI-------QRVVYGN 193
                                       79***************9997554.......4566665 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   2.2e-05      0.05      20      94 ..     123     183 ..     114     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                       EEEEEEEESSSEEEEEEEEEEE-..SSTBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHH CS
                          APOBEC_N  20 cyeVkrssgkrklskkGvLrnqsgaaaskHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaa 94 
                                       c+eV +++++    ++G+ r + +     HaE+  +    + ++ +  +    tlY++ +PC      Ca+ + +
  gi|386000835|ref|YP_005919134.1| 123 CLEVGCRRENV---ESGY-RHELCR--AVHAEQNAII---Q-AAIHGVSTSGATLYCTHQPCIL----CAKIIIN 183
                                       99999995444...8999.777776..8****98443...3.33445788899***********....*998876 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   6.7e-05      0.15      12      62 ..     133     183 ..     124     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                             SNAD4  12 lekgvlkn.kke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiae 62 
                                       +e+g+ ++ ++  haE + + +    ++   +   t+y +  PC  Ca+ i++
  gi|386000835|ref|YP_005919134.1| 133 VESGYRHElCRAvHAEQNAIIQA--AIHGVSTSGATLYCTHQPCILCAKIIIN 183
                                       4455555544447***9999888..7888889999**************9986 PP

>> Inv-AAD  Invertebrate-AID/APOBEC-deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.4   0.00058       1.3      12      63 ..     132     174 ..      99     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00058
                           Inv-AAD  12 ilatGytleleGnthaeqccliklaekhevaeeklaevlpkntvlYttmepC 63 
                                        + +Gy  el    haeq ++i+           ++ v ++ + lY t  pC
  gi|386000835|ref|YP_005919134.1| 132 NVESGYRHELCRAVHAEQNAIIQ---------AAIHGVSTSGATLYCTHQPC 174
                                       34556666666666666665555.........55666666667777777777 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.5   9.3e-05      0.21       4      32 ..     142     184 ..     140     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                                       T-S--SS-E...............E-TTS--B-CHHHHHHHHC CS
                          zf-C3HC4   4 Cleeakepn..............elleCkHsfCskCirkilks 32 
                                       C  + +e+n               +l C+H+ C  C + i++s
  gi|386000835|ref|YP_005919134.1| 142 CRAVHAEQNaiiqaaihgvstsgATLYCTHQPCILCAKIIINS 184
                                       6666666666666677777777789************999994 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00021      0.47      36      91 ..     131     183 ..     120     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                              NAD1  36 ssllkGvlen.eskcHaEllflnkikslklldpsqkykvtwylswSPCseCasklae 91 
                                       ++++ G+ ++  +++HaE+  + +    ++ +  ++   t+y+++ PC  Ca+ +++
  gi|386000835|ref|YP_005919134.1| 131 ENVESGYRHElCRAVHAEQNAIIQA---AI-HGVSTSGATLYCTHQPCILCAKIIIN 183
                                       4555566666433469999875555...33.55578889*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1352.56
//
Query:       gi|386000836|ref|YP_005919135.1|  [L=497]
Description: lysyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-124  414.6   0.0   4.2e-124  414.1   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)
    3.6e-07   29.3   0.0      0.002   16.9   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    0.00044   19.7   0.0       0.34   10.2   0.0    2.2  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.1   0.0    7e-128  4.2e-124       2     336 ..       4     328 ..       3     352 .. 0.96

  Alignments for each domain:
  == domain 1  score: 414.1 bits;  conditional E-value: 7e-128
                      tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvp 78 
                                       +Wad+ aekl   r         ++v++Gi+pSG+iH+Gn+rev+tad+v ra+ +rg e+rli+i+D++D+lR+++
  gi|386000836|ref|YP_005919135.1|   4 HWADVAAEKLA-DR-------SPHTVATGITPSGQIHLGNMREVMTADAVFRAILSRGGEARLIYIADTYDPLRRLY 72 
                                       9*********9.33.......4789**************************************************** PP

                      tRNA-synt_1f  79 enlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekik 155
                                       ++lp++ +e+++gkpl++iP+p+g++esya+hf  ++ +sL++lgi+ e+++a ++Yk+gly +aik+al +r++i+
  gi|386000836|ref|YP_005919135.1|  73 PFLPKS-FEEHVGKPLSEIPCPEGCCESYADHFLLPFFDSLERLGIRPEVYRADRMYKDGLYVDAIKTALLKRDDIA 148
                                       ******.********************************************************************** PP

                      tRNA-synt_1f 156 eilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaa 232
                                       +il+++ g+++ +++sp+ ++ce+cgr+++t+v+ +d e+e+ eY+c +cG++++++ r+g gKL W+vdw++rW++
  gi|386000836|ref|YP_005919135.1| 149 RILKEVSGRDLPADWSPLDAICESCGRLNSTKVTGFDLEGETAEYVC-RCGQSGTASFRGG-GKLAWRVDWPARWSI 223
                                       ***********************************************.**********997.*************** PP

                      tRNA-synt_1f 233 lgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrfli 308
                                       l+V++Ep+GkDha+aGgS+d++++i+ e++g++aP++vvYe+i+lkg+++m+sS+G v+t++d+l+v++pevlr+li
  gi|386000836|ref|YP_005919135.1| 224 LEVTVEPFGKDHATAGGSYDTGKRISeEVYGYPAPYPVVYEWIHLKGKGAMHSSTGIVVTIRDMLDVVPPEVLRYLI 300
                                       ***************************************************************************** PP

                      tRNA-synt_1f 309 lrrkPkkakkldldleilrlvdeYdkle 336
                                       +r+kP+k++++d++l +l l++eYd+  
  gi|386000836|ref|YP_005919135.1| 301 IRTKPEKHIEFDPGLPLLTLIEEYDRRA 328
                                       *************************864 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   4.1e-05      0.25      10      47 ..      27      64 ..      19      66 .. 0.84
   2 !   16.9   0.0   3.4e-07     0.002     317     361 ..     262     307 ..     248     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.1e-05
                                      -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE-- CS
                      tRNA-synt_1g 10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDe 47
                                      ++g++HlG+++ev+ aD++ R    rg e   +   D+
  gi|386000836|ref|YP_005919135.1| 27 PSGQIHLGNMREVMTADAVFRAILSRGGEARLIYIADT 64
                                      5799******************9999998877766666 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.4e-07
                                       EE--EEE---.-----------HHHHHHHH-HHHHHHHHHHHS-TT CS
                      tRNA-synt_1g 317 aheyltvegk.KlSkSrgvvvkakealerldadllRYylaaeapek 361
                                       + e++ ++gk  + +S g+vv+++++l+ +++++lRY +++++pek
  gi|386000836|ref|YP_005919135.1| 262 VYEWIHLKGKgAMHSSTGIVVTIRDMLDVVPPEVLRYLIIRTKPEK 307
                                       679999999735999**************************99987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00049       2.9      14      48 ..      22      56 ..      10      67 .. 0.81
   2 !   10.2   0.0   5.6e-05      0.34     245     292 ..     264     312 ..     252     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00049
                                      EEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 14 vCGptvydashlGhaRslvafDilrrilqalgYdv 48
                                        G+t   ++hlG+ R++++ D + r + ++g + 
  gi|386000836|ref|YP_005919135.1| 22 ATGITPSGQIHLGNMREVMTADAVFRAILSRGGEA 56
                                      6799******************9999888877655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.6e-05
                                       --EEETTB.E--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE- CS
                      tRNA-synt_1e 245 ghlkiege.kmsksLknfitikdvlkkfdprqlRllllsahyrsqldfk 292
                                       ++++++g+  m  s + ++ti+d+l  + p++lR+l++ ++ +++++f+
  gi|386000836|ref|YP_005919135.1| 264 EWIHLKGKgAMHSSTGIVVTIRDMLDVVPPEVLRYLIIRTKPEKHIEFD 312
                                       67788765369999*************************9999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 3621.22
//
Query:       gi|386000837|ref|YP_005919136.1|  [L=174]
Description: Nucleoside 2-deoxyribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-13   50.6   0.0      3e-13   49.9   0.0    1.3  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
    2.6e-07   30.9   0.0    3.8e-07   30.4   0.0    1.2  1  Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   3.3e-17     3e-13       1     106 [.      22     120 ..      22     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3.3e-17
                                       EEEESGGGCSCCCHHHHHHHHHHHHTTTT...EEE-CCTT-TT....--SSHHHHHHHHHHHHHC-SEEEEE--SSS CS
                   Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengl...dglaPldneaelelpaeetaraiyeadialirqaDavianldpfr 74 
                                       +YLAgpl F++++ ++a  lk+ ++++     +++ P+  e+     a+  + +i++a++a + ++ +++a+ld+  
  gi|386000837|ref|YP_005919136.1|  22 VYLAGPL-FSRAEVEWAGSLKREMEAALGeriEVIWPF--EV-----ASGSKGEIFQANLAALIRSPLMVAVLDGPA 90 
                                       8******.***999999999988888766677999***..44.....568999**********************77 PP

                                       SSS--HHHHHHHHHHHHC.T-EEEEE-S-GCGH CS
                   Nuc_deoxyrib_tr  75 gpeaDsGtafEvGyaval.gkpvlayttdarel 106
                                           D+Gta+EvG   al g++ ++ +td r+ 
  gi|386000837|ref|YP_005919136.1|  91 ---VDDGTAWEVGCHFALfGRRAIGIRTDVRKA 120
                                       ...************99779**********994 PP

>> Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   4.2e-11   3.8e-07       2     107 ..      20     116 ..      19     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.2e-11
                                       EEEEEEE---SSSST-HHHHHHHHHHTSSS-EEEEE----SS-----HHHHH.....HHHHHHHHHHHH-SEEEEEE CS
                   Nuc_deoxyri_tr2   2 ksvFLaGsteseaetdWredlteaLsaipklgvtvfnPqredwdseleedrskkrfreqvewelealekAdvvvfvf 78 
                                        +v+LaG+++s+ae +W  +l + ++a   + ++v+ P + +  s+           e+++ +l+al ++ ++v+v+
  gi|386000837|ref|YP_005919136.1|  20 VAVYLAGPLFSRAEVEWAGSLKREMEAALGERIEVIWPFEVASGSKG----------EIFQANLAALIRSPLMVAVL 86 
                                       68*******************9999776699*********9977765..........9******************* PP

                                       -TT---HHHHHHHHHHTTS.S-EEEEE-TT CS
                   Nuc_deoxyri_tr2  79 dgedsatrslvElglaaak.gkkvvlvpkg 107
                                       dg+ ++  + +E+g   a  g++ ++++++
  gi|386000837|ref|YP_005919136.1|  87 DGPAVDDGTAWEVGCHFALfGRRAIGIRTD 116
                                       **88887899******9999***9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1315.92
//
Query:       gi|386000838|ref|YP_005919137.1|  [L=260]
Description: Ser/Thr protein phosphatase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-05   23.9   0.0    5.5e-05   23.4   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.2e-05   24.1   0.0    5.1e-05   23.9   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.034   13.0   0.0      0.054   12.3   0.0    1.2  1  Epimerase_2    UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   9.1e-09   5.5e-05       2      63 ..      20     112 ..      20     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.1e-09
                     Metallophos_2   2 klaiiSDlH................snldaleavlealkevgvdaiihaGD.........leeeep......evlee 47 
                                       k+++ +DlH                + ++ l+ +  ++ ev++d++i++GD         +    +      ++l++
  gi|386000838|ref|YP_005919137.1|  20 KVLVAADLHmgiehqlwlggasvpsQTGKMLAGLKLRVGEVEPDRVILLGDvkhnlpwtsF----QersevpSFLQA 92 
                                       6899999999999999999998888778888888889999***********5555555443....044333379999 PP

                     Metallophos_2  48 llelapvlaVrGNnD....e 63 
                                       l ++ +v++V GN+D    e
  gi|386000838|ref|YP_005919137.1|  93 LSDMVEVEIVAGNHDlgiaE 112
                                       99999**********43330 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.5e-09   5.1e-05       2      89 ..      20     121 ..      19     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.5e-09
                                       EEEEEESBTB..........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH...T CS
                       Metallophos   2 rilvigDlHl..........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky...p 64 
                                       ++lv +DlH           a+ + q  + l+ l+    e +pd v+l+GD+ +  ++ ++ ++  +  +++     
  gi|386000838|ref|YP_005919137.1|  20 KVLVAADLHMgiehqlwlggASVPSQTGKMLAGLKLRVGEVEPDRVILLGDVKHNLPWTSFQERSeVPSFLQAlsdM 96 
                                       89*******9999999877733333333333333333566699********99999888855555554444447777 PP

                                       SEEEEEC-TTSCHHH.HHHHHHHHHH CS
                       Metallophos  65 ipvylllGNHegfee.ellnkygylg 89 
                                       + v +++GNH+ + + el +++ + +
  gi|386000838|ref|YP_005919137.1|  97 VEVEIVAGNHD-LGIaELAPPEVSVH 121
                                       889********.55655555544333 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.1e-06     0.054      34      78 ..      29      72 ..      18      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.1e-06
                                      ----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSH CS
                       Epimerase_2 34 iekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtn 78
                                      +  ++++l  ++ s+  +tg++l gl+  + e++pD v++lGD  
  gi|386000838|ref|YP_005919137.1| 29 M-GIEHQLWLGGASVPSQTGKMLAGLKLRVGEVEPDRVILLGDVK 72
                                      4.678888899999*****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1995.55
//
Query:       gi|386000839|ref|YP_005919138.1|  [L=180]
Description: orotate phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-09   38.0   0.1    1.4e-09   37.7   0.1    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00047   19.6   0.0    0.00062   19.3   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.058   12.9   0.0      0.075   12.5   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase
       0.13   12.1   0.0       0.29   11.0   0.0    1.6  1  BTRD1         Bacterial tandem repeat domain 1
       0.18   12.1   0.0       0.28   11.5   0.0    1.2  1  DUF4112       Domain of unknown function (DUF4112)


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   3.9e-13   1.4e-09      30     133 ..      60     160 ..      39     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.9e-13
                                       GEEEEEEETTTHHHHHHHHHHS.....TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSH CS
                      Pribosyltran  30 pdvvvgiargGvpfakiladeL.....evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGg 101
                                        ++v+g   g+ p++ ++a        ++   ++rk+ + ++++  +          +++p+g+kV +VDD+++tG+
  gi|386000839|ref|YP_005919138.1|  60 AVAVAGMTLGADPIVAAIAVVGhlqgrDLSALIIRKEPKGHGTGKYVE--------GPTLPEGSKVAVVDDVVTTGS 128
                                       556666666666666655543344666666677777777777777775........899****************** PP

                                       HHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHH CS
                      Pribosyltran 102 TllaalelLkekgpeevriavlvdkpateeev 133
                                       +l++ +e+L+ +g   v + +++d+ ++ +e+
  gi|386000839|ref|YP_005919138.1| 129 SLIKSIERLRGEGYRPVQVLAILDREEGGRER 160
                                       ***********************999987765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-07   0.00062      98     166 ..      91     157 ..      64     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                           UPRTase  98 glqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegv 166
                                       ++ r+e + +    y   P+ ++ ++v ++D v+ TG+s+++ i++L+ +g +   + vl++l  eeg 
  gi|386000839|ref|YP_005919138.1|  91 LIIRKEPKGHGTGKYVEGPTLPEGSKVAVVDDVVTTGSSLIKSIERLRGEGYR--PVQVLAILDREEGG 157
                                       3444444566677777889989999************************8875..78888888888775 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05     0.075     120     165 ..     113     157 ..      90     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvslvdwrsee 165
                                       + +++ +vDD ++tG+++++ i++l+ +  r  + v++++d  +  
  gi|386000839|ref|YP_005919138.1| 113 EGSKVAVVDDVVTTGSSLIKSIERLRGEGYR-PVQVLAILDREEGG 157
                                       5678999******************998765.56778888866554 PP

>> BTRD1  Bacterial tandem repeat domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.2e-05      0.29      19      33 ..     134     148 ..     126     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.2e-05
                             BTRD1  19 fdklkakGYrpvhvs 33 
                                       +++l+++GYrpv+v 
  gi|386000839|ref|YP_005919138.1| 134 IERLRGEGYRPVQVL 148
                                       5789*********95 PP

>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.7e-05      0.28      18      53 ..      61      96 ..      51     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
                           DUF4112 18 ipgcglrfGldpiigliPvvGdvisallslylvlea 53
                                      + + g+++G dpi++ i vvG + +  ls++++++ 
  gi|386000839|ref|YP_005919138.1| 61 VAVAGMTLGADPIVAAIAVVGHLQGRDLSALIIRKE 96
                                      4567899**********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1175.43
//
Query:       gi|386000840|ref|YP_005919139.1|  [L=87]
Description: hypothetical protein Mhar_0124 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   14.9   0.2      0.033   14.5   0.2    1.4  1  DUF11            Domain of unknown function DUF11
      0.036   14.3   0.1      0.057   13.7   0.1    1.3  1  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
      0.072   11.9   0.0       0.09   11.6   0.0    1.1  1  Monooxygenase_B  Monooxygenase subunit B protein
       0.18   12.1   0.0        0.2   12.0   0.0    1.1  1  Alpha_adaptinC2  Adaptin C-terminal domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   7.4e-06     0.033      22      78 ..       4      50 ..       1      62 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-06
                             DUF11 22 vtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78
                                      + Ntg +++ +v v   +P+gl+++s+  s        s  ++ +g+sa++++ vr 
  gi|386000840|ref|YP_005919139.1|  4 LGNTGESAL-DVSVVPAVPPGLSAQSAGPS--------S-VNISPGGSAQFAYLVRG 50
                                      669999999.*************9999999........3.3889******9998886 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.3e-05     0.057      17      79 .]       7      65 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                       NPCBM_assoc 17 gtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarlt 79
                                      ++++a +vs+   +P+G ++++ ++ s   + pG ++++   V+   g a+G y v+ ++++t
  gi|386000840|ref|YP_005919139.1|  7 TGESALDVSVVPAVPPGLSAQS-AGPSSVNISPGGSAQFAYLVR---GEAPGLYHVRSQVTYT 65
                                      577899*************555.5555568***********997...66789*****999986 PP

>> Monooxygenase_B  Monooxygenase subunit B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.09      78     110 ..      31      63 ..      24      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                                       SS-B---TT-EEEEEEEEEE-S-EEEEEEEEEE CS
                   Monooxygenase_B  78 prsvslelGedYefkvvlkaRrpGtyhvhpmln 110
                                       p+sv+++ G+  +f   +++  pG yhv +++ 
  gi|386000840|ref|YP_005919139.1|  31 PSSVNISPGGSAQFAYLVRGEAPGLYHVRSQVT 63 
                                       89**************************99886 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.4e-05       0.2      33      96 ..       5      65 ..       1      75 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                                      EE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEEESCTTS-EEEEEEEEEE CS
                   Alpha_adaptinC2 33 tNkssqpisnfsfqaavpkslklqlqppsstvlppnpggqitqvllienpskkplrmrlrisyk 96
                                      +N+  + +  +s   avp +l  q   pss +++p  gg+++  +l+ + +++   +r +++y+
  gi|386000840|ref|YP_005919139.1|  5 GNTGESALD-VSVVPAVPPGLSAQSAGPSSVNISP--GGSAQFAYLVRGEAPGLYHVRSQVTYT 65
                                      565555554.777889******************9..**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       187  (0.01043); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 640.43
//
Query:       gi|386000841|ref|YP_005919140.1|  [L=379]
Description: hypothetical protein Mhar_0125 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2575.53
//
Query:       gi|386000842|ref|YP_005919141.1|  [L=124]
Description: hypothetical protein Mhar_0126 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.1   0.1       0.14   11.9   0.1    1.1  1  BppU_N    BppU N-terminal domain


Domain annotation for each model (and alignments):
>> BppU_N  BppU N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.7e-06      0.14      74     141 ..       5      73 ..       1      78 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.7e-06
                            BppU_N  74 eDavnGilkyvlpde.ilkyvGkveaslyidkndeslittgrFtFeikksliddsipevesyyfndfed 141
                                       ++a++Gi+++  +++ +++ + +++a +++  ++e +++  +F+  i ++  ++ +   ++y+++ ++ 
  gi|386000842|ref|YP_005919141.1|   5 ISATGGIVTISYTNNtVIQLASRNNATVSVALTEEYILVPVTFNLAIPADYESSVLVYDKDYQVSRTNS 73 
                                       3799*******9987479**************99****************9988887777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 816.10
//
Query:       gi|386000843|ref|YP_005919142.1|  [L=296]
Description: Methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-60  204.0   0.0    3.1e-60  203.4   0.0    1.3  1  Met_10           Met-10+ like-protein
    3.4e-05   23.2   0.0      4e-05   23.0   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0011   18.6   0.0     0.0015   18.2   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0045   16.6   0.0     0.0076   15.8   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.021   15.5   0.0      0.036   14.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      0.046   13.4   0.0      0.061   13.0   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
        0.2   11.0   0.0       0.25   10.7   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.4   0.0   1.2e-63   3.1e-60       2     199 .]      44     240 ..      43     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.4 bits;  conditional E-value: 1.2e-63
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +++i G v+i++++ +++  k  ige++l++  ++ +vl +++  +g fR+++ ev+aGs++tet+h+E g+ fklD
  gi|386000843|ref|YP_005919142.1|  44 GWSILGKVIIVKIDPQIESLKARIGEALLEIYpRCSSVLLDRGV-AGPFREPDREVIAGSAKTETVHREDGVVFKLD 119
                                       799*****************************99*****99876.******************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                        +kv+fs ++ +Er+r+ +l   ge+Vvd+fAGiG+f++p+a++s++k+++ai++nP ++ yl en++lN v+ +v 
  gi|386000843|ref|YP_005919142.1| 120 PAKVMFSAGNLQERMRMGRL-GGGETVVDMFAGIGYFTLPMAVHSRPKKIIAIEINPVAYGYLAENVRLNGVDGIVV 195
                                       ****************9886.78****************************************************** PP

                                       EEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       p+ +D+  v+++ +adrvvm+++ ++ ++ld+++aal+ gg  hy
  gi|386000843|ref|YP_005919142.1| 196 PVHGDCDLVTPRAVADRVVMGYVGTTDQYLDAAIAALRAGGALHY 240
                                       *******************************************99 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.6e-08     4e-05      52     150 ..     144     239 ..      70     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-08
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE-- CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDP 128
                                       +v+d +++ G  ++  a+  +  k+++a +i++ A+  + eNv+ln v+ ivv+ ++d  ++    +   d + +  
  gi|386000843|ref|YP_005919142.1| 144 TVVDMFAGIGYFTLPMAVH-SRPKKIIAIEINPVAYGYLAENVRLNGVDGIVVPVHGDCDLVT--PRAVADRVVMGY 217
                                       6888899999999999988.88899*******************************9*99887..666778999999 PP

                                       SS--GGGHHHHHHHEEEEEEEE CS
                               TRM 129 fGspapfldsavqsvkekglLl 150
                                        G++ ++ld+a+++++ +g L 
  gi|386000843|ref|YP_005919142.1| 218 VGTTDQYLDAAIAALRAGGALH 239
                                       *****************99885 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.7e-07    0.0015       2      60 ..     143     203 ..     142     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.7e-07
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       ++++D+f+G G  +  +a +   +k+iaiein+      ++N ++ gv+  + +v+gd+  
  gi|386000843|ref|YP_005919142.1| 143 ETVVDMFAGIGYFTLPMAVHsrPKKIIAIEINPVAYGYLAENVRLNGVDGIVVPVHGDCDL 203
                                       579***************9866789*********************************975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     3e-06    0.0076      33     102 ..     143     214 ..     117     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEE CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdliv 102
                                       ++v+D+ +G+G+ ++ +a +s   ++ +++++  A     en++ n+++  v  v+ d+   ++ +  d +v
  gi|386000843|ref|YP_005919142.1| 143 ETVVDMFAGIGYFTLPMAVHSRPKKIIAIEINPVAYGYLAENVRLNGVDgiVVPVHGDCDLVTPRAVADRVV 214
                                       579******************999*************************65555666666555555556555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05     0.036       1      97 []     145     236 ..     145     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       v+d+ +G G +tl +a +   +k+++++i++ +  + +e+++ +g+   v  v+gd++    + +  D vv+     
  gi|386000843|ref|YP_005919142.1| 145 VVDMFAGIGYFTLPMAVHSRPKKIIAIEINPVAYGYLAENVRLNGVdgIVVPVHGDCDL-VTPRAVADRVVMG---- 216
                                       899*************99768*********************9*998666668898755.5577799999993.... PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       ++    ++++l+ +  +L+ gG
  gi|386000843|ref|YP_005919142.1| 217 YVGT--TDQYLDAAIAALRAGG 236
                                       4443..3366777777777766 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.061      40      94 ..     140     195 ..      97     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       HCC-EEEETT-TTSHHHH..HHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalgl..EAlSRgakkavlvekdkeavkilkenleelkleeeta 94 
                                       + g++v+D+faG G   l     SR  kk++++e ++ a+  l en++  ++++ + 
  gi|386000843|ref|YP_005919142.1| 140 GGGETVVDMFAGIGYFTLpmAVHSRP-KKIIAIEINPVAYGYLAENVRLNGVDGIVV 195
                                       67889*********765520556887.9*******************9998877444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.7e-05      0.25     161     230 ..     141     213 ..      90     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.7e-05
                              PrmA 161 egeevlDvGtGSGiLaia.aakLgakkvvavDiDevAvkvakeNaelNkveakl.evalseellk.eekadvi 230
                                       +ge+v+D+ +G G  ++  a+    kk++a+ i++vA    +eN++lN+v+  +  v+   +l++ ++ ad +
  gi|386000843|ref|YP_005919142.1| 141 GGETVVDMFAGIGYFTLPmAVHSRPKKIIAIEINPVAYGYLAENVRLNGVDGIVvPVHGDCDLVTpRAVADRV 213
                                       6789999999999888752556689*************************99550444444444334555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2048.00
//
Query:       gi|386000844|ref|YP_005919143.1|  [L=118]
Description: Zn-dependent hydrolase of the beta-lactamase fold family, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-18   64.7   0.2    1.1e-17   64.4   0.2    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0016   18.0   0.1      0.002   17.7   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.2   1.3e-21   1.1e-17     104     163 .]       2      61 ..       1      61 [. 0.98

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.3e-21
                     Lactamase_B_3 104 dgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       dg++++hlG+l+h ls+ + ++lg+vDv+++Pvgg +tl++  a++++ +++pk+v+Pmh
  gi|386000844|ref|YP_005919143.1|   2 DGIRVCHLGDLGHLLSERDAAALGDVDVLMIPVGGVYTLDAGGAKKVVGQIRPKVVIPMH 61 
                                       89*********************************************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.2e-07     0.002     133     201 .]       2      62 ..       1      62 [. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.2e-07
                                       TTEEEEEESS-S---.HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 133 ggkrvyyigDtgyip.eeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       +g rv+++gD+g++  e+ ++ lg++d+l+++++         + ++l+ ++a +++ ++++k+++++H+
  gi|386000844|ref|YP_005919143.1|   2 DGIRVCHLGDLGHLLsERDAAALGDVDVLMIPVG---------GVYTLDAGGAKKVVGQIRPKVVIPMHF 62 
                                       5789********998666779*************.........8999**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 913.23
//
Query:       gi|386000845|ref|YP_005919144.1|  [L=58]
Description: hypothetical protein Mhar_0130 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       120  (0.00669307); expected 358.6 (0.02)
Passed bias filter:                      100  (0.00557756); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 383.24
//
Query:       gi|386000846|ref|YP_005919145.1|  [L=396]
Description: Integral membrane protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-44  150.0   2.6    7.7e-44  149.5   2.6    1.2  1  DUF21          Cyclin M transmembrane N-terminal domain
      2e-22   79.0   0.6      2e-22   79.0   0.6    2.5  3  CorC_HlyC      Transporter associated domain
    2.8e-11   43.7   2.2    0.00017   22.0   0.0    3.5  4  CBS            CBS domain
  ------ inclusion threshold ------
      0.011   15.9   1.0      0.021   15.0   0.2    1.8  2  HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
      0.029   13.0   3.4      0.041   12.5   3.4    1.1  1  MurJ           Lipid II flippase MurJ
       0.17   11.7   2.3        5.5    6.8   0.1    3.4  3  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
       0.99    9.8   5.2        1.7    9.0   5.2    1.3  1  MgtE           Divalent cation transporter


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.5   2.6     3e-47   7.7e-44      21     176 .]       1     160 [.       1     160 [. 0.98

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 3e-47
                             DUF21  21 vslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellaegalavviatvivtlli 97 
                                       +sls++rl ++ e++ ++a+ +  l+++p++lL t+l+gn+lvni +s++at+l+++++  g+++v iat i+t l+
  gi|386000846|ref|YP_005919145.1|   1 MSLSKIRLIHMLEEKVRGASVINLLREDPNKLLGTILVGNNLVNISASSIATVLAIKYF--GDAGVGIATGITTALV 75 
                                       79*********************************************************..69************** PP

                             DUF21  98 lvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil......esesepavseeelkklveesee 168
                                       lvf+Ei+Pksla++++ekial++a p+ +l+++l+P+v++++++++l+l       +++ p+++eeelk+lv+++ee
  gi|386000846|ref|YP_005919145.1|  76 LVFAEITPKSLAAQKSEKIALVVAKPIFILTTILAPIVFVFTQIARLFLrllgckYNDNLPTITEEELKSLVNLGEE 152
                                       ******************************************************999******************** PP

                             DUF21 169 egvieeee 176
                                       egvie +e
  gi|386000846|ref|YP_005919145.1| 153 EGVIEDQE 160
                                       ****9887 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.5   3.9e+03      54      79 ..     157     182 ..     140     184 .. 0.68
   2 ?   -0.8   0.0      0.64   1.6e+03      17      34 ..     231     249 ..     228     267 .. 0.88
   3 !   79.0   0.6   7.7e-26     2e-22       3      77 ..     310     382 ..     308     386 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                       EEEETTEEEEEEEEETTCEEEEEEEE CS
                         CorC_HlyC  54 evdleglrftVlemdgrrIkkvrvek 79 
                                       e + + +   V + +++ Ik v +++
  gi|386000846|ref|YP_005919145.1| 157 EDQEKTMICNVFDFKDHLIKDVMIQR 182
                                       33434688999999999999999886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.64
                                       HHHHHHHTS.TTHHCT-SB CS
                         CorC_HlyC  17 deleeelgl.elpeedyeT 34 
                                       ++l+e +++ ++    y+T
  gi|386000846|ref|YP_005919145.1| 231 RDLNEVFDIkKFMKKPYYT 249
                                       79*******7799999988 PP

  == domain 3  score: 79.0 bits;  conditional E-value: 7.7e-26
                                       ECTTEEEEETT-BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEE CS
                         CorC_HlyC   3 ldegsylvdGslpldeleeelglelpeedyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrv 77 
                                       ++eg+y+v+Gs++++el+e++g+++++e ye++gG+++el+gr+Pk+gesve    + +f++++m+++rIkk++v
  gi|386000846|ref|YP_005919145.1| 310 IQEGEYIVNGSTRIEELNELIGTRIESEHYESVGGFIIELMGRLPKQGESVEHM--NTKFIIENMERNRIKKIKV 382
                                       689**********************************************55555..******************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.49   1.3e+03      21      46 ..       6      36 ..       1      39 [. 0.75
   2 !   18.8   0.1   6.4e-07    0.0016       2      52 ..     176     229 ..     175     234 .. 0.81
   3 !   22.0   0.0   6.5e-08   0.00017       3      56 ..     241     293 ..     236     294 .. 0.80
   4 ?   -3.4   0.0       5.6   1.4e+04      11      25 ..     316     330 ..     304     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.49
                                      HHHH.HHHHTSSEEEEE....ETTTBEEEEE CS
                               CBS 21 alel.mrekgvsrlPVV....dedgklvGiv 46
                                      +  + m e++v++  V+    ++ +kl+G +
  gi|386000846|ref|YP_005919145.1|  6 IRLIhMLEEKVRGASVInllrEDPNKLLGTI 36
                                      5555566888999989889998888999988 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.4e-07
                                       HHHSBS..SCEEEETTSBHHHHHHHHHHHT.SSEEEEE.ETTTBEEEEEEHHHHH CS
                               CBS   2 gdimtr..dvvtvppdttleealelmrekg.vsrlPVV.dedgklvGivtlrDll 52 
                                       +d+m    dvv ++ +++  e+++++ +++ +sr+P+  ++ ++++Gi+  + l+
  gi|386000846|ref|YP_005919145.1| 176 KDVMIQrmDVVAININASYDEIINKI-RTEqYSRFPIYsNKIDNIIGILNVKELV 229
                                       6775555599****************.5555******9544447*****999886 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 6.5e-08
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                        +m +++ +  + ++ +e++++m +kg +++ +V de+g   Givt +Dl++ ++
  gi|386000846|ref|YP_005919145.1| 241 KFMKKPY-YTFEYMNTSELFNEM-KKGRTHMAIVlDEYGGTAGIVTFEDLVEEIV 293
                                       4576666.88999999*******.77744665544****************9986 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 5.6
                                       EEETTSBHHHHHHHH CS
                               CBS  11 tvppdttleealelm 25 
                                        v+ +t +ee+ el+
  gi|386000846|ref|YP_005919145.1| 316 IVNGSTRIEELNELI 330
                                       456666688887776 PP

>> HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8   7.1e+03      24      41 ..     183     200 ..     159     209 .. 0.63
   2 ?   15.0   0.2     8e-06     0.021      15      70 ..     281     333 ..     275     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                     HEPN_RES_NTD1  24 lefilegiekeYedaane 41 
                                       ++++   i+  Y++  n+
  gi|386000846|ref|YP_005919145.1| 183 MDVVAININASYDEIINK 200
                                       344444444444444444 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8e-06
                     HEPN_RES_NTD1  15 kkvvsleellefilegiekeYedaanelpydsreggylvgetydtedlleeviele 70 
                                          v++e+l+e i+ +i+ eY+  ++e+    +eg+y+v+ +   e+l +e+i+++
  gi|386000846|ref|YP_005919145.1| 281 G-IVTFEDLVEEIVGEISDEYDMHTKEIEII-QEGEYIVNGSTRIEEL-NELIGTR 333
                                       3.789**********************9998.59****9999555554.4444444 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.4   1.6e-05     0.041     364     435 ..      43     118 ..      34     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                              MurJ 364 lnills....llllpplgvvglalatslsaliglvllyvllrkrlklteargiktflak.lvvllalaavvilllss 435
                                       +ni +s    +l ++++g +g ++at++   + ++++  ++ k+l+ +++++i++++ak + +l++++a ++  + +
  gi|386000846|ref|YP_005919145.1|  43 VNISASsiatVLAIKYFGDAGVGIATGITT-ALVLVFAEITPKSLAAQKSEKIALVVAKpIFILTTILAPIVFVFTQ 118
                                       566666666699*****************9.88888899********************877777777766655544 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0022       5.5      29      55 ..     125     151 ..     123     153 .. 0.89
   2 ?    2.5   0.0     0.048   1.2e+02      32      56 ..     221     245 ..     218     247 .. 0.91
   3 ?   -1.7   0.1      0.96   2.5e+03      31      47 ..     280     296 ..     279     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0022
                                       HHTT--BHHHHHHS-HHHHTTSSS-SS CS
                     RNA_pol_A_CTD  29 kragiktvgeLvklseeeLlkikNlGk 55 
                                       +  g+k+ ++L +++eeeL+++ NlG+
  gi|386000846|ref|YP_005919145.1| 125 RLLGCKYNDNLPTITEEELKSLVNLGE 151
                                       567899999*****************8 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.048
                                       T--BHHHHHHS-HHHHTTSSS-SSH CS
                     RNA_pol_A_CTD  32 giktvgeLvklseeeLlkikNlGkK 56 
                                       gi  v+eLv ++ +e   ik + kK
  gi|386000846|ref|YP_005919145.1| 221 GILNVKELVYRDLNEVFDIKKFMKK 245
                                       8999****************99887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.96
                                       TT--BHHHHHHS-HHHH CS
                     RNA_pol_A_CTD  31 agiktvgeLvklseeeL 47 
                                       agi t ++Lv+    e+
  gi|386000846|ref|YP_005919145.1| 280 AGIVTFEDLVEEIVGEI 296
                                       79999999998655555 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.2   0.00066       1.7       7      93 ..      38     122 ..      35     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHHHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHH.HHHHHHHH CS
                              MgtE   7 lgGnlgaqlasristalhlgelekklkkvllkelrvvlllgvilgllifllalllgw.....slllal.vvglalvl 77 
                                       +g nl++++as i t l+++ +           + v++ +g++ +l++++  ++  +     s ++al v    ++l
  gi|386000846|ref|YP_005919145.1|  38 VGNNLVNISASSIATVLAIKYF---------GDAGVGIATGITTALVLVFAEITPKSlaaqkSEKIALvVAKPIFIL 105
                                       689****************977.........5567777777777777776655433355556555555144555555 PP

                                       HHHHHHHH...HHHHHH CS
                              MgtE  78 vllaaall.ilgvllpl 93 
                                       + ++a ++ +++ +  l
  gi|386000846|ref|YP_005919145.1| 106 TTILAPIVfVFTQIARL 122
                                       55555555544444434 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2506.46
//
Query:       gi|386000847|ref|YP_005919146.1|  [L=491]
Description: Transporter, monovalent cation:proton antiporter-2 (CPA2) family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-55  188.2  40.9    2.4e-55  187.9  40.9    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    5.7e-12   45.3   0.0      1e-11   44.5   0.0    1.4  1  TrkA_C          TrkA-C domain


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9  40.9   2.7e-59   2.4e-55       4     381 .]      13     389 ..       9     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 2.7e-59
                                       HHHHHHHHHHH.HHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHH CS
                    Na_H_Exchanger   4 lillallvgll.arrlklpeivgliiaGlllGpsglg.l.iepseedlevlselglilllFlaGleldlrelrknlk 77 
                                       ++ll+++v    ++ l++p +++++++G+l G  g+g + ++++    + l ++ li++lF  Gl + ++e+r +l+
  gi|386000847|ref|YP_005919146.1|  13 VLLLLSVVSSKaSTQLGVPALLLFLVIGMLAGADGPGgVdFDNP-WLAQALGTVALIFILFSGGLDTRWSEVRPVLW 88 
                                       334344444433*************************5335555.899***************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC..CCCTSTCCCCCCHHHHHHHHHH CS
                    Na_H_Exchanger  78 silllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk.eegrvperlgtlllgesvlnDa 153
                                         +ll+++gvlit+v++G+++y+  +l+++lleall++ai+s td+++v +il+ ++ r++ +l+ ll+ es+ nD 
  gi|386000847|ref|YP_005919146.1|  89 RGVLLSTVGVLITTVIVGYAAYY--VLDFSLLEALLLAAIISSTDAAAVFSILRsRQIRLKGELRPLLELESGSNDP 163
                                       **********************8..89**************************98999******************* PP

                                       HCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 154 vavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaall 229
                                       +a++l+ +l++l+   a+ +ts  +ll if+   ++g ++g  +g  ++++  ++  d r l+++l++ l+l++++l
  gi|386000847|ref|YP_005919146.1| 164 MAIFLTISLIGLI---AAPATSPTALLPIFAQQMALGAVCGHMMGRAMAIAVNRIrLDYRGLYPVLTISLVLFTYGL 237
                                       *************...999**********************9999999999999999******************** PP

                                       HHTSXXXHHHHHHHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 230 aellgvsgilgaflaGlvlseyefsnk..lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvail 304
                                       a +lg  g l++ laGl+l++y+f +k  l ++ +s++ + + +++F+ +Gl + ++ l   +   + +++ +++i+
  gi|386000847|ref|YP_005919146.1| 238 AAILGGNGFLAVYLAGLTLGNYSFIHKrsLMHDHDSLA-WMMQIVMFLTLGLLVYPSQLI--PVAATGLFVCFILIF 311
                                       **********************99999999999*****.********************6..777777777778888 PP

                                       THHHHHHHHHTTTX.SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHHHHHH CS
                    Na_H_Exchanger 305 lgrilavflllrll.glslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGlslkpll 379
                                       ++r+++v+l+l  + +  + e+++i++ gl +g+v ++la +  + g+ +++l ++++++vvl++vlvqG+s+++l 
  gi|386000847|ref|YP_005919146.1| 312 VARPVSVLLCLLPFrKMRFAERIMISWVGL-KGSVPIILATFPLTYGIEKADLiFNIVFFVVLTSVLVQGSSIPFLA 387
                                       9********99999789*************.*******************************************998 PP

                                       HC CS
                    Na_H_Exchanger 380 kk 381
                                       ++
  gi|386000847|ref|YP_005919146.1| 388 RW 389
                                       76 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.1e-15     1e-11       1      67 [.     415     480 ..     415     482 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.1e-15
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       lve++v +gs  vGk +++lnl++ +  ++ +rR+g+++ p+g+tvL++GD l v +s  +l+ lr+
  gi|386000847|ref|YP_005919146.1| 415 LVEFEVMPGSAAVGKQIADLNLPD-DTWIAILRRDGRPLRPGGSTVLQAGDGLSVQSSGPSLELLRS 480
                                       69**********************.****************************99999888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2753.08
//
Query:       gi|386000848|ref|YP_005919147.1|  [L=144]
Description: hypothetical protein Mhar_0133 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.051   12.1   0.6      0.058   11.9   0.6    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   3.2e-06     0.058     457     512 ..      63     119 ..      46     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-06
                                       TTXXXXXXTSX.XXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESS CS
                      tRNA-synt_2c 457 yeeleaeakvl.allkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekeg 512
                                        + +e ++++  ++++ +e   e++e  ++++ Ld+T fY  + G  +D G+i +e+
  gi|386000848|ref|YP_005919147.1|  63 MNVTEQRGRIFnGVVTYTEDGVEMTEEFAGVIALDNTTFYIAEFGSGYDVGTIVSED 119
                                       5555555655424666777778888888999********************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.57
# Mc/sec: 755.14
//
Query:       gi|386000849|ref|YP_005919148.1|  [L=102]
Description: hypothetical protein Mhar_0134 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 606.83
//
Query:       gi|386000850|ref|YP_005919149.1|  [L=720]
Description: catalase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-89  298.5   0.0    8.6e-46  156.5   0.0    2.2  2  peroxidase  Peroxidase


Domain annotation for each model (and alignments):
>> peroxidase  Peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.5   0.0   4.8e-50   8.6e-46       7     228 ..      62     379 ..      49     380 .. 0.89
   2 !  140.1   0.0   4.9e-45   8.8e-41       2     228 ..     386     693 ..     385     694 .. 0.89

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 4.8e-50
                                       HCCCC.TTTHCHHHHHHHHHHHTT.......SSTTSCHHHTCCHHCSGGGTTTHHHHHHHHHHHHHCTT.....S-H CS
                        peroxidase   7 aalka.drdmgpsllrlafhdcfv.......gGcdgsvlllepektapaNaslrkgldvldaikakleaacpgvvSc 75 
                                       +++ a ++++gp ++r+a+h++++       gG+  + ++l+p +++p+N +l+k++++l++ik+k++++    +S+
  gi|386000850|ref|YP_005919149.1|  62 DWWPAdWGHYGPLFIRMAWHSAGTyrlgdgrGGAGSGSQRLAPLNSWPDNVNLDKARRLLWPIKQKYGRK----ISW 134
                                       44444699**********************99999999******************************95....*** PP

                                       HHHHHHHHHHHHHCTT--..--EE---S-SSGGG.S-S....................................... CS
                        peroxidase  76 ADlialaardavelaggplvpvslGRrDatessa.sev.snl................................... 115
                                       ADl++la+++a+e +g +++ +  GR+D +e+++ +++ s+                                    
  gi|386000850|ref|YP_005919149.1| 135 ADLMILAGNCALESMGFKTFGFGGGREDVWEPEEdIYWgSEEewlatsdtpksrysgerdlenplaavqmgliyvnp 211
                                       ******************99**************9***66669*********************************9 PP

                                       ......-.-TS-HHHHHHHHHHHT--HHHHHHH.HGGGGC-EESHH................SS-GGGT.....HHS CS
                        peroxidase 116 ......PdptasvdelrdkfarkgltdeelvaL.sGaHtiGkahcssfs.rlya....aadpaldaayaae.kCasg 179
                                             Pdp as +++r++far+ ++dee+vaL +G+Ht+Gk+h+s  +  +      a++++++ +++++ ++ +g
  gi|386000850|ref|YP_005919149.1| 212 egpdgnPDPVASGRDVRETFARMAMNDEETVALvAGGHTFGKCHGSGPAtHVGPepeaAPIEEQGLGWKSSfRSGKG 288
                                       9999999*************************************875544444257777888888888877755334 PP

                                       ..............EETS-STHHHHHHCC....................................T-EEEHHHHHHH CS
                        peroxidase 180 nte.lvdld.....tptkfdnsyfknlle....................................krgllrsDqvll 214
                                       +++  + l+     +pt++d  y k +++                                    + +++++D++l 
  gi|386000850|ref|YP_005919149.1| 289 GDAiSSGLEgawkpNPTRWDMGYLKVMFKyewervkspagahqwlakdvaeedmvvdahdpskrhRPMMTTADLSLR 365
                                       4445333333344677************************************************************* PP

                                       HSCCCHHHHHHCCC CS
                        peroxidase 215 sdsetralvekyae 228
                                        d+ ++++ ++y e
  gi|386000850|ref|YP_005919149.1| 366 FDPIYEPISRRYLE 379
                                       ***********986 PP

  == domain 2  score: 140.1 bits;  conditional E-value: 4.9e-45
                                       HHHHHHCCCC.TTTHCHHH.........HHHHHHH.......................................HTT CS
                        peroxidase   2 rafvkaalka.drdmgpsl.........lrlafhd.......................................cfv 29 
                                       +af++a++k  +rdmgp           ++l+++d                                       +  
  gi|386000850|ref|YP_005919149.1| 386 DAFARAWFKLtHRDMGPRSrylgpevpaEELIWQDpvpavdhelidaadisalkaeilasglsipelvstawasA-S 461
                                       6899*************55566889999***********************999999999999998887776651.0 PP

                                       ........SSTTSCHHHTCCHHCSGGGT..TTHHHHHHHHHHHHHCTT.......S-HHHHHHHHHHHHHHCT.... CS
                        peroxidase  30 ........gGcdgsvlllepektapaNa..slrkgldvldaikakleaacpg..vvScADlialaardavela.... 90 
                                               gG++g++++l p+k+++aN+  +l+k+l +l+ ik++++ + +g   vS+ADli+l++++a+e a    
  gi|386000850|ref|YP_005919149.1| 462 tfrgsdkrGGANGARIRLPPQKDWEANEpsRLKKVLSTLEGIKEEFNGRASGgkRVSLADLIVLGGCAAIEVAakna 538
                                       46688999*********************9*****************97766546*****************99996 PP

                                       T--...--EE---S-SSGGGS-S......-............-TS-HHH.HHHHHHHHT--HHHHHHH.HGGGGC-E CS
                        peroxidase  91 ggp.lvpvslGRrDatessasevsnl...P...........dptasvde.lrdkfarkgltdeelvaL.sGaHtiGk 150
                                       g+  +vp+++GR+Da+++ +  +s+    P           +   s++e l+d+++ ++lt++e+++L +G++++G+
  gi|386000850|ref|YP_005919149.1| 539 GHNvTVPFTPGRTDASQEMTDAASFAvlePaadgfrnylkaRYAVSAEElLVDRAQLLTLTAPEMTVLvGGMRVLGA 615
                                       666788**************6564445574666666666657799****9*************************** PP

                                       ESHH...........SS-GGGT....HHS........EETS-STHHHHHHCC......................... CS
                        peroxidase 151 ahcssfsrlyaaadpaldaayaaekCasgntelvdldtptkfdnsyfknlle......................... 202
                                       +++                          +++ v++ +p++++n++f+nll+                         
  gi|386000850|ref|YP_005919149.1| 616 NYGG-------------------------SQHGVFTRRPEALTNDFFANLLDmrtvwrataeddgvfegrdrvtgdl 667
                                       **54.........................333688889*************************************** PP

                                       T-EEEHHHHHHHHSCCCHHHHHHCCC CS
                        peroxidase 203 krgllrsDqvllsdsetralvekyae 228
                                       +++++r+D+ ++s+s++ra++e+y +
  gi|386000850|ref|YP_005919149.1| 668 EWTATRVDLIFGSNSQLRAIAEVYGS 693
                                       ************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 4165.17
//
Query:       gi|386000851|ref|YP_005919150.1|  [L=58]
Description: DNA-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.021   15.0   5.8       0.21   11.8   0.3    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.068   12.9   5.5       0.48   10.2   0.1    2.6  2  zinc_ribbon_2   zinc-ribbon domain
      0.095   12.6   7.0       0.14   12.1   0.8    1.7  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.22   11.6   9.0        2.6    8.2   1.2    2.3  2  UPF0547         Uncharacterised protein family UPF0547
       0.24   11.0   4.2        1.1    8.9   0.7    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
          2    8.5   8.9       0.66   10.0   0.7    2.3  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.8    0.0058        17      28      40 .]      20      32 ..      16      33 .. 0.73
   2 ?   11.8   0.3     7e-05      0.21      17      27 ..      47      57 ..      45      58 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0058
                     Auto_anti-p27 28 drkggkvyCvaCd 40
                                      d+++  ++C++C+
  gi|386000851|ref|YP_005919150.1| 20 DQNSSACVCPRCG 32
                                      4467889999996 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7e-05
                     Auto_anti-p27 17 tCpvCgvPLmr 27
                                       Cp+C vPLm 
  gi|386000851|ref|YP_005919150.1| 47 KCPECRVPLMG 57
                                      5*********6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00016      0.48       2       9 ..      28      35 ..      27      37 .. 0.76
   2 ?    4.0   1.4     0.015        45      16      20 ..      48      52 ..      41      55 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                     zinc_ribbon_2  2 CpnCGael 9 
                                      Cp+CG e+
  gi|386000851|ref|YP_005919150.1| 28 CPRCGFEI 35
                                      88888887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                     zinc_ribbon_2 16 CpyCG 20
                                      Cp+C+
  gi|386000851|ref|YP_005919150.1| 48 CPECR 52
                                      66665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   4.6e-05      0.14      35      58 ..      12      37 ..       5      39 .. 0.76
   2 ?   11.0   6.8   0.00011      0.32      26      54 ..      23      53 ..      15      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                    OrfB_Zn_ribbon 35 gsknke..alsgrtfkCpnCgfeadr 58
                                      g+ nk+  ++++   +Cp+Cgfe+ r
  gi|386000851|ref|YP_005919150.1| 12 GKGNKRnrDQNSSACVCPRCGFEIER 37
                                      55555555899999********9987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon 26 yTSktCseCgsknke..alsgrtfkCpnCgf 54
                                       +   C++Cg + ++   ++ r  kCp+C +
  gi|386000851|ref|YP_005919150.1| 23 SSACVCPRCGFEIERapGVNCRSIKCPECRV 53
                                      45568**********999***********75 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2   0.00088       2.6      14      23 ..      25      34 ..      23      36 .. 0.80
   2 ?    7.8   1.3    0.0012       3.6       2       9 ..      47      54 ..      47      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00088
                           UPF0547 14 aqfCphCGyv 23
                                      a +Cp CG++
  gi|386000851|ref|YP_005919150.1| 25 ACVCPRCGFE 34
                                      5679999996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                           UPF0547  2 vCPeCeak 9 
                                      +CPeC+ +
  gi|386000851|ref|YP_005919150.1| 47 KCPECRVP 54
                                      7****975 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.7   0.00036       1.1       4      13 ..      27      36 ..      24      38 .. 0.87
   2 ?    3.7   0.1     0.016        48       2       9 ..      45      52 ..      44      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00036
                            zf_UBZ  4 lCerCgkeip 13
                                      +C+rCg ei+
  gi|386000851|ref|YP_005919150.1| 27 VCPRCGFEIE 36
                                      8*****9997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                            zf_UBZ  2 tylCerCg 9 
                                      ++ C++C 
  gi|386000851|ref|YP_005919150.1| 45 SIKCPECR 52
                                      579****5 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7   0.00022      0.66      20      30 .]      26      36 ..      21      36 .. 0.84
   2 ?    2.7   2.0     0.043   1.3e+02       4       8 ..      47      51 ..      42      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                    PhnA_Zn_Ribbon 20 lvCpeCahEwe 30
                                       vCp C+ E+e
  gi|386000851|ref|YP_005919150.1| 26 CVCPRCGFEIE 36
                                      59*******97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.043
                    PhnA_Zn_Ribbon  4 kCplC 8 
                                      kCp+C
  gi|386000851|ref|YP_005919150.1| 47 KCPEC 51
                                      67777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 419.83
//
Query:       gi|386000852|ref|YP_005919151.1|  [L=202]
Description: hypothetical protein Mhar_0137 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-10   39.8  16.3      2e-06   27.4   4.1    2.9  3  Fer4             4Fe-4S binding domain
    1.2e-09   38.2  12.6    3.4e-05   23.9   1.9    2.4  2  Fer4_9           4Fe-4S dicluster domain
    1.8e-08   34.6   8.0    3.9e-08   33.5   8.0    1.5  1  Fer4_18          4Fe-4S dicluster domain
    3.4e-08   33.3  14.5      2e-06   27.6   4.0    3.5  4  Fer4_5           4Fe-4S binding domain
    7.4e-08   32.9  12.5    0.00052   20.5   2.5    2.6  3  Fer4_7           4Fe-4S dicluster domain
    1.2e-07   31.5  22.1    9.9e-05   22.3   3.3    2.7  2  Fer4_6           4Fe-4S binding domain
    4.8e-07   29.8   8.1     0.0031   17.6   1.1    2.4  2  Fer4_21          4Fe-4S dicluster domain
    3.7e-06   27.0  15.9    3.7e-06   27.0  15.9    2.5  2  Fer4_10          4Fe-4S dicluster domain
    4.3e-06   26.5  18.4    0.00032   20.6   1.4    3.0  3  Fer4_2           4Fe-4S binding domain
    7.3e-05   23.6  16.1     0.0014   19.6   2.5    2.5  2  Fer4_16          4Fe-4S double cluster binding domain
    0.00013   22.7   8.2      0.043   14.7   0.3    2.3  2  Fer4_22          4Fe-4S dicluster domain
    0.00051   20.5  10.6      0.059   13.9   0.7    2.3  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    0.00074   20.0  18.6       0.15   12.6   3.8    2.6  2  Fer4_17          4Fe-4S dicluster domain
     0.0008   20.2   5.5     0.0008   20.2   5.5    3.4  4  Fer4_3           4Fe-4S binding domain
     0.0063   16.9  21.9       0.19   12.3   5.2    3.1  3  Fer4_4           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.075   13.5  20.7       0.13   12.7   3.2    2.5  2  Fer4_8           4Fe-4S dicluster domain
       0.73   10.6  10.6        4.1    8.2   1.4    2.3  2  Fer4_15          4Fe-4S single cluster domain
        1.4    9.1   6.3       0.11   12.6   1.1    1.9  2  DUF2614          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.5   3.5e+03      10      19 ..     136     138 ..     133     142 .. 0.60
   2 !   20.5   0.8     3e-07    0.0003       3      20 ..     155     172 ..     153     173 .. 0.90
   3 !   27.4   4.1     2e-09     2e-06       7      24 .]     184     201 ..     182     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                                       S-THHHHHST CS
                              Fer4  10 gCGaCvevCP 19 
                                               CP
  gi|386000852|ref|YP_005919151.1| 136 L-------CP 138
                                       4.......55 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3e-07
                                       EETTTSSS-THHHHHSTT CS
                              Fer4   3 ideekCigCGaCvevCPv 20 
                                        d+++Ci C +C +vCP 
  gi|386000852|ref|YP_005919151.1| 155 LDQNLCIDCSRCQKVCPM 172
                                       799**************5 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 2e-09
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                       +Ci+CG+Cve+CP gA++
  gi|386000852|ref|YP_005919151.1| 184 DCIKCGRCVEACPKGALR 201
                                       5***************85 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.9   3.4e-08   3.4e-05       8      49 ..     134     173 ..     131     175 .. 0.91
   2 !   19.5   3.3   8.3e-07   0.00083      35      50 ..     184     199 ..     173     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.4e-08
                            Fer4_9   8 CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+  Cp+g+ ++  +++k  l+ +++  Ci+C +C ++Cp +
  gi|386000852|ref|YP_005919151.1| 134 CTL-CPMGTLQRFLGRGKYPLKLDQN-LCIDCSRCQKVCPMQ 173
                                       666.*****************98776.9************87 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 8.3e-07
                            Fer4_9  35 aCigCgaCveaCpkga 50 
                                       +Ci+Cg+CveaCpkga
  gi|386000852|ref|YP_005919151.1| 184 DCIKCGRCVEACPKGA 199
                                       6999999999999987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   8.0   3.9e-11   3.9e-08      58      96 ..     157     196 ..     149     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.9e-11
                           Fer4_18  58 agdcidcescvkvcPtgidirk.Glqleciscllcidacd 96 
                                       ++ cidc+ c kvcP+++d+r  G   +ci+c++c++ac 
  gi|386000852|ref|YP_005919151.1| 157 QNLCIDCSRCQKVCPMQLDVRAvGGDPDCIKCGRCVEACP 196
                                       567******************7699**************6 PP

>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5       9.7   9.7e+03      12      19 ..      10      17 ..       7      21 .. 0.41
   2 !   27.6   4.0     2e-09     2e-06       2      47 ..      26      71 ..      25      72 .. 0.87
   3 !   18.1   2.8   1.9e-06    0.0018       8      39 ..     118     148 ..     106     156 .. 0.76
   4 ?   -1.9   0.0       3.5   3.5e+03      27      33 ..     194     200 ..     191     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.7
                            Fer4_5 12 ivlvtllf 19
                                      i+++ +  
  gi|386000852|ref|YP_005919151.1| 10 IIVLLVSI 17
                                      33333323 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2e-09
                            Fer4_5  2 allllilflaivlvtllfGRafCgWiCPfGalqellakllrrklgk 47
                                      ++++ + fl i++++ + GR+fCg++C  G++ +++   ++r++ +
  gi|386000852|ref|YP_005919151.1| 26 GYVVALVFLSILAISPFRGRWFCGNLCLWGSFNDFWVGKISRHIQI 71
                                      5778899***************************877767777766 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.9e-06
                            Fer4_5   8 lflaivlvtllfGRafCgWiCPfGalqellak 39 
                                         + i++ +++  Ra+C  +CP G+lq +l++
  gi|386000852|ref|YP_005919151.1| 118 ASFSILFGAAYSPRAWCT-LCPMGTLQRFLGR 148
                                       3445666666799*****.**********998 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.5
                            Fer4_5  27 iCPfGal 33 
                                       +CP Gal
  gi|386000852|ref|YP_005919151.1| 194 ACPKGAL 200
                                       8**9998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       8.7   8.6e+03       7      15 ..      47      55 ..      46      80 .. 0.75
   2 !   17.6   2.0   4.5e-06    0.0044      12      50 ..     137     172 ..     129     174 .. 0.73
   3 !   20.5   2.5   5.3e-07   0.00052       2      19 ..     185     202 .]     184     202 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.7
                            Fer4_7  7 aCvaaCpvk 15
                                      +C + C ++
  gi|386000852|ref|YP_005919151.1| 47 FCGNLCLWG 55
                                      566666444 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.5e-06
                            Fer4_7  12 CpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       Cp+++++       +g+  +++d++ C++C +C++vCP 
  gi|386000852|ref|YP_005919151.1| 137 CPMGTLQRFLG---RGKYPLKLDQNLCIDCSRCQKVCPM 172
                                       55555555433...344456889999***********97 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 5.3e-07
                            Fer4_7   2 CigCgaCvaaCpvkaiel 19 
                                       Ci+Cg+Cv+aCp +a+++
  gi|386000852|ref|YP_005919151.1| 185 CIKCGRCVEACPKGALRF 202
                                       99**********999875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   3.3   9.9e-08   9.9e-05       5      22 ..     156     173 ..     156     176 .. 0.95
   2 !   20.6   4.5   3.3e-07   0.00033       9      24 .]     185     200 ..     182     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.9e-08
                            Fer4_6   5 dpdkCigCgdCvrvCPeg 22 
                                       d+++Ci+C +C +vCP++
  gi|386000852|ref|YP_005919151.1| 156 DQNLCIDCSRCQKVCPMQ 173
                                       89**************98 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.3e-07
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci Cg+Cv +CP ga+
  gi|386000852|ref|YP_005919151.1| 185 CIKCGRCVEACPKGAL 200
                                       *************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.1   3.1e-06    0.0031      18      53 ..     137     172 ..     132     177 .. 0.74
   2 !   15.9   0.9   1.1e-05     0.011       7      22 ..     184     199 ..     178     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                           Fer4_21  18 CedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       C+ ++ q   + +k  lk+ ++ C+ C  C +vCP+
  gi|386000852|ref|YP_005919151.1| 137 CPMGTLQRFLGRGKYPLKLDQNLCIDCSRCQKVCPM 172
                                       666666777777777778888888888888888887 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
                           Fer4_21   7 kCigCgkCliaCedts 22 
                                       +Ci+Cg+C+ aC++++
  gi|386000852|ref|YP_005919151.1| 184 DCIKCGRCVEACPKGA 199
                                       7***********9865 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       8.2   8.2e+03      18      21 ..     136     139 ..     131     141 .. 0.61
   2 !   27.0  15.9   3.7e-09   3.7e-06       3      56 .]     154     196 ..     152     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                           Fer4_10  18 aCPa 21 
                                        CP+
  gi|386000852|ref|YP_005919151.1| 136 LCPM 139
                                       3555 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.7e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++d++ Ci C +C+k+CP+             + +  ++  +C++cg CveaCP
  gi|386000852|ref|YP_005919151.1| 154 KLDQNLCIDCSRCQKVCPM-----------QLDVRAVGGDPDCIKCGRCVEACP 196
                                       57999**************...........666666677899***********9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       5.7   5.7e+03      16      21 ..     134     138 ..     131     139 .. 0.62
   2 !   20.6   1.4   3.2e-07   0.00032       2      21 ..     152     171 ..     151     172 .. 0.91
   3 !   15.4   4.1   1.4e-05     0.014       6      21 ..     182     196 ..     178     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.7
                            Fer4_2  16 CvsaCP 21 
                                       C + CP
  gi|386000852|ref|YP_005919151.1| 134 C-TLCP 138
                                       4.4455 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.2e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       p + d + Ci C+ C+++CP
  gi|386000852|ref|YP_005919151.1| 152 PLKLDQNLCIDCSRCQKVCP 171
                                       56889*************** PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.4e-05
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                       d+d Ci Cg Cv aCP
  gi|386000852|ref|YP_005919151.1| 182 DPD-CIKCGRCVEACP 196
                                       677.***********9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.3   8.5e-05     0.085      53      66 ..     159     172 ..     150     174 .. 0.61
   2 !   19.6   2.5   1.4e-06    0.0014       2      18 ..     185     201 ..     184     202 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-05
                           Fer4_16  53 aitgCdiCqdvCPa 66 
                                        ++ C +Cq+vCP+
  gi|386000852|ref|YP_005919151.1| 159 LCIDCSRCQKVCPM 172
                                       45555555555554 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.4e-06
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C++Cg+C+e+CP +a++
  gi|386000852|ref|YP_005919151.1| 185 CIKCGRCVEACPKGALR 201
                                       ***************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   4.3e-05     0.043      74      95 ..     152     173 ..     141     174 .. 0.83
   2 !   11.2   2.5    0.0005       0.5      78      94 ..     181     197 ..     175     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-05
                           Fer4_22  74 kekfgesgCvGCgRCieacpvk 95 
                                         k +++ C+ C RC+++cp++
  gi|386000852|ref|YP_005919151.1| 152 PLKLDQNLCIDCSRCQKVCPMQ 173
                                       5577999************987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0005
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       g   C+ CgRC+eacp+
  gi|386000852|ref|YP_005919151.1| 181 GDPDCIKCGRCVEACPK 197
                                       5678***********97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.7     6e-05     0.059       2      18 ..     156     172 ..     155     181 .. 0.87
   2 !   10.9   3.5   0.00054      0.54       5      18 ..     184     197 ..     182     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6e-05
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D++ Ci+c  C +++P 
  gi|386000852|ref|YP_005919151.1| 156 DQNLCIDCSRCQKVCPM 172
                                       8999************7 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00054
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ci cg Cve++P+
  gi|386000852|ref|YP_005919151.1| 184 DCIKCGRCVEACPK 197
                                       6************6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   7.0   0.00016      0.16      44      61 .]     158     175 ..     132     175 .. 0.89
   2 !   12.6   3.8   0.00015      0.15      45      59 ..     184     198 ..     183     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                           Fer4_17  44 slCieCgeCerkCPqgld 61 
                                       +lCi C +C+++CP++ld
  gi|386000852|ref|YP_005919151.1| 158 NLCIDCSRCQKVCPMQLD 175
                                       89**************97 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00015
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       +Ci+Cg+C+++CP+g
  gi|386000852|ref|YP_005919151.1| 184 DCIKCGRCVEACPKG 198
                                       699*********986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       6.1   6.1e+03       3       8 ..      47      53 ..      46      54 .. 0.69
   2 ?   -1.7   0.8       7.8   7.8e+03       1       4 [.     134     137 ..     134     140 .. 0.64
   3 !   10.7   3.8   0.00083      0.82       1      12 [.     160     171 ..     160     176 .. 0.95
   4 !   20.2   5.5   8.1e-07    0.0008       1      15 []     185     199 ..     185     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.1
                            Fer4_3  3 gCg.aCv 8 
                                       Cg +C+
  gi|386000852|ref|YP_005919151.1| 47 FCGnLCL 53
                                      5876885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.8
                            Fer4_3   1 CtgC 4  
                                       Ct C
  gi|386000852|ref|YP_005919151.1| 134 CTLC 137
                                       6666 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00083
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C++C +vCP
  gi|386000852|ref|YP_005919151.1| 160 CIDCSRCQKVCP 171
                                       9*********** PP

  == domain 4  score: 20.2 bits;  conditional E-value: 8.1e-07
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg+Cve+CP+gA
  gi|386000852|ref|YP_005919151.1| 185 CIKCGRCVEACPKGA 199
                                       **************9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.2   1.2e+03       3       8 ..     133     138 ..     132     139 .. 0.84
   2 !   12.0   4.3   0.00023      0.23       1      17 []     157     173 ..     157     173 .. 0.92
   3 !   12.3   5.2   0.00019      0.19       4      16 ..     185     197 ..     183     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.2
                            Fer4_4   3 rCigCg 8  
                                       +C+ C+
  gi|386000852|ref|YP_005919151.1| 133 WCTLCP 138
                                       899997 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00023
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       q+ Ci+C +C  +CP++
  gi|386000852|ref|YP_005919151.1| 157 QNLCIDCSRCQKVCPMQ 173
                                       688************86 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00019
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci Cg+Cv aCP 
  gi|386000852|ref|YP_005919151.1| 185 CIKCGRCVEACPK 197
                                       ************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.2   0.00014      0.13       4      18 ..     159     173 ..     156     184 .. 0.72
   2 ?   11.7   4.1   0.00026      0.26       5      16 ..     185     196 ..     182     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                            Fer4_8   4 kCieCgaCqsaCpvl 18 
                                        Ci C++Cq+ Cp+ 
  gi|386000852|ref|YP_005919151.1| 159 LCIDCSRCQKVCPMQ 173
                                       588888888888764 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00026
                            Fer4_8   5 CieCgaCqsaCp 16 
                                       Ci+Cg+C +aCp
  gi|386000852|ref|YP_005919151.1| 185 CIKCGRCVEACP 196
                                       666666666665 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.4    0.0041       4.1       2      19 ..     154     171 ..     153     179 .. 0.88
   2 ?    7.1   2.3     0.009         9       7      20 ..     184     197 ..     182     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0041
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       ++D+++Ci c +C +++p
  gi|386000852|ref|YP_005919151.1| 154 KLDQNLCIDCSRCQKVCP 171
                                       68**************98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.009
                           Fer4_15   7 aCigcglCvaeape 20 
                                        Ci cg+Cv+++p+
  gi|386000852|ref|YP_005919151.1| 184 DCIKCGRCVEACPK 197
                                       6***********97 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3         6     6e+03      28      32 ..      20      24 ..       4      40 .. 0.45
   2 ?   12.6   1.1   0.00011      0.11      16      98 ..      82     164 ..      64     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6
                           DUF2614 28 llfke 32
                                      l++ +
  gi|386000852|ref|YP_005919151.1| 20 LWYPK 24
                                      33333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                           DUF2614  16 l.vfiglivmyigllfkeselllvlflllGlllvlastvvyfwiGllstkavqvvcpeceketkvlGrvdlcmhcde 91 
                                       + +fi+++ m i+ +++++  +  l +++ ++ +l+++   ++    s +a    cp  +   ++lGr    ++ d+
  gi|386000852|ref|YP_005919151.1|  82 VpIFIAMMGMNISRIISTEGSVDKLGMVFVTMSILTASFSILFGAAYSPRAWCTLCPM-GTLQRFLGRGKYPLKLDQ 157
                                       3489*********9*************99999998887777777889**********7.56789*****99999999 PP

                           DUF2614  92 pltldks 98 
                                        l +d s
  gi|386000852|ref|YP_005919151.1| 158 NLCIDCS 164
                                       9999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1288.57
//
Query:       gi|386000853|ref|YP_005919152.1|  [L=178]
Description: putative membrane-bound metal-dependent hydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-10   40.2   7.4    2.8e-10   39.8   7.4    1.2  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   7.4   1.6e-14   2.8e-10       1     112 [.       1     171 [.       1     174 [. 0.87

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.6e-14
                              YdjM   1 MdgltHallGaalglalaallgaake.............avllavavlgAllPDiDhpsstlgrklgllskklak.. 62 
                                       M    H+l G+++  ++  +l+  +              a  +++ v+g+ lPD+Dhp + + r  +++ +++    
  gi|386000853|ref|YP_005919152.1|   1 MNYDEHVLAGILTYPIAIFFLAVLDVhlgfpiettfvamALGYVFYVIGSDLPDMDHPEALVHRIAKPFVAVAVGis 77 
                                       6666788888777666666665554456677888888889999999**************99999999888665599 PP

                              YdjM  63 ........................................lvgHRgftHSllflallalvlllllrlfgrsa....l 95 
                                                                               +  HRg+ HS +f+a+ a+++  ++r+ +  a    l
  gi|386000853|ref|YP_005919152.1|  78 afknlgaavlltpypiinlaiawffaalaavvgwnlfrflMPDHRGVVHSPIFAAVYAIIAFTIVRFGFVAApgeaL 154
                                       9**************************************999*******************9999999988888887 PP

                              YdjM  96 rlglllllgvlsHlllD 112
                                       +++l+ +lg+ +HlllD
  gi|386000853|ref|YP_005919152.1| 155 FIALASFLGYNLHLLLD 171
                                       888889999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1231.84
//
Query:       gi|386000854|ref|YP_005919153.1|  [L=509]
Description: hypothetical protein Mhar_0139, partial [Methanosaeta harundinacea 6Ac]
Scores for complete 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-92  310.5   0.0    1.5e-92  310.3   0.0    1.1  1  Type_ISP_C  Type ISP C-terminal specificity domain


Domain annotation for each model (and alignments):
>> Type_ISP_C  Type ISP C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.3   0.0   8.2e-97   1.5e-92       2     343 .]     117     498 ..     116     498 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.3 bits;  conditional E-value: 8.2e-97
                        Type_ISP_C   2 lfplyslGvktnRDawvynfskeelekrikrlideyneevkrkkkktkdstkikwsralkkdlkknkklefdeekiv 78 
                                       lf lys+G++t+RD+ +++   +el++ ++++++++ e v++k+ + kd +++k+++a ++ l+    + +de+ + 
  gi|386000854|ref|YP_005919153.1| 117 LFGLYSSGIQTKRDKIAIAQGISELRAILRDFASMEPEVVRSKFDLPKDGRDWKIKWASEHALA----IVNDEKGLS 189
                                       8*********************************************************888776....9******** PP

                        Type_ISP_C  79 eilYRPFdkqwlyydkr...lierprqlpelfphlskenlvivvsgsgsgkgfs.vlvtdlipdlhlls...krggq 148
                                       +ilYRPFd++w++ d+r   ++ +pr  +++++h++++nl+++++++ s + f+ ++vt++ +d +++s   ++ ++
  gi|386000854|ref|YP_005919153.1| 190 PILYRPFDNRWTVIDDRskgFVAYPR--FDVMRHMKNNNLGLILTRQLSLSTFQhAWVTQNAIDGNTISlqtREYNY 264
                                       *****************9********..*******************99999999****************99**** PP

                        Type_ISP_C 149 vfPlylyeeee.snlaag............erkdnitdellaefrea...........yggatitkedifyYiYAvl 201
                                       +fPlyly++ + ++ +++             r +n+++e++a f+e+           +++at+ +ed+f+YiYAv+
  gi|386000854|ref|YP_005919153.1| 265 LFPLYLYPTPTeDSSRQKsfssadwppgkdGRVPNLSPEFVADFAEKlglsfvpdgrgDSEATFGPEDVFDYIYAVF 341
                                       **********964444448999******************************************************* PP

                        Type_ISP_C 202 hspeYrerYaedLkkdlpRiPltkdfelFkelvelGreLadLhlnyesepleegietepeegdnrvek..mkykk.. 274
                                       hsp+YrerYae+Lk+d+pR+Plt+d+++F++lvelG eL++Lhl+ es+ l + ++++p  gdnrvek  +ky +  
  gi|386000854|ref|YP_005919153.1| 342 HSPSYRERYAEFLKIDFPRVPLTSDRKKFRRLVELGGELVALHLL-ESPLLARPATRYPVVGDNRVEKgyPKYFApg 417
                                       *********************************************.**********************88888889* PP

                        Type_ISP_C 275 ............kkdkgtiiindeitlegvpeeaweYkvgGksale.Wlkdrykrktdkasgilndpnewakleete 338
                                                     + g+++in+++++egvp+++we++vgG+++++ Wlkdr++r++++++  ++++  +a l+et+
  gi|386000854|ref|YP_005919153.1| 418 egepgskagdgaVLEVGRVYINRSQYFEGVPPQVWEFQVGGYQVCDkWLKDRRGRQLSYDDLTVYQKVVVA-LKETI 493
                                       **********9999*********************************************988887777777.***** PP

                        Type_ISP_C 339 ellel 343
                                       +l+e+
  gi|386000854|ref|YP_005919153.1| 494 RLMEE 498
                                       ***85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3429.03
//
Query:       gi|386000855|ref|YP_005919154.1|  [L=593]
Description: hypothetical protein Mhar_0140 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-10   38.3   0.0     0.0017   17.6   0.0    2.7  2  N6_Mtase      N-6 DNA Methylase
     0.0007   19.3   0.0        0.9    9.2   0.0    3.2  3  UPF0020       Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.029   14.9   0.0      0.049   14.1   0.0    1.4  1  Eco57I        Eco57I restriction-modification methylase
      0.038   13.4   0.0      0.067   12.6   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
      0.096   13.2   0.0       0.23   12.0   0.0    1.6  1  Phage_tail_T  Minor tail protein T


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.9e-07    0.0017       2      44 ..     297     339 ..     296     355 .. 0.91
   2 !   17.4   0.0   5.9e-07    0.0021      36     137 ..     376     528 ..     369     565 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-07
                          N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellep 44 
                                       ++d + + YE +l  +  +  ++ G ++TP+ v++ iv+ +++
  gi|386000855|ref|YP_005919154.1| 297 QEDPVVHFYETFLAAYDPKLRERRGVYYTPEPVVSYIVRSVDS 339
                                       6788889*******************************98875 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.9e-07
                          N6_Mtase  36 klivellepksgesvyDpacGsggllvqaekvlkee.............dgktkelsiyGqeknettyrLa..kmNl 97 
                                       kl  ++++++++  ++DpacG+g +l  + ++++++               ++    i+G e+   +y++a  k+ +
  gi|386000855|ref|YP_005919154.1| 376 KLPERVTKTSPKVLILDPACGTGTFLYAVIDHIRQDfmahgnagywsayVRDHLLPRIFGFELLMAPYAVAhfKLGM 452
                                       55567889999999*******************98899999999998877777778899*99999999999444678 PP

                          N6_Mtase  98 llhgieykkvk...............irlgdtlekpkfe.....................kdkkfdvvvaNppfnq 137
                                       +l g +  +++               + l +tle+ +                        d+ + vv+ Npp+++
  gi|386000855|ref|YP_005919154.1| 453 MLAGQDLPEAErgdwiydfksderlgVYLTNTLEEAENPwknlwgyeaigreaqsasvmkRDRPIMVVIGNPPYSN 528
                                       8888887765555555555555555555555555444446667777777777777777776777777777777765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0067        24     121     166 ..     283     325 ..     267     333 .. 0.81
   2 !    9.2   0.0   0.00025       0.9      25      43 ..     383     401 ..     380     403 .. 0.82
   3 ?    1.1   0.0     0.074   2.7e+02     112     132 ..     507     527 ..     489     543 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0067
                                       ---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEEEE CS
                           UPF0020 121 evdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvllt 166
                                       + d+++++  +G+r++++  + ++Y+ fl +    lr+  r v+ t
  gi|386000855|ref|YP_005919154.1| 283 DLDSVLAD--FGKRTKQEDPVVHFYETFLAAYDPKLRE-RRGVYYT 325
                                       57777777..8**********************99999.5666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00025
                                       T--TTS-EEETT-TTSHHH CS
                           UPF0020  25 gwkpgepllDPmCGsGtil 43 
                                       +  p   +lDP CG+Gt+l
  gi|386000855|ref|YP_005919154.1| 383 KTSPKVLILDPACGTGTFL 401
                                       55667789*********97 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.074
                                       GGG--STTS---EEEE----- CS
                           UPF0020 112 aakLrlkegevdvivtnpPYG 132
                                        a++ +++  + v+++npPY 
  gi|386000855|ref|YP_005919154.1| 507 SASVMKRDRPIMVVIGNPPYS 527
                                       4444446668899*******6 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.049       4      64 ..     518     577 ..     511     593 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                            Eco57I   4 dviiGNPPYqeseakkelkaleekakdiyqkFvekalkledkylaliiparflasgkglke 64 
                                        v+iGNPPY +   +++++    + kd  ++  ek l+l+d ++ +i   ++   ++++  
  gi|386000855|ref|YP_005919154.1| 518 MVVIGNPPYSNFGRMNRGEWILDQLKDYKKDLNEKKLNLDDDFIKFIRWGQWR-IEQTGYG 577
                                       59*********998888888899899988999999***********9999997.4444444 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05     0.067     113     146 ..     375     410 ..     372     417 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                           UPRTase 113 nkLPkki..aertvlllDpviaTGgsaaaaiqlLke 146
                                       +kLP+++  ++ +vl+lDp + TG  + a+i+++++
  gi|386000855|ref|YP_005919154.1| 375 SKLPERVtkTSPKVLILDPACGTGTFLYAVIDHIRQ 410
                                       59****9666667*********************98 PP

>> Phage_tail_T  Minor tail protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.5e-05      0.23       1      75 [.     164     245 ..     164     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                      Phage_tail_T   1 klarefrrPdwrrmlaemsstelgewaeffsensfsdall...daefstlkal..vlslvtdk..eldaddfsllsa 70 
                                       +lare++r   ++  ++++stel + ++ f e    d+ l    aef+ + ++  v +l++ +  +  ++ f+ l a
  gi|386000855|ref|YP_005919154.1| 164 RLAREIQRAVVKAFEQDLASTELRNLRRAFAEVLIPDLDLpekTAEFADMYSQtiVYGLFAARcnHAGPEPFRRLGA 240
                                       79***********************************9994445899998654227788887511455678888877 PP

                      Phage_tail_T  71 peave 75 
                                       + ++ 
  gi|386000855|ref|YP_005919154.1| 241 ARSIP 245
                                       77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3728.43
//
Query:       gi|386000856|ref|YP_005919155.1|  [L=133]
Description: putative nucleic acid-binding protein, contains PIN domain [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.9   0.9    1.9e-16   60.6   0.9    1.0  1  PIN       PIN domain
     0.0012   18.5   0.0     0.0026   17.5   0.0    1.6  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.9   2.2e-20   1.9e-16       1     119 [.       2     120 ..       2     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.2e-20
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                       +++D++v+++ll ++e+ae++++ l+ +  +el++++ +++ + ++ +r + k e  ++++ + l+ s++k ++++ 
  gi|386000856|ref|YP_005919155.1|   2 YLVDSNVWLELLLEQERAEEVAQFLQIVgtDELWITEFTIYSIGIIMTR-LNKDEIFEDFLSDVLEDSGVKRVCLSI 77 
                                       68***********************999*********************.6666666666666666*********** PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                       ++++++ ++a+k +l+  Da+ ++ A+++++ l+ +fD df+r+
  gi|386000856|ref|YP_005919155.1|  78 GDLKQVIQVARKFRLDFDDAYQYVAAEKNDLCLV-SFDADFDRA 120
                                       *******************************988.*******97 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.9e-07    0.0026      24      72 ..      83     131 ..      70     133 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-07
                           DUF5615  24 vlhvrelglegasDeeileyAkeedriivTkDkDFgellllggpppgvi 72 
                                       v++v +      +D      A+++d+++v++D+DF +  + +++p  ++
  gi|386000856|ref|YP_005919155.1|  83 VIQVARKFRLDFDDAYQYVAAEKNDLCLVSFDADFDRAEMGRRTPSEIL 131
                                       5666555555689999999****************88766666666765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 829.44
//
Query:       gi|386000857|ref|YP_005919156.1|  [L=299]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-07   30.5   0.0    2.4e-06   28.0   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
     0.0032   17.7   0.1     0.0052   17.1   0.1    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.6e-10   2.4e-06       2     115 ..      75     182 ..      74     212 .. 0.80
   2 ?    0.1   0.0      0.11   9.5e+02     118     144 ..     270     295 ..     234     299 .] 0.77

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.6e-10
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +++ gCnl+C+fC+++   +  g gr++s  +++e +  l a+ g+++v ++  + ++ p + e+l ++ +    g+
  gi|386000857|ref|YP_005919156.1|  75 IFMTGCNLDCVFCQNYDI-SHLGEGREVSATKLAEMMVCL-ADGGCHNVNFVTPTHFV-PQILEALVEATEM---GL 145
                                       799*************97.99*******************.8999*********9999.9999999999998...77 PP

                                       EEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd.eeklerllelgvdrvslgleaadde 115
                                       ++ ++ n +  d  e l++l+   +d +  +++ ++d 
  gi|386000857|ref|YP_005919156.1| 146 SVPLVYNSGGYDsVETLRLLDG-IFDIYMPDAKYGTDA 182
                                       7777777777664555555555.457777766666666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                                       HHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 118 lklmnrghtfeevlealeklreagikr 144
                                        +l  r+ t+ e+ ea+ ++r ag++r
  gi|386000857|ref|YP_005919156.1| 270 PELS-RPITLREYAEAVNLARVAGLDR 295
                                       4556.7789999999999999999985 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.8e-07    0.0052       9      48 ..      74     113 ..      66     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-07
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedl 48 
                                       ++f++gCnl C +C n ++    +g+e++ + l+e++  l
  gi|386000857|ref|YP_005919156.1|  74 TIFMTGCNLDCVFCQNYDISHLGEGREVSATKLAEMMVCL 113
                                       79**************************977766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2079.65
//
Query:       gi|386000858|ref|YP_005919157.1|  [L=609]
Description: hypothetical protein Mhar_0143 [Methanosaeta harundinacea 6Ac]
Scores for 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-187  598.2  68.3    1.8e-12   46.5   0.5   18.0 18  TPR_1            Tetratricopeptide repeat
   4.6e-165  535.1  95.8    5.2e-14   51.6   1.4   17.8 18  TPR_11           TPR repeat
   1.5e-161  511.9  67.4      7e-10   38.3   2.5   18.0 18  TPR_2            Tetratricopeptide repeat
   3.3e-129  421.3  68.1    3.1e-16   59.7   0.8   11.4 13  TPR_16           Tetratricopeptide repeat
   5.8e-124  394.2  49.9    3.7e-08   33.0   0.1   18.0 18  TPR_8            Tetratricopeptide repeat
   2.8e-119  381.3  49.0    7.3e-08   32.3   0.3   17.2 17  TPR_17           Tetratricopeptide repeat
      1e-86  278.1  60.4    1.3e-06   28.7   0.2   17.7 18  TPR_14           Tetratricopeptide repeat
    2.7e-78  258.3  38.5    2.2e-11   43.9   0.1   11.7 11  TPR_12           Tetratricopeptide repeat
    4.4e-65  216.1  61.1    3.8e-09   36.9   3.2   11.8 13  TPR_19           Tetratricopeptide repeat
    9.9e-54  175.5  45.8      0.011   15.7   0.1   17.4 17  TPR_7            Tetratricopeptide repeat
    1.7e-47  159.4  36.6    6.1e-07   29.5   1.0   10.8 13  TPR_9            Tetratricopeptide repeat
    6.6e-47  155.1  38.5     0.0059   17.2   0.6   17.6 18  TPR_6            Tetratricopeptide repeat
    8.4e-40  134.9  18.7    1.6e-07   31.4   0.6    8.5 10  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.6e-38  129.5  70.6     0.0087   15.9   0.1   17.2 17  TPR_10           Tetratricopeptide repeat
    1.4e-33  116.6  14.9    0.00035   19.6   0.0    8.8 10  NARP1            NMDA receptor-regulated protein 1
    1.1e-30  105.1  40.0       0.26   11.3   1.1   16.5 16  TPR_3            Tetratricopeptide repeat
    5.2e-24   84.1  69.6      0.088   12.9   0.2   17.8 18  MIT              MIT (microtubule interacting and transport) 
    3.9e-19   68.5  16.3         15    5.7   0.0   15.9 17  ANAPC5           Anaphase-promoting complex subunit 5
    5.4e-17   62.6  18.9    0.00063   20.2   0.3    7.4  9  BTAD             Bacterial transcriptional activator domain
    2.4e-15   56.8  55.1      0.091   12.5   0.2   14.0 17  TPR_21           Tetratricopeptide repeat-like domain
      1e-14   53.6   0.5        4.6    8.2   0.0   12.2  8  TPR_4            Tetratricopeptide repeat
    2.7e-14   53.5  17.4          1    9.4   0.0   13.3 12  DUF3856          Domain of Unknown Function (DUF3856)
    6.1e-14   52.1  30.4        2.1    8.1   0.0   14.4 16  DUF5113          Domain of unknown function (DUF5113)
    6.8e-13   47.9   1.0         32    5.1   0.0   13.1 12  PPR              PPR repeat
    5.7e-11   42.3  32.4        1.8    8.7   0.0   15.2 16  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    7.3e-11   42.0   4.2       0.11   11.9   0.0    7.8  7  TPR_MalT         MalT-like TPR region
    2.7e-10   40.5  28.1       0.25   11.3   0.1    9.6 11  Wzy_C_2          Virulence factor membrane-bound polymerase, 
      1e-09   37.6  18.0        5.3    6.6   0.0   12.3 12  SHNi-TPR         SHNi-TPR
    3.9e-08   32.8   2.7        5.5    6.0   0.0    8.3 11  Rota_NSP3        Rotavirus non-structural protein NSP3
    6.8e-08   32.2   0.0        4.8    6.8   0.0    7.7 11  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
    9.6e-08   32.0   0.0         16    5.5   0.0    8.0  8  DUF627           Protein of unknown function (DUF627)
    1.1e-07   31.5   4.8         70    3.4   0.0   10.8 12  BPS              BPS (Between PH and SH2)
    2.8e-07   30.2  10.9         11    5.6   0.0    8.6  8  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like
    4.2e-06   27.5   4.3    1.2e+02    3.5   0.0    9.3 11  TetR_C_15        Tetracyclin repressor-like, C-terminal domai
    5.7e-06   26.5   5.8         45    4.4   0.0    9.2  8  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    0.00016   21.0   0.0         13    5.2   0.0    4.1  3  DUF2917          Protein of unknown function (DUF2917)
    0.00017   21.6   1.5         32    4.7   0.0    6.2  4  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
     0.0002   20.7  21.7          4    6.6   0.0    8.5  4  FAT              FAT domain
    0.00023   21.6   9.1        7.1    7.1   0.0    7.3  7  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00034   20.9  22.8          5    7.5   0.8    7.9 11  TPR_20           Tetratricopeptide repeat
    0.00048   19.8   8.7         30    4.5   0.1    8.6  8  PPTA             Protein prenyltransferase alpha subunit repe
    0.00059   19.9   0.2         78    3.4   0.0    8.0 11  MAS20            MAS20 protein import receptor
     0.0008   19.2   3.8       0.27   11.1   0.1    6.8  7  TraD             Conjugal transfer protein TraD
    0.00083   18.9  36.7     0.0016   17.9   4.5    8.2  7  SNAP             Soluble NSF attachment protein, SNAP
     0.0012   19.0  20.5        9.4    6.5   0.0   10.2 13  DUF1510          Domain of unknown function (DUF1510)
     0.0018   18.0  21.8        9.7    5.9   0.7   10.3 12  RPN7             26S proteasome subunit RPN7
     0.0027   17.5  12.6        3.4    7.6   0.0    8.5  8  Imm31            Immunity protein 31
  ------ inclusion threshold ------
      0.015   14.9  19.2         24    4.4   0.1   10.2 12  4HB_MCP_1        Four helix bundle sensory module for signal 
      0.019   15.1   9.2    1.7e+02    2.5   0.0    8.9  9  PPR_2            PPR repeat family
       0.12   12.7   1.2    2.2e+02    2.3   0.0    5.6  4  Ig_2             Immunoglobulin domain
       0.37   10.2   5.5         12    5.2   0.0    4.7  5  Coatomer_E       Coatomer epsilon subunit
       0.44   10.0   5.6         10    5.5   0.2    4.2  6  DUF5112          Domain of unknown function (DUF5112)
       0.45   10.9  10.0         96    3.4   0.0    7.0  5  nos_propeller_2  Nitrous oxide reductase propeller repeat 2
        3.8    7.3  12.8         72    3.2   0.0    7.1  8  Big_3_4          Domain of unknown function


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.1e-06   0.00036      14      34 .]       2      22 ..       1      22 [. 0.95
   2 !   38.2   0.5   2.3e-12   7.6e-10       1      34 []      23      56 ..      23      56 .. 0.98
   3 !   40.7   0.4   3.7e-13   1.2e-10       1      34 []      57      90 ..      57      90 .. 0.97
   4 !   36.7   0.1   6.6e-12   2.2e-09       1      34 []      91     124 ..      91     124 .. 0.97
   5 !   30.9   0.2   4.5e-10   1.5e-07       3      33 ..     127     157 ..     125     158 .. 0.96
   6 !   32.8   0.1   1.1e-10   3.8e-08       1      34 []     159     192 ..     159     192 .. 0.96
   7 !   39.3   0.0     1e-12   3.3e-10       1      34 []     193     226 ..     193     226 .. 0.95
   8 !   46.5   0.5   5.4e-15   1.8e-12       1      34 []     227     260 ..     227     260 .. 0.97
   9 !   23.1   0.0   1.3e-07   4.4e-05       3      33 ..     263     293 ..     261     294 .. 0.92
  10 !   40.6   0.1     4e-13   1.3e-10       1      34 []     295     328 ..     295     328 .. 0.97
  11 !   42.8   0.1   8.2e-14   2.7e-11       1      34 []     329     362 ..     329     362 .. 0.97
  12 !   32.2   0.1   1.8e-10     6e-08       2      33 ..     364     395 ..     363     396 .. 0.95
  13 !   38.0   0.0   2.7e-12     9e-10       1      33 [.     397     429 ..     397     430 .. 0.97
  14 !   38.0   0.0   2.7e-12     9e-10       1      33 [.     431     463 ..     431     464 .. 0.97
  15 !   39.1   0.0   1.2e-12     4e-10       1      34 []     465     498 ..     465     498 .. 0.97
  16 !   44.2   3.2   2.8e-14   9.4e-12       3      34 .]     501     532 ..     499     532 .. 0.96
  17 !   44.2   0.2     3e-14   9.9e-12       2      34 .]     534     566 ..     534     566 .. 0.97
  18 !    8.0   0.2    0.0079       2.6       2      30 ..     568     596 ..     567     596 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-06
                                      TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 14 lgkydeAleyyekALelnPnn 34
                                      +g+y  A+e++++A++l+P++
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPEY 22
                                      9******************86 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 2.3e-12
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+a+y +G+++++ g+y eA+++y++A++l+P++
  gi|386000858|ref|YP_005919157.1| 23 ADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEY 56
                                      89******************************86 PP

  == domain 3  score: 40.7 bits;  conditional E-value: 3.7e-13
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a a++n+G+a+ ++g+yde +++y++A++l+P++
  gi|386000858|ref|YP_005919157.1| 57 ASAWNNKGLALDYQGNYDESIKAYDEAIRLDPEF 90
                                      78******************************86 PP

  == domain 4  score: 36.7 bits;  conditional E-value: 6.6e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a++n+G a+ ++g+y eA  ++++A++l+P++
  gi|386000858|ref|YP_005919157.1|  91 AAAWNNKGIALGNQGNYTEATRCFDEAIRLDPEY 124
                                       78******************************86 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 4.5e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+yn+G a+ + g+y  A+ +y++A++l+P+
  gi|386000858|ref|YP_005919157.1| 127 AWYNKGKALSERGNYTGAILAYDEAIRLDPE 157
                                       9*****************************7 PP

  == domain 6  score: 32.8 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+  +G a+f+ g+y eA++++++A++l+P++
  gi|386000858|ref|YP_005919157.1| 159 AAAWHKKGDALFERGNYTEAIQAFDEAIRLDPED 192
                                       78******************************86 PP

  == domain 7  score: 39.3 bits;  conditional E-value: 1e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a ++yn+G+a+  +g+y eA+ +y++A++l+P++
  gi|386000858|ref|YP_005919157.1| 193 ATTWYNKGVALGMQGNYAEAIPAYDEAIRLDPED 226
                                       568*****************************86 PP

  == domain 8  score: 46.5 bits;  conditional E-value: 5.4e-15
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++n+Gna+ +lgkydeA+ + +kA+el+P++
  gi|386000858|ref|YP_005919157.1| 227 ADAWNNRGNALNELGKYDEAIHALDKAIELDPED 260
                                       89******************************86 PP

  == domain 9  score: 23.1 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++n+G  +  +g+y eA++++++A++l+P+
  gi|386000858|ref|YP_005919157.1| 263 PWNNKGKPLWMKGNYTEAIQAFDEAIRLDPE 293
                                       5999999999********************7 PP

  == domain 10  score: 40.6 bits;  conditional E-value: 4e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+ n+G ++  +gkydeA+++y++A++l Pn+
  gi|386000858|ref|YP_005919157.1| 295 AVAWSNKGTVLADQGKYDEAIQAYDEAIRLHPNY 328
                                       68******************************97 PP

  == domain 11  score: 42.8 bits;  conditional E-value: 8.2e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++a+ n+G a++++g+y eA+++y++A++l+P+n
  gi|386000858|ref|YP_005919157.1| 329 VDAWINKGSALYEQGNYPEAIQAYDEAIRLDPDN 362
                                       58******************************98 PP

  == domain 12  score: 32.2 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++yn+Gna+ +lg+y e + +y++A++l+P+
  gi|386000858|ref|YP_005919157.1| 364 MTWYNKGNALSELGNYTEGILAYDEAIRLDPE 395
                                       68*****************************6 PP

  == domain 13  score: 38.0 bits;  conditional E-value: 2.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+++  +Gn ++ +gkydeA+++y++A++l+P+
  gi|386000858|ref|YP_005919157.1| 397 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 429
                                       799*****************************6 PP

  == domain 14  score: 38.0 bits;  conditional E-value: 2.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+++  +Gn ++ +gkydeA+++y++A++l+P+
  gi|386000858|ref|YP_005919157.1| 431 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 463
                                       799*****************************6 PP

  == domain 15  score: 39.1 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+++  +Gn ++ +gkydeA+++y++A++l+P++
  gi|386000858|ref|YP_005919157.1| 465 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEF 498
                                       799*****************************86 PP

  == domain 16  score: 44.2 bits;  conditional E-value: 2.8e-14
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+yn+Gna++++ kydeA+++y++A++lnP++
  gi|386000858|ref|YP_005919157.1| 501 AWYNKGNALYEQDKYDEAIQAYDEAIRLNPDY 532
                                       9*****************************97 PP

  == domain 17  score: 44.2 bits;  conditional E-value: 3e-14
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a++n+Gna+  +gkydeA+++y++A++l+P++
  gi|386000858|ref|YP_005919157.1| 534 EAWNNKGNALVMQGKYDEAIQAYDEAIRLDPEF 566
                                       69*****************************86 PP

  == domain 18  score: 8.0 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       + ++ +G+++ +lgk  eA e+y kA el
  gi|386000858|ref|YP_005919157.1| 568 YPWFSKGVVLEYLGKVAEANEAYAKAEEL 596
                                       669********************999765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.3   1.8e-10     6e-08       7      39 ..       2      34 ..       1      35 [. 0.97
   2 !   41.5   1.8   2.3e-13   7.7e-11       1      38 [.      30      67 ..      30      68 .. 0.96
   3 !   38.2   0.6   2.5e-12   8.2e-10       7      42 .]      70     105 ..      69     105 .. 0.98
   4 !   30.3   0.1   7.2e-10   2.4e-07       7      38 ..     104     135 ..     103     137 .. 0.96
   5 !   34.0   0.3   5.1e-11   1.7e-08       1      39 [.     132     170 ..     132     170 .. 0.96
   6 !   49.1   0.0   9.6e-16   3.2e-13       1      42 []     166     207 ..     166     207 .. 0.99
   7 !   37.2   1.7   5.2e-12   1.7e-09       7      38 ..     206     237 ..     205     240 .. 0.96
   8 !   38.7   0.4   1.7e-12   5.6e-10       1      42 []     234     275 ..     234     275 .. 0.95
   9 !   29.6   0.0   1.2e-09   4.1e-07       7      42 .]     274     309 ..     268     309 .. 0.97
  10 !   45.3   1.4   1.5e-14     5e-12       1      42 []     302     343 ..     302     343 .. 0.96
  11 !   51.6   1.0   1.6e-16   5.5e-14       1      42 []     336     377 ..     336     377 .. 0.97
  12 !   24.6   0.1   4.6e-08   1.5e-05       1      36 [.     370     405 ..     370     407 .. 0.94
  13 !   37.6   0.1   3.8e-12   1.3e-09       1      36 [.     404     439 ..     404     441 .. 0.94
  14 !   37.6   0.1   3.8e-12   1.3e-09       1      36 [.     438     473 ..     438     475 .. 0.94
  15 !   51.6   1.4   1.6e-16   5.2e-14       1      41 [.     472     512 ..     472     513 .. 0.98
  16 !   46.9   4.3   4.7e-15   1.6e-12       1      42 []     506     547 ..     506     547 .. 0.99
  17 !   41.7   0.1     2e-13   6.7e-11       1      39 [.     540     578 ..     540     581 .. 0.94
  18 ?    0.1   0.9         2   6.7e+02       7      23 ..     580     596 ..     579     596 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.8e-10
                            TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                                      qG+y+ Aiea+ +A++ldP++a+a+y  Gl++y
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPEYADAWYSKGLTLY 34
                                      8*****************************988 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 2.3e-13
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                      G  +y +G+y+eA++aY +A++ldP++a+a++n Gla+
  gi|386000858|ref|YP_005919157.1| 30 GLTLYYRGNYTEAVQAYDEAIRLDPEYASAWNNKGLAL 67
                                      7789*******************************996 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 2.5e-12
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       qG+y+e+i+aY +A++ldP++a a++n G a+ +qG
  gi|386000858|ref|YP_005919157.1|  70 QGNYDESIKAYDEAIRLDPEFAAAWNNKGIALGNQG 105
                                       9********************************998 PP

  == domain 4  score: 30.3 bits;  conditional E-value: 7.2e-10
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       qG+y+eA  ++ +A++ldP++a a+yn G+a+
  gi|386000858|ref|YP_005919157.1| 104 QGNYTEATRCFDEAIRLDPEYAGAWYNKGKAL 135
                                       8*****************************97 PP

  == domain 5  score: 34.0 bits;  conditional E-value: 5.1e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       G+a+ e+G+y++Ai aY +A++ldP+ a a+++ G+a++
  gi|386000858|ref|YP_005919157.1| 132 GKALSERGNYTGAILAYDEAIRLDPELAAAWHKKGDALF 170
                                       89999*******************************986 PP

  == domain 6  score: 49.1 bits;  conditional E-value: 9.6e-16
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       Gda++e+G+y+eAi+a+ +A++ldP++a+ +yn G+a+ +qG
  gi|386000858|ref|YP_005919157.1| 166 GDALFERGNYTEAIQAFDEAIRLDPEDATTWYNKGVALGMQG 207
                                       9**************************************998 PP

  == domain 7  score: 37.2 bits;  conditional E-value: 5.2e-12
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       qG+y eAi aY +A++ldP++a+a++n+G+a+
  gi|386000858|ref|YP_005919157.1| 206 QGNYAEAIPAYDEAIRLDPEDADAWNNRGNAL 237
                                       8*****************************97 PP

  == domain 8  score: 38.7 bits;  conditional E-value: 1.7e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+ e+Gky+eAi a+ kA++ldP++a  ++n G+ ++++G
  gi|386000858|ref|YP_005919157.1| 234 GNALNELGKYDEAIHALDKAIELDPEDAAPWNNKGKPLWMKG 275
                                       9**********************************9887776 PP

  == domain 9  score: 29.6 bits;  conditional E-value: 1.2e-09
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+y+eAi+a+ +A++ldP+ a a++n G +++ qG
  gi|386000858|ref|YP_005919157.1| 274 KGNYTEAIQAFDEAIRLDPELAVAWSNKGTVLADQG 309
                                       8********************************998 PP

  == domain 10  score: 45.3 bits;  conditional E-value: 1.5e-14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G ++ +qGky+eAi+aY +A++l P++++a+ n G a+y+qG
  gi|386000858|ref|YP_005919157.1| 302 GTVLADQGKYDEAIQAYDEAIRLHPNYVDAWINKGSALYEQG 343
                                       56789************************************9 PP

  == domain 11  score: 51.6 bits;  conditional E-value: 1.6e-16
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+yeqG+y+eAi+aY +A++ldPdna  +yn G+a+ ++G
  gi|386000858|ref|YP_005919157.1| 336 GSALYEQGNYPEAIQAYDEAIRLDPDNAMTWYNKGNALSELG 377
                                       89************************************9988 PP

  == domain 12  score: 24.6 bits;  conditional E-value: 4.6e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+a+ e+G+y+e i aY +A++ldP+ a+++   G+
  gi|386000858|ref|YP_005919157.1| 370 GNALSELGNYTEGILAYDEAIRLDPEEADVWVSKGN 405
                                       9*****************************988887 PP

  == domain 13  score: 37.6 bits;  conditional E-value: 3.8e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+ ++ qGky+eAi+aY +A++ldP+ a+++   G+
  gi|386000858|ref|YP_005919157.1| 404 GNSFRMQGKYDEAIQAYDEAIRLDPEEADVWVSKGN 439
                                       99****************************988887 PP

  == domain 14  score: 37.6 bits;  conditional E-value: 3.8e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+ ++ qGky+eAi+aY +A++ldP+ a+++   G+
  gi|386000858|ref|YP_005919157.1| 438 GNSFRMQGKYDEAIQAYDEAIRLDPEEADVWVSKGN 473
                                       99****************************988887 PP

  == domain 15  score: 51.6 bits;  conditional E-value: 1.6e-16
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       G+ ++ qGky+eAi+aY +A++ldP++a a+yn G+a+y+q
  gi|386000858|ref|YP_005919157.1| 472 GNSFRMQGKYDEAIQAYDEAIRLDPEFAGAWYNKGNALYEQ 512
                                       99*************************************98 PP

  == domain 16  score: 46.9 bits;  conditional E-value: 4.7e-15
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+yeq ky+eAi+aY +A++l+Pd+ ea++n G+a+ +qG
  gi|386000858|ref|YP_005919157.1| 506 GNALYEQDKYDEAIQAYDEAIRLNPDYKEAWNNKGNALVMQG 547
                                       9**************************************998 PP

  == domain 17  score: 41.7 bits;  conditional E-value: 2e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       G+a++ qGky+eAi+aY +A++ldP++a  ++  G+++ 
  gi|386000858|ref|YP_005919157.1| 540 GNALVMQGKYDEAIQAYDEAIRLDPEFAYPWFSKGVVLE 578
                                       9**********************************9987 PP

  == domain 18  score: 0.1 bits;  conditional E-value: 2
                            TPR_11   7 qGkyeeAieaYkkAlkl 23 
                                       +Gk  eA eaY kA +l
  gi|386000858|ref|YP_005919157.1| 580 LGKVAEANEAYAKAEEL 596
                                       79************886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.2e-06    0.0021      14      34 .]       2      22 ..       1      22 [. 0.94
   2 !   34.0   0.7   4.7e-11   1.6e-08       1      34 []      23      56 ..      23      56 .. 0.96
   3 !   35.2   0.3     2e-11   6.6e-09       1      33 [.      57      89 ..      57      90 .. 0.96
   4 !   31.8   0.1   2.5e-10   8.4e-08       1      34 []      91     124 ..      91     124 .. 0.96
   5 !   28.1   0.3   3.8e-09   1.2e-06       2      33 ..     126     157 ..     125     158 .. 0.95
   6 !   34.3   0.2   3.9e-11   1.3e-08       1      34 []     159     192 ..     159     192 .. 0.96
   7 !   32.8   0.0   1.1e-10   3.8e-08       2      34 .]     194     226 ..     193     226 .. 0.95
   8 !   33.3   0.4   8.3e-11   2.8e-08       1      34 []     227     260 ..     227     260 .. 0.97
   9 !   22.6   0.0   2.2e-07   7.3e-05       3      33 ..     263     293 ..     261     294 .. 0.90
  10 !   31.8   0.1   2.5e-10   8.2e-08       2      34 .]     296     328 ..     295     328 .. 0.95
  11 !   37.7   0.1   3.1e-12     1e-09       2      34 .]     330     362 ..     329     362 .. 0.97
  12 !   26.8   0.1     1e-08   3.4e-06       3      33 ..     365     395 ..     363     396 .. 0.95
  13 !   30.9   0.0     5e-10   1.6e-07       1      33 [.     397     429 ..     397     430 .. 0.95
  14 !   30.9   0.0     5e-10   1.6e-07       1      33 [.     431     463 ..     431     464 .. 0.95
  15 !   31.2   0.0   3.9e-10   1.3e-07       1      33 [.     465     497 ..     465     498 .. 0.95
  16 !   38.3   2.5   2.1e-12     7e-10       2      34 .]     500     532 ..     499     532 .. 0.95
  17 !   36.6   0.2   6.9e-12   2.3e-09       2      33 ..     534     565 ..     533     566 .. 0.97
  18 !   14.7   0.2   7.2e-05     0.024       2      30 ..     568     596 ..     567     597 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.2e-06
                             TPR_2 14 lgdyeeAleafekAleldPnn 34
                                      +g+y  A+eaf++A++ldP++
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPEY 22
                                      9******************85 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 4.7e-11
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+a+y  Gl +y++g+y eA++a+++A++ldP++
  gi|386000858|ref|YP_005919157.1| 23 ADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEY 56
                                      79******************************85 PP

  == domain 3  score: 35.2 bits;  conditional E-value: 2e-11
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPn 33
                                      a a++n Gla+ ++g+y+e ++a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 57 ASAWNNKGLALDYQGNYDESIKAYDEAIRLDPE 89
                                      679*****************************7 PP

  == domain 4  score: 31.8 bits;  conditional E-value: 2.5e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a++n G a+ ++g+y eA ++f++A++ldP++
  gi|386000858|ref|YP_005919157.1|  91 AAAWNNKGIALGNQGNYTEATRCFDEAIRLDPEY 124
                                       789*****************************85 PP

  == domain 5  score: 28.1 bits;  conditional E-value: 3.8e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        a+yn G+a+ ++g+y  A+ a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 126 GAWYNKGKALSERGNYTGAILAYDEAIRLDPE 157
                                       69*****************************7 PP

  == domain 6  score: 34.3 bits;  conditional E-value: 3.9e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a++  G+a++++g+y eA++af++A++ldP++
  gi|386000858|ref|YP_005919157.1| 159 AAAWHKKGDALFERGNYTEAIQAFDEAIRLDPED 192
                                       689*****************************86 PP

  == domain 7  score: 32.8 bits;  conditional E-value: 1.1e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                         +yn G a+  +g+y+eA+ a+++A++ldP++
  gi|386000858|ref|YP_005919157.1| 194 TTWYNKGVALGMQGNYAEAIPAYDEAIRLDPED 226
                                       68*****************************86 PP

  == domain 8  score: 33.3 bits;  conditional E-value: 8.3e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++n+G+a+ +lg+y+eA++a++kA+eldP++
  gi|386000858|ref|YP_005919157.1| 227 ADAWNNRGNALNELGKYDEAIHALDKAIELDPED 260
                                       79******************************86 PP

  == domain 9  score: 22.6 bits;  conditional E-value: 2.2e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++n G+ ++ +g+y eA++af++A++ldP+
  gi|386000858|ref|YP_005919157.1| 263 PWNNKGKPLWMKGNYTEAIQAFDEAIRLDPE 293
                                       5888888899********************7 PP

  == domain 10  score: 31.8 bits;  conditional E-value: 2.5e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+ n G +++ +g+y+eA++a+++A++l Pn+
  gi|386000858|ref|YP_005919157.1| 296 VAWSNKGTVLADQGKYDEAIQAYDEAIRLHPNY 328
                                       69*****************************96 PP

  == domain 11  score: 37.7 bits;  conditional E-value: 3.1e-12
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+ n G a+y++g+y eA++a+++A++ldP+n
  gi|386000858|ref|YP_005919157.1| 330 DAWINKGSALYEQGNYPEAIQAYDEAIRLDPDN 362
                                       79*****************************98 PP

  == domain 12  score: 26.8 bits;  conditional E-value: 1e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        +yn G+a+ +lg+y e + a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 365 TWYNKGNALSELGNYTEGILAYDEAIRLDPE 395
                                       7*****************************7 PP

  == domain 13  score: 30.9 bits;  conditional E-value: 5e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+++   G++ + +g+y+eA++a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 397 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 429
                                       689999**************************7 PP

  == domain 14  score: 30.9 bits;  conditional E-value: 5e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+++   G++ + +g+y+eA++a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 431 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 463
                                       689999**************************7 PP

  == domain 15  score: 31.2 bits;  conditional E-value: 3.9e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+++   G++ + +g+y+eA++a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 465 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 497
                                       689999**************************7 PP

  == domain 16  score: 38.3 bits;  conditional E-value: 2.1e-12
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+yn G+a+y++++y+eA++a+++A++l+P++
  gi|386000858|ref|YP_005919157.1| 500 GAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDY 532
                                       69*****************************96 PP

  == domain 17  score: 36.6 bits;  conditional E-value: 6.9e-12
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       ea++n G+a+  +g+y+eA++a+++A++ldP+
  gi|386000858|ref|YP_005919157.1| 534 EAWNNKGNALVMQGKYDEAIQAYDEAIRLDPE 565
                                       79*****************************7 PP

  == domain 18  score: 14.7 bits;  conditional E-value: 7.2e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       + ++  G ++++lg+ +eA ea+ kA el
  gi|386000858|ref|YP_005919157.1| 568 YPWFSKGVVLEYLGKVAEANEAYAKAEEL 596
                                       679***********************886 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   1.1   1.5e-13   4.9e-11      10      67 ..       2      56 ..       2      57 .. 0.97
   2 !   47.7   0.9   5.4e-15   1.8e-12       1      65 [.      27      88 ..      27      89 .. 0.97
   3 !   33.1   0.2   1.9e-10   6.5e-08       3      53 ..      63     110 ..      61     110 .. 0.97
   4 !   48.5   0.2     3e-15   9.9e-13       3      65 ..      97     156 ..      95     159 .. 0.96
   5 !   34.8   1.0   5.6e-11   1.9e-08      19      67 ..     147     192 ..     146     193 .. 0.97
   6 !   51.9   0.5   2.7e-16   8.9e-14       2      67 ..     164     226 ..     163     227 .. 0.97
   7 !   47.9   2.2   4.8e-15   1.6e-12       2      67 ..     198     260 ..     197     261 .. 0.91
   8 !   36.5   0.1   1.7e-11   5.5e-09       3      65 ..     233     292 ..     232     295 .. 0.95
   9 !   59.7   0.8   9.4e-19   3.1e-16       3      68 .]     301     363 ..     299     363 .. 0.97
  10 !   45.5   0.0   2.5e-14   8.4e-12       1      67 [.     367     430 ..     367     431 .. 0.97
  11 !   47.4   0.0   6.7e-15   2.2e-12       3      65 ..     437     496 ..     435     497 .. 0.95
  12 !   55.6   0.9   1.8e-17     6e-15       1      65 [.     503     564 ..     503     565 .. 0.98
  13 ?    2.5   0.1      0.69   2.3e+02       8      56 ..     578     596 ..     570     603 .. 0.56

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.5e-13
                            TPR_16 10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      +g+y+ A++a+++a+++d   P+ a+A++ +g+ ++ +g+++eA+++y++a+r +p +
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLD---PEYADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEY 56
                                      8*****************...*********************************9975 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 5.4e-15
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65
                                      + +++ ++++g+y++A+ a+++a+++d   P+ a A++++g+a+  qg+++e + +y++a+r +p
  gi|386000858|ref|YP_005919157.1| 27 YSKGLTLYYRGNYTEAVQAYDEAIRLD---PEYASAWNNKGLALDYQGNYDESIKAYDEAIRLDP 88
                                      678999*********************...*******************************9998 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 1.9e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       +++a+ ++g+yd+ ++a+++a+++d   P+ a+A++++g a+  qg+++eA
  gi|386000858|ref|YP_005919157.1|  63 KGLALDYQGNYDESIKAYDEAIRLD---PEFAAAWNNKGIALGNQGNYTEA 110
                                       7999*********************...*********************98 PP

  == domain 4  score: 48.5 bits;  conditional E-value: 3e-15
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++ a+ ++g+y++A + +++a+++d   P+ a A++++g a+ ++g++++A+ +y++a+r +p
  gi|386000858|ref|YP_005919157.1|  97 KGIALGNQGNYTEATRCFDEAIRLD---PEYAGAWYNKGKALSERGNYTGAILAYDEAIRLDP 156
                                       688999*******************...********************************999 PP

  == domain 5  score: 34.8 bits;  conditional E-value: 5.6e-11
                            TPR_16  19 aleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       a+++a+++d   P+ a+A+  +gda++++g+++eA++++++a+r +p +
  gi|386000858|ref|YP_005919157.1| 147 AYDEAIRLD---PELAAAWHKKGDALFERGNYTEAIQAFDEAIRLDPED 192
                                       79*******...***********************************87 PP

  == domain 6  score: 51.9 bits;  conditional E-value: 2.7e-16
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++a++++g+y++A+ a+++a+++d   P++a  ++++g+a+  qg++aeA+ +y++a+r +p +
  gi|386000858|ref|YP_005919157.1| 164 KKGDALFERGNYTEAIQAFDEAIRLD---PEDATTWYNKGVALGMQGNYAEAIPAYDEAIRLDPED 226
                                       579***********************...***********************************87 PP

  == domain 7  score: 47.9 bits;  conditional E-value: 4.8e-15
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++ a+  +g+y++A++a+++a+++d   P++a+A++++g+a+ ++g ++eA+ ++++a++ +p +
  gi|386000858|ref|YP_005919157.1| 198 NKGVALGMQGNYAEAIPAYDEAIRLD---PEDADAWNNRGNALNELGKYDEAIHALDKAIELDPED 260
                                       556667779*****************...************************8888888999987 PP

  == domain 8  score: 36.5 bits;  conditional E-value: 1.7e-11
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++a+ ++g+yd+A++al+ a+++d   P++a+ ++++g  ++ +g+++eA++++++a+r +p
  gi|386000858|ref|YP_005919157.1| 233 RGNALNELGKYDEAIHALDKAIELD---PEDAAPWNNKGKPLWMKGNYTEAIQAFDEAIRLDP 292
                                       6888889******************...********************************999 PP

  == domain 9  score: 59.7 bits;  conditional E-value: 9.4e-19
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++ ++++g+yd+A+ a+++a++++   P  ++A+ ++g a+++qg+++eA+++y++a+r +pd++
  gi|386000858|ref|YP_005919157.1| 301 KGTVLADQGKYDEAIQAYDEAIRLH---PNYVDAWINKGSALYEQGNYPEAIQAYDEAIRLDPDNA 363
                                       7899*********************...***********************************985 PP

  == domain 10  score: 45.5 bits;  conditional E-value: 2.5e-14
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++++a+ ++g+y++ + a+++a+++d   P+ a+ +  +g+++  qg ++eA+++y++a+r +p +
  gi|386000858|ref|YP_005919157.1| 367 YNKGNALSELGNYTEGILAYDEAIRLD---PEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEE 430
                                       789************************...**********************************976 PP

  == domain 11  score: 47.4 bits;  conditional E-value: 6.7e-15
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++++++ +g+yd+A+ a+++a+++d   P+ a+ +  +g+++  qg ++eA+++y++a+r +p
  gi|386000858|ref|YP_005919157.1| 437 KGNSFRMQGKYDEAIQAYDEAIRLD---PEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP 496
                                       5788888******************...********************************998 PP

  == domain 12  score: 55.6 bits;  conditional E-value: 1.8e-17
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++++a++++ +yd+A+ a+++a++++   Pd  eA++++g+a+  qg ++eA+++y++a+r +p
  gi|386000858|ref|YP_005919157.1| 503 YNKGNALYEQDKYDEAIQAYDEAIRLN---PDYKEAWNNKGNALVMQGKYDEAIQAYDEAIRLDP 564
                                       789************************...********************************998 PP

  == domain 13  score: 2.5 bits;  conditional E-value: 0.69
                            TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaal 56 
                                                                      +lg +a ++  +a+A++l
  gi|386000858|ref|YP_005919157.1| 578 E------------------------------YLGKVAEANEAYAKAEEL 596
                                       3..............................455555555555555544 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00021     0.069      14      33 ..       2      21 ..       2      22 .. 0.94
   2 !   25.2   0.3   3.4e-08   1.1e-05       1      33 [.      23      55 ..      23      56 .. 0.96
   3 !   29.5   0.2   1.4e-09   4.6e-07       1      33 [.      57      89 ..      57      90 .. 0.96
   4 !   22.2   0.0   3.2e-07   0.00011       1      33 [.      91     123 ..      91     124 .. 0.95
   5 !   22.7   0.1   2.2e-07   7.2e-05       1      33 [.     125     157 ..     125     158 .. 0.95
   6 !   28.1   0.0   4.1e-09   1.4e-06       1      34 []     159     192 ..     159     192 .. 0.95
   7 !   23.4   0.0   1.3e-07   4.2e-05       1      34 []     193     226 ..     193     226 .. 0.95
   8 !   33.0   0.1   1.1e-10   3.7e-08       1      34 []     227     260 ..     227     260 .. 0.96
   9 !   17.4   0.0     1e-05    0.0035       4      33 ..     264     293 ..     261     294 .. 0.91
  10 !   22.1   0.0   3.3e-07   0.00011       3      33 ..     297     327 ..     295     328 .. 0.93
  11 !   26.8   0.0   1.1e-08   3.6e-06       2      34 .]     330     362 ..     329     362 .. 0.96
  12 !   24.1   0.0   7.7e-08   2.6e-05       4      33 ..     366     395 ..     364     396 .. 0.96
  13 !   21.6   0.0   4.7e-07   0.00016       1      33 [.     397     429 ..     397     430 .. 0.95
  14 !   21.6   0.0   4.7e-07   0.00016       1      33 [.     431     463 ..     431     464 .. 0.95
  15 !   21.8   0.0   4.3e-07   0.00014       1      33 [.     465     497 ..     465     498 .. 0.95
  16 !   29.2   1.2   1.8e-09   5.8e-07       1      34 []     499     532 ..     499     532 .. 0.95
  17 !   26.8   0.1   1.1e-08   3.6e-06       2      33 ..     534     565 ..     533     566 .. 0.96
  18 ?    7.5   0.1     0.016       5.3       4      30 ..     570     596 ..     567     596 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00021
                                      TT-HHHHHHHHHHHHHHHHH CS
                             TPR_8 14 lgdyeeAkeyyekaleldpd 33
                                      +g+y +A+e++ +a++ldp+
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPE 21
                                      59*****************8 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 3.4e-08
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+a+y +g+++   g+y eA+++y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 23 ADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPE 55
                                      78******************************8 PP

  == domain 3  score: 29.5 bits;  conditional E-value: 1.4e-09
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+a++n+g++++ +g+y+e++++y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 57 ASAWNNKGLALDYQGNYDESIKAYDEAIRLDPE 89
                                      689*****************************7 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 3.2e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a++n+g ++ ++g+y eA  ++ +a++ldp+
  gi|386000858|ref|YP_005919157.1|  91 AAAWNNKGIALGNQGNYTEATRCFDEAIRLDPE 123
                                       579*****************************8 PP

  == domain 5  score: 22.7 bits;  conditional E-value: 2.2e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a+yn+g+++++ g+y  A+ +y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 125 AGAWYNKGKALSERGNYTGAILAYDEAIRLDPE 157
                                       569****************************96 PP

  == domain 6  score: 28.1 bits;  conditional E-value: 4.1e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a a++++g+++++ g+y eA++++ +a++ldp++
  gi|386000858|ref|YP_005919157.1| 159 AAAWHKKGDALFERGNYTEAIQAFDEAIRLDPED 192
                                       579*****************************86 PP

  == domain 7  score: 23.4 bits;  conditional E-value: 1.3e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a  +yn+g ++  +g+y eA+ +y +a++ldp++
  gi|386000858|ref|YP_005919157.1| 193 ATTWYNKGVALGMQGNYAEAIPAYDEAIRLDPED 226
                                       568*****************************86 PP

  == domain 8  score: 33.0 bits;  conditional E-value: 1.1e-10
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a++n g+++ +lg+y+eA+ ++ ka+eldp++
  gi|386000858|ref|YP_005919157.1| 227 ADAWNNRGNALNELGKYDEAIHALDKAIELDPED 260
                                       78******************************86 PP

  == domain 9  score: 17.4 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++n+g+ ++ +g+y eA++++ +a++ldp+
  gi|386000858|ref|YP_005919157.1| 264 WNNKGKPLWMKGNYTEAIQAFDEAIRLDPE 293
                                       8899999999******************96 PP

  == domain 10  score: 22.1 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ n+g ++ ++g+y+eA+++y +a++l p+
  gi|386000858|ref|YP_005919157.1| 297 AWSNKGTVLADQGKYDEAIQAYDEAIRLHPN 327
                                       899************************9887 PP

  == domain 11  score: 26.8 bits;  conditional E-value: 1.1e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+ n+gs++ ++g+y eA+++y +a++ldpdn
  gi|386000858|ref|YP_005919157.1| 330 DAWINKGSALYEQGNYPEAIQAYDEAIRLDPDN 362
                                       79*****************************97 PP

  == domain 12  score: 24.1 bits;  conditional E-value: 7.7e-08
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +yn+g+++++lg+y e + +y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 366 WYNKGNALSELGNYTEGILAYDEAIRLDPE 395
                                       *****************************7 PP

  == domain 13  score: 21.6 bits;  conditional E-value: 4.7e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++ +g+  + +g+y+eA+++y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 397 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 429
                                       689*****************************7 PP

  == domain 14  score: 21.6 bits;  conditional E-value: 4.7e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++ +g+  + +g+y+eA+++y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 431 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 463
                                       689*****************************7 PP

  == domain 15  score: 21.8 bits;  conditional E-value: 4.3e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++++ +g+  + +g+y+eA+++y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 465 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 497
                                       689*****************************7 PP

  == domain 16  score: 29.2 bits;  conditional E-value: 1.8e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a a+yn+g+++ ++ +y+eA+++y +a++l+pd+
  gi|386000858|ref|YP_005919157.1| 499 AGAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDY 532
                                       569*****************************85 PP

  == domain 17  score: 26.8 bits;  conditional E-value: 1.1e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea++n+g+++  +g+y+eA+++y +a++ldp+
  gi|386000858|ref|YP_005919157.1| 534 EAWNNKGNALVMQGKYDEAIQAYDEAIRLDPE 565
                                       79*****************************7 PP

  == domain 18  score: 7.5 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekalel 30 
                                       ++ +g +++ lg+  eA e+y ka el
  gi|386000858|ref|YP_005919157.1| 570 WFSKGVVLEYLGKVAEANEAYAKAEEL 596
                                       99*********************9775 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   1.1e-07   3.7e-05       2      34 .]      12      44 ..      11      44 .. 0.95
   2 !   23.1   0.4   1.8e-07   6.1e-05       1      33 [.      45      77 ..      45      78 .. 0.94
   3 !   23.1   0.2   1.9e-07   6.4e-05       1      32 [.      79     110 ..      79     112 .. 0.96
   4 !   24.1   0.0   9.1e-08     3e-05       1      32 [.     113     144 ..     113     145 .. 0.94
   5 !   20.6   0.1   1.2e-06   0.00039       1      34 []     147     180 ..     147     180 .. 0.97
   6 !   24.4   0.0   7.1e-08   2.3e-05       2      33 ..     182     213 ..     181     213 .. 0.95
   7 !   32.3   0.3   2.2e-10   7.3e-08       1      33 [.     215     247 ..     215     248 .. 0.96
   8 !   15.1   0.1   6.8e-05     0.023       2      32 ..     250     280 ..     249     282 .. 0.78
   9 !   25.4   0.0   3.5e-08   1.2e-05       2      34 .]     284     316 ..     283     316 .. 0.96
  10 !   28.4   0.1   3.7e-09   1.2e-06       1      34 []     317     350 ..     317     350 .. 0.97
  11 !   27.1   0.1   9.7e-09   3.2e-06       1      30 [.     351     380 ..     351     383 .. 0.94
  12 !   21.9   0.0   4.5e-07   0.00015       1      34 []     385     418 ..     385     418 .. 0.97
  13 !   21.9   0.0   4.5e-07   0.00015       1      34 []     419     452 ..     419     452 .. 0.97
  14 !   21.9   0.0   4.5e-07   0.00015       1      34 []     453     486 ..     453     486 .. 0.97
  15 !   26.7   0.5   1.4e-08   4.6e-06       1      34 []     487     520 ..     487     520 .. 0.97
  16 !   28.2   0.4   4.3e-09   1.4e-06       1      34 []     521     554 ..     521     554 .. 0.97
  17 !   15.9   0.0   3.7e-05     0.012       1      32 [.     555     586 ..     555     589 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.1e-07
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      + +a++ldP +ada++ ++ +l+ +G++ +A+q
  gi|386000858|ref|YP_005919157.1| 12 FDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQ 44
                                      889****************************87 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.8e-07
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      +y +a++ldP +a a+nn++ +l  +G++++ +
  gi|386000858|ref|YP_005919157.1| 45 AYDEAIRLDPEYASAWNNKGLALDYQGNYDESI 77
                                      599**************************9976 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 1.9e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +a++ldP  a a+nn++ +l ++G++ +A
  gi|386000858|ref|YP_005919157.1|  79 AYDEAIRLDPEFAAAWNNKGIALGNQGNYTEA 110
                                       599**************************988 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 9.1e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       ++ +a++ldP +a a++n++++l+++G++  A
  gi|386000858|ref|YP_005919157.1| 113 CFDEAIRLDPEYAGAWYNKGKALSERGNYTGA 144
                                       799*************************9877 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 1.2e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP  a a++ ++ +l ++G++ +A+q
  gi|386000858|ref|YP_005919157.1| 147 AYDEAIRLDPELAAAWHKKGDALFERGNYTEAIQ 180
                                       599*****************************98 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 7.1e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +a++ldP +a  ++n++++l ++G++++A+
  gi|386000858|ref|YP_005919157.1| 182 FDEAIRLDPEDATTWYNKGVALGMQGNYAEAI 213
                                       889***************************96 PP

  == domain 7  score: 32.3 bits;  conditional E-value: 2.2e-10
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a++ldP +ada+nn++++l ++G++++A+
  gi|386000858|ref|YP_005919157.1| 215 AYDEAIRLDPEDADAWNNRGNALNELGKYDEAI 247
                                       599****************************97 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 6.8e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + ka+eldP +a ++nn+++ l ++G++ +A
  gi|386000858|ref|YP_005919157.1| 250 LDKAIELDPEDAAPWNNKGKPLWMKGNYTEA 280
                                       579***************9855555555555 PP

  == domain 9  score: 25.4 bits;  conditional E-value: 3.5e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a++ldP  a+a+ n++++l+ +G++++A+q
  gi|386000858|ref|YP_005919157.1| 284 FDEAIRLDPELAVAWSNKGTVLADQGKYDEAIQ 316
                                       889****************************98 PP

  == domain 10  score: 28.4 bits;  conditional E-value: 3.7e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l+Pn++da+ n++ +l+++G++ +A+q
  gi|386000858|ref|YP_005919157.1| 317 AYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQ 350
                                       599*****************************97 PP

  == domain 11  score: 27.1 bits;  conditional E-value: 9.7e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                       +y +a++ldP+na  ++n++++l+++G++ 
  gi|386000858|ref|YP_005919157.1| 351 AYDEAIRLDPDNAMTWYNKGNALSELGNYT 380
                                       599************************986 PP

  == domain 12  score: 21.9 bits;  conditional E-value: 4.5e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP  ad++  +++ ++++G++++A+q
  gi|386000858|ref|YP_005919157.1| 385 AYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQ 418
                                       599*****************************98 PP

  == domain 13  score: 21.9 bits;  conditional E-value: 4.5e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP  ad++  +++ ++++G++++A+q
  gi|386000858|ref|YP_005919157.1| 419 AYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQ 452
                                       599*****************************98 PP

  == domain 14  score: 21.9 bits;  conditional E-value: 4.5e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP  ad++  +++ ++++G++++A+q
  gi|386000858|ref|YP_005919157.1| 453 AYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQ 486
                                       599*****************************98 PP

  == domain 15  score: 26.7 bits;  conditional E-value: 1.4e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP  a a++n++++l+++ ++++A+q
  gi|386000858|ref|YP_005919157.1| 487 AYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQ 520
                                       599*****************************98 PP

  == domain 16  score: 28.2 bits;  conditional E-value: 4.3e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l+P++ +a+nn++++l ++G++++A+q
  gi|386000858|ref|YP_005919157.1| 521 AYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQ 554
                                       599*****************************98 PP

  == domain 17  score: 15.9 bits;  conditional E-value: 3.7e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +a++ldP  a++++ ++++l+ +G+ ++A
  gi|386000858|ref|YP_005919157.1| 555 AYDEAIRLDPEFAYPWFSKGVVLEYLGKVAEA 586
                                       599*********************99998877 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00037      0.12      14      39 ..       2      27 ..       1      31 [. 0.93
   2 !   20.8   0.5   1.4e-06   0.00046       2      39 ..      24      61 ..      23      67 .. 0.92
   3 !   18.9   0.1   5.7e-06    0.0019      10      39 ..      66      95 ..      63     100 .. 0.88
   4 !   17.2   0.0     2e-05    0.0066      10      43 ..     100     133 ..      97     134 .. 0.90
   5 !   20.2   0.5   2.1e-06   0.00071       2      42 ..     126     166 ..     125     168 .. 0.93
   6 !   28.7   0.2     4e-09   1.3e-06       2      42 ..     160     200 ..     159     202 .. 0.93
   7 !   18.1   0.2     1e-05    0.0034      14      39 ..     206     231 ..     200     235 .. 0.91
   8 !   20.4   0.2   1.9e-06   0.00062       3      39 ..     229     265 ..     228     269 .. 0.90
   9 !   15.5   0.0   6.9e-05     0.023      11      38 ..     271     298 ..     271     303 .. 0.91
  10 !   23.5   0.1   1.9e-07   6.3e-05       8      42 ..     302     336 ..     298     338 .. 0.91
  11 !   22.8   0.0   3.1e-07    0.0001       8      41 ..     336     369 ..     334     372 .. 0.92
  12 !   15.5   0.0   6.7e-05     0.022       4      39 ..     366     401 ..     364     405 .. 0.92
  13 !   20.0   0.1   2.4e-06    0.0008       6      39 ..     402     435 ..     397     439 .. 0.86
  14 !   19.1   0.1   4.9e-06    0.0016      11      39 ..     441     469 ..     436     473 .. 0.90
  15 !   20.9   0.1   1.2e-06   0.00041      10      41 ..     474     505 ..     468     508 .. 0.88
  16 !   24.4   0.5   9.5e-08   3.1e-05       2      39 ..     500     537 ..     499     542 .. 0.92
  17 !   16.8   0.0   2.6e-05    0.0086       8      38 ..     540     570 ..     538     575 .. 0.88
  18 ?   -0.0   0.1       6.6   2.2e+03      10      29 ..     576     595 ..     569     597 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00037
                            TPR_14 14 lGdpdeAiallrralalaPddaeawl 39
                                      +G++  Ai+++++a++l+P+ a+aw+
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPEYADAWY 27
                                      799**********************7 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.4e-06
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawl 39
                                      +a++  +  l+ +G++ eA++++++a++l+P+ a aw 
  gi|386000858|ref|YP_005919157.1| 24 DAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEYASAWN 61
                                      79999*******************************95 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 5.7e-06
                            TPR_14 10 allalGdpdeAiallrralalaPddaeawl 39
                                      al  +G++de+i+++++a++l+P++a+aw 
  gi|386000858|ref|YP_005919157.1| 66 ALDYQGNYDESIKAYDEAIRLDPEFAAAWN 95
                                      66679************************6 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 2e-05
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlllaq 43 
                                       al ++G++ eA +++++a++l+P+ a aw+  ++
  gi|386000858|ref|YP_005919157.1| 100 ALGNQGNYTEATRCFDEAIRLDPEYAGAWYNKGK 133
                                       66689************************98876 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 2.1e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                        a++  ++al ++G++ +Ai ++++a++l+P+ a+aw   +
  gi|386000858|ref|YP_005919157.1| 126 GAWYNKGKALSERGNYTGAILAYDEAIRLDPELAAAWHKKG 166
                                       589999*******************************8776 PP

  == domain 6  score: 28.7 bits;  conditional E-value: 4e-09
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +a+ + ++al+++G++ eAi+++++a++l+P+da++w+  +
  gi|386000858|ref|YP_005919157.1| 160 AAWHKKGDALFERGNYTEAIQAFDEAIRLDPEDATTWYNKG 200
                                       79***********************************8765 PP

  == domain 7  score: 18.1 bits;  conditional E-value: 1e-05
                            TPR_14  14 lGdpdeAiallrralalaPddaeawl 39 
                                       +G+++eAi ++++a++l+P+da+aw 
  gi|386000858|ref|YP_005919157.1| 206 QGNYAEAIPAYDEAIRLDPEDADAWN 231
                                       8***********************95 PP

  == domain 8  score: 20.4 bits;  conditional E-value: 1.9e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a+  ++ al +lG++deAi +l++a++l+P+da+ w 
  gi|386000858|ref|YP_005919157.1| 229 AWNNRGNALNELGKYDEAIHALDKAIELDPEDAAPWN 265
                                       677799**************************99885 PP

  == domain 9  score: 15.5 bits;  conditional E-value: 6.9e-05
                            TPR_14  11 llalGdpdeAiallrralalaPddaeaw 38 
                                       l+  G++ eAi+++++a++l+P+ a+aw
  gi|386000858|ref|YP_005919157.1| 271 LWMKGNYTEAIQAFDEAIRLDPELAVAW 298
                                       5778***********************9 PP

  == domain 10  score: 23.5 bits;  conditional E-value: 1.9e-07
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + +l+ +G++deAi+++++a++l+P+  +aw+  +
  gi|386000858|ref|YP_005919157.1| 302 GTVLADQGKYDEAIQAYDEAIRLHPNYVDAWINKG 336
                                       56899**************************9765 PP

  == domain 11  score: 22.8 bits;  conditional E-value: 3.1e-07
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlll 41 
                                       ++al+++G++ eAi+++++a++l+Pd+a +w+  
  gi|386000858|ref|YP_005919157.1| 336 GSALYEQGNYPEAIQAYDEAIRLDPDNAMTWYNK 369
                                       689****************************876 PP

  == domain 12  score: 15.5 bits;  conditional E-value: 6.7e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ++  + al +lG++ e i ++++a++l+P++a++w 
  gi|386000858|ref|YP_005919157.1| 366 WYNKGNALSELGNYTEGILAYDEAIRLDPEEADVWV 401
                                       777899****************************96 PP

  == domain 13  score: 20.0 bits;  conditional E-value: 2.4e-06
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawl 39 
                                         +  ++ +G++deAi+++++a++l+P++a++w 
  gi|386000858|ref|YP_005919157.1| 402 SKGNSFRMQGKYDEAIQAYDEAIRLDPEEADVWV 435
                                       556778899***********************96 PP

  == domain 14  score: 19.1 bits;  conditional E-value: 4.9e-06
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawl 39 
                                       ++ +G++deAi+++++a++l+P++a++w 
  gi|386000858|ref|YP_005919157.1| 441 FRMQGKYDEAIQAYDEAIRLDPEEADVWV 469
                                       6779***********************96 PP

  == domain 15  score: 20.9 bits;  conditional E-value: 1.2e-06
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                                        ++ +G++deAi+++++a++l+P++a aw+  
  gi|386000858|ref|YP_005919157.1| 474 SFRMQGKYDEAIQAYDEAIRLDPEFAGAWYNK 505
                                       57789************************876 PP

  == domain 16  score: 24.4 bits;  conditional E-value: 9.5e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                        a++  + al++++++deAi+++++a++l+Pd  eaw 
  gi|386000858|ref|YP_005919157.1| 500 GAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDYKEAWN 537
                                       589999******************************96 PP

  == domain 17  score: 16.8 bits;  conditional E-value: 2.6e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                                       + al  +G++deAi+++++a++l+P++a  w
  gi|386000858|ref|YP_005919157.1| 540 GNALVMQGKYDEAIQAYDEAIRLDPEFAYPW 570
                                       578999*******************998666 PP

  == domain 18  score: -0.0 bits;  conditional E-value: 6.6
                            TPR_14  10 allalGdpdeAiallrrala 29 
                                       +l+ lG+ +eA +++ +a +
  gi|386000858|ref|YP_005919157.1| 576 VLEYLGKVAEANEAYAKAEE 595
                                       66677777777777777755 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.7   5.5e-07   0.00018      16      76 ..       2      54 ..       1      55 [. 0.90
   2 !   17.3   0.1   1.3e-05    0.0042       3      32 ..      57      86 ..      55      89 .. 0.79
   3 !   27.5   0.4   8.5e-09   2.8e-06       2      76 ..      90     156 ..      89     157 .. 0.92
   4 !   37.6   0.2     6e-12     2e-09       2      76 ..     158     224 ..     157     225 .. 0.93
   5 !   31.4   0.0   5.1e-10   1.7e-07       3      76 ..     227     292 ..     225     293 .. 0.94
   6 !   43.9   0.1   6.7e-14   2.2e-11       2      75 ..     294     359 ..     293     361 .. 0.91
   7 !   27.9   0.1   6.5e-09   2.2e-06       3      76 ..     363     428 ..     361     429 .. 0.92
   8 !   30.6   0.0   9.4e-10   3.1e-07       3      76 ..     397     462 ..     395     463 .. 0.91
   9 !   30.6   0.0   9.5e-10   3.2e-07       3      76 ..     431     496 ..     429     497 .. 0.91
  10 !   37.5   1.3   6.4e-12   2.1e-09       3      76 ..     499     564 ..     497     565 .. 0.92
  11 ?    2.3   0.0      0.63   2.1e+02      52      73 ..     574     595 ..     567     600 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.5e-07
                            TPR_12 16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                                      +g+y+ A+e +++a+++      p+   +a + +  g +++++g+y eA++++ ea+++++
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLD-----PE---YADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDP 54
                                      8*************7777.....76...5999999999999****************9975 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.3e-05
                            TPR_12  3 atalnnlaavlrrlgrydeAlellekalei 32
                                      a+a+nn +++l ++g+yde+++ +++a+++
  gi|386000858|ref|YP_005919157.1| 57 ASAWNNKGLALDYQGNYDESIKAYDEAIRL 86
                                      788888888888888888888888888765 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 8.5e-09
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a+a+nn + +l  +g+y+eA +++++a+++      p++   a + +n g +++++g+y  A+ ++ ea+++++
  gi|386000858|ref|YP_005919157.1|  90 FAAAWNNKGIALGNQGNYTEATRCFDEAIRLD-----PEY---AGAWYNKGKALSERGNYTGAILAYDEAIRLDP 156
                                       5899************************8888.....775...779*************************9975 PP

  == domain 4  score: 37.6 bits;  conditional E-value: 6e-12
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a+a+++ +++l+++g+y+eA++ +++a+++      p+    att +n g ++ ++g+y+eA+ ++ ea+++++
  gi|386000858|ref|YP_005919157.1| 158 LAAAWHKKGDALFERGNYTEAIQAFDEAIRLD-----PE---DATTWYNKGVALGMQGNYAEAIPAYDEAIRLDP 224
                                       7999*9**********************7777.....76...5****************************9975 PP

  == domain 5  score: 31.4 bits;  conditional E-value: 5.1e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a+nn++++l++lg+ydeA+  l+ka+e+      p+    a+  +n g  +++ g+y eA++++ ea+++++
  gi|386000858|ref|YP_005919157.1| 227 ADAWNNRGNALNELGKYDEAIHALDKAIELD-----PED---AAPWNNKGKPLWMKGNYTEAIQAFDEAIRLDP 292
                                       789************************9999.....875...99**************************9975 PP

  == domain 6  score: 43.9 bits;  conditional E-value: 6.7e-14
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a a++n ++vl+ +g+ydeA++ +++a++++        p+++ + +n g +++++g+y eA++++ ea++++
  gi|386000858|ref|YP_005919157.1| 294 LAVAWSNKGTVLADQGKYDEAIQAYDEAIRLH--------PNYVDAWINKGSALYEQGNYPEAIQAYDEAIRLD 359
                                       6899************************5555........55799**************************987 PP

  == domain 7  score: 27.9 bits;  conditional E-value: 6.5e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a +++n +++l +lg+y+e +  +++a+++      p+   +a +    g  +r++g+y+eA++++ ea+++++
  gi|386000858|ref|YP_005919157.1| 363 AMTWYNKGNALSELGNYTEGILAYDEAIRLD-----PE---EADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP 428
                                       67889**********************7777.....65...899**************************9975 PP

  == domain 8  score: 30.6 bits;  conditional E-value: 9.4e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a +++  ++  r +g+ydeA++ +++a+++      p+   +a +    g  +r++g+y+eA++++ ea+++++
  gi|386000858|ref|YP_005919157.1| 397 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLD-----PE---EADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP 462
                                       7788899********************7777.....65...899**************************9975 PP

  == domain 9  score: 30.6 bits;  conditional E-value: 9.5e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a +++  ++  r +g+ydeA++ +++a+++      p+   +a +    g  +r++g+y+eA++++ ea+++++
  gi|386000858|ref|YP_005919157.1| 431 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLD-----PE---EADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP 496
                                       7788899********************7777.....65...899**************************9975 PP

  == domain 10  score: 37.5 bits;  conditional E-value: 6.4e-12
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a++n +++l+++ +ydeA++ +++a+++      pd+    ++ +n g ++ ++g+y+eA++++ ea+++++
  gi|386000858|ref|YP_005919157.1| 499 AGAWYNKGNALYEQDKYDEAIQAYDEAIRLN-----PDY---KEAWNNKGNALVMQGKYDEAIQAYDEAIRLDP 564
                                       66899**********************7777.....885...89**************************9975 PP

  == domain 11  score: 2.3 bits;  conditional E-value: 0.63
                            TPR_12  52 grlyralgryeeAlelleeala 73 
                                       g ++++lg+ +eA e++ +a +
  gi|386000858|ref|YP_005919157.1| 574 GVVLEYLGKVAEANEAYAKAEE 595
                                       4445555555555555555544 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   1.1   1.6e-07   5.2e-05       4      58 ..       2      56 ..       1      60 [. 0.93
   2 !   22.2   1.3   4.6e-07   0.00015       1      60 [.      33      92 ..      33      95 .. 0.93
   3 !   24.3   0.1     1e-07   3.3e-05       4      57 ..      70     123 ..      67     128 .. 0.95
   4 !   24.0   0.1   1.2e-07     4e-05       4      61 ..     104     162 ..     101     166 .. 0.92
   5 !   26.6   0.3     2e-08   6.5e-06       3      59 ..     137     193 ..     135     200 .. 0.95
   6 !   36.9   3.2   1.1e-11   3.8e-09       3      60 ..     205     262 ..     203     266 .. 0.95
   7 !   23.1   0.8   2.4e-07   7.9e-05       2      57 ..     272     327 ..     271     331 .. 0.94
   8 !   30.4   0.7   1.3e-09   4.2e-07       1      46 [.     305     350 ..     305     351 .. 0.96
   9 !   31.3   0.4   6.6e-10   2.2e-07       1      62 [.     339     400 ..     339     403 .. 0.96
  10 !   26.5   1.2     2e-08   6.6e-06       3      62 ..     409     468 ..     407     471 .. 0.96
  11 !   36.2   3.6   1.9e-11   6.4e-09       3      61 ..     477     535 ..     475     542 .. 0.93
  12 !   35.2   2.1     4e-11   1.3e-08       1      57 [.     509     565 ..     509     571 .. 0.95
  13 !   16.2   0.2   3.4e-05     0.011       1      51 [.     543     593 ..     543     598 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.6e-07
                            TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                                      +g+y+ A++++ +a+  dp++a+a++     l+  g+++eA ++ d++ + dp  
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEY 56
                                      9*************************************************99984 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 4.6e-07
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60
                                      l+++g+y+eA++++ +a+  dp++a a+ +   al  +g++de +++ d++ + dp  a+
  gi|386000858|ref|YP_005919157.1| 33 LYYRGNYTEAVQAYDEAIRLDPEYASAWNNKGLALDYQGNYDESIKAYDEAIRLDPEFAA 92
                                      6789*************************************************9998655 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 1e-07
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +g+y+e ++++ +a+  dp+ a+a+ +  +al ++g+++eA ++ d++ + dp 
  gi|386000858|ref|YP_005919157.1|  70 QGNYDESIKAYDEAIRLDPEFAAAWNNKGIALGNQGNYTEATRCFDEAIRLDPE 123
                                       9***********************************************999997 PP

  == domain 4  score: 24.0 bits;  conditional E-value: 1.2e-07
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ary 61 
                                       +g+y+eA + + +a+  dp++a a+++  +al + g+++ A+ + d++ + dp   a++
  gi|386000858|ref|YP_005919157.1| 104 QGNYTEATRCFDEAIRLDPEYAGAWYNKGKALSERGNYTGAILAYDEAIRLDPELaAAW 162
                                       8***************************************************9963444 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 2e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       ++g+y+ A+ ++ +a+  dp+ a+a+    +al++ g+++eA+++ d++ + dp da
  gi|386000858|ref|YP_005919157.1| 137 ERGNYTGAILAYDEAIRLDPELAAAWHKKGDALFERGNYTEAIQAFDEAIRLDPEDA 193
                                       79****************************************************985 PP

  == domain 6  score: 36.9 bits;  conditional E-value: 1.1e-11
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       ++g+yaeA++++ +a+  dp++a+a+ +  +al +lg +deA+ +Ld++ e dp da+
  gi|386000858|ref|YP_005919157.1| 205 MQGNYAEAIPAYDEAIRLDPEDADAWNNRGNALNELGKYDEAIHALDKAIELDPEDAA 262
                                       59****************************************************9964 PP

  == domain 7  score: 23.1 bits;  conditional E-value: 2.4e-07
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++ g+y+eA++++ +a+  dp+ a a+ +   +l  +g +deA+++ d++ +  p+
  gi|386000858|ref|YP_005919157.1| 272 WMKGNYTEAIQAFDEAIRLDPELAVAWSNKGTVLADQGKYDEAIQAYDEAIRLHPN 327
                                       678**********************************************9999998 PP

  == domain 8  score: 30.4 bits;  conditional E-value: 1.3e-09
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       l ++g+y+eA++++ +a+   p++ +a+++   al+++g++ eA++
  gi|386000858|ref|YP_005919157.1| 305 LADQGKYDEAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQ 350
                                       679*****************************************97 PP

  == domain 9  score: 31.3 bits;  conditional E-value: 6.6e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l+++g+y eA++++ +a+  dp+na  +++  +al +lg+++e + + d++ + dp +a+++
  gi|386000858|ref|YP_005919157.1| 339 LYEQGNYPEAIQAYDEAIRLDPDNAMTWYNKGNALSELGNYTEGILAYDEAIRLDPEEADVW 400
                                       789*****************************************************998876 PP

  == domain 10  score: 26.5 bits;  conditional E-value: 2e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       ++g+y+eA++++ +a+  dp+ a+++    +    +g +deA+++ d++ + dp +a+++
  gi|386000858|ref|YP_005919157.1| 409 MQGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEEADVW 468
                                       79****************************************************998886 PP

  == domain 11  score: 36.2 bits;  conditional E-value: 1.9e-11
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       ++g+y+eA++++ +a+  dp+ a a+++  +al+++  +deA+++ d++ + +pd  ++
  gi|386000858|ref|YP_005919157.1| 477 MQGKYDEAIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDYKEA 535
                                       79*****************************************************7544 PP

  == domain 12  score: 35.2 bits;  conditional E-value: 4e-11
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l+++ +y+eA++++ +a+  +p++ ea+ +  +al+ +g +deA+++ d++ + dp 
  gi|386000858|ref|YP_005919157.1| 509 LYEQDKYDEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEAIRLDPE 565
                                       789************************************************999997 PP

  == domain 13  score: 16.2 bits;  conditional E-value: 3.4e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       l+++g+y+eA++++ +a+  dp+ a+ +     +l  lg ++eA ++ +++
  gi|386000858|ref|YP_005919157.1| 543 LVMQGKYDEAIQAYDEAIRLDPEFAYPWFSKGVVLEYLGKVAEANEAYAKA 593
                                       689********************9999998888888888888888876655 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.079        26      12      33 ..       2      21 ..       2      22 .. 0.91
   2 ?    7.2   0.3     0.017       5.6       6      33 ..      30      55 ..      25      56 .. 0.80
   3 !   13.7   0.1   0.00015     0.049       1      33 [.      59      89 ..      59      92 .. 0.92
   4 !   11.0   0.0    0.0011      0.35       1      33 [.      93     123 ..      93     123 .. 0.93
   5 !   11.0   0.1     0.001      0.35       1      33 [.     127     157 ..     127     160 .. 0.92
   6 !   14.5   0.0   8.1e-05     0.027       2      36 .]     162     194 ..     161     194 .. 0.90
   7 !   12.9   0.0   0.00026     0.085       2      35 ..     196     227 ..     195     228 .. 0.87
   8 !   15.7   0.1   3.3e-05     0.011       1      35 [.     229     261 ..     229     262 .. 0.94
   9 ?    5.4   0.0     0.065        21      13      33 ..     275     293 ..     271     296 .. 0.88
  10 !   13.4   0.0   0.00018     0.061       1      30 [.     297     324 ..     297     327 .. 0.84
  11 !   14.5   0.0   7.9e-05     0.026       1      34 [.     331     362 ..     331     364 .. 0.90
  12 ?    6.8   0.1     0.023       7.5       1      35 [.     365     397 ..     365     398 .. 0.90
  13 !   13.2   0.0   0.00021     0.068       6      35 ..     404     431 ..     399     432 .. 0.84
  14 !   13.2   0.0   0.00021     0.068       6      35 ..     438     465 ..     433     466 .. 0.84
  15 !   11.5   0.0   0.00072      0.24       6      33 ..     472     497 ..     467     499 .. 0.84
  16 !   10.6   0.2    0.0014      0.46       1      32 [.     501     530 ..     501     533 .. 0.87
  17 !   15.1   0.0   5.4e-05     0.018       1      33 [.     535     565 ..     535     568 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.079
                             TPR_7 12 lGdyeeAielyeqsLaltkdpe 33
                                      +G+y  Aie + +  a++ dpe
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDE--AIRLDPE 21
                                      7************..9998885 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.017
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdpe 33
                                      + +   +G+y eA++ y +  a++ dpe
  gi|386000858|ref|YP_005919157.1| 30 GLTLYYRGNYTEAVQAYDE--AIRLDPE 55
                                      5555668************..9998885 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00015
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33
                                      a++n + +   +G+y+e i+ y +  a++ dpe
  gi|386000858|ref|YP_005919157.1| 59 AWNNKGLALDYQGNYDESIKAYDE--AIRLDPE 89
                                      78999*******************..9999997 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.0011
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++n + +  ++G+y eA +++ +  a++ dpe
  gi|386000858|ref|YP_005919157.1|  93 AWNNKGIALGNQGNYTEATRCFDE--AIRLDPE 123
                                       78999*******************..9999885 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.001
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++n + + s++G+y  Ai  y +  a++ dpe
  gi|386000858|ref|YP_005919157.1| 127 AWYNKGKALSERGNYTGAILAYDE--AIRLDPE 157
                                       7899********************..9999987 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 8.1e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpedae 36 
                                       ++  +++ +++G+y eAi+ + +  a++ dpeda+
  gi|386000858|ref|YP_005919157.1| 162 WHKKGDALFERGNYTEAIQAFDE--AIRLDPEDAT 194
                                       566799*****************..******9985 PP

  == domain 7  score: 12.9 bits;  conditional E-value: 0.00026
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       ++n +++   +G+y+eAi  y +  a++ dpeda
  gi|386000858|ref|YP_005919157.1| 196 WYNKGVALGMQGNYAEAIPAYDE--AIRLDPEDA 227
                                       67777777779************..*****9986 PP

  == domain 8  score: 15.7 bits;  conditional E-value: 3.3e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++n +++  +lG+y+eAi  + +  a++ dpeda
  gi|386000858|ref|YP_005919157.1| 229 AWNNRGNALNELGKYDEAIHALDK--AIELDPEDA 261
                                       799*********************..999999987 PP

  == domain 9  score: 5.4 bits;  conditional E-value: 0.065
                             TPR_7  13 GdyeeAielyeqsLaltkdpe 33 
                                       G+y eAi+ + +  a++ dpe
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDE--AIRLDPE 293
                                       9***********..9999986 PP

  == domain 10  score: 13.4 bits;  conditional E-value: 0.00018
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       a++n + +  ++G+y+eAi+ y +  a++ 
  gi|386000858|ref|YP_005919157.1| 297 AWSNKGTVLADQGKYDEAIQAYDE--AIRL 324
                                       68899999****************..5554 PP

  == domain 11  score: 14.5 bits;  conditional E-value: 7.9e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a+ n +++  ++G+y eAi+ y +  a++ dp++
  gi|386000858|ref|YP_005919157.1| 331 AWINKGSALYEQGNYPEAIQAYDE--AIRLDPDN 362
                                       577999******************..99999987 PP

  == domain 12  score: 6.8 bits;  conditional E-value: 0.023
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +++n +++ s+lG+y e i  y +  a++ dpe+a
  gi|386000858|ref|YP_005919157.1| 365 TWYNKGNALSELGNYTEGILAYDE--AIRLDPEEA 397
                                       6899*************9999999..999999875 PP

  == domain 13  score: 13.2 bits;  conditional E-value: 0.00021
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       ++ ++ +G+y+eAi+ y +  a++ dpe+a
  gi|386000858|ref|YP_005919157.1| 404 GNSFRMQGKYDEAIQAYDE--AIRLDPEEA 431
                                       5666669************..999999876 PP

  == domain 14  score: 13.2 bits;  conditional E-value: 0.00021
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       ++ ++ +G+y+eAi+ y +  a++ dpe+a
  gi|386000858|ref|YP_005919157.1| 438 GNSFRMQGKYDEAIQAYDE--AIRLDPEEA 465
                                       5666669************..999999876 PP

  == domain 15  score: 11.5 bits;  conditional E-value: 0.00072
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++ ++ +G+y+eAi+ y +  a++ dpe
  gi|386000858|ref|YP_005919157.1| 472 GNSFRMQGKYDEAIQAYDE--AIRLDPE 497
                                       5666669************..9999986 PP

  == domain 16  score: 10.6 bits;  conditional E-value: 0.0014
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n +++  ++ +y+eAi+ y +  a++  p
  gi|386000858|ref|YP_005919157.1| 501 AWYNKGNALYEQDKYDEAIQAYDE--AIRLNP 530
                                       7899********************..766554 PP

  == domain 17  score: 15.1 bits;  conditional E-value: 5.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++n +++ + +G+y+eAi+ y +  a++ dpe
  gi|386000858|ref|YP_005919157.1| 535 AWNNKGNALVMQGKYDEAIQAYDE--AIRLDPE 565
                                       7899********************..9999987 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.4   2.8e-06   0.00093      13      61 ..       7      55 ..       2      60 .. 0.91
   2 !   17.0   0.0   1.5e-05     0.005      10      61 ..      72     123 ..      63     127 .. 0.92
   3 !   19.3   0.1   2.9e-06   0.00096       7      63 ..     103     159 ..      97     161 .. 0.90
   4 !   22.3   0.5   3.2e-07   0.00011       8      64 ..     138     194 ..     133     197 .. 0.91
   5 !   25.4   0.8   3.4e-08   1.1e-05       7      65 ..     171     229 ..     168     231 .. 0.94
   6 !   29.5   1.0   1.8e-09   6.1e-07       9      63 ..     207     261 ..     199     263 .. 0.94
   7 !   13.0   0.4   0.00026     0.085      12      62 ..     244     294 ..     243     301 .. 0.94
   8 !   15.0   0.2   6.3e-05     0.021      10      61 ..     276     327 ..     271     331 .. 0.91
   9 !   28.1   0.2   5.2e-09   1.7e-06       5      62 ..     305     362 ..     302     363 .. 0.95
  10 !   20.6   0.1   1.1e-06   0.00037      10      65 ..     344     399 ..     342     401 .. 0.95
  11 !   13.8   0.1   0.00014     0.047       9      65 ..     411     467 ..     406     469 .. 0.95
  12 !   21.8   0.3   4.5e-07   0.00015       9      62 ..     479     532 ..     474     536 .. 0.94
  13 !   14.7   0.0   7.7e-05     0.026       8      52 ..     546     590 ..     540     596 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-06
                             TPR_9 13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                       a+++ +  + l+P+ ++ ++  Gl l+ +G++ +A+++ + +++l+p+
  gi|386000858|ref|YP_005919157.1|  7 MAIEAFDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPE 55
                                      588999999**************************************97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.5e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++++ +++++  + l+P+ +  +   G++l  +G++ +A ++++ +++l+p+
  gi|386000858|ref|YP_005919157.1|  72 NYDESIKAYDEAIRLDPEFAAAWNNKGIALGNQGNYTEATRCFDEAIRLDPE 123
                                       57788999******************************************96 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 2.9e-06
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       ++ ++ +a ++ +  + l+P+ ++ ++  G +l ++G++ +A+ + + +++l+p+ +
  gi|386000858|ref|YP_005919157.1| 103 NQGNYTEATRCFDEAIRLDPEYAGAWYNKGKALSERGNYTGAILAYDEAIRLDPELA 159
                                       56778899*********************************************9765 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 3.2e-07
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       + ++  a+ +++  + l+P+ +  +   G +l+++G++ +A+++++ +++l+p++++
  gi|386000858|ref|YP_005919157.1| 138 RGNYTGAILAYDEAIRLDPELAAAWHKKGDALFERGNYTEAIQAFDEAIRLDPEDAT 194
                                       5666778889999****************************************9976 PP

  == domain 5  score: 25.4 bits;  conditional E-value: 3.4e-08
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++ ++ +a+++ +  + l+P+d+  ++  G++l  +G++++A+ + + +++l+p+++da
  gi|386000858|ref|YP_005919157.1| 171 ERGNYTEAIQAFDEAIRLDPEDATTWYNKGVALGMQGNYAEAIPAYDEAIRLDPEDADA 229
                                       6778899*************************************************998 PP

  == domain 6  score: 29.5 bits;  conditional E-value: 1.8e-09
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                        ++++a+ +++  + l+P+d++ +  RG +l +lG + +A+ +L+ +++l+p+++
  gi|386000858|ref|YP_005919157.1| 207 GNYAEAIPAYDEAIRLDPEDADAWNNRGNALNELGKYDEAIHALDKAIELDPEDA 261
                                       5789999*********************************************986 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 0.00026
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++a+ +++  + l+P+d+  +   G  l   G++ +A+++++ +++l+p+ 
  gi|386000858|ref|YP_005919157.1| 244 DEAIHALDKAIELDPEDAAPWNNKGKPLWMKGNYTEAIQAFDEAIRLDPEL 294
                                       78999********************************************75 PP

  == domain 8  score: 15.0 bits;  conditional E-value: 6.3e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++ +a+++ +  + l+P+ +  +   G +la +G + +A+++ + +++l p+
  gi|386000858|ref|YP_005919157.1| 276 NYTEAIQAFDEAIRLDPELAVAWSNKGTVLADQGKYDEAIQAYDEAIRLHPN 327
                                       56789999***************************************99996 PP

  == domain 9  score: 28.1 bits;  conditional E-value: 5.2e-09
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++ + ++++a+++++  + l+P+ ++ +   G +l+++G++ +A+++ + +++l+pd+
  gi|386000858|ref|YP_005919157.1| 305 LADQGKYDEAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQAYDEAIRLDPDN 362
                                       577889**************************************************96 PP

  == domain 10  score: 20.6 bits;  conditional E-value: 1.1e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++++a+++++  + l+Pd +  ++  G +l +lG++ +++ + + +++l+p+ +d+
  gi|386000858|ref|YP_005919157.1| 344 NYPEAIQAYDEAIRLDPDNAMTWYNKGNALSELGNYTEGILAYDEAIRLDPEEADV 399
                                       6889***********************************************99885 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 0.00014
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        ++++a+++++  + l+P++++ +   G     +G + +A+++ + +++l+p+ +d+
  gi|386000858|ref|YP_005919157.1| 411 GKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEEADV 467
                                       6799************************************************99885 PP

  == domain 12  score: 21.8 bits;  conditional E-value: 4.5e-07
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                        ++++a+++++  + l+P+ ++ ++  G +l++++ + +A+++ + +++l+pd 
  gi|386000858|ref|YP_005919157.1| 479 GKYDEAIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDY 532
                                       6799************************************************85 PP

  == domain 13  score: 14.7 bits;  conditional E-value: 7.7e-05
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladL 52 
                                       + ++++a+++++  + l+P+ ++ ++  G++l+ lG +++A ++ 
  gi|386000858|ref|YP_005919157.1| 546 QGKYDEAIQAYDEAIRLDPEFAYPWFSKGVVLEYLGKVAEANEAY 590
                                       6789***********************************998765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.48   1.6e+02      13      32 ..       2      21 ..       1      22 [. 0.89
   2 !   12.2   0.3    0.0007      0.23       1      32 [.      24      55 ..      24      56 .. 0.86
   3 ?    8.1   0.1     0.014       4.7       7      31 ..      64      88 ..      62      89 .. 0.89
   4 ?    2.8   0.0      0.68   2.2e+02       7      32 ..      98     123 ..      96     124 .. 0.86
   5 ?    7.5   0.0     0.021       6.9       2      31 ..     127     156 ..     127     157 .. 0.93
   6 !   12.8   0.0   0.00043      0.14       2      32 ..     161     191 ..     160     192 .. 0.90
   7 !    8.7   0.0    0.0092         3       4      32 ..     197     225 ..     195     226 .. 0.91
   8 ?    8.1   0.0     0.014       4.7       6      32 ..     233     259 ..     229     260 .. 0.89
   9 ?    5.7   0.0     0.078        26      14      31 ..     275     292 ..     269     293 .. 0.86
  10 !   13.2   0.0   0.00032      0.11       8      32 ..     303     327 ..     297     328 .. 0.87
  11 !   14.5   0.1   0.00013     0.042       2      33 .]     331     362 ..     330     362 .. 0.89
  12 ?    3.4   0.0      0.43   1.4e+02       4      31 ..     367     394 ..     365     396 .. 0.90
  13 !   12.7   0.0   0.00047      0.16       7      31 ..     404     428 ..     399     430 .. 0.91
  14 !   12.7   0.0   0.00047      0.16       7      31 ..     438     462 ..     433     464 .. 0.91
  15 !   12.5   0.0   0.00053      0.18       7      31 ..     472     496 ..     467     497 .. 0.91
  16 !   17.2   0.6   1.8e-05    0.0059       2      32 ..     501     531 ..     501     532 .. 0.96
  17 !    9.9   0.1    0.0038       1.3       7      31 ..     540     564 ..     538     565 .. 0.87
  18 ?   -0.8   0.0       9.3   3.1e+03      10      25 ..     577     592 ..     572     595 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.48
                                      HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 13 lgdtdkAlealerlikeYPd 32
                                      +g+++ A+ea+++ i+  P+
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPE 21
                                      789************99885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0007
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  1 dAlyklalsyrklgdtdkAlealerlikeYPd 32
                                      dA y  +l ++  g++++A++a+++ i+  P+
  gi|386000858|ref|YP_005919157.1| 24 DAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPE 55
                                      68888898888777*************99885 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.014
                                      HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYP 31
                                      +l++  +g++d++++a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 64 GLALDYQGNYDESIKAYDEAIRLDP 88
                                      78888999*************9888 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.68
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++ ++g++++A + +++ i+  P+
  gi|386000858|ref|YP_005919157.1|  98 GIALGNQGNYTEATRCFDEAIRLDPE 123
                                       66777899*************98885 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       A y+ ++++ + g+++ A+ a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 127 AWYNKGKALSERGNYTGAILAYDEAIRLDP 156
                                       789********99*************9888 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A  k + ++++ g++++A++a+++ i+  P+
  gi|386000858|ref|YP_005919157.1| 161 AWHKKGDALFERGNYTEAIQAFDEAIRLDPE 191
                                       677899*****99*************99886 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       y+ + ++ ++g++++A+ a+++ i+  P+
  gi|386000858|ref|YP_005919157.1| 197 YNKGVALGMQGNYAEAIPAYDEAIRLDPE 225
                                       88999999*9**************99886 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       ++ ++ +lg++d+A+ al++ i+  P+
  gi|386000858|ref|YP_005919157.1| 233 RGNALNELGKYDEAIHALDKAIELDPE 259
                                       678888999*************99886 PP

  == domain 9  score: 5.7 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHHHH-T CS
                             TPR_6  14 gdtdkAlealerlikeYP 31 
                                       g++++A++a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIRLDP 292
                                       6*************9888 PP

  == domain 10  score: 13.2 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                         +  +g++d+A++a+++ i+ +P+
  gi|386000858|ref|YP_005919157.1| 303 TVLADQGKYDEAIQAYDEAIRLHPN 327
                                       5566789*****************8 PP

  == domain 11  score: 14.5 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       A  + + +++++g++ +A++a+++ i+  Pd+
  gi|386000858|ref|YP_005919157.1| 331 AWINKGSALYEQGNYPEAIQAYDEAIRLDPDN 362
                                       56677999*********************995 PP

  == domain 12  score: 3.4 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYP 31 
                                       y+ + ++ +lg++++ + a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 367 YNKGNALSELGNYTEGILAYDEAIRLDP 394
                                       88999999*99*************9888 PP

  == domain 13  score: 12.7 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + s+r++g++d+A++a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 404 GNSFRMQGKYDEAIQAYDEAIRLDP 428
                                       779999***************9888 PP

  == domain 14  score: 12.7 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + s+r++g++d+A++a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 438 GNSFRMQGKYDEAIQAYDEAIRLDP 462
                                       779999***************9888 PP

  == domain 15  score: 12.5 bits;  conditional E-value: 0.00053
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + s+r++g++d+A++a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 472 GNSFRMQGKYDEAIQAYDEAIRLDP 496
                                       779999***************9888 PP

  == domain 16  score: 17.2 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A y+ + ++++++++d+A++a+++ i+  Pd
  gi|386000858|ref|YP_005919157.1| 501 AWYNKGNALYEQDKYDEAIQAYDEAIRLNPD 531
                                       78**************************998 PP

  == domain 17  score: 9.9 bits;  conditional E-value: 0.0038
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + ++ ++g++d+A++a+++ i+  P
  gi|386000858|ref|YP_005919157.1| 540 GNALVMQGKYDEAIQAYDEAIRLDP 564
                                       66778899*************9888 PP

  == domain 18  score: -0.8 bits;  conditional E-value: 9.3
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealer 25 
                                       ++ lg+ ++A ea+ +
  gi|386000858|ref|YP_005919157.1| 577 LEYLGKVAEANEAYAK 592
                                       5557899999999987 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.0   8.8e-07   0.00029       1      81 [.       1      82 [.       1      83 [. 0.96
   2 !   19.1   0.2   3.5e-06    0.0012       1      81 [.     103     184 ..     103     185 .. 0.95
   3 !   24.9   0.0   5.2e-08   1.7e-05       2      81 ..     138     218 ..     137     219 .. 0.95
   4 !   18.3   0.0     6e-06     0.002      23      82 .]     191     253 ..     184     253 .. 0.88
   5 !   13.6   0.0   0.00017     0.058      36      81 ..     274     320 ..     267     321 .. 0.93
   6 !   19.7   0.0   2.2e-06   0.00074      30      81 ..     336     388 ..     323     389 .. 0.92
   7 !   14.9   0.0   6.9e-05     0.023      29      81 ..     403     456 ..     392     457 .. 0.89
   8 !   31.4   0.6   4.8e-10   1.6e-07       2      81 ..     444     524 ..     444     525 .. 0.94
   9 !   30.4   1.4     1e-09   3.4e-07       1      81 [.     477     558 ..     477     559 .. 0.97
  10 ?    7.0   0.1     0.021       6.9      30      78 ..     540     589 ..     527     593 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-07
                                      HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78
                                      +q+ny  Ai  ++ +   ++e +++ y ++l+ly +g+y++A + +++a +l+++   ++  ++ +l  +++y+e i+a
  gi|386000858|ref|YP_005919157.1|  1 MQGNYTMAIEAFDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQAYDEAiRLDPEYASAWNNKGLALDYQGNYDESIKA 79
                                      699*************999***********************************************************9 PP

                                      H-S CS
                            ANAPC3 79 Lek 81
                                      +++
  gi|386000858|ref|YP_005919157.1| 80 YDE 82
                                      876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.5e-06
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       +q+ny +A  +++ +   ++e + + y ++++l ++g+y+ A+  +++a +l+++  +++  ++ +l++ ++y eAi
  gi|386000858|ref|YP_005919157.1| 103 NQGNYTEATRCFDEAIRLDPEYAGAWYNKGKALSERGNYTGAILAYDEAiRLDPELAAAWHKKGDALFERGNYTEAI 179
                                       6899************8889888889999************************************************ PP

                                       HHH-S CS
                            ANAPC3  77 aaLek 81 
                                       +a+++
  gi|386000858|ref|YP_005919157.1| 180 QAFDE 184
                                       **987 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 5.2e-08
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       ++ny  Ai+ ++ +   ++e + + + ++ +l+++g+y++A++ +++a +l++++   +y ++ +l  +++y eAi 
  gi|386000858|ref|YP_005919157.1| 138 RGNYTGAILAYDEAIRLDPELAAAWHKKGDALFERGNYTEAIQAFDEAiRLDPEDATTWYNKGVALGMQGNYAEAIP 214
                                       689************9999999999999************************************************8 PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       a+++
  gi|386000858|ref|YP_005919157.1| 215 AYDE 218
                                       8875 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 6e-06
                                       HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                            ANAPC3  23 pedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                       ++++ ++  + +l  +g+y +A+  +++a +l++++  ++   + +l +L+ky+eAi aL+k+
  gi|386000858|ref|YP_005919157.1| 191 EDATTWYnkGVALGMQGNYAEAIPAYDEAiRLDPEDADAWNNRGNALNELGKYDEAIHALDKA 253
                                       33455555599999**********************************************985 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 0.00017
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        g+y++A++ +++a +l+++   ++  ++ +l +++ky+eAi+a+++
  gi|386000858|ref|YP_005919157.1| 274 KGNYTEAIQAFDEAiRLDPELAVAWSNKGTVLADQGKYDEAIQAYDE 320
                                       699****************************************9986 PP

  == domain 6  score: 19.7 bits;  conditional E-value: 2.2e-06
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       + +ly++g+y +A++ +++a +l++ +   +y ++ +l +L++y e+i a+++
  gi|386000858|ref|YP_005919157.1| 336 GSALYEQGNYPEAIQAYDEAiRLDPDNAMTWYNKGNALSELGNYTEGILAYDE 388
                                       779*********************************************88775 PP

  == domain 7  score: 14.9 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++ ++  +g+y++A++ +++a +l+++   +++ ++ +   ++ky+eAi+a+++
  gi|386000858|ref|YP_005919157.1| 403 KGNSFRMQGKYDEAIQAYDEAiRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDE 456
                                       4778889********************************9**********9986 PP

  == domain 8  score: 31.4 bits;  conditional E-value: 4.8e-10
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       q++y++Ai  ++ +   ++e ++    ++ ++  +g+y++A++ +++a +l+++  g++y ++ +l++++ky+eAi+
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAiRLDPEFAGAWYNKGNALYEQDKYDEAIQ 520
                                       679************8888888888889************************************************* PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       a+++
  gi|386000858|ref|YP_005919157.1| 521 AYDE 524
                                       9986 PP

  == domain 9  score: 30.4 bits;  conditional E-value: 1e-09
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       +q++y++Ai  ++ +   ++e + + y ++ +ly++ +y++A++ +++a +ln+  ++++  ++ +l+ ++ky+eAi
  gi|386000858|ref|YP_005919157.1| 477 MQGKYDEAIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEAiRLNPDYKEAWNNKGNALVMQGKYDEAI 553
                                       6899************9************************************************************ PP

                                       HHH-S CS
                            ANAPC3  77 aaLek 81 
                                       +a+++
  gi|386000858|ref|YP_005919157.1| 554 QAYDE 558
                                       *9986 PP

  == domain 10  score: 7.0 bits;  conditional E-value: 0.021
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       + +l  +g+y++A++ +++a +l+++    ++ ++ +l  L+k+ eA  a
  gi|386000858|ref|YP_005919157.1| 540 GNALVMQGKYDEAIQAYDEAiRLDPEFAYPWFSKGVVLEYLGKVAEANEA 589
                                       56777888888888888888777777777777777777777777777665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.3   1.1e+03      15      30 ..       2      17 ..       1      18 [. 0.91
   2 !   13.0   0.2   0.00021      0.07       9      30 ..      30      51 ..      29      52 .. 0.93
   3 !   11.6   0.2   0.00058      0.19       3      30 ..      58      85 ..      57      86 .. 0.90
   4 !   15.9   0.1   2.6e-05    0.0087       3      30 ..      92     119 ..      90     120 .. 0.90
   5 ?    6.8   0.1     0.019       6.2       8      30 ..     131     153 ..     129     154 .. 0.90
   6 !    9.6   0.1    0.0025      0.84       9      30 ..     166     187 ..     158     188 .. 0.89
   7 !    9.0   0.1    0.0039       1.3       7      30 ..     198     221 ..     193     222 .. 0.90
   8 !   14.4   0.5   7.7e-05     0.026       6      30 ..     231     255 ..     227     256 .. 0.92
   9 ?    3.4   0.0      0.23        77      13      30 ..     272     289 ..     265     290 .. 0.87
  10 !   15.9   0.1   2.7e-05    0.0089       6      32 ..     299     325 ..     294     325 .. 0.90
  11 !   12.9   0.1   0.00022     0.074       7      30 ..     334     357 ..     333     358 .. 0.91
  12 ?    4.9   0.1     0.075        25       7      30 ..     368     391 ..     363     392 .. 0.86
  13 !    8.4   0.1     0.006         2      11      30 ..     406     425 ..     404     426 .. 0.86
  14 !    8.4   0.1     0.006         2      11      30 ..     440     459 ..     438     460 .. 0.86
  15 !    8.4   0.1     0.006         2      11      30 ..     474     493 ..     472     494 .. 0.86
  16 !   13.6   0.8   0.00014     0.046       7      31 ..     504     528 ..     499     529 .. 0.92
  17 !   14.3   0.3   8.6e-05     0.029       6      30 ..     537     561 ..     535     562 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.3
                            TPR_10 15 rgrydeAealleeala 30
                                      +g+y+ A + ++ea++
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIR 17
                                      89************97 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00021
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      + +l+ rg+y+eA++ ++ea++
  gi|386000858|ref|YP_005919157.1| 30 GLTLYYRGNYTEAVQAYDEAIR 51
                                      789*****************97 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00058
                            TPR_10  3 sslnNLanalrqrgrydeAealleeala 30
                                      s+ nN + al  +g+yde+ + ++ea++
  gi|386000858|ref|YP_005919157.1| 58 SAWNNKGLALDYQGNYDESIKAYDEAIR 85
                                      5559**********************97 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 2.6e-05
                            TPR_10   3 sslnNLanalrqrgrydeAealleeala 30 
                                       ++ nN ++al ++g+y+eA + ++ea++
  gi|386000858|ref|YP_005919157.1|  92 AAWNNKGIALGNQGNYTEATRCFDEAIR 119
                                       5569**********************97 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.019
                            TPR_10   8 LanalrqrgrydeAealleeala 30 
                                        + al++rg+y++A   ++ea++
  gi|386000858|ref|YP_005919157.1| 131 KGKALSERGNYTGAILAYDEAIR 153
                                       5889*****************97 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0025
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + al++rg+y+eA + ++ea++
  gi|386000858|ref|YP_005919157.1| 166 GDALFERGNYTEAIQAFDEAIR 187
                                       6699****************97 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0039
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++al  +g+y+eA   ++ea++
  gi|386000858|ref|YP_005919157.1| 198 NKGVALGMQGNYAEAIPAYDEAIR 221
                                       6799******************97 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 7.7e-05
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN +nal ++g+ydeA   l++a++
  gi|386000858|ref|YP_005919157.1| 231 NNRGNALNELGKYDEAIHALDKAIE 255
                                       9**********************98 PP

  == domain 9  score: 3.4 bits;  conditional E-value: 0.23
                            TPR_10  13 rqrgrydeAealleeala 30 
                                       +  g+y+eA + ++ea++
  gi|386000858|ref|YP_005919157.1| 272 WMKGNYTEAIQAFDEAIR 289
                                       5679************97 PP

  == domain 10  score: 15.9 bits;  conditional E-value: 2.7e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealair 32 
                                       +N + +l ++g+ydeA + ++ea++++
  gi|386000858|ref|YP_005919157.1| 299 SNKGTVLADQGKYDEAIQAYDEAIRLH 325
                                       68899*******************975 PP

  == domain 11  score: 12.9 bits;  conditional E-value: 0.00022
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N + al+++g+y eA + ++ea++
  gi|386000858|ref|YP_005919157.1| 334 NKGSALYEQGNYPEAIQAYDEAIR 357
                                       5689******************97 PP

  == domain 12  score: 4.9 bits;  conditional E-value: 0.075
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N +nal+++g+y+e    ++ea++
  gi|386000858|ref|YP_005919157.1| 368 NKGNALSELGNYTEGILAYDEAIR 391
                                       779***********9999999986 PP

  == domain 13  score: 8.4 bits;  conditional E-value: 0.006
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                         r +g+ydeA + ++ea++
  gi|386000858|ref|YP_005919157.1| 406 SFRMQGKYDEAIQAYDEAIR 425
                                       5578**************97 PP

  == domain 14  score: 8.4 bits;  conditional E-value: 0.006
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                         r +g+ydeA + ++ea++
  gi|386000858|ref|YP_005919157.1| 440 SFRMQGKYDEAIQAYDEAIR 459
                                       5578**************97 PP

  == domain 15  score: 8.4 bits;  conditional E-value: 0.006
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                         r +g+ydeA + ++ea++
  gi|386000858|ref|YP_005919157.1| 474 SFRMQGKYDEAIQAYDEAIR 493
                                       5578**************97 PP

  == domain 16  score: 13.6 bits;  conditional E-value: 0.00014
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N +nal+++ +ydeA + ++ea+++
  gi|386000858|ref|YP_005919157.1| 504 NKGNALYEQDKYDEAIQAYDEAIRL 528
                                       679*******************985 PP

  == domain 17  score: 14.3 bits;  conditional E-value: 8.6e-05
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN +nal  +g+ydeA + ++ea++
  gi|386000858|ref|YP_005919157.1| 537 NNKGNALVMQGKYDEAIQAYDEAIR 561
                                       899********************97 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-05     0.008     206     256 ..       3      53 ..       1      57 [. 0.95
   2 !   14.7   0.0   3.3e-05     0.011     202     256 ..      67     121 ..      54     124 .. 0.92
   3 !   11.9   0.0   0.00022     0.074     206     256 ..     105     155 ..      99     157 .. 0.94
   4 !   12.4   0.0   0.00016     0.054     204     259 ..     137     192 ..     124     194 .. 0.92
   5 !   11.9   0.1   0.00023     0.075     205     259 ..     172     226 ..     158     233 .. 0.93
   6 !   15.2   0.0   2.3e-05    0.0076     203     256 ..     238     291 ..     234     294 .. 0.96
   7 !   19.6   0.0     1e-06   0.00035     205     257 ..     308     360 ..     303     369 .. 0.94
   8 !   11.7   0.0   0.00027     0.091     203     257 ..     374     428 ..     361     438 .. 0.89
   9 !   15.4   0.1     2e-05    0.0066     205     256 ..     444     495 ..     438     498 .. 0.94
  10 !   13.1   0.3   9.9e-05     0.033     205     257 ..     512     564 ..     497     568 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       g+++ A+e  d+ai+ +p+  + ++ K+  l   G+ ++A+++ +ea +lD
  gi|386000858|ref|YP_005919157.1|   3 GNYTMAIEAFDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQAYDEAIRLD 53 
                                       67899******************************************9999 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.3e-05
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        d+ g+++++++  d+ai+ +p++   + +K+  l  +G+ ++A+++ +ea +lD
  gi|386000858|ref|YP_005919157.1|  67 LDYQGNYDESIKAYDEAIRLDPEFAAAWNNKGIALGNQGNYTEATRCFDEAIRLD 121
                                       58899**********************************************9999 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00022
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       g++++A+++ d+ai+ +p+    +++K++ l   G+ ++A+ + +ea +lD
  gi|386000858|ref|YP_005919157.1| 105 GNYTEATRCFDEAIRLDPEYAGAWYNKGKALSERGNYTGAILAYDEAIRLD 155
                                       7899*******************************************9999 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00016
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       + g+++ A+   d+ai+ +p+l   +  K+  l   G+ ++A+++ +ea +lD +D
  gi|386000858|ref|YP_005919157.1| 137 ERGNYTGAILAYDEAIRLDPELAAAWHKKGDALFERGNYTEAIQAFDEAIRLDPED 192
                                       5678999**********************************************988 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00023
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        g++++A++  d+ai+ +p+    +++K+  l  +G+  +A+ + +ea +lD +D
  gi|386000858|ref|YP_005919157.1| 172 RGNYTEAIQAFDEAIRLDPEDATTWYNKGVALGMQGNYAEAIPAYDEAIRLDPED 226
                                       57899***********************************************887 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 2.3e-05
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       ++lg++++A++ +dkaie +p+    + +K++ l  +G+ ++A+++ +ea +lD
  gi|386000858|ref|YP_005919157.1| 238 NELGKYDEAIHALDKAIELDPEDAAPWNNKGKPLWMKGNYTEAIQAFDEAIRLD 291
                                       7899**********************************************9999 PP

  == domain 7  score: 19.6 bits;  conditional E-value: 1e-06
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                        g++++A++  d+ai+ +p+ v+ +++K+  l  +G+  +A+++ +ea +lD 
  gi|386000858|ref|YP_005919157.1| 308 QGKYDEAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQAYDEAIRLDP 360
                                       5789*********************************************9995 PP

  == domain 8  score: 11.7 bits;  conditional E-value: 0.00027
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                        +lg++++ +   d+ai+ +p+  ++++ K++ ++ +G  ++A+++ +ea +lD 
  gi|386000858|ref|YP_005919157.1| 374 SELGNYTEGILAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP 428
                                       4678889999999****************************************95 PP

  == domain 9  score: 15.4 bits;  conditional E-value: 2e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        g++++A++  d+ai+ +p+  ++++ K++ ++ +G  ++A+++ +ea +lD
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLD 495
                                       6789********************************************9999 PP

  == domain 10  score: 13.1 bits;  conditional E-value: 9.9e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                         ++++A++  d+ai+ +p   e + +K++ l  +G  ++A+++ +ea +lD 
  gi|386000858|ref|YP_005919157.1| 512 QDKYDEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEAIRLDP 564
                                       45689*******************************************99995 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.13        43      13      25 ..       1      13 [.       1      21 [. 0.88
   2 !   11.2   0.2   0.00083      0.27       2      25 ..      24      47 ..      23      55 .. 0.88
   3 ?   -1.0   0.1       5.7   1.9e+03      15      23 ..      78      86 ..      64      93 .. 0.64
   4 ?    0.6   0.0       1.8   6.1e+02      13      24 ..     103     114 ..     101     122 .. 0.86
   5 ?   -0.8   0.0       4.8   1.6e+03      15      25 ..     139     149 ..     137     161 .. 0.72
   6 ?    6.9   0.0     0.019       6.2      11      35 ..     169     191 ..     157     192 .. 0.81
   7 ?    4.3   0.0      0.12        40      13      35 ..     205     225 ..     200     226 .. 0.80
   8 !    7.9   0.0    0.0091         3      15      36 .]     241     260 ..     239     260 .. 0.88
   9 !    9.3   0.0    0.0035       1.2      12      25 ..     272     285 ..     268     294 .. 0.84
  10 !   10.5   0.3    0.0014      0.47      10      25 ..     304     319 ..     302     321 .. 0.89
  11 !   10.0   0.0     0.002      0.66       9      25 ..     337     353 ..     336     362 .. 0.79
  12 !   10.3   0.0    0.0017      0.56      13      25 ..     409     421 ..     405     429 .. 0.86
  13 !   10.3   0.0    0.0017      0.56      13      25 ..     443     455 ..     439     463 .. 0.86
  14 !   10.3   0.0    0.0017      0.56      13      25 ..     477     489 ..     473     497 .. 0.86
  15 !   11.3   1.1   0.00078      0.26      10      25 ..     508     523 ..     502     524 .. 0.89
  16 !   10.0   0.1    0.0021      0.69      13      25 ..     545     557 ..     542     565 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                                      HTT-HHHHHHH.. CS
                             TPR_3 13 nkkkyqeArelfs 25
                                      ++++y+ A+e+f+
  gi|386000858|ref|YP_005919157.1|  1 MQGNYTMAIEAFD 13
                                      79*********98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00083
                                      HHHHHHHHHHHHTT-HHHHHHH.. CS
                             TPR_3  2 dylysyAaefynkkkyqeArelfs 25
                                      d +ys + ++y  ++y+eA+++++
  gi|386000858|ref|YP_005919157.1| 24 DAWYSKGLTLYYRGNYTEAVQAYD 47
                                      669999****************77 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 5.7
                                      T-HHHHHHH CS
                             TPR_3 15 kkyqeArel 23
                                      k y+eA+ l
  gi|386000858|ref|YP_005919157.1| 78 KAYDEAIRL 86
                                      345555555 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.8
                                       HTT-HHHHHHH. CS
                             TPR_3  13 nkkkyqeArelf 24 
                                       n+++y+eA   f
  gi|386000858|ref|YP_005919157.1| 103 NQGNYTEATRCF 114
                                       89******7665 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 4.8
                                       T-HHHHHHH.. CS
                             TPR_3  15 kkyqeArelfs 25 
                                       ++y+ A+ +++
  gi|386000858|ref|YP_005919157.1| 139 GNYTGAILAYD 149
                                       78888887755 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.019
                                       HHHTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3  11 fynkkkyqeArelfsYallaildke 35 
                                       ++  ++y+eA+++f+   +  ld+e
  gi|386000858|ref|YP_005919157.1| 169 LFERGNYTEAIQAFD--EAIRLDPE 191
                                       6788*********98..66666665 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.12
                                       HTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3  13 nkkkyqeArelfsYallaildke 35 
                                       ++++y eA+ +++   +  ld+e
  gi|386000858|ref|YP_005919157.1| 205 MQGNYAEAIPAYD--EAIRLDPE 225
                                       89*********77..66666665 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0091
                                       T-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  15 kkyqeArelfsYallaildken 36 
                                       +ky+eA+++++   +  ld+e+
  gi|386000858|ref|YP_005919157.1| 241 GKYDEAIHALD--KAIELDPED 260
                                       9********99..999988887 PP

  == domain 9  score: 9.3 bits;  conditional E-value: 0.0035
                                       HHTT-HHHHHHH.. CS
                             TPR_3  12 ynkkkyqeArelfs 25 
                                        +k++y+eA+++f+
  gi|386000858|ref|YP_005919157.1| 272 WMKGNYTEAIQAFD 285
                                       59**********98 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.0014
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++ +++ky+eA+++++
  gi|386000858|ref|YP_005919157.1| 304 VLADQGKYDEAIQAYD 319
                                       6789**********87 PP

  == domain 11  score: 10.0 bits;  conditional E-value: 0.002
                                       HHHHHTT-HHHHHHH.. CS
                             TPR_3   9 aefynkkkyqeArelfs 25 
                                        ++y +++y eA+++++
  gi|386000858|ref|YP_005919157.1| 337 SALYEQGNYPEAIQAYD 353
                                       689************77 PP

  == domain 12  score: 10.3 bits;  conditional E-value: 0.0017
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       +++ky+eA+++++
  gi|386000858|ref|YP_005919157.1| 409 MQGKYDEAIQAYD 421
                                       8**********77 PP

  == domain 13  score: 10.3 bits;  conditional E-value: 0.0017
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       +++ky+eA+++++
  gi|386000858|ref|YP_005919157.1| 443 MQGKYDEAIQAYD 455
                                       8**********77 PP

  == domain 14  score: 10.3 bits;  conditional E-value: 0.0017
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       +++ky+eA+++++
  gi|386000858|ref|YP_005919157.1| 477 MQGKYDEAIQAYD 489
                                       8**********77 PP

  == domain 15  score: 11.3 bits;  conditional E-value: 0.00078
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++y ++ky+eA+++++
  gi|386000858|ref|YP_005919157.1| 508 ALYEQDKYDEAIQAYD 523
                                       79************87 PP

  == domain 16  score: 10.0 bits;  conditional E-value: 0.0021
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       +++ky+eA+++++
  gi|386000858|ref|YP_005919157.1| 545 MQGKYDEAIQAYD 557
                                       89*********77 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.79   2.6e+02      18      32 ..       3      17 ..       2      24 .. 0.84
   2 ?    7.5   0.4     0.013       4.2      17      33 ..      36      52 ..      27      52 .. 0.91
   3 !   10.4   0.6    0.0016      0.52       9      33 ..      62      86 ..      56      86 .. 0.88
   4 ?    6.1   0.0     0.035        12       9      32 ..      96     119 ..      91     120 .. 0.85
   5 ?    4.7   0.1     0.095        32      15      33 ..     136     154 ..     125     154 .. 0.84
   6 ?    5.1   0.0     0.074        25      17      32 ..     172     187 ..     169     188 .. 0.89
   7 !    9.5   0.1     0.003         1       8      33 ..     197     222 ..     191     222 .. 0.82
   8 ?    2.8   0.1      0.37   1.2e+02      17      33 ..     240     256 ..     232     261 .. 0.75
   9 ?    4.7   0.0     0.096        32      17      32 ..     274     289 ..     273     290 .. 0.89
  10 !   12.9   0.2   0.00027     0.088       4      33 ..     295     324 ..     293     325 .. 0.86
  11 !   11.2   0.2   0.00088      0.29      16      33 ..     341     358 ..     331     358 .. 0.84
  12 ?    0.4   0.1         2   6.7e+02      16      32 ..     375     391 ..     361     392 .. 0.80
  13 !    8.9   0.1    0.0046       1.5      17      33 ..     410     426 ..     409     426 .. 0.91
  14 !    8.9   0.1    0.0046       1.5      17      33 ..     444     460 ..     443     460 .. 0.91
  15 !    8.9   0.1    0.0046       1.5      17      33 ..     478     494 ..     477     494 .. 0.91
  16 ?    6.9   0.8     0.019       6.4      17      33 ..     512     528 ..     507     528 .. 0.88
  17 !    8.9   0.1    0.0046       1.5      17      33 ..     546     562 ..     545     562 .. 0.91
  18 ?    2.0   0.3      0.65   2.2e+02       8      31 ..     571     594 ..     567     596 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.79
                               MIT 18 gnyeeAlelYkeale 32
                                      gny  A+e++ ea++
  gi|386000858|ref|YP_005919157.1|  3 GNYTMAIEAFDEAIR 17
                                      899999999999986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.013
                               MIT 17 agnyeeAlelYkealel 33
                                      +gny eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 36 RGNYTEAVQAYDEAIRL 52
                                      69************975 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0016
                               MIT  9 kkAveeDnagnyeeAlelYkealel 33
                                      +k   +D +gny+e +++Y ea++l
  gi|386000858|ref|YP_005919157.1| 62 NKGLALDYQGNYDESIKAYDEAIRL 86
                                      677899****************975 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.035
                               MIT   9 kkAveeDnagnyeeAlelYkeale 32 
                                       +k + + n+gny eA +++ ea++
  gi|386000858|ref|YP_005919157.1|  96 NKGIALGNQGNYTEATRCFDEAIR 119
                                       56777889**************97 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.095
                               MIT  15 DnagnyeeAlelYkealel 33 
                                        ++gny  A+ +Y ea++l
  gi|386000858|ref|YP_005919157.1| 136 SERGNYTGAILAYDEAIRL 154
                                       578*************975 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.074
                               MIT  17 agnyeeAlelYkeale 32 
                                       +gny eA++++ ea++
  gi|386000858|ref|YP_005919157.1| 172 RGNYTEAIQAFDEAIR 187
                                       79***********997 PP

  == domain 7  score: 9.5 bits;  conditional E-value: 0.003
                               MIT   8 vkkAveeDnagnyeeAlelYkealel 33 
                                        +k v +  +gny+eA+ +Y ea++l
  gi|386000858|ref|YP_005919157.1| 197 YNKGVALGMQGNYAEAIPAYDEAIRL 222
                                       5777888889*************975 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.37
                               MIT  17 agnyeeAlelYkealel 33 
                                        g+y+eA+++  +a+el
  gi|386000858|ref|YP_005919157.1| 240 LGKYDEAIHALDKAIEL 256
                                       57777777777777764 PP

  == domain 9  score: 4.7 bits;  conditional E-value: 0.096
                               MIT  17 agnyeeAlelYkeale 32 
                                       +gny eA++++ ea++
  gi|386000858|ref|YP_005919157.1| 274 KGNYTEAIQAFDEAIR 289
                                       69***********997 PP

  == domain 10  score: 12.9 bits;  conditional E-value: 0.00027
                               MIT   4 AlelvkkAveeDnagnyeeAlelYkealel 33 
                                       A++  +k + +  +g+y+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 295 AVAWSNKGTVLADQGKYDEAIQAYDEAIRL 324
                                       66777888888889*************975 PP

  == domain 11  score: 11.2 bits;  conditional E-value: 0.00088
                               MIT  16 nagnyeeAlelYkealel 33 
                                       ++gny+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 341 EQGNYPEAIQAYDEAIRL 358
                                       78*************975 PP

  == domain 12  score: 0.4 bits;  conditional E-value: 2
                               MIT  16 nagnyeeAlelYkeale 32 
                                       + gny e + +Y ea++
  gi|386000858|ref|YP_005919157.1| 375 ELGNYTEGILAYDEAIR 391
                                       6799**********997 PP

  == domain 13  score: 8.9 bits;  conditional E-value: 0.0046
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+y+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 410 QGKYDEAIQAYDEAIRL 426
                                       59************975 PP

  == domain 14  score: 8.9 bits;  conditional E-value: 0.0046
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+y+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDEAIRL 460
                                       59************975 PP

  == domain 15  score: 8.9 bits;  conditional E-value: 0.0046
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+y+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 478 QGKYDEAIQAYDEAIRL 494
                                       59************975 PP

  == domain 16  score: 6.9 bits;  conditional E-value: 0.019
                               MIT  17 agnyeeAlelYkealel 33 
                                       + +y+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 512 QDKYDEAIQAYDEAIRL 528
                                       569***********975 PP

  == domain 17  score: 8.9 bits;  conditional E-value: 0.0046
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+y+eA+++Y ea++l
  gi|386000858|ref|YP_005919157.1| 546 QGKYDEAIQAYDEAIRL 562
                                       59************975 PP

  == domain 18  score: 2.0 bits;  conditional E-value: 0.65
                               MIT   8 vkkAveeDnagnyeeAlelYkeal 31 
                                       ++k v ++  g+ +eA e+Y +a 
  gi|386000858|ref|YP_005919157.1| 571 FSKGVVLEYLGKVAEANEAYAKAE 594
                                       5789999*************9995 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.35   1.2e+02      55      76 ..       3      24 ..       1      33 [. 0.87
   2 ?    3.2   0.0      0.29        95      54      70 ..      36      52 ..      22      61 .. 0.83
   3 ?    3.0   0.0      0.33   1.1e+02      55      70 ..      71      86 ..      54      91 .. 0.82
   4 ?    0.8   0.0       1.6   5.3e+02      55      70 ..     105     120 ..      90     126 .. 0.89
   5 ?   -1.6   0.0       8.5   2.8e+03      55      70 ..     139     154 ..     121     157 .. 0.83
   6 ?    5.3   0.0     0.061        20      55      71 ..     173     189 ..     167     195 .. 0.83
   7 ?    2.6   0.0      0.43   1.4e+02      55      76 ..     207     228 ..     201     231 .. 0.88
   8 ?    3.7   0.0      0.19        64      53      70 ..     239     256 ..     232     261 .. 0.87
   9 ?    4.2   0.0      0.14        46      55      70 ..     275     290 ..     272     295 .. 0.90
  10 ?    5.7   0.0     0.048        16      43      70 ..     297     324 ..     291     331 .. 0.83
  11 ?    4.4   0.0      0.11        38      40      70 ..     328     358 ..     324     366 .. 0.84
  12 ?    2.3   0.0      0.54   1.8e+02      52      76 ..     374     398 ..     363     401 .. 0.87
  13 ?    5.7   0.0     0.045        15      55      76 ..     411     432 ..     405     435 .. 0.87
  14 ?    5.7   0.0     0.045        15      55      76 ..     445     466 ..     439     469 .. 0.87
  15 ?    3.3   0.0      0.25        83      55      70 ..     479     494 ..     473     499 .. 0.87
  16 ?    3.2   0.0      0.28        94      53      70 ..     511     528 ..     495     536 .. 0.82
  17 ?    3.4   0.0      0.24        79      55      70 ..     547     562 ..     529     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.35
                            ANAPC5 55 ghneeAvkaleeairlArenkD 76
                                      g++  A++a+ eairl  e +D
  gi|386000858|ref|YP_005919157.1|  3 GNYTMAIEAFDEAIRLDPEYAD 24
                                      68899**********9877766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.29
                            ANAPC5 54 fghneeAvkaleeairl 70
                                       g++ eAv+a  eairl
  gi|386000858|ref|YP_005919157.1| 36 RGNYTEAVQAYDEAIRL 52
                                      4899***********98 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.33
                            ANAPC5 55 ghneeAvkaleeairl 70
                                      g+++e++ka  eairl
  gi|386000858|ref|YP_005919157.1| 71 GNYDESIKAYDEAIRL 86
                                      89************97 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.6
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g++ eA++ + eairl
  gi|386000858|ref|YP_005919157.1| 105 GNYTEATRCFDEAIRL 120
                                       7899**********98 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 8.5
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g++  A+ a  eairl
  gi|386000858|ref|YP_005919157.1| 139 GNYTGAILAYDEAIRL 154
                                       788999********97 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.061
                            ANAPC5  55 ghneeAvkaleeairlA 71 
                                       g++ eA++a+ eairl 
  gi|386000858|ref|YP_005919157.1| 173 GNYTEAIQAFDEAIRLD 189
                                       899***********985 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.43
                            ANAPC5  55 ghneeAvkaleeairlArenkD 76 
                                       g+++eA+ a  eairl  e +D
  gi|386000858|ref|YP_005919157.1| 207 GNYAEAIPAYDEAIRLDPEDAD 228
                                       789************9888887 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.19
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       ++g+++eA++al  ai+l
  gi|386000858|ref|YP_005919157.1| 239 ELGKYDEAIHALDKAIEL 256
                                       689*************87 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.14
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g++ eA++a+ eairl
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIRL 290
                                       7899**********97 PP

  == domain 10  score: 5.7 bits;  conditional E-value: 0.048
                            ANAPC5  43 alLnlaslhadfghneeAvkaleeairl 70 
                                       a  n  ++ ad g+++eA++a  eairl
  gi|386000858|ref|YP_005919157.1| 297 AWSNKGTVLADQGKYDEAIQAYDEAIRL 324
                                       555677788899**************98 PP

  == domain 11  score: 4.4 bits;  conditional E-value: 0.11
                            ANAPC5  40 yqyalLnlaslhadfghneeAvkaleeairl 70 
                                       y  a +n  s  ++ g++ eA++a  eairl
  gi|386000858|ref|YP_005919157.1| 328 YVDAWINKGSALYEQGNYPEAIQAYDEAIRL 358
                                       556778888888899**************98 PP

  == domain 12  score: 2.3 bits;  conditional E-value: 0.54
                            ANAPC5  52 adfghneeAvkaleeairlArenkD 76 
                                       +++g++ e + a  eairl  e++D
  gi|386000858|ref|YP_005919157.1| 374 SELGNYTEGILAYDEAIRLDPEEAD 398
                                       5789**************9988887 PP

  == domain 13  score: 5.7 bits;  conditional E-value: 0.045
                            ANAPC5  55 ghneeAvkaleeairlArenkD 76 
                                       g+++eA++a  eairl  e++D
  gi|386000858|ref|YP_005919157.1| 411 GKYDEAIQAYDEAIRLDPEEAD 432
                                       89*************9988887 PP

  == domain 14  score: 5.7 bits;  conditional E-value: 0.045
                            ANAPC5  55 ghneeAvkaleeairlArenkD 76 
                                       g+++eA++a  eairl  e++D
  gi|386000858|ref|YP_005919157.1| 445 GKYDEAIQAYDEAIRLDPEEAD 466
                                       89*************9988887 PP

  == domain 15  score: 3.3 bits;  conditional E-value: 0.25
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+++eA++a  eairl
  gi|386000858|ref|YP_005919157.1| 479 GKYDEAIQAYDEAIRL 494
                                       89************97 PP

  == domain 16  score: 3.2 bits;  conditional E-value: 0.28
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       + ++++eA++a  eairl
  gi|386000858|ref|YP_005919157.1| 511 EQDKYDEAIQAYDEAIRL 528
                                       55789***********98 PP

  == domain 17  score: 3.4 bits;  conditional E-value: 0.24
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+++eA++a  eairl
  gi|386000858|ref|YP_005919157.1| 547 GKYDEAIQAYDEAIRL 562
                                       89************97 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.035        12      73     124 ..      34      85 ..      13      92 .. 0.87
   2 !   20.2   0.3   1.9e-06   0.00063      10     124 ..      95     221 ..      86     226 .. 0.90
   3 !   12.1   0.0   0.00061       0.2      54     130 ..     219     294 ..     217     301 .. 0.89
   4 !   12.6   0.0    0.0004      0.13      73     124 ..     306     357 ..     297     361 .. 0.92
   5 ?    7.0   0.0     0.022       7.2      53     125 ..     388     460 ..     362     477 .. 0.74
   6 ?    4.8   0.0      0.11        36      75     124 ..     444     493 ..     440     500 .. 0.92
   7 !    9.0   0.1    0.0055       1.8      75     124 ..     478     527 ..     471     531 .. 0.94
   8 !   10.6   0.5    0.0017      0.56      53     124 ..     490     561 ..     486     567 .. 0.90
   9 ?    3.4   0.1      0.29        96      68     132 ..     539     598 ..     527     605 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.035
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        + G + ea++ ++++++++P    ++    +Al ++G+  e +++Y+++ r
  gi|386000858|ref|YP_005919157.1|  34 YYRGNYTEAVQAYDEAIRLDPEYASAWNNKGLALDYQGNYDESIKAYDEAIR 85 
                                       5679999****************************************99865 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHHTT-HHHHHHHHHHHHTT...--SSTTGGGTT.........STTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BTAD  10 vaagraalaagdpeeaaelleaAlal...wrGpaladlea.........gewleaererleelrlealealaeaelr 74 
                                        ++g a+ ++g  +ea +++++A++l   ++G  +++ +a            + +e+ rl+ +  +a  +  +a+++
  gi|386000858|ref|YP_005919157.1|  95 NNKGIALGNQGNYTEATRCFDEAIRLdpeYAGAWYNKGKAlsergnytgAILAYDEAIRLDPELAAAWHKKGDALFE 171
                                       6678888999999**********997666999999888889999999866677899********************* PP

                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        G + ea++  +++++++P + +++     Al  +G+ aeA+ +Y+++ r
  gi|386000858|ref|YP_005919157.1| 172 RGNYTEAIQAFDEAIRLDPEDATTWYNKGVALGMQGNYAEAIPAYDEAIR 221
                                       *********************************************99865 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                              BTAD  54 rerleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeL 130
                                       + rl+ +  +a   + +a+ +lG+++ea+  l+++++++P + + +    + l   G+  eA+++++++  +L+ eL
  gi|386000858|ref|YP_005919157.1| 219 AIRLDPEDADAWNNRGNALNELGKYDEAIHALDKAIELDPEDAAPWNNKGKPLWMKGNYTEAIQAFDEAI-RLDPEL 294
                                       55778888899999****************************************************9995.455555 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.0004
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +  G+++ea++ +++++++hP   +++     Al+ +G+  eA+++Y+++ r
  gi|386000858|ref|YP_005919157.1| 306 ADQGKYDEAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQAYDEAIR 357
                                       56899******************************************99865 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  53 ererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       e+ rl+ +  ++  +  +     G+++ea++ ++++++++P   + +       + +G+  eA+++Y+++ rl
  gi|386000858|ref|YP_005919157.1| 388 EAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRL 460
                                       5555555555555555555556789999999999999999999999999999999999999999999988776 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.11
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        G+++ea++ ++++++++P   + +       + +G+  eA+++Y+++ r
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIR 493
                                       58999****************************************99865 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0055
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        G+++ea++ ++++++++P    ++     Al+ +++  eA+++Y+++ r
  gi|386000858|ref|YP_005919157.1| 478 QGKYDEAIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEAIR 527
                                       5899*****************************************99866 PP

  == domain 8  score: 10.6 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  53 ererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       e+ rl+ ++  a     +a+ +  +++ea++ ++++++++P   +++     Al  +G+  eA+++Y+++ r
  gi|386000858|ref|YP_005919157.1| 490 EAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEAIR 561
                                       66678888888888889999999********************************************99865 PP

  == domain 9  score: 3.4 bits;  conditional E-value: 0.29
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS- CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgv 132
                                         +a++  G+++ea++ ++++++++P     +      l ++G+ aeA e+Y ++     eeLg 
  gi|386000858|ref|YP_005919157.1| 539 KGNALVMQGKYDEAIQAYDEAIRLDPEFAYPWFSKGVVLEYLGKVAEANEAYAKA-----EELGY 598
                                       5567778888888888888888888888888888888888888888888888877.....55555 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.72   2.4e+02     151     175 ..      28      52 ..       2      65 .. 0.80
   2 ?    0.7   1.1       1.1   3.6e+02     146     174 ..      57      85 ..      33      99 .. 0.66
   3 ?    0.7   0.5       1.1   3.7e+02     126     174 ..      70     119 ..      65     134 .. 0.74
   4 ?    1.6   0.2      0.59     2e+02     151     175 ..     130     154 ..     101     164 .. 0.76
   5 !    7.9   0.1     0.007       2.3     151     179 ..     164     192 ..     158     201 .. 0.85
   6 ?    2.4   0.1      0.33   1.1e+02     152     179 ..     199     226 ..     193     235 .. 0.86
   7 ?    4.7   0.1     0.064        21     145     179 ..     226     260 ..     203     279 .. 0.74
   8 ?    6.4   0.0     0.019       6.4     124     174 ..     238     289 ..     234     296 .. 0.85
   9 !   12.1   0.4   0.00034      0.11     127     174 ..     275     323 ..     271     331 .. 0.72
  10 !    7.7   0.1    0.0078       2.6     152     178 ..     335     361 ..     329     375 .. 0.87
  11 ?   -0.8   0.0       3.2   1.1e+03     152     178 ..     369     395 ..     363     402 .. 0.87
  12 !    7.9   0.1     0.007       2.3     151     178 ..     402     429 ..     396     435 .. 0.86
  13 !    8.1   0.1    0.0058       1.9     151     179 ..     436     464 ..     426     471 .. 0.86
  14 ?    7.0   0.1     0.013       4.3     151     174 ..     470     493 ..     464     499 .. 0.88
  15 !    9.0   4.8    0.0032       1.1     126     174 ..     478     527 ..     478     535 .. 0.83
  16 !   12.5   0.2   0.00028     0.091     151     174 ..     538     561 ..     528     567 .. 0.88
  17 ?    3.1   0.1       0.2        65     152     174 ..     573     595 ..     572     604 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.72
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaa 175
                                        +G  l+ +g+ +eA +aY++A++ 
  gi|386000858|ref|YP_005919157.1|  28 SKGLTLYYRGNYTEAVQAYDEAIRL 52 
                                       47778889999***********975 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                            TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAla 174
                                       a++ + +G +l  qg+ de  +aY++A++
  gi|386000858|ref|YP_005919157.1|  57 ASAWNNKGLALDYQGNYDESIKAYDEAIR 85 
                                       33344577788888888888888888876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
                            TPR_21 126 ekkydeAlktLeak..keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       +++yde +k+ +++   + +faa+ +  +G +l +qg+ +eA   +++A++
  gi|386000858|ref|YP_005919157.1|  70 QGNYDESIKAYDEAirLDPEFAAAWN-NKGIALGNQGNYTEATRCFDEAIR 119
                                       66777777777654114567777665.589999999999999998888886 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.59
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaa 175
                                        +G +l+++g+ + A  aY++A++ 
  gi|386000858|ref|YP_005919157.1| 130 NKGKALSERGNYTGAILAYDEAIRL 154
                                       49********************975 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.007
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleek 179
                                        +GD+l+++g+ +eA +a+++A++   e+
  gi|386000858|ref|YP_005919157.1| 164 KKGDALFERGNYTEAIQAFDEAIRLDPED 192
                                       69********************9876665 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.33
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleek 179
                                       +G +l  qg+ +eA  aY++A++   e+
  gi|386000858|ref|YP_005919157.1| 199 KGVALGMQGNYAEAIPAYDEAIRLDPED 226
                                       7888999**************9876655 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.064
                            TPR_21 145 aalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                       +a + + rG++l + gk deA +a ++A++   e+
  gi|386000858|ref|YP_005919157.1| 226 DADAWNNRGNALNELGKYDEAIHALDKAIELDPED 260
                                       45566789999999999999999999999877665 PP

  == domain 8  score: 6.4 bits;  conditional E-value: 0.019
                            TPR_21 124 laekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        + +kydeA+++L+++ + +  +a+  + +G  l  +g+ +eA +a+++A++
  gi|386000858|ref|YP_005919157.1| 238 NELGKYDEAIHALDKAiELDPEDAAPWNNKGKPLWMKGNYTEAIQAFDEAIR 289
                                       5779*********765155777889999**********************97 PP

  == domain 9  score: 12.1 bits;  conditional E-value: 0.00034
                            TPR_21 127 kkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       ++y eA+++ +++ + +   a +   +G +l+ qgk deA +aY++A++
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIRlDPELAVAWSNKGTVLADQGKYDEAIQAYDEAIR 323
                                       666666666644433133334455679********************96 PP

  == domain 10  score: 7.7 bits;  conditional E-value: 0.0078
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaalee 178
                                       +G +l++qg+  eA +aY++A++   +
  gi|386000858|ref|YP_005919157.1| 335 KGSALYEQGNYPEAIQAYDEAIRLDPD 361
                                       8********************986655 PP

  == domain 11  score: -0.8 bits;  conditional E-value: 3.2
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaalee 178
                                       +G++l++ g+ +e   aY++A++   e
  gi|386000858|ref|YP_005919157.1| 369 KGNALSELGNYTEGILAYDEAIRLDPE 395
                                       8********************987665 PP

  == domain 12  score: 7.9 bits;  conditional E-value: 0.007
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaalee 178
                                        +G+ +  qgk deA +aY++A++   e
  gi|386000858|ref|YP_005919157.1| 402 SKGNSFRMQGKYDEAIQAYDEAIRLDPE 429
                                       5899999***************986655 PP

  == domain 13  score: 8.1 bits;  conditional E-value: 0.0058
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleek 179
                                        +G+ +  qgk deA +aY++A++   e+
  gi|386000858|ref|YP_005919157.1| 436 SKGNSFRMQGKYDEAIQAYDEAIRLDPEE 464
                                       5899999***************9876665 PP

  == domain 14  score: 7.0 bits;  conditional E-value: 0.013
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        +G+ +  qgk deA +aY++A++
  gi|386000858|ref|YP_005919157.1| 470 SKGNSFRMQGKYDEAIQAYDEAIR 493
                                       5899999***************97 PP

  == domain 15  score: 9.0 bits;  conditional E-value: 0.0032
                            TPR_21 126 ekkydeAlktLeak..keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       ++kydeA+++ +++   + +fa++  + +G++l++q+k deA +aY++A++
  gi|386000858|ref|YP_005919157.1| 478 QGKYDEAIQAYDEAirLDPEFAGAWYN-KGNALYEQDKYDEAIQAYDEAIR 527
                                       689999999997752257889888765.9********************97 PP

  == domain 16  score: 12.5 bits;  conditional E-value: 0.00028
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        +G++lv qgk deA +aY++A++
  gi|386000858|ref|YP_005919157.1| 538 NKGNALVMQGKYDEAIQAYDEAIR 561
                                       69********************97 PP

  == domain 17  score: 3.1 bits;  conditional E-value: 0.2
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G +l   gk +eA +aY +A +
  gi|386000858|ref|YP_005919157.1| 573 KGVVLEYLGKVAEANEAYAKAEE 595
                                       78899999************965 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.65   2.2e+02       2      25 ..      92     115 ..      91     116 .. 0.83
   2 ?    3.1   0.1      0.61     2e+02       3      24 ..     161     182 ..     159     184 .. 0.78
   3 ?    5.1   0.0      0.13        44       4      20 ..     196     212 ..     193     218 .. 0.84
   4 ?    3.5   0.1      0.45   1.5e+02       4      20 ..     230     246 ..     227     251 .. 0.88
   5 ?    8.2   0.0     0.014       4.6       1      24 [.     295     318 ..     295     320 .. 0.86
   6 ?    5.2   0.0      0.12        41       3      24 ..     331     352 ..     329     354 .. 0.82
   7 ?    3.4   0.0      0.49   1.6e+02       2      24 ..     500     522 ..     499     524 .. 0.84
   8 ?    3.4   0.0      0.47   1.6e+02       6      24 ..     538     556 ..     534     558 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.65
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       +a  + + al  +G++ eA + ++
  gi|386000858|ref|YP_005919157.1|  92 AAWNNKGIALGNQGNYTEATRCFD 115
                                       56678899***********99876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.61
                             TPR_4   3 allaLArallalGdldeArall 24 
                                       a +  + al+++G++ eA +++
  gi|386000858|ref|YP_005919157.1| 161 AWHKKGDALFERGNYTEAIQAF 182
                                       5566689**********97766 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.13
                             TPR_4   4 llaLArallalGdldeA 20 
                                        ++ + al  +G+++eA
  gi|386000858|ref|YP_005919157.1| 196 WYNKGVALGMQGNYAEA 212
                                       68899***********9 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.45
                             TPR_4   4 llaLArallalGdldeA 20 
                                         +++ al +lG +deA
  gi|386000858|ref|YP_005919157.1| 230 WNNRGNALNELGKYDEA 246
                                       5689************9 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.014
                             TPR_4   1 arallaLArallalGdldeArall 24 
                                       a+a ++ + +l+++G +deA ++ 
  gi|386000858|ref|YP_005919157.1| 295 AVAWSNKGTVLADQGKYDEAIQAY 318
                                       5789999*************7665 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.12
                             TPR_4   3 allaLArallalGdldeArall 24 
                                       a ++ + al+++G+++eA ++ 
  gi|386000858|ref|YP_005919157.1| 331 AWINKGSALYEQGNYPEAIQAY 352
                                       6678889***********7665 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.49
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                        a ++ + al+++  +deA ++ 
  gi|386000858|ref|YP_005919157.1| 500 GAWYNKGNALYEQDKYDEAIQAY 522
                                       688999*************7665 PP

  == domain 8  score: 3.4 bits;  conditional E-value: 0.47
                             TPR_4   6 aLArallalGdldeArall 24 
                                       + + al  +G +deA ++ 
  gi|386000858|ref|YP_005919157.1| 538 NKGNALVMQGKYDEAIQAY 556
                                       56899**********7665 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.29        96     101     126 ..      58      83 ..      21      89 .. 0.79
   2 ?    1.0   0.0       1.3   4.2e+02     101     132 ..      92     123 ..      88     133 .. 0.80
   3 ?   -0.4   0.0       3.3   1.1e+03     102     127 ..     127     152 ..     122     160 .. 0.84
   4 ?    3.5   0.1      0.21        70      64     126 ..     168     219 ..     159     229 .. 0.57
   5 !    9.4   0.0    0.0032         1     104     129 ..     231     256 ..     223     269 .. 0.81
   6 ?    3.7   0.0      0.17        58     104     126 ..     299     321 ..     259     327 .. 0.76
   7 ?    6.0   0.0     0.034        11      60     126 ..     300     355 ..     283     361 .. 0.67
   8 !    8.0   0.1    0.0082       2.7      54     127 ..     362     424 ..     353     431 .. 0.84
   9 ?    5.6   0.1     0.046        15      69     127 ..     411     458 ..     404     466 .. 0.78
  10 ?    6.4   0.1     0.026       8.6      66     128 ..     442     493 ..     431     505 .. 0.76
  11 ?    2.7   0.0      0.36   1.2e+02     102     127 ..     501     526 ..     495     535 .. 0.81
  12 ?    2.7   0.0      0.36   1.2e+02     104     129 ..     571     596 ..     566     600 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrma 126
                                       +a  +++ al+  G++de++ka+  a
  gi|386000858|ref|YP_005919157.1|  58 SAWNNKGLALDYQGNYDESIKAYDEA 83 
                                       55668889999999999999988776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrmagemiae 132
                                       aa  +++ al + G++ ea + f  a  +  e
  gi|386000858|ref|YP_005919157.1|  92 AAWNNKGIALGNQGNYTEATRCFDEAIRLDPE 123
                                       667799***************99998776555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a +++++al+e G++  a+ a+  a 
  gi|386000858|ref|YP_005919157.1| 127 AWYNKGKALSERGNYTGAILAYDEAI 152
                                       6689999******9999999988765 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.21
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       al + g+y ea+++ d+a+r       l+ ++   W    ++++val   G+++ea+ a+  a
  gi|386000858|ref|YP_005919157.1| 168 ALFERGNYTEAIQAFDEAIR-------LDPEDATTW----YNKGVALGMQGNYAEAIPAYDEA 219
                                       44444444444444444443.......444444444....56677777777777777666655 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                        +r+ al+elG++dea++a+ +a e+
  gi|386000858|ref|YP_005919157.1| 231 NNRGNALNELGKYDEAIHALDKAIEL 256
                                       57889999999999999999888886 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.17
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                        ++++ l++ G++dea++a+  a
  gi|386000858|ref|YP_005919157.1| 299 SNKGTVLADQGKYDEAIQAYDEA 321
                                       45666677777777777776655 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.034
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  60 glsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                            la  g+ydea+++ d+a+r       l+ +    W    ++++ al e G++ ea++a+  a
  gi|386000858|ref|YP_005919157.1| 300 NKGTVLADQGKYDEAIQAYDEAIR-------LHPNYVDAW----INKGSALYEQGNYPEAIQAYDEA 355
                                       445556666677777777777765.......444444444....47888888888888888888766 PP

  == domain 8  score: 8.0 bits;  conditional E-value: 0.0082
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  54 dalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       +a+++    +al +lg+y e++ + d+a+r       l+ +e   W+    s++ ++   G++dea++a+  a 
  gi|386000858|ref|YP_005919157.1| 362 NAMTWYNKGNALSELGNYTEGILAYDEAIR-------LDPEEADVWV----SKGNSFRMQGKYDEAIQAYDEAI 424
                                       67778888899999********99999997.......8999999996....799**************998875 PP

  == domain 9  score: 5.6 bits;  conditional E-value: 0.046
                                       T-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  69 grydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       g+ydea+++ d+a+r       l+ +e   W+    s++ ++   G++dea++a+  a 
  gi|386000858|ref|YP_005919157.1| 411 GKYDEAIQAYDEAIR-------LDPEEADVWV----SKGNSFRMQGKYDEAIQAYDEAI 458
                                       677777777777775.......7888888886....79999999999999999998875 PP

  == domain 10  score: 6.4 bits;  conditional E-value: 0.026
                                       HHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  66 aklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                          g+ydea+++ d+a+r       l+ +e   W+    s++ ++   G++dea++a+  a  
  gi|386000858|ref|YP_005919157.1| 442 RMQGKYDEAIQAYDEAIR-------LDPEEADVWV----SKGNSFRMQGKYDEAIQAYDEAIR 493
                                       455777777777777775.......7888888886....689999999999999999988765 PP

  == domain 11  score: 2.7 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a ++++ al e  ++dea++a+  a 
  gi|386000858|ref|YP_005919157.1| 501 AWYNKGNALYEQDKYDEAIQAYDEAI 526
                                       56788999999999999999888775 PP

  == domain 12  score: 2.7 bits;  conditional E-value: 0.36
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                       fs++v le lG+ +ea +a+ +a e+
  gi|386000858|ref|YP_005919157.1| 571 FSKGVVLEYLGKVAEANEAYAKAEEL 596
                                       89********************9986 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.7   1.2e+03      21      41 ..       2      22 ..       1      30 [. 0.77
   2 ?    3.2   0.3      0.21        68       7      36 ..      22      51 ..      20      56 .. 0.90
   3 ?    2.3   0.1      0.38   1.3e+02       7      36 ..      56      85 ..      54      87 .. 0.92
   4 ?    3.5   0.1      0.17        56       8      49 ..      91     132 ..      88     142 .. 0.81
   5 ?    0.8   0.0       1.1   3.7e+02       7      36 ..     124     153 ..     122     154 .. 0.91
   6 ?    4.9   0.0     0.063        21       8      36 ..     159     187 ..     156     189 .. 0.90
   7 ?    1.5   0.0       0.7   2.3e+02       8      36 ..     193     221 ..     190     222 .. 0.88
   8 !    8.1   0.0    0.0063       2.1       8      36 ..     227     255 ..     224     256 .. 0.93
   9 ?    3.9   0.0      0.12        41      10      36 ..     263     289 ..     259     290 .. 0.86
  10 ?    3.7   0.0      0.15        48       8      37 ..     295     324 ..     292     335 .. 0.84
  11 ?    5.0   0.1     0.057        19       9      56 ..     330     376 ..     325     389 .. 0.80
  12 ?    4.0   0.0      0.12        39       7      36 ..     396     425 ..     394     426 .. 0.89
  13 ?    4.0   0.0      0.12        39       7      36 ..     430     459 ..     428     460 .. 0.89
  14 ?    4.1   0.0      0.11        37       7      36 ..     464     493 ..     462     495 .. 0.90
  15 ?    5.5   0.4     0.042        14       7      42 ..     498     532 ..     495     539 .. 0.85
  16 ?    4.2   0.1       0.1        34       9      36 ..     534     561 ..     531     567 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.7
                           DUF5113 21 egeyeeALeyldsaleylNah 41
                                      +g+y+ A+e +d+a+++  ++
  gi|386000858|ref|YP_005919157.1|  2 QGNYTMAIEAFDEAIRLDPEY 22
                                      79************9865555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.21
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsale 36
                                       a+++ + + +l+++g+y+eA++  d+a++
  gi|386000858|ref|YP_005919157.1| 22 YADAWYSKGLTLYYRGNYTEAVQAYDEAIR 51
                                      57888899999*****************96 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.38
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsale 36
                                       a+++ n + +l ++g+y+e+++  d+a++
  gi|386000858|ref|YP_005919157.1| 56 YASAWNNKGLALDYQGNYDESIKAYDEAIR 85
                                      689999*********************996 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.17
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakkk 49 
                                       a ++ n + +l  +g+y+eA +++d+a+++  ++   +++k 
  gi|386000858|ref|YP_005919157.1|  91 AAAWNNKGIALGNQGNYTEATRCFDEAIRLDPEYAGAWYNKG 132
                                       7788899999999***************98777777777665 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.1
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        a+++ n +++l  +g+y+ A+   d+a++
  gi|386000858|ref|YP_005919157.1| 124 YAGAWYNKGKALSERGNYTGAILAYDEAIR 153
                                       689999******************999986 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.063
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       a ++ + + +l+ +g+y+eA++ +d+a++
  gi|386000858|ref|YP_005919157.1| 159 AAAWHKKGDALFERGNYTEAIQAFDEAIR 187
                                       7788899999*****************96 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.7
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       a ++ n + +l ++g+y eA+   d+a++
  gi|386000858|ref|YP_005919157.1| 193 ATTWYNKGVALGMQGNYAEAIPAYDEAIR 221
                                       677889999999**************986 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.0063
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       a+++ n +++ln  g+y+eA++ ld+a+e
  gi|386000858|ref|YP_005919157.1| 227 ADAWNNRGNALNELGKYDEAIHALDKAIE 255
                                       88999**********************97 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.12
                           DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                        + n ++ l ++g+y+eA++ +d+a++
  gi|386000858|ref|YP_005919157.1| 263 PWNNKGKPLWMKGNYTEAIQAFDEAIR 289
                                       5678889999***************96 PP

  == domain 10  score: 3.7 bits;  conditional E-value: 0.15
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaley 37 
                                       a ++ n ++ l  +g+y+eA++  d+a+++
  gi|386000858|ref|YP_005919157.1| 295 AVAWSNKGTVLADQGKYDEAIQAYDEAIRL 324
                                       667889999999***************986 PP

  == domain 11  score: 5.0 bits;  conditional E-value: 0.057
                           DUF5113   9 ndYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldkl 56 
                                       +++ n +++l+ +g+y eA++  d+a+++     +++++k  + l++l
  gi|386000858|ref|YP_005919157.1| 330 DAWINKGSALYEQGNYPEAIQAYDEAIRLDPDNAMTWYNKG-NALSEL 376
                                       67889999*******************98777777777776.466665 PP

  == domain 12  score: 4.0 bits;  conditional E-value: 0.12
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                       +a+ +++ ++   ++g+y+eA++  d+a++
  gi|386000858|ref|YP_005919157.1| 396 EADVWVSKGNSFRMQGKYDEAIQAYDEAIR 425
                                       57788999999****************996 PP

  == domain 13  score: 4.0 bits;  conditional E-value: 0.12
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                       +a+ +++ ++   ++g+y+eA++  d+a++
  gi|386000858|ref|YP_005919157.1| 430 EADVWVSKGNSFRMQGKYDEAIQAYDEAIR 459
                                       57788999999****************996 PP

  == domain 14  score: 4.1 bits;  conditional E-value: 0.11
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                       +a+ +++ ++   ++g+y+eA++  d+a++
  gi|386000858|ref|YP_005919157.1| 464 EADVWVSKGNSFRMQGKYDEAIQAYDEAIR 493
                                       57788999999****************996 PP

  == domain 15  score: 5.5 bits;  conditional E-value: 0.042
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaleylNahy 42 
                                        a+++ n +++l+ +++y+eA++  d+a++ lN  y
  gi|386000858|ref|YP_005919157.1| 498 FAGAWYNKGNALYEQDKYDEAIQAYDEAIR-LNPDY 532
                                       689999**********************97.45554 PP

  == domain 16  score: 4.2 bits;  conditional E-value: 0.1
                           DUF5113   9 ndYanlayylnvegeyeeALeyldsale 36 
                                       +++ n +++l ++g+y+eA++  d+a++
  gi|386000858|ref|YP_005919157.1| 534 EAWNNKGNALVMQGKYDEAIQAYDEAIR 561
                                       568899999*****************96 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       5.8   1.9e+03      14      28 ..       3      17 ..       1      19 [. 0.83
   2 ?    3.0   0.0      0.44   1.5e+02       9      28 ..     100     119 ..      99     121 .. 0.87
   3 ?    2.3   0.0      0.75   2.5e+02       9      28 ..     168     187 ..     167     189 .. 0.85
   4 ?    1.6   0.0       1.2     4e+02       3      25 ..     230     252 ..     228     257 .. 0.78
   5 ?    0.9   0.0       2.1   6.9e+02      13      28 ..     274     289 ..     271     291 .. 0.85
   6 ?    3.0   0.0      0.43   1.4e+02      10      27 ..     305     322 ..     303     325 .. 0.83
   7 ?    0.3   0.0       3.1     1e+03       9      28 ..     338     357 ..     337     359 .. 0.82
   8 ?    2.9   0.0      0.47   1.6e+02      10      28 ..     407     425 ..     405     427 .. 0.81
   9 ?    2.9   0.0      0.47   1.6e+02      10      28 ..     441     459 ..     439     461 .. 0.81
  10 ?    2.9   0.0      0.47   1.6e+02      10      28 ..     475     493 ..     473     495 .. 0.81
  11 ?    0.7   0.0       2.4   7.9e+02       9      28 ..     508     527 ..     507     529 .. 0.80
  12 ?    5.1   0.0     0.095        32       8      28 ..     541     561 ..     540     563 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5.8
                               PPR 14 GkleeAlelfkeMke 28
                                      G++ +A+e f+e ++
  gi|386000858|ref|YP_005919157.1|  3 GNYTMAIEAFDEAIR 17
                                      99999*****99765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.44
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       +++  G++ eA ++f+e ++
  gi|386000858|ref|YP_005919157.1| 100 ALGNQGNYTEATRCFDEAIR 119
                                       68899***********9765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.75
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++   G++ eA++ f+e ++
  gi|386000858|ref|YP_005919157.1| 168 ALFERGNYTEAIQAFDEAIR 187
                                       77889***********9765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 1.2
                               PPR   3 ynslIsgycknGkleeAlelfke 25 
                                       +n   +++   Gk++eA+  +++
  gi|386000858|ref|YP_005919157.1| 230 WNNRGNALNELGKYDEAIHALDK 252
                                       66666888999******988776 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 2.1
                               PPR  13 nGkleeAlelfkeMke 28 
                                       +G++ eA++ f+e ++
  gi|386000858|ref|YP_005919157.1| 274 KGNYTEAIQAFDEAIR 289
                                       79**********9765 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.43
                               PPR  10 ycknGkleeAlelfkeMk 27 
                                       ++  Gk++eA++ ++e +
  gi|386000858|ref|YP_005919157.1| 305 LADQGKYDEAIQAYDEAI 322
                                       6778*********99966 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 3.1
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++   G++ eA++ ++e ++
  gi|386000858|ref|YP_005919157.1| 338 ALYEQGNYPEAIQAYDEAIR 357
                                       67789********9999665 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.47
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       +   Gk++eA++ ++e ++
  gi|386000858|ref|YP_005919157.1| 407 FRMQGKYDEAIQAYDEAIR 425
                                       6678*********999765 PP

  == domain 9  score: 2.9 bits;  conditional E-value: 0.47
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       +   Gk++eA++ ++e ++
  gi|386000858|ref|YP_005919157.1| 441 FRMQGKYDEAIQAYDEAIR 459
                                       6678*********999765 PP

  == domain 10  score: 2.9 bits;  conditional E-value: 0.47
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       +   Gk++eA++ ++e ++
  gi|386000858|ref|YP_005919157.1| 475 FRMQGKYDEAIQAYDEAIR 493
                                       6678*********999765 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 2.4
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++    k++eA++ ++e ++
  gi|386000858|ref|YP_005919157.1| 508 ALYEQDKYDEAIQAYDEAIR 527
                                       6667789*******999766 PP

  == domain 12  score: 5.1 bits;  conditional E-value: 0.095
                               PPR   8 sgycknGkleeAlelfkeMke 28 
                                       ++++  Gk++eA++ ++e ++
  gi|386000858|ref|YP_005919157.1| 541 NALVMQGKYDEAIQAYDEAIR 561
                                       68999***********99765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.43   1.4e+02      15      36 ..       3      24 ..       2      27 .. 0.90
   2 ?    5.3   0.2     0.062        21      13      37 ..      35      59 ..      24      61 .. 0.85
   3 ?    3.1   0.0       0.3     1e+02      14      35 ..      70      91 ..      65      94 .. 0.91
   4 !    8.7   0.0    0.0054       1.8      12      34 ..     102     124 ..      98     127 .. 0.85
   5 ?    3.0   0.0      0.34   1.1e+02      15      34 ..     173     192 ..     168     194 .. 0.91
   6 ?    1.3   0.0       1.1   3.6e+02      13      37 ..     205     229 ..     196     231 .. 0.82
   7 ?    3.4   0.0      0.25        82      14      33 ..     240     259 ..     236     261 .. 0.92
   8 ?    2.1   0.0      0.64   2.1e+02      15      33 ..     275     293 ..     274     297 .. 0.93
   9 ?    1.5   0.0      0.93   3.1e+02      14      34 ..     308     328 ..     306     331 .. 0.89
  10 ?    6.6   0.0     0.024       7.9      10      34 ..     338     362 ..     336     364 .. 0.93
  11 ?   -0.8   0.0       5.1   1.7e+03      14      33 ..     376     395 ..     367     399 .. 0.85
  12 ?    1.3   0.0       1.1   3.7e+02      15      33 ..     411     429 ..     407     433 .. 0.90
  13 ?    1.3   0.0       1.1   3.7e+02      15      33 ..     445     463 ..     441     467 .. 0.90
  14 ?    2.5   0.0      0.46   1.5e+02      15      34 ..     479     498 ..     475     502 .. 0.90
  15 ?    2.7   0.4       0.4   1.3e+02      10      37 ..     508     535 ..     501     537 .. 0.87
  16 ?    2.2   0.0      0.57   1.9e+02      14      34 ..     546     566 ..     542     567 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.43
                                      T-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C 15 geYseArryvdalLeiEPenrQ 36
                                      g+Y++A +  d  ++++Pe   
  gi|386000858|ref|YP_005919157.1|  3 GNYTMAIEAFDEAIRLDPEYAD 24
                                      9*****************9765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.062
                                      HHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQa 37
                                        g+Y+eA +  d  ++++Pe   a
  gi|386000858|ref|YP_005919157.1| 35 YRGNYTEAVQAYDEAIRLDPEYASA 59
                                      559*****************98765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.3
                                      HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPenr 35
                                      +g+Y+e+ +  d  ++++Pe+ 
  gi|386000858|ref|YP_005919157.1| 70 QGNYDESIKAYDEAIRLDPEFA 91
                                      59*****************985 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0054
                                       HHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                         +g+Y+eA r+ d  ++++Pe 
  gi|386000858|ref|YP_005919157.1| 102 GNQGNYTEATRCFDEAIRLDPEY 124
                                       468******************86 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.34
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                       g+Y+eA +  d  ++++Pe 
  gi|386000858|ref|YP_005919157.1| 173 GNYTEAIQAFDEAIRLDPED 192
                                       8*****************85 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 1.1
                                       HHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                                        +g+Y eA    d  ++++Pe   a
  gi|386000858|ref|YP_005919157.1| 205 MQGNYAEAIPAYDEAIRLDPEDADA 229
                                       579*****************98665 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.25
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+Y+eA   +d  +e++Pe
  gi|386000858|ref|YP_005919157.1| 240 LGKYDEAIHALDKAIELDPE 259
                                       89*****************8 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.64
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       g+Y+eA +  d  ++++Pe
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIRLDPE 293
                                       8****************98 PP

  == domain 9  score: 1.5 bits;  conditional E-value: 0.93
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +g+Y+eA +  d  ++++P+ 
  gi|386000858|ref|YP_005919157.1| 308 QGKYDEAIQAYDEAIRLHPNY 328
                                       589****************85 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.024
                                       HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPen 34 
                                       + y +g+Y eA +  d  ++++P+n
  gi|386000858|ref|YP_005919157.1| 338 ALYEQGNYPEAIQAYDEAIRLDPDN 362
                                       67999*******************9 PP

  == domain 11  score: -0.8 bits;  conditional E-value: 5.1
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+Y+e     d  ++++Pe
  gi|386000858|ref|YP_005919157.1| 376 LGNYTEGILAYDEAIRLDPE 395
                                       89****99999999999997 PP

  == domain 12  score: 1.3 bits;  conditional E-value: 1.1
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       g+Y+eA +  d  ++++Pe
  gi|386000858|ref|YP_005919157.1| 411 GKYDEAIQAYDEAIRLDPE 429
                                       89***************98 PP

  == domain 13  score: 1.3 bits;  conditional E-value: 1.1
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       g+Y+eA +  d  ++++Pe
  gi|386000858|ref|YP_005919157.1| 445 GKYDEAIQAYDEAIRLDPE 463
                                       89***************98 PP

  == domain 14  score: 2.5 bits;  conditional E-value: 0.46
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                       g+Y+eA +  d  ++++Pe+
  gi|386000858|ref|YP_005919157.1| 479 GKYDEAIQAYDEAIRLDPEF 498
                                       89****************98 PP

  == domain 15  score: 2.7 bits;  conditional E-value: 0.4
                                       HHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQa 37 
                                       + y + +Y+eA +  d  +++ P+ + a
  gi|386000858|ref|YP_005919157.1| 508 ALYEQDKYDEAIQAYDEAIRLNPDYKEA 535
                                       7788999****************99877 PP

  == domain 16  score: 2.2 bits;  conditional E-value: 0.57
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +g+Y+eA +  d  ++++Pe+
  gi|386000858|ref|YP_005919157.1| 546 QGKYDEAIQAYDEAIRLDPEF 566
                                       699****************97 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.84   2.8e+02      45      69 ..      28      52 ..       1      89 [. 0.68
   2 ?    1.0   0.0      0.66   2.2e+02      42      69 ..      59      86 ..      27     129 .. 0.50
   3 ?    3.5   0.0      0.11        38      14      69 ..     172     222 ..     157     256 .. 0.50
   4 !    9.6   0.0    0.0015      0.51      47     111 ..     268     326 ..     252     359 .. 0.78
   5 ?    2.1   0.0      0.31     1e+02      88     111 ..     405     428 ..     399     433 .. 0.80
   6 !   11.9   0.0   0.00032      0.11      47     157 ..     438     534 ..     432     543 .. 0.80
   7 ?    4.2   0.1     0.069        23      87     111 ..     540     564 ..     535     596 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.84
                          TPR_MalT 45 vlGeasllqGdleaAlqalqeaekl 69
                                      + G +  ++G+ ++A+qa+ ea++l
  gi|386000858|ref|YP_005919157.1| 28 SKGLTLYYRGNYTEAVQAYDEAIRL 52
                                      4566666777777777777777765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.66
                          TPR_MalT 42 atavlGeasllqGdleaAlqalqeaekl 69
                                      a  + G a  +qG+ +++ +a+ ea++l
  gi|386000858|ref|YP_005919157.1| 59 AWNNKGLALDYQGNYDESIKAYDEAIRL 86
                                      3334455555555555565555555554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                          TPR_MalT  14 sgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaekl 69 
                                       +g+ ++a++   +A+ l ped+  +     ++ G a  +qG+ ++A  a+ ea++l
  gi|386000858|ref|YP_005919157.1| 172 RGNYTEAIQAFDEAIRLDPEDATTW-----YNKGVALGMQGNYAEAIPAYDEAIRL 222
                                       4444444444444444444444222.....33333333555555555555555554 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0015
                          TPR_MalT  47 GeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlat 111
                                       G   +++G+ ++A qa+ ea++l        +++++    + +l  qG+ +eA++ y +a++l +
  gi|386000858|ref|YP_005919157.1| 268 GKPLWMKGNYTEAIQAFDEAIRLD----PELAVAWS--NKGTVLADQGKYDEAIQAYDEAIRLHP 326
                                       556799*************99886....55555666..559********************9754 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.31
                          TPR_MalT  88 eilvaqGrLheAletyeqalqlat 111
                                       +  ++qG+ +eA++ y +a++l +
  gi|386000858|ref|YP_005919157.1| 405 NSFRMQGKYDEAIQAYDEAIRLDP 428
                                       556899999999999999999865 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00032
                          TPR_MalT  47 GeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgf 123
                                       G  + +qG+ ++A qa+ ea++l  ++  +    +  ++ ++  ++qG+ +eA++ y +a++l +e  ++      +
  gi|386000858|ref|YP_005919157.1| 438 GNSFRMQGKYDEAIQAYDEAIRLDPEEADV----W--VSKGNSFRMQGKYDEAIQAYDEAIRLDPEFAGA------W 502
                                       777889999999999999999986333332....2..46689999*****************87776665......3 PP

                          TPR_MalT 124 llvlladllyEwndLeeAeqhlqeGielleqlep 157
                                        +   ++ lyE+ + +eA q+ +e+i+l  ++++
  gi|386000858|ref|YP_005919157.1| 503 -Y-NKGNALYEQDKYDEAIQAYDEAIRLNPDYKE 534
                                       .4.55999******************99877655 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.069
                          TPR_MalT  87 aeilvaqGrLheAletyeqalqlat 111
                                       ++ lv+qG+ +eA++ y +a++l +
  gi|386000858|ref|YP_005919157.1| 540 GNALVMQGKYDEAIQAYDEAIRLDP 564
                                       5678999999999999999999755 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.9   6.2e+02     153     181 ..      33      61 ..       2      68 .. 0.77
   2 ?    6.3   0.0     0.024         8     123     181 ..      70     129 ..      62     135 .. 0.87
   3 !    9.1   0.1    0.0034       1.1     123     182 ..     172     232 ..     168     237 .. 0.90
   4 ?    1.3   0.0      0.82   2.7e+02     153     183 ..     237     267 ..     234     271 .. 0.86
   5 !   11.3   0.1   0.00074      0.25     124     182 ..     275     334 ..     272     339 .. 0.87
   6 ?    0.5   0.0       1.5   4.9e+02     122     180 ..     341     400 ..     334     406 .. 0.69
   7 ?    5.9   0.0     0.032        11     151     181 ..     405     435 ..     377     440 .. 0.78
   8 !    8.4   0.4    0.0054       1.8     125     181 ..     412     469 ..     410     474 .. 0.86
   9 ?    6.0   0.6      0.03       9.9     125     180 ..     446     502 ..     444     508 .. 0.82
  10 ?    7.0   1.3     0.015         5     125     182 ..     480     538 ..     476     543 .. 0.84
  11 !    8.1   1.0    0.0067       2.2     122     178 ..     511     568 ..     506     573 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.9
                           Wzy_C_2 153 lallGdedeAeqilararalfpeedakwv 181
                                       l   G   eA q +++a+ l pe++ +w+
  gi|386000858|ref|YP_005919157.1|  33 LYYRGNYTEAVQAYDEAIRLDPEYASAWN 61 
                                       556799999*********99999999995 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                           Wzy_C_2 123 penlaaklalarklihlsPe.pavierlilslallGdedeAeqilararalfpeedakwv 181
                                       + n+++ ++++ ++i+l Pe +a  ++  ++l  +G   eA++  ++a+ l pe++ +w 
  gi|386000858|ref|YP_005919157.1|  70 QGNYDESIKAYDEAIRLDPEfAAAWNNKGIALGNQGNYTEATRCFDEAIRLDPEYAGAWY 129
                                       7899999************9456789999***************************9993 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0034
                           Wzy_C_2 123 penlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakwvq 182
                                       + n+ + +++  ++i+l Pe a + ++  ++l ++G  +eA   +++a+ l pe++ +w++
  gi|386000858|ref|YP_005919157.1| 172 RGNYTEAIQAFDEAIRLDPEDAtTWYNKGVALGMQGNYAEAIPAYDEAIRLDPEDADAWNN 232
                                       67999999***********9761569*********************************54 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.82
                           Wzy_C_2 153 lallGdedeAeqilararalfpeedakwvql 183
                                       l  lG+ deA   l++a+ l pe++a w++ 
  gi|386000858|ref|YP_005919157.1| 237 LNELGKYDEAIHALDKAIELDPEDAAPWNNK 267
                                       5569**********************99664 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00074
                           Wzy_C_2 124 enlaaklalarklihlsPepavi.erlilslallGdedeAeqilararalfpeedakwvq 182
                                        n+ + +++  ++i+l Pe av  ++    la +G+ deA q +++a+ l+p++  +w++
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIRLDPELAVAwSNKGTVLADQGKYDEAIQAYDEAIRLHPNYVDAWIN 334
                                       57788899999999999999985378889999***********************99954 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 1.5
                           Wzy_C_2 122 spenlaaklalarklihlsPepavi.erlilslallGdedeAeqilararalfpeedakw 180
                                       ++ n+++ ++++ ++i+l P  a++ ++   +l  lG   e    +++a+ l pee+  w
  gi|386000858|ref|YP_005919157.1| 341 EQGNYPEAIQAYDEAIRLDPDNAMTwYNKGNALSELGNYTEGILAYDEAIRLDPEEADVW 400
                                       466777888888888888887765436666777777777777777777777777776666 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.032
                           Wzy_C_2 151 lslallGdedeAeqilararalfpeedakwv 181
                                        s  ++G+ deA q +++a+ l pee+  wv
  gi|386000858|ref|YP_005919157.1| 405 NSFRMQGKYDEAIQAYDEAIRLDPEEADVWV 435
                                       6789**********************99994 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.0054
                           Wzy_C_2 125 nlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakwv 181
                                       ++++ ++++ ++i+l Pe+a v      s  ++G+ deA q +++a+ l pee+  wv
  gi|386000858|ref|YP_005919157.1| 412 KYDEAIQAYDEAIRLDPEEAdVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEEADVWV 469
                                       67788999999999999886467778899***********************999994 PP

  == domain 9  score: 6.0 bits;  conditional E-value: 0.03
                           Wzy_C_2 125 nlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       ++++ ++++ ++i+l Pe+a v      s  ++G+ deA q +++a+ l pe + +w
  gi|386000858|ref|YP_005919157.1| 446 KYDEAIQAYDEAIRLDPEEAdVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPEFAGAW 502
                                       677889999999999998764667778999****************99988888777 PP

  == domain 10  score: 7.0 bits;  conditional E-value: 0.015
                           Wzy_C_2 125 nlaaklalarklihlsPe.pavierlilslallGdedeAeqilararalfpeedakwvq 182
                                       ++++ ++++ ++i+l Pe +   ++   +l  +++ deA q +++a+ l p+++++w++
  gi|386000858|ref|YP_005919157.1| 480 KYDEAIQAYDEAIRLDPEfAGAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDYKEAWNN 538
                                       678889999999999998434677788888899************************54 PP

  == domain 11  score: 8.1 bits;  conditional E-value: 0.0067
                           Wzy_C_2 122 spenlaaklalarklihlsP.epavierlilslallGdedeAeqilararalfpeeda 178
                                       +++++++ ++++ ++i+l P ++   ++   +l+++G+ deA q +++a+ l pe ++
  gi|386000858|ref|YP_005919157.1| 511 EQDKYDEAIQAYDEAIRLNPdYKEAWNNKGNALVMQGKYDEAIQAYDEAIRLDPEFAY 568
                                       5678899999999999999944567788999999**********99999988766555 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.22        74      15      30 ..      37      52 ..      35      53 .. 0.88
   2 ?   -1.2   0.0       4.5   1.5e+03      15      29 ..      71      85 ..      70      86 .. 0.85
   3 ?    5.8   0.0     0.028       9.3      12      29 ..     170     187 ..     166     188 .. 0.87
   4 ?    2.3   0.0      0.35   1.2e+02      15      30 ..     241     256 ..     239     256 .. 0.91
   5 ?    1.4   0.0      0.65   2.2e+02      15      30 ..     275     290 ..     274     292 .. 0.88
   6 ?    2.3   0.0      0.36   1.2e+02      14      30 ..     308     324 ..     307     328 .. 0.88
   7 ?    6.6   0.0     0.016       5.3      13      30 ..     341     358 ..     340     358 .. 0.90
   8 ?    2.0   0.0      0.44   1.5e+02      14      30 ..     410     426 ..     407     426 .. 0.88
   9 ?    2.0   0.0      0.44   1.5e+02      14      30 ..     444     460 ..     441     460 .. 0.88
  10 ?    2.0   0.0      0.44   1.5e+02      14      30 ..     478     494 ..     475     494 .. 0.88
  11 ?    4.8   0.2     0.057        19      13      30 ..     511     528 ..     510     535 .. 0.88
  12 ?    2.2   0.0      0.38   1.3e+02      14      30 ..     546     562 ..     544     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                          SHNi-TPR 15 enFpqAveDlrkaLeL 30
                                      +n+++Av+ +++a+ L
  gi|386000858|ref|YP_005919157.1| 37 GNYTEAVQAYDEAIRL 52
                                      7**********99865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.5
                          SHNi-TPR 15 enFpqAveDlrkaLe 29
                                      +n+++ ++ +++a+ 
  gi|386000858|ref|YP_005919157.1| 71 GNYDESIKAYDEAIR 85
                                      79******9999986 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.028
                          SHNi-TPR  12 lEnenFpqAveDlrkaLe 29 
                                       +E++n+++A++ +++a+ 
  gi|386000858|ref|YP_005919157.1| 170 FERGNYTEAIQAFDEAIR 187
                                       89***********99986 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.35
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++++A++ l+ka+eL
  gi|386000858|ref|YP_005919157.1| 241 GKYDEAIHALDKAIEL 256
                                       69************98 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.65
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +n+++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIRL 290
                                       69******99999865 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.36
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 308 QGKYDEAIQAYDEAIRL 324
                                       579**********9876 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.016
                          SHNi-TPR  13 EnenFpqAveDlrkaLeL 30 
                                       E++n+p+A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 341 EQGNYPEAIQAYDEAIRL 358
                                       89***********99865 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.44
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 410 QGKYDEAIQAYDEAIRL 426
                                       579*********99865 PP

  == domain 9  score: 2.0 bits;  conditional E-value: 0.44
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDEAIRL 460
                                       579*********99865 PP

  == domain 10  score: 2.0 bits;  conditional E-value: 0.44
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 478 QGKYDEAIQAYDEAIRL 494
                                       579*********99865 PP

  == domain 11  score: 4.8 bits;  conditional E-value: 0.057
                          SHNi-TPR  13 EnenFpqAveDlrkaLeL 30 
                                       E++++++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 511 EQDKYDEAIQAYDEAIRL 528
                                       89************9877 PP

  == domain 12  score: 2.2 bits;  conditional E-value: 0.38
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386000858|ref|YP_005919157.1| 546 QGKYDEAIQAYDEAIRL 562
                                       689*********99865 PP

>> Rota_NSP3  Rotavirus non-structural protein NSP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.18        60     227     264 ..      33      68 ..      25      84 .. 0.75
   2 ?    4.6   0.0     0.046        15     220     259 ..      60      97 ..      55     111 .. 0.83
   3 ?    0.1   0.0         1   3.4e+02     220     253 ..      94     126 ..      82     157 .. 0.74
   4 ?    0.8   0.0      0.65   2.2e+02     221     257 ..     129     164 ..     125     174 .. 0.84
   5 ?    1.9   0.0       0.3     1e+02     221     250 ..     163     191 ..     156     202 .. 0.87
   6 ?    3.9   0.0     0.072        24     219     250 ..     229     259 ..     209     264 .. 0.91
   7 ?    6.0   0.0     0.017       5.5     220     258 ..     264     301 ..     260     326 .. 0.86
   8 ?   -0.7   0.0       1.9   6.2e+02     219     249 ..     331     360 ..     312     370 .. 0.87
   9 ?    1.1   0.0      0.52   1.7e+02     221     250 ..     367     395 ..     361     423 .. 0.83
  10 ?   -0.5   0.0       1.7   5.5e+02     220     258 ..     468     505 ..     407     531 .. 0.73
  11 ?    1.6   0.0      0.37   1.2e+02     219     251 ..     535     566 ..     528     570 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                         Rota_NSP3 227 lldvGsltsskeiieksieleiPiikadirnnespdfd 264
                                       l+  G++t++++ +  +i l+ P++ + + nn+   +d
  gi|386000858|ref|YP_005919157.1|  33 LYYRGNYTEAVQAYDEAIRLD-PEYASAW-NNKGLALD 68 
                                       55579****************.****999.66654443 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.046
                         Rota_NSP3 220 yneklerlldvGsltsskeiieksieleiPiikadirnne 259
                                       +n+k+  l   G++ +s++ +  +i l+ P++ a + nn+
  gi|386000858|ref|YP_005919157.1|  60 WNNKGLALDYQGNYDESIKAYDEAIRLD-PEFAAAW-NNK 97 
                                       67777665558*****************.****999.554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1
                         Rota_NSP3 220 yneklerlldvGsltsskeiieksieleiPiika 253
                                       +n+k+  l + G++t++   +  +i l+ P++  
  gi|386000858|ref|YP_005919157.1|  94 WNNKGIALGNQGNYTEATRCFDEAIRLD-PEYAG 126
                                       5777777777777777777777777777.76654 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.65
                         Rota_NSP3 221 neklerlldvGsltsskeiieksieleiPiikadirn 257
                                        +k++ l + G++t ++  +  +i l+ P++ a +++
  gi|386000858|ref|YP_005919157.1| 129 YNKGKALSERGNYTGAILAYDEAIRLD-PELAAAWHK 164
                                       4788999999*****************.**9987754 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.3
                         Rota_NSP3 221 neklerlldvGsltsskeiieksieleiPi 250
                                        +k++ l++ G++t++++ +  +i l+ P+
  gi|386000858|ref|YP_005919157.1| 163 HKKGDALFERGNYTEAIQAFDEAIRLD-PE 191
                                       68999**********************.87 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.072
                         Rota_NSP3 219 vyneklerlldvGsltsskeiieksieleiPi 250
                                        +n++++ l ++G++ ++++ + k+iel+ P+
  gi|386000858|ref|YP_005919157.1| 229 AWNNRGNALNELGKYDEAIHALDKAIELD-PE 259
                                       68***************************.86 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.017
                         Rota_NSP3 220 yneklerlldvGsltsskeiieksieleiPiikadirnn 258
                                       +n+k+++l   G++t++++ +  +i l+ P++   + n+
  gi|386000858|ref|YP_005919157.1| 264 WNNKGKPLWMKGNYTEAIQAFDEAIRLD-PELAVAWSNK 301
                                       7***************************.*998777554 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 1.9
                         Rota_NSP3 219 vyneklerlldvGsltsskeiieksieleiP 249
                                        + +k+  l++ G++ ++++ +  +i l+ P
  gi|386000858|ref|YP_005919157.1| 331 AWINKGSALYEQGNYPEAIQAYDEAIRLD-P 360
                                       56789999********************9.6 PP

  == domain 9  score: 1.1 bits;  conditional E-value: 0.52
                         Rota_NSP3 221 neklerlldvGsltsskeiieksieleiPi 250
                                        +k++ l ++G++t+ +  +  +i l+ P+
  gi|386000858|ref|YP_005919157.1| 367 YNKGNALSELGNYTEGILAYDEAIRLD-PE 395
                                       578999999******************.86 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 1.7
                         Rota_NSP3 220 yneklerlldvGsltsskeiieksieleiPiikadirnn 258
                                       +  k++     G++ ++++ +  +i l+ P++   + n+
  gi|386000858|ref|YP_005919157.1| 468 WVSKGNSFRMQGKYDEAIQAYDEAIRLD-PEFAGAWYNK 505
                                       4455554444688888899999999999.8887766554 PP

  == domain 11  score: 1.6 bits;  conditional E-value: 0.37
                         Rota_NSP3 219 vyneklerlldvGsltsskeiieksieleiPii 251
                                        +n+k++ l+  G++ ++++ +  +i l+ P++
  gi|386000858|ref|YP_005919157.1| 535 AWNNKGNALVMQGKYDEAIQAYDEAIRLD-PEF 566
                                       58***************************.998 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.28        94      38      91 ..      16      69 ..       6      84 .. 0.80
   2 ?    1.3   0.0      0.74   2.5e+02      39      72 ..      85     118 ..      74     129 .. 0.84
   3 ?    3.8   0.0      0.13        42      39      72 ..     153     186 ..     134     202 .. 0.85
   4 ?   -1.6   0.0       5.7   1.9e+03      56      72 ..     238     254 ..     217     271 .. 0.76
   5 ?   -0.1   0.0         2   6.5e+02      55      79 ..     271     295 ..     236     312 .. 0.63
   6 ?    2.2   0.0       0.4   1.3e+02      35      72 ..     285     322 ..     272     331 .. 0.74
   7 ?    1.8   0.0      0.53   1.8e+02      28      71 ..     312     355 ..     294     365 .. 0.73
   8 ?   -1.0   0.0       3.7   1.2e+03      39      72 ..     391     424 ..     385     434 .. 0.79
   9 ?   -0.1   0.0         2   6.5e+02      36      72 ..     422     458 ..     405     468 .. 0.74
  10 ?    0.4   0.0       1.4   4.7e+02      36      73 ..     456     493 ..     433     506 .. 0.76
  11 ?    6.8   0.0     0.015       4.8      28      80 ..     516     568 ..     504     570 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.28
                        HrpB1_HrpK 38 rvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaa 91
                                       +L Pe a++    g+ l  rg+++eA+++  e     ++ + a     l+L +
  gi|386000858|ref|YP_005919157.1| 16 IRLDPEYADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEYASAWNNKGLALDY 69
                                      46899999999*******************999887777666665555555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.74
                        HrpB1_HrpK  39 vLrPevaeldllegvlliergrweeAlrlLreve 72 
                                       +L Pe+a++    g+ l ++g+++eA r + e  
  gi|386000858|ref|YP_005919157.1|  85 RLDPEFAAAWNNKGIALGNQGNYTEATRCFDEAI 118
                                       589999999999999999***********99976 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                        HrpB1_HrpK  39 vLrPevaeldllegvlliergrweeAlrlLreve 72 
                                       +L Pe+a++    g  l erg+++eA++++ e  
  gi|386000858|ref|YP_005919157.1| 153 RLDPELAAAWHKKGDALFERGNYTEAIQAFDEAI 186
                                       5899999999999999**************9976 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 5.7
                        HrpB1_HrpK  56 iergrweeAlrlLreve 72 
                                        e g+++eA+++L +  
  gi|386000858|ref|YP_005919157.1| 238 NELGKYDEAIHALDKAI 254
                                       56789999999998765 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 2
                        HrpB1_HrpK  55 liergrweeAlrlLreveaeasgtp 79 
                                       l  +g+++eA++++ e     ++ +
  gi|386000858|ref|YP_005919157.1| 271 LWMKGNYTEAIQAFDEAIRLDPELA 295
                                       4456778888888887766665555 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.4
                        HrpB1_HrpK  35 dalrvLrPevaeldllegvlliergrweeAlrlLreve 72 
                                       d+  +L Pe+a +    g +l  +g+++eA+++  e  
  gi|386000858|ref|YP_005919157.1| 285 DEAIRLDPELAVAWSNKGTVLADQGKYDEAIQAYDEAI 322
                                       44455888888888889999999999999999888766 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.53
                        HrpB1_HrpK  28 edaellLdalrvLrPevaeldllegvlliergrweeAlrlLrev 71 
                                       ++a +  d+  +L P+ +++ +  g  l e+g++ eA+++  e 
  gi|386000858|ref|YP_005919157.1| 312 DEAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQAYDEA 355
                                       44444455566788999999999999999999999999887776 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 3.7
                        HrpB1_HrpK  39 vLrPevaeldllegvlliergrweeAlrlLreve 72 
                                       +L Pe a++ +  g+    +g+++eA+++  e  
  gi|386000858|ref|YP_005919157.1| 391 RLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAI 424
                                       478888888888888888999******9988765 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 2
                        HrpB1_HrpK  36 alrvLrPevaeldllegvlliergrweeAlrlLreve 72 
                                       +  +L Pe a++ +  g+    +g+++eA+++  e  
  gi|386000858|ref|YP_005919157.1| 422 EAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAI 458
                                       4445788888888888888888999999999877765 PP

  == domain 10  score: 0.4 bits;  conditional E-value: 1.4
                        HrpB1_HrpK  36 alrvLrPevaeldllegvlliergrweeAlrlLrevea 73 
                                       +  +L Pe a++ +  g+    +g+++eA+++  e   
  gi|386000858|ref|YP_005919157.1| 456 EAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIR 493
                                       44568888888888888888889999999999888765 PP

  == domain 11  score: 6.8 bits;  conditional E-value: 0.015
                        HrpB1_HrpK  28 edaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpy 80 
                                       ++a +  d+  +L P  +e+    g+ l+ +g+++eA+++  e     ++++y
  gi|386000858|ref|YP_005919157.1| 516 DEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEAIRLDPEFAY 568
                                       4455555666679***************************9998877777665 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.44   1.5e+02      62     101 ..       8      47 ..       1      53 [. 0.73
   2 ?    2.3   0.0       0.5   1.7e+02      61     103 ..      41      83 ..      36      88 .. 0.86
   3 ?    0.0   0.0       2.5   8.4e+02      62      94 ..     110     142 ..     103     155 .. 0.70
   4 ?    5.4   0.0     0.055        18       4      32 ..     168     196 ..     165     211 .. 0.86
   5 ?    5.5   0.0     0.049        16       4      47 ..     270     310 ..     267     359 .. 0.83
   6 ?    1.7   0.0      0.74   2.5e+02       4      47 ..     338     378 ..     335     385 .. 0.71
   7 ?   -0.8   0.0       4.7   1.6e+03      62     103 ..     416     457 ..     413     462 .. 0.85
   8 ?    2.0   0.0       0.6     2e+02      62     103 ..     484     525 ..     480     529 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.44
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkak 101
                                       ++e+f ea +l   yA   +  +  l  +  Y +av+   
  gi|386000858|ref|YP_005919157.1|   8 AIEAFDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQAYD 47 
                                       7888888888888888888877777777777777776554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.5
                            DUF627  61 asvecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                        +v+++ ea +l   yA+   + +  l+ +  Y +++k   +a
  gi|386000858|ref|YP_005919157.1|  41 EAVQAYDEAIRLDPEYASAWNNKGLALDYQGNYDESIKAYDEA 83 
                                       699***************9999999999999999999876655 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.5
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYk 94 
                                       +  cf ea +l   yA   ++ ++ l  +  Y 
  gi|386000858|ref|YP_005919157.1| 110 ATRCFDEAIRLDPEYAGAWYNKGKALSERGNYT 142
                                       456778888888777777777777777666665 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.055
                            DUF627   4 dllargnhikALeiiedlisrhgedeksa 32 
                                       +l++rgn+++A++ ++++i+   ed + +
  gi|386000858|ref|YP_005919157.1| 168 ALFERGNYTEAIQAFDEAIRLDPEDATTW 196
                                       689****************9888877665 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.049
                            DUF627   4 dllargnhikALeiiedlisrhgedeksallhrlqGtifvklak 47 
                                        l+ +gn+++A++ ++++i+   e    a+   ++Gt+++++ k
  gi|386000858|ref|YP_005919157.1| 270 PLWMKGNYTEAIQAFDEAIRLDPE---LAVAWSNKGTVLADQGK 310
                                       578999999999999999999888...67777888999888876 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.74
                            DUF627   4 dllargnhikALeiiedlisrhgedeksallhrlqGtifvklak 47 
                                       +l+++gn+ +A++  +++i+   +    a+  +++G+ + +l +
  gi|386000858|ref|YP_005919157.1| 338 ALYEQGNYPEAIQAYDEAIRLDPD---NAMTWYNKGNALSELGN 378
                                       578899999999999999876666...35566666666666555 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 4.7
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                       +++++ ea +l    A   +  ++ ++ + +Y +a++   +a
  gi|386000858|ref|YP_005919157.1| 416 AIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEA 457
                                       899999999999999999999999999999999998876655 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.6
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                       +++++ ea +l    A   ++ ++ l  + +Y +a++   +a
  gi|386000858|ref|YP_005919157.1| 484 AIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEA 525
                                       89*********************************9876665 PP

>> BPS  BPS (Between PH and SH2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.91     3e+02      20      41 ..       8      29 ..       2      33 .. 0.84
   2 ?   -0.7   0.0         4   1.3e+03      25      41 ..      47      63 ..      37      66 .. 0.83
   3 ?    3.4   0.0      0.21        70       9      41 ..      65      97 ..      58     100 .. 0.90
   4 ?    1.9   0.0      0.59     2e+02      25      42 ..     149     166 ..     139     169 .. 0.85
   5 ?    1.4   0.0      0.85   2.8e+02      21      41 ..     179     199 ..     172     203 .. 0.82
   6 ?    3.2   0.0      0.24        81       9      42 ..     201     234 ..     197     237 .. 0.80
   7 ?    0.3   0.0         2   6.5e+02      21      43 ..     281     303 ..     274     305 .. 0.82
   8 ?   -1.1   0.0       5.3   1.7e+03      21      42 ..     349     370 ..     343     372 .. 0.82
   9 ?    0.7   0.0       1.4   4.7e+02      26      42 ..     388     404 ..     383     411 .. 0.81
  10 ?    2.3   0.0      0.45   1.5e+02      20      42 ..     416     438 ..     407     444 .. 0.78
  11 ?    2.3   0.0      0.45   1.5e+02      20      42 ..     450     472 ..     441     478 .. 0.78
  12 ?   -1.3   0.0       5.9     2e+03      20      42 ..     484     506 ..     477     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.91
                               BPS 20 vIeNptEalsaaleegqaWRkk 41
                                       Ie   Ea   ++e + aW  k
  gi|386000858|ref|YP_005919157.1|  8 AIEAFDEAIRLDPEYADAWYSK 29
                                      699999*************766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4
                               BPS 25 tEalsaaleegqaWRkk 41
                                       Ea   ++e + aW  k
  gi|386000858|ref|YP_005919157.1| 47 DEAIRLDPEYASAWNNK 63
                                      69999999******877 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.21
                               BPS  9 VaMDFSGqkgrvIeNptEalsaaleegqaWRkk 41
                                       a+D+ G+    I    Ea   ++e + aW  k
  gi|386000858|ref|YP_005919157.1| 65 LALDYQGNYDESIKAYDEAIRLDPEFAAAWNNK 97
                                      699***************************887 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.59
                               BPS  25 tEalsaaleegqaWRkks 42 
                                        Ea   ++e + aW kk 
  gi|386000858|ref|YP_005919157.1| 149 DEAIRLDPELAAAWHKKG 166
                                       699999**********96 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.85
                               BPS  21 IeNptEalsaaleegqaWRkk 41 
                                       I    Ea   ++e++ +W  k
  gi|386000858|ref|YP_005919157.1| 179 IQAFDEAIRLDPEDATTWYNK 199
                                       677789************877 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.24
                               BPS   9 VaMDFSGqkgrvIeNptEalsaaleegqaWRkks 42 
                                       Va+   G+    I    Ea   ++e++ aW  + 
  gi|386000858|ref|YP_005919157.1| 201 VALGMQGNYAEAIPAYDEAIRLDPEDADAWNNRG 234
                                       56666677777788889*************9886 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 2
                               BPS  21 IeNptEalsaaleegqaWRkkss 43 
                                       I    Ea   ++e + aW  k +
  gi|386000858|ref|YP_005919157.1| 281 IQAFDEAIRLDPELAVAWSNKGT 303
                                       667789999*********99876 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 5.3
                               BPS  21 IeNptEalsaaleegqaWRkks 42 
                                       I    Ea   +++++ +W  k 
  gi|386000858|ref|YP_005919157.1| 349 IQAYDEAIRLDPDNAMTWYNKG 370
                                       5566799999********8876 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 1.4
                               BPS  26 EalsaaleegqaWRkks 42 
                                       Ea   ++ee+  W  k 
  gi|386000858|ref|YP_005919157.1| 388 EAIRLDPEEADVWVSKG 404
                                       99999********8775 PP

  == domain 10  score: 2.3 bits;  conditional E-value: 0.45
                               BPS  20 vIeNptEalsaaleegqaWRkks 42 
                                        I    Ea   ++ee+  W  k 
  gi|386000858|ref|YP_005919157.1| 416 AIQAYDEAIRLDPEEADVWVSKG 438
                                       577778*************8775 PP

  == domain 11  score: 2.3 bits;  conditional E-value: 0.45
                               BPS  20 vIeNptEalsaaleegqaWRkks 42 
                                        I    Ea   ++ee+  W  k 
  gi|386000858|ref|YP_005919157.1| 450 AIQAYDEAIRLDPEEADVWVSKG 472
                                       577778*************8775 PP

  == domain 12  score: -1.3 bits;  conditional E-value: 5.9
                               BPS  20 vIeNptEalsaaleegqaWRkks 42 
                                        I    Ea   ++e + aW  k 
  gi|386000858|ref|YP_005919157.1| 484 AIQAYDEAIRLDPEFAGAWYNKG 506
                                       5777789999*********8876 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.6   5.2e+02      87     129 ..      19      64 ..      14      79 .. 0.71
   2 ?    3.1   0.0      0.19        62      94     139 ..     161     210 ..     149     215 .. 0.80
   3 ?    2.9   0.0      0.22        72      93     134 ..     228     273 ..     223     286 .. 0.78
   4 ?    0.3   0.0       1.4   4.7e+02     114     135 ..     355     376 ..     327     388 .. 0.71
   5 ?    4.2   0.0     0.086        29     115     137 ..     390     412 ..     388     422 .. 0.83
   6 ?    5.0   0.0      0.05        16     114     137 ..     423     446 ..     409     456 .. 0.78
   7 ?    5.5   0.0     0.034        11     114     137 ..     457     480 ..     434     490 .. 0.74
   8 ?    5.6   0.0     0.032        11      91     142 ..     532     587 ..     522     593 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.6
                     Pyrid_ox_like  87 drakieelWspvvkawfpegkddpnlt....likvtpeeaeyWdsks 129
                                       d++ ++  +s+ +  ++ +g+ ++ ++     i+++pe a  W++k+
  gi|386000858|ref|YP_005919157.1|  19 DPEYADAWYSKGLTLYY-RGNYTEAVQaydeAIRLDPEYASAWNNKG 64 
                                       66666677777777777.67777777533335899999999999876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.19
                     Pyrid_ox_like  94 lWspvvkawfpegkddpnlt....likvtpeeaeyWdsksgklvsllkma 139
                                        W +  +a f++g+ ++ ++     i+++pe+a  W +k+  l +  ++a
  gi|386000858|ref|YP_005919157.1| 161 AWHKKGDALFERGNYTEAIQafdeAIRLDPEDATTWYNKGVALGMQGNYA 210
                                       68888999999999999998333359***********9987776665555 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.22
                     Pyrid_ox_like  93 elWspvvkawfpegkddpnltl....ikvtpeeaeyWdsksgklvs 134
                                       + W++  +a  + gk d+ +      i+++pe+a  W++k++ l +
  gi|386000858|ref|YP_005919157.1| 228 DAWNNRGNALNELGKYDEAIHAldkaIELDPEDAAPWNNKGKPLWM 273
                                       67999999999999999999742222789**********8877655 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.4
                     Pyrid_ox_like 114 likvtpeeaeyWdsksgklvsl 135
                                        i+++p++a  W +k++ l  l
  gi|386000858|ref|YP_005919157.1| 355 AIRLDPDNAMTWYNKGNALSEL 376
                                       599***********99988765 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.086
                     Pyrid_ox_like 115 ikvtpeeaeyWdsksgklvsllk 137
                                       i+++peea +W sk++++ +  k
  gi|386000858|ref|YP_005919157.1| 390 IRLDPEEADVWVSKGNSFRMQGK 412
                                       89************999877655 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.05
                     Pyrid_ox_like 114 likvtpeeaeyWdsksgklvsllk 137
                                        i+++peea +W sk++++ +  k
  gi|386000858|ref|YP_005919157.1| 423 AIRLDPEEADVWVSKGNSFRMQGK 446
                                       599************999877655 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.034
                     Pyrid_ox_like 114 likvtpeeaeyWdsksgklvsllk 137
                                        i+++peea +W sk++++ +  k
  gi|386000858|ref|YP_005919157.1| 457 AIRLDPEEADVWVSKGNSFRMQGK 480
                                       59*************999877655 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.032
                     Pyrid_ox_like  91 ieelWspvvkawfpegkddpnlt....likvtpeeaeyWdsksgklvsllkmakaa 142
                                        +e W++  +a   +gk d+ ++     i+++pe a+ W sk+  l +l k+a+a+
  gi|386000858|ref|YP_005919157.1| 532 YKEAWNNKGNALVMQGKYDEAIQaydeAIRLDPEFAYPWFSKGVVLEYLGKVAEAN 587
                                       6899******************8444459***********9998888888888775 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.8   5.8e+02       9      30 ..       8      29 ..       6      51 .. 0.84
   2 ?   -0.3   0.0       5.3   1.8e+03       8      28 ..      41      61 ..      39      68 .. 0.86
   3 ?    2.5   0.0      0.71   2.4e+02       7      37 ..      74     104 ..      73     120 .. 0.78
   4 ?    1.0   0.0       2.1   6.9e+02      10      37 ..     145     172 ..     142     191 .. 0.72
   5 ?    1.7   0.1       1.3   4.5e+02       8      31 ..     279     302 ..     277     325 .. 0.76
   6 ?    0.7   0.0       2.7     9e+02       7      29 ..     312     334 ..     310     358 .. 0.81
   7 ?    2.2   0.0      0.88   2.9e+02       7      45 ..     414     452 ..     412     460 .. 0.78
   8 ?    2.1   0.0      0.98   3.2e+02       7      43 ..     448     484 ..     446     493 .. 0.77
   9 ?    3.5   0.0      0.35   1.2e+02       7      48 ..     482     523 ..     481     528 .. 0.78
  10 ?    3.3   0.0      0.42   1.4e+02       7      34 ..     516     543 ..     512     562 .. 0.77
  11 ?    0.3   0.0       3.6   1.2e+03       7      31 ..     550     574 ..     548     593 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.8
                         TetR_C_15  9 lvdallaahrenpalrrvllee 30
                                       ++a+ +a r +p++  ++++ 
  gi|386000858|ref|YP_005919157.1|  8 AIEAFDEAIRLDPEYADAWYSK 29
                                      589****************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 5.3
                         TetR_C_15  8 alvdallaahrenpalrrvll 28
                                      + v+a+ +a r +p++  ++ 
  gi|386000858|ref|YP_005919157.1| 41 EAVQAYDEAIRLDPEYASAWN 61
                                      689*************99886 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.71
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel 37 
                                       d+ + a+ +a r +p++ +++     +lg++
  gi|386000858|ref|YP_005919157.1|  74 DESIKAYDEAIRLDPEFAAAWNNKGIALGNQ 104
                                       67799****************9888777776 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 2.1
                         TetR_C_15  10 vdallaahrenpalrrvlleeapslgel 37 
                                       + a+ +a r +p+l +++++   +l e 
  gi|386000858|ref|YP_005919157.1| 145 ILAYDEAIRLDPELAAAWHKKGDALFER 172
                                       6789999***********9876555444 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 1.3
                         TetR_C_15   8 alvdallaahrenpalrrvlleea 31 
                                       + ++a+ +a r +p+l ++++   
  gi|386000858|ref|YP_005919157.1| 279 EAIQAFDEAIRLDPELAVAWSNKG 302
                                       6799***************98765 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 2.7
                         TetR_C_15   7 dalvdallaahrenpalrrvlle 29 
                                       d+ ++a+ +a r +p +  ++  
  gi|386000858|ref|YP_005919157.1| 312 DEAIQAYDEAIRLHPNYVDAWIN 334
                                       7899************9999875 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.88
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeq 45 
                                       d+ ++a+ +a r +p+   v+++   s + +   +++ q
  gi|386000858|ref|YP_005919157.1| 414 DEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQ 452
                                       7899*****************999877777744444444 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.98
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelveal 43 
                                       d+ ++a+ +a r +p+   v+++   s + +   +++
  gi|386000858|ref|YP_005919157.1| 448 DEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEA 484
                                       7899*****************9998777777444444 PP

  == domain 9  score: 3.5 bits;  conditional E-value: 0.35
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeqria 48 
                                       d+ ++a+ +a r +p++  +++    +l e++  +++ q  +
  gi|386000858|ref|YP_005919157.1| 482 DEAIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYD 523
                                       789*******************99887777755555555555 PP

  == domain 10  score: 3.3 bits;  conditional E-value: 0.42
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapsl 34 
                                       d+ ++a+ +a r np++++++     +l
  gi|386000858|ref|YP_005919157.1| 516 DEAIQAYDEAIRLNPDYKEAWNNKGNAL 543
                                       789*****************98766555 PP

  == domain 11  score: 0.3 bits;  conditional E-value: 3.6
                         TetR_C_15   7 dalvdallaahrenpalrrvlleea 31 
                                       d+ ++a+ +a r +p++   +++  
  gi|386000858|ref|YP_005919157.1| 550 DEAIQAYDEAIRLDPEFAYPWFSKG 574
                                       7899*************98887765 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.65   2.2e+02       7      34 ..     158     185 ..     155     192 .. 0.84
   2 ?    3.5   0.0      0.25        84      12      36 ..     231     255 ..     225     262 .. 0.82
   3 ?    3.2   0.0      0.31     1e+02       7      34 ..     294     321 ..     290     328 .. 0.79
   4 ?    0.8   0.0       1.7   5.8e+02      20      34 ..     409     423 ..     401     432 .. 0.81
   5 ?    0.9   0.0       1.6   5.4e+02      20      34 ..     443     457 ..     431     466 .. 0.81
   6 ?    0.7   0.0       1.9   6.4e+02      20      34 ..     477     491 ..     468     496 .. 0.80
   7 ?   -0.9   0.0       6.1     2e+03      15      34 ..     506     525 ..     499     529 .. 0.78
   8 ?    4.4   0.0      0.14        45      12      34 ..     537     559 ..     528     563 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.65
                         NRBF2_MIT   7 lahqqsrkadrllaaGkyeeaischkka 34 
                                       la    +k d l+  G y eai     a
  gi|386000858|ref|YP_005919157.1| 158 LAAAWHKKGDALFERGNYTEAIQAFDEA 185
                                       677778999*************987665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.25
                         NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaa 36 
                                       + + + l   Gky+eai    ka +
  gi|386000858|ref|YP_005919157.1| 231 NNRGNALNELGKYDEAIHALDKAIE 255
                                       5677788889*******99999876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.31
                         NRBF2_MIT   7 lahqqsrkadrllaaGkyeeaischkka 34 
                                       la   s k   l   Gky+eai  +  a
  gi|386000858|ref|YP_005919157.1| 294 LAVAWSNKGTVLADQGKYDEAIQAYDEA 321
                                       555667777788889*******988766 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.7
                         NRBF2_MIT  20 aaGkyeeaischkka 34 
                                         Gky+eai  +  a
  gi|386000858|ref|YP_005919157.1| 409 MQGKYDEAIQAYDEA 423
                                       579******988766 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.6
                         NRBF2_MIT  20 aaGkyeeaischkka 34 
                                         Gky+eai  +  a
  gi|386000858|ref|YP_005919157.1| 443 MQGKYDEAIQAYDEA 457
                                       579******988766 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 1.9
                         NRBF2_MIT  20 aaGkyeeaischkka 34 
                                         Gky+eai  +  a
  gi|386000858|ref|YP_005919157.1| 477 MQGKYDEAIQAYDEA 491
                                       579******987766 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 6.1
                         NRBF2_MIT  15 adrllaaGkyeeaischkka 34 
                                        + l    ky+eai  +  a
  gi|386000858|ref|YP_005919157.1| 506 GNALYEQDKYDEAIQAYDEA 525
                                       566777889****9987765 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.14
                         NRBF2_MIT  12 srkadrllaaGkyeeaischkka 34 
                                       + k + l+  Gky+eai  +  a
  gi|386000858|ref|YP_005919157.1| 537 NNKGNALVMQGKYDEAIQAYDEA 559
                                       56889999*********988766 PP

>> DUF2917  Protein of unknown function (DUF2917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.04        13      34      50 ..     396     412 ..     391     420 .. 0.85
   2 ?    5.2   0.0      0.04        13      34      50 ..     430     446 ..     425     454 .. 0.85
   3 ?    5.2   0.0      0.04        13      34      50 ..     464     480 ..     459     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.04
                           DUF2917  34 peDhwLqaGqslrlarg 50 
                                         D+w  +G s+r++++
  gi|386000858|ref|YP_005919157.1| 396 EADVWVSKGNSFRMQGK 412
                                       68***********9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.04
                           DUF2917  34 peDhwLqaGqslrlarg 50 
                                         D+w  +G s+r++++
  gi|386000858|ref|YP_005919157.1| 430 EADVWVSKGNSFRMQGK 446
                                       68***********9986 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.04
                           DUF2917  34 peDhwLqaGqslrlarg 50 
                                         D+w  +G s+r++++
  gi|386000858|ref|YP_005919157.1| 464 EADVWVSKGNSFRMQGK 480
                                       68***********9986 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.27        89      11      34 ..      28      51 ..      21      84 .. 0.88
   2 ?    0.9   0.0       1.4   4.8e+02      12      65 ..     199     249 ..     188     260 .. 0.70
   3 ?    4.6   0.0       0.1        34      10      60 ..     333     380 ..     327     390 .. 0.78
   4 ?    4.7   0.0     0.098        32      11      64 ..     504     554 ..     498     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.27
                          Rapsyn_N 11 ekGLklyesndtekalrvWrkvLk 34
                                       kGL ly   + ++a++ + ++++
  gi|386000858|ref|YP_005919157.1| 28 SKGLTLYYRGNYTEAVQAYDEAIR 51
                                      69***************9998877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.4
                          Rapsyn_N  12 kGLklyesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkykealef 65 
                                       kG+ l  + +  +a+  + ++++   + ++ ++  G   +a  e+Gky ea++ 
  gi|386000858|ref|YP_005919157.1| 199 KGVALGMQGNYAEAIPAYDEAIRLDPEDADAWNNRG---NALNELGKYDEAIHA 249
                                       666666666666666666666666666666666666...57789******9964 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.1
                          Rapsyn_N  10 iekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkyk 60 
                                       i+kG  lye+ +  +a++ + ++++   d++  +   G   +a se+G y 
  gi|386000858|ref|YP_005919157.1| 333 INKGSALYEQGNYPEAIQAYDEAIRLDPDNAMTWYNKG---NALSELGNYT 380
                                       99******************999998777766655555...3555666655 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.098
                          Rapsyn_N  11 ekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkykeale 64 
                                       +kG  lye+++ ++a++ + ++++   d ++ ++  G    a    Gky ea++
  gi|386000858|ref|YP_005919157.1| 504 NKGNALYEQDKYDEAIQAYDEAIRLNPDYKEAWNNKGN---ALVMQGKYDEAIQ 554
                                       6999*******************999999998888874...5566788888877 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.11        37     269     302 ..      40      73 ..      35     121 .. 0.76
   2 ?    6.6   0.0     0.012         4     254     304 ..     128     177 ..      95     227 .. 0.79
   3 ?    4.6   1.3     0.046        15     247     291 ..     297     334 ..     224     381 .. 0.65
   4 ?    5.3   4.0     0.029       9.6     235     303 ..     483     556 ..     394     580 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                                       SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHH CS
                               FAT 269 eeilqsysaateidpswykawhtwalfnfevvsk 302
                                        e++q+y +a ++dp+ + aw++ +l+ + + + 
  gi|386000858|ref|YP_005919157.1|  40 TEAVQAYDEAIRLDPEYASAWNNKGLALDYQGNY 73 
                                       6888999999999999999998866666655444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                                       CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHH CS
                               FAT 254 wqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskee 304
                                       w ++ + l+ ++ +  ++  +y +a ++dp+++ awh+ +++ fe+ +  e
  gi|386000858|ref|YP_005919157.1| 128 WYNKGKALS-ERGNYTGAILAYDEAIRLDPELAAAWHKKGDALFERGNYTE 177
                                       555555543.44457788889***********************9977765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.046
                                       CCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 247 cylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       +   kG  ++  +k        +e+ q+y +a +++p+  +aw +
  gi|386000858|ref|YP_005919157.1| 297 AWSNKGTVLADQGK-------YDEAIQAYDEAIRLHPNYVDAWIN 334
                                       33333333333333.......566666666666666666666655 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                                       ........HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC......CCHHHHHCCHHH CS
                               FAT 235 tnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawht......walfnfevvske 303
                                       + ++ + + +     + G w ++ + l  +++k +e+ q+y +a +++p+  +aw++      +   ++e+++++
  gi|386000858|ref|YP_005919157.1| 483 EAIQAYDEAIRLDPEFAGAWYNKGNAL-YEQDKYDEAIQAYDEAIRLNPDYKEAWNNkgnalvMQGKYDEAIQAY 556
                                       444444444433445567777777776.45566888888888888888888888888666666666666666666 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.89     3e+02      78     121 ..      32      75 ..       1      81 [. 0.60
   2 ?    3.3   0.1      0.32   1.1e+02      81     118 ..     205     242 ..     125     252 .. 0.61
   3 ?   -1.2   0.0         8   2.7e+03      80     121 ..     272     313 ..     260     319 .. 0.76
   4 ?    7.1   0.0     0.021       7.1      71     121 ..     331     381 ..     327     386 .. 0.91
   5 ?    0.8   0.0       1.9   6.3e+02      73     122 ..     401     450 ..     396     455 .. 0.84
   6 ?    0.8   0.0       1.8     6e+02      72     122 ..     434     484 ..     422     488 .. 0.85
   7 ?    3.9   0.2      0.21        68      74     122 ..     504     552 ..     497     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.89
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       + + +g+y  a++  + ++  dpe a+a + k  al+  g+  e
  gi|386000858|ref|YP_005919157.1|  32 TLYYRGNYTEAVQAYDEAIRLDPEYASAWNNKGLALDYQGNYDE 75 
                                       44556666666666666666666666666666666666655555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.32
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                        +g+y  a+   + ++  dpe+a+a + + +al++lg+
  gi|386000858|ref|YP_005919157.1| 205 MQGNYAEAIPAYDEAIRLDPEDADAWNNRGNALNELGK 242
                                       34445555555555555555556666656566555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 8
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                         +g+y  a++  + ++  dpe a a + k  +l   g+  e
  gi|386000858|ref|YP_005919157.1| 272 WMKGNYTEAIQAFDEAIRLDPELAVAWSNKGTVLADQGKYDE 313
                                       568889999999999999999988888888777777776665 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
                   Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                       + ++k ++ +++g+y  a++  + ++  dp+na +   k +al +lg+ +e
  gi|386000858|ref|YP_005919157.1| 331 AWINKGSALYEQGNYPEAIQAYDEAIRLDPDNAMTWYNKGNALSELGNYTE 381
                                       567889999*************************************98776 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       ++k ++ + +g+y  a++  + ++  dpe+a+    k ++++  g+  e+
  gi|386000858|ref|YP_005919157.1| 401 VSKGNSFRMQGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEA 450
                                       6677788899********************99999999999988887766 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        ++k ++ + +g+y  a++  + ++  dpe+a+    k ++++  g+  e+
  gi|386000858|ref|YP_005919157.1| 434 WVSKGNSFRMQGKYDEAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEA 484
                                       56677788899********************99999999999988887765 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.21
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       +k ++ +++++y  a++  + ++  +p+ +ea + k +al   g+  e+
  gi|386000858|ref|YP_005919157.1| 504 NKGNALYEQDKYDEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEA 552
                                       6788999****************************99999988887766 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.12        38       6      55 ..       7      56 ..       2      69 .. 0.87
   2 ?    2.7   0.1       0.5   1.6e+02      11      53 ..     148     190 ..     139     199 .. 0.83
   3 ?    4.9   0.0       0.1        34       6      42 ..     177     213 ..     172     215 .. 0.93
   4 ?    7.5   0.8     0.015         5       6      52 ..     211     257 ..     206     268 .. 0.87
   5 ?    2.6   0.1      0.52   1.7e+02       7      51 ..     246     290 ..     243     294 .. 0.88
   6 ?    5.0   0.1     0.095        31       6      50 ..     313     357 ..     308     376 .. 0.87
   7 ?   -0.7   0.1       5.4   1.8e+03      12      51 ..     387     426 ..     379     433 .. 0.77
   8 ?    2.1   0.1      0.76   2.5e+02       6      52 ..     415     461 ..     410     476 .. 0.86
   9 ?    2.3   0.1      0.65   2.2e+02       6      54 ..     449     497 ..     444     508 .. 0.85
  10 ?    4.1   0.4      0.17        57       6      56 ..     483     533 ..     478     539 .. 0.87
  11 ?    5.4   0.3     0.067        22       5      52 ..     516     563 ..     512     568 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
                            TPR_20  6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55
                                        ++++++a+  +p+  da +   l l+ +g+y eA+++  e ++ d ++
  gi|386000858|ref|YP_005919157.1|  7 MAIEAFDEAIRLDPEYADAWYSKGLTLYYRGNYTEAVQAYDEAIRLDPEY 56
                                      578999*******************************9887777777665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.5
                            TPR_20  11 leaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                        ++a+  +p+  +a ++  +al+++g+y eA++++ e ++ d 
  gi|386000858|ref|YP_005919157.1| 148 YDEAIRLDPELAAAWHKKGDALFERGNYTEAIQAFDEAIRLDP 190
                                       5677888899999999999*************99988888775 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.1
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAl 42 
                                       + ++++++a+  +p+d  + ++   al ++g+y+eA+
  gi|386000858|ref|YP_005919157.1| 177 EAIQAFDEAIRLDPEDATTWYNKGVALGMQGNYAEAI 213
                                       6799*******************************97 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.015
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       + + + ++a+  +p+d da  +  +al++ g+y+eA+ +L + ++ d
  gi|386000858|ref|YP_005919157.1| 211 EAIPAYDEAIRLDPEDADAWNNRGNALNELGKYDEAIHALDKAIELD 257
                                       56778899999***************************998777665 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.52
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkr 51 
                                        + +l++a++ +p+d +   +  + l ++g+y eA++++ e ++ 
  gi|386000858|ref|YP_005919157.1| 246 AIHALDKAIELDPEDAAPWNNKGKPLWMKGNYTEAIQAFDEAIRL 290
                                       6899*************999****************998877765 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.095
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       + +++ ++a+  +p+ +da ++   al+++g+y eA+++  e ++
  gi|386000858|ref|YP_005919157.1| 313 EAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEAIQAYDEAIR 357
                                       67899999****************************998666665 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 5.4
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilkr 51 
                                       ++a+  +p++ d  +   +   ++g+y+eA+++  e ++ 
  gi|386000858|ref|YP_005919157.1| 387 DEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRL 426
                                       5677778888888888888899999999999876666655 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.76
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       + +++ ++a+  +p++ d  +   +   ++g+y+eA+++  e ++ d
  gi|386000858|ref|YP_005919157.1| 415 EAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLD 461
                                       678999999999************************99876666655 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.65
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       + +++ ++a+  +p++ d  +   +   ++g+y+eA+++  e ++ d +
  gi|386000858|ref|YP_005919157.1| 449 EAIQAYDEAIRLDPEEADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDPE 497
                                       67899999999**************************987777776665 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.17
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                       + +++ ++a+  +p+   a ++  +al+++ +y+eA+++  e ++ + +++
  gi|386000858|ref|YP_005919157.1| 483 EAIQAYDEAIRLDPEFAGAWYNKGNALYEQDKYDEAIQAYDEAIRLNPDYK 533
                                       67899999999**************************99888888777775 PP

  == domain 11  score: 5.4 bits;  conditional E-value: 0.067
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       ++ +++ ++a+  npd  +a  +  +al+++g+y+eA+++  e ++ d
  gi|386000858|ref|YP_005919157.1| 516 DEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEAIRLD 563
                                       56799999******************************9876666655 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.09        30       7      20 ..      48      61 ..      47      63 .. 0.91
   2 ?    1.3   0.0      0.91     3e+02       7      20 ..      82      95 ..      81      97 .. 0.90
   3 ?   -0.5   0.0       3.3   1.1e+03       7      20 ..     116     129 ..     115     130 .. 0.88
   4 ?    2.1   0.0      0.51   1.7e+02       7      20 ..     184     197 ..     183     199 .. 0.90
   5 ?    0.5   0.0       1.7   5.5e+02       7      22 ..     218     233 ..     217     236 .. 0.89
   6 ?    1.7   0.0       0.7   2.3e+02       6      20 ..     251     265 ..     249     266 .. 0.90
   7 ?    2.4   0.1      0.41   1.4e+02       7      20 ..     354     367 ..     353     369 .. 0.89
   8 ?    0.4   0.0       1.7   5.7e+02       7      20 ..     490     503 ..     489     504 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.09
                                      HHHHH-TT-CHHHH CS
                              PPTA  7 kliekdpkNYsaWn 20
                                      ++i++dp   saWn
  gi|386000858|ref|YP_005919157.1| 48 EAIRLDPEYASAWN 61
                                      79***********9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.91
                                      HHHHH-TT-CHHHH CS
                              PPTA  7 kliekdpkNYsaWn 20
                                      ++i++dp    aWn
  gi|386000858|ref|YP_005919157.1| 82 EAIRLDPEFAAAWN 95
                                      79***********9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.3
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       ++i++dp    aW+
  gi|386000858|ref|YP_005919157.1| 116 EAIRLDPEYAGAWY 129
                                       79******999997 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.51
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       ++i++dp + ++W+
  gi|386000858|ref|YP_005919157.1| 184 EAIRLDPEDATTWY 197
                                       79***********8 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.7
                                       HHHHH-TT-CHHHHHH CS
                              PPTA   7 kliekdpkNYsaWnyR 22 
                                       ++i++dp +  aWn R
  gi|386000858|ref|YP_005919157.1| 218 EAIRLDPEDADAWNNR 233
                                       789999999999*998 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.7
                                       HHHHHH-TT-CHHHH CS
                              PPTA   6 ekliekdpkNYsaWn 20 
                                       +k+ie+dp +   Wn
  gi|386000858|ref|YP_005919157.1| 251 DKAIELDPEDAAPWN 265
                                       689*******99999 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.41
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       ++i++dp+N  +W+
  gi|386000858|ref|YP_005919157.1| 354 EAIRLDPDNAMTWY 367
                                       79*******99998 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.7
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       ++i++dp    aW+
  gi|386000858|ref|YP_005919157.1| 490 EAIRLDPEFAGAWY 503
                                       79***********8 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         6     2e+03      84     104 ..     100     120 ..      96     124 .. 0.81
   2 ?    3.4   0.0      0.24        78      80     106 ..     164     190 ..     163     195 .. 0.90
   3 ?   -1.7   0.0       8.6   2.9e+03      82     106 ..     234     258 ..     232     261 .. 0.81
   4 ?   -0.7   0.0       4.2   1.4e+03      81     104 ..     267     290 ..     266     293 .. 0.87
   5 ?   -1.2   0.0         6     2e+03      81     107 ..     301     327 ..     300     330 .. 0.86
   6 ?   -0.8   0.0       4.6   1.5e+03      78     106 ..     332     360 ..     310     376 .. 0.87
   7 ?   -0.4   0.0       3.5   1.2e+03      79     108 ..     401     430 ..     399     436 .. 0.87
   8 ?   -0.5   0.0       3.8   1.3e+03      79     108 ..     435     464 ..     433     468 .. 0.86
   9 ?   -1.6   0.0         8   2.7e+03      79     104 ..     469     494 ..     465     497 .. 0.88
  10 ?   -1.2   0.0       6.2     2e+03      81     106 ..     505     530 ..     503     537 .. 0.83
  11 ?    0.5   0.0       1.8     6e+02      81     104 ..     539     562 ..     536     565 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6
                             MAS20  84 ellaqgeeeeaaehlynAlkv 104
                                        l +qg++ ea+ ++  A+++
  gi|386000858|ref|YP_005919157.1| 100 ALGNQGNYTEATRCFDEAIRL 120
                                       566789**********99987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.24
                             MAS20  80 qlGEellaqgeeeeaaehlynAlkvcp 106
                                       ++G+ l+++g++ ea++++  A+++ p
  gi|386000858|ref|YP_005919157.1| 164 KKGDALFERGNYTEAIQAFDEAIRLDP 190
                                       589********************9866 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.6
                             MAS20  82 GEellaqgeeeeaaehlynAlkvcp 106
                                       G+ l + g+++ea+ +l +A+ + p
  gi|386000858|ref|YP_005919157.1| 234 GNALNELGKYDEAIHALDKAIELDP 258
                                       66677779************98755 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 4.2
                             MAS20  81 lGEellaqgeeeeaaehlynAlkv 104
                                       +G  l ++g++ ea++++  A+++
  gi|386000858|ref|YP_005919157.1| 267 KGKPLWMKGNYTEAIQAFDEAIRL 290
                                       68889999*************987 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 6
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpq 107
                                       +G  l+ qg+++ea+++   A+++ p+
  gi|386000858|ref|YP_005919157.1| 301 KGTVLADQGKYDEAIQAYDEAIRLHPN 327
                                       57778899*************999886 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 4.6
                             MAS20  78 evqlGEellaqgeeeeaaehlynAlkvcp 106
                                        +++G  l +qg++ ea+++   A+++ p
  gi|386000858|ref|YP_005919157.1| 332 WINKGSALYEQGNYPEAIQAYDEAIRLDP 360
                                       5899999**********999999998755 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 3.5
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkvcpqP 108
                                       v++G++  +qg+++ea+++   A+++ p+ 
  gi|386000858|ref|YP_005919157.1| 401 VSKGNSFRMQGKYDEAIQAYDEAIRLDPEE 430
                                       78999999***********99999987765 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 3.8
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkvcpqP 108
                                       v++G++  +qg+++ea+++   A+++ p+ 
  gi|386000858|ref|YP_005919157.1| 435 VSKGNSFRMQGKYDEAIQAYDEAIRLDPEE 464
                                       78999999***********99999987765 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 8
                             MAS20  79 vqlGEellaqgeeeeaaehlynAlkv 104
                                       v++G++  +qg+++ea+++   A+++
  gi|386000858|ref|YP_005919157.1| 469 VSKGNSFRMQGKYDEAIQAYDEAIRL 494
                                       789999999********999999886 PP

  == domain 10  score: -1.2 bits;  conditional E-value: 6.2
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcp 106
                                       +G+ l +q++++ea+++   A+++ p
  gi|386000858|ref|YP_005919157.1| 505 KGNALYEQDKYDEAIQAYDEAIRLNP 530
                                       78999999999999999999998766 PP

  == domain 11  score: 0.5 bits;  conditional E-value: 1.8
                             MAS20  81 lGEellaqgeeeeaaehlynAlkv 104
                                       +G+ l++qg+++ea+++   A+++
  gi|386000858|ref|YP_005919157.1| 539 KGNALVMQGKYDEAIQAYDEAIRL 562
                                       799*************99999886 PP

>> TraD  Conjugal transfer protein TraD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00081      0.27      33      60 ..     143     171 ..     136     172 .. 0.93
   2 ?   -1.0   0.0       4.6   1.5e+03      42      57 ..     220     236 ..     215     238 .. 0.77
   3 ?   -1.2   0.0       5.7   1.9e+03      39      56 ..     251     269 ..     246     271 .. 0.79
   4 ?   -1.0   0.0       4.8   1.6e+03      39      57 ..     387     406 ..     382     407 .. 0.80
   5 ?   -1.8   0.0       8.5   2.8e+03      41      57 ..     423     440 ..     419     441 .. 0.81
   6 ?   -1.8   0.0       8.5   2.8e+03      41      57 ..     457     474 ..     453     475 .. 0.81
   7 ?   -1.7   0.0       7.6   2.5e+03      46      58 ..     530     543 ..     523     545 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00081
                              TraD  33 GaLlelaellredeeeaa.wkrrGkaaFe 60 
                                       Ga l   e+ r d+e aa w+++G+a+Fe
  gi|386000858|ref|YP_005919157.1| 143 GAILAYDEAIRLDPELAAaWHKKGDALFE 171
                                       9***************************8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.6
                              TraD  42 lredeeeaa.wkrrGka 57 
                                        r d+e a+ w +rG+a
  gi|386000858|ref|YP_005919157.1| 220 IRLDPEDADaWNNRGNA 236
                                       5667777778*****98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.7
                              TraD  39 aellredeeeaa.wkrrGk 56 
                                        ++ + d+e aa w ++Gk
  gi|386000858|ref|YP_005919157.1| 251 DKAIELDPEDAApWNNKGK 269
                                       5667778999999*****8 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 4.8
                              TraD  39 aellredeeeaa.wkrrGka 57 
                                        e+ r d+eea+ w  +G+ 
  gi|386000858|ref|YP_005919157.1| 387 DEAIRLDPEEADvWVSKGNS 406
                                       6778889999999*****86 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 8.5
                              TraD  41 llredeeeaa.wkrrGka 57 
                                       + r d+eea+ w  +G+ 
  gi|386000858|ref|YP_005919157.1| 423 AIRLDPEEADvWVSKGNS 440
                                       56778999999*****86 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 8.5
                              TraD  41 llredeeeaa.wkrrGka 57 
                                       + r d+eea+ w  +G+ 
  gi|386000858|ref|YP_005919157.1| 457 AIRLDPEEADvWVSKGNS 474
                                       56778999999*****86 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 7.6
                              TraD  46 eeeaa.wkrrGkaa 58 
                                       + +++ w ++G+a+
  gi|386000858|ref|YP_005919157.1| 530 PDYKEaWNNKGNAL 543
                                       444555*****986 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.2      0.64   2.1e+02      87     103 ..      36      52 ..       2     123 .. 0.58
   2 ?    3.2   0.7      0.15        50      91     147 ..     142     190 ..     103     226 .. 0.50
   3 ?    1.9   1.5      0.37   1.2e+02      91      91 ..     203     203 ..     157     302 .. 0.49
   4 ?    2.6   2.1      0.22        75     129     183 ..     275     323 ..     207     341 .. 0.61
   5 !    7.3   1.1    0.0081       2.7     119     194 ..     300     368 ..     260     376 .. 0.71
   6 !   10.4   0.2   0.00097      0.32      35     102 ..     397     459 ..     392     460 .. 0.88
   7 !   17.9   4.5   4.8e-06    0.0016      35     183 ..     431     561 ..     426     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.64
                                       HT-HHHHHHHHHHHHHH CS
                              SNAP  87 kvspeeAvealekAiei 103
                                       + + +eAv+a+++Ai +
  gi|386000858|ref|YP_005919157.1|  36 RGNYTEAVQAYDEAIRL 52 
                                       44444444444444432 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH CS
                              SNAP  91 eeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeq 147
                                       + A+ a+++Ai +       + aA  +k+   l+e   g++++Ai+a+++A  l + 
  gi|386000858|ref|YP_005919157.1| 142 TGAILAYDEAIRL-----DPELAAAWHKKGDALFER--GNYTEAIQAFDEAIRL-DP 190
                                       3333333333333.....223344444443334443..3555555555555553.33 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.37
                                       H CS
                              SNAP  91 e 91 
                                        
  gi|386000858|ref|YP_005919157.1| 203 L 203
                                       1 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.22
                                       --HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              SNAP 129 gdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvak 183
                                       g++++Ai+a+++A    + e a a +nk       + a+++ky++Ai++y++ ++
  gi|386000858|ref|YP_005919157.1| 275 GNYTEAIQAFDEAIR-LDPELAVAWSNK-----GTVLADQGKYDEAIQAYDEAIR 323
                                       455555555555555.233333333333.....3445667777777777776654 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0081
                                       HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGG CS
                              SNAP 119 eiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvakkslennllkys 194
                                       + + ++ ++ g++++Ai+aY++A  l  +         ++++  +   e+++y++Ai++y++ ++   +n ++ y+
  gi|386000858|ref|YP_005919157.1| 300 NKGTVLADQ-GKYDEAIQAYDEAIRLHPN------YVDAWINKGSALYEQGNYPEAIQAYDEAIRLDPDNAMTWYN 368
                                       555666666.8899999999999987543......33444444555568899999999999999999888888776 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00097
                                       HHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHH CS
                              SNAP  35 adlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAie 102
                                       ad++++ +n+++++ k++eA +a+ +a +++       e a+ +v  +++++++ + +eA++a+++Ai 
  gi|386000858|ref|YP_005919157.1| 397 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP------EEADVWVSKGNSFRMQgKYDEAIQAYDEAIR 459
                                       79999999****************99988766......8899999999999988788999999999986 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 4.8e-06
                                       HHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-H CS
                              SNAP  35 adlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrf 110
                                       ad++++ +n+++++ k++eA +a+ +a +++       e a+ +v  +++++++ + +eA++a+++Ai +       
  gi|386000858|ref|YP_005919157.1| 431 ADVWVSKGNSFRMQGKYDEAIQAYDEAIRLDP------EEADVWVSKGNSFRMQgKYDEAIQAYDEAIRL-----DP 496
                                       7999999******************9988876......8899*********9997999**********87.....45 PP

                                       HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              SNAP 111 rraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvak 183
                                       + a+  +++   lye++  ++++Ai+aY++A  l + + ++a  nk           ++ky++Ai++y++ ++
  gi|386000858|ref|YP_005919157.1| 497 EFAGAWYNKGNALYEQD--KYDEAIQAYDEAIRL-NPDYKEAWNNKGN-----ALVMQGKYDEAIQAYDEAIR 561
                                       667778888888***99..9***********995.4555555555544.....34456888888888888765 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         4   1.3e+03      27      50 ..      38      61 ..      34      65 .. 0.87
   2 ?    0.0   0.0       2.9   9.8e+02      27      51 ..      72      96 ..      66     125 .. 0.76
   3 ?    6.5   0.0     0.028       9.4      27      52 ..     174     199 ..     167     206 .. 0.90
   4 ?   -0.1   0.0       3.2   1.1e+03      27      53 ..     208     234 ..     204     241 .. 0.85
   5 ?    0.1   0.0       2.7   9.1e+02      28      50 ..     243     265 ..     238     271 .. 0.86
   6 ?    1.1   0.0       1.4   4.6e+02      27      51 ..     276     300 ..     272     330 .. 0.80
   7 ?   -1.5   0.0       8.5   2.8e+03      28      50 ..     311     333 ..     301     341 .. 0.78
   8 ?    5.9   0.0     0.041        14      26      54 ..     343     371 ..     335     381 .. 0.86
   9 ?   -0.5   0.0       4.1   1.4e+03      27      54 ..     378     405 ..     374     412 .. 0.86
  10 ?    2.7   0.0      0.44   1.4e+02      27      54 ..     412     439 ..     402     444 .. 0.85
  11 ?    3.0   0.1      0.35   1.2e+02      27      54 ..     446     473 ..     438     491 .. 0.83
  12 ?   -1.5   0.0       8.6   2.9e+03      27      53 ..     480     506 ..     470     516 .. 0.80
  13 ?   -0.9   0.1       5.7   1.9e+03      27      51 ..     514     538 ..     501     543 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4
                           DUF1510 27 DwnEmekavskatglsednmivww 50
                                      +++E ++a  +a+ l+ +    w 
  gi|386000858|ref|YP_005919157.1| 38 NYTEAVQAYDEAIRLDPEYASAWN 61
                                      899************999888875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.9
                           DUF1510 27 DwnEmekavskatglsednmivwwl 51
                                      +++E  ka  +a+ l+ +    w  
  gi|386000858|ref|YP_005919157.1| 72 NYDESIKAYDEAIRLDPEFAAAWNN 96
                                      899999******9999988888764 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.028
                           DUF1510  27 DwnEmekavskatglsednmivwwlg 52 
                                       +++E  +a+ +a+ l+ ++ ++w+ +
  gi|386000858|ref|YP_005919157.1| 174 NYTEAIQAFDEAIRLDPEDATTWYNK 199
                                       89*********************865 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 3.2
                           DUF1510  27 DwnEmekavskatglsednmivwwlgn 53 
                                       ++ E   a  +a+ l+ ++   w  + 
  gi|386000858|ref|YP_005919157.1| 208 NYAEAIPAYDEAIRLDPEDADAWNNRG 234
                                       89999***************9997654 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 2.7
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       ++E  +a+ ka++l+ ++   w 
  gi|386000858|ref|YP_005919157.1| 243 YDEAIHALDKAIELDPEDAAPWN 265
                                       78999************998886 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 1.4
                           DUF1510  27 DwnEmekavskatglsednmivwwl 51 
                                       +++E  +a+ +a+ l+ +  + w  
  gi|386000858|ref|YP_005919157.1| 276 NYTEAIQAFDEAIRLDPELAVAWSN 300
                                       8999***********9988888764 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 8.5
                           DUF1510  28 wnEmekavskatglsednmivww 50 
                                       ++E  +a  +a+ l+ + +  w 
  gi|386000858|ref|YP_005919157.1| 311 YDEAIQAYDEAIRLHPNYVDAWI 333
                                       78999999999999877666664 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.041
                           DUF1510  26 vDwnEmekavskatglsednmivwwlgng 54 
                                        ++ E  +a  +a+ l+ dn ++w+ + +
  gi|386000858|ref|YP_005919157.1| 343 GNYPEAIQAYDEAIRLDPDNAMTWYNKGN 371
                                       4899********************97655 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 4.1
                           DUF1510  27 DwnEmekavskatglsednmivwwlgng 54 
                                       +++E   a  +a+ l+ ++  vw  + +
  gi|386000858|ref|YP_005919157.1| 378 NYTEGILAYDEAIRLDPEEADVWVSKGN 405
                                       78899999**************987654 PP

  == domain 10  score: 2.7 bits;  conditional E-value: 0.44
                           DUF1510  27 DwnEmekavskatglsednmivwwlgng 54 
                                        ++E  +a  +a+ l+ ++  vw  + +
  gi|386000858|ref|YP_005919157.1| 412 KYDEAIQAYDEAIRLDPEEADVWVSKGN 439
                                       589*******************987654 PP

  == domain 11  score: 3.0 bits;  conditional E-value: 0.35
                           DUF1510  27 DwnEmekavskatglsednmivwwlgng 54 
                                        ++E  +a  +a+ l+ ++  vw  + +
  gi|386000858|ref|YP_005919157.1| 446 KYDEAIQAYDEAIRLDPEEADVWVSKGN 473
                                       589*******************988654 PP

  == domain 12  score: -1.5 bits;  conditional E-value: 8.6
                           DUF1510  27 DwnEmekavskatglsednmivwwlgn 53 
                                        ++E  +a  +a+ l+ +    w+ + 
  gi|386000858|ref|YP_005919157.1| 480 KYDEAIQAYDEAIRLDPEFAGAWYNKG 506
                                       58999999999*999998888887654 PP

  == domain 13  score: -0.9 bits;  conditional E-value: 5.7
                           DUF1510  27 DwnEmekavskatglsednmivwwl 51 
                                        ++E  +a  +a+ l+ d    w  
  gi|386000858|ref|YP_005919157.1| 514 KYDEAIQAYDEAIRLNPDYKEAWNN 538
                                       5889999999**9999987777764 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.9   9.7e+02      34      63 ..      21      50 ..      11      54 .. 0.80
   2 ?    0.7   0.0       1.1   3.7e+02     119     137 ..      97     115 ..      59     130 .. 0.83
   3 ?    3.6   0.0      0.15        49      32      63 ..     155     186 ..     147     190 .. 0.89
   4 ?   -0.6   0.0       2.7   9.1e+02      36      64 ..     227     255 ..     215     258 .. 0.84
   5 ?    3.9   0.0      0.12        39      33      63 ..     292     322 ..     273     334 .. 0.87
   6 ?   -0.8   0.0       3.1     1e+03      38      63 ..     331     356 ..     325     359 .. 0.85
   7 ?    2.1   0.0      0.42   1.4e+02      37      63 ..     398     424 ..     388     431 .. 0.85
   8 ?    1.9   0.0      0.49   1.6e+02      37      63 ..     432     458 ..     426     462 .. 0.84
   9 ?    1.9   0.0      0.46   1.5e+02      37      63 ..     466     492 ..     459     496 .. 0.84
  10 ?    0.8   0.4         1   3.4e+02      30      60 ..     493     523 ..     471     530 .. 0.50
  11 ?    5.9   0.7     0.029       9.7      15      63 ..     511     560 ..     500     563 .. 0.81
  12 ?   -0.5   0.0       2.7   8.9e+02      49      73 ..     580     604 ..     572     606 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7 34 eirrakldlaehYlkigdleeAlkaysrir 63
                                      e ++a++ ++   +  g+++eA++ay +++
  gi|386000858|ref|YP_005919157.1| 21 EYADAWYSKGLTLYYRGNYTEAVQAYDEAI 50
                                      567777888888888899999999999864 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                                       HHHHHHHTT-HHHHHHHHC CS
                              RPN7 119 eGlallairkfkeAaelll 137
                                       +G+al  +++++eA++++ 
  gi|386000858|ref|YP_005919157.1|  97 KGIALGNQGNYTEATRCFD 115
                                       7888889999999999885 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  32 keeirrakldlaehYlkigdleeAlkaysrir 63 
                                       + e ++a++++++  ++ g+++eA++a+ +++
  gi|386000858|ref|YP_005919157.1| 155 DPELAAAWHKKGDALFERGNYTEAIQAFDEAI 186
                                       5578999*********************9964 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                       ++a++++++   + g+++eA+ a+ +++e
  gi|386000858|ref|YP_005919157.1| 227 ADAWNNRGNALNELGKYDEAIHALDKAIE 255
                                       67888889999999*******99999865 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysrir 63 
                                        e + a+ +++   ++ g+++eA++ay +++
  gi|386000858|ref|YP_005919157.1| 292 PELAVAWSNKGTVLADQGKYDEAIQAYDEAI 322
                                       577889999******************9964 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrir 63 
                                       a+ +++   ++ g++ eA++ay +++
  gi|386000858|ref|YP_005919157.1| 331 AWINKGSALYEQGNYPEAIQAYDEAI 356
                                       677888999999**********9964 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  37 rakldlaehYlkigdleeAlkaysrir 63 
                                       + +  +++ + + g+++eA++ay +++
  gi|386000858|ref|YP_005919157.1| 398 DVWVSKGNSFRMQGKYDEAIQAYDEAI 424
                                       567789999999***********9964 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  37 rakldlaehYlkigdleeAlkaysrir 63 
                                       + +  +++ + + g+++eA++ay +++
  gi|386000858|ref|YP_005919157.1| 432 DVWVSKGNSFRMQGKYDEAIQAYDEAI 458
                                       556778999999***********9964 PP

  == domain 9  score: 1.9 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  37 rakldlaehYlkigdleeAlkaysrir 63 
                                       + +  +++ + + g+++eA++ay +++
  gi|386000858|ref|YP_005919157.1| 466 DVWVSKGNSFRMQGKYDEAIQAYDEAI 492
                                       566788999999***********9964 PP

  == domain 10  score: 0.8 bits;  conditional E-value: 1
                                       T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHH CS
                              RPN7  30 lgkeeirrakldlaehYlkigdleeAlkays 60 
                                         + e + a++++++  ++  +++eA++ay 
  gi|386000858|ref|YP_005919157.1| 493 RLDPEFAGAWYNKGNALYEQDKYDEAIQAYD 523
                                       3344445555555555555555555555555 PP

  == domain 11  score: 5.9 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  15 eleeLdaelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysrir 63 
                                       e ++ d+ ++ +        + ++a++++++  ++ g+++eA++ay +++
  gi|386000858|ref|YP_005919157.1| 511 EQDKYDEAIQAYDeAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEAI 560
                                       56677777777764556777999***********************9964 PP

  == domain 12  score: -0.5 bits;  conditional E-value: 2.7
                                       CT-HHHHHHHHHTCCCC--SHHHHH CS
                              RPN7  49 igdleeAlkaysrireyctslkhki 73 
                                        g+++eA +ay+++ e   s++  i
  gi|386000858|ref|YP_005919157.1| 580 LGKVAEANEAYAKAEELGYSTGRRI 604
                                       699***********99888888766 PP

>> Imm31  Immunity protein 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.6   1.5e+03      15      47 ..      53      81 ..      36      86 .. 0.68
   2 ?   -0.6   0.0       3.6   1.2e+03      14      33 ..      86     105 ..      81     119 .. 0.80
   3 ?    2.7   0.0      0.35   1.2e+02      13      46 ..     187     216 ..     179     223 .. 0.78
   4 ?    7.6   0.0      0.01       3.4      13      48 ..     289     320 ..     274     325 .. 0.88
   5 ?    1.9   0.0      0.63   2.1e+02      17      48 ..     395     422 ..     388     433 .. 0.72
   6 ?    2.0   0.0      0.56   1.8e+02      19      48 ..     431     456 ..     423     476 .. 0.72
   7 ?    1.4   0.0      0.86   2.8e+02      17      48 ..     463     490 ..     456     495 .. 0.72
   8 ?   -0.8   0.0       4.3   1.4e+03      36      48 ..     546     558 ..     525     564 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.6
                             Imm31 15 dailaelhGerGvvlGrseddqGefeyavfiya 47
                                      d++ a  + ++G       d qG+++ ++ +y 
  gi|386000858|ref|YP_005919157.1| 53 DPEYASAWNNKGLA----LDYQGNYDESIKAYD 81
                                      55555555555544....467888888888875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.6
                             Imm31  14 tdailaelhGerGvvlGrse 33 
                                        d++ a  + ++G+ lG  +
  gi|386000858|ref|YP_005919157.1|  86 LDPEFAAAWNNKGIALGNQG 105
                                       68999999*****9999755 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.35
                             Imm31  13 stdailaelhGerGvvlGrseddqGefeyavfiy 46 
                                         d++ a  + ++Gv lG+     G++  a+ +y
  gi|386000858|ref|YP_005919157.1| 187 RLDPEDATTWYNKGVALGMQ----GNYAEAIPAY 216
                                       5689999***********95....5555555555 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.01
                             Imm31  13 stdailaelhGerGvvlGrseddqGefeyavfiyad 48 
                                         d++la  + ++G vl     dqG+++ a+++y +
  gi|386000858|ref|YP_005919157.1| 289 RLDPELAVAWSNKGTVL----ADQGKYDEAIQAYDE 320
                                       56999**********99....59**********964 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.63
                             Imm31  17 ilaelhGerGvvlGrseddqGefeyavfiyad 48 
                                       + a+++  +    G s   qG+++ a+++y +
  gi|386000858|ref|YP_005919157.1| 395 EEADVWVSK----GNSFRMQGKYDEAIQAYDE 422
                                       555555444....5677779*********965 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.56
                             Imm31  19 aelhGerGvvlGrseddqGefeyavfiyad 48 
                                       a+++  +    G s   qG+++ a+++y +
  gi|386000858|ref|YP_005919157.1| 431 ADVWVSK----GNSFRMQGKYDEAIQAYDE 456
                                       5555444....5677779*********965 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.86
                             Imm31  17 ilaelhGerGvvlGrseddqGefeyavfiyad 48 
                                       + a+++  +    G s   qG+++ a+++y +
  gi|386000858|ref|YP_005919157.1| 463 EEADVWVSK----GNSFRMQGKYDEAIQAYDE 490
                                       555555444....5677779*********964 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 4.3
                             Imm31  36 qGefeyavfiyad 48 
                                       qG+++ a+++y +
  gi|386000858|ref|YP_005919157.1| 546 QGKYDEAIQAYDE 558
                                       899******9964 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.5   5.1e+02     129     149 ..      31      51 ..      21      63 .. 0.82
   2 ?    1.6   0.0      0.52   1.7e+02     126     149 ..      96     119 ..      89     126 .. 0.86
   3 ?    1.1   0.0      0.77   2.6e+02     130     151 ..     168     189 ..     163     199 .. 0.83
   4 ?   -1.1   0.0       3.5   1.2e+03     129     152 ..     201     224 ..     195     247 .. 0.77
   5 ?   -1.8   0.0       5.6   1.9e+03     133     149 ..     273     289 ..     271     293 .. 0.84
   6 ?    4.4   0.1     0.073        24     131     157 ..     305     331 ..     299     342 .. 0.76
   7 ?    2.3   0.0      0.33   1.1e+02     126     153 ..     334     361 ..     325     369 .. 0.80
   8 ?    0.4   0.0       1.2     4e+02     134     149 ..     410     425 ..     406     432 .. 0.82
   9 ?    0.4   0.0       1.2     4e+02     134     149 ..     444     459 ..     440     466 .. 0.82
  10 ?    0.1   0.0       1.5   4.9e+02     134     149 ..     478     493 ..     474     499 .. 0.84
  11 ?   -0.1   0.1       1.8     6e+02     131     149 ..     509     527 ..     504     544 .. 0.77
  12 ?    3.6   0.1      0.13        44     130     149 ..     542     561 ..     531     567 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegr 149
                                       l+l  +g+++eA q+y++ +r
  gi|386000858|ref|YP_005919157.1|  31 LTLYYRGNYTEAVQAYDEAIR 51 
                                       677789**********99886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.52
                         4HB_MCP_1 126 kkvlelakegkkdeAyqlyetegr 149
                                       +k ++l ++g+++eA + +++ +r
  gi|386000858|ref|YP_005919157.1|  96 NKGIALGNQGNYTEATRCFDEAIR 119
                                       67799************9998876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.77
                         4HB_MCP_1 130 elakegkkdeAyqlyetegrpa 151
                                       +l+++g+++eA+q++++ +r  
  gi|386000858|ref|YP_005919157.1| 168 ALFERGNYTEAIQAFDEAIRLD 189
                                       58899**********9998755 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.5
                         4HB_MCP_1 129 lelakegkkdeAyqlyetegrpar 152
                                       ++l  +g++ eA+ +y++ +r   
  gi|386000858|ref|YP_005919157.1| 201 VALGMQGNYAEAIPAYDEAIRLDP 224
                                       68899999**99999999887444 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 5.6
                         4HB_MCP_1 133 kegkkdeAyqlyetegr 149
                                        +g+++eA+q++++ +r
  gi|386000858|ref|YP_005919157.1| 273 MKGNYTEAIQAFDEAIR 289
                                       589********998875 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.073
                         4HB_MCP_1 131 lakegkkdeAyqlyetegrpareklie 157
                                       la +gk+deA+q+y++ +r + + +++
  gi|386000858|ref|YP_005919157.1| 305 LADQGKYDEAIQAYDEAIRLHPNYVDA 331
                                       899*************99865555544 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.33
                         4HB_MCP_1 126 kkvlelakegkkdeAyqlyetegrpare 153
                                       +k  +l ++g++ eA+q+y++ +r   +
  gi|386000858|ref|YP_005919157.1| 334 NKGSALYEQGNYPEAIQAYDEAIRLDPD 361
                                       66678999************99986555 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1.2
                         4HB_MCP_1 134 egkkdeAyqlyetegr 149
                                       +gk+deA+q+y++ +r
  gi|386000858|ref|YP_005919157.1| 410 QGKYDEAIQAYDEAIR 425
                                       89*********99886 PP

  == domain 9  score: 0.4 bits;  conditional E-value: 1.2
                         4HB_MCP_1 134 egkkdeAyqlyetegr 149
                                       +gk+deA+q+y++ +r
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDEAIR 459
                                       89*********99886 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 1.5
                         4HB_MCP_1 134 egkkdeAyqlyetegr 149
                                       +gk+deA+q+y++ +r
  gi|386000858|ref|YP_005919157.1| 478 QGKYDEAIQAYDEAIR 493
                                       89*********99876 PP

  == domain 11  score: -0.1 bits;  conditional E-value: 1.8
                         4HB_MCP_1 131 lakegkkdeAyqlyetegr 149
                                       l ++ k+deA+q+y++ +r
  gi|386000858|ref|YP_005919157.1| 509 LYEQDKYDEAIQAYDEAIR 527
                                       6678899******999887 PP

  == domain 12  score: 3.6 bits;  conditional E-value: 0.13
                         4HB_MCP_1 130 elakegkkdeAyqlyetegr 149
                                       +l+ +gk+deA+q+y++ +r
  gi|386000858|ref|YP_005919157.1| 542 ALVMQGKYDEAIQAYDEAIR 561
                                       7999***********99876 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       6.1     2e+03      13      28 ..     101     116 ..     100     119 .. 0.87
   2 ?    0.6   0.0         2   6.7e+02      12      28 ..     168     184 ..     167     187 .. 0.90
   3 ?    1.3   0.0       1.2     4e+02      13      28 ..     305     320 ..     303     323 .. 0.87
   4 ?   -0.6   0.0       4.8   1.6e+03      12      28 ..     338     354 ..     337     357 .. 0.89
   5 ?    0.3   0.0       2.5   8.3e+02      16      28 ..     410     422 ..     405     425 .. 0.86
   6 ?    0.3   0.0       2.5   8.3e+02      16      28 ..     444     456 ..     439     459 .. 0.86
   7 ?    0.3   0.0       2.5   8.3e+02      16      28 ..     478     490 ..     473     493 .. 0.86
   8 ?    1.1   0.0       1.4   4.5e+02      11      28 ..     507     524 ..     507     529 .. 0.88
   9 ?    2.5   0.0       0.5   1.7e+02      11      28 ..     541     558 ..     535     561 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 6.1
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       l ++g++ eA + f+e
  gi|386000858|ref|YP_005919157.1| 101 LGNQGNYTEATRCFDE 116
                                       5689**********98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2
                             PPR_2  12 glckkgkveeAfklfne 28 
                                       +l+++g++ eA++ f+e
  gi|386000858|ref|YP_005919157.1| 168 ALFERGNYTEAIQAFDE 184
                                       7899***********98 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.2
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       l+ +gk++eA++ ++e
  gi|386000858|ref|YP_005919157.1| 305 LADQGKYDEAIQAYDE 320
                                       6779********9998 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 4.8
                             PPR_2  12 glckkgkveeAfklfne 28 
                                       +l+++g++ eA++ ++e
  gi|386000858|ref|YP_005919157.1| 338 ALYEQGNYPEAIQAYDE 354
                                       7899*********9998 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 2.5
                             PPR_2  16 kgkveeAfklfne 28 
                                       +gk++eA++ ++e
  gi|386000858|ref|YP_005919157.1| 410 QGKYDEAIQAYDE 422
                                       89*******9998 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 2.5
                             PPR_2  16 kgkveeAfklfne 28 
                                       +gk++eA++ ++e
  gi|386000858|ref|YP_005919157.1| 444 QGKYDEAIQAYDE 456
                                       89*******9998 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 2.5
                             PPR_2  16 kgkveeAfklfne 28 
                                       +gk++eA++ ++e
  gi|386000858|ref|YP_005919157.1| 478 QGKYDEAIQAYDE 490
                                       89*******9998 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 1.4
                             PPR_2  11 sglckkgkveeAfklfne 28 
                                       ++l+++ k++eA++ ++e
  gi|386000858|ref|YP_005919157.1| 507 NALYEQDKYDEAIQAYDE 524
                                       578999********9998 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.5
                             PPR_2  11 sglckkgkveeAfklfne 28 
                                       ++l+ +gk++eA++ ++e
  gi|386000858|ref|YP_005919157.1| 541 NALVMQGKYDEAIQAYDE 558
                                       67899*********9998 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.66   2.2e+02      27      51 ..     122     145 ..     116     152 .. 0.78
   2 ?   -0.9   0.0       6.7   2.2e+03      26      45 ..     189     208 ..     181     219 .. 0.78
   3 ?   -0.5   0.0         5   1.7e+03      26      47 ..     291     311 ..     287     322 .. 0.76
   4 ?    2.0   0.0      0.82   2.7e+02      27      48 ..     360     380 ..     350     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.66
                              Ig_2  27 pppkvqwykggevinsspnffinav 51 
                                       p++   wy++g+++++++n ++ a+
  gi|386000858|ref|YP_005919157.1| 122 PEYAGAWYNKGKALSERGN-YTGAI 145
                                       566668***********99.76555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.7
                              Ig_2  26 npppkvqwykggevinsspn 45 
                                       +p++  +wy++g ++  ++n
  gi|386000858|ref|YP_005919157.1| 189 DPEDATTWYNKGVALGMQGN 208
                                       5778899****999987776 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 5
                              Ig_2  26 npppkvqwykggevinsspnff 47 
                                       +p+  v w+++g+v+ ++++ +
  gi|386000858|ref|YP_005919157.1| 291 DPELAVAWSNKGTVLADQGK-Y 311
                                       5777899********99887.4 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.82
                              Ig_2  27 pppkvqwykggevinsspnffi 48 
                                       p+  ++wy++g+++++ +n ++
  gi|386000858|ref|YP_005919157.1| 360 PDNAMTWYNKGNALSELGN-YT 380
                                       66679*********98887.44 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       6.7   2.2e+03      12      23 ..      34      45 ..      32      81 .. 0.65
   2 ?    5.2   0.0     0.037        12     182     255 ..     174     247 ..     150     260 .. 0.77
   3 ?    1.9   0.0      0.36   1.2e+02     209     254 ..     303     348 ..     273     368 .. 0.73
   4 ?    0.1   0.1       1.3   4.3e+02     213     237 ..     443     467 ..     399     522 .. 0.60
   5 ?    0.1   0.1       1.2   4.1e+02     213     256 ..     511     554 ..     465     562 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.7
                                      HHTT-HHHHHHH CS
                        Coatomer_E 12 fYlGaYqkaine 23
                                      +Y G+Y++a+  
  gi|386000858|ref|YP_005919157.1| 34 YYRGNYTEAVQA 45
                                      666777666643 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 182 kiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                       ++ +A   f+e     ++   +   k v+  ++g+y+eA     ea+  d++d+++  N   a ++lgk +e++
  gi|386000858|ref|YP_005919157.1| 174 NYTEAIQAFDEAIRLDPEDATTWYNKGVALGMQGNYAEAIPAYDEAIRLDPEDADAWNNRGNALNELGKYDEAI 247
                                       56666666666655545555566667777778899************************999999999998876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.36
                                       HHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHH CS
                        Coatomer_E 209 vvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaev 254
                                        v   +g+y+eA +   ea+   +++ ++ iN   a  + g  +e+
  gi|386000858|ref|YP_005919157.1| 303 TVLADQGKYDEAIQAYDEAIRLHPNYVDAWINKGSALYEQGNYPEA 348
                                       4555678888888888888888888888888877666666666555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.3
                                       HTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeet 237
                                       ++g+y+eA +   ea+  d++++++
  gi|386000858|ref|YP_005919157.1| 443 MQGKYDEAIQAYDEAIRLDPEEADV 467
                                       2344444444444444444444444 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.2
                                       HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                        +++y+eA +   ea+  ++ ++e+  N   a    gk +e+++
  gi|386000858|ref|YP_005919157.1| 511 EQDKYDEAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQ 554
                                       46788888888888888888888888888777777777777665 PP

>> DUF5112  Domain of unknown function (DUF5112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1       0.2        66      21      65 ..      40      84 ..      36      89 .. 0.91
   2 ?   -0.0   0.1       1.5   4.9e+02      25      64 ..      78     117 ..      61     120 .. 0.86
   3 ?   -2.3   0.0       7.6   2.5e+03      22      65 ..     211     254 ..     205     261 .. 0.78
   4 ?   -1.5   0.0       4.1   1.4e+03      23      65 ..     246     288 ..     229     303 .. 0.86
   5 ?   -0.6   0.0       2.2   7.5e+02      21      75 ..     278     332 ..     271     335 .. 0.84
   6 ?    5.5   0.2     0.031        10      22      64 ..     517     559 ..     510     563 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                           DUF5112 21 laAekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkeve 65
                                      + A +a+ +a   + ++a A Nn +     + +y+e+ k ++e+ 
  gi|386000858|ref|YP_005919157.1| 40 TEAVQAYDEAIRLDPEYASAWNNKGLALDYQGNYDESIKAYDEAI 84
                                      67999**********************************999875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.5
                           DUF5112  25 kalklaegysagkaeAlNnlaFvaiarmdyeeaekllkev 64 
                                       ka+ +a   + + a A Nn +     + +y ea+++++e+
  gi|386000858|ref|YP_005919157.1|  78 KAYDEAIRLDPEFAAAWNNKGIALGNQGNYTEATRCFDEA 117
                                       7888888888999**********************99986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7.6
                           DUF5112  22 aAekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkeve 65 
                                        A  a+ +a   + + a+A Nn +       +y+ea + l+++ 
  gi|386000858|ref|YP_005919157.1| 211 EAIPAYDEAIRLDPEDADAWNNRGNALNELGKYDEAIHALDKAI 254
                                       56668888888888999999999888777778888888887765 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.1
                           DUF5112  23 AekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkeve 65 
                                       A +al  a + + + a   Nn +    ++ +y ea + ++e+ 
  gi|386000858|ref|YP_005919157.1| 246 AIHALDKAIELDPEDAAPWNNKGKPLWMKGNYTEAIQAFDEAI 288
                                       6678888888888899999999999999999999999998865 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.2
                           DUF5112  21 laAekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkeveektdneielL 75 
                                       + A +a+ +a   + + a A  n + v   + +y+ea + ++e+ +   n ++  
  gi|386000858|ref|YP_005919157.1| 278 TEAIQAFDEAIRLDPELAVAWSNKGTVLADQGKYDEAIQAYDEAIRLHPNYVDAW 332
                                       568888899999999999999999999999999********99999888888765 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.031
                           DUF5112  22 aAekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkev 64 
                                        A +a+ +a   +  + eA Nn +   +++ +y+ea + ++e+
  gi|386000858|ref|YP_005919157.1| 517 EAIQAYDEAIRLNPDYKEAWNNKGNALVMQGKYDEAIQAYDEA 559
                                       57899999999999999***********************987 PP

>> nos_propeller_2  Nitrous oxide reductase propeller repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       8.3   2.7e+03      32      52 ..     129     149 ..     122     153 .. 0.84
   2 ?    1.8   0.0      0.91     3e+02      31      53 ..     230     252 ..     223     257 .. 0.88
   3 ?    3.2   0.0      0.34   1.1e+02      26      52 ..     259     285 ..     252     298 .. 0.88
   4 ?    3.4   0.0      0.29        96      26      52 ..     293     319 ..     288     323 .. 0.89
   5 ?    0.9   0.1       1.8   5.9e+02      31      52 ..     502     523 ..     495     537 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 8.3
                   nos_propeller_2  32 pndGrdlddpekyvslfsaid 52 
                                        n G+ l +  +y+  + a d
  gi|386000858|ref|YP_005919157.1| 129 YNKGKALSERGNYTGAILAYD 149
                                       699**********98887766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.91
                   nos_propeller_2  31 lpndGrdlddpekyvslfsaida 53 
                                        +n G+ l++  ky   + a+d 
  gi|386000858|ref|YP_005919157.1| 230 WNNRGNALNELGKYDEAIHALDK 252
                                       5799**************99985 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.34
                   nos_propeller_2  26 EfrvPlpndGrdlddpekyvslfsaid 52 
                                       E+ +P +n G+ l  + +y+  ++a d
  gi|386000858|ref|YP_005919157.1| 259 EDAAPWNNKGKPLWMKGNYTEAIQAFD 285
                                       8999*****************999988 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.29
                   nos_propeller_2  26 EfrvPlpndGrdlddpekyvslfsaid 52 
                                       E  v   n G++l d+ ky   ++a d
  gi|386000858|ref|YP_005919157.1| 293 ELAVAWSNKGTVLADQGKYDEAIQAYD 319
                                       7788999*************9999877 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.8
                   nos_propeller_2  31 lpndGrdlddpekyvslfsaid 52 
                                         n G+ l +++ky   ++a d
  gi|386000858|ref|YP_005919157.1| 502 WYNKGNALYEQDKYDEAIQAYD 523
                                       579************9999977 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 ?   -2.0   0.0       9.1     3e+03      23      46 ..      60      83 ..      42      84 .. 0.77
   2 ?    3.2   0.0      0.22        72      20      46 ..     125     151 ..     115     153 .. 0.90
   3 ?    2.2   0.0      0.45   1.5e+02      21      46 ..     194     219 ..     182     223 .. 0.84
   4 ?    1.9   0.0      0.53   1.8e+02      14      46 ..     254     287 ..     247     289 .. 0.82
   5 ?   -1.6   0.0       6.6   2.2e+03      23      46 ..     366     389 ..     355     393 .. 0.85
   6 ?   -0.7   0.0       3.5   1.2e+03      14      46 ..     390     423 ..     382     427 .. 0.83
   7 ?   -0.7   0.0       3.5   1.2e+03      14      46 ..     424     457 ..     416     461 .. 0.83
   8 ?   -0.9   0.0       4.1   1.4e+03      14      46 ..     458     491 ..     454     493 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
                           Big_3_4 23 iWnvpvPldedGeyvvellaedea 46
                                      + n  + ld +G+y   + a dea
  gi|386000858|ref|YP_005919157.1| 60 WNNKGLALDYQGNYDESIKAYDEA 83
                                      445678999999999999999998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.22
                           Big_3_4  20 eGdiWnvpvPldedGeyvvellaedea 46 
                                        G ++n    l e G+y  ++la dea
  gi|386000858|ref|YP_005919157.1| 125 AGAWYNKGKALSERGNYTGAILAYDEA 151
                                       6999**********************8 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.45
                           Big_3_4  21 GdiWnvpvPldedGeyvvellaedea 46 
                                         ++n  v l ++G+y  ++ a dea
  gi|386000858|ref|YP_005919157.1| 194 TTWYNKGVALGMQGNYAEAIPAYDEA 219
                                       458899******************98 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.53
                           Big_3_4  14 vefdrseGdiWn.vpvPldedGeyvvellaedea 46 
                                       +e+d  +   Wn    Pl ++G+y  ++ a dea
  gi|386000858|ref|YP_005919157.1| 254 IELDPEDAAPWNnKGKPLWMKGNYTEAIQAFDEA 287
                                       6777777777761568****************98 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 6.6
                           Big_3_4  23 iWnvpvPldedGeyvvellaedea 46 
                                       ++n    l e G+y   +la dea
  gi|386000858|ref|YP_005919157.1| 366 WYNKGNALSELGNYTEGILAYDEA 389
                                       77888889999***********98 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 3.5
                           Big_3_4  14 vefdrseGdiWnvp.vPldedGeyvvellaedea 46 
                                       + +d  e d+W      + ++G y  ++ a dea
  gi|386000858|ref|YP_005919157.1| 390 IRLDPEEADVWVSKgNSFRMQGKYDEAIQAYDEA 423
                                       67888899999654268999*****99***9998 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 3.5
                           Big_3_4  14 vefdrseGdiWnvp.vPldedGeyvvellaedea 46 
                                       + +d  e d+W      + ++G y  ++ a dea
  gi|386000858|ref|YP_005919157.1| 424 IRLDPEEADVWVSKgNSFRMQGKYDEAIQAYDEA 457
                                       77888899999654268999*****9****9998 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 4.1
                           Big_3_4  14 vefdrseGdiWnvp.vPldedGeyvvellaedea 46 
                                       + +d  e d+W      + ++G y  ++ a dea
  gi|386000858|ref|YP_005919157.1| 458 IRLDPEEADVWVSKgNSFRMQGKYDEAIQAYDEA 491
                                       67888899999654268999**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 1.15u 0.30s 00:00:01.45 Elapsed: 00:00:00.71
# Mc/sec: 2592.41
//
Query:       gi|386000859|ref|YP_005919158.1|  [L=419]
Description: Alkaline phosphatase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-93  312.3   1.0    3.4e-86  289.8   1.5    2.1  2  Alk_phosphatase  Alkaline phosphatase
      1e-07   31.6   0.0    1.9e-07   30.7   0.0    1.4  1  Metalloenzyme    Metalloenzyme superfamily
    0.00046   19.7   0.0      0.006   16.0   0.0    2.2  1  Sulfatase        Sulfatase
  ------ inclusion threshold ------
      0.055   13.1   0.3       0.21   11.1   0.3    1.8  1  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph


Domain annotation for each model (and alignments):
>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.8   1.5   7.6e-90   3.4e-86       1     314 [.      36     342 ..      36     360 .. 0.94
   2 !   20.1   0.0   5.5e-08   0.00025     374     415 ..     376     418 ..     372     419 .] 0.89

  Alignments for each domain:
  == domain 1  score: 289.8 bits;  conditional E-value: 7.6e-90
                                       -SEEEEEEETT-SHHHHHHHHHHHCHCTCSSSTTS.TTGGG-SEEEEEESSECSTTSSGHHHHHHHHHHSSBTBTT- CS
                   Alk_phosphatase   1 aknvilligDGmgvstvtaaRslkeqakdklgeetllamdrfplvglsktyavdkqvtDSaataTAyacgvktynga 77 
                                       a++vi+ligDGmg +++taaR  k +++ +   +++l md +++ g s t + d+ vtDSaa++T +a+g kt  g 
  gi|386000859|ref|YP_005919158.1|  36 ARSVIFLIGDGMGFAQMTAARWAKADENLSNYTDAELFMDGMEYAGYSSTSSADSFVTDSAAAGTTLATGHKTKLGI 112
                                       699*************************9999********************************************* PP

                                       BSB-TTS......T-B---HHHHHHHTT-EEEEEEEEETTSHHHHTTTTTBSSTTSSSHHHSTCCCHHTTS-SHHHH CS
                   Alk_phosphatase  78 igvdaaa......gkevksvleaAkkaGkstGlVtTtritdAtPaalvahvesRkwkedaavpaealeegkkdiaeq 148
                                       ig d+ +      g++++++le A ++Gk+tG+Vt  rit+AtPa+++ahv++R    d           ++ iaeq
  gi|386000859|ref|YP_005919158.1| 113 IGQDETSifgvqdGENLTTILELAEAEGKATGVVTNMRITHATPASFYAHVNDR----DK----------ENRIAEQ 175
                                       *****999**********************************************....33..........36788** PP

                                       HHHCST-SEEEEESCGGGSB..CSBCTS....STCCT.SBHHHHHCCTTCEEE-SHHHHHHHCTSTSSCEEEESSSS CS
                   Alk_phosphatase 149 likakkidvllGGGrkeffp..aeyatd....GerkdGrnlieeakkkgyqyvsdrkeLlkakeenvkplLGLFadg 219
                                        ++   +dv lGGG  +f    +  ++      +r d ++l  +a+  gy +v +r+eLlk ++e++++lLGLF  +
  gi|386000859|ref|YP_005919158.1| 176 FLAS-GVDVALGGGLCYFVGinE--TDPlggaSSRDDDQDLLAQAQDLGYVFVYNRTELLKIDPEETEKLLGLFGSS 249
                                       ***9.*************77431..3325544689999*************************************** PP

                                       SCS-CCCSCTCCE..--HHHHHHHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHH CS
                   Alk_phosphatase 220 dlkveldrdeatd..PsLkemtevAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakk 294
                                       +l +el+r ++td  PsL+emte+Ai++Ls++e+GFFL+VEG+ IDha H  +  +   E+++fdeAvkaal++ ++
  gi|386000859|ref|YP_005919158.1| 250 HLVFELRRRNETDrePSLSEMTEKAIEILSHDEDGFFLMVEGGTIDHACHIRSYENTAAETLAFDEAVKAALDYGER 326
                                       ********9988777************************************************************** PP

                                       CTTEEEEEEESSEESEEEES CS
                   Alk_phosphatase 295 eketlvvvTaDHshvfsfgg 314
                                         +tlvvvT+DH+     gg
  gi|386000859|ref|YP_005919158.1| 327 SGDTLVVVTSDHEA----GG 342
                                       ************98....44 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.5e-08
                                       ..SSHTEE-SSEEEEEESTTGGGG.SCEEECCHHHHHHHHHCT CS
                   Alk_phosphatase 374 pltseeHtgedvavfAygpkaelv.rGvqeqteiakvlaaale 415
                                       p    +Ht++dv+++A gp ae++ rG +++tei++ ++ +++
  gi|386000859|ref|YP_005919158.1| 376 PTGMSTHTAVDVPLMASGPGAERFsRGRIDNTEIFYLMKEVMG 418
                                       667789****************9956************98765 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   4.3e-11   1.9e-07     111     218 ..     262     398 ..     220     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.3e-11
                                       STT--HHHHHHHHHHHH.CC.-S..EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEE.EEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                     Metalloenzyme 111 qpemkavevaekaldailsgkfd..lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgil.vvtAD 184
                                        +e +  e++eka++ + s++ d  +++v     D + H + +e+t+a   a+Deavk  ld  e ++++l vvt+D
  gi|386000859|ref|YP_005919158.1| 262 DREPSLSEMTEKAIEIL-SHDEDgfFLMVEGGTIDHACHIRSYENTAAETLAFDEAVKAALDYGERSGDTLvVVTSD 337
                                       556678899*****999.5557779999999********************************99987655178*** PP

                                       SB--TTTSS...................................-----EEEEEESTT--- CS
                                       xxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 185 Hgnaedmvkrdk...........................qplTsHtlepVPilivgkglap 218
                                       H     + +  +                           + ++ Ht+  VP++  g+g ++
  gi|386000859|ref|YP_005919158.1| 338 HEAGGLVLGAVDfddysagvpvfasglafipgegynltpTGMSTHTAVDVPLMASGPGAER 398
                                       *98887777444777999******************99999999*********99999664 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-06     0.006       3     286 ..      39     398 ..      37     419 .] 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                                       EEEEEESSE-TTGSGGGTTTSCSSHHHHHHH.HTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT... CS
                         Sulfatase   3 vvliladdlgagdlglyggktattpnldrla.eeglrftnfysaaplcspsraalltgryphnsgvasntevgg... 75 
                                       v+++++d +g++++++  +  a   nl++ + +e ++    y++  +++ s  ++ t   ++ +  a+ ++  +   
  gi|386000859|ref|YP_005919158.1|  39 VIFLIGDGMGFAQMTAARWAKAD-ENLSNYTdAELFMDGMEYAG-YSSTSSADSFVTDSAAAGTTLATGHK--Tklg 111
                                       89999999999999999999985.88877774444444444444.46666777777777666655444443..2347 PP

                                       ...........HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC................CTTTSEEEETS CS
                         Sulfatase  76 ...........gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk................nrgfdrflgfp 125
                                                  ++ +++ +t++el  + G +t+++ +   ++    s+y                 + g        
  gi|386000859|ref|YP_005919158.1| 112 iigqdetsifgVQDGENLTTILELAEAEGKATGVVTNMRITHATPASFYAhvndrdkenriaeqflASGV------- 181
                                       8888999999999999999999999999999999999999999888844444444444444444442222....... PP

                                       SSCHHTCCCCCCCCCECTCCC....................TTTTCSHHHHHHHHHHHHH...........HCCCTS CS
                         Sulfatase 126 tgsaalkdpekseyngevlrv....................ppeggysddrlldealefl...........larndk 171
                                                                                  + + +d++ll +a+++            +  +++
  gi|386000859|ref|YP_005919158.1| 182 --------------------DvalggglcyfvginetdplgGASSRDDDQDLLAQAQDLGyvfvynrtellKIDPEE 238
                                       ....................234555555555555555555333444444444444443222334444443444444 PP

                                       SEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH............................HHHHHHHHHHHH CS
                         Sulfatase 172 pfflylatlapHappeapdeyakkyatffddgseaar............................qlleaylnsvey 220
                                          l   + ++H  +e  ++ ++    +++++se ++                            +++e+ ++    
  gi|386000859|ref|YP_005919158.1| 239 TEKLLGLFGSSHLVFELRRRNETD---REPSLSEMTEkaieilshdedgfflmveggtidhachiRSYENTAAETLA 312
                                       444455578888766666666554...44444444445567788888888888888888888666777777777777 PP

                                       HHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG.......................HHTTSSSCTTCSSSHHHHB CS
                         Sulfatase 221 vDdligrvlaaLeenglldntlvvftSDhgaslee.......................sngplrggkganayeggtr 274
                                        D++++  l++    + + +tlvv+tSDh a                            +  + ++++  +++  + 
  gi|386000859|ref|YP_005919158.1| 313 FDEAVKAALDYG---ERSGDTLVVVTSDHEAGGLVlgavdfddysagvpvfasglafiPGEGYNLTPTGMSTHTAVD 386
                                       788888877777...78889*********995444778888888888888888888874455555555577777788 PP

                                       EEEEEEETTTSH CS
                         Sulfatase 275 vPllvwwpgeka 286
                                       vPl+  +pg  +
  gi|386000859|ref|YP_005919158.1| 387 VPLMASGPGAER 398
                                       888888777665 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   4.7e-05      0.21      30     233 ..      80     339 ..      39     355 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                                       HSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSS...EEETTTTEEEEEETTTTGG..........GGGCTTS CS
                      Phosphodiest  30 egvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNt...fydrktgeyvvfvtededa..........prwwqge 93 
                                        g+s++    +f t+++++ ++l+TG+   + Gi+g++   ++  ++ge+++   e ++a                 
  gi|386000859|ref|YP_005919158.1|  80 AGYSSTSSADSFVTDSAAAGTTLATGHKT-KLGIIGQDetsIFGVQDGENLTTILELAEAegkatgvvtnM------ 149
                                       56666666678888888888888888875.57888843111223333332222222222233332222220...... PP

                                       -HHHHHHHTHTTCEEEESE.....TTTTSEBTTCT.SC.TBHHSBTCT.CSTTS....................... CS
                      Phosphodiest  94 piwdtaakarglkaaalfw.....pgsevdystyyylvsetppryleddfnakv....................... 142
                                                               p s  ++ + ++++  + +++l+  ++ ++                       
  gi|386000859|ref|YP_005919158.1| 150 ------------------RithatPASFYAHVNDRDKENRIAEQFLASGVDVALggglcyfvginetdplggassrd 208
                                       ..................12233344444444444444433333333333333333333333333333333333333 PP

                                       .............................................CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSES CS
                      Phosphodiest 143 .............................................pledkvdkavlqtwldaafakvvlekelekpd 174
                                                                                    +l+++  +++ +++ ++ +++ ++  + e+  
  gi|386000859|ref|YP_005919158.1| 209 ddqdllaqaqdlgyvfvynrtellkidpeetekllglfgsshlvfELRRRNETDREPSLSEMTEKAIEILSHDEDGF 285
                                       3333333333334444444444445555555555556666666679999999999999999999999998888999* PP

                                       EEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 175 lllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                       +l+v    +D++ H      ++++++    D+a++  l++ ++    ++t ++++SDH 
  gi|386000859|ref|YP_005919158.1| 286 FLMVEGGTIDHACHIR--SYENTAAETLAFDEAVKAALDYGERS---GDTLVVVTSDHE 339
                                       **************55..46778999999******999998887...9**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2865.31
//
Query:       gi|386000860|ref|YP_005919159.1|  [L=90]
Description: hypothetical protein Mhar_0145 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 684.19
//
Query:       gi|386000861|ref|YP_005919160.1|  [L=491]
Description: hypothetical protein Mhar_0146 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 3710.99
//
Query:       gi|386000862|ref|YP_005919161.1|  [L=495]
Description: type-2 seryl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for 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-55  184.9   0.1    1.3e-54  184.4   0.1    1.2  1  tRNA_bind_4   tRNA-binding domain
      6e-11   42.6   0.0    9.3e-11   42.0   0.0    1.2  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
     0.0019   17.7   0.0     0.0039   16.7   0.0    1.5  1  tRNA-synt_2d  tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_bind_4  tRNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.1   2.1e-58   1.3e-54       1     160 [.       1     154 [.       1     155 [. 0.98

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 2.1e-58
                                       EEEEEEEEEEESS-SCCCHHHHHHHHHHHCCTGGGTTSSTTT.S.SSEEEEEEE-SSEEEEEEEEESSS-HHHHHHH CS
                       tRNA_bind_4   1 lkfelkgklklskdieeaeeeieefieeanktiLkkGvpegkeeegakitewkiegnelkleieSgryvRahdallr 77 
                                       +kf+l+++++ls+d+ +ae+e++ef++ a+ ++LkkG+  gk   ga++ +w++ + e+++ ieS+ryvRahdallr
  gi|386000862|ref|YP_005919161.1|   1 MKFHLEASFRLSADAGAAETELREFFNGAA-DLLKKGAAGGK---GAEVLSWNLGEAEISVVIESDRYVRAHDALLR 73 
                                       9*************************9866.5*******998...******************************** PP

                                       HHHHHHHHCCCCCS--EEEEEEEEEEEEEE-SS--HH---TTECEEEEETTEEEEEEES--HHHHHTTHHHHHHHHH CS
                       tRNA_bind_4  78 lkkplaeklGkkyriGvRgikveeyeieiesekelkaekipeveeveveegkitlelkdvdeselkkrvvdRiiklv 154
                                       l++pla++lGkkyr+GvRgi+v +yeie+es+ ++ ++kip+v+e+ +++g++tl+l dvde++l+++v+dRi++l+
  gi|386000862|ref|YP_005919161.1|  74 LRRPLADLLGKKYRVGVRGIEVAKYEIEVESKISI-DHKIPHVREMVHRDGTLTLSL-DVDEADLRNQVPDRIVSLL 148
                                       *********************************99.9********************.******************* PP

                                       HHHHCC CS
                       tRNA_bind_4 155 eekiek 160
                                       +eki++
  gi|386000862|ref|YP_005919161.1| 149 DEKIQA 154
                                       ***987 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.6e-14   9.3e-11      24     178 ..     308     469 ..     300     470 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.6e-14
                                       HHHHHEEEBGGSSEEEEE.EEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SC. CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      tRNA-synt_2b  24 lirdevlrskrLPlklyq.iqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglef. 98 
                                        ++ ++l s +LP+++++  +t +R+E   ++G+ Rv eFh  + + ++++++++++ ++l   + rife+++ e  
  gi|386000862|ref|YP_005919161.1| 308 FFQGRTLPSDDLPIRIFDrSGTSHRYESGGIHGIERVDEFHRIEIVWMGTQEQVKEEAEKLKDCYRRIFEEIL-ELr 383
                                       56666678899*****97368*******99*****************************************96.332 PP

                                       ..........EEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE CS
                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  99 ..........raiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaa 165
                                                  a ++ ++  ++ ++ + + ea+ +  ++ ie    +  g+++++ +++++    ++      +c +
  gi|386000862|ref|YP_005919161.1| 384 wrmawvtpwfMAQEGKTGLSEMTGAGTVDYEALLPYNGSWIEFQNLSINGDKYPRGFNVKA----QSGDPLWSGCSG 456
                                       34444444333333335555699***********************************999....444455679999 PP

                                       EEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                      tRNA-synt_2b 166 igveRllsaileq 178
                                       +g+eR  sa l+q
  gi|386000862|ref|YP_005919161.1| 457 VGLERWASAFLAQ 469
                                       *****99999887 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.5e-07    0.0039      91     203 ..     310     419 ..     307     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-07
                                       HHHHHTTS-SSEEEEE.EEEEEBSST...-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEE CS
                      tRNA-synt_2d  91 qirtlekkkppikiis.igrvfRrda...vDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrp 163
                                       q rtl + ++pi+i+   g  +R ++       +  eFh +e ++++++ ++++    l++ ++++f++ +++r+r 
  gi|386000862|ref|YP_005919161.1| 310 QGRTLPSDDLPIRIFDrSGTSHRYESggiHGIERVDEFHRIEIVWMGTQEQVKEEAEKLKDCYRRIFEEILELRWRM 386
                                       6689999999****9636899999996656778999***************************************98 PP

                                       CEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHT CS
                      tRNA-synt_2d 164 syfpftePsaevdvylvekkkkwlEllgaGmvrpevleav 203
                                       ++   ++P +   +   e k++  E+ gaG v+ e+l ++
  gi|386000862|ref|YP_005919161.1| 387 AW---VTPWF---MAQ-EGKTGLSEMTGAGTVDYEALLPY 419
                                       75...44533...323.45667777777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 3451.07
//
Query:       gi|386000863|ref|YP_005919162.1|  [L=75]
Description: hypothetical protein Mhar_0148 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 571.23
//
Query:       gi|386000864|ref|YP_005919163.1|  [L=430]
Description: Phosphoesterase, RecJ domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-14   52.4   0.2    1.3e-13   51.5   0.2    1.5  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
       0.07   13.4   0.1       0.14   12.4   0.1    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.2   1.5e-17   1.3e-13      49     137 ..     329     419 ..     296     420 .. 0.73

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.5e-17
                                       CCHHH.HHHHHH.HHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEE CS
                             DHHA1  49 eewda.galgia.adklksklkkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaG 119
                                       +e+da g++ ++ + +l    ++p+ ++  +e g  vkvsar ++     g+d++ ++k aa+++gg+GGGH  A+G
  gi|386000864|ref|YP_005919163.1| 329 NEMDAaGVVCGLsVRYLYA--DRPMLILNRSE-G-IVKVSARGNRLlvfcGLDLSSALKGAAEAVGGNGGGHSVASG 401
                                       3333333333333666666..56666666655.4.*********88******************************* PP

                                       EEEEHCHHHHHHHHHHHH CS
                             DHHA1 120 agipaekleealealeea 137
                                       a+ip ++ ee+++a++ a
  gi|386000864|ref|YP_005919163.1| 402 ASIPLGSEEEFIAAVDGA 419
                                       **************9976 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.6e-05      0.14       4      57 ..      23     105 ..      20     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       EE-ECSSSHHHHHHHHHHHH.............................CECS--TCGGCGCCHHCCCSEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   4 ivghknpDtDsigSaialan.............................llvDhneksqavegeakeeaedviiiDH 51 
                                       +  + + D+D+i+Sa ++                               + +D+++ +   +    + + +v + DH
  gi|386000864|ref|YP_005919163.1|  23 V--ISHNDADGITSAGLICTalrranipfhatlvsrldqqvidsveppvVFCDMGSGKPHLIS---KIEGEVFVFDH 94 
                                       5..6789*******877777678888888888888888888888888888*****99999988...7788899**** PP

                                       S---S.....S CS
                                       xxxxx.....x RF
                               DHH  52 Hrlge.....e 57 
                                       H +        
  gi|386000864|ref|YP_005919163.1|  95 HTPVGdidcvH 105
                                       *9976554330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 3270.01
//
Query:       gi|386000865|ref|YP_005919164.1|  [L=124]
Description: 30S ribosomal protein S15P/S13e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-17   62.5   1.9    4.5e-17   62.0   1.9    1.2  1  Ribosomal_S15    Ribosomal protein S15
    5.5e-08   32.7   0.0    7.2e-07   29.2   0.0    2.4  2  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
  ------ inclusion threshold ------
      0.022   14.6   0.2      0.032   14.1   0.2    1.2  1  Remorin_C        Remorin, C-terminal region


Domain annotation for each model (and alignments):
>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   1.9   7.5e-21   4.5e-17       8      79 ..      47     120 ..      42     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 7.5e-21
                                       HSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCT CS
                     Ribosomal_S15   8 fqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklg 79 
                                       + r++    ++++++a+l++++  +++hl++nkkD h+rr L+++++k+r+l kY++r+ +  e++++  e+++
  gi|386000865|ref|YP_005919164.1|  47 YLRENAEVQEIPEDLANLMRKAIGMRKHLESNKKDLHNRRWLQLTENKIRRLAKYYRRTGRlpENWQYRPETAE 120
                                       5566677889**************************************************99******999986 PP

>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.2e-10   7.2e-07      28      60 .]       1      33 [.       1      33 [. 0.96
   2 ?    0.8   0.0     0.083     5e+02      23      44 ..      85     106 ..      80     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-10
                                      --HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N 28 lskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      ++kee+ +++++l+  G+ p +IG++LRDqyGv
  gi|386000865|ref|YP_005919164.1|  1 MNKEELGKHVLRLHGSGVAPTMIGLTLRDQYGV 33
                                      5799****************************8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.083
                                       -TTS---HHHHHHHHHHHHHTT CS
                   Ribosomal_S13_N  23 psWlklskeeveelivklakkG 44 
                                        +Wl+l+++++  l   +++ G
  gi|386000865|ref|YP_005919164.1|  85 RRWLQLTENKIRRLAKYYRRTG 106
                                       68*****999988776666655 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   5.4e-06     0.032      57     106 ..      52     110 ..      47     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-06
                         Remorin_C  57 kaleklknklariekkAeekRasaeakr.........reeelktkekankirstgklps 106
                                       ++ +++ ++la   +kA ++R++ e+++         +  e k+ + a+++r+tg+lp+
  gi|386000865|ref|YP_005919164.1|  52 AEVQEIPEDLANLMRKAIGMRKHLESNKkdlhnrrwlQLTENKIRRLAKYYRRTGRLPE 110
                                       5679999********************999999999989999**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 864.91
//
Query:       gi|386000866|ref|YP_005919165.1|  [L=250]
Description: hypothetical protein Mhar_0151 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-46  156.2   0.0    5.5e-46  155.9   0.0    1.1  1  DUF116    Protein of unknown function DUF116


Domain annotation for each model (and alignments):
>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9   0.0   3.1e-50   5.5e-46       2     155 .]      75     228 ..      74     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 3.1e-50
                            DUF116   2 llkllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklteeglnCkrCgkCkigelkk 78 
                                       l+k ++r+++ d+  +++v ++++n ++++kf+ vp+++r++++P+Clr+ dCpaklt+egl+C +Cg+C++g +k 
  gi|386000866|ref|YP_005919165.1|  75 LIKSIFRTFRADDAIVDDVGVKLRNYINAEKFEAVPMDERAIFIPQCLRSVDCPAKLTPEGLRCVNCGRCEVGPAKI 151
                                       6899************************************************************************* PP

                            DUF116  79 laeklgykvyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveeleell 155
                                        ae+lgy+++ ++g+++++++ik+++p+ai+gv C ++++eg++ ++++++++++v+l ++gC++T++d+ +++e++
  gi|386000866|ref|YP_005919165.1| 152 FAEDLGYRFFLAPGSSVIKRMIKKYRPRAIVGVGCPMEIKEGLELCQGHDIPAIGVPLLTNGCVSTTLDWGRFYEVI 228
                                       ************************************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1792.78
//
Query:       gi|386000867|ref|YP_005919166.1|  [L=889]
Description: hypothetical protein Mhar_0152 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-274  912.1   1.4   3.7e-274  911.6   1.4    1.2  1  UPF0182   Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  911.6   1.4  2.1e-278  3.7e-274       7     758 .]      10     747 ..       5     747 .. 0.95

  Alignments for each domain:
  == domain 1  score: 911.6 bits;  conditional E-value: 2.1e-278
                           UPF0182   7 vlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerlelleklerlreale 83 
                                        l++ll+    +a l+te+ wf++lgy+svf+t l +r +lf+++++++ +++l+nl+l  +               
  gi|386000867|ref|YP_005919166.1|  10 GLILLLISSGQMAYLITEWRWFSSLGYSSVFWTILAARSALFLLATMAFGAVTLANLRLVGER-------------- 72 
                                       567778889999*********************************************998877.............. PP

                           UPF0182  84 kklkllllaialvlsllvglvassqwekvllflnstsfgvkDpifgkDisFYvFklPflelllslllalvllaliav 160
                                         + + l+ i++++s+l+gl+a++ we+vll+ln+++fg +Dp+fg+D++F+vF+lP+l  l  +++a+v++ l+++
  gi|386000867|ref|YP_005919166.1|  73 --P-RQLAWIVVLISVLFGLAAQAGWERVLLALNAQPFGATDPLFGNDVGFFVFTLPLLWSLWYAVFAAVMVNLALA 146
                                       ..2.3455677889********************************************9999999999999988888 PP

                           UPF0182 161 llvyllsgeslgirl...........kfaelskaarrhlsvllallllllalsywLdryellyskrgvvtGagYtdv 226
                                       + +yl+ +  +   l              ++ k+a  h+ +ll++l+ll +++y+Ldryell++  gvv+GagY dv
  gi|386000867|ref|YP_005919166.1| 147 AGAYLYLHADR---LifgpeggdyleIARSIPKRAIGHIGALLGVLALLFSARYLLDRYELLFTGGGVVYGAGYADV 220
                                       88877666444...2235677888997789***********************************9*********** PP

                           UPF0182 227 navlpaktilavialvvavlllvaivlkklklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIe 303
                                        a+lp+  ++a++a++ a+ll++ ++ ++   + +a+a+lv+ a ++g+++p ++q+++V Pnel++E+p+i++nI+
  gi|386000867|ref|YP_005919166.1| 221 YARLPFLYVFAAVAAISALLLFAYAAGRRSPKIPLAIAVLVVGAGAAGTIYPVVIQQYSVAPNELTLERPFIAHNIN 297
                                       ***********************99777766777777788888888******************************* PP

                           UPF0182 304 aTreAygLdkveveefeaeaeltaedleenaetienirLlDprplletfrqlqqirnYYkFedldvdrYtidgeerq 380
                                       +Tr AygLd+v v++f+++ +lt +d+++naet++nir++D+rpll+t++qlq+ir YY+F d+dvdrY +dg++rq
  gi|386000867|ref|YP_005919166.1| 298 YTRLAYGLDDVVVKDFPVDYNLTGADVRRNAETVDNIRIWDWRPLLTTYKQLQEIRLYYEFLDADVDRYVVDGRKRQ 374
                                       ***************************************************************************** PP

                           UPF0182 381 vviaaREldysalpeeaktwvnkhlvYTHGyGvvaspvnkvteeGlpeflvkdipseeeeslkieepriYfGeltnd 457
                                       v+++aRE+++++lpe+aktw+n hl YTHGyGv++spvn +teeGlpe+++k+ip+ e+e  +i++p+iY+Ge  +d
  gi|386000867|ref|YP_005919166.1| 375 VMLSAREISTDRLPEQAKTWQNVHLFYTHGYGVAMSPVNAATEEGLPEYFIKNIPP-ESEVGDIHRPEIYYGEGRKD 450
                                       *******************************************************9.55666889************ PP

                           UPF0182 458 yvivgtkvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnikeRvekvaP 534
                                       y+iv+t+v Efdyp g++nvy+tY G+gGv + +++ +ll+a++  ++k+lls+e+t es+i+++R+i eR ++vaP
  gi|386000867|ref|YP_005919166.1| 451 YAIVKTQVLEFDYPMGDQNVYTTYAGTGGVVL-DPVMKLLMAYRHMSPKILLSKELTGESRIMIHRDILERAQTVAP 526
                                       ********************************.99****************************************** PP

                           UPF0182 535 fLtlDsdpYlvvadgrlyWivDaYTtsdrYPySepeeatsgeeevnYiRNSVKvvvDAydGtvklYvvdeeDPiika 611
                                       fL +D+dpY+v+adgrl+Wi+DaYT s rYPySep      + ++nYiRN+VKvv+DAy+Gtv++Yv++ +DP+i+a
  gi|386000867|ref|YP_005919166.1| 527 FLAYDRDPYVVLADGRLFWIIDAYTLSGRYPYSEP------SGRFNYIRNPVKVVIDAYNGTVSYYVIE-DDPLIRA 596
                                       ***********************************......689************************8.8****** PP

                           UPF0182 612 wskiFpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpke...eeeqpvePyYlilk 685
                                       ++ iFp+lf+p+ +mpe L +h+rYP dlF++q+ ++++YH+tdp+ FYn+ed+We+p e    ++qp+ePyY+i+k
  gi|386000867|ref|YP_005919166.1| 597 YEAIFPDLFQPIGSMPEGLLAHMRYPVDLFRIQAGIYQNYHMTDPQIFYNKEDAWETPMEiyqGRSQPMEPYYVIMK 673
                                       *************************************************************999999********** PP

                           UPF0182 686 lpg.eekeefillspftpssrenliawlaarsdgenygklllyelpkqelvyGpeqiearinqdpeisqqlsLw 758
                                       +p+ e  eef+l++pftp++r+n+iaw++a++d+ nyg++l+y++pk++lvyGp+qieari+q++eis+ql+Lw
  gi|386000867|ref|YP_005919166.1| 674 IPEsEVAEEFMLIQPFTPRTRNNMIAWMSAKCDQPNYGQILVYRFPKDQLVYGPMQIEARIDQSTEISEQLTLW 747
                                       **845689****************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 6272.99
//
Query:       gi|386000868|ref|YP_005919167.1|  [L=58]
Description: Ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-19   66.6  16.7      2e-09   36.9   4.2    2.1  2  Fer4          4Fe-4S binding domain
    5.8e-13   48.3  17.2    2.3e-06   27.4   4.9    2.1  2  Fer4_6        4Fe-4S binding domain
    3.4e-12   45.7  15.6    5.6e-07   29.3   3.7    2.1  2  Fer4_2        4Fe-4S binding domain
    1.1e-11   44.7  12.9    1.4e-11   44.3  12.9    1.2  1  Fer4_9        4Fe-4S dicluster domain
    7.2e-11   42.5  13.9    1.1e-10   41.9  14.0    1.3  1  Fer4_7        4Fe-4S dicluster domain
    7.5e-11   42.0  13.9      1e-10   41.6  13.9    1.3  1  Fer4_10       4Fe-4S dicluster domain
    1.2e-10   41.4  14.7    1.3e-10   41.3  14.7    1.0  1  Fer4_21       4Fe-4S dicluster domain
    2.4e-10   41.2  13.5    1.4e-05   25.9   2.0    2.0  2  Fer4_16       4Fe-4S double cluster binding domain
    3.4e-07   30.2  15.9    0.00063   20.1   5.5    2.1  2  Fer4_4        4Fe-4S binding domain
    5.2e-07   30.1  17.4    0.00033   21.1   4.7    2.2  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    1.7e-06   28.4  15.9    0.00058   20.3   3.0    2.0  2  Fer4_17       4Fe-4S dicluster domain
    2.2e-06   28.2  18.6     0.0016   19.2   5.2    2.2  2  Fer4_3        4Fe-4S binding domain
    1.1e-05   25.7  17.1     0.0015   18.9   4.0    2.1  2  Fer4_8        4Fe-4S dicluster domain
    3.9e-05   24.3  15.5    0.00011   22.9   2.3    2.6  2  Fer4_15       4Fe-4S single cluster domain
    0.00032   21.5   8.7      0.072   13.9   1.6    2.0  2  Fer4_22       4Fe-4S dicluster domain
     0.0034   17.5   7.1     0.0039   17.3   7.1    1.1  1  Fer4_11       4Fe-4S dicluster domain
     0.0035   17.5  15.4      0.033   14.4   3.6    2.0  2  Fer4_18       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.029   14.5   6.1      0.056   13.6   6.1    1.4  1  Furin-like_2  Furin-like repeat, cysteine-rich
        4.7    7.1   8.1        4.1    7.3   0.9    2.2  2  zf-C2H2_11    zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   4.6   3.8e-12   3.6e-09       2      24 .]       4      26 ..       3      26 .. 0.95
   2 !   36.9   4.2   2.1e-12     2e-09       2      24 .]      34      56 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.8e-12
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v++ e C+ CG+Cve CP +AIt
  gi|386000868|ref|YP_005919167.1|  4 VVNREECVSCGTCVEECPENAIT 26
                                      89********************7 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 2.1e-12
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v++ +kC+ CG Cve+CP +AI+
  gi|386000868|ref|YP_005919167.1| 34 VVNVDKCTECGSCVEACPSEAIS 56
                                      89*******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   4.4   2.8e-09   2.7e-06       2      24 .]       3      25 ..       2      25 .. 0.96
   2 !   27.4   4.9   2.5e-09   2.3e-06       1      24 []      32      55 ..      32      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.8e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      ++++++ C++Cg Cv  CPe+ai
  gi|386000868|ref|YP_005919167.1|  3 AVVNREECVSCGTCVEECPENAI 25
                                      799*******************8 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.5e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++++ dkC+ Cg Cv +CP  ai
  gi|386000868|ref|YP_005919167.1| 32 IAVVNVDKCTECGSCVEACPSEAI 55
                                      689*****************9998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   4.1   8.1e-08   7.7e-05       2      22 .]       2      22 ..       1      22 [. 0.92
   2 !   29.3   3.7   5.9e-10   5.6e-07       2      21 ..      32      51 ..      31      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.1e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      p+vv+++ C++Cg+Cv  CP+
  gi|386000868|ref|YP_005919167.1|  2 PAVVNREECVSCGTCVEECPE 22
                                      5799****************5 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 5.9e-10
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                       +vv+ d+C++Cg+Cv aCP
  gi|386000868|ref|YP_005919167.1| 32 IAVVNVDKCTECGSCVEACP 51
                                      5799**************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3  12.9   1.5e-14   1.4e-11       1      51 []       9      55 ..       7      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.5e-14
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C++Cg+Cve Cp +++++d+ e  + +      +C++Cg+CveaCp++ai
  gi|386000868|ref|YP_005919167.1|  9 ECVSCGTCVEECPENAITMDDEEIAVVNVD----KCTECGSCVEACPSEAI 55
                                      5********************999999876....6*************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9  14.0   1.2e-13   1.1e-10       2      52 .]      10      54 ..       9      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.2e-13
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ Cg Cv+ Cp +ai++d+e      e ++++ +kC+ Cg+Cv++CP++a
  gi|386000868|ref|YP_005919167.1| 10 CVSCGTCVEECPENAITMDDE------EIAVVNVDKCTECGSCVEACPSEA 54
                                      ******************997......578899***************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6  13.9   1.1e-13     1e-10       3      56 .]       4      51 ..       2      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.1e-13
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      v++++ C+ Cg+Cv+ CP        +++++++e++ + +v+kCt+cg+CveaCP
  gi|386000868|ref|YP_005919167.1|  4 VVNREECVSCGTCVEECPE-------NAITMDDEEIAVvNVDKCTECGSCVEACP 51
                                      7899***************.......66666666666669**************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3  14.7   1.4e-13   1.3e-10       1      58 [.       3      56 ..       3      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.4e-13
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      A++++++C++Cg C+  C++   +ai++d+++++ v  d+C+ C  C++ CP +++i+
  gi|386000868|ref|YP_005919167.1|  3 AVVNREECVSCGTCVEECPE---NAITMDDEEIAVVNVDKCTECGSCVEACP-SEAIS 56
                                      899****************7...9****************************.58886 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   2.0   1.5e-08   1.4e-05       2      22 ..      10      30 ..       9      37 .. 0.85
   2 !   21.2   4.0   4.4e-07   0.00041       1      18 [.      39      56 ..      39      58 .] 0.92

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.5e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekke 22
                                      C++Cg C+e CP+nai+++ e
  gi|386000868|ref|YP_005919167.1| 10 CVSCGTCVEECPENAITMDDE 30
                                      *****************9944 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 4.4e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg C+e+CP++ai+
  gi|386000868|ref|YP_005919167.1| 39 KCTECGSCVEACPSEAIS 56
                                      6***************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.6   1.3e-05     0.012       2      16 ..       8      22 ..       7      29 .. 0.90
   2 !   20.1   5.5   6.7e-07   0.00063       2      16 ..      38      52 ..      38      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C+ Cg Cv  CP 
  gi|386000868|ref|YP_005919167.1|  8 EECVSCGTCVEECPE 22
                                      78************5 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.7e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C++CgsCv aCP+
  gi|386000868|ref|YP_005919167.1| 38 DKCTECGSCVEACPS 52
                                      79************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   4.7   3.5e-07   0.00033       1      27 [.       5      32 ..       5      36 .. 0.76
   2 !   15.6   4.9   1.9e-05     0.018       1      18 [.      35      52 ..      35      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-07
                           Fer4_13  1 VDrdtCiacgaCvelaPdv.Feeddegg 27
                                      V+r++C++cg+Cve +P+    +dde+ 
  gi|386000868|ref|YP_005919167.1|  5 VNREECVSCGTCVEECPENaITMDDEEI 32
                                      89***************85245555544 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.9e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      V+ d+C++cg+Cve++P 
  gi|386000868|ref|YP_005919167.1| 35 VNVDKCTECGSCVEACPS 52
                                      7789*************5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   5.0   3.7e-05     0.035      44      59 ..       8      23 ..       3      25 .. 0.88
   2 !   20.3   3.0   6.2e-07   0.00058      37      59 ..      31      53 ..      23      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C++Cg C+++CP++
  gi|386000868|ref|YP_005919167.1|  8 EECVSCGTCVEECPEN 23
                                      68***********987 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.2e-07
                           Fer4_17 37 aekeekaslCieCgeCerkCPqg 59
                                      +++  ++++C+eCg C+++CP++
  gi|386000868|ref|YP_005919167.1| 31 EIAVVNVDKCTECGSCVEACPSE 53
                                      34446899*************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.5   3.4e-05     0.032       1      15 []      10      24 ..      10      24 .. 0.97
   2 !   19.2   5.2   1.7e-06    0.0016       1      15 []      40      54 ..      40      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg+Cve CP++A
  gi|386000868|ref|YP_005919167.1| 10 CVSCGTCVEECPENA 24
                                      99***********98 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg Cve+CP+ A
  gi|386000868|ref|YP_005919167.1| 40 CTECGSCVEACPSEA 54
                                      ************876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   5.1   9.1e-05     0.086      50      64 ..       9      23 ..       5      25 .. 0.80
   2 !   18.9   4.0   1.6e-06    0.0015      47      63 ..      36      52 ..      24      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-05
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                      +C++cg C+e+Cp++
  gi|386000868|ref|YP_005919167.1|  9 ECVSCGTCVEECPEN 23
                                      788888888888876 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-06
                            Fer4_8 47 alwsCttcgaCtevCpv 63
                                      ++++Ct+cg+C+e+Cp 
  gi|386000868|ref|YP_005919167.1| 36 NVDKCTECGSCVEACPS 52
                                      47888888888888886 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.3   1.1e-07   0.00011       2      35 ..       4      38 ..       3      39 .. 0.88
   2 !    9.3   5.4     0.002       1.9       2      19 ..      34      51 ..      33      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                           Fer4_15  2 vvDrdaCigcglCvaea.pevfeldedglasvlld 35
                                      vv+r++C +cg Cv+e+ ++ +++d++ +a+v +d
  gi|386000868|ref|YP_005919167.1|  4 VVNREECVSCGTCVEECpENAITMDDEEIAVVNVD 38
                                      699**************55689********88775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      vv+ d+C+ cg Cv+++p
  gi|386000868|ref|YP_005919167.1| 34 VVNVDKCTECGSCVEACP 51
                                      57889************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.6   7.6e-05     0.072      77      95 ..       5      23 ..       1      24 [. 0.85
   2 !   12.3   0.9   0.00024      0.23      78      94 ..      36      52 ..      26      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-05
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      ++++ Cv Cg C+e cp++
  gi|386000868|ref|YP_005919167.1|  5 VNREECVSCGTCVEECPEN 23
                                      57899***********986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00024
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      +  +C+ Cg C+eacp+
  gi|386000868|ref|YP_005919167.1| 36 NVDKCTECGSCVEACPS 52
                                      56778888888888876 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   7.1   4.1e-06    0.0039       8      58 ..       8      54 ..       3      58 .] 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                           Fer4_11  8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPyki 58
                                      e+C  C    Cv+ +p++ai+ d+e+ aV+ + +++  e+ ++veacP ++
  gi|386000868|ref|YP_005919167.1|  8 EECVSC--GTCVEECPENAITMDDEEIAVV-NVDKCT-ECGSCVEACPSEA 54
                                      456666..47**************776666.555665.8*********776 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   4.1   0.00077      0.73      58      73 ..       7      22 ..       3      29 .. 0.81
   2 !   14.4   3.6   3.5e-05     0.033      47      74 ..      26      53 ..      22      58 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00077
                           Fer4_18 58 agdcidcescvkvcPt 73
                                        +c++c++cv+ cP 
  gi|386000868|ref|YP_005919167.1|  7 REECVSCGTCVEECPE 22
                                      6799999999999996 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.5e-05
                           Fer4_18 47 lkekeerkekgagdcidcescvkvcPtg 74
                                      +++ ee +  ++ +c++c+scv+ cP +
  gi|386000868|ref|YP_005919167.1| 26 TMDDEEIAVVNVDKCTECGSCVEACPSE 53
                                      5667778888999*************75 PP

>> Furin-like_2  Furin-like repeat, cysteine-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   6.1   5.9e-05     0.056      23      65 ..       4      50 ..       2      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                      Furin-like_2 23 lleregirqiGvclascpaGyfgvrnkev.....nrctkckaeecesc 65
                                      +++re+    G+c+++cp+    +  +e+     ++ct+c +   e+c
  gi|386000868|ref|YP_005919167.1|  4 VVNREECVSCGTCVEECPENAITMDDEEIavvnvDKCTECGS-CVEAC 50
                                      57899****************999988862222245666655.34555 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.2      0.05        47       7      13 ..      10      16 ..       8      17 .. 0.93
   2 ?    7.3   0.9    0.0043       4.1       6      13 ..      39      46 ..      36      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.05
                        zf-C2H2_11  7 CleCGlc 13
                                      C+ CG c
  gi|386000868|ref|YP_005919167.1| 10 CVSCGTC 16
                                      *****99 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0043
                        zf-C2H2_11  6 qCleCGlc 13
                                      +C+eCG c
  gi|386000868|ref|YP_005919167.1| 39 KCTECGSC 46
                                      8*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 465.10
//
Query:       gi|386000869|ref|YP_005919168.1|  [L=1235]
Description: Anaerobic ribonucleoside-triphosphate reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-148  496.5   0.0    1.9e-83  281.2   0.0    2.1  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct
    3.7e-17   62.5   0.0    7.9e-17   61.5   0.0    1.5  1  Intein_splicing  Intein splicing domain
     0.0003   21.1   0.0      0.075   13.4   0.0    2.7  2  LAGLIDADG_3      LAGLIDADG-like domain
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.21   11.2   0.1    1.4  1  TackOD1          Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.3   0.0   1.5e-66   6.8e-63       1     258 [.     133     417 ..     133     419 .. 0.95
   2 !  281.2   0.0   4.2e-87   1.9e-83     253     561 .]     886    1231 ..     866    1231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 213.3 bits;  conditional E-value: 1.5e-66
                                       .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SS CS
                              NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgng 77 
                                       enan+ +++++++++k a+++ske +l  l+p+ +++ h  gd+HiHDl+y+ +  ++C+++dl++++ +Gl+  +g
  gi|386000869|ref|YP_005919168.1| 133 ENANL-QENAETSHKKKADKISKEQYLL-LIPPYLSDHHLAGDLHIHDLEYFGT-RPFCQDWDLRYFFYYGLMP-DG 205
                                       8****.*********************5.************************9.77***************65.66 PP

                                       S......-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTT CS
                              NRDD  78 v......srppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynln 148
                                       +      + p+k+ e+a+ +av++l+++q+++aGgq++++f+t+lap++  +      +l+++ei q mq+fvy+++
  gi|386000869|ref|YP_005919168.1| 206 SgtkasvAGPAKKPEVAMLHAVKALASAQTNFAGGQGFYNFLTFLAPYL--E------GLDYSEICQLMQMFVYEMT 274
                                       6689999******************************************..6......78***************** PP

                                       S-S..SSSS---EEEEEE.-HH......................................HHHHHTTTTS-HCH--- CS
                              NRDD 149 tlpsrrGaQvpFtninlgldtp.......................tegrfee..kliikallevmleGdgnkgtpft 200
                                       +++++rG+Qv+F++++l  ++p                       t+g+fe+  +l +kal+evmleGd++ g+pf+
  gi|386000869|ref|YP_005919168.1| 275 QMMVARGGQVVFSSVQLSPGVPklwrdkpvvyqgkvwdgegaplrTYGEFEKevRLGFKALMEVMLEGDYW-GKPFN 350
                                       ***********************************************************************.***** PP

                                       -SEEEEEEEEETETTH...............HHHHHHHHHHTTT--EEE.......EEES--GGGTT- CS
                              NRDD 201 FPilifklkedfnleeed..........pnydlfklalevtakrgfpyffnlledlepedekevasmg 258
                                       FP++ ++++ df  e+ d          ++ dl+ l +++++k g+py+ n+l+ +++  +  +++++
  gi|386000869|ref|YP_005919168.1| 351 FPKPEISIEPDFMAED-DgfnaahpevpTYRDLYLLSFQLASKFGTPYYDNQLPAYRGAGKGISCYQC 417
                                       ***********95555.67********99***********************9877887777777777 PP

  == domain 2  score: 281.2 bits;  conditional E-value: 4.2e-87
                                        GGGTT-------....-............S---....EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHH CS
                              NRDD  253 evasmgCRlrld....ege..........rlgg....rgslgvvtiNlprlaleakgdeekffelLdellelake 309 
                                         v+  +C +++     + +          +  g    +gs++vv++N+pr a++a+gd++ +fe L+ l++ a e
  gi|386000869|ref|YP_005919168.1|  886 IVTGNCCAYQFAatfeS-DaafedkllfkE--GmhfsMGSWQVVSLNCPRAAYLARGDDDLLFEYLRGLMDTAVE 957 
                                        46778*******54431.133445565541..25567************************************** PP

                                        HHHHHHHHHHHHHHTT.-HHH.HTTSS-G.E..............EEEEEEE-HHHHHHHTTEEEE..-HHHHHH CS
                              NRDD  310 aleerrkilekllakg.lpflmgkgylks.r.kkkdeveevlkngtltiGfiGlaEalkaltgkkigeseeakef 381 
                                        +++ +r+++++++++  +pf+ +++   + r +kk +++  l++ ++tiG++G++E+++++tg++++es+ea+++
  gi|386000869|ref|YP_005919168.1|  958 IFKVKREWMNQVIKNRrMPFA-TQRPK-DpRtGKKGTLAVDLESLVYTIGVVGVNEMVQFHTGSQMHESKEAWKL 1030
                                        ***************9****6.55555.33668899*************************************** PP

                                        HHHHHHHHHHHHHHHHHHHSS-EEEEE---TTHHHHHHHHH....HH...........................H CS
                              NRDD  382 alkvlkhmrekadelkeetglnfsleatPaEslsgrfakldk..kkfgeipgv.dke................py 437 
                                        a++++++m+ +a+el++++g++++l +tPaE++ +rfa  d   +kf++      k+                +y
  gi|386000869|ref|YP_005919168.1| 1031 AVRAMTEMEIYAKELSRRHGMTIALARTPAETVVQRFAVSDLlsEKFRDCAARvVKGdldtamkrihqtrdlpVY 1105
                                        *****************************************9889**55444334446777777788889999** PP

                                        HG-SSSS-TTSSB-HHHHHHHHHHHTGGGTT-S-EEEEBSS--SSHHHHHHHHH.HHHHTT--EEEEE--EEEET CS
                              NRDD  438 YtNsfhvpvdekislfekikleaefqklttGGailyieldeekknpealeklvk.iakktgigYfsinpkidvCn 511 
                                        YtN +h+p + ++s+fe+ kle+ f ++++GG+i++i+l+e+ ++p+ l+++   +a+ t+igYf+++ +++vC 
  gi|386000869|ref|YP_005919168.1| 1106 YTNGTHIPPSLDVSIFERAKLEHIFFPIVDGGNIFHIFLGESAPDPQGLMDFAMnLARSTQIGYFAFTRDMTVCL 1180
                                        *****************************************************99******************** PP

                                        T.--..EESSSB-TTT--BE.EEEEEESSSSEEEHHHHHHHHHHHSGG---B CS
                              NRDD  512 ecgy..kgeiekCpkCgseeevevirRitGYlrpvsswnkgkkaElkdRvkh 561 
                                        +c     g++e+Cp+Cgs++ +e+++R+tGYl++vs wn++kk+El+dR k+
  gi|386000869|ref|YP_005919168.1| 1181 SCFCvsPGLKEECPRCGSDH-LEYLSRVTGYLQSVSGWNEAKKQELRDRNKY 1231
                                        ***99999*********666.****************************998 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   1.8e-20   7.9e-17       8     132 ..     433     888 ..     425     890 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.8e-20
                                       EE.EEHHHHCC.................ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT CS
                                       xx.xxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   8 ek.vkieelve.................kegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpe 65 
                                       ++ ++i+e+++                 +      s+n+++l+    + k +++ + + el++i l+sgr+i++Tp+
  gi|386000869|ref|YP_005919168.1| 433 IHvKQISEIFSeaeeygketdpfgvefvRFQGRTPSVNFDTLEASLREFKGVMRQRCEgELLKIVLKSGRRIRVTPN 509
                                       554566666666666666666666666644445557999999999999***************************** PP

                                       -EEEECCTTEEEEEECCC--TT-EEEEE................................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                   Intein_splicing  66 HkllvvrdegivEkradeLkegdliavp................................................. 93 
                                       H++ v+++++ v k+a +L++gd++ +                                                  
  gi|386000869|ref|YP_005919168.1| 510 HPVYVLDKGNFVKKQACDLNVGDFLPLLtdvdfglaplasidvettllkagyadeivvhnesvnvknakkpglpkni 586
                                       ******77*****************9999************************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|386000869|ref|YP_005919168.1| 587 sitselvrflgyylaegcsdqsgrrysvrlsfgkhesgliddamacikslglepkvseektatnvvvnskllyllid 663
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|386000869|ref|YP_005919168.1| 664 algcghdahtksvpdllfnvdpslvgeyiccafrgdgnvnvqkgelngrphtahviriglvsrdavqrliwlaqrig 740
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|386000869|ref|YP_005919168.1| 741 vqmnymvrdetvrhpqtgnpyrltsyscyvtsqdqienfysrtgyggcavsddrkevggvftripienaglehadlk 817
                                       ***************************************************************************** PP

                                       ..............................HSCEEEEEEEEEEEEECEEEEEEE.EETTT-EEEE.CTTEE CS
                                       ..............................xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxx RF
                   Intein_splicing  94 ..............................dadvvwdkvksievedeeeyVYdl.tvednhNFva.ngiiv 132
                                                                      +dv   ++++ieve++ +yVYdl  v ++hNF    gi+ 
  gi|386000869|ref|YP_005919168.1| 818 ypsqyrsqghkcvnqrhidssgspiierliGGDVHVLEIREIEVEEYGGYVYDLvDVSETHNFSNaMGIVT 888
                                       *****************************************************858*******88777775 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.7e-05     0.075       8      63 ..     596     652 ..     591     663 .. 0.83
   2 !    4.7   0.0    0.0085        38      10      81 ..     695     782 ..     687     784 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                       HHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCC CS
                       LAGLIDADG_3   8 rGlfdaDGsvskskkkgvs.isltssskelledvqrlLlrlGIestiyekkkakgrg 63 
                                        G++ a+G+ + s+++ +  +s++ ++  l++d +   + lG+e ++ e+k a + +
  gi|386000869|ref|YP_005919168.1| 596 LGYYLAEGCSDQSGRRYSVrLSFGKHESGLIDDAMACIKSLGLEPKVSEEKTATNVV 652
                                       6**********999775558******************************5554444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0085
                                       HHHHCCECCECSTTTTS.......EEEEES-HHHHHHHHHHHHHCT.HSCEEEE.....EEE-SCCCC......... CS
                       LAGLIDADG_3  10 lfdaDGsvskskkkgvs.......isltssskelledvqrlLlrlGIestiyek.....kkakgrgvy......... 65 
                                        f +DG v+++k+  ++       i+++  s++ ++ +  l +r+G+  +   +     +   +             
  gi|386000869|ref|YP_005919168.1| 695 AFRGDGNVNVQKGELNGrphtahvIRIGLVSRDAVQRLIWLAQRIGVQMNYMVRdetvrH--PQ---Tgnpyrltsy 766
                                       599*********9988899999************************99887777445321..22...1344567777 PP

                                       ECCCHCHCTTCGGGTT CS
                       LAGLIDADG_3  66 rlliisgenlkrFlek 81 
                                          ++s++++++F+++
  gi|386000869|ref|YP_005919168.1| 767 SCYVTSQDQIENFYSR 782
                                       7778888888888876 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.7e-05      0.21      58      99 ..    1160    1202 ..    1141    1210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                           TackOD1   58 elvkrglle.eelvdrirlCpsCksghlnvrevCpkCkSidie 99  
                                        +l+++  +    +   + +C sC + +  ++e+Cp C+S ++e
  gi|386000869|ref|YP_005919168.1| 1160 NLARSTQIGyFAFTRDMTVCLSCFCVSPGLKEECPRCGSDHLE 1202
                                        555555555566788899*********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 7420.99
//
Query:       gi|386000870|ref|YP_005919169.1|  [L=187]
Description: hypothetical protein Mhar_0155 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-31  108.9   0.0    2.3e-31  108.7   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    1.1e-07   31.7   0.0    1.5e-07   31.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0   2.5e-35   2.3e-31       1     151 [.       8     145 ..       8     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.5e-35
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadali 77 
                                       m i +i G++r+g+ ++k+a+++++ ++e g+e e+id++d+ lp  + d+ +     ts+++++l+e++  ad+++
  gi|386000870|ref|YP_005919169.1|   8 MYIPIILGTARAGRESEKVARFMLAKAAEFGLESEIIDVRDYRLP--ATDDSK-----TSEAAKRLKERVLRADGIV 77 
                                       56779**********************999***************..888666.....9****************** PP

                                       EEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEET CS
                           FMN_red  78 ivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavg 151
                                       iv+PeYn++y+g lK +lD+l     + e  gKpv++ +v++g+ gg+r+ e+l   +  +++ + ++ +++++
  gi|386000870|ref|YP_005919169.1|  78 IVSPEYNHGYPGELKMMLDLL-----YVEYFGKPVGICGVSSGVFGGARMIEHLVATCVRFHMLPTGE-VLYFP 145
                                       *********************.....9********************************999999888.66665 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.7e-11   1.5e-07       3     108 ..      10     103 ..       8     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.7e-11
                                       EEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHHHHHHHCSS CS
                      Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaad 79 
                                       i ii +  r  +  s ++a+ +++++++ g  e +++d+ +  lp  +         +++ +  +++ + e++l+ad
  gi|386000870|ref|YP_005919169.1|  10 IPIILGTARA-GRESEKVARFMLAKAAEFG-LESEIIDVRDYRLPATDD--------SKT-SEAAKRLK-ERVLRAD 74 
                                       6688889998.5888***************.9*********87777774........222.35666666.99***** PP

                                       EEEEEEE-BTTB--HHHHHHHHHHS-TTT CS
                      Flavodoxin_2  80 aivlqfPlwwfgvPailKgwiDrvltagf 108
                                        iv+++P ++ g+P  lK  +D  ++  f
  gi|386000870|ref|YP_005919169.1|  75 GIVIVSPEYNHGYPGELKMMLDLLYVEYF 103
                                       **********************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 1108.97
//
Query:       gi|386000871|ref|YP_005919170.1|  [L=173]
Description: 3-demethylubiquinone-9 3-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-32  110.2   0.1    1.4e-29  103.0   0.1    2.1  1  3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase
  ------ inclusion threshold ------
      0.054   14.1   0.0      0.095   13.3   0.0    1.4  1  PSCyt1        Planctomycete cytochrome C
      0.081   12.0   0.0      0.091   11.8   0.0    1.1  1  Filo_VP35     Filoviridae VP35


Domain annotation for each model (and alignments):
>> 3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.1   2.3e-33   1.4e-29       2     115 ..       3     135 ..       2     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 2.3e-33
                      3-dmu-9_3-mt   2 kitpcLlfdgeaeeAaefYvsvfe....nseilsvarypee..............e.pskegkvltveFtlagqefv 59 
                                        i +c+ f+geaeeAa++Yv  f+    +s+il+++ y++e              + p+++g+v  v+F l+g e++
  gi|386000871|ref|YP_005919170.1|   3 TIRTCIGFHGEAEEAANLYVDAFSrafgDSKILKITYYGDEelealrevpdvteeFmPGPPGSVKDVRFLLNGDELM 79 
                                       5789***************9875433339*****9998765222222222221112345789*************** PP

                      3-dmu-9_3-mt  60 alnggpef.kfneavSllveckdqeevdrlwnalseeggeeskcgWvkDkfGvswQi 115
                                       a+ngg  f +f+e+vSl+v+ck+q+++d lw++lse g  e++cgW+kD+fGvswQi
  gi|386000871|ref|YP_005919170.1|  80 AFNGGGYFgNFTESVSLYVSCKTQDQIDGLWEKLSEGG-IEQQCGWLKDRFGVSWQI 135
                                       ****955538*************************986.788**************9 PP

>> PSCyt1  Planctomycete cytochrome C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.6e-05     0.095       1      56 [.       7      60 ..       7      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                            PSCyt1  1 CyeCHgpddaegglrLdsrdaalkggesg.aaivpgdpeeselierilsddedmeMP 56
                                      C+  Hg++++ ++l +d ++ a+  g+s    i+    ee e+++++  d++++ MP
  gi|386000871|ref|YP_005919170.1|  7 CIGFHGEAEEAANLYVDAFSRAF--GDSKiLKITYYGDEELEALREV-PDVTEEFMP 60
                                      8888*******************..6888889999999999******.889999999 PP

>> Filo_VP35  Filoviridae VP35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.5e-05     0.091     161     285 ..      17     141 ..       5     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX----S-HHHHHHHHH.CTSSSSSBH..HHHHHHH CS
                         Filo_VP35 161 qpalykelavaqkieskdetvknavreaadklskvlelseetfskpdlsakdlallly.dhlpGfnta..fhilvqv 234
                                          ly ++  +    sk   +     e ++ l +v +++ee +  p  s kd++ ll  d l  fn    f  +++ 
  gi|386000871|ref|YP_005919170.1|  17 AANLYVDAFSRAFGDSKILKITYYGDEELEALREVPDVTEEFMPGPPGSVKDVRFLLNgDELMAFNGGgyFGNFTES 93 
                                       555666665566666666666666778889999*********************99975789999865226666666 PP

                                       HHHHHHHTCHHCCHHHHHHHHHHTT--H.HHHHHHHHHHSGGGTTB---EEE CS
                         Filo_VP35 235 lsklayksGkdsasldefqailaeGesa.qaalirlskrvdifldvvppvir 285
                                       +s l y s k  + +d + + l+eG    q+    l  r+ +  +++p +i+
  gi|386000871|ref|YP_005919170.1|  94 VS-L-YVSCKTQDQIDGLWEKLSEGGIEqQCGW--LKDRFGVSWQIAPEIIQ 141
                                       65.4.89*****************986515654..56788888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 944.31
//
Query:       gi|386000872|ref|YP_005919171.1|  [L=151]
Description: endoribonuclease L-PSP [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-20   71.3   0.0    8.3e-20   71.0   0.0    1.1  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   4.6e-24   8.3e-20      10     121 .]      30     145 ..      25     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 4.6e-24
                                       S-BSEEE...ETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGG.HHH CS
                     Ribonuc_L-PSP  10 pYsqavk...agnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladied.fae 81 
                                       ++sqav      +++yv Gq ++d  +g++v egdv  qt+q+l+n++ +Laaaga+l+dvVk +v+++  +     
  gi|386000872|ref|YP_005919171.1|  30 AFSQAVVvtgPAKTIYVGGQDAVD-GSGNIVgEGDVGLQTEQVLKNIQTALAAAGADLADVVKWNVYVVAGQPlQPG 105
                                       6899777555678***********.6999999************************************999885779 PP

                                       HHHHHHHHSSSSTS--EEEEEE-SBSG.GG-SEEEEEEEE- CS
                     Ribonuc_L-PSP  82 vnevyaeafdelkeaParsaveVaaLp.kgakvEIeaiavv 121
                                       +++ + ++ + + ++Pa ++  V+ L+ ++++vEI+a+avv
  gi|386000872|ref|YP_005919171.1| 106 FEAFMRGWGRRP-NPPAITMAFVSGLArPEYLVEIDAVAVV 145
                                       999*********.7*************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1097.88
//
Query:       gi|386000873|ref|YP_005919172.1|  [L=338]
Description: hypothetical protein Mhar_0158 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.034   13.5   0.0    1.3  1  NucS      Endonuclease NucS


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-06     0.034     141     213 ..      43     114 ..      36     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-06
                              NucS 141 iLgkdeegklvivelkrrkaevdaveqLkryvellkedsvld.kvrGvlvapsittdaekllkeeglefkeldp 213
                                       ++ +d +gk+ +ve+kr    ++a ++L     ll+ d++ + ++  v+v + it++a + +++ g++f +l  
  gi|386000873|ref|YP_005919172.1|  43 LIIED-DGKTYVVEIKRI-VRLEALSRLGLLKLLLNADNISNyDIEFVMVGKRITPEAAEAAEKTGMRFIKLPA 114
                                       55444.689999****98.99*******9988899998875438*************************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2226.10
//
Query:       gi|386000874|ref|YP_005919173.1|  [L=245]
Description: hypothetical protein Mhar_0159 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0075   16.2   0.0      0.034   14.1   0.0    1.9  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.9e-06     0.034      13     145 ..      25     141 ..      15     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-06
                            AbiEii  13 dklvFkGGTa...LslayglipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigegedyegl 86 
                                       +  v+ GG a    +++yg     S+DIDl++    +++   +l ++l++  +++ +++ +v             + 
  gi|386000874|ref|YP_005919173.1|  25 PVTVLIGGWAvysYNKWYG-----SVDIDLVT----NNKTKHQLMKRLRDERGFVHQRDPMVP------------TT 80 
                                       556788888877789****.....******74....777777788888888888888888754............44 PP

                            AbiEii  87 rlrypaefggyarqkikieigfreavppaerreippyleel........ggpafevpvysleellae 145
                                        +       + ++ ki +++g+re++  +e r+ +  ++ l         +p+ +v v  +e++l  
  gi|386000874|ref|YP_005919173.1|  81 VV------KNVQEEKILLDFGSREDISRFEGRDEQLPFSLLdgrteareISPSSSVSVIVPERTLLM 141
                                       44......44455555556666666633333333333322233345555577777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1817.34
//
Query:       gi|386000875|ref|YP_005919174.1|  [L=52]
Description: hypothetical protein Mhar_0160 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   15.1   0.0      0.019   15.0   0.0    1.1  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.1e-06     0.019      86     121 .]      15      50 ..       7      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                                       HHHHSSSSTS--EEEEEE-SBSG.GG-SEEEEEEEE- CS
                     Ribonuc_L-PSP  86 yaeafdelkeaParsaveVaaLp.kgakvEIeaiavv 121
                                       +  + + + ++Pa ++  V+ L+ ++++vEI+a+avv
  gi|386000875|ref|YP_005919174.1|  15 MRAWGRRP-NPPAITMAFVSGLArPEYLVEIDAVAVV 50 
                                       45555666.69************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       131  (0.0073066); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 391.97
//
Query:       gi|386000876|ref|YP_005919175.1|  [L=226]
Description: type II site-specific deoxyribonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete 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-98  326.9   0.0    5.2e-98  326.6   0.0    1.0  1  XhoI      Restriction endonuclease XhoI


Domain annotation for each model (and alignments):
>> XhoI  Restriction endonuclease XhoI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.6   0.0  2.9e-102   5.2e-98       2     186 ..      15     198 ..      14     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 326.6 bits;  conditional E-value: 2.9e-102
                              XhoI   2 qkesgkadqGersavtgGkqldGfielllelllaaGlaekeiyvkkelelPGffrptkewdllvvkegkllaaielk 78 
                                       q+++g +dqG+rsavtgGkq+dGf+++++el++a+G++e +iy+kk++ lPGffrp+k wd++vv++g l+aaielk
  gi|386000876|ref|YP_005919175.1|  15 QERRGGSDQGARSAVTGGKQMDGFVRKIIELMTASGVDEGNIYTKKTH-LPGFFRPVKGWDIVVVVDGVLMAAIELK 90 
                                       8999******************************************99.**************************** PP

                              XhoI  79 sqvgpsfGnnfnnrteealGsaldlwtayregafkesprPflGylllledaeasrksvrvsephfevleefkgasyv 155
                                       sqvg sfGnnfnnrteea+G+ald+wtayregaf++sp+P+lGyl+lled+++sr++vr++e+hf+v+eef+gasy+
  gi|386000876|ref|YP_005919175.1|  91 SQVGLSFGNNFNNRTEEAMGTALDIWTAYREGAFCTSPAPWLGYLFLLEDCPESRSPVRTQETHFPVFEEFRGASYA 167
                                       ***************************************************************************** PP

                              XhoI 156 kryellcrklvrerlytaaalivsdredgak 186
                                       kryel+crklvrer+y+aa++i++dre++++
  gi|386000876|ref|YP_005919175.1| 168 KRYELFCRKLVRERQYNAACFIIADREKSNS 198
                                       ***************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1730.56
//
Query:       gi|386000877|ref|YP_005919176.1|  [L=325]
Description: DNA methylase N-4/N-6 domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-36  126.7   0.0    1.6e-36  126.2   0.0    1.2  1  N6_N4_Mtase      DNA methylase
      0.004   16.9   0.0      0.037   13.7   0.0    2.1  2  UPF0020          Putative RNA methylase family UPF0020
     0.0078   16.8   0.0       0.21   12.2   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.097   13.4   0.0         12    6.7   0.0    2.6  2  Methyltransf_25  Methyltransferase domain
       0.16   11.7   0.0       0.31   10.7   0.0    1.4  1  Met_10           Met-10+ like-protein


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   4.5e-40   1.6e-36       1     229 [.      75     306 ..      75     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 4.5e-40
                                       EEEEEE--SSSSSCS......GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT............. CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy.endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk............. 63 
                                       v+l vt+pPY+t k+y +n+ q++  ++ye++l+ l +v+++v rvL ++g +++ ++d    +             
  gi|386000877|ref|YP_005919176.1|  75 VHLAVTSPPYWTLKEYpANEGQLGSVEDYEQFLDELDRVWRNVFRVLVPGGRLVVVVGDVCLPRrcfgrhvvfplha 151
                                       79**********************************************************99999999*****7443 PP

                                       HHHHHHHHHTT.-EEEEEEEEEEES............SSTTTSTCC........S-B--EEEEEEEESSTT-..--- CS
                       N6_N4_Mtase  64 elkaladeifg.gffllnvivwkkp............nsmpesnkd........rltsthEyilvfsknkkyllkfn 119
                                           + + + + gf  l  i+w k                               ++++ Eyil+ +k++ y     
  gi|386000877|ref|YP_005919176.1| 152 S---IQERCRKiGFDNLAPIIWYKIanarfesnngskF-------LgkpyepnaIVKNDIEYILFQRKPGGY----- 213
                                       3...33344445699999******98666555555541.......044444444999999999999999999..... PP

                                       GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEE CS
                       N6_N4_Mtase 120 ldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivl 196
                                           ++p ++ + l+       + +++++++iW    i           ++kHpa++P+al+erlI++++  gd+vl
  gi|386000877|ref|YP_005919176.1| 214 ----RKPSNAARLLSVIP---EDLHKEWFQQIW---TITGAS-------TRKHPAPFPLALAERLIRMFSFVGDTVL 273
                                       ....44444444444433...5566678*****...333332.......245************************* PP

                                       ETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 197 DpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                       DpF+G+GtT  aa + gr ++G+eie+ y+e+a
  gi|386000877|ref|YP_005919176.1| 274 DPFMGTGTTNLAAGQWGRSSVGFEIEPTYFEMA 306
                                       ******************************976 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.094   3.4e+02     119     158 ..      72     116 ..      51     132 .. 0.72
   2 !   13.7   0.0     1e-05     0.037       6      58 ..     247     297 ..     243     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.094
                                       TS---EEEE----------HHHH.HHH.....HHHHHHHHHHH-TT CS
                           UPF0020 119 egevdvivtnpPYGerlgskkal.ekL.....Yseflrelkrvlrg 158
                                       +++v + vt pPY   l++ +a+  +L     Y++fl+el rv r+
  gi|386000877|ref|YP_005919176.1|  72 DESVHLAVTSPPYWT-LKEYPANeGQLgsvedYEQFLDELDRVWRN 116
                                       568999999999965.444444335555556688888888888776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1e-05
                                       SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT CS
                           UPF0020   6 fngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgll 58 
                                       +++pap   +LA  l+r+     g++ lDP+ G+Gt  + a++ g++ + g+ 
  gi|386000877|ref|YP_005919176.1| 247 RKHPAPFPLALAERLIRMFSF-VGDTVLDPFMGTGTTNLAAGQWGRSSV-GFE 297
                                       578999999999999999876.688999**************9999988.333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.9e-05      0.21      72      96 .]     105     129 ..      45     129 .. 0.91
   2 ?    2.3   0.0     0.076   2.7e+02       5      43 ..     277     315 ..     273     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                                       CC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgGllvi 96 
                                       +++++++++++++ RvL pgG+lv+
  gi|386000877|ref|YP_005919176.1| 105 QFLDELDRVWRNVFRVLVPGGRLVV 129
                                       45689*****************996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.076
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT- CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl 43 
                                       +GtG    a  + g++ vg+++ ++  ++a+++ ++ ++
  gi|386000877|ref|YP_005919176.1| 277 MGTGTTNLAAGQWGRSSVGFEIEPTYFEMASNRLNKIRN 315
                                       67777777777899****************998877654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.021        74      80      97 .]     108     125 ..      47     125 .. 0.92
   2 ?    6.7   0.0    0.0033        12       1      43 [.     272     312 ..     272     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                       ++l+++ ++++rvL pgG
  gi|386000877|ref|YP_005919176.1| 108 DELDRVWRNVFRVLVPGG 125
                                       468899***********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0033
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee 43 
                                       vLd   GtG++ la+ +  g  + +g++i +++ e a +r+++
  gi|386000877|ref|YP_005919176.1| 272 VLDPFMGTGTTNLAAGQW-G-RSSVGFEIEPTYFEMASNRLNK 312
                                       899999***998888888.5.9****************99965 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.8e-05      0.31      92     151 ..     259     315 ..     256     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                                       HHHHTT--.TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                            Met_10  92 erlaklve.egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                       erl+++++  g++V+d f G G   ++++++++ +  ++ +++P+ +++  +  +lNk+ +
  gi|386000877|ref|YP_005919176.1| 259 ERLIRMFSfVGDTVLDPFMGTGTTNLAAGQWGRSS--VGFEIEPTYFEMASN--RLNKIRN 315
                                       7999996537********************88888..99*****98885443..6788766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2616.13
//
Query:       gi|386000878|ref|YP_005919177.1|  [L=319]
Description: Delta-aminolevulinic acid dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-145  484.1   0.1   1.9e-145  483.9   0.1    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.9   0.1  1.1e-149  1.9e-145       2     316 ..       2     315 ..       1     316 [. 0.99

  Alignments for each domain:
  == domain 1  score: 483.9 bits;  conditional E-value: 1.1e-149
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                       +r+rrlrk + lr++v+etr+sa+dli+plfv+e+ +++ +i+smpg+ r+s+++l+keveel +lg++av+lFg+p
  gi|386000878|ref|YP_005919177.1|   2 RRMRRLRK-PGLRRIVAETRVSADDLIMPLFVDERLKRPIKIESMPGQNRHSLESLAKEVEELEELGVPAVILFGLP 77 
                                       68999986.67****************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT- CS
                              ALAD  79 eekdeegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGa 155
                                       e+kde gs a++++g+vqra ++ike++++++vi+D+clceytshGhcg+++++ev ndetl ll k avsqa+aGa
  gi|386000878|ref|YP_005919177.1|  78 EKKDEVGSGAYDPQGVVQRAAERIKETTSKVIVIADLCLCEYTSHGHCGLIKNQEVANDETLPLLGKAAVSQARAGA 154
                                       ***************************************************************************** PP

                                       SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHH CS
                              ALAD 156 divapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealrevel 232
                                       d+vapS+mmD +vaair aLd++gf++++ilsY+aKyaS+fYgPFr+aaes  sfgdr+ Yqmdpan+ eal ev+l
  gi|386000878|ref|YP_005919177.1| 155 DVVAPSGMMDHMVAAIRGALDDEGFTDTPILSYAAKYASSFYGPFREAAESGYSFGDRSGYQMDPANALEALWEVRL 231
                                       ***************************************************************************** PP

                                       HHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEET CS
                              ALAD 233 dleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltY 309
                                       d+eeGAD++mvKPa++ylDi+r vk+ef +p+aayqvSGEY+mi+aaae+gw+d +k++ E+l+sikRAGad+iltY
  gi|386000878|ref|YP_005919177.1| 232 DIEEGADMIMVKPAMPYLDIVRMVKDEFGMPTAAYQVSGEYSMIMAAAERGWIDGEKAMGEALTSIKRAGADMILTY 308
                                       ***************************************************************************** PP

                                       THHHHHH CS
                              ALAD 310 fakevak 316
                                       +ak++a+
  gi|386000878|ref|YP_005919177.1| 309 YAKKFAR 315
                                       ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2593.62
//
Query:       gi|386000879|ref|YP_005919178.1|  [L=412]
Description: glutamyl-tRNA reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-39  134.5   0.1    4.9e-39  133.5   0.1    1.5  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
    2.1e-35  121.7   0.0    3.7e-35  120.8   0.0    1.4  1  GlutR_N        Glutamyl-tRNAGlu reductase, N-terminal domain
    8.4e-21   74.2   0.8    1.8e-20   73.2   0.8    1.6  1  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
    3.9e-05   24.2   0.5    0.00033   21.2   0.0    2.7  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.061   12.7   0.0       0.16   11.3   0.0    1.7  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.18   11.1   0.0        2.2    7.6   0.0    2.5  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.1   1.6e-42   4.9e-39       1     138 []     154     289 ..     154     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 1.6e-42
                                       HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77 
                                       +la+++l+sl++++vl+iGaG ++el+ k+Ll+k++ +++v+NRt+ ra +la  l++e   a++++ +ke+++ +d
  gi|386000879|ref|YP_005919178.1| 154 DLAEEILGSLEGRRVLVIGAGDTGELISKALLSKNIGELLVTNRTFGRALALAAGLGAE---AVPFDRMKEMIRTSD 227
                                       59******************************************************888...*************** PP

                                       EEEE-SSSSS-SB-HHHHHCCHHH.S...EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                      Shikimate_DH  78 vvisataseepilekeeveealkkrk.kplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                       +visat+++++il+++++ee++++r+   ll++Dia+PRd++++v+e+ +v+l ++D L+e+
  gi|386000879|ref|YP_005919178.1| 228 LVISATSAPHYILRRDDLEEVMARRTkGTLLMIDIANPRDIAEDVGEIPGVELRNIDALREI 289
                                       ************************996777*****************************987 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   0.0   1.2e-38   3.7e-35       3     146 .]       1     139 [.       1     139 [. 0.83

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.2e-38
                           GlutR_N   3 inhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelk.e 76 
                                       ++h++a+++  e+++  +  l++llk + ++  v+e ++L+TCNR+Eiy+++ +    ++ l+el +   +++++ +
  gi|386000879|ref|YP_005919178.1|   1 MTHRKANIDEIERAWHGD--LEALLKWIsSSdLVEESAVLKTCNRVEIYVVSPR---GEKVLFELAK---KARISsR 69 
                                       58************9964..445555553233678**************76654...4444445442...3344437 PP

                           GlutR_N  77 klyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                        + +++++e+++Hl+r+asGL+S+++GEdqIlgQ+ke y++ak+a+t+g +L++ f+kai+v+krvr et
  gi|386000879|ref|YP_005919178.1|  70 IIDFHDHDESLNHLLRLASGLESMIIGEDQILGQMKELYNMAKAAETTGWTLDVAFKKAISVGKRVRRET 139
                                       899*****************************************************************98 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.8     6e-24   1.8e-20       1      97 []     303     404 ..     303     404 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 6e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHH CS
                       GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllhep 73 
                                       +AeaiI+ee++ ++a++k++++++++ +++ +aeei+++e  ra++kl+    l + ++++l ++++s+vnk++ ep
  gi|386000879|ref|YP_005919178.1| 303 RAEAIIDEELALLKAKYKRRRAEDLLGRIYLQAEEIKAQECMRAMNKLGarhtLGEIEERVLMDMSHSIVNKIFAEP 379
                                       59*************************************************9666666666**************** PP

                                       HHHHHSS.-TTTTHHHHHHHHH... CS
                       GlutR_dimer  74 tarLkea.edeeeellealrrlFnl 97 
                                       t++L++a e+ ++ +l+++++lF+l
  gi|386000879|ref|YP_005919178.1| 380 TKALRRAaERGDDGCLNFIEELFGL 404
                                       *******555555**********97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.8   2.4e+03      25      49 ..      43      67 ..      30      76 .. 0.78
   2 !   21.2   0.0   1.1e-07   0.00033       2      96 ..     168     264 ..     167     265 .. 0.79
   3 ?   -1.6   0.0       1.4   4.3e+03      39      71 ..     286     319 ..     278     344 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.8
                                      GGCEEEEEESSCCCHHHHHHHHC-E CS
                     F420_oxidored 25 pheivvansrnpekaeelaeelgvk 49
                                        ei+v++ r ++ + ela+++ ++
  gi|386000879|ref|YP_005919178.1| 43 RVEIYVVSPRGEKVLFELAKKARIS 67
                                      5689999999999999999988754 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.1e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECH.HHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdn.eeaaeeadvvvlavkpedveev 77 
                                       + +iGaG+ ge + + ll+++    e++v ++r+  +a +la+ lg+++ + d  +e+++ +d v+ a    ++   
  gi|386000879|ref|YP_005919178.1| 168 VLVIGAGDTGELISKALLSKN--IGELLV-TNRTFGRALALAAGLGAEAVPFDRmKEMIRTSDLVISATSAPHYILR 241
                                       669*****************9..899995.5***************99999875389**********9999888654 PP

                                       HHHC...GHHHHTTS.EEEEESS CS
                     F420_oxidored  78 lsel...akdalkgk.lvisvla 96 
                                        ++l   +++  kg+ l i++++
  gi|386000879|ref|YP_005919178.1| 242 RDDLeevMARRTKGTlLMIDIAN 264
                                       44444445555555414577776 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                                       HHHHH.HHHC-EEECECHHHHHHH-SEEEE-S-H CS
                     F420_oxidored  39 aeela.eelgvkvtavdneeaaeeadvvvlavkp 71 
                                       ++e+  e++  ++ +++ +ea+ + +  +l  k+
  gi|386000879|ref|YP_005919178.1| 286 LREISaENMRLRMAEMARAEAIIDEELALLKAKY 319
                                       5555425556777777778887777777776554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.4e-05      0.16      31      99 ..     160     233 ..     134     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                                       BS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee....eeeelgvelvsleellaesDivslhl 99 
                                         +l+g++v +iG+G+ G+ + k l + ++ ++++++r+  +         ++ v ++ ++e++++sD v+ ++
  gi|386000879|ref|YP_005919178.1| 160 LGSLEGRRVLVIGAGDTGELISKALLSKNIgELLVTNRTFGRALalaaGLGAEAVPFDRMKEMIRTSDLVISAT 233
                                       4479*******************99988887888888876655455555556666788999*******998655 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.61   1.8e+03      35      51 ..      88     104 ..      81     120 .. 0.74
   2 ?    7.6   0.0   0.00074       2.2      21      93 ..     150     239 ..     127     249 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.61
                                       TT-EEEEE---TTTHHH CS
                     THF_DHG_CYH_C  35 egkkvvvvGrsnivgkp 51 
                                       +g + +++G+ +i+g+ 
  gi|386000879|ref|YP_005919178.1|  88 SGLESMIIGEDQILGQM 104
                                       6888999**99999974 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00074
                                       HHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT.................T-EEEEE-TTS.....CCHHH CS
                     THF_DHG_CYH_C  21 kgvvellketgielegkkvvvvGrsnivgkplallLlek.................natVtvchskt.....kdlae 75 
                                        + v+l +e   +leg++v+v+G++++ +   ++lL+++                  a        +     + ++e
  gi|386000879|ref|YP_005919178.1| 150 SAAVDLAEEILGSLEGRRVLVIGAGDTGELISKALLSKNigellvtnrtfgralalAAGLG-----AeavpfDRMKE 221
                                       5677888888889999999999998874444444454434444444455553322222222.....12234478899 PP

                                       HHCCSSEEEE-SS-TT-B CS
                     THF_DHG_CYH_C  76 itreadivvvavGkpeli 93 
                                       ++r++d+v++a+  p+ i
  gi|386000879|ref|YP_005919178.1| 222 MIRTSDLVISATSAPHYI 239
                                       999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 3272.53
//
Query:       gi|386000880|ref|YP_005919179.1|  [L=131]
Description: hypothetical protein Mhar_0165, partial [Methanosaeta harundinacea 6Ac]
Scores for 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-07   28.5   0.2    1.7e-06   27.7   0.2    1.5  1  CysG_dimeriser  Sirohaem synthase dimerisation region
    2.6e-05   23.5   0.1    4.3e-05   22.9   0.1    1.4  1  Sirohm_synth_M  Sirohaem biosynthesis protein central


Domain annotation for each model (and alignments):
>> CysG_dimeriser  Sirohaem synthase dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2   1.9e-10   1.7e-06       1      42 [.      53      95 ..      53     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.9e-10
                                      THHHHHHHHHHHHHHHHHH-SSHHHHHH.HHHHHT-HHHHHHH CS
                    CysG_dimeriser  1 slGrLAelagrlRdrVkarlpdvaaRRr.FWerffdgpvaelv 42
                                      ++G++A+l+g++R   k+r++d ++RRr  We + dg+v  l+
  gi|386000880|ref|YP_005919179.1| 53 GYGDMARLLGEMRGVMKERVADQEERRRiLWEIISDGEVWRLL 95
                                      69**********************9988358877799887665 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   4.8e-09   4.3e-05       1      27 [.      22      48 ..      22      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-09
                    Sirohm_synth_M  1 rGpLQIaiSTnGksPrLAaliRreier 27
                                      rGp  +aiST G sP+L++ +R +ie+
  gi|386000880|ref|YP_005919179.1| 22 RGPVVVAISTFGESPALSKSLRMRIEE 48
                                      89999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 988.06
//
Query:       gi|386000881|ref|YP_005919180.1|  [L=65]
Description: hypothetical protein Mhar_0166 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      119  (0.00663729); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 503.98
//
Query:       gi|386000882|ref|YP_005919181.1|  [L=163]
Description: AsnC family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-31  108.9   0.0    1.7e-31  108.2   0.0    1.3  1  AsnC_trans_reg2  AsnC-like ligand binding domain
    1.1e-06   28.4   1.2    0.00026   20.8   0.8    2.5  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.2   0.4       0.29   10.7   0.2    2.3  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.082   12.8   0.0       0.12   12.2   0.0    1.3  1  DUF3015          Protein of unknown function (DUF3015)


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.0   3.8e-35   1.7e-31       2      82 .]      73     157 ..      72     157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 3.8e-35
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyev 74 
                                       lG+ ana+++w+vp e+ e+v+ ++a+++evtHcYeR    ewpynly++vh +s+ee+++v+aei++++g+++y+v
  gi|386000882|ref|YP_005919181.1|  73 LGIVANAMIVWRVPPEDAERVGGIMASFDEVTHCYERaerpEWPYNLYTVVHSPSREECRKVAAEISRKVGITEYQV 149
                                       8************************************98888*********************************** PP

                   AsnC_trans_reg2  75 LpstrefK 82 
                                       L+s+refK
  gi|386000882|ref|YP_005919181.1| 150 LFSEREFK 157
                                       *******9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.8   5.7e-08   0.00026       2      41 ..      13      55 ..      12      56 .. 0.97
   2 !    5.6   0.0    0.0031        14      16      34 ..     131     149 ..     128     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.7e-08
                     HTH_AsnC-type  2 DeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrL 41
                                      D++D+++++a q     ++++y++LA+++ + e +vl+R+ rL
  gi|386000882|ref|YP_005919181.1| 13 DDLDLALIRAAQGGialSSRPYEALAKELAIGEGEVLERLSRL 55
                                      9*****************************************9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0031
                     HTH_AsnC-type  16 aRisyaeLAervGlSestv 34 
                                       +R   ae++++vG++e +v
  gi|386000882|ref|YP_005919181.1| 131 CRKVAAEISRKVGITEYQV 149
                                       677789********99776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   6.5e-05      0.29      20      48 .]      34      62 ..      30      62 .. 0.93
   2 ?    2.3   0.0     0.027   1.2e+02      21      30 ..     136     145 ..     128     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.5e-05
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +  LA++l +  + v++rl rL e ++I+
  gi|386000882|ref|YP_005919181.1| 34 YEALAKELAIGEGEVLERLSRLLELEVIR 62
                                      568************************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.027
                            HTH_24  21 reLAerlglS 30 
                                       +e+++++g++
  gi|386000882|ref|YP_005919181.1| 136 AEISRKVGIT 145
                                       7*******98 PP

>> DUF3015  Protein of unknown function (DUF3015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.12      69      97 ..      33      61 ..      20      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                           DUF3015 69 nleeLaediakGeGealaalavllgveae 97
                                       +e+La++ a GeGe l+ l++ll+ e  
  gi|386000882|ref|YP_005919181.1| 33 PYEALAKELAIGEGEVLERLSRLLELEVI 61
                                      5899*******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1189.95
//
Query:       gi|386000883|ref|YP_005919182.1|  [L=678]
Description: Cell surface protein, putative [Methanosaeta harundinacea 6Ac]
Scores for 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-77  257.7  60.6    7.5e-22   77.8   2.6    5.8  6  NosD             Periplasmic copper-binding protein (NosD)
    3.2e-56  189.5  57.3    1.4e-16   60.8   9.3    5.1  5  Beta_helix       Right handed beta helix region
     0.0014   18.5  19.2       0.42   10.4   0.3    5.6  6  Pectate_lyase_3  Pectate lyase superfamily protein
  ------ inclusion threshold ------
       0.76    9.8   2.1        7.1    6.6   0.0    2.6  3  zf-DNL           DNL zinc finger


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 !   17.1   0.3   5.5e-07    0.0025      50     146 ..      31     140 ..      12     141 .. 0.77
   2 !   77.8   2.6   1.7e-25   7.5e-22      29     174 ..     113     255 ..     103     257 .. 0.92
   3 !   50.1   2.5   4.6e-17   2.1e-13      62     150 ..     211     299 ..     211     329 .. 0.94
   4 !   41.0   0.6   2.8e-14   1.3e-10      18     154 ..     349     485 ..     310     488 .. 0.90
   5 !   73.7   4.4   2.8e-24   1.3e-20       3     172 ..     424     592 ..     422     596 .. 0.94
   6 !   66.0  14.7   6.7e-22     3e-18      18     212 ..     460     648 ..     460     673 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-07
                              NosD  50 titgntienlryGihlenses.ntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNti.. 123
                                       +i+g  ++   +G+ +e  ++  ti+++++++ + Gi+ ++s  n + ++ i +++  G+lls+ +  ++++  +  
  gi|386000883|ref|YP_005919182.1|  31 NISGFEMRGTGTGVGVELRSKeATIRGCIIRNFSTGILSSDSD-NAVVGSAIEGCSV-GVLLSGGTVRDLQESSVsg 105
                                       5666666666666666644444799999999999999999999.6666999999999.9999999999999888877 PP

                              NosD 124 ...........s.nnnkGiflensssntitgNrie 146
                                                  + + ++G+ + n s+  ++++ i+
  gi|386000883|ref|YP_005919182.1| 106 vealgpaisncTiSGGTGVVIANCSGCAVSDSLIT 140
                                       77788888777448888888888888888888776 PP

  == domain 2  score: 77.8 bits;  conditional E-value: 1.7e-25
                              NosD  29 isnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnen 105
                                       isn +is + +g+ + n+s++ ++++ i   r+G+ +++s ++++++n++ss e+Gia+++s+++ +  N++++ +n
  gi|386000883|ref|YP_005919182.1| 113 ISNCTIS-GGTGVVIANCSGCAVSDSLI-TARTGVLITDSPRTRVRGNEISSPERGIAVERSEESEILENVVTGATN 187
                                       5455544.5667779**********766.668*********************************999********* PP

                              NosD 106 yGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnse 174
                                         ill +s n+t+++N ++ +n Gi+l++s+ n+i +Nr e++   Gi+ l++s+gn + +N + +n e
  gi|386000883|ref|YP_005919182.1| 188 VAILLLASGNSTVAENSALGCNVGIRLKDSTANRILKNRMEESAVAGIW-LEGSKGNVVAGNLLSGNVE 255
                                       *************************************************.**************99975 PP

  == domain 3  score: 50.1 bits;  conditional E-value: 4.6e-17
                              NosD  62 Gihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensss 137
                                       Gi+l++s  n+i +n ++++  +Gi+l+ s++n++ +N +s+n +  i+ s+ss+n+i +N+i++n++G++l +s  
  gi|386000883|ref|YP_005919182.1| 211 GIRLKDSTANRILKNRMEESAvAGIWLEGSKGNVVAGNLLSGNVEGLIFRSGSSGNSILENQILKNGRGLTLLGSGA 287
                                       9********************************************78899*************************** PP

                              NosD 138 ntitgNriesnqk 150
                                       n +++N+ e+n  
  gi|386000883|ref|YP_005919182.1| 288 NLLRKNQMEDN-H 299
                                       **********9.4 PP

  == domain 4  score: 41.0 bits;  conditional E-value: 2.8e-14
                              NosD  18 giqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnnt 94 
                                        + l + ++ ++++ ++sn+++g l+ nss++t ++ t+  +++G+++ ++ ++ +e + +++++ G++++  ++  
  gi|386000883|ref|YP_005919182.1| 349 LLALVGCTNVTVESLALSNNSAGALIVNSSSCTARNLTLLGNDAGVRMLWTAGCGVEASRADNCTIGFLVQGGKGAS 425
                                       4556677999****************************************************************99* PP

                              NosD  95 lenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                       +e++ + +++++G+l+++s+ + +++ ++s+   Gi++ ns+s+ti + r  +n++ Gi 
  gi|386000883|ref|YP_005919182.1| 426 IEGSSALRSSEAGFLVQGSEASALRGVEASEGLVGISVVNSTSTTILQARAMGNTEEGIK 485
                                       ********************************************************9997 PP

  == domain 5  score: 73.7 bits;  conditional E-value: 2.8e-24
                              NosD   3 naisgdevlvsargngiqlensegseisnneisnsrdgilldnssnntitgn.tienlryGihlensesntiedntl 78 
                                        +i+g++ l+s +++g  +++se s +++ e s++  gi + ns++ ti +  ++ n ++Gi ++ s ++++++n++
  gi|386000883|ref|YP_005919182.1| 424 ASIEGSSALRS-SEAGFLVQGSEASALRGVEASEGLVGISVVNSTSTTILQArAMGNTEEGIKISRSPRSVLNNNIA 499
                                       57888886555.789******************************9999999455566******************* PP

                              NosD  79 ssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGill 155
                                       s+n+ Gi  + s ++++  + +s+n+++G  l + s  t+++  + +n++G+fl++  + +i+gN++++n+ +G+  
  gi|386000883|ref|YP_005919182.1| 500 SGNRWGIRASGSDGTMVVRSHLSENRDAGLALLQLSAATVAGSSAFDNGDGVFLQAVVGAKIEGNNLSNNRRYGLR- 575
                                       ********************************99999***************************************. PP

                              NosD 156 lsssegntiynNyFinn 172
                                       +s+s + ++y+N+F++n
  gi|386000883|ref|YP_005919182.1| 576 MSYSREGKVYGNTFVKN 592
                                       **************999 PP

  == domain 6  score: 66.0 bits;  conditional E-value: 6.7e-22
                              NosD  18 giqlensegsei.snneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssn 92 
                                       gi + ns+  +i +  ++ n+++gi ++ s    + +n  + +r Gi+ ++s+++ +  + ls+n+ +G+al + s+
  gi|386000883|ref|YP_005919182.1| 460 GISVVNSTSTTIlQARAMGNTEEGIKISRSPRSVLNNNIASGNRWGIRASGSDGTMVVRSHLSENRdAGLALLQLSA 536
                                       6777788777777999************************************************************9 PP

                              NosD  93 ntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNy 168
                                        t+ ++ + +n + G++l++  + +i++N+ s n  +G++++ s + ++ gN++ +n + G   l +++g  i  N+
  gi|386000883|ref|YP_005919182.1| 537 ATVAGSSAFDNGD-GVFLQAVVGAKIEGNNLSnNRRYGLRMSYSREGKVYGNTFVKN-GLGGTGLVDCTGCIIRHNN 611
                                       9***********9.******************9999*********************.888888************* PP

                              NosD 169 Finnsenvkydgsn...nneWnttktsgtniiggpylgGNyWsdydg 212
                                       Fi+n + ++ ++     +n+W+          gg  +gGN+Wsd + 
  gi|386000883|ref|YP_005919182.1| 612 FIDNGNPMSPQNAVdngDNSWD----------GGAEVGGNFWSDHQV 648
                                       ****999988777677899**3..........57799*******875 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 !   53.8   3.7   4.2e-18   1.9e-14       2     157 ..      45     204 ..      21     205 .. 0.83
   2 !   46.4   1.0   8.1e-16   3.6e-12       3     124 ..     190     308 ..     189     329 .. 0.88
   3 !   37.3   2.9   5.2e-13   2.3e-09       6     156 ..     353     497 ..     347     498 .. 0.94
   4 !   60.8   9.3   3.1e-20   1.4e-16       2     158 .]     460     612 ..     459     612 .. 0.95
   5 !   48.1   9.7   2.5e-16   1.1e-12      13     149 ..     493     632 ..     491     643 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 4.2e-18
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-..............EEES-EEES...-SS-SEEE-TT-S-EEES- CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssn.............vvienneian...nsgsGiyilgssnntisnn 62 
                                       g+++++ +  ti++++i+n  ++Gi   +s+n             v++++ ++ +   +s sG++     +  isn+
  gi|386000883|ref|YP_005919182.1|  45 GVELRSKEA-TIRGCIIRNF-STGILSSDSDNavvgsaiegcsvgVLLSGGTVRDlqeSSVSGVEA---LGPAISNC 116
                                       455555555.*********5.***********5555444444444444444444444444444444...579***** PP

                                       EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SS CS
                        Beta_helix  63 tisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkg 139
                                       tis+++  g+ + + s+  ++++ it +   G+ +++s+++++++N i++ +  Gi ++ s+ + ++  N++t++ +
  gi|386000883|ref|YP_005919182.1| 117 TISGGT--GVVIANCSGCAVSDSLITART--GVLITDSPRTRVRGNEISSPE-RGIAVERSE-ESEILENVVTGATN 187
                                       ***888..********************5..8999*************9999.*********.9999********** PP

                                       EEEE-TT-SS--EEES-E CS
                        Beta_helix 140 aGiavvgsssnvtvrnNt 157
                                       ++i +  s++  tv++N+
  gi|386000883|ref|YP_005919182.1| 188 VAILLLASGN-STVAENS 204
                                       ***8888888.***9996 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 8.1e-16
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S- CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasn 79 
                                       i++  s+n t+  n   + ++ Gi l++s+ ++i +n+++ +   Gi+++gs++n++ +n  s+n +g i  +g+s+
  gi|386000883|ref|YP_005919182.1| 190 ILLLASGNSTVAENSALG-CNVGIRLKDSTANRILKNRMEESAVAGIWLEGSKGNVVAGNLLSGNVEGLIFRSGSSG 265
                                       555566777899999999.69**********99999***************************9998888888**** PP

                                       -EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT CS
                        Beta_helix  80 nlienneitdnggsGiylnyssnntienNiidnnagsGividdss 124
                                       n i  n i +ng+ G++l +s  n +++N++++n   ++ +d ++
  gi|386000883|ref|YP_005919182.1| 266 NSILENQILKNGR-GLTLLGSGANLLRKNQMEDNH-RAFRVDRED 308
                                       ***********99.9*9999999*******99998.777777665 PP

  == domain 3  score: 37.3 bits;  conditional E-value: 5.2e-13
                                       -SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EE CS
                        Beta_helix   6 ngssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnli 82 
                                        g++nvt++   +sn +++G  + +ss+++ +n ++ + ++ G+++l ++++ ++ ++  +++  g+ ++g+++  i
  gi|386000883|ref|YP_005919182.1| 353 VGCTNVTVESLALSN-NSAGALIVNSSSCTARNLTLLG-NDAGVRMLWTAGCGVEASRADNCT-IGFLVQGGKGASI 426
                                       68999**********.6*********************.************************.************* PP

                                       ES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix  83 enneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                       e++   + +++G+ +++s+   +++  +++    Gi++ +s  ++t+ + ++ +n  +Gi++ +s +  +++nN
  gi|386000883|ref|YP_005919182.1| 427 EGSSALRSSEAGFLVQGSEASALRGVEASEGL-VGISVVNST-STTILQARAMGNTEEGIKISRSPR-SVLNNN 497
                                       ********************************.*********.999*******************99.555554 PP

  == domain 4  score: 60.8 bits;  conditional E-value: 3.1e-20
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78 
                                       gis+ +s+++ti     +++   Gi++  s + v+  n+ia+ +  Gi+ +gs+++ + +++ s+n + g+al + s
  gi|386000883|ref|YP_005919182.1| 460 GISVVNSTSTTILQARAMGNTEEGIKISRSPRSVLN-NNIASGNRWGIRASGSDGTMVVRSHLSENRDAGLALLQLS 535
                                       8999999999**********************6666.777777********************************** PP

                                       --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES CS
                        Beta_helix  79 nnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrn 155
                                         ++ ++  +dng+ G++l+     +ie+N+++nn+++G+ +++s  + +v +Nt+++n+  G  +v+  + + +r+
  gi|386000883|ref|YP_005919182.1| 536 AATVAGSSAFDNGD-GVFLQAVVGAKIEGNNLSNNRRYGLRMSYSR-EGKVYGNTFVKNGLGGTGLVDCTG-CIIRH 609
                                       ************99.*******************************.999**********99998888888.99999 PP

                                       -E. CS
                        Beta_helix 156 Nti 158
                                       N++
  gi|386000883|ref|YP_005919182.1| 610 NNF 612
                                       997 PP

  == domain 5  score: 48.1 bits;  conditional E-value: 2.5e-16
                                       EESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES CS
                        Beta_helix  13 iknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitd 89 
                                       + nn+i + ++ Gi + gs+++ + +++++ n++ G+++l+ s +t+ +++  dn+ +g+ l++  +  ie+n+ ++
  gi|386000883|ref|YP_005919182.1| 493 VLNNNIASGNRWGIRASGSDGTMVVRSHLSENRDAGLALLQLSAATVAGSSAFDNG-DGVFLQAVVGAKIEGNNLSN 568
                                       66888888899999999999988888999999999999999999999999999999.99999999999999999999 PP

                                       -SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-S.....SEEEE-TT-SS CS
                        Beta_helix  90 nggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnk.....gaGiavvgsss 149
                                       n+++G++++ys   ++ +N++  n+  G  + d   ++ +++N++ +n+     ++++++ ++s+
  gi|386000883|ref|YP_005919182.1| 569 NRRYGLRMSYSREGKVYGNTFVKNGLGGTGLVDCT-GCIIRHNNFIDNGnpmspQNAVDNGDNSW 632
                                       99999999999999999999999998888888888.89999999999998888855555555544 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1   0.00057       2.6     160     214 ..      36      88 ..       8      89 .. 0.70
   2 !    5.5   0.1     0.003        13     143     202 ..     162     222 ..      98     236 .. 0.61
   3 ?   -0.4   0.0      0.19   8.7e+02     145     195 ..     254     305 ..     215     329 .. 0.65
   4 !   10.4   0.3   9.3e-05      0.42     156     214 ..     358     416 ..     252     417 .. 0.62
   5 !    4.5   0.3    0.0061        27     146     201 ..     459     516 ..     439     551 .. 0.68
   6 ?   -0.4   0.5      0.19   8.6e+02     136     173 ..     562     601 ..     537     637 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00057
                                       S-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEE CS
                   Pectate_lyase_3 160 dlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlknvkinncegGi 214
                                       +++ +g  + g++++++++t+r + + n +tgi  + +++  +++  i++c +G+
  gi|386000883|ref|YP_005919182.1|  36 EMRGTG-TGVGVELRSKEATIRGCIIRNFSTGILSS-DSDNAVVGSAIEGCSVGV 88 
                                       333444.67788888******************999.555566677999999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.003
                                       ---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEE CS
                   Pectate_lyase_3 143 tkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtl 202
                                         + gi +e+++++ + + v++g  + +i +  + ++tv ++   +++ gi+++++++  +
  gi|386000883|ref|YP_005919182.1| 162 SPERGIAVERSEESEILENVVTGATNVAILLlASGNSTVAENSALGCNVGIRLKDSTANRI 222
                                       3344666666666555555555556666666556666666666666666666666555444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.19
                                       -TT---SS--E..EEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE- CS
                   Pectate_lyase_3 145 hqgifiengsg..gflndlvfsglgdigiav.gnqqftvrnitfnnattgievl 195
                                        +g++ ++gs+  ++l++ + ++  + g+++ g+ +  +r+++++++ ++++v+
  gi|386000883|ref|YP_005919182.1| 254 VEGLIFRSGSSgnSILENQILKN--GRGLTLlGSGANLLRKNQMEDNHRAFRVD 305
                                       33555555555333336666655..34444446666666666666666666655 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 9.3e-05
                                       EEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEE CS
                   Pectate_lyase_3 156 gflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinncegGi 214
                                        +++ l  s+    g+ +  +   t+rn+t  ++  g+++lw+ g  +++ + +nc+ G+
  gi|386000883|ref|YP_005919182.1| 358 VTVESLALSN-NSAGALIvNSSSCTARNLTLLGNDAGVRMLWTAGCGVEASRADNCTIGF 416
                                       2335555566.455555548999**********************************996 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.0061
                                       TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E.EE CS
                   Pectate_lyase_3 146 qgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg.wt 201
                                       +gi + n+ + ++  +++ g+ + gi++ ++  ++++n+  +++  gi+++ + g ++
  gi|386000883|ref|YP_005919182.1| 459 VGISVVNSTSTTILQARAMGNTEEGIKIsRSPRSVLNNNIASGNRWGIRASGSDGtMV 516
                                       4666666666666666666777777777556777777777777777777765444233 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 0.19
                                       EEE-SSS---TT---SS--EEEE.ES-EEES.-SS-SEEE CS
                   Pectate_lyase_3 136 emseasgtkhqgifiengsggfl.ndlvfsg.lgdigiav 173
                                       e ++ s++   g++++++ +g +  + ++++ lg++g+  
  gi|386000883|ref|YP_005919182.1| 562 EGNNLSNNRRYGLRMSYSREGKVyGNTFVKNgLGGTGLVD 601
                                       4444444666799999887754446666655355555533 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0016       7.1      24      36 ..     122     134 ..     118     153 .. 0.83
   2 ?   -3.5   0.0       2.3     1e+04      23      37 ..     369     383 ..     355     385 .. 0.71
   3 ?    1.9   0.1     0.048   2.1e+02      25      38 ..     596     609 ..     588     615 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0016
                            zf-DNL  24 kGvVivqCpgCkn 36 
                                       +GvVi +C+gC+ 
  gi|386000883|ref|YP_005919182.1| 122 TGVVIANCSGCAV 134
                                       69*********85 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                            zf-DNL  23 ekGvVivqCpgCknr 37 
                                         G  iv+ ++C +r
  gi|386000883|ref|YP_005919182.1| 369 SAGALIVNSSSCTAR 383
                                       568889999999876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.048
                            zf-DNL  25 GvVivqCpgCknrH 38 
                                       G+ +v C gC  rH
  gi|386000883|ref|YP_005919182.1| 596 GTGLVDCTGCIIRH 609
                                       7779******9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 4585.33
//
Query:       gi|386000884|ref|YP_005919183.1|  [L=454]
Description: Response regulator domain with PAS sensor, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-18   65.0   0.0      1e-17   64.3   0.0    1.3  1  Response_reg  Response regulator receiver domain
    2.5e-08   34.1   0.0    6.4e-08   32.8   0.0    1.7  1  PAS_4         PAS fold
    9.3e-08   32.1   0.0    2.4e-07   30.7   0.0    1.6  1  PAS           PAS fold
    6.1e-07   29.3   0.0    1.7e-06   27.9   0.0    1.7  1  PAS_8         PAS domain
    1.3e-06   28.6   0.0    2.8e-06   27.5   0.0    1.6  1  PAS_9         PAS domain
     0.0001   22.5   0.0    0.00024   21.3   0.0    1.6  1  PAS_3         PAS fold


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 !   64.3   0.0   3.4e-21     1e-17       1     103 [.      17     119 ..      17     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 3.4e-21
                                       EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvii 76 
                                       +li++D+p+ +el+   +  ++++  v++a++g+e l+ + ++++dl+ +D  +pg++Gl++l+eir+ d+++pv++
  gi|386000884|ref|YP_005919183.1|  17 ILIIEDNPDDVELILLGFSkHDEF-FVDVATTGEEGLDRVATSRYDLVSVDFALPGISGLDVLEEIRTSDQDVPVVM 92 
                                       8*************9999956777.9*************************************************** PP

                                       EESSTSHHHHHHHHHCTESEEEESSG- CS
                      Response_reg  77 ltahseeedavealkagaddflsKpfd 103
                                       +t++++ee  v a++  a  +++K +d
  gi|386000884|ref|YP_005919183.1|  93 VTGRGTEELQVVAFEKFATSYVMKSVD 119
                                       ************************986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   2.2e-11   6.4e-08       1     110 []     159     270 ..     159     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.2e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...daarleralrrvlegeepiefleelll 74 
                                       l+++p +++vl  +g +  +N ++ae+fg++ e+l+G+++++l+ +e   + ++ e++  +v +   + + +e+ ++
  gi|386000884|ref|YP_005919183.1| 159 LENSPTGIYVL-QNGCFKMVNSRFAEIFGCDKEDLIGEHFWSLADPEsfeCEEAAEEPCLEVGADLPRTKVHEFGVT 234
                                       67888888886.5788899****************************777666666666666666666666666666 PP

                             PAS_4  75 ..pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         +g+ r++e r+  l+d   e + vl+ ++D T+r+r
  gi|386000884|ref|YP_005919183.1| 235 rrDGSKRWVEARIASLDD--QEERWVLGNVVDATDRKR 270
                                       999*************66..66679*********9986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   8.1e-11   2.4e-07       6     103 ..     158     257 ..     156     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.1e-11
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC. CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl. 81 
                                       ile++p++i v+  +g++  vN+ ++e++G + e+++g+++  l        ++e +e+ +++ e++  +  ++++ 
  gi|386000884|ref|YP_005919183.1| 158 ILENSPTGIYVL-QNGCFKMVNSRFAEIFGCDKEDLIGEHFWSLA-------DPESFECEEAAEEPCLEVGADLPRt 226
                                       89**********.*****************************998.......8899999999999999999999999 PP

                                       .........TTSSEEEEEEEEEEEEETTEEE CS
                               PAS  82 .........rdgrpihlevraspvrdaggei 103
                                                rdg+++++e r +++ d ++++
  gi|386000884|ref|YP_005919183.1| 227 kvhefgvtrRDGSKRWVEARIASLDDQEERW 257
                                       9999999*****************9999985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   5.8e-10   1.7e-06       4      60 ..     156     212 ..     153     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.8e-10
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplledae 60 
                                       r ++e+sp gi v+ +g  + +vN +++e++G + +dl+ge ++ l +    ++e+a 
  gi|386000884|ref|YP_005919183.1| 156 RYILENSPTGIYVLQNGC-FKMVNSRFAEIFGCDkEDLIGEHFWSLADPESFECEEAA 212
                                       789*********99999*.*************99999999999988888888888443 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   9.5e-10   2.8e-06       3     103 ..     165     266 ..     163     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.5e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirknget 75 
                                       gi +   +g    +N  +++++G ++e+++g +++ l   ++ + ++  ++ +le g +    +  e   +r++g++
  gi|386000884|ref|YP_005919183.1| 165 GIYVL-QNGCFKMVNSRFAEIFGCDKEDLIGEHFWSLAdpESFECEEAAEEPCLEVGADlpRTKVHEFGVTRRDGSK 240
                                       66655.77756689************************766666667777777777777*999999999******** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDit 103
                                        wv+++++ + d++++ v+  + ++D t
  gi|386000884|ref|YP_005919183.1| 241 RWVEARIASLDDQEERWVL--GNVVDAT 266
                                       **********988888888..9999987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.1e-08   0.00024       4      80 ..     177     255 ..     174     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.1e-08
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge...py.egeyRirrkdGeyrwveararvir 76 
                                       v+ r+ ei+G ++e+l+g   ++ +l  pe  e  ++a + +l+ g+   +   +e+ + r+dG+ rwvear+  + 
  gi|386000884|ref|YP_005919183.1| 177 VNSRFAEIFGCDKEDLIGE--HFWSLADPESFECEEAAEEPCLEVGAdlpRTkVHEFGVTRRDGSKRWVEARIASLD 251
                                       899****************..**********************7776332223578*****************9995 PP

                             PAS_3  77 deng 80 
                                       d++ 
  gi|386000884|ref|YP_005919183.1| 252 DQEE 255
                                       5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 3451.26
//
Query:       gi|386000885|ref|YP_005919184.1|  [L=174]
Description: hypothetical protein Mhar_0170 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   72.5   0.0    6.4e-20   72.0   0.0    1.2  1  AAA_18    AAA domain
    0.00033   20.8   0.1       0.82    9.8   0.1    2.4  2  AAA_33    AAA domain
     0.0033   17.9   0.6      0.014   15.8   0.5    2.1  1  AAA_17    AAA domain
     0.0044   16.4   0.0     0.0058   16.0   0.0    1.2  1  ATPase    KaiC
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.025   14.3   0.0    1.3  1  AAA_24    AAA domain
      0.026   14.8   4.6       0.12   12.6   4.6    2.3  1  AAA_28    AAA domain
       0.03   14.8   0.0      0.054   13.9   0.0    1.6  1  AAA       ATPase family associated with various cellular acti
      0.082   13.3   1.1       0.29   11.5   1.1    1.9  1  AAA_16    AAA ATPase domain
      0.085   13.1   0.0       0.17   12.1   0.0    1.5  1  DUF1884   Domain of unknown function (DUF1884)
       0.13   12.6   0.1        0.3   11.3   0.0    1.6  2  AAA_22    AAA domain
       0.61    9.6   3.4        0.4   10.2   0.6    2.0  3  AAA_25    AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   3.9e-23   6.4e-20       3     130 .]       5     118 ..       4     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.9e-23
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvi 79 
                                       ltGtpG+GKtt+a  L  r   +++++ +++e+gl+ + d+   + ++++d + l++ +++l       + ++ +v+
  gi|386000885|ref|YP_005919184.1|   5 LTGTPGTGKTTVAALLPFR---VIEINALVREEGLSVGIDEG--RGCLIADVEALEARIEELAPE----GAEEIVVL 72 
                                       9***************999...9*******************..**********99999999995....679999** PP

                            AAA_18  80 dghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                       +gh ++ + ++a     +vL+++p +l+eRl++Rgy e+ki+en eae+ld
  gi|386000885|ref|YP_005919184.1|  73 EGHFSHRFAPEA-----IVLRTRPAVLRERLARRGYPERKIRENLEAEALD 118
                                       **********88.....9******************************985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0     0.001       1.7       4      18 ..       5      19 ..       3      34 .. 0.87
   2 !    9.8   0.1   0.00051      0.82      96     134 ..      79     118 ..      65     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                            AAA_33  4 lvGlpGsGKstlaer 18
                                      l G pG+GK+t+a  
  gi|386000885|ref|YP_005919184.1|  5 LTGTPGTGKTTVAAL 19
                                      579*********975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00051
                            AAA_33  96 gvpvrivvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                        ++ +++v++t +++l+eRla+R  ++ + r +++ eald
  gi|386000885|ref|YP_005919184.1|  79 RFAPEAIVLRTRPAVLRERLARRGYPErKIRENLEAEALD 118
                                       566799******************9974456667776665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   8.6e-06     0.014       1      81 [.       6      77 ..       6     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-06
                                      EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79
                                      +G PG GK+t++      + f +++   l+ree  + g     de r   + + ++ ++  +e++a e +++ v+++gh
  gi|386000885|ref|YP_005919184.1|  6 TGTPGTGKTTVA----ALLPFRVIEINALVREEGLSVGI----DEGRGCLIADVEA-LEARIEELAPEGAEEIVVLEGH 75
                                      69**********....567******99999999877787....6665444444444.4444556777788899****** PP

                                      SE CS
                            AAA_17 80 pr 81
                                      ++
  gi|386000885|ref|YP_005919184.1| 76 FS 77
                                      96 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.5e-06    0.0058      23      94 ..       4      78 ..       2     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
                            ATPase 23 litGepGtGKtifal..qFlikgae.kygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaee 94
                                       +tG+pGtGKt++a+   F +  ++  + e+g+ v ++e    l+ ++++l   +e+l  eg   i+ +  + ++
  gi|386000885|ref|YP_005919184.1|  4 ALTGTPGTGKTTVAAllPFRVIEINaLVREEGLSVGIDEGRGCLIADVEALEARIEELAPEGAEEIVVLEGHFSH 78
                                      589**********9722465443331346******************************9998888877766655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.025       4      30 ..       2      28 ..       1      73 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfid 30
                                      + +++G +g+GKTt+a+ l+ +++ i+
  gi|386000885|ref|YP_005919184.1|  2 RAALTGTPGTGKTTVAALLPFRVIEIN 28
                                      6799**************977777764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.6   7.6e-05      0.12       2      22 ..       3      23 ..       2     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                       ++tG+++tGKTt+++ L  r
  gi|386000885|ref|YP_005919184.1|  3 AALTGTPGTGKTTVAALLPFR 23
                                      589************999755 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.054       3      18 ..       5      20 ..       3      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                                      EESSTTSSHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakav 18
                                      l+G+pGtGKT++a  +
  gi|386000885|ref|YP_005919184.1|  5 LTGTPGTGKTTVAALL 20
                                      89*********99765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   0.00018      0.29      28      49 ..       4      25 ..       2     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                            AAA_16 28 llsGesGvGKsslvrellrale 49
                                       l+G +G+GK++++  l+ ++ 
  gi|386000885|ref|YP_005919184.1|  4 ALTGTPGTGKTTVAALLPFRVI 25
                                      599***********99985443 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.17       2      42 ..      45      85 ..      44      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHHHHHHHHHHTT----EEEE-HHHHHHHHHHH CS
                           DUF1884  2 gdlirilevieekineLkleGfePdiiLvGkeaieflkeal 42
                                      g li   e +e++i+eL  eG e  ++L G+   +f +ea+
  gi|386000885|ref|YP_005919184.1| 45 GCLIADVEALEARIEELAPEGAEEIVVLEGHFSHRFAPEAI 85
                                      667777899***************************99986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019       0.3       9      25 ..       4      20 ..       3      35 .. 0.91
   2 ?   -2.4   0.0       3.3   5.3e+03      46      46 ..     123     123 ..      94     154 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_22  9 vvtGesGtGKTtllrrl 25
                                      ++tG +GtGKTt+++ l
  gi|386000885|ref|YP_005919184.1|  4 ALTGTPGTGKTTVAALL 20
                                      69***********9865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                            AAA_22  46 t 46 
                                       +
  gi|386000885|ref|YP_005919184.1| 123 E 123
                                       1 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00024       0.4      36      53 ..       3      20 ..       1      38 [. 0.86
   2 ?   -1.5   0.0      0.95   1.5e+03     126     140 ..      47      61 ..      27      73 .. 0.75
   3 ?   -1.9   0.0       1.3   2.1e+03     141     159 ..     115     133 ..      90     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                            AAA_25 36 allaGapgtGKttlaldl 53
                                      a+l+G pgtGKtt+a  l
  gi|386000885|ref|YP_005919184.1|  3 AALTGTPGTGKTTVAALL 20
                                      78************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.95
                            AAA_25 126 ltadvdaleaaieev 140
                                       l adv+alea+iee 
  gi|386000885|ref|YP_005919184.1|  47 LIADVEALEARIEEL 61 
                                       457889999998885 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                            AAA_25 141 egvrlvviDplsralggde 159
                                       e +++v +  +  +++ +e
  gi|386000885|ref|YP_005919184.1| 115 EALDVVLVEAVEGCHRVSE 133
                                       4444444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1107.30
//
Query:       gi|386000886|ref|YP_005919185.1|  [L=354]
Description: histidinol-phosphate aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-43  148.6   0.0    5.5e-43  147.5   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
     0.0046   15.9   0.0     0.0069   15.3   0.0    1.1  1  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.036   13.8   0.1      0.082   12.7   0.1    1.5  1  DUF4051          Protein of unknown function (DUF4051)
       0.32    9.5   0.0       0.45    9.0   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.0   1.2e-46   5.5e-43       3     362 ..      38     346 ..      36     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 1.2e-46
                                       EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                       +++Lgsne++++    ++p+v +a +          +y+ +     l eala ++g        +e  vv g G + 
  gi|386000886|ref|YP_005919185.1|  38 IVKLGSNENPYG----PSPKVYEAIAS-----ARPERYPEPG---RLVEALAGYAG------APPE-DVVIGAGMDG 95 
                                       789*********....****9999955.....5667899999...9**********......5566.********** PP

                                       HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
                     Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilves 156
                                       + ++l++l+ l+pgd+ ++  pt++ y+     +g+     p      ++  +e   e + +       +k+i+++s
  gi|386000886|ref|YP_005919185.1|  96 VMDTLTRLF-LDPGDRAVIYPPTFSYYEILTVTAGADPLFLP------RGPEFEVPSE-VPS------GIKMIFICS 158
                                       *********.********************************......4555555555.333......559****** PP

                                       S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEE CS
                     Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyi 233
                                       p+NPtG+ +++e+l+ +   +++ + ++f+DeaYa+f  ++      +++ve+++nl++ ++ sKafGlaG R+Gy+
  gi|386000886|ref|YP_005919185.1| 159 PNNPTGDTIPEEDLRGI---VEAAEGIVFLDEAYAEFSDQNF-----LPLVEDYDNLVVGRTTSKAFGLAGMRLGYA 227
                                       *****************...88889***************55.....9***************************** PP

                                       EEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEE CS
                     Aminotran_1_2 234 lgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfll 309
                                       ++ +++++  r+++ pf   +++  aa  aal+d +    ++  +++ + ++r++l +++     + + + +g fl+
  gi|386000886|ref|YP_005919185.1| 228 VAPDWIAREYRRAAPPFFGvTTPSVAAGIAALEDLE----HMRRSVEAIRHERDRLMAAI-----PEFRPSGGNFLY 295
                                       ******************9***************88....9******************8.....666666666666 PP

                                       EEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 310 tdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +++ +    e+++ Ll + gv+v+ + sf+      lR+tv  +t+ee+ +++ea
  gi|386000886|ref|YP_005919185.1| 296 METAEP-SGEVAERLLGR-GVIVRDCYSFRGagDRALRVTV--GTPEENGRFLEA 346
                                       666655.59*********.**********9999889*****..******999998 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-06    0.0069     142     209 ..     155     230 ..     141     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-06
                                       EEESS-TTT--.----....---TT-EEEEEE-TT-...STTTS---S-B--SEEEEEHHHHHS-GGG-EEEEEES CS
                       Alliinase_C 142 lvtsPnnPdgl.lrea....vvkgseakviyDlayY...WPhytpitskadedimLftlskltGhaGsrlGWalvk 209
                                       ++ sPnnP g  + e+    +v+  e++v  D ay      ++ p+ +  d+ ++  t+sk  G aG rlG+a+  
  gi|386000886|ref|YP_005919185.1| 155 FICSPNNPTGDtIPEEdlrgIVEAAEGIVFLDEAYAefsDQNFLPLVEDYDNLVVGRTTSKAFGLAGMRLGYAVAP 230
                                       689*****985244332333889**********9952223579999999**99********************865 PP

>> DUF4051  Protein of unknown function (DUF4051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.8e-05     0.082      20      38 ..     263     281 ..     257     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                           DUF4051  20 chlkRycrAfRqdRDAllE 38 
                                        h++R   A+R++RD l+ 
  gi|386000886|ref|YP_005919185.1| 263 EHMRRSVEAIRHERDRLMA 281
                                       69*************8865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   9.9e-05      0.45      71     175 ..      87     188 ..      68     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9.9e-05
                                       EEESSHHHHHHHHHHTTS-T.TEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS CS
                   Cys_Met_Meta_PP  71 lavssGmaAiaaailallka.GdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtp 146
                                       +++ +Gm  ++ ++++l+   Gd+ v    +Y +t+++ + ++   g +  f     + e+ + + +  k++++ +p
  gi|386000886|ref|YP_005919185.1|  87 VVIGAGMDGVMDTLTRLFLDpGDRAV----IYPPTFSYYEILTVTAGADPLFLPRGPEFEVPSEVPSGIKMIFICSP 159
                                       67788999999999887544499988....7********************************************** PP

                                       -TTTT----HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 147 tnpllkvvDiekiaklakkagvlvvvDnt 175
                                        np+ +++  e++  ++ +a+ +v++D +
  gi|386000886|ref|YP_005919185.1| 160 NNPTGDTIPEEDLRGIVEAAEGIVFLDEA 188
                                       ***99887656555555566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 2321.79
//
Query:       gi|386000887|ref|YP_005919186.1|  [L=413]
Description: Acetylornithine aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-107  359.8   0.0   2.7e-107  359.0   0.0    1.3  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.028   13.7   0.0      0.042   13.1   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.0   0.0    3e-111  2.7e-107       8     402 ..      48     406 ..      42     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: 359.0 bits;  conditional E-value: 3e-111
                                       -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT CS
                       Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklap 84 
                                         ++++ ++ G++++d+ g++y+D+v++ av+n+Gh+h  vv+a+++qa++l h+s +++ +e+++ lae+l +l++
  gi|386000887|ref|YP_005919186.1|  48 RQPILLVRGSGARVWDASGREYIDFVAGVAVNNVGHCHASVVEAIRQQAKELIHTS-NLYYTENQVLLAEELKALTG 123
                                       4468999*************************************************.*******************9 PP

                                       -..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE- CS
                       Aminotran_3  85 kgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlk 161
                                          d+ f++nsG+e+ve+AlKlark      at ++ki+a  ++fHGrtlg+l++t + + y++ f p++ e  +++
  gi|386000887|ref|YP_005919186.1| 124 M--DRAFFCNSGAESVEAALKLARK------ATGRSKIVAAIHSFHGRTLGSLGATYK-PMYREPFRPLQ-EADFVP 190
                                       9..**********************......***************************.********984.567788 PP

                                       TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT CS
                       Aminotran_3 162 ypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf 238
                                       ++d                  eal ++ + e++Avi+Ep+qgegGv v++p +l+++re+c++ ++l+i DEvqtGf
  gi|386000887|ref|YP_005919186.1| 191 FDD-----------------PEALAAAVSTETSAVILEPVQGEGGVHVPKPRYLRAAREICDDCGALFILDEVQTGF 250
                                       887.................3567778899*********************************************** PP

                                       TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHH CS
                       Aminotran_3 239 GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeeklle 315
                                       GrTGk+f+ eh gv pD mtlaK+++gGlp+ a+la + v ++++ g+h+sTfgG pl  a+ala++ +i ee l+e
  gi|386000887|ref|YP_005919186.1| 251 GRTGKWFGKEHSGVMPDAMTLAKGIAGGLPMGAMLAAESVSDVFKRGDHASTFGGGPLVSAAALASIGAIREERLVE 327
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--H CS
                       Aminotran_3 316 naqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitd 392
                                       + +e+g++l+++L+e  ++     +vRg+Glm+++el ++      ei+++a+e Gvl+  + d+v+r++ppl++  
  gi|386000887|ref|YP_005919186.1| 328 RSEEMGRYLRSRLSEEIDAI----DVRGLGLMVGVELAANCP----EIVNRARERGVLLNATSDHVLRMVPPLVVGR 396
                                       ***************99775....9****************9....8****************************** PP

                                       HHHHHHHHHH CS
                       Aminotran_3 393 eeidelleil 402
                                        eid +++ l
  gi|386000887|ref|YP_005919186.1| 397 GEIDRVVKVL 406
                                       ***9998766 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-06     0.042       6     144 ..      92     244 ..      87     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH.TTTTTT-EEEEESSS-THHHHHHH CS
                   DegT_DnrJ_EryC1   6 eleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLra.lgvgpgdeVIvpsltFvatanavl 81 
                                       + ++++e++++  l   ++   ++++++a +g++ a  ++sG ++++ aL+   +++ + +++ + ++F +     l
  gi|386000887|ref|YP_005919186.1|  92 IRQQAKELIHTSNLYYTENQVLLAEELKALTGMDRAFFCNSGAESVEAALKLaRKATGRSKIVAAIHSFHGRTLGSL 168
                                       56667777766666666777789****************************9555666677888889****999999 PP

                                       HTT-EEEEE-....B-TTTSSB..-GGGCGGG--TTEEEEEEB-GGG.......B---HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1  82 elgakpvfvD....vdpdtyni..dpaaieaaitertkaIlpVhlyG.......qvadmdalkaiaakhglkvieD 144
                                        + +kp++ +     +++++ +  dp+a++aa+ ++t+a+++  + G       ++  + a ++i+++ g  +i D
  gi|386000887|ref|YP_005919186.1| 169 GATYKPMYREpfrpLQEADFVPfdDPEALAAAVSTETSAVILEPVQGeggvhvpKPRYLRAAREICDDCGALFILD 244
                                       9999999887333357888887779**************9964444411222223445666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2758.42
//
Query:       gi|386000888|ref|YP_005919187.1|  [L=223]
Description: Metallo-beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-33  116.9   1.1    1.3e-33  116.7   1.1    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    8.2e-10   38.5   0.0    1.2e-09   38.0   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00039   19.9   0.0    0.00058   19.4   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.066   13.1   0.0       0.13   12.2   0.0    1.6  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   1.1   2.9e-37   1.3e-33       3     197 .]      21     200 ..      19     200 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 2.9e-37
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       p+ +n+yli  d+  iL+D+G+++e ++ +    +++++p +++ ++lTH H+DH +g++ l+eat++ v +++eea
  gi|386000888|ref|YP_005919187.1|  21 PFDGNVYLI-LDEVPILVDAGMEPESTLRKI---KKYIDPQEIEMIVLTHCHHDHSAGVPRLKEATGARVLIHEEEA 93 
                                       6779*****.9*****************997...******************************************* PP

                                       HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SH CS
                       Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.ag 155
                                        +l +++a  a+ ++     ++ ++  d ++ e+d+ ++g + l v ++pgh++g+++++ + +kvlf+GD+++ +g
  gi|386000888|ref|YP_005919187.1|  94 GSLGDDMATVAYLFG----LPAQEIEADGTLKEGDVLDLGEWKLSVLHTPGHSPGGICLYEPKAKVLFSGDTVFpQG 166
                                       ********9999997....69*****************************************************666 PP

                                       HCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 156 etgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++gr+dl        +++  +++++s+++l +l++evl+pgH
  gi|386000888|ref|YP_005919187.1| 167 NIGRTDL--------FAGCDADLIRSIERLTALDVEVLYPGH 200
                                       6666666........99999********************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   2.6e-13   1.2e-09       3     159 ..      35     179 ..      34     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.6e-13
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       iL+Dag +   + +++l++ ++  ++++i++++lth+H DH ag++ l+e ++  ++++ +++ +  l + +   a 
  gi|386000888|ref|YP_005919187.1|  35 ILVDAGME---P-ESTLRKIKKYIDPQEIEMIVLTHCHHDHSAGVPRLKEATG--ARVLIHEEEAGSLGDDMATVAY 105
                                       89*****9...4.33443445677899***********************655..5677777766666666543333 PP

                                       HTTTTEEEEEE-TTSEEEE......CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHH CS
                     Lactamase_B_2  80 eeepavnvheldwgesfel......gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeei 150
                                          ++++++e++++++++       g  + ++ +   ++ s+           G ++ +++ +v+++gDt + ++ i
  gi|386000888|ref|YP_005919187.1| 106 L--FGLPAQEIEADGTLKEgdvldlG--EWKLSVLHTPGHSPG----------GICLYEPKAKVLFSGDTVFPQGNI 168
                                       3..35777777777777663333114..344555555555655..........9*****************888888 PP

                                       H..HHHCT-SE CS
                     Lactamase_B_2 151 g..erlggadl 159
                                       g  ++++g+d 
  gi|386000888|ref|YP_005919187.1| 169 GrtDLFAGCDA 179
                                       85566777665 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-07   0.00058       2      56 ..      28      79 ..      27      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-07
                     Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekvi..ptvdliLLshatlehlGayally 56
                                      L ld+v iL+D G++ +     s+l++++k+i  +++++i+L+h   +h ++ + l 
  gi|386000888|ref|YP_005919187.1| 28 LILDEVPILVDAGMEPE-----STLRKIKKYIdpQEIEMIVLTHCHHDHSAGVPRLK 79
                                      568************86.....5799*****9777**************99977665 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.13      16      70 ..      32      92 ..      22     167 .. 0.70
   2 ?   -2.7   0.0       1.1   4.9e+03     105     115 ..     192     202 ..     186     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                     Lactamase_B_3 16 garilvDPf......kanlgyeppaeeaDlvlisqaledHah.letlkqlaenvkvleeges 70
                                      ++ ilvD +       ++++ +++++e++++++++ + dH + +++lk+ a+ ++vl ++e+
  gi|386000888|ref|YP_005919187.1| 32 EVPILVDAGmepestLRKIKKYIDPQEIEMIVLTHCHHDHSAgVPRLKE-ATGARVLIHEEE 92
                                      5667888776666543378888899************777542445555.445555544333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                     Lactamase_B_3 105 gltiyhlGhla 115
                                       +++++++Gh+ 
  gi|386000888|ref|YP_005919187.1| 192 DVEVLYPGHME 202
                                       68899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1482.61
//
Query:       gi|386000889|ref|YP_005919188.1|  [L=55]
Description: hypothetical protein Mhar_0174 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       112  (0.00624686); expected 358.6 (0.02)
Passed bias filter:                       97  (0.00541023); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 413.68
//
Query:       gi|386000890|ref|YP_005919189.1|  [L=103]
Description: Addiction module toxin, RelE/StbE family [Methanosaeta harundinacea 6Ac]
Scores for 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-09   35.8   0.3    1.1e-08   35.6   0.3    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    7.9e-06   25.8   0.1      1e-05   25.4   0.1    1.3  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
    0.00032   20.9   0.1    0.00044   20.5   0.1    1.2  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s
  ------ inclusion threshold ------
      0.084   13.1   0.0      0.093   13.0   0.0    1.1  1  DUF3014          Protein of unknown function (DUF3014)
        0.1   13.1   0.0        0.1   13.1   0.0    1.2  1  RPAP3_C          Potential Monad-binding region of RPAP3
       0.11   12.8   0.2       0.31   11.4   0.2    1.8  1  Pea-VEAacid      Pea-VEAacid family


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 !   35.6   0.3   3.6e-12   1.1e-08       4      88 ..      15      89 ..      12      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.6e-12
                                      EHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC...CTTEEEEEECTEEEEEEEETSTTEEE CS
                        ParE_toxin  4 tprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg...lkglrririgdyriiYriddeelvvv 79
                                      t ++++++kk+ +         + + d+l +++++++ +p++g+p    +   l+++r  ++++y+i+Y + ++++++ 
  gi|386000890|ref|YP_005919189.1| 15 TTEFERQFKKLTKK-------DRALRDRLLRKINQILSDPEIGEP----KshaLRHIRGSHVDPYVIVYVF-NGNTIT- 80
                                      67889999999986.......9999********************....334477***************9.576777. PP

                                      EEEEEEHHH CS
                        ParE_toxin 80 ilrvlhrse 88
                                      ++ v h++ 
  gi|386000890|ref|YP_005919189.1| 81 FIYVDHHDA 89
                                      ******975 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 !   25.4   0.1   3.4e-09     1e-05       3      50 ..      14      64 ..      12      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.4e-09
                   ParE-like_toxin  3 qtrrfkkalkklkek...lkadldkavkeiiedPelGeeKkGDLsgvfvyk 50
                                       t++f+++ kkl +k   l+ +l +++++i++dPe+Ge+K   L+ ++ ++
  gi|386000890|ref|YP_005919189.1| 14 STTEFERQFKKLTKKdraLRDRLLRKINQILSDPEIGEPKSHALRHIRGSH 64
                                      6899********9885556778999****************9999998765 PP

>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.5e-07   0.00044       2      85 ..      11      89 ..      10      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.5e-07
                                      EEEEEHHHHHHHHHHHHTT--HH.HHHHHHHHHHTT-S--GGG--EE-SSS-TTEEEEEEETTEEEEEEE-SSEEEEEE CS
                        YafQ_toxin  2 kikptkqfkkdlkrlkkrkkdle.klkevlklLaegepLpekyrdHaLkgnwkgyrecHikpDllLiYrleddelvlvr 79
                                      ++  t++f++++k+l k+ + l  +l + ++ ++++ ++  + + HaL      +r  H+ p  +++Y  + ++++++ 
  gi|386000890|ref|YP_005919189.1| 11 EYASTTEFERQFKKLTKKDRALRdRLLRKINQILSDPEI-GEPKSHALR----HIRGSHVDP-YVIVYVFNGNTITFIY 83
                                      67789***********66555544777777777777777.56799***9....68999**99.899************* PP

                                      EE-HHH CS
                        YafQ_toxin 80 lGsHse 85
                                      ++ H+ 
  gi|386000890|ref|YP_005919189.1| 84 VDHHDA 89
                                      ***986 PP

>> DUF3014  Protein of unknown function (DUF3014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05     0.093      76     110 ..      18      52 ..       5      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                           DUF3014  76 lqeayeeLGypkasFndrlvaaidellaaPepeep 110
                                       +++ ++ L +++++++drl++ i+++l+ Pe+ ep
  gi|386000890|ref|YP_005919189.1|  18 FERQFKKLTKKDRALRDRLLRKINQILSDPEIGEP 52 
                                       8999***************************9887 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.4e-05       0.1       4      31 ..      14      42 ..      11      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                           RPAP3_C  4 tayeFeklwrklkredkdlkavllq.inp 31
                                      + +eFe++++kl ++d++l+ +ll+ in+
  gi|386000890|ref|YP_005919189.1| 14 STTEFERQFKKLTKKDRALRDRLLRkINQ 42
                                      789*********99999999999988876 PP

>> Pea-VEAacid  Pea-VEAacid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2    0.0001      0.31       6      13 ..      62      69 ..      61      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                       Pea-VEAacid  6 GSHVDSYV 13
                                      GSHVD YV
  gi|386000890|ref|YP_005919189.1| 62 GSHVDPYV 69
                                      9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 694.78
//
Query:       gi|386000891|ref|YP_005919190.1|  [L=161]
Description: transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-20   74.4   0.1    1.3e-20   74.3   0.1    1.0  1  GyrI-like  GyrI-like small molecule binding domain
    1.4e-07   31.8   0.0    1.6e-07   31.6   0.0    1.1  1  Cass2      Integron-associated effector binding protein


Domain annotation for each model (and alignments):
>> GyrI-like  GyrI-like small molecule binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   1.5e-24   1.3e-20       2     154 ..       5     159 ..       4     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.5e-24
                                       CEEEEEE--EEEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCTT..--SSEEEEEEEEE-STTCCCEEEEEEEECC CS
                         GyrI-like   2 eveivelpafrvvgirhrgdyneeggipklweelyawaseiklsn..avspligvssdepeetedeelkydigvtve 76 
                                       ++ei+ +pa+rv+++ ++g +    +ipk++eel aw +++ +     ++  +++++d+p ++ +ee+++++++ v 
  gi|386000891|ref|YP_005919190.1|   5 DIEIKSVPALRVASLWGKGLPFA-VTIPKAYEELAAWMAKKSIPAlsGSPMGLALYYDDPASVAPEEVRFKVAMPVA 80 
                                       689****************9888.34*************999988988888899**********************9 PP

                                       CCC..CGBTTSEEEEE-SEEEEEEEEECEGGGHHHHHHHHHHTHHHHTT-EEEESEEEEEEECCCTS.SCGCEEEEE CS
                         GyrI-like  77 irv..egpeglefleipageyAvfrhkGpyddlqatyaklygewlpesgyerrdgpsiEiYlsdpre.reeelktei 150
                                       ++    + +g  + ++p+ e+A ++ +Gpy +l+++y  lyg w+ ++g  + ++  +E+Y       ++ee++tei
  gi|386000891|ref|YP_005919190.1|  81 AETpeFAEGGAAVEVLPEAEVAYLTVRGPYTNLEDAYSQLYG-WVFSNGF-QPADAAREVYVRWSESmPPEEWVTEI 155
                                       99987889999*******************************.*******.88888899998877778********* PP

                                       EEEE CS
                         GyrI-like 151 yipv 154
                                       ++pv
  gi|386000891|ref|YP_005919190.1| 156 QVPV 159
                                       ***8 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.8e-11   1.6e-07       1     149 []       7     159 ..       7     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.8e-11
                                       EEEEE--EEEEEEEEETTCCCCH...HHHHHHHHHHHHH...HHCTTSBSTEEEEEEEC-TT....-CCGEEEEEEE CS
                             Cass2   1 rIvelpeftvaGiryegskeeedlnkeigklwreflekg...rlkkikkdkrvfgiyhdyes....eenkfsyyagv 70 
                                       +I+++p+ +va++   g   + +    i+k+++e+ +++    ++ ++ +   +++y+d ++    ee  f++  ++
  gi|386000891|ref|YP_005919190.1|   7 EIKSVPALRVASLWGKGLPFAVT----IPKAYEELAAWMakkSIPALSGSPMGLALYYDDPAsvapEEVRFKV--AM 77 
                                       68888888888887777777775....888888888777444666666667778888888889*555555555..44 PP

                                       EE-TT..SSS-TT-EEEEE--EEEEEEEEESSSTT-HHHHHHHHHHCHCCHCTEEE-SSEEEEEE....STTHHHTE CS
                             Cass2  71 evpsd..sevpeglvkkeiPggkYavftiegdfeedlaeaweaiygellpnsnyerrggpdfEvy....keepaeks 141
                                       +v  +  ++ + g  + ++P+ + a  t++g+  + l++a+ ++yg+++ ++++++++ +  Evy     + p e++
  gi|386000891|ref|YP_005919190.1|  78 PVAAEtpEFAEGGAAVEVLPEAEVAYLTVRGPYTN-LEDAYSQLYGWVF-SNGFQPAD-AAREVYvrwsESMPPEEW 151
                                       4444444899************************9.************9.69****55.99****88775555669* PP

                                       EEEEEEEE CS
                             Cass2 142 eielyIPv 149
                                         e+++Pv
  gi|386000891|ref|YP_005919190.1| 152 VTEIQVPV 159
                                       *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1241.87
//
Query:       gi|386000892|ref|YP_005919191.1|  [L=74]
Description: hypothetical protein Mhar_0177 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      936  (0.0522059); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 577.91
//
Query:       gi|386000893|ref|YP_005919192.1|  [L=204]
Description: isoprenylcysteine carboxyl methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-15   55.6   0.1    1.1e-14   54.6   0.1    1.5  1  ICMT        Isoprenylcysteine carboxyl methyltransferase (ICM
    8.4e-09   35.8   0.0    1.4e-08   35.1   0.0    1.3  1  PEMT        Phospholipid methyltransferase
    9.7e-06   25.3   0.1    1.1e-05   25.1   0.1    1.3  1  DUF1295     Protein of unknown function (DUF1295)
     0.0002   21.0   2.7     0.0002   21.0   2.7    1.8  2  NnrU        NnrU protein
  ------ inclusion threshold ------
       0.11   11.3   0.0       0.18   10.5   0.0    1.5  1  ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family


Domain annotation for each model (and alignments):
>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   3.1e-18   1.1e-14       4      92 ..      93     180 ..      89     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.1e-18
                              ICMT   4 lvllaqalrlvvmatlGeiwttrvailpdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvall 80 
                                       l+l a +l++   a l ++++  ++i+++h lv++g+y+ +rHP Y+++++++ a llLl na  +a   ++++ l 
  gi|386000893|ref|YP_005919192.1|  93 LFLQALILLWRSHADLAKSFSPGLQIRKGHLLVTTGVYERIRHPMYAAHLLWATAQLLLLQNA--IAGPAFLVASLP 167
                                       6788889999999**************************************************..************ PP

                              ICMT  81 lf.vRikeEekaL 92 
                                       l+  Ri  Ee+++
  gi|386000893|ref|YP_005919192.1| 168 LYaARIPREEEMM 180
                                       **********988 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   3.8e-12   1.4e-08       5     106 .]      89     188 ..      85     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.8e-12
                              PEMT   5 lGlllialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllall 81 
                                       lG++l++  l+l + s+ +l +      ++  ++ + lvt+G+Y+ +++P+y + +l   +  L+ ++a +  + l+
  gi|386000893|ref|YP_005919192.1|  89 LGAALFLQALILLWRSHADLAKSFSPGLQI--RKGHLLVTTGVYERIRHPMYAAHLLWATAQLLLLQNAIAGPAFLV 163
                                       7999****************9999998887..9999**************************999998888666666 PP

                              PEMT  82 vllvylialkfvEephlakiYgkre 106
                                       + l  ++a++  Ee+++  ++g+++
  gi|386000893|ref|YP_005919192.1| 164 ASLPLYAARIPREEEMMLDQFGEEY 188
                                       66666677777**********9976 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   3.1e-09   1.1e-05     120     235 .]      86     195 ..      19     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.1e-09
                           DUF1295 120 ldviglalwlvgivl..ealaDqQlsafkkdpankgk.vldsGLwrysRHPNYfgealiWwglflialealegleal 193
                                       + ++g+al+l +++l     aD  +s        kg+ ++++G+++  RHP Y +  l+W    l+ l++       
  gi|386000893|ref|YP_005919192.1|  86 AGSLGAALFLQALILlwRSHADLAKSFSPGLQIRKGHlLVTTGVYERIRHPMYAAH-LLWATAQLLLLQN------- 154
                                       5567777777776551145566655443444456888899************9775.5676655554444....... PP

                           DUF1295 194 aiagplll.tlllvfvsgipllEkkalkkykdkeeyreYqkkt 235
                                       aiagp +l   l ++ + ip  E+++l +++  eeyr+Y ++t
  gi|386000893|ref|YP_005919192.1| 155 AIAGPAFLvASLPLYAARIPREEEMMLDQFG--EEYRRYSERT 195
                                       566665541567789999************9..*******997 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.41   1.5e+03      34      49 ..      10      25 ..       4      61 .. 0.66
   2 !   21.0   2.7   5.5e-08    0.0002      70     129 ..      87     151 ..      34     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.41
                              NnrU 34 ykilyslvsllglvll 49
                                      y i++ ++s++ l +l
  gi|386000893|ref|YP_005919192.1| 10 YLIGFGAASAIRLLWL 25
                                      5566666666666655 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.5e-08
                              NnrU  70 rhlalllmlvafillaaallpgnplsvglka......dlaetgivritrHPmllgvaiWAlaHlla 129
                                         l ++l l a+ill  +++   + s++          l +tg+++ +rHPm ++  +WA+a ll 
  gi|386000893|ref|YP_005919192.1|  87 GSLGAALFLQALILLWRSHADLAK-SFSPGLqirkghLLVTTGVYERIRHPMYAAHLLWATAQLLL 151
                                       344567888899999999988776.3332223566767889*********************9875 PP

>> ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     5e-05      0.18     343     422 ..     116     194 ..      50     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5e-05
                        ERG4_ERG24 343 iqtktGskLlvsGWyglarkinYlgDwlqslswsLatgfqsvlpyfyvlyFlvlLvhRelRDeekCkkkYGedweeY 419
                                       +q ++G+ L+++G y   r++ Y + +l + +  L    ++  p f  +  l l   R  R+ee    ++Ge++ +Y
  gi|386000893|ref|YP_005919192.1| 116 LQIRKGHLLVTTGVYERIRHPMYAAHLLWATAQLLLLQNAIAGPAFL-VASLPLYAARIPREEEMMLDQFGEEYRRY 191
                                       7899************************9999888777666666655.55677888999999999999999999999 PP

                        ERG4_ERG24 420 kkk 422
                                         +
  gi|386000893|ref|YP_005919192.1| 192 SER 194
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1638.29
//
Query:       gi|386000894|ref|YP_005919193.1|  [L=215]
Description: Metallo-beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-32  112.6   1.7    2.7e-32  112.4   1.7    1.0  1  Lactamase_B     Metallo-beta-lactamase superfamily
    1.7e-08   34.2   0.1    3.9e-08   33.0   0.1    1.7  1  Lactamase_B_2   Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.015   14.8   0.1       0.02   14.3   0.1    1.2  1  Lactamase_B_6   Metallo-beta-lactamase superfamily domain
      0.019   14.7   0.3      0.032   14.0   0.3    1.4  1  CheB_methylest  CheB methylesterase


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   1.7   6.1e-36   2.7e-32       5     197 .]      15     192 ..      11     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 6.1e-36
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        +n+yli  d+ v LiD+G+++ea++       + ++p +++ +ilTH H+DH++g++ l+ at+++v + + e + 
  gi|386000894|ref|YP_005919193.1|  15 EGNVYLI-IDEVVALIDAGMDAEATMRN---VEKLIDPAKIEFIILTHCHHDHTAGVPALKAATGAKVLIGEGEVCD 87 
                                       58*****.9*************999985...89******************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       l ++ a ++++++++    + +++ d ++ee+d++ +g +al v+ +pgh++g+++++ + +kvlf+GD+ll++ ++
  gi|386000894|ref|YP_005919193.1|  88 LGDDIATGSYQYGED----PAEFGIDGTLEEGDVINLGEWALSVIRTPGHSPGSISLYEPRAKVLFSGDTLLPHGNI 160
                                       ************975....*****************************************************65555 PP

                                       CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         ++       r +  ++++ +s+++la l++ vl+pgH
  gi|386000894|ref|YP_005919193.1| 161 GRTR-------RSGEMVRELVRSVERLASLEVRVLYPGH 192
                                       5555.......8*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   8.7e-12   3.9e-08       4     144 ..      28     154 ..      27     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 8.7e-12
                                       EES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH...HCCTTCGHH CS
                     Lactamase_B_2   4 LiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla...vleanfvyl 77 
                                       LiDag d  +  +r    ve++ ++++i++++lth+H DH+ag++ l++ ++ k+ l++  +v +   ++++++ + 
  gi|386000894|ref|YP_005919193.1|  28 LIDAGMDAEAT-MRN---VEKLIDPAKIEFIILTHCHHDHTAGVPALKAATGAKV-LIGEGEVCDlgdDIATGSYQY 99 
                                       8******5555.444...4567899************************655432.336644433222555554444 PP

                                       HCHTTTTEEEE.EE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2  78 aleeepavnvh.eldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                         +++ +  +  +l+ g+ + lg+    + ++  ++ s+           +  + +++ +v+++gDt 
  gi|386000894|ref|YP_005919193.1| 100 GEDPA-EFGIDgTLEEGDVINLGE--WALSVIRTPGHSPG----------SISLYEPRAKVLFSGDTL 154
                                       44444.222221455555555554..33555555666665..........666667777777777775 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.6e-06      0.02       2      59 ..      20      74 ..      19      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-06
                     Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekvi..ptvdliLLshatlehlGayallyakf 59
                                      L +d+v  L+D G+d +      +++++ek i   +++ i+L+h   +h ++ + l a+ 
  gi|386000894|ref|YP_005919193.1| 20 LIIDEVVALIDAGMDAE-----ATMRNVEKLIdpAKIEFIILTHCHHDHTAGVPALKAAT 74
                                      5689***********86.....35889999986569**************9998887665 PP

>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   7.1e-06     0.032      52     133 ..       2      76 ..       1      91 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-06
                                       SEEEE--TT-B--TTEEEE--TTSEEEEE....EE-.-SS-HHHHHHHHHHHH.G.GEEEEE-SBSS-TTHHHHHHH CS
                    CheB_methylest  52 lkVkeaedgeelepgrvyvapgdkhllielalsakkgerpsiDvlfesaaeayge.raigviLtGmgsDGaeGlkai 127
                                       ++V++++ g ++++g+vy++  +   li+        + + ++ +++ + + ++  ++  +iLt   +D ++G+ a+
  gi|386000894|ref|YP_005919193.1|   2 VEVHKVNGGGPVHEGNVYLIIDEVVALID--------AGMDAEATMRNVEKLIDPaKIEFIILTHCHHDHTAGVPAL 70 
                                       5899999****************988888........34678999999999999999999***************** PP

                                       HHTT-E CS
                    CheB_methylest 128 keaggl 133
                                       k+a g 
  gi|386000894|ref|YP_005919193.1|  71 KAATGA 76 
                                       *98664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1690.56
//
Query:       gi|386000895|ref|YP_005919194.1|  [L=433]
Description: Thiamine biosynthesis protein ThiC [Methanosaeta harundinacea 6Ac]
Scores for complete 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-170  566.9   0.0   2.7e-170  566.7   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family
  ------ inclusion threshold ------
      0.037   14.2   0.0       0.15   12.2   0.0    2.1  1  AbiEi_4       Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.7   0.0  3.1e-174  2.7e-170       1     417 [.       2     414 ..       2     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 566.7 bits;  conditional E-value: 3.1e-174
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeE 77 
                                       t +e+a+kg++ +e+e+va+ke+v+p  +++ va+Gr+vip+n +++ +p++iG++l+tkvn niG+s+ + d ++E
  gi|386000895|ref|YP_005919194.1|   2 TLIEDAKKGKTPPEVEAVARKEGVDPAALTRLVARGRVVIPRNARRDIRPTGIGETLTTKVNLNIGSSRGVADPAAE 78 
                                       7899************************************************************************* PP

                      ThiC_Rad_SAM  78 veKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdf 154
                                       veK+ va++agadtvmdLstggd+de+r+kil+++++pvgtvpiYqa +     + +lt++ l++++e+qa+dGvdf
  gi|386000895|ref|YP_005919194.1|  79 VEKAVVAMEAGADTVMDLSTGGDLDEMRRKILKAVEIPVGTVPIYQAEV-----AGDLTSQGLFDALERQAKDGVDF 150
                                       **********************************************986.....6799******************* PP

                      ThiC_Rad_SAM 155 ltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDa 231
                                       +t+H+gv+l++ e+lk+++R++g+vSrgGsl+ ++m ++++enp+y+efd+llei++e+++tlSlgdglRpG+i+Da
  gi|386000895|ref|YP_005919194.1| 151 VTVHVGVNLNSFERLKRSHRIMGVVSRGGSLTLKYMSETGEENPYYAEFDHLLEIAREHELTLSLGDGLRPGCIEDA 227
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 232 tdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiG 308
                                       +d+a+++e+i+lgelv+rar+agvq+mveGPGHvp deie++vk++k ++++aP+y+lGp+vtD+apgYDhit+aiG
  gi|386000895|ref|YP_005919194.1| 228 SDRAKYMEFIMLGELVDRARRAGVQAMVEGPGHVPADEIETSVKAMKYVTDGAPLYLLGPIVTDVAPGYDHITAAIG 304
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 309 aalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakg..lkkarerdkalskaRkeldwekqfela 383
                                       + +a+++Gad+lC  tp+EHl lP++ed+ eG i+++iaahaadlak   +++ar +d++++ aR++ldw +qf+la
  gi|386000895|ref|YP_005919194.1| 305 GVIAGMSGADFLCATTPSEHLDLPTKEDIFEGTIVTRIAAHAADLAKAgvKDRARLWDRKMAAARRDLDWPSQFDLA 381
                                       ***********************************************866788999********************* PP

                      ThiC_Rad_SAM 384 ldpekareireeklpeeeeaCsmCgekCavkive 417
                                       ++p+ areir+++   e ++C+mC e Ca+++++
  gi|386000895|ref|YP_005919194.1| 382 INPAIAREIRHRRGV-EVDTCTMCNELCAIRLAR 414
                                       ***********9986.99************9876 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.7e-05      0.15      19      39 ..      19      40 ..      12      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                           AbiEi_4 19 lea.aGispsalrrLvrkGwLv 39
                                      +++  G++p al+rLv +G++v
  gi|386000895|ref|YP_005919194.1| 19 VARkEGVDPAALTRLVARGRVV 40
                                      46669**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2587.49
//
Query:       gi|386000896|ref|YP_005919195.1|  [L=200]
Description: hypothetical protein Mhar_0181 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-48  165.0   0.0    1.3e-48  164.8   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.0   7.2e-53   1.3e-48       1     166 []      11     182 ..      11     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 7.2e-53
                                       HHHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEEEE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS-- CS
                           AMMECR1   1 lklareaieealkeekkle.eeakeelkekaglFVtlkekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFsp 76 
                                       ++larea++++++++++++ e+ +++++ekag+FVtl+ k+geLRGCiG+ ep ++L+ ++++ A++a+++DpRF++
  gi|386000896|ref|YP_005919195.1|  11 VHLAREALTAYVDRRERIApEDLPPAFSEKAGVFVTLH-KAGELRGCIGYPEPVMDLGVAIVDSAINAGVNDPRFPR 86 
                                       579*****99******999899999*************.77************************************ PP

                                       --HHHHTTEEEEEEEE---EE--......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS- CS
                           AMMECR1  77 vtaeElpeleveVsvLtepepiv......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglr 147
                                       v +eEl+++e+eV+vL++p+p +      +  ++vg+hG+i+++g  s++lLPqva+e+g d ++fl +++ Kagl+
  gi|386000896|ref|YP_005919195.1|  87 VGREELSRIEIEVTVLSPPRPYSvrnrdlPGAVQVGRHGIIVRRGIWSGLLLPQVATEWGFDATDFLCQTCIKAGLP 163
                                       **********************5443344555********************************************* PP

                                       TTCCCSTTSEEEEE-EEEE CS
                           AMMECR1 148 pdewkdseikltryevekf 166
                                       pd w d+e+++  +e+++f
  gi|386000896|ref|YP_005919195.1| 164 PDSWIDEETEVLFFEGQAF 182
                                       ***99**********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1163.09
//
Query:       gi|386000897|ref|YP_005919196.1|  [L=239]
Description: hypothetical protein Mhar_0182 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        3.4    6.9   6.4       0.67    9.2   1.7    2.0  2  Glucos_trans_II  Glucosyl transferase GtrII


Domain annotation for each model (and alignments):
>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2     0.059   1.1e+03     251     270 ..       4      23 ..       1      27 [. 0.62
   2 ?    9.2   1.7   3.8e-05      0.67     183     272 ..      87     198 ..      75     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.059
                   Glucos_trans_II 251 kkkkkksllllllllllllp 270
                                        +++k+ ++l+l++ll+l+ 
  gi|386000897|ref|YP_005919196.1|   4 SIYRKSFAALVLIVLLALSV 23 
                                       56666665577777777765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 3.8e-05
                   Glucos_trans_II 183 iisfvlylllyki.ilklfglelsy..................isellqnlkryys..isnygvkpkklllililli 238
                                       +i +v++l+ ++i + ++ g  ++y                    e  + +k ++s     +g   +  + i +++i
  gi|386000897|ref|YP_005919196.1|  87 FIVMVIALVPFSIvFVNVLGAYHYYgkrqdilekllakngstsQDETQSLIKEFISmePIGVGGVARAAMAIGVIVI 163
                                       45566666666664444455554446666777777777777774444666666666554556666788899999999 PP

                   Glucos_trans_II 239 liilllalllkkkkkkkksll.llllllllllpfa 272
                                       + +++++ll+++ ++ k+ +  +ll+l  +l++++
  gi|386000897|ref|YP_005919196.1| 164 VGVAVVFLLVNASEGDKDIVKeILLILSGALSSVI 198
                                       99*************99988899999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1493.94
//
Query:       gi|386000898|ref|YP_005919197.1|  [L=166]
Description: rubrerythrin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-22   80.3  12.9    2.3e-21   76.7  12.9    2.0  1  Rubrerythrin     Rubrerythrin
     0.0037   17.1   1.4       0.45   10.3   1.7    2.1  2  Haem_oxygenas_2  Iron-containing redox enzyme
     0.0088   16.0   6.1      0.021   14.7   6.1    1.6  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.013   14.3   0.3      0.019   13.8   0.3    1.3  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
      0.061   13.6   0.3         12    6.2   0.1    2.7  2  zf-nanos         Nanos RNA binding domain
      0.081   12.8   0.8          4    7.4   0.1    2.5  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.091   12.4   0.5       0.22   11.1   0.5    1.6  1  RecR             RecR protein
       0.12   12.4   2.2         12    6.0   0.3    2.4  2  Rubredoxin       Rubredoxin
       0.14   12.2   9.7       0.52   10.4   2.0    2.5  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.18   11.8   1.1       0.51   10.3   1.1    1.8  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.19   11.7   0.7        3.8    7.5   0.1    2.4  2  zf_CopZ          Zinc binding domain
       0.21   11.5   0.7         12    5.8   0.0    2.5  2  zf-C2H2_9        C2H2 type zinc-finger (1 copy)
       0.24   11.9   1.0        3.1    8.4   0.1    2.3  2  zf-H2C2_2        Zinc-finger double domain
       0.34   10.8   3.9        3.6    7.5   0.2    2.4  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
        1.2    9.5   7.8        1.3    9.4   1.4    2.3  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        1.5    8.6   4.8          4    7.2   0.3    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        3.6    7.6   5.3         11    6.1   0.3    2.5  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7  12.9   2.1e-24   2.3e-21       1     136 [.       6     120 ..       6     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 2.1e-24
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       + L++A+agE +a r Y ++aeka+ egypq a+lF++ Ae+E+ Ha ++ +++++++ ++e               
  gi|386000898|ref|YP_005919197.1|   6 DALKEAFAGEAQANRKYLAFAEKADqEGYPQAARLFRAAAEAEAVHAINHLRAMNAVKTTKE--------------- 67 
                                       689*****************************************************999988............... PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                              nL+eai+g+++e +emy+ +  +a+ eg+  a++ f+++ + E+ H++++ ++
  gi|386000898|ref|YP_005919197.1|  68 -------NLREAIAGETHEFKEMYPGMIGAAQAEGDRAAERAFRYANDVEEIHARLYHEM 120
                                       .......*************************************************9887 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.7   0.00043      0.45     104     167 ..      13      74 ..       8      84 .. 0.89
   2 ?    4.7   0.0     0.021        23      46      63 ..     108     125 ..      94     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00043
                   Haem_oxygenas_2 104 alEllvsletlklaeelrelgldeeapeyfdlHvtiDnaHaamaleaviellateepeeqedvl 167
                                       a E+++++ +l++ae+  + g + +a + f++ ++++++Ha   l +++++++t++++++e+++
  gi|386000898|ref|YP_005919197.1|  13 AGEAQANRKYLAFAEKADQEGYP-QAARLFRAAAEAEAVHAINHL-RAMNAVKTTKENLREAIA 74 
                                       5699*******************.899******************.*********977777766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                   Haem_oxygenas_2  46 dlernHvelyrrllkalG 63 
                                       d e+ H++ly++++++l 
  gi|386000898|ref|YP_005919197.1| 108 DVEEIHARLYHEMMESLE 125
                                       55777**********997 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   6.1     2e-05     0.021       2     104 ..       6     122 ..       5     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH....... CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee....... 71 
                                       +aL e++a e +a  +yla+a  ++++g+++ a +f+  ae e  ha   +  ++a       t+  l e       
  gi|386000898|ref|YP_005919197.1|   6 DALKEAFAGEAQANRKYLAFAEKADQEGYPQAARLFRAAAEAEAVHAINHLRAMNAVKT----TKENLREaiageth 78 
                                       79*********************************************988888888877....33322223334455 PP

                                       .........C-SSSS..CSSHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  72 .........ieapke..fgsveevleaalehekkvteslrelie 104
                                                i a +   +  +e +++ a + e+   + ++e++e
  gi|386000898|ref|YP_005919197.1|  79 efkemypgmIGAAQAegDRAAERAFRYANDVEEIHARLYHEMME 122
                                       55556666643333343446777777777777777777777666 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.8e-05     0.019     505     537 ..     132     165 ..     114     166 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                       --EEEETT.--EESS...SB-TTT--BE.EEEEEES CS
                              NRDD 505 pkidvCnecgykgei...ekCpkCgseeevevirRi 537
                                        ++ vC+ cg++ e+   e+Cp+Cg +   +++rRi
  gi|386000898|ref|YP_005919197.1| 132 FPYYVCPVCGMTAEReppERCPVCGVK--GDRFRRI 165
                                       57789******888779*99*****44..6999998 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.011        12      34      44 ..     135     145 ..     131     147 .. 0.87
   2 ?    4.6   0.0     0.036        37      35      45 ..     151     161 ..     149     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                          zf-nanos  34 yvCpiCgatgd 44 
                                       yvCp+Cg t +
  gi|386000898|ref|YP_005919197.1| 135 YVCPVCGMTAE 145
                                       9******9976 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.036
                          zf-nanos  35 vCpiCgatgdk 45 
                                        Cp+Cg +gd+
  gi|386000898|ref|YP_005919197.1| 151 RCPVCGVKGDR 161
                                       6********96 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0037         4      11      22 ..     132     143 ..     128     143 .. 0.77
   2 ?    3.4   0.1     0.065        69      14      21 ..     150     157 ..     144     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                         zf-C2H2_3  11 fgasqCkeCgMv 22 
                                       f    C++CgM+
  gi|386000898|ref|YP_005919197.1| 132 FPYYVCPVCGMT 143
                                       55566******7 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.065
                         zf-C2H2_3  14 sqCkeCgM 21 
                                       ++C++Cg 
  gi|386000898|ref|YP_005919197.1| 150 ERCPVCGV 157
                                       67****96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00021      0.22      19      34 ..     137     155 ..     135     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                       -TTT--EESSSS...-CCC CS
                              RecR  19 CsrCgnlteedl...CaIC 34 
                                       C++Cg  +e+++   C++C
  gi|386000898|ref|YP_005919197.1| 137 CPVCGMTAEREPperCPVC 155
                                       ***********7777**** PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.013        13      35      44 ..     135     144 ..     130     146 .. 0.81
   2 ?    6.0   0.3     0.012        12      36      47 .]     151     162 ..     149     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                                       -BBTTTB-BG CS
                        Rubredoxin  35 WvCPdCgvek 44 
                                       +vCP+Cg++ 
  gi|386000898|ref|YP_005919197.1| 135 YVCPVCGMTA 144
                                       7999999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                                       BBTTTB-BGGGE CS
                        Rubredoxin  36 vCPdCgvekeqF 47 
                                       +CP+Cgv+ + F
  gi|386000898|ref|YP_005919197.1| 151 RCPVCGVKGDRF 162
                                       6******98877 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 ?   10.4   2.0    0.0005      0.52       2      13 ..     137     148 ..     136     150 .. 0.91
   2 ?    6.1   1.1     0.011        12       1       6 [.     151     156 ..     151     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
                    DNA_ligase_ZBD   2 CPvCGsavvRee 13 
                                       CPvCG  ++Re+
  gi|386000898|ref|YP_005919197.1| 137 CPVCGMTAEREP 148
                                       **********86 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                    DNA_ligase_ZBD   1 hCPvCG 6  
                                       +CPvCG
  gi|386000898|ref|YP_005919197.1| 151 RCPVCG 156
                                       5****9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   0.00049      0.51      31      58 ..     137     161 ..     135     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00049
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfeadr 58 
                                       C++Cg + ++   +   +Cp Cg++ dr
  gi|386000898|ref|YP_005919197.1| 137 CPVCGMTAER---EPPERCPVCGVKGDR 161
                                       **********...44457******9998 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.17   1.8e+02       3      11 ..     136     144 ..     134     146 .. 0.79
   2 ?    7.5   0.1    0.0036       3.8       2      15 ..     150     163 ..     149     166 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.17
                                       B-TTT--B- CS
                           zf_CopZ   3 kCPvCgkkG 11 
                                        CPvCg  +
  gi|386000898|ref|YP_005919197.1| 136 VCPVCGMTA 144
                                       6****9765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
                                       -B-TTT--B-EEE- CS
                           zf_CopZ   2 kkCPvCgkkGkkVk 15 
                                       ++CPvCg kG + +
  gi|386000898|ref|YP_005919197.1| 150 ERCPVCGVKGDRFR 163
                                       58********9866 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.056        59       3      11 ..     136     144 ..     134     147 .. 0.83
   2 ?    5.8   0.0     0.011        12       3      15 ..     151     163 ..     149     166 .] 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.056
                                       B-TTT--B- CS
                         zf-C2H2_9   3 lCPvCevkf 11 
                                       +CPvC +  
  gi|386000898|ref|YP_005919197.1| 136 VCPVCGMTA 144
                                       7****9976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                       B-TTT--B-SSHH CS
                         zf-C2H2_9   3 lCPvCevkfnswk 15 
                                       +CPvC vk + ++
  gi|386000898|ref|YP_005919197.1| 151 RCPVCGVKGDRFR 163
                                       7******987665 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0029       3.1      11      23 ..     129     143 ..     113     146 .. 0.74
   2 ?    1.9   0.1      0.33   3.5e+02      16      22 ..     151     157 ..     149     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                         zf-H2C2_2  11 ge.kp.yeCplCdka 23 
                                       ge +p y Cp+C+ +
  gi|386000898|ref|YP_005919197.1| 129 GEsFPyYVCPVCGMT 143
                                       6735689*****976 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.33
                         zf-H2C2_2  16 eCplCdk 22 
                                        Cp+C+ 
  gi|386000898|ref|YP_005919197.1| 151 RCPVCGV 157
                                       5****86 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0034       3.6       3      14 ..     136     147 ..     136     147 .. 0.87
   2 ?    4.2   0.4     0.038        40       2       8 ..     150     156 ..     150     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0034
                                       B-TTT--BBEEE CS
                      zf-FPG_IleRS   3 pCpRCwryierv 14 
                                       +Cp+C+++ er+
  gi|386000898|ref|YP_005919197.1| 136 VCPVCGMTAERE 147
                                       6******99885 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                                       SB-TTT- CS
                      zf-FPG_IleRS   2 epCpRCw 8  
                                       e+Cp+C+
  gi|386000898|ref|YP_005919197.1| 150 ERCPVCG 156
                                       79****9 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6     0.078        82       6      10 ..     137     141 ..     135     143 .. 0.90
   2 ?    9.4   1.4    0.0012       1.3       6      17 ..     152     165 ..     147     166 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.078
                                       -TTTT CS
                    Prim_Zn_Ribbon   6 CPvCG 10 
                                       CPvCG
  gi|386000898|ref|YP_005919197.1| 137 CPVCG 141
                                       ****9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                       -TTTT-T.TTEE.E CS
                    Prim_Zn_Ribbon   6 CPvCGGr.DrFr.f 17 
                                       CPvCG + DrFr +
  gi|386000898|ref|YP_005919197.1| 152 CPVCGVKgDRFRrI 165
                                       *****9879**955 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5     0.076        80       6      11 ..     136     141 ..     136     143 .. 0.93
   2 ?    7.2   0.3    0.0038         4       4      17 ..     149     164 ..     146     166 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.076
                           zf-RRN7   6 pCgvCg 11 
                                       +C+vCg
  gi|386000898|ref|YP_005919197.1| 136 VCPVCG 141
                                       7****9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0038
                           zf-RRN7   4 gppCgvCgc..rsftl 17 
                                        ++C+vCg   ++f+ 
  gi|386000898|ref|YP_005919197.1| 149 PERCPVCGVkgDRFRR 164
                                       589*****76667766 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.6     0.069        72      20      27 ..     136     143 ..     127     147 .. 0.83
   2 ?    6.1   0.3     0.011        11      20      32 ..     151     165 ..     144     166 .] 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.069
                     Zn_Tnp_IS1595  20 vCPhCgsr 27 
                                       vCP Cg +
  gi|386000898|ref|YP_005919197.1| 136 VCPVCGMT 143
                                       8****965 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                     Zn_Tnp_IS1595  20 vCPhCgsr..kayri 32 
                                       +CP Cg++  +++ri
  gi|386000898|ref|YP_005919197.1| 151 RCPVCGVKgdRFRRI 165
                                       6*****997666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      789  (0.0440069); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 976.38
//
Query:       gi|386000899|ref|YP_005919198.1|  [L=318]
Description: Phosphoribulokinase/uridine kinase family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-41  142.1   0.0    2.8e-41  141.4   0.0    1.3  1  PRK             Phosphoribulokinase / Uridine kinase family
    0.00057   20.4   0.0    0.00087   19.8   0.0    1.4  1  AAA_18          AAA domain
     0.0037   17.2   0.0     0.0061   16.6   0.0    1.3  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
     0.0065   16.2   0.0     0.0091   15.7   0.0    1.2  1  AAA_30          AAA domain
     0.0076   16.1   0.2      0.015   15.1   0.2    1.4  1  zf-CGNR         CGNR zinc finger
     0.0089   16.4   0.0      0.016   15.6   0.0    1.5  1  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.025   14.5   0.0    1.3  1  NACHT           NACHT domain
      0.024   13.9   0.0      0.043   13.1   0.0    1.4  1  Zeta_toxin      Zeta toxin
      0.026   15.0   0.0      0.049   14.1   0.0    1.4  1  ABC_tran        ABC transporter
      0.027   14.6   0.0      0.051   13.7   0.0    1.5  1  AAA_33          AAA domain
      0.029   14.6   0.0      0.051   13.8   0.0    1.4  1  AAA_22          AAA domain
      0.035   13.8   0.1        2.2    8.0   0.0    2.1  2  Cytidylate_kin  Cytidylate kinase
      0.065   13.3   0.1       0.14   12.3   0.1    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.078   12.1   0.1       0.11   11.7   0.1    1.2  1  NB-ARC          NB-ARC domain
       0.08   13.4   0.0       0.13   12.7   0.0    1.3  1  AAA_23          AAA domain
       0.14   10.8   0.0       0.19   10.3   0.0    1.1  1  AAA_13          AAA domain
       0.14   11.9   0.0       0.39   10.5   0.0    1.7  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
       0.15   11.9   0.1       0.26   11.0   0.1    1.4  1  AAA_29          P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   2.8e-44   2.8e-41       1     189 [.      13     187 ..      13     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 2.8e-44
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyev 77 
                                       v++vag+SG+Gktt++r ++ ++g+e+v          ++     +d+++ +r+++  + ++ l+pean +dll e 
  gi|386000899|ref|YP_005919198.1|  13 VVAVAGDSGSGKTTLSRGIRRLLGEEAVS--------TFS----MDDYHSLDREERRVRGMTPLNPEANRLDLLAEH 77 
                                       79**********************77776........444....579****************************** PP

                               PRK  78 lkelkegkkvdkpiYsheteeaapdkeeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDiae 154
                                       l++l+ g+++ kp+Y+h+ +e     +    +  vl++EGlh+ly ++++  +d+ i+vd+s  ++  +k+ RD  +
  gi|386000899|ref|YP_005919198.1|  78 LRSLRLGETIAKPVYDHSVGEFRE--PVPFRSGPVLILEGLHPLYTQKLRREVDFGIFVDPSRAVKRRWKIRRDCGD 152
                                       *********************988..56667789******************************************* PP

                               PRK 155 RGrsleavldsilrrkpdyvnyikpqfseadliiq 189
                                       RG++++ v+++il+r pdy+ y++ q+ +a+++++
  gi|386000899|ref|YP_005919198.1| 153 RGYQRDLVMAEILAREPDYKLYVDVQKVYAEAVVK 187
                                       ********************************997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.7e-07   0.00087       1      52 [.      14      62 ..      14     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.7e-07
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrl 52
                                      ++++G +G+GKttl++ ++++l  g++  ++++ +++   + +e  +     
  gi|386000899|ref|YP_005919198.1| 14 VAVAGDSGSGKTTLSRGIRRLL--GEEAVSTFSMDDYHSLDREE-RRVRGMT 62
                                      689******************9..99999999999999888888.3444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.1e-06    0.0061      20      54 ..      12      44 ..       1      58 [. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.1e-06
                                      EEEEEEESTTSSHHHHHHHHHHHTT------TTTT CS
                              TsaE 20 dvilLeGdLGaGKTtlvrglakalgveevkSPTFt 54
                                       v++  Gd G+GKTtl+rg+ + lg e+v+  TF+
  gi|386000899|ref|YP_005919198.1| 12 FVVAVAGDSGSGKTTLSRGIRRLLGEEAVS--TFS 44
                                      36999******************9987664..555 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   9.2e-06    0.0091      15      80 ..       7      94 ..       1     126 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.2e-06
                            AAA_30 15 tsgdr.vavltGpAGtGKttalkalreaweaag................grviglAptgkaAkvLa...eelgi..eas 71
                                      +sg+  v+++ G  G+GKtt+ +++r+++ ++                 +rv g++p +  A++L    e+l     ++
  gi|386000899|ref|YP_005919198.1|  7 GSGRVfVVAVAGDSGSGKTTLSRGIRRLLGEEAvstfsmddyhsldreeRRVRGMTPLNPEANRLDllaEHLRSlrLGE 85
                                      5555415667899****************99988999999999999999999999999999999873333322233566 PP

                            AAA_30 72 tiakllkrl 80
                                      tiak ++ +
  gi|386000899|ref|YP_005919198.1| 86 TIAKPVYDH 94
                                      666666555 PP

>> zf-CGNR  CGNR zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.5e-05     0.015      13      35 ..     132     154 ..     131     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                       EEE--SSS-----SSHH.HHHHH CS
                           zf-CGNR  13 vfvDtSrngsrrWCsmraCGnra 35 
                                       +fvD Sr+ +rrW   r+CG r 
  gi|386000899|ref|YP_005919198.1| 132 IFVDPSRAVKRRWKIRRDCGDRG 154
                                       6*******************995 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.016      25      58 ..      12      43 ..       3     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrg 58
                                       +v + G+sG+GK++l r ++r l ++   + + 
  gi|386000899|ref|YP_005919198.1| 12 FVVAVAGDSGSGKTTLSRGIRRLLGEEA--VSTF 43
                                      5799*****************8888873..3333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.5e-05     0.025       2      28 ..      13      39 ..      12      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                      +v++ G++GsGKTtL +++ +++ e+ 
  gi|386000899|ref|YP_005919198.1| 13 VVAVAGDSGSGKTTLSRGIRRLLGEEA 39
                                      689****************99988776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-05     0.043      18      57 ..      13      51 ..       3      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      ++ ++G +G+GK++l++ +++ l+ ++ v +++ Dd+ +l
  gi|386000899|ref|YP_005919198.1| 13 VVAVAGDSGSGKTTLSRGIRRLLG-EEAVSTFSMDDYHSL 51
                                      7889*****************995.666668899998776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     5e-05     0.049      13      39 ..      13      39 ..      10      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpte 39
                                      +va+ G++G+GK+tL + + +ll  ++
  gi|386000899|ref|YP_005919198.1| 13 VVAVAGDSGSGKTTLSRGIRRLLGEEA 39
                                      689**************9999986533 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.1e-05     0.051       1      35 [.      13      50 ..      13      92 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg...avllssdtlrr 35
                                      +v + G +GsGK+tl++++ + lg   + + s d++++
  gi|386000899|ref|YP_005919198.1| 13 VVAVAGDSGSGKTTLSRGIRRLLGeeaVSTFSMDDYHS 50
                                      78899***********9886666644366666666444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.1e-05     0.051       8      65 ..      14      82 ..      12     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsst.sskdllrellralg 65
                                      ++v G sG+GKTtl r +++ l eea  +           e+++v  +t+ +++ ++ dll e lr l 
  gi|386000899|ref|YP_005919198.1| 14 VAVAGDSGSGKTTLSRGIRRLLGEEAVSTFsmddyhsldrEERRVRGMTPLNPEaNRLDLLAEHLRSLR 82
                                      6899*****************988766666888888888666666677777777777777777666665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0022       2.2       1      32 [.      14      45 ..      14      64 .. 0.89
   2 ?    3.8   0.0     0.042        42     129     197 ..     127     194 ..     111     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgal 32
                                      +a+ G +gsGK +++r + + lg + ++t ++
  gi|386000899|ref|YP_005919198.1| 14 VAVAGDSGSGKTTLSRGIRRLLGEEAVSTFSM 45
                                      7999****************999999998776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.042
                                       T-SEEEEEE--HHHHHHHHHHHHHHTT--.--HHHHHHHHHHHHHHHHCTSSS-S.---TT-EEEETTTS- CS
                    Cytidylate_kin 129 daelKifldAsveeRakRRlkqlkakgts.vsleellaeikeRDklDkerevgpL.klaedaliidtsklt 197
                                       + ++ if+d s    +kRR+k +++ g    + + ++aei +R   D +  v+   + ae ++ id ++l+
  gi|386000899|ref|YP_005919198.1| 127 EVDFGIFVDPSR--AVKRRWKIRRDCGDRgYQRDLVMAEILAREP-DYKLYVDVQkVYAEAVVKIDDTRLG 194
                                       566777877664..579*****99999998999999*******75.4444444330446666667777765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.14       2      27 ..      14      39 ..      13      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      EEEESSTTSSHHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrg 27
                                      +++++ +G+GKTtl+ ++ r+l ++ 
  gi|386000899|ref|YP_005919198.1| 14 VAVAGDSGSGKTTLSRGIRRLLGEEA 39
                                      7899*************999998855 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.11      18      41 ..       9      32 ..       1      42 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      SCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqil 41
                                         +vva+ G  G+GKttl++ i 
  gi|386000899|ref|YP_005919198.1|  9 GRVFVVAVAGDSGSGKTTLSRGIR 32
                                      34589**************99875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.13      23      48 ..      15      41 ..      12      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            AAA_23 23 lItGpNGaGKTTildAiklaLyget.p 48
                                      ++ G+ G+GKTT+ + i+  L++e+ +
  gi|386000899|ref|YP_005919198.1| 15 AVAGDSGSGKTTLSRGIRRLLGEEAvS 41
                                      678******************998733 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.19      23      52 ..      18      47 ..      16      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkfangs 52
                                      G  G+GKTtLSr +r l  +e+++ f++  
  gi|386000899|ref|YP_005919198.1| 18 GDSGSGKTTLSRGIRRLLGEEAVSTFSMDD 47
                                      667**************9889888887665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.39       2      25 ..      14      37 ..      13      73 .. 0.79
   2 ?   -2.1   0.0       2.6   2.6e+03      63     108 ..     196     241 ..     164     255 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                       ++ G+ gsGK++L + ++ l + 
  gi|386000899|ref|YP_005919198.1| 14 VAVAGDSGSGKTTLSRGIRRLLGE 37
                                      5789***************99764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                            AAA_21  63 eeflsqgvryryglrlersqv.eeklssvetllesgllldkrsleee 108
                                       +  +++++  ry++rl ++ + + +  +  +  +s l++ ++ ++++
  gi|386000899|ref|YP_005919198.1| 196 P-SFLEDPGERYSVRLIQEVLeAGPSAVDLKIDLSALFSLPDGEFSI 241
                                       3.344444444555554444444444444444444444444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00026      0.26      25      39 ..      14      28 ..       4      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                            AAA_29 25 tlltGpsGsGKSTll 39
                                      + ++G+sGsGK+Tl 
  gi|386000899|ref|YP_005919198.1| 14 VAVAGDSGSGKTTLS 28
                                      6799*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1961.95
//
Query:       gi|386000900|ref|YP_005919199.1|  [L=145]
Description: HTH-type transcriptional regulatory protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   13.3   0.0      0.067   13.0   0.0    1.1  1  Antibiotic_NAT  Aminoglycoside 3-N-acetyltransferase


Domain annotation for each model (and alignments):
>> Antibiotic_NAT  Aminoglycoside 3-N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-06     0.067     111     191 ..      58     136 ..      48     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-06
                                       TTSHHHHHHHSTEEEEEEB--GGG-TTHHHHTTSS..S---EEEEEEEEEE.TTEEEEEEEEEE-.--GCGHHHHHH CS
                    Antibiotic_NAT 111 egSplgrlyelggkvLllGvglernTalHlaEeradvpnkrldeeeapvieeegervwveyedve.ldsedfeklga 186
                                        +Sp+  + + +  v+l Gvg  + T+l  a  + ++  + +++++++vi  +ge++  ++e+++  +s+++e++g+
  gi|386000900|ref|YP_005919199.1|  58 AQSPFNAITQKEDLVVLTGVGKFSSTMLKKARLMSSL--SIVTKTFSAVIV-DGESKVERVEETAvIESRELERIGK 131
                                       69*******************9999******999975..445888888885.6666777888877455599**9999 PP

                                       HHHTT CS
                    Antibiotic_NAT 187 aleee 191
                                         e +
  gi|386000900|ref|YP_005919199.1| 132 TSEFA 136
                                       87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 957.79
//
Query:       gi|386000901|ref|YP_005919200.1|  [L=138]
Description: HTH-type transcriptional regulatory protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 932.37
//
Query:       gi|386000902|ref|YP_005919201.1|  [L=418]
Description: tRNA(Ile2) 2-agmatinylcytidine synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-42  142.5   0.0      1e-41  141.7   0.0    1.5  1  DUF1743          Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.036   14.1   0.0    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.087   12.8   0.4       0.17   11.8   0.4    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.28   10.6   2.0       0.54    9.6   2.0    1.4  1  zf-TFIIB         Transcription factor zinc-finger
       0.42   10.6   3.8       0.87    9.6   3.8    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.73    9.8   9.0        1.5    8.8   9.0    1.6  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   0.0   3.4e-45     1e-41       2     116 .]     137     248 ..     136     248 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 3.4e-45
                                       THHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEE CS
                           DUF1743   2 rgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlf 77 
                                       rg+iGA+aa+ga++  +d+tyEllaYr+perwg +re+de sv++ade typ+t+d+vD+++++vv +Ph+ dpvlf
  gi|386000902|ref|YP_005919201.1| 137 RGLIGALAAVGAEF--SDWTYELLAYRRPERWGtPREIDEASVWRADELTYPRTWDTVDHHNQKVVFAPHSGDPVLF 211
                                       89**********55..58*********************************************************** PP

                                       EEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  78 Girgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       Girge pe l++a+++i s  e +e+++++rtnqgtdah
  gi|386000902|ref|YP_005919201.1| 212 GIRGEGPEPLREALEAIGS--EAYERAVIYRTNQGTDAH 248
                                       *******************..****************99 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.2e-05     0.036      15      61 ..     277     327 ..     263     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       ETTEEEEEEE..ETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEEC CS
                   tRNA_anti-codon  15 ggkvifidlr..Dgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrr 61 
                                       +g++if+ l+  Dg   i++ +f   +++++    l +Gd+++v+G vkr 
  gi|386000902|ref|YP_005919201.1| 277 EGGHIFFPLEaeDGNSAINCAAFEptKNFRDRVRALLPGDLIEVYGAVKRG 327
                                       6788888765116678999999997777777777788************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   5.8e-05      0.17      26      55 ..     345     374 ..     331     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                    OrfB_Zn_ribbon  26 yTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                        T   C+ C +++k a  g+ ++C++C ++
  gi|386000902|ref|YP_005919201.1| 345 PTAPLCPSCRRRMKSAGRGQGYRCRRCRTR 374
                                       47789**********************976 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.0   0.00018      0.54       2      26 ..     350     372 ..     349     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                          zf-TFIIB   2 CPkCqdeleeser.ggveidyCpqCr 26 
                                       CP+C+  ++ + r +g   ++C +Cr
  gi|386000902|ref|YP_005919201.1| 350 CPSCRRRMKSAGRgQG---YRCRRCR 372
                                       ************9666...5555554 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 ?    9.6   3.8   0.00029      0.87      16      45 ..     345     373 ..     338     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
                     Zn_Tnp_IS1595  16 pngfvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       p+ + CP C  r  +a r    + ++C++Cr+
  gi|386000902|ref|YP_005919201.1| 345 PTAPLCPSCRRRmkSAGRG---QGYRCRRCRT 373
                                       56689*****664333333...45******97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.0   0.00051       1.5       7      33 ..     350     374 ..     349     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00051
                    Zn_ribbon_SprT   7 CtgCgreythhlsi.rrhnYrCrrCkgt 33 
                                       C++C+    +  s  r + YrCrrC+ +
  gi|386000902|ref|YP_005919201.1| 350 CPSCR---RRMKSAgRGQGYRCRRCRTR 374
                                       *****...88888856666******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2891.86
//
Query:       gi|386000903|ref|YP_005919202.1|  [L=272]
Description: Manganese-dependent inorganic pyrophosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-23   82.5   0.3    5.5e-23   81.7   0.3    1.4  1  DHHA2     DHHA2 domain
    1.2e-19   70.4   0.1      2e-19   69.7   0.1    1.4  1  DHH       DHH family
  ------ inclusion threshold ------
      0.081   12.6   0.0       0.11   12.2   0.0    1.2  1  CHASE2    CHASE2 domain
      0.093   12.5   0.0       0.14   11.9   0.0    1.4  1  DSBA      DSBA-like thioredoxin domain


Domain annotation for each model (and alignments):
>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.3   1.2e-26   5.5e-23       2     143 .]     147     270 ..     146     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 1.2e-26
                                       HHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHHHHHHHHHHH.HHT-SEEEEEEE.. CS
                             DHHA2   2 elkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkgellaalekfaeerkldllvlmttfe 78 
                                       ++ +aksd+s++++ ++++ DyK f+   g k g+++++v++ + l+  rk+e+l+++ek++++++l ++++m+t  
  gi|386000903|ref|YP_005919202.1| 147 AMLTAKSDISSKTAMEIVKGDYKHFD-FAGTKAGVGQIEVMDLSVLVP-RKKEILETMEKVRKDEGLSFVLIMLT-- 219
                                       5899**********************.****************99998.99***********9999*********.. PP

                                       ...ETTT..EEEEEE...STTHHHHHT---B.T.EEET...............T---HHHHTHHHHHHH CS
                             DHHA2  79 eegdirr..elllaaldaaeklaealekase.e.leLeewkegaewrrvykqgnvkasRKqvaPllrea 143
                                          d+++  + ll++ + ++k+++a+e + e + +                 ++v +++Kqv+P l++a
  gi|386000903|ref|YP_005919202.1| 220 ---DVMKeaSDLLFVGSPVDKFEKAFEGKMEnNaIY---------------KKGVLSRKKQVIPPLEAA 270
                                       ...777769666666466688999999885433233...............34************9875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.1   4.5e-23     2e-19      24     101 .]      36     110 ..       5     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.5e-23
                                       CECS--TCGGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  24 llvDhneksqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllg 100
                                       +lvDhne  qave+  ++ea + ++iDHH++g +++t +pi+f+nepvgsta+iv  ++++ k+ iske+a++++++
  gi|386000903|ref|YP_005919202.1|  36 VLVDHNEVGQAVEN--IKEATIFEVIDHHKIG-DITTPNPIFFHNEPVGSTATIVSAMYDQYKVPISKEMAGVMMSA 109
                                       89************..****************.*******************************************9 PP

                                       H CS
                                       x RF
                               DHH 101 i 101
                                       i
  gi|386000903|ref|YP_005919202.1| 110 I 110
                                       8 PP

>> CHASE2  CHASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.11     167     222 ..      51     116 ..       3     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                            CHASE2 167 ptvsladvle.........vppeefkdkiVliGata...tglkdlfstPfssempgveihAnalsnll 222
                                       ++ ++++v++          +p++f++    +G+ta   + ++d++ +P+s+em+gv++ A   +++l
  gi|386000903|ref|YP_005919202.1|  51 KEATIFEVIDhhkigdittPNPIFFHNEP--VGSTAtivSAMYDQYKVPISKEMAGVMMSAILSDTVL 116
                                       55555566544555554434445666666..599988889**********99*********9999999 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.14      30      79 ..     164     216 ..     127     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                       EEEEEEE-SSSCHHHHCT.S.GGG...SHHHHHHHHHHHHHHHHHHT....GG CS
                              DSBA  30 vkvvlrpfelagakkasgnvgpse...lpeklkylledlkrlaeaegiplrfp 79 
                                       vk  +++f++ag+k  +g + + +   l ++ k++le ++++++ eg+++ + 
  gi|386000903|ref|YP_005919202.1| 164 VKGDYKHFDFAGTKAGVGQIEVMDlsvLVPRKKEILETMEKVRKDEGLSFVLI 216
                                       55579********77666655555999999******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1970.04
//
Query:       gi|386000904|ref|YP_005919203.1|  [L=228]
Description: thymidylate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  109.9   0.0    1.4e-31  109.6   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
     0.0057   16.8   0.1      0.042   14.0   0.1    2.2  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.037   14.4   0.0       0.22   12.0   0.0    2.3  2  AAA_17           AAA domain
      0.054   13.8   0.0       0.42   10.9   0.0    2.0  2  AAA_22           AAA domain
        0.2   11.6   0.0       0.46   10.4   0.0    1.6  2  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0     4e-35   1.4e-31       1     183 [.       8     215 ..       8     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 4e-35
                                       EEESTTSSHHHHHHHHHHHHHH.....TTE.EEEESSSTTSHHHHHHHHHHH.......TCS---HHH.....HHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlke.....egikvvltrepggteiGekirelll.......keeeleeqt.....eall 60 
                                       +EG+DG+GK+t ++ +++  +e     eg++ ++t ep+ ++ G+++re l             + ++     e++l
  gi|386000904|ref|YP_005919203.1|   8 FEGIDGSGKSTALAGVARMASEgelavEGRRFLFTAEPTYGDEGRLLRERLRgpaaeggG---AAAMRagqmeELFL 81 
                                       8************9999875542222278889*******************998753331...2222256678**** PP

                                       HHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHHHHHHT.TTTTTCHHHHHHGGGTTS...E-SEEEEEESSHHHHHT CS
                   Thymidylate_kin  61 faadriehleekikpalkqgktvivdRylfSslaYqga.kegvdldlvlslnedvll...kPdltflldvdpevalk 133
                                       f+ad+++hl+e ++pal+ g +v++dRy +S +aYqga  ++v  d + +++e   +    Pd t+l+++dp+ a++
  gi|386000904|ref|YP_005919203.1|  82 FMADHARHLAETVIPALEGGMVVVSDRYSDSRAAYQGAtLREVFSDPMERVRELHRPwsvVPDRTILFSIDPALAVE 158
                                       **************************************77888888877777765556779**************** PP

                                       SCCTTSS......TTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHHH CS
                   Thymidylate_kin 134 Rlakrde......ldeeeeeqldflrkvrerylelak.ederiliidasksieevhe 183
                                       R+  r+e      +  e++e+++flr v e+++ la+ e+ r+++idas++i ev +
  gi|386000904|ref|YP_005919203.1| 159 RCLSRGEadpsapKGPEKFEREEFLRLVAENFKTLARlEPRRFVVIDASRPIAEVLA 215
                                       *******9998877799***********************************99965 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.2e-05     0.042       1     122 [.       5     167 ..       5     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg..........avllssdt.......lrrrlfg..........tdqqskt.... 46 
                                       l+ + G  GsGKst + ++++             + + +++t       lr+rl+g                +    
  gi|386000904|ref|YP_005919203.1|   5 LITFEGIDGSGKSTALAGVARMASegelavegrrFLFTAEPTygdegrlLRERLRGpaaegggaaaM-----Ragqm 76 
                                       7899***************877666333333344444444447777777666666654443333321.....03333 PP

                            AAA_33  47 .dytrvldrlyqilnelarkalsagrnvildat...............nlsrrerarflklarrlg.vpvrivvvet 106
                                        ++  +  +  ++l+e++  al+ g  v+ d                 + ++  ++r+++l r ++ vp+r + ++ 
  gi|386000904|ref|YP_005919203.1|  77 eELFLFMADHARHLAETVIPALEGGMVVVSDRYsdsraayqgatlrevFSDP--MERVRELHRPWSvVPDRTILFSI 151
                                       3444444555556666665555555555553333444444444444434444..44555554444426899999999 PP

                            AAA_33 107 deetlkeRlakRaang 122
                                       d++++ eR   R ++ 
  gi|386000904|ref|YP_005919203.1| 152 DPALAVERCLSRGEAD 167
                                       9999999998888864 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     6e-05      0.22       2     123 ..      10     165 ..       9     178 .. 0.70
   2 ?   -1.5   0.0      0.87   3.1e+03      95     113 ..     191     209 ..     172     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                                       E-TTSSHHHHHHHHHH................HHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklve................kygfthlsaGdllreeakrggl.akardemrklpleekkelqkea 61 
                                       G+ GsGK+t+++ +++                  + t+   G llre  +   + +    +mr +++ee   +++  
  gi|386000904|ref|YP_005919203.1|  10 GIDGSGKSTALAGVARmasegelavegrrflfTAEPTYGDEGRLLRERLRGPAAeGGGAAAMRAGQMEELFLFMADH 86 
                                       899***********986667766666665555557777888999999988775534457889999999988777777 PP

                                       HHHHHHHH...HSSE.EEEEE-SEEEETTEEEESSHHHHHH.............HH..SEEEEEE--HHHHHHHHHH CS
                            AAA_17  62 aekiaeea...kkkg.vlvdghprikeqagfldglpkevle.............elkpdaiilleadpeeilerrlk 121
                                       a+++ae+     ++g v+v   ++ + +a +     +ev+              ++ pd  il+++dp   +er+l+
  gi|386000904|ref|YP_005919203.1|  87 ARHLAETVipaLEGGmVVVSDRYS-DSRAAYQGATLREVFSdpmervrelhrpwSVVPDRTILFSIDPALAVERCLS 162
                                       777777644554444255555554.45566666667788754444455455555556999*********99999999 PP

                                       H.T CS
                            AAA_17 122 d.r 123
                                       + +
  gi|386000904|ref|YP_005919203.1| 163 RgE 165
                                       733 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.87
                                       HHHHHH..SEEEEEE--HH CS
                            AAA_17  95 evleelkpdaiilleadpe 113
                                       ++l+ l+p  +++++a+  
  gi|386000904|ref|YP_005919203.1| 191 KTLARLEPRRFVVIDASRP 209
                                       4567888999999998864 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.42       9      91 ..       7      92 ..       2      99 .. 0.78
   2 ?    0.6   0.0      0.18   6.3e+02      71      98 ..     175     205 ..     150     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...erlsseellealeq 84
                                      +  G  G+GK+t l+ +++ + e + a e r+ +++ +++ + + + l+++l     +++ a   + ++ eel+  +++
  gi|386000904|ref|YP_005919203.1|  7 TFEGIDGSGKSTALAGVARMASEGELAVEGRRFLFTAEPTYGDEGRLLRERLRGPAAEGGGAaamRAGQMEELFLFMAD 85
                                      566999***************9888777766666677777777888888888777776666688888888888888888 PP

                            AAA_22 85 alrarav 91
                                      ++r+ a 
  gi|386000904|ref|YP_005919203.1| 86 HARHLAE 92
                                      8888776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                            AAA_22  71 erlsseellealeqalrarav...ielliiD 98 
                                       e  ++ee+l+++++++++ a+   +++++iD
  gi|386000904|ref|YP_005919203.1| 175 EKFEREEFLRLVAENFKTLARlepRRFVVID 205
                                       4457788889999999999999999999998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.46       3      38 ..       6      41 ..       4      50 .. 0.85
   2 ?   -3.3   0.0         2   7.3e+03      71      89 ..     188     206 ..     178     222 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEE CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpqgafklvF 38
                                      +  +G  GsGK+t l+++a+ + eg+l  +  +++F
  gi|386000904|ref|YP_005919203.1|  6 ITFEGIDGSGKSTALAGVARMASEGELAVEGRRFLF 41
                                      667999*******************99876666666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                                       CCHHHHCCSCCCEEEEEE- CS
                             NACHT  71 evwavllelperlLlilDg 89 
                                       e ++ l++l+ r   ++D+
  gi|386000904|ref|YP_005919203.1| 188 ENFKTLARLEPRRFVVIDA 206
                                       4455666666666667765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1744.17
//
Query:       gi|386000905|ref|YP_005919204.1|  [L=228]
Description: hypothetical protein Mhar_0190 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-25   88.6   0.0    1.6e-24   86.6   0.0    1.7  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.027   14.5   0.0      0.049   13.7   0.0    1.4  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   1.7e-28   1.6e-24      14     168 ..      43     198 ..      38     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.7e-28
                        MAF_flag10  14 slkellnkfkgnkpaiivgaGPSLeknlel.lkelr........dkaviiaadtalkaLlkegIkPDivvs.lDpqe 80 
                                       s+kel + ++g ++++++g+GPSL   l+  l   +        +++viiaad+a+++ l +g  PD++v+ lD+  
  gi|386000905|ref|YP_005919204.1|  43 SIKELASMIRG-RKVLVCGNGPSLPRGLAEaLGGGEgspeplkrSDLVIIAADGATTPILAAGALPDVIVTdLDG-- 116
                                       47888888899.************988654155544667777779******************************.. PP

                        MAF_flag10  81 asyevfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfk 157
                                           ++   +++g++ +v+a+g+n  +lk+y +++  ++ ++tq ++ l   +++ +fgG++++++a++lA+++g+ 
  gi|386000905|ref|YP_005919204.1| 117 -FLPDILASNRRGSAAVVHAHGDNLAALKEYVPRLTRVL-ATTQ-SRPL---EGVYNFGGFTDGDRAVFLARRFGAG 187
                                       .888999999999*********************99544.4455.3333...3559********************* PP

                        MAF_flag10 158 eIiliGqDlay 168
                                       eI+l+G+D+  
  gi|386000905|ref|YP_005919204.1| 188 EIHLVGFDFDD 198
                                       ********976 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-06     0.049       9      62 ..      88     136 ..      81     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                     TPK_catalytic   9 slrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyeskgteivkkp 62 
                                        ++++aDg++  ++     +++ lpdviv DlD   p+++   +    ++v+ +
  gi|386000905|ref|YP_005919204.1|  88 LVIIAADGATTPIL-----AAGALPDVIVTDLDGFLPDILASNRRGSAAVVHAH 136
                                       4689**********.....99**************9999998888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1543.06
//
Query:       gi|386000906|ref|YP_005919205.1|  [L=303]
Description: hypothetical protein Mhar_0191 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1972.64
//
Query:       gi|386000907|ref|YP_005919206.1|  [L=311]
Description: Sulfite reductase, beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-19   69.1   0.0    5.3e-19   68.3   0.0    1.4  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    8.9e-14   51.1   0.0    1.7e-13   50.2   0.0    1.5  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    1.7e-13   49.8  16.4    2.8e-07   30.1   4.7    2.4  2  Fer4          4Fe-4S binding domain
    3.1e-12   46.0  17.9    2.7e-07   30.4   2.9    2.8  3  Fer4_6        4Fe-4S binding domain
    2.1e-09   36.9  14.5    0.00011   22.1   3.1    2.6  2  Fer4_2        4Fe-4S binding domain
      1e-08   35.2  13.3    0.00033   20.7   2.8    2.8  3  Fer4_21       4Fe-4S dicluster domain
    1.2e-08   35.4  15.1    0.00079   20.0   7.6    2.6  2  Fer4_7        4Fe-4S dicluster domain
    3.8e-08   33.3  25.3      6e-06   26.3  15.3    2.7  3  Fer4_10       4Fe-4S dicluster domain
    4.1e-07   30.1  12.6    9.4e-07   28.9  12.6    1.7  1  Fer4_9        4Fe-4S dicluster domain
    3.9e-05   24.3  21.5      0.023   15.6   6.9    2.7  2  Fer4_3        4Fe-4S binding domain
    4.5e-05   23.8  11.1     0.0064   16.9   0.1    2.5  2  Fer4_8        4Fe-4S dicluster domain
    0.00019   22.1  12.4      0.035   14.8   2.0    2.8  2  Fer4_15       4Fe-4S single cluster domain
    0.00061   20.6  11.2      0.081   13.8   2.2    3.0  3  Fer4_22       4Fe-4S dicluster domain
     0.0011   19.3  19.9      0.023   15.2   4.6    2.7  2  Fer4_4        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.019   15.5  13.3      0.053   14.1   0.2    3.2  4  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
      0.025   15.5  14.3        1.1   10.3   3.4    2.4  3  Fer4_16       4Fe-4S double cluster binding domain
       0.13   12.8  17.5       0.34   11.5   2.5    2.7  2  Fer4_17       4Fe-4S dicluster domain
       0.35   11.1  12.7       0.96    9.7  12.7    1.6  1  Fer4_18       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   5.3e-22   5.3e-19       4     152 ..     113     303 ..     110     309 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 5.3e-22
                                       SCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           NIR_SIR   4 nlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei. 79 
                                       + rnv++c g+  c +a+ +tt+lak++     + +  ++ P  +K+ + gcp  c + ++n ig++g +++e    
  gi|386000907|ref|YP_005919206.1| 113 TFRNVVSCLGSDYCFKAAAETTSLAKEVA----EAFTGEKTPGPLKVGIGGCPFPCTRPQFNEIGIMGRVRPEMDTe 185
                                       679**************************....99**************************************999* PP

                                       ...................................................EEEEEE--B-SSSTC-TCEEEEEEEE CS
                                       ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 ...................................................gfnilvGGglgrthgakktsarlgfv 105
                                                                                          g+ ++vGG+ +  + ++  ++   fv
  gi|386000907|ref|YP_005919206.1| 186 kctgcercvavckvgaasvvdgkavidydkcimcgrcvvncpggarysaedGYMLFVGGRGSWPPFEGWILR--DFV 260
                                       **************************************************************9999998888..7** PP

                                       EGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 106 peeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                         ee+l+++  i+evy     + ++   Rl+++++ +G+e+Fr+ v 
  gi|386000907|ref|YP_005919206.1| 261 GREEILPLIGRILEVYG----AGAKPGMRLREFIKTIGFEEFRRRVA 303
                                       *****************....***********************994 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.7e-16   1.7e-13       2      69 .]      39     103 ..      38     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.7e-16
                      NIR_SIR_ferr   2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLaea 69 
                                       k kdgk  + + + v +G +++ q r++ ++aekyg ge+++T rQ l + gvpee+l+  l++Laea
  gi|386000907|ref|YP_005919206.1|  39 KRKDGK--FEIKILVTGGMLSPGQVRRIGEVAEKYG-GEVHITVRQELSILGVPEERLDLALQDLAEA 103
                                       678887..799*************************.***************************9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   3.8   8.6e-09   8.6e-06       3      22 ..     182     201 ..     180     203 .. 0.91
   2 !   30.1   4.7   2.8e-10   2.8e-07       2      23 ..     210     231 ..     209     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.6e-09
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                        d+ekC+gC +Cv vC vgA
  gi|386000907|ref|YP_005919206.1| 182 MDTEKCTGCERCVAVCKVGA 201
                                       69*****************9 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.8e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       vid++kCi CG+Cv  CP gA 
  gi|386000907|ref|YP_005919206.1| 210 VIDYDKCIMCGRCVVNCPGGAR 231
                                       8*******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         8   7.9e+03       8      18 ..     119     129 ..     118     129 .. 0.77
   2 !   24.2   3.5   2.5e-08   2.5e-05       2      23 ..     180     201 ..     179     202 .. 0.93
   3 !   30.4   2.9   2.7e-10   2.7e-07       1      22 [.     208     229 ..     208     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8
                            Fer4_6   8 kCigCgdCvrv 18 
                                       +C+g + C+++
  gi|386000907|ref|YP_005919206.1| 119 SCLGSDYCFKA 129
                                       59988889875 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.5e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       +e d +kC+gC++Cv+vC  ga
  gi|386000907|ref|YP_005919206.1| 180 PEMDTEKCTGCERCVAVCKVGA 201
                                       799***************9987 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 2.7e-10
                            Fer4_6   1 vveidpdkCigCgdCvrvCPeg 22 
                                       +++id+dkCi Cg+Cv++CP g
  gi|386000907|ref|YP_005919206.1| 208 KAVIDYDKCIMCGRCVVNCPGG 229
                                       689*****************55 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.7   6.2e-07   0.00061       3      21 ..     180     198 ..     178     199 .. 0.91
   2 !   22.1   3.1   1.1e-07   0.00011       2      21 ..     208     227 ..     207     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.2e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++ dt++C+gC+ Cv +C 
  gi|386000907|ref|YP_005919206.1| 180 PEMDTEKCTGCERCVAVCK 198
                                       789***************5 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.1e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++v+d d+Ci Cg Cv +CP
  gi|386000907|ref|YP_005919206.1| 208 KAVIDYDKCIMCGRCVVNCP 227
                                       579****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.8   1.8e+03       7      22 ..     119     134 ..     116     144 .. 0.73
   2 !   20.7   2.8   3.3e-07   0.00033      12      53 ..     158     199 ..     155     204 .. 0.88
   3 !   20.2   1.1   4.9e-07   0.00049       1      21 [.     209     229 ..     209     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.8
                           Fer4_21   7 kCigCgkCliaCedts 22 
                                       +C+g   C++a  +t+
  gi|386000907|ref|YP_005919206.1| 119 SCLGSDYCFKAAAETT 134
                                       5788888888776654 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.3e-07
                           Fer4_21  12 gkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       g C   C     + i i ++ + ++ +++C+GC+ C++vC v
  gi|386000907|ref|YP_005919206.1| 158 GGCPFPCTRPQFNEIGIMGRVRPEMDTEKCTGCERCVAVCKV 199
                                       6688899999999999999999999***************88 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 4.9e-07
                           Fer4_21   1 AridedkCigCgkCliaCedt 21 
                                       A+id dkCi Cg+C++ C+ +
  gi|386000907|ref|YP_005919206.1| 209 AVIDYDKCIMCGRCVVNCPGG 229
                                       89****************965 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   7.6     8e-07   0.00079      12      52 .]     160     201 ..     119     201 .. 0.65
   2 !   19.6   0.8     1e-06   0.00099      33      52 .]     211     230 ..     204     238 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8e-07
                            Fer4_7  12 Cpvkaieldeeenek.....gtekveidpekClgCgaCvavCPtga 52 
                                       Cp  + + +     +     g+ ++e+d ekC+gC++CvavC +ga
  gi|386000907|ref|YP_005919206.1| 160 CPFPCTRPQF----NeigimGRVRPEMDTEKCTGCERCVAVCKVGA 201
                                       3433333332....02223366888******************997 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1e-06
                            Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                       id++kC+ Cg+Cv  CP ga
  gi|386000907|ref|YP_005919206.1| 211 IDYDKCIMCGRCVVNCPGGA 230
                                       56666666666666666554 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.3   1.3e+03       6      18 ..     117     129 ..     113     152 .. 0.83
   2 !   26.3  15.3     6e-09     6e-06       3      56 .]     181     227 ..     179     227 .. 0.93
   3 !   20.1   2.3     5e-07    0.0005       1      21 [.     208     228 ..     208     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                           Fer4_10   6 ddtCirCgkCvka 18 
                                         +C++   C ka
  gi|386000907|ref|YP_005919206.1| 117 VVSCLGSDYCFKA 129
                                       5679999999886 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 6e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       + d+++C++C++Cv++C       ++ ++   +++  ++++kC++cg Cv  CP
  gi|386000907|ref|YP_005919206.1| 181 EMDTEKCTGCERCVAVC-------KVGAASVVDGKAVIDYDKCIMCGRCVVNCP 227
                                       5799*************.......78999999999999***************9 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 5e-07
                           Fer4_10   1 kvvidddtCirCgkCvkaCPa 21 
                                       k+vid d+Ci Cg+Cv  CP 
  gi|386000907|ref|YP_005919206.1| 208 KAVIDYDKCIMCGRCVVNCPG 228
                                       579*****************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9  12.6   9.5e-10   9.4e-07       1      49 [.     186     229 ..     159     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 9.5e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       kCtgC +Cv++C+ g+++  +++  + ++     +Ci+Cg+Cv  Cp g
  gi|386000907|ref|YP_005919206.1| 186 KCTGCERCVAVCKVGAASVVDGKAVIDYD-----KCIMCGRCVVNCPGG 229
                                       7************************9995.....5************87 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   6.6   7.9e-05     0.079       1      15 []     187     201 ..     187     201 .. 0.98
   2 !   15.6   6.9   2.3e-05     0.023       1      15 []     216     230 ..     216     230 .. 0.98

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.9e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgC++Cv vC vgA
  gi|386000907|ref|YP_005919206.1| 187 CTGCERCVAVCKVGA 201
                                       *************98 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.3e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++Cg+Cv+ CP gA
  gi|386000907|ref|YP_005919206.1| 216 CIMCGRCVVNCPGGA 230
                                       **************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   7.1    0.0029       2.9      46      64 ..     182     200 ..     117     201 .. 0.79
   2 !   16.9   0.1   6.4e-06    0.0064       3      16 ..     214     227 ..     212     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                            Fer4_8  46 ealwsCttcgaCtevCpvg 64 
                                          ++Ct+c++C+ vC+vg
  gi|386000907|ref|YP_005919206.1| 182 MDTEKCTGCERCVAVCKVG 200
                                       4578899999999999886 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.4e-06
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       +kCi Cg+C  +Cp
  gi|386000907|ref|YP_005919206.1| 214 DKCIMCGRCVVNCP 227
                                       78999999999998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   3.0   0.00017      0.17       3      31 ..     182     210 ..     181     211 .. 0.83
   2 !   14.8   2.0   3.5e-05     0.035       2      20 ..     210     228 ..     209     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedglas 31 
                                        D ++C+gc++Cva+++       dg+a+
  gi|386000907|ref|YP_005919206.1| 182 MDTEKCTGCERCVAVCKVGAASVVDGKAV 210
                                       699*************9777777788885 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.5e-05
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       v+D d+Ci+cg+Cv ++p 
  gi|386000907|ref|YP_005919206.1| 210 VIDYDKCIMCGRCVVNCPG 228
                                       69***************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.1   2.1e+03      31      52 ..     111     132 ..      99     149 .. 0.70
   2 !   13.8   2.2   8.1e-05     0.081      73      94 ..     178     199 ..     162     201 .. 0.87
   3 !   10.4   1.4   0.00092      0.91      77      94 ..     211     228 ..     203     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                           Fer4_22  31 gervrvwdsClleeftkvagge 52 
                                       g  +r++ sCl +++   a+ e
  gi|386000907|ref|YP_005919206.1| 111 GMTFRNVVSCLGSDYCFKAAAE 132
                                       5667788888888776655543 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.1e-05
                           Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                       ++ ++++++C+GC RC+++c+v
  gi|386000907|ref|YP_005919206.1| 178 VRPEMDTEKCTGCERCVAVCKV 199
                                       5668899*************87 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00092
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++  +C+ CgRC+ +cp 
  gi|386000907|ref|YP_005919206.1| 211 IDYDKCIMCGRCVVNCPG 228
                                       577889999999999986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   4.6   2.4e-05     0.023       2      16 ..     185     199 ..     184     200 .. 0.91
   2 !   14.9   1.6   2.9e-05     0.029       1      15 [.     213     227 ..     213     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C+gC +Cva+C++
  gi|386000907|ref|YP_005919206.1| 185 EKCTGCERCVAVCKV 199
                                       89***********97 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.9e-05
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +++Ci Cg+Cv  CP
  gi|386000907|ref|YP_005919206.1| 213 YDKCIMCGRCVVNCP 227
                                       59************* PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       8.6   8.6e+03      17      25 ..      35      43 ..      33      48 .. 0.79
   2 ?   -2.2   0.1       6.2   6.2e+03       6      18 ..     120     132 ..     118     144 .. 0.77
   3 ?    7.0   3.6    0.0083       8.3       2      16 ..     183     197 ..     182     199 .. 0.93
   4 ?   14.1   0.2   5.3e-05     0.053       1      29 [.     211     239 ..     211     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.6
                           Fer4_13 17 PdvFeedde 25
                                      P vF+++d 
  gi|386000907|ref|YP_005919206.1| 35 PAVFKRKDG 43
                                      99**99984 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                           Fer4_13   6 CiacgaCvelaPd 18 
                                       C + + C ++a +
  gi|386000907|ref|YP_005919206.1| 120 CLGSDYCFKAAAE 132
                                       8888888888765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0083
                           Fer4_13   2 DrdtCiacgaCvela 16 
                                       D ++C++c+ Cv+++
  gi|386000907|ref|YP_005919206.1| 183 DTEKCTGCERCVAVC 197
                                       889**********99 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 5.3e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggas 29 
                                       +D d+Ci cg Cv  +P   ++  e+g++
  gi|386000907|ref|YP_005919206.1| 211 IDYDKCIMCGRCVVNCPGGARYSAEDGYM 239
                                       799**************877777777766 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.9    0.0031       3.1      51      65 ..     184     198 ..     177     200 .. 0.71
   2 ?   10.3   3.4    0.0011       1.1       1      18 [.     186     203 ..     186     215 .. 0.77
   3 ?    9.9   3.3    0.0014       1.4       1      16 [.     215     230 ..     215     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                           Fer4_16  51 qeaitgCdiCqdvCP 65 
                                        e++tgC +C++vC 
  gi|386000907|ref|YP_005919206.1| 184 TEKCTGCERCVAVCK 198
                                       467888888888885 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       +C++C++C+ vC ++a +
  gi|386000907|ref|YP_005919206.1| 186 KCTGCERCVAVCKVGAAS 203
                                       5999*******9999865 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0014
                           Fer4_16   1 rCgtCgkCaevCPtna 16 
                                       +C+ Cg+C+  CP +a
  gi|386000907|ref|YP_005919206.1| 215 KCIMCGRCVVNCPGGA 230
                                       5************987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.3     0.015        15      33      57 ..     174     198 ..     119     202 .. 0.79
   2 ?   11.5   2.5   0.00034      0.34      43      59 ..     213     229 ..     203     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                           Fer4_17  33 lleeaekeekaslCieCgeCerkCP 57 
                                       +++++  e+  ++C++C++C+++C 
  gi|386000907|ref|YP_005919206.1| 174 IMGRVRPEMDTEKCTGCERCVAVCK 198
                                       4555555678899999999999995 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00034
                           Fer4_17  43 aslCieCgeCerkCPqg 59 
                                        ++Ci Cg+C+  CP g
  gi|386000907|ref|YP_005919206.1| 213 YDKCIMCGRCVVNCPGG 229
                                       589************76 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  12.7   0.00097      0.96      56      95 ..     182     226 ..     174     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00097
                           Fer4_18  56 kgagdcidcescvkvcPtg....idirkGlql.eciscllcidac 95 
                                        ++ +c+ ce cv+vc +g    +d +  + + +ci c++c+  c
  gi|386000907|ref|YP_005919206.1| 182 MDTEKCTGCERCVAVCKVGaasvVDGKAVIDYdKCIMCGRCVVNC 226
                                       56789***********998433344455555556********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1863.65
//
Query:       gi|386000908|ref|YP_005919207.1|  [L=286]
Description: Putative phosphoserine phosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
          1    9.1  48.7        2.8    7.7  28.2    2.1  2  ERM             Ezrin/radixin/moesin family
        1.9    9.1  20.6       0.35   11.5   3.9    3.4  3  DUF5344         Family of unknown function (DUF5344)
        2.1    8.1  34.7       0.99    9.2   8.6    3.2  2  KASH_CCD        Coiled-coil region of CCDC155 or KASH
        4.5    7.7  22.4        3.3    8.2   5.8    4.6  3  DUF1771         Domain of unknown function (DUF1771)


Domain annotation for each model (and alignments):
>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  28.2   0.00064       2.8      58     199 ..       4     160 ..       2     168 .. 0.53
   2 ?    6.0  16.0     0.002       9.1      12     115 ..     157     258 ..     153     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00064
                               ERM  58 eaeeeiqrlkesaekeeeekeklerklreaeleaarleeeser...keeeaerLke....eleeareaeeeakekll 127
                                       e+ee+++rlk++a + +e++++l++++ +  +e ++l ++ ++   +++e ++L++    ++ ea+ +  e +ek  
  gi|386000908|ref|YP_005919207.1|   4 ELEEKKARLKQQAVDYKESRSQLNAEASKWAAERNELNKKTKElidQAQELKTLRDeynkNVAEAKLKRDEYNEKTN 80 
                                       66666666666666666666666666666666666666655553334444444444222135555666666666666 PP

                               ERM 128 ealstpskseseenveeseteeeeenseeesaeletdeveklsleieee..............Rvtylekskrlqeq 190
                                       ++ ++  +  +++n + + +      +e  + e+++++ e ls+++e++              R + +ek++ l++ 
  gi|386000908|ref|YP_005919207.1|  81 DFYAQIDEIRKKHNLTGDRSIRGL-RREIDHMEFKQQT-EVLSPDKEKQlvekisalraefktRKEQMEKNEVLRDL 155
                                       666666332334444444444444.3344567777663.34555555555555555555555588888888877766 PP

                               ERM 191 LkeLksele 199
                                       L+    e +
  gi|386000908|ref|YP_005919207.1| 156 LD----EAQ 160
                                       65....444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.002
                               ERM  12 erLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreae 88 
                                       ++ ++l+++a +  +  ++s e a+++  k+    +ea++  + a +a++e  + +e+a k+++e  + +r++r+++
  gi|386000908|ref|YP_005919207.1| 157 DEAQKLRDQASEYHDLVTKSAELAQEYHDKMIATFKEADQVRAAADAAHREFVKAQEAADKQHREFIRTQREIRDFD 233
                                       5668999999999999************************************************************* PP

                               ERM  89 leaarleeeserkeeeaerLkeeleea 115
                                         ++ l++++++k e+  + k+e+++ 
  gi|386000908|ref|YP_005919207.1| 234 KIITGLRKKNREKRED--KVKAEVRKE 258
                                       *****99887775554..334443332 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.6    0.0077        35       7      63 ..       8      65 ..       3      78 .. 0.88
   2 ?   11.5   3.9   7.8e-05      0.35      17      82 ..     127     196 ..     123     201 .. 0.88
   3 ?   -0.1   0.1      0.33   1.5e+03      15      52 ..     229     266 ..     206     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0077
                           DUF5344  7 nqaeVeqkLselktaaeelktsipetisgknsldv.vekineleeeleellkaYktll 63
                                      ++a ++q+  ++k++ ++l++++++ ++++n+l+  ++++ + ++el++l++ Y + +
  gi|386000908|ref|YP_005919207.1|  8 KKARLKQQAVDYKESRSQLNAEASKWAAERNELNKkTKELIDQAQELKTLRDEYNKNV 65
                                      5788999999***********************85378899*************8654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.8e-05
                           DUF5344  17 elktaaeelktsipetisgknsldvvekineleeeleellkaYktlllknvedte....saVdslkeaDe 82 
                                       +l +++++l++++++  ++ ++ +v++ + + +++l ++ + Y++l++k++e ++    +++ ++keaD+
  gi|386000908|ref|YP_005919207.1| 127 QLVEKISALRAEFKTRKEQMEKNEVLRDLLDEAQKLRDQASEYHDLVTKSAELAQeyhdKMIATFKEADQ 196
                                       78899*********************************************99888333357888888887 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.33
                           DUF5344  15 Lselktaaeelktsipetisgknsldvvekineleeel 52 
                                       + +  + +++l++++ e+ ++k + +v ++++e+  ++
  gi|386000908|ref|YP_005919207.1| 229 IRDFDKIITGLRKKNREKREDKVKAEVRKEAEEILTQF 266
                                       55555556667777777777777777777777766665 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  13.3   0.00055       2.5      79     172 ..       5      91 ..       1     117 [. 0.79
   2 ?    9.2   8.6   0.00022      0.99      94     158 ..     123     185 ..     101     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00055
                          KASH_CCD  79 leEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekeallee 155
                                       leEk+arlk+q+          ++   +L+ e  k +ae++el+kk+keL+++ +eLk+  +e+++ +ae      e
  gi|386000908|ref|YP_005919207.1|   5 LEEKKARLKQQAVDY-------KESRSQLNAEASKWAAERNELNKKTKELIDQAQELKTLRDEYNKNVAEAKLKRDE 74 
                                       455555555444443.......33345789999********************************999998888888 PP

                          KASH_CCD 156 ktkqieeLkltieEyss 172
                                        +++++++ ++i+E+++
  gi|386000908|ref|YP_005919207.1|  75 YNEKTNDFYAQIDEIRK 91 
                                       89999999988888775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00022
                          KASH_CCD  94 ekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektk 158
                                       +ke+q L++ki +L  e +k + e+ e ++ l++Ll+e ++L+ q+ e++ l+++  +l++e   
  gi|386000908|ref|YP_005919207.1| 123 DKEKQ-LVEKISALRAE-FKTRKEQMEKNEVLRDLLDEAQKLRDQASEYHDLVTKSAELAQEYHD 185
                                       56665.8999****987.68888999999999********************9988887777554 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.8   0.00073       3.3       3      57 ..      11      67 ..       9      73 .. 0.91
   2 ?    4.6   0.3    0.0098        44       2      24 ..     160     182 ..     150     185 .. 0.83
   3 ?    3.1   4.1     0.028   1.2e+02       7      32 ..     179     204 ..     175     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00073
                           DUF1771  3 rlRaeAdeharkrnelfekAaeAyrrGd..gaaAkelseqGkehgekmeeanreAae 57
                                      rl ++A ++ + r++l ++A++  ++ +   ++ kel +q++e++   +e+n++ ae
  gi|386000908|ref|YP_005919207.1| 11 RLKQQAVDYKESRSQLNAEASKWAAERNelNKKTKELIDQAQELKTLRDEYNKNVAE 67
                                      788999**************99888888899*********************98776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0098
                           DUF1771   2 erlRaeAdeharkrnelfekAae 24 
                                       ++lR++A e++++  +  e A+e
  gi|386000908|ref|YP_005919207.1| 160 QKLRDQASEYHDLVTKSAELAQE 182
                                       57899999999888888888876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.028
                           DUF1771   7 eAdeharkrnelfekAaeAyrrGdga 32 
                                        A+e+++k+   f++A + +++ d a
  gi|386000908|ref|YP_005919207.1| 179 LAQEYHDKMIATFKEADQVRAAADAA 204
                                       799***************99887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3013  (0.168052); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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):               4  [number of targets reported over threshold]
# CPU time: 1.03u 0.37s 00:00:01.40 Elapsed: 00:00:00.58
# Mc/sec: 1484.65
//
Query:       gi|386000909|ref|YP_005919208.1|  [L=226]
Description: hypothetical protein Mhar_0194 [Methanosaeta harundinacea 6Ac]
Scores for 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-25   87.4   0.0    1.1e-24   87.1   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    6.6e-23   81.3   0.2    8.3e-23   81.0   0.2    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    7.2e-12   45.7   2.3    1.2e-11   45.1   2.4    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   1.9e-28   1.1e-24       1     163 []       2     189 ..       2     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.9e-28
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfka...nlgyeppaeeaDlvlisqaledHa.hletlkqlaenvkvlee...... 67 
                                       ++twl h++f l ++  r+l+DP+ +    +   p++ ++D++ ++++++dH  ++e++++  +  +vl+       
  gi|386000909|ref|YP_005919208.1|   2 KITWLSHSCFEL-VETMRVLIDPYLRgnpAAPASPEELDPDAIAVTHGHADHLgDAEEIAR-RTGSPVLAVsevarf 76 
                                       69********98.4679*******65544667777779**************626667777.666777777677777 PP

                     Lactamase_B_3  68 .............geslevggleiravatshdavggser.....genngflleqdgltiyhlGhlahelsseelkel 126
                                                    g++l++++++++ +++ h ++   +      ge  gf++ +dg+++yh G++a   ++  +  l
  gi|386000909|ref|YP_005919208.1|  77 ldrrgvrsegmniGGTLRIADVSFTMTRAVHSSGITVTDppacgGEAAGFVI-DDGVRVYHAGDTALFGDMRLIGDL 152
                                       7778888888888899***************555322223345577999999.67************9999****** PP

                     Lactamase_B_3 127 grvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                        r++v l+P+gg +t+g++ea+ +a++++p+lv+Pmh
  gi|386000909|ref|YP_005919208.1| 153 LRPEVALLPIGGRYTMGPREAAIAASWIRPHLVIPMH 189
                                       ************************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.2   1.4e-26   8.3e-23       2     201 .]      18     190 ..      17     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.4e-26
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                       r+LiD+ +   +  ++a  P+++ +   + da+ +th+H+DHl ++  ++++++   p++a  +v++ l+++     
  gi|386000909|ref|YP_005919208.1|  18 RVLIDPYLR--G--NPAA-PASPEEL--DPDAIAVTHGHADHLGDAEEIARRTG--SPVLAVSEVARFLDRR----- 80 
                                       89***9988..3..4564.5555555..88*********************655..5888888888888888..... PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C...TCCE-TTTSEEEEEECTTEEEEEESS-S---HH..H CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgr...rldrnagdtlGlriegggkrvyyigDtgyipee..i 150
                                            +v+ + +++g++++++  ++++t+t a h+sg    +     g+++G++i+ +g rvy++gDt+ + ++  i
  gi|386000909|ref|YP_005919208.1|  81 -----GVRSEGMNIGGTLRIA--DVSFTMTRAVHSSGItvtDPPACGGEAAGFVID-DGVRVYHAGDTALFGDMrlI 149
                                       .....678899*********9..578************6543344445********.9**************66547 PP

                                       HHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 151 gerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       g++l+ ++++ll+i+         + +++ p+ea+ aa  ++++ ++++H+
  gi|386000909|ref|YP_005919208.1| 150 GDLLR-PEVALLPIG---------GRYTMGPREAAIAASWIRPHLVIPMHY 190
                                       76666.9********.........899***********************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   2.4   1.9e-15   1.2e-11      17     163 ..      18     161 ..       4     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.9e-15
                                       EEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHH CS
                       Lactamase_B  17 viLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasr 93 
                                        +LiD+ + +  a  a        + +d+da+ +TH+H+DH G++++++++t+ pv av+e+a+ l ++++  + + 
  gi|386000909|ref|YP_005919208.1|  18 RVLIDPYLRGNPAAPA------SPEELDPDAIAVTHGHADHLGDAEEIARRTGSPVLAVSEVARFLDRRGVRSEGMN 88 
                                       7899999999999996......899**********************************************999999 PP

                                       CCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCCCCCC....... CS
                       Lactamase_B  94 kglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallagetgridl....... 162
                                        g+          ++d   + + a +  +  vt  p+ g+  + + + +g +v  +GD+ l g+  +i+        
  gi|386000909|ref|YP_005919208.1|  89 IGG-------TLRIADVSFTMTRAVHSSGITVTDPPACGGEAAGFVIdDGVRVYHAGDTALFGDMRLIGDllrpeva 158
                                       763.......4445555555555555555555555555444333333266778888888888887777764444445 PP

                                       ... CS
                       Lactamase_B 163 ..t 163
                                         +
  gi|386000909|ref|YP_005919208.1| 159 llP 161
                                       552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1303.80
//
Query:       gi|386000910|ref|YP_005919209.1|  [L=149]
Description: hypothetical protein Mhar_0195 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-08   35.5   0.0    5.6e-08   33.1   0.0    1.8  1  CGI-121       Kinase binding protein CGI-121
  ------ inclusion threshold ------
       0.17    9.9   0.0       0.19    9.8   0.0    1.1  1  RAG1          Recombination-activation protein 1 (RAG1), reco
       0.22   11.6   0.0       0.31   11.2   0.0    1.2  1  RC-P840_PscD  Photosystem P840 reaction centre protein PscD


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   9.4e-12   5.6e-08      25     105 ..      24      99 ..      10     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 9.4e-12
                                       EE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS--HH CS
                           CGI-121  25 fldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvssseadee 101
                                         dasl++ + h   A+ +a+ a ++ +   k l  Eil + s++++I+ al  +g+s+ t+++ ++ ++++     
  gi|386000910|ref|YP_005919209.1|  24 AMDASLVVGERHAAFAAEKAVRAFTERRNVAKDLGLEILRYASGQRQIERALS-MGVSEATERVALIVMGTP----P 95 
                                       57**************************************************9.***************998....3 PP

                                       HHHH CS
                           CGI-121 102 evlk 105
                                       ++++
  gi|386000910|ref|YP_005919209.1|  96 DISD 99 
                                       3333 PP

>> RAG1  Recombination-activation protein 1 (RAG1), recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   3.1e-05      0.19     202     259 ..      76     133 ..      36     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.1e-05
                              RAG1 202 gledsactegfsvvvkescdgmgdvsekhgsgpvvpekavrfsftvmsvsvladdeee 259
                                        +  s +te ++++v  +   + d+ e  g gp   e avr +f +  + + a  ee 
  gi|386000910|ref|YP_005919209.1|  76 SMGVSEATERVALIVMGTPPDISDILELDGEGPRWSEAAVREAFDIGDLEIEAAGEER 133
                                       4666888999*************************************99999998884 PP

>> RC-P840_PscD  Photosystem P840 reaction centre protein PscD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.1e-05      0.31      27      87 ..      39      98 ..      20     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.1e-05
                      RC-P840_PscD 27 avhkaekyfitsakrdrsgklqleis.pasgrrklsptkeliekliegeielfvlttqpdia 87
                                      a+ ka + f  + +r+  ++l lei   asg+r++  +  +    +  ++ l+v+ t pdi+
  gi|386000910|ref|YP_005919209.1| 39 AAEKAVRAF--TERRNVAKDLGLEILrYASGQRQIERALSMGVSEATERVALIVMGTPPDIS 98
                                      444444444..45778889999998527*************9999999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1078.00
//
Query:       gi|386000911|ref|YP_005919210.1|  [L=201]
Description: hypothetical protein Mhar_0196 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-65  220.0   0.4    2.8e-65  219.8   0.4    1.0  1  DUF2150   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.8   0.4   1.6e-69   2.8e-65       1     188 []       4     191 ..       4     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 219.8 bits;  conditional E-value: 1.6e-69
                           DUF2150   1 eFYteeRwqNWlnrvkeedldleedseeleaavllnlqdDvilavlkiikaveeeelskeeAleeleevreivleev 77 
                                       eFYt+ RwqNW+n++ke+ + l+e++e+ +aav+++ +dDv+la+lk+i+++e+++++keeA+++++e+reiv e+ 
  gi|386000911|ref|YP_005919210.1|   4 EFYTRGRWQNWINKIKESGFTLQESEEDPSAAVFVYAMDDVVLACLKVIARCEHGTITKEEAISTIDEIREIVSERD 80 
                                       7**********************9999999*********************************************** PP

                           DUF2150  78 eeddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpe 154
                                       ++  e+++ ++es++ sl +vf a+++yi+gg++++++++++v++aa+ae+++++e+al+i+++iGa+vi ge++pe
  gi|386000911|ref|YP_005919210.1|  81 DSLGEDATLMLESLNASLSAVFLASQRYIDGGYDQKTPLADMVRKAATAEEAGRMEEALGILSDIGARVIGGEAVPE 157
                                       ***************************************************************************** PP

                           DUF2150 155 kvledleyglvaewldgidslaaamsssesveee 188
                                       +++ +l+y++ ae+ldgid+++aa ++++s++e+
  gi|386000911|ref|YP_005919210.1| 158 EAFAELPYCMTAELLDGIDAISAAQVGDDSYKED 191
                                       ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1383.86
//
Query:       gi|386000912|ref|YP_005919211.1|  [L=293]
Description: Methionine aminopeptidase, type II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-38  132.8   0.0    1.4e-38  132.7   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.0   7.7e-43   1.4e-38       1     191 [.       7     195 ..       7     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 7.7e-43
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB--TTE CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrvlkegd 75 
                                       e++r a++i ++++e+++++i  gv+  e+a+++e +   r  ++++afp  + ++    ++h tp   d  +  ++
  gi|386000912|ref|YP_005919211.1|   7 EKYRTAGEILARVREEAASMIDVGVSILEVAEFVEGK--TRALGGEPAFP--CNISRDRVAAHDTPrpADGAVFGEE 79 
                                       689********************************88..6667899****..888899999999885456667788* PP

                                       EEEEEEEEEETTEEEEEEEEE.ECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSS CS
                     Peptidase_M24  76 lvlidagaeydgyasDitrTv.lvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffph 151
                                       +v++d+g+++dgy++D ++Tv l G  +p   +l+ea ++++ aai++v+pG+++++++aa++e ++ +g+ + + +
  gi|386000912|ref|YP_005919211.1|  80 MVKLDIGVHVDGYIADAAVTVdLGG--HP---DLVEASKAGLAAAIELVEPGASTADLGAAIEEAIRGYGY-SSVAN 150
                                       *********************5555..45...6**************************************.999** PP

                                       CSEEEESS.SSSEEEEEESS.STTCSSB--TTBEEEEEE....EEE CS
                     Peptidase_M24 152 glGHgvGl.evhdegpsvsr.esndgrkleeGmvftiEp....giy 191
                                       ++GHg+G+ + h+e ps+++ +  +g++l +G+v++iEp    gi 
  gi|386000912|ref|YP_005919211.1| 151 LTGHGLGRyRAHGE-PSIPNrAVEKGVELSPGDVIAIEPfatdGIG 195
                                       *******99****9.**975344489*************7777444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 2103.35
//
Query:       gi|386000913|ref|YP_005919212.1|  [L=384]
Description: Peptidase M24 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-39  133.4   0.0      1e-38  133.1   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0   5.7e-43     1e-38       1     208 [.     151     368 ..     151     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 5.7e-43
                                       HHHHHHHHHHHHHHHHHHHHHHT........T.....CBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTT CS
                     Peptidase_M24   1 elirkaariasaaleavleaikp........g.....vterelaaeieattlkrhgarglafppivasgenaavlhy 64 
                                       e+ir ++r++++a++ ++e+i++        +      t++ +  +ie   l + g++     +iva g++aa +h 
  gi|386000913|ref|YP_005919212.1| 151 EAIRYSQRACEEAMKVAIEMIRRsrpageflFleggpLTSERVRSAIEVS-LLEWGCEAE--GTIVAGGPEAADPHL 224
                                       5799******************84445444404444469*********66.788888777..599************ PP

                                       BCSSSB--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHH CS
                     Peptidase_M24  65 tpndrvlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarev 139
                                       +  + +l ++ +++id+ ++ +  +y +D+trTvl G+ +pe  e+ye+vl+aq a+i+av++G++++ ++ +++e 
  gi|386000913|ref|YP_005919212.1| 225 VG-SGPLPRDAPIVIDIFPRSKrtRYFADMTRTVLRGEAEPEVLEIYEVVLAAQVAGIAAVRAGASGRMVHSKVCEA 300
                                       99.59*****************9****************************************************** PP

                                       HHHTTB....CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 140 lesagl....akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       +e++g+    ++ f h+ GHgvGl vh+  ps+s     g  l++  v+t+Epg+y  p+ ggvr+ed+++v+
  gi|386000913|ref|YP_005919212.1| 301 FEERGYpereGRGFIHSSGHGVGLAVHER-PSLS---EVGKALRAESVVTVEPGLY-YPELGGVRLEDLLVVR 368
                                       **********9999*************98.**99...4589***************.99************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2801.91
//
Query:       gi|386000914|ref|YP_005919213.1|  [L=250]
Description: geranylgeranylglyceryl phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-62  210.8   0.0    2.1e-62  210.5   0.0    1.0  1  PcrB            PcrB family
     0.0002   20.9   0.1    0.00041   19.9   0.0    1.5  2  His_biosynth    Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.023   13.7   4.2      0.029   13.4   0.3    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
      0.075   12.3   0.1       0.11   11.7   0.1    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.078   12.2   0.3       0.13   11.5   0.3    1.3  1  DHO_dh          Dihydroorotate dehydrogenase
       0.17   12.3   0.1        0.6   10.5   0.1    2.0  1  LEP503          Lens epithelial cell protein LEP503
       0.17   11.0   3.5       0.59    9.3   0.3    2.3  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
       0.23   10.8   0.1       0.38   10.1   0.1    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.44    9.8   4.8        1.1    8.5   0.8    2.2  2  ThiG            Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.5   0.0   1.1e-65   2.1e-62       7     224 ..      19     245 ..      12     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 1.1e-65
                                       SEEEEE-TTSS-CHHH...HHHHHCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSE CS
                              PcrB   7 rhltklDPeeenpdEi...veiviesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvryaDa 77 
                                        hlt++DP+ + p+ +   +++++++gtDa+m+gGs    +  l++tvr ++     +lP++l+ps v+g+  +aDa
  gi|386000914|ref|YP_005919213.1|  19 AHLTLIDPDSQGPEAAgrmAKAAAKGGTDAIMVGGSVgaaGRALEDTVRSIRAE--SGLPVILFPSGVSGLCSNADA 93 
                                       4**********999752227888*************97667789********99..9******************** PP

                                       EEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT CS
                              PcrB  78 lFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllg 153
                                       +F+msllns  a +++  +alg+  v k+   +e+++++Y++veP+++v++v++ak ++++k+++aa+++la k++g
  gi|386000914|ref|YP_005919213.1|  94 VFFMSLLNSRSASYLIENQALGAPLVYKYG--LEPIPMAYIIVEPGGTVGWVGDAKlIPRDKPELAAAYALAGKYFG 168
                                       ******************************..********************************************* PP

                                       -SEEEEE-.TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..HCHHHHHHH CS
                              PcrB 154 lrliYlEa.sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..erkidaile 224
                                       +r++YlEa sGa ++v  + v+a+k+ + +a livGGGirs++ A++ vea A++iv+G+ ve ++  e  +++i+ 
  gi|386000914|ref|YP_005919213.1| 169 MRMVYLEAgSGAGDPVppKMVAATKRAIGDALLIVGGGIRSGDAARRLVEAgAEIIVTGTGVERSEdvEAFVREITS 245
                                       ************999987899999999************************************88856777777766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   2.8e+03      35      79 ..      10      52 ..       4      62 .. 0.55
   2 !   19.9   0.0   2.1e-07   0.00041      56     109 ..     180     234 ..     140     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                      HHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEE CS
                      His_biosynth 35 akryeeegadelhvvDldaakegreanldlveeiaeevfipvqvG 79
                                      a++ e +ga  l+++D d  ++g ea   + ++ a+  +  ++vG
  gi|386000914|ref|YP_005919213.1| 10 ATAVETAGAAHLTLIDPD--SQGPEAAGRMAKAAAKGGTDAIMVG 52
                                      555566666666666654..2344444444444444444445555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.1e-07
                                       TTHHHHHHHHHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  56 egreanldlveeiaeevf.ipvqvGGGIrsledveelleagadkviigtaavknp 109
                                       +g ++  ++v+++ +++  + + vGGGIrs +++++l+eaga+ ++ gt + ++ 
  gi|386000914|ref|YP_005919213.1| 180 AGDPVPPKMVAATKRAIGdALLIVGGGIRSGDAARRLVEAGAEIIVTGTGVERSE 234
                                       66666677888888887657899********************999999765444 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4     0.049        98     217     241 ..      32      57 ..      11      74 .. 0.80
   2 ?   13.4   0.3   1.4e-05     0.029     134     175 ..     187     229 ..     167     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.049
                                       -SHHHHHHHHHTT.-SEEEESCCCTT CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             IMPDH 217 kysgdivkAlaaG.adavmlGsllag 241
                                       +  g ++kA a G +da+m+G  + +
  gi|386000914|ref|YP_005919213.1|  32 EAAGRMAKAAAKGgTDAIMVGGSVGA 57 
                                       56788999999752689999987654 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 134 eavkeikkkvee.veviaGnvataegakaLieagadavkvGiG 175
                                       ++v++ k+++ + + +++G + + ++a++L+eaga+++  G G
  gi|386000914|ref|YP_005919213.1| 187 KMVAATKRAIGDaLLIVGGGIRSGDAARRLVEAGAEIIVTGTG 229
                                       78999999999989999*********************99998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.7e-05      0.11     161     205 ..     194     238 ..     178     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                       Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesd 205
                                          g+ ++++Gg+  + DaA  lv++gae+ v   g e++++ + 
  gi|386000914|ref|YP_005919213.1| 194 RAIGDALLIVGGGIRSGDAARRLVEAGAEIIVTGTGVERSEDVEA 238
                                       4557889************************99998876665444 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   6.4e-05      0.13     232     277 ..     187     231 ..     173     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                       k++ + ++ + + + i+g GGi sg+ a   +eaGA ++  +t++ 
  gi|386000914|ref|YP_005919213.1| 187 KMVAATKRAIGDALLIVG-GGIRSGDAARRLVEAGAEIIVTGTGVE 231
                                       556666666665665555.************************984 PP

>> LEP503  Lens epithelial cell protein LEP503
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0003       0.6       6      39 ..     183     214 ..     180     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                            LEP503   6 PlaqalPssfrralGdaalrvGtGkrllggnmay 39 
                                       P++  +  + +ra+Gda l vG G r   g+ a 
  gi|386000914|ref|YP_005919213.1| 183 PVPPKMVAATKRAIGDALLIVGGGIR--SGDAAR 214
                                       888899999***************99..676665 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.043        86       4     174 ..      37      53 ..      28      78 .. 0.68
   2 ?    9.3   0.3    0.0003      0.59     146     187 ..     200     240 ..     187     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.043
                                       HHHHHHHHT-SEEEEESHHHHHHHHTT--S-EEEE-B---TTS---BS-SHHHHHHHHTTT-SEEEEE--SS--T-- CS
                              NanE   4 makaaeqaGavgiriegvedikaikavvdlPiiGivkrdlpdsevritatlkdideLaaagadiialDatdrerpvt 80 
                                       makaa+++G+ +i                                                                
  gi|386000914|ref|YP_005919213.1|  37 MAKAAAKGGTDAIM--------------------------------------------------------------- 50 
                                       55666666555554............................................................... PP

                                       HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHH CS
                              NanE  81 ieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintPe 157
                                                                                                                    
  gi|386000914|ref|YP_005919213.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHTT--SEEEE-H CS
                              NanE 158 kakkaieiGvdavvvGs 174
                                                     vG+
  gi|386000914|ref|YP_005919213.1|  51 --------------VGG 53 
                                       ..............444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0003
                                       -EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHH CS
                              NanE 146 kviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfv 187
                                        +i+ G i + + a++ +e G++ +v G+ + r e++ + fv
  gi|386000914|ref|YP_005919213.1| 200 LLIVGGGIRSGDAARRLVEAGAEIIVTGTGVERSEDV-EAFV 240
                                       4799999**************************9987.4455 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00019      0.38     165     197 ..     197     230 ..     185     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                       ---EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 165 ldlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                        d  + v GG++  d++++++eaga+++V+g++v
  gi|386000914|ref|YP_005919213.1| 197 GDALLIVGGGIRSgDAARRLVEAGAEIIVTGTGV 230
                                       578899*****86488999************986 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.029        57     136     184 ..      37      84 ..      31     101 .. 0.69
   2 ?    8.5   0.8   0.00054       1.1     156     224 ..     177     247 ..     169     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                                       HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEE.ES-- CS
                              ThiG 136 larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPviv.DAGi 184
                                       +a++  + G+ a+m  ++ +G+  G + + +++ i++e  +Pvi+   G+
  gi|386000914|ref|YP_005919213.1|  37 MAKAAAKGGTDAIMVGGS-VGA-AGRALEDTVRSIRAESGLPVILfPSGV 84 
                                       567777789999996655.664.46667788999********99733343 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00054
                                       TS----.S-HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                              ThiG 156 GsglGl.lnkealkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                       Gsg G  + ++++    + + +  +iv  Gi+s   a   +e Ga+ ++  t v +++d  a  r ++ a+
  gi|386000914|ref|YP_005919213.1| 177 GSGAGDpVPPKMVAATKRAIgDALLIVGGGIRSGDAARRLVEAGAEIIVTGTGVERSEDVEAFVREITSAM 247
                                       6666641344555555555578889**********************************998888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1797.44
//
Query:       gi|386000915|ref|YP_005919214.1|  [L=407]
Description: NAD-dependent malic enzyme [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-31  109.0   0.0    1.4e-28   99.9   0.0    2.4  1  malic          Malic enzyme, N-terminal domain
    7.1e-22   77.9   4.4    2.5e-20   72.8   4.4    2.6  1  Malic_M        Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
      0.044   13.0   0.2       0.06   12.6   0.2    1.2  1  FAD_binding_3  FAD binding domain
      0.054   13.2   0.2       0.11   12.2   0.2    1.6  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
      0.065   13.6   0.9       0.15   12.4   0.9    1.6  1  TraC           TraC-like protein
       0.18   11.0   3.0       0.49    9.6   3.0    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   4.7e-32   1.4e-28       4     182 .]      18     148 ..      15     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 4.7e-32
                                       ECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTT CS
                             malic   4 netlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLG 80 
                                       + +  + +++++  e+l+++YtP+v+e+c+e+++++++ + +y+++++                 v+vvtdg+++LG
  gi|386000915|ref|YP_005919214.1|  18 IAIKSKVPCSTR--EDLSLAYTPGVAEPCREIENDPDRIY-DYTAKGNL----------------VAVVTDGTAVLG 75 
                                       555666667777..**************************.********................************ PP

                                       TBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHHH CS
                             malic  81 lGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavke 156
                                       lGd+G +a++++m+GK++L++++a++d   ++p+++d +                           +   +ve+ k+
  gi|386000915|ref|YP_005919214.1|  76 LGDIGpAAAMPVMEGKAILFKEFADVD---AFPICIDSK---------------------------DPSVVVEVTKR 122
                                       ***************************...*********...........................67788999999 PP

                                       HHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 157 lfppkaliqfEDfkaknafeileryr 182
                                       +   +++i++ED++a+++fei++r++
  gi|386000915|ref|YP_005919214.1| 123 ISTVFGGINLEDISAPRCFEIEDRLK 148
                                       99999******************986 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   4.4   8.4e-24   2.5e-20       3     257 ..     162     380 ..     160     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 8.4e-24
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--- CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekle 79 
                                       gTa+v++a+l++al i gk + e ++v  GaG+ag+ +++ +++  v          +++ l DrkG+++e+r +l+
  gi|386000915|ref|YP_005919214.1| 162 GTAVVTAAALINALTIVGKGFDEVRVVTSGAGAAGVAVSNFLMSFGV----------EDLILCDRKGVVHEGRGDLN 228
                                       9***********************************99998776544..........5699**************** PP

                                       TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHH CS
                           Malic_M  80 eekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataed 156
                                       + k++ ak ++ +  +    +L+ +++   ++v +G+s+ +g+ +ee+vr+mak     i++++ NP    E +++ 
  gi|386000915|ref|YP_005919214.1| 229 PSKMEMAKITNPTGVT---GSLACALEG--ADVFVGVSA-PGIVSEEMVRSMAKD---SIVFAMANPVP--EIMPD- 293
                                       ********99999844...678877775..79*****97.89**********986...5********97..55554. PP

                                       HHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT CS
                           Malic_M 157 vlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkeg 233
                                       + k   g+ ++a+G          +   ++Q NN++ fPg+  g++ +ra+ i++em +aaa+a+a+l+++ +  e+
  gi|386000915|ref|YP_005919214.1| 294 LAKK-AGARVIATG----------RSDFPNQVNNVLGFPGIFRGALDVRARDINEEMKMAAARAIATLAEPIS--ED 357
                                       4443.566777887..........456689*************************************998766..56 PP

                                       -SS--GGGHHHHHHHHHHHHHHHH CS
                           Malic_M 234 sllPelseirevslkvavavakaa 257
                                       ++ P+  + r v  kva ava+aa
  gi|386000915|ref|YP_005919214.1| 358 RIIPSPFD-RRVVPKVAEAVARAA 380
                                       99998655.667788999999887 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     2e-05      0.06       2      52 ..     185     234 ..     184     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHH CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmel 52 
                                       + V+  GaG aG+  +++L + Gv+ +++  r+  v ++r+d ln+  me+
  gi|386000915|ref|YP_005919214.1| 185 VRVVTSGAGAAGVAVSNFLMSFGVEDLILCDRKGVVHEGRGD-LNPSKMEM 234
                                       567777**********************************99.56666776 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.8e-05      0.11      21      74 ..     174     226 ..     156     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                                       HHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE CS
                     ELFV_dehydrog  21 mlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGl 74 
                                       +l  ++ + +++ rv++sG G  g ++ ++l++ g + + + D +Gv+++  G 
  gi|386000915|ref|YP_005919214.1| 174 ALTIVG-KGFDEVRVVTSGAGAAGVAVSNFLMSFGVEDLILCDRKGVVHEGRGD 226
                                       333323.36999*************************************98884 PP

>> TraC  TraC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   5.1e-05      0.15      20      50 ..     367     397 ..     365     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                              TraC  20 qaevreAeRigRiAlkaGLgeieieeeelda 50 
                                       +++ + Ae ++R+A+ +G++ +e++ +e+ +
  gi|386000915|ref|YP_005919214.1| 367 RVVPKVAEAVARAAIESGVARLEVDPAEVGR 397
                                       566789*******************999965 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.0   0.00016      0.49      28     128 ..     184     284 ..     164     286 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                                       --EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTTTCECEE.....HCHHHHHHHHHHHH-SEEEE- CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgak.VtvlDvrparleqleslgakfvev.....lksqeellaeavkeadvvigt 98 
                                       + +v+  G+G aG++  +  +++g +   ++D +  + e   +l+ + +e+      +    +la a++ adv +  
  gi|386000915|ref|YP_005919214.1| 184 EVRVVTSGAGAAGVAVSNFLMSFGVEdLILCDRKGVVHEGRGDLNPSKMEMakitnPTGVTGSLACALEGADVFV-- 258
                                       556666666666666666666666541344455555555444444433443211112223344555555666655.. PP

                                       --BTTSS---SC-HHHHHTS-TTEEEEETT CS
                       AlaDh_PNT_C  99 vlipGkkaPkLvteemvksMkpgsVivDvA 128
                                           G +aP +v+eemv+sM + s++  +A
  gi|386000915|ref|YP_005919214.1| 259 ----GVSAPGIVSEEMVRSMAKDSIVFAMA 284
                                       ....569******************97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3220.70
//
Query:       gi|386000916|ref|YP_005919215.1|  [L=182]
Description: hypothetical protein Mhar_0201 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-08   34.3   0.0      3e-08   33.9   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.1e-08   32.4   0.0    7.7e-07   29.1   0.0    2.0  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.5e-05   25.4   0.2    4.3e-05   23.8   0.0    1.7  2  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   5.1e-12     3e-08      16     117 .]      25     148 ..      11     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 5.1e-12
                                       HHHHHHHHHHHH.HHSTTCEEEE....EEETTEEEEEEEEEEEET..................TSTTEEEEEEEEES CS
                    Acetyltransf_1  16 nedaseeefees.fsleaegllv....aeedgeliGfisllkipd..................ekggvayieslaVs 69 
                                        +da++++f +  + +e  +ll+    + + + ++Gf +++ +                    ++++++ i +la++
  gi|386000916|ref|YP_005919215.1|  25 SGDAELDDFLKNdALKEQQELLSkthlCFYKNHVAGFFTITADSIrvkkdrldesqivedseyPAYPCILIARLAID 101
                                       566777775555222333355555555679999*****666555566666778888888899999************ PP

                                       GGGTTSSHHHHHHHHHHHHHHHT..TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  70 peyrgkGlGsaLlealeeraree..gikkivlaveedndaairlYeklGF 117
                                       +  +++G+G+ Ll  ++ +a+e   g++++ +   ++ + a ++Y+k+GF
  gi|386000916|ref|YP_005919215.1| 102 KRVHKRGIGKFLLLLIIGFALEGplGCRYLSV---DPKTDALEYYKKFGF 148
                                       ***********************999977666...77999*****88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.3e-10   7.7e-07      17     108 ..      34     150 ..      15     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.3e-10
                   Acetyltransf_10  17 ispealrerieegealllvaeeggkivGvielrdgs.........................hisllfVdpeyrgqGi 68 
                                       ++++al+e+  e   ++++++ ++ ++G+ +++ +s                          i++l++d+  +++Gi
  gi|386000916|ref|YP_005919215.1|  34 LKNDALKEQQ-ELLSKTHLCFYKNHVAGFFTITADSirvkkdrldesqivedseypaypciLIARLAIDKRVHKRGI 109
                                       5555555554.4444455555555666666553333355555556666666666666666679************** PP

                   Acetyltransf_10  69 gkaLleaveeeaekdgikl.eltvnaspyavpfYeklGFka 108
                                       gk Ll  ++  a + +++   l+v+ ++ a ++Y+k+GF  
  gi|386000916|ref|YP_005919215.1| 110 GKFLLLLIIGFALEGPLGCrYLSVDPKTDALEYYKKFGFNF 150
                                       ************9999999********************75 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.47   2.8e+03      55      72 ..      39      57 ..       9      61 .. 0.46
   2 !   23.8   0.0   7.3e-09   4.3e-05      26      74 ..      94     148 ..      64     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.47
                                      EE.EEEE.THHHHHHHHHHT CS
                    Acetyltransf_7 55 le.qlel.naekaikfYekl 72
                                      l+ q el ++ + + fY+ +
  gi|386000916|ref|YP_005919215.1| 39 LKeQQELlSK-THLCFYKNH 57
                                      2233333222.334488765 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 7.3e-09
                                       CTEEEEE-GGGTTSSHHHHHHHHTT.......SEEEEEEEEE..THH.HHHHHHHHTTE CS
                    Acetyltransf_7  26 eitrlaVdpeyrgkGiGraLleaae.......kgiileqlel..nae.kaikfYeklGF 74 
                                        i rla+d+  +++GiG+ Ll +++        g++    +l  +++  a+++Y+k+GF
  gi|386000916|ref|YP_005919215.1|  94 LIARLAIDKRVHKRGIGKFLLLLIIgfalegpLGCR----YLsvDPKtDALEYYKKFGF 148
                                       4667*****************863344454566675....3332333589********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1399.50
//
Query:       gi|386000917|ref|YP_005919216.1|  [L=76]
Description: hypothetical protein Mhar_0202 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.4   0.0      0.049   14.1   0.0    1.1  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-06     0.049     104     145 ..      22      63 ..      21      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-06
                               NYN 104 gDgDFaplveklrergkrVevllaeeastsseLisaad.efis 145
                                       gDgDF+++++  ++r kr +v++++ + +++eL++++  +f++
  gi|386000917|ref|YP_005919216.1|  22 GDGDFEQPLKPFQARVKRFMVMSTK-RFIARELREVSGmHFVD 63 
                                       9**********************55.8********99777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 522.74
//
Query:       gi|386000918|ref|YP_005919217.1|  [L=171]
Description: hypothetical protein Mhar_0203 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-12   45.2   0.1    2.1e-10   40.4   0.1    2.0  1  Malic_M      Malic enzyme, NAD binding domain
     0.0062   15.9   0.1      0.012   15.0   0.1    1.4  1  AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   2.3e-14   2.1e-10      69     237 ..       2     145 ..       1     165 [. 0.79

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.3e-14
                                       EE-BTT-S---TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--S CS
                           Malic_M  69 GLltedrekleeekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSN 145
                                       G+++ +r++l++ k++ a+ +++ +++    +++e+++   ++v +G+s+ +g+ +ee+vr+mak     i++++ N
  gi|386000918|ref|YP_005919217.1|   2 GVIHPGRSDLNSSKMEMARITNRKDKT---GSIAEAMDG--ADVFVGVSA-PGIVSEEMVRSMAKD---SILFAMAN 69 
                                       788888889999998888887777644...688888875..69*****97.89**********986...5******* PP

                                       SGGGSSS-HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHH CS
                           Malic_M 146 PtskaEataedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaeala 222
                                       P    E +++ + k   g+ ++a+G          +    +Q NN++ fPg+  g++ +ra++i+++m +aaa+a+a
  gi|386000918|ref|YP_005919217.1|  70 PVP--EIMPD-LAK-KAGARVIATG----------RSDFLNQVNNVLGFPGIFRGALDVRAREINEDMKMAAARAIA 132
                                       *97..55554.444.3567778887..........456689************************************ PP

                                       TT--HHHHHTT-SS- CS
                           Malic_M 223 elvseeelkegsllP 237
                                       +l+++ +   + + P
  gi|386000918|ref|YP_005919217.1| 133 RLAEPISE--ECIIP 145
                                       *9876553..34444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.3e-06     0.012      73     128 ..      19      68 ..       7      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-06
                                       CECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETT CS
                       AlaDh_PNT_C  73 kfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvA 128
                                         ++ +k +  ++aea+  adv +g       +aP +v+eemv+sM + s++  +A
  gi|386000918|ref|YP_005919217.1|  19 ARITNRKDKTGSIAEAMDGADVFVGV------SAPGIVSEEMVRSMAKDSILFAMA 68 
                                       44666788888999999999999865......9*****************986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 1327.81
//
Query:       gi|386000919|ref|YP_005919218.1|  [L=169]
Description: hypothetical protein Mhar_0204 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-30  105.9   0.0    3.1e-30  105.6   0.0    1.0  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.0   1.7e-34   3.1e-30       1     144 [.       2     156 ..       2     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 1.7e-34
                               NYN   1 rvavfiDgenlpvpak...gkevdyrklleeirs..kgelvraraygn...wedeeqnkfqdalsstgikvkhkplk 69 
                                       +++vf+Dg+n+++ +k   ++ ++++kll++i++  +ge++ a++y+    + d++q++f +al+++g+++ +k lk
  gi|386000919|ref|YP_005919218.1|   2 KISVFVDGANVFYMQKdelKWWINFEKLLRWIENrtGGEIIDAYYYVGeenPPDTRQQGFLTALADIGYSIITKELK 78 
                                       799**********999855555************99999*********88877888********************8 PP

                               NYN  70 krg.....gsgkkavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaad 141
                                        ++     + +k + D+e+++d++  +   +yd ++LvsgDgDF+++++ lr+rgkr +v++++ + +++eL++++ 
  gi|386000919|ref|YP_005919218.1|  79 IIVlddgrEIRKANLDIEIVLDMFNTI--ENYDMAILVSGDGDFERPLRLLRARGKRFMVMSTK-RFIARELREVSG 152
                                       888****999*****************..77*******************************55.8*******9987 PP

                               NYN 142 .efi 144
                                        +f+
  gi|386000919|ref|YP_005919218.1| 153 mHFV 156
                                       6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1108.51
//
Query:       gi|386000920|ref|YP_005919219.1|  [L=177]
Description: Transcriptional regulator, Fur family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28   99.7   0.0    1.5e-28   99.4   0.0    1.1  1  FUR       Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0   8.3e-33   1.5e-28       2     118 ..      39     154 ..      38     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 8.3e-33
                                       TTHCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSE CS
                               FUR   2 aglklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehh 78 
                                       +g+k+T+qR +i +++ +++eh++a++ + e+k+++p++slaTVY t+++l+++glv el++++ge+ry+ + +e h
  gi|386000920|ref|YP_005919219.1|  39 RGYKATPQRIAISRYILSNHEHPTAQKAHLEVKKTHPTVSLATVYSTIRILKDMGLVMELNLSQGETRYDPN-TEAH 114
                                       79**********************************************************************.6*** PP

                                       EEEEETTT--EEEE--HHHHHHHHHHHHHTT-EEEEEEEE CS
                               FUR  79 dhlicekCgkviefkddeiekiqeeiaekegfklvshrle 118
                                       +hl c +Cg  i+ +d+ + ++ ++++++ +f+++  +l 
  gi|386000920|ref|YP_005919219.1| 115 AHLLCIRCGCLIDWSDPIMGELISKVSAEANFTVIGSSLD 154
                                       ********************************99887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 1210.40
//
Query:       gi|386000921|ref|YP_005919220.1|  [L=193]
Description: Peroxiredoxin, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-29  100.5   0.0    1.6e-28   99.1   0.0    1.6  2  AhpC-TSA    AhpC/TSA family
    2.4e-11   43.5   0.0    3.5e-11   43.0   0.0    1.2  1  Redoxin     Redoxin
      7e-11   41.8   0.6    1.1e-10   41.1   0.6    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
      0.059   13.5   0.0      0.069   13.3   0.0    1.2  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.0   3.5e-32   1.6e-28      22     123 ..       7     115 ..       2     116 .. 0.96
   2 ?   -1.7   0.0      0.58   2.6e+03      89     111 ..     128     149 ..     127     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 3.5e-32
                                       HHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.......SSEEEE-TTS CS
                          AhpC-TSA  22 dykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes......lnfpllsDeeg 92 
                                       dykgk++vlf +p+d++pvCtte  a++k+ eef+++++e+ig+s+d+++sh k+ e ++      ++fp+++D +g
  gi|386000921|ref|YP_005919220.1|   7 DYKGKWIVLFSHPADFTPVCTTEFVAFEKRREEFDKLNCELIGLSIDQVFSHMKWTEWIRenikveIKFPIIADDQG 83 
                                       9**************************************************************************** PP

                                       HHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  93 kvakaygvlkee.kglalratfvidkegkiry 123
                                        +a+ +g++++     ++ra+f+id+e +ir 
  gi|386000921|ref|YP_005919220.1|  84 RIAEMLGMIHPGkGSNTVRAVFIIDPEATIRL 115
                                       *********99978899*************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.58
                                       -TTSHHHHHTT-EETTTTECSCE CS
                          AhpC-TSA  89 Deegkvakaygvlkeekglalra 111
                                       De   v ka++v++e+ ++a +a
  gi|386000921|ref|YP_005919220.1| 128 DEIVRVLKALQVVDEK-KVAAPA 149
                                       6666788999999776.666665 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   7.7e-15   3.5e-11      25     128 ..       7     114 ..       2     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 7.7e-15
                                       HHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH......TT-TSEEEE-TTS CS
                           Redoxin  25 efkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk......eglkfpvlsDgsa 95 
                                       ++kgk +v+++ p+ f+P+C++e +++ek  e++ + + + +++++d+    +++ +        ++kfp+++D ++
  gi|386000921|ref|YP_005919220.1|   7 DYKGKWIVLFSHPADFTPVCTTEFVAFEKRREEFDKLNCELIGLSIDQVFSHMKWTEWirenikVEIKFPIIADDQG 83 
                                       59********************************************998884444333556999788********** PP

                                       HHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEE CS
                           Redoxin  96 aftkalGlrleedaseglrtpryavidedgkvv 128
                                        ++++lG+     ++++   +++++id +  ++
  gi|386000921|ref|YP_005919220.1|  84 RIAEMLGMIHP-GKGSN-TVRAVFIIDPEATIR 114
                                       *******6643.33443.8999****9888775 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.6   2.5e-14   1.1e-10       1      35 [.     136     174 ..     136     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.5e-14
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavk 35 
                                       ALQ++d+++va PAnW p     Gd+vi+pPp +e+ a  
  gi|386000921|ref|YP_005919220.1| 136 ALQVVDEKKVAAPANW-PnneliGDHVIIPPPGDEKTAAT 174
                                       9***************.99****************98765 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.069       4      80 ..      35     137 ..      32     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.s...akkFvkl...tgfpfelyvDpsaklyqalglk................... 54 
                                       ++ +e+d+ +++l++ +i+++ s     +++++   ++++f++++D ++ + + lg+                    
  gi|386000921|ref|YP_005919220.1|  35 KRREEFDKLNCELIGLSIDQVfShmkWTEWIREnikVEIKFPIIADDQGRIAEMLGMIhpgkgsntvravfiidpea 111
                                       56799****************997556678877888999*****************987777777777777777665 PP

                        AhpC-TSA_2  55 rglklklaplslqkalenllkrlkei 80 
                                       + + + + p++  + ++++++ lk++
  gi|386000921|ref|YP_005919220.1| 112 TIRLILFYPQEVGRNMDEIVRVLKAL 137
                                       33444444555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1327.44
//
Query:       gi|386000922|ref|YP_005919221.1|  [L=99]
Description: hypothetical protein Mhar_0207 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.9   0.1      0.013   15.5   0.1    1.2  1  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   7.5e-07     0.013       9      63 ..       8      60 ..       2      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.5e-07
                                      EESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHH CS
                               ABM  9 rvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaal 63
                                      r + +   a++++f ++ e + ++  G+ g+el+ ++  ++ +vv+++ +++ a+
  gi|386000922|ref|YP_005919221.1|  8 RHRVEDFPAWRKKFDDRME-I-RKSNGWSGHELYYDEGKKEAYVVHTVHDDKLAM 60
                                      556677889**********.9.6*************************9996662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 705.61
//
Query:       gi|386000923|ref|YP_005919222.1|  [L=204]
Description: Superoxide dismutase (Mn/Fe) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-33  113.5   0.2    6.9e-33  112.9   0.2    1.3  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    4.9e-30  103.8   0.3      8e-30  103.1   0.3    1.3  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.2   7.6e-37   6.9e-33       1     102 []      96     198 ..      96     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 7.6e-37
                                       --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTH CS
                          Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYy 76 
                                       p+g+la+a++e+fgs+ +fkkef+aaa++ +gsGwa L++    ++  i+++++++ ++      l++lDvwehAYy
  gi|386000923|ref|YP_005919222.1|  96 PKGALADALKEEFGSFARFKKEFSAAAATAEGSGWAALAWCGMtNRPVIMQIEKHNVNVYPMFRILMVLDVWEHAYY 172
                                       899*************************************87647899********999998999************ PP

                                       HHHTT-HHHHHHHHGGGBBHHHHHHH CS
                          Sod_Fe_C  77 ldyqnkradYieafwnvvnWkeveer 102
                                       ldy+n+r++++eafw++v+W+ev++r
  gi|386000923|ref|YP_005919222.1| 173 LDYKNERPKFVEAFWKIVDWDEVSRR 198
                                       ***********************986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.3   8.9e-34     8e-30       2      82 .]       7      87 ..       6      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 8.9e-34
                                      ------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          Sod_Fe_N  2 yeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwkn 80
                                      y+LpeLpYay+aLeP+is+ +l lHhdkHh++Yvn++N++le+l++a+++  +l++k++ k+l+++aggh++Hslfw+n
  gi|386000923|ref|YP_005919222.1|  7 YSLPELPYAYNALEPQISEAQLRLHHDKHHAAYVNGANAILERLDKAREAGADLDMKATLKELSFQAGGHLLHSLFWRN 85
                                      99****************************************************************************9 PP

                                      B- CS
                          Sod_Fe_N 81 ls 82
                                      l+
  gi|386000923|ref|YP_005919222.1| 86 LA 87
                                      95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1482.30
//
Query:       gi|386000924|ref|YP_005919223.1|  [L=262]
Description: Dienelactone hydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-28   97.7   0.0    1.1e-25   90.5   0.0    2.0  1  DLH              Dienelactone hydrolase family
    1.1e-09   38.1   0.0    4.1e-06   26.4   0.0    2.1  2  Peptidase_S9     Prolyl oligopeptidase family
     0.0049   15.8   0.0     0.0071   15.3   0.0    1.2  1  Chlorophyllase2  Chlorophyllase enzyme
  ------ inclusion threshold ------
       0.01   14.9   0.0      0.015   14.4   0.0    1.3  1  Chlorophyllase   Chlorophyllase
      0.038   13.8   0.0       0.19   11.6   0.0    1.9  2  Abhydrolase_3    alpha/beta hydrolase fold
      0.059   12.6   0.0        1.8    7.8   0.0    2.1  2  Hydrolase_4      Serine aminopeptidase, S33
      0.064   13.4   0.0       0.13   12.4   0.0    1.4  1  Abhydrolase_4    TAP-like protein
      0.096   12.6   0.0        1.5    8.7   0.0    2.2  2  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0     5e-29   1.1e-25       9     216 ..      64     260 ..      50     261 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 5e-29
                               DLH   9 knakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaa 85 
                                       +++ +p++v+i+ + G++   +d ++rla  G v++aP+  + +       + + ++++elv+              
  gi|386000924|ref|YP_005919223.1|  64 DDPTYPGIVMIHSFNGLEPGYRDLADRLAASGHVVIAPEWQTFNR------TPRDEVVEELVRTS------------ 122
                                       45689*********************************9644444......45556666666655............ PP

                               DLH  86 vaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG.......lspekeleeaakikapilalfgeeD 155
                                        ayl  +++v+ + +g++GfC GG+ ++l+    +e+   va+YG       +   ++ + ++ ++apil+++g++D
  gi|386000924|ref|YP_005919223.1| 123 AAYLVDREDVDGDSLGLTGFCAGGRYTMLFLPGMEEFRSGVAWYGfpysggfNDEARPADLIDGLAAPILIIHGTRD 199
                                       3566666778999*************************************999999********************* PP

                               DLH 156 efipadevekleealkaanvdlelkvYpgagHaFandsresyneeaaedawervlelfkqv 216
                                        + p + + +   al aa++ +elkvY+g gH+F+ +s e ++  aa+da  ++  +f++ 
  gi|386000924|ref|YP_005919223.1| 200 VPSPISGIYDYSAALDAAGKYFELKVYQGEGHGFMIASGEREVSFAARDAEGEMARFFERT 260
                                       **********************************************************975 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00022      0.49      51      98 ..     122     168 ..     102     171 .. 0.85
   2 !   26.4   0.0   1.8e-09   4.1e-06     142     189 ..     187     234 ..     171     262 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                                       HHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE- CS
                      Peptidase_S9  51 aaealakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpv 98 
                                        a +l++++ vd + l++tG  +GG  t+  l    + F+ +va +++
  gi|386000924|ref|YP_005919223.1| 122 SAAYLVDREDVDGDSLGLTGFCAGGRYTMLFLP-GMEEFRSGVAWYGF 168
                                       5889*********************99999998.89999999987776 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.8e-09
                                       ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTT CS
                      Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvg 189
                                         +p+L+ihG+ D   p++  + + aaL+ +gk ++l+++ +egHg+ 
  gi|386000924|ref|YP_005919223.1| 187 LAAPILIIHGTRDVPSPISGIYDYSAALDAAGKYFELKVYQGEGHGFM 234
                                       678******************************************654 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.2e-06    0.0071      15      64 ..      66     115 ..      49     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
                   Chlorophyllase2  15 geYpvllflhGylllnslYsqlLkhiashgfivvapqlykvaeadakeik 64 
                                        +Yp ++++h ++ l+  Y++l  ++a  g++v+ap+ ++++ +  +e+ 
  gi|386000924|ref|YP_005919223.1|  66 PTYPGIVMIHSFNGLEPGYRDLADRLAASGHVVIAPEWQTFNRTPRDEVV 115
                                       48**********************************99998666545442 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.5e-06     0.015      44      90 ..      62     114 ..      29     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-06
                    Chlorophyllase  44 G....typvvlflhGtllsnkfyskllnhiashGfivvaP..qlykllpPsaq 90 
                                       G    typ ++++h +   +  y +l + +a+ G++v+aP  q ++  p ++ 
  gi|386000924|ref|YP_005919223.1|  62 GgddpTYPGIVMIHSFNGLEPGYRDLADRLAASGHVVIAPewQTFNRTPRDEV 114
                                       434448**********************************3334455553333 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   7.8e+02      31      82 ..      97     146 ..      69     153 .. 0.61
   2 ?   11.6   0.0   8.3e-05      0.19     166     210 ..     188     234 ..     169     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                                       EEEEEE---TTTS-TTHHHHHHHH.HHHHHHHTHHHHTETTCEEEEEEETHHH CS
                     Abhydrolase_3  31 vvvsvdYrlAPehpfPaavedala.alrwlaeqawelgadpsrivlaGdSaGG 82 
                                       vv++++ +    +p    ve+ ++ ++ +l+++     +d +++ l G  aGG
  gi|386000924|ref|YP_005919223.1|  97 VVIAPEWQTFNRTPRDEVVEELVRtSAAYLVDR---EDVDGDSLGLTGFCAGG 146
                                       444444444444444444444433134445554...46888888888888888 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.3e-05
                                       ---EEEEEETT-TTHHHH..HHHHHHHHHTT--EEEEEETTEETTGG CS
                     Abhydrolase_3 166 lpptlvvvaefDplrdeg..eayaerlraagvevelieyegmvHgfa 210
                                       ++p+l++ +++D+ +  +   +y+++l aag+  el++y+g+ Hgf+
  gi|386000924|ref|YP_005919223.1| 188 AAPILIIHGTRDVPSPISgiYDYSAALDAAGKYFELKVYQGEGHGFM 234
                                       568888888888877654225799**********************7 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.028        62       7      39 ..      71     103 ..      66     124 .. 0.87
   2 ?    7.8   0.0   0.00081       1.8     190     234 ..     187     233 ..     176     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.028
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDh 39 
                                       +v++H ++     y +la++Laa G  v+a  +
  gi|386000924|ref|YP_005919223.1|  71 IVMIHSFNGLEPGYRDLADRLAASGHVVIAPEW 103
                                       7888999999999*************9999776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00081
                       Hydrolase_4 190 itlPllllhGeaDkvvdpeas...relyerlgskdktlklypglyHel 234
                                       + +P+l++hG++D   + ++     ++++++g k  +lk+y+g  H  
  gi|386000924|ref|YP_005919223.1| 187 LAAPILIIHGTRDVPSPISGIydySAALDAAG-KYFELKVYQGEGHGF 233
                                       459***********999999955555555555.388999**9999976 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.7e-05      0.13      33      78 ..     186     237 ..     164     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
                     Abhydrolase_4  33 g.aapvLllqnerDpaTPyegakklakalgga....vlvtvegeGHgala.a 78 
                                       g aap+L++ ++rD   P +g    + al  a    +l +++geGHg+++ +
  gi|386000924|ref|YP_005919223.1| 186 GlAAPILIIHGTRDVPSPISGIYDYSAALDAAgkyfELKVYQGEGHGFMIaS 237
                                       2369**************************9789988999*******99844 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00065       1.5       9      38 ..     122     151 ..     116     158 .. 0.91
   2 ?    1.2   0.0      0.13   2.9e+02     115     162 ..     188     232 ..     177     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00065
                                       HHHHHHCSTTB--SSEEEEEETHHHHHHHH CS
                            BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelall 38 
                                        ++yl +++ v +d  gl G + Gg +++l
  gi|386000924|ref|YP_005919223.1| 122 SAAYLVDREDVDGDSLGLTGFCAGGRYTML 151
                                       578***********************9987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                       -SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S- CS
                            BAAT_C 115 kgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHl 162
                                        +pil++ g+ D   p +    + s+ L +agk  e++   Y++ GH 
  gi|386000924|ref|YP_005919223.1| 188 AAPILIIHGTRDVPSPISGI-YDYSAALDAAGKYFELK--VYQGEGHG 232
                                       57999999999976665544.589999******95555..56888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1984.98
//
Query:       gi|386000925|ref|YP_005919224.1|  [L=134]
Description: hypothetical protein Mhar_0210 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   11.7   0.0       0.31   11.4   0.0    1.2  1  TraA      TraA


Domain annotation for each model (and alignments):
>> TraA  TraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05      0.31      56      91 ..      46      81 ..       5      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                              TraA 56 tatdlmksgdatvkatfgkdssvvkwvvlaevlvga 91
                                      +  +l + g+ tv +t+ +d   +   +l +vl+g+
  gi|386000925|ref|YP_005919224.1| 46 GEMELQQHGNNTVTGTYTHDNGRISGTILGDVLIGT 81
                                      4568999**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 1050.56
//
Query:       gi|386000926|ref|YP_005919225.1|  [L=242]
Description: Thymidylate synthase, methanogen type [Methanosaeta harundinacea 6Ac]
Scores for 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-19   69.2   0.0    4.3e-19   68.7   0.0    1.2  1  Thymidylat_synt  Thymidylate synthase
  ------ inclusion threshold ------
       0.14   12.4   0.1       0.39   11.0   0.0    1.8  2  Myb_DNA-binding  Myb-like DNA-binding domain


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   4.8e-23   4.3e-19      90     224 ..      82     235 ..      23     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 4.8e-23
                                       -SSSHHHHHHHBTST......................TTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS- CS
                   Thymidylat_synt  90 lgpvYGkqwrkfkae......................egkkidqlakvidqlkenpdsRriivsawnpaeldkmaLp 144
                                        +  YG  +r+++ +                       g  +dq+++v+++l++np+sRr     w p    +    
  gi|386000926|ref|YP_005919225.1|  82 FEYTYGERLRSWSLPcpgkergvrddrggekgidgegAGGAVDQIEYVVRRLRSNPNSRRASAVTWIPPVDTEKEEV 158
                                       6778********99999****************99999999*************************98764458899 PP

                                       -SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHH CS
                   Thymidylat_synt 145 pChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvke 221
                                       pC+++  f++++   g+L+l+   RS D++ + p N+     L++ +a+  g +pg+++ +   aHiY+   + v e
  gi|386000926|ref|YP_005919225.1| 159 PCMMVDDFKIRQ---GRLHLTALFRSHDFAGAYPANLYGLTRLLEYVAERAGAEPGSIATVSCSAHIYDHDWDWVAE 232
                                       **********44...57******************************************************999998 PP

                                       HHT CS
                   Thymidylat_synt 222 qle 224
                                       +++
  gi|386000926|ref|YP_005919225.1| 233 MVT 235
                                       876 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.63   5.7e+03      25      35 ..      29      39 ..      28      40 .. 0.82
   2 ?   11.0   0.0   4.3e-05      0.39      11      38 ..     197     242 .]     195     242 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.63
                                      HHHHHHTSS-H CS
                   Myb_DNA-binding 25 kIaerlggRte 35
                                      +I ++ g+Rt+
  gi|386000926|ref|YP_005919225.1| 29 EITDERGTRTR 39
                                      6889999**98 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHH..................HTTCHHHHHHHHTSS-HHHH CS
                   Myb_DNA-binding  11 lLleavkk..................hGnrWkkIaerlggRtekqc 38 
                                       +Lle+v++                  +  +W+ +ae++ gR+e+++
  gi|386000926|ref|YP_005919225.1| 197 RLLEYVAEragaepgsiatvscsahiYDHDWDWVAEMVTGRSEEEI 242
                                       788888888888888888888888889999************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1746.05
//
Query:       gi|386000927|ref|YP_005919226.1|  [L=164]
Description: hypothetical protein Mhar_0212 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.048   13.6   0.0    1.6  1  Hjc       Archaeal holliday junction resolvase (hjc)


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-06     0.048      38      83 ..      47     103 ..      11     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-06
                                       TTEEEEEEEEEESSS...EEEE........EHHHHHHHHHHHHHHTCEEEEEEEETT CS
                               Hjc  38 gdvvlviEvKsskke...riyl........kkeqvekllefarkaggelllavklqg 83 
                                        + +l+iE+Ks   +   ++y           +q+e++ +f ++ g + +lav l++
  gi|386000927|ref|YP_005919226.1|  47 PAYYLAIECKSIDARkakTLYFtqhfsaagGVHQMERIDQFIDRTGRRGFLAVELRR 103
                                       4569******965551126666****999999**************99999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1197.50
//
Query:       gi|386000928|ref|YP_005919227.1|  [L=176]
Description: hypothetical protein Mhar_0213 [Methanosaeta harundinacea 6Ac]
Scores for 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-07   28.8   0.0    1.3e-06   28.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.1e-06   27.2   0.0      3e-06   26.7   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    8.5e-06   26.4   0.0    1.2e-05   25.9   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.1e-05   25.0   0.0    1.4e-05   24.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    5.2e-05   23.1   0.0    5.2e-05   23.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00017   21.4   0.0    0.00022   21.0   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0002   21.9   0.0    0.00033   21.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0021   17.6   0.0      0.003   17.1   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.024   14.3   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.054   13.0   0.0      0.074   12.6   0.0    1.1  1  DOT1             Histone methylation protein DOT1
       0.23   10.5   0.0       0.31   10.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0     8e-10   1.3e-06       2      47 ..      23      65 ..      22      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8e-10
                   Methyltransf_31  2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAren 47
                                      + g+++lD GCG+G+ ++++    ++  +++GiD+ +ea+e +r++
  gi|386000928|ref|YP_005919227.1| 23 RPGMTFLDMGCGSGAVSLAAS---RFTDQIFGIDRRPEAVEISRAR 65
                                      5789**************999...45679************99986 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.8e-09     3e-06      46     104 ..       8      65 ..       5      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHH CS
                              CMAS  46 AqlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkr 104
                                        q + ++++++kl+++pGmt Ld+GcG G++   a++r+  +++g+    e  + +++r
  gi|386000928|ref|YP_005919227.1|   8 TQPENVQIAIGKLDIRPGMTFLDMGCGSGAVSL-AASRFTDQIFGIDRRPEAVEISRAR 65 
                                       688999***********************9765.7789999999997666666666665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   7.5e-09   1.2e-05       2      57 ..      29      78 ..      28     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.5e-09
                                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG CS
                   Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed 57
                                      Ld+GcG+G ++la+++     ++ g+D  +e++e+ r+r+    +  +f++g+a  
  gi|386000928|ref|YP_005919227.1| 29 LDMGCGSGAVSLAASRFT--DQIFGIDRRPEAVEISRARV----PAGTFLCGEAAG 78
                                      9************99775..*******************9....677888877755 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   8.8e-09   1.4e-05     159     202 ..      22      64 ..      11      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 8.8e-09
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvake 202
                                       +++g ++lD+G+GSG  ++aa+++  ++++++D  + Av+++++
  gi|386000928|ref|YP_005919227.1|  22 IRPGMTFLDMGCGSGAVSLAASRFT-DQIFGIDRRPEAVEISRA 64 
                                       678999*****************96.78************9985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.2e-08   5.2e-05      21      62 ..      23      70 ..      10     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.2e-08
                   Methyltransf_23 21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......k 62
                                      r+g+  Ld+GcG+G ++  ++++  ++ g+D +peavei +      +
  gi|386000928|ref|YP_005919227.1| 23 RPGMTFLDMGCGSGAVSLAASRFTDQIFGIDRRPEAVEISRarvpagT 70
                                      788899********99999998888*************9765554440 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07   0.00022      55     119 ..       6      67 ..       1     119 [. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                       EE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHH CS
                              PCMT  55 tiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlk 119
                                       t  +p  v +a+  l++++g+  L++G+GsG  +   +r+  + +   +i+r +e ve +++++ 
  gi|386000928|ref|YP_005919227.1|   6 TATQPENVQIAIGKLDIRPGMTFLDMGCGSGAVSLAASRFTDQIF---GIDRRPEAVEISRARVP 67 
                                       6789999999999******************99888888877666...*************9985 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     2e-07   0.00033       1      51 [.      29      75 ..      29      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEE CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvad 51
                                      Ld+GcG+G+++ a  +   +++g+D  +e++++++++++       f++++
  gi|386000928|ref|YP_005919227.1| 29 LDMGCGSGAVSLAASRFTDQIFGIDRRPEAVEISRARVPAGT----FLCGE 75
                                      8**************999****************99987764....45555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.9e-06     0.003      29      75 ..      22      66 ..      13      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                                      CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHH CS
                               MTS 29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenl 75
                                       +   + lD+GcG G++++a+ +++++  +  +d   +A+e++++ +
  gi|386000928|ref|YP_005919227.1| 22 IRPGMTFLDMGCGSGAVSLAASRFTDQ--IFGIDRRPEAVEISRARV 66
                                      5566678****************9999..99**********999865 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.024      42      82 ..      25      64 ..      16      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                                      C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHH CS
                     Cons_hypoth95 42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilke 82
                                      g ++LD+ +GsGa++l A+SR  +++  +++ +eav+i ++
  gi|386000928|ref|YP_005919227.1| 25 GMTFLDMGCGSGAVSL-AASRFTDQIFGIDRRPEAVEISRA 64
                                      6789************.88*****************98776 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.5e-05     0.074      26      79 ..       8      59 ..       6      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                      B-HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHH CS
                              DOT1 26 llpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnas 79
                                      ++pe ++  + k+++++  +F+D+G G G v l a+  +   + +G++   +a 
  gi|386000928|ref|YP_005919227.1|  8 TQPENVQIAIGKLDIRPGMTFLDMGCGSGAVSLAAS-RFT-DQIFGIDRRPEAV 59
                                      5788899999*******************9876544.443.3467777665555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00019      0.31      18      70 ..      12      64 ..       7      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                      HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHC CS
                            RrnaAD 18 vineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqk 70
                                       ++ ++ kl++++ +t l++g G G+ +       +q   +  +++ +++ ++
  gi|386000928|ref|YP_005919227.1| 12 NVQIAIGKLDIRPGMTFLDMGCGSGAVSLAASRFTDQIFGIDRRPEAVEISRA 64
                                      5677899******************9986655555777777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1240.09
//
Query:       gi|386000929|ref|YP_005919228.1|  [L=202]
Description: Uroporphyrin-III C/tetrapyrrole methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-31  109.1   0.6    9.7e-31  107.4   0.6    1.6  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.6   5.4e-35   9.7e-31       1     209 [.       1     186 [.       1     189 [. 0.91

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 5.4e-35
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l++V +GpGdpel+T +A ral++ad v+ +++ a +++++++++e  l +pm  +k++l e ++e+a+++a  ++
  gi|386000929|ref|YP_005919228.1|   1 MLIGVSLGPGDPELITRKAERALAAADKVFVPGEMAADLVRRYAEPE-LLDFPMISDKRRLLEIWAENADRVASWAA 76 
                                       79*******************************77999999999776.9***********************99999 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                        g  ++++++GD + ++t+s+l + + +r++++e+e+iPGv  + a+aarlg++l+e++ v++ + p          
  gi|386000929|ref|YP_005919228.1|  77 GGA-AAFACIGDVNTFSTFSHLKRLVIERHPEVEIETIPGVGTVPALAARLGVDLSESFLVSDGS-PV--------- 142
                                       996.********************9999****************************999888888.43......... PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtl 209
                                               t++ +ka+r +ae+a++L+++  + + +  ++ r+  +de vvrg +
  gi|386000929|ref|YP_005919228.1| 143 -------NTVIRMKAVR-PAEMAKELAAE--GFD-EFLLGVRLYAPDEVVVRGEM 186
                                       .......7888898888.99999999888..544.89999999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1398.85
//
Query:       gi|386000930|ref|YP_005919229.1|  [L=236]
Description: Precorrin-4 C11-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-48  164.5   1.7    3.8e-48  164.3   1.7    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.043   12.6   0.0      0.061   12.1   0.0    1.1  1  VipB          Type VI secretion protein, EvpB/VC_A0108, tail 


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.3   1.7   4.2e-52   3.8e-48       1     212 [.       2     201 ..       2     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 4.2e-52
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+++VG+GpGdp+l+Tvr++r+l++ad+v++++s++   ll+ l           + ++++  + eei+  +  alr
  gi|386000930|ref|YP_005919229.1|   2 KVHFVGAGPGDPDLITVRGARLLAEADLVVYAGSLVNPALLEGLSA---------ELVDSNKINLEEINGLMLSALR 69 
                                       799******************************9966666665543.........579999999************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeer 152
                                       +g++Vv+l+sGDP++yg+  e ++ l++  ag+evev+PGvssl a+aa+l++ lt +g++ s++  +p+  + +++
  gi|386000930|ref|YP_005919229.1|  70 RGERVVRLHSGDPSLYGAILEQMRPLEE--AGVEVEVVPGVSSLFAVAAALKTQLTLKGVSESLIvtRPAGTTLARD 144
                                       ****************************..*************************************9999****** PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                        +++l+  g+t++++ + +k+ e+ e+L e   +++tp+avv +a+++de+v++gt+e++
  gi|386000930|ref|YP_005919229.1| 145 SIRELSRFGTTMAIFLGADKIRETTERL-EV--PKQTPAAVVYHASWPDEQVIVGTVEDI 201
                                       ****************************.55..6788********************997 PP

>> VipB  Type VI secretion protein, EvpB/VC_A0108, tail sheath
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.8e-06     0.061     375     415 ..      91     131 ..      83     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-06
                              VipB 375 aryPLreakveVeevpgkpGayraklslrPhfqleeltvsl 415
                                         +PL+ea veVe vpg    +++++ l+ ++ l++++ sl
  gi|386000930|ref|YP_005919229.1|  91 QMRPLEEAGVEVEVVPGVSSLFAVAAALKTQLTLKGVSESL 131
                                       569*********************************99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1707.84
//
Query:       gi|386000931|ref|YP_005919230.1|  [L=254]
Description: Cobalamin (Vitamin B12) biosynthesis CbiG protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-25   89.5   0.1    3.2e-25   88.9   0.1    1.3  1  CbiG_C    Cobalamin synthesis G C-terminus
    2.5e-25   88.3   0.2    2.5e-25   88.3   0.2    2.2  2  CbiG_N    Cobalamin synthesis G N-terminal


Domain annotation for each model (and alignments):
>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.1   3.6e-29   3.2e-25       1     115 [.     140     252 ..     140     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 3.6e-29
                                       EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT- CS
                            CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnps 77 
                                       +vvG+G+rrg++a+e+ ea+ +al   g s e+++a+at ++K+depg+ e+ae+lg p++++++e+L+a +  ++s
  gi|386000931|ref|YP_005919230.1| 140 IVVGLGARRGVDASEVLEAVGSALVSVGRSFEEIRAIATAEIKRDEPGISEAAERLGRPVVYLDEEVLNAQSPTTES 216
                                       79*******************************************************************98753444 PP

                                       CHHHCCCSSS-HHHHHHHHHC.EECSCEEEETTEEEEE CS
                            CbiG_C  78 efvkkevGvpsVaEaaAllaaarllvpKqakggvTvAi 115
                                          ++ +G+ +VaE+aAl+ ++rl++pK+a+g+vTvA+
  gi|386000931|ref|YP_005919230.1| 217 R--ARDLGLVGVAEPAALALSERLIMPKKAYGRVTVAL 252
                                       3..468*******************************7 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.2   2.8e-29   2.5e-25       5      82 .]       2      78 ..       1      78 [. 0.97
   2 ?   -1.8   0.2      0.37   3.3e+03      36      50 ..     128     142 ..     118     167 .. 0.63

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 2.8e-29
                                      HHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
                            CbiG_N  5 elfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82
                                      e++ + d +v+++a+GivvR+++p l++K+tD +Vv+vd++ r ++++++Gh +g+n+lA ++ + lga p++Ttatd
  gi|386000931|ref|YP_005919230.1|  2 EAVGRFDLVVAVMAVGIVVRILCPALREKWTDAPVVAVDSSLRSAVPVVGGH-HGGNDLAYHLYEKLGAYPAVTTATD 78
                                      56788999********************************************.************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.37
                                       --EEEEE-TT--EEE CS
                            CbiG_N  36 DpaVvvvdeagrfvi 50 
                                       D +V v+  +g  v+
  gi|386000931|ref|YP_005919230.1| 128 DEGVAVLRRRGGIVV 142
                                       445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1786.37
//
Query:       gi|386000932|ref|YP_005919231.1|  [L=513]
Description: Cobalt-precorrin-3B C(17)-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-64  217.9   5.3    7.5e-34  117.5   0.6    2.1  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.35   11.0   2.9         11    6.3   0.4    2.8  3  Adeno_PIX     Adenovirus hexon-associated protein (IX)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.6   8.4e-38   7.5e-34       1     212 [.       6     212 ..       6     213 .. 0.84
   2 !  103.0   0.4   2.4e-33   2.1e-29       1     212 [.     278     475 ..     278     476 .. 0.84

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 8.4e-38
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal..aea 75 
                                       +ly+VG+GpG++ llT rA +al +a  v+g++  +l +++dll+          k + ++++  +e+++a   +++
  gi|386000932|ref|YP_005919231.1|   6 RLYIVGIGPGGRGLLTRRAEEALLEARSVVGYG-PYLNLVKDLLPG---------K-VVRSTGMGREVERAReaVDL 71 
                                       69*******************************.**********85.........3.33444445555555562666 PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagie.veviPGvsslqaaaarlgiplteggevlsvl..lpglake 149
                                       l++g dV+l++sGDP+vyg+++  +e ++ r  ++e vev+PG++s++aaa+r+gi   e   v s++  l++++++
  gi|386000932|ref|YP_005919231.1|  72 LAEG-DVALISSGDPNVYGMAGLGLEVASGR-VELErVEVVPGITSFSAAASRAGITFREAVAVISLSdlLTPWERI 146
                                       6666.9**************99999766654.34545*********************************9**9977 PP

                      TP_methylase 150 eereleallangdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtleel 212
                                       e+r ++  +++ +  +++++pr +     l++l+++     ++ ++++ v++++++++e+++ +t +e+
  gi|386000932|ref|YP_005919231.1| 147 EDRARA--ASELGMPMAIYNPRsRrrtwqLERLLDIVTGG-GEGERHLLVAKNVSRPGEALWWTTAGEV 212
                                       766664..46677777777999646788899999999888.99999****************9999886 PP

  == domain 2  score: 103.0 bits;  conditional E-value: 2.4e-33
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+ lVGvGpGdp +lT++A  +++ +d++lg++ r+l+++ +l+     ++     ++ + ee+  +  +a  ea+ 
  gi|386000932|ref|YP_005919231.1| 278 KIRLVGVGPGDPRHLTLEAEGLIRGSDLLLGAE-RHLASVGALPGGL-GARSLSISPTGRFEERVGARLAAAEEAAG 352
                                       6789*****************************.******8776543.5555555555667777777777779**** PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       +g+++ +l++GDP  ++++ + +   ++  +g  ++v PGv ++ aaaar+g+pl++++  ls l    + e++++ 
  gi|386000932|ref|YP_005919231.1| 353 RGETASILFGGDPGTFSSAWRGL---SR--PG--IRVSPGVGAFAAAAARVGAPLVNDFALLSGL----DGEAPEKA 418
                                       ******************99985...88..77..**********************999999999....44566666 PP

                      TP_methylase 155 eallangdtlvllkapr..klaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       ++ll++ ++ v++++ +   l+ +a++ +    d+++p a+v++a+++der+  g+ ++l
  gi|386000932|ref|YP_005919231.1| 419 RRLLEA-GFAVVFYNQSsgGLEAIADAASSL--DPERPFALVQDATRPDERIAIGRASDL 475
                                       677775.555555566646699999999999..7788*****************999987 PP

>> Adeno_PIX  Adenovirus hexon-associated protein (IX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1    0.0065        58      37      73 ..      98     134 ..      86     152 .. 0.83
   2 ?    6.3   0.4    0.0012        11      56      84 ..     387     415 ..     378     427 .. 0.79
   3 ?   -1.9   0.0       0.4   3.6e+03      31      60 ..     419     447 ..     415     459 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0065
                         Adeno_PIX  37 nsttltyetvsgtpletaasaaasaaaatargivtdf 73 
                                        s  +  e v   p  t+ saaas a  t r  v+ +
  gi|386000932|ref|YP_005919231.1|  98 ASGRVELERVEVVPGITSFSAAASRAGITFREAVAVI 134
                                       5666778999999999*************99988754 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0012
                         Adeno_PIX  56 saaasaaaatargivtdfaflsplassaa 84 
                                        a a+aaa     +v dfa+ls l   a 
  gi|386000932|ref|YP_005919231.1| 387 GAFAAAAARVGAPLVNDFALLSGLDGEAP 415
                                       46677777778889********9987765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.4
                         Adeno_PIX  31 rpvlpansttltyetvsgtpletaasaaas 60 
                                       r +l a  + + y+  sg  le+ a aa+s
  gi|386000932|ref|YP_005919231.1| 419 RRLLEAGFAVVFYNQSSG-GLEAIADAASS 447
                                       566777777788887777.59999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 3043.94
//
Query:       gi|386000933|ref|YP_005919232.1|  [L=212]
Description: precorrin-8X methylmutase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-58  195.7   2.1    6.9e-58  195.5   2.1    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.5   2.1   3.9e-62   6.9e-58       1     196 []      18     205 ..      18     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.5 bits;  conditional E-value: 3.9e-62
                                       HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HH CS
                              CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkk 77 
                                       eI+++S ++i   +g++   + e+++ +R++ at+d+++ae+lrf+ d  +agl+al+a a i++D++mv+aG+ k+
  gi|386000933|ref|YP_005919232.1|  18 EIYNRSRSLIAGIVGDR---TPEDRIKQRCVIATGDLSVAEILRFQGDPAAAGLAALEAAAAIFVDIRMVEAGVLKR 91 
                                       69************988...999***************************************************999 PP

                                       HHHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE--- CS
                              CbiC  78 rleklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPv 154
                                        +++   ++++++      +la+++gitr++a++ ++a el+g+ivviGnAP+ALl++++l+e+g+++palvigvPv
  gi|386000933|ref|YP_005919232.1|  92 GHNS---PIITAIGRG--DRLAEKEGITRTSAGFVELAGELSGSIVVIGNAPSALLTVCDLMERGEAEPALVIGVPV 163
                                       9877...899999998..7899******************************************************* PP

                                       -SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHHH CS
                              CbiC 155 GFvgaaesKealaesevpyitveGrkGGsavAaaivnaLlel 196
                                       GFv+aaesKe+l++  vp+i + G++GG+++A+a++n+++++
  gi|386000933|ref|YP_005919232.1| 164 GFVNAAESKERLRKIAVPSISTVGTRGGTPIAVAAINEIINM 205
                                       **************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1331.19
//
Query:       gi|386000934|ref|YP_005919233.1|  [L=409]
Description: Putative cobalt-precorrin-6A synthase (Deacetylating) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-43  147.8   2.8    4.5e-43  147.4   2.8    1.1  1  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   2.8   2.5e-47   4.5e-43       1     222 [.      70     318 ..      70     333 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 2.5e-47
                              CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleeeaavikdaGddp.DvTngaeivae 76 
                                       lr+G+TtG++AaAAak+A++ l  g  + +v+i +p+g+++++p+e     + +++ +k +Gd+  DvT ga+++a+
  gi|386000934|ref|YP_005919233.1|  70 LRRGLTTGTTAAAAAKGAVISL--GGPVFTVSILTPAGIRVSVPVEGR---RGTCTAVKIGGDHAsDVTAGAALMAR 141
                                       699*******************..78889***************6544...457*********866*********** PP

                              CbiD  77 ve......................................eeieiegGeGvGrvtkpgLevevgeaAInpvprkmie 115
                                        e                                      ++ie+ +G G+Gr+  +gL+v+ g++AI+p +r  ie
  gi|386000934|ref|YP_005919233.1| 142 AEaigaeagyeaaagedpgplgsddtrhaegtgpggegpgKRIELVAGAGIGRIGAAGLTVPLGKPAISPSARGEIE 218
                                       ****************************************88*********************************** PP

                              CbiD 116 enveevleea.kegvevtisvpeGeelAkkTlNprlGivgGiSiLGTtGivepmSeeallesireelkvaaaeglke 191
                                       +++ee +eea  e v+v++ v +Ge++A++TlNp++G++gGiSiLG tG vep+ e+ l es ++e+        ++
  gi|386000934|ref|YP_005919233.1| 219 TAIEEGMEEAgLEAVRVELEVINGEAIARETLNPKVGVLGGISILGSTGFVEPWNEH-LAESREAEVLE-----ADR 289
                                       ********998779***************************************9765.55555544433.....479 PP

                              CbiD 192 lvlvtGnkgeklakkklglpeealvkvsnfv 222
                                       +v++tG+ g ++ +    +p+ ++v ++n +
  gi|386000934|ref|YP_005919233.1| 290 VVVTTGRVGLRYSRF--LFPKFRVVLLGNQL 318
                                       9**********9886..57888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 3150.41
//
Query:       gi|386000935|ref|YP_005919234.1|  [L=194]
Description: Precorrin-6y C5,15-methyltransferase (Decarboxylating) domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-21   77.8   1.1    4.4e-21   75.8   1.1    1.9  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   1.1   2.5e-25   4.4e-21       1     209 [.       2     173 ..       2     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 2.5e-25
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+++VG+GpG    lT +A++a+k+a ++ g++ ra e++++ ++                + + +ei++  a +  
  gi|386000935|ref|YP_005919234.1|   2 KIVGVGAGPGM---LTFEAAEAVKEARLIRGSR-RAIELVREVID---------------PGCDVAEIEDYRALREL 59 
                                       78999999988...*******************.******76653...............34445566555544444 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                          ++v+l++GDP+++g g  +             eviPG+ss+q a++rl+++l +   ++ +  ++++  +e  +
  gi|386000935|ref|YP_005919234.1|  60 -PPEAVVLSTGDPMLSGLGYLEG------------EVIPGISSMQVACSRLKVSLLKVVPITVHG-RRMD--PEPIV 120
                                       .4569*************76653............8********************999999999.7755..89999 PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtl 209
                                       e+++  +   +l++   +l+ l++lL e+  +  ++vav  ++g+++e+++rg+ 
  gi|386000935|ref|YP_005919234.1| 121 EEVARGRAVFLLVDEATDLPGLCRLLEER--GLSRDVAVLTDLGYPKEEIRRGST 173
                                       998885555555555558***********..8899****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1473.88
//
Query:       gi|386000936|ref|YP_005919235.1|  [L=350]
Description: hypothetical protein Mhar_0221 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-08   33.8   0.1    4.3e-08   33.1   0.1    1.3  1  Ada_Zn_binding  Metal binding domain of Ada


Domain annotation for each model (and alignments):
>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.4e-12   4.3e-08      18      64 ..     302     349 ..     295     350 .] 0.91

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.4e-12
                                       EEEETTTTEEE-TT-SS.S-S-SCCEEEESSHHHHHHTT-EEETTTTT CS
                    Ada_Zn_binding  18 vyavkttgiyCrpsCpa.rlPkrenveFfdtaaeAeaagfrpCkrcrP 64 
                                       +++ kt   y rp+C++ ++ k+en   f+++ eA++ag+ pCk c+P
  gi|386000936|ref|YP_005919235.1| 302 YVGSKTSDKYHRPDCKSaKKIKPENRITFSDVWEAREAGYSPCKVCNP 349
                                       799************9725567*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2701.42
//
Query:       gi|386000937|ref|YP_005919236.1|  [L=185]
Description: hypothetical protein Mhar_0222 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-11   43.4   0.9    4.2e-11   42.8   0.9    1.3  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.9   2.4e-15   4.2e-11       1      39 [.       8      43 ..       8      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.4e-15
                     Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                      k+m +lL +G tMLa++++ Cg+PL+r+  +g+v+C++C
  gi|386000937|ref|YP_005919236.1|  8 KRMTRLLEMGGTMLATHHE-CGAPLFRY--KGEVVCPVC 43
                                      79**************995.*******6..579****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1379.72
//
Query:       gi|386000938|ref|YP_005919237.1|  [L=69]
Description: hypothetical protein Mhar_0223 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-30  104.2   2.2      3e-30  104.1   2.2    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   2.2   1.7e-34     3e-30      16      81 .]       1      66 [.       1      66 [. 0.98

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 1.7e-34
                                      HT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                           UPF0147 16 iedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                      ++d++vPrniRr+a+ +k++L + +es a+raa+aisiLdeisnDpn+Plh+Rtliw+v s+LEt+
  gi|386000938|ref|YP_005919237.1|  1 MSDDTVPRNIRRSADSVKATLLNVQESEAIRAASAISILDEISNDPNIPLHTRTLIWNVASQLETV 66
                                      689*************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 487.42
//
Query:       gi|386000939|ref|YP_005919238.1|  [L=406]
Description: Orc1/cdc6 family replication initiation protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-22   77.4   0.1    2.1e-21   75.7   0.0    2.0  2  Cdc6_C           CDC6, C terminal winged helix domain
    3.2e-13   50.1   0.0    7.7e-13   48.9   0.0    1.5  1  AAA_22           AAA domain
    9.2e-12   45.7   0.8    2.2e-08   34.7   0.0    2.8  3  AAA_16           AAA ATPase domain
    6.1e-09   36.4   0.0    1.5e-08   35.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
    3.5e-05   23.6   0.0    7.9e-05   22.4   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
      4e-05   23.1   0.0    7.3e-05   22.3   0.0    1.4  1  TniB             Bacterial TniB protein
    0.00014   21.8   0.0    0.00027   20.9   0.0    1.5  1  NACHT            NACHT domain
    0.00015   21.5   0.0       0.02   14.6   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00031   20.8   0.2     0.0015   18.5   0.2    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00055   19.2   0.0    0.00087   18.5   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
     0.0036   17.1   0.0     0.0062   16.3   0.0    1.4  1  AAA_24           AAA domain
     0.0069   15.7   0.0     0.0093   15.2   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.025   14.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.019   15.3   0.3      0.055   13.8   0.3    1.8  1  AAA_assoc_2      AAA C-terminal domain
      0.021   15.3   0.2       0.06   13.9   0.2    1.9  1  AAA_18           AAA domain
      0.038   14.0   0.0       0.08   13.0   0.0    1.5  1  AAA_14           AAA domain
      0.046   14.1   0.0       0.14   12.6   0.0    1.8  1  RNA_helicase     RNA helicase
      0.053   13.3   3.9        1.3    8.7   0.1    2.9  3  DEAD             DEAD/DEAH box helicase
      0.055   13.5   0.3       0.41   10.6   0.3    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
      0.066   12.6   0.9       0.76    9.1   0.1    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.069   13.2   0.0       0.13   12.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.14   11.1   0.2       0.39    9.6   0.1    1.7  2  AAA_10           AAA-like domain
       0.16   11.2   0.2        9.9    5.3   0.0    2.1  2  KAP_NTPase       KAP family P-loop domain
       0.17   11.6   2.1       0.27   10.9   0.1    2.3  3  IstB_IS21        IstB-like ATP binding protein
       0.23   10.1   0.0       0.37    9.4   0.0    1.2  1  AAA_13           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 ?   -2.6   0.0       7.7   5.5e+03      27      42 ..     261     276 ..     237     279 .. 0.62
   2 !   75.7   0.0     3e-24   2.1e-21       1      78 [.     303     378 ..     303     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.7
                                       HHHHHTT-----HHHH CS
                            Cdc6_C  27 slCesegvdpltqrev 42 
                                       +l+e++g + +t+ +v
  gi|386000939|ref|YP_005919238.1| 261 ELAERTGSNRVTEDQV 276
                                       5666666666666665 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 3e-24
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L++++ll++ +g + vttg vy +Yk+lC   ++d lt+r++ dl++eL+mlgi+ + ++skGr +grt++isL+++
  gi|386000939|ref|YP_005919238.1| 303 LYSVLLLEE-QGIKNVTTGAVYGMYKQLCPLVDLDFLTHRRIADLIAELDMLGIIHTVVVSKGR-YGRTKEISLSIP 377
                                       89*****99.*****************************************************9.*********987 PP

                                       C CS
                            Cdc6_C  78 p 78 
                                        
  gi|386000939|ref|YP_005919238.1| 378 L 378
                                       5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.1e-15   7.7e-13       4     129 ..      53     179 ..      50     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.1e-15
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelkaerlsseell 79 
                                       ta+ ++++G +GtGKT +++ + ++l+++ +     + +++++++ +  ++  +l +l+r +g+e    +  +++++
  gi|386000939|ref|YP_005919238.1|  53 TASNVLIYGKTGTGKTAVAKYVGSELEAAGAK-SaSNCSFIYINCEVIDTQYRVLAHLARCFGREVPMTGWPTDQVY 128
                                       78999*********************655444.36********************************9889999999 PP

                            AAA_22  80 ealeqalraravielliiDEaqhlr.s.eealeeL.rsllnlsrkgvqliLvG 129
                                       e +++ l++ ++ +++++DE+++l+ + +++l +L r+ ++   ++  + L+G
  gi|386000939|ref|YP_005919238.1| 129 EEVRKSLDEDRRMVVMVLDEVDKLTrKgDDILYNLtRINSD--LDQAGVSLIG 179
                                       ********99999***********76269999999455566..4555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.1e-11   2.2e-08       2      79 ..      31     116 ..      30     127 .. 0.88
   2 !    8.4   0.1    0.0036       2.5     129     163 ..     134     168 ..     123     178 .. 0.78
   3 ?   -1.3   0.0       3.6   2.6e+03     106     107 ..     250     272 ..     193     304 .. 0.45

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.1e-11
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipy.. 69 
                                       l+ Re++++ ++s+l ++ +g++ ++vl++G  G+GK+++++ +  +le++      ++ f++ +c+    ++ y  
  gi|386000939|ref|YP_005919238.1|  31 LPHREDQINGMASILVPALRGETaSNVLIYGKTGTGKTAVAKYVGSELEAAgaksasNCSFIYINCEVI--DTQYrv 105
                                       789*******************************************999999999988999********..555555 PP

                            AAA_16  70 sa.laqalare 79 
                                       +a la+++ re
  gi|386000939|ref|YP_005919238.1| 106 LAhLARCFGRE 116
                                       55588888664 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0036
                            AAA_16 129 llsrderplvlvlDdlqwadeaslqllaaLlrlle 163
                                        l +d+r +v+vlD+++++     ++l++L r  +
  gi|386000939|ref|YP_005919238.1| 134 SLDEDRRMVVMVLDEVDKLTRKGDDILYNLTRINS 168
                                       55666677**********************98754 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.6
                            AAA_16 106 a.....................a 107
                                       +                      
  gi|386000939|ref|YP_005919238.1| 250 RraldllrvsgelaertgsnrvT 272
                                       11111112222222333333333 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 !   35.1   0.0   2.1e-11   1.5e-08       1     112 [.      57     187 ..      57     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.1e-11
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS....................STTHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk....................yvgesekkire 48 
                                       vl+yG  GtGKT++ak v +el         + +f+ i++  +  +                       +  +++r+
  gi|386000939|ref|YP_005919238.1|  57 VLIYGKTGTGKTAVAKYVGSELeaagaksasNCSFIYINCEVIDTQyrvlahlarcfgrevpmtgwPTDQVYEEVRK 133
                                       79*******************8555444444477******99997799********999888665444555555555 PP

                                       HHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...G CS
                               AAA  49 lfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...p 112
                                        ++e +   + +++++DE+d+l+++         ++++  L +  +++++  + v +ig++n+    
  gi|386000939|ref|YP_005919238.1| 134 SLDEDR---RMVVMVLDEVDKLTRKG--------DDILYNLTRINSDLDQ--AGVSLIGISNDlkfT 187
                                       555533...459**********9888........8899999999888888..579******994444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-07   7.9e-05      20      64 ..      52     102 ..      35     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                                       TSSS-EEEECSTTSSHHHHHHHHHH......HSTTTTS-EEEEETTTS-TT CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraihe......askrkekpfvavncaaipee 64 
                                       +t ++vli G++GtGK+ +a+ + +      a++ ++ +f+ +nc  i ++
  gi|386000939|ref|YP_005919238.1|  52 ETASNVLIYGKTGTGKTAVAKYVGSeleaagAKSASNCSFIYINCEVIDTQ 102
                                       46789******************7766666666667779******977554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     1e-07   7.3e-05      29     132 ..      48     153 ..      32     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1e-07
                              TniB  29 ypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkar.arv 104
                                       + + +  +n+l++G++ +GKt++++   ++ +++  ++a+++  +++++    ++ r  a++ + +g ++  + + +
  gi|386000939|ref|YP_005919238.1|  48 ALRGETASNVLIYGKTGTGKTAVAKYVGSELEAAGAKSASNCSFIYINCEVIDTQYRVLAHLARCFGREVPMTgWPT 124
                                       45566679**************9988888888888999****************************99987763688 PP

                              TniB 105 skleqqvlrllre.lkvrvLiiDEihnll 132
                                       ++ +++v + l+e  ++ v+++DE+++l 
  gi|386000939|ref|YP_005919238.1| 125 DQVYEEVRKSLDEdRRMVVMVLDEVDKLT 153
                                       99999**9999752678899******987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.8e-07   0.00027       3      98 ..      57     157 ..      55     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.8e-07
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....CHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse....vwa 74 
                                       v++ G+ G GKT+ ++ + +++ +   ++   + ++++++  + ++ ++  +la+   ++ p  + p ++    v++
  gi|386000939|ref|YP_005919238.1|  57 VLIYGKTGTGKTAVAKYVGSELEAAGAKSASNCSFIYINCEVIDTQYRVlAHLARCFGREVPMTGWPTDQvyeeVRK 133
                                       89*********************9999998899999*********99989999999999999998888888888999 PP

                                       HHCCSCCCEEEEEE-STT-SS-TC CS
                             NACHT  75 vllelperlLlilDglDelvtdlg 98 
                                        l e ++ ++++lD +D+l ++ +
  gi|386000939|ref|YP_005919238.1| 134 SLDEDRRMVVMVLDEVDKLTRKGD 157
                                       99999*************998655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.9e-05      0.02      28      60 ..      49      81 ..      35      92 .. 0.83
   2 ?    4.2   0.0     0.046        33      62     106 ..     118     162 ..     104     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                            RuvB_N 28 kreealdhvllyGpPGlGkttlakiiakelgvk 60
                                       r+e+   vl+yG  G Gkt++ak + +el++ 
  gi|386000939|ref|YP_005919238.1| 49 LRGETASNVLIYGKTGTGKTAVAKYVGSELEAA 81
                                      69999*************************975 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.046
                            RuvB_N  62 kitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                        +t  P+ +   ++   l + ++  v+ +de+ +l+r+ +++ly+
  gi|386000939|ref|YP_005919238.1| 118 PMTGWPTDQVYEEVRKSLDEDRRMVVMVLDEVDKLTRKGDDILYN 162
                                       555555555556666666666777899*****************6 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   2.1e-06    0.0015      14     147 ..      48     165 ..      33     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                          ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkae 90 
                                        l+ e+++ ++iYG  g GKta+ k + ++le  + +     ++  ++ + +d+     ++   l++ +g +vp + 
  gi|386000939|ref|YP_005919238.1|  48 ALRGETASNVLIYGKTGTGKTAVAKYVGSELEAAGAKSASNCSFIYINCEVIDTQ---YRVLAHLARCFGREVPMTG 121
                                       46889999***********************999885555555555555555554...4555788999999999877 PP

                          ATPase_2  91 leeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLln 147
                                                   ++  e++ +++ ++++ +++++De+ kl     ++  + +++L +
  gi|386000939|ref|YP_005919238.1| 122 W---------PTDQVYEEVRKSLDEDRRMVVMVLDEVDKLT----RKGDDILYNLTR 165
                                       6.........5589999999999999999*********999....556667776665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06   0.00087      46      92 ..      47      99 ..      24     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                            DUF815 46 qfleglpannvLLwGarGtGKSslvkallneyaeeg......Lrlievekedl 92
                                        l+g++a+nvL++G+ GtGK ++ k + +e++++g        +i ++ e +
  gi|386000939|ref|YP_005919238.1| 47 PALRGETASNVLIYGKTGTGKTAVAKYVGSELEAAGaksasnCSFIYINCEVI 99
                                      5689***********************99999887755555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.7e-06    0.0062       3      85 ..      55     160 ..      53     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.7e-06
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie...........................swedf 52 
                                        ++liyG+ g+GKT +ak    + l     k++ +  ++    i+                             +++
  gi|386000939|ref|YP_005919238.1|  55 SNVLIYGKTGTGKTAVAKYV-GSELEAAGAKSASNCSFIY---INcevidtqyrvlahlarcfgrevpmtgwPTDQV 127
                                       589*****************.5555544444444444444...3333666766666677777788888887766778 PP

                            AAA_24  53 ldevvelaaeladyktlviDtideleelclaev 85 
                                       ++ev +  +e+++  + v+D +d+l +  ++ +
  gi|386000939|ref|YP_005919238.1| 128 YEEVRKSLDEDRRMVVMVLDEVDKLTRKGDDIL 160
                                       888888899999999999999999988655555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05    0.0093       3     105 ..      56     157 ..      54     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakke..ekkkkkeafeklssfinnls 75 
                                        vl+ G++GtGKt v+  +  el     ++ ++  +++ N + +++ ++ la  +   +++   +    +++ ++++
  gi|386000939|ref|YP_005919238.1|  56 NVLIYGKTGTGKTAVAKYVGSELeaAGAKSASNCSFIYINCEVIDTQYRVLAHLArcFGREVPMTGWPTDQVYEEVR 132
                                       689********************6555667777789*************9998884444444444444555555555 PP

                           DUF2075  76 efkkaeekkeepkedvvivDEAhrlltksd 105
                                            ++ +e++++ v++ DE  +l+ k+d
  gi|386000939|ref|YP_005919238.1| 133 -----KSLDEDRRMVVMVLDEVDKLTRKGD 157
                                       .....777888999999****999998776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.5e-05     0.025      33      60 ..      54      81 ..      45     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldke 60
                                        +vl++G+tGtGKt+++k + ++l+  
  gi|386000939|ref|YP_005919238.1| 54 ASNVLIYGKTGTGKTAVAKYVGSELEAA 81
                                      679***************9999888844 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   7.7e-05     0.055      13      55 ..     239     280 ..     231     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleeal 55 
                                       +ala+  +GDaR+aL lL +  e ae+ +g++++t++++++a 
  gi|386000939|ref|YP_005919238.1| 239 SALAAQEHGDARRALDLLRVSGELAER-TGSNRVTEDQVRAAR 280
                                       67899999***********99999986.999999999998654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   8.4e-05      0.06       1      25 [.      57      97 ..      57     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.4e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf................g 25
                                      +l+ G+ G+GKt +ak++ ++l+                  
  gi|386000939|ref|YP_005919238.1| 57 VLIYGKTGTGKTAVAKYVGSELEAagaksasncsfiyincE 97
                                      79****************76663334444444454444440 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011      0.08       5      78 ..      57     154 ..      54     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            AAA_14   5 lvitGaRrvGKTtllkqlikell......vkkesilyinldderd...........kkladpe...........kll 53 
                                       ++i G   +GKT ++k + +el       +++ s++yin++  ++                             +++
  gi|386000939|ref|YP_005919238.1|  57 VLIYGKTGTGKTAVAKYVGSELEaagaksASNCSFIYINCEVIDTqyrvlahlarcF-----GrevpmtgwptdQVY 128
                                       7899999********99999988***9999999********9999555555444441.....033444555555777 PP

                            AAA_14  54 elileklke.ekktylflDEiqevpe 78 
                                       e+++++l e +++ +++lDE+ ++++
  gi|386000939|ref|YP_005919238.1| 129 EEVRKSLDEdRRMVVMVLDEVDKLTR 154
                                       777777433478899******98754 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00019      0.14       1      26 [.      57      82 ..      57     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      +++yG++g+GK+ +ak++ ++l+ + 
  gi|386000939|ref|YP_005919238.1| 57 VLIYGKTGTGKTAVAKYVGSELEAAG 82
                                      689**************999998655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0019       1.3      14      31 ..      54      71 ..      36      84 .. 0.81
   2 ?    4.4   0.1     0.039        28     122     150 ..     141     167 ..     123     184 .. 0.74
   3 ?   -0.8   0.1       1.6   1.1e+03      83     128 ..     339     387 ..     272     389 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                      TCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                              DEAD 14 ggdvlvaaeTGsGKTlaf 31
                                        +vl+ ++TG+GKT+++
  gi|386000939|ref|YP_005919238.1| 54 ASNVLIYGKTGTGKTAVA 71
                                      479************997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlp 150
                                       + ++VlDE+d+l  +  +d+i   l++++
  gi|386000939|ref|YP_005919238.1| 141 MVVMVLDEVDKLTRK--GDDILYNLTRIN 167
                                       4579*********98..555555555553 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.6
                                       TTSSHHHHHHHHH.TT.CSEEEEEHHHHHHHHH.CTSSHCTTEEEEEEE CS
                                       xxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                              DEAD  83 ggvaardqlskld.ng.vdivvgtpgrlddlls.tgklnlsqvrflVlD 128
                                       +  +  d +++ld  g ++ vv   gr  +  + + ++ l +++ ++lD
  gi|386000939|ref|YP_005919238.1| 339 THRRIADLIAELDmLGiIHTVVVSKGRYGRTKEiSLSIPLAKLKAMILD 387
                                       4455556666665333677888888887774421223448888888888 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 ?   10.6   0.3   0.00057      0.41       1      80 [.      56     155 ..      56     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00057
                                       EEEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--T.T--HHHHH--B--.............------- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.........nreveyvqltr.dtteedlkgrreik....ngttslvdsplvraa 63 
                                       +vl+ G++GtgK+ +a+++ + l         n+++ y+++   dt+++ l    +      +  t +    +++++
  gi|386000939|ref|YP_005919238.1|  56 NVLIYGKTGTGKTAVAKYVGSELeaagaksasNCSFIYINCEViDTQYRVLAHLARCFgrevP-MTGWPTDQVYEEV 131
                                       69***************9987777777777777777777776524444444333332244422.2333333344455 PP

                                       -.......G-SEEEEESGGG--HH CS
                             AAA_5  64 r.......egeilvlDEveraese 80 
                                       r       +  ++vlDEv+++ ++
  gi|386000939|ref|YP_005919238.1| 132 RksldedrRMVVMVLDEVDKLTRK 155
                                       556666666667777777776655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0011      0.76      38      55 ..      52      70 ..      34     120 .. 0.75
   2 ?    1.8   0.1      0.18   1.3e+02     134     165 ..     128     162 ..      96     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                                      S-..SEEEE--TTSSHHHH CS
                      FtsK_SpoIIIE 38 ma.shllvaGatgsGKSta 55
                                       + s++l+ G tg+GK+ +
  gi|386000939|ref|YP_005919238.1| 52 ETaSNVLIYGKTGTGKTAV 70
                                      4459************965 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHTT---B-TT-................ CS
                      FtsK_SpoIIIE 134 ydgeiaedpldifgdvflvlDnyddlaaene....r 165
                                       y+++ ++  +d + +v++vlD+ d+l  ++      
  gi|386000939|ref|YP_005919238.1| 128 YEEVRKSLDED-RRMVVMVLDEVDKLTRKGDdilyN 162
                                       66666666666.5799***********999866553 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.13       5      50 ..      36      85 ..      33     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT------ CS
                              TsaE  5 eetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgveevkS 50
                                      ++++ +++ l  al    ++ +l++G+ G+GKT+ ++ + ++l+ +  kS
  gi|386000939|ref|YP_005919238.1| 36 DQINGMASILVPALrgetASNVLIYGKTGTGKTAVAKYVGSELEAAGAKS 85
                                      566666777777666543455*******************9998763333 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00055      0.39      15      51 ..      50      84 ..      45      95 .. 0.88
   2 ?   -2.5   0.0       2.5   1.8e+03     242     269 ..     142     167 ..     128     218 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00055
                            AAA_10 15 kgsktnasasliiGdlGnGKSvlakllvlyisllggk 51
                                      +g  ++as++li G++G GK  +ak++   + ++g k
  gi|386000939|ref|YP_005919238.1| 50 RG--ETASNVLIYGKTGTGKTAVAKYVGSELEAAGAK 84
                                      55..789999*****************9998888866 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                            AAA_10 242 kvvifDEawiftssaeGkkllkelvRiG 269
                                        v+++DE+  +t   +G  +l +l Ri 
  gi|386000939|ref|YP_005919238.1| 142 VVMVLDEVDKLT--RKGDDILYNLTRIN 167
                                       456667766665..35666666666654 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.014       9.9       5      46 ..      38      80 ..      34     111 .. 0.81
   2 ?    4.0   0.1     0.034        24     159     187 ..     126     154 ..     115     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                        KAP_NTPase  5 asaladilseptl..atpivvgLygkWGsGKssllnkledelke 46
                                      ++ +a il+ p+l  +t + v +ygk G+GK+++ + + +el+ 
  gi|386000939|ref|YP_005919238.1| 38 INGMASILV-PALrgETASNVLIYGKTGTGKTAVAKYVGSELEA 80
                                      566677777.6667789999*************99988888765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.034
                        KAP_NTPase 159 elladmektLdalqkrlVvviDdLDrcet 187
                                       +++++  k+Ld+  + +V+v+D+ D ++ 
  gi|386000939|ref|YP_005919238.1| 126 QVYEEVRKSLDEDRRMVVMVLDEVDKLTR 154
                                       57788999****9************9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00038      0.27      46      75 ..      53      82 ..      46      94 .. 0.88
   2 ?   -2.2   0.1       4.1   2.9e+03      99     121 ..     131     153 ..     125     167 .. 0.74
   3 ?   -3.1   0.0       7.5   5.4e+03     106     122 ..     378     394 ..     367     399 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgveavrag 75
                                      ++ n+++ G +G+GK+ +a  +g e  +ag
  gi|386000939|ref|YP_005919238.1| 53 TASNVLIYGKTGTGKTAVAKYVGSELEAAG 82
                                      678****************99998876666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.1
                         IstB_IS21  99 laralkrllkvdllilDdlgllp 121
                                       + + l++  ++ +++lD++  l+
  gi|386000939|ref|YP_005919238.1| 131 VRKSLDEDRRMVVMVLDEVDKLT 153
                                       56777888899999999986554 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 7.5
                         IstB_IS21 106 llkvdllilDdlgllpl 122
                                       l+k + +ilDd+ l++l
  gi|386000939|ref|YP_005919238.1| 378 LAKLKAMILDDYRLKDL 394
                                       56788899999988765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00051      0.37      20      57 ..      58      95 ..      53     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00051
                            AAA_13 20 liYGwNGaGKTtLSrllrslelgetepkfangsieitn 57
                                      liYG+ G+GKT ++++  s  + +  +  +n+s+++ n
  gi|386000939|ref|YP_005919238.1| 58 LIYGKTGTGKTAVAKYVGSELEAAGAKSASNCSFIYIN 95
                                      7***************9874444555667888886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.61
# Mc/sec: 2000.55
//
Query:       gi|386000940|ref|YP_005919239.1|  [L=299]
Description: Thioredoxin reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-35  122.9   5.1    1.7e-35  122.7   5.1    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-21   76.3   2.2    2.9e-16   59.6   0.0    2.4  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    9.2e-08   31.6  12.0    2.4e-05   23.6   1.7    3.6  4  FAD_binding_2  FAD binding domain
    1.6e-06   27.1   3.7    0.00043   19.1   0.4    2.6  3  HI0933_like    HI0933-like protein
    2.6e-05   23.5   9.4     0.0068   15.5   0.4    3.6  4  GIDA           Glucose inhibited division protein A
    8.5e-05   21.9   0.3    0.00017   20.9   0.3    1.5  1  Thi4           Thi4 family
    0.00055   19.4   0.2    0.00055   19.4   0.2    1.6  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0016   18.1  11.4       0.06   12.9   0.1    2.5  3  DAO            FAD dependent oxidoreductase
     0.0017   17.7   0.8     0.0032   16.8   0.8    1.4  1  FAD_binding_3  FAD binding domain
     0.0091   16.2   0.4     0.0091   16.2   0.4    2.4  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.081   12.9   0.0    1.3  1  HU-DNA_bdg     DNA-binding domain
      0.066   12.3   3.9       0.34   10.0   0.0    2.4  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.79   10.3   6.0        6.3    7.4   0.1    3.1  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   5.1   1.3e-38   1.7e-35       1     294 []       2     287 ..       2     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.3e-38
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgie 68 
                                       +dv++iG+GpAGl+a ++ a+ g k++++   g++ + + ++   ++++++++e ++          + kk++++++
  gi|386000940|ref|YP_005919239.1|   2 YDVIIIGAGPAGLTAGMYCARGGKKILIL---GNVYGSQQSMGGLYENYPGFPEGIQgielsermvAQAKKYGAELH 75 
                                       69***************************...99999999**99999999999999999888777766666666643 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkri 145
                                             v k+   ++ + +++  e++  ++++ +l+lA+G++ r+l ipG+ e+++++v++++ +++    ++   +
  gi|386000940|ref|YP_005919239.1|  76 EEV---VAKVVSLNGVFRVKT--ESW--EYQARALILAMGARHRTLSIPGEVEYATRGVSYCAYCDGALFRNKT--V 143
                                       333...344444456677732..234..8***************************************999988..* PP

                                       EEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx. RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge....kle. 217
                                       +v+G G+ +     +la l ++v+l+  r+ l+      ++a++ ++++    +++    v+ i   g+     +e 
  gi|386000940|ref|YP_005919239.1| 144 AVIGYGNGAARAVLYLAGLCARVHLLNVREDLV------AEAIYLDRIKSL-TNFVATPGVEPISILGDgfvtGVEf 213
                                       ********************************9......899999999887.7788777777666666665877777 PP

                                       EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                          ++ +++++d v+v  Gv+p+ el+  +lg+el+++g+++v++   +tn+pg++a+GDv+   gg +++++Av +
  gi|386000940|ref|YP_005919239.1| 214 RARGKVRTLKVDGVFVEMGVSPNVELA-ADLGVELTKGGFVKVNRLTqETNIPGVFAAGDVT---GGRMQVTTAVGA 286
                                       88899999*******************.*****************984699***********...888888888776 PP

                                       H CS
                                       x RF
                       Pyr_redox_2 294 G 294
                                       G
  gi|386000940|ref|YP_005919239.1| 287 G 287
                                       6 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.0     6e-06    0.0083       1      27 [.       5      30 ..       5      48 .. 0.89
   2 !   59.6   0.0   2.1e-19   2.9e-16      88     305 .]      62     271 ..      59     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                      iIiGaGPaGl+a++ + + g  ++lil
  gi|386000940|ref|YP_005919239.1|  5 IIIGAGPAGLTAGMYCARGGK-KILIL 30
                                      8****************9998.79998 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 2.1e-19
                       Pyr_redox_3  88 revaksfelpiklfeeV.esvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefh 160
                                       r va+ +++  +l+eeV  +v + ++ f+v+t++ +y+A+ +i+A+G   + ++l+ipGe +     + y  + + +
  gi|386000940|ref|YP_005919239.1|  62 RMVAQAKKYGAELHEEVvAKVVSLNGVFRVKTESWEYQARALILAMGA--RHRTLSIPGEVEyatRGVSYCAYCDGA 136
                                       56888888888888876489***************************9..99999*****97333456888888999 PP

                       Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke......ekikvlf 231
                                        ++++ v+ViG +n a+ a l l+   a+V+++  ++ + +e         +++ +r+++l +       e i +l 
  gi|386000940|ref|YP_005919239.1| 137 LFRNKTVAVIGYGNGAARAVLYLAGLCARVHLLNVREDLVAE---------AIYLDRIKSLTNFvatpgvEPISILG 204
                                       9********************************999865554.........45555555544311112223455555 PP

                       Pyr_redox_3 232 naevkeikekeeeykvktedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +  v+ ++ +        ++gk  + k d v++ +G +p++++ ++ ++el++ g+++++  t+etn+pg+f aG
  gi|386000940|ref|YP_005919239.1| 205 DGFVTGVEFR--------ARGKVRTLKVDGVFVeMGVSPNVELAADLGVELTKGGFVKVNRLTQETNIPGVFAAG 271
                                       5555555543........3334444455666666***************************************99 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.7   1.7e-08   2.4e-05       1      32 [.       3      34 ..       3      44 .. 0.88
   2 !    5.5   0.1    0.0054       7.5     139     205 ..      55     115 ..      36     165 .. 0.74
   3 ?   -0.8   0.0      0.44     6e+02     155     204 ..     210     254 ..     202     263 .. 0.73
   4 !    7.9   0.1     0.001       1.4     388     413 ..     260     285 ..     253     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.7e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dvi+iG+G AGL+A++ +a+ G+k++++ ++ 
  gi|386000940|ref|YP_005919239.1|  3 DVIIIGAGPAGLTAGMYCARGGKKILILGNVY 34
                                      9*************************997765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG... CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr..a 205
                                       +g +l +r+v++a+k+g +++e+  a+ +       +G+      + +  +++a+a++la g+ +r  +
  gi|386000940|ref|YP_005919239.1|  55 QGIELSERMVAQAKKYGAELHEEVVAKVVSL-----NGVFRV---KTESWEYQARALILAMGARHRtlS 115
                                       677888999999*999999999999988855.....675444...566677999********9999442 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.44
                                       TEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES.EEEE-----GG CS
                     FAD_binding_2 155 gvdfqerteadeLivedgrvtGavvenpesgrevrirak.avvlatgGfgr 204
                                       gv+f++r ++++L     +v G+ ve +  + +v+++a+ +v l++gGf +
  gi|386000940|ref|YP_005919239.1| 210 GVEFRARGKVRTL-----KVDGVFVE-MGVSPNVELAADlGVELTKGGFVK 254
                                       5777777777777.....78888888.544555778999999999999976 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.001
                                       EEESSBTEEE-STCEESSSSTTS--T CS
                     FAD_binding_2 388 dgqpipGLYAaGevaaggvhganrlg 413
                                       ++++ipG +AaG v++g ++ + + g
  gi|386000940|ref|YP_005919239.1| 260 QETNIPGVFAAGDVTGGRMQVTTAVG 285
                                       5789***********99998877655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   3.1e-07   0.00043       1      30 [.       2      31 ..       2      40 .. 0.93
   2 !    8.2   0.0   0.00063      0.87     103     164 ..      51     109 ..      49     118 .. 0.79
   3 ?   -2.0   0.1      0.78   1.1e+03     356     384 ..     248     273 ..     245     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllle 30
                                      +dvi+iG+G+AGl a + +a+ gk++l+l 
  gi|386000940|ref|YP_005919239.1|  2 YDVIIIGAGPAGLTAGMYCARGGKKILILG 31
                                      59************************9985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00063
                                       ETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 103 pvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       p+  +  ++ + +++++k+ g +l+ e   k v  + +g+frvkt ++ e++a++l+lA+G 
  gi|386000940|ref|YP_005919239.1|  51 PEGIQGIELSERMVAQAKKYGAELHEEVVAKVV--SLNGVFRVKT-ESWEYQARALILAMGA 109
                                       555566667777889999999999876644444..67889*****.9*************97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.78
                                       EEEE.E-GGGB-TTT-BBTTSTTEEE-GGG CS
                       HI0933_like 356 TaGG.VdlkevssktmeskkvpgLffaGEv 384
                                       T+GG V+++ + ++t    ++pg+f aG v
  gi|386000940|ref|YP_005919239.1| 248 TKGGfVKVNRLTQET----NIPGVFAAGDV 273
                                       666645555555554....59*******87 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   4.9e-06    0.0068       1      28 [.       3      30 ..       3      46 .. 0.86
   2 ?   -0.3   0.0      0.31   4.2e+02     112     163 ..      73     122 ..      56     131 .. 0.67
   3 ?    0.8   0.1      0.15     2e+02       2      45 ..     143     186 ..     142     198 .. 0.85
   4 !   10.3   0.2   0.00019      0.26     350     389 ..     260     299 .]     252     299 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.9e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dvi+iG+G AG+ A + +ar G k+l++
  gi|386000940|ref|YP_005919239.1|  3 DVIIIGAGPAGLTAGMYCARGGKKILIL 30
                                      8**********************99987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                                       EEEES-EEEEEECTTEEEEEEE..TTS-EEEECEEEE--TT-BT-EEEETTEEE CS
                              GIDA 112 eiieeeveeliveekkvkgvvt..edgetikakavviatGtflkgkihigekel 163
                                       e+ ee v++++     ++gv    ++  +++a+a ++a G+  +  ++ ge e+
  gi|386000940|ref|YP_005919239.1|  73 ELHEEVVAKVVS----LNGVFRvkTESWEYQARALILAMGARHRTLSIPGEVEY 122
                                       566666777744....56654300344578999*******96666666666555 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.15
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsig 45 
                                       v ViG G     A l +a l a+v L+  + d +ae  + + i+
  gi|386000940|ref|YP_005919239.1| 143 VAVIGYGNGAARAVLYLAGLCARVHLLNVREDLVAEAIYLDRIK 186
                                       89*************************98888888876665555 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00019
                                       SBBSSSBTEEE-CGGGTB-S.HHHHHHHHHHHHHHHHHHHC CS
                              GIDA 350 LetkkvkgLflAGqinGteG.YeEaaaqGllAGinaarkak 389
                                        et+ ++g+f+AG+++G     + a++ G+ A+i a r+++
  gi|386000940|ref|YP_005919239.1| 260 QETN-IPGVFAAGDVTGGRMqVTTAVGAGTSAAISAMRHIQ 299
                                       4554.9***********9651567888**********9986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   1.2e-07   0.00017      19      49 ..       3      32 ..       1      46 [. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailer 49
                                      Dv+i+GaG++GLta+ y a+  + k++il +
  gi|386000940|ref|YP_005919239.1|  3 DVIIIGAGPAGLTAGMYCARG-GKKILILGN 32
                                      9*******************9.999999864 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2     4e-07   0.00055       1      29 [.       3      31 ..       3      81 .. 0.89
   2 ?   -3.4   0.6       3.3   4.5e+03      10      20 ..     286     296 ..     285     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve 29
                                      Dv+++G+gpaG++A + +ar G+k l++ 
  gi|386000940|ref|YP_005919239.1|  3 DVIIIGAGPAGLTAGMYCARGGKKILILG 31
                                      9************************9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.3
                      FAD_oxidored  10 aGvaAAiaAar 20 
                                       aG+ AAi+A r
  gi|386000940|ref|YP_005919239.1| 286 AGTSAAISAMR 296
                                       799******98 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   2.7   0.00014       0.2       1      26 [.       3      30 ..       3      43 .. 0.87
   2 !   12.9   0.1   4.4e-05      0.06     151     225 ..      62     129 ..      49     146 .. 0.70
   3 ?   -2.8   0.1       2.6   3.6e+03     156     160 ..     240     244 ..     209     292 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                      EEEEECTSHHHHHHHHHHHHTT..EEEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtll 26
                                      dv+iiG+G +Gl++ ++ ar g  +++l
  gi|386000940|ref|YP_005919239.1|  3 DVIIIGAGPAGLTAGMYCARGGkkILIL 30
                                      9*****************8877988887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHTT-EEEESECEEEE.EEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEE CS
                               DAO 151 alaraaealGveilegtevtgl.eeedgkvwgverttp.gendaadavVnaaGawsd.llgllkeldlpispvrgqv 224
                                        + ++a++ G+e++e+  v ++ +   ++v +v +t++ +   +a+a+++a+Ga  + l+    + ++  +++rg +
  gi|386000940|ref|YP_005919239.1|  62 RMVAQAKKYGAELHEE-VVAKVvSL--NGVFRV-KTESwEY--QARALILAMGARHRtLS---IPGEVE-YATRGVS 128
                                       68899**********9.55554132..246666.6666565..47********9977544...212223.7777766 PP

                                       E CS
                               DAO 225 l 225
                                       +
  gi|386000940|ref|YP_005919239.1| 129 Y 129
                                       5 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.6
                                       HHHTT CS
                               DAO 156 aealG 160
                                       a++lG
  gi|386000940|ref|YP_005919239.1| 240 AADLG 244
                                       22233 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8   2.3e-06    0.0032       2      30 ..       2      30 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlv 30
                                      +dV+I+GaGpaGl++++  ++ G + +++
  gi|386000940|ref|YP_005919239.1|  2 YDVIIIGAGPAGLTAGMYCARGGKKILIL 30
                                      69******************999998887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   6.6e-06    0.0091       1      25 [.       6      30 ..       6      47 .. 0.94
   2 ?   -3.4   0.0       8.9   1.2e+04      25      35 ..     268     278 ..     267     280 .. 0.78
   3 ?   -1.7   0.2       2.5   3.5e+03       2      13 ..     284     295 ..     284     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                      I+GaG +Gl+a  ++a+ g+++l+l
  gi|386000940|ref|YP_005919239.1|  6 IIGAGPAGLTAGMYCARGGKKILIL 30
                                      9*********************997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.9
                                       E-SSSSSSGGG CS
                     NAD_binding_8  25 lekrdrlGGra 35 
                                       + ++d +GGr+
  gi|386000940|ref|YP_005919239.1| 268 FAAGDVTGGRM 278
                                       66789999998 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.5
                                       E--SHHHHHHHH CS
                     NAD_binding_8   2 vGaGlsGlvaAy 13 
                                       vGaG s++  A 
  gi|386000940|ref|YP_005919239.1| 284 VGAGTSAAISAM 295
                                       8****9988775 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.9e-05     0.081      53     102 ..      56     105 ..      52     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHHHHHTTT-EEE-SSEEEEEEEES-BC..CCC--TTT-EEEE CS
                        HU-DNA_bdg  53 ilnlykrevseaileGysVntglgrasltikGvfegkeekFdpkkhslnv 102
                                        ++l +r v++a + G ++  +++  +++++Gvf  k+e+++ ++  l +
  gi|386000940|ref|YP_005919239.1|  56 GIELSERMVAQAKKYGAELHEEVVAKVVSLNGVFRVKTESWEYQARALIL 105
                                       58999*************************************98877765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.022        30       2      16 ..       1      15 [.       1      28 [. 0.87
   2 ?   10.0   0.0   0.00025      0.34     128     212 ..      84     161 ..      60     176 .. 0.68
   3 ?   -4.1   0.2       4.9   6.7e+03     195     204 ..     282     291 ..     277     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                       K_oxygenase  2 ilDligiGiGpsnLs 16
                                      ++D+i+iG+Gp+ L+
  gi|386000940|ref|YP_005919239.1|  1 MYDVIIIGAGPAGLT 15
                                      59*********9987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00025
                       K_oxygenase 128 eeeelltveskdaegeeeelearnlvlgvGtep...kiPevleklegkervvHsseylerkeellakkriaVvGsGq 201
                                       + + +++v++     e+ e++ar+l+l++G +    +iP  +e  +   r v    y     +l ++k++aV+G G 
  gi|386000940|ref|YP_005919239.1|  84 SLNGVFRVKT-----ESWEYQARALILAMGARHrtlSIPGEVEYAT---RGVSYCAYCDG--ALFRNKTVAVIGYGN 150
                                       3336788887.....799************6541226788777654...33333333333..47889********** PP

                       K_oxygenase 202 Saaeifedllr 212
                                        aa  +  l+ 
  gi|386000940|ref|YP_005919239.1| 151 GAARAVLYLAG 161
                                       ***98887765 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 4.9
                       K_oxygenase 195 aVvGsGqSaa 204
                                       + vG+G Saa
  gi|386000940|ref|YP_005919239.1| 282 TAVGAGTSAA 291
                                       569*****98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4      0.04        55       2      27 ..       4      29 ..       3      32 .. 0.88
   2 ?   -0.9   0.1       1.9   2.6e+03      41      66 ..      58      83 ..      52      95 .. 0.64
   3 ?    7.4   0.1    0.0046       6.3       2      79 ..     143     214 ..     142     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
                                      EEEECSSHHHHHHHHHHHHTTSEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtv 27
                                      v+++G+G  gl ++ + a+ gkk+ +
  gi|386000940|ref|YP_005919239.1|  4 VIIIGAGPAGLTAGMYCARGGKKILI 29
                                      89**********99999999998765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHTTEEEECSEEEEEE CS
                         Pyr_redox 41 easkilqeklekngievllntkveei 66
                                      e+s+++  + +k g e++ + +++ +
  gi|386000940|ref|YP_005919239.1| 58 ELSERMVAQAKKYGAELHEEVVAKVV 83
                                      67788888888888888765444433 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0046
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvk 77 
                                       v+v+G G+ +  +  +la l ++V+++  ++ l       a++i  ++++ +  +++    ve i   +dg v++v+
  gi|386000940|ref|YP_005919239.1| 143 VAVIGYGNGAARAVLYLAGLCARVHLLNVREDLV------AEAIYLDRIKSL-TNFVATPGVEPISILGDGfVTGVE 212
                                       89********************************......999999999988.555555555555555666677777 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       ++
  gi|386000940|ref|YP_005919239.1| 213 FR 214
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2133.37
//
Query:       gi|386000941|ref|YP_005919240.1|  [L=313]
Description: hypothetical protein Mhar_0227 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-05   22.9   0.0    0.00017   22.0   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.85   10.0   3.2        1.3    9.4   0.3    2.5  3  DUF1677      Protein of unknown function (DUF1677)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.9e-08   0.00017       3     149 ..      23     170 ..      21     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-08
                                       EESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS....TTHHHHHHHHHHTC CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlr.CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly....pdfvellerlakla 74 
                                        trgC+ r C+ C   +     +   +  + +  +  k l+ e++v  +  +g   +      p  v++l+ la+  
  gi|386000941|ref|YP_005919240.1|  23 RTRGCRWRrCTVCGYASE--GAPATGDDLLVQFRAATKDLSPEDRVVKIYTSGSFFDPLevppPARVRILDGLAAA- 96 
                                       79****999*******85..999999999999999999998444377777777777776999999999******99. PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdri 149
                                           ++ +e+ +  ++ e +e+ + +  + v++gle+ +d  v+++   +g +fee+ +a +  ++ag+ + ++ +
  gi|386000941|ref|YP_005919240.1|  97 -GVEKLIIESRPEYVTGEAVEESVARIRTEVAVGLETSNDL-VRDRSIsKGFSFEEFAAAAKVVHAAGGSVKTYLL 170
                                       .8***************************************.6666666******************999544444 PP

>> DUF1677  Protein of unknown function (DUF1677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.61   5.5e+03       5      14 ..      31      40 ..      28      45 .. 0.73
   2 ?   -0.1   0.0      0.14   1.2e+03      37      50 ..     112     125 ..      89     160 .. 0.69
   3 ?    9.4   0.3   0.00015       1.3      29      47 ..     253     271 ..     249     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.61
                           DUF1677  5 kCecCgltee 14
                                      +C  Cg   e
  gi|386000941|ref|YP_005919240.1| 31 RCTVCGYASE 40
                                      7888887766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.14
                           DUF1677  37 aeavkeelerskkk 50 
                                       +eav+e ++r +++
  gi|386000941|ref|YP_005919240.1| 112 GEAVEESVARIRTE 125
                                       57888877773222 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00015
                           DUF1677  29 GkwvCGLCaeavkeelers 47 
                                       G   CGLC eav + ++ +
  gi|386000941|ref|YP_005919240.1| 253 GPHNCGLCDEAVAKAIREH 271
                                       5667********9988763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2392.14
//
Query:       gi|386000942|ref|YP_005919241.1|  [L=287]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-38  132.8   0.3    6.9e-19   68.8   0.3    2.1  2  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   3.8e-21   6.8e-17       1     134 [.       1     129 [.       1     136 [. 0.94
   2 !   68.8   0.3   3.9e-23   6.9e-19       4     141 .]     156     282 ..     154     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 3.8e-21
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++++lV++D+s++s+k+le    l   +  +++ll+vi p ++ a+ + + +  + ++++ +++++++   +a+  
  gi|386000942|ref|YP_005919241.1|   1 MFETVLVPTDFSKYSDKVLECVGGLPGVK--KVVLLNVIGPVDPLATIWNPGARLKVAKKKLLDQAKLL---EAQGL 72 
                                       99**************************8..6******************9999999999999999876...7**** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTS CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhap 134
                                       +++++    +eg+  + i ev eee+++l+V+G+rg++ l+ ++lG+v+++vlr  +
  gi|386000942|ref|YP_005919241.1|  73 EVEQRAEPMLEGEIFRNIQEVSEEEGVNLVVMGARGKGFLQNIFLGNVAKNVLRYGD 129
                                       ************************************999999***********9765 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 3.9e-23
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       ++l+++D+se s++A+++   +   r  e++ll+v+ + +s+a  da+ ++++e l   ++  e           g+
  gi|386000942|ref|YP_005919241.1| 156 KVLCPTDFSEPSEEAIRFVKGMIGVR--EVVLLNVVFSGESQAHVDAKMKEAREKLNAIKEGFE---------RDGI 221
                                       8********************99998..7*******************9999999999998775.........67** PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       k  v + +gdpaeei+ vae+e+++l+ + s+g+++ ++ ++GSv   v ++ ++pVlv r
  gi|386000942|ref|YP_005919241.1| 222 KASVLISMGDPAEEIIAVAEDENVSLVAMSSHGKGWMKQHIVGSVVYEVSKNGTKPVLVLR 282
                                       ***********************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2365.50
//
Query:       gi|386000943|ref|YP_005919242.1|  [L=349]
Description: hypothetical protein Mhar_0229 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.9e-117  390.9  27.7   7.3e-117  390.6  27.7    1.0  1  DUF1646   Protein of unknown function (DUF1646)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.6  27.7  4.1e-121  7.3e-117       4     347 .]       9     349 .]       7     349 .] 0.97

  Alignments for each domain:
  == domain 1  score: 390.6 bits;  conditional E-value: 4.1e-121
                           DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfe 80 
                                       l+ i++lvl+ P+  +kvee le+fl++mgv avt+ + + +el+iea+++p++         gi+ avl+aGl+f+
  gi|386000943|ref|YP_005919242.1|   9 LFGIFLLVLLCPFFIKKVEEQLEAFLFVMGVSAVTIANAWHMELVIEAIEEPIMK--------GIVPAVLVAGLLFY 77 
                                       667999**********************************************864........7************* PP

                           DUF1646  81 llkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaal 157
                                       + +++ + +++  ldk++lk++vfl++vilGl++s+i+ai+aa++l+e+v+l+pl+r++k+kl+v+a+f+iGlGaal
  gi|386000943|ref|YP_005919242.1|  78 YGRSHAQRIMNVLLDKVPLKILVFLIVVILGLSASLITAIIAALVLVEVVSLMPLDRNTKIKLTVVACFSIGLGAAL 154
                                       ***************************************************************************** PP

                           DUF1646 158 tPvGePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevlirav 229
                                       tPvGePlstia++kl     +++f++l+d++g+yii+++l+++ll+++ + ++++ +e+  + +  ++l++v ir+ 
  gi|386000943|ref|YP_005919242.1| 155 TPVGEPLSTIAITKLqgppyHAGFTFLLDTIGVYIIPGMLAFGLLSTIIVGKKTVAKETDTFAKGGDTLRDVGIRGA 231
                                       **************955554589*****************************999999999999************* PP

                           DUF1646 230 kvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliP 306
                                       kv++f++al llG+gfk +i++y++++++ ilywvn+ sav+dnatl+aaei+P++   qi+ailm+ll++GG+liP
  gi|386000943|ref|YP_005919242.1| 232 KVYLFVMALLLLGSGFKIIIDTYLIHIPAMILYWVNMSSAVLDNATLTAAEIGPSMDIFQIKAILMGLLVAGGMLIP 308
                                       ***************************************************************************** PP

                           DUF1646 307 GniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       GniPni+sa kl i+skeWar gvP+g++++++yf  ++++
  gi|386000943|ref|YP_005919242.1| 309 GNIPNIISANKLGITSKEWARTGVPIGLVTMLVYFGWIFYI 349
                                       ***********************************988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2747.01
//
Query:       gi|386000944|ref|YP_005919243.1|  [L=290]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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  140.2   2.4    3.4e-21   76.2   0.1    2.2  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.054   13.7   0.5         15    5.8   0.0    3.1  3  UPF0180   Uncharacterised protein family (UPF0180)
      0.077   12.8   0.0        3.7    7.4   0.0    2.9  3  RQC       RQC domain
        0.2   11.8   0.3          8    6.6   0.0    2.4  2  DUF3347   Protein of unknown function (DUF3347)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   7.6e-25   3.4e-21       1     141 []       1     136 [.       1     136 [. 0.97
   2 !   64.0   0.4   4.6e-21   2.1e-17       3     141 .]     157     285 ..     156     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 7.6e-25
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+++lV++D+s++++k++e   +    +  e++llhv+d+  ++++++ + +  e+++ + ++ +e++   + +  
  gi|386000944|ref|YP_005919243.1|   1 MYEKVLVPTDFSKYAQKVIECIGDVPGLK--EIVLLHVVDATHPSKRGWTRGPKVEDAKIDLADIKERL---ENLGF 72 
                                       9***********************99998..7*********************************9987...69999 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++  +  v++e d++++i +va+ee+++liV+G+ g++++s++llGS s  v+r +++++l+ r
  gi|386000944|ref|YP_005919243.1|  73 KVTPRLEVITEADVSRTIQRVADEENVSLIVMGALGKGRVSGILLGSASTGVVRFSNKDTLIMR 136
                                       999999******************************************************9976 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 4.6e-21
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                        ++l+ +D+se+s+  + +   l k+  +e+il +v++  + +++ ++  ++++e l + ++ l         + +g
  gi|386000944|ref|YP_005919243.1| 157 SKVLCTTDFSEASQSSISMIKGL-KDVVGEVILEYVVSKGETQEEIEGYVAEAKEKLGEIKEDL---------ASAG 223
                                       689999********999888886.7767899999999999999999988888888888888766.........578* PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        kv+++v +g+p+e i+ +a  ed++liV+ s g+++++++++GS++  v+r a+ pVl+Vr
  gi|386000944|ref|YP_005919243.1| 224 LKVRTHVDVGNPREQITSLATTEDVSLIVISSQGKGWIKQMMVGSTTFDVVRTAERPVLIVR 285
                                       *************************************************************8 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0033        15       8      25 ..      59      76 ..      56     113 .. 0.81
   2 ?   -1.6   0.0      0.69   3.1e+03      62      74 ..     193     205 ..     191     208 .. 0.78
   3 ?    4.5   0.1    0.0088        40       7      45 ..     210     258 ..     207     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0033
                           UPF0180  8 gLsnvkeaLrekGYeVvd 25
                                      +L ++ke L++ G++V++
  gi|386000944|ref|YP_005919243.1| 59 DLADIKERLENLGFKVTP 76
                                      699*************86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.69
                           UPF0180  62 AsgktaeeIlqev 74 
                                        +g t+eeI+  v
  gi|386000944|ref|YP_005919243.1| 193 SKGETQEEIEGYV 205
                                       5799****98766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0088
                           UPF0180   7 egLsnvkeaLrekGYeVvdlet..........eedaqsvdaiVvtGqdt 45 
                                       e+L ++ke L++ G +V +  +           +++++v+ iV+++q +
  gi|386000944|ref|YP_005919243.1| 210 EKLGEIKEDLASAGLKVRTHVDvgnpreqitsLATTEDVSLIVISSQGK 258
                                       6899***********9965444444777777655678888888866654 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00082       3.7       5      33 ..       9      39 ..       7      54 .. 0.85
   2 ?   -0.9   0.0      0.29   1.3e+03      24      45 ..     106     127 ..      84     133 .. 0.80
   3 ?    1.4   0.0     0.057   2.5e+02       4      27 ..     162     185 ..     161     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00082
                                      EE-HHHHHHHHHHHHHT.T.S-SBHHHHHHH CS
                               RQC  5 vDvteeaqkilscvyrt.g.qrfgaghivdv 33
                                       D++++aqk+++c+ ++ g + + + h+vd 
  gi|386000944|ref|YP_005919243.1|  9 TDFSKYAQKVIECIGDVpGlKEIVLLHVVDA 39
                                      59*************9974578888888886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                                       -SBHHHHHHHHHT---CCCCCT CS
                               RQC  24 rfgaghivdvLrGsktkkirql 45 
                                        +g+g ++ +L Gs++  + ++
  gi|386000944|ref|YP_005919243.1| 106 ALGKGRVSGILLGSASTGVVRF 127
                                       5789999999999999888765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.057
                                       EEE-HHHHHHHHHHHHHTTS-SBH CS
                               RQC   4 tvDvteeaqkilscvyrtgqrfga 27 
                                       t D++e++q  +s+++ +++ +g 
  gi|386000944|ref|YP_005919243.1| 162 TTDFSEASQSSISMIKGLKDVVGE 185
                                       68*************999877764 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0018         8     139     157 ..     139     157 ..     127     159 .. 0.73
   2 ?    3.2   0.0      0.02        92      86     129 ..     199     242 ..     157     258 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                           DUF3347 139 afglkekalYvqfCPmann 157
                                       + +  e+a Y++fCPm ++
  gi|386000944|ref|YP_005919243.1| 139 MLEGLEGATYEKFCPMIFS 157
                                       444556679*******986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                           DUF3347  86 vdtsklkekekkelkeiseelkekaekiaeskdieeqReaFkkl 129
                                        +++ + +++k++l ei+e+l+++  k++++ d+ + Re+ ++l
  gi|386000944|ref|YP_005919243.1| 199 EEIEGYVAEAKEKLGEIKEDLASAGLKVRTHVDVGNPREQITSL 242
                                       23455556666666666666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2160.16
//
Query:       gi|386000945|ref|YP_005919244.1|  [L=343]
Description: hypothetical protein Mhar_0231 [Methanosaeta harundinacea 6Ac]
Scores for 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-116  387.1  29.1   9.5e-116  387.0  29.1    1.0  1  DUF1646   Protein of unknown function (DUF1646)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.0  29.1  5.3e-120  9.5e-116       4     347 .]       3     343 .]       1     343 [] 0.96

  Alignments for each domain:
  == domain 1  score: 387.0 bits;  conditional E-value: 5.3e-120
                           DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfe 80 
                                       l+ i++lvl+ P+  +kvee le+fl++mgv avt+ + + +el+iea+++p++         gi+ avl+aGl+f+
  gi|386000945|ref|YP_005919244.1|   3 LFGIFLLVLLCPFFIKKVEEQLEAFLFVMGVSAVTIANAWHMELVIEAIEEPIMK--------GIVPAVLVAGLLFY 71 
                                       667999**********************************************864........7************* PP

                           DUF1646  81 llkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaal 157
                                       + +++ + +++  ldk++lk++vfl++vilGl++s+i+ai+aa++l+e+v+l+pl+r++k+kl+v+a+f+iGlGaal
  gi|386000945|ref|YP_005919244.1|  72 YGRSHAQRIMNVLLDKVPLKILVFLIVVILGLSASLITAIIAALVLVEVVSLMPLDRNTKIKLTVVACFSIGLGAAL 148
                                       ***************************************************************************** PP

                           DUF1646 158 tPvGePlstiavskln.....edflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevlirav 229
                                       tPvGePlstia++kl+     ++f++l++++g+y+i+++l+++ll+++ + ++++ +e+       ++l++v ir+ 
  gi|386000945|ref|YP_005919244.1| 149 TPVGEPLSTIAITKLQgppyyAGFTFLLETIGMYVIPGILAFGLLSTIIVGKKTVAKETDILARGGDTLRDVGIRGA 225
                                       ***************85555579***************************99877775555577899********** PP

                           DUF1646 230 kvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliP 306
                                       kv++f++al llG+gfk +i++y++++++ ilywvn+ sav+dnatl+aaei+P++   qi+ailm+ll++GG+liP
  gi|386000945|ref|YP_005919244.1| 226 KVYLFVMALLLLGSGFKIIIDTYLIHIPAMILYWVNMSSAVLDNATLTAAEIGPSMDIFQIKAILMGLLVAGGMLIP 302
                                       ***************************************************************************** PP

                           DUF1646 307 GniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       GniPni+sa kl i+skeWar gvP+g++++++yf  ++++
  gi|386000945|ref|YP_005919244.1| 303 GNIPNIISANKLGITSKEWARTGVPIGLVTMLVYFGWIFYI 343
                                       ***********************************988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2496.48
//
Query:       gi|386000946|ref|YP_005919245.1|  [L=290]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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  140.2   2.4    3.4e-21   76.2   0.1    2.2  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.054   13.7   0.5         15    5.8   0.0    3.1  3  UPF0180   Uncharacterised protein family (UPF0180)
      0.077   12.8   0.0        3.7    7.4   0.0    2.9  3  RQC       RQC domain
        0.2   11.8   0.3          8    6.6   0.0    2.4  2  DUF3347   Protein of unknown function (DUF3347)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   7.6e-25   3.4e-21       1     141 []       1     136 [.       1     136 [. 0.97
   2 !   64.0   0.4   4.6e-21   2.1e-17       3     141 .]     157     285 ..     156     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 7.6e-25
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+++lV++D+s++++k++e   +    +  e++llhv+d+  ++++++ + +  e+++ + ++ +e++   + +  
  gi|386000946|ref|YP_005919245.1|   1 MYEKVLVPTDFSKYAQKVIECIGDVPGLK--EIVLLHVVDATHPSKRGWTRGPKVEDAKIDLADIKERL---ENLGF 72 
                                       9***********************99998..7*********************************9987...69999 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++  +  v++e d++++i +va+ee+++liV+G+ g++++s++llGS s  v+r +++++l+ r
  gi|386000946|ref|YP_005919245.1|  73 KVTPRLEVITEADVSRTIQRVADEENVSLIVMGALGKGRVSGILLGSASTGVVRFSNKDTLIMR 136
                                       999999******************************************************9976 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 4.6e-21
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                        ++l+ +D+se+s+  + +   l k+  +e+il +v++  + +++ ++  ++++e l + ++ l         + +g
  gi|386000946|ref|YP_005919245.1| 157 SKVLCTTDFSEASQSSISMIKGL-KDVVGEVILEYVVSKGETQEEIEGYVAEAKEKLGEIKEDL---------ASAG 223
                                       689999********999888886.7767899999999999999999988888888888888766.........578* PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        kv+++v +g+p+e i+ +a  ed++liV+ s g+++++++++GS++  v+r a+ pVl+Vr
  gi|386000946|ref|YP_005919245.1| 224 LKVRTHVDVGNPREQITSLATTEDVSLIVISSQGKGWIKQMMVGSTTFDVVRTAERPVLIVR 285
                                       *************************************************************8 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0033        15       8      25 ..      59      76 ..      56     113 .. 0.81
   2 ?   -1.6   0.0      0.69   3.1e+03      62      74 ..     193     205 ..     191     208 .. 0.78
   3 ?    4.5   0.1    0.0088        40       7      45 ..     210     258 ..     207     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0033
                           UPF0180  8 gLsnvkeaLrekGYeVvd 25
                                      +L ++ke L++ G++V++
  gi|386000946|ref|YP_005919245.1| 59 DLADIKERLENLGFKVTP 76
                                      699*************86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.69
                           UPF0180  62 AsgktaeeIlqev 74 
                                        +g t+eeI+  v
  gi|386000946|ref|YP_005919245.1| 193 SKGETQEEIEGYV 205
                                       5799****98766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0088
                           UPF0180   7 egLsnvkeaLrekGYeVvdlet..........eedaqsvdaiVvtGqdt 45 
                                       e+L ++ke L++ G +V +  +           +++++v+ iV+++q +
  gi|386000946|ref|YP_005919245.1| 210 EKLGEIKEDLASAGLKVRTHVDvgnpreqitsLATTEDVSLIVISSQGK 258
                                       6899***********9965444444777777655678888888866654 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00082       3.7       5      33 ..       9      39 ..       7      54 .. 0.85
   2 ?   -0.9   0.0      0.29   1.3e+03      24      45 ..     106     127 ..      84     133 .. 0.80
   3 ?    1.4   0.0     0.057   2.5e+02       4      27 ..     162     185 ..     161     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00082
                                      EE-HHHHHHHHHHHHHT.T.S-SBHHHHHHH CS
                               RQC  5 vDvteeaqkilscvyrt.g.qrfgaghivdv 33
                                       D++++aqk+++c+ ++ g + + + h+vd 
  gi|386000946|ref|YP_005919245.1|  9 TDFSKYAQKVIECIGDVpGlKEIVLLHVVDA 39
                                      59*************9974578888888886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                                       -SBHHHHHHHHHT---CCCCCT CS
                               RQC  24 rfgaghivdvLrGsktkkirql 45 
                                        +g+g ++ +L Gs++  + ++
  gi|386000946|ref|YP_005919245.1| 106 ALGKGRVSGILLGSASTGVVRF 127
                                       5789999999999999888765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.057
                                       EEE-HHHHHHHHHHHHHTTS-SBH CS
                               RQC   4 tvDvteeaqkilscvyrtgqrfga 27 
                                       t D++e++q  +s+++ +++ +g 
  gi|386000946|ref|YP_005919245.1| 162 TTDFSEASQSSISMIKGLKDVVGE 185
                                       68*************999877764 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0018         8     139     157 ..     139     157 ..     127     159 .. 0.73
   2 ?    3.2   0.0      0.02        92      86     129 ..     199     242 ..     157     258 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                           DUF3347 139 afglkekalYvqfCPmann 157
                                       + +  e+a Y++fCPm ++
  gi|386000946|ref|YP_005919245.1| 139 MLEGLEGATYEKFCPMIFS 157
                                       444556679*******986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                           DUF3347  86 vdtsklkekekkelkeiseelkekaekiaeskdieeqReaFkkl 129
                                        +++ + +++k++l ei+e+l+++  k++++ d+ + Re+ ++l
  gi|386000946|ref|YP_005919245.1| 199 EEIEGYVAEAKEKLGEIKEDLASAGLKVRTHVDVGNPREQITSL 242
                                       23455556666666666666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2240.02
//
Query:       gi|386000947|ref|YP_005919246.1|  [L=343]
Description: hypothetical protein Mhar_0233 [Methanosaeta harundinacea 6Ac]
Scores for 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-116  387.1  29.1   9.5e-116  387.0  29.1    1.0  1  DUF1646   Protein of unknown function (DUF1646)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.0  29.1  5.3e-120  9.5e-116       4     347 .]       3     343 .]       1     343 [] 0.96

  Alignments for each domain:
  == domain 1  score: 387.0 bits;  conditional E-value: 5.3e-120
                           DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplailevgaipigitqavllaGlvfe 80 
                                       l+ i++lvl+ P+  +kvee le+fl++mgv avt+ + + +el+iea+++p++         gi+ avl+aGl+f+
  gi|386000947|ref|YP_005919246.1|   3 LFGIFLLVLLCPFFIKKVEEQLEAFLFVMGVSAVTIANAWHMELVIEAIEEPIMK--------GIVPAVLVAGLLFY 71 
                                       667999**********************************************864........7************* PP

                           DUF1646  81 llkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGlGaal 157
                                       + +++ + +++  ldk++lk++vfl++vilGl++s+i+ai+aa++l+e+v+l+pl+r++k+kl+v+a+f+iGlGaal
  gi|386000947|ref|YP_005919246.1|  72 YGRSHAQRIMNVLLDKVPLKILVFLIVVILGLSASLITAIIAALVLVEVVSLMPLDRNTKIKLTVVACFSIGLGAAL 148
                                       ***************************************************************************** PP

                           DUF1646 158 tPvGePlstiavskln.....edflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevlirav 229
                                       tPvGePlstia++kl+     ++f++l++++g+y+i+++l+++ll+++ + ++++ +e+       ++l++v ir+ 
  gi|386000947|ref|YP_005919246.1| 149 TPVGEPLSTIAITKLQgppyyAGFTFLLETIGMYVIPGILAFGLLSTIIVGKKTVAKETDILARGGDTLRDVGIRGA 225
                                       ***************85555579***************************99877775555577899********** PP

                           DUF1646 230 kvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliP 306
                                       kv++f++al llG+gfk +i++y++++++ ilywvn+ sav+dnatl+aaei+P++   qi+ailm+ll++GG+liP
  gi|386000947|ref|YP_005919246.1| 226 KVYLFVMALLLLGSGFKIIIDTYLIHIPAMILYWVNMSSAVLDNATLTAAEIGPSMDIFQIKAILMGLLVAGGMLIP 302
                                       ***************************************************************************** PP

                           DUF1646 307 GniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                       GniPni+sa kl i+skeWar gvP+g++++++yf  ++++
  gi|386000947|ref|YP_005919246.1| 303 GNIPNIISANKLGITSKEWARTGVPIGLVTMLVYFGWIFYI 343
                                       ***********************************988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2555.76
//
Query:       gi|386000948|ref|YP_005919247.1|  [L=290]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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  140.2   2.4    3.4e-21   76.2   0.1    2.2  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.054   13.7   0.5         15    5.8   0.0    3.1  3  UPF0180   Uncharacterised protein family (UPF0180)
      0.077   12.8   0.0        3.7    7.4   0.0    2.9  3  RQC       RQC domain
        0.2   11.8   0.3          8    6.6   0.0    2.4  2  DUF3347   Protein of unknown function (DUF3347)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   7.6e-25   3.4e-21       1     141 []       1     136 [.       1     136 [. 0.97
   2 !   64.0   0.4   4.6e-21   2.1e-17       3     141 .]     157     285 ..     156     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 7.6e-25
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+++lV++D+s++++k++e   +    +  e++llhv+d+  ++++++ + +  e+++ + ++ +e++   + +  
  gi|386000948|ref|YP_005919247.1|   1 MYEKVLVPTDFSKYAQKVIECIGDVPGLK--EIVLLHVVDATHPSKRGWTRGPKVEDAKIDLADIKERL---ENLGF 72 
                                       9***********************99998..7*********************************9987...69999 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++  +  v++e d++++i +va+ee+++liV+G+ g++++s++llGS s  v+r +++++l+ r
  gi|386000948|ref|YP_005919247.1|  73 KVTPRLEVITEADVSRTIQRVADEENVSLIVMGALGKGRVSGILLGSASTGVVRFSNKDTLIMR 136
                                       999999******************************************************9976 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 4.6e-21
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                        ++l+ +D+se+s+  + +   l k+  +e+il +v++  + +++ ++  ++++e l + ++ l         + +g
  gi|386000948|ref|YP_005919247.1| 157 SKVLCTTDFSEASQSSISMIKGL-KDVVGEVILEYVVSKGETQEEIEGYVAEAKEKLGEIKEDL---------ASAG 223
                                       689999********999888886.7767899999999999999999988888888888888766.........578* PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        kv+++v +g+p+e i+ +a  ed++liV+ s g+++++++++GS++  v+r a+ pVl+Vr
  gi|386000948|ref|YP_005919247.1| 224 LKVRTHVDVGNPREQITSLATTEDVSLIVISSQGKGWIKQMMVGSTTFDVVRTAERPVLIVR 285
                                       *************************************************************8 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0033        15       8      25 ..      59      76 ..      56     113 .. 0.81
   2 ?   -1.6   0.0      0.69   3.1e+03      62      74 ..     193     205 ..     191     208 .. 0.78
   3 ?    4.5   0.1    0.0088        40       7      45 ..     210     258 ..     207     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0033
                           UPF0180  8 gLsnvkeaLrekGYeVvd 25
                                      +L ++ke L++ G++V++
  gi|386000948|ref|YP_005919247.1| 59 DLADIKERLENLGFKVTP 76
                                      699*************86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.69
                           UPF0180  62 AsgktaeeIlqev 74 
                                        +g t+eeI+  v
  gi|386000948|ref|YP_005919247.1| 193 SKGETQEEIEGYV 205
                                       5799****98766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0088
                           UPF0180   7 egLsnvkeaLrekGYeVvdlet..........eedaqsvdaiVvtGqdt 45 
                                       e+L ++ke L++ G +V +  +           +++++v+ iV+++q +
  gi|386000948|ref|YP_005919247.1| 210 EKLGEIKEDLASAGLKVRTHVDvgnpreqitsLATTEDVSLIVISSQGK 258
                                       6899***********9965444444777777655678888888866654 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00082       3.7       5      33 ..       9      39 ..       7      54 .. 0.85
   2 ?   -0.9   0.0      0.29   1.3e+03      24      45 ..     106     127 ..      84     133 .. 0.80
   3 ?    1.4   0.0     0.057   2.5e+02       4      27 ..     162     185 ..     161     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00082
                                      EE-HHHHHHHHHHHHHT.T.S-SBHHHHHHH CS
                               RQC  5 vDvteeaqkilscvyrt.g.qrfgaghivdv 33
                                       D++++aqk+++c+ ++ g + + + h+vd 
  gi|386000948|ref|YP_005919247.1|  9 TDFSKYAQKVIECIGDVpGlKEIVLLHVVDA 39
                                      59*************9974578888888886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                                       -SBHHHHHHHHHT---CCCCCT CS
                               RQC  24 rfgaghivdvLrGsktkkirql 45 
                                        +g+g ++ +L Gs++  + ++
  gi|386000948|ref|YP_005919247.1| 106 ALGKGRVSGILLGSASTGVVRF 127
                                       5789999999999999888765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.057
                                       EEE-HHHHHHHHHHHHHTTS-SBH CS
                               RQC   4 tvDvteeaqkilscvyrtgqrfga 27 
                                       t D++e++q  +s+++ +++ +g 
  gi|386000948|ref|YP_005919247.1| 162 TTDFSEASQSSISMIKGLKDVVGE 185
                                       68*************999877764 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0018         8     139     157 ..     139     157 ..     127     159 .. 0.73
   2 ?    3.2   0.0      0.02        92      86     129 ..     199     242 ..     157     258 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                           DUF3347 139 afglkekalYvqfCPmann 157
                                       + +  e+a Y++fCPm ++
  gi|386000948|ref|YP_005919247.1| 139 MLEGLEGATYEKFCPMIFS 157
                                       444556679*******986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                           DUF3347  86 vdtsklkekekkelkeiseelkekaekiaeskdieeqReaFkkl 129
                                        +++ + +++k++l ei+e+l+++  k++++ d+ + Re+ ++l
  gi|386000948|ref|YP_005919247.1| 199 EEIEGYVAEAKEKLGEIKEDLASAGLKVRTHVDVGNPREQITSL 242
                                       23455556666666666666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2175.37
//
Query:       gi|386000949|ref|YP_005919248.1|  [L=426]
Description: hypothetical protein Mhar_0235 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-06   27.7   0.2         13    6.2   0.0    5.8  6  Colicin_E5    Colicin E5 ribonuclease domain
  ------ inclusion threshold ------
       0.01   15.1   0.0    1.6e+02    1.7   0.0    4.9  6  mRNA_decap_C  mRNA-decapping enzyme C-terminus


Domain annotation for each model (and alignments):
>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.019   1.7e+02      41      71 ..      34      64 ..      18      71 .. 0.82
   2 !    4.5   0.0    0.0047        42      32      70 ..      88     126 ..      86     132 .. 0.88
   3 ?    3.5   0.0      0.01        92      32      67 ..     140     175 ..     138     180 .. 0.92
   4 !    6.2   0.0    0.0015        13      32      70 ..     203     241 ..     196     250 .. 0.91
   5 ?    1.5   0.0      0.04   3.6e+02      32      68 ..     307     343 ..     305     348 .. 0.89
   6 ?   -0.6   0.0      0.18   1.6e+03      32      67 ..     370     405 ..     367     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.019
                        Colicin_E5 41 anktsDglrrndsAtvYgekdgkYvvvndrt 71
                                      + +t  g + +   +v   kdg+Y+v    t
  gi|386000949|ref|YP_005919248.1| 34 WVRTFGGAGEDVGTSVQETKDGGYIVTGSTT 64
                                      556778889999999***********97766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0047
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvndr 70 
                                       kt s+ ++ +++t  g++++    v   kdg+Y++    
  gi|386000949|ref|YP_005919248.1|  88 KTDSEGNTLWERTFGGMGKDIGFMVQETKDGGYIIAGAT 126
                                       78999999**************************98655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.01
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s+ +  ++kt  g + + + ++    dg+Y++ 
  gi|386000949|ref|YP_005919248.1| 140 KTDSEGNPEWDKTFGGRGNDWPNAIQQTADGGYIIA 175
                                       788999999*************************96 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0015
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvndr 70 
                                       kt s+ + ++++t  g + ++  +v    dg+Y+v    
  gi|386000949|ref|YP_005919248.1| 203 KTDSEGNIAWDRTFGGSGFDEGSSVQETDDGGYIVTGYT 241
                                       78999999***************************8655 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.04
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvvn 68 
                                       kt s+  k ++kt  g + ++  +v    d++Y++  
  gi|386000949|ref|YP_005919248.1| 307 KTDSNGTKEWDKTFGGPGFDEGIAVKETGDDGYIIAG 343
                                       688889999*************************975 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.18
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s+ +k +++t  g +   + +v   +dg Y++ 
  gi|386000949|ref|YP_005919248.1| 370 KTDSKGEKEWDRTFGGRGNGWANAVDETTDGSYIIT 405
                                       678888899999988988888889999999999986 PP

>> mRNA_decap_C  mRNA-decapping enzyme C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.018   1.6e+02      14      22 ..      84      92 ..      84      93 .. 0.90
   2 ?    1.7   0.0     0.018   1.6e+02      14      22 ..     136     144 ..     136     144 .. 0.89
   3 ?    1.4   0.0     0.022     2e+02      14      22 ..     199     207 ..     195     207 .. 0.84
   4 ?   -3.5   0.0      0.78     7e+03      14      21 ..     251     258 ..     251     258 .. 0.86
   5 ?    1.3   0.0     0.023   2.1e+02      15      22 ..     304     311 ..     303     313 .. 0.88
   6 ?    0.4   0.0     0.046   4.1e+02      15      21 ..     367     373 ..     366     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.018
                      mRNA_decap_C 14 iHLIknDss 22
                                      i LIk+Ds+
  gi|386000949|ref|YP_005919248.1| 84 IWLIKTDSE 92
                                      89*****95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.018
                      mRNA_decap_C  14 iHLIknDss 22 
                                       i LIk+Ds+
  gi|386000949|ref|YP_005919248.1| 136 IWLIKTDSE 144
                                       89*****95 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.022
                      mRNA_decap_C  14 iHLIknDss 22 
                                       + LIk+Ds+
  gi|386000949|ref|YP_005919248.1| 199 LWLIKTDSE 207
                                       78*****95 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 0.78
                      mRNA_decap_C  14 iHLIknDs 21 
                                       i L+k+D+
  gi|386000949|ref|YP_005919248.1| 251 IWLVKTDP 258
                                       78****95 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.023
                      mRNA_decap_C  15 HLIknDss 22 
                                        LIk+Ds+
  gi|386000949|ref|YP_005919248.1| 304 WLIKTDSN 311
                                       7*****97 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.046
                      mRNA_decap_C  15 HLIknDs 21 
                                        LIk+Ds
  gi|386000949|ref|YP_005919248.1| 367 WLIKTDS 373
                                       7*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2994.27
//
Query:       gi|386000950|ref|YP_005919249.1|  [L=103]
Description: V-type ATP synthase subunit G [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0014   19.0  19.0     0.0024   18.3  19.0    1.3  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
     0.0019   18.3  19.3      0.053   13.6   8.4    2.0  2  ATP-synt_B    ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.032   14.7  13.3      0.038   14.5  13.3    1.1  1  V-ATPase_G    Vacuolar (H+)-ATPase G subunit
      0.035   13.5  16.6       0.17   11.3   2.1    2.1  2  DUF3552       Domain of unknown function (DUF3552)
       0.06   14.0   0.2      0.074   13.7   0.2    1.3  1  DUF643        Protein of unknown function (DUF643)
       0.86   10.2   9.9        2.8    8.5   0.9    2.1  2  YtxH          YtxH-like protein
       0.97   10.1   8.5        8.3    7.1   8.4    2.0  1  DUF883        Bacterial protein of unknown function (DUF883)
          2    8.6   7.1       0.69   10.1   1.9    2.2  2  CinA_KH       Damage-inducible protein CinA KH domain
          3    7.9  14.1         73    3.4  14.1    2.1  1  DivIVA        DivIVA protein


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  19.0   1.2e-06    0.0024       8     102 ..       7     101 ..       3     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   8 keLaerEaeLdqrlEaArkeaerev....eaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaea 80 
                                       k ++  E+e   +lE A k+ae+ v    +aAe + +++++eA+a+++al ++   ++  + +r ++e+ +++e ea
  gi|386000950|ref|YP_005919249.1|   7 KMVKGAERESLSKLERANKDAEELVikanKAAEEQVNKVIEEADAEVEALIED---KI-SQAKRSANEIITEGEREA 79 
                                       556667888899***********994433455666678999999999999754...33.45677889999******* PP

                                       HHHHHHHHCSHHHHHHHHHHHH CS
                      V-ATPase_G_2  81 qavrkraearlqqAvelilkaV 102
                                       +++++ra+ ++++A + +  +V
  gi|386000950|ref|YP_005919249.1|  80 RQLSERAQSKISDAGAFVASQV 101
                                       **************88777666 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   8.4   2.7e-05     0.053      52      99 ..      12      59 ..       4      61 .. 0.68
   2 !   11.0   4.0   0.00017      0.34      57      89 ..      58      90 ..      55     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                        ATP-synt_B 52 llaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkes 99
                                      ++ e   +l+ A ++A+e++ +A+k+ae++ ++ ++ea ae+e l+e+
  gi|386000950|ref|YP_005919249.1| 12 AERESLSKLERANKDAEELVIKANKAAEEQVNKVIEEADAEVEALIED 59
                                      444555677777777777777777777777777777777777777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00017
                        ATP-synt_B 57 eqqlkeAraeAaeiiknAkkeaeklkeeieaea 89
                                      e++  +A++ A+eii ++++ea++l e ++ + 
  gi|386000950|ref|YP_005919249.1| 58 EDKISQAKRSANEIITEGEREARQLSERAQSKI 90
                                      456677777777777777777777777776654 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  13.3   1.9e-05     0.038       5      82 ..      16      93 ..      12     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHH CS
                        V-ATPase_G  5 gIqqLLqAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikel 82
                                      ++ +L +A k+A+e v +A k+ ++++ +  eeA +E+e+  + k  + k++ +e +++ e  ++++ +++++ki++ 
  gi|386000950|ref|YP_005919249.1| 16 SLSKLERANKDAEELVIKANKAAEEQVNKVIEEADAEVEALIEDKISQAKRSANEIITEGEREARQLSERAQSKISDA 93
                                      6678899*******************************************************************9875 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.2   0.00079       1.6      23      62 ..      14      53 ..       8      57 .. 0.85
   2 ?   11.3   2.1   8.5e-05      0.17      24      54 ..      56      86 ..      53      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00079
                           DUF3552 23 kiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeei 62
                                      + + +k+++A+++A++++ +A+k Ae++  + + ea  e+
  gi|386000950|ref|YP_005919249.1| 14 RESLSKLERANKDAEELVIKANKAAEEQVNKVIEEADAEV 53
                                      566789999*****************99999999998776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.5e-05
                           DUF3552 24 iaekkiaeAeeeAkkiieeAkkeAeakkkea 54
                                        e ki++A+++A++ii e ++eA ++ + a
  gi|386000950|ref|YP_005919249.1| 56 LIEDKISQAKRSANEIITEGEREARQLSERA 86
                                      6799********************9987766 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.7e-05     0.074      24      77 ..       8      61 ..       3      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                            DUF643 24 eteqltleqkkqlysavkkiqeykiktGksveeiindiiepekefikdvlkdkn 77
                                       ++ +  e  ++l +a k ++e +ik+ k+ ee +n++ie +   +   + dk 
  gi|386000950|ref|YP_005919249.1|  8 MVKGAERESLSKLERANKDAEELVIKANKAAEEQVNKVIEEADAEVEALIEDKI 61
                                      566677788889999*************************99988887777774 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.7    0.0037       7.3      33      73 ..      19      59 ..       7      60 .. 0.90
   2 ?    8.5   0.9    0.0014       2.8      25      70 ..      52      93 ..      51      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0037
                              YtxH 33 kaddlkekakelleeakekakekaedlkekvkekadelkek 73
                                      k++ + ++a+el+ +a++ a+e+++++ e+++ +++ l e+
  gi|386000950|ref|YP_005919249.1| 19 KLERANKDAEELVIKANKAAEEQVNKVIEEADAEVEALIED 59
                                      68899999**************************9998875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                              YtxH 25 etRkdlkekaddlkekakelleeakekakekaedlkekvkekadel 70
                                      e+ + + +k +++k +a+e+++e     +++a +l+e +++k++++
  gi|386000950|ref|YP_005919249.1| 52 EVEALIEDKISQAKRSANEIITEG----EREARQLSERAQSKISDA 93
                                      66678999999******9999999....999999999999988775 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.4    0.0042       8.3       5      66 ..      18      87 ..      14     101 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                            DUF883  5 aeleslladleellkeaadeageeaeelRerleerlera.rerlrdaeea.......vaerakeaaeaad 66
                                      + le + +d+eel+ +a++ a+e+++++ e++++++e++  +++++a+++        +++a++ +e+a+
  gi|386000950|ref|YP_005919249.1| 18 SKLERANKDAEELVIKANKAAEEQVNKVIEEADAEVEALiEDKISQAKRSaneiiteGEREARQLSERAQ 87
                                      5677888899999999999999988888888777666542445555555511111115555555555555 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 ?   10.1   1.9   0.00035      0.69      39      71 ..      29      61 ..       9      61 .. 0.90
   2 ?    1.4   0.3      0.18   3.5e+02      50      66 ..      66      82 ..      62      93 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                                      EEEEE...EEHHHHHHHHH....HHHHHTTTTE CS
                           CinA_KH 39 tvRltakaaneeeaealiapveeeirerlgdyv 71
                                      ++ + a+ a ee+++++i+++ +e+++ + d++
  gi|386000950|ref|YP_005919249.1| 29 ELVIKANKAAEEQVNKVIEEADAEVEALIEDKI 61
                                      7899***********************999876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                                      HHHHHHHH....HHHHH CS
                           CinA_KH 50 eeaealiapveeeirer 66
                                      + a+++i + e+e r+ 
  gi|386000950|ref|YP_005919249.1| 66 RSANEIITEGEREARQL 82
                                      56666666666666653 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  14.1     0.037        73      57     117 ..      19      87 ..       4      97 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.037
                                       XXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  57 eykeleetLkktlvvaqetaee....vkanakkeaeliik....eAekkaekiveeaeeeakkiaeeie 117
                                       + + ++++ ++ ++ a ++aee    v ++a +e e +i+    +A+ +a++i+ e e+ea++++e+ +
  gi|386000950|ref|YP_005919249.1|  19 KLERANKDAEELVIKANKAAEEqvnkVIEEADAEVEALIEdkisQAKRSANEIITEGEREARQLSERAQ 87 
                                       444444444444454444444311113334444444433211114555555555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2588  (0.144347); expected 358.6 (0.02)
Passed bias filter:                      975  (0.0543812); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 784.57
//
Query:       gi|386000951|ref|YP_005919250.1|  [L=641]
Description: V-type ATP synthase subunit I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-30  104.7   0.0    1.3e-16   59.7   0.0    2.7  2  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
        1.2    9.4   2.9        1.1    9.6   0.0    2.5  2  DUF948      Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.5e-20   1.3e-16     157     415 ..     142     400 ..      89     417 .. 0.63
   2 !   41.8   0.1   4.1e-15   3.6e-11     721     812 ..     549     633 ..     537     634 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.5e-20
                        V_ATPase_I 157 e................lsfvaGvikrekveaferilwralrgnlflrqaeieepledpetgekveksvfiiffqg. 216
                                       +                l++++G+ ++e+++ +   l  ++ g +++ +++i++          +e  v ++ ++  
  gi|386000951|ref|YP_005919250.1| 142 KirdfrvdladvvktdlLTVLIGIAPKERASDMTSKLSEITNGICYIGSKDISQ----------IESVVLVVALSEv 208
                                       022223333344444558889999999999999999999999999999999998..........4555666655544 PP

                        V_ATPase_I 217 .eqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkeka 292
                                        + +++ +++i        +e  +  +  + + +e  +++ + +  l + ee l+++++++a+++++    v++e  
  gi|386000951|ref|YP_005919250.1| 209 sKDVSDSLRRI-------GFERMD-VSGLSGTPAEALSTLGERKASLASEEEFLRSEIKKLAERWRDKL-LVHRELL 276
                                       44555555555.......333222.22233333444444555555555556666666666655554433.3333333 PP

                        V_ATPase_I 293 iy..htLnl.fnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQe 366
                                       +   + L++  n+ +t++++i egW+p++++ ++++ + e+t  ++ sv +  n   + ++ P y +   f + fQ 
  gi|386000951|ref|YP_005919250.1| 277 LIerDRLDVqTNFMRTDETFILEGWIPAKSIGSVKEEVLEVT--KGYSVVKESNPNPSPDDIPVYLQNPPFIRHFQV 351
                                       221123443134467889**********************99..455666666666667788*************** PP

                        V_ATPase_I 367 ivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvl 415
                                       + + YG ++Y+E+ p+++    F   F++M  D+  G+++++++l+l+ 
  gi|386000951|ref|YP_005919250.1| 352 LTELYGRPKYHEIDPTFMLAPVFMLFFGIMLTDAVYGVMMAAVGLMLLR 400
                                       *********************************************9975 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 4.1e-15
                        V_ATPase_I 721 ASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWVEfq 797
                                        SY RL AL LA + ++     m+++  l+++   +  i +v++ +vf+v  ++    m+gl  f H +RLh VEf 
  gi|386000951|ref|YP_005919250.1| 549 LSYARLLALGLATSGIA-----MTVNI-LSSMVDSVPFIGIVLGAIVFVVGHIF-NWGMNGLGGFVHGIRLHYVEFF 618
                                       59**********98876.....55555.43445556667777777777766555.579******************* PP

                        V_ATPase_I 798 sKFykgdGykFepfs 812
                                       +KFy+g G +++p+ 
  gi|386000951|ref|YP_005919250.1| 619 NKFYEGGGSEYRPYR 633
                                       *************96 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00012       1.1      45      87 ..     101     140 ..      95     155 .. 0.62
   2 ?   -4.0   0.9         2   1.8e+04      10      24 ..     461     475 ..     461     481 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00012
                            DUF948  45 ilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +l+ +e+ll+++n+    v+e  e+++++t+++++++++v++l
  gi|386000951|ref|YP_005919250.1| 101 LLERSERLLEEANA---AVREPEERLNRVTSELGEISTKVESL 140
                                       44445555555555...55555666666666666666666655 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2
                            DUF948  10 FvvLviflivvllkl 24 
                                       F++Lv+++  + l+l
  gi|386000951|ref|YP_005919250.1| 461 FLILVLVIGLIHLNL 475
                                       778888887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4508.99
//
Query:       gi|386000952|ref|YP_005919251.1|  [L=211]
Description: V-type ATP synthase subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete 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-31  108.7  12.1    2.7e-31  108.5  12.1    1.0  1  vATP-synt_E    ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
       0.12   11.9   0.8       0.17   11.4   0.8    1.2  1  Unpaired       Unpaired protein
       0.39   11.0   2.5       0.72   10.1   2.5    1.4  1  Ribosomal_L22  Ribosomal protein L22p/L17e
        2.4    8.2  15.0       0.91    9.6   9.7    2.5  2  ATP-synt_B     ATP synthase B/B' CF(0)


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5  12.1     6e-35   2.7e-31       8     199 .]      19     207 ..      12     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 6e-35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   8 ekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeeaekk 84 
                                       +++e I ++a ++++ + ++ +++++ k+  ++ k ++qae+++++++  a+++ ++k+  ++e++++++f +ae +
  gi|386000952|ref|YP_005919251.1|  19 AQVELILQQARKDADDIRGESEKKAQAKKSVILGKGQQQAEREYQRILADAKMQVKRKIFDVKEDLIKKAFVDAEAR 95 
                                       678999*********************************************************************** PP

                                       HHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCT.HCCCCCCHHCCSSSS--SEEEEESSEBTTS CS
                       vATP-synt_E  85 LaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveea.ldkaaeeykaktkkktvevagdeedfledv 160
                                       L+ +++++ eY ++lkk+iv+  v ++++ + v +r++D+ l++e  l ++aee+ ++t+k+t ++  +e    +++
  gi|386000952|ref|YP_005919251.1|  96 LKRLADTS-EYGDVLKKMIVESGVVVGGGPLEVLVRERDRALLSEKaLADLAEEISKATGKDTALELSEE---VITT 168
                                       *****999.********************************9976559**************99998888...89** PP

                                       SSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 161 lGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                       +GG v+++++gki+ +nT+e+r++++  +l+ ++++ LF
  gi|386000952|ref|YP_005919251.1| 169 IGGAVVRSKSGKIEADNTIESRISRIGSELRFKVAEILF 207
                                       ***********************************9999 PP

>> Unpaired  Unpaired protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   3.8e-05      0.17      42      92 ..      39      89 ..      29     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                          Unpaired 42 ekakrckkrkkilkqLkrkagrElrelnaedkatednkaiDirekekwslh 92
                                      +++k+ +k+  il + +++a+rE++ + a+ k + ++k  D++e  + + +
  gi|386000952|ref|YP_005919251.1| 39 SEKKAQAKKSVILGKGQQQAEREYQRILADAKMQVKRKIFDVKEDLIKKAF 89
                                      344555788999******************************997665555 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.5   0.00016      0.72      10      80 ..      25      99 ..      17     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHTTSBHHHHHH....HHHT-SSTTHHHHHHHHHHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22 10 fkklrevarlIrgmkveeAlk....yLkfskkkaakfvlklLknaeanaelkgldvdslvIeeiqvnkgpklkrr 80
                                       +++r+ a+ Irg + ++A +    +L + +++a ++  ++L  a+ + + k  dv++  I++++v+   +lkr+
  gi|386000952|ref|YP_005919251.1| 25 LQQARKDADDIRGESEKKAQAkksvILGKGQQQAEREYQRILADAKMQVKRKIFDVKEDLIKKAFVDAEARLKRL 99
                                      577888999999988888875333367779999***********************************9999996 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   9.7    0.0002      0.91      59     118 ..      24      87 ..      14     100 .. 0.71
   2 ?    0.6   0.2      0.12   5.4e+02      74     121 ..     154     204 ..     130     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                        ATP-synt_B  59 qlkeAraeAaeiiknAkkeaeklkeei....eaeaeaeaerlkesAaaeIeqekdralaeLreq 118
                                        l++Ar++A++i+ + +k+a+  k  i    +++ae+e +r+ ++A+ ++++    ++++L ++
  gi|386000952|ref|YP_005919251.1|  24 ILQQARKDADDIRGESEKKAQAKKSVIlgkgQQQAEREYQRILADAKMQVKRKIFDVKEDLIKK 87 
                                       5889999999999888888887777662222567788888888888888887776666666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                        ATP-synt_B  74 Akkeaeklkeeieaeaeaeaerlke...sAaaeIeqekdralaeLreqvva 121
                                       +k+ a +l ee ++    ++ r k+   +A ++Ie   +r+ +eLr +v++
  gi|386000952|ref|YP_005919251.1| 154 GKDTALELSEEVITTIGGAVVRSKSgkiEADNTIESRISRIGSELRFKVAE 204
                                       355566666777666666666665433367778888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1249  (0.0696637); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1583.07
//
Query:       gi|386000953|ref|YP_005919252.1|  [L=357]
Description: V-type ATP synthase subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-78  263.3   0.1    4.5e-78  263.1   0.1    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.026   15.0   0.0         21    5.6   0.0    3.4  3  HTH_40          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.1   0.1   5.1e-82   4.5e-78       2     335 ..      17     350 ..      16     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: 263.1 bits;  conditional E-value: 5.1e-82
                                       HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H. CS
                    vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp 78 
                                       + r+ +m+s++++ee+++++++++sl++v++ L+ tdY+ +l +  +     ++ie+al+++ a+ ++++ +++p +
  gi|386000953|ref|YP_005919252.1|  17 NSRIQVMSSRIIPEEKLKEMIEASSLAEVVAALEPTDYSPYLHEMME--ERSEAIERALNRHTADSYREVATMVPMD 91 
                                       789**************************************877775..5789************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHH CS
                    vATP-synt_AC39  79 srefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyleea 155
                                       ++ +l +ll+++di N+kl+lrg+++ +++++e++++l+p+gel + ++ +l+ea+s+eel+++l gtpy++ +e+ 
  gi|386000953|ref|YP_005919252.1|  92 LKAVLAVLLRKWDIYNIKLILRGVYA-ERSPDEIRADLVPVGELAPSKIGELAEARSLEELVSNLDGTPYSRLAES- 166
                                       99************************.5999*****************************************9999. PP

                                       HCC...--SHHHHHHHHHHHHHHHHHHHHHTSS.-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--S CS
                    vATP-synt_AC39 156 ldeleetgdleiienaLdkayledllkfckklg.getaeilreilgfeiDlrniniilrskkygelskedrkkllip 231
                                       l+ +++t++l  +e+ Ld+  +ed++k   ++  +e+   l+++l++ iD+ n++ ++r+kk+g l+  +++ +l++
  gi|386000953|ref|YP_005919252.1| 167 LQLFDQTRNLTVLEARLDNILYEDAWKDMTSKPlDENLLALKNYLATNIDVVNLKFLFRAKKDG-LTAGSIEGYLVK 242
                                       9***************************77666688889***********************87.566669999*** PP

                                       S-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT-...-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHH CS
                    vATP-synt_AC39 232 ggslypeglealaeaedveellaalkyteygelleealee...agslksledaldealvkllkk.afrqqfsvgvfy 304
                                       gg l ++ +++++e+++v++++aal+ t+y + +  a+ e   +gs   +e ald +lv++ k+ + +q+f++g+++
  gi|386000953|ref|YP_005919252.1| 243 GGGLQESLIKSILEMDTVDNVVAALEGTKYYQPVLGAVPEyesTGSVLPIELALDGYLVRVGKNiSITQPFGIGPAI 319
                                       *************************999999988878777898888******************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 305 aYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       +Yl  ke Eirn+r++a+gi++gl++++Ir+
  gi|386000953|ref|YP_005919252.1| 320 GYLSMKEMEIRNVRTLARGIEAGLSPDEIRN 350
                                       *****************************97 PP

>> HTH_40  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    0.0024        21      32      88 ..      41     111 ..      25     112 .. 0.74
   2 ?   -1.5   0.0       0.4   3.6e+03      57      57 ..     186     186 ..     138     223 .. 0.55
   3 ?    5.2   0.0    0.0032        29      19      71 ..     226     275 ..     226     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0024
                            HTH_40  32 HLaelieegeeidlerlv...seeeekeIeeaiekvgsek...........lkpikealpeevsydeIrlv 88 
                                        Lae + + e+ d++ ++    ee+ ++Ie a++++  ++           lk++ + l  + + + I+l+
  gi|386000953|ref|YP_005919252.1|  41 SLAEVVAALEPTDYSPYLhemMEERSEAIERALNRHTADSyrevatmvpmdLKAVLAVLLRKWDIYNIKLI 111
                                       588888888999998885444889999*******9998885666666666677777777777777777765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.4
                            HTH_40  57 I 57 
                                       I
  gi|386000953|ref|YP_005919252.1| 186 I 186
                                       1 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0032
                            HTH_40  19 AkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvgseklkp 71 
                                       Ak+ gl+ + Ieg+L++    +e   ++ +++ ++ +++ +a+e  +   ++p
  gi|386000953|ref|YP_005919252.1| 226 AKKDGLTAGSIEGYLVKGGGLQE-SLIKSILEMDTVDNVVAALEGTK--YYQP 275
                                       7899*************988854.66777777788888888887643..3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2097.58
//
Query:       gi|386000954|ref|YP_005919253.1|  [L=108]
Description: V-type ATP synthase subunit F [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-19   68.9   1.5    4.1e-19   68.7   1.5    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   1.5   2.3e-23   4.1e-19       1      89 [.       6      98 ..       6     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 2.3e-23
                                      EEEEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS...SSSEEEEESC CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiaeeirelideykee...alPaileIPs 75
                                      iavIGd+dtv gfrl Gv+  + v  ee ie +l el+ +e +g+i+ite++a+  r+ ide+++    ++P+++eI +
  gi|386000954|ref|YP_005919253.1|  6 IAVIGDSDTVSGFRLGGVTRSYvVRVEEPIEVILAELIGDETVGVIAITERLADANRSAIDEITKGkkaVTPILVEISD 84
                                      8******************9995666899**********************************998889********** PP

                                      SCCGGSHHCHHHHH CS
                        ATP-synt_F 76 kegpydeekdsvrk 89
                                      k+gp  +e d +++
  gi|386000954|ref|YP_005919253.1| 85 KNGPIVREVDPLKA 98
                                      ****9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 803.50
//
Query:       gi|386000955|ref|YP_005919254.1|  [L=587]
Description: V-type ATP synthase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-88  294.3   0.0    2.5e-86  288.8   0.0    2.2  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    2.7e-41  140.2   0.0    6.1e-41  139.1   0.0    1.6  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
      1e-14   54.8   1.3    3.1e-14   53.3   1.3    1.9  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.025   13.6   0.0      0.044   12.8   0.0    1.3  1  TrfA             TrfA protein
      0.089   12.6   0.3       0.32   10.8   0.0    1.9  3  PhoQ_Sensor      PhoQ Sensor
       0.17   12.2   0.0       0.36   11.1   0.0    1.5  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.8   0.0   8.3e-90   2.5e-86       1     213 []     213     437 ..     213     437 .. 0.98
   2 ?    3.4   0.0     0.017        52     142     172 ..     524     554 ..     518     564 .. 0.87

  Alignments for each domain:
  == domain 1  score: 288.8 bits;  conditional E-value: 8.3e-90
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH.......SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe.......gtimk 70 
                                       G+r+ D++fp+++G+  +ipg+fg+Gktv +++l+k+++s+ +++yvg+Gergne++evl++fp        +++m+
  gi|386000955|ref|YP_005919254.1| 213 GQRIYDTFFPLAKGGSAAIPGGFGTGKTVSQHQLAKWADSQ-VVVYVGCGERGNEMTEVLDTFPLlddpttgEKLME 288
                                       99***********************************9999.**********************9999987666*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       r++l+antsn+pvaareas+ytg+tlAE++rd+g++v ++ads+srwaeA+re+s+rl+emp+++gypayl++++a 
  gi|386000955|ref|YP_005919254.1| 289 RSTLIANTSNMPVAAREASVYTGVTLAEFYRDMGYDVAVMADSTSRWAEAMREVSGRLEEMPGEEGYPAYLASRVAD 365
                                       ***************************************************************************** PP

                                       HHTTSEEE......TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka......pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        yER+g++      ++r Gsv+ v avsp+ggD+s+pv+++tl+++ +f+ Ld++la+r+hfPain+l S+S
  gi|386000955|ref|YP_005919254.1| 366 YYERSGRVitlgsgEERLGSVSLVGAVSPPGGDLSEPVSQNTLRVVSVFWALDSTLADRRHFPAINWLRSYS 437
                                       *************9999******************************************************9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                                       HHHHHHHHTTSEEETSSEEEEEEEEEEE-GG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 142 gaklaslyERagkapdrtGsvtivaavspag 172
                                       + ++  +y+Ra ka d   s+  + ++++++
  gi|386000955|ref|YP_005919254.1| 524 ARTILAFYDRALKAMDAGASIAKIETIQVKD 554
                                       556778*********************9875 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1   0.0   2.1e-44   6.1e-41       1     121 []      85     204 ..      85     204 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 2.1e-44
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvke 77 
                                       yDGiqrpLe ++e++g++i+rG++vp+l+ e+ w+++p +++g++v++gd+lGtv+et++i+h+++vpp+++gk+++
  gi|386000955|ref|YP_005919254.1|  85 YDGIQRPLEGLREAAGDYITRGLTVPPLNPETVWDYTPVAAEGSSVETGDVLGTVPETKVITHRVLVPPGIRGKLTK 161
                                       9**************************************************************************** PP

                                       E--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  78 iaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       +  eg+ +v+d +a++++e+gke++lt+ ++wPvr prp+k+kl
  gi|386000955|ref|YP_005919254.1| 162 VR-EGKLHVTDSVATLTKEDGKEANLTMSHRWPVRVPRPYKRKL 204
                                       *9.**************************************996 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   1.3     1e-17   3.1e-14       1      69 []       7      69 ..       7      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1e-17
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++++Gp+v +e+++g  + +y++++v+  +   +l+g+ ++l++d++ ++v++ t+Gl++G++V+ TG
  gi|386000955|ref|YP_005919254.1|  7 IYKISGPLVVAEDVKG--CVMYEVVKVG--D--IGLMGETIRLDGDRAYIQVYEATEGLKPGEPVETTG 69
                                      689*************..**********..9..**********************************98 PP

>> TrfA  TrfA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.044      66     151 ..      15      99 ..       4     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                              TrfA  66 vprealqnkviyhvnkdvkitytgvelradddelvfaqvleyakrtalgepvsftfyelcqdldwsingryytkaee 142
                                       v  e +++ v+y v k  +i   g  +r d d   + qv e +++   gepv  t   l  dl+  i   +y   + 
  gi|386000955|ref|YP_005919254.1|  15 VVAEDVKGCVMYEVVKVGDIGLMGETIRLDGDR-AYIQVYEATEGLKPGEPVETTGSPLTADLGPGILKNFYDGIQR 90 
                                       556778999********************9986.799******************************9999988888 PP

                              TrfA 143 clsrlqasa 151
                                        l  l+ +a
  gi|386000955|ref|YP_005919254.1|  91 PLEGLREAA 99 
                                       777776666 PP

>> PhoQ_Sensor  PhoQ Sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.7   8.2e+03      52      63 ..     245     256 ..     243     259 .. 0.83
   2 ?   -2.5   0.0       1.3   3.8e+03     102     130 ..     444     472 ..     436     486 .. 0.65
   3 ?   10.8   0.0   0.00011      0.32      90     131 ..     488     529 ..     481     553 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                       PhoQ_Sensor  52 slaqwedgklti 63 
                                       +la+w d+++ +
  gi|386000955|ref|YP_005919254.1| 245 QLAKWADSQVVV 256
                                       79******9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                       PhoQ_Sensor 102 keWlkke...glyeldtdvktssallknnpea 130
                                        +W kk+   ++ye+ td+     ll++++e+
  gi|386000955|ref|YP_005919254.1| 444 GDWYKKNvseDFYEVRTDMM---VLLQKEAEL 472
                                       56777643337888887753...445555554 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00011
                       PhoQ_Sensor  90 qrevpelekkikkeWlkkeglyeldtdvktssallknnpeaq 131
                                       +r v e+++++++++l++++++e+d+  +++++l+  ++ ++
  gi|386000955|ref|YP_005919254.1| 488 ERLVLEVSRMVREDYLQQNAYHEIDSYCSKEKQLMMARTILA 529
                                       66788999*********************9999998776554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.36       5      51 ..     226     264 ..     224     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst 51 
                                        g+ ++ G  GtGKT++  +l++++d         ++vv +v + + +
  gi|386000955|ref|YP_005919254.1| 226 GGSAAIPGGFGTGKTVSQHQLAKWAD---------SQVVvYVGCGERG 264
                                       68899*******************95.........4444488777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.52
# Mc/sec: 3399.59
//
Query:       gi|386000956|ref|YP_005919255.1|  [L=464]
Description: V-type ATP synthase subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-64  215.9   0.0    6.5e-64  215.5   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.3e-10   41.6   5.9    1.3e-10   41.6   5.9    1.8  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.26   11.4   1.9       0.62   10.2   1.9    1.6  1  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.0   1.1e-67   6.5e-64       1     213 []     135     353 ..     135     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 1.1e-67
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D   ++v+Gq++ i++++g++++ +++++++q++ +       ++++++G  ++e++ ++++f+++++++r 
  gi|386000956|ref|YP_005919255.1| 135 GISTIDGNNTLVRGQKLPIMSGAGLPHNDLAAQIARQAKVRgteePfSVVFAAMGITHEEASFFMRDFERTGALERI 211
                                       899**********************************98889986479***************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v ++n +++p+++r++++++++t+AEy+++  ++++l++++++++++eAlreis++ +e+p+++gyp+y++++la+l
  gi|386000956|ref|YP_005919255.1| 212 VAFINLADDPAIERIITPRMALTAAEYLAYtCDMHILVVLTDMTNYCEALREISAAREEVPGRRGYPGYMYTDLATL 288
                                       ******************************99********************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+++  +Gs+t+v+++s++++D+++p+++ t +it+g++vL++++++r+++P++++l S+S
  gi|386000956|ref|YP_005919255.1| 289 YERAGRVRGAKGSITQVPILSMPDDDITHPIPDLTGYITEGQFVLSREMHRRGIYPPVDILPSLS 353
                                       ***************************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   5.9   2.2e-14   1.3e-10       2      69 .]      13      78 ..      12      78 .. 0.94
   2 ?   -3.1   0.0         2   1.2e+04      23      44 ..     415     434 ..     413     434 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.2e-14
                                      EEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                     ATP-synt_ab_N  2 vqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                       +v Gp++ ve+++g+++g+++ +  +  + g   +g++l+ + ++++v+v+++t+G++   t+V++TG
  gi|386000956|ref|YP_005919255.1| 13 REVAGPLMVVEGVEGVAYGEIVDVVLP--D-GGTKRGQVLESRKGVAVVQVFEGTSGIDTlSTKVRFTG 78
                                      589************999999999999..9.88889********************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                       EEEEECCETCSTEEEEEEEEEE CS
                     ATP-synt_ab_N  23 nalevelvefgtlllgvalnlg 44 
                                       + ++ e  ++++ ++++ l lg
  gi|386000956|ref|YP_005919255.1| 415 EYVTQE--RDEDRTIEQTLDLG 434
                                       667777..45899999999886 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9    0.0001      0.62      11      61 ..      16      68 ..       5      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0001
                        HAS-barrel 11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn..selsndlalvl 61
                                       +++++veg+++v +Ge V + lpdg+   G+v+  r+g    + +  +++++
  gi|386000956|ref|YP_005919255.1| 16 AGPLMVVEGVEGVAYGEIVDVVLPDGGTKRGQVLESRKGVavVQVFEGTSGID 68
                                      68999****************************99888544444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 3474.39
//
Query:       gi|386000957|ref|YP_005919256.1|  [L=219]
Description: V-type ATP synthase subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-57  192.4   8.7    8.3e-57  192.2   8.7    1.0  1  ATP-synt_D     ATP synthase subunit D
     0.0057   16.8   3.5       0.88    9.7   0.9    2.4  2  ApoLp-III      Apolipophorin-III precursor (apoLp-III)
  ------ inclusion threshold ------
      0.012   15.6   0.4      0.023   14.7   0.4    1.5  1  Peptidase_A17  Pao retrotransposon peptidase
      0.014   15.0   3.0      0.022   14.4   0.3    2.0  2  Filament       Intermediate filament protein
      0.066   13.4   0.9        2.1    8.6   0.1    2.4  2  DUF2703        Domain of unknown function (DUF2703)
       0.16   12.3   2.5        1.2    9.5   0.2    2.5  2  DUF948         Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   8.7   2.8e-60   8.3e-57       1     196 []      14     207 ..      14     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 2.8e-60
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eL++l +r+kla++gh+lLk+KrdaL+ ef +++++++e r+  +e+l++a + l +a+a++g++++ ++++ +   
  gi|386000957|ref|YP_005919256.1|  14 ELLKLGRRIKLAEKGHKLLKEKRDALVSEFLDVVQRVQESRDSTNEKLEAAFKDLLMAQAVMGSDAVWQISQVTG-- 88 
                                       799*****************************************************************9999666.. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                        +++k+++ t n++GVkvp + +e+  +s   + yg+++t+++ld+a ++++e++ ++++la++++s+++L+ e+ k
  gi|386000957|ref|YP_005919256.1|  89 -QEIKIDVDTMNIMGVKVPMIVIEDVkRSMVDRGYGFADTSSKLDDASRNFEEAIGEVIKLAEVQQSVQSLASEVIK 164
                                       .569*****************7765553444567******************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+rRvNaLe++vIPrl++t   I+++L E+ere+f+rlkk+k+
  gi|386000957|ref|YP_005919256.1| 165 TKRRVNALEYIVIPRLKATAIHIRMRLAEMERENFTRLKKIKA 207
                                       *****************************************95 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0015       4.6      21      63 ..      26      68 ..      12      75 .. 0.69
   2 !    9.7   0.9   0.00029      0.88      74     112 ..     131     171 ..     111     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
                         ApoLp-III 21 eevvetiKensenlvdqlkqvikslqeelkkksdeleealkev 63
                                      e   + +Ke+ + lv++  +v + +qe+   ++++le a+k++
  gi|386000957|ref|YP_005919256.1| 26 EKGHKLLKEKRDALVSEFLDVVQRVQESRDSTNEKLEAAFKDL 68
                                      5555667777777777777777777777777777777777664 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
                         ApoLp-III  74 lseenPevkkkaqel..qekvQsgvqslvkesqklaeslke 112
                                       l  ++ + ++++ e    ++vQ++vqsl++e+ k+  ++++
  gi|386000957|ref|YP_005919256.1| 131 LDDASRNFEEAIGEVikLAEVQQSVQSLASEVIKTKRRVNA 171
                                       44444455555544422468**************9999875 PP

>> Peptidase_A17  Pao retrotransposon peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   7.7e-06     0.023      91     150 ..     140     200 ..     113     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.7e-06
                     Peptidase_A17  91 kaygavvYl.rvekedgevevslllaKsrvaPlkkltiprlELlaallaarlakkvkkelk 150
                                       +a g v+ l  v+++ ++  ++ +  K rv  l+ + iprl  +a+++ +rla++ +++++
  gi|386000957|ref|YP_005919256.1| 140 EAIGEVIKLaEVQQSVQSLASEVIKTKRRVNALEYIVIPRLKATAIHIRMRLAEMERENFT 200
                                       566666655145667889999*******************************998777665 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2     0.066     2e+02     212     271 ..       9      68 ..       3      79 .. 0.79
   2 ?   14.4   0.3   7.2e-06     0.022     185     269 ..     130     214 ..      83     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.066
                                       XX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 212 rsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeel 271
                                       + ++ e+ +l r+i+  e   + lk+++++l ++  ++ +r+++ +++++ekl++  ++l
  gi|386000957|ref|YP_005919256.1|   9 SPTRMELLKLGRRIKLAEKGHKLLKEKRDALVSEFLDVVQRVQESRDSTNEKLEAAFKDL 68 
                                       567888888888888888888889999999999999999999999999999888765555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 185 nreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsle.ieleslkkqkasleaqlaeleerleaelekl 260
                                       + ++a +++++ + e+ + ae + ++++s  +e+ +++r++++le i +  lk+++  ++ +lae+e +  + l+k+
  gi|386000957|ref|YP_005919256.1| 130 KLDDASRNFEEAIGEVIKLAEVQ-QSVQSLASEVIKTKRRVNALEyIVIPRLKATAIHIRMRLAEMERENFTRLKKI 205
                                       56789999999999999888765.689*****************9567999************************** PP

                                       HHHHHHHHH CS
                          Filament 261 qeklselee 269
                                       ++++++ ee
  gi|386000957|ref|YP_005919256.1| 206 KAAIEAGEE 214
                                       ***998876 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00069       2.1      14      81 ..      50     114 ..      41     123 .. 0.79
   2 ?    3.0   0.1     0.036   1.1e+02      12      57 ..     156     201 ..     145     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00069
                           DUF2703  14 tCercgeTgktleeavkelkeaLealgievelekvelseeelareflesntilingrpleellgvevk 81 
                                       + e  ++T+++le+a k+l +a + +g + +++  +++ +e++   + ++t+ i g+++  ++ ++vk
  gi|386000957|ref|YP_005919256.1|  50 VQESRDSTNEKLEAAFKDLLMAQAVMGSDAVWQISQVTGQEIK---IDVDTMNIMGVKVPMIVIEDVK 114
                                       5566789**************************8888888888...7888888888877666555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                           DUF2703  12 getCercgeTgktleeavkelkeaLealgievelekvelseeelar 57 
                                       ++ ++++ +T++ ++++   + ++L+a+ i+++++  e+++e+++r
  gi|386000957|ref|YP_005919256.1| 156 QSLASEVIKTKRRVNALEYIVIPRLKATAIHIRMRLAEMERENFTR 201
                                       5567888999999999999999*****************9999984 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0004       1.2      21      69 ..      15      63 ..      11      85 .. 0.90
   2 ?    2.5   0.1     0.058   1.7e+02      36      49 ..     149     162 ..     108     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0004
                            DUF948 21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69
                                      llkl++ ++ a++  + l+++ d+++ e  d+++ v+e  +  nekle+
  gi|386000957|ref|YP_005919256.1| 15 LLKLGRRIKLAEKGHKLLKEKRDALVSEFLDVVQRVQESRDSTNEKLEA 63
                                      89********************************************997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.058
                            DUF948  36 eelekqvdpilkev 49 
                                       +e+++ v+++  ev
  gi|386000957|ref|YP_005919256.1| 149 AEVQQSVQSLASEV 162
                                       22333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.48
# Mc/sec: 1382.92
//
Query:       gi|386000958|ref|YP_005919257.1|  [L=128]
Description: hypothetical protein Mhar_0244 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-16   60.3   0.0    1.5e-16   60.0   0.0    1.1  1  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   8.4e-21   1.5e-16      19     106 .]      20     106 ..       4     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 8.4e-21
                             DUF22  19 vepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvldvvekgkpkkveeerei 95 
                                         pf + ++ ++++ +liA+ed+++++G+ k +kik++ +p+nti+      rh +g+v++++e + + +ve +r  
  gi|386000958|ref|YP_005919257.1|  20 RVPFDFALQGTCHIDYLIAEEDKKFRSGDAKPVKIKKVAIPRNTILLISPYGRHGIGQVISIGE-EIAMPVELDRSA 95 
                                       46999**********************************************************9.************ PP

                             DUF22  96 teavflpvedG 106
                                       ++a+f++  dG
  gi|386000958|ref|YP_005919257.1|  96 DHALFVAGVDG 106
                                       *****998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 919.45
//
Query:       gi|386000959|ref|YP_005919258.1|  [L=139]
Description: hypothetical protein Mhar_0245 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-44  151.1   0.4    1.7e-44  150.9   0.4    1.0  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9   0.4   9.5e-49   1.7e-44       2     127 .]       6     134 ..       5     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 9.5e-49
                                       S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGG....GT-EESEEEEE-SS CS
                             DUF61   2 rilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelw....dklkLPIllemdpe 74 
                                       r++ak ++s+n+hlP+erktL+elL eekp iv++dgs+hr+++eele++++ +++ +w    dklkLPIl+em p+
  gi|386000959|ref|YP_005919258.1|   6 RVFAKLVRSLNDHLPVERKTLRELLGEEKPRIVCRDGSTHRIRREELETIER-ISRLKWgkeaDKLKLPILIEMAPD 81 
                                       899***********************************************99.6666676777************** PP

                                       SSE..EEEES-HHHHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TEE CS
                             DUF61  75 lgesvylvrgkaevkvvskilgkereeedelviykpevrelrrklptatqliF 127
                                       +g+s++++rg+ ++++v++il++er+++de+vi +p++r+lrr+lp+atq++F
  gi|386000959|ref|YP_005919258.1|  82 YGRSAARIRGRVYCDIVQEILKEERKTTDEMVIFRPDIRRLRRELPSATQYAF 134
                                       ****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1013.00
//
Query:       gi|386000960|ref|YP_005919259.1|  [L=173]
Description: Acetyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-12   46.9   0.0    1.6e-11   44.3   0.0    1.8  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      1e-11   45.1   0.0    2.1e-11   44.1   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.7e-09   36.5   0.0    7.9e-09   35.8   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.5e-05   23.7   0.0    0.00011   22.1   0.0    2.0  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.053   13.4   0.0       0.54   10.2   0.0    2.1  2  PLD_C            Phospholipase D C terminal


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   4.6e-15   1.6e-11       2     127 ..       4     128 ..       3     129 .. 0.93
   2 ?    0.5   0.0      0.17   6.1e+02      32      63 ..     135     166 ..     130     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.6e-15
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEE..EE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaa..gv 76 
                                       ire ++ed++++ ++  +aF++  ++  e+  ++r+ + +   l+ae++ge+vg++ + p ++   G+t + a  g+
  gi|386000960|ref|YP_005919259.1|   4 IREERPEDVEAIRQINLAAFNQPAEA--EVVDRLRESCRDLLSLVAEEGGEVVGHILFSPASIGGEGATPPLAgmGL 78 
                                       79999********************9..799999999999999************************8877761156 PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT-EE CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGyei 127
                                       +  av pe +g+g+ s L++  ++ +re+g p ++  ++ +++Y rfG+e 
  gi|386000960|ref|YP_005919259.1|  79 APMAVLPERQGQGIGSLLIHNGIKMLRERGCPYIIVLGY-PEYYPRFGFER 128
                                       679************************************.*********96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHTTSEEEEEEETTEEEEEEEEEEEE CS
                    Acetyltransf_9  32 reyfrklleesrvlgaedngelvgqlallple 63 
                                       + +++++ +e+ ++++ ++  +vg  ++ +++
  gi|386000960|ref|YP_005919259.1| 135 HSQWSEVPDEAFMILILNKTAIVGASGVASYR 166
                                       566889999999***********999887765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   5.9e-15   2.1e-11       4     117 .]      15     126 ..      12     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.9e-15
                                       HHHHHHHHTHHHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET......TSTTEEEEEEEEESGGGT CS
                    Acetyltransf_1   4 lvellvesffppnedaseeefeesfsleae.gllvaeedgeliGfisllkipd......ekggvayieslaVspeyr 73 
                                       ++++  + f  p e + +++ +es     +   lvaee+ge++G+i +++         +    + +  +aV pe++
  gi|386000960|ref|YP_005919259.1|  15 IRQINLAAFNQPAEAEVVDRLRES---CRDlLSLVAEEGGEVVGHILFSPASIggegatPPLAGMGLAPMAVLPERQ 88 
                                       555555565566666666666666...55557777***********8888888888888777889999********* PP

                                       TSSHHHHHHHHHHHHHHHTTESEE.EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  74 gkGlGsaLlealeerareegikki.vlaveedndaairlYeklGF 117
                                       g+G+Gs+L+   ++ +re+g+ +i vl          ++Y ++GF
  gi|386000960|ref|YP_005919259.1|  89 GQGIGSLLIHNGIKMLRERGCPYIiVLG-------YPEYYPRFGF 126
                                       *********************6654872.......2345555665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.2e-12   7.9e-09       6      76 .]      45     128 ..      40     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.2e-12
                                       EEEEETTEEEEEEEEEEES..........TCTEE.....EEE-GGGTTSSHHHHHHH..HTT....SEEEEEEEEE. CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld..........aeitr.....laVdpeyrgkGiGraLle..aae....kgiileqlel. 60 
                                       +Vae++g++vG i +s+ +          a   +     +aV+pe +g+GiG+ L+   + +    +g+  +   l 
  gi|386000960|ref|YP_005919259.1|  45 LVAEEGGEVVGHILFSPASiggegatpplA---GmglapMAVLPERQGQGIGSLLIHngI-KmlreRGCPYI-IVLg 116
                                       69**********999999988777776552...144577*****************8332.13445776533.2342 PP

                                       THHHHHHHHHHTTEEE CS
                    Acetyltransf_7  61 naekaikfYeklGFee 76 
                                             ++Y ++GFe+
  gi|386000960|ref|YP_005919259.1| 117 Y----PEYYPRFGFER 128
                                       2....45*******95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.1e-08   0.00011      20      85 ..      33     109 ..       5     142 .. 0.75
   2 ?   -0.6   0.0      0.33   1.2e+03     101     111 ..     121     131 ..     119     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.1e-08
                   Acetyltransf_10  20 ealrerieegealllvaeeggkivGvi.....elrdgs............hisllfVdpeyrgqGigkaLleaveee 79 
                                       ++lre +   + l lvaeegg++vG+i     +                  ++ ++V pe +gqGig+ L+++ ++ 
  gi|386000960|ref|YP_005919259.1|  33 DRLRESC--RDLLSLVAEEGGEVVGHIlfspaS----IggegatpplagmGLAPMAVLPERQGQGIGSLLIHNGIKM 103
                                       5666666..99999*************554443....255568**9*99999999******************9999 PP

                   Acetyltransf_10  80 aekdgi 85 
                                       ++++g 
  gi|386000960|ref|YP_005919259.1| 104 LRERGC 109
                                       987754 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.33
                   Acetyltransf_10 101 YeklGFkavge 111
                                       Y ++GF++ ++
  gi|386000960|ref|YP_005919259.1| 121 YPRFGFERASR 131
                                       66666665443 PP

>> PLD_C  Phospholipase D C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.061   2.2e+02       5      20 ..       7      22 ..       6      23 .. 0.88
   2 ?   10.2   0.0   0.00015      0.54       3      59 ..      22      77 ..      20      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.061
                             PLD_C  5 eePesleCvrkvnkia 20
                                      e+Pe++e +r++n +a
  gi|386000960|ref|YP_005919259.1|  7 ERPEDVEAIRQINLAA 22
                                      58**********9776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                             PLD_C  3 lfeePesleCvrkvnkiaeenWkayaseeveelkghLlkYPvevdkdGkvkelpgae 59
                                      +f++P + e v ++++  ++  +  ++ee  e+ gh+l  P +++ +G   +l g  
  gi|386000960|ref|YP_005919259.1| 22 AFNQPAEAEVVDRLRESCRDLLSL-VAEEGGEVVGHILFSPASIGGEGATPPLAGMG 77
                                      69****************999887.56677799***************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.46
# Mc/sec: 1131.21
//
Query:       gi|386000961|ref|YP_005919260.1|  [L=255]
Description: hypothetical protein Mhar_0247 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1905.65
//
Query:       gi|386000962|ref|YP_005919261.1|  [L=125]
Description: hypothetical protein Mhar_0248 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.15   11.8   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.4e-06      0.15     102     144 ..      23      68 ..       9      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-06
                                       TSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH...C CS
                      TPP_enzyme_C 102 gpagkdlkpvdfaklaealGakgarvekadveeleealkeal...e 144
                                       +p+++dl++vd  ++a+ ++a g r ++++ ee+e+al++al   e
  gi|386000962|ref|YP_005919261.1|  23 EPSEEDLYQVDEDEIAREMEALGSRKRSRHREEIEAALRAALdrgE 68 
                                       45555799**************887778889***********5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 910.40
//
Query:       gi|386000963|ref|YP_005919262.1|  [L=187]
Description: hypothetical protein Mhar_0249 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   11.9   0.0        1.4    8.0   0.0    2.0  2  BPL_N     Biotin-protein ligase, N terminal


Domain annotation for each model (and alignments):
>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   7.6e-05       1.4      45      84 ..      36      78 ..      25      83 .. 0.82
   2 ?    1.9   0.0    0.0053        94     200     220 ..     149     168 ..     139     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 7.6e-05
                             BPL_N 45 PWastcallVlPgG.aDlpYvreln..gegnrkikeyVekGGk 84
                                      P      +lV+P G a+  Y ++l+  +++ ++i++++ekGG 
  gi|386000963|ref|YP_005919262.1| 36 PFLPRFRVLVIPTGfANPEYSKALSslRAARSRIADFLEKGGI 78
                                      66777789****9945666*****9778999***********5 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.0053
                             BPL_N 200 aAvvlckvgeGkalLtgvhpE 220
                                          vl kvg+Gk++ t++h E
  gi|386000963|ref|YP_005919262.1| 149 PVLVLGKVGRGKVVATTIH-E 168
                                       567999**********999.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1309.92
//
Query:       gi|386000964|ref|YP_005919263.1|  [L=140]
Description: Transcriptional regulator, CopG family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-34  116.4   5.7    6.4e-34  116.0   5.7    1.2  1  NikR_C           NikR C terminal nickel binding domain
    3.7e-08   33.0   0.0    6.8e-08   32.2   0.0    1.4  1  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.025   14.7   0.0    1.6  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
       0.03   14.5   0.1       0.06   13.5   0.0    1.6  2  RHH_8            Ribbon-Helix-Helix transcriptional regulator


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   5.7   1.4e-37   6.4e-34       1      77 []      58     134 ..      58     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.4e-37
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltli 77 
                                       vGvit+vy hhqr+l + lt+iqhe+ d+i+s+lhvhldhdncLe++ l+Ge++e+++ aek++alkgVkhvklt++
  gi|386000964|ref|YP_005919263.1|  58 VGVITMVYSHHQRGLVDALTNIQHEFTDIIQSTLHVHLDHDNCLEIVTLRGEGQEVRKAAEKMMALKGVKHVKLTTT 134
                                       7**************************************************************************86 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.5e-11   6.8e-08       1      37 [.       7      44 ..       7      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.5e-11
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      r+ ++l+e+ll r+d +++ rg +SrSe IR+A+r+y+
  gi|386000964|ref|YP_005919263.1|  7 RIGVSLPESLLTRFDGIIEQRGySSRSEGIRDAIRNYI 44
                                      899*********************************97 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.5e-06     0.025      87     118 ..       3      35 ..       1      40 [. 0.86
   2 ?   -2.4   0.0       1.1   4.7e+03      82      82 ..      95      95 ..      72     127 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                   HicB_lk_antitox  87 gkaeriNitlpervlkriDaavkaag.esRSgf 118
                                       ++  ri ++lpe++l+r D +++++g +sRS  
  gi|386000964|ref|YP_005919263.1|   3 QELMRIGVSLPESLLTRFDGIIEQRGySSRSEG 35 
                                       56789*********************679*975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                   HicB_lk_antitox 82 l 82
                                      l
  gi|386000964|ref|YP_005919263.1| 95 L 95
                                      2 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.3e-05      0.06       8      46 ..      10      48 ..       3      87 .. 0.81
   2 ?   -1.3   0.0      0.53   2.4e+03      47      47 ..      99      99 ..      61     132 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                             RHH_8  8 inlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                      + l    L++ D ++e+  Ys+R++ ir air+ + +++
  gi|386000964|ref|YP_005919263.1| 10 VSLPESLLTRFDGIIEQRGYSSRSEGIRDAIRNYIVHYE 48
                                      5555566899999********************987664 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.53
                             RHH_8 47 d 47
                                      +
  gi|386000964|ref|YP_005919263.1| 99 N 99
                                      1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1108.20
//
Query:       gi|386000965|ref|YP_005919264.1|  [L=230]
Description: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-65  220.5   0.0    4.5e-65  218.9   0.0    1.6  1  Fibrillarin      Fibrillarin
     0.0084   16.8   0.0      0.014   16.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.022   14.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
      0.066   13.3   0.0      0.092   12.8   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.18   12.6   0.0       0.64   10.8   0.0    2.0  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.9   0.0   1.3e-68   4.5e-65       5     225 ..       5     226 ..       1     227 [. 0.91

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 1.3e-68
                                       CSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT.........-S--S--TTS CS
                       Fibrillarin   5 eklegvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkg.........lkelpikkgs 72 
                                       e l+g+ +++  g+ar+at+  vp   vYgE++++      R+W+p+rsKlaa + k          +++l +++gs
  gi|386000965|ref|YP_005919264.1|   5 EDLSGILVLDLFGEARIATRPKVP-VPVYGERIVD----GLRIWDPHRSKLAALLNKSllagglagfVRDLNLSPGS 76 
                                       6678999999889999****9999.57******97....59***********97765411112223357899***** PP

                                       EEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESS CS
                       Fibrillarin  73 kvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDva 149
                                        vLYlGaa+Gtt+sHvsD+v  +g+vyave spr++r+l+ +++ R nivPi+eDA +Pe+Y+ l+e vD++++D+a
  gi|386000965|ref|YP_005919264.1|  77 AVLYLGAATGTTASHVSDLVP-DGLVYAVELSPRAIRDLLGLCQGRDNIVPIIEDAFHPERYAPLLEPVDLVYQDLA 152
                                       ********************9.******************************************************* PP

                                       STTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                       Fibrillarin 150 qpdqarilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                       q +qa+i+ +n+  +lk gg l+++ikars+dvt++p+ev k ev +l+  g++v+ + +l py++dh +vv++++
  gi|386000965|ref|YP_005919264.1| 153 QRNQAEIANLNVGRYLKPGGALVLMIKARSVDVTADPKEVAKGEVARLE--GVEVVSVTDLRPYHQDHWAVVARKR 226
                                       **********************************************996..789******************9875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     4e-06     0.014       1      97 []      78     172 ..      78     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC...CGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda...edlpfedgsfDlvvssgal 74 
                                       vL lG+ tG+++ ++++ ++++ v++v++s+++++     ++ ++ n+  +  da   e++    + +Dlv+    l
  gi|386000965|ref|YP_005919264.1|  78 VLYLGAATGTTASHVSDLVPDGLVYAVELSPRAIRDLLGLCQGRD-NIVPIIEDAfhpERYAPLLEPVDLVYQD--L 151
                                       899****************99********************7655.88888888867766777888******94..4 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                          +++++e a  ++ r LkpgG
  gi|386000965|ref|YP_005919264.1| 152 A--QRNQAEIANLNVGRYLKPGG 172
                                       4..44566778899********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.2e-06     0.022       4     109 ..      75     176 ..      72     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-06
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklled..ekfDl 77 
                                       g  vl lG++tG+ +      l p++ v+ ++ s++ai+     +q  g dn+   ++d+++     +++  e++Dl
  gi|386000965|ref|YP_005919264.1|  75 GSAVLYLGAATGTTASHVS-DLVPDGLVYAVELSPRAIRDLLGLCQ--GRDNIVPIIEDAFHpER--YAPllEPVDL 146
                                       6678999***********9.7889*******************966..**************444..77778***** PP

                   Methyltransf_31  78 ilsnevlnaladpdkile.eiervlkpggilli 109
                                       +  +    a+ ++++i + ++ r+lkpgg+l++
  gi|386000965|ref|YP_005919264.1| 147 VYQD---LAQRNQAEIANlNVGRYLKPGGALVL 176
                                       **99...46677777776699********9985 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.092      19      97 ..      72     153 ..      49     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEECS-CCCSSHHHHHCHCHHHS CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgditdpetiekikealser 86 
                                       ++pg +v+ lgaa+G  +  ++  +   g v+av l p          + ++++  i  d ++pe    ++e     
  gi|386000965|ref|YP_005919264.1|  72 LSPGSAVLYLGAATGTTASHVSDLVPD-GLVYAVELSPRairdllglcQGRDNIVPIIEDAFHPERYAPLLE----- 142
                                       568999******************976.********999777666555555788888*******99998885..... PP

                                       SEEEEEE--S- CS
                              FtsJ  87 kvdlvvsDgap 97 
                                       +vdlv  D+a 
  gi|386000965|ref|YP_005919264.1| 143 PVDLVYQDLAQ 153
                                       8*******995 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.64       3      42 ..      81     119 ..      79     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                   Methyltransf_12   3 iGcGtGsllralleklpdieytgvDispsaiedakeklak 42 
                                       +G+ tG++++++ +  pd  +++v++sp+ai +    l +
  gi|386000965|ref|YP_005919264.1|  81 LGAATGTTASHVSDLVPDGLVYAVELSPRAI-RDLLGLCQ 119
                                       8******************************.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1625.06
//
Query:       gi|386000966|ref|YP_005919265.1|  [L=258]
Description: Signal sequence peptidase I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0031   17.5   0.0      0.007   16.3   0.0    1.6  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.9e-07     0.007       2      24 ..      47      86 ..      46     105 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-07
                                      XXSSTTCCTXXTTXEEEEECTS.................- CS
                     Peptidase_S24  2 vpGdSMeptlldGdlilVdkfs.................e 24
                                      v+++SM+p ++ Gd+i++   s                  
  gi|386000966|ref|YP_005919265.1| 47 VESGSMYPNMKVGDIIVIQGASrtevipwdegeaenyttF 86
                                      89****************9666666666664444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1866.47
//
Query:       gi|386000967|ref|YP_005919266.1|  [L=637]
Description: DNA polymerase D, small subunit DP1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-11   43.7   0.0    6.6e-11   43.1   0.0    1.3  1  Metallophos      Calcineurin-like phosphoesterase
    5.4e-10   39.0   0.0    9.1e-10   38.2   0.0    1.3  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    1.4e-05   25.4   0.0    3.8e-05   23.9   0.0    1.7  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    0.00023   21.1   1.3    0.00028   20.8   0.4    1.6  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0086   16.1   0.1      0.098   12.7   0.1    2.1  2  DUF4539          Domain of unknown function (DUF4539)


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.8e-14   6.6e-11       4     203 ..     367     570 ..     366     571 .. 0.69

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.8e-14
                                       EEEESBTB...TTCCTHHHHHHHHHHHHHHH........TTESEEEEESTSSSSS..............HHHHHHHH CS
                       Metallophos   4 lvigDlHl...algggqlddllkllddllre........ekpdlvllaGDlvdrg..............dlekelle 55 
                                       l+++D+H+      +  +d+++ ++   + e        +k+ + ++aGDlvd+                +e+ +++
  gi|386000967|ref|YP_005919266.1| 367 LLLSDVHVgstYFMEDAWDRFIGWI---RGEvedplgiaSKVKYAVIAGDLVDGIgiypgqegdlaikdIWEQ-YER 439
                                       689****744444444444444444...3333334455578899999*******88***********997777.777 PP

                                       HHHHHHHH...TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETH CS
                       Metallophos  56 llaalvky...pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellv 129
                                         a+lv++   +i ++l +GNH+      +++ +  ++  +++++++++++n+ ++ lg+   + l++hG s+++  
  gi|386000967|ref|YP_005919266.1| 440 A-AELVAEipdRISIVLSPGNHD-VVRQAEPQPALPERLRPLFKKNVTFVGNPASFILGGV--DWLVYHGRSIDD-- 510
                                       7.5555555667888********.4446666666667779999999999999999999999..999999996555.. PP

                                       HHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEE.ESSSS CS
                       Metallophos 130 sldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvis.GHtHv 203
                                        + k+ +l++  +++    e+lk+             + sp+y g+  + ++e+ + ll + ++ +v++ GH+H+
  gi|386000967|ref|YP_005919266.1| 511 LVLKIPGLSYAEPEKAM-VEMLKR------------RHLSPIY-GNRVSIAPEEED-LLVIRRPPAVLHsGHVHT 570
                                       34444444444444444.777777............4555666.666666666666.7777777777777***96 PP

>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.5e-13   9.1e-10      72     201 ..     442     564 ..     401     570 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.5e-13
                                       HHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---E CS
                       DNA_pol_E_B  72 silesllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkre 148
                                       + + ++   +++vl Pg  D++ + + Pq++lp+ l +  k++   +++v NP ++ l +v+ +++ +  ++dl  +
  gi|386000967|ref|YP_005919266.1| 442 ELVAEIPDRISIVLSPGNHDVVRQ-AEPQPALPERLRPLFKKN---VTFVGNPASFILGGVDWLVYHGRSIDDLVLK 514
                                       45566668899*************.*****************8...99****************************9 PP

                                       EESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE CS
                       DNA_pol_E_B 149 slkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlv 201
                                       +   s     + +k++  +l+ rhl+P++   +++  ++ d lv+   P vl 
  gi|386000967|ref|YP_005919266.1| 515 IPGLSY---AEPEKAMVEMLKRRHLSPIYGNRVSIAPEEEDLLVIRRPPAVLH 564
                                       999999...799*********************************98898875 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.1e-08   3.8e-05       4     150 ..     367     591 ..     366     606 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.1e-08
                     Metallophos_2   4 aiiSDlH..snldaleav..............lealkevgvdaiihaGD....................l..eeeep 42 
                                       +++SD+H  s ++  +a+              l ++++v   + + aGD                    +  +e++ 
  gi|386000967|ref|YP_005919266.1| 367 LLLSDVHvgSTYFMEDAWdrfigwirgevedpLGIASKV--KYAVIAGDlvdgigiypgqegdlaikdiWeqYERAA 441
                                       679999999777777777777888888888877777777..********8888888888888888777535667777 PP

                     Metallophos_2  43 evleellelapvlaVrGNnD.......eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl......... 102
                                       e ++e+ ++  ++  +GN+D       +   + e++   +++  t + + a + l+g++ l++Hg            
  gi|386000967|ref|YP_005919266.1| 442 ELVAEIPDRISIVLSPGNHDvvrqaepQ-PaLPERLRPLFKKNVTFVGNPASFILGGVDWLVYHGRSIddlvlkipg 517
                                       888888888899999*****88776532.24677777777777777789999999**********977********* PP

                     Metallophos_2 103 ...........................gvkdalaellke...aeegsdvvvcGHtHvpevekeggvlvvnPGsvgep 149
                                                                  + + + +    +      + +v+ +GH H+ ++ + +gv+ +n G  + +
  gi|386000967|ref|YP_005919266.1| 518 lsyaepekamvemlkrrhlspiygnrvSIAPEEE----DllvIRRPPAVLHSGHVHTVGMARYKGVTAINSGTWQSQ 590
                                       ****777777777777777777754443333333....2544467788************************98776 PP

                     Metallophos_2 150 r 150
                                        
  gi|386000967|ref|YP_005919266.1| 591 T 591
                                       4 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.4   1.2e+04      23      41 ..     227     245 ..     227     249 .. 0.75
   2 !   20.8   0.4   7.8e-08   0.00028       2      57 ..     281     336 ..     280     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.4
                                       EEETTEEEEEEEETHHHHH CS
                   tRNA_anti-codon  23 lrDgtgriqvvlfreeatk 41 
                                       lrD tgr ++v   +++ +
  gi|386000967|ref|YP_005919266.1| 227 LRDITGRSTCVGEYQDFVR 245
                                       7999999999987755555 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 7.8e-08
                                       EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGr 57 
                                       ++ G+v+ ++ +s ++   ++l+D tg++++++ +    ++  e+l  + vv+vtG+
  gi|386000967|ref|YP_005919266.1| 281 SIIGMVMEVR-TSAKGNRVVELEDPTGMVTAIFQKgVPGSEEVETLVSDEVVGVTGT 336
                                       89*******9.999******************************************8 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   2.7e-05     0.098       6      52 ..     282     328 ..     280     333 .. 0.78
   2 ?    0.6   0.0      0.17     6e+02      44      64 ..     356     376 ..     345     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                           DUF4539   6 lvviiksintlnslgdalvtlkDptGeidgtihrkvl.eeygkdlsvG 52 
                                       +++++ ++  ++ +g+  v l+DptG +++++++ v  +e  + l+++
  gi|386000967|ref|YP_005919266.1| 282 IIGMVMEV-RTSAKGNRVVELEDPTGMVTAIFQKGVPgSEEVETLVSD 328
                                       57889999.66666699*******************985555555544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                           DUF4539  44 eygkdlsvGavllLkqVsvfs 64 
                                       +  +++  G +llL +V+v s
  gi|386000967|ref|YP_005919266.1| 356 RSAAAFGEGGALLLSDVHVGS 376
                                       55677899**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 4567.16
//
Query:       gi|386000968|ref|YP_005919267.1|  [L=231]
Description: hypothetical protein Mhar_0254 [Methanosaeta harundinacea 6Ac]
Scores for 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-68  229.3  28.2    3.4e-68  229.1  28.2    1.0  1  DUF1538   Protein of unknown function (DUF1538)
  ------ inclusion threshold ------
        3.1    6.5   9.0      0.088   11.6   3.0    1.4  2  DUF2206   Predicted membrane protein (DUF2206)


Domain annotation for each model (and alignments):
>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.1  28.2   3.8e-72   3.4e-68       1     210 [.      19     228 ..      19     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 3.8e-72
                           DUF1538   1 ivlvlllfqllvlklslkelaeillGlllvvlGlalFllGvelgllplGeqvgsklakkkklllvllvafllGflvt 77 
                                       i lv+ll+ql+++  +++++a++ll++++v lG+++Fl+Gv++g+lp+Ge++g +lak++++l+++lv+f++ fl+t
  gi|386000968|ref|YP_005919267.1|  19 ISLVVLLIQLFLVGSPPEKIATFLLSAFMVGLGFTFFLMGVKVGMLPMGEAIGGELAKHGSVLFLVLVTFVISFLAT 95 
                                       6789************************************************************************* PP

                           DUF1538  78 lAEPalsvlakqveevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaia 154
                                       lAEP+++vl++++ +vs + i++ +l++++a+Gvg++++l++lri++g+++kyl + +yllv++l++++p++++ai+
  gi|386000968|ref|YP_005919267.1|  96 LAEPDVRVLTSTITSVSGEVISRVALLVSIAFGVGIFVVLSMLRIVYGVPIKYLYAGSYLLVIALSFFTPPDYLAIS 172
                                       ***************************************************************************** PP

                           DUF1538 155 fDsgGvttgpitvplilalglGvasalegknalvdgFGlvalaslgPilavlllgl 210
                                       fDsgGvttgp+tvplilalg+Gvas++ g++al+dgFGl+++as+gPil v+llg+
  gi|386000968|ref|YP_005919267.1| 173 FDSGGVTTGPMTVPLILALGTGVASVMAGRSALSDGFGLIGFASIGPILGVMLLGV 228
                                       *******************************************************8 PP

>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.4      0.41   3.7e+03     221     233 ..      20      32 ..      11      56 .. 0.59
   2 ?   11.6   3.0   9.8e-06     0.088      79     167 ..      79     168 ..      69     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.41
                           DUF2206 221 svflvvllLfnsG 233
                                       s++++++ Lf +G
  gi|386000968|ref|YP_005919267.1|  20 SLVVLLIQLFLVG 32 
                                       4444444444333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.8e-06
                           DUF2206  79 sivnkilssiateflnptttqglavitkqissllhtvskylhliiqfliviGvlsvlflrkkkyrlsieylaivlvl 155
                                       s++  +l + + +fl+  ++  + v+t+ i+s++ +v   + l++    ++G++ vl + +  y + i+yl +  +l
  gi|386000968|ref|YP_005919267.1|  79 SVLFLVLVTFVISFLATLAEPDVRVLTSTITSVSGEVISRVALLVSIAFGVGIFVVLSMLRIVYGVPIKYLYAGSYL 155
                                       566678888999999999*************************************87776799************** PP

                           DUF2206 156 lvilvasivlp.y 167
                                       lvi++ ++++p y
  gi|386000968|ref|YP_005919267.1| 156 LVIALSFFTPPdY 168
                                       ******9998845 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1702.75
//
Query:       gi|386000969|ref|YP_005919268.1|  [L=242]
Description: hypothetical protein Mhar_0255 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-67  225.7  21.9    4.5e-67  225.4  21.9    1.0  1  DUF1538      Protein of unknown function (DUF1538)


Domain annotation for each model (and alignments):
>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.4  21.9   2.5e-71   4.5e-67       2     211 .]      24     233 ..      23     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.4 bits;  conditional E-value: 2.5e-71
                           DUF1538   2 vlvlllfqllvlklslkelaeillGlllvvlGlalFllGvelgllplGeqvgsklakkkklllvllvafllGflvtl 78 
                                       vl++l+fq++ l+ + ++++++l+G++l+++G++lFl Gv lg+lp G+++g+ + + ++ +++l+v++llGfl+t+
  gi|386000969|ref|YP_005919268.1|  24 VLFFLVFQVFHLRYPRRHVMRLLFGIALTTVGMVLFLAGVFLGFLPTGQEMGRFFGSYEEGWVLLAVGVLLGFLATY 100
                                       799************************************************************************** PP

                           DUF1538  79 AEPalsvlakqveevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaiaf 155
                                       AEPa++vl  qve+ s+g ik++++++++++Gv++ + +g++ri +gi++ ++++pgy+l+++l + ++++fv+i+f
  gi|386000969|ref|YP_005919268.1| 101 AEPAVRVLCYQVEKASSGYIKSSLMLYTLSLGVAVLVGIGMARIHYGIPILHIVIPGYILAIILLFASDRDFVGISF 177
                                       ***************************************************************************** PP

                           DUF1538 156 DsgGvttgpitvplilalglGvasalegknalvdgFGlvalaslgPilavlllgll 211
                                       D+gGv+tgp++v++++++++G+as++eg+++lvdgFGl+al++l+Pi++vl lg++
  gi|386000969|ref|YP_005919268.1| 178 DAGGVATGPMAVTFLMSVAVGAASVMEGSDPLVDGFGLIALIALAPIIFVLSLGVI 233
                                       *****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1803.70
//
Query:       gi|386000970|ref|YP_005919269.1|  [L=130]
Description: Nitrogen regulatory protein P-II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   15.1   0.2      0.037   14.6   0.2    1.2  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   2.1e-06     0.037       1      95 [.      10      99 ..      10     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-06
                                      EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH- CS
                              P-II  1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaak 79
                                      i +i+++   +e+  a  +ag +g t+   +G G  ++ ++l  + + e    +k ++  vvs  ++++v+ea++ka k
  gi|386000970|ref|YP_005919269.1| 10 IVTIVKKGWGDEILCASMDAGAEGGTILFGRGVGVREQ-KKL-LNIMIE---PEKEVVLTVVSTCEADRVLEAVVKAGK 83
                                      56788888888888888888899988888777776662.232.222333...3477777888***************** PP

                                      SSSTTSEEEEEEEESE CS
                              P-II 80 tgeiGDGkiFvlpvee 95
                                       +e+G G  F l +++
  gi|386000970|ref|YP_005919269.1| 84 LEEPGKGIAFELRIDK 99
                                      *******999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1097.93
//
Query:       gi|386000971|ref|YP_005919270.1|  [L=343]
Description: 2-dehydropantoate 2-reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-32  112.3   0.0    2.1e-32  111.9   0.0    1.2  1  ApbA_C         Ketopantoate reductase PanE/ApbA C terminal
    5.5e-18   65.0   0.0    9.9e-18   64.2   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.015   15.8   0.0      0.026   15.0   0.0    1.4  1  NAD_binding_7  Putative NAD(P)-binding
      0.063   13.4   0.0       0.54   10.3   0.0    2.1  1  Octopine_DH    NAD/NADP octopine/nopaline dehydrogenase, alph


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   4.8e-36   2.1e-32       4     125 .]     206     331 ..     203     331 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 4.8e-36
                            ApbA_C   4 larweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlek....taa 76 
                                       ++ w K+l+n+a+npl+a++++++g+l e  + r++++al+ E++av+ea+g++      +e+ + + ek    ta+
  gi|386000971|ref|YP_005919270.1| 206 KDLWAKMLYNCALNPLGAIFGVPYGDLAEVSASREIMEALIGEIFAVMEAAGYRTHWSTPDEYRAVFYEKllppTAR 282
                                       578*************************************************8866665788888888889999999 PP

                            ApbA_C  77 nrsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellkale 125
                                       + sS+lqD++a++ tEi+++ Gavv+l+e++gv+tP+n++ly+++k +e
  gi|386000971|ref|YP_005919270.1| 283 HESSTLQDIRAKKSTEIEALSGAVVRLGEEVGVPTPTNATLYRMVKFME 331
                                       *********************************************9875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   2.2e-21   9.9e-18       2     148 ..       4     174 ..       3     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.2e-21
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH................. CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsae................. 61 
                                       +i G Ga+G  +a +L   ga+v +i+r+  + al+k Gl  t+  g++ + p+   +++                 
  gi|386000971|ref|YP_005919270.1|   4 LIYGGGAVGLGIASCLILSGAKVDIIAREGTVSALRKGGLARTGIFGSVEVGPEGFGAFAsldellrlggrrlqdgg 80 
                                       699**************************************99999*********999999**************** PP

                                       ...SCCCCS-ESEEEE-SSGGGHHHHHHHH...GGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEE CS
                              ApbA  62 ...ekselepidlvivtvKayqteealeei...kplldpntvvlllqNGlgheeelrealpkprvlggvtthgatre 132
                                          ++  + ++d+v++++K+    +a++++   +++l++  +++l+qNG+g++e+++e++pk++++++ +  g+ r 
  gi|386000971|ref|YP_005919270.1|  81 lnrDRDFGCDYDYVLICTKSHGSPAAAADLsrhRKILGDGGKIVLFQNGWGNAEIFAEHFPKDQIYSARVITGFSRP 157
                                       **9889999***********99888877752227789**************************************** PP

                                       ETTEEEECS.--EEEEE CS
                              ApbA 133 gpgevhhag.kgeikig 148
                                       +++ v+ +   ++i++g
  gi|386000971|ref|YP_005919270.1| 158 ENNVVEVTVhADSIHLG 174
                                       ***99988656777776 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   5.8e-06     0.026       9      87 ..       2     116 ..       1     118 [. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.8e-06
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele..............................elvklaeee. 54 
                                       k l+ GgG v++  ++ l+ +gakv ++a e    ++                              el++l  +  
  gi|386000971|ref|YP_005919270.1|   2 KALIYGGGAVGLGIASCLILSGAKVDIIAREG--TVSalrkgglartgifgsvevgpegfgafasldELLRLGGRRl 76 
                                       689****************************4..4443445666666666555555555555555554444433331 PP

                     NAD_binding_7  55 ....lekd...legadlviaatddrelneriaeaakarri 87 
                                           l++d     ++d v+++t+ +   ++ a++ + r+i
  gi|386000971|ref|YP_005919270.1|  77 qdggLNRDrdfGCDYDYVLICTKSHGSPAAAADLSRHRKI 116
                                       1111322222222588888888888887777777777766 PP

>> Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.54      46     146 ..     237     327 ..     226     330 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                       Octopine_DH  46 svaevlealdeErlaiakalgl..evlplaerlldaYgdeikdksslaevirtneaykgikaPmsldhRyltEDipy 120
                                       ++ e++eal  E++a+ +a g+  ++ + +e+ +++Y+     k    ++ +++  +++i+a +s+       +i+ 
  gi|386000971|ref|YP_005919270.1| 237 ASREIMEALIGEIFAVMEAAGYrtHWSTPDEYRAVFYE-----KLLPPTARHESSTLQDIRAKKST-------EIEA 301
                                       57799***************984345577777777774.....22222233457788888887765.......7889 PP

                       Octopine_DH 121 gLvvlkslAellgvptpvidsviela 146
                                           ++ l+e +gvptp+   ++++ 
  gi|386000971|ref|YP_005919270.1| 302 LSGAVVRLGEEVGVPTPTNATLYRMV 327
                                       99999999999999999988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2563.07
//
Query:       gi|386000972|ref|YP_005919271.1|  [L=235]
Description: hypothetical protein Mhar_0258 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.3   0.0     0.0027   17.8   0.0    1.3  1  DUF2953   Protein of unknown function (DUF2953)
  ------ inclusion threshold ------
        1.1    9.5   7.5        2.4    8.5   6.4    2.0  2  KASH      Nuclear envelope localisation domain


Domain annotation for each model (and alignments):
>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     3e-07    0.0027       3      52 ..     151     193 ..     149     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-07
                           DUF2953   3 iGleDaadTgilyGliwaikgllygllsnlfnikkpeievtPvFneevfe 52 
                                       +Gl+D+adT+ ++Gl  a+  +l ++       +  + ev P+F ee + 
  gi|386000972|ref|YP_005919271.1| 151 VGLSDPADTAEAFGLMMAVLMPLEAV-------TPLRAEVAPSFAEERLA 193
                                       7**********************999.......9**********999875 PP

>> KASH  Nuclear envelope localisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.4   0.00027       2.4       8      26 ..      10      28 ..       8      38 .. 0.67
   2 ?   -1.5   0.0      0.34   3.1e+03      14      45 ..     165     196 ..     160     203 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00027
                              KASH  8 aalpLqllLllllllalLv 26
                                      aal LqllLll++llalL+
  gi|386000972|ref|YP_005919271.1| 10 AALILQLLLLLFVLLALLL 28
                                      7899997777777666654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.34
                              KASH  14 llLllllllalLvplseedesCslaNnfarSf 45 
                                       l++ +l+ l  + pl  e     +  ++a Sf
  gi|386000972|ref|YP_005919271.1| 165 LMMAVLMPLEAVTPLRAEVAPSFAEERLAGSF 196
                                       45555555555555554544444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1817.92
//
Query:       gi|386000973|ref|YP_005919272.1|  [L=140]
Description: hypothetical protein Mhar_0259 [Methanosaeta harundinacea 6Ac]
Scores for 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-19   70.5   3.8      1e-19   70.5   3.8    1.8  2  Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)


Domain annotation for each model (and alignments):
>> Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   3.8   5.6e-24     1e-19       3      80 .]      30     107 ..      29     107 .. 0.95
   2 ?   -0.8   0.5     0.099   1.8e+03      26      45 ..     118     137 ..     113     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 5.6e-24
                        Spore_YtfJ   3 tgdgtviiPvskvsfGfgaGgsefkskkekepfgggsgaGvsitPvAfLvikkgevkllpvkk...ssldklidlvp 76 
                                       t+ g+++iP+ +v+ GfgaG++ +   ke+e+ ggg+g+G++i+PvA+++i++++v++ pv+k   s +++l d++p
  gi|386000973|ref|YP_005919272.1|  30 TAGGKTVIPLLSVGAGFGAGAGAG---KEDEGTGGGAGGGFGIKPVAVIIIEEESVRVEPVEKkpgSLIEQLADKIP 103
                                       5678********************...8899******************************99************** PP

                        Spore_YtfJ  77 dvvd 80 
                                       ++++
  gi|386000973|ref|YP_005919272.1| 104 SLIK 107
                                       *985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.099
                        Spore_YtfJ  26 fkskkekepfgggsgaGvsi 45 
                                       +k+k+++e+ gg +g G +i
  gi|386000973|ref|YP_005919272.1| 118 GKEKEAEEKSGGEKGKGKEI 137
                                       34444677778888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 841.71
//
Query:       gi|386000974|ref|YP_005919273.1|  [L=226]
Description: hypothetical protein Mhar_0260 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00041   21.0   0.0      0.001   19.7   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
     0.0013   19.3   0.0     0.0025   18.4   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0041   16.7   0.0     0.0064   16.1   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.13   10.8   0.0       0.18   10.4   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.3e-07     0.001       1      92 [.      83     168 ..      83     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       +Ld++cG+      la  +   +v g D s++++e+  er       +  + +d++dl+++++sf +vvs +  +  
  gi|386000974|ref|YP_005919273.1|  83 ILDVACGPV----SLACLY--DDVCGHDNSPAFVEHLVERG------IPARLADITDLDYPSESFSYVVSLNPpMKP 147
                                       8******94....334345..7899**************99......89999******************8877764 PP

                                       SS.....HHHHHHHHHHHHHH CS
                   Methyltransf_25  77 ls.....dedlekalkeiarv 92 
                                       +      ++ ++++++e+ r+
  gi|386000974|ref|YP_005919273.1| 148 FRrrgdpRAGVRRFVEEMLRI 168
                                       431110022345666666666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.6e-07    0.0025       1      68 [.      84     141 ..      84     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.6e-07
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                       Ldv+cG  +la+ +     +v g D s+++++      +e+g  +  + ad+++l ++++sf  vvs 
  gi|386000974|ref|YP_005919273.1|  84 LDVACGPVSLACLYD----DVCGHDNSPAFVEHL----VERG--IPARLADITDLDYPSESFSYVVSL 141
                                       8***********999....99**********554....5555..55699****************996 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-06    0.0064      12     107 ..      78     174 ..      71     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                              MetW  12 kpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvv.lsqtlqa 87 
                                       + + r+ld+ cG  +l  l  +       G +++ + v + v++G+     d+ +dl+ ++++sf yvv l+  ++ 
  gi|386000974|ref|YP_005919273.1|  78 DLEGRILDVACGPVSLACLYDD-----VCGHDNSPAFVEHLVERGIPARLADI-TDLD-YPSESFSYVVsLNPPMKP 147
                                       55789********998777744.....56889****************99999.5775.9*******9978888988 PP

                              MetW  88 trn...p....kevldellrigrraiv 107
                                        r+   p    ++ ++e+lri+r+ ++
  gi|386000974|ref|YP_005919273.1| 148 FRRrgdPragvRRFVEEMLRIARKRVI 174
                                       775233332336799*******87544 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.9e-05      0.18     121     184 ..      83     137 ..      66     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.9e-05
                   Methyltransf_29 121 vlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdl 184
                                       +lDv Cg  s++  l   dv       +D+  a v   +eRg+pa la ++   l yPs+sf  
  gi|386000974|ref|YP_005919273.1|  83 ILDVACGPVSLAC-L-YDDV-----CGHDNSPAFVEHLVERGIPARLADIT--DLDYPSESFSY 137
                                       6888888888754.3.3444.....5689999***************9886..69*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1393.71
//
Query:       gi|386000975|ref|YP_005919274.1|  [L=87]
Description: FeoA family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-17   61.0   0.2    1.1e-16   60.9   0.2    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.2   5.9e-21   1.1e-16       2      73 ..      13      82 ..      12      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 5.9e-21
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      pL++l eGe+g +++++   + l++rL emGl+p +++ v+ r+  +gp+++  +++r+aLgr++ ++IlV 
  gi|386000975|ref|YP_005919274.1| 13 PLAFLLEGEEGNVVEVRGG-RGLAQRLSEMGLTPSTKVLVL-RSCPQGPMLISFRGSRIALGRGITMKILVS 82
                                      9***************998.99*******************.77889************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       143  (0.0079759); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 553.46
//
Query:       gi|386000976|ref|YP_005919275.1|  [L=233]
Description: Ferrous iron transport protein B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-66  221.5   0.1    4.8e-66  221.1   0.1    1.1  1  FeoB_N       Ferrous iron transport protein B
    2.1e-19   69.7   0.0    3.4e-19   69.0   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    1.7e-12   47.7   0.3    3.5e-12   46.7   0.3    1.6  1  FeoB_Cyto    FeoB cytosolic helical domain
    1.3e-06   28.0   0.0    1.8e-06   27.5   0.0    1.3  1  SRPRB        Signal recognition particle receptor beta subuni
    0.00056   19.9   0.1       0.86    9.5   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
     0.0023   17.5   0.0       0.31   10.6   0.0    2.7  1  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0024   17.2   0.0     0.0035   16.7   0.0    1.2  1  AIG1         AIG1 family
     0.0095   16.2   0.1      0.021   15.0   0.1    1.8  1  Roc          Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.031   13.9   0.0    1.4  1  Ras          Ras family
      0.042   13.3   0.1        2.4    7.5   0.0    2.9  3  TniB         Bacterial TniB protein


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.1   0.1   2.7e-69   4.8e-66       2     156 .]       3     157 ..       2     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.1 bits;  conditional E-value: 2.7e-69
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       tva++GnpnvGkt lfn+ltg+kq+vgNwpGvtvekk+gkl ++g+e+e+vDlPG+Ysl a++++e v+r+++lee+
  gi|386000976|ref|YP_005919275.1|   3 TVAIIGNPNVGKTELFNRLTGMKQHVGNWPGVTVEKKTGKLVHRGEEIEVVDLPGTYSLAATAKDELVSRSYILEER 79 
                                       79*************************************************************************** PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                       pdvvv++vdat+lernLyLtl llel++++v+aln +d a+++gi id++kLse Lgvpvv+t+a ++eg+e+l++a
  gi|386000976|ref|YP_005919275.1|  80 PDVVVDIVDATSLERNLYLTLLLLELEANLVVALNRWDMARERGIVIDTEKLSELLGVPVVPTVAPSGEGVERLKDA 156
                                       **************************************************************************997 PP

                                       H CS
                            FeoB_N 156 i 156
                                       +
  gi|386000976|ref|YP_005919275.1| 157 V 157
                                       5 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   1.9e-22   3.4e-19       2      96 ..       4      97 ..       3     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.9e-22
                                      EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCTSE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleeadl 78
                                      vai+G+pNvGK+ L+n+ltg k +v+++pg+T + ++g++ ++g+eie+vD+pG ++     +++ +++++   e+ d+
  gi|386000976|ref|YP_005919275.1|  4 VAIIGNPNVGKTELFNRLTGMKQHVGNWPGVTVEKKTGKLVHRGEEIEVVDLPGTYSlaATAKDELVSRSYILEERPDV 82
                                      9****************************************999**********98664344444799999988889** PP

                                      EEEEEETTTTCSHHHHHH CS
                          MMR_HSR1 79 illvvdaseeklkpldee 96
                                      ++ +vda+ + l+++   
  gi|386000976|ref|YP_005919275.1| 83 VVDIVDAT-S-LERN-LY 97
                                      ******77.3.3222.33 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.3     2e-15   3.5e-12       1      54 [.     174     228 ..     174     233 .] 0.90

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2e-15
                         FeoB_Cyto   1 YgeeiEkaiekleellkes.nlkaklppRwlAlklLegDeelleelkedpelrae 54 
                                       Ygee E ai+++e++++++ +l +++ppRwlA++lLe+De +l+ ++++p  r+ 
  gi|386000976|ref|YP_005919275.1| 174 YGEEAEIAIAEVEDAVRKDaELSRRYPPRWLAIRLLEDDEHVLKLIETSPHQRTI 228
                                       9**********************************************97765554 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0     1e-09   1.8e-06       5      92 ..       3      96 ..       1     119 [. 0.73

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1e-09
                                      EEEEE-STTSSHHHHHHHHHHSS---B-...--SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE.. CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvkktv...tSqessaalkvksekgskltliDfPGheklrqklleklkaksslkg.. 78
                                      +v ++G  + GKT lf+rLt  + +      + +e+++ + v  ++g++++++D+PG  +l+   +++l+ +s +    
  gi|386000976|ref|YP_005919275.1|  3 TVAIIGNPNVGKTELFNRLTGMKQHVGNwpgVTVEKKTGKLV--HRGEEIEVVDLPGTYSLAATAKDELVSRSYILEer 79
                                      789****************97744433211134455555555..9*****************99999988887753222 PP

                                      ...EEEEEETTS-HHHH CS
                             SRPRB 79 ...lvfvvDStidpkev 92
                                         +v +vD+t  ++++
  gi|386000976|ref|YP_005919275.1| 80 pdvVVDIVDATSLERNL 96
                                      23266677777666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0011       1.9     101     129 ..       3      30 ..       1      63 [. 0.69
   2 !    9.5   0.0   0.00048      0.86      41      97 ..     101     157 ..      82     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                                       EEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktge 129
                                       t++++G+  vGK+ L n+l++  ++++g+
  gi|386000976|ref|YP_005919275.1|   3 TVAIIGNPNVGKTELFNRLTGM-KQHVGN 30 
                                       7899****************97.555554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00048
                                       HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  41 laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                       l+ e ++++v++ln+ D++ e+  + ++++  e lg++v+ + a ++eg+e+lk+++
  gi|386000976|ref|YP_005919275.1| 101 LLLELEANLVVALNRWDMARERGIVIDTEKLSELLGVPVVPTVAPSGEGVERLKDAV 157
                                       34567889***************99999999999*******************9875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00017      0.31      53     190 ..      33     159 ..       1     163 [. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                                       TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHH.....HHHHHHT-SEEEEEEETTTBSTHH.HHHHHHHHHHTTT CS
                          GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFske.....virglrvlDgavlvvdaveGvepq.teevlrlalkegv 123
                                       g+T++ ++ +l    +  +i ++D PG  +   +     v+r++   +   +vvd+v+         +  l+l+++ 
  gi|386000976|ref|YP_005919275.1|  33 GVTVEKKTGKLV--HRGEEIEVVDLPGTYSLAATakdelVSRSYILEERPDVVVDIVDATSLErNLYLTLLLLELEA 107
                                       778888888888..888888888888887776541122255554333333345555544333303344556677888 PP

                                       EEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 124 piivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                       +++v++N  D+++++   i +e  ++l      l          vpvv++ a +gegv+ l +a+ e
  gi|386000976|ref|YP_005919275.1| 108 NLVVALNRWDMARERGIVIDTEKLSEL------L---------GVPVVPTVAPSGEGVERLKDAVLE 159
                                       899999999999777666655555555......2.........478899999999998888888876 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.9e-06    0.0035       2      92 ..       3      88 ..       2     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                                      EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHC CS
                              AIG1  2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcllls 80
                                      t+ ++G   +Gk    N + g k+   +    +vt + ++ + + +g++i+V+D Pg  +l ++a++  + ++r++ l 
  gi|386000976|ref|YP_005919275.1|  3 TVAIIGNPNVGKTELFNRLTGMKQHVGNW--PGVTVEKKTGKLVHRGEEIEVVDLPGTYSLAATAKD--ELVSRSYILE 77
                                      6778999999*********9999998885..89999999**********************998773..4456667776 PP

                                      TT-ESEEEEEEE CS
                              AIG1 81 eegihalllvls 92
                                      e  +++++ +++
  gi|386000976|ref|YP_005919275.1| 78 ER-PDVVVDIVD 88
                                      66.888875544 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.2e-05     0.021       2      38 ..       4      40 ..       3     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdflt 38
                                      v ++G+ +vGKt l++r++  k +  + + + v+ +t
  gi|386000976|ref|YP_005919275.1|  4 VAIIGNPNVGKTELFNRLTGMKQHVGNWPGVTVEKKT 40
                                      789***************9776665554444444333 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.031       2     157 ..       4     158 ..       3     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                       EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE.. CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil.. 76 
                                       + ++G+ +vGKt l +r +  k +    + + v+++t ++  +g+e+  e+ D  G     + ++  + + + il  
  gi|386000976|ref|YP_005919275.1|   4 VAIIGNPNVGKTELFNRLTGMKQHVGNWPGVTVEKKTGKLVHRGEEI--EVVDLPGTYSLAATAKDELVSRSYILee 78 
                                       679*****************999999999999999999999888876..6788888887777666666666666555 PP

                                       ...EEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHH CS
                               Ras  77 ...lvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenve 150
                                          +v di +++s+e+   + + +    e   ++v+  n+ D++++r +  ++ e+l++ lg++ + t A + e+ve
  gi|386000976|ref|YP_005919275.1|  79 rpdVVVDIVDATSLERNLYL-TLLLLELE--ANLVVALNRWDMARERGIVIDT-EKLSELLGVPVVPTVAPSGEGVE 151
                                       55588999999999974433.33333333..4677777999999999998876.66999999999999999999998 PP

                                       HHHHHHH CS
                               Ras 151 eafeell 157
                                        + +++l
  gi|386000976|ref|YP_005919275.1| 152 RLKDAVL 158
                                       7665555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0013       2.4      35      59 ..       1      25 [.       1      38 [. 0.85
   2 ?    1.2   0.0      0.12   2.1e+02      70     101 ..     137     168 ..     120     173 .. 0.85
   3 ?    0.3   0.0      0.22     4e+02     163     182 ..     183     202 ..     171     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                              TniB 35 mpnlllvGdsnnGKtmivekFarlh 59
                                      m  + ++G++n+GKt ++++ + ++
  gi|386000976|ref|YP_005919275.1|  1 MTTVAIIGNPNVGKTELFNRLTGMK 25
                                      67899*************9987665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                              TniB  70 vpvlvvqappkpdekrlyaaiLealgaplkar 101
                                       vpv+   ap+    +rl +a+Lea +a+  +r
  gi|386000976|ref|YP_005919275.1| 137 VPVVPTVAPSGEGVERLKDAVLEAAKAEGGKR 168
                                       799999*****************999886655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.22
                              TniB 163 eealralrtDpqlasRFepi 182
                                        e+ +a+r+D++l++R+ p 
  gi|386000976|ref|YP_005919275.1| 183 AEVEDAVRKDAELSRRYPPR 202
                                       577899**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1458.60
//
Query:       gi|386000977|ref|YP_005919276.1|  [L=434]
Description: Ferrous iron transport protein B [Methanosaeta harundinacea 6Ac]
Scores for complete 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-42  142.7  22.3    4.6e-28   97.7   4.5    3.0  3  Gate      Nucleoside recognition
    1.4e-19   69.5   1.9    1.4e-19   69.5   1.9    3.7  4  FeoB_C    Ferrous iron transport protein B C terminus
  ------ inclusion threshold ------
       0.84    9.4   4.2         12    5.8   0.2    3.1  2  PMP1_2    ATPase proteolipid family


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   2.2   2.7e-19   1.6e-15       2     111 ..     114     208 ..     113     209 .. 0.96
   2 !   97.7   4.5   7.7e-32   4.6e-28       1     111 [.     276     402 ..     276     403 .. 0.93
   3 ?   -3.5   1.0         2   1.2e+04      85     109 ..     407     431 ..     406     433 .. 0.54

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.7e-19
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       l ++p i+++++ +++l++s++l+r++++++ +++ lg  l++++++++++gf+   +++++++ ++         +
  gi|386000977|ref|YP_005919276.1| 114 LVFVPPIFMLFFALSILEDSGYLSRAAFVMDRLMHSLG--LHGRSFIPMMMGFG---CNIPAIMATR---------S 176
                                       66899*********************************..**************...*********9.........* PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelgs 111
                                       +d++k++++++l++ l + c+a+l+v+v ++g+
  gi|386000977|ref|YP_005919276.1| 177 IDGEKDRMITILVNPLIS-CGARLPVYVLMAGA 208
                                       ****************87.*********99986 PP

  == domain 2  score: 97.7 bits;  conditional E-value: 7.7e-32
                              Gate   1 llkagpiillasiliwflss.............ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtl 64 
                                       l +ag+ii+  ++++wfls+             ss+++ +g +lep+f+p+g   dw a+v+ll+g++akevvv+t 
  gi|386000977|ref|YP_005919276.1| 276 LARAGTIIFGTVLVVWFLSAhpweatgggelieSSYIASLGHALEPIFKPFG--WDWMAAVALLFGLLAKEVVVATY 350
                                       579*************************************************..*********************** PP

                              Gate  65 gtly.....tsalgellqgfdtpksalafllfvllytpcvatlavivrelgs 111
                                       g l      +   + ++ g +tp + +af+ fvl+y+pc+at++vi+re++s
  gi|386000977|ref|YP_005919276.1| 351 GILLgveeaSLGESLVSLGLFTPLTGFAFMAFVLIYVPCIATIGVIARETNS 402
                                       *9999995533334456699*****************************986 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2
                              Gate  85 alafllfvllytpcvatlavivrel 109
                                       a+a+  +v+l++     ++ ++r+l
  gi|386000977|ref|YP_005919276.1| 407 AFAMTYLVVLAFLVSGLIIGFGRML 431
                                       5566666666665555555566655 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   1.9   2.4e-23   1.4e-19       1      53 []     219     271 ..     219     271 .. 0.98
   2 ?   -3.2   0.1       1.2   7.1e+03       9      20 ..     283     294 ..     281     298 .. 0.69
   3 ?   -1.3   0.4      0.31   1.9e+03       9      22 ..     332     345 ..     330     349 .. 0.82
   4 ?   -2.1   2.9      0.54   3.2e+03       1      19 [.     407     425 ..     407     430 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 2.4e-23
                            FeoB_C   1 lfslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                       +fs+Yllgi++a+++al++++ t ++gepspfv+ELP Y +P++k  ++++w R
  gi|386000977|ref|YP_005919276.1| 219 IFSIYLLGIALAVIMALIFRR-TlFRGEPSPFVLELPAYSVPTAKAAVVHMWAR 271
                                       69*******************.99****************************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                            FeoB_C   9 ilvallvalllk 20 
                                       i+ ++lv ++l+
  gi|386000977|ref|YP_005919276.1| 283 IFGTVLVVWFLS 294
                                       666777777776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.31
                            FeoB_C   9 ilvallvalllkkt 22 
                                        +vall +ll+k +
  gi|386000977|ref|YP_005919276.1| 332 AAVALLFGLLAKEV 345
                                       58999999999874 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.54
                            FeoB_C   1 lfslYllgilvallvalll 19 
                                       +f++  l +l++l+++l++
  gi|386000977|ref|YP_005919276.1| 407 AFAMTYLVVLAFLVSGLII 425
                                       5899999999999999997 PP

>> PMP1_2  ATPase proteolipid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5     0.012        72       8      32 ..     216     239 ..     212     243 .. 0.86
   2 ?    5.8   0.2     0.002        12       4      28 ..     372     396 ..     370     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                            PMP1_2   8 GGviLvFvLvGLACvAivltilYRk 32 
                                       G vi    L G+A +A+++ +++R+
  gi|386000977|ref|YP_005919276.1| 216 GTVIFSIYLLGIA-LAVIMALIFRR 239
                                       88999999****9.78999999986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.002
                            PMP1_2   4 stLPGGviLvFvLvGLACvAivlti 28 
                                       + L G   + FvL+ + C+A +  i
  gi|386000977|ref|YP_005919276.1| 372 TPLTGFAFMAFVLIYVPCIATIGVI 396
                                       6788888999**********99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2602.93
//
Query:       gi|386000978|ref|YP_005919277.1|  [L=139]
Description: hypothetical protein Mhar_0264 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.6   0.7       0.16   12.4   0.1    1.7  2  DUF805    Protein of unknown function (DUF805)
        1.5    8.7   4.8        1.8    8.4   0.5    2.3  2  DUF4538   Domain of unknown function (DUF4538)


Domain annotation for each model (and alignments):
>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.24   2.1e+03      39      39 ..      39      39 ..      10      61 .. 0.41
   2 ?   12.4   0.1   1.8e-05      0.16       4      63 ..      64     133 ..      62     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                            DUF805 39 v 39
                                      +
  gi|386000978|ref|YP_005919277.1| 39 I 39
                                      2 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.8e-05
                            DUF805   4 fkGRasRsefwwfvlfllllvivlallaavlaa..........aavasalsvvlallllvps..lavtvRRl 63 
                                       f+GR +   f +  lfl++++ vl ll++ +++              + +     ++++++s  la+ vRRl
  gi|386000978|ref|YP_005919277.1|  64 FQGRHEGLSFVMGGLFLTAVFGVLYLLMMGADGlmyllgeaeaL--PALTDARPEIWIFILSlpLALKVRRL 133
                                       99*********999***999999999998887798888887552..3333333334444444449******8 PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3     0.023     2e+02       2      21 ..       7      26 ..       6      27 .. 0.88
   2 ?    8.4   0.5    0.0002       1.8       9      22 ..      43      56 ..      42      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.023
                           DUF4538  2 rglkyvllvggvvgliglal 21
                                      ++ k  ++ ++v+g+i la+
  gi|386000978|ref|YP_005919277.1|  7 KTGKRLAIYASVLGVISLAI 26
                                      678889999********995 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0002
                           DUF4538  9 lvggvvgliglalY 22
                                      l+gg+v ++++a+Y
  gi|386000978|ref|YP_005919277.1| 43 LFGGFVLVVMAATY 56
                                      69***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 884.46
//
Query:       gi|386000979|ref|YP_005919278.1|  [L=163]
Description: Iron-dependent repressor [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-22   77.3   0.1    1.6e-21   76.3   0.2    1.5  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    4.7e-14   52.2   0.0    1.7e-13   50.5   0.0    1.8  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    1.4e-05   24.9   0.0    2.5e-05   24.1   0.0    1.3  1  MarR_2          MarR family
     0.0011   18.8   0.0     0.0021   17.9   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0024   18.4   0.0     0.0055   17.2   0.0    1.6  2  HTH_27          Winged helix DNA-binding domain
     0.0026   17.5   0.0     0.0058   16.4   0.0    1.6  1  LexA_DNA_bind   LexA DNA binding domain
      0.006   16.5   0.0      0.012   15.6   0.0    1.5  1  MarR            MarR family
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.018   15.4   0.0    1.3  1  Rrf2            Transcriptional regulator
       0.05   13.8   0.5      0.086   13.1   0.5    1.4  1  Ldl_recept_a    Low-density lipoprotein receptor domain class
      0.059   13.2   0.0        0.1   12.4   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.069   12.7   0.0       0.16   11.6   0.0    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.2   9.5e-25   1.6e-21       1      60 []       3      62 ..       3      62 .. 0.98
   2 ?   -3.4   0.0       7.2   1.2e+04      19      30 ..     148     159 ..     147     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 9.5e-25
                                      X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +L++++EdYLe+I+++seek+++++ d+++ L+++p+sV em+kkL++ Gyv+++k+ g+
  gi|386000979|ref|YP_005919278.1|  3 KLSRKAEDYLEAIFEISEEKGYARVRDISQKLDIRPPSVVEMVKKLDDLGYVVHKKQEGV 62
                                      699*****************************************************9997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.2
                                       HHSSB-HHHHHH CS
                    Fe_dep_repress  19 ekkvvktkdlae 30 
                                       +++ +++ ++ae
  gi|386000979|ref|YP_005919278.1| 148 SGGCISRRRIAE 159
                                       567899999998 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.6e+03      17      32 ..       7      22 ..       3      35 .. 0.70
   2 !   50.5   0.0     1e-16   1.7e-13       1      61 [.      65     124 ..      65     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                      HHHHHHHHHCT--CCC CS
                     Fe_dep_repr_C 17 llerfLvdvlgvdwee 32
                                       +e++L  ++++++e+
  gi|386000979|ref|YP_005919278.1|  7 KAEDYLEAIFEISEEK 22
                                      4567777777776665 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 1e-16
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpee 61 
                                       T+kG+e+++ +++rh +++ fL   ++v++ +a+++A+ +Eh l+ +++e++ +l++f + 
  gi|386000979|ref|YP_005919278.1|  65 TPKGEEIGRVIKDRHDTIKAFL-MLINVPEPIADKDACIMEHKLDTKTVEQIKNLVKFVQL 124
                                       9*********************.89********************************9875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.5e-08   2.5e-05      10      54 ..      14      57 ..      11      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++++  + g+  +v+++ ++l++ +++v  ++k+L + G+v+ +
  gi|386000979|ref|YP_005919278.1| 14 AIFEISEEKGY-ARVRDISQKLDIRPPSVVEMVKKLDDLGYVVHK 57
                                      6899******9.6*****************************876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0021      20      58 ..      22      60 ..      17      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +g a++++i+++l++  ++v e++++L d G+V  +k++
  gi|386000979|ref|YP_005919278.1| 22 KGYARVRDISQKLDIRPPSVVEMVKKLDDLGYVVHKKQE 60
                                      68899****************************988765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.4e-06    0.0055      14      68 .]      20      68 ..      11      68 .. 0.81
   2 ?   -2.9   0.0       6.1     1e+04      14      27 ..     105     118 ..     101     123 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-06
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++ + ++ +d++++l++   ++++++kkL   G+v++++ e       v lT+kG
  gi|386000979|ref|YP_005919278.1| 20 EEKGYARVRDISQKLDIRPPSVVEMVKKLDDLGYVVHKKQE------GVFLTPKG 68
                                      66677889***************************777776......56667776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                            HTH_27  14 hrrrrkkladlcgr 27 
                                       h +++k+ +++   
  gi|386000979|ref|YP_005919278.1| 105 HKLDTKTVEQIKNL 118
                                       66777777777654 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.6e-06    0.0058       1      57 [.       1      55 [.       1      60 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                                      XX---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind  1 mkkLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyie 57
                                      m+kL+++ ++ l+ i +  ee+gy+  +r+i+++l ++ p +v e  k+L   Gy+ 
  gi|386000979|ref|YP_005919278.1|  1 MSKLSRKAEDYLEAIFEISEEKGYA-RVRDISQKLDIR-PPSVVEMVKKLDDLGYVV 55
                                      89**********************9.79**********.778888999999999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.2e-06     0.012      14      48 ..      20      55 ..      12      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                                      HSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 14 eqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                      e+ + ++v ++  kl + +++v +++++L + G++ 
  gi|386000979|ref|YP_005919278.1| 20 EEKGyARVRDISQKLDIRPPSVVEMVKKLDDLGYVV 55
                                      4444499**********************9999985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.1e-05     0.018       2      58 ..       3      57 ..       1      72 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      ---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2  2 klsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      kls+k e  l a+ ++++e++   +++++i+++ +i p+ +  +++kL   g+v  +
  gi|386000979|ref|YP_005919278.1|  3 KLSRKAEDYLEAIFEISEEKGY--ARVRDISQKLDIRPPSVVEMVKKLDDLGYVVHK 57
                                      5899999999999999999995..6****************************9766 PP

>> Ldl_recept_a  Low-density lipoprotein receptor domain class A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   5.3e-05     0.086       3      19 ..     139     155 ..     137     163 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                                       SSSSCEEETTSEEEEGG CS
                      Ldl_recept_a   3 CepnefqCgsgeCIprs 19 
                                       C+  e+ Cgsg CI+r+
  gi|386000979|ref|YP_005919278.1| 139 CRTGEHVCGSGGCISRR 155
                                       **************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.2e-05       0.1      16      49 ..      22      55 ..      13      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                       +  +++++++++++ +++v  +++ L  lGyv 
  gi|386000979|ref|YP_005919278.1| 22 KGYARVRDISQKLDIRPPSVVEMVKKLDDLGYVV 55
                                      444699**************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.6e-05      0.16      14      47 ..      21      54 ..      12      55 .. 0.87
   2 ?   -3.6   0.0       5.4   8.8e+03      18      25 ..     152     159 ..     150     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.6e-05
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +++    r+++++l++ p+ v + +k+L + G++
  gi|386000979|ref|YP_005919278.1| 21 EKGYARVRDISQKLDIRPPSVVEMVKKLDDLGYV 54
                                      4677889**************************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.4
                            HTH_24  18 isqreLAe 25 
                                       is r +Ae
  gi|386000979|ref|YP_005919278.1| 152 ISRRRIAE 159
                                       78888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1050.33
//
Query:       gi|386000980|ref|YP_005919279.1|  [L=232]
Description: hypothetical protein Mhar_0266 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.15   11.6   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.5e-06      0.15     110     222 ..      27     128 ..      11     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-06
                                       HTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEEC CS
                         OMPdecase 110 kwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetlnateedaddfihltpgigleqggdg 186
                                         g  g  ila+ s   +++  +    ++ v+ a +h a+    Gf   +++       d+f  +++ ++ +  gd 
  gi|386000980|ref|YP_005919279.1|  27 PEG--GFEILAESSVSLEMDQLR--SSDDRVQMADQHLAA---EGFSPDKEMT-----SDNFFGMRQSYNRTGEGDE 91 
                                       444..666777777766666666..777777777777755...6888877777.....69***********9***** PP

                                       TTCCGGGHHHHHHHTTCSEE.EESHHHHTSSSHHHHH CS
                         OMPdecase 187 kgqqyntpekligiagadii.ivGRgIlkagdpveea 222
                                        +q y+ + ++ +  g+d++  vGR  +k++d + +a
  gi|386000980|ref|YP_005919279.1|  92 ADQTYEFFIQEYSNPGSDMAaAVGRMAVKSSDGAYAA 128
                                       *****************975279*******9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1416.19
//
Query:       gi|386000981|ref|YP_005919280.1|  [L=348]
Description: extracellular ligand-binding receptor [Methanosaeta harundinacea 6Ac]
Scores for complete 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-47  162.3   0.2    2.8e-47  162.1   0.2    1.0  1  Peripla_BP_6  Periplasmic binding protein
    2.7e-20   72.8   0.0    2.6e-19   69.6   0.0    1.9  1  ANF_receptor  Receptor family ligand binding region
    7.4e-15   54.8   0.0    3.6e-08   32.8   0.0    2.2  2  Peripla_BP_5  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.2   4.7e-51   2.8e-47       3     338 ..       2     331 ..       1     335 [. 0.91

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 4.7e-51
                                       EEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSH CS
                      Peripla_BP_6   3 kiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgplss 79 
                                       kiG+++ l G  a++  ++ +ga++a+eeiNaaGGi+Gr+++l+ +D ++dp++  ++  +l + ++  + +g   +
  gi|386000981|ref|YP_005919280.1|   2 KIGAIYNLEGSQAPLDLPSSRGARLAVEEINAAGGIDGRRVDLLLCDGKSDPAEVRRCSLDLAE-ENLSGMIGLSDT 77 
                                       9***************************************************************.************ PP

                                       HHHHHHHHHHHHHT-EEEESS-HHC..CTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEES.SHHHHHHHH CS
                      Peripla_BP_6  80 avaaavaevlakdgvpvigpagltg..ekcspyvfslgpsysaqasalveylakelggkkvalvyad.yafgregia 153
                                       + + a+a+ +a +g+p+++ +++++   ++++  f +++ ++ qa+a++e++ +  +  + al+      + r ++ 
  gi|386000981|ref|YP_005919280.1|  78 DMVVAAAPGAAGAGIPFLTSGATSPrlPEVYDGLFLACFGDDVQAAAGAEHAFE-MDLLTCALLVEGeMEYARLLAG 153
                                       *******************888776447***********************777.6877777665444********* PP

                                       HHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC.-CH CS
                      Peripla_BP_6 154 alkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvsws.gse 229
                                        +++  +a+Gge+   ++  l+++d +a+v++i +a +d ++la++++ +a ++ ++++aG+    i++++ + ++ 
  gi|386000981|ref|YP_005919280.1| 154 YFRERYQALGGEIA--FEAFLNGSDKEALVQAIGEASPDMIYLAAGPDLAAEVVGEVRDAGIE---IPVFGGDsLDS 225
                                       ************97..44556799***************************************...88887774666 PP

                                       HHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHH CS
                      Peripla_BP_6 230 edlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreavra 306
                                       ++l++ g      +++++    d ++ ++  fv+ay   yg  pp ++faa gy+a++ll+ea+ +ags ++ea+ +
  gi|386000981|ref|YP_005919280.1| 226 PELRRGGT---GRIVFSAHALLDENSSRSGPFVRAYDGLYGH-PPENAFAALGYDAVMLLAEAMDRAGSEDPEAILE 298
                                       66766665...5788888888899*****************9.578******************************* PP

                                       HHHHS-.BECCCTCCBEECTTSBEE--EEEEEE CS
                      Peripla_BP_6 307 aleslg.fdgllgplkftaedhqasrpvyvvqv 338
                                       al++ + f g++g+++++   + +++ v++  +
  gi|386000981|ref|YP_005919280.1| 299 ALQNTTgFVGVTGDISYDGGRRIPNKGVTMISL 331
                                       ****999********999877777777766655 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   4.3e-23   2.6e-19       5     343 ..      23     322 ..      20     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 4.3e-23
                                       HHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS CS
                      ANF_receptor   5 AmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisyg 81 
                                        ++lAveein+ +++  g+++++   d ++d++ +++ +ld+ + +  ++iG s  +++ a+a  a+ + iP+++ g
  gi|386000981|ref|YP_005919280.1|  23 GARLAVEEINAAGGID-GRRVDLLLCDGKSDPAEVRRCSLDLAEENLSGMIGLSDTDMVVAAAPGAAGAGIPFLTSG 98 
                                       689*********6665.67*************************99******************************* PP

                                       ---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESS.HHHHHHHHHHHHHHHHTT-EEEEEEEES CS
                      ANF_receptor  82 stspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdd.dygesglqaleeeleergicvalkekip 157
                                       +tsp l +   y+ ++     d  qa A ++   ++   + al+++ + +y + ++ +++e+ ++ g ++a+++ ++
  gi|386000981|ref|YP_005919280.1|  99 ATSPRLPE--VYDGLFLACFGDDVQAAAGAEHAFEMDLLTCALLVEGEmEYARLLAGYFRERYQALGGEIAFEAFLN 173
                                       *****766..5889999999999*************************9**************************** PP

                                       TCHHHCHHHHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT CS
                      ANF_receptor 158 essnddevvrkllkeiks.karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaeg 233
                                         s+++ +v+++    ++ +++ i+l + ++ a e++ ++r++g+     v+ +        +ld+pe   ++   g
  gi|386000981|ref|YP_005919280.1| 174 -GSDKEALVQAI----GEaSPDMIYLAAGPDLAAEVVGEVRDAGIEI--PVFGG-------DSLDSPE--LRRGGTG 234
                                       .65677777777....55588*************************9..47773.......4455554..3333555 PP

                                       -EEEEE...--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HH CS
                      ANF_receptor 234 vlgfrl...kdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscnt 307
                                        ++f+     d ns +   f+         ++    +g+ + +++aal YdaV+llaeA+++++             
  gi|386000981|ref|YP_005919280.1| 235 RIVFSAhalLDENSSRSGPFV---------RAYDGLYGHPPENAFAALGYDAVMLLAEAMDRAG------------- 289
                                       555555566566666666666.........55556778888999********************............. PP

                                       HHCCHHHHHHHHHHHT-E.EEETTSCEEB-TTSBBE- CS
                      ANF_receptor 308 lkpweggqkllrylrnvn.feGltGdvkfdengdrvp 343
                                           e+ +++l++l+n++ f G+tGd+++ + g+r+p
  gi|386000981|ref|YP_005919280.1| 290 ---SEDPEAILEALQNTTgFVGVTGDISY-DGGRRIP 322
                                       ...6788888999998755**********.5666665 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0     6e-12   3.6e-08       1      66 [.       1      66 [.       1      75 [. 0.92
   2 !   19.7   0.0   5.7e-08   0.00034     138     311 ..     139     304 ..     119     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6e-12
                      Peripla_BP_5  1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaekliee 66
                                      +k+G ++ l G+ a  +    ++a+la+eeinaagG++gr+++  + d++sd++  ++ + +l ee
  gi|386000981|ref|YP_005919280.1|  1 MKIGAIYNLEGSQAPLDLPSSRGARLAVEEINAAGGIDGRRVDLLLCDGKSDPAEVRRCSLDLAEE 66
                                      69****************************************************999988888764 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.7e-08
                      Peripla_BP_5 138 flvGsdyvypretnrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagi 214
                                       +lv  +  y+r  +  +++  +a gge+  e +  l+ sd +++v++i +a+pd+++     d +++   e+++agi
  gi|386000981|ref|YP_005919280.1| 139 LLVEGEMEYARLLAGYFRERYQALGGEIAFEAF--LNGSDKEALVQAIGEASPDMIYLAAGPDLAAEVVGEVRDAGI 213
                                       566667778888888899999999999999987..678999***********************************9 PP

                      Peripla_BP_5 215 kaekipvvs.lsvaeeelaaidaealvGhlaawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaq 290
                                       +   ipv+   s+   el++ ++  +v  ++a   +   ++ ++  fv+++   +g+    n+ +   y +v+l+a+
  gi|386000981|ref|YP_005919280.1| 214 E---IPVFGgDSLDSPELRRGGTGRIV--FSAHALLD-ENSSRSGPFVRAYDGLYGH-PPENAFAALGYDAVMLLAE 283
                                       5...999862589999****9998887..44544444.46677889*********98.678999999********** PP

                      Peripla_BP_5 291 Avekagstdvekvreallgqe 311
                                       A+ +ags+d+e++ eal++++
  gi|386000981|ref|YP_005919280.1| 284 AMDRAGSEDPEAILEALQNTT 304
                                       ***************998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2131.62
//
Query:       gi|386000982|ref|YP_005919281.1|  [L=124]
Description: hypothetical protein Mhar_0268 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-31  109.0   0.2    2.6e-31  108.8   0.2    1.0  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
      0.076   12.6   0.4      0.098   12.2   0.4    1.2  1  AAA_25    AAA domain


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.2   2.9e-35   2.6e-31       1     122 []       3     111 ..       3     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 2.9e-35
                            DUF488   1 slervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweeffer 75 
                                       +++r yd + + dg r+lvD RlwPr    g+ kealk d         w ke +ps+ lr+w++hdp rweef++r
  gi|386000982|ref|YP_005919281.1|   3 RIKRAYDpPAPGDGKRFLVD-RLWPR----GIGKEALKVDG--------WTKEAAPSDGLRRWYGHDPsRWEEFRRR 66 
                                       589*****************.*****....***********........*******************99******* PP

                            DUF488  76 Yaaeleskeaakealeelkelakkg.vaLlcaekdperchrvvlaeyl 122
                                       Y++ele +   ++a+e l e+a++g ++L+++++d+er+++ vl+e l
  gi|386000982|ref|YP_005919281.1|  67 YREELEAN---RAAWEPLLEAARSGdLTLVYSARDEERNNAAVLQEHL 111
                                       ******93...69*******************************9975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   1.1e-05     0.098      75     139 ..      52     113 ..      31     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                            AAA_25  75 lyvsaEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaiee 139
                                       +y +   + +e+rrR+r+ +ea+ + a++++l +a++++l+L+++ r++++ +a+v  l++++e+
  gi|386000982|ref|YP_005919281.1|  52 WYGHDPSRWEEFRRRYREELEAN-RAAWEPLLEAARSGDLTLVYSARDEERNNAAV--LQEHLER 113
                                       44444444569******999996.78*******9999************9966665..5555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 747.43
//
Query:       gi|386000983|ref|YP_005919282.1|  [L=194]
Description: hypothetical protein Mhar_0269 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1227.77
//
Query:       gi|386000984|ref|YP_005919283.1|  [L=225]
Description: hypothetical protein Mhar_0270 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-50  167.9  10.6    1.4e-18   67.0   0.1    3.9  4  HEAT_2         HEAT repeats
    4.8e-46  150.8  21.5    1.7e-07   31.2   0.0    7.2  7  HEAT_PBS       PBS lyase HEAT-like repeat
      8e-34  112.8   0.3    8.7e-05   22.5   0.0    7.1  7  HEAT           HEAT repeat
    1.7e-18   66.7   8.6      0.013   16.0   0.0    7.0  7  HEAT_EZ        HEAT-like repeat
    5.5e-13   48.5   0.1      0.038   14.0   0.0    6.0  7  Arm            Armadillo/beta-catenin-like repeat
      5e-11   42.9   0.0     0.0017   18.4   0.0    5.2  4  Cnd1           non-SMC mitotic condensation complex subunit 1
    0.00024   19.8   0.0      0.056   12.0   0.0    2.8  3  Adaptin_N      Adaptin N terminal region
  ------ inclusion threshold ------
      0.031   14.4   0.0         22    5.1   0.0    3.8  4  Aconitase_B_N  Aconitate B N-terminal domain
      0.052   13.2   0.0         23    4.7   0.0    3.3  3  DSX_dimer      Doublesex dimerisation domain
       0.25   11.9   0.0         55    4.5   0.0    3.7  5  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1     7e-08   0.00013      34      73 ..       5      44 ..       4      44 .. 0.87
   2 !   60.2   0.1   1.1e-19     2e-16       3      75 ..      37     108 ..      35     111 .. 0.96
   3 !   67.0   0.1   7.8e-22   1.4e-18       2      74 ..      98     169 ..      97     171 .. 0.97
   4 !   42.3   1.4   4.2e-14   7.5e-11       3      60 ..     161     217 ..     160     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7e-08
                            HEAT_2 34 paLvellededpavRraaaeaLgaigdpealpaLkelldd 73
                                      + L+++++  d + R++aa aLg+igdp+a+  L e+l+d
  gi|386000984|ref|YP_005919283.1|  5 DDLLRAVKGGDLHARQMAAYALGRIGDPRAVGPLIEALKD 44
                                      5688999999999999999999999999999999999875 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.1e-19
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddd 75 
                                       +L++al +d d +vr +a+++Lg+ig+p+a + ++e+l+d +++vR  aa aLg +gdp a + L ++l d++
  gi|386000984|ref|YP_005919283.1|  37 PLIEAL-KDGDGKVRERAAWSLGKIGDPRATEPIIEALKDGEMMVRSRAAFALGLLGDPGATDPLIRALEDER 108
                                       79****.9*************************************************************9876 PP

  == domain 3  score: 67.0 bits;  conditional E-value: 7.8e-22
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddd 74 
                                       d+L+ al +d+   vr++a++aLgrig+p+  + L+e+l d+ + vR  aa++Lg+igdp+a+  L  +l+d+
  gi|386000984|ref|YP_005919283.1|  98 DPLIRAL-EDERRGVRWRAVEALGRIGDPRGAEPLIEALGDPVWSVRSRAAWSLGKIGDPRAVGPLIGALKDP 169
                                       89*****.9*************************************************************986 PP

  == domain 4  score: 42.3 bits;  conditional E-value: 4.2e-14
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigd 60 
                                       +L+ al +dp + vrr+a++aL rig+ +a + L e+l de p v++aaaeaL +i+ 
  gi|386000984|ref|YP_005919283.1| 161 PLIGAL-KDPYEHVRRNAAIALCRIGDARATRPLAEALHDEAPSVQAAAAEALERIRG 217
                                       578899.9*********************************************99953 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 !   26.6   0.2   3.1e-09   5.5e-06       2      27 .]      19      44 ..      18      44 .. 0.94
   2 !   31.2   0.0   9.7e-11   1.7e-07       1      27 []      49      75 ..      49      75 .. 0.98
   3 !   22.9   0.1   4.6e-08   8.3e-05       1      27 []      80     106 ..      80     106 .. 0.98
   4 !   28.3   0.1   8.3e-10   1.5e-06       1      27 []     111     137 ..     111     137 .. 0.96
   5 !   26.4   0.0   3.4e-09   6.1e-06       1      27 []     142     168 ..     142     168 .. 0.97
   6 !   19.0   1.0   8.6e-07    0.0015       1      27 []     173     199 ..     173     199 .. 0.96
   7 !    7.1   0.0    0.0058        10       1      14 [.     204     217 ..     204     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.1e-09
                                      HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  2 RraAakaLgqlgdeeaipaLleaLqd 27
                                      R  Aa+aLg++gd++a+ +L+eaL+d
  gi|386000984|ref|YP_005919283.1| 19 RQMAAYALGRIGDPRAVGPLIEALKD 44
                                      778*********************98 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 9.7e-11
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR +Aa++Lg++gd++a ++++eaL+d
  gi|386000984|ref|YP_005919283.1| 49 VRERAAWSLGKIGDPRATEPIIEALKD 75
                                      9************************98 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 4.6e-08
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +Aa+aLg lgd+ a ++L++aL+d
  gi|386000984|ref|YP_005919283.1|  80 VRSRAAFALGLLGDPGATDPLIRALED 106
                                       9************************98 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 8.3e-10
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR++A++aLg++gd++ +++L+eaL d
  gi|386000984|ref|YP_005919283.1| 111 VRWRAVEALGRIGDPRGAEPLIEALGD 137
                                       9***********************976 PP

  == domain 5  score: 26.4 bits;  conditional E-value: 3.4e-09
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +Aa++Lg++gd++a+ +L+ aL+d
  gi|386000984|ref|YP_005919283.1| 142 VRSRAAWSLGKIGDPRAVGPLIGALKD 168
                                       9************************98 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 8.6e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vRr+Aa aL ++gd +a  +L eaL d
  gi|386000984|ref|YP_005919283.1| 173 VRRNAAIALCRIGDARATRPLAEALHD 199
                                       9***********************976 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHCTS CS
                          HEAT_PBS   1 vRraAakaLgqlgd 14 
                                       v++aAa+aL +++ 
  gi|386000984|ref|YP_005919283.1| 204 VQAAAAEALERIRG 217
                                       89**********97 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.019        33      17      27 ..      19      29 ..       7      31 .. 0.87
   2 !   17.1   0.0   2.7e-06    0.0048       4      27 ..      37      60 ..      35      62 .. 0.90
   3 !   14.6   0.0   1.6e-05     0.028       4      27 ..      68      91 ..      67      93 .. 0.90
   4 !   11.3   0.0   0.00019      0.35       4      27 ..      99     122 ..      97     124 .. 0.91
   5 !   22.5   0.0   4.9e-08   8.7e-05       4      27 ..     130     153 ..     129     155 .. 0.91
   6 !   17.0   0.0   2.8e-06    0.0051       4      28 ..     161     185 ..     159     187 .. 0.90
   7 !   15.7   0.1   7.2e-06     0.013       5      27 ..     193     215 ..     191     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHH CS
                              HEAT 17 ReaAakaLgal 27
                                      R++Aa+aLg++
  gi|386000984|ref|YP_005919283.1| 19 RQMAAYALGRI 29
                                      9********99 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.7e-06
                                      HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  4 lllkllsDpspeVReaAakaLgal 27
                                      +l+++l+D + +VRe Aa++Lg++
  gi|386000984|ref|YP_005919283.1| 37 PLIEALKDGDGKVRERAAWSLGKI 60
                                      57899*****************98 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.6e-05
                                      HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  4 lllkllsDpspeVReaAakaLgal 27
                                      +++++l+D ++ VR+ Aa aLg l
  gi|386000984|ref|YP_005919283.1| 68 PIIEALKDGEMMVRSRAAFALGLL 91
                                      58899****************976 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00019
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+++l+D+   VR  A++aLg++
  gi|386000984|ref|YP_005919283.1|  99 PLIRALEDERRGVRWRAVEALGRI 122
                                       58899*****************99 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 4.9e-08
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+++l Dp ++VR+ Aa++Lg++
  gi|386000984|ref|YP_005919283.1| 130 PLIEALGDPVWSVRSRAAWSLGKI 153
                                       58899*****************98 PP

  == domain 6  score: 17.0 bits;  conditional E-value: 2.8e-06
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +l+ +l+Dp  +VR++Aa aL+++ 
  gi|386000984|ref|YP_005919283.1| 161 PLIGALKDPYEHVRRNAAIALCRIG 185
                                       57899*****************995 PP

  == domain 7  score: 15.7 bits;  conditional E-value: 7.2e-06
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       l ++l+D++p+V +aAa+aL ++
  gi|386000984|ref|YP_005919283.1| 193 LAEALHDEAPSVQAAAAEALERI 215
                                       7899****************876 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.062   1.1e+02      43      55 .]      17      29 ..       7      29 .. 0.84
   2 !   16.0   0.0   7.1e-06     0.013      27      55 .]      32      60 ..      31      60 .. 0.94
   3 !    7.0   0.0    0.0049       8.7      31      54 ..      67      90 ..      63      91 .. 0.83
   4 !   10.4   0.0   0.00041      0.73      30      55 .]      97     122 ..      94     122 .. 0.89
   5 !    9.8   0.0   0.00061       1.1      28      55 .]     130     153 ..     123     153 .. 0.83
   6 !    9.5   0.0   0.00076       1.4      27      52 ..     156     181 ..     155     184 .. 0.92
   7 !    9.4   0.2   0.00085       1.5      31      55 .]     191     215 ..     187     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.062
                           HEAT_EZ 43 eVRaaAagaLgnl 55
                                      + R+ Aa+aLg++
  gi|386000984|ref|YP_005919283.1| 17 HARQMAAYALGRI 29
                                      67999*****997 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.1e-06
                           HEAT_EZ 27 peilpaLlalLnddsdeVRaaAagaLgnl 55
                                      p+++ +L+ +L+d + +VR+ Aa+ Lg++
  gi|386000984|ref|YP_005919283.1| 32 PRAVGPLIEALKDGDGKVRERAAWSLGKI 60
                                      68899********999***********97 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0049
                           HEAT_EZ 31 paLlalLnddsdeVRaaAagaLgn 54
                                       + + +L+d + +VR  Aa aLg 
  gi|386000984|ref|YP_005919283.1| 67 EPIIEALKDGEMMVRSRAAFALGL 90
                                      566889999999**********96 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00041
                           HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                        ++L+++L+d+   VR+ A+ aLg++
  gi|386000984|ref|YP_005919283.1|  97 TDPLIRALEDERRGVRWRAVEALGRI 122
                                       5689999*****************97 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00061
                           HEAT_EZ  28 eilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                        ++ aL+     d+  +VR  Aa+ Lg++
  gi|386000984|ref|YP_005919283.1| 130 PLIEALG-----DPVwSVRSRAAWSLGKI 153
                                       4778888.....8889***********97 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.00076
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaL 52 
                                       p+++ +L+ +L+d+  +VR +Aa+aL
  gi|386000984|ref|YP_005919283.1| 156 PRAVGPLIGALKDPYEHVRRNAAIAL 181
                                       68899******99999*********9 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.00085
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaLgnl 55 
                                       ++L+ +L d+ ++V+aaAa aL+++
  gi|386000984|ref|YP_005919283.1| 191 RPLAEALHDEAPSVQAAAAEALERI 215
                                       578888989999***********97 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.4   2.5e+03      19      39 ..       9      29 ..       7      31 .. 0.75
   2 !   14.0   0.0   2.1e-05     0.038      10      38 ..      31      59 ..      28      62 .. 0.90
   3 ?   -0.4   0.0      0.75   1.3e+03      12      37 ..      64      89 ..      58      92 .. 0.80
   4 ?    5.1   0.0     0.013        24       8      38 ..      91     121 ..      89     124 .. 0.85
   5 ?    2.8   0.0     0.072   1.3e+02      15      38 ..     129     152 ..     121     155 .. 0.82
   6 !    9.4   0.0   0.00059       1.1      10      37 ..     155     182 ..     152     186 .. 0.87
   7 !    9.6   0.1   0.00051      0.92       9      37 ..     185     213 ..     183     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                                      HHTTTSSHHHHHHHHHHHHHH CS
                               Arm 19 rLLssedeevqeeAawALsNL 39
                                      r  + +d   ++ Aa AL+ +
  gi|386000984|ref|YP_005919283.1|  9 RAVKGGDLHARQMAAYALGRI 29
                                      4555778888999****9966 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.1e-05
                                      HTTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm 10 eaGavppLvrLLssedeevqeeAawALsN 38
                                      +  av pL++ L+++d +v+e Aaw L+ 
  gi|386000984|ref|YP_005919283.1| 31 DPRAVGPLIEALKDGDGKVRERAAWSLGK 59
                                      6779**********************986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.75
                                      THHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm 12 GavppLvrLLssedeevqeeAawALs 37
                                       a +p ++ L+++  +v+  Aa AL+
  gi|386000984|ref|YP_005919283.1| 64 RATEPIIEALKDGEMMVRSRAAFALG 89
                                      56789999999999999999987765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.013
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawALsN 38 
                                       + + Ga +pL+r L++e  +v+  A+ AL+ 
  gi|386000984|ref|YP_005919283.1|  91 LGDPGATDPLIRALEDERRGVRWRAVEALGR 121
                                       6799***********9999998888888875 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.072
                                       HHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm  15 ppLvrLLssedeevqeeAawALsN 38 
                                       +pL++ L ++  +v+  Aaw L+ 
  gi|386000984|ref|YP_005919283.1| 129 EPLIEALGDPVWSVRSRAAWSLGK 152
                                       6888888888889********985 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.00059
                                       HTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLssedeevqeeAawALs 37 
                                       +  av pL+  L+++ e v+++Aa AL+
  gi|386000984|ref|YP_005919283.1| 155 DPRAVGPLIGALKDPYEHVRRNAAIALC 182
                                       6779*******************97776 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.00051
                                       HHTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm   9 ieaGavppLvrLLssedeevqeeAawALs 37 
                                        +a a +pL + L++e ++vq +Aa AL 
  gi|386000984|ref|YP_005919283.1| 185 GDARATRPLAEALHDEAPSVQAAAAEALE 213
                                       5788999********************95 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0028       5.1      22      48 ..      34      60 ..      16      67 .. 0.80
   2 !    8.3   0.0    0.0012       2.2      23      75 ..      66     112 ..      63     127 .. 0.70
   3 ?    1.5   0.0      0.15   2.7e+02      24      48 ..     129     153 ..     125     159 .. 0.86
   4 !   18.4   0.0   9.6e-07    0.0017      23      88 ..     159     218 ..     156     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
                              Cnd1 22 lvepLrkrLkDedpyVRktaaivvakL 48
                                       v pL ++LkD d  VR+ aa  + k+
  gi|386000984|ref|YP_005919283.1| 34 AVGPLIEALKDGDGKVRERAAWSLGKI 60
                                      578999***************999886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVv 75 
                                       +ep+ ++LkD +++VR  aa+++  L +++        + l ++leDe + V+
  gi|386000984|ref|YP_005919283.1|  66 TEPIIEALKDGEMMVRSRAAFALGLLGDPG------ATDPLIRALEDERRGVR 112
                                       789999***************998775553......33445555555555555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.15
                              Cnd1  24 epLrkrLkDedpyVRktaaivvakL 48 
                                       epL ++L D+   VR  aa  + k+
  gi|386000984|ref|YP_005919283.1| 129 EPLIEALGDPVWSVRSRAAWSLGKI 153
                                       79999*************9998886 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 9.6e-07
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                       v pL  +LkD+ ++VR++aai+++++ ++           la++l+De p+V+a a  al+ i  +
  gi|386000984|ref|YP_005919283.1| 159 VGPLIGALKDPYEHVRRNAAIALCRIGDARA------TRPLAEALHDEAPSVQAAAAEALERIRGQ 218
                                       679999******************9866555......55799******************999765 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0061        11      86     138 ..      40      88 ..       9     133 .. 0.71
   2 ?    1.4   0.0      0.05        89      81     137 ..      97     149 ..      90     155 .. 0.76
   3 !   12.0   0.0   3.1e-05     0.056     119     183 ..     162     219 ..     133     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0061
                                       HHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHH CS
                         Adaptin_N  86 kDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalai 138
                                        +lkd +  +r  A  +L++i++p+ +e     i ++lkd + +vr+ Aa a+
  gi|386000984|ref|YP_005919283.1|  40 EALKDGDGKVRERAAWSLGKIGDPRATEP----IIEALKDGEMMVRSRAAFAL 88 
                                       56777777777777777777777765554....45566778888888888776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.05
                                       CHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHH CS
                         Adaptin_N  81 tnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAala 137
                                       t+ l ++l+d    +r  A+ +L++i++p+ ae l +a    l d+  +vr+ Aa +
  gi|386000984|ref|YP_005919283.1|  97 TDPLIRALEDERRGVRWRAVEALGRIGDPRGAEPLIEA----LGDPVWSVRSRAAWS 149
                                       56677889999999999999999999999998887765....455555666666655 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 3.1e-05
                                       HHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCC CS
                         Adaptin_N 119 ikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleeikknd 183
                                       +  +lkd+   vr++Aa+a+ ++ ++ +          + e+l+d+ p+v++aA  +le+i+ ++
  gi|386000984|ref|YP_005919283.1| 162 LIGALKDPYEHVRRNAAIALCRIGDARATR-------PLAEALHDEAPSVQAAAAEALERIRGQP 219
                                       44568899999********99997665554.......589*********************4433 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.012        22      80     119 ..      19      58 ..       7      61 .. 0.85
   2 ?    0.3   0.0      0.37   6.6e+02      79     119 ..      80     120 ..      67     123 .. 0.70
   3 ?    1.7   0.0      0.14   2.5e+02      83     118 ..     146     181 ..     140     185 .. 0.83
   4 ?    0.9   0.0      0.24   4.3e+02      96     120 ..     190     214 ..     184     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                     Aconitase_B_N  80 peeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       ++ A   Lg +    +v +Li++lk+ d +++e aa  L 
  gi|386000984|ref|YP_005919283.1|  19 RQMAAYALGRIGDPRAVGPLIEALKDGDGKVRERAAWSLG 58 
                                       5667778888888899*******************98886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                     Aconitase_B_N  79 speeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                        +++A   Lg +    + ++Li +l+++++ ++  a+eaL 
  gi|386000984|ref|YP_005919283.1|  80 VRSRAAFALGLLGDPGATDPLIRALEDERRGVRWRAVEALG 120
                                       45555566665555567889999999999989988888885 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.14
                     Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                       A   Lg++    +v +Li +lk+  e+++++aa aL
  gi|386000984|ref|YP_005919283.1| 146 AAWSLGKIGDPRAVGPLIGALKDPYEHVRRNAAIAL 181
                                       5666777777789******************99988 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.24
                     Aconitase_B_N  96 vksLidllkekdeelaeeaaeaLkk 120
                                        ++L ++l+++  +++++aaeaL++
  gi|386000984|ref|YP_005919283.1| 190 TRPLAEALHDEAPSVQAAAAEALER 214
                                       5789999**9999*********986 PP

>> DSX_dimer  Doublesex dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.28   5.1e+02       8      37 ..      22      50 ..      18      52 .. 0.82
   2 ?    4.1   0.0     0.021        37       5      24 ..      50      69 ..      46      81 .. 0.81
   3 ?    4.7   0.0     0.013        23       6      25 ..     144     163 ..     141     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                         DSX_dimer  8 aqWlleklGyPWemmPlmyvilksadGdvq 37
                                      a + l ++G P  + Pl+   lk  dG v+
  gi|386000984|ref|YP_005919283.1| 22 AAYALGRIGDPRAVGPLIE-ALKDGDGKVR 50
                                      6677889999999999986.5899999886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                         DSX_dimer  5 vkraqWlleklGyPWemmPl 24
                                        ra W l k+G P    P+
  gi|386000984|ref|YP_005919283.1| 50 RERAAWSLGKIGDPRATEPI 69
                                      57**********99877776 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.013
                         DSX_dimer   6 kraqWlleklGyPWemmPlm 25 
                                        ra W l k+G P  + Pl+
  gi|386000984|ref|YP_005919283.1| 144 SRAAWSLGKIGDPRAVGPLI 163
                                       59***********9999986 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.23   4.2e+02      29      51 ..      35      57 ..      14      62 .. 0.86
   2 ?   -0.9   0.0       1.4   2.6e+03      30      47 ..      67      84 ..      62      88 .. 0.82
   3 ?    4.5   0.0      0.03        55      30      51 ..      98     119 ..      95     125 .. 0.90
   4 ?   -1.4   0.0       2.1   3.7e+03      29      54 ..     159     184 ..     157     199 .. 0.77
   5 ?   -1.8   0.0       2.7   4.8e+03      75      92 ..     195     213 ..     187     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                     Vac14_Fab1_bd 29 vkpvlkcfsDkdsrvRyyacEsl 51
                                      v p++++++D d +vR  a+ sl
  gi|386000984|ref|YP_005919283.1| 35 VGPLIEALKDGDGKVRERAAWSL 57
                                      77999**********97776665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                     Vac14_Fab1_bd 30 kpvlkcfsDkdsrvRyya 47
                                      +p++++++D +  vR  a
  gi|386000984|ref|YP_005919283.1| 67 EPIIEALKDGEMMVRSRA 84
                                      799999***999999665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.03
                     Vac14_Fab1_bd  30 kpvlkcfsDkdsrvRyyacEsl 51 
                                       +p++++++D+ + vR+ a+E+l
  gi|386000984|ref|YP_005919283.1|  98 DPLIRALEDERRGVRWRAVEAL 119
                                       6899****************99 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.1
                     Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEslyni 54 
                                       v p++ +++D  ++vR  a+ +l  i
  gi|386000984|ref|YP_005919283.1| 159 VGPLIGALKDPYEHVRRNAAIALCRI 184
                                       56788888999999988777776555 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 2.7
                     Vac14_Fab1_bd  75 klvaDsdesvksg.aelld 92 
                                       + + D+ +sv+ + ae l+
  gi|386000984|ref|YP_005919283.1| 195 EALHDEAPSVQAAaAEALE 213
                                       4455666677654134555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1321.74
//
Query:       gi|386000985|ref|YP_005919284.1|  [L=1070]
Description: Carbamoyl-phosphate synthase, large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-101  338.4   0.6    2.7e-67  226.3   0.1    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    5.8e-41  139.7   0.0    1.4e-40  138.4   0.0    1.7  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    4.2e-19   68.5   1.0    6.9e-18   64.6   0.1    3.4  3  MGS              MGS-like domain
    9.3e-17   61.1   0.1    3.4e-09   36.5   0.0    2.5  2  ATP-grasp        ATP-grasp domain
    1.6e-15   57.2   0.0    1.3e-06   28.1   0.0    2.6  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.5e-14   53.9   0.0    4.7e-06   26.4   0.0    2.7  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    2.9e-13   50.2   0.2    5.1e-06   26.6   0.0    2.5  2  ATP-grasp_3      ATP-grasp domain
    2.4e-08   34.0   0.1      0.003   17.3   0.0    2.7  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0007   19.1   0.0      0.029   13.8   0.0    2.7  2  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.28   11.0   0.0    2.9  2  HTH_23           Homeodomain-like domain
      0.014   15.0   0.0          3    7.4   0.0    2.8  2  ATP-grasp_2      ATP-grasp domain
      0.021   14.7   0.0       0.16   11.9   0.0    2.3  2  HTH_25           Helix-turn-helix domain
      0.025   14.6   0.1      0.075   13.1   0.1    1.8  1  DUF3071          Protein of unknown function (DUF3071)
      0.041   13.8   0.0       0.13   12.2   0.0    1.8  1  ComX             Bacillus competence pheromone ComX
       0.17   12.0   0.0        1.8    8.7   0.0    2.8  3  Peptidase_S66    LD-carboxypeptidase N-terminal domain
       0.18   12.4   0.0        1.4    9.5   0.0    2.6  2  TIR_2            TIR domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   0.1   2.4e-70   2.7e-67       1     210 [.     128     331 ..     128     332 .. 0.99
   2 !  110.4   0.1   7.2e-35     8e-32       1     210 [.     669     871 ..     669     872 .. 0.95

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 2.4e-70
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D++ +k+a+ +i++pv +s a+  ++ e a ++ ke+g P ii++a++lGG+G++ a++eee+  +v+++++ ++  
  gi|386000985|ref|YP_005919284.1| 128 DRDLFKSAMIRIGEPVPRSRAV--DSPEGAKEALKELGLPLIIRPAYTLGGSGGGSAETEEEFFRIVEMGMKRSR-- 200
                                       9*******************99..**************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                          +qvlve+sl g+ e+E+ev+rD+++++it+c++en++++  +t+++i+v P qtLtdee q+lr+aa++++r++
  gi|386000985|ref|YP_005919284.1| 201 --IHQVLVEESLVGWTELEYEVMRDRNDTCITICNMENMDPMgiHTGESIVVTPIQTLTDEEVQTLRTAAINIIRAL 275
                                       ..9************************************************************************** PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +++g+++++f+ +  ++ey viEvN+R+s++sala+kaTG++++ ++akia+g++L+e
  gi|386000985|ref|YP_005919284.1| 276 KIEGGCNIQFAAK--DGEYRVIEVNPRVSRSSALASKATGYPIARVTAKIAVGMTLDE 331
                                       ***********99..6****************************************97 PP

  == domain 2  score: 110.4 bits;  conditional E-value: 7.2e-35
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+e+++ al+++++p  ++  a  ++ eea a a++igyPv++++++ lGG+ m ++++e el+  +++a++ ++  
  gi|386000985|ref|YP_005919284.1| 669 DRERFNLALREMGIPQPEAGYA--TSPEEAKAEARRIGYPVLVRPSYVLGGRAMEIVYDERELVVYMREAVRVSP-- 741
                                       99*************9999888..9*************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         ++ +l++ +l++  ei+v+ ++D ++  i    +e + +   + +++  + P qt+ ++  +++re   k++ ++
  gi|386000985|ref|YP_005919284.1| 742 --EHPILIDDFLQNAVEIDVDAVSDGHDVLIGA-IMEHIEEAgiHSGDSACIIPPQTIPAAVQDTVREYVKKIALAL 815
                                       ..9************************987765.5777777678********************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +v+g  +++ +++  ++  yv+E N+R s+  +  +k+ Gl+l+k+aa + +g++L e
  gi|386000985|ref|YP_005919284.1| 816 EVKGILNIQMAYK--DGIVYVLEANPRSSRTIPFVSKTVGLPLAKIAAGVMAGKSLAE 871
                                       ************9..59*************************************9986 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.0   1.2e-43   1.4e-40       3     122 .]     422     537 ..     420     537 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 1.2e-43
                       CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiael 79 
                                       l++ptdeR+fai+ealrrg++veei++lt i+p+F++++e+++e+e+e+++    l+  +lr+ak++GfsD++i ++
  gi|386000985|ref|YP_005919284.1| 422 LATPTDERLFAIYEALRRGVTVEEISDLTGIHPYFIARIENVIEMEREIAAG---LSVPVLRRAKRMGFSDERIGKI 495
                                       899*********************************************9987...79******************** PP

                       CPSase_L_D3  80 leeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       l+ +++ee+++lr + gilp++k+vDtcAaeF+a+tpY+Ys+Y
  gi|386000985|ref|YP_005919284.1| 496 LG-KRREEIADLRIESGILPTFKMVDTCAAEFAARTPYYYSSY 537
                                       87.66677**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.88   9.9e+02      50      74 ..      23      55 ..       5     105 .. 0.77
   2 ?   -2.5   0.0       5.6   6.2e+03      50      92 ..     281     326 ..     243     328 .. 0.56
   3 !   64.6   0.1   6.2e-21   6.9e-18       3      95 .]     953    1037 ..     951    1037 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.88
                                      H........HHHHHHHTTSCCEEEEE--THHHH CS
                               MGS 50 v........eildaikngeidlvintlypfkat 74
                                               +  + ++++++++v ++ +p + +
  gi|386000985|ref|YP_005919284.1| 23 AaefdfsgsQACKSLREEGVEVVLVNSNPATIM 55
                                      355555555777888999999999998887655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                                       HHHHHHHHTTSCCEEEEE--THHHHHH...CHHHHHHHHHHHTTSH CS
                               MGS  50 veildaikngeidlvintlypfkatva...kdgykirraaenidIp 92 
                                       ++i+ a k+ge+ ++ +++   ++        gy i+r+  +i ++
  gi|386000985|ref|YP_005919284.1| 281 CNIQFAAKDGEYRVIEVNPRVSRSSALaskATGYPIARVTAKIAVG 326
                                       3455555555555555555444443333444566666666666666 PP

  == domain 3  score: 64.6 bits;  conditional E-value: 6.2e-21
                                        HHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHC CS
                               MGS    3 velakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvak 77  
                                        +e+a+kl++ g +++AT+GTa++l++ g++ ++ vek+  g +++    +ld +k ge++l+int++++++ +  
  gi|386000985|ref|YP_005919284.1|  953 AEVARKLADSGLSIIATQGTAEFLTKMGVA-VKRVEKIYVG-SPN----VLDYMKRGEVSLIINTPTTKQSVK-- 1019
                                        699***************************.6666677777.789....9******************99886.. PP

                                        HHHHHHHHHHHTTSHEES CS
                               MGS   78 dgykirraaenidIplpt 95  
                                        dg++irr a+++++p++t
  gi|386000985|ref|YP_005919284.1| 1020 DGFQIRRNAVDYHVPYIT 1037
                                        ****************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.5e-08   9.5e-05       5     161 ..     140     302 ..     136     310 .. 0.82
   2 !   36.5   0.0     3e-12   3.4e-09       2     160 ..     678     841 ..     677     844 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.5e-08
                                       T--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEE CS
                         ATP-grasp   5 glpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekE 77 
                                       g pvpr  av+s e ++ea++elglp++++ +     G G    + ee+  +++e+     + ++v+vEe     +E
  gi|386000985|ref|YP_005919284.1| 140 GEPVPRSRAVDSPEGAKEALKELGLPLIIR-PAYTLGGSGGGSAETEEEFFRIVEMGmkrsRIHQVLVEESLVGWTE 215
                                       6699*************************9.7666777777777788887777776666657789*****999999* PP

                                       EEEEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT CS
                         ATP-grasp  78 lsvlvvrsaeGetafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledge 150
                                       l   v+r+++ +  ++  +e++   gi     ++v p +  ++ + ++ ++ a +i+++L + G   +  F  +dge
  gi|386000985|ref|YP_005919284.1| 216 LEYEVMRDRNDTCITICNMENMDPMGIHTgesIVVTPIQTLTDeEVQTLRTAAINIIRALKIEGGCNIQ-FAAKDGE 291
                                       ***********99999999****9999753336788877655515566666677*************98.5566*** PP

                                       EEEEEEESS-- CS
                         ATP-grasp 151 llvnElapRpH 161
                                         v E+ pR+ 
  gi|386000985|ref|YP_005919284.1| 292 YRVIEVNPRVS 302
                                       *********85 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 3e-12
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       +++g+p p+  +++s ee+++ a+++g+pv+v+ +     G+   +v +e +l   ++++     e+++++ +f + 
  gi|386000985|ref|YP_005919284.1| 678 REMGIPQPEAGYATSPEEAKAEARRIGYPVLVR-PSYVLGGRAMEIVYDERELVVYMREAvrvsPEHPILIDDFLQN 753
                                       68899****************************.99999************9877777766776999********** PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                        +E+ v +v + +  + + +++e+++e gi        + p++++++ q +++e++kki+ +L++ G++ + + ++ 
  gi|386000985|ref|YP_005919284.1| 754 AVEIDVDAVSDGHD-VLIGAIMEHIEEAGIHsgdsACIIPPQTIPAAVQDTVREYVKKIALALEVKGILNIQMAYK- 828
                                       *********99887.888999999998877622215677899*******************************999. PP

                                       TCTEEEEEEESS- CS
                         ATP-grasp 148 dgellvnElapRp 160
                                       dg ++v E  pR 
  gi|386000985|ref|YP_005919284.1| 829 DGIVYVLEANPRS 841
                                       999******9995 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   4.6e-09   5.2e-06      26     174 ..     153     299 ..     137     303 .. 0.79
   2 !   28.1   0.0   1.2e-09   1.3e-06      26     174 ..     694     839 ..     676     864 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.6e-09
                                       HHHHHHHHHC-SSEEEEESS.SSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCEE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpar.eGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgneklev 98 
                                       e  ++  +elg+p++++pa  +G S G   +e+eee+ + +e  +k+   ++vlvEe +    e+e  v+ + + ++
  gi|386000985|ref|YP_005919284.1| 153 EGAKEALKELGLPLIIRPAYtLGGSGG-GSAETEEEFFRIVEMGMKRSriHQVLVEESLvGWTELEYEVMRDRNDTC 228
                                       556788899**********62577755.568999********9998763369*****99799*********888777 PP

                                       EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                        ++ ++   +        ++++++ ++   +l++e+ ++++++a+++ +al+++G + + f  + +ge  + EvN+
  gi|386000985|ref|YP_005919284.1| 229 ITICNMENMDP----MGIHTGESIVVTPIQTLTDEEVQTLRTAAINIIRALKIEGGCNIQFAAK-DGEYRVIEVNP 299
                                       77766655443....233344555555555799999************************9876.9*********6 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.2e-09
                                       HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCEE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgneklev 98 
                                       e  +++  ++gypv+V+p+       ++ v  e el  +++ea++   ++ +l++ ++ ++ ei+v av +  ++ +
  gi|386000985|ref|YP_005919284.1| 694 EEAKAEARRIGYPVLVRPSYVLGGRAMEIVYDERELVVYMREAVRVspEHPILIDDFLqNAVEIDVdAVSDGHDVLI 770
                                       445566889**********9888889*****************98733577*******99******55666667999 PP

                                       EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                         + e++ + g+       s+d+a +  p +++++v+++++e+++k+  al+++G+  + + ++ +g +++ E N+
  gi|386000985|ref|YP_005919284.1| 771 GAIMEHIEEAGIH------SGDSACIIPPQTIPAAVQDTVREYVKKIALALEVKGILNIQMAYK-DGIVYVLEANP 839
                                       9999999999986......678999999********************************9987.9********96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.6e-08   1.7e-05      47     117 ..     262     333 ..     251     345 .. 0.80
   2 !   26.4   0.0   4.2e-09   4.7e-06      44     118 ..     799     874 ..     742     888 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-08
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeve 117
                                       + l  +a +++++++++g  n+Q+  ++++++++E+NpR+s      s ++G  ++++ +k + g+  +e+ 
  gi|386000985|ref|YP_005919284.1| 262 QTLRTAAINIIRALKIEGGCNIQFAAKDGEYRVIEVNPRVSRSSAlASKATGYPIARVTAKIAVGMTLDEIG 333
                                       56778999********************************96555156677999999999999998666555 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4.2e-09
                      ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgleteevee 118
                                         ++ + e+++++a +++++g+ n+Q+ ++++  ++LE NpR s ++   s   G+ l+++a+  + g++ +e   
  gi|386000985|ref|YP_005919284.1| 799 AVQDTVREYVKKIALALEVKGILNIQMAYKDGIVYVLEANPRSSRTIPFvSKTVGLPLAKIAAGVMAGKSLAEQGV 874
                                       44677899***************************************9626666*********9999984444433 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.2e-07   0.00025      16     158 ..     149     301 ..     141     304 .. 0.74
   2 !   26.6   0.0   4.5e-09   5.1e-06       3     157 ..     669     840 ..     667     844 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                                       S---....-EESS--SSSEEEEESS-------B--SS--TTE...............EEEE---S.EEEEEEEEE.S CS
                       ATP-grasp_3  16 vkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kplSvsllsdg 83 
                                       v  P +  +e l+e   +l++ p++  gg++   +e +ee ++++e+          lv e + G ++l  +++ d 
  gi|386000985|ref|YP_005919284.1| 149 VDSP-EGAKEALKELGLPLIIRPAYTLGGSGGGSAETEEEFFRIVEMGMkrsrihqvLVEESLVGwTELEYEVMRDR 224
                                       5556.56667778888999**********999999999988888777657788666655555555457777888888 PP

                                       SSEEEEEEEEEEEET....TEEEEE...EES----HHHHHHHH...HHHHHTTSTT--EEEEEEEEESS.SEEEEEE CS
                       ATP-grasp_3  84 ekvlvlavnrqliekaekefvyaGn...vtpietelkeevvel...aeevvekleglaGyvGvDlvlkdeepyviEv 154
                                       ++  +  +n + ++      + +G+   vtpi+t  +eev++l   a +++++l ++ G   + +  kd+e  viEv
  gi|386000985|ref|YP_005919284.1| 225 NDTCITICNMENMDPM---GIHTGEsivVTPIQTLTDEEVQTLrtaAINIIRAL-KIEGGCNIQFAAKDGEYRVIEV 297
                                       7777777777777764...55666533379999988777765411177777777.9999999*************** PP

                                       ESS- CS
                       ATP-grasp_3 155 NPRl 158
                                       NPR+
  gi|386000985|ref|YP_005919284.1| 298 NPRV 301
                                       ***8 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.5e-09
                                       SHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE............... CS
                       ATP-grasp_3   3 dKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........ 64 
                                       d  ++  +L+e g++ P        +  ++e+++  +++ v p++  gg ++ +v +++e+   + e          
  gi|386000985|ref|YP_005919284.1| 669 DRERFNLALREMGIPQPeagyatsPEEAKAEARRIGYPVLVRPSYVLGGRAMEIVYDERELVVYMREAVrvspehpi 745
                                       55566678999999999888775545556677788***************************999998899****** PP

                                       EEEE---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H......HHHHHHHHHHHHTTSTT- CS
                       ATP-grasp_3  65 lvqefie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel......keevvelaeevveklegl 134
                                       l+ +f++   ++ v+++sdg++vl+ a+ + + e      + +G ++ i   +      ++ v+e ++++  +l ++
  gi|386000985|ref|YP_005919284.1| 746 LIDDFLQnAVEIDVDAVSDGHDVLIGAIMEHIEEA----GIHSGDSACIIPPQtipaavQDTVREYVKKIALAL-EV 817
                                       ******73579*********999999888776655....55555554433332231233666677777777777.** PP

                                       -EEEEEEEEESS.SEEEEEEESS CS
                       ATP-grasp_3 135 aGyvGvDlvlkdeepyviEvNPR 157
                                       +G++ + + +kd+  yv+E NPR
  gi|386000985|ref|YP_005919284.1| 818 KGILNIQMAYKDGIVYVLEANPR 840
                                       *********************** PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.4e-05     0.038       6     148 ..     132     266 ..     127     300 .. 0.78
   2 !   17.3   0.0   2.7e-06     0.003      10     186 ..     677     838 ..     672     843 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSS CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagek 82 
                                        k+ + ++g p ++ +a+++pe ake ++e++ +  +++++   +g g   a++eee +++v+  +++ +     ++
  gi|386000985|ref|YP_005919284.1| 132 FKSAMIRIGEPVPRSRAVDSPEGAKEALKELGLPL-IIRPAYTLGGSGGGSAETEEEFFRIVEMGMKRSR----IHQ 203
                                       577888999999***********************.9999999999999**************9998544....57* PP

                                       EEEEE---S.EEEEEEEEECTTE.EEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHH CS
                            GARS_A  83 vviEelleG.eEvsllalvdgkt.vkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekike 148
                                       v++Ee l G +E+   ++ d ++ ++++    +         g  TG   +++p+ ++t+e++++ ++
  gi|386000985|ref|YP_005919284.1| 204 VLVEESLVGwTELEYEVMRDRNDtCITICNMENMD-----PMGIHTGESIVVTPIQTLTDEEVQTLRT 266
                                       ********966999999998654044444433332.....2466666666666666666666666655 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.7e-06
                                       HHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEE CS
                            GARS_A  10 lkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviE 86 
                                       l+++gip +e    t+peeak+  ++ + ++  v+++ + +g+ + ++ +e+e + +++e ++     + ++ ++i+
  gi|386000985|ref|YP_005919284.1| 677 LREMGIPQPEAGYATSPEEAKAEARRIGYPV-LVRPSYVLGGRAMEIVYDERELVVYMREAVR----VSPEHPILID 748
                                       6789***************************.99**************************997....46799***** PP

                                       E---.SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHHCTT CS
                            GARS_A  87 elle.GeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptveglkkeg 162
                                       ++l+   E+ + a++dg++v   ++  +h  +   + g   G   ++ p  +++ +++++++e  +++++ +l+   
  gi|386000985|ref|YP_005919284.1| 749 DFLQnAVEIDVDAVSDGHDVLIGAIM-EH--IE--EAGIHSGDSACIIPPQTIPAAVQDTVRE-YVKKIALALE--- 816
                                       ***7358***********99754443.33..33..3466666666666655555555555555.4444444443... PP

                                       ---EEEEEEEEEEETTE.EEEEEEE CS
                            GARS_A 163 ipfkGvLyaglmlvedg.pkvlefn 186
                                          kG+L  ++   +dg  +vle n
  gi|386000985|ref|YP_005919284.1| 817 --VKGILNIQMAY-KDGiVYVLEAN 838
                                       ..34666555443.33335666665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   1.3e+02      21      51 ..     138     168 ..     116     171 .. 0.83
   2 !   13.8   0.0   2.6e-05     0.029      19      51 ..     677     709 ..     666     712 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                       ATP-grasp_5  21 aygipvvetrlassaeeaveaaeeigypvvl 51 
                                        +g pv+++r ++s+e a ea +e+g p  +
  gi|386000985|ref|YP_005919284.1| 138 RIGEPVPRSRAVDSPEGAKEALKELGLPLII 168
                                       467799*********************9877 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.6e-05
                       ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvl 51 
                                       l+ +gip +e  +a+s+eea + a++igypv +
  gi|386000985|ref|YP_005919284.1| 677 LREMGIPQPEAGYATSPEEAKAEARRIGYPVLV 709
                                       7899**************************976 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.28       5      37 ..     427     460 ..     424     463 .. 0.89
   2 ?    0.5   0.0       0.5   5.6e+02      11      28 ..     479     497 ..     477     504 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                            HTH_23   5 reRlrillllae.GlsvreIAreLgvsrrTvyrw 37 
                                       +eRl +++ +++ G +v+eI+++ g+++  + r+
  gi|386000985|ref|YP_005919284.1| 427 DERLFAIYEALRrGVTVEEISDLTGIHPYFIARI 460
                                       6899999999999**************9888887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                            HTH_23  11 llllae.GlsvreIAreLg 28 
                                       l+ +++ G s ++I ++Lg
  gi|386000985|ref|YP_005919284.1| 479 LRRAKRmGFSDERIGKILG 497
                                       6667779**********99 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.021        23      13      56 ..     138     180 ..     123     235 .. 0.82
   2 ?    7.4   0.0    0.0027         3      11      53 ..     677     718 ..     674     728 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                                       CTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCT CS
                       ATP-grasp_2  13 kygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKa 56 
                                       + g +vp+++ ++s+e a+ea+k+lg    +++     GG G +
  gi|386000985|ref|YP_005919284.1| 138 RIGEPVPRSRAVDSPEGAKEALKELGLPL-IIRPAYTLGGSGGG 180
                                       456689********************988.88888888887755 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                                       HHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTC CS
                       ATP-grasp_2  11 lakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGR 53 
                                       l++ g++ pe+  a+s+eea++ a+++g  +  v+     GGR
  gi|386000985|ref|YP_005919284.1| 677 LREMGIPQPEAGYATSPEEAKAEARRIGYPV-LVRPSYVLGGR 718
                                       7899*************************99.56666666777 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.16       8      32 ..     438     462 ..     437     464 .. 0.95
   2 ?   -0.9   0.0       1.4   1.5e+03      44      58 ..     804     818 ..     794     819 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                       TTT--HHHHHHHSS--HHHHHHHHC CS
                            HTH_25   8 arglsleevaketkIrkdylealEe 32 
                                       +rg ++ee+++ t I++  + ++E+
  gi|386000985|ref|YP_005919284.1| 438 RRGVTVEEISDLTGIHPYFIARIEN 462
                                       79**********************7 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHTT-- CS
                            HTH_25  44 lrgylrnYArlLgld 58 
                                       +r y++++A +L+++
  gi|386000985|ref|YP_005919284.1| 804 VREYVKKIALALEVK 818
                                       89*******999876 PP

>> DUF3071  Protein of unknown function (DUF3071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.7e-05     0.075      48     101 ..     422     475 ..     361     505 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                           DUF3071  48 aeeesslrpreIQariRaGasveevaeeagvsververyahPvlaERariaela 101
                                        +++++ r   I + +R G +vee+++ +g++   + r ++ + +ER+ +a l 
  gi|386000985|ref|YP_005919284.1| 422 LATPTDERLFAIYEALRRGVTVEEISDLTGIHPYFIARIENVIEMEREIAAGLS 475
                                       445555667789999*********************************999875 PP

>> ComX  Bacillus competence pheromone ComX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.13      10      44 ..     991    1025 ..     984    1032 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                              ComX   10 venPdvleklqeGklsLvGlsetEqkailDVfqee 44  
                                        v +P+vl  ++ G++sL+  + t+++ + D+fq +
  gi|386000985|ref|YP_005919284.1|  991 VGSPNVLDYMKRGEVSLIINTPTTKQSVKDGFQIR 1025
                                        99******************************965 PP

>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.7   4.1e+03      21      39 ..      32      50 ..      23     102 .. 0.64
   2 ?   -2.4   0.0       4.2   4.7e+03      18      63 ..     390     439 ..     381     460 .. 0.57
   3 ?    8.7   0.0    0.0016       1.8      21     101 ..     573     660 ..     562     661 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.7
                                      HHHHHHHHCTEEEEEGCTC CS
                     Peptidase_S66 21 raievleelglevvlgksa 39
                                      +a++ l+e g+evvl +s+
  gi|386000985|ref|YP_005919284.1| 32 QACKSLREEGVEVVLVNSN 50
                                      6777787778888744432 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHHC...TEEEEEGCTC.--TTTTCSS-HHHHHHHHHHHHC- CS
                     Peptidase_S66  18 eleraievleel...glevvlgksa.aksagylagtdeeRaadLnealad 63 
                                       +l +a++ le     g+  + ++ + ++ ++ la   +eR+ ++ eal++
  gi|386000985|ref|YP_005919284.1| 390 ALMKAVRSLEIDkdlGYAGKYEPWTdEELRHLLATPTDERLFAIYEALRR 439
                                       55555555533222366666555331222224555667777777777654 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0016
                                       HHHHHHHHCTEEEEEGCTC.......--TTTTCSS-HHHHHHHHHHHHC-TTECEEEES--SS-CHHCHHHH-HCCH CS
                     Peptidase_S66  21 raievleelglevvlgksa.......aksagylagtdeeRaadLnealadpeikaiicarGGygaarllpyldfdai 90 
                                       +a+++l+elg+e+++++++       ++++ +    +   ++d +++++++  + ++   GG++a++l   l+ +  
  gi|386000985|ref|YP_005919284.1| 573 HAVQALRELGIEAHIANNNpetvstdYDTS-DKLFFEPLTLEDVMNIIEKERHDGVMVQFGGQTAMNLAIPLEREIA 648
                                       689999999***998885544333222211.2222555789***************************999987766 PP

                                       HC.S--EEEE-C CS
                     Peptidase_S66  91 kk.npkiliGyS 101
                                       ++  p  ++G S
  gi|386000985|ref|YP_005919284.1| 649 RRgLPTKILGTS 660
                                       667777777766 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.7   8.6e+03      10      25 ..     805     820 ..     801     848 .. 0.84
   2 ?    9.5   0.0    0.0013       1.4       1      63 [.     940     997 ..     940    1038 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.7
                             TIR_2  10 kewaeklaeaLeaagi 25 
                                       +e+++k+a aLe +gi
  gi|386000985|ref|YP_005919284.1| 805 REYVKKIALALEVKGI 820
                                       7899999999999996 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                             TIR_2   1 VFiSyssedkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspayl 63 
                                       VFiS + edk  + ++a++L ++g+++   +       ++ +++  a+++ +  + v sp+ l
  gi|386000985|ref|YP_005919284.1| 940 VFISVRDEDKGPVAEVARKLADSGLSIIATQ----GTAEFLTKMGVAVKRVE-KIYVGSPNVL 997
                                       9************************986444....23477777777777765.4555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1070 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.49
# Mc/sec: 6522.32
//
Query:       gi|386000986|ref|YP_005919285.1|  [L=363]
Description: Carbamoyl-phosphate synthase, small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-45  153.5   0.0    3.7e-45  152.9   0.0    1.2  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    1.1e-37  129.7   0.0    1.6e-37  129.2   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    1.7e-08   34.5   0.3    6.1e-06   26.1   0.3    2.3  1  Peptidase_C26    Peptidase C26
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.38   10.5   0.0    1.5  1  DJ-1_PfpI        DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0   8.3e-49   3.7e-45       3     127 ..       4     129 ..       3     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 8.3e-49
                   CPSase_sm_chain   3 vLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvv 78 
                                       vL LedGt +eG +fg  + ++GE+vf T m+GY+e+ltDpsY+gq+l++typl+GnyGv+ ++++s++i +a++v+
  gi|386000986|ref|YP_005919285.1|   4 VLGLEDGTRVEGVGFGaPGVVSGELVFVTVMSGYEEALTDPSYKGQLLTFTYPLMGNYGVSGDHFQSDRIGAAAMVC 80 
                                       799*************55999******************************************************** PP

                   CPSase_sm_chain  79 relseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                       +e+ ++p ++r+++++s++l+ee++pgi+g+DTR+Lt k+r++gam+++
  gi|386000986|ref|YP_005919285.1|  81 KEIWNRPLHHRSTRTISQFLEEEGVPGIHGLDTRMLTIKIRNQGAMRAA 129
                                       **********************************************997 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.0   3.5e-41   1.6e-37       3     178 ..     180     344 ..     178     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 3.5e-41
                                       EESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEET CS
                            GATase   3 iDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGIC 78 
                                       +D +  +++n++++++  g+++ vvp d+ ++ i  ++ +p+++++s+Gpg+p+ ++ +iea+k++++ ++P++GIC
  gi|386000986|ref|YP_005919285.1| 180 MDLG--IKRNILDSMACQGFDIVVVPSDSRISDI--ERYDPEALFISNGPGDPEkAGRAIEAVKHFAG-EKPVFGIC 251
                                       5667..9**********************99999..489*****************************.******** PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       LG+Q++++++g++++k k ++hhgg+++++d       +++ ++i++++H++++ p++ e +gl++t ++++d++++
  gi|386000986|ref|YP_005919285.1| 252 LGLQVICLALGAETYKLK-FGHHGGNQPVKD------LESGIVYITSQNHNFALRPQSAEGTGLKITQVNANDGTVE 321
                                       ******************.************......67779*******************************9888 PP

                                       EEEEETTTEEEESSBTTSTTSTT CS
                            GATase 156 eiiekknpfvgvQFHPEststpe 178
                                       +++     + +vQ+HPE++++p 
  gi|386000986|ref|YP_005919285.1| 322 AVRSSYLGMEAVQYHPEARPGPL 344
                                       88888889**********99986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.3   1.4e-09   6.1e-06     102     216 .]     241     338 ..     222     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.4e-09
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqai 178
                                        + ++P++giC+Glq++  alG ++y+  +    + +h        ++ vk  ++++++   +         H++a+
  gi|386000986|ref|YP_005919285.1| 241 FAGEKPVFGICLGLQVICLALGAETYKL-K----FGHH------GGNQPVKDLESGIVYITSQ--------NHNFAL 298
                                       56689*****************999963.4....2333......4467777666666655555........355555 PP

                     Peptidase_C26 179 ke...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       +     +++l+++ v + Dg++Ea++s      + +vQ+HPE
  gi|386000986|ref|YP_005919285.1| 299 RPqsaEGTGLKITQVNAnDGTVEAVRSSYL--GMEAVQYHPE 338
                                       432225789999998877*********994..599******9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.6e-05      0.38      46     107 ..     200     257 ..     172     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.6e-05
                                       EEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHH CS
                         DJ-1_PfpI  46 lkvtvdaslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlL 107
                                       + v+ d  ++d++  +  al +  G   pe+     +++e vk+fa  +k+v+ IC g q+ 
  gi|386000986|ref|YP_005919285.1| 200 VVVPSDSRISDIERYDPEALFISNGPGDPEKAG---RAIEAVKHFA-GEKPVFGICLGLQVI 257
                                       66778999**************99988777666...89*****987.679********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 2186.26
//
Query:       gi|386000987|ref|YP_005919286.1|  [L=412]
Description: saccharopine dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for 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-39  135.7   0.0    3.8e-39  135.4   0.0    1.1  1  Sacchrp_dh_C     Saccharopine dehydrogenase C-terminal domain
    2.6e-07   31.0   0.0    4.7e-07   30.1   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0052   17.6   0.0     0.0083   16.9   0.0    1.3  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0089   15.5   0.0      0.013   15.0   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.022   14.7   0.6      0.035   14.0   0.6    1.3  1  NAD_binding_10   NAD(P)H-binding
      0.026   14.4   0.4      0.047   13.6   0.4    1.3  1  KR               KR domain
      0.052   13.0   0.1      0.091   12.2   0.1    1.4  1  adh_short        short chain dehydrogenase
        0.2   11.7   0.5       0.35   11.0   0.5    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.27   10.6   0.0       0.37   10.2   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
        4.7    7.6   9.2       0.16   12.2   0.5    3.3  4  DUF4129          Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> Sacchrp_dh_C  Saccharopine dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.0   2.1e-42   3.8e-39       1     265 []     150     402 ..     150     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 2.1e-42
                                       BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCC.ESTTCEEESS-HHHHHHHCCSEEEEEETTEEEECT CS
                      Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeas.dnplgYkfsWspegvlreltnpakvlengqvkevp 76 
                                       G++PG+++ ++ ++id ++     +e  ++++gg+p+ ea+ ++pl Y+++Ws   vlre++  ++vl++g+++ev 
  gi|386000987|ref|YP_005919286.1| 150 GFAPGLSNASIGRGIDLLDS----AERATARVGGVPSKEAAaRHPLWYTVTWSFGHVLREYMVRPRVLRGGRIVEVA 222
                                       9***************8866....679**************99*****************************99998 PP

                                       .CCCSGCC.TCEEEC.C.CCCEECTTECEEECTHCHHHHHHC.SCSEEEEEEEEEHHHHHHHHHHHTTT--SCECCC CS
                      Sacchrp_dh_C  77 .gsellkgakkpiyi.l.pglslegypnrdslpyeelyglpeaktlfrgtlrypgfsellkslkelGllseepkeea 150
                                        ++e      +   +   +  ++e+ ++  ++p   ly+ p + +++ +t+r+pg++e ++ l+++Gll+ ep    
  gi|386000987|ref|YP_005919286.1| 223 pLTER-----ERFVFgPlG-EEFEAAATP-GMPS-LLYTRPGLAEFTEKTVRWPGHWEGIDLLRRCGLLDLEP---- 287
                                       45553.....333333332.377755444.3444.3556666679***************************9.... PP

                                       CCCHHSTT.C.EHHHHHHHHCCHHCCCCTTEEEEEEEEEEEEEETTSEEEEEEE..EEEEEE.EHH..SSSHHHHHH CS
                      Sacchrp_dh_C 151 lkawlseg.e.spldvlaalLekklalepgerDlvvlqhefgiesdgkkkekkt..stlvgy.dee..gssamaktv 220
                                       +++   +g + sp++++ ++ e +l+  pge+Dl+++ +++ + + g+    ++    l++  d +  g sama+++
  gi|386000987|ref|YP_005919286.1| 288 MEV---AGcSiSPRELFISVVEPRLRPLPGETDLCIMANSVQGLKGGEA---ARvdHLLLAGpD-QvaGVSAMARVT 357
                                       666...667789*****************************55555554...442233332122.367********* PP

                                       HHHHHHHHHHHHTTSCTSSEEEEGGGS.CHHHHHHHHHHHHHCT- CS
                      Sacchrp_dh_C 221 GvpaaiaaklildgkikkrGvvtpeelvdpeiyeplleeLekeGi 265
                                       G  aa+aa+++ +g++++rG+v+pe+ ++  +ye +l eLe +Gi
  gi|386000987|ref|YP_005919286.1| 358 GSSAAVAARILGRGELRGRGIVAPEDGIRGAVYEGYLRELELRGI 402
                                       ****************************888**********9997 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.6e-10   4.7e-07       1     128 [.       3     144 ..       3     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.6e-10
                                       EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--T..TTHHHHHHHHHTTSSEEE CS
                   Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialda..enyeavLaallkegdlvv 74 
                                       vl+iG+ G++G+a+a++la +++v+  + ++++   +le++aa++ g ++  + +d+   + ++ + +l++++d+ v
  gi|386000987|ref|YP_005919286.1|   3 VLVIGGaGRIGSAAARDLAGSGEVE-VVGLVGPRAGRLERAAAWIGGDKLRLHPCDVggGDARE-VRRLMEGYDVGV 77 
                                       7899988*****************5.889****************7666666666662268888.99********** PP

                                       E-SSGG.GHHHHHHHHHHHT-EEEE..SS-.............BCGCCSCHCCSHHHHHTHHHHHHCTSE CS
                   Sacchrp_dh_NADP  75 nlsppi.ssldvlkaCietgvhyvd..tsi.............skeertnyalreavlklkekakeagvt 128
                                        ++p+   s   l+a+i++  + vd   ++              +++ t+    e+  +l+++a+e+gvt
  gi|386000987|ref|YP_005919286.1|  78 IALPDRrTSYRALEAAIDASLDAVDvlEEYhrrpdpyeteglpVPASMTP---DEYGESLHRRAEENGVT 144
                                       *****99999***************6534466665555443332222222...33334566666677776 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.6e-06    0.0083       2      87 ..       2      98 ..       1     107 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.6e-06
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS............HHHHHTCTTESEEE CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd............leelladpeidavi 67
                                      rv++iG+ G+igs  +r l  s  + evv+l+ p+a r e++a+  g +                +++l++    d+ +
  gi|386000987|ref|YP_005919286.1|  2 RVLVIGGaGRIGSAAARDLAGS-GEVEVVGLVGPRAGRLERAAAWIGGDKLRLhpcdvgggdareVRRLME--GYDVGV 77
                                      77777777********999999.999****************88888773333334456666555777777..788888 PP

                                      E-S-G.GGHHHHHHHHHHTT- CS
                      GFO_IDH_MocA 68 vatpn.gtheelakaaleagk 87
                                      +a p  +t ++  +aa+ a  
  gi|386000987|ref|YP_005919286.1| 78 IALPDrRTSYRALEAAIDASL 98
                                      888887777777777777765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     7e-06     0.013       1      66 [.       3      74 ..       3     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7e-06
                                      EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC......EEEE--TT-HH..HHHHHHHHHT-S CS
                         Epimerase  1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledl......elveldltdrs..alerlfkeeqpd 66
                                      +lV+G++G iGsa ++ l+  g +ev+gl    +a++ +r +        +l+ +d+  ++  +++rl++  + d
  gi|386000987|ref|YP_005919286.1|  3 VLVIGGAGRIGSAAARDLAGSGeVEVVGLVGP-RAGRLERAAAWiggdklRLHPCDVGGGDarEVRRLME--GYD 74
                                      79********************8889999876.3444443333367777888888887666447888887..444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.9e-05     0.035       1      84 [.       7      96 ..       7     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETT....HHHCHHHHCTTTCEEEE--TT..-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRn....peklaeleaeeglevvegdvt..dvedlaealkgadaVvsalggggk 73
                                      G+ G++G+++++ l+ +g++ev+ lv       e++a+    ++l++   dv   d+ ++++ ++g+d+ v+al  +++
  gi|386000987|ref|YP_005919286.1|  7 GGAGRIGSAAARDLAGSGEVEVVGLVGPragrLERAAAWIGGDKLRLHPCDVGggDAREVRRLMEGYDVGVIALPDRRT 85
                                      99***********************95422335677766677888888888854499************9999998888 PP

                                      HHHHHHHHHHH CS
                    NAD_binding_10 74 deegaknivda 84
                                        ++ ++++da
  gi|386000987|ref|YP_005919286.1| 86 SYRALEAAIDA 96
                                      77877777776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   2.6e-05     0.047       3      62 ..       3      58 ..       2      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                                      EEEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----T CS
                                KR  3 ylitGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDv 62
                                      +l++GG+G +G + ar la +g  + + l++ +a   e+++a+i      g + ++ ++Dv
  gi|386000987|ref|YP_005919286.1|  3 VLVIGGAGRIGSAAARDLAGSGeVEVVGLVGPRAGRLERAAAWIG-----GDKLRLHPCDV 58
                                      69********************44555599999877777776664.....45555555555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.1e-05     0.091       3      69 ..       3      71 ..       1      78 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                                      EEEESTTSHHHHHHHHHHHHTT.-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTT..SHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeG.akvvv.vdrseekleevakelkeegakalaiqvDvt..dreevealve 69
                                      vlv+G+++ IG a a+ la +G ++vv  v+ ++ +le++a+ ++   +k+   ++Dv   d++ev++l+e
  gi|386000987|ref|YP_005919286.1|  3 VLVIGGAGRIGSAAARDLAGSGeVEVVGlVGPRAGRLERAAAWIGG--DKLRLHPCDVGggDAREVRRLME 71
                                      8******************9993455558****************6..57777777776668888888887 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5    0.0002      0.35       1      34 [.       1      34 [.       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEET CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdr 34
                                      ++v+v+G +Gr+G++ ++ +  + ++e+v+ v  
  gi|386000987|ref|YP_005919286.1|  1 MRVLVIGGAGRIGSAAARDLAGSGEVEVVGLVGP 34
                                      89**************************998865 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 ?   10.2   0.0    0.0002      0.37       1      76 [.       4      75 ..       4      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                      EEETTTSHHHHHHHHHHHHCT.-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--T..T-HHHHHHHHHHHT- CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekg.yevhgivrrsssfntgriehlakdpkeeleenlklhkgDl..tDssslerllaevqp 76
                                      L+ G+aG iGs  a+ L   g  ev+g+v    + +++r +++         ++l+lh +D+   D+++++rl++ +++
  gi|386000987|ref|YP_005919286.1|  4 LVIGGAGRIGSAAARDLAGSGeVEVVGLVGPR-AGRLERAAAWIG------GDKLRLHPCDVggGDAREVRRLMEGYDV 75
                                      899***************98636999988644.345556655553......4679999999955589999999987765 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         8   1.4e+04      24      44 ..      27      44 ..      17      46 .. 0.59
   2 ?   -1.8   0.0       2.1   3.8e+03      56      68 ..      61      73 ..      52      74 .. 0.74
   3 ?   12.2   0.5     9e-05      0.16      10      34 ..     115     140 ..      99     193 .. 0.79
   4 ?   -3.2   0.2       5.8     1e+04      29      41 ..     353     366 ..     333     368 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8
                           DUF4129 24 Eyarrvriapspaaalaalae 44
                                      E++  v   ++ a +l+++a+
  gi|386000987|ref|YP_005919286.1| 27 EVVGLV---GPRAGRLERAAA 44
                                      555555...445555555554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                           DUF4129 56 asaeeyrrlveal 68
                                      ++a e+rrl+e +
  gi|386000987|ref|YP_005919286.1| 61 GDAREVRRLMEGY 73
                                      5777888887754 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 9e-05
                           DUF4129  10 aergldrrpgeTprEyarrv.riaps 34 
                                       +  gl+ ++++Tp Ey + + r+a +
  gi|386000987|ref|YP_005919286.1| 115 ETEGLPVPASMTPDEYGESLhRRAEE 140
                                       456*****************765544 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 5.8
                           DUF4129  29 v.riapspaaalaa 41 
                                         r+++s aa +a+
  gi|386000987|ref|YP_005919286.1| 353 MaRVTGSSAAVAAR 366
                                       13555666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2428.71
//
Query:       gi|386000988|ref|YP_005919287.1|  [L=117]
Description: hypothetical protein Mhar_0276 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 685.58
//
Query:       gi|386000989|ref|YP_005919288.1|  [L=577]
Description: Glycyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-24   84.1   0.0    1.5e-23   82.7   0.0    1.8  1  HGTP_anticodon  Anticodon binding domain
    2.3e-10   40.7   0.1    7.9e-09   35.7   0.0    2.3  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.011   15.5   2.4      0.017   14.8   0.1    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.017   15.2   0.0        2.8    8.1   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.06   12.8   0.8       0.24   10.9   0.2    2.1  2  zf-ribbon_3     zinc-ribbon domain
        0.1   13.1   2.8        1.4    9.5   0.0    3.4  3  zf-C2H2         Zinc finger, C2H2 type
       0.47   10.5   1.5       0.84    9.7   0.2    2.1  2  ADK_lid         Adenylate kinase, active site lid
       0.77   10.8   3.7         22    6.2   0.0    3.9  4  zf-C2H2_4       C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0   6.8e-27   1.5e-23       1      93 [.     470     560 ..     470     561 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 6.8e-27
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv+v+pl + + el   a+++a+eLr  ++rve+d s++sig+++r+ d++g+p+ v+v++++le+gtvt+rdrd++
  gi|386000989|ref|YP_005919288.1| 470 QVAVLPLMD-RPELIGPAEEIARELRSLDLRVEYD-SSGSIGRRYRRNDEVGTPYSVTVDYETLEEGTVTIRDRDSM 544
                                       8*******9.999*********************7.9**************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       +q+r++++++++++ +
  gi|386000989|ref|YP_005919288.1| 545 AQIRIARSDVAKIVAS 560
                                       ***********99875 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   3.5e-12   7.9e-09      12      76 ..     157     223 ..     151     235 .. 0.83
   2 ?    2.4   0.0     0.058   1.3e+02     149     178 ..     416     445 ..     404     446 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.5e-12
                                       EE-SSSHHHHHHHHHHHEEEBGG..SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                      tRNA-synt_2b  12 iLkPtneetfvelirdevlrskr..LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easl 76 
                                       +L+P+  +++   ++   lr +r  LP+  +qi+  yR+E s  +G++R+reF q ++++f   ++++
  gi|386000989|ref|YP_005919288.1| 157 YLRPETAQGMFVNFQRL-LRHYRdrLPFGAVQIGKSYRNEISPRQGVIRLREFSQAEAEIFINpQDKS 223
                                       79999999998888855.9984447****************9566****************9966655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.058
                                       EECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 149 vldennreksvimicaaigveRllsaileq 178
                                       + +  ++e  +++i  ++g+ R+l  +le+
  gi|386000989|ref|YP_005919288.1| 416 TEEVRGEEVVPHVIEPSFGIDRILYSVLEH 445
                                       4455679999***************99997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3      0.48   1.1e+03       2       7 ..      88      93 ..      87      95 .. 0.67
   2 ?   14.8   0.1   7.6e-06     0.017       9      20 ..     120     131 ..     118     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.48
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +CG+
  gi|386000989|ref|YP_005919288.1| 88 CRECGE 93
                                      666664 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.6e-06
                     zinc_ribbon_2   9 lqdnakFCpyCG 20 
                                       +q+n++FCp+CG
  gi|386000989|ref|YP_005919288.1| 120 IQENDVFCPECG 131
                                       89*********9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.017        37      23      34 ..      82      93 ..      69     101 .. 0.76
   2 ?    8.1   0.0    0.0013       2.8      21      38 ..     119     136 ..     112     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                       Zn-ribbon_8 23 dapltaCPeCgs 34
                                       +plt+C eCg+
  gi|386000989|ref|YP_005919288.1| 82 SDPLTECRECGE 93
                                      468899999996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8  21 isdapltaCPeCgsevrr 38 
                                       + +++++ CPeCg+++  
  gi|386000989|ref|YP_005919288.1| 119 VIQENDVFCPECGGDLSE 136
                                       44444455*****98865 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.52   1.2e+03       5      10 ..      88      93 ..      85      98 .. 0.66
   2 ?   10.9   0.2   0.00011      0.24      12      26 .]     120     134 ..     119     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.52
                       zf-ribbon_3  5 CPnCGa 10
                                      C +CG+
  gi|386000989|ref|YP_005919288.1| 88 CRECGE 93
                                      555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                       zf-ribbon_3  12 lssddnvCpyCGtkl 26 
                                       +++ d++Cp CG++l
  gi|386000989|ref|YP_005919288.1| 120 IQENDVFCPECGGDL 134
                                       68889*******987 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00063       1.4       2      20 ..      87     104 ..      86     106 .. 0.94
   2 ?   -1.5   0.1         2   4.5e+03       3       7 ..     127     131 ..     126     141 .. 0.86
   3 ?    2.0   0.1      0.16   3.5e+02      11      21 ..     326     336 ..     326     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00063
                                       EETTTTEEESSHHHHHHHH CS
                           zf-C2H2   2 kCpdCgksFkrksnLkrHi 20 
                                       +C +Cg+ + r ++L +Hi
  gi|386000989|ref|YP_005919288.1|  87 ECRECGEIY-RADHLIKHI 104
                                       6********.********8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                       ETTTT CS
                           zf-C2H2   3 CpdCg 7  
                                       Cp+Cg
  gi|386000989|ref|YP_005919288.1| 127 CPECG 131
                                       ****8 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.16
                                       SSHHHHHHHHH CS
                           zf-C2H2  11 krksnLkrHir 21 
                                       +++++L++H+ 
  gi|386000989|ref|YP_005919288.1| 326 RTNYDLRSHMA 336
                                       589******95 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00038      0.84       4      31 ..      88     134 ..      87     136 .. 0.72
   2 ?   -2.0   0.1       1.6   3.6e+03      29      36 .]     355     362 ..     354     362 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00038
                                       -TTT--EE.......ETTTB--S.............STTB-TTT--.- CS
                           ADK_lid   4 CpkCGrsY.......hvvfnpPk.............veglCDkCGepL 31 
                                       C+ CG++Y       h+v   P              ++ +C +CG++L
  gi|386000989|ref|YP_005919288.1|  88 CRECGEIYradhlikHIV-EVPDalaneeiyrviqeNDVFCPECGGDL 134
                                       9*******7774444422.22335666777777777999******998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                                       -.-B--GG CS
                           ADK_lid  29 epLvqRsD 36 
                                       e Lv+R+D
  gi|386000989|ref|YP_005919288.1| 355 ERLVVRPD 362
                                       68*****9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0097        22       2      21 ..      87     105 ..      86     108 .. 0.90
   2 ?    1.6   0.1      0.31   6.9e+02       3      15 ..     127     139 ..     125     142 .. 0.80
   3 ?    0.1   0.0      0.92   2.1e+03       9      21 ..     166     178 ..     164     180 .. 0.85
   4 ?   -0.3   0.0       1.2   2.7e+03      12      21 ..     327     336 ..     326     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0097
                         zf-C2H2_4   2 kCpiCgksFsskkaLlrHlk 21 
                                       +C+ Cg+ + + ++L +H+ 
  gi|386000989|ref|YP_005919288.1|  87 ECRECGEIY-RADHLIKHIV 105
                                       7********.********85 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.31
                         zf-C2H2_4   3 CpiCgksFsskka 15 
                                       Cp Cg+  s  ++
  gi|386000989|ref|YP_005919288.1| 127 CPECGGDLSEIYE 139
                                       *****99877665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.92
                         zf-C2H2_4   9 sFsskkaLlrHlk 21 
                                        F + ++LlrH +
  gi|386000989|ref|YP_005919288.1| 166 MFVNFQRLLRHYR 178
                                       799999*****86 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.2
                         zf-C2H2_4  12 skkaLlrHlk 21 
                                       ++++L++H++
  gi|386000989|ref|YP_005919288.1| 327 TNYDLRSHMA 336
                                       6789****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 3954.43
//
Query:       gi|386000990|ref|YP_005919289.1|  [L=218]
Description: membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.023   14.7   0.3    1.6  1  MHC2-interact  CLIP, MHC2 interacting


Domain annotation for each model (and alignments):
>> MHC2-interact  CLIP, MHC2 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   1.3e-06     0.023      24      55 ..      15      46 ..       2      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-06
                     MHC2-interact 24 rsslkralkvaglsiLvalLiAGQavTaYfvy 55
                                       ++ ++a+ ++gls+ +alL+ G a+ + fv 
  gi|386000990|ref|YP_005919289.1| 15 TEARRKAIHLTGLSVPAALLLFGKAAAIGFVA 46
                                      3456799*******************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1586.20
//
Query:       gi|386000991|ref|YP_005919290.1|  [L=214]
Description: adenylate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-59  200.4   0.0    1.8e-59  200.2   0.0    1.0  1  ADK              Adenylate kinase
    2.7e-27   95.9   0.1    5.4e-27   94.9   0.0    1.4  2  AAA_17           AAA domain
    1.6e-16   60.0   2.0    2.7e-16   59.2   1.4    1.7  2  ADK_lid          Adenylate kinase, active site lid
    2.8e-05   24.3   0.0    8.6e-05   22.7   0.0    1.8  2  AAA_33           AAA domain
    2.9e-05   24.6   0.0    6.1e-05   23.6   0.0    1.5  1  AAA_18           AAA domain
    7.4e-05   23.1   0.1      0.076   13.3   0.0    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0016   18.2   0.0     0.0025   17.6   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
     0.0025   18.2   0.0     0.0056   17.1   0.0    1.6  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   16.0   0.0       0.27   11.5   0.0    2.2  2  AAA_28           AAA domain
      0.025   14.3   0.0      0.042   13.6   0.0    1.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.035   13.8   0.0        1.3    8.6   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.041   13.6   0.2       0.19   11.4   0.0    2.1  3  AAA_24           AAA domain
       0.11   13.0   0.0       0.14   12.6   0.0    1.4  1  ABC_tran         ABC transporter
       0.19   11.8   0.0       0.32   11.0   0.0    1.4  1  Pox_A3L          Poxvirus A3L Protein


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.0   1.4e-62   1.8e-59       1     150 [.       5     189 ..       5     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 1.4e-62
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       llG+Pg+GKGtqa+ +++kyg++h+stGd+lR++v++gt+lG eak++m++g+lvpd+++++++k++l+k+d k g+
  gi|386000991|ref|YP_005919290.1|   5 LLGPPGSGKGTQAKMIADKYGVVHISTGDILRENVRNGTPLGVEAKKFMEAGKLVPDSLLIDIIKDRLAKDDVKGGW 81 
                                       79*************************************************************************** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       +lDG+PRt++qaea++++l + ++k+d+vl++dvp++ lv+R+tg                                
  gi|386000991|ref|YP_005919290.1|  82 MLDGYPRTMPQAEAMDKILPNLGQKIDVVLNIDVPDAELVKRVTGrrmckcgttyhvqfnppkvagkcdacgadlyq 158
                                       ***************************************************************************** PP

                                       ...GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ...DneetvkkRletykkqtkplidyykkkg 150
                                          D+eetvk+Rl++y++qt+plidyy+k+g
  gi|386000991|ref|YP_005919290.1| 159 radDTEETVKERLQAYHAQTQPLIDYYDKRG 189
                                       ****************************987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   4.2e-30   5.4e-27       1     123 [.       6     128 ..       6     132 .. 0.95
   2 ?   -2.9   0.0       6.7   8.5e+03     127     136 .]     159     168 ..     157     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 4.2e-30
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS..HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl..akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       lG+PGsGKgtq++ +++kyg+ h+s+Gd+lre++++g    ++a++ m+ ++l+++  l +++++++a+++ k+g++
  gi|386000991|ref|YP_005919290.1|   6 LGPPGSGKGTQAKMIADKYGVVHISTGDILRENVRNGTPlgVEAKKFMEAGKLVPDSLLIDIIKDRLAKDDVKGGWM 82 
                                       7*********************************9997446899999999*************************** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       +dg+pr+  qa+++d++  +  +++  d+++ +++++ e+++r+  +r
  gi|386000991|ref|YP_005919290.1|  83 LDGYPRTMPQAEAMDKILPNLGQKI--DVVLNIDVPDAELVKRVTGRR 128
                                       *********************9999..****************98875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
                                       -TS-SHHHHH CS
                            AAA_17 127 rdddneesik 136
                                       r+dd+ee++k
  gi|386000991|ref|YP_005919290.1| 159 RADDTEETVK 168
                                       6666666654 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       9.1   1.2e+04      25      34 ..     114     123 ..     114     123 .. 0.82
   2 !   59.2   1.4   2.1e-19   2.7e-16       1      36 []     127     161 ..     127     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9.1
                                       TTT--.-B-- CS
                           ADK_lid  25 DkCGepLvqR 34 
                                       D++  +Lv+R
  gi|386000991|ref|YP_005919290.1| 114 DVPDAELVKR 123
                                       7778899998 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 2.1e-19
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr+C kCG++Yhv+fnpPkv g+CD CG +L+qR+D
  gi|386000991|ref|YP_005919290.1| 127 RRMC-KCGTTYHVQFNPPKVAGKCDACGADLYQRAD 161
                                       9***.6*****************************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.7e-08   8.6e-05       2     119 ..       3     128 ..       3     139 .. 0.76
   2 ?   -2.2   0.0       3.4   4.3e+03     108     117 ..     164     173 ..     154     181 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.7e-08
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllss.dtlrrrlfg...tdqqsktdytrvldr.....lyqilnelarkalsa 69 
                                       ++l G+pGsGK t a+ ++ k g+v++s+ d+lr+++++    +++ k +  ++ +      l++i++++++ +   
  gi|386000991|ref|YP_005919290.1|   3 IVLLGPPGSGKGTQAKMIADKYGVVHISTgDILRENVRNgtpLGVEAK-KFMEAGKLvpdslLIDIIKDRLA-KDDV 77 
                                       5789***********************983556668888776333333.33333333222256777777774.4566 PP

                            AAA_33  70 grnvildatnlsrrerarflklarrlgvpvri.vvvetdeetlkeRlakRa 119
                                       +++ +ld   ++  + ++++k++++lg ++ + + +++++++l +R+  R 
  gi|386000991|ref|YP_005919290.1|  78 KGGWMLDGYPRTMPQAEAMDKILPNLGQKIDVvLNIDVPDAELVKRVTGRR 128
                                       7889999999999999999****9999998662569999999999999985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                            AAA_33 108 eetlkeRlak 117
                                       eet keRl++
  gi|386000991|ref|YP_005919290.1| 164 EETVKERLQA 173
                                       4444444443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.7e-08   6.1e-05       1     114 [.       3     128 ..       3     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.7e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       I+l G+pG+GK t ak ++++ g+     g++lr++++++ +l  + ++ +   +++ d    d + d l + +   
  gi|386000991|ref|YP_005919290.1|   3 IVLLGPPGSGKGTQAKMIADKYGVvhistGDILRENVRNGTPLGVEAKKfMEAGKLVPDSLLIDIIKDRLAKDD--- 76 
                                       89*******************87799999*********988888777777666666677777777777777764... PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRg 114
                                        +g++  +dg +  + +++a d+              +++++ el +R+  R+
  gi|386000991|ref|YP_005919290.1|  77 VKGGW-MLDGYPRTMPQAEAMDKILpnlgqkidvvLNIDVPDAELVKRVTGRR 128
                                       34444.889988888888777776688888888667789999*******9997 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   5.9e-05     0.076       2      50 ..       3      50 ..       2      55 .. 0.88
   2 !    7.8   0.0    0.0029       3.7     170     197 ..      58      85 ..      53      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgnssaGlrAr 50
                                      i++ G+P sGK + a  +a kY+   ++  +++ e + +g ++ G+ A+
  gi|386000991|ref|YP_005919290.1|  3 IVLLGPPGSGKGTQAKMIADKYGVVHISTGDILRENVRNG-TPLGVEAK 50
                                      8899*******************************99886.56677766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                         Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                       + P+ ll++I+ +Rl  +d   G ++Dg
  gi|386000991|ref|YP_005919290.1|  58 LVPDSLLIDIIKDRLAKDDVKGGWMLDG 85 
                                       57*****************999999998 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0025       2      34 ..       4      36 ..       3      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYR 34
                                       + GP gsGK++ a+++a+k g+  ++tg + R
  gi|386000991|ref|YP_005919290.1|  4 VLLGPPGSGKGTQAKMIADKYGVVHISTGDILR 36
                                      566**************************9988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.3e-06    0.0056       1      37 [.       3      37 ..       3      78 .. 0.76
   2 ?   -3.4   0.0       9.3   1.2e+04     111     130 ..      95     113 ..      92     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgsellsk 37
                                      ++l GppG GK + ak +a + gv  + is  ++l +
  gi|386000991|ref|YP_005919290.1|  3 IVLLGPPGSGKGTQAKMIADKYGV--VHISTGDILRE 37
                                      5799*****************765..78888777744 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.3
                                       SGGGSTHHHHSTTSSEEEET CS
                               AAA 111 rpdkldpallrgRfdrkiei 130
                                        +dk+ p l  +++d++++i
  gi|386000991|ref|YP_005919290.1|  95 AMDKILPNLG-QKIDVVLNI 113
                                       5788888888.888888776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.27       1      37 [.       2      41 ..       2      61 .. 0.79
   2 ?    2.4   0.0      0.13   1.7e+02     124     162 ..     162     202 ..     137     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareilee 37
                                      +iv++G++++GK t ++ +a++ g++++   ++ re +++
  gi|386000991|ref|YP_005919290.1|  2 NIVLLGPPGSGKGTQAKMIADKyGVVHIstGDILRENVRN 41
                                      69******************87687766556666665555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                            AAA_28 124 dgeR..redleereaiderlrealrelgipviivpsgdvee 162
                                       d+e   +e+l++  a ++ l++ ++++gi  ++v  gd++e
  gi|386000991|ref|YP_005919290.1| 162 DTEEtvKERLQAYHAQTQPLIDYYDKRGIVATVVGVGDIKE 202
                                       3333223566666677788999************9999876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.3e-05     0.042      36      69 ..       3      35 ..       1      42 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkitsgPvl 69
                                      ++l GpPG Gk t ak+ia++ gv ++i++g +l
  gi|386000991|ref|YP_005919290.1|  3 IVLLGPPGSGKGTQAKMIADKYGV-VHISTGDIL 35
                                      7899****************9998.455556555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0011       1.3       3      65 ..       7      71 ..       7      83 .. 0.80
   2 ?    3.4   0.0     0.042        54     104     140 ..      93     129 ..      77     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                      ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadr 65
                                      G  G+GK tqa+++++++   +i+   +++     gt++G  +++ ++ + +l + ++++ + +dr
  gi|386000991|ref|YP_005919290.1|  7 GPPGSGKGTQAKMIADKYGVVHIStgdILRENVRNGTPLGVEAKKFME-AGKLVPDSLLIDIIKDR 71
                                      5669**************999998865566666688999999988888.77777777777666666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.042
                                       CHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS CS
                   Thymidylate_kin 104 ldlvlslnedvllkPdltflldvdpevalkRlakrde 140
                                       ++++ ++ ++++ k d+++ +dv+ ++ +kR++ r++
  gi|386000991|ref|YP_005919290.1|  93 AEAMDKILPNLGQKIDVVLNIDVPDAELVKRVTGRRM 129
                                       567778888887799******************9998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.19       4      30 ..       2      30 ..       1      55 [. 0.84
   2 ?   -0.5   0.0      0.67   8.6e+02     152     181 ..      95     128 ..      65     142 .. 0.70
   3 ?   -3.6   0.0       5.8   7.4e+03      81     106 ..     152     176 ..     149     186 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                            AAA_24  4 kiliyGpsgiGKTtlakel..gpkplfid 30
                                      +i++ Gp+g+GK t+ak++  ++ ++ i 
  gi|386000991|ref|YP_005919290.1|  2 NIVLLGPPGSGKGTQAKMIadKYGVVHIS 30
                                      79***************996666565555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.67
                            AAA_24 152 lgkktanelkeevDlvlranlkred....kvger 181
                                         +k  ++l ++ D+vl +++  ++     +g+r
  gi|386000991|ref|YP_005919290.1|  95 AMDKILPNLGQKIDVVLNIDVPDAElvkrVTGRR 128
                                       4455677788889999998886655666544444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.8
                            AAA_24  81 claevirqnekaeskedkgdgkGyge 106
                                       c a++++++ + ++++ k ++++y +
  gi|386000991|ref|YP_005919290.1| 152 CGADLYQRADD-TEETVKERLQAYHA 176
                                       66666666666.55556666666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011      0.14      14      42 ..       3      34 ..       1     122 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEEESTTSSHHHHHHHHTTSS--...SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkp...teGei 42
                                      ++++G+ G+GK t +k++a ++       G+i
  gi|386000991|ref|YP_005919290.1|  3 IVLLGPPGSGKGTQAKMIADKYGVvhiSTGDI 34
                                      789***************98874433355555 PP

>> Pox_A3L  Poxvirus A3L Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.32       2      36 ..     136     173 ..     135     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                           Pox_A3L   2 YkveLdppr...rCskCaanlveylkeDretikmiles 36 
                                       Y+v+ +pp+   +C +C a+l++   + +et+k  l++
  gi|386000991|ref|YP_005919290.1| 136 YHVQFNPPKvagKCDACGADLYQRADDTEETVKERLQA 173
                                       9*******98889***********99999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1599.30
//
Query:       gi|386000992|ref|YP_005919291.1|  [L=241]
Description: Uridylate kinase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-28   98.3   5.2    6.2e-27   94.7   5.2    1.9  1  AA_kinase       Amino acid kinase family
  ------ inclusion threshold ------
       0.11   12.9   2.2       0.21   12.0   2.1    1.5  1  K-cyclin_vir_C  K cyclin, C terminal


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   5.2   6.9e-31   6.2e-27       1     240 [.      20     219 ..      20     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 6.9e-31
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHH CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeageva 77 
                                       +++V  lGGs+l+  +++sl+ +a  +++l  +++++ vV+Ggg+++++++a+++ l ++e+         +     
  gi|386000992|ref|YP_005919291.1|  20 MILVYSLGGSILAGRDAESLKGYAHALKEL-AEEHQVFVVVGGGKIAREYIAKARALAASEAF--------C----- 82 
                                       689**********888899***********.9999******************6666666664........3..... PP

                                       HHHHHHHHHHHHHHHHHHTTH..GEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHH.HTT-EEEEESEEEEET CS
                         AA_kinase  78 trdalaslgerlvaallaagl..pavglsaaaldateagrdegsdgnvesvdaeaieell.eagvvpvltgfiglde 151
                                         d+l++ +++++a+ll a+l  +a + +a+++                       + +  + g+++vl+g++    
  gi|386000992|ref|YP_005919291.1|  83 --DLLGIGATKMNAMLLIAALgrAAAPEPAESYA---------------------GALSAsAGGKIVVLGGMA---- 132
                                       ..9******************5333333333332.....................223331457********9.... PP

                                       TTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHH CS
                         AA_kinase 152 egelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaa 226
                                       +g+    ++D +aallAe++gAd+li++t+V+GVy+adp ++p a+++++++++++     + e+  g+  +++p a
  gi|386000992|ref|YP_005919291.1| 133 PGQ----TTDAVAALLAEYVGADRLIVATSVEGVYSADPEIDPGAKKFDKMTAKDLVRlaMETEMKAGSRSPVDPLA 205
                                       999....9********************************************************************* PP

                                       HHHHHCTT-EEEEE CS
                         AA_kinase 227 laaarrggipvvIt 240
                                       +++++r++ip+ ++
  gi|386000992|ref|YP_005919291.1| 206 AKILERSRIPAAVV 219
                                       **********9875 PP

>> K-cyclin_vir_C  K cyclin, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   2.3e-05      0.21      46      98 ..     114     165 ..      96     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                    K-cyclin_vir_C  46 PaslvaaagcallvlaaviPqdahsggvvprlaeilGvdvavlaaavesvlts 98 
                                         +l a+ag  ++vl+ ++P ++ + +v   lae +G d  ++a++ve v ++
  gi|386000992|ref|YP_005919291.1| 114 AGALSASAGGKIVVLGGMAPGQT-TDAVAALLAEYVGADRLIVATSVEGVYSA 165
                                       55677899**************9.899*********************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1887.68
//
Query:       gi|386000993|ref|YP_005919292.1|  [L=274]
Description: Putative signal transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-26   91.8   0.0    2.6e-26   91.1   0.0    1.4  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
    1.8e-10   41.1   1.1    0.00014   22.3   0.1    3.0  3  CBS           CBS domain
    9.4e-06   25.9   0.0    2.1e-05   24.8   0.0    1.6  1  Rrf2          Transcriptional regulator
    3.9e-05   23.5   0.0    8.1e-05   22.5   0.0    1.5  1  HTH_11        HTH domain


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   5.9e-30   2.6e-26      17      77 ..       2      62 ..       1      64 [. 0.95

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 5.9e-30
                      HrcA_DNA-bdg 17 yrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqt 77
                                      +r+++ravKgeeiA++++rn+Gt+RNq+qsLkal LvegvpGPkGGYk  ++ayea++++ 
  gi|386000993|ref|YP_005919292.1|  2 QRREGRAVKGEEIADIIDRNPGTIRNQMQSLKALHLVEGVPGPKGGYKAIAAAYEAINLDA 62
                                      6899*****************************************************9875 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.6   7.3e+03      41      50 ..     127     136 ..     123     136 .. 0.71
   2 !   16.5   0.0   1.9e-06    0.0084       6      54 ..     161     208 ..     154     211 .. 0.83
   3 !   22.3   0.1     3e-08   0.00014       5      55 ..     222     271 ..     214     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                                       BEEEEEEHHH CS
                               CBS  41 klvGivtlrD 50 
                                       ++ G+vt rD
  gi|386000993|ref|YP_005919292.1| 127 HIKGVVTGRD 136
                                       4899*99777 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.9e-06
                                       BSSCEEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   6 trdvvtvppdttleealelmrekg..vsrlPVVdedgklvGivtlrDllra 54 
                                        r+ +t++p+ +l ea  ++  ++    r   V ++g+  G+++l+ ++r 
  gi|386000993|ref|YP_005919292.1| 161 ARPAITIDPEISLLEACSKL--HHlkA-RAALVGKNGNRSGVISLENIVRG 208
                                       57889***************..88433.5558899**999*******9986 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 3e-08
                                       SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       m rd++tv  d++l+ a+ ++ e+g s++ VV e++ + G++  rDl+r +
  gi|386000993|ref|YP_005919292.1| 222 MERDYPTVEGDEPLHVAISKLGETGASQV-VVTESDVPFGMLDARDLIRCM 271
                                       99*******************999999**.8889**999*********965 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.7e-09   2.1e-05      20      76 ..       3      60 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.7e-09
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE.ESSHCCCSBH CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr.LakppeeItl 76
                                      ++e++ v+ eeia+  + +p  ++  ++ L+   lv+ v G++GGy+ +a + e I+l
  gi|386000993|ref|YP_005919292.1|  3 RREGRAVKGEEIADIIDRNPGTIRNQMQSLKALHLVEGVPGPKGGYKaIAAAYEAINL 60
                                      345566****************************************735666666665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.8e-08   8.1e-05      14      55 .]       6      49 ..       2      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.8e-08
                            HTH_11 14 gp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                      g  + gee+A+ +++   t+r+ +++L++l   +e++pg+  GY+
  gi|386000993|ref|YP_005919292.1|  6 GRaVKGEEIADIIDRNPGTIRNQMQSLKAL-HLVEGVPGPkgGYK 49
                                      4449**************************.5*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 2249.49
//
Query:       gi|386000994|ref|YP_005919293.1|  [L=425]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-21   76.8   0.0    4.6e-21   75.9   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    7.2e-09   36.0   0.2    1.4e-08   35.1   0.2    1.5  1  SPASM        Iron-sulfur cluster-binding domain
     0.0025   18.1   0.0     0.0041   17.4   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.18   11.9   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
       0.15   12.3   0.0       0.48   10.7   0.0    1.9  1  Chorion_S16  Chorion protein S16


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   1.3e-24   4.6e-21       1     166 [.     105     259 ..     105     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.3e-24
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       +++t+ C++rC +Ca p      gr++ l vee+++ v ++  + g+  vi+ ggep+ y+++ +l+++  ++    
  gi|386000994|ref|YP_005919293.1| 105 ISITEECPNRCLHCALPD----SGRHHRLEVEEVEDVVSQV-LDLGTTLVIFDGGEPTTYRELPDLVRAVDER---A 173
                                       67999************6....7******************.8********************9999999998...8 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                       +++ +++ ++   e+ ++ l+++g+  v+++l++a +   +++m+ r + f + ++a+e + +ag+   vd + +l+
  gi|386000994|ref|YP_005919293.1| 174 VSTIFTSGAGFT-ERLARNLKDAGLYAVNVSLDSAAEA-EHDRMRgRAGAFRDAMRAVEEALAAGLL--VDLYAVLR 246
                                       999999999997.*************************.5555555******************999..9******* PP

                                       TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleellel 166
                                         n +e+e++ +l
  gi|386000994|ref|YP_005919293.1| 247 RDNVSEIEAFHRL 259
                                       *******998776 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   3.9e-12   1.4e-08       1      46 [.     319     358 ..     319     377 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.9e-12
                             SPASM   1 CfapsrslfInsdGdVvpC.cvdkktyveelklGnireesleeIwns 46 
                                       Cfa+++ + I+++GdV+pC c+       + ++Gn+r+es++ Iw+ 
  gi|386000994|ref|YP_005919293.1| 319 CFAGRSWMHITPEGDVYPCaCL-------PKVVGNVRKESVKRIWRR 358
                                       9******************444.......49**************75 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0041      13     132 ..     109     217 ..      96     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                       + C+ +C  C   ++ +  +++  + e  e ++ ++ +   + +++ GGEP     +++l +lv+ v e+++  + +
  gi|386000994|ref|YP_005919293.1| 109 EECPNRCLHC---ALPDSGRHHRLEVEEVEDVVSQVLDLGTTLVIFDGGEPTT---YRELPDLVRAVDERAV--STI 177
                                       5677777775...588999999999888889999999****************...999************9..466 PP

                           Fer4_12  90 lytgytleelskkekeellkeidvlvdGkfeesledeslrfrg 132
                                        ++g  + e +++   +l +    +v + ++ + e e+ r+rg
  gi|386000994|ref|YP_005919293.1| 178 FTSGAGFTERLAR---NLKDAGLYAVNVSLDSAAEAEHDRMRG 217
                                       6777777777644...322333346666666666666666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.1e-05      0.18       5      77 ..     108     172 ..     105     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                           Fer4_14   5 lsgCnlsCkgCdnketwks.elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       +  C+  C  C   ++ +  +l+ +++e++++q+l      +     + + GGeP  y + ++l   v+ + e+
  gi|386000994|ref|YP_005919293.1| 108 TEECPNRCLHCALPDSGRHhRLEVEEVEDVVSQVL------DLGTTLVIFDGGEPTTYRELPDL---VRAVDER 172
                                       568********966643330444444444444444......3444557889*****99665555...5555544 PP

>> Chorion_S16  Chorion protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.48      43      75 ..     277     309 ..     250     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                       Chorion_S16  43 nrygweqgrpllakpygpldklyaaalpprsfv 75 
                                        r+  e g  l +  y  ld++ +aa ppr+f 
  gi|386000994|ref|YP_005919293.1| 277 GRWSEEVGSILSVEDYAALDEFVSAAPPPRTFS 309
                                       5778899999*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2936.59
//
Query:       gi|386000995|ref|YP_005919294.1|  [L=115]
Description: phosphoribosyl-AMP cyclohydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-36  123.8   0.1    2.1e-36  123.6   0.1    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.1   1.2e-40   2.1e-36       1      74 []      22      95 ..      22      95 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 1.2e-40
                                      EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH  1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74
                                      mlaymn+eal+ktletgka+y+Srsr klW KGe+Sg++q+v+e r+DcD Da+llkv+q g aCHtg++sCFy
  gi|386000995|ref|YP_005919294.1| 22 MLAYMNREALAKTLETGKAHYWSRSRGKLWLKGESSGHFQRVVEARIDCDLDAILLKVDQLGGACHTGYRSCFY 95
                                      9************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 788.15
//
Query:       gi|386000996|ref|YP_005919295.1|  [L=415]
Description: hypothetical protein Mhar_0284 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-81  272.9   0.0    3.2e-71  240.3   0.0    2.1  2  Nre_N     Archaeal Nre, N-terminal
    2.1e-37  127.4   0.1    3.2e-37  126.8   0.1    1.3  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.4e-11     3e-07      25      56 ..       9      40 ..       2      53 .. 0.88
   2 !  240.3   0.0   3.6e-75   3.2e-71      58     270 .]      84     295 ..      72     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.4e-11
                             Nre_N 25 skeleGsspPsvfVGrygYPkVsvgplvppve 56
                                      +++leG spP+vfVGr gYP+Vs+gpl+p + 
  gi|386000996|ref|YP_005919295.1|  9 GTTLEGPSPPEVFVGRFGYPRVSAGPLLPAQG 40
                                      5789***********************99865 PP

  == domain 2  score: 240.3 bits;  conditional E-value: 3.6e-75
                             Nre_N  58 dasvldspekwlglslediiklrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdev 133
                                       ++s + +p++++++ + di++lr+s+vr++++v+v +ak + klle  qe+a+s++pv++ev+++k+p+ +l+fd++
  gi|386000996|ref|YP_005919295.1|  84 SPSLFTRPAELAEMGVGDIVALRSSMVRSSTRVEVWDAKnPGKLLEMAQEIAISSTPVETEVTFAKPPRGRLRFDGF 160
                                       5788999******************************9989999********************************* PP

                             Nre_N 134 laPvGpsaeleklkvaenpkvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsI 210
                                       + P Gp +++e++++++np+vprkv+++v Dtdl A+ av eL+++gv+v+ i+rlLS+GlLG+  +r+lVPTrWsI
  gi|386000996|ref|YP_005919295.1| 161 MMPSGPVGTVEEMEIISNPTVPRKVDEVVGDTDLLATAAVGELFEAGVEVDGISRLLSLGLLGK--NRKLVPTRWSI 235
                                       ***************************************************************8..*********** PP

                             Nre_N 211 TAvddivgkelkkeikdlpeidevevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       TA ddi gk+l+  i+d p++ ++ +fsge l N+f ++LaPg++++el+E+w p+s+w+
  gi|386000996|ref|YP_005919295.1| 236 TASDDIAGKHLAAAIQDDPPVGDYLLFSGERLANHFEILLAPGSFTYELIEIWLPRSVWS 295
                                       ***********************************************************6 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.1   3.5e-41   3.2e-37       4     110 .]     309     414 ..     306     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 3.5e-41
                             Nre_C   4 egrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeev 80 
                                         +k+ys++aG+Yyaarlavle L++++rq+ ++ +reit+eYwaP+GvW+vRea+r+al+++p++fe+le+al+e+
  gi|386000996|ref|YP_005919295.1| 309 GPKKGYSDLAGGYYAARLAVLERLADMRRQSAILAVREITEEYWAPLGVWVVREAARAALAGEPRSFETLEAALAEM 385
                                       6799************************************************************************* PP

                             Nre_C  81 seklklplkkllkkskllkelkkqktLddF 110
                                       +++l++p+++++ +s+l+++   q+tL +F
  gi|386000996|ref|YP_005919295.1| 386 ATRLRTPAREWRPHSELARGA-GQTTLARF 414
                                       ********************9.89999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2704.86
//
Query:       gi|386000997|ref|YP_005919296.1|  [L=58]
Description: hypothetical protein Mhar_0285 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 386.92
//
Query:       gi|386000998|ref|YP_005919297.1|  [L=194]
Description: Heat shock protein Hsp20 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-11   44.0   0.6    8.3e-10   38.7   0.6    2.2  1  HSP20       Hsp20/alpha crystallin family
    7.8e-07   28.6   0.0    1.2e-06   28.0   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
  ------ inclusion threshold ------
      0.016   16.2   0.1      0.023   15.7   0.1    1.2  1  CS          CS domain
      0.018   15.4   0.0      0.028   14.8   0.0    1.2  1  PIH1_CS     PIH1 CS-like domain
       0.12   12.9   0.2       0.35   11.3   0.2    1.9  1  HMA         Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.6   2.3e-13   8.3e-10       1      99 [.     110     193 ..     110     194 .] 0.91

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.3e-13
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       d++e+ + +++ +++pg++ke++k++ ++++v ++ + e               +kF ++++L  +vd+d+ kas+k
  gi|386000998|ref|YP_005919297.1| 110 DVMEDGDLYKIFAELPGVEKENIKLDSTERSVRIETTGE---------------KKFAKTIALDAEVDPDSAKASYK 171
                                       67899999**************************99999...............69********************* PP

                                       TTEEEEEEEBSS--..------ CS
                             HSP20  78 dGvLtvtvpkkepekkkkerki 99 
                                       +GvL+++++kk +++k ke+ki
  gi|386000998|ref|YP_005919297.1| 172 NGVLSIELEKKLKAEKGKEIKI 193
                                       ***********99976555555 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   3.2e-10   1.2e-06       2      63 .]     116     179 ..     115     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.2e-10
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig...nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       d y++ ++LP+v+ke+i+l  ++    I+     +f ++i+L   ++ + + +A++++gvL I++
  gi|386000998|ref|YP_005919297.1| 116 DLYKIFAELPGVEKENIKLDSTERSVRIETTgekKFAKTIALDAEVDPDSA-KASYKNGVLSIEL 179
                                       5688999******************99999888899999**********77.***********86 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.1   6.3e-06     0.023      14      76 .]     120     181 ..     113     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.3e-06
                                       EEEE-TTCTTTTTCEEEEEETTEEEEEE.TSCEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS  14 vtiyvkkvnikkkdvkvefkerslkvki.gkeklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       +  ++++v  +k+++k++ +ers++++  g++k+ +   L +++dp++++ + ++  + i L+K
  gi|386000998|ref|YP_005919297.1| 120 IFAELPGV--EKENIKLDSTERSVRIETtGEKKFAKTIALDAEVDPDSAKASYKNGVLSIELEK 181
                                       55667777..******************76678888888**********************999 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.7e-06     0.028      34      87 ..     119     172 ..     115     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
                           PIH1_CS  34 aieielPllksikevklrvgerrleleskk.akyfLslkLpYpvdedkveAkFvk 87 
                                       +i  elP++ + +++kl+ +er++ +e+ + +k+  ++ L+ +vd d+++A +++
  gi|386000998|ref|YP_005919297.1| 119 KIFAELPGV-EKENIKLDSTERSVRIETTGeKKFAKTIALDAEVDPDSAKASYKN 172
                                       566689999.7899*************9998899999**************9964 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   9.9e-05      0.35      19      56 ..     120     155 ..     115     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                               HMA  19 vLselpgV..esvkvdlatktvtVegdaestklrkiieai 56 
                                        ++elpgV  e++k+d  +++v +e++ e+ k+    ++i
  gi|386000998|ref|YP_005919297.1| 120 IFAELPGVekENIKLDSTERSVRIETTGEK-KF---AKTI 155
                                       578*****999999***************8.44...4433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 1392.92
//
Query:       gi|386000999|ref|YP_005919298.1|  [L=81]
Description: Putative transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.017   15.0   0.0    1.2  1  MarR      MarR family
      0.033   14.2   0.0       0.04   13.9   0.0    1.2  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.9e-06     0.017       4      48 ..      14      58 ..      12      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +++++L+i++++gp+   + ak+  ++ + v r+l +   kGl++
  gi|386000999|ref|YP_005919298.1| 14 QRIKVLEIIESKGPQPADKVAKFGRLTGPVVGRALEEVAGKGLLR 58
                                      6789**************************************986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.5e-06      0.04      11      71 ..      18      79 ..      13      81 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-06
                            HTH_45 11 ILeais.egeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklke 71
                                      +Le+i+ +g +   k+ +   L+  ++ + L+    kgl++++++ ++ T+ G el ++lk+
  gi|386000999|ref|YP_005919298.1| 18 VLEIIEsKGPQPADKVAKFGRLTGPVVGRALEEVAGKGLLREKGGVWEFTDLGVELSKELKK 79
                                      6777764555666677777778888889999***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 597.35
//
Query:       gi|386001000|ref|YP_005919299.1|  [L=170]
Description: Nitroreductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-37  127.1   2.6    1.8e-19   70.5   0.3    2.0  2  Nitroreductase  Nitroreductase family
    6.8e-23   81.4   0.0    2.7e-11   43.5   0.0    3.1  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.3     2e-23   1.8e-19       1      66 [.       7      72 ..       7      73 .. 0.95
   2 !   60.5   0.1   2.2e-20     2e-16      83     170 .]      65     147 ..      63     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2e-23
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHT CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaea 66
                                      i+kRrSiRk+  ++v+ ++l+++lea+r aPsa+nlq+wrfvvv+d+  r++laeaa++++ ++ea
  gi|386001000|ref|YP_005919299.1|  7 IKKRRSIRKYLTRKVENDKLDRVLEAGRLAPSAKNLQEWRFVVVRDEGRRKRLAEAAKGQTFVGEA 72
                                      89******************************************999999********99887765 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 2.2e-20
                                       HHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S.. CS
                    Nitroreductase  83 aqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpde 159
                                        q ++++apv+i +   +++ +++ +  ++ +  +d+++a++ ++L+A+a+Glg+c+ig+f+e++  v+k+l++p+e
  gi|386001000|ref|YP_005919299.1|  65 GQTFVGEAPVVIAA---CATVTDYVMTCGQLTYPIDLAIAVEHMVLTAAAEGLGTCWIGAFYEEE--VKKILNIPPE 136
                                       6899**********...************************************************..********** PP

                                       SEEEEEEEEE- CS
                    Nitroreductase 160 eeivvliavGy 170
                                        ++v+l+++Gy
  gi|386001000|ref|YP_005919299.1| 137 VRVVALLPLGY 147
                                       **********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   8.6e-07    0.0077       1      27 [.       2      28 ..       2      30 .. 0.90
   2 !   21.7   0.0   1.4e-08   0.00012     158     186 ..      24      52 ..      22      67 .. 0.87
   3 !   43.5   0.0     3e-15   2.7e-11      66     152 ..      82     167 ..      55     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-07
                                      -HHHHHHH--B---B--S---HHHHHH CS
                    TM1586_NiRdase  1 nlyeaiekRhsvRkYkdealeeellee 27
                                      +l eai+kR+s+RkY  +++e+++l++
  gi|386001000|ref|YP_005919299.1|  2 DLAEAIKKRRSIRKYLTRKVENDKLDR 28
                                      578******************999886 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHTS--GGG----EEE.E-S CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdd 186
                                       ++++++lea rlAPsA N q wrf ++ d
  gi|386001000|ref|YP_005919299.1|  24 DKLDRVLEAGRLAPSAKNLQEWRFVVVRD 52 
                                       68899********************8875 PP

  == domain 3  score: 43.5 bits;  conditional E-value: 3e-15
                                       SSEEEE----SSHHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----.-- CS
                    TM1586_NiRdase  66 vpnyialvgekkedleekaGYygeqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklveak 141
                                       v++y++ +g+    +   +    e++vL + a+GlgtcW+g+ y++ +k+ ++++ + ++v+++ lGy++++ +++ 
  gi|386001000|ref|YP_005919299.1|  82 VTDYVMTCGQLT--YPIDLAIAVEHMVLTAAAEGLGTCWIGAFYEEeVKKILNIPPEVRVVALLPLGYPDESPHPRP 156
                                       556666666554..334444578*********************99777889************************* PP

                                       ---HHHHBSS- CS
                    TM1586_NiRdase 142 rkpleelcevk 152
                                       rk++ e+++++
  gi|386001000|ref|YP_005919299.1| 157 RKEIGEIVAFE 167
                                       ******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1271.00
//
Query:       gi|386001001|ref|YP_005919300.1|  [L=138]
Description: Peptide methionine sulfoxide reductase msrB [Methanosaeta harundinacea 6Ac]
Scores for 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-54  183.8   0.0    1.2e-54  183.6   0.0    1.0  1  SelR            SelR domain
     0.0024   17.6   1.0      0.051   13.3   0.0    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
     0.0035   17.5   0.0     0.0061   16.8   0.0    1.4  1  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
  ------ inclusion threshold ------
       0.14   12.1   1.2        1.3    9.0   1.2    2.3  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6   0.0   2.6e-58   1.2e-54       1     121 []      11     130 ..      11     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 2.6e-58
                                       HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEEC CS
                              SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdts 77 
                                       e+k+ Lt+e+y v+r++gte+pftg+y+++k kG+y+c++cg++Lfss++kfdsg+GwpsF e+i+e+av+e++d+s
  gi|386001001|ref|YP_005919300.1|  11 EWKNLLTREEYIVTRRRGTEPPFTGKYYDFKGKGIYRCVACGNDLFSSKAKFDSGSGWPSFVEPISEDAVAEREDES 87 
                                       7**************************************************************************** PP

                                       TTSEEEEEEETTCECEEEEEECTSSSSS.SEEEEE-CCCEEEEE CS
                              SelR  78 lgmertevvcakcdahlGhvFedgpkpttgkrycinsvslkfkp 121
                                       +gm+r+ev+ca+cd+hlGhvFedgp+p tg+rycins++lkf+p
  gi|386001001|ref|YP_005919300.1|  88 YGMVRVEVICAQCDSHLGHVFEDGPPP-TGLRYCINSAALKFVP 130
                                       *************************99.5*************86 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.023     1e+02      44      51 ..      45      52 ..      37      54 .. 0.87
   2 !   13.3   0.0   1.1e-05     0.051      12      37 ..      84     109 ..      80     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.023
                    zinc_ribbon_10 44 kyrCpkCg 51
                                       yrC  Cg
  gi|386001001|ref|YP_005919300.1| 45 IYRCVACG 52
                                      6******9 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
                    zinc_ribbon_10  12 ddetsaknryalICskChshnGlapk 37 
                                       +de+  + r+ +IC +C sh G + +
  gi|386001001|ref|YP_005919300.1|  84 EDESYGMVRVEVICAQCDSHLGHVFE 109
                                       5677778899************9854 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0061       3      80 ..      46     121 ..      44     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                                       EEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCC..CC CS
                      Yippee-Mis18   3 fqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteee..lk 77 
                                       ++C  C ++l  s + +++g  +   ++++++++ v ++e ++         ++ C++C+s+lG ++++ ++   l+
  gi|386001001|ref|YP_005919300.1|  46 YRCVACGNDLFSSKAKFDSGSGWPS-FVEPISEDAVAEREDESY---GMVRVEVICAQCDSHLGHVFEDGPPPtgLR 118
                                       7899999999999999999999555.567777777766666666...4777899*************9987653455 PP

                                       CCC CS
                      Yippee-Mis18  78 ykr 80 
                                       y++
  gi|386001001|ref|YP_005919300.1| 119 YCI 121
                                       554 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.2   0.00029       1.3       4      34 ..      45     104 ..      45     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                    Zn_ribbon_SprT   4 vYrCtgCgreythhlsirrhn................................YrCrrCkgtL 34 
                                       +YrC+ Cg   +  +s++                                    +C +C ++L
  gi|386001001|ref|YP_005919300.1|  45 IYRCVACG---NDLFSSKAKFdsgsgwpsfvepisedavaeredesygmvrveVICAQCDSHL 104
                                       6*******...7777777666666666666666666666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1057.49
//
Query:       gi|386001002|ref|YP_005919301.1|  [L=298]
Description: Putative methanogenesis marker protein 8 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-86  287.8   0.1    6.9e-86  287.6   0.1    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.6   0.1   3.8e-90   6.9e-86       1     256 [.       4     264 ..       4     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 287.6 bits;  conditional E-value: 3.8e-90
                           DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGa 77 
                                       H++e++g+  v+v+dg+++ +++pk+++CPl + l+g    ++++++++++ ++ e+G++ ++R+le +++ vsfGa
  gi|386001002|ref|YP_005919301.1|   4 HMLEMAGA-LVRVRDGEIEVLTDPKVRWCPLRSGLYGHGVESRKTVESVLRGHMVELGMYGPHRVLELSDRPVSFGA 79 
                                       9*****98.9******************************************************************* PP

                           DUF2099  78 sEilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveG 154
                                       sE++++a+++gl+daav+vc+gaGtv++++pe+v +lg++++Gl++TePiee+++ ++e+g+i+ld++ ++idqveG
  gi|386001002|ref|YP_005919301.1|  80 SEMIADAMRSGLVDAAVVVCEGAGTVVAARPEVVAALGAHMTGLIRTEPIEEIQAGLRERGCILLDDR-GSIDQVEG 155
                                       *****************************************************************988.9******* PP

                           DUF2099 155 vkkAiekgykkiavtvae..aedakklrelek.....eegvkilifavhttgiskeeaeelveaaDlvtacAskeir 224
                                       +++A+++gy++i+vt++   a +a ++r+l++     ++g   +ifavh+  + +++ae l+e++D+v++cAs+e+r
  gi|386001002|ref|YP_005919301.1| 156 YRRALAAGYQRIVVTITGkrAFEAGEIRKLSSasacgQAGEGPVIFAVHNLDVAEDQAEVLAETCDVVWGCASREVR 232
                                       ****************996677899*****9999999999************************************* PP

                           DUF2099 225 eivkkkallqvgksvpvfaltekGkelilerl 256
                                       e+v+k+a+lq+g s+pv+alt++Gk+l+l+r+
  gi|386001002|ref|YP_005919301.1| 233 EVVGKRAKLQIGISIPVYALTDSGKRLVLNRA 264
                                       *****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1994.61
//
Query:       gi|386001003|ref|YP_005919302.1|  [L=357]
Description: Archaeal sugar kinase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-06   26.8   0.1    8.9e-06   25.9   0.1    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1     5e-10   8.9e-06      12      66 .]     130     193 ..     126     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5e-10
                                       SSSCHHHHHHHHHHHHHHHHTTEHH.HH.......HHHHHHHH.HHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N  12 aGLGSSAAlavalvaAllallglsl.ee.......aklaleae.rlaqggngsggDvaasvyGg 66 
                                        GLGS +++ val+ A++++lg +l ++       ++   e e   + +g   g+  aa++yGg
  gi|386001003|ref|YP_005919302.1| 130 VGLGSTGSVLVALANAMNEALGGPLtKDeirlligNNYVEETEdGRVTLGFETGVGPAAVTYGG 193
                                       6*********************998744589999999999999899999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2632.70
//
Query:       gi|386001004|ref|YP_005919303.1|  [L=596]
Description: ATP-dependent OLD family endonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-35  123.0   0.4    1.5e-34  120.4   0.0    2.2  2  AAA_15    AAA ATPase domain
    5.1e-20   72.1   0.2    1.2e-10   41.3   0.1    2.4  2  DUF2813   Protein of unknown function (DUF2813)
    2.9e-17   63.5   2.6    3.5e-15   56.6   2.6    2.4  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    4.7e-09   37.0   0.9    6.8e-09   36.5   0.1    1.8  2  AAA_23    AAA domain
    1.2e-06   28.2   0.0    5.8e-06   25.9   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0006   19.5   0.0     0.0013   18.4   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.061   13.4   0.0       0.15   12.1   0.0    1.8  1  MMR_HSR1  50S ribosome-binding GTPase
        0.1   12.2   0.0       0.22   11.1   0.0    1.5  1  AAA_27    AAA domain
       0.15   12.5   0.0        0.4   11.2   0.0    1.7  1  ABC_tran  ABC transporter


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   7.4e-38   1.5e-34       2     369 .]      11     354 ..      11     354 .. 0.72
   2 ?   -3.5   0.1       3.1   6.2e+03     166     167 ..     540     541 ..     497     581 .. 0.47

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 7.4e-38
                            AAA_15   2 kIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnk.ekkn..kkvikiekedleifenisesk 75 
                                       kI++++i+NFRslk+v+++l+  ltv+iG+Nn+GK+s+l+al  F      ++n  ++ i++++++++  ++++  +
  gi|386001004|ref|YP_005919303.1|  11 KIEEVRIRNFRSLKEVDVKLDW-LTVIIGENNAGKTSFLDAL--FVAIGaGRHNisSDDIFLAQSETKAPKEREVII 84 
                                       89********************.*******************..555331344444445555555555555555555 PP

                            AAA_15  76 dikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks.....kkel 147
                                       d+ I+                                ++  ++i  +   ++++el+ e is +++ +     + + 
  gi|386001004|ref|YP_005919303.1|  85 DLLIRPI------------------------------DKGGNIIDIFPEGCYWIELYGEGISQDDDGNefvaiRTQM 131
                                       5555555..............................5677889999999999999999999999999988885555 PP

                            AAA_15 148 pkekeeklekekeelkid.kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklke 223
                                        + ++e   + + ++  d ++ ++  ++k + s+++++        +   l+l  akR++++e+    +s+  kl++
  gi|386001004|ref|YP_005919303.1| 132 RWDSTEGGYEVERKFLADwQDPNRLNLSKVKGSVSSYQ-------IKPLALYLLDAKRDIKEEFQSR-NSFWYKLIS 200
                                       55555555555555555567777777777888888777.......8888899999999999988777.777778888 PP

                            AAA_15 224 kileealqekl...........eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik.. 287
                                       ++  e+++              +++    l ++qe l++++k+++ + +++ + +i              +++++  
  gi|386001004|ref|YP_005919303.1| 201 DLGLENGKITEieaelgrinegIISGSGVLGHLQEHLNDLYKTIGGDSESVSITPIPR-----------HLRDLSkg 266
                                       7776666522234444444444444445555555555555555555555444444444...........44444455 PP

                            AAA_15 288 ........ddeelplnknGsGvqrllllillileaekk..dekeeknvilliEEPEahLHpqaqkvlikllkeland 354
                                                 +++pl++ G G+++l  ++++++++  k  +++++    l++EEPE hLHpqaq+ l+ ++ e+   
  gi|386001004|ref|YP_005919303.1| 267 vdvnystkGAQSFPLSRHGMGTRSLAAVLTFRAYMTWKqrNSNDNIHPMLALEEPESHLHPQAQRALFSQIEEIPG- 342
                                       5555556699**************************9964555555669*********************999965. PP

                            AAA_15 355 nktQviitTHSphii 369
                                          Q ii+THSp+i+
  gi|386001004|ref|YP_005919303.1| 343 ---QRIISTHSPYIA 354
                                       ...55********96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.1
                            AAA_15 166 ke 167
                                        +
  gi|386001004|ref|YP_005919303.1| 540 TN 541
                                       11 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   4.9e-10   9.8e-07       3      70 ..      12      77 ..      10      91 .. 0.80
   2 !   41.3   0.1   5.8e-14   1.2e-10     264     366 ..     294     395 ..     277     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.9e-10
                           DUF2813  3 LerieisGFRGinrLSlsleentvLiGENaWGKSSLldALslilnvekelyqFtlkDFhvdeseeeeq 70
                                      +e++ i  FR ++   ++l+ +tv+iGEN  GK S ldAL +++ +    ++ +++D ++ +se++  
  gi|386001004|ref|YP_005919303.1| 12 IEEVRIRNFRSLKEVDVKLDWLTVIIGENNAGKTSFLDALFVAIGAG--RHNISSDDIFLAQSETKAP 77
                                      578999**********************************9987765..5788888877766555443 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 5.8e-14
                           DUF2813 264 lgllatllqakgkvelkriarPilllEdpearLHPtmlaiaWellellPlQkiltTNSveLlsqvplesirrLvRes 340
                                       + ++ ++++ k++++ +   +P+l lE+pe++LHP+    +++ +e +P Q+i++T S  + +q+++++ r   +  
  gi|386001004|ref|YP_005919303.1| 294 VLTFRAYMTWKQRNS-NDNIHPMLALEEPESHLHPQAQRALFSQIEEIPGQRIISTHSPYIAGQTDVSKFRHFRKVG 369
                                       456788999998887.66678****************************************************999* PP

                           DUF2813 341 drtqayslerkslskedlRriaFHir 366
                                       ++t ++++  ++l ++d+ +i   + 
  gi|386001004|ref|YP_005919303.1| 370 ENTMVTQMDTSELEADDIHKIDRMVM 395
                                       *******************9976555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   2.6   1.8e-18   3.5e-15       1     301 [.      33     353 ..      33     354 .. 0.58

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.8e-18
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl.....drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72 
                                       l+v+iG N++GK+++Ldal ++ ++      +d ++l  ++++  ++r+++  l  + +++ +++ ++ f++ +   
  gi|386001004|ref|YP_005919303.1|  33 LTVIIGENNAGKTSFLDALFVAIGAgrhniSSDDIFLAQSETKAPKEREVIIDLLIRPIDKGGNIIDI-FPEGCYW- 107
                                       79*****************7775555555522222222222222244444444444444444444444.4444444. PP

                            AAA_21  73 ryglrlersqv...eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltd 146
                                                 +   +e +s+ +++ e   ++     +++   + ++r + +++++  + +ls+       +g++  +
  gi|386001004|ref|YP_005919303.1| 108 ----------IelyGEGISQDDDGNEFVAIRTQMRWDSTEGGYEVERKFLADWQDPNRLNLSK------VKGSVSSY 168
                                       ..........44555555555566666666666666666666666666666666666666554......33444444 PP

                            AAA_21 147 itsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.... 219
                                        +++++ +ll+       r    +++ ++ +++k++  l+   +++ ++e+el  ++eg+ +   v   l+e     
  gi|386001004|ref|YP_005919303.1| 169 QIKPLALYLLDAK-----RDIKEEFQSRNSFWYKLISDLGLENGKITEIEAELGRINEGIISGSGVLGHLQEHlndl 240
                                       4444444444433.....33334444444444444444444444444444444444444433333333333334455 PP

                            AAA_21 220 ..........................gvvflengdgqelparelSdGtkrllallt....allralkkg....slll 262
                                                                   v +  ++ q +p++  ++Gt++l+a+lt    + + ++ ++    + l+
  gi|386001004|ref|YP_005919303.1| 241 yktiggdsesvsitpiprhlrdlskgVDVNYSTKGAQSFPLSRHGMGTRSLAAVLTfrayMTWKQRNSNdnihPMLA 317
                                       55566666666777788889999987777888899999999999*******8555511113444444448******* PP

                            AAA_21 263 iDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                       ++EpE++LHP+++r l+  ++e      Q i++THSp++
  gi|386001004|ref|YP_005919303.1| 318 LEEPESHLHPQAQRALFSQIEEIPG---QRIISTHSPYI 353
                                       *****************99988866...*********97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   3.4e-12   6.8e-09       2      85 ..      15      94 ..      14     242 .. 0.64
   2 ?   -3.3   0.1       5.5   1.1e+04     150     150 ..     531     531 ..     468     567 .. 0.53

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.4e-12
                            AAA_23  2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfe 80
                                      ++i+nfrs++++++ ++  lt+I+G+N aGKT++ldA+  a +   ++ s+++   ++ +  e +  ++ + +++l ++
  gi|386001004|ref|YP_005919303.1| 15 VRIRNFRSLKEVDVKLD-WLTVIIGENNAGKTSFLDALFVAIGAGRHNISSDD---IFLAQSETKAPKEREVIIDLLIR 89
                                      79**************9.9***********************98666665543...33333332233333333555444 PP

                            AAA_23 81 nkdgr 85
                                       +d++
  gi|386001004|ref|YP_005919303.1| 90 PIDKG 94
                                      44443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.5
                            AAA_23 150 d 150
                                       +
  gi|386001004|ref|YP_005919303.1| 531 A 531
                                       1 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.9e-09   5.8e-06       2      49 ..      12      56 ..      11      85 .. 0.80
   2 ?   -1.3   0.0      0.62   1.2e+03     158     201 ..     312     353 ..     287     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                                      EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLG 49
                                      +++++i+nF+s+  k+v+++++  +t+i+G+N +GK+++ldA+   +G
  gi|386001004|ref|YP_005919303.1| 12 IEEVRIRNFRSL--KEVDVKLDW-LTVIIGENNAGKTSFLDALFVAIG 56
                                      899*********..577777776.89*****************44556 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.62
                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkeksknaQfivislreem 201
                                        +p+  l e +++L  +  +++ + ++e     Q i+ +++  +
  gi|386001004|ref|YP_005919303.1| 312 IHPMLALEEPESHLHPQAQRALFSQIEEIP--GQRIISTHSPYI 353
                                       5799999999****9999999999999988..999999998665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.5e-07    0.0013       8      47 ..      19      56 ..      12      66 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.5e-07
                            AAA_29  8 NWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                      N  ++  ++++++l+  t+++G++ +GK+++lDA+ + + 
  gi|386001004|ref|YP_005919303.1| 19 NFRSL--KEVDVKLDWLTVIIGENNAGKTSFLDALFVAIG 56
                                      44444..44555544689****************976554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.5e-05      0.15       3      28 ..      35      65 ..      33     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.5e-05
                                      EEEESTTSSHHHHHHHHH.....TSTEEESS CS
                          MMR_HSR1  3 aivGrpNvGKStLinalt.....gekaivsd 28
                                      +i+G  N+GK++++ al+     g++ i sd
  gi|386001004|ref|YP_005919303.1| 35 VIIGENNAGKTSFLDALFvaigaGRHNISSD 65
                                      79***************83333223344444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.22      11      46 ..      20      51 ..      10      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                            AAA_27 11 yGkftdrsldfsaeeadlhliyGpNEAGKstalrAi 46
                                      + ++++  ++++     l++i+G N AGK++ l+A+
  gi|386001004|ref|YP_005919303.1| 20 FRSLKEVDVKLD----WLTVIIGENNAGKTSFLDAL 51
                                      555555555554....79***************997 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002       0.4       6      34 ..      26      54 ..      23      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                      EEEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStLlkllagl 34
                                      +++k + +++i+Gen aGK+++l +l   
  gi|386001004|ref|YP_005919303.1| 26 VDVKLDWLTVIIGENNAGKTSFLDALFVA 54
                                      67888999***************999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 4193.60
//
Query:       gi|386001005|ref|YP_005919304.1|  [L=633]
Description: UvrD/REP helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-57  194.1   0.1    1.3e-56  192.5   0.1    1.8  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.2e-32  113.7   0.0      5e-31  108.4   0.0    2.5  2  UvrD_C           UvrD-like helicase C-terminal domain
    1.9e-30  106.1   0.0    4.5e-30  104.9   0.0    1.6  2  AAA_19           AAA domain
    2.4e-08   34.5   1.1    0.00023   21.6   0.0    3.3  2  AAA_16           AAA ATPase domain
    4.1e-08   32.9   0.1    1.4e-07   31.2   0.1    1.9  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    4.4e-08   33.1   0.0    1.8e-05   24.5   0.0    2.4  2  AAA_30           AAA domain
    2.7e-06   27.3   0.0       0.72    9.5   0.0    3.4  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    9.5e-05   22.3   0.0     0.0015   18.3   0.0    2.2  2  AAA_11           AAA domain
     0.0095   14.7   0.0      0.017   13.9   0.0    1.4  1  SNF2_N           SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.037   14.3   0.1       0.86    9.9   0.0    2.9  2  AAA_22           AAA domain
      0.038   13.9   0.0       0.18   11.7   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
      0.062   13.3   0.0       0.17   11.8   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
      0.072   12.3   0.1         16    4.6   0.0    3.2  3  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.086   12.8   0.0       0.75    9.8   0.0    2.1  2  Flavi_DEAD       Flavivirus DEAD domain


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.5   0.1     1e-59   1.3e-56       2     314 ..       6     271 ..       5     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 1e-59
                                       SHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT CS
                     UvrD-helicase   2 npeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessd 78 
                                       ++ qr+++++ +gp+lv+A++GsGKT+vl+er+ rl++e  +   ril++TFTnkAa+E+keR+ e+ + +      
  gi|386001005|ref|YP_005919304.1|   6 SETQRKIVEHGEGPLLVVAGPGSGKTRVLTERVRRLLNED-TGHFRILALTFTNKAANEMKERLSEIPNIE------ 75 
                                       689************************************9.*************************86554...... PP

                                       -HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSC.HSHTTTTHHHHHH CS
                     UvrD-helicase  79 derlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkellek.saddslnldkkkl 154
                                                  ++a i+TlHsfc ++l +  + +g+d+  +i+++ +    ++q l+++ + + + + +ln+  ++ 
  gi|386001005|ref|YP_005919304.1|  76 -----------KRAFIGTLHSFCMEVLANRGKPVGIDELPNIFESYQD---RKQVLFQAAMANpYLRHKLNIILDAN 138
                                       ...........69*****************************998882...44445555554344444455544444 PP

                                       HHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCEE CS
                     UvrD-helicase 155 eklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeenalD 231
                                                           + + ++    ++s ak++++ p+  ++         +  +++++ y + ++ + a+D
  gi|386001005|ref|YP_005919304.1| 139 T-------------------QDRLLNRWLDMISSAKNNLFVPEMMDN---------ETDRQVYEAYNNGLRVSYAID 187
                                       3...................45678899999************9998.........56899**************** PP

                                       HHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHT.TTTTEEEEE-GGG--GGGGTB-THHH CS
                     UvrD-helicase 232 fsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllas.gheelfmvGDpkQsIYgFRgAdielf 307
                                       f+dll+ +++l++e +++a+++r++y++i iDE QD+n++Qy++++ l+  +h+++++vGD+kQ+I+ + gA+++ +
  gi|386001005|ref|YP_005919304.1| 188 FDDLLLLTYRLFQERPKIADFYRRQYRYICIDEGQDLNEAQYQVISALCGlEHRNVMIVGDKKQAIFVWNGANPKYL 264
                                       *************************************************835566********************** PP

                                       HHHHHHS CS
                     UvrD-helicase 308 lkkkkdf 314
                                        ++++df
  gi|386001005|ref|YP_005919304.1| 265 DQFERDF 271
                                       ***9998 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.8   3.6e+03      36      94 ..      12      70 ..       4      86 .. 0.70
   2 !  108.4   0.0   3.9e-34     5e-31       2     347 ..     277     594 ..     276     596 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.8
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 36 tvekgekivvleaeteeeEaekiaatikallekneklediavLvRsnkdadkiskaLkk 94
                                       ve ge   +  a   +  ++   + +++ll++++   +i  L+ +nk a+++++ L++
  gi|386001005|ref|YP_005919304.1| 12 IVEHGEGPLLVVAGPGSGKTRVLTERVRRLLNEDTGHFRILALTFTNKAANEMKERLSE 70
                                      55556655555555556666777778888886666666677777778888888888876 PP

  == domain 2  score: 108.4 bits;  conditional E-value: 3.9e-34
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnrralekekktvekgekivvleaeteeeEaekiaatikall.......eknek 71 
                                        ++ N+RS++ +++aa+++++++  +        +     +i+++e  +e++Ea+ + + i++ll       e  + 
  gi|386001005|ref|YP_005919304.1| 277 FMNDNFRSSQVVVNAAKSLVSEYEVE-------GQLPIAGSIELMEGIDEQHEARLVLDYIQNLLneghrdvEGPIT 346
                                       5789****************666655.......33344446************************999999888899 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                            UvrD_C  72 lediavLvRsnkdadkiskaLkkegipf.nvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlg.igka 146
                                       le++a+L R+ +    ++++L+k + p+ ++++ ++  + + i+d+   l+llan++d + ++ ++ r  ++   ++
  gi|386001005|ref|YP_005919304.1| 347 LERCALLGRNRYVLSAVEDELNKRHWPYyKQLSAQQESESSLIQDFELCLRLLANPRDRLHFSMLIARWDMReDASD 423
                                       *************************9972467799999999***********************8888766504444 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 147 tveriseelkklglsltDfikedtleygeeFieliraleeknlelllkkiektaeerqalvskyadlfkelaeklae 223
                                         +++     + gl+l   +k  t++  ++ +  i ale+ +                    + + +fk++ e l++
  gi|386001005|ref|YP_005919304.1| 424 FGQHV-----SDGLRLLSALKRRTSD-NDRLA-VILALESMDWT------------------EENFKFKNAMEYLYD 475
                                       55555.....7899999988888866.33333.23333332222..................224579999999**9 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 224 lkekseskrkkeeklenlreLysllkelekkeeeeeveeklneileiatLseseleeskkkekipiiTiHqAKGlEF 300
                                         e++es+++++  +e +r+  +  +++ + +++ +++  l+ +l + +L  +++    ++e   ++T+H+AKGlEF
  gi|386001005|ref|YP_005919304.1| 476 YSETKESQEERALIIEDIRTWQKHWNYYLR-SQPGGYH-TLTSFLGQVALGTTQQ---PRQEGLALLTVHSAKGLEF 547
                                       9999999995555*****************.5555555.5**********99998...55599************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 301 dvVflagleegtfPsyrskkekrleEEkRlfYVaiTRAkkrLfisys 347
                                       dvV+++g++egtfP yr+++   leEE+R  +Va+TR k+ L +sy 
  gi|386001005|ref|YP_005919304.1| 548 DVVVVMGMAEGTFPDYRARDGPALEEEMRDAFVAVTRSKRLLAFSYP 594
                                       ********************************************995 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   3.5e-33   4.5e-30       1     144 [.       9     255 ..       9     257 .. 0.94
   2 ?   -3.4   0.0       8.4   1.1e+04      85     108 ..     467     490 ..     431     502 .. 0.63

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 3.5e-33
                            AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.......at 70 
                                       qr++v ++ e++llv+aGpG+GKTrvl+++v+ l+++ + +  +il+++ft++Aa+e++erl+++  +       + 
  gi|386001005|ref|YP_005919304.1|   9 QRKIV-EHGEGPLLVVAGPGSGKTRVLTERVRRLLNEDTGH-FRILALTFTNKAANEMKERLSEI--PniekrafIG 81 
                                       89999.******************************99875.********************554..34589999** PP

                            AAA_19  71 TiHrlal...................................................................... 77 
                                       T+H++ +                                                                      
  gi|386001005|ref|YP_005919304.1|  82 TLHSFCMevlanrgkpvgidelpnifesyqdrkqvlfqaamanpylrhklniildantqdrllnrwldmissaknnl 158
                                       *****99********************************************************************** PP

                            AAA_19  78 ...........................ldfddlltealelle.eaeeekklqeee.llivDEfqdvdelqyrLlkal 125
                                                                  +dfddll  +  l++ + +  ++ ++++ ++ +DE qd++e qy++++al
  gi|386001005|ref|YP_005919304.1| 159 fvpemmdnetdrqvyeaynnglrvsyaIDFDDLLLLTYRLFQeRPKIADFYRRQYrYICIDEGQDLNEAQYQVISAL 235
                                       **********************************9999988853455667788999********************* PP

                            AAA_19 126 lgek.kklllvGDpdQliyv 144
                                       +g +  ++++vGD++Q+i+v
  gi|386001005|ref|YP_005919304.1| 236 CGLEhRNVMIVGDKKQAIFV 255
                                       *999777***********97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.4
                            AAA_19  85 tealelleeaeeekklqeeelliv 108
                                       ++a+e+l + +e+k+ qee +li+
  gi|386001005|ref|YP_005919304.1| 467 KNAMEYLYDYSETKESQEERALII 490
                                       334444445556666656666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.8e-07   0.00023      14     170 .]       7     246 ..       3     246 .. 0.62
   2 !    7.2   0.2    0.0047         6      51     149 ..     355     462 ..     339     489 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-07
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslv.rellralekdggif.lrgkcdqlesa.........ipysalaqalare 79 
                                       ++ +++ +++++ +l++  +G+GK++++ ++++r l++d g+f + + +  +++a         i      ++  ++
  gi|386001005|ref|YP_005919304.1|   7 ETQRKIVEHGEGPLLVVAGPGSGKTRVLtERVRRLLNEDTGHFrILALTFTNKAAnemkerlseI-----PNIE-KR 77 
                                       55566777778889999999********7788888888868888444333442332333333331.....3333.22 PP

                            AAA_16  80 ellrqllde...............aesaeleawrekleeala................................... 106
                                        ++  l++                +               l                                    
  gi|386001005|ref|YP_005919304.1|  78 AFIGTLHSFcmevlanrgkpvgidE---------------LPnifesyqdrkqvlfqaamanpylrhklniildant 139
                                       3333333332112212333333331...............2233334444444444466666666666666666777 PP

                            AAA_16 107 ...........................................avpelagaea...........srllellkrllal 129
                                                                                  +                     rl+++  +++++
  gi|386001005|ref|YP_005919304.1| 140 qdrllnrwldmissaknnlfvpemmdnetdrqvyeaynnglrvS--------YaidfddlllltYRLFQERPKIADF 208
                                       77777777777777778998888887777776666655444431........0455555567789999999999999 PP

                            AAA_16 130 lsrderplvlvlDdlqwadeaslqllaaLlrlleskpllvv 170
                                       ++r +   ++++D+ q++ ea+ q+++aL+ l   +++++v
  gi|386001005|ref|YP_005919304.1| 209 YRR-QY-RYICIDEGQDLNEAQYQVISALCGLEH-RNVMIV 246
                                       999.66.8**********************9944.587775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0047
                            AAA_16  51 dggiflrgkcdql.esaipy.sa.laqalareellrqlldeaesaeleawrekleeala.....avpelagaeasrl 119
                                       ++ ++l++  d+l ++  py  +  aq+ ++++l+++ +  ++  + +++r ++   +a     + +++ g++ s+ 
  gi|386001005|ref|YP_005919304.1| 355 RNRYVLSAVEDELnKRHWPYyKQlSAQQESESSLIQDFELCLRLLANPRDRLHFSMLIArwdmrEDASDFGQHVSDG 431
                                       45777777777776777888744588888888888888777666555555555555555776666666667777999 PP

                            AAA_16 120 lellkrllallsrderp.lvlvlDdlqwade 149
                                       l+ll++l +++s ++r  ++l l+ ++w +e
  gi|386001005|ref|YP_005919304.1| 432 LRLLSALKRRTSDNDRLaVILALESMDWTEE 462
                                       999999997777767745**********887 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.1e-10   1.4e-07       3      49 ..     535     589 ..     533     591 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.1e-10
                          UvrD_C_2   3 yaltihkaQGsefpaVivfd......pdlaaarmgel..rrrlLYtavTRArekl 49 
                                       + lt+h a+G+ef++V+v        pd+ a+++++l    r +++avTR+++ l
  gi|386001005|ref|YP_005919304.1| 535 ALLTVHSAKGLEFDVVVVMGmaegtfPDYRARDGPALeeEMRDAFVAVTRSKRLL 589
                                       679***************752222226777777776699*************987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.4e-08   1.8e-05       2      67 ..       5      69 ..       4     124 .. 0.74
   2 !    6.4   0.0     0.005       6.5      69     140 ..     136     264 ..      94     305 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                            AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaa.g.grviglAptgkaAkvLaeelg 67
                                      l++ Q+++ve    +g+   ++++++G+GKt +l++  r++++++ g +r+++l+ t+kaA++++e l 
  gi|386001005|ref|YP_005919304.1|  5 LSETQRKIVE----HGEGPLLVVAGPGSGKTRVLTERvRRLLNEDtGhFRILALTFTNKAANEMKERLS 69
                                      6666776665....444568999***********876488888886579****************9876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.005
                            AAA_30  69 eastiakllkrlk..........................................................grarle 87 
                                       +a+t ++ll+r+                                                           +    +
  gi|386001005|ref|YP_005919304.1| 136 DANTQDRLLNRWLdmissaknnlfvpemmdnetdrqvyeaynnglrvsyaidfddlllltyrlfqerpkiaD-FY-R 210
                                       555555555555555555555555555555555555555555555555555555566666666666665531.22.3 PP

                            AAA_30  88 pg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdl 140
                                       ++ + + +DE   ++ +q + + + +  ++  v++vGD++Q   V +G+  + l
  gi|386001005|ref|YP_005919304.1| 211 RQyRYICIDEGQDLNEAQYQVISALCGLEHRNVMIVGDKKQAIFVWNGANPKYL 264
                                       3448999************99999999999***********9888888654444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00057      0.72       2      70 ..      21     102 ..      20     112 .. 0.68
   2 !    5.6   0.0    0.0092        12      61     120 ..     211     269 ..     159     334 .. 0.76
   3 !    8.2   0.0    0.0015       1.9     179     231 ..     531     590 ..     501     592 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00057
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts..........liltvnrptaelltegk....pklpnlsvrtvdsflmalvkstkgk 64 
                                       +v + pG+GK++++ + +r            l lt  +++a+  +e++    + +++  + t+ sf m  ++  +gk
  gi|386001005|ref|YP_005919304.1|  21 LVVAGPGSGKTRVLTERVRRLlnedtghfriLALTFTNKAANEMKERLseipNIEKRAFIGTLHSFCMEVLAN-RGK 96 
                                       56678********998888755566888777777777777777777775554444444555566666666654.566 PP

                   Viral_helicase1  65 ililDE 70 
                                        + +DE
  gi|386001005|ref|YP_005919304.1|  97 PVGIDE 102
                                       666666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0092
                   Viral_helicase1  61 tkgkililDEylllhaGyilllaal..skaklvilfGDplQipfhsrnasfllahlpsslsh 120
                                        +++++ +DE + l+ ++ +++ al   + ++v+++GD +Q  f   n    ++++  ++++
  gi|386001005|ref|YP_005919304.1| 211 RQYRYICIDEGQDLNEAQYQVISALcgLEHRNVMIVGDKKQAIFVW-N--GANPKYLDQFER 269
                                       569999*********99998855541155589*********88774.2..255555555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0015
                   Viral_helicase1 179 algvrevttvhevqGltfdkVtlvllketdlelis........esrenllvAlTRhrkslv 231
                                       + g    +tvh++ Gl+fd+V++    e +   ++        e+    +vA TR+++ l 
  gi|386001005|ref|YP_005919304.1| 531 QEGLA-LLTVHSAKGLEFDVVVVMGMAEGTFPDYRardgpaleEEMRDAFVAVTRSKRLLA 590
                                       34444.99*************9986655443333356667666678889999999998775 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0015      18      76 ..      17      70 ..       2      82 .. 0.77
   2 ?    1.3   0.0      0.19   2.5e+02     217     253 ..     212     251 ..     200     252 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                            AAA_11 18 e..itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76
                                      e  + ++ GP G+gKT++++e +++l       +e +++ riL+ + +N+A +e+ erl++
  gi|386001005|ref|YP_005919304.1| 17 EgpLLVVAGP-GSGKTRVLTERVRRL------LNEDTGHFRILALTFTNKAANEMKERLSE 70
                                      2324556666.***************......56899**********************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.19
                            AAA_11 217 kfdvviIDEA.....aqavEpstliPlrlgakkvvLvGDpkQ 253
                                       +++++ IDE      aq   +s+l  l ++  +v +vGD kQ
  gi|386001005|ref|YP_005919304.1| 212 QYRYICIDEGqdlneAQYQVISALCGLEHR--NVMIVGDKKQ 251
                                       667777777622222344444555555555..9********9 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.3e-05     0.017     150     211 ..     189     246 ..     133     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                       --EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 150 ydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwil 211
                                        d ++ tY   +++     k+  + +++ +++++DEg+ l+  + ++  a++ L+ +n +i+
  gi|386001005|ref|YP_005919304.1| 189 DDLLLLTYRLFQERP----KIADFYRRQYRYICIDEGQDLNEAQYQVISALCGLEHRNVMIV 246
                                       467888888888666....78999*******************************9999887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00067      0.86       4      32 ..      16      44 ..      13     137 .. 0.72
   2 ?    0.0   0.0      0.73   9.4e+02      82     115 ..     205     235 ..     197     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00067
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldee 32
                                      ++g l+v++ +G+GKT++l + +++l +e
  gi|386001005|ref|YP_005919304.1| 16 GEGPLLVVAGPGSGKTRVLTERVRRLLNE 44
                                      78999************998887777544 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.73
                            AAA_22  82 leqalraravielliiDEaqhlrseealeeLrsl 115
                                       +++  r++++   + iDE q l +e++++ ++ l
  gi|386001005|ref|YP_005919304.1| 205 IADFYRRQYR--YICIDEGQDL-NEAQYQVISAL 235
                                       5666777777..99********.77776666555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.18      13      97 ..      11     111 ..       7     146 .. 0.65
   2 ?   -3.0   0.0       4.3   5.5e+03     181     227 ..     353     402 ..     348     404 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialr..eesiskldefie...eeeekkklekal.. 82 
                                       +i+e ++ + +++ Gp gsGKt++l e + +l++ d  ++ + al   +++ ++++e +    +      +ek +  
  gi|386001005|ref|YP_005919304.1|  11 KIVEHGEGPLLVVAGP-GSGKTRVLTERVRRLLNEDTGHFRILALTftNKAANEMKERLSeipN------IEKRAfi 80 
                                       7999999********9.9**************88777555555544004444444444333322......3333333 PP

                          ATPase_2  83 ..............giavpkaeleeilk..e 97 
                                                     g++v+ +el +i++  +
  gi|386001005|ref|YP_005919304.1|  81 gtlhsfcmevlanrGKPVGIDELPNIFEsyQ 111
                                       3345666666666666666666666666553 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                          ATPase_2 181 egrhky..ilvddldketalnflkegfkeleel..skedfeeiyryvGGkP 227
                                        gr +y    v+d   +  +   k+++ + e++    +dfe++ r++  +P
  gi|386001005|ref|YP_005919304.1| 353 LGRNRYvlSAVEDELNKRHWPYYKQLSAQQESEssLIQDFELCLRLL-ANP 402
                                       56666632223322255667777777777644434456777777776.555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.17      14      76 ..       7      70 ..       3     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                      HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGG CS
                            ResIII 14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkk 76
                                      ++  k+ ++++  +l+++  G+GKT+v+++ ++rll++     ++l l  +++  + ++e++++
  gi|386001005|ref|YP_005919304.1|  7 ETQRKIVEHGEGPLLVVAGPGSGKTRVLTERVRRLLNEDTGHfRILALTFTNKAANEMKERLSE 70
                                      556667768888999*******************999866545788777777777777766644 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.013        16       6      51 ..      22      68 ..      19      97 .. 0.67
   2 ?    1.3   0.0      0.12   1.6e+02      85     185 ..     209     297 ..     178     313 .. 0.74
   3 ?    2.1   0.0     0.072        92     234     297 ..     477     552 ..     428     557 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                           DUF2075  6 VtGvaGtGKtvvllnllaeleddeeertavylsv.Nhplvlvlreal 51
                                      V  ++G+GKt vl + + +l +++ ++ +++++   ++  + ++e+l
  gi|386001005|ref|YP_005919304.1| 22 VVAGPGSGKTRVLTERVRRLLNEDTGHFRILALTfTNKAANEMKERL 68
                                      4457****************777777776665431333344445544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                           DUF2075  85 eepkedvvivDEAhrlltksdqaekqseenqlkelmkr.akvvvalvDegQelntgeigteeelkklakklevelee 160
                                        +++ + + +DE + l++         + + +  l     + v+++ D++Q++   + ++ + l+++ ++ +++   
  gi|386001005|ref|YP_005919304.1| 209 YRRQYRYICIDEGQDLNE--------AQYQVISALCGLeHRNVMIVGDKKQAIFVWNGANPKYLDQFERDFGAKK-- 275
                                       566777778888888888........2234555555554556777889999999999888888999988888885.. PP

                           DUF2075 161 kvhLksqfRvaaseaviewvdalld 185
                                        + ++  fR+  s+ v++  ++l++
  gi|386001005|ref|YP_005919304.1| 276 -IFMNDNFRS--SQVVVNAAKSLVS 297
                                       .568888888..6666666666655 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.072
                           DUF2075 234 krlaekkkkkskekdvkiee.gdfklpWnleek................elkkpwaessdtleevgseytiQGleld 293
                                       + +    k++++e+   ie    ++ +Wn++                   l +    +++ l +  +++++ Gle+d
  gi|386001005|ref|YP_005919304.1| 477 SET----KESQEERALIIEDiRTWQKHWNYYLRsqpggyhtltsflgqvALGTTQQPRQEGL-ALLTVHSAKGLEFD 548
                                       222....2222222222322355999999998877787777777776553333333344444.34588888888888 PP

                           DUF2075 294 yvgv 297
                                        v+v
  gi|386001005|ref|YP_005919304.1| 549 VVVV 552
                                       7766 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00059      0.75      11      57 ..      24      72 ..      18      82 .. 0.82
   2 ?   -0.1   0.0      0.66   8.4e+02      35      76 ..     349     390 ..     346     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00059
                                      --TTS-TTTTHHHHHHHHHHHT...T--EEEEESSHHHHHHHHHHTTTS- CS
                        Flavi_DEAD 11 lhPGaGktrkvlpelvkeaier...rlrtlvLaPtrvvlaemeealkgle 57
                                      + PG+Gktr vl e v++ +++   + r l L+ t   ++em+e l++ +
  gi|386001005|ref|YP_005919304.1| 24 AGPGSGKTR-VLTERVRRLLNEdtgHFRILALTFTNKAANEMKERLSEIP 72
                                      57******7.8889999887762235799***************998765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.66
                                       -EEEEESSHHHHHHHHHHTTTS-EEE-------------SEE CS
                        Flavi_DEAD  35 rtlvLaPtrvvlaemeealkglevryktsavkeektgrelvd 76 
                                       r  +L   r vl+ +e+ l++ +  y +++  +++++ +l++
  gi|386001005|ref|YP_005919304.1| 349 RCALLGRNRYVLSAVEDELNKRHWPYYKQLSAQQESESSLIQ 390
                                       566788899*********************999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 4222.26
//
Query:       gi|386001006|ref|YP_005919305.1|  [L=153]
Description: riboflavin synthase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-15   55.6   0.0    5.4e-15   55.4   0.0    1.0  1  DMRL_synthase   6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
       0.12   12.9   0.5       0.23   12.0   0.5    1.3  1  EF-G-binding_N  Elongation factor G-binding protein, N-termin


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0     6e-19   5.4e-15       3     137 ..       2     127 ..       1     131 [. 0.82

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 6e-19
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphf 79 
                                       +i+i  ++f      ++ ++a++elk+     ++i+++tVPG+ +lp+aak l+e++++ + v+alG  + G  p +
  gi|386001006|ref|YP_005919305.1|   2 KIGIADTNF---ARYDMARAAIKELKRGCS--AEIVRYTVPGVKDLPVAAKILIEERGC-ELVMALG--MPGPKPID 70 
                                       788888888...788999********9664..69*********************6445.*******..9******* PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTCCCHHHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvdteeqaleraggkagnkGeeaaeaalema 137
                                       + +a+++s gl+ ++l t++ ++   +  d+ e  +e a + a+ + +e+ae+a++++
  gi|386001006|ref|YP_005919305.1|  71 KTCAHEASTGLIMAQLMTNTHILEVFVHEDEAESEKELA-SLAERRTREHAENAIKLL 127
                                       *******************65554444433444444444.445************986 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   2.6e-05      0.23      34      74 ..      85     126 ..      81     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                    EF-G-binding_N  34 kalaaekIlelfpelseeq.kelLeqiddiktkekaeklLee 74 
                                       + ++++ Ile+f+++ e++ ++ L+++++ +t+e+ae++ + 
  gi|386001006|ref|YP_005919305.1|  85 QLMTNTHILEVFVHEDEAEsEKELASLAERRTREHAENAIKL 126
                                       7899********9988877788899************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 1021.62
//
Query:       gi|386001007|ref|YP_005919306.1|  [L=656]
Description: Ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Methanosaeta harundinacea 6Ac]
Scores for complete 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-149  497.2   0.0   1.3e-146  489.3   0.0    2.1  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    8.9e-20   70.5   0.0    1.9e-19   69.5   0.0    1.5  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
       0.12   11.2   0.0       0.76    8.5   0.0    1.9  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.3   0.0  2.1e-150  1.3e-146       1     524 []     161     620 ..     161     620 .. 0.97

  Alignments for each domain:
  == domain 1  score: 489.3 bits;  conditional E-value: 2.1e-150
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfvl veds+++I+ ++ke+a+++++ggG+G+++s+lR+kg++v+ t+g asGpvsfm+++da ++v+kqgG+Rr
  gi|386001007|ref|YP_005919306.1| 161 SACFVLPVEDSMDGIFGALKEMAKIHQSGGGTGFSFSRLRPKGDPVRATGGVASGPVSFMEVFDAATEVIKQGGRRR 237
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GA+m++l+++HpDi++f++aKe+       rl+n+n+svg++d+ m++++++++  L++Prt        g      
  gi|386001007|ref|YP_005919306.1| 238 GANMAVLRADHPDILDFVRAKER-----AGRLQNFNLSVGITDDQMRRARSGRKLDLINPRT--------G------ 295
                                       *********************66.....56*******************************3........2...... PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 155 yeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCn 231
                                                   ++++a  L++e+a saw+ g+Pgvlf D+iN +++l     g+I+atN+CgE+pll+yes   Cn
  gi|386001007|ref|YP_005919306.1| 296 ---------QVAEKIEAAGLLQEVAASAWRRGDPGVLFLDRINDAHPL----PGTIEATNPCGEQPLLPYES---CN 356
                                       .........23459**********************************....48******************...** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 232 LasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgip 308
                                       L+s+nL++f      g+ e+dwd l+ + +l++r+Ld+v++vn++pl++i+++t k+R+iGlGvmg+a++l++lgi 
  gi|386001007|ref|YP_005919306.1| 357 LGSVNLSRFA-----GRGEVDWDGLEGTARLAIRFLDDVLEVNRFPLRRIREETLKSRKIGLGVMGFAEMLIELGIS 428
                                       **********.....789*********************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 309 ydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnam 385
                                       y s+ea+ +a++++++++ +a ++S  l +erg+fpl e+s                  dw+          +rna+
  gi|386001007|ref|YP_005919306.1| 429 YASKEAVGMAEEAMKFIAAAARDESRLLGEERGSFPLLEESSL----------------DWDA---------MRNAT 480
                                       *************************************998864................4777.........9**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 386 vtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki.lesvqgleeipeei 461
                                       vt++aPTgsiSliagts gieP+f l y++    +e++ +np fe+  k++gl +  +++   +++ +g+e +p+++
  gi|386001007|ref|YP_005919306.1| 481 VTTIAPTGSISLIAGTSPGIEPLFGLSYSRDLLGEEMVAMNPLFERMAKDRGLGDGLIRTVAaQGTLDGAEGVPDDL 557
                                       ******************************************************988888887788*********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 462 krvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       k++f+ta+++ + +h+k+qaa q++ d+++Skt+nlp eatve+v +++ lA++lG+Kg+t+Y
  gi|386001007|ref|YP_005919306.1| 558 KELFVTAMEVAPAQHVKIQAAFQRFTDNGVSKTVNLPPEATVENVLNIFALAYDLGCKGITVY 620
                                       **************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   3.1e-23   1.9e-19       4      83 .]      81     158 ..      79     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.1e-23
                   Ribonuc_red_lgN   4 tynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmnaGt 80 
                                       + +a + l++rYl++d  g+++E+ ++mf RvA+++a ae  +  + ++ ++a +f dlm+   flp+sPtlmnaG 
  gi|386001007|ref|YP_005919306.1|  81 GPFAPELLRKRYLRRDVSGDVAETAEEMFSRVARTVARAEGRF--GGDASAMAARFRDLMAGGLFLPNSPTLMNAGL 155
                                       6677789*********************************975..78*****************************8 PP

                   Ribonuc_red_lgN  81 elg 83 
                                        lg
  gi|386001007|ref|YP_005919306.1| 156 SLG 158
                                       875 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00013      0.76     345     395 ..     403     451 ..     379     457 .. 0.88
   2 ?    0.1   0.0     0.043   2.6e+02     449     499 ..     566     615 ..     561     624 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00013
                                       .......EEEEEEE-HHHHHHHTTEEEE..-HHHHHHHHHHHHHHHHHHHH CS
                              NRDD 345 eevlkngtltiGfiGlaEalkaltgkkigeseeakefalkvlkhmrekade 395
                                       ee+lk+  + +G++G+aE+l  l g ++ +s+ea  +a +++k++  +a++
  gi|386001007|ref|YP_005919306.1| 403 EETLKSRKIGLGVMGFAEMLIEL-GISY-ASKEAVGMAEEAMKFIAAAARD 451
                                       6789999****************.9999.99**************988775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.043
                                       SB-HHHHHHHHHHHTGGGTT-S-EEEEBSS--SSHHHHHHHHHHHHHTT-- CS
                              NRDD 449 kislfekikleaefqklttGGailyieldeekknpealeklvkiakktgig 499
                                       ++ +++ +k++a fq++t+ G+   ++l+ e   +e + ++  +a++ g+ 
  gi|386001007|ref|YP_005919306.1| 566 EVAPAQHVKIQAAFQRFTDNGVSKTVNLPPE-ATVENVLNIFALAYDLGCK 615
                                       5678999*********************954.5788888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 4466.76
//
Query:       gi|386001008|ref|YP_005919307.1|  [L=226]
Description: CODH nickel-insertion accessory protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-05   24.8   0.0      2e-05   24.6   0.0    1.2  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    9.5e-05   22.3   0.1    0.00013   21.9   0.1    1.2  1  AAA_26    AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.3e-09     2e-05      54     127 ..      80     189 ..       3     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.3e-09
                                       H...............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEE CS
                                       x...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  54 p...............................................dlkrllellealgkkkalllkiagvvlnr 83 
                                                                                       +l+r+++l+++lg++       ++ v+n+
  gi|386001008|ref|YP_005919307.1|  80 AllrhvilrekdlvildmeagiehlgrgttrgvdvmiavvepglrsveTLERIKRLAKDLGIE------RVMAVINK 150
                                       055555555555555666666666666666666667777777777777788888888888865......89****** PP

                                       ESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS.- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                              CbiA  84 vdgeneetllkealeelkqrygvpvlgviprdeavaeaparge.p 127
                                         +e  +++++e l+e     +vpvlg+ip+d ++++a+  g+ p
  gi|386001008|ref|YP_005919307.1| 151 APEE--QAKIREKLAEM----NVPVLGMIPFDRSLMDADLAGMsP 189
                                       8887..99999999997....8****************9999855 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.5e-08   0.00013     131     196 ..     115     181 ..     109     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-08
                            AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnp.envetlekksgipvlGvvPylpdlea 196
                                       +i V+ +gl++++ l     ++++ +++ ++ ++Nk +++ +++++  +  ++pvlG +P +++l++
  gi|386001008|ref|YP_005919307.1| 115 MIAVVEPGLRSVETLERIKRLAKDLGIERVMAVINKAPEEqAKIREKLAEMNVPVLGMIPFDRSLMD 181
                                       4779999999998888888888999***9999****766656888888889**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1626.84
//
Query:       gi|386001009|ref|YP_005919308.1|  [L=61]
Description: hypothetical protein Mhar_0298 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.021   15.1   0.0    1.1  1  DUF1884       Domain of unknown function (DUF1884)
       0.05   14.4   0.0      0.073   13.9   0.0    1.5  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.3e-06     0.021      40      72 ..      13      45 ..       4      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-06
                                      HHHHHHHT--.----EETTEEEEE-GGGTTEEEE CS
                           DUF1884 40 ealkkeleee.eevtelsnlkveileeLGgDavv 72
                                      + l+  ++ e e  +e+ n ++  leeLG +a+v
  gi|386001009|ref|YP_005919308.1| 13 KRLRL-FGREgESCVEILNRRMDSLEELGVEAIV 45
                                      44553.555515679*****************97 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.1e-06     0.073       3      32 ..       5      34 ..       3      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-06
                      VAPB_antitox  3 IsIsdevYekLkklKregeSFsdvIerLle 32
                                      I +++ v+++L+ + regeS+ ++++r ++
  gi|386001009|ref|YP_005919308.1|  5 IQVDEGVKKRLRLFGREGESCVEILNRRMD 34
                                      999**********************99554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 458.44
//
Query:       gi|386001010|ref|YP_005919309.1|  [L=330]
Description: Phosphoribosylformylglycinamidine cyclo-ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-23   83.1   0.1    3.8e-23   82.4   0.1    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    6.7e-16   58.7   1.3    1.1e-15   58.0   1.3    1.3  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.1   4.2e-27   3.8e-23       3     148 ..     171     320 ..     169     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 4.2e-27
                                       TEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHH CS
                            AIRS_C   3 GdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaalkglvkaahDvTgGGLl 73 
                                        dv+++++s+Gl+++g+sl+rki+ee++  ++      ++ +g++llept+iy  +++  +k +v++++++Tg GLl
  gi|386001010|ref|YP_005919309.1| 171 EDVVVGLPSSGLHSNGFSLARKIVEESSYTYFdrmpgsEKTIGELLLEPTRIYMEALAVIQKADVHGMAHITGSGLL 247
                                       7***************************9999*****6666************99877777*************999 PP

                                       HHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEE CS
                            AIRS_C  74 galaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavI 142
                                         l+++   sg+g+eid +    pif  l+      + em++++n+G + v+v +e++ davl++ +       +v+
  gi|386001010|ref|YP_005919309.1| 248 K-LHRI---SGFGFEIDDPiePQPIFRFLQeeggvAEDEMYRTFNMGMGWVFVLSEDDvDAVLKMTDG------KVV 314
                                       5.6777...8899****9999999999999999*************************9999998884......588 PP

                                       EEEEES CS
                            AIRS_C 143 Gevtak 148
                                       Ge++++
  gi|386001010|ref|YP_005919309.1| 315 GEIVDE 320
                                       888876 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   1.3   1.2e-19   1.1e-15       4      93 ..      54     156 ..      39     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.2e-19
                                       EEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT- CS
                              AIRS   4 avvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgv 71 
                                       a+++ttd+++++vl++        +G  ++a+n++Dl+a GA+Pla++++lal+       ++++ gl+++a+ ++v
  gi|386001010|ref|YP_005919309.1|  54 AIAMTTDGVGSKVLIASAMRkwdtVGIDCMAMNVNDLLAIGAEPLAFVDYLALErvdpeMTAQIAVGLERGAKIANV 130
                                       579************664445577***********************************99**************** PP

                                       EEEEEEEEEESS....EEEEEEEEEE CS
                              AIRS  72 plvgGdtsfsne....ptisvtavGl 93 
                                       ++vgG+t++ +e    + ++ ta+G+
  gi|386001010|ref|YP_005919309.1| 131 SIVGGETASLPEiirgFDLAGTAIGM 156
                                       *********99999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2393.06
//
Query:       gi|386001011|ref|YP_005919310.1|  [L=461]
Description: Aspartokinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-45  154.6   0.0    3.3e-45  154.6   0.0    2.0  2  AA_kinase  Amino acid kinase family
    8.8e-23   79.8   3.8    2.1e-10   40.2   0.2    3.0  3  ACT        ACT domain
    1.6e-22   79.1   2.3    1.9e-11   43.6   0.5    2.5  2  ACT_7      ACT domain
    0.00043   21.2   0.4     0.0087   17.0   0.4    2.4  2  LytR_C     LytR cell envelope-related transcriptional attenua
  ------ inclusion threshold ------
       0.11   12.5   0.3        9.7    6.3   0.0    2.8  2  ACT_6      ACT domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0   9.1e-49   3.3e-45       5     240 ..       1     281 [.       1     282 [. 0.87
   2 ?   -1.8   0.5      0.53   1.9e+03      23      46 ..     380     401 ..     317     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 9.1e-49
                                       EEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH....TCCCCCHHHC............. CS
                         AA_kinase   5 vKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal....ksglssgelaa............ 64 
                                       +K+GGss++d+ +  lr++ e ++ l + +n++vvV+++ g++td ll+     +     ++ +             
  gi|386001011|ref|YP_005919310.1|   1 MKFGGSSVADGAK--LRNVGELVKSL-SGENEIVVVTSAlGGVTDDLLQCartsA-----EGGKVediatfvdrlsk 69 
                                       6**********99..***********.9999******************943331.....33332234445555544 PP

                                       ..........E..HHHHHHHHH.......................................HHHHHHHHHHHHHHHH CS
                         AA_kinase  65 .......glrstleeagevatr.......................................dalaslgerlvaalla 95 
                                              +                                                     d + s+gerl a +l+
  gi|386001011|ref|YP_005919310.1|  70 rhvqalmD-------------AvldpdiakelkeiitqrlgelekayigicylgelsprsiDRISSFGERLAAPILS 133
                                       44444440.............0444444445555566699999999******************************* PP

                                       TTHGEEEE-GGGTCEECCCE.....HHHTTTCEEECCHHHHHHHT.T-EEEEESEEEEETTTE...EEEE-HHHHHH CS
                         AA_kinase  96 aglpavglsaaaldateagr...degsdgnvesvdaeaieellea.gvvpvltgfigldeege...lgrgssDtiaa 165
                                         l++ gl+++++   eag    ++  +++  + + + +   l   + vpv+tgfig de g    lgrg+sD +a+
  gi|386001011|ref|YP_005919310.1| 134 GVLRDLGLKSRYYSGGEAGVitnSDYGNAKPLEKSYDLLSSRLTPiDGVPVVTGFIGEDERGNittLGRGGSDFSAS 210
                                       ***********************8888888888899999999988778***************************** PP

                                       HHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 166 llAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvIt 240
                                       l+++a+gAd++++++d+ GV++ dpk+v+ a+ +p is++ea+e    ++++G+kv+hp+a+++a r+gipv+++
  gi|386001011|ref|YP_005919310.1| 211 LIGAAIGADEIWFWKDTTGVLTTDPKIVSEAKNIPVISYREAME----MSYFGAKVLHPRAIEPAIRNGIPVRVK 281
                                       ********************************************....*************************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHTTEEEEEE--HHH CS
                         AA_kinase  23 laeqiaalkesgnklvvVhGggsf 46 
                                       ++++++    ++  ++ V+G+g +
  gi|386001011|ref|YP_005919310.1| 380 IVREVSHN--KDVAVIAVVGAGMV 401
                                       33444433..55666777777644 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.96   3.4e+03      42      61 ..      59      78 ..      50      92 .. 0.59
   2 !   40.2   0.2   5.8e-14   2.1e-10       8      63 ..     324     373 ..     320     376 .. 0.85
   3 !   39.6   0.1   8.9e-14   3.2e-10       2      65 ..     395     452 ..     394     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.96
                                      EEEEEEEEEEHHHHHHHHHH CS
                               ACT 42 givfvvivvdeedleevlea 61
                                      +i+++v+  + ++++++++a
  gi|386001011|ref|YP_005919310.1| 59 DIATFVDRLSKRHVQALMDA 78
                                      46666666666666665554 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 5.8e-14
                                       ESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHH CS
                               ACT   8 pDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealk 63 
                                        + PG++ar f+ala++g+Ni++i+q+ss      ++++ +vvde ++e+++ al+
  gi|386001011|ref|YP_005919310.1| 324 IGTPGIAARAFSALANAGVNIVMISQGSS------EANISVVVDEPQVEAAEIALR 373
                                       578**************************......788888888888888775555 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 8.9e-14
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       v+  g+ + PG+++rvfga+++  iN+ +i+q+ss      ++++ +vv+  ++e ++++l++ 
  gi|386001011|ref|YP_005919310.1| 395 VVGAGMVGTPGVAGRVFGAMGRSKINVLMISQGSS------EHNISFVVSIGEAERAVQELHRE 452
                                       56678999***************************......89999999999999999999876 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.5   5.4e-15   1.9e-11       5      64 ..     312     373 ..     308     374 .. 0.94
   2 !   35.0   0.1   2.6e-12   9.3e-09       2      65 .]     386     451 ..     385     451 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 5.4e-15
                                       EEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   5 gwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                        ++ l+++g+g+ + ++Gi+a+ +s+La+ag++i +iS   ++  ++++V+e ++e+A  aL+
  gi|386001011|ref|YP_005919310.1| 312 KVALLTISGAGMIG-TPGIAARAFSALANAGVNIVMISqgsSEANISVVVDEPQVEAAEIALR 373
                                       67889*******88.*******************************************99987 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 2.6e-12
                                       EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                       ++++++++ vvg+g+ + ++G++ +++++  + +I++++iS   +++ ++++V   ++e+Av+ Lh+
  gi|386001011|ref|YP_005919310.1| 386 HNKDVAVIAVVGAGMVG-TPGVAGRVFGAMGRSKINVLMISqgsSEHNISFVVSIGEAERAVQELHR 451
                                       57899**********88.*********************************************9995 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   2.4e-06    0.0087      11      82 ..     325     397 ..     322     399 .. 0.67
   2 ?    1.1   0.0      0.22   7.9e+02      11      64 ..     402     455 ..     401     460 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                            LytR_C  11 gvsGlAarvadaLeerGftvgevgn.agnadee.ttivyreaaa.aaak.alaaalglgelqedsvkdas..vtvvl 81 
                                       g++G+Aar+ +aL+++G +++ +++ +++a  + +++v  ++++ +aa+ al+a+++ +  + + + +++  v  v+
  gi|386001011|ref|YP_005919310.1| 325 GTPGIAARAFSALANAGVNIVMISQgSSEA--NiSVVV--DEPQvEAAEiALRAEFPTTI-VREVSHNKDvaVIAVV 396
                                       89********************88524444..347887..55664455568888886443.3333333334566666 PP

                            LytR_C  82 G 82 
                                       G
  gi|386001011|ref|YP_005919310.1| 397 G 397
                                       6 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.22
                            LytR_C  11 gvsGlAarvadaLeerGftvgevgn.agnadeettivy.reaaaaaakalaaalgl 64 
                                       g++G+A+rv  a+ +   +v  +++ +++++  + +v  +ea++ a ++l +++gl
  gi|386001011|ref|YP_005919310.1| 402 GTPGVAGRVFGAMGRSKINVLMISQgSSEHNI-SFVVSiGEAER-AVQELHREFGL 455
                                       799********999999999998752333333.33333345444.88888888876 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0027       9.7      12      37 ..     326     351 ..     314     369 .. 0.86
   2 ?    3.2   0.0     0.025        90      13      61 ..     404     452 ..     392     457 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0027
                             ACT_6  12 rpGltasLtsvlaefgvnilDieqav 37 
                                        pG+ a+ +s+la  gvni+ i q  
  gi|386001011|ref|YP_005919310.1| 326 TPGIAARAFSALANAGVNIVMISQGS 351
                                       59******************999965 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.025
                             ACT_6  13 pGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarleka 61 
                                       pG+  +++++  ++++n+l i q   + + s+++ +   e+a+++l ++
  gi|386001011|ref|YP_005919310.1| 404 PGVAGRVFGAMGRSKINVLMISQGSSEHNISFVVSIGEAERAVQELHRE 452
                                       99999****************************9999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3384.39
//
Query:       gi|386001012|ref|YP_005919311.1|  [L=731]
Description: Elongation factor 2 [Methanosaeta harundinacea 6Ac]
Scores for 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-63  211.4   0.0    1.4e-62  210.7   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    6.5e-27   93.7   0.4    3.6e-26   91.3   0.1    2.5  3  EFG_IV       Elongation factor G, domain IV
    2.4e-25   88.4   0.3    7.4e-25   86.8   0.3    1.9  1  EFG_II       Elongation Factor G, domain II
      8e-23   80.3   0.0    2.6e-22   78.6   0.0    2.0  1  EFG_C        Elongation factor G C-terminus
    4.2e-14   52.7   0.4    1.4e-13   51.0   0.4    2.0  1  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0003   20.9   0.0    0.00064   19.8   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0029   17.6   0.0     0.0075   16.2   0.0    1.7  1  DUF2888      Protein of unknown function (DUF2888)
     0.0041   16.9   0.0     0.0098   15.7   0.0    1.7  1  RF3_C        Class II release factor RF3, C-terminal domain
  ------ inclusion threshold ------
      0.031   13.9   0.0      0.067   12.8   0.0    1.5  1  Ras          Ras family
       0.13   12.3   0.0       0.58   10.1   0.0    2.2  2  DUF3748      Protein of unknown function (DUF3748)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.7   0.0   7.6e-66   1.4e-62       3     193 ..      21     257 ..      19     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 7.6e-66
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEEE CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliDt 77 
                                       irnigi++h+DhGKtTL+d+Ll+ +g+is+  e a+++ ++D+ + E++rgiTi++a++s+  + ++k+ylin+iDt
  gi|386001012|ref|YP_005919311.1|  21 IRNIGIVAHIDHGKTTLSDNLLAGSGMISM--ELAGKQLFMDFDELEQARGITIDAANVSMVhEyQGKEYLINMIDT 95 
                                       8*****************************..889999************************6269*********** PP

                                       SSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH. CS
                          GTP_EFTU  78 PGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk. 153
                                       PGHvdF  +v+r++r++Dgav+vvdaveG +pqte+vlr+alke+v++++f+NK+Drl +elk  ++e++ +l +  
  gi|386001012|ref|YP_005919311.1|  96 PGHVDFGGDVTRAMRAVDGAVVVVDAVEGAMPQTETVLRQALKENVHPVLFVNKVDRLLNELKVDKQEMQLRLGKLi 172
                                       *************************************************************************8885 PP

                                       ...........HHHHHHHHHTTT..........TTEEEEEEBTTTTBTHH........................... CS
                          GTP_EFTU 154 ...........eeklekygekge..........kevpvvfgSalkgegvk........................... 182
                                                  e          e          +  +v+fgSal +++++                           
  gi|386001012|ref|YP_005919311.1| 173 dninklirgmnE----------EkykagwrvdaSAGSVAFGSALYNWAISvpqmkstgigfgevydycqvgdmktla 239
                                       555555544432..........14555555556899***********988777777777777777777777777777 PP

                                       .......HHHHHHHHHSH CS
                          GTP_EFTU 183 .......tllealvellp 193
                                              ++ ++++++lp
  gi|386001012|ref|YP_005919311.1| 240 qkcplylAVNDMVIRFLP 257
                                       777777667777777666 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   2.3e+03       3      54 ..     464     506 ..     462     510 .. 0.54
   2 !   91.3   0.1     2e-29   3.6e-26      12     120 ..     514     618 ..     503     619 .. 0.93
   3 ?   -3.2   0.0       3.9     7e+03      24      59 ..     684     719 ..     677     723 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                       CESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--ST CS
                            EFG_IV   3 VayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkg 54 
                                       V yrE+i+ ++++ +e         ++  + ++eiePle     e+vd++k 
  gi|386001012|ref|YP_005919311.1| 464 VVYRESITGKTTGPVEGKS-----PNHHNRFYIEIEPLE----PEVVDAIKA 506
                                       6677777666663222211.....234456677777775....556666655 PP

  == domain 2  score: 91.3 bits;  conditional E-value: 2e-29
                                       -CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEE CS
                            EFG_IV  12 pvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkv 88 
                                       ++ er+++l+  +g+d+++a+ i  + +     +n+f+++tkg+q++ke++e+  +Gf ea+k+Gp+++epv++vk+
  gi|386001012|ref|YP_005919311.1| 514 EELERRNILIS-KGMDKEEARNISGVFE-----TNVFINMTKGVQYLKETMELMLEGFMEATKNGPICREPVQGVKA 584
                                       44456777777.7***************.....8******************************************* PP

                                       EEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  89 tLldgslhe..vdsseaafkpaarralkeallkA 120
                                       +L+d++lhe  +++++a+++pa+r+a+++++l+A
  gi|386001012|ref|YP_005919311.1| 585 KLMDIKLHEdaIHRGPAQVIPAVRQAVQAGILMA 618
                                       ******************************9998 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.9
                                       TSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHC CS
                            EFG_IV  24 sggdgqyakvileiePleegsgnefvdetkggqvpk 59 
                                       ++g+  +++    +eP ++ + +e v +++g + +k
  gi|386001012|ref|YP_005919311.1| 684 TEGRSLWSTEFAGFEPIPPAAMLETVRQIRGRKGLK 719
                                       567788888888999999999999999888876555 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.3   4.1e-28   7.4e-25       1      74 [.     387     460 ..     387     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 4.1e-28
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePv+++a+e+k+ +d  kl ++L+++++EDptl+++ +eeT+e +++GmGelHleiv+ r++r+ +ve++++
  gi|386001012|ref|YP_005919311.1| 387 VSEPVVTVAVEAKNTRDLPKLVEVLRQVAKEDPTLNITINEETGEHLMAGMGELHLEIVAYRIQRDKGVEITTS 460
                                       689********************************************************************986 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   1.5e-25   2.6e-22       2      85 ..     622     704 ..     621     708 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.5e-25
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       +lEP+++v i+vp+e +g ++s+++ rrG i++me++ ++++ii+a++P++el+gfa ++r +T+G+  +s+ef+g+
  gi|386001012|ref|YP_005919311.1| 622 ILEPFQNVFIQVPQEQMGGAMSEIQGRRGMILSMETE-GDMIIIKAKAPVSELFGFAGAIRGATEGRSLWSTEFAGF 697
                                       89***********************************.*************************************** PP

                                       EE--HHH CS
                             EFG_C  79 eevpgdk 85 
                                       e++p   
  gi|386001012|ref|YP_005919311.1| 698 EPIPPAA 704
                                       **99865 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.4   7.9e-17   1.4e-13       1      73 [.     306     372 ..     306     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 7.9e-17
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G+va+gr++sGtl++G+e+ i  +++ k+    r++++  f++  + +v+  +aG+i+a+ gl da  vG+t+
  gi|386001012|ref|YP_005919311.1| 306 GEVATGRLFSGTLERGMELFI--SGVAKS---NRVQQTGIFMGADRVEVEKIPAGNIAAVTGLRDA-YVGSTV 372
                                       89*******************..888899...*********************************8.999997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.6e-07   0.00064       2     113 ..      24     148 ..      23     149 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                                       EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGlie 58 
                                       ++iv +   GK+tL   l+                 +  + ++  g T+d     +      k+  i+++DtpG ++
  gi|386001012|ref|YP_005919311.1|  24 IGIVAHIDHGKTTLSDNLLAgsgmismelagkqlfmDFDELEQARGITIDAANVSMVheyqGKEYLINMIDTPGHVD 100
                                       7888888999999999998544455555555444323457778888888885554442532222559*******665 PP

                                       HHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH.HHHHHHTTSEEEEEEE CS
                          MMR_HSR1  59 gaseekglgkaflaleeadlillvvdaseeklkpldeel.eelleeakkplilvln 113
                                           + ++++a++    +d +++vvda e+   p+ e++  + l+e+  p +l +n
  gi|386001012|ref|YP_005919311.1| 101 ---FGGDVTRAMR---AVDGAVVVVDAVEG-AMPQTETVlRQALKENVHP-VLFVN 148
                                       ...2223444444...58********9955.5555555504444444444.45555 PP

>> DUF2888  Protein of unknown function (DUF2888)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.2e-06    0.0075       9      97 ..      60     147 ..      56     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                           DUF2888   9 dlceipfnrnftidlvnlsvstefqvkitmtphhdlgtfvvepknvfsikravkgdaafkveraagwlpdtpqvltl 85 
                                       d+ e+   r +tid  n+s+  e+q k  +    d    v    +v    rav g a + v+   g +p+t  vl  
  gi|386001012|ref|YP_005919311.1|  60 DFDELEQARGITIDAANVSMVHEYQGKEYLINMIDTPGHVDFGGDVTRAMRAVDG-AVVVVDAVEGAMPQTETVLRQ 135
                                       566788899********************************************99.567899*************** PP

                           DUF2888  86 fvyerlnpvewh 97 
                                        + e + pv + 
  gi|386001012|ref|YP_005919311.1| 136 ALKENVHPVLFV 147
                                       ********9765 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.5e-06    0.0098      13      80 ..     394     461 ..     381     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                                       EEEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE CS
                             RF3_C  13 arvrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrles 80 
                                         v++k++    +l + l+q+a+E  +  ++ +e++ e +++ +G+L +e+v++R+++  gve+++++
  gi|386001012|ref|YP_005919311.1| 394 VAVEAKNTRDLPKLVEVLRQVAKEDPTLNITINEETGEHLMAGMGELHLEIVAYRIQRDKGVEITTSP 461
                                       5788999999999***********99988888888999************************998876 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05     0.067      25     126 ..      65     163 ..      55     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                       SSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHS CS
                               Ras  25 keeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrva 101
                                       ++    Ti +++ +   e++gke+ +++ DT G  +f    +  +r ++g+++v d  + +   + ++    +++  
  gi|386001012|ref|YP_005919311.1|  65 EQARGITIDAANVSMVHEYQGKEYLINMIDTPGHVDFGGDVTRAMRAVDGAVVVVDAVEGA-MPQTETV---LRQAL 137
                                       5666789999999999**************************************9977654.3333333...34444 PP

                                       TTTSEEEEEEETTT.GGGG-SS-HHH CS
                               Ras 102 eenvpivLvGnKvD.leekravstee 126
                                       +env+ vL  nKvD l ++ +v+++e
  gi|386001012|ref|YP_005919311.1| 138 KENVHPVLFVNKVDrLLNELKVDKQE 163
                                       56777889999999444555666555 PP

>> DUF3748  Protein of unknown function (DUF3748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7   4.9e+03      45      67 ..     113     135 ..     107     143 .. 0.82
   2 ?   10.1   0.0   0.00033      0.58       4      70 ..     615     685 ..     612     695 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                           DUF3748  45 pekastldalditpPytpGaLrG 67 
                                       +++++ +da++ + P t+ +Lr 
  gi|386001012|ref|YP_005919311.1| 113 DGAVVVVDAVEGAMPQTETVLRQ 135
                                       6678899********99999995 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                           DUF3748   4 vvtvsPv..eperlvfihGpenpdeqWkydfsrrrGviveeaepekastldalditpP.y.tpGaLrGGsh 70 
                                       +  ++P+  ep + vfi+ p+++      +++ rrG+i++ ++++ ++ + a + ++  +  +Ga+rG + 
  gi|386001012|ref|YP_005919311.1| 615 ILMANPAilEPFQNVFIQVPQEQMGGAMSEIQGRRGMILSMETEGDMIIIKAKAPVSElFgFAGAIRGATE 685
                                       55556643378999*************9***********************9986654143589***9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 5200.00
//
Query:       gi|386001013|ref|YP_005919312.1|  [L=422]
Description: Elongation factor 1-alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-56  191.5   0.0    1.8e-56  190.8   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.6e-39  134.6   0.5    6.9e-39  132.6   0.2    2.2  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    2.6e-16   59.8   1.5    8.4e-16   58.1   1.5    2.0  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.6e-06   27.5   0.0    3.9e-05   23.7   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
    0.00037   20.3   1.5      0.001   18.9   1.5    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4
     0.0055   16.6   0.0       0.41   10.6   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
     0.0077   15.8   0.1       0.17   11.4   0.1    2.6  2  FeoB_N       Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.055   12.4   0.0        0.1   11.6   0.0    1.3  1  AMA-1        Apical membrane antigen 1
      0.064   12.6   0.0       0.23   10.8   0.0    1.8  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
       0.14   12.3   0.0         17    5.4   0.0    2.5  2  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.0     1e-59   1.8e-56       1     183 [.       5     206 ..       5     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 1e-59
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHST.............HCHSHHHHHHTSCSSCEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeerv.............lDtlkeErergiTiksaaisl 63 
                                       k+++n+++ighvDhGK+TL++rL++++ga+s +  ++ + +++             +D+lkeErerg+Ti++ +  +
  gi|386001013|ref|YP_005919312.1|   5 KPHMNLAFIGHVDHGKSTLVGRLMFEAGAVSPHIVEQyK-KEAeakgkgsfefawvMDSLKEERERGVTIDIGHQRF 80 
                                       579****************************97776642.222467999**************************** PP

                                       ETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...H CS
                          GTP_EFTU  64 eketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...k 136
                                       +  t+ky ++++D+PGH+dF+k++i+g++++D avlv++a +Gv++qt+e++ la+++g++ +i++iNKmD +   +
  gi|386001013|ref|YP_005919312.1|  81 D--TDKYYFTIVDCPGHRDFIKNMITGASQADSAVLVIAAPDGVMAQTREHVFLARTLGINqLIIAINKMDAAkysE 155
                                       *..************************************************************************9* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............H CS
                          GTP_EFTU 137 aelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............t 183
                                       a++ke++eev  kl      l+ +g+k   e+p++++Sa+ g++v             t
  gi|386001013|ref|YP_005919312.1| 156 ARFKEVKEEVG-KL------LQMVGYKVA-EIPFIPVSAFVGDNVIargdnltwysgpT 206
                                       ***********.55......588899985.9************9875555555555554 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.9e+03      36      70 ..     262     287 ..     246     295 .. 0.55
   2 !  132.6   0.2   3.8e-42   6.9e-39       3     111 ..     313     419 ..     311     420 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                       -EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CE CS
                       GTP_EFTU_D3  36 advtgkvveLlskldkktekvsekkpefvkpGdnv 70 
                                       a+vtg+v+++    +      +++++e + pGdn+
  gi|386001013|ref|YP_005919312.1| 262 ANVTGEVKTI----E-----MHHEEAEEALPGDNI 287
                                       4555555555....1.....112223445555555 PP

  == domain 2  score: 132.6 bits;  conditional E-value: 3.8e-42
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+Aq+++l++  +++i agY+pv++++ta+++++ +e+++kld++t+ v+e++p f+k Gd++iv+v ++kp
  gi|386001013|ref|YP_005919312.1| 313 TVAKEFTAQIVVLQH--PSAISAGYTPVFHCHTAQIACTLTEIKAKLDPRTGAVKEQNPAFIKAGDAAIVTVMPTKP 387
                                       6789***********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       +++ek++e+pqlGrFaiR++g+T+aaG+ ++i
  gi|386001013|ref|YP_005919312.1| 388 MVIEKVKEIPQLGRFAIRDMGQTIAAGMCMNI 419
                                       ***************************99887 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   1.5   4.7e-19   8.4e-16       1      73 [.     239     305 ..     239     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.7e-19
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  grv++G++kkGd++ + + n t      ++++ +e++he+ +ea +g+n+G +v+++g +d i++Gd+ 
  gi|386001013|ref|YP_005919312.1| 239 GTVPVGRVETGIIKKGDKIIFEPaNVT------GEVKTIEMHHEEAEEALPGDNIGWNVRGIGKKD-IKRGDVC 305
                                       99*******************887776......99*******************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.2e-08   3.9e-05       2      96 ..      10     128 ..       9     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                                       EEEEESTTSSHHHHHHHHH.....................T..........STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt.....................g..........ekaivsdkpgtTrdinegrvklkgke 47 
                                        a++G+   GKStL+ +l+                     g          +  + +++ g+T+di + r+++++  
  gi|386001013|ref|YP_005919312.1|  10 LAFIGHVDHGKSTLVGRLMfeagavsphiveqykkeaeakGkgsfefawvmDSLKEERERGVTIDIGHQRFDTDKYY 86 
                                       699***************988877777777777666655515566665553467889999************99999 PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHH CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldee 96 
                                       +++vD+pG  +    +  +++ +    +ad ++lv+ a  +++ ++ +e
  gi|386001013|ref|YP_005919312.1|  87 FTIVDCPG--H----RDFIKNMITGASQADSAVLVIAAP-DGVMAQTRE 128
                                       ********..3....223555555566788889888765.333333333 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.5   5.6e-07     0.001      21      84 ..     243     304 ..     231     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-07
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                       vG +v +G+ik g k+i e  +  Ge++ i+ ++++ eea  G++++  ++g    ++ik gd+
  gi|386001013|ref|YP_005919312.1| 243 VG-RVETGIIKKGDKIIFEPANVTGEVKTIEMHHEEAEEALPGDNIGWNVRGIG-KKDIKRGDV 304
                                       88.9**********************************************9933.467999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.031        56     102     123 ..      10      31 ..       3      53 .. 0.80
   2 !   10.6   0.0   0.00023      0.41      13      79 ..     106     176 ..      84     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.031
                                       EEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                        +++G+   GKStL+ +l+ e+
  gi|386001013|ref|YP_005919312.1|  10 LAFIGHVDHGKSTLVGRLMFEA 31 
                                       5799***********9998764 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00023
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.....HHHHHHHHHHHTTSEE CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee.....eleelkeelealgyev 79 
                                       ++  d +++v+++   +  + +    ++la + gi +++i++nK+D ++ +e       ee+ + l+ +gy+v
  gi|386001013|ref|YP_005919312.1| 106 ASQADSAVLVIAAP--DGVMAQTREHVFLARTLGInQLIIAINKMDAAKYSEarfkeVKEEVGKLLQMVGYKV 176
                                       67889999999987..444445555666778888868999********9998755533344445556666666 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.17     3e+02       2      21 ..       9      28 ..       8      49 .. 0.85
   2 !   11.4   0.1   9.5e-05      0.17      32     125 ..      70     158 ..      68     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.17
                                      EEEEEESTTSSHHHHHHHHH CS
                            FeoB_N  2 tvalvGnpnvGkttlfnalt 21
                                      ++a++G  + Gk+tl+ +l 
  gi|386001013|ref|YP_005919312.1|  9 NLAFIGHVDHGKSTLVGRLM 28
                                      6799***********99886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.5e-05
                                       TSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHHHHHHHTTS CS
                            FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardflleeepdvvvnvvdatnlernLyLtlqllelgv 106
                                       Gvt++  + +++++++ ++ivD PG  ++  + ++   +    +l+   pd v+         r+ +++++ l ++ 
  gi|386001013|ref|YP_005919312.1|  70 GVTIDIGHQRFDTDKYYFTIVDCPGHRDFikNMITGASQADSAVLVIAAPDGVMA------QTREHVFLARTLGIN- 139
                                       9************************987744556666666666777777776653......334444455555554. PP

                                       SEEEEEETHHHHHHTTEEE CS
                            FeoB_N 107 pvvlalnmideaekkgiei 125
                                       ++++a+n++d+a+ ++ + 
  gi|386001013|ref|YP_005919312.1| 140 QLIIAINKMDAAKYSEARF 158
                                       6889999999988766554 PP

>> AMA-1  Apical membrane antigen 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05       0.1     228     290 ..     138     201 ..     120     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHHS--SS-SS--SS--HHHHHHTT--BCSSSB---T.TSTTSTTSSCTT--TT-SS-E CS
                             AMA-1 228 Cakiifeesasddikqyeeeledleklkeglknknlsliksa.flPvgayksdrikskGrGlnW 290
                                        +++i      d  k  e +++++++    l +    +++++ f Pv+a+ +d+++++G  l W
  gi|386001013|ref|YP_005919312.1| 138 INQLIIAINKMDAAKYSEARFKEVKEEVGKLLQMVGYKVAEIpFIPVSAFVGDNVIARGDNLTW 201
                                       68999999999***************999999****************************9999 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.23      28      67 ..      66     104 ..      50     118 .. 0.84
   2 ?   -1.1   0.0      0.54   9.7e+02     115     148 ..     142     173 ..     120     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                         Gtr1_RagA  28 tlrlgatidveksevrflgnltlnlwDcgGqeafveeyls 67 
                                        ++ g+tid+ ++++  +++ ++ ++Dc+G ++f++++++
  gi|386001013|ref|YP_005919312.1|  66 ERERGVTIDIGHQRF-DTDKYYFTIVDCPGHRDFIKNMIT 104
                                       566689******999.58999***************9765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.54
                         Gtr1_RagA 115 fvlihKmDliqedereeifeerkeeireeiekle 148
                                        + i+KmD    +  e  f+e kee+ + ++ ++
  gi|386001013|ref|YP_005919312.1| 142 IIAINKMDAA--KYSEARFKEVKEEVGKLLQMVG 173
                                       5678999987..5667778888888877766554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0094        17       1      19 [.      10      28 ..      10      40 .. 0.85
   2 ?    4.5   0.0     0.019        33      64     151 ..      55     133 ..      32     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0094
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      +a++G++ +GKS+++  L+
  gi|386001013|ref|YP_005919312.1| 10 LAFIGHVDHGKSTLVGRLM 28
                                      589***********98887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.019
                                       -CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS CS
                         Dynamin_N  64 dfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanh 140
                                       +f  v + +++e+e+         ++ i ++ ++ ++   t+vD PG  +  k   ++++ + +  +++l++ + + 
  gi|386001013|ref|YP_005919312.1|  55 EFAWVMDSLKEERERGV-------TIDIGHQRFDTDKYYFTIVDCPGHRDFIK---NMITGASQADSAVLVIAAPDG 121
                                       55555555555555544.......346778888999999********988544...456666666666666665555 PP

                                       -CCC-.CHHHHH CS
                         Dynamin_N 141 dlsns.ealfla 151
                                        ++++ e  fla
  gi|386001013|ref|YP_005919312.1| 122 VMAQTrEHVFLA 133
                                       555554555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2908.14
//
Query:       gi|386001014|ref|YP_005919313.1|  [L=102]
Description: 30S ribosomal protein S10P [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-26   92.6   0.0    1.6e-26   92.4   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.058   14.2   0.0       0.12   13.2   0.0    1.5  2  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   1.7e-30   1.6e-26       1      97 [.       5      98 ..       5      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.7e-30
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      rirl+++d+++L+++++++  +a+++g+ + gp+plPtkr  v+++ksp ++ + +++++e+r+hkR+id+ da+++ +
  gi|386001014|ref|YP_005919313.1|  5 RIRLSGTDPRSLDEICSQVRGIAQRTGVHMAGPIPLPTKRMVVPTRKSPDGEgTATWDHWEMRVHKRMIDL-DADERAL 82
                                      8**********************************************************************.8****** PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      ++l++   +++p+ V++e+
  gi|386001014|ref|YP_005919313.1| 83 RQLMR---IQVPKNVNIEI 98
                                      *****...*********97 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05      0.12       6      51 ..       4      45 ..       1      50 [. 0.93
   2 ?   -2.3   0.0      0.93   8.4e+03      68      74 ..      81      87 ..      70      98 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                            PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiaki 51
                                      a+ir+sg+d + + e +++++ + ++    ++v++ gp+p p +++
  gi|386001014|ref|YP_005919313.1|  4 ARIRLSGTDPRSLDEICSQVRGIAQR----TGVHMAGPIPLPTKRM 45
                                      89*********************999....6799********9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.93
                            PriA_C 68 alqkllk 74
                                      al++l++
  gi|386001014|ref|YP_005919313.1| 81 ALRQLMR 87
                                      3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 795.59
//
Query:       gi|386001015|ref|YP_005919314.1|  [L=93]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-21   75.8   0.2      3e-21   75.5   0.2    1.1  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.2   1.7e-25     3e-21       2      61 ..      19      88 ..      18      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.7e-25
                                      -HHHHHHHHHHHHHHHHHHTTCGCS--TT----S.......-EB-S--.....HHHHHTT-SSEETTEEE CS
                       Glu-tRNAGln  2 seeEleklakelnsildyveqLqevdttgveplthp.....vlReDev.....reelLknApetedgyfv 61
                                      se E e +   +ns+ldy+ qL+e+dt++vep++++     v+ReD+v     +ee+L+nAp te+gyf+
  gi|386001015|ref|YP_005919314.1| 19 SEVEREGFVASFNSVLDYFHQLDELDTEDVEPTYRVvdltnVFREDVVgeslsSEEALSNAPRTENGYFK 88
                                      7889******************************************98889*9999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 689.06
//
Query:       gi|386001016|ref|YP_005919315.1|  [L=475]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.8e-154  514.4   0.0   3.1e-154  514.2   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.2   0.0  1.7e-158  3.1e-154       3     451 .]      19     454 ..      17     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 514.2 bits;  conditional E-value: 1.7e-158
                                       HHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-S CS
                           Amidase   3 veaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypae 79 
                                       v+a++++i++  ++lna++ +  e+al++A+++d++     + g L+GvPi++K +i++kg++t ++s++l++y+++
  gi|386001016|ref|YP_005919315.1|  19 VSALFSKINK--SRLNAYNVLSEEAALERAREYDRSP----WGGLLAGVPIAIKSSISTKGIETNCSSRILTGYIPP 89 
                                       5667777777..89********************997....6*********************************** PP

                                       S--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTT CS
                           Amidase  80 kDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSi 156
                                       +Datv+erLk++Ga+i+gkTnmdefamg+ste+s+fgpt+NPwd +r+pGGSSGGsAAavAag +p a+G+DtGGSi
  gi|386001016|ref|YP_005919315.1|  90 YDATVIERLKEEGAIIIGKTNMDEFAMGTSTETSCFGPTKNPWDADRVPGGSSGGSAAAVAAGEAPCALGSDTGGSI 166
                                       ***************************************************************************** PP

                                       HHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT- CS
                           Amidase 157 RiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkk 233
                                       R+PAsfcg+vGlKPtyg+vSr+g+v++++sl+++Gpl+ sved+al+l+vi+g+dp+dsts+ +   ++ + ++ + 
  gi|386001016|ref|YP_005919315.1| 167 RCPASFCGIVGLKPTYGLVSRYGLVSYANSLEQIGPLTLSVEDAALVLDVIAGHDPRDSTSARS---EGGYFARIEG 240
                                       **************************************************************94...5888899999 PP

                                       --TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS.- CS
                           Amidase 234 slkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry.e 309
                                         +gl  Gv++e++ + +dp v++av +a+ +Le +G+  ++v+lp+  +al++yy+i+++eassnlar++g ry  
  gi|386001016|ref|YP_005919315.1| 241 GVDGLTLGVPQEYFGEGVDPLVEKAVWDAISKLEGLGASWKKVSLPHTRYALAAYYIIAMSEASSNLARFDGLRYgL 317
                                       99*************************************************************************** PP

                                       --SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCC..BSEEEEESSSS CS
                           Amidase 310 rlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafee..lDvllsPtapt 384
                                       rl  +++++++++ +ra+++g+evkrri lg+yalsa++++ yylka kvr+l++++f +a+ +   D+l++Pt+p 
  gi|386001016|ref|YP_005919315.1| 318 RLGADQDWHTTFSDIRAAGFGPEVKRRILLGTYALSAGYYGRYYLKALKVRTLIKQDFERALSAggADLLVTPTMPF 394
                                       ***************************************************************************** PP

                                       S--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 385 paprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                       pa+r+ge+    +++++ly  ++ft   vp nlag pa+svp+g+  dglP+G+q+ig++f+e+++L
  gi|386001016|ref|YP_005919315.1| 395 PAFRIGERI---EDPLSLYMADVFT---VPINLAGVPAISVPCGFA-DGLPIGLQIIGRHFDEAAVL 454
                                       ******997...69***********...****************96.6****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 3542.41
//
Query:       gi|386001017|ref|YP_005919316.1|  [L=480]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete 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-100  335.7   0.0   2.7e-100  335.3   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    3.8e-40  137.2   0.0    5.6e-40  136.6   0.0    1.3  1  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.018   15.1   0.2      0.041   14.0   0.2    1.6  1  YqeY       Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.3   0.0  4.5e-104  2.7e-100       1     269 [.       6     284 ..       6     287 .. 0.97

  Alignments for each domain:
  == domain 1  score: 335.3 bits;  conditional E-value: 4.5e-104
                                       EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRK 76 
                                       ++iGlE+H+ql++ +sKlF+++st  +++ pn+++++v+l+lPGtlPv+nk+ave+ai++alalnc i+ e+ f+RK
  gi|386001017|ref|YP_005919316.1|   6 VIIGLEVHVQLNKlNSKLFCGCSTDYHDSPPNTHTCPVCLGLPGTLPVVNKRAVEYAIRVALALNCAIQGETLFYRK 82 
                                       58*********998*********7767777*********************************************** PP

                                       E-TCTTCTTSEEEEESSS.SEEEEEEEE......TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                            GatB_N  77 nyfypdlpkgyQitqkeeplakeGslel......ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiE 143
                                       ny+ypdlpk++Qitq++ pl  +Gs+ +      e+++ri+r+h+EeD ++ vh    +++++s+vd+nR+G++L+E
  gi|386001017|ref|YP_005919316.1|  83 NYYYPDLPKAFQITQYDFPLGLGGSILIkgedgeERRIRITRVHMEEDPGRLVHagtiDRAKYSMVDYNRCGMALLE 159
                                       **************************99999999999*****************99987888*************** PP

                                       EEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 144 ivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaiey 220
                                       +vtepdlrsp+ear++++klr++l++l+v dgn+ eG++R+D N+S+         g+r E+Kn++s k +eka++y
  gi|386001017|ref|YP_005919316.1| 160 VVTEPDLRSPKEARSFLDKLRNILEYLDVFDGNL-EGAMRIDSNISLVG-------GERAEVKNISSHKGVEKALAY 228
                                       **********************************.7************4.......49******************* PP

                                       HHHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--H CS
                                       xxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 221 eierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleise 269
                                       ei+rq ++        qeTr++de +g tv++R+keea+dYryfpepdl+p++i +
  gi|386001017|ref|YP_005919316.1| 229 EITRQRSARrrgvaqvQETRHYDELRGITVTIRTKEEAHDYRYFPEPDLVPMRIAD 284
                                       *******999******************************************9976 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.0   9.4e-44   5.6e-40       3     148 .]     327     474 ..     325     474 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 9.4e-44
                                       HHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH....HH.TX CS
                         GatB_Yqey   3 feevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleell....ee.gk 74 
                                       f evv+e+a ++laa+w+++ l geln+++++ie+  ++p+q++ +l+li+ gkI++k a ev++++l    e+ + 
  gi|386001017|ref|YP_005919316.1| 327 FYEVVAERAPPRLAAAWIADVLKGELNYRDVTIER--FSPDQMVVILDLIEGGKITEKGAVEVIRTILdgpgETtEA 401
                                       789999999**************************..9******************************888844589 PP

                                       XHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  75 speeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       +p++i+  kgL  ++d ++++++v  +++e ++av+dy++g+eka++f+vG vMkkt+G+adp ++n+l++e L
  gi|386001017|ref|YP_005919316.1| 402 DPAAIVATKGLSRVED-DAVMAAVRAAVEESSQAVADYRAGNEKAINFIVGVVMKKTRGRADPGEANRLVREAL 474
                                       99**************.******************************************************987 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   6.9e-06     0.041      93     143 .]     417     474 ..     406     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-06
                                       HHHHHHHHHHHHHHTT--.......BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH- CS
                              YqeY  93 eeeiealvkeaiaevgae.......smkdmGkvmkalkpkvkGkaDgkkvsalvkekL 143
                                       ++ + a+v++a++e +++       + k++  +++++++k++G+aD +++++lv+e L
  gi|386001017|ref|YP_005919316.1| 417 DDAVMAAVRAAVEESSQAvadyragNEKAINFIVGVVMKKTRGRADPGEANRLVREAL 474
                                       666666666666666444445555599****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3524.84
//
Query:       gi|386001018|ref|YP_005919317.1|  [L=364]
Description: hypothetical protein Mhar_0307 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2365.73
//
Query:       gi|386001019|ref|YP_005919318.1|  [L=441]
Description: Phenylacetate-coenzyme A ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-33  114.0   0.2    6.2e-33  113.0   0.2    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
      1e-15   57.3   0.2    1.2e-14   53.7   0.0    2.2  2  AMP-binding      AMP-binding enzyme
    0.00042   19.3   0.0       0.54    9.1   0.0    2.1  2  GH3              GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.2     1e-36   6.2e-33       1      96 []     343     439 ..     343     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 1e-36
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       G+nvfPsq+e+vl++i+ev+++Yqi+v+r+g lD ++v vEv+e gfsd++++l +l+k+i+k+lk +l+v ++vel
  gi|386001019|ref|YP_005919318.1| 343 GINVFPSQVESVLMTIPEVGDHYQIIVDRKGPLDIMKVMVEVTEtGFSDKISDLMSLSKRISKELKGVLNVVADVEL 419
                                       99******************************************99******************************* PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                       vepg +prsegKa rviDkR
  gi|386001019|ref|YP_005919318.1| 420 VEPGRIPRSEGKAVRVIDKR 439
                                       *******************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0     2e-18   1.2e-14     166     370 ..      98     294 ..      22     297 .. 0.80
   2 ?    1.5   0.0     0.015        88     409     423 .]     328     342 ..     306     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2e-18
                                       EE--SSSS-EEEEEEHHHH.HHHHHHHH.HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC CS
                       AMP-binding 166 YTSGTTGkPKGVmlshrnl.vanvaslk.letrfklkeddvv.lsilplahifglilelllallsGatvvllpkdaa 239
                                        +SGTTGkP  V ++ + + +    sl+   t  +l+++dv+ + +    +  gl    ++a   Gatv   +++  
  gi|386001019|ref|YP_005919318.1|  98 VSSGTTGKPTVVGYTKDDIeM-WSDSLArALTSIGLGRGDVIqVGYGYGLFTGGL-GLHYGAEKIGATVLP-TGTGN 171
                                       58**************99953.335554322236677899996666666677776.999999999998755.55555 PP

                                       CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEE CS
                       AMP-binding 240 ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegY 315
                                       ++ +  + l+++l+ t ia++P+ + +++e +++    ++ +d  sl++ ++g+ep s e+ r++++ +g + ++++
  gi|386001019|ref|YP_005919318.1| 172 TERQ--IMLMQDLGSTAIACTPSYFLHIAEvAERMG--VSIRDDTSLKVGVFGAEPWSDETRRRIEEATGIKAYDIF 244
                                       4434..56********************99776555..56678899******************************* PP

                                       EEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                       G +E++g ++  +++e+    g +        ++++D++tge +pdge+Gel++ 
  gi|386001019|ref|YP_005919318.1| 245 GTSEMSGPLF-TECQEQ---NG-IHIWSDMFLIEVIDPKTGEVLPDGETGELVIT 294
                                       ********98.564444...22.444445778999******************96 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.015
                                       EEEEEEECCCEEEET CS
                       AMP-binding 409 yleivgRkkdliklr 423
                                        ++i+gR++d+i++r
  gi|386001019|ref|YP_005919318.1| 328 LMRILGRTDDMIVIR 342
                                       589*********986 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0     9e-05      0.54      73     108 ..      90     124 ..      85     199 .. 0.84
   2 !    8.3   0.0   0.00015      0.89     357     419 ..     286     357 ..     273     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 9e-05
                                       SSS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.H CS
                               GH3  73 sepiklfalsSGTtsgksKliPvteeslkelallvl 108
                                       +++i+++  sSGTt gk+ ++ +t++  + ++  ++
  gi|386001019|ref|YP_005919318.1|  90 RNRIVRYHVSSGTT-GKPTVVGYTKDDIEMWSDSLA 124
                                       6789**********.**********99988776544 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00015
                                       TSEEEEEEESTT....S-SSEEECEEEEEEE....EETTEE.EEEEEECCTEEE-SSSS-CCHHHHHHHHH. CS
                               GH3 357 GkeYelvvTtfa....GLyRYrigDvvrvtg....fynkaP.rleFvgRknvvlsidgeklteeelqkavee 419
                                       G++ elv+Tt +     L RYrigD+ ++ +       + P  ++++gR++ ++ i+g  +  +++++++ +
  gi|386001019|ref|YP_005919318.1| 286 GETGELVITTLSkwaiPLIRYRIGDLTKIDSepcpCGRTHPrLMRILGRTDDMIVIRGINVFPSQVESVLMT 357
                                       77779999997644447************9833334567897789**************9999999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3312.72
//
Query:       gi|386001020|ref|YP_005919319.1|  [L=144]
Description: Amino acid-binding ACT domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-17   61.2   0.0    2.3e-09   36.9   0.0    2.4  2  ACT       ACT domain
    2.5e-06   28.0   0.3      0.014   16.0   0.1    2.2  2  ACT_4     ACT domain
    2.1e-05   24.2   0.1     0.0058   16.4   0.0    2.8  2  ACT_7     ACT domain
  ------ inclusion threshold ------
      0.056   14.0   0.2        8.9    7.0   0.1    2.3  2  P-II      Nitrogen regulatory protein P-II
      0.098   12.7   0.0       0.33   11.0   0.0    1.8  2  ACT_6     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   6.3e-13   2.3e-09       3      53 ..       7      54 ..       5      60 .. 0.86
   2 !   22.0   0.0   2.8e-08   9.9e-05       3      51 ..      73     119 ..      72     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.3e-13
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHH CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdee 53
                                      ++++v+++PG +a+v+ +l+d+g+Ni+ +++++ +d     v+ ++v d+e
  gi|386001020|ref|YP_005919319.1|  7 ISLFVENKPGRMAKVSKTLSDAGVNIRALTVAEAGD---FGVIRMVVDDPE 54
                                      8899*******************************9...777777776665 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.8e-08
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEE CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvd 51 
                                       l v+++D PG L ++ ++l++  +N+d +  + +    a+++ ++i vd
  gi|386001020|ref|YP_005919319.1|  73 LAVEMKDIPGGLYEIVNTLGESEVNVDYAYAFVTTK--AERALLIIRVD 119
                                       6699******************************99..89999888887 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.9e-06     0.014       8      53 ..       6      49 ..       4      52 .. 0.86
   2 !   10.2   0.0   0.00025      0.91       9      65 ..      73     127 ..      70     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikit 53
                                      ++++ +e+++g +a++++++s++++ni+++++ +  +  +  i++ 
  gi|386001020|ref|YP_005919319.1|  6 QISLFVENKPGRMAKVSKTLSDAGVNIRALTVAE--AGDFGVIRMV 49
                                      68999**************************998..4457777665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                             ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrv 65 
                                       l ve++d +g L +i++++ e+++n+    a  +   +  +  + + V ++e+ +rv
  gi|386001020|ref|YP_005919319.1|  73 LAVEMKDIPGGLYEIVNTLGESEVNVDYAYAFVTT--KAERALLIIRVDNLEKARRV 127
                                       78999*********************987777744..34566777777777776666 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.6e-06    0.0058      20      44 ..      14      39 ..       4      62 .. 0.86
   2 !    5.2   0.1    0.0049        18      19      64 ..      79     129 ..      66     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                      S--HHHHHHHHHHTTT---EEEE.-S CS
                             ACT_7 20 vtGivaklaspLaeagIsifqiS.ty 44
                                       +G++ak+++ L++ag++i +++  +
  gi|386001020|ref|YP_005919319.1| 14 KPGRMAKVSKTLSDAGVNIRALTvAE 39
                                      69*****************9887555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0049
                                       SS--HHHHHHHHHHTTT---.....EEEE-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7  19 dvtGivaklaspLaeagIsi.....fqiStyrtdyiLVpeedlekAveaLh 64 
                                       d++G + ++++ L e  +++     f+++ +    ++++ ++lekA ++L+
  gi|386001020|ref|YP_005919319.1|  79 DIPGGLYEIVNTLGESEVNVdyayaFVTTKAERALLIIRVDNLEKARRVLT 129
                                       578888888888888888874443344445666788999999999999997 PP

>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0096        34       6      35 ..      14      45 ..      13      75 .. 0.86
   2 ?    7.0   0.1    0.0025       8.9       4      29 ..     115     140 ..     113     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0096
                                      EGGGHHHHHHHHHHTT..GGCEEEEEEEEEES CS
                              P-II  6 rpekleevkeaLekag..vkgltvtevkGrGk 35
                                      +p ++ +v ++L++ag  +++ltv e   +G 
  gi|386001020|ref|YP_005919319.1| 14 KPGRMAKVSKTLSDAGvnIRALTVAEAGDFGV 45
                                      68899**********96678999999877775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0025
                                       EEEGGGHHHHHHHHHHTTGGCEEEEE CS
                              P-II   4 iirpekleevkeaLekagvkgltvte 29 
                                       iir ++le+ + +L++agvk  t  e
  gi|386001020|ref|YP_005919319.1| 115 IIRVDNLEKARRVLTDAGVKLATREE 140
                                       9******************9998766 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.2e-05      0.33       6      51 ..       8      53 ..       6      63 .. 0.85
   2 ?   -1.6   0.0      0.76   2.7e+03      11      30 ..      79      98 ..      70      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
                             ACT_6  6 tvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp 51
                                      +++ +++pG  a+++++l++ gvni  + +a  ++  ++ ++v+ p
  gi|386001020|ref|YP_005919319.1|  8 SLFVENKPGRMAKVSKTLSDAGVNIRALTVAEAGDFGVIRMVVDDP 53
                                      555679********************99999999988888888765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.76
                             ACT_6 11 drpGltasLtsvlaefgvni 30
                                      d pG + ++  +l e+ vn+
  gi|386001020|ref|YP_005919319.1| 79 DIPGGLYEIVNTLGESEVNV 98
                                      67888889999998888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 1054.64
//
Query:       gi|386001021|ref|YP_005919320.1|  [L=394]
Description: hypothetical protein Mhar_0310 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.7    6.4   9.3        2.4    8.2   0.3    3.5  3  DUF4227   Protein of unknown function (DUF4227)


Domain annotation for each model (and alignments):
>> DUF4227  Protein of unknown function (DUF4227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3   0.00014       2.4      10      38 ..      26      53 ..      23      55 .. 0.84
   2 ?    1.0   0.1     0.024   4.2e+02      10      34 ..     115     139 ..     108     143 .. 0.84
   3 ?   -0.1   1.0     0.051   9.2e+02       3      34 ..     243     274 ..     241     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00014
                           DUF4227 10 flLFtvltllfyyallwlneeyepyhrYd 38
                                      +++F ++ +l+y +l  l e + +yh++d
  gi|386001021|ref|YP_005919320.1| 26 LIIF-ICCCLIYIILSVLVESLPDYHDWD 53
                                      4555.57799****************998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.024
                           DUF4227  10 flLFtvltllfyyallwlneeyepy 34 
                                       f + ++l+++ +y++ ++  e+++y
  gi|386001021|ref|YP_005919320.1| 115 FYIILILAIIPFYGIDLIRGEVRSY 139
                                       667789999*********9999887 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.051
                           DUF4227   3 llerlkvflLFtvltllfyyallwlneeyepy 34 
                                       +++ + ++ +   +t+ f+ +  ++ +e+ ++
  gi|386001021|ref|YP_005919320.1| 243 MFHEIIFLSILFSITVYFFISSWFIIQELLEA 274
                                       56667777776777888887777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2984.09
//
Query:       gi|386001022|ref|YP_005919321.1|  [L=193]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1386.09
//
Query:       gi|386001023|ref|YP_005919322.1|  [L=991]
Description: hypothetical protein Mhar_0312 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  127.1   0.7    2.9e-08   33.4   0.2    4.7  4  PKD             PKD domain
    4.9e-06   27.0   0.0    1.3e-05   25.6   0.0    1.7  1  Transglut_core  Transglutaminase-like superfamily
     0.0012   18.5   0.3       0.11   12.1   0.1    3.6  4  ChitinaseA_N    Chitinase A, N-terminal domain
  ------ inclusion threshold ------
      0.019   15.2   0.4        5.1    7.3   0.0    2.9  3  DUF4625         Domain of unknown function (DUF4625)
       0.11   12.8   1.9         14    6.1   0.1    4.5  5  Colicin_E5      Colicin E5 ribonuclease domain
       0.14   11.7   0.1        3.1    7.3   0.0    2.8  4  TcfC            E-set like domain
       0.14   11.6   0.1          1    8.8   0.1    2.2  1  DUF553          Transglutaminase-like domain
       0.16   10.7   5.3         19    3.9   0.0    4.6  5  REJ             REJ domain
        8.8    6.2   9.3         27    4.6   0.0    4.5  6  DUF1314         Protein of unknown function (DUF1314)


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   7.3e-11   1.5e-07      23      67 ..     293     334 ..     277     338 .. 0.87
   2 !   33.4   0.2   1.5e-11   2.9e-08      14      65 ..     366     421 ..     361     425 .. 0.90
   3 !   28.8   0.0     4e-10   7.9e-07      20      67 ..     461     508 ..     446     512 .. 0.85
   4 !   28.0   0.0   7.3e-10   1.5e-06      16      69 ..     542     596 ..     528     598 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.3e-11
                                       SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
                               PKD  23 ganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                                       g ++ y+Wdfgd   +  + +p v+htY++ G Y V +++++  g
  gi|386001023|ref|YP_005919322.1| 293 GGIADYEWDFGD---GVREKGPVVNHTYRKGGPYPVMLKVTDVEG 334
                                       77899*******...**************************9766 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.5e-11
                                       EEEEEES.....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-S CS
                               PKD  14 vaftaav....pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasna 65 
                                       ++f a+     +dg+ ++++W+fgdg ++  ls   +t  Y++ G+++V++t++++
  gi|386001023|ref|YP_005919322.1| 366 ITFDASEsydeEDGEVASFTWNFGDGHTTMELSDGLATNFYPRSGTFNVSLTVKDS 421
                                       678888888889******************************************97 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 4e-10
                                       S....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
                               PKD  20 v...pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                                           +dg+++ y+W+fgd   + + ++p + h Yl+ G++ +++   ++  
  gi|386001023|ref|YP_005919322.1| 461 QsldADGKITEYRWNFGD---GKTARGPQAIHNYLKGGNFIIKLEIIDDND 508
                                       33479*************...*********************998877765 PP

  == domain 4  score: 28.0 bits;  conditional E-value: 7.3e-10
                                       EEEES....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EE CS
                               PKD  16 ftaav...pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsa 69 
                                       f a      dg++v y+Wdfg    + ++   +v ++Y + G Y V +t+++++g+ 
  gi|386001023|ref|YP_005919322.1| 542 FDADEsedLDGRIVDYLWDFGE--GGRKQGFACVDYKYIKGGVYSVVLTVTDDDGAK 596
                                       5555544448************..89999************************9975 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.5e-09   1.3e-05       3     103 ..      91     190 ..      89     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.5e-09
                    Transglut_core   3 laeeltagakdplekakaiyewvrknveys.aprrtpgsrdaeavle.......tgkGncedfaslfvallRalGip 71 
                                       la+++    +++ e++ +i e++++n +y+ +pr +  +r a+++++       +g+G+c dfa l++al  ++G  
  gi|386001023|ref|YP_005919322.1|  91 LAQRF--PGDHSVEQVCEIFEYLKNNWNYTgDPRCGEFYRYANQTIRlgeeigrAGAGDCDDFAILMAALIENIGGT 165
                                       66666..5667779****************988888888889999996666555666******************** PP

                    Transglut_core  72 aRvvtgylsgeeekeqsvasedaHawvevyl....e 103
                                       +++   y +           ++ Ha++ev++     
  gi|386001023|ref|YP_005919322.1| 166 TKINLVYDE-----------WQGHAYTEVCIgkhnS 190
                                       ***988866...........999*******955550 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.52     1e+03      37      57 ..     165     185 ..     156     211 .. 0.67
   2 ?    0.1   0.0       0.3   5.9e+02      76     106 ..     314     344 ..     303     348 .. 0.80
   3 ?   -0.7   0.0      0.52     1e+03      72     104 ..     484     516 ..     471     520 .. 0.79
   4 !   12.1   0.1   5.5e-05      0.11      75     111 ..     573     609 ..     550     615 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.52
                      ChitinaseA_N  37 eaevsvewnvWsGeagdkakv 57 
                                       + ++++ ++ W G+a +++ +
  gi|386001023|ref|YP_005919322.1| 165 TTKINLVYDEWQGHAYTEVCI 185
                                       578999*******99877766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
                      ChitinaseA_N  76 tfkvkkgGryqlevelCdaeGCsksapkeiv 106
                                       + +++kgG y + +++ d eG  + + ++i 
  gi|386001023|ref|YP_005919322.1| 314 NHTYRKGGPYPVMLKVTDVEGKENRTISSIE 344
                                       6789***************997766666655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.52
                      ChitinaseA_N  72 kesatfkvkkgGryqlevelCdaeGCsksapke 104
                                         +a  ++ kgG++ +++e+ d +   +s++  
  gi|386001023|ref|YP_005919322.1| 484 GPQAIHNYLKGGNFIIKLEIIDDNDAVNSTTRD 516
                                       4578899*************9999888887665 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 5.5e-05
                      ChitinaseA_N  75 atfkvkkgGryqlevelCdaeGCsksapkeivvaDtD 111
                                         +k+ kgG y++ + + d +G  +s++k+++v + +
  gi|386001023|ref|YP_005919322.1| 573 VDYKYIKGGVYSVVLTVTDDDGAKSSNSKKVTVGEKE 609
                                       57999***************************98766 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0026       5.1     106     131 ..     320     345 ..     313     346 .. 0.91
   2 ?   -3.8   0.0       7.1   1.4e+04      31      49 ..     490     508 ..     482     518 .. 0.67
   3 ?    4.8   0.1     0.015        31     104     130 ..     578     604 ..     575     606 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
                           DUF4625 106 aGdYhlvirvtDasGneteesreiki 131
                                        G Y ++++vtD +G e+++  +i++
  gi|386001023|ref|YP_005919322.1| 320 GGPYPVMLKVTDVEGKENRTISSIEV 345
                                       599****************9999986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.1
                           DUF4625  31 vlkiGetlhfeaklsdnea 49 
                                        + +G ++ ++++++d+++
  gi|386001023|ref|YP_005919322.1| 490 NYLKGGNFIIKLEIIDDND 508
                                       5567888888888876543 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.015
                           DUF4625 104 aeaGdYhlvirvtDasGneteesreik 130
                                       ++ G Y +v++vtD +G ++  s +++
  gi|386001023|ref|YP_005919322.1| 578 IKGGVYSVVLTVTDDDGAKSSNSKKVT 604
                                       678***************999887765 PP

>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   4.2e+03      41      67 ..     634     660 ..     624     663 .. 0.83
   2 ?    6.1   0.1     0.007        14      32      67 ..     727     762 ..     695     767 .. 0.91
   3 ?    1.6   0.0      0.18   3.5e+02      38      67 ..     784     813 ..     777     818 .. 0.85
   4 ?   -1.6   0.0       1.7   3.4e+03      39      67 ..     887     915 ..     879     918 .. 0.80
   5 ?   -1.3   0.0       1.4   2.9e+03      32      67 ..     931     966 ..     930     969 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                        Colicin_E5  41 anktsDglrrndsAtvYgekdgkYvvv 67 
                                       + +t  g +++   +v    dg+Y++ 
  gi|386001023|ref|YP_005919322.1| 634 WSRTFGGAGQDGGYSVEQTADGGYIIA 660
                                       66788899999999999999****985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.007
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt s  ++ +++t  g ++++  +v    dg+Y++ 
  gi|386001023|ref|YP_005919322.1| 727 KTDSAGNRVWDRTFGGSGQDEGNSVQQTADGGYIIA 762
                                       899999****************************95 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                        Colicin_E5  38 dkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       d  +++t  g ++++  +v+   dg+Yv+ 
  gi|386001023|ref|YP_005919322.1| 784 DLVWERTFGGKGHEQGDSVWQTDDGGYVIT 813
                                       55688899999*****************96 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.7
                        Colicin_E5  39 kranktsDglrrndsAtvYgekdgkYvvv 67 
                                         ++++  g ++++  +v    dg+Y++ 
  gi|386001023|ref|YP_005919322.1| 887 SEWERAFGGAGQEEGHSVQQTVDGGYIIT 915
                                       5667777899999999**********995 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.4
                        Colicin_E5  32 ktkssddkranktsDglrrndsAtvYgekdgkYvvv 67 
                                       kt ss  + +++t  g +++   +v   +d++Y++ 
  gi|386001023|ref|YP_005919322.1| 931 KTDSSGYRVWDRTFGGAGQEVGFSVQQTTDEGYIIT 966
                                       67788888999999999***9*************95 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.2   8.3e+03      44      54 ..     321     331 ..     320     336 .. 0.82
   2 ?   -3.1   0.0       2.9   5.8e+03      43      57 ..     409     423 ..     401     425 .. 0.79
   3 ?    0.7   0.0      0.19   3.8e+02      41      63 ..     492     514 ..     480     521 .. 0.73
   4 ?    7.3   0.0    0.0016       3.1      31      67 ..     568     604 ..     565     605 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.2
                              TcfC  44 GiYeveirvye 54 
                                       G Y+v ++v +
  gi|386001023|ref|YP_005919322.1| 321 GPYPVMLKVTD 331
                                       89******987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                              TcfC  43 sGiYeveirvyengq 57 
                                       sG+++v + v ++++
  gi|386001023|ref|YP_005919322.1| 409 SGTFNVSLTVKDSNR 423
                                       6999****9999664 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.19
                              TcfC  41 LPsGiYeveirvyengqvvrteq 63 
                                       L  G++ +++++++++  v++++
  gi|386001023|ref|YP_005919322.1| 492 LKGGNFIIKLEIIDDNDAVNSTT 514
                                       6679999*******555555444 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0016
                              TcfC  31 aGnqeidtssLPsGiYeveirvyengqvvrteqqkft 67 
                                        G   +d++    G+Y+v + v ++++  +++++k+t
  gi|386001023|ref|YP_005919322.1| 568 QGFACVDYKYIKGGVYSVVLTVTDDDGAKSSNSKKVT 604
                                       688889********************99999998886 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00053         1       5     118 ..      90     185 ..      86     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00053
                            DUF553   5 klaeklkkensketiinvlewvdenikYdye.kaevvetllvlWatfftlskvdskilklietpkeilktkkgiCrD 80 
                                       +la+++ +  s e++ ++ e++++n +Y  + ++       + +              + i+  +ei +  +g C D
  gi|386001023|ref|YP_005919322.1|  90 SLAQRFPGDHSVEQVCEIFEYLKNNWNYTGDpRCGEF----YRY------------ANQTIRLGEEIGRAGAGDCDD 150
                                       5566666666666666666666666666543122222....221............123455667778889999*** PP

                            DUF553  81 YaiLTaalLlnln.iskvylvsvtfenskvgHaavavki 118
                                       +aiL aal+ n +  +k+ lv+ ++     gHa   v i
  gi|386001023|ref|YP_005919322.1| 151 FAILMAALIENIGgTTKINLVYDEW----QGHAYTEVCI 185
                                       *******999876145666666664....4577666655 PP

>> REJ  REJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.44   8.8e+02      98     111 ..     278     291 ..     267     304 .. 0.76
   2 ?    1.1   0.0     0.065   1.3e+02     278     313 ..     316     350 ..     311     352 .. 0.86
   3 ?    2.3   0.6     0.029        58     101     128 ..     366     389 ..     353     474 .. 0.72
   4 ?   -1.7   0.0      0.48   9.7e+02      99     126 ..     453     475 ..     440     486 .. 0.82
   5 ?    3.9   0.0    0.0094        19     388     417 ..     584     613 ..     578     622 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.44
                               REJ  98 rgnltLdGseSyDp 111
                                       r+ +++d+s+SyD 
  gi|386001023|ref|YP_005919322.1| 278 REPIIFDASQSYDL 291
                                       5889*********8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.065
                               REJ 278 kLqsgesyaltlrvtdkegkksglasisfkvnepPt 313
                                       + ++g  y + l+vtd egk++  +  s++vnepP+
  gi|386001023|ref|YP_005919322.1| 316 TYRKGGPYPVMLKVTDVEGKEN-RTISSIEVNEPPV 350
                                       5577889999************.8888999****97 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.029
                               REJ 101 ltLdGseSyDpdeddhsqsqlsYeWlcr 128
                                       +t+d+seSyD ++ +      s++W + 
  gi|386001023|ref|YP_005919322.1| 366 ITFDASESYDEEDGE----VASFTWNFG 389
                                       777888888774443....335666553 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.48
                               REJ  99 gnltLdGseSyDpdeddhsqsqlsYeWl 126
                                       + + +d+s+S D d + ++     Y+W 
  gi|386001023|ref|YP_005919322.1| 453 EGIAVDASQSLDADGKITE-----YRWN 475
                                       5689**********99877.....5554 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.0094
                               REJ 388 tvmvsVyDnkgarvsvsltitVkppavnns 417
                                       +v+ +V+D +ga +s s+++tV + +++++
  gi|386001023|ref|YP_005919322.1| 584 SVVLTVTDDDGAKSSNSKKVTVGEKESSTA 613
                                       7999******************99999887 PP

>> DUF1314  Protein of unknown function (DUF1314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.013        27       8      27 ..     659     678 ..     657     684 .. 0.88
   2 ?   -0.8   0.0      0.61   1.2e+03       8      26 ..     761     779 ..     759     782 .. 0.88
   3 ?    3.2   0.1     0.035        70       7      27 ..     811     831 ..     810     838 .. 0.89
   4 ?   -3.5   0.0         4     8e+03       8      28 ..     863     883 ..     862     886 .. 0.85
   5 ?   -1.1   0.1      0.74   1.5e+03       8      27 ..     914     933 ..     912     952 .. 0.83
   6 ?   -1.4   0.0      0.91   1.8e+03       8      27 ..     965     984 ..     963     987 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                           DUF1314   8 laGrtvdlPGGGdlhitatk 27 
                                       +aGrt+d  GG dl+++ t+
  gi|386001023|ref|YP_005919322.1| 659 IAGRTLDAFGGDDLWLIKTN 678
                                       79*************99886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.61
                           DUF1314   8 laGrtvdlPGGGdlhitat 26 
                                       +aG t+d  GG dl+++ t
  gi|386001023|ref|YP_005919322.1| 761 IAGYTLDNFGGDDLWLIKT 779
                                       799************9877 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.035
                           DUF1314   7 vlaGrtvdlPGGGdlhitatk 27 
                                       v++Grt+d  GG dl+++ t 
  gi|386001023|ref|YP_005919322.1| 811 VITGRTLDNFGGDDLWLIKTD 831
                                       689*************98875 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 4
                           DUF1314   8 laGrtvdlPGGGdlhitatkt 28 
                                       ++G t+d  GG dl+++ t +
  gi|386001023|ref|YP_005919322.1| 863 ITGYTLDDFGGKDLYLIKTDS 883
                                       579999*********998875 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.74
                           DUF1314   8 laGrtvdlPGGGdlhitatk 27 
                                       ++G t+d  GG dl+++ t 
  gi|386001023|ref|YP_005919322.1| 914 ITGYTLDDFGGDDLWLIKTD 933
                                       67999**********99875 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 0.91
                           DUF1314   8 laGrtvdlPGGGdlhitatk 27 
                                       ++G t+d  GG dl+++ t 
  gi|386001023|ref|YP_005919322.1| 965 ITGYTLDNFGGDDLWLIKTD 984
                                       6799***********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (991 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 5861.59
//
Query:       gi|386001024|ref|YP_005919323.1|  [L=86]
Description: hypothetical protein Mhar_0313 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.38
# Mc/sec: 679.09
//
Query:       gi|386001025|ref|YP_005919324.1|  [L=334]
Description: RNA methylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-26   92.6   0.0    2.4e-25   89.4   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    3.4e-09   37.0   0.0      6e-09   36.1   0.0    1.4  1  THUMP            THUMP domain
    6.9e-06   26.7   0.0    1.9e-05   25.3   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    0.00026   21.6   0.1    0.00086   19.9   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
     0.0026   17.5   0.0     0.0063   16.2   0.0    1.6  2  N6_N4_Mtase      DNA methylase
     0.0082   16.0   0.0      0.013   15.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.097   12.3   0.0    1.9  2  Cons_hypoth95    Conserved hypothetical protein 95
      0.087   12.1   0.0       0.14   11.4   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0   1.1e-28   2.4e-25       1     195 [.     163     328 ..     163     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.1e-28
                                       -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH- CS
                           UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearael 77 
                                       +++++f++p+++ ++LA+alv+l+++++ge+llDP+ G+G++l+Ea+l++ + +                       
  gi|386001025|ref|YP_005919324.1| 163 PHKKPFFHPGAILPKLARALVNLSQVREGERLLDPFAGTGGFLVEAGLMAVRGV----------------------- 216
                                       5789************************************************99....................... PP

                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-------.---HHHHHHHHHHHHHHHH CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGer.lgskkalekLYseflrelk 153
                                          g+D ++r+v+ga +N+e    +    + + da  L+lk+++v++ v++ PYG++ l ++++ ++L    l el 
  gi|386001025|ref|YP_005919324.1| 217 ---GVDVQWRIVRGAASNLEGLDCT----LIVGDAMRLPLKDESVEAAVSDAPYGRSaLIQAGSRDELLTGSLAELR 286
                                       ...****************976655....5568999***9999************9736788999************ PP

                                       HH-TT..-EEEEEESSHHHHHCC---..ESEEEEEEETTEEEEE CS
                           UPF0020 154 rvlrgggrlvlltsenkalekaleer..alrkvkeknvklglll 195
                                       rvl       ++  e++ +  a+ee+  ++ ++++++v+ +l++
  gi|386001025|ref|YP_005919324.1| 287 RVLVP--GRRMIYVEDRPVGGAIEEAgfEILEAHQERVHRSLTR 328
                                       *****..77788899999*******9788889999999999987 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.7e-12     6e-09      31     141 ..      40     147 ..      23     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.7e-12
                                       EEEEETHHHHHHHHHTST....TECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHH CS
                             THUMP  31 ekpeedeellkealekar....giqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsre 103
                                       ++++++++ l+  l ++      ++rv+ v ++ e +   + +aa e++ +       +++Vr+kr g+    +s e
  gi|386001025|ref|YP_005919324.1|  40 RHFVVEAKDLDLSLDRLGarmaMVHRVVEVAAEAEPTAVGVARAAAELDLPDR-----SYRVRAKRLGEA-PLGSDE 110
                                       44555555554444444444446666666655555555666666666666554.....***********9.****** PP

                                       HHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEE CS
                             THUMP 104 inrevGkaivektglkVdlenPdivvrveiikdkayis 141
                                       ++r+vG  +++++  k dl +P+i +r+ +  + ++++
  gi|386001025|ref|YP_005919324.1| 111 VERMVGSVLWRRGY-KADLADPQIEIRAVVTSEGVLLG 147
                                       **************.******************99987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.4   1.2e+04      36      65 ..      65      94 ..      59      98 .. 0.56
   2 !   25.3   0.0   8.4e-09   1.9e-05       2      96 ..     195     292 ..     194     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.4
                                      HHHHHHHHTTTTEEEEESBCCGBSSSTTTE CS
                   Methyltransf_25 36 aareraeeeglnvefvqgdaedlpfedgsf 65
                                      ++ e a+e+++ +  v   a +l+++d+s+
  gi|386001025|ref|YP_005919324.1| 65 RVVEVAAEAEPTAVGVARAAAELDLPDRSY 94
                                      444555555555555555556666666665 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 8.4e-09
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE.....EST CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs.....sga 73 
                                       Ld  +GtG ++ ++     + + +gvD++ + ++ a++++  egl++++++gda +lp++d+s+ + vs     + a
  gi|386001025|ref|YP_005919324.1| 195 LDPFAGTGGFLVEAGLM--AVRGVGVDVQWRIVRGAASNL--EGLDCTLIVGDAMRLPLKDESVEAAVSdapygRSA 267
                                       67778999999998866..4999*****************..799************************77776334 PP

                                       .GGG.SSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  74 .lhh.lsdedlekalkeiarvLkpg 96 
                                        ++    de l   l+e++rvL pg
  gi|386001025|ref|YP_005919324.1| 268 lIQAgSRDELLTGSLAELRRVLVPG 292
                                       3666444555677899999999887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.7     1e+04      34      61 ..      70      93 ..      58      96 .. 0.48
   2 !   19.9   0.0   3.8e-07   0.00086       5      91 ..     199     292 ..     195     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.7
                                      HHHHCCHHT-EEEETTEECCCTSS-TT- CS
                   Methyltransf_11 34 akekaseeglkvefvvadaeklpfedns 61
                                      a e+ +++   v + +a ae l ++d s
  gi|386001025|ref|YP_005919324.1| 70 AAEAEPTA---VGVARAAAE-LDLPDRS 93
                                      33333332...333333333.6777765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.8e-07
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.....-CCC-.. CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.....vlhhv.. 74 
                                       +GtG ++ +    + r vgvD+  + ++ a ++ ++ +  ++++v+da +lp++d+s+ + vs       +l     
  gi|386001025|ref|YP_005919324.1| 199 AGTGGFLVEAGLMAVRGVGVDVQWRIVRGAASNLEGLD--CTLIVGDAMRLPLKDESVEAAVSDApygrsALIQAgs 273
                                       68888888888778999*************99999998..99*********************99776664444457 PP

                                       ..CCHHHHHHHHHHHEEEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLkpg 91 
                                         e +   l+e++RvL pg
  gi|386001025|ref|YP_005919324.1| 274 rdELLTGSLAELRRVLVPG 292
                                       7667888999999999998 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.8e-06    0.0063     170     227 ..     168     226 ..     119     231 .. 0.86
   2 ?   -2.2   0.0       1.2   2.8e+03      33      52 ..     276     295 ..     269     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                                       ---SS---HHHHHHHHHHH.S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHH CS
                       N6_N4_Mtase 170 kkHpaqkPvallerlIkls.tkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyve 227
                                         Hp     +l++ l++ls  ++g+  lDpFaG+G  +v+a  +  + +G+++++++v+
  gi|386001025|ref|YP_005919324.1| 168 FFHPGAILPKLARALVNLSqVREGERLLDPFAGTGGFLVEAGLMAVRGVGVDVQWRIVR 226
                                       55788888899999**7763678********************************9998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHEEEEEEE CS
                       N6_N4_Mtase  33 eflekvlkevrrvLkddgsi 52 
                                       e+l++ l+e+rrvL ++  +
  gi|386001025|ref|YP_005919324.1| 276 ELLTGSLAELRRVLVPGRRM 295
                                       678999********998765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.9e-06     0.013       4     108 ..     191     296 ..     189     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.9e-06
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g r+lD+ +GtG ++ e+  +  +  + vG+D + + ++ A +n++  gld +++ +gd+  l+  l+de++   +s
  gi|386001025|ref|YP_005919324.1| 191 GERLLDPFAGTGGFLVEAG-L--MAVRGVGVDVQWRIVRGAASNLE--GLD-CTLIVGDAMRLP--LKDESVEAAVS 259
                                       7899************999.4..45789****************88..887.99**********..99********* PP

                   Methyltransf_31  81 nevl.........naladpdkileeiervlkpggill 108
                                       +++               +   l e+ rvl pg +++
  gi|386001025|ref|YP_005919324.1| 260 DAPYgrsaliqagSRDELLTGSLAELRRVLVPGRRMI 296
                                       9555444444433444444444448888888887776 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05     0.097      38     130 ..     187     270 ..     178     276 .. 0.78
   2 ?   -0.1   0.0      0.27   6.1e+02      22      42 ..     301     321 ..     289     326 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                       CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                       +  eg+r+LD faG+G+  +EA    a + v v+ + + v+    nle l+++     ++ da++  lk     e++
  gi|386001025|ref|YP_005919324.1| 187 QVREGERLLDPFAGTGGFLVEAG-LMAVRGVGVDVQWRIVRGAASNLEGLDCT----LIVGDAMRLPLKD----ESV 254
                                       4568899**************94.46778899999999999999999999955....6777777666555....455 PP

                                       EEEEE--SSSTTCH.H CS
                     Cons_hypoth95 115 divflDPPyakellie 130
                                       +    D Py +++li+
  gi|386001025|ref|YP_005919324.1| 255 EAAVSDAPYGRSALIQ 270
                                       6667788888776655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.27
                                       XSSSHHHHHHHHHHHCCCHCC CS
                     Cons_hypoth95  22 RPttdrvrealFnilaaeieg 42 
                                       RP    + ea F+il+a+ e+
  gi|386001025|ref|YP_005919324.1| 301 RPVGGAIEEAGFEILEAHQER 321
                                       9**************988555 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.3e-05      0.14      33      64 ..     177     208 ..     164     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                          N6_Mtase  33 evsklivellepksgesvyDpacGsggllvqa 64 
                                       ++ + +v+l + ++ge  +Dp +G+gg+lv+a
  gi|386001025|ref|YP_005919324.1| 177 KLARALVNLSQVREGERLLDPFAGTGGFLVEA 208
                                       3456677777********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 2609.15
//
Query:       gi|386001026|ref|YP_005919325.1|  [L=365]
Description: hypothetical protein Mhar_0315 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-07   29.4   0.0    1.1e-06   28.7   0.0    1.4  1  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   6.4e-11   1.1e-06     139     207 ..     198     266 ..     110     301 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.4e-11
                                       CCTCC..HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHC CS
                               APH 139 selld..lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlav 207
                                       +++l+  +l+++e++  +++++l+ +  + +  HgD+hp+N++++++ +    v+D  +  +g ++ D+  
  gi|386001026|ref|YP_005919325.1| 198 PAFLKpgELAAIEKRCVDWRWRLREKTHRLCMAHGDFHPWNVMFRSGTDFS--VLDRSRGEWGEAADDVTA 266
                                       2233357899***************99999999************776666..999777777777777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2859.38
//
Query:       gi|386001027|ref|YP_005919326.1|  [L=417]
Description: adenosylhomocysteinase [Methanosaeta harundinacea 6Ac]
Scores for 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-64  218.6   0.0    6.5e-37  127.3   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    1.2e-50  171.8   0.4    2.6e-50  170.6   0.4    1.6  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.4e-08   33.1   0.2    7.8e-08   31.9   0.2    1.6  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.9e-07   28.8   0.0      2e-06   27.5   0.0    1.6  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0065   16.7   0.0      0.023   14.9   0.0    2.0  1  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
       0.13   11.5   3.2       0.76    9.0   3.2    2.1  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.0   2.2e-40   6.5e-37       3     138 ..       4     134 ..       2     139 .. 0.97
   2 !   89.9   0.0   5.4e-29   1.6e-25     175     287 ..     138     412 ..     134     417 .] 0.98

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 2.2e-40
                                       B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   3 kvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifst 79 
                                        +kd +lae G+k+ie a + mp l ++reeya+e+pl+g+r++ +lh+t++ta L+ tL+a Gae+  a  n  st
  gi|386001027|ref|YP_005919326.1|   4 VIKDPKLAEKGKKRIEWARRHMPVLQKIREEYAAERPLEGVRVVACLHVTVETANLLSTLTAGGAEIAVAGSNPLST 80 
                                       689************************************************************************** PP

                                       -HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  80 qdeaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                       qd++aaa+ae+g+ v+a++ge+ +ey +ci++al+      +p++ lDdG D  +++h+
  gi|386001027|ref|YP_005919326.1|  81 QDDVAAALAEDGMRVYAFHGENDQEYYDCINRALEI-----RPHVTLDDGADTIATIHR 134
                                       **********************************66.....79***********99997 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 5.4e-29
                                       CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                         AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............................... 220
                                       +l+++i G  eetttGv rL  la++gkLl p i vnd+ tk  fD                               
  gi|386001027|ref|YP_005919326.1| 138 DLAAEILGGCEETTTGVIRLRALADAGKLLYPVIAVNDAETKMMFDnrygtgqstihgimnatnflfagktvvvggy 214
                                       5788999********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|386001027|ref|YP_005919326.1| 215 gwcgrglatrargmganvivveveprkaleaamdgfrvmsmtaaaplgdlfvtvtgnvsvireehvelmkdqaivan 291
                                       ***************************************************************************** PP

                                       ......................................................S-HHHHHHHHHHHHHHHHHHHHT CS
                                       ......................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ......................................................hpsfvmsasftnqvlaqielfkk 243
                                                                                             hp  vm++sf+nq+l+   + ++
  gi|386001027|ref|YP_005919326.1| 292 sghfnveidipaleemasgvsevqenvleykmadgrriyllaegrlinlaaaygHPPEVMDMSFANQALSVRYIAEN 368
                                       ***************************************************************************** PP

                                       TSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 244 ekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigv 287
                                        ++ ++kvy +p ++D +va+l+l+++g+++++lt eq +y++ 
  gi|386001027|ref|YP_005919326.1| 369 GRRLDRKVYSVPSEIDKRVAALKLAAMGIEIESLTPEQDKYLHS 412
                                       999**************************************975 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   0.4   8.8e-54   2.6e-50       1     161 [.     184     344 ..     184     345 .. 0.99

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 8.8e-54
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s + gi+ at++l+aGk++vv GyG  G+G a+  +g+Ga viv ev+P  al aam+Gf+v+ +  ++ 
  gi|386001027|ref|YP_005919326.1| 184 NRYGTGQSTIHGIMNATNFLFAGKTVVVGGYGWCGRGLATRARGMGANVIVVEVEPRKALEAAMDGFRVMSMTAAAP 260
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +d++vt+tGn  +i+ eh++ mkd+aiv+n Ghf+ eid+ ale++a  ++ev+ +v +++++dg++i llaeGrl
  gi|386001027|ref|YP_005919326.1| 261 LGDLFVTVTGNVSVIREEHVELMKDQAIVANSGHFNVEIDIPALEEMASGVSEVQENVLEYKMADGRRIYLLAEGRL 337
                                       ***************************************************************************** PP

                                       CHHHTS- CS
                     AdoHcyase_NAD 155 lnlgcat 161
                                       +nl++a 
  gi|386001027|ref|YP_005919326.1| 338 INLAAAY 344
                                       ***9986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.2   2.6e-11   7.8e-08      34     128 ..     204     294 ..     179     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.6e-11
                                       GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBS CS
                      2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlin 110
                                        +gktv + G+G  G+ +a r++++g++vi++++ ++k  e++  g++++s+ ++    D  + ++     +  +i 
  gi|386001027|ref|YP_005919326.1| 204 FAGKTVVVGGYGWCGRGLATRARGMGANVIVVEVEPRKALEAAMDGFRVMSMTAAAPLGDLFVTVTG----NVSVIR 276
                                       689**********************************99999999***************9887765....889*** PP

                                       HHHHHCSTTTEEEEESS- CS
                      2-Hacid_dh_C 111 aeelakmkkgailiNtaR 128
                                       +e+ ++mk++ai+ N + 
  gi|386001027|ref|YP_005919326.1| 277 EEHVELMKDQAIVANSGH 294
                                       *************99875 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   6.6e-10     2e-06       3     101 ..     205     299 ..     203     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.6e-10
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyee 79 
                                        gk+++v GyG  G+  a+  r  g +v+v   e +k + +A  +gf+v++++ a+   d+ ++++    + +v++e
  gi|386001027|ref|YP_005919326.1| 205 AGKTVVVGGYGWCGRGLATRARGMGANVIVVEVEPRKAL-EAAMDGFRVMSMTAAAPLGDLFVTVTG---NVSVIRE 277
                                       79****************************999888555.66779***************9998875...4678888 PP

                                       HTGGG--TT-EEEESSSHHHHT CS
                              IlvN  80 eiepnlkegkalafahGfnihf 101
                                       e  + +k+++++a +  fn+  
  gi|386001027|ref|YP_005919326.1| 278 EHVELMKDQAIVANSGHFNVEI 299
                                       888999*****999999*9976 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.8e-06     0.023       1      49 [.     209     257 ..     209     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.8e-06
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-T CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgda 49 
                                       +++ G+G  Gr la + +  g  +v+v++ +++++ e++ +g++v+   a
  gi|386001027|ref|YP_005919326.1| 209 VVVGGYGWCGRGLATRARGmGA-NVIVVEVEPRKALEAAMDGFRVMSMTA 257
                                       6899***************666.6******************99987665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.2   0.00026      0.76      27      67 ..     204     245 ..     182     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                                       ---EEEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C  27 epakvlviGg.GvaGlqAiatakglgakVtvlDvrparleql 67 
                                        ++k++v+Gg G  G   +  a+g+ga+V v++v+p+++ + 
  gi|386001027|ref|YP_005919326.1| 204 FAGKTVVVGGyGWCGRGLATRARGMGANVIVVEVEPRKALEA 245
                                       37888888877***********************99876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2704.93
//
Query:       gi|386001028|ref|YP_005919327.1|  [L=300]
Description: Metallo-beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-25   89.2   0.0    3.3e-25   88.8   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    2.5e-13   50.5   0.3      2e-12   47.5   0.3    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00017   21.6   0.0    0.00034   20.6   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.025   14.0   0.0        1.4    8.4   0.0    2.2  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   7.3e-29   3.3e-25       3     200 ..      83     263 ..      82     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 7.3e-29
                                       EEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC....C--EEEEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre....lrpkklplyapkgvlavleanf 74 
                                       iL+D+g + +   a+          ++ ++d+Vllth H DH+ +ll l++    + ++++++y+p+g++   ea  
  gi|386001028|ref|YP_005919327.1|  83 ILFDCGAGALLRlAEA-------GLSPLEVDLVLLTHLHLDHVSDLLPLAKarwlMGESEMEVYGPEGTAGWFEAVR 152
                                       89******54441222.......345668**********************999533444***********999876 PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig 151
                                             ++  v+++ +++g++f l+  gl+i+a +a h+ +          lG+rie+++k+v+y+gDt+ ++ +i+
  gi|386001028|ref|YP_005919327.1| 153 GLYSYLKDLDVSFTVVNPGDEFCLN--GLRIRAREAVHSIPA---------LGYRIESETKSVVYSGDTEPVE-SIR 217
                                       66666666799*************9..89************9.........*******************999.999 PP

                                       HHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 152 erlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                        + +gadll++++ + e+        H+tp+     ++ +g+kr vl+H
  gi|386001028|ref|YP_005919327.1| 218 LLAEGADLLVHECSFPEPFV---ITNHATPRRLGLTFKGAGVKRIVLTH 263
                                       9*************999977...679*********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.3   4.5e-16     2e-12      10     162 ..      75     221 ..      69     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 4.5e-16
                                       EEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                       Lactamase_B  10 liegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                       l+   ++ iL+D+G ++   +a      +gl p++vd v+lTHlHlDH+++l  l++a++     + e++    + +
  gi|386001028|ref|YP_005919327.1|  75 LVIRAEEPILFDCGAGALLRLAE-----AGLSPLEVDLVLLTHLHLDHVSDLLPLAKARWLMGESEMEVYGPEGTAG 146
                                       666788999*****999999997.....8*******************************99888888777666666 PP

                                       HHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B  87 addaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                          +a+r+   +  + + +  v+  ++++ + g r       +   ++++++e++ ++v+++GD+ +++++ ++ +
  gi|386001028|ref|YP_005919327.1| 147 WF-EAVRGLYSYLKDLDVSFTVVNPGDEFCLNGLRIRAREAVHSIPALGYRIESETKSVVYSGDTEPVESIRLLAE 221
                                       63.33333332555566666666666666788888888899999999********************999988877 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   7.5e-08   0.00034      31     117 ..      99     213 ..      75     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.5e-08
                     Lactamase_B_3  31 eppaeeaDlvlisqaledHah.letlkql..................................aenvkvleegesle 72 
                                       + ++ e+Dlvl+++ + dH   l +l+++                                  +  ++v+++g+++ 
  gi|386001028|ref|YP_005919327.1|  99 GLSPLEVDLVLLTHLHLDHVSdLLPLAKArwlmgesemevygpegtagwfeavrglysylkdlDVSFTVVNPGDEFC 175
                                       455689*************75155666669*********************************99************ PP

                     Lactamase_B_3  73 vggleiravatshdavggsergenngflleqdgltiyhlGhlahe 117
                                       ++gl+ira ++ h         +  g+++e++  ++++ G++   
  gi|386001028|ref|YP_005919327.1| 176 LNGLRIRAREAVH-------SIPALGYRIESETKSVVYSGDTEPV 213
                                       ***********99.......577899***************9864 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0003       1.4       9      71 ..      83     140 ..      77     146 .. 0.65
   2 ?    3.4   0.0    0.0099        44     128     161 ..     176     209 ..     148     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0003
                     Lactamase_B_6   9 iLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvya 71 
                                       iL D+G     +     l+e      +vdl+LL+h  l+h++ +  l ++      ++++vy+
  gi|386001028|ref|YP_005919327.1|  83 ILFDCGAGAL-L----RLAEAGLSPLEVDLVLLTHLHLDHVSDLLPLAKARWLMGESEMEVYG 140
                                       6666666654.2....23333333458***************875555443334456677776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0099
                     Lactamase_B_6 128 ldgltitaynaGhtlGGtiWkiskesekivYavd 161
                                       l+gl i a +a h++ +  ++i++e++++vY  d
  gi|386001028|ref|YP_005919327.1| 176 LNGLRIRAREAVHSIPALGYRIESETKSVVYSGD 209
                                       399****************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2134.87
//
Query:       gi|386001029|ref|YP_005919328.1|  [L=192]
Description: Tungsten formylmethanofuran dehydrogenase, subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete 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-41  140.0   0.0    5.5e-41  139.7   0.0    1.1  1  FmdE           FmdE, Molybdenum formylmethanofuran dehydrogen
    2.9e-05   23.9   3.3    2.9e-05   23.9   3.3    2.2  2  zf-dskA_traR   Prokaryotic dksA/traR C4-type zinc finger
     0.0089   16.2   0.4      0.018   15.2   0.4    1.5  1  LIM            LIM domain
  ------ inclusion threshold ------
      0.047   13.8   1.7      0.047   13.8   1.7    1.8  2  Zn-ribbon_8    Zinc ribbon domain
      0.078   12.9   0.0       0.14   12.1   0.0    1.4  1  L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI
       0.11   12.1   1.0       0.25   10.9   1.0    1.6  1  TF_Zn_Ribbon   TFIIB zinc-binding
       0.12   12.5   0.8       0.36   11.0   0.8    1.8  1  FYVE           FYVE zinc finger
       0.15   12.5   0.8       0.38   11.3   0.0    2.0  2  Ribosomal_L44  Ribosomal protein L44
       0.27   11.3   3.8        2.1    8.5   0.4    2.3  2  XPA_N          XPA protein N-terminal


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.0   2.8e-44   5.5e-41       1     130 [.      11     140 ..      11     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 2.8e-44
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEETT CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkrk 77 
                                       fHGH+Cpg+++Gyr+a++++++++    ++deelvaive++sC +DAiq l+gct+Gkgn+i++d+gk+++tf++r+
  gi|386001029|ref|YP_005919328.1|  11 FHGHTCPGIAIGYRVARYVKNHYKR---SEDEELVAIVENSSCSVDAIQSLLGCTFGKGNFIFKDHGKHVYTFYSRD 84 
                                       9**********************84...347********************************************** PP

                                       T-EEEEEEE-....CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHH CS
                              FmdE  78 tgkavrlklk....eelpelreklakgkakeekeeeeleeeleeaikkilnapeeel 130
                                        +ka+r+++k    +  p+ ++++++g++++e e+e++ +++eea + il+ap+e+l
  gi|386001029|ref|YP_005919328.1|  85 HNKAIRIYVKnvlpRTDPTAMKRFFAGEMTPE-ERERFLKLREEATNYILTAPDEDL 140
                                       *************99999***********999.8999******************98 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.12   2.4e+02      10      20 ..     111     121 ..     111     126 .. 0.88
   2 !   23.9   3.3   1.4e-08   2.9e-05       4      34 ..     158     190 ..     155     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                      zf-dskA_traR  10 GEpIpeaRlra 20 
                                       GE+ pe+R r 
  gi|386001029|ref|YP_005919328.1| 111 GEMTPEERERF 121
                                       9*******986 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.4e-08
                      zf-dskA_traR   4 gs..CeeCGEpIpeaRlralPgarlCveCqeka 34 
                                        s  C eCGE  +e R r   g+++C eC +k+
  gi|386001029|ref|YP_005919328.1| 158 PSleCQECGEAFMEVRGRTAAGKIVCEECYQKF 190
                                       5566**************************985 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   9.2e-06     0.018      27      56 ..     160     189 ..     155     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.2e-06
                                       SB-TTT-SB-CTT.CEEETTEEEEHHHHHH CS
                               LIM  27 FtCsdCqkeLkegsfyekdgklyCkkdylk 56 
                                       + C++C++ + e +     gk++C+++y+k
  gi|386001029|ref|YP_005919328.1| 160 LECQECGEAFMEVRGRTAAGKIVCEECYQK 189
                                       78***********9999999********86 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.3   6.6e+03      15      30 ..       5      17 ..       3      18 .. 0.66
   2 ?   13.8   1.7   2.4e-05     0.047       7      34 ..     161     188 ..     159     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.3
                       Zn-ribbon_8 15 fevlqsisdapltaCP 30
                                      f+++++++     +CP
  gi|386001029|ref|YP_005919328.1|  5 FNEVVKFH---GHTCP 17
                                      77777777...55688 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.4e-05
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       +C+eCg+ f +++  + a +++C eC +
  gi|386001029|ref|YP_005919328.1| 161 ECQECGEAFMEVRGRTAAGKIVCEECYQ 188
                                       8***********9888888899****65 PP

>> L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.8e-05      0.14      15      41 ..      85     125 ..      83     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                                       T-TTSEEEEEE.SS-SS-EEEEE-SS-.............- CS
                     L51_S25_CI-B8  15 kNPavpivvrr.rsgdgPallaiYfng.............r 41 
                                       +N a++i+v++    ++P+++ ++f g             r
  gi|386001029|ref|YP_005919328.1|  85 HNKAIRIYVKNvLPRTDPTAMKRFFAGemtpeererflklR 125
                                       9**********888888**********88887755555551 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.0   0.00012      0.25       2      25 ..     161     186 ..     160     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                       EETTTTCEECHEE..TSTTCEEESSS CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveD..pergelvCtdC 25 
                                        C +Cg  ++++   ++ g +vC++C
  gi|386001029|ref|YP_005919328.1| 161 ECQECGEAFMEVRgrTAAGKIVCEEC 186
                                       5********999999*********** PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00018      0.36      11      44 ..     161     191 ..     155     192 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                       B-TTT--B--SSS--EE-TTT--EE-STTS-EEE CS
                              FYVE  11 kCeiCakkFsllrrrhhCrlCGkvvCekCssklv 44 
                                       +C++C ++F  +r r    + Gk+vCe+C +k+v
  gi|386001029|ref|YP_005919328.1| 161 ECQECGEAFMEVRGRT---AAGKIVCEECYQKFV 191
                                       7999999997666664...689*******99876 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.38      49      70 ..     155     176 ..     149     182 .. 0.86
   2 ?   -1.1   0.2       1.4   2.7e+03      53      62 ..     180     189 ..     177     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                       B--EEEEETTT--EEE----BB CS
                     Ribosomal_L44  49 KivlrleCteCkkkrlkalkRa 70 
                                       +i++ leC+eC+++ ++   R+
  gi|386001029|ref|YP_005919328.1| 155 RIHPSLECQECGEAFMEVRGRT 176
                                       899*************998887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                       EEEETTT--E CS
                     Ribosomal_L44  53 rleCteCkkk 62 
                                       ++ C+eC +k
  gi|386001029|ref|YP_005919328.1| 180 KIVCEECYQK 189
                                       689****876 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4     0.001       2.1       3      12 ..     161     170 ..     159     172 .. 0.89
   2 ?    3.8   0.2      0.03        60       3      11 ..     182     190 ..     180     192 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                             XPA_N   3 kCdeCgkefl 12 
                                       +C+eCg++f+
  gi|386001029|ref|YP_005919328.1| 161 ECQECGEAFM 170
                                       8********8 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.03
                             XPA_N   3 kCdeCgkef 11 
                                       +C+eC ++f
  gi|386001029|ref|YP_005919328.1| 182 VCEECYQKF 190
                                       6****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1399.86
//
Query:       gi|386001030|ref|YP_005919329.1|  [L=108]
Description: hypothetical protein Mhar_0319 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   60.5   0.0    1.7e-16   60.2   0.0    1.1  1  DUF3467   Protein of unknown function (DUF3467)
    0.00048   19.9   0.0    0.00051   19.8   0.0    1.2  1  LolA      Outer membrane lipoprotein carrier protein LolA


Domain annotation for each model (and alignments):
>> DUF3467  Protein of unknown function (DUF3467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   1.9e-20   1.7e-16      19      91 .]       8      90 ..       2      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 1.9e-20
                           DUF3467 19 vdesvaggsYsngaivmtspsEfiidF........lq...lvpgrpearvksrvvlspaaakqlvaaLqknldlyetrf 86
                                      v+ ++++++Y+ ga+  +sp++f+  F        +q   +v  ++e rv  + +lsp aak+l+++L++++++ye +f
  gi|386001030|ref|YP_005919329.1|  8 VKADKFRQIYAVGAMGGHSPYDFRMAFyndspkavVQdgkQV-SVMERRVETELILSPLAAKELADWLNNHIKEYERQF 85
                                      78899**********************777755442254455.6778889999************************** PP

                           DUF3467 87 Geikl 91
                                      Geik+
  gi|386001030|ref|YP_005919329.1| 86 GEIKK 90
                                      ***96 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.7e-08   0.00051      33      68 ..      26      61 ..       8      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-08
                                      TTTEEEEEE-TTS-EEEEEETTEEEEEETTTTEEEE CS
                              LolA 33 rPgkfrweytsPdeqlivsdgktvwlydpdleqvti 68
                                       P  fr+++++ ++ ++v dgk+v ++++++e+ +i
  gi|386001030|ref|YP_005919329.1| 26 SPYDFRMAFYNDSPKAVVQDGKQVSVMERRVETELI 61
                                      699****************************99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 778.65
//
Query:       gi|386001031|ref|YP_005919330.1|  [L=178]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-24   82.7   0.0    1.4e-10   40.5   0.1    4.1  4  TPR_1            Tetratricopeptide repeat
    1.3e-22   78.0   0.1    1.5e-08   34.1   0.3    4.1  4  TPR_2            Tetratricopeptide repeat
    2.7e-18   66.2   0.2    7.8e-10   39.1   0.1    2.2  2  TPR_19           Tetratricopeptide repeat
    3.4e-17   62.8   0.6    1.8e-12   47.7   0.1    2.5  2  TPR_16           Tetratricopeptide repeat
    1.5e-15   57.2   1.7    1.6e-08   34.7   0.2    3.9  3  TPR_12           Tetratricopeptide repeat
    2.9e-15   55.7   0.1    2.6e-07   30.2   0.0    4.0  4  TPR_11           TPR repeat
    1.3e-14   53.1   0.0    2.9e-05   23.9   0.0    4.2  4  TPR_8            Tetratricopeptide repeat
    1.3e-13   50.9   4.6    1.1e-06   28.7   0.1    3.0  3  TPR_9            Tetratricopeptide repeat
      5e-13   48.7   4.4    0.00045   20.8   1.0    4.1  4  TPR_14           Tetratricopeptide repeat
    1.8e-10   40.0   0.2       0.06   13.4   0.0    3.9  4  TPR_7            Tetratricopeptide repeat
    2.4e-10   40.1   0.2    5.8e-07   29.4   0.0    3.0  3  TPR_17           Tetratricopeptide repeat
    4.6e-09   35.8   5.5     0.0078   16.1   0.3    4.3  4  TPR_10           Tetratricopeptide repeat
    1.8e-07   31.3   0.0       0.16   12.6   0.1    4.0  4  TPR_6            Tetratricopeptide repeat
    3.5e-07   30.2   4.7      0.024   15.2   0.3    3.6  3  TPR_4            Tetratricopeptide repeat
      1e-06   29.2   1.9      0.004   17.6   0.0    2.5  3  BTAD             Bacterial transcriptional activator domain
      1e-05   25.6   0.0     0.0069   16.6   0.0    2.1  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00018   21.5   1.8         15    6.1   0.0    4.2  4  PPR              PPR repeat
    0.00055   20.0   0.0       0.67   10.1   0.0    2.9  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0036   16.3   0.0       0.54    9.1   0.0    2.0  2  NARP1            NMDA receptor-regulated protein 1
     0.0078   16.2   0.0      0.024   14.7   0.0    1.7  2  SRP_TPR_like     Putative TPR-like repeat
     0.0079   16.2   0.2        6.4    6.9   0.1    3.8  5  MIT              MIT (microtubule interacting and transport) 
  ------ inclusion threshold ------
       0.01   16.3   0.0        0.2   12.1   0.0    2.1  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.011   15.8   0.4       0.97    9.5   0.0    2.9  3  DUF3856          Domain of Unknown Function (DUF3856)
      0.012   15.6   0.1       0.84    9.5   0.1    2.1  2  Wzy_C_2          Virulence factor membrane-bound polymerase, 
      0.015   14.8   0.0       0.62    9.4   0.0    2.0  2  Coatomer_E       Coatomer epsilon subunit
      0.019   14.2   0.2      0.076   12.2   0.1    1.8  2  TPR_15           Tetratricopeptide repeat
      0.075   12.7   0.3       0.41   10.3   0.1    2.2  2  TPR_21           Tetratricopeptide repeat-like domain
        0.2   11.6   0.2       0.36   10.8   0.2    1.4  1  SpoOE-like       Spo0E like sporulation regulatory protein


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.5e-06    0.0016       6      34 .]      10      38 ..       6      38 .. 0.86
   2 !   40.5   0.1   2.2e-13   1.4e-10       1      33 [.      39      71 ..      39      72 .. 0.97
   3 !   13.6   0.0   7.1e-05     0.046       5      25 ..      77      97 ..      74     103 .. 0.93
   4 ?    5.4   0.0     0.027        18       6      33 ..     111     138 ..     108     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                                      HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  6 nlGnayfklgkydeAleyyekALelnPnn 34
                                       +G+   k ++++eA+ +++++Le nP+n
  gi|386001031|ref|YP_005919330.1| 10 HKGMDRVKRNEFEEAIGFFDQVLEMNPEN 38
                                      567777799******************97 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 2.2e-13
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPn 33
                                      a+a++n+G+a+f+lg+++eAl++y++A + +P+
  gi|386001031|ref|YP_005919330.1| 39 ADAWNNKGVALFQLGRPEEALAAYDRAHQADPE 71
                                      89*****************************97 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 7.1e-05
                                      HHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1  5 ynlGnayfklgkydeAleyye 25
                                       n++ +++ +g+++eAle ye
  gi|386001031|ref|YP_005919330.1| 77 RNRAFVLRTMGRFEEALEVYE 97
                                      69****************997 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.027
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                                       nl+ ++  +g ++eAl +  +A  ++P+
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALMEAANIEPS 138
                                       9999************999999888885 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.2e-06    0.0059       5      34 .]       9      38 ..       6      38 .. 0.88
   2 !   34.1   0.3   2.3e-11   1.5e-08       1      33 [.      39      71 ..      39      72 .. 0.96
   3 !   15.7   0.0   1.9e-05     0.012       4      32 ..      76     104 ..      74     106 .. 0.85
   4 ?    6.7   0.0     0.014       9.2       5      33 ..     110     138 ..     106     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.2e-06
                             TPR_2  5 ynlGlayyklgdyeeAleafekAleldPnn 34
                                         G+   k++++eeA+ +f+++le +P+n
  gi|386001031|ref|YP_005919330.1|  9 VHKGMDRVKRNEFEEAIGFFDQVLEMNPEN 38
                                      5677888899******************97 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 2.3e-11
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPn 33
                                      a+a++n G a+++lg++eeAl+a+++A + dP+
  gi|386001031|ref|YP_005919330.1| 39 ADAWNNKGVALFQLGRPEEALAAYDRAHQADPE 71
                                      79******************************7 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.9e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       l n++ +++ +g++eeAle +e  +  +P
  gi|386001031|ref|YP_005919330.1|  76 LRNRAFVLRTMGRFEEALEVYEGIITEEP 104
                                       789******************96666665 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.014
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldPn 33 
                                        nl+ ++  +g +eeAl a+ +A  ++P 
  gi|386001031|ref|YP_005919330.1| 110 RNLATVLVGMGLLEEALGALMEAANIEPS 138
                                       699999******************99995 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   1.2e-12   7.8e-10       3      58 ..      17      72 ..      15      77 .. 0.94
   2 !   25.2   0.0   2.6e-08   1.7e-05       3      56 ..      85     137 ..      83     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.2e-12
                            TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                                      +++ ++eA+ ++ q+l+ +p+na+a+ +   al++lg+++eA a+ d++ ++dp +
  gi|386001031|ref|YP_005919330.1| 17 KRNEFEEAIGFFDQVLEMNPENADAWNNKGVALFQLGRPEEALAAYDRAHQADPES 72
                                      57789************************************************983 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 2.6e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                        +g+++eAl+ +e +++e+p+ ++ r  LA +l+ +g l+eA  +L ++ + +p
  gi|386001031|ref|YP_005919330.1|  85 TMGRFEEALEVYEGIITEEPEASDFRN-LATVLVGMGLLEEALGALMEAANIEP 137
                                       69*************************.*****************998887766 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   2.8e-15   1.8e-12       4      65 ..      12      70 ..      11      72 .. 0.94
   2 !   12.8   0.0   0.00022      0.14       7      59 ..      83     132 ..      78     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.8e-15
                            TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65
                                      ++++++++++++A+  ++++l+++   P++a+A++++g+a++++gr +eA+a+y++a +a+p
  gi|386001031|ref|YP_005919330.1| 12 GMDRVKRNEFEEAIGFFDQVLEMN---PENADAWNNKGVALFQLGRPEEALAAYDRAHQADP 70
                                      7899********************...************************99999978877 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00022
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyra 59 
                                       ++  g++++A++++e  +      P+a +++ +l+ ++   g l+eA+ al +a
  gi|386001031|ref|YP_005919330.1|  83 LRTMGRFEEALEVYEGIITEE---PEASDFR-NLATVLVGMGLLEEALgALMEA 132
                                       5678*****************...7666665.4566666666666666666655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.1e-08   1.3e-05       5      75 ..       7      69 ..       4      71 .. 0.84
   2 !   34.7   0.2   2.5e-11   1.6e-08       3      69 ..      39      97 ..      37     101 .. 0.94
   3 !    7.9   0.0    0.0056       3.6       8      32 ..     111     135 ..     103     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.1e-08
                            TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                      +l++ ++   ++ +++eA+ +++++le+      p++   a + +n g ++++lgr+eeAl+++ +a +++
  gi|386001031|ref|YP_005919330.1|  7 ILVHKGMDRVKRNEFEEAIGFFDQVLEMN-----PEN---ADAWNNKGVALFQLGRPEEALAAYDRAHQAD 69
                                      66777888888899999999999999999.....887...8899999999999999999999999998875 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2.5e-11
                            TPR_12  3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69
                                      a a+nn +++l++lgr +eAl+ +++a+++      p++    + lrn + ++r +gr+eeAle +e
  gi|386001031|ref|YP_005919330.1| 39 ADAWNNKGVALFQLGRPEEALAAYDRAHQAD-----PES---REPLRNRAFVLRTMGRFEEALEVYE 97
                                      789************************9999.....876...789*******************998 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0056
                            TPR_12   8 nlaavlrrlgrydeAlellekalei 32 
                                       nla+vl  +g ++eAl  l +a +i
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALMEAANI 135
                                       6777777777777777777777654 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.1e-10   2.6e-07       5      42 .]      16      53 ..      12      53 .. 0.95
   2 !   21.5   0.0   2.1e-07   0.00013       3      41 ..      48      86 ..      46      87 .. 0.91
   3 !    7.1   0.0    0.0069       4.4       5      18 ..      84      97 ..      82      97 .. 0.85
   4 ?    1.2   0.0      0.47     3e+02       8      26 ..     120     138 ..     115     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.1e-10
                            TPR_11  5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      ++++++eeAi  + + l+ +P+na+a++n G+a++++G
  gi|386001031|ref|YP_005919330.1| 16 VKRNEFEEAIGFFDQVLEMNPENADAWNNKGVALFQLG 53
                                      799*********************************99 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.1e-07
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                                      a++++G+ eeA++aY +A + dP++ e + n+++++  +
  gi|386001031|ref|YP_005919330.1| 48 ALFQLGRPEEALAAYDRAHQADPESREPLRNRAFVLRTM 86
                                      89******************************9998655 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0069
                            TPR_11  5 yeqGkyeeAieaYk 18
                                      +  G++eeA+e+Y+
  gi|386001031|ref|YP_005919330.1| 84 RTMGRFEEALEVYE 97
                                      668**********6 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.47
                            TPR_11   8 GkyeeAieaYkkAlkldPd 26 
                                       G +eeA+ a+ +A ++ P+
  gi|386001031|ref|YP_005919330.1| 120 GLLEEALGALMEAANIEPS 138
                                       6689*********999995 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0028       1.8      14      34 .]      18      38 ..       6      38 .. 0.88
   2 !   23.9   0.0   4.5e-08   2.9e-05       1      33 [.      39      71 ..      39      72 .. 0.94
   3 !    9.6   0.0    0.0017       1.1       7      30 ..      79     102 ..      78     105 .. 0.81
   4 ?    5.6   0.0     0.035        22       6      33 ..     111     138 ..     111     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0028
                                      TT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 14 lgdyeeAkeyyekaleldpdn 34
                                       +++eeA+ ++ ++le++p+n
  gi|386001031|ref|YP_005919330.1| 18 RNEFEEAIGFFDQVLEMNPEN 38
                                      6889***************86 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.5e-08
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+a++n+g ++++lg+ eeA ++y +a ++dp+
  gi|386001031|ref|YP_005919330.1| 39 ADAWNNKGVALFQLGRPEEALAAYDRAHQADPE 71
                                      79*************************888886 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0017
                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekalel 30 
                                        + +++++g++eeA e+ye  ++ 
  gi|386001031|ref|YP_005919330.1|  79 RAFVLRTMGRFEEALEVYEGIITE 102
                                       5678999***********977665 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.035
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                       nl+ ++  +g +eeA  ++++a  ++p+
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALMEAANIEPS 138
                                       799999*****************99995 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.6e-09   1.1e-06       8      62 ..      18      72 ..      16      74 .. 0.94
   2 !   26.6   0.6   7.5e-09   4.8e-06      11      70 ..      55     114 ..      54     116 .. 0.93
   3 !    8.7   0.0    0.0028       1.8      28      69 ..     105     149 ..      99     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.6e-09
                             TPR_9  8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                                      ++++e+a+   + +l ++P+ ++ +   G++l+qlG++++Ala+ +++ + +p+ 
  gi|386001031|ref|YP_005919330.1| 18 RNEFEEAIGFFDQVLEMNPENADAWNNKGVALFQLGRPEEALAAYDRAHQADPES 72
                                      7899*********************************************999976 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 7.5e-09
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeaira 70 
                                        e+ala+++r  + +P++ e +r R+++l  +G++++Al+  e  +  +p+a d + ++ 
  gi|386001031|ref|YP_005919330.1|  55 PEEALAAYDRAHQADPESREPLRNRAFVLRTMGRFEEALEVYEGIITEEPEASDFRNLAT 114
                                       589*************************************************99887765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0028
                             TPR_9  28 dpeerrdRGlllaqlGclsaAladLeaylalap...dapdaeair 69 
                                       ++++ r  + +l+ +G l++Al +L  ++ ++p     +++ea+r
  gi|386001031|ref|YP_005919330.1| 105 EASDFRNLATVLVGMGLLEEALGALMEAANIEPsisIEREIEALR 149
                                       57899************************9999666444444444 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00015     0.096      14      39 ..      18      43 ..      15      47 .. 0.90
   2 !   20.8   1.0     7e-07   0.00045      10      40 ..      48      78 ..      45      81 .. 0.88
   3 !   12.7   0.0   0.00028      0.18       6      38 ..      78     110 ..      73     116 .. 0.84
   4 ?    2.1   0.0      0.73   4.7e+02       7      30 ..     112     135 ..     107     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00015
                            TPR_14 14 lGdpdeAiallrralalaPddaeawl 39
                                      + +++eAi  ++++l+ +P++a+aw 
  gi|386001031|ref|YP_005919330.1| 18 RNEFEEAIGFFDQVLEMNPENADAWN 43
                                      679*********************95 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 7e-07
                            TPR_14 10 allalGdpdeAiallrralalaPddaeawll 40
                                      al++lG+p+eA+a+++ra +++P+++e ++ 
  gi|386001031|ref|YP_005919330.1| 48 ALFQLGRPEEALAAYDRAHQADPESREPLRN 78
                                      89**********************9986665 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00028
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeaw 38 
                                        +a +l++ G+++eA+++++ ++   P+  +++
  gi|386001031|ref|YP_005919330.1|  78 NRAFVLRTMGRFEEALEVYEGIITEEPEASDFR 110
                                       57899*******************999877665 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.73
                            TPR_14   7 laeallalGdpdeAiallrralal 30 
                                       la +l   G ++eA+ +l +a   
  gi|386001031|ref|YP_005919330.1| 112 LATVLVGMGLLEEALGALMEAANI 135
                                       788899999999999998777555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00026      0.17      10      32 ..      16      36 ..      12      40 .. 0.78
   2 !   13.4   0.0   9.3e-05      0.06       1      34 [.      41      72 ..      41      74 .. 0.87
   3 !    9.6   0.0    0.0015      0.97      10      32 ..      84     104 ..      78     107 .. 0.82
   4 ?   -0.7   0.0       2.9   1.9e+03      12      27 ..     119     128 ..     109     137 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                             TPR_7 10 srlGdyeeAielyeqsLaltkdp 32
                                      ++++++eeAi+++ q+L++   p
  gi|386001031|ref|YP_005919330.1| 16 VKRNEFEEAIGFFDQVLEM--NP 36
                                      5789***********5555..44 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.3e-05
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                                      a++n +++ ++lG+ eeA+  y +  a   dpe 
  gi|386001031|ref|YP_005919330.1| 41 AWNNKGVALFQLGRPEEALAAYDR--AHQADPES 72
                                      799********************9..87777665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0015
                             TPR_7  10 srlGdyeeAielyeqsLaltkdp 32 
                                       + +G++eeA+e+ye    +t++p
  gi|386001031|ref|YP_005919330.1|  84 RTMGRFEEALEVYEG--IITEEP 104
                                       559***********8..666665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.9
                             TPR_7  12 lGdyeeAielyeqsL.a 27 
                                       +G  eeA       L a
  gi|386001031|ref|YP_005919330.1| 119 MGLLEEA-------LgA 128
                                       4544554.......444 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   9.1e-10   5.8e-07       2      33 ..      28      59 ..      27      60 .. 0.94
   2 ?    7.3   0.0     0.011       6.8       2      34 .]      62      94 ..      61      94 .. 0.87
   3 ?   -0.9   0.0       4.5   2.9e+03      12      26 ..     112     126 ..     109     133 .. 0.47

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.1e-10
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      + ++le +P nada+nn++++l ++G++++A+
  gi|386001031|ref|YP_005919330.1| 28 FDQVLEMNPENADAWNNKGVALFQLGRPEEAL 59
                                      7899**************************97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      y +a + dP + +++ n+A +l+  G++++A++
  gi|386001031|ref|YP_005919330.1| 62 YDRAHQADPESREPLRNRAFVLRTMGRFEEALE 94
                                      66777789999999****************985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.5
                            TPR_17  12 nadaynnLAelllkn 26 
                                        a ++  ++ l + +
  gi|386001031|ref|YP_005919330.1| 112 LATVLVGMGLLEEAL 126
                                       333444444444455 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.16     1e+02      14      31 ..      17      34 ..      12      35 .. 0.90
   2 !   16.1   0.3   1.2e-05    0.0078       6      30 ..      43      67 ..      39      68 .. 0.90
   3 !   11.4   0.0   0.00036      0.23       6      26 ..      77      97 ..      76     101 .. 0.88
   4 ?    5.2   0.2     0.031        20       7      31 ..     111     135 ..     109     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                            TPR_10 14 qrgrydeAealleealai 31
                                      +r++++eA  +++++l++
  gi|386001031|ref|YP_005919330.1| 17 KRNEFEEAIGFFDQVLEM 34
                                      589************997 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                            TPR_10  6 nNLanalrqrgrydeAealleeala 30
                                      nN ++al+q+gr +eA+a +++a +
  gi|386001031|ref|YP_005919330.1| 43 NNKGVALFQLGRPEEALAAYDRAHQ 67
                                      99*******************9965 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00036
                            TPR_10  6 nNLanalrqrgrydeAealle 26
                                       N a +lr +gr++eA++ +e
  gi|386001031|ref|YP_005919330.1| 77 RNRAFVLRTMGRFEEALEVYE 97
                                      68899*************998 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.031
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       NLa +l  +g ++eA+  l ea +i
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALMEAANI 135
                                       9***************998888765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0       0.1        64      10      32 ..      15      37 ..       7      38 .. 0.80
   2 !   12.6   0.1   0.00026      0.16       7      33 .]      46      72 ..      44      72 .. 0.93
   3 !    8.4   0.0    0.0057       3.6       7      32 ..      80     105 ..      77     106 .. 0.85
   4 ?    0.1   0.0       2.6   1.6e+03       9      27 ..     115     133 ..     111     138 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrklgdtdkAlealerlikeYPd 32
                                      + k ++ ++A+  ++++++  P+
  gi|386001031|ref|YP_005919330.1| 15 RVKRNEFEEAIGFFDQVLEMNPE 37
                                      5666799***********98876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00026
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPdS 33
                                      + ++++lg++++Al+a++r  +  P+S
  gi|386001031|ref|YP_005919330.1| 46 GVALFQLGRPEEALAAYDRAHQADPES 72
                                      8899**99**************99988 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       a  +r +g+ ++Ale +e +i+e P+
  gi|386001031|ref|YP_005919330.1|  80 AFVLRTMGRFEEALEVYEGIITEEPE 105
                                       55667799**************9996 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealerli 27 
                                        +  +g  ++Al al +  
  gi|386001031|ref|YP_005919330.1| 115 VLVGMGLLEEALGALMEAA 133
                                       4445556666766665554 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   3.7e-05     0.024       6      26 .]      44      64 ..      39      64 .. 0.87
   2 !   11.4   0.0   0.00065      0.42       4      25 ..      76      97 ..      74      97 .. 0.90
   3 ?    3.5   0.3      0.23   1.5e+02       6      21 ..     111     126 ..     110     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.7e-05
                             TPR_4  6 aLArallalGdldeAraller 26
                                      + + al++lG+++eA+a+ +r
  gi|386001031|ref|YP_005919330.1| 44 NKGVALFQLGRPEEALAAYDR 64
                                      6789*************9886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00065
                             TPR_4  4 llaLArallalGdldeAralle 25
                                      l ++A +l   G+++eA+++ e
  gi|386001031|ref|YP_005919330.1| 76 LRNRAFVLRTMGRFEEALEVYE 97
                                      789***************9876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.23
                             TPR_4   6 aLArallalGdldeAr 21 
                                       +LA +l   G l+eA+
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEAL 126
                                       8**************8 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.2e-06     0.004      73     123 ..      16      66 ..       6      72 .. 0.90
   2 !   17.5   0.6   6.6e-06    0.0042      72     121 ..      49      98 ..      48     106 .. 0.91
   3 ?    7.1   0.3     0.011       6.9      72     116 ..      83     126 ..      66     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.2e-06
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++ ++ eea++  ++ ++++P + +++     Al+++Gr +eAL++Y+r+ 
  gi|386001031|ref|YP_005919330.1|  16 VKRNEFEEAIGFFDQVLEMNPENADAWNNKGVALFQLGRPEEALAAYDRAH 66 
                                       5567889999999***********************************986 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 6.6e-06
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       +++lGr eeala ++++ +++P   +  r     l+ +Gr +eALevYe 
  gi|386001031|ref|YP_005919330.1|  49 LFQLGRPEEALAAYDRAHQADPESREPLRNRAFVLRTMGRFEEALEVYEG 98 
                                       689*******************988888888889**************96 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                       + ++Gr eeal+ +e++++e+P   ++ r l + l  +G  +eAL
  gi|386001031|ref|YP_005919330.1|  83 LRTMGRFEEALEVYEGIITEEPEASDF-RNLATVLVGMGLLEEAL 126
                                       334566666666666666666655555.34445555555555555 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0069      35      81 ..      17      64 ..      15      65 .. 0.93
   2 !    8.8   0.0    0.0028       1.8      12      81 ..      62     131 ..      61     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                      HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      +++++++A+ ++++  + n+++  ++  ++ +l++L++ eeA+aa+++
  gi|386001031|ref|YP_005919330.1| 17 KRNEFEEAIGFFDQVlEMNPENADAWNNKGVALFQLGRPEEALAAYDR 64
                                      6899****************************************9876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
                                       HHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  12 aerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++r+++a++es e +   A +l  +g++++A+e+++   +++        +A +l+ ++ +eeA+ aL +
  gi|386001031|ref|YP_005919330.1|  62 YDRAHQADPESREPLRNRAFVLRTMGRFEEALEVYEGIITEEPEASDFRNLATVLVGMGLLEEALGALME 131
                                       68999899999999888999******************6666666677778999999*******999965 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.057        36      12      29 ..      17      34 ..      16      35 .. 0.85
   2 ?    5.2   0.0     0.046        29       9      25 ..      48      64 ..      47      68 .. 0.86
   3 ?    6.1   0.0     0.024        15      13      25 ..      86      98 ..      83     102 .. 0.86
   4 ?    1.4   0.0      0.77   4.9e+02      10      23 ..     116     129 ..     109     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.057
                               PPR 12 knGkleeAlelfkeMkek 29
                                      k +++eeA+ +f++ +e+
  gi|386001031|ref|YP_005919330.1| 17 KRNEFEEAIGFFDQVLEM 34
                                      7899*********98876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.046
                               PPR  9 gycknGkleeAlelfke 25
                                      ++ + G++eeAl  +++
  gi|386001031|ref|YP_005919330.1| 48 ALFQLGRPEEALAAYDR 64
                                      67899*******98876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                               PPR 13 nGkleeAlelfke 25
                                       G++eeAle+++ 
  gi|386001031|ref|YP_005919330.1| 86 MGRFEEALEVYEG 98
                                      59********985 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.77
                               PPR  10 ycknGkleeAlelf 23 
                                       ++  G+leeAl  +
  gi|386001031|ref|YP_005919330.1| 116 LVGMGLLEEALGAL 129
                                       66689*****9765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0     0.001      0.67      13      37 ..      17      41 ..      15      43 .. 0.91
   2 ?   -1.7   0.0       5.1   3.3e+03       9      33 ..      47      71 ..      46      74 .. 0.71
   3 ?    6.4   0.0     0.015       9.3      14      42 ..      86     114 ..      83     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                                      HHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQa 37
                                      k  e++eA  + d++Le+ Pen  a
  gi|386001031|ref|YP_005919330.1| 17 KRNEFEEAIGFFDQVLEMNPENADA 41
                                      7789******************876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.1
                                      HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  9 lGhyklgeYseArryvdalLeiEPe 33
                                      ++ + lg+ +eA+   d+  + +Pe
  gi|386001031|ref|YP_005919330.1| 47 VALFQLGRPEEALAAYDRAHQADPE 71
                                      5666777778888888888777777 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.015
                                       HT-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLke 42 
                                       +g+++eA++  + ++  EPe +  ++L +
  gi|386001031|ref|YP_005919330.1|  86 MGRFEEALEVYEGIITEEPEASDFRNLAT 114
                                       799*****************999999976 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00086      0.55     204     259 ..      15      72 ..       6      74 .. 0.83
   2 !    9.1   0.0   0.00085      0.54      18      78 ..      53     112 ..      51     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00086
                                       HHT-SH..HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 204 klgsre..kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       ++++ e  +A+ + d+ +e +p+  + + +K+  l + G +++A ++ ++a + D + 
  gi|386001031|ref|YP_005919330.1|  15 RVKRNEfeEAIGFFDQVLEMNPENADAWNNKGVALFQLGRPEEALAAYDRAHQADPES 72 
                                       5554444499999999999999999999999999999999999999999999998765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                                       THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHH CS
                             NARP1  18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegl 78 
                                       g+ eeAl+  +++++   +  + + ++a +l  +gr+eeA ++ye +++  pe s++ ++l
  gi|386001031|ref|YP_005919330.1|  53 GRPEEALAAYDRAHQADPESREPLRNRAFVLRTMGRFEEALEVYEGIITEEPEASDF-RNL 112
                                       67889999999999999999999999**************************99885.444 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.7e-05     0.024       5      75 ..      28     103 ..      17     134 .. 0.77
   2 ?    1.4   0.0      0.47     3e+02       5      51 ..      96     143 ..      93     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                      SRP_TPR_like   5 yekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveaee 75 
                                       ++++l+++ ++ + +  k val +l++ eeaL + + ++     s +    +a+vl  + ++++al++ + + +ee
  gi|386001031|ref|YP_005919330.1|  28 FDQVLEMNPENADAWnnKGVALFQLGRPEEALAAYDRAHqadPESREPLRNRAFVLRTMGRFEEALEVYEGIITEE 103
                                       577777777776666669***************999887433456666789****************999887776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                      SRP_TPR_like   5 yekilrlegkelkkfk..vvaliklekyeeaLkllkkgsalsedvrfEk 51 
                                       ye i+  e++e + f+  ++ l+ ++  eeaL +l ++ +++ ++  E+
  gi|386001031|ref|YP_005919330.1|  96 YEGIIT-EEPEASDFRnlATVLVGMGLLEEALGALMEAANIEPSISIER 143
                                       666664.667777776225668899999****99999887877777775 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.4   9.3e+02       8      28 ..       9      29 ..       8      34 .. 0.64
   2 ?    1.3   0.0      0.56   3.6e+02      27      50 ..      21      43 ..      18      51 .. 0.75
   3 ?    0.0   0.1       1.4   9.2e+02      17      30 ..      52      65 ..      44      68 .. 0.75
   4 ?    2.0   0.0      0.35   2.3e+02      17      28 ..      86      97 ..      75      98 .. 0.79
   5 !    6.9   0.1      0.01       6.4      28      62 ..     123     161 ..     120     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.4
                               MIT  8 vkkAveeDnagnyeeAlelYk 28
                                      v+k +++ +++++eeA+  + 
  gi|386001031|ref|YP_005919330.1|  9 VHKGMDRVKRNEFEEAIGFFD 29
                                      566666667778888876654 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.56
                               MIT 27 YkealelLlqalkekneerrellr 50
                                      ++ea++ + q+l   n+e  +++ 
  gi|386001031|ref|YP_005919330.1| 21 FEEAIGFFDQVLE-MNPENADAWN 43
                                      5799999999996.5666666555 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.4
                               MIT 17 agnyeeAlelYkea 30
                                       g  eeAl +Y  a
  gi|386001031|ref|YP_005919330.1| 52 LGRPEEALAAYDRA 65
                                      56779999999988 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.35
                               MIT 17 agnyeeAlelYk 28
                                       g +eeAle Y+
  gi|386001031|ref|YP_005919330.1| 86 MGRFEEALEVYE 97
                                      6899*******6 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.01
                               MIT  28 kealelLlqalk.e...kneerrellrekieeYleRaee 62 
                                       +eal+ L++a + e   + e+  e+lr+ ++e   Rae+
  gi|386001031|ref|YP_005919330.1| 123 EEALGALMEAANiEpsiSIEREIEALRRVMMEVAIRAEF 161
                                       689*********9876666699***************95 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00032       0.2      69     123 ..       5      59 ..       1      63 [. 0.90
   2 ?    2.5   0.0      0.28   1.8e+02      90     124 ..      60      94 ..      56     109 .. 0.82
   3 ?    0.5   0.0       1.2   7.8e+02      81     108 ..      85     112 ..      72     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++ ++ k  + +k+++++ a+ + +++++ +pena+a + k  al qlg+ +e+ 
  gi|386001031|ref|YP_005919330.1|   5 EKILVHKGMDRVKRNEFEEAIGFFDQVLEMNPENADAWNNKGVALFQLGRPEEAL 59 
                                       566788999999*************************************998876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.28
                                       HHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  90 ellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                          + + +adpe +e  + +a +l+ +g+++e+  
  gi|386001031|ref|YP_005919330.1|  60 AAYDRAHQADPESREPLRNRAFVLRTMGRFEEALE 94 
                                       5567788899999999999**********999865 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakel 108
                                       + g ++ a+e+ + +++++pe ++ ++l
  gi|386001031|ref|YP_005919330.1|  85 TMGRFEEALEVYEGIITEEPEASDFRNL 112
                                       5678888999999999999998888876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0015      0.97      79     127 ..      22      66 ..      18      77 .. 0.82
   2 ?    2.8   0.0      0.18   1.1e+02     105     124 ..      78      97 ..      74     106 .. 0.85
   3 ?   -0.9   0.0       2.4   1.5e+03      60      79 ..     111     130 ..      97     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       ++a+ +f++  e++ ++   W     +++val +lGr +eal a+  a 
  gi|386001031|ref|YP_005919330.1|  22 EEAIGFFDQVLEMNPENADAW----NNKGVALFQLGRPEEALAAYDRAH 66 
                                       567777777777777777777....58******************9886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                                       HHHHHHHHTT-HHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafr 124
                                       +ra  l  +Gr +eal+ ++
  gi|386001031|ref|YP_005919330.1|  78 NRAFVLRTMGRFEEALEVYE 97 
                                       79999999*******99986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHTT-HHHHHHHHH CS
                           DUF3856  60 glsealaklgrydealesad 79 
                                        l+  l+++g  +eal +  
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALM 130
                                       56666666666666665543 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0013      0.84     121     178 ..      16      74 ..       6      84 .. 0.84
   2 ?    4.3   0.0     0.054        35     127     170 ..      90     133 ..      83     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                           Wzy_C_2 121 lspenlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeeda 178
                                       +++   ++ +++  ++++  Pe a   ++  ++l +lG+++eA+  ++ra+ + pe+++
  gi|386001031|ref|YP_005919330.1|  16 VKRNEFEEAIGFFDQVLEMNPENAdAWNNKGVALFQLGRPEEALAAYDRAHQADPESRE 74 
                                       6777788888999999999999764779999********************99888765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.054
                           Wzy_C_2 127 aaklalarklihlsPepavierlilslallGdedeAeqilarar 170
                                       ++ l++++ +i   Pe+   ++l+  l++ G  +eA+  l +a 
  gi|386001031|ref|YP_005919330.1|  90 EEALEVYEGIITEEPEASDFRNLATVLVGMGLLEEALGALMEAA 133
                                       678999******************************98887765 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00097      0.62     202     256 ..       6      60 ..       2      73 .. 0.88
   2 ?    1.8   0.0       0.2   1.3e+02     181     229 ..      87     134 ..      80     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00097
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 202 lllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                        +l +k +  ++ +++eeA     + L+ +++++++  N  va  +lg+++e+ +
  gi|386001031|ref|YP_005919330.1|   6 KILVHKGMDRVKRNEFEEAIGFFDQVLEMNPENADAWNNKGVALFQLGRPEEALA 60 
                                       67888888999999***********************************998865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                                       THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLd 229
                                       +++++A+ +++ +    ++        A v + +g  eeA   L ea +
  gi|386001031|ref|YP_005919330.1|  87 GRFEEALEVYEGIITE-EPEASDFRNLATVLVGMGLLEEALGALMEAAN 134
                                       4567777888877777.44444445567888888888888888888865 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012     0.076     211     270 ..      36      95 ..       8     104 .. 0.75
   2 ?   -0.1   0.0      0.66   4.2e+02      13      40 ..     111     137 ..      99     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                            TPR_15 211 esdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrl 270
                                        ++a+ w+  + Al  Lgrp++AL+ + +  ++ +++   l   A +l + gr++eA ++
  gi|386001031|ref|YP_005919330.1|  36 PENADAWNNKGVALFQLGRPEEALAAYDRAHQADPESREPLRNRAFVLRTMGRFEEALEV 95 
                                       5677888888999999********999996666666655556666699999999999876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.66
                            TPR_15  13 klatllykqgdvkkAlevLkeaaqkaap 40 
                                       +lat+l + g +++Al +L e a++++p
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALME-AANIEP 137
                                       67999999999*******965.555545 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00065      0.41     146     180 ..      39      73 ..      16      85 .. 0.79
   2 ?   -0.2   0.0       1.1   6.8e+02     118     138 ..     111     131 ..      86     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00065
                            TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                       a + + +G +l++ g+ +eA aaY++A +a  e+ 
  gi|386001031|ref|YP_005919330.1|  39 ADAWNNKGVALFQLGRPEEALAAYDRAHQADPESR 73 
                                       555678999********************999885 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                            TPR_21 118 RLarvllaekkydeAlktLea 138
                                        La vl+ ++ ++eAl +L +
  gi|386001031|ref|YP_005919330.1| 111 NLATVLVGMGLLEEALGALME 131
                                       489999999999999988865 PP

>> SpoOE-like  Spo0E like sporulation regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00057      0.36       1      18 [.     141     158 ..     141     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00057
                                       HHHHHHHHHHHHHHHHHH CS
                        SpoOE-like   1 LlkeIEelRkeLnelaek 18 
                                       +++eIE+lR+ ++e a++
  gi|386001031|ref|YP_005919330.1| 141 IEREIEALRRVMMEVAIR 158
                                       79************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1229.10
//
Query:       gi|386001032|ref|YP_005919331.1|  [L=72]
Description: Transcriptional regulatory protein, AsnC family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-09   37.5   0.1      2e-09   37.3   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.061   13.4   0.3      0.079   13.0   0.3    1.2  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   2.2e-13     2e-09       3      73 ..       2      68 ..       1      69 [. 0.94

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.2e-13
                                      EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      ++ epg+    +++ +al ++  V+e+  v G+ d+++++ v+ +++l+ ++ + ++++ gv++tet + +
  gi|386001032|ref|YP_005919331.1|  2 INAEPGS---EKAVYDALTAIRGVREVVPVYGETDFIAIADVEGIADLNMIVLK-VREIHGVTSTETILGM 68
                                      6778888...99******************************************.************9876 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   8.8e-06     0.079       8      68 ..       2      63 ..       1      66 [. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-06
                              NapD  8 Vqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsas 68
                                      ++a p++ +av +al+a+ gv Ev  + +e   + + + e   +l  ++ +++++ gV s++
  gi|386001032|ref|YP_005919331.1|  2 INAEPGSEKAVYDALTAIRGVrEVVPVYGETDFIAIADVEGIADLNMIVLKVREIHGVTSTE 63
                                      7899****************999************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 498.57
//
Query:       gi|386001033|ref|YP_005919332.1|  [L=893]
Description: DNA mismatch repair protein MutS [Methanosaeta harundinacea 6Ac]
Scores for complete 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-83  279.7   0.3    1.9e-83  279.1   0.3    1.3  1  MutS_V    MutS domain V
    1.9e-41  140.8   0.0    3.9e-41  139.8   0.0    1.6  1  MutS_I    MutS domain I
    8.3e-39  133.8   0.1    1.3e-38  133.2   0.1    1.3  1  MutS_III  MutS domain III
      6e-31  106.7   0.0    1.1e-30  105.8   0.0    1.5  1  MutS_IV   MutS family domain IV
    1.8e-18   67.2   0.0    3.4e-18   66.3   0.0    1.5  1  MutS_II   MutS domain II
     0.0016   18.4   0.0     0.0088   16.1   0.0    2.1  2  AAA_14    AAA domain
     0.0089   15.6   0.0      0.022   14.4   0.0    1.6  1  AAA_27    AAA domain
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.24   11.9   0.0    1.4  1  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.3   8.7e-87   1.9e-83       1     188 []     613     800 ..     613     800 .. 0.99

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 8.7e-87
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       +++tGpnmaGksty+rq+al+++laqiGsfvpa+ a+is+vd+iftRvga Ddl+ g+stFm+Em+E+a+il++at+
  gi|386001033|ref|YP_005919332.1| 613 IILTGPNMAGKSTYMRQIALAIILAQIGSFVPAAFASISPVDRIFTRVGAYDDLSAGQSTFMIEMTELAKILSSATS 689
                                       599************************************************************************** PP

                                       TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEE CS
                            MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvk 154
                                       ksl++lDE+GRGtst+dGlaia++v+e+++++++ k++fatHyh+lt+la  l+ vkn+++avkee e++ fl++v 
  gi|386001033|ref|YP_005919332.1| 690 KSLILLDEIGRGTSTFDGLAIAWSVTEHIHNRVRGKAVFATHYHQLTQLAGVLPGVKNYNMAVKEEGETVLFLRTVV 766
                                       ***************************************************************************** PP

                                       ES--SS--HHHHHHHTT--HHHHHHHHHHHHHTT CS
                            MutS_V 155 egaaeksyGikvaklaglPesvverArevlkele 188
                                       +ga+++syGi+vaklag+Pe+vv+rA+e+l+e+e
  gi|386001033|ref|YP_005919332.1| 767 PGATDRSYGIHVAKLAGVPEAVVARAKEILREIE 800
                                       ******************************9986 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   1.8e-44   3.9e-41       2     111 ..       6     116 ..       5     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 1.8e-44
                                       HHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC..EEEEEEEHHHHHHHHHHHHHTT CS
                            MutS_I   2 plmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkksseke.ipmagvPehalekylrkLvekg 77 
                                       plm qy+ +k++  da+l+fr+GdfYe+fg DA+iaar+l+itlt+r+k++e + ip ag+P+hal+ yl kLv++g
  gi|386001033|ref|YP_005919332.1|   6 PLMDQYFGMKEECGDALLLFRMGDFYETFGPDAEIAARVLNITLTSRQKDKEGNrIPLAGIPHHALDAYLPKLVAAG 82 
                                       9***********************************************7777777********************** PP

                                       -EEEEEEE-S-HHHHS.S--EEEEEEEBTTC-TT CS
                            MutS_I  78 ykVavveqtetpaekkgvvkrevvrviTpGtltd 111
                                       ykVa++eq+e+p ++kg+vkre++rviTpGt+++
  gi|386001033|ref|YP_005919332.1|  83 YKVAICEQVEDPRKAKGLVKREIIRVITPGTILE 116
                                       *******************************986 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.1   5.7e-42   1.3e-38       1     191 []     268     561 ..     268     561 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 5.7e-42
                                       HHHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          MutS_III   1 aTlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrr 76 
                                       +TlrnLei++n+r+ sk+g+L+ +ld+T T+ G+R Lr+wl  Pl++ e+I++RldaVee + ++ lr++lre+lr 
  gi|386001033|ref|YP_005919332.1| 268 TTLRNLEIFRNIRDRSKRGTLVDFLDETTTPGGSRTLRKWLQMPLLSHEDIERRLDAVEElVGDPLLRADLREALRG 344
                                       59*********99999********************************************999*************9 PP

                                       ---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH.............HHHHHHHHHHB-SS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxx RF
                          MutS_III  77 lpDleRllsrislgkakardlkallealkaleelvallekeklaesee.............eslaelleeaideepl 140
                                        +DleR++ r s g+a+++dl+al  +++ l+ +va+l + +++   e              ++a+l+ +ai ++p+
  gi|386001033|ref|YP_005919332.1| 345 GGDLERVVGRTSCGTASPKDLRALKGSIEGLPRIVAILTAARSE---ElvrlrerleigplGEVADLIGRAIADDPP 418
                                       99***************************999999999666554...3456887777776655679*********** PP

                                       SSGGGS--B-T.................................................................. CS
                                       xxxxxxxxxxx.................................................................. RF
                          MutS_III 141 alekegedlra.................................................................. 151
                                       ++ +eg+++r+                                                                  
  gi|386001033|ref|YP_005919332.1| 419 SAIREGGIIRDgydpeldglrsllregrgwiarmerqerdrtgikslrvgynnvfgyyievtkanlsavppeyirkq 495
                                       ***************************************************************************** PP

                                       ..........................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ..........................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                                   +le+e+f ++++e ++++ ++++  eal eLDvl+ lA
  gi|386001033|ref|YP_005919332.1| 496 tlaggerfitpelkemesrvlsaqerSASLEEEIFISVRREAAAKSREILERGEALGELDVLVTLA 561
                                       ************************9999999***********9999*****************998 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0     5e-34   1.1e-30       1      92 []     430     521 ..     430     521 .. 0.99

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 5e-34
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       g+d+eLd lr++l+e + +++++e++er ++giksl+v+yn+v+Gyy+evt+ + + vp+e+ir+qtl ++er++t+
  gi|386001033|ref|YP_005919332.1| 430 GYDPELDGLRSLLREGRGWIARMERQERDRTGIKSLRVGYNNVFGYYIEVTKANLSAVPPEYIRKQTLAGGERFITP 506
                                       8**************************************************************************** PP

                                       CHHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaeee 92 
                                       elk++e ++l+a+e+
  gi|386001033|ref|YP_005919332.1| 507 ELKEMESRVLSAQER 521
                                       ************986 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.5e-21   3.4e-18       1     136 [.     126     251 ..     126     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.5e-21
                                       -EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE.-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEE CS
                           MutS_II   1 nylaAisekregrrvGlafiDlstgefvvsefed.feeleaeLsrlsPkElllpedlsestaeeessklrelrsrvg 76 
                                       nyla+i+e  ++  +Gl+ +D+stgef  +e      +l +eL+++ P+E+l+p ++++  +         + + v+
  gi|386001033|ref|YP_005919332.1| 126 NYLASIVE--DDGKIGLSLLDVSTGEFLATELLAtGGKLSTELAKFRPAECLIPRSAESL-V------GDGEGMMVQ 193
                                       8*******..9999*****************997799*******************8655.3......467889999 PP

                                       EESCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCSCCCCT-C CS
                           MutS_II  77 vretvefesekaserleedfsvedldgfglekekklalaAlgalisYleetqkekelshl 136
                                       + ++++f++  a+ rl+++f++e ++ +gl   ++ a +A+ga++ Yl+   +   l h+
  gi|386001033|ref|YP_005919332.1| 194 RLDDADFALVGARARLADHFGGERVERWGL-PAHPAAARACGAVLTYLQSARLP-ALDHI 251
                                       9*****************************.999***************99988.77776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.7   1.6e+03      31      73 ..     249     295 ..     231     309 .. 0.66
   2 !   16.1   0.0   3.9e-06    0.0088       2      81 ..     610     706 ..     609     754 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.7
                            AAA_14  31 esilyinldderdkkladpe..kllelilek..lkeekktylflDEi 73 
                                       ++i ++ l +++d +  d++  ++le++++    +++++ + flDE 
  gi|386001033|ref|YP_005919332.1| 249 DHIAEVRLYSPEDFMVLDETtlRNLEIFRNIrdRSKRGTLVDFLDET 295
                                       67888888888886666554454556666653222245666789986 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.9e-06
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderd...............kkladpe.....kllelil 57 
                                       ++++++tG+  +GK+t+++q++   + ++  s++  ++ + +                +             ++++ 
  gi|386001033|ref|YP_005919332.1| 610 NRVIILTGPNMAGKSTYMRQIALAIIlAQIGSFVPAAFASISPvdriftrvgayddlsA-----GqstfmIEMTELA 681
                                       799******************97777966666666666666554444555544433221.....0221221122222 PP

                            AAA_14  58 eklke.....ekktylflDEiqevpewek 81 
                                           +       k++++lDEi + ++ ++
  gi|386001033|ref|YP_005919332.1| 682 ----KilssaTSKSLILLDEIGRGTSTFD 706
                                       ....12333568999*****987666555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   9.8e-06     0.022      12      46 ..     596     630 ..     589     635 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-06
                            AAA_27  12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAi 46 
                                       G f  + +d++  ++++ ++ GpN AGKst +r i
  gi|386001033|ref|YP_005919332.1| 596 GGFVANDVDLDGRSNRVIILTGPNMAGKSTYMRQI 630
                                       7899999************************9976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.24      15      42 ..     603     633 ..     596     641 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            AAA_23  15 idF...skgltlItGpNGaGKTTildAikla 42 
                                       +d+   s+ + ++tGpN aGK+T ++ i la
  gi|386001033|ref|YP_005919332.1| 603 VDLdgrSNRVIILTGPNMAGKSTYMRQIALA 633
                                       5666678899***************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (893 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 5928.06
//
Query:       gi|386001034|ref|YP_005919333.1|  [L=595]
Description: DNA mismatch repair protein MutL [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-38  130.0   0.0    4.9e-38  129.5   0.0    1.3  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    7.2e-36  123.2   0.0    1.4e-35  122.3   0.0    1.4  1  MutL_C          MutL C terminal dimerisation domain
    1.8e-10   40.8   0.1    3.3e-10   39.9   0.1    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    3.1e-07   30.9   0.0      6e-07   30.0   0.0    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0   1.1e-41   4.9e-38       3     118 ..     215     330 ..     213     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 1.1e-41
                                       HHHHHHHHCCEEEEEEEETTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEE CS
                    DNA_mis_repair   3 avlgkevaenlleiekeeeqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvLn 79 
                                       ++lg+eva+nl+++e+e  +++i+G+ ++++++rs++d+++++vNgRlv+s+ l++a+ eaY++l+p+gr+p++v++
  gi|386001034|ref|YP_005919333.1| 215 RILGREVARNLVPFEAEARSVSISGVAARETATRSSPDWIITYVNGRLVRSRALSRAVAEAYRTLIPTGRHPIAVVS 291
                                       799************************************************************************** PP

                                       EEESSGGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                    DNA_mis_repair  80 leidpeevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                       l+idp++vDvNvhP+K+eVrf +eeev  ++++a++ al
  gi|386001034|ref|YP_005919333.1| 292 LRIDPSQVDVNVHPAKTEVRFLREEEVAALVTDAIRAAL 330
                                       ***********************************9987 PP

>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0     3e-39   1.4e-35       4     145 ..     409     550 ..     407     552 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 3e-39
                                       EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHCT CS
                            MutL_C   4 kalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLaklG 80 
                                       + lgq  + yi+ae ++glvlvDqhaA eri ye l +++++++  sQ+L+ P++lelsp+ea llee   +La++G
  gi|386001034|ref|YP_005919333.1| 409 RLLGQALQLYIVAEGPEGLVLVDQHAAAERIRYEILSKKYASGT-ISQELIEPVTLELSPKEAVLLEEWGPTLAEMG 484
                                       689**************************************975.******************************** PP

                                       -EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS.-H-HCCHHHHHHHHCTTSSSSSS- CS
                            MutL_C  81 feleefgpnslivravPallrqqnleelirelleelaekgk.esleekleellatmachssvkagr 145
                                       f++++fg+n+++vr+vPa+ r  + +e+++++l +l + g+  +     ee+l+ +ac++s+kag 
  gi|386001034|ref|YP_005919333.1| 485 FDVQPFGKNAYTVRSVPAIGRRLDSPEAVHDVLRDLFALGRvGTGSTAKEEILKLLACRGSIKAGA 550
                                       **************************************99984457899**************985 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 !   39.9   0.1   7.4e-14   3.3e-10       4      94 ..      25     116 ..      21     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 7.4e-14
                       HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakr....kstslGkkGiG 76 
                                        +++ elv+Ns+dA a+++ +ev++    +g i+++DdG Gm++e+   a++ + +sk + +       slG +G  
  gi|386001034|ref|YP_005919333.1|  25 ASVVKELVENSIDAGATRILVEVEEG--GKGLIRVTDDGCGMDREDAALAIERHATSKISGPgdleRIASLGFRGEA 99 
                                       689*********************95..68*****************999976666666554233257779999988 PP

                       HATPase_c_3  77 lklAslslgkkltvitkk 94 
                                         +++ s+++ l+++tk 
  gi|386001034|ref|YP_005919333.1| 100 -LSSIASVAEALELVTKV 116
                                       .78899999999999975 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 !   30.0   0.0   1.3e-10     6e-07       5      64 ..      23      83 ..      19     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.3e-10
                                      HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTCSTTCH....H CS
                         HATPase_c  5 rLrqiisnlvdNavkfatkageieveikase.ddlvisveDnGiGipkedlkklfekfsq....d 64
                                      r   ++++lv+N++++   a++i ve++  e ++  i+v+D+G+G+++ed  +  e++ +     
  gi|386001034|ref|YP_005919333.1| 23 RPASVVKELVENSIDA--GATRILVEVE--EgGKGLIRVTDDGCGMDREDAALAIERHATskisG 83
                                      56689**********6..799*******..448*****************997777666633331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3818.42
//
Query:       gi|386001035|ref|YP_005919334.1|  [L=386]
Description: Formate dehydrogenase, beta subunit (F420) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-27   94.0   0.0    1.4e-26   93.2   0.0    1.4  1  FrhB_FdhB_C      Coenzyme F420 hydrogenase/dehydrogenase, bet
    3.2e-18   65.6   0.0    8.9e-18   64.2   0.0    1.8  1  FrhB_FdhB_N      Coenzyme F420 hydrogenase/dehydrogenase, bet
    9.5e-09   35.3  11.3    0.00041   20.4   1.2    3.1  3  Fer4_10          4Fe-4S dicluster domain
    1.8e-08   34.8   5.5    1.8e-08   34.8   5.5    2.1  2  Fer4_17          4Fe-4S dicluster domain
    3.4e-08   34.0  20.6    5.6e-07   30.1  10.3    2.6  3  Fer4_7           4Fe-4S dicluster domain
    1.1e-07   31.8   9.3     0.0021   18.2   0.6    3.0  3  Fer4_9           4Fe-4S dicluster domain
    3.1e-07   29.9  19.3    0.00047   19.9   4.0    2.9  3  Fer4             4Fe-4S binding domain
    4.6e-07   30.2   8.5    9.8e-07   29.1   6.8    2.4  3  Fer4_8           4Fe-4S dicluster domain
    3.6e-06   26.8  19.6     0.0026   17.8   3.9    3.4  3  Fer4_2           4Fe-4S binding domain
    6.2e-06   26.4   3.0      0.023   14.9   0.1    2.6  2  Fer4_18          4Fe-4S dicluster domain
    3.5e-05   24.2  11.2     0.0075   16.8   1.2    2.5  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    4.6e-05   23.5   9.5      0.025   14.7   0.6    2.7  2  Fer4_21          4Fe-4S dicluster domain
    0.00011   22.0  19.0    0.00086   19.3   2.5    3.1  3  Fer4_6           4Fe-4S binding domain
    0.00031   20.5   5.8       0.07   12.9   0.7    2.3  2  Fer4_20          Dihydroprymidine dehydrogenase domain II, 4F
     0.0019   18.5  19.9      0.055   14.0   1.8    3.3  3  Fer4_4           4Fe-4S binding domain
     0.0042   17.8   6.9       0.31   11.8   0.9    2.8  2  Fer4_15          4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.013   16.4  22.0      0.026   15.5   4.0    3.0  2  Fer4_3           4Fe-4S binding domain
      0.045   14.7  16.8       0.59   11.1  14.7    3.0  3  Fer4_16          4Fe-4S double cluster binding domain
       0.16   12.2   6.0        1.5    9.1   0.3    2.4  2  c-SKI_SMAD_bind  c-SKI Smad4 binding domain
       0.24   12.3   9.6       0.75   10.7   0.6    2.5  2  Fer4_22          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.0   1.6e-29   1.4e-26       3     151 ..      89     239 ..      87     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 1.6e-29
                       FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk.kklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkgkfrvelkd. 76 
                                       kv+ v+++C+ +++ + +k  ++ ++ ll+ gl+Cgg+  p+++r+ + e  g +p+ v+k  + +kg+f+++++  
  gi|386001035|ref|YP_005919334.1|  89 KVGAVVKGCDLMGIFEQAKrGEVDRNNLLLFGLNCGGSIAPSMMRRiISEAFGEEPSAVTKETI-HKGRFHITVRGe 164
                                       799***********9999996667777*******************999999999*********.9******99999 PP

                       FrhB_FdhB_C  77 ekeislkelee...firpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagelele 150
                                       +k++++ e+e     +r++C++Ck k+++ AD+++G+++ +e+     +++++v v t++g++ll++a+eag++ + 
  gi|386001035|ref|YP_005919334.1| 165 HKDLPIREIEGaglGRRENCRRCKLKVPRGADLACGNWGVREEL---VGEATFVEVTTDRGRDLLRRALEAGAIGIA 238
                                       99*****9999999************************777766...46***********************99876 PP

                       FrhB_FdhB_C 151 e 151
                                       +
  gi|386001035|ref|YP_005919334.1| 239 S 239
                                       6 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   9.9e-21   8.9e-18       1      70 [.       1      71 [.       1      78 [. 0.92

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 9.9e-21
                       FrhB_FdhB_N  1 vvaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYt.l 70
                                      +++ ++td+ +r++++sGG+vtallk +Leegi+d+v+ v++++d  + +p +  +++e+ + aGs++  +
  gi|386001035|ref|YP_005919334.1|  1 MIYVWATDPGVRRRGESGGAVTALLKFALEEGIVDAVLGVKRGADLTDGRPHLTADPKEVEEMAGSIHGgT 71
                                      7899***************************************9999********************9844 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.5   1.3e+03      40      48 ..     179     187 ..     165     201 .. 0.66
   2 !   20.2   0.6   5.3e-07   0.00047       2      21 ..     280     299 ..     279     314 .. 0.82
   3 !   20.4   1.2   4.6e-07   0.00041       6      23 ..     330     347 ..     325     376 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                           Fer4_10  40 kkvekCtgc 48 
                                       +  e+C +c
  gi|386001035|ref|YP_005919334.1| 179 GRRENCRRC 187
                                       555566665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.3e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                       v+ ++ +Ci+C +Cv++CPa
  gi|386001035|ref|YP_005919334.1| 280 VIEETARCIKCYACVEVCPA 299
                                       5677889************9 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 4.6e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                       +d+Ci+Cg+C++ CP+ +
  gi|386001035|ref|YP_005919334.1| 330 ADSCINCGQCQELCPMEI 347
                                       799*************55 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       8.6   7.7e+03      49      53 ..     184     188 ..     182     195 .. 0.63
   2 !   34.8   5.5     2e-11   1.8e-08       1      60 [.     286     347 ..     286     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.6
                           Fer4_17  49 CgeCe 53 
                                       C++C+
  gi|386001035|ref|YP_005919334.1| 184 CRRCK 188
                                       55554 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 2e-11
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraaklglleeaeke.ekaslCieCgeCerkCPqgl 60 
                                       rCi+C +C+++Cp + + ++ ++ ++   + +gl     +  ++a++Ci+Cg+C++ CP+++
  gi|386001035|ref|YP_005919334.1| 286 RCIKCYACVEVCPALFNtTGPYRTSFPGLVPPGLEFHLTRYaHVADSCINCGQCQELCPMEI 347
                                       7************977725557778888888874444444339*****************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         6   5.4e+03      37      41 ..     183     187 ..     170     195 .. 0.74
   2 !   17.4   2.6   5.8e-06    0.0052      28      50 ..     276     299 ..     254     301 .. 0.68
   3 !   30.1  10.3   6.2e-10   5.6e-07       1      51 [.     286     346 ..     286     347 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6
                            Fer4_7  37 kClgC 41 
                                       +C  C
  gi|386001035|ref|YP_005919334.1| 183 NCRRC 187
                                       34433 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.8e-06
                            Fer4_7  28 tekvei.dpekClgCgaCvavCPt 50 
                                       +++++i +  +C+ C+aCv+vCP+
  gi|386001035|ref|YP_005919334.1| 276 RMRAVIeETARCIKCYACVEVCPA 299
                                       33444414679***********95 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 6.2e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.......gt....ekveidpekClgCgaCvavCPtg 51 
                                       rCi+C aCv++Cp+   ++ ++   +       g      ++++++++C++Cg+C++ CP +
  gi|386001035|ref|YP_005919334.1| 286 RCIKCYACVEVCPALFNTTGPYR-TSfpglvppGLefhlTRYAHVADSCINCGQCQELCPME 346
                                       8************6666655542.12234444411445588999****************76 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.9   1.7e+03      34      39 ..     182     187 ..     149     195 .. 0.70
   2 !   18.2   0.6   2.3e-06    0.0021      33      48 ..     279     299 ..     244     303 .. 0.75
   3 !   16.8   1.5   6.3e-06    0.0056       2      19 ..     333     350 ..     320     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                            Fer4_9  34 eaCigC 39 
                                       e+C  C
  gi|386001035|ref|YP_005919334.1| 182 ENCRRC 187
                                       455555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.3e-06
                            Fer4_9  33 e.....eaCigCgaCveaCpk 48 
                                       +      +Ci+C aCve+Cp 
  gi|386001035|ref|YP_005919334.1| 279 AvieetARCIKCYACVEVCPA 299
                                       033344789999999999995 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 6.3e-06
                            Fer4_9   2 CtgCgaCveaCpagvvve 19 
                                       C++Cg+C+e Cp+++ + 
  gi|386001035|ref|YP_005919334.1| 333 CINCGQCQELCPMEIPNA 350
                                       888888888888887765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2         5   4.5e+03       6      11 ..     182     187 ..     181     189 .. 0.60
   2 !   19.9   4.0   5.2e-07   0.00047       6      19 ..     285     298 ..     280     300 .. 0.89
   3 !   19.6   2.4   6.3e-07   0.00057       5      21 ..     330     346 ..     326     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5
                                       TTSSS- CS
                              Fer4   6 ekCigC 11 
                                       e C +C
  gi|386001035|ref|YP_005919334.1| 182 ENCRRC 187
                                       556666 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.2e-07
                                       TTSSS-THHHHHST CS
                              Fer4   6 ekCigCGaCvevCP 19 
                                        +Ci+C aCvevCP
  gi|386001035|ref|YP_005919334.1| 285 ARCIKCYACVEVCP 298
                                       69************ PP

  == domain 3  score: 19.6 bits;  conditional E-value: 6.3e-07
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                        + Ci+CG+C e CP +
  gi|386001035|ref|YP_005919334.1| 330 ADSCINCGQCQELCPME 346
                                       699************76 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.1   3.7e+03      52      57 ..     182     187 ..     151     194 .. 0.56
   2 !   13.9   1.8   6.5e-05     0.058      45      63 ..     281     299 ..     246     302 .. 0.66
   3 !   29.1   6.8   1.1e-09   9.8e-07       3      65 .]     285     347 ..     283     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.1
                            Fer4_8  52 ttcgaC 57 
                                        +c++C
  gi|386001035|ref|YP_005919334.1| 182 ENCRRC 187
                                       444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.5e-05
                            Fer4_8  45 eealwsCttcgaCtevCpv 63 
                                        e   +C  c aC+evCp 
  gi|386001035|ref|YP_005919334.1| 281 IEETARCIKCYACVEVCPA 299
                                       5666778888888888874 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 1.1e-09
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                        +Ci+C aC + Cp+l +t    + + +g +     e + +  ++ ++sC +cg+C+e Cp++i
  gi|386001035|ref|YP_005919334.1| 285 ARCIKCYACVEVCPALFNTTgPYRTSFPGLVPP-GLEFHLTRYAHVADSCINCGQCQELCPMEI 347
                                       69************8888776777777777766.333333333788***************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3      0.99   8.9e+02       8      14 ..     182     188 ..     181     191 .. 0.74
   2 !   17.8   3.9   2.9e-06    0.0026       6      22 .]     283     299 ..     278     299 .. 0.85
   3 !   17.3   2.1     4e-06    0.0036       3      21 ..     326     344 ..     324     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.99
                            Fer4_2   8 drCigCg 14 
                                       ++C +C+
  gi|386001035|ref|YP_005919334.1| 182 ENCRRCK 188
                                       6788885 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.9e-06
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       +t+rCi C aCv +CPa
  gi|386001035|ref|YP_005919334.1| 283 ETARCIKCYACVEVCPA 299
                                       689*************8 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 4e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++ ++d+Ci+Cg C+  CP
  gi|386001035|ref|YP_005919334.1| 326 YAHVADSCINCGQCQELCP 344
                                       66789************** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.6e-05     0.023      53      73 ..     279     299 ..     257     304 .. 0.78
   2 !   11.1   0.3   0.00037      0.34      56      75 ..     328     347 ..     320     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                           Fer4_18  53 rkekgagdcidcescvkvcPt 73 
                                          ++++ ci+c +cv+vcP 
  gi|386001035|ref|YP_005919334.1| 279 AVIEETARCIKCYACVEVCPA 299
                                       44578999************7 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00037
                           Fer4_18  56 kgagdcidcescvkvcPtgi 75 
                                       + a  ci+c++c ++cP++i
  gi|386001035|ref|YP_005919334.1| 328 HVADSCINCGQCQELCPMEI 347
                                       45678************998 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.2   8.3e-06    0.0075       4      23 ..     285     304 ..     281     312 .. 0.85
   2 !   11.8   3.0   0.00029      0.26       4      17 ..     331     344 ..     329     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-06
                           Fer4_13   4 dtCiacgaCvelaPdvFeed 23 
                                        +Ci c aCve++P +F   
  gi|386001035|ref|YP_005919334.1| 285 ARCIKCYACVEVCPALFNTT 304
                                       68***************865 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00029
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       d+Ci+cg+C el+P
  gi|386001035|ref|YP_005919334.1| 331 DSCINCGQCQELCP 344
                                       89************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.4   4.3e-05     0.039      30      52 ..     274     298 ..     266     302 .. 0.72
   2 !   14.7   0.6   2.8e-05     0.025      34      53 ..     326     345 ..     319     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                           Fer4_21  30 aktvlkvved..eCvGCnlCssvCP 52 
                                        +++ +v+e+  +C+ C  C++vCP
  gi|386001035|ref|YP_005919334.1| 274 RDRMRAVIEEtaRCIKCYACVEVCP 298
                                       5566666643238999999999999 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.8e-05
                           Fer4_21  34 lkvvedeCvGCnlCssvCPv 53 
                                       +++v+d+C+ C  C + CP+
  gi|386001035|ref|YP_005919334.1| 326 YAHVADSCINCGQCQELCPM 345
                                       45678888888888888886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4       4.3   3.9e+03      12      15 ..     184     187 ..     181     189 .. 0.66
   2 !   19.3   2.5   9.6e-07   0.00086       7      21 ..     285     299 ..     281     302 .. 0.92
   3 !   12.6   2.6   0.00012      0.11       6      22 ..     330     346 ..     327     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.3
                            Fer4_6  12 CgdC 15 
                                       C++C
  gi|386001035|ref|YP_005919334.1| 184 CRRC 187
                                       7777 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 9.6e-07
                            Fer4_6   7 dkCigCgdCvrvCPe 21 
                                        +Ci C++Cv vCP+
  gi|386001035|ref|YP_005919334.1| 285 ARCIKCYACVEVCPA 299
                                       58************7 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00012
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                       +d+Ci Cg C   CP+ 
  gi|386001035|ref|YP_005919334.1| 330 ADSCINCGQCQELCPME 346
                                       79*************85 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.7   7.9e-05      0.07      15      40 ..     278     301 ..     263     305 .. 0.78
   2 !    9.9   0.5   0.00064      0.58      18      51 ..     327     358 ..     318     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                                       HHHHHHHTT----TT-HHHHCSTT-- CS
                           Fer4_20  15 eealeeAsRClqCkkapcvkgCPvei 40 
                                       ++++ee +RC++C    cv+ CP+  
  gi|386001035|ref|YP_005919334.1| 278 RAVIEETARCIKC--YACVEVCPALF 301
                                       46799********..78******865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00064
                                       HHHHTT----TT-HHHHCSTT---HHHHHHHHHT CS
                           Fer4_20  18 leeAsRClqCkkapcvkgCPveidipefikkiae 51 
                                       ++ A+ C++C   +c++ CP+ei   + +++ia+
  gi|386001035|ref|YP_005919334.1| 327 AHVADSCINC--GQCQELCPMEIPNARIMHAIAT 358
                                       567999****..78********999888888876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.7       1.1   9.6e+02       2       8 ..     182     188 ..     181     190 .. 0.78
   2 !   14.0   1.8   6.1e-05     0.055       3      15 ..     286     298 ..     284     308 .. 0.90
   3 !   13.4   3.5   9.3e-05     0.083       2      16 ..     331     345 ..     330     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.1
                            Fer4_4   2 erCigCg 8  
                                       e+C +C+
  gi|386001035|ref|YP_005919334.1| 182 ENCRRCK 188
                                       6788887 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.1e-05
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       rCi C +Cv +CP
  gi|386001035|ref|YP_005919334.1| 286 RCIKCYACVEVCP 298
                                       9************ PP

  == domain 3  score: 13.4 bits;  conditional E-value: 9.3e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++Ci+Cg+C   CP+
  gi|386001035|ref|YP_005919334.1| 331 DSCINCGQCQELCPM 345
                                       89************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.9   0.00034      0.31       5      23 ..     284     302 ..     280     306 .. 0.86
   2 !    8.4   0.6    0.0041       3.6       6      20 ..     331     345 ..     330     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                           Fer4_15   5 rdaCigcglCvaeapevfe 23 
                                         +Ci c +Cv+++p +f 
  gi|386001035|ref|YP_005919334.1| 284 TARCIKCYACVEVCPALFN 302
                                       569**************97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0041
                           Fer4_15   6 daCigcglCvaeape 20 
                                       d Ci cg+C +++p 
  gi|386001035|ref|YP_005919334.1| 331 DSCINCGQCQELCPM 345
                                       89***********95 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   4.0   2.9e-05     0.026       1      12 [.     287     298 ..     287     301 .. 0.97
   2 ?   11.7   3.9   0.00046      0.41       1      12 [.     333     344 ..     333     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-05
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C+aCvevCP
  gi|386001035|ref|YP_005919334.1| 287 CIKCYACVEVCP 298
                                       ***********9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00046
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C++Cg+C e CP
  gi|386001035|ref|YP_005919334.1| 333 CINCGQCQELCP 344
                                       ************ PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         4   3.6e+03      37      61 ..     164     188 ..     138     190 .. 0.66
   2 ?    9.1   4.9    0.0027       2.4       1      14 [.     286     299 ..     239     300 .. 0.85
   3 ?   11.1  14.7   0.00066      0.59       1      66 [.     286     345 ..     286     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4
                           Fer4_16  37 ekkdlaedeekckkqeaitgCdiCq 61 
                                       e+kdl+++e +    ++   C++C+
  gi|386001035|ref|YP_005919334.1| 164 EHKDLPIREIEGAGLGRRENCRRCK 188
                                       4566666666666566667777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0027
                           Fer4_16   1 rCgtCgkCaevCPt 14 
                                       rC++C +C+evCP+
  gi|386001035|ref|YP_005919334.1| 286 RCIKCYACVEVCPA 299
                                       47777777777774 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00066
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       rC++C +C+evCP+   ++       +r+++   ++   +++ ++ ++  +  ++ C+ Cq+ CP+
  gi|386001035|ref|YP_005919334.1| 286 RCIKCYACVEVCPALFNTTG-----PYRTSFPGLVPPGLEFHLTRYAHV-ADSCINCGQCQELCPM 345
                                       6************8655444.....4667777789999******99998.999************7 PP

>> c-SKI_SMAD_bind  c-SKI Smad4 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.1      0.03        27      23      36 ..     282     295 ..     276     302 .. 0.81
   2 ?    9.1   0.3    0.0017       1.5      16      49 ..     321     357 ..     318     374 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                   c-SKI_SMAD_bind  23 sseakCikCleCkl 36 
                                       +++a+CikC+ C  
  gi|386001035|ref|YP_005919334.1| 282 EETARCIKCYACVE 295
                                       6899********65 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                   c-SKI_SMAD_bind  16 fvpelyssseakCikCleCkllfs...pqkFvvHsHr 49 
                                       f  ++y +   +Ci+C +C+ l     p+  ++H+  
  gi|386001035|ref|YP_005919334.1| 321 FHLTRYAHVADSCINCGQCQELCPmeiPNARIMHAIA 357
                                       5668999************986543337777887655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.8     0.049        44       1      14 [.     286     299 ..     286     305 .. 0.89
   2 ?   10.7   0.6   0.00083      0.75      79      96 .]     330     347 ..     320     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.049
                           Fer4_22   1 rClsCgaCtlvCpt 14 
                                       rC++C aC  vCp+
  gi|386001035|ref|YP_005919334.1| 286 RCIKCYACVEVCPA 299
                                       7***********97 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00083
                           Fer4_22  79 esgCvGCgRCieacpvki 96 
                                       + +C+ Cg C+e cp++i
  gi|386001035|ref|YP_005919334.1| 330 ADSCINCGQCQELCPMEI 347
                                       567888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2392.06
//
Query:       gi|386001036|ref|YP_005919335.1|  [L=695]
Description: Formate dehydrogenase, alpha subunit (F420) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-92  308.5   0.0    9.8e-92  308.2   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    4.1e-33  113.7   0.0    8.3e-33  112.7   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.5e-21   76.1   0.2    2.8e-21   75.3   0.2    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.2   0.0   1.6e-95   9.8e-92       1     431 [.      62     486 ..      62     487 .. 0.90

  Alignments for each domain:
  == domain 1  score: 308.2 bits;  conditional E-value: 1.6e-95
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rlk+P+++   r  G Fv++sWdeAl+lia++l      y p++v++ +s +++ +e+ ++++k+++ +++  ++++
  gi|386001036|ref|YP_005919335.1|  62 RLKTPLIK---R-GGSFVPASWDEALQLIARRLSS----YRPEEVFFLASAKAT-NEENYLFQKFARVVMK--TNNV 127
                                       9*******...9.9*********************....*******99999999.999999**********..9*** PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+l+++s++    +++gs+     +++n++ dle+++ i+++GsN  e +p+  +r +  a++++akvi+ +pr
  gi|386001036|ref|YP_005919335.1| 128 DHCARLCHSSTVsalaKAFGSG-----AMTNSILDLEEARCIFVIGSNTFEQHPLI-GRRLVLARRRGAKVISADPR 198
                                       ***********96555555554.....6788999**********************.55555566668********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCS..HHHHHHCCHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleee..tgkkkevvariar 225
                                       ++ ++k+ad++l+i+pgtd+al++++   i++ +++d  f++ +t g+e +++ + ++ +    t+   + v +  +
  gi|386001036|ref|YP_005919335.1| 199 LTPTAKEADLHLPIRPGTDVALINGLVRRIIEGGWEDRGFIEERTRGFETLRETVMKEESTLpgTS-RITGVPEGDI 274
                                       ************************************************999887765555442133.4466777778 PP

                                       HHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCC CS
                     Molybdopterin 226 elarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvk 302
                                       e a+++++t + ++ ++ +g++++++g +++ a++nL++l+gn+g+pg+g++ l+Gq++++g a+++galp   s +
  gi|386001036|ref|YP_005919335.1| 275 EAAAEMIATLKPAALLYSMGVTQHTSGVENVLALANLMMLTGNIGRPGSGVNPLRGQNNVQG-ACDMGALPNVFSGY 350
                                       888888888888**************************************************.************** PP

                                       CCTT....HHHHHCCCTTTCST.SS--ECGGCHHHHHHT..TSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEE CS
                     Molybdopterin 303 slke....ekikfaaeqpgnlg.nfprnlfversnllks..sgkkvlyllgnnpevdhadenevekalekldlvvvl 372
                                       +++e    ++  ++ ++ ++lg    +++++e+++ l +  + +k+lyl+g+np+++ ad+n+v +al + ++ v  
  gi|386001036|ref|YP_005919335.1| 351 QSVEedgcRRRMKRVWGVEELGeARAGITSTEMMEILADrpGRMKALYLMGENPMISEADQNRVRRALDNVEFMVSQ 427
                                       ***99**9555555555555541457899999999997533789********************************* PP

                                       ESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 373 dgrltstalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       ++++t+t + aD++LPaa++ Ek++++tn+++r+q+l++a++ppgea +dw+Il+ La+
  gi|386001036|ref|YP_005919335.1| 428 EIFMTETTELADVVLPAASFAEKDGTFTNTDRRVQRLRKAIDPPGEAMPDWEILSRLAR 486
                                       ********************************************************996 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   1.4e-36   8.3e-33       1     111 []     574     680 ..     574     680 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1.4e-36
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l+L+tgrsl+++h++ +tr++ +l+ + +   ve+n+edA+++Gi dG+ V+v+srrG++e++a+vt ++++Gv+f+
  gi|386001036|ref|YP_005919335.1| 574 LILTTGRSLWHWHAGSMTRRSKSLGGEVEtGWVEMNEEDAEEMGIGDGEVVRVSSRRGRIELPARVTSEIKRGVIFV 650
                                       79**********************999999*********************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksva 111
                                       pf++ e      +aN+lt++a+dp+s++pefk++a
  gi|386001036|ref|YP_005919335.1| 651 PFHFAE-----CPANRLTNAALDPVSKIPEFKACA 680
                                       ****99.....*********************996 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.2   4.6e-25   2.8e-21       1      54 [.       5      58 ..       5      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.6e-25
                                      SEEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCC CS
                    Molybdop_Fe4S4  1 ekvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervy 54
                                      +k+v t+CpyCgvgCgl++ v+d+++v ve+++ hp+neg+lC KGr ++++++
  gi|386001036|ref|YP_005919335.1|  5 MKFVATTCPYCGVGCGLLLAVRDERVVGVEPWQAHPINEGKLCQKGRYAHQFIH 58
                                      799************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 4853.77
//
Query:       gi|386001037|ref|YP_005919336.1|  [L=442]
Description: AIR synthase related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-16   58.6   3.7    1.6e-15   57.6   3.7    1.6  1  AIRS_C    AIR synthase related protein, C-terminal domain
    8.6e-08   32.7   0.4      2e-07   31.6   0.4    1.6  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   3.7   1.8e-19   1.6e-15       2     155 ..     230     379 ..     229     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.8e-19
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                       pGdv+++t++ G g +  +++   +++e        ++d+ +  + ++++ al +++ +++a++DvT+GG+ g+++e
  gi|386001037|ref|YP_005919336.1| 230 PGDVILMTEGAGGGTVC-AAALYYGRHE--------VVDETMNIKFLEAASALLEQEVEIHAMTDVTNGGIRGDAKE 297
                                       9*********8888888.5555455444........899************************************** PP

                                       HHHTTTEEEEEECG......THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                            AIRS_C  79 mapasgvgaeidld......kvpifdele.splemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                       + + +gv++ ++++      + ++++ le +++++l   +   ll+++pp +a +++++++ +g+ e   IG+v+++
  gi|386001037|ref|YP_005919336.1| 298 ISKTAGVKLIFQEErmarlvNRRVLEMLEdLEIDYLG-VSIDALLIIAPPSSAGEIVRAVRGAGV-EIDAIGRVEEG 372
                                       **************76665555555555444455554.5555699********************.8********** PP

                                       SSEEEEE CS
                            AIRS_C 149 eelsviv 155
                                       ++++++v
  gi|386001037|ref|YP_005919336.1| 373 RGVELHV 379
                                       *999887 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.4   2.2e-11     2e-07       4      92 ..     109     217 ..      96     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.2e-11
                                       E........EEEEEEEEE.EECCTCCCC.HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHH CS
                              AIRS   4 a........vvvttdshnrpvlvepvhf.iGakavavnlsDlaamGArPlalllslalp......wleevvrglaea 65 
                                       +        +v+t+d++   + ++++ f +G  +  ++l+D+++m ArP+a++  + l        l + ++g+a+ 
  gi|386001037|ref|YP_005919336.1| 109 GaveaggryIVLTVDGMH--SRLSDYPFlAGFHVTRATLRDIYVMRARPVAMFSDIHLAddgdlsRLFDHLAGIAAV 183
                                       333334444589999554..4455555556********************9999999989**999999999****** PP

                                       HHHTT-EEEEEEEEEESS.......EEEEEEEEE CS
                              AIRS  66 aeelgvplvgGdtsfsne.......ptisvtavG 92 
                                       +e  gvpl++G t +  +       +t +v+avG
  gi|386001037|ref|YP_005919336.1| 184 GELTGVPLITGSTLRIGGdmvigdrLTGCVGAVG 217
                                       ***********99876444555555666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 3133.14
//
Query:       gi|386001038|ref|YP_005919337.1|  [L=165]
Description: transcription factor E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-19   68.9   0.6      4e-19   68.4   0.6    1.2  1  TFIIE_alpha   TFIIE alpha subunit
    0.00021   20.7   0.7    0.00049   19.6   0.7    1.7  1  TF_Zn_Ribbon  TFIIB zinc-binding
      0.008   16.3   0.1      0.085   13.0   0.0    2.1  2  FUR           Ferric uptake regulator family
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.053   13.6   0.0    1.5  1  HTH_9         RNA polymerase III subunit RPC82 helix-turn-hel
      0.034   13.6   0.0      0.056   12.9   0.0    1.3  1  RepL          Firmicute plasmid replication protein (RepL)
      0.046   13.5   0.1       0.26   11.1   0.0    2.2  2  HTH_IclR      IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.6   1.3e-22     4e-19       7     105 .]      13     110 ..       8     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.3e-22
                                       HHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCC CS
                       TFIIE_alpha   7 vrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvd 83 
                                       +rk  gee  +++d++    evt+e +a+ ++i ln +r+ L+ Lye rl+ky+r+rd+e +w +y w +  ++l  
  gi|386001038|ref|YP_005919337.1|  13 LRKLVGEEGLQIVDCMP-AEEVTDEYVAEITGISLNTVRRTLYLLYEHRLAKYRRERDPESGWLTYLWTLCSDNLDR 88 
                                       68999**********99.88********************************************************* PP

                                       CHHHHHHHHHHHHHHHHCCCTS CS
                       TFIIE_alpha  84 vvkrkleevvkkLeeklekeen 105
                                       ++  + +++++kLee l  e++
  gi|386001038|ref|YP_005919337.1|  89 ALESEARKLLRKLEERLAYEKE 110
                                       *****************99875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   1.6e-07   0.00049      10      39 ..     122     152 ..     114     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.6e-07
                                       ECHEE.TSTTCEEESSSSBEEEECCCCCCCH CS
                      TF_Zn_Ribbon  10 nlveD.pergelvCtdCGlVlednsidegpe 39 
                                       ++v+D +++++++C++CG+ le++ +d  ++
  gi|386001038|ref|YP_005919337.1| 122 RFVFDeASENNFICPFCGAGLEYMENDRIVT 152
                                       478886788889************9998765 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.8e-05     0.085      25      57 ..      29      61 ..      18      72 .. 0.90
   2 ?    1.2   0.0      0.13   3.9e+02      68      95 ..     121     147 ..     108     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      EHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTS CS
                               FUR 25 saeevykelkeedpeislaTVYrtLklleeagl 57
                                       aeev++e + e   isl TV rtL ll e  l
  gi|386001038|ref|YP_005919337.1| 29 PAEEVTDEYVAEITGISLNTVRRTLYLLYEHRL 61
                                      69*************************988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                       EEEEESSSSSEEEEEETTT--EEEE--H CS
                               FUR  68 sryelakkehhdhlicekCgkviefkdd 95 
                                       +r+ +  +   +++ic  Cg   e +++
  gi|386001038|ref|YP_005919337.1| 121 ARFVFD-EASENNFICPFCGAGLEYMEN 147
                                       566666.466789999999986665543 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.053      36      59 ..      41      64 ..      34      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      HHSSTHHHHHHHHHHHHHTTSEEE CS
                             HTH_9 36 ktkLsldqVkksLvvLiqhrlVqy 59
                                       t++sl+ V+++L++L  hrl++y
  gi|386001038|ref|YP_005919337.1| 41 ITGISLNTVRRTLYLLYEHRLAKY 64
                                      478********************9 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.056      77     104 ..      34      61 ..      31      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                              RepL  77 tnRelaeetgislktvsetlkileeani 104
                                       t   +ae tgisl+tv++tl  l e  +
  gi|386001038|ref|YP_005919337.1|  34 TDEYVAEITGISLNTVRRTLYLLYEHRL 61 
                                       67789***************99988766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.9e-05      0.26      24      50 ..      38      64 ..      21      66 .. 0.91
   2 ?   -0.7   0.0      0.41   1.2e+03      33      45 ..      92     104 ..      91     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                                      HHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 24 lArrtglpkStvhRlLqtLvelGyveq 50
                                      +A+ tg++  tv+R L  L e+++ ++
  gi|386001038|ref|YP_005919337.1| 38 VAEITGISLNTVRRTLYLLYEHRLAKY 64
                                      79*********************9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHT CS
                          HTH_IclR  33 StvhRlLqtLvel 45 
                                       S ++ lL+ L+e+
  gi|386001038|ref|YP_005919337.1|  92 SEARKLLRKLEER 104
                                       88999****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      822  (0.0458475); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1081.36
//
Query:       gi|386001039|ref|YP_005919338.1|  [L=133]
Description: hypothetical protein Mhar_0328 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.2   0.0       0.15   12.0   0.0    1.6  2  TrmB      Sugar-specific transcriptional regulator TrmB


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 ?   -2.8   0.0      0.34   6.2e+03      18      32 ..       4      18 ..       4      22 .. 0.68
   2 ?   12.0   0.0   8.4e-06      0.15      28      60 ..      73     105 ..      64     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.34
                                      HHHCCCHHCHHCCCT CS
                              TrmB 18 lklgpatadeiaeel 32
                                      +k+ p ta+++  ++
  gi|386001039|ref|YP_005919338.1|  4 VKNAPRTATTLKIRS 18
                                      577888888876555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.4e-06
                                       HCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  28 iaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                         e+lgv+rs  Y + ++L+ +Gl+ ++ g+++
  gi|386001039|ref|YP_005919338.1|  73 MMEDLGVSRSAFYFMRNKLLGAGLIAVRSGEYR 105
                                       5799************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 790.30
//
Query:       gi|386001040|ref|YP_005919339.1|  [L=108]
Description: hypothetical protein Mhar_0329 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-29  100.8   0.2    4.6e-29  100.5   0.2    1.1  1  DUF2551          Protein of unknown function (DUF2551)
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.033   14.6   0.0    1.3  1  Penicillinase_R  Penicillinase repressor
      0.026   14.3   0.1      0.031   14.0   0.1    1.1  1  DUF1758          Putative peptidase (DUF1758)


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.2   7.7e-33   4.6e-29       1      83 []      12      94 ..      12      94 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 7.7e-33
                           DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeey 79
                                      L ++l+ D++G Rr vL ++lea+++tv+++y+++ke+f+ s+k+vas++G+i+s+lGIl+++k+s++ ++vY Lkeey
  gi|386001040|ref|YP_005919339.1| 12 LVQFLDLDTDGRRRFVLGVILEAGEITVSSLYKAVKEQFETSRKVVASLLGYICSKLGILSAHKKSYRLPTVYVLKEEY 90
                                      679**************************************************************************** PP

                           DUF2551 80 adlv 83
                                      adlv
  gi|386001040|ref|YP_005919339.1| 91 ADLV 94
                                      **98 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-06     0.033       8      57 ..      27      77 ..      23     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHT.TS-EEEEET CS
                   Penicillinase_R  8 vmeilwekgeatvkevveeleeekelaysTVktllrrLvkK.gllsrekeg 57
                                      v+ ++ e+ge+tv+++ ++++e+ e++++ V++ll+  + K g+ls++k+ 
  gi|386001040|ref|YP_005919339.1| 27 VLGVILEAGEITVSSLYKAVKEQFETSRKVVASLLGYICSKlGILSAHKKS 77
                                      8999***********************************997888888864 PP

>> DUF1758  Putative peptidase (DUF1758)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.2e-06     0.031      21      88 ..       3      69 ..       1      79 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-06
                           DUF1758 21 selsYiseRlinaLgLartpsriLvigisadkaeairgssrlviksrlsddtlavrahvlkkitssLe 88
                                      s +s i+ Rl++ L L +   r  v g+  +  e ++ s    +k + +   ++v a+ l+ i s L 
  gi|386001040|ref|YP_005919339.1|  3 SMQSEIASRLVQFLDLDTDGRRRFVLGVILEAGEITVSSLYKAVKEQFETS-RKVVASLLGYICSKLG 69
                                      77899**************************99999999888999888765.567799******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 733.21
//
Query:       gi|386001041|ref|YP_005919340.1|  [L=235]
Description: hypothetical protein Mhar_0330 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-11   43.1   0.0    5.6e-11   42.5   0.0    1.2  1  Mrr_cat   Restriction endonuclease
  ------ inclusion threshold ------
       0.24   11.8   0.0       0.34   11.3   0.0    1.3  1  BRCT      BRCA1 C Terminus (BRCT) domain


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 !   42.5   0.0   6.3e-15   5.6e-11       4     114 ..      28     139 ..      26     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.3e-15
                                       T-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEE.TTEEEE.EEEEEEE--TS-B-HHHHHHHHHHCTTS.. CS
                           Mrr_cat   4 mspkeFeklvaellealGykeveltgrsgDggiDliakk.dplgse.rilvqaKryknkvgvkeVqeligalkkrga 78 
                                       +++  Fe+   +l+e +Gyk v  + rs+Dgg +l a++ d+ g++ ++++  K + ++v++ +V++ + a + +  
  gi|386001041|ref|YP_005919340.1|  28 VEGSGFEEEFSDLIELNGYK-VAKAARSEDGGSELFASRtDEVGHQvTYVIHLKPSGAAVDEAAVERAARARDRHPG 103
                                       67889**************9.***************966377777689***************************99 PP

                                       SEEEEEE.SS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  79 dkgifvt.tsdftkaAreeaeelnkieLldgdeLael 114
                                       + +++v+ +s+f+++  + a++  +++L+  +e+ +l
  gi|386001041|ref|YP_005919340.1| 104 SISVVVSpSSEFARSVVDLADR-RGVRLWGEEEIRRL 139
                                       99**9994566***********.******99999876 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.8e-05      0.34      22      54 ..      34      82 ..      26     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                                      HHHHHHHHHHTTCEE.................ESSCSTTSSEEEESSSHS CS
                              BRCT 22 rdeleelikehGGkv.................ttevskktthlvvgepes 54
                                       +e  +li+++G kv                 t+ev +++t++++ +p s
  gi|386001041|ref|YP_005919340.1| 34 EEEFSDLIELNGYKVakaarsedggselfasrTDEVGHQVTYVIHLKP-S 82
                                      578899***************************************999.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 1405.19
//
Query:       gi|386001042|ref|YP_005919341.1|  [L=266]
Description: hypothetical protein Mhar_0331 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-56  184.2   8.5    1.4e-09   37.3   0.0    7.1  7  TPR_1         Tetratricopeptide repeat
    1.6e-46  152.6  20.0    7.2e-07   28.8   0.0    7.1  7  TPR_2         Tetratricopeptide repeat
      4e-43  142.0   2.7    8.9e-07   28.6   0.2    7.1  7  TPR_8         Tetratricopeptide repeat
      3e-36  123.8  41.1    3.6e-11   43.5   6.5    4.3  5  TPR_16        Tetratricopeptide repeat
      2e-33  113.8   7.7    5.9e-08   32.3   0.0    7.4  7  TPR_11        TPR repeat
    1.3e-29  100.4   1.4    0.00032   20.9   0.0    6.9  7  TPR_17        Tetratricopeptide repeat
    2.8e-25   88.4  14.2    8.3e-07   29.2   2.0    5.4  5  TPR_12        Tetratricopeptide repeat
    5.1e-25   86.0  27.2    2.8e-05   24.6   1.1    7.1  7  TPR_14        Tetratricopeptide repeat
    4.9e-24   84.3  17.0    4.2e-07   30.0   2.1    5.1  5  TPR_9         Tetratricopeptide repeat
    1.4e-22   79.9  19.2    2.2e-08   34.5   0.8    4.2  5  TPR_19        Tetratricopeptide repeat
    1.2e-16   59.4   6.7      0.002   18.0   0.1    6.3  6  TPR_7         Tetratricopeptide repeat
    7.7e-12   45.0  11.1      0.011   16.4   0.4    6.9  7  TPR_6         Tetratricopeptide repeat
    1.1e-10   41.0  23.9      0.025   14.4   0.2    7.2  7  TPR_10        Tetratricopeptide repeat
    8.1e-09   35.7   9.0      0.005   16.9   0.1    6.0  5  DUF3856       Domain of Unknown Function (DUF3856)
    2.6e-08   34.0   4.0    0.00035   20.7   0.1    4.2  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    7.8e-08   32.9  14.0       0.14   12.6   1.1    4.3  4  BTAD          Bacterial transcriptional activator domain
    1.1e-07   31.7  24.7       0.62   10.9   0.9    7.0  7  TPR_4         Tetratricopeptide repeat
    7.8e-05   22.0   2.7      0.003   16.8   1.1    3.1  3  TPR_15        Tetratricopeptide repeat
    8.2e-05   21.7   0.0        1.4    7.8   0.0    3.5  4  NARP1         NMDA receptor-regulated protein 1
     0.0002   21.3   5.7        4.8    7.3   0.2    4.9  5  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    0.00021   21.3  13.1       0.24   11.5   0.0    5.1  5  MIT           MIT (microtubule interacting and transport) dom
    0.00033   20.9   1.5      0.012   15.8   0.0    3.4  3  TPR_5         Tetratrico peptide repeat
    0.00071   19.0   0.2        2.1    7.9   0.0    3.3  3  SHNi-TPR      SHNi-TPR
     0.0013   18.7   4.1        2.8    8.0   0.0    4.0  3  TPR_3         Tetratricopeptide repeat
     0.0015   18.0   0.2        2.2    7.6   0.0    3.0  3  TPR_MalT      MalT-like TPR region
     0.0053   16.7   0.4        1.7    8.5   0.0    3.1  3  Wzy_C_2       Virulence factor membrane-bound polymerase, C-t
     0.0067   16.4   0.0       0.12   12.4   0.0    2.7  2  SRP_TPR_like  Putative TPR-like repeat
  ------ inclusion threshold ------
       0.13   12.6   3.2       0.32   11.4   0.1    2.9  2  TPR_20        Tetratricopeptide repeat
       0.28   10.6   1.2         11    5.3   0.1    3.0  2  SNAP          Soluble NSF attachment protein, SNAP
        0.9    9.9   9.0         32    5.1   0.0    5.1  4  PPR           PPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1     1e-06   0.00061       2      32 ..      28      58 ..      27      60 .. 0.95
   2 !   30.0   0.4   4.8e-10   2.9e-07       2      34 .]      62      94 ..      61      94 .. 0.96
   3 !   21.5   0.0   2.3e-07   0.00014       2      34 .]      96     128 ..      95     128 .. 0.94
   4 !   28.9   0.0   1.1e-09   6.8e-07       1      32 [.     129     160 ..     129     160 .. 0.97
   5 !   37.3   0.0   2.4e-12   1.4e-09       2      32 ..     167     197 ..     166     199 .. 0.95
   6 !   31.5   0.0   1.6e-10   9.6e-08       2      34 .]     201     233 ..     200     233 .. 0.95
   7 !   14.2   0.0   4.7e-05     0.028       3      30 ..     236     263 ..     234     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-06
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnP 32
                                      + +y +G+a++  g ++eA +   +A+e +P
  gi|386001042|ref|YP_005919341.1| 28 DYWYKRGAAHYGSGLFEEAADSLARAIEADP 58
                                      78**************************999 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 4.8e-10
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      +a y lG a++k+g+y+ A+e y+ AL l P++
  gi|386001042|ref|YP_005919341.1| 62 EARYLLGEALRKKGRYQAAVESYDAALDLKPDH 94
                                      789****************************96 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +++ ++++a+ +l +++eAle  ++AL l+P +
  gi|386001042|ref|YP_005919341.1|  96 RSWRGRAVALNELDRHEEALESADRALGLDPRD 128
                                       7899***************************75 PP

  == domain 4  score: 28.9 bits;  conditional E-value: 1.1e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+++  +G+a++ lg++ eA e y++ALe++P
  gi|386001042|ref|YP_005919341.1| 129 ARCWIVKGYAFHALGRFSEAAESYDRALEIEP 160
                                       789***************************99 PP

  == domain 5  score: 37.3 bits;  conditional E-value: 2.4e-12
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a++n+G+a+ +lg+++eAle+y++ + ++P
  gi|386001042|ref|YP_005919341.1| 167 RAWNNKGAALDNLGRHEEALECYDESILIDP 197
                                       79****************************9 PP

  == domain 6  score: 31.5 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++++n+G+ +  l++++eA+e++ kA+el P +
  gi|386001042|ref|YP_005919341.1| 201 YTWNNKGVSLIALKRPEEAVECFGKAVELFPGY 233
                                       58****************************975 PP

  == domain 7  score: 14.2 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       a+ n+++a+ +lg+  eA+e+ ++A  l
  gi|386001042|ref|YP_005919341.1| 236 AWRNRALALKSLGREGEAEEALDRARDL 263
                                       9***********************9665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   8.4e-08     5e-05       1      32 [.      27      58 ..      27      59 .. 0.97
   2 !   27.9   0.9   2.5e-09   1.5e-06       2      34 .]      62      94 ..      61      94 .. 0.95
   3 !   14.4   0.0   5.2e-05     0.031       2      34 .]      96     128 ..      95     128 .. 0.92
   4 !   24.9   0.1   2.2e-08   1.3e-05       1      32 [.     129     160 ..     129     161 .. 0.96
   5 !   28.8   0.0   1.2e-09   7.2e-07       2      32 ..     167     197 ..     166     199 .. 0.95
   6 !   28.3   0.0   1.9e-09   1.1e-06       2      33 ..     201     232 ..     200     233 .. 0.94
   7 !   14.5   0.3   4.6e-05     0.027       3      30 ..     236     263 ..     234     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.4e-08
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldP 32
                                      ++++y +G a+y +g +eeA++ + +A+e dP
  gi|386001042|ref|YP_005919341.1| 27 PDYWYKRGAAHYGSGLFEEAADSLARAIEADP 58
                                      589***************************99 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.5e-09
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ea y lG+a++k+g+y+ A+e +++Al l P++
  gi|386001042|ref|YP_005919341.1| 62 EARYLLGEALRKKGRYQAAVESYDAALDLKPDH 94
                                      789****************************97 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.2e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       + +  ++ a+ +l+++eeAle  ++Al ldP++
  gi|386001042|ref|YP_005919341.1|  96 RSWRGRAVALNELDRHEEALESADRALGLDPRD 128
                                       67999999999********************86 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 2.2e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a+++   G+a  +lg++ eA+e +++Ale++P
  gi|386001042|ref|YP_005919341.1| 129 ARCWIVKGYAFHALGRFSEAAESYDRALEIEP 160
                                       679999************************99 PP

  == domain 5  score: 28.8 bits;  conditional E-value: 1.2e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +a++n G a+ +lg++eeAle++++++ +dP
  gi|386001042|ref|YP_005919341.1| 167 RAWNNKGAALDNLGRHEEALECYDESILIDP 197
                                       69****************************9 PP

  == domain 6  score: 28.3 bits;  conditional E-value: 1.9e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       + ++n G ++++l+++eeA+e+f kA+el P+
  gi|386001042|ref|YP_005919341.1| 201 YTWNNKGVSLIALKRPEEAVECFGKAVELFPG 232
                                       57*****************************7 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 4.6e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       a+ n++la+  lg+  eA+ea+++A  l
  gi|386001042|ref|YP_005919341.1| 236 AWRNRALALKSLGREGEAEEALDRARDL 263
                                       8************************877 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   6.9e-05     0.041       2      32 ..      28      58 ..      27      60 .. 0.95
   2 !   28.6   0.2   1.5e-09   8.9e-07       2      34 .]      62      94 ..      61      94 .. 0.96
   3 !   12.4   0.0   0.00023      0.14       7      33 ..     101     127 ..      95     128 .. 0.89
   4 !   21.8   0.0   2.4e-07   0.00014       1      32 [.     129     160 ..     129     160 .. 0.97
   5 !   27.6   0.0   3.3e-09     2e-06       2      33 ..     167     198 ..     166     199 .. 0.96
   6 !   21.9   0.0   2.2e-07   0.00013       3      32 ..     202     231 ..     200     233 .. 0.94
   7 !    9.1   0.0    0.0027       1.6       3      27 ..     236     260 ..     234     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.9e-05
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldp 32
                                      +++y+ g ++   g +eeA  ++ +a+e+dp
  gi|386001042|ref|YP_005919341.1| 28 DYWYKRGAAHYGSGLFEEAADSLARAIEADP 58
                                      68****************************9 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.5e-09
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      ea y+lg +++k+g+y++A+e+y  al+l+pd+
  gi|386001042|ref|YP_005919341.1| 62 EARYLLGEALRKKGRYQAAVESYDAALDLKPDH 94
                                      789****************************97 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00023
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                        + ++ +l ++eeA e+  +al ldp 
  gi|386001042|ref|YP_005919341.1| 101 RAVALNELDRHEEALESADRALGLDPR 127
                                       578899*******************96 PP

  == domain 4  score: 21.8 bits;  conditional E-value: 2.4e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+ +  +g++ + lg++ eA e+y +ale++p
  gi|386001042|ref|YP_005919341.1| 129 ARCWIVKGYAFHALGRFSEAAESYDRALEIEP 160
                                       789***************************98 PP

  == domain 5  score: 27.6 bits;  conditional E-value: 3.3e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n+g ++++lg++eeA e+y + + +dp 
  gi|386001042|ref|YP_005919341.1| 167 RAWNNKGAALDNLGRHEEALECYDESILIDPF 198
                                       89****************************96 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                        ++n+g  ++ l++ eeA+e++ ka+el p
  gi|386001042|ref|YP_005919341.1| 202 TWNNKGVSLIALKRPEEAVECFGKAVELFP 231
                                       69*************************987 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                       a+ n ++++++lg+  eA+e++ +a
  gi|386001042|ref|YP_005919341.1| 236 AWRNRALALKSLGREGEAEEALDRA 260
                                       56689****************9988 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.8   8.4e-06     0.005      26      65 ..      19      58 ..      16      58 .. 0.90
   2 !   43.5   6.5     6e-14   3.6e-11       1      68 []      31      95 ..      31      95 .. 0.98
   3 !   43.4   6.8   6.4e-14   3.9e-11       1      67 [.      65     128 ..      65     129 .. 0.97
   4 !   37.4   0.3     5e-12     3e-09       4      61 ..     136     193 ..     133     199 .. 0.90
   5 !   29.0   0.4   2.1e-09   1.3e-06       3      61 ..     206     261 ..     204     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.4e-06
                            TPR_16 26 rdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65
                                      ++++  ++++ ++ +g a++  g ++eAa+ +++a++a+p
  gi|386001042|ref|YP_005919341.1| 19 SGGEGLLDPDYWYKRGAAHYGSGLFEEAADSLARAIEADP 58
                                      677788899********************99999999998 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 6e-14
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68
                                      ++++ a++ +g +++Aa  l +a+++d   P   eA++llg+a+ ++gr+++A++ y+aal+  pd+p
  gi|386001042|ref|YP_005919341.1| 31 YKRGAAHYGSGLFEEAADSLARAIEAD---PIFFEARYLLGEALRKKGRYQAAVESYDAALDLKPDHP 95
                                      78999**********************...***********************************987 PP

  == domain 3  score: 43.4 bits;  conditional E-value: 6.4e-14
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       + l+ a+++ g+y++A++ ++aal++    Pd+++++ ++++a+ ++ r++eA++  ++al+ +p +
  gi|386001042|ref|YP_005919341.1|  65 YLLGEALRKKGRYQAAVESYDAALDLK---PDHPRSWRGRAVALNELDRHEEALESADRALGLDPRD 128
                                       789************************...***********************************87 PP

  == domain 4  score: 37.4 bits;  conditional E-value: 5e-12
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++a+ ++g++ +Aa+ +++al+  p  P+a +A++++g a+  +gr++eA++ y++ +
  gi|386001042|ref|YP_005919341.1| 136 GYAFHALGRFSEAAESYDRALEIEPLGPRAGRAWNNKGAALDNLGRHEEALECYDESI 193
                                       5666689********************************************9888765 PP

  == domain 5  score: 29.0 bits;  conditional E-value: 2.1e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       ++ ++++++++++A++ +  a++++   P    A+ ++++a+  +gr  eA++++++a 
  gi|386001042|ref|YP_005919341.1| 206 KGVSLIALKRPEEAVECFGKAVELF---PGYTTAWRNRALALKSLGREGEAEEALDRAR 261
                                       5678999******************...************************9999986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.3    0.0042       2.5      27      42 .]      26      41 ..      26      41 .. 0.91
   2 !   18.1   0.4   2.7e-06    0.0016       8      42 .]      41      75 ..      38      75 .. 0.93
   3 !   32.3   0.0   9.9e-11   5.9e-08       1      38 [.      68     105 ..      68     109 .. 0.94
   4 ?    6.6   0.0      0.01         6       4      29 ..     105     130 ..     104     133 .. 0.88
   5 !   22.7   0.1   9.6e-08   5.8e-05       1      29 [.     136     164 ..     136     176 .. 0.87
   6 !   17.1   0.0   5.2e-06    0.0031       7      37 ..     179     209 ..     173     214 .. 0.92
   7 !   15.8   0.0   1.4e-05    0.0084       8      42 .]     214     248 ..     207     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0042
                            TPR_11 27 naeayynLGlayykqG 42
                                      +++ +y++G+a+y  G
  gi|386001042|ref|YP_005919341.1| 26 DPDYWYKRGAAHYGSG 41
                                      79***********876 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.7e-06
                            TPR_11  8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      G +eeA  ++ +A++ dP + ea y LG+a+ k+G
  gi|386001042|ref|YP_005919341.1| 41 GLFEEAADSLARAIEADPIFFEARYLLGEALRKKG 75
                                      668***************************99988 PP

  == domain 3  score: 32.3 bits;  conditional E-value: 9.9e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G a++++G+y +A+e+Y +Al+l+Pd ++ + ++++a+
  gi|386001042|ref|YP_005919341.1|  68 GEALRKKGRYQAAVESYDAALDLKPDHPRSWRGRAVAL 105
                                       899*****************************999987 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.01
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnae 29 
                                       + e+ + eeA+e+  +Al ldP +a+
  gi|386001042|ref|YP_005919341.1| 105 LNELDRHEEALESADRALGLDPRDAR 130
                                       5677899****************996 PP

  == domain 5  score: 22.7 bits;  conditional E-value: 9.6e-08
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnae 29 
                                       G+a++++G++ eA e+Y +Al++ P  ++
  gi|386001042|ref|YP_005919341.1| 136 GYAFHALGRFSEAAESYDRALEIEPLGPR 164
                                       99**********************96665 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 5.2e-06
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       +G+ eeA+e+Y + + +dP +   ++n G+ 
  gi|386001042|ref|YP_005919341.1| 179 LGRHEEALECYDESILIDPFDFYTWNNKGVS 209
                                       79*************************9976 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 1.4e-05
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        + eeA+e++ kA++l P + +a+ n++la+  +G
  gi|386001042|ref|YP_005919341.1| 214 KRPEEAVECFGKAVELFPGYTTAWRNRALALKSLG 248
                                       5669**************************99887 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.9   2.3e+03      12      27 ..      26      41 ..      25      47 .. 0.75
   2 !   20.9   0.0   5.3e-07   0.00032       4      34 .]      52      82 ..      50      82 .. 0.95
   3 !   12.7   0.0   0.00021      0.13       2      34 .]      84     116 ..      83     116 .. 0.95
   4 !    7.8   0.0    0.0083       4.9       3      32 ..     119     148 ..     118     150 .. 0.89
   5 !   15.0   0.0     4e-05     0.024       2      34 .]     152     187 ..     151     187 .. 0.88
   6 !   17.8   0.0   4.9e-06     0.003       1      34 []     188     221 ..     188     221 .. 0.96
   7 !   17.9   0.0   4.6e-06    0.0028       1      34 []     222     255 ..     222     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.9
                            TPR_17 12 nadaynnLAelllknG 27
                                      ++d ++ ++ +++  G
  gi|386001042|ref|YP_005919341.1| 26 DPDYWYKRGAAHYGSG 41
                                      7899999999887666 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.3e-07
                            TPR_17  4 kaleldPnnadaynnLAelllknGdlmtArq 34
                                      +a+e dP  ++a ++L+e+l+k+G+++ A++
  gi|386001042|ref|YP_005919341.1| 52 RAIEADPIFFEARYLLGEALRKKGRYQAAVE 82
                                      8**************************9975 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00021
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y  al+l P+++ ++  +A++l ++ ++++A++
  gi|386001042|ref|YP_005919341.1|  84 YDAALDLKPDHPRSWRGRAVALNELDRHEEALE 116
                                       899***************************985 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0083
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                        +al ldP +a  +  ++++++ +G++ +A
  gi|386001042|ref|YP_005919341.1| 119 DRALGLDPRDARCWIVKGYAFHALGRFSEA 148
                                       588999*******************98776 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 4e-05
                            TPR_17   2 ylkaleldPnn...adaynnLAelllknGdlmtArq 34 
                                       y +ale++P       a+nn++ +l ++G++++A++
  gi|386001042|ref|YP_005919341.1| 152 YDRALEIEPLGpraGRAWNNKGAALDNLGRHEEALE 187
                                       899****9666566********************85 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 4.9e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +++ +dP +++ +nn+++ l  ++++++A++
  gi|386001042|ref|YP_005919341.1| 188 CYDESILIDPFDFYTWNNKGVSLIALKRPEEAVE 221
                                       8*****************************9975 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 4.6e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ ka+el P +  a+ n+A +l+++G+ ++A++
  gi|386001042|ref|YP_005919341.1| 222 CFGKAVELFPGYTTAWRNRALALKSLGREGEAEE 255
                                       678***************************9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.012         7      44      75 ..      26      57 ..      11      59 .. 0.78
   2 !   29.2   2.0   1.4e-09   8.3e-07       6      74 ..      64     124 ..      61     127 .. 0.92
   3 !   25.0   1.0   2.8e-08   1.7e-05       6      74 ..      98     158 ..      94     160 .. 0.86
   4 !   17.9   0.1   4.7e-06    0.0028       4      32 ..     167     195 ..     164     196 .. 0.90
   5 !   25.9   0.0   1.5e-08   9.2e-06       5      73 ..     202     262 ..     200     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                            TPR_12 44 tattlrnLgrlyralgryeeAlelleealaia 75
                                         + +  g +++ +g +eeA + l +a++++
  gi|386001042|ref|YP_005919341.1| 26 DPDYWYKRGAAHYGSGLFEEAADSLARAIEAD 57
                                      55566778999999999999999999999875 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.4e-09
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        + l+++lr+ gry+ A e +++al++      pdhp    + r+ + ++ +l+r+eeAle   +al +
  gi|386001042|ref|YP_005919341.1|  64 RYLLGEALRKKGRYQAAVESYDAALDLK-----PDHPR---SWRGRAVALNELDRHEEALESADRALGL 124
                                       568*************************.....***66...9************************966 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 2.8e-08
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ++ +a++l++l r++eAle  ++al +      p     a++ +  g +++algr+ eA e + +al+i
  gi|386001042|ref|YP_005919341.1|  98 WRGRAVALNELDRHEEALESADRALGLD-----P---RDARCWIVKGYAFHALGRFSEAAESYDRALEI 158
                                       6568888888999888888888886666.....5...57****************************97 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 4.7e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekalei 32 
                                       +a+nn +a+l  lgr++eAle++++++ i
  gi|386001042|ref|YP_005919341.1| 167 RAWNNKGAALDNLGRHEEALECYDESILI 195
                                       7999********************99865 PP

  == domain 5  score: 25.9 bits;  conditional E-value: 1.5e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       ++nn ++ l +l+r +eA e++ ka+e++   +G     + t+ rn + ++  lgr  eA+e+l +a +
  gi|386001042|ref|YP_005919341.1| 202 TWNNKGVSLIALKRPEEAVECFGKAVELF---PG-----YTTAWRNRALALKSLGREGEAEEALDRARD 262
                                       789**************************...44.....45899**********************987 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.8   9.9e-07   0.00059       1      42 [.      27      68 ..      27      68 .. 0.95
   2 !   24.6   1.1   4.6e-08   2.8e-05       2      42 ..      62     102 ..      61     103 .. 0.93
   3 !   20.6   0.9   8.5e-07   0.00051       1      42 [.      95     136 ..      95     138 .. 0.93
   4 !   14.6   0.3   7.5e-05     0.045       8      38 ..     136     169 ..     132     175 .. 0.76
   5 !   10.1   0.0     0.002       1.2       7      34 ..     172     199 ..     167     208 .. 0.82
   6 !   15.4   0.0   4.2e-05     0.025      11      42 ..     210     241 ..     206     243 .. 0.91
   7 !    8.3   2.0    0.0076       4.6       3      29 ..     236     262 ..     235     266 .] 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.9e-07
                            TPR_14  1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42
                                      p+ ++++++a++ +G ++eA++ l ra++++P + ea++ll+
  gi|386001042|ref|YP_005919341.1| 27 PDYWYKRGAAHYGSGLFEEAADSLARAIEADPIFFEARYLLG 68
                                      678**********************************99986 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 4.6e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ea+++l+eal+  G++++A++ +++al+l Pd+++ w+  a
  gi|386001042|ref|YP_005919341.1|  62 EARYLLGEALRKKGRYQAAVESYDAALDLKPDHPRSWRGRA 102
                                       89********************************9998665 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 8.5e-07
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       p+ ++ +a al +l++++eA++ ++ral l+P da+ w+  +
  gi|386001042|ref|YP_005919341.1|  95 PRSWRGRAVALNELDRHEEALESADRALGLDPRDARCWIVKG 136
                                       678999********************************9876 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 7.5e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaP...ddaeaw 38 
                                       + a+ alG++ eA++ ++ral+  P      +aw
  gi|386001042|ref|YP_005919341.1| 136 GYAFHALGRFSEAAESYDRALEIEPlgpRAGRAW 169
                                       67899*****************665211555555 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.002
                            TPR_14   7 laeallalGdpdeAiallrralalaPdd 34 
                                        ++al +lG+++eA++++++ +  +P d
  gi|386001042|ref|YP_005919341.1| 172 KGAALDNLGRHEEALECYDESILIDPFD 199
                                       578999**************99998855 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 4.2e-05
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawllla 42 
                                       l al +p+eA++++ +a++l+P+  +aw+  a
  gi|386001042|ref|YP_005919341.1| 210 LIALKRPEEAVECFGKAVELFPGYTTAWRNRA 241
                                       7899************************8766 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0076
                            TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                       a++ +a al  lG+  eA+++l+ra +
  gi|386001042|ref|YP_005919341.1| 236 AWRNRALALKSLGREGEAEEALDRARD 262
                                       8999********************965 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   2.1e-05     0.012      28      60 ..      26      58 ..      25      72 .. 0.89
   2 !   23.2   1.0   9.5e-08   5.6e-05       4      50 ..      70     116 ..      67     116 .. 0.91
   3 !   30.0   2.1   7.1e-10   4.2e-07       9      67 ..     109     167 ..     104     169 .. 0.93
   4 !   18.6   0.0   2.5e-06    0.0015       9      60 ..     180     231 ..     173     236 .. 0.92
   5 !   11.2   0.4   0.00053      0.32      22      56 ..     227     261 ..     225     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                             TPR_9 28 dpeerrdRGlllaqlGclsaAladLeaylalap 60
                                      dp+ ++ RG +++ +G +++A++ L ++++ +p
  gi|386001042|ref|YP_005919341.1| 26 DPDYWYKRGAAHYGSGLFEEAADSLARAIEADP 58
                                      7889***************************99 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 9.5e-08
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                       ++  + ++++a + ++  l l+Pd+p+ +r R+++l +l++ ++Al+
  gi|386001042|ref|YP_005919341.1|  70 ALRKKGRYQAAVESYDAALDLKPDHPRSWRGRAVALNELDRHEEALE 116
                                       5667889**********************************999985 PP

  == domain 3  score: 30.0 bits;  conditional E-value: 7.1e-10
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaea 67 
                                       +++e+al+ ++r l l+P+d++ +   G + + lG++s+A++  +++l+++p  p a +
  gi|386001042|ref|YP_005919341.1| 109 DRHEEALESADRALGLDPRDARCWIVKGYAFHALGRFSEAAESYDRALEIEPLGPRAGR 167
                                       899*************************************************8888765 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 2.5e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        ++e+al++++  +l++P d + +   G+ l  l ++++A++++  +++l p
  gi|386001042|ref|YP_005919341.1| 180 GRHEEALECYDESILIDPFDFYTWNNKGVSLIALKRPEEAVECFGKAVELFP 231
                                       689*****************************************99998765 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.00053
                             TPR_9  22 lllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                       + l+P     +r R+l+l  lG+  +A ++L+++ 
  gi|386001042|ref|YP_005919341.1| 227 VELFPGYTTAWRNRALALKSLGREGEAEEALDRAR 261
                                       568999999**********************9975 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.8   3.6e-11   2.2e-08       4      62 ..      40      98 ..      37     104 .. 0.93
   2 !   30.8   0.4   5.2e-10   3.1e-07       2      62 ..      72     132 ..      71     138 .. 0.94
   3 !   18.6   0.1   3.3e-06     0.002       6      60 ..     110     164 ..     105     171 .. 0.92
   4 !   11.9   0.1   0.00041      0.24       4      56 ..     142     197 ..     139     204 .. 0.86
   5 !   22.5   0.2     2e-07   0.00012       1      54 [.     210     263 ..     210     266 .] 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.6e-11
                            TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      +g ++eA++ l++a+++dp   ear+lL eal + g++++A +  da+++ +pd++r +
  gi|386001042|ref|YP_005919341.1| 40 SGLFEEAADSLARAIEADPIFFEARYLLGEALRKKGRYQAAVESYDAALDLKPDHPRSW 98
                                      67899*************************************************99866 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 5.2e-10
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        + g+y++A++ + +al+ +p++++ + + A al +l + +eA +  d+++  dp dar +
  gi|386001042|ref|YP_005919341.1|  72 RKKGRYQAAVESYDAALDLKPDHPRSWRGRAVALNELDRHEEALESADRALGLDPRDARCW 132
                                       678*****************************************************99865 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 3.3e-06
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       +++eAl+   +al  dp +a+ ++    a  alg++ eA +  d+++e +p  +r
  gi|386001042|ref|YP_005919341.1| 110 RHEEALESADRALGLDPRDARCWIVKGYAFHALGRFSEAAESYDRALEIEPLGPR 164
                                       799*********************************************9997665 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00041
                            TPR_19   4 egdyaeAlalleqalqedpk...naearllLAeallalgqldeAealLdalpeedp 56 
                                        g++ eA++ + +al+ +p     ++a+ +   al +lg+ +eA ++ d+  + dp
  gi|386001042|ref|YP_005919341.1| 142 LGRFSEAAESYDRALEIEPLgprAGRAWNNKGAALDNLGRHEEALECYDESILIDP 197
                                       699**************66644499999999****************999888777 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 2e-07
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                       l+a ++++eA++ + +a +  p++  a+ + A al +lg+  eAe++Ld++ + 
  gi|386001042|ref|YP_005919341.1| 210 LIALKRPEEAVECFGKAVELFPGYTTAWRNRALALKSLGREGEAEEALDRARDL 263
                                       577789********************************************9875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.55   3.3e+02       8      31 ..      36      57 ..      31      58 .. 0.79
   2 !   18.0   0.1   3.3e-06     0.002       3      35 ..      65      95 ..      63      96 .. 0.88
   3 ?    2.6   0.2      0.29   1.7e+02       6      34 ..     102     128 ..      99     130 .. 0.75
   4 !   13.4   0.0    0.0001     0.061       6      32 ..     136     160 ..     132     164 .. 0.81
   5 !   15.4   0.0   2.4e-05     0.014       1      26 [.     168     193 ..     168     199 .. 0.86
   6 ?    5.6   0.0      0.03        18       1      28 [.     202     227 ..     202     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.55
                             TPR_7  8 lysrlGdyeeAielyeqsLaltkd 31
                                      ++   G +eeA++ + +  a++ d
  gi|386001042|ref|YP_005919341.1| 36 AHYGSGLFEEAADSLAR--AIEAD 57
                                      5666799********99..77766 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.3e-06
                             TPR_7  3 lnLarlysrlGdyeeAielyeqsLaltkdpeda 35
                                      + L+++ ++ G+y+ A+e y +  al+  p+++
  gi|386001042|ref|YP_005919341.1| 65 YLLGEALRKKGRYQAAVESYDA--ALDLKPDHP 95
                                      579*******************..888887776 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.29
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++  +l ++eeA+e   +  al  dp d
  gi|386001042|ref|YP_005919341.1| 102 AVALNELDRHEEALESADR--ALGLDPRD 128
                                       5666678999*****9999..55555555 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 0.0001
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       + ++++lG+++eA+e y +  al+ +p
  gi|386001042|ref|YP_005919341.1| 136 GYAFHALGRFSEAAESYDR--ALEIEP 160
                                       568999*************..555444 PP

  == domain 5  score: 15.4 bits;  conditional E-value: 2.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsL 26 
                                       a++n + +  +lG++eeA+e+y +s+
  gi|386001042|ref|YP_005919341.1| 168 AWNNKGAALDNLGRHEEALECYDESI 193
                                       799*******************9944 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.03
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       +++n ++   +l + eeA+e++ +  a+
  gi|386001042|ref|YP_005919341.1| 202 TWNNKGVSLIALKRPEEAVECFGK--AV 227
                                       6789999999999*********99..43 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.045        27       3      31 ..      30      58 ..      28      58 .. 0.88
   2 !   16.4   0.4   1.8e-05     0.011       1      32 [.      62      93 ..      62      94 .. 0.90
   3 ?    1.4   0.0       1.1   6.3e+02       7      28 ..     102     123 ..     100     128 .. 0.80
   4 ?    5.6   0.0     0.046        28       7      31 ..     136     160 ..     135     161 .. 0.88
   5 ?    3.1   0.0       0.3   1.8e+02       8      25 ..     174     191 ..     167     197 .. 0.84
   6 !   10.8   0.0    0.0011      0.63       7      32 ..     207     232 ..     205     233 .. 0.92
   7 ?    2.6   0.2      0.45   2.7e+02       5      27 ..     239     261 ..     236     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.045
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  3 lyklalsyrklgdtdkAlealerlikeYP 31
                                       yk++ +++  g  ++A + l r i+  P
  gi|386001042|ref|YP_005919341.1| 30 WYKRGAAHYGSGLFEEAADSLARAIEADP 58
                                      69*******977************99766 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  1 dAlyklalsyrklgdtdkAlealerlikeYPd 32
                                      +A y+l++++rk g++++A+e ++  ++  Pd
  gi|386001042|ref|YP_005919341.1| 62 EARYLLGEALRKKGRYQAAVESYDAALDLKPD 93
                                      79**********99*********999886665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       a ++ +l+++++Ale  +r + 
  gi|386001042|ref|YP_005919341.1| 102 AVALNELDRHEEALESADRALG 123
                                       77888899*******9998775 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       ++++ +lg+ ++A e ++r ++  P
  gi|386001042|ref|YP_005919341.1| 136 GYAFHALGRFSEAAESYDRALEIEP 160
                                       78899999***********998766 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealer 25 
                                        ++ +lg++++Ale +++
  gi|386001042|ref|YP_005919341.1| 174 AALDNLGRHEEALECYDE 191
                                       5677889*******9975 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + s+++l+++++A+e + + ++ +P+
  gi|386001042|ref|YP_005919341.1| 207 GVSLIALKRPEEAVECFGKAVELFPG 232
                                       88999*99*****************6 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       ++al++++lg+  +A eal+r +
  gi|386001042|ref|YP_005919341.1| 239 NRALALKSLGREGEAEEALDRAR 261
                                       57899999888888888888875 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.57   3.4e+02       9      30 ..      34      55 ..      33      56 .. 0.90
   2 !   11.4   0.1   0.00037      0.22       8      31 ..      67      90 ..      63      95 .. 0.92
   3 ?    6.0   0.2     0.019        11       9      29 ..     102     122 ..     101     128 .. 0.75
   4 !    7.3   0.2    0.0072       4.3      10      31 ..     137     158 ..     136     159 .. 0.89
   5 !   14.4   0.2   4.2e-05     0.025       6      29 ..     170     193 ..     167     195 .. 0.94
   6 !    7.1   0.0    0.0083         5       6      30 ..     204     228 ..     202     229 .. 0.94
   7 ?    4.6   1.3     0.053        31       7      28 ..     239     260 ..     238     265 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.57
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      ++a++  g ++eA + l +a++
  gi|386001042|ref|YP_005919341.1| 34 GAAHYGSGLFEEAADSLARAIE 55
                                      789999********99999997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00037
                            TPR_10  8 LanalrqrgrydeAealleealai 31
                                      L+ alr+ gry++A++ ++ al++
  gi|386001042|ref|YP_005919341.1| 67 LGEALRKKGRYQAAVESYDAALDL 90
                                      9*******************9975 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.019
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       a+al ++ r++eA++ +++al
  gi|386001042|ref|YP_005919341.1| 102 AVALNELDRHEEALESADRAL 122
                                       677888888888888777776 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0072
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        a +++gr+ eA + +++al+i
  gi|386001042|ref|YP_005919341.1| 137 YAFHALGRFSEAAESYDRALEI 158
                                       56789***************97 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 4.2e-05
                            TPR_10   6 nNLanalrqrgrydeAealleeal 29 
                                       nN ++al ++gr++eA++ ++e++
  gi|386001042|ref|YP_005919341.1| 170 NNKGAALDNLGRHEEALECYDESI 193
                                       999*******************98 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0083
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN ++ l +++r +eA++ + +a++
  gi|386001042|ref|YP_005919341.1| 204 NNKGVSLIALKRPEEAVECFGKAVE 228
                                       899999*****************98 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.053
                            TPR_10   7 NLanalrqrgrydeAealleea 28 
                                       N a al ++gr  eAe+ l++a
  gi|386001042|ref|YP_005919341.1| 239 NRALALKSLGREGEAEEALDRA 260
                                       7799**************9998 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.9     0.012         7      60     121 ..      66     116 ..      30     117 .. 0.84
   2 !   13.2   0.4   0.00012     0.072      61     128 ..     101     157 ..      96     159 .. 0.85
   3 !   16.9   0.1   8.4e-06     0.005      54     124 ..     128     190 ..     123     195 .. 0.90
   4 ?    1.7   0.0       0.4   2.4e+02     105     129 ..     205     229 ..     201     233 .. 0.90
   5 ?    4.8   0.0     0.046        27     102     127 ..     236     261 ..     231     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  60 glsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealk 121
                                        l eal k gry++a+es d al       +l+ d  + W      raval+el r++eal+
  gi|386001042|ref|YP_005919341.1|  66 LLGEALRKKGRYQAAVESYDAAL-------DLKPDHPRSWR----GRAVALNELDRHEEALE 116
                                       488999999*********99999.......68888888884....68889999999988886 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  61 lsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                        + al +l r++ealesad+al        l+  + + Wi     ++ a++ lGr +ea +++  a e
  gi|386001042|ref|YP_005919341.1| 101 RAVALNELDRHEEALESADRALG-------LDPRDARCWIV----KGYAFHALGRFSEAAESYDRALE 157
                                       57799999999999999999995.......77778899985....89999999999999999999887 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856  54 dalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                       da c+ +   a+  lgr+ ea es d+al+       l    G+ W     ++++al++lGr++eal+ + 
  gi|386001042|ref|YP_005919341.1| 128 DARCWIVKGYAFHALGRFSEAAESYDRALEI----EPLGPRAGRAW----NNKGAALDNLGRHEEALECYD 190
                                       999**************************86....46888899999....69***************9986 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.4
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagem 129
                                       +++v+l  l r +ea++ f +a+e+
  gi|386001042|ref|YP_005919341.1| 205 NKGVSLIALKRPEEAVECFGKAVEL 229
                                       7999999***************997 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a  +ra al++lGr+ ea +a+  a 
  gi|386001042|ref|YP_005919341.1| 236 AWRNRALALKSLGREGEAEEALDRAR 261
                                       5569*************999888776 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.5   0.00026      0.16      27      79 ..      29      84 ..      26      87 .. 0.83
   2 !   20.7   0.1   5.9e-07   0.00035      14      78 ..      52     117 ..      40     121 .. 0.88
   3 !   12.1   0.0    0.0003      0.18      32      80 ..     104     153 ..     101     155 .. 0.89
   4 ?    5.6   0.0     0.031        18      35      81 ..     178     225 ..     172     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                      HHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3 27 yll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79
                                      y++  + ++y +g +++A + l +a + ++   ++ryl++++l k ++y+ A+  +
  gi|386001042|ref|YP_005919341.1| 29 YWYkrGAAHYGSGLFEEAADSLARAiEADPIFFEARYLLGEALRKKGRYQAAVESY 84
                                      67667899999**************66666666****************9998766 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.9e-07
                                       HHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  14 rllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       r+ +a++   e++yll+++l + g+y+ A e ++ a +l++ +++++   A +l +L+++eeA+  
  gi|386001042|ref|YP_005919341.1|  52 RAIEADPIFFEARYLLGEALRKKGRYQAAVESYDAAlDLKPDHPRSWRGRAVALNELDRHEEALES 117
                                       445677777799***************************************************975 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.0003
                                       HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +l ++ ++++A+e +++a +l++++ +c+++++ +  +L+++ eA   ++
  gi|386001042|ref|YP_005919341.1| 104 ALNELDRHEEALESADRAlGLDPRDARCWIVKGYAFHALGRFSEAAESYD 153
                                       555677899************************************98766 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.031
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++g++++A+e ++++  +++ +   +  ++ +l++Lk+ eeA+ +++k
  gi|386001042|ref|YP_005919341.1| 178 NLGRHEEALECYDESiLIDPFDFYTWNNKGVSLIALKRPEEAVECFGK 225
                                       566666777777776555555556666678999************998 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.4   0.00032      0.19      69     122 ..      34      87 ..      30      94 .. 0.89
   2 !   12.6   1.1   0.00023      0.14      68     123 ..     101     156 ..      96     168 .. 0.91
   3 !   10.4   0.4    0.0011      0.68      74     121 ..     141     191 ..     138     201 .. 0.85
   4 !   10.2   0.2    0.0013      0.75      73     125 ..     211     263 ..     202     266 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        +a+   G  eea++ l+++++++P   +++ +l +Al++ Gr ++A e Y+ +
  gi|386001042|ref|YP_005919341.1|  34 GAAHYGSGLFEEAADSLARAIEADPIFFEARYLLGEALRKKGRYQAAVESYDAA 87 
                                       56677778899****************************************986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00023
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       +a a+ +l r+eeal+ +++++ ++P + r +     A +++Gr +eA e Y+r+ 
  gi|386001042|ref|YP_005919341.1| 101 RAVALNELDRHEEALESADRALGLDPRDARCWIVKGYAFHALGRFSEAAESYDRAL 156
                                       56677899********************************************9985 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0011
                                       HTT-HHHHHHHHHHHHHHSTT...-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPl...rErlhrqlmrAlarsGrqaeALevYer 121
                                       +lGr +ea++ ++++++ +Pl     r++    +Al  +Gr +eALe Y++
  gi|386001042|ref|YP_005919341.1| 141 ALGRFSEAAESYDRALEIEPLgprAGRAWNNKGAALDNLGRHEEALECYDE 191
                                       79****************9982224567888899***************87 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0013
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       ++l r eea++   ++v++ P   +++r   +Al  +Gr++eA e+ +r+r+l
  gi|386001042|ref|YP_005919341.1| 211 IALKRPEEAVECFGKAVELFPGYTTAWRNRALALKSLGREGEAEEALDRARDL 263
                                       6778889999999999*******************************999975 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.21   1.3e+02       7      26 .]      33      52 ..      28      52 .. 0.87
   2 ?    6.6   0.2     0.024        14       3      22 ..      63      82 ..      62      86 .. 0.90
   3 !   10.9   0.9     0.001      0.62       1      26 []      95     120 ..      95     120 .. 0.90
   4 ?    6.9   0.0      0.02        12       1      25 [.     129     153 ..     129     154 .. 0.85
   5 !    9.6   0.1    0.0027       1.6       2      25 ..     167     190 ..     166     191 .. 0.84
   6 ?   -1.5   0.0       9.8   5.9e+03      10      22 ..     209     221 ..     205     224 .. 0.73
   7 ?    5.0   3.1     0.082        49       3      26 .]     236     259 ..     235     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.21
                             TPR_4  7 LArallalGdldeAraller 26
                                      ++ a++  G ++eA++ l+r
  gi|386001042|ref|YP_005919341.1| 33 RGAAHYGSGLFEEAADSLAR 52
                                      799***********998875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.024
                             TPR_4  3 allaLArallalGdldeAra 22
                                      a+++L++al   G++ +A +
  gi|386001042|ref|YP_005919341.1| 63 ARYLLGEALRKKGRYQAAVE 82
                                      89***************986 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.001
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       +r   ++A al +l +++eA++ ++r
  gi|386001042|ref|YP_005919341.1|  95 PRSWRGRAVALNELDRHEEALESADR 120
                                       677889***************98876 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.02
                             TPR_4   1 arallaLArallalGdldeAralle 25 
                                       ar+ ++ + a +alG++ eA++  +
  gi|386001042|ref|YP_005919341.1| 129 ARCWIVKGYAFHALGRFSEAAESYD 153
                                       578889999***********98665 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0027
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       ra  + + al  lG+++eA++  +
  gi|386001042|ref|YP_005919341.1| 167 RAWNNKGAALDNLGRHEEALECYD 190
                                       56678899************9876 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 9.8
                             TPR_4  10 allalGdldeAra 22 
                                        l al +++eA +
  gi|386001042|ref|YP_005919341.1| 209 SLIALKRPEEAVE 221
                                       56666699**987 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.082
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       a  ++A al  lG+  eA+++l+r
  gi|386001042|ref|YP_005919341.1| 236 AWRNRALALKSLGREGEAEEALDR 259
                                       567999999999999999999987 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.1   5.1e-06     0.003     131     242 ..      41     157 ..      27     164 .. 0.77
   2 !    7.0   0.2     0.005         3     148     238 ..      97     190 ..      95     203 .. 0.67
   3 ?    1.6   0.0      0.22   1.3e+02     160     203 ..     214     257 ..     199     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                            TPR_15 131 ellksle.e.eeaaeqsaafllar...aelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrel 202
                                        l++++  +   a e ++ f+ ar   +e+ r++g+ +aA++ y  Al+l+pd      +   +l++l+r +e+ e 
  gi|386001042|ref|YP_005919341.1|  41 GLFEEAAdSlARAIEADPIFFEARyllGEALRKKGRYQAAVESYDAALDLKPDHPRSWRGRAVALNELDRHEEALES 117
                                       566665423234477899999665333899**************************9999999*********93333 PP

                            TPR_15 203 lkawkaraesdasLwgplaaAlllLgrpkkALeylrkqak 242
                                         +  +   +da+ w + + A  +Lgr ++A e + + ++
  gi|386001042|ref|YP_005919341.1| 118 ADRALGLDPRDARCWIVKGYAFHALGRFSEAAESYDRALE 157
                                       333334449******************9999888877665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.005
                            TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsse..lraallWlliDlgrrae.Lrellkawkara..esdasLwgp 219
                                        +  ra +  + +++++Al+ + +Al l+p ++   + +++ +  +  gr  e + ++ +a++ +    +  + w+ 
  gi|386001042|ref|YP_005919341.1|  97 SWRGRAVALNELDRHEEALESADRALGLDPRDARcwIVKGYAFHAL--GRFSEaAESYDRALEIEPlgPRAGRAWNN 171
                                       6777888888888899999999999999988876334556666555..44444123333344433377777777777 PP

                            TPR_15 220 laaAlllLgrpkkALeylr 238
                                        +aAl  Lgr ++ALe + 
  gi|386001042|ref|YP_005919341.1| 172 KGAALDNLGRHEEALECYD 190
                                       8888888888888887765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.22
                            TPR_15 160 gqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrell 203
                                        ++++A++++ +A++l+p+ +++  +   +l  lgr+ e+ e+l
  gi|386001042|ref|YP_005919341.1| 214 KRPEEAVECFGKAVELFPGYTTAWRNRALALKSLGREGEAEEAL 257
                                       57899999999999999998887666666666666666666666 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.061        36     207     254 ..      42      89 ..      29      94 .. 0.82
   2 !    7.8   0.0    0.0023       1.4     202     254 ..     105     157 ..     101     174 .. 0.91
   3 ?   -1.0   0.0         1     6e+02      43      63 ..     171     191 ..     164     209 .. 0.69
   4 !    6.2   0.0    0.0068         4     206     256 ..     214     264 ..     208     266 .] 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.061
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                         e+A + + +aie +p + e  +  ++ l+++G  ++A+e  + a  
  gi|386001042|ref|YP_005919341.1|  42 LFEEAADSLARAIEADPIFFEARYLLGEALRKKGRYQAAVESYDAALD 89 
                                       457889999999*********999999999999*99999999998754 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0023
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeeark 254
                                        ++l + e+Ale  d+a+  +p    ++++K+  +   G +++Aae  ++a +
  gi|386001042|ref|YP_005919341.1| 105 LNELDRHEEALESADRALGLDPRDARCWIVKGYAFHALGRFSEAAESYDRALE 157
                                       67888999**************************************9999865 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1
                                       HHHHHHHHTT-HHHHHHHHHH CS
                             NARP1  43 tkaelllkLgrkeeAeatyea 63 
                                       +k+  l +Lgr+eeA + y +
  gi|386001042|ref|YP_005919341.1| 171 NKGAALDNLGRHEEALECYDE 191
                                       566667777777777777765 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0068
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       ++ e+A+e+  ka+e  p  +  + ++a  lk  G   +A e++++ar l 
  gi|386001042|ref|YP_005919341.1| 214 KRPEEAVECFGKAVELFPGYTTAWRNRALALKSLGREGEAEEALDRARDLE 264
                                       56789*******************************************996 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.15        87       2      33 ..      28      59 ..      27      64 .. 0.88
   2 !    7.3   0.2    0.0081       4.8       2      33 ..      62      93 ..      61      95 .. 0.93
   3 ?    3.0   0.0      0.18   1.1e+02       8      33 ..     102     127 ..     101     130 .. 0.88
   4 ?    5.9   0.0     0.023        14      14      32 ..     142     160 ..     137     162 .. 0.94
   5 ?    0.1   0.0       1.4   8.6e+02      14      32 ..     179     197 ..     175     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  2 eclYylAlGhyklgeYseArryvdalLeiEPe 33
                                      ++ Y    +hy  g ++eA   + + +e +P 
  gi|386001042|ref|YP_005919341.1| 28 DYWYKRGAAHYGSGLFEEAADSLARAIEADPI 59
                                      78899999*************99999999995 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0081
                                      HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  2 eclYylAlGhyklgeYseArryvdalLeiEPe 33
                                      e  Y+l  +  k g+Y+ A +  da L + P+
  gi|386001042|ref|YP_005919341.1| 62 EARYLLGEALRKKGRYQAAVESYDAALDLKPD 93
                                      568*************************9997 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.18
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPe 33 
                                       A++   l +++eA++ +d+ L ++P+
  gi|386001042|ref|YP_005919341.1| 102 AVALNELDRHEEALESADRALGLDPR 127
                                       677778999***************97 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.023
                                       HT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                       lg++seA +  d+ LeiEP
  gi|386001042|ref|YP_005919341.1| 142 LGRFSEAAESYDRALEIEP 160
                                       899***************9 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.4
                                       HT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                       lg+++eA+++ d  + i+P
  gi|386001042|ref|YP_005919341.1| 179 LGRHEEALECYDESILIDP 197
                                       899*******998888887 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0055       3.3      16      33 ..      73      90 ..      69      90 .. 0.92
   2 ?   -2.3   0.1       8.3     5e+03      11      26 ..     102     117 ..     101     124 .. 0.65
   3 ?    2.5   0.0      0.26   1.6e+02      18      32 ..     143     157 ..     140     158 .. 0.88
   4 !   11.5   0.0    0.0004      0.24       9      31 ..     171     193 ..     167     195 .. 0.91
   5 ?    5.2   0.0     0.037        22      19      63 ..     215     263 ..     205     265 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0055
                               MIT 16 nagnyeeAlelYkealel 33
                                      ++g y++A+e Y  al+l
  gi|386001042|ref|YP_005919341.1| 73 KKGRYQAAVESYDAALDL 90
                                      689*************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.3
                               MIT  11 AveeDnagnyeeAlel 26 
                                       Av + +    eeAle 
  gi|386001042|ref|YP_005919341.1| 102 AVALNELDRHEEALES 117
                                       6666666777777775 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.26
                               MIT  18 gnyeeAlelYkeale 32 
                                       g ++eA e Y  ale
  gi|386001042|ref|YP_005919341.1| 143 GRFSEAAESYDRALE 157
                                       7899*********98 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.0004
                               MIT   9 kkAveeDnagnyeeAlelYkeal 31 
                                       +k + +Dn g  eeAle+Y e++
  gi|386001042|ref|YP_005919341.1| 171 NKGAALDNLGRHEEALECYDESI 193
                                       577899**************997 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.037
                               MIT  19 nyeeAlelYkealelLlqalk.ekne...errellrekieeYleRaeeL 63 
                                         eeA+e++ +a+el+    +   n     +    + ++ee l+Ra  L
  gi|386001042|ref|YP_005919341.1| 215 RPEEAVECFGKAVELFPGYTTaWRNRalaLKSLGREGEAEEALDRARDL 263
                                       569************9877774333224455555666777777777666 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4      0.84     5e+02      18      28 ..      78      88 ..      40     125 .. 0.61
   2 !   15.8   0.0   2.1e-05     0.012      10     113 ..     138     238 ..     131     244 .. 0.76
   3 ?    2.0   0.0       0.4   2.4e+02      80      93 ..     240     253 ..     209     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.84
                             TPR_5 18 dkavplYrraL 28
                                      ++av+ Y  aL
  gi|386001042|ref|YP_005919341.1| 78 QAAVESYDAAL 88
                                      33333333333 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.1e-05
                             TPR_5  10 arDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraelea.psdelddalaaflaLvLs 85 
                                       a+   G+  +a++ Y raL+    g r++ra     ++L nlG+ eeal+  ++ +   p d ++        + L+
  gi|386001042|ref|YP_005919341.1| 138 AFHALGRFSEAAESYDRALEIEPLGPRAGRAWNNKGAALDNLGRHEEALECYDESILIdPFDFYTW---NNKGVSLI 211
                                       67788999*****************************************99887654315555554...45556778 PP

                             TPR_5  86 dlgrereavsivllalaehlprYqRsvt 113
                                       +l+r++eav    +a +e +p Y  + +
  gi|386001042|ref|YP_005919341.1| 212 ALKRPEEAVECFGKA-VELFPGYTTAWR 238
                                       888888888765444.455666665555 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.4
                             TPR_5  80 laLvLsdlgrerea 93 
                                       +aL+L +lgre ea
  gi|386001042|ref|YP_005919341.1| 240 RALALKSLGREGEA 253
                                       68888888888887 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0063       3.8      14      31 ..      74      91 ..      64      94 .. 0.84
   2 !    7.9   0.0    0.0035       2.1      15      30 ..     143     158 ..     142     159 .. 0.94
   3 ?   -2.1   0.0       4.6   2.8e+03      18      30 ..     217     229 ..     217     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0063
                          SHNi-TPR 14 nenFpqAveDlrkaLeLr 31
                                       +++  Ave +++aL+L+
  gi|386001042|ref|YP_005919341.1| 74 KGRYQAAVESYDAALDLK 91
                                      689**************8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       ++F++A+e +++aLe+
  gi|386001042|ref|YP_005919341.1| 143 GRFSEAAESYDRALEI 158
                                       59************98 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.6
                          SHNi-TPR  18 pqAveDlrkaLeL 30 
                                       ++Ave + ka+eL
  gi|386001042|ref|YP_005919341.1| 217 EEAVECFGKAVEL 229
                                       5899999999998 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.076        45       1      22 [.      27      48 ..      27      54 .. 0.93
   2 ?    5.2   0.1     0.036        21      14      25 ..      74      85 ..      71      91 .. 0.85
   3 !    8.0   0.0    0.0047       2.8       8      25 ..     136     153 ..     136     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.076
                                      HHHHHHHHHHHHHTT-HHHHHH CS
                             TPR_3  1 ldylysyAaefynkkkyqeAre 22
                                      +dy+y+ +a+ y ++ ++eA++
  gi|386001042|ref|YP_005919341.1| 27 PDYWYKRGAAHYGSGLFEEAAD 48
                                      69****************9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.036
                                      TT-HHHHHHH.. CS
                             TPR_3 14 kkkyqeArelfs 25
                                      k++yq A+e ++
  gi|386001042|ref|YP_005919341.1| 74 KGRYQAAVESYD 85
                                      9********988 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0047
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       +++f+  ++++eA+e ++
  gi|386001042|ref|YP_005919341.1| 136 GYAFHALGRFSEAAESYD 153
                                       79*************976 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0037       2.2      61     113 ..      41      94 ..      29     100 .. 0.80
   2 ?    5.6   0.0     0.014       8.5      15      66 ..     109     155 ..     100     160 .. 0.57
   3 ?    0.8   0.0      0.42   2.5e+02      17      59 ..     216     260 ..     207     265 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                          TPR_MalT  61 qalqeae.klarqadslhvallallqqaeilvaqGrLheAletyeqalqlateq 113
                                         ++ea  +lar++++ ++   a + ++e l+++Gr ++A+e y  al l +++
  gi|386001042|ref|YP_005919341.1|  41 GLFEEAAdSLARAIEADPIFFEARYLLGEALRKKGRYQAAVESYDAALDLKPDH 94 
                                       556666625788888888888888999*********************999887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                          TPR_MalT  15 gdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqea 66 
                                        + e+ale A +AL l p d+   r  +  v G+a++  G++ +A +++  a
  gi|386001042|ref|YP_005919341.1| 109 DRHEEALESADRALGLDPRDA---RCWI--VKGYAFHALGRFSEAAESYDRA 155
                                       555666666666666666666...3333..4566666666666666655443 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.42
                          TPR_MalT  17 aeralelArqALallpeddllar..iaatavlGeasllqGdleaA 59 
                                       +e+a+e   +A++l+p     +r  ++a+ +lG+    ++ l++A
  gi|386001042|ref|YP_005919341.1| 216 PEEAVECFGKAVELFPGYTTAWRnrALALKSLGREGEAEEALDRA 260
                                       555555556666666655555543355555555333333333333 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.042        25     122     180 ..      73     132 ..      40     137 .. 0.85
   2 ?   -0.5   0.0       1.6   9.7e+02     151     180 ..     174     203 ..     146     210 .. 0.79
   3 !    8.5   0.0    0.0029       1.7     134     171 ..     224     262 ..     196     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                           Wzy_C_2 122 spenlaaklalarklihlsP.epavierlilslallGdedeAeqilararalfpeedakw 180
                                       ++  ++a ++ + +++ l+P  p+  +  +++l  l++++eA+   +ra  l p ++  w
  gi|386001042|ref|YP_005919341.1|  73 KKGRYQAAVESYDAALDLKPdHPRSWRGRAVALNELDRHEEALESADRALGLDPRDARCW 132
                                       667789999999999999994589999********************9988877777666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                           Wzy_C_2 151 lslallGdedeAeqilararalfpeedakw 180
                                        +l  lG+++eA+  +++ + + p + ++w
  gi|386001042|ref|YP_005919341.1| 174 AALDNLGRHEEALECYDESILIDPFDFYTW 203
                                       578899*******99998877666666666 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0029
                           Wzy_C_2 134 rklihlsPepav.ierlilslallGdedeAeqilarara 171
                                        k+++l+P+ ++  ++ +l+l  lG+e eAe  l+rar 
  gi|386001042|ref|YP_005919341.1| 224 GKAVELFPGYTTaWRNRALALKSLGREGEAEEALDRARD 262
                                       57889999765526899*******************996 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00019      0.12       5      66 ..      84     150 ..      80     160 .. 0.75
   2 ?    0.7   0.0      0.86   5.1e+02      26      39 ..     178     191 ..     151     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                      SRP_TPR_like   5 yekilrle..gkelkkfkvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalk 66 
                                       y+  l l+  ++   + ++val +l+++eeaL+ ++ +      +  +   k Y++  l ++ +a++
  gi|386001042|ref|YP_005919341.1|  84 YDAALDLKpdHPRSWRGRAVALNELDRHEEALESADRALgldPRDARCWIVKGYAFHALGRFSEAAE 150
                                       555555541134444559*****************9998333345789999***********99986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.86
                      SRP_TPR_like  26 klekyeeaLkllkk 39 
                                       +l+++eeaL+  ++
  gi|386001042|ref|YP_005919341.1| 178 NLGRHEEALECYDE 191
                                       55555555554443 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00053      0.32       9      43 ..      48      82 ..      44      89 .. 0.92
   2 ?    1.1   0.1      0.85   5.1e+02      13      44 ..      86     117 ..      81     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00053
                            TPR_20  9 aeleaalaanpddldarldlAlallaagryeeAle 43
                                      ++l +a++a+p   +ar+ l +al ++gry++A+e
  gi|386001042|ref|YP_005919341.1| 48 DSLARAIEADPIFFEARYLLGEALRKKGRYQAAVE 82
                                      67899****************************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.85
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleq 44 
                                       aal  +pd        A al++  r+eeAle 
  gi|386001042|ref|YP_005919341.1|  86 AALDLKPDHPRSWRGRAVALNELDRHEEALES 117
                                       66666677777777778888888888888875 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.15        87     120     144 ..      67      90 ..      43      97 .. 0.88
   2 ?    5.3   0.1     0.019        11      88     127 ..     208     254 ..     135     263 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                                       HHHHHHHTT--HHHHHHHHHHHHHH CS
                              SNAP 120 iaelyekelgdlekAieaYekAael 144
                                       ++e + k+ g++++A+e+Y+ A +l
  gi|386001042|ref|YP_005919341.1|  67 LGEALRKK-GRYQAAVESYDAALDL 90 
                                       68888888.9999999999999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                       T......-HHHHHHHHHHHHHHHHH.TT-HHHHHHHHHHHHHHHHHT CS
                              SNAP  88 v......speeAvealekAieiyte.kgrfrraAklkkeiaelyeke 127
                                       v      +peeAve++ kA+e++      +r+ A   k+++   e e
  gi|386001042|ref|YP_005919341.1| 208 VslialkRPEEAVECFGKAVELFPGyTTAWRNRALALKSLGREGEAE 254
                                       04444448999999999999998541344566666666666655555 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.5   3.3e+03       9      21 ..      70      82 ..      67      86 .. 0.82
   2 ?    5.1   0.0     0.054        32      13      25 ..     179     191 ..     178     193 .. 0.90
   3 ?    3.2   0.0      0.22   1.3e+02      14      25 ..     214     225 ..     209     229 .. 0.81
   4 ?    3.1   0.1      0.22   1.3e+02       8      21 ..     245     258 ..     243     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.5
                               PPR  9 gycknGkleeAle 21
                                      ++ k+G+++ A+e
  gi|386001042|ref|YP_005919341.1| 70 ALRKKGRYQAAVE 82
                                      67799***99987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.054
                               PPR  13 nGkleeAlelfke 25 
                                        G++eeAle+++e
  gi|386001042|ref|YP_005919341.1| 179 LGRHEEALECYDE 191
                                       69*********98 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.22
                               PPR  14 GkleeAlelfke 25 
                                        ++eeA+e+f +
  gi|386001042|ref|YP_005919341.1| 214 KRPEEAVECFGK 225
                                       799*******87 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.22
                               PPR   8 sgycknGkleeAle 21 
                                       ++++++G+ eeAl+
  gi|386001042|ref|YP_005919341.1| 245 KSLGREGEAEEALD 258
                                       789*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1405.75
//
Query:       gi|386001043|ref|YP_005919342.1|  [L=327]
Description: hypothetical protein Mhar_0332 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-12   47.8   0.0    3.5e-12   46.7   0.0    1.5  1  LTD       Lamin Tail Domain
      6e-05   23.5   0.0      9e-05   22.9   0.0    1.2  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   3.9e-16   3.5e-12       7     107 ..     165     252 ..     159     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 3.9e-16
                               LTD   7 dvvIsevmedgagnnan.efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngsk 81 
                                       +vvI+ev ++++g++++ e+velyN + ++  ++gw+l+ a g    +  gt +l  g+ ++v +++          
  gi|386001043|ref|YP_005919342.1| 165 RVVINEVEANPPGSDEGgEWVELYNDGFEEAAIGGWTLTAAGGSvVGISPGT-VLVGGGFLLVKADG---------- 230
                                       8************9999*************************7777777777.88888888888873.......... PP

                               LTD  82 asssavwnnggdava.Lydasgevvds 107
                                             w  ++d+++ L+d +g +vd+
  gi|386001043|ref|YP_005919342.1| 231 -----YWLRNDDELVtLRDGAGMEVDR 252
                                       .....35555555444***99999997 PP

>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     1e-08     9e-05      25      82 ..      75     143 ..      57     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1e-08
                                       HHHHHHHHHHHHCSSEEEEE-S...SBSTTSEEEEEEEET........TEEHHHHHHHTTSSEE---BT CS
                             SNase  25 eAkeflkklvlqkkvvvleldk...kkDkygrllayvyln........kknineeLvkeGlArvyevye 82 
                                        A+ f+++l+++++v ++++d+    +D +grlla vyl+         + +n  Lv++GlA v   + 
  gi|386001043|ref|YP_005919342.1|  75 VARTFAESLLKNRTVSLDIDDRtegGRDPQGRLLAVVYLSdpagglnlSHPLNRLLVEAGLAEVCDLEA 143
                                       6999*************9999999999*******************99999***********9887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1893.85
//
Query:       gi|386001044|ref|YP_005919343.1|  [L=351]
Description: Tetratricopeptide TPR_2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-58  191.9   8.6      1e-11   44.1   0.1    7.2  7  TPR_1         Tetratricopeptide repeat
    9.8e-54  178.8  14.6    1.3e-12   47.2   0.0    6.2  6  TPR_11        TPR repeat
      2e-49  166.0  40.1    1.3e-12   48.1   0.7    4.9  6  TPR_16        Tetratricopeptide repeat
    7.1e-47  153.8  15.1      1e-08   34.6   0.1    7.0  7  TPR_2         Tetratricopeptide repeat
    1.7e-38  127.6   4.2    2.5e-07   30.4   0.0    6.7  6  TPR_8         Tetratricopeptide repeat
    3.1e-38  127.4  12.9    6.3e-09   35.6   0.0    7.6  7  TPR_17        Tetratricopeptide repeat
    7.3e-29   99.7  20.9    8.6e-12   45.0   2.3    5.0  6  TPR_9         Tetratricopeptide repeat
      1e-28   97.5  22.5    1.1e-05   25.8   0.2    6.3  6  TPR_14        Tetratricopeptide repeat
      3e-26   91.5  18.9      5e-10   39.5   0.2    5.3  5  TPR_12        Tetratricopeptide repeat
    1.9e-24   85.9   9.1    6.9e-08   32.9   0.3    3.2  3  TPR_19        Tetratricopeptide repeat
    5.9e-22   76.0  12.1     0.0011   18.9   0.0    6.3  6  TPR_7         Tetratricopeptide repeat
      2e-13   49.6  12.8       0.27   12.0   0.2    6.8  6  TPR_4         Tetratricopeptide repeat
    3.2e-12   47.1  11.6    0.00084   19.8   1.1    4.2  4  BTAD          Bacterial transcriptional activator domain
    2.9e-11   42.8  25.9      0.056   13.3   0.1    6.7  6  TPR_10        Tetratricopeptide repeat
    5.6e-10   39.5   4.1       0.17   12.0   0.2    5.5  4  DUF3856       Domain of Unknown Function (DUF3856)
    6.1e-10   39.2   0.3     0.0016   18.6   0.2    2.9  3  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    2.3e-09   36.9   4.2      4e-05   23.0   1.3    2.9  2  TPR_15        Tetratricopeptide repeat
    5.2e-07   29.9  12.6       0.38   11.5   0.1    6.2  6  TPR_6         Tetratricopeptide repeat
      2e-06   27.7   1.5       0.88    9.6   0.0    4.5  4  TPR_3         Tetratricopeptide repeat
    2.4e-06   27.4   2.5         12    6.4   0.1    5.9  6  PPR           PPR repeat
    4.8e-05   23.3   8.9        1.9    8.6   0.0    5.3  5  MIT           MIT (microtubule interacting and transport) dom
    8.3e-05   21.7   0.0      0.015   14.2   0.0    3.0  3  NARP1         NMDA receptor-regulated protein 1
    0.00014   22.1   0.6         20    5.6   0.0    4.3  4  TPR_20        Tetratricopeptide repeat
    0.00016   21.7   4.4          3    8.0   0.0    5.0  6  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
     0.0002   20.8   0.0       0.99    8.8   0.0    2.9  3  Coatomer_E    Coatomer epsilon subunit
    0.00039   20.6   1.0         18    5.6   0.0    4.4  4  NRBF2_MIT     MIT domain of nuclear receptor-binding factor 2
    0.00059   19.3   0.4      0.074   12.5   0.0    3.0  3  SNAP          Soluble NSF attachment protein, SNAP
  ------ inclusion threshold ------
      0.013   15.3   7.3        1.4    8.6   0.1    4.1  4  TPR_21        Tetratricopeptide repeat-like domain
      0.013   14.7   0.6         19    4.4   0.0    3.3  4  FAT           FAT domain
      0.042   13.9   0.0        1.7    8.7   0.0    3.0  4  SRP_TPR_like  Putative TPR-like repeat
       0.15   11.8   0.3         11    5.7   0.0    3.5  4  RPN7          26S proteasome subunit RPN7


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   2.8e-07   0.00016       2      31 ..      41      70 ..      40      73 .. 0.91
   2 !   40.0   0.0   3.5e-13     2e-10       1      32 [.      74     105 ..      74     107 .. 0.94
   3 !   24.5   0.0   2.8e-08   1.6e-05       2      33 ..     109     140 ..     108     141 .. 0.90
   4 !   25.4   0.0   1.5e-08   8.5e-06       1      34 []     142     175 ..     142     175 .. 0.96
   5 !   44.1   0.1   1.7e-14     1e-11       1      34 []     176     209 ..     176     209 .. 0.97
   6 !   32.3   0.0   9.5e-11   5.5e-08       2      32 ..     211     241 ..     210     242 .. 0.97
   7 ?    2.8   0.3       0.2   1.1e+02       2       9 ..     245     252 ..     244     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.8e-07
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALeln 31
                                      k +  +Gna  + g+y+eA++ y++A  l+
  gi|386001044|ref|YP_005919343.1| 41 KDWSDMGNAQARRGEYQEAVASYDRATALD 70
                                      56999*********************9998 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 3.5e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       ++++yn+G+a+ +lg+y+eAle+y++  +++P
  gi|386001044|ref|YP_005919343.1|  74 PDIWYNRGLALSSLGRYEEALECYQRGAKIEP 105
                                       589**************************999 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 2.8e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       + + + G a+ +lg+y+eAle y++A e + +
  gi|386001044|ref|YP_005919343.1| 109 DLWLGTGSALSSLGRYEEALESYNRAAEFDSK 140
                                       678888*********************99976 PP

  == domain 4  score: 25.4 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++a++++G ++ +lg+++eAl+  + AL  +P++
  gi|386001044|ref|YP_005919343.1| 142 PDAWNGRGTVLARLGRLEEALASTDTALAMDPED 175
                                       68******************************86 PP

  == domain 5  score: 44.1 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++ +G+++++lg+++eAl++y++A+e++P++
  gi|386001044|ref|YP_005919343.1| 176 ADAWNSKGAILLQLGRPEEALACYDRAIEIDPED 209
                                       89******************************86 PP

  == domain 6  score: 32.3 bits;  conditional E-value: 9.5e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       + ++n+G a+++lg+y+eA + y+ A+ l+P
  gi|386001044|ref|YP_005919343.1| 211 DLWNNRGSALHQLGRYQEAQDSYSWAIALDP 241
                                       79****************************9 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.2
                                       HHHHHHHH CS
                             TPR_1   2 kalynlGn 9  
                                       +a+yn+G+
  gi|386001044|ref|YP_005919343.1| 245 YAWYNRGL 252
                                       69*****8 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.2   2.1e-13   1.2e-10       1      42 []      47      88 ..      47      88 .. 0.95
   2 !   27.0   0.0   4.4e-09   2.5e-06       6      42 .]      86     122 ..      83     122 .. 0.92
   3 !   41.5   0.0   1.3e-13   7.8e-11       1      42 []     115     156 ..     115     156 .. 0.96
   4 !   25.9   0.0   9.8e-09   5.7e-06       3      42 .]     151     190 ..     149     190 .. 0.94
   5 !   47.2   0.0   2.3e-15   1.3e-12       1      42 []     183     224 ..     183     224 .. 0.96
   6 !   26.5   0.5   6.4e-09   3.7e-06       1      37 [.     217     253 ..     217     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.1e-13
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      G+a   +G+y eA+++Y +A +ld  n++++yn+Gla+  +G
  gi|386001044|ref|YP_005919343.1| 47 GNAQARRGEYQEAVASYDRATALDAYNPDIWYNRGLALSSLG 88
                                      899999*******************************98777 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 4.4e-09
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++G+yeeA+e+Y++  k+ P +++++++ G a+  +G
  gi|386001044|ref|YP_005919343.1|  86 SLGRYEEALECYQRGAKIEPFDPDLWLGTGSALSSLG 122
                                       79**************************999987776 PP

  == domain 3  score: 41.5 bits;  conditional E-value: 1.3e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+ ++G+yeeA+e+Y++A ++d+++++a++++G +++++G
  gi|386001044|ref|YP_005919343.1| 115 GSALSSLGRYEEALESYNRAAEFDSKDPDAWNGRGTVLARLG 156
                                       778889*********************************998 PP

  == domain 4  score: 25.9 bits;  conditional E-value: 9.8e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++  +G++eeA+++  +Al+ dP++a+a++  G++++++G
  gi|386001044|ref|YP_005919343.1| 151 VLARLGRLEEALASTDTALAMDPEDADAWNSKGAILLQLG 190
                                       67789*********************************98 PP

  == domain 5  score: 47.2 bits;  conditional E-value: 2.3e-15
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G ++ ++G+ eeA+++Y +A+++dP+++++++n+G a++++G
  gi|386001044|ref|YP_005919343.1| 183 GAILLQLGRPEEALACYDRAIEIDPEDPDLWNNRGSALHQLG 224
                                       66899***********************************99 PP

  == domain 6  score: 26.5 bits;  conditional E-value: 6.4e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G a++++G+y eA  +Y+ A++ldP    a+yn+Gl+
  gi|386001044|ref|YP_005919343.1| 217 GSALHQLGRYQEAQDSYSWAIALDPLHEYAWYNRGLL 253
                                       899********************************86 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   3.2     1e-12   5.9e-10       2      68 .]      45     108 ..      44     108 .. 0.92
   2 !   44.2   0.6   3.7e-14   2.2e-11       1      68 []      78     142 ..      78     143 .. 0.96
   3 !   35.9   2.4   1.5e-11   8.9e-09      11      67 ..     122     175 ..     121     176 .. 0.92
   4 !   48.1   0.7   2.3e-15   1.3e-12       3      68 .]     148     210 ..     146     211 .. 0.97
   5 !   38.3   0.2   2.7e-12   1.5e-09       3      53 ..     182     229 ..     180     229 .. 0.94
   6 !   20.0   0.8   1.4e-06   0.00083       3      43 ..     216     253 ..     214     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1e-12
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++++a +r+g+y++A+a +++a+++d+  Pd    ++++g+a+  +gr++eA++ y++ ++  p++p
  gi|386001044|ref|YP_005919343.1|  45 DMGNAQARRGEYQEAVASYDRATALDAYNPD---IWYNRGLALSSLGRYEEALECYQRGAKIEPFDP 108
                                       5799**********************87777...********************9999888888776 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 3.7e-14
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++++a+  +g+y++A++ +++  k     P++++ +l+ g a+  +gr++eA++ y++a++ ++++p
  gi|386001044|ref|YP_005919343.1|  78 YNRGLALSSLGRYEEALECYQRGAKIE---PFDPDLWLGTGSALSSLGRYEEALESYNRAAEFDSKDP 142
                                       78999**********************...******************************99998887 PP

  == domain 3  score: 35.9 bits;  conditional E-value: 1.5e-11
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       g+y++A++ +++a + d   + +++A++++g +++r+grl+eA+a  + al+ +p +
  gi|386001044|ref|YP_005919343.1| 122 GRYEEALESYNRAAEFD---SKDPDAWNGRGTVLARLGRLEEALASTDTALAMDPED 175
                                       9****************...55556*****************************987 PP

  == domain 4  score: 48.1 bits;  conditional E-value: 2.3e-15
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++ ++r+g+ ++A+a  ++al++d   P++a+A++ +g ++l++gr +eA+a y++a++ +p +p
  gi|386001044|ref|YP_005919343.1| 148 RGTVLARLGRLEEALASTDTALAMD---PEDADAWNSKGAILLQLGRPEEALACYDRAIEIDPEDP 210
                                       68899********************...***********************************998 PP

  == domain 5  score: 38.3 bits;  conditional E-value: 2.7e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       ++ ++l++g++++A+a +++a++ d   P++++ ++++g a+ ++gr++eA
  gi|386001044|ref|YP_005919343.1| 182 KGAILLQLGRPEEALACYDRAIEID---PEDPDLWNNRGSALHQLGRYQEA 229
                                       57789********************...88888*****************9 PP

  == domain 6  score: 20.0 bits;  conditional E-value: 1.4e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43 
                                       ++ a+ ++g+y++A+  + +a+++d   P++  A++++g++
  gi|386001044|ref|YP_005919343.1| 216 RGSALHQLGRYQEAQDSYSWAIALD---PLHEYAWYNRGLL 253
                                       67778899*****************...***********86 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.5   4.2e-07   0.00024       1      31 [.      40      70 ..      40      73 .. 0.92
   2 !   33.4   0.1   4.4e-11   2.5e-08       1      32 [.      74     105 ..      74     107 .. 0.94
   3 !   21.0   0.0     4e-07   0.00023       2      33 ..     109     140 ..     108     141 .. 0.90
   4 !   24.9   0.0   2.4e-08   1.4e-05       1      34 []     142     175 ..     142     175 .. 0.96
   5 !   34.6   0.1   1.8e-11     1e-08       1      34 []     176     209 ..     176     209 .. 0.97
   6 !   23.8   0.0   5.1e-08   2.9e-05       1      33 [.     210     242 ..     210     243 .. 0.94
   7 ?   -0.5   0.2       3.2   1.8e+03       2       9 ..     245     252 ..     244     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.2e-07
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleld 31
                                      a+ +  +G+a +++g+y+eA++ +++A +ld
  gi|386001044|ref|YP_005919343.1| 40 AKDWSDMGNAQARRGEYQEAVASYDRATALD 70
                                      567999**********************998 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 4.4e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       ++++yn+Gla+  lg+yeeAle++++  +++P
  gi|386001044|ref|YP_005919343.1|  74 PDIWYNRGLALSSLGRYEEALECYQRGAKIEP 105
                                       579***************************99 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 4e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++   G a+  lg+yeeAle +++A e d +
  gi|386001044|ref|YP_005919343.1| 109 DLWLGTGSALSSLGRYEEALESYNRAAEFDSK 140
                                       689999*********************98865 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 2.4e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++a++ +G ++++lg++eeAl+  + Al+ dP++
  gi|386001044|ref|YP_005919343.1| 142 PDAWNGRGTVLARLGRLEEALASTDTALAMDPED 175
                                       689*****************************86 PP

  == domain 5  score: 34.6 bits;  conditional E-value: 1.8e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++  G ++++lg++eeAl+++++A+e+dP++
  gi|386001044|ref|YP_005919343.1| 176 ADAWNSKGAILLQLGRPEEALACYDRAIEIDPED 209
                                       79******************************86 PP

  == domain 6  score: 23.8 bits;  conditional E-value: 5.1e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++++n+G a+ +lg+y+eA + +  A++ldP 
  gi|386001044|ref|YP_005919343.1| 210 PDLWNNRGSALHQLGRYQEAQDSYSWAIALDPL 242
                                       579****************************95 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 3.2
                             TPR_2   2 ealynlGl 9  
                                       +a+yn+Gl
  gi|386001044|ref|YP_005919343.1| 245 YAWYNRGL 252
                                       69****97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00092      0.53       6      32 ..      45      71 ..      43      73 .. 0.88
   2 !   28.5   0.0   1.7e-09     1e-06       2      33 ..      75     106 ..      74     107 .. 0.94
   3 !   20.3   0.0   7.3e-07   0.00042       4      33 ..     111     140 ..     108     141 .. 0.88
   4 !   12.8   0.0   0.00019      0.11       2      34 .]     143     175 ..     142     175 .. 0.95
   5 !   30.4   0.0   4.3e-10   2.5e-07       1      34 []     176     209 ..     176     209 .. 0.96
   6 !   20.4   0.0   6.7e-07   0.00039       2      32 ..     211     241 ..     210     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00092
                                      HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  6 nlgsiylklgdyeeAkeyyekaleldp 32
                                       +g++    g+y+eA+++y +a+ ld 
  gi|386001044|ref|YP_005919343.1| 45 DMGNAQARRGEYQEAVASYDRATALDA 71
                                      578999999**************9996 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.7e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++yn g+++++lg+yeeA e+y++  +++p 
  gi|386001044|ref|YP_005919343.1|  75 DIWYNRGLALSSLGRYEEALECYQRGAKIEPF 106
                                       69***************************996 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 7.3e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++  gs++++lg+yeeA e+y++a e d +
  gi|386001044|ref|YP_005919343.1| 111 WLGTGSALSSLGRYEEALESYNRAAEFDSK 140
                                       66669*********************9987 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00019
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a++  g ++  lg++eeA ++   al +dp++
  gi|386001044|ref|YP_005919343.1| 143 DAWNGRGTVLARLGRLEEALASTDTALAMDPED 175
                                       79*****************************85 PP

  == domain 5  score: 30.4 bits;  conditional E-value: 4.3e-10
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a++ +g i+l+lg+ eeA ++y +a+e+dp++
  gi|386001044|ref|YP_005919343.1| 176 ADAWNSKGAILLQLGRPEEALACYDRAIEIDPED 209
                                       78******************************86 PP

  == domain 6  score: 20.4 bits;  conditional E-value: 6.7e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++++n gs++++lg+y+eA+ +y  a+ ldp
  gi|386001044|ref|YP_005919343.1| 211 DLWNNRGSALHQLGRYQEAQDSYSWAIALDP 241
                                       68*********************99999998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.24   1.4e+02      16      33 ..      43      60 ..      38      61 .. 0.86
   2 !   21.9   0.2   2.5e-07   0.00014       2      34 .]      63      95 ..      62      95 .. 0.96
   3 !   17.1   0.0   8.6e-06     0.005       1      34 []      96     129 ..      96     129 .. 0.97
   4 !   23.6   0.0   7.5e-08   4.3e-05       2      33 ..     131     162 ..     130     163 .. 0.96
   5 !   22.2   0.1   2.1e-07   0.00012       4      33 ..     167     196 ..     166     197 .. 0.94
   6 !   35.6   0.0   1.1e-11   6.3e-09       1      33 [.     198     230 ..     198     231 .. 0.97
   7 ?    5.8   0.0     0.035        20       5      22 ..     236     253 ..     236     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.24
                            TPR_17 16 ynnLAelllknGdlmtAr 33
                                      +  ++++++++G++++A+
  gi|386001044|ref|YP_005919343.1| 43 WSDMGNAQARRGEYQEAV 60
                                      7789************97 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.5e-07
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      y +a +ld  n+d ++n++ +l+++G++++A++
  gi|386001044|ref|YP_005919343.1| 63 YDRATALDAYNPDIWYNRGLALSSLGRYEEALE 95
                                      99*****************************85 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 8.6e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y++ ++++P ++d++   + +l+++G++++A++
  gi|386001044|ref|YP_005919343.1|  96 CYQRGAKIEPFDPDLWLGTGSALSSLGRYEEALE 129
                                       8*******************************85 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 7.5e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +a+e d +++da+n ++++l+++G+l++A+
  gi|386001044|ref|YP_005919343.1| 131 YNRAAEFDSKDPDAWNGRGTVLARLGRLEEAL 162
                                       99****************************97 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 2.1e-07
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                        al+ dP +ada+n ++ +ll++G++++A+
  gi|386001044|ref|YP_005919343.1| 167 TALAMDPEDADAWNSKGAILLQLGRPEEAL 196
                                       699*************************97 PP

  == domain 6  score: 35.6 bits;  conditional E-value: 1.1e-11
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a+e+dP ++d++nn++ +l+++G++++A+
  gi|386001044|ref|YP_005919343.1| 198 CYDRAIEIDPEDPDLWNNRGSALHQLGRYQEAQ 230
                                       8*******************************8 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.035
                            TPR_17   5 aleldPnnadaynnLAel 22 
                                       a++ldP + +a++n++ l
  gi|386001044|ref|YP_005919343.1| 236 AIALDPLHEYAWYNRGLL 253
                                       799************976 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.4   0.00016     0.095      29      64 ..      40      75 ..      38      76 .. 0.91
   2 !   27.9   2.6   3.4e-09     2e-06       6      64 ..      51     109 ..      47     112 .. 0.94
   3 !   29.0   0.5   1.6e-09     9e-07       9      65 ..      88     144 ..      82     144 .. 0.95
   4 !   33.7   1.4   5.3e-11   3.1e-08       9      65 ..     122     178 ..     115     180 .. 0.95
   5 !   45.0   2.3   1.5e-14   8.6e-12       3      60 ..     184     241 ..     183     250 .. 0.95
   6 ?    2.5   0.1      0.28   1.6e+02      22      40 ..     237     255 ..     233     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                             TPR_9 29 peerrdRGlllaqlGclsaAladLeaylalapdapd 64
                                      + ++ d G ++a++G +++A+a  +++ al+  +pd
  gi|386001044|ref|YP_005919343.1| 40 AKDWSDMGNAQARRGEYQEAVASYDRATALDAYNPD 75
                                      679************************999987776 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.4e-09
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       +r+ ++++a a ++r  +l+   p+ ++ RGl+l  lG++++Al++ ++ + ++p +pd
  gi|386001044|ref|YP_005919343.1|  51 ARRGEYQEAVASYDRATALDAYNPDIWYNRGLALSSLGRYEEALECYQRGAKIEPFDPD 109
                                       78999********************************************9999998877 PP

  == domain 3  score: 29.0 bits;  conditional E-value: 1.6e-09
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        ++e+al++++r   + P dp++++  G +l  lG++++Al+  +++++ + ++pda
  gi|386001044|ref|YP_005919343.1|  88 GRYEEALECYQRGAKIEPFDPDLWLGTGSALSSLGRYEEALESYNRAAEFDSKDPDA 144
                                       689************************************************999997 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 5.3e-11
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        ++e+al+ ++r   ++++dp+ +  RG +la+lG+l++Ala  +++la++p+++da
  gi|386001044|ref|YP_005919343.1| 122 GRYEEALESYNRAAEFDSKDPDAWNGRGTVLARLGRLEEALASTDTALAMDPEDADA 178
                                       689***************************************************998 PP

  == domain 5  score: 45.0 bits;  conditional E-value: 1.5e-14
                             TPR_9   3 aiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ai+++  + e+ala+++r + ++P+dp+++  RG +l+qlG++++A +   +++al+p
  gi|386001044|ref|YP_005919343.1| 184 AILLQLGRPEEALACYDRAIEIDPEDPDLWNNRGSALHQLGRYQEAQDSYSWAIALDP 241
                                       6899999*************************************************99 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.28
                             TPR_9  22 lllaPddpeerrdRGllla 40 
                                       ++l+P + + ++ RGll  
  gi|386001044|ref|YP_005919343.1| 237 IALDPLHEYAWYNRGLLVP 255
                                       6799999*********965 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.4   1.4e-06   0.00082       3      40 ..      42      79 ..      40      82 .. 0.92
   2 !   19.8   0.0   1.6e-06   0.00092       1      39 [.      74     112 ..      74     115 .. 0.94
   3 !   20.0   0.1   1.4e-06   0.00082       1      38 [.     108     145 ..     108     149 .. 0.93
   4 !   20.9   1.3   7.1e-07   0.00041       1      38 [.     142     179 ..     142     184 .. 0.95
   5 !   25.8   0.2     2e-08   1.1e-05       3      38 ..     178     213 ..     177     217 .. 0.90
   6 !   18.7   0.4   3.7e-06    0.0021       1      41 [.     210     250 ..     210     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-06
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawll 40
                                       + +++ a +++G+++eA+a ++ra al+  ++++w+ 
  gi|386001044|ref|YP_005919343.1| 42 DWSDMGNAQARRGEYQEAVASYDRATALDAYNPDIWYN 79
                                      5999*******************************986 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.6e-06
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       p+ ++ ++ al  lG+++eA+++++r  +  P d+++wl
  gi|386001044|ref|YP_005919343.1|  74 PDIWYNRGLALSSLGRYEEALECYQRGAKIEPFDPDLWL 112
                                       6789********************************997 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1.4e-06
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       p+++l  ++al  lG+++eA++ ++ra + + +d++aw
  gi|386001044|ref|YP_005919343.1| 108 PDLWLGTGSALSSLGRYEEALESYNRAAEFDSKDPDAW 145
                                       689**************************999999999 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 7.1e-07
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       p+a+  ++ +l++lG+++eA+a  + ala +P+da+aw
  gi|386001044|ref|YP_005919343.1| 142 PDAWNGRGTVLARLGRLEEALASTDTALAMDPEDADAW 179
                                       689999*******************************9 PP

  == domain 5  score: 25.8 bits;  conditional E-value: 2e-08
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       a+   +++ll+lG+p+eA+a+++ra++ +P+d+++w
  gi|386001044|ref|YP_005919343.1| 178 AWNSKGAILLQLGRPEEALACYDRAIEIDPEDPDLW 213
                                       56667899**************************99 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 3.7e-06
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       p+++  +++al +lG+++eA + + +a+al+P ++ aw+  
  gi|386001044|ref|YP_005919343.1| 210 PDLWNNRGSALHQLGRYQEAQDSYSWAIALDPLHEYAWYNR 250
                                       5778889******************************9865 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.4    0.0008      0.46      49      74 ..      44      69 ..      35      71 .. 0.76
   2 !   28.0   1.8   3.4e-09     2e-06       5      74 ..      76     137 ..      72     140 .. 0.91
   3 !   24.1   0.8   5.6e-08   3.2e-05       8      75 ..     113     172 ..     107     174 .. 0.82
   4 !   32.5   0.1   1.4e-10   7.8e-08       5      76 ..     144     207 ..     141     208 .. 0.94
   5 !   39.5   0.2   8.6e-13     5e-10       3      75 ..     176     240 ..     174     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0008
                            TPR_12 49 rnLgrlyralgryeeAlelleealai 74
                                       ++g ++ ++g+y+eA++ + +a+a+
  gi|386001044|ref|YP_005919343.1| 44 SDMGNAQARRGEYQEAVASYDRATAL 69
                                      56788888888888888888888876 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 3.4e-09
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +++n++++l  lgry+eAle++++   i      p  p+      + g +++ lgryeeAle +++a + 
  gi|386001044|ref|YP_005919343.1|  76 IWYNRGLALSSLGRYEEALECYQRGAKIE-----PFDPD---LWLGTGSALSSLGRYEEALESYNRAAEF 137
                                       789**********************8888.....88888...599*********************9875 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 5.6e-08
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                         +++l  lgry+eAle +++a e  ++   pd      + ++ g+++ +lgr+eeAl+    ala++
  gi|386001044|ref|YP_005919343.1| 113 GTGSALSSLGRYEEALESYNRAAEFDSKD--PD------AWNGRGTVLARLGRLEEALASTDTALAMD 172
                                       5689999***************9999666..55......58888888888888888888888888776 PP

  == domain 4  score: 32.5 bits;  conditional E-value: 1.4e-10
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+n +++vl+rlgr++eAl+  ++al++      p+    a + +  g ++++lgr+eeAl+ + +a++i++
  gi|386001044|ref|YP_005919343.1| 144 AWNGRGTVLARLGRLEEALASTDTALAMD-----PED---ADAWNSKGAILLQLGRPEEALACYDRAIEIDP 207
                                       7888*************************.....875...99***************************986 PP

  == domain 5  score: 39.5 bits;  conditional E-value: 8.6e-13
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a a+n  +a+l++lgr +eAl+++++a+ei      p+ p+     +n g ++++lgry+eA++ +  a+a++
  gi|386001044|ref|YP_005919343.1| 176 ADAWNSKGAILLQLGRPEEALACYDRAIEID-----PEDPD---LWNNRGSALHQLGRYQEAQDSYSWAIALD 240
                                       789988*************************.....99988...5**********************999975 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   1.4e-09     8e-07       4      62 ..      53     111 ..      50     114 .. 0.95
   2 !   32.9   0.3   1.2e-10   6.9e-08       5      65 ..     122     182 ..     118     185 .. 0.94
   3 !   28.2   0.3   3.4e-09     2e-06       1      55 [.     186     240 ..     186     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.4e-09
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +g y+eA+a + +a + d+ n++++++   al +lg+++eA ++ ++  + +p d++++
  gi|386001044|ref|YP_005919343.1|  53 RGEYQEAVASYDRATALDAYNPDIWYNRGLALSSLGRYEEALECYQRGAKIEPFDPDLW 111
                                       79************************************************999998876 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 1.2e-10
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       g+y+eAl+ + +a + d k+++a+ +   +l  lg+l+eA a  d+++++dp da++++ +
  gi|386001044|ref|YP_005919343.1| 122 GRYEEALESYNRAAEFDSKDPDAWNGRGTVLARLGRLEEALASTDTALAMDPEDADAWNSK 182
                                       99****************************************************9998755 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 3.4e-09
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       ll+ g+++eAla + +a++ dp++++++ +   al +lg+++eA++  + + + d
  gi|386001044|ref|YP_005919343.1| 186 LLQLGRPEEALACYDRAIEIDPEDPDLWNNRGSALHQLGRYQEAQDSYSWAIALD 240
                                       7899****************************************98766555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   8.1e-06    0.0047       4      35 ..      45      74 ..      43      75 .. 0.89
   2 !   18.9   0.0   1.9e-06    0.0011       2      34 ..      77     107 ..      76     109 .. 0.85
   3 !   14.4   0.1     5e-05     0.029       6      33 ..     115     142 ..     111     144 .. 0.87
   4 ?    3.5   0.0      0.15        88       5      34 ..     148     175 ..     144     177 .. 0.76
   5 !   15.7   0.0   1.9e-05     0.011       1      35 [.     178     210 ..     178     211 .. 0.85
   6 !   10.2   0.2    0.0011      0.64       2      30 ..     213     239 ..     212     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.1e-06
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdpeda 35
                                       +++++ r+G+y+eA+  y +  a++ d +++
  gi|386001044|ref|YP_005919343.1| 45 DMGNAQARRGEYQEAVASYDR--ATALDAYNP 74
                                      69*******************..999988765 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.9e-06
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ++n + + s+lG+yeeA+e+y++  +   +p+d
  gi|386001044|ref|YP_005919343.1|  77 WYNRGLALSSLGRYEEALECYQR--GAKIEPFD 107
                                       679999****************9..76666665 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +++ s+lG+yeeA+e y ++ ++++ + 
  gi|386001044|ref|YP_005919343.1| 115 GSALSSLGRYEEALESYNRAAEFDSKDP 142
                                       7899***************988887665 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.15
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdped 34 
                                        + +  rlG+ eeA+       al+ dped
  gi|386001044|ref|YP_005919343.1| 148 RGTVLARLGRLEEALASTDT--ALAMDPED 175
                                       5778899********99999..66666665 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.9e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++  + +  +lG+ eeA+ +y +  a++ dped+
  gi|386001044|ref|YP_005919343.1| 178 AWNSKGAILLQLGRPEEALACYDR--AIEIDPEDP 210
                                       57788999****************..777777765 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.0011
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       ++n +++ ++lG+y+eA + y    a++ 
  gi|386001044|ref|YP_005919343.1| 213 WNNRGSALHQLGRYQEAQDSYSW--AIAL 239
                                       799**************988865..5555 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0053       3.1       6      25 ..      45      64 ..      43      65 .. 0.85
   2 !    9.5   0.0     0.003       1.7       5      25 ..      78      98 ..      74      99 .. 0.88
   3 ?    3.4   0.0      0.28   1.6e+02      10      22 ..     117     129 ..     110     133 .. 0.81
   4 !   12.0   0.2   0.00046      0.27       6      22 ..     147     163 ..     142     166 .. 0.88
   5 !   11.4   0.2   0.00069       0.4       8      26 .]     183     201 ..     174     201 .. 0.89
   6 ?    7.8   0.0      0.01       5.8       6      22 ..     215     231 ..     212     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0053
                             TPR_4  6 aLArallalGdldeAralle 25
                                      +++ a++++G++ eA a  +
  gi|386001044|ref|YP_005919343.1| 45 DMGNAQARRGEYQEAVASYD 64
                                      6799***********99766 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.003
                             TPR_4  5 laLArallalGdldeAralle 25
                                      ++++ al  lG+++eA++  +
  gi|386001044|ref|YP_005919343.1| 78 YNRGLALSSLGRYEEALECYQ 98
                                      899**************9876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.28
                             TPR_4  10 allalGdldeAra 22 
                                       al  lG+++eA++
  gi|386001044|ref|YP_005919343.1| 117 ALSSLGRYEEALE 129
                                       67779******97 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00046
                             TPR_4   6 aLArallalGdldeAra 22 
                                       +++ +l++lG+l+eA+a
  gi|386001044|ref|YP_005919343.1| 147 GRGTVLARLGRLEEALA 163
                                       7899***********98 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00069
                             TPR_4   8 ArallalGdldeAraller 26 
                                       +  ll+lG+++eA+a  +r
  gi|386001044|ref|YP_005919343.1| 183 GAILLQLGRPEEALACYDR 201
                                       6789***********9876 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.01
                             TPR_4   6 aLArallalGdldeAra 22 
                                       +++ al++lG++ eA++
  gi|386001044|ref|YP_005919343.1| 215 NRGSALHQLGRYQEAQD 231
                                       6888***********85 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.1   1.5e-06   0.00084      67     123 ..      45     101 ..      36     104 .. 0.93
   2 ?    7.2   0.0     0.011       6.6      91     123 ..     103     135 ..      99     142 .. 0.83
   3 !   17.0   0.3     1e-05    0.0059      69     123 ..     149     203 ..     142     208 .. 0.92
   4 !    8.4   0.0    0.0046       2.6      67     100 ..     215     248 ..     211     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++ +a++r G+++ea+a +++++a++ ++ + +    +Al  +Gr +eALe Y+r  
  gi|386001044|ref|YP_005919343.1|  45 DMGNAQARRGEYQEAVASYDRATALDAYNPDIWYNRGLALSSLGRYEEALECYQRGA 101
                                       5678999***********************************************975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                                       HSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  91 ehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        +P++ +l+     Al  +Gr +eALe Y+r+ 
  gi|386001044|ref|YP_005919343.1| 103 IEPFDPDLWLGTGSALSSLGRYEEALESYNRAA 135
                                       56777777777778****************985 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                          ++rlGr eeala  + ++a++P + +++    + l ++Gr +eAL+ Y+r+ 
  gi|386001044|ref|YP_005919343.1| 149 GTVLARLGRLEEALASTDTALAMDPEDADAWNSKGAILLQLGRPEEALACYDRAI 203
                                       556789*********************************************9985 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0046
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHH CS
                              BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhr 100
                                        +  a+ +lGr++ea++ ++ ++a++Pl+E ++ 
  gi|386001044|ref|YP_005919343.1| 215 NRGSALHQLGRYQEAQDSYSWAIALDPLHEYAWY 248
                                       57788999**********************9985 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.5   0.00039      0.22       7      28 ..      45      66 ..      44      69 .. 0.90
   2 !   11.4   0.2   0.00039      0.22       7      27 ..      79      99 ..      78     103 .. 0.90
   3 !    7.7   0.1    0.0057       3.3       9      29 ..     115     135 ..     115     137 .. 0.86
   4 ?    4.0   0.1     0.082        47       9      23 ..     149     163 ..     146     171 .. 0.81
   5 !   13.3   0.1   9.8e-05     0.056       8      31 ..     182     205 ..     176     205 .. 0.90
   6 !   10.3   0.5   0.00087       0.5       6      22 ..     214     230 ..     214     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                            TPR_10  7 NLanalrqrgrydeAealleea 28
                                      +++na  +rg+y+eA+a +++a
  gi|386001044|ref|YP_005919343.1| 45 DMGNAQARRGEYQEAVASYDRA 66
                                      68***************99998 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00039
                            TPR_10  7 NLanalrqrgrydeAeallee 27
                                      N + al+++gry+eA++ +++
  gi|386001044|ref|YP_005919343.1| 79 NRGLALSSLGRYEEALECYQR 99
                                      7799*************9987 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0057
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       + al+++gry+eA++ + +a 
  gi|386001044|ref|YP_005919343.1| 115 GSALSSLGRYEEALESYNRAA 135
                                       679***********9887775 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.082
                            TPR_10   9 analrqrgrydeAea 23 
                                       + +l ++gr++eA+a
  gi|386001044|ref|YP_005919343.1| 149 GTVLARLGRLEEALA 163
                                       7899*********98 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 9.8e-05
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                        +++l q+gr +eA+a +++a++i
  gi|386001044|ref|YP_005919343.1| 182 KGAILLQLGRPEEALACYDRAIEI 205
                                       5899******************97 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00087
                            TPR_10   6 nNLanalrqrgrydeAe 22 
                                       nN + al+q+gry+eA 
  gi|386001044|ref|YP_005919343.1| 214 NNRGSALHQLGRYQEAQ 230
                                       999*************6 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2    0.0014       0.8      87     125 ..      65      99 ..      39     104 .. 0.71
   2 !   12.0   0.2   0.00029      0.17      53     127 ..     106     169 ..     102     174 .. 0.70
   3 !    8.0   0.0    0.0047       2.7      58     128 ..     145     204 ..     136     209 .. 0.74
   4 !    9.2   0.0     0.002       1.2      78     126 ..     192     236 ..     176     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                                       HH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  87 rrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                       r   l+  +  +W    ++r+ al++lGr++eal+ ++ 
  gi|386001044|ref|YP_005919343.1|  65 RATALDAYNPDIW----YNRGLALSSLGRYEEALECYQR 99 
                                       4445555555666....79****************9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  53 fdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       fd   + g  +al  lgry+eales       +nr  e+++ +   W      r++ l+ lGr +eal +  +a 
  gi|386001044|ref|YP_005919343.1| 106 FDPDLWLGTGSALSSLGRYEEALES-------YNRAAEFDSKDPDAWN----GRGTVLARLGRLEEALASTDTAL 169
                                       5555666777888888888888777.......6777777777777774....57777777777777777766665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  58 haglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       + g    la+lgr +eal s+d+al        ++ ++   W     s+++ l +lGr +eal  +  a e
  gi|386001044|ref|YP_005919343.1| 145 WNGRGTVLARLGRLEEALASTDTALA-------MDPEDADAW----NSKGAILLQLGRPEEALACYDRAIE 204
                                       55666788999999999999999996.......455566666....4678888888888888888887777 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                        ++al  ++r  e++ ++  lW     +r+ al++lGr++ea +++  a
  gi|386001044|ref|YP_005919343.1| 192 PEEALACYDRAIEIDPEDPDLW----NNRGSALHQLGRYQEAQDSYSWA 236
                                       5789999999999999999999....58**************9999766 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   2.8e-06    0.0016       3      80 ..      54     132 ..      52     134 .. 0.94
   2 ?    7.1   0.0     0.011       6.5      30      77 ..     115     163 ..     104     168 .. 0.88
   3 !   17.2   0.0   7.5e-06    0.0044       4      81 ..     157     235 ..     155     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.8e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       + y++A+  ++r+ a ++++p+  y  +l+l ++g+y++A+e +++  k+++ ++  ++ ++ +l  L++yeeA+  
  gi|386001044|ref|YP_005919343.1|  54 GEYQEAVASYDRATALDAYNPDIWYNRGLALSSLGRYEEALECYQRGaKIEPFDPDLWLGTGSALSSLGRYEEALES 130
                                       679********************************************9**************************987 PP

                                       H- CS
                            ANAPC3  79 Le 80 
                                       + 
  gi|386001044|ref|YP_005919343.1| 131 YN 132
                                       65 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       + +l ++g+y++A+e +++a + +sk++ ++   + +l  L+++eeA+a
  gi|386001044|ref|YP_005919343.1| 115 GSALSSLGRYEEALESYNRAaEFDSKDPDAWNGRGTVLARLGRLEEALA 163
                                       5678889999999999999999999999999999999999999999997 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 7.5e-06
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       ++++A+   + +la+++e++++   ++  l+++g+ ++A+  +++a +++++++  +   + +l +L++y+eA + +
  gi|386001044|ref|YP_005919343.1| 157 RLEEALASTDTALAMDPEDADAWNSKGAILLQLGRPEEALACYDRAiEIDPEDPDLWNNRGSALHQLGRYQEAQDSY 233
                                       567888888999999**********************************************************8877 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       ++
  gi|386001044|ref|YP_005919343.1| 234 SW 235
                                       65 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.3     7e-08     4e-05     146     249 ..      40     143 ..      37     163 .. 0.87
   2 !   15.6   0.4   1.3e-05    0.0073     144     233 ..     140     229 ..     132     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7e-08
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgp 219
                                       a  ++ +++++ ++g+ ++A+  y +A al++ + ++  +   +l  lgr++e   +l+ +++ a     d++Lw+ 
  gi|386001044|ref|YP_005919343.1|  40 AKDWSDMGNAQARRGEYQEAVASYDRATALDAYNPDIWYNRGLALSSLGRYEE---ALECYQRGAkiePFDPDLWLG 113
                                       55689999999**************************99999999999****7...88888877777799******* PP

                            TPR_15 220 laaAlllLgrpkkALeylrkqakenrkdpl 249
                                        ++Al+ Lgr+++ALe +++ a+  +kdp 
  gi|386001044|ref|YP_005919343.1| 114 TGSALSSLGRYEEALESYNRAAEFDSKDPD 143
                                       *********************999999985 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.3e-05
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLw 217
                                       +++  +  r+ +  + g+ ++Al     Ala++p+++++ +    +l+ lgr +e   +l+ + ++     +d++Lw
  gi|386001044|ref|YP_005919343.1| 140 KDPDAWNGRGTVLARLGRLEEALASTDTALAMDPEDADAWNSKGAILLQLGRPEE---ALACYDRAIeidPEDPDLW 213
                                       6788888888888899999999999999999999999888888888888888886...8888887777888888999 PP

                            TPR_15 218 gplaaAlllLgrpkkA 233
                                       +  ++Al  Lgr+++A
  gi|386001044|ref|YP_005919343.1| 214 NNRGSALHQLGRYQEA 229
                                       9999999999998888 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.051        29       6      26 ..      46      66 ..      45      69 .. 0.89
   2 !   11.5   0.1   0.00066      0.38       3      25 ..      77      99 ..      75      99 .. 0.93
   3 ?    6.0   0.0     0.036        21       4      26 ..     112     134 ..     109     136 .. 0.82
   4 ?    0.3   0.0       2.3   1.4e+03       3      20 ..     152     169 ..     148     173 .. 0.62
   5 !    7.9   0.0    0.0095       5.5      10      32 ..     186     208 ..     182     209 .. 0.85
   6 ?    1.0   0.1       1.4   8.1e+02       7      23 ..     217     233 ..     215     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.051
                                      HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  6 lalsyrklgdtdkAlealerl 26
                                      ++ ++ + g++++A++ ++r 
  gi|386001044|ref|YP_005919343.1| 46 MGNAQARRGEYQEAVASYDRA 66
                                      789999989*********986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00066
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  3 lyklalsyrklgdtdkAlealer 25
                                       y+++l++ +lg++++Ale ++r
  gi|386001044|ref|YP_005919343.1| 77 WYNRGLALSSLGRYEEALECYQR 99
                                      69********99*********97 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerl 26 
                                       +  + ++ +lg++++Ale ++r 
  gi|386001044|ref|YP_005919343.1| 112 LGTGSALSSLGRYEEALESYNRA 134
                                       55677888899*********997 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAl 20 
                                       l +l+++ ++l  td+Al
  gi|386001044|ref|YP_005919343.1| 152 LARLGRLEEALASTDTAL 169
                                       557777777753555444 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                                       +++lg++++Al+ ++r i+  P+
  gi|386001044|ref|YP_005919343.1| 186 LLQLGRPEEALACYDRAIEIDPE 208
                                       56678*************99886 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAleal 23 
                                       + ++ +lg++++A + +
  gi|386001044|ref|YP_005919343.1| 217 GSALHQLGRYQEAQDSY 233
                                       66777788999998876 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0083       4.8      10      36 .]      49      73 ..      41      73 .. 0.82
   2 ?    3.7   0.0      0.11        62      14      25 ..      87      98 ..      75     102 .. 0.87
   3 ?    2.2   0.0      0.33   1.9e+02      14      34 ..     121     139 ..     116     141 .. 0.75
   4 !    9.6   0.0    0.0015      0.88       9      33 ..     218     240 ..     217     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0083
                                      HHHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3 10 efynkkkyqeArelfsYallaildken 36
                                      ++   ++yqeA+  ++   +++ld++n
  gi|386001044|ref|YP_005919343.1| 49 AQARRGEYQEAVASYD--RATALDAYN 73
                                      566679********77..*******99 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                      TT-HHHHHHH.. CS
                             TPR_3 14 kkkyqeArelfs 25
                                       ++y+eA+e ++
  gi|386001044|ref|YP_005919343.1| 87 LGRYEEALECYQ 98
                                      69********88 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.33
                                       TT-HHHHHHH..HHHHHHH-T CS
                             TPR_3  14 kkkyqeArelfsYallaildk 34 
                                        ++y+eA+e   Y  +a  d+
  gi|386001044|ref|YP_005919343.1| 121 LGRYEEALES--YNRAAEFDS 139
                                       589****999..656666555 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0015
                                       HHHHHTT-HHHHHHH..HHHHHHH- CS
                             TPR_3   9 aefynkkkyqeArelfsYallaild 33 
                                        ++++ ++yqeA + +s   + +ld
  gi|386001044|ref|YP_005919343.1| 218 SALHQLGRYQEAQDSYS--WAIALD 240
                                       689************88..888887 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       2.3   1.3e+03       6      21 ..      46      61 ..      43      65 .. 0.77
   2 ?    6.4   0.1     0.021        12       9      24 ..      83      98 ..      83      99 .. 0.89
   3 ?    5.3   0.0     0.048        28       8      24 ..     116     132 ..     116     137 .. 0.87
   4 ?    3.1   0.0      0.23   1.3e+02       9      20 ..     151     162 ..     144     163 .. 0.85
   5 ?    5.3   0.0     0.047        27      11      27 ..     187     203 ..     184     206 .. 0.84
   6 ?   -0.9   0.0       4.4   2.5e+03       7      20 ..     217     230 ..     212     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.3
                               PPR  6 lIsgycknGkleeAle 21
                                      + ++ ++ G+++eA+ 
  gi|386001044|ref|YP_005919343.1| 46 MGNAQARRGEYQEAVA 61
                                      6678899*******86 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                               PPR  9 gycknGkleeAlelfk 24
                                      ++++ G++eeAle+++
  gi|386001044|ref|YP_005919343.1| 83 ALSSLGRYEEALECYQ 98
                                      68999********997 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.048
                               PPR   8 sgycknGkleeAlelfk 24 
                                       s++++ G++eeAle ++
  gi|386001044|ref|YP_005919343.1| 116 SALSSLGRYEEALESYN 132
                                       6899*********9766 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.23
                               PPR   9 gycknGkleeAl 20 
                                       ++++ G+leeAl
  gi|386001044|ref|YP_005919343.1| 151 VLARLGRLEEAL 162
                                       689********8 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.047
                               PPR  11 cknGkleeAlelfkeMk 27 
                                        + G++eeAl ++++ +
  gi|386001044|ref|YP_005919343.1| 187 LQLGRPEEALACYDRAI 203
                                       689**********9865 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 4.4
                               PPR   7 IsgycknGkleeAl 20 
                                        s++ + G+++eA 
  gi|386001044|ref|YP_005919343.1| 217 GSALHQLGRYQEAQ 230
                                       5788899*****96 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.09        52      16      30 ..      52      66 ..      40      69 .. 0.87
   2 !    8.6   0.0    0.0033       1.9      17      31 ..      87     101 ..      79     103 .. 0.86
   3 ?    6.9   0.2     0.011       6.4      18      32 ..     122     136 ..     117     137 .. 0.89
   4 ?    3.0   0.0      0.19   1.1e+02      17      32 ..     189     204 ..     181     205 .. 0.85
   5 ?    1.7   0.0      0.46   2.7e+02      16      32 ..     222     238 ..     216     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.09
                               MIT 16 nagnyeeAlelYkea 30
                                      ++g+y+eA+  Y  a
  gi|386001044|ref|YP_005919343.1| 52 RRGEYQEAVASYDRA 66
                                      689*********998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0033
                               MIT  17 agnyeeAlelYkeal 31 
                                        g yeeAle+Y+ + 
  gi|386001044|ref|YP_005919343.1|  87 LGRYEEALECYQRGA 101
                                       589*********986 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                               MIT  18 gnyeeAlelYkeale 32 
                                       g yeeAle Y  a e
  gi|386001044|ref|YP_005919343.1| 122 GRYEEALESYNRAAE 136
                                       89*********9987 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.19
                               MIT  17 agnyeeAlelYkeale 32 
                                        g  eeAl +Y  a+e
  gi|386001044|ref|YP_005919343.1| 189 LGRPEEALACYDRAIE 204
                                       57779*********98 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.46
                               MIT  16 nagnyeeAlelYkeale 32 
                                       + g y+eA + Y+ a+ 
  gi|386001044|ref|YP_005919343.1| 222 QLGRYQEAQDSYSWAIA 238
                                       5699********98885 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.089        51     204     259 ..      86     141 ..      76     142 .. 0.91
   2 !   14.2   0.0   2.7e-05     0.015     204     279 ..     154     229 ..     150     235 .. 0.78
   3 ?    1.9   0.0      0.14        83      42      82 ..     214     256 ..     211     284 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.089
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        lg++e+Ale+ ++  + +p   +l+l  +  l   G  ++A e  ++a ++D +D
  gi|386001044|ref|YP_005919343.1|  86 SLGRYEEALECYQRGAKIEPFDPDLWLGTGSALSSLGRYEEALESYNRAAEFDSKD 141
                                       578999999999999999***********************************998 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.7e-05
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHTT-HHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcakymLradeveeA 279
                                       +lg+ e+Al   d+a++ +p+  + +  K+ il + G +++A ++ ++a ++D +D  + ++    + + ++++eA
  gi|386001044|ref|YP_005919343.1| 154 RLGRLEEALASTDTALAMDPEDADAWNSKGAILLQLGRPEEALACYDRAIEIDPEDPDLWNNRGSALHQLGRYQEA 229
                                       6788999999999999999999999999999999999999999999999999998865544444444444555555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHTT-HHHHHHHHHHHH..HH-TT-CHHHHHHHHHT CS
                             NARP1  42 etkaelllkLgrkeeAeatyeaLl..ernpenskYyeglekak 82 
                                       +++++ l +Lgr++eA+  y+  +  +  +e   Y +gl    
  gi|386001044|ref|YP_005919343.1| 214 NNRGSALHQLGRYQEAQDSYSWAIalDPLHEYAWYNRGLLVPT 256
                                       579999*************987651145556666777766544 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.17        97       8      43 ..      60      95 ..      54      97 .. 0.87
   2 ?    2.5   0.0      0.32   1.9e+02      15      44 ..     101     130 ..      95     147 .. 0.83
   3 ?    5.4   0.1     0.039        23       7      42 ..     161     196 ..     158     199 .. 0.92
   4 ?    5.6   0.0     0.035        20      12      43 ..     200     231 ..     196     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.17
                            TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAle 43
                                      +a+ ++a a +  + d+ ++  lal + gryeeAle
  gi|386001044|ref|YP_005919343.1| 60 VASYDRATALDAYNPDIWYNRGLALSSLGRYEEALE 95
                                      666777888899999*******************97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.32
                            TPR_20  15 laanpddldarldlAlallaagryeeAleq 44 
                                       ++ +p d d+ l    al + gryeeAle 
  gi|386001044|ref|YP_005919343.1| 101 AKIEPFDPDLWLGTGSALSSLGRYEEALES 130
                                       5668999999999999************96 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.039
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAl 42 
                                        la+ ++ala +p+d da       ll+ gr eeAl
  gi|386001044|ref|YP_005919343.1| 161 ALASTDTALAMDPEDADAWNSKGAILLQLGRPEEAL 196
                                       5788899****************************8 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.035
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAle 43 
                                       ++a++ +p+d d+  +   al++ gry+eA +
  gi|386001044|ref|YP_005919343.1| 200 DRAIEIDPEDPDLWNNRGSALHQLGRYQEAQD 231
                                       578999************************76 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.2   7.1e+02      10      25 ..      49      64 ..      47      73 .. 0.79
   2 !    7.8   0.0     0.006       3.5       2      32 ..      75     105 ..      74     108 .. 0.90
   3 ?   -0.8   0.1       2.9   1.7e+03      14      23 ..     121     130 ..     117     138 .. 0.79
   4 !    8.0   0.0    0.0052         3      12      37 ..     153     178 ..     152     185 .. 0.91
   5 ?    1.4   0.0      0.57   3.3e+02      15      34 ..     190     209 ..     186     212 .. 0.85
   6 ?   -2.4   0.0       9.2   5.3e+03      13      23 ..     222     232 ..     218     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                                      HHHHHT-HHHHHHHHH CS
                        Fis1_TPR_C 10 GhyklgeYseArryvd 25
                                      ++++ geY+eA    d
  gi|386001044|ref|YP_005919343.1| 49 AQARRGEYQEAVASYD 64
                                      78999****9976555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEP 32 
                                       +  Y   l+   lg+Y+eA+++ ++  +iEP
  gi|386001044|ref|YP_005919343.1|  75 DIWYNRGLALSSLGRYEEALECYQRGAKIEP 105
                                       56799999****************9999999 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.9
                                       HT-HHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArry 23 
                                       lg+Y+eA++ 
  gi|386001044|ref|YP_005919343.1| 121 LGRYEEALES 130
                                       8999999975 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0052
                                       HHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQa 37 
                                       ++lg+ +eA+  +d+ L+++Pe   a
  gi|386001044|ref|YP_005919343.1| 153 ARLGRLEEALASTDTALAMDPEDADA 178
                                       79*******************98766 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.57
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                       g+ +eA+ + d+ +ei+Pe 
  gi|386001044|ref|YP_005919343.1| 190 GRPEEALACYDRAIEIDPED 209
                                       55589*************85 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 9.2
                                       HHT-HHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArry 23 
                                        lg+Y+eA   
  gi|386001044|ref|YP_005919343.1| 222 QLGRYQEAQDS 232
                                       58999999765 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0052         3     181     238 ..      88     145 ..      81     161 .. 0.73
   2 !    6.3   0.1    0.0099       5.7     183     237 ..     124     178 ..     122     181 .. 0.86
   3 !    8.8   0.0    0.0017      0.99     205     256 ..     180     231 ..     173     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0052
                                       THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHH CS
                        Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetL 238
                                       +++++A+  +q  +   +  p+l  g   +   lgryeeA ++ + a + d+kd+++ 
  gi|386001044|ref|YP_005919343.1|  88 GRYEEALECYQRGAKIEPFDPDLWLGTGSALSSLGRYEEALESYNRAAEFDSKDPDAW 145
                                       67788888888766544444444444444455679********************985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeet 237
                                       +++A+  ++  +e  ++ p+  ng+  v   lgr eeA  +  +aL  d++d+++
  gi|386001044|ref|YP_005919343.1| 124 YEEALESYNRAAEFDSKDPDAWNGRGTVLARLGRLEEALASTDTALAMDPEDADA 178
                                       67777777777777778899999***************************99997 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 205 ngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       n k ++ l+lgr+eeA      a++ d++d++   N   a ++lg+ +e+++
  gi|386001044|ref|YP_005919343.1| 180 NSKGAILLQLGRPEEALACYDRAIEIDPEDPDLWNNRGSALHQLGRYQEAQD 231
                                       67888999******************************999****9998876 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.8   1.1e+03      22      36 ..      54      68 ..      46      72 .. 0.83
   2 ?    5.6   0.0     0.031        18      19      36 ..      85     102 ..      78     104 .. 0.82
   3 ?    4.0   0.0     0.098        57      19      38 ..     119     138 ..     115     142 .. 0.84
   4 ?    5.0   0.0     0.049        28      13      37 ..     181     205 ..     174     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.8
                         NRBF2_MIT 22 Gkyeeaischkkaaa 36
                                      G y+ea++ + +a+a
  gi|386001044|ref|YP_005919343.1| 54 GEYQEAVASYDRATA 68
                                      899999999999886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.031
                         NRBF2_MIT  19 laaGkyeeaischkkaaa 36 
                                        + G+yeea+ c+++ a+
  gi|386001044|ref|YP_005919343.1|  85 SSLGRYEEALECYQRGAK 102
                                       5679*********99875 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.098
                         NRBF2_MIT  19 laaGkyeeaischkkaaayl 38 
                                        + G+yeea+  +++aa++ 
  gi|386001044|ref|YP_005919343.1| 119 SSLGRYEEALESYNRAAEFD 138
                                       5679*************975 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.049
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkkaaay 37 
                                        k   ll  G+ eea++c+ +a ++
  gi|386001044|ref|YP_005919343.1| 181 SKGAILLQLGRPEEALACYDRAIEI 205
                                       56677999***********999765 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1       0.3   1.8e+02     252     270 ..      55      73 ..      44      79 .. 0.68
   2 ?    0.9   0.0      0.42   2.4e+02      29      43 ..      88     102 ..      80     103 .. 0.71
   3 !   12.5   0.0   0.00013     0.074      24     127 ..     118     230 ..     110     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.3
                                       THHHHHHHHTTSS---HHH CS
                              SNAP 252 kfteavkefDkiskldkWk 270
                                       +++eav+ +D+ + ld+++
  gi|386001044|ref|YP_005919343.1|  55 EYQEAVASYDRATALDAYN 73 
                                       5667777777777777665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHH CS
                              SNAP  29 skaeeAadlyeqAAn 43 
                                        ++eeA ++y++ A+
  gi|386001044|ref|YP_005919343.1|  88 GRYEEALECYQRGAK 102
                                       478888888888775 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00013
                                       H--SHHHHHHHHHHHHHHHH.HHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT........-HH CS
                              SNAP  24 fgsksskaeeAadlyeqAAn.ayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv........spe 91 
                                       ++s + ++eeA + y++AA+   k   +w+  g++ +++ +++e l ++d+a  +  e a + +++        +pe
  gi|386001044|ref|YP_005919343.1| 118 LSSLG-RYEEALESYNRAAEfDSKDPDAWNGRGTVLARLGRLEEALASTDTALAMDPEDADAWNSKgaillqlgRPE 193
                                       55544.9************84468889******************999988866655555555444467888889** PP

                                       HHHHHHHHHHHH.HHHTT-HHHHHHHHHHHHHHHHHT CS
                              SNAP  92 eAvealekAiei.ytekgrfrraAklkkeiaelyeke 127
                                       eA +++++Aiei   + + +++ ++   +++   e +
  gi|386001044|ref|YP_005919343.1| 194 EALACYDRAIEIdPEDPDLWNNRGSALHQLGRYQEAQ 230
                                       ***********93344455566666666666665555 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4     0.092        53     123     172 ..      50     100 ..      44     107 .. 0.81
   2 ?    1.2   0.1      0.44   2.5e+02     151     175 ..     113     137 ..      88     146 .. 0.74
   3 ?    8.6   0.1    0.0024       1.4     122     175 ..     151     205 ..     149     212 .. 0.75
   4 ?    3.2   0.0      0.11        62     151     174 ..     215     238 ..     210     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.092
                            TPR_21 123 llaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaA 172
                                       ++  ++y+eA++  +++++ +a++  +   rG +l++ g+ +eA + Yq++
  gi|386001044|ref|YP_005919343.1|  50 QARRGEYQEAVASYDRATAlDAYNPDIWYNRGLALSSLGRYEEALECYQRG 100
                                       677889999999997665438999999999999999999999999999986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.44
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaa 175
                                         G +l++ g+ +eA + Y++A + 
  gi|386001044|ref|YP_005919343.1| 113 GTGSALSSLGRYEEALESYNRAAEF 137
                                       5699999*************99865 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0024
                            TPR_21 122 vllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       vl+  + ++eAl+  +++ + +  +a + + +G il++ g+ +eA a Y++A++ 
  gi|386001044|ref|YP_005919343.1| 151 VLARLGRLEEALASTDTALAmDPEDADAWNSKGAILLQLGRPEEALACYDRAIEI 205
                                       5666667777777666554313446777789*********************975 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.11
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        rG +l + g+ +eA++ Y+ A+a
  gi|386001044|ref|YP_005919343.1| 215 NRGSALHQLGRYQEAQDSYSWAIA 238
                                       59*****************99986 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.11        66     258     296 ..      46      84 ..      31      99 .. 0.79
   2 ?    3.5   0.0     0.057        33     254     290 ..     117     146 ..      90     154 .. 0.84
   3 ?    4.4   0.0     0.032        19     250     303 ..     181     227 ..     164     234 .. 0.80
   4 ?   -0.8   0.2       1.2   6.7e+02     252     291 ..     217     249 ..     213     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                       CCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHH CS
                               FAT 258 lqkldwseekieeilqsysaateidpswykawhtwalfn 296
                                       +++++ ++ + +e+++sy +at +d    + w++ +l+ 
  gi|386001044|ref|YP_005919343.1|  46 MGNAQARRGEYQEAVASYDRATALDAYNPDIWYNRGLAL 84 
                                       444577888899********************9855554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
                                       CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 254 wqealqkldwseekieeilqsysaateidpswykawh 290
                                        +++l++        ee+l+sy +a+e+d +  +aw+
  gi|386001044|ref|YP_005919343.1| 117 ALSSLGR-------YEEALESYNRAAEFDSKDPDAWN 146
                                       4555555.......89*******************96 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.032
                                       TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHH CS
                               FAT 250 kkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvske 303
                                        kG  + +l++       +ee+l++y +a eidp+  + w++ + +  +  + +
  gi|386001044|ref|YP_005919343.1| 181 SKGAILLQLGR-------PEEALACYDRAIEIDPEDPDLWNNRGSALHQLGRYQ 227
                                       56666777777.......9****************9999998777776665555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.2
                                       CCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 252 Gewqealqkldwseekieeilqsysaateidpswykawht 291
                                       G+ +++l++        +e+ +sys+a  +dp  + aw++
  gi|386001044|ref|YP_005919343.1| 217 GSALHQLGR-------YQEAQDSYSWAIALDPLHEYAWYN 249
                                       565666666.......89999**********999999986 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0     0.003       1.7      20      56 ..      80     131 ..      54     141 .. 0.75
   2 ?    2.9   0.0      0.18   1.1e+02      23      64 ..     117     161 ..     101     198 .. 0.73
   3 ?    1.3   0.0      0.58   3.3e+02      24      40 ..     186     202 ..     130     236 .. 0.60
   4 ?   -0.2   0.0       1.7   9.8e+02      16      34 ..     212     230 ..     197     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs...............alsedvrfEkaYvlY 56 
                                       + +al +l++yeeaL+  + g                als+  r+E+a   Y
  gi|386001044|ref|YP_005919343.1|  80 RGLALSSLGRYEEALECYQRGAkiepfdpdlwlgtgsALSSLGRYEEALESY 131
                                       889999**********999998788777777777777777777777776665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                      SRP_TPR_like  23 aliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykka 64 
                                       al +l++yeeaL+  + +    + + d    +  vl +l ++++a
  gi|386001044|ref|YP_005919343.1| 117 ALSSLGRYEEALESYNRAAefdSKDPDAWNGRGTVLARLGRLEEA 161
                                       566788999998877665522222333444455555555555554 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.58
                      SRP_TPR_like  24 liklekyeeaLkllkkg 40 
                                       l++l++ eeaL   + +
  gi|386001044|ref|YP_005919343.1| 186 LLQLGRPEEALACYDRA 202
                                       44445555555444433 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.7
                      SRP_TPR_like  16 lkkfkvvaliklekyeeaL 34 
                                       l + +  al +l++y+ea 
  gi|386001044|ref|YP_005919343.1| 212 LWNNRGSALHQLGRYQEAQ 230
                                       4455777888899998885 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.6   9.3e+02      41      62 ..      45      66 ..      37      76 .. 0.78
   2 ?   -0.5   0.0       1.5   8.5e+02      48      60 ..      86      98 ..      75     103 .. 0.63
   3 ?   -0.3   0.0       1.3   7.4e+02      49      64 ..     121     136 ..     112     140 .. 0.85
   4 ?    5.7   0.0     0.019        11      14      64 ..     153     204 ..     146     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                                      HHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7 41 dlaehYlkigdleeAlkaysri 62
                                      d ++  ++ g+++eA++ y r+
  gi|386001044|ref|YP_005919343.1| 45 DMGNAQARRGEYQEAVASYDRA 66
                                      5566667889999999999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                                      HCT-HHHHHHHHH CS
                              RPN7 48 kigdleeAlkays 60
                                      + g +eeAl++y+
  gi|386001044|ref|YP_005919343.1| 86 SLGRYEEALECYQ 98
                                      3456666666665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.3
                                       CT-HHHHHHHHHTCCC CS
                              RPN7  49 igdleeAlkaysrire 64 
                                        g +eeAl+ y+r+ e
  gi|386001044|ref|YP_005919343.1| 121 LGRYEEALESYNRAAE 136
                                       68999*******9865 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  14 keleeLdaelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       ++l +L++ l        ++ e ++a++ ++   l+ g  eeAl++y r++e
  gi|386001044|ref|YP_005919343.1| 153 ARLGRLEEALASTDtALAMDPEDADAWNSKGAILLQLGRPEEALACYDRAIE 204
                                       56667777777766445577888999**********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2060.79
//
Query:       gi|386001045|ref|YP_005919344.1|  [L=430]
Description: hypothetical protein Mhar_0334 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      108  (0.00602376); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 2551.14
//
Query:       gi|386001046|ref|YP_005919345.1|  [L=113]
Description: hypothetical protein Mhar_0335 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 754.41
//
Query:       gi|386001047|ref|YP_005919346.1|  [L=171]
Description: hypothetical protein Mhar_0336 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.9   1.6        0.2   11.6   0.1    1.9  2  NdhL      NADH dehydrogenase transmembrane subunit


Domain annotation for each model (and alignments):
>> NdhL  NADH dehydrogenase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.36   6.5e+03      61      71 ..     107     117 ..      98     120 .. 0.54
   2 ?   11.6   0.1   1.1e-05       0.2      18      55 ..     127     166 ..     122     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.36
                              NdhL  61 llllaPflNlR 71 
                                       +lll  +l +R
  gi|386001047|ref|YP_005919346.1| 107 ILLLGALLAFR 117
                                       44555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.1e-05
                              NdhL  18 alsvlYllviPlilylwlrkRWyvaskiErll..iymlvf 55 
                                       al ++ l+++P+il l+l   W     iE +   +y+ vf
  gi|386001047|ref|YP_005919346.1| 127 ALQAASLVLVPMILALYLYAGWKALTAIEDYNerLYVTVF 166
                                       677889***********************88522466555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1301.99
//
Query:       gi|386001048|ref|YP_005919347.1|  [L=1302]
Description: Cna B domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-06   28.4  15.1        5.7    7.0   0.1    8.1  7  Y_Y_Y        Y_Y_Y domain
     0.0063   16.7   3.8         14    5.9   0.5    7.2  8  He_PIG       Putative Ig domain
  ------ inclusion threshold ------
       0.97   10.0  18.5         20    5.7   0.9    4.4  4  EB1_binding  EB-1 Binding Domain
        2.4    8.1  14.8         14    5.6   0.0    5.7  7  CBM_20       Starch binding domain


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 !    5.7   0.0    0.0031        14       8      50 ..      69     115 ..      64     128 .. 0.88
   2 !    5.7   0.0    0.0031        14       8      50 ..     176     222 ..     171     235 .. 0.88
   3 !    4.3   0.4    0.0087        39       4      52 ..     279     333 ..     276     350 .. 0.80
   4 ?    2.0   0.0     0.046   2.1e+02      30      50 ..     416     436 ..     391     446 .. 0.82
   5 ?    3.9   0.1     0.011        51       8      52 ..     497     547 ..     492     553 .. 0.76
   6 ?    1.4   0.1     0.071   3.2e+02      34      50 ..     749     765 ..     713     774 .. 0.63
   7 !    7.0   0.1    0.0013       5.7       8      50 ..     827     875 ..     823     883 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0031
                                       EEEEEEEETTE..SSEEEESSTS...EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y   8 llYrYrlegid..keWveasdysq..easytnlppGdYtlkVkakdn 50 
                                       ++Y++ l+g +  + W++ +d s   +  + +   GdY++ V ++d 
  gi|386001048|ref|YP_005919347.1|  69 ISYKFFLKGPStgDAWQQVQDWSAtnFWDWVPAQQGDYEVNVWIRDG 115
                                       789999999998889999999988999****************9995 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0031
                                       EEEEEEEETTE..SSEEEESSTS...EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y   8 llYrYrlegid..keWveasdysq..easytnlppGdYtlkVkakdn 50 
                                       ++Y++ l+g +  + W++ +d s   +  + +   GdY++ V ++d 
  gi|386001048|ref|YP_005919347.1| 176 ISYKFFLKGPStgDAWQQVQDWSAtnFWDWVPAQQGDYEVNVWIRDG 222
                                       789999999998889999999988999****************9995 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0087
                                       CCTTEEEEEEEETTE..SSEEEESSTS.....EEEEES--SEEEEEEEEEEETTS CS
                             Y_Y_Y   4 nperllYrYrlegid..keWveasdysq....easytnlppGdYtlkVkakdndg 52 
                                       +++ + Yr+ l+g    ++Wve ++ s+    + + t+  +G+ ++ V ++d + 
  gi|386001048|ref|YP_005919347.1| 279 DGDTVFYRFFLKGPGtsNNWVEKRGWSNiptwSWTTTPADEGNNQVNVWIRDQNH 333
                                       67889999999975444********9999*77777788889*********99875 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.046
                                       EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y  30 easytnlppGdYtlkVkakdn 50 
                                          +++   GdY++ V ++d 
  gi|386001048|ref|YP_005919347.1| 416 WWDWKPSQQGDYEVNVWIRDG 436
                                       66799999*********9996 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.011
                                       EEEEEEEETTE..SSEEEESSTS.....EEEEES--SEEEEEEEEEEETTS CS
                             Y_Y_Y   8 llYrYrlegid..keWveasdysq....easytnlppGdYtlkVkakdndg 52 
                                       +lYr+++ g +  + W+  +d s+    + s ++ + G+Y + V+++d + 
  gi|386001048|ref|YP_005919347.1| 497 ILYRFWMRGPStgNVWKVVRDWSTsrtwTWSTSPGEIGQYDFCVYVRDGKH 547
                                       6788888888776778777777776656677778889**********9765 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.071
                                       ES--SEEEEEEEEEEET CS
                             Y_Y_Y  34 tnlppGdYtlkVkakdn 50 
                                       t+   G+Y ++V+++d 
  gi|386001048|ref|YP_005919347.1| 749 TPGDVGNYDVYVYVRDG 765
                                       55567*********995 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0013
                                       EEEEEEEETTE..SSEEEESSTS.....EEEEES--SEEEEEEEEEEET CS
                             Y_Y_Y   8 llYrYrlegid..keWveasdysq....easytnlppGdYtlkVkakdn 50 
                                       +lYr++l+g    + W+  +d s+    + +  +  +G+Y l+V+++d 
  gi|386001048|ref|YP_005919347.1| 827 ILYRFWLKGPAtgNAWKVVQDWSTsrawTWTSAPADAGEYSLYVYVRDG 875
                                       7899999998777889999888888844444445668**********95 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4   6.4e+03      30      47 ..     101     115 ..      98     116 .. 0.79
   2 ?   -2.6   0.0       1.4   6.4e+03      30      47 ..     208     222 ..     205     223 .. 0.79
   3 ?   -1.3   0.0      0.58   2.6e+03      33      47 ..     422     436 ..     418     438 .. 0.81
   4 ?    1.2   0.0     0.098   4.4e+02      23      48 ..     522     546 ..     518     547 .. 0.74
   5 ?   -1.0   0.1      0.48   2.1e+03      30      47 ..     639     655 ..     629     656 .. 0.72
   6 ?    0.0   0.1      0.22     1e+03      29      47 ..     750     765 ..     702     767 .. 0.76
   7 ?   -0.2   0.0      0.26   1.2e+03      25      48 ..     854     876 ..     849     877 .. 0.72
   8 !    5.9   0.5    0.0032        14      16      40 ..    1246    1270 ..    1234    1289 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                            He_PIG  30 dqtvapGsytftVtatdg 47 
                                           ++G y + V   dg
  gi|386001048|ref|YP_005919347.1| 101 A---QQGDYEVNVWIRDG 115
                                       4...55*******99987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                            He_PIG  30 dqtvapGsytftVtatdg 47 
                                           ++G y + V   dg
  gi|386001048|ref|YP_005919347.1| 208 A---QQGDYEVNVWIRDG 222
                                       4...55*******99987 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.58
                            He_PIG  33 vapGsytftVtatdg 47 
                                       +++G y + V   dg
  gi|386001048|ref|YP_005919347.1| 422 SQQGDYEVNVWIRDG 436
                                       367*******99998 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.098
                            He_PIG  23 GtitGtpdqtvapGsytftVtatdgs 48 
                                        t t++ +++ + G y+f V + dg 
  gi|386001048|ref|YP_005919347.1| 522 RTWTWSTSPG-EIGQYDFCVYVRDGK 546
                                       5556775555.55*******999985 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.48
                            He_PIG  30 dqtvapGsytftVtatdg 47 
                                        ++  +G y++ V + dg
  gi|386001048|ref|YP_005919347.1| 639 HPG-DAGPYDVYVYVRDG 655
                                       333.23*******99997 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 0.22
                            He_PIG  29 pdqtvapGsytftVtatdg 47 
                                       p      G y++ V + dg
  gi|386001048|ref|YP_005919347.1| 750 PGDV---GNYDVYVYVRDG 765
                                       3333...999999999998 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 0.26
                            He_PIG  25 itGtpdqtvapGsytftVtatdgs 48 
                                        t+t  ++  +G+y+  V + dg 
  gi|386001048|ref|YP_005919347.1| 854 WTWTSAPA-DAGEYSLYVYVRDGK 876
                                       57884444.33********99985 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.0032
                            He_PIG   16 LtLdsstGtitGtpdqtvapGsytf 40  
                                        Lt ++++ ++tG+    v +Gsy+ 
  gi|386001048|ref|YP_005919347.1| 1246 LTWNPADAHLTGSTLRKVSTGSYSL 1270
                                        7889999999999999999999986 PP

>> EB1_binding  EB-1 Binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.9    0.0044        20      99     124 ..       8      33 ..       5      67 .. 0.76
   2 ?    5.5   1.0    0.0051        23      99     124 ..     115     140 ..     112     172 .. 0.78
   3 ?    5.0   0.1    0.0074        33      99     121 ..     222     244 ..     219     267 .. 0.92
   4 ?    3.9   0.3     0.016        73      99     123 ..     436     460 ..     433     481 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0044
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       EB1_binding  99 skhsspsGavaarvtpfnynpsprks 124
                                        kh++p    a +vtpf  np+p   
  gi|386001048|ref|YP_005919347.1|   8 GKHAAPDSWDAFKVTPFKVNPAPAAN 33 
                                       69*******************99754 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0051
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       EB1_binding  99 skhsspsGavaarvtpfnynpsprks 124
                                        kh++p    a +vtpf  np+p   
  gi|386001048|ref|YP_005919347.1| 115 GKHAAPDSWDAFKVTPFKVNPAPAAN 140
                                       69*******************99754 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0074
                                       XXXXXXXXXXXXXXXXXXXXXXX CS
                       EB1_binding  99 skhsspsGavaarvtpfnynpsp 121
                                        kh++p    a +vtpf  np+p
  gi|386001048|ref|YP_005919347.1| 222 GKHAAPDSWDAFKVTPFKVNPAP 244
                                       69*******************98 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                       EB1_binding  99 skhsspsGavaarvtpfnynpsprk 123
                                        kh+ p    a ++tpf  np+p  
  gi|386001048|ref|YP_005919347.1| 436 GKHAGPDSWDAYKITPFKVNPAPTP 460
                                       69*******************9864 PP

>> CBM_20  Starch binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0032        14      45      83 ..      52      90 ..      39      96 .. 0.83
   2 ?    5.6   0.0    0.0033        15      46      83 ..     160     197 ..     146     203 .. 0.83
   3 ?   -2.4   0.1         1   4.7e+03      44      79 ..     265     300 ..     252     316 .. 0.73
   4 ?   -2.4   0.1      0.99   4.4e+03      49      79 ..     376     407 ..     367     416 .. 0.73
   5 ?   -2.2   0.0      0.86   3.9e+03      49      78 ..     484     513 ..     478     523 .. 0.84
   6 ?    1.3   0.0     0.074   3.3e+02      45      79 ..     700     734 ..     689     744 .. 0.81
   7 ?    0.6   0.1      0.12   5.3e+02      44      79 ..     809     844 ..     794     857 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0032
                            CBM_20 45 ssyplWsttvslpagtkieYkyikkdsdgsvtWesgenr 83
                                      ++   W++++s p g  i+Yk+  k  +    W++ ++ 
  gi|386001048|ref|YP_005919347.1| 52 GTPIKWTAAASDPDGDPISYKFFLKGPSTGDAWQQVQDW 90
                                      45557***********************999**997765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0033
                            CBM_20  46 syplWsttvslpagtkieYkyikkdsdgsvtWesgenr 83 
                                       +   W++++s p g  i+Yk+  k  +    W++ ++ 
  gi|386001048|ref|YP_005919347.1| 160 TPIKWTAAASDPDGDPISYKFFLKGPSTGDAWQQVQDW 197
                                       4557***********************999**997765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1
                            CBM_20  44 tssyplWsttvslpagtkieYkyikkdsdgsvtWes 79 
                                       +++  +W+++ +   g ++ Y++  k    s  W +
  gi|386001048|ref|YP_005919347.1| 265 AGTTVVWTASSTDTDGDTVFYRFFLKGPGTSNNWVE 300
                                       456778888888888889999999999988888865 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.99
                            CBM_20  49 lWsttv.slpagtkieYkyikkdsdgsvtWes 79 
                                        W++++ + + g  +++k+  +  +    We 
  gi|386001048|ref|YP_005919347.1| 376 RWTADAtDPNPGDVVQFKFHLRGPSTGGAWEV 407
                                       6888662445599999**99999888888886 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 0.86
                            CBM_20  49 lWsttvslpagtkieYkyikkdsdgsvtWe 78 
                                       +W++t+s p g  i Y++  +  +   +W+
  gi|386001048|ref|YP_005919347.1| 484 TWTATASDPDGDPILYRFWMRGPSTGNVWK 513
                                       79***************9998888777776 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.074
                            CBM_20  45 ssyplWsttvslpagtkieYkyikkdsdgsvtWes 79 
                                       +   +W++t+s p g  i Yk+  +       W+ 
  gi|386001048|ref|YP_005919347.1| 700 GARITWTATASDPDGDPILYKFWLRGPATGNAWKV 734
                                       45679*****************9988877777765 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.12
                            CBM_20  44 tssyplWsttvslpagtkieYkyikkdsdgsvtWes 79 
                                       ++s  +W++t+s p+g  i Y++  k       W+ 
  gi|386001048|ref|YP_005919347.1| 809 AGSTIVWTATASDPEGDPILYRFWLKGPATGNAWKV 844
                                       467889*****************9999888777865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 8536.16
//
Query:       gi|386001049|ref|YP_005919348.1|  [L=338]
Description: Cna B domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-10   42.0  12.4     0.0023   18.7   1.0    3.3  3  Big_9       Bacterial Ig domain
    0.00045   20.8   9.5       0.72   10.5   0.2    3.4  3  Cadherin_4  Bacterial cadherin-like domain
     0.0054   16.6   0.0         12    5.8   0.0    3.3  3  CBM_20      Starch binding domain
     0.0085   16.0   0.0       0.17   11.8   0.1    2.7  3  Y_Y_Y       Y_Y_Y domain
  ------ inclusion threshold ------
       0.13   12.3   1.6       0.22   11.5   1.6    1.2  1  DUF2909     Protein of unknown function (DUF2909)


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   2.6e-06    0.0094      11      88 ..      49     132 ..      42     134 .. 0.68
   2 !   18.7   1.0   6.3e-07    0.0023       5      89 ..     149     242 ..     144     243 .. 0.70
   3 !   13.2   0.2   3.1e-05      0.11       6      41 ..     257     299 ..     253     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                             Big_9  11 vndaPvavdds...vtvtedsv....landtdpdgdaltvtsltvtlvtapanGtvtinadgt..ltytpnagfsgt 78 
                                       +n +P+a d +    + +e ++    +a++tdpdgd++++  + +++ ++++  + + + +gt  + +tp+++  g+
  gi|386001049|ref|YP_005919348.1|  49 ANVPPTALDLTpdkGSPQEVGTaikwTASATDPDGDPISYR-FFLKGPSTGDAWQQVQDWSGTnsWDWTPTQD--GS 122
                                       6889999885555566665555677899**********987.5555555544444444445552277777666..99 PP

                             Big_9  79 dsftYtvsDg 88 
                                       +++++ + Dg
  gi|386001049|ref|YP_005919348.1| 123 YEVNVWIRDG 132
                                       9999988887 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6.3e-07
                             Big_9   5 tvtvtp.vndaPvavddsvtvt.edsv......landtdpdgdaltvtsltvtlvta..panGtvtinadgtltytp 71 
                                       +v+ +p  n++Pva++ + + +  +++      +a+++dpdgda+ ++ + +++ ++  +   t   +++ t+t+t 
  gi|386001049|ref|YP_005919348.1| 149 SVNPAPvPNQPPVANSLNPNAAsPQDPgtpiiwTASASDPDGDAILYK-FFLKGPATsnSWAETRGWDPSPTWTWTT 224
                                       444455889999999988444323333456**9***********9655.54443322222233334567778***** PP

                             Big_9  72 nagfsgtdsftYtvsDgs 89 
                                       ++  +g  ++++ v Dg+
  gi|386001049|ref|YP_005919348.1| 225 SPADAGANQVNVWVRDGN 242
                                       ****************97 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 3.1e-05
                             Big_9   6 vtvtpvndaPvavddsvtvt.edsv......landtdpdgdal 41 
                                       + +++ n++Pva++ + + +  +++      +a+++dpdgda+
  gi|386001049|ref|YP_005919348.1| 257 FVINAPNQPPVANSLNPNAAsPQDPgtpiiwTASASDPDGDAI 299
                                       7899**********88444323333456**9**********97 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.2    0.0017       6.1      19      53 ..      61      91 ..      46     125 .. 0.63
   2 !    7.5   0.6    0.0018       6.4       8      48 ..     151     193 ..     144     236 .. 0.66
   3 !   10.5   0.2    0.0002      0.72       4      48 ..     256     299 ..     253     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                        Cadherin_4 19 dsatvte.dtpltitagnvlandtDvdgddltvtav 53
                                      d ++  e +t++       +a +tD+dgd++++  +
  gi|386001049|ref|YP_005919348.1| 61 DKGSPQEvGTAI-----KWTASATDPDGDPISYRFF 91
                                      444444422333.....4589*********998654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                        Cadherin_4   8 tgv...ndaPvavdds..atvte..dtpltitagnvlandtDvdgddl 48 
                                       +++   n++Pva+  +  a+ ++  +tp+       +a ++D+dgd++
  gi|386001049|ref|YP_005919348.1| 151 NPApvpNQPPVANSLNpnAASPQdpGTPIIW-----TASASDPDGDAI 193
                                       4433359999999765113444422455544.....89********95 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0002
                        Cadherin_4   4 titvtgvndaPvavdds..atvte..dtpltitagnvlandtDvdgddl 48 
                                       ++ +++ n++Pva+  +  a+ ++  +tp+       +a ++D+dgd++
  gi|386001049|ref|YP_005919348.1| 256 DFVINAPNQPPVANSLNpnAASPQdpGTPIIW-----TASASDPDGDAI 299
                                       6789**********865114444422455555.....89********85 PP

>> CBM_20  Starch binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.01        37      45      82 ..      69     106 ..      53     122 .. 0.85
   2 !    5.8   0.0    0.0035        12      45      79 ..     176     210 ..     161     225 .. 0.84
   3 ?    2.3   0.0     0.043   1.6e+02      45      71 ..     282     308 ..     268     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.01
                            CBM_20  45 ssyplWsttvslpagtkieYkyikkdsdgsvtWesgen 82 
                                       ++   W+++++ p g  i+Y++  k  +    W++ ++
  gi|386001049|ref|YP_005919348.1|  69 GTAIKWTASATDPDGDPISYRFFLKGPSTGDAWQQVQD 106
                                       55668**********************99999998665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0035
                            CBM_20  45 ssyplWsttvslpagtkieYkyikkdsdgsvtWes 79 
                                       ++  +W++++s p g +i Yk+  k    s  W +
  gi|386001049|ref|YP_005919348.1| 176 GTPIIWTASASDPDGDAILYKFFLKGPATSNSWAE 210
                                       45568********************9999999976 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.043
                            CBM_20  45 ssyplWsttvslpagtkieYkyikkds 71 
                                       ++  +W++++s p g +i Yk+  k  
  gi|386001049|ref|YP_005919348.1| 282 GTPIIWTASASDPDGDAILYKFFLKGP 308
                                       45568*****************98765 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 !   11.8   0.1   4.9e-05      0.17       7      49 ..      85     131 ..      81     146 .. 0.85
   2 ?    0.5   0.0      0.17   6.2e+02       5      29 ..     190     216 ..     187     259 .. 0.63
   3 ?   -1.9   0.0      0.94   3.4e+03       5      16 ..     296     307 ..     294     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                                       TEEEEEEEETTE..SSEEEESSTS...EEEEES--SEEEEEEEEEEE CS
                             Y_Y_Y   7 rllYrYrlegid..keWveasdysq..easytnlppGdYtlkVkakd 49 
                                        ++Yr+ l+g +  + W++ +d s   +  +t+   G+Y++ V ++d
  gi|386001049|ref|YP_005919348.1|  85 PISYRFFLKGPStgDAWQQVQDWSGtnSWDWTPTQDGSYEVNVWIRD 131
                                       5899999*9999888999999876679*****************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                       CTTEEEEEEEETTE..SSEEEESSTS. CS
                             Y_Y_Y   5 perllYrYrlegid..keWveasdysq 29 
                                       ++ +lY++ l+g    ++W e+++  +
  gi|386001049|ref|YP_005919348.1| 190 GDAILYKFFLKGPAtsNSWAETRGWDP 216
                                       678899999988543366666655444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.94
                                       CTTEEEEEEEET CS
                             Y_Y_Y   5 perllYrYrleg 16 
                                       ++ +lY++ l+g
  gi|386001049|ref|YP_005919348.1| 296 GDAILYKFFLKG 307
                                       6789****9987 PP

>> DUF2909  Protein of unknown function (DUF2909)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   6.1e-05      0.22      34      56 ..      25      47 ..      23      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.1e-05
                           DUF2909 34 vraLalRVgLSillflllllalk 56
                                      +r La+R++LS+l+f ++l  ++
  gi|386001049|ref|YP_005919348.1| 25 SRTLARRLALSLLIFGMILTSAA 47
                                      689****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2061.87
//
Query:       gi|386001050|ref|YP_005919349.1|  [L=168]
Description: Formaldehyde-activating enzyme, tetrahydromethanopterin-dependent [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-70  236.8   1.4    1.1e-70  236.6   1.4    1.0  1  Fae       Formaldehyde-activating enzyme (Fae)
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.17   11.8   0.0    1.2  1  DUF4291   Domain of unknown function (DUF4291)


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.6   1.4   1.3e-74   1.1e-70       1     158 [.      10     167 ..      10     168 .] 0.99

  Alignments for each domain:
  == domain 1  score: 236.6 bits;  conditional E-value: 1.3e-74
                               Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfG 77 
                                       vGEalvgeg+evAhidl+iG+k+++v++Af+ ala++++ghtpllavl+pnl+ kPatlmvnkvti+n++qa l+fG
  gi|386001050|ref|YP_005919349.1|  10 VGEALVGEGPEVAHIDLVIGRKGSAVEDAFVAALASPRMGHTPLLAVLEPNLIPKPATLMVNKVTITNATQALLIFG 86 
                                       8**************************************************************************** PP

                               Fae  78 paQaavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdka 154
                                       paQaavakav+d+v+eg+ip+++a+dl+iivsvf++++a+dkkk+ +yny+AtklAi+rA+k+eP+++e l++kd+a
  gi|386001050|ref|YP_005919349.1|  87 PAQAAVAKAVMDSVAEGTIPEADAEDLLIIVSVFLQWDAEDKKKVADYNYRATKLAIERAMKGEPTVKEALARKDSA 163
                                       ***************************************************************************** PP

                               Fae 155 khpf 158
                                       khpf
  gi|386001050|ref|YP_005919349.1| 164 KHPF 167
                                       ***9 PP

>> DUF4291  Domain of unknown function (DUF4291)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17      99     137 ..     109     147 ..      77     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                           DUF4291  99 ewkkelkkskvrvQWdperdlrleklekrsiqiGlkgel 137
                                       + ++ l   +v +QWd e + +++  ++r+ ++ +++++
  gi|386001050|ref|YP_005919349.1| 109 DAEDLLIIVSVFLQWDAEDKKKVADYNYRATKLAIERAM 147
                                       445555566899*********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1026.67
//
Query:       gi|386001051|ref|YP_005919350.1|  [L=235]
Description: flavoprotein [Methanosaeta harundinacea 6Ac]
Scores for 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-15   55.1   0.0    3.4e-14   52.9   0.0    1.8  2  Flavoprotein  Flavoprotein
    5.7e-09   35.4  13.2    5.5e-06   26.0   1.4    3.3  2  Fer4          4Fe-4S binding domain
    1.7e-07   30.9  12.2    0.00085   19.3   1.1    2.5  2  Fer4_2        4Fe-4S binding domain
    3.6e-07   30.7   4.6     0.0082   16.7   0.2    2.3  2  Fer4_7        4Fe-4S dicluster domain
    1.7e-06   28.1   4.0      0.026   14.7   0.7    2.3  2  Fer4_9        4Fe-4S dicluster domain
    0.00012   22.9   6.5      0.008   17.1   0.2    2.4  2  Fer4_16       4Fe-4S double cluster binding domain
    0.00016   22.2   3.2       0.14   12.7   0.3    2.3  2  Fer4_17       4Fe-4S dicluster domain
    0.00034   20.6  10.1      0.028   14.5   0.6    2.4  2  Fer4_10       4Fe-4S dicluster domain
     0.0015   18.5  13.8      0.022   14.8   3.9    2.8  2  Fer4_6        4Fe-4S binding domain
  ------ inclusion threshold ------
       0.21   11.8  11.0        3.7    7.8  11.0    2.3  1  Fer4_21       4Fe-4S dicluster domain
        1.3    9.8  12.0          2    9.2   0.3    3.4  3  Fer4_15       4Fe-4S single cluster domain
        2.4    8.9  14.2        1.1    9.9   2.1    2.8  2  Fer4_4        4Fe-4S binding domain
        3.1    8.3  10.5        2.9    8.4   0.8    2.4  2  Fer4_8        4Fe-4S dicluster domain
        6.9    7.3  11.4        4.8    7.8   0.7    2.9  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
        9.2    7.5  15.6        6.7    7.9   4.8    3.3  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   2.9e-17   3.4e-14       1     106 [.       2     128 ..       2     141 .. 0.82
   2 ?   -0.3   0.0      0.67     8e+02     113     133 ..     197     219 ..     193     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.9e-17
                                       EEEEEEE-SSCGGGCH.HHHHHHHHHTTEEEEEEESCHHHHCCHHG....GS....TCSSHHHHHHCT......... CS
                      Flavoprotein   1 kkillgiTGsvaaika.lellekLkkegievqvvltkaAkkfiske....klklaaredpilhielrr......... 63 
                                       k++++++TG+ + + + +  + k+ + + +v  ++++a++++++      +lk  + ++ ++++ l+r         
  gi|386001051|ref|YP_005919350.1|   2 KNVAWAVTGAGHYLAEsVAAMGKISQ-KNRVCTFVSEAGEEVLRMYglfdRLKEISGGGYLEEVFLEReegssspka 77 
                                       689********999887777777776.99***************776655555555667777777766788888888 PP

                                       ......TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE CS
                      Flavoprotein  64 ......wadllviaPasantlakianGiadnlltlilra..takkpiliaP 106
                                             ++dll++aPa+ant+aki++Giad+l t+ + +  +a +p +++P
  gi|386001051|ref|YP_005919350.1|  78 grfmmnKFDLLIVAPATANTVAKIVCGIADTLPTNAAALanKAAVPLYVLP 128
                                       999999*****************************9944477778888888 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.67
                                       CTCSTCHHHHHHH.H.T...... CS
                      Flavoprotein 113 yenpqtlknlekl.e.egvtvik 133
                                        ++p + +n+e+l + +gvtv+ 
  gi|386001051|ref|YP_005919350.1| 197 ASRPLDRENIERLgRiPGVTVLA 219
                                       578999*******9899999985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   4.5   0.00013      0.16       2      23 ..     142     165 ..     141     166 .. 0.87
   2 !   26.0   1.4   4.6e-09   5.5e-06       2      24 .]     168     190 ..     167     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                       EEETTTSSS-THHHH..HSTTTEE CS
                              Fer4   2 videekCigCGaCve..vCPvgAI 23 
                                       +id ++C +C aC+   +CP gAI
  gi|386001051|ref|YP_005919350.1| 142 TIDRDLCLRCEACEPraACPRGAI 165
                                       79***********95449999998 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 4.6e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       +id  +C gCG+C   CP gAI+
  gi|386001051|ref|YP_005919350.1| 168 QIDLLRCDGCGICRGLCPQGAIR 190
                                       69999*****************6 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   4.1   7.4e-06    0.0088       1      21 [.     139     161 ..     139     162 .. 0.88
   2 !   19.3   1.1   7.1e-07   0.00085       4      22 .]     168     186 ..     167     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.4e-06
                            Fer4_2   1 apvvvdtdrCigCgaC..vsaCP 21 
                                       +p+ +d+d C++C+aC  + aCP
  gi|386001051|ref|YP_005919350.1| 139 PPFTIDRDLCLRCEACepRAACP 161
                                       5799************66699*9 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.1e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       ++d  rC gCg+C+  CP+
  gi|386001051|ref|YP_005919350.1| 168 QIDLLRCDGCGICRGLCPQ 186
                                       58999*************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   1.7e-05      0.02      16      52 .]     126     164 ..     100     164 .. 0.74
   2 !   16.7   0.2   6.8e-06    0.0082       1      20 [.     173     192 ..     173     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                            Fer4_7  16 aieldeeenekgtekveidpekClgCgaCva..vCPtga 52 
                                       ++ +d  e++++ +  +id + Cl C+aC+   +CP ga
  gi|386001051|ref|YP_005919350.1| 126 VLPTDVLERAETEPPFTIDRDLCLRCEACEPraACPRGA 164
                                       4444445555566778*************97669**997 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.8e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaield 20 
                                       rC gCg C   Cp++ai+  
  gi|386001051|ref|YP_005919350.1| 173 RCDGCGICRGLCPQGAIRRG 192
                                       8***************9965 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.8e-05     0.033      33      51 .]     141     165 ..     108     165 .. 0.76
   2 !   14.7   0.7   2.1e-05     0.026      35      51 .]     173     189 ..     166     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                            Fer4_9  33 e....eaCigCgaCv..eaCpkgai 51 
                                            + C+ C+aC+  +aCp+gai
  gi|386001051|ref|YP_005919350.1| 141 FtidrDLCLRCEACEprAACPRGAI 165
                                       0333358*******9889****997 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                            Fer4_9  35 aCigCgaCveaCpkgai 51 
                                       +C gCg C   Cp+gai
  gi|386001051|ref|YP_005919350.1| 173 RCDGCGICRGLCPQGAI 189
                                       69999999999999886 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.8    0.0045       5.4       2      20 ..     148     168 ..     147     171 .. 0.84
   2 !   17.1   0.2   6.7e-06     0.008       1      24 [.     173     195 ..     173     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                           Fer4_16   2 CgtCgkCa..evCPtnaikek 20 
                                       C +C++C    +CP +ai e+
  gi|386001051|ref|YP_005919350.1| 148 CLRCEACEprAACPRGAIGEQ 168
                                       99*****63379******987 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.7e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       rC +Cg C   CP++ai+   + +
  gi|386001051|ref|YP_005919350.1| 173 RCDGCGICRGLCPQGAIRRG-AIS 195
                                       6****************988.333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2   0.00088       1.1      33      59 ..     131     163 ..     102     165 .. 0.62
   2 !   12.7   0.3   0.00012      0.14       1      19 [.     173     191 ..     173     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                           Fer4_17  33 lleeaeke....ekaslCieCgeCe..rkCPqg 59 
                                        le+ae+e       +lC+ C+ Ce  ++CP g
  gi|386001051|ref|YP_005919350.1| 131 VLERAETEppftIDRDLCLRCEACEprAACPRG 163
                                       555555554332245789999999877788865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                           Fer4_17   1 rCiqCgyClpeCpsyeayd 19 
                                       rC +Cg C+  Cp++++++
  gi|386001051|ref|YP_005919350.1| 173 RCDGCGICRGLCPQGAIRR 191
                                       699*********9987754 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.9   0.00034       0.4       4      21 ..     143     162 ..     141     170 .. 0.77
   2 !   14.5   0.6   2.4e-05     0.028       4      26 ..     169     191 ..     166     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                           Fer4_10   4 idddtCirCgkCvk..aCPa 21 
                                       id+d C+rC++C    aCP 
  gi|386001051|ref|YP_005919350.1| 143 IDRDLCLRCEACEPraACPR 162
                                       89**********75448**8 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                           Fer4_10   4 idddtCirCgkCvkaCPadltsv 26 
                                       id  +C +Cg C+  CP+ + + 
  gi|386001051|ref|YP_005919350.1| 169 IDLLRCDGCGICRGLCPQGAIRR 191
                                       78899*************65333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.9   1.8e-05     0.022       3      24 .]     142     165 ..     140     165 .. 0.85
   2 !    8.5   2.3    0.0018       2.2       4      24 .]     169     189 ..     168     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                            Fer4_6   3 eidpdkCigCgdC..vrvCPegai 24 
                                       +id+d+C+ C++C   ++CP gai
  gi|386001051|ref|YP_005919350.1| 142 TIDRDLCLRCEACepRAACPRGAI 165
                                       8************54477999997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       id  +C+gCg C   CP gai
  gi|386001051|ref|YP_005919350.1| 169 IDLLRCDGCGICRGLCPQGAI 189
                                       56669*******777777776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.0    0.0031       3.7       2      58 ..     142     190 ..     141     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                           Fer4_21   2 ridedkCigCgkCl..iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +id+d C+ C+ C    aC+     ai  +      +   +C GC +C   CP +++i+
  gi|386001051|ref|YP_005919350.1| 142 TIDRDLCLRCEACEprAACPR---GAIGEQ------IDLLRCDGCGICRGLCP-QGAIR 190
                                       59***********63378994...566433......34458************.68885 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.5     0.035        42       2      15 ..     142     155 ..     141     159 .. 0.87
   2 ?    0.5   0.1       0.9   1.1e+03      57      64 ..     158     165 ..     155     166 .. 0.90
   3 ?    9.2   0.3    0.0016         2       3      20 ..     169     186 ..     168     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.035
                           Fer4_15   2 vvDrdaCigcglCv 15 
                                       ++Drd+C  c++C 
  gi|386001051|ref|YP_005919350.1| 142 TIDRDLCLRCEACE 155
                                       79***********6 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.9
                           Fer4_15  57 raCPvdAI 64 
                                       +aCP +AI
  gi|386001051|ref|YP_005919350.1| 158 AACPRGAI 165
                                       79*****9 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +D  +C+gcg C  ++p+
  gi|386001051|ref|YP_005919350.1| 169 IDLLRCDGCGICRGLCPQ 186
                                       7889*********99985 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   4.6      0.11   1.3e+02       2      11 ..     146     155 ..     144     163 .. 0.74
   2 ?    9.9   2.1   0.00093       1.1       3      17 .]     173     187 ..     171     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                            Fer4_4   2 erCigCgsCv 11 
                                       + C++C +C+
  gi|386001051|ref|YP_005919350.1| 146 DLCLRCEACE 155
                                       67*******8 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00093
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       rC gCg C+  CPqg
  gi|386001051|ref|YP_005919350.1| 173 RCDGCGICRGLCPQG 187
                                       8************96 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.1     0.067        80       5      16 ..     148     161 ..     144     168 .. 0.79
   2 ?    8.4   0.8    0.0024       2.9       2      17 ..     171     186 ..     170     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.067
                            Fer4_8   5 CieCgaCq..saCp 16 
                                       C +C+aC+  +aCp
  gi|386001051|ref|YP_005919350.1| 148 CLRCEACEprAACP 161
                                       88999998777787 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0024
                            Fer4_8   2 lekCieCgaCqsaCpv 17 
                                       l +C +Cg C+  Cp 
  gi|386001051|ref|YP_005919350.1| 171 LLRCDGCGICRGLCPQ 186
                                       5678888888888882 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   3.8       0.1   1.2e+02       1      17 [.     143     161 ..     143     163 .. 0.79
   2 ?   -0.6   0.1       1.6     2e+03      49      57 ..     158     166 ..     155     166 .. 0.85
   3 ?    7.8   0.7    0.0041       4.8       1      18 [.     169     186 ..     169     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                           Fer4_13   1 VDrdtCiacgaC..velaP 17 
                                       +Drd C  c+aC  ++++P
  gi|386001051|ref|YP_005919350.1| 143 IDRDLCLRCEACepRAACP 161
                                       8***********4445555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                           Fer4_13  49 daCPvesIg 57 
                                       +aCP  +Ig
  gi|386001051|ref|YP_005919350.1| 158 AACPRGAIG 166
                                       79***9996 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0041
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D  +C +cg+C+ l+P+
  gi|386001051|ref|YP_005919350.1| 169 IDLLRCDGCGICRGLCPQ 186
                                       67779************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.1      0.26   3.1e+02       1      15 []     148     164 ..     148     164 .. 0.70
   2 ?    7.9   4.8    0.0056       6.7       1      15 []     174     188 ..     174     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.26
                            Fer4_3   1 CtgCgaCv..evCPvgA 15 
                                       C+ C+aC+   +CP gA
  gi|386001051|ref|YP_005919350.1| 148 CLRCEACEprAACPRGA 164
                                       88899997334788776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg C   CP gA
  gi|386001051|ref|YP_005919350.1| 174 CDGCGICRGLCPQGA 188
                                       *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1465.50
//
Query:       gi|386001052|ref|YP_005919351.1|  [L=181]
Description: GMP synthase subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-34  118.5   0.0    3.2e-34  118.4   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.6e-14   53.0   0.9    3.7e-13   49.7   0.4    2.5  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.048   13.2   0.5       0.18   11.4   0.5    1.9  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.0   5.3e-38   3.2e-34       2     187 ..       5     176 ..       4     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 5.3e-38
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                       +++ny ++++ ++++++ l     ++ ++++aeei     ++dg+++ gGp    ++ + e +++    +iPiLGIC
  gi|386001052|ref|YP_005919351.1|   5 VVNNYGQFNHLIHRSIRDLV-PARMISNQTPAEEI-----EADGLILGGGPTLERAGRCSEYLTR---LEIPILGIC 72 
                                       899*******9999999886.9999999*******.....69*********99998888777776...679****** PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       LG+Q++a+ fg+ v+k    ++   + ++ + e ++l+gl ++++++ +H + v     +p +++v+a+se  +e++
  gi|386001052|ref|YP_005919351.1|  73 LGLQVMAETFGGRVEKGAVGGYAEVEVEVLE-EDDILKGLAPRIKTWASHADQVVS---LPPDFRVLARSEV-CEIE 144
                                       ******************9999999999999.67*********************9...***********55.79** PP

                                       EEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 156 eiiekknpfvgvQFHPEststpegpellfnfl 187
                                       ++ +kk+p++gvQ+HPE+++t++g +ll+nfl
  gi|386001052|ref|YP_005919351.1| 145 AMGHKKRPLYGVQWHPEVVHTEGGIKLLENFL 176
                                       ******************************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.18   1.1e+03      59      71 ..      40      52 ..      22      55 .. 0.81
   2 !   49.7   0.4   6.3e-17   3.7e-13     103     216 .]      63     161 ..      57     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                     Peptidase_C26 59 ldgllltGgqdve 71
                                       dgl+l Gg+++e
  gi|386001052|ref|YP_005919351.1| 40 ADGLILGGGPTLE 52
                                      69*******9875 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 6.3e-17
                     Peptidase_C26 103 ergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavk.vekgsllaellgseeievnslHhqai 178
                                       + ++PilgiC+Glq+++ ++GG++ + +    g+           + +v+ +e++ +l+ l+   +i++   H   +
  gi|386001052|ref|YP_005919351.1|  63 RLEIPILGICLGLQVMAETFGGRVEKGAVG--GYA----------EVEVEvLEEDDILKGLAP--RIKTWASHADQV 125
                                       5689*******************9888774..222..........223331679999999998..9999******** PP

                     Peptidase_C26 179 kelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                         l +++rv A++e   iEa+ ++++  +++gvQwHPE
  gi|386001052|ref|YP_005919351.1| 126 VSLPPDFRVLARSEVCEIEAMGHKKR--PLYGVQWHPE 161
                                       **********************9994..6********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   3.1e-05      0.18      33      94 ..      34      84 ..       2     103 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                          GATase_3 33 kdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeied 94
                                      + e++  +ad +il+Gg + +++          e +++    ++p+lgiC Glq++ e++  
  gi|386001052|ref|YP_005919351.1| 34 PAEEI--EADGLILGGGPTLERAGR------CSEYLTR---LEIPILGICLGLQVMAETFGG 84
                                      33333..489999999876544444......4444555...579************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1127.49
//
Query:       gi|386001053|ref|YP_005919352.1|  [L=227]
Description: hypothetical protein Mhar_0342 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-09   38.7   0.8    4.3e-09   36.9   0.9    1.8  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.9   2.4e-13   4.3e-09       2      72 ..      46     135 ..      45     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.4e-13
                          CxxCxxCC   2 CkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak......................adgrCvfldeetk 54 
                                       C++Cg+CC+  e++v + + +++ + a e+    e++ ++a                       ++ +C++++e+  
  gi|386001053|ref|YP_005919352.1|  46 CRRCGDCCRgeENSVVVFPFEIRVIIADET---GESWLEVAGppeegewdcegnfhtlewrlrkTGRDCRYYSEN-- 117
                                       *********877788888899888888877...4444444445568999999***********999*********.. PP

                          CxxCxxCC  55 lCkiYeeRpkicrlfpas 72 
                                        C+iY  Rp+ c ++p+ 
  gi|386001053|ref|YP_005919352.1| 118 GCRIYGARPLLCTTYPFY 135
                                       8***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1348.53
//
Query:       gi|386001054|ref|YP_005919353.1|  [L=382]
Description: Pentapeptide repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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  107.4  26.3      1e-11   44.2   1.5    4.7  4  Pentapeptide    Pentapeptide repeats (8 copies)
    6.1e-10   39.1   0.0    1.6e-05   25.0   0.0    2.8  2  Pentapeptide_4  Pentapeptide repeats (9 copies)
    7.9e-10   38.7   0.0     0.0081   16.3   0.0    4.3  4  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   2.3   4.5e-13   2.7e-09       2      40 .]      35      73 ..      35      73 .. 0.94
   2 !   44.2   1.5   1.7e-15     1e-11       5      39 ..      58      92 ..      57      92 .. 0.95
   3 !   31.1   2.0   2.2e-11   1.3e-07       1      38 [.      84     121 ..      84     123 .. 0.92
   4 !   33.0   0.3   5.7e-12   3.4e-08       1      37 [.     124     160 ..     124     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.5e-13
                                      B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide  2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40
                                      +LsgAnLsganLsga l ++   gAnlsgA+Ls+a L g
  gi|386001054|ref|YP_005919353.1| 35 DLSGANLSGANLSGAWLFNTHVVGANLSGANLSEAQLGG 73
                                      79********************************98865 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 1.7e-15
                                      T-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide  5 gAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39
                                      gAnLsganLs+a l gAnL+gAnls+A+L++a L+
  gi|386001054|ref|YP_005919353.1| 58 GANLSGANLSEAQLGGANLIGANLSKANLRRAYLR 92
                                      8*******************************997 PP

  == domain 3  score: 31.1 bits;  conditional E-value: 2.2e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       AnL++A+L+ a+Ls+a+++ A+L++++l++A+L  ++L
  gi|386001054|ref|YP_005919353.1|  84 ANLRRAYLRFADLSDADMNAADLSKSDLIFAKLFLTKL 121
                                       9*******************************976666 PP

  == domain 4  score: 33.0 bits;  conditional E-value: 5.7e-12
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsgan 37 
                                       A+Ls A L +a+L++a+l+ A+L++Anl+gA+L  ++
  gi|386001054|ref|YP_005919353.1| 124 AILSKAALMEASLREADLEFADLSEANLEGAQLVKTR 160
                                       7899999999999999999999999999999997765 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.7e-09   1.6e-05       6      64 ..      54     112 ..      49     124 .. 0.90
   2 !   11.3   0.0     5e-05       0.3      10      56 ..     123     169 ..     114     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.7e-09
                    Pentapeptide_4   6 csfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlk 64 
                                        +  +++ls++n+sea+l ++n+ +++ls +n++++ l+ +d++++d++ a +s ++l 
  gi|386001054|ref|YP_005919353.1|  54 THVVGANLSGANLSEAQLGGANLIGANLSKANLRRAYLRFADLSDADMNAADLSKSDLI 112
                                       577899*************************************************9985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5e-05
                    Pentapeptide_4  10 ncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkra 56 
                                       +++ls++ + ea lr+++++ ++ls++n++ ++l +++++++ +++ 
  gi|386001054|ref|YP_005919353.1| 123 GAILSKAALMEASLREADLEFADLSEANLEGAQLVKTRVEGALFTNC 169
                                       55666666666666666666666666666666666666666666654 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   2.2e-05      0.13       2      38 ..      37      76 ..      33      82 .. 0.44
   2 !   16.3   0.0   1.4e-06    0.0081       2      45 ..      67     107 ..      57     110 .. 0.56
   3 !    9.7   0.0   0.00015      0.91      19      45 ..     133     157 ..     118     170 .. 0.49
   4 !    9.2   0.0   0.00022       1.3       2      29 ..     147     173 ..     146     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                    Pentapeptide_3  2 sganFsgaadFr.....gatFsgaasFsnadFgsadFsgarF 38
                                      sgan+sga +++     +++  ga + s+a++++a + ga+ 
  gi|386001054|ref|YP_005919353.1| 37 SGANLSGA-NLSgawlfNTHVVGA-NLSGANLSEAQLGGANL 76
                                      44444444.444333334444444.44444444444444444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.4e-06
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                                       s+a++ ga ++ ga+ s+a + ++a ++ ad+s+a ++ ++d+s
  gi|386001054|ref|YP_005919353.1|  67 SEAQLGGA-NLIGANLSKA-NLRRAYLRFADLSDADMN-AADLS 107
                                       44444455.5555555555.566666666666666666.66665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00015
                    Pentapeptide_3  19 gaasFsnadFgsadFsgarFtgdvdFs 45 
                                        a s ++ad++ ad+s+a+ + ++++ 
  gi|386001054|ref|YP_005919353.1| 133 EA-SLREADLEFADLSEANLE-GAQLV 157
                                       34.455555555555555554.44333 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00022
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadF.g 29 
                                       s+an++ga ++ +++ +ga  F+n++  g
  gi|386001054|ref|YP_005919353.1| 147 SEANLEGA-QLVKTRVEGAL-FTNCRVyG 173
                                       899*****.**********6.****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2287.98
//
Query:       gi|386001055|ref|YP_005919354.1|  [L=79]
Description: hypothetical protein Mhar_0344 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0001   21.8   0.0    0.00013   21.5   0.0    1.1  1  Hfq       Hfq protein


Domain annotation for each model (and alignments):
>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.2e-09   0.00013      14      57 ..      26      70 ..      21      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.2e-09
                                      -EEEEEETTS-EEEEEEEEE-SSEEEEE.ETTEEEEEEGGGEEEE CS
                               Hfq 14 ipvtifLvnGiklkGviksfDnftvlLe.sdgkqqlvYKhaisti 57
                                       +vti L+ G  l  ++++  n+ +lL+  +gk ++v+Khai t+
  gi|386001055|ref|YP_005919354.1| 26 QKVTIRLLDGRPLIAKLEAQNNYELLLDlGKGKKMIVFKHAIGTL 70
                                      68*************************83566788*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 545.55
//
Query:       gi|386001056|ref|YP_005919355.1|  [L=246]
Description: tRNA(His)-5'-guanylyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.5   0.0    2.2e-16   60.0   0.0    1.2  1  Thg1      tRNAHis guanylyltransferase
    1.8e-06   28.1   0.0    2.4e-06   27.7   0.0    1.2  1  Thg1C     Thg1 C terminal domain


Domain annotation for each model (and alignments):
>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   2.5e-20   2.2e-16      12     110 ..      13     108 ..       4     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.5e-20
                              Thg1  12 kllpntlivvRiDGrgFhkfskkhkfekPnDeralklmneaakelvkefe.divlaYgqSDEislvlsketklynrr 87 
                                       +l  + ++vvR DGrgF k+ +  k +kP+D +++++m +aa+++v+     + +a+++SDE+sl++ ++   +n+r
  gi|386001056|ref|YP_005919355.1|  13 DLRVRAPLVVRADGRGFGKLLR--KANKPYDLEFARAMATAARAFVEGSGlAPAIAFTFSDEVSLLFGEAP--FNGR 85 
                                       56778899**************..99********************998669*****************99..**** PP

                              Thg1  88 aqklvslvaslftaafvkllska 110
                                        +k+ s+va+ ++      l ka
  gi|386001056|ref|YP_005919355.1|  86 LEKIDSVVAGSLSGLLSIGLGKA 108
                                       *********99987766666665 PP

>> Thg1C  Thg1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   2.7e-10   2.4e-06       2      78 ..     122     196 ..     121     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.7e-10
                             Thg1C   2 nlrDYlsWRqvDchinnlYNttFWalvqkgglteqeaeeeLkgtlskdkneiLfsefginYnnepeifrkGsvlvre 78 
                                       ++ +Y++ Rq ++  n ++   F+alv  +g  ++ea  +L+g   ++ +e+Lf++ g n ++ p+  r+G  + r 
  gi|386001056|ref|YP_005919355.1| 122 EVVEYFAARQDEAWRNHVFSSGFYALV-AEGFAPREAMGRLRGMKEAEIHEMLFRR-GANLAKSPAWQRRGILIRRV 196
                                       6889***********************.79************************76.99********9999766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1634.96
//
Query:       gi|386001057|ref|YP_005919356.1|  [L=88]
Description: PRC-barrel domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-12   47.9   1.6    1.2e-12   47.7   1.6    1.2  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   1.6   6.9e-17   1.2e-12       3      73 ..       2      73 ..       1      86 [. 0.95

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 6.9e-17
                                      ECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEET CS
                               PRC  3 efrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivd 73
                                      +++++ l +++Vyt  G  +G+V Dvv+d++ g+v +l ++  ++ ++  +++ ++iP++  v +++d+ii +
  gi|386001057|ref|YP_005919356.1|  2 QIEITALLDQDVYTQRGIFVGRVDDVVLDPDVGEVSGLALGNVNRSFLdlKGRGIIIPYR-GVTAVGDIIITK 73
                                      5778999*************************************9888************.*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 646.09
//
Query:       gi|386001058|ref|YP_005919357.1|  [L=439]
Description: Cna B domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-09   37.9  11.5      0.022   15.5   0.2    4.4  4  Big_9            Bacterial Ig domain
  ------ inclusion threshold ------
       0.27   11.0   1.7         24    4.7   0.1    2.6  2  T2SS-T3SS_pil_N  Pilus formation protein N terminal region


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.52   4.7e+03      51      69 ..      43      62 ..      35      82 .. 0.57
   2 !   15.5   0.2   2.4e-06     0.022      12      89 ..     119     204 ..     116     205 .. 0.71
   3 !   15.1   0.4   3.3e-06     0.029       3      89 ..     218     312 ..     216     313 .. 0.68
   4 !   12.1   0.1   2.9e-05      0.26      10      89 ..     331     420 ..     325     421 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.52
                             Big_9 51 vtapanGtvtinadgt.lty 69
                                      ++a a G +ti ++g+  ty
  gi|386001058|ref|YP_005919357.1| 43 SSANAAGIATIQSTGSgMTY 62
                                      34455555555555543333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.4e-06
                             Big_9  12 ndaPvavddsvtvt....edsv...landtdpdgdaltvtsltvtlvtapanGtvtinadgt.....ltytpnagfs 76 
                                       n++Pva+d   +v+    ++++   +a +tdpdgda+ ++ + ++   +p+ G +  + +g      +t+  +++ +
  gi|386001058|ref|YP_005919357.1| 119 NQQPVATDLYPNVAgpapAGTAvtwTAMATDPDGDAILYK-FWLK---GPSTGWAWKDMTGWtasnrWTWRTAPSDA 191
                                       999*****8866665565555567799*********9654.4333...3333333333333334444********** PP

                             Big_9  77 gtdsftYtvsDgs 89 
                                       gt s+ ++v+Dg+
  gi|386001058|ref|YP_005919357.1| 192 GTSSVCVSVKDGR 204
                                       ***********96 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.3e-06
                             Big_9   3 tvtvtvtpvndaPvavdds.......vtvtedsv..landtdpdgdaltvtsltvtlvtapanGtvtinadgt.... 66 
                                       ++tv    +n +P+a+  s       +     sv  +a++tdpdgd++ +  + ++   +p+ G +    +g     
  gi|386001058|ref|YP_005919357.1| 218 EFTVALPRTNGPPTATGLSpsrgspaLP--GASVtwTATATDPDGDQIFYR-FWLK---GPSTGDAWREMTGWtasn 288
                                       677777789********99777653333..33335599*********9654.4333...333333333323333333 PP

                             Big_9  67 .ltytpnagfsgtdsftYtvsDgs 89 
                                        +t++ +a+ +gt ++++ + Dg+
  gi|386001058|ref|YP_005919357.1| 289 rWTWQTTASDAGTSQVNVWIRDGN 312
                                       3*********************97 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 2.9e-05
                             Big_9  10 p..vndaPvavdds.......vtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgt.....ltytpn 72 
                                       +  +n++P+a+  +       v  ++ + +a ++dpdgd++ +  + +    +p+ G +    +g      +t++ +
  gi|386001058|ref|YP_005919357.1| 331 AprANRPPTATGLEpnwrsplVAGSAVTWTAKAVDPDGDQIFYR-FWL---RGPSTGDAWREMTGWtasnrWTWQTT 403
                                       4458999999998877776666666666699*********9654.433...33333333333333333334****** PP

                             Big_9  73 agfsgtdsftYtvsDgs 89 
                                       a+ +gt ++++ + Dg+
  gi|386001058|ref|YP_005919357.1| 404 ASDAGTSQVNVWIRDGN 420
                                       ***************97 PP

>> T2SS-T3SS_pil_N  Pilus formation protein N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0027        24      45      62 ..     295     312 ..     286     318 .. 0.86
   2 ?    4.7   0.1    0.0027        24      45      62 ..     403     420 ..     394     426 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0027
                   T2SS-T3SS_pil_N  45 tGksvGtTnlivwdaggr 62 
                                       t+  +Gt+++ vw ++g+
  gi|386001058|ref|YP_005919357.1| 295 TASDAGTSQVNVWIRDGN 312
                                       78899********99998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0027
                   T2SS-T3SS_pil_N  45 tGksvGtTnlivwdaggr 62 
                                       t+  +Gt+++ vw ++g+
  gi|386001058|ref|YP_005919357.1| 403 TASDAGTSQVNVWIRDGN 420
                                       78899********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 3095.26
//
Query:       gi|386001059|ref|YP_005919358.1|  [L=481]
Description: hypothetical protein Mhar_0348 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   17.2   0.0     0.0093   16.2   0.0    1.4  1  DUF11     Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.086   13.1   0.1       0.92    9.8   0.0    2.3  2  Stirrup   Stirrup


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-06    0.0093       3      79 ..     207     284 ..     205     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.qgtasaltsvgsLeagesatlsftvrv 78 
                                       K  ++s++  G+++tyt+t  N    + +++v+     + +++vs+     +  s  +++g+L +ge  ++ + +++
  gi|386001059|ref|YP_005919358.1| 207 KEGKPSRISQGGKITYTITYGNDLLEPITNLVIVEDYDPRMSIVSADPPpDPGTSNVWTIGTLLPGEYGQIVVVMKM 283
                                       77788999********************998887778999******99986667778888******99999888876 PP

                             DUF11  79 t 79 
                                        
  gi|386001059|ref|YP_005919358.1| 284 V 284
                                       5 PP

>> Stirrup  Stirrup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.11   9.9e+02      10      22 ..     108     120 ..     103     123 .. 0.86
   2 ?    9.8   0.0    0.0001      0.92      23      54 ..     308     338 ..     303     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHTTT-E CS
                           Stirrup  10 edfkewaskygve 22 
                                        d+k ++s+ygve
  gi|386001059|ref|YP_005919358.1| 108 SDLKLFTSRYGVE 120
                                       68999*******9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0001
                                       EEEETTEEEEEETTEEEE-TTHHHHS-EEHHH CS
                           Stirrup  23 fktngsqtlaiikdekvslgqwhrrnrvskav 54 
                                       f tn   tl i+++ ++s  q+ rr+rv+  v
  gi|386001059|ref|YP_005919358.1| 308 FTTNREPTL-IVNQVRISCDQFERRGRVATPV 338
                                       788888887.89****************8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 3438.27
//
Query:       gi|386001060|ref|YP_005919359.1|  [L=304]
Description: GMP synthase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-32  110.5   0.0    5.8e-32  109.6   0.0    1.5  1  GMP_synt_C       GMP synthase C terminal domain
    5.7e-12   45.3   0.0    1.9e-11   43.6   0.0    1.7  1  NAD_synthase     NAD synthase
     0.0017   17.9   0.0     0.0044   16.5   0.0    1.7  2  QueC             Queuosine biosynthesis protein QueC
     0.0024   16.7   0.0       0.02   13.7   0.0    1.9  2  tRNA_Me_trans    tRNA methyl transferase
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.031   13.9   0.0    1.6  2  ThiI             Thiamine biosynthesis protein (ThiI)
      0.017   14.5   0.0      0.024   14.0   0.0    1.2  1  Arginosuc_synth  Arginosuccinate synthase
      0.028   14.1   0.0      0.047   13.4   0.0    1.3  1  Asn_synthase     Asparagine synthase


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   2.2e-35   5.8e-32      13      92 .]     225     303 ..     212     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 2.2e-35
                                       SEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS- CS
                        GMP_synt_C  13 wQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpat 89 
                                       wQafa++l  k++Gv+gd R+y+yvva+Rav+s+Damtadv+elp+evL++is+ri  e+++v+rvvyd+t kPp+t
  gi|386001060|ref|YP_005919359.1| 225 WQAFAAVLG-KATGVKGDIRAYGYVVAVRAVSSRDAMTADVIELPWEVLRRISHRIAGEIPEVSRVVYDLTPKPPGT 300
                                       9*******9.9****************************************************************** PP

                                       S-- CS
                        GMP_synt_C  90 iEw 92 
                                       iE+
  gi|386001060|ref|YP_005919359.1| 301 IEF 303
                                       **7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   7.4e-15   1.9e-11      16     177 ..      19     186 ..       4     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 7.4e-15
                                       CTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHH.HHHH CS
                      NAD_synthase  16 agakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivr.afeq 90 
                                       +    +v+GlSGGvDSs+ a la++al  ++ + +++  + +  +e+++ a ++ +    +  t+  ++    a+  
  gi|386001060|ref|YP_005919359.1|  19 TVKGRAVIGLSGGVDSSVCAFLAREAL-GDRLIPVYVDsGLMRLNESKKIAEMFSDF---NLITVTAEDRFLgALAG 91 
                                       444579*********************.67999999983444455555555555443...44444444433303333 PP

                                       HHHHHH......-HHHHHHHHHHHHHHHHHHHHHH.HTEEEB--.-BHHHHTTT-S-TTTTT--SBETTTTS-HHHH CS
                      NAD_synthase  91 elkeak......edlakgNlkaRiRmailyaiank.lnllvlgT.gnksElvvGyfTkyGDgaadlapiaellKtev 159
                                        +++++      e + +   +   R  + y i +  +  l+ +  g ks   vG   ++ D  + ++p+ +l+K ev
  gi|386001060|ref|YP_005919359.1|  92 VTDPEEkrkvvgETFIRVFEEEARRVGAEYLIQGTiYPDLIESEgGIKSHHNVGGLPLHMDFKGIVEPLRDLYKDEV 168
                                       333333334666555554444445888888887661566776651679***************************** PP

                                       HHHHHHTT--HHHHCS-- CS
                      NAD_synthase 160 keLakelnvPervlkkpP 177
                                       ++ a+ l +P ++ ++ P
  gi|386001060|ref|YP_005919359.1| 169 RAVARGLSMPTEICERMP 186
                                       ****************99 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.7e-06    0.0044       1      53 [.      23      76 ..      23     113 .. 0.80
   2 ?   -1.8   0.0      0.72   1.8e+03     154     177 ..     156     179 ..     123     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                                      EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT-- CS
                              QueC  1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgv 53
                                      +av+ lSGG+DS+++++la+++ g++++ + +d g  + +e ++ +++++++++
  gi|386001060|ref|YP_005919359.1| 23 RAVIGLSGGVDSSVCAFLAREAlGDRLIPVYVDSGLMRLNESKKIAEMFSDFNL 76
                                      699****************98625899999999888888888888877777776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.72
                                       EE-TTTT--HHHHHHHHHHTTHHH CS
                              QueC 154 ieaPlidlsKaeivklgkelgvpl 177
                                       i+ Pl dl K e+ +++  l +p+
  gi|386001060|ref|YP_005919359.1| 156 IVEPLRDLYKDEVRAVARGLSMPT 179
                                       889999999999999988887765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.8e-06      0.02       3      23 ..      24      44 ..      22      81 .. 0.81
   2 ?    0.7   0.0     0.069   1.8e+02     164     186 ..     156     178 ..     150     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq 23
                                       v++lSgGVDSsv a+l +e+
  gi|386001060|ref|YP_005919359.1| 24 AVIGLSGGVDSSVCAFLAREA 44
                                      589*************99886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.069
                     tRNA_Me_trans 164 llfPlgeltKeevrkiAkeagla 186
                                       ++ Pl +l K+evr++A+  +++
  gi|386001060|ref|YP_005919359.1| 156 IVEPLRDLYKDEVRAVARGLSMP 178
                                       6679************9877665 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.031       2     115 ..      20     125 ..      19     130 .. 0.70
   2 ?   -3.8   0.0       3.2   8.3e+03     140     158 ..     156     174 ..     153     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                              ThiI   2 tqgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       ++g+++  lSgG+DS V a+l+ +  G r   v++++ ++      +  +k+ae++++++      ++v   ++ l 
  gi|386001060|ref|YP_005919359.1|  20 VKGRAVIGLSGGVDSSVCAFLAREAlGDRLIPVYVDSGLMR----LNESKKIAEMFSDFNL-----ITVTAEDRFLG 87 
                                       6899****************987534889999999765554....4455678888888873.....34444445556 PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtG 115
                                        +   ++++ +  ++  +++r+ e+ a++ ga+ l++G
  gi|386001060|ref|YP_005919359.1|  88 ALAGVTDPEEKRKVVGETFIRVFEEEARRVGAEYLIQG 125
                                       66655555555555566777777777777777777777 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.2
                              ThiI 140 ilrPLigldKeeiiklAke 158
                                       i++PL  l K+e+ ++A+ 
  gi|386001060|ref|YP_005919359.1| 156 IVEPLRDLYKDEVRAVARG 174
                                       7889999999999999985 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.2e-06     0.024       1      64 [.      25      86 ..      25      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.2e-06
                   Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefv 64
                                      v+  sGG+D sv+  l +e lg+  i v vd G     l+e k+ a+ +++ + ++v a++ f 
  gi|386001060|ref|YP_005919359.1| 25 VIGLSGGVDSSVCAFLAREALGDRLIPVYVDSGLM--RLNESKKIAEMFSDFNLITVTAEDRFL 86
                                      5678*****************************99..9********************999986 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.047      23      52 ..      27      56 ..      13      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                      Asn_synthase 23 lLSGGlDSSliaalaarqsksplktFsigf 52
                                       LSGG+DSS+ a+la++ +  +l  + ++ 
  gi|386001060|ref|YP_005919359.1| 27 GLSGGVDSSVCAFLAREALGDRLIPVYVDS 56
                                      59*************998875555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2316.99
//
Query:       gi|386001061|ref|YP_005919360.1|  [L=188]
Description: imidazoleglycerol-phosphate dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-44  150.6   0.1    4.5e-44  150.2   0.1    1.2  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   0.1   2.5e-48   4.5e-44       2     144 .]      32     170 ..      31     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 2.5e-48
                                       ...HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE CS
                              IGPD   2 gigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevald 78 
                                       g gfldhmL++la+ +g+dl+ k+ g +       +  +g+alG+a+++algdkrgi+R+g+a++pmDeala++ald
  gi|386001061|ref|YP_005919360.1|  32 GSGFLDHMLSALARMSGIDLSAKAGGGISAQR---SRALGLALGEAIASALGDKRGIRRYGWAAAPMDEALASAALD 105
                                       789************************99666...899*************************************** PP

                                       --SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  79 lsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       lsgr+ylv+++e+  + +g+l t+ v  f+ +l+e  +itlh++   gen+hh++e +fKa++ aL
  gi|386001061|ref|YP_005919360.1| 106 LSGRAYLVMRGEFAGDLVGDLPTQDVAAFLSALTEGGRITLHIRFE-GENDHHQAEIIFKALGLAL 170
                                       ********************************************88.*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1472.91
//
Query:       gi|386001062|ref|YP_005919361.1|  [L=241]
Description: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-66  224.4   0.5    1.4e-66  224.2   0.5    1.0  1  His_biosynth  Histidine biosynthesis protein
    2.7e-06   26.9   1.7    0.00035   20.0   0.1    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    5.3e-06   26.0   8.5    4.5e-05   23.0   2.7    2.1  2  NMO           Nitronate monooxygenase
    3.4e-05   23.1   0.2      0.014   14.5   0.0    2.2  2  Dus           Dihydrouridine synthase (Dus)
    7.4e-05   22.1   0.3     0.0072   15.6   0.1    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0011   18.3   0.7     0.0059   15.8   0.0    2.0  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0011   18.5   0.0     0.0021   17.6   0.0    1.5  1  PcrB          PcrB family
     0.0018   17.6   2.2      0.021   14.2   0.5    2.1  2  TMP-TENI      Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.043   12.8   4.7       0.32    9.9   5.2    1.8  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.054   12.5   6.6      0.073   12.1   0.4    2.1  2  FMN_dh        FMN-dependent dehydrogenase
      0.082   12.1   0.0        1.2    8.2   0.0    2.0  2  IGPS          Indole-3-glycerol phosphate synthase
       0.12   11.5   0.1        0.2   10.7   0.1    1.3  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.2   0.5   9.5e-70   1.4e-66       2     228 ..       5     230 ..       4     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 9.5e-70
                                       EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                      His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                       ++pa+Dl+ G++V+lv G+  +e +  +dp++ a r++e g   lh++Dld+a +g ++n  +++ei+e++++ +qv
  gi|386001062|ref|YP_005919361.1|   5 LFPAVDLRGGRCVQLVGGVPGTEVVSLDDPLAEAVRWAEMGSSTLHIIDLDGAIQGVRINGPILQEIVETLDLFIQV 81 
                                       78*************************************************************************** PP

                                       ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHH CS
                      His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakk 155
                                       GGGIrs ed+++ll +g+d+vi+gtaa+ +pe+++e+ae+fg+++++va+D+rrg kv+++gw+++ +  a+el   
  gi|386001062|ref|YP_005919361.1|  82 GGGIRSPEDAASLLGLGVDRVILGTAALARPEMVTEVAEEFGKERVMVALDVRRG-KVTTEGWQRNLEKGAIELGLL 157
                                       *******************************************************.********************* PP

                                       HHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 156 leelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       ++e+gag+il+t+id +G   G+d e t++l eav+ipv+a+GGv+++ dl  l+ +g+++++vg+a+y+g+l
  gi|386001062|ref|YP_005919361.1| 158 FQERGAGSILFTNIDVEGQVRGIDPEPTRRLVEAVEIPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAIYTGKL 230
                                       **********************************************************************997 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.3e-07   0.00035     156     220 ..      56     122 ..      28     143 .. 0.79
   2 !    6.5   0.1    0.0031       4.7     164     209 ..     182     227 ..     158     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                       TS----S.-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH.HHTSSSHHHHHHHH CS
                              ThiG 156 GsglGll.nkealkiiieeakvPvivDAGigspsdaaqamelGadavllnta.vaeakdpvamAraf 220
                                       G+ +G++ n   l+ i+e++++ + v  Gi+sp+daa  + lG+d v+l ta +a+ +   ++A+ f
  gi|386001062|ref|YP_005919361.1|  56 GAIQGVRiNGPILQEIVETLDLFIQVGGGIRSPEDAASLLGLGVDRVILGTAaLARPEMVTEVAEEF 122
                                       6667775366789***********************************9986266666666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                              ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                                       +e  + ++e +++Pv+   G+ +  d       Ga + ++ ta+ +
  gi|386001062|ref|YP_005919361.1| 182 PEPTRRLVEAVEIPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAIYT 227
                                       55567899***********************************976 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.3    0.0032       4.8     185     234 ..      68     117 ..      56     139 .. 0.86
   2 !   23.0   2.7     3e-08   4.5e-05     187     225 ..     187     225 ..     182     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0032
                               NMO 185 vpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdak 234
                                       ++++++ +d+ +   GGi   ++ a  L lG   v +gt+ L+  e  ++
  gi|386001062|ref|YP_005919361.1|  68 LQEIVETLDLFIQVGGGIRSPEDAASLLGLGVDRVILGTAALARPEMVTE 117
                                       678888899999999*************************9988776554 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3e-08
                               NMO 187 qvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                       + ++av+iPv+AaGG+ +  ++     +GA+g+ +gt+ 
  gi|386001062|ref|YP_005919361.1| 187 RLVEAVEIPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAI 225
                                       5789*******************999***********96 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   9.5e-06     0.014     175     227 ..      68     120 ..      58     147 .. 0.83
   2 !    6.6   0.1    0.0024       3.6     177     217 ..     187     226 ..     179     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.5e-06
                                       HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HH CS
                               Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.st 227
                                        +e+ + + + + + G+I+++eda   l   G+d v+ g +al +P ++ e  +
  gi|386001062|ref|YP_005919361.1|  68 LQEIVETLDLFIQVGGGIRSPEDAASLLGL-GVDRVILGTAALARPEMVTEvAE 120
                                       5688889999999*************9999.******************85333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
                                       HHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                               Dus 177 evkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                        + +av+ipv+a G+++++ d+  +l+  Ga g ++g + +
  gi|386001062|ref|YP_005919361.1| 187 RLVEAVEIPVVAAGGVTTVGDLL-VLRGAGAAGAVVGTAIY 226
                                       67899****************97.67777999999998765 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.01        16     246     291 ..      78     122 ..      61     125 .. 0.81
   2 !   15.6   0.1   4.8e-06    0.0072     235     282 ..     186     230 ..     176     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                                       -EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHH CS
                            DHO_dh 246 piIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkel 291
                                        i   GGi s eDa   +  G   v ++ta   + p ++ ++ +e 
  gi|386001062|ref|YP_005919361.1|  78 FIQVGGGIRSPEDAASLLGLGVDRVILGTAA-LARPEMVTEVAEEF 122
                                       4555699**********************99.77888888888876 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.8e-06
                                       HHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTC CS
                            DHO_dh 235 relykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpk 282
                                       r+l + ++  ip+++ GG+++  D l    aGA+   v+ta+ ++g  
  gi|386001062|ref|YP_005919361.1| 186 RRLVEAVE--IPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAI-YTGKL 230
                                       55666666..*******************************9.87765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.9e-06    0.0059     143     184 ..      75     117 ..      51     125 .. 0.84
   2 ?    0.7   0.2      0.17   2.6e+02     143     176 ..     192     225 ..     164     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.9e-06
                                       TT--EEEES---SHHHHHHHHTT--SEEEE-H.HHH-HHHHHH CS
                              NanE 143 aglkviaeGrintPekakkaieiGvdavvvGs.aitrleeiak 184
                                        +l++ + G i +Pe a++ + +Gvd v++G+ a++r+e +++
  gi|386001062|ref|YP_005919361.1|  75 LDLFIQVGGGIRSPEDAASLLGLGVDRVILGTaALARPEMVTE 117
                                       46788899***********************7369***99886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                                       TT--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 143 aglkviaeGrintPekakkaieiGvdavvvGsai 176
                                        ++ v+a G + t          G++  vvG+ai
  gi|386001062|ref|YP_005919361.1| 192 VEIPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAI 225
                                       36889999999999999999999********998 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0021     177     220 ..      74     116 ..      19     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                       HHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHH CS
                              PcrB 177 klekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkid 220
                                        l+   + vGGGirs+E+A+  ++   D ++ G++    +e+ + 
  gi|386001062|ref|YP_005919361.1|  74 TLD-LFIQVGGGIRSPEDAASLLGLgVDRVILGTAALARPEM-VT 116
                                       332.34569****************9********98888854.44 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.037        55     141     177 ..      67     104 ..      61     108 .. 0.85
   2 !   14.2   0.5   1.4e-05     0.021     121     181 .]     162     225 ..     160     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.037
                          TMP-TENI 141 glkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                                        l+e++e+l + + + GGi+ +e++a++l  g+d+v +
  gi|386001062|ref|YP_005919361.1|  67 ILQEIVETLDLFIQVGGGIRsPEDAASLLGLGVDRVIL 104
                                       5899999999999999**96479999999999999865 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                          TMP-TENI 121 gvGpifpTdtKkdaeplgl..eglkelaealeiPvvaiGGitl.envaevleagadgvavvsai 181
                                       g+G+i  T+   + +++g+  e  ++l+ea+eiPvva GG+t+  ++  ++ aga+g  v +ai
  gi|386001062|ref|YP_005919361.1| 162 GAGSILFTNIDVEGQVRGIdpEPTRRLVEAVEIPVVAAGGVTTvGDLLVLRGAGAAGAVVGTAI 225
                                       6788888888888877776226789***************987256777778999998887776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.2   0.00022      0.32     106     238 ..      88     224 ..      79     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHTT-SEEEEE-STSSSHHHHHHH.HHH.HHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE-S..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                             IMPDH 106 lervkalveagvdvlvvdsahghsekvleav.kei.kkkvee.veviaGnvataegakaLieagadavkvGi..... 174
                                        e ++ l+  gvd +++ +a     ++++ v +e  k++v   ++v  G v+t+   ++L e ga  +  G+     
  gi|386001062|ref|YP_005919361.1|  88 PEDAASLLGLGVDRVILGTAALARPEMVTEVaEEFgKERVMVaLDVRRGKVTTEGWQRNL-EKGA--IELGLlfqer 161
                                       5778999999******99988666555544415552455543488899999876655555.5555..5555444555 PP

                                       S-STTBHHHHHCSB---HHHHH..HHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 175 GpGsiCttrvvagvGvpqltAv..aevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                       G+Gsi  t +      +q+  +    + + ++  ++pv+a GG+++ gd+     aGa   ++G  
  gi|386001062|ref|YP_005919361.1| 162 GAGSILFTNIDV---EGQVRGIdpEPTRRLVEAVEIPVVAAGGVTTVGDLLVLRGAGAAGAVVGTA 224
                                       ********9844...2455555215677799999****************9999999999999875 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   4.9e-05     0.073     260     304 ..      67     109 ..      53     132 .. 0.85
   2 ?    3.5   1.2      0.02        29     264     306 ..     188     228 ..     176     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                                       CHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 260 vLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       +L+eive ++  + + v gGir+ +D++  l lG d v+lG ++l
  gi|386001062|ref|YP_005919361.1|  67 ILQEIVETLD--LFIQVGGGIRSPEDAASLLGLGVDRVILGTAAL 109
                                       5889999996..9999*************************8875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.02
                                       HHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
                            FMN_dh 264 iveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                                       +veav+  i+v++ gG+++  D l     GA + ++G ++  g
  gi|386001062|ref|YP_005919361.1| 188 LVEAVE--IPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAIYTG 228
                                       466665..9****************************988665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.079   1.2e+02     216     248 ..      83     115 ..      67     121 .. 0.80
   2 ?    8.2   0.0   0.00081       1.2     195     243 ..     181     227 ..     178     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.079
                                       SSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHH CS
                              IGPS 216 SGiktredveklkeegvnafLvGeslmrqedve 248
                                        Gi+++ed+ +l   gv+ ++ G++ ++ +++ 
  gi|386001062|ref|YP_005919361.1|  83 GGIRSPEDAASLLGLGVDRVILGTAALARPEMV 115
                                       69*********************9977776655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00081
                                       -CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                              IGPS 195 dlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                                       d + t++L++ v+  + +va  G++t  d+  l+ +g+ +  vG+++  
  gi|386001062|ref|YP_005919361.1| 181 DPEPTRRLVEAVE--IPVVAAGGVTTVGDLLVLRGAGAAGAVVGTAIYT 227
                                       6677899999887..99****************************9965 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00014       0.2     275     307 ..      77     109 ..      45     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                       -EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 275 vsliadGglktgadvvkalalGAdavgigtaal 307
                                       + +++ Gg+++++d +  l lG d v +gtaal
  gi|386001062|ref|YP_005919361.1|  77 LFIQVGGGIRSPEDAASLLGLGVDRVILGTAAL 109
                                       6799***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1682.35
//
Query:       gi|386001063|ref|YP_005919362.1|  [L=996]
Description: ATP-dependent RNA helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.8e-31  107.0   0.1    2.1e-30  106.0   0.1    1.6  1  DEAD_assoc  DEAD/H associated
    1.2e-29  103.3   0.0    2.7e-29  102.2   0.0    1.6  2  DEAD        DEAD/DEAH box helicase
    6.2e-23   81.3   0.0    6.6e-21   74.7   0.1    2.9  3  Helicase_C  Helicase conserved C-terminal domain
      2e-05   24.7   0.0      0.025   14.6   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.018   15.4   0.1        2.9    8.2   0.0    3.1  3  AAA_19      AAA domain
      0.019   13.7   0.0      0.027   13.2   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
      0.023   14.2   2.0       0.54    9.8   0.0    3.4  3  AAA_25      AAA domain
      0.048   13.4   1.6       0.11   12.2   1.6    1.5  1  YdjO        Cold-inducible protein YdjO
      0.091   13.0   0.0         16    5.8   0.0    2.5  2  AAA_22      AAA domain
       0.13   12.8   0.1         40    4.8   0.0    3.2  2  FliG_N      FliG N-terminal domain
       0.15   11.6   1.2       0.61    9.7   0.2    2.2  2  WcbI        Polysaccharide biosynthesis enzyme WcbI


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.1   1.3e-33   2.1e-30       1     190 [.     666     836 ..     666     837 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.3e-33
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +P++rt++vE    ++   ++ +++++G+++neal+++l+a ls+r+g++v++ +++++i l++p +  lp+++ +l
  gi|386001063|ref|YP_005919362.1| 666 VPDERTIVVEGD--GT---YITINACLGHQANEALGRVLTALLSARLGTSVALDVDPYRIGLETP-RPILPEEVAAL 736
                                       8*********86..45...9******************************************884.24677888999 PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       l+ ++pd+l+ +le  l++++lf +r+ +vA+r+++l r+ +        + ++ ++ l  +    d ++ +ea+re
  gi|386001063|ref|YP_005919362.1| 737 LAGTDPDHLAPILEMTLKNTSLFTWRMVHVARRFGALRRDLDR-------EVVSLKRVLGLFV---DGVIGEEAMRE 803
                                       ***************************************9877.......8899999999999...*********** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpSpf 190
                                       vl d +D +r++e+l+ ++ag+i +++   +++Sp+
  gi|386001063|ref|YP_005919362.1| 804 VLFDRIDADRAREVLEGLRAGKIAITT---SSASPI 836
                                       ************************997...777775 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   1.7e-32   2.7e-29       1     170 [.      24     244 ..      24     250 .. 0.87
   2 ?   -3.5   0.0       4.6   7.5e+03      30      76 ..     298     339 ..     296     358 .. 0.67

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.7e-32
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx........................... RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktg........................... 47 
                                       t+ Q++aiplil g+++l+ a+TG+GKT+a+++p++++++++       +                           
  gi|386001063|ref|YP_005919362.1|  24 TAPQERAIPLILAGEHLLLIAPTGTGKTEAAALPLFNRILRDrarP---Ragtagmeagggrprgeersspgdgdgm 97 
                                       567************************************9975541...2556778889999999999********* PP

                                       ..........................-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSH.HHHHHHHHTT CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                              DEAD  48 ..........................pkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaa.rdqlskldng 97 
                                                                   a++v+P+r+L +++l++l++++++++++v +  g++++ ++  + l + 
  gi|386001063|ref|YP_005919362.1|  98 rwetrsrgrmqgrerpgtdedegpgrISAIYVTPLRALNRDMLSRLRSWGEELGVSVAVRHGDTTQaERRAQSL-RP 173
                                       ****************************************************9999987777555414444444.67 PP

                                       CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  98 vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +d++++tp+ l+ +l+ ++l+  l+ vr++V+DE+++l  ++++ ++  +l+++++   +     q + lSAT+ 
  gi|386001063|ref|YP_005919362.1| 174 PDLLITTPETLQVMLTGKRLResLRGVRTVVIDEVHELAASKRGSQLALVLERMAEVAGE----FQRVGLSATVG 244
                                       *************9955555556*******************************655554....55*******86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  30 aflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       a++i v+++       ++ ++l+ + tr+ ae   + ++ +++ i++
  gi|386001063|ref|YP_005919362.1| 298 AAQIRVIREA-----VRRERCLVFVNTRQAAEVLGSSFRILGERIGV 339
                                       5555666444.....56778999999999988888888877777664 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.084   1.4e+02      32      57 ..     143     168 ..     123     182 .. 0.76
   2 !   74.7   0.1   4.1e-24   6.6e-21       9     108 ..     303     402 ..     296     406 .. 0.90
   3 ?   -2.4   0.0       3.8   6.2e+03       6      29 ..     857     880 ..     854     898 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.084
                                       HHHHHHHTTSTEEEESTTSTHHHHHH CS
                        Helicase_C  32 vklllekkgikvavlhgelpqneree 57 
                                       ++   e+ g++vav hg+++q er++
  gi|386001063|ref|YP_005919362.1| 143 LRSWGEELGVSVAVRHGDTTQAERRA 168
                                       344455569**************986 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 4.1e-24
                                       HHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                        Helicase_C   9 llkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                        + + ++++++l+fvnt++ +   ++l +++   g ++ v+hg+l+++ r+e+ e+f++g+ + Li+t+ +e Gidi
  gi|386001063|ref|YP_005919362.1| 303 VIREAVRRERCLVFVNTRQAA---EVLGSSFrilGERIGVHHGSLSKEARIEAEEAFKAGRLRGLICTSSMELGIDI 376
                                       4467789************99...56655555669****************************************** PP

                                       TTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtg 108
                                        +v++Vi+++ pr+v++++qr+GR g
  gi|386001063|ref|YP_005919362.1| 377 GDVEHVIQYSSPREVSRLVQRVGRSG 402
                                       ************************87 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.8
                                       HHHHHHHTTTTSEEEEEESSHHHH CS
                        Helicase_C   6 llellkleeeggkilifvntidrl 29 
                                       +++llk +  ++++++f+ +++  
  gi|386001063|ref|YP_005919362.1| 857 VIDLLKDRIMNDRVILFCVQCKGW 880
                                       67888999999******9888843 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0021       3.4      25      42 ..      38      56 ..      21      70 .. 0.76
   2 !   14.6   0.0   1.5e-05     0.025     100     169 ..     170     243 ..     124     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                      SEEEEEESTTSTHHHHH.H CS
                            ResIII 25 krglikmaTGtGKTlva.a 42
                                      +++l+ ++TGtGKT  a +
  gi|386001063|ref|YP_005919362.1| 38 EHLLLIAPTGTGKTEAAaL 56
                                      6899**********98844 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.5e-05
                                       ....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS- CS
                            ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATp 169
                                       +    ++l+tt ++l+  +   + ++ + +      ++iDE+H l+a+k         ++ +e   e+ ++gl+AT 
  gi|386001063|ref|YP_005919362.1| 170 SLRPPDLLITTPETLQVML---TGKRLRESLRGVRTVVIDEVHELAASKrgsqlalVLERMAEVAGEFQRVGLSATV 243
                                       4455578999999999999...77888888888889***********9655544444444455556699*******6 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0018       2.9       1      25 [.      27      52 ..      27      64 .. 0.91
   2 ?   -1.1   0.0       1.3   2.1e+03      94     115 ..     191     212 ..     161     229 .. 0.74
   3 ?    3.2   0.0     0.063     1e+02      38      84 ..     306     350 ..     296     467 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                            AAA_19  1 qreave.alkekvllvtaGpGtGKTr 25
                                      q++a+   l+ ++ll++a+ GtGKT+
  gi|386001063|ref|YP_005919362.1| 27 QERAIPlILAGEHLLLIAPTGTGKTE 52
                                      8899988999***************7 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                            AAA_19  94 aeeekklqeee.llivDEfqdvd 115
                                       ++ ++ l ++  ++++DE+ ++ 
  gi|386001063|ref|YP_005919362.1| 191 KRLRESL-RGVrTVVIDEVHELA 212
                                       4455677.555599999998876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.063
                            AAA_19  38 ggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddll 84 
                                       + v  e++l+   t++Aa+ l  + + lg+++   H+   l  + ++
  gi|386001063|ref|YP_005919362.1| 306 EAVRRERCLVFVNTRQAAEVLGSSFRILGERIGVHHGS--LSKEARI 350
                                       3345699*****************99999998888866..4444444 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 ?   13.2   0.0   1.7e-05     0.027     101     199 ..     128     221 ..      46     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       EE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S- CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 101 ivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqv 176
                                        v P  +l +   + ++++ ++  + v v +g++++ ++     ++ l+  d +itt ++l+     +  r+ l  v
  gi|386001063|ref|YP_005919362.1| 128 YVTPLrALNRDMLSRLRSWGEELGVSVAVRHGDTTQAER----RAQSLRPPDLLITTPETLQVMLTGKRLRESLRGV 200
                                       56666566666667889999************9855555....8899***************999777888888776 PP

                                       S-SEEEES-GGGT--TTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 177 ewkrvvlDEghtlknstskaaea 199
                                         + vv+DE h l  s++  + a
  gi|386001063|ref|YP_005919362.1| 201 --RTVVIDEVHELAASKRGSQLA 221
                                       ..57**********997544433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00033      0.54      12      50 ..      16      54 ..       5      70 .. 0.77
   2 ?    1.2   0.1      0.15   2.4e+02      88     159 ..     141     216 ..     136     243 .. 0.58
   3 ?   -0.4   0.1      0.45   7.3e+02      87     142 ..     257     312 ..     251     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                            AAA_25 12 vad.laapppprrwlvkgllpagelallaGapgtGKttla 50
                                      +++ +a p +p++  ++ +l age  ll++++gtGKt +a
  gi|386001063|ref|YP_005919362.1| 16 ARQgIAEPTAPQERAIPLIL-AGEHLLLIAPTGTGKTEAA 54
                                      55525556666666666665.9***************776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                            AAA_25  88 rRlravgeal......rddarllvldlagv.eslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsral 155
                                        Rlr +ge+l      r+ ++ ++  +a++  + +L+ ++ +  +  lt++  +l++      gvr vviD + ++ 
  gi|386001063|ref|YP_005919362.1| 141 SRLRSWGEELgvsvavRHGDTTQAERRAQSlRPPDLLITTPETLQvmLTGK--RLRES---LRGVRTVVIDEVHELA 212
                                       577778877777777655555555555555556666554433322123443..34444...445999***9998877 PP

                            AAA_25 156 ggde 159
                                       +   
  gi|386001063|ref|YP_005919362.1| 213 ASKR 216
                                       6644 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.45
                            AAA_25  87 rrRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieeveg 142
                                       rrR r v +++++ ar +v++ + + ++  L+++   ++ l+a+++ +++a+++ e+
  gi|386001063|ref|YP_005919362.1| 257 RRRCRIVQTDVEREARFRVISPQPEaGDYALAKELECDPSLAAQIRVIREAVRR-ER 312
                                       79999999***********************999999999999*9999998888.53 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.6   6.7e-05      0.11      25      53 ..     876     906 ..     873     909 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                              YdjO  25 dCngW..mRdnFsfeeePtCplCkseMvkev 53 
                                       +C+gW  +R   ++ e P Cp+C+s+Mv   
  gi|386001063|ref|YP_005919362.1| 876 QCKGWksLRMVKNVPEVPECPVCGSRMVAAL 906
                                       699997778888899************9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0096        16       7      22 ..      39      54 ..      36      67 .. 0.89
   2 ?    4.4   0.0     0.026        42      80     110 ..     191     221 ..     134     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0096
                            AAA_22  7 ilvvtGesGtGKTtll 22
                                      +l++++++GtGKT  +
  gi|386001063|ref|YP_005919362.1| 39 HLLLIAPTGTGKTEAA 54
                                      899**********876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                            AAA_22  80 ealeqalraravielliiDEaqhlr...seeale 110
                                       ++l++ lr  ++   ++iDE++ l    +  +l 
  gi|386001063|ref|YP_005919362.1| 191 KRLRESLRGVRT---VVIDEVHELAaskRGSQLA 221
                                       555555555555...********97743244444 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.05        81      71      98 ..     797     824 ..     793     827 .. 0.90
   2 ?    4.8   0.0     0.025        40       9      31 ..     950     974 ..     938     977 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHSHHHHHHHCHHHHXX CS
                            FliG_N  71 geeyarelLekalgeekaeellerltae 98 
                                       gee++re+L   +++++a+e+le l+a+
  gi|386001063|ref|YP_005919362.1| 797 GEEAMREVLFDRIDADRAREVLEGLRAG 824
                                       899********************99876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                                       HHHHHH..CXHHHHHHHHTTSXHHH CS
                            FliG_N   9 Aillla..LgeeeaaevlkhLdeee 31 
                                       A+ l++  Lg+e+aa+++++L+++e
  gi|386001063|ref|YP_005919362.1| 950 AVALASrgLGPETAARLMRNLRRDE 974
                                       3333324488888888888888887 PP

>> WcbI  Polysaccharide biosynthesis enzyme WcbI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.47   7.6e+02      16      50 ..     192     226 ..     185     235 .. 0.75
   2 ?    9.7   0.2   0.00037      0.61     106     156 ..     940     991 ..     932     993 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.47
                              WcbI  16 lLessapaevrtvrvppvheltaedlp.qleellar 50 
                                        L++s  + vrtv ++ vhel a++   ql+  l+r
  gi|386001063|ref|YP_005919362.1| 192 RLRESL-RGVRTVVIDEVHELAASKRGsQLALVLER 226
                                       455555.68999999999999998877676666655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00037
                              WcbI 106 pplvdYhdlrllaaaarglsaeeavalfrr.dvfsaegvralaeaslaelrr 156
                                       + + +Y  + ++a+a+rgl +e+a++l+r+ +  +a+ +r++ +a+++  r+
  gi|386001063|ref|YP_005919362.1| 940 NLVLTYGKAAAVALASRGLGPETAARLMRNlRRDEADFYRDILKAEREYART 991
                                       56789****************************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (996 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 6594.21
//
Query:       gi|386001064|ref|YP_005919363.1|  [L=151]
Description: hypothetical protein Mhar_0353 [Methanosaeta harundinacea 6Ac]
Scores for complete 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  141.6   4.7    1.8e-41  141.4   4.7    1.0  1  LDcluster4       SLOG cluster4 family
      1e-07   32.1   0.8    1.4e-07   31.7   0.4    1.4  1  Lysine_decarbox  Possible lysine decarboxylase
      1e-05   24.9   1.8      2e-05   24.0   1.5    1.6  2  DNA_processg_A   DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   4.7     3e-45   1.8e-41       2     133 ..       1     126 [.       1     143 [. 0.90

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 3e-45
                        LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdi 78 
                                       ++++V+G+++  ++e+  +la elGr iA+ g+vl+tGg +Gvmeaa++Ga+eagG+tvG+lp+  eke++n++v +
  gi|386001064|ref|YP_005919363.1|   1 MQVAVVGAGD--YEERRCSLAMELGRKIAEGGHVLITGGLGGVMEAACQGAREAGGVTVGVLPG--EKEAANPFVAV 73 
                                       58********..89999***********************************************..88999****** PP

                        LDcluster4  79 iiyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgtdell 133
                                       +i TG+g+  Rn ilv+s+dvvia++g +GTlsEialal+ gk vi l  +++++
  gi|386001064|ref|YP_005919363.1|  74 AIGTGMGHG-RNAILVRSADVVIALPGLYGTLSEIALALKMGKLVIDLG-DWNVD 126
                                       *******77.************************************998.44333 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.4   2.4e-11   1.4e-07       1      75 [.      42     113 ..      38     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.4e-11
                                       HHHHHHHHHHTTS-EEEEEECCHHH.HHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkilla.eeapneevnelvivedmeeRkealveladafvilPGGiGTleElleiltl 75 
                                       mea+ +ga eagg ++G+ p    + +ea+n+ v   + +   + R++ lv+ ad +++lPG +GTl E+  +l +
  gi|386001064|ref|YP_005919363.1|  42 MEAACQGAREAGGVTVGVLP----GeKEAANPFVAVAIGTGMGHGRNAILVRSADVVIALPGLYGTLSEIALALKM 113
                                       88899999999999999944....3488899***999999999**************************9877765 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   1.5   3.3e-09     2e-05      44     111 ..       2      69 ..       1      88 [. 0.92
   2 ?   -1.4   0.0      0.19   1.1e+03     158     183 ..      93     118 ..      81     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.3e-09
                    DNA_processg_A  44 avaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgtgldkiyP 111
                                       +va+VG+ +  e+  ++a +l +++ae g++ + G+  G+ +aa ++a eagg tv+vl++  +   P
  gi|386001064|ref|YP_005919363.1|   2 QVAVVGAGDYEERRCSLAMELGRKIAEGGHVLITGGLGGVMEAACQGAREAGGVTVGVLPGEKEAANP 69 
                                       69*********************************************************987666555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.19
                    DNA_processg_A 158 lvveaaekSGalitaelAlelgrevf 183
                                       +v+  +   G+l  + lAl++g+ v+
  gi|386001064|ref|YP_005919363.1|  93 VVIALPGLYGTLSEIALALKMGKLVI 118
                                       55556666799999999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1067.51
//
Query:       gi|386001065|ref|YP_005919364.1|  [L=453]
Description: histidyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-59  202.1   3.5    6.6e-58  196.4   3.5    2.1  1  tRNA-synt_His    Histidyl-tRNA synthetase
    1.7e-13   51.0   0.0    2.5e-13   50.4   0.0    1.3  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    1.2e-10   41.4   0.3    1.1e-09   38.3   0.0    2.3  2  HGTP_anticodon   Anticodon binding domain
    9.1e-05   21.7   0.2      0.018   14.1   0.0    2.6  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    0.00026   20.6   0.0     0.0018   17.8   0.0    2.0  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.056   12.9   0.0       0.35   10.3   0.0    2.0  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   3.5   2.2e-61   6.6e-58       1     309 [.       8     343 ..       8     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 2.2e-61
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd+lp+++ +++++rrr+++++e+wGY++Vs+P++E+l+ ++ ++g +  d+++ + D+ gr l+lR+++T++v 
  gi|386001065|ref|YP_005919364.1|   8 GTRDFLPMDSFRRNAVRRRMQEILEQWGYSEVSTPTFEHLELFTIKSGPSiIDEIYAFQDKGGRDLALRPELTASVM 84 
                                       78*********************************************9995689*********************** PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R++   l+ + +plRl+Y+G+++r ++ + gr re+ Q+GaEl+G++ ++a++E + l+ e+++ +agv +  l lg
  gi|386001065|ref|YP_005919364.1|  85 RMYVGELQkAAKPLRLHYFGNCFRYERPQRGRFREFWQLGAELVGSDRPDAEAEAIALAQELIK-SAGV-SGDLHLG 159
                                       *******99******************************************************7.****.889**** PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTH..........................HHCCHCC CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglk..........................ealrell 203
                                         gl+ra+++ ++  +s++ +l++++++k+++ l+e ++e g +                          ++  ++l
  gi|386001065|ref|YP_005919364.1| 160 YLGLIRAMMRTIP--ASERPTLMRFIDKKERTLLAEKLQEIGRDhlgllelidlkgrraldraaemaedlAKMSDAL 234
                                       **********977..888*************9999999986655899********************6665555555 PP

                                       ....HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS CS
                     tRNA-synt_His 204 kal.elygdaevleealealaaapalqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq 279
                                            ++gd ++  +a  ++a++++++ a  +l++ a+l++ la+++v+ t+D+  +rg+eYytG+vF++ya g g+
  gi|386001065|ref|YP_005919364.1| 235 LDDgVAAGDSDTASAAGDRAARSDRAAPADLDLAHFAELVDLLATYGVEATVDFEIVRGLEYYTGTVFEIYATGLGA 311
                                       44478999*********************************999899*************************99875 PP

                                       ..-SEEEEEECTTTGGG.T---EEEEEEEEHHH CS
                     tRNA-synt_His 280 ..aiarGGrYdelgaaf.grarpAtGfsldlea 309
                                         +i +GG+Y  l a + g++  +tGf +  ++
  gi|386001065|ref|YP_005919364.1| 312 qnQICGGGTY-SLAALLgGQETRSTGFGIGFDR 343
                                       55********.78888899********987776 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   8.4e-17   2.5e-13       1     131 [.      63     315 ..      63     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 8.4e-17
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       Y ++d+ +r+++L+P+ ++ +++++  e l++   Pl+l++++ ++R+E++ +rG  R reF q +++ ++++   +
  gi|386001065|ref|YP_005919364.1|  63 YAFQDKGGRDLALRPELTASVMRMYVGE-LQKAAKPLRLHYFGNCFRYERP-QRG--RFREFWQLGAELVGSDR--P 133
                                       899*************************.655445****************.***..**************998..9 PP

                                       HHHHHHHHHHHHHHHHTT.SC.......EEEEEEGTTSC...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx...................................... RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglef.......raiielmsaks...................................... 109
                                       d  ++ i +++++ ++ g++          i                                              
  gi|386001065|ref|YP_005919364.1| 134 DAEAEAIALAQELIKSAGVSGdlhlgylGLI-------Rammrtipaserptlmrfidkkertllaeklqeigrdhl 203
                                       9************999999885544443222.......222233346667777777777777777777777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                      tRNA-synt_2b 110 ............................................................................. 109
                                                                                                                    
  gi|386001065|ref|YP_005919364.1| 204 gllelidlkgrraldraaemaedlakmsdallddgvaagdsdtasaagdraarsdraapadldlahfaelvdllaty 280
                                       77777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                       .............BTTSEEEEEEEEETTTSEEEEE CS
                                       .............xxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 110 .............adykdkkefeavsesltkgiei 131
                                                    ++y+  ++fe++   l+++ +i
  gi|386001065|ref|YP_005919364.1| 281 gveatvdfeivrgLEYYTGTVFEIYATGLGAQNQI 315
                                       77777777777777777777777777777777766 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.28   8.3e+02      13      50 ..     222     259 ..     211     262 .. 0.79
   2 !   38.3   0.0   3.6e-13   1.1e-09      32      92 ..     385     445 ..     358     447 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHH CS
                    HGTP_anticodon  13 eleeyakklaeeLraagirvelddsnesigkkireadl 50 
                                       e+ e   k  ++L+++g+ +   d ++  g + +++d+
  gi|386001065|ref|YP_005919364.1| 222 EMAEDLAKMSDALLDDGVAAGDSDTASAAGDRAARSDR 259
                                       45566677888999999988888899999999999887 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 3.6e-13
                                       EEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  32 velddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklk 92 
                                       ++ld  ++ +g ++++a  +g  fav+vG+ke+e+g +t+r++ t++qe++ l e++e l 
  gi|386001065|ref|YP_005919364.1| 385 IVLDVMGRGLGAQLKQASAIGASFAVIVGPKEVEEGRLTLREMSTGSQESLRLGEVAERLA 445
                                       456668999***********************************************99886 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   6.1e-06     0.018      25     124 ..      20     129 ..      17     153 .. 0.78
   2 !    4.5   0.0    0.0051        15     284     300 ..     334     350 ..     320     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                                       HHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT..TEEE..............-E-S-.SHHHH.H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..............xxxxx.xxxxx.x RF
                       tRNA-synt_2  25 rstvtkavrkyleengfieietPiLsksdteegarlFkvksrek.ekeff..............aLtqs.pqlyl.e 84 
                                       r+ v + ++++le+ g+ e+ tP++ +       +lF++ks     +e +               Lt s + +y  e
  gi|386001065|ref|YP_005919364.1|  20 RNAVRRRMQEILEQWGYSEVSTPTFEHL------ELFTIKSGPSiIDEIYafqdkggrdlalrpELTASvMRMYVgE 90 
                                       7889999*****************9999......9999988776634555567888888878887887745788624 PP

                                       HHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  85 llivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsf 124
                                       l  +a+  r   ++++FR E+ +  r   EF+q+ ae+  
  gi|386001065|ref|YP_005919364.1|  91 LQKAAKPLRLHYFGNCFRYERPQRGRFR-EFWQLGAELVG 129
                                       445566789**************99998.*******9854 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0051
                                       EEEEEEEHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 284 hgGlglGldRlvmlllg 300
                                         G+g+G+dR++ +++ 
  gi|386001065|ref|YP_005919364.1| 334 STGFGIGFDRIMEIVTL 350
                                       68*********999885 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     6e-07    0.0018      21     133 ..      22     129 ..      11     153 .. 0.82
   2 ?   -0.1   0.1      0.18   5.4e+02     207     222 ..     330     345 ..     302     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6e-07
                                       HHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH.. CS
                      tRNA-synt_2d  21 kvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl.. 95 
                                        v+++++ei+ + g++ev+ p         ++L++   ++  ++ d  y  +++    ++l LR   ta  +r+   
  gi|386001065|ref|YP_005919364.1|  22 AVRRRMQEILEQWGYSEVSTPTF-------EHLELFTIKSGPSIIDEIYAFQDKG--GRDLALRPELTASVMRMYvg 89 
                                       57788999999999999988875.......5666666666667778878777777..789*********99999888 PP

                                       ..TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEE CS
                      tRNA-synt_2d  96 ..ekkkppikiisigrvfRrdavDathlaeFhqveglvvd 133
                                         +k  +p+++  +g++fR +   + +  eF q+   +v+
  gi|386001065|ref|YP_005919364.1|  90 elQKAAKPLRLHYFGNCFRYERPQRGRFREFWQLGAELVG 129
                                       889999**************************98765555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.18
                                       TTSEEEEEEEEHHHHH CS
                      tRNA-synt_2d 207 eevsgfafGlGveRla 222
                                       +e++  +fG+G++R+ 
  gi|386001065|ref|YP_005919364.1| 330 QETRSTGFGIGFDRIM 345
                                       5788999*******97 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.35      18     159 ..      20     152 ..      14     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                   tRNA_synthFbeta  18 eqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlargn 94 
                                       ++++rr+++++l + G++Ev t +f + + +      +  ++    +   + d  +lR+ L+++++      l++  
  gi|386001065|ref|YP_005919364.1|  20 RNAVRRRMQEILEQWGYSEVSTPTFEHLELFTIKSGPSIIDEIYAFQDKGGRD-LALRPELTASVMRMYVGELQKAA 95 
                                       67899999999999999999999998888876664444444455555555555.479***********999999999 PP

                   tRNA_synthFbeta  95 edvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgi 159
                                       + +rl  +g++f+ +  +  +++e ++l++ l+g++         r+   +++ +++++l +s g+
  gi|386001065|ref|YP_005919364.1|  96 KPLRLHYFGNCFRYErPQRGRFREFWQLGAELVGSD---------RPDAEAEAIALAQELIKSAGV 152
                                       99*************999999**************9.........555555666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 3327.02
//
Query:       gi|386001066|ref|YP_005919365.1|  [L=183]
Description: TATA-box-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-56  186.3   0.3    5.5e-27   93.5   0.2    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    2.4e-09   37.2   0.0    0.00063   19.8   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.2   6.2e-31   5.5e-27       2      84 ..       5      85 ..       4      86 .. 0.96
   2 !   91.3   0.0   3.1e-30   2.7e-26       2      81 ..      97     176 ..      96     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 6.2e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+Nvvas++l  e+dL k++ ++  ++aeY++e+fpglvyr+++p++++liF+sGkvv+tGak++e++r+++ ++a+
  gi|386001066|ref|YP_005919365.1|  5 INIENVVASTKLAEEFDLIKIEAEL--EGAEYNKEKFPGLVYRVKSPRAAFLIFTSGKVVCTGAKNVEDVRTVITNMAQ 81
                                      79*******************8777..**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                       lk 
  gi|386001066|ref|YP_005919365.1| 82 TLKS 85
                                      9986 PP

  == domain 2  score: 91.3 bits;  conditional E-value: 3.1e-30
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       +++qN+vasa+l+ +l+ +++al +  +n+eYepe+fpglvyr++ pkv++liFssGk+v+tG ks+ee++e +k +
  gi|386001066|ref|YP_005919365.1|  97 IHVQNIVASADLKTDLNPNAIALGLGLENIEYEPEQFPGLVYRIKTPKVVVLIFSSGKLVVTGGKSPEECEEGVKIV 173
                                       78********************9988***********************************************9987 PP

                                       HHH CS
                               TBP  79 api 81 
                                          
  gi|386001066|ref|YP_005919365.1| 174 RVQ 176
                                       655 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-06     0.017      22      56 ..      34      68 ..      17      85 .. 0.83
   2 !   19.8   0.0     7e-08   0.00063      24      59 ..     130     165 ..     125     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                           DUF3378 22 lrskkppyavfaakkndttItaYtSgKVlFQGkna 56
                                       +++k p+ v++ k++ +   ++tSgKV+  G++ 
  gi|386001066|ref|YP_005919365.1| 34 YNKEKFPGLVYRVKSPRAAFLIFTSGKVVCTGAKN 68
                                      345679***********************999765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 7e-08
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59 
                                        ++ p+ v+++k++++++ ++ SgK+++ G +  +e
  gi|386001066|ref|YP_005919365.1| 130 PEQFPGLVYRIKTPKVVVLIFSSGKLVVTGGKSPEE 165
                                       5789************************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 1311.73
//
Query:       gi|386001067|ref|YP_005919366.1|  [L=404]
Description: hypothetical protein Mhar_0356 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-35  120.5   0.1    9.6e-35  119.0   0.0    1.8  2  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
      0.001   18.8   0.4      0.026   14.3   0.0    2.3  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.0   1.1e-38   9.6e-35       6     100 .]       1      95 [.       1      95 [. 0.99
   2 ?   -2.4   0.0      0.74   6.7e+03       6      32 ..     297     324 ..     296     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 1.1e-38
                                       EEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEEC CS
                    Saccharop_dh_N   6 leGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedvkle 82 
                                       +eGhliDs++l+k+ld+i+++gg+fe+++f+vGkkk+dtSy+ + +s+ed+++L++il +l+ lga+++e+edv+le
  gi|386001067|ref|YP_005919366.1|   1 MEGHLIDSLTLTKALDKIMSMGGEFEIKKFRVGKKKHDTSYVMIAISGEDSDHLDRILLALHPLGARVIEAEDVHLE 77 
                                       79*************************************************************************** PP

                                       ESSCTTB--TTB----SS CS
                    Saccharop_dh_N  83 kaekdgvlpedFYsttnh 100
                                        a++d+v+p++FYsttnh
  gi|386001067|ref|YP_005919366.1|  78 IAPQDRVVPRGFYSTTNH 95 
                                       *****************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.74
                                       EEEXXTTSSHHHHHH.HHHHHTTXEEEE CS
                    Saccharop_dh_N   6 leGhliDsgilnkvl.dlileaggsfev 32 
                                       l G + D g l+ v+ d++l++++ fe 
  gi|386001067|ref|YP_005919366.1| 297 LAGSIRDDGPLPDVItDTVLAQKAMFEA 324
                                       6788888888888755899999999975 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.012     1e+02       2      37 ..     177     216 ..     176     253 .. 0.71
   2 !   14.3   0.0   2.9e-06     0.026      67     137 .]     317     388 ..     299     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.012
                                       HHHHHHHHH-S....SEEEEE-CHHCHTTGHHHHHHHHHH CS
                      TPP_enzyme_M   2 ekaaellkaak....rpvilvGggvarsgaseelrelaek 37 
                                       +++ae + a k    +++++ G g++  ga+e+l+ l++ 
  gi|386001067|ref|YP_005919366.1| 177 KQLAEEILATKraggKIAVVGGPGIIHTGAAEALAGLIRD 216
                                       5666666666644446799***************999876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-06
                                       SCHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  67 gskaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketleaL 137
                                       ++ka  eal+  D v++  + ++ i t++  p   ++ k i +di+p+++ k        ++++v d++ +l +L
  gi|386001067|ref|YP_005919366.1| 317 AQKAMFEALRGVDMVIMMATMLHSIATGNLLP---SRVKTICVDINPSTVTKLMdrgtAQAIGLVTDIGIFLPRL 388
                                       56777899****************87766444...33489*********99988444335699999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2971.59
//
Query:       gi|386001068|ref|YP_005919367.1|  [L=373]
Description: hypothetical protein Mhar_0357 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-43  145.6   0.9    1.9e-42  144.2   0.2    2.1  2  Lig_C           Ligase Pab1020 C-terminal region
    4.4e-13   49.8   0.0    7.7e-13   49.1   0.0    1.3  1  RNA_ligase      RNA ligase
     0.0039   16.9   0.0        1.2    8.8   0.0    2.3  2  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.38   2.3e+03      17      44 ..     189     215 ..     183     235 .. 0.71
   2 !  144.2   0.2   3.1e-46   1.9e-42       1     125 []     247     371 ..     247     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHH--SHHHHHHHHHHHHH CS
                             Lig_C  17 RviReafqavefeeseeelrerakeLGe 44 
                                       R +R  f  + +++  +e+re +++LG 
  gi|386001068|ref|YP_005919367.1| 189 RAVR-LFGEFGLQQAAAEIREIVRDLGA 215
                                       5566.56666677777777777777774 PP

  == domain 2  score: 144.2 bits;  conditional E-value: 3.1e-46
                                       HHCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHH CS
                             Lig_C   1 vafsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeni 77 
                                       +af+y++++g+dF+fsRv+Re+fqa+e++e e+e+ er+ +LG+s+L+pm et+++   +e + +e+++ ++d +++
  gi|386001068|ref|YP_005919367.1| 247 YAFRYYNDYGQDFFFSRVVREGFQAAEWAEGEAEFLERCLRLGRSMLTPMRETVEAKMVGEPIVQEVEILVRDLQTA 323
                                       8**************************************************************************** PP

                                       HHHHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                             Lig_C  78 eellehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                       ++++eh+rr+gv+a+++ ++++ g ++vk+k+++ st+dk++s++eG+
  gi|386001068|ref|YP_005919367.1| 324 RDFEEHFRRMGVRAIFDPPRNSRGGHLVKIKRLVLSTNDKTESIVEGQ 371
                                       **********************************************96 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.3e-16   7.7e-13       3     156 ..      82     231 ..      81     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.3e-16
                                       EEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH...ECCEEEEEEEES...SS.. CS
                        RNA_ligase   3 vvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla.neelilyGElig..hsi.k 73 
                                       v v+EK++G n+r+  v e   + +R++++ p         +   +a+++  +e+++ +++l+l GE++g  +++ +
  gi|386001068|ref|YP_005919367.1|  82 VLVEEKMNGHNVRVARVGEsTVALTRGGFIcP---------YSTEVAREQIPPEIFRdHPDLVLSGEMVGpkNPYvP 149
                                       679**************4459999******53.........22222333322344447788*********6433334 PP

                                       .TTSS.EEEEEEEEEEECTTBECE--HHHH.HHHHHCCT..B..EEEEE.SS.HHHHHCCC..HHHHTC--EEEEEE CS
                        RNA_ligase  74 ygglpkefyvFdifdirdkeeqrylspdev.ealakglg..tvpvlyegkfl.aaeellell.lskgnkrEGlVikp 145
                                        + +p+e + F++fd++ ++ +r l+   + +ala+++g   v++++e++ + aa+e++e++ +   + rEG+++k+
  gi|386001068|ref|YP_005919367.1| 150 KEVYPAEAMDFYLFDTS-RKGRRDLEGPLRtHALAEEYGirAVRLFGEFGLQqAAAEIREIVrDLGARGREGVIVKD 225
                                       44499988888888887.5588888887777****************999998888888885447889********9 PP

                                       SSSSBETTEBS CS
                        RNA_ligase 146 eselyknkgra 156
                                       +++l      +
  gi|386001068|ref|YP_005919367.1| 226 PENL-----AR 231
                                       9887.....44 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0002       1.2      14      82 ..      74     142 ..      65     159 .. 0.86
   2 !    5.6   0.0    0.0018        11     164     189 ..     203     228 ..     197     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0002
                                       HHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEE CS
                    DNA_ligase_A_M  14 lkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElva 82 
                                       l+++ ++ ++vE+K++G  ++v + g++   ++R +   +++ +   +++   ++ d  +++l GE+v 
  gi|386001068|ref|YP_005919367.1|  74 LRRHFSSGVLVEEKMNGHNVRVARVGESTVALTRGGFICPYSTEVAREQIPPEIFRDHPDLVLSGEMVG 142
                                       5666678889*******************************888888999888888889********96 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHTTECEEEEEETT- CS
                    DNA_ligase_A_M 164 veeleelleeaiseglEGlvvKnpds 189
                                       + e++e+++   + g EG++vK+p+ 
  gi|386001068|ref|YP_005919367.1| 203 AAEIREIVRDLGARGREGVIVKDPEN 228
                                       67999******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2480.97
//
Query:       gi|386001069|ref|YP_005919368.1|  [L=258]
Description: hypothetical protein Mhar_0358 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-40  136.0  11.6    1.4e-10   41.4   0.3    4.1  4  CBS             CBS domain
  ------ inclusion threshold ------
       0.05   14.1   0.0         23    5.5   0.0    2.9  3  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
      0.087   12.7   0.0       0.94    9.4   0.0    2.4  2  DUF746          Domain of Unknown Function (DUF746)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.4   3.3e-14     2e-10       1      55 [.       3      55 ..       3      56 .. 0.92
   2 !   21.3   0.1   4.6e-08   0.00028       9      55 ..      78     121 ..      70     123 .. 0.82
   3 !   41.4   0.3   2.4e-14   1.4e-10       2      55 ..     128     179 ..     127     181 .. 0.93
   4 !   38.3   0.0   2.3e-13   1.3e-09       1      55 [.     200     254 ..     200     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.3e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                                      V+dim+++v t++ ++ ++ al+ m++ + ++rl+V+ +dgkl G +t+r ++r+l
  gi|386001069|ref|YP_005919368.1|  3 VKDIMSTPV-TIDKSERIAHALDVMEK-NdLRRLLVT-SDGKLAGTITMRQIARVL 55
                                      89*****99.***************55.55****888.9**************987 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.6e-08
                                       CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       v  v+p++ +eea+ l+ +    +++VV e+++++G v  +D l+al
  gi|386001069|ref|YP_005919368.1|  78 VTKVHPEMKVEEAVVLLQK--T-SVLVVMEEEEILGWVRPKDMLKAL 121
                                       568**************44..5.6668756777************98 PP

  == domain 3  score: 41.4 bits;  conditional E-value: 2.4e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +d m++++ t++p++ l  + + m +++v+rlPV+ e+gklvGi+++rD+++ l
  gi|386001069|ref|YP_005919368.1| 128 ADAMRTPL-TATPSDRLIHVRRVMLDRDVGRLPVM-ENGKLVGIISERDVAKSL 179
                                       68899999.***************9**********.9*************9876 PP

  == domain 4  score: 38.3 bits;  conditional E-value: 2.3e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+d+m+r v ++  dt+leea ++m e++++++PV++ +++lvG++t+r  +++l
  gi|386001069|ref|YP_005919368.1| 200 VSDVMSRGVKSIMIDTPLEEARKMMLEEDLGGMPVLNQNNELVGMLTRRCFFDYL 254
                                       89**********************************************9777666 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0038        23      22      44 ..      36      58 ..      14      92 .. 0.77
   2 ?   -0.7   0.0      0.35   2.1e+03      22      46 ..     102     125 ..      75     132 .. 0.74
   3 ?    5.1   0.0    0.0053        32      22      43 ..     160     181 ..     155     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0038
                                      B-TT-BBSS---HHHHHHHHHHH CS
                    Ribosomal_L9_C 22 agedgklFGsVtakdIaealkkk 44
                                      + +dgkl G++t ++Ia  l + 
  gi|386001069|ref|YP_005919368.1| 36 VTSDGKLAGTITMRQIARVLGTR 58
                                      4679*************988655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.35
                                       B-TT-BBSS---HHHHHHHHHHHT- CS
                    Ribosomal_L9_C  22 agedgklFGsVtakdIaealkkklg 46 
                                       + e++++ G V +kd  +al+   g
  gi|386001069|ref|YP_005919368.1| 102 VMEEEEILGWVRPKDMLKALRMT-G 125
                                       35677888889999998888765.5 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0053
                                       B-TT-BBSS---HHHHHHHHHH CS
                    Ribosomal_L9_C  22 agedgklFGsVtakdIaealkk 43 
                                       + e+gkl G ++++d+a+ l++
  gi|386001069|ref|YP_005919368.1| 160 VMENGKLVGIISERDVAKSLRA 181
                                       569***************9976 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.14   8.5e+02      12      28 ..      45      61 ..      41      62 .. 0.82
   2 ?    9.4   0.0   0.00016      0.94      13      53 ..     158     195 ..     156     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                            DUF746 12 plslaeaadllgtdegi 28
                                       + + ++a+ lgt +++
  gi|386001069|ref|YP_005919368.1| 45 TITMRQIARVLGTRQRM 61
                                      57889*******98875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00016
                            DUF746  13 lslaeaadllgt.degiiakwvreFrewllqLDPSGqleari 53 
                                       l+++e ++l+g  +e+++ak +r Fr+++    PS q eari
  gi|386001069|ref|YP_005919368.1| 158 LPVMENGKLVGIiSERDVAKSLRAFRDLV----PSSQQEARI 195
                                       89*********6489***********987....777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1835.65
//
Query:       gi|386001070|ref|YP_005919369.1|  [L=285]
Description: Putative signal transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-44  149.8  14.0    6.9e-15   55.2   0.1    4.3  4  CBS              CBS domain
  ------ inclusion threshold ------
       0.18   11.7   0.0        5.4    7.0   0.0    2.9  4  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   2.2e-13     2e-09       1      53 [.       4      55 ..       4      58 .. 0.91
   2 !   55.2   0.1   7.7e-19   6.9e-15       4      56 ..      77     129 ..      72     130 .. 0.94
   3 !   31.5   1.7     2e-11   1.8e-07       1      51 [.     137     187 ..     137     189 .. 0.93
   4 !   32.0   0.1   1.4e-11   1.2e-07       1      53 [.     228     279 ..     227     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.2e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      V+d+m ++v +++ ++++  a +lm ++ +srl+V+d  ++l Givt++D+  
  gi|386001070|ref|YP_005919369.1|  4 VKDYMQSPVYVIDKEEPVQRARNLMLKHYISRLLVMD-GDRLAGIVTKHDISH 55
                                      89**********************99999****9996.556*********965 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 7.7e-19
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +mt++++t++p +t+e+a+e+m+e+g+++lPV  ++g++vGi+t rDll++ +
  gi|386001070|ref|YP_005919369.1|  77 VMTERPITIYPGATVEQAAEIMAENGIDGLPVERDEGEIVGIITSRDLLSYFV 129
                                       7*********************9999******988**************9975 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 2e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDl 51 
                                       Vgd+m   vv+v+   t+  +l++m+e+gv+r+ VV +++  +vG++t + l
  gi|386001070|ref|YP_005919369.1| 137 VGDLMAQGVVSVHRHHTIDHVLDEMVENGVDRV-VVcEDNATPVGVITHTNL 187
                                       89*******************************.77788999******9877 PP

  == domain 4  score: 32.0 bits;  conditional E-value: 1.4e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllr 53 
                                       ++d+m+ ++++  p+    +a++++ ek+ + +lPVV +dgk+vG ++ rD+  
  gi|386001070|ref|YP_005919369.1| 228 AEDVMSYPIIFTGPEVKAIDAAKILLEKEiC-GLPVV-DDGKVVGFFSTRDITA 279
                                       469*********************99***89.*****.6*************76 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.15   1.4e+03      20      48 ..      22      50 ..       4      71 .. 0.62
   2 ?    0.1   0.0     0.082   7.4e+02      24      49 ..      96     122 ..      84     129 .. 0.72
   3 ?    7.0   0.0    0.0006       5.4      17      48 ..     153     184 ..     137     193 .. 0.74
   4 ?   -3.0   0.0      0.71   6.4e+03      36      50 ..     262     276 ..     247     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                   Acetyltransf_10 20 ealrerieegealllvaeeggkivGviel 48
                                      ++ r+ + ++    l++ +g++++G+++ 
  gi|386001070|ref|YP_005919369.1| 22 QRARNLMLKHYISRLLVMDGDRLAGIVTK 50
                                      45555554555555666678888888743 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.082
                   Acetyltransf_10  24 eri.eegealllvaeeggkivGvielr 49 
                                       e + e+g   l v  ++g+ivG+i+ r
  gi|386001070|ref|YP_005919369.1|  96 EIMaENGIDGLPVERDEGEIVGIITSR 122
                                       444356666677888999*****9765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0006
                   Acetyltransf_10  17 ispealrerieegealllvaeeggkivGviel 48 
                                         ++ l+e++e+g   ++v+e++ ++vGvi+ 
  gi|386001070|ref|YP_005919369.1| 153 TIDHVLDEMVENGVDRVVVCEDNATPVGVITH 184
                                       3346778888********************54 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 0.71
                   Acetyltransf_10  36 aeeggkivGvielrd 50 
                                       + ++gk+vG+ ++rd
  gi|386001070|ref|YP_005919369.1| 262 VVDDGKVVGFFSTRD 276
                                       346779999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2064.74
//
Query:       gi|386001071|ref|YP_005919370.1|  [L=318]
Description: Putative signal transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-47  157.8   5.1    1.5e-13   51.0   0.1    4.2  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.3e-10   2.3e-06       4      55 ..      40      92 ..      34      94 .. 0.86
   2 !   51.0   0.1   8.3e-18   1.5e-13       1      56 [.     117     172 ..     117     173 .. 0.96
   3 !   37.6   0.0   1.2e-13   2.1e-09       1      55 [.     180     234 ..     180     236 .. 0.95
   4 !   41.1   0.1   9.9e-15   1.8e-10       5      56 ..     260     310 ..     248     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-10
                                      HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHHH CS
                               CBS  4 imtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllral 55
                                      i t +vvt+pp+tt+  a+++m+++g++rlP+  + g  +l+G vt  D++++l
  gi|386001071|ref|YP_005919370.1| 40 IATNEVVTAPPTTTIIGAIKIMTSYGFGRLPIA-DAGtrRLLGFVTGVDVVDFL 92
                                      36779***************************9.577778******99999887 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 8.3e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +++im+++++++ + +++eeal+lm ek+v++lPVVd++g++  +vt++D +++++
  gi|386001071|ref|YP_005919370.1| 117 IREIMSPRLISIGEKASVEEALRLMYEKNVGGLPVVDDEGRIKALVTEHDFAKLVA 172
                                       589************************************************99875 PP

  == domain 3  score: 37.6 bits;  conditional E-value: 1.2e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                       V+++m++ v+t++ + ++e+  ++m++ g ++ lPVV  d  l+G+vt +D++r+l
  gi|386001071|ref|YP_005919370.1| 180 VEEFMSPSVITANGQISIEKTTKIMVQPGgFRKLPVV-QDSILIGMVTASDIMRYL 234
                                       899************************999*******.6889************98 PP

  == domain 4  score: 41.1 bits;  conditional E-value: 9.9e-15
                                       SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                        +rd+v+   d++l+ a+e+m +kgv++lPV+ + g l+Gi+t+rD +ra +
  gi|386001071|ref|YP_005919370.1| 260 VRRDIVSTEKDADLGWAAETMMDKGVGALPVM-DRGSLLGIITKRDFIRAFA 310
                                       345779**************88**********.6999************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2422.95
//
Query:       gi|386001072|ref|YP_005919371.1|  [L=258]
Description: Putative signal transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-48  162.8   8.5    2.3e-13   50.3   0.2    4.1  4  CBS       CBS domain
    0.00039   20.4   2.6       0.14   12.2   0.1    2.7  3  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.3     8e-16   7.2e-12       1      54 [.       5      58 ..       5      60 .. 0.96
   2 !   29.5   0.0   8.2e-11   7.4e-07      11      55 ..      76     122 ..      67     124 .. 0.87
   3 !   40.3   0.0   3.7e-14   3.3e-10       1      53 [.     132     184 ..     132     185 .. 0.96
   4 !   50.3   0.2   2.6e-17   2.3e-13       1      56 [.     200     254 ..     200     255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8e-16
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      V++im++d+v+v + + +  a +l+r++ +++lP+++++g++vGivt+rD l++
  gi|386001072|ref|YP_005919371.1|  5 VEEIMSKDPVSVEEGDFVTRARQLIRDNQLRGLPILNGEGRVVGIVTDRDMLKV 58
                                      89***********************9999**********************985 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 8.2e-11
                                       EEETTSBHHHHHHHHHHHTSSEE.EEE..ETTTBEEEEEEHHHHHHHH CS
                               CBS  11 tvppdttleealelmrekgvsrl.PVV..dedgklvGivtlrDllral 55 
                                        v+p t+++ea++l+ ++++ ++ PVV   ed +l+G+v+  D+++++
  gi|386001072|ref|YP_005919371.1|  76 LVTPKTDMAEAAKLLLSANY-AIlPVVpsSEDRRLLGVVSPIDIFKKI 122
                                       699***********99****.665***8777779***********987 PP

  == domain 3  score: 40.3 bits;  conditional E-value: 3.7e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       ++d m+r+  t++p++++ ++ + m++++++++PVVde ++++G++t+ D+++
  gi|386001072|ref|YP_005919371.1| 132 AKDAMSRETKTCSPQDPVTKVWDAMVDSDFTGMPVVDERERPLGMITRFDIIK 184
                                       5799***********************************************97 PP

  == domain 4  score: 50.3 bits;  conditional E-value: 2.6e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+ +m+++++tv p+++l++a +lm +++++r+ VV edgklvGi+ + D+++a+ 
  gi|386001072|ref|YP_005919371.1| 200 VEKLMSTPLFTVAPESSLRDASKLMLDREIGRISVV-EDGKLVGIIDRYDVIKAIF 254
                                       7789*********************9**********.9***************985 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   1.6e-05      0.14       4      27 ..      29      52 ..      26      54 .. 0.94
   2 !    7.8   0.0   0.00039       3.5       6      29 ..     158     181 ..     154     189 .. 0.84
   3 ?   -2.9   0.2      0.82   7.4e+03      17      25 ..     236     244 ..     226     250 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                      CCS---TT-EEEETTSSEEEEEEE CS
                               PRC  4 frasdliGkeVytedGeklGkVkD 27
                                      +r ++l+G+++ +++G+ +G V+D
  gi|386001072|ref|YP_005919371.1| 29 IRDNQLRGLPILNGEGRVVGIVTD 52
                                      7899******************99 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00039
                                       S---TT-EEEETTSSEEEEEEEEE CS
                               PRC   6 asdliGkeVytedGeklGkVkDvv 29 
                                        sd+ G++V++e  + lG ++ + 
  gi|386001072|ref|YP_005919371.1| 158 DSDFTGMPVVDERERPLGMITRFD 181
                                       69****************998764 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.82
                                       TTSSEEEEE CS
                               PRC  17 edGeklGkV 25 
                                       edG+ +G +
  gi|386001072|ref|YP_005919371.1| 236 EDGKLVGII 244
                                       345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1915.41
//
Query:       gi|386001073|ref|YP_005919372.1|  [L=172]
Description: Putative signal-transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-23   82.8   4.6    3.8e-16   59.3   0.5    2.3  2  CBS       CBS domain
  ------ inclusion threshold ------
        0.1   12.5   0.9        8.5    6.3   0.1    2.2  2  MreC      rod shape-determining protein MreC
       0.15   11.7   1.8       0.38   10.3   1.8    1.7  1  RecR      RecR protein


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   2.6e-09   1.6e-05      10      55 ..       2      46 ..       1      48 [. 0.84
   2 !   59.3   0.5   6.3e-20   3.8e-16       1      53 [.      58     110 ..      58     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.6e-09
                                      EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS 10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      +t++   ++ +a+++m +++v++l V+  d+++ Gi+t+rDl+ ++
  gi|386001073|ref|YP_005919372.1|  2 ITIDSKVDVVKAANKMFSANVGSLIVI-HDDQPMGIITERDLVGKI 46
                                      78888999889998855899****999.5677**********9887 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 6.3e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+d+m+++++tv+pd +l+ea+ +m ++gv rlPV+ +dgklvGi+t++Dl++
  gi|386001073|ref|YP_005919372.1|  58 VRDVMSSPLITVHPDVSLSEAAIKMLKSGVKRLPVISSDGKLVGIITDTDLVS 110
                                       89***********************9************************985 PP

>> MreC  rod shape-determining protein MreC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0036        21      10      45 ..      15      52 ..      10      79 .. 0.74
   2 ?    6.3   0.1    0.0014       8.5      25      43 ..      88     107 ..      83     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0036
                                      TTEEEES--GGGT--TT..-EEEETTEEEEEEEEE-SS CS
                              MreC 10 nssltIdkGskdgvkkg..mpVvsgkglVGkVtevgkn 45
                                      n+++  ++Gs   ++ +  m ++++  lVGk++   +n
  gi|386001073|ref|YP_005919372.1| 15 NKMFSANVGSLIVIHDDqpMGIITERDLVGKIVARAAN 52
                                      566677778877777662266899999*****875444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0014
                                       TT-EEEETTE.EEEEEEEE- CS
                              MreC  25 kgmpVvsgkg.lVGkVtevg 43 
                                       k  pV+s++g lVG++t++ 
  gi|386001073|ref|YP_005919372.1|  88 KRLPVISSDGkLVGIITDTD 107
                                       4579****99******9875 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.8   6.4e-05      0.38      19      39 ..     145     172 .]     141     172 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.4e-05
                                       -TTT--EESSS.......S-CCCCSTTS CS
                              RecR  19 CsrCgnlteed.......lCaICsdprR 39 
                                       C+rCg ++++        lC  C+d +R
  gi|386001073|ref|YP_005919372.1| 145 CERCGQISDSLesvngelLCWSCRDGNR 172
                                       *********9559999999******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1189.59
//
Query:       gi|386001074|ref|YP_005919373.1|  [L=158]
Description: Molybdenum cofactor synthesis domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-26   93.1   0.0    1.4e-26   92.9   0.0    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   7.7e-31   1.4e-26       2     141 ..       5     148 ..       4     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 7.7e-31
                                       EEEE-HHHH........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   2 vitvGdell........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       v++v+++++        ++ +eD +g  + ++l+++g +   y+++pD  ee+++a+l++  eadv++++GGtG++p
  gi|386001074|ref|YP_005919373.1|   5 VVVVSTSRFrrfgaaaePKGAEDLSGRAILDRLEAAGRSFT-YRLIPDGAEEVRRAILES--EADVVVLCGGTGLAP 78 
                                       789999999888888886668*************9998776.99*************888..55************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGG CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpa 141
                                        D+t e  ++lf+k+++gf+e+fr+ s+++     v++ ail ra      g ++++LPGsp+a+  ++++il  +
  gi|386001074|ref|YP_005919373.1|  79 GDMTIEGAEPLFDKTIPGFGEIFRQRSQEE-----VGTRAILTRAAagvvgGVPVFCLPGSPSAASLGIDLIL-AE 148
                                       *****************************9.....99999****99****6666****************999.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.56
# Mc/sec: 850.77
//
Query:       gi|386001075|ref|YP_005919374.1|  [L=66]
Description: hypothetical protein Mhar_0364, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-16   60.1   0.0    2.1e-16   60.0   0.0    1.0  1  CGGC         CGGC domain
  ------ inclusion threshold ------
      0.088   12.5   0.0        0.1   12.2   0.0    1.1  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   2.4e-20   2.1e-16      42     106 .]       1      66 []       1      66 [] 0.97

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.4e-20
                              CGGC  42 fvtCggCpgkkvveklkelkkegvdvihlssCiktk.kakkeCpeieeikeaieeklgievvegth 106
                                       +++CggCpg+++v+++ke++++g++vi+ls+C++++  ++++C + eei+ ai++++g++vv+gth
  gi|386001075|ref|YP_005919374.1|   1 MASCGGCPGRDAVRQAKEMVRRGAEVIFLSTCMTKPiPSEPACRYSEEIAGAIRKNAGVPVVMGTH 66 
                                       679******************************8888999*************************9 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.1e-05       0.1      22      68 ..      11      53 ..       8      65 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHH CS
                       Pterin_bind 22 kalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvleal 68
                                      +a+ qa++mv+ GA+++ ++   t+P    +++e + +   ++  a+
  gi|386001075|ref|YP_005919374.1| 11 DAVRQAKEMVRRGAEVIFLSTCMTKP----IPSEPACRYSEEIAGAI 53
                                      79***************999999955....45555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 497.59
//
Query:       gi|386001076|ref|YP_005919375.1|  [L=192]
Description: Mn2+-dependent serine/threonine protein kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-10   40.6   0.2    2.1e-05   24.5   0.1    2.3  2  APH             Phosphotransferase enzyme family
    4.5e-09   36.2   0.0    6.8e-09   35.6   0.0    1.2  1  RIO1            RIO1 family
    1.5e-06   27.8   0.0    1.5e-05   24.4   0.0    2.1  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    2.5e-05   23.8   0.0    5.8e-05   22.6   0.0    1.6  1  Pkinase         Protein kinase domain
    7.9e-05   22.4   0.0    9.8e-05   22.1   0.0    1.1  1  WaaY            Lipopolysaccharide core biosynthesis protein 
  ------ inclusion threshold ------
      0.085   12.1   0.0       0.13   11.5   0.0    1.3  1  Pkinase_Tyr     Protein tyrosine kinase
      0.089   12.1   0.0       0.12   11.7   0.0    1.2  1  EcKinase        Ecdysteroid kinase
       0.11   12.1   0.0       0.14   11.7   0.0    1.3  1  Choline_kinase  Choline/ethanolamine kinase
       0.16   11.3   0.0       0.17   11.2   0.0    1.2  1  DUF4135         Domain of unknown function (DUF4135)


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.023      33     108 ..      34     103 ..       9     105 .. 0.78
   2 !   24.5   0.1   1.1e-08   2.1e-05     168     237 ..     105     175 ..     103     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                       -HHHHHHHHHHH.....HHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCC CS
                               APH  33 aaeeirrevall.....rlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaa 104
                                       ++e+irre  ++        ++ gvp+P vl+    d +++     +e v+g  l +    +++p+l e +ge+ ++
  gi|386001076|ref|YP_005919375.1|  34 LDERIRRERTVMesriiSEARRCGVPTPIVLD---VDSFSL----TMEHVEGVKLKD----RIDPALTEGVGELVGR 99 
                                       55555655555444222777788889999999...556666....7***********....9*************** PP

                                       HHCH CS
                               APH 105 lhqv 108
                                       lh++
  gi|386001076|ref|YP_005919375.1| 100 LHAC 103
                                       ***9 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.1e-08
                                       EE-SS-SGGGEEEC..TTEEEEE---TT-EEEECC....HHHHCCH...HHCSCHCCCHCHHHHHHHHCS-HHHHCC CS
                               APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglgppl....yDlavll...rswtseldpeflaallrayeqeaglarl 237
                                       ++HgDl + N++++  + ++ ++iDf++a +   +    +D+ v+    r  ++++ +e+  a++r+y+  + +ar+
  gi|386001076|ref|YP_005919375.1| 105 IVHGDLTTSNMILQ--GEKI-YFIDFGLAFHDQGIeaqgVDVHVFFqtvR-SCHDRPEELISAFGRGYA--RTYARA 175
                                       89************..9999.******99887433111156655556633.699999999999999998..777765 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   3.4e-12   6.8e-09      53     151 ..      41     129 ..      27     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.4e-12
                                       HHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEE CS
                              RIO1  53 lwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvH 129
                                         +  E r+++++++ gvp P ++++ +  l me ++  gv   klkd       + ++ e + e+   ++ +g+vH
  gi|386001076|ref|YP_005919375.1|  41 ERTVMESRIISEARRCGVPTPIVLDVDSFSLTMEHVE--GV---KLKDRI-----DPALTEGVGELVGRLHACGIVH 107
                                       55567999999*************************9..54...555544.....5566777777777889****** PP

                                       SS-STTSEEEETTEEEE--GTT CS
                              RIO1 130 aDLSeyNvlvdedkvviIDvsQ 151
                                       +DL   N++++ +k+++ID++ 
  gi|386001076|ref|YP_005919375.1| 108 GDLTTSNMILQGEKIYFIDFGL 129
                                       *******************985 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   7.8e-09   1.5e-05     112     166 ..      78     127 ..      19     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7.8e-09
                               Kdo 112 waelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                       + +l+++   al + vg l+ +lh+ g+ H+dl   n+ lq e+     i++iD+
  gi|386001076|ref|YP_005919375.1|  78 GVKLKDRIDPALTEGVGELVGRLHACGIVHGDLTTSNMILQGEK-----IYFIDF 127
                                       444788899999****************************9996.....*****9 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.9e-08   5.8e-05       5     146 ..       3     131 ..       1     150 [. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.9e-08
                                       EEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--T CS
                           Pkinase   5 eklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyve 81 
                                       e++G+G+ +++ ka e+ t+            ++  +++++++E +i+ + +   + +   ++ + d++ l +e+ve
  gi|386001076|ref|YP_005919375.1|   3 EEIGRGAEAVITKAGERVTKWRLPKGYRMAALDERIRRERTVMESRIISEARRCGVPT--PIVLDVDSFSLTMEHVE 77 
                                       5677777777777776555544433222222333333356666666666666666654..45667888999999999 PP

                                       TEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                           Pkinase  82 ggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlak 146
                                       g +l+d++             +++ + e +  lH+ gi+H Dl ++N++++  +++  +DFGla 
  gi|386001076|ref|YP_005919375.1|  78 GVKLKDRIDP----------ALTEGVGELVGRLHACGIVHGDLTTSNMILQ-GEKIYFIDFGLAF 131
                                       9999998873..........667778888899******************9.899********95 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.9e-08   9.8e-05     115     178 ..      66     127 ..      35     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.9e-08
                              WaaY 115 vkvyimiieyiegielvdmpeiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriidl 178
                                       v+ + + +e++eg++l d   id ++ + + + + +lh+ g+v gd    n+i++++++  id+
  gi|386001076|ref|YP_005919375.1|  66 VDSFSLTMEHVEGVKLKD--RIDPALTEGVGELVGRLHACGIVHGDLTTSNMILQGEKIYFIDF 127
                                       6788999**********9..699***************************************96 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.4e-05      0.13     119     151 ..     100     131 ..      63     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                                       HHHTTEEEST-SGGGEEEEETTEEEE-STTTHE CS
                       Pkinase_Tyr 119 LeskklvHrdlaarNvLlsenkvvkisDfGLar 151
                                       L++  +vH dl++ N++l+ ++++   DfGLa 
  gi|386001076|ref|YP_005919375.1| 100 LHACGIVHGDLTTSNMILQ-GEKIYFIDFGLAF 131
                                       88999***********999.6677778****85 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.9e-05      0.12     213     251 ..     101     133 ..      66     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                          EcKinase 213 efnvlnHGDlwvnNimfkydeegepedvilvDFQlsryg 251
                                       + + ++HGDl ++N++++ +      +++++DF l+++ 
  gi|386001076|ref|YP_005919375.1| 101 HACGIVHGDLTTSNMILQGE------KIYFIDFGLAFHD 133
                                       567799***********774......89*****998764 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.1e-05      0.14     148     172 ..     106     128 ..      74     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                                       E-S--SGGGEEE.-CTTEEEE--GT CS
                    Choline_kinase 148 cHnDlqegNillnkeekklvlIDFE 172
                                        H Dl  +N++l  + +k+++IDF 
  gi|386001076|ref|YP_005919375.1| 106 VHGDLTTSNMIL--QGEKIYFIDFG 128
                                       5***********..9*********5 PP

>> DUF4135  Domain of unknown function (DUF4135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.6e-05      0.17     138     184 ..      92     138 ..      43     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.6e-05
                           DUF4135 138 raGallallyllgg..tDlheeNliasgeqpvliDlEtlltheaeksae 184
                                        +G+l+  l++ g+   Dl   N+i +ge++++iD+  +++   + ++ 
  gi|386001076|ref|YP_005919375.1|  92 GVGELVGRLHACGIvhGDLTTSNMILQGEKIYFIDFGLAFHD--QGIEA 138
                                       57888888888887446***********************43..33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1330.00
//
Query:       gi|386001077|ref|YP_005919376.1|  [L=89]
Description: DNA/RNA-binding protein Alba [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-19   67.4   0.3    9.2e-19   67.0   0.3    1.1  1  Alba      Alba
  ------ inclusion threshold ------
      0.021   14.2   0.2      0.024   14.0   0.2    1.1  1  DUF4097   Putative adhesin
      0.025   14.5   0.1       0.03   14.3   0.1    1.4  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.3   1.5e-22   9.2e-19       2      67 .]       6      68 ..       5      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.5e-22
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEEE CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltsss 67
                                      +++V+s +p+m+yv+++++++ n++++eV + a+GraIs+Av+vae+ ++rf+ g ++v+++++s+
  gi|386001077|ref|YP_005919376.1|  6 VVFVGS-KPVMNYVLAVVTQF-NSGAGEVKIMARGRAISRAVDVAEVSRSRFL-GDVKVKDIQIST 68
                                      799***.**************.******************************8.66*****99985 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   3.9e-06     0.024      90     142 ..      29      86 ..      18      89 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-06
                           DUF4097  90 sGdlsvek.....atklkaetlelksss..GdltlsnvsaktltvksesGdvtiegseak 142
                                        G++++        + + + +++ +  +  Gd+++++++++t t++++ G+ +++ +e++
  gi|386001077|ref|YP_005919376.1|  29 AGEVKIMArgraiSRAVDVAEVSRS--RflGDVKVKDIQISTETLNTDRGETNVSAIEIT 86 
                                       4566644334422233333333333..255***********************9999987 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     5e-06      0.03      59      87 ..      27      55 ..       4      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                             Rpp20 59 lkkeeVfvkatGrAiekalsvgrwfqeke 87
                                          eV + a GrAi +a+ v++  +++ 
  gi|386001077|ref|YP_005919376.1| 27 SGAGEVKIMARGRAISRAVDVAEVSRSRF 55
                                      56789****************98764443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 564.41
//
Query:       gi|386001078|ref|YP_005919377.1|  [L=205]
Description: Phosphoribosylglycinamide formyltransferase [Methanosaeta harundinacea 6Ac]
Scores for 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-51  172.2   0.0    9.9e-51  172.0   0.0    1.0  1  Formyl_trans_N  Formyl transferase
     0.0096   15.7   0.0       0.03   14.1   0.0    1.9  2  ubiquitin       Ubiquitin family
  ------ inclusion threshold ------
       0.15   12.4   1.1       0.76   10.1   0.1    2.3  3  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0   0.0   1.7e-54   9.9e-51       2     181 .]       4     182 ..       3     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 1.7e-54
                                       EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCT CS
                    Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkel 78 
                                       +i v+ sg g+nl+++++a ++g l a+v++v+ ++++a  l+ a+ a+i +  ++  +l +  +++  lae l+ +
  gi|386001078|ref|YP_005919377.1|   4 RIGVISSGRGENLRHIIEAISSGRLPAEVAVVLADQPEAGALRIARGAGIEAAFVDPTGLGRA-EYDARLAEHLDRA 79 
                                       7889*******************************************************9987.9************ PP

                                       T-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE CS
                    Formyl_trans_N  79 kadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkve 155
                                       ++dl+vl gym++l++e+v+++r++ +niHp+LLP+f+G++a q+al  G+k+tG+t+h vdee+D+G+i++q +ve
  gi|386001078|ref|YP_005919377.1|  80 GVDLVVLTGYMRILTPEFVRRFRGRTINIHPALLPSFPGLDAFQQALDYGVKVTGTTVHLVDEEVDHGPIIHQVAVE 156
                                       ***************************************************************************** PP

                                       --TT--HHHHHHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 156 iiaedtkeeleqrvadaehkalveal 181
                                       + ++dt e+l++r+++ae +a++eal
  gi|386001078|ref|YP_005919377.1| 157 VREDDTHESLKARIQEAEYRAYPEAL 182
                                       ***********************986 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.43   2.6e+03      56      68 ..     127     140 ..     123     144 .. 0.73
   2 !   14.1   0.0   4.9e-06      0.03      10      41 ..     152     184 ..     130     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.43
                                       GHTTSTT.EEEEEE CS
                         ubiquitin  56 eygiqdg.stlhlv 68 
                                       +yg++   +t+hlv
  gi|386001078|ref|YP_005919377.1| 127 DYGVKVTgTTVHLV 140
                                       67776444999997 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.9e-06
                                       EEEEEEETTSBHHHHHHHHHHHH.TSSGGGEEE CS
                         ubiquitin  10 kitleveesdtveelKekiaeke.gipaeqqrL 41 
                                       ++ +ev e+dt e+lK++i+e e +  +e +rL
  gi|386001078|ref|YP_005919377.1| 152 QVAVEVREDDTHESLKARIQEAEyRAYPEALRL 184
                                       7899*****************997777777777 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.21   1.2e+03     104     146 ..       5      55 ..       3      65 .. 0.69
   2 ?   10.1   0.1   0.00013      0.76      85     123 ..      63     102 ..      35     113 .. 0.75
   3 ?   -0.1   0.1      0.18   1.1e+03      66      95 ..     159     186 ..     119     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.21
                               HAD 104 vvvvSgg....lrplvepll.aelg..adevlatelevdd.rltgelgleg 146
                                       + v+S+g    lr+++e++   +l   +  vla + e  + r+ +++g+e 
  gi|386001078|ref|YP_005919377.1|   5 IGVISSGrgenLRHIIEAISsGRLPaeVAVVLADQPEAGAlRIARGAGIEA 55 
                                       566766656668888888885477777777788888877777766666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                               HAD  85 lldpgalellaahr.aaGdrvvvvSgglrplvepllaelg 123
                                       l + +  ++la+h+ +aG+ +vv++g +r+l+ ++ +++ 
  gi|386001078|ref|YP_005919377.1|  63 LGRAEYDARLAEHLdRAGVDLVVLTGYMRILTPEFVRRFR 102
                                       444566778888888*****************99997764 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.18
                               HAD  66 seelaaelerfvaevirpklldpgalella 95 
                                       +++ ++ l++ ++e+  ++ + p+al+l+ 
  gi|386001078|ref|YP_005919377.1| 159 EDDTHESLKARIQEAEYRA-Y-PEALRLFI 186
                                       4555666666665555544.4.77777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1357.25
//
Query:       gi|386001079|ref|YP_005919378.1|  [L=162]
Description: Histidine triad (HIT) protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-12   46.6   0.0    6.2e-12   46.1   0.0    1.3  1  HIT       HIT domain
    1.7e-06   28.5   0.0    2.4e-06   28.0   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    0.00027   20.8   0.1    0.00041   20.2   0.1    1.4  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0     1e-15   6.2e-12      14      95 ..      43     125 ..      31     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1e-15
                                       SEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSS.S-E CS
                               HIT  14 lvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsva.hlH 89 
                                       + +++ +  p   ghl v+p++h+s+l   + ee+a++l++++  ++ l+k+++ +g+++ in g+ ag  +a h+H
  gi|386001079|ref|YP_005919378.1|  43 HHFIIMNAYPYNNGHLMVVPRRHTSTLAGWSSEERAEFLELADLAVAILKKTMNPDGFNIGINMGECAGAGIAsHIH 119
                                       568999*************************************************************9997744*** PP

                                       EEEEEC CS
                               HIT  90 iHvipr 95 
                                       +Hv+pr
  gi|386001079|ref|YP_005919378.1| 120 LHVVPR 125
                                       ****98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     4e-10   2.4e-06       2     100 ..      21     123 ..      20     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4e-10
                                       -HHHH.HHTTSS-B-EEEE-.SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C   2 wvfni.lakgkepervvyed.ekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       ++f++ + +++++e+++++   +  ++  ++p ++ hl+v+p+r+ ++l   ++e+     e+ + a +++++ +  
  gi|386001079|ref|YP_005919378.1|  21 CIFCEkIDEDRDAENLILHRgVHHFIIMNAYPYNNGHLMVVPRRHTSTLAGWSSEERAEFLELADLAVAILKKTM-- 95 
                                       777751566666999988777666666789**********************9999999999*********9988.. PP

                                       -EEEEE--SCCCT-.....-S-S--EEEE CS
                            DcpS_C  77 vdaeelrvgvhyqP.....svyhlHlHvi 100
                                        +++ +++g+++         +h+HlHv+
  gi|386001079|ref|YP_005919378.1|  96 -NPDGFNIGINMGEcagagIASHIHLHVV 123
                                       .67888888888877777899*******8 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   6.8e-08   0.00041       8      75 ..      15      84 ..       9     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.8e-08
                                      HHHHHH-S--..--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHH CS
                          CwfJ_C_1  8 kasldsClfC..lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfr 75
                                      +++ + C fC  +++ + +++li+  g + ++ +   p ++gH++++p  H+s+l   + e++ e  +  
  gi|386001079|ref|YP_005919378.1| 15 SEKAGACIFCekIDEDRDAENLILHRGVHHFIIMNAYPYNNGHLMVVPRRHTSTLAGWSSEERAEFLELA 84
                                      667899****888999999************************************999999888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 974.41
//
Query:       gi|386001080|ref|YP_005919379.1|  [L=94]
Description: hypothetical protein Mhar_0369 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.16   12.1   0.0    1.1  1  GH114_assoc  N-terminal glycosyl-hydrolase-114-associated dom


Domain annotation for each model (and alignments):
>> GH114_assoc  N-terminal glycosyl-hydrolase-114-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.1e-06      0.16      23      68 ..      19      64 ..      10      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-06
                       GH114_assoc 23 sggaqaefefslPsavadadvssltlevsalvptk.sgdrWkvdlfl 68
                                      +gg ++e ef   +a  +a++ sl+ e+  l++ + s ++W++++  
  gi|386001080|ref|YP_005919379.1| 19 TGGEKFEQEFYMTAAEVAATLRSLADEIEGLGRVEaSTGDWTLGV-S 64
                                      569999************************************998.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 729.66
//
Query:       gi|386001081|ref|YP_005919380.1|  [L=148]
Description: hypothetical protein Mhar_0370 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-05   24.6   0.0    4.8e-05   23.4   0.0    1.5  1  DUF523    Protein of unknown function (DUF523)


Domain annotation for each model (and alignments):
>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.7e-09   4.8e-05      36     125 ..      32     128 ..       6     134 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.7e-09
                            DUF523  36 lvpv.CPEvaggLptPRepaelakrvlkkegedvtealekgaeealeelkeeeikg.ailkekSPSCGveki...Y. 106
                                       ++++ CPE    L+  R ++  + ++   + + + +++ +  ++++e l++++ k+ ++  +kSPSCG  ++   Y 
  gi|386001081|ref|YP_005919380.1|  32 IIQLpCPEAG-HLGLDRWEVTKN-QIDVPSYRRYCRQVFAHQADLIELLAKKGHKIeVVGVAKSPSCGAASTtegYt 106
                                       4555599975.577788777775.4444455555555555555556655555544415678*********9999996 PP

                            DUF523 107 ....dgtfskklvegeGvfaall 125
                                           +   ++++v+g+G+f++ +
  gi|386001081|ref|YP_005919380.1| 107 ggriR-PQEHDHVSGMGIFMEEV 128
                                       54431.22455699*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 978.10
//
Query:       gi|386001082|ref|YP_005919381.1|  [L=147]
Description: hypothetical protein Mhar_0371 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.7   0.1       0.08   13.3   0.1    1.2  1  bPH_3     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.5e-06      0.08      22      75 ..      60     112 ..      40     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-06
                             bPH_3  22 pglivvTnkRiifldpkmfggkdfeeipYksIksvdlkkgllgakitletsgkt 75 
                                       +++iv+T+  ++f++++ + +++++ +++  I+ +++ k+  +++++++++   
  gi|386001082|ref|YP_005919381.1|  60 SSWIVATEGEVVFIRAG-LIRNRVDRFSLPRITGIEYVKEFQDNTLKIRIGEAA 112
                                       789**************.779***********************9999985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 1173.14
//
Query:       gi|386001083|ref|YP_005919382.1|  [L=373]
Description: hypothetical protein Mhar_0372 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-77  258.6   0.0    3.7e-77  258.1   0.0    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    3.8e-46  156.0   0.0    6.2e-46  155.3   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.1   0.0   4.1e-81   3.7e-77       1     188 []     182     373 .]     182     373 .] 0.99

  Alignments for each domain:
  == domain 1  score: 258.1 bits;  conditional E-value: 4.1e-81
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-. CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelev. 76 
                                       e++ek+e ll++g+i+++ l+ a+ie+yv+G  fnl++fysp+ ++vellgid+R+es+ldg+vr+pa +ql+l++ 
  gi|386001083|ref|YP_005919382.1| 182 EYREKSELLLKHGVIDQDGLDLARIERYVIGPVFNLDFFYSPILDQVELLGIDWRFESSLDGHVRIPAPQQLTLNEa 258
                                       799*********************************************************************99988 PP

                                       ..---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT CS
                           DUF1297  77 ..epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme 151
                                         +pey+v+G+++++lREsllek+f+l+ek+vea+k  ++pGiiGpFcLq++v+kdl++ ++dv++Ri+ggtnv+m+
  gi|386001083|ref|YP_005919382.1| 259 qvSPEYTVCGHNSATLRESLLEKAFDLAEKYVEATKVHYSPGIIGPFCLQTCVDKDLNFSIYDVAPRIGGGTNVHMA 335
                                       889************************************************************************** PP

                                       .--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 152 .gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                                        g+py + l+++++s+Grr+ +E++ a+ekd le+ivt
  gi|386001083|ref|YP_005919382.1| 336 vGHPYGNALWRTSMSTGRRLMREVRIALEKDALEKIVT 373
                                       *************************************8 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.0     7e-50   6.2e-46       1     121 [.      14     149 ..      14     150 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 7e-50
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT............TT-SEEEE.S.S..TTSS--HHHHHHT CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf............kvidevivldkfkdilkeevqeklree 65 
                                       i+++aSHsal++++gA +egfrtlavc+kgrek+Y k+            +v+dev +l++f+d++++e+q+ l+++
  gi|386001083|ref|YP_005919382.1|  14 IGVVASHSALDTCDGAVEEGFRTLAVCQKGREKTYAKYfrttrvggrvasGVVDEVRILNRFSDLVRSEQQDALISK 90 
                                       89*************************************************************************** PP

                                       TCEE--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--B CS
                           DUF1246  66 nailvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkk 121
                                       n+++vP++sf++Y+gi+++e e++vp++G+r+llr+Eer e++++y  LekAg+++P++
  gi|386001083|ref|YP_005919382.1|  91 NVLFVPNRSFTSYCGIDSVEdEFEVPLLGSRNLLRSEERGEEQDYYwiLEKAGLPFPET 149
                                       *********************************************99**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 2460.38
//
Query:       gi|386001084|ref|YP_005919383.1|  [L=256]
Description: Tungsten formylmethanofuran dehydrogenase, subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.5  21.4    4.2e-06   26.5  10.1    4.0  2  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   2.8   0.00011         2     132     161 ..      80     109 ..      75     111 .. 0.77
   2 !   26.5  10.1   2.3e-10   4.2e-06      34     146 ..     108     214 ..     107     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00011
                                       TTTT-EEEEEEE-S-B-SSBTTT--EEEEE CS
                             GXGXG 132 gceYmtGGvvvvLgktgrnfaaGmsgGiay 161
                                       ++e mt G++ v g+ g++ + Gm gG + 
  gi|386001084|ref|YP_005919383.1|  80 IGEKMTCGMIEVDGDLGMHAGNGMAGGEIS 109
                                       578888888888888888888888888764 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.3e-10
                                       EEEEEEE-TTTTTT--TTEEEEEEEEE-STTTT.......T-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--SEE CS
                             GXGXG  34 iklkGsaGqslgaflakGltleleGdandyvGk.......glsgGkivikpskeskfkaeeniivGnvvlygatgGk 103
                                       i+++G aG+ lg  + +G  ++++Gda dyvG        g+ gG+i i++++            G+ +     gGk
  gi|386001084|ref|YP_005919383.1| 108 ISIRGGAGDWLGREM-RGGLINVSGDAGDYVGAgyrgescGMRGGEIRIEGDA------------GDYLGEHLCGGK 171
                                       899************.8889************833333335888888888888............************ PP

                                       EEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S- CS
                             GXGXG 104 lfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgk 146
                                       + + g+ag+  ++ n+g +++++g  +  +  m+ G++ v+g+
  gi|386001084|ref|YP_005919383.1| 172 ITVLGDAGDFPGIANRGGVIIIGGDAHLPGAEMASGTITVFGR 214
                                       ****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1837.90
//
Query:       gi|386001085|ref|YP_005919384.1|  [L=561]
Description: Tungsten formylmethanofuran dehydrogenase, subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-84  284.2   0.4    3.5e-84  284.0   0.4    1.1  1  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.016   14.5   0.0        5.3    6.2   0.0    2.7  3  Amidohydro_1  Amidohydrolase family
       0.03   14.0   0.1        1.3    8.8   0.0    2.6  2  Cupin_2       Cupin domain


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.0   0.4   5.8e-88   3.5e-84       3     473 .]      39     496 ..      37     496 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.0 bits;  conditional E-value: 5.8e-88
                      Amidohydro_3   3 iDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwi.vgeGwdeaqfaeerfp 77 
                                       iDa+G+lv+PG+ D+H+H+ag++vn  r +r++d r+  +e+ +             +++   +G+++++ ++ +++
  gi|386001085|ref|YP_005919384.1|  39 IDARGMLVMPGGLDAHAHIAGAKVNTgRIMRPEDGRRG-AEART-------------KLLrPQSGYTVPNCYAIGYR 101
                                       9*********************************5553.33333.............345567789*********** PP

                      Amidohydro_3  78 yalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlapla 154
                                       ya+ ++++++e+a+++l+a++tH+++  +++ d+            g++  ++n++++++ +r+g           +
  gi|386001085|ref|YP_005919384.1| 102 YARLGYTTAFEAATPILEARHTHEELEEIPIVDK------------GALTLFGNNWEVLECVRDG-----------D 155
                                       **********************************............*******************...........* PP

                      Amidohydro_3 155 reaeaaavaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls. 223
                                         ++aa+va++l+a ++yG+++v       ++ ggnv + dd++p f++t++e      ii +l+ a+e lglp+s 
  gi|386001085|ref|YP_005919384.1| 156 LGKLAAFVAWGLRASRGYGVKVVnpgggeaWGFGGNVKGIDDPVPNFGVTPRE------IIRGLMRANEALGLPHSv 226
                                       *****************************************************......9***************** PP

                      Amidohydro_3 224 .........pgseeltigavklfadgvl..gsrtalltepyf.....tgwpdfedea..laelvaaadergldvaih 282
                                                pg++e+t++++++ +d++   +++++++t+ +f     tgw+dfe++a  +a +++++++ ++d++++
  gi|386001085|ref|YP_005919384.1| 227 hlhtnnlgkPGNYETTLETLRAVEDIAAsrDRQVLHVTHMQFsayggTGWKDFESKApeIAGYFNRHQQFTMDMGQL 303
                                       *************************65544999******************************************** PP

                      Amidohydro_3 283 aigdaavd..dvldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlgp 351
                                       ++g a+++  d++ ++ +a   ++k++n+d  +le ++gv    +  + ++ a+q+a+g++                
  gi|386001085|ref|YP_005919384.1| 304 IFGSATTMtaDAPLEYGNArllKAKWSNHDI-ELEESSGVvplVYGRKMPINAIQWAIGLE---------------- 363
                                       *******************************.********9********************................ PP

                      Amidohydro_3 352 erargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.............evlrpdeelsleeal 414
                                               +++l++++++v++++D +++gpf ++p+++a++m+++ r++              ++ +++e+ +e+++
  gi|386001085|ref|YP_005919384.1| 364 --------LALLTEDPWQVIMTTDhPNGGPFVNYPEVIALLMSRAKREEelaslhelassrsSLPSIEREMGWEDIA 432
                                       ........*************************************9999**************************** PP

                      Amidohydro_3 415 alyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear......vrltvvdGrvvy 473
                                         +++gpA++lgl+++ G+L+ Gad+D+ ++d+dp ++dp++++e +      +++t+++G+vv+
  gi|386001085|ref|YP_005919384.1| 433 IVTRAGPARILGLPEK-GHLGFGADGDVSIYDIDPKKLDPSKDHERVkaalsrAKYTIKGGEVVV 496
                                       ***************8.****************************99****************97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0017        10       1      16 [.      45      60 ..      45     103 .. 0.85
   2 ?   -1.8   0.0      0.25   1.5e+03     113     148 ..     224     260 ..     201     341 .. 0.75
   3 ?    6.2   0.0   0.00089       5.3     268     322 ..     415     476 ..     353     502 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0017
                                      EEEE-EEEEEEECETT CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqs 16
                                      +v+PG+ DaH H+ + 
  gi|386001085|ref|YP_005919384.1| 45 LVMPGGLDAHAHIAGA 60
                                      59***********754 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.25
                                       TTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEE CS
                      Amidohydro_1 113 adgvvk.valapheapafsdeelkealkeakkrdlpv 148
                                       +++ +    l+ ++ ++++ e+l+++ + a+ rd +v
  gi|386001085|ref|YP_005919384.1| 224 HSVHLHtNNLGKPGNYETTLETLRAVEDIAASRDRQV 260
                                       4444444556666666666666666666555555544 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.00089
                                       HHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT.........C CS
                      Amidohydro_1 268 qrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi.........l 322
                                       +r++l + e+  + ++++  ++  ++A++lgl+ ++G +  G d D  + d d+          
  gi|386001085|ref|YP_005919384.1| 415 SRSSLPSIER-EMGWEDIAIVTRAGPARILGLP-EKGHLGFGADGDVSIYDIDPkkldpskdhE 476
                                       4455555223.356677555666799******7.***************999444455555441 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.023   1.4e+02      12      33 ..     120     141 ..     113     155 .. 0.84
   2 ?    8.8   0.0   0.00022       1.3      30      64 ..     485     521 ..     484     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.023
                                       EEECSSSEEEEEEEEESEEEEE CS
                           Cupin_2  12 pshrHpgedeffyVleGegelt 33 
                                        +h+H++ +e+ +V +G ++l 
  gi|386001085|ref|YP_005919384.1| 120 ARHTHEELEEIPIVDKGALTLF 141
                                       489999999********99985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00022
                                       EEEEECTEEEEEETTEEEEE-TT-EEEEEE..-SSS- CS
                           Cupin_2  30 geltvdgeeveleaGdsvyfpagtpHrfrN..tgdep 64 
                                       +++t+ g ev++++G++v +p g+  ++    ++de+
  gi|386001085|ref|YP_005919384.1| 485 AKYTIKGGEVVVRDGEIVAVPQGRTYWVDAsvPEDEA 521
                                       689999*****************88887443355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 4205.32
//
Query:       gi|386001086|ref|YP_005919385.1|  [L=430]
Description: Tungsten formylmethanofuran dehydrogenase, subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-16   60.0   0.0    6.7e-15   55.0   0.0    2.3  1  Molybdopterin  Molybdopterin oxidoreductase
      0.005   16.6   0.7        1.6    8.4   0.2    3.7  3  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   7.5e-19   6.7e-15       1     417 [.      46     409 ..      46     412 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 7.5e-19
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R   PmvR    g+G++v+ + +eA++  a+ lk+    + p        ++++s++     +kl  ll  ++++++
  gi|386001086|ref|YP_005919385.1|  46 RTAAPMVR----GDGELVETTYEEAYDRAARILKE---AKRP------LLYGWCSTVC--ETAKLGILLAEEVGGVV 107
                                       5668****....8**********************...8888......3455554332..2345555555555569* PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG.-SEEEEESS-HHHHSHHHHHHHHHHHHTTC........-EEE CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlen.sdliilwGsNvreerpilnarirkaalkkk........akvi 145
                                       d+ a ++++     ig +++     + +l+++ n +dli+ wG+N++e +p  ++r    a+  +         kvi
  gi|386001086|ref|YP_005919385.1| 108 DSTATVCHGPS--IIGIEEK--GMAGATLGQIKNrADLIVFWGANPAEAHPRHTGRYSSNARG-MftpegrggRKVI 179
                                       ********997..6777655..66667799998779*****************5554444433.456667789**** PP

                                       EECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHH CS
                     Molybdopterin 146 vigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvar 222
                                       v++ r + ++k ad+ + i+pgtd +++ a++  ++ ++k                           + +  + va+
  gi|386001086|ref|YP_005919385.1| 180 VVDVRETRTAKNADKFILIRPGTDYEVLSALR--MIVKGKGEI------------------------VPETVAGVAK 230
                                       ***************************88888..777777777........................2234455666 PP

                                       HHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCC CS
                     Molybdopterin 223 iarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvll 299
                                          e a+ +  +a+   +++G gl+h++    ++  +++L++ ++   +    + +++G +++ag        ++ +
  gi|386001086|ref|YP_005919385.1| 231 SDLEEAAAMMMAAKFGVVLIGLGLTHSRGRYKNVDNALSLVADLNGFTK--FVVMAMRGHYNVAG---FGQVCAWST 302
                                       66666666666666699999*******7777777777777664331111..12223333222333...333334444 PP

                                       CCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCS CS
                     Molybdopterin 300 svkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrl 376
                                        ++        +++  +g   ++p++++    +ll +++ ++l ++  +p  + + +  +         v+ +d + 
  gi|386001086|ref|YP_005919385.1| 303 GFP-------MAVDLSRGAPYFNPGETAA--CDLLARKEADALMVVAADPASNFPRATVE---AMAEIPVIQIDPFP 367
                                       555.......5555666666666666665..67888888899966664443333333333...348899******** PP

                                       SHHHHTSSEEEEBE-C.CGSEEEEE-TTSEEEEEEESSS-ST CS
                     Molybdopterin 377 tstalyaDiiLPaatw.yEkedlytndegrfqhlkqavsppg 417
                                       + t l aD++ P+a   +E e++   ++g   ++k++v++p+
  gi|386001086|ref|YP_005919385.1| 368 NPTTLLADVVIPTAVCgIEAEGTAYRMDGLSLRMKKVVDSPY 409
                                       ************996538*********************996 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2   0.00018       1.6       2     120 ..      68     192 ..      67     210 .. 0.66
   2 ?    2.5   0.0     0.012   1.1e+02       1      26 [.     233     258 ..     233     275 .. 0.85
   3 ?   -0.7   0.0      0.12   1.1e+03      75     113 ..     329     367 ..     314     371 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00018
                                       HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE...EEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHH CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv...vttlmgkgvipedhplylgmlglhgskaaneal 75 
                                       ++aa +lk+akrp+++ G      ++++    lae++g  v   +t  +g ++i  +++   gm+g     +  ++ 
  gi|386001086|ref|YP_005919385.1|  68 DRAARILKEAKRPLLY-GWCSTVCETAKLGILLAEEVGGVVdstATVCHGPSIIGIEEK---GMAGA----TLGQIK 136
                                       6899999999999887.555555678888888888888888654444566777776666...55554....456666 PP

                                       HH-SEEEEES-S...SSTCCCTT....TTT.TTTTT...-.EEEEEESSCCCCTTCC CS
                      TPP_enzyme_M  76 eeaDlvlalGar...fddirttg....sep.efape...a.kiihididpaeigkny 120
                                       ++aDl+++ Ga+    +  r+tg    + +  f pe   + k+i +d+ ++   kn 
  gi|386001086|ref|YP_005919385.1| 137 NRADLIVFWGANpaeAHP-RHTGryssNARgMFTPEgrgGrKVIVVDVRETRTAKNA 192
                                       778999999988554333.55663333333344444776457999999988888885 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.012
                                       HHHHHHHHHH-SSEEEEE-CHHCHTT CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsg 26 
                                       +e+aa+++ aak  v+l+G g   s+
  gi|386001086|ref|YP_005919385.1| 233 LEEAAAMMMAAKFGVVLIGLGLTHSR 258
                                       589****************9998774 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.12
                                       H.HH-SEEEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSC CS
                      TPP_enzyme_M  75 l.eeaDlvlalGarfddirttgsepefapea.kiihididp 113
                                       + +eaD ++++ a+    +  ++ +++a  +  +i+id+ p
  gi|386001086|ref|YP_005919385.1| 329 ArKEADALMVVAADPASNFPRATVEAMA--EiPVIQIDPFP 367
                                       3378999999997743311111222222..33688888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 3382.07
//
Query:       gi|386001087|ref|YP_005919386.1|  [L=135]
Description: Tungsten formylmethanofuran dehydrogenase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   41.6   0.0    1.4e-10   41.2   0.0    1.2  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   7.6e-15   1.4e-10       3     108 ..      12     106 ..      10     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 7.6e-15
                                       EEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                   Molydop_binding   3 LitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                       +i+gr+l+q  +  ++++ +  ++++  ++ +   d  alGi ++ +V v++ +G+v+v ak + +++pG +f+p+g
  gi|386001087|ref|YP_005919386.1|  12 MISGRTLGQGATCEAKMSPEFFRATS--TCSLADSDYDALGIPEDGNVLVRNGFGEVVVSAKRDGGLPPGLIFIPMG 86 
                                       67888888887776666555555544..89999******************************************** PP

                                       HCC.....S-GHCTS--SCSTTT--CSTT CS
                   Molydop_binding  80 wweagekggnaNaltddatdplsgtpefk 108
                                        w+        Na++ ++t   +gtp fk
  gi|386001087|ref|YP_005919386.1|  87 PWA--------NAVVGPET-GGCGTPLFK 106
                                       ***........99984443.445666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1101.78
//
Query:       gi|386001088|ref|YP_005919387.1|  [L=164]
Description: 3-isopropylmalate dehydratase small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-19   69.4   0.1    1.2e-18   67.8   0.2    1.6  2  Aconitase_C    Aconitase C-terminal domain
     0.0023   17.6   0.0     0.0057   16.3   0.0    1.7  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   2.3e+03      14      47 ..       9      42 ..       6      54 .. 0.76
   2 !   67.8   0.2   1.3e-22   1.2e-18      75     123 ..      53     100 ..      48     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                      HHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSB CS
                       Aconitase_C 14 deksnvdtdlkipkqfegtianiglgnelveekr 47
                                      ++k+ vdtd++ip+  + + +  gl   ++e++r
  gi|386001088|ref|YP_005919387.1|  9 KFKDDVDTDAIIPGRYLVINDPEGLARYVFEGVR 42
                                      5788999999999988777766666666666665 PP

  == domain 2  score: 67.8 bits;  conditional E-value: 1.3e-22
                                       -EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                       Aconitase_C  75 klvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                       ++vv+ g nfG+GSSRehA+++l+  G+kav+a SF+rIf +n+i+ gl
  gi|386001088|ref|YP_005919387.1|  53 DFVVA-GRNFGCGSSREHAPLGLKGAGVKAVVARSFARIFFRNAINIGL 100
                                       55555.5****************************************96 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.3e-07    0.0057      96     167 ..      82     154 ..      52     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.3e-07
                                       EEEEEE-HHHHHHHHHTT.-EEEE---TT--TT-EEEEETTTTEEEE.TT--EEEE---S-TCHHHHHHHTSHH CS
                     Aconitase_2_N  96 vlGgkiaPiFfntvedsG.alpieadvskletGdvieikpkegkikk.eegevvsefklkpetlldevraggri 167
                                       v+  + a iFf  + + G  l i+ dv++++ Gd iei++ +g i + ++ge   +  l p  l++ v agg +
  gi|386001088|ref|YP_005919387.1|  82 VVARSFARIFFRNAINIGlPLFISPDVERIRDGDEIEIDADAGVIFNrSRGENYPTTPL-PPFLQEIVEAGGLV 154
                                       55667899999766666636999**********************99667777777776.67899999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1207.78
//
Query:       gi|386001089|ref|YP_005919388.1|  [L=375]
Description: 3-isopropylmalate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for 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-99  332.5   0.0    3.4e-99  332.3   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.3   0.0  1.9e-103   3.4e-99       1     348 []       4     367 ..       4     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 332.3 bits;  conditional E-value: 1.9e-103
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.S CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.e 76 
                                       k+++++gdgiGpe+v++  kv +aa+ek+g e+e+  + +G+  + etge + e+tl+ + +++++ lg++g p  +
  gi|386001089|ref|YP_005919388.1|   4 KVPVIPGDGIGPEIVAEGQKVAEAAAEKHGFEIEWTTFSLGADHYLETGELVGEDTLKDLSRYRAIYLGSIGDPRvK 80 
                                       699************************************************************************77 PP

                                       SSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET.......... CS
                            Iso_dh  77 kevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg.......... 143
                                        +v  +  Lla+r  +d ++nlrpvk++  ++v +plk++ ++++d+v+vRe+t++ Y+g+ + ++           
  gi|386001089|ref|YP_005919388.1|  81 PGVLEKGVLLAMRFYFDQYVNLRPVKLL--EGVWTPLKDKGPKDIDFVVVRENTEDFYIGIGSRARAgrsraefevi 155
                                       77777779********************..89*****************************99998889******** PP

                                       .............TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC CS
                            Iso_dh 144 .............sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee 206
                                                    s +++e a+++ ++s+e+++r++++af+lA +r +k++ +vdKanvl+    +wr+++e +a+ 
  gi|386001089|ref|YP_005919388.1| 156 rtlyqvkfgldvdS-ESDEIAYQIGMISKEGTRRVIKYAFDLATAR-RKHLSSVDKANVLSDIYgFWREEFEALAT- 229
                                       **********9743.789****************************.*************98877***********. PP

                                       TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCT CS
                            Iso_dh 207 eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdia 283
                                       eyp++  +  +vD+++m  vk+p+ fdV+v++N+fGDi+ D+ a++ G+lGl+p+a+++++++ +fE++HGsap++ 
  gi|386001089|ref|YP_005919388.1| 230 EYPEVSTDFNFVDAITMWFVKNPEWFDVVVAPNMFGDIITDLGAMIQGGLGLAPGANINPEGTSMFEPIHGSAPKYK 306
                                       ***************************************************************************** PP

                                       TSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 284 gkdkaNpiavilSaalmLryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgdav 348
                                       g++k+Npia+i + a++L++ lg+ eaA+++ +A+e +++  +++T+D++g+a    +tse+gd++
  gi|386001089|ref|YP_005919388.1| 307 GQNKVNPIATIWAGAMLLEH-LGEGEAAEDVVRAIETNIKRgKVRTYDMGGSA----TTSEVGDDI 367
                                       ********************.********************899*********....******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 2755.30
//
Query:       gi|386001090|ref|YP_005919389.1|  [L=78]
Description: DNA-directed RNA polymerase subunit H [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-28   98.0   0.0    2.2e-28   97.9   0.0    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   1.2e-32   2.2e-28       3      73 .]       6      76 ..       4      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.2e-32
                                      -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      +++H+lvP+h +l++ee++e+++ ++++  qLPki+++Dpv++++g k GdvvkI r+s+t+ge+v YRlV
  gi|386001090|ref|YP_005919389.1|  6 LQDHDLVPEHILLTPEEAEEVFRAYGVDSAQLPKIHATDPVVKEIGGKVGDVVKIKRNSPTSGESVFYRLV 76
                                      579*******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 592.57
//
Query:       gi|386001091|ref|YP_005919390.1|  [L=496]
Description: DNA-directed RNA polymerase, subunit B' [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-52  177.4   0.1    2.9e-52  177.1   0.1    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    6.4e-27   94.4   0.1    9.6e-27   93.8   0.1    1.2  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    2.8e-26   91.5   0.0    5.2e-26   90.6   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
  ------ inclusion threshold ------
       0.14   10.9   0.0       0.23   10.1   0.0    1.2  1  Acetate_kinase  Acetokinase family


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   0.1   6.5e-56   2.9e-52       2     202 ..      17     384 ..      16     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 6.5e-56
                                       TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYs 78 
                                       Lv+ +++SFn+f++  l+k+i+e   ie++ e+       ++k++sir+++P+v+e+d+s +++yP++arlrnltY 
  gi|386001091|ref|YP_005919390.1|  17 LVHHHINSFNDFIDSGLQKVIDEVGIIETNIEE------TYVKLGSIRVENPTVTEADGSVERLYPNDARLRNLTYA 87 
                                       99***********************99999997......69************************************ PP

                                       EEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  79 aplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek 155
                                       +pl+++++ v      ++e+++ e  iG lP+M+ s+ c+ls++s +e++e +E+pld+GGyF++nG+e+vi+ +e+
  gi|386001091|ref|YP_005919390.1|  88 SPLRLEMTIVE----GETEKEPVEAMIGMLPIMIMSQVCNLSGLSRDEMIEFGEDPLDPGGYFVVNGSERVIMTLED 160
                                       *********99....8999********************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|386001091|ref|YP_005919390.1| 161 lspnkilveynqryddfievakvfsqrqgyrslvivergrrsilevsfpsvsgrlnfvtlaralgletdmeivqavs 237
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|386001091|ref|YP_005919390.1| 238 enpeiikfmlenleeaevatkeealekiggrvaagqakeyqkkraayvldryllphigvdegdryakglflarmaea 314
                                       ***************************************************************************** PP

                                       .......................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .......................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                              l G+L+++lfrv++ +l+rd+k +l++   ++++l++  +v+a+ +t
  gi|386001091|ref|YP_005919390.1| 315 cfelalgkrgeddkdhyankrlkLSGDLMEDLFRVAFSRLTRDIKYQLERASMRNRELNVITTVRADVLT 384
                                       *****************************************************************99876 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.1   2.1e-30   9.6e-27       9     190 .]     159     337 ..     152     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.1e-30
                                       E-SSSSSE.............SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHH CS
                    RNA_pol_Rpb2_2   9 kekdknki.............satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIler 72 
                                        + ++nki             +a+v s +  +r++v++++  +++l ++ +s+  + ++v + +Algl +d eI+++
  gi|386001091|ref|YP_005919390.1| 159 EDLSPNKIlveynqryddfieVAKVFSQRQGYRSLVIVERGRRSILEVSFPSVSGRLNFVTLARALGLETDMEIVQA 235
                                       5555566666666666666999999**************************************************** PP

                                       HTSSSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSS CS
                    RNA_pol_Rpb2_2  73 icydsedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglse 149
                                       ++   e+++++ +++ e+ e++e++t+eeal++ig +va+++ +e + ++a  +l         +r+ l+ h+g++e
  gi|386001091|ref|YP_005919390.1| 236 VS---ENPEII-KFMLENLEEAEVATKEEALEKIGGRVAAGQAKEYQKKRAAYVL---------DRYLLP-HIGVDE 298
                                       **...455555.5666666778899***********9999999999999999998.........8*****.****** PP

                                       STCHH...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 150 slenkr.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                           +r +k  +++ m+++ ++l+lg+r +DD+Dh++nkR++
  gi|386001091|ref|YP_005919390.1| 299 G---DRyAKGLFLARMAEACFELALGKRGEDDKDHYANKRLK 337
                                       *...5669********************************96 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   1.2e-29   5.2e-26       1      64 [.     405     465 ..     405     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.2e-29
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLal 64 
                                       q+ldr+ ++++lshlrrv s+   ls+++ ++e+Rdlhp++wGriCp+eTPEG+ncGlvk++a+
  gi|386001091|ref|YP_005919390.1| 405 QLLDRTDYMASLSHLRRVISP---LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQ 465
                                       89*******************...**************************************97 PP

>> Acetate_kinase  Acetokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0     5e-05      0.23      51      98 ..     230     277 ..     216     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5e-05
                    Acetate_kinase  51 eaektaiadheealklilntlkeekvikdlkeiaaighRvvhggekft 98 
                                        ++ +a+++  e +k++l++l+e +v ++ + ++ ig+Rv+ g+ k+ 
  gi|386001091|ref|YP_005919390.1| 230 MEIVQAVSENPEIIKFMLENLEEAEVATKEEALEKIGGRVAAGQAKEY 277
                                       5667788888999*****************************998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3678.39
//
Query:       gi|386001092|ref|YP_005919391.1|  [L=607]
Description: DNA-directed RNA polymerase subunit B' [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.1e-123  411.0   0.0   6.5e-123  410.6   0.0    1.1  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    2.3e-30  104.8   0.1    5.2e-30  103.7   0.1    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    2.4e-20   72.5   1.2    4.1e-20   71.8   0.4    1.8  2  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    3.7e-09   37.0   6.4    1.4e-08   35.1   6.4    2.0  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
        0.1   12.5   0.2         22    5.1   0.0    2.7  2  Nudix_N_2       Nudix N-terminal
       0.14   11.8   1.9       0.81    9.3   0.1    2.3  2  RecR            RecR protein
       0.24   11.5   0.0        0.4   10.8   0.0    1.3  1  Y1_Tnp          Transposase IS200 like
          1    9.6   4.1       0.68   10.1   1.6    2.0  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.6   0.0  2.9e-126  6.5e-123       3     390 .]     140     510 ..     138     510 .. 0.96

  Alignments for each domain:
  == domain 1  score: 410.6 bits;  conditional E-value: 2.9e-126
                                       HT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEE CS
                    RNA_pol_Rpb2_6   3 klapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGq 79 
                                        l+p++eh+ spr+++ a m kq lg+  +n   r +++ + l+++q++l++++ +++a++        ++e ++Gq
  gi|386001092|ref|YP_005919391.1| 140 GLVPYPEHNASPRNTMGAGMIKQCLGTPLANTKLRPDTRGHYLHYPQRALCRSR-TADAVG--------FDERPAGQ 207
                                       678***************************************************.999999........******** PP

                                       EEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB CS
                    RNA_pol_Rpb2_6  80 navVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGi 151
                                       n+vVAv+ yeGYniEDa+iln+ +++r++ +s++++  e e r++++g+e+ ++ ++ +     + ea+++Ld+dG+
  gi|386001092|ref|YP_005919391.1| 208 NFVVAVLVYEGYNIEDALILNRGSIERGLGRSHFFRVSEAEERKYPGGQEDKFEIPDMEvrgarGTEAYSQLDDDGL 284
                                       *************************************************8877777666899999************ PP

                                       --SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--E CS
                    RNA_pol_Rpb2_6 152 vrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnk 228
                                       v+++a v ++d+l+gk+  ++ ++ +e     ++fg + ++ ++ts++++s+e+gvVd+v++       ++++++n+
  gi|386001092|ref|YP_005919391.1| 285 VNPNAVVAPNDVLIGKT--SPPRFLEE----PTEFGITPQQRRETSVTMRSNEKGVVDTVIL-------TESSNGNR 348
                                       ****************8..88888744....356777778889*******************.......8999**** PP

                                       EEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSS CS
                    RNA_pol_Rpb2_6 229 lvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaaleg 305
                                       l+kv+++++R +++GDKfasrhGqKGv++li+p  DmPf+e G v+D+++NP+++PSRmt+g++lE++ gk+++leg
  gi|386001092|ref|YP_005919391.1| 349 LAKVKTRDQRVPELGDKFASRHGQKGVIGLIVPPADMPFTEAGQVPDLIVNPHAIPSRMTVGHVLEMIGGKMGSLEG 425
                                       ***************************************************************************** PP

                                       S--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT- CS
                    RNA_pol_Rpb2_6 306 kkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltq 382
                                       ++vdat+F g++e++++ +L++ g++++G+ev+y+G++Ge++ a++fvGvi y+kL+h+v+ K+haRs+Gp+++lt+
  gi|386001092|ref|YP_005919391.1| 426 RFVDATAFLGEEETDMRAALTKFGFSHTGREVMYNGINGEQIMADVFVGVILYQKLYHMVAGKMHARSRGPVQVLTR 502
                                       ***************************************************************************** PP

                                       -B-SCGGG CS
                    RNA_pol_Rpb2_6 383 QPlgGkaq 390
                                       QP++G+a+
  gi|386001092|ref|YP_005919391.1| 503 QPTEGRAR 510
                                       ******96 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.1   2.3e-33   5.2e-30       1      86 [.     512     603 ..     512     604 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 2.3e-33
                                       BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                    RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklL 71 
                                       GGlrfGEMErd+lia+Gaa  Lkerl+++SD+v+  vc+rc+++a+ +      +C+++ s+++i +ve+++afklL
  gi|386001092|ref|YP_005919391.1| 512 GGLRFGEMERDVLIAHGAALALKERLVDESDKVTELVCSRCGMIAIHDkrrnvdYCSVCGSDTEIYPVEMSYAFKLL 588
                                       9*********************************************999**************************** PP

                                       HHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7  72 lqeLqslgialklll 86 
                                       l+e++slg+a++l+l
  gi|386001092|ref|YP_005919391.1| 589 LDEIKSLGVAPRLVL 603
                                       ***********9976 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.4   1.8e-23   4.1e-20       1      62 []       9      70 ..       9      70 .. 0.99
   2 ?   -3.1   0.0       4.5     1e+04      32      45 ..     116     129 ..     108     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.8e-23
                                      EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                      VfvNG+ +G+ +dp +l++++R+lRR gkis+++++++  +++e+ i+tD+GR++RPli+Ve
  gi|386001092|ref|YP_005919391.1|  9 VFVNGEFVGTNSDPISLAKEMRRLRRGGKISNQINVSYFARTNEILINTDSGRARRPLIVVE 70
                                      9************************************************************7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.5
                                       TT-EEEE-TTT--E CS
                    RNA_pol_Rpb2_4  32 eevsivlnekqkev 45 
                                       ee++i++++++ ev
  gi|386001092|ref|YP_005919391.1| 116 EEMEITPDHTHMEV 129
                                       78999***999887 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   6.4   6.4e-12   1.4e-08       1      58 []      91     131 ..      91     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.4e-12
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                       +ddL+reg+vEylDaeEEe+a++a+ + +++                   +TH+E++P
  gi|386001092|ref|YP_005919391.1|  91 FDDLVREGLVEYLDAEEEENALVAIEEMEITPD-----------------HTHMEVDP 131
                                       9************************99999665.................68888877 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0099        22      16      31 ..     540     555 ..     531     556 .. 0.77
   2 ?    4.5   0.0     0.015        33       2      11 ..     566     575 ..     565     579 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0099
                                       TT-SS-EEEETTTTEE CS
                         Nudix_N_2  16 dgDnreRlvCpaCgti 31 
                                       + D+ + lvC++Cg+i
  gi|386001092|ref|YP_005919391.1| 540 ESDKVTELVCSRCGMI 555
                                       56666779******99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       +Cs CG+ +e
  gi|386001092|ref|YP_005919391.1| 566 YCSVCGSDTE 575
                                       9*****9876 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.038        85      19      26 ..     549     556 ..     530     560 .. 0.71
   2 ?    9.3   0.1   0.00036      0.81       8      24 ..     556     572 ..     554     576 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.038
                                       -TTT--EE CS
                              RecR  19 CsrCgnlt 26 
                                       CsrCg ++
  gi|386001092|ref|YP_005919391.1| 549 CSRCGMIA 556
                                       *****997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                                       HHHHHHHH-EE-TTT-- CS
                              RecR   8 aLqeakekvrhCsrCgn 24 
                                       a+++ +++v +Cs+Cg 
  gi|386001092|ref|YP_005919391.1| 556 AIHDKRRNVDYCSVCGS 572
                                       789999*********96 PP

>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018       0.4      15      57 ..      86     130 ..      81     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                            Y1_Tnp  15 Rrkvltge.veerlkeii.keiaekkevkilelelmpDHvHllve 57 
                                       R +++ ++ v+e l e++ +e  e+  v i e+e+ pDH H+ v+
  gi|386001092|ref|YP_005919391.1|  86 RGEITFDDlVREGLVEYLdAEEEENALVAIEEMEITPDHTHMEVD 130
                                       55666666699999999945555566678889*********9776 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4     3e+03      20      29 ..     162     172 ..     155     179 .. 0.78
   2 ?   10.1   1.6   0.00031      0.68      16      40 .]     547     571 ..     543     571 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                     Auto_anti-p27  20 vC.gvPLmrdr 29 
                                       +C g+PL  ++
  gi|386001092|ref|YP_005919391.1| 162 QClGTPLANTK 172
                                       599***98876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00031
                     Auto_anti-p27  16 etCpvCgvPLmrdr.kggkvyCvaCd 40 
                                        +C++Cg++   d+   +  yC +C+
  gi|386001092|ref|YP_005919391.1| 547 LVCSRCGMIAIHDKrR-NVDYCSVCG 571
                                       68************54.555*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 4180.20
//
Query:       gi|386001093|ref|YP_005919392.1|  [L=878]
Description: DNA-directed RNA polymerase subunit A' [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   7.6e-104  347.4   0.0   1.1e-103  346.9   0.0    1.2  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    3.1e-69  232.4   0.1    4.7e-69  231.9   0.1    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    2.9e-32  111.8   0.0    5.5e-32  110.9   0.0    1.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    7.2e-32  109.6   0.0    1.6e-31  108.5   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    2.1e-27   96.3   0.0    3.3e-27   95.6   0.0    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.9   0.0    3e-107  1.1e-103       2     312 .]       7     311 ..       6     311 .. 0.93

  Alignments for each domain:
  == domain 1  score: 346.9 bits;  conditional E-value: 3e-107
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i +i+fg++sp+e+r++Svv++ +a+t++++  +P e+Gl+D+rlg+id  l+C+ Cg    eC+ghfGhi+L +
  gi|386001093|ref|YP_005919392.1|   7 KRIGKISFGLISPQEFRRMSVVKIITADTYDDDG-FPIEMGLMDPRLGVIDPGLRCRSCGGRPGECPGHFGHIDLIA 82 
                                       899*****************************95.****************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH..HHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllsklk..krekleelkkrlkaieelckkinlcekCgavqpkle 153
                                       Pv+h+gf kli+kil+ +c+ cs+l+l e++k+++ ++    ++  + + + ++++ +  +k+++c  Cg  +p+ e
  gi|386001093|ref|YP_005919392.1|  83 PVIHVGFAKLIRKILRAICRDCSRLMLLENEKRMYLEQIetLVRLGQTTDDVVNKVFSEARKHKVCPYCG--APQQE 157
                                       ***************************9999987766552123333555689999***************..55565 PP

                                       EETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 154 eegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrs 230
                                        ++e+  a +++ ++     l+++++++ +++i+ded++v+g++++ +rPew++ltvlPVpP+++RPs++l++g+rs
  gi|386001093|ref|YP_005919392.1| 158 IKFERPLAYVEEGHK-----LTPSDIRDRFEKIPDEDIKVMGMNPDTARPEWMLLTVLPVPPVTMRPSITLESGQRS 229
                                       566666666666666.....********************************************************* PP

                                       BECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 231 edDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGr 307
                                       edDlt+kl+dii++N+r+++++e+gap+liie+ +elLQ+h++t++dn +sg++pa+++s+rplk+lsqrLkGKeGr
  gi|386001093|ref|YP_005919392.1| 230 EDDLTHKLVDIIRINQRFQENREAGAPQLIIEDLWELLQYHITTFLDNTVSGVPPARHRSGRPLKTLSQRLKGKEGR 306
                                       ***************************************************************************** PP

                                       CCCCT CS
                                       xxxxx RF
                    RNA_pol_Rpb1_1 308 fRgnL 312
                                       fRg+L
  gi|386001093|ref|YP_005919392.1| 307 FRGSL 311
                                       ***98 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.9   0.1   1.3e-72   4.7e-69       1     166 []     313     479 ..     313     479 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.9 bits;  conditional E-value: 1.3e-72
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdpnl+++evgvP ++a+ l+vp +v+  ni+ +r++v++g +++Pg +yv+r+dg++ k++  
  gi|386001093|ref|YP_005919392.1| 313 GKRVNFSARTVISPDPNLSINEVGVPLEIAMELSVPLVVNGRNIEVMRDFVRRGADKHPGVNYVTRADGRRVKVTDR 389
                                       9**************************************************************************99 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       ++ ++a++le g++v r+++dgd+vl+NRqPsLh++sim+hrv v+++kt+rln +v+ +yNaDFDGDemnlh+pq+
  gi|386001093|ref|YP_005919392.1| 390 NAeEVADQLEPGWKVDRQLMDGDIVLFNRQPSLHRMSIMSHRVIVMPHKTFRLNPAVCPPYNADFDGDEMNLHVPQT 466
                                       9978************************************************************************* PP

                                       HHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 154 eearaEaeelllv 166
                                       eearaEae l+ v
  gi|386001093|ref|YP_005919392.1| 467 EEARAEAEILMRV 479
                                       *********9975 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   1.5e-35   5.5e-32       1     156 [.     482     647 ..     482     648 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.5e-35
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSE...BEEHHHHHHCC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpke...lwtgkqtfsri 74 
                                       nilsp+ g P+ig ++D ++G++llT+ d  i+r e++++l+k      + ++++ ++  ++     wtgkq+fs+i
  gi|386001093|ref|YP_005919392.1| 482 NILSPRFGGPIIGGIHDYVTGNFLLTHGDRRISRIEVMEVLKKL-----HHLEIPEPVGWNEAgepYWTGKQIFSLI 553
                                       9*******************************************.....67899999998866677*********** PP

                                       CHCCCCEEEE.....SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  75 lpneinyerk.....neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslq 138
                                       lp+ +n+e k     n+++        d +v+i++g +++G+id ++vg + +g++ + ++keyg++  + f+d ++
  gi|386001093|ref|YP_005919392.1| 554 LPRGLNLEFKasfckNCDSckreacddDAYVVIRDGKILTGTIDAAAVG-AFKGKITDRVIKEYGPTVGAGFIDGMT 629
                                       ***999999988555444488999*99**********************.999************************ PP

                                       HHHHHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 139 rlgfkyllqsgftigigD 156
                                       +++++ ++ +gf++gi+D
  gi|386001093|ref|YP_005919392.1| 630 QMAIRGIMLAGFSFGIDD 647
                                       *****************9 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.0   4.3e-35   1.6e-31       4     108 .]     676     779 ..     672     779 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 4.3e-35
                                       HCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTT CS
                    RNA_pol_Rpb1_4   4 aerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnveg 80 
                                       ++  g+le+lpg++l+e++e++i++ l kard+ag+ia ++l ++Ns ++M+ sGa+Gs++n++q+a+c+Gqq+v+g
  gi|386001093|ref|YP_005919392.1| 676 YKA-GELEPLPGRTLDETLEMRIMQTLGKARDNAGSIAGRYLGIDNSGVVMAVSGARGSMLNLTQMAACVGQQSVRG 751
                                       444.99*************************************77******************************** PP

                                       BSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  81 kripkgfsgrtlphfkkidespesrGFv 108
                                       +ri +g++grtlphf++ d ++e++GFv
  gi|386001093|ref|YP_005919392.1| 752 ERIRRGYEGRTLPHFRRGDLGAEAHGFV 779
                                       ***************************8 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0   9.3e-31   3.3e-27       1      66 [.     786     851 ..     786     870 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 9.3e-31
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL+++efffh+ ggReGL+DtA++T++sGYlqRrl++al+d+ v+yd+tv+++ g ivqf ygedg
  gi|386001093|ref|YP_005919392.1| 786 GLNPTEFFFHAIGGREGLVDTAIRTSQSGYLQRRLINALQDLEVQYDGTVKETRGIIVQFSYGEDG 851
                                       9****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 6218.51
//
Query:       gi|386001094|ref|YP_005919393.1|  [L=378]
Description: DNA-directed RNA polymerase subunit A'' [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-54  185.2   0.2    1.9e-54  184.9   0.2    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.034   14.5   0.1      0.084   13.3   0.1    1.7  1  Secretin_N      Bacterial type II/III secretion system short 
       0.14   12.2   0.2       0.36   10.8   0.2    1.7  1  NAC             NAC domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9   0.2   3.2e-58   1.9e-54      66     265 ..      38     326 ..      12     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 3.2e-58
                                       S...............B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEE CS
                                       x...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  66 g...............lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvsknikskslt 127
                                       +                vep eavG++aaQSiGePgTQ+t++TFH+aGva+ nvtlG+prl ei+++ k+ +++++t
  gi|386001094|ref|YP_005919393.1|  38 EfcevadlvladyersKVEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKIPSTPTMT 114
                                       23333333444444447************************************************************ PP

                                       EEB-SSSSSCHHHCHHHHHHHSE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                    RNA_pol_Rpb1_5 128 vllvdeeakelekakkvkkaiek...................................................... 150
                                       ++l +e+a +++ a++v+ +ie+                                                      
  gi|386001094|ref|YP_005919393.1| 115 IRLDKEYALDRDIAREVAWSIEStnilhlgsiatdlaemnvvidlneeallqrkitasevaerlaegtklsadqrgn 191
                                       *****************999999999*************************************************** PP

                                       ...........................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEES CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ...........................gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsn 200
                                                                  gi++ikr++++     ke  +e+vl teg +l++v++ ++ vd +++ +n
  gi|386001094|ref|YP_005919393.1| 192 qiimtppepsyrdllqlvekiktislkGIEGIKRVVIR-----KEG-DEYVLYTEGSALKDVIQFKG-VDPTRTKTN 261
                                       ****************9999999999999999999998.....222.5679****************.********* PP

                                       SHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 201 diaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                       +i ei  +lgieaar+a+++e ++++++qg+sv+ rH++l++d+mt+ ge+++++r+G+  ++ s
  gi|386001094|ref|YP_005919393.1| 262 NITEIGDVLGIEAARNAIINEATDTLREQGLSVDVRHIMLVADIMTCDGEVKQIGRHGVSGEKAS 326
                                       **********************************************************9887765 PP

>> Secretin_N  Bacterial type II/III secretion system short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.4e-05     0.084      39      76 ..     175     212 ..     135     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       SSTT-TTSEEEEETTTTEEEEEECHHHHHHHHHHHHHH CS
                        Secretin_N  39 gallgkggrvvadprtNsllvrgspervarirqlikqL 76 
                                       ++ l++g++++ad r N+++++ +++ ++ + ql++++
  gi|386001094|ref|YP_005919393.1| 175 AERLAEGTKLSADQRGNQIIMTPPEPSYRDLLQLVEKI 212
                                       56678899***************************986 PP

>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2     6e-05      0.36       7      31 ..     211     234 ..     207     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6e-05
                               NAC   7 alkklglkeipgieeVtirksdgkv 31 
                                        +k + lk i+gi++V+irk+++ +
  gi|386001094|ref|YP_005919393.1| 211 KIKTISLKGIEGIKRVVIRKEGD-E 234
                                       5778889*************994.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2703.28
//
Query:       gi|386001095|ref|YP_005919394.1|  [L=103]
Description: 50S ribosomal protein L30e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-13   47.8   0.0    1.1e-12   47.5   0.0    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.054   13.2   0.0      0.065   13.0   0.0    1.2  1  Ysc84           Las17-binding protein actin regulator


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.2e-16   1.1e-12       3      94 ..       4      91 ..       2      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.2e-16
                                      HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81
                                      i ++l+ + ++gk+vlG + ++ a  +g+akl+i A d+++e   +      +e +v+ +++ + k+LG ++gk++ v+
  gi|386001095|ref|YP_005919394.1|  4 IDRALRSSIRTGKVVLGSNLALEAGAKGQAKLIISAVDCPEEVAAE---LKRAEVPVYSYSGRG-KDLGSACGKPFSVA 78
                                      677899999*******************************999888...555699999999999.************** PP

                                      EEEEEESTTTHHH CS
                    Ribosomal_L7Ae 82 alaikdegdskdl 94
                                      ala++++g+s+++
  gi|386001095|ref|YP_005919394.1| 79 ALAVIEPGESEIM 91
                                      **********987 PP

>> Ysc84  Las17-binding protein actin regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-06     0.065      20      70 ..       2      61 ..       1      80 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-06
                             Ysc84 20 lntkealeaftkktrvslGgdlsvaaGpvg.........aggeaeaaaaak..........lkapvysys 70
                                      +n ++al++  ++++v lG++l++ aG  g                    +          ++ pvysys
  gi|386001095|ref|YP_005919394.1|  2 INIDRALRSSIRTGKVVLGSNLALEAGAKGqakliisavD----------CpeevaaelkrAEVPVYSYS 61
                                      88899****9999**************9885444444440..........23445555544778889997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 661.54
//
Query:       gi|386001096|ref|YP_005919395.1|  [L=143]
Description: Transcription termination factor NusA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-22   78.1   4.8    9.1e-16   57.5   1.4    2.1  2  KH_2      KH domain
    1.5e-15   57.0   5.1    1.9e-15   56.7   2.2    2.0  2  KH_5      NusA-like KH domain
    8.4e-10   38.4   1.1    8.5e-05   22.4   0.1    2.2  2  KH_4      KH domain
    0.00012   21.8   3.4    0.00095   18.9   1.3    2.4  2  KH_1      KH domain
  ------ inclusion threshold ------
      0.032   13.2   0.0       0.04   12.9   0.0    1.1  1  DUF3843   Protein of unknown function (DUF3843)


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   1.4   2.5e-19   9.1e-16       3      64 ..      13      74 ..      11      75 .. 0.95
   2 !   22.0   0.1   2.9e-08    0.0001       2      51 ..      77     128 ..      76     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 2.5e-19
                                      HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTT CS
                              KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegk 64
                                      +++l++++++  +++++I+++++r+i+vi+++ +g +IG++Gsni++++k ++k+ie++e++
  gi|386001096|ref|YP_005919395.1| 13 YIALFESLTGGVARDCIIDDENDRIIFVIKKGDMGAAIGRKGSNINRVKKSIGKQIEIVEHS 74
                                      789999999999************************************************98 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHHTECETEEEEEEECCS.CEEEEEEEESC.HHHHHTGGGHHHHHHH CS
                              KH_2   2 ipeslaveikkagvskveIerta.nrviiviresq.pgivIGkgGsnikkig 51 
                                       ++e+l+++++ a +++v I  ++ +r+ +v+ +++ +gi+IG+ G+ni k +
  gi|386001096|ref|YP_005919395.1|  77 VKEFLENVFQPASIKNVTIVSKNnKRLAYVEVANRdKGIAIGRDGRNILKAK 128
                                       679999*99**********99777******9988669***********8876 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   2.2   5.4e-19   1.9e-15       2      69 .]      34      95 ..      33      95 .. 0.97
   2 ?    1.0   0.0      0.13   4.6e+02       9      31 ..     108     125 ..     101     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 5.4e-19
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                      ++r+++++k+++     +Ga++g+kGs+i+ v++ + g++i++ve s+D++ef +n+++Pa +++V+i
  gi|386001096|ref|YP_005919395.1| 34 NDRIIFVIKKGD-----MGAAIGRKGSNINRVKKSI-GKQIEIVEHSDDVKEFLENVFQPASIKNVTI 95
                                      689*********.....*******************.****************************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                              KH_5   9 VkshnpnvdpvGaivgkkGsrik 31 
                                       V +++      G ++g+ G++i 
  gi|386001096|ref|YP_005919395.1| 108 VANRD-----KGIAIGRDGRNIL 125
                                       55555.....7999******995 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   4.8e-06     0.017      21      52 ..      27      58 ..      15      61 .. 0.88
   2 !   22.4   0.1   2.4e-08   8.5e-05       2      51 ..      75     124 ..      74     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                              KH_4 21 teeeeeeeveielnvegedlGrvIGkrGrtld 52
                                      ++ +++e+++i   +++ d+G  IG++G +++
  gi|386001096|ref|YP_005919395.1| 27 DCIIDDENDRIIFVIKKGDMGAAIGRKGSNIN 58
                                      6778999*********************9986 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.4e-08
                              KH_4   2 elvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtl 51 
                                       + v+++l+++++ +   +vt+  +++++   ++v+  d+G+ IG++Gr++
  gi|386001096|ref|YP_005919395.1|  75 DDVKEFLENVFQPASIKNVTIVSKNNKRLAYVEVANRDKGIAIGRDGRNI 124
                                       579999***9964456679999999***********************87 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.3   2.7e-07   0.00095       4      40 ..      39      76 ..      28     101 .. 0.85
   2 ?    2.8   0.0     0.029     1e+02       4      22 ..     106     124 ..     104     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.7e-07
                                      EEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEES.STT CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreet.gakIkvpk.sed 40
                                      + +++  +g+ IG++GsnI++ ++ + g +I +++ s+d
  gi|386001096|ref|YP_005919395.1| 39 FVIKKGDMGAAIGRKGSNINRVKK-SiGKQIEIVEhSDD 76
                                      57888899****************.99*****9975554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.029
                                       EEEGGGHHHHHHTGGGHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnI 22 
                                       ++v ++  g  IG+ G+nI
  gi|386001096|ref|YP_005919395.1| 106 VEVANRDKGIAIGRDGRNI 124
                                       67888889999*******9 PP

>> DUF3843  Protein of unknown function (DUF3843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05      0.04     284     343 ..      61     121 ..      56     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                           DUF3843 284 katggkelvylesekelkeFLteklkyeekenlelpqikaekglvl.mvspekgllvakdl 343
                                       k++ gk++ ++e+++++keFL ++ +  + +n+++ + ++++   + ++++ kg+ +  d 
  gi|386001096|ref|YP_005919395.1|  61 KKSIGKQIEIVEHSDDVKEFLENVFQPASIKNVTIVSKNNKRLAYVeVANRDKGIAIGRDG 121
                                       7889******************************999777775554267888999997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1002.16
//
Query:       gi|386001097|ref|YP_005919396.1|  [L=120]
Description: 30S ribosomal protein S12 [Methanosaeta harundinacea 6Ac]
Scores for 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-46  154.2   0.8      1e-45  154.0   0.8    1.0  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0   0.8   5.6e-50     1e-45       1     113 [.       5     118 ..       5     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 5.6e-50
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r++l+++ k+d+l gap +rG+vlekv+veak+PnsA+Rk+vr++Likng++vtaf+pg+ga+ f+dEhdev+v+ i
  gi|386001097|ref|YP_005919396.1|   5 RRALKLNVKADPLGGAPRARGIVLEKVGVEAKQPNSAIRKCVRIQLIKNGRQVTAFCPGDGAIGFIDEHDEVVVERI 81 
                                       6788999********************************************************************99 PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g a++D+pGvr++vv v++v l++++ ++kekp
  gi|386001097|ref|YP_005919396.1|  82 GGRmGGAKGDIPGVRFQVVAVNNVALNEMVSGRKEKP 118
                                       9888*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 833.25
//
Query:       gi|386001098|ref|YP_005919397.1|  [L=187]
Description: 30S ribosomal protein S7 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-40  137.4   4.4    3.5e-40  137.1   4.4    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1   4.4     2e-44   3.5e-40      16     149 .]      45     187 .]      36     187 .] 0.95

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 2e-44
                                       SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEE CS
                      Ribosomal_S7  16 pkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvp 88 
                                       +k ++++ve+link+m+    +Gkk + +kiv++aldi++++tk++pl+vl +A++n+ Pr+ev ++++GG+t++ +
  gi|386001098|ref|YP_005919397.1|  45 KKSEQHIVERLINKMMQgednTGKKMKTYKIVEEALDIVHQRTKENPLSVLAKAISNAGPREEVVRLKYGGITVPKA 121
                                       358999*********************************************************************** PP

                                       EEE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  89 vevrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       v+ +p+Rr+++Al++i+++a   ++++++s+a +La+E+i+A++g+  + a+++++ ++r+A+a+r
  gi|386001098|ref|YP_005919397.1| 122 VDTAPQRRVDVALNFIATGAqrsAFKSKRSAASCLADEIIAASKGDvrSFAMNRKDSVERVAKAAR 187
                                       ********************99899999*****************999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1245.33
//
Query:       gi|386001099|ref|YP_005919398.1|  [L=367]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-41  141.9   0.1    3.1e-41  141.5   0.1    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.9e-16   60.4   1.4    3.4e-12   46.8   0.0    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.8e-05   24.5   1.3       0.48   10.0   0.0    3.1  3  DAO            FAD dependent oxidoreductase
    0.00018   20.8   0.0       0.13   11.4   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    0.00075   19.7   0.3          1    9.6   0.0    2.8  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.011   15.8   0.2        6.8    6.7   0.1    2.6  3  NAD_binding_9  FAD-NAD(P)-binding
      0.035   13.3   0.1       0.63    9.2   0.0    2.3  2  Thi4           Thi4 family
       0.12   11.4   0.4        1.1    8.2   0.1    2.1  2  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   0.1   1.4e-44   3.1e-41       2     279 ..      10     281 ..       9     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 1.4e-44
                                       SEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq.agakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielll 71 
                                       +vvv+GgG++G ++ +++a+  g++ +lve ++     + l++  l g  + +e  +      +         +l+ 
  gi|386001099|ref|YP_005919398.1|  10 RVVVVGGGIGGAELLRNAATkEGLELVLVEPKD-RIECQALYPDYLGGEIGVEEMTApldpfcR----RMGAAHLRD 81 
                                       79******************55*******6444.445555555666666666654445854331....333344555 PP

                                       CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC..TTBEECCSECHHHHHHCCSS-TSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.aenvgklvrtldsaealklkllpkrivv 147
                                          ++++d++ ++v++e      +++++yd lvl +G+ ++ +g++G+ +  ++  +++   a+++ +  +p+ri+v
  gi|386001099|ref|YP_005919398.1|  82 --RALRVDFADRRVTCE------KNDLDYDILVLVPGAVQNYFGVEGAeKAFTINTLEETVRARRFIERARPERIAV 150
                                       ..5*************4......347*********************9344444455555556777777778***** PP

                                       ES-SHHHHHHHHHHHHH.T-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 148 vGgGyiGvElAaalakl.gkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledg 223
                                       +G+G++GvE+ ++la   g+++ +ve +drll++l k+ s  +e+ l  +Gvev +g++v  i++ g    v   dg
  gi|386001099|ref|YP_005919398.1| 151 IGSGPTGVETVCFLAARpGSKISIVEMMDRLLPTLSKNSSILMEKILSGKGVEVLTGKRVSSIREGG----VAFADG 223
                                       **********99977766******************************************9999666....8***** PP

                                       CEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBES.STTEEE-GGGC....T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx....x RF
                       Pyr_redox_2 224 eeidadlvvvavGvrpstelleeklglelderggivvdeflrtn.vpgiyaiGDva....g 279
                                       +++d+++ ++ +G+rp + +  e l l+  ++g++++d++lr++  ++++a GD a    +
  gi|386001099|ref|YP_005919398.1| 224 TSLDCEMTIWTAGIRPAPLI--EGLDLPK-KKGWLLTDQYLRVQgREDVFAFGDGAwieiD 281
                                       *****************866..9999998.*************99*********9977662 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   8.3e-05      0.19       1      36 [.      10      47 ..      10      64 .. 0.83
   2 !   46.8   0.0   1.5e-15   3.4e-12       1      70 [.     147     217 ..     147     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.3e-05
                                      EEEEECSSHHHHHHHHHH.HHTTSEEEEEESSSSSS.T CS
                         Pyr_redox  1 kvvvvGgGyiglElAgal.aelgkkVtvversdkll.r 36
                                      +vvvvGgG  g El  ++ ++ g +  +ve +d++  +
  gi|386001099|ref|YP_005919398.1| 10 RVVVVGGGIGGAELLRNAaTKEGLELVLVEPKDRIEcQ 47
                                      79***********9987747799***********9852 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 1.5e-15
                                       EEEEECSSHHHHHHHHHHHH.TTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalae.lgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                                       +++v+G+G +g+E  ++la+  g+k+++ve++d+ll+ l +  s ++++ l+ +g+evl++++v +i++ +
  gi|386001099|ref|YP_005919398.1| 147 RIAVIGSGPTGVETVCFLAArPGSKISIVEMMDRLLPTLSKNSSILMEKILSGKGVEVLTGKRVSSIREGG 217
                                       79****************76589********************************************9654 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3   0.00039      0.87       1      32 [.      10      44 ..      10      48 .. 0.85
   2 !   10.0   0.0   0.00021      0.48       2      38 ..     148     186 ..     147     197 .. 0.80
   3 ?    3.3   0.0     0.023        52     156     213 ..     197     246 ..     190     275 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00039
                                      EEEEECTSHHHHHHHHHHHHT.T..EEEEESSSST CS
                               DAO  1 dvviiGGGiiGlstAyeLarr.g..Vtllekgdia 32
                                      +vv++GGGi G+   + +a++ g   +l+e +d++
  gi|386001099|ref|YP_005919398.1| 10 RVVVVGGGIGGAELLRNAATKeGleLVLVEPKDRI 44
                                      59****************965489*9999988765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                                       EEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGG CS
                               DAO   2 vviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSg 38 
                                       +++iG+G +G+ t  +La+r+   + ++e+ d++   + +
  gi|386001099|ref|YP_005919398.1| 148 IAVIGSGPTGVETVCFLAARPgskISIVEMMDRLL-PTLS 186
                                       9*****************99559*****9976655.4555 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.023
                                       HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEE..EEE--GGGHH.HHHTTCTT CS
                               DAO 156 aealGveilegtevtgleeedgkvwgverttpgendaada..vVnaaGawsd.llgllkel 213
                                       +  +Gve+l+g +v +++e  g+v+   +   g+    d+   + +aG+    l+   + l
  gi|386001099|ref|YP_005919398.1| 197 LSGKGVEVLTGKRVSSIRE--GGVAFA-D---GTS--LDCemTIWTAGIRPApLI---EGL 246
                                       6778*************54..232222.2...654..444448888888766666...434 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0     0.001       2.3     192     214 ..       9      31 ..       2      45 .. 0.80
   2 !   11.4   0.0   5.7e-05      0.13     187     243 ..     141     199 ..     115     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.001
                       K_oxygenase 192 kriaVvGsGqSaaeifedllrrq 214
                                        r++VvG+G  +ae+++++++++
  gi|386001099|ref|YP_005919398.1|   9 LRVVVVGGGIGGAELLRNAATKE 31 
                                       69**************9998765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.7e-05
                       K_oxygenase 187 ellakkriaVvGsGqSaaeifedllrr.qkkvel.klvtrsealeplddspfvneifsP 243
                                       e+++++riaV+GsG ++ e +  l++r  +k ++ +++ r       ++s ++ +i+s 
  gi|386001099|ref|YP_005919398.1| 141 ERARPERIAVIGSGPTGVETVCFLAARpGSKISIvEMMDRLLPTLSKNSSILMEKILSG 199
                                       47899******************999954444440444443333344444455555555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1     0.003       6.8       1      31 [.      13      44 ..      13      49 .. 0.83
   2 !    9.6   0.0   0.00046         1       1      31 [.     150     181 ..     150     182 .. 0.93
   3 ?   -2.6   0.0         3   6.8e+03      34      53 ..     209     234 ..     206     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.003
                                      EE--SHHHHHHHHHHH.CCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLa.kagfdvlllekrdrl 31
                                      +vG+G++G+ + + +a k+g++ +l+e  dr+
  gi|386001099|ref|YP_005919398.1| 13 VVGGGIGGAELLRNAAtKEGLELVLVEPKDRI 44
                                      8*******98877655156******9999886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00046
                                       EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLaka.gfdvlllekrdrl 31 
                                       ++G+G +G  + ++La + g ++ ++e+ drl
  gi|386001099|ref|YP_005919398.1| 150 VIGSGPTGVETVCFLAARpGSKISIVEMMDRL 181
                                       8**************9998********98875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3
                                       GG-EECE......TTCEECTS---EE CS
                     NAD_binding_8  34 raasyev......pgvrvdygahifh 53 
                                       r++s++       +g  +d+ ++i++
  gi|386001099|ref|YP_005919398.1| 209 RVSSIREggvafaDGTSLDCEMTIWT 234
                                       66677663333334577777777775 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.003       6.8       1      40 [.      12      47 ..      12      57 .. 0.77
   2 ?   -3.2   0.0       3.2   7.2e+03     118     147 ..      77     103 ..      66     110 .. 0.60
   3 ?    6.5   0.0    0.0035       7.7       1      28 [.     149     174 ..     149     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.003
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                      ++vG+G+ G+ +l++ + +    + le+ l++p+   + +
  gi|386001099|ref|YP_005919398.1| 12 VVVGGGIGGAELLRNAATK----EGLELVLVEPKDRIECQ 47
                                      69*******8777666655....7*********8765444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                     NAD_binding_9 118 evhraevvdleeradgqavlladgaslaad 147
                                        ++r+++++++ ++++++    +++ l++d
  gi|386001099|ref|YP_005919398.1|  77 AHLRDRALRVDFADRRVTC---EKNDLDYD 103
                                       5677777777777666433...44445555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0035
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkksplei 28 
                                       a++G Gp+G+ ++  L+ar   +s+++i
  gi|386001099|ref|YP_005919398.1| 149 AVIGSGPTGVETVCFLAARP--GSKISI 174
                                       89****************96..555444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.069   1.6e+02      20      49 ..      11      40 ..       2      44 .. 0.89
   2 ?    9.2   0.0   0.00028      0.63      20      49 ..     148     177 ..     135     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.069
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailer 49
                                      vv+vG+G  G    +  a+k +l+++++e 
  gi|386001099|ref|YP_005919398.1| 11 VVVVGGGIGGAELLRNAATKEGLELVLVEP 40
                                      99*********99999999999*9999985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00028
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvailer 49 
                                       ++++G+G++G+ +   la +p+ k+ i+e 
  gi|386001099|ref|YP_005919398.1| 148 IAVIGSGPTGVETVCFLAARPGSKISIVEM 177
                                       89*************************995 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0005       1.1       2      36 ..      11      44 ..      10      51 .. 0.90
   2 ?    1.1   0.0     0.072   1.6e+02       2      36 ..     148     181 ..     147     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      vvv+G+G  g  l  +  + k gl++vl+e+ + +
  gi|386001099|ref|YP_005919398.1| 11 VVVVGGGIGGAELLRNA-ATKEGLELVLVEPKDRI 44
                                      8************8777.99**********98876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.072
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       ++viG+Gp g+     l +a+pg k+ ++e  + l
  gi|386001099|ref|YP_005919398.1| 148 IAVIGSGPTGVETVCFL-AARPGSKISIVEMMDRL 181
                                       78********9999888.89999999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 3055.81
//
Query:       gi|386001100|ref|YP_005919399.1|  [L=363]
Description: Chorismate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.8e-144  478.6   0.1   7.7e-144  478.4   0.1    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.4   0.1  4.3e-148  7.7e-144       1     327 []      10     356 ..      10     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 478.4 bits;  conditional E-value: 4.3e-148
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       +r+tt+GeShg+++g+v+dg+pagl+l+ee +q eLdrRrpgqs+++tqrkE+D+veilsG+f+g+t+Gtpi++l++
  gi|386001100|ref|YP_005919399.1|  10 FRITTWGESHGSGVGVVVDGCPAGLALSEEVVQGELDRRRPGQSSISTQRKEEDRVEILSGTFDGVTTGTPISMLVW 86 
                                       89*************************************************************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       N+d++s+ y+ ++++pRpgHADlty ++Yg+rd+rgggr+SaReT++rvaaGavak+lL+e gi +++yv ++g++ 
  gi|386001100|ref|YP_005919399.1|  87 NRDAKSSAYDALRDRPRPGHADLTYLARYGVRDHRGGGRASARETVGRVAAGAVAKRLLAERGILVAGYVLELGGVr 163
                                       **************************************************************************888 PP

                                       .............CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHH CS
                   Chorismate_synt 154 .............ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakal 217
                                                    e +++npvrcpd+ aa++m +aie+a+++gdslGg+ e+v+ gvp+GlGepvfdkld++La+al
  gi|386001100|ref|YP_005919399.1| 164 adllegldlsalrEGAEKNPVRCPDQIAAAKMVRAIEAAREAGDSLGGIAEIVAVGVPPGLGEPVFDKLDGDLARAL 240
                                       8888888888775334788********************************************************** PP

                                       HTSTTEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBT CS
                   Chorismate_synt 218 msipAvkgveiGsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdl 288
                                       m+i+Avk+veiG+G+eaa+++Gs++nD+i         +tnnaGGi+GGis+G+piv+r+avKp+psi+++q+tvdl
  gi|386001100|ref|YP_005919399.1| 241 MGIGAVKAVEIGAGVEAARMRGSDMNDPILpgpegpRFETNNAGGILGGISTGAPIVCRIAVKPTPSISRPQRTVDL 317
                                       ******************************77665433*************************************** PP

                                       TS-E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 289 etkeevelevkgrhDpcvvpravvvveamvalvladall 327
                                       ++ e+ve+e+kgrhDp++ pr+v+v+eamvalvlad+ll
  gi|386001100|ref|YP_005919399.1| 318 SRGEAVEIEIKGRHDPVIPPRIVPVAEAMVALVLADHLL 356
                                       *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 2854.51
//
Query:       gi|386001101|ref|YP_005919400.1|  [L=603]
Description: Molybdenum cofactor biosynthesis protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-41  142.0   3.1    1.3e-41  142.0   3.1    1.8  2  MoeA_N         MoeA N-terminal region (domain I and II)
    2.7e-24   85.5   0.0    6.5e-24   84.2   0.0    1.6  1  MoCF_biosynth  Probable molybdopterin binding domain
      1e-14   54.1   1.2    2.8e-14   52.7   1.2    1.7  1  PBP_like       PBP superfamily domain
    3.5e-11   43.1   0.1    3.5e-11   43.1   0.1    2.7  3  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   3.1   2.9e-45   1.3e-41       2     157 .]      10     173 ..       9     173 .. 0.92
   2 ?   -3.1   0.0       1.3   5.7e+03       8      41 ..     420     452 ..     418     453 .. 0.68

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 2.9e-45
                                       -HHHHHHHHHHH-HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--.............. CS
                            MoeA_N   2 sveealaiilaaleleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........s 69 
                                       s++ea++i+laa++   +e vpl ++algrvlae v + +dvP+f+++amDGYA+r++++ +a+e++p        +
  gi|386001101|ref|YP_005919400.1|  10 SLDEAIEIVLAAVPEAGAEaVPL-ERALGRVLAERVASGIDVPGFHRAAMDGYALRSAETVAAREDRPiafalvgrV 85 
                                       89***********5556666***.99**************************************************9 PP

                                       .....-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTB CS
                            MoeA_N  70 aageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragt 143
                                       ++g+epe ++ +g av++ TG+++P g daVv+vE+ e +    +   + ++v+ gen +raG d++ Ge++l  g+
  gi|386001101|ref|YP_005919400.1|  86 PMGREPEVVVGEGeAVEVSTGSMMPGGSDAVVMVEHSEvD--GSSLL-IrRPVHFGENTHRAGGDVAMGETVLLPGR 159
                                       99999999999999**********************8532..22222.2489************************* PP

                                       B--CCCHHHHHHCT CS
                            MoeA_N 144 rltpaeigllasvG 157
                                       rl+++eiglla+vG
  gi|386001101|ref|YP_005919400.1| 160 RLSAREIGLLAAVG 173
                                       *************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                       HHHHHH-HH-EEEEEGGCG-TT-BBSS-EE-SS- CS
                            MoeA_N   8 aiilaaleleeeevplaaealgrvlaedvvAped 41 
                                       ++ilaal+ +   vp   +  g ++aed vA+++
  gi|386001101|ref|YP_005919400.1| 420 ETILAALPFPVRFVPT-GSRRGAISAEDGVAEVA 452
                                       5566666554444888.55679999999999876 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   1.5e-27   6.5e-24       6     143 ..     199     323 ..     186     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.5e-27
                                       -HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHH CS
                     MoCF_biosynth   6 GdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealaklf 82 
                                       G+el  g+i+D n++ +a+++++ g + + y+++pDd++ ++e lla +ee+d+++++G t+++  D++++++++++
  gi|386001101|ref|YP_005919400.1| 199 GSELSLGQIYDINSYSIAAAVEDCGGTPRIYGILPDDPDSMAEGLLAMAEESDLVLVSGSTSAGIGDMVYRVVEEFG 275
                                       78999****************************************9999999************************* PP

                                       SEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  83 ekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       e       ++f++++lkpgkp++++ +   ++   k++igLPG+p ++ +++ ++  pa++
  gi|386001101|ref|YP_005919400.1| 276 E-------VVFHGINLKPGKPTLFGSV---GG---KPFIGLPGYPTSALTVFGLLAAPAIR 323
                                       *.......8**************9999...44...58******************999987 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   1.2   6.3e-18   2.8e-14      13     192 ..     430     591 ..     424     592 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 6.3e-18
                                       EEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC CS
                          PBP_like  13 vavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdl 89 
                                       v++  +Gs  G  +  +g a++a +++   ++ +++ + l+      +   v +++re  +++ak+ p     + dl
  gi|386001101|ref|YP_005919400.1| 430 VRFVPTGSRRGAISAEDGVAEVAVVSRSVGQEPGWDESVLE------P---VGGYSREL-VMMAKD-P----EILDL 491
                                       788999*********************99999999999888......2...56777765.777777.3....45555 PP

                                       .-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTT CS
                          PBP_like  90 .adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldfvp 165
                                          ++  +v+  ++S     + ++l++ g +k+++ g   +ar+h avaaaV+agrad g++++ +aee +gl   +
  gi|386001101|ref|YP_005919400.1| 492 aGAEDSKVVGWSRDSEMSRILGRVLAESGSEKAKLVG---TARTHAAVAAAVKAGRADLGLAVREAAEE-EGLAARK 564
                                       3348889*********************999999999...79*************************98.8****** PP

                                       CE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 166 laeerydlvvrkealddpevqaflefl 192
                                       +ae +  ++vr e++ +++v+afle+l
  gi|386001101|ref|YP_005919400.1| 565 VAEDEILFLVRPERMGREAVRAFLEAL 591
                                       ************************987 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.22     1e+03       3      23 ..      39      59 ..      38      69 .. 0.87
   2 ?   -3.9   0.3       3.6   1.6e+04      61      69 ..      95     103 ..      86     104 .. 0.76
   3 !   43.1   0.1   7.9e-15   3.5e-11       2      72 .]     337     401 ..     336     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.22
                                      EESS-EE--SSS-EEEEEEEE CS
                            MoeA_C  3 rlaedlksdpgrreflRvilt 23
                                      +lae+++s  + + f+R+ ++
  gi|386001101|ref|YP_005919400.1| 39 VLAERVASGIDVPGFHRAAMD 59
                                      58999*************987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.6
                                       E-TT-EEEE CS
                            MoeA_C  61 leaGeeVev 69 
                                       + +Ge Vev
  gi|386001101|ref|YP_005919400.1|  95 VGEGEAVEV 103
                                       789999998 PP

  == domain 3  score: 43.1 bits;  conditional E-value: 7.9e-15
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       +rla++++s++ rr++l v +    g+ +++p+  +gSg +++la A+g + ip+ +e l+ GeeV v+l+
  gi|386001101|ref|YP_005919400.1| 337 GRLARPVRSEG-RRQMLAVAVV---GD-WVYPV-DKGSGSITTLAAADGVVDIPSSVELLDRGEEVTVHLF 401
                                       699******99.**********...88.*****.**********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.22s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4103.97
//
Query:       gi|386001102|ref|YP_005919401.1|  [L=186]
Description: hypothetical protein Mhar_0392 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 1319.22
//
Query:       gi|386001103|ref|YP_005919402.1|  [L=333]
Description: DNA primase, large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-33  115.9   0.0    7.8e-33  114.0   0.0    1.7  2  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   4.4e-37   7.8e-33       4     206 ..     128     307 ..     125     312 .. 0.91
   2 ?   -0.6   0.0      0.04   7.1e+02     256     266 .]     313     323 ..     308     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 4.4e-37
                                       EEEHHHHHHHTT-G........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHH CS
                   DNA_primase_lrg   4 kvpfedvldlvkrr........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekle 72 
                                       +vpf+d+l+ ++r         ++ l++G++ ++ +el +ll+e+ r+r++++l    + +p++     e+ r  l 
  gi|386001103|ref|YP_005919402.1| 128 RVPFSDYLKAAARMkspgwklvNRSLEAGWVAVTGSELARLLEERARDRVARGLPL--KVSPDV----CEKLRPDLA 198
                                       79******999844589***************************************..777888....888888899 PP

                                       HHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHC CS
                   DNA_primase_lrg  73 ellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeile 149
                                       e+ e+l+           e ++ ++ +++++++++fPpC+r  l  +  + +l+h++r++lt+Fl  +g+++de++ 
  gi|386001103|ref|YP_005919402.1| 199 EVVEELR-----------ERRAEERVDLGEVTEGAFPPCIRGFLAAVANGANLAHTARFALTTFLLAVGMNVDEVVG 264
                                       9999999...........55556667789************************************************ PP

                                       CCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-H CS
                   DNA_primase_lrg 150 lwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cp 206
                                       ++ ++     ++Fd+ ++ry+++h++G   ++t y+p+sC+++          ++g Cp
  gi|386001103|ref|YP_005919402.1| 265 VFGRS-----PDFDEeKTRYQVEHIAG--KGGTAYKPPSCATM---------ATYGnCP 307
                                       ****8.....*****************..7789**********.........8888887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.04
                                       TT-SSCHHHCC CS
                   DNA_primase_lrg 256 rdeikhPlqYy 266
                                       +  ++hPl+Yy
  gi|386001103|ref|YP_005919402.1| 313 CRWVSHPLSYY 323
                                       5679******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2191.80
//
Query:       gi|386001104|ref|YP_005919403.1|  [L=247]
Description: DNA polymerase sliding clamp [Methanosaeta harundinacea 6Ac]
Scores for complete 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-14   53.2   0.1    7.6e-14   51.5   0.1    1.8  2  PCNA_N         Proliferating cell nuclear antigen, N-terminal
      2e-11   44.1   0.0    1.8e-07   31.4   0.0    3.7  3  PCNA_C         Proliferating cell nuclear antigen, C-terminal
    0.00084   18.9   0.0     0.0013   18.2   0.0    1.3  1  Rad9           Rad9
  ------ inclusion threshold ------
      0.018   15.2   0.2       0.21   11.8   0.1    2.5  2  DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal do


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1   1.7e-17   7.6e-14       8     101 ..       7      99 ..       1     108 [. 0.90
   2 ?   -1.4   0.0      0.39   1.7e+03      76      99 ..     139     163 ..     135     181 .. 0.53

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.7e-17
                                       SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                            PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                        a  l+  +ea+  lv+e+ f  +++G++l+a+D + va+vs++l+se+fe ++   +  +gv+l  l+ +l +a+ 
  gi|386001104|ref|YP_005919403.1|   7 SAETLRDAVEAVSSLVDEVKFTLSENGVELKAVDPANVAMVSFRLNSEAFEYFKA-TPGEIGVDLVRLADVLSMADR 82 
                                       46678999*******************************************9997.5789***************** PP

                                       TSEEEEEEETTSSEEEE CS
                            PCNA_N  85 edsvtlkaedeadtlal 101
                                        ++vtl+ ++e+ +l++
  gi|386001104|ref|YP_005919403.1|  83 GENVTLELDEENHKLKI 99 
                                       ********999988876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                                       HHHHTTSTT.TSEEEEEEETTSSEE CS
                            PCNA_N  76 skilkcann.edsvtlkaedeadtl 99 
                                        k ++ a++ +d v+l   d+++  
  gi|386001104|ref|YP_005919403.1| 139 RKAVRAAEKvSDHVVLGVTDDPEDQ 163
                                       5666666542566666666555543 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.27   1.2e+03      22      45 ..      15      38 ..       4      57 .. 0.71
   2 !    5.5   0.0    0.0039        18      45      76 ..      62      93 ..      52     114 .. 0.88
   3 !   31.4   0.0     4e-11   1.8e-07       2     127 ..     122     242 ..     121     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.27
                                      HHHHTTT-SEEEEEEETTEEEEEE CS
                            PCNA_C 22 crdlsqlsdsvvisvtkegvkfsa 45
                                      +  +s+l d+v  +++ +gv  +a
  gi|386001104|ref|YP_005919403.1| 15 VEAVSSLVDEVKFTLSENGVELKA 38
                                      555677777777777777777665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                                      EEETTEEEEEEE--BEESSSGGGCBEEEESS- CS
                            PCNA_C 45 asGdiGsasivlkqvkdvdkeeeavklelkep 76
                                      + G+iG   + l++v ++++  e v+lel+e 
  gi|386001104|ref|YP_005919403.1| 62 TPGEIGVDLVRLADVLSMADRGENVTLELDEE 93
                                      56***************************985 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 4e-11
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETT...EEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtke...gvkfsasGdiGsasivlkqvkdvdkeeeavklelke 75 
                                       +p+++  a v lp +   + +r   ++sd vv+ vt +        a+Gdi s ++++          e   l+  +
  gi|386001104|ref|YP_005919403.1| 122 VPELDLPAHVILPGAHLRKAVRAAEKVSDHVVLGVTDDpedQFYMEAKGDIDSLKLKMPG-------AELLGLKPGK 191
                                       7999999****************************975211566789****988444433.......3455666666 PP

                                       -EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  76 pvtltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                       + +  f+l+Yla++ ka   +++v+l++  + Pl + +k+ ++  ++ylla+
  gi|386001104|ref|YP_005919403.1| 192 ARS-LFSLDYLADMSKAIGKAQEVKLEMGVDYPLRISFKLGQGVEINYLLAP 242
                                       554.5*********************************************98 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     3e-07    0.0013       4      58 ..      14      67 ..      11     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3e-07
                              Rad9  4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqir 58
                                      a++++s + de+ +  se+g+el++v+ ++ a +++ l+++ F+ + k + ++i 
  gi|386001104|ref|YP_005919403.1| 14 AVEAVSSLVDEVKFTLSENGVELKAVDPANVAMVSFRLNSEAFEYF-KATPGEIG 67
                                      78999***************************************99.55655554 PP

>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.6e-05      0.21      23     109 ..      24     108 ..       2     117 .. 0.68
   2 ?   -0.0   0.0      0.21   9.2e+02      74      92 ..     200     218 ..     192     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                                       STTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEEE......EE-EEEEEEHHHHHHHHHHSSTTSEEEEEEE CS
                     DNA_pol3_beta  23 nRntlpiLsgvllevkdsqlsltgtDleisiestisaese......eeegkvlvparllldivkaLpndkkvkisvn 93 
                                       +         v+ + +++++ l++ D    + +++ ++se      +++g++ v    l+d+++  + +++v+++++
  gi|386001104|ref|YP_005919403.1|  24 E---------VKFTLSENGVELKAVDPANVAMVSFRLNSEafeyfkATPGEIGVDLVRLADVLSMADRGENVTLELD 91 
                                       3.........555666666666666654444444444444466666799**************************** PP

                                       TTEEEEE.EETTEEEEE CS
                     DNA_pol3_beta  94 eqkllii.ksgssrfsl 109
                                       e++ +++ ++ s  ++l
  gi|386001104|ref|YP_005919403.1|  92 EENHKLKiGVNSLSYTL 108
                                       *7776650244445555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                                       HHHHHHHHSSTTSEEEEEE CS
                     DNA_pol3_beta  74 llldivkaLpndkkvkisv 92 
                                       +l+d+ ka+ + ++vk+++
  gi|386001104|ref|YP_005919403.1| 200 YLADMSKAIGKAQEVKLEM 218
                                       799*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1682.28
//
Query:       gi|386001105|ref|YP_005919404.1|  [L=93]
Description: DNA-directed RNA polymerase subunit M [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-18   64.1   8.4    1.7e-17   63.0   4.7    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
    4.5e-05   23.3   3.1     0.0012   18.8   0.9    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00031   20.4   1.6        2.6    7.9   0.0    3.1  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
     0.0008   19.5   3.0       0.91    9.7   0.0    3.2  3  Zn-ribbon_8      Zinc ribbon domain
     0.0018   18.2   3.5       0.28   11.2   0.6    2.7  2  Nudix_N_2        Nudix N-terminal
     0.0018   17.8   5.5      0.093   12.3   2.1    2.9  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0028   17.7   1.7      0.012   15.6   0.1    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0055   17.4   0.7      0.049   14.4   0.1    2.0  2  zinc_ribbon_15   zinc-ribbon family
  ------ inclusion threshold ------
      0.011   15.4   2.8        2.2    8.0   0.0    3.1  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.012   15.7   3.7      0.084   12.9   3.7    2.1  1  DZR              Double zinc ribbon
      0.012   16.0   1.2       0.29   11.6   1.2    2.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.023   14.1   6.6        1.1    8.8   0.4    2.8  3  zf-ribbon_3      zinc-ribbon domain
      0.023   15.0   2.7        4.4    7.7   0.1    3.0  3  C1_2             C1 domain
      0.026   14.4   6.0        2.4    8.1   0.9    3.2  3  zinc_ribbon_4    zinc-ribbon domain
      0.029   14.1   7.7          2    8.2   0.6    3.2  3  zinc_ribbon_2    zinc-ribbon domain
      0.037   13.9   0.3       0.14   12.0   0.0    1.9  2  zf-ZPR1          ZPR1 zinc-finger domain
       0.04   14.3   1.1       0.99    9.7   0.5    2.0  2  DUF3268          zinc-finger-containing domain
      0.051   13.5   2.8       0.99    9.4   0.9    2.6  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.076   12.9   9.3       0.16   11.8   0.4    3.1  3  zf-HIT           HIT zinc finger
       0.09   12.8   5.1        4.3    7.4   1.9    2.7  2  Elf1             Transcription elongation factor Elf1 like
      0.098   12.3   8.1        5.3    6.7   0.1    3.1  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.12   12.3   8.5       0.61   10.1   3.1    2.7  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.13   12.3   3.7       0.17   11.9   0.4    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.13   11.9  10.5       0.49   10.1   0.2    3.1  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        0.2   11.7   5.1       0.22   11.5   0.0    2.7  3  DUF1451          Zinc-ribbon containing domain
       0.24   11.1   0.2       0.24   11.1   0.2    2.4  2  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
       0.26   11.2  14.3        1.6    8.7   0.9    3.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.27   10.6   5.1       0.37   10.1   2.2    2.4  2  zf-TFIIB         Transcription factor zinc-finger
       0.35   11.6   5.6         15    6.4   2.4    2.7  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.39   10.4   4.6          1    9.0   0.1    3.0  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.41   10.7   3.2        2.8    8.0   0.9    2.7  2  CpXC             CpXC protein
       0.44   11.1   5.9         14    6.4   0.1    3.2  3  zf-C2H2          Zinc finger, C2H2 type
       0.47   10.8   5.1        1.5    9.2   0.8    2.7  2  GFA              Glutathione-dependent formaldehyde-activatin
       0.52   10.3   5.7        6.7    6.7   0.4    3.1  3  HalOD2           Halobacterial output domain 2
       0.68   10.1   7.5        9.7    6.4   2.1    2.8  2  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.84   10.6   7.4         41    5.4   0.2    3.2  3  zf-C2H2_4        C2H2-type zinc finger
        1.2    9.0   3.5         28    4.6   0.0    2.7  3  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
        1.5    8.9   6.2         30    4.7   6.3    2.5  1  zinc-ribbons_6   zinc-ribbons
        2.1    8.2  13.9        1.2    8.9   1.1    3.1  3  Rubredoxin_2     Rubredoxin metal binding domain
        3.6    7.6   7.7          6    6.9   0.2    3.0  3  YhfH             YhfH-like protein
        3.8    7.8   8.7    5.3e+02    0.9   8.9    2.8  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
        3.8    7.6   6.5         15    5.8   0.4    3.0  3  zf-C2H2_6        C2H2-type zinc finger
        4.8    7.8   9.4        8.4    7.0   3.3    2.6  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        5.9    6.9  10.6         41    4.1   0.1    3.2  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.27   1.1e+02      31      37 ..      10      16 ..       7      18 .. 0.62
   2 !   63.0   4.7   4.2e-20   1.7e-17       2      39 .]      53      90 ..      52      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.27
                           TFIIS_C 31 CtkCghr 37
                                      C  Cg+r
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKR 16
                                      5556554 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 4.2e-20
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                      kCp+Cg++ ay++ +Q+RsaDE++++f++CtkC+++Wr
  gi|386001105|ref|YP_005919404.1| 53 KCPECGNDTAYWWLRQLRSADESEVRFFRCTKCNFTWR 90
                                      8************************************8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.058        24      20      29 ..       9      19 ..       3      34 .. 0.73
   2 !   18.8   0.9   2.8e-06    0.0012      19      45 ..      52      87 ..      43      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.058
                     Zn_Tnp_IS1595 20 vCPhCgsr.ka 29
                                      +C +Cg+r + 
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRlEM 19
                                      69999987654 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.8e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45
                                        CP Cg++  ++ +++         + f+C +C+ 
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGNDtAYWWLRQlrsadeseVRFFRCTKCNF 87
                                      57*******66666666999**************85 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.078        32      22      31 ..       7      16 ..       2      28 .. 0.78
   2 !    7.9   0.0    0.0063       2.6      42      51 ..      49      58 ..      43      60 .. 0.85
   3 ?    6.3   0.1      0.02       8.1      40      52 ..      74      87 ..      68      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.078
                    zinc_ribbon_10 22 alICskChsh 31
                                       lIC+ C + 
  gi|386001105|ref|YP_005919404.1|  7 VLICRRCGKR 16
                                      59*****875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0063
                    zinc_ribbon_10 42 evkyrCpkCg 51
                                      ++ky+Cp+Cg
  gi|386001105|ref|YP_005919404.1| 49 TTKYKCPECG 58
                                      679******9 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.02
                    zinc_ribbon_10 40 leev.kyrCpkCga 52
                                       +ev  +rC kC++
  gi|386001105|ref|YP_005919404.1| 74 ESEVrFFRCTKCNF 87
                                      4555369*****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.042        17       8      16 ..      10      18 ..       7      32 .. 0.76
   2 !    9.7   0.0    0.0022      0.91       5      14 ..      51      60 ..      37      77 .. 0.75
   3 ?    3.6   0.3      0.18        74       6      12 ..      80      86 ..      79      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.042
                       Zn-ribbon_8  8 CeeCghefe 16
                                      C++Cg++ e
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLE 18
                                      999999988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8  5 eYrCeeCghe 14
                                       Y+C eCg++
  gi|386001105|ref|YP_005919404.1| 51 KYKCPECGND 60
                                      4666666654 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.18
                       Zn-ribbon_8  6 YrCeeCg 12
                                      +rC++C+
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCN 86
                                      8*****8 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.013       5.3       3      14 ..      10      21 ..       9      24 .. 0.87
   2 !   11.2   0.6   0.00068      0.28       3      30 ..      54      87 ..      51      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                                      -TTT--B-EEE- CS
                         Nudix_N_2  3 CsqCGtpvelri 14
                                      C+ CG+++e++ 
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLEMKR 21
                                      ********9886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00068
                                      -TTT--B-E.....EE--TT-SS-EE.EETTTTE CS
                         Nudix_N_2  3 CsqCGtpve.....lripdgDnreRl.vCpaCgt 30
                                      C++CG+ ++     +   +++++ R+ +C++C++
  gi|386001105|ref|YP_005919404.1| 54 CPECGNDTAywwlrQLRSADESEVRFfRCTKCNF 87
                                      *******998887444558889999648****97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.026        10      17      31 ..       5      19 ..       3      30 .. 0.78
   2 !   12.3   2.1   0.00023     0.093       1      25 [.      52      85 ..      52      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                                      TTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon 17 rgelvCtdCGlVled 31
                                      +g l+C +CG  le 
  gi|386001105|ref|YP_005919404.1|  5 EGVLICRRCGKRLEM 19
                                      67799****987776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                                      EEETTTTCEE.C.......HEETSTTCE.EESSS CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.l.......veDpergel.vCtdC 25
                                      ykCP+Cg+++ +         D+++  + +Ct+C
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGNDTaYwwlrqlrSADESEVRFfRCTKC 85
                                      8*******98669999977555555555599999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     3e-05     0.012      68      95 ..       5      60 ..       1      70 [. 0.88
   2 ?    1.9   0.2      0.55   2.3e+02      71      81 ..      80      90 ..      67      93 .] 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-05
                                      --EEEETTTS-EEECHHH.HH...........................S-TTTSSS CS
                              HypA 68 pvkvrCreCgkefeleek.al...........................rCpkCgsa 95
                                      + ++ Cr+Cgk+ e++++ +l                           +Cp+Cg+ 
  gi|386001105|ref|YP_005919404.1|  5 EGVLICRRCGKRLEMKRSeSLvsrteqrgrtmtviedsegaglpttkyKCPECGND 60
                                      56789*********887533478999****************************86 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.55
                                      EEETTTS-EEE CS
                              HypA 71 vrCreCgkefe 81
                                      +rC++C+ +++
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCNFTWR 90
                                      68888887775 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   0.00012     0.049      36      75 ..       6      61 ..       2      64 .. 0.78
   2 ?    1.5   0.0       1.3   5.2e+02      65      72 ..      79      86 ..      66      92 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00012
                    zinc_ribbon_15 36 pylacskCkslleaskelgkeiekkesse.................kkeCknCgkev 75
                                       +l c++C+++le+++++ + ++++e++                  k++C++Cg+ +
  gi|386001105|ref|YP_005919404.1|  6 GVLICRRCGKRLEMKRSE-SLVSRTEQRGrtmtviedsegaglpttKYKCPECGNDT 61
                                      5789********999843.33333333335789*********************976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.3
                    zinc_ribbon_15 65 kkeCknCg 72
                                        +C +C+
  gi|386001105|ref|YP_005919404.1| 79 FFRCTKCN 86
                                      44555554 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0055       2.2      19      28 ..       5      14 ..       3      18 .. 0.80
   2 ?    5.4   0.1     0.036        15       7      13 ..      54      60 ..      51      64 .. 0.80
   3 ?    0.8   0.1         1   4.1e+02       6      11 ..      81      86 ..      79      93 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0055
                           zf-RRN7 19 dGfyyCrrCh 28
                                      +G  +CrrC+
  gi|386001105|ref|YP_005919404.1|  5 EGVLICRRCG 14
                                      67789****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.036
                           zf-RRN7  7 CgvCgcr 13
                                      C++Cg++
  gi|386001105|ref|YP_005919404.1| 54 CPECGND 60
                                      *****94 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1
                           zf-RRN7  6 pCgvCg 11
                                      +C  C+
  gi|386001105|ref|YP_005919404.1| 81 RCTKCN 86
                                      799888 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7   0.00021     0.084      14      37 ..       9      60 ..       3      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                               DZR 14 fCseCgtklkavaa............................edrCpsCgek 37
                                       C +Cg++l+   +                            +++Cp+Cg +
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLEMKRSeslvsrteqrgrtmtviedsegaglpttKYKCPECGND 60
                                      7********8544499*********************************986 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.2    0.0007      0.29       6      36 ..      10      87 ..       5      93 .] 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0007
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigq...............................................cvyCadCga 36
                                      C  Cg+r +++rs++ v+  +q                                               ++ C++C+ 
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLEMKRSESLVSRTEQrgrtmtviedsegaglpttkykcpecgndtaywwlrqlrsadesevrFFRCTKCNF 87
                                      666777777777777777777777777777777777777775555555555555555555555555578888888876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0047       1.9      13      26 .]       4      17 ..       2      17 .. 0.88
   2 ?    8.8   0.4    0.0026       1.1       3      10 ..      52      59 ..      50      61 .. 0.77
   3 ?   -1.1   0.3       3.5   1.4e+03       5       8 ..      82      85 ..      79      86 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0047
                       zf-ribbon_3 13 ssddnvCpyCGtkl 26
                                      s+++ +C  CG++l
  gi|386001105|ref|YP_005919404.1|  4 SEGVLICRRCGKRL 17
                                      89999******997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0026
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++CP+CG+
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGN 59
                                      68888886 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.5
                       zf-ribbon_3  5 CPnC 8 
                                      C +C
  gi|386001105|ref|YP_005919404.1| 82 CTKC 85
                                      5555 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.1   4.4e+02      16      27 ..       5      16 ..       2      22 .. 0.73
   2 ?    5.0   0.1     0.077        31      31      38 ..      50      57 ..      41      63 .. 0.78
   3 ?    7.7   0.1     0.011       4.4      31      41 ..      78      88 ..      70      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.1
                              C1_2 16 sesfnCsaCgrk 27
                                      ++   C+ Cg+ 
  gi|386001105|ref|YP_005919404.1|  5 EGVLICRRCGKR 16
                                      566679999986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.077
                              C1_2 31 ffYsCseC 38
                                      ++Y+C+eC
  gi|386001105|ref|YP_005919404.1| 50 TKYKCPEC 57
                                      459**999 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.011
                              C1_2 31 ffYsCseCdfs 41
                                       f++C++C+f+
  gi|386001105|ref|YP_005919404.1| 78 RFFRCTKCNFT 88
                                      459*******8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.33   1.3e+02      27      33 ..       9      15 ..       2      18 .. 0.68
   2 ?    5.1   0.0     0.053        21      25      33 ..      51      59 ..      41      60 .. 0.84
   3 ?    8.1   0.9     0.006       2.4      26      36 .]      80      90 ..      74      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.33
                     zinc_ribbon_4 27 rCskCgh 33
                                       C +Cg+
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGK 15
                                      4777775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.053
                     zinc_ribbon_4 25 kvrCskCgh 33
                                      k +C+ Cg+
  gi|386001105|ref|YP_005919404.1| 51 KYKCPECGN 59
                                      778999986 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.006
                     zinc_ribbon_4 26 vrCskCghvFr 36
                                       rC+kC+ ++r
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCNFTWR 90
                                      69*****9996 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.026        10       2       9 ..      10      17 ..       5      21 .. 0.80
   2 ?    8.2   0.6     0.005         2       1       7 [.      53      59 ..      48      60 .. 0.80
   3 ?    3.1   0.2      0.21        84       1       5 [.      81      85 ..      74      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C +CG+ l
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRL 17
                                      88888876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.005
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +Cp+CG+
  gi|386001105|ref|YP_005919404.1| 53 KCPECGN 59
                                      6888887 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                     zinc_ribbon_2  1 fCpnC 5 
                                      +C++C
  gi|386001105|ref|YP_005919404.1| 81 RCTKC 85
                                      46666 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.9   7.6e+02      33      41 ..      10      18 ..       7      44 .. 0.51
   2 ?   12.0   0.0   0.00035      0.14       2      42 ..      53      91 ..      52      93 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.9
                           zf-ZPR1 33 CehCgyknn 41
                                      C++Cg + +
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLE 18
                                      666665532 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00035
                           zf-ZPR1  2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42
                                      +Cp+Cg  n + + +l ++    e  +  f+C +C+++ +e
  gi|386001105|ref|YP_005919404.1| 53 KCPECG--NDTAYWWLRQLRSADESEVRFFRCTKCNFTWRE 91
                                      7****8..458999999*******************98776 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.25     1e+02       4      24 ..       9      29 ..       6      43 .. 0.71
   2 ?    9.7   0.5    0.0024      0.99       3      37 ..      52      86 ..      50      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.25
                           DUF3268  4 rCpyCGekvilvsaseiYker 24
                                      +C+ CG++  +++++++ +  
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLEMKRSESLVSRT 29
                                      699999999988887776333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                       +Cp CG+ +++   +++ ++ + +  ++ C+kC+
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGNDTAYWWLRQLRSADESEVRFFRCTKCN 86
                                      68*****************9999999********8 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.23        95      18      26 ..       6      14 ..       3      15 .. 0.84
   2 ?    9.4   0.9    0.0024      0.99       4      15 ..      53      75 ..      47      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.23
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                       +l+C  C+
  gi|386001105|ref|YP_005919404.1|  6 GVLICRRCG 14
                                      69******7 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0024
                    PhnA_Zn_Ribbon  4 kCplCaSeytY...........e 15
                                      kCp+C+ +++Y            
  gi|386001105|ref|YP_005919404.1| 53 KCPECGNDTAYwwlrqlrsadeS 75
                                      9*******999887777775443 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.21        86      16      22 ..      10      16 ..       7      17 .. 0.86
   2 ?   11.8   0.4    0.0004      0.16      12      21 ..      50      59 ..      46      61 .. 0.85
   3 ?    2.6   0.3      0.31   1.3e+02      15      20 ..      81      86 ..      80      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.21
                                      -TTT--E CS
                            zf-HIT 16 CpkCntr 22
                                      C++C+ r
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKR 16
                                      9***987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0004
                                      -SEE-TTT-- CS
                            zf-HIT 12 akYkCpkCnt 21
                                       kYkCp C+ 
  gi|386001105|ref|YP_005919404.1| 50 TKYKCPECGN 59
                                      69******96 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.31
                                      E-TTT- CS
                            zf-HIT 15 kCpkCn 20
                                      +C kCn
  gi|386001105|ref|YP_005919404.1| 81 RCTKCN 86
                                      688887 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.036        15      44      59 ..       6      21 ..       3      30 .. 0.84
   2 ?    7.4   1.9     0.011       4.3      19      52 ..      49      86 ..      28      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.036
                              Elf1 44 aevsCkvCgesfetkv 59
                                      +++ C+ Cg+++e+k 
  gi|386001105|ref|YP_005919404.1|  6 GVLICRRCGKRLEMKR 21
                                      8899*******99984 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                              Elf1 19 ptkFdCpfCnheksv....evkldkkekiaevsCkvCg 52
                                       tk++Cp C+++++     + +   ++++   +C++C+
  gi|386001105|ref|YP_005919404.1| 49 TTKYKCPECGNDTAYwwlrQLRSADESEVRFFRCTKCN 86
                                      689********976411112333333347777888887 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.013       5.3       4      14 ..       9      19 ..       7      23 .. 0.85
   2 ?    6.7   0.3     0.013       5.4       2       9 ..      51      58 ..      50      62 .. 0.87
   3 ?    2.6   0.2      0.26     1e+02       3      10 ..      80      87 ..      78      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C rCgk++++
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLEM 19
                                      7******9876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                            zf_UBZ  2 tylCerCg 9 
                                       y C++Cg
  gi|386001105|ref|YP_005919404.1| 51 KYKCPECG 58
                                      69*****9 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.26
                            zf_UBZ  3 ylCerCgk 10
                                      + C +C+ 
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCNF 87
                                      78****95 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 ?    3.7   0.3      0.14        57      30      45 ..       9      24 ..       8      37 .. 0.74
   2 ?    5.4   0.2     0.043        18      42      54 ..      47      59 ..      31      63 .. 0.78
   3 ?   10.1   3.1    0.0015      0.61      30      56 ..      53      89 ..      49      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgr 45
                                       C +Cg++++ ++s+ 
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLEMKRSES 24
                                      5999**9999855544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.043
                    OrfB_Zn_ribbon 42 lsgrtfkCpnCgf 54
                                      l + ++kCp+Cg 
  gi|386001105|ref|YP_005919404.1| 47 LPTTKYKCPECGN 59
                                      5677888888886 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0015
                    OrfB_Zn_ribbon 30 tCseCgsknke..........alsgrtfkCpnCgfea 56
                                      +C+eCg    +          + + r f+C++C+f++
  gi|386001105|ref|YP_005919404.1| 53 KCPECGNDTAYwwlrqlrsadESEVRFFRCTKCNFTW 89
                                      7******999999999999999999*********997 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.82   3.3e+02       2      17 ..      10      25 ..       9      34 .. 0.80
   2 ?   11.9   0.4   0.00042      0.17       1      35 [.      53      87 ..      53      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.82
                         Ogr_Delta  2 CPhCgapaaartsrnl 17
                                      C  Cg++    +s+ l
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLEMKRSESL 25
                                      888***9999999876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00042
                         Ogr_Delta  1 rCPhCgapaaartsrnl.skdvre.ryyqCsnfeCga 35
                                      +CP+Cg+  a +  r+l s+d  e r++ C+   C +
  gi|386001105|ref|YP_005919404.1| 53 KCPECGNDTAYWWLRQLrSADESEvRFFRCTK--CNF 87
                                      6******9999888887366666699999998..655 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0012      0.49      17      31 ..       7      21 ..       2      24 .. 0.77
   2 ?    5.3   0.8     0.039        16       1      10 [.      52      61 ..      52      63 .. 0.80
   3 ?    2.1   0.2      0.38   1.5e+02      19      24 ..      81      86 ..      76      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                                      ----SSS-----B-- CS
                    DNA_RNApol_7kD 17 piRCkeCGhRilYKk 31
                                      ++ C+ CG R+ +K+
  gi|386001105|ref|YP_005919404.1|  7 VLICRRCGKRLEMKR 21
                                      677999999987775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.039
                                      -B-SSS--B- CS
                    DNA_RNApol_7kD  1 YiCgeCgaev 10
                                      Y+C eCg+++
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGNDT 61
                                      8899998875 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.38
                                      --SSS- CS
                    DNA_RNApol_7kD 19 RCkeCG 24
                                      RC++C 
  gi|386001105|ref|YP_005919404.1| 81 RCTKCN 86
                                      999995 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00054      0.22     111     132 ..       4      25 ..       2      35 .. 0.90
   2 ?    1.3   0.3       0.8   3.2e+02     134     141 ..      53      60 ..      46      68 .. 0.80
   3 ?   -0.4   0.2       2.7   1.1e+03     115     122 ..      80      87 ..      67      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00054
                           DUF1451 111 glGtlvCekCgkelalkkteei 132
                                       + G+l+C++Cgk+l++k++e +
  gi|386001105|ref|YP_005919404.1|   4 SEGVLICRRCGKRLEMKRSESL 25 
                                       68***************99876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.8
                           DUF1451 134 pCpkCgat 141
                                       +Cp+Cg++
  gi|386001105|ref|YP_005919404.1|  53 KCPECGND 60 
                                       68888876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.7
                           DUF1451 115 lvCekCgk 122
                                       ++C+kC+ 
  gi|386001105|ref|YP_005919404.1|  80 FRCTKCNF 87 
                                       57888865 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.81   3.3e+02      36      41 ..       9      14 ..       6      15 .. 0.82
   2 ?   11.1   0.2    0.0006      0.24      22      41 ..      67      86 ..      66      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.81
                     Baculo_LEF5_C 36 yCskCg 41
                                       C++Cg
  gi|386001105|ref|YP_005919404.1|  9 ICRRCG 14
                                      7****9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0006
                     Baculo_LEF5_C 22 iQnRagDEi.vsfvryCskCg 41
                                      +Q+R+ DE  v f r C kC+
  gi|386001105|ref|YP_005919404.1| 67 RQLRSADESeVRFFR-CTKCN 86
                                      7*******7477776.****9 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.9     0.004       1.6      26      38 .]       9      21 ..       6      21 .. 0.90
   2 ?    4.7   6.5     0.068        28       4      31 ..      51      86 ..      51      90 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                    Zn_ribbon_SprT 26 rCrrCkgtLrgke 38
                                      +CrrC+ +L++k+
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLEMKR 21
                                      8********9985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.068
                    Zn_ribbon_SprT  4 vYrCtgCgreyth....hlsirrhn.......YrCrrCk 31
                                      +Y+C+ Cg+   +    +l++   +        rC +C 
  gi|386001105|ref|YP_005919404.1| 51 KYKCPECGNDTAYwwlrQLRS---AdesevrfFRCTKCN 86
                                      7*******9877622224444...144467778888876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.3   5.1e+02      22      26 ..      10      14 ..       7      28 .. 0.63
   2 ?   10.1   2.2   0.00092      0.37       1      25 [.      53      85 ..      53      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                          zf-TFIIB 22 CpqCr 26
                                      C +C+
  gi|386001105|ref|YP_005919404.1| 10 CRRCG 14
                                      44443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00092
                          zf-TFIIB  1 kCPkCqdele.....eser...ggveidyCpqC 25
                                      kCP C+++       ++++   ++v +++C++C
  gi|386001105|ref|YP_005919404.1| 53 KCPECGNDTAywwlrQLRSadeSEVRFFRCTKC 85
                                      8****986666888755556669********** PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.068        28       4      15 ..       9      20 ..       7      37 .. 0.76
   2 ?    6.4   2.4     0.036        15       4      14 ..      53      68 ..      50      85 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.068
                           zf-ISL3  4 rCPnCgsk..tvvk 15
                                       C++Cg++  +  k
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRleM--K 20
                                      5******9532..3 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.036
                           zf-ISL3  4 rCPnCgsktv.....v 14
                                      +CP+Cg+ t+     +
  gi|386001105|ref|YP_005919404.1| 53 KCPECGNDTAywwlrQ 68
                                      6******998566653 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.98     4e+02       9      14 ..      10      15 ..       3      20 .. 0.60
   2 ?    9.0   0.1    0.0026         1       5      14 ..      50      59 ..      48      61 .. 0.89
   3 ?    0.7   0.2         1   4.1e+02       6      12 ..      79      85 ..      74      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.98
                                      -TTT-- CS
                   Desulfoferrod_N  9 CevCGn 14
                                      C  CG 
  gi|386001105|ref|YP_005919404.1| 10 CRRCGK 15
                                      555654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0026
                                      -EEE-TTT-- CS
                   Desulfoferrod_N  5 evYkCevCGn 14
                                       +YkC  CGn
  gi|386001105|ref|YP_005919404.1| 50 TKYKCPECGN 59
                                      58*******9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1
                                      EEE-TTT CS
                   Desulfoferrod_N  6 vYkCevC 12
                                       ++C+ C
  gi|386001105|ref|YP_005919404.1| 79 FFRCTKC 85
                                      69**999 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.9    0.0068       2.8       3      47 ..      10      61 ..       8      65 .. 0.67
   2 ?    1.4   0.1      0.79   3.2e+02      34      46 ..      76      88 ..      67      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0068
                              CpXC  3 CpaCgkefeaeiwts.idadedpelkeklldgs......lfeatCpkCgata 47
                                      C +Cgk+ e++  +s +  +e+      ++++s       ++++Cp+Cg+++
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLEMKRSESlVSRTEQRGRTMTVIEDSegaglpTTKYKCPECGNDT 61
                                      88888888887665514555666666677776544454468999****9876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.79
                              CpXC 34 slfeatCpkCgat 46
                                      +++ ++C kC+ t
  gi|386001105|ref|YP_005919404.1| 76 EVRFFRCTKCNFT 88
                                      677899****876 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.58   2.4e+02       3       9 ..      10      16 ..       8      25 .. 0.80
   2 ?    6.4   0.1     0.034        14       1       7 [.      52      58 ..      52      66 .. 0.85
   3 ?    4.0   0.4      0.19        77       1       8 [.      80      87 ..      80      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.58
                                      ETTTTEE CS
                           zf-C2H2  3 CpdCgks 9 
                                      C  Cgk+
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKR 16
                                      8899986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.034
                                      EEETTTT CS
                           zf-C2H2  1 ykCpdCg 7 
                                      ykCp+Cg
  gi|386001105|ref|YP_005919404.1| 52 YKCPECG 58
                                      9*****9 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.19
                                      EEETTTTE CS
                           zf-C2H2  1 ykCpdCgk 8 
                                      ++C++C+ 
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCNF 87
                                      89****96 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8    0.0037       1.5      25      59 ..      29      61 ..      10      72 .. 0.70
   2 ?    0.3   0.2       2.2   8.9e+02      42      56 ..      72      86 ..      64      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0037
                               GFA 25 ealelleg.elkeykktadsgnkvtrsfCpeCgspl 59
                                      ++ +   g +++++++++  g + t++ CpeCg   
  gi|386001105|ref|YP_005919404.1| 29 TEQR---GrTMTVIEDSEGAGLPTTKYKCPECGNDT 61
                                      3333...458899999999999**********9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.2
                               GFA 42 dsgnkvtrsfCpeCg 56
                                      + +++v+   C +C 
  gi|386001105|ref|YP_005919404.1| 72 ADESEVRFFRCTKCN 86
                                      567778888899996 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.2   4.8e+02      34      40 ..      10      16 ..       6      24 .. 0.79
   2 ?    4.4   0.1     0.085        35       4      11 ..      53      60 ..      41      74 .. 0.79
   3 ?    6.7   0.4     0.016       6.7       4      13 ..      81      90 ..      78      93 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.2
                            HalOD2 34 CtrCGev 40
                                      C rCG+ 
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKR 16
                                      9999975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.085
                            HalOD2  4 kCseCsld 11
                                      kC+eC+ d
  gi|386001105|ref|YP_005919404.1| 53 KCPECGND 60
                                      67777766 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.016
                            HalOD2  4 kCseCsldWt 13
                                      +C++C++ W 
  gi|386001105|ref|YP_005919404.1| 81 RCTKCNFTWR 90
                                      8********5 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3      0.06        25      36      61 ..      10      36 ..       4      40 .. 0.82
   2 ?    6.4   2.1     0.024       9.7      32      48 ..      50      66 ..      47      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.06
                                      ESSSSSS.EEEEEETTEEEETTTTEEE CS
                   Ribosomal_L37ae 36 Cpfcgkt.kvkRkavgiwkCkkcgktv 61
                                      C +cgk+ ++kR+   + + ++ g+t+
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRlEMKRSESLVSRTEQRGRTM 36
                                      99****99****988887777777766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                                      S-BEESSSSSSEEEEEE CS
                   Ribosomal_L37ae 32 akytCpfcgktkvkRka 48
                                      +ky+Cp+cg+++  ++ 
  gi|386001105|ref|YP_005919404.1| 50 TKYKCPECGNDTAYWWL 66
                                      69*******99876654 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.34   1.4e+02       2      11 ..       9      18 ..       8      27 .. 0.81
   2 ?    5.4   0.2       0.1        41       1       7 [.      52      58 ..      52      64 .. 0.86
   3 ?    4.6   0.7      0.18        73       1      12 [.      80      88 ..      80      93 .] 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.34
                         zf-C2H2_4  2 kCpiCgksFs 11
                                      +C+ Cgk+  
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLE 18
                                      7*****9975 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.1
                         zf-C2H2_4  1 fkCpiCg 7 
                                      +kCp Cg
  gi|386001105|ref|YP_005919404.1| 52 YKCPECG 58
                                      8*****7 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.18
                         zf-C2H2_4  1 fkCpiCgksFss 12
                                      f+C+ C  +F +
  gi|386001105|ref|YP_005919404.1| 80 FRCTKC--NF-T 88
                                      89****..66.3 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       6.6   2.7e+03      16      20 ..      10      14 ..       4      14 .. 0.79
   2 ?    4.6   0.2     0.072        29      13      20 ..      51      58 ..      45      58 .. 0.75
   3 ?    4.6   0.0     0.069        28      14      23 ..      80      89 ..      69      93 .] 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.6
                         zf-C2H2_3 16 CkeCg 20
                                      C  Cg
  gi|386001105|ref|YP_005919404.1| 10 CRRCG 14
                                      999*8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.072
                         zf-C2H2_3 13 asqCkeCg 20
                                      + +C+eCg
  gi|386001105|ref|YP_005919404.1| 51 KYKCPECG 58
                                      356****8 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.069
                         zf-C2H2_3 14 sqCkeCgMvY 23
                                       +C++C+ ++
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCNFTW 89
                                      35*****987 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   6.3     0.073        30       2      26 ..       9      61 ..       8      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.073
                                      --SSS-S--E.E-S...........................SEEE-TTT--EE CS
                    zinc-ribbons_6  2 kCpeCqqele.krg...........................eqyhCeaCqedl 26
                                      +C++C + le kr+                           ++y+C +C +d 
  gi|386001105|ref|YP_005919404.1|  9 ICRRCGKRLEmKRSeslvsrteqrgrtmtviedsegaglptTKYKCPECGNDT 61
                                      69999999885444888888888888888888888888888888888888754 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.35   1.4e+02       3       7 ..      10      14 ..       9      16 .. 0.73
   2 ?    8.9   1.1    0.0029       1.2       1      14 [.      52      65 ..      52      65 .. 0.90
   3 ?    5.2   0.7     0.044        18       1       9 [.      80      88 ..      80      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.35
                      Rubredoxin_2  3 CsqCG 7 
                                      C++CG
  gi|386001105|ref|YP_005919404.1| 10 CRRCG 14
                                      88888 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                      Rubredoxin_2  1 YvCsqCGfesakwf 14
                                      Y C +CG+++a w+
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGNDTAYWW 65
                                      99******999996 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.044
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      ++C +C+f+
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCNFT 88
                                      8******98 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1       0.1        41      16      24 ..      10      18 ..       9      24 .. 0.85
   2 ?    6.9   0.2     0.015         6      15      22 ..      53      60 ..      47      62 .. 0.85
   3 ?   -0.6   0.4       3.3   1.3e+03      16      19 ..      82      85 ..      74      85 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                              YhfH 16 CteCGkeie 24
                                      C  CGk +e
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLE 18
                                      9*****986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                              YhfH 15 kCteCGke 22
                                      kC+eCG++
  gi|386001105|ref|YP_005919404.1| 53 KCPECGND 60
                                      8*****86 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.3
                              YhfH 16 CteC 19
                                      Ct+C
  gi|386001105|ref|YP_005919404.1| 82 CTKC 85
                                      4444 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   8.9       1.3   5.3e+02      21      33 ..      49      61 ..       7      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.3
                      NOB1_Zn_bind 21 mtkkFCpkCGnkt 33
                                      +tk  Cp+CGn+t
  gi|386001105|ref|YP_005919404.1| 49 TTKYKCPECGNDT 61
                                      6788899999998 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.3   5.5e+02       4      12 ..      10      18 ..       9      19 .. 0.80
   2 ?    5.8   0.4     0.036        15       2       9 ..      52      59 ..      51      60 .. 0.89
   3 ?    3.2   0.3      0.23        92       2       8 ..      80      86 ..      79      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.3
                         zf-C2H2_6  4 CsvCsksFp 12
                                      C  C+k+++
  gi|386001105|ref|YP_005919404.1| 10 CRRCGKRLE 18
                                      888***976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.036
                         zf-C2H2_6  2 heCsvCsk 9 
                                      ++C++C++
  gi|386001105|ref|YP_005919404.1| 52 YKCPECGN 59
                                      9*****95 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.23
                         zf-C2H2_6  2 heCsvCs 8 
                                      ++C+ C+
  gi|386001105|ref|YP_005919404.1| 80 FRCTKCN 86
                                      89****8 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.3     0.021       8.4       4      20 ..       6      22 ..       5      54 .. 0.68
   2 ?    2.8   2.3      0.43   1.7e+02       5      31 ..      51      84 ..      47      90 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.021
                   Zn_ribbon_recom  4 GllrCgeCGspmtrrkr 20
                                      G+l+C +CG+++  +++
  gi|386001105|ref|YP_005919404.1|  6 GVLICRRCGKRLEMKRS 22
                                      89*********655433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.43
                   Zn_ribbon_recom  5 llrCgeCGspmtr......rkrk.gkrhyYrCst 31
                                      + +C eCG+   +      r++  ++ + +rC +
  gi|386001105|ref|YP_005919404.1| 51 KYKCPECGNDTAYwwlrqlRSADeSEVRFFRCTK 84
                                      568****997433333222222233335566655 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1       0.1        41      13      28 ..       3      14 ..       1      24 [. 0.67
   2 ?    2.9   2.7      0.24     1e+02       4       9 ..      54      59 ..      54      59 .. 0.98
   3 ?    3.9   0.1      0.12        49      16      28 ..      73      86 ..      69      88 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                                      EEECSCCCEEEESSSS CS
                    RNA_POL_M_15KD 13 pkedkegknfeCrqCg 28
                                      p e+++     Cr Cg
  gi|386001105|ref|YP_005919404.1|  3 PSEGVLI----CRRCG 14
                                      5666666....88886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.24
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      Cp+CgN
  gi|386001105|ref|YP_005919404.1| 54 CPECGN 59
                                      *****9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                                      CSCCCE.EEESSSS CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCg 28
                                      d++ ++ f C +C 
  gi|386001105|ref|YP_005919404.1| 73 DESEVRfFRCTKCN 86
                                      34444469999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 675.91
//
Query:       gi|386001106|ref|YP_005919405.1|  [L=236]
Description: Amino acid-binding ACT domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-69  232.8   4.4    1.1e-69  232.8   4.4    1.4  2  DUF5612       Domain of unknown function (DUF5612)
      2e-07   30.6   0.2    9.3e-07   28.5   0.0    2.3  3  ACT           ACT domain
    9.9e-05   22.9   0.0     0.0002   21.9   0.0    1.5  1  ACT_4         ACT domain
     0.0076   15.7   0.1      0.011   15.2   0.1    1.4  1  Peripla_BP_1  Periplasmic binding proteins and sugar binding 
  ------ inclusion threshold ------
       0.11   12.9   0.1        2.3    8.6   0.0    2.1  2  DUF1178       Protein of unknown function (DUF1178)


Domain annotation for each model (and alignments):
>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   7.2e+03      93     113 ..      21      41 ..      14      52 .. 0.69
   2 !  232.8   4.4   3.1e-73   1.1e-69       1     142 [.      94     234 ..      94     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                                       .T-EEEEES-BSSHHHHSSEE CS
                           DUF5612  93 kdiivislnmaGsvtevadlv 113
                                       + + +i+ n +G + + a +v
  gi|386001106|ref|YP_005919405.1|  21 TALNLICENRPGVLRDIAGVV 41 
                                       456677777777777777665 PP

  == domain 2  score: 232.8 bits;  conditional E-value: 3.1e-73
                                       E--HHHHT-EEEEEEE-HHHHHHHHHHHHHHHHHHHCTSS-EEEEEEE--SHHHHHHHHHHGGGSTTEEEEEEESSB CS
                           DUF5612   1 hkslkeifGkrviilGGGaqvaqvalGaiseadrhnirGerisvdtiplvGeeelaeaveavsrlprvkvlvlaGsl 77 
                                       h+s++ei+G+rvii+GGGaqvaq a+Ga++eadrhn+rGerisvdtiplvGe+ +a+av+av rl+r++vlvlaG+l
  gi|386001106|ref|YP_005919405.1|  94 HQSFDEIYGSRVIIIGGGAQVAQAAVGAVNEADRHNLRGERISVDTIPLVGEDPIADAVNAVGRLHRASVLVLAGAL 170
                                       689************************************************************************** PP

                                       --THHHHHHHHHHHT.T-EEEEES-BSSHHHHSSEEESSHHHHHHHHHHHH-TTS---GGGCSS- CS
                           DUF5612  78 mGGkiteavkklkeekdiivislnmaGsvtevadlvvtdpvqaGvlavmavadtavfdiervkgk 142
                                       mGG+i+++v++l+ee +i+vi+l+maGsv+  adlvvtdp+qaG++avm+va+ta fdi+rv+g 
  gi|386001106|ref|YP_005919405.1| 171 MGGRISDEVQRLQEE-GIPVIALKMAGSVPRRADLVVTDPIQAGTFAVMHVAKTAIFDINRVRGM 234
                                       **************9.**********************************************985 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.6e-10   9.3e-07       2      40 ..      22      61 ..      21      86 .. 0.83
   2 ?   -2.3   0.0       1.2   4.1e+03      29      61 ..      89     121 ..      87     126 .. 0.61
   3 ?   -1.6   0.0      0.66   2.4e+03      44      64 ..     137     157 ..     131     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.6e-10
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.E CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk.v 40
                                       l++ +++rPG+L +++g++a +g Ni+  +q+  e++ +
  gi|386001106|ref|YP_005919405.1| 22 ALNLICENRPGVLRDIAGVVASLGGNIEYTQQFVLERGvH 61
                                      6899************************999998888753 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                       EEEEEEEESTTECEEEEEEEEEEHHHHHHHHHH CS
                               ACT  29 dsieqrssedkvagivfvvivvdeedleevlea 61 
                                         ++++ s d++ g  +++i ++++++++++ a
  gi|386001106|ref|YP_005919405.1|  89 MEVTVHQSFDEIYGSRVIIIGGGAQVAQAAVGA 121
                                       556777777775566666666666666666655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.66
                                       EEEEEEEEHHHHHHHHHHHHT CS
                               ACT  44 vfvvivvdeedleevlealkk 64 
                                       v+++ +v+e++++++++a+ +
  gi|386001106|ref|YP_005919405.1| 137 VDTIPLVGEDPIADAVNAVGR 157
                                       677888888888888887655 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.6e-08    0.0002       7      79 ..      21      92 ..      18      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.6e-08
                             ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisVe 79
                                      + l++++e+r+g+L+di+ v+++ ++ni+  +    +  g+ ++k tv  +  +  + +++ L+a+p+V++V+
  gi|386001106|ref|YP_005919405.1| 21 TALNLICENRPGVLRDIAGVVASLGGNIEYTQQFVLE-RGVHRGKATVYMEIDQLAAGMVEDLEALPSVMEVT 92
                                      67999**************************999986.89*********987777778999********9995 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.1e-06     0.011      55     110 ..     159     217 ..     109     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-06
                                       TT-SEEEEE-..S-GG.HHHHHHHHHHT-EEEEESS--B-TTTS-EEEE-HHHHHHHHH CS
                      Peripla_BP_1  55 kgidgliiat..sdts.fdditakaesgipvialedaidapdgvPcvipddtqageest 110
                                       +++  l++a+  ++++ +d++++ +e+gipvial+ a+  p   ++v+ d  qag+ + 
  gi|386001106|ref|YP_005919405.1| 159 HRASVLVLAGalMGGRiSDEVQRLQEEGIPVIALKMAGSVPRRADLVVTDPIQAGTFAV 217
                                       6777788884236777899***********************************98665 PP

>> DUF1178  Protein of unknown function (DUF1178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.064   2.3e+02     116     148 ..     111     143 ..      92     145 .. 0.87
   2 ?    8.6   0.0   0.00063       2.3     124     147 ..     171     194 ..     166     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.064
                           DUF1178 116 geaeeraIrGeataeeakeLleeGievlplpll 148
                                       g + ++a  G  +++++++L+ e i+v ++pl+
  gi|386001106|ref|YP_005919405.1| 111 GAQVAQAAVGAVNEADRHNLRGERISVDTIPLV 143
                                       556677788999*****************9986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00063
                           DUF1178 124 rGeataeeakeLleeGievlplpl 147
                                       +G   ++e+++L+eeGi+v++l +
  gi|386001106|ref|YP_005919405.1| 171 MGGRISDEVQRLQEEGIPVIALKM 194
                                       5677789*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1652.48
//
Query:       gi|386001107|ref|YP_005919406.1|  [L=85]
Description: glutaredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-06   28.5   0.0    1.6e-06   28.2   0.0    1.3  1  Glutaredoxin  Glutaredoxin
     0.0074   16.7   0.0     0.0081   16.5   0.0    1.1  1  DUF836        Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.8e-10   1.6e-06       2      41 ..       6      44 ..       5      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.8e-10
                                      EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHH CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireel 41
                                      v++t+  Cp C ++kr+L   g++f+++d     e+  el
  gi|386001107|ref|YP_005919406.1|  6 VVYTTADCPRCEQVKRVLAGWGAEFDTVDMATA-EALTEL 44
                                      89***************************9986.555555 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     9e-07    0.0081       3      57 ..       6      61 ..       4      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9e-07
                                      EEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHC.....CCCTTTTEEEECT CS
                            DUF836  3 tLyskpgChlCeqakekLkelkleegleleviDIakdeelea.....kYgleipvlaleg 57
                                      + y++  C+ Ceq+k +L+ ++ e     +++D a+ e l +      + l  pvl+  +
  gi|386001107|ref|YP_005919406.1|  6 VVYTTADCPRCEQVKRVLAGWGAE----FDTVDMATAEALTElrvngVFTLSAPVLMAGE 61
                                      579****************77644....55888888888776666778888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 644.81
//
Query:       gi|386001108|ref|YP_005919407.1|  [L=115]
Description: hypothetical protein Mhar_0398 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 867.89
//
Query:       gi|386001109|ref|YP_005919408.1|  [L=77]
Description: histone [Methanosaeta harundinacea 6Ac]
Scores for complete 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-18   65.1   0.1    5.9e-18   64.9   0.1    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.1e-11   45.2   0.0    1.2e-11   45.0   0.0    1.0  1  Histone        Core histone H2A/H2B/H3/H4
    1.7e-08   34.4   0.0      2e-08   34.1   0.0    1.0  1  Bromo_TP       Bromodomain associated
      1e-07   32.1   0.0    1.2e-07   31.8   0.0    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    1.7e-05   24.9   0.0    2.1e-05   24.6   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    2.1e-05   24.6   0.1    2.3e-05   24.5   0.1    1.1  1  TAF            TATA box binding protein associated factor (TA
    0.00024   21.4   0.0    0.00028   21.2   0.0    1.1  1  CENP-S         CENP-S protein
       0.01   14.6   0.0      0.012   14.4   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin
  ------ inclusion threshold ------
      0.035   14.0   0.2      0.048   13.6   0.2    1.2  1  Tail_P2_I      Phage tail protein (Tail_P2_I)
      0.047   14.2   0.0      0.056   13.9   0.0    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
      0.055   13.5   0.0      0.062   13.3   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
       0.11   11.3   0.4       0.12   11.2   0.4    1.2  1  AAA_32         AAA domain


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.1     4e-21   5.9e-18       3      65 .]       4      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 4e-21
                                      XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                      LP+a+v ++++++ +a+++++ A++ +ae++e +  e+a+eA+e ++++krKt+kae+i+ Av
  gi|386001109|ref|YP_005919408.1|  4 LPVAPVSRLIREA-GAKRVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAV 65
                                      9************.**********************************************998 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   8.2e-15   1.2e-11      65     129 ..       7      66 ..       1      68 [. 0.86

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 8.2e-15
                                       HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       +p++R++re        +r+s  a +al+e+lE + +e++eeA   a+haKR+T+ ++Di+ A++
  gi|386001109|ref|YP_005919408.1|   7 APVSRLIRE-----AGAKRVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVK 66 
                                       455555555.....556**********************************************98 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.3e-11     2e-08      12      70 ..       9      67 ..       5      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                                      HHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHH CS
                          Bromo_TP 12 vsqileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLqe 70
                                      vs + +eaG +++ e+a ++L e++++Y  e++e+a ++a+ha R +++ +D++ + ++
  gi|386001109|ref|YP_005919408.1|  9 VSRLIREAGAKRVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVKR 67
                                      8999**************************************************98877 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   7.8e-11   1.2e-07       6      78 ..       2      69 ..       1      74 [. 0.92

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 7.8e-11
                          CENP-T_C  6 pslPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkrqr 78
                                      p lP+a v++l +++       +++++ a +al ++++ +   v+e+   +a+Ha+RKt++++D+   +kr r
  gi|386001109|ref|YP_005919408.1|  2 PILPVAPVSRLIREA-----GAKRVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVKRVR 69
                                      89999***9999887.....4569*****************************************99999977 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.4e-08   2.1e-05      11      68 ..       9      66 ..       5      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.4e-08
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                      ++ ++++ g + ++e   + L ++   y ++v e+A   a+hak+k+v+++d+r A++
  gi|386001109|ref|YP_005919408.1|  9 VSRLIREAGAKRVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVK 66
                                      6789999*************************************************97 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   1.5e-08   2.3e-05      17      66 .]      17      66 ..       1      66 [. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                      T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                               TAF 17 GitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                      G + +s+ a  +Lae +e    e+++ea+ + +h+kR++  ++D+ +A++
  gi|386001109|ref|YP_005919408.1| 17 GAKRVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVK 66
                                      7777888999999999999999************************9986 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.9e-07   0.00028      25      71 ..      20      66 ..       6      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                            CENP-S 25 eatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                      ++++ +  al+e+      ++a+    +a+HAkR+t++++D+   ++
  gi|386001109|ref|YP_005919408.1| 20 RVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVK 66
                                      466666778888888888899********************965555 PP

>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.8e-06     0.012     254     308 ..      12      66 ..       6      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-06
                                       EEES--GGGGH.HH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGST CS
                     EPSP_synthase 254 tvenvginslq.Gdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpd 308
                                       +++++g++ +  G + al e+le  g+e+ +e++++    +  +++k++di+++++
  gi|386001109|ref|YP_005919408.1|  12 LIREAGAKRVSeGARDALAEVLESYGMEVAEEAVEWANHAK-RKTVKAEDIREAVK 66 
                                       588999999999*********************99999999.8*********9986 PP

>> Tail_P2_I  Phage tail protein (Tail_P2_I)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.2e-05     0.048      64     106 ..      12      56 ..       9      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                         Tail_P2_I  64 vikeaielhrlkGTpaavrrvlealgfg..veitEWweyrkpytf 106
                                       +i+ea + +   G + a+ +vle++g++   e +EW++ +k  t 
  gi|386001109|ref|YP_005919408.1|  12 LIREAGAKRVSEGARDALAEVLESYGMEvaEEAVEWANHAKRKTV 56 
                                       89*********************9999743578889887444443 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.8e-05     0.056      17      64 ..      20      67 ..       9      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.8e-05
                                      ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH CS
                       TFIID_20kDa 17 kldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhler 64
                                      ++ e  +d L+e+ + +  +v + a++ a h k +++ + Di+  ++r
  gi|386001109|ref|YP_005919408.1| 20 RVSEGARDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAVKR 67
                                      56778899**********************************977777 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.2e-05     0.062      25      64 ..      26      65 ..      12      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                                      HHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXX CS
                       TFIID-18kDa 25 vqlledlvrgyliellqqaakvaklrgsrkitlEDllfli 64
                                       + l ++++ y +e+ ++a++ a++ +++ ++ ED+  ++
  gi|386001109|ref|YP_005919408.1| 26 RDALAEVLESYGMEVAEEAVEWANHAKRKTVKAEDIREAV 65
                                      578999*****************************97665 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   7.9e-05      0.12     481     510 ..      38      67 ..       8      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-05
                            AAA_32 481 adllrEAdywakkegaevveaehVekAlee 510
                                       +++ +EA  wa+++++++v+ae++++A+++
  gi|386001109|ref|YP_005919408.1|  38 MEVAEEAVEWANHAKRKTVKAEDIREAVKR 67 
                                       58999**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 568.42
//
Query:       gi|386001110|ref|YP_005919409.1|  [L=630]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-67  228.3   0.0    1.4e-67  227.9   0.0    1.1  1  GatB_N     GatB/GatE catalytic domain
    1.1e-16   61.1   0.0    1.8e-16   60.3   0.0    1.4  1  GatB_Yqey  GatB domain
    2.5e-13   50.1   0.0    5.8e-13   48.9   0.0    1.6  1  GAD        GAD domain
     0.0017   18.4   0.1     0.0032   17.5   0.1    1.4  1  YqeY       Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.9   0.0   3.2e-71   1.4e-67       1     271 [.      12     444 ..      12     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.9 bits;  conditional E-value: 3.2e-71
                                       EEEEEEEEEEB--SB-SSSSSBSS....SSCE..........STTSS--TTTTTS...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx....xxxx..........xxxxxxxxxxxxx...................... RF
                            GatB_N   1 lviGlEiHaqlktksKlFssaste....eege..........epnsevsevdlal...................... 41 
                                       lv+G+EiH+ql+t+ KlF++++t+    e  e           ++se++e+d a+                      
  gi|386001110|ref|YP_005919409.1|  12 LVCGIEIHQQLDTAAKLFCGCPTRirevE--EsdhqffrylrPARSELGEIDRAAleevlvtrkfiyksydstclve 86 
                                       58********************8765431..145678889845999*******99********************** PP

                                       ....TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEE CS
                                       ....xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                            GatB_N  42 ....PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrier 112
                                           P   P  ln ea+e+ + ++  l ++ia+e++++RK+++++++++g+Q+t+    la++Gs+++   +v++e+
  gi|386001110|ref|YP_005919409.1|  87 adeeP---PGeLNPEALEIGLIVSRLLSMKIADEVHTMRKIVIDGSNTSGFQRTA---YLASHGSIDTsCGRVGMET 157
                                       *9995...6559*******************************************...699******97789***** PP

                                       EEEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 113 ihlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvS 189
                                       i+lEe+aa+ v+++ +e++++l+R+G+pL+Ei+t+pd+ sp++ar+v+ +l+++lr++g +++++  G++R+DvNvS
  gi|386001110|ref|YP_005919409.1| 158 ICLEEEAARIVEDRGDEVVYSLDRLGIPLVEICTSPDIVSPAHAREVAGRLGMILRSTGRVKRGL--GTIRQDVNVS 232
                                       *****************************************************************..********** PP

                                       ECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH..................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                            GatB_N 190 vreeekgeeegtrvEiKnlnslksiekaieyeierqiell..................................... 229
                                       +r        g+rvEiK++++l+ ie+++++e+erq  ll                                     
  gi|386001110|ref|YP_005919409.1| 233 IRG-------GARVEIKGVQDLNLIETIVAVEAERQHLLLeirdellrrgamvsdrvadvtgifgpteskvirsalr 302
                                       **4.......59***************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|386001110|ref|YP_005919409.1| 303 kggavlavklagfadligaeiqpgrrlgselsdrakragvggifhsdelpaygittkeveavrselgagegdgfamv 379
                                       ***************************************************************************** PP

                                       ..........................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHH CS
                                       ..........................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ..........................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseel 271
                                                                 +eTr++ ++ g+++++R+ + +a   r++pe+d+pp+++s e 
  gi|386001110|ref|YP_005919409.1| 380 aapldraeaamkavleraaealvgvpEETRRALPE-GTSEYMRPLPgSA---RMYPETDVPPVVVSPED 444
                                       ***********************************.**********555...*************9875 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   4.1e-20   1.8e-16       2     148 .]     483     624 ..     482     624 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4.1e-20
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                       +fee+v+  + ++ ++  +l+ + +el+  g+++++  l++++l+e l+l+a  +++k+ + ++le+++ + g s++
  gi|386001110|ref|YP_005919409.1| 483 LFEEAVRDLSLPPALVVRTLEMIPRELEGVGVPVSR--LPESRLKEALALVAGRRVAKEGIPKLLEAMAMNpGLSAS 557
                                       8********99*************************..9******************************999***** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       e+ +  gL  + + + +e++v+ ++a      e ++++ e al+ l+G vMk+++Gkad++l++  l++++
  gi|386001110|ref|YP_005919409.1| 558 EAASATGLSGVGE-GDVEAVVAAIVAGR---EEFVRERGEAALGPLMGLVMKELRGKADGALISAALRREI 624
                                       ***********98.**************...677899***************************9999875 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.3e-16   5.8e-13       1      95 []     297     390 ..     297     390 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-16
                                       HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT-- CS
                               GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgae 76 
                                       +++al +gg v a+++ g +a+l++ ei+++++++ el+++++   +v+g +++++++++ +t +ev+ ++  +ga 
  gi|386001110|ref|YP_005919409.1| 297 IRSALRKGGAVLAVKLAG-FADLIGAEIQPGRRLGSELSDRAKRA-GVGGIFHSDELPAYgITTKEVEAVRSELGAG 371
                                       6899**************.8**********************976.******************************* PP

                                       TTEEEEEEEEEHHHHHHHH CS
                               GAD  77 egDillfvAdkkktvnkal 95 
                                       egD + +vA + + ++ a+
  gi|386001110|ref|YP_005919409.1| 372 EGDGFAMVAAPLDRAEAAM 390
                                       **********999988876 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.2e-07    0.0032      96     141 ..     573     622 ..     567     624 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHHHHH....TT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHH CS
                              YqeY  96 iealvkeaiae....vgaesmkdmGkvmkalkpkvkGkaDgkkvsalvke 141
                                       +ea+v++++a     v +++ +++G +m++++++++GkaDg+ +sa++++
  gi|386001110|ref|YP_005919409.1| 573 VEAVVAAIVAGreefVRERGEAALGPLMGLVMKELRGKADGALISAALRR 622
                                       5666666665411114677999************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 4443.22
//
Query:       gi|386001111|ref|YP_005919410.1|  [L=348]
Description: Cell division control protein 6 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-08   34.5   0.4    3.6e-06   27.5   0.0    2.8  2  AAA_16        AAA ATPase domain
    1.1e-07   32.2   0.0    2.2e-07   31.2   0.0    1.5  1  AAA_22        AAA domain
    1.4e-05   25.0   0.0    4.7e-05   23.3   0.0    2.0  1  Cdc6_C        CDC6, C terminal winged helix domain
    1.9e-05   25.1   0.0    4.3e-05   23.9   0.0    1.6  1  AAA           ATPase family associated with various cellular 
    0.00034   20.2   0.0     0.0045   16.5   0.0    2.0  2  AAA_7         P-loop containing dynein motor region
      0.001   18.9   0.0     0.0017   18.2   0.0    1.3  1  AAA_11        AAA domain
     0.0018   18.0   0.0      0.077   12.7   0.0    2.3  2  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.1       0.39   11.3   0.0    2.5  2  AAA_18        AAA domain
      0.021   14.0   0.0      0.031   13.5   0.0    1.2  1  NB-ARC        NB-ARC domain
      0.022   14.0   0.0        0.4    9.9   0.0    2.4  2  Zeta_toxin    Zeta toxin
      0.027   14.4   0.0      0.042   13.8   0.0    1.2  1  NACHT         NACHT domain
      0.029   14.4   0.0      0.064   13.3   0.0    1.7  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.045   12.6   0.0        0.1   11.4   0.0    1.5  2  AAA_35        AAA-like domain
      0.048   13.4   0.0      0.073   12.8   0.0    1.3  1  AAA_24        AAA domain
      0.056   13.6   0.1       0.22   11.7   0.0    1.9  2  TIP49_C       TIP49 AAA-lid domain
       0.12   11.8   0.0       0.18   11.2   0.0    1.2  1  RecA          recA bacterial DNA recombination protein
       0.15   11.2   0.0        0.2   10.8   0.0    1.2  1  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.17   12.3   0.0       0.35   11.3   0.0    1.5  1  RNA_helicase  RNA helicase
       0.19   12.1   0.0       0.36   11.2   0.0    1.5  1  AAA_19        AAA domain
       0.19   11.3   0.0       0.35   10.5   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   4.1e-09   3.6e-06      10     163 ..       2     130 ..       1     140 [. 0.67
   2 ?   -1.0   0.1       2.3     2e+03     159     159 ..     253     253 ..     191     305 .. 0.58

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.1e-09
                            AAA_16  10 eqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellr 83 
                                       e+L+ +++ ++  grp + l+ G++G+GK++ + +l+ ++e++   +  +  +c+         +   a+ + +++ 
  gi|386001111|ref|YP_005919410.1|   2 EALKFCVRpALQGGRPVSALCLGPPGTGKTTAIFKLFSEMEAHSSKVvpVHVNCQMD-------HTRHAI-FLRIYS 70 
                                       6889999944555566*****************999999998832221233333333.......334455.335666 PP

                            AAA_16  84 qlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq.wadeaslql.laaL 158
                                       +ll +         +               a+  ++ ++l r+++ l++d r lv+ lDd+   + e   +  l++L
  gi|386001111|ref|YP_005919410.1|  71 KLLGH--------SPP--------------ASGVSFKRVLERIAKTLAKDNRVLVVALDDVNyLFPEKEVDRvLYTL 125
                                       66666........222..............22257888999999777777888999999999444445555558888 PP

                            AAA_16 159 lrlle 163
                                       lr  e
  gi|386001111|ref|YP_005919410.1| 126 LRGHE 130
                                       88766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                            AAA_16 159 l 159
                                       l
  gi|386001111|ref|YP_005919410.1| 253 L 253
                                       2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   2.5e-10   2.2e-07       8     113 ..      20     126 ..      15     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.5e-10
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellral.glelkaerlsseellea 81 
                                        ++ G++GtGKTt + +l+++ +++      +++vv  +v+++ + ++  ++ ++ ++l g++  a++ s +++le+
  gi|386001111|ref|YP_005919410.1|  20 ALCLGPPGTGKTTAIFKLFSEMEAH------SSKVVpvHVNCQMDHTRHAIFLRIYSKLlGHSPPASGVSFKRVLER 90 
                                       6899*****************9876......8888899*************77777765155555589999999999 PP

                            AAA_22  82 leqalraravielliiDEaqhlr.s...eealeeLr 113
                                       +++ l +  ++ ++ +D++ +l+ +   +++l +L 
  gi|386001111|ref|YP_005919410.1|  91 IAKTLAKDNRVLVVALDDVNYLFpEkevDRVLYTLL 126
                                       9999999999999********997324555555554 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.2e-08   4.7e-05      38      82 ..     289     332 ..     261     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.2e-08
                                       -HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                            Cdc6_C  38 tqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                                         ++++++l++L++ +++++  s+ G r gr+r +++++dp++vl
  gi|386001111|ref|YP_005919410.1| 289 GYTRFHEILNKLDAARLVDTDFSGPGHR-GRSRVVRIRYDPKEVL 332
                                       679***********************97.**************98 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 !   23.9   0.0   4.8e-08   4.3e-05       2      96 ..      21     132 ..      20     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.8e-08
                                       EEESSTTSSHHHHHHHHHHHHTHE....................EEEEETTTCSSS............STTHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgve....................fleisgsellsk............yvgesekki 46 
                                       l  GppGtGKT+++  + +e++++                    f                         g s k++
  gi|386001111|ref|YP_005919410.1|  21 LCLGPPGTGKTTAIFKLFSEMEAHsskvvpvhvncqmdhtrhaiF----------LriyskllghsppASGVSFKRV 87 
                                       678*****************9655445554444444444444434..........0555555555577667777776 PP

                                       HHHHHH..HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  47 relfke..akekakpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                        e +++  ak + +  ++ +D++  l++++      e +rv+ +Ll+  + +
  gi|386001111|ref|YP_005919410.1|  88 LERIAKtlAKDN-RVLVVALDDVNYLFPEK------EVDRVLYTLLRGHEAF 132
                                       666655222333.479*************9......6777777777655555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     5e-06    0.0045      35      74 ..      19      60 ..       3      73 .. 0.69
   2 ?    1.3   0.0      0.24   2.1e+02      97     128 ..      97     128 ..      84     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-06
                             AAA_7 35 pvllvGptGtGKtviikdllkkld..kekylsltinfsaqts 74
                                      + l+ Gp GtGKt+ i +l+++++  ++k++++++n++   +
  gi|386001111|ref|YP_005919410.1| 19 SALCLGPPGTGKTTAIFKLFSEMEahSSKVVPVHVNCQMDHT 60
                                      359***************999999334455555555554444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.24
                             AAA_7  97 pggkklvvFvDDlnmpakekygaqppiellRq 128
                                       + ++ lvv +DD+n   +ek  ++   +llR 
  gi|386001111|ref|YP_005919410.1|  97 KDNRVLVVALDDVNYLFPEKEVDRVLYTLLRG 128
                                       5678899********99999999999998885 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.9e-06    0.0017      20      43 ..      20      56 ..       4     111 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                            AAA_11 20 tliqGPPGtgKTktivellsqll.............s 43
                                      +l  GPPGtgKT++i +l+s++              +
  gi|386001111|ref|YP_005919410.1| 20 ALCLGPPGTGKTTAIFKLFSEMEahsskvvpvhvncQ 56
                                      5677******************744444444444440 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   8.6e-05     0.077      21      50 ..      20      49 ..       6      55 .. 0.75
   2 ?    2.9   0.1     0.087        78     139     188 ..     202     248 ..     188     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrvi 50
                                      a+  Gp+GtGKtta+ +l   +ea+  +v+
  gi|386001111|ref|YP_005919410.1| 20 ALCLGPPGTGKTTAIFKLFSEMEAHSSKVV 49
                                      4568***********999888887776766 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.087
                            AAA_30 139 dlveaagigtaeLtevvRqkeseeraaalalregdaeealealadrgrih 188
                                       dl+e ag   + ++ + R   ++er+a++++++ d+++a   +++   +h
  gi|386001111|ref|YP_005919410.1| 202 DLTERAGDLRVGIDLLKRAGMEAERRASRRISDEDVDRA---YERSRLVH 248
                                       444446667788889999999***************966...66666666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00043      0.39       4      32 ..      23      49 ..      21      71 .. 0.74
   2 ?    2.3   0.1      0.26   2.3e+02      96     117 ..     296     342 ..     214     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                            AAA_18  4 tGtpGvGKttlakeL.skrlgfgvnlrdva 32
                                       G+pG+GKtt    L s++     ++++v+
  gi|386001111|ref|YP_005919410.1| 23 LGPPGTGKTTAIFKLfSEM---EAHSSKVV 49
                                      59**********9995554...34444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.26
                            AAA_18  96 k.........................vvLtaspeelleRlekRgyee 117
                                                                 v ++ +p+e l R++k +  +
  gi|386001111|ref|YP_005919410.1| 296 IlnkldaarlvdtdfsgpghrgrsrvVRIRYDPKEVLARVKKERDPP 342
                                       04445555555555555555566666999999999999999987665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.031      26     112 ..      23     109 ..      17     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                                       EESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESX..XHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHC CS
                            NB-ARC  26 vGmgGvGKttlakqilnksdevegrFdsvawvvvskt..dkseeiletilkeLslseddleekeeveslkrklvrlL 100
                                        G +G GKtt + + +++   +e +   v+ v v  +   + + i+ +i  +L  ++   +  +  +   +++ + L
  gi|386001111|ref|YP_005919410.1|  23 LGPPGTGKTTAIFKLFSE---MEAHSSKVVPVHVNCQmdHTRHAIFLRIYSKLLGHSPPASGVS-FKRVLERIAKTL 95 
                                       599*******77777766...55565666666555441156799*********77755555555.55599******* PP

                                       CCT.TEEEE.EEEE CS
                            NB-ARC 101 ltk.rfllv.lDDV 112
                                        +  r+l+v lDDV
  gi|386001111|ref|YP_005919410.1|  96 AKDnRVLVVaLDDV 109
                                       98867777679**9 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00045       0.4      12      47 ..      13      48 ..       5      64 .. 0.82
   2 ?    0.8   0.0      0.29   2.6e+02      31      60 ..      86     115 ..      72     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvv 47
                                      ++ rP++ l  G pG GK++++ +l  e+e++++ v
  gi|386001111|ref|YP_005919410.1| 13 QGGRPVSALCLGPPGTGKTTAIFKLFSEMEAHSSKV 48
                                      5689*************************9554433 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.29
                        Zeta_toxin  31 elaellkdelerqgnvvrldpDdlRelhPe 60 
                                       +++e +++ l+++++v+++  Dd+  l+Pe
  gi|386001111|ref|YP_005919410.1|  86 RVLERIAKTLAKDNRVLVVALDDVNYLFPE 115
                                       57888999999999***********99998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.7e-05     0.042       6     115 ..      23     128 ..      19     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                                       EC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-C...CHHHHC CS
                             NACHT   6 qGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvse...vwavll 77 
                                        G++G GKTt + kl +++ +   +     ++ +++++++ ++ ++  r   +ll    p+++   ++    +a  l
  gi|386001111|ref|YP_005919410.1|  23 LGPPGTGKTTAIFKLFSEMEAHSSK----VVPVHVNCQMDHTRHAIflRIYSKLLGHSPPASGVSFKRvleRIAKTL 95 
                                       79*****************998844....489999999999999889677777777777777777777554333333 PP

                                       CSCCCEE.EEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  78 elperlL.lilDglDelvtdlgqkekqpvrtlLselirk 115
                                       +  +r+L   lD++++l  +      ++v+++L +l+r+
  gi|386001111|ref|YP_005919410.1|  96 AKDNRVLvVALDDVNYLFPE------KEVDRVLYTLLRG 128
                                       44444443668999888873......4568888888886 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.1e-05     0.064       9      55 ..      27     120 ..      24     340 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt   +L   +  +  +V++v +  q+  ++++  l+++ +                                
  gi|386001111|ref|YP_005919410.1|  27 GTGKTTAIFKLFSEMEAHSSKVVPVHVNCQMDHTRHAIFLRIYSKLlghsppasgvsfkrvleriaktlakdnrvlv 103
                                       9*****************************99999944444444444666678766555555555555555555555 PP

                                       ................C CS
                                       ................x RF
                              CbiA  55 ................d 55 
                                                        
  gi|386001111|ref|YP_005919410.1| 104 valddvnylfpekevdR 120
                                       55555555555555550 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.4   2.1e+03      39      68 ..      25      54 ..      22      67 .. 0.77
   2 ?   11.4   0.0   0.00012       0.1     122     154 ..      95     127 ..      79     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                            AAA_35 39 pkkmGKtSLlarilakakqqgyktvsldlq 68
                                      p  +GKt  + ++ +++++++ k+v + ++
  gi|386001111|ref|YP_005919410.1| 25 PPGTGKTTAIFKLFSEMEAHSSKVVPVHVN 54
                                      777899999999999999988887766544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                            AAA_35 122 LkeidkplvLaldevdrlfeypeiakdflslLR 154
                                       L++ ++ lv+ald+v+ lf ++e+ + + +lLR
  gi|386001111|ref|YP_005919410.1|  95 LAKDNRVLVVALDDVNYLFPEKEVDRVLYTLLR 127
                                       6777999*************************9 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05     0.073       3      75 ..      18     110 ..      16     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdie.............swedfldevv 57 
                                       ++ l+ Gp+g+GKTt + +l         +  p+ +++ +  +++  + f +i              s++ +l+ ++
  gi|386001111|ref|YP_005919410.1|  18 VSALCLGPPGTGKTTAIFKLfsemeahssKVVPVHVNCQM--DHTRHAIFLRIYskllghsppasgvSFKRVLERIA 92 
                                       567899************9977766664433334444433..55555555555578888888888888888888888 PP

                            AAA_24  58 elaaeladyktlviDtid 75 
                                       +  a++++  ++ +D ++
  gi|386001111|ref|YP_005919410.1|  93 KTLAKDNRVLVVALDDVN 110
                                       888888888888888776 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         4   3.6e+03      39      58 ..      91     110 ..      88     113 .. 0.77
   2 ?   11.7   0.0   0.00025      0.22      18      62 ..     197     242 ..     193     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4
                           TIP49_C  39 pasilakkrkkkevevedve 58 
                                       +a++lak +    v+++dv+
  gi|386001111|ref|YP_005919410.1|  91 IAKTLAKDNRVLVVALDDVN 110
                                       67888888888888888886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                           TIP49_C  18 ldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveevee 62 
                                       ld+ a++ ++ + LR  i Ll+ a + a++r +++++ edv +++e
  gi|386001111|ref|YP_005919410.1| 197 LDKVADLTERAGdLRVGIDLLKRAGMEAERRASRRISDEDVDRAYE 242
                                       6677777766644******************************996 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.18      59     150 ..      23     119 ..      10     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                       EESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HH.HHHHTT--GGG-EEE--SSH...HHHHH.HHHHHHTTT CS
                              RecA  59 yGpessGkttlalhaiaeaqkkggvaafidaehaldpk.yakklGvdidellvsqpdtG...eqale.iadalvrsg 130
                                        Gp  +Gktt  +++ +e++ ++  ++ + ++  +d + +a  l +  + l  s p +G   ++ le ia++l + +
  gi|386001111|ref|YP_005919410.1|  23 LGPPGTGKTTAIFKLFSEMEAHSSKVVPVHVNCQMDHTrHAIFLRIYSKLLGHSPPASGvsfKRVLErIAKTLAKDN 99 
                                       6999*******************************975267788888888889999999333456766888999999 PP

                                       --SEEEEE-TTT---STT-- CS
                              RecA 131 aidlivvdsvaalvpkaeie 150
                                        + ++ +d v  l p+ e++
  gi|386001111|ref|YP_005919410.1| 100 RVLVVALDDVNYLFPEKEVD 119
                                       999***************98 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023       0.2       8      50 ..      24      63 ..      18     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                           DUF2075  8 GvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrea 50
                                      G +GtGKt   ++l+ e+  +++ +++v + vN  ++++ r+a
  gi|386001111|ref|YP_005919410.1| 24 GPPGTGKTTAIFKLFSEM--EAHSSKVVPVHVNC-QMDHTRHA 63
                                      99***************9..55555555555553.44555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.35       4      26 ..      23      45 ..      20      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                      RNA_helicase  4 yGpsgeGKStlakeLakallkkl 26
                                       Gp+g+GK+t++ +L ++++ ++
  gi|386001111|ref|YP_005919410.1| 23 LGPPGTGKTTAIFKLFSEMEAHS 45
                                      7*****************99887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004      0.36      14      38 ..      21      45 ..      11     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                            AAA_19 14 lvtaGpGtGKTrvlkhivallvelg 38
                                      l +++pGtGKT+ + +  +++++  
  gi|386001111|ref|YP_005919410.1| 21 LCLGPPGTGKTTAIFKLFSEMEAHS 45
                                      6789**********99988887655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.35       4      33 ..      20      49 ..      17      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvl 33
                                       l +G+ G+GKTt++ KL   ++++  kv+
  gi|386001111|ref|YP_005919410.1| 20 ALCLGPPGTGKTTAIFKLFSEMEAHSSKVV 49
                                      6789***************99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2444.52
//
Query:       gi|386001112|ref|YP_005919411.1|  [L=286]
Description: Phosphate binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-40  137.5   2.8    2.1e-39  135.9   2.8    1.6  1  PBP_like_2  PBP superfamily domain
    9.3e-20   70.6   0.1    1.2e-19   70.2   0.1    1.2  1  PBP_like    PBP superfamily domain
    2.2e-11   44.0   0.1    3.6e-11   43.3   0.1    1.3  1  SBP_bac_11  Bacterial extracellular solute-binding protein
     0.0036   17.3   0.8      0.016   15.1   0.8    1.9  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.027   13.9   0.0    1.3  1  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.9   2.8   5.9e-43   2.1e-39       6     282 .]      34     273 ..      30     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 5.9e-43
                        PBP_like_2   6 atsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaanga 82 
                                       a+ ++ +++aGstt+ p+++++a+ f++ ++ ++v ++++G+g gik +++g++d+a+++r+++ +eia    a g 
  gi|386001112|ref|YP_005919411.1|  34 APKAAGVTVAGSTTVMPLVEAAAEEFNRIQKEVRVSVTGGGTGVGIKNVAGGTADIAMASRDVKPEEIA----AYG- 105
                                       5556669***********************************************************995....344. PP

                        PBP_like_2  83 ggliqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstala 155
                                        g+ ++ va++aia+vv+++   ++ + lsre++ +I+sg ItnW+ +lg+p d+ I v +r+ gsgt+++f ++++
  gi|386001112|ref|YP_005919411.1| 106 DGFQEHLVAYDAIAVVVSQPiyeGGITdLSREEVLAIYSGDITNWK-GLGGP-DERIYVAAREVGSGTRDTFNEMVM 180
                                       7799*******************9999*******************.69999.************************ PP

                        PBP_like_2 156 eqgpwtasgigasg..segvasavsn.ngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasn 229
                                        +  +++ g+ +    + +v++av++   aigy+ ++y +                           al ++ + + 
  gi|386001112|ref|YP_005919411.1| 181 GTVEAETPGVTTYHgsNAEVKTAVTGsSRAIGYLGLNYLE-------------------------GGALRAVALGG- 231
                                       9955554444433366888888887778888888888666.........................44555555433. PP

                        PBP_like_2 230 plawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsde 282
                                            + p+ e+i+dg yPlsr++ +++  ++      a++a++F+d+l s e
  gi|386001112|ref|YP_005919411.1| 232 -----VTPSPETIKDGQYPLSRALKLYTFGDP------APGAEKFIDFLQSAE 273
                                       .....99***********************99......***********9975 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   3.3e-23   1.2e-19       1     151 [.      56     216 ..      56     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 3.3e-23
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS.---CCCHHCCCCCEEE...EEEEEEEE........E- CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshl.ldketeeynapalrka...ldgievvl........vn 65 
                                       aee+++ +++vrv+v++ G+g G+k+++ g+adia++++  ++e+ ++    ++++   +d+i+vv+        ++
  gi|386001112|ref|YP_005919411.1|  56 AEEFNRIQKEVRVSVTGGGTGVGIKNVAGGTADIAMASRdVKPEEIAAYGDGFQEHlvaYDAIAVVVsqpiyeggIT 132
                                       79*************************************65555544333344444111567766669999999999 PP

                                       CC-HCHCCCCHCCHHHS--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCH CS
                          PBP_like  66 larreqglvvakgnpkkitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaV 140
                                        ++re+ l +++g   +itnwk l  +d+++ ++ Re GSGtrd f+e++   g  +++ +g++++  s+ +v++aV
  gi|386001112|ref|YP_005919411.1| 133 DLSREEVLAIYSG---DITNWKGLggPDERIYVAAREVGSGTRDTFNEMVM--GTVEAETPGVTTYHGSNAEVKTAV 204
                                       9999999999999...8*********************************5..5799******************** PP

                                       CCETTCCEC.CC CS
                          PBP_like 141 aagradvgv.gi 151
                                            ++g+ g+
  gi|386001112|ref|YP_005919411.1| 205 TGSSRAIGYlGL 216
                                       ****99996454 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1     1e-14   3.6e-11       1     229 [.      40     283 ..      40     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1e-14
                                       .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpl 76 
                                       +tva ++++ + ++++a++F + + +v+v v++gg g  ++ +a+g  +D+  +     +e++aa g +   ++  +
  gi|386001112|ref|YP_005919411.1|  40 VTVAGSTTVMPLVEAAAEEFnRIQKEVRVSVTGGGTGVGIKNVAGG-TADIAMASRDVKPEEIAAYGDGF--QEHLV 113
                                       59******************555***********************.9999999999999***9999999..9**** PP

                                       EEEEEEEEESTT-T.................T---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHH CS
                        SBP_bac_11  77 assplviavpkgnp.................kkikgwadLlkpglklavadPttspsGlaalalleaagaqellkal 136
                                       a+  ++++v ++ +                  +i++w+ L++p+ ++ va  +  ++ + +++ +   g   +++a 
  gi|386001112|ref|YP_005919411.1| 114 AYDAIAVVVSQPIYeggitdlsreevlaiysGDITNWKGLGGPDERIYVAAREVGSGTRDTFNEMVM-G---TVEAE 186
                                       *************54455555555555555459******************9998888888877776.8...99999 PP

                                       HHTEEEEESSHHHHHHHHHTTT-S...EEEEEHHHHH..HSTTSSEEEE--TTT--.......EEEEEEEE-TT--H CS
                        SBP_bac_11 137 ekkvvklgessrqlltaveagead...agivyeseakaaengdkleavylpeglnld....pldypaavlkkaakre 206
                                         +v+++ +s   + tav   + +   +g+ y+   ++  ++  l  v++++++  +    pl  ++ + + ++ + 
  gi|386001112|ref|YP_005919411.1| 187 TPGVTTYHGSNAEVKTAVTGSSRAigyLGLNYLEGGAL--RAVALGGVTPSPETI-KdgqyPLSRALKLYTFGDPAP 260
                                       9****************887765512256666554444..344555566655554.312225666666666888999 PP

                                       HHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 207 aAraFlafLrspeaqailrkyGf 229
                                        A++F++fL+s+e+q+i+++ Gf
  gi|386001112|ref|YP_005919411.1| 261 GAEKFIDFLQSAEGQRIVAESGF 283
                                       **********************9 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   4.6e-06     0.016       6     314 ..      48     275 ..      43     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE....CGGHHHHHHHT..TSBECCHH CS
                         SBP_bac_1   6 egaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav....dndwiarlaka..glllpldp 76 
                                        +   +a++ ++f++  + + V ++ +g+g ++      +a+G+ + D+++      +  ia + ++    l   d+
  gi|386001112|ref|YP_005919411.1|  48 VMPLVEAAA-EEFNRIQKEVRVSVTGGGTGVGIK----NVAGGT-A-DIAMAsrdvKPEEIAAYGDGfqEHLVAYDA 117
                                       555566666.99*998867777777777777777....999999.6.999999999999999999999999999999 PP

                                       HHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTH CS
                         SBP_bac_1  77 yvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpi 153
                                       +++    p+++ +  +ls + + +i+             g i+              +W+ l  +++++  + +   
  gi|386001112|ref|YP_005919411.1| 118 IAVVVSQPIYEGGITDLSREEVLAIYS------------GDIT--------------NWKGLGGPDERIYVAAREV- 167
                                       999999999888788877777655555............3333..............9**8887777777777777. PP

                                       CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHH CS
                         SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalf 230
                                              +sgt + f                                   + ++ +++e +g++++  ++a++++++
  gi|386001112|ref|YP_005919411.1| 168 -------GSGTRDTFN---------------------------------EMVMGTVEAETPGVTTYHGSNAEVKTAV 204
                                       .......555555554.................................3344556799****************** PP

                                       HTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHH CS
                         SBP_bac_1 231 eaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldf 307
                                       +    a+++ gl++ +  ++ a + + ++++++  ++  +           +   +  l +++  +   +A+kF+df
  gi|386001112|ref|YP_005919411.1| 205 TGSSRAIGYLGLNYLEGGALRAVALGGVTPSPETIKDGQY-----------P--LSRALKLYTFGDPAPGAEKFIDF 268
                                       *999999999999955555555555555555555444444...........4..9********************** PP

                                       HTSHHHH CS
                         SBP_bac_1 308 llspeaq 314
                                       l+s+e+q
  gi|386001112|ref|YP_005919411.1| 269 LQSAEGQ 275
                                       *****99 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.4e-06     0.027     190     218 ..     259     286 .]     251     286 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.4e-06
                         SBP_bac_6 190 kelakafidfllspevqailakaggvfPv 218
                                       ++ a++fidfl s+e+q+i+a++g+ +Pv
  gi|386001112|ref|YP_005919411.1| 259 APGAEKFIDFLQSAEGQRIVAESGF-VPV 286
                                       5679********************9.886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1885.41
//
Query:       gi|386001113|ref|YP_005919412.1|  [L=332]
Description: hypothetical protein Mhar_0403 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-09   37.4   0.0    5.6e-09   36.5   0.0    1.5  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   3.1e-13   5.6e-09       1     156 [.      30     227 ..      30     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.1e-13
                                       EEEE--CCC...--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE......... CS
                                       xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys...lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddsek 74 
                                       dlHvHt +s   l   +l++e+l +kak++g+  + +TDh+ + +     + +     ++  ++ G+e+ + d +  
  gi|386001113|ref|YP_005919412.1|  30 DLHVHTLFShdvLPVPSLHPEALYRKAKKMGMGYVTFTDHDTMRA----HQVL----GDRDGLVTGVEIRIMDPELV 98 
                                       89********985558999**********************9875....5555....344578************** PP

                                       .........E....EHHHH....................................................HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx....................................................xxxxxx RF
                               PHP  75 erpshltllaknqeGyknl....................................................lkllsk 99 
                                        ++ h++++  ++e++ +l                                                    ++  ++
  gi|386001113|ref|YP_005919412.1|  99 GHTVHVNVYDLDEEEFAELeeiaelegdlrafvgllkrrglpftynhpfwfepgerpnlraipeivelfpvVEYNMH 175
                                       ***************8888999999************************************9998776665444444 PP

                                       HHH..........HHHHHHS..................TTGGHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 100 aylegfyrkpridkellekhsegLivlsgclkGevfealdlieveekaeealeelak 156
                                       + +    +k+++ +++ +++++gL++++ +++G ++++l+l + +   +e ++ +a+
  gi|386001113|ref|YP_005919412.1| 176 RVT----KKNELAMAMAQRYEKGLVAVTDTHSGMIGKVLTLSKGDS-FREYFRNIAE 227
                                       444....777777888888******************999886666.7777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2345.67
//
Query:       gi|386001114|ref|YP_005919413.1|  [L=122]
Description: hypothetical protein Mhar_0404 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.046   13.3   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.049   13.5   0.0       0.42   10.5   0.0    2.0  2  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.1e-06     0.046      16      45 ..      77     106 ..      68     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-06
                            HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeG 45 
                                       pr+s  e+ er+g +  +v+  +kr+ ++G
  gi|386001114|ref|YP_005919413.1|  77 PRLSTLEIGERIGYPYEAVSGAIKRMLQKG 106
                                       9**************************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.05   4.5e+02      12      27 ..      10      25 ..       8      31 .. 0.75
   2 ?   10.5   0.0   4.7e-05      0.42      20      53 ..      76     109 ..      67     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.05
                                      CHCHHHHHHCCCHHCH CS
                              TrmB 12 kvYlaLlklgpatade 27
                                      +vY+aLl + + + ++
  gi|386001114|ref|YP_005919413.1| 10 SVYQALLIEARHRQQD 25
                                      5899999887766666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.7e-05
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVe 53 
                                       + ++++ ei e++g p+  v  +++++++kG  e
  gi|386001114|ref|YP_005919413.1|  76 YPRLSTLEIGERIGYPYEAVSGAIKRMLQKGDLE 109
                                       5677889************************766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 843.77
//
Query:       gi|386001115|ref|YP_005919414.1|  [L=323]
Description: hypothetical protein Mhar_0405 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2655.88
//
Query:       gi|386001116|ref|YP_005919415.1|  [L=297]
Description: Phosphate ABC transporter substrate-binding protein, PhoT family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-37  128.2   5.0    1.9e-36  126.2   5.0    1.7  1  PBP_like_2       PBP superfamily domain
    7.1e-23   80.7   0.3      1e-22   80.2   0.3    1.2  1  PBP_like         PBP superfamily domain
      5e-07   29.7   0.1    2.6e-06   27.3   0.1    1.9  1  SBP_bac_11       Bacterial extracellular solute-binding prote
     0.0021   18.1   1.3     0.0053   16.8   1.3    1.7  1  SBP_bac_1        Bacterial extracellular solute-binding prote
  ------ inclusion threshold ------
      0.033   13.5   0.0       0.17   11.2   0.0    2.0  1  LysR_substrate   LysR substrate binding domain
      0.082   12.7   0.0       0.13   12.1   0.0    1.4  1  SBP_bac_8        Bacterial extracellular solute-binding prote


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   5.0   6.3e-40   1.9e-36       5     281 ..      44     282 ..      41     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 6.3e-40
                        PBP_like_2   5 eatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaang 81 
                                       +  +++ + ++Gstt+ p+    a+ f+ a++ ++v ++++GSg gik +++g  d+a+++rp+++se  + +    
  gi|386001116|ref|YP_005919415.1|  44 G--TAAALSVSGSTTVLPFGASCAEEFNAAQSAVQVSVTGGGSGVGIKNVAEGISDVAMASRPVKDSEK-EAYP--- 114
                                       3..44459***********************************************************99.4333... PP

                        PBP_like_2  82 aggliqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstal 154
                                       + ++++v +a++a++++v++     +++ ls+e++++I+ g+It+W + lg + d+ I v  r+ gsgt+++f + +
  gi|386001116|ref|YP_005919415.1| 115 DEEFVEVLAAYDAVCIAVSQAvydAGVTeLSAEEVRAIYNGEITSWAQ-LG-GDDEKIYVLGREVGSGTRDTFNEIV 189
                                       567****************9988877779*******************.55.56*********************** PP

                        PBP_like_2 155 aeqgpwtasgigasg..segvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakias 228
                                       +   ++++ g+ +s   + +v++a+ + + aigy+ ++y  +                          al ++    
  gi|386001116|ref|YP_005919415.1| 190 MGSDKAETPGVTTSHgsNAEVKTALtKSDRAIGYLGLNYIMDG-------------------------ALAAIAF-- 239
                                       ***9999888877768899999999788**********99933.........................3333222.. PP

                        PBP_like_2 229 nplawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsd 281
                                          ++ ++p+ e+i+dg+yPl r +y+++y ++       + a+aFld+++ d
  gi|386001116|ref|YP_005919415.1| 240 ---EG-VEPSAETIKDGSYPLARELYMVTYGEP------TEDAQAFLDFVTGD 282
                                       ...23.99***********************99......999*******9976 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.3   3.4e-26     1e-22       1     192 [.      65     279 ..      65     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 3.4e-26
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH..HCCCCCEEEEEEEEEEEE-CC-HCHCCCC CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketee..ynapalrkaldgievvlvnlarreqglvv 75 
                                       aee++++++ v+v+v++ Gsg G+k++++g  d+a+++++ k++e+  y  +++ + l++ ++v + + +   +  v
  gi|386001116|ref|YP_005919415.1|  65 AEEFNAAQSAVQVSVTGGGSGVGIKNVAEGISDVAMASRPVKDSEKeaYPDEEFVEVLAAYDAVCIAVSQAVYDAGV 141
                                       79**************************************7766662244444444555555666555555555555 PP

                                       HCCHHHS........--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCC CS
                          PBP_like  76 akgnpkk........itnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaa 142
                                        +    +        it+w++l   d+++ + +Re GSGtrd f+e +   g +k++ +g+++   s+ +v++a  +
  gi|386001116|ref|YP_005919415.1| 142 TELSAEEvraiyngeITSWAQLggDDEKIYVLGREVGSGTRDTFNEIV--MGSDKAETPGVTTSHGSNAEVKTALTK 216
                                       555444245555555*********************************..557******************999999 PP

                                       ETTCCE................C.CCGG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 143 gradvg................v.gieavaeelkgldfvplaeerydlvvrkealddpevqaflefl 192
                                        + ++g                + g+e+ ae++k++++ pla+e y + + +     +  qafl+f+
  gi|386001116|ref|YP_005919415.1| 217 SDRAIGylglnyimdgalaaiaFeGVEPSAETIKDGSY-PLARELYMVTYGEP---TEDAQAFLDFV 279
                                       99999988888888888887775588999999977776.99996666555555...45688888876 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   8.7e-10   2.6e-06      14     229 ..      62     293 ..      49     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.7e-10
                                       HHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEE.EEEEEEEEESTT CS
                        SBP_bac_11  14 relaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpl.assplviavpkg 88 
                                       + +a++F +a++ v+v v++ggsg  ++ +a+g   Dv  +     +++ +++ + ++e  ++l a+  ++iav + 
  gi|386001116|ref|YP_005919415.1|  62 ASCAEEFnAAQSAVQVSVTGGGSGVGIKNVAEG-ISDVAMAS--RPVKDSEKEAYPDEEFVEVLaAYDAVCIAVSQA 135
                                       678****888999********************.56665554..479999999999988888873567799***999 PP

                                       -.........T........T---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHH CS
                        SBP_bac_11  89 n.........p........kkikgwadLlkpglklavadPttspsGlaalalleaagaqellkalekkvvklgessr 148
                                                 +          i++wa+L++++ k+ v   +  ++ + +++ +   g   ++ka   +v+++ +s  
  gi|386001116|ref|YP_005919415.1| 136 VydagvtelsAeevraiynGEITSWAQLGGDDEKIYVLGREVGSGTRDTFNEIVM-G---SDKAETPGVTTSHGSNA 208
                                       9555444444044444443479***************998888888877765555.7...88888888888888888 PP

                                       HHHHHHHTTT-SEEEEEHHHH......H..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHH CS
                        SBP_bac_11 149 qlltaveageadagivyesea......kaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspe 219
                                        + ta+   + ++g   ++ +      + a +g + +a ++++g +  pl+  + +++ +   e A+aFl+f+++++
  gi|386001116|ref|YP_005919415.1| 209 EVKTALTKSDRAIGYLGLNYImdgalaAIAFEGVEPSAETIKDGSY--PLARELYMVTYGEPTEDAQAFLDFVTGDD 283
                                       8888877766555544444443444322222455666668888888..799999999999999************** PP

                                       HHHHHHHTT- CS
                        SBP_bac_11 220 aqailrkyGf 229
                                       +qai+++ Gf
  gi|386001116|ref|YP_005919415.1| 284 GQAIAEELGF 293
                                       *******999 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.3   1.8e-06    0.0053     134     315 .]     159     286 ..      58     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                                       BHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHH CS
                         SBP_bac_1 134 tWdelveaakklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanlt 210
                                       +W +l   ++k+   g+          +sgt + f + ++                                 + ++
  gi|386001116|ref|YP_005919415.1| 159 SWAQLGGDDEKIYVLGREV--------GSGTRDTFNEIVM---------------------------------GSDK 194
                                       5555555555554444444........3333333332222.................................2335 PP

                                       HHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEE CS
                         SBP_bac_1 211 kelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgay 287
                                       +e +g++++  ++a++++++++ + a+++ gl+++ + +++a+++  ++++ +  ++  ++                
  gi|386001116|ref|YP_005919415.1| 195 AETPGVTTSHGSNAEVKTALTKSDRAIGYLGLNYIMDGALAAIAFEGVEPSAETIKDGSYPL------------ARE 259
                                       799999999**************************999999999999999999998888886............777 PP

                                       EEEEBTTCSTHHHHHHHHHHHTSHHHHH CS
                         SBP_bac_1 288 glaipkgsknpeaAkkFldfllspeaqa 315
                                        +++ +g +  e A++Fldf++++++qa
  gi|386001116|ref|YP_005919415.1| 260 LYMVTYGEPT-EDAQAFLDFVTGDDGQA 286
                                       7888888888.669***********996 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.7e-05      0.17      25     203 ..      65     278 ..      46     282 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSS........CCTTEEEEEEEEEEEEEEEETTS..... CS
                    LysR_substrate  25 larfraryPevelelvegdseelldllaegelDlairagpp........edsglearpLaeeplvlvaspdh..... 88 
                                        ++f a+   v+++++ g s   ++ +aeg  D+a +++p         +d++++ +  a + +++++s++      
  gi|386001116|ref|YP_005919415.1|  65 AEEFNAAQSAVQVSVTGGGSGVGIKNVAEGISDVAMASRPVkdsekeayPDEEFVEVLAAYDAVCIAVSQAVydagv 141
                                       57899************************************777777777777766666677777777766667777 PP

                                       .........GGGGSSSECGGGGCT..SEEEEE..STTSTHHHHHHHHHHCTTEECEEEEEE...SSHHHHHHHHHTT CS
                    LysR_substrate  89 .........pLargepvsledLad..eplill..eegsglrdlledalreaglkprvalev...nsleallalvaaG 149
                                                ++ +ge +s+++L +  e+  +l  e gsg+rd++++    +  + ++++++   +++e   al ++ 
  gi|386001116|ref|YP_005919415.1| 142 telsaeevrAIYNGEITSWAQLGGddEKIYVLgrEVGSGTRDTFNEIVMGSDKAETPGVTTshgSNAEVKTALTKSD 218
                                       76666655544446666666666544444444224555566666666666644443333331113445555666666 PP

                                       S-BEEEEGGGHHCCCHTTTEEEEEESST............TCEEEEEEEEETTCCCHHHHHHHHHH CS
                    LysR_substrate 150 lGiallprsavrdeladgrlvalplpep............plprelylvyrkgrelspavrafidf 203
                                         i++l   ++     dg l a+ +++             pl rely+v+  +   ++ ++af+df
  gi|386001116|ref|YP_005919415.1| 219 RAIGYLGLNYIM----DGALAAIAFEGVepsaetikdgsyPLARELYMVTYGEP--TEDAQAFLDF 278
                                       666666655553....35555555555555555666665555566666665553..5566666665 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05      0.13     136     262 ..     154     294 ..     107     297 .] 0.54

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                                       GGGGGTHHETTEE---H...........HHH.HHHHHHHHHHHHTT-EE..-S..--SSTTTTTSBSEEE...E-T. CS
                         SBP_bac_8 136 wlqaallakdgksldddg.........gkdglkealellkklkdngkty..dtgadavsefanGevafti...ngs. 197
                                       +++++ +a++g + ++ +         ++d++ e++   +k    g+t+  +++a++  ++++ + a+++   n+  
  gi|386001116|ref|YP_005919415.1| 154 NGEITSWAQLGGDDEKIYvlgrevgsgTRDTFNEIVMGSDKAETPGVTTshGSNAEVKTALTKSDRAIGYlglNYIm 230
                                       56666666555555555556444433333333444333333333333443434444444444444444442333331 PP

                                       .THHHHHH-TTTSEEEE--S--.EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH--- CS
                         SBP_bac_8 198 .wdiaaaqkagkklgaivpkqg.sfaggkglavpknaknedlaAldFlkwltspenqaalaektgyi 262
                                        +++aa++ +g +  a  +k+g +++  + ++v+ + + ed  A++Fl ++t +++qa  ae  g++
  gi|386001116|ref|YP_005919415.1| 231 dGALAAIAFEGVEPSAETIKDGsYPLARELYMVTYGEPTED--AQAFLDFVTGDDGQA-IAEELGFV 294
                                       12233333444443444568883455555666677788888..**************9.66667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2042.54
//
Query:       gi|386001117|ref|YP_005919416.1|  [L=337]
Description: Phosphate binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-33  114.5   0.2    3.3e-32  112.3   0.2    1.8  1  PBP_like_2  PBP superfamily domain
    2.8e-13   49.4   0.1    4.1e-13   48.9   0.1    1.3  1  PBP_like    PBP superfamily domain
    0.00035   20.4   0.0     0.0022   17.8   0.0    2.0  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    0.00053   19.9   0.3      0.001   19.0   0.3    1.5  1  PLDc_N      Phospholipase_D-nuclease N-terminal


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.2   7.4e-36   3.3e-32       8     279 ..      91     319 ..      86     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 7.4e-36
                        PBP_like_2   8 svgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangagg 84 
                                       ++++i +aGstt+ p+ ++ a  f k + +a v++a++G+ agi++l++g +d+a+++r++ e e  +   + g   
  gi|386001117|ref|YP_005919416.1|  91 ASSTISVAGSTTVLPLAEACAREFHKGQRDAVVTVAGGGTDAGIEELAAGKIDIAMASRKVGEGEM-E---GLG-AS 162
                                       4567*****************99*****************************************88.3...333.67 PP

                        PBP_like_2  85 liqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeq 157
                                       + ++p+a +++a+vv+++    ++  lsr ++++I+sg + +W+d lg+p d  I  v+rs gsgt + fs+ +a+ 
  gi|386001117|ref|YP_005919416.1| 163 FEEHPIALDGVAIVVSRPifeAGVDeLSRHQVSAIYSGDVASWKD-LGGP-DLEIVAVSRSHGSGTGEIFSERVATP 237
                                       789****************9955555*******************.8888.************************88 PP

                        PBP_like_2 158 gpwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplaw 233
                                       g     ++       v+ +v + + aigy+ ++         l            ++     ++l v+ +++     
  gi|386001117|ref|YP_005919416.1| 238 GVSIYLDS----GADVERYVaRSDRAIGYIGLN---------L------------AF----DDELGVIAYEG----- 280
                                       33332222....55677777688******9998.........2............33....67777766644..... PP

                        PBP_like_2 234 slqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyll 279
                                        ++p+ +++ dg+yPl r++y+++  +        ++  aFl++++
  gi|386001117|ref|YP_005919416.1| 281 -VVPSAASVRDGSYPLARTLYMYTLGEA------DPEEVAFLEFVT 319
                                       .999999999**************9976......788888888876 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   9.1e-17   4.1e-13       1     150 [.     111     264 ..     111     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 9.1e-17
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH....HCCCCCEEEEEEEEEEE........E- CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketee....ynapalrkaldgievvl........vn 65 
                                       a+e+++ +++  v+va+ G+ +G++ l+ag++dia++++   e e     + +++   aldg ++v+        v 
  gi|386001117|ref|YP_005919416.1| 111 AREFHKGQRDAVVTVAGGGTDAGIEELAAGKIDIAMASRKVGEGEMeglgASFEEHPIALDGVAIVVsrpifeagVD 187
                                       67999999*******************************76655544455666666888999654445555555555 PP

                                       CC-HCHCCCCHCCHHHS--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCH CS
                          PBP_like  66 larreqglvvakgnpkkitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaV 140
                                        ++r+q   +++g   ++++wkdl  +d +++ v R +GSGt   f e ++         +g++ + +s  +v ++V
  gi|386001117|ref|YP_005919416.1| 188 ELSRHQVSAIYSG---DVASWKDLggPDLEIVAVSRSHGSGTGEIFSERVAT--------PGVSIYLDSGADVERYV 253
                                       5555555555555...7*********************************44........78888899999999999 PP

                                       CCETTCCEC.C CS
                          PBP_like 141 aagradvgv.g 150
                                       a+ + ++g+ g
  gi|386001117|ref|YP_005919416.1| 254 ARSDRAIGYiG 264
                                       99999999533 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.8e-07    0.0022       1     127 [.      95     237 ..      95     333 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.8e-07
                                       .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpl 76 
                                       + va ++++ +  +++a +F + + +  v+v +gg  + ++ +a+g + D+  +     + + + +gl+++ ++ p+
  gi|386001117|ref|YP_005919416.1|  95 ISVAGSTTVLPLAEACAREFhKGQRDAVVTVAGGGTDAGIEELAAG-KIDIAMASR--KVGEGEMEGLGASFEEHPI 168
                                       57899999999999******555999********************.899877665..58999999****99***** PP

                                       EEEEEEEEESTT-.................TT---SHHHHHHSS--.EEEE--T-TTTTHH.HHHHGGG CS
                        SBP_bac_11  77 assplviavpkgn.................pkkikgwadLlkpglk.lavadPttspsGlaalalleaa 127
                                       a   ++i+v ++                    ++ +w+dL++p+l+ +av+  + s++G    + ++  
  gi|386001117|ref|YP_005919416.1| 169 ALDGVAIVVSRPIfeagvdelsrhqvsaiySGDVASWKDLGGPDLEiVAVSRSHGSGTGEIFSERVATP 237
                                       ************98888777776666555225899**********647788777799888666666555 PP

>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   2.3e-07     0.001       7      41 ..      46      80 ..      42      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-07
                            PLDc_N  7 lidiird.rnpssklaWllvilflPvlGailYllfG 41
                                      l  ++++ ++p+s l W++v +f+   Ga+lYl++G
  gi|386001117|ref|YP_005919416.1| 46 LREVLKRmTRPESVLTWVVVAVFVA-AGAVLYLIAG 80
                                      3445666999************999.********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2529.86
//
Query:       gi|386001118|ref|YP_005919417.1|  [L=87]
Description: Transcriptional regulatory protein, AsnC family, partial [Methanosaeta harundinacea 6Ac]
Scores for 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-09   35.3   0.0      1e-08   35.0   0.0    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   5.7e-13     1e-08       1      71 [.       6      72 ..       6      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.7e-13
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                                      +++++ pgh    +++ +al+ l  +   y + Gd+d+ll v v+ l al+ ++++ +++++gv  t+t +
  gi|386001118|ref|YP_005919417.1|  6 IMLKTVPGH---ERRVHAALRGLSGINRMYILFGDFDLLLDVQVEGLLALNGLVDT-VREVEGVVATRTIL 72
                                      678899999...*****************************************999.************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 635.55
//
Query:       gi|386001119|ref|YP_005919418.1|  [L=419]
Description: Alkaline phosphatase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-98  328.0   0.5    1.5e-90  304.2   0.5    2.1  2  Alk_phosphatase  Alkaline phosphatase
    2.3e-12   46.8   0.0    3.8e-12   46.1   0.0    1.4  1  Metalloenzyme    Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.027   13.9   0.0       0.35   10.2   0.0    2.2  1  Sulfatase        Sulfatase
      0.063   12.9   0.1       0.17   11.5   0.0    1.7  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph


Domain annotation for each model (and alignments):
>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.2   0.5   3.3e-94   1.5e-90       1     320 [.      37     348 ..      37     371 .. 0.91
   2 !   21.8   0.0   1.7e-08   7.5e-05     376     415 ..     378     418 ..     370     419 .] 0.89

  Alignments for each domain:
  == domain 1  score: 304.2 bits;  conditional E-value: 3.3e-94
                                       -SEEEEEEETT-SHHHHHHHHHHHCHCTCSSS........TTS.TTGGG-SEEEEEESSECSTTSSGHHHHHHHHHH CS
                   Alk_phosphatase   1 aknvilligDGmgvstvtaaRslkeqakdklg........eetllamdrfplvglsktyavdkqvtDSaataTAyac 69 
                                       ak+vi+ligDGmg +++taaR  k +  d++g        + t+l md +++ g+  t++ d+ +tDSaa+ TA+a+
  gi|386001119|ref|YP_005919418.1|  37 AKSVIFLIGDGMGYAQLTAARWEKAG-GDQPGyqptldnyQTTRLYMDGMEYAGHISTHSLDSWITDSAAAVTAMAT 112
                                       79*******************98876.3333311112222467889******************************* PP

                                       SSBTBTT-BSB-TTS..............T-B---HHHHHHHTT-EEEEEEEEETTSHHHHTTTTTBSSTTSSSHHH CS
                   Alk_phosphatase  70 gvktyngaigvdaaa..............gkevksvleaAkkaGkstGlVtTtritdAtPaalvahvesRkwkedaa 132
                                       g ktyn++i+v + +                ++k++le+A +aGk+tG+V+T+rit+AtPa++++hv+ R+w++++a
  gi|386001119|ref|YP_005919418.1| 113 GQKTYNDVISVGNITahgeimgrnnatlyAVPLKTILEMADEAGKATGVVSTSRITHATPAGYYSHVAFRDWEDEIA 189
                                       ***********999999**********9999***************************************9987666 PP

                                       STCCCHHTTS-SHHHHHHHCST-SEEEEESCGGGSBCSBCTSSTCCT.SBHHHHHCCTTCEEE-SHHHHHHHCTSTS CS
                   Alk_phosphatase 133 vpaealeegkkdiaeqlikakkidvllGGGrkeffpaeyatdGerkdGrnlieeakkkgyqyvsdrkeLlkakeenv 209
                                                     eq i+  +++v +GGG+++f         ++ + r l eea + g+ +v++ +eL +++++++
  gi|386001119|ref|YP_005919418.1| 190 --------------EQCIES-DMEVAMGGGASKF---------SFDN-RSLLEEAPSLGWTVVRNGRELSAVDPAST 241
                                       ..............9*****.*************.........6666.***************************** PP

                                       SCEEEESSSSSCS-CCCSCTCCE--HHHHHHHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHH CS
                   Alk_phosphatase 210 kplLGLFadgdlkveldrdeatdPsLkemtevAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvk 286
                                       + lLG+F d+++ +eldrd+a++PsL+emte+Ai++Ls++++GFFL+VEG+rIDha+H+ d ++a++++++fdeAvk
  gi|386001119|ref|YP_005919418.1| 242 DRLLGIFTDSHMSYELDRDPAAEPSLAEMTEKAIEILSRDDDGFFLIVEGARIDHAGHARDYKRAVGDTLAFDEAVK 318
                                       ***************************************************************************** PP

                                       HHHHHCHHCTTEEEEEEESSEESEEEESTTSTT. CS
                   Alk_phosphatase 287 aalefakkeketlvvvTaDHshvfsfggyttrge 320
                                        al++a ++ etlvvvTaDH+     gg++++ +
  gi|386001119|ref|YP_005919418.1| 319 VALDYAAENPETLVVVTADHEC----GGLVLGAN 348
                                       ********************99....55555533 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.7e-08
                                       SSHTEE-SSEEEEEESTTGGGG.SCEEECCHHHHHHHHHCT CS
                   Alk_phosphatase 376 tseeHtgedvavfAygpkaelv.rGvqeqteiakvlaaale 415
                                       ++  Ht+ dv++fA gp a ++ rG++++te++++l+aa++
  gi|386001119|ref|YP_005919418.1| 378 EEASHTATDVPIFASGPGAIEFsRGLIDNTEVFEILKAAMG 418
                                       6789***************76647*************9976 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   8.5e-16   3.8e-12       2     217 ..      39     397 ..      38     411 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 8.5e-16
                                       EEEEEEETTBB----.....GGGTTHHHS--HHHHHH..................HHH.......SEEEEEESSS.T CS
                                       xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxx.x RF
                     Metalloenzyme   2 kvvlvvlDGlGeapa.....delnaihvAktPtldkL..................kkeaPerwlikahgtavglp.e 54 
                                        v+ ++ DG+G+a+      +++++ +    Ptld+                         +w i+ +  av+ +  
  gi|386001119|ref|YP_005919418.1|  39 SVIFLIGDGMGYAQLtaarwEKAGGDQPGYQPTLDNYqttrlymdgmeyaghistH--SLDSW-ITDSAAAVTAMaT 112
                                       56777788888877755555444445555577777777777777777766665320..22333.3334444444335 PP

                                       T----HH.......HHHHHH......................................................... CS
                                       xxxxxxx.......xxxxxx......................................................... RF
                     Metalloenzyme  55 ddmgnse.......vgHlel......................................................... 67 
                                       +++   +       ++H e+                                                         
  gi|386001119|ref|YP_005919418.1| 113 GQKTYNDvisvgniTAHGEImgrnnatlyavplktilemadeagkatgvvstsrithatpagyyshvafrdwedeia 189
                                       55555556665555777777888888888888888888888888888888888888888888888888888888888 PP

                                       .......................HHHHTT-----EEEEEEEE-S---SS..HHHHHT--EEEE--SHH....STT-- CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx....xxxxx RF
                     Metalloenzyme  68 .......................lrisetvkfahvtffwnggrsgyfnp..leereeipsdtvitfdl....qpemk 115
                                                                + e+      t ++ng +   ++p   ++  +i  d+ + ++l    + e +
  gi|386001119|ref|YP_005919418.1| 190 eqciesdmevamgggaskfsfdnRSLLEEAPSLGWTVVRNGRELSAVDPasTDRLLGIFTDSHMSYELdrdpAAEPS 266
                                       88888888888888888888876333455555556778888888888887455557899999999999777777788 PP

                                       HHHHHHHHHHHH.CC.-S..EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS.-TTTEEEEEE-SSB--T CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 116 avevaekaldailsgkfd..lvvvniknaDmvGHtgdleatiaaieaaDeavkeildai.eqvdgilvvtADHgnae 189
                                         e++eka++ + s + d  +++v  +  D +GH++d+++++    a+Deavk  ld   e+ ++++vvtADH +  
  gi|386001119|ref|YP_005919418.1| 267 LAEMTEKAIEIL-SRDDDgfFLIVEGARIDHAGHARDYKRAVGDTLAFDEAVKVALDYAaENPETLVVVTADHECGG 342
                                       899******999.555678999********************************999651556778899******** PP

                                       TTSS...................................-----EEEEEESTT-- CS
                                       xxxxxxx.........................xxx..xxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 190 dmvkrdk.........................qpl..TsHtlepVPilivgkgla 217
                                        + + +                          q+l   sHt+  VPi+  g+g  
  gi|386001119|ref|YP_005919418.1| 343 LVLGANSseyiegwapnfgsgaypvsdsyadlQILeeASHTATDVPIFASGPGAI 397
                                       ***98889************************5553389**********999854 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   7.7e-05      0.35       3     250 ..      40     339 ..      38     418 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.7e-05
                                       EEEEEESSE-TTGSGGGTTTS......CSSHHH.....HHHHHTSEEESSEE-SSSS......HHHHHHHHHHSS-H CS
                         Sulfatase   3 vvliladdlgagdlglyggkt......attpnl.....drlaeeglrftnfysaapl......cspsraalltgryp 62 
                                       v+++++d +g+++l++  ++        + p+l     +rl   g+ +  ++s+++l      ++ ++ a+ tg+  
  gi|386001119|ref|YP_005919418.1|  40 VIFLIGDGMGYAQLTAARWEKaggdqpGYQPTLdnyqtTRLYMDGMEYAGHISTHSLdswitdSAAAVTAMATGQKT 116
                                       67777777777744444444422222233666622232333344444444444432222222244444555555544 PP

                                       HHHTHSSCCSTTT....................HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC..... CS
                         Sulfatase  63 hnsgvasntevgg....................gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk..... 114
                                                   +                       +    t++e+  eaG +t+++     ++    + y+     
  gi|386001119|ref|YP_005919418.1| 117 Y-----------NdvisvgnitahgeimgrnnaTLYAVPLKTILEMADEAGKATGVVSTSRITHATPAGYYShvafr 182
                                       4...........23333333333666777777666666777788888888888877777777776555555555444 PP

                                       ...........CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC.................................. CS
                         Sulfatase 115 ...........nrgfdrflgfptgsaalkdpekseyngevlrv.................................. 146
                                                  + +++  +g+ +                   +                                  
  gi|386001119|ref|YP_005919418.1| 183 dwedeiaeqciESDMEVAMGGGA-------------------Skfsfdnrslleeapslgwtvvrngrelsavdpas 240
                                       45555555555333333333333...................13333333333333333345666666888888888 PP

                                       ...................TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCC CS
                         Sulfatase 147 ...................ppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkyatffddg 203
                                                          +p+ + s ++++++a+e+l  r+ d  f+++      Ha++      a          
  gi|386001119|ref|YP_005919418.1| 241 tdrllgiftdshmsyeldrDPAAEPSLAEMTEKAIEIL-SRDdDGFFLIVEGARIDHAGH------AR--------- 301
                                       88888888888888888888888888888888888885.555244444444555566522......12......... PP

                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSS CS
                         Sulfatase 204 seaarqlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhg 250
                                             + +a +++++  D++++  l+++    ++ +tlvv+t+Dh 
  gi|386001119|ref|YP_005919418.1| 302 -----DYKRAVGDTLAF-DEAVKVALDYA---AENPETLVVVTADHE 339
                                       .....334556677766.99999999999...899999999999994 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   1.1e+03      37      56 ..      95     114 ..      48     123 .. 0.66
   2 ?   11.5   0.0   3.7e-05      0.17     143     251 ..     254     359 ..     148     405 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                       EE-SSS-SHHHHHHHHHHSS CS
                      Phosphodiest  37 lrpvfPtlTfpnhaslvTGl 56 
                                        + ++ t+++++ ++++TG+
  gi|386001119|ref|YP_005919418.1|  95 SLDSWITDSAAAVTAMATGQ 114
                                       34455566666666666664 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.7e-05
                                       CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      Phosphodiest 143 pledkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderg 219
                                       ++e + d a+ +++ ++ +++ ++  + ++  +l+v    +D++gH    ++ +v d+l   D+a++  l+++ e+ 
  gi|386001119|ref|YP_005919418.1| 254 SYELDRDPAAEPSLAEMTEKAIEILSRDDDGFFLIVEGARIDHAGHAR-DYKRAVGDTL-AFDEAVKVALDYAAEN- 327
                                       55666666788888899998888877779999**************88.6788888887.58**************. PP

                                       GTTTEEEEEEES---EEEH.T.TSEEEGGGTSTG CS
                      Phosphodiest 220 lsaetniilvSDHGmadvs.d.dkvielndllee 251
                                          et +++++DH  + +    +   +++ ++++
  gi|386001119|ref|YP_005919418.1| 328 --PETLVVVTADHECGGLVlGaNSSEYIEGWAPN 359
                                       ..9**********766665544555555666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3110.04
//
Query:       gi|386001120|ref|YP_005919419.1|  [L=305]
Description: phosphate ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-28   98.8   8.1      3e-28   98.8   8.1    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        4.7    7.2   9.4       0.33   10.9   2.9    2.6  3  DUF2755       Protein of unknown function (DUF2755)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.9  11.9         2   1.8e+04      30      63 ..      24      83 ..       6      94 .. 0.47
   2 !   98.8   8.1   3.4e-32     3e-28       1     182 [.      95     301 ..      95     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: -5.9 bits;  conditional E-value: 2
                      BPD_transp_1 30 lPsfvlaillvlvf..........................vilsilghlilpviilllls 63
                                      + + ++a +lv+v+                           ++ +  ++++p+i+ +++ 
  gi|386001120|ref|YP_005919419.1| 24 FFFAAIASILVMVLifyflireslvafqevgvfdlvfgmkWHSAGEIFGMTPIIVGSIMV 83
                                      333333333333333333477777777777777776444322222223333333333332 PP

  == domain 2  score: 98.8 bits;  conditional E-value: 3.4e-32
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrli 71 
                                       g++l++++    + + + +l p i++l ++Ps+v ++l vl++      +++   g +il++ ill ++++p  + i
  gi|386001120|ref|YP_005919419.1|  95 GVPLAVYLSELAGPRSRSILKPAIELLAGVPSIVYGFLGVLILvaylerSFDMLTGRSILAGSILLGIMFIPALTTI 171
                                       799999999999**********************8888888888899**9***********999999999999999* PP

                      BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                       +++alr++p++++e ++alGa+rwq++r+v+lP+a + ii+ ++l++g+++g++++++++ ++    +l   +   +
  gi|386001120|ref|YP_005919419.1| 172 CEDALRAVPREFKEGSLALGATRWQTVRRVTLPAASSGIIAAVVLNVGNIIGETMAALLVVGNV--ARLPSPIFDVF 246
                                       *************************************************************664..44444444444 PP

                      BPD_transp_1 149 dyseis.....................nggvlalviavlllnlvadilqrlldpr 182
                                       d s+i                      +++ ++l+++v lln++ad++ +++ ++
  gi|386001120|ref|YP_005919419.1| 247 DPSAIFtsviagemgevphgsihyhalFAVGFVLLAIVTLLNISADLVRAAIKKK 301
                                       44444466788999*********99999999999999999999999999999887 PP

>> DUF2755  Protein of unknown function (DUF2755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.9   3.7e-05      0.33      44      95 ..      37      91 ..      20      94 .. 0.72
   2 ?   -2.4   0.1      0.52   4.6e+03      63      82 ..     116     136 ..     109     143 .. 0.49
   3 ?   -3.0   0.1      0.81   7.2e+03      80      90 ..     274     284 ..     254     291 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                           DUF2755 44 lvhapGvlerlmqaqesarpqveisl...avGtlfglvpflaGlvilgvlalilr 95
                                      l+    + e l+  qe +   + +++   + G +fg+ p+++G ++++ lali+ 
  gi|386001120|ref|YP_005919419.1| 37 LIFYFLIRESLVAFQEVGVFDLVFGMkwhSAGEIFGMTPIIVGSIMVTLLALIIN 91
                                      4555555666777777776666655433378*********************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.52
                           DUF2755  63 pqveislavG.tlfglvpfla 82 
                                       p++e+  +v  +++g++ +l+
  gi|386001120|ref|YP_005919419.1| 116 PAIELLAGVPsIVYGFLGVLI 136
                                       555555555312344444433 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.81
                           DUF2755  80 flaGlvilgvl 90 
                                       f +G v+l+++
  gi|386001120|ref|YP_005919419.1| 274 FAVGFVLLAIV 284
                                       33344444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2091.20
//
Query:       gi|386001121|ref|YP_005919420.1|  [L=308]
Description: phosphate ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-30  104.1  10.9    7.4e-30  104.1  10.9    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        1.8    8.6   7.9       0.25   11.3   1.1    2.9  3  DUF2755       Protein of unknown function (DUF2755)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.2   8.7         2   1.8e+04      37     173 ..      38      94 ..      19      97 .. 0.37
   2 !  104.1  10.9   8.3e-34   7.4e-30       1     183 [.      98     305 ..      98     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: -6.2 bits;  conditional E-value: 2
                      BPD_transp_1  37 illvlvf.............vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrk 100
                                       +ll++ f             v                                                        
  gi|386001121|ref|YP_005919420.1|  38 MLLIFYFltfesflafrevgV-------------------------------------------------------- 58 
                                       222222222233333333331........................................................ PP

                      BPD_transp_1 101 vvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis............nggvlalviav 165
                                                                                        +++ +            +++++a+ +++
  gi|386001121|ref|YP_005919420.1|  59 -------------------------------------------------FDMLLgqkwhpagevfgMAPIIAGSVLI 86 
                                       .................................................1111133333333333444444444444 PP

                      BPD_transp_1 166 lllnlvad 173
                                         + l+++
  gi|386001121|ref|YP_005919420.1|  87 TTIALIIN 94 
                                       44444444 PP

  == domain 2  score: 104.1 bits;  conditional E-value: 8.3e-34
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrli 71 
                                       g++l+i++    +++ +++l p i++l ++Ps+v ++l vlv+      +++   g +il+++ill ++++p  + i
  gi|386001121|ref|YP_005919420.1|  98 GVPLAIYLSELAGRRSREFLKPAIELLAGVPSIVYGFLGVLVLvvylerSFNMLTGRSILAGAILLGIMFIPALTTI 174
                                       899******9************************88888877788999*9999************************ PP

                      BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailg 147
                                       +++alr++pk+++e ++alGa+rwq++r+v+lP+a + ii+ +il++g+++g++++++++ ++ + l +++++a   
  gi|386001121|ref|YP_005919420.1| 175 CEDALRAVPKEFKEGSLALGATRWQTVRRVTLPAASSGIIAAVILNVGRIIGETMAALLVVGNVArLPSPIFDAFDR 251
                                       *************************************************************8866655555555555 PP

                      BPD_transp_1 148 ydyseis.....................nggvlalviavlllnlvadilqrlldprv 183
                                         +                         +++ ++l+++v +ln++ad++ +++++r+
  gi|386001121|ref|YP_005919420.1| 252 GAI---FtsviagemgevahgsihyhalFAVGFVLLAIVTILNISADLVRAAIQKRF 305
                                       555...344589999************999999999****************99996 PP

>> DUF2755  Protein of unknown function (DUF2755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.1   2.8e-05      0.25      71      95 ..      70      94 ..      25      97 .. 0.85
   2 ?   -0.7   0.1      0.15   1.3e+03      70      95 ..     120     143 ..     108     147 .. 0.51
   3 ?   -1.9   0.1      0.37   3.3e+03      27      38 ..     275     287 ..     255     298 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                           DUF2755 71 vGtlfglvpflaGlvilgvlalilr 95
                                       G +fg+ p++aG v+++ +ali+ 
  gi|386001121|ref|YP_005919420.1| 70 AGEVFGMAPIIAGSVLITTIALIIN 94
                                      699*******************996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.15
                           DUF2755  70 avGtlfglvpflaGlvilgvlalilr 95 
                                       a+ +l g+  ++ G  +lgvl+l++ 
  gi|386001121|ref|YP_005919420.1| 120 AIELLAGVPSIVYG--FLGVLVLVVY 143
                                       44444443333334..4455555544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.37
                           DUF2755  27 alfvl.lclwaGa 38 
                                       alf + + l a  
  gi|386001121|ref|YP_005919420.1| 275 ALFAVgFVLLAIV 287
                                       4442213333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2102.49
//
Query:       gi|386001122|ref|YP_005919421.1|  [L=424]
Description: Phosphate ABC transporter, inner membrane subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-24   85.5  10.0    3.5e-24   85.5  10.0    3.2  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.24   11.6   0.1       0.24   11.6   0.1    3.4  4  HemY_N        HemY protein N-terminus


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   3.6      0.47   4.2e+03     117     136 ..      13      31 ..       6      96 .. 0.46
   2 ?   -3.0   5.1      0.57   5.1e+03       3      44 ..     122     187 ..     106     217 .. 0.57
   3 !   85.5  10.0   3.9e-28   3.5e-24       4     183 ..     217     422 ..     214     424 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.47
                      BPD_transp_1 117 afggllggavlleflgswpG 136
                                       a+++++  ++l+++++ +pG
  gi|386001122|ref|YP_005919421.1|  13 AVALVILTSSLVYLVL-QPG 31 
                                       3333333333333333.222 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.57
                      BPD_transp_1   3 llGilaa........lnrnkkldkllrpliivllslPsfvlaillvlvf................v 44 
                                       ++G+++a        + ++++++++l + +  l+++ +++l+  ++ v+                 
  gi|386001122|ref|YP_005919421.1| 122 FIGSFLAikdsinllYGYSSRGREVLVFSMVRLSAVFTLLLLGGIISVIlfrgigaiswefltqpH 187
                                       566666666666666667777777777777777777777733222222223555555555544440 PP

  == domain 3  score: 85.5 bits;  conditional E-value: 3.9e-28
                      BPD_transp_1   4 lGilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraa 75 
                                       lGi aa     ++r++ l++++++ + +l ++Ps+v +++ ++  ++   +g + l++ i+l l+++p+++l+ ++a
  gi|386001122|ref|YP_005919421.1| 217 LGIGAAiylneYSRHSGLKRVVTIAVGCLNGVPSVVYGLFGLA--FLVATFGLSLLAGSIILGLMNLPTIILTSQEA 291
                                       5555555565**************************8888775..46689*************************** PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyse 152
                                       l+s+p +l+e + alGasrwq++rkvv+P+alp ++tgli+ ++++ g+++ + +++    ++ + ++ + g   + 
  gi|386001122|ref|YP_005919421.1| 292 LKSVPNSLREGSVALGASRWQTVRKVVIPSALPGVLTGLIIGVARAAGETAPIMWTA--VTFSATPVTMYYGVVPDV 366
                                       ***************************************************999999..325555555555555555 PP

                      BPD_transp_1 153 is.........................nggvlalviavlllnlvadilqrlldprv 183
                                       ++                         +g++l+l+++vl +n va ++  +  +++
  gi|386001122|ref|YP_005919421.1| 367 TQpvnnlcyhllnliyflgawdveekaWGTALVLLALVLSINMVAIFVRNHYRKKI 422
                                       55999999***************************************999998887 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4      0.45   4.1e+03      19      34 ..      13      28 ..       9      32 .. 0.64
   2 ?   -3.5   1.8       1.3   1.2e+04      18      32 ..     157     171 ..     147     183 .. 0.50
   3 ?   11.6   0.1   2.7e-05      0.24      19      80 ..     257     316 ..     253     323 .. 0.92
   4 ?   -1.4   0.3       0.3   2.7e+03      10      33 ..     387     410 ..     381     419 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.45
                            HemY_N 19 avlllvllfvllylll 34
                                      av+l++l+  l+yl+l
  gi|386001122|ref|YP_005919421.1| 13 AVALVILTSSLVYLVL 28
                                      5666666666666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
                            HemY_N  18 vavlllvllfvllyl 32 
                                       v+ lll+++++ ++l
  gi|386001122|ref|YP_005919421.1| 157 VFTLLLLGGIISVIL 171
                                       223333333333333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 2.7e-05
                            HemY_N  19 avlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseGlialaeGdfarAek 80 
                                        +++lv++f l +l+ +++ +l++lp+ +     +   +   + l+eG +al++ ++++ +k
  gi|386001122|ref|YP_005919421.1| 257 GLAFLVATFGLSLLAGSIILGLMNLPTIILTS--QEALKSVPNSLREGSVALGASRWQTVRK 316
                                       6889*************************998..88889999****************9998 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.3
                            HemY_N  10 yrietslvvavlllvllfvllyll 33 
                                       +++e   +  +l+l++l++ + ++
  gi|386001122|ref|YP_005919421.1| 387 WDVEEKAWGTALVLLALVLSINMV 410
                                       556666665555555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3048.07
//
Query:       gi|386001123|ref|YP_005919422.1|  [L=464]
Description: Carbohydrate kinase, YjeF related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-46  158.6   0.4      1e-45  156.1   0.2    2.1  2  Carb_kinase  Carbohydrate kinase
    1.8e-41  141.9   1.6    9.8e-41  139.5   0.0    2.3  2  YjeF_N       YjeF-related protein N-terminus
    0.00076   18.9   0.1     0.0014   18.1   0.1    1.3  1  HK           Hydroxyethylthiazole kinase family
  ------ inclusion threshold ------
      0.057   13.5   0.0        2.4    8.3   0.0    2.6  2  DUF498       Protein of unknown function (DUF498/DUF598)


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.15   6.6e+02     142     172 ..      59      88 ..      46      96 .. 0.73
   2 !  156.1   0.2   2.3e-49     1e-45       1     243 [.     223     459 ..     223     460 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.15
                                       SHHHHHHHHHHHHTTEEEEESTTSEEEECTT CS
                       Carb_kinase 142 drlelarelaqklnavvllkgekdvivspeg 172
                                       d l +ar   + l+++v l g +  i+++e+
  gi|386001123|ref|YP_005919422.1|  59 DALVAAR-HLADLEVTVFLLGRSREIATQEA 88 
                                       4444444.456799**********9999864 PP

  == domain 2  score: 156.1 bits;  conditional E-value: 2.3e-49
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEE CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavv 72 
                                       vlvigG   y+GA+ laa aalr+ga+l +va+ ++ +  +   +p++iv pl+    +  +   i e+l r d+vv
  gi|386001123|ref|YP_005919422.1| 223 VLVIGG-GPYSGAPALAAMAALRAGADLATVAAPRNVAGIIAGLSPNLIVRPLSddhlSPGDLdLIRELLPRHDVVV 298
                                       689999.9****************************9*****************8888444455799********** PP

                                       E-TT-SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHH CS
                       Carb_kinase  73 iGpGLgrdekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelare 149
                                       +G+GLgr++++ ++l e   +    viDAd+L              + i+TPh  Ef r +   v  +    e+   
  gi|386001123|ref|YP_005919422.1| 299 VGMGLGRHPETREALAELIPECGKAVIDADALLPGI--------PLQGIITPHESEFRRVSTIRVPPGRVEKETLMS 367
                                       *************99999988777********7544........4579*************99999999999***** PP

                                       HHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHC CS
                       Carb_kinase 150 laqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaa 226
                                       +a+ +  +vllkg++d+i + +  v  n tg++++++GG+GDvLaG+ ga+  ++++++ aa+aaa+++g+a+d+a+
  gi|386001123|ref|YP_005919422.1| 368 FARDMTLTVLLKGKVDLITD-GSVVRGNATGNAGMTVGGTGDVLAGIAGAFY-SKAPPLRAAVAAAFVNGTAGDLAF 442
                                       ******************99.999999*******************988875.5667******************** PP

                                       CCT-TS-HCHHHHHHHC CS
                       Carb_kinase 227 ekkgvgmlatelskiip 243
                                        +kg+++lat+++++ip
  gi|386001123|ref|YP_005919422.1| 443 VEKGYSLLATDVIEKIP 459
                                       **************997 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.5   0.0   2.2e-44   9.8e-41       3     170 ..      25     179 ..      23     180 .. 0.91
   2 ?    0.7   0.6     0.097   4.3e+02      24      57 ..     218     250 ..     206     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 2.2e-44
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellk 79 
                                       +Lmenag+a+a  +r+++     +kk+ v++G+gnnGgd+l+aArhLa  +++V + l +++e  +++a++++e+l+
  gi|386001123|ref|YP_005919422.1|  25 QLMENAGSALASEARRRA----RGKKIAVVAGRGNNGGDALVAARHLADLEVTVFL-LGRSREIATQEARQNWEILE 96 
                                       7*****************....9************************655555555.788899************** PP

                            YjeF_N  80 kaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgta 156
                                       +++ ++ e   +e+le     ++dl++DA++G+g+rg++r+  ae+i+ +nss++pvl+vD+PSGl ++    +  a
  gi|386001123|ref|YP_005919422.1|  97 HLNFDLREVRCSEELEPLS--RYDLILDAIFGTGVRGPVRGLEAEAIDAINSSGRPVLSVDVPSGLGTE----K--A 165
                                       *******999999987554..7********************************************554....4..8 PP

                            YjeF_N 157 vkadvtvtfgapkr 170
                                       v++d+tvtf+ pk 
  gi|386001123|ref|YP_005919422.1| 166 VEPDATVTFHRPKV 179
                                       99********9995 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.097
                            YjeF_N  24 paekkvlvlvGsgnnGgdglaaArhLaqegakVt 57 
                                        ++ +vlv+ G+  +G+ +laa + L ++ga+  
  gi|386001123|ref|YP_005919422.1| 218 GENGRVLVIGGGPYSGAPALAAMAAL-RAGADLA 250
                                       34556666666669********9999.7777644 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     3e-07    0.0014     145     222 ..     366     441 ..     355     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3e-07
                                       HHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.H CS
                                HK 145 qkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgke 221
                                        + A+ + ++v++ G+vD+++dg+ v     G+  ++ + ++G +l+ + +af + k  +l aav+a  +  +Ag+ 
  gi|386001123|ref|YP_005919422.1| 366 MSFARDMTLTVLLKGKVDLITDGSVVRGNATGNAGMT-VGGTGDVLAGIAGAFYS-KAPPLRAAVAAAFVNGTAGDL 440
                                       568999****************************997.9*************998.457888889999999999966 PP

                                       H CS
                                HK 222 a 222
                                       a
  gi|386001123|ref|YP_005919422.1| 441 A 441
                                       5 PP

>> DUF498  Protein of unknown function (DUF498/DUF598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.041   1.8e+02      53      86 ..     117     155 ..      64     162 .. 0.72
   2 ?    8.3   0.0   0.00053       2.4      36      77 ..     277     315 ..     251     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.041
                                       .SEE...EEE-TTS..-----HHHHHHHHCCTSEEEEE- CS
                            DUF498  53 pell...ilGtGkr..qlplspevrealnelgigvevmd 86 
                                        +l+   i+GtG r  ++ l+ e ++a+n+ g  v   d
  gi|386001123|ref|YP_005919422.1| 117 YDLIldaIFGTGVRgpVRGLEAEAIDAINSSGRPVLSVD 155
                                       444433389******9*************9997776665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00053
                                       TCEECHHHHHHCT..T..SEEEEE-TTS-----HHHHHHHHC CS
                            DUF498  36 edlteeslellellepkpellilGtGkrqlplspevrealne 77 
                                       ++l++ +l+l+  l p+ +++++G+G   +p   e+real e
  gi|386001123|ref|YP_005919422.1| 277 DHLSPGDLDLIRELLPRHDVVVVGMGLGRHP---ETREALAE 315
                                       678899999999999***********99776...66666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3071.83
//
Query:       gi|386001124|ref|YP_005919423.1|  [L=155]
Description: Molybdenum cofactor biosynthesis protein C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-47  159.1   0.6    7.1e-47  158.9   0.6    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.6     4e-51   7.1e-47       1     136 []      13     153 ..      13     153 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 4e-51
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mv+++ek+++ r+AvA+g+++l+ +t+e i+e+ +kkGdvl+var+a+i+a+K+++++iplcHp+p+t vev++ l 
  gi|386001124|ref|YP_005919423.1|  13 MVEITEKPVVGRRAVASGIIRLKGSTVESIREGGVKKGDVLTVARVAAIQAVKEAPRTIPLCHPIPITGVEVDFVLL 89 
                                       9*************************************************************************987 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEESS CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsgG 136
                                           +v+ +++v+  g+tGvemEAL +vs+a+l+v+DmvK ++k+       + iee+r+veK++G
  gi|386001124|ref|YP_005919423.1|  90 --PAAVRATVAVTSVGRTGVEMEALAGVSAALLNVWDMVKYLEKDgtgnypsTSIEEIRVVEKRKG 153
                                       ..799***********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1133.11
//
Query:       gi|386001125|ref|YP_005919424.1|  [L=67]
Description: hypothetical protein Mhar_0415 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       106  (0.00591221); expected 358.6 (0.02)
Passed bias filter:                       93  (0.00518713); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 482.11
//
Query:       gi|386001126|ref|YP_005919425.1|  [L=435]
Description: tryptophanyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-40  137.5   0.0    8.2e-23   81.1   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.072   12.8   0.0    2.2  3  NETI          NETI protein


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0   9.2e-27   8.2e-23       2     177 ..      62     231 ..      60     247 .. 0.89
   2 !   54.5   0.0   1.2e-18   1.1e-14     178     292 ..     301     414 ..     276     415 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 9.2e-27
                                       HHS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b   2 kerplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlak 78 
                                       +++p++v+sG++P+g++HlG  ++++ +++ qk+g ++f+ iaD++A  ++   +  r  +   e++  +   ++a 
  gi|386001126|ref|YP_005919425.1|  62 EKSPFAVMSGFMPSGRVHLGGKMVMEEIIWHQKHGGDAFVAIADMEAHSVRGI-SWQRCREMGIEEYILS---IIAL 134
                                       4789****************9999***************************99.4445555556777777...**** PP

                                       TCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSE CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadl 153
                                       gl+p  a++++qse  +  +la  l+  +++ +l+ ++ f   ++++++     ++ +++++p+L ++     k+ +
  gi|386001126|ref|YP_005919425.1| 135 GLEP-SATIYFQSECGAVRDLAFELAAAARFSELAAIYGFSG-ETNVAHmVsVMVQSADILHPQLPENGGP--KPVV 207
                                       ****.89***********************************.8888885346788999999999999998..999* PP

                                       EEEEGGGHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 154 vpgGsDQkqnielgrdlarrfnkk 177
                                        p+GsDQ+ +i+l+rdla r++k 
  gi|386001126|ref|YP_005919425.1| 208 IPVGSDQDAHIRLTRDLAGRMRKF 231
                                       ********************9987 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 1.2e-18
                                       STTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHHCHHHHHH CS
                      tRNA-synt_1b 178 evfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsnelierle 252
                                         f +p +l+++++tgl+G+ KmS+S ++s I L++++e+++kk+ kavt  ++    +k l + +e +  ++e l 
  gi|386001126|ref|YP_005919425.1| 301 YGFVPPASLYHRFMTGLTGG-KMSSSRPESHIALTEDPEEARKKVMKAVTGGRQslVEQKKLGGEPEKCT-VYELLL 375
                                       67999***************.*********************************87788999999***99.****** PP

                                       HHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 253 avsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                        ++++++  e+ e+   +++++ ++g +kk++ae ++++l
  gi|386001126|ref|YP_005919425.1| 376 FHLSEDD-AELGEVFDGCKSGTRTCGSCKKEAAERIKAFL 414
                                       *999999.9****************************998 PP

>> NETI  NETI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.2   1.1e+04      46      53 ..      41      48 ..      38      49 .. 0.85
   2 ?   -2.5   0.0      0.51   4.6e+03      20      28 ..      70      78 ..      69      80 .. 0.86
   3 ?   12.8   0.0     8e-06     0.072       8      32 ..     250     274 ..     247     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.2
                              NETI 46 pvrqkIvF 53
                                      +++++I+F
  gi|386001126|ref|YP_005919425.1| 41 YMKRHIIF 48
                                      7899***9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.51
                              NETI 20 eGYmPvrRi 28
                                       G+mP  R+
  gi|386001126|ref|YP_005919425.1| 70 SGFMPSGRV 78
                                      6****9996 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 8e-06
                              NETI   8 eTIedcLeRmkkeGYmPvrRiEkPv 32 
                                       e I++  +R+k++GY+ v+R E+ +
  gi|386001126|ref|YP_005919425.1| 250 ELIDAAAARLKEMGYRKVKRYEEHI 274
                                       66888899**************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 3233.81
//
Query:       gi|386001127|ref|YP_005919426.1|  [L=225]
Description: Phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-21   75.8   0.0    3.7e-21   75.3   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00044   19.8   0.0    0.00062   19.3   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   4.2e-25   3.7e-21      11     150 ..      20     158 ..      13     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.2e-25
                                       EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.............EE- CS
                      Pribosyltran  11 ildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.....rll 82 
                                       ++d ++ l++ i  + +++pd+vv+i rgG+++a  + d L    + + + k++++g   + r     +      l+
  gi|386001127|ref|YP_005919426.1|  20 FYDLARTLSRIIKAS-GWRPDLVVAIGRGGYVPARVVCDFLV--HDLLTSIKVEHWGIAAQRRE----RasvrfPLA 89 
                                       444555555555555.*************************7..44555555555554444432....11233469* PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEE CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfva 150
                                       +   g++Vl+VDD+ dtG Tl aa+  Lk+ g+ evr+avl  k ++++e+d++a r++    ++  +a
  gi|386001127|ref|YP_005919426.1|  90 TAASGQRVLVVDDVTDTGETLAAATGYLKSLGAGEVRTAVLQHKASSTIEPDYYAERIDLWRwIIYPWA 158
                                       *********************************************************996665555555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.9e-08   0.00062      83     157 ..      58     130 ..      37     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-08
                           UPRTase  83 ealrellpearvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                         +++ll +++v h g+  +  +     +   L +  + ++vl++D v  TG+++aaa   Lk+ g+ge +  vl
  gi|386001127|ref|YP_005919426.1|  58 FLVHDLLTSIKVEHWGIAAQRRERA--SVRFPLATAASGQRVLVVDDVTDTGETLAAATGYLKSLGAGEVRTAVL 130
                                       45789999********999996654..444458888899**************************9998777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1709.34
//
Query:       gi|386001128|ref|YP_005919427.1|  [L=129]
Description: hypothetical protein Mhar_0418 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-05   24.7   0.2    8.4e-05   22.4   0.2    2.2  3  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0061   16.7   0.0      0.011   15.9   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.021   14.7   0.1       0.05   13.6   0.0    1.6  1  PadR      Transcriptional regulator PadR-like family
      0.056   13.1   0.1      0.068   12.8   0.1    1.3  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
       0.11   12.4   0.0       0.19   11.7   0.0    1.4  1  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.16   5.8e+02      23      37 ..      14      28 ..       6      33 .. 0.76
   2 !   22.4   0.2   2.3e-08   8.4e-05       2      65 ..      21      91 ..      20      93 .. 0.87
   3 ?    1.6   0.0      0.07   2.5e+02      38      48 ..      86      96 ..      80      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
                                      CHHCHHCCCTTSSCH CS
                              TrmB 23 atadeiaeelgvprs 37
                                       +  e+ ++lg+pr+
  gi|386001128|ref|YP_005919427.1| 14 REFVEVLRDLGIPRN 28
                                      566799999999997 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.3e-08
                                      HHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE- CS
                              TrmB  2 qklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYrav 65
                                      ++lG+  + a++ ++L + ++at +ei   +++ ++ v  ++r L + G+Ve ++ +        k+Yr +
  gi|386001128|ref|YP_005919427.1| 21 RDLGIPRNVASMITYLANVQEATSREIEIGSNLRQPEVSIAMRALRNNGWVEEREVKkdgkgrpMKVYRLI 91
                                      5677777777778899999************************************9889999955588876 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.07
                                      CHHHHHHHHHH CS
                              TrmB 38 kvYevLrsLed 48
                                      kvY+ +rsLe+
  gi|386001128|ref|YP_005919427.1| 86 KVYRLIRSLEE 96
                                      8********96 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     3e-06     0.011       5      61 ..      32      90 ..      30      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie...vdkefkgkkprtllri 61
                                      +++yLa v+ea+ +e+    ++ + + s+ +++L ++g++e   v+k+ kg+ p+ ++r+
  gi|386001128|ref|YP_005919427.1| 32 MITYLANVQEATSREIEIGSNLRQPEVSIAMRALRNNGWVEereVKKDGKGR-PMKVYRL 90
                                      689*************************************733255666665.8888876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05      0.05      38      65 ..      62      90 ..      52      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                      HHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                              PadR 38 LkrLekeglvesewees.gegpprkyYrl 65
                                      ++ L+++g+ve++++++ g+g+p k+Yrl
  gi|386001128|ref|YP_005919427.1| 62 MRALRNNGWVEEREVKKdGKGRPMKVYRL 90
                                      688***********9999*********98 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.9e-05     0.068      87     140 ..      31      89 ..      14     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                          SMC_ScpB  87 etLaiIaykqpvtraeie...eiRGvnsdsvvrtLlerglieekgrkee.pgrpil.Yg 140
                                        ++ + a  q  t+ eie   ++R  +++ ++r L + g++ee++ k+  +grp+  Y+
  gi|386001128|ref|YP_005919427.1|  31 SMITYLANVQEATSREIEigsNLRQPEVSIAMRALRNNGWVEEREVKKDgKGRPMKvYR 89 
                                       45666777888899999655589*******************998665549**985465 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.2e-05      0.19       2      61 ..      24      81 ..      23      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      g+++  a  + +L++  +   t +e++   +l ++ vs + + L   G+ve+r+   D++
  gi|386001128|ref|YP_005919427.1| 24 GIPRNVASMITYLANVQE--ATSREIEIGSNLRQPEVSIAMRALRNNGWVEEREVKKDGK 81
                                      677777788888888888..89999****************************9988987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 983.97
//
Query:       gi|386001129|ref|YP_005919428.1|  [L=70]
Description: hypothetical protein Mhar_0419 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.2   0.1      0.046   13.8   0.1    1.4  1  DprA_WH   DprA winged helix domain


Domain annotation for each model (and alignments):
>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.5e-06     0.046      15      40 ..      39      64 ..      25      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-06
                           DprA_WH 15 rrvLaaLgpePvhvDqLvrrtglpaa 40
                                      ++v+a+L+  Pv+ D+Lv++  l++ 
  gi|386001129|ref|YP_005919428.1| 39 ETVVALLEGHPVPADDLVEAKDLEIV 64
                                      689***************99777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 457.84
//
Query:       gi|386001130|ref|YP_005919429.1|  [L=296]
Description: hypothetical protein Mhar_0420 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0025   17.7   0.0     0.0058   16.5   0.0    1.5  2  Methyltransf_23  Methyltransferase domain
     0.0075   17.0   0.0      0.015   16.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.85   7.6e+03     107     145 ..      62      97 ..      57     108 .. 0.59
   2 !   16.5   0.0   6.5e-07    0.0058      13      91 ..     139     223 ..     131     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.85
                   Methyltransf_23 107 tllkp.gGylllseplaslkedrllldwlylvpagrhisf 145
                                       +l++p +++lll++     ++ +++ld  +++ a r++++
  gi|386001130|ref|YP_005919429.1|  62 RLTEPaDTWLLLTDR----YSGSRALDGYLQDGAARVVRV 97 
                                       566663577777776....555555555555555555555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.5e-07
                   Methyltransf_23  13 lerll.pklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq.......eaaepqg 81 
                                       ler+l p l+ag++vL++ cG+G  ++ l++ gf     Dl++  + +a   k  + d+ +++       ++ +p +
  gi|386001130|ref|YP_005919429.1| 139 LERFLrPLLPAGSEVLEVCCGSGMGTQALKRLGFRPWTEDLDSCEICMA--LKAGHLDSDRAMvldarllDRFFPPR 213
                                       5666634479*********************999766666666666665..22223333333344444445556999 PP

                   Methyltransf_23  82 kfdlIvlrev 91 
                                       +fd++v ++v
  gi|386001130|ref|YP_005919429.1| 214 RFDVVVGFMV 223
                                       ******9997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-06     0.015       1      78 [.     153     227 ..     153     244 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       vL+++cG+G  t+al + +   + +  D+++  +  a +  + ++ ++ ++ + + d  f+ ++fD+vv +++ l  
  gi|386001130|ref|YP_005919429.1| 153 VLEVCCGSGMGTQALKRLG--FRPWTEDLDSCEICMALKAGHLDSDRAMVLDARLLDRFFPPRRFDVVVGFMVgL-- 225
                                       9***************995..666666665555544444443232255556566666569*********965543.. PP

                                       SS CS
                   Methyltransf_25  77 ls 78 
                                       ++
  gi|386001130|ref|YP_005919429.1| 226 ID 227
                                       33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 2331.61
//
Query:       gi|386001131|ref|YP_005919430.1|  [L=672]
Description: DNA mismatch repair protein, MutS family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-05   25.0   0.0    2.8e-05   24.2   0.0    1.4  1  MutS_V    MutS domain V
    0.00023   21.7   1.2    0.00055   20.5   0.2    2.3  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.02   15.3   0.1      0.087   13.3   0.0    2.1  2  AAA       ATPase family associated with various cellular acti
       0.17   11.9   1.1       0.51   10.3   0.0    2.4  3  HTH_15    Helix-turn-helix domain of alkylmercury lyase


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   6.2e-09   2.8e-05       2      47 ..     488     533 ..     487     631 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.2e-09
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEE CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftR 47 
                                       ++ G n +Gk ++l  va +++la++G  vpa+++++s++++++  
  gi|386001131|ref|YP_005919430.1| 488 ILSGVNSGGKTALLELVAQVAVLAHMGLPVPARSCRLSLFESLYHF 533
                                       899**************************************99964 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   1.2e-07   0.00055       3      56 ..       2      58 ..       1      59 [. 0.89
   2 ?   -2.9   0.1       2.5   1.1e+04      17      29 ..     241     254 ..     236     264 .. 0.45

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                                      HHHTSTT--HHHHHHHHTTT--....SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGie....svedlaaadveeLakipGiGkktAeriilelk 56
                                      +Ll+v+G+G k+  +l+   ++     +e+l++ dv+ L ++ G+++++A  +++ ++
  gi|386001131|ref|YP_005919430.1|  2 KLLDVPGVGSKLSERLITR-YGdeeaALEALLRGDVAGLIEMRGMSERQATALVQRAR 58
                                      69*****************.663344499**********************9999886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                       HHHTT.T--SHHHH CS
                             HHH_5  17 allsa.Giesvedl 29 
                                       all+a  i  v+++
  gi|386001131|ref|YP_005919430.1| 241 ALLKAaEILEVAEV 254
                                       33333223333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   6.4e+03      37      74 ..      41      82 ..      25     119 .. 0.63
   2 ?   13.3   0.0   1.9e-05     0.087       2      98 ..     488     593 ..     487     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                      SSTTHHHHHHHHHHHHHHHTS...TS.EEEEEETGGGHHHHH CS
                               AAA 37 kyvgesekkirelfkeakeka...kp.silfiDEidalaksr 74
                                      ++ g se++  +l+++a+  +   +p   l  +E+ ++ +s 
  gi|386001131|ref|YP_005919430.1| 41 EMRGMSERQATALVQRARGASygvSPaAFLATEEAARIYSSL 82
                                      456777777777777777666666555555555555555554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.9e-05
                                       EEESSTTSSHHHHHHHHHHHH.....T....HEEEEEETTTCSSS........STTHHHHHHHHHHHHHHHTSTSEE CS
                               AAA   2 llyGppGtGKTllakavakel.....g....vefleisgsellsk........yvgesekkirelfkeakekakpsi 61 
                                       +l+G    GKT+l + va+ +     g    ++ +++s+ e l +          g+ e+ ir++ + a e +  + 
  gi|386001131|ref|YP_005919430.1| 488 ILSGVNSGGKTALLELVAQVAvlahmGlpvpARSCRLSLFESLYHfgksrgtlGAGAFEATIRKFSALAGEGR--KL 562
                                       68999999************64444433322444555555555337888888889999999999999999987..9* PP

                                       EEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  62 lfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       ++ DE++a+++         + r+++ Ll el++  +
  gi|386001131|ref|YP_005919430.1| 563 VLADELEAMTEPG------ASARIIASLLGELSRGGS 593
                                       *********8877......899999999999887655 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7   7.6e+03      32      57 ..     261     286 ..     260     290 .. 0.71
   2 ?   -3.9   0.0       3.1   1.4e+04      18      31 ..     413     426 ..     409     427 .. 0.80
   3 ?   10.3   0.0   0.00011      0.51       6      50 ..     564     610 ..     561     615 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                            HTH_15  32 kGepVtveeLAaatgrsveevrqaLa 57 
                                       +G   ++++LA++    v + ++ +a
  gi|386001131|ref|YP_005919430.1| 261 EGLSLSMAKLAEEGDPEVQRLERLMA 286
                                       56677888888888777777776655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.1
                            HTH_15  18 ssaellrpLlrlLa 31 
                                       +++el+++L + L+
  gi|386001131|ref|YP_005919430.1| 413 GMWELVVALHERLL 426
                                       68999999998876 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00011
                            HTH_15   6 lseslakgeeggssaellrpLlrlLakGepVt..veeLAaatgrsve 50 
                                       l+++l    e+g sa ++ +Ll +L  G  V+  v +LA++++r  e
  gi|386001131|ref|YP_005919430.1| 564 LADELEAMTEPGASARIIASLLGELSRGGSVAifVSHLAEEVARFAE 610
                                       789999**********************9998446899999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 4833.16
//
Query:       gi|386001132|ref|YP_005919431.1|  [L=91]
Description: hypothetical protein Mhar_0422 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.4   0.7      0.072   12.8   0.7    1.3  1  Doppel    Prion-like protein Doppel
      0.067   12.9   0.0      0.074   12.7   0.0    1.1  1  DUF4956   Domain of unknown function (DUF4956)
      0.084   11.6   0.1       0.12   11.2   0.1    1.1  1  CreD      Inner membrane protein CreD


Domain annotation for each model (and alignments):
>> Doppel  Prion-like protein Doppel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   1.2e-05     0.072       4      17 ..      26      39 ..      25      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                      S-SSCCHHHHHHHH CS
                            Doppel  4 hLgtWwlAivCvLL 17
                                      hL++W +A++C L 
  gi|386001132|ref|YP_005919431.1| 26 HLEIWHIAVICLLM 39
                                      9**********997 PP

>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.074      72     134 ..      11      71 ..       5      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                           DUF4956  72 vtYlFvaialglinglaslslvellvlnvlivlvlallesprllkkerrklvtldrieliape 134
                                       v Yl   + l l+    +l+++ ++v+++l++ ++++++  ++ k+ ++++++ dr+e  +++
  gi|386001132|ref|YP_005919431.1|  11 VLYL--QVYLYLMGPPYHLEIWHIAVICLLMLPAFFIANYLLVKKMVQERRIREDRVERFVAA 71 
                                       5444..5556677888899*************************************9987654 PP

>> CreD  Inner membrane protein CreD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.9e-05      0.12       5      48 ..      31      76 ..      28      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.9e-05
                              CreD  5 Kllviallll..llliplalikslvkeReerqeevveeiaeswgge 48
                                       ++vi+ll+l   ++   +l+k++v+eR+ r++ v + +a+s++++
  gi|386001132|ref|YP_005919431.1| 31 HIAVICLLMLpaFFIANYLLVKKMVQERRIREDRVERFVAASVSRD 76
                                      56677777763256667899********************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 585.48
//
Query:       gi|386001133|ref|YP_005919432.1|  [L=198]
Description: Response regulator receiver domain-containing protein (CheY-like) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-09   35.8   0.0    9.9e-05   22.0   0.0    2.9  2  HTH_23          Homeodomain-like domain
    6.8e-08   32.0   0.0      0.002   17.7   0.0    2.7  2  GerE            Bacterial regulatory proteins, luxR family
    6.2e-07   29.0   0.1     0.0075   15.9   0.1    2.6  2  Sigma70_r4_2    Sigma-70, region 4
      8e-07   28.7   0.0    0.00026   20.7   0.0    2.5  2  HTH_38          Helix-turn-helix domain
    0.00014   21.9   0.0     0.0019   18.3   0.0    2.5  3  HTH_28          Helix-turn-helix domain
    0.00021   21.3   0.2     0.0037   17.3   0.0    2.7  3  HTH_3           Helix-turn-helix
    0.00032   20.9   0.0      0.016   15.5   0.0    2.6  2  HTH_Tnp_1       Transposase
    0.00067   19.6   0.0      0.014   15.4   0.0    2.4  2  HTH_29          Winged helix-turn helix
    0.00091   18.7   0.2       0.11   12.0   0.1    2.9  2  Sigma70_r4      Sigma-70, region 4
     0.0017   18.3   0.1       0.27   11.1   0.1    2.3  2  Sigma70_ECF     ECF sigma factor
     0.0033   17.3   0.0        3.8    7.5   0.0    2.6  2  Terminase_5     Putative ATPase subunit of terminase (gpP-lik
     0.0068   16.5   0.0        1.1    9.4   0.0    2.5  2  HTH_7           Helix-turn-helix domain of resolvase
     0.0083   15.7   0.1       0.17   11.5   0.0    2.6  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.01   15.4   0.0       0.36   10.5   0.0    2.7  3  CENP-B_N        CENP-B N-terminal DNA-binding domain
      0.016   15.4   2.1       0.15   12.3   0.0    3.2  4  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.024   15.1   0.1       0.63   10.5   0.0    2.5  2  HTH_40          Helix-turn-helix domain
      0.027   14.2   0.2       0.36   10.7   0.0    2.8  3  HTH_10          HTH DNA binding domain
      0.034   13.5   0.0        3.8    7.0   0.0    2.9  3  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.035   14.5   0.1        1.4    9.4   0.0    2.7  2  HTH_31          Helix-turn-helix domain
      0.064   13.7   0.2       0.45   10.9   0.0    2.0  2  GcrA            GcrA cell cycle regulator
      0.092   12.9   0.0       0.38   10.9   0.0    2.0  2  MerR_1          MerR HTH family regulatory protein


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00043      0.37       8      28 ..      65      85 ..      59     106 .. 0.94
   2 !   22.0   0.0   1.2e-07   9.9e-05       6      44 ..     113     151 ..     109     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                            HTH_23  8 lrillllaeGlsvreIAreLg 28
                                      + +++l+ +Gls +eIA++Lg
  gi|386001133|ref|YP_005919432.1| 65 AAVVRLFYKGLSDTEIAEQLG 85
                                      6799****************8 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.2e-07
                            HTH_23   6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkryree 44 
                                       e+++ l+l a G+sv+e +++Lgv ++T++ +++ +++ 
  gi|386001133|ref|YP_005919432.1| 113 EKQEFLRLSAAGHSVKEMSERLGVAPSTISEYKNIFECQ 151
                                       7999*****************************999754 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00022      0.19       3      28 ..      59      85 ..      57      98 .. 0.81
   2 !   17.7   0.0   2.3e-06     0.002       9      38 ..     116     145 ..     114     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                                      S-HHHH.HHHHHHCTTS-HHHHHHHHT CS
                              GerE  3 LskREr.evLrllaeGksnkeIAeeln 28
                                      L+++++  v rl+++G+s +eIAe+l+
  gi|386001133|ref|YP_005919432.1| 59 LTPQQLaAVVRLFYKGLSDTEIAEQLG 85
                                      6666642699***************97 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.3e-06
                                       HHHHHHCTTS-HHHHHHHHTS-HHHHHHHH CS
                              GerE   9 evLrllaeGksnkeIAeelniSekTVkvhk 38 
                                       e Lrl a+G s+ke +e+l++++ T++ +k
  gi|386001133|ref|YP_005919432.1| 116 EFLRLSAAGHSVKEMSERLGVAPSTISEYK 145
                                       789***********************9887 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   8.8e-06    0.0075      10      54 .]      58     100 ..      57     102 .. 0.92
   2 !   10.4   0.0   0.00046      0.39      19      43 ..     117     141 ..     110     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.8e-06
                                       TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                       +L+++q ++++  +++gls  EIAe+lg  +++ ++ +sRAr kL
  gi|386001133|ref|YP_005919432.1|  58 KLTPQQLAAVVRLFYKGLSDTEIAEQLG--DRALNKTVSRARIKL 100
                                       7999***********************6..999999999999887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00046
                                       HHHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2  19 fllryleglsykEIAellgisegtV 43 
                                       fl     g+s kE +e+lg+ ++t+
  gi|386001133|ref|YP_005919432.1| 117 FLRLSAAGHSVKEMSERLGVAPSTI 141
                                       55556789***************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.016        13       3      31 ..      57      85 ..      55      88 .. 0.90
   2 !   20.7   0.0   3.1e-07   0.00026       9      38 ..     113     142 ..     111     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                            HTH_38  3 khLsleeReeIerllaeGlslreIArrLg 31
                                      ++L++++     rl  +Gls  eIA +Lg
  gi|386001133|ref|YP_005919432.1| 57 TKLTPQQLAAVVRLFYKGLSDTEIAEQLG 85
                                      67888888888999*************98 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.1e-07
                            HTH_38   9 eReeIerllaeGlslreIArrLgrspsTIs 38 
                                       e +e  rl a+G+s++e+  rLg++psTIs
  gi|386001133|ref|YP_005919432.1| 113 EKQEFLRLSAAGHSVKEMSERLGVAPSTIS 142
                                       7778889**********************8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.1   9.3e+02      19      38 ..      50      73 ..      46      79 .. 0.74
   2 ?   -0.9   0.0       2.2   1.9e+03      11      23 ..      73      85 ..      62      85 .. 0.68
   3 !   18.3   0.0   2.3e-06    0.0019       1      34 [.     113     146 ..     113     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                            HTH_28 19 Arelgi....srrtvyrWikryee 38
                                      A++++i    +++++   ++ + +
  gi|386001133|ref|YP_005919432.1| 50 AQRYNIqtklTPQQLAAVVRLFYK 73
                                      666666666699999999999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                            HTH_28 11 aGhsvreaArelg 23
                                      +G s +e+A++lg
  gi|386001133|ref|YP_005919432.1| 73 KGLSDTEIAEQLG 85
                                      6778899999997 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 2.3e-06
                            HTH_28   1 qRleiikllaaGhsvreaArelgisrrtvyrWik 34 
                                       ++ e ++l aaGhsv+e +++lg+ ++t++   +
  gi|386001133|ref|YP_005919432.1| 113 EKQEFLRLSAAGHSVKEMSERLGVAPSTISEYKN 146
                                       588999***********************86665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.6     4e+03       8      19 ..      57      68 ..      51      70 .. 0.73
   2 ?    0.6   0.0      0.73   6.2e+02       8      20 ..      73      85 ..      73      98 .. 0.77
   3 !   17.3   0.0   4.3e-06    0.0037       4      30 ..     118     145 ..     116     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.6
                                      TTHHHHHHHHHH CS
                             HTH_3  8 lglsqeeLAekl 19
                                       +l+ ++LA+++
  gi|386001133|ref|YP_005919432.1| 57 TKLTPQQLAAVV 68
                                      578888888865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.73
                                      TTHHHHHHHHHHT CS
                             HTH_3  8 lglsqeeLAeklG 20
                                      +gls +e+Ae lG
  gi|386001133|ref|YP_005919432.1| 73 KGLSDTEIAEQLG 85
                                      699999***9999 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 4.3e-06
                                       HHH.HTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3   4 lRk.qlglsqeeLAeklGvsrstisriE 30 
                                       lR+ ++g s +e++e+lGv +stis + 
  gi|386001133|ref|YP_005919432.1| 118 LRLsAAGHSVKEMSERLGVAPSTISEYK 145
                                       678899*******************996 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.17   1.4e+02      24      57 ..      44      81 ..      39      97 .. 0.65
   2 !   15.5   0.0   1.9e-05     0.016      11      48 ..     113     149 ..     110     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                         HTH_Tnp_1 24 ksvsevArrhgvs....pnqLykWrrqyregeeaspae 57
                                      + vs+ A+r++++    p+qL + +r++ +g++ +++ 
  gi|386001133|ref|YP_005919432.1| 44 VVVSDMAQRYNIQtkltPQQLAAVVRLFYKGLSDTEIA 81
                                      66777777777642222667777777766666666555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-05
                         HTH_Tnp_1  11 fKariVreslepgksvsevArrhgvspnqLykWrrqyr 48 
                                       +K++++r+s  +g sv+e  +r+gv p++ +  +  ++
  gi|386001133|ref|YP_005919432.1| 113 EKQEFLRLS-AAGHSVKEMSERLGVAPSTISEYKNIFE 149
                                       7999*****.*******************999887665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.43   3.7e+02       2      23 ..      65      85 ..      65      85 .. 0.91
   2 !   15.4   0.0   1.6e-05     0.014       3      34 ..     116     146 ..     114     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.43
                            HTH_29  2 aqallllaeGvstvsqiAkllg 23
                                      a++++l ++G+s   +iA++lg
  gi|386001133|ref|YP_005919432.1| 65 AAVVRLFYKGLS-DTEIAEQLG 85
                                      67999******8.******998 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-05
                            HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlk 34 
                                       + l+l+a G+s v+++ ++lg+ ++t+  +++
  gi|386001133|ref|YP_005919432.1| 116 EFLRLSAAGHS-VKEMSERLGVAPSTISEYKN 146
                                       5799******8.***************98887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00013      0.11       4      31 ..      58      85 ..      57     104 .. 0.88
   2 ?    3.5   0.0     0.058        50      19      38 ..     123     142 ..     117     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      HS-HHHHHHHHHHHTTT--HHHHHHHHT CS
                        Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlg 31
                                      +L++++   ++  f++gl+  EI+e+lg
  gi|386001133|ref|YP_005919432.1| 58 KLTPQQLAAVVRLFYKGLSDTEIAEQLG 85
                                      79*************************8 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.058
                                       TT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVr 38 
                                        g++ +E +erlg+  ++++
  gi|386001133|ref|YP_005919432.1| 123 AGHSVKEMSERLGVAPSTIS 142
                                       57899*********999997 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00031      0.27     123     180 ..      46     101 ..      16     107 .. 0.80
   2 ?    5.3   0.0     0.019        16     150     169 ..     123     142 ..     109     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                       Sigma70_ECF 123 lleLdealerllsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawle 180
                                       + ++++  +  ++l p+q+  v   + +Gls +EiAe+lg   r+ ++    aR +l+
  gi|386001133|ref|YP_005919432.1|  46 VSDMAQRYNIQTKLTPQQLAAVVRLFYKGLSDTEIAEQLG--DRALNKTVSRARIKLH 101
                                       556666666667899*******99*************996..7888888777777665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                       Sigma70_ECF 150 eGlsveEiAeklgvskrtve 169
                                       +G sv+E++e+lgv+ +t+ 
  gi|386001133|ref|YP_005919432.1| 123 AGHSVKEMSERLGVAPSTIS 142
                                       79****************96 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0044       3.8       7      26 ..      68      87 ..      62      95 .. 0.80
   2 !    7.1   0.0    0.0057       4.9      13      38 ..     124     149 ..     119     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0044
                       Terminase_5  7 rlLYwqGyrvaeIAeelglk 26
                                      + L+++G + +eIAe lg  
  gi|386001133|ref|YP_005919432.1| 68 VRLFYKGLSDTEIAEQLGDR 87
                                      469**************965 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0057
                       Terminase_5  13 GyrvaeIAeelglkeatVysWkkrde 38 
                                       G +v+e +e lg+ + t+  +k+ +e
  gi|386001133|ref|YP_005919432.1| 124 GHSVKEMSERLGVAPSTISEYKNIFE 149
                                       899*******************9766 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.039        34       5      32 ..      58      85 ..      56      85 .. 0.90
   2 !    9.4   0.0    0.0013       1.1      12      38 ..     115     141 ..     104     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                                      SS-HHHHGGGGSSTTTT--STTTSSSS- CS
                             HTH_7  5 klskndinrvvkLleeGisiskIAkevn 32
                                      kl++ +++ vv+L  +G s ++IA++++
  gi|386001133|ref|YP_005919432.1| 58 KLTPQQLAAVVRLFYKGLSDTEIAEQLG 85
                                      778889999****************975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                       GGGGSSTTTT--STTTSSSS---SSSS CS
                             HTH_7  12 nrvvkLleeGisiskIAkevnisRsTv 38 
                                       ++ ++L ++G+s+++  +++++++sT+
  gi|386001133|ref|YP_005919432.1| 115 QEFLRLSAAGHSVKEMSERLGVAPSTI 141
                                       5668999*******************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.38   3.2e+02      17      28 ..      74      85 ..      73      85 .. 0.88
   2 !   11.5   0.0    0.0002      0.17      16      37 ..     123     144 ..     120     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.38
                            HTH_24 17 risqreLAerlg 28
                                      ++s +e+Ae+lg
  gi|386001133|ref|YP_005919432.1| 74 GLSDTEIAEQLG 85
                                      67889*****98 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                            HTH_24  16 prisqreLAerlglSpstvnrr 37 
                                       ++ s +e +erlg+ pst++++
  gi|386001133|ref|YP_005919432.1| 123 AGHSVKEMSERLGVAPSTISEY 144
                                       789****************986 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.67   5.7e+02      26      35 ..      47      56 ..      36      68 .. 0.80
   2 ?    1.1   0.0      0.37   3.2e+02       5      32 ..      57      84 ..      54      94 .. 0.89
   3 ?   10.5   0.0   0.00042      0.36      11      43 ..     113     145 ..     111     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.67
                                      HHHHHHHT-- CS
                          CENP-B_N 26 aelarrfnvp 35
                                       + a+r+n+ 
  gi|386001133|ref|YP_005919432.1| 47 SDMAQRYNIQ 56
                                      5789999984 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                                      SS--HHHHHHHHHHHHCTT-HHHHHHHH CS
                          CENP-B_N  5 rsLTlreKievIqrleegeSkaelarrf 32
                                      + LT+++  +v+++   g S  e+a ++
  gi|386001133|ref|YP_005919432.1| 57 TKLTPQQLAAVVRLFYKGLSDTEIAEQL 84
                                      789****99****999999999999776 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00042
                                       HHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHH CS
                          CENP-B_N  11 eKievIqrleegeSkaelarrfnvpestlsdil 43 
                                       eK e  +++  g S++e   r++v +st+s+ +
  gi|386001133|ref|YP_005919432.1| 113 EKQEFLRLSAAGHSVKEMSERLGVAPSTISEYK 145
                                       89999999999******************9865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       7.4   6.3e+03      19      34 ..      40      55 ..      37      57 .. 0.70
   2 ?   -2.5   0.0       7.4   6.3e+03      25      33 ..      77      85 ..      74      95 .. 0.80
   3 ?   12.3   0.0   0.00017      0.15      24      41 ..     126     143 ..     119     144 .. 0.91
   4 ?    0.2   0.0         1   8.7e+02      28      50 ..     172     184 ..     164     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.4
                                      HHSSB-HHHHHHHHTS CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnv 34
                                      ++  v ++d+a+r n+
  gi|386001133|ref|YP_005919432.1| 40 SRLQVVVSDMAQRYNI 55
                                      5556778888888877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.4
                                      HHHHHHHHT CS
                    Fe_dep_repress 25 tkdlaerLn 33
                                       +++ae L+
  gi|386001133|ref|YP_005919432.1| 77 DTEIAEQLG 85
                                      688999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00017
                                       -HHHHHHHHTS-HHHHHH CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVse 41 
                                       ++k+++erL+v+ps++se
  gi|386001133|ref|YP_005919432.1| 126 SVKEMSERLGVAPSTISE 143
                                       789*************98 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1
                                       HHHHHTS-HHHHHHHHHHHHHTT CS
                    Fe_dep_repress  28 laerLnvspssVsemlkkLekdG 50 
                                       ++er          m+   +kdG
  gi|386001133|ref|YP_005919432.1| 172 VSER----------MVTHISKDG 184
                                       4444..........555555555 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.33   2.8e+02       6      22 ..      68      87 ..      63     106 .. 0.80
   2 ?   10.5   0.0   0.00074      0.63       3      39 ..     115     153 ..     113     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                            HTH_40  6 lelleeglsieeIAke...r 22
                                       +l+ +gls  eIA++   r
  gi|386001133|ref|YP_005919432.1| 68 VRLFYKGLSDTEIAEQlgdR 87
                                      68999*********995554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00074
                            HTH_40   3 eetlelleeglsieeIAkerglkesTIegH..Laeliee 39 
                                       +e l+l   g+s++e +++ g+++sTI ++  + e+  +
  gi|386001133|ref|YP_005919432.1| 115 QEFLRLSAAGHSVKEMSERLGVAPSTISEYknIFECQAA 153
                                       666888999******************998556666666 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         2   1.7e+03       1       8 [.      59      66 ..      43      73 .. 0.67
   2 ?   -0.0   0.1      0.93   7.9e+02      27      34 ..      78      85 ..      59     100 .. 0.63
   3 ?   10.7   0.0   0.00043      0.36      25      43 ..     126     144 ..     122     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2
                            HTH_10  1 LTdkqlev 8 
                                      LT++ql++
  gi|386001133|ref|YP_005919432.1| 59 LTPQQLAA 66
                                      56666555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.93
                            HTH_10 27 keLAkelG 34
                                       e+A++lG
  gi|386001133|ref|YP_005919432.1| 78 TEIAEQLG 85
                                      35555555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00043
                            HTH_10  25 tlkeLAkelGIskstlseh 43 
                                       ++ke++++lG+++st+se+
  gi|386001133|ref|YP_005919432.1| 126 SVKEMSERLGVAPSTISEY 144
                                       689*************996 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         4   3.4e+03      31      38 ..      78      85 ..      72      87 .. 0.76
   2 ?    7.0   0.0    0.0045       3.8      24      44 ..     122     141 ..     115     144 .. 0.83
   3 ?    3.1   0.0     0.072        62       6      18 ..     153     165 ..     151     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                      HTH_Tnp_ISL3 31 kavArqlg 38
                                      +++A+qlg
  gi|386001133|ref|YP_005919432.1| 78 TEIAEQLG 85
                                      57777776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0045
                      HTH_Tnp_ISL3  24 llesrsvkavArqlgvSwtTV 44 
                                       +  + svk+ +++lgv ++T+
  gi|386001133|ref|YP_005919432.1| 122 AAGH-SVKEMSERLGVAPSTI 141
                                       5566.***************9 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.072
                      HTH_Tnp_ISL3   6 arrrsriTlrlea 18 
                                       a++r ++T+r+e+
  gi|386001133|ref|YP_005919432.1| 153 AAERDGFTKRFED 165
                                       78999******95 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.32   2.7e+02      13      30 ..      73      97 ..      50     100 .. 0.71
   2 ?    9.4   0.0    0.0016       1.4      12      34 ..     122     144 ..     115     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.32
                            HTH_31 13 aGLsqeevAerlg.......vsest 30
                                       GLs +e Ae+lg       vs+++
  gi|386001133|ref|YP_005919432.1| 73 KGLSDTEIAEQLGdralnktVSRAR 97
                                      3777788888877777777777665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                            HTH_31  12 raGLsqeevAerlgvsestlsrl 34 
                                       +aG s +e+ erlgv +st+s +
  gi|386001133|ref|YP_005919432.1| 122 AAGHSVKEMSERLGVAPSTISEY 144
                                       79******************987 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.4   1.2e+03       6      24 ..       3      21 ..       1      63 [. 0.78
   2 ?   10.9   0.0   0.00052      0.45       9      39 ..      65      95 ..      57     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                              GcrA  6 ErvelLkklwleGlSasqi 24
                                      +++e+Lk+l+l+  S +++
  gi|386001133|ref|YP_005919432.1|  3 DKTEQLKELFLKISSSTKV 21
                                      6788888888875555444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00052
                              GcrA  9 elLkklwleGlSasqiaaqlggvsRnAViGk 39
                                      ++  +l+ +GlS ++ia+qlg  + n  + +
  gi|386001133|ref|YP_005919432.1| 65 AAVVRLFYKGLSDTEIAEQLGDRALNKTVSR 95
                                      566689***************5444443333 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.9   2.5e+03      44      63 ..      62      81 ..      57      84 .. 0.81
   2 ?   10.9   0.0   0.00045      0.38       2      30 ..     126     154 ..     125     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHTT--GGG-- CS
                            MerR_1 44 erLklikyLlkrGltlkgik 63
                                      ++L+ + +L ++Gl+  +i+
  gi|386001133|ref|YP_005919432.1| 62 QQLAAVVRLFYKGLSDTEIA 81
                                      67899999999999977776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00045
                                       EHHHHHHHHTS-HHHHHHHHHHTT-S-EE CS
                            MerR_1   2 sigevakilgvtthtlrywekegllkpkr 30 
                                       s++e +++lgv ++t+  + + + ++ + 
  gi|386001133|ref|YP_005919432.1| 126 SVKEMSERLGVAPSTISEYKNIFECQAAA 154
                                       789*****************999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.61
# Mc/sec: 982.67
//
Query:       gi|386001134|ref|YP_005919433.1|  [L=254]
Description: UbiA prenyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-18   65.3  14.7    5.6e-18   65.2  14.7    1.1  1  UbiA             UbiA prenyltransferase family
     0.0065   16.9   0.8     0.0065   16.9   0.8    3.0  3  Caps_synth_CapC  Capsule biosynthesis CapC


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2  14.7   6.2e-22   5.6e-18      24     239 ..      13     225 ..       1     243 [. 0.74

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 6.2e-22
                              UbiA  24 llllgtllaaaaanalNdyfDreiDadmertpnRPlv.sGrispkealifaivllilgllllalllnpltallglla 99 
                                       l++++++l++++++ lN + D  +D++  + p+R     Gr      li+a+ +++l++ l+ +++ pl++ ++++ 
  gi|386001134|ref|YP_005919433.1|  13 LICMAVFLITFSTYSLNKLTDMAEDSI--NVPERINFiYGRKQ--FILITALGSYLLSIPLV-FFAAPLAVPIVFVP 84 
                                       678899*********************..*****544566655..8999************9.************** PP

                              UbiA 100 lllyvvYt.....g.lrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalavflltwaialan.dlrdr 168
                                       +l+ ++Y      g  rlK+++++++v+++i+++l+ +l   + +++  +++++ll l ++l+ + i ++  d+rd+
  gi|386001134|ref|YP_005919433.1|  85 ILANLLYGskllpGiPRLKDIPVMKNVIVAISWALVCTLLPSVeISNV-PMATILLVLYFMLVKVFINTILyDIRDV 160
                                       *999***999999677***************************76665.777777777755555555554469**** PP

                              UbiA 169 egDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrda 239
                                       egDr ag+kt+p +l   ++    +ll++   l  +l+++ +     ll+a++l ++++++    +r+r++
  gi|386001134|ref|YP_005919433.1| 161 EGDRVAGVKTIPSLLNTPRTTM--LLLVINSALTAILAFINQPIR-SLLMAMILYGYFCII---YFRKRRN 225
                                       ***************7777776..333333332212333333333.444444444444444...2444444 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   7.3e-07    0.0065      24      82 ..       2      71 ..       1      99 [. 0.78
   2 ?   -4.8   6.8         2   1.8e+04      33      42 ..     178     187 ..     104     218 .. 0.60
   3 ?    0.6   1.5     0.079   7.1e+02      35      76 ..     180     217 ..     168     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.3e-07
                   Caps_synth_CapC 24 Gylalvl.dqplsllvtllialltylivrl..........lsrflilyGrrrfvavlllgvlvklllell 82
                                      Gy+ l +  +pl +++++li++ ty + +l           +r+ ++yGr++f+++ +lg  +  +  ++
  gi|386001134|ref|YP_005919433.1|  2 GYILLGAtPNPLICMAVFLITFSTYSLNKLtdmaedsinvPERINFIYGRKQFILITALGSYLLSIPLVF 71
                                      888888889********************99977777665567777********9999987654444433 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 2
                   Caps_synth_CapC  33 plsllvtlli 42 
                                       p + +++l+i
  gi|386001134|ref|YP_005919433.1| 178 PRTTMLLLVI 187
                                       3333333322 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.079
                   Caps_synth_CapC  35 sllvtllialltylivrllsrflilyGrrrfvavlllgvlvk 76 
                                       + +++l+i  ++ +i++++++ +    r  ++a++l g+++ 
  gi|386001134|ref|YP_005919433.1| 180 TTMLLLVINSALTAILAFINQPI----RSLLMAMILYGYFCI 217
                                       44444444444444444444432....455566666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1586.60
//
Query:       gi|386001135|ref|YP_005919434.1|  [L=270]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-19   67.6   0.8    1.4e-18   66.8   0.2    1.7  2  DUF1724         Domain of unknown function (DUF1724)
    0.00038   20.3   0.9      0.015   15.2   0.1    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00061   19.6   0.4     0.0014   18.4   0.4    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0024   17.9   0.3        1.1    9.3   0.4    2.6  2  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.025   14.6   0.0    1.4  1  HTH_20          Helix-turn-helix domain
      0.014   15.4   4.8      0.038   14.0   1.1    2.4  2  HTH_45          Winged helix-turn-helix
      0.064   13.5   0.4       0.88    9.8   0.1    2.7  3  Rio2_N          Rio2, N-terminal
      0.065   13.1   0.6       0.21   11.4   0.4    2.0  2  HxlR            HxlR-like helix-turn-helix
      0.084   12.8   1.5       0.11   12.4   0.6    1.7  2  MarR            MarR family
      0.089   11.9   0.0       0.11   11.6   0.0    1.2  1  Ldh_2           Malate/L-lactate dehydrogenase


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.1   9.1e+03      24      39 ..     185     200 ..     176     203 .. 0.64
   2 !   66.8   0.2   7.8e-22   1.4e-18       1      61 [.     205     265 ..     205     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.1
                           DUF1724  24 lslfdkdgkydhkdli 39 
                                       l + ++d +y  kdl+
  gi|386001135|ref|YP_005919434.1| 185 LEVIFRDHEYLIKDLM 200
                                       5556666666666666 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 7.8e-22
                           DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSe 61 
                                       +kly ++e + +l++tvt+k+l ++ +++dg+yd + dli+ +esA+kWG+eLF+yY+++S+
  gi|386001135|ref|YP_005919434.1| 205 FKLYEIQEYV-TLAFTVTEKILDFGAYRSDGTYDLScDLICIGESAVKWGRELFDYYRNKSR 265
                                       689999**99.*************************************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.4e-06     0.015      16      58 ..      29      71 ..      27      89 .. 0.93
   2 ?    3.2   0.1     0.045        81       1      18 [.     200     217 ..     199     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.4e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       Llk+g+++++++ ee g+  +++  +++++++  lV+r ++ 
  gi|386001135|ref|YP_005919434.1| 29 LLLKEGNKSTSDLEEEMGIRNTTILHAIKEMIKSKLVTRAEKG 71
                                      589**********************************998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.045
                                       HHHCHHHHHCCCHCHHHH CS
                              TrmB   1 LqklGLseyEakvYlaLl 18 
                                       ++k +++ yE++ Y++L 
  gi|386001135|ref|YP_005919434.1| 200 MKKSNFKLYEIQEYVTLA 217
                                       45889**********995 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4     8e-07    0.0014       2      45 ..      22      65 ..      21      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8e-07
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      + R +IL lL eg+++ ++l ee+g+   t+ h  k + ++ LV
  gi|386001135|ref|YP_005919434.1| 22 KVRTEILLLLKEGNKSTSDLEEEMGIRNTTILHAIKEMIKSKLV 65
                                      6799***************************9988888777776 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.4   0.00062       1.1       8      56 ..      25      73 ..      16      79 .. 0.88
   2 !    5.8   0.0    0.0078        14      29      49 ..     109     128 ..      80     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00062
                    Sulfolobus_pRN  8 ekillilsrrcatleeleektGiekeellvyltrlykrGlisrkWrkia 56
                                        ill l  +  +  +lee  Gi   ++l  +  + k  l+ r  + ++
  gi|386001135|ref|YP_005919434.1| 25 TEILLLLKEGNKSTSDLEEEMGIRNTTILHAIKEMIKSKLVTRAEKGYG 73
                                      5799************************************999877665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0078
                    Sulfolobus_pRN  29 GiekeellvyltrlykrGlis 49 
                                       Gi+ +ellv + rlyk  +i 
  gi|386001135|ref|YP_005919434.1| 109 GIP-DELLVKMGRLYKSEIIE 128
                                       565.68**********99996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.4e-05     0.025       9      59 ..      21      70 ..      15      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++vR +il +L  ++  + s+l e+++++ +t+ + ++++ +  Lv++ + 
  gi|386001135|ref|YP_005919434.1| 21 SKVRTEILLLL-KEGNKSTSDLEEEMGIRNTTILHAIKEMIKSKLVTRAEK 70
                                      589********.**********************************99766 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.1   2.1e-05     0.038       4      74 ..      20      90 ..      19      92 .. 0.91
   2 ?    2.2   0.1       0.1   1.8e+02       7      40 ..     180     214 ..     175     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                            HTH_45  4 kleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                      + ++  +IL  ++eg+++ + +  +  +   ++   ++ +++ +l++  ++ Y lT+ G+   + l e+++
  gi|386001135|ref|YP_005919434.1| 20 RSKVRTEILLLLKEGNKSTSDLEEEMGIRNTTILHAIKEMIKSKLVTRAEKGYGLTNLGRMQASMLSEIID 90
                                      667889*****************************************************988888877765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                            HTH_45   7 IiadILeais.egeakkTkimykanLsykllnkYL 40 
                                       ++++ILe+i  + e     +m+k+n +   +++Y+
  gi|386001135|ref|YP_005919434.1| 180 VTSEILEVIFrDHEYLIKDLMKKSNFKLYEIQEYV 214
                                       67899999973555567789999999999999886 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00049      0.88      28      70 ..      39      78 ..      36      79 .. 0.86
   2 ?   -0.5   0.0      0.84   1.5e+03      25      43 ..     110     128 ..     103     155 .. 0.71
   3 ?   -0.9   0.0       1.1     2e+03      15      32 ..     185     202 ..     179     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                            Rio2_N 28 elieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeG 70
                                      + +ee  +++++ + +++++++k kl+ r +   +GY Lt  G
  gi|386001135|ref|YP_005919434.1| 39 SDLEEEMGIRNTTILHAIKEMIKSKLVTRAE---KGYGLTNLG 78
                                      56778889999******************87...799998876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.84
                            Rio2_N  25 Vptelieeisrlkeeevkk 43 
                                       +p el+ ++ rl ++e+ +
  gi|386001135|ref|YP_005919434.1| 110 IPDELLVKMGRLYKSEIIE 128
                                       7888888888888766543 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.1
                            Rio2_N  15 vEmgmrnhevVpteliee 32 
                                       +E+  r+he+  ++l+++
  gi|386001135|ref|YP_005919434.1| 185 LEVIFRDHEYLIKDLMKK 202
                                       578888888887776654 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00012      0.21       8      82 ..      25      91 ..      20     106 .. 0.84
   2 ?   -2.5   0.0       2.7   4.9e+03      28      53 ..     107     131 ..      95     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHH CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkw 82
                                      + il  l +g+k +s+l++++ +i + ++ + ++e+ +++l+ r +         Y lt+ Gr  + +l+e+ ++
  gi|386001135|ref|YP_005919434.1| 25 TEILLLLKEGNKSTSDLEEEM-GIRNTTILHAIKEMIKSKLVTRAEK-------GYGLTNLGRMQASMLSEIIDF 91
                                      568999***************.99999999************99754.......488888888777777777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                       STTS-HHHHHHHHHHHHHTTSEEEEE CS
                              HxlR  28 lpkisqkmLaqrLreLeqdglierev 53 
                                       + +i+ ++L++ + +L ++++ie++ 
  gi|386001135|ref|YP_005919434.1| 107 ISGIPDELLVK-MGRLYKSEIIEADS 131
                                       56666666654.55677778887765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   6.4e-05      0.11      10      50 ..      29      68 ..      21      70 .. 0.87
   2 ?   -3.5   0.0       5.7     1e+04      27      39 ..      78      90 ..      74      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-05
                                      HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                        l  +g+ s s+L + +g+ ++t+  ++++++k  l++R 
  gi|386001135|ref|YP_005919434.1| 29 L-LLKEGNKSTSDLEEEMGIRNTTILHAIKEMIKSKLVTRA 68
                                      3.445799******************************995 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.7
                                      HTS-HHHHHHHHH CS
                              MarR 27 lgvskstvtrvld 39
                                        ++ s++++++d
  gi|386001135|ref|YP_005919434.1| 78 GRMQASMLSEIID 90
                                      4577788888876 PP

>> Ldh_2  Malate/L-lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.1e-05      0.11     276     323 ..     130     177 ..      69     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.1e-05
                                       .HHHHHHHHHHHHHHHHTS-BSTTTSS---TTHHHHHHHHHHHHH-EE CS
                             Ldh_2 276 daeefkervdalldelrasppaegadevllPGereaaaraerlkeGip 323
                                       d+ e+ ++vd +++el++s++++g +++++PG  e  a   r++  i+
  gi|386001135|ref|YP_005919434.1| 130 DSSELLKTVDYFIAELKKSNRIQGVSPIIVPGYAEVIAHCVRNNAEIE 177
                                       6788999*************************9998887766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1593.51
//
Query:       gi|386001136|ref|YP_005919435.1|  [L=382]
Description: Sep-tRNA:Cys-tRNA synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-41  140.2   0.0      9e-41  139.8   0.0    1.1  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    6.3e-11   42.1   0.0    9.3e-11   41.5   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    2.3e-10   40.0   0.0    3.2e-10   39.5   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.078   12.3   0.0       0.12   11.7   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.13   10.9   0.0       0.19   10.4   0.0    1.2  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   2.5e-44     9e-41     107     388 ..     107     376 ..      91     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 2.5e-44
                                       EEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH...HCCTCCCEEEEEECSSTTTTB----HHHHHHH CS
                           SepSecS 107 vridekSslkavelaGleialvekvlegDelitdvedveeii...ekkreevilavlstlsffaprspDdvkeiaki 180
                                          ++  +l a+elaGl++ lv+  +     ++d+   +e+i   + ++e v +avl++++++++++ D  k++++i
  gi|386001136|ref|YP_005919435.1| 107 DGNAHYTTLLAAELAGLKVELVPASEG-PGYRVDPGGYQEAIsraRGRGERVAMAVLTYPDGNYGNLVD-PKAVSEI 181
                                       4556778999************98655.55688888888888442234577889***************.7****** PP

                                       HHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCCHCCCHCHCTSCH CS
                           SepSecS 181 CaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikeiskeypgrasaap 257
                                       C + ++P+ vNgAY++               GR++v+ ksl+++++v++G++++a+s++++i +  +e + r+ +++
  gi|386001136|ref|YP_005919435.1| 182 CTDAGLPLAVNGAYSV---------------GRMPVSAKSLGADVIVGSGHKSMASSGPIGIIGATEELATRIFRRS 243
                                       ****************...............********************************************** PP

                                       CCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC..............EEESSSTT-SSEEEEE-CCCH CS
                           SepSecS 258 skdvlisllllGskaykkllkeqkesfkllreklkklaeeve..............ekllevpeNpissaltletld 320
                                       +    ++l++lG++ +++ + + ++sf+ + e+ ++++eeve              +  +++p+ +++++++ e l+
  gi|386001136|ref|YP_005919435.1| 244 KLVPKKELEMLGCTLRGAGILTMMASFPAVVERTRRWDEEVEkarwfagemerlgmDLQGDQPHGHDLMFFKSEILY 320
                                       *******************************************************9999****************** PP

                                       CCCC...THHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHHHHHHHH CS
                           SepSecS 321 eikk...karldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvlerldeil 388
                                       ei+k   k+r +l++eL++r++ G++      ++lT        r +k+ s++ l+ e++++vl +++ei+
  gi|386001136|ref|YP_005919435.1| 321 EISKtakKGRYFLYRELKKRNIFGIK------PGLT--------RQFKL-SSYQLSREELETVLSAFEEIV 376
                                       **999999******************......****........899**.*****************9986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.6e-14   9.3e-11      35     242 ..      53     238 ..      25     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
                                       TSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                     Aminotran_1_2  35 gtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                       g+l e++++ +   ++eal +fl          + +v  + Ga ++i a++ +l ++ g+ ++++   +     +++
  gi|386001136|ref|YP_005919435.1|  53 GSLEEIQTPPIKEFVREALPQFLE--------VD-EVRISHGAREGIFAAMHAL-CQGGETVIADGNAHYTTLLAAE 119
                                       66777788888888999999***9........77.*******************.8********************* PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                       l+g++v  +p ++ +++++d  +++ea+++a  +  ++ + +++ p  + G + +++ + ++   ++  +l l v  
  gi|386001136|ref|YP_005919435.1| 120 LAGLKVELVPASEGPGYRVDPGGYQEAISRARGRGERVAMAVLTYPDGNYGNLVDPKAVSEI---CTDAGLPLAVNG 193
                                       **********9999************************************************...************ PP

                                       TTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHH CS
                     Aminotran_1_2 189 aYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsq 242
                                       aY+++ +        +  ++   +++ivgs  K++++ G  +G+i ++++++  
  gi|386001136|ref|YP_005919435.1| 194 AYSVGRMP-------V-SAKSLGADVIVGSGHKSMASSG-PIGIIGATEELATR 238
                                       *****998.......3.33333346**************.9***9999988765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   8.9e-14   3.2e-10      48     220 ..      67     238 ..      56     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.9e-14
                                       HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET. CS
                       Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkviplde. 123
                                       +re + +++++++   +   +G+ e+i +++++l    + g++++   + h  +l  ++ela   g+kv+ +p+ e 
  gi|386001136|ref|YP_005919435.1|  67 VREALPQFLEVDE---VRISHGAREGIFAAMHAL---CQGGETVIADGNAHYTTL-LAAELA---GLKVELVPASEg 133
                                       6778888888874...667889999*********...778888887777777777.566665...666666666551 PP

                                       .TSCBEGGGHHHH-......-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTES CS
                       Aminotran_5 124 .egeldldelekll......nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvD 193
                                        + ++d+  +++++       e++++  +t      G++ + +++ +++ ++g  ++v +a +vg +p+  k lg+D
  gi|386001136|ref|YP_005919435.1| 134 pGYRVDPGGYQEAIsrargrGERVAMAVLTYPDGNYGNLVDPKAVSEICTDAGLPLAVNGAYSVGRMPVSAKSLGAD 210
                                       1566777788999988888779999**************************************************** PP

                                       EEEEETTTTTSSTT.-EEEEEEHHHHHT CS
                       Aminotran_5 194 flafsghKllgPtG.iGvlyvrkellek 220
                                       +++ sghK ++ +G iG++ + +el  +
  gi|386001136|ref|YP_005919435.1| 211 VIVGSGHKSMASSGpIGIIGATEELATR 238
                                       ********99999989999888887765 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.3e-05      0.12      31     150 ..      70     198 ..      50     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                                       HHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B.-TTTSSB-GGGCGG CS
                   DegT_DnrJ_EryC1  31 afaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDv.dpdtynidpaaiea 106
                                       a+ ++l+v+ +     + +++  a++al  g g++VI   +   +t  a+  +g+k+ +v   +   y +dp   ++
  gi|386001136|ref|YP_005919435.1|  70 ALPQFLEVDEVRISHGAREGIFAAMHALCQG-GETVIADGNAHYTTLLAAELAGLKVELVPAsEGPGYRVDPGGYQE 145
                                       4566666666555555668999*****9999.****************************8625689********** PP

                                       G--TTE....EEEEEB-G.....GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 107 aitert....kaIlpVhl.....yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                       ai + +    +  ++V +     yG+ +d +a+ +i+++ gl++    A ++G
  gi|386001136|ref|YP_005919435.1| 146 AISRARgrgeRVAMAVLTypdgnYGNLVDPKAVSEICTDAGLPLAVNGAYSVG 198
                                       ****99999955555543222238*******************9888777776 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.4e-05      0.19     151     238 ..     107     196 ..      93     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.4e-05
                                       ETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HH..HHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHH CS
                     Pyridoxal_deC 151 sdqahssvekaalvlgvklrvipldengklrga..alekaieedkekGlipffvvatlGttvlgaFddlkelgdice 225
                                         +ah+    aa+++g+k+ ++p+ e   +r++    ++ai ++  +G  + ++v t    ++g+  d+k + +ic 
  gi|386001136|ref|YP_005919435.1| 107 DGNAHYTTLLAAELAGLKVELVPASEGPGYRVDpgGYQEAISRARGRGERVAMAVLTYPDGNYGNLVDPKAVSEICT 183
                                       4579********************99655665522579***********999************************* PP

                                       HCT-EEEEE-TTG CS
                     Pyridoxal_deC 226 kydlwlHvDAAya 238
                                         +l+l v  Ay 
  gi|386001136|ref|YP_005919435.1| 184 DAGLPLAVNGAYS 196
                                       ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2456.43
//
Query:       gi|386001137|ref|YP_005919436.1|  [L=309]
Description: glycerophosphoryl diester phosphodiesterase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  129.5   0.0    1.5e-26   93.7   0.0    2.2  2  GDPD      Glycerophosphoryl diester phosphodiesterase family
    7.3e-27   93.1   3.7    1.1e-26   92.5   3.7    1.2  1  zf-like   Cysteine-rich small domain
    0.00077   19.8   0.7     0.0025   18.2   0.7    1.9  1  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   2.4e-30   1.5e-26       1     119 [.       7     111 ..       7     152 .. 0.82
   2 !   34.4   0.0   3.1e-12   1.9e-08     210     257 ..     167     212 ..     109     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 2.4e-30
                                       TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTC CS
                              GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiaken 77 
                                       HRGa +  pEnTl+s+++A   Gad++E+Dv+lTkDg +Vv+HD ++drttd++g  +v+++ lee++ ld +++  
  gi|386001137|ref|YP_005919436.1|   7 HRGARSIAPENTLASIRAAGGCGADLVEVDVRLTKDGFLVVIHDASVDRTTDGSG--KVEEMALEEIRALD-AGQ-- 78 
                                       *******************************************************..**************.434.. PP

                                       CCCSCCCSSGCCB...BHHHHHHH..HHHCCSEEEEEEECCCCC CS
                              GDPD  78 kaqlsenrvrlefpfptleevlkk..pqnvglnieikipmlsea 119
                                            ++rv      ptl+e+++   + ++g+ +e k + l+  
  gi|386001137|ref|YP_005919436.1|  79 -----GERV------PTLAEAVRLaeDLDLGIVVEMKEEGLEDL 111
                                       .....4455......99999998766666666666665555554 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 3.1e-12
                                       CCCEB.CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC-SEEEES-H CS
                              GDPD 210 eglgdpdlVkraksrglvvhvytvnnedeeemkrlleagvdgvitDfp 257
                                       + l++p l  +a+++g++v+++t n++  +e+++l+++g  g++tD+p
  gi|386001137|ref|YP_005919436.1| 167 PQLTNPNLFIAARRAGVEVYPWTINDP--DEVRWLNRLGAAGIVTDDP 212
                                       3445788999*****************..*****************98 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   3.7   1.8e-30   1.1e-26       6      80 ..     227     302 ..     223     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.8e-30
                           zf-like   6 snkeCeyyPCHktedenClfCyCPlYaledeelGefveteng.kvkdCskCllvHkkevadellkklkeileelkk 80 
                                       +  eC+yyPCH+ e+++C+fC+CPlY+++d elG+f+ ++ g ++++C +C+lvH+++va +l +++ +++eelk+
  gi|386001137|ref|YP_005919436.1| 227 RAGECQYYPCHHFEGQDCTFCFCPLYPCKDPELGRFIRSRRGkRLWSCVDCTLVHRPSVARYLSDHPAATTEELKR 302
                                       5679**************************************9*****************************9997 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.7   4.3e-07    0.0025       1      29 [.     184     212 ..     184     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.3e-07
                            GDPD_2   1 kvrfWttddeavwrelvgaGVdgInTDdl 29 
                                       +v+ Wt++d+++ r l ++G+ gI TDd+
  gi|386001137|ref|YP_005919436.1| 184 EVYPWTINDPDEVRWLNRLGAAGIVTDDP 212
                                       5888************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 2220.45
//
Query:       gi|386001138|ref|YP_005919437.1|  [L=157]
Description: hypothetical protein Mhar_0429 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.8   0.3       0.39   10.7   0.3    2.2  1  PSDC      Phophatidylserine decarboxylase


Domain annotation for each model (and alignments):
>> PSDC  Phophatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   2.2e-05      0.39      70     112 ..      66     109 ..      25     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                              PSDC  70 evglvgvPlna.lLdwpmgtpsGyalFldpevNkalkkiLneWg 112
                                       +     +P+n   +d  m t++  ++Fld+ vN+   +i  +W 
  gi|386001138|ref|YP_005919437.1|  66 QGAFLDLPVNEsQIDTNMTTTASQQAFLDQPVNQSKIDIQPSWT 109
                                       5556667776425899*****************98777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1167.46
//
Query:       gi|386001139|ref|YP_005919438.1|  [L=270]
Description: xylose isomerase domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-22   80.3   0.0    1.6e-22   80.0   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   9.1e-27   1.6e-22       3     208 ..      22     218 ..      20     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 9.1e-27
                                       HHHHCT-SEEEEECCTCSHHHHC.HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHH CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvsel.sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiel 78 
                                        +aeaG+  +E++  ++  +     +e+++ +r+ l ++  ++++  +  ++++ ++  + a      ++  +ai+l
  gi|386001139|ref|YP_005919438.1|  22 VIAEAGVGEMEFWAETPWYWEGGrRPEGAELIREVLGRRITTLHAPVMDLNPSSYNDLVCLAT----MEEGISAIRL 94 
                                       689************99999888*******************************999988888....********** PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTT CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavds 153
                                       a  LGa+++v+hpG      +  +ee +e+l++ l+ ++d a +egv lalE+l +++++l    +e+ r+ld+ ++
  gi|386001139|ref|YP_005919438.1|  95 AGLLGARVVVVHPG-KRTAKRPAREEEREKLRRYLEVCLDRAVEEGVLLALENLEPAPWNLCSepDEMGRFLDEHPR 170
                                       **************.33555556669*********************************9888************98 PP

                                       TTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSS CS
                      AP_endonuc_2 154 pnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeG 208
                                         +g++lD++H+     +  ++++al+dri  vH++         + rh+p+  G
  gi|386001139|ref|YP_005919438.1| 171 --LGMTLDISHATPPPSRALAFVEALGDRILDVHVS-----ATIDGVRHLPVSSG 218
                                       ..*********************************3.....33346666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2070.21
//
Query:       gi|386001140|ref|YP_005919439.1|  [L=92]
Description: hypothetical protein Mhar_0431 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 786.50
//
Query:       gi|386001141|ref|YP_005919440.1|  [L=117]
Description: Nascent polypeptide associated complex NAC [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   66.9   1.2      2e-18   66.1   1.2    1.4  1  NAC       NAC domain
  ------ inclusion threshold ------
      0.058   13.2   0.0      0.087   12.7   0.0    1.3  1  UBA_4     UBA-like domain
       0.29   11.1   1.3       0.72    9.8   0.0    2.0  2  DUF2786   Protein of unknown function (DUF2786)


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   1.2   3.4e-22     2e-18       1      56 [.      12      70 ..      12      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 3.4e-22
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                      +kK+++++k++g+  +ei+g+eeV++r++d  +++f++++V+  +++g+ +y+v+G+a+e
  gi|386001141|ref|YP_005919440.1| 12 PKKMKQMMKQMGIsiEEIEGVEEVIFRTAD-REIFFQDASVTvmDAQGNRSYQVVGTAQE 70
                                      7*****************************.***************************98 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.087       9      33 ..      87     111 ..      79     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                             UBA_4   9 aiTGadeekArqlLeannWdLerAi 33 
                                       a TG+++++A+  L+ +++dL  Ai
  gi|386001141|ref|YP_005919440.1|  87 AQTGSTPQEAKAALKDAGGDLAEAI 111
                                       56********************998 PP

>> DUF2786  Protein of unknown function (DUF2786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.16   9.3e+02      28      39 ..      14      25 ..      13      25 .. 0.87
   2 ?    9.8   0.0   0.00012      0.72      13      27 ..      87     101 ..      84     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                           DUF2786 28 kAqeLmarynld 39
                                      k  ++m++ +++
  gi|386001141|ref|YP_005919440.1| 14 KMKQMMKQMGIS 25
                                      7889****9997 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00012
                           DUF2786  13 AesstneaEAeaAla 27 
                                       A+ +++++EA+aAl 
  gi|386001141|ref|YP_005919440.1|  87 AQTGSTPQEAKAALK 101
                                       77799********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 948.28
//
Query:       gi|386001142|ref|YP_005919441.1|  [L=174]
Description: GPR1/FUN34/yaaH family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-32  111.9  21.5    3.5e-32  111.7  21.5    1.0  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7  21.5     2e-36   3.5e-32      30     194 ..       1     160 [.       1     172 [. 0.90

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 2e-36
                   Gpr1_Fun34_YaaH  30 lttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsy.aailipgfgilaa 105
                                       +tt +l+++n+g  ++ +  +++++ +fyGG++q++aGi+e+  gntFg+ta++sYG Fwl++ a+il+p++  +a 
  gi|386001142|ref|YP_005919441.1|   1 MTTVLLNMHNAGWFELGS--MILAMGIFYGGVAQIIAGIMEWKKGNTFGTTAFTSYGLFWLTLvALILLPNTTWAAG 75 
                                       578888999988888776..9****************************************9637788899888776 PP

                   Gpr1_Fun34_YaaH 106 YeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvlkAggvfgiiaafla 182
                                            ++ +  l  y+++w +ftf +++ tl+ + al ++ff+l++ f+llai ++tgsa++ +  g+ gi+++f+a
  gi|386001142|ref|YP_005919441.1|  76 T----KTSDPGLIAYFFMWGLFTFYMFIGTLKLNRALQVVFFTLTILFWLLAIRDYTGSATIATITGYEGIFCGFTA 148
                                       6....456667778999************************************************************ PP

                   Gpr1_Fun34_YaaH 183 wYnalaglatke 194
                                        Y+a+a+++++ 
  gi|386001142|ref|YP_005919441.1| 149 IYAACAQVLNEV 160
                                       ********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1296.79
//
Query:       gi|386001143|ref|YP_005919442.1|  [L=297]
Description: hypothetical protein Mhar_0434 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.092   12.8   0.0       0.15   12.1   0.0    1.4  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
       0.21   11.9   0.0       0.43   10.9   0.0    1.5  1  TetR_C_10        Tetracyclin repressor-like, C-terminal domai


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05      0.15      59     101 ..     212     249 ..     167     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                       HHHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S CS
                   Nuc_deoxyrib_tr  59 lirqaDavianldpfrgpeaDsGtafEvGyavalgkpvlaytt 101
                                        i +a +v+++l++      D+ +++E+G+a a gk  l+++ 
  gi|386001143|ref|YP_005919442.1| 212 DICRARMVVVDLTG-----SDPLVMYELGIAHAVGKESLVLCR 249
                                       67889999999999.....89***************9888775 PP

>> TetR_C_10  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.43      58     104 ..      18      65 ..      14      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                         TetR_C_10  58 eeskelfeelmdfltdlie.kGkekGvirslpskaliaivygallkly 104
                                       e+ + l++++m++++ l e k +++Gv+rs ++++++a+   a l + 
  gi|386001143|ref|YP_005919442.1|  18 EKVDSLLDQFMGIVDGLAEeKKIQRGVVRSQNPSSIVAVLDAATLYIL 65 
                                       6778899********998625679**************9877665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2088.61
//
Query:       gi|386001144|ref|YP_005919443.1|  [L=191]
Description: carbonate dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-14   51.5   9.7    0.00012   21.7   0.4    4.6  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    1.3e-12   47.2   8.0    0.00049   19.8   0.0    4.8  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.12   12.2   0.2       0.67    9.8   0.1    2.1  2  DUF1952    Domain of unknown function (DUF1952)


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   6.5e-08   0.00039       3      35 ..      18      50 ..      16      51 .. 0.89
   2 !    9.8   0.1   0.00011      0.66      18      35 ..      55      72 ..      50      73 .. 0.83
   3 !   21.7   0.4     2e-08   0.00012       2      35 ..      79     112 ..      78     113 .. 0.94
   4 !    3.8   0.0    0.0084        50       3      34 ..     115     145 ..     113     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-08
                                      EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                      +I + ++++p a++ g+V IG++v++++g+ ++
  gi|386001144|ref|YP_005919443.1| 18 TIAKTAYVDPAATVIGDVRIGERVYVAPGASVR 50
                                      57777899*********************9886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00011
                                      TTEEE-TTEEEETTEEEE CS
                           Hexapep 18 gnVkIGdnvkIgagvvig 35
                                       +++IGd++ +  g+v +
  gi|386001144|ref|YP_005919443.1| 55 TPIIIGDDCNVQDGAVFH 72
                                      578999999999999976 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++G+ v I ++avi+g+ +IGd + +g ++v++
  gi|386001144|ref|YP_005919443.1|  79 IRLGKRVSIAHGAVIHGPLEIGDESFVGFNAVVH 112
                                       678*****************************97 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.0084
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++G+ +++g+ a +  +V + d++ + +g+v+
  gi|386001144|ref|YP_005919443.1| 115 TLGKRCFVGHLALV-VGVRLRDGSFVPPGAVV 145
                                       57888888887777.67778888888888887 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 !    8.7   0.1   0.00023       1.4      15      32 ..      31      49 ..      27      51 .. 0.81
   2 !   10.1   1.9   9.1e-05      0.54       1      32 [.      56      93 ..      56      94 .. 0.79
   3 !    8.6   0.0   0.00025       1.5       1      16 [.      96     111 ..      96     116 .. 0.90
   4 !   19.8   0.0   8.3e-08   0.00049       4      34 .]     116     147 ..     114     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00023
                                      EES.EEE-TT-EE-TT-EE CS
                         Hexapep_2 15 giG.vslGdncvvgaGvvi 32
                                      +iG v +G+++ v++G  +
  gi|386001144|ref|YP_005919443.1| 31 VIGdVRIGERVYVAPGASV 49
                                      5866************877 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.1e-05
                                      .EEE-TT-EE-TT-E....ES..EEE-TT-EE-TT-EE CS
                         Hexapep_2  1 pviIGdnCliGanag....iG..vslGdncvvgaGvvi 32
                                      p+iIGd+C++   a+     G  + lG+++ ++ G vi
  gi|386001144|ref|YP_005919443.1| 56 PIIIGDDCNVQDGAVfhglEGtsIRLGKRVSIAHGAVI 93
                                      89*******99999964432455999999999988887 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00025
                                       .EEE-TT-EE-TT-EE CS
                         Hexapep_2   1 pviIGdnCliGanagi 16 
                                       p+ IGd +++G na++
  gi|386001144|ref|YP_005919443.1|  96 PLEIGDESFVGFNAVV 111
                                       788***********96 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 8.3e-08
                                       E-TT-EE-TT-EE.SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   4 IGdnCliGanagi.GvslGdncvvgaGvvita 34 
                                        G++C++G  a + Gv l+d++ v +G v++a
  gi|386001144|ref|YP_005919443.1| 116 LGKRCFVGHLALVvGVRLRDGSFVPPGAVVDA 147
                                       59**********55****************96 PP

>> DUF1952  Domain of unknown function (DUF1952)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00011      0.67      17      45 ..      33      61 ..      28      89 .. 0.87
   2 ?   -0.3   0.0      0.17     1e+03      18      34 ..     130     146 ..     124     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                           DUF1952 17 GaveedeGvyrldGavvrfrelePlkvGs 45
                                      G v+ +e vy  +Ga vr  e  P  +G 
  gi|386001144|ref|YP_005919443.1| 33 GDVRIGERVYVAPGASVRADEATPIIIGD 61
                                      889**********************9996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.17
                           DUF1952  18 aveedeGvyrldGavvr 34 
                                       +v+  +G +  +Gavv 
  gi|386001144|ref|YP_005919443.1| 130 GVRLRDGSFVPPGAVVD 146
                                       788899999999*9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1324.21
//
Query:       gi|386001145|ref|YP_005919444.1|  [L=422]
Description: Transporter, major facilitator family [Methanosaeta harundinacea 6Ac]
Scores for 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-22   77.8  59.3    1.7e-10   40.4  32.5    2.3  2  MFS_1         Major Facilitator Superfamily
     0.0067   15.9  10.0     0.0067   15.9  10.0    2.9  2  Nodulin-like  Nodulin-like


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4  32.5   1.9e-14   1.7e-10      27     229 ..      48     254 ..      14     269 .. 0.68
   2 !   37.5  25.7   1.4e-13   1.3e-09      29     178 ..     268     420 ..     236     422 .] 0.74

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.9e-14
                             MFS_1  27 lg..ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslw.lllvlrvlqGlga 99 
                                       lg   ++ ++ + + ++ + +a++++++G+ ++++G+ +v ++g +l ++g +l++ fass + l+ +  v+ G+g 
  gi|386001145|ref|YP_005919444.1|  48 LGqdPTAMAMTWPFIVFLAMFALTMPLAGPYIQKVGPTKVCMAGGVLCGVG-WLAAsFASSPTmLIPLYGVIGGVGV 123
                                       332244555888999999999******************************.8888895554545668899****** PP

                             MFS_1 100 galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafvlfllllpee 175
                                       g+++ a ++  a+wfp+ +rg+a+gl  +gf++++++   ++ +++ s++    ++  +++++++  v+  ++l + 
  gi|386001145|ref|YP_005919444.1| 124 GIAYGAPIYTSAQWFPD-KRGLAVGLTVLGFGFSSAIITYASRFMLGSGWdIMNIMRTFGVAFIIITVILSVFLKC- 198
                                       *****************.****************************444334445666666666666654444433. PP

                             MFS_1 176 pperkrkspkeeekgtgpaplvp.....awkallkdpvlw.illialllfffgfsglltl 229
                                       pp+  ++ +++      p+  v+        ++ k + ++ ++l+  +++ +g++++ + 
  gi|386001145|ref|YP_005919444.1| 199 PPSGCKPGGWTA----PPSTTVTrkvdfMRNEMSKTKTFYgLWLCYTIGALAGLTAIGIA 254
                                       333333344444....44444443333333444444444334444444444455555554 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.4e-13
                             MFS_1  29 ispseigllltl...yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa..sslwlllvlrvlqGlgag 100
                                        ++ +  + + l   +a++ +++ +++G+l+d++ +r   +l+++l ++++ll+  +  ss+++ +++ ++   + g
  gi|386001145|ref|YP_005919444.1| 268 TAEEATKWTFLLilpFAIFNGAGRPIFGSLTDKLTPRNAAILSYVLILAACLLIY-TnySSFYAYVASFAILWGCLG 343
                                       344446776666678***********************99999999999944444.443777755555555555557 PP

                             MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafvlfllllpeep 176
                                       + ++++ +++a  f  ++ ++ +gl+ +++++Gai+g ++++   ++lg ++  f+i+a++++l++v+  ++++ +p
  gi|386001145|ref|YP_005919444.1| 344 GWLAIAPTATASFFGMKDNAKNYGLVFTAYGAGAIIGGIVSAQAKDLLGaFQPFFLIVAALAVLGIVV--AFVMLKP 418
                                       77777778888888889*************************999999989999**********9887..7777777 PP

                             MFS_1 177 pe 178
                                       pe
  gi|386001145|ref|YP_005919444.1| 419 PE 420
                                       76 PP

>> Nodulin-like  Nodulin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  10.0   7.5e-07    0.0067       1     182 [.      14     195 ..      14     207 .. 0.78
   2 !    2.5   2.5    0.0097        87      39     126 ..     248     336 ..     244     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-07
                      Nodulin-like   1 rWlvlvaaiwiqsiaGanylFsaySsal.Kss..lgisQkqlnl...LavakdlGkalGllsGllaevlplwvvllv 71 
                                       rW++++  ++iq + Ga y ++++   l      lg + + +++   + v+  + +    l+G  ++++ ++ v ++
  gi|386001145|ref|YP_005919444.1|  14 RWMIVIVGLIIQLCLGAIYAYGVLRTPLlNHFkaLGQDPTAMAMtwpFIVFLAMFALTMPLAGPYIQKVGPTKVCMA 90 
                                       79999999999999999999997765541444114444455554223346666666666788998999999999999 PP

                      Nodulin-like  72 gaamglvGYgvvwLvvtesiaklpywllfllillaanseawlnTaslvtcirnFpesrgvvvgllkgyaGlsaaiyt 148
                                       g + + vG    wL+ +    + p +l+ l+ ++++ +   +  a + t+ + Fp  rg++vgl++   G s+ai+t
  gi|386001145|ref|YP_005919444.1|  91 GGVLCGVG----WLAASFA--SSPTMLIPLYGVIGGVGVGIAYGAPIYTSAQWFPDKRGLAVGLTVLGFGFSSAIIT 161
                                       99988655....7776655..5699999**************9**********************9999******** PP

                      Nodulin-like 149 qlyeailgsdaksllllvalvplvvslvvlylvr 182
                                        + + +lgs  + + ++ +++++++ ++v+ +v 
  gi|386001145|ref|YP_005919444.1| 162 YASRFMLGSGWDIMNIMRTFGVAFIIITVILSVF 195
                                       *********9999999999999998888877663 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0097
                      Nodulin-like  39 lnlLavakdlGkalGllsGllaevlplwvvllvgaamglvGYgv.vwLvvtesiaklpywllfllillaanseawln 114
                                       l+ +++a  +G  +   +G+ ae +  w+ ll+  ++ + G g  ++ ++t++++  +   l  +++laa    + n
  gi|386001145|ref|YP_005919444.1| 248 LTAIGIAGPVGLEVFANAGMTAEEATKWTFLLILPFAIFNGAGRpIFGSLTDKLTPRNAAILSYVLILAACLLIYTN 324
                                       7889999999*9999*******************9999999996478899999998788888888888999999999 PP

                      Nodulin-like 115 TaslvtcirnFp 126
                                        +s+   + +F+
  gi|386001145|ref|YP_005919444.1| 325 YSSFYAYVASFA 336
                                       999988888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 2580.16
//
Query:       gi|386001146|ref|YP_005919445.1|  [L=357]
Description: hypothetical protein Mhar_0437 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.5   3.0       0.68   10.5   0.1    2.9  4  FliG_N    FliG N-terminal domain


Domain annotation for each model (and alignments):
>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       0.9   1.6e+04      17      29 ..      74      86 ..      66      90 .. 0.60
   2 ?   10.5   0.1   3.8e-05      0.68      49      96 ..     159     206 ..     128     211 .. 0.88
   3 ?    1.2   0.0      0.03   5.3e+02      41      66 ..     258     283 ..     242     301 .. 0.80
   4 ?   -2.8   0.0      0.51   9.1e+03      51      73 ..     330     352 ..     326     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.9
                                      HHHHHHHHTTSXH CS
                            FliG_N 17 eeeaaevlkhLde 29
                                      e eaae+   L+e
  gi|386001146|ref|YP_005919445.1| 74 ESEAAEIADSLKE 86
                                      4455555555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHHHHHSHHHHHHHCHHHH CS
                            FliG_N  49 eveaVleefleeleaqeylseggeeyarelLekalgeekaeellerlt 96 
                                        +e+++e+  ++++++ + + +g+e a  +L++ lg+ +a + l+ + 
  gi|386001146|ref|YP_005919445.1| 159 RMEDIFEDVSKIAKKSRESTPSGIEEASAILTNLLGAAEALQFLDAAL 206
                                       6899************************************99999765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.03
                                       CHTTXXHHHHHHHHHHHHHHHHCCCC CS
                            FliG_N  41 slksvskeeveaVleefleeleaqey 66 
                                       +l++++   +++V +ef ee++++ y
  gi|386001146|ref|YP_005919445.1| 258 RLDEMTTPLAKNVADEFAEEFAEEYY 283
                                       56777777889999999999987654 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHCCCCHHCHHHH CS
                            FliG_N  51 eaVleefleeleaqeylseggee 73 
                                        aV ee   +l+++  +  +g++
  gi|386001146|ref|YP_005919445.1| 330 TAVAEEMARTLKKEGVIKFKGDK 352
                                       57888888888888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 2462.74
//
Query:       gi|386001147|ref|YP_005919446.1|  [L=327]
Description: Diaminopimelate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-74  249.3   0.0    1.7e-74  248.8   0.0    1.2  1  DAPDH_C        Diaminopimelic acid dehydrogenase C-terminal d
    6.3e-05   23.5   0.0    0.00012   22.6   0.0    1.4  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.05   14.0   0.0       0.13   12.6   0.0    1.7  2  HAD            haloacid dehalogenase-like hydrolase
       0.12   13.1   0.0       0.98   10.1   0.0    2.3  3  CoA_binding    CoA binding domain
       0.13   12.3   0.0       0.22   11.6   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.16   12.8   0.0       0.27   12.1   0.0    1.4  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
       0.19   11.3   0.0       0.31   10.6   0.0    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind


Domain annotation for each model (and alignments):
>> DAPDH_C  Diaminopimelic acid dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.8   0.0   6.5e-78   1.7e-74       1     154 []     123     276 ..     123     276 .. 1.00

  Alignments for each domain:
  == domain 1  score: 248.8 bits;  conditional E-value: 6.5e-78
                                       STTTTHHHHHHHHHHHHSSSEEEEEEE-SEE-HHHHHHHCTSTTECEEEEEEEE-HHHHHHHHTT--TT--HHHHEE CS
                           DAPDH_C   1 GWdPGlfslnrllaeailpegktytfWGkGvsqghsdairriegvkdavqytiPveealekvrsgekpelttrekht 77 
                                       GWdPGlfsl rll ea+lpeg++ytfWG Gvsqghsda+rr+egv+da+qytiP+e+++++vrsge+p+l+tre+h 
  gi|386001147|ref|YP_005919446.1| 123 GWDPGLFSLIRLLEEAVLPEGTDYTFWGPGVSQGHSDAVRRVEGVRDARQYTIPIEDTVARVRSGEAPSLSTRERHL 199
                                       9**************************************************************************** PP

                                       EEEEEEE.SCCGHHHHHHHHHT-TTTTTTSEEEEEE--HHHHHHHSSSB-EEEEEEEEEECTTCEEEEEEEEEEESS CS
                           DAPDH_C  78 recyvvaeegadkekiekeiktmpnyfadydttvhfiseeelkkehsglphggfvirsgktgeekeevieyslklds 154
                                       r+cyvvaeegad  +i+++i++mpnyfadydt+v+fis+ee++++h+++phggfv+r+gkt++++ +v+e++lklds
  gi|386001147|ref|YP_005919446.1| 200 RRCYVVAEEGADPGEIREKIRSMPNYFADYDTKVSFISQEEMERSHNRMPHGGFVMRAGKTADGTGHVLEFRLKLDS 276
                                       ***************************************************************************97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.5e-08   0.00012       1      68 [.       5      70 ..       5      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.5e-08
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvla 68
                                      +igi+G+Gn+g+a+ + l ++      +v  ++r+p  ++ l   l ++ ++ ++e  a+e dv vl+
  gi|386001147|ref|YP_005919446.1|  5 RIGIVGYGNVGRAVELSLRQNPDMMAAVV-LTRRDPRGIRTLTPGLMASSIE-EAERYASEVDVAVLC 70
                                      79**************9999986666677.66***************99999.9************98 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.4   6.2e+03     158     184 ..      54      77 ..      22      79 .. 0.53
   2 ?   12.6   0.0   5.3e-05      0.13      82     176 ..      97     182 ..      83     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.4
                               HAD 158 lrewlaaegegidleevvayGDspsDl 184
                                       ++e   ae ++ + +  v +G s +Dl
  gi|386001147|ref|YP_005919446.1|  54 IEE---AERYASEVDVAVLCGGSATDL 77 
                                       333...333333444455555555555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.3e-05
                               HAD  82 rpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaal 158
                                       +p+ + p+  ++++ ++++G r+++vS g++p +  l ++l  ++vl +        +   +++g +   ++ v+++
  gi|386001147|ref|YP_005919446.1|  97 HPR-I-PEYFAAVDSAARRGRRTAIVSTGWDPGLFSLIRLLE-EAVLPE------GTDYTFWGPGVSQGHSDAVRRV 164
                                       566.5.89999999999*********************9999.999888......4444455677777777778999 PP

                               HAD 159 rewlaaegegidleevva 176
                                       +   +a+ + i++e++va
  gi|386001147|ref|YP_005919446.1| 165 EGVRDARQYTIPIEDTVA 182
                                       999999999999999987 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00038      0.98       3      69 ..       3      70 ..       1      76 [. 0.82
   2 ?   -3.7   0.0         7   1.8e+04      56      74 ..     221     240 ..     214     245 .. 0.65
   3 ?   -0.6   0.0      0.84   2.2e+03      19      41 ..     292     314 ..     287     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00038
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC.-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEE CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygikavfgv.nprkvgtevlglpvyksvdeleekt.evdvavit 69
                                      + +++++G g+ g+a+ ++ +++ ++   +v    +pr + t   gl++  s++e+e    evdvav++
  gi|386001147|ref|YP_005919446.1|  3 KLRIGIVGYGNVGRAVELSLRQNPDMMAAVVLTRrDPRGIRTLTPGLMAS-SIEEAERYAsEVDVAVLC 70
                                      6799*************999999999988666550555445555599999.*********88*****97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7
                                       HHHHHC.TTTEEEEES-HHH CS
                       CoA_binding  56 eleekt.evdvavitvPaes 74 
                                        +++   + d++v ++++e+
  gi|386001147|ref|YP_005919446.1| 221 SMPNYFaDYDTKVSFISQEE 240
                                       44455545888888888776 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.84
                                       HHHHHHHHHECEEEEEEC-TTTT CS
                       CoA_binding  19 lyhfkeklkygikavfgvnprkv 41 
                                       +y+ +++  +g + vf+v p ++
  gi|386001147|ref|YP_005919446.1| 292 AYRLHQEGAIGARTVFDVPPAHL 314
                                       48999999999*******99876 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.22      28      88 ..       8      73 ..       3      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                      EE--SHHHHHHHHHHHH...CT-EEEEE-S-H..HHHHHHHCTT-EE--HHHCTTT-SEEEE-SSS CS
                     AdoHcyase_NAD 28 vaGyGdvGkGcaaslkg...lGarvivtevdP..icalqaameGfevvtleevvkkadivvtttGn 88
                                      ++GyG+vG+    sl++   + a v++t  dP  i +l   +   ++ + e  ++++d+ v + G+
  gi|386001147|ref|YP_005919446.1|  8 IVGYGNVGRAVELSLRQnpdMMAAVVLTRRDPrgIRTLTPGLMASSIEEAERYASEVDVAVLCGGS 73
                                      89*************973335799********5556666666666666666678899999999886 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.27       1      70 [.       4      71 ..       4      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivat 70
                                      lr++i+G+G++g+    +l+++ +    v l  +d+   +++   +++++ ++ e+ ++  e+d+++ + 
  gi|386001147|ref|YP_005919446.1|  4 LRIGIVGYGNVGRAVELSLRQNPDMMAAVVLTRRDPRGIRTLTPGLMASSIEEAERYAS--EVDVAVLCG 71
                                      69*********999988*****9999****************99999999999999999..888888775 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.31       4      62 ..       3      62 ..       1      69 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                      TS-EEEES-SHHHHHHHHHHHHT.T--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-S CS
                              IlvN  4 gkkiaviGyGsqGhaqalnlrds.gldvvvglregsksvkkAkeegfevltvaeavkkad 62
                                      + +i ++GyG+ G+a  l lr++  +  +v l + +    +    g+   +++ea + a 
  gi|386001147|ref|YP_005919446.1|  3 KLRIGIVGYGNVGRAVELSLRQNpDMMAAVVLTRRDPRGIRTLTPGLMASSIEEAERYAS 62
                                      6789*****************873455666666666667777788888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 2370.18
//
Query:       gi|386001148|ref|YP_005919447.1|  [L=222]
Description: hypothetical protein Mhar_0439 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-11   43.3   4.4    4.4e-11   43.3   4.4    1.9  2  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.12   2.1e+03       2      31 ..       9      39 ..       8      56 .. 0.59
   2 !   43.3   4.4   2.4e-15   4.4e-11       2      84 ..      86     181 ..      85     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                          CxxCxxCC  2 Cke.CgaCCkelkvklteedlerlkaaevae 31
                                      C + C++ C e k      +l +++++  + 
  gi|386001148|ref|YP_005919447.1|  9 CHGsCAEGCVEMKRAGLHLKLLEMRPHWSVL 39
                                      7777988888665555555555555554444 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 2.4e-15
                          CxxCxxCC   2 CkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak........adgrCvfldeetklCkiYeeRpkicrl 68 
                                       C++Cg CCk   ++ +l  ed+er+ ++     ++ +   +           ++C+f+d+e+  C+iY  Rpk+c  
  gi|386001148|ref|YP_005919447.1|  86 CTGCGLCCKtpGAGLYLDREDMERICRHLGWPMKRLEALCRYdrqlkawaLRQPCPFYDPEE-GCTIYPARPKTCTR 161
                                       *********888999**********8888855555544443367999*9999*********6.************** PP

                          CxxCxxCC  69 fpas....ekeellaraetC 84 
                                       +p +    e  + la++ +C
  gi|386001148|ref|YP_005919447.1| 162 YPLHpplrEVPYHLAVDAFC 181
                                       **976665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1550.31
//
Query:       gi|386001149|ref|YP_005919448.1|  [L=222]
Description: phosphoglycolate phosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   87.6   0.0    1.4e-15   57.7   0.0    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    9.9e-09   35.8   3.1    4.6e-05   23.8   0.1    2.9  3  Hydrolase        haloacid dehalogenase-like hydrolase
    4.3e-06   26.0   0.0      0.003   16.7   0.0    2.1  2  Trehalose_PPase  Trehalose-phosphatase
    9.2e-06   26.2   6.1       0.01   16.3   0.0    3.1  3  HAD              haloacid dehalogenase-like hydrolase
    0.00023   20.8   0.0    0.00047   19.8   0.0    1.5  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
    0.00055   20.1   0.1     0.0053   16.9   0.0    2.0  2  HAD_2            Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.8e-10   1.4e-06       2      84 ..       2      85 ..       1     116 [. 0.85
   2 !   57.7   0.0   4.7e-19   1.4e-15     175     244 ..     133     202 ..      96     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.8e-10
                                      EEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE..ECTTTEEEEE-- CS
                       Hydrolase_3  2 alDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali..ddekgkilykst 78
                                      alD+DGT+ +++  ++++++ea+ +l     +v++ +G+ + +++  +  lg + ++ia NG++i   + + ++l++  
  gi|386001149|ref|YP_005919448.1|  2 ALDIDGTITDDQRLLHPRAVEAVGRLN-SRTTVILVSGNVHCFTRAAAVLLGTSRTFIAENGGVIswGEGEMELLSDPA 79
                                      89**********99************9.5689*********************************65555555555555 PP

                                      B-HHHH CS
                       Hydrolase_3 79 iskedv 84
                                      i +e++
  gi|386001149|ref|YP_005919448.1| 80 ICQEAY 85
                                      555555 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 4.7e-19
                                       STTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE- CS
                       Hydrolase_3 175 skgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtk 244
                                       s++ + i  ++v+Kg al k++ +l++s+eev+a+GD+  D++M+ +ag+  A++n+ +e+k++Adyv++
  gi|386001149|ref|YP_005919448.1| 133 SGFAVHIKDRKVDKGRALAKVMDRLGLSQEEVAAVGDSISDLPMFRVAGFRAAVANGVPELKAKADYVSG 202
                                       4567889999**********************************************************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5     0.042   1.2e+02       5      17 ..       2      14 ..       1      17 [. 0.82
   2 !   10.7   0.3   0.00016      0.47     114     186 ..      11      88 ..       5      99 .. 0.71
   3 !   23.8   0.1   1.5e-08   4.6e-05     155     210 .]     124     181 ..      94     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.042
                                      EEESBTTTBCHHH CS
                                      xxxxxxxxxxxxx RF
                         Hydrolase  5 vfDkdGTLttgep 17
                                      ++D+dGT+t+ ++
  gi|386001149|ref|YP_005919448.1|  2 ALDIDGTITDDQR 14
                                      68*******9875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                       HHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES.STTT....SHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxx....xxxxxxxxxx RF
                         Hydrolase 114 adplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet.vakp....spegkvaair 184
                                        d++ + p a+eav +L+++   v+l++g+ + + ++aa  lG  ++f a+ ++ i+   ++     +p + ++a r
  gi|386001149|ref|YP_005919448.1|  11 DDQRLLHPRAVEAVGRLNSRTT-VILVSGNVHCFTRAAAVLLGtSRTFIAENGGVISWgEGEMellsDPAICQEAYR 86 
                                       4777899***********9977.999999999999999999**7666633333333322333344556666666666 PP

                                       HH CS
                                       xx RF
                         Hydrolase 185 eL 186
                                       +L
  gi|386001149|ref|YP_005919448.1|  87 RL 88 
                                       66 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 1.5e-08
                                       TT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        G  +d +d  +a+ i+  +  + +++ +++++L+ + eeva+VGD++ D+++++ Ag
  gi|386001149|ref|YP_005919448.1| 124 WGleADLVDSGFAVHIKDRKVDKGRALAKVMDRLGLSQEEVAAVGDSISDLPMFRVAG 181
                                       555445556667777777666789999****************************998 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00065       1.9       2      52 ..       3      46 ..       2      94 .. 0.73
   2 !   16.7   0.0     1e-06     0.003     155     206 ..     137     187 ..     125     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00065
                                      EETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHH CS
                   Trehalose_PPase  2 lDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeel 52
                                      lD+dGT+++  +      +++++++++ +L s+    v++vSG    ++++
  gi|386001149|ref|YP_005919448.1|  3 LDIDGTITDDQR-----LLHPRAVEAVGRLNSRTT--VILVSGNVHCFTRA 46
                                      89****987555.....**************9955..******87777444 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1e-06
                                       EEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT.... CS
                   Trehalose_PPase 155 vevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktk..e 206
                                       v ++ ++v KG a+++++++lg +   ++ v ++GD ++D  mF+v   ++   
  gi|386001149|ref|YP_005919448.1| 137 VHIKDRKVDKGRALAKVMDRLGLS---QEEVAAVGDSISDLPMFRVAGFRAavA 187
                                       899********************9...7778899***********987775444 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.1      0.12   3.5e+02       3      13 ..       3      13 ..       1      15 [. 0.85
   2 !   10.6   0.2   0.00019      0.56      84     130 ..      14      60 ..      11     101 .. 0.75
   3 !   16.3   0.0   3.4e-06      0.01     147     188 .]     143     178 ..     123     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                               HAD  3 fDfDgTLldgd 13
                                      +D+DgT++d++
  gi|386001149|ref|YP_005919448.1|  3 LDIDGTITDDQ 13
                                      7*******986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00019
                               HAD  84 klldpgalellaahraaGdrvvvvSgglrplvepllaelg.adevlat 130
                                       +ll+p a+e++  ++    +v++vSg+   ++++ + +lg + +++a+
  gi|386001149|ref|YP_005919448.1|  14 RLLHPRAVEAVG-RLNSRTTVILVSGNVHCFTRAAAVLLGtSRTFIAE 60 
                                       6899********.4466689********************65555555 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 3.4e-06
                               HAD 147 kpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       k+ +g    +al++   +   g++ eev a+GDs+sDlp++r
  gi|386001149|ref|YP_005919448.1| 143 KVDKG----RALAK--VMDRLGLSQEEVAAVGDSISDLPMFR 178
                                       44555....77777..77778888899*************97 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.84   2.5e+03       6      21 ..       2      15 ..       1      38 [. 0.60
   2 !   19.8   0.0   1.6e-07   0.00047      95     212 ..      79     192 ..      67     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.84
                                      EE-TBTTTB.S-HHHH CS
                              S6PP  6 vsdLDntlvdgdneal 21
                                      + d+D+t++  d++ l
  gi|386001149|ref|YP_005919448.1|  2 ALDIDGTIT--DDQRL 15
                                      579999999..33333 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHT-TTEEE--GGG-BTTBEEEEE-TTS-THHHHHHHHHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHH CS
                              S6PP  95 qavvealaklpeLtlQpeeeqrehKvSyfvdkekaaevlkeleqlLekreldvkviyssgkdlDvlPkraskgeAlr 171
                                        + +ea ++l+e+ + ++++ r +++  +v +++ +   +e e +L+  +l+++++  sg ++ +  ++ +kg+Al+
  gi|386001149|ref|YP_005919448.1|  79 AICQEAYRRLKEVYPLAKKDSR-YRITDLVVESNFEI--QEAESRLRGWGLEADLV-DSGFAVHIKDRKVDKGRALA 151
                                       5666777777777776665554.88888887777766..99999999999999998.568899************** PP

                                       HHHHHHT--GGGEEEEE-SGGGHHHH.TSSSEEEE-TT--HH CS
                              S6PP 172 yLakkleleleqilvcGdsgnDeell.ignvlgVvVgnaqee 212
                                         +++l+l +e++  +Gds  D  ++ ++++++  V+n  +e
  gi|386001149|ref|YP_005919448.1| 152 KVMDRLGLSQEEVAAVGDSISDLPMFrVAGFRA-AVANGVPE 192
                                       **************************6666665.56776666 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.14   4.2e+02       4      16 ..       4      16 ..       2      28 .. 0.87
   2 !   16.9   0.0   1.8e-06    0.0053     139     176 ..     148     185 ..     133     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.14
                             HAD_2  4 DlDgTlldteeli 16
                                      D+DgT+ d + l+
  gi|386001149|ref|YP_005919448.1|  4 DIDGTITDDQRLL 16
                                      9*******98775 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.8e-06
                             HAD_2 139 eviekaleklklkkeeviyvGDsptDieaakkagikvi 176
                                       + ++k++++l+l++eev  vGDs++D+   + ag +++
  gi|386001149|ref|YP_005919448.1| 148 RALAKVMDRLGLSQEEVAAVGDSISDLPMFRVAGFRAA 185
                                       56899**********************99999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1672.76
//
Query:       gi|386001150|ref|YP_005919449.1|  [L=326]
Description: DNA repair and recombination protein RadA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-82  275.5   0.0    4.5e-82  275.1   0.0    1.1  1  Rad51            Rad51
    1.6e-13   51.0   0.4    4.8e-13   49.5   0.4    1.8  1  HHH_5            Helix-hairpin-helix domain
    1.7e-13   50.7   0.2    4.5e-06   26.3   0.1    2.1  2  RecA             recA bacterial DNA recombination protein
      9e-09   34.8   0.6    0.00084   19.1   0.1    2.5  2  HHH              Helix-hairpin-helix motif
      3e-07   30.0   0.2    8.5e-07   28.5   0.2    1.7  1  ATPase           KaiC
    4.5e-06   26.4   0.0    6.8e-06   25.8   0.0    1.3  1  AAA_25           AAA domain
    1.3e-05   25.2   0.2      3e-05   24.0   0.2    1.5  1  HHH_2            Helix-hairpin-helix motif
    0.00016   21.4   0.0     0.0022   17.8   0.0    2.4  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00081   19.6   0.0     0.0015   18.7   0.0    1.4  1  Cdd1             Pathogenicity locus
      0.001   18.6   0.1      0.014   14.9   0.0    2.1  2  CobU             Cobinamide kinase / cobinamide phosphate gua
     0.0017   18.8   0.0     0.0063   16.9   0.0    1.9  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.014   15.7   0.4      0.032   14.5   0.1    1.7  2  DUF4332          Domain of unknown function (DUF4332)
      0.014   15.3   0.0      0.021   14.7   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.018   15.5   0.0      0.032   14.7   0.0    1.5  1  HhH-GPD          HhH-GPD superfamily base excision DNA repair
      0.021   15.1   0.0      0.052   13.8   0.0    1.7  1  AAA_22           AAA domain
      0.038   13.7   0.0      0.084   12.6   0.0    1.7  1  AAA_24           AAA domain
      0.038   14.3   0.1          6    7.3   0.0    2.6  2  HHH_8            Helix-hairpin-helix domain
      0.079   13.2   0.1         21    5.5   0.0    2.5  2  HHH_3            Helix-hairpin-helix motif
       0.14   12.7   0.1        2.7    8.5   0.0    3.1  2  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.1   0.0   4.8e-85   4.5e-82       2     254 ..      65     326 .]      64     326 .] 0.93

  Alignments for each domain:
  == domain 1  score: 275.1 bits;  conditional E-value: 4.8e-85
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf ++  ++e+r+ + ++ttGs+++D+l+gGG+et++i e++Gef+sGktq++h+++v vqlp e gG +g ++ id
  gi|386001150|ref|YP_005919449.1|  65 GFETGDMVMERRKLVGKVTTGSETFDALMGGGFETQAIVEVYGEFGSGKTQVAHQVAVNVQLPAEEGGLNGSVIIID 141
                                       7888889999999999************************************************************* PP

                                       SSS---GGGGHHHH.........HHTT--HHHHGGGEEEEE--STTHHHHHHH...HTHHHHHHS..-EEEEEEETT CS
                             Rad51  79 tegtfrperlveia.........erykldkeevlenvayaRaytiehqeellq...qaaallaed..kfallivDsv 141
                                       te tfrper+ ++          e    ++ee l n+ +aRay+++hq  l +    +a++++++    +llivDs+
  gi|386001150|ref|YP_005919449.1| 142 TENTFRPERIAQMVeglppsgepE-KPREPEEFLRNIHVARAYNSNHQILLAEsalDLAEKMKKSgkPARLLIVDSL 217
                                       *************97777776422.256899*****************9998744456888876532689******* PP

                                       TGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEE CS
                             Rad51 142 talyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRl 218
                                       ta++R+++ grg la+Rqqkl+k+l+tL ++ad  ++ v++tnqv+a++d+    f +dp+kP+gG++++h++t R+
  gi|386001150|ref|YP_005919449.1| 218 TAHFRAEYVGRGTLADRQQKLNKHLHTLMRFADLNNAVVLVTNQVMAKPDA----FFGDPTKPVGGHIVGHTATFRI 290
                                       ***************************************************....99******************** PP

                                       EEEE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 219 alrkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                                       +lrk kge+Ri++++dsPnlp+ eavfa+++ G++d
  gi|386001150|ref|YP_005919449.1| 291 YLRKSKGEKRIARLIDSPNLPDGEAVFAVTSAGLMD 326
                                       *********************************987 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.4   5.1e-16   4.8e-13       3      56 ..       5      58 ..       3      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5.1e-16
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                      +L ++sG+Gp+tA +l +aG+ sve+la a++++La+  ++G+ tA +ii +++
  gi|386001150|ref|YP_005919449.1|  5 LLEDLSGVGPATAEKLREAGFASVEALAVASPAQLAACADVGESTAAKIIASAR 58
                                      5889**********************************************9998 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   4.8e-09   4.5e-06      28      96 ..      76     149 ..      65     156 .. 0.80
   2 !   22.3   0.0   8.3e-08   7.8e-05     116     226 ..     192     299 ..     185     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.8e-09
                                       -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----HH CS
                              RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehaldpk 96 
                                       ++ v  +++Gs ++d  +G GG+    i+e+yG   sGkt +a ++ +++q   ++g   g +  id+e ++ p+
  gi|386001150|ref|YP_005919449.1|  76 RKLVGKVTTGSETFDALMG-GGFETQAIVEVYGEFGSGKTQVAHQVAVNVQlpaEEGglnGSVIIIDTENTFRPE 149
                                       4568899********9999.***********************99999998443333121567888999887776 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8.3e-08
                                       HHHHHHHHHHHHTTT-.-SEEEEE-TTT---STT--..---------HHHHHHHHHHHHHHHHHTTT--EEEEEEE- CS
                              RecA 116 Geqaleiadalvrsga.idlivvdsvaalvpkaeie..Gemgdskvglqarlmsqalrkltgaisksntvvifinqi 189
                                        e+al++a+++ +sg    l++vds++a   +ae    G ++d +     + + + l  l    + +n+vv+  nq+
  gi|386001150|ref|YP_005919449.1| 192 AESALDLAEKMKKSGKpARLLIVDSLTAHF-RAEYVgrGTLADRQ-----QKLNKHLHTLMRFADLNNAVVLVTNQV 262
                                       699***********96478*******9976.66664014444444.....34567888899999999********** PP

                                       ----------------HHHHHHH-SEEEEEEEES--- CS
                              RecA 190 rekiGvmfgnpetttGGralkfyasvrldvrrieeik 226
                                         k    fg+p    GG+ +   a+ r+ +r+++  k
  gi|386001150|ref|YP_005919449.1| 263 MAKPDAFFGDPTKPVGGHIVGHTATFRIYLRKSKGEK 299
                                       *******************************987655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.4e-05     0.042      13      29 ..       6      22 ..       5      23 .. 0.89
   2 !   19.1   0.1   8.9e-07   0.00084       1      29 [.      27      55 ..      27      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                      HHTSTT-SHHHHHHHHH CS
                               HHH 13 LlalPGVGpktAeaIls 29
                                      L++l+GVGp+tAe+ ++
  gi|386001150|ref|YP_005919449.1|  6 LEDLSGVGPATAEKLRE 22
                                      889**********9875 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 8.9e-07
                                      SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH  1 sleglipasreeLlalPGVGpktAeaIls 29
                                      s+e+l  as+++L+a+  VG++tA +I++
  gi|386001150|ref|YP_005919449.1| 27 SVEALAVASPAQLAACADVGESTAAKIIA 55
                                      679999*********************86 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2     9e-10   8.5e-07       1     200 [.      82     305 ..      82     308 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 9e-10
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikg...aekygepgvfvtveepa.......edlrena 67 
                                       v tg e +D ++ gG+  +++v ++Ge G+GKt +a q +++    ae+ g +g  + ++ ++        ++ e  
  gi|386001150|ref|YP_005919449.1|  82 VTTGSETFDALMGGGFETQAIVEVYGEFGSGKTQVAHQVAVNVqlpAEEGGLNGSVIIIDTENtfrperiAQMVEGL 158
                                       679**************************************953336777777766666665555774555555555 PP

                            ATPase  68 kslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitgl.aye....... 134
                                          G   +  e e+ l  i++++  +     +++  l e + +lae +k+ +   + +++Ds+t++   e       
  gi|386001150|ref|YP_005919449.1| 159 PPSGEPEKPREPEEFLRNIHVARAYNS----NHQILLAESALDLAEKMKKSGKpaRLLIVDSLTAHfRAEyvgrgtl 231
                                       555666666666666666666555544....3445555555556666655544338889999998742211122211 PP

                            ATPase 135 .ekeavaReilrqlvrvlkklgvTailvsekss........seeaaggygveefivdgvivLdlkeieeelvRtl 200
                                        ++++++ + l++l+r+   ++ + + ++++            + +gg+ v +  ++  i L++ + e+++ R +
  gi|386001150|ref|YP_005919449.1| 232 aDRQQKLNKHLHTLMRFADLNNAVVLVTNQVMAkpdaffgdPTKPVGGHIVGH-TATFRIYLRKSKGEKRIARLI 305
                                       14566667777777777777777777777766567777766556677777777.777777777777777777766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   7.2e-09   6.8e-06      24     157 ..      91     223 ..      72     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.2e-09
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal... 97 
                                        l++g    ++++ ++G  g+GKt +a ++a+ v +  +  g     +g V+++++E++    ++R++++ e l   
  gi|386001150|ref|YP_005919449.1|  91 ALMGGGFETQAIVEVYGEFGSGKTQVAHQVAVNVQLPAEEGG----LNGSVIIIDTENTF--RPERIAQMVEGLpps 161
                                       567766688889999********************7554434....69***********8..79**********999 PP

                            AAA_25  98 .......rddarllvldlagveslpLfakdrggtl.ltadvdaleaaieeveg.vrlvviDplsralgg 157
                                              ++ + l+ +++a+       ++ +++ + l++   +l++++++  + +rl+++D+l++ +++
  gi|386001150|ref|YP_005919449.1| 162 gepekprEPEEFLRNIHVARA------YNSNHQ-IlLAESALDLAEKMKKSGKpARLLIVDSLTAHFRA 223
                                       888755433344444444443......334444.44889999********6558*********997766 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   3.1e-08     3e-05      10      52 ..      11      54 ..       9      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.1e-08
                             HHH_2 10 hVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52
                                       VG +tA++L ++ F s++aL+ as  +L++  d+Ge +A++i+
  gi|386001150|ref|YP_005919449.1| 11 GVGPATAEKLREAgFASVEALAVASPAQLAACADVGESTAAKII 54
                                      69********9866***************************997 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0022       5      36 ..       8      40 ..       4      48 .. 0.80
   2 ?    2.0   0.0      0.21   1.9e+02       2      19 ..      38      55 ..      37      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                   DNA_pol_lambd_f  5 kvyGVGpktAkkwyakGirtledlra.krakLt 36
                                         GVGp+tA+k+ ++G+ ++e l    +a+L 
  gi|386001150|ref|YP_005919449.1|  8 DLSGVGPATAEKLREAGFASVEALAVaSPAQLA 40
                                      568*******************99775556665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                   DNA_pol_lambd_f  2 lFtkvyGVGpktAkkwya 19
                                      ++  + +VG +tA k +a
  gi|386001150|ref|YP_005919449.1| 38 QLAACADVGESTAAKIIA 55
                                      5677899******99875 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.6e-06    0.0015       8      42 ..       6      40 ..       2      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-06
                              Cdd1  8 lqdiPniGkalaedlvelGirsveelkgedpeely 42
                                      l+d+ ++G+a+ae+l+e G+ sve l+  +p++l 
  gi|386001150|ref|YP_005919449.1|  6 LEDLSGVGPATAEKLREAGFASVEALAVASPAQLA 40
                                      899*****************************996 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.25   2.4e+02       3      22 ..     105     124 ..     103     129 .. 0.84
   2 !   14.9   0.0   1.5e-05     0.014      56     127 ..     191     263 ..     171     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.25
                              CobU   3 vtGgarSGKSefAeklaees 22 
                                       v G   SGK ++A ++a + 
  gi|386001150|ref|YP_005919449.1| 105 VYGEFGSGKTQVAHQVAVNV 124
                                       789999*********99765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                              CobU  56 tveepldlaealkeeek.kevvLvDcltlwltnllleeeaek.veekleeeveellealkelkatvvlVsnEvg 127
                                       + e+ ldlae++k++ k ++ ++vD+lt       + + + +  ++kl++++++l++ +++l++ vvlV+n v 
  gi|386001150|ref|YP_005919449.1| 191 LAESALDLAEKMKKSGKpARLLIVDSLTAHFRAEYVGRGTLAdRQQKLNKHLHTLMR-FADLNNAVVLVTNQVM 263
                                       568889******9999999*********99887777655433377788888877776.5678999******995 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.7e-06    0.0063       3     114 ..     105     265 ..     103     271 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-06
                                       EESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS................................. CS
                               AAA   3 lyGppGtGKTllakavakelgve.........fleisgsellsk................................. 37 
                                       +yG  G GKT +a++va +++ +         ++ i+  + +                                   
  gi|386001150|ref|YP_005919449.1| 105 VYGEFGSGKTQVAHQVAVNVQLPaeegglngsVIIIDTENTFRPeriaqmveglppsgepekprepeeflrnihvar 181
                                       79*****************8644444555555555555555522466666666666666666666666666666666 PP

                                       ........STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHHHHHHTTTSSST CS
                               AAA  38 ........yvgesekkirelfkeakekakp.silfiDEidalaksr...sgseseeeervvnqLlteldgvkkkesk 102
                                               ++ es+ +++e +k+  +   p   l++D + a ++++   +g+  + ++++ ++L + l ++ + ++ 
  gi|386001150|ref|YP_005919449.1| 182 aynsnhqiLLAESALDLAEKMKKSGK---PaRLLIVDSLTAHFRAEyvgRGTLADRQQKLNKHL-HTLMRFADLNN- 253
                                       66667766666666666666666554...559**************995444555555555555.55555555545. PP

                                       EEEEEEESS.GGG CS
                               AAA 103 vivigatnr.pdk 114
                                         v+++tn+ + k
  gi|386001150|ref|YP_005919449.1| 254 -AVVLVTNQvMAK 265
                                       .677778873444 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.4e-05     0.032      58      90 ..       9      41 ..       2      52 .. 0.90
   2 ?   -3.2   0.0       9.8   9.2e+03      34      55 ..     230     251 ..     222     260 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                           DUF4332 58 ikgigeeyaeLLeaaGvdsvaeLaqrnpanLhq 90
                                        g+g++ ae L +aG +sv++La  +pa+L +
  gi|386001150|ref|YP_005919449.1|  9 LSGVGPATAEKLREAGFASVEALAVASPAQLAA 41
                                      679***************************975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.8
                           DUF4332  34 alaeklgisernvlklanlAdL 55 
                                       +la++ +   + + +l   AdL
  gi|386001150|ref|YP_005919449.1| 230 TLADRQQKLNKHLHTLMRFADL 251
                                       4444444445555555555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05     0.021      18     127 ..      98     217 ..      96     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefie......eeeekkklekal 82 
                                       e++ i+ +YG  gsGKt++  +++ n +   +       vi ++  ++ + +++ +++e      e e+ ++ e+ l
  gi|386001150|ref|YP_005919449.1|  98 ETQAIVEVYGEFGSGKTQVAHQVAVNVQLPAEegglngSVIIIDTENTFRPERIAQMVEglppsgEPEKPREPEEFL 174
                                       78999******************999855444477785666666666666777888888888996555555555555 PP

                          ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkk.iiiiiDel 127
                                         ++  a++   +++++ l+++a++ l ek+kk+gk    +i+D l
  gi|386001150|ref|YP_005919449.1| 175 -RNIHVARA-YNSNHQILLAESALD-LAEKMKKSGKPaRLLIVDSL 217
                                       .45555555.223466677777776.55788888887778888877 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.4e-05     0.032      18      88 ..      17     188 ..      12     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                           HhH-GPD  18 ierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............................ 66 
                                        e+l+e+ gf ++e+la a++++L+++   + ++++ a  i++ Ar+ +                            
  gi|386001150|ref|YP_005919449.1|  17 AEKLREA-GFASVEALAVASPAQLAAC---ADVGESTAAKIIASARAAAdiggfetgdmvmerrklvgkvttgsetf 89 
                                       5778888.8******************...9999***************9999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                           HhH-GPD  67 ............................................................................. 66 
                                                                                                                    
  gi|386001150|ref|YP_005919449.1|  90 dalmgggfetqaivevygefgsgktqvahqvavnvqlpaeegglngsviiidtentfrperiaqmveglppsgepek 166
                                       99999988888888888888887777777777777777777777666666666666666666666666666666666 PP

                                       .S-SSS--TTSHHHHHHHHHHTT CS
                                       .xxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 .gkpdvlivvDvhvrrilkrlrs 88 
                                        + p+  +   +hv+r+ +  ++
  gi|386001150|ref|YP_005919449.1| 167 pREPE-EFLRNIHVARAYNSNHQ 188
                                       54444.45556666666555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.5e-05     0.052       4      79 ..      99     191 ..      97     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelka....... 70 
                                       t+ i+ v+Ge G+GKT ++ +++ + +  a   e    + +v+ ++  +   ++ +++++     ++  +       
  gi|386001150|ref|YP_005919449.1|  99 TQAIVEVYGEFGSGKTQVAHQVAVNVQLPA---EeggLNGSVIIIDTENTFRPERIAQMVEGLPPSGEPEkprepee 172
                                       678999*****************9975443...23468999999999999988888888877666555555455555 PP

                            AAA_22  71 ..........erlsseell 79 
                                                 ++ + + ll
  gi|386001150|ref|YP_005919449.1| 173 flrnihvaraYNSNHQILL 191
                                       5555555544444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.9e-05     0.084       6      76 ..     104     219 ..      99     258 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.9e-05
                            AAA_24   6 liyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie...................... 47 
                                        +yG+ g+GKT +a +                ++++idte+ +    + ++ ++                       
  gi|386001150|ref|YP_005919449.1| 104 EVYGEFGSGKTQVAHQVavnvqlpaeegglNGSVIIIDTENTF---RPERIAQMVeglppsgepekprepeeflrni 177
                                       59***************89999999988888889999999844...4444443334555666666666444444333 PP

                            AAA_24  48 .swedfldevvel......................aaeladyktlviDtide 76 
                                                                          ++  ++ + l++D+++ 
  gi|386001150|ref|YP_005919449.1| 178 hV----------AraynsnhqillaesaldlaekmKKSGKPARLLIVDSLTA 219
                                       30..........2333333344444444444444466667777777777765 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0063         6      49      65 ..       6      22 ..       1      23 [. 0.87
   2 ?    4.3   0.0     0.055        52      42      64 ..      33      54 ..      26      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0063
                                      CTTSTT--HHHHHHHHH CS
                             HHH_8 49 ltklpgiGkkiaakiee 65
                                      l++l g+G+++a+k++e
  gi|386001150|ref|YP_005919449.1|  6 LEDLSGVGPATAEKLRE 22
                                      688************99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.055
                                      HHHHTTHCTTSTT--HHHHHHHH CS
                             HHH_8 42 itsleeeltklpgiGkkiaakie 64
                                      ++s ++ l +   +G+++aaki 
  gi|386001150|ref|YP_005919449.1| 33 VASPAQ-LAACADVGESTAAKII 54
                                      566567.99999*********95 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.022        21      15      32 ..       5      22 ..       2      33 .. 0.76
   2 ?    5.4   0.1     0.023        22      11      32 ..      34      55 ..      30      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                             HHH_3 15 eLqklpGlgpklAknIva 32
                                      +L+ l+G+gp++A+++ +
  gi|386001150|ref|YP_005919449.1|  5 LLEDLSGVGPATAEKLRE 22
                                      7999*********99755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                             HHH_3 11 AsaeeLqklpGlgpklAknIva 32
                                      As ++L+  + +g+++A +I+a
  gi|386001150|ref|YP_005919449.1| 34 ASPAQLAACADVGESTAAKIIA 55
                                      99******************98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.2   2.1e+03       6      35 ..      42      75 ..      39      82 .. 0.76
   2 ?    8.5   0.0    0.0029       2.7       1      90 [.     103     225 ..     103     312 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.2
                            AAA_18  6 tpGvGKttlakeLskrlgf....gvnlrdvaken 35
                                      ++ vG +t ak +++  +     g++ +d++ e+
  gi|386001150|ref|YP_005919449.1| 42 CADVGESTAAKIIASARAAadigGFETGDMVMER 75
                                      667999*******887633477888888888776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0029
                            AAA_18   1 IlltGtpGvGKttlakeL.......skrlgf..............gvnlrdvakenglllevdpe.....aldeskr 51 
                                       + + G  G+GKt++a+ +       ++++g+               +++ +++    ++ e +++      l++ ++
  gi|386001150|ref|YP_005919449.1| 103 VEVYGEFGSGKTQVAHQVavnvqlpAEEGGLngsviiidtentfrPERIAQMVEGLPPSGEPEKPrepeeFLRNIHV 179
                                       5688999*********9944444444443335555555555554422222222222222222222333322222222 PP

                            AAA_18  52 ldedkldklldaleenss.................aleegknl.vidghlaelesea 90 
                                       ++  +  +         +                 +++++  l ++d++ a+++ e+
  gi|386001150|ref|YP_005919449.1| 180 ARAYN--S---------NhqillaesaldlaekmkKSGKPARLlIVDSLTAHFRAEY 225
                                       22222..2.........1222233333567776664444444448888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2025.20
//
Query:       gi|386001151|ref|YP_005919450.1|  [L=371]
Description: OB-fold nucleic acid binding domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-24   84.6   8.9      2e-08   34.1   0.3    4.4  5  tRNA_anti-codon  OB-fold nucleic acid binding domain
    6.7e-09   35.8   0.0     0.0027   17.5   0.0    3.2  3  CDC24_OB3        Cell division control protein 24, OB domain 
    5.4e-07   29.4   0.1       0.99    9.4   0.0    3.3  3  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
      0.017   15.4   2.5        9.5    6.6   0.1    3.5  3  MlaD             MlaD protein
       0.28   11.3   2.9        5.1    7.3   0.1    3.5  3  PRC              PRC-barrel domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.28     1e+03      52      74 ..      29      60 ..      22      62 .. 0.62
   2 !   34.1   0.3   5.7e-12     2e-08       1      71 [.      66     144 ..      66     154 .. 0.85
   3 !   24.3   0.0   6.5e-09   2.3e-05       7      72 ..     186     250 ..     183     254 .. 0.82
   4 ?   -1.1   0.0      0.52   1.9e+03      38      59 ..     265     286 ..     258     295 .. 0.84
   5 !   28.2   0.2   3.8e-10   1.4e-06       5      69 ..     289     355 ..     275     357 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.28
                                      EEEEEEEEECTTS.........SEEEEEEEEE CS
                   tRNA_anti-codon 52 vrvtGrvkrrpgg.........elelkveeie 74
                                      v+  G++  r++          e+elk+++i+
  gi|386001151|ref|YP_005919450.1| 29 VELMGELCDRRTAamlvarefgEVELKIDRIR 60
                                      55555555554444444444449*****9997 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 5.7e-12
                                       EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTT.S-TTSEEEEEEEEEECTTSSEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaen.lkeGdvvrvtGrvkrrpggelel 68 
                                       Vt++G+v++is         ++ g+v++++l D+tg++++vl++e a+ +    l  ++ +rv+G  ++ + g  e+
  gi|386001151|ref|YP_005919450.1|  66 VTFVGKVVAISevhefprsGGGVGRVANVTLADETGSVRIVLWDELAEPVSTGeLHLDQTLRVRGFTREGYFG-TEV 141
                                       89**************77555558999*****************444444433588*****************.999 PP

                                       EEE CS
                   tRNA_anti-codon  69 kve 71 
                                       +v+
  gi|386001151|ref|YP_005919450.1| 142 TVD 144
                                       987 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 6.5e-09
                                       EEEEE..EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                   tRNA_anti-codon   7 vtsis..drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                       v+  s  d+s g v +++l D +g+i+++l++   +k   +l eGd ++vt  ++r + g +e+++  
  gi|386001151|ref|YP_005919450.1| 186 VREFSrrDGSVGLVRSVILGDSSGKIRLTLWN---EKAEIDLAEGDALEVTNALSRERYGSVEVQAGG 250
                                       5555555777788999****************...9***************7777776666**99865 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.52
                                       HHHHHHTTS-TTSEEEEEEEEE CS
                   tRNA_anti-codon  38 eatklaenlkeGdvvrvtGrvk 59 
                                       e++ + ++l  G++  ++G v+
  gi|386001151|ref|YP_005919450.1| 265 EKMTQVSDLAAGSICSISGFVS 286
                                       56677889999*******9985 PP

  == domain 5  score: 28.2 bits;  conditional E-value: 3.8e-10
                                       EEEEEEE..EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon   5 Grvtsis..drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                       G+v+  +  d+  g+v++i + Dgtgr++v l++ ++ +l e+l+ G+ + +  +  ++  +g++el+
  gi|386001151|ref|YP_005919450.1| 289 GEVREFErdDGTVGRVANIYVSDGTGRVRVALWN-DQVRLIEDLDLGSRIDIVdCMARAGWNGDVELS 355
                                       4445555878888*********************.****************99998888866667776 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.5e-07    0.0027       3      57 ..      60     117 ..      58     133 .. 0.75
   2 !    5.9   0.0    0.0025       9.1       3      53 ..     168     221 ..     166     241 .. 0.76
   3 !    8.7   0.0   0.00035       1.2      16      63 ..     279     335 ..     263     344 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.5e-07
                         CDC24_OB3   3 rekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfk 57 
                                       r+++ +vt +G+vvai     f  ++++  + ++ +++++D+tG+++++lw+e ++ + +
  gi|386001151|ref|YP_005919450.1|  60 RPETGKVTFVGKVVAIsevheF-PRSGG-GVGRVANVTLADETGSVRIVLWDELAEPVST 117
                                       566778**********775443.23333.456666******************8876655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0025
                         CDC24_OB3   3 rekmlnvtLlGrvvai..freknsek.kkmdryslrieDttGaidatlweeagk 53 
                                       r+ m ++ +l+rv +   +re +  +  +  ++s+ + D++G+i++tlw+e ++
  gi|386001151|ref|YP_005919450.1| 168 RADMGDIHILARVLDPgtVREFSRRDgSVGLVRSVILGDSSGKIRLTLWNEKAE 221
                                       667888888888888766334444444566778****************99654 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00035
                         CDC24_OB3  16 vai............freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGh 63 
                                         i            f e+++++ + ++ ++ + D tG ++++lw+  ++l++  l +G 
  gi|386001151|ref|YP_005919450.1| 279 CSIsgfvsglgevreF-ERDDGT-VGRVANIYVSDGTGRVRVALWNDQVRLIED-LDLGS 335
                                       5555555555664322.555655.55556**********************999.88886 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00097       3.5      16      66 ..      69     117 ..      60     146 .. 0.71
   2 !    9.4   0.0   0.00028      0.99      22      62 ..     183     221 ..     164     236 .. 0.75
   3 !    8.7   0.0   0.00045       1.6       3      63 ..     269     327 ..     267     353 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00097
                         REPA_OB_2  16 igvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfes 66 
                                       +g v  ++ev+e+ +  ++   +  ++tl De+g sv++ lW++ ae +++
  gi|386001151|ref|YP_005919450.1|  69 VGKVVAISEVHEFPRSGGG-VGRVANVTLADETG-SVRIVLWDELAEPVST 117
                                       5666666777776666555.556679******99.7********8887663 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00028
                         REPA_OB_2  22 veevseitskstekelkkreltlvDesgasvevtlWgkeae 62 
                                        + v+e+ +++++     r++ l D+sg ++++tlW+++ae
  gi|386001151|ref|YP_005919450.1| 183 PGTVREFSRRDGS-VGLVRSVILGDSSG-KIRLTLWNEKAE 221
                                       5566666666666.45567888988887.69*******986 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00045
                         REPA_OB_2   3 elenvekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaek 63 
                                       +++++ ++si+ + g v+ ++ev+e+ + +++   +  ++ + D +g+ v+v+lW+++ + 
  gi|386001151|ref|YP_005919450.1| 269 QVSDLAAGSICSISGFVSGLGEVREFERDDGT-VGRVANIYVSDGTGR-VRVALWNDQVRL 327
                                       78899999******************999888.677789999999986.9******98654 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0052        19      25      46 ..      85     106 ..      83     157 .. 0.87
   2 ?    0.6   0.0       0.2     7e+02      27      62 ..     195     229 ..     191     250 .. 0.77
   3 ?    6.6   0.1    0.0027       9.5      27      47 ..     300     320 ..     296     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0052
                              MlaD  25 GvtvGrVtsitldpdtrrvtvt 46 
                                       G  vGrV+++tl ++t +v++ 
  gi|386001151|ref|YP_005919450.1|  85 GGGVGRVANVTLADETGSVRIV 106
                                       5569********9999988765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                              MlaD  27 tvGrVtsitldpdtrrvtvtvdldkksetsipedsr 62 
                                        vG V+s+ l + + ++++t+  + k e+++ e+  
  gi|386001151|ref|YP_005919450.1| 195 SVGLVRSVILGDSSGKIRLTLWNE-KAEIDLAEGDA 229
                                       5999******99999998888877.66666666544 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0027
                              MlaD  27 tvGrVtsitldpdtrrvtvtv 47 
                                       tvGrV++i++++ t rv+v +
  gi|386001151|ref|YP_005919450.1| 300 TVGRVANIYVSDGTGRVRVAL 320
                                       8***********999998876 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.072   2.6e+02      22      40 ..      88     106 ..      83     113 .. 0.86
   2 ?   -0.5   0.0      0.36   1.3e+03      21      38 ..     195     212 ..     189     232 .. 0.84
   3 ?    7.3   0.1    0.0014       5.1      18      40 ..     297     319 ..     294     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.072
                                       EEEEEEEEEETTTTEEEEE CS
                               PRC  22 lGkVkDvvidekegrvral 40 
                                       +G+V +v + +++g vr +
  gi|386001151|ref|YP_005919450.1|  88 VGRVANVTLADETGSVRIV 106
                                       9*************99977 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.36
                                       EEEEEEEEEEETTTTEEE CS
                               PRC  21 klGkVkDvvidekegrvr 38 
                                        +G V  v++ + +g++r
  gi|386001151|ref|YP_005919450.1| 195 SVGLVRSVILGDSSGKIR 212
                                       689999999999888886 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0014
                                       TSSEEEEEEEEEEETTTTEEEEE CS
                               PRC  18 dGeklGkVkDvvidekegrvral 40 
                                       d+  +G+V ++++ +++grvr +
  gi|386001151|ref|YP_005919450.1| 297 DDGTVGRVANIYVSDGTGRVRVA 319
                                       56689***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 2727.96
//
Query:       gi|386001152|ref|YP_005919451.1|  [L=576]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-58  197.5   0.0    4.2e-28   98.6   0.0    2.3  2  ABC_tran     ABC transporter
    4.5e-12   46.4   2.9      0.009   15.9   0.0    4.2  4  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.7e-08   32.1   1.6      0.012   15.5   0.0    2.6  2  RsgA_GTPase  RsgA GTPase
    1.3e-06   28.0   2.7     0.0069   15.8   0.0    3.6  3  SMC_N        RecF/RecN/SMC N terminal domain
    3.3e-06   26.7   1.9      0.033   13.9   0.0    2.5  2  AAA_29       P-loop containing region of AAA domain
    0.00016   21.5   0.7       0.38   10.5   0.0    3.0  3  AAA_30       AAA domain
    0.00031   21.2   0.7       0.81   10.1   0.0    2.8  3  AAA_16       AAA ATPase domain
    0.00049   20.3   1.0       0.21   11.9   0.0    4.2  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
    0.00083   19.9   2.3        0.6   10.6   0.0    2.6  2  AAA_23       AAA domain
    0.00094   19.5   1.4        2.6    8.3   0.0    3.4  3  AAA_22       AAA domain
     0.0016   18.2   0.1       0.23   11.1   0.0    3.0  3  IstB_IS21    IstB-like ATP binding protein
     0.0017   17.8   1.7        0.7    9.3   0.0    3.6  4  TniB         Bacterial TniB protein
      0.004   17.4   0.0        2.9    8.1   0.0    2.7  2  AAA_28       AAA domain
     0.0047   16.9   0.1        0.6   10.0   0.0    2.4  2  Rad17        Rad17 P-loop domain
     0.0049   16.2   3.9      0.084   12.2   0.4    3.1  3  ATPase       KaiC
  ------ inclusion threshold ------
       0.01   15.0   0.9       0.96    8.6   0.2    2.4  2  NB-ARC       NB-ARC domain
       0.02   14.6   0.8        1.2    8.8   0.0    2.6  3  AAA_15       AAA ATPase domain
      0.056   13.4   2.5        3.6    7.5   0.0    2.7  2  NACHT        NACHT domain
      0.063   13.2   1.6        6.2    6.7   0.1    2.5  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.075   13.6   3.0        4.8    7.7   0.0    3.5  3  AAA_18       AAA domain
      0.079   11.7   2.5        5.3    5.7   0.3    3.0  3  ABC_ATPase   Predicted ATPase of the ABC class
      0.091   12.2   0.1         14    5.0   0.0    2.3  2  PhoH         PhoH-like protein
      0.093   12.3   7.2        8.2    6.0   0.2    4.6  5  AAA_25       AAA domain
        0.1   13.0   0.2         56    4.2   0.1    3.6  2  AAA          ATPase family associated with various cellular a
        0.1   11.7   0.3        9.2    5.3   0.0    2.3  2  G-alpha      G-protein alpha subunit
        0.2   11.3   0.4         18    5.0   0.1    2.3  2  PRK          Phosphoribulokinase / Uridine kinase family
       0.22   11.3   1.7        5.9    6.6   0.1    2.5  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.24   11.6   0.5         22    5.3   0.0    2.4  2  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.25   11.4   1.5        2.4    8.3   0.1    2.7  2  MMR_HSR1     50S ribosome-binding GTPase
       0.28   10.0   1.3        4.3    6.1   0.0    2.1  2  DLIC         Dynein light intermediate chain (DLIC)
        1.5    8.4   3.7        7.9    6.0   0.2    2.4  2  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   2.4e-30   1.4e-27       1     136 [.      21     180 ..      21     181 .. 0.86
   2 !   98.6   0.0   7.2e-31   4.2e-28       2     136 ..     285     490 ..     284     491 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 2.4e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfp 72 
                                       lk vs++ +ege+++ivG++G GKStLlk+l g ++ ++G+i++dg ++      +l + ++++  ++ +    l+ 
  gi|386001152|ref|YP_005919451.1|  21 LKGVSFTAEEGEILGIVGKSGGGKSTLLKILRGIETFDSGKIEIDGLEIVPnsgPDLVHRQRQVTAIHLQrdFGLWT 97 
                                       799*******************************************9999988866666666666665543555555 PP

                                       TSBHHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSE CS
                                       xxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkl 129
                                       e  +++                     e+++ +e+a++ l+l++  d+++k+ ++ LSgG+kqr+ +ar l+kkpkl
  gi|386001152|ref|YP_005919451.1|  98 EPAIKNVarrvysritgyetipteydlEYEAVMEEAMDYLKLVG-LDKKAKHLATILSGGEKQRLLIARQLAKKPKL 173
                                       55444437789999*********999999999************.667778999*********************** PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       lllDEp 
  gi|386001152|ref|YP_005919451.1| 174 LLLDEPA 180
                                       ******6 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 7.2e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfp 72 
                                       ++++l+++ege++ ++G++G GK+tLlk++ g  +p+eG++ ++ g+ + +     +e+  +r++ig++ qe  lfp
  gi|386001152|ref|YP_005919451.1| 285 EDLNLEIREGEITSLIGSSGGGKTTLLKIIQGIARPDEGSVFYRlGDGWVDmveysRERMGVRRNIGIMYQEFALFP 361
                                       689**************************************66666665556666669999**************** PP

                                       TSBHHHH......................................HHHTCHHHHHHHSTTGG............... CS
                                       xxxxxxx......................................xxxxxxxxxxxxxxxxx............... RF
                          ABC_tran  73 eltvren......................................esdeeiekalsklglke............... 96 
                                       + tv e+                                        +ee++++l+klgl+                
  gi|386001152|ref|YP_005919451.1| 362 RETVLEQiayklgvkgqdvidyarkvaeemgisdkildviytltdMTEEEAKTVLDKLGLTReifeelfprfpetea 438
                                       *******************************99999999999998777889999999999999999*********** PP

                                       ............TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  97 ............lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   l+ +++++ p++LSgG+k+rv++a ++++kp +l+lDEp+
  gi|386001152|ref|YP_005919451.1| 439 rryaepvfkvldLDPSILEKYPHQLSGGEKVRVSIALLMASKPGILILDEPF 490
                                       *********9999999999999*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.5e-05     0.015       2      40 ..      34      62 ..      33      90 .. 0.72
   2 ?    2.4   0.0      0.19   1.1e+02     246     299 ..     161     213 ..     146     215 .. 0.67
   3 !   15.9   0.0   1.6e-05     0.009       1      24 [.     296     319 ..     296     342 .. 0.80
   4 !   10.4   0.1   0.00069       0.4     236     298 ..     462     522 ..     404     527 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40
                                       +++G+ g GKS+LL++l+++  +          +sg+ 
  gi|386001152|ref|YP_005919451.1| 34 LGIVGKSGGGKSTLLKILRGIETF----------DSGKI 62
                                      579***************998544..........22222 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                            AAA_21 246 alltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                        l++   +++kk++lll+DEp +   P+   ++l+ +k+ +r  g+  i+++H p
  gi|386001152|ref|YP_005919451.1| 161 LLIAR--QLAKKPKLLLLDEPATMACPATKQEVLDAIKNVNReLGITTIVVSHLP 213
                                       44444..4456669*******8777777777777777666666777777777766 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.6e-05
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllar 24 
                                       ++ liG  g GK++LL++++++ar
  gi|386001152|ref|YP_005919451.1| 296 ITSLIGSSGGGKTTLLKIIQGIAR 319
                                       689****************99986 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00069
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       +lS G k   ++  all a k+ ++l++DEp   ++P  lr ++  + +++++ ++ ++l++H 
  gi|386001152|ref|YP_005919451.1| 462 QLSGGEKV--RVSIALLMASKP-GILILDEPFGDIDPITLRGVANAIkRINAEFNTTILLVSHH 522
                                       55555553..567788887777.************************65555599********6 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.1e-05     0.018      79     129 ..      10      61 ..       3      68 .. 0.78
   2 !   15.5   0.0   2.1e-05     0.012      89     125 ..     283     320 ..     264     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                                       EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  79 vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       v+ ++ ++ e+l+ ++   ++ ++  +vG+SG GKStL++ l++ ++   g+
  gi|386001152|ref|YP_005919451.1|  10 VYQLKDRQVEALKGVSFTAEEgEILGIVGKSGGGKSTLLKILRGIETFDSGK 61 
                                       56666666777777777777779999****************9976666555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.1e-05
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                        +e+l+ ++++ +++ l+G+SG GK+tL++ +++ ++ 
  gi|386001152|ref|YP_005919451.1| 283 RIEDLNLEIREgEITSLIGSSGGGKTTLLKIIQGIARP 320
                                       678898889888******************99986555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.4     0.004       2.3      28     200 ..      35     214 ..      20     228 .. 0.63
   2 ?    1.4   0.1      0.32   1.9e+02      25      44 ..     295     314 ..     285     317 .. 0.85
   3 !   15.8   0.0   1.2e-05    0.0069     117     205 ..     406     529 ..     370     539 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTC.......HCCCCCC--BTTCSSTTEEEEEEEE...EETTEESSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrs.......eklsdlihkskekasvkkaeveitf...dnedkklkiek 94 
                                        ivG+ G GKs ll  ++ +  ++s  k+         ++  dl+h+   +++v+  +++  f   +++  ++k  +
  gi|386001152|ref|YP_005919451.1|  35 GIVGKSGGGKSTLLKILRGIETFDSG-KIEIdgleivpNSGPDLVHR---QRQVTAIHLQRDFglwTEP--AIKNVA 105
                                       67888888888887777644444444.33330000000333344443...3333333333333211111..123334 PP

                                       SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  95 eevsisrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllD 165
                                        +v+ + + +++  +ey ++ + v  +e ++ l+ +g++k+       LSgGek+     Ll+A q +k+  l llD
  gi|386001152|ref|YP_005919451.1| 106 RRVYSRITGYETIPTEYDLEYEAVM-EEAMDYLKLVGLDKKakhlatILSGGEKQ----RLLIARQLAKKPKLLLLD 177
                                       4455555555666688888877665.5667788888888888888889******8....78899999999999999* PP

                                       TTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 166 eidaaLDeknvkkvaellkekskn..aQfivislree 200
                                       e +     +  ++v + +k+ + +     iv+s+  e
  gi|386001152|ref|YP_005919451.1| 178 EPATMACPATKQEVLDAIKNVNRElgITTIVVSHLPE 214
                                       9999888999999999999777664466788887655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                                       SEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                       ++t+++G+ G GK+ ll  i
  gi|386001152|ref|YP_005919451.1| 295 EITSLIGSSGGGKTTLLKII 314
                                       689***********998765 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.2e-05
                                       EE-HHHHHHHHHCTT-STT.....................................CS-HHHHHHHHHHHHHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 117 evtkkevsellesagiske.....................................lLSgGektLvalaLlfAiqkv 156
                                       ++t++e + +l + g+++e                                     +LSgGek  v++aLl+A    
  gi|386001152|ref|YP_005919451.1| 406 DMTEEEAKTVLDKLGLTREifeelfprfpetearryaepvfkvldldpsilekyphQLSGGEKVRVSIALLMAS--- 479
                                       67778888888888888889999999999999999999999999999999999999***************885... PP

                                       S--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 157 kpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemleka 205
                                        +  + +lDe    +D    + va+ +k  +++ n+ ++ +s++ +++++ 
  gi|386001152|ref|YP_005919451.1| 480 -KPGILILDEPFGDIDPITLRGVANAIKriNAEFNTTILLVSHHVDFVREI 529
                                       .45799*********************944444457888888888777665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.5   0.00034       0.2      18      39 ..      27      48 ..      19      51 .. 0.77
   2 !   13.9   0.0   5.8e-05     0.033      17      48 ..     289     320 ..     283     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                      + ++ ++  ++G+sG GKSTll
  gi|386001152|ref|YP_005919451.1| 27 TAEEGEILGIVGKSGGGKSTLL 48
                                      455344788************8 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.8e-05
                            AAA_29  17 ieidlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                       +ei++ ++t l+G sG GK+Tll  iq +  p
  gi|386001152|ref|YP_005919451.1| 289 LEIREGEITSLIGSSGGGKTTLLKIIQGIARP 320
                                       6777555***************9766666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00065      0.38       2      41 ..      13      54 ..      12      67 .. 0.80
   2 ?   -0.4   0.0       1.4   7.9e+02      69     113 ..     145     196 ..     103     211 .. 0.67
   3 !    7.5   0.0    0.0054       3.1      19      48 ..     295     324 ..     289     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                            AAA_30  2 lnaeQaaave..alltsgdrvavltGpAGtGKttalkalrea 41
                                      l++ Q +a++  ++++++  +  ++G  G GK+t+lk lr +
  gi|386001152|ref|YP_005919451.1| 13 LKDRQVEALKgvSFTAEEGEILGIVGKSGGGKSTLLKILRGI 54
                                      77888888873346788888*****************99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            AAA_30  69 eastiakllkrlk......grarlepg.tllivDE.agmvdtkqlaallkaae 113
                                       +a+ +a +l+  +      +  +l+++ +ll+ DE a m+  ++ +++l+a++
  gi|386001152|ref|YP_005919451.1| 145 KAKHLATILSGGEkqrlliA-RQLAKKpKLLLLDEpATMACPATKQEVLDAIK 196
                                       55555555544446677754.46666679999999445554455555555554 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0054
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggr 48 
                                        ++ l G  G GKtt+lk ++ +++ ++g+
  gi|386001152|ref|YP_005919451.1| 295 EITSLIGSSGGGKTTLLKIIQGIARPDEGS 324
                                       478899**************9988776555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1     0.004       2.3       6      44 ..      15      51 ..      13      65 .. 0.82
   2 ?   -2.3   0.0       8.7     5e+03     138     149 ..     223     234 ..     143     255 .. 0.47
   3 !   10.1   0.0    0.0014      0.81      23      55 ..     293     325 ..     279     450 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.004
                            AAA_16  6 eeeleqLlsalervrsgrpelvllsGesGvGKsslvrel 44
                                      ++++e+L+ +  ++ +g  e++ ++G sG GKs+l++ l
  gi|386001152|ref|YP_005919451.1| 15 DRQVEALKGVSFTAEEG--EILGIVGKSGGGKSTLLKIL 51
                                      77888888776666666..89**************9765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.7
                            AAA_16 138 vlvlDdlqwade 149
                                        ++lD  + +de
  gi|386001152|ref|YP_005919451.1| 223 MIWLDKGEILDE 234
                                       333333333333 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0014
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif 55 
                                       ++e++ l+G sG GK++l++ ++  ++ d+g +
  gi|386001152|ref|YP_005919451.1| 293 EGEITSLIGSSGGGKTTLLKIIQGIARPDEGSV 325
                                       44899**************99998888774333 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.22   1.3e+02      25      42 ..     145     162 ..     120     197 .. 0.72
   2 !   11.9   0.0   0.00036      0.21      31      89 ..     461     506 ..     451     507 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                           SbcCD_C  25 elsrssgtlSGGekqfla 42 
                                       + ++ ++ lSGGekq l+
  gi|386001152|ref|YP_005919451.1| 145 KAKHLATILSGGEKQRLL 162
                                       555666678999998765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00036
                           SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                        +lSGGek + +++al+      + s      ++++++LDE F+ +D+ +++ + ++++
  gi|386001152|ref|YP_005919451.1| 461 HQLSGGEK-VRVSIALL------MAS------KPGILILDEPFGDIDPITLRGVANAIK 506
                                       57899999.77777777......223......589*************99998887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0     0.001       0.6      20      46 ..      32      58 ..       2     205 .. 0.71
   2 !    7.8   1.3    0.0074       4.3      13      40 ..     287     315 ..     281     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                            AAA_23 20 gltlItGpNGaGKTTildAiklaLyge 46
                                       +  I+G+ G GK+T+l  ++ + + +
  gi|386001152|ref|YP_005919451.1| 32 EILGIVGKSGGGKSTLLKILRGIETFD 58
                                      5778*************9998765555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0074
                            AAA_23  13 qeidF.skgltlItGpNGaGKTTildAik 40 
                                        +++  +  +t ++G  G GKTT+l  i+
  gi|386001152|ref|YP_005919451.1| 287 LNLEIrEGEITSLIGSSGGGKTTLLKIIQ 315
                                       44555556799**************9886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1     0.009       5.2       5      25 ..      31      51 ..      28      68 .. 0.88
   2 ?    0.3   0.0       1.3   7.6e+02      81     114 ..     157     197 ..     123     219 .. 0.59
   3 !    8.3   0.0    0.0044       2.6       4      24 ..     293     313 ..     290     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                            AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                        il ++G sG GK+tll+ l
  gi|386001152|ref|YP_005919451.1| 31 GEILGIVGKSGGGKSTLLKIL 51
                                      567889***********9976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                            AAA_22  81 aleqalrarav...ielliiDEaqhlr....seealeeLrs 114
                                         ++ l ar+    ++ll++DE   +     ++e+l  +++
  gi|386001152|ref|YP_005919451.1| 157 EKQRLLIARQLakkPKLLLLDEPATMAcpatKQEVLDAIKN 197
                                       44444444444455569999998888665433666666544 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0044
                            AAA_22   4 tagilvvtGesGtGKTtllrr 24 
                                       +  i+ ++G sG GKTtll+ 
  gi|386001152|ref|YP_005919451.1| 293 EGEITSLIGSSGGGKTTLLKI 313
                                       567899************986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00041      0.23      28      63 ..      11      47 ..       4      60 .. 0.84
   2 ?   -1.0   0.0       2.1   1.2e+03     103     130 ..     165     192 ..     140     222 .. 0.67
   3 ?    3.1   0.0      0.12        67      44      80 ..     291     327 ..     284     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                         IstB_IS21 28 rsldkrkvkeLatlsfiekk.enivllGpsGvGKshl 63
                                       +l+ r+v++L + sf++++ e + ++G sG GKs l
  gi|386001152|ref|YP_005919451.1| 11 YQLKDRQVEALKGVSFTAEEgEILGIVGKSGGGKSTL 47
                                      57889***********987615556*********987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                         IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaell 130
                                        +   k++ll+lD+ ++      ++e+l
  gi|386001152|ref|YP_005919451.1| 165 RQLAKKPKLLLLDEPATMACPATKQEVL 192
                                       3445678999999999887766555554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                       i++ e   l+G sG GK+ l   +   a  ++ sv++
  gi|386001152|ref|YP_005919451.1| 291 IREGEITSLIGSSGGGKTTLLKIIQGIARPDEGSVFY 327
                                       566777889*********9977666555556666666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1         1   5.8e+02      38      53 ..      34      49 ..      17      56 .. 0.88
   2 !    9.3   0.0    0.0012       0.7     117     160 ..     168     209 ..     148     220 .. 0.81
   3 ?   -1.5   0.0       2.4   1.4e+03      39      53 ..     298     312 ..     289     320 .. 0.88
   4 ?    4.3   0.0      0.04        23     105     160 ..     466     519 ..     453     527 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                              TniB 38 lllvGdsnnGKtmive 53
                                      l +vG+s  GK+++++
  gi|386001152|ref|YP_005919451.1| 34 LGIVGKSGGGKSTLLK 49
                                      669**********986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                              TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       + k+++L++DE   +  + a +++e+l a+k+ ++el i+ ++v
  gi|386001152|ref|YP_005919451.1| 168 AKKPKLLLLDEPATMA-CPA-TKQEVLDAIKNVNRELGITTIVV 209
                                       4589*******99887.555.55689*************99877 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                              TniB  39 llvGdsnnGKtmive 53 
                                        l+G s  GKt++++
  gi|386001152|ref|YP_005919451.1| 298 SLIGSSGGGKTTLLK 312
                                       589*********986 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.04
                              TniB 105 skleqqvlrllrelkvrvLiiDE.ihnllagsarkqreflnalksLgnelkipivlv 160
                                        ++ +  ++ll + k+ +Li+DE + ++      + r + na+k+++ e++ +i lv
  gi|386001152|ref|YP_005919451.1| 466 GEKVRVSIALLMASKPGILILDEpFGDI---DPITLRGVANAIKRINAEFNTTILLV 519
                                       566777899**************44444...57788999999999999999988876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.017       9.7       4      46 ..      36      89 ..      34     116 .. 0.74
   2 !    8.1   0.0     0.005       2.9       4      20 ..     299     315 ..     297     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                            AAA_28  4 itGgestGKTtlleaLa..ar.........gypvvpEaareileeklakgedal 46
                                      i+G +++GK+tll+ L   ++         g ++vp ++ +++  + + +  +l
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLKILRgiETfdsgkieidGLEIVPNSGPDLVHRQRQVTAIHL 89
                                      78999***********97722334445556777888777777777766665555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.005
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       ++G +++GKTtll+ ++
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKIIQ 315
                                       89***********9877 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.001       0.6      33      67 ..      19      53 ..       7      62 .. 0.84
   2 ?    4.2   0.0     0.062        36      39      66 ..     288     315 ..     266     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      e+lk  +   ++ +iL i G sG gkst +k+L  
  gi|386001152|ref|YP_005919451.1| 19 EALKGVSFTAEEGEILGIVGKSGGGKSTLLKILRG 53
                                      57888888888899******************965 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.062
                             Rad17  39 vLesrkkriLLisGPsGCgkstvvkvLs 66 
                                        Le r+ +i  + G sG gk+t +k++ 
  gi|386001152|ref|YP_005919451.1| 288 NLEIREGEITSLIGSSGGGKTTLLKIIQ 315
                                       4667777799999************975 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.55   3.2e+02      18      35 ..      30      47 ..      27      59 .. 0.87
   2 ?    2.4   0.0      0.15        84     141     191 ..     189     230 ..     165     248 .. 0.70
   3 !   12.2   0.4   0.00014     0.084      16     147 ..     291     419 ..     284     425 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.55
                            ATPase 18 egrvvlitGepGtGKtif 35
                                      eg++  i+G++G GK+++
  gi|386001152|ref|YP_005919451.1| 30 EGEILGIVGKSGGGKSTL 47
                                      688999*********997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                            ATPase 141 ReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlke 191
                                        e l+ +++v ++lg+T+i vs           ++v  +++d +i Ld+ e
  gi|386001152|ref|YP_005919451.1| 189 QEVLDAIKNVNRELGITTIVVSHL---------PEVHRYLADRMIWLDKGE 230
                                       4556667777799********994.........556666666666666655 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00014
                            ATPase  16 ipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGw..dlekleeegklaiidas 89 
                                       i eg+++ + G++G GKt++ +  +i+g+++ +e  vf  +    +d+ e  + ++G+  ++  + +e  +a+    
  gi|386001152|ref|YP_005919451.1| 291 IREGEITSLIGSSGGGKTTLLK--IIQGIARPDEGSVFYRLGDGWVDMVEYSReRMGVrrNIGIMYQE--FALFPRE 363
                                       7899***************998..9********************99999887689983355555665..7777777 PP

                            ATPase  90 esaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrql 147
                                       +  e+ ++ k   + + +i+  +++ +e++++  ++D i +l ++++e++a++ l++l
  gi|386001152|ref|YP_005919451.1| 364 TVLEQ-IAYKLGVKGQDVIDYARKVAEEMGISDKILDVIYTL-TDMTEEEAKTVLDKL 419
                                       77665.3447888999999***********************.999999999999887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0017      0.96       4      38 ..      17      49 ..      14      59 .. 0.81
   2 ?    4.4   0.0     0.032        18      22      40 ..     296     314 ..     282     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                                      HHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC  4 svekviekLlekdelqslvvalvGmgGvGKttlak 38
                                      +ve++++  +  +e +  ++++vG+ G GK+tl+k
  gi|386001152|ref|YP_005919451.1| 17 QVEALKGVSFTAEEGE--ILGIVGKSGGGKSTLLK 49
                                      6777777777677777..***************86 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.032
                                       EEEEEESTTSSHHHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqi 40 
                                       + +l G  G GKttl+k i
  gi|386001152|ref|YP_005919451.1| 296 ITSLIGSSGGGKTTLLKII 314
                                       789************9865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.11        63      26      44 ..      34      52 ..      22      74 .. 0.83
   2 ?   -2.3   0.0       4.8   2.8e+03     320     350 ..     167     197 ..      99     212 .. 0.61
   3 ?    8.8   0.0     0.002       1.2      14      44 ..     284     315 ..     283     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            AAA_15 26 tvliGkNnsGKSsileald 44
                                        ++Gk + GKS++l++l 
  gi|386001152|ref|YP_005919451.1| 34 LGIVGKSGGGKSTLLKILR 52
                                      569*************995 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.8
                            AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllke 350
                                         +k+++ll++EP +   p  ++++ +++k+
  gi|386001152|ref|YP_005919451.1| 167 LAKKPKLLLLDEPATMACPATKQEVLDAIKN 197
                                       3445566666666555555555555555554 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.002
                            AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsileald 44 
                                       ++d  +++ e  +t liG  + GK+++l++++
  gi|386001152|ref|YP_005919451.1| 284 IEDLNLEIREGeITSLIGSSGGGKTTLLKIIQ 315
                                       567777777777******************97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.7     0.044        25       5      18 ..      36      49 ..      32      55 .. 0.86
   2 ?    7.5   0.0    0.0062       3.6       4      26 ..     298     319 ..     295     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.044
                                      EEC-TTTCHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlq 18
                                      + G++G GK+tLl+
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLK 49
                                      89**********97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0062
                                       EEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawae 26 
                                        l G +G GKTtLl+ +++ +a+
  gi|386001152|ref|YP_005919451.1| 298 SLIGSSGGGKTTLLK-IIQGIAR 319
                                       589**********96.5566655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.011       6.2       1      19 [.      33      51 ..      33      65 .. 0.85
   2 ?    5.2   0.1     0.032        18       3      17 ..     298     312 ..     296     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                              MobB  1 vlgivgksgsGKTtLlekl 19
                                      +lgivgksg GK tLl+ l
  gi|386001152|ref|YP_005919451.1| 33 ILGIVGKSGGGKSTLLKIL 51
                                      79*************9865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.032
                              MobB   3 givgksgsGKTtLle 17 
                                       +++g sg GKTtLl+
  gi|386001152|ref|YP_005919451.1| 298 SLIGSSGGGKTTLLK 312
                                       789**********96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0083       4.8       3      19 ..      36      52 ..      34      91 .. 0.85
   2 ?    0.0   0.0         2   1.2e+03      27      93 ..     163     223 ..     144     246 .. 0.67
   3 ?    3.4   0.5      0.18     1e+02       3      19 ..     299     315 ..     298     429 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0083
                            AAA_18  3 ltGtpGvGKttlakeLs 19
                                      + G++G GK+tl k L+
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLKILR 52
                                      89*************96 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2
                            AAA_18  27 nlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakd 93 
                                       + r++ak+  lll ++p+ +  +   ++++ld++ + ++e         ++v++ +++ +++ a++ 
  gi|386001152|ref|YP_005919451.1| 163 IARQLAKKPKLLLLDEPA-TMACPATKQEVLDAIKNVNRELGI-----TTIVVSHLPEVHRYLADRM 223
                                       678888888888888888.777777777776666666666644.....6778888777777665554 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.18
                            AAA_18   3 ltGtpGvGKttlakeLs 19 
                                       l G +G GKttl k ++
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKIIQ 315
                                       67999*******99884 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.041        24     244     264 ..      30      51 ..      12      70 .. 0.84
   2 ?   -0.1   0.0      0.53   3.1e+02     376     412 ..     191     227 ..     154     237 .. 0.77
   3 ?    5.7   0.3    0.0092       5.3     241     265 ..     290     315 ..     288     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.041
                                       SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAl 264
                                       +G +  IvG    GKsTLL+ l
  gi|386001152|ref|YP_005919451.1|  30 EGeILGIVGKSGGGKSTLLKIL 51 
                                       566889*************976 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                                       HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                        ABC_ATPase 376 lvdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                       ++d ++++ ++lg++ti+v+   +    +Ad++i ++
  gi|386001152|ref|YP_005919451.1| 191 VLDAIKNVNRELGITTIVVSHLPEVHRYLADRMIWLD 227
                                       5678888889999999999877777777788888776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0092
                                       EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                        i++G +t ++G+   GK+TLL+ ++
  gi|386001152|ref|YP_005919451.1| 290 EIREGeITSLIGSSGGGKTTLLKIIQ 315
                                       589999****************9886 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.025        14       8      49 ..      16      62 ..       9      65 .. 0.74
   2 ?    4.7   0.0     0.031        18      16      35 ..     291     310 ..     284     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                                      HHHHHHHHHH....H-SEEEEE--TTSST.THHHHHHHHHHHHTTS- CS
                              PhoH  8 eQkeylealk....kndivfaiGpaGtGK.tylavalavealkkkkv 49
                                      +Q e+l+ ++    + +i+ ++G++G GK t+l +  ++e + ++k+
  gi|386001152|ref|YP_005919451.1| 16 RQVEALKGVSftaeEGEILGIVGKSGGGKsTLLKILRGIETFDSGKI 62
                                      55555555555544667************668899999999888776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.031
                                       HHH-SEEEEE--TTSSTTHH CS
                              PhoH  16 lkkndivfaiGpaGtGKtyl 35 
                                       +++ +i+  iG++G GKt l
  gi|386001152|ref|YP_005919451.1| 291 IREGEITSLIGSSGGGKTTL 310
                                       67889************865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.39   2.2e+02      32      50 ..      30      48 ..      23      51 .. 0.88
   2 ?    2.5   0.0      0.16        95     166     189 ..     189     212 ..     177     214 .. 0.90
   3 ?   -2.9   0.0       7.2   4.2e+03      80     117 ..     234     276 ..     234     289 .. 0.75
   4 ?    6.0   0.2     0.014       8.2      30      50 ..     291     311 ..     284     313 .. 0.92
   5 ?    2.1   0.0      0.21   1.2e+02     168     188 ..     501     521 ..     494     523 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.39
                            AAA_25 32 agelallaGapgtGKttla 50
                                      +ge+  ++G +g GK+tl+
  gi|386001152|ref|YP_005919451.1| 30 EGEILGIVGKSGGGKSTLL 48
                                      67788899*********96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                            AAA_25 166 galvealeriarrtgaavllvhHv 189
                                       +++++a++++ r++g+++++v H+
  gi|386001152|ref|YP_005919451.1| 189 QEVLDAIKNVNRELGITTIVVSHL 212
                                       7899*******************7 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.2
                            AAA_25  80 EdsedelrrRlravgeal....rddarllvldlagv.eslpLf 117
                                       E+  +e+ rR+  ++ ++    ++++ l+++ ++g  +++ L+
  gi|386001152|ref|YP_005919451.1| 234 EGEPEEVLRRFLSLLGDAeplvPRPQALPAIRIVGLhKRNYLV 276
                                       6677789999999999998888888888888877765655554 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.014
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       +++ge++ l+G +g GKttl+
  gi|386001152|ref|YP_005919451.1| 291 IREGEITSLIGSSGGGKTTLL 311
                                       579****************96 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.21
                            AAA_25 168 lvealeriarrtgaavllvhH 188
                                       + +a++ri ++++ ++llv H
  gi|386001152|ref|YP_005919451.1| 501 VANAIKRINAEFNTTILLVSH 521
                                       789****************99 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 ?    4.2   0.1     0.097        56       4      72 ..      37     184 ..      34     223 .. 0.57
   2 ?    4.1   0.0     0.099        57       3      20 ..     299     316 ..     297     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.097
                                       ESSTTSSHHHHHHHHHHH..HTHEEEEEETTTCS.SS........................................ CS
                               AAA   4 yGppGtGKTllakavake..lgvefleisgsell.sk........................................ 37 
                                       +G  G GK++l k +     +++  +ei+g e++ ++                                        
  gi|386001152|ref|YP_005919451.1|  37 VGKSGGGKSTLLKILRGIetFDSGKIEIDGLEIVpNSgpdlvhrqrqvtaihlqrdfglwtepaiknvarrvysrit 113
                                       68888888888888765532345556666666663335555555566666666666666666666666666666666 PP

                                       ...........................STTHHHHHHHHHHHHHHHTS.........TSEEEEEETGGGHHH CS
                               AAA  38 ...........................yvgesekkirelfkeakeka.........kpsilfiDEidalak 72 
                                                                   + +++k+++ +++  ++++         kp+ l++DE   +a 
  gi|386001152|ref|YP_005919451.1| 114 gyetipteydleyeavmeeamdylklvGLDKKAKHLATILSGGEKQRlliarqlakKPKLLLLDEPATMAC 184
                                       66666666666666666666666665533444444444444433333344444445577777777666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.099
                                       EESSTTSSHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavak 20 
                                       l+G  G GKT+l k +  
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKIIQG 316
                                       89***********99865 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.038        22      28      47 ..      36      55 ..      14      66 .. 0.83
   2 ?    5.3   0.0     0.016       9.2      28      48 ..     299     319 ..     289     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.038
                                      EEESTTSSHHHHHHHHHHHC CS
                           G-alpha 28 llGqseSGKsTilkqlklly 47
                                      ++G+s++GKsT+lk l+ ++
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLKILRGIE 55
                                      79************988665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                                       EEESTTSSHHHHHHHHHHHCS CS
                           G-alpha  28 llGqseSGKsTilkqlkllyk 48 
                                       l+G+s++GK+T+lk ++ + +
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKIIQGIAR 319
                                       89************9997665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.031        18       1      20 [.      33      52 ..      33      71 .. 0.84
   2 ?    4.2   0.0     0.053        31       3      22 ..     298     317 ..     296     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.031
                               PRK  1 vIgvagsSGaGkttvarkle 20
                                      ++g+ g+SG Gk+t+ + l+
  gi|386001152|ref|YP_005919451.1| 33 ILGIVGKSGGGKSTLLKILR 52
                                      789***********988776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.053
                               PRK   3 gvagsSGaGkttvarkleki 22 
                                       ++ gsSG Gktt+ + ++ i
  gi|386001152|ref|YP_005919451.1| 298 SLIGSSGGGKTTLLKIIQGI 317
                                       789*********99988766 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.13        74       6      24 ..      36      54 ..      32      61 .. 0.87
   2 ?    6.6   0.1      0.01       5.9       6      23 ..     299     316 ..     295     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                         PduV-EutP  6 liGkvgsGKttLtqalkge 24
                                      ++Gk+g GK tL + l+g 
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLKILRGI 54
                                      69************99985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                         PduV-EutP   6 liGkvgsGKttLtqalkg 23 
                                       liG++g GKttL + ++g
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKIIQG 316
                                       9************99987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.037        22       4      39 ..      36      72 ..      34      92 .. 0.72
   2 ?    4.0   0.1     0.093        54       4      18 ..     299     313 ..     297     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.037
                                      EESSTTSSHHHHHHCHCT.-CCC-EEETTTTEEEEEE CS
                               Roc  4 lvGdsgvGKtsllkrfve.dkfsekekstigvdfltk 39
                                      +vG+sg GK++llk +   ++f++ + ++ g++++ +
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLKILRGiETFDSGKIEIDGLEIVPN 72
                                      8************988765777777777777776665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.093
                                       EESSTTSSHHHHHHC CS
                               Roc   4 lvGdsgvGKtsllkr 18 
                                       l+G sg GKt+llk 
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKI 313
                                       8***********985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0041       2.4       3      21 ..      35      53 ..      33      69 .. 0.85
   2 ?    0.8   0.1      0.85   4.9e+02       4      19 ..     299     314 ..     297     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0041
                                      EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                      +ivG++  GKStL++ l g
  gi|386001152|ref|YP_005919451.1| 35 GIVGKSGGGKSTLLKILRG 53
                                      8*************98865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.85
                                       EEESTTSSHHHHHHHH CS
                          MMR_HSR1   4 ivGrpNvGKStLinal 19 
                                       ++G +  GK+tL++ +
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKII 314
                                       89**********9866 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.084        49      30      55 ..      36      61 ..      27      70 .. 0.85
   2 ?    6.1   0.0    0.0074       4.3      30      55 ..     299     324 ..     291     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.084
                              DLIC 30 vlGedgsGkttliaklqGveeekkGr 55
                                      ++G++g Gk+tl+  l+G+e    G+
  gi|386001152|ref|YP_005919451.1| 36 IVGKSGGGKSTLLKILRGIETFDSGK 61
                                      789*****************987775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0074
                              DLIC  30 vlGedgsGkttliaklqGveeekkGr 55 
                                       ++G +g Gkttl+  +qG+  +  G+
  gi|386001152|ref|YP_005919451.1| 299 LIGSSGGGKTTLLKIIQGIARPDEGS 324
                                       78*****************9998887 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5      0.13        75       3      19 ..      34      50 ..      32      61 .. 0.87
   2 ?    6.0   0.2     0.014       7.9       2      19 ..     296     313 ..     295     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                                      EEEEESTTCCHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnh 19
                                      ++++G  G GK+tLl+ 
  gi|386001152|ref|YP_005919451.1| 34 LGIVGKSGGGKSTLLKI 50
                                      7899**********975 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                                       EEEEEESTTCCHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnh 19 
                                       +t l G+ G GKTtLl+ 
  gi|386001152|ref|YP_005919451.1| 296 ITSLIGSSGGGKTTLLKI 313
                                       57899***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 4549.38
//
Query:       gi|386001153|ref|YP_005919452.1|  [L=674]
Description: methionyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.6e-148  494.7   0.0   1.9e-148  494.4   0.0    1.0  1  tRNA-synt_1g  tRNA synthetases class I (M)
    7.6e-26   90.1   0.0    1.3e-25   89.3   0.0    1.4  1  tRNA_bind     Putative tRNA binding domain
    4.2e-16   58.3   0.1    1.7e-07   29.9   0.0    3.8  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    9.1e-13   48.4   0.0    1.5e-12   47.8   0.0    1.4  1  Anticodon_1   Anticodon-binding domain of tRNA
    1.3e-08   34.5   0.0    0.00029   20.3   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
     0.0033   16.4   0.0       0.85    8.5   0.0    2.4  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.44   10.6   5.8        1.5    8.9   5.9    1.9  1  DZR           Double zinc ribbon
        4.2    7.6   6.6          1    9.6   0.1    3.2  4  zf-RING_7     C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.4   0.0  8.4e-152  1.9e-148       1     390 [.       8     393 ..       8     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 494.4 bits;  conditional E-value: 8.4e-152
                                       EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikel 77 
                                       +lvt++lpYang+ H+Ghl+++++aDif+R  ++ ge  +f+cg+D+hGtpi ++Ae++g+tp elv+++h++++e+
  gi|386001153|ref|YP_005919452.1|   8 ILVTCGLPYANGPCHIGHLRTYVPADIFVRGLKKMGEAPHFICGSDSHGTPIVVNAEERGTTPTELVTRYHDHFDEV 84 
                                       69*************************************************************************** PP

                                       HHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.- CS
                      tRNA-synt_1g  78 fkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.e 153
                                       f++++++fd++g+t++ ++++ +q+i+++l e+g++y +ei+ +ycp+++rflpdryveg CP+c  + argd+c +
  gi|386001153|ref|YP_005919452.1|  85 FRRMGVEFDYFGNTDDPSNHRRTQAIVEALMEEGHVYPREIQLAYCPSCDRFLPDRYVEGICPYCS-SPARGDECdQ 160
                                       *****************************************************************9.67******88 PP

                                       TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS CS
                      tRNA-synt_1g 154 ecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrd 230
                                        cg++lep e+ +p+++++gs +e+++++h+ff+ls+f+++l +++  ++   ++n++++++ew++++Lkd++i+r+
  gi|386001153|ref|YP_005919452.1| 161 GCGRHLEPGEISEPVCKVCGSGAEYRTQRHYFFRLSSFSDFLVDYL--QSLGGTTNARNYALEWVRQELKDWCITRN 235
                                       9*********************************************..44469************************ PP

                                       -SSS-EETTECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHT CS
                      tRNA-synt_1g 231 ldwGipvPgaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillga 307
                                       l wG+++Pg+e+ v+YVW+dA+igYis+t+e+a    ++ +w++yW   k +++vhfig di+++H+ifwPa+l+ga
  gi|386001153|ref|YP_005919452.1| 236 LGWGVKFPGSEDLVVYVWVDAPIGYISFTEEWA--LRTNGDWERYW--RKPSRIVHFIGGDIVYHHCIFWPAMLKGA 308
                                       ********************************9..44578******..569************************** PP

                                       T----S-EEEE--EEE--------------H.HHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCH CS
                      tRNA-synt_1g 308 elklpkkvvaheyltvegkKlSkSrgvvvka.kealer.ldadllRYylaaeapekkDldfswedfvervNseLadk 382
                                       +++lp++vva+++l++++k +SkSrg+vv++ +++le+ l++dllRYyla+ ++++k+l+fsw+ f e+vN eL+++
  gi|386001153|ref|YP_005919452.1| 309 GYTLPSAVVASGMLKIDNKTFSKSRGYVVWViDDYLEQgLHPDLLRYYLASYTSHTKELNFSWKIFAEKVNGELVGA 385
                                       ******************************8799***99************************************** PP

                                       HHHHHHHH CS
                      tRNA-synt_1g 383 lgnlvnRv 390
                                       lgn+vnR+
  gi|386001153|ref|YP_005919452.1| 386 LGNFVNRA 393
                                       *******7 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.0   5.8e-29   1.3e-25       1      96 []     580     672 ..     580     672 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 5.8e-29
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       lrvG+v  ae +++++kLl+l vd+G+ee rqiv+g+++   pe+l+++ vvv+anl+p+kl GveS+GM+l+a+  
  gi|386001153|ref|YP_005919452.1| 580 LRVGEVKAAEGIKGSEKLLRLLVDIGSEE-RQIVAGIAKTHRPEDLLGRRVVVLANLEPAKLFGVESRGMLLAAD-- 653
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                       +++e  +l +++++++G+k
  gi|386001153|ref|YP_005919452.1| 654 ADGEAVLLAPDKATPPGTK 672
                                       8****************86 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   7.8e-11   1.7e-07      26     174 ..       9     138 ..       3     144 .. 0.87
   2 !   21.3   0.0     3e-08   6.7e-05     354     432 ..     165     243 ..     158     267 .. 0.88
   3 ?   -0.1   0.0     0.093   2.1e+02     560     602 .]     325     370 ..     313     370 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 7.8e-11
                       tRNA-synt_1  26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefre 102
                                        ++ g Py++G  HiGh  + +  di +r  +  G+  ++  G D +G +i  + e++ g++               
  gi|386001153|ref|YP_005919452.1|   9 LVTCGLPYANGPCHIGHLRTYVPADIFVRGLKKMGEAPHFICGSDSHGTPIVVNAEER-GTT--------------- 69 
                                       567789********************************************97776666.222............... PP

                       tRNA-synt_1 103 kvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktals 174
                                          e +++y+++  + ++r+Gv +D+  +  T d++ +  ++ +   l+++g++y ++  + +++++   l 
  gi|386001153|ref|YP_005919452.1|  70 -PTELVTRYHDHFDEVFRRMGVEFDYFGN--TDDPSNHRRTQAIVEALMEEGHVYPREIQLAYCPSCDRFLP 138
                                       .3478999**************9999765..88999999999999********************9987665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3e-08
                       tRNA-synt_1 354 kaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhr 430
                                       + e+ e s p+c+  +   +yr +  +f r++++ d +++ +++   + + ++   +   ++ +dWci R++ WG++
  gi|386001153|ref|YP_005919452.1| 165 HLEPGEISEPVCKVCGSGAEYRTQRHYFFRLSSFSDFLVDYLQSLGGTTNARNYALEWVRQELKDWCITRNLGWGVK 241
                                       678889999**********************************99988887766655445689*************9 PP

                       tRNA-synt_1 431 ip 432
                                        p
  gi|386001153|ref|YP_005919452.1| 242 FP 243
                                       87 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.093
                       tRNA-synt_1 560 eGrKmSKslgNvidpld..vikkygadalRltli.lsdvgrdinls 602
                                       + +  SKs g v+  +d  + + +  d lR++l+ +++ ++++n+s
  gi|386001153|ref|YP_005919452.1| 325 DNKTFSKSRGYVVWVIDdyLEQGLHPDLLRYYLAsYTSHTKELNFS 370
                                       55678999998876554113344557********9******99986 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   6.5e-16   1.5e-12       1     116 [.     411     521 ..     411     596 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 6.5e-16
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrl 76 
                                       d ++ ++++ +v+ v+ a+eey+f+k a+ ++ +   d+ ++y++ ++p+   +s+ d+  a+ +++l ++++l +l
  gi|386001153|ref|YP_005919452.1| 411 DPEVMAKIEGTVSLVRSALEEYEFKKLADGAMAL--ADFGNVYFQGSEPWKLAKSDRDRcGAVLRNCLQIAKALAIL 485
                                       678899***************************8..9**************998876664445588889999***** PP

                       Anticodon_1  77 laPfmPfitEelwqreeeelgkkesimlaewpekaeel.ek 116
                                       l+P+mP  +E +w    ++lg + +   a +  +a    e+
  gi|386001153|ref|YP_005919452.1| 486 LQPVMPGKMEVAW----RQLGLDGTAADARFD-DAHLPiEA 521
                                       *************....889988888888887.34222333 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00029      14     125 ..      11     124 ..       8     132 .. 0.85
   2 !   11.9   0.0   4.7e-05      0.11     242     295 ..     317     373 ..     286     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                       EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdlea 89 
                                       +CG p +   +h+Gh R++v  Di+ r l+++g   +f+         i+ +a+e++++ +el+ ++ ++f + ++ 
  gi|386001153|ref|YP_005919452.1|  11 TCGlPYANGPCHIGHLRTYVPADIFVRGLKKMGEAPHFICGSDSHGTPIVVNAEERGTTPTELVTRYHDHFDEVFRR 87 
                                       57733456689*****************************9999999****************************** PP

                                       TT----SB.--BGGGGHHHHHHHHHHHHHTTSEEE-T CS
                      tRNA-synt_1e  90 Lnvlkptl.eprvsekvdeiielvekliekgyaYavs 125
                                       ++v    + ++    +      +ve l+e+g+ Y+ +
  gi|386001153|ref|YP_005919452.1|  88 MGVEFDYFgNTDDPSNHRRTQAIVEALMEEGHVYPRE 124
                                       ***9765523444555667788899999999999765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.7e-05
                                       EEE--EEETTBE--TTTT---.BHHHHHTT.S-HHHHHHHHHSS.-TTS-EEE-HHH CS
                      tRNA-synt_1e 242 lhnghlkiegekmsksLknfi.tikdvlkk.fdprqlRllllsa.hyrsqldfkeel 295
                                       + +g+lki+++  sks + ++ +i d l++  +p  lR++l+s   + ++l+f+ + 
  gi|386001153|ref|YP_005919452.1| 317 VASGMLKIDNKTFSKSRGYVVwVIDDYLEQgLHPDLLRYYLASYtSHTKELNFSWKI 373
                                       678***************998356888976489********9852678899998665 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00038      0.85      24      70 ..       7      54 ..       2      57 .. 0.86
   2 ?   -3.6   0.0       1.8   4.1e+03     110     148 ..      76     114 ..      71     120 .. 0.71
   3 !    5.1   0.0    0.0039       8.8     277     325 ..     324     373 ..     307     378 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00038
                      tRNA-synt_1f 24 evvvesGis.pSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70
                                       ++v  G+  + G+ HiG lr  + ad+ +r l+k+ge+ ++i+ sD 
  gi|386001153|ref|YP_005919452.1|  7 PILVTCGLPyANGPCHIGHLRTYVPADIFVRGLKKMGEAPHFICGSDS 54
                                      567777775257*******************************99985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                      tRNA-synt_1f 110 hfnaelvesLdelgievefisatelYksglydeaikeal 148
                                       +++ ++ e+ +++g+e+++  +t+  ++ + ++ai eal
  gi|386001153|ref|YP_005919452.1|  76 RYHDHFDEVFRRMGVEFDYFGNTDDPSNHRRTQAIVEAL 114
                                       566778888889999999888877766666666666666 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0039
                      tRNA-synt_1f 277 kggekmssSkGnvl.tledwlev.aepevlrflilrrkPkkakkldldlei 325
                                         ++  s+S+G v+  ++d le  ++p++lr+++++    + k+l+++ +i
  gi|386001153|ref|YP_005919452.1| 324 IDNKTFSKSRGYVVwVIDDYLEQgLHPDLLRYYLAS-YTSHTKELNFSWKI 373
                                       344599*****98735788888637*********99.77778888887666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.9   0.00066       1.5       1      49 []     130     180 ..     130     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00066
                               DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCps.Cgekvdpearf...CpeCG 49 
                                       Cp+C + lp++     C++C ++ +     d C++ Cg+ ++p++     C+ CG
  gi|386001153|ref|YP_005919452.1| 130 CPSCDRFLPDRYVegICPYCSSPAR----GDECDQgCGRHLEPGEISepvCKVCG 180
                                       ***********9888*********9....8***866**99999865445599998 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00046         1      22      33 .]     126     137 ..     114     137 .. 0.92
   2 ?   -1.2   0.5       1.1   2.4e+03      26      30 ..     146     150 ..     145     151 .. 0.85
   3 ?   -1.3   0.1       1.2   2.6e+03       3      16 ..     160     173 ..     160     173 .. 0.86
   4 ?   -2.9   0.0       3.6     8e+03       8      19 ..     409     420 ..     409     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                                       B-EE-TTT--EE CS
                         zf-RING_7  22 evvtCpeCGRIL 33 
                                       ++++Cp+C R+L
  gi|386001153|ref|YP_005919452.1| 126 QLAYCPSCDRFL 137
                                       689*******98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       -TTT- CS
                         zf-RING_7  26 CpeCG 30 
                                       Cp+C+
  gi|386001153|ref|YP_005919452.1| 146 CPYCS 150
                                       ****6 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                                       TTT--B--CCHHHH CS
                         zf-RING_7   3 gGChmelppqvlse 16 
                                       +GC+ +l p+++se
  gi|386001153|ref|YP_005919452.1| 160 QGCGRHLEPGEISE 173
                                       79999999999886 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.6
                                       B--CCHHHHHCC CS
                         zf-RING_7   8 elppqvlselra 19 
                                       el+p+v +++ +
  gi|386001153|ref|YP_005919452.1| 409 ELDPEVMAKIEG 420
                                       79****999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 4803.74
//
Query:       gi|386001154|ref|YP_005919453.1|  [L=446]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-16   57.7   0.0    2.7e-15   56.2   0.0    1.8  2  DUF1724       Domain of unknown function (DUF1724)
    2.2e-12   47.1   0.0    3.4e-12   46.5   0.0    1.3  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0     3e-19   2.7e-15       1      62 []     204     265 ..     204     265 .. 0.96
   2 ?   -3.1   0.0      0.99   8.9e+03       8      21 ..     339     352 ..     334     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3e-19
                           DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSep 62 
                                       ++l+++ e++ +l+l vt++fl+l+l+++dg yd     i  +esA+ WG eLFeyY +rS++
  gi|386001154|ref|YP_005919453.1| 204 FRLRLIGEDL-KLALFVTESFLYLGLYRHDGVYDVGtGAIYLGESAVAWGMELFEYYAQRSRE 265
                                       5789999***.*************************99***********************85 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.99
                           DUF1724   8 eeikplsltvtDkf 21 
                                       e  + ++l+v+D+ 
  gi|386001154|ref|YP_005919453.1| 339 ESYGRPFLVVADYL 352
                                       56678999***986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   3.8e-16   3.4e-12       1     103 [.     298     404 ..     298     414 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.8e-16
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHH..ESEEEEESSCSSSEHHHHHHHH.HHCTTTS CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeek..vdlillDinmpgmdGlellkei.reedpel 72 
                                       v+iv+Dd   ++l+r+++e  +    +v+ a++ ++al++++e+   + l++ D  +p+  Gl+l+ +  r  +   
  gi|386001154|ref|YP_005919453.1| 298 VMIVEDDLGHATLIRRIFEesSPR-WRVHHASQLQDALRWIEESYgrPFLVVADYLLPDGCGLDLAGKAeRPLEVGF 373
                                       89*****************53344.49**************998777********************996777799* PP

                                       EEEEEESSTSHHHHHHHHHCTESEEEESSG- CS
                      Response_reg  73 pviiltahseeedavealkagaddflsKpfd 103
                                       p iilt+ ++e+ a +a+k ga+d+++K+ d
  gi|386001154|ref|YP_005919453.1| 374 PLIILTGFGSEKIAAQAFKSGAMDYVVKEAD 404
                                       ****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2654.33
//
Query:       gi|386001155|ref|YP_005919454.1|  [L=886]
Description: Multi-sensor signal transduction histidine kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-33  116.1   0.0    9.3e-33  113.3   0.0    2.3  2  CHASE4       CHASE4 domain
    4.3e-25   88.4   0.0    9.2e-25   87.3   0.0    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      2e-17   63.4   0.1    5.4e-17   62.0   0.0    1.8  2  PAS_4        PAS fold
    4.6e-11   42.6   0.4    1.9e-09   37.4   0.0    2.7  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.9e-09   37.7   0.0    5.8e-09   36.2   0.0    1.9  1  PAS_9        PAS domain
    2.1e-09   38.1   0.0    8.3e-09   36.2   0.0    2.1  2  GAF          GAF domain
    3.5e-09   36.7   0.0      1e-08   35.1   0.0    1.9  1  PAS          PAS fold
    3.8e-06   27.2   0.0    2.8e-05   24.4   0.0    2.3  2  GAF_2        GAF domain
    2.7e-05   24.5   0.1    6.9e-05   23.1   0.1    1.8  1  HAMP         HAMP domain
    4.4e-05   23.4   0.0    0.00017   21.5   0.0    2.1  1  PAS_8        PAS domain
    0.00022   21.1   0.0    0.00045   20.1   0.0    1.4  1  HATPase_c_5  GHKL domain
     0.0013   18.6   0.0     0.0023   17.7   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0028   18.0   0.0      0.084   13.2   0.0    2.5  2  GAF_3        GAF domain
     0.0084   16.1   0.0      0.018   15.0   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.014   15.2   0.2          3    7.6   0.0    3.2  3  dCache_1     Cache domain


Domain annotation for each model (and alignments):
>> CHASE4  CHASE4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   7.8e-36   9.3e-33       2     136 ..      53     205 ..      52     206 .. 0.92
   2 ?   -0.8   0.0       1.3   1.6e+03      21      63 ..     334     384 ..     332     463 .. 0.60

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 7.8e-36
                            CHASE4   2 lqaeldqlerllkdwavWDdtyafvqdrdpdyiesnlgdetletlgldlvlfldadgklvy....dqengq...... 68 
                                       lq++l++l+r ++dw  W+dt +fv +++ +yi++nl+++tl+ l++d+++++d++g+l y    ++++g+      
  gi|386001155|ref|YP_005919454.1|  53 LQEDLSSLKRAAEDWGHWNDTRDFVIGENDQYIQDNLNSWTLSGLDVDFMIYYDRSGNLFYsrafNHATGEevpapg 129
                                       899**********************************************************7766333333788888 PP

                            CHASE4  69 ........ekllseaeeesgrsgllkldggpalvaaapIltsegegpsrGtlvfgryldeallsrlseltlldlel 136
                                               ++l +++++e+g++g+++ ++g++lv++++Il+s+ +gp +Gt+++gr+ld+a+ + l++l++ dl++
  gi|386001155|ref|YP_005919454.1| 130 rllslakdDPLIAHSSPEDGLTGIVSDPEGLLLVSSTTILDSHWKGPISGTFIVGRRLDGARAEGLARLSGIDLRM 205
                                       8888888877888888889******************************************************997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                            CHASE4  21 dtyafvqdrdpdyiesnlgdetletlgldlvlfldadgklvy........d 63 
                                       ++ +++++ +++ + s    +t  +  +d++++ d++ + v          
  gi|386001155|ref|YP_005919454.1| 334 EMLDHLESYNQKLAMSEKRFRTIVDTAHDCIFIKDPKSRYVLvnpvmeriF 384
                                       556677777777777777778889999999999999999886433333330 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 !   87.3   0.0   7.7e-28   9.2e-25       2     110 ..     778     885 ..     777     886 .] 0.92

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 7.7e-28
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76 
                                       d  r+++++ nl+dN++k+ ++ ++ e+e+  +   ++ v+ v+DnGiG+++++ +k+f+ f++    + +++g+G+
  gi|386001155|ref|YP_005919454.1| 778 DRLRVQEALTNLLDNSIKYMGDRPHPEIEVGWRPegEETVFFVRDNGIGMDPDQWEKVFGLFYK---IDPDSEGSGV 851
                                       67799**************8899999999987324689999***********************...677899**** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       Gl+iv++++e +gG+iw+ese+grGt++ ftlp 
  gi|386001155|ref|YP_005919454.1| 852 GLAIVRRIIEVHGGRIWIESEEGRGTCVLFTLPT 885
                                       *******************************995 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   4.5e-20   5.4e-17       2     107 ..     358     463 ..     357     466 .. 0.96
   2 ?   -3.4   0.0       9.4   1.1e+04      29      60 ..     757     790 ..     750     792 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 4.5e-20
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       d   d+++++dp +r++ +N+ ++++f++p+  +lG++++ ++++e aar+++ ++ vl+ge ++ ++  +++ g+ 
  gi|386001155|ref|YP_005919454.1| 358 DTAHDCIFIKDPKSRYVLVNPVMERIFQLPASKMLGERDEVFFSAETAARIREKDAGVLSGEPFVGEVSAHTRAGSS 434
                                       66789************************************************************99999999**** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTe 107
                                        ++   ++Plrd++G+v g+++i+rDiT+
  gi|386001155|ref|YP_005919454.1| 435 MTFHAVKVPLRDDRGQVTGICGIARDITD 463
                                       ****************************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.4
                             PAS_4  29 gappeellGktlaellpee..daarleralrrvl 60 
                                       g  + + +  +lae +p    d+ r+++al+ +l
  gi|386001155|ref|YP_005919454.1| 757 GELRSRGIKVSLAEGWPRVrvDRLRVQEALTNLL 790
                                       5567788888999999999888888888887766 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.13   1.6e+02      16      51 ..     295     339 ..     292     360 .. 0.65
   2 !   37.4   0.0   1.6e-12   1.9e-09       2      64 ..     668     732 ..     667     734 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHC.............T-HSSCHHHHHHHHHHHHHH CS
                             HisKA  16 PLsailgnaeaLkre...........gklteelkeyletiesearrl 51 
                                       PL++i   +ea++++           g+   el+ + e+i +  ++l
  gi|386001155|ref|YP_005919454.1| 295 PLATITSSVEAIREQekgqgsriptvGP--AELATLAESINEMLDHL 339
                                       9***********8877788877665422..34444444444433333 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsri 64 
                                       ++rf+ +v+H+Lr PL +i+g++  L+++  +   ++ k  l+ ie+ +  +dhl++d L lsr 
  gi|386001155|ref|YP_005919454.1| 668 MERFVYTVSHDLRSPLVTIQGFVGFLREDlsALDGDKIKIDLAMIEEAVLKMDHLLKDTLSLSRV 732
                                       689***********************99777444467777***********************96 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   4.8e-12   5.8e-09       2     104 .]     362     463 ..     361     463 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4.8e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d+i+i +p+ r + +N+ ++r+++  +  +lg + + +f  ++e++ r+r+      + +++ +ev   ++ g+ + 
  gi|386001155|ref|YP_005919454.1| 362 DCIFIKDPKSRYVLVNPVMERIFQLPASKMLGERDEVFF--SAETAARIREKDAGVLSgEPFVGEVSAHTRAGSSMT 436
                                       89***99***************************99999..6666666666666666678***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       +++  +p++dd g ++gi +i rDit+
  gi|386001155|ref|YP_005919454.1| 437 FHAVKVPLRDDRGQVTGICGIARDITD 463
                                       **************************6 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.7     8e+03      90     109 ..     439     459 ..     413     473 .. 0.71
   2 !   36.2   0.0   6.9e-12   8.3e-09       1     132 [.     493     637 ..     493     638 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.7
                                       EEEEEEEE.TTEEEEEEEEEE CS
                               GAF  90 slvvPlvn.dgelwGllvlhn 109
                                       ++ vPl++ +g++ G+  + +
  gi|386001155|ref|YP_005919454.1| 439 AVKVPLRDdRGQVTGICGIAR 459
                                       567999977999998876655 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 6.9e-12
                                       SHHHHHHHHHHHHHHHHTESEEEEEE.EEETTEEECEEEEECC....EEEETTSHHHH............HHHHHSS CS
                               GAF   1 dleelldtvveelrellgadrvalyl.pdydGlhydipqasrw....lfmkngrgicg............qvlatgq 60 
                                       d++++   v++ l+e+++adr+ ++  ++ dG     +q  +w    ++++ + ++ +            ++++ g+
  gi|386001155|ref|YP_005919454.1| 493 DIDQIIIDVLQLLGEAVEADRAYIFEnQTVDGEVL-MSQRYEWtkgeVEPQINNPVLQslpyhpdsstfyEIISRGR 568
                                       78999999****************98755677444.55555555554222223332223333334444557777788 PP

                                       SEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHH CS
                               GAF  61 plvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvava 132
                                       p v       +      +r +l++ gi+s l vP++++++lwG + ++++++   ++  e+ +lqv a  ++ a
  gi|386001155|ref|YP_005919454.1| 569 PYVGL---VKDLPES--ERAYLAPQGIVSILIVPIFVEDRLWGFIGFDDCHRerFWSNGEISVLQVAAGSIGGA 637
                                       87755...2333222..468999**************************7777567************988765 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   8.6e-12     1e-08       2     113 .]     352     461 ..     351     461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 8.6e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+i+++++d if+ D + r ++vN+ +e++++l+++ +lg+    +++ e+ a + ++     ++g e+  ge+s
  gi|386001155|ref|YP_005919454.1| 352 RFRTIVDTAHDCIFIKDPKSRYVLVNPVMERIFQLPASKMLGERDEVFFSAET-AARIREKDAGVLSG-EPFVGEVS 426
                                       79****************************************98776777663.22333333444555.55555999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         +r g+   ++   +p+rd  g+++g++g++rdi
  gi|386001155|ref|YP_005919454.1| 427 AHTRAGSSMTFHAVKVPLRDDRGQVTGICGIARDI 461
                                       999*******************************8 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   1.5e+03      94     126 ..     440     472 ..     394     474 .. 0.78
   2 !   24.4   0.0   2.4e-08   2.8e-05      11     136 ..     501     637 ..     492     638 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                       EEEEE-T.TS---EEEEES......--HHHHHHH CS
                             GAF_2  94 lavPlis.egrvvGvlnlyankppafdeedlelL 126
                                       + vPl++ +g+v G+ ++ a +  +  e+ +elL
  gi|386001155|ref|YP_005919454.1| 440 VKVPLRDdRGQVTGICGI-ARDITDIKEAGVELL 472
                                       669****88*****9998.777777777777776 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.4e-08
                                       HHHHHHH.SS..EEEEEEE-.TTS-EEEE.......EEEES-TTSTT-S-B--....-TTHHHHHHHHTS-EE.ES- CS
                             GAF_2  11 vldelve.lgaalgyillvd.ddgglrla.......awgeaeeefgaaldrpl....geglvgealrtgrpvi.lnd 73 
                                       vl+ l e + a+ +yi + +  dg+  ++       + ge e++ +  + ++l    +++ + e++  grp + l  
  gi|386001155|ref|YP_005919454.1| 501 VLQLLGEaVEADRAYIFENQtVDGE--VLmsqryewTKGEVEPQINNPVLQSLpyhpDSSTFYEIISRGRPYVgL-- 573
                                       5666655345667777774433333..223354434333333333222222223343444688999999999953.. PP

                                       GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......-.-HHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppaf.deedlelLeelaeqiaia 136
                                       +++ p + ++ ++  g+ s+l+vP++ e+r+ G++++   ++++f +  ++++L+  a+ i+ a
  gi|386001155|ref|YP_005919454.1| 574 VKDLPESERAYLAPQGIVSILIVPIFVEDRLWGFIGFDDCHRERFwSNGEISVLQVAAGSIGGA 637
                                       77788889999999*************99********888888877************999865 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   5.8e-08   6.9e-05       5      52 ..     291     340 ..     287     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.8e-08
                                       TTHHHHHHHHHHHHHHTT..TBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   5 rilrPLrrLaraarriaa..GdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       +il PL  +++++++i++      +r+p+ g+ E+++La+++N+Mld+L+
  gi|386001155|ref|YP_005919454.1| 291 SILMPLATITSSVEAIREqeKGQGSRIPTVGPAELATLAESINEMLDHLE 340
                                       677799***********744244559**********************97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.4e-07   0.00017       2      48 ..     352     395 ..     351     411 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgql 48 
                                       r+r+++++++d i++ d   r v vN+ +++++ ++   ++g    ++
  gi|386001155|ref|YP_005919454.1| 352 RFRTIVDTAHDCIFIKDPKSRYVLVNPVMERIFQLPaSKMLG----ER 395
                                       9*************6664449*************77433333....33 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.8e-07   0.00045       9      92 ..     785     874 ..     778     881 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-07
                       HATPase_c_5   9 ilgnlLdNAieacskieeekrfIrltvrekk.ksliisieNsyegek.......kklesskskkeehGiGlksirei 77 
                                        l nlLdN+i  + + +  +++I++  r +  +++++  +N +  +        + + +   ++e  G+Gl  +r+i
  gi|386001155|ref|YP_005919454.1| 785 ALTNLLDNSIKYMGDRP--HPEIEVGWRPEGeETVFFVRDNGIGMDPdqwekvfGLFYKIDPDSEGSGVGLAIVRRI 859
                                       589************99..8********76626677777888766442243233334477999************** PP

                       HATPase_c_5  78 vkkykgnlsieaedg 92 
                                       ++ ++g ++ie e+g
  gi|386001155|ref|YP_005919454.1| 860 IEVHGGRIWIESEEG 874
                                       ***********9987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     2e-06    0.0023       4      56 ..     783     838 ..     780     852 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                       HATPase_c_3   4 ekAlaelvdNsld..Adaenvkievnknr.gktgeivieDdGkGmseeelknalrl 56 
                                       ++Al+ l+dNs+   +d  + +iev  ++ g+++ + ++D+G Gm++++ ++++ l
  gi|386001155|ref|YP_005919454.1| 783 QEALTNLLDNSIKymGDRPHPEIEVGWRPeGEETVFFVRDNGIGMDPDQWEKVFGL 838
                                       78*********9988888886666664433899***************99998764 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.25     3e+02      64     103 ..     418     460 ..     406     478 .. 0.72
   2 !   13.2   0.0     7e-05     0.084       1     126 [.     493     637 ..     493     638 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
                             GAF_3  64 gevvsepsfaeedg..lpdraalavPLvagr.qviGvlalast 103
                                       ge++++  +a++ +  + + +a+ vPL++ r qv G+ ++a++
  gi|386001155|ref|YP_005919454.1| 418 GEPFVGEVSAHTRAgsSMTFHAVKVPLRDDRgQVTGICGIARD 460
                                       6666666665542211233455669****99******999875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7e-05
                             GAF_3   1 sldellekllkllvkllgaevgalll...ldedgnkl.qvaagw.dgkpalse.......sld..edsalarralss 63 
                                       ++d+++ ++l+ll +++ a+++ +++   +d  g+ l   +  w +g+  + +       sl+   ds+ + + +s+
  gi|386001155|ref|YP_005919454.1| 493 DIDQIIIDVLQLLGEAVEADRAYIFEnqtVD--GEVLmSQRYEWtKGEVEP-QinnpvlqSLPyhPDSSTFYEIISR 566
                                       6899*********************975533..333324445554333333.23446666888777777777999** PP

                             GAF_3  64 gevvse.....psfaeedglpd..raalavPLvagrqviGvlalastkpra.fdaedlelleslArqiata 126
                                       g ++++     p+++++   p+   ++l+vP+ +++++ G++++   + +  +++ + + l+  A+ i+ a
  gi|386001155|ref|YP_005919454.1| 567 GRPYVGlvkdlPESERAYLAPQgiVSILIVPIFVEDRLWGFIGFDDCHRERfWSNGEISVLQVAAGSIGGA 637
                                       ***99977666555554444433378899***************877766647999999999999988876 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 !   15.0   0.0   1.5e-05     0.018      33     112 ..     779     863 ..     748     883 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                       HATPase_c_2  33 rlaveEactNave..hayleap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep....keslkegGrGl 102
                                       rl v+Ea+tN       y +++ + ++ev ++ ++e+ ++ v+D+G g dp ++++     +    + + + +G+Gl
  gi|386001155|ref|YP_005919454.1| 779 RLRVQEALTNLLDnsIKYMGDRpHPEIEVGWRPEGEETVFFVRDNGIGMDPDQWEKVFG--LfykiDPDSEGSGVGL 853
                                       56688999888752234555555899**************************9988644..24577999999***** PP

                       HATPase_c_2 103 alikglvDev 112
                                       a+++++ +  
  gi|386001155|ref|YP_005919454.1| 854 AIVRRIIEVH 863
                                       ****998765 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0025         3      33      97 ..      64     121 ..      41     172 .. 0.74
   2 ?    0.7   0.0      0.32   3.8e+02     118     164 ..     408     465 ..     319     473 .. 0.55
   3 ?    2.7   0.1     0.075        90      56     157 ..     494     611 ..     469     611 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0025
                          dCache_1  33 aetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvdadGqviassdpssppn 97 
                                       ae  +   + +d++        ++++ +q+ l+s+  s  d++ + ++d++G++++s   +    
  gi|386001155|ref|YP_005919454.1|  64 AEDWGHWNDTRDFVI------GENDQYIQDNLNSWTLSGLDVDFMIYYDRSGNLFYSRAFN-HAT 121
                                       444444455555555......5689*********9999999***************65444.333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.32
                          dCache_1 118 g.........gkpvisdpy..vdqtggkpvi..tiavpiyddsgkfiGvlaadldldnlq 164
                                                 g+p+++++   +  + g +++  ++ vp++dd g+++G+ +++ d++++ 
  gi|386001155|ref|YP_005919454.1| 408 IrekdagvlsGEPFVGEVSahT--RAGSSMTfhAVKVPLRDDRGQVTGICGIARDITDIK 465
                                       3344555556677777775322..223333301444677889999999999888888776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.075
                          dCache_1  56 sreslqallksilksnpdisgvylvda...dGqviassdpssppnleg...........tddpadrdwykealaggg 118
                                       +++++ + l+ + ++ +  +  y++ +   dG+v++s ++++ ++ ++            + p ++  + e++++g 
  gi|386001155|ref|YP_005919454.1| 494 IDQIIIDVLQLLGEAVE-ADRAYIFENqtvDGEVLMSQRYEWTKGEVEpqinnpvlqslPYHPDSST-FYEIISRG- 567
                                       56666666666655553.45566665556699*****999999888779*66666655544443333.66788888. PP

                          dCache_1 119 gkpvisdpy...vdqt......ggkpvitiavpiyddsgkfiGvlaad 157
                                        +p+++ +       +       +  v  ++vpi+++  + +G +++d
  gi|386001155|ref|YP_005919454.1| 568 -RPYVGLVKdlpE--SeraylaPQGIVSILIVPIFVE-DRLWGFIGFD 611
                                       .887777765442..1446775556999999****96.7899988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 5277.49
//
Query:       gi|386001156|ref|YP_005919455.1|  [L=155]
Description: Response regulator receiver protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-20   72.4   0.0    3.8e-20   72.1   0.0    1.1  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   2.1e-24   3.8e-20       1     111 [.      19     138 ..      19     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 2.1e-24
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH......ESEEEEESSCSSSEHHHHHHHHHHCT. CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek......vdlillDinmpgmdGlellkeireed. 69 
                                       +l+v+D+ + ++l+ +++e+ g+  +++  +dgk+al++l+ ++      + ++llD+++p++dG+e+l++i++ + 
  gi|386001156|ref|YP_005919455.1|  19 ILLVEDNNAHAMLIMRAFERLGFtGRIEWLRDGKAALDYLRLHEgggrslPRMVLLDLRLPKVDGHEVLSQIKRSEr 95 
                                       89*******************99669**************8888889999**********************99988 PP

                                       .TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  70 .pelpviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                        + +pv++lt+ ++++d+ +a++  ++ +l Kp++ e+L+  +
  gi|386001156|ref|YP_005919455.1|  96 lRAIPVVVLTTSTSDDDLRRAYSNHVNSYLIKPLSFEDLKRTV 138
                                       999************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 960.79
//
Query:       gi|386001157|ref|YP_005919456.1|  [L=254]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for 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-14   51.3  12.2    5.8e-13   48.6   1.9    4.2  4  Fer4_5         4Fe-4S binding domain
    1.8e-11   44.5   4.7    6.2e-06   26.7   0.2    2.7  2  Fer4_7         4Fe-4S dicluster domain
      2e-11   43.8  22.0    1.4e-09   37.9   9.8    2.6  3  Fer4_9         4Fe-4S dicluster domain
    7.5e-09   35.6  21.5    5.9e-08   32.7  11.3    2.8  4  Fer4_10        4Fe-4S dicluster domain
    7.6e-09   35.0  22.3    0.00014   21.6   2.2    3.9  4  Fer4           4Fe-4S binding domain
    1.2e-06   28.5  18.2     0.0084   16.5   1.5    3.8  3  Fer4_4         4Fe-4S binding domain
    1.4e-06   28.1  19.6    7.5e-05   22.6   1.4    3.0  3  Fer4_6         4Fe-4S binding domain
    1.5e-06   28.6  12.4     0.0068   16.9   4.8    2.8  2  Fer4_17        4Fe-4S dicluster domain
    1.7e-06   28.9   7.8       0.01   16.8   0.3    3.3  4  Fer4_16        4Fe-4S double cluster binding domain
    2.3e-06   27.8   5.7    2.3e-06   27.8   5.7    2.5  3  Fer4_18        4Fe-4S dicluster domain
    4.1e-06   26.8  13.1     0.0023   18.0   3.4    3.1  3  Fer4_21        4Fe-4S dicluster domain
    1.6e-05   24.7  11.7    4.3e-05   23.4   1.8    3.4  4  Fer4_2         4Fe-4S binding domain
    0.00013   21.0   1.6     0.0002   20.3   1.6    1.2  1  MscS_TM        Mechanosensitive ion channel inner membrane do
    0.00037   20.9  15.7     0.0048   17.3  12.7    2.7  3  Fer4_8         4Fe-4S dicluster domain
     0.0019   19.0  12.4     0.0058   17.5   0.8    2.7  2  Fer4_22        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.3  10.2       0.18   12.6   1.7    2.5  2  Fer4_15        4Fe-4S single cluster domain
      0.039   14.5  16.0       0.08   13.5   0.9    3.2  3  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
      0.056   14.4   5.3      0.056   14.4   5.3    3.6  4  Fer4_3         4Fe-4S binding domain
       0.19   11.5   5.3       0.21   11.4   0.2    2.7  3  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
       0.19   10.9   8.1      0.034   13.4   4.1    1.6  2  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   1.9   6.4e-16   5.8e-13       4      45 ..      46      87 ..      43      89 .. 0.88
   2 ?   -0.6   0.5       1.5   1.3e+03       3      14 ..      99     110 ..      92     116 .. 0.63
   3 !   15.2   2.9   1.7e-05     0.016      10      46 ..     145     182 ..     137     184 .. 0.67
   4 ?   -0.0   0.0      0.99   8.8e+02      24      32 ..     201     209 ..     201     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 6.4e-16
                            Fer4_5  4 lllilflaivlvtllfGRafCgWiCPfGalqellakllrrkl 45
                                       +l  f++i++ +l++GR++CgW+CP G lqe+++++  rk 
  gi|386001157|ref|YP_005919456.1| 46 GGLMVFILIFISSLFLGRLWCGWLCPAGGLQEIYFQINDRKT 87
                                      578999*****************************9776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                            Fer4_5   3 llllilflaivl 14 
                                       ++ll+++++i++
  gi|386001157|ref|YP_005919456.1|  99 IFLLLFAPLILA 110
                                       455555556655 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.7e-05
                            Fer4_5  10 l.aivlvtllfGR.afCgWiCPfGalqellakllrrklg 46 
                                       + +i ++++  GR  fC ++CP+ +++ + +k +r  ++
  gi|386001157|ref|YP_005919456.1| 145 ItFITIFAIAAGRrGFCHYFCPIAVIMIIGRK-IRNLFR 182
                                       41444444447777*********999887776.666555 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.99
                            Fer4_5  24 CgWiCPfGa 32 
                                       C+  CP G+
  gi|386001157|ref|YP_005919456.1| 201 CSTTCPMGL 209
                                       9999**996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   6.9e-09   6.2e-06       6      51 ..     159     208 ..     158     209 .. 0.76
   2 !   19.0   0.2   1.8e-06    0.0016       2      17 ..     225     240 ..     210     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 6.9e-09
                            Fer4_7   6 gaCvaaCpvkaieldeeenek..gt..ekveidpekClgCgaCvavCPtg 51 
                                       g+C   Cp  +i++  ++  +  +    ++  d ++C+gCg+C ++CP g
  gi|386001157|ref|YP_005919456.1| 159 GFCHYFCPIAVIMIIGRKIRNlfRWpaLRLFADGDRCTGCGRCSTTCPMG 208
                                       79***********9987444434222133466889*************87 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                            Fer4_7   2 CigCgaCvaaCpvkai 17 
                                       Ci Cg Cv+aCp ++i
  gi|386001157|ref|YP_005919456.1| 225 CILCGGCVDACPKGVI 240
                                       6666666666666665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.6   4.1e+03       8      23 ..      66      81 ..      65      89 .. 0.68
   2 !   19.0   4.2   1.3e-06    0.0012       8      49 ..     161     208 ..     157     208 .. 0.92
   3 !   37.9   9.8   1.6e-12   1.4e-09       1      51 []     194     240 ..     194     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.6
                            Fer4_9  8 CveaCpagvvvedaae 23
                                      C   Cpag  +e  ++
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAGGLQEIYFQ 81
                                      5556998888776665 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.3e-06
                            Fer4_9   8 CveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkg 49 
                                       C++ Cp  v++    +  +  r+         ++C+gCg+C   Cp g
  gi|386001157|ref|YP_005919456.1| 161 CHYFCPIAVIMIIGRKIRNLFRWPALrlfadgDRCTGCGRCSTTCPMG 208
                                       9************99999999887779*****9*************86 PP

  == domain 3  score: 37.9 bits;  conditional E-value: 1.6e-12
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +CtgCg+C + Cp+g+ v d ++r +  +a    +Ci Cg Cv+aCpkg+i
  gi|386001157|ref|YP_005919456.1| 194 RCTGCGRCSTTCPMGLDVLDMVQRRRMEDA----ECILCGGCVDACPKGVI 240
                                       6*********************99987655....5*************976 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.3   3.9e+03      18      32 ..      69      78 ..      66      89 .. 0.53
   2 ?   -1.9   0.0       4.1   3.7e+03      15      21 ..     161     167 ..     159     178 .. 0.75
   3 !   32.7  11.3   6.6e-11   5.9e-08       4      56 .]     190     236 ..     187     236 .. 0.85
   4 !   15.7   2.5   1.3e-05     0.012       5      21 ..     221     237 ..     217     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.3
                           Fer4_10 18 aCPadltsvgakgea 32
                                       CPa     g+ +e+
  gi|386001157|ref|YP_005919456.1| 69 LCPA-----GGLQEI 78
                                      6999.....333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                           Fer4_10  15 CvkaCPa 21 
                                       C  +CP 
  gi|386001157|ref|YP_005919456.1| 161 CHYFCPI 167
                                       7778887 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 6.6e-11
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        d d+C++Cg+C + CP+      + +  +  ++ r    +C+ cg Cv+aCP
  gi|386001157|ref|YP_005919456.1| 190 ADGDRCTGCGRCSTTCPM------GLDVLDMVQRRRMEDAECILCGGCVDACP 236
                                       6889**************......55666666666778889***********9 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 1.3e-05
                           Fer4_10   5 dddtCirCgkCvkaCPa 21 
                                       +d  Ci Cg Cv+aCP 
  gi|386001157|ref|YP_005919456.1| 221 EDAECILCGGCVDACPK 237
                                       67789999999999997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.8   1.6e+03      14      21 ..      66      73 ..      65      76 .. 0.79
   2 ?    1.7   0.2      0.29   2.6e+02      12      23 ..     159     170 ..     159     171 .. 0.86
   3 !   21.6   2.2   1.5e-07   0.00014       4      21 ..     191     208 ..     189     209 .. 0.91
   4 !   21.3   5.1   1.8e-07   0.00016       7      23 ..     224     240 ..     221     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                                      HHHHSTTT CS
                              Fer4 14 CvevCPvg 21
                                      C   CP g
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAG 73
                                      7788**87 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                                       THHHHHSTTTEE CS
                              Fer4  12 GaCvevCPvgAI 23 
                                       G C   CP  +I
  gi|386001157|ref|YP_005919456.1| 159 GFCHYFCPIAVI 170
                                       78******9887 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.5e-07
                                       ETTTSSS-THHHHHSTTT CS
                              Fer4   4 deekCigCGaCvevCPvg 21 
                                       d ++C+gCG+C   CP g
  gi|386001157|ref|YP_005919456.1| 191 DGDRCTGCGRCSTTCPMG 208
                                       569*************86 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 1.8e-07
                                       TSSS-THHHHHSTTTEE CS
                              Fer4   7 kCigCGaCvevCPvgAI 23 
                                        Ci CG Cv++CP g+I
  gi|386001157|ref|YP_005919456.1| 224 ECILCGGCVDACPKGVI 240
                                       6**************99 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.063        57       8      15 ..     159     166 ..     157     179 .. 0.90
   2 !   14.8   4.4   3.4e-05     0.031       2      17 .]     193     208 ..     192     208 .. 0.94
   3 !   16.5   1.5   9.3e-06    0.0084       3      16 ..     224     237 ..     219     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.063
                            Fer4_4   8 gsCvaaCP 15 
                                       g C+++CP
  gi|386001157|ref|YP_005919456.1| 159 GFCHYFCP 166
                                       57*****9 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.4e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       +rC+gCg+C  +CP+g
  gi|386001157|ref|YP_005919456.1| 193 DRCTGCGRCSTTCPMG 208
                                       8*************86 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 9.3e-06
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        Ci Cg Cv+aCP 
  gi|386001157|ref|YP_005919456.1| 224 ECILCGGCVDACPK 237
                                       5************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3       9.3   8.4e+03      15      23 ..     161     169 ..     159     170 .. 0.67
   2 !   22.6   1.4   8.4e-08   7.5e-05       5      22 ..     191     208 ..     189     212 .. 0.89
   3 !   14.9   5.2   2.3e-05     0.021       9      24 .]     225     240 ..     222     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.3
                            Fer4_6  15 CvrvCPega 23 
                                       C   CP ++
  gi|386001157|ref|YP_005919456.1| 161 CHYFCPIAV 169
                                       777799666 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 8.4e-08
                            Fer4_6   5 dpdkCigCgdCvrvCPeg 22 
                                       d d+C+gCg+C + CP+g
  gi|386001157|ref|YP_005919456.1| 191 DGDRCTGCGRCSTTCPMG 208
                                       669*************97 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 2.3e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci Cg Cv++CP g+i
  gi|386001157|ref|YP_005919456.1| 225 CILCGGCVDACPKGVI 240
                                       ************9997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   4.8   7.6e-06    0.0068      44      61 .]     193     210 ..     159     210 .. 0.87
   2 !   15.5   0.8   2.1e-05     0.018      44      60 ..     223     239 ..     212     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.6e-06
                           Fer4_17  44 slCieCgeCerkCPqgld 61 
                                       ++C++Cg+C++ CP+gld
  gi|386001157|ref|YP_005919456.1| 193 DRCTGCGRCSTTCPMGLD 210
                                       79**************98 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.1e-05
                           Fer4_17  44 slCieCgeCerkCPqgl 60 
                                        +Ci Cg+C+ +CP+g+
  gi|386001157|ref|YP_005919456.1| 223 AECILCGGCVDACPKGV 239
                                       68************986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.4   6.6e+03       8      20 ..      66      78 ..      65      91 .. 0.63
   2 ?   -1.2   0.0       4.5     4e+03       8      15 ..     161     168 ..     156     172 .. 0.65
   3 !   14.8   0.3   4.5e-05      0.04      52      66 ..     193     207 ..     184     219 .. 0.79
   4 !   16.8   0.3   1.1e-05      0.01       2      19 ..     225     242 ..     224     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.4
                           Fer4_16  8 CaevCPtnaikek 20
                                      C   CP++ ++e 
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAGGLQEI 78
                                      5556888877766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.5
                           Fer4_16   8 CaevCPtn 15 
                                       C   CP +
  gi|386001157|ref|YP_005919456.1| 161 CHYFCPIA 168
                                       55666655 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 4.5e-05
                           Fer4_16  52 eaitgCdiCqdvCPa 66 
                                        ++tgC++C ++CP+
  gi|386001157|ref|YP_005919456.1| 193 DRCTGCGRCSTTCPM 207
                                       567777777777776 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 1.1e-05
                           Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                       C+ Cg C+++CP ++i+ 
  gi|386001157|ref|YP_005919456.1| 225 CILCGGCVDACPKGVIHY 242
                                       ***************985 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.8e+03       6      21 ..      66      81 ..      64      94 .. 0.76
   2 ?   -0.4   0.2       1.5   1.3e+03       4      14 ..     159     169 ..     157     176 .. 0.80
   3 !   27.8   5.7   2.6e-09   2.3e-06      58     101 ..     192     242 ..     172     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                           Fer4_18  6 cvyvcPyarvqsvlyd 21
                                      c  +cP + +q + ++
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAGGLQEIYFQ 81
                                      8899999999998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                           Fer4_18   4 dvcvyvcPyar 14 
                                        +c y cP a 
  gi|386001157|ref|YP_005919456.1| 159 GFCHYFCPIAV 169
                                       6899***9875 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 2.6e-09
                           Fer4_18  58 agdcidcescvkvcPtgidirkGlq......leciscllcidacdk.vmek 101
                                          c+ c+ c + cP+g+d+ + +q       eci c+ c+dac k v++ 
  gi|386001157|ref|YP_005919456.1| 192 GDRCTGCGRCSTTCPMGLDVLDMVQrrrmedAECILCGGCVDACPKgVIHY 242
                                       456****************98877744433469***********7635554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.9   2.6e+03      14      29 ..      66      81 ..      64      91 .. 0.67
   2 !   18.0   3.4   2.6e-06    0.0023      13      53 ..     160     207 ..     158     214 .. 0.63
   3 !   11.2   2.5   0.00034      0.31       3      21 ..     220     238 ..     218     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                           Fer4_21 14 CliaCedtshqaieid 29
                                      C   C+ ++ q i ++
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAGGLQEIYFQ 81
                                      7777888888888544 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.6e-06
                           Fer4_21  13 kCliaCedtshqai..eidaktvl.......kvvedeCvGCnlCssvCPv 53 
                                        C+  C+ + +  i  +   ++ +           d+C+GC  Cs+ CP+
  gi|386001157|ref|YP_005919456.1| 160 FCHYFCPIAVIMIIgrK--IRNLFrwpalrlFADGDRCTGCGRCSTTCPM 207
                                       69999996555555432..22211233332245689*************8 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00034
                           Fer4_21   3 idedkCigCgkCliaCedt 21 
                                       +++++Ci Cg C+ aC+++
  gi|386001157|ref|YP_005919456.1| 220 MEDAECILCGGCVDACPKG 238
                                       5678888888888888864 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3       8.4   7.5e+03      16      22 .]      66      72 ..      66      72 .. 0.68
   2 ?   -1.1   0.1       2.9   2.6e+03      14      21 ..     159     166 ..     159     166 .. 0.84
   3 !   23.4   1.8   4.8e-08   4.3e-05       3      21 ..     188     206 ..     186     207 .. 0.91
   4 !   13.7   2.6   5.5e-05     0.049       7      21 ..     223     236 ..     218     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.4
                            Fer4_2 16 CvsaCPa 22
                                      C + CPa
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPA 72
                                      5567997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                            Fer4_2  14 gaCvsaCP 21 
                                       g C   CP
  gi|386001157|ref|YP_005919456.1| 159 GFCHYFCP 166
                                       679999*9 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 4.8e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                        ++d drC+gCg C + CP
  gi|386001157|ref|YP_005919456.1| 188 LFADGDRCTGCGRCSTTCP 206
                                       68899************** PP

  == domain 4  score: 13.7 bits;  conditional E-value: 5.5e-05
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       ++ Ci Cg Cv+aCP
  gi|386001157|ref|YP_005919456.1| 223 AE-CILCGGCVDACP 236
                                       45.***********9 PP

>> MscS_TM  Mechanosensitive ion channel inner membrane domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.6   2.3e-07    0.0002     119     218 ..       8     117 ..       6     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                           MscS_TM 119 vrrlrralkrlilvllplllvlilaealsdalard.vlGrlaflllllllavflarl....lrpalglyankkeeek 190
                                       ++rlr+al  l +vl+p+ +v i       ++ ++ v+G l++++l ++ ++fl rl    l pa+gl++ + + ++
  gi|386001157|ref|YP_005919456.1|   8 RQRLRKALIILSFVLMPITFVYISCPIITRGASEGiVTGGLMVFILIFISSLFLGRLwcgwLCPAGGLQEIYFQIND 84 
                                       689*****************888888887777776245666666677777777766523336799999998888777 PP

                           MscS_TM 191 nsl.....rlrrllylllvlaPlalavlaalGY 218
                                       +++      + + l +ll++aPl+lav +a G+
  gi|386001157|ref|YP_005919456.1|  85 RKTnrvrlNWLKYLIFLLLFAPLILAVHSAGGF 117
                                       77775633344557789999**********998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       8.2   7.4e+03      57      63 ..     161     167 ..     158     170 .. 0.62
   2 !   17.3  12.7   5.3e-06    0.0048       3      65 .]     193     239 ..     191     239 .. 0.82
   3 !   11.9   2.0   0.00027      0.24      50      64 ..     224     238 ..     222     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.2
                            Fer4_8  57 CtevCpv 63 
                                       C   Cp+
  gi|386001157|ref|YP_005919456.1| 161 CHYFCPI 167
                                       6666665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.3e-06
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       ++C++Cg+C ++Cp+  +  ++ +  r e                  +C  cg C+++Cp+g+
  gi|386001157|ref|YP_005919456.1| 193 DRCTGCGRCSTTCPMGLDVLDMVQRRRMED----------------AECILCGGCVDACPKGV 239
                                       69************9999977655444443................36************986 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00027
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                       +C  cg C+++Cp+g
  gi|386001157|ref|YP_005919456.1| 224 ECILCGGCVDACPKG 238
                                       466666666666665 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.8   6.5e-06    0.0058      78      95 ..     191     208 ..     174     209 .. 0.85
   2 !    8.7   1.5    0.0034         3      75      95 ..     218     238 ..     212     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.5e-06
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       +   C+GCgRC+++cp++
  gi|386001157|ref|YP_005919456.1| 191 DGDRCTGCGRCSTTCPMG 208
                                       5678***********976 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                           Fer4_22  75 ekfgesgCvGCgRCieacpvk 95 
                                       ++++   C+ Cg C++acp++
  gi|386001157|ref|YP_005919456.1| 218 RRMEDAECILCGGCVDACPKG 238
                                       5678899***********986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.7    0.0002      0.18       4      19 ..     191     206 ..     189     216 .. 0.90
   2 ?    7.9   1.6    0.0057       5.1       5      20 ..     222     237 ..     219     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                           Fer4_15   4 DrdaCigcglCvaeap 19 
                                       D d+C+gcg+C + +p
  gi|386001157|ref|YP_005919456.1| 191 DGDRCTGCGRCSTTCP 206
                                       89************98 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0057
                           Fer4_15   5 rdaCigcglCvaeape 20 
                                         +Ci cg Cv+++p+
  gi|386001157|ref|YP_005919456.1| 222 DAECILCGGCVDACPK 237
                                       568***********97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       4.8   4.3e+03      12      17 ..      66      71 ..      64      73 .. 0.88
   2 ?   13.5   0.9   8.9e-05      0.08       2      18 ..     191     207 ..     190     217 .. 0.90
   3 ?    9.4   2.7    0.0017       1.6       4      18 ..     223     237 ..     220     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.8
                           Fer4_13 12 CvelaP 17
                                      C++l+P
  gi|386001157|ref|YP_005919456.1| 66 CGWLCP 71
                                      *****9 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.9e-05
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D d+C++cg C  ++P 
  gi|386001157|ref|YP_005919456.1| 191 DGDRCTGCGRCSTTCPM 207
                                       889*************6 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0017
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                        +Ci cg Cv+++P+
  gi|386001157|ref|YP_005919456.1| 223 AECILCGGCVDACPK 237
                                       79************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       6.1   5.5e+03       7      14 ..      66      73 ..      64      74 .. 0.70
   2 ?   -1.7   0.1         9   8.1e+03       7      12 ..     161     166 ..     159     167 .. 0.80
   3 ?    9.9   6.1    0.0017       1.5       1      14 [.     195     208 ..     195     208 .. 0.94
   4 ?   14.4   5.3   6.3e-05     0.056       1      14 [.     225     238 ..     225     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6.1
                            Fer4_3  7 CvevCPvg 14
                                      C   CP g
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAG 73
                                      66678855 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 9
                            Fer4_3   7 CvevCP 12 
                                       C   CP
  gi|386001157|ref|YP_005919456.1| 161 CHYFCP 166
                                       778898 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0017
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       CtgCg+C   CP g
  gi|386001157|ref|YP_005919456.1| 195 CTGCGRCSTTCPMG 208
                                       ************65 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 6.3e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ Cg Cv++CP+g
  gi|386001157|ref|YP_005919456.1| 225 CILCGGCVDACPKG 238
                                       ************98 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.7   3.3e+03      71      96 ..      66      91 ..      60      99 .. 0.63
   2 ?   11.4   0.2   0.00023      0.21      19      48 ..     190     217 ..     185     224 .. 0.82
   3 ?    0.7   1.8      0.46   4.2e+02      20      39 ..     221     238 ..     215     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.7
                                      HHHHS-GGGTGCCS-GGGTTB.---- CS
                           Fer4_20 71 cgrvCpqeelCegaCvlekkgkepva 96
                                      cg +Cp   l e    +++++++ v+
  gi|386001157|ref|YP_005919456.1| 66 CGWLCPAGGLQEIYFQINDRKTNRVR 91
                                      88888876666655555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00023
                                       HHHTT----TT-HHHHCSTT---HHHHHHH CS
                           Fer4_20  19 eeAsRClqCkkapcvkgCPveidipefikk 48 
                                       ++ +RC  C    c+++CP+ +d+ +++++
  gi|386001157|ref|YP_005919456.1| 190 ADGDRCTGC--GRCSTTCPMGLDVLDMVQR 217
                                       5779*****..78**********9888876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.46
                                       HHTT----TT-HHHHCSTT- CS
                           Fer4_20  20 eAsRClqCkkapcvkgCPve 39 
                                       e + C+ C    cv++CP  
  gi|386001157|ref|YP_005919456.1| 221 EDAECILC--GGCVDACPKG 238
                                       4456****..78******76 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.4   1.2e+03     195     212 ..      14      31 ..       3      43 .. 0.59
   2 ?   13.4   4.1   3.8e-05     0.034     115     216 ..      47     151 ..      40     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                     MIG-14_Wnt-bd 195 ilkilaiilavlyflyLl 212
                                       +l+il ++l+ + f+y+ 
  gi|386001157|ref|YP_005919456.1|  14 ALIILSFVLMPITFVYIS 31 
                                       445555555555555554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.8e-05
                     MIG-14_Wnt-bd 115 wflllldiifqsiFlsvLllFwlvff...eslrdeqnrr..ktlsfylpklllvlllwlvllvlalyerleqlkdpf 186
                                        +++++ i++ s+Fl  L + wl+ +   +++  + n+r  +++++ + k l++lll++ l++      + +  dpf
  gi|386001157|ref|YP_005919456.1|  47 GLMVFILIFISSLFLGRLWCGWLCPAgglQEIYFQINDRktNRVRLNWLKYLIFLLLFAPLILAVHSAGGFTAIDPF 123
                                       57999*********************77744445555555689********************************** PP

                     MIG-14_Wnt-bd 187 ysiwss.alilkilaiilavlyflyLlylif 216
                                       y ++ + +   ++  ++ +++y+ + ++ if
  gi|386001157|ref|YP_005919456.1| 124 YYTD-HgI--SIAKEGAYTIFYAQITFITIF 151
                                       *665.432..333333444444433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1458.09
//
Query:       gi|386001158|ref|YP_005919457.1|  [L=401]
Description: hypothetical protein Mhar_0449 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-37  129.1   0.0    3.6e-37  128.8   0.0    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    3.6e-19   69.7   0.0    5.1e-11   42.9   0.0    2.2  2  AAA_15    AAA ATPase domain
    2.9e-12   46.5   0.0    1.1e-10   41.4   0.0    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
    6.3e-06   25.7   0.9      0.045   13.0   0.0    2.4  3  DUF2813   Protein of unknown function (DUF2813)
    3.6e-05   24.4   0.1    4.6e-05   24.0   0.1    1.5  1  AAA_23    AAA domain
    0.00016   21.3   0.0    0.00037   20.2   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0016   19.0   0.0     0.0047   17.4   0.0    1.7  2  ABC_tran  ABC transporter


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.0   1.4e-40   3.6e-37       1     303 []      34     349 ..      34     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 1.4e-40
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       lnvliGpNgsGKSnL++a++ll   ++   +   + ++ggg ++++++  ++ + + ++   ++ ++   r+   +r
  gi|386001158|ref|YP_005919457.1|  34 LNVLIGPNGSGKSNLIEAISLL---RAAPGDIRAVIRRGGGASDWIWKGKPDGEASIDVVISNLRGNLPLRHVLAFR 107
                                       7*********************...7788888888888888889999999999988888888889999999999999 PP

                            AAA_21  78 lersqv...eeklssvet.llesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsr 150
                                        e++ +    e++ ++e+ ++ ++++++++     +v n   +g ++   +++lk+ +v+ +++    ++  + + +
  gi|386001158|ref|YP_005919457.1| 108 EENQTFrlaDERIENKEPfPGFDRPYFYYSYQHGNPVLNVSTKGLHEETEERKLKPETVETDQSILAQRRDPEAYPE 184
                                       9999999996666666663888****************************************999888888888888 PP

                            AAA_21 151 awsllllldglrke...rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer..... 219
                                        ++l++  d++  +   ++g+  if++  + ++++++l++  + l l  ++l+   ++++ i ++ ++l e      
  gi|386001158|ref|YP_005919457.1| 185 VSYLASVYDKIKIYrewYFGRSAIFREPQKADMRNDRLEEDFSNLGLFLNRLRGVPKAKKAILEALHDLYEGlddfd 261
                                       88877777777777*************************999999999999999999998888888888777***** PP

                            AAA_21 220 ......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                             +v  +  +++  +pa+ lSdGt+r+l++l++l +  ++ +l++i+EpE+gLHP +l+++++ll+++s+ ++
  gi|386001158|ref|YP_005919457.1| 262 vsikggTVQVFFTEGDFTIPATRLSDGTLRYLCMLAILCDPTPP-PLICIEEPELGLHPDILPKVADLLNAASE-RT 336
                                       *******************************8888887776666.*****************************.** PP

                            AAA_21 291 QviltTHSpllld 303
                                       Q+i+tTHS  l+d
  gi|386001158|ref|YP_005919457.1| 337 QLIVTTHSDILVD 349
                                       ********98876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   8.8e-09   2.2e-05      19      46 ..      29      55 ..      25      58 .. 0.91
   2 !   42.9   0.0     2e-14   5.1e-11     261     369 .]     238     348 ..     170     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 8.8e-09
                            AAA_15 19 idlseeltvliGkNnsGKSsilealdlF 46
                                      i l++ l+vliG+N+sGKS+++ea+ l+
  gi|386001158|ref|YP_005919457.1| 29 IALES-LNVLIGPNGSGKSNLIEAISLL 55
                                      78999.*******************886 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 2e-14
                            AAA_15 261 k.kilkkkidkikkfnykgkkneeieik..........ddeelplnknGsGvqrllllillileaekkdekeeknvi 326
                                          + kk i +     y g +++ + ik           d+ +p+++ ++G+ r l +  l + +        ++ +
  gi|386001158|ref|YP_005919457.1| 238 GvPKAKKAILEALHDLYEGLDDFDVSIKggtvqvffteGDFTIPATRLSDGTLRYLCM--LAILCDPT-----PPPL 307
                                       25556666666666667777777777777777777788**************997665..45555555.....88** PP

                            AAA_15 327 lliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                       ++iEEPE+ LHp+    +++ll  +++ +  Q+i+tTHS+ ++
  gi|386001158|ref|YP_005919457.1| 308 ICIEEPELGLHPDILPKVADLLNAASERT--QLIVTTHSDILV 348
                                       ****************************9..********9875 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   4.2e-14   1.1e-10       2     205 ..      11     351 ..      10     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.2e-14
                                       EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHC...TT.TTTTTTCHCCCCCC--BTTCSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvL...Gersakklrseklsdlihkskekasvk 75 
                                       +++++ +n  s+  +t  + + +s+++++GpNGSGKsnl++Ai+ +    G+  a   r   +sd i k   ++   
  gi|386001158|ref|YP_005919457.1|  11 VREIRPRNLLSFGPDTEPIAL-ESLNVLIGPNGSGKSNLIEAISLLRaapGDIRAVIRRGGGASDWIWK---GKPDG 83 
                                       677888888899755555555.55*******************65431112222322245567888887...88899 PP

                                       EEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                             SMC_N  76 kaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske................. 135
                                       +a+++++++n   +l+ +       + ++r++++++++ ++++++ke    + +  ++ +                 
  gi|386001158|ref|YP_005919457.1|  84 EASIDVVISNLRGNLPLR------HVLAFREENQTFRLADERIENKEPFPGFDRPYFYYSyqhgnpvlnvstkglhe 154
                                       9******99999982221......23455666667777777777777777777777777777777777777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001158|ref|YP_005919457.1| 155 eteerklkpetvetdqsilaqrrdpeaypevsylasvydkikiyrewyfgrsaifrepqkadmrndrleedfsnlgl 231
                                       7888888888******************************************************************* PP

                                       ....................................................CS-HHH.HHHHHHHHHHHHHCCS-- CS
                                       ....................................................xxxxxx.xxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ....................................................lLSgGe.ktLvalaLlfAiqkvkpa 159
                                                                                            LS G  + L++la+l       p 
  gi|386001158|ref|YP_005919457.1| 232 flnrlrgvpkakkailealhdlyeglddfdvsikggtvqvfftegdftipatRLSDGTlRYLCMLAIL---CDPTPP 305
                                       *******************************************************9973568888887...788999 PP

                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                       pl ++ e +  L      kva+ll+++s+++Q+iv+++++ ++  +
  gi|386001158|ref|YP_005919457.1| 306 PLICIEEPELGLHPDILPKVADLLNAASERTQLIVTTHSDILVDAM 351
                                       **************************************99888777 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.7e-05     0.045      19      45 ..      29      55 ..      27      62 .. 0.91
   2 ?   -3.0   0.0       1.3   3.4e+03     164     225 ..     151     211 ..     140     254 .. 0.51
   3 !   10.8   0.1   8.2e-05      0.21     284     328 ..     305     351 ..     298     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                           DUF2813 19 lsleentvLiGENaWGKSSLldALsli 45
                                      + le+++vLiG N  GKS L++A+sl+
  gi|386001158|ref|YP_005919457.1| 29 IALESLNVLIGPNGSGKSNLIEAISLL 55
                                      6899*********************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                           DUF2813 164 rlredtleaelkeerlerrlenllrrllskpqklse.delkselqalssllehYfleksasrk 225
                                        l+e+t+e +lk e +e  ++ l++r  ++p+ + e + l s +  ++   e+Yf   +  r+
  gi|386001158|ref|YP_005919457.1| 151 GLHEETEERKLKPETVETDQSILAQR--RDPEAYPEvSYLASVYDKIKIYREWYFGRSAIFRE 211
                                       56666666666666666666555443..33444433344455555555555566654433333 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 8.2e-05
                           DUF2813 284 rPilllEdpearLHPtmlaiaWellellP..lQkiltTNSveLlsqv 328
                                        P++ +E+pe  LHP  l  + +ll+     +Q i+tT S  L+ ++
  gi|386001158|ref|YP_005919457.1| 305 PPLICIEEPELGLHPDILPKVADLLNAASerTQLIVTTHSDILVDAM 351
                                       59***********************987533899******9888766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.8e-08   4.6e-05       5      41 ..      17      54 ..      13     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.8e-08
                            AAA_23  5 enfrsf..rdqe.idFskgltlItGpNGaGKTTildAikl 41
                                      +n+ sf  + +e i ++  l++++GpNG+GK+ +++Ai l
  gi|386001158|ref|YP_005919457.1| 17 RNLLSFgpD-TEpIALE-SLNVLIGPNGSGKSNLIEAISL 54
                                      677777433.4448887.7*******************86 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.5e-07   0.00037      18      45 ..      28      55 ..      15      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-07
                            AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqal 45
                                      +i l++  +l+Gp+GsGKS l+ Ai+ l
  gi|386001158|ref|YP_005919457.1| 28 PIALESLNVLIGPNGSGKSNLIEAISLL 55
                                      566667789****************987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0047      13      42 ..      34      62 ..      28      99 .. 0.85
   2 ?   -2.8   0.0       3.3   8.5e+03     107     125 ..     283     301 ..     257     313 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGei 42
                                      + +++G+nG+GKS L+++++ l   + G+i
  gi|386001158|ref|YP_005919457.1| 34 LNVLIGPNGSGKSNLIEAISLLRA-APGDI 62
                                      5689***************97643.56665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.3
                                       GGS-HHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 107 ssLSgGqkqrvalarallk 125
                                       + LS G  + +++ ++l+ 
  gi|386001158|ref|YP_005919457.1| 283 TRLSDGTLRYLCMLAILCD 301
                                       6799999998888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2275.33
//
Query:       gi|386001159|ref|YP_005919458.1|  [L=332]
Description: putative tRNA pseudouridine synthase B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-25   89.2   0.2    2.6e-25   88.3   0.2    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    1.4e-23   83.9   0.1    1.9e-14   54.3   0.0    3.2  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    2.3e-20   72.4   0.1    1.5e-18   66.6   0.0    2.3  2  DKCLD     DKCLD (NUC011) domain
      2e-18   66.1   1.0    3.4e-18   65.4   1.0    1.4  1  PUA       PUA domain


Domain annotation for each model (and alignments):
>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.2   5.8e-29   2.6e-25       1      63 [.     175     241 ..     175     242 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 5.8e-29
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                       R+Lc+DiG+aLg gAh+eeLRRtr+gpf ++e +vtl++L+da  +++e  de+ L+r +lP+e+al
  gi|386001159|ref|YP_005919458.1| 175 RKLCHDIGLALGSGAHMEELRRTRSGPFrEDETLVTLHELQDAKVIWREtgDETpLRRAVLPVERAL 241
                                       9***************************999999***************98888***********98 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   4.1e-18   1.9e-14       1      53 [.      61     113 ..      61     118 .. 0.96
   2 !   24.6   0.0   5.8e-09   2.6e-05      73     149 .]     115     174 ..     111     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 4.1e-18
                                       HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEE CS
                            TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgae 53 
                                       kr+l+++ +Gh+GtLDp++tG+L+ ++g+ T+++e ll+a KeY++ +rl+a+
  gi|386001159|ref|YP_005919458.1|  61 KRILEIETAGHSGTLDPKVTGILPTMLGDSTRVVETLLSAGKEYVCLMRLHAT 113
                                       89************************************************986 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.8e-09
                                       -HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                            TruB_N  73 teekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                        ++++ ev+++f G i+q+pp  S+vk                 r+ r+ +iy le+le+e p+v + v c++GtYi
  gi|386001159|ref|YP_005919458.1| 115 PRKRVMEVCSEFAGVIYQRPPLKSSVK-----------------RALRTREIYYLEVLEIEGPRVLFLVGCEAGTYI 174
                                       578899*********************.................899*****************************9 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   3.4e-22   1.5e-18      10      58 .]       9      57 ..       2      57 .. 0.94
   2 ?    3.4   0.0     0.017        78       7      36 ..     213     242 ..     210     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 3.4e-22
                                      XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                             DKCLD 10 nydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                      ++++ lvr+e  t+ ++G+sP  Rp++++i+ G+inLDKP +P+SHEVV
  gi|386001159|ref|YP_005919458.1|  9 RTRETLVRREGRTDPRYGVSPEGRPLDQHIRLGCINLDKPPGPTSHEVV 57
                                      78999*******************************************9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                                       ...XXX-EEESS-----TTSS--GGG--HH CS
                             DKCLD   7 lLknydkllvrtehytplpaGssPlkRpie 36 
                                       +L++ + ++  t+ +tpl+  + P++R ++
  gi|386001159|ref|YP_005919458.1| 213 ELQDAKVIWRETGDETPLRRAVLPVERALS 242
                                       577788888899***************997 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   1.0   7.7e-22   3.4e-18       1      73 [.     245     317 ..     245     318 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 7.7e-22
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       +++v+ dgAv+a+++ga L apG+++ e  +eeg+ V+i++ +ge+vav++a + se+++k + g+++++ rv
  gi|386001159|ref|YP_005919458.1| 245 PTLVISDGAVDAICHGAPLAAPGLLRLESGIEEGEKVVIYTLKGEAVAVAVAAMGSEDMMKSATGIVAKTSRV 317
                                       679*****************************************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2514.56
//
Query:       gi|386001160|ref|YP_005919459.1|  [L=179]
Description: cytidylate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-21   76.9   1.1    1.7e-12   47.9   0.6    2.0  2  Cytidylate_kin2  Cytidylate kinase-like family
    2.4e-12   47.0   0.6    5.8e-05   22.9   0.2    2.1  2  Cytidylate_kin   Cytidylate kinase
    5.2e-12   46.4   0.2    7.4e-12   45.9   0.2    1.2  1  AAA_18           AAA domain
    1.4e-07   32.0   0.3    3.4e-07   30.8   0.2    1.7  1  AAA_17           AAA domain
      1e-06   29.1   0.8    4.1e-06   27.1   0.7    2.1  1  AAA_28           AAA domain
     0.0011   19.2   0.4     0.0075   16.4   0.4    1.9  1  SKI              Shikimate kinase
     0.0026   17.9   0.4      0.022   14.9   0.0    2.0  2  ADK              Adenylate kinase
     0.0027   17.8   0.2       0.11   12.7   0.0    2.2  2  AAA_33           AAA domain
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.25   11.3   0.0    1.3  1  Rad17            Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   8.9e-10   1.8e-06       1      54 [.       2      57 ..       2      66 .. 0.89
   2 !   47.9   0.6   8.4e-16   1.7e-12      87     178 ..      65     153 ..      57     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.9e-10
                   Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevde.rs 54
                                      iIT+s+  G+g +t+ + L+++Lgl+ ++  e+++++a++ g+s  e+ ++ e  +
  gi|386001160|ref|YP_005919459.1|  2 IITVSGAPGTGTSTLSRILSKELGLRWVNSgELFRKIASDRGISLGELGRIAEeGP 57
                                      8**********************************************966655254 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 8.4e-16
                   Cytidylate_kin2  87 rvirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgq 163
                                       ++ re+aae ++++ GR + ++L      l+++l a++  r++r+a+re+   e+a ++ k +++ +a +y+ky++ 
  gi|386001160|ref|YP_005919459.1|  65 DAQREMAAEAGGIFEGRLSGHVLDA---DLKILLKADRRLRAERIATREKKLLEDALQEAKGREECEARRYEKYYNI 138
                                       5679999999*************99...8********************9999************************ PP

                   Cytidylate_kin2 164 dwgdaenYdlvlnts 178
                                       d+ d + Ydlv++t 
  gi|386001160|ref|YP_005919459.1| 139 DVRDLSVYDLVIDTG 153
                                       *************95 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.1e-08   6.1e-05       1      37 [.       3      39 ..       3      43 .. 0.96
   2 !   22.9   0.2   2.9e-08   5.8e-05      96     170 ..      57     124 ..      49     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.1e-08
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      i++ G  g+G s+++r+l+++lgl+++++g+l+R +a
  gi|386001160|ref|YP_005919459.1|  3 ITVSGAPGTGTSTLSRILSKELGLRWVNSGELFRKIA 39
                                      8999******************************997 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHH CS
                    Cytidylate_kin  96 pavRailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeR 170
                                       p++  i+ + +re++ +a+ ++eGR  g +v+ da+lKi l+A  + Ra+R ++  ++k     le+ l+e k R
  gi|386001160|ref|YP_005919459.1|  57 PEIDYIIDDAQREMAAEAGGIFEGRLSG-HVL-DADLKILLKADRRLRAERIATR-EKK----LLEDALQEAKGR 124
                                       6777889999***************655.554.9****************97665.333....344444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.2   3.7e-15   7.4e-12       1     122 [.       3     123 ..       3     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3.7e-15
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G+pG+G +tl++ Lsk+lg+     g+  r++a+++g++l++    + e+  + +   d +++++ +      
  gi|386001160|ref|YP_005919459.1|   3 ITVSGAPGTGTSTLSRILSKELGLrwvnsGELFRKIASDRGISLGELGR-IAEEGPEIDYIIDDAQREMAA------ 72 
                                       89********************99***********************99.444444444443445555544...... PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik.....e 122
                                       e++  +++g+l+ ++ +a+ +   + L+a+   ++eR+++R+++  + +     +
  gi|386001160|ref|YP_005919459.1|  73 EAGG-IFEGRLSGHVLDADLK---ILLKADRRLRAERIATREKKLLEDAlqeakG 123
                                       3456.9*********998876...*****************98755544555554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.2   1.7e-10   3.4e-07       2      80 ..       7      82 ..       6     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.7e-10
                                      E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79
                                      G PG G +t+++ l +++g+  ++ G+l+r+ a+++g    + ++++++  e++     ++ ++ +e+a++ g +++g 
  gi|386001160|ref|YP_005919459.1|  7 GAPGTGTSTLSRILSKELGLRWVNSGELFRKIASDRGIsLGELGRIAEEGPEIDY----IIDDAQREMAAEAGGIFEGR 81
                                      9***********************************9834455555555555554....33333344444455566665 PP

                                      S CS
                            AAA_17 80 p 80
                                       
  gi|386001160|ref|YP_005919459.1| 82 L 82
                                      4 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.7   2.1e-09   4.1e-06       2      70 ..       3      74 ..       2     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.1e-09
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaa 70
                                      i ++G+++tG++tl++ L+++ g ++v   E +r+i ++++ + ++  + +e+  ++ + + ++q+e +a+a
  gi|386001160|ref|YP_005919459.1|  3 ITVSGAPGTGTSTLSRILSKElGLRWVnsGELFRKIASDRGISLGELGRIAEEGPEIDYIIDDAQREMAAEA 74
                                      789****************888*******************8888755555888888888888887777666 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   3.8e-06    0.0075       1     136 [.       9     140 ..       9     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCS.SEEEEE-TTGGGSH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleee.glViatGGGavlse 76 
                                       +G+G st+ ++l+k+lgl+++ + el+ k +     + +   ge g  ++E   ++ +++   +   a  GG+++ +
  gi|386001160|ref|YP_005919459.1|   9 PGTGTSTLSRILSKELGLRWVNSGELFRKIASD---RGI-SLGELGRIAEEGPEIDYIIDDAqREMAAEAGGIFEGR 81 
                                       699************************999883...233.247777777788888888877777889999****999 PP

                                       HHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSC CS
                               SKI  77 enrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaad 136
                                        + ++l    + i+L++++   +er++ +++  ll++  +e + +ee + +r + y +++ 
  gi|386001160|ref|YP_005919459.1|  82 LSGHVLD-ADLKILLKADRRLRAERIATREK-KLLEDALQEAKGREECEaRRYEKYYNIDV 140
                                       9999999.9*****************99999.47777777777777777788888887765 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.022       1      37 [.       5      41 ..       5      59 .. 0.84
   2 ?    1.6   0.1      0.13   2.6e+02      74     133 ..      58     133 ..      49     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                                      + GaPg+G  t ++ l k++gl  + +G+l+R+  + 
  gi|386001160|ref|YP_005919459.1|  5 VSGAPGTGTSTLSRILSKELGLRWVNSGELFRKIASD 41
                                      57******************************96643 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                                       TTEEEEESB-SSHHH..HHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT..............GSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxx RF
                               ADK  74 kkgfllDGfPRtveq..aealeelleeekvkldlvleldvpeevlveRltg..............DneetvkkRle 133
                                       + ++++D   R+++   +  +e  l+ +  + dl + l+++  +  eR++                +ee  ++R e
  gi|386001160|ref|YP_005919459.1|  58 EIDYIIDDAQREMAAeaGGIFEGRLSGHVLDADLKILLKADRRLRAERIATrekklledalqeakGREECEARRYE 133
                                       5678888888877531145688889999999999999999999999999985555555555555444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.3e-05      0.11       2      53 ..       3      54 ..       2      80 .. 0.75
   2 ?    3.1   0.3      0.05        99     102     121 ..      93     112 ..      85     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvld 53
                                      + + G+pG+G stl++ l k+lg   ++s +l+r+++ +   s+ ++ r+++
  gi|386001160|ref|YP_005919459.1|  3 ITVSGAPGTGTSTLSRILSKELGLRWVNSGELFRKIASDRGISLGELGRIAE 54
                                      5678****************************99999877777666655544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.05
                            AAA_33 102 vvvetdeetlkeRlakRaan 121
                                       + +++d+++ +eR+a R+++
  gi|386001160|ref|YP_005919459.1|  93 ILLKADRRLRAERIATREKK 112
                                       6799*************996 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.25      47      73 ..       2      28 ..       1      40 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                             Rad17 47 iLLisGPsGCgkstvvkvLskelgikl 73
                                      i+ +sG +G g st  ++Lskelg + 
  gi|386001160|ref|YP_005919459.1|  2 IITVSGAPGTGTSTLSRILSKELGLRW 28
                                      6789********************864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1214.05
//
Query:       gi|386001161|ref|YP_005919460.1|  [L=202]
Description: hypothetical protein Mhar_0451 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-46  155.8   1.5    1.1e-45  155.4   1.5    1.2  1  EMC3_TMCO1    Integral membrane protein EMC3/TMCO1-like
    5.5e-05   23.6   3.4     0.0004   20.8   3.4    2.0  1  DUF4199       Protein of unknown function (DUF4199)
  ------ inclusion threshold ------
      0.092   11.9   1.9      0.093   11.9   1.4    1.3  1  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   1.5   1.9e-49   1.1e-45       9     169 ..      48     199 ..      40     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 1.9e-49
                        EMC3_TMCO1   9 rdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqs 85 
                                           +lP+++v++ ++++tgl+++l+qk+++d++ +++ q++++ +qk++r++q  gdk ++++l+ +q e+ +dqs
  gi|386001161|ref|YP_005919460.1|  48 G---ILPFHVVLFALAAITGLYASLIQKYTMDWDYLKRQQETMRSFQKEFRAAQLAGDKARQQQLQVQQREMLGDQS 121
                                       4...89*********************************************************************** PP

                        EMC3_TMCO1  86 emmmdqmkpmivtmipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqii 162
                                       +mm++q+kpm++++i++i++f+w + +++++++  l fp++g    ++    +++ +++ ++++wYf+cs+ +sqii
  gi|386001161|ref|YP_005919460.1| 122 KMMKMQLKPMAYIGIVSIPLFMWAYLYIEEHAI-LLSFPFWGVHP-IS----DTVLGPIFYWFYWYFICSIPVSQII 192
                                       ******************************999.789*****888.99....************************* PP

                        EMC3_TMCO1 163 rklLgea 169
                                       rk+L+++
  gi|386001161|ref|YP_005919460.1| 193 RKALDIG 199
                                       ****986 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   3.4   6.6e-08    0.0004      41     168 .]      16     194 ..       4     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.6e-08
                           DUF4199  41 lllvpfl.vylalkkyrkknlgGfisfgqafgfgflislvagllsavfqyiyfnfidpd.....fienyiaeilekl 111
                                        + + ++ +++  +++r+++ g+++    +++ g+l++ v  +  a+++ +y ++i++      +++++ +++  ++
  gi|386001161|ref|YP_005919460.1|  16 GVGIALMvGIMVSMEFRHNV-GEVMEAVLGWLPGILPFHVVLFALAAITGLYASLIQKYtmdwdYLKRQQETM-RSF 90 
                                       33333330566666*****9.8899999999999999888888888888777755544434444777777765.455 PP

                           DUF4199 112 eeakeesae.eenaemseeeike............alesls.................................... 139
                                       +++  +++  + +a +++ + ++            +    +                                    
  gi|386001161|ref|YP_005919460.1|  91 QKEFRAAQLaGDKARQQQLQVQQremlgdqskmmkM----Qlkpmayigivsiplfmwaylyieehaillsfpfwgv 163
                                       555555554444444444444445555554543330....2456666666667777777777777778888888888 PP

                           DUF4199 140 .piiv.alqsflgnliiGlilsliiAlilkk 168
                                        pi+  +l  +++ + +++i s++++ i++k
  gi|386001161|ref|YP_005919460.1| 164 hPISDtVLGPIFYWFYWYFICSIPVSQIIRK 194
                                       88877799999999999*********99997 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.4   1.6e-05     0.093     129     241 ..      13     125 ..       2     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2 129 llksllkvvlvgavaylvlkseleellalaeldleaalelllslllkllllvllallviallDlllqrwefekklkM 205
                                       ll  +  +++vg+++ + ++++++e+++     +  +l  +l + + l++l+++  l  +l+      w++ k+   
  gi|386001161|ref|YP_005919460.1|  13 LLLGVGIALMVGIMVSMEFRHNVGEVME----AVLGWLPGILPFHVVLFALAAITGLYASLIQKYTMDWDYLKRQQE 85 
                                       4444444555555555555555555554....45778888889999999999999999******************* PP

                                       XXXXXXXXXXXXX..X-HHHHHHHHHHHHHHH..HHHHHH CS
                      Bac_export_2 206 tkqEvKdEyKesE..GdpeiKsrirqlqrela..rrrmma 241
                                       t +  ++E++ ++  Gd   +++++ +qre++  +++mm+
  gi|386001161|ref|YP_005919460.1|  86 TMRSFQKEFRAAQlaGDKARQQQLQVQQREMLgdQSKMMK 125
                                       **********66444****************866667765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1309  (0.0730102); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1529.73
//
Query:       gi|386001162|ref|YP_005919461.1|  [L=539]
Description: Preprotein translocase, SecY subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-65  220.6  21.8      5e-65  219.7  21.8    1.4  1  SecY             SecY translocase
    1.4e-09   37.7   4.0    4.2e-09   36.1   4.0    1.9  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7  21.8   5.6e-69     5e-65       1     306 []      75     516 ..      75     516 .. 0.81

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 5.6e-69
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg......... 65 
                                       s++ LGI+P++tasI+lqLl ++     +++k +  ++++++ +++++++l++v+++v+al  +++ g         
  gi|386001162|ref|YP_005919461.1|  75 SLMLLGIGPIVTASIVLQLLvGA-----DIIKlNLrDPRDQAIFQGTQKLLVFVMIIVEALPQVTG-Gyllpdqsla 145
                                       89******************999.....555554559***********************996543.4688899999 PP

                                       ........HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS...............-HHH CS
                              SecY  66 ........lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals...............glie 119
                                               l+ lli++q+++g+vl+++++E+++++GiG+G+ l+i+ag++++l++ l                +   
  gi|386001162|ref|YP_005919461.1| 146 salgvslgLISLLIFVQICIGGVLVLFMDEVVSKWGIGSGVGLFIVAGVSQSLITGLFnwtigdqglpigiipK--- 219
                                       99999999889*******************************************66663666666666543330... PP

                                       H..............SS.........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETT CS
                              SecY 120 l..............ale.......gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlkln 174
                                       +              + +        i   +l+l++t+++il+vv+ve+++++ip+ ++  r    g+++++P+kl+
  gi|386001162|ref|YP_005919461.1| 220 WvfiftndvlgledvF-TtsglervFIDGGILALITTIVIILFVVLVESTRVEIPLAHSaVR----GARGRFPVKLV 291
                                       2555555555545441.14455544333789***************************9778....9********** PP

                                       CCCSCHHHHHHHHHH.............................................................. CS
                              SecY 175 yagviPiIfasslla.............................................................. 189
                                       ya+v+P+I++++l+a                                                              
  gi|386001162|ref|YP_005919461.1| 292 YASVLPMILVRALQAniqmigtllagkigtmttasttdtasgvnivytayssilgtftstssydmvtgelvgatspq 368
                                       ***************88888888888888888888888888888877777777777777776666666666666554 PP

                                       ....HHHCCCCS..............................TCCCS....THHHHHHHHHHHHHH....HHHHHHT CS
                              SecY 190 ....lpstiaqfl.............................lalls....psvlyvvlyvlliif....Fayfyte 225
                                           l       +                                      + +l+v++ ++++i+    Fa+f++e
  gi|386001162|ref|YP_005919461.1| 369 pisgL-------MyylspinsphdwipglvassnpgmellglP---PiagwQIWLHVFTDAAVLIIggviFAMFWIE 435
                                       44440.......2555555555555555555555775555542...044558899999988887777999******* PP

                                       CT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHH CS
                              SecY 226 it.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVg 300
                                       +t + +k+va +++ sg ++pg+r +  +++k L ++++++t+iG+++++l++++++l+g+  +g  ggt+lL++V+
  gi|386001162|ref|YP_005919461.1| 436 TTgMGAKSVAAKIHASGLQVPGHRrNPVSIEKLLLRYIPKVTVIGGVIIGLLTLVASLMGT--LGGAGGTGLLLAVS 510
                                       ************************999**********************************..999*********** PP

                                       HHHHHH CS
                              SecY 301 valetv 306
                                       ++++++
  gi|386001162|ref|YP_005919461.1| 511 IVYRLY 516
                                       **9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   4.0   4.7e-13   4.2e-09       1      35 []      41      74 ..      41      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.7e-13
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      +lY+ ls++ L+G+s ++s+D+f+ +Ra fA+++G
  gi|386001162|ref|YP_005919461.1| 41 ILYFALSNVSLFGLS-PASIDLFGMYRAFFAGSFG 74
                                      89************9.9****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3243.70
//
Query:       gi|386001163|ref|YP_005919462.1|  [L=125]
Description: 50S ribosomal protein L15 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-17   65.0   3.7    1.9e-17   64.1   3.7    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   3.7   1.1e-21   1.9e-17       2     127 ..      27     123 ..      26     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.1e-21
                                       GGGTSSTTTTTTTTT-S--......S--.........---GGG..---EEEEHHHHHHTTTTGTTS------EEEGG CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkkkpgfeGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerleladeaeeidle 78 
                                       G++gG G++G  k++ v        G++     + k+Gf + ++++e  v+n++dLd++++ee          idl 
  gi|386001163|ref|YP_005919462.1|  27 GSRGGTGNAGGCKHHFVRD-MML--GRV-----MGKHGFFK-HNAREVDVINVGDLDSMATEEG--------RIDLG 86 
                                       99************97553.333..333.....7888*985.4479***********8877765........5**** PP

                                       GTTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  79 elaeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       ++            Kvlgkg+++++++v+a++fS++A++kIe++GG+v+
  gi|386001163|ref|YP_005919462.1|  87 KM------------KVLGKGSISRPVTVTAKAFSAAARAKIEEVGGEVV 123
                                       **............*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 928.21
//
Query:       gi|386001164|ref|YP_005919463.1|  [L=151]
Description: 50S ribosomal protein L30 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-19   68.5   0.3    1.2e-18   66.7   0.1    2.0  2  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.1   6.8e-23   1.2e-18       1      51 []       2      52 ..       2      52 .. 0.96
   2 ?   -1.1   0.0       0.1   1.8e+03      30      38 ..      80      88 ..      75      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 6.8e-23
                                      EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                      ++++r r+ ++++p++++tL lL+L++in+ vv++++p +rGm++kVk++V
  gi|386001164|ref|YP_005919463.1|  2 YAIVRLRGSVNTKPDIKDTLDLLRLHRINHCVVVPDNPHYRGMIQKVKDYV 52
                                      579**************************99999999*************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.1
                                      EEEE--SSH CS
                     Ribosomal_L30 30 gtvvklntp 38
                                      + ++k+nt 
  gi|386001164|ref|YP_005919463.1| 80 DQFIKENTS 88
                                      679****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1157.79
//
Query:       gi|386001165|ref|YP_005919464.1|  [L=200]
Description: 30S ribosomal protein S5 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-25   85.8   0.8    1.6e-24   85.1   0.8    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    7.6e-24   83.5   2.2    1.5e-23   82.6   0.8    2.1  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.8   1.8e-28   1.6e-24       2      65 ..     134     198 ..     133     200 .] 0.97

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.8e-28
                                       EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT CS
                    Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrsp 65 
                                       gk g+v ++l+paprG Gi agg++++v+e+aGi+Dv++ks g +r+++n++kAt++AL+++ ++
  gi|386001165|ref|YP_005919464.1| 134 GKAGSVSITLIPAPRGLGIAAGGTAKKVMEMAGIRDVWTKSSGnTRTTLNFAKATYNALRNTVTM 198
                                       89***********************************************************9886 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.8   1.6e-27   1.5e-23       1      65 []      48     112 ..      48     112 .. 0.98
   2 ?   -0.7   0.0      0.16   1.4e+03      51      64 ..     185     198 ..     182     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.6e-27
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                       l+++vl+i++vq++t++Grr +f+a+v+vG+++G+vG+G g  ++v  Airk+i+ Ak+n+++v+
  gi|386001165|ref|YP_005919464.1|  48 LEDEVLDINMVQRMTDSGRRVKFRATVIVGNKDGYVGIGQGRDNQVGPAIRKGIDVAKLNIIKVN 112
                                       799************************************************************96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.16
                                       HHHHHHHHHTEEE- CS
                      Ribosomal_S5  51 rkAiekAkknlvpv 64 
                                        kA+ +A +n v +
  gi|386001165|ref|YP_005919464.1| 185 AKATYNALRNTVTM 198
                                       699******98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1458.99
//
Query:       gi|386001166|ref|YP_005919465.1|  [L=169]
Description: 50S ribosomal protein L18 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-32  113.0   0.2    2.4e-21   76.4   0.1    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
     0.0003   21.2   0.0    0.00039   20.8   0.0    1.3  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.1   2.7e-25   2.4e-21       2      97 ..       6      94 ..       5      99 .. 0.96
   2 !   35.1   0.0   1.4e-12   1.2e-08     129     163 .]      99     133 ..      94     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 2.7e-25
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r++v frrrreg+tdY+ r +li          k Rlv+r  nk+i  q++ a+  gd++l +++s+el+k+g++ +  
  gi|386001166|ref|YP_005919465.1|  6 RYKVPFRRRREGRTDYHFRYKLILS-------RKPRLVIRKGNKNISLQLIVAEPVGDRTLLTVNSQELKKLGFDQNTG 77
                                      9**********************85.......678******************************************** PP

                     Ribosomal_L5e 81 nyaaaYatglllarrll 97
                                      n  aaY+tgll+++r+ 
  gi|386001166|ref|YP_005919465.1| 78 NVPAAYLTGLLFGKRMK 94
                                      **************986 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.4e-12
                     Ribosomal_L5e 129 fkaiLdvGLartttgakvfgalkgavdgglsiphs 163
                                        +aiLd+G++  t+g+++++alkg+vd+g++iphs
  gi|386001166|ref|YP_005919465.1|  99 TEAILDMGIHANTRGNRIYSALKGVVDAGIEIPHS 133
                                       689*******************************7 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-08   0.00039       7      94 ..      12     106 ..       7     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-08
                                       HCHHHHHHTTT--...TTSSS-EEEEEE-SS-EEEEEE..-TTT--EEEEECS-SCC.CT.S-SSSCHHHHHHHHHH CS
                    Ribosomal_L18p   7 rkrRhkRirkkls...gtaerprlvvfrsnrhiyaQvi..ddvkgktlasastleke.lk.lkstknkeaakkvgel 76 
                                       r+rR+ R   + +     + +prlv+ + n++i+ Q+i  + v ++tl ++++ e + l   ++t+n  aa   g l
  gi|386001166|ref|YP_005919465.1|  12 RRRREGRTDYHFRyklILSRKPRLVIRKGNKNISLQLIvaEPVGDRTLLTVNSQELKkLGfDQNTGNVPAAYLTGLL 88 
                                       556666655554443345679***************87447899999999888775415578999************ PP

                                       HHHHHCHHCHTC-EE--T CS
                    Ribosomal_L18p  77 iAerakekgiekvvfDrg 94 
                                       + +r k+ g ++++ D g
  gi|386001166|ref|YP_005919465.1|  89 FGKRMKAMGGTEAILDMG 106
                                       *********999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1054.68
//
Query:       gi|386001167|ref|YP_005919466.1|  [L=153]
Description: 50S ribosomal protein L19e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-55  186.4   7.4      3e-55  186.3   7.4    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3   7.4   1.7e-59     3e-55       2     143 ..       4     147 ..       3     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 1.7e-59
                                       THHHHHHHHHHTTS-GGGEEE..-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SG CS
                    Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwl..dpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgs 76 
                                       +++qkrlaasvl vG++r+w+  dpe + eia++itredir+ i+ g I++kpkkgnsrar r r++k+++g+++g+
  gi|386001167|ref|YP_005919466.1|   4 FSTQKRLAASVLAVGESRIWInpDPEVAGEIADSITREDIRSQIEAGNIKAKPKKGNSRARYRVRAAKRAYGHQKGQ 80 
                                       789******************7778999************************************************* PP

                                       GG--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                    Ribosomal_L19e  77 GkrkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                       G+rkG+k++R p+k++W+++iRalR+ Lkelre+++id++tYr+lYrkakGge++++a+L++yi++k
  gi|386001167|ref|YP_005919466.1|  81 GRRKGAKGSRSPRKVVWMTKIRALRSNLKELREEGEIDRHTYRMLYRKAKGGEYRSTAHLNAYIKAK 147
                                       ****************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 1214.44
//
Query:       gi|386001168|ref|YP_005919467.1|  [L=128]
Description: 50S ribosomal protein L32e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-33  115.7   0.2    1.7e-33  115.3   0.2    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.2   9.3e-38   1.7e-33       1     108 []      19     122 ..      19     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 9.3e-38
                                       ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenk 77 
                                       +++F+r +s++++kl+ swr+prG++n++r+++ ++ +++k+GYgsp+ +rg++p G+k+vlV+n+++L++   +  
  gi|386001168|ref|YP_005919467.1|  19 KPEFNRCDSHKKKKLSPSWRRPRGLHNKLRQQIAAKGKLVKAGYGSPRGVRGYHPCGMKEVLVKNPDDLKNAEGC-- 93 
                                       689*******************************************************************88666.. PP

                                       ..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  78 syaaeiahsVsskkrkeiverAaelgikVtN 108
                                         a++ia++V++kkr ei++ A+e+++kV+N
  gi|386001168|ref|YP_005919467.1|  94 --AVRIAATVGMKKRDEIEAMAREMNLKVLN 122
                                       ..89**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 969.93
//
Query:       gi|386001169|ref|YP_005919468.1|  [L=177]
Description: 50S ribosomal protein L6 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-26   93.3   1.5    9.3e-14   51.9   0.1    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
       0.26   11.0   2.3         11    5.8   0.4    2.3  2  DUF3060       Protein of unknown function (DUF3060)


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1     1e-17   9.3e-14       1      76 []      11      84 ..      11      84 .. 0.97
   2 !   41.1   0.1   2.4e-14   2.2e-10       1      76 []      96     170 ..      96     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1e-17
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP+gv v+i ++ +v+v+Gp g+++r++++   +e+ +e+ +++v      +++++ + gt+ ++ +nmikGV eg
  gi|386001169|ref|YP_005919468.1| 11 IPEGVAVEIGDDATVTVTGPLGTVSRRLWYP-GIEIRKEDSTLVVDAEITRKRHRS-MAGTIAAHLKNMIKGVNEG 84
                                      8*****************************9.88888*******************.****************998 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 2.4e-14
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+  ++s  +  + ++lG++++++++i  g +ve+k     ++ ++v+gidke v    A+i++++++   +i+++
  gi|386001169|ref|YP_005919468.1|  96 FPIQLKASKGELLISNFLGERKPRSAKIMGGSQVEIK-----GDTVIVTGIDKELVgqtmANIEQATKVRGFDIRVF 167
                                       677778888888899********************99.....*********************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|386001169|ref|YP_005919468.1| 168 QDG 170
                                       *98 PP

>> DUF3060  Protein of unknown function (DUF3060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0028        25       3      17 ..      20      34 ..      19      35 .. 0.88
   2 ?    5.8   0.4    0.0013        11       7      45 ..     128     168 ..     125     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0028
                           DUF3060  3 GssNtvtltGeCeav 17
                                      G+++tvt+tG  ++v
  gi|386001169|ref|YP_005919468.1| 20 GDDATVTVTGPLGTV 34
                                      999*******99888 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0013
                           DUF3060   7 tvtltGeCeavtVsGssNtVtvdsvdk....itvsGldNtVty 45 
                                       +v+++G+  +v V+G++   + +++ +     +v+G+d +V++
  gi|386001169|ref|YP_005919468.1| 128 QVEIKGD--TVIVTGIDKELVGQTMANieqaTKVRGFDIRVFQ 168
                                       6888888..99*******9999988883334469999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1408.40
//
Query:       gi|386001170|ref|YP_005919469.1|  [L=120]
Description: 30S ribosomal protein S8 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-22   79.9   0.0    2.1e-22   79.4   0.0    1.2  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   1.2e-26   2.1e-22       8     127 .]       2     120 .]       1     120 [] 0.82

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.2e-26
                                       HHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE-SBTTC-- CS
                      Ribosomal_S8   8 trirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrvskpgrrv 82 
                                       + i+Nae ++k  + + paskl+ + lkv+ + Gyi dfe++ + k+ ++k++l+ + ++++vik     + + ++ 
  gi|386001170|ref|YP_005919469.1|   2 SIIKNAEDVGKGGCIIqPASKLIGNTLKVMADLGYIGDFEFVdDGKSGMFKVNLQGKINRCGVIKPRFSTQVADLEK 78 
                                       78***************************************9666666666666555566****9555555555552 PP

                                       EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  83 YakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       + +++ lp   +++G++i+sTs+Gv+++ +Ar++++GG++layv+
  gi|386001170|ref|YP_005919469.1|  79 W-EKRFLP--SRNFGVLIMSTSQGVISHVDARERGIGGQLLAYVY 120
                                       2.223344..578*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 931.98
//
Query:       gi|386001171|ref|YP_005919470.1|  [L=50]
Description: 30S ribosomal protein S14 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-14   53.8   3.2    1.2e-14   53.8   3.2    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
      0.011   15.7   0.2      0.015   15.3   0.2    1.2  1  DZR            Double zinc ribbon
      0.026   14.2   0.3      0.034   13.8   0.3    1.2  1  zf-P11         P-11 zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   3.2     2e-18   1.2e-14       9      54 .]       6      50 .]       1      50 [] 0.94

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 2e-18
                                      S..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                     Ribosomal_S14  9 ssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                      +s +r+ n C+ +Gr+ G+irk+g+  +R+cfRe A +   +G++K+S
  gi|386001171|ref|YP_005919470.1|  6 KSFGRGANACKRCGRRPGLIRKYGIylCRQCFREIAPE---MGFEKYS 50
                                      5689**********************************...******8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   2.5e-06     0.015      10      41 ..      10      43 ..       5      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-06
                               DZR 10 pdarfCseCgtk..lkavaaedrCpsCgekvdpe 41
                                       +a+ C++Cg +  l +    + C +C +++ pe
  gi|386001171|ref|YP_005919470.1| 10 RGANACKRCGRRpgLIRKYGIYLCRQCFREIAPE 43
                                      58999*******55554555*******9998876 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   5.6e-06     0.034       1      28 [.      11      37 ..      11      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-06
                                      -SSSBTTTSS--SSEEE-SSSEEEHHHH CS
                            zf-P11  1 GplsCksCWfkdksLveCsdHYLClrCl 28
                                      G   Ck C  +  +L++    YLC++C+
  gi|386001171|ref|YP_005919470.1| 11 GANACKRCG-RRPGLIRKYGIYLCRQCF 37
                                      6789****7.5689*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 363.32
//
Query:       gi|386001172|ref|YP_005919471.1|  [L=168]
Description: 50S ribosomal protein L5 [Methanosaeta harundinacea 6Ac]
Scores for 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-26   90.2   0.0    1.2e-25   89.5   0.0    1.4  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
      1e-14   54.6   0.0    1.6e-14   53.9   0.0    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.0   1.3e-29   1.2e-25       1      82 [.      56     144 ..      56     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 1.3e-29
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       piG++vtLrg++++efl+ +lev+   lr      +ssfd++Gn+sfG++e+++fp+++y++d+gifGmd+++ +++
  gi|386001172|ref|YP_005919471.1|  56 PIGCRVTLRGRDAEEFLKVALEVAGSALR------RSSFDDTGNFSFGVEEHTDFPGMKYEPDIGIFGMDVSVALKR 126
                                       8****************************......****************************************** PP

                    Ribosomal_L5_C  78 k...tde..........e 82 
                                       +   +++           
  gi|386001172|ref|YP_005919471.1| 127 PgyrVARrrvarakmasT 144
                                       *76622234554555534 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   1.8e-18   1.6e-14       3      57 .]       1      52 [.       1      52 [. 0.98

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.8e-18
                                      TTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  3 MqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      M +Pr++K+++++g+Ge+g++   l +a+ +L eIt   Pv++ akk+ ++F+i+
  gi|386001172|ref|YP_005919471.1|  1 MLEPRIDKVTVHIGTGESGQR---LVNAETILGEITSRSPVRSIAKKTLPGFGIK 52
                                      889******************...*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1249.51
//
Query:       gi|386001173|ref|YP_005919472.1|  [L=211]
Description: 30S ribosomal protein S4e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-22   78.3   0.0    4.8e-22   77.6   0.0    1.4  1  Ribosomal_S4e  Ribosomal family S4e
    1.7e-07   30.9   0.4    3.5e-07   29.8   0.4    1.6  1  S4             S4 domain
     0.0011   18.9   0.8     0.0027   17.6   0.8    1.8  1  KOW            KOW motif
      0.007   14.8   0.0      0.011   14.2   0.0    1.2  1  DUF515         Protein of unknown function (DUF515)
  ------ inclusion threshold ------
      0.043   13.6   0.1       0.17   11.7   0.0    2.0  2  S4_2           S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   1.3e-25   4.8e-22       2      75 .]      69     140 ..      68     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.3e-25
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                       ++n+rll d kgrf lh+ ++ ea+ KLc+i+kkt+ ++g++ql+++dG++i+ + + + +  +v +++++++I
  gi|386001173|ref|YP_005919472.1|  69 DKNFRLLTDAKGRFNLHELEAGEAR-KLCRIEKKTVLQGGKTQLNLNDGTNILAEGD-YTTRSSVILSIPDKEI 140
                                       79***********************.******************************8.**************98 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.4   9.7e-11   3.5e-07       3      48 .]      17      63 ..      15      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.7e-11
                                      HHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4  3 Ldkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      L +v+   lgl+   reA++   +G+VlV+Gk +kd +++V+  Dvi
  gi|386001173|ref|YP_005919472.1| 17 LVVVVrDLLGLVDNSREAKRVLHEGGVLVDGKARKDLNFPVGIFDVI 63
                                      777777669*********************************99997 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   7.5e-07    0.0027       2      31 ..     149     182 ..     148     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.5e-07
                                       TSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                       G+  +Vv+G+h G++G+++ ++  k    +rV++
  gi|386001173|ref|YP_005919472.1| 149 GNLAMVVGGTHSGEVGTIKVIEVVKssrpNRVII 182
                                       9*****************9777777777777765 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.9e-06     0.011     396     447 ..     103     155 ..      83     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-06
                            DUF515 396 lgnYGkellelEdntqllal.dEnvkllvivevPsekvpdilevedeivvikv 447
                                       + + Gk  l+l d t++la  d +++  vi+++P++ ++d++e ++  + ++v
  gi|386001173|ref|YP_005919472.1| 103 VLQGGKTQLNLNDGTNILAEgDYTTRSSVILSIPDKEISDVIEFKEGNLAMVV 155
                                       45569999*********87436799*******************998877665 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.9e-05      0.17      17      41 ..      25      49 ..      23      52 .. 0.89
   2 ?   -2.2   0.0         1   3.7e+03      27      38 ..     101     112 ..      98     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                              S4_2 17 aglvesGgeaKafiaegeVkvNGev 41
                                      +glv++  eaK ++ eg V+v+G+ 
  gi|386001173|ref|YP_005919472.1| 25 LGLVDNSREAKRVLHEGGVLVDGKA 49
                                      68999999***************86 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                              S4_2  27 KafiaegeVkvN 38 
                                       K++++ g+ ++N
  gi|386001173|ref|YP_005919472.1| 101 KTVLQGGKTQLN 112
                                       677777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1526.04
//
Query:       gi|386001174|ref|YP_005919473.1|  [L=116]
Description: 50S ribosomal protein L24 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-28   97.9   0.9    4.2e-28   97.6   0.9    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    1.8e-05   24.5   0.1    3.2e-05   23.7   0.1    1.4  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.9   4.7e-32   4.2e-28       1      81 [.       3     116 .]       3     116 .] 0.98

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 4.7e-32
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s+++rkqrK +f+ap+h+r+k+m+a LskeLre+ + rs +++                                gv
  gi|386001174|ref|YP_005919473.1|   3 SKQPRKQRKERFSAPLHKRQKYMHAALSKELREEMKARSAQVKkgdtvqlmrgdhagtegevqkadlksgtihvaGV 79 
                                       89*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLer 81 
                                       ++ +a+gt+vp++++pS+v+Itk+++ D++rkki +r
  gi|386001174|ref|YP_005919473.1|  80 SVFRADGTEVPRPVQPSNVIITKMEMdDEERKKIFSR 116
                                       **************************999***99765 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   3.5e-09   3.2e-05       1      31 [.      46      76 ..      46      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.5e-09
                                      TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                               KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                      +Gd+V+ ++G h+G +G+V k d +  +++v
  gi|386001174|ref|YP_005919473.1| 46 KGDTVQLMRGDHAGTEGEVQKADLKSGTIHV 76
                                      7***********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 890.68
//
Query:       gi|386001175|ref|YP_005919474.1|  [L=132]
Description: 50S ribosomal protein L14 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  127.3   1.1    3.7e-37  127.1   1.1    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   1.1   2.1e-41   3.7e-37       2     121 ..      12     131 ..      11     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 2.1e-41
                                       .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS CS
                     Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdG 74 
                                       i+ ++rl++aDN+ga+ +e+i+v +++    + + a vGd+ivvsvkk++p   ++++++++av+vr++ke+rr+dG
  gi|386001175|ref|YP_005919474.1|  12 INAGARLECADNTGARVLEIISVKRYRgvknRMPCAGVGDMIVVSVKKGTP---EMRKQIMTAVIVRQRKEFRRPDG 85 
                                       67899*******************8877665569*****************...99********************* PP

                                       -EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                     Ribosomal_L14  75 svirfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                       + ++f+dnaaV+ ++ g p+G++i+gpvare++e+ + ki+s A+ +
  gi|386001175|ref|YP_005919474.1|  86 MRVKFEDNAAVITDALGIPKGSEIKGPVAREVAER-YGKIASAASII 131
                                       **********************************9.********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 759.91
//
Query:       gi|386001176|ref|YP_005919475.1|  [L=109]
Description: 30S ribosomal protein S17 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-27   93.1   3.7      1e-26   92.8   3.7    1.1  1  Ribosomal_S17    Ribosomal protein S17
    6.8e-07   29.6   0.1    1.4e-06   28.6   0.0    1.6  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   3.7   1.2e-30     1e-26       1      68 []      38     106 ..      38     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 1.2e-30
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       G+Vvsdkm+ TvvV +e   k  ky +y+krr+k++ah++++  +kvGD+V+++ecrPlSktk+fvvve
  gi|386001176|ref|YP_005919475.1|  38 GKVVSDKMTDTVVVLREFERKMTKYDRYEKRRSKLHAHNPPCLkAKVGDVVKVAECRPLSKTKSFVVVE 106
                                       99*****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.5e-10   1.4e-06      32      69 .]       3      36 ..       1      36 [. 0.94
   2 ?   -3.0   0.0       1.1   9.9e+03      30      32 ..      63      65 ..      50      74 .. 0.51

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.5e-10
                                      ------TT----GGGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 32 yvknvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                      ++++vglg k P++A +    D KCPF G+ s+rG+++
  gi|386001176|ref|YP_005919475.1|  3 IMRDVGLGVKSPEKACD----DPKCPFHGELSVRGQVF 36
                                      689**************....9*************996 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                                      --- CS
                   Ribosomal_S17_N 30 kry 32
                                       ry
  gi|386001176|ref|YP_005919475.1| 63 DRY 65
                                      333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 788.01
//
Query:       gi|386001177|ref|YP_005919476.1|  [L=97]
Description: ribonuclease P protein component 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-24   85.9   0.0    1.5e-24   85.7   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.0   8.1e-29   1.5e-24       1      84 []       6      88 ..       6      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 8.1e-29
                                      HHHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHH CS
                           UPF0086  1 ekLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpa 79
                                      e+L++++l+G++veV+r +np++ gi+G+Vv+Et+nt+ i+t +s+vk+vpK+   F f++++ l+v+ +Gs l ++p+
  gi|386001177|ref|YP_005919476.1|  6 ENLVRHELIGLPVEVARGTNPAQAGISGRVVDETRNTFLIET-RSGVKCVPKSCNCFIFTLSQGLKVKAEGSVLVSQPE 83
                                      68****************************************.9*********************************** PP

                                      HHHCH CS
                           UPF0086 80 dRaer 84
                                      +R+++
  gi|386001177|ref|YP_005919476.1| 84 NRINK 88
                                      ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 718.32
//
Query:       gi|386001178|ref|YP_005919477.1|  [L=67]
Description: 50S ribosomal protein L29 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-21   73.8   0.2    8.9e-21   73.6   0.2    1.0  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.025   14.8   0.1    1.4  1  DUF3213        Protein of unknown function (DUF3213)
      0.058   13.8   0.1      0.065   13.6   0.1    1.1  1  Radical_SAM    Radical SAM superfamily
      0.059   13.5   0.2        0.1   12.7   0.2    1.6  1  MRP-L47        Mitochondrial 39-S ribosomal protein L47 (MRP-
       0.78    9.8   5.3       0.79    9.8   0.1    2.1  2  DUF1192        Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.2   2.5e-24   8.9e-21       2      57 .]       8      64 ..       7      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 2.5e-24
                                      HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                      elr++s eeL e+l++lk eL + r   ++g ++enp+rir+++++IARikT+++er
  gi|386001178|ref|YP_005919477.1|  8 ELRNMSPEELGEELEKLKGELVRERGLVVSGgAPENPGRIREIKRSIARIKTIQKER 64
                                      9******************************9************************8 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   6.8e-06     0.025      45      70 ..      11      36 ..       2      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.8e-06
                                      S-SHHHHHHHT...TT-SS------- CS
                           DUF3213 45 kvnieelkkkleelkgevveekeltl 70
                                       ++ eel ++le+lkge+v e+ l +
  gi|386001178|ref|YP_005919477.1| 11 NMSPEELGEELEKLKGELVRERGLVV 36
                                      4677*****************99877 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.8e-05     0.065      26      73 ..       9      57 ..       4      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 26 grslsveeileevkelk.aekgvkevilgggepllypdfvellerlakl 73
                                       r++s+ee+ ee+++lk +  + ++++++gg p    ++ e+ + +a++
  gi|386001178|ref|YP_005919477.1|  9 LRNMSPEELGEELEKLKgELVRERGLVVSGGAPENPGRIREIKRSIARI 57
                                      699**************99999***********9977777766666665 PP

>> MRP-L47  Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.9e-05       0.1      64      87 .]      41      64 ..       3      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                           MRP-L47 64 mpsperlkkvkesMeniktVlkeR 87
                                       ++p+r+ ++k+s+++ikt+ keR
  gi|386001178|ref|YP_005919477.1| 41 PENPGRIREIKRSIARIKTIQKER 64
                                      5799*****************999 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00022      0.79      15      39 ..       7      31 ..       2      40 .. 0.89
   2 ?    1.7   2.0     0.078   2.8e+02      29      51 ..      47      65 ..      45      67 .] 0.49

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                           DUF1192 15 qDLslLSveELeerIalLeaEIaRl 39
                                      ++L ++S eEL e  ++L+ E  R 
  gi|386001178|ref|YP_005919477.1|  7 DELRNMSPEELGEELEKLKGELVRE 31
                                      57999****************9995 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.078
                           DUF1192 29 IalLeaEIaRleaaiakkkasra 51
                                      I + +  IaR++    + ++ ra
  gi|386001178|ref|YP_005919477.1| 47 IREIKRSIARIK----TIQKERA 65
                                      555555555555....4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:01.67
# Mc/sec: 121.42
//
Query:       gi|386001179|ref|YP_005919478.1|  [L=302]
Description: 30S ribosomal protein S3 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-21   74.8   0.1    1.2e-20   73.8   0.1    1.5  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    2.9e-14   52.6   0.5    7.1e-14   51.4   0.0    1.8  2  KH_2            KH domain
  ------ inclusion threshold ------
      0.029   14.2   0.5       0.35   10.7   0.1    2.5  3  KH_1            KH domain
      0.078   13.1   0.1       0.27   11.3   0.0    1.8  2  PUFD            BCORL-PCGF1-binding domain
       0.16   11.9   2.4       0.22   11.4   0.2    2.2  2  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1   3.3e-24   1.2e-20       1      83 []      99     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 3.3e-24
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a++le+++ fR+a ++++rr+m++ga G++i++sG+L+ + ++r ek+  G+v++  ++ ++ +d+++a a  k G
  gi|386001179|ref|YP_005919478.1|  99 LASSLERGWYFRKAGQTTLRRVMESGALGCEIILSGKLT-GPRSRVEKFLSGYVKHsgKPSQEIVDHGYAVAVKKLG 174
                                       5899***********************************.9************************************ PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       +iG++V+I
  gi|386001179|ref|YP_005919478.1| 175 TIGCQVRI 182
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0     2e-17   7.1e-14       2      72 ..      17      84 ..      16      90 .. 0.91
   2 ?   -2.2   0.2       1.1   3.8e+03      51      72 ..     213     234 ..     209     241 .. 0.57

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2e-17
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEE CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivk 72
                                      + e+l +e++ ag++++  +rt+ ++ i++++++pg+vIGkgG+ i+k++ +l ++++ l + ++ ++  +
  gi|386001179|ref|YP_005919478.1| 17 VHEYLSKELSRAGYGGMTMNRTPMGIQITVYAEKPGMVIGKGGKLIRKLTRDLDRNFR-LDNPQIDVQ--D 84
                                      5799*****************************************************6.999999954..3 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHTTCEEEEEEE CS
                              KH_2  51 gkelrkdieklegkkVklnivk 72 
                                       + el++ +e   ++ V++ +++
  gi|386001179|ref|YP_005919478.1| 213 RDELEELLESGAEGAVEVTVEE 234
                                       4556666666666666666663 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   9.6e-05      0.35       8      27 ..      48      67 ..      42      75 .. 0.83
   2 ?   -3.0   0.0       1.8   6.5e+03      21      31 ..     116     125 ..     113     142 .. 0.67
   3 ?    0.3   0.0      0.17   6.2e+02      29      60 ..     175     206 ..     173     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.6e-05
                                      GGHHHHHHTGGGHHHHHHHH CS
                              KH_1  8 sslvgriIGkgGsnIkeIre 27
                                      +++ g +IGkgG+ I+++ +
  gi|386001179|ref|YP_005919478.1| 48 AEKPGMVIGKGGKLIRKLTR 67
                                      556699***********987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                                       HHHHHHHHHT- CS
                              KH_1  21 nIkeIreetga 31 
                                       ++++ +e +ga
  gi|386001179|ref|YP_005919478.1| 116 TLRRVME-SGA 125
                                       7788887.443 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.17
                                       H.T-EEEEESSTT...T.-EEEEEE.SHHHHHHH CS
                              KH_1  29 t.gakIkvpksedegsderevtisG.speavekA 60 
                                       t g++++++++++   +++ ++i   s+e+ e+A
  gi|386001179|ref|YP_005919478.1| 175 TiGCQVRIVPPDAV--PPDRFEIVPpSKEQAEEA 206
                                       66999999964443..677777766666666655 PP

>> PUFD  BCORL-PCGF1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.7e-05      0.27      44      82 ..      70     108 ..      61     123 .. 0.85
   2 ?   -1.6   0.1       0.8   2.9e+03      86     108 ..     201     223 ..     191     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.7e-05
                              PUFD  44 srifrarfPhlevvslaeaefyrqvslsqllsseeelea 82 
                                        r fr  +P+++v+ + +ae+  qv + +l+ss e+   
  gi|386001179|ref|YP_005919478.1|  70 DRNFRLDNPQIDVQDVGKAELNAQVVANRLASSLERGWY 108
                                       589**************************9999887655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.8
                              PUFD  86 pdskelveLvelepelqslLGss 108
                                       ++++e + + e  +el++lL s 
  gi|386001179|ref|YP_005919478.1| 201 EQAEEALPVEEKRDELEELLESG 223
                                       55667777778888888888775 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.2e-05      0.22      29      51 ..      40      62 ..      30      65 .. 0.85
   2 ?   -1.0   0.2      0.45   1.6e+03       4      24 ..     216     234 ..     213     244 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                              KH_4 29 veielnvegedlGrvIGkrGrtl 51
                                        i+++v  e+ G vIGk G+ +
  gi|386001179|ref|YP_005919478.1| 40 MGIQITVYAEKPGMVIGKGGKLI 62
                                      568999**************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.45
                              KH_4   4 vedilkalvddpeevevteee 24 
                                       +e++l++ +  + +vevt+ee
  gi|386001179|ref|YP_005919478.1| 216 LEELLESGA--EGAVEVTVEE 234
                                       566666643..3455555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2186.11
//
Query:       gi|386001180|ref|YP_005919479.1|  [L=154]
Description: 50S ribosomal protein L22 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-28   98.7   0.1    2.3e-28   98.4   0.1    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.1   1.3e-32   2.3e-28       1     103 []      19     151 ..      19     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.3e-32
                                       EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHH CS
                     Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklL 47 
                                       a+g + ++s+k++ e++++Irgm +e A++yL++  +kk+                            aak vl +L
  gi|386001180|ref|YP_005919479.1|  19 AMGTEHHISPKHALEICNAIRGMRAEAAKTYLEEviAKKRpvpfkhhnkkvphrhglvgwdagrypqkAAKAVLGVL 95 
                                       578899*****************************88888************************************* PP

                                       HHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  48 knaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvlk 103
                                        na +nae+kgld+  + I+++  ++g++l+++++rA+Gr++p   ++++ie++l+
  gi|386001180|ref|YP_005919479.1|  96 VNATSNAEYKGLDPAGMKITHVSTKQGRTLRGWMPRAMGRATPKDTETVSIEMILT 151
                                       ******************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 1200.21
//
Query:       gi|386001181|ref|YP_005919480.1|  [L=136]
Description: 30S ribosomal protein S19 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-29   99.4   0.2    1.1e-28   98.9   0.2    1.2  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.2   6.2e-33   1.1e-28       1      81 []      44     119 ..      40     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 6.2e-33
                                       .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTr 76 
                                       r+lk+g ++ +++ll +v      k++ev++th+Rd+++lPemvg t+++ynGk f++vei +emvGh+LgE+s+Tr
  gi|386001181|ref|YP_005919480.1|  44 RRLKRGlTKDHKRLLSRV------KDREVVRTHLRDMIVLPEMVGKTIEIYNGKAFNRVEIMPEMVGHYLGEYSLTR 114
                                       456666444445555544......4678************************************************* PP

                                       ----S CS
                     Ribosomal_S19  77 kpvkh 81 
                                        +v+h
  gi|386001181|ref|YP_005919480.1| 115 ARVTH 119
                                       **999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1041.88
//
Query:       gi|386001182|ref|YP_005919481.1|  [L=205]
Description: 50S ribosomal protein L2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-45  154.5   0.8    2.1e-45  154.0   0.8    1.2  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    7.4e-14   51.5   0.1    2.4e-13   49.9   0.1    1.9  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0   0.8   2.3e-49   2.1e-45       1     121 [.      58     189 ..      58     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 2.3e-49
                                       SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCT CS
                    Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehk 77 
                                       k+Gn lpl++ipeG  ++nie++p+ gg++ars+G y+ ++a++  k++v+lpSge+++++ +c+AtiGvv++g+++
  gi|386001182|ref|YP_005919481.1|  58 KPGNSLPLAEIPEGIPICNIESNPRAGGQFARSSGVYGILIAHDVGKTVVQLPSGEMKWLNPQCMATIGVVAGGGRT 134
                                       68******************************************9******************************** PP

                                       T----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSSST CS
                    Ribosomal_L2_C  78 ekklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrkap 121
                                       +k+++kAg+k+++     g++p+vrGvamn vdHp+GGG     G+  t+sr++p
  gi|386001182|ref|YP_005919481.1| 135 DKPFVKAGKKYHKmkskaGKYPRVRGVAMNVVDHPFGGGGwqhpGRpkTVSRNTP 189
                                       ***************************************9777766546666655 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1   2.6e-17   2.4e-13      31      76 ..       5      50 ..       1      51 [. 0.92
   2 ?   -1.7   0.0      0.33     3e+03      19      30 ..     143     155 ..     118     170 .. 0.60

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.6e-17
                                      SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2 31 ekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      ++v g+V+ei +Dp+R Ap+A+v++ ++e+ryi+ peg+ vG+++ 
  gi|386001182|ref|YP_005919481.1|  5 QTVLGVVKEIVHDPARCAPVARVVLDNDEERYILVPEGVYVGQEIA 50
                                      56889**************************************996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.33
                                       --EE-B--S-.-- CS
                      Ribosomal_L2  19 kkyrlidfkr.nk 30 
                                       kky  +++k  ++
  gi|386001182|ref|YP_005919481.1| 143 KKYHKMKSKAgKY 155
                                       4555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1576.19
//
Query:       gi|386001183|ref|YP_005919482.1|  [L=68]
Description: 50S ribosomal protein L23 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-10   40.5   0.4    5.8e-10   39.4   0.4    1.5  1  Ribosomal_L23   Ribosomal protein L23
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.049   13.6   0.1    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.4   6.4e-14   5.8e-10      18      61 ..       5      48 ..       1      60 [. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 6.4e-14
                                      TE.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESS CS
                     Ribosomal_L23 18 knkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrv 61
                                      +n++ F V+  anK eik+ +e l++V+V +V+t++  + +k+ 
  gi|386001183|ref|YP_005919482.1|  5 DNTMEFLVEIGANKKEIKEELERLYDVEVISVRTMITSKGEKKA 48
                                      47899*******************************98877764 PP

>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.4e-06     0.049      13      48 ..      17      50 ..      13      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-06
                                      -HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEE CS
                    Ribosomal_S24e 13 skteireklakmykvdpdlvvvfgfrthfGggkttG 48
                                      +k+ei+e+l ++y+v  +++ v+++ t+ G+ k+ +
  gi|386001183|ref|YP_005919482.1| 17 NKKEIKEELERLYDV--EVISVRTMITSKGEKKAAV 50
                                      79***********98..9************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 502.02
//
Query:       gi|386001184|ref|YP_005919483.1|  [L=253]
Description: 50S ribosomal protein L4P [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-48  162.8   0.1    8.4e-48  162.6   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.1   4.7e-52   8.4e-48       3     191 ..      18     249 ..      16     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 4.7e-52
                                       E-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT-- CS
                      Ribosomal_L4   3 LspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGg 71 
                                       L p+vF++++r+dli+rav+a +anr q+++ +  a+ ++s+   ++++  G+G +Rv++i        +p+a+gG+
  gi|386001184|ref|YP_005919483.1|  18 L-PSVFDEEFRPDLIKRAVLAAQANRLQPYGPSDlAGLKTSA--LSWGT--GRGASRVPRILngrraarVPQAKGGR 89 
                                       7.9****************************9999*******..6****..**********99999*********** PP

                                       -SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-...-S........S--HHHHHHHHHHTT-... CS
                      Ribosomal_L4  72 vahgpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.e..ple........esktkelvellkklgl... 134
                                       +ah+pkp+ d ++k+n K+rr+A+rsa++a+a+++l++ +++l +  p++         +kt e++++l + g    
  gi|386001184|ref|YP_005919483.1|  90 RAHPPKPQTDRTEKVNAKERRKAIRSAIAATANADLVRGRGHLfSgePIVvakddlegVEKTAEVRKFLAACGRwdd 166
                                       *****************************************76442344488888889999**********544455 PP

                                       .......................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHH CS
                      Ribosomal_L4 135 .......................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitks 184
                                                              ++ks+Liv+++ + +l++a+rnlpgv+v++v++lnv+ l+++++    +v+t+s
  gi|386001184|ref|YP_005919483.1| 167 vmrakdgktvragrgkmrgrrykQPKSLLIVAGR-EGGLIRASRNLPGVDVTTVDRLNVELLAPGTHagrlTVWTES 242
                                       5555667777778888888999999*******98.99**************************************** PP

                                       HHHHHHH CS
                      Ribosomal_L4 185 aveklee 191
                                        +++l e
  gi|386001184|ref|YP_005919483.1| 243 SLRWLGE 249
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1848.78
//
Query:       gi|386001185|ref|YP_005919484.1|  [L=297]
Description: 50S ribosomal protein L3P [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-81  273.7   0.0    1.1e-80  271.4   0.0    1.8  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.4   0.0   6.2e-85   1.1e-80      44     369 .]       2     296 ..       1     296 [. 0.93

  Alignments for each domain:
  == domain 1  score: 271.4 bits;  conditional E-value: 6.2e-85
                                       SEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCST CS
                      Ribosomal_L3  44 taflGyKaGmthiVrevdkpgskldkkevveavtvvetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyk 120
                                        +f+GyKaGmthi+  +dkp+s ++++e+ ++vt++etpp+ i++++ y++ + G+r+  + w+++l  ++ r +  
  gi|386001185|ref|YP_005919484.1|   2 DGFAGYKAGMTHIIMIDDKPNSLTEGMEISVPVTILETPPLSIAALRVYEKYNGGVRAAGEAWSDKLDPSLARSI-- 76 
                                       69***********************************************************************99.. PP

                                       STTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHH CS
                      Ribosomal_L3 121 nwykskkkaftkyskkyeskdvkklieadleeikkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldf 197
                                                    + k +     + i a +e +++     r+iaht  + ++++ +K+++l+EiqvngG+ia+++++
  gi|386001185|ref|YP_005919484.1|  77 ------------TVPKNKRGAAIDEIGAIIEDMEE----LRLIAHTNPKLLTGVPKKNPDLMEIQVNGGNIANQFEL 137
                                       ............12222233444455555555655....9************************************* PP

                                       HHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSSS..SSS-S-SS-SSSSS--TTS--SEE CS
                      Ribosomal_L3 198 arealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthrg..lRkvaaigawdparVsstvaraGq 272
                                       a++ l   v+++++F +g +iDv ++tkGkG++G+vkRWg++ ++rk+ rg  +R+++++g+w+p +V++tv+  Gq
  gi|386001185|ref|YP_005919484.1| 138 AKSLLGSSVPISSIFSPGSIIDVSAITKGKGVQGPVKRWGINLQKRKHSRGgkRRHIGNLGPWNPHHVRWTVPLLGQ 214
                                       ***************************************************99999********************* PP

                                       ESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGG CS
                      Ribosomal_L3 273 kGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqt 349
                                       +Gyh+Rte+nk++  ig+              +  itP+GGf+ yG++++++ ++ GsvpGp krlv++r +++++ 
  gi|386001185|ref|YP_005919484.1| 215 MGYHQRTEFNKRVLAIGS-------------DGGAITPDGGFPGYGIIRGEYAILSGSVPGPSKRLVRMRSAVRAKD 278
                                       ******************.............4678****************************************99 PP

                                       SCCCSS-EEEEEE-TTCTSS CS
                      Ribosomal_L3 350 srkaeeevslkfidtaskfg 369
                                        + + ++v   +++  sk+g
  gi|386001185|ref|YP_005919484.1| 279 ADLKTPQV--LYVSRDSKQG 296
                                       99999999..8999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1940.61
//
Query:       gi|386001186|ref|YP_005919485.1|  [L=279]
Description: hypothetical protein Mhar_0477 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-55  187.4   0.0    4.8e-55  187.1   0.0    1.1  1  Methyltrn_RNA_3  Putative RNA methyltransferase
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.52   10.5   0.0    1.8  2  SpoU_methylase   SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.1   0.0   5.4e-59   4.8e-55       2     285 ..       7     270 ..       6     271 .. 0.89

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 5.4e-59
                   Methyltrn_RNA_3   2 vsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFp 78 
                                        si+iPss + + ++++ +t ++g+IARaaa+F+Vd+iv+++d+e +      +s f++r+LqY+etP+YLrk+lFp
  gi|386001186|ref|YP_005919485.1|   7 TSILIPSSATMESRDERVRTLKVGMIARAAAVFRVDRIVIYRDEEFD------DSRFISRVLQYAETPQYLRKRLFP 77 
                                       69*****************************************9966......579********************* PP

                   Methyltrn_RNA_3  79 lhkelkyaglLppldaphhl.....rsseegeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVk 150
                                        ++ l+y+g+Lppl++phh      ++ + geyr G+vv++  ++     +V+iG+++++ l ++++ ++g R  V+
  gi|386001186|ref|YP_005919485.1|  78 RERALRYVGILPPLRTPHHPksskvSTLKVGEYRVGLVVDEVGSDDG--AWVEIGVERPLPLRTAKRFSAGQRLNVR 152
                                       ********************766544445789*******99876555..6**********999999*********** PP

                   Methyltrn_RNA_3 151 lsseesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkk.efkh 226
                                       + s ++  a+ V+ se      +ywGY+ +++ +l++ +  s       l+++ts+ g++ +  l +   ++ + + 
  gi|386001186|ref|YP_005919485.1| 153 VFSLKPLAAEPVDRSEI----PHYWGYETEVIPDLDEHVRSS-----GRLVVATSRLGTPATPDLLARVVRQgQGRG 220
                                       *99999******99998....5***************99987.....68999*******65555555545555899* PP

                   Methyltrn_RNA_3 227 llivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLal 285
                                       l +v+G+  rg++a+l ++        ++e    +++nt+p+qg++t+r+EEa++++L++
  gi|386001186|ref|YP_005919485.1| 221 LELVYGSpARGVDAFLSSE--------TMEG--CCVINTIPHQGTETVRLEEAIFATLSQ 270
                                       *******999999999555........3333..378**********************96 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.8e-05      0.52      15      44 ..      29      56 ..      27      72 .. 0.80
   2 ?   -1.2   0.0      0.23   2.1e+03      74      89 ..     190     205 ..     137     256 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.8e-05
                                      HHHHHHHHHHTT-SEEEEESGSSCTCGSHH CS
                    SpoU_methylase 15 lGaiaRtakafgaselvlvkprsadllnpe 44
                                      +G+iaR+a++f ++++v+ +++++  ++++
  gi|386001186|ref|YP_005919485.1| 29 VGMIARAAAVFRVDRIVIYRDEEF--DDSR 56
                                      7*****************987766..4444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.23
                                       CTEEEEEESTT-SEGC CS
                    SpoU_methylase  74 egfalvatslkgksls 89 
                                       +g  +vats+ g++ +
  gi|386001186|ref|YP_005919485.1| 190 SGRLVVATSRLGTPAT 205
                                       3334555555444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2155.22
//
Query:       gi|386001187|ref|YP_005919486.1|  [L=186]
Description: hypothetical protein Mhar_0478 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-11   44.5   0.0    2.9e-11   44.0   0.0    1.1  1  TIR_2            TIR domain
      0.005   16.8   0.0     0.0073   16.3   0.0    1.3  1  TIR-like         Predicted nucleotide-binding protein contain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.024   14.7   0.0    1.4  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
       0.07   12.6   0.6        8.4    6.0   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   6.5e-15   2.9e-11       1     114 [.       5     117 ..       5     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 6.5e-15
                             TIR_2   1 VFiSyssedkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaale 77 
                                       V+i +s+ed++ a++laeaL + g++ ++  +    g +  e+++ +i+++d+v+++l+ + + s+++++e+  a  
  gi|386001187|ref|YP_005919486.1|   5 VYITHSEEDEPLARELAEALWRVGLESFVAIYRRARGISPGERVRFGIRHCDCVIALLTLDGVVSPRVNQEIGFAAG 81 
                                       89************************998887778899999***********************************7 PP

                             TIR_2  78 aaeegkkrlipvllep.ekpp.laslqyidlskk.deeal 114
                                            ++ +ip+l ++ e p  +++l+ i +s++ + +al
  gi|386001187|ref|YP_005919486.1|  82 ----IDQLVIPLLEKEaELPVmIRHLKPITFSREgYSDAL 117
                                       ....3666****99953556545*********77776666 PP

>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-06    0.0073       1      66 [.       4      70 ..       4      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                          TIR-like  1 kvFivhg.edeeaaeevkelLeklglepiileeqvnkgktiiekleealksvdfaivlltpdDivak 66
                                      kv+i h+ ede +a+e++e+L ++gle ++   +  +g +  e ++  ++++d +i llt d +v  
  gi|386001187|ref|YP_005919486.1|  4 KVYITHSeEDEPLARELAEALWRVGLESFVAIYRRARGISPGERVRFGIRHCDCVIALLTLDGVVSP 70
                                      8***********************************************************9988765 PP

>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.4e-06     0.024      59     112 ..      51     102 ..       8     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-06
                                       HHHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGHHHHHTS CS
                   Nuc_deoxyrib_tr  59 lirqaDavianldpfrgpeaDsGtafEvGyavalgkpvlayttdarelrervea 112
                                       +ir++D+via l+        + +  E+G+a+++   v+ + +++ el   +++
  gi|386001187|ref|YP_005919486.1|  51 GIRHCDCVIALLTLDG--VVSPRVNQEIGFAAGIDQLVIPLLEKEAELPVMIRH 102
                                       79***********966..6888999************99999988886665555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0044        20       3      10 ..     135     142 ..     133     145 .. 0.64
   2 ?    6.0   0.1    0.0019       8.4      15      24 ..     164     173 ..     162     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0044
                       zf-ribbon_3   3 vrCPnCGa 10 
                                       ++CP CG+
  gi|386001187|ref|YP_005919486.1| 135 IKCPLCGE 142
                                       56666664 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0019
                       zf-ribbon_3  15 ddnvCpyCGt 24 
                                        d++C+yC +
  gi|386001187|ref|YP_005919486.1| 164 LDTICTYCES 173
                                       59******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1304.71
//
Query:       gi|386001188|ref|YP_005919487.1|  [L=163]
Description: N-acetyltransferase GCN5 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-14   54.2   0.0      2e-14   53.9   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.2e-14   53.0   0.0    4.7e-14   52.8   0.0    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.6e-09   37.4   0.0      5e-09   37.0   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    7.2e-08   32.7   0.0    1.6e-07   31.6   0.0    1.6  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.4e-07   29.5   0.0    8.9e-07   28.8   0.0    1.2  1  FR47             FR47-like protein
    7.6e-06   25.9   0.0    9.5e-06   25.6   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00018   21.2   0.0    0.00023   20.8   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.026   14.6   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.081   13.0   0.0       0.15   12.2   0.0    1.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   9.8e-18     2e-14       3     117 .]      18     137 ..      14     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 9.8e-18
                                       HHHHHHHHHTHHHHHHHHHHH.HHHHHHSTTC..EEEEEEET..TEEEEEEEEEEEET.TSTTEEEEEEEEESGGGT CS
                    Acetyltransf_1   3 dlvellvesffppnedaseee.feesfsleae..gllvaeed..geliGfisllkipd.ekggvayieslaVspeyr 73 
                                       ++++++v+  f  ++++ +   f++ + +       +v  ++  g+++Gf  l+   + ++  +++ + ++V+pe r
  gi|386001188|ref|YP_005919487.1|  18 EIFNFYVDNSFAAFPEDRVPGkFFDLLMEASRgyPAFV-ARGarGQVLGFGLLRSHHPmPAFSRTAEITIFVHPESR 93 
                                       56677777777777777777755555333333233333.3334699*****9999999*777788888********* PP

                                       TSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  74 gkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       g+G+G+ L   l+++a+ +gi+ i + +++ nd++i+++++lGF
  gi|386001188|ref|YP_005919487.1|  94 GMGIGRSLALRLIDEAKGRGITSILAGISSRNDGSIAFHRRLGF 137
                                       ***********************99999999********88**9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   2.4e-17   4.7e-14       4     155 .]       8     158 ..       5     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.4e-17
                    Acetyltransf_4   4 ateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkr.akdwka 78 
                                       +  eD +ei +i ++yv n +  f ++    + f+ ++ea    +   f +    +++ G   l+  ++  a +  a
  gi|386001188|ref|YP_005919487.1|   8 ISSEDREEIVEIFNFYVDNSFAAFPEDRVPGKFFDLLMEAS--RGYPAFVARGaRGQVLGFGLLRSHHPMpAFSRTA 82 
                                       5679999*********9999999888888888999999995..44444555559*********************** PP

                    Acetyltransf_4  79 elsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDmiw 155
                                       e+++++    ++ +g+gr l   l++ +k  +i+++la i s n+ si+fh +lGF+  g+fk ++ k g+ +D +w
  gi|386001188|ref|YP_005919487.1|  83 EITIFVH-PESRGMGIGRSLALRLIDEAKGRGITSILAGISSRNDGSIAFHRRLGFRERGRFKAIGRKWGEDFDVVW 158
                                       ******5.89****************************************************************999 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   2.5e-12     5e-09       2     138 .]       3     138 ..       2     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.5e-12
                    Acetyltransf_3   2 LlLrplteeDlealfe...lrsdpevmrylpepltleeaeewlerawaeeseeegyg.waivlkdtgviGsvglrdl 74 
                                       L L p+++eD e+++e   ++ d  +   +pe++ + +  ++l +      +++gy  ++ +   ++v+G+  lr+ 
  gi|386001188|ref|YP_005919487.1|   3 LELEPISSEDREEIVEifnFYVDNSFAA-FPEDRVPGKFFDLLME------ASRGYPaFVARGARGQVLGFGLLRSH 72 
                                       8899**9999999987222466877775.5776766666666663......34889845553333336******999 PP

                    Acetyltransf_3  75 eeedee...aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       ++ + +   ae+ + ++p+++g G+++  +  l++ a +  g++ + a i+ +N +Si+ +++lGf+
  gi|386001188|ref|YP_005919487.1|  73 HPMPAFsrtAEITIFVHPESRGMGIGRSLALRLIDEA-KGRGITSILAGISSRNDGSIAFHRRLGFR 138
                                       988877999****************************.8888************************6 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.7   9.4e+03      26      35 ..      18      27 ..      10      29 .. 0.67
   2 !   31.6   0.0   8.3e-11   1.6e-07       6      76 .]      54     139 ..      37     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.7
                                      CTEEEEE-GG CS
                    Acetyltransf_7 26 eitrlaVdpe 35
                                      ei +++Vd +
  gi|386001188|ref|YP_005919487.1| 18 EIFNFYVDNS 27
                                      5667888876 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 8.3e-11
                                       EEEEET.TEEEEEEEEEEES.......TCTEEEEE-GGGTTSSHHHHH.HHH..TT..SEEE.EEEEEE......TH CS
                    Acetyltransf_7   6 fVaedd.gkivGfialslld.......aeitrlaVdpeyrgkGiGraL.lea..ae..kgii.leqlel......na 62 
                                       fVa+   g+++Gf  l  +        + ++ ++V+pe rg GiGr L l++  ++  +gi+ +    l      n+
  gi|386001188|ref|YP_005919487.1|  54 FVARGArGQVLGFGLLRSHHpmpafsrTAEITIFVHPESRGMGIGRSLaLRLidEAkgRGITsI----LagissrND 126
                                       56644468889998888888998876666666****************7565331235664431....222322133 PP

                                       HHHHHHHHHTTEEE CS
                    Acetyltransf_7  63 ekaikfYeklGFee 76 
                                         +i+f ++lGF+e
  gi|386001188|ref|YP_005919487.1| 127 -GSIAFHRRLGFRE 139
                                       .8999*******96 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   4.4e-10   8.9e-07      27      80 ..      86     140 ..      80     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.4e-10
                                       EEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEE CS
                              FR47  27 lqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfeki 80 
                                       + v+pe r++G g++l+  l+ e   rg+t++ + +   N+ si++  +lGf+++
  gi|386001188|ref|YP_005919487.1|  86 IFVHPESRGMGIGRSLALRLIDEAKGRGITSIlAGISSRNDGSIAFHRRLGFRER 140
                                       789**************************975167999***************97 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.8e-09   9.5e-06      33     111 ..      53     142 ..      10     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.8e-09
                   Acetyltransf_10  33 llvaeeg.gkivGvielrdgs........hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                                        +va    g+++G++ lr+++            +fV+pe rg Gig++L  ++++ea+ +gi      + + +   +
  gi|386001188|ref|YP_005919487.1|  53 AFVARGArGQVLGFGLLRSHHpmpafsrtAEITIFVHPESRGMGIGRSLALRLIDEAKGRGITSiLAGISSRNdGSI 129
                                       4444433377778887777666775553322235***************************9999888999999*** PP

                   Acetyltransf_10  99 pfYeklGFkavge 111
                                       +f ++lGF++ g+
  gi|386001188|ref|YP_005919487.1| 130 AFHRRLGFRERGR 142
                                       *********9876 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.2e-07   0.00023     179     242 ..      79     145 ..      74     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                   GNAT_acetyltran 179 ekgieieidTkedyrrkgLAtivaaalileclkrglyPsWDaa...neaSvaLaekLGYefekeYkv 242
                                       ++ +ei i  +++ r+ g  + +a +li+e+  rg++         n  S+a  ++LG++   ++k+
  gi|386001188|ref|YP_005919487.1|  79 SRTAEITIFVHPESRGMGIGRSLALRLIDEAKGRGITSILAGIssrNDGSIAFHRRLGFRERGRFKA 145
                                       6789*******************************99988555777**************9988876 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.026      30      59 ..      86     115 ..      79     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                   Acetyltransf_CG  30 TeVpeelrGkGiAkkLvkaalddareeglk 59 
                                       ++V++e rG Gi++ L+ + +d+a+ +g +
  gi|386001188|ref|YP_005919487.1|  86 IFVHPESRGMGIGRSLALRLIDEAKGRGIT 115
                                       79**********************999865 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.4e-05      0.15      79     126 ..      86     138 ..      81     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--......SSHHHHHTTT-E CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfP......ssipiYrrfGye 126
                                       + v+pe rg g+ ++L  r+++e++ +g++ s+l +       si++ rr+G++
  gi|386001188|ref|YP_005919487.1|  86 IFVHPESRGMGIGRSLALRLIDEAKGRGIT-SILAGissrndGSIAFHRRLGFR 138
                                       679***********************9986.44444334444445788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 1010.35
//
Query:       gi|386001189|ref|YP_005919488.1|  [L=76]
Description: Deoxyribonuclease/rho motif-related TRAM [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-12   45.3   0.7    7.5e-12   45.1   0.7    1.1  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.7   4.2e-16   7.5e-12       2      61 ..      20      75 ..      19      76 .] 0.94

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.2e-16
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                      ++ G++++V++e+ s ++g+gi+r++ g+v+fvp +    Gd+ ++ ++kv  +++ ++ 
  gi|386001189|ref|YP_005919488.1| 20 VETGKEYDVEIEDIS-KQGDGIARIE-GFVIFVPETGV--GDKTKIMVDKVMQRFAIAHK 75
                                      678************.**********.********988..**************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 480.79
//
Query:       gi|386001190|ref|YP_005919489.1|  [L=133]
Description: hypothetical protein Mhar_0481 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.9   0.1       0.27   11.3   0.1    1.2  1  DUF982    Protein of unknown function (DUF982)


Domain annotation for each model (and alignments):
>> DUF982  Protein of unknown function (DUF982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.5e-05      0.27      13      47 ..      14      48 ..       9      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.5e-05
                                      EEEEEEHHHHHHHHHH--S---SHHHHHHHHHHHH CS
                            DUF982 13 vreissveeAldfLleeWPvsrgpayeaAlkaCrd 47
                                       r+++ +++ +++  + WPv +g + e Al+ C  
  gi|386001190|ref|YP_005919489.1| 14 KRIVAEIADKIEWTPQGWPVVEGLEGELALQKCYS 48
                                      57899****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 826.26
//
Query:       gi|386001191|ref|YP_005919490.1|  [L=139]
Description: hypothetical protein Mhar_0482 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-13   50.0   0.1    4.1e-13   49.5   0.1    1.2  1  4HBT      Thioesterase superfamily
      2e-06   27.9   0.1    2.6e-06   27.6   0.1    1.2  1  DUF4442   Domain of unknown function (DUF4442)
    3.3e-05   24.3   0.0    5.2e-05   23.6   0.0    1.3  1  4HBT_3    Thioesterase-like superfamily
  ------ inclusion threshold ------
      0.093   11.9   0.0        0.1   11.8   0.0    1.2  1  PS-DH     Polyketide synthase dehydratase


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.1   9.2e-17   4.1e-13       1      78 [.      48     122 ..      48     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 9.2e-17
                                       TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       +G  hgG++++l+Dea  +a +s+g    + v++++s++++++ + g++l +ea+ +  ++++a+++++v++ +g l
  gi|386001191|ref|YP_005919490.1|  48 FGMAHGGAIFSLIDEAFEVASNSHGT---VSVALSMSVTYVSSPKKGETLQAEAEEVSRSNRVATYDIRVKTAGGDL 121
                                       699**********************6...9******************************************99988 PP

                                       E CS
                              4HBT  78 v 78 
                                       +
  gi|386001191|ref|YP_005919490.1| 122 I 122
                                       6 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   5.9e-10   2.6e-06      12     112 ..      15     115 ..       3     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.9e-10
                                       HSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-. CS
                           DUF4442  12 kaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlak. 87 
                                         PY   +g++  e++ g+a v+++   +++N +g  H++Ai++l + a+ +    +  ++ + +  +m+v Y++  
  gi|386001191|ref|YP_005919490.1|  15 EEPYAEKMGLKLVEVAEGYALVEMRFTEEMENIFGMAHGGAIFSLIDEAFEVA---SNSHGTVSVALSMSVTYVSSp 88 
                                       46***********************************************9875...45678899999******9863 PP

                                       --S.-EEEEEE.-TTS-TT--EEEEEE CS
                           DUF4442  88 atg.dltavae.lepedvgekeelvve 112
                                       ++g +l+a+ae ++++++ ++++++v+
  gi|386001191|ref|YP_005919490.1|  89 KKGeTLQAEAEeVSRSNRVATYDIRVK 115
                                       444257777751333455555555554 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-08   5.2e-05      11      88 ..      51     134 ..      41     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                                       .-HHHHHHHHHHHHHHT....-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEE.EETTEEEEEEEE CS
                            4HBT_3  11 gyGGyvlAlalraaqrtv...pdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvel.sqggrpiftata 81 
                                       ++GG++ +l+ +a + +     ++ +  s++v+++   + g  ++ ++e+v +  +++t+ +++ + gg  i++++a
  gi|386001191|ref|YP_005919490.1|  51 AHGGAIFSLIDEAFEVASnshGTVSVaLSMSVTYVSSPKKGeTLQAEAEEVSRSNRVATYDIRVkTAGGDLIAICQA 127
                                       4********9999996554432223356************************************4456999999999 PP

                                       EEE---T CS
                            4HBT_3  82 sfgraes 88 
                                          r+++
  gi|386001191|ref|YP_005919490.1| 128 LVYRKRD 134
                                       9887764 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05       0.1     208     286 ..      59     128 ..      23     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHG..GG----------EEEEEEEEEEE-S...-BTS--EEEEEE----SS-EEEEEEEE-SS-BEEEEEE CS
                             PS-DH 208 llDaalQllaaalsaeaekadaaylPvaierlrvyrpssaageelwvharleeegarsivadltlvdedGrvvaeie 284
                                       l+D a+ +        +++++++ + ++++  +v+   +++ge+l+++a+  ++++r +++d+++ ++ G ++a  +
  gi|386001191|ref|YP_005919490.1|  59 LIDEAFEVA-------SNSHGTVSVALSMSVTYVSS--PKKGETLQAEAEEVSRSNRVATYDIRVKTAGGDLIAICQ 126
                                       455555544.......36777777777777777764..678******************************999776 PP

                                       SE CS
                             PS-DH 285 gl 286
                                        l
  gi|386001191|ref|YP_005919490.1| 127 AL 128
                                       66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 989.07
//
Query:       gi|386001192|ref|YP_005919491.1|  [L=182]
Description: N-acetyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-13   49.6   0.1    5.3e-13   49.2   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      1e-09   38.7   0.0    1.7e-09   38.0   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.3e-08   32.4   0.0    8.6e-08   32.2   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.8e-07   30.0   0.0    5.8e-07   29.4   0.0    1.3  1  FR47             FR47-like protein
     0.0028   17.7   0.0     0.0098   16.0   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.055   13.6   0.2       0.38   10.9   0.2    2.1  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   1.8e-16   5.3e-13      25     117 .]      65     158 ..      42     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.8e-16
                                       HHHHHSTTCEEEEEEET....TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                    Acetyltransf_1  25 eesfsleaegllvaeed....geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki 97 
                                       +   + e e+++++e +    g+++G + + k  +   ++a ++ l  +pe rg GlG++L e+++e+ r+ g+  i
  gi|386001192|ref|YP_005919491.1|  65 FATSRSERERIWIVEVEkageGRVVGSAAVVKASE---EEAQLRWLLLAPEVRGLGLGRRLAEEAVEFSRSVGYPSI 138
                                       33335566678885555567788************...89************************************* PP

                                       EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                       +l++    +aa  lYe lGF
  gi|386001192|ref|YP_005919491.1| 139 FLWTVRGLEAAESLYESLGF 158
                                       **9*999********99**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   5.6e-13   1.7e-09       2      76 .]      72     160 ..      71     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.6e-13
                                       TEEEEEEEET....TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEE...EE.EEEETH CS
                    Acetyltransf_7   2 kgevfVaedd....gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.ae....kgii...le.qlelna 62 
                                       +++++++e +    g++vG +a++  +   a++ +l  +pe rg G+Gr+L e  +e     g+    l+ +  l+ 
  gi|386001192|ref|YP_005919491.1|  72 RERIWIVEVEkageGRVVGSAAVVKASeeeAQLRWLLLAPEVRGLGLGRRLAEEaVEfsrsVGYPsifLWtVRGLE- 147
                                       6899****999**9*****9999988887777777*****************953223434442232234222232. PP

                                       HHHHHHHHHTTEEE CS
                    Acetyltransf_7  63 ekaikfYeklGFee 76 
                                        +a+++Ye+lGFee
  gi|386001192|ref|YP_005919491.1| 148 -AAESLYESLGFEE 160
                                       .6889*******96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   2.9e-11   8.6e-08      29     115 ..      71     167 ..      43     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.9e-11
                   Acetyltransf_10  29 gealllvaeeg....gkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnasp 95 
                                       ++  ++++e++    g++vG +++ + ++   ++  l  +pe rg G+g++L e++ e  +  g+      tv+   
  gi|386001192|ref|YP_005919491.1|  71 ERERIWIVEVEkageGRVVGSAAVvKASEeeaQLRWLLLAPEVRGLGLGRRLAEEAVEFSRSVGYPSifLWTVRGLE 147
                                       45555555554444489999998876666788***************************999998877999****** PP

                   Acetyltransf_10  96 yavpfYeklGFkavgeeqee 115
                                       +a+++Ye+lGF++++e++ e
  gi|386001192|ref|YP_005919491.1| 148 AAESLYESLGFEETEEKTSE 167
                                       **************665544 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.9e-10   5.8e-07      21      82 ..     101     163 ..      85     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.9e-10
                                       TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfekiee 82 
                                         +l  l + pe+r+ Glg+rl+++  +  +  g+  ++l++v + +++++lye+lGfe+ ee
  gi|386001192|ref|YP_005919491.1| 101 EAQLRWLLLAPEVRGLGLGRRLAEEAVEFSRSVGYpSIFLWTVRGLEAAESLYESLGFEETEE 163
                                       46788999*****************99999998873689999*****************9965 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.3e-06    0.0098      75     127 ..     103     160 ..      26     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-06
                                       EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       ++ +   ape rg g+ ++L ++a+e  r+ g+p ++l+      +++++Y+++G+e 
  gi|386001192|ref|YP_005919491.1| 103 QLRWLLLAPEVRGLGLGRRLAEEAVEFSRSVGYPSIFLWTvrgleAAESLYESLGFEE 160
                                       56667789********************************99988889********96 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.22   6.6e+02      26      49 ..      74      97 ..      59     108 .. 0.73
   2 ?   10.9   0.2   0.00013      0.38      33      57 ..     110     134 ..      78     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
                   Acetyltransf_CG 26 dfthTeVpeelrGkGiAkkLvkaa 49
                                       ++ +eV+++ +G+ ++++ v +a
  gi|386001192|ref|YP_005919491.1| 74 RIWIVEVEKAGEGRVVGSAAVVKA 97
                                      567789999999999998766555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                   Acetyltransf_CG  33 peelrGkGiAkkLvkaalddareeg 57 
                                        +e+rG G++++L+++a+++ r+ g
  gi|386001192|ref|YP_005919491.1| 110 APEVRGLGLGRRLAEEAVEFSRSVG 134
                                       699****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1242.66
//
Query:       gi|386001193|ref|YP_005919492.1|  [L=113]
Description: hypothetical protein Mhar_0484 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-06   26.2   0.4    8.6e-06   25.7   0.4    1.2  1  HTH_20        Helix-turn-helix domain
     0.0031   17.2   0.2      0.036   13.9   0.1    2.2  2  HTH_23        Homeodomain-like domain
     0.0055   16.5   0.0     0.0072   16.2   0.0    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.036   13.6   0.0      0.075   12.6   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.037   13.7   0.0      0.053   13.2   0.0    1.3  1  Sigma70_r4_2  Sigma-70, region 4
       0.16   12.0   0.0       0.22   11.6   0.0    1.1  1  HTH_45        Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.4   2.9e-09   8.6e-06      10      57 ..      39      85 ..      32      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.9e-09
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      + Rr+il++  ++++ +++e+ae l+++   + +HL+ Le+a  ve v
  gi|386001193|ref|YP_005919492.1| 39 RARRAILKMV-DEGAGSPEEIAEKLGIDGGLAAFHLAMLERALVVEAV 85
                                      78********.*******************************999976 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   1.2e-05     0.036       4      29 ..      38      64 ..      35      65 .. 0.85
   2 ?    1.2   0.0      0.12   3.6e+02       3      15 ..      74      86 ..      72      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                            HTH_23  4 ereRlrillllae.GlsvreIAreLgv 29
                                       r R  il++++e   s++eIA++Lg+
  gi|386001193|ref|YP_005919492.1| 38 LRARRAILKMVDEgAGSPEEIAEKLGI 64
                                      456777*******966**********8 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                            HTH_23  3 sereRlrilllla 15
                                       ++eR++++ +++
  gi|386001193|ref|YP_005919492.1| 74 AMLERALVVEAVD 86
                                      5899****99998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.4e-06    0.0072       3      42 ..      40      79 ..      39      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLrea 42
                                      +R+ ILk++ eg  +  e+ae+lg+  +    HL++L+ a
  gi|386001193|ref|YP_005919492.1| 40 ARRAILKMVDEGAGSPEEIAEKLGIDGGLAAFHLAMLERA 79
                                      599**********************************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05     0.075      19      43 ..      54      78 ..      38      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLee 43
                                      s  e+Ae+lg+  +    +l  Le+
  gi|386001193|ref|YP_005919492.1| 54 SPEEIAEKLGIDGGLAAFHLAMLER 78
                                      778********************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.053      15      39 ..      41      65 ..      35      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHTS---HHHHHHHHT-- CS
                      Sigma70_r4_2 15 qreifllryleglsykEIAellgis 39
                                      +r+i+ + ++   s +EIAe+lgi 
  gi|386001193|ref|YP_005919492.1| 41 RRAILKMVDEGAGSPEEIAEKLGID 65
                                      89*********************96 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.2e-05      0.22      10      69 ..      43     102 ..      38     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlellekl 69 
                                       +IL++++eg  ++ +i  k  ++  l+   L mL    +++  ++ Y+ T  G+ ++e++
  gi|386001193|ref|YP_005919492.1|  43 AILKMVDEGAGSPEEIAEKLGIDGGLAAFHLAMLERALVVEAVDGVYRSTPTGRLYIERV 102
                                       7**********************************99999*************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 940.16
//
Query:       gi|386001194|ref|YP_005919493.1|  [L=219]
Description: CDP-alcohol phosphatidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-07   30.8   1.5    3.8e-07   30.8   1.5    2.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.5   2.1e-11   3.8e-07       2      66 .]      25      88 ..      24      88 .. 0.84
   2 ?   -0.2   0.4     0.099   1.8e+03      13      13 ..     165     165 ..      94     203 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.1e-11
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                       Pna T l l+ ++  ++ l +  +l+ ++ll+l+++ +D +DG +AR ++ +s  G++lD ++D
  gi|386001194|ref|YP_005919493.1| 25 SPNAWTGLALAVALGGFVAL-WRGQLLPGLLLFLVSGGLDVVDGAVARTTGRTSVAGAFLDGVLD 88
                                      59999999999877666544.5555899999999**999*************777******9988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.099
                                       H CS
                   CDP-OH_P_transf  13 l 13 
                                       +
  gi|386001194|ref|YP_005919493.1| 165 A 165
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1865.93
//
Query:       gi|386001195|ref|YP_005919494.1|  [L=409]
Description: Aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-71  239.4   0.0    7.5e-71  239.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.2e-07   31.4   0.0    1.9e-07   30.7   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    3.9e-06   26.1   0.0    7.1e-06   25.2   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
     0.0011   17.6   0.0     0.0019   16.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.031   13.2   0.0      0.082   11.8   0.0    1.6  2  Alliinase_C      Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.2   0.0   2.1e-74   7.5e-71       2     363 .]      51     400 ..      50     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 2.1e-74
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi Lg++e+++     t+ ++++a +   l++g  ++y+ ++gl el+e la+ ++++ +l++++e +++ ++G +
  gi|386001195|ref|YP_005919494.1|  51 DVISLGVGEPDFP----TPWHIREACIY-SLECG-HTSYTSNKGLIELREILAESAKEELELDYDPEEEILITTGVS 121
                                       89**********9....**********9.66666.578*******************999***************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++ +++++++ lnpgde++vp+p y  y +++ l+gg   +++++ +e+f+l  e++ +a+ e      +tk +++ 
  gi|386001195|ref|YP_005919494.1| 122 EAVDLAFRAT-LNPGDEVIVPQPCYVAYVPDVLLAGGVPKPVATRLSEEFKLRPEDFRDAIGE------RTKALVLS 191
                                       **********.****************************************************......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                        p+NPtG+++t+e+le+++dl+ ++ ll+++De+Y ++ ++ + a +   +   ++ ++++++lsK+ +++G+R+Gy
  gi|386001195|ref|YP_005919494.1| 192 YPNNPTGAIMTREDLEEIADLVVENDLLVISDEVYDKLTYDGKHA-SFAQLEGMRDRTVLLNGLSKSCAMTGWRIGY 267
                                       ****************************************98743.3233333344489****************** PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       +lg++a++ +++k+++      ++ +q a+++al+  +    e+++m++++ +rr+ +++eL++lgl++++++++++
  gi|386001195|ref|YP_005919494.1| 268 ALGDSAIIGAMTKVHQYTMLcaPTMAQVAAVEALRRGES---EVKAMKREYDRRRRLFVSELERLGLPCFEPKGAFY 341
                                       ***************9888789**************996...9********************************** PP

                                       EEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                        +  ++    t +e++++Ll+e+ v+ +pg+ f+   +g+lR ++ ++++ee+ e+v+++
  gi|386001195|ref|YP_005919494.1| 342 AFPSIEGTglTSEEFAEELLKEQRVAAVPGNAFGEsgEGFLRCSY-ATSREEILEAVDRI 400
                                       ******9999***********************************.***********998 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   5.4e-11   1.9e-07      45     144 ..     118     223 ..     105     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.4e-11
                                       SSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE...E CS
                   DegT_DnrJ_EryC1  45 ssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl...p 117
                                       +  ++A+ la ra  ++pgdeVIvp+  +va +  vl +g +p +v     + + + p++ + ai ertka +   p
  gi|386001195|ref|YP_005919494.1| 118 TGVSEAVDLAFRA-TLNPGDEVIVPQPCYVAYVPDVLLAGGVPKPVATRlSEEFKLRPEDFRDAIGERTKALVlsyP 193
                                       4446899999998.4899**************************999873689******************984444 PP

                                       B-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 118 VhlyGqva...dmdalkaiaakhglkvieD 144
                                        +  G+++   d++++ ++  + +l vi+D
  gi|386001195|ref|YP_005919494.1| 194 NNPTGAIMtreDLEEIADLVVENDLLVISD 223
                                       577888776679999999999999999999 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     2e-09   7.1e-06      60     177 ..     110     225 ..      95     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2e-09
                                       TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH- CS
                       Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll 136
                                        eeei+ t G +ea+ l+ ++    l+pgde++v +  + a + p + la     k +  +l ee +l+++++++++
  gi|386001195|ref|YP_005919494.1| 110 PEEEILITTGVSEAVDLAFRAT---LNPGDEVIVPQPCYVAYV-PDVLLA-GGVPKPVATRLSEEFKLRPEDFRDAI 181
                                       579*****************99...***************999.999998.44456667899*************** PP

                                       -TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 137 nektklvaithvsnvtGti...qpveeigklakkkgalvlvDaa 177
                                        e+tk++ ++  +n tG i   +++eei++l+ +++ lv+ D +
  gi|386001195|ref|YP_005919494.1| 182 GERTKALVLSYPNNPTGAImtrEDLEEIADLVVENDLLVISDEV 225
                                       *****************852336999999999999999999865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.2e-07    0.0019      72     175 ..     115     225 ..     103     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.2e-07
                                       EESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHH..HHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEE CS
                   Cys_Met_Meta_PP  72 avssGma.AiaaailallkaGdeivvsddlYggt..qrllkkvlkk.lgievkfvdtsdleelekaikentklvylE 144
                                       ++++G++ A+++a++a l+ Gde++v + +Y       ll   ++k +  + +   +  +e+++ ai e+tk++ l 
  gi|386001195|ref|YP_005919494.1| 115 LITTGVSeAVDLAFRATLNPGDEVIVPQPCYVAYvpDVLLAGGVPKpVATRLSEEFKLRPEDFRDAIGERTKALVLS 191
                                       556665549999*******************86421566777676624444444445789***************** PP

                                       SS-TTTT---...-HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 145 tptnpllkvv...DiekiaklakkagvlvvvDnt 175
                                        p np+  ++   D+e+ia+l+ ++++lv+ D +
  gi|386001195|ref|YP_005919494.1| 192 YPNNPTGAIMtreDLEEIADLVVENDLLVISDEV 225
                                       ****996664444***************999976 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05     0.082     142     239 ..     188     300 ..     165     323 .. 0.65
   2 ?   -2.0   0.0      0.36   1.3e+03     317     351 ..     357     392 ..     348     403 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                                       EEES.S-TTT---..---......---TT-EEEEEE-TT....-...STTTS---S-B--SEEEEEHHHHHS-GGG- CS
                       Alliinase_C 142 lvts.PnnPdgll..rea......vvkgseakviyDlay....Y...WPhytpitskadedimLftlskltGhaGsr 202
                                       lv s PnnP g++  re       +v +++  vi D +y    Y      +++++   d  + L  lsk    +G r
  gi|386001195|ref|YP_005919494.1| 188 LVLSyPNNPTGAImtREDleeiadLVVENDLLVISDEVYdkltYdgkHASFAQLEGMRDRTVLLNGLSKSCAMTGWR 264
                                       5555599999987333322222222344444455554442222733334578889999******************* PP

                                       EEEEEES-HHHHHHHHHHHHHHHSS--HHHHHHHHHH CS
                       Alliinase_C 203 lGWalvkdkevakklveyieknsiGvskesqlrvlki 239
                                       +G+al  d+++   +++  + +       +q+ +++ 
  gi|386001195|ref|YP_005919494.1| 265 IGYAL-GDSAIIGAMTKVHQYTMLCAPTMAQVAAVEA 300
                                       ****8.5777777777666655555555555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.36
                                       HHHHHHTTTEEEEEGGGGT.S-TTEEEEESSS-HHH CS
                       Alliinase_C 317 caevlrekkiltrsGevfe.aesryvrlsllkrddd 351
                                        +e+l+e+++ +  G+ f+ +++ + r s   + ++
  gi|386001195|ref|YP_005919494.1| 357 AEELLKEQRVAAVPGNAFGeSGEGFLRCSYATSREE 392
                                       578999999999999999625677888877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2907.92
//
Query:       gi|386001196|ref|YP_005919495.1|  [L=163]
Description: AsnC family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for 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-14   54.2   0.1    1.8e-14   53.4   0.1    1.4  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.2e-08   33.5   0.0    4.4e-08   32.6   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00036   20.5   0.0    0.00063   19.7   0.0    1.3  1  HTH_20           Helix-turn-helix domain
     0.0004   20.2   0.1     0.0011   18.8   0.0    1.8  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0081   16.0   0.1      0.021   14.7   0.1    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.034   14.4   0.0      0.059   13.6   0.0    1.3  1  RNase_3_N        Ribonuclease III N-terminal domain
      0.057   13.2   0.0        0.1   12.4   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      0.067   13.1   0.0       0.14   12.1   0.0    1.5  1  MarR             MarR family
      0.076   12.9   0.0       0.16   11.9   0.0    1.4  1  MarR_2           MarR family
       0.12   12.3   0.0       0.33   10.9   0.0    1.7  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
       0.15   11.7   0.0       0.41   10.3   0.0    1.7  2  DUF4423          Domain of unknown function (DUF4423)
       0.16   11.8   0.0       0.26   11.2   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   1.2e-17   1.8e-14       3      74 ..      72     141 ..      68     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.2e-17
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       vsl++++   +++++e++ ++ eV+++  ++Gd+d+ + v+ r++++   f+ ek+a+l+gv+ t t++vl+
  gi|386001196|ref|YP_005919495.1|  72 VSLSRDK--GYDAIAERISRFSEVQSVRLISGDHDISFTVRGRSMKDVAFFVTEKIATLEGVEATCTHFVLK 141
                                       6666666..9*************************************************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.9e-11   4.4e-08       2      48 .]       2      48 ..       1      48 [. 0.95

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.9e-11
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++  ++ILe+L++n+r +  e+A  lg + + v + +k Le++G+I+
  gi|386001196|ref|YP_005919495.1|  2 RDFAKEILEVLEENARATPGEIATLLGRPEGEVAAEIKSLEDSGIIR 48
                                      566789****************************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.2e-07   0.00063      14      55 ..       7      48 ..       4      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +il  L +++ +t++e+a +l+ +  ++   ++ Le+ g+++
  gi|386001196|ref|YP_005919495.1|  7 EILEVLEENARATPGEIATLLGRPEGEVAAEIKSLEDSGIIR 48
                                      69999***********************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     7e-07    0.0011       7      42 .]       7      42 ..       3      42 .. 0.93
   2 ?   -2.5   0.0       3.2   4.8e+03      33      39 ..      82      88 ..      80      89 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7e-07
                     HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                       ILe L+e+aR++  e+A  +G  e +v++ ++ Le
  gi|386001196|ref|YP_005919495.1|  7 EILEVLEENARATPGEIATLLGRPEGEVAAEIKSLE 42
                                      7***************************99888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.2
                     HTH_AsnC-type 33 tvlrRvr 39
                                      ++++R+ 
  gi|386001196|ref|YP_005919495.1| 82 AIAERIS 88
                                      5666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.4e-05     0.021      16      54 ..      11      49 ..       6      71 .. 0.85
   2 ?   -2.7   0.0       3.7   5.5e+03      29      59 ..     126     156 ..     122     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      +L ++ +at  eia  lg+p+  v   ++sLed G++++
  gi|386001196|ref|YP_005919495.1| 11 VLEENARATPGEIATLLGRPEGEVAAEIKSLEDSGIIRK 49
                                      4458999*****************************987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                                       CCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  29 aeelgvprskvYevLrsLedkGlVerekgrp 59 
                                       a   gv+ +    vL+s ++ G++   + +p
  gi|386001196|ref|YP_005919495.1| 126 ATLEGVEATCTHFVLKSYKEHGVILYDRVQP 156
                                       5555566666666777777777765555555 PP

>> RNase_3_N  Ribonuclease III N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05     0.059      37      83 ..      12      58 ..       5      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                                      HHHSGCSS-GGGHHHHCSHHHHHHHHHHHHHHTT--THHHHHHHHHH CS
                         RNase_3_N 37 aleneeklpveilpalsRykLklAaelksleelgklplleeisnyes 83
                                      + en  ++p ei   l R +  +Aae+ksle++g ++ + ++ n+e+
  gi|386001196|ref|YP_005919495.1| 12 LEENARATPGEIATLLGRPEGEVAAEIKSLEDSGIIRKYMTMINWEK 58
                                      34578899*************************99998888888875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.8e-05       0.1       7      49 ..       7      48 ..       5      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iL+ l+e +++ t  e+A  +g p   v   +++L+  G+++
  gi|386001196|ref|YP_005919495.1|  7 EILEVLEENARA-TPGEIATLLGRPEGEVAAEIKSLEDSGIIR 48
                                      69*********8.***********************9999987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.3e-05      0.14       8      50 ..       8      50 ..       6      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      iL+ l+e+  ++  e+a  lg   + v   ++ Le+ G i+++
  gi|386001196|ref|YP_005919495.1|  8 ILEVLEENARATPGEIATLLGRPEGEVAAEIKSLEDSGIIRKY 50
                                      8999************************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      10      53 ..       8      49 ..       7      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L +L  + +   t+ge+a  lg + + v   +k L++ G +++
  gi|386001196|ref|YP_005919495.1|  8 ILEVLEENAR--ATPGEIATLLGRPEGEVAAEIKSLEDSGIIRK 49
                                      6888999997..9****************************986 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.33      48      98 ..      12      58 ..       9      75 .. 0.91
   2 ?   -2.1   0.0       2.3   3.4e+03      32      49 ..     137     152 ..     115     157 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                   Phage_rep_org_N 48 lsenipytaemlalifnreletvrlaLkvlkdlelieisedkvikiknwek 98
                                      l+en   t  ++a+++ r+ ++v + +k l+d ++i +     +++ nwek
  gi|386001196|ref|YP_005919495.1| 12 LEENARATPGEIATLLGRPEGEVAAEIKSLEDSGIIRKY----MTMINWEK 58
                                      789999999***************************987....77778877 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                   Phage_rep_org_N  32 kllvlaGKlnenGelyls 49 
                                       + ++++  ++e+G + ++
  gi|386001196|ref|YP_005919495.1| 137 HFVLKS--YKEHGVILYD 152
                                       344555..5555555555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.41      34      72 ..      15      51 ..       4      64 .. 0.83
   2 ?   -1.5   0.0       1.2   1.7e+03      22      47 ..      63      88 ..      51      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                           DUF4423 34 dfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                      +++a+p e+a  l+   ++ ev++ ++ L+++g+++k  
  gi|386001196|ref|YP_005919495.1| 15 NARATPGEIATLLG--RPEGEVAAEIKSLEDSGIIRKYM 51
                                      3469**********..*******************9965 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                           DUF4423 22 yypvirel.lplkdfkadpeelakrlr 47
                                      y  +i el ++l    + ++++a+r+ 
  gi|386001196|ref|YP_005919495.1| 63 YVYAIVELkVSLSRD-KGYDAIAERIS 88
                                      555566654555555.56666666654 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.26       6      47 .]       7      49 ..       5      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +IL  L+e   ++ +e+a  lg +++ v    k L+++G+++k
  gi|386001196|ref|YP_005919495.1|  7 EILEVLEEnARATPGEIATLLGRPEGEVAAEIKSLEDSGIIRK 49
                                      8*******666*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1135.01
//
Query:       gi|386001197|ref|YP_005919496.1|  [L=109]
Description: hypothetical protein Mhar_0488 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       143  (0.0079759); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 851.05
//
Query:       gi|386001198|ref|YP_005919497.1|  [L=305]
Description: PP-loop domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-11   42.7   0.0    1.8e-10   40.9   0.0    1.8  1  ATP_bind_3       PP-loop family
    9.3e-07   27.9   0.0    1.2e-06   27.6   0.0    1.1  1  tRNA_Me_trans    tRNA methyl transferase
    1.5e-05   24.4   0.5    1.5e-05   24.4   0.5    2.8  4  zn-ribbon_14     Zinc-ribbon
  ------ inclusion threshold ------
      0.076   12.7   0.2       0.17   11.5   0.2    1.5  1  Asn_synthase     Asparagine synthase
       0.16   12.0   0.0       0.26   11.3   0.0    1.4  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
       0.59   10.6   3.0         36    4.8   0.1    3.2  3  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   6.1e-14   1.8e-10       2     163 ..      51     223 ..      50     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 6.1e-14
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       ++vAvSgG DS  Ll +l+ l ++ +  +lva+ +d g+     +  ++ ++++k l++++++ +++          
  gi|386001198|ref|YP_005919497.1|  51 IAVAVSGGKDSSSLLSILHALFSSREDvELVAVSIDEGIAGYRPRTLAAAASVAKGLGVEHVVRSLEGefgvttdll 127
                                       78****************9987655444*************************************998888888776 PP

                                       .HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.CCEE-C CS
                        ATP_bind_3  69 .akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.irlvRP 143
                                        ++ + ++       lR  +l++++++ +++ ++++h+ dD a t++l+  +g   + l+ +++++ + + +  + P
  gi|386001198|ref|YP_005919497.1| 128 aSSGQPQGPCSFCGVLRKGLLNRTARELSADAVATGHNLDDEAQTVMLNYLKGDV-DRLYRLRPRRALPGmVPRIKP 203
                                       5333445555677889************************************876.68889999998877688999* PP

                                       CCT--HHHHHHHHHHTT--- CS
                        ATP_bind_3 144 lLkvskeeleeylkekkikw 163
                                       l  v  +e+  y+  + i++
  gi|386001198|ref|YP_005919497.1| 204 LRRVPEKEMGVYAIAHAIPF 223
                                       ********999999999887 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0     4e-10   1.2e-06       2     125 ..      50     165 ..      49     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4e-10
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                       +++va+SgG DSs  + +l+  + + + v l  ++  de   +    + l+ a +va+ lg+++ v ++e e+   v
  gi|386001198|ref|YP_005919497.1|  50 RIAVAVSGGKDSSSLLSILHALFSSREDVELVAVSI-DEGI-AGYRPRTLAAAASVAKGLGVEHVVRSLEGEFG--V 122
                                       799**************************9988776.4444.678899*************************5..8 PP

                     tRNA_Me_trans  79 feefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                         ++l +  +G+   P+  C    + g+l ++a e l ada+atGH 
  gi|386001198|ref|YP_005919497.1| 123 TTDLLAS--SGQPQGPCSFCGVL-RKGLLNRTARE-LSADAVATGHN 165
                                       9999985..899999*****865.44667777776.**********6 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.3       1.7   5.1e+03       2       6 ..       3       7 ..       3       8 .. 0.86
   2 ?   -1.9   0.1      0.85   2.5e+03       3       8 ..     137     142 ..     135     143 .. 0.79
   3 ?   -2.8   0.0       1.6   4.7e+03      20      29 ..     242     251 ..     242     253 .. 0.85
   4 !   24.4   0.5     5e-09   1.5e-05       3      25 ..     278     300 ..     276     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                      zn-ribbon_14 2 kCerC 6
                                     +C rC
  gi|386001198|ref|YP_005919497.1| 3 RCDRC 7
                                     7**** PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.85
                      zn-ribbon_14   3 CerCGy 8  
                                       C+ CG 
  gi|386001198|ref|YP_005919497.1| 137 CSFCGV 142
                                       999*97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                      zn-ribbon_14  20 LLegLnkgrp 29 
                                       LL++L++ +p
  gi|386001198|ref|YP_005919497.1| 242 LLNDLEAKHP 251
                                       8999*99888 PP

  == domain 4  score: 24.4 bits;  conditional E-value: 5e-09
                      zn-ribbon_14   3 CerCGylSSqkiCkACvLLegLn 25 
                                       C+rCG  SS  +C  C LLe+L+
  gi|386001198|ref|YP_005919497.1| 278 CTRCGEPSSDGVCATCRLLERLR 300
                                       *********************97 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   5.6e-05      0.17      20      78 ..      51     115 ..      48     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                      Asn_synthase  20 vGalLSGGlDSSliaalaarqsk..splktFsigfee....kgsdeakyakevaehlgtehtelv 78 
                                       +++  SGG DSS++ +++ +     +++  +++  +e     +   +++a+ va+ lg+eh+   
  gi|386001198|ref|YP_005919497.1|  51 IAVAVSGGKDSSSLLSILHALFSsrEDVELVAVSIDEgiagYRPRTLAAAASVAKGLGVEHVVRS 115
                                       67889**************988778889999999966774455566788999********97655 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.8e-05      0.26       2     156 ..      51     224 ..      50     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinae 71 
                                       ++v+vsgGkds+ ll ++   f  +       v +d g     p t++    +++ +g++  v + e e+       
  gi|386001198|ref|YP_005919497.1|  51 IAVAVSGGKDSSSLLSILHALFSSRedvelVAVSIDEGIAgyRPRTLAAAASVAKGLGVEHVVRSLEGEFGVTTDLL 127
                                       789************99999998876777779999999863368888899999999988844444444443333333 PP

                                       H-S-THHHC...HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S...........CEEE- CS
                       PAPS_reduct  72 khgsslyee...aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek...........slrvf 134
                                          ss   +    ++ + +   l+++ ++l++da+ tG   d++++   l++++ d d              + r+ 
  gi|386001198|ref|YP_005919497.1| 128 A--SSGQPQgpcSFCGVLRKGLLNRTARELSADAVATGHNLDDEAQTVMLNYLKGDVDRLYrlrprralpgmVPRIK 202
                                       3..33333367789999999999999999999999999999999988888888877774446777777777666777 PP

                                       CCCT--HHHHHHHHHHCT--B- CS
                       PAPS_reduct 135 PllnWteedvwqyilrenipyn 156
                                       Pl    e++   y+ ++ ip  
  gi|386001198|ref|YP_005919497.1| 203 PLRRVPEKEMGVYAIAHAIPFE 224
                                       7777777777777777777765 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.032        95       5      20 ..       3      18 ..       1      25 [. 0.86
   2 ?    0.5   0.0      0.26   7.8e+02       5      10 ..     136     141 ..     134     160 .. 0.89
   3 ?    4.8   0.1     0.012        36      13      38 ..     263     285 ..     252     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.032
                   Lar_restr_allev  5 pCPfCggravlersqr 20
                                       C+ C gra ++++++
  gi|386001198|ref|YP_005919497.1|  3 RCDRCSGRAAIFQRYS 18
                                      5********9999876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.26
                   Lar_restr_allev   5 pCPfCg 10 
                                       pC fCg
  gi|386001198|ref|YP_005919497.1| 136 PCSFCG 141
                                       999999 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.012
                   Lar_restr_allev  13 avlersqrvvaeigqcvyCadCgast 38 
                                       ++l r++ +++e   +v+C+ Cg  +
  gi|386001198|ref|YP_005919497.1| 263 KILARDPPGSYE---VVACTRCGEPS 285
                                       566777777787...********833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2070.66
//
Query:       gi|386001199|ref|YP_005919498.1|  [L=348]
Description: Cell division protein pelota [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-25   89.4   0.0    2.6e-25   88.9   0.0    1.2  1  eRF1_1    eRF1 domain 1
    7.3e-20   71.6   0.0    3.6e-19   69.3   0.0    2.2  2  eRF1_3    eRF1 domain 3
    6.7e-06   26.4   0.0    1.4e-05   25.4   0.0    1.6  1  eRF1_2    eRF1 domain 2
  ------ inclusion threshold ------
        0.1   13.0   0.0       0.28   11.5   0.0    1.7  1  DinI      DinI-like family


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   5.8e-29   2.6e-25       1     128 [.       1     124 [.       1     125 [. 0.93

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 5.8e-29
                                       HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqre.sstgsreservklkLtikvekvdfdk 76 
                                       m++lk++l++d +g ++L+ e+ +dlwhl  liapgd v a t+rk + +  +    + er  ++L i+ve+v+f++
  gi|386001199|ref|YP_005919498.1|   1 MRVLKKSLRGD-EGEISLVTESIDDLWHLKYLIAPGDLVFALTHRKATPSaDKLRPEKLERRPVRLGIRVESVEFHT 76 
                                       9********88.9*********************************9884133333447****************** PP

                                       TSSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  77 dagvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                       +++ lr++G +  +++   + ++htl+le++ +++i k +w    l r++ea
  gi|386001199|ref|YP_005919498.1|  77 SSSWLRVHGVIEVGQD---VSSYHTLNLEPGSDLSIVK-RWRPDELARIREA 124
                                       ****************...9******************.9*********998 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   6.3e+03      25      42 ..     232     249 ..     227     250 .. 0.80
   2 !   69.3   0.0     8e-23   3.6e-19       4     113 .]     257     346 ..     254     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                                       SHHHHHHHHHTT-EEEEE CS
                            eRF1_3  25 GveevlkalemgAvetLL 42 
                                       Gv   +++l+ gA++++L
  gi|386001199|ref|YP_005919498.1| 232 GVSGFQEVLRRGAIDQIL 249
                                       666678889999999987 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 8e-23
                                       HHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHH CS
                            eRF1_3   4 ekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvee 80 
                                       e+ lle +l+e+a+d g+a+YG  ev+ a+e gAvetL+vs+e  rs      +             +++l+++v++
  gi|386001199|ref|YP_005919498.1| 257 ETTLLEALLREIATD-GRAAYGPAEVRGAAEQGAVETLMVSDEQVRSP-----E-------------MDRLMRSVSD 314
                                       8899***********.***************************99996.....2.............89******** PP

                                       TT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  81 sgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                        +++v+i+sse+e G++l +a+gG+aai Ryk+
  gi|386001199|ref|YP_005919498.1| 315 ARGRVVIFSSEFEPGKRL-SALGGVAAITRYKI 346
                                       ******************.************97 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.1e-09   1.4e-05       3     127 ..     134     244 ..     132     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.1e-09
                                       EEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESE CS
                            eRF1_2   3 glivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkg 79 
                                        + +++ege+ ig+l++  +e++++i +   +K + G    r     r e l+e  k++a  a ++           
  gi|386001199|ref|YP_005919498.1| 134 VIALVEEGETAIGVLRQFGVETVSEIRMG-GGKGMSGRGGDR-----RTEFLDEAAKEIARVAASD---------SK 195
                                       56789*********************998.577777777777.....4667777888888777777.........56 PP

                                       EEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC.C CS
                            eRF1_2  80 iilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek.a 127
                                       +ilagpgf+ke++ +   + +   +  i+l d+s  g sg++evl+  a
  gi|386001199|ref|YP_005919498.1| 196 VILAGPGFTKEDLKRRVDAAYPGLAPRIVLCDASAMGVSGFQEVLRRgA 244
                                       9********************************************9853 PP

>> DinI  DinI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.2e-05      0.28      10      54 ..     206     251 ..     203     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHHH-SS-EEEEEEESS-EEEEES.--HHHHHHHHHHHHH CS
                              DinI  10 aELskRiqevfPdaevrvrkasanglsveG.askedkeriseiLQe 54 
                                       ++L++R++  +P    r++   a+++ v+G ++   + +i++iL+e
  gi|386001199|ref|YP_005919498.1| 206 EDLKRRVDAAYPGLAPRIVLCDASAMGVSGfQEVLRRGAIDQILEE 251
                                       68****************************9*99**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.61
# Mc/sec: 1717.57
//
Query:       gi|386001200|ref|YP_005919499.1|  [L=738]
Description: DNA topoisomerase I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   8.6e-118  393.9   0.0   1.1e-117  393.6   0.0    1.1  1  Topoisom_bac    DNA topoisomerase
    5.3e-15   55.5   0.0    2.3e-14   53.5   0.1    2.1  2  Toprim          Toprim domain
    5.9e-13   48.4   3.1    1.7e-12   46.9   0.3    2.3  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
    1.2e-08   35.5   3.1    2.8e-08   34.2   2.0    2.3  2  HHH_5           Helix-hairpin-helix domain
     0.0058   16.9   0.1      0.013   15.8   0.1    1.5  1  DUF4332         Domain of unknown function (DUF4332)
     0.0088   15.9   0.2      0.027   14.3   0.2    1.9  1  HHH             Helix-hairpin-helix motif
     0.0098   16.1   0.0      0.021   15.1   0.0    1.5  1  Cdd1            Pathogenicity locus
  ------ inclusion threshold ------
      0.046   14.1   0.8        0.1   13.0   0.1    2.0  2  IMS_HHH         IMS family HHH motif


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.6   0.0  4.9e-121  1.1e-117       2     412 ..     150     546 ..     149     547 .. 0.93

  Alignments for each domain:
  == domain 1  score: 393.6 bits;  conditional E-value: 4.9e-121
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                       ++++l+ ++eaR+++D+++G++l+r+++ +  +  k++ls+GRVq+ptLaliv+Re+eie+F+p++ywe++a l+k+
  gi|386001200|ref|YP_005919499.1| 150 VDFDLASSGEARQVVDLIWGAALTRFISITSGRlgKGFLSVGRVQSPTLALIVDREKEIEAFKPQPYWEISACLEKD 226
                                       6889************************94444569***********************************987555 PP

                      Topoisom_bac  77 kkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqk 153
                                        +      k++k+ri++ + a++i+e+l +  a+v+s+++k+++++pp pfdtt++ ++as + g+sa+++++ia+ 
  gi|386001200|ref|YP_005919499.1| 227 LR-----VKHEKGRIWEGDLARSIFEELGE-VATVVSIKEKTRTDRPPAPFDTTAFISAASGI-GFSAANAMRIAEW 296
                                       43.....589******************55.6******************************8.************* PP

                      Topoisom_bac 154 LYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklk 230
                                       LY++ g+i+YpRT++t+++++ +l+a+++ ++k   + ++e ae++l+ +  + ++++   ++H++I+Pt+ ++k  
  gi|386001200|ref|YP_005919499.1| 297 LYTS-GFISYPRTENTVYPKTLDLRALVSIFKKG--P-FREDAERVLSGPMVP-TRGKRFSTDHPPIYPTAPAAK-A 367
                                       ***7.****************77******99995..5.999999*99977755.5555555*********88775.8 PP

                      Topoisom_bac 231 elsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegee 307
                                       + + d++k+Yel+vrrfla+l+ + ++  ++v++e++++ f+a+g + +e+G+++ y+++k+ ee   lp+l+ege+
  gi|386001200|ref|YP_005919499.1| 368 DMKPDQWKIYELVVRRFLATLSGPSRWIVMNVRVEIDGQPFRATGARQIEAGWRACYPYSKAAEE--ILPQLSEGEK 442
                                       999********************************************************999987..6********* PP

                      Topoisom_bac 308 vkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.k 383
                                       ++v + eleek+T+pp+ry +++L+k+m++ g+Gt++Tr+eii+kl+ r Yv+ +   ++pt+++ a+ve+l++  +
  gi|386001200|ref|YP_005919499.1| 443 LRVLGKELEEKETQPPSRYGQGRLVKLMDELGLGTKSTRHEIISKLYARAYVQGNP--MKPTNTAYAVVEALQQHsP 517
                                       *****************************************************966..9*************7777* PP

                      Topoisom_bac 384 dlvspelTaeleekLdeIaegkadakevl 412
                                       ++++p++T+ lee++ +Ia+g   +++v+
  gi|386001200|ref|YP_005919499.1| 518 NITKPDMTRTLEEDMTKIANGHVGEEAVI 546
                                       **********************9999997 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1     1e-17   2.3e-14       2     103 .]       3     135 ..       2     135 .. 0.89
   2 ?   -2.2   0.0       2.2   4.9e+03      22      46 ..     340     362 ..     318     380 .. 0.72

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1e-17
                                       EEEESSHHHHHHHHHTHT................STEEEEEEESSSSEEEHS..........TTEEEEE........ CS
                            Toprim   2 lvivEgpsdaktiakalg................sgfqavtaslGhildlet..........efkpvye........ 44 
                                       l+i+E+ + ak ia++l                  ++++v+ ++Ghi+ ++           +              
  gi|386001200|ref|YP_005919499.1|   3 LIIAEKHNVAKRIAQILAgskpkvkrvhgieafyFDDKVVMGLSGHIVGVDYppgynnwqkvD-----Yrdlihaev 74 
                                       8****************9****************999***************77776555551.....145555666 PP

                                       .ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESSS CS
                            Toprim  45 .eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefsei 103
                                         ++++ k+++al+ l k+ad+i +atD DreGe i+ e+l  ++++++  k  rv+fs i
  gi|386001200|ref|YP_005919499.1|  75 vTRPTQGKIVSALHDLGKDADRITIATDYDREGELIGVEALRIAEDANPTiKADRVRFSAI 135
                                       69***************************************99998777788899999976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
                                       EEEEEEESSSSEEEHSTTEEEEEEC CS
                            Toprim  22 fqavtaslGhildletefkpvyeei 46 
                                        + +++++G+ ++ ++  +p+y   
  gi|386001200|ref|YP_005919499.1| 340 SGPMVPTRGKRFSTDH--PPIYPTA 362
                                       5679999***999999..7776633 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.3   7.5e-16   1.7e-12       2      38 ..     582     619 ..     581     620 .. 0.95
   2 ?    1.5   0.2      0.12   2.6e+02       4      10 ..     652     659 ..     650     667 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 7.5e-16
                                       EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       + C  Cg +L+++rg++G +F+GC  YP+C+ft +l+k
  gi|386001200|ref|YP_005919499.1| 582 GLCQICGHELIIRRGRRGsRFIGCAGYPDCTFTLPLPK 619
                                       78*********************************986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.12
                                       -SSS-.-E CS
                    zf-C4_Topoisom   4 CPkCg.gd 10 
                                       CPkC+ ++
  gi|386001200|ref|YP_005919499.1| 652 CPKCNfDQ 659
                                       99998555 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.1   6.9e+03      37      44 ..     277     284 ..     241     296 .. 0.48
   2 !   34.2   2.0   1.3e-11   2.8e-08       2      53 ..     675     726 ..     674     730 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                                       HHTSTTS- CS
                             HHH_5  37 LakipGiG 44 
                                       ++++ GiG
  gi|386001200|ref|YP_005919499.1| 277 ISAASGIG 284
                                       55555554 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1.3e-11
                                       HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       ++L +++GiGpkt  +l  aG+++  dla a++e+La+ +G+ kk+  ++ l
  gi|386001200|ref|YP_005919499.1| 675 DLLAKIPGIGPKTLEKLGAAGVKTALDLAGAEAEALAEKTGLTKKKISSWQL 726
                                       5799******************************************999976 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   5.6e-06     0.013       1      54 [.     681     729 ..     673     735 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                           DUF4332   1 pgigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAd 54 
                                       pgig++  ekL +aG+kt+ dL+ ++   ++  alaek+g++ +++ +++ lA+
  gi|386001200|ref|YP_005919499.1| 681 PGIGPKTLEKLGAAGVKTALDLAGAE---AE--ALAEKTGLTKKKISSWQLLAK 729
                                       67888888888888888888888773...33..477788888888888887776 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   1.2e-05     0.027      10      25 ..     674     689 ..     667     691 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                       HHHHHTSTT-SHHHHH CS
                               HHH  10 reeLlalPGVGpktAe 25 
                                       ++ L+++PG+Gpkt e
  gi|386001200|ref|YP_005919499.1| 674 VDLLAKIPGIGPKTLE 689
                                       68899*********76 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.2e-06     0.021       3      45 ..     672     714 ..     670     722 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.2e-06
                              Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelyekl 45 
                                       ++++ l +iP+iG+++ e+l + G+++  +l+g ++e+l ek 
  gi|386001200|ref|YP_005919499.1| 672 TEVDLLAKIPGIGPKTLEKLGAAGVKTALDLAGAEAEALAEKT 714
                                       5677899*******************************99886 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.9   1.3e+04      15      25 ..     442     452 ..     441     453 .. 0.60
   2 ?   13.0   0.1   4.6e-05       0.1      14      32 .]     678     696 ..     677     696 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.9
                           IMS_HHH  15 kipGiGgklge 25 
                                       k++ +G+ l+e
  gi|386001200|ref|YP_005919499.1| 442 KLRVLGKELEE 452
                                       55666766666 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.6e-05
                           IMS_HHH  14 tkipGiGgklgekLeklGi 32 
                                        kipGiG+k+ ekL + G+
  gi|386001200|ref|YP_005919499.1| 678 AKIPGIGPKTLEKLGAAGV 696
                                       69************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 4146.62
//
Query:       gi|386001201|ref|YP_005919500.1|  [L=434]
Description: Methyl-coenzyme M reductase, beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-139  463.9   8.0     2e-139  463.3   8.0    1.3  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    2.1e-82  275.2   1.8    4.6e-82  274.1   1.8    1.6  1  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.3   8.0  2.3e-143    2e-139       1     248 [.     186     433 ..     186     434 .] 1.00

  Alignments for each domain:
  == domain 1  score: 463.3 bits;  conditional E-value: 2.3e-143
                          MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtv 77 
                                       G+alrni+anh++aitk+na+naaalssi+eq+++femG+a+G fer+++lglayqGlnann+vydlvk+ngk+gt+
  gi|386001201|ref|YP_005919500.1| 186 GFALRNIMANHIAAITKRNAMNAAALSSIYEQIGNFEMGNAIGIFERYQMLGLAYQGLNANNMVYDLVKSNGKTGTI 262
                                       8**************************************************************************** PP

                          MCR_beta  78 GtvveslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleke 154
                                       Gtvv+s+vera+edkvik+ +klpsg+ +ye+ dv++wnay+aaG+laa++vn+ga r aqavsstlly+nd++eke
  gi|386001201|ref|YP_005919500.1| 263 GTVVHSVVERAVEDKVIKAGEKLPSGFVMYEAVDVPMWNAYCAAGTLAATMVNCGALRGAQAVSSTLLYFNDVIEKE 339
                                       ***************************************************************************** PP

                          MCR_beta 155 tglpGvdfGrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgev 231
                                       t+lpG+d+G+v+GtavGfsffshsiyGGGGpG+fnGnhvvtrhs+Gfaipcv+aavaldaGtq+f+pe+tsglvg v
  gi|386001201|ref|YP_005919500.1| 340 TALPGCDWGKVMGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVSAAVALDAGTQMFTPEMTSGLVGAV 416
                                       ***************************************************************************** PP

                          MCR_beta 232 fgeidefreplkavaea 248
                                       +gei+efrep+ avaea
  gi|386001201|ref|YP_005919500.1| 417 YGEIKEFREPIVAVAEA 433
                                       **************986 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.1   1.8   5.1e-86   4.6e-82       1     182 []       3     184 ..       3     184 .. 1.00

  Alignments for each domain:
  == domain 1  score: 274.1 bits;  conditional E-value: 5.1e-86
                        MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivena 77 
                                       Dkidly+d+G ll+sdv+l+a+sPlkn+a+kk+++++krtvavnlagie+alktgkvgg++++i+Grel++d+v+na
  gi|386001201|ref|YP_005919500.1|   3 DKIDLYSDRGVLLKSDVDLSAVSPLKNAAMKKLINLTKRTVAVNLAGIENALKTGKVGGQGRQIKGRELKYDVVANA 79 
                                       9**************************************************************************** PP

                        MCR_beta_N  78 daiaekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaa 154
                                       +a+a++ik+l+qve++ddt+v++l+gGkqllvq+P++R++aa+e+ v+++ataaa++ea++++f+ +mf+a++v+aa
  gi|386001201|ref|YP_005919500.1|  80 NALAAEIKKLLQVEAGDDTNVQVLGGGKQLLVQIPTARVDAASEFVVGMTATAAATCEALVTQFKAGMFEAPMVHAA 156
                                       ***************************************************************************** PP

                        MCR_beta_N 155 vlGryPqtvdlaggnvasilsipqkneG 182
                                       v+G+yPqtv +aggn+as+l+ipq++eG
  gi|386001201|ref|YP_005919500.1| 157 VWGQYPQTVPMAGGNIASVLNIPQNDEG 184
                                       ***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2817.40
//
Query:       gi|386001202|ref|YP_005919501.1|  [L=164]
Description: Methyl-coenzyme M reductase, protein D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-53  180.4   0.0    1.8e-53  180.2   0.0    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.2   0.0     1e-57   1.8e-53       1     141 [.      11     151 ..      11     153 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 1e-57
                             MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGril 77 
                                       ++eifp+R+Lkp+t+++lL+e+++  gi r++i+Gp+LPk+vpygp kG+++e++ + ++e++++++eL+vkvGri+
  gi|386001202|ref|YP_005919501.1|  11 QIEIFPQRFLKPDTAQRLLEEIYSSGGILRIMIQGPNLPKSVPYGPGKGIPIEEHLNMLLELGDSALELRVKVGRIW 87 
                                       89*************************************************************************** PP

                             MCR_D  78 leledeeviekieeiceevlpfsyeikegkfirkkktvsDyakyGeeeadkrllGlvDpkskle 141
                                       lel++ee ie ++++ce+vlp++++ik+ + +++k+tvsDyakyG+e  dkr+lGlvDpk+k e
  gi|386001202|ref|YP_005919501.1|  88 LELDSEERIEGVKAACERVLPCTFSIKRKQLFHTKPTVSDYAKYGSEVEDKRILGLVDPKAKRE 151
                                       *************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1269.23
//
Query:       gi|386001203|ref|YP_005919502.1|  [L=236]
Description: Methyl-coenzyme M reductase, gamma subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.2e-106  354.7   0.0   2.4e-106  354.5   0.0    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit


Domain annotation for each model (and alignments):
>> MCR_gamma  Methyl-coenzyme M reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.5   0.0  1.3e-110  2.4e-106      22     246 .]       3     234 ..       1     234 [. 0.99

  Alignments for each domain:
  == domain 1  score: 354.5 bits;  conditional E-value: 1.3e-110
                         MCR_gamma  22 aeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGakaGdrvryiqfadsmyfaPaqPy 98 
                                        +leklr+isd dvv+i+ghraPG++y+s+hPPl+em ep++pir+lv+P++Ga aGdr+ry qfadsmy+aPa Py
  gi|386001203|ref|YP_005919502.1|   3 SDLEKLRDISDADVVTIMGHRAPGADYPSTHPPLAEMGEPDCPIRQLVTPTPGAAAGDRIRYSQFADSMYNAPAIPY 79 
                                       689************************************************************************** PP

                         MCR_gamma  99 qrarlellryrgvdtGtlsGrqiievrerdlekiskelletelfdpartgirGatvhGhslrldenGlmfdalqrlv 175
                                        r++++++++rg d+GtlsGrqi+e+rerd+e+++k +++te+ dpa +++rG+tvhGhslrlde+G+mfd+l+r+ 
  gi|386001203|ref|YP_005919502.1|  80 FRSYWAAINCRGSDPGTLSGRQIVEARERDIEQYTKIMMDTEMCDPALATMRGCTVHGHSLRLDEDGMMFDMLARTE 156
                                       ***************************************************************************** PP

                         MCR_gamma 176 ldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgval........rddkevvevvkrihelrtklg 244
                                       l  +dg+v yvkdqvg+pld+kv+ Gkp++e+e kk+tti+r d+v++        r  +e + ++++++e r+k+g
  gi|386001203|ref|YP_005919502.1| 157 LG-SDGNVYYVKDQVGIPLDRKVNAGKPMSEAEAKKRTTIFRCDNVSFggpctadkRTFDEGLVTLHHMWERRSKWG 232
                                       *8.9************************************************99999999***************** PP

                         MCR_gamma 245 fk 246
                                       f+
  gi|386001203|ref|YP_005919502.1| 233 FR 234
                                       95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1765.61
//
Query:       gi|386001204|ref|YP_005919503.1|  [L=559]
Description: Methyl-coenzyme M reductase, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.6e-147  489.4   0.1   9.2e-147  487.6   0.2    1.7  2  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
      8e-66  220.3   3.3    1.7e-65  219.2   3.3    1.6  1  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter
  ------ inclusion threshold ------
      0.077   12.6   0.1       0.69    9.5   0.0    2.4  2  MCR_beta_N   Methyl-coenzyme M reductase beta subunit, N-term


Domain annotation for each model (and alignments):
>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.6   0.2  1.5e-150  9.2e-147       1     270 []       7     276 ..       7     276 .. 0.98
   2 ?   -1.2   0.0      0.18   1.1e+03      91     105 ..     522     536 ..     519     543 .. 0.85

  Alignments for each domain:
  == domain 1  score: 487.6 bits;  conditional E-value: 1.5e-150
                                       XX--HHHHHHH-S.S.-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH-S----TTS....S--S-SS---EEE CS
                       MCR_alpha_N   1 eklflkalkkkfkke.dpeekktkfykfeGlkqserkrefveaakkiakkrgislynpdilhl.GvplGqrklmpyk 75 
                                       +klf+kal+kkf ++ d + +kt + ++ G +q++rkref+ea+kk++ krgis+ynp +lh+ GvplGqr+l+pyk
  gi|386001204|ref|YP_005919503.1|   7 KKLFVKALNKKFGRDfDLSGTKTVY-ERLGPEQNARKREFMEASKKLEGKRGISMYNP-YLHAgGVPLGQRQLVPYK 81 
                                       689**********997777777776.********************************.78999************* PP

                                       BTTS--EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT- CS
                       MCR_alpha_N  76 vsgtdvlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehm 152
                                       +s+t+++vegddlhfvnn+a+qq+wddirrt++vgld+ahevlekrlGkevtPetin+yle+lnha+PG+avvqehm
  gi|386001204|ref|YP_005919503.1|  82 LSTTEYIVEGDDLHFVNNPAMQQMWDDIRRTIVVGLDMAHEVLEKRLGKEVTPETINNYLEILNHAMPGAAVVQEHM 158
                                       ***************************************************************************** PP

                                       ----TTT-TT-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHH CS
                       MCR_alpha_N 153 vethPalvedcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrws 229
                                       vethPalv+dc v++ftGdd+ladeid+q+lid+nk+fp+eqae++k+a+Gk+ +q+++iPtivsrtcdGgttsrws
  gi|386001204|ref|YP_005919503.1| 159 VETHPALVDDCNVRMFTGDDDLADEIDDQYLIDVNKLFPAEQAEEIKAAMGKTSWQAIHIPTIVSRTCDGGTTSRWS 235
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHT--SS-TTHHHHHHHHHTTSEEES---B- CS
                       MCR_alpha_N 230 amqigmsfisayklcaGeaavadlayaakhaeviemgellP 270
                                       amq++m+fi+ay++caGeaavadla+aakha+vi+m+++lP
  gi|386001204|ref|YP_005919503.1| 236 AMQLSMTFIDAYNMCAGEAAVADLAFAAKHAAVIQMADMLP 276
                                       ****************************************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.18
                                       GG-HHHHHHHHHHHT CS
                       MCR_alpha_N  91 vnnaalqqlwddirr 105
                                         n+al   wddir+
  gi|386001204|ref|YP_005919503.1| 522 FANPALIFTWDDIRK 536
                                       5699999*******8 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2   3.3   2.9e-69   1.7e-65       1     127 []     324     450 ..     324     450 .. 1.00

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 2.9e-69
                         MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdkygglakvkatlevvkdiatevtlyaleqyekyptl 77 
                                       dqiwlGsymsGGvGftqyataayt+++lddf+yy++dy  dk+g++ k++atle+ kdiate+tlya+eqye++ptl
  gi|386001204|ref|YP_005919503.1| 324 DQIWLGSYMSGGVGFTQYATAAYTNDVLDDFSYYACDYGVDKFGDWGKAPATLETSKDIATETTLYAMEQYESFPTL 400
                                       9**************************************************************************** PP

                         MCR_alpha  78 ledhfGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                       ledhfGGsqr+av+aaa++i++a+ tgns++Gl++wyls+l+hk++++r+
  gi|386001204|ref|YP_005919503.1| 401 LEDHFGGSQRSAVMAAASAIGSACLTGNSQSGLAAWYLSHLIHKDGWGRM 450
                                       ************************************************97 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00012      0.69      22      58 ..      94     129 ..      84     181 .. 0.77
   2 ?   -1.9   0.1      0.37   2.2e+03     129     165 ..     342     378 ..     335     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                        MCR_beta_N  22 isPlknpaikkivkdvkrtvavnlagiekalktgkvg 58 
                                       +  ++npa++++ +d++rt+ v l+   + l++ ++g
  gi|386001204|ref|YP_005919503.1|  94 LHFVNNPAMQQMWDDIRRTIVVGLDMAHEVLEK-RLG 129
                                       55689*******************998888865.444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.37
                        MCR_beta_N 129 taaavveaiidefdvdmfdasvvkaavlGryPqtvdl 165
                                       ++aa ++ ++d f   + d  v k   +G+ P t++ 
  gi|386001204|ref|YP_005919503.1| 342 ATAAYTNDVLDDFSYYACDYGVDKFGDWGKAPATLET 378
                                       557889999999999999999999999*****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 4315.74
//
Query:       gi|386001205|ref|YP_005919504.1|  [L=172]
Description: hypothetical protein Mhar_0499 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-10   40.8   0.0      3e-10   40.5   0.0    1.2  1  DUF1863   MTH538 TIR-like domain (DUF1863)
     0.0038   17.8   0.1     0.0055   17.3   0.1    1.5  1  TIR_2     TIR domain
  ------ inclusion threshold ------
       0.04   14.0   0.1      0.048   13.8   0.1    1.1  1  ORF45     Family of unknown function


Domain annotation for each model (and alignments):
>> DUF1863  MTH538 TIR-like domain (DUF1863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0     5e-14     3e-10      49     113 ..      80     140 ..      47     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 5e-14
                           DUF1863  49 rdrdedsaaedikeairdaldrssvliVLvgsetatsrWvdwEIaaslkkgkrllgvsldrlkqr 113
                                       +++++     ++++ i ++++ ss++ VLvg+  ++ +WvdwE+ +sl  +k+l++ +l +  + 
  gi|386001205|ref|YP_005919504.1|  80 KNENAV----YVRRCITKRIEASSIVFVLVGKTFQDCEWVDWEVRESLLMKKNLVALRLSDEPSL 140
                                       555555....************************************************9887655 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   9.2e-07    0.0055      41     104 ..      88     147 ..      43     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.2e-07
                             TIR_2  41 eeeieeaiessdvvlvvlspaylesewcreeleaaleaaeegkkrlipvllepekppl.aslqyi 104
                                       ++ i + ie s++v v++++ +++ ew++ e++  l      kk+l+ ++l  ++p+l a +   
  gi|386001205|ref|YP_005919504.1|  88 RRCITKRIEASSIVFVLVGKTFQDCEWVDWEVRESLL----MKKNLVALRLS-DEPSLkAPKVLR 147
                                       566899****************************996....4677*******.467664333333 PP

>> ORF45  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     8e-06     0.048     125     174 ..      76     125 ..      41     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8e-06
                             ORF45 125 vkmyspefgfyvnskimfvltesvlaficlkhsfgkcewldkniktvclq 174
                                          +  e  +yv   i   +  s + f+ + ++f  cew+d +++   l 
  gi|386001205|ref|YP_005919504.1|  76 KVHFKNENAVYVRRCITKRIEASSIVFVLVGKTFQDCEWVDWEVRESLLM 125
                                       334678999********************************999876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1330.17
//
Query:       gi|386001206|ref|YP_005919505.1|  [L=205]
Description: ExsB family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-26   93.7   0.0    2.3e-26   92.6   0.0    1.4  1  QueC         Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.011   15.8   0.0        3.4    7.7   0.0    2.3  2  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
      0.026   14.3   0.0        6.7    6.4   0.0    2.3  2  ATP_bind_3   PP-loop family
      0.059   12.9   0.0       0.83    9.2   0.0    2.4  3  ThiI         Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.0     5e-30   2.3e-26       2     203 ..       4     192 ..       3     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 5e-30
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       +v ++SG +DS ++  + ++e +e + + +d+gq   ++e ea ++++++ ++   + +dl+ + +  +s       
  gi|386001206|ref|YP_005919505.1|   4 VVPIVSGDIDSLVMCKILNNERQEQHPIFIDFGQIsGDEEWEACRSVFERCDLPPPERIDLSGYCRSIESD------ 74 
                                       5679******************************9899**********************99444433332...... PP

                                       ------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EE CS
                              QueC  78 evpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkiei 154
                                        v+     +++  n f p+RNl+ l  aasya+++g++ +++++ + ++  +PD ++ef+ ++n a+n + ++ i+i
  gi|386001206|ref|YP_005919505.1|  75 -VQG--ECKASYINAFLPGRNLMALMAAASYAYQRGIKIVALALLSDESRRFPDQTEEFLVNANFAINSAFGDFITI 148
                                       .333..23567889*************************************************************** PP

                                       E-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHH CS
                              QueC 155 eaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRk 203
                                        +Pli+++K+++++++  +g+p+eet+ C  g ++    g C +C+ Rk
  gi|386001206|ref|YP_005919505.1| 149 LTPLINFTKEDVLNTARWYGLPIEETFCCHPG-RN----GICRSCTARK 192
                                       *******************************9.44....7788888887 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0026        12       5      34 ..       7      36 ..       3      43 .. 0.90
   2 ?    7.7   0.0   0.00076       3.4     121     155 ..     136     171 ..     121     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                                      E--SSCTCHHHHHHHHHHCTTHEEEEEE-S CS
                       PAPS_reduct  5 svsgGkdslVllhLalkafkpvpvvfvdtg 34
                                       vsg +dslV+ +++ +  ++ + +f+d g
  gi|386001206|ref|YP_005919505.1|  7 IVSGDIDSLVMCKILNNERQEQHPIFIDFG 36
                                      68*************************987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00076
                                       EEECTTT-SCEEE-.CCCT--HHHHHHHHHHCT--B CS
                       PAPS_reduct 121 veidedfekslrvf.PllnWteedvwqyilrenipy 155
                                       + i+++f +++ ++ Pl+n+t+edv + ++  ++p+
  gi|386001206|ref|YP_005919505.1| 136 FAINSAFGDFITILtPLINFTKEDVLNTARWYGLPI 171
                                       678899999****99**********99888777776 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0021       9.4       6      35 ..       8      33 ..       3      57 .. 0.74
   2 ?    6.4   0.0    0.0015       6.7     133     162 ..     140     170 ..      95     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0021
                                      --SCHHHHHHHHHHHHHCTTTTTEEEEEEE CS
                        ATP_bind_3  6 vSgGlDSmaLllllaklkkklgiklvaihv 35
                                      vSg +DS++++++l++++++++     i +
  gi|386001206|ref|YP_005919505.1|  8 VSGDIDSLVMCKILNNERQEQH----PIFI 33
                                      9**************9988643....3444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0015
                                       EEETT.CCEE-CCCT--HHHHHHHHHHTT-- CS
                        ATP_bind_3 133 seias.irlvRPlLkvskeeleeylkekkik 162
                                       s + + i+++ Pl++++ke++ +++++ +++
  gi|386001206|ref|YP_005919505.1| 140 SAFGDfITILTPLINFTKEDVLNTARWYGLP 170
                                       44555599******************99876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.28   1.3e+03       6      20 ..       4      18 ..       2      50 .. 0.82
   2 ?    0.1   0.0      0.12   5.3e+02      19      37 ..      99     117 ..      97     129 .. 0.82
   3 ?    9.2   0.0   0.00019      0.83     138     158 ..     146     166 ..     131     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.28
                              ThiI  6 vlaLlSgGiDSpVaa 20
                                      v+ ++Sg iDS V  
  gi|386001206|ref|YP_005919505.1|  4 VVPIVSGDIDSLVMC 18
                                      788899999998865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                              ThiI  19 aaylllkRGcrvvlvhlkn 37 
                                       aa+ + +RG+++v++ l +
  gi|386001206|ref|YP_005919505.1|  99 AASYAYQRGIKIVALALLS 117
                                       778889*******998865 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00019
                              ThiI 138 llilrPLigldKeeiiklAke 158
                                       ++il PLi + Ke++ ++A+ 
  gi|386001206|ref|YP_005919505.1| 146 ITILTPLINFTKEDVLNTARW 166
                                       68*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1449.52
//
Query:       gi|386001207|ref|YP_005919506.1|  [L=145]
Description: Protein ArsC (Arsenate reductase) (Arsenical pumpmodifier) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-13   50.4   0.0    3.3e-13   50.2   0.0    1.1  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.8e-17   3.3e-13       1     136 [.       7     129 ..       7     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.8e-17
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       v+f +  N++RS+mAe l+r++  +     +  + SaG+     +++dp ave+++e+gi++s ++++  ++ +   
  gi|386001207|ref|YP_005919506.1|   7 VIFLSAHNSARSQMAEGLLRHLYSD-----RYLAFSAGVD---PREVDPLAVEAMAERGIDISRQRSKSSKELWGTA 75 
                                       79********************666.....68899*****...899******************************* PP

                                       SSEEEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkreleslapekekakvkllgeyteqldieDPyygeieafeevldeiee 136
                                       +D++  + +    e+++l p+   ++ +++   ++   +eDP+      + +++d++e+
  gi|386001207|ref|YP_005919506.1|  76 VDVVAKIRDFDS-EACPLFPS---GRWRAFLPLEDPSMVEDPAERR-RVLSAARDRLER 129
                                       *******88877.9*******...3455566656778888887654.555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1123.59
//
Query:       gi|386001208|ref|YP_005919507.1|  [L=431]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-28   98.9   0.0    8.7e-28   97.8   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    5.5e-07   29.6   1.5    8.4e-05   22.6   0.8    3.4  3  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   9.7e-32   8.7e-28       2     166 ..     156     324 ..     155     325 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 9.7e-32
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerl 70 
                                       ++ rgC ++C+fC++p+    ++  rs+s+e+il+ev+e+ +++gv  v ++gg+ +l           f+ ll+ l
  gi|386001208|ref|YP_005919507.1| 156 ETHRGCLGGCTFCQVPRF--FGRSIRSRSLENILAEVREM-KRRGVTRVAVSGGTGSLFgygkevnkEAFITLLKGL 229
                                       6789*************8..********************.7***99999999999998777777776677777777 PP

                                       HHTCCCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  71 aklavpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                       a++        ++++ +++d   ee+le+ +++ v +v +g+e++++  +l+ m++g t+e+ lea+e+++++g+k+
  gi|386001208|ref|YP_005919507.1| 230 AEI---LGPKNLSVPDMRVDfvdEEILEAVRRYTVGWVFFGIESGSPG-ILRAMKKGTTPEKSLEAVELAHQSGVKV 302
                                       777...88999999999999****************************.**************************** PP

                                       EEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGendeeleellel 166
                                         ++ivg pGe +e+++++l++
  gi|386001208|ref|YP_005919507.1| 303 GGSFIVGYPGEMEEDYQATLDF 324
                                       ********************98 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.8   9.3e-09   8.4e-05      53     120 ..      40     101 ..       3     102 .. 0.72
   2 ?   -3.5   0.0       1.2     1e+04      62      86 ..     180     203 ..     171     208 .. 0.46
   3 ?    0.3   0.0     0.074   6.7e+02      20      57 ..     229     266 ..     226     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.3e-09
                       B12-binding  53 dvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       d+ +lS+ +tsql    e+ el+ r+ p  ++ vGG+ + l pe +l + l++d vvvgege+ +++l
  gi|386001208|ref|YP_005919507.1|  40 DLTLLSLFSTSQL-LDPEIRELASRA-P--RIYVGGP-VGLVPEIVLGE-LEVDAVVVGEGEEVVADL 101
                                       6667777444444.456777776555.5..89****8.6*********9.*************99987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                       B12-binding  62 tsqleavkelvellkrirprvkvvv 86 
                                       + +le++ + v++ kr++  ++v+v
  gi|386001208|ref|YP_005919507.1| 180 SRSLENILAEVREMKRRGV-TRVAV 203
                                       4455555444444444333.23333 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.074
                       B12-binding  20 laaalrdagfeVqllganvenedivaairaekpdvvgl 57 
                                       la++l  ++ +V ++ +++ +e+i++a+r+  +  v +
  gi|386001208|ref|YP_005919507.1| 229 LAEILGPKNLSVPDMRVDFVDEEILEAVRRYTVGWVFF 266
                                       67777777888888888888899999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 3232.50
//
Query:       gi|386001209|ref|YP_005919508.1|  [L=407]
Description: Putative methanogenesis marker protein 10 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-15   55.8   3.9    2.5e-13   50.7   2.2    3.2  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   2.2   1.4e-17   2.5e-13       7     158 ..      15     189 ..      11     198 .. 0.82
   2 ?    0.3   0.0     0.044   7.8e+02      65      65 ..     326     326 ..     189     379 .. 0.56

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.4e-17
                                       ESS--TTTSCCTT.........................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTG CS
                                       xxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                       Radical_SAM   7 CnlrCsfCarpet.........................vrregrgrslsveeileevkelkaekg.vkevilgggep 57 
                                       C + Cs+C+++                              e ++ ++++  ++ ev  +++ ++  k+ i+ggg+ 
  gi|386001209|ref|YP_005919508.1|  15 CKGFCSYCYFKGVktnelkpfgckrclpfqkgcdycsrAIAEAYPGFKPMATVAMEVAGAAFGRRpDKVTISGGGDL 91 
                                       55556666666556666666666666666666666666558999999999999999999986666799********* PP

                                       GGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  58 llypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevleal 134
                                       + yp++ el+++  +     i++ +++  +  + + +e l e+gv  vs+++ ++d+   ++ ++    +e+ l++l
  gi|386001209|ref|YP_005919508.1|  92 SCYPHLLELARMVGQG-GVPIHLGYTSGKGFTRGDEAEDLIEAGVKEVSFTVFSTDPA-LRREHMNDRHPEAALANL 166
                                       ******9999999998.4888888888888888*************************.777777889********* PP

                                       HHHHHTTSETEEEEEEEBTTTSH.H CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Radical_SAM 135 eklreagikrvvdrivglpGend.e 158
                                       ++++e  ++ v+   v++pG+nd  
  gi|386001209|ref|YP_005919508.1| 167 RRFAEG-CD-VYAASVLIPGVNDgP 189
                                       *****9.**.************943 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.044
                                       H CS
                                       x RF
                       Radical_SAM  65 e 65 
                                       +
  gi|386001209|ref|YP_005919508.1| 326 D 326
                                       0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3223.58
//
Query:       gi|386001210|ref|YP_005919509.1|  [L=394]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-14   52.5   0.0    3.8e-13   50.2   0.0    2.2  3  Radical_SAM  Radical SAM superfamily
    7.1e-06   26.5   0.4    1.9e-05   25.1   0.4    1.8  1  SPASM        Iron-sulfur cluster-binding domain
     0.0013   19.0   0.0      0.008   16.4   0.0    2.0  2  Fer4_12      4Fe-4S single cluster domain
     0.0071   16.5   0.0      0.016   15.4   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   8.5e-17   3.8e-13       1     151 [.      18     162 ..      18     178 .. 0.84
   2 ?   -1.1   0.0      0.48   2.2e+03     105     144 ..     190     234 ..     158     245 .. 0.68
   3 ?   -1.8   0.1      0.77   3.4e+03       3      13 ..     316     326 ..     315     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 8.5e-17
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTC. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx. RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggeplly.pdfvellerlakla. 74 
                                       +++t gC+  Cs+C+ +      +r+ ++++e ++e v +l+ ++++  +++++ggepll  +df++++++l+ +  
  gi|386001210|ref|YP_005919509.1|  18 IIPTLGCPSSCSYCWSSD-----ERSPIMTIETVKEMVHWLReFRDDPVTFTFHGGEPLLAgADFYREALALITEGl 89 
                                       57999************5.....99*****************77777***********9866888888888888879 PP

                                       .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                         ++i +++ tn  + ++e++  l+e+    +  +++ + d    +l +  + f++++++ + ++e+g+  v  +i 
  gi|386001210|ref|YP_005919509.1|  90 rPRKIAFALQTNLWKMTPEMASVLAEYQ-IPIGSSIDGPKDL--NDLQRSAGYFDKTMAGYRVAKEHGLS-V-QFIC 161
                                       99************************99.8888888888885..566667799**************999.3.3333 PP

                                       E CS
                                       x RF
                       Radical_SAM 151 g 151
                                        
  gi|386001210|ref|YP_005919509.1| 162 T 162
                                       3 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                                       EEEEEBSSSHH.......HHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 105 vslgleaadde.......kvlklmnrghtfeevlealeklreagikr 144
                                          +l++ d++       k+ +l+   + ++++le+++k+  ++i++
  gi|386001210|ref|YP_005919509.1| 190 ALPSLKSDDPDkwalppeKYGELL-V-YLLDKYLENMDKIEVRNIND 234
                                       556777778888888777888888.5.88899999999988888776 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.77
                                       EESEESS--TT CS
                                       xxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsf 13 
                                       ++r C+++C++
  gi|386001210|ref|YP_005919509.1| 316 HLRYCRGGCPY 326
                                       5789*****99 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.4   4.3e-09   1.9e-05       4      67 ..     253     314 ..     247     320 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.3e-09
                             SPASM   4 psrslfInsdGdVvpCcvdkktyvee.lklGnirees.leeIw...nseeyqefrkskkfplielCrnC 67 
                                       +  ++++ +dG ++pC   ++ +  + +++Gnir+ +  +++     + ++qef+ ++ +     C+ C
  gi|386001210|ref|YP_005919509.1| 253 MDDTFAVGPDGSIYPC---YRFVGMPeWVMGNIRDRPsQADLAgsgAGRRMQEFK-RRVD---VACKGC 314
                                       678999**********...44555558******7766333444333666777777.3333...448888 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.8e-06     0.008      12      67 ..      21      74 ..      11     133 .. 0.72
   2 ?   -0.3   0.1      0.27   1.2e+03      10      36 ..     309     337 ..     295     363 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-06
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpe 67
                                      + gC+ sC++C   + +s+    e+ ke+   + +++  +    +t+ GGEPll  
  gi|386001210|ref|YP_005919509.1| 21 TLGCPSSCSYCWSSDERSPIMTIETVKEMVHWL-REF-RDDPVTFTFHGGEPLLAG 74
                                      569********9777777666666666655444.334.244478999******943 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                           Fer4_12  10 lfvsgCnl..sCkgCfnketwsfksgkef 36 
                                       +  +gC++   C+g    ++  +++g+  
  gi|386001210|ref|YP_005919509.1| 309 VACKGCRHlrYCRGGCPYNAIAPSGGELL 337
                                       44566666656666555556666655555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.5e-06     0.016       6      61 ..      22      73 ..      17     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                           Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhy 61
                                       gC+ sC  C  ++  +s   +++t +++++ l+++ ++ +     ++ GGePL+ 
  gi|386001210|ref|YP_005919509.1| 22 LGCPSSCSYCWSSD-ERSPIMTIETVKEMVHWLREFRDDPV---TFTFHGGEPLLA 73
                                      69*********999.56666666666667788888888877...589*******53 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3063.93
//
Query:       gi|386001211|ref|YP_005919510.1|  [L=318]
Description: CaCA family Na+/Ca+ antiporter [Methanosaeta harundinacea 6Ac]
Scores for complete 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-50  171.3  40.1    1.7e-26   93.0  13.1    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein
  ------ inclusion threshold ------
       0.22   11.7   0.4          1    9.5   0.1    2.0  2  IF-2      Translation-initiation factor 2
        5.4    7.6   8.1        2.4    8.7   2.6    3.1  2  DUF2061   Predicted membrane protein (DUF2061)


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0  13.1   2.9e-30   1.7e-26       3     146 ..      16     153 ..      14     157 .. 0.92
   2 !   84.5  19.0   1.2e-27   6.9e-24       4     147 ..     177     312 ..     175     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.9e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHT..TTHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaalt..gevdlaignvlGsnif 77 
                                       f++f++sl++++ +a+ +++sa ++ak+lgis+ v+G t++A+g+ lpE+ +si+a++   g +++a gnvlGs+++
  gi|386001211|ref|YP_005919510.1|  16 FLTFAVSLVALYYGAKAITDSAVHFAKVLGISEFVIGATVVAFGTALPEFSTSIVAMMVdgGAPEIAAGNVLGSILA 92 
                                       899*******************************************************63255************** PP

                                       HHHTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  78 nlllviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                       n++l +G +a + ++++d++ l+ dl  +ll+++l++ +v+l         r+t+ egl+l+++Y+ +l
  gi|386001211|ref|YP_005919510.1|  93 NTGLALGAAAALYGIYIDRKILETDL-SFLLASMLAIYVVFL-D------YRITWIEGLLLIAIYLSFL 153
                                       **************************.889999999665554.5......8***************998 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 1.2e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       ++f++++ll++++a+++++++ +i+++lgi++ v++++llA g+slpE+ ++i+aa++g +d+a+g ++G+n+fn l
  gi|386001211|ref|YP_005919510.1| 177 GIFFAGILLLAIGANYMIEAILSISSTLGIPEGVVAVLLLAVGTSLPEISTAIVAAKSGRGDIAMGDIMGANAFNAL 253
                                       79*************************************************************************** PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylv 147
                                       +++G + l+g +   +  + ++l++ +l++lll +  ++l       +r+t++eg +l+++Y+l ++
  gi|386001211|ref|YP_005919510.1| 254 IILGAASLVGDVAASEAFVSVTLPVVVLISLLLGF--MVLG------NRITRFEGSMLVAIYLLEVI 312
                                       *********99655555566666665665555533..3334......***************98665 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   1.2e+03      42      74 ..      21      60 ..      11      71 .. 0.73
   2 ?    9.5   0.1   0.00017         1      36      70 ..     224     255 ..     202     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                                      TEEEECEEEESSB-HHHHHHHHH...ST....EEEEEESS CS
                              IF-2 42 vkvkvihsgvGaitesDvelasa...sn....aiiigFnv 74
                                      v++  ++ g  ait+s v+ a++   s+    a++++F +
  gi|386001211|ref|YP_005919510.1| 21 VSLVALYYGAKAITDSAVHFAKVlgiSEfvigATVVAFGT 60
                                      6666778888999999999999966533555577777765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                                       CTT.SSTEEEECEEEESSB-HHHHHHHHHSTEEEE CS
                              IF-2  36 kleseevkvkvihsgvGaitesDvelasasnaiii 70 
                                       ++   +  +   +sg G+i   D++ a+a na+ii
  gi|386001211|ref|YP_005919510.1| 224 EI---STAIVAAKSGRGDIAMGDIMGANAFNALII 255
                                       33...233555678899**************9998 PP

>> DUF2061  Predicted membrane protein (DUF2061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.6    0.0004       2.4       2      45 ..      30      73 ..      30      74 .. 0.95
   2 ?   -0.4   0.3      0.28   1.7e+03      19      41 ..     252     274 ..     249     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0004
                           DUF2061  2 lKtlswrvihtvvtflvaylltgslalAgaialvEpvvktvlYy 45
                                      +K+++  ++h++ +++++ +++g  ++A+  al E+ + +v+++
  gi|386001211|ref|YP_005919510.1| 30 AKAITDSAVHFAKVLGISEFVIGATVVAFGTALPEFSTSIVAMM 73
                                      699999**********************************9986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.28
                           DUF2061  19 aylltgslalAgaialvEpvvkt 41 
                                       a+++ g ++l g +a  E++v +
  gi|386001211|ref|YP_005919510.1| 252 ALIILGAASLVGDVAASEAFVSV 274
                                       689999999********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2042.62
//
Query:       gi|386001212|ref|YP_005919511.1|  [L=1171]
Description: Chromosome segregation protein SMC [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-71  240.1   0.1    2.2e-71  239.8   0.1    1.1  1  SMC_N            RecF/RecN/SMC N terminal domain
      3e-28   98.5   0.0    9.1e-28   96.9   0.0    1.9  1  SMC_hinge        SMC proteins Flexible Hinge Domain
    3.1e-10   40.9  13.3    3.1e-10   40.9  13.3    4.9  2  AAA_23           AAA domain
    1.6e-09   38.0   0.0      4e-09   36.6   0.0    1.7  1  AAA_15           AAA ATPase domain
    1.9e-09   37.8   8.2    2.4e-05   24.3   0.0    3.4  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.9e-08   31.8   0.0    1.7e-07   30.9   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.037   14.1   1.1        3.1    7.9   0.1    3.3  3  Flagellin_N      Bacterial flagellin N-terminal helical regio
      0.053   13.8   0.3        1.5    9.1   0.0    3.1  2  AAA_22           AAA domain
      0.053   13.5   0.1       0.12   12.3   0.1    1.6  1  Levi_coat        Levivirus coat protein
       0.12   12.9   7.3       0.95   10.0   0.0    4.7  4  ABC_tran         ABC transporter
        1.6    9.1  14.4        9.2    6.6   0.3    6.0  5  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.8    9.1  24.5        4.2    7.8   0.2    6.9  7  Snapin_Pallidin  Snapin/Pallidin


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.8   0.1   1.4e-74   2.2e-71       1     219 [.       2    1163 ..       2    1164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 239.8 bits;  conditional E-value: 1.4e-74
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvk 75  
                                        ++k++e+ nFks+ g+++++p+ + f a++GpNGSGKsn++dA+lF L+ +s++++r+e+l dli++ +++++ +
  gi|386001212|ref|YP_005919511.1|    2 HIKEIELVNFKSF-GRRAVIPLRNDFIAVTGPNGSGKSNVVDALLFALSLSSSRAMRAERLPDLIYRGDNGKNPD 75  
                                        599**********.5************************************************************ PP

                                        EEEEEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT............ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                             SMC_N   76 kaeveitfdnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske............ 135 
                                        +a+v++ fdn+++ ++++++ v+isr+v  +++   s y++ng+ +t++e+++ l++agi++e            
  gi|386001212|ref|YP_005919511.1|   76 FAQVTVKFDNSERGVPVDEDVVEISRKVRLTKNkyqSIYYFNGNPCTQTEIHDHLSRAGITPEgynvvmqgdvtr 150 
                                        **************************997766556799************************************* PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  151 iiemtplerrrivdeiagvaefdekkkkaleelevvreridrgdvilveveaqlarlaeerdralayqaqreekr 225 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  226 rmeaflllaklkeaesdladldtelldlrsidsdligrldrgraelssleenlkglndeitrkgedeqievkrrm 300 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  301 vevkgsikadegriemaegeiaaleaeqrsdyleadrlgreaeelsmrirdgsirkasilaeiqereealasyre 375 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  376 kiaradaryaevrdrlavvkreveeaksraadlmrerdrhldaarrrsiereeaaieisearetmagldrergri 450 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  451 grqrqeleerislfeeerddldsarisirremarvdetlqrlqmeraraeaslrsagegtgysraveairsamsq 525 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  526 ghltglfgtiaelgevgedyatalevaaggrlqsivaetdgdaaraietlkrskagratflplnkmasgtppalp 600 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  601 kepgvvdyainlvafdprflpafwhvfrdtlvvkeldvarrlmgryrmvtldgdlvekggamtggtfksrlkfaa 675 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  676 derqkleeatrrvlaaqaerdslierldrvegevssvrrgveelgrevsrievrleeidgqkvrlerliqdrerr 750 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  751 lleleadaagvmerldllerdirereaeargaeerarslerdlegseipelsaladgleaeirslsrkaseieae 825 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  826 itghrlreeshsarraelsgrreareerkraaiekksaaadrigkadlaladlgqrereievelselkgtrsrll 900 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  901 devmaksrevdsadrerervrariaaaegaaaemrsaadglraeiesfgidaseeppksqtiirkihalersmee 975 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001212|ref|YP_005919511.1|  976 lepvnmlaieeydrvfdrretlrdrretlqreredllakldqyeemkreafmaafeginenfrdtfnqlsdgege 1050
                                        *************************************************************************** PP

                                        .............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                        .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 .............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181 
                                                                     ++SgGek+L+al+++fAiq+++pap+y lDeid+ LD +nv++va+
  gi|386001212|ref|YP_005919511.1| 1051 lileneedplaggmtirarparkafhrleAMSGGEKSLTALSFIFAIQRFRPAPFYALDEIDMFLDGANVERVAK 1125
                                        *************************************************************************** PP

                                        HHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  182 llkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                        l+k   + aQfiv+slr+ m+++a+ +vgvt++en++s
  gi|386001212|ref|YP_005919511.1| 1126 LIKGIAQAAQFIVVSLRKPMIQEAKYVVGVTMQENNIS 1163
                                        **********************************9987 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   6.1e-31   9.1e-28       2     116 ..     529     642 ..     528     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 6.1e-31
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +g++G++a+l ev e y +A+e+a+g+rlq++v e++ +a ++ie lk+ +agratflpl+++ +  ++  +++ + 
  gi|386001212|ref|YP_005919511.1| 529 TGLFGTIAELGEVGEDYATALEVAAGGRLQSIVAETDGDAARAIETLKRSKAGRATFLPLNKMASGTPPALPKEPG- 604
                                       689***************************************************************9999999988. PP

                         SMC_hinge  79 gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        + ++i+lv +d+++ +a+ ++++dtlvv+ ld+A++l
  gi|386001212|ref|YP_005919511.1| 605 VVDYAINLVAFDPRFLPAFWHVFRDTLVVKELDVARRL 642
                                       ************************************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9  13.3   2.1e-13   3.1e-10       2     199 ..       6     250 ..       5     496 .. 0.77
   2 ?   -1.4   7.0       1.9   2.9e+03      57     187 ..     867    1020 ..     847    1045 .. 0.54

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.1e-13
                            AAA_23   2 Lkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       +++ nf+sf r+  i + + + ++tGpNG+GK+ ++dA+ +aL   ++r  r ++     + +  +++gk++ ++++
  gi|386001212|ref|YP_005919511.1|   6 IELVNFKSFgRRAVIPLRNDFIAVTGPNGSGKSNVVDALLFALSLSSSRAMRAER---LPDLIYRGDNGKNPDFAQV 79 
                                       8899*****77789*******************************9999999654...5566667778899999777 PP

                            AAA_23  78 tfenkdgry.....trsiererelskkkg..kttkkaklelleideleqfise........llgskkiilnlilflg 139
                                       t++ ++ ++      + +e +r+++ +k+  ++++  +++ ++ +e  + +s+        ++  + +  ++i + +
  gi|386001212|ref|YP_005919511.1|  80 TVKFDNSERgvpvdEDVVEISRKVRLTKNkyQSIYYFNGNPCTQTEIHDHLSRagitpegyNVVMQGDVTRIIEMTP 156
                                       77777777756776333333333333332002222223333333333333333555555777777777999999999 PP

                            AAA_23 140 qer............feefelkdkke...................rleelekeleeledekkllekleqekekek.. 183
                                        er            f   ++k+kk                    ++e+    l e+ d++   +++  ++ek+   
  gi|386001212|ref|YP_005919511.1| 157 LERrrivdeiagvaeF---DEKKKKAleelevvreridrgdvilvEVEAQLARLAEERDRALAYQAQ--REEKRRme 228
                                       9998888888885432...433333355566777777777775553333333333333333333333..22222244 PP

                            AAA_23 184 ......eleeleeeleeilkel 199
                                             +l+e e++l +++ el
  gi|386001212|ref|YP_005919511.1| 229 aflllaKLKEAESDLADLDTEL 250
                                       5666665555555555554443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                            AAA_23   57 gfeksdveiesegkvkayveltfenkdgry.............trsiererelskkkgkttkkaklellei.del 117 
                                        ++ k+d ++++ g+ ++ +e++++  +g++              +s +rere+ +       +a+ e  +  d l
  gi|386001212|ref|YP_005919511.1|  867 RIGKADLALADLGQREREIEVELSELKGTRsrlldevmaksreVDSADRERERVRARIAAAEGAAAEMRSAaDGL 941 
                                        556777778888999999999988877777788888888765555555555555555555555544444334555 PP

                            AAA_23  118 eqfisellgskki........ilnlilflgqerfeefel...........kdkkerleelekeleeledekklle 173 
                                        + +i++    + i        + ++i  +++ +  ++el            + ++r e l++  e+l+ e++ l 
  gi|386001212|ref|YP_005919511.1|  942 RAEIES----FGIdaseeppkSQTIIRKIHALERSMEELepvnmlaieeyDRVFDRRETLRDRRETLQREREDLL 1012
                                        555554....33333366886556666666666545555344433333333333333333333333333322222 PP

                            AAA_23  174 kleqekekekelee 187 
                                        ++       +++ee
  gi|386001212|ref|YP_005919511.1| 1013 AK------LDQYEE 1020
                                        22......222222 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   2.7e-12     4e-09       1     229 [.       1     304 [.       1     404 [. 0.58

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.7e-12
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                       M Ik+i++ NF+s+   + i+l +++  + G+N+sGKS++++al + l+ +++                        
  gi|386001212|ref|YP_005919511.1|   1 MHIKEIELVNFKSFGRrAVIPLRNDFIAVTGPNGSGKSNVVDALLFALSLSSSRAmraerlpdliyrgdngknpdfa 77 
                                       99************999***************************888887744447788888888888888888887 PP

                            AAA_15  55 .........................kkvikiekedleifeniseskdikIdvef....................... 83 
                                                                +  +                                                
  gi|386001212|ref|YP_005919511.1|  78 qvtvkfdnsergvpvdedvveisrkVRLT------------------------Knkyqsiyyfngnpctqteihdhl 130
                                       76555555555555555555554431122........................122333333333333333333344 PP

                            AAA_15  84 ...........................................aek.ekakeyektlkskekkkadlllkkkesdlk 116
                                                                                  + k +ka e+++  +++ ++  d++l + e +l 
  gi|386001212|ref|YP_005919511.1| 131 sragitpegynvvmqgdvtriiemtplerrrivdeiagvaefdE-KkKKALEELEVVRERIDR-GDVILVEVEAQLA 205
                                       77777777777777777777777777777777777777775531.223333333333333333.3345555555566 PP

                            AAA_15 117 ktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksa 193
                                        + ++++ +l      ++    ek+  + +l   k +++e++ ++l+++  dl+++ ++l+  l             
  gi|386001212|ref|YP_005919511.1| 206 RLAEERDRALA-----YQAQREEKRRMEAFLLLAKLKEAESDLADLDTELLDLRSIDSDLIGRLDRGR--------- 268
                                       55555555554.....2222233333344455555555555555555555666666665555554444......... PP

                            AAA_15 194 iiklllisakRnvsdedsekkssllgklkekileea 229
                                       ++++ l ++ +  +de + k ++  +++k++ +e +
  gi|386001212|ref|YP_005919511.1| 269 AELSSLEENLKGLNDEITRKGEDEQIEVKRRMVEVK 304
                                       444445555555555555554444444444444443 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.6e-08   2.4e-05       1      46 [.      26      74 ..      26     127 .. 0.66
   2 ?   -2.9   2.2         3   4.5e+03      43      87 ..     254     300 ..     227     510 .. 0.52
   3 !   17.2   0.2   2.4e-06    0.0035     181     296 ..    1057    1140 ..     946    1140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.6e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkip 46
                                      + +++GpNgsGKSn+ dal ++ +l   +++   + ++l  +g+++k p
  gi|386001212|ref|YP_005919511.1| 26 FIAVTGPNGSGKSNVVDALLFALSLsssRAMRAERLPDLIYRGDNGKNP 74
                                      5789******************998887444444444444444444443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                            AAA_21  43 rkipslldlydpeipfefeieeflsqgvryryglrlersqv..eekl 87 
                                       r+i+s l ++ +++++e++  e +++g + +   + e++q+  +++ 
  gi|386001212|ref|YP_005919511.1| 254 RSIDSDLIGRLDRGRAELSSLEENLKGLNDEITRKGEDEQIevKRRM 300
                                       55555555555555555555555555555555555555555331111 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.4e-06
                            AAA_21  181 ekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrl..lalltallr 253 
                                        e +l+++ + + ++++   + l                                  +S G k+l  l ++ a+ r
  gi|386001212|ref|YP_005919511.1| 1057 EDPLAGGMTIRARPARKAFHRL--------------------------------EAMSGGEKSLtaLSFIFAIQR 1099
                                        3333333333333333333333................................346*******74599999999 PP

                            AAA_21  254 alkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                         ++  +++++DE++ +L+ + ++r+++l+k  ++  aQ+i+++
  gi|386001212|ref|YP_005919511.1| 1100 FRPA-PFYALDEIDMFLDGANVERVAKLIKGIAQ-AAQFIVVS 1140
                                        9999.************************66666.6****986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.1e-10   1.7e-07       2      47 ..       4      49 ..       3      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.1e-10
                            AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                      k+++lvN  +f +  +i+++ ++++ +tGp+GsGKS ++DA+ + L 
  gi|386001212|ref|YP_005919511.1|  4 KEIELVNFKSFGRrAVIPLR-NDFIAVTGPNGSGKSNVVDALLFALS 49
                                      789**********8888987.669******************98875 PP

>> Flagellin_N  Bacterial flagellin N-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.063        95      63     101 ..     256     294 ..     242     303 .. 0.86
   2 ?   -3.2   0.0       5.6   8.4e+03     107     125 ..     690     708 ..     674     713 .. 0.59
   3 ?    7.9   0.1    0.0021       3.1      52      90 ..     905     943 ..     899     976 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TTTS CS
                       Flagellin_N  63 nnslgisrlqtaqgalselsdilqrlkelavaasndsns 101
                                        +s+ i+rl++ +  ls+l+++l+ l++ ++ +++d++ 
  gi|386001212|ref|YP_005919511.1| 256 IDSDLIGRLDRGRAELSSLEENLKGLNDEITRKGEDEQI 294
                                       568889**********************99999999875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHHHHHHHH CS
                       Flagellin_N 107 slqaelqqLtdelnriant 125
                                       ++qae ++L++ l+r+  +
  gi|386001212|ref|YP_005919511.1| 690 AAQAERDSLIERLDRVEGE 708
                                       4566666666666666544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_N  52 sqiaglsqlvrnnslgisrlqtaqgalselsdilqrlke 90 
                                       +++++++++ r+++ + +r+++a+ga  e++++++ l++
  gi|386001212|ref|YP_005919511.1| 905 AKSREVDSADRERERVRARIAAAEGAAAEMRSAADGLRA 943
                                       678999****************************99665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00098       1.5       6      38 ..      25      72 ..      22     198 .. 0.77
   2 ?    0.9   0.3      0.33     5e+02      57     111 ..     941     999 ..     861    1014 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00098
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee...............e 38
                                       +++vtG+ G+GK+ ++  ll  l   ++ ++               +
  gi|386001212|ref|YP_005919511.1| 25 DFIAVTGPNGSGKSNVVDALLFALSLSSSRAMraerlpdliyrgdngK 72
                                      689*************99998777655555555555555555555554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.33
                            AAA_22  57 lrellralglelka...erlsseellealeqalrarav...ielliiDEaqhlr.seealee 111
                                       lr+  + +g ++++   + ++  + ++ale+ ++       + +l i+E ++++ + e l++
  gi|386001212|ref|YP_005919511.1| 941 LRAEIESFGIDASEeppKSQTIIRKIHALERSME---ElepVNMLAIEEYDRVFdRRETLRD 999
                                       3333333333333322222222222244444444...2555999999999997545555544 PP

>> Levi_coat  Levivirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.4e-05      0.12      32      81 ..    1123    1170 ..    1114    1171 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
                                        EEEEEESSSTTTS-E.EEEEEEEESSSEEEEEEEEEEEEEEEEEETTEEE CS
                         Levi_coat   32 vaelieanavsalekrvtisvrqssanrkkykvkvkvqkvasqtvsGved 81  
                                        va+li+  a  ++ + + +s+r++  ++ ky v v +q+    tv+Gv++
  gi|386001212|ref|YP_005919511.1| 1123 VAKLIKGIA--QAAQFIVVSLRKPMIQEAKYVVGVTMQENNISTVTGVCL 1170
                                        777776544..5556689******************************97 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00064      0.95      13      32 ..      26      45 ..      23     131 .. 0.89
   2 ?   -2.3   0.0       3.9   5.8e+03      85      89 ..     321     325 ..     257     409 .. 0.57
   3 ?    0.7   0.1      0.47   6.9e+02      52     112 ..     452     526 ..     419     531 .. 0.49
   4 ?    2.2   0.1      0.16   2.4e+02      51     119 ..     971    1091 ..     952    1110 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00064
                                      EEEEEESTTSSHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlklla 32
                                       +a++G+nG+GKS ++ +l+
  gi|386001212|ref|YP_005919511.1| 26 FIAVTGPNGSGKSNVVDALL 45
                                      5899***********99986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
                                       HHHHH CS
                                       xxxxx RF
                          ABC_tran  85 iekal 89 
                                       i+++ 
  gi|386001212|ref|YP_005919511.1| 321 IAALE 325
                                       22222 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.47
                                       B-HHHCCHCEEEE-SS--S-TTSBHHHH.........................HHHTCHHHHHHHSTTGGTTCBGES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  52 qeleslrkeigvlpqepqlfpeltvren.........................esdeeiekalsklglkelkdtvvk 103
                                       +++++l+++i+ +++e           +                          +++++e+ l++ g      + v+
  gi|386001212|ref|YP_005919511.1| 452 RQRQELEERISLFEEE-----------RddldsarisirremarvdetlqrlqMERARAEASLRSAGEGTGYSRAVE 517
                                       3455555555555555...........03333333333322454444444443333334444444444445555554 PP

                                       TTSGGS-HH CS
                                       xxxxxxxxx RF
                          ABC_tran 104 sspssLSgG 112
                                          s +S+G
  gi|386001212|ref|YP_005919511.1| 518 AIRSAMSQG 526
                                       444666666 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.16
                                        GB-HHHCCHCEEEE-SS--S-TTSB.HHHH..HHHTCHHHHHHHSTTGG.......................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.xxxx..xxxxxxxxxxxxxxxxx.......................... RF
                          ABC_tran   51 eqeleslrkeigvlpqepqlfpelt.vren..esdeeiekalsklglke.......................... 96  
                                        +  +e    ++  +++ +++f++ + +r++  + ++e e++l+kl++ e                          
  gi|386001212|ref|YP_005919511.1|  971 RSMEELEPVNMLAIEEYDRVFDRREtLRDRreTLQREREDLLAKLDQYEemkreafmaafeginenfrdtfnqls 1045
                                        444555555555555554444443325555663333344444444443333333333333332233333334444 PP

                                        ....................TTCBGESTTS...GGS-HHHHHHHHH CS
                                        ....................xxxxxxxxxx...xxxxxxxxxxxxx RF
                          ABC_tran   97 ....................lkdtvvkssp...ssLSgGqkqrval 119 
                                                            ++++++++     + +SgG+k+  al
  gi|386001212|ref|YP_005919511.1| 1046 dgegelileneedplaggmtIRARPARKAFhrlEAMSGGEKSLTAL 1091
                                        4445555555555555555533333333333346777777776666 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1       0.2     3e+02      31      60 ..     379     408 ..     358     420 .. 0.77
   2 ?   -2.0   0.0       3.1   4.6e+03      41      86 ..     428     473 ..     417     483 .. 0.62
   3 ?    4.9   0.3     0.022        32      44      95 ..     679     730 ..     668     745 .. 0.74
   4 ?   -0.2   0.1      0.86   1.3e+03      33      81 ..     776     819 ..     750     827 .. 0.44
   5 ?    6.6   0.3    0.0062       9.2      15      70 ..     966    1021 ..     957    1025 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekyeel 60 
                                       +a ++y++++d++a +++++e+ +++ + l
  gi|386001212|ref|YP_005919511.1| 379 RADARYAEVRDRLAVVKREVEEAKSRAADL 408
                                       466789999999999999999888887765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                           BLOC1_2  41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       ++a ++++  e +  ++ e     +q +++e++++ +ee  + LD+
  gi|386001212|ref|YP_005919511.1| 428 EAAIEISEARETMAGLDRERGRIGRQRQELEERISLFEEERDDLDS 473
                                       4555555555555555555555555666677777777776666665 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.022
                           BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                       ++le+   ++ + ++e +++++++d++e +v++    v+eL   ++++E+++
  gi|386001212|ref|YP_005919511.1| 679 QKLEEATRRVLAAQAERDSLIERLDRVEGEVSSVRRGVEELGREVSRIEVRL 730
                                       5666666666677777788888888888888888888888887777777765 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.86
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       +++    +++a sle++le  +       ++    d +e+++++L   +
  gi|386001212|ref|YP_005919511.1| 776 EAEARGAEERARSLERDLEGSEI-----PELSALADGLEAEIRSLSRKA 819
                                       44444444444444444443221.....222222233333333333333 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0062
                           BLOC1_2   15 leatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqi 70  
                                        + a    ++ Le +N  a+e+y+ + d+ + l++  e l+++ e l  +l+q +++
  gi|386001212|ref|YP_005919511.1|  966 IHALERSMEELEPVNMLAIEEYDRVFDRRETLRDRRETLQREREDLLAKLDQYEEM 1021
                                        5667778899*******************************999999999986665 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0028       4.2      11      81 ..     239     309 ..     234     316 .. 0.78
   2 ?    4.6   0.4     0.029        44      42      87 ..     359     399 ..     344     409 .. 0.64
   3 ?   -2.6   0.0       5.1   7.7e+03      35      72 ..     423     457 ..     421     462 .. 0.79
   4 ?    2.9   0.3     0.098   1.5e+02      67      84 ..     477     494 ..     472     499 .. 0.89
   5 ?    3.6   0.1      0.06        89      40      89 ..     685     733 ..     675     734 .. 0.65
   6 ?    2.5   0.1      0.13   1.9e+02      17      76 ..     919     977 ..     884     980 .. 0.91
   7 ?   -2.1   0.1       3.6   5.4e+03      25      51 ..     997    1023 ..     988    1030 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeya.kKLvnikkrmsslnerlqk 81 
                                        e++l +ld++l +lr   ++L  +ldr +++L +lee+ +  +  ++ +   +  +++k+rm +++ +++ 
  gi|386001212|ref|YP_005919511.1| 239 AESDLADLDTELLDLRSIDSDLIGRLDRGRAELSSLEENLK-GLNDEITRKGeDEQIEVKRRMVEVKGSIKA 309
                                       678999*******************************9998.444555444336677788888877776665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.029
                   Snapin_Pallidin  42 kLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                        L+e++e +e      l +y++K++++  r  ++ +rl  +k+ +e
  gi|386001212|ref|YP_005919511.1| 359 ILAEIQEREE-----ALASYREKIARADARYAEVRDRLAVVKREVE 399
                                       4666666666.....6666666666666666666666665555443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.1
                   Snapin_Pallidin  35 qldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrm 72 
                                       +++r+ ++++ ++ea e  +++ l++ + ++ + ++++
  gi|386001212|ref|YP_005919511.1| 423 SIEREEAAIE-ISEARE--TMAGLDRERGRIGRQRQEL 457
                                       7888888885.888888..8999999999888888776 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.098
                   Snapin_Pallidin  67 nikkrmsslnerlqklkk 84 
                                       +i+++m ++ e+lq+l+ 
  gi|386001212|ref|YP_005919511.1| 477 SIRREMARVDETLQRLQM 494
                                       79**************95 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.06
                   Snapin_Pallidin  40 nekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                       ++++  ++ +  ++++++l++    ++++++ +++l   +++++ R+e++
  gi|386001212|ref|YP_005919511.1| 685 TRRVLAAQAER-DSLIERLDRVEGEVSSVRRGVEELGREVSRIEVRLEEI 733
                                       34333333333.36777888888888888888888888888888888776 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.13
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssln 76 
                                       ++++++++ +    e+++  d l+++++++  +++ e +p+ ++ ++K++++++ m++l+
  gi|386001212|ref|YP_005919511.1| 919 RVRARIAAAEGAAAEMRSAADGLRAEIESFGIDAS-EEPPKSQTIIRKIHALERSMEELE 977
                                       67788888888889999999999999999988888.78******************9885 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 3.6
                   Snapin_Pallidin   25 lrqsQeeLleqldrlnekLkeleeaqe 51  
                                        lr+  e L+ + + l +kL+++ee++ 
  gi|386001212|ref|YP_005919511.1|  997 LRDRRETLQREREDLLAKLDQYEEMKR 1023
                                        555666666666667777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1362  (0.0759663); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 1.54u 0.36s 00:00:01.90 Elapsed: 00:00:00.66
# Mc/sec: 5384.80
//
Query:       gi|386001213|ref|YP_005919512.1|  [L=236]
Description: Chromosome segregation and condensation protein ScpA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   48.1   0.0    1.2e-10   41.7   0.0    2.5  1  SMC_ScpA  Segregation and condensation protein ScpA


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   6.8e-15   1.2e-10       1     238 [.      29     224 ..      29     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 6.8e-15
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXX.XXX CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeelelee.lrd 76 
                                       L+ ++e+d++d ++  vt++fl+ i++l  + +l   +  l+ as l+++K++s+   e+++eee ee+ +    r 
  gi|386001213|ref|YP_005919512.1|  29 LARRGEIDPWDLDLSAVTEKFLERIEAL-GNRDLPALGRTLLYASILLRMKSDSME-GEEEPEEEFEEFDDPPvFRR 103
                                       67799***********************.567**********************85.56677778888777541577 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA  77 kLiarLleYrkykeeaklfkeleaerlksfskarsdleefikeveevavkieksvfklieafnkllkrakivalaek 153
                                       ++++ L+       +  ++++          +++++lee+i+e+ + +   e +v  +        ++ ++v  a  
  gi|386001213|ref|YP_005919512.1| 104 RIVEGLP-------SPPIRRRA---------RRPVTLEELISELRRAETVAERKVGRER------ARPEPTVEEAME 158
                                       8888888.......44444433.........5679999999999998887787743333......333333333333 PP

                                       XX...HHHHHHHHHHHH...............HHHTS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEES CS
                          SMC_ScpA 154 qiseleisieeqleellaqleqflqarlkevLldlrswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQe 230
                                       + +e    ie +   l  ++  +l a           ++++s+L +          v  ++ lL +   + + leQ 
  gi|386001213|ref|YP_005919512.1| 159 RAHEE--GIEGRIRTLRGTIFEMLAAEE---------RISFSDLPER--------DVLSYVSLLFMAGRREIWLEQD 216
                                       46766..788888888888888887654.........5899988655........6888999999999999999999 PP

                                       STTS-EEE CS
                          SMC_ScpA 231 eflddLqv 238
                                         +++L++
  gi|386001213|ref|YP_005919512.1| 217 ALFGELYI 224
                                       99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1416.11
//
Query:       gi|386001214|ref|YP_005919513.1|  [L=357]
Description: Chromosome segregation and condensation protein ScpB [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-35  122.3   0.0    3.2e-35  121.1   0.0    1.6  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
    0.00045   20.2   1.7       0.43   10.7   0.2    3.0  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.15   12.0   0.2        5.7    6.9   0.1    2.9  2  TrmB      Sugar-specific transcriptional regulator TrmB
       0.49   10.2   0.1       0.49   10.2   0.1    3.1  4  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   7.1e-39   3.2e-35       2     152 ..      22     164 ..      21     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 7.1e-39
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkk 78 
                                       ++EA+Lf+ag+pl+++e+a++++l  + + +  ++L +ey+e+  g+e++e +g+y +++++ +a+ v+k+ ++   
  gi|386001214|ref|YP_005919513.1|  22 VVEAALFAAGRPLTAAEIAELTDLPIRVAMRFADSLVREYSERAGGIEVRESEGRYVMQVRSTVADRVSKVGPQ--- 95 
                                       79***********************************************************************9... PP

                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglk 152
                                        +L+   l+tLa+Ia +qp+ ++e+ ++RG +s+++vr+Llergli+ ++    +gr+ + +tT+ F eyfgl+
  gi|386001214|ref|YP_005919513.1|  96 -ELDPPLLRTLAVIARHQPIPQSELVRVRGNKSYGHVRELLERGLIRAEK----EGRTKIITTTKGFAEYFGLD 164
                                       .***********************************************99....9*****************95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1   0.00086       3.9      15      39 ..      23      48 ..      17      54 .. 0.85
   2 !   10.7   0.2   9.6e-05      0.43      33      61 .]     119     147 ..     102     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00086
                                      HHHHH.STCTTB-HHHHHHHHTS-HH CS
                            HTH_20 15 ilraL.araegltaselaerldlskn 39
                                      +++aL a +++lta+e+ae+ dl+  
  gi|386001214|ref|YP_005919513.1| 23 VEAALfAAGRPLTAAEIAELTDLPIR 48
                                      67788899************999865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.6e-05
                                       HHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  33 rldlskntlsyHLrvLeeagLvevvregr 61 
                                       +++++ n  + H+r+L e gL++ ++egr
  gi|386001214|ref|YP_005919513.1| 119 LVRVRGNKSYGHVRELLERGLIRAEKEGR 147
                                       45788888999****************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.053   2.4e+02      21      39 ..      32      50 ..      23      80 .. 0.79
   2 ?    6.9   0.1    0.0013       5.7      32      60 ..     120     148 ..     117     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.053
                                      CCCHHCHHCCCTTSSCHCH CS
                              TrmB 21 gpatadeiaeelgvprskv 39
                                       p+ta eiae +++p   +
  gi|386001214|ref|YP_005919513.1| 32 RPLTAAEIAELTDLPIRVA 50
                                      689********99997655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0013
                                       TTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  32 lgvprskvYevLrsLedkGlVerekgrpk 60 
                                       + v  +k Y  +r+L+++Gl++ ek+ ++
  gi|386001214|ref|YP_005919513.1| 120 VRVRGNKSYGHVRELLERGLIRAEKEGRT 148
                                       55667788999*************97754 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00011      0.49      14      44 ..      29      59 ..      25      60 .. 0.79
   2 ?   -2.1   0.0      0.78   3.5e+03      20      33 ..     104     117 ..      96     121 .. 0.60
   3 ?   -2.4   0.1      0.98   4.4e+03      37      49 ..     129     141 ..     128     143 .. 0.80
   4 ?   -3.2   0.0       1.7   7.8e+03      20      31 ..     297     308 ..     285     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHH CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLve 44
                                      +a+++lt +e+A+ t+lp   + R+  +Lv+
  gi|386001214|ref|YP_005919513.1| 29 AAGRPLTAAEIAELTDLPIRVAMRFADSLVR 59
                                      56778*************8777777777776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.78
                                       BHHHHHHHHTS-HH CS
                          HTH_IclR  20 tlselArrtglpkS 33 
                                       tl+ +Ar+  +p S
  gi|386001214|ref|YP_005919513.1| 104 TLAVIARHQPIPQS 117
                                       56666666555555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.98
                                       HHHHHHHHTTSEE CS
                          HTH_IclR  37 RlLqtLvelGyve 49 
                                       ++++ L e+G+++
  gi|386001214|ref|YP_005919513.1| 129 GHVRELLERGLIR 141
                                       6788899999987 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.7
                                       BHHHHHHHHTS- CS
                          HTH_IclR  20 tlselArrtglp 31 
                                        + e+A  +g+p
  gi|386001214|ref|YP_005919513.1| 297 MVEEIALDLGVP 308
                                       578999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 2504.80
//
Query:       gi|386001215|ref|YP_005919514.1|  [L=272]
Description: Metal-dependent phosphohydrolase, HD subdomain protein [Methanosaeta harundinacea 6Ac]
Scores for 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-09   35.7   0.3    1.3e-08   35.1   0.3    1.3  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.3   7.3e-13   1.3e-08       3     120 ..      36     160 ..      35     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 7.3e-13
                                       HHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH...HHHCTCCHHHHHHHHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk...eeefekflaHekvgaeilrevekrlg 75 
                                       eH+ +V + +  +++ lg+ ++d  l++++aL+HD+G  p++     +   +   ++  +H+  ++ +l +++ ++ 
  gi|386001215|ref|YP_005919514.1|  36 EHTARVRREISDIGRTLGLaDDDLRLAEAMALFHDLGRFPQYA---TYgtfS--DRRSCDHAALSVGVLIDSGVLDA 107
                                       89999999999*****************************776...444432..444569****************9 PP

                                       HH...HHHHHHHHHTTCCHHHHHHHHH.....HHHCCTSCHHHHHHHHHHHHH CS
                                HD  76 ld...ledvaklirehheswegkkrpr.....glaerqlslearivklaDrla 120
                                       ld    e+++k+i++h++    +++ +     ++  r+ +++++ + l+D+++
  gi|386001215|ref|YP_005919514.1| 108 LDpeeRELILKAISRHNRAGLPEEESDrcllfSKLLRDADKLDIWAVLLDYYQ 160
                                       99******************966444234455666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1726.20
//
Query:       gi|386001216|ref|YP_005919515.1|  [L=662]
Description: Glycoside hydrolase 15-related protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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   20.8   0.3       0.15   10.8   0.0    3.4  3  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.031   13.4   0.0      0.047   12.9   0.0    1.2  1  DUF608          Glycosyl-hydrolase family 116, catalytic regi


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.013   1.1e+02      23      52 ..     316     350 ..     299     369 .. 0.73
   2 !   10.8   0.0   1.7e-05      0.15     167     343 ..     446     581 ..     391     596 .. 0.73
   3 !    4.3   0.0    0.0015        14     413     446 ..     607     639 ..     597     641 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.013
                                       TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHH CS
                    Glyco_hydro_15  23 tGlliASpstsdp.....DYrytWvRDsvyvilav 52 
                                        G  iAS + +        Y y+W RD++    a+
  gi|386001216|ref|YP_005919515.1| 316 NGSAIASCDSDIRqfgadVYSYCWPRDAAWASIAL 350
                                       5667777764443677755*********9877666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 1.7e-05
                                       TS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECE CS
                    Glyco_hydro_15 167 ktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntyli 243
                                        +++f+lWEe++g   +  s   + ++l  a+++a ++g++   + ++  ++ +   +     ++r +++  + + +
  gi|386001216|ref|YP_005919515.1| 446 PRASFDLWEERKGVFTY--SASTVYAGLRGAAELALALGNDRLFEAWSAGAERVRAAI-----VDRLYDDRLGRFRR 515
                                       5689***********99..555667888899999999999999999999999999999.....88888888888888 PP

                                       CSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--S CS
                    Glyco_hydro_15 244 ldgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrR 320
                                         ++              +d+sl  +   ++ p++d          pr+  ++ +++++ll+ g          v R
  gi|386001216|ref|YP_005919515.1| 516 SGED------------GTVDSSLFGVWWFGVLPPND----------PRVARTMEAVERELLRPGG--------GVAR 562
                                       7777............88899998888899999999..........9999999999999888877........3888 PP

                                       BTT--CGSSSBSCT--BHHHHHH CS
                    Glyco_hydro_15 321 ysedvkpdklglsGrpyylctlw 343
                                       y+ d +    g+  +++ ++tlw
  gi|386001216|ref|YP_005919515.1| 563 YEGDEY----GGRMNSWIISTLW 581
                                       888887....5666777777777 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0015
                                       S-TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                    Glyco_hydro_15 413 dnslgvLteevdvylgeliraqpllfsealllri 446
                                        + +g+L e+v + +g +++  pl++s+a+++ +
  gi|386001216|ref|YP_005919515.1| 607 HPTTGLLPEQVAD-DGSPRSVLPLMWSHAAFILA 639
                                       567899****987.9***************9965 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-06     0.047     147     241 ..     441     534 ..     438     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-06
                            DUF608 147 enegfadqtYDaws.vkGvsaycgglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnGeYfkydess 222
                                       +++g +  ++D w+  kGv +y+++  +a L+ a+e+a  lg+++  e +++  e+ + +  ++L+  +  ++ +s 
  gi|386001216|ref|YP_005919515.1| 441 DDSGLPRASFDLWEeRKGVFTYSASTVYAGLRGAAELALALGNDRLFEAWSAGAERVRAAIVDRLYDDRLGRFRRSG 517
                                       789999*******7368*****************************************************9999755 PP

                            DUF608 223 sesesimadqlaGqwylra 241
                                         ++  +   l G w+  +
  gi|386001216|ref|YP_005919515.1| 518 --EDGTVDSSLFGVWWFGV 534
                                       ..55666668999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 4921.68
//
Query:       gi|386001217|ref|YP_005919516.1|  [L=328]
Description: Peptidase S8 and S53 subtilisin kexin sedolisin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.5   0.3    4.6e-09   36.8   0.1    2.0  3  Ig_3      Immunoglobulin domain
    1.2e-07   31.8   0.1    2.6e-07   30.7   0.1    1.6  1  ig        Immunoglobulin domain
    3.9e-07   30.0   0.1    2.1e-06   27.7   0.1    2.2  1  I-set     Immunoglobulin I-set domain
    3.2e-06   27.4   0.2      7e-06   26.3   0.2    1.5  1  Ig_2      Immunoglobulin domain
    0.00041   20.5   0.1     0.0059   16.8   0.1    2.5  2  V-set     Immunoglobulin V-set domain


Domain annotation for each model (and alignments):
>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         4   1.4e+04      61      74 ..      46      59 ..      38      62 .. 0.78
   2 ?   -3.7   0.0         5   1.8e+04      58      68 ..     164     174 ..     159     180 .. 0.75
   3 !   36.8   0.1   1.3e-12   4.6e-09       5      78 ..     235     301 ..     233     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                                      EESS--GGG-EEEE CS
                              Ig_3 61 tisnvtksdsGtYt 74
                                      +++ ++k d+ tY+
  gi|386001217|ref|YP_005919516.1| 46 QVKGISKADETTYQ 59
                                      67788899999996 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5
                                       TEEEESS--GG CS
                              Ig_3  58 ssLtisnvtks 68 
                                       ++Lti++v+++
  gi|386001217|ref|YP_005919516.1| 164 GKLTIHEVRPD 174
                                       78999999875 PP

  == domain 3  score: 36.8 bits;  conditional E-value: 1.3e-12
                                       ECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS...TTCSEEESSEECCCTEEEESS--GGG-EEEEEEEE CS
                              Ig_3   5 tvppsstvvtegesvtLtCeaegnppptitWykngeklssnstsssissegssssLtisnvtksdsGtYtCvAs 78 
                                       +vp++     ege++tL+  ++g   p ++W+k+ +   +  ts     + ++s ++i+nv+++d+G YtC+++
  gi|386001217|ref|YP_005919516.1| 235 VVPNEVK--CEGETATLRALVSGCYDPIYQWFKGITS--EDGTS---IPGATGSVYIIRNVSPEDEGYYTCKVT 301
                                       5555444..7***********************9883..32333...469999******************986 PP

>> ig  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   7.2e-11   2.6e-07       4      80 ..     237     306 ..     234     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 7.2e-11
                                       SEEEEETTS-EEEEEEEESSSCTSEEEEEESSSSCSEEEEEEEEETTCEEEEEEEECSSTGGGTEEEEEEEEETTEE CS
                                ig   4 plvlvleGesatLtCsvstqtkptdvtWkkegqtkiesqkvvkegnrrkgssslliskvteedaGtYtCevnnsgss 80 
                                       p+ +  eGe+atL+  vs +  ++++ W+k  +++  ++          + s  +i++v++ed+G YtC+v  +g s
  gi|386001217|ref|YP_005919516.1| 237 PNEVKCEGETATLRALVS-GCYDPIYQWFKGITSEDGTSI------PGATGSVYIIRNVSPEDEGYYTCKVTCNGNS 306
                                       6677779***********.***********9999999988......9999********************9877665 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   5.8e-10   2.1e-06      14      85 ..     243     310 ..     234     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.8e-10
                                       TTS-EEEEEEEECSSS-EEEEEETTCB-STSSSEEEEEETTEEEEEESSB-GGGGEEEEEEEEETSEEEEEE CS
                             I-set  14 eGesvelectveGepepsvsWakdgselkssqrvkvtveeaeytLtIsnvevsDeGkYtckatnsagkaeak 85 
                                       eGe+++l++ v+G+ +p  +W+k+   ++s++  ++      +  +I+nv+++DeG Ytck+t++  ++e  
  gi|386001217|ref|YP_005919516.1| 243 EGETATLRALVSGCYDPIYQWFKG---ITSEDGTSIPGAT-GSVYIIRNVSPEDEGYYTCKVTCNGNSDEDA 310
                                       8*********************98...5555555665555.46779******************99988865 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   1.9e-09     7e-06       6      70 ..     236     308 ..     231     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                              Ig_2   6 psptvvtegepvtLtCsapgnpppkvqwykgg.....evin.sspn.ffinavsaedsgtYtCra.rntkgge 70 
                                       +++ v  ege+ tL+  ++g+ +p +qw+kg      + i+  +++ ++i++vs+ed g YtC++ +n++  e
  gi|386001217|ref|YP_005919516.1| 236 VPNEVKCEGETATLRALVSGCYDPIYQWFKGItsedgTSIPgATGSvYIIRNVSPEDEGYYTCKVtCNGNSDE 308
                                       5556668999999999999**99******999776666666544557888***************66655555 PP

>> V-set  Immunoglobulin V-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.22   7.9e+02      49      83 ..     137     174 ..     125     177 .. 0.73
   2 !   16.8   0.1   1.6e-06    0.0059      77      99 ..     285     307 ..     266     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.22
                                       ECT...TEEEEESTTTEEEEEEGTTTEEEEEESSESGG CS
                             V-set  49 ysn...kskeekkkgrfslrkdpskgdfsltiqnltls 83 
                                       ys+   ++k  +++grf  +  +   d+ lti++++++
  gi|386001217|ref|YP_005919516.1| 137 YSTnvrTTKLVIQRGRFAKELIIPGMDGKLTIHEVRPD 174
                                       44446555666668888888888999*******99985 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-06
                                       ESSESGGG-EEEEEEEECSSEEE CS
                             V-set  77 iqnltlsDsGtYtCavvpsgegv 99 
                                       i+n++++D+G+YtC+v  +g ++
  gi|386001217|ref|YP_005919516.1| 285 IRNVSPEDEGYYTCKVTCNGNSD 307
                                       89*************94444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2353.51
//
Query:       gi|386001218|ref|YP_005919517.1|  [L=1471]
Description: hypothetical protein Mhar_0512 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-31  110.4   0.2    1.9e-31  109.6   0.2    1.4  1  Peptidase_C25  Peptidase family C25
    0.00083   19.6   0.0     0.0092   16.3   0.0    2.8  2  DUF11          Domain of unknown function DUF11
     0.0029   16.7   0.0     0.0059   15.7   0.0    1.4  1  GHL10          Glycosyl hydrolase-like 10
  ------ inclusion threshold ------
      0.016   15.9   0.2       0.08   13.6   0.2    2.2  1  CW_binding_2   Putative cell wall binding repeat 2
      0.063   13.5   0.1         17    5.7   0.1    2.5  2  PucR           Purine catabolism regulatory protein-like fami
       0.18   12.0   0.8         24    5.2   0.0    3.1  3  VERL           Vitelline envelope receptor for lysin


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.2   6.4e-35   1.9e-31      52     377 ..     861    1179 ..     792    1180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 6.4e-35
                                        HHHHHHHHHHTT.--SEEEEES-T.............TTS--EE-.....TTT-SEESHHHHS-T.....TSSS- CS
                     Peptidase_C25   52 flkyayknwsas.klkYllLvGdtsivvkvkspitksdliptyqiakslgnestiptDdyyasldgnedsddltp 125 
                                         l++++++   +  ++Yl+ vG                +i t + ++  g  ++ ++  y + ld     dd ++
  gi|386001218|ref|YP_005919517.1|  861 DLQTLVEDL--EiSPRYLMVVGGP----------GSLPFISTGMKQA-AGVFEYDVCREYGIELD-----DDGYQ 917 
                                        556666666..2357899999988..........3444555555333.77888899999999999.....9**** PP

                                        SSEEEEE--SSHHHHHHHHHHHHHHHCT--S-G....GGGEEEEEE--.........HHTHHHHHHHHHHHTSSG CS
                     Peptidase_C25  126 dlavGRipvtsaaeaaavvnKiiaYerntengsaagqwrnkvlliagdvvgeweaadgneiagttaettpseynv 200 
                                        d+a+GRi   s+ +a+++v+++ aY++    g   g wr  +l+i+             + +++t ++ p  + +
  gi|386001218|ref|YP_005919517.1|  918 DVATGRIIGLSVYDASQMVARTFAYDDI---G---GEWRGSALVISSP-----------ADYPSTWPQSPIPLRI 975 
                                        **************************76...3...56***********...........5589************ PP

                                        GGT-SEEEEE-SS--.............TTTTHHHHH--SEEEEES-EETTEE.......TTTTEEHHHHHT--- CS
                     Peptidase_C25  201 nklyadlaayeaetetevpaanqpllttqnllkalnqGvlfvnytGHGsetaw.......adeslstndisaltn 268 
                                         +++    a  ++++   ++++++  t+q++ +++n G+++v +  HG  ++w        d+  + +++++lt 
  gi|386001218|ref|YP_005919517.1|  976 GEYLRA--AGLNAEN---LRWEEA--TYQRVSSKMNSGQSLVYFDYHGVDWGWqlsiwalMDQLMDEEQVKQLTL 1043
                                        ***999..9999999...445555..778*************************99998666666********** PP

                                        TT--EEEEEESSSTT-TTSSS-.................-HHHHHHHSTTSSEEEEEEESS---SS--SHHHHHH CS
                     Peptidase_C25  269 tnklpiaitaaCltgafdeetkr................sfgeklvlnangGavayigatrlgysgvndrlsraf 327 
                                        ++  + ++t aClt+++ +++++                s++ +++   ++Gav+y g + ++++ v+d+++  +
  gi|386001218|ref|YP_005919517.1| 1044 AP--QTTTTSACLTTKL-KGQTFpyrdgidvyiptrledSMALAFL---KAGAVNYAGPSANSWIFVSDDYVGRM 1112
                                        99..*************.666667***********99888888888...************************** PP

                                        HHHHHHHHH...T-S-SS-HHHHHHH................................EEEEE-TT-- CS
                     Peptidase_C25  328 fealfadaartlGealllaknelletgl...............aqsiskgm.nkrt..fnllGDPalr 377 
                                        ++al+ ++a t+Gea+++a+n ++++++               ++ + ++m n++   f+l+GDPa+r
  gi|386001218|ref|YP_005919517.1| 1113 HQALVFENA-TIGEAMMAANNLYASKIQategidlekideyqpWYLSIEEMlNQTAsiFTLFGDPAFR 1179
                                        *********.5*************9999**********99965444477776777799********98 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.9   5.6e+03      14      27 ..     360     373 ..     325     397 .. 0.72
   2 !   16.3   0.0   3.1e-06    0.0092      12      76 ..     592     677 ..     579     686 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                             DUF11  14 dtvtytltvtNtgp 27 
                                       d ++yt+ ++N  +
  gi|386001218|ref|YP_005919517.1| 360 DYIEYTISTQNVEG 373
                                       45677777777544 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.1e-06
                             DUF11  12 pGdtvtytltvtNtgpasangvvvtDtl.Paglayvsvsas....................qgtasaltsvgsLeag 67 
                                        G+ v+  +t++N+g + ++++ +tD+  Pa + +  +sas                     +  +  +++ +L + 
  gi|386001218|ref|YP_005919517.1| 592 EGEIVRLKITLKNSGKDELKDLALTDLIlPARMVAWWSSASgkvvltdpstglsptpdsafFSGTNLSWTIDRLGPR 668
                                       58899999******************855877777777777777777777777666666665555578888999999 PP

                             DUF11  68 esatlsftv 76 
                                       e atl+++v
  gi|386001218|ref|YP_005919517.1| 669 EFATLNLEV 677
                                       999998877 PP

>> GHL10  Glycosyl hydrolase-like 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-06    0.0059     131     214 ..     209     296 ..     191     315 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                             GHL10 131 lnPliPevqdfitklvvevvkrYdvDgvqlDDyfyl.pesfGydlidvalYrqetk...kealsnkeddlwidWRrd 203
                                       l P+ P+++d +   v+ev+  Y  Dgv l ++  l  ++   d+ + + Y+  +    +   s+ + +lw +W+ +
  gi|386001218|ref|YP_005919517.1| 209 LCPIDPDARDHLYDRVEEVIDDYAADGVVLYNFGFLdENHCFCDVCKEEFYNDTGVdlsRVGSSSYNRQLWSRWKEE 285
                                       5699**************************9996551555667899999999888511134567788889******* PP

                             GHL10 204 kisqlvkklna 214
                                       ++ + v ++ +
  gi|386001218|ref|YP_005919517.1| 286 QVLEVVDEVRR 296
                                       **999998865 PP

>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.7e-05      0.08       6      68 ..     440     508 ..     436     510 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                       SHHHHHHHHHHH.........EEET..THHHHHHHHHHHHHT--EEEE-TSSS.-.HHHHHHHEEEES-TTTS-H CS
                      CW_binding_2   6 DRyeTaaaiaka.........latg..faDALsaaalaakknaPiLLtdkldtal.kalksatvyilGGegvvsd 68 
                                       D +e a ++a +         +  g  +   L+aaa+a+ +n P+L++ ++   l +++++  +  lG + vvs 
  gi|386001218|ref|YP_005919517.1| 440 DSIEMASKVAAKwdespgavlI--GdnYSAGLTAAAIASYLNWPVLFVGDS---LsNSTEDD-LARLGSTTVVSA 508
                                       6677777777755777776432..5568889*****************733...22223333.668999999985 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0056        17      62      94 ..      94     126 ..      80     128 .. 0.89
   2 ?    4.9   0.0     0.011        31      52      79 ..     366     394 ..     362     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0056
                              PucR  62 lvrelaeagvaaLviklgreipeelieaadelg 94 
                                        + ++a+a+++aLvi  + e+ ++l++aa++ g
  gi|386001218|ref|YP_005919517.1|  94 ALHAMAAANISALVIDAEGELAKSLVKAAQKEG 126
                                       57899************77**********9987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
                              PucR  52 l.kddpealaelvrelaeagvaaLviklg 79 
                                       + +++ e   + +++la+ g+a++v++++
  gi|386001218|ref|YP_005919517.1| 366 IsTQNVEGTVRRIEDLAKEGAAGMVFEYD 394
                                       545677888899***************95 PP

>> VERL  Vitelline envelope receptor for lysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   4.4e+03      45      67 ..     393     415 ..     389     420 .. 0.80
   2 ?    3.5   0.0     0.028        84      29      59 ..     428     458 ..     423     467 .. 0.79
   3 ?    5.2   0.0    0.0081        24      35      51 ..    1399    1415 ..    1383    1423 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                              VERL  45 ytvtvrlkWsegtPtylsleCyl 67 
                                       y v    +Wse  P   s++  +
  gi|386001218|ref|YP_005919517.1| 393 YDVVYTPLWSELQPPSASVQWLM 415
                                       88888999***999999988766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.028
                              VERL  29 vfrGPysv.PkndtvvlytvtvrlkWsegtPt 59 
                                       vf+ P  v   nd++++ +  v+ kW e + +
  gi|386001218|ref|YP_005919517.1| 428 VFWDPDGViEYNDSIEMAS-KVAAKWDESPGA 458
                                       89999876267******75.67889*988755 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0081
                              VERL   35 svPkndtvvlytvtvrl 51  
                                         vP+n+tv l +vtvr 
  gi|386001218|ref|YP_005919517.1| 1399 GVPTNETVSLANVTVRA 1415
                                        69*************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 9429.98
//
Query:       gi|386001219|ref|YP_005919518.1|  [L=528]
Description: hypothetical protein Mhar_0513 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00069   19.8   0.2        0.6   10.4   0.0    3.4  3  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
     0.0092   16.6   4.1       0.29   11.8   0.1    2.9  3  CW_binding_2  Putative cell wall binding repeat 2
  ------ inclusion threshold ------
        0.1   12.6   0.0        0.2   11.7   0.0    1.4  1  Inp1          Inheritance of peroxisomes protein 1
       0.12   13.2   0.0       0.28   11.9   0.0    1.6  1  N_BRCA1_IG    Ig-like domain from next to BRCA1 gene
       0.14   12.2   0.0       0.37   10.8   0.0    1.6  1  CtaG_Cox11    Cytochrome c oxidase assembly protein CtaG/Cox1


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00017       0.6      41      71 ..      72     102 ..      32     103 .. 0.74
   2 !    5.6   0.0    0.0054        19      24      54 ..     168     199 ..     146     203 .. 0.70
   3 ?   -2.9   0.0       2.3   8.4e+03       3      18 ..     215     230 ..     214     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                       NPCBM_assoc  41 pasaaslapGetveatvkVtppagaaaGdye 71 
                                         +++ lapGe+v++++k + p+++ +G+y+
  gi|386001219|ref|YP_005919518.1|  72 ISKFEILAPGEEVKVKIKFSTPPEISPGTYP 102
                                       556778***********************96 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0054
                       NPCBM_assoc  24 vslsl.slPeGWtvvevspasaaslapGetve 54 
                                       +sl++  lP+ Wt++ +++++  + +++ t++
  gi|386001219|ref|YP_005919518.1| 168 ISLDVpHLPPRWTATLFDGTETVEMPYNLTLS 199
                                       45554146****************99998876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.3
                       NPCBM_assoc   3 pGetvtltltvtndgt 18 
                                       pG+t t+ + +t+ g+
  gi|386001219|ref|YP_005919518.1| 215 PGDTRTIGIQATSLGD 230
                                       8999999999999874 PP

>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.8   1.4e+04      38      44 ..      10      17 ..       6      30 .. 0.55
   2 !   11.8   0.1   8.1e-05      0.29      25      71 .]     364     416 ..     338     416 .. 0.64
   3 !    5.3   0.2    0.0085        30       1      45 [.     427     483 ..     427     514 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.8
                                      -EEEE-.T CS
                      CW_binding_2 38 PiLLtd.k 44
                                      P+LL+  +
  gi|386001219|ref|YP_005919518.1| 10 PLLLVAvS 17
                                      56666421 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHHHHHT--EEEE-..TS..SS..-.HHHH.HHHEEEES-TTTS-HHHH CS
                      CW_binding_2  25 ALsaaalaakknaPiLLtd..kl..dt.al.kalk.satvyilGGegvvsdsve 71 
                                       AL+ a   a++  P++     +l  d+ +l ++l+ ++ v+ilG e+vvs++ve
  gi|386001219|ref|YP_005919518.1| 364 ALAYAEGLANDTVPVITLRggDLseDDlQLlEELPlAK-VVILGNESVVSSEVE 416
                                       55544444455689999986422555666666666444.99**********997 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0085
                                       EE--SSHHHHHHHHHH.H........EEET..THHHHHHHHHHHHHT--EEEE-.TS CS
                      CW_binding_2   1 RiaGaDRyeTaaaiak.a........latg..faDALsaaalaakknaPiLLtd.kl 45 
                                       RiaG+   eT+   a+ +        +  g     A +a   a++ +aP++     l
  gi|386001219|ref|YP_005919518.1| 427 RIAGDEICETSWLFASaFspagteavVIAGadEMEAFAAYEEAKRIGAPLIICGtPL 483
                                       9***************5599998886455634556999999999999***9997422 PP

>> Inp1  Inheritance of peroxisomes protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05       0.2      81     113 ..     292     326 ..     282     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                              Inp1  81 iLpklqvwrvddee...skfvlrienperywrIelp 113
                                       ++pk+qv+ v +e+   ++f l + +p   +rIe+ 
  gi|386001219|ref|YP_005919518.1| 292 VMPKSQVISVGEEKsgiGEFTLLATKPG-RYRIEFL 326
                                       79********55556999******9999.78***93 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-05      0.28       7      78 ..      31     101 ..      27     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                        N_BRCA1_IG   7 vvppgteftktWrlrNtGseaWpagtklvfvgGdkmg.sasaeessvsvpavapgeevevsvelkaP..skpgry 78 
                                       +++pg+  ++t  l+N+G+++   g++   v+G++   +     +  + + +apgeev+v++++ +P   +pg+y
  gi|386001219|ref|YP_005919518.1|  31 ELHPGEITERTLILKNSGNQPI-FGITTMPVAGKAKElV-LM--EISKFEILAPGEEVKVKIKFSTPpeISPGTY 101
                                       6789999999**********97.7777777777777433.32..3344666****************43345555 PP

>> CtaG_Cox11  Cytochrome c oxidase assembly protein CtaG/Cox11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.37      59     131 ..      28      96 ..      15     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                        CtaG_Cox11  59 rslevkpGetalafytaknksdkpiigqavysvaPeeaakyfnKieCFCFeeqkLkpgeevdlpvlFfidpel 131
                                        ++e++pGe+++ +   kn+ ++pi g+ ++ va +     +  i  F    + L+pgeev++ + F   pe+
  gi|386001219|ref|YP_005919518.1|  28 FEVELHPGEITERTLILKNSGNQPIFGITTMPVAGKAKELVLMEISKF----EILAPGEEVKVKIKFSTPPEI 96 
                                       47999*****************************99999999999877....689999999999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3505.38
//
Query:       gi|386001220|ref|YP_005919519.1|  [L=263]
Description: hypothetical protein Mhar_0514 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1709.56
//
Query:       gi|386001221|ref|YP_005919520.1|  [L=153]
Description: hypothetical protein Mhar_0515 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-42  145.0   0.1    1.3e-42  144.8   0.1    1.0  1  DUF2240      Uncharacterized protein conserved in archaea (DU
     0.0062   16.7   0.1      0.086   13.1   0.0    2.4  2  SelB-wing_2  Elongation factor SelB, winged helix


Domain annotation for each model (and alignments):
>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.1   1.5e-46   1.3e-42       2     143 ..       5     142 ..       4     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.5e-46
                           DUF2240   2 lkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpde 78 
                                        ++ va pfkk+ k++l+ sdfvfalsld+kw +p+++++ll++a+ egL++ +++++ ++fd ++ e+P gFkp+ 
  gi|386001221|ref|YP_005919520.1|   5 RAYLVATPFKKRDKRSLKISDFVFALSLDLKWGPPEKVRALLQEAADEGLVRIEGDYVHAAFDDSQAEVPVGFKPQ- 80 
                                       6789************************************************************************. PP

                           DUF2240  79 ellkekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                          ke++ fe++l+ ++++tg+ +kev++++ne+q++l glv+++a+al+vak+ g +v+dl+ e
  gi|386001221|ref|YP_005919520.1|  81 ---KEEDLFEKALRLVVSTTGMGRKEVISMVNERQDSLMGLVNLDAVALLVAKEVGAEVTDLAGE 142
                                       ...99********************************************************9987 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   9.6e-06     0.086      31      56 ..      38      63 ..       1      63 [. 0.72
   2 ?    1.3   0.0     0.044   3.9e+02      16      31 ..      98     113 ..      96     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-06
                                      -HCCHHHHHHHHHHTTSEEE-SSEEE CS
                       SelB-wing_2 31 paklfqallealvargilavegdwvh 56
                                      p++ + all++++++g + +egd+vh
  gi|386001221|ref|YP_005919520.1| 38 PPEKVRALLQEAADEGLVRIEGDYVH 63
                                      377799*******************9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.044
                                       -EEHHHHHHHCSSSS- CS
                       SelB-wing_2  16 GmskeeLrsrlaprlp 31 
                                       Gm++ e  s++  r +
  gi|386001221|ref|YP_005919520.1|  98 GMGRKEVISMVNERQD 113
                                       9********9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:01.14
# Mc/sec: 404.21
//
Query:       gi|386001222|ref|YP_005919521.1|  [L=163]
Description: hypothetical protein Mhar_0516 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1171.02
//
Query:       gi|386001223|ref|YP_005919522.1|  [L=246]
Description: hypothetical protein Mhar_0517 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-22   78.8   2.6    8.8e-22   78.5   2.6    1.0  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   2.6   4.9e-26   8.8e-22       1     200 []      18     242 ..      18     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 4.9e-26
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtss.lslkpeysy...... 70 
                                       +tV G++ v v++D++++++++++++++++ a++e +e++n+ +eal ++g++e  ++ ++  s+++ ++       
  gi|386001223|ref|YP_005919522.1|  18 LTVVGEGVVLVPADVVYVSITATVQDENLTVASSESSEALNRTIEALIEAGVDEGAFTAGRgRSVSTIQTAsrvcnn 94 
                                       59**********************************************88998877644444333222222223322 PP

                             SIMPL  71 engknkitgye...........asqsltvkfrdldklgevldaavka.ane.in.gvsf.slsdedelrdeareeAv 132
                                       +         +           ++ ++t++f+   + ++++++  +    e  + g+    l d+ ++ +eare+A+
  gi|386001223|ref|YP_005919522.1|  95 S---------TcvvvsdgavnlVREEVTIRFDA--REEALINRSFEVaRSEgAEaGIAGyALVDRRAAIAEAREKAI 160
                                       0.........02223344445599999999933..3444555554432221222244444566889999******** PP

                             SIMPL 133 kdArakAealAkalgvklgkvvsise..sgsnpyappapamaaaaaa............aasaatpfepgeievtas 195
                                       ++A+a A alA+a+g+klg+ ++i e  s+  +++++a ++ ++ +               ++a + epg +ev  +
  gi|386001223|ref|YP_005919522.1| 161 QNAEAEAGALASAAGLKLGERLEIFErsSPLIREPSYAFDPLGMRMTdlfdlswpvavdPFETASSAEPGMMEVISQ 237
                                       *******************999**996322223444444444444449999999998884444444458999***** PP

                             SIMPL 196 Vtvvf 200
                                       V v++
  gi|386001223|ref|YP_005919522.1| 238 VFVTY 242
                                       ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1973.79
//
Query:       gi|386001224|ref|YP_005919523.1|  [L=326]
Description: hypothetical protein Mhar_0518 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.004   17.4   4.9     0.0069   16.7   4.9    1.4  1  Bactofilin  Polymer-forming cytoskeletal
  ------ inclusion threshold ------
       0.45   10.0   3.2       0.66    9.4   3.2    1.1  1  MTABC_N     Mitochondrial ABC-transporter N-terminal five TM 
        1.3    7.5   4.4        1.6    7.3   4.4    1.1  1  FapA        Flagellar Assembly Protein A
          2    6.6  12.0        2.7    6.2  12.0    1.1  1  DUF2070     Predicted membrane protein (DUF2070)
          9    5.9   5.9        3.8    7.2   3.0    1.7  1  DUF2101     Predicted membrane protein (DUF2101)


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.9   1.9e-06    0.0069      12      96 ..      55     141 ..      44     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                        Bactofilin  12 elevegdlridGkveGdi.eakgklvvgeggkvegnika..eevvvaGtvkGnveaee.kvelkktakveGdikaks 84 
                                        + v gd+ id+ ++Gd+  a+g++ +  ++ v g+i a  +++ ++G v+ nv + + +v++ +t+++  d     
  gi|386001224|ref|YP_005919523.1|  55 AVIVGGDVLIDAPIRGDLlVAGGTVDI--NSDVGGKILAagGTINLRGDVERNVVMAGgTVKVLPTSNIGMDAALTG 129
                                       567889************877888877..8899***88756779999****99999988****************** PP

                        Bactofilin  85 leieegavfeGk 96 
                                        e+++g+++ G+
  gi|386001224|ref|YP_005919523.1| 130 TEVQNGGNVAGT 141
                                       *********997 PP

>> MTABC_N  Mitochondrial ABC-transporter N-terminal five TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2   0.00018      0.66      62     189 ..     176     297 ..     165     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                           MTABC_N  62 rlyklqlvlallllllalarlilraallksgevygylilalvlsllawlfsllllllerrkllpslptrgHglvlLl 138
                                       + ++l ++l +l++ l+ +rl+  ++ + +gev  +    ++l l   + + +l++++  +++         l lL 
  gi|386001224|ref|YP_005919523.1| 176 STFSLLMILGFLIVGLVSLRLFPGVFSAVDGEVRRSPAARALLGLGLMVAATILVIVSALSVVGIP-L---ALLLLA 248
                                       567788999999999999999999999999999999999999999999999999999888887555.3...478888 PP

                           MTABC_N 139 fwtlafvaenlafvswnsedwWfklktlkdqvefglfvvryvvtlllfvlG 189
                                       + + a++a nl fvs++  +w      ++d ++++ fv+ y+v+ llf++ 
  gi|386001224|ref|YP_005919523.1| 249 LAAAALLAANL-FVSFSLGRW-IVSALNRDLADLSAFVIGYLVLSLLFLIP 297
                                       88888888888.899877665.56677899******************986 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.4   0.00043       1.6     180     240 ..      52     115 ..      24     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00043
                              FapA 180 VdpvleikgdV..dlst.GnIkfkG.sViikGnVeegmkVkasgditikGvvesatieAggnIti 240
                                       Vd+ + + gdV  d  + G++ + G +V i+ +V  g    a+g i+  G ve+  + Agg +++
  gi|386001224|ref|YP_005919523.1|  52 VDSAVIVGGDVliDAPIrGDLLVAGgTVDINSDV-GGKILAAGGTINLRGDVERNVVMAGGTVKV 115
                                       5666666666522333467777777789999999.777888888999999999999999998877 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  12.0   0.00074       2.7      38     162 ..     180     310 ..     144     320 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00074
                           DUF2070  38 lfgillfglpalvaflltlpvlrilggrltykrs....lflalltelivviisllaillsall..qalvllalvlsl 108
                                       l  il f++  lv++ l+  v + + g +  +rs    ++l l  ++ + i++++++l    +    l ll l+l+ 
  gi|386001224|ref|YP_005919523.1| 180 LLMILGFLIVGLVSLRLFPGVFSAVDGEV--RRSpaarALLGLGLMVAATILVIVSALS---VvgIPLALLLLALAA 251
                                       67788899999999999999999998885..5555244555554444444433333333...223566666666666 PP

                           DUF2070 109 alvfalrllvlvavsdesllkav.....lpaliqpllailllvlyfspesfllllllsl 162
                                       a+ +a +l+v ++++++ ++        l a+++ +l++ ll+l+    s + l+ + l
  gi|386001224|ref|YP_005919523.1| 252 AALLAANLFVSFSLGRWIVSALNrdladLSAFVIGYLVLSLLFLIPYAGSLMELISIGL 310
                                       66677777776666665333333554554444444444444444422344444444444 PP

>> DUF2101  Predicted membrane protein (DUF2101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.0    0.0011       3.8      23     107 ..     209     303 ..     202     308 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                           DUF2101  23 krnltehelvsLkLqlifllyliislvlvf...lksllvlllaa.......lleflllryilirniellidfeayra 89 
                                       +r+++ + l+ L L +++ + +i+s ++v    l  ll  l aa       ++ f l r+i+    + l d  a+  
  gi|386001224|ref|YP_005919523.1| 209 RRSPAARALLGLGLMVAATILVIVSALSVVgipLALLLLALAAAallaanlFVSFSLGRWIVSALNRDLADLSAFVI 285
                                       67778888889999999998888777666531122222222222110001123455557777777777789999999 PP

                           DUF2101  90 fylavsviailaylgyvl 107
                                        yl++s++ ++ y g+++
  gi|386001224|ref|YP_005919523.1| 286 GYLVLSLLFLIPYAGSLM 303
                                       9************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2259.51
//
Query:       gi|386001225|ref|YP_005919524.1|  [L=391]
Description: cell division protein FtsZ [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-42  144.1   0.0    8.8e-42  143.5   0.0    1.3  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    8.7e-33  112.5   0.8    2.2e-32  111.2   0.8    1.7  1  FtsZ_C          FtsZ family, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.4   0.7      0.097   12.6   0.1    2.3  2  NAD_binding_10  NAD(P)H-binding
      0.081   12.3   0.0       0.15   11.4   0.0    1.4  1  ThiF            ThiF family
        2.1    7.4   8.7       0.53    9.4   2.1    2.3  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5   0.0   2.4e-45   8.8e-42       2     196 ..      59     218 ..      58     219 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 2.4e-45
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       i v+g+G++G++++++l e      gi             +g +e++    a++td+q+l +i a+      +++l+
  gi|386001225|ref|YP_005919524.1|  59 IRVVGCGGGGSNTIERLAE-----TGI-------------EG-AELF----AMNTDAQHLLHISAD------RRVLI 106
                                       789****************.....6**.............88.8888....***************......***** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                       g   ++++gag+ p++g+eaa+e+ +eir +ve++d+   +fit +lgGGTG+G++pv++ev++e+  +al+++vv+
  gi|386001225|ref|YP_005919524.1| 107 GRRTTRGLGAGSLPSIGEEAARESIDEIRAAVEGADM---VFITCGLGGGTGTGAAPVVAEVAREM--GALTISVVT 178
                                       *************************************...**************************..********* PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                       lP+   e+ +++ na  +lk+l++ sd+viv++Nd+Ll+++
  gi|386001225|ref|YP_005919524.1| 179 LPFAA-EGAIRMANADVGLKRLRDVSDTVIVVPNDRLLEVV 218
                                       ***99.*******************************9986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.8   6.3e-36   2.2e-32       1      94 [.     266     359 ..     266     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 6.3e-36
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvAm+g+Gea+ge ++++++ +a++spLLdvd+sgA+++lvn+ gg+++t++++e+v+e+++e++++ea++i+Ga+i
  gi|386001225|ref|YP_005919524.1| 266 GVAMIGLGEAQGEMKSKDSVIKALRSPLLDVDISGATSALVNVVGGPNMTISDAETVVEEVYERINPEARIIWGAQI 342
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                       d++le+ ir++ v+tg+
  gi|386001225|ref|YP_005919524.1| 343 DPNLENGIRTMLVVTGV 359
                                       ****************8 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.1   3.6e+02      48      81 ..      42      79 ..       5     100 .. 0.68
   2 ?   12.6   0.1   2.7e-05     0.097      49      96 ..     129     177 ..     124     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.1
                                      TT-CCHHHHHHTT-SEEEES-...--TCC.HHHHHHHH CS
                    NAD_binding_10 48 vtdvedlaealkgadaVvsal...ggggk.deegakni 81
                                       ++ +dla++l++  +V+  +   ggg++  e+ a++ 
  gi|386001225|ref|YP_005919524.1| 42 KENDDDLAAVLEQLTTVIRVVgcgGGGSNtIERLAETG 79
                                      46789999999999988777744222222344444444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.7e-05
                                       T-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEE CS
                    NAD_binding_10  49 tdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlv 96 
                                       ++ +++++a++gad V+++ g gg++ +g a  ++++a+e g   + +v
  gi|386001225|ref|YP_005919524.1| 129 ESIDEIRAAVEGADMVFITCGLGGGTGTGaAPVVAEVAREMGALTISVV 177
                                       6889************999977777556624444455666665555554 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.2e-05      0.15      19      44 ..      57      82 ..      34      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.2e-05
                                      SEEEEE--SHHHHHHHHHHHHHTTTE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgk 44
                                      + + +vG+Gg Gs+ ++ La +G++ 
  gi|386001225|ref|YP_005919524.1| 57 TVIRVVGCGGGGSNTIERLAETGIEG 82
                                      56779******************974 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.6     0.043   1.5e+02       2      19 ..      61      78 ..      61     102 .. 0.86
   2 ?    9.4   2.1   0.00015      0.53     129     182 ..     128     168 ..     105     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.043
                         Tubulin_2  2 viGLGGtGgkvlaelrrr 19
                                      v+G+GG G++++++l++ 
  gi|386001225|ref|YP_005919524.1| 61 VVGCGGGGSNTIERLAET 78
                                      79************9875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00015
                         Tubulin_2 129 fanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrk 182
                                        ++           i+++r    +e+   vf+ ++L GGTG G +  va + r+
  gi|386001225|ref|YP_005919524.1| 128 RES-----------IDEIRAA--VEGADMVFITCGLGGGTGTGAAPVVAEVARE 168
                                       333...........3333331..223358**************98877777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2829.57
//
Query:       gi|386001226|ref|YP_005919525.1|  [L=106]
Description: hypothetical protein Mhar_0520 [Methanosaeta harundinacea 6Ac]
Scores for complete 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   36.1   0.0    5.1e-09   35.9   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.032   14.3   0.0    1.3  1  DUF5338   Family of unknown function (DUF5338)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   5.7e-13   5.1e-09       3      76 ..       2      76 ..       1      82 [. 0.94

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.7e-13
                           DUF1699  3 irvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgielle.gdv 76
                                      +r++ s  ++++l ++++ + +af p n++i +++++c klk++ + +   k +    ++ l +q++el+  gdv
  gi|386001226|ref|YP_005919525.1|  2 MRILNSEFDLARLLPSDEELAIAFVPTNREIYRMLQACHKLKTVYIHPDTFKEFPCVGQTLLYMQKVELVVdGDV 76
                                      69999999************************************************************9754998 PP

>> DUF5338  Family of unknown function (DUF5338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.6e-06     0.032      21      48 ..      21      48 ..      12      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-06
                           DUF5338 21 nrvaFLavrkdikealkaGyalktiweh 48
                                       + aF + +++i ++l+a ++lkt++ h
  gi|386001226|ref|YP_005919525.1| 21 LAIAFVPTNREIYRMLQACHKLKTVYIH 48
                                      5679*********************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 768.67
//
Query:       gi|386001227|ref|YP_005919526.1|  [L=125]
Description: hypothetical protein Mhar_0521 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-06   26.6   0.1    4.9e-06   26.0   0.1    1.3  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0014   18.9   0.1     0.0023   18.2   0.1    1.3  1  Rrf2      Transcriptional regulator
     0.0017   18.3   0.0     0.0036   17.3   0.0    1.6  1  HTH_20    Helix-turn-helix domain
     0.0023   18.3   0.0     0.0038   17.6   0.0    1.3  1  FaeA      FaeA-like protein
     0.0023   17.8   0.2     0.0039   17.0   0.2    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
      0.003   17.4   0.0     0.0046   16.8   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0035   17.4   0.1     0.0049   16.9   0.1    1.3  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22
     0.0039   16.8   0.1      0.006   16.2   0.1    1.3  1  GntR      Bacterial regulatory proteins, gntR family
     0.0098   15.6   0.0        1.3    8.9   0.0    2.3  2  MerR      MerR family regulatory protein
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.028   14.3   0.1    1.9  1  HTH_12    Ribonuclease R winged-helix domain
      0.024   14.5   0.0      0.035   14.0   0.0    1.3  1  MarR_2    MarR family
      0.037   13.8   0.0      0.059   13.2   0.0    1.3  1  HTH_IclR  IclR helix-turn-helix domain
      0.046   13.7   0.1      0.053   13.5   0.1    1.2  1  DUF977    Bacterial protein of unknown function (DUF977)
       0.11   12.0   0.0       0.13   11.7   0.0    1.3  1  RepL      Firmicute plasmid replication protein (RepL)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   3.8e-09   4.9e-06       5      47 ..      42      84 ..      38      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.8e-09
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++ IL+ +++n  i +  LAe++g+++  v++ l+ Le+eGlI
  gi|386001227|ref|YP_005919526.1| 42 HLIILKHVMENEPIGILKLAEETGIPSHKVRYSLRVLEQEGLI 84
                                      666***************************************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.8e-06    0.0023       4      57 ..      33      86 ..      31      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                      -HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  4 sskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++++e+  + l++L++  e+ep+ + ++ae+++i+ + ++  l+ L+++gl+ +
  gi|386001227|ref|YP_005919526.1| 33 KRELEMLKRHLIILKHVMENEPIGILKLAEETGIPSHKVRYSLRVLEQEGLIAA 86
                                      66677777899*****************************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.8e-06    0.0036      15      55 ..      45      85 ..      40      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-06
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      il++ +++e+     lae+ +++   ++y LrvLe+ gL+ 
  gi|386001227|ref|YP_005919526.1| 45 ILKHVMENEPIGILKLAEETGIPSHKVRYSLRVLEQEGLIA 85
                                      78888999999999*************************97 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.9e-06    0.0038       5      48 ..      45      87 ..      41      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                      Il+++ + + p     +A+ +g+    +Ry L  Le+eg i  s
  gi|386001227|ref|YP_005919526.1| 45 ILKHVME-NEPIGILKLAEETGIPSHKVRYSLRVLEQEGLIAAS 87
                                      899****.*******************************99765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2     3e-06    0.0039       5      45 ..      43      84 ..      40      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      l ILk ++e ++  +  laee+g++  +v++ L++L+++GL+
  gi|386001227|ref|YP_005919526.1| 43 LIILKHVMEnEPIGILKLAEETGIPSHKVRYSLRVLEQEGLI 84
                                      56888888856688889************************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.6e-06    0.0046      16      54 ..      48      86 ..      34      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                       +++++p  + ++aee+g+p  kv  +Lr Le+ Gl+  
  gi|386001227|ref|YP_005919526.1| 48 HVMENEPIGILKLAEETGIPSHKVRYSLRVLEQEGLIAA 86
                                      5789999999**************************976 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 !   16.9   0.1   3.8e-06    0.0049       2      56 ..      34      88 ..      33     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-06
                           DUF2250  2 eeleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      +ele  +++l +lkh+ + ++   + +a+e+ ip ++vr  l+ Le+ GL+    
  gi|386001227|ref|YP_005919526.1| 34 RELEMLKRHLIILKHVMENEPIGILKLAEETGIPSHKVRYSLRVLEQEGLIAASA 88
                                      6889999********************************************8766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.7e-06     0.006      10      55 ..      41      85 ..      29      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.7e-06
                                      HHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 10 redIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      r++I+ ++++ ++++    +La+e g+  + vR +Lr Le+egl+ 
  gi|386001227|ref|YP_005919526.1| 41 RHLIILKHVMENEPI-GILKLAEETGIPSHKVRYSLRVLEQEGLIA 85
                                      6789999********.****************************96 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.001       1.3       4      18 ..      59      73 ..      55      73 .. 0.90
   2 ?    4.4   0.0     0.026        33      16      26 ..      75      85 ..      74      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                                      HHHHHHTTTHHHHHH CS
                              MerR  4 evAeltGvsprtLRy 18
                                       +Ae tG++++++Ry
  gi|386001227|ref|YP_005919526.1| 59 KLAEETGIPSHKVRY 73
                                      58************9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                                      HHHHHHTTSST CS
                              MerR 16 LRyYEreGLip 26
                                      LR +E+eGLi 
  gi|386001227|ref|YP_005919526.1| 75 LRVLEQEGLIA 85
                                      899*******4 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.2e-05     0.028       3      61 ..      45      96 ..      43     101 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                            HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEk 61
                                      ILk++ e+ +pig  ++aee       i    vRy Lr+le++gl+      g+  tE+
  gi|386001227|ref|YP_005919526.1| 45 ILKHVMEN-EPIGILKLAEE-----TGIPSHKVRYSLRVLEQEGLIAASAP-GAVTTER 96
                                      56666554.46776666665.....34666889************975543.4677776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.7e-05     0.035      26      54 ..      59      87 ..      41     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                                      HHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 26 elarrlglsksavsrilkrLvaaGLverr 54
                                       la+++g++ + v + l+ L++ GL+  +
  gi|386001227|ref|YP_005919526.1| 59 KLAEETGIPSHKVRYSLRVLEQEGLIAAS 87
                                      59************************765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.059       4      48 ..      41      84 ..      38      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                      HHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  4 RalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      R l iL+++ e  +  ++  lA++tg+p  +v+  L+ L+++G++
  gi|386001227|ref|YP_005919526.1| 41 RHLIILKHVMENEP-IGILKLAEETGIPSHKVRYSLRVLEQEGLI 84
                                      55668888888777.8999************************98 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.1e-05     0.053       5      75 ..      31     102 ..      27     125 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                            DUF977   5 ktqeereelkeriiGl..vkkneritisdleritGvgrtsvrkylvdvlerGdlirpGkyGvfrdervvrvwr 75 
                                       k + e e+lk  +i l  v +ne i i +l   tG+  + vr  l+ vle+ +li     G  + er     r
  gi|386001227|ref|YP_005919526.1|  31 KVKRELEMLKRHLIILkhVMENEPIGILKLAEETGIPSHKVRYSLR-VLEQEGLIAASAPGAVTTERTEAFLR 102
                                       56667777887766654499*********************98876.89*********999999999877444 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.13      80     113 ..      59      92 ..      27     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                              RepL  80 elaeetgislktvsetlkileeanilkkkanGvl 113
                                       +laeetgi  + v+  l++le+ +++   a G++
  gi|386001227|ref|YP_005919526.1|  59 KLAEETGIPSHKVRYSLRVLEQEGLIAASAPGAV 92 
                                       79************************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1008.29
//
Query:       gi|386001228|ref|YP_005919527.1|  [L=432]
Description: DNA ligase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-23   83.2   0.0      1e-22   81.3   0.0    1.8  2  DNA_ligase_A_N  DNA ligase N terminus
    2.6e-17   63.1   0.0    4.3e-17   62.4   0.0    1.3  1  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   1.1e-26     1e-22       1     172 [.       3     172 ..       3     173 .. 0.91
   2 !    6.4   0.0    0.0012        11      55      98 ..     158     202 ..     157     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.1e-26
                                       BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT CS
                    DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealg 73 
                                       p+ e+a+++e++++ + +r +k + la++++ +   + e+l p++rL     +P ++ re+gig+ +l  +l e++g
  gi|386001228|ref|YP_005919527.1|   3 PYLEIARALEAVSR-EERRGAKAERLAALIKPL---PAEMLRPTVRLisgrPWPPWEPRELGIGPETLDAVLEEISG 75 
                                       68899999*****9.77899**********776...5789************************************* PP

                                       --HHHHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHH CS
                    DNA_ligase_A_N  74 lskkkikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEa 148
                                       + +  ++++     D g+ ae++++ rs++  ++s++   +v+e+L++++a  g gs  ++++ilk+ll +asp+Ea
  gi|386001228|ref|YP_005919527.1|  76 RVPS-SEERA---ADPGDRAERMVRGRSQRtLAPSTMDSLHVYESLRQISAQrGPGSLSRRRAILKGLLLAASPLEA 148
                                       8777.66655...79999999999888888889999*************86689*********************** PP

                                       HHHHHHHCT---SS--HHHHHHHH CS
                    DNA_ligase_A_N 149 kyliriilkdlriglsektvldal 172
                                       kyl+r +l++   gl+  ++  a+
  gi|386001228|ref|YP_005919527.1| 149 KYLARAVLGRTTAGLGPSLISAAI 172
                                       *****************9998886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0012
                                       -.-----HHHHHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHC CS
                    DNA_ligase_A_N  55 r.eygigesllakalaealglskkkikdalakvgDlgevaeevls 98 
                                       r + g+g+sl++ a+++a+ ++   +k a+  + Dlg va ++++
  gi|386001228|ref|YP_005919527.1| 158 RtTAGLGPSLISAAIGKAFDVDYSLVKRAYSYLPDLGMVALNARQ 202
                                       44889*****************99999999999******877665 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   4.8e-21   4.3e-17      24     197 ..     239     408 ..     219     411 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 4.8e-21
                                       EEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHHHCHHH CS
                    DNA_ligase_A_M  24 vEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpfqklasrk 100
                                       + + y G R+qvhk +d+v++++ +l+++t+ + +l ++++ a      +++++GEl++v    g+i p+ ++  r+
  gi|386001228|ref|YP_005919527.1| 239 YVVRYGGLRVQVHKFNDRVYIYTSQLRNVTRPLRDLAEEVAMA--GG--EFVMEGELILV--RGGRISPRSETVGRI 309
                                       557899******************************9999444..33..7*********7..678999998888887 PP

                                       HCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB.....--BTTTEEE--EEEESSHHHHHHHHH CS
                    DNA_ligase_A_M 101 kkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeil.....kesedrvelaeslevkdveeleelle 172
                                       + + + +     a ++l + D+Lyl+g +l+++ ++eRr lL ++l     ++ + r+ lae+ ++ d + +ee+l+
  gi|386001228|ref|YP_005919527.1| 310 NLRGRSR---GGAMPSLAASDLLYLNGGDLLQRGYEERRGLLAKALkgvegRPLSSRIFLAEEEVIGDGQRAEEFLR 383
                                       3333222...346799******************************999999999********************** PP

                                       HHHHTTECEEEEEETT-CC-TTCEE CS
                    DNA_ligase_A_M 173 eaiseglEGlvvKnpdskYepgkrs 197
                                       ++++ g  G  +++ d+ Y pg+ s
  gi|386001228|ref|YP_005919527.1| 384 RSLDRGFGGAWIRDLDGLYIPGEMS 408
                                       *********************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 3147.39
//
Query:       gi|386001229|ref|YP_005919528.1|  [L=463]
Description: hypothetical protein Mhar_0523 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-31  108.3   0.0    5.5e-31  107.4   0.0    1.4  1  Fasciclin       Fasciclin domain
  ------ inclusion threshold ------
        3.2    8.4  24.0      6e+02    1.0   0.0    4.8  2  DNA_pol_B_N     DNA polymerase beta N-terminal domain


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0   6.2e-35   5.5e-31       2     128 .]     314     430 ..     313     430 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 6.2e-35
                                       GGHHHHHHHHTTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHHEE CS
                         Fasciclin   2 dlstfvsllekaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkaset 78 
                                       +l+++v+++e+agla+ L  ++g++TvFaPt+eAf  l++  l+    d ++l+eiL+yHv+++++++++++++ ++
  gi|386001229|ref|YP_005919528.1| 314 NLNDLVTAVEAAGLADFL-AGEGPFTVFAPTDEAFGLLGEIDLN----DTDALTEILTYHVADGALMAADVVNM-TS 384
                                       68999*************.777*************988544444....78************************.** PP

                                       EECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  79 latllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       ++t leg++l+++++  ++  +vng ar+v++d+ ++ngv+h+id vL+p
  gi|386001229|ref|YP_005919528.1| 385 IET-LEGSSLTIEVT--DEGAFVNG-ARIVQTDVVCSNGVVHIIDAVLMP 430
                                       ***.***********..999*****.**********************98 PP

>> DNA_pol_B_N  DNA polymerase beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.067     6e+02      65      87 ..     133     154 ..     110     160 .. 0.79
   2 ?   -9.4  24.0         2   1.8e+04      48      85 ..     217     256 ..     152     299 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.067
                       DNA_pol_B_N  65 rsisIpLtvdasaatgavPvVdr 87 
                                       +  sI + v+a a+tg++P+V  
  gi|386001229|ref|YP_005919528.1| 133 QAYSIGMGVPA-ASTGSCPIVAP 154
                                       55678899999.*********75 PP

  == domain 2  score: -9.4 bits;  conditional E-value: 2
                       DNA_pol_B_N  48 dtdtgedgeglsvpl....avrsisIpLtvdasaatgavPvV 85 
                                        +dt +++++ +  +    + +++++p+ +d +a++ +vPvV
  gi|386001229|ref|YP_005919528.1| 217 VADTEAEDVEVP--VvadtEAEDVEVPIVADTEAEDVEVPVV 256
                                       111111111111..1111122344444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2744.21
//
Query:       gi|386001230|ref|YP_005919529.1|  [L=97]
Description: hypothetical protein Mhar_0524 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.8e-07   29.8   0.1    8.9e-07   29.4   0.1    1.2  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.16   12.0   0.0    1.2  1  Toxin_YhaV  Toxin with endonuclease activity, of toxin-antito


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 !   29.4   0.1   9.9e-11   8.9e-07      26      83 ..      20      84 ..       5      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.9e-11
                                      HHHHHHHHHHHHHHHHHTTTSEECTSTC......CTTEEEEEEC.TEEEEEEEETSTTEEEEEEE CS
                        ParE_toxin 26 krfldaleealellaenpalgrprrelg......lkglrririg.dyriiYriddeelvvvilrv 83
                                      ++    + +++ +l ++p +g +r + +       k+l+r+++g  y ++Yri ++e+vv il++
  gi|386001230|ref|YP_005919529.1| 20 EKSRRLVADRCLALSDDPFPGGERGDRKalhlagHKKLYRLHVGrSYTVFYRIYEDEKVVSILAI 84
                                      4556788999*************44444577***88*****************77888888**98 PP

>> Toxin_YhaV  Toxin with endonuclease activity, of toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05      0.16      67      97 ..      53      83 ..      32      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                        Toxin_YhaV 67 kykhwkrakllqryRLFFRydseskiivlaW 97
                                       +k++ r+ +++ y  F+R+ +++k++ ++ 
  gi|386001230|ref|YP_005919529.1| 53 GHKKLYRLHVGRSYTVFYRIYEDEKVVSILA 83
                                      6899*********************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 627.67
//
Query:       gi|386001231|ref|YP_005919530.1|  [L=63]
Description: hypothetical protein Mhar_0525 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00037   21.2   0.0    0.00042   21.0   0.0    1.1  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.3e-08   0.00042       1      39 [.       7      45 ..       7      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-08
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkk 39
                                      K I ++ ev e L++lKr+ge F  ++ +++e +kk++ 
  gi|386001231|ref|YP_005919530.1|  7 KRIPVTREVWEDLSDLKRPGETFAGLLAEMIEHEKKRRL 45
                                      78999***************************8888753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 413.67
//
Query:       gi|386001232|ref|YP_005919531.1|  [L=74]
Description: hypothetical protein Mhar_0526 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-20   71.8   0.5    3.1e-20   71.6   0.5    1.0  1  UPF0175   Uncharacterised protein family (UPF0175)


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.5   1.7e-24   3.1e-20       1      70 [.       1      70 [.       1      72 [. 0.97

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.7e-24
                           UPF0175  1 ipdellqalklteeelerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeele 70
                                      +p+++l + k +e+ + relri++ vklYe grlS+g+Aaelag++r efl  L r+++ +++ +  +le
  gi|386001232|ref|YP_005919531.1|  1 MPEKVLLSEKTDEKAFGRELRILASVKLYELGRLSSGRAAELAGMPRFEFLLTLERYKAFPLEAELRDLE 70
                                      69**********************************************************9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 450.17
//
Query:       gi|386001233|ref|YP_005919532.1|  [L=367]
Description: hypothetical protein Mhar_0527 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 2055.23
//
Query:       gi|386001234|ref|YP_005919533.1|  [L=405]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-58  196.5   0.0    6.8e-58  195.3   0.0    1.6  2  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
      1e-35  123.3   0.0    1.2e-35  123.1   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.081   12.5   0.0       0.26   10.8   0.0    1.8  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.64   3.8e+03      32      45 ..      15      28 ..      13      29 .. 0.84
   2 !  195.3   0.0   1.1e-61   6.8e-58       1     170 []      37     200 ..      37     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.64
                                      HHCH---HHHHHHH CS
                      PhosphMutase 32 pkkyytGRGplEAl 45
                                      p +  +G+ plEA+
  gi|386001234|ref|YP_005919533.1| 15 PIEALEGKTPLEAA 28
                                      567789*******7 PP

  == domain 2  score: 195.3 bits;  conditional E-value: 1.1e-61
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTG CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrra 77 
                                       A++G+ Gl+++vp+ ++pgSdvAnls++Gydp++yytGR+plEA+++G++l+p+dvafRcnlv+vd ++g+++d++a
  gi|386001234|ref|YP_005919533.1|  37 AREGRGGLARNVPPRMPPGSDVANLSVMGYDPRRYYTGRAPLEAAAMGVSLGPEDVAFRCNLVNVDLDRGVMVDYSA 113
                                       89****************************************************************99********* PP

                                       GG-.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE..--S-B--S--..SSTTS------BS.SGGGHHHHHH CS
                      PhosphMutase  78 gristeeakeLikalneeleegvevkfypgveyrhllvl..lsdkitdtdpphdkegkeikellplkseeaketael 152
                                       g+is+ee++eLi+al++      ++++ypgv+yr+llv    +     ++pphd++g++i+ +lp k    +e a++
  gi|386001234|ref|YP_005919533.1| 114 GHISSEEGRELIAALQKSDP---KARLYPGVSYRNLLVRggDEGLQAVCTPPHDISGQPIDGYLP-K----GEGAAA 182
                                       *****************886...8***************886666789*****************.7....9***** PP

                                       HHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 153 lnelieksqeiLedhpvN 170
                                       l+e++++s  iL++hpvN
  gi|386001234|ref|YP_005919533.1| 183 LREMMLASVPILAEHPVN 200
                                       *****************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0     2e-39   1.2e-35       1     247 [.       1     395 [.       1     396 [. 0.96

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 2e-39
                                       -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel....... 67 
                                       +k+v+++ DG+++ p + l++   ++ A+tP++d+++ e       +  g+a  +p  + ++s+v++l++       
  gi|386001234|ref|YP_005919533.1|   1 MKLVILLGDGMADHPIEALEGktpLEAAETPNMDRIARE-------GRGGLARNVPPRMPPGSDVANLSVmgydprr 70 
                                       57899999*******************************.......789**************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|386001234|ref|YP_005919533.1|  71 yytgrapleaaamgvslgpedvafrcnlvnvdldrgvmvdysaghisseegreliaalqksdpkarlypgvsyrnll 147
                                       ***************************************************************************** PP

                                       ......................................................HHHHTT-----EEEEEEEE-S-- CS
                                       ......................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ......................................................lrisetvkfahvtffwnggrsgy 90 
                                                                                              r  e+++ a+++++w++g+ ++
  gi|386001234|ref|YP_005919533.1| 148 vrggdeglqavctpphdisgqpidgylpkgegaaalremmlasvpilaehpvnlRRAREGKRTANMIWLWGQGKAPS 224
                                       *****************************************************9999******************** PP

                                       -SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  91 fnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGH 147
                                       ++++ e ++++++++ ++dl                      +++++ ++ + l+a+  ++ d+v+++++ +D+++H
  gi|386001234|ref|YP_005919533.1| 225 MPKFRELWGVEGAVISAVDLlkgmgvyaglevinvpgatgVLDTNYEGKVAACLEAL--DRVDFVYLHVEAPDEMSH 299
                                       ***************************************999***************..679*************** PP

                                       TT-HHHHHHHHHHHHH.HHHHHHTTS-TTTE..EEEEE-SSB--TTTSS........-----EEEEEESTT----S- CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 148 tgdleatiaaieaaDe.avkeildaieqvdg..ilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkv 221
                                       +g+le++i+ai+++De  v+ +l  +e +++   ++v++DH+++  + +        Ht+epVP++++g g++ d +
  gi|386001234|ref|YP_005919533.1| 300 DGKLEEKIEAIQRFDErVVGLVLAGLERSGHqwRVAVLPDHPTPIALRT--------HTAEPVPFAMIGSGIEADGM 368
                                       ****************667889999999887335899************........****************9888 PP

                                       -S.SHHHHTT-TTEEEEGGGHHHHHHH CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 222 ke.gakfrekggLanvaatllnllgle 247
                                       +  ++++ ++gg +++++  l+ +++e
  gi|386001234|ref|YP_005919533.1| 369 EAfSEREGARGGCGTIDGWRLMGMMVE 395
                                       887777777999999999988888776 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.24   1.4e+03      16      40 ..      27      48 ..       3      54 .. 0.68
   2 ?   10.8   0.0   4.4e-05      0.26     163     218 ..     273     328 ..     182     340 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.24
                                      HHGSTSHHHHHHHHHSEEESEEE-S CS
                      Phosphodiest 16 rlaellpnlaaLakegvsapnlrpv 40
                                      +   ++pn++++a+eg  +   r+v
  gi|386001234|ref|YP_005919533.1| 27 A--AETPNMDRIAREGRGGL-ARNV 48
                                      2..499********998776.5555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.4e-05
                                       SHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHH.HHHHHHHHHHT CS
                      Phosphodiest 163 kvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDka.igdLlealder 218
                                       kv++++e  ++ d++++++e++D ++H    + +e  +a++r D+  +g  l++l++ 
  gi|386001234|ref|YP_005919533.1| 273 KVAACLEAlDRVDFVYLHVEAPDEMSHDG--KLEEKIEAIQRFDERvVGLVLAGLERS 328
                                       333444447******************65..666778889999865156667777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2507.12
//
Query:       gi|386001235|ref|YP_005919534.1|  [L=251]
Description: Riboflavin biosynthesis protein RibD C-domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-24   84.9   0.0    8.9e-24   84.4   0.0    1.2  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   4.9e-28   8.9e-24       2     198 ..      15     236 ..      14     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 4.9e-28
                                       EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH..HTT.G.. CS
                            RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae..adaea.. 74 
                                        v++   +SlDG++++  ++ + +     + ++  +  +adail G++t+     +   +++k++++   +++    
  gi|386001235|ref|YP_005919534.1|  15 RVTIYNLASLDGRVDRVADSPEAM---LLYYELS-YHWKADAILAGSETIFVLGGHEEEEMAKEEPPPprKEP-Ppg 86 
                                       68888899******9999888832...2333333.33458899999966555444444444444444321222.145 PP

                                       .......SS-EEEEEETTS-S-TTSHHHHSS...S-EEEEESSCSCHHHHHHCC.......E....SE-HHHHHHHH CS
                            RibD_C  75 .......rqpvrvVvdstlrvpldakvltdd...aptlvatteeadkekveklk.......v....rvdlkelleeL 130
                                                p+ vV+ds+ r+  + ++l+++   ++++v+ +++++  +++ l        +    +vdl ++leeL
  gi|386001235|ref|YP_005919534.1|  87 tegliyePRPLLVVPDSRGRIH-NWRLLQQEpwwRKIVVLCSKATPPSYLDYLGkrhleyfIvgedHVDLRQALEEL 162
                                       67788999************54.455666664544677888888888888888788776662699************ PP

                                       HHT.T--EEEEEETHHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS....EEEEEEEEEEETTEE CS
                            RibD_C 131 ker.girsllveGGatLagsllraglvDelrlyiaPkllGg.agktlfdgegfka....lklklvksealgegv 198
                                       k+r g rs+ + +G+ L+g llraglvDe+ ++i P+l+Gg  g++lf+++++++    ++l+l+++e++  g+
  gi|386001235|ref|YP_005919534.1| 163 KARyGARSVRTDCGGRLNGVLLRAGLVDEVSVLISPTLVGGrRGTSLFEEGEIESggefVHLRLTHMERVRGGF 236
                                       *******************************************************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1887.60
//
Query:       gi|386001236|ref|YP_005919535.1|  [L=243]
Description: Methyl-coenzyme M reductase operon protein C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-07   29.5   3.9    4.2e-06   26.1   3.9    2.4  1  MCR_C     Methyl-coenzyme M reductase operon protein C
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.22   12.0   0.0    1.5  1  MobC      Bacterial mobilisation protein (MobC)
       0.32   11.1   2.5       0.67   10.1   2.5    1.4  1  DUF5595   Domain of unknown function (DUF5595)


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   3.9     7e-10   4.2e-06      73     172 ..      38     148 ..      32     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7e-10
                             MCR_C  73 avvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvg.........kr...iaqikeeekrlinehDlavfvlG 137
                                         ++++  r+h+  ++C+++  lrr+G +t ++ l  G+g         k    +  ++ +e + i+ h +av  lG
  gi|386001236|ref|YP_005919535.1|  38 IAIAMSPGRRHITKPVCEITYGLRREGVQTSVLVLEAGAGvpdsfpsasKGfgpTFGLSPKEIEQIERHKIAVIHLG 114
                                       45788999*************************9999988333222221211112357889**************** PP

                             MCR_C 138 nfkdCikkkkeklfedievPvvvtggPeelkleev 172
                                       n ++ +  k ++++   evP v+++    ++ e+ 
  gi|386001236|ref|YP_005919535.1| 115 NIRSHVVYKAKEVLALAEVPAVIVCQS-PVDFEDF 148
                                       ********************8887764.4666665 PP

>> MobC  Bacterial mobilisation protein (MobC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.6e-05      0.22      11      25 ..     189     202 ..     189     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                              MobC  11 lNQIAraaNsgqgsq 25 
                                       lNQ+A+++N ++++ 
  gi|386001236|ref|YP_005919535.1| 189 LNQLAKVLN-HHLAR 202
                                       8********.55444 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.5   0.00011      0.67      40      72 ..     187     219 ..     184     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                           DUF5595  40 skLkelynvdeaqlesleeeekrLeeEierlek 72 
                                       +kL++l +v + +l+++e+ee++  eE e  e+
  gi|386001236|ref|YP_005919535.1| 187 AKLNQLAKVLNHHLARMEREERKRREEEEMPEA 219
                                       79********************99999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1485  (0.0828267); expected 358.6 (0.02)
Passed bias filter:                      830  (0.0462937); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1382.79
//
Query:       gi|386001237|ref|YP_005919536.1|  [L=266]
Description: Diphthine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-16   61.4   0.1    1.3e-16   61.2   0.1    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1   7.5e-21   1.3e-16       1     168 [.       1     170 [.       1     223 [. 0.80

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 7.5e-21
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l++VG+G+ d  +++v++l++++++d+v+++   ++++l  + +e+  l +  g+e+++l+++  e++   +   +
  gi|386001237|ref|YP_005919536.1|   1 MLTFVGLGLYDERDVSVKGLQTIRDSDLVYAEF--YTSRLMGATPEK--LAQLYGREVKVLTREEVEVSPEGWLGRA 73 
                                       799**************************7666..555555555553..5555667799999999999999977777 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl........lpgl 146
                                       + ++V++lv+GDP++++t+  l   lra + gie++++   s+++a+   +g+  + +g ++s+         +   
  gi|386001237|ref|YP_005919536.1|  74 KEEKVAFLVGGDPMISTTHLDLR--LRALRMGIETRIVHSSSIVTAVSGMTGLQNYRFGRSTSIPypyvaggrRIVA 148
                                       7788******************6..99999*********************************99777777763333 PP

                      TP_methylase 147 akeeereleallangdtlvllk 168
                                         +++  +++l+ + +tl++l+
  gi|386001237|ref|YP_005919536.1| 149 MSPRDVVVDNLARDLHTLLFLD 170
                                       3345666777777777777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1792.88
//
Query:       gi|386001238|ref|YP_005919537.1|  [L=59]
Description: Putative CopG/Arc/MetJ family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 463.55
//
Query:       gi|386001239|ref|YP_005919538.1|  [L=114]
Description: Queuosine biosynthesis protein QueD [Methanosaeta harundinacea 6Ac]
Scores for complete 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-34  117.9   0.0    2.9e-34  117.7   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.0   1.6e-38   2.9e-34       6     118 ..       5     111 ..       3     114 .] 0.95

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 1.6e-38
                                       EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.-- CS
                              PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkflnaddpeleellspT 82 
                                        eFdaaHrl++++gkc+++HGH+y+vev veg+++++tg+++df +lkeal+++leelDh+ ln   + l+   +pT
  gi|386001239|ref|YP_005919538.1|   5 LEFDAAHRLPGYDGKCARVHGHTYEVEVVVEGQVDEKTGFLMDFYDLKEALRSVLEELDHRDLN---EILD---NPT 75 
                                       69**************************************************************...4555...4** PP

                                       HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEE CS
                              PTPS  83 aEnlaklifeelkerlqekevklskvrvwEtpnswa 118
                                       aE++a+ i + l+e+l ++++ l +v++wE +++w+
  gi|386001239|ref|YP_005919538.1|  76 AECIAEQIRAGLEEQLLGSNAALVSVKLWEGKGKWV 111
                                       ********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 689.52
//
Query:       gi|386001240|ref|YP_005919539.1|  [L=225]
Description: 7-cyano-7-deazaguanine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-53  179.8   0.0    5.5e-53  179.6   0.0    1.0  1  QueC           Queuosine biosynthesis protein QueC
      6e-08   32.5   0.0    5.2e-07   29.4   0.0    2.1  2  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.028   14.1   0.0    1.2  1  Asn_synthase   Asparagine synthase
      0.033   13.0   0.0      0.058   12.2   0.0    1.4  2  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.6   0.0   1.2e-56   5.5e-53       1     209 [.       4     216 ..       4     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 1.2e-56
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdee 76 
                                       kav+l SGGlDSt++++ a+++g e+ + ++ Ygq+ +++e +a +++a +lg +e +  ++dl+++++   Lt++ 
  gi|386001240|ref|YP_005919539.1|   4 KAVCLCSGGLDSTVAATKALNDGFEISIFHVLYGQKaEEREKRAIAEVAGALGAVEVRFAKTDLFRKMTP--LTTAG 78 
                                       79**********************************99****************************9986..55555 PP

                                       -------.......--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH.. CS
                              QueC  77 ievpkeelee....eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg.. 147
                                       + +p  +  +    + +p+t+V  RNl+f s+aa+yae++gae++++G+n+e+   YPD+r+efv+ +n +l+ +  
  gi|386001240|ref|YP_005919539.1|  79 APIPMGREVDirgpRATPSTWVYCRNLVFGSMAAAYAESVGAERVYVGFNAEEGRSYPDNRPEFVDRFNLLLEKAva 155
                                       56665222223456999**********************************************************76 PP

                                       .HTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 148 .edkkieieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                         + + ++eaPl++l+K eivklg +lg+p+ +t+sCY ++  + +CgeC+aC+ R  gf ea
  gi|386001240|ref|YP_005919539.1| 156 sFSIPPRVEAPLVHLQKPEIVKLGSDLGAPMALTWSCYLDG--ALHCGECEACQHRMFGFLEA 216
                                       64557799********************************4..46**************9886 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.2e-10   5.2e-07       5      75 ..       4      70 ..       1     126 [. 0.84
   2 ?    1.1   0.0     0.058   2.6e+02     140     160 ..     163     183 ..     148     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-10
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkev 75
                                      k+++L SgG+DS Vaa  +l+ G+++ + h+    + +++++   + +ae+    ++ +ev++   d+ + 
  gi|386001240|ref|YP_005919539.1|  4 KAVCLCSGGLDSTVAATKALNDGFEISIFHVL---YGQKAEEREKRAIAEVAGALGA-VEVRFAKTDLFRK 70
                                      89**************************9994...5555555555789999988886.9999998886555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.058
                              ThiI 140 ilrPLigldKeeiiklAkeig 160
                                       +  PL+ l+K ei+kl  ++g
  gi|386001240|ref|YP_005919539.1| 163 VEAPLVHLQKPEIVKLGSDLG 183
                                       557************998887 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.3e-06     0.028      22      89 ..       7      72 ..       3      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-06
                      Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgtehtelvlteeelldalp 89
                                      +l SGGlDS++ a  a      ++  F++ + + ++  e ++ +eva +lg    e+++ + +l++ + 
  gi|386001240|ref|YP_005919539.1|  7 CLCSGGLDSTVAATKALNDGF-EISIFHVLYGQkAEEREKRAIAEVAGALGAV--EVRFAKTDLFRKMT 72
                                      677*****9877776666665.9********5449999*************98..78888888887665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.3e-05     0.058       3      53 ..       5      50 ..       3      72 .. 0.72
   2 ?   -3.8   0.0      0.92   4.1e+03      91     124 ..      95     127 ..      94     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.3e-05
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkd 53
                                       v++ SgG DS+vaa+   + g+e+  +++   ++++e +     ++ +++
  gi|386001240|ref|YP_005919539.1|  5 AVCLCSGGLDSTVAATKALNDGFEISIFHVLYGQKAEERE-----KRAIAE 50
                                      68999*******************9888877666655444.....333444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.92
                     tRNA_Me_trans  91 TPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                       TP+  v C + + fg ++ +  e+ ga+ +  G 
  gi|386001240|ref|YP_005919539.1|  95 TPSTWVYCRNLV-FGSMAAAYAESVGAERVYVGF 127
                                       777777885554.777777777778888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1338.05
//
Query:       gi|386001241|ref|YP_005919540.1|  [L=239]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.4e-17   61.9   0.0    1.9e-16   60.9   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    3.4e-09   37.1   0.0    4.9e-09   36.6   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
      6e-09   36.1   0.0    1.4e-08   34.8   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.04   14.3   0.3       0.51   10.7   0.1    2.4  2  HTH_31       Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   4.3e-20   1.9e-16       2     160 ..      22     182 ..      21     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 4.3e-20
                                       EEESEESS--TTTSCCTT............HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHH CS
                                       xxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet............vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvel 66 
                                       v t gCnl+C +C+  +             + r++ +  +s+   +eev++l + +g++ v ++ggepl +p+fve+
  gi|386001241|ref|YP_005919540.1|  22 VRTAGCNLACAYCDSAKFrrevtfcdviapGLRRRAENPVSLAWTMEEVRAL-WGRGTHSVSITGGEPLCQPEFVEA 97 
                                       6899************99***********9999999999*************.************************ PP

                                       HHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  67 lerlaklavpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                       l+r++    +g+ + +etng+ +     +r+ ++   +d  +++++ ++ +    + +  + +e  l+++e++ ++g
  gi|386001241|ref|YP_005919540.1|  98 LARACSA--EGMPVYLETNGFSH-----RRFSKMIpwIDIAAVDIKLPSAF---SRGGSEELVENELASIEAASRRG 164
                                       *******..8************8.....55555555568888888888876...33337777888888888888888 PP

                                       SETEEEEEEEBTTTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikrvvdrivglpGendeel 160
                                       +  ++  +v+l    ++e+
  gi|386001241|ref|YP_005919540.1| 165 VF-TIAKVVVLASTPRAEI 182
                                       88.7777777666666665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.1e-12   4.9e-09       2     116 ..       9     134 ..       8     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.1e-12
                           Fer4_12   2 nGeG...vr..lslfvsgCnlsCkgCfnketw.............sfksgkeftkelleeiiedlkkesiegltllG 60 
                                       +GeG   +r  ++++++gCnl+C++C   + +             + +++++++ +   e ++ l  +    ++++G
  gi|386001241|ref|YP_005919540.1|   9 QGEGpllGRrqVFVRTAGCNLACAYCDSAKFRrevtfcdviapglRRRAENPVSLAWTMEEVRALWGRGTHSVSITG 85 
                                       6777666442368889**********98888866666666666666669999998888888888989********** PP

                           Fer4_12  61 GEPllpenaeallelvkevkeekpekdiwlytgytleelskkekeellkeidv.lvd 116
                                       GEPl   + e +  l++ + +e++ ++ ++++g++   +s     +++  id+ +vd
  gi|386001241|ref|YP_005919540.1|  86 GEPLC--QPEFVEALARACSAEGM-PVYLETNGFSHRRFS-----KMIPWIDIaAVD 134
                                       *****..999*************9.8**********9998.....455555544455 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   3.2e-12   1.4e-08       1      96 [.      20     122 ..      20     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3.2e-12
                           Fer4_14   1 lfvrlsgCnlsCkgCdnketwks..............elgkpqteelleqilkdlkkseikiqglvltGGePLhyen 63 
                                       +fvr++gCnl+C  Cd  + ++               ++++p +     ++++ l  +    + +++tGGePL   +
  gi|386001241|ref|YP_005919540.1|  20 VFVRTAGCNLACAYCDSAK-FRRevtfcdviapglrrRAENPVSLAWTMEEVRALWGRGT--HSVSITGGEPL--CQ 91 
                                       6***************555.3333555779999998888999998888888877777766..88*********..34 PP

                           Fer4_14  64 kkellklvkrlkeeypekkiwletngtleiele 96 
                                        + +  l +    e+  +++ letng  +  + 
  gi|386001241|ref|YP_005919540.1|  92 PEFVEALARACSAEG--MPVYLETNGFSHRRFS 122
                                       444455556666666..*********9887776 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00011      0.51      15      57 ..      65     105 ..      51     109 .. 0.66
   2 ?    0.7   0.0      0.16   7.1e+02      37      53 ..     203     218 ..     199     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                            HTH_31  15 LsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                       ++ eev ++  + + t s   +G +++++p+++ealara+ ++
  gi|386001241|ref|YP_005919540.1|  65 WTMEEVRAL--WGRGTHSVSITGGEPLCQPEFVEALARACSAE 105
                                       555555222..444444444688888**************876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                            HTH_31  37 Grrgrpspavlealara 53 
                                       G   rpsp+ l+ l +a
  gi|386001241|ref|YP_005919540.1| 203 GDG-RPSPEKLTELFEA 218
                                       555.9*******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:01.56
# Mc/sec: 464.43
//
Query:       gi|386001242|ref|YP_005919541.1|  [L=124]
Description: hypothetical protein Mhar_0536 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.91
# Mc/sec: 410.04
//
Query:       gi|386001243|ref|YP_005919542.1|  [L=153]
Description: hypothetical protein Mhar_0538 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-50  170.2   0.0    2.4e-50  170.1   0.0    1.0  1  DUF2124   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.0   1.4e-54   2.4e-50       1     140 [.       8     146 ..       8     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 1.4e-54
                                       EHHHHHHHHHHHHTTT-SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEETT-GGG-EEEEEETTEEEEEEE-.-S CS
                           DUF2124   1 kglsgllrefkelvkesekivfvGspgvCtpfaellayaiRdlekelvfvpdldlekarklevtdvGmqleeeaeee 77 
                                       kgl+g+l+ f++lvke+e+i+fvG+pg+Ctpfa++l++ +R+  k+l+fvp l++e++r+l++t +Gm+l+++a + 
  gi|386001243|ref|YP_005919542.1|   8 KGLGGMLNGFRDLVKEDESITFVGTPGFCTPFATFLGFPVRE--KRLAFVPGLKVEETRALVATGYGMELGKAA-SP 81 
                                       8*****************************************..9***************************99.** PP

                                       -EEEEEEEGGGGSTTTS--HHHHHHHHHHHEEEEEEEEEETTHHHHTTHHH..HS--SEEEEEEE CS
                           DUF2124  78 kadvvvllGGlampkikveaedvkeliekiekkkviGvcfmsifekagWld..kidFdliidakl 140
                                       +advvv+lGG+ampki+v++e++++l+ ki++kk+iGvcfm i+e+agW++  ++ F+++++++l
  gi|386001243|ref|YP_005919542.1|  82 DADVVVILGGMAMPKIGVSIEEMAALLGKIQHKKLIGVCFMGILEQAGWCGtpALGFNYVMNTNL 146
                                       *************************************************99667*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 1048.04
//
Query:       gi|386001244|ref|YP_005919543.1|  [L=221]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-08   34.9   0.0    3.9e-08   33.8   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      4e-05   24.2   0.0    7.7e-05   23.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.016   15.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.015   14.9   0.0      0.022   14.3   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   8.6e-12   3.9e-08      35      87 ..      72     126 ..      58     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.6e-12
                                       HHHCCHHT-.EEEETTEECCCT.SS-TT-EEEEEEES-CCC-...CCHHHHHHHHHHH CS
                   Methyltransf_11  35 kekaseegl.kvefvvadaekl.pfednsfDlvvssevlhhv...edpekalkeiaRv 87 
                                       ++ ++   + ++++v +da+++  f+d+ fD+ +s++v++hv    ++++  +e++Rv
  gi|386001244|ref|YP_005919543.1|  72 RTDSH---HsNIRLVAGDARDMrGFADGAFDVAFSNSVIEHVggpSEQRRMAREVMRV 126
                                       33333...34699*********89********************99***********9 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.7e-08   7.7e-05      43      92 ..      75     126 ..      61     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.7e-08
                                       HTTTTEEEEESBCCGBS.SSTTTEEEEEEESTGGG.SSHHHHHHHHHHHHHH CS
                   Methyltransf_25  43 eeglnvefvqgdaedlp.fedgsfDlvvssgalhh.lsdedlekalkeiarv 92 
                                       +++ n+++v gda+d+  f+dg fD+ +s+ +++h   +++++++ +e+ rv
  gi|386001244|ref|YP_005919543.1|  75 SHHSNIRLVAGDARDMRgFADGAFDVAFSNSVIEHvGGPSEQRRMAREVMRV 126
                                       34459**********9879**********76799944678999*******98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-06     0.016      52     113 ..      76     136 ..      62     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                   Methyltransf_31  52 gldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggilliedpr 113
                                         +n+++ +gd+ ++   ++d  fD+ +sn+v+ ++  p +  + + +v++ g ++ +++p+
  gi|386001244|ref|YP_005919543.1|  76 HHSNIRLVAGDARDMRG-FADGAFDVAFSNSVIEHVGGPSEQRRMAREVMRVGRRYFVQTPN 136
                                       34599*********775.9***********************************99999998 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     5e-06     0.022      59     114 ..      82     139 ..      72     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                              MetW  59 viqgdldkdlenfedksfdyvvlsqtlqatrnp...kevldellrigrraivsfPnfGh 114
                                       ++ gd+ +d+  f+d +fd++  +  +  +  p   +++ +e++r+grr  v  Pn+ +
  gi|386001244|ref|YP_005919543.1|  82 LVAGDA-RDMRGFADGAFDVAFSNSVIEHVGGPseqRRMAREVMRVGRRYFVQTPNWSF 139
                                       566665.68999***************9997662226899****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1591.30
//
Query:       gi|386001245|ref|YP_005919544.1|  [L=933]
Description: Oligosaccharyl transferase, STT3 subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-30  104.7  23.0    1.5e-29  103.3  23.0    1.6  1  STT3          Oligosaccharyl transferase STT3 subunit
    1.4e-25   89.4   0.5    4.8e-25   87.7   0.5    2.0  1  AglB_L1       Archaeal glycosylation protein B long periphera
    0.00025   21.3  11.2    0.00025   21.3  11.2    3.4  3  PMT_2         Dolichyl-phosphate-mannose-protein mannosyltran
     0.0036   17.0   9.0     0.0036   17.0   9.0    4.5  5  DUF4203       Domain of unknown function (DUF4203)
  ------ inclusion threshold ------
       0.16   12.3   0.1       0.46   10.8   0.1    1.7  1  Big_6         Bacterial Ig domain
       0.88    9.3   8.0         14    5.4   0.0    3.9  4  TMEM208_SND2  SRP-independent targeting protein 2/TMEM208


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3  23.0   4.9e-33   1.5e-29      58     460 ..     117     591 ..     104     635 .. 0.77

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 4.9e-33
                                       HHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC.HHHHHHH.HCCHHHHHHHHCHHHHHHHHHHS-CCCHH CS
                              STT3  58 kknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld.vsirevc.lwlpallgsLlaIpiyflvrelksdiaGl 132
                                       +++wfd+ +++P G  +++gp+ ++   ++s++  + ++ ++  ev+  +lpa++g Ll+ ++yf+ rel +  aG+
  gi|386001245|ref|YP_005919544.1| 117 QRPWFDPMTFFPRGTEITFGPFNSWAIAILSYMADLGTPsMHTVEVVgAVLPAVFGALLVFVVYFIGRELGGRTAGF 193
                                       789*******************98885666666666666855555542679************************** PP

                                       HHHHHCCC-CC.CCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCS.................TTCHHHHHHHHHH CS
                              STT3 133 lAAlllaiaPg.YlsrtvaGfyDtdmfeivlllfvlffflkaiktks.................nkislaviaalii 191
                                       +AA+++a+ Pg +lsr+  Gf+D+++ e++l+  ++ ff+ a  ++                  ++ ++ ++a+l++
  gi|386001245|ref|YP_005919544.1| 194 MAAVMIAVLPGqFLSRSLIGFADHHAAEVLLSTTAMLFFILAFRSGAgkltfaairrmdltalkRPLAYCLLAGLFL 270
                                       ***************************************************************************** PP

                                       HHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHH CS
                              STT3 192 flivlaWggyailiyallllfilalLiigrfelklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgl 268
                                        l++ aW+    l++ ++l+f+ +  i+  +  +    v++s +iaf+v   +vl+f+  +    + + ++++   +
  gi|386001245|ref|YP_005919544.1| 271 GLYIDAWSSG-HLFVGIILAFVTVQSIVDHMRGRNADYVGISGAIAFFVTLLLVLPFVRAENGFGFTLYSLFQ---P 343
                                       ********99.8999***************99999999***********999999999999644334444443...3 PP

                                       HHHHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGGHHHHHHHHHHHHC........................ CS
                              STT3 269 lqlvafgsvvvlvaelkfyqfislfqpgilsevlgligevvtalavlglialw........................ 321
                                        +l++   +++ ++ l+++ ++  ++ +++  ++  + +vv+++ +l+++                           
  gi|386001245|ref|YP_005919544.1| 344 TILIVGIIFMLFLSVLSSQLVQRKMDRSYFPLIVIGSIVVVFVILMLAVPQFTgaltaglkifqprtgggatiseas 420
                                       44444444445555588888888888886665555558888888888888888899999999*************** PP

                                       .........................CCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHH.. CS
                              STT3 322 .........................lgilyslldleyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgi.. 370
                                                                l+ l  ll +  ++ +++  +l+  w ++ l+++++  rf+  ++v++++  
  gi|386001245|ref|YP_005919544.1| 421 rilergsiqrnfpgivpilspfwltLIALPLLLLRYRRDDSRNGDMLILAWTVIILALTFAQNRFAyYYAVNVAFla 497
                                       ***************8888777775333333333355778888899999999999********************89 PP

                                       HCHHCCHHCTCHHHHHHH.................HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHH CS
                              STT3 371 ifvgllleflavfvkiys.................vsqilfsgvvvillmltllpvlallaavkiskifstykdeke 430
                                        ++g++l  +  f+                      + i f++v +    ++l +  +++  v+  ki s y ++  
  gi|386001245|ref|YP_005919544.1| 498 GYLGSVLLEKTRFLEVEDalvrmargsskeapdqnRAIINFVVVAFL---VVLFVYPSMFGSVQGVKIGSFYSQNQV 571
                                       55555443333333333355667779999999865444444444444...444444444555555555555555433 PP

                                       HHHHHHHHHHHHHHCT.TTTTHHH.TTHHHC CS
                              STT3 431 akikvaakavaptksnglkeslew.kantnr 460
                                        ++              ++es++w + nt++
  gi|386001245|ref|YP_005919544.1| 572 GPMN-----------SDWYESMYWlRDNTPS 591
                                       3333...........2555666666555554 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.5   1.6e-28   4.8e-25       1      92 []     839     931 ..     839     931 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.6e-28
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETT.EE CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagn.vt 76 
                                       GAtitG+a++g+ v++sv+++t++gr+f Y++++ a++dG+f+l+vPYsteg e+ +tn++v + gpY++++g+ + 
  gi|386001245|ref|YP_005919544.1| 839 GATITGTASPGTDVVISVPISTGRGRSFVYQKSTAAGSDGQFSLVVPYSTEGPESWSTNFDVGPVGPYTLRVGTvQY 915
                                       9************************************************************************9455 PP

                                       EEE---HHHHHHT-EE CS
                           AglB_L1  77 aeveVpEeaVlsgetv 92 
                                       +ev+VpE aV +g+++
  gi|386001245|ref|YP_005919544.1| 916 EEVRVPEGAVIAGSSI 931
                                       79**********9987 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3  11.2   8.4e-08   0.00025      18     153 ..     158     293 ..     137     298 .. 0.83
   2 ?   -2.6   5.0       1.9   5.8e+03     105     154 ..     332     385 ..     312     392 .. 0.60
   3 ?    2.4   0.9     0.056   1.7e+02      79     113 ..     466     500 ..     444     503 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.4e-08
                             PMT_2  18 gfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa...lftpdaplvllwalalylllr 91 
                                       +  e++  +++a++g+l ++++y++ r+l g++a+++aa+++av+p  + +        + a+ vll + a+++++ 
  gi|386001245|ref|YP_005919544.1| 158 HTVEVVGAVLPAVFGALLVFVVYFIGRELGGRTAGFMAAVMIAVLPGQFLSRSligFADHHAAEVLLSTTAMLFFIL 234
                                       45677788999***********************************655544457778889**************** PP

                             PMT_2  92 aleknklkywllagvlfGlgflsKytaallliaallyllisarrilkekkpylalllalllf 153
                                       a  ++  k  ++a   + l  l ++ a +ll +++l l+i+    + + +++++++la++ +
  gi|386001245|ref|YP_005919544.1| 235 AFRSGAGKLTFAAIRRMDLTALKRPLAYCLLAGLFLGLYID---AWSSGHLFVGIILAFVTV 293
                                       *****987777777788888888888888888777799999...888999999999988876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                             PMT_2 105 gvlfGlgflsKytaallliaallyllis....arrilkekkpylalllalllfs 154
                                       g+ f+l  l+ +t+++++i ++l+l +      +r++  +++ l+++  +++++
  gi|386001245|ref|YP_005919544.1| 332 GFGFTLYSLFQPTILIVGIIFMLFLSVLssqlVQRKMDRSYFPLIVIGSIVVVF 385
                                       556677777788888777754443333322454444444444443333333333 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.056
                             PMT_2  79 vllwalalylllraleknklkywllagvlfGlgfl 113
                                       +l +a+++ +l+    +n++ y++++ v+f +g+l
  gi|386001245|ref|YP_005919544.1| 466 MLILAWTVIILALTFAQNRFAYYYAVNVAFLAGYL 500
                                       78889999999999999999999999998876665 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.4   7.2e+03     114     133 ..      66      86 ..      58      90 .. 0.60
   2 !   17.0   9.0   1.2e-06    0.0036      38     128 ..     143     237 ..     133     248 .. 0.84
   3 ?   -2.9   8.6       1.5   4.6e+03      59     133 ..     262     333 ..     240     350 .. 0.48
   4 ?   -7.1  17.2         6   1.8e+04      79     129 ..     345     392 ..     263     402 .. 0.55
   5 ?   -2.6   0.8       1.2   3.5e+03      37      70 ..     471     504 ..     464     514 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                           DUF4203 114 vivvlgllga.vlslklqkll 133
                                       ++v+lg+++   l+l+  k++
  gi|386001245|ref|YP_005919544.1|  66 IYVGLGVVFLfSLYLRVYKPM 86 
                                       345555555536777767766 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.2e-06
                           DUF4203  38 lvlilkvvvlpsslvqgaslvaalvvGllgGllallfwelglfllgalgGlllallilsllegglitslpskaif.. 112
                                       ++++ ++ +l +  ++++ +v+a++  ++g+ll+++++ +g  l+g  +G++ a++i +l  g++++   s + f  
  gi|386001245|ref|YP_005919544.1| 143 IAILSYMADLGTPSMHTVEVVGAVLPAVFGALLVFVVYFIGRELGGRTAGFMAAVMIAVLP-GQFLSR--SLIGFad 216
                                       45556666666999*******************************************9999.777763..3344567 PP

                           DUF4203 113 .....lvivvlgllgavlslk 128
                                            ++++  ++l+++l+++
  gi|386001245|ref|YP_005919544.1| 217 hhaaeVLLSTTAMLFFILAFR 237
                                       89999999*********9996 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                           DUF4203  59 aalvvGllgGllallfwelglfllgalgGlllallilsllegglitslpskaif..............lvivvlgll 121
                                        +l++Gl++Gl +   w+ g ++    +G++la++++ ++             +              ++i+ ++ l
  gi|386001245|ref|YP_005919544.1| 262 YCLLAGLFLGLYI-DAWSSGHLF----VGIILAFVTVQSI-------------VdhmrgrnadyvgisGAIAFFVTL 320
                                       4555555555552.222222222....3345555555555.............033333333222224444444444 PP

                           DUF4203 122 gavlslkl.qkll 133
                                         vl ++  ++ +
  gi|386001245|ref|YP_005919544.1| 321 LLVLPFVRaENGF 333
                                       4444444445555 PP

  == domain 4  score: -7.1 bits;  conditional E-value: 6
                           DUF4203  79 lfllgalgGlllallilsllegglitslpskaif..lvivvlgllgavlslkl 129
                                       ++    ++G+++ +l+ls+l+ +l++   +++ f  +vi+++++++++l+l  
  gi|386001245|ref|YP_005919544.1| 345 IL----IVGIIF-MLFLSVLSSQLVQRKMDRSYFplIVIGSIVVVFVILMLAV 392
                                       22....333333.4555555677778888888888777777777777777765 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 1.2
                           DUF4203  37 vlvlilkvvvlpsslvqgaslvaalvvGllgGll 70 
                                        +v+il ++  ++ + +   + +a+++G lg +l
  gi|386001245|ref|YP_005919544.1| 471 WTVIILALTFAQNRFAYYYAVNVAFLAGYLGSVL 504
                                       3333333333346666777777777777777665 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00015      0.46      14      54 ..     839     886 ..     834     896 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                             Big_6  14 gttltGkaeagatVtvkdadgtvlgtg.......tadadGeFsvtlep 54 
                                       g+t+tG+a +g+ V+++ +  t  g++        a++dG+Fs+ ++ 
  gi|386001245|ref|YP_005919544.1| 839 GATITGTASPGTDVVISVPISTGRGRSfvyqkstAAGSDGQFSLVVPY 886
                                       899***********99766433333334444443679******98865 PP

>> TMEM208_SND2  SRP-independent targeting protein 2/TMEM208
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.94   2.8e+03      28      73 ..     112     158 ..     103     164 .. 0.65
   2 ?   -1.2   1.7      0.52   1.5e+03      23      72 ..     344     395 ..     336     403 .. 0.51
   3 ?    5.4   0.2    0.0048        14      96     139 ..     465     510 ..     463     516 .. 0.75
   4 ?    5.4   0.0    0.0047        14       1      31 [.     520     550 ..     520     557 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.94
                      TMEM208_SND2  28 nalylllrlll.rsslrprslllylllslpalllyyvlekmgrpkyd 73 
                                       ++l l + ++     +   + +++  ++  a++++ +++ +g+p+++
  gi|386001245|ref|YP_005919544.1| 112 TVLNLQRPWFDpMTFFPRGTEITFGPFNSWAIAILSYMADLGTPSMH 158
                                       44444444444333344447778888999999999******999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.52
                      TMEM208_SND2  23 islavnalylllrlllrsslrpr....slllylllslpalllyyvlekmgrpky 72 
                                       ++l+v ++++l+  +l+s+l  r    s+++++++    +++++v+  ++ p++
  gi|386001245|ref|YP_005919544.1| 344 TILIVGIIFMLFLSVLSSQLVQRkmdrSYFPLIVIGS--IVVVFVILMLAVPQF 395
                                       5566666666666666333322222225665555433..333333333455555 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0048
                      TMEM208_SND2  96 Dviyltwivqvlsilfg.nkfWllylv.iPayalYklwglilgpaf 139
                                       D+++l w v +l++ f  n+f + y+v +   a+Y+  +l+ +  f
  gi|386001245|ref|YP_005919544.1| 465 DMLILAWTVIILALTFAqNRFAYYYAVnVAFLAGYLGSVLLEKTRF 510
                                       99**************988887777772455567877776655555 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0047
                      TMEM208_SND2   1 mAkksaKkiaeeNkatLknlrlislavnaly 31 
                                       mA+ s+K+  ++N+a+++++  ++l+v ++y
  gi|386001245|ref|YP_005919544.1| 520 MARGSSKEAPDQNRAIINFVVVAFLVVLFVY 550
                                       9*************************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 5852.40
//
Query:       gi|386001246|ref|YP_005919545.1|  [L=237]
Description: creatininase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-62  211.4   0.1    1.5e-62  211.2   0.1    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.2   0.1   8.4e-67   1.5e-62       1     240 [.       5     227 ..       5     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 211.2 bits;  conditional E-value: 8.4e-67
                      Creatininase   1 eeltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTi 77 
                                       ee+tw+e+e+al+ ++++ilPvG+tE+HGphlp+ tDt++a ++a++va++ +  ++v+P+++yGv+ + +gfpGTi
  gi|386001246|ref|YP_005919545.1|   5 EEMTWTEIEAALEVTRTLILPVGATEEHGPHLPTFTDTIQALEVAKEVARRRA--VFVAPPVHYGVCRSTRGFPGTI 79 
                                       69**********************************************99966..9***********999******* PP

                      Creatininase  78 slspetliavlrdileslarhGfrrivlvngHgg..nsaalkeaarelraehdaaavrvtaaekelaaalkleeaae 152
                                       s+sp  l+++++d+l+ ++++Gf+r+++++gH g  + +alkeaa+++ a   ++ v+++  ++ +++         
  gi|386001246|ref|YP_005919545.1|  80 SISPGALRDLVSDLLTAFHDSGFERVLILTGHAGgqHLSALKEAAEKAVAIR-DIRVSLVSDFDLIDP--------- 146
                                       ********************************9989**********999988.777665555555555......... PP

                      Creatininase 153 aaeeseeee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakegvstaedaeelspsGvlGdpskataekGea 228
                                           +e e+ g+gHAge+EtS ml +r++lV+    +++++ ++    +   +d+++l  +Gv+Gdps+at+ekGe+
  gi|386001246|ref|YP_005919545.1| 147 ----REVETpGDGHAGEIETSRMLVIREDLVKGLPEKHFPPRPR----YLIMRDVRPLMGNGVMGDPSRATREKGER 215
                                       ....666777**********************776555544433....4689999**99****************** PP

                      Creatininase 229 lleaaveelael 240
                                       ++e av+ ++e+
  gi|386001246|ref|YP_005919545.1| 216 FMEMAVQGVLEA 227
                                       *******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1561.04
//
Query:       gi|386001247|ref|YP_005919546.1|  [L=507]
Description: Phenylalanyl-tRNA synthetase alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-93  312.2   0.0    3.2e-93  311.7   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.5e-10   40.2   0.0    9.1e-07   28.5   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00015   21.2   0.0    0.00034   20.1   0.0    1.5  1  GerE             Bacterial regulatory proteins, luxR family
    0.00031   21.2   0.2          1    9.9   0.0    2.4  2  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.067   12.9   0.2       0.41   10.4   0.0    2.3  2  Sigma70_r4_2     Sigma-70, region 4
      0.079   12.0   0.1        0.2   10.7   0.0    1.6  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
       0.13   12.2   0.4        2.3    8.2   0.0    2.6  2  MarR_2           MarR family
        0.2   12.0   1.6        2.6    8.4   0.4    2.8  3  PheRS_DBD3       PheRS DNA binding domain 3
       0.22   11.8   0.8        0.6   10.4   0.0    2.1  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.7   0.0   1.6e-96   3.2e-93       2     244 ..     235     500 ..     234     501 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.7 bits;  conditional E-value: 1.6e-96
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       +dv+lp++ri++gk+hp++++l++++ei+le+gf+e++g+ v+s+f+nfdaL++pqdhpaR+mqdtFyl++ +++  
  gi|386001247|ref|YP_005919546.1| 235 YDVALPAERIYPGKVHPYQRLLSRMREIMLEMGFSEIKGEVVQSSFWNFDALFQPQDHPAREMQDTFYLDSRAEIpd 311
                                       9********************************************************************888777** PP

                                       ..........................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEE CS
                      tRNA-synt_2d  77 ..........................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhq 126
                                                                 v+++ +LRthtt+v+i++l ++++pp+k +si+rv+Rr+a+D th++eF q
  gi|386001247|ref|YP_005919546.1| 312 hsrvkemhehggevgstgwggtwdpeVARREVLRTHTTSVTIKYLaDHPNPPVKAFSIDRVYRREAIDPTHTPEFEQ 388
                                       **************************999****************88899*************************** PP

                                       EEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHT CS
                      tRNA-synt_2d 127 veglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleav 203
                                       +eg+++de++s+a+l+gvl+e++ k+ g+e +vrfrp yfp+tePs+e +vy+  ++ +w+El+gaG++r ev++++
  gi|386001247|ref|YP_005919546.1| 389 LEGVIMDEGLSFANLLGVLREFYAKM-GFE-EVRFRPGYFPYTEPSVEPEVYI--QGLGWVELGGAGVFRREVTAPF 461
                                       **************************.***.**********************..9********************* PP

                                       T-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 204 gideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       gi  + +++a+GlGv Rlaml++g++D+R l+++d+ +lr+
  gi|386001247|ref|YP_005919546.1| 462 GI--DHPVLAWGLGVGRLAMLRLGLKDLRLLYQSDIGWLRD 500
                                       **..**********************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00031      0.62       5      38 ..     239     272 ..     236     303 .. 0.80
   2 !   28.5   0.0   4.6e-10   9.1e-07      74     209 ..     344     469 ..     328     473 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00031
                   tRNA_synthFbeta   5 lPkapttegelnkeqklrrklrdllagaGlnEvi 38 
                                       lP + + +g+ ++ q+l  ++r+++ ++G++E+ 
  gi|386001247|ref|YP_005919546.1| 239 LPAERIYPGKVHPYQRLLSRMREIMLEMGFSEIK 272
                                       89999*************************9863 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 4.6e-10
                   tRNA_synthFbeta  74 lRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgi 149
                                       lRt  ++    ++++  ++ n+ v++F i +v++ +  + +   e ++l +v++ +             +f++l g+
  gi|386001247|ref|YP_005919546.1| 344 LRTHTTSV---TIKYLADHPNPPVKAFSIDRVYRREaIDPTHTPEFEQLEGVIMDEG-----------LSFANLLGV 406
                                       55554444...455556899****************97778899*************...........********* PP

                   tRNA_synthFbeta 150 vealleslgiekvefepaehpalhpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                       ++++ +++g+e+v+f+p   p+ +p    e++++g    e+G +G +  ev + f+++++v +
  gi|386001247|ref|YP_005919546.1| 407 LREFYAKMGFEEVRFRPGYFPYTEPSVEPEVYIQGLgwvELGGAGVFRREVTAPFGIDHPVLA 469
                                       *********************************885556********************9976 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.7e-07   0.00034       2      34 ..      10      43 ..       9      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.7e-07
                                      SS-HHHHHHHHHHCTTS-H.HHHHHHHTS-HHHH CS
                              GerE  2 sLskRErevLrllaeGksn.keIAeelniSekTV 34
                                       Ls+R r+vL+ + +G++   +IAe+l+i+e +V
  gi|386001247|ref|YP_005919546.1| 10 ALSPRDRQVLKEISDGLTDpRKIAEKLGIKEVSV 43
                                      6****************96489*********988 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00092       1.8       2      68 .]      12      72 ..      11      72 .. 0.81
   2 !    9.9   0.0   0.00052         1      18      68 .]     136     183 ..     132     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00092
                            HTH_27  2 trqqalvLhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrre.krvrlTdkG 68
                                      ++ +++vL  i    ++ +  + ++++l +   ++++s + L e+GL+       d+r    ++lT++G
  gi|386001247|ref|YP_005919546.1| 12 SPRDRQVLKEIS---DGLTDpRKIAEKLGIKEVSVISSAEGLAEMGLI-----GLDKRVeEVYALTEEG 72
                                      677788888888...45555599*************************.....4455544899999998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00052
                            HTH_27  18 rkkladlcgrlnvedshis.yslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       + +l +l++   ++ s+   ++lk L  +GLve+ +    +++  +++Td+G
  gi|386001247|ref|YP_005919546.1| 136 EEILGALSFQGETSGSALDsEALKLLKGRGLVESRA----QKSWSLEITDAG 183
                                       56668899999999999988************4444....569999999998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.41       8      43 ..       8      43 ..       5      45 .. 0.92
   2 ?   -1.3   0.0       0.9   1.8e+03      11      32 ..      58      78 ..      55      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                      HTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2  8 laeLperqreifllryleglsykEIAellgisegtV 43
                                      l++L++r+r+++  +     + + IAe+lgi+e++V
  gi|386001247|ref|YP_005919546.1|  8 LSALSPRDRQVLKEISDGLTDPRKIAEKLGIKEVSV 43
                                      899************988889************998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.9
                                      S-HHHHHHHHHHHTS---HHHH CS
                      Sigma70_r4_2 11 LperqreifllryleglsykEI 32
                                      L +r  e++ l  +eg  y+EI
  gi|386001247|ref|YP_005919546.1| 58 LDKRVEEVYAL-TEEGARYAEI 78
                                      77888899999.69*******9 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.3   4.5e+03      29      46 ..     256     273 ..     253     280 .. 0.79
   2 ?   10.7   0.0    0.0001       0.2      93     119 ..     365     390 ..     364     411 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHTT-EE--- CS
                                       xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  29 tkavrkyleengfieiet 46 
                                       ++ +r+++ e gf ei+ 
  gi|386001247|ref|YP_005919546.1| 256 LSRMREIMLEMGFSEIKG 273
                                       677999999999999975 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
                                       EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       + f+i r++R E ++ ++ + EF q+e
  gi|386001247|ref|YP_005919546.1| 365 KAFSIDRVYRREAIDPTHTP-EFEQLE 390
                                       68******************.****98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0012       2.3       1      51 [.       9      56 ..       9      73 .. 0.89
   2 ?    0.9   0.1      0.21   4.3e+02      39      55 ..     155     171 ..     155     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      ++l+p +++vL ++ ++      ++ +a++lg++  +v    + L + GL+
  gi|386001247|ref|YP_005919546.1|  9 SALSPRDRQVLKEISDGLT---DPRKIAEKLGIKEVSVISSAEGLAEMGLI 56
                                      589***********99984...9************9999999999999999 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                                       HHHHHHHHHTTSEEEEE CS
                            MarR_2  39 srilkrLvaaGLverrp 55 
                                       s +lk L  +GLve r+
  gi|386001247|ref|YP_005919546.1| 155 SEALKLLKGRGLVESRA 171
                                       56899*********885 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4    0.0013       2.6      13      48 ..      91     122 ..      81     128 .. 0.77
   2 ?    1.1   0.0      0.24   4.8e+02       2      35 ..     384     417 ..     383     418 .. 0.80
   3 ?   -2.6   0.0       3.5     7e+03      41      54 ..     443     455 ..     442     458 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                        PheRS_DBD3  13 eggisqkelkklggdpvakiGfskAmknkWikkdkg 48 
                                       +gg++++e+    +dp  k+G++   k++W +++ g
  gi|386001247|ref|YP_005919546.1|  91 AGGVPISEI----EDPALKVGIGWLKKKGWAAVEAG 122
                                       578999999....3466*************999654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                        PheRS_DBD3   2 hEarvfaavppeggisqkelkklggdpvakiGfs 35 
                                       +E+   + v  ++g+s + l  ++ + +ak+Gf 
  gi|386001247|ref|YP_005919546.1| 384 PEFEQLEGVIMDEGLSFANLLGVLREFYAKMGFE 417
                                       56666666655789******999999******95 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.5
                        PheRS_DBD3  41 kWikkdkgdgkvvr 54 
                                       +W+++  g g + r
  gi|386001247|ref|YP_005919546.1| 443 GWVEL-GGAGVFRR 455
                                       8****.44444555 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003       0.6      17      53 ..      20      57 ..      18      62 .. 0.88
   2 ?   -2.7   0.1       3.6   7.2e+03      49      57 ..     220     228 ..     219     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                                      HH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 17 se.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      +e + +   + ++ae L+++  sV  + + L+++G++ 
  gi|386001247|ref|YP_005919546.1| 20 KEiSDGLTDPRKIAEKLGIKEVSVISSAEGLAEMGLIG 57
                                      67778888999************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                                       TTSEEEETT CS
                    Fe_dep_repress  49 dGyveyeky 57 
                                        Gyv y++ 
  gi|386001247|ref|YP_005919546.1| 220 GGYVSYKGS 228
                                       59****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 3160.01
//
Query:       gi|386001248|ref|YP_005919547.1|  [L=546]
Description: Phenylalanyl-tRNA synthetase, beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-34  118.5   0.0    3.6e-34  118.1   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    3.9e-14   52.7   0.0    3.7e-13   49.6   0.0    2.5  2  B5               tRNA synthetase B5 domain
    9.5e-14   51.4   0.0    1.5e-13   50.8   0.0    1.2  1  B3_4             B3/4 domain
    0.00041   19.9   0.0      0.036   13.5   0.0    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.12   12.6   0.0        0.3   11.3   0.0    1.7  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0     1e-37   3.6e-34       3     213 ..     345     536 ..     343     537 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1e-37
                   tRNA_synthFbeta   3 stlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldkll.eddderkavelanPlsedqsvlRtsL 78 
                                       ++lPk++t+++ +++ + ++  lr++++g+G+ E++ ++++se ++ +++ +  de  a ++++P+se ++++Rts+
  gi|386001248|ref|YP_005919547.1| 345 PVLPKTVTVGE-PHPLEVRKSDLREIMVGLGYLETMPFTLTSERVNFEMMgRPRDEAAATRVLHPISELHTMVRTSI 420
                                       57999999999.99************************************9999*********************** PP

                   tRNA_synthFbeta  79 lpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealle 155
                                       lp+lLe  a N+++ ++  r+F +g+v +        + ++ la++  +++           vd +++  +v al++
  gi|386001248|ref|YP_005919547.1| 421 LPSLLEIFAINQHHPLP-QRIFALGDVLIGG------RTRQELAAASIHSS-----------VDLAEVRSVVGALFR 479
                                       *****************.*************......8899**********...........*************** PP

                   tRNA_synthFbeta 156 slgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       +l + + e+ p+e+ a+  gr  ++ v+g++vG +G ++p+vl++f+l+q+++++El 
  gi|386001248|ref|YP_005919547.1| 480 ELDL-TPEIIPSEDGAFLAGRRGDLLVEGTKVGSFGFFSPQVLQSFGLDQPAVGLELR 536
                                       ****.***************************************************96 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.47   1.7e+03      11      52 ..      14      54 ..       4      60 .. 0.70
   2 !   49.6   0.0     1e-16   3.7e-13       3      67 .]     277     340 ..     276     340 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.47
                                      HHTS---HHHHHHHHHHTT-E..EESSTTCEEEE--TT-TT-- CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                                B5 11 llGidlseeeiikiLkrlgce.riekdkdlllVtvPswRsDle 52
                                      ++G   s++ei   +  +g +  +++ +d ++V+  + R+Dl 
  gi|386001248|ref|YP_005919547.1| 14 MVG--ASRDEIMARMAMMGADiGKSNAEDYVDVEFFPDRPDLY 54
                                      555..47889999999999873346667788888777788875 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 1e-16
                                       EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++ve++++l+G +ls+ee +  L+r+ + +    + +l+V vP++R D+ + +D+ E+ a  yGY
  gi|386001248|ref|YP_005919547.1| 277 VEVEEARSLIGFNLSAEELAASLERMRFGV-RPLGRELEVLVPAYRADIMHSWDIFEDAAKGYGY 340
                                       67999************************8.999999***************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   4.2e-17   1.5e-13      34     130 ..     111     234 ..      95     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4.2e-17
                                       -.--HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEEEBTTS-.EEEE-T............... CS
                              B3_4  34 p.innvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakegeklvtldgk.erelde............... 88 
                                       p i+++ D+++ ++  lg+     +++++D++++ ++++   a   +++v+ld + +  ++e               
  gi|386001248|ref|YP_005919547.1| 111 PaIESLMDLQEDLHWGLGRnrrkvAIGVHDISRVVPPFTYFAADPSFEFVPLDFEeSLSMEEilrrhpkgvsyasil 187
                                       3499************************************************9662444466*************** PP

                                       ....TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HH CS
                              B3_4  89 ....edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpv 130
                                           ++++i+d+++ v s +++++ge ++v +dT++ f+ +++ dpv
  gi|386001248|ref|YP_005919547.1| 188 egfdRYPLITDANGDVlSFPPIINGELTRVRDDTRDLFIDVTGTDPV 234
                                       **************999***************************995 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     1e-05     0.036       8     110 ..     348     446 ..     341     452 .. 0.82
   2 ?    3.5   0.0     0.012        42     189     214 ..     510     533 ..     497     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                                       TSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE- CS
                      tRNA-synt_2d   8 gkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLR 84 
                                        k ++ g+ hpl+  +++++ei++ lg+ e+    + se  nf+++  p+d++a +     +l +p +  e ++++R
  gi|386001248|ref|YP_005919547.1| 348 PKTVTVGEPHPLEVRKSDLREIMVGLGYLETMPFTLTSERVNFEMMGRPRDEAAAT----RVL-HPIS--ELHTMVR 417
                                       56788999*****************************************9998843....233.3334..5578889 PP

                                       SSTHHHHHHHH...TTS-SSEEEEEEEEE CS
                      tRNA-synt_2d  85 thttavqirtl...ekkkppikiisigrv 110
                                       t   +  +      +++ +p++i+++g v
  gi|386001248|ref|YP_005919547.1| 418 TSILPSLLEIFainQHHPLPQRIFALGDV 446
                                       98877777666667777789999988866 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                                       EEEEEEE-HHHHHHTT-.TTSEEEEE CS
                      tRNA-synt_2d 189 llgaGmvrpevleavgideevsgfaf 214
                                       ++ +G ++p+vl+++g+d  ++++++
  gi|386001248|ref|YP_005919547.1| 510 VGSFGFFSPQVLQSFGLD--QPAVGL 533
                                       7899*************5..554444 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.4e-05       0.3      47      82 ..      33      68 ..       8      69 .. 0.81
   2 ?   -4.0   0.0         5   1.8e+04      58      68 ..     315     325 ..     313     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.4e-05
                         PhetRS_B1 47 adkkseeviykidipAnryDLLcleglaralkvFlg 82
                                       +k++ e ++ ++    r+DL + eg+aral+ Fl+
  gi|386001248|ref|YP_005919547.1| 33 IGKSNAEDYVDVEFFPDRPDLYSSEGVARALQGFLD 68
                                      56778899999*********************9985 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5
                         PhetRS_B1  58 idipAnryDLL 68 
                                       + +pA r D++
  gi|386001248|ref|YP_005919547.1| 315 VLVPAYRADIM 325
                                       668*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 3327.61
//
Query:       gi|386001249|ref|YP_005919548.1|  [L=139]
Description: Putative signal-transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-21   75.0   1.1    2.1e-12   47.3   0.1    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   2.6e-10   4.6e-06       5      53 ..       1      51 [.       1      54 [. 0.91
   2 !   47.3   0.1   1.2e-16   2.1e-12       3      54 ..      67     118 ..      64     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.6e-10
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT...BEEEEEEHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedg...klvGivtlrDllr 53
                                      mt +++ v  +tt+ ea+++m+++g ++++VV e g   ++vGivt + l+r
  gi|386001249|ref|YP_005919548.1|  1 MTYPILAVGVETTVFEAIQMMVREGKGSVLVV-EGGllkEVVGIVTTSGLFR 51
                                      888999****************99999**9**.7889978******988876 PP

  == domain 2  score: 47.3 bits;  conditional E-value: 1.2e-16
                                       HHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   3 dimtr.dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       ++mt+ ++vt+ p++t + a+e+m e++v+rlPVV e g lvGi+t +Dllr 
  gi|386001249|ref|YP_005919548.1|  67 EVMTPaPLVTIGPNETTRRAAEMMLEHKVRRLPVV-ECGALVGIITSKDLLRC 118
                                       799998889**************************.8999***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 990.76
//
Query:       gi|386001250|ref|YP_005919549.1|  [L=348]
Description: hypothetical protein Mhar_0546 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0037   17.5   0.0      0.009   16.3   0.0    1.7  1  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.031   14.5   0.5      0.031   14.5   0.5    1.8  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
      0.099   12.8   0.9       0.43   10.8   0.1    2.5  2  He_PIG       Putative Ig domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-06     0.009       6      40 ..      73     141 ..      68     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvtDtl...................................P 40 
                                       d+  ++pG t++y++tv N g ++a +v++  ++                                   P
  gi|386001250|ref|YP_005919549.1|  73 DQNYATPGKTLEYIVTVENLGCSDA-DVKLVAVPkncrpgwfgwtelvmtvaagsvgtevlpvtpdmkaP 141
                                       455799*******************.99998766666666666666666666666666666666666662 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 ?   -3.7   0.0       2.5   1.5e+04       3      19 ..      20      36 ..      18      39 .. 0.62
   2 ?   14.5   0.5   5.1e-06     0.031       1      77 [.      77     152 ..      77     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.5
                       NPCBM_assoc  3 pGetvtltltvtndgta 19
                                      +G + + +l+++ +g a
  gi|386001250|ref|YP_005919549.1| 20 QGPESEWNLEAAATGPA 36
                                      56666666666666654 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.1e-06
                       NPCBM_assoc   1 vepGetvtltltvtndg..taaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtak 75 
                                       ++pG+t ++ +tv n g  +a ++ v +   + +GW      ++ + ++a+G   +  + Vtp  +a +Gdy+ +++
  gi|386001250|ref|YP_005919549.1|  77 ATPGKTLEYIVTVENLGcsDADVKLVAVPKNCRPGWF---GWTELVMTVAAGSVGTEVLPVTPDMKAPPGDYDFQVT 150
                                       589************999788899999*****99999...5566777*************************99999 PP

                       NPCBM_assoc  76 ar 77 
                                       a+
  gi|386001250|ref|YP_005919549.1| 151 AS 152
                                       87 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.61   3.6e+03      22      43 ..      37      64 ..      34      70 .. 0.62
   2 ?   10.8   0.1   7.2e-05      0.43      27      47 ..     134     154 ..     126     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.61
                            He_PIG 22 tGtitGtpdqtvap......GsytftVt 43
                                      +G ++G ++ tv p      G++ + V+
  gi|386001250|ref|YP_005919549.1| 37 SGPVSGPVSGTVWPsaprilGELRVSVD 64
                                      5666677766665544566666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.2e-05
                            He_PIG  27 GtpdqtvapGsytftVtatdg 47 
                                       +tpd    pG y+f Vta++ 
  gi|386001250|ref|YP_005919549.1| 134 VTPDMKAPPGDYDFQVTASAP 154
                                       7999999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2658.64
//
Query:       gi|386001251|ref|YP_005919550.1|  [L=188]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1430.76
//
Query:       gi|386001252|ref|YP_005919551.1|  [L=266]
Description: hypothetical protein Mhar_0548 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2069.36
//
Query:       gi|386001253|ref|YP_005919552.1|  [L=259]
Description: hypothetical protein Mhar_0549 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.24   11.6   0.0    1.3  1  RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.4e-05      0.24      48      92 ..     105     151 ..      95     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                   RNase_Zc3h12a_2  48 dlvafqklidldfi..kfiteaenfkwfnvvadladrigavfvssae 92 
                                       d + f+k  +++++   + t +++ kw+++++ +   igav v    
  gi|386001253|ref|YP_005919552.1| 105 DYINFNKEAEFEYMpvSYQTGTYDQKWIEKLCVQNYYIGAVVVEMYT 151
                                       67899999999**954668999*******************996533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1695.00
//
Query:       gi|386001254|ref|YP_005919553.1|  [L=330]
Description: hypothetical protein Mhar_0552 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-79  265.8   0.0    3.5e-79  265.5   0.0    1.1  1  NRD1_2    NrpR regulatory domains NRD1 and 2
    3.4e-23   81.4   0.4    7.5e-23   80.3   0.4    1.6  1  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.5   0.0   3.9e-83   3.5e-79       1     237 [.      89     327 ..      89     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 265.5 bits;  conditional E-value: 3.9e-83
                                       ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE.......... CS
                            NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegk 75 
                                       vgfv+++iee++y+++fdp +++ +V+vN+sl+dk+d e+al ++k v+++g++vs+rv i +ege+  + +vp+g 
  gi|386001254|ref|YP_005919553.1|  89 VGFVNARIEEYMYRSSFDPGSENNRVVVNTSLLDKRDSERALAAMKAVFDAGFAVSRRVLIQDEGEEmgGAAVPRGF 165
                                       79*************************************************************************** PP

                                       EEEEEE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEE CS
                            NRD1_2  76 vgiatvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkil 152
                                       +gi tvCSit+dg+Ll+ GIpv+++++G++++++++  +Ft+l++Y g+s+dP++v++s+k + ++ +++tg+g +l
  gi|386001254|ref|YP_005919553.1| 166 LGISTVCSITVDGMLLRGGIPVNTTFAGVVDVREGSLYQFTDLLAYAGSSLDPIRVLMSRKAARITGAVKTGNGGLL 242
                                       ***************************************************************************** PP

                                       EEEEEEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEE CS
                            NRD1_2 153 AnlReipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsg 229
                                       AnlReipv+a  +++e+le +k agi gv++i+ep+e+ +g+pv  +kvgi++++G+n++ a++e+g +++++++s+
  gi|386001254|ref|YP_005919553.1| 243 ANLREIPVAAIGQARELLEMAKGAGIDGVMRISEPGEPNMGCPVGAGKVGIALCAGVNAVLAAEELGAEIRTTPISS 319
                                       ***************************************************************************** PP

                                       EEEGGGSE CS
                            NRD1_2 230 lidiselk 237
                                       + ++ ++k
  gi|386001254|ref|YP_005919553.1| 320 IQEYGRMK 327
                                       *******8 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.4   8.3e-27   7.5e-23       1      66 []      15      80 ..      15      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 8.3e-27
                            HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                      +eIL++++ ++kpiga++i +eL  rgy++geravRy L++++e g+t++ gy+gr lt  G  eL
  gi|386001254|ref|YP_005919553.1| 15 IEILRVINAAEKPIGARAISDELSSRGYEVGERAVRYNLKIMDELGFTKKEGYSGRVLTPLGRREL 80
                                      79**********************************************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2478.72
//
Query:       gi|386001255|ref|YP_005919554.1|  [L=409]
Description: hypothetical protein Mhar_0553 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-11   42.7   0.2    1.2e-10   41.1   0.1    1.8  2  PEGA      PEGA domain


Domain annotation for each model (and alignments):
>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   6.5e-15   1.2e-10       5      64 ..     145     205 ..     142     209 .. 0.87
   2 ?   -2.1   0.0      0.21   3.8e+03      48      64 ..     343     359 ..     341     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6.5e-15
                              PEGA   5 tirSnpeGatVyidGkylGkTPvtlsleaGnyslrvekeGYedlektvtvt.agetvklnl 64 
                                        + S+p+Ga+VyidG y G TP   ++e+ ++ ++   eGY +++  +++t ++ tv ++l
  gi|386001255|ref|YP_005919554.1| 145 PVVSDPSGAEVYIDGIYSGITPFIATVEPESHLVEAYREGYWNWFNVIEFTpSTGTVPITL 205
                                       588************************************************5555555544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.21
                              PEGA  48 lektvtvtagetvklnl 64 
                                       ++++++v++g++++++ 
  gi|386001255|ref|YP_005919554.1| 343 WSTRCDVEEGTVYRIYA 359
                                       789999**999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 3172.21
//
Query:       gi|386001256|ref|YP_005919555.1|  [L=129]
Description: 30S ribosomal protein S6e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-41  140.8   0.1    2.3e-41  140.7   0.1    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7   0.1   1.3e-45   2.3e-41       1     124 [.       3     123 ..       3     124 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 1.3e-45
                                       -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEE CS
                     Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLls 77 
                                       ++++i+dp++gk++++e++++ +++++g+++g+ +dgda+G  ++gy ++itggsd++Gfp+++++++++r+++L++
  gi|386001256|ref|YP_005919555.1|   3 FRVVICDPQSGKAYQVEAKDAAANKFLGRKVGDVIDGDAVG--MPGYSIEITGGSDREGFPLRRDLPGSKRRKVLIA 77 
                                       689**************************************..********************************** PP

                                       TTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                     Ribosomal_S6e  78 kggvgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                       + g+gy+p +kG r+rksv+G+ +sad+ q+n++i ++g+k++e+l+
  gi|386001256|ref|YP_005919555.1|  78 G-GTGYNPSEKGRRRRKSVHGRDISADVGQINVKIAERGAKPVEELL 123
                                       9.*******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 842.91
//
Query:       gi|386001257|ref|YP_005919556.1|  [L=436]
Description: putative transporter protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-35  122.4  36.8    1.4e-20   73.9   6.5    3.9  4  MgtE             Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4     0.052   9.3e+02      35      56 ..      46      67 ..      13      83 .. 0.54
   2 !   61.3   4.3   6.4e-21   1.2e-16       1     123 [.      85     215 ..      85     216 .. 0.83
   3 !    3.7   3.8    0.0043        77      14      72 ..     234     291 ..     230     297 .. 0.62
   4 !   73.9   6.5   7.7e-25   1.4e-20       1     123 [.     297     427 ..     297     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.052
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                              MgtE 35 vllkelrvvlllgvilgllifl 56
                                      ++ +++ ++++++v+ +++ f+
  gi|386001257|ref|YP_005919556.1| 46 IVKQSFFALVICSVTSMVAGFS 67
                                      2222222222222222222222 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 6.4e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllalllgw.....slllalv 70 
                                       iP  ++++G +  ++ +r+ t+lh+ge+++     + l++++  v ++ + ++l+++l++  lg      +l +  +
  gi|386001257|ref|YP_005919556.1|  85 IPGAIDMRGTIFGTFGARLGTSLHTGEISPPlaRSEPLRQQVGGVAVQVLSVSLILALVVKGLGLavgldTLSIYDL 161
                                       68889***********************9997668889999999888888888888888554444555555555556 PP

                                       HHHHHHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  71 vglalvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       v ++++  +++ ++l  ++ l++  ++++g+DPdn+++P++t++gD++++ +l+
  gi|386001257|ref|YP_005919556.1| 162 VLISVLSSIFSGLILlGFTLLVIEKSFRRGWDPDNISVPFITVAGDVITIPILF 215
                                       99999988888888877777777899***************************9 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHTTSS.-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHH CS
                              MgtE  14 qlasristalhlgel.ekk..lkkvllkelrvvlllgvilgllifllalllgwslllalvvg 72 
                                        l   ista ++  + + +  l   ++++ + vl+++++ +++++l++ ++ +   ++l+++
  gi|386001257|ref|YP_005919556.1| 234 LLFLFISTAAAVYSIgS-NhqLMARIVRQSMPVLMIATLFSTVAGLFMGVYEE---MLLAFS 291
                                       55556888888888853.33667777777788888888888888888666544...333332 PP

  == domain 4  score: 73.9 bits;  conditional E-value: 7.7e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.........CTS CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllalllgw........slll 67 
                                       iPv++++gGnlg +l+sr+++a hlg+++ +  l      ++   l+l+++l+  ++lla++++            l
  gi|386001257|ref|YP_005919556.1| 297 IPVFNAVGGNLGGILSSRLTSAYHLGLIKMDgrLEGETKINFGCTLVLSAFLFPTLGLLAFVVSRasgmdalgFGDL 373
                                       7*************************995555467777778888999999999999999998877777775554444 PP

                                       HHHHHHHHHHHHHHHHHH..HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  68 alvvglalvlvllaaallilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       ++++ la +++ l+a+++  +++ ++++ k+g+DPdn++iP +t+++D+lgt+ l+
  gi|386001257|ref|YP_005919556.1| 374 LMICLLAGLFTTLLAIFV--TYYFTYFFVKIGVDPDNVTIPTITSMMDVLGTASLI 427
                                       444555555556666666..99999***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3126.24
//
Query:       gi|386001258|ref|YP_005919557.1|  [L=389]
Description: geranylgeranyl reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-11   43.0  11.4    1.2e-05   24.7   0.6    2.9  2  FAD_binding_3   FAD binding domain
    3.8e-07   29.8   2.3    3.8e-07   29.8   2.3    2.2  3  FAD_oxidored    FAD dependent oxidoreductase
    8.3e-07   28.0   0.9    1.3e-06   27.4   0.9    1.3  1  HI0933_like     HI0933-like protein
    3.3e-06   26.5   1.2    4.4e-06   26.1   0.1    1.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.8e-06   26.2   0.2    7.3e-06   25.3   0.0    1.6  2  GIDA            Glucose inhibited division protein A
    9.1e-06   25.8   0.4    9.1e-06   25.8   0.4    3.0  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.5e-05   22.5   0.3      0.028   13.3   0.2    2.5  2  Trp_halogenase  Tryptophan halogenase
    8.7e-05   23.0   0.4    0.00022   21.7   0.4    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0001   21.7   2.0     0.0001   21.7   2.0    2.0  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.001   18.2   2.2      0.001   18.2   2.2    2.0  2  FAD_binding_2   FAD binding domain
     0.0011   18.2   0.3     0.0011   18.2   0.3    1.9  2  Thi4            Thi4 family
     0.0012   17.9   5.8      0.015   14.4   5.7    2.2  1  Lycopene_cycl   Lycopene cyclase protein
     0.0063   16.4   0.2      0.012   15.5   0.2    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.011   15.3   9.2      0.013   15.1   1.9    2.3  2  DAO             FAD dependent oxidoreductase
      0.031   13.6   0.0       0.05   12.9   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.045   13.8   0.6        4.7    7.2   0.2    3.1  3  NAD_binding_9   FAD-NAD(P)-binding
      0.054   12.7   0.4      0.082   12.1   0.4    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.6   1.1e-08   1.2e-05       1      35 [.       7      41 ..       7      51 .. 0.93
   2 !   20.0   4.3   3.2e-07   0.00034     150     326 ..     145     318 ..     109     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      e++V++VGaGpaG ++a   ++ G +vvl+e+ ++
  gi|386001258|ref|YP_005919557.1|  7 EVEVAVVGAGPAGSVAAETAARLGAEVVLIERKRE 41
                                      689*****************************876 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.2e-07
                                       EEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEE.EEEEEEEEEEC-SCCCTTCCEEEEECCTTEE.EEEECCETEE CS
                     FAD_binding_3 150 eetvrakYlvGaDGgrStvrktlgiefegeetvy.eagvldvlfdadlsdiveplvlilsaesrgv.mviPlentle 224
                                         t++a+ ++GaDG  S++++ +g+  +ge +v  e ++++v +d       +++++ +++ ++g   +iPl +   
  gi|386001258|ref|YP_005919557.1| 145 SGTMDAEVVIGADGPGSATARGAGLAARGEVGVClEYEMAGVDIDPAA----AEMYFGTASAPGGYaWIIPLGEDVA 217
                                       3588*************************9998314455555555533....345666666666655899****444 PP

                                       EEEEEEECCE-GGGSCCCHHHHHHHHH..HHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-ST CS
                     FAD_binding_3 225 rfyvqvearaekeersekfteeevkar..lreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPt 299
                                       ++ v  +  +  ++   ++ ++ ++++  ++e  +e  +++ ++    +  a  +    ++g+v+laGDAa ++  t
  gi|386001258|ref|YP_005919557.1| 218 NVGVGTRPPYLLGRGLREVLDSFISEHpiAKEKLQEGSVTAVMRG---LVPAGGMPPAIQRGNVLLAGDAAGMVMAT 291
                                       444444444445555666666666554113333333333333333...23344567889****************** PP

                                       TSHHHHHHHHHHHHHHHHHHHHHTTSS CS
                     FAD_binding_3 300 gGqGlNtaiqDavnLawkLaavlkGeA 326
                                        G G+ +a+      +   a  + GeA
  gi|386001258|ref|YP_005919557.1| 292 SGGGIPLAMVGGRAAGEVAARYIGGEA 318
                                       *******99877777777777777666 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   2.3   3.6e-10   3.8e-07       1      35 [.       9      43 ..       9      52 .. 0.96
   2 ?   -3.8   0.4       5.7     6e+03      15      26 ..     115     126 ..     115     127 .. 0.86
   3 ?   -0.2   0.6      0.47   4.9e+02     397     423 ..     296     322 ..     261     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.6e-10
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      +v VvG+gpaG +AA +Aar Ga+v+L+e+++ +G
  gi|386001258|ref|YP_005919557.1|  9 EVAVVGAGPAGSVAAETAARLGAEVVLIERKREIG 43
                                      599*****************************998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.7
                      FAD_oxidored  15 AiaAaraGakvl 26 
                                       A  AaraGa+vl
  gi|386001258|ref|YP_005919557.1| 115 AWRAARAGARVL 126
                                       678*******98 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.47
                      FAD_oxidored 397 epvcmalGqAaGvaAalaleegvaprd 423
                                        p  m+ G AaG +Aa  +  + a+++
  gi|386001258|ref|YP_005919557.1| 296 IPLAMVGGRAAGEVAARYIGGEAALQE 322
                                       68999999****999988877776665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.9   1.2e-09   1.3e-06       2      43 ..       9      50 ..       8      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.2e-09
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +v+v+G+G+AG  aA++aa+ g++V+l+e+++++g+ ++  G
  gi|386001258|ref|YP_005919557.1|  9 EVAVVGAGPAGSVAAETAARLGAEVVLIERKREIGSPVQCGG 50
                                      79*********************************9777655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   4.2e-09   4.4e-06       2      33 ..       9      40 ..       8      81 .. 0.88
   2 ?   -2.9   0.1       2.9     3e+03       4      21 ..     152     169 ..     114     196 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.2e-09
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      +v+v+G+GpAG  aa+t+a+ ga+v+l+e+++
  gi|386001258|ref|YP_005919557.1|  9 EVAVVGAGPAGSVAAETAARLGAEVVLIERKR 40
                                      599*************************8544 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                                       EEE--SHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   4 vviGgGpAGlaaaltlaq 21 
                                       vviG+   G a+a+ ++ 
  gi|386001258|ref|YP_005919557.1| 152 VVIGADGPGSATARGAGL 169
                                       455554444444444443 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   6.9e-09   7.3e-06       2      31 ..      10      39 ..       9     111 .. 0.87
   2 ?   -2.5   0.0         2   2.1e+03      15      27 ..     115     127 ..     113     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.9e-09
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithk 31
                                      v V+G+G AG+ AA +aarlGa+v+Li  k
  gi|386001258|ref|YP_005919557.1| 10 VAVVGAGPAGSVAAETAARLGAEVVLIERK 39
                                      89*************************444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       HHHHHHTT--EEE CS
                              GIDA  15 AlaaarlGakvlL 27 
                                       A+ aar+Ga+vl 
  gi|386001258|ref|YP_005919557.1| 115 AWRAARAGARVLV 127
                                       999******9986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.4   8.6e-09   9.1e-06       1      32 [.      12      43 ..      12      51 .. 0.95
   2 ?   -0.1   0.4         1   1.1e+03      12      35 ..     115     144 ..     113     163 .. 0.65
   3 ?   -2.6   0.1       6.2   6.5e+03       3      14 ..     302     313 ..     301     329 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.6e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G+vaA ++a+ g++v+l+e+ + +G
  gi|386001258|ref|YP_005919557.1| 12 VVGAGPAGSVAAETAARLGAEVVLIERKREIG 43
                                      8****************************999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                                       HHHHHCC......TEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  12 AylLaka......gfdvlllekrdrlGGra 35 
                                       A+++a+a      g++ +l e r +l+Gra
  gi|386001258|ref|YP_005919557.1| 115 AWRAARAgarvlvGVRAELQEGRLHLSGRA 144
                                       788888722233444555555555555555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.2
                                       --SHHHHHHHHH CS
                     NAD_binding_8   3 GaGlsGlvaAyl 14 
                                       G+ ++G vaA++
  gi|386001258|ref|YP_005919557.1| 302 GGRAAGEVAARY 313
                                       555555555554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   2.6e-05     0.028       2      51 ..      10      57 ..       9      68 .. 0.80
   2 !    6.9   0.0    0.0024       2.5     248     372 ..     196     332 ..     104     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE.-SSS---SS-EE--THHHH CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlve.seeigtvgvGeatipsirk 51
                                      + +vG+G+aG++aA + a+ +   +ev l+e + eig      + +p+i++
  gi|386001258|ref|YP_005919557.1| 10 VAVVGAGPAGSVAAETAARLG---AEVVLIErKREIGSPVQCGGFLPEIEE 57
                                      89*****************99...89****934578765444466777766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0024
                                       SEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS...-HHHHHHHHHHHCT--TTTS-EEEE---EE........... CS
                    Trp_halogenase 248 ytrataekaGWtWkiPLqhrlgn.Gyvyssaha...dddeAlaellaeldgkleaeprkirfttGr........... 309
                                       y +      G  W iPL + + n G+  +  ++      e l+ +++e + ++e      +++ G            
  gi|386001258|ref|YP_005919557.1| 196 YFGTASAPGGYAWIIPLGEDVANvGVGTRPPYLlgrGLREVLDSFISEHPIAKE------KLQEGSvtavmrglvpa 266
                                       555556667888888888888887777776666444222233333333332222......22222222333345555 PP

                                       ...ES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHHHHHHHHH CS
                    Trp_halogenase 310 ...rkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaiaefnrevarele 372
                                             + + nv++ G+a+g v +  + +i l++++ r   ++ ++    +aa++e+ +++a+e++
  gi|386001258|ref|YP_005919557.1| 267 ggmPPAIQRGNVLLAGDAAGMVMATSGGGIPLAMVGGRAAGEVAARYIGGEAALQEYPEWIAEEMG 332
                                       5557888899**************************9999999999999999*****999999987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.4   2.1e-07   0.00022       2      35 ..      10      43 ..       9      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+vvG+G  g  +A+++a+lg++V ++er+ ++ 
  gi|386001258|ref|YP_005919557.1| 10 VAVVGAGPAGSVAAETAARLGAEVVLIERKREIG 43
                                      89****************************9987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.0   9.5e-08    0.0001      20      62 ..       2      41 ..       1      51 [. 0.87
   2 ?   -1.8   1.1       1.5   1.6e+03      12      36 ..     133     156 ..     125     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.5e-08
                                      TCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 20 aGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                      aGg+    + +v v+G+G aG  A++ta++lga+V++++ + +
  gi|386001258|ref|YP_005919557.1|  2 AGGLD---EVEVAVVGAGPAGSVAAETAARLGAEVVLIERKRE 41
                                      56666...889*************************9998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       GCTSEEETTCEETCB---EEEEEST CS
                       AlaDh_PNT_C  12 ffggkgtlaGgvpgvepakvlviGg 36 
                                        ++g+  l G+ +g+  a+v++ G+
  gi|386001258|ref|YP_005919557.1| 133 LQEGRLHLSGRASGTMDAEVVI-GA 156
                                       5789999999999999999865.54 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.2   9.7e-07     0.001       2      36 ..      10      44 ..       9      51 .. 0.91
   2 ?   -1.4   0.2      0.92   9.7e+02      15      46 ..     115     149 ..     113     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.7e-07
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      v V+G+G AG +AA +aa+ G++v+++e + e g+
  gi|386001258|ref|YP_005919557.1| 10 VAVVGAGPAGSVAAETAARLGAEVVLIERKREIGS 44
                                      89**************************9998776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.92
                                       HHHHHHTTT-EEEEESSSGGGSGGGG-...-S-EE CS
                     FAD_binding_2  15 AleaaeaGlkvavvekeqefggataws...qGgid 46 
                                       A +aa+aG++v+v   ++ ++g ++ s   +G++d
  gi|386001258|ref|YP_005919557.1| 115 AWRAARAGARVLVGVRAELQEGRLHLSgraSGTMD 149
                                       7899*********9999999996666522267666 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   1.1e-06    0.0011      17      63 ..       7      52 ..       4      55 .. 0.92
   2 ?   -2.5   0.2       2.3   2.4e+03      21      40 ..     299     318 ..     297     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                      e +v++vGaG++G  aa + a+  + +v+++er+  +G  +  GG l
  gi|386001258|ref|YP_005919557.1|  7 EVEVAVVGAGPAGSVAAETAARL-GAEVVLIERKREIGSPVQCGGFL 52
                                      789***************99999.**************999999975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                       EEE--SHHHHHHHHHHHHCT CS
                              Thi4  21 vivGaGssGLtaayylakkp 40 
                                       ++vG+ ++G  aa+y++ + 
  gi|386001258|ref|YP_005919557.1| 299 AMVGGRAAGEVAARYIGGEA 318
                                       579999*********99765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   5.7   1.4e-05     0.015       2     295 ..      10     315 ..       9     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga..............leecvehsWs 63 
                                       v+v+GaGpAg   A+    a+ g +vvlie   ++  p +      e e+l++               e +v h+ +
  gi|386001258|ref|YP_005919557.1|  10 VAVVGAGPAGSVAAETA--ARLGAEVVLIERKREIGSPVQCgGFLPEIEELEGllpkakipealadlPEGLVLHRTR 84 
                                       89********6655555..****************999999999999999999999***999977755668999999 PP

                     Lycopene_cycl  64 gtivylddgkkillgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggr..kirarlvvda 138
                                         ++  + g++++ +   + + ++ + ++l+ r + +g++ l +  ++ +e      +  l+g    +++a +v+ a
  gi|386001258|ref|YP_005919557.1|  85 VQRICSPSGRSKEFSVLGRVIDRRSFDRHLAWRAARAGARVLVGVRAELQE-----GRLHLSGRAsgTMDAEVVIGA 156
                                       99999**********999999*************98888777664444444.....44466655556********** PP

                     Lycopene_cycl 139 rglaslk.karrlglQtfyGvevevdnppfdldkmv.lMDfrveqklkgltFlYalPldsdrllvEeT...elaskp 210
                                        g +s++ ++  l      Gv +e +    d+d +   M f ++  ++g++  +++Pl++d + v       +  + 
  gi|386001258|ref|YP_005919557.1| 157 DGPGSATaRGAGLAARGEVGVCLEYEMAGVDIDPAAaEMYFGTASAPGGYA--WIIPLGEDVANVGVGtrpPYLLGR 231
                                       **6666666677777788999999998888888654158888988888876..568999888877643112244444 PP

                     Lycopene_cycl 211 eLpadalkkrlaaylra.lglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapl 285
                                        L +++l + +++   a   l++ +v    +g++P   gg +p+++   vl +G aag+v  + G  ++ ++   + 
  gi|386001258|ref|YP_005919557.1| 232 GL-REVLDSFISEHPIAkEKLQEGSVTAVMRGLVPA--GGMPPAIQRGnVLLAGDAAGMVMATSGGGIPLAMVGGRA 305
                                       45.456777776554443889999999999******..999999987659999**********99999999988775 PP

                     Lycopene_cycl 286 lasaiaaalr 295
                                         ++ a++ +
  gi|386001258|ref|YP_005919557.1| 306 AGEVAARYIG 315
                                       5555555554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.1e-05     0.012       2      33 ..      10      41 ..       9      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      vav+GaG  G+  a+ +a+ g eVvl+++++e
  gi|386001258|ref|YP_005919557.1| 10 VAVVGAGPAGSVAAETAARLGAEVVLIERKRE 41
                                      9***************************9887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.9   1.3e-05     0.013       2      33 ..      10      43 ..       9      50 .. 0.93
   2 ?    4.6   1.0     0.019        20     103     207 ..      65     164 ..      46     309 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      v+++G+G +G+ +A  +ar g  V+l+e+++++g
  gi|386001258|ref|YP_005919557.1| 10 VAVVGAGPAGSVAAETAARLGaeVVLIERKREIG 43
                                      9****************999**********9998 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                                       HHHH..HHTTTTE.EEEEHHHHHHHSTTST.TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEE CS
                               DAO 103 lall..leaglda.elldaeevrelepalp.gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleee 175
                                       ++ +  l a+l++  +l + +v+++++  p g  +  f+  + ++d + + + la +a+++G+++l g +++ l  +
  gi|386001258|ref|YP_005919557.1|  65 AKIPeaL-ADLPEgLVLHRTRVQRICS--PsGRSKE-FSVLGRVIDRRSFDRHLAWRAARAGARVLVGVRAE-L--Q 134
                                       4444433.4444423688877888885..3232333.44444888***********************4443.4..3 PP

                                       ETCEEEEEEECTEEEEEEEEEEE--GGGHHHH CS
                               DAO 176 dgkvwgverttpgendaadavVnaaGawsdll 207
                                       +g+++     ++g+ da + v+ a G++s  +
  gi|386001258|ref|YP_005919557.1| 135 EGRLHLS-GRASGTMDA-EVVIGADGPGSATA 164
                                       4453322.333365333.66999999998643 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.8e-05      0.05      34      91 ..       5      64 ..       1      68 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                      GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC..EECSHHHHHHH CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv..elvsleellae 91
                                      l + +v+++G+G  G+ +a++++ +g++v+ ++r+++  + ++  g+  e ++le ll +
  gi|386001258|ref|YP_005919557.1|  5 LDEVEVAVVGAGPAGSVAAETAARLGAEVVLIERKREIGSPVQCGGFlpEIEELEGLLPK 64
                                      667899****************************98866644443433355566666655 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0045       4.7       1      37 [.      11      43 ..      11      47 .. 0.80
   2 ?    1.5   0.0      0.24   2.5e+02      89     121 ..     103     135 ..      69     164 .. 0.84
   3 ?    1.1   0.0      0.32   3.4e+02      95     121 ..     319     345 ..     307     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0045
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepg 37
                                      a+vGaGp+G  ++e  ++        e+ l+++ +e+g
  gi|386001258|ref|YP_005919557.1| 11 AVVGAGPAGSVAAETAARL-----GAEVVLIERkREIG 43
                                      89*********99999888.....58888888844445 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.24
                     NAD_binding_9  89 dfvpRalyGrYlrdlfeellarlpegvtvevhr 121
                                       +++ R+ + r+l+++++++ ar+  gv+ e+ +
  gi|386001258|ref|YP_005919557.1| 103 RVIDRRSFDRHLAWRAARAGARVLVGVRAELQE 135
                                       567899999999999999999987777766655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.32
                     NAD_binding_9  95 lyGrYlrdlfeellarlpegvtvevhr 121
                                        +++Y ++++ee+ ++l ++v+++ + 
  gi|386001258|ref|YP_005919557.1| 319 ALQEYPEWIAEEMGRELANSVRIREVV 345
                                       6789***************99999875 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   7.8e-05     0.082       2      33 ..      12      43 ..      11      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg.nig 33
                                      ++GaGPaG  aa ++ ++g  +++ +E++ +ig
  gi|386001258|ref|YP_005919557.1| 12 VVGAGPAGSVAAETAARLGA-EVVLIERKrEIG 43
                                      8*******************.6999**985665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2876.12
//
Query:       gi|386001259|ref|YP_005919558.1|  [L=673]
Description: Na+/solute symporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-29  103.3  34.5    1.9e-29  102.8  34.5    1.2  1  SSF       Sodium:solute symporter family
    5.6e-05   22.3  29.2    0.00011   21.3  29.2    1.5  1  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8  34.5   2.1e-33   1.9e-29       1     406 []      69     459 ..      69     459 .. 0.80

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 2.1e-33
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       ++lagr+++   +gls+aas + a+ ++   G+    G++ v++ +   ++ ll++  +a+r r+  a+T p++l+ 
  gi|386001259|ref|YP_005919558.1|  69 FWLAGREIGAANIGLSAAASWLTASALLLATGLFLYIGVGSVWVWVFPNVAGLLIIAGIAKRVRRIPAMTQPELLEI 145
                                       89********************************99****9999888888889999999****************** PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                       R++     +   a+++ + ++l    d++g    + + +G+    avll+a+++ +Y+ +GG++Avv+td +q +l 
  gi|386001259|ref|YP_005919558.1| 146 RYHPIV--RAPVAVAIAITMVLFAVTDFIGFKLVLATFFGVPPLYAVLLMAVAVSIYVSLGGFRAVVWTDAVQ-FLF 219
                                       **7654..444444555555555567***********************************************.556 PP

                               SSF 155 lvgalilliivllevGgleslveklkeaapkv.vdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakd 230
                                       l+g  + +   +l+  +  +   +l++a+ ++ +d  +   l +l   + al+l l+l+ G +  +   +++ a  d
  gi|386001259|ref|YP_005919558.1| 220 LAGVAVGVA--FLATRASVAGGITLAAASASLgSDWWN---LFILGGVTGALVLQLALLPGWVAEQDPWQKIWASRD 291
                                       666554333..333322222222233333322244433...33455579999************************* PP

                               SSF 231 akailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaims 307
                                        +a+++g++ + ++l++v++      + a +l g+ p  +g+   ++++ y + +++ lp +l +l+     Aa ms
  gi|386001259|ref|YP_005919558.1| 292 DRAARRGLILGAVLLAVVYLA---CLVAAVALRGIYPLPAGE--IEAEMLYLTFIQESLPGGLVALFAIGFAAASMS 363
                                       ******************999...566789999**9988886..5789******************988888899** PP

                               SSF 308 tltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlav 384
                                         ++   s++s +++D+ ++ +r + a+ ke++ + r +v+v+i++a ++a++ e+   +  v +a+ + +   +  
  gi|386001259|ref|YP_005919558.1| 364 CADTFATSGASCISRDIVQRHIRPQ-ASMKEMLVINRALVIVMIAIAAAVALHVESI--VEAVIIATVIGTTSYFFP 437
                                       *****************99877766.5666666666666666667777777766665..444444444444555555 PP

                               SSF 385 illalfwkrvneqGAlagliiG 406
                                       i+ +lfwkr+++ GAla++i+G
  gi|386001259|ref|YP_005919558.1| 438 IIGGLFWKRATRWGALAAVIVG 459
                                       678*****************99 PP

>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3  29.2   1.2e-08   0.00011      16     329 ..     110     429 ..     104     440 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-08
                             Nramp  16 lwvlllstllaillq.elsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAialnllfgipl 91 
                                       +wv ++ +++++l+   ++ r   +  ++ +el++ r+ + v++ +++++ + ++++ ++++iG  ++l ++fg+p 
  gi|386001259|ref|YP_005919558.1| 110 VWVWVFPNVAGLLIIaGIAKRVRRIPAMTQPELLEIRYHPIVRAPVAVAIAITMVLFAVTDFIGFKLVLATFFGVPP 186
                                       677777777776554145666777777888899999***************************************** PP

                             Nramp  92 lvgvlitavlvllllflekggyrkl...E..aliialvlvialsFiaelflvkpdwgevlkglvvPslpg.keslll 162
                                       l++vl++av v + +    gg+r +      +++++  ++++++F+a+ + v   ++ +++++    l +   +l++
  gi|386001259|ref|YP_005919558.1| 187 LYAVLLMAVAVSIYVS--LGGFRAVvwtDavQFLFLAGVAVGVAFLATRASVAGGITLAAASAS---LGSdWWNLFI 258
                                       **************99..6666654222311233333344558888888888877777777755...3333469*** PP

                             Nramp 163 avgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAa..vly..sggkdv 235
                                       + g+ Ga v   +l       q+ +++i +s+++   + +r   i+++++  ++ la l++a a   +y  + g + 
  gi|386001259|ref|YP_005919558.1| 259 LGGVTGALVLQLALLPGWVAEQDPWQKIWASRDD---RAARRGLILGAVLLAVVYLACLVAAVAlrGIYplPAG-E- 330
                                       *********9888877777777777666555555...9999999999999888888777655541156653222.3. PP

                             Nramp 236 esledaa.eaLepllGskaasvlFaigLlaaGlsStitgtlagqyvm.egflglrislwlrrlitralafvpalivi 310
                                        ++e ++   +++ l      +lFaig  aa++s + t +++g+  +  ++++ +i+++++  ++++l +  al+++
  gi|386001259|ref|YP_005919558.1| 331 IEAEMLYlTFIQESLP-GGLVALFAIGFAAASMSCADTFATSGASCIsRDIVQRHIRPQAS--MKEMLVINRALVIV 404
                                       3444444134455555.3799******************9999976625788777777433..36666666666555 PP

                             Nramp 311 lligaele......lvkllvlsqvl 329
                                       +++ a+ +      +v++ +++ v+
  gi|386001259|ref|YP_005919558.1| 405 MIAIAAAValhvesIVEAVIIATVI 429
                                       5555555512223345555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 4832.17
//
Query:       gi|386001260|ref|YP_005919559.1|  [L=548]
Description: Dihydroxy-acid dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.8e-211  701.6   0.8   6.6e-211  701.4   0.8    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  701.4   0.8  3.7e-215  6.6e-211       1     516 [.      31     544 ..      31     545 .. 0.97

  Alignments for each domain:
  == domain 1  score: 701.4 bits;  conditional E-value: 3.7e-215
                          ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmlea 77 
                                       +p+++++ns++e++p+h hl+++a+avk+g++ aggvp+ef+tig++Dgiamg++gm+ysLpsRe+i d++e+m+ea
  gi|386001260|ref|YP_005919559.1|  31 RPFVAVVNSWNEFIPGHIHLDKIAQAVKAGIRMAGGVPFEFHTIGICDGIAMGHRGMKYSLPSREIIEDTIEVMVEA 107
                                       7**************************************************************************** PP

                          ILVD_EDD  78 qllDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaa 152
                                       ++lD++vlis+CDKivPg+lmaa rl++Pai v+gGpm +g +   +ldl++vfe +++        e le le+ a
  gi|386001260|ref|YP_005919559.1| 108 HQLDGMVLISSCDKIVPGHLMAAGRLDLPAIAVTGGPMYPGFACdqELDLIDVFEGWQKG------GEVLEVLENLA 178
                                       ****************************************76333589999999999864......578999***** PP

                          ILVD_EDD 153 cpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvl 229
                                       cpgaGsC+g++TAntmacl+e+lGlslpg+a+++a +a+++++a+++g +ivel+e+ +++r+++t++++eNAi ++
  gi|386001260|ref|YP_005919559.1| 179 CPGAGSCAGLFTANTMACLTETLGLSLPGCATAHAADAKKMRIAKKSGLKIVELIERGITAREVVTRKSIENAIRMD 255
                                       ***************************************************************************** PP

                          ILVD_EDD 230 lalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvl 306
                                       +a+GGStN++lH++A+A+e++++++l+dfd+lsr++p+l++l+P g +++ dl+raGG+pav+k+L+++  lh+dvl
  gi|386001260|ref|YP_005919559.1| 256 MAIGGSTNTALHIPAVASEFEIDIDLEDFDRLSRETPHLVNLRPGGPHHIIDLERAGGIPAVMKRLQSK--LHRDVL 330
                                       *******************************************************************65..****** PP

                          ILVD_EDD 307 tvtgktlaenlee..aev...keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdsee 378
                                       tvtg+tl+e++++    +   +  +v+r+le+p+++egg+a+LkG+LapeG+vvK++av++e+++++g+A+v+dsee
  gi|386001260|ref|YP_005919559.1| 331 TVTGRTLGEEIAAfsP-AnpeTFAKVVRTLESPVHPEGGIAILKGSLAPEGSVVKQTAVSQEMRRHTGKAKVYDSEE 406
                                       ***********88641.2455889***************************************************** PP

                          ILVD_EDD 379 eaveailkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegG 455
                                       +a++ i+ g++ ag+vvviryeGPkGgpGm+E l+ptsa+ g glg++valitDGRfSG+++g++ighv+PEAa+gG
  gi|386001260|ref|YP_005919559.1| 407 DALAGIVGGEVVAGNVVVIRYEGPKGGPGMRETLSPTSAIQGIGLGNSVALITDGRFSGGTRGPCIGHVCPEAAVGG 483
                                       ***************************************************************************** PP

                          ILVD_EDD 456 pialvedGDiieidiekrtlelevseeelaaRraawkp.ekkvktrgllakyaklvssaseG 516
                                       pialvedGD i+idi++r+++l+v++ +++ Rr aw+p e+kv ++g+la+y+++v+sas+G
  gi|386001260|ref|YP_005919559.1| 484 PIALVEDGDEIRIDIDARRIDLLVDAGTIEGRRGAWRPpEPKV-AKGMLARYSRSVTSASRG 544
                                       *********************************99***55555.4***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3799.22
//
Query:       gi|386001261|ref|YP_005919560.1|  [L=198]
Description: 2'-5' RNA ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-26   92.4   0.1    1.6e-14   53.8   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
      4e-09   36.6   0.0    5.3e-09   36.2   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   1.8e-18   1.6e-14       1      87 []      24     103 ..      24     103 .. 0.95
   2 !   36.9   0.0   3.4e-13     3e-09      10      87 .]     109     187 ..     104     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.8e-18
                                       EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEE CS
                        LigT_PEase   1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglf 77 
                                       +++p +i++  ar++ae++     +g+++v p   HiTL+flg+v+++kv ++ eal+++  ++ +f+ +v+gvg+f
  gi|386001261|ref|YP_005919560.1|  24 VDLPGPIRDGMARVQAEIA----LPGVRLVNPGLIHITLKFLGDVPPSKVGRVDEALRRV--RRSSFTARVRGVGAF 94 
                                       678999*************....89***********************************..888************ PP

                                       EECCSCCEEE CS
                        LigT_PEase  78 psrlrprviy 87 
                                       p r + rv++
  gi|386001261|ref|YP_005919560.1|  95 PGR-SIRVVW 103
                                       986.788888 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 3.4e-13
                                       HHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCC CS
                        LigT_PEase  10 elarlaaeleralaklglkpv.rpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl.rpr 84 
                                       e + l++ +e+al  lg++ + r+f+ H T+a++    +e+ + l e+la + +++   e++v++++l +s+l +++
  gi|386001261|ref|YP_005919560.1| 109 EFEGLFSAVEEALVPLGFPREgRRFTSHATIARVARPGPETTALLAERLAPF-REIDLGEFRVEEFSLKKSTLtPGG 184
                                       56779999****************************9999888888888888.4666668***************** PP

                                       EEE CS
                        LigT_PEase  85 viy 87 
                                       +iy
  gi|386001261|ref|YP_005919560.1| 185 PIY 187
                                       **9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   5.9e-13   5.3e-09      26     145 ..      54     175 ..      39     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.9e-13
                   2_5_RNA_ligase2  26 pHitLlypfvededl.adlaellsrlaketepfevrldgfgvFehkks.vvylsvsdsealqalraallealpeagd 100
                                        HitL+++++ +++   +++e+l+r+    + f++r+ g+g F++++  vv++ +  + +++ l +a++eal + g 
  gi|386001261|ref|YP_005919560.1|  54 IHITLKFLGDVPPSKvGRVDEALRRVR--RSSFTARVRGVGAFPGRSIrVVWIGA--EGEFEGLFSAVEEALVPLGF 126
                                       6********999988899999999995..668*************7777******..99****************** PP

                   2_5_RNA_ligase2 101 kedsgeftPHlTiaqsadstsa..aellekl..aqalpplefevdeval 145
                                        ++ ++ft H+Tia+ a++ +   a l e+l   ++ +  ef+v+e++l
  gi|386001261|ref|YP_005919560.1| 127 PREGRRFTSHATIARVARPGPEttALLAERLapFREIDLGEFRVEEFSL 175
                                       **99*************99998664444555666777778899998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 1381.17
//
Query:       gi|386001262|ref|YP_005919561.1|  [L=451]
Description: CCA-adding enzyme [Methanosaeta harundinacea 6Ac]
Scores for 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  145.2   0.0    1.4e-42  144.5   0.0    1.3  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    8.4e-14   51.6   0.0    1.6e-13   50.7   0.0    1.5  1  NTP_transf_2     Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   0.0   1.6e-46   1.4e-42       1     113 []     135     245 ..     135     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 1.6e-46
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEET CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDP 77 
                                       dev llK+f+kg+gvYGsel++ GfsGYlaEllv++ygsf  vle  + w+p+ +idle++++  +++++plvv+DP
  gi|386001262|ref|YP_005919561.1| 135 DEVLLLKQFMKGVGVYGSELRIGGFSGYLAELLVIRYGSFVGVLEGSSLWRPGEAIDLEDHSS--RSHEDPLVVVDP 209
                                       89***********************************************************99..999********* PP

                                       TEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                   tRNA_NucTransf2  78 vDpkRNvaaalsleklaefilaareflkkpseefff 113
                                       vDp RNvaaal+l+++  f +a+r fl++ps+efff
  gi|386001262|ref|YP_005919561.1| 210 VDPGRNVAAALTLDRMFAFAAASRLFLREPSLEFFF 245
                                       ***********************************6 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.8e-17   1.6e-13       7      94 ..      24     121 ..      19     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.8e-17
                                       HHHHHTT.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH........HHHEHHHHHHHHCCCEEECTTEEEEE CS
                      NTP_transf_2   7 elkelep.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre........kkeegleklaeiikfleellglevdl 73 
                                       el +  + + ++vl+GS+arGt+l+g +D+D+++ +pe +s          + +e +e++ae+ +++ ++ g evd+
  gi|386001262|ref|YP_005919561.1|  24 ELMRAAGiGGEAVLVGSAARGTWLSGdHDLDVFIGVPEGSSLLpalevarlVAPEFEERYAEHAYVHALFEGFEVDI 100
                                       4444445599*****************************7776********888899******************** PP

                                       ECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  74 vtrekledpllvksileerpl 94 
                                       v+++ +ed + ++s+++++p+
  gi|386001262|ref|YP_005919561.1| 101 VPCYLVEDASEIISAVDRTPF 121
                                       *****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 3286.78
//
Query:       gi|386001263|ref|YP_005919562.1|  [L=340]
Description: Histone deacetylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-85  286.2   0.0    4.9e-85  285.7   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.7   0.0   2.8e-89   4.9e-85       1     305 [.      20     303 ..      20     305 .. 0.95

  Alignments for each domain:
  == domain 1  score: 285.7 bits;  conditional E-value: 2.8e-89
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hpe+++Rl+++le +++s gl   le l++p++at ee+++vHs+ Y+++++++s++ +                 l
  gi|386001263|ref|YP_005919562.1|  20 HPERKERLISALEMIRSS-GLE--LE-LVTPRPATLEEVRAVHSPGYIDQVRTISERGGGY---------------L 77 
                                       899999999999999887.764..44.599**********************999876655...............4 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrv 154
                                       d dt+vs ++++aal+a+g+v++++++v +g +++af+lvrPpgHHa +++ +GFC++Nnvai+++ +q+  +++rv
  gi|386001263|ref|YP_005919562.1|  78 DLDTVVSRRSYEAALMAAGGVITGIERVNDG-LENAFALVRPPGHHALPNRGMGFCIFNNVAIGARFAQR-MGMERV 152
                                       679**************************99.9***********************************99.899*** PP

                                       EEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 155 ailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                       +i+D+DvHhGnGt+++fy+d +v+++S+H++++  yPgtg +++lg + ++gf++nvpl+ gtgd+ y ++feeil+
  gi|386001263|ref|YP_005919562.1| 153 LIVDWDVHHGNGTSAIFYDDRSVMYFSTHQFPH--YPGTGRVKELGMDGAEGFTVNVPLPWGTGDSGYFAAFEEILK 227
                                       ******************************777..****************************************** PP

                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlealaravtavls 305
                                       p++ ef+Pd++lvsaG D ++ dpl+++nl+   ++++   ++e+ad++ + ++v+ leGGYnl+ala+++ avl+
  gi|386001263|ref|YP_005919562.1| 228 PLALEFDPDIVLVSAGQDPHQADPLSGMNLTCGAFGYMAAAVKEVADRCcGgRLVAALEGGYNLSALAESIVAVLR 303
                                       *************************************************999******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1984.54
//
Query:       gi|386001264|ref|YP_005919563.1|  [L=671]
Description: S-layer protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.5e-173  573.6  37.4    3.6e-87  291.7  15.4    2.0  2  S-layer       S-layer protein
    2.4e-08   33.7   0.9    4.3e-08   32.9   0.9    1.4  1  PGF-CTERM     PGF-CTERM motif
     0.0054   15.7   0.0       0.69    8.8   0.0    2.1  2  DAGAT         Diacylglycerol acyltransferase
  ------ inclusion threshold ------
      0.026   14.0   0.6        3.2    7.1   0.1    2.2  2  2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catal
      0.053   13.8   2.3        6.3    7.1   0.1    3.8  2  DUF2525       Protein of unknown function (DUF2525)
      0.057   13.6   0.1         19    5.5   0.0    3.2  2  PrcB_C        PrcB C-terminal
      0.061   13.3   2.6        1.3    8.9   0.2    2.9  2  DHOase        Dihydro-orotase-like
      0.061   13.3   8.0       0.37   10.8   1.5    2.7  2  DUF5004       Domain of unknown function (DUF5004)
          1    9.1   6.1        8.8    6.1   0.1    3.1  3  Amidase02_C   N-acetylmuramoyl-l-alanine amidase
        1.2    9.2   3.8         35    4.5   0.2    3.4  3  RNase_PH_C    3' exoribonuclease family, domain 2
        1.9    8.7   6.6        8.6    6.6   0.2    3.9  4  ZoocinA_TRD   Target recognition domain of lytic exoenzyme
        2.9    8.2   5.6        6.5    7.1   0.3    3.4  3  Myco_19_kDa   Mycobacterium 19 kDa lipoprotein antigen
        3.6    7.4  16.9        6.2    6.6  16.9    1.3  1  CT47          Cancer/testis gene family 47
        5.7    7.3   7.1        6.4    7.2   1.2    2.8  2  PDZ_2         PDZ domain


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 !  288.2  14.0   3.3e-89   4.3e-86       5     258 .]       5     267 ..       1     267 [. 0.96
   2 !  291.7  15.4   2.8e-90   3.6e-87       9     258 .]     304     562 ..     296     562 .. 0.96

  Alignments for each domain:
  == domain 1  score: 288.2 bits;  conditional E-value: 3.3e-89
                           S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfa 81 
                                       e+ + +tw +++F+gfyydidd++++Es+tl+++  +d   ++ +++Y+t +++kef+f++wg+Y++igfla++Yfa
  gi|386001264|ref|YP_005919563.1|   5 EDGKVVTWGPQEFAGFYYDIDDNIGTESITLTVT--GDALEKDTGVIYETAAQNKEFDFDDWGEYKTIGFLADEYFA 79 
                                       5667789*************************76..7999999********************************** PP

                           S-layer  82 gydnsa...etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskv 155
                                        y++ +   ++s+d++l++de+Lskvl+d+de++t++sg+ l+L+e+Yel i+ iD+dg+kv+++L+k g+ vds+v
  gi|386001264|ref|YP_005919563.1|  80 AYNEGThlaTESTDANLMKDEQLSKVLMDDDEDRTFTSGTPLKLAEDYELAIQAIDLDGNKVYVQLMKSGAVVDSAV 156
                                       **55555789999**************************************************************** PP

                           S-layer 156 issska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvse 227
                                       +++sk+     d tyvy+kdlgd++++v+iavh++++frg+e +l++i+gi+qisd ++++++++e++km+++sv+ 
  gi|386001264|ref|YP_005919563.1| 157 VEPSKTgatlkDMTYVYKKDLGDTKKIVVIAVHFKNAFRGAEVDLATIDGIWQISDAITDVSQDTEYDKMTIQSVNA 233
                                       ***9999********************************************************************98 PP

                           S-layer 228 n..eiemendds.itLsrdktieimddlkfkvaD 258
                                          +i+m+ndd+ itL++ k+i +m++l++k+aD
  gi|386001264|ref|YP_005919563.1| 234 AamTITMNNDDEkITLTKKKDILLMENLRIKTAD 267
                                       7669*****9988********************8 PP

  == domain 2  score: 291.7 bits;  conditional E-value: 2.8e-90
                           S-layer   9 eltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy.d 84 
                                       +++w+a++F+gfyydidd+l+ E+lt++++  +d   ++ +++Y+t+++ ++fe+e+wg+Y++igfla++Yfa y +
  gi|386001264|ref|YP_005919563.1| 304 TVEWDATTFAGFYYDIDDNLGREKLTMTIT--GDALEKDTGVIYETSAELNDFELEDWGQYRTIGFLADEYFAAYaE 378
                                       788*************************76..799999*************************************76 PP

                           S-layer  85 nsa..etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvisss 159
                                        s+  ++s+d++l++de+Lskvl+d+de+ t++sg+ l+L+e+Yel i+ iD+dg+kv+++L+k+g+ vds+v+++s
  gi|386001264|ref|YP_005919563.1| 379 GSFlaTESTDANLMKDEQLSKVLMDDDEDMTFYSGTPLKLAEDYELAIQAIDLDGNKVYVQLMKNGAVVDSAVVEPS 455
                                       666889999*******************************************************************9 PP

                           S-layer 160 ka.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsen..e 229
                                       k+     d+ty+y+kdlgd++++v+iavh++++frg++++l++++gi+qisd+v+++++++e++km++++v+    +
  gi|386001264|ref|YP_005919563.1| 456 KDgavtkDKTYIYKKDLGDTKKIVVIAVHFKNAFRGANQDLATVNGIWQISDTVTDVSQDTEYDKMTIQTVNGAtmT 532
                                       999********************************************************************987668 PP

                           S-layer 230 iemendds.itLsrdktieimddlkfkvaD 258
                                       i+m+ndd+ itLs+dk+i +m+++++k+aD
  gi|386001264|ref|YP_005919563.1| 533 ITMNNDDEkITLSKDKDILLMEKIRIKTAD 562
                                       9****9988********************8 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.9   3.3e-11   4.3e-08       1      23 []     647     669 ..     647     669 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.3e-11
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       +PGF+av+Al+GLLa+ +L+ R+
  gi|386001264|ref|YP_005919563.1| 647 IPGFEAVFALTGLLAVSYLVLRK 669
                                       7********************97 PP

>> DAGAT  Diacylglycerol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0094        12      85     170 ..     167     254 ..     116     260 .. 0.81
   2 !    8.8   0.0   0.00054      0.69      82     169 ..     459     548 ..     415     556 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0094
                             DAGAT  85 tdatgvkekfpgirfnlatLagqfrtpfrr...eillllGlievsresieyvLdkeekGravvlvvGGaeealeahp 158
                                        d t v++k  g   +++++a +f+ +fr    ++ ++ G+ ++s ++i+ v + +e  +  +  v  a+ ++ +++
  gi|386001264|ref|YP_005919563.1| 167 KDMTYVYKKDLGDTKKIVVIAVHFKNAFRGaevDLATIDGIWQIS-DAITDVSQDTEYDKMTIQSVNAAAMTITMNN 242
                                       4777888888888899************95322577888999988.678888888888899**************** PP

                             DAGAT 159 gketltLkkrkG 170
                                       + e++tL+k+k 
  gi|386001264|ref|YP_005919563.1| 243 DDEKITLTKKKD 254
                                       ********9985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00054
                             DAGAT  82 alatdatgvkekfpgirfnlatLagqfrtpfr...reillllGlievsresieyvLdkeekGravvlvvGGaeeale 155
                                       a++ d t +++k  g   +++++a +f+ +fr   +++ ++ G+ ++s ++++ v + +e  +  +  v Ga  ++ 
  gi|386001264|ref|YP_005919563.1| 459 AVTKDKTYIYKKDLGDTKKIVVIAVHFKNAFRganQDLATVNGIWQIS-DTVTDVSQDTEYDKMTIQTVNGATMTIT 534
                                       567788999999899999************98555689999****999.566666666666699999********** PP

                             DAGAT 156 ahpgketltLkkrk 169
                                       ++++ e++tL+k k
  gi|386001264|ref|YP_005919563.1| 535 MNNDDEKITLSKDK 548
                                       **********9977 PP

>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.012        15     101     154 ..     186     239 ..     171     241 .. 0.87
   2 ?    7.1   0.1    0.0025       3.2     118     154 ..     498     534 ..     462     536 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                                       EE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE CS
                      2-oxoacid_dh 101 vAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftis 154
                                       +Av+ ++    + +  a   ++++i+++++++++ +   k++ ++++ + +ti+
  gi|386001264|ref|YP_005919563.1| 186 IAVHFKNAFRGAEVDLATIDGIWQISDAITDVSQDTEYDKMTIQSVNAAAMTIT 239
                                       666666666667777788889*******************************98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                                       GG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE CS
                      2-oxoacid_dh 118 dkkslleiakelkelaekaregklkpedleggtftis 154
                                          ++++i++ ++++++ +   k++ + ++g+t+ti+
  gi|386001264|ref|YP_005919563.1| 498 TVNGIWQISDTVTDVSQDTEYDKMTIQTVNGATMTIT 534
                                       55689*******************************8 PP

>> DUF2525  Protein of unknown function (DUF2525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0049       6.3      13      51 ..      89     132 ..      83     136 .. 0.86
   2 ?    3.8   0.1     0.057        73      13      51 ..     384     427 ..     382     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0049
                           DUF2525  13 sesevqefidnddahrvtvdgreydtyr.....ELaeaFELDIr 51 
                                       +es+  + +++++ ++v +d  e +t++      Lae +EL I+
  gi|386001264|ref|YP_005919563.1|  89 TESTDANLMKDEQLSKVLMDDDEDRTFTsgtplKLAEDYELAIQ 132
                                       788888899*****************99555556*******996 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.057
                           DUF2525  13 sesevqefidnddahrvtvdgreydtyr.....ELaeaFELDIr 51 
                                       +es+  + +++++ ++v +d  e  t+       Lae +EL I+
  gi|386001264|ref|YP_005919563.1| 384 TESTDANLMKDEQLSKVLMDDDEDMTFYsgtplKLAEDYELAIQ 427
                                       6777777889999999999998888774233337*******986 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.036        46      13      34 ..     125     146 ..     120     166 .. 0.82
   2 ?    5.5   0.0     0.015        19      13      50 ..     420     466 ..     413     466 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
                            PrcB_C  13 gGYsievdkvyetenaiyvktt 34 
                                       ++Y + ++ + +++n++yv++ 
  gi|386001264|ref|YP_005919563.1| 125 EDYELAIQAIDLDGNKVYVQLM 146
                                       79*****************986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                            PrcB_C  13 gGYsievdkvyetenaiyvkt.........tllgPepgeevtqalty 50 
                                       ++Y + ++ + +++n++yv++          + +P+++  vt+  ty
  gi|386001264|ref|YP_005919563.1| 420 EDYELAIQAIDLDGNKVYVQLmkngavvdsAVVEPSKDGAVTKDKTY 466
                                       78999*************99955555555555566666666666555 PP

>> DHOase  Dihydro-orotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2     0.001       1.3      48      97 ..      73     122 ..      44     151 .. 0.88
   2 ?    3.3   0.1     0.055        70      49      97 ..     369     417 ..     342     462 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                            DHOase  48 dseeafiltddtvyvtiqllefeglkkaeLdqalkaiaeDDevtnqsavq 97 
                                        ++e f++ +++  +  ++ +++ +k ++L+++l +  eD + t++++ +
  gi|386001264|ref|YP_005919563.1|  73 LADEYFAAYNEGTHLATESTDANLMKDEQLSKVLMDDDEDRTFTSGTPLK 122
                                       57899*****************************************9875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.055
                            DHOase  49 seeafiltddtvyvtiqllefeglkkaeLdqalkaiaeDDevtnqsavq 97 
                                       ++e f++  ++ ++  ++ +++ +k ++L+++l +  eD +  ++++ +
  gi|386001264|ref|YP_005919563.1| 369 ADEYFAAYAEGSFLATESTDANLMKDEQLSKVLMDDDEDMTFYSGTPLK 417
                                       678999999999***********************99999998888764 PP

>> DUF5004  Domain of unknown function (DUF5004)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.6     0.014        18      21      66 ..     203     252 ..     195     267 .. 0.80
   2 ?   10.8   1.5   0.00029      0.37      21      68 ..     498     549 ..     487     562 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                           DUF5004  21 klsGeWql....tkltrndeldltddeednetdLfeqfdfkdfkitFneD 66 
                                        ++G Wq+    t + +++e d+ + +  n  +++  ++ +d kit+ + 
  gi|386001264|ref|YP_005919563.1| 203 TIDGIWQIsdaiTDVSQDTEYDKMTIQSVNAAAMTITMNNDDEKITLTKK 252
                                       58999997222245677889999999999999999999999999998664 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00029
                           DUF5004  21 klsGeWql....tkltrndeldltddeednetdLfeqfdfkdfkitFneDrs 68 
                                        ++G Wq+    t + +++e d+ + ++ n+  ++  ++ +d kit+++D+ 
  gi|386001264|ref|YP_005919563.1| 498 TVNGIWQIsdtvTDVSQDTEYDKMTIQTVNGATMTITMNNDDEKITLSKDKD 549
                                       6899999722224577899*******************************86 PP

>> Amidase02_C  N-acetylmuramoyl-l-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0069       8.8      18      32 ..     213     227 ..     210     228 .. 0.94
   2 ?   -2.2   0.1       2.7   3.5e+03      10      29 ..     337     357 ..     331     362 .. 0.70
   3 ?    4.8   0.2     0.017        22      19      32 ..     509     522 ..     507     523 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0069
                       Amidase02_C  18 fiTeptsdteLdkit 32 
                                       +iT++ +dte dk+t
  gi|386001264|ref|YP_005919563.1| 213 AITDVSQDTEYDKMT 227
                                       69************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                       Amidase02_C  10 lqpd.GltYfiTeptsdteLd 29 
                                       l++d G+ Y  +  + d eL+
  gi|386001264|ref|YP_005919563.1| 337 LEKDtGVIYETSAELNDFELE 357
                                       355669999888888887776 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.017
                       Amidase02_C  19 iTeptsdteLdkit 32 
                                       +T++ +dte dk+t
  gi|386001264|ref|YP_005919563.1| 509 VTDVSQDTEYDKMT 522
                                       8************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.9   8.9e+03      36      48 ..     137     149 ..     126     154 .. 0.78
   2 ?    3.7   0.1     0.051        65      27      46 ..     232     251 ..     213     263 .. 0.84
   3 ?    4.5   0.2     0.027        35      28      46 ..     528     546 ..     509     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.9
                                       ETTSEEEEEEEEC CS
                        RNase_PH_C  36 agtkevvtlmkeg 48 
                                       +g+k  v+lmk+g
  gi|386001264|ref|YP_005919563.1| 137 DGNKVYVQLMKSG 149
                                       6778778888887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.051
                                       SSEEEEEEEETTSEEEEEEE CS
                        RNase_PH_C  27 segdltlavagtkevvtlmk 46 
                                         + +t+++++++e++tl k
  gi|386001264|ref|YP_005919563.1| 232 NAAAMTITMNNDDEKITLTK 251
                                       5579***********99965 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.027
                                       SEEEEEEEETTSEEEEEEE CS
                        RNase_PH_C  28 egdltlavagtkevvtlmk 46 
                                        + +t+++++++e++tl+k
  gi|386001264|ref|YP_005919563.1| 528 GATMTITMNNDDEKITLSK 546
                                       469*************987 PP

>> ZoocinA_TRD  Target recognition domain of lytic exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.4   1.8e+03      40      60 ..     131     151 ..     128     186 .. 0.72
   2 ?    1.7   0.0      0.22   2.8e+02       8      30 ..     200     221 ..     194     269 .. 0.72
   3 ?    0.4   0.1      0.54   6.9e+02      40      91 ..     426     475 ..     422     490 .. 0.68
   4 ?    6.6   0.2    0.0067       8.6       7      28 ..     494     514 ..     486     540 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                       ZoocinA_TRD  40 idkvdanGnliadqvlkvGdy 60 
                                       i  +d +Gn +  q +k G  
  gi|386001264|ref|YP_005919563.1| 131 IQAIDLDGNKVYVQLMKSGAV 151
                                       78899**********999963 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.22
                       ZoocinA_TRD   8 dlkvvnGvWqvkndvlvpvdfdW 30 
                                       dl +++G+Wq+  d +++v  d 
  gi|386001264|ref|YP_005919563.1| 200 DLATIDGIWQIS-DAITDVSQDT 221
                                       68999*****96.4555554443 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.54
                       ZoocinA_TRD  40 idkvdanGnliadqvlkvGdyfvfnPksvlsveepiygvaGltfakvkfaeg 91 
                                       i  +d +Gn +  q +k G   v + + v+  ++++++   +++ k  + ++
  gi|386001264|ref|YP_005919563.1| 426 IQAIDLDGNKVYVQLMKNGA--VVDSAVVEPSKDGAVTKDKTYIYKKDLGDT 475
                                       7899*************996..445555555555545444555555555555 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0067
                       ZoocinA_TRD   7 ddlkvvnGvWqvkndvlvpvdf 28 
                                       +dl +vnG+Wq+  d++++v  
  gi|386001264|ref|YP_005919563.1| 494 QDLATVNGIWQIS-DTVTDVSQ 514
                                       6899*******96.55555444 PP

>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.25   3.2e+02      47      85 ..     214     253 ..     196     256 .. 0.75
   2 ?   -2.3   0.1         4   5.1e+03      86      99 ..     289     302 ..     286     312 .. 0.79
   3 ?    7.1   0.3    0.0051       6.5      46      85 ..     508     548 ..     491     551 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.25
                       Myco_19_kDa  47 lt.dgdeptvesvgigdvdGftltyaegtgggsaevtkdg 85 
                                       +t  +++ + ++++i+ v+  ++t++ +++ +++++tk+ 
  gi|386001264|ref|YP_005919563.1| 214 ITdVSQDTEYDKMTIQSVNAAAMTITMNNDDEKITLTKKK 253
                                       4434566778888888888888888888888889998875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                       Myco_19_kDa  86 ntYtitGtaegads 99 
                                        tY+i G+++   +
  gi|386001264|ref|YP_005919563.1| 289 GTYEIRGNVQDLGM 302
                                       59******987766 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0051
                       Myco_19_kDa  46 vlt.dgdeptvesvgigdvdGftltyaegtgggsaevtkdg 85 
                                       ++t  +++ + ++++i++v+G t+t++ +++ ++++++kd 
  gi|386001264|ref|YP_005919563.1| 508 TVTdVSQDTEYDKMTIQTVNGATMTITMNNDDEKITLSKDK 548
                                       566457888999******************9999**99997 PP

>> CT47  Cancer/testis gene family 47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  16.9    0.0049       6.2     190     244 ..     588     642 ..     537     651 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0049
                              CT47 190 eeaasv....eEpaveadlaem..aeEpaeeaaeeeaaeeaaeeaaaeElaaeaaEEPale 244
                                       eeaa +    + pave+  ae   aeEpa ea   + +e  aee+aaeE a    EEPa+e
  gi|386001264|ref|YP_005919563.1| 588 EEAAPApveaPAPAVEEPVAEEpvAEEPAAEAP--AVEEPVAEEPAAEEHA----EEPAAE 642
                                       222211111133333333333333333333333..2334444444444444....444443 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.18   2.3e+02      10      77 ..     177     248 ..     160     253 .. 0.69
   2 ?    7.2   1.2     0.005       6.4      10      78 ..     472     544 ..     454     545 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                                       ---..-EEEEEE-TTSGGGGT...--TT-EEEEETT..B--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEE CS
                             PDZ_2  10 eedtggvlvvsVkeggPaakag..lkagDvilkvdg..kkvksledlislllkkkpGdtVkltvlRdgkkkt 77 
                                       + dt++++v+ V+ ++ + +a   l++ D i ++ +  ++v+++++ +++  +  +    ++t+  d++k t
  gi|386001264|ref|YP_005919563.1| 177 LGDTKKIVVIAVHFKNAFRGAEvdLATIDGIWQISDaiTDVSQDTEYDKMTIQSVNAAAMTITMNNDDEKIT 248
                                       334999************999866777888888887333555555555666666666666666666666655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.005
                                       ---..-EEEEEE-TTSGGGGT...--TT-EEEEETTB--..SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEE CS
                             PDZ_2  10 eedtggvlvvsVkeggPaakag..lkagDvilkvdgkkv..ksledlislllkkkpGdtVkltvlRdgkkktv 78 
                                       + dt++++v+ V+ ++ + +a+  l++   i ++ +++   +++++ +++  ++ +G t ++t+  d++k t+
  gi|386001264|ref|YP_005919563.1| 472 LGDTKKIVVIAVHFKNAFRGANqdLATVNGIWQISDTVTdvSQDTEYDKMTIQTVNGATMTITMNNDDEKITL 544
                                       344899************999888************8773366666667777****************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4292.36
//
Query:       gi|386001265|ref|YP_005919564.1|  [L=336]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-18   67.3   0.0    2.9e-18   66.8   0.0    1.3  1  Radical_SAM     Radical SAM superfamily
     0.0029   17.9   0.0     0.0065   16.7   0.0    1.5  1  Fer4_12         4Fe-4S single cluster domain
     0.0034   17.1   1.2       0.23   11.3   0.0    2.7  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.023   14.1   5.9          1    8.9   0.1    3.1  3  zf-ribbon_3     zinc-ribbon domain
      0.029   14.3   8.7         12    5.9   0.0    5.2  6  zinc_ribbon_4   zinc-ribbon domain
      0.036   14.1   0.1      0.036   14.1   0.1    3.0  3  DZR             Double zinc ribbon
      0.057   13.5   2.7        5.5    7.1   0.1    2.8  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.079   12.3   1.6       0.11   11.8   0.5    1.9  2  zf-TFIIB        Transcription factor zinc-finger
       0.14   11.5   0.0       0.27   10.5   0.0    1.4  1  CcmH            Cytochrome C biogenesis protein
       0.52   10.5   0.1       0.52   10.5   0.1    3.9  4  Zn-ribbon_8     Zinc ribbon domain
        1.1    9.4   5.0        3.8    7.6   0.0    3.2  3  ADK_lid         Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   1.8e-21   2.9e-18       3     166 ..      81     239 ..      79     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.8e-21
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                        t gCn+rC +C++        ++   rg+ + +e++++e+ ++     ++ v  +  ep+   +++ ++ rla+  
  gi|386001265|ref|YP_005919564.1|  81 ATVGCNFRCLHCQNADIsqipaEGGAIRGERVEPERVVAEALSAG----CRSVAYTYTEPTIFFEYALDVSRLAAD- 152
                                       689************99************************9998....***************************. PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                        +g+++++++ng++  ee  +++ ++  d ++++l+  d + ++k + +   ++ v++++e++  +gi  v +++++
  gi|386001265|ref|YP_005919564.1| 153 -RGLKNVFVSNGYMS-EEATRTIEPYL-DAINVDLKGNDGF-YRKVC-G-ARLDPVKRTIELMWGLGIW-VEVTTLV 222
                                       .8************8.*********99.*************.*****.4.89*****************.9****** PP

                                       BTTTSH..HHHHHHHHH CS
                                       xxxxxx..xxxxxxxxx RF
                       Radical_SAM 152 lpGend..eeleellel 166
                                       +pG+nd  e+l+e++e+
  gi|386001265|ref|YP_005919564.1| 223 IPGYNDsdEDLREIAEF 239
                                       *****955666666666 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     4e-06    0.0065       8     117 ..      78     186 ..      72     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfk.sgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                       +s+ + gCn++C  C n ++ +   +g  +   +   e++++++     + + ++  EP      e  l++ +    
  gi|386001265|ref|YP_005919564.1|  78 YSIATVGCNFRCLHCQNADISQIPaEGGAIRgeRVEPERVVAEALSAGCRSVAYTYTEPTI--FFEYALDVSRLAAD 152
                                       677889************9986542555554324455788888889999************..88999********* PP

                           Fer4_12  82 ekpekdiwlytgytleelskkekeellkeidvlvdG 117
                                       +++ k++++++gy+ ee +++  e+ l+ i+v ++G
  gi|386001265|ref|YP_005919564.1| 153 RGL-KNVFVSNGYMSEEATRT-IEPYLDAINVDLKG 186
                                       **9.79************986.99999999998877 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00014      0.23       3      16 ..     299     312 ..     297     314 .. 0.89
   2 ?    3.5   0.6     0.039        63       2       9 ..     323     330 ..     322     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       E-SSS--EEEEEE- CS
                    zf-C4_Topoisom   3 kCPkCggdLvlkrg 16 
                                       +CP+Cg+ Lv++ g
  gi|386001265|ref|YP_005919564.1| 299 TCPACGETLVERFG 312
                                       8**********976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.039
                                       EE-SSS-- CS
                    zf-C4_Topoisom   2 ekCPkCgg 9  
                                       + CP+Cg+
  gi|386001265|ref|YP_005919564.1| 323 GRCPSCGE 330
                                       78*****5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.6   4.2e+03       8      11 ..     195     199 ..     194     201 .. 0.56
   2 ?    8.9   0.1   0.00061         1       3      12 ..     298     308 ..     295     310 .. 0.74
   3 ?    6.2   1.0    0.0044       7.2       4      11 ..     324     332 ..     324     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                       zf-ribbon_3   8 CGa.p 11 
                                       CGa +
  gi|386001265|ref|YP_005919564.1| 195 CGArL 199
                                       66633 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00061
                       zf-ribbon_3   3 vrCPnCGa.pl 12 
                                       ++CP+CG+ ++
  gi|386001265|ref|YP_005919564.1| 298 TTCPACGEtLV 308
                                       68999998666 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0044
                       zf-ribbon_3   4 rCPnCGa.p 11 
                                       rCP+CG+ +
  gi|386001265|ref|YP_005919564.1| 324 RCPSCGEgI 332
                                       799999755 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.016        25      22      33 ..      14      25 ..      12      26 .. 0.89
   2 ?    0.9   0.7      0.27   4.4e+02      25      33 ..      86      94 ..      80      95 .. 0.77
   3 ?   -2.5   0.0       3.1     5e+03      17      27 ..      98     108 ..      96     108 .. 0.85
   4 ?   -1.4   0.0       1.5   2.4e+03      11      23 ..     141     153 ..     140     156 .. 0.79
   5 ?    5.9   0.0    0.0077        12      19      34 ..     291     306 ..     286     308 .. 0.83
   6 ?    2.5   0.1     0.085   1.4e+02      27      32 ..     324     329 ..     315     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                     zinc_ribbon_4 22 kgvkvrCskCgh 33
                                      +g+ vrC  C+h
  gi|386001265|ref|YP_005919564.1| 14 DGGAVRCGLCNH 25
                                      5899******99 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                     zinc_ribbon_4 25 kvrCskCgh 33
                                      + rC +C++
  gi|386001265|ref|YP_005919564.1| 86 NFRCLHCQN 94
                                      679999987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.1
                     zinc_ribbon_4  17 eklpakgvkvr 27 
                                       +++pa+g+ +r
  gi|386001265|ref|YP_005919564.1|  98 SQIPAEGGAIR 108
                                       79****99987 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.5
                     zinc_ribbon_4  11 kyeiddeklpakg 23 
                                       +y++d ++l+a++
  gi|386001265|ref|YP_005919564.1| 141 EYALDVSRLAADR 153
                                       7*******99665 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0077
                     zinc_ribbon_4  19 lpakgvkvrCskCghv 34 
                                       +p++g + +C++Cg++
  gi|386001265|ref|YP_005919564.1| 291 IPGEGENTTCPACGET 306
                                       8899999999999976 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.085
                     zinc_ribbon_4  27 rCskCg 32 
                                       rC+ Cg
  gi|386001265|ref|YP_005919564.1| 324 RCPSCG 329
                                       566665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   3.7       6.2     1e+04      29      35 ..      87      93 ..      12      99 .. 0.60
   2 ?   -1.5   0.0       1.6   2.6e+03      17      25 ..     194     202 ..     191     212 .. 0.78
   3 ?   14.1   0.1   2.2e-05     0.036      11      36 ..     296     330 ..     291     334 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                               DZR 29 drCpsCg 35
                                       rC +C+
  gi|386001265|ref|YP_005919564.1| 87 FRCLHCQ 93
                                      3555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                               DZR  17 eCgtklkav 25 
                                        Cg++l++v
  gi|386001265|ref|YP_005919564.1| 194 VCGARLDPV 202
                                       588888765 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.2e-05
                               DZR  11 darfCseCgtklkavaa...........edrCpsCge 36 
                                       ++ +C++Cg++l +  +             rCpsCge
  gi|386001265|ref|YP_005919564.1| 296 ENTTCPACGETLVE--RfgfrvarngivDGRCPSCGE 330
                                       5679*******974..34599999***99******98 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0034       5.5       2      11 ..     298     307 ..     298     310 .. 0.86
   2 ?    5.6   0.4     0.011        17       3      11 ..     324     332 ..     324     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0034
                            zf-ACC   2 tKCpsCgeml 11 
                                       t Cp+Cge+l
  gi|386001265|ref|YP_005919564.1| 298 TTCPACGETL 307
                                       68******98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                            zf-ACC   3 KCpsCgeml 11 
                                       +CpsCge +
  gi|386001265|ref|YP_005919564.1| 324 RCPSCGEGI 332
                                       6*****975 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       5.6   9.2e+03      27      32 ..     213     218 ..     213     221 .. 0.75
   2 ?   11.8   0.5   6.7e-05      0.11       2      26 ..     300     329 ..     299     336 .] 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.6
                          zf-TFIIB  27 GvWldr 32 
                                       G+W++ 
  gi|386001265|ref|YP_005919564.1| 213 GIWVEV 218
                                       9**975 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.7e-05
                          zf-TFIIB   2 CPkCqdele.....eserggveidyCpqCr 26 
                                       CP+C+ +l+      + r+g+   +Cp+C+
  gi|386001265|ref|YP_005919564.1| 300 CPACGETLVerfgfRVARNGIVDGRCPSCG 329
                                       *********888777778***********7 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.27      15      48 ..      66      99 ..      53     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                      GGGS--SSHHHHHHHHHHHHHEE-TTSSS-BTTT CS
                              CcmH 15 eedeelkdpaqeararalseeLRClvCqnqsiad 48
                                      ++ +++   ++  ++ ++  ++RCl Cqn +i++
  gi|386001265|ref|YP_005919564.1| 66 KPLYHFMPGHLSYSIATVGCNFRCLHCQNADISQ 99
                                      555666666667777888999**********987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.1         6   9.7e+03       7      13 ..      19      25 ..      18      30 .. 0.81
   2 ?    0.1   0.1      0.56   9.1e+02       6      13 ..      87      94 ..      86     100 .. 0.83
   3 ?   10.5   0.1   0.00032      0.52      23      38 ..     294     310 ..     289     311 .. 0.78
   4 ?    2.9   0.1     0.075   1.2e+02      28      34 ..     324     330 ..     315     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6
                       Zn-ribbon_8  7 rCeeCgh 13
                                      rC  C+h
  gi|386001265|ref|YP_005919564.1| 19 RCGLCNH 25
                                      8999996 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.56
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      +rC  C++
  gi|386001265|ref|YP_005919564.1| 87 FRCLHCQN 94
                                      89999984 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00032
                       Zn-ribbon_8  23 dapltaCPeCgs.evrr 38 
                                       + ++t+CP+Cg+  v+r
  gi|386001265|ref|YP_005919564.1| 294 EGENTTCPACGEtLVER 310
                                       667899******66665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.075
                       Zn-ribbon_8  28 aCPeCgs 34 
                                        CP+Cg+
  gi|386001265|ref|YP_005919564.1| 324 RCPSCGE 330
                                       4888885 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.5       0.9   1.5e+03      11      24 ..      24      37 ..      18      39 .. 0.69
   2 ?    7.6   0.0    0.0023       3.8      20      34 ..     296     310 ..     257     311 .. 0.83
   3 ?    2.0   0.2      0.13   2.1e+02      20      29 ..     321     330 ..     317     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.9
                                      EETTTB--SSTTB- CS
                           ADK_lid 11 YhvvfnpPkveglC 24
                                       h   ++P + g+C
  gi|386001265|ref|YP_005919564.1| 24 NHFCRIKPEKRGIC 37
                                      46444899999999 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0023
                                       STTB-TTT--.-B-- CS
                           ADK_lid  20 veglCDkCGepLvqR 34 
                                       ++  C  CGe+Lv R
  gi|386001265|ref|YP_005919564.1| 296 ENTTCPACGETLVER 310
                                       6778999****9988 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.13
                                       STTB-TTT-- CS
                           ADK_lid  20 veglCDkCGe 29 
                                       v+g C  CGe
  gi|386001265|ref|YP_005919564.1| 321 VDGRCPSCGE 330
                                       5778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 2316.20
//
Query:       gi|386001266|ref|YP_005919565.1|  [L=421]
Description: Thiamine biosynthesis protein ThiC [Methanosaeta harundinacea 6Ac]
Scores for complete 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-142  475.3   0.0   1.8e-142  475.1   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.1   0.0  9.8e-147  1.8e-142       3     417 ..      10     417 ..       8     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 475.1 bits;  conditional E-value: 9.8e-147
                      ThiC_Rad_SAM   3 leaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEve 79 
                                       l+aa +gi  +++++va +e+++p ++ + va+Gr+vi+++  ++  p++iG+glrtkvnan+Gtsad  d + Eve
  gi|386001266|ref|YP_005919565.1|  10 LQAAIRGIEPPAVRMVAGAEGLSPAVLLKLVAAGRAVIMQRDGKP--PLGIGEGLRTKVNANVGTSADLIDPDGEVE 84 
                                       68999**********************************988765..9***************************** PP

                      ThiC_Rad_SAM  80 KlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdflt 156
                                       K+ +a+k+gadtv dLs+gg idei ++i e+++vp++tvpiYqa++ ++++++++t  e+l++i++q+  G + + 
  gi|386001266|ref|YP_005919565.1|  85 KAMAAEKYGADTVTDLSMGGPIDEIFRRIKEATSVPLTTVPIYQAVA-EKGSFSSITGGEILRTIRKQIGAGASSVV 160
                                       **********************************************9.569************************** PP

                      ThiC_Rad_SAM 157 iHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatd 233
                                       +Ha++tle+l  lk++kR++g+vS+gGs+++awml++++enp++++fde++ +l+e d +lSlg+++R+G+i+D +d
  gi|386001266|ref|YP_005919565.1| 161 VHAAITLEMLVDLKRSKRIMGVVSKGGSFTSAWMLQKGEENPFLSHFDEICGVLAERDAVLSLGNTMRSGCISDPMD 237
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 234 eaqlaelivlgelvkrareagvqvmveG.PGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGa 309
                                       ++q+ae++++++l+kra++ gvqv+veG  GHv+ d+i + v l k+ ++  P++v Gpl++Di++gYDhi++++G+
  gi|386001266|ref|YP_005919565.1| 238 AVQVAEMEMNADLAKRANDLGVQVIVEGmGGHVRPDRIPEYVALYKRRTSFRPLFVAGPLPIDIGVGYDHISGSVGG 314
                                       ****************************889********************************************** PP

                      ThiC_Rad_SAM 310 alaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldp 386
                                       a+aa aGad+lCy+tp+EHl+lPd+ +v+eGv+a+kiaah++d++k     r +d+ l+++R+  dwe+qf+la+d 
  gi|386001266|ref|YP_005919565.1| 315 AMAAGAGADYLCYITPSEHLALPDVGQVREGVVAFKIAAHIGDTMKYG--PRLEDEMLARYRRVRDWENQFKLAIDA 389
                                       **********************************************95..5689*********************** PP

                      ThiC_Rad_SAM 387 ekareireeklpeeeeaCsmCgekCavkive 417
                                       ++a eir++     ++ C+mCg++Ca+ i+e
  gi|386001266|ref|YP_005919565.1| 390 DRAMEIRSRGG---TDGCTMCGKYCAIAIME 417
                                       *******9876...79***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 3091.84
//
Query:       gi|386001267|ref|YP_005919566.1|  [L=218]
Description: Sulfite reductase, assimilatory-type [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-31  107.6   0.0    6.7e-31  106.9   0.0    1.3  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    2.8e-13   49.5   0.0    4.8e-13   48.7   0.0    1.4  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   7.5e-35   6.7e-31       4     151 ..      86     217 ..      83     218 .] 0.96

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 7.5e-35
                                       SCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   4 nlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeig 80 
                                       ++r+v++cpg+++c+  l D+  +  +++    ++y+ +++P KfKi vsgcpn c++  ++D+gl+g+ k     g
  gi|386001267|ref|YP_005919566.1|  86 CVRSVKICPGTTFCKRGLQDSVGVGLKLD----EKYHGMEMPSKFKIGVSGCPNSCAEPAVKDLGLMGTAK-----G 153
                                       89***************************....**************************************.....* PP

                                       EEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  81 fnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv 151
                                       +++lvGG++ r+++ +  +a    + +ee l++ve+++ +y+      n +k+Rl++++e++G+ekF+ +v
  gi|386001267|ref|YP_005919566.1| 154 WTVLVGGNAARKPRLGVVLA--EALSDEEALALVEKVIGYYK-----ANAEKQRLGEFIEEIGFEKFKGAV 217
                                       ********************..5788888*************.....99******************9776 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   5.4e-17   4.8e-13       3      66 ..      13      75 ..      11      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 5.4e-17
                      NIR_SIR_ferr  3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66
                                      q+d+++y ++  ++ +G+i+++ l+++a++aeky    +++T+ Q + + g+++edl+  +++L
  gi|386001267|ref|YP_005919566.1| 13 QRDKETY-AIAPHIAGGIIDPASLKRIAEVAEKYKAAALKITSAQRIAIVGLKPEDLDGAWADL 75
                                      8998887.*****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1557.45
//
Query:       gi|386001268|ref|YP_005919567.1|  [L=278]
Description: Thymidylate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-68  230.6   0.0    1.8e-68  230.4   0.0    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.4   0.0     1e-72   1.8e-68       1     219 [.       4     255 ..       4     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 230.4 bits;  conditional E-value: 1e-72
                            DUF166   1 lvltsgeyGervvenilnepdfersl.................ivavvevpe..eldefiedpeelLpe.lkeaDiv 57 
                                       +vl++ge+G+++++n+ n + f++s+                 ++ v+e+p+   l++fi+d++ ++p+ ++eaDi+
  gi|386001268|ref|YP_005919567.1|   4 VVLYNGEFGRTLIGNLINFSGFCISCgdgctlckagkyslaedLLSVIEMPDpeGLEDFIDDVSPYIPAeIPEADIA 80 
                                       69*****************************************999999999989*************99******* PP

                            DUF166  58 iaytlhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCslee.egkpkideFle 130
                                       i + +hpD+ + l+ ++kek++k +i ++e pk    glr +l e++ ++g+e+a+ kpfC+l++ +  p i++F++
  gi|386001268|ref|YP_005919567.1|  81 IVVHVHPDIIFGLLSILKEKGYKGIIGGSEMPKdlpLGLRTQLAEEARRMGLEAAFAKPFCALRPdPATPAINAFMQ 157
                                       ***********************************99****************************99********** PP

                            DUF166 131 e..fGkPelevevk.....dgkikkVeVlrsapCGstwyvakklkGkeveeaeeka..geahqsYpClAsmerdfel 198
                                       +  fG+Pe+e+  +     +++i   +V+rsapCGstwyvak++ G e ++ ++++  +eah++YpC+Asme+d+el
  gi|386001268|ref|YP_005919567.1| 158 KahFGEPEIEIVAQesrpgKETILAANVVRSAPCGSTWYVAKRMAGLETDQPDLREriAEAHHAYPCTASMEQDPEL 234
                                       99*********998555433445899***********************977666666******************* PP

                            DUF166 199 ketklhkAgyihkeavekAlk 219
                                       k+t+lh+Agyi++eave+A+k
  gi|386001268|ref|YP_005919567.1| 235 KDTILHRAGYIIREAVEDAIK 255
                                       *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1972.09
//
Query:       gi|386001269|ref|YP_005919568.1|  [L=119]
Description: HxlR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-23   81.0   0.4    5.5e-23   80.6   0.4    1.1  1  HxlR          HxlR-like helix-turn-helix
    0.00025   21.0   0.1    0.00037   20.5   0.1    1.3  1  HTH_20        Helix-turn-helix domain
    0.00057   19.7   0.2     0.0014   18.5   0.1    1.7  1  MarR_2        MarR family
     0.0018   18.4   0.0      0.002   18.2   0.0    1.1  1  Replic_Relax  Replication-relaxation
     0.0027   17.2   0.1     0.0055   16.2   0.1    1.6  1  HTH_24        Winged helix-turn-helix DNA-binding
     0.0053   16.9   0.0     0.0075   16.4   0.0    1.2  1  HTH_34        Winged helix DNA-binding domain
     0.0086   16.0   0.0      0.012   15.5   0.0    1.4  1  PadR          Transcriptional regulator PadR-like family
     0.0097   15.6   0.0      0.012   15.4   0.0    1.1  1  DUF4423       Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.037   14.0   0.0    1.5  1  HTH_45        Winged helix-turn-helix
      0.023   14.6   0.1      0.051   13.6   0.1    1.7  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.037   12.4   0.0      0.037   12.4   0.0    1.0  1  DUF505        Protein of unknown function (DUF505)
      0.047   13.6   0.0      0.093   12.7   0.0    1.6  1  MarR          MarR family
      0.074   13.0   0.7       0.34   10.9   0.2    2.3  2  HTH_12        Ribonuclease R winged-helix domain
       0.14   12.2   0.0       0.61   10.3   0.0    1.9  2  DprA_WH       DprA winged helix domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.4   4.3e-26   5.5e-23       2      87 ..      14     103 ..      13     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 4.3e-26
                                       HHSTTHHHHHHHHTTS-...EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE.SSSS-EEEEEE-TCGGGGHH CS
                              HxlR   2 iggkWkllilvellkgk...kRfselkralpkisqkmLaqrLreLeqdglierevy.pevPpkveYsltekGrslep 74 
                                       i  kW+ll+l el kg+   +Rfselk  l +i+ k+L++rL+eLe++gl++r+    + P + eYslte G ++ +
  gi|386001269|ref|YP_005919568.1|  14 IARKWTLLVLLELYKGEghvRRFSELKSCLSGITPKVLSARLKELEREGLVKRRFDgRSFPARAEYSLTESGLEIVE 90 
                                       789************854459*******************************99752789***************** PP

                                       HHHHHHHHHHHHH CS
                              HxlR  75 vlqelkkwgeeyl 87 
                                       +++e+k w+ ++ 
  gi|386001269|ref|YP_005919568.1|  91 IVKEMKRWALKWK 103
                                       *********9985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.9e-07   0.00037      27      61 .]      36      71 ..      22      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-07
                                      HHHHHHHH.TS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 27 aselaerl.dlskntlsyHLrvLeeagLvevvregr 61
                                      +sel+ +l +++++ ls +L++Le+ gLv+++  gr
  gi|386001269|ref|YP_005919568.1| 36 FSELKSCLsGITPKVLSARLKELEREGLVKRRFDGR 71
                                      69******88********************997775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.1e-06    0.0014       9      60 ..      21      70 ..      17      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHCTTTSEEEHHHHHH.HHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelar.rlglsksavsrilkrLvaaGLverrpgpeDk 60
                                       vL++L+ ++g   + +el     g+++  +s +lk+L++ GLv rr    D+
  gi|386001269|ref|YP_005919568.1| 21 LVLLELYKGEGHVRRFSELKScLSGITPKVLSARLKELEREGLVKRRF---DG 70
                                      69999999999844*******666*********************995...34 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-06     0.002      27      97 ..      51     117 ..      33     119 .] 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                      Replic_Relax  27 arrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarllaaqraepeprskrdrrereassrflpHt 97 
                                       ++ rL++L+++gl++r ++ r  +     +++ Y Lt+ G ++++ ++++++++ k+++++ e s ++ +++
  gi|386001269|ref|YP_005919568.1|  51 LSARLKELEREGLVKRrFDGR--SF---PARAEYSLTESGLEIVEIVKEMKRWALKWKITNIECSCQDCSEC 117
                                       789*************99999..33...3478************7776699999999988888777666655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.3e-06    0.0055      27      48 .]      44      65 ..      43      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
                            HTH_24 27 lglSpstvnrrlkrLeeeGlIk 48
                                      +g++p  +++rlk+Le+eGl+k
  gi|386001269|ref|YP_005919568.1| 44 SGITPKVLSARLKELEREGLVK 65
                                      69******************97 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.9e-06    0.0075      16      70 ..      35      90 ..      20      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.9e-06
                            HTH_34 16 dfvelkeal.eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafk 70
                                       f+elk++l ++t   Ls+ lk Le  g ++++ + ++   r  +++T+ G+e  +
  gi|386001269|ref|YP_005919568.1| 35 RFSELKSCLsGITPKVLSARLKELEREGLVKRRFDGRSFPARAEYSLTESGLEIVE 90
                                      69******9459999********************999999**********99665 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.6e-06     0.012      37      70 ..      54      86 ..      37      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.6e-06
                                      HHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                              PadR 37 aLkrLekeglveseweesgegpprkyYrlTdaGr 70
                                       Lk+Le+eglv+++ +  ++ p+r  Y lT+ G 
  gi|386001269|ref|YP_005919568.1| 54 RLKELEREGLVKRRFDG-RSFPARAEYSLTESGL 86
                                      69************998.69***********995 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     9e-06     0.012      17      88 ..      14      84 ..       6     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9e-06
                           DUF4423 17 yfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttsse 88
                                      + ++W  +v++el + +   +  +el+ +l   i+ +  ++ l+ L++ gl+k+  dg+  ++++  + +++
  gi|386001269|ref|YP_005919568.1| 14 IARKWTLLVLLELYKGEGHVRRFSELKSCLS-GITPKVLSARLKELEREGLVKRRFDGRSFPARAEYSLTES 84
                                      6799**************************9.9**********************99998777777663332 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.9e-05     0.037      35      75 ..      50      98 ..      44     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                            HTH_45 35 llnkYLdmLvekgli.......kk.skekYvlTekGlelleklkeleel 75
                                      +l+  L+ L  +gl+       +     +Y+lTe Gle++e +ke+++ 
  gi|386001269|ref|YP_005919568.1| 50 VLSARLKELEREGLVkrrfdgrSFpARAEYSLTESGLEIVEIVKEMKRW 98
                                      56667899999999988777763347889****************9985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     4e-05     0.051      30      54 ..      43      67 ..      21      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                                      HTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 30 mlGltretvsrilseLkreglisrg 54
                                      + G+t+  +s  l+eL+regl++r+
  gi|386001269|ref|YP_005919568.1| 43 LSGITPKVLSARLKELEREGLVKRR 67
                                      689*******************965 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.9e-05     0.037      36      70 ..      54      95 ..      17     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                            DUF505 36 illeLelagLvr.......leepekielTyaGkklaelldel 70
                                       l+eLe  gLv+       ++  ++++lT++G +++e+++e+
  gi|386001269|ref|YP_005919568.1| 54 RLKELEREGLVKrrfdgrsFPARAEYSLTESGLEIVEIVKEM 95
                                      388999999998777776567888999999999999999999 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.3e-05     0.093      26      50 ..      43      67 ..      19      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                                      HHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 26 klgvskstvtrvldrLekkGlieRs 50
                                       +g+++  ++  l++Le++Gl++R+
  gi|386001269|ref|YP_005919568.1| 43 LSGITPKVLSARLKELEREGLVKRR 67
                                      6789999****************97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.2   2.8e+03      32      38 ..       8      14 ..       4      18 .. 0.78
   2 ?   10.9   0.2   0.00027      0.34      37      64 ..      53      87 ..      37      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                            HTH_12 32 eravRyr 38
                                      +r+vRy 
  gi|386001269|ref|YP_005919568.1|  8 NRTVRYI 14
                                      6999995 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00027
                            HTH_12 37 yrLrkleergltrrvgya.......greltEkGle 64
                                       rL+ le++gl++r   +          ltE Gle
  gi|386001269|ref|YP_005919568.1| 53 ARLKELEREGLVKRRFDGrsfparaEYSLTESGLE 87
                                      69**********99754444665556778888887 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.6e+03      44      51 ..      19      26 ..      14      36 .. 0.72
   2 ?   10.3   0.0   0.00047      0.61      35      58 ..      44      67 ..      42      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                           DprA_WH 44 aaLleLEL 51
                                      ++L+ LEL
  gi|386001269|ref|YP_005919568.1| 19 TLLVLLEL 26
                                      57899998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00047
                           DprA_WH 35 tglpaaevsaaLleLELaGlverl 58
                                      +g+++ ++sa L eLE +Glv+r+
  gi|386001269|ref|YP_005919568.1| 44 SGITPKVLSARLKELEREGLVKRR 67
                                      89*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 864.59
//
Query:       gi|386001270|ref|YP_005919569.1|  [L=114]
Description: hypothetical protein Mhar_0568 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 841.56
//
Query:       gi|386001271|ref|YP_005919570.1|  [L=1832]
Description: hypothetical protein Mhar_0569 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-35  120.3  32.9    8.9e-11   42.0   0.3    9.5  9  DUF11          Domain of unknown function DUF11
    2.8e-05   24.3   1.8        1.4    9.2   0.0    6.5  6  CARDB          CARDB
    0.00031   21.0  10.5        6.8    7.0   0.0    6.4  7  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
      0.002   17.9   0.2        0.8    9.4   0.0    3.7  3  DUF4139        Domain of unknown function (DUF4139)
     0.0027   17.8   0.2        2.8    8.1   0.0    3.9  3  Fn3-like       Fibronectin type III-like domain
     0.0049   17.0   3.1       0.14   12.4   0.0    5.0  4  He_PIG         Putative Ig domain
      0.006   16.4   0.1        5.1    7.0   0.0    3.1  2  Myosin_N       Myosin N-terminal SH3-like domain
  ------ inclusion threshold ------
      0.015   15.5   0.0        1.6    8.9   0.0    2.7  2  Collagen_bind  Collagen binding domain
      0.081   13.6   0.1         34    5.2   0.0    3.2  2  SAF            SAF domain
        0.7   10.6  10.0         31    5.3   0.0    5.6  5  fn3_5          Fn3-like domain
        1.3    9.0   4.5        3.2    7.7   0.1    3.4  2  LBP_C          Lacto-N-biose phosphorylase C-terminal domain
        1.3    9.4  15.8         18    5.7   0.2    5.5  4  SpaA           Prealbumin-like fold domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.6   1.1e+04       9      75 ..     239     251 ..     215     253 .. 0.63
   2 ?    1.1   0.0      0.34     5e+02      33      75 ..     302     343 ..     291     348 .. 0.67
   3 ?    1.5   0.0      0.26   3.8e+02      24      74 ..     384     434 ..     382     447 .. 0.75
   4 !   42.0   0.3   5.9e-14   8.9e-11       1      76 [.     547     630 ..     547     636 .. 0.89
   5 ?    2.5   2.2      0.12   1.8e+02       1      37 [.     872     908 ..     872     967 .. 0.76
   6 !   11.4   0.7    0.0002       0.3       3      37 ..     982    1016 ..     980    1091 .. 0.70
   7 !   17.2   0.4     3e-06    0.0045       1      40 [.    1098    1168 ..    1098    1255 .. 0.65
   8 !   38.9   0.0   5.2e-13   7.8e-10      14      88 ..    1573    1647 ..    1563    1654 .. 0.90
   9 !   20.0   0.1   4.2e-07   0.00063      16      91 .]    1698    1774 ..    1686    1774 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.6
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsft 75 
                                       ++                                                      ++ge+a+++ft
  gi|386001271|ref|YP_005919570.1| 239 TI------------------------------------------------------APGETARVNFT 251
                                       44......................................................55555555554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.34
                             DUF11  33 vvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsft 75 
                                       ++++ + P+g ++     + ++   + +  +L +ge+at++ft
  gi|386001271|ref|YP_005919570.1| 302 YTIEEIIPEGWTLADINGAASIEGSKAT-VNLGPGETATVNFT 343
                                       5666666777666655555223333333.599********998 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.26
                             DUF11  24 Ntgpasa.ngvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsf 74 
                                       N ++     +++++ + P+g ++  v  + ++   + +  +L +ge+at++f
  gi|386001271|ref|YP_005919570.1| 384 NASGLLVpGTYTIEEIIPEGWTLADVNGAASIEGSKAT-VDLGPGETATVNF 434
                                       66555554678999999999999998888444444444.59********998 PP

  == domain 4  score: 42.0 bits;  conditional E-value: 5.9e-14
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas........qgtasaltsv.gsLeage 68 
                                       +tKt ++++  p  +vt+t++v+Ntg +++  + v+DtlPag++y+s+s +         gt +  +   g L +g+
  gi|386001271|ref|YP_005919570.1| 547 VTKTASPTAGVPHTEVTFTIVVRNTGKVPL-ALEVNDTLPAGMSYISASPApdrvienaDGTTEIFWDGlGALGPGN 622
                                       79****************************.*******************999998877777766666699999999 PP

                             DUF11  69 satlsftv 76 
                                       ++t+ + +
  gi|386001271|ref|YP_005919570.1| 623 ETTILVVA 630
                                       99987665 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.12
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtD 37 
                                       ltK  ++ +++ G  +ty   v N g+++ +++++ D
  gi|386001271|ref|YP_005919570.1| 872 LTKVASPIPAAVGTVITYSYAVENVGGTTIANITLFD 908
                                       688889999********************99988855 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.0002
                             DUF11    3 KtvdksevrpGdtvtytltvtNtgpasangvvvtD 37  
                                        Kt d+++v+ G+ vty  +v+N g a+ +g+ + D
  gi|386001271|ref|YP_005919570.1|  982 KTPDRTNVTVGEVVTYSFVVQNVGIAPVEGLLLYD 1016
                                        999*************************9998876 PP

  == domain 7  score: 17.2 bits;  conditional E-value: 3e-06
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtl..................................P 40  
                                        +tKt  +++vrpGd+vty++tv   gpa   +v v+D+                                    
  gi|386001271|ref|YP_005919570.1| 1098 VTKTALQKAVRPGDEVTYNITVC--GPAGT-RVNVRDLFdrpvefvcaeprplkigdrwqewnltlpggnnttC 1168
                                        79********************6..55544.7788887755555555555555555555555555544444440 PP

  == domain 8  score: 38.9 bits;  conditional E-value: 5.2e-13
                             DUF11   14 dtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatlsftvrvtrtaasga 86  
                                         +v+y +tvtN g+a++++++v+D+ P+ ++y+s+s +   ++ +a +sv  L ag++  +++ ++v   + s+ 
  gi|386001271|ref|YP_005919570.1| 1573 SQVRYAITVTNDGNAPLEDITVEDVFPPRTSYISSSLRpeIAADRAVWSVSPLGAGGRFEIELVLEVIEDGGSL- 1646
                                        59************************************988889999999***************999988874. PP

                             DUF11   87 lt 88  
                                          
  gi|386001271|ref|YP_005919570.1| 1647 -V 1647
                                        .4 PP

  == domain 9  score: 20.0 bits;  conditional E-value: 4.2e-07
                             DUF11   16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas.....qgtasaltsvgsLeagesatlsftvrvtrtaasg 85  
                                        +ty ltv+N  + +   + + DtlP+gl++  +s       ++ ++  + + +L++ e +t+++ v+++++++  
  gi|386001271|ref|YP_005919570.1| 1698 ITYRLTVQNLQNETV-VANIVDTLPSGLSLLGASVMpaeydRSRGRISWVIADLNPREVRTIEYLVEARTRGR-- 1769
                                        89*************.9****************999888887788888888*******************999.. PP

                             DUF11   86 altnva 91  
                                         + nva
  gi|386001271|ref|YP_005919570.1| 1770 -FLNVA 1774
                                        .77775 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.3     5e+03      54      69 ..     330     344 ..     316     355 .. 0.77
   2 !    9.2   0.0   0.00094       1.4       2      33 ..     543     574 ..     542     626 .. 0.91
   3 ?    2.3   0.0      0.13     2e+02       7      37 ..     873     903 ..     861     913 .. 0.84
   4 ?   -0.1   0.0      0.77   1.1e+03      12      33 ..     986    1007 ..     977    1037 .. 0.88
   5 ?    0.9   0.0      0.36   5.4e+02       3      27 ..    1095    1119 ..    1092    1120 .. 0.93
   6 ?    2.6   0.0      0.11   1.6e+02      14      41 ..    1568    1595 ..    1557    1655 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.3
                                       ESEE-CTEEEEEEEEE CS
                             CARDB  54 vpsLaagesttvsftw 69 
                                       v +L +ge++tv+ft 
  gi|386001271|ref|YP_005919570.1| 330 V-NLGPGETATVNFTN 344
                                       3.89999999999985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00094
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGta 33 
                                       p L+vt+t++p++ ++ +e+t+t+ v+N+G+ 
  gi|386001271|ref|YP_005919570.1| 543 PGLEVTKTASPTAGVPHTEVTFTIVVRNTGKV 574
                                       789***************************85 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
                                       .EEEC-SEEETTSEEEEEEEEEE-SSS-EEE CS
                             CARDB   7 tntlnpseafvgeentitvtvkNqGtaasga 37 
                                       t+ ++p +a vg+ +t ++ v+N G  +  +
  gi|386001271|ref|YP_005919570.1| 873 TKVASPIPAAVGTVITYSYAVENVGGTTIAN 903
                                       6667889999***************877655 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.77
                                        -SEEETTSEEEEEEEEEE-SSS CS
                             CARDB   12 pseafvgeentitvtvkNqGta 33  
                                         ++++vge +t ++ v+N G a
  gi|386001271|ref|YP_005919570.1|  986 RTNVTVGEVVTYSFVVQNVGIA 1007
                                        67899***************87 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.36
                                        -EEE.EEEC-SEEETTSEEEEEEEE CS
                             CARDB    3 DLtvtntlnpseafvgeentitvtv 27  
                                        DLtvt+t+  +++ +g+e+t ++tv
  gi|386001271|ref|YP_005919570.1| 1095 DLTVTKTALQKAVRPGDEVTYNITV 1119
                                        **********************998 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.11
                                        EEETTSEEEEEEEEEE-SSS-EEEEEEE CS
                             CARDB   14 eafvgeentitvtvkNqGtaasgatkva 41  
                                        +  + ++++  +tv+N G+a  ++++v+
  gi|386001271|ref|YP_005919570.1| 1568 ADKNSSQVRYAITVTNDGNAPLEDITVE 1595
                                        3445566777779*******99988875 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 ?   -2.8   0.0       5.2   7.7e+03      46      58 ..     239     251 ..     236     251 .. 0.84
   2 !    5.9   0.0      0.01        15      30      58 ..     308     343 ..     302     348 .. 0.88
   3 !    6.0   0.0    0.0093        14      30      57 ..     400     434 ..     395     436 .. 0.83
   4 ?   -0.6   0.0       1.1   1.7e+03       6      32 ..     561     586 ..     557     596 .. 0.78
   5 ?   -2.3   0.0       3.7   5.6e+03       2      24 ..     990    1012 ..     989    1014 .. 0.87
   6 ?    1.9   0.3      0.18   2.8e+02      35      65 ..    1097    1125 ..    1073    1131 .. 0.77
   7 !    7.0   0.0    0.0045       6.8       5      31 ..    1573    1599 ..    1570    1619 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.2
                       NPCBM_assoc  46 slapGetveatvk 58 
                                       ++apGet++++++
  gi|386001271|ref|YP_005919570.1| 239 TIAPGETARVNFT 251
                                       799*****99885 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                       NPCBM_assoc  30 lPeGWt......vvevspasaa.slapGetveatvk 58 
                                        PeGWt      + ++++ +a+  l pGet++++++
  gi|386001271|ref|YP_005919570.1| 308 IPEGWTladingAASIEGSKATvNLGPGETATVNFT 343
                                       6*****99988888888888889**********986 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0093
                       NPCBM_assoc  30 lPeGWt......vvevspasaa.slapGetveatv 57 
                                        PeGWt      + ++++ +a+ +l pGet+++++
  gi|386001271|ref|YP_005919570.1| 400 IPEGWTladvngAASIEGSKATvDLGPGETATVNF 434
                                       6*****99977777777777779********9986 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.1
                       NPCBM_assoc   6 tvtltltvtndgtaaatnvslslslPe 32 
                                       +vt+t++v n+g+ ++ +++++ +lP+
  gi|386001271|ref|YP_005919570.1| 561 EVTFTIVVRNTGKVPL-ALEVNDTLPA 586
                                       799*********9997.4555555555 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 3.7
                       NPCBM_assoc    2 epGetvtltltvtndgtaaatnv 24  
                                        + Ge vt+ ++v n g a+++++
  gi|386001271|ref|YP_005919570.1|  990 TVGEVVTYSFVVQNVGIAPVEGL 1012
                                        679999*************9976 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.18
                       NPCBM_assoc   35 tvvevspasaa.slapGetveatvkVtppaga 65  
                                        t   v+ + ++ +++pG++v+ +++V  pag+
  gi|386001271|ref|YP_005919570.1| 1097 T---VTKTALQkAVRPGDEVTYNITVCGPAGT 1125
                                        4...3334444489************999987 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0045
                       NPCBM_assoc    5 etvtltltvtndgtaaatnvslslslP 31  
                                        ++v++ +tvtndg+a+++++ ++  +P
  gi|386001271|ref|YP_005919570.1| 1573 SQVRYAITVTNDGNAPLEDITVEDVFP 1599
                                        689999**************9986666 PP

>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.096   1.4e+02     131     156 ..     560     585 ..     547     589 .. 0.90
   2 ?    1.1   0.0      0.19   2.8e+02     128     156 ..    1570    1599 ..    1563    1605 .. 0.84
   3 !    9.4   0.0   0.00054       0.8     130     203 ..    1695    1763 ..    1679    1766 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.096
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 131 veyaytitvkNtksepvtlkvedqvP 156
                                        e+++ti v+Nt + p  l+v+d +P
  gi|386001271|ref|YP_005919570.1| 560 TEVTFTIVVRNTGKVPLALEVNDTLP 585
                                       57889********************9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                                        xxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                           DUF4139  128 qrrveyaytitvkNtksepv.tlkvedqvP 156 
                                        ++  +++y itv+N  + p  +++ved +P
  gi|386001271|ref|YP_005919570.1| 1570 KNSSQVRYAITVTNDGNAPLeDITVEDVFP 1599
                                        677899***********7753799999888 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00054
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                           DUF4139  130 rveyaytitvkNtksepvtlkvedqvPvSrdeeikveledaepskaevdkdtgilewkl.klapgekkkiefsye 203 
                                        +  ++y++tv+N ++e+v  +++d +P      + +    a+  +ae+d+++g++ w + +l p+e ++ie+ +e
  gi|386001271|ref|YP_005919570.1| 1695 ENIITYRLTVQNLQNETVVANIVDTLPS----GLSL--LGASVMPAEYDRSRGRISWVIaDLNPREVRTIEYLVE 1763
                                        56689**********************4....5666..66777888***********7648*********99876 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 !    8.1   0.0    0.0019       2.8      23      40 ..     234     251 ..     233     254 .. 0.94
   2 ?    2.1   0.0      0.14   2.1e+02      27      40 ..     330     343 ..     327     346 .. 0.90
   3 ?    2.4   0.0      0.11   1.7e+02      27      40 ..     422     435 ..     420     464 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                                       EEEEEEE-TT-EEEEEEE CS
                          Fn3-like  23 gFekveLapGesktvtft 40 
                                       gF kv++apGe+++v+ft
  gi|386001271|ref|YP_005919570.1| 234 GFIKVTIAPGETARVNFT 251
                                       8***************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                                       EEE-TT-EEEEEEE CS
                          Fn3-like  27 veLapGesktvtft 40 
                                       v+L pGe++tv+ft
  gi|386001271|ref|YP_005919570.1| 330 VNLGPGETATVNFT 343
                                       89**********97 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.11
                                       EEE-TT-EEEEEEE CS
                          Fn3-like  27 veLapGesktvtft 40 
                                       v+L pGe++tv+f 
  gi|386001271|ref|YP_005919570.1| 422 VDLGPGETATVNFI 435
                                       99*********995 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.4   6.6e+03      16      27 ..     140     151 ..     139     176 .. 0.85
   2 ?   -2.9   0.1       5.5   8.2e+03      18      40 ..     229     250 ..     229     251 .. 0.72
   3 ?    0.2   0.0      0.59   8.8e+02       7      19 ..     579     602 ..     552     607 .. 0.69
   4 !   12.4   0.0   9.4e-05      0.14       9      29 ..    1717    1747 ..    1699    1754 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.4
                            He_PIG  16 LtLdsstGtitG 27 
                                       Lt+ + t++it+
  gi|386001271|ref|YP_005919570.1| 140 LTIQPQTCSITV 151
                                       899999***997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.5
                            He_PIG  18 LdsstGtitGtpdqtvapGsytf 40 
                                       ++s++G i +t+ ++ ++ + +f
  gi|386001271|ref|YP_005919570.1| 229 FSSGDGFIKVTIAPG-ETARVNF 250
                                       6899999****8887.3335555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.59
                            He_PIG   7 pgsngLPsGLtL...........d 19 
                                       + +++LP+G++            +
  gi|386001271|ref|YP_005919570.1| 579 EVNDTLPAGMSYisaspapdrviE 602
                                       457899999997655555555555 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 9.4e-05
                            He_PIG    9 sngLPsGLtL..........dsstGtitGtp 29  
                                         ++LPsGL+L          d s G+i++++
  gi|386001271|ref|YP_005919570.1| 1717 VDTLPSGLSLlgasvmpaeyDRSRGRISWVI 1747
                                        589**************************96 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0034       5.1      11      39 ..     310     341 ..     310     342 .. 0.95
   2 !    5.9   0.0    0.0074        11      11      39 ..     402     433 ..     402     434 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                                       TS-EEEEEE...EEESSEEEEEETTSEEEEEE CS
                          Myosin_N  11 egyvkGeIk...eeeGdkvtVetedGktvtVk 39 
                                       eg+  + I    ++eG k+tV +  G+t tV+
  gi|386001271|ref|YP_005919570.1| 310 EGWTLADINgaaSIEGSKATVNLGPGETATVN 341
                                       899999999999******************97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0074
                                       TS-EEEEEE...EEESSEEEEEETTSEEEEEE CS
                          Myosin_N  11 egyvkGeIk...eeeGdkvtVetedGktvtVk 39 
                                       eg+  + +    ++eG k+tV +  G+t tV+
  gi|386001271|ref|YP_005919570.1| 402 EGWTLADVNgaaSIEGSKATVDLGPGETATVN 433
                                       799999999999******************97 PP

>> Collagen_bind  Collagen binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011       1.6       3      51 ..    1561    1609 ..    1559    1630 .. 0.85
   2 ?    3.5   0.0      0.05        74       5      56 ..    1685    1736 ..    1681    1762 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                        SEEEEEEE-STT-E.EEEEEEE.-TT---BS-EEEEEEE-TTEEE-TT-- CS
                     Collagen_bind    3 avdKvGsvdkennelihWevni.NkalqeienavltDvigegqelvkdSi 51  
                                        ++ K G +dk++++ ++  +++ N   +++e+++++Dv +  +   ++S+
  gi|386001271|ref|YP_005919570.1| 1561 SISKIGEADKNSSQ-VRYAITVtNDGNAPLEDITVEDVFPPRTSYISSSL 1609
                                        589***********.******966778889********998877666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.05
                                        EEEEEE-STT-E.EEEEEEE-TT---BS-EEEEEEE-TTEEE-TT--EEEEE CS
                     Collagen_bind    5 dKvGsvdkennelihWevniNkalqeienavltDvigegqelvkdSievyel 56  
                                         K Gsvd   +++i+  +++ + ++e   a + D++++g  l   S+  +e 
  gi|386001271|ref|YP_005919570.1| 1685 SKTGSVDPVLENIITYRLTVQNLQNETVVANIVDTLPSGLSLLGASVMPAEY 1736
                                        79******************999999999999**********9999876665 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.036        54      21      55 ..     302     336 ..     294     341 .. 0.88
   2 ?    5.2   0.0     0.023        34      21      55 ..     394     428 ..     388     434 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.036
                                       EEEECECGG.CCTSCCCGGHHHHTTEEESS-B-TT- CS
                               SAF  21 ltlkrpias.hkigllpiaygeviGkratrdikaGe 55 
                                       +t++++i++ +  +++  a   + G++at ++ +Ge
  gi|386001271|ref|YP_005919570.1| 302 YTIEEIIPEgWTLADINGA-ASIEGSKATVNLGPGE 336
                                       6899999999999999997.***************9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.023
                                       EEEECECGG.CCTSCCCGGHHHHTTEEESS-B-TT- CS
                               SAF  21 ltlkrpias.hkigllpiaygeviGkratrdikaGe 55 
                                       +t++++i++ +  +++  a   + G++at d+ +Ge
  gi|386001271|ref|YP_005919570.1| 394 YTIEEIIPEgWTLADVNGA-ASIEGSKATVDLGPGE 428
                                       6899999999999999997.***************9 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   3.2e+03      65      79 ..     237     251 ..     232     263 .. 0.89
   2 ?    5.3   0.0     0.021        31      56      79 ..     319     343 ..     283     364 .. 0.83
   3 ?    2.4   0.0      0.16   2.4e+02      56      78 ..     408     434 ..     369     451 .. 0.82
   4 ?    2.3   0.0      0.17   2.5e+02       8      32 ..     560     585 ..     557     645 .. 0.76
   5 ?    0.9   0.7      0.49   7.3e+02      16      50 ..    1199    1233 ..    1192    1248 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                             fn3_5  65 kvtvpAnssktvtvt 79 
                                       kvt+ +++++ v++t
  gi|386001271|ref|YP_005919570.1| 237 KVTIAPGETARVNFT 251
                                       79***********98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                             fn3_5  56 e.aaltfetskvtvpAnssktvtvt 79 
                                       + a+++ ++++v +++++++tv++t
  gi|386001271|ref|YP_005919570.1| 319 GaASIEGSKATVNLGPGETATVNFT 343
                                       2689*******************98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.16
                             fn3_5  56 e....aaltfetskvtvpAnssktvtv 78 
                                       +    a+++ ++++v +++++++tv++
  gi|386001271|ref|YP_005919570.1| 408 DvngaASIEGSKATVDLGPGETATVNF 434
                                       0444589******************98 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.17
                             fn3_5   8 dkfsftltlkNtsnkaltykvsan.d 32 
                                       ++ +ft+ ++Nt++ +l ++v+++ +
  gi|386001271|ref|YP_005919570.1| 560 TEVTFTIVVRNTGKVPLALEVNDTlP 585
                                       5689****************999853 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.49
                             fn3_5   16 lkNtsnkaltykvsandvlTdladkeegklilkaa 50  
                                        ++ +++++++y+++++  +Tdl  ++++ ++++  
  gi|386001271|ref|YP_005919570.1| 1199 ANDYNTEPPSYTLTNVVTATDLNKTNNTDTDTETV 1233
                                        4669999*********8899997666666655544 PP

>> LBP_C  Lacto-N-biose phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0021       3.2      10      36 ..     126     152 ..     116     157 .. 0.89
   2 ?    0.1   0.9      0.52   7.8e+02      23      40 ..    1224    1241 ..    1223    1245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                             LBP_C  10 vayYpesgklvViNNsdeeqtTtvytg 36 
                                       v +Yp+ + l+ iN + ++qt +++  
  gi|386001271|ref|YP_005919570.1| 126 VKAYPACNGLALINLTIQPQTCSITVI 152
                                       789******************999865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.52
                             LBP_C   23 NNsdeeqtTtvytgdgkr 40  
                                        NN+d++ +T+   + g++
  gi|386001271|ref|YP_005919570.1| 1224 NNTDTDTETVLVSEAGTE 1241
                                        *********998888865 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.025        37      43      63 ..     179     200 ..     171     223 .. 0.87
   2 ?    2.8   0.2     0.097   1.4e+02      42      66 ..     287     311 ..     209     324 .. 0.82
   3 ?    5.7   0.2     0.012        18      37      67 ..     374     404 ..     312     417 .. 0.76
   4 ?    3.2   0.0     0.073   1.1e+02      36      61 ..     478     502 ..     456     505 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                                       TSEE.EEEEEESEEEEEEEEE- CS
                              SpaA  43 nGka.tfegLplGtYllvEtka 63 
                                        G+a tf+gLp+G+Y++ E +a
  gi|386001271|ref|YP_005919570.1| 179 GGEAeTFGGLPPGSYVIGEEEA 200
                                       56664789*********99987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.097
                                       TTSEEEEE.EEESEEEEEEEEE-STT CS
                              SpaA  42 enGkatfe.gLplGtYllvEtkaPeg 66 
                                       ++G+++ +  L +GtY+++E+  Peg
  gi|386001271|ref|YP_005919570.1| 287 KDGETNASvLLVPGTYTIEEI-IPEG 311
                                       6888888745678*******8.5555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.012
                                       EEE-BTTSEEEEEEE.ESEEEEEEEEE-STTE CS
                              SpaA  37 tlttdenGkatfegL.plGtYllvEtkaPegY 67 
                                       ++   ++G+++ +gL  +GtY+++E+  Peg 
  gi|386001271|ref|YP_005919570.1| 374 QKILLKDGETNASGLlVPGTYTIEEI-IPEGW 404
                                       4555589****9986256*******8.56665 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.073
                                       SEEE-BTTSEEEEEEEESEEEEEEEE CS
                              SpaA  36 ttlttdenGkatfegLplGtYllvEt 61 
                                       +t+ +d  G + +++L++G Y + E 
  gi|386001271|ref|YP_005919570.1| 478 KTVGSD-GGVLAWNDLAPGVYNVSEK 502
                                       444455.68899***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1832 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 1.00u 0.32s 00:00:01.32 Elapsed: 00:00:00.52
# Mc/sec: 10534.57
//
Query:       gi|386001272|ref|YP_005919571.1|  [L=535]
Description: hypothetical protein Mhar_0570 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-19   67.1  11.5    9.4e-08   31.8   0.1    4.5  4  PKD           PKD domain
    0.00092   19.3   4.5        1.2    9.4   0.1    3.9  4  He_PIG        Putative Ig domain
      0.001   18.5   1.4      0.044   13.3   0.2    3.2  3  TcfC          E-set like domain
     0.0024   18.1   0.0        2.1    8.6   0.0    3.1  3  DUF4625       Domain of unknown function (DUF4625)
     0.0074   16.2   0.4          3    7.9   0.1    3.5  4  Y_Y_Y         Y_Y_Y domain
  ------ inclusion threshold ------
      0.036   14.4   1.0        0.1   13.0   0.1    2.2  2  Ig_2          Immunoglobulin domain
      0.039   13.6   0.1          7    6.3   0.0    3.1  3  ChitinaseA_N  Chitinase A, N-terminal domain
       0.19   11.8   0.0         35    4.5   0.0    3.2  3  BiPBP_C       Penicillin-Binding Protein C-terminus Family
        0.3   11.2   4.9         22    5.3   1.5    3.3  3  DUF5011       Domain of unknown function (DUF5011)


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.8   3.1e-09   6.1e-06       8      70 ..     189     256 ..     183     257 .. 0.79
   2 !   31.8   0.1   4.7e-11   9.4e-08      13      67 ..     281     341 ..     275     343 .. 0.83
   3 !    8.9   0.2   0.00066       1.3       4      61 ..     362     417 ..     356     420 .. 0.87
   4 ?    5.0   0.0     0.011        22      15      34 ..     453     472 ..     438     504 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.1e-09
                                       -BSSEEEEEEEES...-SS-SEEEEE--SS...--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD   8 lvpgatvaftaav..pdganvtysWdfgdg...svvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                       ++ g +++ft          ++  W+fgd    s+   + +  +  tY+spG Y+Vt++++++ g ++
  gi|386001272|ref|YP_005919571.1| 189 VCLGGSIQFTDLTtgGYKPYASSVWTFGDAttySCSSASPCNPPPKTYASPGRYTVTLRVTDNKGVVS 256
                                       678889999999943333444555*****77777777777777889*****************99776 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 4.7e-11
                                       EEEEEEES....-....SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
                               PKD  13 tvaftaav...pd....ganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                                       +v+f+  +   p+    +++++ sWdf+  + + ++s +++ +t+++pG+Y V++t++++ g
  gi|386001272|ref|YP_005919571.1| 281 EVQFSDLStatPTadvmPTITAQSWDFDG-GGAIDSSMQSPEYTFPAPGTYPVRLTVTDSHG 341
                                       677777776442255668899999****9.****************************9865 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00066
                                       --S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S...SEEEEEEEE CS
                               PKD   4 sptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls...pGeYeVtvt 61 
                                       s ++++ g t+++ ++  dg  ++ysW+      ++ +s +++t+ +++   +G+Y+++v+
  gi|386001272|ref|YP_005919571.1| 362 SNSPVCEGSTINLYGGP-DGL-ISYSWTGPE---GFASSLQNTTIYPATlanAGTYTLKVV 417
                                       37889999999999999.665.79*******...999999999999999999******996 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.011
                                       EEEEES.-SS-SEEEEE--S CS
                               PKD  15 aftaavpdganvtysWdfgd 34 
                                        + a++ +g ++ty+W++  
  gi|386001272|ref|YP_005919571.1| 453 ILIAGSNSGGPATYLWTTSG 472
                                       5678899**********977 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0007       1.4      31      49 .]     235     253 ..     224     253 .. 0.85
   2 !    9.4   0.1    0.0006       1.2      34      49 .]     326     341 ..     311     341 .. 0.88
   3 ?   -1.5   0.1       1.5   3.1e+03      32      42 ..     406     416 ..     383     417 .. 0.68
   4 ?   -3.1   0.0       4.8   9.5e+03      34      44 ..     494     504 ..     486     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0007
                            He_PIG  31 qtvapGsytftVtatdgsg 49 
                                       +   pG+yt+t+++td+ g
  gi|386001272|ref|YP_005919571.1| 235 TYASPGRYTVTLRVTDNKG 253
                                       45579***********875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0006
                            He_PIG  34 apGsytftVtatdgsg 49 
                                       apG+y +++t+td+ g
  gi|386001272|ref|YP_005919571.1| 326 APGTYPVRLTVTDSHG 341
                                       68***********865 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                            He_PIG  32 tvapGsytftV 42 
                                         ++G+yt  V
  gi|386001272|ref|YP_005919571.1| 406 LANAGTYTLKV 416
                                       34569999877 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.8
                            He_PIG  34 apGsytftVta 44 
                                       ++G+ ++t+ta
  gi|386001272|ref|YP_005919571.1| 494 EAGRVNITLTA 504
                                       56999999998 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.72   1.4e+03      13      21 ..      93     101 ..      91     103 .. 0.86
   2 !   13.3   0.2   2.2e-05     0.044      44      65 ..     240     261 ..     238     263 .. 0.92
   3 ?    1.8   0.0     0.083   1.7e+02      43      56 ..     327     340 ..     321     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.72
                              TcfC  13 grveiyRdg 21 
                                       ++v+iyR++
  gi|386001272|ref|YP_005919571.1|  93 SVVDIYRGD 101
                                       78*****97 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.2e-05
                              TcfC  44 GiYeveirvyengqvvrteqqk 65 
                                       G Y+v++rv +n++vv+t++q 
  gi|386001272|ref|YP_005919571.1| 240 GRYTVTLRVTDNKGVVSTKSQS 261
                                       99*****************995 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.083
                              TcfC  43 sGiYeveirvyeng 56 
                                        G+Y+v++ v ++ 
  gi|386001272|ref|YP_005919571.1| 327 PGTYPVRLTVTDSH 340
                                       6*********9875 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001       2.1     104     129 ..     237     262 ..     219     265 .. 0.85
   2 ?    1.5   0.0      0.16   3.2e+02     105     122 ..     326     343 ..     302     352 .. 0.84
   3 ?    4.0   0.0     0.027        55      98     129 ..     401     430 ..     384     433 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                           DUF4625 104 aeaGdYhlvirvtDasGneteesrei 129
                                       a +G Y +++rvtD++G  + +s ++
  gi|386001272|ref|YP_005919571.1| 237 ASPGRYTVTLRVTDNKGVVSTKSQSY 262
                                       89***************999888776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                           DUF4625 105 eaGdYhlvirvtDasGne 122
                                       ++G Y + ++vtD +G +
  gi|386001272|ref|YP_005919571.1| 326 APGTYPVRLTVTDSHGCT 343
                                       58************9975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.027
                           DUF4625  98 ieiPadaeaGdYhlvirvtDasGneteesrei 129
                                       i + + a+aG Y   ++v+D++G ete ++++
  gi|386001272|ref|YP_005919571.1| 401 IYPATLANAGTYT--LKVVDEEGCETEAKTTV 430
                                       444444899*996..5789*******998875 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 ?   -3.5   0.0       5.3   1.1e+04      30      42 ..     194     206 ..     189     206 .. 0.86
   2 !    7.9   0.1    0.0015         3      36      53 ..     237     254 ..     235     262 .. 0.84
   3 ?    2.9   0.0     0.052     1e+02      30      63 ..     319     352 ..     307     354 .. 0.79
   4 ?    0.7   0.0      0.27   5.3e+02      34      45 ..     405     416 ..     381     423 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.3
                                       EEEEES--SEEEE CS
                             Y_Y_Y  30 easytnlppGdYt 42 
                                       ++ +t l  G Y+
  gi|386001272|ref|YP_005919571.1| 194 SIQFTDLTTGGYK 206
                                       7899****99996 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                                       --SEEEEEEEEEEETTS- CS
                             Y_Y_Y  36 lppGdYtlkVkakdndgq 53 
                                        +pG+Yt++++++dn+g 
  gi|386001272|ref|YP_005919571.1| 237 ASPGRYTVTLRVTDNKGV 254
                                       58*************986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.052
                                       EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEE CS
                             Y_Y_Y  30 easytnlppGdYtlkVkakdndgqwnyditslsf 63 
                                       + +yt   pG+Y +++ ++d+ g   +  + +++
  gi|386001272|ref|YP_005919571.1| 319 SPEYTFPAPGTYPVRLTVTDSHGCTGFIVKDVTV 352
                                       6789999*************99988877776665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.27
                                       ES--SEEEEEEE CS
                             Y_Y_Y  34 tnlppGdYtlkV 45 
                                       t  ++G+YtlkV
  gi|386001272|ref|YP_005919571.1| 405 TLANAGTYTLKV 416
                                       55678******9 PP

>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.3   4.6e+03      17      22 ..     219     224 ..     207     262 .. 0.61
   2 ?   13.0   0.1     5e-05       0.1      21      77 ..     367     430 ..     351     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                              Ig_2  17 vtLtCs 22 
                                        t +Cs
  gi|386001272|ref|YP_005919571.1| 219 TTYSCS 224
                                       333444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5e-05
                              Ig_2  21 Csap.....gnpp..pkvqwykggevinsspnffinavsaedsgtYtCrarntkggevsrpvel 77 
                                       C+++     g p+  ++++w+  + + +s +n +i  +++ ++gtYt ++    g+e++ ++++
  gi|386001272|ref|YP_005919571.1| 367 CEGStinlyGGPDglISYSWTGPEGFASSLQNTTIYPATLANAGTYTLKVVDEEGCETEAKTTV 430
                                       55454555555555699***************66699*************99999999999887 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2   3.9e+02      79     102 ..     236     261 ..     222     271 .. 0.81
   2 ?    6.3   0.0    0.0035         7      67     107 ..     311     352 ..     289     363 .. 0.85
   3 ?    2.0   0.0     0.073   1.4e+02      78     107 ..     405     432 ..     386     435 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                      ChitinaseA_N  79 vkkgGryqlevelCdaeG..Csksap 102
                                       +   Gry +++++ d++G   +ks++
  gi|386001272|ref|YP_005919571.1| 236 YASPGRYTVTLRVTDNKGvvSTKSQS 261
                                       6778**************54455555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0035
                      ChitinaseA_N  67 gaas.akesatfkvkkgGryqlevelCdaeGCsksapkeivv 107
                                       ga++ + +s ++++   G y +++ + d++GC+    k ++v
  gi|386001272|ref|YP_005919571.1| 311 GAIDsSMQSPEYTFPAPGTYPVRLTVTDSHGCTGFIVKDVTV 352
                                       677734556699*********************988888877 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.073
                      ChitinaseA_N  78 kvkkgGryqlevelCdaeGCsksapkeivv 107
                                       ++ ++G y l  ++ d+eGC + a +++ v
  gi|386001272|ref|YP_005919571.1| 405 TLANAGTYTL--KVVDEEGCETEAKTTVLV 432
                                       4566777765..568*****9999888876 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.091   1.8e+02      69      86 ..     238     257 ..     211     260 .. 0.83
   2 ?    0.1   0.0      0.43   8.6e+02      67      82 ..     324     341 ..     295     344 .. 0.72
   3 ?    4.5   0.0     0.018        35      69      83 ..     408     422 ..     394     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.091
                           BiPBP_C  69 epGrhrLtv..vDaaGrvdd 86 
                                       +pGr+++t+  +D++G v++
  gi|386001272|ref|YP_005919571.1| 238 SPGRYTVTLrvTDNKGVVST 257
                                       799998887669**998765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                           BiPBP_C  67 qpepGrh..rLtvvDaaG 82 
                                        p pG++  rLtv+D +G
  gi|386001272|ref|YP_005919571.1| 324 FPAPGTYpvRLTVTDSHG 341
                                       457777544899999998 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.018
                           BiPBP_C  69 epGrhrLtvvDaaGr 83 
                                       + G+++L vvD++G 
  gi|386001272|ref|YP_005919571.1| 408 NAGTYTLKVVDEEGC 422
                                       78***********95 PP

>> DUF5011  Domain of unknown function (DUF5011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.5     0.011        22      44      66 ..     237     259 ..     235     264 .. 0.85
   2 ?    4.3   0.0     0.023        45      46      71 .]     327     352 ..     324     352 .. 0.86
   3 ?    0.7   0.1       0.3     6e+02      45      71 .]     408     432 ..     405     432 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                                       TS-EEEEEEEEEE-TTSEEEEEE CS
                           DUF5011  44 skvGtYtitYtvtdssgneatvt 66 
                                         +G Yt+t  vtd++g  +t++
  gi|386001272|ref|YP_005919571.1| 237 ASPGRYTVTLRVTDNKGVVSTKS 259
                                       579**************988875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
                                       -EEEEEEEEEE-TTSEEEEEEEEEEE CS
                           DUF5011  46 vGtYtitYtvtdssgneatvtRtVkV 71 
                                       +GtY +  tvtds+g +  +  +V+V
  gi|386001272|ref|YP_005919571.1| 327 PGTYPVRLTVTDSHGCTGFIVKDVTV 352
                                       8**************98877777766 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.3
                                       S-EEEEEEEEEE-TTSEEEEEEEEEEE CS
                           DUF5011  45 kvGtYtitYtvtdssgneatvtRtVkV 71 
                                       ++GtYt++  v d++g e++++ tV V
  gi|386001272|ref|YP_005919571.1| 408 NAGTYTLK--VVDEEGCETEAKTTVLV 432
                                       68999995..99999999999888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 4020.90
//
Query:       gi|386001273|ref|YP_005919572.1|  [L=150]
Description: hypothetical protein Mhar_0571 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1067.67
//
Query:       gi|386001274|ref|YP_005919573.1|  [L=336]
Description: hypothetical protein Mhar_0572 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2578.10
//
Query:       gi|386001275|ref|YP_005919574.1|  [L=557]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-66  222.1  86.5    1.4e-25   89.9  26.8    3.8  4  Beta_helix       Right handed beta helix region
    7.8e-51  172.7  66.2    7.6e-18   64.7  13.2    3.8  3  NosD             Periplasmic copper-binding protein (NosD)
    8.7e-13   48.2  39.6      2e-06   27.3   4.6    6.0  3  DUF1565          Protein of unknown function (DUF1565)
    4.9e-08   33.1  34.3    2.6e-06   27.4  12.5    4.1  3  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   8.0     2e-16     9e-13      31     124 ..      90     185 ..      34     186 .. 0.82
   2 !   89.9  26.8   3.2e-29   1.4e-25       9     158 .]     117     263 ..      95     263 .. 0.95
   3 !   71.2  21.5   1.9e-23   8.4e-20      13     142 ..     258     385 ..     254     389 .. 0.95
   4 !   55.3   6.2   1.4e-18   6.5e-15      15     143 ..     375     507 ..     373     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2e-16
                                       SS-.....EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S-- CS
                        Beta_helix  31 ssn....vvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnn 103
                                       s+      +i +++  ++    +++l+ ++++i nnti+++ + gi l ++s+ li++n+i+dn ++Gi+l ++++ 
  gi|386001275|ref|YP_005919574.1|  90 SGVvldgFIIAGCTNDSCDSASVSVLS-DGCKILNNTIYGSMSHGISLLNSSGHLISKNRIHDNFRAGIQLAGANSS 165
                                       333223245666666667778888885.9999999999999999999999999999999999999999999999999 PP

                                       EEES-EEESTT--SEE---TT CS
                        Beta_helix 104 tienNiidnnagsGividdss 124
                                       +i++N i++n+ +Gi+i++s+
  gi|386001275|ref|YP_005919574.1| 166 QISDNEIRGNG-YGIYIEASE 185
                                       99999999999.999999886 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 3.2e-29
                                       -E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES- CS
                        Beta_helix   9 snvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienn 85 
                                       ++++i nnti++s ++Gi l +ss+++i++n+i++n   Gi + g++ ++is+n+i++n+ +gi+++++ + +i +n
  gi|386001275|ref|YP_005919574.1| 117 DGCKILNNTIYGSMSHGISLLNSSGHLISKNRIHDNFRAGIQLAGANSSQISDNEIRGNG-YGIYIEASEGAVIAYN 192
                                       3479********************************************************.**************** PP

                                       EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix  86 eitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                       +i+ ng +Gi +  ss  +i++N i+nn+++G++  ds+ n+ +  Nti ++++ Gi+vv+s s + ++ Nti
  gi|386001275|ref|YP_005919574.1| 193 DISANGADGIAIVASSGQQITGNEIHNNSENGVYHLDSK-NNIIVANTIQDCRNSGIDVVRSFS-TLIVFNTI 263
                                       ***************************************.999*********************.88888886 PP

  == domain 3  score: 71.2 bits;  conditional E-value: 1.9e-23
                                       EESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEES-EEE CS
                        Beta_helix  13 iknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gasnnlienneit 88 
                                       i  nti+++g  Gi l++++n+v+ +n ++ n  +G++ilgs+++tisnn+++ n + gi l+ ++ n++i nn+i+
  gi|386001275|ref|YP_005919574.1| 258 IVFNTIERCGEMGINLDETDNIVVNRNFLSANDINGVSILGSDHSTISNNVVEKNRDNGISLRrDSRNSMIANNTIS 334
                                       5669*****************9999999999********************************************** PP

                                       S-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEE CS
                        Beta_helix  89 dnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGi 142
                                       +n+++G+ l+ s+ n++++N+i++n+ +Giv+++s+ ++ v  N++ +n+  G+
  gi|386001275|ref|YP_005919574.1| 335 ENKRYGLILDESNLNSVQENQIHHNT-NGIVMRYSA-GNSVVENVVRDNG-FGL 385
                                       **************************.*********.8889********7.665 PP

  == domain 4  score: 55.3 bits;  conditional E-value: 1.4e-18
                                       SEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-S CS
                        Beta_helix  15 nntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdng 91 
                                        n +++ +g G+ l+  +nvv+++neian+s +Gi+++++++++i  n+i d+ ++gi++  +  +++++n+i + g
  gi|386001275|ref|YP_005919574.1| 375 ENVVRD-NGFGLSLEMVDNVVVSKNEIANSSRDGISLNRCDHSKIWANRILDSAADGIHIIRSTATIVSDNDILRSG 450
                                       577888.6********************************************************************* PP

                                       S-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-S.....SEEEE CS
                        Beta_helix  92 gsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnk.....gaGia 143
                                       ++G+++  +s++n +  N i + a  Gi++ +++ n+  + N + +nk     ++G +
  gi|386001275|ref|YP_005919574.1| 451 EYGVQILdQSTQNLLLANLIQDSALGGIYLFEGEFNL-ASFNALIDNKkfngwDNGGN 507
                                       ******956999**********************555.55555555554444444444 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7  13.2   1.7e-21   7.6e-18      39     178 ..      90     226 ..      39     228 .. 0.80
   2 !   62.8  23.2   6.1e-21   2.7e-17      35     168 ..     219     355 ..     218     356 .. 0.95
   3 !   63.6  20.8   3.4e-21   1.5e-17      43     212 ..     343     519 ..     342     538 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.7e-21
                              NosD  39 dgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdss 114
                                       +g+     +++ i g+t  +++++ + + s+++ i +nt++++   Gi+l +ss+  +++N+i +n ++Gi l +++
  gi|386001275|ref|YP_005919574.1|  90 SGV---VLDGFIIAGCTNDSCDSASVSVLSDGCKILNNTIYGSMsHGISLLNSSGHLISKNRIHDNFRAGIQLAGAN 163
                                       444...3456777777778887777777888999999999998889********99**********999******** PP

                              NosD 115 nntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvky 178
                                       +++is+N+i  n++Gi++e+s++ +i  N i++n+  Gi  + +s+g++i++N   nnsen  y
  gi|386001275|ref|YP_005919574.1| 164 SSQISDNEIRGNGYGIYIEASEGAVIAYNDISANGADGIA-IVASSGQQITGNEIHNNSENGVY 226
                                       **********************************999999.99999999*****9999999765 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 6.1e-21
                              NosD  35 snsrdgilldnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGil 109
                                       +ns++g+++ +s+nn i  nti+++ ++Gi ++ s s+ i  nt+++++ +Gi l+++ n +++ N +s n+++G++
  gi|386001275|ref|YP_005919574.1| 219 NNSENGVYHLDSKNNIIVANTIQDCrNSGIDVVRSFSTLIVFNTIERCGeMGINLDETDNIVVNRNFLSANDINGVS 295
                                       6899*********************889*******************************99**************** PP

                              NosD 110 lsdssnntisnNtis.nnnkGiflensssnt.itgNriesnqkiGilllsssegntiynNy 168
                                       + +s+ +tisnN++  n ++Gi+l+++s+n  i +N+i++n+ +G+  l++s+ n++ +N+
  gi|386001275|ref|YP_005919574.1| 296 ILGSDHSTISNNVVEkNRDNGISLRRDSRNSmIANNTISENKRYGLI-LDESNLNSVQENQ 355
                                       **************99**********96665166*************.**********997 PP

  == domain 3  score: 63.6 bits;  conditional E-value: 3.4e-21
                              NosD  43 ldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntis 119
                                       ld+s+ n++++n+i+++++Gi++ +s +n + +n++++n+ G++l++  n ++++N+i n+++ Gi+l++++ ++i 
  gi|386001275|ref|YP_005919574.1| 343 LDESNLNSVQENQIHHNTNGIVMRYSAGNSVVENVVRDNGFGLSLEMVDNVVVSKNEIANSSRDGISLNRCDHSKIW 419
                                       7899*********************************************99************************** PP

                              NosD 120 nNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsn...nneWnttkts 192
                                        N+i+ + ++Gi++ +s+ + +++N i +++++G+ +l++s++n++  N   ++     y  ++     ++n    +
  gi|386001275|ref|YP_005919574.1| 420 ANRILdSAADGIHIIRSTATIVSDNDILRSGEYGVQILDQSTQNLLLANLIQDSALGGIYLFEGefnLASFNALIDN 496
                                       **********************************************9999855554433333222443333322211 PP

                              NosD 193 ...gtniiggpylgGNyWsdydg 212
                                          +   +gg+   GNy+sd ++
  gi|386001275|ref|YP_005919574.1| 497 kkfNGWDNGGNLWDGNYYSDHQC 519
                                       10122235778888888888776 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   4.6   4.5e-10     2e-06       6     199 ..      23     185 ..      18     210 .. 0.56
   2 !    6.4  25.0    0.0011         5      84     225 ..     194     343 ..     186     384 .. 0.58
   3 !    8.1   0.9   0.00034       1.5     113     195 ..     380     456 ..     371     492 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.5e-10
                           DUF1565   6 antGsksaPfktiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagkkvgplisgg 82 
                                       + +Gs  + f  i  A+ +++ag+ i + +GtY e+    +P++++          g G+   + + + ++p+i  +
  gi|386001275|ref|YP_005919574.1|  23 QVDGSGTKDFSKIQDAIDASEAGDEIVVKNGTYAESLVVDWPITLR----------GEGM-PLVEGCNATSPVITIN 88 
                                       67899999************************************94..........3344.2222222333333222 PP

                           DUF1565  83 gddlsgvqnvtivlaneatiaGvtitNpnilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGn 159
                                       ++          v+ +   iaG t  N     + +v++ s + ki nNti g + +Gi+  +        g+ is n
  gi|386001275|ref|YP_005919574.1|  89 ASG---------VVLDGFIIAGCT--ND-SCDSASVSVLSDGCKILNNTIYGSMSHGISLLNS------SGHLISKN 147
                                       222.........333344444432..33.2345555555566666666666666666655444......35555666 PP

                           DUF1565 160 silfekn.GiaisgasaavenkienNiivkNliGvvanala 199
                                        i ++ + Gi+  ga+ +   +i +N i  N +G+ + a +
  gi|386001275|ref|YP_005919574.1| 148 RIHDNFRaGIQLAGANSS---QISDNEIRGNGYGIYIEASE 185
                                       655555545555555555...56666666666655544444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0011
                           DUF1565  84 ddlsgvqnvtivlaneatiaGvtitNp....................nilkgtgv.liesasakianNtitgniadG 139
                                        + +g +  +iv  +  +i+G +i N                     +  ++ g+ +++s+s+ i  Nti+ +++ G
  gi|386001275|ref|YP_005919574.1| 194 ISANGADGIAIVASSGQQITGNEIHNNsengvyhldsknniivantiQDCRNSGIdVVRSFSTLIVFNTIERCGEMG 270
                                       4555777889****************955555555555555555433224445552233335555555555555555 PP

                           DUF1565 140 ievsiyeaktgaggniisGnsilfeknGiaisgasaavenkienNiivkNli.GvvanalalDlGsgsegsaGnNif 215
                                       i+ + ++ +  ++ n  s     +++nG+ i g+ ++    i nN++ kN+  G+  +  +     +s   + nN++
  gi|386001275|ref|YP_005919574.1| 271 INLDETD-NIVVNRNFLSA----NDINGVSILGSDHS---TISNNVVEKNRDnGISLRRDS----RNSM--IANNTI 333
                                       5554432.22222222222....33457777666666...677777777766666644444....3344..666777 PP

                           DUF1565 216 snnaeaDini 225
                                       s n++  +  
  gi|386001275|ref|YP_005919574.1| 334 SENKRYGLIL 343
                                       7776665544 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00034
                           DUF1565 113 lkgtgvliesa.sakianNtitgniadGievsiyeaktgaggniisGnsil.feknGiaisgasaavenki.enNii 186
                                        +g g+++e + + ++++N i +  +dGi+ +  + ++      i  n il ++ +Gi i  ++a+    + +n i+
  gi|386001275|ref|YP_005919574.1| 380 DNGFGLSLEMVdNVVVSKNEIANSSRDGISLNRCDHSK------IWANRILdSAADGIHIIRSTAT---IVsDNDIL 447
                                       567899999999999***************98776222......2333332133345555554444...22122233 PP

                           DUF1565 187 vkNliGvva 195
                                           +Gv++
  gi|386001275|ref|YP_005919574.1| 448 RSGEYGVQI 456
                                       333334332 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  12.5   5.9e-10   2.6e-06      14     215 .]      28     249 ..      15     249 .. 0.61
   2 !   11.5   6.7   4.3e-05      0.19     126     209 ..     300     380 ..     273     386 .. 0.69
   3 !    3.9   1.3    0.0093        42      95     211 ..     379     503 ..     367     507 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.9e-10
                                       EEE-HHHHHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-........TTTEEEEE-TT-.SS--SEE CS
                   Pectate_lyase_3  14 vtDdtaaiqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvGdg........ngrpvlkaaaaf.vgaglid 81 
                                        t d   iq+ai   +a++ g+ + +  GtY  s  +     ++L G+g         + pv+  +a+  v +g i 
  gi|386001275|ref|YP_005919574.1|  28 GTKDFSKIQDAI---DASEAGDEIVVKNGTYAESLVV--DWPITLRGEGmplvegcnATSPVITINASGvVLDGFII 99 
                                       3556778*****...9999999999******877666..88999999996666666655555555444332222222 PP

                                       ES-TTT-..-EEEEEEEEEEE..GGGG-SS---S........SEEE.............ES-EEEEEEEEEEES-SS CS
                   Pectate_lyase_3  82 gdpyvsggsealiatnnfyrq..irnlkiditav........apga.............tgihwqtaqatslenvef 135
                                       +  ++++   +  ++++++++  i n +i             ++++             +gi+   a   +++++e+
  gi|386001275|ref|YP_005919574.1| 100 AGCTNDS--CDSASVSVLSDGckILNNTIYG--SmshgisllNSSGhlisknrihdnfrAGIQLAGANSSQISDNEI 172
                                       2222212..2223333333332211212211..11112233322222222211222222444444444444444433 PP

                                       EEE-SSS---TT---SS--EEEE..ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEES CS
                   Pectate_lyase_3 136 emseasgtkhqgifiengsggfl..ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinn 209
                                       +       ++ gi+ie ++g ++  nd+ ++g ++i+i   + qq+t ++i  n+ ++g++ l++++ ++++++i++
  gi|386001275|ref|YP_005919574.1| 173 R------GNGYGIYIEASEGAVIayNDISANGADGIAIVAsSGQQITGNEIHNNS-ENGVYHLDSKNNIIVANTIQD 242
                                       3......45678*****99988888*******7777766656*********9999.9******999988889***** PP

                                       SSE.EEE CS
                   Pectate_lyase_3 210 ceg.Gid 215
                                       c + Gid
  gi|386001275|ref|YP_005919574.1| 243 CRNsGID 249
                                       **99986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.3e-05
                                       EEEEEES-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EE CS
                   Pectate_lyase_3 126 qatslenvefemseasgtkhqgifiengsggfl.ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgw 200
                                       +  +++n+++e +       +gi ++++s++ +  + ++s + ++g+ +  ++   v++++++++t+gi + ++ g 
  gi|386001275|ref|YP_005919574.1| 300 DHSTISNNVVEKN-----RDNGISLRRDSRNSMiANNTISENKRYGLILdESNLNSVQENQIHHNTNGIVMRYSAGN 371
                                       4444444444444.....44489999999977777777777799999997788888899999999999999998887 PP

                                       EEEEEEEES CS
                   Pectate_lyase_3 201 tlknvkinn 209
                                       +++ + + +
  gi|386001275|ref|YP_005919574.1| 372 SVVENVVRD 380
                                       766665544 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0093
                                       EEEEEEEE...GGGG-SS---S.SEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-S CS
                   Pectate_lyase_3  95 atnnfyrq...irnlkiditav.apgatgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglg 167
                                        +n f  +   + n++++ +++ +++ +gi  + ++  ++ ++ +  s a+     gi i ++   +++d  + + g
  gi|386001275|ref|YP_005919574.1| 379 RDNGFGLSlemVDNVVVSKNEIaNSSRDGISLNRCDHSKIWANRILDSAAD-----GIHIIRSTATIVSDNDILRSG 450
                                       555554444457788888888844444888888888888877766555555.....888888888888666666667 PP

                                       S-SEEE.S..-EEEEEES-EEE-S--SEEE-T.T-E.EEEEEE....EEESSS CS
                   Pectate_lyase_3 168 digiav.g..nqqftvrnitfnnattgievlw.gwg.wtlknv....kinnce 211
                                       ++g+++    +q+  + n+   +a  gi++ + + +  +++++    k+n++ 
  gi|386001275|ref|YP_005919574.1| 451 EYGVQIlDqsTQNLLLANLIQDSALGGIYLFEgEFNlASFNALidnkKFNGWD 503
                                       88888853668888888888888888888887455544444332223455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3863.47
//
Query:       gi|386001276|ref|YP_005919575.1|  [L=549]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-53  180.2  63.8    5.6e-21   74.9  16.4    3.8  3  NosD          Periplasmic copper-binding protein (NosD)
    2.5e-52  176.9  73.8    1.1e-22   80.6  30.2    3.5  3  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 !   61.6  17.6   7.2e-21   6.5e-17      41     173 ..      84     213 ..      34     215 .. 0.86
   2 !   62.0  20.7   5.4e-21   4.9e-17      36     173 ..     189     329 ..     187     331 .. 0.96
   3 !   74.9  16.4   6.2e-25   5.6e-21      16     229 ..     330     528 ..     327     542 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 7.2e-21
                              NosD  41 illdnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnn 116
                                       +     +++ i g+t  ++++G +l+ s++++i +nt+++++  Gi++ +ss+  ++nN+i +n ++Gi l + +++
  gi|386001276|ref|YP_005919575.1|  84 V---VLDGFIIGGCTNDSCNSGSVLVLSDGSRIMNNTIYGSTsHGICVLNSSDHLISNNRIHDNFKAGIRLAGVNES 157
                                       4...446788999999999*********************999*********99*********************** PP

                              NosD 117 tisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinns 173
                                        i++N+isnn++G+f+e+s++n ++++ i +n+  G+  ++ss+g +++ N+   n 
  gi|386001276|ref|YP_005919575.1| 158 RIAKNNISNNGYGVFIERSHDNWVSNSDIWGNGADGVT-IASSTGSELTSNSIHSNA 213
                                       ********************************888888.************997776 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 5.4e-21
                              NosD  36 nsrdgilldnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGill 110
                                       n+ dg+++ +s++ ++t n i+++ ++G++l++s++n++ +n ++++  sGi +++s   ++  N i +++++Gi +
  gi|386001276|ref|YP_005919575.1| 189 NGADGVTIASSTGSELTSNSIHSNaDNGVYLVDSNNNILVGNRIRDCMnSGIDIYRSFSIMIASNAIEGCDGMGINV 265
                                       7789***************999998**********************99*********99***************** PP

                              NosD 111 sdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinns 173
                                       +  +nn  + N ++ n+ +Gi++ ++s+nti++N + sn++ Gi l  +s++n +  N++ +n+
  gi|386001276|ref|YP_005919575.1| 266 DSGDNNVMAWNSVLnNDLDGISILGASYNTISHNVVRSNRESGISLRLDSKRNMVIYNNLSENK 329
                                       **************9999***************************9999999999999997775 PP

  == domain 3  score: 74.9 bits;  conditional E-value: 6.2e-25
                              NosD  16 gngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsss 91 
                                        +gi+ ++s+ + ++ nei+n ++++ + +ss+n+i +n+i ++  G+ le  +++++++n++ +++ +Gi l +  
  gi|386001276|ref|YP_005919575.1| 330 RYGIVFDESDSNFVQANEIDNHSTALIIRYSSDNSIVENRIIDSGFGLSLEVVDNVVVSKNEIVNSTrDGIRLFRCD 406
                                       579***********************************************************999998********* PP

                              NosD  92 nntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflens.ssntitgNriesnqkiGilllsssegntiyn 166
                                       n+ +  N+i n+   G+ + +s+++ +s+N i+ + ++Gi++ ++  +n + +N i++++  Gi+ l ++e n+++ 
  gi|386001276|ref|YP_005919575.1| 407 NSNIWSNRIPNSAADGVHIIRSTGTIVSDNDILgSGEYGIQVLDQsAQNLFLSNLIQNSGLGGIY-LFDGEFNLVMS 482
                                       99**************************************976654999999*******777788.99999****** PP

                              NosD 167 NyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeind 229
                                       N +i+n++ ++  ++++n+W                +GNy+sd++++   g  ++ +pYei +
  gi|386001276|ref|YP_005919575.1| 483 NGLIDNKK-FNGRDNGGNRW----------------AGNYYSDFECREMIGTMVCAEPYEIRG 528
                                       ***99984.44444449***................9**********************9975 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 !   80.6  30.2   1.3e-26   1.1e-22       5     158 .]     106     255 ..      87     255 .. 0.95
   2 !   65.4  18.5   5.9e-22   5.3e-18       1     140 [.     238     375 ..     238     380 .. 0.92
   3 !   56.1  14.6   4.2e-19   3.8e-15       4     148 ..     356     500 ..     353     508 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.3e-26
                                       E-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                        Beta_helix   5 ingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                       + ++++  i nnti++s ++Gi++ +ss+++i+nn+i++n   Gi++ g++++ i +n+is+n+ +g+ ++ ++ n 
  gi|386001276|ref|YP_005919575.1| 106 VLSDGS-RIMNNTIYGSTSHGICVLNSSDHLISNNRIHDNFKAGIRLAGVNESRIAKNNISNNG-YGVFIERSHDNW 180
                                       445555.7*******************************************************9.************ PP

                                       EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                       ++n++i+ ng +G+++ +s+   ++ N i++na +G+++ ds+ n+   +N+i ++++ Gi++++s s + ++ N i
  gi|386001276|ref|YP_005919575.1| 181 VSNSDIWGNGADGVTIASSTGSELTSNSIHSNADNGVYLVDSN-NNILVGNRIRDCMNSGIDIYRSFS-IMIASNAI 255
                                       *******************************************.999*******************99.99999975 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 5.9e-22
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.- CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.g 76 
                                       sgi i++s ++ i  n i+++ g Gi +++++n+v+  n + nn  +Gi+ilg+s+ntis+n+++ n ++gi l+ +
  gi|386001276|ref|YP_005919575.1| 238 SGIDIYRSFSIMIASNAIEGCDGMGINVDSGDNNVMAWNSVLNNDLDGISILGASYNTISHNVVRSNRESGISLRlD 314
                                       69999********************************6666666********************************* PP

                                       -S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSE CS
                        Beta_helix  77 asnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkga 140
                                       +++n++ +n+ ++n+++Gi ++ s++n ++ N idn +  ++ i++ss ++ +  N+i +++  
  gi|386001276|ref|YP_005919575.1| 315 SKRNMVIYNNLSENKRYGIVFDESDSNFVQANEIDNHS-TALIIRYSS-DNSIVENRIIDSG-F 375
                                       **********************************9999.999999999.7778999988875.4 PP

  == domain 3  score: 56.1 bits;  conditional E-value: 4.2e-19
                                       EE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S-- CS
                        Beta_helix   4 singssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnn 80 
                                       +i+ ss+ +i  n i + +g G+ l+  +nvv+++nei n++ +Gi++ +++n++i  n+i ++ ++g+++  + ++
  gi|386001276|ref|YP_005919575.1| 356 IIRYSSDNSIVENRIID-SGFGLSLEVVDNVVVSKNEIVNSTRDGIRLFRCDNSNIWSNRIPNSAADGVHIIRSTGT 431
                                       566666679********.7********************************************************** PP

                                       EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-S CS
                        Beta_helix  81 lienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgss 148
                                       ++++n+i   g++Gi++  +s +n +  N i n +  Gi++ d++ n++++n  i+n k +G ++ g+ 
  gi|386001276|ref|YP_005919575.1| 432 IVSDNDILGSGEYGIQVLdQSAQNLFLSNLIQNSGLGGIYLFDGEFNLVMSNGLIDNKKFNGRDNGGNR 500
                                       *****************955888**********************999999999999998887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3639.83
//
Query:       gi|386001277|ref|YP_005919576.1|  [L=385]
Description: Pentapeptide repeat protein [Methanosaeta harundinacea 6Ac]
Scores for 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-82  271.1  38.8    8.9e-12   44.4   1.7   10.2 10  Pentapeptide    Pentapeptide repeats (8 copies)
    2.7e-38  130.0   0.0    6.5e-08   32.6   0.0    5.6  5  Pentapeptide_4  Pentapeptide repeats (9 copies)
    3.3e-34  116.8   0.0    0.00033   20.7   0.3    8.5 10  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.19   11.7   0.0         27    4.7   0.0    3.2  4  CfAFP           Choristoneura fumiferana antifreeze protein (


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.6   4.2e-15   1.9e-11       1      39 [.      38      76 ..      38      76 .. 0.98
   2 !   44.4   1.7     2e-15   8.9e-12       1      39 [.      68     106 ..      68     106 .. 0.98
   3 !   37.9   0.0   2.1e-13   9.4e-10       2      40 .]     109     147 ..     109     147 .. 0.98
   4 !   26.0   0.0   1.2e-09   5.2e-06       1      40 []     148     187 ..     148     187 .. 0.96
   5 !   27.8   0.1     3e-10   1.4e-06       2      40 .]     179     217 ..     178     217 .. 0.92
   6 !   37.0   1.6   4.1e-13   1.8e-09       1      40 []     213     252 ..     213     252 .. 0.98
   7 !   37.1   0.5   3.8e-13   1.7e-09       1      40 []     258     297 ..     258     297 .. 0.97
   8 !   32.3   0.0   1.2e-11   5.5e-08       5      40 .]     292     327 ..     288     327 .. 0.96
   9 !   32.0   0.6   1.5e-11   6.8e-08       1      32 [.     323     354 ..     323     360 .. 0.82
  10 !    4.8   0.0    0.0051        23       6      17 ..     361     372 ..     357     375 .. 0.43

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 4.2e-15
                                      -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide  1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39
                                      ++L+ A+Lsg +L ga+l++++L+gA+lsgAdL++a L+
  gi|386001277|ref|YP_005919576.1| 38 CDLRSADLSGRDLVGAHLNQSDLSGADLSGADLRDAYLR 76
                                      9***********************************997 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 2e-15
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       A+L++A+L+ + L ganl+ AnL gA+lsgAdLs+a+Ls
  gi|386001277|ref|YP_005919576.1|  68 ADLRDAYLRSTWLLGANLKKANLAGADLSGADLSEADLS 106
                                       8************************************97 PP

  == domain 3  score: 37.9 bits;  conditional E-value: 2.1e-13
                                       B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       +Ls+A L+ga+ sga+l +A+Lt+A+l+++d ++a+L+g
  gi|386001277|ref|YP_005919576.1| 109 DLSEAKLWGAKISGASLVDATLTKADLTRTDITDADLTG 147
                                       79************************************8 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 1.2e-09
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A++++A+L  a+L+ga ++g  L+g n+ gA ++ a ++g
  gi|386001277|ref|YP_005919576.1| 148 AEMTNARLFRADLTGATMTGVYLIGGNFVGAHMNWAEMRG 187
                                       789********************************99987 PP

  == domain 5  score: 27.8 bits;  conditional E-value: 3e-10
                                       B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                        +++A  +g++L++  +s+A ++g++lsg+dLs++++s+
  gi|386001277|ref|YP_005919576.1| 179 HMNWAEMRGSYLNRGQFSRAEFYGTDLSGSDLSDSDFSR 217
                                       57788899*****************************95 PP

  == domain 6  score: 37.0 bits;  conditional E-value: 4.1e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       +++s+A+L  anLs+anl+ A + +A+l+ A+Ls++ L+g
  gi|386001277|ref|YP_005919576.1| 213 SDFSRAYLMRANLSDANLNWALFAYADLTEAKLSRSTLRG 252
                                       69************************************98 PP

  == domain 7  score: 37.1 bits;  conditional E-value: 3.8e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A+L+gA+Lsga+L++a+l+   L+++nls++++ +a L+g
  gi|386001277|ref|YP_005919576.1| 258 ADLTGADLSGADLTDADLTAIRLIKSNLSNTKMGRAYLQG 297
                                       89**********************************9987 PP

  == domain 8  score: 32.3 bits;  conditional E-value: 1.2e-11
                                       T-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   5 gAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       +A+L+g +L+g++lsgA L++A++ ++ L++anL+g
  gi|386001277|ref|YP_005919576.1| 292 RAYLQGLDLRGVDLSGAYLRDATIDRTYLTDANLTG 327
                                       8**********************************8 PP

  == domain 9  score: 32.0 bits;  conditional E-value: 1.5e-11
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-E CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAd 32 
                                       AnL+gA+L+ga Ls + ++gA+L gAnl++A+
  gi|386001277|ref|YP_005919576.1| 323 ANLTGADLRGATLSSVEMTGADLAGANLIRAK 354
                                       78889999999999999999999999988887 PP

  == domain 10  score: 4.8 bits;  conditional E-value: 0.0051
                                       -B-CCSCCEECC CS
                      Pentapeptide   6 AnLsganLsgan 17 
                                       + Ls anL+g+ 
  gi|386001277|ref|YP_005919576.1| 361 VSLSKANLEGTL 372
                                       444444444443 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   8.1e-10   3.6e-06       5      72 ..      37     105 ..      36     107 .. 0.92
   2 !   19.2   0.0   2.2e-07     0.001       9      62 ..     101     154 ..      98     156 .. 0.75
   3 !   32.6   0.0   1.4e-11   6.5e-08       1      76 [.     148     224 ..     148     225 .. 0.95
   4 !   27.9   0.0   4.4e-10     2e-06       4      74 ..     226     297 ..     223     300 .. 0.87
   5 !   22.5   0.0   2.1e-08   9.6e-05       8      73 ..     300     373 ..     289     379 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.1e-10
                    Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.kl 72 
                                       rc ++ ++ls+ ++  a+l+ +++++++ls + ++++ l+++ + +++lk+a++ g +l+++ +s+  l
  gi|386001277|ref|YP_005919576.1|  37 RCDLRSADLSGRDLVGAHLNQSDLSGADLSGADLRDAYLRSTWLLGANLKKANLAGADLSGADLSEaDL 105
                                       89999*********************************************************9965355 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.2e-07
                    Pentapeptide_4   9 nncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcn 62 
                                        +++ls+v++sea+l ++ ++++ l+++++++++l  +d++++dl+ a+ ++ +
  gi|386001277|ref|YP_005919576.1| 101 SEADLSEVDLSEAKLWGAKISGASLVDATLTKADLTRTDITDADLTGAEMTNAR 154
                                       567888888888888888888888888888888888888888887777666654 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 1.4e-11
                    Pentapeptide_4   1 aeftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                       ae+t++ + +++l++++++ ++l++ nF++++++ ++++ + l+  +f+ +++  + +sg++l+++ fs+  l++++
  gi|386001277|ref|YP_005919576.1| 148 AEMTNARLFRADLTGATMTGVYLIGGNFVGAHMNWAEMRGSYLNRGQFSRAEFYGTDLSGSDLSDSDFSRaYLMRAN 224
                                       68999999************************************************************874798876 PP

  == domain 4  score: 27.9 bits;  conditional E-value: 4.4e-10
                    Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkd 74 
                                       +++ +n + +++++++ea+l ++++++++ls++ ++ ++ls +d++++dl+ +++  +nl+n++  ++ l +
  gi|386001277|ref|YP_005919576.1| 226 SDANLNWALFAYADLTEAKLSRSTLRGTKLSYADLTGADLSGADLTDADLTAIRLIKSNLSNTKMgRAYLQG 297
                                       56677778899***************************************************9985555655 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 2.1e-08
                    Pentapeptide_4   8 fnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkra........sFsgcnlknvnfsdklk 73 
                                       +++++ls++ ++ a++ ++ +t+++l+ + ++ ++ls+v+ +++dl+ a        +F+ + l+++n++++l 
  gi|386001277|ref|YP_005919576.1| 300 LRGVDLSGAYLRDATIDRTYLTDANLTGADLRGATLSSVEMTGADLAGAnlirakvdQFTLVSLSKANLEGTLL 373
                                       45666666667777777777777777777788888888888888888888888888877777777777777654 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   1.8e-05     0.079       8      47 ..      36      73 ..      33      74 .. 0.85
   2 !   12.7   0.0   2.5e-05      0.11       3      36 ..      82     113 ..      76     118 .. 0.70
   3 !   17.6   0.0     7e-07    0.0031       3      47 ..     117     158 ..     115     159 .. 0.92
   4 !    9.2   0.0    0.0003       1.3       6      44 ..     155     195 ..     150     197 .. 0.71
   5 !   20.7   0.3   7.4e-08   0.00033       1      39 [.     195     231 ..     186     239 .. 0.59
   6 !   16.0   0.0   2.2e-06    0.0097       2      46 ..     236     277 ..     235     279 .. 0.85
   7 !   17.1   0.0     1e-06    0.0046       4      48 .]     293     334 ..     272     334 .. 0.87
   8 !   18.4   0.0   3.9e-07    0.0017       2      47 ..     301     343 ..     300     344 .. 0.90
   9 !   12.1   0.0   3.8e-05      0.17       4      38 ..     318     350 ..     314     356 .. 0.60
  10 ?    1.6   0.0     0.069   3.1e+02       5      39 ..     339     369 ..     335     375 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                    Pentapeptide_3  8 gaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47
                                      + +d+r a  sg  +  +a+++ +d+sga  + ++d+++a
  gi|386001277|ref|YP_005919576.1| 36 DRCDLRSADLSGR-DLVGAHLNQSDLSGADLS-GADLRDA 73
                                      5569999999999.999999999999999999.9999886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsga 36 
                                       gan+++a ++ ga  sga + s+ad++++d+s+a
  gi|386001277|ref|YP_005919576.1|  82 GANLKKA-NLAGADLSGA-DLSEADLSEVDLSEA 113
                                       5666777.7777777777.777777777777665 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 7e-07
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       ga  sga ++ +at ++a + +++d+++ad+ ga +t ++++ +a
  gi|386001277|ref|YP_005919576.1| 117 GAKISGA-SLVDATLTKA-DLTRTDITDADLTGAEMT-NARLFRA 158
                                       7889999.**********.******************.9998776 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0003
                    Pentapeptide_3   6 FsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdF 44 
                                       + +a d++gat +g      +F +a+++ a  +g+  + + +F
  gi|386001277|ref|YP_005919576.1| 155 LFRA-DLTGATMTGVYliggNFVGAHMNWAEMRGSYLN-RGQF 195
                                       4455.6666666666555558*********99999877.6666 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 7.4e-08
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFt 39 
                                       Fs+a+F+g+ d++g+  s++ +Fs+a + +a++s+a+ +
  gi|386001277|ref|YP_005919576.1| 195 FSRAEFYGT-DLSGSDLSDS-DFSRAYLMRANLSDANLN 231
                                       555555555.5555555555.566655555555555555 PP

  == domain 6  score: 16.0 bits;  conditional E-value: 2.2e-06
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                                         a ++ a  ++++t +g+   s ad+++ad+sga  t d+d+++
  gi|386001277|ref|YP_005919576.1| 236 AYADLTEA-KLSRSTLRGT-KLSYADLTGADLSGADLT-DADLTA 277
                                       55667777.9999999999.7*****************.**9975 PP

  == domain 7  score: 17.1 bits;  conditional E-value: 1e-06
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48 
                                       a ++g  d+rg+  sga + ++a++++  + +a+ t ++d++gat
  gi|386001277|ref|YP_005919576.1| 293 AYLQGL-DLRGVDLSGA-YLRDATIDRTYLTDANLT-GADLRGAT 334
                                       667778.8899999999.899999999999999999.99998886 PP

  == domain 8  score: 18.4 bits;  conditional E-value: 3.9e-07
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       +g+ +sga ++r+at +++ + ++a++++ad++ga+ +  v+++ga
  gi|386001277|ref|YP_005919576.1| 301 RGVDLSGA-YLRDATIDRT-YLTDANLTGADLRGATLS-SVEMTGA 343
                                       57789999.**********.9***************99.9988876 PP

  == domain 9  score: 12.1 bits;  conditional E-value: 3.8e-05
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarF 38 
                                       + +++a +++ga  +ga+  s+  +++ad++ga+ 
  gi|386001277|ref|YP_005919576.1| 318 TYLTDA-NLTGADLRGAT-LSSVEMTGADLAGANL 350
                                       555555.66666666663.6666666666666654 PP

  == domain 10  score: 1.6 bits;  conditional E-value: 0.069
                    Pentapeptide_3   5 nFsgaadFrgatFsgaa..sFsnadFgsadFsgarFt 39 
                                       +++ga d+ ga+ ++a    F     + +++s+a+ +
  gi|386001277|ref|YP_005919576.1| 339 EMTGA-DLAGANLIRAKvdQF-----TLVSLSKANLE 369
                                       44444.555555555543223.....44444444443 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.86   3.9e+03      45      83 ..      56      94 ..      46     122 .. 0.71
   2 ?    4.7   0.0     0.006        27      51      94 ..     127     170 ..     101     181 .. 0.62
   3 ?   -0.7   0.0      0.28   1.2e+03      56      84 ..     212     240 ..     197     279 .. 0.50
   4 ?    2.6   0.0     0.028   1.3e+02      64     106 ..     305     347 ..     240     356 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.86
                             CfAFP 45 dnselessictrsqysdayvkksvttdcnidksqlygtt 83
                                      ++s+l  +  + ++  day++++    +n++k++l g+ 
  gi|386001277|ref|YP_005919576.1| 56 NQSDLSGADLSGADLRDAYLRSTWLLGANLKKANLAGAD 94
                                      566666666666777777777777777777777766554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.006
                             CfAFP  51 ssictrsqysdayvkksvttdcnidksqlygttctgsrydGvyi 94 
                                        ++ t+++ + + ++++  t +++ +++l+ +  tg+   Gvy+
  gi|386001277|ref|YP_005919576.1| 127 DATLTKADLTRTDITDADLTGAEMTNARLFRADLTGATMTGVYL 170
                                       34445555555555555566666666666666666666666665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.28
                             CfAFP  56 rsqysdayvkksvttdcnidksqlygttc 84 
                                        s++s ay++++  +d+n++ + +  +  
  gi|386001277|ref|YP_005919576.1| 212 DSDFSRAYLMRANLSDANLNWALFAYADL 240
                                       44445555555555554444332222222 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.028
                             CfAFP  64 vkksvttdcnidksqlygttctgsrydGvyitsstttgtrisG 106
                                       +  +   d+ id++ l  +  tg+   G ++ s   tg+ ++G
  gi|386001277|ref|YP_005919576.1| 305 LSGAYLRDATIDRTYLTDANLTGADLRGATLSSVEMTGADLAG 347
                                       2333344566666666666667777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2544.13
//
Query:       gi|386001278|ref|YP_005919577.1|  [L=226]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1758.11
//
Query:       gi|386001279|ref|YP_005919578.1|  [L=405]
Description: hypothetical protein Mhar_0577 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2488.00
//
Query:       gi|386001280|ref|YP_005919579.1|  [L=182]
Description: Phosphoesterase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-23   81.6   0.0      8e-23   81.4   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00029   21.4   0.1      0.034   14.6   0.0    2.2  2  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.0     9e-27     8e-23       2     163 ..       3     148 ..       1     150 [. 0.86

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 9e-27
                     Metallophos_2   2 klaiiSDlH.snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaael 77 
                                       k+++iSD+H ++++ +++ l +l+++ +d+++haGD+  +++e+ e++++l p++aV GN D              +
  gi|386001280|ref|YP_005919579.1|   3 KILAISDTHlQEGAGVPKPLIDLSGE-ADLVLHAGDF--VSLEAYEAFRDLVPFEAVSGNSD-----------DPAV 65 
                                       799******96666666666666665.6*********..***********************...........7889 PP

                     Metallophos_2  78 gtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdp 154
                                       +  lp+++++e+++++++l+H    +++   a+ll + e+++d +v+GH H+p +e   ++l++ PGs++epr + p
  gi|386001280|ref|YP_005919579.1|  66 AALLPQRRVVEVEEVRIGLVHRPSFSADLLGADLLAR-EMEADALVFGHLHRPLLEGG-DRLLICPGSPTEPRLSPP 140
                                       9999******************966555555666666.78888**********99976.89***********99999 PP

                     Metallophos_2 155 etyaildtd 163
                                         +a+l+++
  gi|386001280|ref|YP_005919579.1| 141 -AVAVLEVE 148
                                       .99999987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.8e-06     0.034       2      56 ..       3      50 ..       2      69 .. 0.79
   2 !    4.8   0.0    0.0039        35     166     204 .]      84     117 ..      72     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-06
                                      EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH CS
                       Metallophos  2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellel 56
                                      +il i+D+Hl +g g    l++l        ++dlvl+aGD+v    +e  + +l
  gi|386001280|ref|YP_005919579.1|  3 KILAISDTHLQEGAGVPKPLIDLSG------EADLVLHAGDFVSLEAYEA-FRDL 50
                                      8********9888899999999994......45*********98776666.5555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0039
                                       EESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 166 lgHsplyrgsgylfgdealedllkkygvdlvisGHtHvy 204
                                       l H+p    s +l g + l+   ++ ++d+ ++GH H++
  gi|386001280|ref|YP_005919579.1|  84 LVHRPSF--SADLLGADLLA---REMEADALVFGHLHRP 117
                                       5677777..66666666666...78899*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       158  (0.00881254); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 1269.76
//
Query:       gi|386001281|ref|YP_005919580.1|  [L=396]
Description: Sugar phosphate isomerase involved in capsule formation-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-09   36.8   0.0     0.0005   19.9   0.0    2.9  2  SIS           SIS domain
  ------ inclusion threshold ------
      0.068   12.9   0.0         15    5.3   0.0    2.4  2  Flavoprotein  Flavoprotein


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 !   13.0   0.0   7.8e-06      0.07      10      95 ..      52     134 ..      45     138 .. 0.81
   2 !   19.9   0.0   5.5e-08    0.0005       7      96 ..     236     319 ..     230     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-06
                                       EEESHHHHH.HHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEE CS
                               SIS  10 vlGaGtsya.iakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiia 85 
                                        l+aG+s+  + ++l+l +++++ +++ +ed  + +       +++ l i++s sget+ +++ +e   ++g+ i +
  gi|386001281|ref|YP_005919580.1|  52 GLAAGRSALsLYSFLQLLYNHFNAFPCTMEDPVQKHF----RSTRKNLGIAVSGSGETPAVNKYIEDIINQGGDITL 124
                                       5667777766667777777888888888888888444....489999****************************** PP

                                       EESSTTSHHH CS
                               SIS  86 ITdskgspla 95 
                                       IT +++ ++ 
  gi|386001281|ref|YP_005919580.1| 125 ITANEDGTAH 134
                                       ****998765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.5e-08
                                       EEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEE CS
                               SIS   7 riyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergaki 83 
                                       r ++ G G+s+ +a+ + + + ++++  +   d  +      +  + +d+ + i+ sg+t + ++ ++ a +rga +
  gi|386001281|ref|YP_005919580.1| 236 RYIIGGVGRSGLVARAFEMRFTHLNKTSYWERDFNT------PSFQIGDVYVPITGSGNTYECLEGVRSAFKRGADV 306
                                       7789999**************888887766555444......678899***************************** PP

                                       EEEESSTTSHHHH CS
                               SIS  84 iaITdskgsplar 96 
                                       + IT +++s l++
  gi|386001281|ref|YP_005919580.1| 307 LPITTNPTSELVE 319
                                       *********9986 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0017        15       1      34 [.      93     126 ..      93     155 .. 0.92
   2 ?    5.2   0.0    0.0018        16       4      43 ..     280     319 ..     278     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0017
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvl 34 
                                       k++ ++++Gs  +  + +++e ++++g +++++ 
  gi|386001281|ref|YP_005919580.1|  93 KNLGIAVSGSGETPAVNKYIEDIINQGGDITLIT 126
                                       5789**************************9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0018
                                       EEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCH CS
                      Flavoprotein   4 llgiTGsvaaikalellekLkkegievqvvltkaAkkfis 43 
                                        + iTGs  +++ le +++  k+g++v  + t+   ++++
  gi|386001281|ref|YP_005919580.1| 280 YVPITGSGNTYECLEGVRSAFKRGADVLPITTNPTSELVE 319
                                       5779**************************9987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2547.26
//
Query:       gi|386001282|ref|YP_005919581.1|  [L=411]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-57  192.8   0.0    5.7e-57  192.3   0.0    1.1  1  DUF1297      Domain of unknown function (DUF1297)
    3.1e-41  140.2   0.0    5.1e-41  139.5   0.0    1.3  1  DUF1246      Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.025   14.6   0.0    1.6  1  ATP-grasp_3  ATP-grasp domain
       0.18   11.3   0.0       0.34   10.4   0.0    1.4  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.3   0.0   1.3e-60   5.7e-57      18     187 ..     234     410 ..     223     411 .] 0.95

  Alignments for each domain:
  == domain 1  score: 192.3 bits;  conditional E-value: 1.3e-60
                                       HHHCCEEEEE---SEEEEEEEEEETTT........TEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-.---EEEEEE CS
                           DUF1297  18 edlkkasieeyvvGanfnlnyfysplk........eevellgidrRyesnldglvrlpakeqlelev.epeyvvvGn 85 
                                       +++++ +i+e+++G++++++yfysp++        +++e+lgidrR+esn d++ r+ + ++le+    p++vv+Gn
  gi|386001282|ref|YP_005919581.1| 234 DATQRHTIQEFILGTRYYIHYFYSPIRshgytlskGTLEMLGIDRRVESNADEIFRIGSMDELEAAGiFPSFVVTGN 310
                                       5667889***************************99***********************9999976559******** PP

                                       EEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS CS
                           DUF1297  86 ipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfge 162
                                       ip+vlREsll+k+f+lge++vea+ +l+  G+iGpFcL+++vt+dl++ vf++saRiv+gtnv+++gspys l  ++
  gi|386001282|ref|YP_005919581.1| 311 IPLVLRESLLPKAFDLGERVVEASLDLFG-GMIGPFCLETIVTDDLKFKVFEISARIVAGTNVFISGSPYSDL-IER 385
                                       **************************997.*****************************************87.588 PP

                                       ---HHHHHHHHHHHHHHCT-GGGCE CS
                           DUF1297 163 plsmGrrialEikeaiekdrleeiv 187
                                        ls G+ria Ei  a +++rl+ei+
  gi|386001282|ref|YP_005919581.1| 386 DLSNGKRIAQEISLARDQGRLSEII 410
                                       9***********************9 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.5   0.0   1.1e-44   5.1e-41       1     122 []      76     197 ..      76     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 1.1e-44
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-..SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvi..devivldkfkdilkeevqeklreenailvPhgsf 75 
                                       iat++SHs+lqi++gA+++gfrtl +c  +  k+Y++f+++  d+++ ld++  +l e+  ++l+eenai+vPhgs+
  gi|386001282|ref|YP_005919581.1|  76 IATVCSHSSLQIFHGARQKGFRTLGICLGRPPKFYDAFPLAkpDTFLSLDSYGALLGES--DRLVEENAIVVPHGSL 150
                                       89************************************99989*************998..**************** PP

                                       HHHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                           DUF1246  76 veYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                       veY+g+e++ee+ vp+fGnr+ l wE++re++r++L kAgi +P+++
  gi|386001282|ref|YP_005919581.1| 151 VEYLGTERFEEMPVPTFGNRRSLAWESDREMEREWLLKAGIDLPRRF 197
                                       ********************************************986 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.6e-06     0.025       8      97 ..     183     272 ..     177     369 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.6e-06
                                       HHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.........EEEE---SEEEEEEEEE. CS
                       ATP-grasp_3   8 ykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..lvqefieGkplSvsllsd 82 
                                        ++L +ag+ +P   + + +ee + +++vK   + gg++ ++ + k e  ++++ ++   +qefi G+ + +    +
  gi|386001282|ref|YP_005919581.1| 183 REWLLKAGIDLP--RRFATPEEIDRPVIVKYHGAKGGKGFFISKSKGEYLSKVDATQrhTIQEFILGTRYYIHYFYS 257
                                       57999999****..89999*************************999999888877778*********998877766 PP

                                       SSSEEEEEEEEEEEE CS
                       ATP-grasp_3  83 gekvlvlavnrqlie 97 
                                         + +  ++++  +e
  gi|386001282|ref|YP_005919581.1| 258 PIRSHGYTLSKGTLE 272
                                       666665555555555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.5e-05      0.34      32      78 ..     198     244 ..     189     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.5e-05
                                       HHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  32 aiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       a  +ei  Pvi+k   + GGkG  + +++ e    v ++++++   f
  gi|386001282|ref|YP_005919581.1| 198 ATPEEIDRPVIVKYHGAKGGKGFFISKSKGEYLSKVDATQRHTIQEF 244
                                       5568999**********************999999998888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2993.33
//
Query:       gi|386001283|ref|YP_005919582.1|  [L=180]
Description: Imidazoleglycerol-phosphate dehydratase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-30  106.7   0.0    2.6e-30  105.6   0.0    1.5  2  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.25   4.4e+03      70      82 ..      11      23 ..       5      28 .. 0.80
   2 !  105.6   0.0   1.4e-34   2.6e-30       1     144 []      30     166 ..      30     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.25
                                      TEEEEEEEE--SS CS
                              IGPD 70 ealaevaldlsgr 82
                                      e+ +ev++dl+g 
  gi|386001283|ref|YP_005919582.1| 11 ETKVEVSIDLEGS 23
                                      7889999999875 PP

  == domain 2  score: 105.6 bits;  conditional E-value: 1.4e-34
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       Tg+ +ld +L+ la+ +gfdl+v+++gdl   dHhtvedv+i +Gqal++     +g   +gs  +p  eala +a+
  gi|386001283|ref|YP_005919582.1|  30 TGVRLLDEILRLLARGSGFDLRVRASGDLPTGDHHTVEDVAISFGQALAQVA--VAG---IGSSSVPSGEALAFAAV 101
                                       9*************************************************98..566...599************** PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                        +  + y + e++++r+++  +d e++ +f+++la + g+tlh++++ g ++  +veal+ a++raL
  gi|386001283|ref|YP_005919582.1| 102 RFGATGYRE-EVDISRRSLEGMDLENLGHFMRTLAYNGGLTLHLRAS-GGDDWQKVEALATALGRAL 166
                                       *******99.556********************************99.9999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1231.83
//
Query:       gi|386001284|ref|YP_005919583.1|  [L=163]
Description: hypothetical protein Mhar_0582 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1167.86
//
Query:       gi|386001285|ref|YP_005919584.1|  [L=475]
Description: Ketoisovalerate oxidoreductase subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-37  127.0   0.0    1.2e-36  126.5   0.0    1.3  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    7.6e-22   77.7   0.0    1.2e-21   77.1   0.0    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0   1.3e-40   1.2e-36       1     176 [.     306     468 ..     306     469 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1.3e-40
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv+++g  la+aa r+G  v+++++yg+e+rGg s++ v is e +v s+ v+++d+lva++  +l+++++++ 
  gi|386001285|ref|YP_005919584.1| 306 GGQGVLSMGLALAQAAYRSGRFVSWYPDYGPEQRGGTSNCSVVISGE-RVGSPVVDRPDILVAFNRPSLEKFAADVP 381
                                       9**********************************************.9**************************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT..S-HHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg..lplealee 152
                                       +gg+i+y++      e ++ +              ++v+at+ia   g+ e a+Nt+m+Gal+  ++  lp+ea+  
  gi|386001285|ref|YP_005919584.1| 382 KGGLILYDA-LAGAFEPPEGVT------------AIPVPATEIALSRGV-EQATNTAMFGALMERGNlgLPREAFGG 444
                                       *********.445555555444............58************9.************9999966777***** PP

                                       HHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 153 aikkrfpkkkeviekNlkafragy 176
                                       a +++f+kk ++i +Nl+ ++ag 
  gi|386001285|ref|YP_005919584.1| 445 AFERTFAKKPKLIPLNLEILEAGA 468
                                       **********************95 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   1.4e-25   1.2e-21       2     152 ..      62     220 ..      61     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.4e-25
                                       SSHHHHHHHHHHTTSSSSEEECET.TTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsg.glgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       +Gc+ +           + yl++g + +++G++ ++A+G+++a+ d+  +++ GDG+++ i l+e+++a++r+ ++ 
  gi|386001285|ref|YP_005919584.1|  62 VGCSVF----------AYYYLDCGhVQAAHGRAPAIATGLSRAEDDAILISYQGDGDLASIgLNETVQAANRGEKMA 128
                                       566666..........567888555999***************99******************************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.....BS----HHHHHHHTTSEEE..EESSH.HHHH...HHHHHH CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagk....dlkpvdfaklaealGakga..rvekadveel...eealke 141
                                       v+ +nN +ygmtggq   ++  g+ + ++pag+     ++p+++++l   l a+++  rv+ ++++++   ++a+++
  gi|386001285|ref|YP_005919584.1| 129 VFFVNNTVYGMTGGQmapTTLVGEVTATTPAGRdprdSGYPIHLCELLDTLRAPVFieRVSLSNINHIrraRRAVRR 205
                                       ******************99***********99**977****************777*9999998888444667777 PP

                                       HH....CSSSEEEEE CS
                      TPP_enzyme_C 142 al....ekkgpalie 152
                                       al    +kkg a++e
  gi|386001285|ref|YP_005919584.1| 206 ALeiqrDKKGYAFVE 220
                                       779999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 3263.31
//
Query:       gi|386001286|ref|YP_005919585.1|  [L=347]
Description: Ketoisovalerate ferredoxin oxidoreductase, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-53  180.1   0.0    7.1e-53  179.7   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.1e-22   80.3   0.0    2.1e-22   79.4   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    9.3e-05   22.3   0.0    0.00018   21.4   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.7   0.0   1.2e-56   7.1e-53       2     195 ..      15     210 ..      14     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 1.2e-56
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++ag+d +++YPITP+sei++e++++ +k++    ++vq+esE +ai++v GAaaaG r++ a+Sg+G++L++e 
  gi|386001286|ref|YP_005919585.1|  15 GAMYAGCDCYFGYPITPASEILHEASKYFPKVGR---KFVQAESEEAAINMVYGAAAAGHRVLAASSGPGMSLKQEG 88 
                                       799******************************7...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH......S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar......dtglivlasenvqeafdlalvAfnlAekvrvPv 149
                                       + ++ag+elP+viv++aRa+p    +i ++qsD ++a        +  +vla+++vqe+ d++++Af lA+k+r P+
  gi|386001286|ref|YP_005919585.1|  89 ISYIAGAELPCVIVDIARAGPGL-GNIGPEQSDYNQAVkggghgCYRNLVLAPNSVQEMCDFTIKAFDLAFKYRNPA 164
                                       ***********************.9****************77777779**************************** PP

                                       EEEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX..SXXXBX CS
                             POR_N 150 ivlfDgfllshevekvelpdeedelklikekleeyerkey..aldpek 195
                                       ++l Dg+l+ h+ve +++p++  +  +i++ +  + +ke   +l +  
  gi|386001286|ref|YP_005919585.1| 165 VILADGVLG-HMVELLTFPKRA-IEPVIDDSWAVRGNKETrgNLVTSI 210
                                       *********.*********999.8888888887777776534333333 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   3.5e-26   2.1e-22       1     101 [.     246     338 ..     246     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 3.5e-26
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Aevv+v +G++++ aksavd++R+egi +Gl+r+++l+PFP++el+ ++++ +++++++++      Gq+ e+++ a
  gi|386001286|ref|YP_005919585.1| 246 AEVVLVSYGISSRIAKSAVDAARREGIAAGLFRPISLFPFPSRELRAFADRGSRFISVEMSD-----GQMREDIRLA 317
                                       9*************************************************************.....********** PP

                                       TGGGTSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditved 101
                                       + ++    v +v++ gG++i+ ++
  gi|386001286|ref|YP_005919585.1| 318 TGCR---EVALVSRYGGNLIQRHQ 338
                                       9988...9999*******998776 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     3e-08   0.00018       6      68 ..     242     304 ..     238     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3e-08
                                       EETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C   6 lregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                       ++e  +v+lv+yG   + a  A++++++egi a +  ++++ p+  + +++ + +  r++ ve
  gi|386001286|ref|YP_005919585.1| 242 RCEDAEVVLVSYGISSRIAKSAVDAARREGIAAGLFRPISLFPFPSRELRAFADRGSRFISVE 304
                                       57899**************************************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 2748.66
//
Query:       gi|386001287|ref|YP_005919586.1|  [L=628]
Description: AMP-forming acetyl-CoA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-76  256.5   0.0    4.6e-76  256.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.2e-23   82.1   0.5    1.2e-22   80.7   0.5    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.8e-08   33.8   8.4    7.5e-08   32.8   8.4    1.5  1  Fer4_7         4Fe-4S dicluster domain
    2.3e-06   27.2  16.6      0.001   18.8   4.1    2.4  2  Fer4           4Fe-4S binding domain
    3.8e-06   26.9   7.0      1e-05   25.5   7.1    1.7  1  Fer4_21        4Fe-4S dicluster domain
    6.4e-06   26.2   9.5    2.2e-05   24.5   9.7    1.8  2  Fer4_10        4Fe-4S dicluster domain
    3.3e-05   23.9   8.4    0.00021   21.4   9.2    1.9  2  Fer4_9         4Fe-4S dicluster domain
    6.6e-05   23.4   3.2       0.16   12.5   0.3    2.5  2  Fer4_17        4Fe-4S dicluster domain
    6.6e-05   22.8  13.3      0.017   15.2   1.6    2.6  2  Fer4_2         4Fe-4S binding domain
    0.00015   21.7  16.1      0.037   14.1   3.5    2.4  2  Fer4_6         4Fe-4S binding domain
    0.00048   20.5   4.4       0.27   11.7   0.6    2.4  2  Fer4_8         4Fe-4S dicluster domain
    0.00079   20.2   2.7       0.55   11.1   0.5    2.4  2  Fer4_22        4Fe-4S dicluster domain
     0.0013   19.0  12.4      0.036   14.6   2.3    2.5  2  Fer4_4         4Fe-4S binding domain
     0.0019   18.7   9.3     0.0054   17.2   1.1    2.6  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
     0.0027   18.6  12.6      0.024   15.6   2.3    2.5  3  Fer4_16        4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
       0.33   11.7   4.1       0.77   10.5   0.2    2.6  2  Fer4_15        4Fe-4S single cluster domain
        6.2    8.0  16.1        5.4    8.2   4.4    2.4  2  Fer4_3         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.1   0.0   4.3e-79   4.6e-76       5     422 ..      43     454 ..      39     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 256.1 bits;  conditional E-value: 4.3e-79
                                       HHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   5 aaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       a++ p kvalv+   sg+ + lT+++++++++r+A++++ +G++kgd V++ l+ ++e+ ++++++ k+Gav++p  
  gi|386001287|ref|YP_005919586.1|  43 AEEDPHKVALVWcndSGDEKILTFGDMKRESDRAANFFKGHGIRKGDAVMLSLKSRYEFWISMIGLHKIGAVAIPAT 119
                                       7899***********999*********************88************************************ PP

                                       TTS-HHHHHHHHHHHTESEEE...ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TS CS
                       AMP-binding  79 ptltaeelayiledseakvli...atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpe 151
                                         l+++++ y ++ ++ k++i   +    e   e+++ a ++l++  +      +++++  +l+ +ee e+++++ e
  gi|386001287|ref|YP_005919586.1| 120 HMLKRKDIVYRIRRADLKMIIsiaE----EGvPEEVDGACKELRDAGVLKAFVGEGARDG-WLNLREELEAASPEFE 191
                                       *********************5541....4434444444444333333222333333333.3333333333332355 PP

                                       CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHT CS
                       AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllalls 227
                                       ++e +k++d+++  +TSGTTG+PK V + + + +  + ++    + ++++++   +++++  +  ++   l++  ++
  gi|386001287|ref|YP_005919586.1| 192 RPEGTKSSDILLAYFTSGTTGNPKMVNHDQSYSLGHILTAR---YwQNVEDGGLHYTVADTGWGKAVWGKLYGQWIA 265
                                       67789*************************88877777753...42446556667999********9999******* PP

                                       T-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                       AMP-binding 228 GatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffr 304
                                       G++v +++ d ++d+++++++ +k++vt+++++P++++ +++++ ++    ++d+s lr+++++gepl+p++ ++f 
  gi|386001287|ref|YP_005919586.1| 266 GSAVFVYDYD-RFDAGRMMDMAAKYRVTTFCAPPTIYRFMIKED-IS----RYDFSTLRYAVTAGEPLNPSIYEKFL 336
                                       **99999966.669999*********************999953.33....45************************ PP

                                       HHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET.....TS-S CS
                       AMP-binding 305 alfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp.....gvmk 376
                                       a +g +++eg+G+TEt +++++ + ++ ++k+gs Gkp pg e+ +vD +  + ++ geeGe++++       g++ 
  gi|386001287|ref|YP_005919586.1| 337 AATGLRLMEGFGQTETVVAIAN-Y-PWMDPKPGSMGKPSPGYEIVLVDKN-DRICEVGEEGEIVIKTDkgkpiGLFV 410
                                       ***99***************84.4.344458******************9.9**************98777888*** PP

                                       EBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 377 gYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                        Y+ +pe+ + ++   +++++TGD +++dedGy+++vgR++d+ik+
  gi|386001287|ref|YP_005919586.1| 411 DYHLDPEKMRNTWH--DDYYHTGDTAWMDEDGYFWFVGRADDIIKS 454
                                       ************97..57**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.5   1.1e-25   1.2e-22       1      76 []     463     541 ..     463     541 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.1e-25
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsal++hpaV e+a+ Gvpd+++G++++a Vvl +g  + e+l++eL+ hv++  +py+ p+ v+f +elpkt s
  gi|386001287|ref|YP_005919586.1| 463 EVESALLTHPAVLECAITGVPDPLRGQVVKATVVLTKGsaPsEELKNELQNHVKAITAPYKYPRIVEFAEELPKTIS 539
                                       8**********************************768442344********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|386001287|ref|YP_005919586.1| 540 GK 541
                                       *9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   8.4   7.1e-11   7.5e-08       2      49 ..     562     609 ..     561     611 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 7.1e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       C  C++C  aCp++++ l ee n++g +++ ++ e C+gCg+C  +CP
  gi|386001287|ref|YP_005919586.1| 562 CKACERCIIACPTNVLALGEELNARGYHYAIYSGEGCIGCGNCYYTCP 609
                                       9*************************999999**************** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   4.1   9.8e-07     0.001       1      23 [.     555     577 ..     555     578 .. 0.93
   2 !   14.0   4.6   3.3e-05     0.034       6      19 ..     596     609 ..     591     611 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.8e-07
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       +vi+   C +C +C+ +CP++++
  gi|386001287|ref|YP_005919586.1| 555 PVINALECKACERCIIACPTNVL 577
                                       68999***************986 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.3e-05
                                       TTSSS-THHHHHST CS
                              Fer4   6 ekCigCGaCvevCP 19 
                                       e CigCG+C+  CP
  gi|386001287|ref|YP_005919586.1| 596 EGCIGCGNCYYTCP 609
                                       56************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   7.1   9.9e-09     1e-05       2      57 ..     556     614 ..     555     616 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.9e-09
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai..eidakt..vlkvvedeCvGCnlCssvCPvedci 57 
                                       +i+  +C  C++C+iaC+ t + a+  e++a+   ++ +  + C+GC  C+  CP   +i
  gi|386001287|ref|YP_005919586.1| 556 VINALECKACERCIIACP-TNVLALgeELNARGyhYAIYSGEGCIGCGNCYYTCPEPFAI 614
                                       688899************.5666776634444411445569**************65555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   9.7   2.1e-08   2.2e-05       3      56 .]     556     609 ..     554     609 .. 0.73
   2 !   13.1   1.8   7.2e-05     0.076       5      21 ..     594     610 ..     590     622 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.1e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       vi++  C  C++C  aCP+++    ++ +a+g+   +       e C+gcg+C+  CP
  gi|386001287|ref|YP_005919586.1| 556 VINALECKACERCIIACPTNVlalgEELNARGYHYAIYS----GEGCIGCGNCYYTCP 609
                                       799999*************77543333333333333333....466***********9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.2e-05
                           Fer4_10   5 dddtCirCgkCvkaCPa 21 
                                         + Ci+Cg+C   CP 
  gi|386001287|ref|YP_005919586.1| 594 SGEGCIGCGNCYYTCPE 610
                                       55678888888888887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.4   0.00018      0.19      33      49 ..     552     575 ..     536     577 .. 0.68
   2 !   21.4   9.2     2e-07   0.00021       2      48 ..     562     610 ..     561     614 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            Fer4_9  33 e.......eaCigCgaCveaCpkg 49 
                                       +        +C  C++C+ aCp++
  gi|386001287|ref|YP_005919586.1| 552 KpypvinaLECKACERCIIACPTN 575
                                       1444444457***********998 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2e-07
                            Fer4_9   2 CtgCgaCveaCpagvv..vedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       C  C +C+ aCp++v    e+ ++r   + ++s e CigCg C+  Cp+
  gi|386001287|ref|YP_005919586.1| 562 CKACERCIIACPTNVLalGEELNARGYHYAIYSGEGCIGCGNCYYTCPE 610
                                       **************985566667777777777779*************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.2   0.00046      0.49      31      60 ..     547     576 ..     523     577 .. 0.66
   2 !   12.5   0.3   0.00015      0.16      44      58 ..     596     610 ..     579     613 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                           Fer4_17  31 lglleeaeke...ekaslCieCgeCerkCPqgl 60 
                                       + ++++        +a +C  C++C  +CP ++
  gi|386001287|ref|YP_005919586.1| 547 IREKDK---PypvINALECKACERCIIACPTNV 576
                                       222222...23336899*************986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00015
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       + Ci+Cg+C + CP+
  gi|386001287|ref|YP_005919586.1| 596 EGCIGCGNCYYTCPE 610
                                       67************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   4.3   0.00014      0.15       1      22 []     553     574 ..     553     574 .. 0.93
   2 !   15.2   1.6   1.6e-05     0.017       9      22 .]     597     610 ..     589     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                            Fer4_2   1 apvvvdtdrCigCgaCvsaCPa 22 
                                       +++v+++  C +C+ C+ aCP+
  gi|386001287|ref|YP_005919586.1| 553 PYPVINALECKACERCIIACPT 574
                                       5799**999************7 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.6e-05
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                        CigCg C+  CP+
  gi|386001287|ref|YP_005919586.1| 597 GCIGCGNCYYTCPE 610
                                       5************5 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   3.5   3.5e-05     0.037       3      24 .]     556     577 ..     554     577 .. 0.83
   2 !   12.8   4.8   9.1e-05     0.096       9      21 ..     598     610 ..     598     614 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       +i++  C  C++C+++CP++++
  gi|386001287|ref|YP_005919586.1| 556 VINALECKACERCIIACPTNVL 577
                                       556666*************986 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.1e-05
                            Fer4_6   9 CigCgdCvrvCPe 21 
                                       CigCg+C+  CPe
  gi|386001287|ref|YP_005919586.1| 598 CIGCGNCYYTCPE 610
                                       ************8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2     0.001       1.1      47      65 .]     558     576 ..     526     576 .. 0.79
   2 !   11.7   0.6   0.00026      0.27       4      16 ..     597     609 ..     594     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                            Fer4_8  47 alwsCttcgaCtevCpvgi 65 
                                       ++ +C +c++C  +Cp+++
  gi|386001287|ref|YP_005919586.1| 558 NALECKACERCIIACPTNV 576
                                       5668************986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00026
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                        Ci+Cg C  +Cp
  gi|386001287|ref|YP_005919586.1| 597 GCIGCGNCYYTCP 609
                                       6***********8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0032       3.4      73      95 ..     553     575 ..     513     576 .. 0.75
   2 !   11.1   0.5   0.00052      0.55      77      94 ..     593     610 ..     583     614 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0032
                           Fer4_22  73 fkekfgesgCvGCgRCieacpvk 95 
                                           +++  C  C RCi acp++
  gi|386001287|ref|YP_005919586.1| 553 PYPVINALECKACERCIIACPTN 575
                                       44556778899999999999876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00052
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++ +gC+GCg C  +cp+
  gi|386001287|ref|YP_005919586.1| 593 YSGEGCIGCGNCYYTCPE 610
                                       566899999999999986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   2.7    0.0019         2       4      17 .]     562     575 ..     558     575 .. 0.89
   2 !   14.6   2.3   3.5e-05     0.036       3      15 ..     597     609 ..     595     616 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C  C +C++aCP++
  gi|386001287|ref|YP_005919586.1| 562 CKACERCIIACPTN 575
                                       99999*******86 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.5e-05
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        CigCg C+++CP
  gi|386001287|ref|YP_005919586.1| 597 GCIGCGNCYYTCP 609
                                       6************ PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.6     0.034        35       3      18 ..     559     574 ..     557     581 .. 0.88
   2 !   17.2   1.1   5.1e-06    0.0054       4      23 ..     596     615 ..     595     620 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.034
                           Fer4_13   3 rdtCiacgaCvelaPd 18 
                                         +C ac+ C  ++P 
  gi|386001287|ref|YP_005919586.1| 559 ALECKACERCIIACPT 574
                                       568************6 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.1e-06
                           Fer4_13   4 dtCiacgaCvelaPdvFeed 23 
                                       + Ci+cg+C+ ++P+ F+++
  gi|386001287|ref|YP_005919586.1| 596 EGCIGCGNCYYTCPEPFAIE 615
                                       78***************976 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.3   2.3e-05     0.024       2      24 ..     562     582 ..     561     591 .. 0.83
   2 !    7.6   2.8    0.0069       7.3      50      65 ..     594     609 ..     585     611 .. 0.71
   3 ?    6.4   3.4     0.016        17       2      14 ..     598     610 ..     597     625 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                       C+ C++C+ +CPtn++     +e
  gi|386001287|ref|YP_005919586.1| 562 CKACERCIIACPTNVLALG--EE 582
                                       ***************9887..44 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0069
                           Fer4_16  50 kqeaitgCdiCqdvCP 65 
                                       ++e ++gC++C  +CP
  gi|386001287|ref|YP_005919586.1| 594 SGEGCIGCGNCYYTCP 609
                                       5666777777777777 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.016
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C++Cg+C  +CP+
  gi|386001287|ref|YP_005919586.1| 598 CIGCGNCYYTCPE 610
                                       9999999999997 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.47     5e+02       6      21 ..     560     575 ..     556     587 .. 0.81
   2 ?   10.5   0.2   0.00073      0.77       6      25 ..     596     615 ..     593     621 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.47
                           Fer4_15   6 daCigcglCvaeapev 21 
                                        +C  c++C+ ++p+ 
  gi|386001287|ref|YP_005919586.1| 560 LECKACERCIIACPTN 575
                                       57**********9975 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00073
                           Fer4_15   6 daCigcglCvaeapevfeld 25 
                                       + Cigcg+C+  +pe f ++
  gi|386001287|ref|YP_005919586.1| 596 EGCIGCGNCYYTCPEPFAIE 615
                                       57*************99875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.9     0.044        46       1      14 [.     562     575 ..     562     576 .. 0.91
   2 ?    8.2   4.4    0.0052       5.4       1      12 [.     598     609 ..     598     611 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.044
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C  C++C  +CP++
  gi|386001287|ref|YP_005919586.1| 562 CKACERCIIACPTN 575
                                       888*********97 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0052
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+gCg C   CP
  gi|386001287|ref|YP_005919586.1| 598 CIGCGNCYYTCP 609
                                       ************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 3353.10
//
Query:       gi|386001288|ref|YP_005919587.1|  [L=182]
Description: transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-15   55.7   0.0    8.7e-15   54.2   0.0    1.7  2  Cupin_2         Cupin domain
      3e-09   36.8   0.1    4.7e-09   36.1   0.1    1.3  1  HTH_19          Helix-turn-helix domain
    5.5e-05   23.1   0.1    8.2e-05   22.6   0.1    1.3  1  HTH_3           Helix-turn-helix
    0.00077   19.8   0.0     0.0013   19.0   0.0    1.5  1  HTH_31          Helix-turn-helix domain
     0.0033   17.3   0.0     0.0053   16.7   0.0    1.3  1  AraC_binding    AraC-like ligand binding domain
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.065   13.1   0.0    1.3  1  Asp_Arg_Hydrox  Aspartyl/Asparaginyl beta-hydroxylase
      0.043   13.6   0.1      0.083   12.7   0.1    1.4  1  YycC            YycC-like protein
      0.072   12.7   0.0      0.097   12.3   0.0    1.3  1  Cupin_1         Cupin
      0.081   13.2   0.0       0.12   12.6   0.0    1.5  1  CENP-C_C        Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   2.7e+03      42      59 ..      81      98 ..      77     102 .. 0.76
   2 !   54.2   0.0   4.4e-18   8.7e-15       2      70 ..     112     180 ..     111     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                      ETTEEEEE-TT-EEEEEE CS
                           Cupin_2 42 eaGdsvyfpagtpHrfrN 59
                                      ++G+ v +++ +  r+ N
  gi|386001288|ref|YP_005919587.1| 81 RKGEGVEVERRRQYRYQN 98
                                      678888888888888887 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 4.4e-18
                                       EEEEETTEEEEEEC.SSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshr.HpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       +v+++p ++ p+ + Hpg+ ef yVleG +++ + ++e++l++Gds++f++   H+++   d pa++lvv
  gi|386001288|ref|YP_005919587.1| 112 IVTIEPKREKPAAYsHPGQ-EFDYVLEGSLKFSIHDHEIVLNEGDSILFDSSFLHAMEAQDDRPAKMLVV 180
                                       799*****7776666****.************************************************98 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   2.4e-12   4.7e-09       3      64 ..      11      71 ..       9      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.4e-12
                            HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqged 64
                                      r++e+Re  + t ee+ae+l++    ++ +E gk+ +++a++l  i + l++d + ll+ge+
  gi|386001288|ref|YP_005919587.1| 11 RIREMRELSKVTAEEMAEHLKVPLETYNCYEEGKM-EIPASKLIEIGQRLEVDMNLLLTGEE 71
                                      9**********************************.999********************985 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   4.1e-08   8.2e-05       1      54 [.      12      65 ..      12      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.1e-08
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                      ++e+R+  + + ee+Ae l v+  t++ +E G+ ++  ++l+++ + L v++  
  gi|386001288|ref|YP_005919587.1| 12 IREMRELSKVTAEEMAEHLKVPLETYNCYEEGKMEIPASKLIEIGQRLEVDMNL 65
                                      8*********************************************99999865 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.6e-07    0.0013       2      59 ..       8      64 ..       7      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.6e-07
                            HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpa 59
                                      ++ + r++Re + ++ ee+Ae+l v   t++ +E G+  + + + l  + + l +d +
  gi|386001288|ref|YP_005919587.1|  8 IATRIREMRELSKVTAEEMAEHLKVPLETYNCYEEGKM-EIPASKLIEIGQRLEVDMN 64
                                      68899*******************************99.6778888877777777765 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.6e-06    0.0053      21      71 ..     127     177 ..     118     182 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                                       T-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEE CS
                      AraC_binding  21 hdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwey 71 
                                       h+  ++ yv+eG+ ++++ +++  l++Gd +L+    +H +e+ ++ + ++
  gi|386001288|ref|YP_005919587.1| 127 HPGQEFDYVLEGSLKFSIHDHEIVLNEGDSILFDSSFLHAMEAQDDRPAKM 177
                                       8888999************************************99777655 PP

>> Asp_Arg_Hydrox  Aspartyl/Asparaginyl beta-hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.065     113     151 ..     141     179 ..     132     182 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                       EEEETTEEE---TTEEEEE-TTS-EEEEE-SSS-EEEEE CS
                    Asp_Arg_Hydrox 113 eirvggetrtweeGevllfDdsfeHevwnetdeeRvvLl 151
                                       ++ +++++   +eG+++lfD sf+H +  + d++  +L+
  gi|386001288|ref|YP_005919587.1| 141 KFSIHDHEIVLNEGDSILFDSSFLHAMEAQDDRPAKMLV 179
                                       67788999999***************9999988766665 PP

>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.2e-05     0.083       6      23 ..      18      35 ..      15      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                              YycC  6 iSpeTAvkLskkLnvPLE 23
                                      +S  TA +++++L+vPLE
  gi|386001288|ref|YP_005919587.1| 18 LSKVTAEEMAEHLKVPLE 35
                                      7999*************9 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.9e-05     0.097      50     113 ..     125     181 ..      97     182 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                                       EESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEE CS
                           Cupin_1  50 yhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivvf 113
                                       y+    e  yvl+G++ + +       +d + +l+eGd + + + + h++ +++d pa ++vv+
  gi|386001288|ref|YP_005919587.1| 125 YSHPGQEFDYVLEGSLKFSI-------HDHEIVLNEGDSILFDSSFLHAMEAQDDRPAKMLVVV 181
                                       55566677788888888222.......244567*************************999985 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.2e-05      0.12      16      61 ..     112     157 ..      88     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                                       EEEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EE CS
                          CENP-C_C  16 ilkLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvF 61 
                                       i++++p+ eK    s+  +   yV++G ++ ++++++ v+ +g++ 
  gi|386001288|ref|YP_005919587.1| 112 IVTIEPKREKPAAYSHPGQEFDYVLEGSLKFSIHDHEIVLNEGDSI 157
                                       799*************************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1079.29
//
Query:       gi|386001289|ref|YP_005919588.1|  [L=145]
Description: hypothetical protein Mhar_0587 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-42  143.3   0.0    6.8e-42  143.0   0.0    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   0.0   3.8e-46   6.8e-42       2     138 .]       5     145 .]       5     145 .] 0.94

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 3.8e-46
                                       EE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S-- CS
                          Archease   2 eyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfk 78 
                                       eyl+htADv+++++G+slee+fesa+lal+ +m+d s+v+ +e+  +e+eae+le+lL+++L+e+lylf++e  +f+
  gi|386001289|ref|YP_005919588.1|   5 EYLEHTADVKFRVRGRSLEELFESAGLALIGAMIDPSTVRVEESWPVEIEAESLEALLYEWLSEILYLFEVELAAFS 81 
                                       8**************************************************************************** PP

                                       --EEEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEET....TEEEEEEEEE- CS
                          Archease  79 evkvdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeed....dgweayvvvDi 138
                                       e++v  +   ++++l++++ ge++d+e+h ++tevKAvT+h+++i +e+    + w+a+vv+D+
  gi|386001289|ref|YP_005919588.1|  82 EFEVALDGGPDGWSLSGRVGGERIDPERHLFETEVKAVTLHQFEIGREEvggeEIWTAQVVLDV 145
                                       **9965568899*****************999*************8875222256********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 901.22
//
Query:       gi|386001290|ref|YP_005919589.1|  [L=473]
Description: hypothetical protein Mhar_0588 [Methanosaeta harundinacea 6Ac]
Scores for 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-163  542.4   0.0   9.3e-163  542.2   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.2   0.0  5.2e-167  9.3e-163       1     412 []      43     473 .]      43     473 .] 0.99

  Alignments for each domain:
  == domain 1  score: 542.2 bits;  conditional E-value: 5.2e-167
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q++nva+lpgiv++++amPD+HlG+g+piG+V+a++   gvi+P++VG+DI CGvr+l+t+l ae++ + +++lv++
  gi|386001290|ref|YP_005919589.1|  43 QVANVATLPGIVNYSMAMPDAHLGYGFPIGGVAAFRedgGVISPGGVGFDInCGVRMLRTDLLAEDVAPMMTNLVED 119
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l+++vp+g+g k+++++s++el+e++++ga+wave g+g  edle++ee g++++a++++vs ka++r+r+qlGtlG
  gi|386001290|ref|YP_005919589.1| 120 LFHDVPSGVGAKGRLRVSEHELDEAFTRGAAWAVEAGFGVPEDLEHCEEGGRMEGAKPDQVSLKARKRGRPQLGTLG 196
                                       ***************************************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+E+q v+ei+d+++ak++gl +gq++vm+H+GSRg Ghqi++d+l+++++a+kk+gi+lpd++La++p+g++
  gi|386001290|ref|YP_005919589.1| 197 SGNHFLEIQRVDEIFDDDLAKRFGLFRGQITVMIHCGSRGAGHQICTDHLQVLSRAVKKYGIELPDKQLACAPLGTP 273
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                       e+++Y+ am+aaanyA+aNRq+i +++re++e+++     d +l+lv+dvaHN+ak Eehe d   e+++VhRKGAt
  gi|386001290|ref|YP_005919589.1| 274 EAENYFGAMAAAANYAWANRQIISAWTREVFERYFP----DARLDLVYDVAHNVAKVEEHEvDgsrERLYVHRKGAT 346
                                       ***********************************5....567899***************96799*********** PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       rA             ++gqpviipGsmgt Sy++ G   a+  +fgS++HGAGR+msR++akk++ ++evk+ l+++
  gi|386001290|ref|YP_005919589.1| 347 RAfgpgrpeipmayrEAGQPVIIPGSMGTPSYVLCGSAGAMrlTFGSACHGAGRIMSRTQAKKTYAGAEVKDVLTRR 423
                                       ***************************************************************************** PP

                                       T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       gi+v+a++ + ++eEape YK+  eVv+++++ +++++va++ p++v kg
  gi|386001290|ref|YP_005919589.1| 424 GIKVMATHPKMLAEEAPEVYKPSFEVVDVVHHLDIARKVAKVVPLGVSKG 473
                                       ***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2954.75
//
Query:       gi|386001291|ref|YP_005919590.1|  [L=267]
Description: RNA methyltransferase, TrmH family, group 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-32  110.1   0.0    1.4e-31  109.6   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.31   10.9   0.0    1.7  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   1.6e-35   1.4e-31       2     142 .]       3     154 ..       2     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.6e-35
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       ++vvlve+ ++gN+G++aR++k+fg+s+lvlv+p++    ++  +++a++a+ev+e ++vvd l ea+++ + +   
  gi|386001291|ref|YP_005919590.1|   3 IRVVLVEPLYEGNVGSVARAMKNFGFSDLVLVRPCEI---EDFGLAMASHAREVIEgARVVDGLGEAISAANLV--- 73 
                                       79*******************************8886...777899**************************99... PP

                                       EEEEST.T-SEGC......CSHHH.............TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HH CS
                    SpoU_methylase  78 lvatsl.kgksls......eidlk.............ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNva 134
                                        v+t++ +g++++                        ++val++G+Ed+Gls e+l+++d +v+Ip+s+e++ +N++
  gi|386001291|ref|YP_005919590.1|  74 -VGTTGvRGRTTDrhlrvpS---LspkelaerlqggrGEVALLLGREDDGLSCEELAACDVVVSIPTSPEYPIMNLS 146
                                       .5555554444332122321...02334457788999**************************************** PP

                                       HHHHHHHH CS
                    SpoU_methylase 135 vAvailly 142
                                       +A+a+lly
  gi|386001291|ref|YP_005919590.1| 147 HAAAVLLY 154
                                       ******98 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.5e-05      0.31      65     177 ..      40     153 ..      10     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                                       TSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS.--SS-B-HHHHHHHHHH--S-EEEEE--. CS
                   Methyltrn_RNA_4  65 egagaeynpdRkealslvkvvesleealeeiekeegkkplvvatsAr.kkentvsyeelrelleeeekpvlllfGt. 139
                                       e++g ++  + +e ++  +vv+ l ea+++ +   g++ +   t+ r  +  ++s +el e+l+  + +v ll+G  
  gi|386001291|ref|YP_005919590.1|  40 EDFGLAMASHAREVIEGARVVDGLGEAISAANLVVGTTGVRGRTTDRhLRVPSLSPKELAERLQGGRGEVALLLGRe 116
                                       567788888889999999***********999999998777665555278899**********************72 PP

                                       TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHHH CS
                   Methyltrn_RNA_4 140 gwGlaeevlekadyiLepirgaseynHLsvrsAvaiil 177
                                         Gl+ e l+++d+++ +i +  ey  +    A+a++l
  gi|386001291|ref|YP_005919590.1| 117 DDGLSCEELAACDVVV-SIPTSPEYPIMNLSHAAAVLL 153
                                       57***********987.699999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1647.53
//
Query:       gi|386001292|ref|YP_005919591.1|  [L=142]
Description: RDD domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-23   81.0   3.7    1.2e-22   80.7   3.7    1.1  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   3.7   6.4e-27   1.2e-22       1     141 []      16     136 ..      16     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 6.4e-27
                               RDD   1 laslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGkl 77 
                                       las+g+R++ +liD v++ +i+ +l+++ +            v  +l  + +++ +lv + y+++++  +gqT+G++
  gi|386001292|ref|YP_005919591.1|  16 LASVGSRFIGYLIDSVIVGVIGSILSYASMN-----------VGETLGGINAFLGFLVSVGYYTYFFG-NGQTPGMM 80 
                                       599****************************...........77888888888999999999999875.8******* PP

                               RDD  78 llglkvvd.edgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDklag 141
                                       ++++k+v  + ++++g+++ ++R++         ++ ++  ++l+g+l++l+++k+q++hDk+ag
  gi|386001292|ref|YP_005919591.1|  81 AMKIKLVGtDGTYPIGYGKGFLRWI---------GMGISTAVILLGYLWILIDKKKQGWHDKIAG 136
                                       ********5556799*********9.........99***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 907.94
//
Query:       gi|386001293|ref|YP_005919592.1|  [L=151]
Description: RDD domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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   85.2   3.6    5.5e-24   85.0   3.6    1.1  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   3.6   3.1e-28   5.5e-24       1     141 []      15     145 ..      15     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 3.1e-28
                               RDD   1 laslgrRllAfliDlvllliislllallivallnakasaneavag..slllllllvlllvllvyqllllskkgqTlG 75 
                                       la++g+R +++l Dlv+l+ii++ l++l+       + +++a++g  s ++ ++l+++++++ y+++++ + gqT+G
  gi|386001293|ref|YP_005919592.1|  15 LAGIGQRMASYLMDLVVLSIIYIALVFLFDL---PAEDWSLAWSGlpSDYPPIYLLMAAIGIGYYTYFFGA-GQTPG 87 
                                       599****************************...4566666666522567889999999999999999875.9**** PP

                               RDD  76 klllglkvvdedg.rklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDklag 141
                                       ++ll +k+v++dg +++gl + ++R++         ++ +++++l++g+l++l++r+rq++hDk+ag
  gi|386001293|ref|YP_005919592.1|  88 MRLLEIKLVRADGiEPIGLRRGFLRWV---------GMEISGVVLFLGYLWILIDRRRQGWHDKIAG 145
                                       **********8875799*********9.........99***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 997.05
//
Query:       gi|386001294|ref|YP_005919593.1|  [L=61]
Description: hypothetical protein Mhar_0592 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 433.06
//
Query:       gi|386001295|ref|YP_005919594.1|  [L=278]
Description: hypothetical protein Mhar_0593 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-69  232.1   0.0    6.1e-69  231.9   0.0    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.9   0.0   3.4e-73   6.1e-69       2     219 ..       5     255 ..       4     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 231.9 bits;  conditional E-value: 3.4e-73
                            DUF166   2 vltsgeyGervvenilnepdfersl.................ivavvevpe..eldefiedpeelLpe.lkeaDivi 58 
                                       v+++ge+G+++++n+ n + f++s+                 +v v+e+p+   l++fi+d++ ++p+ ++eaDi+i
  gi|386001295|ref|YP_005919594.1|   5 VFYNGEFGRTLIGNLINFSGFCISCgdgctlckagkyslaedLVSVIEMPDpeGLEDFIDDVSPYIPAeIPEADIAI 81 
                                       89************************************************9999*************99******** PP

                            DUF166  59 aytlhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCslee.egkpkideFlee 131
                                        + +hpD+ + l+ ++kek++k +i ++e pk    glr +l e++ ++g+e+a+ kpfC+l++ +  p i++F+++
  gi|386001295|ref|YP_005919594.1|  82 VVHVHPDIIFGLLSILKEKGYKGIIGGSEMPKdlpLGLRTQLAEEARRMGLEAAFAKPFCALRPdPATPAINAFMQK 158
                                       **********************************99****************************99**********9 PP

                            DUF166 132 ..fGkPelevevk.....dgkikkVeVlrsapCGstwyvakklkGkeveeaeeka..geahqsYpClAsmerdfelk 199
                                         fG+Pe+e+  +     +++i   +V+rsapCGstwyvak+++G + ++ ++++  +eah++YpC+Asm++d+elk
  gi|386001295|ref|YP_005919594.1| 159 ahFGEPEIEIVAQesrpgKETILAANVVRSAPCGSTWYVAKRMTGLDTDQPDLREriSEAHHAYPCTASMDQDPELK 235
                                       9*********998555433445899***********************977666666******************** PP

                            DUF166 200 etklhkAgyihkeavekAlk 219
                                       +t+lh+Agyi++eave+A+k
  gi|386001295|ref|YP_005919594.1| 236 DTILHRAGYIIREAVEDAIK 255
                                       ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1736.80
//
Query:       gi|386001296|ref|YP_005919595.1|  [L=487]
Description: Aminoacyl-histidine dipeptidase [Methanosaeta harundinacea 6Ac]
Scores for complete 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   78.9   0.0    7.9e-22   78.0   0.0    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
    0.00056   19.7   0.4     0.0011   18.7   0.1    1.7  2  Peptidase_M28  Peptidase family M28
     0.0078   16.1   0.1      0.021   14.7   0.1    1.8  1  M20_dimer      Peptidase dimerisation domain
       0.01   14.9   0.1       0.23   10.5   0.1    2.6  3  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   1.8e-25   7.9e-22       1     206 [.      73     482 ..      73     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.8e-25
                                       EEEEES-BSSTTCGGGSSSTTSEE.....ETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslt.....eedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEE 72 
                                       ll++HlD+V+e++  g ++ fs +     +edG++ + G++ +    +++++al+ l+d g    g+++llf++dEE
  gi|386001296|ref|YP_005919595.1|  73 LLQAHLDMVCEKDR-GSDHDFSRDpilvqVEDGFVSAVGTTLGADNGIGVAAALAVLADPGAV-HGPLELLFTVDEE 147
                                       699*******4444.43346666666667*******************************987.6************ PP

                                       STTTHHHHHHH.......HHHT...TTCESEEE.EEEEESSSBTCHSTETEEEE....................... CS
                                       xxxxxxxxxxx.......xxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxx....................... RF
                     Peptidase_M20  73 ggrgGakalle.......glee...rekvdavf.elhieepgileagklaigvv....................... 115
                                        g++Ga+a+ e               ++++av+ ++  +e+++l                                 
  gi|386001296|ref|YP_005919595.1| 148 EGMSGAGAVQEgqiaarmM--InldTDDPHAVYvGCAGGETSNLR--------Lpmrwdrpdpagasafevvvggls 214
                                       8779998888854444442..033344555544244433333333........023455666777888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|386001296|ref|YP_005919595.1| 215 gghsgvdihlqrgnaikllglllwaagervfpglsslrggekhnaipreaeavvvvpreeaeafsslveaearalre 291
                                       88888888899****************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|386001296|ref|YP_005919595.1| 292 eyravdpglwvevsavemparvaspegsrraiglvaalpngvlrwspeipdlvetstnlsvafteeedlylqtasrs 368
                                       ***************************************************************************** PP

                                       ....................EEEEEEEEEESHEEEC..CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH.TTT CS
                                       ....................xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                     Peptidase_M20 116 ....................kvevelleggapvtln..dsplvkalaeaaeelfgekvelivsgpggtdarff.agi 169
                                                            ++ve +++ +p +l+  ds+l  a+++a ++lfg+++e++  + +g +++++ ++ 
  gi|386001296|ref|YP_005919595.1| 369 sskvgleattatiraaaalaGARVE-RGDRYPGRLPdlDSELLSACRAAHRNLFGRDPEVKSIH-AGLEMGIIgEKF 443
                                       *******************769999.77777888877******************999999999.********9999 PP

                                       EEE.EE.EESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 170 ptv.mi.fgpgsglaHspnEyvdledlekgikvlarlle 206
                                       p + m+ +g+  +  Hsp E+v+++++++ ++++ ++le
  gi|386001296|ref|YP_005919595.1| 444 PDMdMVsLGTLIEHPHSPAERVKISAVAEFYRFILAALE 482
                                       *88455688444********************9999886 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.5e-07    0.0011       7      99 ..      64     171 ..      55     205 .. 0.80
   2 ?   -3.7   0.0       1.8   8.1e+03      62      82 ..     349     369 ..     345     390 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                                       STTCESEEEEEEEE--B-TTT......................TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSS CS
                     Peptidase_M28   7 egkatdevlllgAHyDsvgvg......................rgp.ifvGAdDnAsgvaalLelarvlaasgsrpk 60 
                                       +g++ ++ +ll AH+D v ++                      ++  +  GA Dn+ gvaa L ++          +
  gi|386001296|ref|YP_005919595.1|  64 PGREGSRAVLLQAHLDMVCEKdrgsdhdfsrdpilvqvedgfvSAVgTTLGA-DNGIGVAAALAVLADPG----AVH 135
                                       44444889***********99999*999998888887664443222556676.9*******998755444....578 PP

                                       EEEEEEEESSCSGSSHHHHHHHHHHCCCTTEEEEEEECS CS
                     Peptidase_M28  61 rgvrflffdaEEagllGSkafakakpelkkiaavlnlDm 99 
                                         + +lf+  EE+g+ G+ a   +   + + ++++nlD 
  gi|386001296|ref|YP_005919595.1| 136 GPLELLFTVDEEEGMSGAGAVQ-E--GQIAARMMINLDT 171
                                       99****************9998.4..4567788888885 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                                       EEEEEEESSCSGSSHHHHHHH CS
                     Peptidase_M28  62 gvrflffdaEEagllGSkafa 82 
                                       ++ ++f+  E+ +l+ +++  
  gi|386001296|ref|YP_005919595.1| 349 NLSVAFTEEEDLYLQTASRSS 369
                                       566677777777776666554 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.8e-06     0.021      19     106 ..     226     294 ..     208     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-06
                                       EGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHHHHHHH CS
                         M20_dimer  19 HsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRllpgedpeevle 95 
                                       +++       Ai++l  ll +  +               + +++++gG + n+ip+eaea + +  +  e   ++ e
  gi|386001296|ref|YP_005919595.1| 226 RGN-------AIKLLGLLLWAAGER------------VFPGLSSLRGGEKHNAIPREAEAVVVVPREEAEAFSSLVE 283
                                       444.......666666666666666............33467899*******************9999999999988 PP

                                       HHHHHHTSCCS CS
                         M20_dimer  96 eieeilekeap 106
                                       + + +l++e++
  gi|386001296|ref|YP_005919595.1| 284 AEARALREEYR 294
                                       88888888876 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.17   7.5e+02       7      25 ..      63      81 ..      54      82 .. 0.76
   2 !   10.5   0.1   5.1e-05      0.23     133     190 ..     115     171 ..      96     179 .. 0.84
   3 ?    0.7   0.0     0.047   2.1e+02     261     289 ..     445     473 ..     432     476 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                                      EESSTTSSEEEEEEE--B- CS
                     Peptidase_M42  7 kkgkekepkvmiaAHmDei 25
                                       +g+e + +v++ AH+D +
  gi|386001296|ref|YP_005919595.1| 63 TPGREGSRAVLLQAHLDMV 81
                                      46788999*********76 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHH.HH--SEEEEEEE CS
                     Peptidase_M42 133 lDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsae.kikpdiaiavDv 190
                                        D+ +gva++l++l      +    + l++tv EE G+ Ga +++e +i   ++i +D+
  gi|386001296|ref|YP_005919595.1| 115 ADNGIGVAAALAVLADPGAVH--GPLELLFTVDEEEGMSGAGAVQEgQIAARMMINLDT 171
                                       499**********99887765..99999*************988763567777777776 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.047
                                       TSEEEEEEEEEBSTTSTTEEEEHHHHHHH CS
                     Peptidase_M42 261 gvptalisiptryiHspvevahlddleat 289
                                       ++  + +++ +++ Hsp+e+++++++++ 
  gi|386001296|ref|YP_005919595.1| 445 DMDMVSLGTLIEHPHSPAERVKISAVAEF 473
                                       5677899999*************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2998.67
//
Query:       gi|386001297|ref|YP_005919596.1|  [L=142]
Description: hypothetical protein Mhar_0595 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-10   40.1   2.1     0.0011   18.9   0.1    3.3  3  NHL             NHL repeat
    2.2e-09   37.3   0.4    0.00078   19.1   0.0    2.1  2  SGL             SMP-30/Gluconolactonase/LRE-like region
      0.004   17.1   0.1        1.7    8.5   0.0    2.0  2  Phytase-like    Esterase-like activity of phytase
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.054   12.7   0.0    1.6  2  SdiA-regulated  SdiA-regulated
      0.039   13.7   0.0        1.2    8.8   0.0    2.2  2  ComJ            Competence protein J (ComJ)


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.6e-05     0.056       6      28 .]      37      59 ..      35      59 .. 0.94
   2 !   18.9   0.1   3.1e-07    0.0011       5      28 .]      78     101 ..      78     101 .. 0.95
   3 !    5.8   0.0    0.0042        15       5      17 ..     118     130 ..     118     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                      EEEEETTTEEEEEECCCTEEEEE CS
                               NHL  6 GvavdsnGdiyVaDsenhrvqvF 28
                                      G+a+ ++G++yV+ +++h v+++
  gi|386001297|ref|YP_005919596.1| 37 GIAIGPGGEVYVTINNSHKVVKY 59
                                      9*****************99987 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.1e-07
                                       EEEEEETTTEEEEEECCCTEEEEE CS
                               NHL   5 hGvavdsnGdiyVaDsenhrvqvF 28 
                                       +G+av ++G++yV+ ++nh v+++
  gi|386001297|ref|YP_005919596.1|  78 NGIAVGPGGEVYVTINNNHKVVKY 101
                                       69*******************997 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0042
                                       EEEEEETTTEEEE CS
                               NHL   5 hGvavdsnGdiyV 17 
                                       +G+a+ +nG iy+
  gi|386001297|ref|YP_005919596.1| 118 NGIAAGPNGLIYI 130
                                       69**********9 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.2e-07   0.00078     188     223 ..      37      72 ..      26      78 .. 0.91
   2 !   17.0   0.1   9.5e-07    0.0034     188     223 ..      79     114 ..      72     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.2e-07
                               SGL 188 GlavDaeGnvwvAvwgggkvvrfdpdGklieeiklp 223
                                       G+a+   G+v+v++ +++kvv+++p+G+ ++e++++
  gi|386001297|ref|YP_005919596.1|  37 GIAIGPGGEVYVTINNSHKVVKYSPEGERLAEWDVD 72 
                                       999******************************997 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 9.5e-07
                               SGL 188 GlavDaeGnvwvAvwgggkvvrfdpdGklieeiklp 223
                                       G+av   G+v+v++ +++kvv+++ +G+ ++e++++
  gi|386001297|ref|YP_005919596.1|  79 GIAVGPGGEVYVTINNNHKVVKYSSEGEKLDEWAVD 114
                                       99*******************************997 PP

>> Phytase-like  Esterase-like activity of phytase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0012       4.2      72     107 ..      37      72 ..      35      78 .. 0.92
   2 !    8.5   0.0   0.00049       1.7      72     108 ..      79     115 ..      72     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                      Phytase-like  72 giavapdgtfwvssEggpfilefdadGkllrelplp 107
                                       gia+ p+g+++v+    + +++++++G+ l+e+ + 
  gi|386001297|ref|YP_005919596.1|  37 GIAIGPGGEVYVTINNSHKVVKYSPEGERLAEWDVD 72 
                                       89*****************************99876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00049
                      Phytase-like  72 giavapdgtfwvssEggpfilefdadGkllrelplpa 108
                                       giav p+g+++v+   ++ +++++ +G+ l+e+++  
  gi|386001297|ref|YP_005919596.1|  79 GIAVGPGGEVYVTINNNHKVVKYSSEGEKLDEWAVDG 115
                                       9*****************************9998865 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05     0.054      37      94 ..      46     103 ..      42     109 .. 0.91
   2 ?    4.1   0.0    0.0065        23      38      67 ..      89     118 ..      85     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                    SdiA-regulated  37 LfavtnkpeelveLskeGevlrriplkgfkdpEaveylgdgrlaivdEreqalvvvkv 94 
                                        ++++n+ +++v+ s eGe l++ +++g+ ++ ++++  +g++ ++   ++++v+++ 
  gi|386001297|ref|YP_005919596.1|  46 VYVTINNSHKVVKYSPEGERLAEWDVDGVIETNGIAVGPGGEVYVTINNNHKVVKYSS 103
                                       56789**************************************999999999998875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0065
                    SdiA-regulated  38 favtnkpeelveLskeGevlrriplkgfkd 67 
                                       ++++n+++++v+ s eGe l + +++g+ +
  gi|386001297|ref|YP_005919596.1|  89 YVTINNNHKVVKYSSEGEKLDEWAVDGMMN 118
                                       6789****************9999999754 PP

>> ComJ  Competence protein J (ComJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00034       1.2      20      59 ..      26      65 ..      21      76 .. 0.89
   2 ?    2.6   0.0     0.029     1e+02      13      46 ..     101     134 ..      89     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00034
                                      -----HHHHHHTEEEETTEEEEE-SSSSEEEEEEEES--- CS
                              ComJ 20 vvdWtdedieqGyaladgavsFealedvkaevtvslnkei 59
                                        +W+ ed+  G a+++g   + ++++ +  v+ s++ e 
  gi|386001297|ref|YP_005919596.1| 26 LAQWSLEDLVGGIAIGPGGEVYVTINNSHKVVKYSPEGER 65
                                      679******************************9998775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.029
                                       ETTS--------HHHHHHTEEEETTEEEEE-SSS CS
                              ComJ  13 qkdleppvvdWtdedieqGyaladgavsFealed 46 
                                        ++  ++  +W+ + +  G a++++ +++ +  +
  gi|386001297|ref|YP_005919596.1| 101 YSSEGEKLDEWAVDGMMNGIAAGPNGLIYISFTN 134
                                       4455678999*************99988766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 929.90
//
Query:       gi|386001298|ref|YP_005919597.1|  [L=66]
Description: hypothetical protein Mhar_0596 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   16.2   0.0      0.016   16.0   0.0    1.1  1  DUF1998   Domain of unknown function (DUF1998)


Domain annotation for each model (and alignments):
>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.0   8.9e-07     0.016       5      65 ..       3      61 ..       1      64 [. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-07
                           DUF1998  5 linalplflqcdesdlgteckapedeprkrpariliydavpgGaGi....aekaaelleellraa 65
                                      li++ p+flq+d++ l ++c a+      +++ ili  +     G+    ae++a ll+ +l++a
  gi|386001298|ref|YP_005919597.1|  3 LISVDPIFLQIDQKTLTATCAAA------KRRNILIGSERAPLHGYqartAEELAALLPAVLERA 61
                                      78999***************743......677888877777777772222444555555566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 518.38
//
Query:       gi|386001299|ref|YP_005919598.1|  [L=422]
Description: hypothetical protein Mhar_0597 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-26   91.0  31.5      6e-10   39.1   3.3    4.8  5  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
        2.3    8.0  17.2        3.9    7.2   3.6    6.5  6  Pentapeptide    Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.3   1.1e+04      34      45 ..      44      55 ..      44      56 .. 0.65
   2 !   19.3   0.3     1e-07   0.00093      11      46 ..      66     102 ..      61     104 .. 0.73
   3 !   19.3   0.2   1.1e-07   0.00094       4      44 ..     113     154 ..     112     156 .. 0.92
   4 !   27.0   9.3   4.2e-10   3.8e-06       1      47 [.     154     202 ..     154     203 .. 0.95
   5 !   39.1   3.3   6.7e-14     6e-10       1      47 [.     211     258 ..     211     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                    Pentapeptide_3 34 sgarFtgdvdFs 45
                                      +ga+++g +d++
  gi|386001299|ref|YP_005919598.1| 44 DGAIINGSLDLR 55
                                      477777777776 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1e-07
                    Pentapeptide_3  11 dFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsg 46 
                                         +++  +g+++F + +F g +dFsg++F+++v++ +
  gi|386001299|ref|YP_005919598.1|  66 KITNSIINGPVNFAGKTFeGQVDFSGTTFNDEVTLFD 102
                                       5677778888888888887788888888886677765 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.1e-07
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdF 44 
                                       ++F++ +++ +++F+++a+F+  +F g+ +F++  F+g + F
  gi|386001299|ref|YP_005919598.1| 113 TIFEKKVHLVDTHFIKDADFKYVQFdGGNSFDRISFDGKALF 154
                                       79***********************99*********987766 PP

  == domain 4  score: 27.0 bits;  conditional E-value: 4.2e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.g.sadFsgarFtgdvdFsga 47 
                                       F+ a Fs+ adF++a F++ a+F++  F + s  F+++ F++d+ F+ a
  gi|386001299|ref|YP_005919598.1| 154 FNYAKFSNGADFDDAQFKDIAFFTGVIFsNaSTIFQNSCFEKDALFNYA 202
                                       99***************************77*************99876 PP

  == domain 5  score: 39.1 bits;  conditional E-value: 6.7e-14
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F+ a Fsg a+Fr+a F+g+a F+ + F g+a+F +a+F++ + ++g+
  gi|386001299|ref|YP_005919598.1| 211 FNSAKFSGVANFRNAEFNGDAQFNYTLFnGDASFIDAIFDQMLYLKGS 258
                                       99**************************88**********98998887 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.1     9e+02      32      39 ..      88      95 ..      86      96 .. 0.37
   2 ?   -1.4   0.0      0.21   1.9e+03      21      30 ..     130     139 ..     128     141 .. 0.49
   3 ?    3.3   0.4    0.0075        67      16      25 ..     163     172 ..     152     194 .. 0.59
   4 ?    7.2   3.6   0.00043       3.9      14      35 ..     207     229 ..     195     229 .. 0.75
   5 ?   -2.6   0.0      0.51   4.5e+03      21      28 ..     242     249 ..     241     251 .. 0.36
   6 ?   -1.0   0.0      0.17   1.5e+03      23      29 ..     307     313 ..     293     316 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.1
                                      EECCEEEC CS
                      Pentapeptide 32 dLsganLs 39
                                      d+sg+ ++
  gi|386001299|ref|YP_005919598.1| 88 DFSGTTFN 95
                                      33333333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.21
                                       EEECT-B-TT CS
                      Pentapeptide  21 AnLtgAnlsg 30 
                                       A++ ++ + g
  gi|386001299|ref|YP_005919598.1| 130 ADFKYVQFDG 139
                                       5555555544 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0075
                                       CCCESEEECT CS
                      Pentapeptide  16 anlsgAnLtg 25 
                                       a++ +A + +
  gi|386001299|ref|YP_005919598.1| 163 ADFDDAQFKD 172
                                       3333333332 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.00043
                                       EECCCESEEECT-.B-TT-EECC CS
                      Pentapeptide  14 sganlsgAnLtgA.nlsgAdLsg 35 
                                        +an++ A+++g+ n+++A ++g
  gi|386001299|ref|YP_005919598.1| 207 HDANFNSAKFSGVaNFRNAEFNG 229
                                       46777777777777777777765 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 0.51
                                       EEECT-B- CS
                      Pentapeptide  21 AnLtgAnl 28 
                                       A++++A +
  gi|386001299|ref|YP_005919598.1| 242 ASFIDAIF 249
                                       33333333 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.17
                                       ECT-B-T CS
                      Pentapeptide  23 LtgAnls 29 
                                       L+++nls
  gi|386001299|ref|YP_005919598.1| 307 LRRSNLS 313
                                       4555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2674.43
//
Query:       gi|386001300|ref|YP_005919599.1|  [L=262]
Description: hypothetical protein Mhar_0598 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00024   21.7   0.0    0.00063   20.4   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
     0.0033   18.2   0.0     0.0074   17.0   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
     0.0084   15.4   0.0      0.011   15.0   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.016   14.7   0.0    1.4  1  MTS              Methyltransferase small domain
      0.042   13.6   0.0      0.071   12.9   0.0    1.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.7e-07   0.00063       1      94 [.      52     145 ..      52     147 .. 0.76
   2 ?   -2.6   0.0       2.5   9.1e+03      86      90 ..     189     193 ..     163     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.7e-07
                                       EEEET-TTSHHHHHHHCTS..TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl..gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       + dlG GtG ++++l++r   +  +++ vDise++l a+      e+l ++  +   +dl  e +s  lv     lh
  gi|386001300|ref|YP_005919599.1|  52 IADLGGGTGFILKELLRRRplEGVRLVDVDISEAQLSACDDGRI-ERLAASAATLTRRDLGAEGRSLLLVAR-SLLH 126
                                       78****************755369*************9986552.345555555555677766666655555.4699 PP

                                       GSSHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLk 94 
                                       ++ ++ l+ +l++++  L+
  gi|386001300|ref|YP_005919599.1| 127 YFGRAGLQPLLRHLRGQLQ 145
                                       9999999999998876665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       HHHHH CS
                   Methyltransf_25  86 lkeia 90 
                                       l+e+ 
  gi|386001300|ref|YP_005919599.1| 189 LEEAG 193
                                       33333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.1e-06    0.0074       2      94 ..      54     145 ..      53     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                   Methyltransf_12   2 eiGcGtGsllrallekl..pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       ++G+GtG +l++ll++   ++++++ vDis++++   +    ++e++ ++  +l+ +dl+ +   +   l va ++l
  gi|386001300|ref|YP_005919599.1|  54 DLGGGTGFILKELLRRRplEGVRLVDVDISEAQL--SACDDGRIERLAASAATLTRRDLGAE---GRSLLLVARSLL 125
                                       89**************999***************..44444566666667777777776533...366788899999 PP

                   Methyltransf_12  77 hhl..kdirevldnirklLk 94 
                                       h++  + ++ +l+++r  L 
  gi|386001300|ref|YP_005919599.1| 126 HYFgrAGLQPLLRHLRGQLQ 145
                                       99999999999999987765 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.1e-06     0.011      51     209 ..      37     194 ..      21     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-06
                                       HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS.-----TTEEEEES-TTTS--- CS
                    Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl.sageeervefvgGdffkdslP 126
                                       ++ +l+a++ ++  ++ D+GGGtG ++k+  +  P   v + D+   +++A+    + g  er++  +  + +  l 
  gi|386001300|ref|YP_005919599.1|  37 TAAILQAVEASRPDVIADLGGGTGFILKELLRRRPLEGVRLVDVD--ISEAQLSAcDDGRIERLAASAATLTRRDLG 111
                                       5679999999999**********************8777666653..333332222345566666666666666666 PP

                                       .--SEEEE..ESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCSS-----HHHH CS
                    Methyltransf_2 127 .eaDaill..krvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqteGkeRteaey 200
                                        e+  +ll   ++lh +  +  + lL++++  l+ag + i   a  + ++++   +++   + ++ te +  t  e 
  gi|386001300|ref|YP_005919599.1| 112 aEGRSLLLvaRSLLHYFGRAGLQPLLRHLRGQLQAGEAFIHQSACFADEGDAACLNRI---YGMMGTEKWYSTIDEL 185
                                       5444443311357777777777777777777777766666665555555554443333...5555556666666666 PP

                                       HHHHHHCT- CS
                    Methyltransf_2 201 eellseaGf 209
                                       e+ l+eaGf
  gi|386001300|ref|YP_005919599.1| 186 EAALEEAGF 194
                                       666666666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.6e-06     0.016      20      66 ..      37      83 ..      25     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                                      HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHH CS
                               MTS 20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdar 66
                                      ++ +l+++++++ + ++DlG G+G++  +l+++ p   v lvdvd  
  gi|386001300|ref|YP_005919599.1| 37 TAAILQAVEASRPDVIADLGGGTGFILKELLRRRPLEGVRLVDVDIS 83
                                      677899999999999*********************99****99975 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.071       6      49 ..      51      96 ..      47     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                   Methyltransf_31  6 rvlDlGCGtGeltfelae.elgpkaevvGiDiseeaielAre.naq 49
                                      ++ DlG GtG++++el + +  ++ ++v +Dise  ++ +   + +
  gi|386001300|ref|YP_005919599.1| 51 VIADLGGGTGFILKELLRrRPLEGVRLVDVDISEAQLSACDDgRIE 96
                                      689**************765555999**********9987654555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1959.07
//
Query:       gi|386001301|ref|YP_005919600.1|  [L=387]
Description: Filament induced by cAMP protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-20   71.8   0.0    1.9e-19   70.3   0.0    1.8  1  Fic       Fic/DOC family
     0.0012   17.9   0.1     0.0024   16.9   0.1    1.5  1  DUF3375   Protein of unknown function (DUF3375)
     0.0025   17.9   0.5     0.0076   16.4   0.5    1.9  1  HTH_28    Helix-turn-helix domain
     0.0058   16.7   0.0      0.014   15.4   0.0    1.6  1  Fic_N     Fic/DOC family N-terminal
  ------ inclusion threshold ------
      0.021   14.6   0.3      0.099   12.5   0.3    2.1  1  HTH_23    Homeodomain-like domain
       0.15   12.0   1.8       0.34   10.8   0.8    2.2  2  MarR_2    MarR family
       0.17   12.1   0.9        3.1    8.1   0.1    2.4  2  PaaX      PaaX-like protein


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   7.4e-23   1.9e-19       1      97 []     106     223 ..     106     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 7.4e-23
                                       --SHHHHHHHHCHS-S----........--TS--SS-S............T..EEEE---SCCCHHHHHHHHHHHHC CS
                               Fic   1 pltledllelhrlllqdige........eagefrdeev............segklesalappeevpaeleelleyln 57 
                                       pl++e +++lh+l+++++g+        + g  r +++              g + + ++ +++vpa ++e++ + +
  gi|386001301|ref|YP_005919600.1| 106 PLSEELIRRLHALVTKGTGSetgprgeaR-GGARPKPTpyrdgqnvirdsATGAIVYLPPEAKDVPALMAEMVGWAQ 181
                                       699*****************999766641.333443335555555888776699999999***************** PP

                                       ..HHT-S-HHHHHHHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                               Fic  58 ..elekeeplekaaalhyefekiHPFaDGNgRtarlllnllL 97 
                                         e+e  ++ + a  +hy+f++iHP+ DGNgRtarl++ ++L
  gi|386001301|ref|YP_005919600.1| 182 eaEREGLPVPIIAGLVHYQFVTIHPYYDGNGRTARLIATFIL 223
                                       99999999******************************9987 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.5e-07    0.0024      36      97 ..     310     373 ..     302     382 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.5e-07
                           DUF3375  36 paeelheaLedeLeelr..eeeeeealp.ksAreylrdWvkegWLrrrydegsdeevyelTaaae 97 
                                       p+++++ aL   +e++r  + +e+  l+ + Ar ++r Wv++gWL+ r +++ +   yel+a  +
  gi|386001301|ref|YP_005919600.1| 310 PRARAVLALFTKMERIRtsDVAEALGLSdRMARVLIRGWVSDGWLVLRDPSK-RARSYELSAIYR 373
                                       7888999999999999966444555667788****************98888.*******98655 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5     3e-06    0.0076       2      52 .]     311     364 ..     311     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                            HTH_28   2 Rleiiklla..aGh.svreaArelgisrrtvyrWikryeegGiagLvprrrrpr 52 
                                       R++++++l     + + +++A++lg+s r+ +++i+ + + G+  L++ ++r r
  gi|386001301|ref|YP_005919600.1| 311 RARAVLALFtkMERiRTSDVAEALGLSDRMARVLIRGWVSDGWLVLRDPSKRAR 364
                                       7888888884234578888****************************9999875 PP

>> Fic_N  Fic/DOC family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.6e-06     0.014      39      77 ..      55      94 ..      43      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                             Fic_N 39 SSeIEgtqttlddlleaeadeeeeks.kdvkEVlnYvkAl 77
                                      S++IEg + tl++  ea + +e e + +dv EV nY +Al
  gi|386001301|ref|YP_005919600.1| 55 STRIEGNRLTLAEAEEAISGREIEGReRDVAEVRNYWAAL 94
                                      9*************99999888874449*********998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   3.9e-05     0.099       7      45 ..     311     352 ..     306     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                            HTH_23   7 Rlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                       R+r++l+l     +++++++A++Lg s r  +  ++ ++ +G
  gi|386001301|ref|YP_005919600.1| 311 RARAVLALFTkmeRIRTSDVAEALGLSDRMARVLIRGWVSDG 352
                                       9999999995567******************99999997665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   2.8e+03       3      17 ..      12      26 ..      12      34 .. 0.83
   2 ?   10.8   0.8   0.00013      0.34      17      59 ..     308     362 ..     303     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                                      --HHHHHHHHHHHCT CS
                            MarR_2  3 ltpaqarvLaaLgrr 17
                                      +tpa+ar L+++ ++
  gi|386001301|ref|YP_005919600.1| 12 ITPAIARSLMEIEAA 26
                                      589999999999765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                                       TTTS............EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  17 rpgr............dltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59 
                                        ++r            +++ +++a++lgls   +  +++  v+ G+++ r+ +  
  gi|386001301|ref|YP_005919600.1| 308 LDPRaravlalftkmeRIRTSDVAEALGLSDRMARVLIRGWVSDGWLVLRDPSKR 362
                                       444444444444444459******************************9976443 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.099   2.5e+02      43      59 ..     281     297 ..     275     299 .. 0.85
   2 ?    8.1   0.1    0.0012       3.1      30      68 ..     331     370 ..     328     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.099
                              PaaX  43 alsRlakaGwlvrekeg 59 
                                        ++R+a++G  ++++eg
  gi|386001301|ref|YP_005919600.1| 281 RVFRMAREGAQRSAREG 297
                                       48*******99999988 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                              PaaX  30 laelGiseslvRaalsRlakaGwlvrekegr.rsfYrLsd 68 
                                        ++lG+s+++ R+ +   + +Gwlv  +  + + +Y+Ls+
  gi|386001301|ref|YP_005919600.1| 331 AEALGLSDRMARVLIRGWVSDGWLVLRDPSKrARSYELSA 370
                                       589*********************98777664789***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 2770.12
//
Query:       gi|386001302|ref|YP_005919601.1|  [L=295]
Description: hypothetical protein Mhar_0600 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.52   10.6   0.0    1.9  1  ABC_tran_CTD  ABC transporter C-terminal domain
        0.6   10.1   2.8        3.8    7.6   0.4    2.5  2  HLH           Helix-loop-helix DNA-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.8e-05      0.52       6      36 ..     165     195 ..     162     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpel 36 
                                       e+r+++ + + I++L +ei++l ++l dp  
  gi|386001302|ref|YP_005919601.1| 165 EKRQIADVLSSINELRQEIQKLGNRLTDPKS 195
                                       89***************************85 PP

>> HLH  Helix-loop-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.022     2e+02       9      30 ..     165     186 ..     163     199 .. 0.80
   2 ?    7.6   0.4   0.00042       3.8      14      37 ..     228     251 ..     227     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHCSTCS CS
                               HLH   9 ErrRRdriNsaleeLrellPsl 30 
                                       E+r  +++ s+++eLr+ + +l
  gi|386001302|ref|YP_005919601.1| 165 EKRQIADVLSSINELRQEIQKL 186
                                       899999999*******999844 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00042
                                       HHHHHHHHHHHHCSTCSTTSS-ST CS
                               HLH  14 driNsaleeLrellPslppskKls 37 
                                       ++iN+ l++L+ +l s  +s Kl+
  gi|386001302|ref|YP_005919601.1| 228 NKINKTLDQLKNHLLSVDNSNKLD 251
                                       69*************888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1996.46
//
Query:       gi|386001303|ref|YP_005919602.1|  [L=117]
Description: Putative CoB-CoM heterodisulfide reductase, subunit B, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   19.2   0.4     0.0025   18.0   0.1    1.7  2  CCG       Cysteine-rich domain
  ------ inclusion threshold ------
      0.028   14.1   0.1      0.058   13.1   0.1    1.5  1  zf-CSL    CSL zinc finger


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.8e-07    0.0025      50      85 .]      14      49 ..       2      49 .. 0.80
   2 ?   -1.1   0.0      0.25   2.2e+03      18      37 ..      95     114 ..      87     117 .] 0.53

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-07
                               CCG 50 keelaealakrnvetaeetgadaivtacpgCllqlk 85
                                      +ee a +   r +++a+e gad++v+ cp C+l+l+
  gi|386001303|ref|YP_005919602.1| 14 EEEGAAETLIRILRNAKESGADFVVALCPLCHLMLD 49
                                      45556666678899********************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.25
                               CCG  18 rkalkkllealgveleelek 37 
                                       r +l+kl +a+g e ee   
  gi|386001303|ref|YP_005919602.1|  95 RPVLEKLEGAEGEEAEEEGA 114
                                       44555555555555555444 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.4e-06     0.058      19      54 ..       3      48 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-06
                                      EEETTSSEEEEEHHHHHTT..............--EEEETTSSEEE CS
                            zf-CSL 19 ypCRCgdeFelteedleegae..........gaevvvqCssCSLwi 54
                                      ++CRCg  F  +ee   e  +             vv+ C+ C L++
  gi|386001303|ref|YP_005919602.1|  3 MKCRCGPIFMPEEEGAAETLIrilrnakesgADFVVALCPLCHLML 48
                                      79*******999998888766999*****988889999****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 840.17
//
Query:       gi|386001304|ref|YP_005919603.1|  [L=73]
Description: hypothetical protein Mhar_0602 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-13   49.5   0.0    4.6e-13   49.3   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   2.6e-17   4.6e-13       1      58 [.       3      60 ..       3      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.6e-17
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipep 58
                                      y i+i++ e+  y   vP lpGc+s g+t++e ++n+kea+e+hl +l e++ + p  
  gi|386001304|ref|YP_005919603.1|  3 YTILIHQAEEGGYWSEVPALPGCYSQGETIDETLSNTKEAVEAHLMALKEEEVAAPIE 60
                                      99*********************************************99998887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 468.58
//
Query:       gi|386001305|ref|YP_005919604.1|  [L=52]
Description: hypothetical protein Mhar_0603 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-07   30.9   0.8    2.3e-07   30.7   0.1    1.4  2  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   1.3e-11   2.3e-07      17      58 .]       3      41 ..       1      41 [. 0.95
   2 ?   -2.4   0.0      0.28   5.1e+03       2       9 ..      44      51 ..      44      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.3e-11
                                      EEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin 17 rqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      r kG+Hv  k p+++ ivt+p     +lk+g+lks +k+aGl
  gi|386001305|ref|YP_005919604.1|  3 RGKGDHVNIKMPNGQ-IVTIPIS--GDLKIGLLKSAIKKAGL 41
                                      67***********99.9****99..****************7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.28
                                      HCHHHHHH CS
                        HicA_toxin  2 reviklLe 9 
                                      +e+i+lL+
  gi|386001305|ref|YP_005919604.1| 44 DEFIALLK 51
                                      69999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 377.21
//
Query:       gi|386001306|ref|YP_005919605.1|  [L=295]
Description: CoB-CoM heterodisulfide reductase, subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete 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   76.4   0.2    1.6e-09   37.8   0.0    2.7  2  CCG            Cysteine-rich domain
  ------ inclusion threshold ------
       0.32   11.5   2.0        2.1    8.8   1.6    2.5  2  B12-binding_2  B12 binding domain
        1.1    9.3   4.8         14    5.8   0.8    2.2  2  DUF4110        Domain of unknown function (DUF4110)


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   9.6e-13   5.7e-09       2      84 ..       4      79 ..       3      80 .. 0.91
   2 !   37.8   0.0   2.7e-13   1.6e-09       4      85 .]     142     227 ..     139     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 9.6e-13
                               CCG  2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgC 80
                                      ay++gC ++r   +e++ ++ ++ +alg+el e ++ +CCGa ++  ++e ++ ala+rn+   e     ++++ c+ C
  gi|386001306|ref|YP_005919605.1|  4 AYYPGC-VARSTGREYEISTLAVSRALGIELSEIDDWNCCGATHV--SNEVVSTALAARNLVRTEL----PVMASCSIC 75
                                      8*****.**********************************9988..7777999****99987776....899999999 PP

                               CCG 81 llql 84
                                      +  l
  gi|386001306|ref|YP_005919605.1| 76 YSRL 79
                                      8766 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 2.7e-13
                               CCG   4 fdgChllraa....ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivt 75 
                                       ++gC l r+     +pe + +l+ l++ lg+e  ++  k +CC  +++   +e  a +   r +++a+  gad++v+
  gi|386001306|ref|YP_005919605.1| 142 YYGCLLTRPGggidSPENPSILEDLIRTLGAEPTDFrLKMKCCCGPIFMPEEE-AAAETLIRILRNARASGADFVVA 217
                                       89**999999**************************99999*99999866666.677778899************** PP

                               CCG  76 acpgCllqlk 85 
                                        cp C+l+l+
  gi|386001306|ref|YP_005919605.1| 218 LCPLCHLMLD 227
                                       ********96 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6   0.00036       2.1       4      44 ..      78     121 ..      76     136 .. 0.75
   2 ?   -1.5   0.0      0.59   3.5e+03      53      71 ..     186     204 ..     185     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00036
                     B12-binding_2   4 rlhwaivhgdkegieelidealaqgsa....avdvlndvllpamk 44 
                                       rl+ a++++++++++e ++eal+++++    +++v++  + +a+ 
  gi|386001306|ref|YP_005919605.1|  78 RLRAAMIRLKDRKLRERVNEALEKKYEeekeVLHVIE-MITKALA 121
                                       89********************855444455666653.4444444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.59
                     B12-binding_2  53 gelflpqvllsaevmkkav 71 
                                       g +f p++  +ae++ + +
  gi|386001306|ref|YP_005919605.1| 186 GPIFMPEEEAAAETLIRIL 204
                                       5678888888888876655 PP

>> DUF4110  Domain of unknown function (DUF4110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.8    0.0024        14      43      76 ..      86     119 ..      72     132 .. 0.73
   2 ?    5.2   0.2    0.0037        22      63      84 ..     272     293 ..     270     295 .] 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0024
                           DUF4110  43 kseKelkkeafelAeerywelrpvLeelralede 76 
                                        ++++l+ +  e+ e++y+e ++vL  ++ + + 
  gi|386001306|ref|YP_005919605.1|  86 LKDRKLRERVNEALEKKYEEEKEVLHVIEMITKA 119
                                       6788999999999999999999888777776665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0037
                           DUF4110  63 lrpvLeelraledeqeeagige 84 
                                        rpvLe+l+++e ++ e++  e
  gi|386001306|ref|YP_005919605.1| 272 TRPVLEKLEKIEGKKAEEEGAE 293
                                       69***********976666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2057.44
//
Query:       gi|386001307|ref|YP_005919606.1|  [L=219]
Description: CoB-CoM heterodisulfide reductase, subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-10   40.8   5.8    4.7e-10   39.8   5.8    1.5  1  Fer4_8    4Fe-4S dicluster domain
    2.4e-08   34.0   5.8    7.6e-08   32.4   6.1    1.7  1  Fer4_9    4Fe-4S dicluster domain
    5.6e-08   33.2   5.5    1.3e-07   32.0   5.6    1.6  1  Fer4_17   4Fe-4S dicluster domain
    1.3e-05   25.6   6.9    3.9e-05   24.1   7.0    1.8  1  Fer4_7    4Fe-4S dicluster domain
    1.8e-05   24.8  11.8    4.5e-05   23.5  11.2    1.9  2  Fer4_10   4Fe-4S dicluster domain
    8.9e-05   22.1  10.6     0.0038   17.0   2.3    2.3  2  Fer4      4Fe-4S binding domain
    0.00013   22.0   9.2    0.00036   20.6   9.2    1.7  1  Fer4_21   4Fe-4S dicluster domain
     0.0017   18.3  14.7     0.0041   17.1   3.4    2.3  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.8   2.3      0.011   15.8   2.3    2.3  2  Fer4_6    4Fe-4S binding domain
      0.011   16.1   2.6      0.011   16.1   2.6    2.4  2  Fer4_4    4Fe-4S binding domain
      0.061   14.3  13.8        1.9    9.5  13.4    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
       0.11   13.5  15.0        0.5   11.4   4.4    2.3  2  Fer4_3    4Fe-4S binding domain
       0.41   11.4   4.2         18    6.2   0.3    2.7  2  Fer4_15   4Fe-4S single cluster domain
       0.67   10.2   9.3       0.79    9.9   1.3    3.0  3  Fer4_18   4Fe-4S dicluster domain
          2    9.3  13.5       0.29   12.0   3.0    2.5  2  Fer4_22   4Fe-4S dicluster domain
        4.2    8.0  12.4       0.61   10.7   2.9    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   5.8   4.2e-13   4.7e-10       2      65 .]      40     101 ..      39     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.2e-13
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       ++ Ci+Cg C ++Cp+++ ++   ++  +   ++   e+ + ++ +++w Ct+c  Ct++Cp +i
  gi|386001307|ref|YP_005919606.1|  40 VKTCIQCGTCSASCPTASLMDvPIRKLVKLVLEG---EKAAAMASRSIWLCTSCLLCTVRCPRKI 101
                                       689****************995555555555444...4444456789***************997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   6.1   6.8e-11   7.6e-08       2      49 ..      43     100 ..      42     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.8e-11
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkg 49 
                                       C++Cg+C ++Cp+   ++   ++ ++l  ++e          + C++C  C+ +Cp++
  gi|386001307|ref|YP_005919606.1|  43 CIQCGTCSASCPTASLMDVPIRKLVKLVLEGEkaaamasrsiWLCTSCLLCTVRCPRK 100
                                       ***********9999999999999998888888999********************98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   5.6   1.2e-10   1.3e-07       2      60 ..      43     101 ..      42     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.2e-10
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                       CiqCg C ++Cp+   +d   +kl++ +  g++ +a++++ + lC++C +C+ +CP ++
  gi|386001307|ref|YP_005919606.1|  43 CIQCGTCSASCPTASLMDVPIRKLVKLVLEGEKAAAMASRSIWLCTSCLLCTVRCPRKI 101
                                       *******************99999999888999999999*****************876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   7.0   3.5e-08   3.9e-05       1      51 [.      42     100 ..      42     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.5e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaielde........eenekgtekveidpekClgCgaCvavCPtg 51 
                                       +Ci+Cg C a Cp+  ++  +         e ek  + +  + + C++C  C  +CP +
  gi|386001307|ref|YP_005919606.1|  42 TCIQCGTCSASCPTASLMDVPirklvklvLEGEKAAAMASRSIWLCTSCLLCTVRCPRK 100
                                       6************88877554222322222233333444556788************76 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5  11.2     4e-08   4.5e-05       5      56 .]      39      98 ..      35      98 .. 0.79
   2 !    9.7   2.3   0.00081      0.91       9      24 ..      87     104 ..      79     124 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4e-08
                           Fer4_10  5 dddtCirCgkCvkaCPadl.......tsvgakge.aseeeavrkkvekCtgcgaCveaCP 56
                                      + +tCi+Cg+C ++CP+         + v+   e ++  ++ +  ++ Ct c  C+  CP
  gi|386001307|ref|YP_005919606.1| 39 EVKTCIQCGTCSASCPTASlmdvpirKLVKLVLEgEKAAAMASRSIWLCTSCLLCTVRCP 98
                                      6799*************77*****9955544444044445555589*************9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00081
                           Fer4_10   9 CirCgkCvkaCPadl..t 24 
                                       C+ C  C+  CP ++   
  gi|386001307|ref|YP_005919606.1|  87 CTSCLLCTVRCPRKIrpM 104
                                       999999999999877553 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.3   3.4e-06    0.0038       7      20 ..      42      55 ..      40      58 .. 0.90
   2 !    9.9   1.3   0.00059      0.66       7      20 ..      86      99 ..      86     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                                      TSSS-THHHHHSTT CS
                              Fer4  7 kCigCGaCvevCPv 20
                                       Ci CG+C   CP+
  gi|386001307|ref|YP_005919606.1| 42 TCIQCGTCSASCPT 55
                                      5************9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00059
                                      TSSS-THHHHHSTT CS
                              Fer4  7 kCigCGaCvevCPv 20
                                      +C+ C +C   CP 
  gi|386001307|ref|YP_005919606.1| 86 LCTSCLLCTVRCPR 99
                                      6************7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   9.2   3.2e-07   0.00036       6      52 ..      41      98 ..      36     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.2e-07
                           Fer4_21  6 dkCigCgkCliaCedtshqai..........eidaktvlkvv...edeCvGCnlCssvCP 52
                                      ++Ci+Cg C  +C+++s   +          e  +++ +++       C+ C lC+  CP
  gi|386001307|ref|YP_005919606.1| 41 KTCIQCGTCSASCPTASLMDVpirklvklvlE--GEKAAAMAsrsIWLCTSCLLCTVRCP 98
                                      69*************99988877888877443..33333333111468************ PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.4   3.7e-06    0.0041       6      22 .]      39      55 ..      34      55 .. 0.85
   2 !    6.7   3.6    0.0074       8.3      10      21 ..      87      98 ..      85      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                            Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                      +  +Ci+Cg+C  +CP+
  gi|386001307|ref|YP_005919606.1| 39 EVKTCIQCGTCSASCPT 55
                                      5679*******888**7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0074
                            Fer4_2 10 CigCgaCvsaCP 21
                                      C++C  C+  CP
  gi|386001307|ref|YP_005919606.1| 87 CTSCLLCTVRCP 98
                                      *******666*9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   2.3   9.9e-06     0.011       8      22 ..      42      56 ..      40      58 .. 0.90
   2 ?    4.0   2.6     0.053        60       8      20 ..      86      98 ..      86     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.9e-06
                            Fer4_6  8 kCigCgdCvrvCPeg 22
                                       Ci+Cg C + CP++
  gi|386001307|ref|YP_005919606.1| 42 TCIQCGTCSASCPTA 56
                                      5************96 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                            Fer4_6  8 kCigCgdCvrvCP 20
                                      +C++C  C++ CP
  gi|386001307|ref|YP_005919606.1| 86 LCTSCLLCTVRCP 98
                                      6***********9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   2.6     1e-05     0.011       3      16 ..      42      55 ..      41      60 .. 0.92
   2 ?    3.5   1.1      0.12   1.3e+02       4      16 ..      87      99 ..      81     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +Ci+Cg C a+CP+
  gi|386001307|ref|YP_005919606.1| 42 TCIQCGTCSASCPT 55
                                      7************6 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ C  C+  CP 
  gi|386001307|ref|YP_005919606.1| 87 CTSCLLCTVRCPR 99
                                      99******99995 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  13.4    0.0017       1.9       1      65 [.      42      98 ..      42     100 .. 0.72
   2 ?    5.9   3.1     0.023        26       2      16 ..      87     101 ..      86     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C++Cg C  +CPt+ +         +r+ ++  + e +++a  + +  + + +t C  C+  CP
  gi|386001307|ref|YP_005919606.1| 42 TCIQCGTCSASCPTASLMDV-----PIRKLVKL-VLEGEKAAAMASR--SIWLCTSCLLCTVRCP 98
                                      5**************99888.....45555555.3333444433333..4599***********9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.023
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++C  C+  CP + 
  gi|386001307|ref|YP_005919606.1|  87 CTSCLLCTVRCPRKI 101
                                       ************875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.4   0.00044       0.5       1      13 [.      43      55 ..      43      57 .. 0.95
   2 ?    7.7   2.9    0.0069       7.7       1      14 [.      87     100 ..      87     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C++Cg+C  +CP+
  gi|386001307|ref|YP_005919606.1| 43 CIQCGTCSASCPT 55
                                      ************6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0069
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct C +C + CP +
  gi|386001307|ref|YP_005919606.1|  87 CTSCLLCTVRCPRK 100
                                       9***********87 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.016        18       6      21 ..      41      56 ..      39      76 .. 0.88
   2 ?    5.9   0.4      0.02        22       7      21 ..      86     100 ..      84     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                           Fer4_15  6 daCigcglCvaeapev 21
                                      ++Ci cg C a +p+ 
  gi|386001307|ref|YP_005919606.1| 41 KTCIQCGTCSASCPTA 56
                                      58***********976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                           Fer4_15   7 aCigcglCvaeapev 21 
                                       +C++c lC  ++p+ 
  gi|386001307|ref|YP_005919606.1|  86 LCTSCLLCTVRCPRK 100
                                       7***********975 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3    0.0007      0.79      55      74 ..      37      56 ..       6      71 .. 0.74
   2 ?    3.2   0.8     0.084        95      59      75 ..      85     101 ..      64     106 .. 0.79
   3 ?   -0.0   0.0      0.88   9.8e+02      26      47 ..     174     195 ..     162     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0007
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                       +++  ci+c++c + cPt 
  gi|386001307|ref|YP_005919606.1| 37 GAEVKTCIQCGTCSASCPTA 56
                                      456789************85 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.084
                           Fer4_18  59 gdcidcescvkvcPtgi 75 
                                         c++c  c   cP +i
  gi|386001307|ref|YP_005919606.1|  85 WLCTSCLLCTVRCPRKI 101
                                       56999999999999877 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.88
                           Fer4_18  26 lvvydakrGekiagrkkekkal 47 
                                          ++a+rGe+i g+++ ++  
  gi|386001307|ref|YP_005919606.1| 174 ELGFEAARGERIEGTEEMRRIF 195
                                       5668999****99988877655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.0   0.00026      0.29       1      20 [.      42      61 ..      42      83 .. 0.83
   2 ?    3.5   1.5      0.11   1.3e+02      82      94 ..      87      99 ..      60     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                           Fer4_22  1 rClsCgaCtlvCptCsCfdv 20
                                      +C++Cg+C++ Cpt s +dv
  gi|386001307|ref|YP_005919606.1| 42 TCIQCGTCSASCPTASLMDV 61
                                      5*************987776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                           Fer4_22 82 CvGCgRCieacpv 94
                                      C+ C  C+ +cp 
  gi|386001307|ref|YP_005919606.1| 87 CTSCLLCTVRCPR 99
                                      5555555555554 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.9   0.00054      0.61       4      18 ..      41      55 ..      39      60 .. 0.91
   2 ?    2.0   2.1      0.28   3.2e+02       6      17 ..      87      98 ..      86     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      +tCi cg+C + +P 
  gi|386001307|ref|YP_005919606.1| 41 KTCIQCGTCSASCPT 55
                                      69************6 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.28
                           Fer4_13  6 CiacgaCvelaP 17
                                      C++c +C   +P
  gi|386001307|ref|YP_005919606.1| 87 CTSCLLCTVRCP 98
                                      ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 1536.77
//
Query:       gi|386001308|ref|YP_005919607.1|  [L=448]
Description: Formylmethanofuran dehydrogenase, subunit F [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-43  143.7  79.7    1.2e-08   34.4   3.1    8.3  8  Fer4      4Fe-4S binding domain
    1.1e-34  118.8  54.5    3.4e-11   43.5   5.4    4.7  4  Fer4_7    4Fe-4S dicluster domain
      2e-30  103.5  78.6    2.7e-08   33.5   2.4    8.4  8  Fer4_6    4Fe-4S binding domain
    8.6e-28   96.2  55.0    1.9e-07   31.1   7.9    5.8  5  Fer4_21   4Fe-4S dicluster domain
    8.7e-28   96.3  55.9      1e-08   35.2   3.6    5.3  5  Fer4_9    4Fe-4S dicluster domain
    6.9e-27   93.3  55.9    5.4e-05   23.2   9.1    6.9  7  Fer4_10   4Fe-4S dicluster domain
    4.5e-21   73.6  72.1    4.7e-06   26.4   1.2    8.3  8  Fer4_2    4Fe-4S binding domain
    4.9e-20   72.2  53.8     0.0013   19.7   0.2    7.9  9  Fer4_16   4Fe-4S double cluster binding domain
    2.5e-14   53.4  57.2     0.0012   19.3   9.3    6.6  6  Fer4_8    4Fe-4S dicluster domain
    3.3e-13   49.0  75.9     0.0016   18.8   1.8    8.2  8  Fer4_4    4Fe-4S binding domain
    7.6e-10   39.4  58.3     0.0039   17.9   1.2    8.2  6  Fer4_15   4Fe-4S single cluster domain
    1.4e-09   38.3  61.4    0.00051   20.5   5.9    7.0  7  Fer4_17   4Fe-4S dicluster domain
    1.4e-07   32.2  47.0      0.018   15.9   0.5    8.2  8  Fer4_22   4Fe-4S dicluster domain
    1.5e-06   28.7  67.2      0.029   14.9   1.3    8.4  7  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.7e-05   25.4 103.4     0.0017   19.2   3.3    8.3  8  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
        7.2    6.9  58.2        2.1    8.6   1.2    7.3  8  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   2.1   1.6e-10   1.8e-07       3      23 ..      31      51 ..      29      52 .. 0.93
   2 !   30.9   2.4   1.3e-10   1.5e-07       2      23 ..      69      90 ..      68      91 .. 0.92
   3 !   14.4   4.4   2.1e-05     0.024       6      24 .]     116     134 ..     115     134 .. 0.92
   4 !   19.5   3.9   5.2e-07   0.00059       1      18 [.     159     176 ..     159     178 .. 0.93
   5 !   30.2   2.4   2.3e-10   2.5e-07       3      24 .]     199     220 ..     197     220 .. 0.95
   6 !   34.4   3.1   1.1e-11   1.2e-08       1      23 [.     238     260 ..     238     261 .. 0.93
   7 !   11.6   2.4   0.00017      0.19      10      22 ..     284     296 ..     283     298 .. 0.89
   8 !   15.2   4.4   1.2e-05     0.014       2      18 ..     306     322 ..     305     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.6e-10
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      +d+ kC gCG+Cv  CPv+A+
  gi|386001308|ref|YP_005919607.1| 31 YDYKKCNGCGICVALCPVNAL 51
                                      799*****************8 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 1.3e-10
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       id +kC++CG C+  CPv+A 
  gi|386001308|ref|YP_005919607.1| 69 LIDLDKCVFCGMCAAFCPVDAY 90
                                      59******************96 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.1e-05
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       ekC  C +C+ vCP++AIt
  gi|386001308|ref|YP_005919607.1| 116 EKCLPCALCEPVCPTEAIT 134
                                       78888*************7 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 5.2e-07
                                       EEEETTTSSS-THHHHHS CS
                              Fer4   1 vvideekCigCGaCvevC 18 
                                       +++d+ekC  CG+C++ C
  gi|386001308|ref|YP_005919607.1| 159 IEVDPEKCNLCGKCAKFC 176
                                       689*************** PP

  == domain 5  score: 30.2 bits;  conditional E-value: 2.3e-10
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       +dee+C +CG+Cv +CP +AI+
  gi|386001308|ref|YP_005919607.1| 199 VDEELCDHCGLCVGICPEEAIK 220
                                       8********************6 PP

  == domain 6  score: 34.4 bits;  conditional E-value: 1.1e-11
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       +++d++kCigCG+C  vCP++A 
  gi|386001308|ref|YP_005919607.1| 238 IEVDQDKCIGCGRCLLVCPYDAM 260
                                       589******************96 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 0.00017
                                       S-THHHHHSTTTE CS
                              Fer4  10 gCGaCvevCPvgA 22 
                                       gC aC +vCP ++
  gi|386001308|ref|YP_005919607.1| 284 GCHACFNVCPSDC 296
                                       9*********998 PP

  == domain 8  score: 15.2 bits;  conditional E-value: 1.2e-05
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                       ++ ++ Ci+CGaC++ C
  gi|386001308|ref|YP_005919607.1| 306 KVEKDQCIFCGACANSC 322
                                       7889***********99 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   5.4   3.1e-14   3.4e-11       1      52 []      35      89 ..      35      89 .. 0.90
   2 !   35.0   5.5   1.4e-11   1.6e-08       1      48 [.     117     176 ..      90     178 .. 0.85
   3 !   42.4   4.4   6.7e-14   7.6e-11       2      52 .]     204     259 ..     203     259 .. 0.83
   4 !   16.0  15.3   1.2e-05     0.014       3      49 ..     283     323 ..     280     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 3.1e-14
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52
                                      +C gCg Cva Cpv+a++l ++ + ++    + v id +kC++Cg+C+a CP++a
  gi|386001308|ref|YP_005919607.1| 35 KCNGCGICVALCPVNALQLGPVIEIATGldaPPVLIDLDKCVFCGMCAAFCPVDA 89
                                      7********************98877444558889******************97 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.4e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaield............eeenekgtekveidpekClgCgaCvavC 48 
                                       +C  C  C+++Cp++ai++             eee+ +g+ k+e+dpekC  Cg+C++ C
  gi|386001308|ref|YP_005919607.1| 117 KCLPCALCEPVCPTEAITVVfrptrdvfgplrEEERGEGKGKIEVDPEKCNLCGKCAKFC 176
                                       7*****************77333333333333455555889*****************99 PP

  == domain 3  score: 42.4 bits;  conditional E-value: 6.7e-14
                            Fer4_7   2 CigCgaCvaaCpvkaield..eeenekgt...ekveidpekClgCgaCvavCPtga 52 
                                       C +Cg Cv  Cp +ai+++  + e e+++    ++e+d++kC+gCg+C  vCP++a
  gi|386001308|ref|YP_005919607.1| 204 CDHCGLCVGICPEEAIKVEgnPLELEEEFvfsGEIEVDQDKCIGCGRCLLVCPYDA 259
                                       ****************9874434444444667899******************997 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.2e-05
                            Fer4_7   3 igCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       +gC+aC ++Cp+++ ++ e+       +++++ ++C++CgaC++ C 
  gi|386001308|ref|YP_005919607.1| 283 MGCHACFNVCPSDCWYVGED------GRIKVEKDQCIFCGACANSCH 323
                                       69***************997......48999***************5 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.3   2.1e-07   0.00023       4      24 .]      31      51 ..      28      51 .. 0.92
   2 !   14.2   3.4     3e-05     0.034       2      24 .]      68      90 ..      67      90 .. 0.92
   3 !   13.7   4.6   4.5e-05      0.05       7      24 .]     116     133 ..     115     133 .. 0.95
   4 !   22.6   1.2   7.1e-08     8e-05       1      21 [.     158     178 ..     158     181 .. 0.92
   5 !   27.3   1.7   2.2e-09   2.5e-06       4      24 .]     199     219 ..     197     219 .. 0.96
   6 !   33.5   2.4   2.4e-11   2.7e-08       2      23 ..     238     259 ..     237     260 .. 0.94
   7 !    8.8   3.9    0.0016       1.8       3      21 ..     274     294 ..     272     297 .. 0.84
   8 ?    4.8   5.4      0.03        33       2      20 ..     305     323 ..     304     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.1e-07
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      +d+ kC+gCg Cv+ CP +a+
  gi|386001308|ref|YP_005919607.1| 31 YDYKKCNGCGICVALCPVNAL 51
                                      7999**************997 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      v id dkC+ Cg C++ CP +a+
  gi|386001308|ref|YP_005919607.1| 68 VLIDLDKCVFCGMCAAFCPVDAY 90
                                      679****************9985 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 4.5e-05
                            Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                       +kC+ C  C+ vCP+ ai
  gi|386001308|ref|YP_005919607.1| 116 EKCLPCALCEPVCPTEAI 133
                                       79*************998 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 7.1e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                       ++e+dp+kC+ Cg+C++ C +
  gi|386001308|ref|YP_005919607.1| 158 KIEVDPEKCNLCGKCAKFCEA 178
                                       69***************9975 PP

  == domain 5  score: 27.3 bits;  conditional E-value: 2.2e-09
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       +d+++C++Cg Cv +CPe ai
  gi|386001308|ref|YP_005919607.1| 199 VDEELCDHCGLCVGICPEEAI 219
                                       8******************98 PP

  == domain 6  score: 33.5 bits;  conditional E-value: 2.4e-11
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       +e+d+dkCigCg+C  vCP++a
  gi|386001308|ref|YP_005919607.1| 238 IEVDQDKCIGCGRCLLVCPYDA 259
                                       89******************98 PP

  == domain 7  score: 8.8 bits;  conditional E-value: 0.0016
                            Fer4_6   3 eidpdkCi..gCgdCvrvCPe 21 
                                       e +  +C+  gC +C++vCP 
  gi|386001308|ref|YP_005919607.1| 274 ERQLPLCDpmGCHACFNVCPS 294
                                       566689**999*********7 PP

  == domain 8  score: 4.8 bits;  conditional E-value: 0.03
                            Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                       + + +d Ci Cg+C++ C 
  gi|386001308|ref|YP_005919607.1| 305 IKVEKDQCIFCGACANSCH 323
                                       56889************95 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4   5.7e-07   0.00064      29      57 ..      24      51 ..      11      53 .. 0.73
   2 !   30.4   7.4   2.8e-10   3.1e-07       3      58 ..      70     134 ..      68     135 .. 0.71
   3 !   25.1   6.3   1.2e-08   1.4e-05       3      58 ..     161     220 ..     159     221 .. 0.79
   4 !   31.1   7.9   1.7e-10   1.9e-07       3      56 ..     240     296 ..     238     299 .. 0.73
   5 !   12.1   3.1   0.00014      0.16       3      30 ..     307     331 ..     305     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-07
                           Fer4_21 29 daktvlkvvedeCvGCnlCssvCPvedci 57
                                      d+ +vl +  ++C GC +C++ CPv +++
  gi|386001308|ref|YP_005919607.1| 24 DSVKVLDYDYKKCNGCGICVALCPV-NAL 51
                                      34455666789*************9.665 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 2.8e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqai.......eidaktvl........kvv..edeCvGCnlCssvCPvedcie 58 
                                       id dkC+ Cg C+  C+  ++          e      +        +    +++C  C+lC  vCP+ ++i+
  gi|386001308|ref|YP_005919607.1|  70 IDLDKCVFCGMCAAFCPVDAYRMTandrdykE------MeeyphlvsR-AepNEKCLPCALCEPVCPT-EAIT 134
                                       999**************888877744332211......1233433332.13589*************7.8987 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1.2e-08
                           Fer4_21   3 idedkCigCgkCliaCedtshqai.....eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d++kC  CgkC++ Ce    q       ++ + ++l v e+ C  C lC+ +CP e++i+
  gi|386001308|ref|YP_005919607.1| 161 VDPEKCNLCGKCAKFCEAFLLQEKeptptDLVPFEQLLVDEELCDHCGLCVGICP-EEAIK 220
                                       89***************87777663333233344566889***************.79997 PP

  == domain 4  score: 31.1 bits;  conditional E-value: 1.7e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqaie.idak.tvlkvvedeC..vGCnlCssvCPvedc 56 
                                       +d+dkCigCg+Cl++C+  +++  + ++++ + ++ +   C  +GC+ C +vCP +dc
  gi|386001308|ref|YP_005919607.1| 240 VDQDKCIGCGRCLLVCPYDAMDVTKpFEGDiRLVERQLPLCdpMGCHACFNVCP-SDC 296
                                       89***************877777753333312223333456559**********.588 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00014
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieida 30 
                                       +++d+Ci Cg C+ +C+     a+e+d 
  gi|386001308|ref|YP_005919607.1| 307 VEKDQCIFCGACANSCHC---FAVEVDR 331
                                       789*************94...4555544 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   3.6   9.2e-12     1e-08       1      50 [.      35      89 ..      35      90 .. 0.93
   2 !   23.0  11.0   6.1e-08   6.8e-05       1      51 []      74     133 ..      74     133 .. 0.89
   3 !   31.8   5.4   1.1e-10   1.2e-07       1      51 []     165     219 ..     165     219 .. 0.94
   4 !   29.7   8.9   4.6e-10   5.2e-07       1      49 [.     244     295 ..     244     297 .. 0.94
   5 !   15.8  15.8   1.1e-05     0.012       4      47 ..     284     323 ..     283     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 9.2e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50
                                      kC+gCg Cv+ Cp ++ +   + ++a    a       ++C++Cg C++ Cp +a
  gi|386001308|ref|YP_005919607.1| 35 KCNGCGICVALCPVNALQLGPVIEIATGLDAPPvlidlDKCVFCGMCAAFCPVDA 89
                                      7************************99976666*******************986 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 6.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkgai 51 
                                       kC+ Cg C + Cp +++++ a+ r  +  ++++          e+C+ C  C+ +Cp++ai
  gi|386001308|ref|YP_005919607.1|  74 KCVFCGMCAAFCPVDAYRMTANDRDYKE-MEEYphlvsraepnEKCLPCALCEPVCPTEAI 133
                                       7****************99888888764.444478***********************987 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 1.1e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                                       kC+ Cg+C + C+a + +e++ + ++ +  ++     e C +Cg Cv +Cp++ai
  gi|386001308|ref|YP_005919607.1| 165 KCNLCGKCAKFCEAFLLQEKEPTPTDLVPFEQLlvdeELCDHCGLCVGICPEEAI 219
                                       7************************99977666*******************987 PP

  == domain 4  score: 29.7 bits;  conditional E-value: 4.6e-10
                            Fer4_9   1 kCtgCgaCveaCpagvv.vedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                       kC+gCg+C  +Cp++++ v + +e+ +rl +++   C  +gC+aC+++Cp++
  gi|386001308|ref|YP_005919607.1| 244 KCIGCGRCLLVCPYDAMdVTKPFEGDIRLVERQLPLCdpMGCHACFNVCPSD 295
                                       7****************89999*******9999999*8889*********98 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 1.1e-05
                            Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                       gC+aC ++Cp++ +   + +r+   +     +Ci+CgaC++ C 
  gi|386001308|ref|YP_005919607.1| 284 GCHACFNVCPSDCWYVGEDGRIKVEKD----QCIFCGACANSCH 323
                                       8*************8888888877654....6***********7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.9e-06    0.0033       4      22 ..      31      49 ..      20      66 .. 0.80
   2 !   21.5   0.3   1.7e-07   0.00019       2      30 ..      68      96 ..      67     109 .. 0.73
   3 !   23.2   9.1   4.9e-08   5.4e-05       6      55 ..     115     176 ..     111     177 .. 0.93
   4 !   16.7   0.1   5.2e-06    0.0058       4      30 ..     199     225 ..     196     235 .. 0.77
   5 !   22.6  10.7   7.3e-08   8.2e-05       2      56 .]     238     293 ..     237     293 .. 0.74
   6 !   13.0  14.5   7.2e-05     0.081       9      55 ..     280     322 ..     272     323 .. 0.74
   7 !   10.4   4.4   0.00049      0.55       2      27 ..     305     328 ..     304     347 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
                           Fer4_10  4 idddtCirCgkCvkaCPad 22
                                      +d ++C +Cg Cv+ CP++
  gi|386001308|ref|YP_005919607.1| 31 YDYKKCNGCGICVALCPVN 49
                                      5788999999999999984 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.7e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakg 30
                                      v id d+C+ Cg C ++CP+d+ ++ a++
  gi|386001308|ref|YP_005919607.1| 68 VLIDLDKCVFCGMCAAFCPVDAYRMTAND 96
                                      679*****************773333333 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 4.9e-08
                           Fer4_10   6 ddtCirCgkCvkaCPadl............tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        ++C+ C+ C  +CP+ +               + ++  ++++++++++ekC  cg+C++ C
  gi|386001308|ref|YP_005919607.1| 115 NEKCLPCALCEPVCPTEAitvvfrptrdvfGPLREEERGEGKGKIEVDPEKCNLCGKCAKFC 176
                                       689*************99********999988889999999999****************99 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 5.2e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakg 30 
                                       +d++ C +Cg Cv  CP  + +v++++
  gi|386001308|ref|YP_005919607.1| 199 VDEELCDHCGLCVGICPEEAIKVEGNP 225
                                       7999**************766555555 PP

  == domain 5  score: 22.6 bits;  conditional E-value: 7.3e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                       +++d+d+Ci+Cg+C  +CP+d+  v  k+++ ++  v+  +  C+   c aC  +CP
  gi|386001308|ref|YP_005919607.1| 238 IEVDQDKCIGCGRCLLVCPYDAMDVT-KPFEGDIRLVERQLPLCDPmgCHACFNVCP 293
                                       5789****************554444.44444455555568888754499******9 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 7.2e-05
                           Fer4_10   9 C..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       C  ++C +C ++CP+    +  +  +++  +v+k  ++C++cgaC+ +C
  gi|386001308|ref|YP_005919607.1| 280 CdpMGCHACFNVCPS----DCWYVGEDGRIKVEK--DQCIFCGACANSC 322
                                       65589**********....444444444444444..89*********** PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.00049
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvg 27 
                                       +++++d+Ci Cg+C ++C  +  +v+
  gi|386001308|ref|YP_005919607.1| 305 IKVEKDQCIFCGACANSC--HCFAVE 328
                                       567889999999999999..554444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.6   3.7e-07   0.00042       5      21 ..      31      47 ..      27      48 .. 0.89
   2 !   13.5   2.7   5.3e-05     0.059       1      21 [.      66      86 ..      66      87 .. 0.93
   3 ?    2.6   5.1      0.15   1.7e+02       8      22 .]     116     130 ..     111     130 .. 0.90
   4 !   19.7   1.5   5.5e-07   0.00061       2      21 ..     158     177 ..     157     178 .. 0.91
   5 !   19.4   0.9   6.9e-07   0.00077       4      22 .]     198     216 ..     195     216 .. 0.92
   6 !   26.4   1.2   4.2e-09   4.7e-06       3      22 .]     238     257 ..     236     257 .. 0.92
   7 ?    4.0   4.8     0.057        63      11      21 ..     283     293 ..     280     294 .. 0.92
   8 !    8.6   2.1    0.0019       2.2       2      20 ..     304     322 ..     303     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.7e-07
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      +d  +C+gCg+Cv  CP
  gi|386001308|ref|YP_005919607.1| 31 YDYKKCNGCGICVALCP 47
                                      7899************* PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.3e-05
                            Fer4_2  1 apvvvdtdrCigCgaCvsaCP 21
                                      +pv +d d+C+ Cg C   CP
  gi|386001308|ref|YP_005919607.1| 66 PPVLIDLDKCVFCGMCAAFCP 86
                                      5899************999** PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.15
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       ++C+ C  C  +CP+
  gi|386001308|ref|YP_005919607.1| 116 EKCLPCALCEPVCPT 130
                                       68999*********7 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 5.5e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       +++vd+++C+ Cg+C + C 
  gi|386001308|ref|YP_005919607.1| 158 KIEVDPEKCNLCGKCAKFCE 177
                                       689****************5 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 6.9e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                        vd++ C +Cg Cv  CP+
  gi|386001308|ref|YP_005919607.1| 198 LVDEELCDHCGLCVGICPE 216
                                       69****************5 PP

  == domain 6  score: 26.4 bits;  conditional E-value: 4.2e-09
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++vd d+CigCg C+ +CP+
  gi|386001308|ref|YP_005919607.1| 238 IEVDQDKCIGCGRCLLVCPY 257
                                       789****************5 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.057
                            Fer4_2  11 igCgaCvsaCP 21 
                                       +gC aC ++CP
  gi|386001308|ref|YP_005919607.1| 283 MGCHACFNVCP 293
                                       59********* PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.0019
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       +++v+ d Ci CgaC ++C
  gi|386001308|ref|YP_005919607.1| 304 RIKVEKDQCIFCGACANSC 322
                                       689999************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.6e-06    0.0017       1      26 [.      35      58 ..       7      65 .. 0.84
   2 !   19.0   9.1   1.8e-06     0.002       1      66 [.      74     130 ..      74     131 .. 0.70
   3 !   14.9  10.1   3.5e-05     0.039       1      64 [.     117     176 ..     117     179 .. 0.72
   4 ?    6.8   2.5     0.012        13       1      20 [.     165     184 ..     165     190 .. 0.82
   5 !   16.2   0.2   1.4e-05     0.015       2      20 ..     204     222 ..     203     240 .. 0.85
   6 !   19.7   0.2   1.1e-06    0.0013       1      27 [.     244     270 ..     244     278 .. 0.85
   7 ?    5.7   2.7     0.026        30      55      65 ..     283     293 ..     273     295 .. 0.72
   8 ?    4.6   4.0     0.056        63       4      14 ..     284     294 ..     279     310 .. 0.70
   9 !    7.8   2.4    0.0056       6.2       1      42 [.     311     349 ..     311     361 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeie 26
                                      +C +Cg C+  CP+na++    ++ie
  gi|386001308|ref|YP_005919607.1| 35 KCNGCGICVALCPVNALQLG--PVIE 58
                                      58888888888888888877..5555 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       +C+ Cg Ca  CP++a +++ ++  +++e ++y        ++   + + +e++  C+ C+ vCP 
  gi|386001308|ref|YP_005919607.1|  74 KCVFCGMCAAFCPVDAYRMT-ANDRDYKEMEEY--------PHLVSRAEPNEKCLPCALCEPVCPT 130
                                       5*****************99.333343333333........3333333336679***********6 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.5e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek...kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                       +C  C  C  vCPt+ai+     ++ ++ + +++ ++ ++k +++ d ekc+       C++C++ C
  gi|386001308|ref|YP_005919607.1| 117 KCLPCALCEPVCPTEAITVVfrpTRDVFGPLREE-ERGEGKGKIEVDPEKCN------LCGKCAKFC 176
                                       5999**************7732244444444443.34777777777777777......********* PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.012
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C  CgkCa+ C +  ++ek
  gi|386001308|ref|YP_005919607.1| 165 KCNLCGKCAKFCEAFLLQEK 184
                                       599*********88777776 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.4e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C  Cg C+ +CP++aik +
  gi|386001308|ref|YP_005919607.1| 204 CDHCGLCVGICPEEAIKVE 222
                                       ****************977 PP

  == domain 6  score: 19.7 bits;  conditional E-value: 1.1e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                                       +C++Cg+C+ vCP +a++ +k +e ++
  gi|386001308|ref|YP_005919607.1| 244 KCIGCGRCLLVCPYDAMDVTKPFEGDI 270
                                       5****************9887666655 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.026
                           Fer4_16  55 tgCdiCqdvCP 65 
                                       +gC +C +vCP
  gi|386001308|ref|YP_005919607.1| 283 MGCHACFNVCP 293
                                       67777777777 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.056
                           Fer4_16   4 tCgkCaevCPt 14 
                                       +C++C +vCP+
  gi|386001308|ref|YP_005919607.1| 284 GCHACFNVCPS 294
                                       46666666665 PP

  == domain 9  score: 7.8 bits;  conditional E-value: 0.0056
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdla 42 
                                       +C+ Cg+Ca++C   a++ +  +++ +++ +++ t+  ++++
  gi|386001308|ref|YP_005919607.1| 311 QCIFCGACANSCHCFAVEVD--RSAVTHTPVKE-TPWAEEWK 349
                                       59**********99999999..55555555544.45555554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   5.6e-05     0.062       3      63 ..      34      48 ..       6      60 .. 0.71
   2 !   19.3   9.3     1e-06    0.0012       2      64 ..      72     131 ..      71     132 .. 0.73
   3 !   12.6  11.7   0.00013      0.14       3      62 ..     116     177 ..     115     180 .. 0.67
   4 !   12.6   8.7   0.00012      0.14       3      64 ..     164     217 ..     162     219 .. 0.87
   5 !    9.6  11.7    0.0011       1.3       2      63 ..     242     294 ..     241     296 .. 0.64
   6 !   14.5   0.8   3.1e-05     0.035       3      23 ..     310     330 ..     308     363 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      +kC++Cg C + Cp                                              v
  gi|386001308|ref|YP_005919607.1| 34 KKCNGCGICVALCP----------------------------------------------V 48
                                      45555555555555..............................................4 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1e-06
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       l+kC+ Cg+C + Cp + + ++  +d  ++ +e +    v + +e  ++C+ c  C+ vCp++
  gi|386001308|ref|YP_005919607.1|  72 LDKCVFCGMCAAFCP-VDAYRMTANDRDYKEME-EYPHLV-SRAEPNEKCLPCALCEPVCPTE 131
                                       79*************.44455666666666666.333333.336789**************85 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00013
                            Fer4_8   3 ekCieCgaCqsaCp......vlrrtkkhlldargeaae.dvqeeqvleeeealwsCttcgaCtevCp 62 
                                       ekC  C +C+  Cp      v+r t++     r+e  +  + +      e   ++C+ cg+C++ C 
  gi|386001308|ref|YP_005919607.1| 116 EKCLPCALCEPVCPteaitvVFRPTRDVFGPLREEERGeGKGKI-----EVDPEKCNLCGKCAKFCE 177
                                       69***********9887776666665433333333333112222.....34579************7 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00012
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ekC+ Cg C + C ++  + k++  +     e +   ++       + C +cg C+  Cp++
  gi|386001308|ref|YP_005919607.1| 164 EKCNLCGKCAKFCEAFLLQEKEPTPTDLVPFE-QLLVDE-------ELCDHCGLCVGICPEE 217
                                       79**************9999999999888888.555555.......79************85 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0011
                            Fer4_8   2 lekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsC..ttcgaCtevCpv 63 
                                        +kCi+Cg+C   Cp  ++  tk +     ++ +   +e+q       l  C  ++c+aC +vCp 
  gi|386001308|ref|YP_005919607.1| 242 QDKCIGCGRCLLVCPydAMDVTKPF-----EGDIR-LVERQ-------LPLCdpMGCHACFNVCPS 294
                                       589***********93333333333.....33333.23333.......34565599********97 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 3.1e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkk 23 
                                       ++Ci CgaC ++C+ +  + +
  gi|386001308|ref|YP_005919607.1| 310 DQCIFCGACANSCHCFAVEVD 330
                                       68***********96665443 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.7   1.3e-05     0.015       2      17 .]      34      49 ..      33      49 .. 0.91
   2 !   13.7   1.4   6.3e-05      0.07       2      16 ..      73      87 ..      72      93 .. 0.91
   3 !    7.7   2.5    0.0051       5.7       2      16 ..     116     130 ..     115     134 .. 0.92
   4 !   14.1   1.8   4.7e-05     0.052       1      15 [.     163     177 ..     163     186 .. 0.92
   5 !   14.0   1.7   4.8e-05     0.054       2      16 ..     202     216 ..     201     222 .. 0.90
   6 !   18.8   1.8   1.5e-06    0.0016       1      16 [.     242     257 ..     242     260 .. 0.94
   7 ?    2.7   5.1      0.21   2.3e+02       5      16 ..     283     294 ..     278     298 .. 0.86
   8 ?    3.5   5.6      0.11   1.3e+02       2      15 ..     310     323 ..     309     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+gCg Cva CP++
  gi|386001308|ref|YP_005919607.1| 34 KKCNGCGICVALCPVN 49
                                      89************75 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.3e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C+ Cg C a+CP+
  gi|386001308|ref|YP_005919607.1| 73 DKCVFCGMCAAFCPV 87
                                      89************6 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0051
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C+ C  C+ +CP+
  gi|386001308|ref|YP_005919607.1| 116 EKCLPCALCEPVCPT 130
                                       79************7 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 4.7e-05
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +e+C+ Cg+C  +C+
  gi|386001308|ref|YP_005919607.1| 163 PEKCNLCGKCAKFCE 177
                                       69************8 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 4.8e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C +Cg Cv +CP 
  gi|386001308|ref|YP_005919607.1| 202 ELCDHCGLCVGICPE 216
                                       67************5 PP

  == domain 6  score: 18.8 bits;  conditional E-value: 1.5e-06
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       q++CigCg+C  +CP+
  gi|386001308|ref|YP_005919607.1| 242 QDKCIGCGRCLLVCPY 257
                                       79*************7 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.21
                            Fer4_4   5 igCgsCvaaCPq 16 
                                        gC +C ++CP+
  gi|386001308|ref|YP_005919607.1| 283 MGCHACFNVCPS 294
                                       59*********7 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.11
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       + Ci Cg+C ++C 
  gi|386001308|ref|YP_005919607.1| 310 DQCIFCGACANSCH 323
                                       56999********5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.6   0.00035      0.39       3      19 ..      31      47 ..      29      53 .. 0.91
   2 ?    2.9  11.3      0.17   1.9e+02       1      33 [.      68     103 ..      68     135 .. 0.56
   3 !   11.0   0.3    0.0005      0.56       1      23 [.     159     181 ..     159     189 .. 0.83
   4 !   11.8   1.0   0.00028      0.31       3      20 ..     199     216 ..     197     224 .. 0.91
   5 !   17.9   1.2   3.5e-06    0.0039       1      19 [.     238     256 ..     238     271 .. 0.89
   6 !   14.1   1.0   5.3e-05     0.059       1      32 [.     305     335 ..     305     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      +D ++C gcg Cva++p
  gi|386001308|ref|YP_005919607.1| 31 YDYKKCNGCGICVALCP 47
                                      6999************8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                           Fer4_15   1 VvvDrdaCigcglCvaea...pevfeldedglasvl 33 
                                       V +D d+C  cg+C+a +     + + ++++++++ 
  gi|386001308|ref|YP_005919607.1|  68 VLIDLDKCVFCGMCAAFCpvdAYRMTANDRDYKEME 103
                                       78****************554334555556666666 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0005
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfe 23 
                                       ++vD ++C  cg C++ ++ +  
  gi|386001308|ref|YP_005919607.1| 159 IEVDPEKCNLCGKCAKFCEAFLL 181
                                       79***************976554 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00028
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       vD+++C+ cglCv  +pe
  gi|386001308|ref|YP_005919607.1| 199 VDEELCDHCGLCVGICPE 216
                                       9***************86 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 3.5e-06
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       ++vD+d+Cigcg+C+ ++p
  gi|386001308|ref|YP_005919607.1| 238 IEVDQDKCIGCGRCLLVCP 256
                                       79***************97 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 5.3e-05
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasv 32 
                                       ++v++d+Ci cg+C+  +   f  + d  a++
  gi|386001308|ref|YP_005919607.1| 305 IKVEKDQCIFCGACANSCH-CFAVEVDRSAVT 335
                                       79***************96.666555555544 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2    0.0001      0.12      45      58 ..      35      48 ..       7      55 .. 0.71
   2 !   13.9  10.9   5.3e-05      0.06       1      59 [.      74     131 ..      74     133 .. 0.71
   3 !   10.9  11.4   0.00045       0.5       1      57 [.     117     177 ..     117     181 .. 0.66
   4 ?    6.2   3.1     0.014        16       1      22 [.     165     186 ..     165     192 .. 0.74
   5 !   20.5   5.9   4.6e-07   0.00051       2      59 ..     204     258 ..     203     260 .. 0.83
   6 ?    2.2   2.8      0.25   2.8e+02       4      15 ..     284     295 ..     279     309 .. 0.74
   7 ?    6.4   3.4     0.012        13       1      19 [.     311     329 ..     311     360 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C++Cg C++ CP 
  gi|386001308|ref|YP_005919607.1| 35 KCNGCGICVALCPV 48
                                      55555555555553 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.3e-05
                           Fer4_17   1 rCiqCgyClpeCps..yeaydnepk.kllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +C  Cg+C++ Cp   y+ + n+++ k +++ +++l+ +    e  ++C+ C +Ce +CP +
  gi|386001308|ref|YP_005919607.1|  74 KCVFCGMCAAFCPVdaYRMTANDRDyKEMEE-YPHLVSR---AEPNEKCLPCALCEPVCPTE 131
                                       699**********743444444444144444.4455544...58899*************75 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00045
                           Fer4_17   1 rCiqCgyClpeCpsyeaydn.epk....kllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       +C  C+ C+p+Cp+ +++   +p      +lr+ + g+ ++ + e   ++C+ Cg+C++ C 
  gi|386001308|ref|YP_005919607.1| 117 KCLPCALCEPVCPTEAITVVfRPTrdvfGPLREEERGEGKG-KIEVDPEKCNLCGKCAKFCE 177
                                       6*************999543133321223444433333332.234588*************7 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.014
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnep 22 
                                       +C+ Cg C++ C  +   ++ep
  gi|386001308|ref|YP_005919607.1| 165 KCNLCGKCAKFCEAFLLQEKEP 186
                                       5888888888888777766655 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 4.6e-07
                           Fer4_17   2 CiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       C +Cg C+  Cp  ++  + +p +l +++ ++   e   e   ++Ci+Cg+C  +CP++
  gi|386001308|ref|YP_005919607.1| 204 CDHCGLCVGICPEEAIkVEGNPLELEEEFVFSG--E--IEVDQDKCIGCGRCLLVCPYD 258
                                       ************988756678999999998852..2..2346799************97 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.25
                           Fer4_17   4 qCgyClpeCpsy 15 
                                       +C +C ++Cps 
  gi|386001308|ref|YP_005919607.1| 284 GCHACFNVCPSD 295
                                       677777777764 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.012
                           Fer4_17   1 rCiqCgyClpeCpsyeayd 19 
                                       +Ci Cg+C+++C  ++   
  gi|386001308|ref|YP_005919607.1| 311 QCIFCGACANSCHCFAVEV 329
                                       59999***99999877733 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3    0.0003      0.33      76      95 ..      30      49 ..       6      50 .. 0.78
   2 !    8.1   0.2    0.0043       4.9      81      94 ..      74      87 ..      68     105 .. 0.70
   3 !    7.2   0.4    0.0081       9.1       1      14 [.     117     130 ..     117     152 .. 0.89
   4 ?    4.4   0.8     0.061        69      78      93 ..     162     177 ..     155     180 .. 0.77
   5 ?    3.9   0.2      0.09     1e+02      78      94 ..     200     216 ..     191     218 .. 0.78
   6 !   15.9   0.5   1.6e-05     0.018      76      94 ..     239     257 ..     230     259 .. 0.86
   7 ?    2.1   1.4      0.31   3.5e+02       3      14 ..     283     294 ..     279     310 .. 0.74
   8 !    8.5   1.4    0.0032       3.6       1      24 [.     311     331 ..     311     363 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                       ++ ++C GCg C++ cpv+
  gi|386001308|ref|YP_005919607.1| 30 DYDYKKCNGCGICVALCPVN 49
                                      56899************986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0043
                           Fer4_22 81 gCvGCgRCieacpv 94
                                      +Cv Cg C + cpv
  gi|386001308|ref|YP_005919607.1| 74 KCVFCGMCAAFCPV 87
                                      45555555555554 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0081
                           Fer4_22   1 rClsCgaCtlvCpt 14 
                                       +Cl C+ C  vCpt
  gi|386001308|ref|YP_005919607.1| 117 KCLPCALCEPVCPT 130
                                       7************9 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.061
                           Fer4_22  78 gesgCvGCgRCieacp 93 
                                       + ++C  Cg+C + c 
  gi|386001308|ref|YP_005919607.1| 162 DPEKCNLCGKCAKFCE 177
                                       5677888999999886 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.09
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       +e+ C  Cg C+  cp+
  gi|386001308|ref|YP_005919607.1| 200 DEELCDHCGLCVGICPE 216
                                       67788888888888886 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 1.6e-05
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                       ++++ +C+GCgRC  +cp 
  gi|386001308|ref|YP_005919607.1| 239 EVDQDKCIGCGRCLLVCPY 257
                                       568999***********96 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.31
                           Fer4_22   3 lsCgaCtlvCpt 14 
                                       ++C aC  vCp+
  gi|386001308|ref|YP_005919607.1| 283 MGCHACFNVCPS 294
                                       678899999986 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0032
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedet 24 
                                       +C+ CgaC+     C+Cf ve + 
  gi|386001308|ref|YP_005919607.1| 311 QCIFCGACANS---CHCFAVEVDR 331
                                       69999999875...6777776544 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   1.2    0.0014       1.6       2      17 ..      32      47 ..      31      49 .. 0.90
   2 ?    3.7  14.5     0.081        90       1      58 []      70     135 ..      70     135 .. 0.73
   3 !    7.4   0.6    0.0058       6.5       1      18 [.     161     178 ..     161     185 .. 0.89
   4 !    8.7   2.4    0.0022       2.5       1      18 [.     199     216 ..     199     217 .. 0.96
   5 !   14.9   1.3   2.6e-05     0.029       1      17 [.     240     256 ..     240     257 .. 0.97
   6 ?    2.2   1.0      0.23   2.6e+02       8      18 ..     284     294 ..     282     304 .. 0.87
   7 !   12.4   2.7   0.00016      0.17       1      40 [.     307     343 ..     307     357 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++C +cg+Cv+l+P
  gi|386001308|ref|YP_005919607.1| 32 DYKKCNGCGICVALCP 47
                                      5679***********9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.081
                           Fer4_13   1 VDrdtCiacgaCvelaP.dvFeeddeggasvvaeq.pts....eeekadaeeAada..CPvesIgv 58 
                                       +D d+C+ cg C++++P d +++  ++  +  +e+ p+     e  ++++  A+ +  CP+e+I+v
  gi|386001308|ref|YP_005919607.1|  70 IDLDKCVFCGMCAAFCPvDAYRMTANDRDYKEMEEyPHLvsraEPNEKCLPCALCEpvCPTEAITV 135
                                       899**************99****99988776665323224444555677666665344****9986 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0058
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD ++C  cg+C++++  
  gi|386001308|ref|YP_005919607.1| 161 VDPEKCNLCGKCAKFCEA 178
                                       8**************965 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0022
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD++ C  cg+Cv ++P+
  gi|386001308|ref|YP_005919607.1| 199 VDEELCDHCGLCVGICPE 216
                                       9****************7 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 2.6e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD+d+Ci+cg C  ++P
  gi|386001308|ref|YP_005919607.1| 240 VDQDKCIGCGRCLLVCP 256
                                       9***************9 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.23
                           Fer4_13   8 acgaCvelaPd 18 
                                       +c+aC +++P 
  gi|386001308|ref|YP_005919607.1| 284 GCHACFNVCPS 294
                                       8*********5 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00016
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseee 40 
                                       V++d+Ci cgaC++ + ++F+ + +  +s+v++ p++e+ 
  gi|386001308|ref|YP_005919607.1| 307 VEKDQCIFCGACANSC-HCFAVEVD--RSAVTHTPVKETP 343
                                       89************98.78888887..6778888887443 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   6.6   0.00042      0.47       1      15 []      36      50 ..      36      50 .. 0.98
   2 !    7.4   6.1    0.0085       9.5       1      15 []      75      89 ..      75      89 .. 0.97
   3 ?    4.5   6.2     0.072        81       4      15 .]     121     132 ..     118     132 .. 0.83
   4 ?    3.7   4.1      0.13   1.5e+02       1      11 [.     166     176 ..     166     177 .. 0.97
   5 !   14.0   4.5   6.5e-05     0.073       1      15 []     204     218 ..     204     218 .. 0.93
   6 !   19.2   3.3   1.5e-06    0.0017       1      15 []     245     259 ..     245     259 .. 0.98
   7 ?    6.4   8.7     0.019        21       1      14 [.     280     295 ..     280     296 .. 0.84
   8 ?    3.3   8.3      0.18     2e+02       1      11 [.     312     322 ..     312     326 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv  CPv+A
  gi|386001308|ref|YP_005919607.1| 36 CNGCGICVALCPVNA 50
                                      *************99 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0085
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg C   CPv+A
  gi|386001308|ref|YP_005919607.1| 75 CVFCGMCAAFCPVDA 89
                                      *************98 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.072
                            Fer4_3   4 CgaCvevCPvgA 15 
                                       C +C+ vCP+ A
  gi|386001308|ref|YP_005919607.1| 121 CALCEPVCPTEA 132
                                       99*******876 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.13
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ Cg C + C
  gi|386001308|ref|YP_005919607.1| 166 CNLCGKCAKFC 176
                                       *********99 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 6.5e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++Cg+Cv  CP+ A
  gi|386001308|ref|YP_005919607.1| 204 CDHCGLCVGICPEEA 218
                                       ************866 PP

  == domain 6  score: 19.2 bits;  conditional E-value: 1.5e-06
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg+C+ vCP++A
  gi|386001308|ref|YP_005919607.1| 245 CIGCGRCLLVCPYDA 259
                                       *************98 PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.019
                            Fer4_3   1 Ct..gCgaCvevCPvg 14 
                                       C+  gC aC++vCP++
  gi|386001308|ref|YP_005919607.1| 280 CDpmGCHACFNVCPSD 295
                                       66659*********87 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.18
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ CgaC ++C
  gi|386001308|ref|YP_005919607.1| 312 CIFCGACANSC 322
                                       *********** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0024       2.7      56      74 ..      31      49 ..       6      66 .. 0.74
   2 ?    2.9   2.3       0.1   1.2e+02      59      74 ..      73      88 ..      68      94 .. 0.89
   3 ?    7.4   1.3    0.0042       4.8      53      74 ..     110     131 ..      89     136 .. 0.76
   4 ?   -0.1   0.8      0.92     1e+03      59      72 ..     164     177 ..     149     184 .. 0.72
   5 ?    0.9   0.4      0.46   5.1e+02      84      99 ..     165     180 ..     161     197 .. 0.62
   6 ?    4.1   1.6     0.044        50      60      74 ..     203     217 ..     191     229 .. 0.83
   7 ?    8.6   1.2    0.0018       2.1      57      77 ..     241     262 ..     223     270 .. 0.81
   8 ?    4.9  10.3     0.025        28      57      97 ..     278     324 ..     268     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                           Fer4_18 56 kgagdcidcescvkvcPtg 74
                                       +  +c  c+ cv++cP++
  gi|386001308|ref|YP_005919607.1| 31 YDYKKCNGCGICVALCPVN 49
                                      45678************85 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                       +c+ c++c + cP++
  gi|386001308|ref|YP_005919607.1| 73 DKCVFCGMCAAFCPVD 88
                                      57************85 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0042
                           Fer4_18  53 rkekgagdcidcescvkvcPtg 74 
                                        +++++ +c+ c  c  vcPt+
  gi|386001308|ref|YP_005919607.1| 110 SRAEPNEKCLPCALCEPVCPTE 131
                                       56788999************96 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.92
                           Fer4_18  59 gdcidcescvkvcP 72 
                                        +c  c++c k c 
  gi|386001308|ref|YP_005919607.1| 164 EKCNLCGKCAKFCE 177
                                       45777777777774 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.46
                           Fer4_18  84 eciscllcidacdkvm 99 
                                       +c  c++c   c+  +
  gi|386001308|ref|YP_005919607.1| 165 KCNLCGKCAKFCEAFL 180
                                       5677777777777655 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.044
                           Fer4_18  60 dcidcescvkvcPtg 74 
                                        c +c+ cv +cP +
  gi|386001308|ref|YP_005919607.1| 203 LCDHCGLCVGICPEE 217
                                       5999*********75 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0018
                           Fer4_18  57 gagdcidcescvkvcPtg.idi 77 
                                       ++ +ci c+ c+ vcP + +d+
  gi|386001308|ref|YP_005919607.1| 241 DQDKCIGCGRCLLVCPYDaMDV 262
                                       5778************742565 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.025
                           Fer4_18  57 gagdcidcescvkvcPtgi.....dirkGl.qleciscllcidacdk 97 
                                       +  d + c++c +vcP +      d r  + + +ci c+ c ++c+ 
  gi|386001308|ref|YP_005919607.1| 278 PLCDPMGCHACFNVCPSDCwyvgeDGRIKVeKDQCIFCGACANSCHC 324
                                       5678899*********764222226664441568***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3270.44
//
Query:       gi|386001309|ref|YP_005919608.1|  [L=790]
Description: CoB-CoM heterodisulfide reductase, subunit A [Methanosaeta harundinacea 6Ac]
Scores for 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-51  171.1   3.9      2e-49  166.6   0.2    3.7  4  FlpD           Methyl-viologen-reducing hydrogenase, delta su
    3.8e-20   70.8  55.1    1.5e-07   30.9   3.8    5.4  4  Fer4           4Fe-4S binding domain
    1.6e-18   66.9   0.0    8.6e-18   64.6   0.0    1.9  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.1e-16   60.2  30.3    1.1e-06   29.1  12.9    5.4  5  Fer4_7         4Fe-4S dicluster domain
    4.1e-14   52.4  42.8    3.8e-09   36.5  13.1    5.5  5  Fer4_21        4Fe-4S dicluster domain
    1.1e-13   50.5  56.4    3.5e-05   23.7   3.9    5.8  6  Fer4_6         4Fe-4S binding domain
    4.8e-13   49.0  33.5    2.4e-06   27.6  13.6    4.6  5  Fer4_10        4Fe-4S dicluster domain
    9.7e-12   45.6  26.8    0.00081   20.3   0.2    5.1  4  Fer4_16        4Fe-4S double cluster binding domain
    1.1e-11   44.0  44.9    0.00054   19.9   4.0    5.5  5  Fer4_2         4Fe-4S binding domain
    1.9e-11   44.0  32.3      4e-07   30.1  10.4    3.8  3  Fer4_9         4Fe-4S dicluster domain
    3.1e-08   33.5  30.4    0.00056   20.2   2.1    5.0  4  Fer4_4         4Fe-4S binding domain
    6.4e-07   29.1   0.2    1.3e-06   28.1   0.2    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
      1e-06   29.1  26.7     0.0048   17.3   0.0    5.2  5  Fer4_8         4Fe-4S dicluster domain
    7.6e-06   25.7   1.9     0.0083   15.7   1.0    2.5  2  DAO            FAD dependent oxidoreductase
    1.1e-05   24.8   0.5    2.1e-05   23.8   0.5    1.4  1  FAD_binding_2  FAD binding domain
    9.1e-05   22.6   0.0    0.00069   19.8   0.0    2.3  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    9.4e-05   22.9   0.5    0.00029   21.4   0.2    1.9  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00011   22.8  30.8      0.039   14.7   1.6    5.1  4  Fer4_15        4Fe-4S single cluster domain
    0.00021   21.8  30.7       0.17   12.4   1.6    5.2  6  Fer4_17        4Fe-4S dicluster domain
    0.00067   18.9   0.1    0.00067   18.9   0.1    1.8  2  GIDA           Glucose inhibited division protein A
    0.00079   20.2  22.1       0.62   10.9   1.3    4.7  4  Fer4_22        4Fe-4S dicluster domain
     0.0015   19.0  33.6      0.015   15.9   2.9    4.4  3  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
     0.0038   16.5   0.5     0.0062   15.8   0.5    1.3  1  FAD_binding_3  FAD binding domain
     0.0066   15.2   0.2      0.011   14.5   0.2    1.3  1  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
       0.01   16.7   5.5       0.01   16.7   5.5    6.3  5  Fer4_3         4Fe-4S binding domain
      0.015   14.6   0.1      0.029   13.7   0.1    1.4  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.027   13.7   0.0      0.089   12.0   0.0    1.8  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.035   13.3   0.1      0.068   12.4   0.1    1.4  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.5   4.2e+03      90     114 ..      93     117 ..      77     120 .. 0.72
   2 ?   -0.4   0.0       1.7   1.1e+03       3      47 ..     395     442 ..     394     450 .. 0.73
   3 ?    2.8   0.0      0.17   1.1e+02      47      78 ..     522     557 ..     519     563 .. 0.68
   4 !  166.6   0.2   3.2e-52     2e-49       1     123 []     649     771 ..     649     771 .. 1.00

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.5
                              FlpD  90 iepeRvrleevsaaegekfaevike 114
                                       + + R ++++v ++e+++ +e++k+
  gi|386001309|ref|YP_005919608.1|  93 MANIREQCSWVHMDEPPQAQEKAKD 117
                                       4455677888888888888887776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                              FlpD   3 aFlCnwcayaaadlagvsrlqypp...nvriirvpCsgrvdpefilka 47 
                                       a++ + c+  a+++a++ + +yp+   +++ i ++  g+  +ef ++a
  gi|386001309|ref|YP_005919608.1| 395 AYCSRVCCMYALKNAQLIKEKYPEtevSIHYIDLRAGGEGYEEFYMRA 442
                                       678889999999999999999998433477777777776666665555 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.17
                              FlpD  47 alekGadgVlvlgChpgd....ChyvkGnekaerrv 78 
                                         e+ ++gV+++gC  g         +G+  a++ +
  gi|386001309|ref|YP_005919608.1| 522 PVEAHIEGVFIAGCASGPkeiqVSIAQGEAAAAKAM 557
                                       5677899*******9875444444446666666555 PP

  == domain 4  score: 166.6 bits;  conditional E-value: 3.2e-52
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       i++FlCnwc+ya+adlag+sr+qyp+n+r irv+C+grvdp+f+l+al+ GadgVl++gC+ g+Chy+kGn++a +r
  gi|386001309|ref|YP_005919608.1| 649 IVGFLCNWCSYAGADLAGTSRIQYPTNMRAIRVMCAGRVDPAFVLEALKGGADGVLISGCRLGECHYNKGNYQAYQR 725
                                       89*************************************************************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       v+ l+ +le++gi+p Rv++ +++a+ege +a+ +++fv+++ke+G
  gi|386001309|ref|YP_005919608.1| 726 VQVLRGVLEKVGINPGRVKIIWCAASEGEILAKEVRKFVSELKEMG 771
                                       ********************************************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   6.6     0.078        50       3      22 ..     238     258 ..     236     260 .. 0.86
   2 !   30.4   9.3   3.4e-10   2.2e-07       3      23 ..     286     306 ..     284     307 .. 0.93
   3 !   30.9   3.8   2.3e-10   1.5e-07       2      24 .]     573     595 ..     572     595 .. 0.94
   4 !   28.1   6.0   1.9e-09   1.2e-06       3      24 .]     602     623 ..     600     623 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.078
                                       EETTTSSS-.THHHHHSTTTE CS
                              Fer4   3 ideekCigC.GaCvevCPvgA 22 
                                       +de +C gC ++C+ vCPv++
  gi|386001309|ref|YP_005919608.1| 238 VDEKLCKGClNECAGVCPVEV 258
                                       8999*****668******986 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.4e-10
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                       id++ CigCG+C+e+CPv+A 
  gi|386001309|ref|YP_005919608.1| 286 IDPSACIGCGLCAEACPVDAV 306
                                       9*******************7 PP

  == domain 3  score: 30.9 bits;  conditional E-value: 2.3e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       v+d+ekCigC++Cv+ CP  AI+
  gi|386001309|ref|YP_005919608.1| 573 VVDQEKCIGCKLCVDTCPGKAIS 595
                                       89*******************95 PP

  == domain 4  score: 28.1 bits;  conditional E-value: 1.9e-09
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       +de  C gCG+C+ +CPv+AI+
  gi|386001309|ref|YP_005919608.1| 602 VDEAACKGCGTCAAACPVDAID 623
                                       8*******************95 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   1.3e-20   8.6e-18       2     294 .]     142     549 ..     141     549 .. 0.74

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.3e-20
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx....... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias....... 57 
                                       +v+viGgG+AG++a+l+la  g+ v+lve           l++ +++++c++   +++++ v  ++ i +       
  gi|386001309|ref|YP_005919608.1| 142 EVLVIGGGVAGIQASLDLADCGLSVHLVErrptiggymalLTDVFPTNDCSIcvlAPKMTDVYNHPLIDLvtyaeil 218
                                       699*************************99999999*************988555778888888887777****999 PP

                                       ......................................HHHHCHHHHCCCCHC........CT.CEEEEESCEEEEE CS
                                       ......................................xxxxxxxxxxxxxxx........xx.xxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ......................................evvkklnqgielllg........ee.vvkidpgkkkvkl 87 
                                                                             ev + ++ g+ ++++        ++ v  idp       
  gi|386001309|ref|YP_005919608.1| 219 niegsvgrftvsgvrkarfvdeklckgclnecagvcpvEVPDDYEFGLGKRKAiympipqaVPlVACIDPS------ 289
                                       99999999999999999999888888888888888877555556666555555556666654433333333...... PP

                                       TEEEC.....................TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T. CS
                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2  88 ekkke.....................gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp. 142
                                                                 ++e++++ +++++AtG +++d+  + +  +++   r + sa ++++ l+  
  gi|386001309|ref|YP_005919608.1| 290 ----AcigcglcaeacpvdavkydqrQEEFRFDVGAIIVATGWQSFDPARKEE--YGYGRYRDVISALQVERLLNAa 360
                                       ....1333344455667788888888999999****************66655..3333335555555554444445 PP

                                       ..........................SEEEEES-SHHHHHHHHHHHHHT-.........EEEEEESSSSSS...TTS CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx...xxx RF
                       Pyr_redox_2 143 ..........................krivvvGgGyiGvElAaalaklgk.........evtlveardrll...ral 181
                                                                  r   vG+ y++ ++++++ k ++         ev +       +   ra 
  gi|386001309|ref|YP_005919608.1| 361 gptggevvrpstgevaksvaflqcvgSRDETVGNAYCSRVCCMYALKNAQlikekypetEVSIH------YidlRAG 431
                                       5566666666666666555554477766699*************74444445555555544433......2233677 PP

                                       -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelle..eklgle 251
                                       ++  ++++++a +  G+++  + +v e+++ +     ++e + l+  ++ ++dlvv+++G++p+++     + lgl+
  gi|386001309|ref|YP_005919608.1| 432 GEGYEEFYMRAQR-LGINFI-RGRVSEVEEVDGslrvNYEdTLLGGFRSKPYDLVVLSAGLEPNKDADVvgNLLGLA 506
                                       9999***998765.5*****.6667788877774434444777777777***************998559999**** PP

                                       EEETTEEE--.TTS...BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxx.xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 252 lderggivvd.efl...rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                         ++g++++  +++   +  ++g++ +G +a   +gp+ +q++++qG
  gi|386001309|ref|YP_005919608.1| 507 KRPDGFFEIAhPKMrpvEAHIEGVFIAG-CA---SGPKEIQVSIAQG 549
                                       *******6651567544568********.88...8*******99998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.8    0.0011      0.68      27      52 .]     231     258 ..     189     258 .. 0.69
   2 !   26.0   0.3   1.6e-08     1e-05       1      27 [.     290     316 ..     290     340 .. 0.86
   3 ?    1.3   0.2      0.84   5.4e+02       6      26 ..     395     415 ..     383     440 .. 0.71
   4 !   29.1  12.9   1.7e-09   1.1e-06       1      52 []     578     621 ..     578     621 .. 0.94
   5 !   19.5   2.8   1.7e-06    0.0011       1      28 [.     606     633 ..     606     658 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                            Fer4_7  27 gtekvei.dpekClgCga.CvavCPtga 52 
                                       g++k+++ d+  C gC + C+ vCP+++
  gi|386001309|ref|YP_005919608.1| 231 GVRKARFvDEKLCKGCLNeCAGVCPVEV 258
                                       667777625667****988******975 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.6e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekg 27 
                                       +CigCg C++aCpv+a+++d++++e +
  gi|386001309|ref|YP_005919608.1| 290 ACIGCGLCAEACPVDAVKYDQRQEEFR 316
                                       5********************987755 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.84
                            Fer4_7   6 gaCvaaCpvkaieldeeenek 26 
                                        +C ++C ++a++  +  +ek
  gi|386001309|ref|YP_005919608.1| 395 AYCSRVCCMYALKNAQLIKEK 415
                                       49*****99888866554433 PP

  == domain 4  score: 29.1 bits;  conditional E-value: 1.7e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +CigC+ Cv++Cp kai+++          + +d+  C gCg C+a+CP++a
  gi|386001309|ref|YP_005919608.1| 578 KCIGCKLCVDTCPGKAISVNGT--------ALVDEAACKGCGTCAAACPVDA 621
                                       7******************775........7899****************97 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 1.7e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt 28 
                                       +C gCg C+aaCpv+ai+++ +++e+ +
  gi|386001309|ref|YP_005919608.1| 606 ACKGCGTCAAACPVDAIDMTLFSDEQIM 633
                                       5*****************9977666544 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       1.2   7.6e+02      17      33 ..      42      58 ..      40      69 .. 0.67
   2 !   11.6   0.7   0.00036      0.23      33      54 ..     234     257 ..     221     259 .. 0.76
   3 !   20.5   2.2     6e-07   0.00038       1      31 [.     284     311 ..     284     318 .. 0.77
   4 ?    0.7   0.7      0.89   5.7e+02      38      52 ..     388     402 ..     374     407 .. 0.82
   5 !   36.5  13.1   5.9e-12   3.8e-09       1      59 []     572     624 ..     572     624 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                           Fer4_21 17 aCedtshqaieidaktv 33
                                      +C+dt+ + i+ d +++
  gi|386001309|ref|YP_005919608.1| 42 TCSDTGQDMIKEDIAEH 58
                                      8*********8664443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00036
                           Fer4_21  33 vlkvv.edeCvGC.nlCssvCPve 54 
                                       +++ v e+ C GC n C+ vCPve
  gi|386001309|ref|YP_005919608.1| 234 KARFVdEKLCKGClNECAGVCPVE 257
                                       444442789****889******95 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 6e-07
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidak 31 
                                       A id++ CigCg+C+ aC+   ++a+++d++
  gi|386001309|ref|YP_005919608.1| 284 ACIDPSACIGCGLCAEACP---VDAVKYDQR 311
                                       6788888888888888888...677777765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.89
                           Fer4_21  38 edeCvGCnlCssvCP 52 
                                        de vG + Cs vC 
  gi|386001309|ref|YP_005919608.1| 388 RDETVGNAYCSRVCC 402
                                       68999*********6 PP

  == domain 5  score: 36.5 bits;  conditional E-value: 5.9e-12
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       A++d++kCigC++C+ +C+    +ai++++ +   v e  C GC  C++ CPv d+i+m
  gi|386001309|ref|YP_005919608.1| 572 AVVDQEKCIGCKLCVDTCP---GKAISVNGTAL--VDEAACKGCGTCAAACPV-DAIDM 624
                                       89*****************...599*9986655..99***************9.99998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2         9   5.8e+03      11      17 ..     190     196 ..     189     197 .. 0.80
   2 !   12.6   2.5   0.00017      0.11       4      22 ..     238     257 ..     237     259 .. 0.90
   3 !   19.7   8.5   9.8e-07   0.00063       4      23 ..     286     305 ..     284     306 .. 0.95
   4 ?   -0.3   1.1       2.1   1.4e+03      15      24 .]     397     406 ..     393     406 .. 0.86
   5 !   23.7   3.9   5.4e-08   3.5e-05       1      24 []     571     594 ..     571     594 .. 0.91
   6 !   22.5   4.4   1.2e-07     8e-05       3      24 .]     601     622 ..     599     622 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9
                            Fer4_6  11 gCgdCvr 17 
                                       +C  Cv 
  gi|386001309|ref|YP_005919608.1| 190 DCSICVL 196
                                       8999*96 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                            Fer4_6   4 idpdkCigC.gdCvrvCPeg 22 
                                       +d+ +C gC ++C+ vCP  
  gi|386001309|ref|YP_005919608.1| 238 VDEKLCKGClNECAGVCPVE 257
                                       89*******999******86 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 9.8e-07
                            Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                       idp++CigCg C+ +CP +a
  gi|386001309|ref|YP_005919608.1| 286 IDPSACIGCGLCAEACPVDA 305
                                       8****************987 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.1
                            Fer4_6  15 CvrvCPegai 24 
                                       C rvC ++a+
  gi|386001309|ref|YP_005919608.1| 397 CSRVCCMYAL 406
                                       *****99886 PP

  == domain 5  score: 23.7 bits;  conditional E-value: 5.4e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       v+++d++kCigC  Cv+ CP +ai
  gi|386001309|ref|YP_005919608.1| 571 VAVVDQEKCIGCKLCVDTCPGKAI 594
                                       689*****************7776 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 1.2e-07
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                        +d+ +C gCg C+++CP +ai
  gi|386001309|ref|YP_005919608.1| 601 LVDEAACKGCGTCAAACPVDAI 622
                                       69*****************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.3   0.00096      0.61       4      22 ..     238     257 ..     235     278 .. 0.81
   2 !   23.2   1.2   8.8e-08   5.6e-05       4      32 ..     286     314 ..     283     327 .. 0.77
   3 ?   -1.8   0.4       5.7   3.6e+03      13      30 ..     395     413 ..     383     425 .. 0.65
   4 !   27.6  13.6   3.7e-09   2.4e-06       3      56 .]     573     618 ..     571     618 .. 0.97
   5 !   17.0   2.9   7.7e-06    0.0049       3      24 ..     601     627 ..     599     646 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00096
                           Fer4_10   4 idddtCirCg.kCvkaCPad 22 
                                       +d++ C +C  +C  +CP+ 
  gi|386001309|ref|YP_005919608.1| 238 VDEKLCKGCLnECAGVCPVE 257
                                       68899****88*******93 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 8.8e-08
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgea 32 
                                       id++ Ci+Cg C +aCP+d+ ++++++e+
  gi|386001309|ref|YP_005919608.1| 286 IDPSACIGCGLCAEACPVDAVKYDQRQEE 314
                                       89****************66544444443 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.7
                           Fer4_10  13 gkCvkaCPadl.tsvgakg 30 
                                       + C ++C +++ ++ + ++
  gi|386001309|ref|YP_005919608.1| 395 AYCSRVCCMYAlKNAQLIK 413
                                       4799999554454444333 PP

  == domain 4  score: 27.6 bits;  conditional E-value: 3.7e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+d+++Ci+C+ Cv+ CP         +++s +++  ++  +C gcg C++aCP
  gi|386001309|ref|YP_005919608.1| 573 VVDQEKCIGCKLCVDTCPG--------KAISVNGTALVDEAACKGCGTCAAACP 618
                                       789****************........**************************9 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 7.7e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.....t 24 
                                        +d+  C +Cg+C +aCP+d+      
  gi|386001309|ref|YP_005919608.1| 601 LVDEAACKGCGTCAAACPVDAidmtlF 627
                                       578999*************66554440 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.8     0.061        39       2      66 ..     243     256 ..     232     263 .. 0.63
   2 !   20.3   0.2   1.3e-06   0.00081       2      23 ..     291     312 ..     290     340 .. 0.83
   3 !   16.5   1.5   1.9e-05     0.012       1      20 [.     578     597 ..     578     605 .. 0.86
   4 !   18.8   2.1   3.7e-06    0.0024       2      21 ..     607     628 ..     606     657 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.061
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C++C +                                                    C+ vCP+
  gi|386001309|ref|YP_005919608.1| 243 CKGCLN---------------------------------------------------ECAGVCPV 256
                                       555533...................................................45555554 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.3e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                       C++Cg Cae+CP++a+k ++++
  gi|386001309|ref|YP_005919608.1| 291 CIGCGLCAEACPVDAVKYDQRQ 312
                                       ****************988433 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.9e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C+ C+++CP +ai+ +
  gi|386001309|ref|YP_005919608.1| 578 KCIGCKLCVDTCPGKAISVN 597
                                       5****************976 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 3.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek..k 21 
                                       C++Cg Ca +CP++ai+++  +
  gi|386001309|ref|YP_005919608.1| 607 CKGCGTCAAACPVDAIDMTlfS 628
                                       ****************988333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2         4   2.5e+03      12      18 ..     190     196 ..     189     197 .. 0.77
   2 !    9.6   1.6    0.0015      0.98       4      21 ..     237     255 ..     234     256 .. 0.87
   3 !   17.4   6.5   5.1e-06    0.0033       3      21 ..     284     302 ..     282     303 .. 0.91
   4 !   19.9   4.0   8.5e-07   0.00054       3      21 ..     572     590 ..     569     590 .. 0.93
   5 !   17.9   4.3   3.8e-06    0.0024       4      21 ..     601     618 ..     599     619 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4
                            Fer4_2  12 gCgaCvs 18 
                                        C++Cv 
  gi|386001309|ref|YP_005919608.1| 190 DCSICVL 196
                                       79***86 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                            Fer4_2   4 vvdtdrCigC.gaCvsaCP 21 
                                       +vd+  C gC + C  +CP
  gi|386001309|ref|YP_005919608.1| 237 FVDEKLCKGClNECAGVCP 255
                                       799*******659****** PP

  == domain 3  score: 17.4 bits;  conditional E-value: 5.1e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       + +d+ +CigCg C  aCP
  gi|386001309|ref|YP_005919608.1| 284 ACIDPSACIGCGLCAEACP 302
                                       579**************** PP

  == domain 4  score: 19.9 bits;  conditional E-value: 8.5e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +vvd ++CigC+ Cv+ CP
  gi|386001309|ref|YP_005919608.1| 572 AVVDQEKCIGCKLCVDTCP 590
                                       789***************9 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 3.8e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                        vd+++C gCg+C  aCP
  gi|386001309|ref|YP_005919608.1| 601 LVDEAACKGCGTCAAACP 618
                                       589*************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   7.9   1.1e-07   7.2e-05       2      50 ..     243     305 ..     241     312 .. 0.91
   2 ?   -0.9   0.3       2.9   1.9e+03       7      24 ..     396     419 ..     383     427 .. 0.70
   3 !   30.1  10.4   6.2e-10     4e-07       1      51 []     578     622 ..     568     622 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                            Fer4_9   2 CtgCga.CveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkga 50 
                                       C gC + C  +Cp +v  + +++   r  ++               +aCigCg C+eaCp +a
  gi|386001309|ref|YP_005919608.1| 243 CKGCLNeCAGVCPVEVPDDYEFGLGKRKAIYMPipqavplvacidpSACIGCGLCAEACPVDA 305
                                       99**644*************9999999888777999************************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                            Fer4_9   7 aCveaC......pagvvvedaaer 24 
                                       +C ++C      +a++++e+  e+
  gi|386001309|ref|YP_005919608.1| 396 YCSRVCcmyalkNAQLIKEKYPET 419
                                       799999666666666666665555 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 6.2e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC+gC+ Cv+ Cp ++++    +  ++       aC gCg+C++aCp +ai
  gi|386001309|ref|YP_005919608.1| 578 KCIGCKLCVDTCPGKAISVNGTALVDEA------ACKGCGTCAAACPVDAI 622
                                       7****************99988888886......7*************987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   2.2       2.5   1.6e+03       4      16 ..     243     256 ..     240     261 .. 0.78
   2 !   14.1   2.1   7.9e-05      0.05       2      16 ..     289     303 ..     288     311 .. 0.89
   3 !   20.2   2.1   8.8e-07   0.00056       1      15 [.     576     590 ..     576     598 .. 0.93
   4 !   14.5   1.7   5.8e-05     0.037       3      16 ..     606     619 ..     604     626 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.5
                            Fer4_4   4 CigCg.sCvaaCPq 16 
                                       C gC   C  +CP+
  gi|386001309|ref|YP_005919608.1| 243 CKGCLnECAGVCPV 256
                                       77887569999996 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.9e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + CigCg C  aCP+
  gi|386001309|ref|YP_005919608.1| 289 SACIGCGLCAEACPV 303
                                       68************6 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 8.8e-07
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       qe+CigC+ Cv++CP
  gi|386001309|ref|YP_005919608.1| 576 QEKCIGCKLCVDTCP 590
                                       79************* PP

  == domain 4  score: 14.5 bits;  conditional E-value: 5.8e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C gCg C aaCP+
  gi|386001309|ref|YP_005919608.1| 606 ACKGCGTCAAACPV 619
                                       6************7 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2     2e-09   1.3e-06       1      38 [.     142     179 ..     142     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2e-09
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                       +v+V+GGg+aG+ A +  a  G +v Lve+r+ +GG +
  gi|386001309|ref|YP_005919608.1| 142 EVLVIGGGVAGIQASLDLADCGLSVHLVERRPTIGGYM 179
                                       59**********************************88 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.6      0.16     1e+02      50      65 .]     242     258 ..     226     258 .. 0.82
   2 !   17.3   0.0   7.5e-06    0.0048       3      18 ..     289     304 ..     287     355 .. 0.80
   3 ?   -0.9   0.0       3.6   2.3e+03       7      24 ..     393     410 ..     391     439 .. 0.75
   4 ?    5.7  13.6     0.032        21       2      64 ..     576     620 ..     575     621 .. 0.73
   5 !    8.3   4.3    0.0049       3.1       4      17 ..     606     619 ..     603     659 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.16
                            Fer4_8  50 sCttcga.CtevCpvgi 65 
                                        C +c + C+ vCpv++
  gi|386001309|ref|YP_005919608.1| 242 LCKGCLNeCAGVCPVEV 258
                                       68888655999999975 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 7.5e-06
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       ++Ci+Cg+C +aCpv 
  gi|386001309|ref|YP_005919608.1| 289 SACIGCGLCAEACPVD 304
                                       68***********963 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.6
                            Fer4_8   7 eCgaCqsaCpvlrrtkkh 24 
                                       ++ +C   C ++  ++  
  gi|386001309|ref|YP_005919608.1| 393 GNAYCSRVCCMYALKNAQ 410
                                       678999999988777643 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.032
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        ekCi+C +C ++Cp          + +g a     +e          +C +cg C+ +Cpv+
  gi|386001309|ref|YP_005919608.1| 576 QEKCIGCKLCVDTCP------GKAISVNGTALV---DE---------AACKGCGTCAAACPVD 620
                                       689***********9......333444555333...22.........4799*********986 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0049
                            Fer4_8   4 kCieCgaCqsaCpv 17 
                                       +C +Cg C +aCpv
  gi|386001309|ref|YP_005919608.1| 606 ACKGCGTCAAACPV 619
                                       68888888888873 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.0   1.3e-05    0.0083       2      33 ..     143     176 ..     142     179 .. 0.93
   2 !    8.2   0.0    0.0026       1.6     151     205 ..     414     493 ..     306     527 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       v++iGGG++G+ + ++La  g  V l+e+++ +g
  gi|386001309|ref|YP_005919608.1| 143 VLVIGGGVAGIQASLDLADCGlsVHLVERRPTIG 176
                                       99***************9889*********9988 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                                       H.......................HHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT..EEE.EEEEEEEE-- CS
                               DAO 151 a.......................laraaealGveilegtevtgleeedgkvwgve.rttp..gen.daadavVnaa 200
                                                               ++ +a++lG+++++g +v ++ee dg + +v  ++t   g + + +d vV++a
  gi|386001309|ref|YP_005919608.1| 414 EkypetevsihyidlraggegyeeFYMRAQRLGINFIRG-RVSEVEEVDGSL-RVNyEDTLlgGFRsKPYDLVVLSA 488
                                       0555555555555555555555557889***********.*****9987663.3435444443444448899***** PP

                                       GGGHH CS
                               DAO 201 Gawsd 205
                                       G+  +
  gi|386001309|ref|YP_005919608.1| 489 GLEPN 493
                                       *9755 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.5   3.2e-08   2.1e-05       2      36 ..     143     177 ..     142     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.2e-08
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       v+ViG+G+AG  A+l +a++Gl+v +ve  +  gg
  gi|386001309|ref|YP_005919608.1| 143 VLVIGGGVAGIQASLDLADCGLSVHLVERRPTIGG 177
                                       9***************************9998887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06   0.00069       1      36 [.     145     180 ..     145     214 .. 0.87
   2 ?   -0.4   0.0       2.2   1.4e+03      39      55 ..     311     327 ..     283     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                       ++G+G++G  a   La+ g++v+l+e+r+ +GG +a
  gi|386001309|ref|YP_005919608.1| 145 VIGGGVAGIQASLDLADCGLSVHLVERRPTIGGYMA 180
                                       8********************************997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.2
                                       CETTCEECTS---EEET CS
                     NAD_binding_8  39 evpgvrvdygahifhgs 55 
                                       + +++r+d+ga i++++
  gi|386001309|ref|YP_005919608.1| 311 RQEEFRFDVGAIIVATG 327
                                       335599****9999764 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   4.5e-07   0.00029       2      35 ..     143     176 ..     142     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.5e-07
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       v+v+GgG+ g+ +   la+ g +V++ver++++ 
  gi|386001309|ref|YP_005919608.1| 143 VLVIGGGVAGIQASLDLADCGLSVHLVERRPTIG 176
                                       89*****************************997 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.6      0.56   3.6e+02       3      21 ..     238     256 ..     237     268 .. 0.76
   2 !   12.9   2.2   0.00023      0.14       3      19 ..     286     302 ..     285     320 .. 0.89
   3 !   14.7   1.6   6.1e-05     0.039       2      19 ..     573     590 ..     572     596 .. 0.93
   4 ?    7.3   4.9     0.012       7.9       3      19 ..     602     618 ..     601     625 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.56
                           Fer4_15   3 vDrdaCigc.glCvaeapev 21 
                                       vD+++C gc + C+ ++p v
  gi|386001309|ref|YP_005919608.1| 238 VDEKLCKGClNECAGVCP-V 256
                                       89******9556988887.3 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00023
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       +D +aCigcglC++++p
  gi|386001309|ref|YP_005919608.1| 286 IDPSACIGCGLCAEACP 302
                                       89**************7 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 6.1e-05
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       vvD+++Cigc lCv+ +p
  gi|386001309|ref|YP_005919608.1| 573 VVDQEKCIGCKLCVDTCP 590
                                       69***************8 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.012
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       vD+ aC gcg C+a++p
  gi|386001309|ref|YP_005919608.1| 602 VDEAACKGCGTCAAACP 618
                                       89*************98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.3       1.2   7.8e+02      45      60 ..     242     258 ..     230     259 .. 0.73
   2 ?    5.2  12.1     0.047        30       2      58 ..     243     303 ..     242     306 .. 0.62
   3 !   11.6   2.2    0.0005      0.32       2      16 ..     291     305 ..     290     321 .. 0.66
   4 ?    0.1   0.1       1.9   1.2e+03       6      19 ..     395     408 ..     392     432 .. 0.76
   5 !   11.8   0.3   0.00043      0.28      44      58 ..     577     591 ..     556     594 .. 0.85
   6 !   12.4   1.6   0.00027      0.17       1      36 [.     606     644 ..     606     659 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                           Fer4_17  45 lCieC.geCerkCPqgl 60 
                                       lC +C +eC+ +CP ++
  gi|386001309|ref|YP_005919608.1| 242 LCKGClNECAGVCPVEV 258
                                       56666567777777665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.047
                           Fer4_17   2 CiqCgy.ClpeCpsyeaydnepk.kllraaklglleeaeke..ekaslCieCgeCerkCPq 58 
                                       C +C   C+ +Cp     d e     ++a+++ + +++        s Ci+Cg+C+++CP 
  gi|386001309|ref|YP_005919608.1| 243 CKGCLNeCAGVCPVEVPDDYEFGlGKRKAIYMPIPQAVPLVacIDPSACIGCGLCAEACPV 303
                                       88898559999998666444322123333444444443222224789*************6 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0005
                           Fer4_17   2 CiqCgyClpeCpsye 16 
                                       Ci+Cg C+++Cp  +
  gi|386001309|ref|YP_005919608.1| 291 CIGCGLCAEACPVDA 305
                                       777777777777644 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.9
                           Fer4_17   6 gyClpeCpsyeayd 19 
                                       +yC ++C +y+  +
  gi|386001309|ref|YP_005919608.1| 395 AYCSRVCCMYALKN 408
                                       69***999998754 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00043
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       ++Ci+C++C+  CP 
  gi|386001309|ref|YP_005919608.1| 577 EKCIGCKLCVDTCPG 591
                                       578888888888885 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00027
                           Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraakl.gllee 36 
                                       +C +Cg C+++Cp  ++  + +  +++++++++ + +++
  gi|386001309|ref|YP_005919608.1| 606 ACKGCGTCAAACPVDAIdmTLFSDEQIMAQVRAaTAVKG 644
                                       5************97775566778888888877334444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     1e-06   0.00067       2      29 ..     143     170 ..     142     195 .. 0.84
   2 ?   -2.9   0.2       4.3   2.7e+03     355     386 ..     527     558 ..     524     561 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                       v ViGgG AG+ A+l +a  G++v L+ 
  gi|386001309|ref|YP_005919608.1| 143 VLVIGGGVAGIQASLDLADCGLSVHLVE 170
                                       89************************93 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                                       SBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHH CS
                              GIDA 355 vkgLflAGqinGteGYeEaaaqGllAGinaar 386
                                       ++g+f+AG  +G +    ++aqG  A+  a r
  gi|386001309|ref|YP_005919608.1| 527 IEGVFIAGCASGPKEIQVSIAQGEAAAAKAMR 558
                                       7999********99899999***999999876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.0      0.97   6.2e+02      77      95 ..     238     257 ..     226     258 .. 0.79
   2 !   10.9   1.3   0.00097      0.62      78      95 ..     287     304 ..     276     305 .. 0.86
   3 !   10.1   0.1    0.0018       1.1      72      94 ..     569     591 ..     540     593 .. 0.76
   4 !    9.6   1.5    0.0025       1.6      77      95 ..     602     620 ..     595     621 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.97
                           Fer4_22  77 fgesgCvGC.gRCieacpvk 95 
                                       ++e+ C GC + C  +cpv+
  gi|386001309|ref|YP_005919608.1| 238 VDEKLCKGClNECAGVCPVE 257
                                       48899****778**999987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00097
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       + s+C+GCg C eacpv+
  gi|386001309|ref|YP_005919608.1| 287 DPSACIGCGLCAEACPVD 304
                                       6789***********985 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0018
                           Fer4_22  72 efkekfgesgCvGCgRCieacpv 94 
                                        +++ +++++C+GC  C+++cp 
  gi|386001309|ref|YP_005919608.1| 569 PVVAVVDQEKCIGCKLCVDTCPG 591
                                       556677999************97 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0025
                           Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                       ++e +C GCg C +acpv+
  gi|386001309|ref|YP_005919608.1| 602 VDEAACKGCGTCAAACPVD 620
                                       57899***********985 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.4   7.4e-05     0.047       1      17 [.     286     302 ..     286     319 .. 0.86
   2 !   15.9   2.9   2.3e-05     0.015       1      17 [.     574     590 ..     574     591 .. 0.97
   3 ?    6.9   5.1     0.014       8.9       1      17 [.     602     618 ..     602     622 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D + Ci+cg+C+e++P
  gi|386001309|ref|YP_005919608.1| 286 IDPSACIGCGLCAEACP 302
                                       7999************* PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.3e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD+++Ci+c++Cv+++P
  gi|386001309|ref|YP_005919608.1| 574 VDQEKCIGCKLCVDTCP 590
                                       9***************9 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.014
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD+  C +cg+C++++P
  gi|386001309|ref|YP_005919608.1| 602 VDEAACKGCGTCAAACP 618
                                       899*************9 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   9.7e-06    0.0062       3      34 ..     142     173 ..     140     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.7e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                       +Vl++G+G aG+ ++l L+  G +v+lve+r 
  gi|386001309|ref|YP_005919608.1| 142 EVLVIGGGVAGIQASLDLADCGLSVHLVERRP 173
                                       7*****************************96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.7e-05     0.011       2      36 ..     142     176 ..     141     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +v+viGgG AG+ a++ +a+ g +V l+e+ +++g
  gi|386001309|ref|YP_005919608.1| 142 EVLVIGGGVAGIQASLDLADCGLSVHLVERRPTIG 176
                                       799***************************99988 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   5.4      0.79     5e+02       1      13 [.     243     256 ..     243     258 .. 0.91
   2 ?   16.7   5.5   1.6e-05      0.01       1      15 []     291     305 ..     291     305 .. 0.98
   3 ?   -1.0   1.8       7.4   4.8e+03       7      12 ..     397     402 ..     383     405 .. 0.76
   4 ?   13.1   4.3   0.00024      0.15       1      15 []     579     593 ..     579     593 .. 0.97
   5 ?   10.2   7.4    0.0019       1.2       1      15 []     607     621 ..     607     621 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.79
                            Fer4_3   1 CtgC.gaCvevCPv 13 
                                       C gC + C  vCPv
  gi|386001309|ref|YP_005919608.1| 243 CKGClNECAGVCPV 256
                                       99**889******7 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.6e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg+C e+CPv+A
  gi|386001309|ref|YP_005919608.1| 291 CIGCGLCAEACPVDA 305
                                       *************98 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 7.4
                            Fer4_3   7 CvevCP 12 
                                       C +vC+
  gi|386001309|ref|YP_005919608.1| 397 CSRVCC 402
                                       999997 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00024
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gC +Cv+ CP +A
  gi|386001309|ref|YP_005919608.1| 579 CIGCKLCVDTCPGKA 593
                                       ************998 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0019
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg+C  +CPv+A
  gi|386001309|ref|YP_005919608.1| 607 CKGCGTCAAACPVDA 621
                                       9************98 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.5e-05     0.029      30      62 ..     142     174 ..     112     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                       +vlviGgGvaG+qA    +  g +V +++ rp+
  gi|386001309|ref|YP_005919608.1| 142 EVLVIGGGVAGIQASLDLADCGLSVHLVERRPT 174
                                       79*************999999999999999886 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014     0.089     166     198 ..     142     174 ..     134     193 .. 0.75
   2 ?   -2.2   0.0         3   1.9e+03     234     305 .]     453     534 ..     439     534 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                       +v+ViGg+  ++ a l+l++ g +V++v r+ +
  gi|386001309|ref|YP_005919608.1| 142 EVLVIGGGVAGIQASLDLADCGLSVHLVERRPT 174
                                       677777777777777777777777777777655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                       Pyr_redox_3 234 evkeikekeeeykvkted....gkkvevkddvvlatGykpd..lsflkk.slfeldedgrpvlteete...etnvpg 300
                                       +v e++e + + +v+ ed    g + + +d vvl  G +p+  ++++ +  +++++ dg+ ++   ++   e  ++g
  gi|386001309|ref|YP_005919608.1| 453 RVSEVEEVDGSLRVNYEDtllgGFRSKPYDLVVLSAGLEPNkdADVVGNlLGLAKRPDGFFEIAHPKMrpvEAHIEG 529
                                       67888888888888877722223344557777788999887335667777667777777666655444333788888 PP

                       Pyr_redox_3 301 lflaG 305
                                       +f+aG
  gi|386001309|ref|YP_005919608.1| 530 VFIAG 534
                                       88887 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00011     0.068      18      59 ..     141     181 ..     134     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                              Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59 
                                        +v+++G+G +G+ a+  la   +l v ++er+ ++GG + l
  gi|386001309|ref|YP_005919608.1| 141 REVLVIGGGVAGIQASLDLADC-GLSVHLVERRPTIGGYMAL 181
                                       689******************9.***************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (790 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 5091.10
//
Query:       gi|386001310|ref|YP_005919609.1|  [L=400]
Description: Phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-48  165.1   0.2      3e-47  160.9   0.0    2.1  2  DFP             DNA / pantothenate metabolism flavoprotein
    5.6e-36  123.7   0.4    9.5e-36  122.9   0.4    1.4  1  Flavoprotein    Flavoprotein
  ------ inclusion threshold ------
      0.013   16.0   0.8      0.097   13.2   0.0    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.098   12.6   1.4         19    5.2   0.1    3.2  2  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.033   1.5e+02      33      55 ..      32      54 ..      29      74 .. 0.76
   2 !  160.9   0.0   6.7e-51     3e-47       1     186 []     190     371 ..     190     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.033
                                      HHHHHHHHHTT-EEEEEE-S-SS CS
                               DFP 33 yalAeaaaarGaeVtlvsgpvsl 55
                                      + lA+ +++rGa V+ v +  ++
  gi|386001310|ref|YP_005919609.1| 32 VDLARDLIRRGAAVHSVMSGAAT 54
                                      579************99755333 PP

  == domain 2  score: 160.9 bits;  conditional E-value: 6.7e-51
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       l+g++vlvt+G+T E++Dp+R+++Nr+SGk+G+++A +a++rGaeVtlv+   +l  p  ++ v vesae+ml+av 
  gi|386001310|ref|YP_005919609.1| 190 LAGRRVLVTGGATAERVDPIRILTNRASGKTGAEIALEARRRGAEVTLVHRG-RLGLP--LKEVYVESAEDMLRAVL 263
                                       689**********************************************976.56667..889************** PP

                                       HHHTT-..SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-S.S...-H CS
                               DFP  78 ealkea..divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaet.e...el 148
                                       ++l+    d++++aAAv+Dy+ +  +++Kik    + el l+l+++ +i+a + ++++++  +vGF+aet     el
  gi|386001310|ref|YP_005919609.1| 264 AELEGGgyDAIVAAAAVSDYTRDP-SADKIKS---GGELVLRLRPTSKIIAAV-RASHPEIKMVGFKAETfLsdeEL 335
                                       **966556*************975.667**95...457***************.55567667*******852567** PP

                                       HHHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                               DFP 149 lenareklerkgldlivaNdvskeeagfgsdenevtll 186
                                       + +are +e+++ld++v Ndv++   g+g+++n+v++l
  gi|386001310|ref|YP_005919609.1| 336 IFRARESMEKNRLDIVVGNDVGRG--GMGTEDNRVLIL 371
                                       **********************98..********9985 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.4   2.1e-39   9.5e-36       3     156 ..      18     183 ..      16     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 2.1e-39
                                       EEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESEEE CS
                      Flavoprotein   3 illgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadllv 69 
                                       i+l++TGs+aa+ +++l + L+++g+ v+ v++ aA+++++++ l+ a+       ++++++h+e+     +adll+
  gi|386001310|ref|YP_005919609.1|  18 IVLAVTGSIAAVRTVDLARDLIRRGAAVHSVMSGAATEILHPHALEYASgnpvvtrITGRVEHVEFcgvGGRADLLL 94 
                                       99***************************************9988887799999999*********66656****** PP

                                       EEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................ CS
                      Flavoprotein  70 iaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgk 143
                                       iaPa+ant++kia Gi d+++t+ +    ++ +p++++Pam+ amy++p+++ nle l + gv+v++P   +++k+k
  gi|386001310|ref|YP_005919609.1|  95 IAPATANTIGKIAWGIDDTPVTTYATTalGSGVPVVVVPAMHEAMYRHPAVMSNLEALrSMGVVVLDPR-IEEEKAK 170
                                       *********************998844479****************************66*********.8899999 PP

                                       GHHHHHHHHHHCH CS
                      Flavoprotein 144 maeieeivgkild 156
                                       +ae  ++v ++ +
  gi|386001310|ref|YP_005919609.1| 171 IAESRTVVLEVER 183
                                       9999999988765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05     0.097       8      32 ..     218     242 ..     217     263 .. 0.89
   2 ?   -2.2   0.0       1.4   6.2e+03       6      21 ..     268     283 ..     268     287 .. 0.86
   3 ?   -1.2   0.0      0.72   3.2e+03      38      63 ..     331     356 ..     319     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                                       SHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox   8 GyiglElAgalaelgkkVtvversd 32 
                                       G +g E A ++++ g++Vt+v+r+ 
  gi|386001310|ref|YP_005919609.1| 218 GKTGAEIALEARRRGAEVTLVHRGR 242
                                       899*******************975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                       CSSHHHHHHHHHHHHT CS
                         Pyr_redox   6 GgGyiglElAgalael 21 
                                       GgGy ++ +A+a +++
  gi|386001310|ref|YP_005919609.1| 268 GGGYDAIVAAAAVSDY 283
                                       9******999998876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.72
                                       SSHHHHHHHHHHHHHTTEEEECSEEE CS
                         Pyr_redox  38 lDeeaskilqeklekngievllntkv 63 
                                        Dee+  + +e++ekn  +++ ++ v
  gi|386001310|ref|YP_005919609.1| 331 SDEELIFRARESMEKNRLDIVVGNDV 356
                                       56677777788888888888877666 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0042        19       5      33 ..      28      56 ..      27      97 .. 0.78
   2 ?    4.2   0.1    0.0087        39      10      38 ..     223     253 ..     220     363 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0042
                    Glyco_transf_4  5 erhvleLaraLarrGheVtvvtpgddgpl 33
                                      ++ +++Lar L rrG  V+ v +g   ++
  gi|386001310|ref|YP_005919609.1| 28 AVRTVDLARDLIRRGAAVHSVMSGAATEI 56
                                      68899**************9966555444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0087
                    Glyco_transf_4  10 eLaraLarrGheVtvvtpgddgpleeev..e 38 
                                       e+a + +rrG eVt+v +g+ g + +ev  e
  gi|386001310|ref|YP_005919609.1| 223 EIALEARRRGAEVTLVHRGRLGLPLKEVyvE 253
                                       5677788899999999998888888884330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2381.84
//
Query:       gi|386001311|ref|YP_005919610.1|  [L=276]
Description: GHMP kinase ATP-binding protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.5   6.8    0.00053   20.2   6.8    1.7  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   6.8     3e-08   0.00053       2      66 .]      75     139 ..      73     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-08
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       ++++  +P+g+G+G S+A a++ ++A++ ++gl l  +  +  a+ + +   ++ gDv a   Gg
  gi|386001311|ref|YP_005919610.1|  75 VETELSMPLGSGFGASGAGALSSAYAINGAFGLGLTANAVGEAAHVAEVASGTGLGDVLAQNTGG 139
                                       5566677*************************998544444444433333569999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1686.22
//
Query:       gi|386001312|ref|YP_005919611.1|  [L=259]
Description: pantothenate synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-76  254.9   0.1    3.7e-76  254.6   0.1    1.1  1  PPS_PS        Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.034   13.9   0.0    1.4  1  Amidohydro_2  Amidohydrolase
       0.13   12.0   0.5       0.37   10.5   0.1    1.9  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.6   0.1   6.2e-80   3.7e-76       1     175 [.      71     245 ..      71     246 .. 0.99

  Alignments for each domain:
  == domain 1  score: 254.6 bits;  conditional E-value: 6.2e-80
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       llla++pv+svNGN+aaLv++e+v+La+++ga+levN+fyrteeRv++ia++l++ gaeev g++ da++p+l+++R
  gi|386001312|ref|YP_005919611.1|  71 LLLAERPVLSVNGNAAALVPREMVDLARKIGAPLEVNIFYRTEERVRRIADHLRSFGAEEVFGETPDASVPGLDHAR 147
                                       79*************************************************************************** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       +k+s+ Gi++aDvv+vplEDGDR+eaLv+mgK+v+++DLNPlsRtart+t+tivdnvvRalpnl++ v e+  ++++
  gi|386001312|ref|YP_005919611.1| 148 GKASRGGIFDADVVFVPLEDGDRCEALVRMGKRVVTVDLNPLSRTARTSTVTIVDNVVRALPNLISLVGEMGGQREA 224
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealke 175
                                       el+eiv+++dn++vl++++++
  gi|386001312|ref|YP_005919611.1| 225 ELREIVASYDNRAVLRRSVEA 245
                                       ****************99986 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-06     0.034     125     210 ..     164     237 ..     138     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-06
                                       TTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHH CS
                      Amidohydro_2 125 llgdrldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraale 201
                                       +l+d+  ++ + +++++ ++vd+             + t+r++   ++++v+r +Pnl   + ++Gg   r ++++e
  gi|386001312|ref|YP_005919611.1| 164 PLEDGDRCEALVRMGKRVVTVDLN----------PLSRTARTSTVTIVDNVVRALPNLISLVGEMGGQ--REAELRE 228
                                       555666699999999999999999..........45889999**************************..9889888 PP

                                       HHHHHHHCC CS
                      Amidohydro_2 202 llarrpnvy 210
                                       ++a ++n  
  gi|386001312|ref|YP_005919611.1| 229 IVASYDNRA 237
                                       888888755 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   6.1e-05      0.37       3      42 ..      66     104 ..      65     111 .. 0.93
   2 ?   -1.3   0.0      0.29   1.7e+03     104     115 ..     179     190 ..     122     211 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE CS
                      TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPv 42 
                                       +aa+ll  a+rpv+ v g +a + + +e+++la+k+g+P 
  gi|386001312|ref|YP_005919611.1|  66 AAAALLLLAERPVLSVNGNAA-ALVPREMVDLARKIGAPL 104
                                       79***************9999.99**************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.29
                                       -EEEEEESSCCC CS
                      TPP_enzyme_M 104 akiihididpae 115
                                       ++++ +d +p +
  gi|386001312|ref|YP_005919611.1| 179 KRVVTVDLNPLS 190
                                       256666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1809.18
//
Query:       gi|386001313|ref|YP_005919612.1|  [L=195]
Description: hypothetical protein Mhar_0611 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1411.47
//
Query:       gi|386001314|ref|YP_005919613.1|  [L=977]
Description: Excinuclease ABC, subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete 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-32  110.4   0.0    2.9e-30  104.9   0.0    2.7  2  UvrA_DNA-bind    UvrA DNA-binding domain
    8.7e-27   93.4   0.1    4.8e-26   91.0   0.1    2.3  2  UvrA_inter       UvrA interaction domain
    1.5e-20   74.1   0.3    3.1e-08   34.2   0.1    4.7  3  ABC_tran         ABC transporter
    2.2e-10   40.3   0.0      0.055   12.9   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    8.6e-10   38.9   3.0      0.038   13.8   0.0    4.6  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      5e-09   36.8   0.4     0.0088   16.4   0.5    3.9  3  AAA_16           AAA ATPase domain
    1.1e-08   34.6   0.1     0.0059   16.3   0.1    2.5  2  AAA_29           P-loop containing region of AAA domain
    2.2e-06   28.3   0.1     0.0045   17.5   0.0    2.5  2  AAA_23           AAA domain
    2.2e-05   24.7   0.4       0.29   11.4   0.0    3.6  3  AAA_22           AAA domain
      3e-05   24.0   0.0       0.19   11.6   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    3.1e-05   23.7   0.0       0.45   10.1   0.0    3.1  2  AAA_25           AAA domain
    3.5e-05   23.8   0.0       0.49   10.4   0.0    3.2  3  AAA_14           AAA domain
    4.8e-05   23.2   6.6      0.019   14.9   0.8    2.7  2  BCA_ABC_TP_C     Branched-chain amino acid ATP-binding casset
    5.4e-05   23.1   0.3          7    6.3   0.0    4.1  4  AAA_15           AAA ATPase domain
    6.8e-05   22.7   0.0       0.12   12.1   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00016   21.1   0.0       0.16   11.3   0.0    2.6  2  ATPase           KaiC
    0.00017   22.1   0.1       0.35   11.4   0.1    3.1  2  AAA_18           AAA domain
    0.00035   19.9   0.1       0.28   10.4   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00051   20.0   0.1        1.1    9.1   0.0    2.8  3  APS_kinase       Adenylylsulphate kinase
    0.00061   20.1   4.9      0.023   15.1   0.2    3.5  3  DnaJ_CXXCXGXG    DnaJ central domain
    0.00086   18.4   0.1       0.74    8.8   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
    0.00095   18.8   0.4       0.52    9.9   0.1    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0016   18.4   0.1       0.99    9.3   0.0    2.5  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0017   18.1   0.5        3.9    7.1   0.0    3.1  3  AAA_24           AAA domain
     0.0034   17.3   0.0       0.93    9.4   0.0    2.5  2  NACHT            NACHT domain
     0.0049   17.0   5.5       0.85    9.8   0.5    3.5  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.015   14.3   0.1        7.2    5.5   0.0    2.9  3  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.016   15.6   0.0        3.3    8.1   0.0    2.5  2  RNA_helicase     RNA helicase
      0.021   14.6   0.1         10    5.8   0.0    2.7  2  AAA_30           AAA domain
      0.034   14.0   1.6        9.7    6.1   0.0    3.1  2  NTPase_1         NTPase
      0.099   12.8   8.4        1.5    9.0   0.3    3.5  3  Zn-ribbon_8      Zinc ribbon domain
       0.11   12.7   1.9          5    7.3   0.0    3.2  3  AAA_28           AAA domain
       0.12   11.5   0.1        5.8    6.0   0.1    2.3  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.17   12.0   0.1         25    5.0   0.0    3.1  3  MMR_HSR1         50S ribosome-binding GTPase
       0.21   10.7   0.0         13    4.9   0.0    2.4  2  NB-ARC           NB-ARC domain
       0.31   11.0   9.7        4.3    7.4   0.6    3.8  4  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        6.1    7.3   8.1        3.9    7.9   0.1    3.2  3  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.38   1.8e+02      78     108 ..      35      65 ..      15      67 .. 0.86
   2 !  104.9   0.0   5.9e-33   2.9e-30       1     110 []     312     422 ..     312     422 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.38
                                       .......---HHHHHHHHHH-------HHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreel 108
                                       + + +  f+ +  + +rry e+ S ++r+ l
  gi|386001314|ref|YP_005919613.1|  35 SGKSTLAFDTIYAEGQRRYVESLSAYARQFL 65 
                                       5677889999******************966 PP

  == domain 2  score: 104.9 bits;  conditional E-value: 5.9e-33
                                       -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............ CS
                     UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgee.kikveyksgg 76 
                                       Dp+l++pdp+ s+a+gA+a ++++ + ++ q l+ava+h+g+++ tp+k+L+eeq+  lLyGs e+ ++ ++ k+g 
  gi|386001314|ref|YP_005919613.1| 312 DPSLIIPDPEISIADGAVALYHNHVDGWRGQHLAAVAKHFGFSIFTPIKDLTEEQRSSLLYGSREKiRFDMSMKNGD 388
                                       9**************************************************************8752455666679* PP

                                       ........---HHHHHHHHHH-------HHHHHH CS
                     UvrA_DNA-bind  77 rkrsyektfeGvipnlerryreteSeavreelek 110
                                         +s+++++eG+ip+ er y++t+Se+ reele+
  gi|386001314|ref|YP_005919613.1| 389 AYWSHHGHWEGLIPQSERLYHQTSSEYRREELER 422
                                       ********************************96 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.1   9.9e-29   4.8e-26      16     106 ..     171     260 ..     131     263 .. 0.91
   2 ?   -2.0   0.0       7.6   3.7e+03      81     107 ..     543     569 ..     533     571 .. 0.82

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 9.9e-29
                        UvrA_inter  16 gtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydldedieldknkkhsievvvDrlvvkkeersrlaesv 92 
                                       g ++++laP++r++kg++ +ll++l  +Gf rvr+Dg i ++de+++ld+++kh+ievv+Drl  ++ ersrl e+v
  gi|386001314|ref|YP_005919613.1| 171 GGMVTVLAPIIRQKKGTYGQLLKDLDYEGFARVRVDGLIQRTDEEVDLDRYRKHDIEVVIDRLDPRE-ERSRLVEAV 246
                                       45799***********************************************************975.69******* PP

                        UvrA_inter  93 etAlklgeglvivs 106
                                       e Al+ g gl+iv 
  gi|386001314|ref|YP_005919613.1| 247 EAALERGGGLLIVV 260
                                       ***********996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.6
                        UvrA_inter  81 kkeersrlaesvetAlklgeglvivse 107
                                       ++++++rl e +++  +lg+ l++v++
  gi|386001314|ref|YP_005919613.1| 543 HQRDNARLIETLKKLRDLGNTLIVVEH 569
                                       566789**************9999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-05    0.0074       1      28 [.      14      41 ..      14     102 .. 0.93
   2 !   15.5   0.0   3.8e-05     0.018      68     136 ..     463     539 ..     370     540 .. 0.75
   3 !   34.2   0.1   6.5e-11   3.1e-08       1     136 [.     644     880 ..     644     881 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-05
                                      EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                      lk+++++l ++++++i+G +G+GKStL+
  gi|386001314|ref|YP_005919613.1| 14 LKDITIELPRDRLIVITGVSGSGKSTLA 41
                                      799***********************95 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.8e-05
                                       --S-TTSBHHHH...HHHTC.HHHHHHHSTTGG...TTCBGESTTSGGS-HHHHHHHHHHHHHHHTS..SEEEEEST CS
                                       xxxxxxxxxxxx...xxxxx.xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...esdee.iekalsklglke...lkdtvvksspssLSgGqkqrvalarallkkp..kllllDEp 135
                                         lf++l + e+    ++ + +++++s+lg  e   l   ++++s+ +LSgG+ qr+ la  + ++    l++lDEp
  gi|386001314|ref|YP_005919613.1| 463 LALFDGLALSEReeeIAR-QvLKEIRSRLGFLEhvgLSYLTLSRSAGTLSGGEAQRIRLATQIGSNLmgVLYVLDEP 538
                                       444555544444554222.235555555554444446667777788***************9998852269999999 PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       +
  gi|386001314|ref|YP_005919613.1| 539 S 539
                                       5 PP

  == domain 3  score: 34.2 bits;  conditional E-value: 6.5e-11
                                       EEEEEEEEETTSEEEEEESTTSSHHHHH.HHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLl.kllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpelt 75 
                                       lkn+s  +  g  ++++G +G+GKStL+  +l++ l     +i    +++   +++ s+++ei  +   +q   + t
  gi|386001314|ref|YP_005919613.1| 644 LKNLSARIPIGVFTVVTGVSGSGKSTLIyDTLYRALM---KKIYRS-TETPGlHDRLSFDSEIDKVIVIDQSPIGRT 716
                                       799***********************98345666554...577333.333223566666666666666666666666 PP

                                       HHHH......................................................................... CS
                                       xxxx......................................................................... RF
                          ABC_tran  76 vren......................................................................... 79 
                                        r+n                                                                         
  gi|386001314|ref|YP_005919613.1| 717 PRSNpatytkvfdpirqafsgtkearvrgykpgrfsfnlkggrceacqgdglikiemnflpdvyveceeckgtryna 793
                                       677777777777778888888888888999*******************************************9999 PP

                                       ..................HHHTCHHHHHHHSTTGG.............TTCBGESTTSGGS-HHHHHHHHHHHHHHH CS
                                       ..................xxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ..................esdeeiekalsklglke.............lkdtvvksspssLSgGqkqrvalarallk 125
                                                         +    +e+a+++++++              l   ++++s ++LSgG+ qr++l r l k
  gi|386001314|ref|YP_005919613.1| 794 etlevkyrdrsiaevlemT----VEEAREHFKNVPairskldtlmgvgLGYIKLGQSSTTLSGGEAQRIKLTRELSK 866
                                       9999986666666544330....55555555555555565555556668889999999*****************98 PP

                                       TS...SEEEEESTT CS
                                       xx...xxxxxxxxx RF
                          ABC_tran 126 kp...kllllDEpt 136
                                       k+   +++llDEpt
  gi|386001314|ref|YP_005919613.1| 867 KAtgrTIYLLDEPT 880
                                       853337*******9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0032       1.6       3      47 ..       2      47 ..       1      77 [. 0.78
   2 !   12.9   0.0   0.00011     0.055     135     211 ..     334     583 ..      79     588 .. 0.71
   3 !    6.8   0.0     0.008       3.9      22      42 ..     653     672 ..     636     694 .. 0.79
   4 !    7.7   0.0    0.0045       2.2     135     210 ..     848     923 ..     699     930 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0032
                                      EEEEEESETTEECEEEEEET.TSSEEEEEESTTSSHHHH.HHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N  3 krleienFksyagktvilpf.sksftaivGpNGSGKsnl.ldAilFv 47
                                      k+++i++ +  + k +++++  +++ +i+G  GSGKs l +d i + 
  gi|386001314|ref|YP_005919613.1|  2 KSIVIKGAREHNLKDITIELpRDRLIVITGVSGSGKSTLaFDTI-YA 47
                                      678888888887777777762457999**********9834665.55 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                                       T............................................................................ CS
                                       x............................................................................ RF
                             SMC_N 135 e............................................................................ 135
                                       +                                                                            
  gi|386001314|ref|YP_005919613.1| 334 Nhvdgwrgqhlaavakhfgfsiftpikdlteeqrssllygsrekirfdmsmkngdaywshhghweglipqserlyhq 410
                                       05555555555555555555555555555555555555555555555566666666666666666666666666666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001314|ref|YP_005919613.1| 411 tsseyrreelerfmkvlpcprcggkrlkekvlavkvagmsiaevadlsiseslalfdglalsereeeiarqvlkeir 487
                                       66666666666666666666666666666666666666666666666666777777777777777777777777777 PP

                                       .....................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.S CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                             SMC_N 136 .....................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.a 190
                                                            +LSgGe + + la    i +     ly+lDe    L ++  +++ e lk+ ++   
  gi|386001314|ref|YP_005919613.1| 488 srlgflehvglsyltlsrsagTLSGGEAQRIRLATQ--IGSNLMGVLYVLDEPSIGLHQRDNARLIETLKKLRDLgN 562
                                       777777777777777777777999**9987777766..56666779*************************998768 PP

                                       EEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 191 Qfivislreemlekadklvgv 211
                                        +iv+ ++ee+++ ad++v +
  gi|386001314|ref|YP_005919613.1| 563 TLIVVEHDEETIRAADHVVDM 583
                                       89**************99865 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.008
                                       TTSSEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  22 fsksftaivGpNGSGKsnlld 42 
                                       +   ft+++G  GSGKs l+ 
  gi|386001314|ref|YP_005919613.1| 653 IGV-FTVVTGVSGSGKSTLIY 672
                                       444.9************9875 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0045
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvg 210
                                       ++LSgGe + + l   ++ +k+  + +yllDe    L ++ v+k+  +l+   ++   ++vi ++ ++++ ad ++ 
  gi|386001314|ref|YP_005919613.1| 848 TTLSGGEAQRIKLTRELS-KKATGRTIYLLDEPTTGLHFEDVSKLIGVLNDLVDRgNTVVVIEHNLDVIKAADYVID 923
                                       3899**999999988876.6677889************************998875789999999999999998775 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.095        46       1      15 [.      26      40 ..      26      96 .. 0.91
   2 !   11.1   0.1   0.00053      0.26     121     295 ..     401     567 ..     361     575 .. 0.71
   3 !    7.3   0.0    0.0076       3.7       1      17 [.     656     672 ..     656     693 .. 0.95
   4 !   13.8   0.0   7.8e-05     0.038     255     298 ..     868     911 ..     847     916 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.095
                            AAA_21  1 lnvliGpNgsGKSnL 15
                                      l v++G  gsGKS+L
  gi|386001314|ref|YP_005919613.1| 26 LIVITGVSGSGKSTL 40
                                      579***********8 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00053
                            AAA_21 121 gvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklvei 197
                                       + ++++l++ + se+ +++ +++   ++++ +  + l+++ +  +  ++ ++++++   ++ + l  + +  +  + 
  gi|386001314|ref|YP_005919613.1| 401 IPQSERLYHQTSSEYRREELERFMKVLPCPRCGGKRLKEKVL--AVKVAGMSIAEVADLSISESLALFDGLALSER- 474
                                       567777777777777777777777777777777777777777..55555555555555555554444444444443. PP

                            AAA_21 198 elsdlgegeeliasvderlrer.gvvflengdgqelparel...SdGtkrllalltallralkkgsllliDEpEngL 270
                                               ee+ia+  + ++++   ++++ g  + + +r++   S G  + ++l+t + + l    l+++DEp  gL
  gi|386001314|ref|YP_005919613.1| 475 --------EEEIARQVLKEIRSrLGFLEHVGLSYLTLSRSAgtlSGGEAQRIRLATQIGSNLMG-VLYVLDEPSIGL 542
                                       ........333333333333333556666666666666666666***99999***********9.9*********** PP

                            AAA_21 271 HPkllrrllellkelsrngaQvilt 295
                                       H +  +rl+e lk+l++ g  +i++
  gi|386001314|ref|YP_005919613.1| 543 HQRDNARLIETLKKLRDLGNTLIVV 567
                                       **999*********99999999886 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0076
                            AAA_21   1 lnvliGpNgsGKSnLLd 17 
                                       ++v++G  gsGKS+L++
  gi|386001314|ref|YP_005919613.1| 656 FTVVTGVSGSGKSTLIY 672
                                       89*************85 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 7.8e-05
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +  ++++l+DEp +gLH + +++l+++l++l ++g  v++  H+
  gi|386001314|ref|YP_005919613.1| 868 ATGRTIYLLDEPTTGLHFEDVSKLIGVLNDLVDRGNTVVVIEHN 911
                                       33449************************999999999887666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   1.8e-05    0.0088      23      76 ..      23      79 ..      10     260 .. 0.73
   2 !   14.4   0.0   7.9e-05     0.038      21      51 ..     653     682 ..     639     713 .. 0.76
   3 ?   -2.0   0.0       8.4   4.1e+03      60     143 ..     783     878 ..     775     908 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-05
                            AAA_16 23 rpelvllsGesGvGKsslv.rellralekdggif..lrgkcdql..esaipysalaqal 76
                                      r +l++++G sG+GKs+l+ ++++   e+++ ++  l++ ++q+  +++ p +  ++ l
  gi|386001314|ref|YP_005919613.1| 23 RDRLIVITGVSGSGKSTLAfDTIYA--EGQRRYVesLSAYARQFlgQMNKPDVDSIEGL 79
                                      3489***************766664..44455666699999999888886654455555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.9e-05
                            AAA_16  21 sgrpelvllsGesGvGKsslv.rellralekd 51 
                                        g    ++++G sG+GKs+l+ ++l+ral k+
  gi|386001314|ref|YP_005919613.1| 653 IG--VFTVVTGVSGSGKSTLIyDTLYRALMKK 682
                                       33..7899*************99999888777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.4
                            AAA_16  60 cdqlesaipysa.laqalareellrqllde......aesaeleawrekleeala..........avpelagaeasrl 119
                                       c+++ ++++y a  +++  r++ ++++l++      +  ++++a r kl++ ++          ++  l+g ea   
  gi|386001314|ref|YP_005919613.1| 783 CEEC-KGTRYNAeTLEVKYRDRSIAEVLEMtveearEHFKNVPAIRSKLDTLMGvglgyiklgqSSTTLSGGEA--Q 856
                                       5555.555553334444445455555554433222233345555555555555577777766554444444433..3 PP

                            AAA_16 120 lellkrllallsrderplvlvlDd 143
                                       + +l+r l++ ++ +r ++ +lD+
  gi|386001314|ref|YP_005919613.1| 857 RIKLTRELSKKAT-GR-TIYLLDE 878
                                       3344455533333.44.5555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-05      0.01      14      38 ..      16      40 ..       9      47 .. 0.78
   2 !   16.3   0.1   1.2e-05    0.0059      23      39 ..     654     671 ..     643     682 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTl 38
                                      + tie+ ++  +++tG sGsGKSTl
  gi|386001314|ref|YP_005919613.1| 16 DITIELPRDRLIVITGVSGSGKSTL 40
                                      456777766699************9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.2e-05
                            AAA_29  23 g.atlltGpsGsGKSTll 39 
                                       g +t++tG sGsGKSTl+
  gi|386001314|ref|YP_005919613.1| 654 GvFTVVTGVSGSGKSTLI 671
                                       5589*************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.3e-06    0.0045       1      35 [.       3      40 ..       3      43 .. 0.94
   2 !    8.3   0.0    0.0063         3      21      48 ..     656     684 ..     654     826 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.3e-06
                            AAA_23  1 kLkienfrsf..rdqeidF.skgltlItGpNGaGKTTi 35
                                      ++ i++ r +  +d +i++  + l +ItG  G+GK+T+
  gi|386001314|ref|YP_005919613.1|  3 SIVIKGAREHnlKDITIELpRDRLIVITGVSGSGKSTL 40
                                      68999*****999******999***************8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0063
                            AAA_23  21 ltlItGpNGaGKTTil.dAiklaLygetp 48 
                                       +t++tG  G+GK+T++ d +  aL  +  
  gi|386001314|ref|YP_005919613.1| 656 FTVVTGVSGSGKSTLIyDTLYRALMKKIY 684
                                       599************96766666666654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00059      0.29       5      30 ..      24      49 ..      21     115 .. 0.76
   2 ?   -1.9   0.0       7.5   3.6e+03      70      96 ..     222     259 ..     188     261 .. 0.73
   3 !    9.0   0.0    0.0033       1.6       7      23 ..     656     672 ..     654     709 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00059
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                      ++++v+tG sG+GK+tl+    +   
  gi|386001314|ref|YP_005919613.1| 24 DRLIVITGVSGSGKSTLAFDTIYAEG 49
                                      679*************9866555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.5
                            AAA_22  70 a............erlsseellealeqalraravielli 96 
                                       +            +r ++++l+ea+e al++ +   l++
  gi|386001314|ref|YP_005919613.1| 222 RkhdievvidrldPREERSRLVEAVEAALERGGG-LLIV 259
                                       2444445555555678899999999999999998.6665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0033
                            AAA_22   7 ilvvtGesGtGKTtllr 23 
                                       ++vvtG sG+GK+tl+ 
  gi|386001314|ref|YP_005919613.1| 656 FTVVTGVSGSGKSTLIY 672
                                       789***********985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00039      0.19      81     116 ..       5      41 ..       1      60 [. 0.81
   2 !    9.7   0.0    0.0015      0.74      87     117 ..     641     672 ..     627     689 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                       +++  ++++l++++ +l   +++v+ G SG GKStL 
  gi|386001314|ref|YP_005919613.1|   5 VIKGAREHNLKDITIELPRdRLIVITGVSGSGKSTLA 41 
                                       55566678999999888766***************95 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLin 117
                                       +++l++l++++    ++v+ G SG GKStLi 
  gi|386001314|ref|YP_005919613.1| 641 ENNLKNLSARIPIgVFTVVTGVSGSGKSTLIY 672
                                       56777777777765789*************94 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     0.001       0.5      30      53 ..      21      44 ..       8      50 .. 0.86
   2 !   10.1   0.0   0.00093      0.45      24      55 ..     645     676 ..     622     691 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      lp++ l++++G +g+GK+tla d 
  gi|386001314|ref|YP_005919613.1| 21 LPRDRLIVITGVSGSGKSTLAFDT 44
                                      599******************986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00093
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlal 55 
                                       + +   +p g +++++G +g+GK+tl +d  +
  gi|386001314|ref|YP_005919613.1| 645 KNLSARIPIGVFTVVTGVSGSGKSTLIYDTLY 676
                                       455567899*****************999765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     0.001      0.49       3      27 ..      25      49 ..      23      76 .. 0.84
   2 !    9.3   0.0    0.0023       1.1       5      48 ..     657     697 ..     654     732 .. 0.79
   3 ?   -0.9   0.0       3.3   1.6e+03      52      92 ..     860     903 ..     840     910 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                      +++vitG+  +GK+tl+++ i+ + 
  gi|386001314|ref|YP_005919613.1| 25 RLIVITGVSGSGKSTLAFDTIYAEG 49
                                      789****************998766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0023
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkklad 48 
                                        v+tG+  +GK+tl+++ +++ l    + +y + +++ + ++  
  gi|386001314|ref|YP_005919613.1| 657 TVVTGVSGSGKSTLIYDTLYRAL---MKKIYRSTETPGLHDRLS 697
                                       69***************999999...677777777776655444 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.3
                            AAA_14  52 llelileklkeekktylflDEiqev......pewekalkslvdegkn 92 
                                       l +++ +k+   ++t+ +lDE          +++  +l++lvd+g n
  gi|386001314|ref|YP_005919613.1| 860 LTRELSKKA--TGRTIYLLDEPTTGlhfedvSKLIGVLNDLVDRG-N 903
                                       344444442..4788899999665433333366666777777777.4 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.8     4e-05     0.019       2      16 ..     594     608 ..     594     608 .. 0.94
   2 !   10.8   0.6   0.00074      0.36       1      12 [.     934     945 ..     934     946 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-05
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndPr 16 
                                       v AeGtP+Ev +dP+
  gi|386001314|ref|YP_005919613.1| 594 VVAEGTPEEVEADPE 608
                                       78************6 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00074
                      BCA_ABC_TP_C   1 rvIAeGtPaEvr 12 
                                       r+ AeGtP+Ev 
  gi|386001314|ref|YP_005919613.1| 934 RIVAEGTPEEVA 945
                                       799*******96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.12        57      14      39 ..      14      40 ..       1      42 [. 0.86
   2 ?    4.9   0.0     0.038        18     324     357 ..     530     563 ..     513     573 .. 0.82
   3 ?    3.3   0.0      0.12        56      10      41 ..     643     672 ..     641     726 .. 0.76
   4 ?    6.3   0.0     0.014         7     318     361 ..     865     908 ..     854     915 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsi 39
                                      lkd++i+l  + l v+ G  +sGKS++
  gi|386001314|ref|YP_005919613.1| 14 LKDITIELPRDrLIVITGVSGSGKSTL 40
                                      7999****9999*************98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.038
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                        v+++++EP + LH      li++lk+l + ++t
  gi|386001314|ref|YP_005919613.1| 530 GVLYVLDEPSIGLHQRDNARLIETLKKLRDLGNT 563
                                       589************************9888773 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.12
                            AAA_15  10 NFRslkdveidlseeltvliGkNnsGKSsile 41 
                                       N + l+ + i++   +tv+ G  +sGKS++++
  gi|386001314|ref|YP_005919613.1| 643 NLKNLS-ARIPIGV-FTVVTGVSGSGKSTLIY 672
                                       777777.5999999.**************874 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.014
                            AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                       ++k +   i+l++EP + LH +  + li  l +l++ ++t v+i
  gi|386001314|ref|YP_005919613.1| 865 SKKATGRTIYLLDEPTTGLHFEDVSKLIGVLNDLVDRGNTVVVI 908
                                       56667789*****************************9954443 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0039       1.9       1      19 [.      27      45 ..      27      85 .. 0.70
   2 !   12.1   0.0   0.00025      0.12       1      21 [.     657     677 ..     657     695 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                   Viral_helicase1  1 ivvhGvpGcGKStlirkll 19
                                      iv+ Gv G+GKStl  + +
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLAFDTI 45
                                      79***********866555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllrt 21 
                                       +vv Gv G+GKStli + l  
  gi|386001314|ref|YP_005919613.1| 657 TVVTGVSGSGKSTLIYDTLYR 677
                                       69*************888755 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00033      0.16      16      41 ..      21      46 ..      13      78 .. 0.87
   2 !    6.9   0.0    0.0071       3.4      14      45 ..     649     680 ..     641     689 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                            ATPase 16 ipegrvvlitGepGtGKtifalqFli 41
                                      +p++r + itG++G+GK+++a   ++
  gi|386001314|ref|YP_005919613.1| 21 LPRDRLIVITGVSGSGKSTLAFDTIY 46
                                      89******************987666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0071
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFlikgae 45 
                                         ip g  + +tG++G+GK+++    l++ ++
  gi|386001314|ref|YP_005919613.1| 649 ARIPIGVFTVVTGVSGSGKSTLIYDTLYRALM 680
                                       57899999*************98887777665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00073      0.35       1      15 [.      27      41 ..      27      52 .. 0.95
   2 ?    7.1   0.0     0.015       7.4       2      15 ..     658     671 ..     658     703 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00073
                            AAA_18  1 IlltGtpGvGKttla 15
                                      I++tG++G+GK+tla
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLA 41
                                      99***********98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                            AAA_18   2 lltGtpGvGKttla 15 
                                       ++tG++G+GK+tl 
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLI 671
                                       59**********85 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00058      0.28       2      25 ..      25      48 ..      24      99 .. 0.79
   2 !    7.3   0.0     0.005       2.4       4      25 ..     657     678 ..     654     697 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                           DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                      +++++tGv+G+GK+ +++  +++ 
  gi|386001314|ref|YP_005919613.1| 25 RLIVITGVSGSGKSTLAFDTIYAE 48
                                      689***************999886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.005
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                        +VtGv+G+GK+ +    l+++
  gi|386001314|ref|YP_005919613.1| 657 TVVTGVSGSGKSTLIYDTLYRA 678
                                       69************99999987 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0023       1.1       4      21 ..      26      43 ..      23      56 .. 0.85
   2 !    7.6   0.0    0.0066       3.2       5      32 ..     657     685 ..     653     700 .. 0.78
   3 ?   -2.4   0.0       8.3     4e+03      31      57 ..     845     872 ..     841     876 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0023
                                      EEEEESSTTSSHHHHHHH CS
                        APS_kinase  4 vvwltGlsgsGKstiana 21
                                       + +tG+sgsGKst+a+ 
  gi|386001314|ref|YP_005919613.1| 26 LIVITGVSGSGKSTLAFD 43
                                      689************974 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0066
                                       EEEESSTTSSHHHHHH.HHHHHHHHTT-- CS
                        APS_kinase   5 vwltGlsgsGKstian.alekkLvekgis 32 
                                         +tG+sgsGKst+ + +l ++L++k ++
  gi|386001314|ref|YP_005919613.1| 657 TVVTGVSGSGKSTLIYdTLYRALMKKIYR 685
                                       568**********8652788888887655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.3
                                       --EEEEE.HHHHTTTTTTT--SSHHHHH CS
                        APS_kinase  31 isvylLd.GdnvRhgLnkdLgfseedRk 57 
                                       +s ++L  G+  R +L+++L+ ++  R+
  gi|386001314|ref|YP_005919613.1| 845 QSSTTLSgGEAQRIKLTRELSKKATGRT 872
                                       44555541678899******99988886 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.5      0.45   2.2e+02      16      25 ..     298     307 ..     275     316 .. 0.75
   2 ?    1.7   0.0       0.7   3.4e+02      16      24 ..     428     436 ..     412     452 .. 0.66
   3 !   15.1   0.2   4.7e-05     0.023      16      52 ..     759     791 ..     746     797 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.45
                     DnaJ_CXXCXGXG  16 tCktCkGsGv 25 
                                        C++C+G G 
  gi|386001314|ref|YP_005919613.1| 298 ACEACNGLGI 307
                                       4777777772 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.7
                     DnaJ_CXXCXGXG  16 tCktCkGsG 24 
                                        C++C+G+ 
  gi|386001314|ref|YP_005919613.1| 428 PCPRCGGKR 436
                                       344444443 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 4.7e-05
                     DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGk 52 
                                       +C++C+G G ++ e++    f   +  +C+eC+Gt  
  gi|386001314|ref|YP_005919613.1| 759 RCEACQGDGLIKIEMN----FLPDVYVECEECKGTRY 791
                                       6********7666653....44466789******975 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0015      0.74     110     147 ..       6      42 ..       1      52 [. 0.71
   2 !    7.2   0.0    0.0049       2.4     130     150 ..     655     675 ..     626     685 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                             T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKttlly 147
                                       +++a +++++++  +   +  li+++G  gsGK+tl+ 
  gi|386001314|ref|YP_005919613.1|   6 IKGAREHNLKDITIEL-PRDRLIVITGVSGSGKSTLAF 42 
                                       5555566666553333.48899*************974 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0049
                             T2SSE 130 glilvsGgTgsGKttllyall 150
                                          +v+G  gsGK+tl+y  l
  gi|386001314|ref|YP_005919613.1| 655 VFTVVTGVSGSGKSTLIYDTL 675
                                       5679*************9776 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.011       5.3       3      23 ..      27      47 ..      25      54 .. 0.78
   2 !    9.9   0.1    0.0011      0.52       2      23 ..     656     677 ..     655     684 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      +v+tG  GsGK+tL   ++  
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLAFDTIYA 47
                                      79************8777744 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                       EEEEEESTTCCHHHHHHHHHCT CS
                              cobW   2 vtvltGflGsGKTtLlnhllen 23 
                                        tv+tG  GsGK+tL+  +l +
  gi|386001314|ref|YP_005919613.1| 656 FTVVTGVSGSGKSTLIYDTLYR 677
                                       589*************999844 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.002      0.99       4      48 ..      10      52 ..       9     116 .. 0.62
   2 ?    6.5   0.0     0.015       7.1       5      50 ..     641     684 ..     640     702 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                          ATPase_2  4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkd 48
                                      Re  lk++   l r  ++ ++i+G  gsGK++L    i    +  
  gi|386001314|ref|YP_005919613.1| 10 REHNLKDITIELPR--DRLIVITGVSGSGKSTLAFDTIYAEGQRR 52
                                      88888888755555..99***************988887664433 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                          ATPase_2   5 ekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdky 50 
                                       e+ lk+l   +      + +++G  gsGK++L+   + + + k+ y
  gi|386001314|ref|YP_005919613.1| 641 ENNLKNLSARIPI--GVFTVVTGVSGSGKSTLIYDTLYRALMKKIY 684
                                       5555555555554..5789**************9888777666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0081       3.9       5      20 ..      27      42 ..      23      51 .. 0.88
   2 ?   -0.2   0.0       1.5   7.1e+02     110     133 ..     549     572 ..     541     579 .. 0.80
   3 !    7.0   0.0     0.009       4.4       6      28 ..     658     680 ..     654     739 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0081
                            AAA_24  5 iliyGpsgiGKTtlak 20
                                      i+i+G sg+GK+tla 
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLAF 42
                                      89************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.5
                            AAA_24 110 efrrllkklqelrknvifiahekt 133
                                       +++++lkkl++l+++ i++ h ++
  gi|386001314|ref|YP_005919613.1| 549 RLIETLKKLRDLGNTLIVVEHDEE 572
                                       567888899999999999999776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.009
                            AAA_24   6 liyGpsgiGKTtlakelgpkplf 28 
                                       +++G sg+GK+tl++   +++l+
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLIYDTLYRALM 680
                                       899***********998777776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0019      0.93       1      18 [.      25      42 ..      25      79 .. 0.88
   2 ?    5.1   0.0     0.039        19       4      17 ..     658     671 ..     656     687 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                                      SCEEEEC-TTTCHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlq 18
                                      rl++++G +GsGK+tL+ 
  gi|386001314|ref|YP_005919613.1| 25 RLIVITGVSGSGKSTLAF 42
                                      789*************85 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.039
                                       EEEC-TTTCHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLl 17 
                                       +++G +GsGK+tL+
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLI 671
                                       89**********97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.5    0.0018      0.85       1      20 [.      26      45 ..      26     159 .. 0.82
   2 !    8.2   0.0    0.0055       2.7       3      18 ..     658     673 ..     656     745 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      l+++ G++GsGKstla   +
  gi|386001314|ref|YP_005919613.1| 26 LIVITGVSGSGKSTLAFDTI 45
                                      78999**********96654 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0055
                            AAA_33   3 llvGlpGsGKstlaer 18 
                                       ++ G++GsGKstl+  
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLIYD 673
                                       678********98643 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.015       7.2      20      46 ..      15      41 ..       8      53 .. 0.80
   2 ?   -2.2   0.0       3.2   1.6e+03       6      34 ..     470     498 ..     467     501 .. 0.88
   3 ?    5.3   0.0     0.017       8.1      34      53 ..     659     679 ..     642     687 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                                      HHHGGG-S-SEEEEEEE-TTSSHHHHH CS
                              MeaB 20 erllakaGraqvvGltGvPGaGkstlv 46
                                      + ++ +  r + + +tGv G+Gkstl 
  gi|386001314|ref|YP_005919613.1| 15 KDITIELPRDRLIVITGVSGSGKSTLA 41
                                      55666667888999***********85 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                                       HHHH--SHHHHHHHHHHGGG-S-SEEEEE CS
                              MeaB   6 tlveserpeakellerllakaGraqvvGl 34 
                                        l e e+  a+++l++++++ G  + vGl
  gi|386001314|ref|YP_005919613.1| 470 ALSEREEEIARQVLKEIRSRLGFLEHVGL 498
                                       678889999*************9999998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.017
                                       EEE-TTSSHHHHH.HHHHHHH CS
                              MeaB  34 ltGvPGaGkstlv.ealglel 53 
                                       +tGv G+Gkstl+ + l   l
  gi|386001314|ref|YP_005919613.1| 659 VTGVSGSGKSTLIyDTLYRAL 679
                                       8**********9934555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.068        33       1      17 [.      27      43 ..      27      64 .. 0.85
   2 ?    8.1   0.0    0.0069       3.3       2      27 ..     658     684 ..     657     705 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.068
                      RNA_helicase  1 iwlyGpsgeGKStlake 17
                                      i+++G sg GKStla +
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLAFD 43
                                      789***********976 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0069
                      RNA_helicase   2 wlyGpsgeGKStlake.Lakallkklk 27 
                                       +++G sg GKStl+++ L +al+kk+ 
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLIYDtLYRALMKKIY 684
                                       689**********99889999999983 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.021        10      18      34 ..      24      40 ..      19      64 .. 0.86
   2 ?    5.5   0.1     0.025        12      20      36 ..     656     672 ..     653     689 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                            AAA_30 18 drvavltGpAGtGKtta 34
                                      dr+ v+tG+ G+GK+t+
  gi|386001314|ref|YP_005919613.1| 24 DRLIVITGVSGSGKSTL 40
                                      6899***********97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                            AAA_30  20 vavltGpAGtGKttalk 36 
                                       ++v+tG+ G+GK+t++ 
  gi|386001314|ref|YP_005919613.1| 656 FTVVTGVSGSGKSTLIY 672
                                       689***********985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0      0.02       9.7       2      17 ..      27      42 ..      26      52 .. 0.87
   2 ?    5.8   0.0     0.024        12       3      18 ..     658     673 ..     656     686 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                                      EEEE--TTSSHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvk 17
                                      ++iTG +G+GK+Tl  
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLAF 42
                                      79***********975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                                       EEE--TTSSHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkk 18 
                                       ++TG +G+GK+Tl+  
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLIYD 673
                                       79***********964 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0032       1.5       7      34 ..     274     304 ..     268     308 .. 0.80
   2 ?    5.8   0.1      0.03        15      20      37 ..     422     438 ..     412     441 .. 0.67
   3 ?    0.8   0.5       1.1   5.3e+02       7      34 ..     759     788 ..     759     792 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0032
                       Zn-ribbon_8   7 rCeeCghefevlqsis...dapltaCPeCgs 34 
                                        C  Cg +fe+lq+ +    +p  aC +C++
  gi|386001314|ref|YP_005919613.1| 274 ACPLCGIVFEELQPRTfsfNSPFGACEACNG 304
                                       5*********998754436778888999986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.03
                       Zn-ribbon_8  20 sisdaplta.CPeCgs.evr 37 
                                       +++   ++  CP+Cg+ +++
  gi|386001314|ref|YP_005919613.1| 422 RFM---KVLpCPRCGGkRLK 438
                                       444...3333******8876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                       Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgs 34 
                                       rCe+C+ +  +  +++  ++  + C eC++
  gi|386001314|ref|YP_005919613.1| 759 RCEACQGDGLIKIEMNfLPDVYVeCEECKG 788
                                       788888777766666655566667998876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0      0.01         5       2      16 ..      27      41 ..      26      89 .. 0.78
   2 ?   -1.9   0.1       7.3   3.6e+03     129     163 .]     234     267 ..     216     267 .. 0.66
   3 ?    3.2   0.1       0.2        95       3      16 ..     658     671 ..     656     687 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.01
                            AAA_28  2 ivitGgestGKTtll 16
                                      ivitG +++GK+tl+
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTLA 41
                                      9*************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.3
                            AAA_28 129 edleereaiderlrealrelgipviivpsgdveeR 163
                                       +  eer ++ e++++al++ g  +i+v  +d e+R
  gi|386001314|ref|YP_005919613.1| 234 DPREERSRLVEAVEAALERGGGLLIVV-GTDGEDR 267
                                       334667777777777777777777777.6666665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.2
                            AAA_28   3 vitGgestGKTtll 16 
                                       v+tG +++GK+tl+
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLI 671
                                       89**********98 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.1        51      26      39 ..      27      40 ..      14      48 .. 0.86
   2 ?    6.0   0.1     0.012       5.8      27      51 ..     658     682 ..     655     684 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                                      EEEE-SSSSSTTTT CS
                              DAP3 26 lvltGekgsGKSvl 39
                                      +v+tG  gsGKS+l
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTL 40
                                      689*********98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                                       EEE-SSSSSTTTTHHHHHHHGGGS- CS
                              DAP3  27 vltGekgsGKSvlLlqalayAlekg 51 
                                       v+tG  gsGKS+l+  +l  Al k+
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLIYDTLYRALMKK 682
                                       99**************999999886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.22     1e+02       2      15 ..      27      40 ..      26      55 .. 0.91
   2 ?   -1.5   0.0       5.3   2.6e+03      48      91 ..     532     575 ..     502     584 .. 0.65
   3 ?    5.0   0.0     0.052        25       3      21 ..     658     676 ..     656     712 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.22
                                      EEEEESTTSSHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStL 15
                                      ++i G + +GKStL
  gi|386001314|ref|YP_005919613.1| 27 IVITGVSGSGKSTL 40
                                      799**********9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.3
                                       EEEEECGGCSS.HHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSH CS
                          MMR_HSR1  48 ielvDtpGlie.gaseekglgkaflaleeadlillvvdaseeklk 91 
                                       ++++D p  i   ++++ +l +++++l++    l+vv+  ee+++
  gi|386001314|ref|YP_005919613.1| 532 LYVLDEPS-IGlHQRDNARLIETLKKLRDLGNTLIVVEHDEETIR 575
                                       56677776.542244444788888888887777777774444444 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.052
                                       EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                       ++ G + +GKStLi   + 
  gi|386001314|ref|YP_005919613.1| 658 VVTGVSGSGKSTLIYDTLY 676
                                       689**********965443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.026        13      22      38 ..      26      42 ..      14      53 .. 0.83
   2 ?    3.0   0.0     0.098        48      21      39 ..     655     673 ..     641     686 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                                      EEEEEESTTSSHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlak 38
                                      ++ + G  G+GK+tla 
  gi|386001314|ref|YP_005919613.1| 26 LIVITGVSGSGKSTLAF 42
                                      6889***********85 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.098
                                       EEEEEEESTTSSHHHHHHH CS
                            NB-ARC  21 lvvalvGmgGvGKttlakq 39 
                                       ++  + G  G+GK+tl+ +
  gi|386001314|ref|YP_005919613.1| 655 VFTVVTGVSGSGKSTLIYD 673
                                       566789*********9865 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       9.2   4.5e+03      29      37 ..     271     279 ..     264     280 .. 0.81
   2 ?    0.5   0.0       1.3   6.1e+02      12      23 ..     298     309 ..     297     323 .. 0.72
   3 ?    6.5   0.1     0.017       8.3      30      41 ..     426     437 ..     417     440 .. 0.85
   4 ?    7.4   0.6    0.0088       4.3      12      40 ..     759     790 ..     757     795 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.2
                                       ...E-TTTT CS
                         Anti-TRAP  29 asleCPkCs 37 
                                       + + CP C+
  gi|386001314|ref|YP_005919613.1| 271 SKMACPLCG 279
                                       5699**996 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.3
                                       E-TTTTTTSEET CS
                         Anti-TRAP  12 kCdaCngsGkie 23 
                                       +C+aCng G   
  gi|386001314|ref|YP_005919613.1| 298 ACEACNGLGIKM 309
                                       69****999654 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.017
                                       ..E-TTTTTSSE CS
                         Anti-TRAP  30 sleCPkCsGkgl 41 
                                        l+CP+C+Gk l
  gi|386001314|ref|YP_005919613.1| 426 VLPCPRCGGKRL 437
                                       69*******986 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0088
                                       E-TTTTTTSEETTE.........E-TTTTTSS CS
                         Anti-TRAP  12 kCdaCngsGkiepe...eprasleCPkCsGkg 40 
                                        C+aC+g G i+ e    p   +eC +C+G  
  gi|386001314|ref|YP_005919613.1| 759 RCEACQGDGLIKIEmnfLPDVYVECEECKGTR 790
                                       6********9998877778999*******975 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.6       5.5   2.7e+03       6      35 ..     275     303 ..     273     313 .. 0.61
   2 ?    7.9   0.1    0.0081       3.9       2      17 ..     425     440 ..     424     448 .. 0.83
   3 ?    2.6   0.2      0.36   1.8e+02       6      37 ..     760     794 ..     755     808 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.5
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCg 35 
                                       CP Cg     e ++r+ +  +++ +C+ C+
  gi|386001314|ref|YP_005919613.1| 275 CPLCG-IVFEELQPRTFSFNSPFGACEACN 303
                                       99997.344444555555555555666665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0081
                   Lar_restr_allev   2 eLkpCPfCggravler 17 
                                       +++pCP Cgg+  +e+
  gi|386001314|ref|YP_005919613.1| 425 KVLPCPRCGGKRLKEK 440
                                       679*******987776 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.36
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCga.....s 37 
                                       C  C g++ ++ + +   +   +v+C++C+       
  gi|386001314|ref|YP_005919613.1| 760 CEACQGDGLIKIEMNFLPD--VYVECEECKGtrynaE 794
                                       7777777766555443332..2*******98443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (977 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.86u 0.33s 00:00:01.19 Elapsed: 00:00:00.52
# Mc/sec: 5620.55
//
Query:       gi|386001315|ref|YP_005919614.1|  [L=93]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for 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-14   51.6   0.0    9.6e-14   51.5   0.0    1.0  1  NTP_transf_2   Nucleotidyltransferase domain
    2.8e-09   37.0   0.0      3e-09   36.8   0.0    1.1  1  Polbeta        Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.069   12.6   0.1      0.084   12.3   0.1    1.1  1  tRNA-synt_2d   tRNA synthetases class II core domain (F)
      0.098   12.3   0.0       0.12   12.0   0.0    1.1  1  Amidoligase_2  Putative amidoligase enzyme


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   2.1e-17   9.6e-14       3      94 ..       9      91 ..       7      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.1e-17
                                      HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                      NTP_transf_2  3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled 81
                                      +  +e+k++++v k+ +fGS a G+ +++SDiD+lv ++e++         ++ +   +fleel+g+evdlvt   l  
  gi|386001315|ref|YP_005919614.1|  9 ENEREIKSRFSVRKIGIFGSNAGGEGRETSDIDVLVEFEEPTF--------RNFMGLVFFLEELFGREVDLVTTRGLS- 78
                                      5568999**********************************76........79*******************999999. PP

                                      CTEEEEEECEEEH CS
                      NTP_transf_2 82 pllvksileerpl 94
                                      p+++  +++e ++
  gi|386001315|ref|YP_005919614.1| 79 PYIRPAVEKEVVW 91
                                      8888888888776 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   6.7e-13     3e-09       9      82 ..      16      87 ..       6      93 .] 0.87

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.7e-13
                                      HHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHH CS
                           Polbeta  9 kekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilk 82
                                      ++ +++ + +FGS a g+ re SDiD+ v ++e  ++ + + l   le++  g++vDlv+ +  +p+++  + k
  gi|386001315|ref|YP_005919614.1| 16 SRFSVRKIGIFGSNAGGEGRETSDIDVLVEFEEP-TFRNFMGLVFFLEEL-FGREVDLVTTRGLSPYIRPAVEK 87
                                      444899999************************9.***************.99*******99777888776655 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.9e-05     0.084     127     179 ..      40      91 ..      35      93 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       EEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEE CS
                      tRNA-synt_2d 127 veglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvyl 179
                                       ++ lv  e+ ++++ +g++  +l++lfg+ev++      +p+  P +e +v++
  gi|386001315|ref|YP_005919614.1|  40 IDVLVEFEEPTFRNFMGLV-FFLEELFGREVDLVTTRGLSPYIRPAVEKEVVW 91 
                                       6677777888899988865.699**************************9988 PP

>> Amidoligase_2  Putative amidoligase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.7e-05      0.12     125     167 ..      45      87 ..      41      93 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                     Amidoligase_2 125 dleaetlrnllkilalledwleklldvdlarrlnpyckpldee 167
                                       ++e +t+rn+++ +++le+++  ++d  ++r l+py++p  e+
  gi|386001315|ref|YP_005919614.1|  45 EFEEPTFRNFMGLVFFLEELFGREVDLVTTRGLSPYIRPAVEK 87 
                                       68899********************************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 653.83
//
Query:       gi|386001316|ref|YP_005919615.1|  [L=179]
Description: hypothetical protein Mhar_0614 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1143.71
//
Query:       gi|386001317|ref|YP_005919616.1|  [L=66]
Description: hypothetical protein Mhar_0615 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-13   50.5   4.2    2.1e-13   50.2   4.2    1.1  1  ATPase_gene1     Putative F0F1-ATPase subunit Ca2+/Mg2+ trans
    0.00098   18.9   2.6     0.0014   18.4   2.6    1.3  1  Rick_17kDa_Anti  Glycine zipper 2TM domain
  ------ inclusion threshold ------
       0.01   15.5   0.8       0.01   15.5   0.8    1.0  1  DUF4203          Domain of unknown function (DUF4203)
      0.026   14.3   4.4      0.053   13.3   4.4    1.5  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
       0.04   13.9   7.5      0.076   13.0   6.8    1.7  2  Gly-zipper_Omp   Glycine zipper
      0.066   13.3   5.0      0.086   13.0   5.0    1.2  1  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea
      0.085   12.7   1.0        8.4    6.3   0.0    2.1  2  LapA_dom         Lipopolysaccharide assembly protein A domain
       0.11   12.9   0.5       0.11   12.9   0.5    2.2  2  Romo1            Reactive mitochondrial oxygen species modula
       0.22   11.4   0.8       0.22   11.4   0.8    2.1  2  MadM             Malonate/sodium symporter MadM subunit
        1.8    8.6   3.8         16    5.6   0.3    2.1  2  UPF0154          Uncharacterised protein family (UPF0154)
        2.3    8.7   6.7       0.84   10.0   0.8    2.0  2  Tim17            Tim17/Tim22/Tim23/Pmp24 family
        3.3    8.3   7.8        6.1    7.5   0.2    2.2  2  YtxH             YtxH-like protein
        3.4    7.7   4.9        8.6    6.4   0.2    2.1  2  DUF1043          Protein of unknown function (DUF1043)
        4.6    6.7   7.8         22    4.5   8.0    1.8  1  DUF3169          Protein of unknown function (DUF3169)


Domain annotation for each model (and alignments):
>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   4.2   1.6e-16   2.1e-13       2      53 ..      10      63 ..       9      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.6e-16
                      ATPase_gene1  2 alasqiGielvapillggllGywLDkkf..gtspwfliiglllGlaaGfynvyr 53
                                      ++a + Gie++++il+g ++Gy   ++f  g+++++l+ig +lGl++G yn+yr
  gi|386001317|ref|YP_005919616.1| 10 FKAASAGIEMAISILIGSVVGYVGGRFFdeGSGYIGLVIGAVLGLISGTYNLYR 63
                                      6899*******************999999899*********************9 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.6   1.1e-06    0.0014       4      37 ..      24      56 ..      21      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                   Rick_17kDa_Anti  4 liGAaaGgvaGaaigggggrvlGavvGAaaGava 37
                                      liG ++G v G+ ++  g +++G v+GA++G + 
  gi|386001317|ref|YP_005919616.1| 24 LIGSVVGYVGGRFFDE-GSGYIGLVIGAVLGLIS 56
                                      89**********9977.8*************665 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.8   8.1e-06      0.01      49      93 ..      11      55 ..       1      63 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.1e-06
                           DUF4203 49 sslvqgaslvaalvvGllgGllallfwelglfllgalgGlllall 93
                                      + ++ g+ +++++++G ++G++   f+  g++ +g++ G +l+l+
  gi|386001317|ref|YP_005919616.1| 11 KAASAGIEMAISILIGSVVGYVGGRFFDEGSGYIGLVIGAVLGLI 55
                                      7889999****************999999*************997 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.4   4.2e-05     0.053       7      41 ..      19      58 ..      11      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                                      XXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  7 AaiGAaaGAvvGaliG.....sgggkGAaiGAaaGalaGg 41
                                       ai   +G vvG + G     ++g  G +iGA+ G + G+
  gi|386001317|ref|YP_005919616.1| 19 MAISILIGSVVGYVGGrffdeGSGYIGLVIGAVLGLISGT 58
                                      5666677777777777775455555678******999986 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.9     0.012        15      24      35 ..      23      34 ..      12      42 .. 0.67
   2 ?   13.0   6.8   5.9e-05     0.076       5      35 ..      25      57 ..      20      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                    Gly-zipper_Omp 24 aliGAavGaavG 35
                                      +liG +vG ++G
  gi|386001317|ref|YP_005919616.1| 23 ILIGSVVGYVGG 34
                                      566776666665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.9e-05
                    Gly-zipper_Omp  5 iGAaaGaliGga..vggrgtGaliGAavGaavG 35
                                      iG+++G + G     g  ++G +iGA++G ++G
  gi|386001317|ref|YP_005919616.1| 25 IGSVVGYVGGRFfdEGSGYIGLVIGAVLGLISG 57
                                      6777777777643334458************99 PP

>> Bacteriocin_IIc  Bacteriocin class II with double-glycine leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.0   6.7e-05     0.086      27      61 ..      18      59 ..      11      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
                   Bacteriocin_IIc 27 givggalaGaatGaa.......tlgilgaavGavvGavvGai 61
                                        + ++l+G+++G++         g +g ++Gav+G ++G +
  gi|386001317|ref|YP_005919616.1| 18 EMAISILIGSVVGYVggrffdeGSGYIGLVIGAVLGLISGTY 59
                                      5678899999999999999********************975 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.011        14      16      36 ..      12      32 ..       6      36 .. 0.85
   2 ?    6.3   0.0    0.0066       8.4      27      43 ..      46      62 ..      43      66 .] 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                          LapA_dom 16 elpLsllllvafgiGallgwl 36
                                       ++ ++ ++++++iG ++g++
  gi|386001317|ref|YP_005919616.1| 12 AASAGIEMAISILIGSVVGYV 32
                                      5788999*********99975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0066
                          LapA_dom 27 fgiGallgwllslwsyl 43
                                      ++iGa+lg++ +++   
  gi|386001317|ref|YP_005919616.1| 46 LVIGAVLGLISGTYNLY 62
                                      68999999998887544 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.8     0.075        96       6      24 ..      19      37 ..      14      43 .. 0.81
   2 ?   12.9   0.5   8.6e-05      0.11      11      31 ..      43      63 ..      39      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.075
                             Romo1  6 ikmGalmGaaVGlaiGllf 24
                                      +   +l+G++VG + G +f
  gi|386001317|ref|YP_005919616.1| 19 MAISILIGSVVGYVGGRFF 37
                                      5667899999999988765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.6e-05
                             Romo1 11 lmGaaVGlaiGllfGtfsalr 31
                                       +G ++G+++Gl+ Gt++++r
  gi|386001317|ref|YP_005919616.1| 43 YIGLVIGAVLGLISGTYNLYR 63
                                      68***************9987 PP

>> MadM  Malonate/sodium symporter MadM subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   0.00017      0.22      42      57 ..      20      35 ..      17      36 .. 0.93
   2 ?    0.1   2.6      0.57   7.3e+02      43      58 ..      44      59 ..      40      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                              MadM 42 AiAIllGLvlAYiGGv 57
                                      Ai Il+G v+ Y+GG 
  gi|386001317|ref|YP_005919616.1| 20 AISILIGSVVGYVGGR 35
                                      9**************6 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.57
                              MadM 43 iAIllGLvlAYiGGvv 58
                                      i +++G vl  i G++
  gi|386001317|ref|YP_005919616.1| 44 IGLVIGAVLGLISGTY 59
                                      6789999999999986 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.027        34       3      18 ..      21      36 ..      19      39 .. 0.69
   2 ?    5.6   0.3     0.012        16       3      15 ..      44      56 ..      42      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                           UPF0154  3 ialivGlvlGffiark 18
                                      i +++G v+G++  r 
  gi|386001317|ref|YP_005919616.1| 21 ISILIGSVVGYVGGRF 36
                                      6777888888777664 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                           UPF0154  3 ialivGlvlGffi 15
                                      i+l++G+vlG + 
  gi|386001317|ref|YP_005919616.1| 44 IGLVIGAVLGLIS 56
                                      7888888888775 PP

>> Tim17  Tim17/Tim22/Tim23/Pmp24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.6      0.15   1.9e+02       4      25 ..      14      35 ..      11      39 .. 0.76
   2 ?   10.0   0.8   0.00066      0.84       7      27 ..      40      60 ..      36      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                             Tim17  4 ktglsgvlGallGavfglvkgs 25
                                      ++g+ +++++l+G+v g v g 
  gi|386001317|ref|YP_005919616.1| 14 SAGIEMAISILIGSVVGYVGGR 35
                                      6778888888888888888775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00066
                             Tim17  7 lsgvlGallGavfglvkgsrr 27
                                      +sg++G+++Gav gl++g+++
  gi|386001317|ref|YP_005919616.1| 40 GSGYIGLVIGAVLGLISGTYN 60
                                      689***************987 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0047       6.1       2      23 ..      21      42 ..      20      43 .. 0.86
   2 ?    2.7   4.2      0.14   1.8e+02       6      16 ..      44      54 ..      40      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0047
                              YtxH  2 lglliGaavGaaaglLlAPksG 23
                                      + +liG +vG + g ++   sG
  gi|386001317|ref|YP_005919616.1| 21 ISILIGSVVGYVGGRFFDEGSG 42
                                      679*************986665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                              YtxH  6 iGaavGaaagl 16
                                      iG+++Ga++gl
  gi|386001317|ref|YP_005919616.1| 44 IGLVIGAVLGL 54
                                      67777777776 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0067       8.6       2      20 ..      20      38 ..      19      41 .. 0.88
   2 ?    3.6   0.7      0.05        65       3      14 ..      44      55 ..      42      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0067
                           DUF1043  2 liglvvGiiiGalilrltn 20
                                       i++++G ++G++  r+++
  gi|386001317|ref|YP_005919616.1| 20 AISILIGSVVGYVGGRFFD 38
                                      5999***********9976 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.05
                           DUF1043  3 iglvvGiiiGal 14
                                      iglv+G+++G++
  gi|386001317|ref|YP_005919616.1| 44 IGLVIGAVLGLI 55
                                      899999999986 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   8.0     0.017        22       9      50 ..      17      57 ..      10      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                           DUF3169  9 llmliggliGgiiGfllgafeaekgleelsaalkelllligs 50
                                      + m+i++liG ++G+++g f +e g +++  ++ ++l li+ 
  gi|386001317|ref|YP_005919616.1| 17 IEMAISILIGSVVGYVGGRFFDE-GSGYIGLVIGAVLGLISG 57
                                      56999999999999999999788.688899999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 457.94
//
Query:       gi|386001318|ref|YP_005919617.1|  [L=650]
Description: hypothetical protein Mhar_0616 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 4828.02
//
Query:       gi|386001319|ref|YP_005919618.1|  [L=332]
Description: hypothetical protein Mhar_0617 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2217.20
//
Query:       gi|386001320|ref|YP_005919619.1|  [L=265]
Description: Methyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   54.0   0.0    4.7e-14   52.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    1.4e-11   44.8   0.0    2.4e-11   44.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    5.7e-09   35.6   0.0    8.5e-09   35.1   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.8e-09   35.9   0.0    3.7e-08   34.0   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
    6.4e-08   32.6   0.0    8.4e-08   32.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      2e-05   24.4   0.0      4e-05   23.5   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0012   18.2   0.0     0.0017   17.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0035   17.1   0.0     0.0047   16.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.014   14.4   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.033   14.1   0.0      0.058   13.3   0.0    1.5  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   2.6e-17   4.7e-14       1      97 []      77     179 ..      77     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.6e-17
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH....TTT.....TEEEEESBCCGBSSSTTTEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee....egl.....nvefvqgdaedlpfedgsfDlv 68 
                                       vL+lGcGtG++ +a+  r+  + v++ D+s+ ml++are+aee            ++e+v+g + +++ + +  D+v
  gi|386001320|ref|YP_005919619.1|  77 VLELGCGTGEFPIAAVGRC--SWVIAADVSKPMLRYAREKAEErlreG-GagdldRIEYVRGGFLTYQHQGEPLDAV 150
                                       9***************998..9******************98877642.25789*********************** PP

                                       EEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  69 vssgalhhlsdedlekalkeiarvLkpgG 97 
                                       v ++alhhl+d   + al +ia +Lkp G
  gi|386001320|ref|YP_005919619.1| 151 VTQFALHHLPDFWKQVALIRIAGMLKPAG 179
                                       **********999999***********98 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.3e-14   2.4e-11       1      96 []      78     183 ..      78     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.3e-14
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-........EEEETTEECCCTSS-TT-EEEEEEES CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl........kvefvvadaeklpfednsfDlvvsse 69 
                                       L++GcGtG +  a   r++ v++ D+sk ml++a+eka+e+          ++e+v++ + + + + +  D+vv ++
  gi|386001320|ref|YP_005919619.1|  78 LELGCGTGEFPIAAVGRCSWVIAADVSKPMLRYAREKAEERLReggagdldRIEYVRGGFLTYQHQGEPLDAVVTQF 154
                                       89*************999****************9999998779999****************************** PP

                                       -CCC-CCH..HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  70 vlhhvedp..ekalkeiaRvLkpgGllvi 96 
                                       +lhh++d   + al  ia +Lkp G+l+i
  gi|386001320|ref|YP_005919619.1| 155 ALHHLPDFwkQVALIRIAGMLKPAGKLFI 183
                                       *****6541155889***********986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   4.8e-12   8.5e-09      39     233 .]      65     261 ..      30     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 4.8e-12
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.......TEEEEE--TT CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.......nieflqanae 108
                                       v +l    + a+vl++ +Gtg++ ++   +vg+   v+ +D+++ mL+ +++k++e+          +ie++ +   
  gi|386001320|ref|YP_005919619.1|  65 VLDLLDLSPEATVLELGCGTGEFPIA---AVGRCSWVIAADVSKPMLRYAREKAEERLREggagdldRIEYVRGGFL 138
                                       334444455569**********9885...7899999***********999888776533333358889********* PP

                                       T-TTS-T-EEEEEEES-GGG-S-..HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS CS
                   Ubie_methyltran 109 eLpfeddsfDvvtvsfGlrnvtD..klkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllak 183
                                         + + +  D v   f l  ++D  k+ aL  +  +lkp G+l++ +   v+       ye ++ + l ++ ++  +
  gi|386001320|ref|YP_005919619.1| 139 TYQHQGEPLDAVVTQFALHHLPDfwKQVALIRIAGMLKPAGKLFIRD---VIYSFDAAGYEGFFDRYLSRMAEMGGE 212
                                       ***********************444568899999*******98754...445555566999999999999999887 PP

                                       -HHHHHHHHHHHHHS--HH.HHHHHHHHTTEEEEEEEEEGGGTEEEEEEEE CS
                   Ubie_methyltran 184 dldsyryLvesirafPdqe.tlkeliedaGfksveyesltgGvvaihigvk 233
                                              Lv+   ++      ++ +ie aGf+ +e  ++ +G +a+++ vk
  gi|386001320|ref|YP_005919619.1| 213 G-TPRDILVHIRDEHSTIGwMMEGMIERAGFS-IERADYRAGFIASYLCVK 261
                                       7.666788887777777652678999999995.677888888888887766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.8   3.2e+03      27      60 ..      41      70 ..      27      76 .. 0.58
   2 !   34.0   0.0   2.1e-11   3.7e-08       1      99 []      78     181 ..      78     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                   Methyltransf_12 27 Dispsaiedakeklakrennnnnnvelealdlld 60
                                      D+s+  i    +++ak+++  +++   e+ldlld
  gi|386001320|ref|YP_005919619.1| 41 DVSEIRI--YDQRMAKIRD--VAKEVGEVLDLLD 70
                                      5555555..7777777774..4444445555544 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2.1e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsai....edakeklakrennnnnnvelealdlldldgg.ssfDlvva 72 
                                       Le+GcGtG++  a   +   + +++ D+s+ ++    e+a+e+l++ ++ + +++e+     l  + + +  D+vv 
  gi|386001320|ref|YP_005919619.1|  78 LELGCGTGEFPIAAVGR--CSWVIAADVSKPMLryarEKAEERLREGGAGDLDRIEYVRGGFLTYQHQgEPLDAVVT 152
                                       8*******999999888..89999*********999999999999999999999999988877666557******** PP

                   Methyltransf_12  73 snvlhhlkdir..evldnirklLkpgGrl 99 
                                        ++lhhl+d     +l +i+ +Lkp G+l
  gi|386001320|ref|YP_005919619.1| 153 QFALHHLPDFWkqVALIRIAGMLKPAGKL 181
                                       *******6655227777*********987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   4.7e-11   8.4e-08       8     121 ..      61     187 ..      48     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.7e-11
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae....................... 61 
                                       e+ + l+ ll+ l + + vL++GcGtG++   +  +   v++ D s  +   a+                       
  gi|386001320|ref|YP_005919619.1|  61 EVGEVLD-LLD-LSPEATVLELGCGTGEFPIAAVGRCSWVIAADVSKPMLRYARekaeerlreggagdldrieyvrg 135
                                       4444444.444.88999**********99887755544789*****9988877666666666666666655555444 PP

                   Methyltransf_23  62 kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpd..ppellrqiatllkpgGylllsepl 121
                                       ++ ++q++ +            d +v  + l+h+pd     +l +ia +lkp G l+++++ 
  gi|386001320|ref|YP_005919619.1| 136 GFLTYQHQGE----------PLDAVVTQFALHHLPDfwKQVALIRIAGMLKPAGKLFIRDVI 187
                                       4444444444..........***************986779999**************9964 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.2e-08     4e-05       4     112 ..      74     186 ..      71     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.2e-08
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqkl.......gldnveFeqgdieelekllede 73 
                                       + +vl+lGCGtGe+ +++    g  + v+  D s+ ++++Are+a++         ld++e  +g + + +   + e
  gi|386001320|ref|YP_005919619.1|  74 EATVLELGCGTGEFPIAAV---GRCSWVIAADVSKPMLRYAREKAEERlreggagDLDRIEYVRGGFLTYQ--HQGE 145
                                       679**********999999...44567****************7775422222223558888888888877..3459 PP

                   Methyltransf_31  74 kfDlilsnevlnalad..pdkileeiervlkpggilliedp 112
                                       + D ++++ +l++l+d  ++ +l +i   lkp g l i+d+
  gi|386001320|ref|YP_005919619.1| 146 PLDAVVTQFALHHLPDfwKQVALIRIAGMLKPAGKLFIRDV 186
                                       9*************994445566799999999999999875 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.2e-07    0.0017      52     140 ..      63     159 ..      48     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.2e-07
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS....-SSS-EEEEE.....S CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdel....dlerkvevkl.....l 119
                                         +l+ l+l p  t+L++GcG G+  + av r    v++  +Sk   ++a+++ +e+    +  +  ++++     l
  gi|386001320|ref|YP_005919619.1|  63 GEVLDLLDLSPEATVLELGCGTGEFPIAAVGR-CSWVIAADVSKPMLRYAREKAEERlregGAGDLDRIEYvrggfL 138
                                       568999**************************.7899*******998888766554322225555555543111225 PP

                                       -GGG-----SEEEEES-GGGT CS
                              CMAS 120 dyedldekvdrvvsvgafehv 140
                                        y+   e++d+vv+  a+ h+
  gi|386001320|ref|YP_005919619.1| 139 TYQHQGEPLDAVVTQFALHHL 159
                                       788888888888887777776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.6e-06    0.0047      62     159 ..      62     163 ..      22     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.......SEEEEES CS
                              PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.......nvivvvg 131
                                       v+ +l+ll+l++ a vLe+G+G+G         vg+   v++ + +k + + a+++ ++  +e       ++  v g
  gi|386001320|ref|YP_005919619.1|  62 VGEVLDLLDLSPEATVLELGCGTGEFPI---AAVGRCSWVIAADVSKPMLRYAREKAEERLREggagdldRIEYVRG 135
                                       56789*******************6543...4567777777777777776655555444433334445545555554 PP

                                       -GGGTTGGG.-SEEEEEESSBBSS--HHH CS
                              PCMT 132 DGrkGyeek.aPYdaihvgaaapeiPeal 159
                                        G   y+++  P da+++  a +++P+ +
  gi|386001320|ref|YP_005919619.1| 136 -GFLTYQHQgEPLDAVVTQFALHHLPDFW 163
                                       .6666665425888888888888777655 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     8e-06     0.014     202     243 ..      74     115 ..      48     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                   tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfekvlateiakssveaaqyni 243
                                       +  +lel cG G+f +a   + + v+a++++k+ +  a+   
  gi|386001320|ref|YP_005919619.1|  74 EATVLELGCGTGEFPIAAVGRCSWVIAADVSKPMLRYAREKA 115
                                       4479*****************************999987665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.058      14      61 ..      73     118 ..      59     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakenieka 61 
                                       ++++v+  G+  g  pi++v  g+++ via+D+++  l+ a+e++e+ 
  gi|386001320|ref|YP_005919619.1|  73 PEATVLELGCGTGEFPIAAV--GRCSWVIAADVSKPMLRYAREKAEER 118
                                       5779999************9..99******************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1986.93
//
Query:       gi|386001321|ref|YP_005919620.1|  [L=145]
Description: hypothetical protein Mhar_0619 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-36  122.7   9.2    1.6e-35  121.5   9.2    1.5  1  DUF4870   Domain of unknown function (DUF4870)
     0.0011   18.8   0.5     0.0015   18.4   0.5    1.1  1  Atthog    Attenuator of Hedgehog
      0.004   17.6   0.7      0.004   17.6   0.7    2.1  2  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
      0.026   13.3   3.1      0.029   13.1   3.1    1.2  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   9.2   3.6e-39   1.6e-35       2     108 ..       9     142 ..       8     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 3.6e-39
                           DUF4870   2 rnlaalihlsal.sklliplgniilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvli....... 70 
                                       r++a+l+hlsal + l +plgn+++Plv+wl+k++++ fvd+qgkealNFq+s+++y +++++l +++ +       
  gi|386001321|ref|YP_005919620.1|   9 RTWATLCHLSALlMLLGVPLGNVLGPLVVWLVKRNQHTFVDDQGKEALNFQLSVTLYWVLAGIL-VFLSVgsiaffw 84 
                                       89**********888889*******************************************999.55555689999* PP

                           DUF4870  71 ......................gflllllllllllnlvlviiaaikanegeeyrypltir 108
                                                             gf  ll++ ll++++++ iiaai+a++ge yrypltir
  gi|386001321|ref|YP_005919620.1|  85 paahpgmidfwnpmampfamilGF--LLIFGLLAFSVIFAIIAAIRASNGEAYRYPLTIR 142
                                       **************9988877777..*********************************8 PP

>> Atthog  Attenuator of Hedgehog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5   3.3e-07    0.0015      26     110 ..      52     139 ..      29     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.3e-07
                            Atthog  26 grdqvcfspelqaewllt..lvliivGiicita.tvillvlshwerevvkyarwlgfsamvlfclaavifpigfevd 99 
                                       g++ + f+ +++  w+l+  lv+++vG i+    +    ++ +w+  ++++a  lgf  +  +   +vif i   + 
  gi|386001321|ref|YP_005919620.1|  52 GKEALNFQLSVTLYWVLAgiLVFLSVGSIAFFWpAAHPGMIDFWNPMAMPFAMILGFLLIFGLLAFSVIFAIIAAIR 128
                                       56667788889999999843555666666554414566799*****************99999999*********** PP

                            Atthog 100 eiGGepyqlpk 110
                                          Ge+y+ p 
  gi|386001321|ref|YP_005919620.1| 129 ASNGEAYRYPL 139
                                       ********996 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   8.9e-07     0.004      25      84 ..      18      80 ..       6      88 .. 0.78
   2 ?    0.6   7.0      0.17   7.8e+02      64      88 ..     104     127 ..      80     133 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.9e-07
                              FtsX 25 illitlvalviGlglgllaaqllsdvllssvfs...selkisidlitvliiivlllllallag 84
                                      ++l+ l++ ++G +lg l+ +l+    +++v+     +l +++++  +++++++l++l + ++
  gi|386001321|ref|YP_005919620.1| 18 SALLMLLGVPLGNVLGPLVVWLVKRNQHTFVDDqgkEALNFQLSVTLYWVLAGILVFLSVGSI 80
                                      78999*************************997877777777777777777777777766552 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                              FtsX  64 idlitvliiivlllllallagllsi 88 
                                       +  + +l+i++ll + +++a++++i
  gi|386001321|ref|YP_005919620.1| 104 MI-LGFLLIFGLLAFSVIFAIIAAI 127
                                       32.3345555555555555534443 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.1   6.5e-06     0.029     368     435 ..      43     126 ..       9     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-06
                           DUF2207 368 ergyfdkkgkkklkklsalglgliilglilillallllvll.......................lvfllilllilll 421
                                       +++ f +++ k++  +++  +++++l+ il++l++++++++                            +ll++ ll
  gi|386001321|ref|YP_005919620.1|  43 NQHTFVDDQGKEALNFQLSVTLYWVLAGILVFLSVGSIAFFwpaahpgmidfwnpmampfamilG----FLLIFGLL 115
                                       456666666788888888888888888888888888888889***********999866633322....22222222 PP

                           DUF2207 422 iaiivlllfsrllg 435
                                       ++++++++   +  
  gi|386001321|ref|YP_005919620.1| 116 AFSVIFAI---IAA 126
                                       22222222...222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1129.62
//
Query:       gi|386001322|ref|YP_005919621.1|  [L=142]
Description: Phenylacetic acid degradation protein PaaD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-09   37.7   0.0    2.7e-09   37.2   0.0    1.2  1  4HBT            Thioesterase superfamily
     0.0034   17.5   0.0     0.0051   16.9   0.0    1.3  1  DUF4442         Domain of unknown function (DUF4442)
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.09   13.0   0.0    1.1  1  4HBT_3          Thioesterase-like superfamily
      0.074   13.2   0.0       0.17   12.1   0.0    1.7  2  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   6.1e-13   2.7e-09       2      78 ..      55     128 ..      54     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 6.1e-13
                                       SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                              4HBT   2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                       G  hgG++++l+Dea gaa +s+g    ++ +++ +i+f++p  + + l++ea+ ++  +++  +e++v+ e gr v
  gi|386001322|ref|YP_005919621.1|  55 GMTHGGALFSLVDEAFGAAGNSRGS---VALALNVQITFVAPPSPREILRAEAKEIKREGRISNFEIRVKGEAGRIV 128
                                       899*********************7...9****************************************99988766 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0051      12     124 ..      21     129 ..      17     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                       HSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-- CS
                           DUF4442  12 kaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlaka 88 
                                       + PY + +g+r  +l pg a+ ++    +++  +g  H++A+++l++ a+G+  +    ++ + +  ++++ ++a+ 
  gi|386001322|ref|YP_005919621.1|  21 REPYSRILGIRLVDLGPGWAVTEMDCTEEMEDLLGMTHGGALFSLVDEAFGAAGN---SRGSVALALNVQITFVAPP 94 
                                       67*************************************************8544...3567777777777787775 PP

                                       -S-EEEEEE-TTS-TT--EEEEEEEEEEETTE.EEE CS
                           DUF4442  89 tgdltavaelepedvgekeelvvevevrdekgeevv 124
                                         +   +ae+++ +++ ++  ++e++v+ e+g+ v+
  gi|386001322|ref|YP_005919621.1|  95 SPREILRAEAKEIKRE-GRISNFEIRVKGEAGRIVA 129
                                       5554444444444443.4445555556666665555 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05      0.09      11      82 ..      57     134 ..      50     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                       .-HHHHHHHHHHHHHHT....-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEET.TEEEEEEEE CS
                            4HBT_3  11 gyGGyvlAlalraaqrtv...pdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqg.grpiftata 81 
                                        +GG++ +l+ +a  ++     ++ l  +++++F++p ++   ++ +++++++  ++s  ++++  + gr +++a+ 
  gi|386001322|ref|YP_005919621.1|  57 THGGALFSLVDEAFGAAGnsrGSVALaLNVQITFVAPPSPReILRAEAKEIKREGRISNFEIRVKGEaGRIVAMALG 133
                                       3999999999888887654443333467*************999********************9877999999887 PP

                                       E CS
                            4HBT_3  82 s 82 
                                       +
  gi|386001322|ref|YP_005919621.1| 134 T 134
                                       6 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.94   4.2e+03     126     136 ..      28      38 ..      18      41 .. 0.83
   2 ?   12.1   0.0   3.7e-05      0.17      48      90 ..      90     135 ..      53     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.94
                    Acetyltransf_6 126 eGlrrfdlggg 136
                                        G+r +dlg+g
  gi|386001322|ref|YP_005919621.1|  28 LGIRLVDLGPG 38 
                                       58999999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.7e-05
                    Acetyltransf_6  48 vfadpltraflrdllaalaargalrlyvlrld...grpvAvalglr 90 
                                         a+p +r++lr+ +++  ++g++  +++r++   gr+vA+alg  
  gi|386001322|ref|YP_005919621.1|  90 FVAPPSPREILRAEAKEIKREGRISNFEIRVKgeaGRIVAMALGTA 135
                                       6789***************************534589*****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 1136.09
//
Query:       gi|386001323|ref|YP_005919622.1|  [L=529]
Description: Na+/solute symporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-61  208.9  45.9    1.4e-61  208.6  45.9    1.1  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.6  45.9     8e-66   1.4e-61       1     406 []      35     452 ..      35     452 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 8e-66
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllel.galllvlllllllaerlr....nagalTlp 72 
                                       y+++gr++ ++v+++s +a+ is + +vG  G++ + G++ ++l + ++ +++ ++++++++r r    n+ a+T+p
  gi|386001323|ref|YP_005919622.1|  35 YMVGGRKIHPYVMAMSYGATFISTSAIVGFGGTAGLFGMGLLWLTFlNIFVGIFIAFVVFGKRTRkmgyNLSAMTFP 111
                                       99*****************************************98537888999999999***999999999***** PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                       ++l+ Rf+++  + y+s l++++ + ++ sv l+g+a++ie++l +++++a++l+ +++a Y+viGGl  v+ytd  
  gi|386001323|ref|YP_005919622.1| 112 ELLARRFESRF-IQYFSGLVIFVGMPMYASVVLIGAARFIETTLAIDFNLALMLFSLIIAAYVVIGGLKGVMYTDAF 187
                                       *********99.99*************************************************************** PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkv.vdl..........ltpdslkllrdpltalslwlglvlGv 215
                                       qa++m vg  +ll+++ +++Gg+ ++ + l++ a  v ++l          + + +       +++l+l  g+++Gv
  gi|386001323|ref|YP_005919622.1| 188 QATIMFVGMAFLLVMTYSHLGGITQAHQALTNLAALVpANLaamghlgwtaMPAAGSAWWWTLVSTLVL--GVGIGV 262
                                       ********************************9998875556778877654334444455555555555..999999 PP

                               SSF 216 aglphilvRflaakdakailkgvlkltivlilvligmisiilfaiklagavp..kavgtevgvsniaypeLvvkllp 290
                                         +p  +vRf+++k+++++ ++vl++ ++++++   +++++  ++ +++      a+ +++g+s+ ++p  ++  +p
  gi|386001323|ref|YP_005919622.1| 263 LAMPQLVVRFMTVKSGRELNRAVLIGGVFILMMTGVAFVVGALSNVYFFERDgvIAIAAAAGNSDSIIPVYINTAMP 339
                                       *************************988777777777777777777777666677888999**************** PP

                               SSF 291 nllaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvl 367
                                       +++  +++   lAa mstl+s++ +  +a+ +D+Y+ ++     +   + +++ ii +vv++++      +++  ++
  gi|386001323|ref|YP_005919622.1| 340 SWFVYIFMLTLLAAAMSTLSSQFHAQGTAIGRDVYETVVGTRGGRSILITRIGIIIAVVVAVIL--GYFLPPSI-IA 413
                                       ***************************************9998888888888888888777654..45566676.99 PP

                               SSF 368 klvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                          ++ f+  a+a+l++   alfwkr+++ GA+agl++G
  gi|386001323|ref|YP_005919622.1| 414 PGTAIFFGLCAAAFLPMYTCALFWKRATRAGAIAGLVTG 452
                                       99999999****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3685.98
//
Query:       gi|386001324|ref|YP_005919623.1|  [L=62]
Description: hypothetical protein Mhar_0622 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 418.16
//
Query:       gi|386001325|ref|YP_005919624.1|  [L=145]
Description: Large-conductance mechanosensitive channel [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-43  147.5   1.1    2.3e-43  147.3   1.1    1.0  1  MscL             Large-conductance mechanosensitive channel, 
    1.9e-05   24.6   5.0    3.1e-05   24.0   5.0    1.2  1  UPF0547          Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.019   15.0   0.0    1.3  1  DUF4577          Domain of unknown function (DUF4577)
      0.016   15.2   2.0      0.023   14.7   2.0    1.2  1  DZR              Double zinc ribbon
      0.037   14.2   0.4       0.06   13.5   0.4    1.4  1  zf-UDP           Zinc-binding RING-finger
      0.043   14.0   0.0      0.059   13.6   0.0    1.2  1  UPF0239          Uncharacterised protein family (UPF0239)
      0.072   12.6   0.0       0.13   11.8   0.0    1.4  1  YoaP             YoaP-like
       0.23   11.3   2.7        0.5   10.2   2.4    1.7  2  zinc_ribbon_2    zinc-ribbon domain
        0.3   11.5   5.3       0.37   11.2   2.1    2.6  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.58   10.1   5.2        8.3    6.3   1.1    2.1  2  DUF3487          Protein of unknown function (DUF3487)
       0.63    9.5   4.9        1.8    8.1   4.9    1.7  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   1.1   1.4e-46   2.3e-43       1     115 [.       3     128 ..       3     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 1.4e-46
                              MscL   1 llkeFkefilrGnvidLAvgviiGaaftkiVtslvkdiimpliglllggvdfselkikl............kaeaav 65 
                                       ++keFkef+++Gnv+d+A+g+i+G af+kiVtslv+diimp++g+llggvdf++l+i+l            +a+a +
  gi|386001325|ref|YP_005919624.1|   3 MIKEFKEFAMKGNVLDMAIGIILGLAFGKIVTSLVNDIIMPPVGMLLGGVDFTNLFISLsgtsyatlaeaqAAGAPT 79 
                                       89*******************************************************************998899** PP

                              MscL  66 lkygafiqavinFliiafviFlivkainkkkkeeeeeeeaeekeeellte 115
                                       ++yg fi+++i+Fli+afviFl+v+++nk k++ee+++++ +ke+ +++e
  gi|386001325|ref|YP_005919624.1|  80 INYGLFINTIIDFLIVAFVIFLMVRQVNKMKRKEEAAPPN-TKECPYCKE 128
                                       *****************************76666665444.455544444 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   5.0   1.9e-08   3.1e-05       1      20 [.     121     140 ..     121     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.9e-08
                           UPF0547   1 KvCPeCeakvPvaaqfCphC 20 
                                       K+CP C +++P+aa +C+hC
  gi|386001325|ref|YP_005919624.1| 121 KECPYCKETIPLAATRCSHC 140
                                       99****************** PP

>> DUF4577  Domain of unknown function (DUF4577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.2e-05     0.019      65      93 ..      82     110 ..      57     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                           DUF4577  65 vgliivlivslalvsfvifliiqtgskmd 93 
                                        gl i  i+ + +v+fvifl+++  +km 
  gi|386001325|ref|YP_005919624.1|  82 YGLFINTIIDFLIVAFVIFLMVRQVNKMK 110
                                       59999***********************6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.0   1.4e-05     0.023       9      36 ..     117     142 ..     107     145 .] 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                               DZR   9 ppdarfCseCgtklkavaaedrCpsCge 36 
                                       pp+ + C++C+++++   a++rC++C++
  gi|386001325|ref|YP_005919624.1| 117 PPNTKECPYCKETIP--LAATRCSHCTS 142
                                       555555666666554..44556666655 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   3.7e-05      0.06      27      59 ..      92     129 ..      87     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                            zf-UDP  27 Fvacnecafpvcrpcyeyerk.....dgnqsCPqCktr 59 
                                       F ++  + f+++r++ +++rk       ++ CP Ck +
  gi|386001325|ref|YP_005919624.1|  92 FLIVAFVIFLMVRQVNKMKRKeeaapPNTKECPYCKET 129
                                       8889999**************6666646799****965 PP

>> UPF0239  Uncharacterised protein family (UPF0239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.6e-05     0.059      21      60 ..      80     120 ..      65     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                           UPF0239  21 lrYGLflGAifqlvCilAiillpsskseesv.eeeaessee 60 
                                       + YGLf+  i  ++ ++ +i+l + + ++ + +eea + ++
  gi|386001325|ref|YP_005919624.1|  80 INYGLFINTIIDFLIVAFVIFLMVRQVNKMKrKEEAAPPNT 120
                                       89************999999777776666430344444444 PP

>> YoaP  YoaP-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.1e-05      0.13       7      28 ..      66      87 ..      61      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                              YoaP  7 letlEqAqnaPcpfttyalFyn 28
                                      + tl +Aq+a +p  +y lF n
  gi|386001325|ref|YP_005919624.1| 66 YATLAEAQAAGAPTINYGLFIN 87
                                      57999***************87 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5    0.0045       7.3      10      19 ..     117     126 ..     116     130 .. 0.87
   2 ?   10.2   2.4    0.0003       0.5       2      22 ..     123     143 ..     122     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0045
                     zinc_ribbon_2  10 qdnakFCpyC 19 
                                       ++n k CpyC
  gi|386001325|ref|YP_005919624.1| 117 PPNTKECPYC 126
                                       689999**** PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0003
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                       Cp C ++++  a+ C++C ++
  gi|386001325|ref|YP_005919624.1| 123 CPYCKETIPLAATRCSHCTSE 143
                                       ******************776 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.1   1.8e+03       5      20 ..      21      36 ..      18      39 .. 0.57
   2 ?   11.2   2.1   0.00023      0.37       2      36 ..      87     140 ..      86     145 .] 0.67

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                   FeoB_associated  5 Vgliiaaavafvirrl 20
                                      +g+i+ +a + ++ +l
  gi|386001325|ref|YP_005919624.1| 21 IGIILGLAFGKIVTSL 36
                                      5555556666556555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                   FeoB_associated   2 tiIVgliiaaavafvirrlikk.kkkG........sCg..........ggCsgC 36 
                                       + I+  +i+a v+f+++r + k k+k+        +C             Cs+C
  gi|386001325|ref|YP_005919624.1|  87 NTIIDFLIVAFVIFLMVRQVNKmKRKEeaappntkECPycketiplaaTRCSHC 140
                                       779999999999999999999954444678887775543335555555555555 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.1    0.0051       8.3      29      60 ..      19      50 ..       3      59 .. 0.59
   2 ?    6.1   0.3     0.006       9.8      30      78 ..      63     112 ..      50     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0051
                           DUF3487 29 aglglvvglvlglllallvgslaliptialll 60
                                      + +g+++gl+ g +++ lv+ +++ p ++ll+
  gi|386001325|ref|YP_005919624.1| 19 MAIGIILGLAFGKIVTSLVNDIIMPPVGMLLG 50
                                      45666666666666666666666666666554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.006
                           DUF3487  30 glglvvglvlglllallvgslaliptia.lllvllvvlvggkllarlKRg 78 
                                       g++ ++ + +    a+++++ ++i ti+ +l+v++v++++ + ++++KR 
  gi|386001325|ref|YP_005919624.1|  63 GTSYATLAEAQAAGAPTINYGLFINTIIdFLIVAFVIFLMVRQVNKMKRK 112
                                       56666666666677788999999999997888888999999*******96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.9    0.0011       1.8       2      22 ..     120     140 ..     119     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                       zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyC 22 
                                       t++CP+C++ +    ++ C +C
  gi|386001325|ref|YP_005919624.1| 120 TKECPYCKEtI-PLAATRCSHC 140
                                       89*******55.9999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1044.41
//
Query:       gi|386001326|ref|YP_005919625.1|  [L=475]
Description: Putative cache sensor protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-49  166.9   0.0    6.7e-19   68.3   0.0    3.6  3  sCache_2         Single Cache domain 2
      1e-41  143.0   0.0    5.4e-20   71.7   0.0    3.4  2  dCache_2         Cache domain
    0.00074   18.9   0.0       0.07   12.4   0.0    2.1  2  Cache_3-Cache_2  Cache 3/Cache 2 fusion domain


Domain annotation for each model (and alignments):
>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   1.1e-22   6.7e-19      35     149 ..      69     185 ..      48     190 .. 0.85
   2 !   26.6   0.0   7.6e-10   4.5e-06      36     142 ..     207     322 ..     200     331 .. 0.75
   3 !   67.3   0.0   2.3e-22   1.3e-18      53     145 ..     379     469 ..     367     475 .] 0.94

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.1e-22
                          sCache_2  35 eeaqeevkelvnglkfgdG...kgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvt 108
                                       e+ +e++ e  n+++ +       Y+f++d++gt+l++Pf+p  +Gkn+++l+D nG  ++++l + a+ +gggf++
  gi|386001326|ref|YP_005919625.1|  69 ENGRERALEEFNDPRGQFVvgdLRYVFAYDSNGTCLAQPFRPGSVGKNQIDLRDENGFLFVQNLNRLAS-QGGGFAY 144
                                       444444444444444322244488*********************************************.******* PP

                          sCache_2 109 ylwkkpge.geveeklayvkyfepWdwvigtgvylddinkav 149
                                       y  ++p   +++e kl+y + +   dw++gtgv+l+d+++ +
  gi|386001326|ref|YP_005919625.1| 145 YVRPNPLHhDSPELKLSYIARVDD-DWWLGTGVWLSDVSAVF 185
                                       *******999************98.*************9976 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 7.6e-10
                          sCache_2  36 eaqeevkelvngl..kfgdGkgYffvlde.dgtllvhPfnpqleGknasnlkDanG......kyiirelvkeakkkg 103
                                       + ++++ e+ n+    f dG+ Y+f++d  +  +l+hPf+p+l+Gk +    D  G      + +    ++e++ +g
  gi|386001326|ref|YP_005919625.1| 207 NERKRALEAFNDRngSFVDGNQYLFAYDFdENRVLAHPFQPDLVGKVRRGGLDIYGfamdpsVETGLGGIREVAIDG 283
                                       55555555555431146788********7356799***********99988887773331112233333455557** PP

                          sCache_2 104 ggfvtylwkkpge.geveeklayvkyfepWdwvigtgvyl 142
                                        g+v+y++ +p+  +++  kl yv+ +   dw++g+g+y 
  gi|386001326|ref|YP_005919625.1| 284 TGLVYYMYLDPARdTTPAIKLGYVRAVDD-DWWLGSGIYP 322
                                       ************999************98.********95 PP

  == domain 3  score: 67.3 bits;  conditional E-value: 2.3e-22
                          sCache_2  53 GkgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvtylwkkpgegeveeklayvkyf 129
                                       G+ Y+f+ d +gt+l+ Pf p+ +G+n+ +l++++G++i re+ + a+ +g gf++ylw++p +g +e+k +yv ++
  gi|386001326|ref|YP_005919625.1| 379 GDVYIFAADFNGTSLALPFLPSAVGTNRLDLQNSEGVRINREMRAIAE-DGSGFFEYLWTNPLTGGEEPKTSYVTKV 454
                                       588*********************************************.**************************** PP

                          sCache_2 130 epWdwvigtgvylddi 145
                                          +w++g+g+yl d 
  gi|386001326|ref|YP_005919625.1| 455 DD-GWWLGAGIYLRDE 469
                                       98.9*********995 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   9.1e-24   5.4e-20      94     292 ..      91     322 ..      68     325 .. 0.90
   2 !   66.5   0.0   3.7e-22   2.2e-18      90     190 ..     376     474 ..     366     475 .] 0.96

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 9.1e-24
                          dCache_2  94 egyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeGfveytwpkp.dekkprkkisyvkyf 169
                                         y+f++ds+gt++++p++p   Gkn +dl+d++G  +++++ +la ++g Gf  y  p+p   + p+ k+sy++  
  gi|386001326|ref|YP_005919625.1|  91 LRYVFAYDSNGTCLAQPFRPGSVGKNQIDLRDENGFLFVQNLNRLA-SQGGGFAYYVRPNPlHHDSPELKLSYIARV 166
                                       57********************************999999999999.6677************************** PP

                          dCache_2 170 epldwiIGtgaylddieeelk.......................qellktlksir...ygnngyifiydtdg.niil 219
                                          dw +Gtg++l+d+ +                          + +l+ +++ +   ++ n y+f+yd d  ++++
  gi|386001326|ref|YP_005919625.1| 167 DD-DWWLGTGVWLSDVSAVFSadarldlvrfvdgavdyarenerKRALEAFNDRNgsfVDGNQYLFAYDFDEnRVLA 242
                                       98.**************99999999*******************9999999998744345679********98899* PP

                          dCache_2 220 hplkkelngknll.evkdkkgkl........lqelleaakkkgegfveYkwpkpsgd.kerkKisyvryfppwdWii 286
                                       hp +++l+gk +   ++   g          l  + e a + g g v Y++ +p +d ++  K+ yvr + + dW +
  gi|386001326|ref|YP_005919625.1| 243 HPFQPDLVGKVRRgGLDI-YGFAmdpsvetgLGGIREVAID-GTGLVYYMYLDPARDtTPAIKLGYVRAVDD-DWWL 316
                                       ************944444.4433899*99988888887775.569************9**************.**** PP

                          dCache_2 287 gtgvyl 292
                                       g+g+y 
  gi|386001326|ref|YP_005919625.1| 317 GSGIYP 322
                                       ****95 PP

  == domain 2  score: 66.5 bits;  conditional E-value: 3.7e-22
                          dCache_2  90 ydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeGfveytwpkpdekkprkkisyv 166
                                       +++g+ y+f++d +gt ++ p+ ps  G+n ldl++++G  i rem  +a ++g+Gf ey w++p ++ +++k+syv
  gi|386001326|ref|YP_005919625.1| 376 FVRGDVYIFAADFNGTSLALPFLPSAVGTNRLDLQNSEGVRINREMRAIA-EDGSGFFEYLWTNPLTGGEEPKTSYV 451
                                       789**********************************************9.************************** PP

                          dCache_2 167 kyfepldwiIGtgaylddieeelk 190
                                        +    +w +G+g+yl d e+ +k
  gi|386001326|ref|YP_005919625.1| 452 TKVDD-GWWLGAGIYLRDEERATK 474
                                       ***98.9***********999887 PP

>> Cache_3-Cache_2  Cache 3/Cache 2 fusion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   1.2e-05      0.07     189     286 ..      84     185 ..      71     189 .. 0.82
   2 !    4.3   0.0    0.0034        20     200     281 ..     382     468 ..     378     475 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                   Cache_3-Cache_2 189 kklkvGktGylyvldgkgdkkgkliihptlk...gknvldlkdadgesvvkkl...lkkksgsleyelk....kdek 255
                                       ++++vG+  y++++d++    g+ ++ p +    gkn +dl d++g  +v++l    ++  g+++y ++      + 
  gi|386001326|ref|YP_005919625.1|  84 GQFVVGDLRYVFAYDSN----GTCLAQPFRPgsvGKNQIDLRDENGFLFVQNLnrlASQGGGFAYY-VRpnplHHDS 155
                                       577899999********....****999888889*************8888763313445555555.5569999999 PP

                   Cache_3-Cache_2 256 greklavftyfepwdWvivasvyedefqeev 286
                                       ++ kl++  +++  dW ++++v+ +++ ++ 
  gi|386001326|ref|YP_005919625.1| 156 PELKLSYIARVDD-DWWLGTGVWLSDVSAVF 185
                                       ***********97.9**********998876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0034
                   Cache_3-Cache_2 200 yvldgkgdkkgkliihptlk...gknvldlkdadge...svvkkllkkksgsleyelk..kdekgreklavftyfep 268
                                       y++ ++   +g+ ++ p l    g+n ldl++++g      +  + +  sg++ey ++   +  ++ k++++t+++ 
  gi|386001326|ref|YP_005919625.1| 382 YIFAAD--FNGTSLALPFLPsavGTNRLDLQNSEGVrinREMRAIAEDGSGFFEYLWTnpLTGGEEPKTSYVTKVDD 456
                                       555444..235555444444445*******999998666777778888**********9767777778888888887 PP

                   Cache_3-Cache_2 269 wdWvivasvyede 281
                                        +W ++a+ y  +
  gi|386001326|ref|YP_005919625.1| 457 -GWWLGAGIYLRD 468
                                       .466677766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 3468.21
//
Query:       gi|386001327|ref|YP_005919626.1|  [L=1065]
Description: WD repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-97  317.1  21.8    5.7e-09   36.5   0.1   11.5 11  WD40           WD domain, G-beta repeat
    1.5e-32  112.8   0.0    2.2e-32  112.2   0.0    1.2  1  NB-ARC         NB-ARC domain
      5e-16   58.8   7.8       0.45   10.8   0.1    9.2 10  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma
    5.2e-12   46.0  15.3        4.9    7.3   0.5    9.9 10  DUF5570        Family of unknown function (DUF5570)
    1.1e-11   44.8   0.0      2e-11   44.0   0.0    1.4  1  APAF1_C        APAF-1 helical domain
    1.2e-10   41.0  11.1       0.59    9.3   0.1    7.7  8  120_Rick_ant   120 KDa Rickettsia surface antigen
    1.3e-08   34.0  10.3        4.4    5.8   0.0    9.2 10  Nup160         Nucleoporin Nup120/160
      4e-07   28.9   6.3       0.49    8.9   0.1    5.0  5  Cytochrom_D1   Cytochrome D1 heme domain
    8.4e-07   28.1   0.3        1.6    7.4   0.0    4.4  6  Nucleoporin_N  Nup133 N terminal like
    1.2e-05   25.1   0.1         79    3.4   0.0    8.2 10  PD40           WD40-like Beta Propeller Repeat
    7.6e-05   22.8   0.4        1.2    9.3   0.0    5.4  5  RBB1NT         RBB1NT (NUC162) domain
     0.0001   22.6   0.0    2.8e+02    2.0   0.0    7.9 10  WYL_2          WYL_2, Sm-like SH3 beta-barrel fold
    0.00023   20.6   0.0          4    6.7   0.0    4.4  5  WD40_like      WD40-like domain
     0.0011   18.8   0.1    1.9e+02    2.0   0.0    6.2  7  HIRA_B         HIRA B motif
  ------ inclusion threshold ------
       0.15   11.9   0.0        0.3   10.9   0.0    1.4  1  DUF2378        Protein of unknown function (DUF2378)
       0.47   10.8   2.7       0.99    9.8   0.3    2.8  2  AAA_16         AAA ATPase domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   1.3e-11   1.5e-08       3      38 .]     605     641 ..     604     641 .. 0.94
   2 !   36.5   0.1   5.1e-12   5.7e-09       1      38 []     645     683 ..     645     683 .. 0.95
   3 !   35.7   0.1   8.9e-12     1e-08       1      38 []     687     725 ..     687     725 .. 0.96
   4 !   27.4   0.0   3.7e-09   4.1e-06       2      38 .]     730     767 ..     729     767 .. 0.90
   5 !   27.0   0.0     5e-09   5.6e-06       2      38 .]     772     809 ..     771     809 .. 0.90
   6 !   29.9   0.0   5.9e-10   6.6e-07       1      38 []     813     851 ..     813     851 .. 0.91
   7 !   33.3   0.1   5.1e-11   5.7e-08       1      38 []     855     893 ..     855     893 .. 0.92
   8 !   28.9   0.0   1.3e-09   1.4e-06       1      38 []     897     935 ..     897     935 .. 0.91
   9 !   31.2   0.0   2.3e-10   2.6e-07       1      38 []     939     977 ..     939     977 .. 0.93
  10 !   29.6   0.1   7.5e-10   8.4e-07       1      38 []     981    1019 ..     981    1019 .. 0.92
  11 !    8.1   0.0    0.0047       5.3       3      35 ..    1025    1057 ..    1023    1058 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.3e-11
                                       EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       +lrtl+GH s+v+++a+spdg+  +s+s+D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 605 LLRTLKGHsSWVNAVAVSPDGRRAVSASYDNTLKVWD 641
                                       589*****777*************9***********9 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 5.1e-12
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ +rtl+GH ++v+++a+spdg+  +sGs+D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 645 GEEIRTLKGHsNWVSAVAVSPDGRRALSGSYDNTLKVWD 683
                                       5789******999************99***********9 PP

  == domain 3  score: 35.7 bits;  conditional E-value: 8.9e-12
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ +rtl+GH ++v+++a+spdg+  +sGs+D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 687 GEEIRTLKGHyGWVSAVAVSPDGRRAVSGSYDNTLKVWD 725
                                       5789******999*************************9 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 3.7e-09
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       + + tl+GH  sv+++a+ pdg+  +s+s D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 730 EEILTLKGHsASVRAVAVTPDGRKAVSASGDQTLKVWD 767
                                       67889****777************998877*******9 PP

  == domain 5  score: 27.0 bits;  conditional E-value: 5e-09
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       + + tl+GH  sv+++a+ pdg+  +s+s D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 772 EEILTLKGHsASVSAVAVTPDGRKAVSASGDQTLKVWD 809
                                       67889****777************998877*******9 PP

  == domain 6  score: 29.9 bits;  conditional E-value: 5.9e-10
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ +rtl+GH  sv+++a+ pdg+  +s+s D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 813 GEEIRTLKGHsASVRAVAVTPDGRKAVSSSGDQTLKVWD 851
                                       5789******777************998877*******9 PP

  == domain 7  score: 33.3 bits;  conditional E-value: 5.1e-11
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ lrtl+GH ++v+++a+ pdg+  +s+s D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 855 GEELRTLKGHsNWVNAVAVTPDGRKAVSSSGDKTLKVWD 893
                                       5789******999************998877*******9 PP

  == domain 8  score: 28.9 bits;  conditional E-value: 1.3e-09
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ l+tl+GH  sv+++a  pdg+  +s+s D+t+++Wd
  gi|386001327|ref|YP_005919626.1| 897 GEELQTLKGHsASVSAVALTPDGRKAVSSSGDKTLKVWD 935
                                       57899*****777************998877*******9 PP

  == domain 9  score: 31.2 bits;  conditional E-value: 2.3e-10
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ +rtl+GH  sv+++a+ pdg+  +s++dD+t+++Wd
  gi|386001327|ref|YP_005919626.1| 939 GEEIRTLKGHsASVSAVAVTPDGRKAISACDDRTLKVWD 977
                                       5789******777************999999*******9 PP

  == domain 10  score: 29.6 bits;  conditional E-value: 7.5e-10
                                        TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40    1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38  
                                        g+ lrtl+GH ++v+++ + pdg+  +s+sdD+t+++Wd
  gi|386001327|ref|YP_005919626.1|  981 GEELRTLKGHsDWVNAVVVTPDGQKTVSASDDQTLKVWD 1019
                                        5789******666************8899*********9 PP

  == domain 11  score: 8.1 bits;  conditional E-value: 0.0047
                                        EEEEEESSSSEEEEEEETTSSEEEEE.ETTSEEE CS
                              WD40    3 clrtltGHssvtslafspdgawlasG.sdDgtvr 35  
                                         + t+t+ +++ ++a  pdga +++G s  g ++
  gi|386001327|ref|YP_005919626.1| 1025 VIATFTADGPILCCAIAPDGATIVAGeS-SGRIH 1057
                                        5778887788**************9966.77776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0     2e-35   2.2e-32      22     251 ..     161     377 ..     137     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 2e-35
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslseddleekeeveslkrklv 97 
                                        v+l+GmgG+GK+++a+ + ++ +e+++ F+ ++ w++++ + k  + + +++  L++  +  +  +e++    +l 
  gi|386001327|ref|YP_005919626.1| 161 KVGLHGMGGIGKSVMAAAVARD-EETQRAFPdGILWLTLGINPKLLQRQSDLAVMLGDVPHAFNDIQEGK---SHLS 233
                                       489*******************.*******77**********9999999999999998877776666555...9*** PP

                                       HHCCCTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS CS
                            NB-ARC  98 rlLltkrfllvlDDVweeedwdkigvvlparenrlrvllTTRdeevanavsatsekievelLekdeawellenkvfe 174
                                        lL +k  l++lDDVw+ e  +     +    +++++l+TTRd ++  a  a  + +++ +L +dea+ ll +   +
  gi|386001327|ref|YP_005919626.1| 234 SLLADKVCLIILDDVWNVEHVE----GFNILGSGSKMLITTRDAKIITALDA--QEHRLGVLDDDEALSLLAKWTGQ 304
                                       ******************9984....5566677*************777777..99*****************9988 PP

                                       -GGCHH..CHHHHHHHHHHCTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHHCTGCC.TS--S.SSSSSSHHHHHHHH CS
                            NB-ARC 175 kkleekesleevakeivekckGlPlalkvlggllstkktveewkkvleklesklle.vekst.skslesvasilqls 249
                                        k e    l+ +a e++++c+ lPlal+++g++++   + + w  +le+l++  le ++ +  ++ +  + +++q+s
  gi|386001327|ref|YP_005919626.1| 305 SKEE----LPSLALEVAKECGNLPLALAMVGAMVK--GMPDLWTVALERLQNADLEkIREQFpDYPYPDLLKAIQVS 375
                                       8777....99********************99987..*******************987766267899999999999 PP

                                       HH CS
                            NB-ARC 250 ye 251
                                       ++
  gi|386001327|ref|YP_005919626.1| 376 VD 377
                                       97 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0029       3.3      36      81 ..     611     656 ..     605     663 .. 0.88
   2 ?    4.9   0.0     0.028        31      38      79 ..     655     696 ..     652     703 .. 0.87
   3 !    9.0   0.1    0.0015       1.7      28      84 ..     680     742 ..     677     748 .. 0.80
   4 !   10.8   0.1    0.0004      0.45      29      86 ..     723     786 ..     718     791 .. 0.82
   5 !    9.9   0.1    0.0008       0.9      26      84 ..     771     826 ..     760     832 .. 0.82
   6 !    7.6   0.1    0.0042       4.7      28      81 ..     806     866 ..     795     874 .. 0.82
   7 !    9.3   0.3    0.0012       1.3      28      85 ..     890     953 ..     848     958 .. 0.82
   8 !    8.6   0.1     0.002       2.3      30      81 ..     934     992 ..     931    1000 .. 0.83
   9 ?    3.0   0.0      0.11   1.3e+02      41      81 ..     994    1034 ..     990    1039 .. 0.85
  10 ?    4.7   0.0     0.032        36      29      70 ..    1017    1064 ..    1009    1065 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                       ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       +++s v+++a +pdg+  + a  d+++++ d e g+ +++l+ +s+
  gi|386001327|ref|YP_005919626.1| 611 GHSSWVNAVAVSPDGRRAVSASYDNTLKVWDLERGEEIRTLKGHSN 656
                                       56778999*******************************9998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.028
                       ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                       ++ v+++a +pdg+    +  d+++++ d e g+ +++l+ +
  gi|386001327|ref|YP_005919626.1| 655 SNWVSAVAVSPDGRRALSGSYDNTLKVWDLERGEEIRTLKGH 696
                                       566899999**************************9998765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0015
                       ANAPC4_WD40  28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                       +vw+l       + +++ + v+++a +pdg+  + +  d+++++ d e+g+ + +l+ +s + v
  gi|386001327|ref|YP_005919626.1| 680 KVWDLergeeirTLKGHYGWVSAVAVSPDGRRAVSGSYDNTLKVWDLEKGEEILTLKGHSAS-V 742
                                       566665555555456777889999*****************************999988874.4 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.0004
                       ANAPC4_WD40  29 vwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtc 86 
                                       vw+l       + ++++ +vr++a  pdg+  + a  d ++++ d e+g+ + +l+ +s + v+ 
  gi|386001327|ref|YP_005919626.1| 723 VWDLekgeeilTLKGHSASVRAVAVTPDGRKAVSASGDQTLKVWDLEKGEEILTLKGHSAS-VSA 786
                                       55555554444448999************************************99999885.665 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0008
                       ANAPC4_WD40  26 gqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                       g+++ tl  ++++ +v+++a  pdg+  + a  d ++++ d e+g+ +++l+ +s + v
  gi|386001327|ref|YP_005919626.1| 771 GEEILTL--KGHSASVSAVAVTPDGRKAVSASGDQTLKVWDLEKGEEIRTLKGHSAS-V 826
                                       3445555..89999************************************9998875.5 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0042
                       ANAPC4_WD40  28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       +vw+l       + ++++ +vr++a  pdg+  + +  d ++++ d e g+ +++l+ +s+
  gi|386001327|ref|YP_005919626.1| 806 KVWDLekgeeirTLKGHSASVRAVAVTPDGRKAVSSSGDQTLKVWDLERGEELRTLKGHSN 866
                                       4555555555555588999**********************************99988776 PP

  == domain 7  score: 9.3 bits;  conditional E-value: 0.0012
                       ANAPC4_WD40  28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavt 85 
                                       +vw+l       + ++++ +v+++a  pdg+  + +  d ++++ d e+g+ +++l+ +s + v+
  gi|386001327|ref|YP_005919626.1| 890 KVWDLergeelqTLKGHSASVSAVALTPDGRKAVSSSGDKTLKVWDLEKGEEIRTLKGHSAS-VS 953
                                       56666666665555778889999999999999999999999999999999999999888874.65 PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.002
                       ANAPC4_WD40  30 wtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       w+l       + ++++ +v+++a  pdg+    a++d ++++ d e g+ +++l+ +s+
  gi|386001327|ref|YP_005919626.1| 934 WDLekgeeirTLKGHSASVSAVAVTPDGRKAISACDDRTLKVWDLERGEELRTLKGHSD 992
                                       555555555445788999**********************************9998877 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.11
                       ANAPC4_WD40   41 vrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81  
                                        v+++   pdg+  + a +d ++++ d  +g+v+ +++++  
  gi|386001327|ref|YP_005919626.1|  994 VNAVVVTPDGQKTVSASDDQTLKVWDLGKGEVIATFTADGP 1034
                                        666677899**************************998755 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.032
                       ANAPC4_WD40   29 vwtl......eedkedsevrsLaWkpdgklLavaysdgevrlldaesg 70  
                                        vw+l      ++ + d+ + + a  pdg  ++ + s g+++ll  e++
  gi|386001327|ref|YP_005919626.1| 1017 VWDLgkgeviATFTADGPILCCAIAPDGATIVAGESSGRIHLLRLENA 1064
                                        454444444444678999999999*******************99986 PP

>> DUF5570  Family of unknown function (DUF5570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.016        18      19      47 ..     621     649 ..     612     662 .. 0.86
   2 ?    3.8   0.0     0.053        60      19      47 ..     663     691 ..     653     696 .. 0.88
   3 ?    5.3   0.0     0.017        19      19      46 ..     705     732 ..     699     747 .. 0.82
   4 !    6.3   0.1     0.009        10      14      46 ..     742     774 ..     736     789 .. 0.82
   5 !    7.3   0.5    0.0044       4.9      17      74 ..     787     841 ..     780     846 .. 0.76
   6 ?    4.9   0.1     0.024        27      14      46 ..     826     858 ..     822     867 .. 0.86
   7 ?    4.3   0.1     0.037        42      19      47 ..     873     901 ..     864     914 .. 0.84
   8 ?    5.7   0.0     0.013        15      18      47 ..     914     943 ..     899     955 .. 0.84
   9 ?    2.4   0.0      0.14   1.6e+02      17      46 ..     955     984 ..     947     992 .. 0.86
  10 ?    3.2   0.1     0.078        87      19      70 ..     999    1046 ..     990    1057 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgqdvh 47 
                                        sp gr a + s  +t  +wd+  g++++
  gi|386001327|ref|YP_005919626.1| 621 VSPDGRRAVSASYDNTLKVWDLERGEEIR 649
                                       49***********************9985 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.053
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgqdvh 47 
                                        sp gr a + s  +t  +wd+  g++++
  gi|386001327|ref|YP_005919626.1| 663 VSPDGRRALSGSYDNTLKVWDLERGEEIR 691
                                       49**********************99885 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.017
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgqdv 46 
                                        sp gr a + s  +t  +wd+ +g+++
  gi|386001327|ref|YP_005919626.1| 705 VSPDGRRAVSGSYDNTLKVWDLEKGEEI 732
                                       49***********************997 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.009
                           DUF5570  14 piilldspsgrsasarsegstaslwdvsdgqdv 46 
                                        + +  +p gr a + s  +t  +wd+ +g+++
  gi|386001327|ref|YP_005919626.1| 742 VRAVAVTPDGRKAVSASGDQTLKVWDLEKGEEI 774
                                       5666779***********************998 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0044
                           DUF5570  17 lldspsgrsasarsegstaslwdvsdgqdvhahaivtrtcesvlssavytqgcgyvrs 74 
                                       +  +p gr a + s  +t  +wd+ +g+++    ++     sv + av  +g   v s
  gi|386001327|ref|YP_005919626.1| 787 VAVTPDGRKAVSASGDQTLKVWDLEKGEEI---RTLKGHSASVRAVAVTPDGRKAVSS 841
                                       4559************************99...4555666677777766666655555 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.024
                           DUF5570  14 piilldspsgrsasarsegstaslwdvsdgqdv 46 
                                        + +  +p gr a + s  +t  +wd+  g+++
  gi|386001327|ref|YP_005919626.1| 826 VRAVAVTPDGRKAVSSSGDQTLKVWDLERGEEL 858
                                       5666779*********************99886 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.037
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgqdvh 47 
                                        +p gr a + s  +t  +wd+  g++++
  gi|386001327|ref|YP_005919626.1| 873 VTPDGRKAVSSSGDKTLKVWDLERGEELQ 901
                                       49*********************998874 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.013
                           DUF5570  18 ldspsgrsasarsegstaslwdvsdgqdvh 47 
                                         +p gr a + s  +t  +wd+ +g++++
  gi|386001327|ref|YP_005919626.1| 914 ALTPDGRKAVSSSGDKTLKVWDLEKGEEIR 943
                                       459***********************9985 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.14
                           DUF5570  17 lldspsgrsasarsegstaslwdvsdgqdv 46 
                                       +  +p gr a +  +  t  +wd+  g+++
  gi|386001327|ref|YP_005919626.1| 955 VAVTPDGRKAISACDDRTLKVWDLERGEEL 984
                                       4559*********************99886 PP

  == domain 10  score: 3.2 bits;  conditional E-value: 0.078
                           DUF5570   19 dspsgrsasarsegstaslwdvsdgqdvhahaivtrtcesvlssavytqgcg 70  
                                         +p g+ + + s+ +t  +wd+ +g+ +   a+ t   + +l  a+  +g  
  gi|386001327|ref|YP_005919626.1|  999 VTPDGQKTVSASDDQTLKVWDLGKGEVI---ATFTA-DGPILCCAIAPDGAT 1046
                                        5899***999***************877...55543.356777777766655 PP

>> APAF1_C  APAF-1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   1.8e-14     2e-11       1      74 [.     453     530 ..     453     548 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.8e-14
                           APAF1_C   1 LqdLHkklveryekkykeeelskl....dkddlywysyleyHlakanlveelkallldldwieakvkltgpsslled 73 
                                       L+ LH +l+e y++ky +++ s+      + d y++++l+ Hl++a++ +el+all+d++wi+ak+  t   sll d
  gi|386001327|ref|YP_005919626.1| 453 LKTLHDQLLESYSAKYLNNSRSPSawaeGPKDGYFFQHLARHLKEAGQEDELRALLFDFNWIKAKLAATDVPSLLVD 529
                                       789************988877664221157899************************************99999999 PP

                           APAF1_C  74 y 74 
                                       y
  gi|386001327|ref|YP_005919626.1| 530 Y 530
                                       9 PP

>> 120_Rick_ant  120 KDa Rickettsia surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.13   1.5e+02      78     116 ..     628     667 ..     621     678 .. 0.83
   2 ?    3.4   0.0     0.033        37      79     113 ..     713     747 ..     701     754 .. 0.83
   3 !    8.1   0.1    0.0012       1.3      78     113 ..     754     789 ..     748     796 .. 0.87
   4 !    9.3   0.1   0.00053      0.59      77     118 ..     795     836 ..     789     841 .. 0.84
   5 ?    4.8   0.0     0.012        13      78     113 ..     838     873 ..     832     881 .. 0.85
   6 !    7.1   0.1    0.0025       2.8      77     116 ..     879     918 ..     873     925 .. 0.84
   7 !    8.6   0.1   0.00083      0.93      78     124 ..     922     968 ..     916     975 .. 0.86
   8 ?    1.5   0.0      0.13   1.4e+02      79     122 ..     965    1008 ..     958    1015 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                      120_Rick_ant  78 qvsavgdlrakvvkndaGeklvdLvetsvktklva.kvdG 116
                                        vsa+ d + kv   + Ge++ +L  +s  +  va + dG
  gi|386001327|ref|YP_005919626.1| 628 AVSASYDNTLKVWDLERGEEIRTLKGHSNWVSAVAvSPDG 667
                                       58999999********************999955515566 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.033
                      120_Rick_ant  79 vsavgdlrakvvkndaGeklvdLvetsvktklvak 113
                                       vs + d + kv   ++Ge++ +L  +s +++ va 
  gi|386001327|ref|YP_005919626.1| 713 VSGSYDNTLKVWDLEKGEEILTLKGHSASVRAVAV 747
                                       56667889999999*****************7774 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0012
                      120_Rick_ant  78 qvsavgdlrakvvkndaGeklvdLvetsvktklvak 113
                                        vsa+gd + kv   ++Ge++ +L  +s ++  va 
  gi|386001327|ref|YP_005919626.1| 754 AVSASGDQTLKVWDLEKGEEILTLKGHSASVSAVAV 789
                                       699***************************997764 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00053
                      120_Rick_ant  77 tqvsavgdlrakvvkndaGeklvdLvetsvktklvakvdGtt 118
                                       + vsa+gd + kv   ++Ge++ +L  +s +++ va     +
  gi|386001327|ref|YP_005919626.1| 795 KAVSASGDQTLKVWDLEKGEEIRTLKGHSASVRAVAVTPDGR 836
                                       5699*****************************888654444 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.012
                      120_Rick_ant  78 qvsavgdlrakvvkndaGeklvdLvetsvktklvak 113
                                        vs++gd + kv   + Ge+l +L  +s  ++ va 
  gi|386001327|ref|YP_005919626.1| 838 AVSSSGDQTLKVWDLERGEELRTLKGHSNWVNAVAV 873
                                       689*************************99997764 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0025
                      120_Rick_ant  77 tqvsavgdlrakvvkndaGeklvdLvetsvktklvakvdG 116
                                       + vs++gd + kv   + Ge+l +L  +s ++  va    
  gi|386001327|ref|YP_005919626.1| 879 KAVSSSGDKTLKVWDLERGEELQTLKGHSASVSAVALTPD 918
                                       5689****************************98886544 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.00083
                      120_Rick_ant  78 qvsavgdlrakvvkndaGeklvdLvetsvktklvakvdGttktitky 124
                                        vs++gd + kv   ++Ge++ +L  +s ++  va     +k i+ +
  gi|386001327|ref|YP_005919626.1| 922 AVSSSGDKTLKVWDLEKGEEIRTLKGHSASVSAVAVTPDGRKAISAC 968
                                       689*****************************999877777777766 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.13
                      120_Rick_ant   79 vsavgdlrakvvkndaGeklvdLvetsvktk.lvakvdGttktit 122 
                                         sa  d + kv   + Ge+l +L  +s  ++ +v   dG +kt++
  gi|386001327|ref|YP_005919626.1|  965 ISACDDRTLKVWDLERGEELRTLKGHSDWVNaVVVTPDG-QKTVS 1008
                                        67888999999999**************99966666666.55655 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.013        15     232     255 ..     627     650 ..     612     656 .. 0.80
   2 ?    1.5   0.0     0.081        91     234     255 ..     671     692 ..     654     695 .. 0.79
   3 ?    1.1   0.0       0.1   1.2e+02     237     253 ..     716     732 ..     701     744 .. 0.83
   4 ?    3.1   0.0     0.026        29     229     253 ..     750     774 ..     736     780 .. 0.75
   5 !    4.7   0.0    0.0088       9.8     225     255 ..     789     818 ..     778     837 .. 0.78
   6 ?    1.7   0.0     0.072        81     233     255 ..     838     860 ..     820     887 .. 0.79
   7 ?    0.5   0.0      0.16   1.8e+02     234     254 ..     881     901 ..     868     906 .. 0.77
   8 ?    1.5   0.0     0.081        91     234     255 ..     923     944 ..     904     949 .. 0.78
   9 !    5.8   0.0     0.004       4.4     225     255 ..     957     986 ..     942     992 .. 0.74
  10 ?    4.0   0.0     0.014        15     228     257 ..    1000    1030 ..     990    1034 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                                       EEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 232 ylfalsrdgkLrvWnlltgkclat 255
                                        ++++s d++L+vW+l+ g  ++t
  gi|386001327|ref|YP_005919626.1| 627 RAVSASYDNTLKVWDLERGEEIRT 650
                                       57899***********98877766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.081
                                       EEEETT-EEEEEETTTTEEEEE CS
                            Nup160 234 falsrdgkLrvWnlltgkclat 255
                                       ++ s d++L+vW+l+ g  ++t
  gi|386001327|ref|YP_005919626.1| 671 LSGSYDNTLKVWDLERGEEIRT 692
                                       55588*********98877665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.1
                                       ETT-EEEEEETTTTEEE CS
                            Nup160 237 srdgkLrvWnlltgkcl 253
                                       s d++L+vW+l+ g  +
  gi|386001327|ref|YP_005919626.1| 716 SYDNTLKVWDLEKGEEI 732
                                       78*********987665 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.026
                                       TTTEEEEEETT-EEEEEETTTTEEE CS
                            Nup160 229 gqtylfalsrdgkLrvWnlltgkcl 253
                                       +   ++++s d++L+vW+l+ g  +
  gi|386001327|ref|YP_005919626.1| 750 DGRKAVSASGDQTLKVWDLEKGEEI 774
                                       666688999**********987655 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0088
                                       ....TTTEEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 225 vveigqtylfalsrdgkLrvWnlltgkclat 255
                                       v+  +   ++++s d++L+vW+l+ g  ++t
  gi|386001327|ref|YP_005919626.1| 789 VTP-DGRKAVSASGDQTLKVWDLEKGEEIRT 818
                                       332.77778999************9988877 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.072
                                       EEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 233 lfalsrdgkLrvWnlltgkclat 255
                                       +++ s d++L+vW+l+ g  l+t
  gi|386001327|ref|YP_005919626.1| 838 AVSSSGDQTLKVWDLERGEELRT 860
                                       666788*********99888777 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 0.16
                                       EEEETT-EEEEEETTTTEEEE CS
                            Nup160 234 falsrdgkLrvWnlltgkcla 254
                                       ++ s d++L+vW+l+ g  l 
  gi|386001327|ref|YP_005919626.1| 881 VSSSGDKTLKVWDLERGEELQ 901
                                       55678*********9876665 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.081
                                       EEEETT-EEEEEETTTTEEEEE CS
                            Nup160 234 falsrdgkLrvWnlltgkclat 255
                                       ++ s d++L+vW+l+ g  ++t
  gi|386001327|ref|YP_005919626.1| 923 VSSSGDKTLKVWDLEKGEEIRT 944
                                       56678*********99887776 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.004
                                       ....TTTEEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 225 vveigqtylfalsrdgkLrvWnlltgkclat 255
                                       v+  +   + +++ d++L+vW+l+ g  l+t
  gi|386001327|ref|YP_005919626.1| 957 VTP-DGRKAISACDDRTLKVWDLERGEELRT 986
                                       333.77778999***********98877766 PP

  == domain 10  score: 4.0 bits;  conditional E-value: 0.014
                                        ..TTTEEEEEETT-EEEEEETTTTEEEEEEE CS
                            Nup160  228 i.gqtylfalsrdgkLrvWnlltgkclatid 257 
                                        + + +  +++s d++L+vW+l  g ++at++
  gi|386001327|ref|YP_005919626.1| 1000 TpDGQKTVSASDDQTLKVWDLGKGEVIATFT 1030
                                        44333445789**********9999999965 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00043      0.49      40      96 ..     618     675 ..     605     678 .. 0.88
   2 !    4.9   0.0    0.0068       7.6      16      93 ..     678     756 ..     676     760 .. 0.84
   3 !    7.0   0.1    0.0016       1.8       9      94 ..     755     841 ..     748     860 .. 0.83
   4 !    5.3   0.0    0.0052       5.8       9      92 ..     881     965 ..     875     968 .. 0.79
   5 ?    1.9   0.0     0.057        64      12      94 ..     968    1050 ..     963    1053 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00043
                                       EEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEE.EEE--TTSEEEEEEE CS
                      Cytochrom_D1  40 srvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnars.vavSqddryvivgnY 96 
                                       ++  ++dgR +  ++ D ++++ DL + e ++++k  +n  s vavS d+r ++ g+Y
  gi|386001327|ref|YP_005919626.1| 618 AVAVSPDGRRAVSASYDNTLKVWDLERGEEIRTLKGHSNWVSaVAVSPDGRRALSGSY 675
                                       567899*****************************999976549*************9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0068
                                       EEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-S.SEEEEEEE--TTSEE CS
                      Cytochrom_D1  16 kvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiG.lnarsvavSqddryv 91 
                                        +++ d ++ e++ +l+++y    ++  ++dgR +   + D ++++ DL + e + ++k      r vav  d+r +
  gi|386001327|ref|YP_005919626.1| 678 TLKVWDLERGEEIRTLKGHYGWVSAVAVSPDGRRAVSGSYDNTLKVWDLEKGEEILTLKGHsASVRAVAVTPDGRKA 754
                                       57788889999***********9999***********************9999777777440455889999999877 PP

                                       EE CS
                      Cytochrom_D1  92 iv 93 
                                       + 
  gi|386001327|ref|YP_005919626.1| 755 VS 756
                                       65 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0016
                                       EEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SS.EEEEEEE CS
                      Cytochrom_D1   9 vverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGl.narsvav 84 
                                       v  +++  +++ d ++ e++ +l+++ a   ++  ++dgR +  ++ D ++++ DL + e ++++k  +   r vav
  gi|386001327|ref|YP_005919626.1| 755 VSASGDQTLKVWDLEKGEEILTLKGHSASVSAVAVTPDGRKAVSASGDQTLKVWDLEKGEEIRTLKGHSaSVRAVAV 831
                                       56678888999999999999999999999999999999999999999999999999999999998855414588899 PP

                                       --TTSEEEEE CS
                      Cytochrom_D1  85 Sqddryvivg 94 
                                         d+r ++ +
  gi|386001327|ref|YP_005919626.1| 832 TPDGRKAVSS 841
                                       9999987765 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0052
                                       EEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEE.EEE CS
                      Cytochrom_D1   9 vverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnars.vav 84 
                                       v  +++  +++ d ++ e+l++l+++ a   ++  ++dgR +   + D ++++ DL + e ++++k  + + s vav
  gi|386001327|ref|YP_005919626.1| 881 VSSSGDKTLKVWDLERGEELQTLKGHSASVSAVALTPDGRKAVSSSGDKTLKVWDLEKGEEIRTLKGHSASVSaVAV 957
                                       56678888899999999999999999999888999999999999999999999999999988888866665543666 PP

                                       --TTSEEE CS
                      Cytochrom_D1  85 Sqddryvi 92 
                                         d+r +i
  gi|386001327|ref|YP_005919626.1| 958 TPDGRKAI 965
                                       67777665 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.057
                                        GGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEEEEE-- CS
                      Cytochrom_D1   12 rdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnarsvavSq 86  
                                         d+  +++ d ++ e+l +l+++ +   ++v ++dg     ++ D ++++ DL + e++a+  + +     a++ 
  gi|386001327|ref|YP_005919626.1|  968 CDDRTLKVWDLERGEELRTLKGHSDWVNAVVVTPDGQKTVSASDDQTLKVWDLGKGEVIATFTADGPILCCAIAP 1042
                                        68889999999***************9******************************999999888888888888 PP

                                        TTSEEEEE CS
                      Cytochrom_D1   87 ddryvivg 94  
                                        d+  +++g
  gi|386001327|ref|YP_005919626.1| 1043 DGATIVAG 1050
                                        88888777 PP

>> Nucleoporin_N  Nup133 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0014       1.6     205     274 ..     617     685 ..     603     717 .. 0.86
   2 ?    0.7   0.0      0.16   1.7e+02     207     274 ..     703     769 ..     698     796 .. 0.60
   3 ?    1.7   0.0     0.074        83     203     273 ..     741     810 ..     729     837 .. 0.66
   4 !    4.8   0.0    0.0088       9.9     201     293 ..     781     877 ..     772     880 .. 0.73
   5 !    6.6   0.0    0.0025       2.9     203     274 ..     825     895 ..     814     922 .. 0.83
   6 !    6.0   0.0    0.0038       4.2     200     273 ..     948    1020 ..     923    1021 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                                       EEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEE CS
                     Nucleoporin_N 205 vqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildis 274
                                        ++++++  r+ +++s + +++v+dl+  ++ ++lk++ ++ ++++ + + + +a + +++++lk++d++
  gi|386001327|ref|YP_005919626.1| 617 NAVAVSPDGRRAVSASYDNTLKVWDLERGEEIRTLKGHSNWVSAVAVS-PDGRRALSGSYDNTLKVWDLE 685
                                       567888888999***************77779*************977.99999999*********9985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                                       EEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEE.EEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEE CS
                     Nucleoporin_N 207 lridssrrilytlsskgvirvydlsasngesslksd.idirqilleaitesliasaplaskslkildis 274
                                       +++++  r+ ++ s + +++v+dl++ ++  +lk++ +++r + +  ++ + +a + +++ +lk++d++
  gi|386001327|ref|YP_005919626.1| 703 VAVSPDGRRAVSGSYDNTLKVWDLEKGEEILTLKGHsASVRAVAV--TPDGRKAVSASGDQTLKVWDLE 769
                                       556666666677777777777777755555555443133333333..3566666666777777777664 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.074
                                       -EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEE CS
                     Nucleoporin_N 203 eivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildi 273
                                       ++ ++++ +  r  +++s + +++v+dl++ ++  +lk++    ++++  ++ + +a + +++ +lk++d+
  gi|386001327|ref|YP_005919626.1| 741 SVRAVAVTPDGRKAVSASGDQTLKVWDLEKGEEILTLKGHSASVSAVAV-TPDGRKAVSASGDQTLKVWDL 810
                                       5666666666677788888888888888855445555544333333332.466666666777777777776 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0088
                                       GG-EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEE.EEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEEES CS
                     Nucleoporin_N 201 reeivqlridssrrilytlsskgvirvydlsasngesslksd.idirqilleaitesliasaplaskslkildispv 276
                                       + ++ ++++ +  r  +++s + +++v+dl++ ++ ++lk++ +++r + +  ++ + +a +++++ +lk++d++  
  gi|386001327|ref|YP_005919626.1| 781 SASVSAVAVTPDGRKAVSASGDQTLKVWDLEKGEEIRTLKGHsASVRAVAV--TPDGRKAVSSSGDQTLKVWDLERG 855
                                       556777888888899999*************77766666654155555555..589999999999999***999765 PP

                                       -TT.....TSSCEEEEEEECSS CS
                     Nucleoporin_N 277 sae.....essllhlvaitsng 293
                                       ++      +s+++ +va+t +g
  gi|386001327|ref|YP_005919626.1| 856 EELrtlkgHSNWVNAVAVTPDG 877
                                       5545555567777777777666 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0025
                                       -EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEE CS
                     Nucleoporin_N 203 eivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildis 274
                                       ++ ++++ +  r  ++ s + +++v+dl+  ++ ++lk++ ++ ++++ + + + +a +++++k+lk++d++
  gi|386001327|ref|YP_005919626.1| 825 SVRAVAVTPDGRKAVSSSGDQTLKVWDLERGEELRTLKGHSNWVNAVAVT-PDGRKAVSSSGDKTLKVWDLE 895
                                       566666777777888889999********66669**************88.999999999*********985 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.0038
                                        -GG-EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEE CS
                     Nucleoporin_N  200 ereeivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildi 273 
                                         + ++ ++++ +  r  +++  +++++v+dl+  ++ ++lk++ d+ ++++ + + + ++ + + + +lk++d+
  gi|386001327|ref|YP_005919626.1|  948 HSASVSAVAVTPDGRKAISACDDRTLKVWDLERGEELRTLKGHSDWVNAVVVT-PDGQKTVSASDDQTLKVWDL 1020
                                        556677888888889999**************66669**************88.66666666788888888875 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.077        86      15      24 ..     620     629 ..     613     635 .. 0.87
   2 ?    2.4   0.0      0.14   1.5e+02      15      23 ..     662     670 ..     656     671 .. 0.85
   3 ?    3.4   0.0     0.071        79      13      23 ..     702     712 ..     696     713 .. 0.81
   4 ?   -0.6   0.0       1.2   1.3e+03      15      23 ..     746     754 ..     742     755 .. 0.82
   5 ?   -0.6   0.0       1.2   1.4e+03      15      23 ..     788     796 ..     784     797 .. 0.82
   6 ?   -0.3   0.0         1   1.1e+03      15      24 ..     830     839 ..     825     842 .. 0.84
   7 ?   -0.5   0.0       1.1   1.3e+03      15      24 ..     872     881 ..     869     884 .. 0.83
   8 ?   -0.4   0.0       1.1   1.2e+03      15      24 ..     914     923 ..     910     926 .. 0.83
   9 ?   -0.8   0.0       1.4   1.6e+03      15      23 ..     956     964 ..     952     965 .. 0.82
  10 ?   -3.3   0.0       8.7   9.8e+03      15      24 ..    1039    1048 ..    1031    1048 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.077
                                       EE-TTSSEEE CS
                              PD40  15 sfSPDGkrla 24 
                                       ++SPDG+r +
  gi|386001327|ref|YP_005919626.1| 620 AVSPDGRRAV 629
                                       89*****986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                                       EE-TTSSEE CS
                              PD40  15 sfSPDGkrl 23 
                                       ++SPDG+r 
  gi|386001327|ref|YP_005919626.1| 662 AVSPDGRRA 670
                                       89*****96 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.071
                                       EEEE-TTSSEE CS
                              PD40  13 aPsfSPDGkrl 23 
                                       a ++SPDG+r 
  gi|386001327|ref|YP_005919626.1| 702 AVAVSPDGRRA 712
                                       5689*****97 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.2
                                       EE-TTSSEE CS
                              PD40  15 sfSPDGkrl 23 
                                       +++PDG++ 
  gi|386001327|ref|YP_005919626.1| 746 AVTPDGRKA 754
                                       789****97 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.2
                                       EE-TTSSEE CS
                              PD40  15 sfSPDGkrl 23 
                                       +++PDG++ 
  gi|386001327|ref|YP_005919626.1| 788 AVTPDGRKA 796
                                       789****97 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1
                                       EE-TTSSEEE CS
                              PD40  15 sfSPDGkrla 24 
                                       +++PDG++ +
  gi|386001327|ref|YP_005919626.1| 830 AVTPDGRKAV 839
                                       789****975 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 1.1
                                       EE-TTSSEEE CS
                              PD40  15 sfSPDGkrla 24 
                                       +++PDG++ +
  gi|386001327|ref|YP_005919626.1| 872 AVTPDGRKAV 881
                                       789****975 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 1.1
                                       EE-TTSSEEE CS
                              PD40  15 sfSPDGkrla 24 
                                       +++PDG++ +
  gi|386001327|ref|YP_005919626.1| 914 ALTPDGRKAV 923
                                       789****975 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 1.4
                                       EE-TTSSEE CS
                              PD40  15 sfSPDGkrl 23 
                                       +++PDG++ 
  gi|386001327|ref|YP_005919626.1| 956 AVTPDGRKA 964
                                       789****86 PP

  == domain 10  score: -3.3 bits;  conditional E-value: 8.7
                                        EE-TTSSEEE CS
                              PD40   15 sfSPDGkrla 24  
                                        ++ PDG +++
  gi|386001327|ref|YP_005919626.1| 1039 AIAPDGATIV 1048
                                        789***8875 PP

>> RBB1NT  RBB1NT (NUC162) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.22   2.4e+02      18      44 ..     611     637 ..     606     639 .. 0.85
   2 ?    1.4   0.0      0.32   3.5e+02      17      43 ..     652     678 ..     638     681 .. 0.80
   3 ?   -0.7   0.0       1.4   1.6e+03      19      43 ..     696     720 ..     674     723 .. 0.80
   4 ?    1.9   0.0      0.22   2.5e+02      17      44 ..     862     889 ..     824     891 .. 0.85
   5 !    9.3   0.0    0.0011       1.2      17      44 ..     988    1015 ..     968    1017 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.22
                            RBB1NT  18 kkkswfpaLvvsPscqddvtvkkdeil 44 
                                        ++sw+ a+ vsP+    v+   d+ l
  gi|386001327|ref|YP_005919626.1| 611 GHSSWVNAVAVSPDGRRAVSASYDNTL 637
                                       5789***********999999887765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                            RBB1NT  17 kkkkswfpaLvvsPscqddvtvkkdei 43 
                                       k +++w+ a+ vsP+    ++   d+ 
  gi|386001327|ref|YP_005919626.1| 652 KGHSNWVSAVAVSPDGRRALSGSYDNT 678
                                       45789**********998887776665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                            RBB1NT  19 kkswfpaLvvsPscqddvtvkkdei 43 
                                       +  w+ a+ vsP+    v+   d+ 
  gi|386001327|ref|YP_005919626.1| 696 HYGWVSAVAVSPDGRRAVSGSYDNT 720
                                       557**********999988877765 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.22
                            RBB1NT  17 kkkkswfpaLvvsPscqddvtvkkdeil 44 
                                       k +++w+ a+ v+P+  + v+   d+ l
  gi|386001327|ref|YP_005919626.1| 862 KGHSNWVNAVAVTPDGRKAVSSSGDKTL 889
                                       46789***********999998877765 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0011
                            RBB1NT   17 kkkkswfpaLvvsPscqddvtvkkdeil 44  
                                        k +++w+ a+vv+P+ q++v+  +d+ l
  gi|386001327|ref|YP_005919626.1|  988 KGHSDWVNAVVVTPDGQKTVSASDDQTL 1015
                                        36789********************987 PP

>> WYL_2  WYL_2, Sm-like SH3 beta-barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.99   1.1e+03      49      64 ..     631     646 ..     607     654 .. 0.83
   2 ?    0.2   0.0      0.89   9.9e+02      46      64 ..     670     688 ..     646     694 .. 0.69
   3 ?    0.8   0.0      0.56   6.3e+02      40      64 ..     706     730 ..     689     731 .. 0.64
   4 ?    0.1   0.0      0.94   1.1e+03      48      64 ..     756     772 ..     735     773 .. 0.80
   5 ?    0.2   0.0      0.87   9.8e+02      46      64 ..     796     814 ..     776     815 .. 0.78
   6 ?    2.0   0.0      0.25   2.8e+02      24      64 ..     816     856 ..     813     862 .. 0.80
   7 ?    0.4   0.0      0.75   8.5e+02      40      64 ..     874     898 ..     857     902 .. 0.71
   8 ?    1.0   0.0      0.49   5.5e+02      43      64 ..     919     940 ..     899     946 .. 0.75
   9 ?    1.7   0.0      0.31   3.4e+02      24      64 ..     942     982 ..     940     988 .. 0.82
  10 ?   -1.7   0.0       3.5   3.9e+03      44      63 ..    1004    1023 ..     983    1024 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.99
                             WYL_2  49 kknkstvvYfDlekqg 64 
                                        + ++t+ ++Dle+++
  gi|386001327|ref|YP_005919626.1| 631 ASYDNTLKVWDLERGE 646
                                       567899*******986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.89
                             WYL_2  46 ykrkknkstvvYfDlekqg 64 
                                         + + ++t+ ++Dle+++
  gi|386001327|ref|YP_005919626.1| 670 ALSGSYDNTLKVWDLERGE 688
                                       55566789********986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.56
                             WYL_2  40 kefkgkykrkknkstvvYfDlekqg 64 
                                       +  ++   + + ++t+ ++Dlek++
  gi|386001327|ref|YP_005919626.1| 706 SPDGRRAVSGSYDNTLKVWDLEKGE 730
                                       55555566667889********986 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.94
                             WYL_2  48 rkknkstvvYfDlekqg 64 
                                       + + ++t+ ++Dlek++
  gi|386001327|ref|YP_005919626.1| 756 SASGDQTLKVWDLEKGE 772
                                       5667899*******986 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.87
                             WYL_2  46 ykrkknkstvvYfDlekqg 64 
                                         + + ++t+ ++Dlek++
  gi|386001327|ref|YP_005919626.1| 796 AVSASGDQTLKVWDLEKGE 814
                                       556677899*******986 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.25
                             WYL_2  24 irlakGtlkedlipaekefkgkykrkknkstvvYfDlekqg 64 
                                       ir+ kG+ ++  + a +  ++k  +++ ++t+ ++Dle+++
  gi|386001327|ref|YP_005919626.1| 816 IRTLKGHSASVRAVAVTPDGRKAVSSSGDQTLKVWDLERGE 856
                                       77777777666666667788888899999*********986 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.75
                             WYL_2  40 kefkgkykrkknkstvvYfDlekqg 64 
                                       +  ++k  +++ ++t+ ++Dle+++
  gi|386001327|ref|YP_005919626.1| 874 TPDGRKAVSSSGDKTLKVWDLERGE 898
                                       45566777788899********986 PP

  == domain 8  score: 1.0 bits;  conditional E-value: 0.49
                             WYL_2  43 kgkykrkknkstvvYfDlekqg 64 
                                       ++k  +++ ++t+ ++Dlek++
  gi|386001327|ref|YP_005919626.1| 919 GRKAVSSSGDKTLKVWDLEKGE 940
                                       55666777899********986 PP

  == domain 9  score: 1.7 bits;  conditional E-value: 0.31
                             WYL_2  24 irlakGtlkedlipaekefkgkykrkknkstvvYfDlekqg 64 
                                       ir+ kG+ ++  + a +  ++k  +  ++ t+ ++Dle+++
  gi|386001327|ref|YP_005919626.1| 942 IRTLKGHSASVSAVAVTPDGRKAISACDDRTLKVWDLERGE 982
                                       78888888777777778888999999999*********986 PP

  == domain 10  score: -1.7 bits;  conditional E-value: 3.5
                             WYL_2   44 gkykrkknkstvvYfDlekq 63  
                                        +k  + ++++t+ ++Dl k+
  gi|386001327|ref|YP_005919626.1| 1004 QKTVSASDDQTLKVWDLGKG 1023
                                        5566678899******9986 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.47   5.3e+02       6      78 ..     619     692 ..     616     696 .. 0.68
   2 !    6.7   0.0    0.0036         4       5      91 ..     702     790 ..     699     793 .. 0.84
   3 ?    0.9   0.0       0.2   2.3e+02       6      78 ..     787     860 ..     782     876 .. 0.80
   4 ?    2.0   0.0     0.093     1e+02       6      91 ..     871     958 ..     866     961 .. 0.80
   5 ?    4.7   0.0     0.014        16       6     110 ..     955    1062 ..     950    1064 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.47
                         WD40_like   6 idiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillslleneeeven 78 
                                       + +s++g   +  + d++++v +le +e++  +++ ++ v  v +  d    l ++ D t+   +le +ee+++
  gi|386001327|ref|YP_005919626.1| 619 VAVSPDGRRAVSASYDNTLKVWDLERGEEIRTLKGHSNWVSAVAVSPDGrRALSGSYDNTLKVWDLERGEEIRT 692
                                       55666666666667777777788888887777777777777776654433777777777777777777777765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0036
                         WD40_like   5 sidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillslleneeevenek 80 
                                       ++ +s++g   + G+ d++++v +le +e++  +++ + Sv  v +  d  + + ++ D t+   +le++ee+ + k
  gi|386001327|ref|YP_005919626.1| 702 AVAVSPDGRRAVSGSYDNTLKVWDLEKGEEILTLKGHSASVRAVAVTPDGrKAVSASGDQTLKVWDLEKGEEILTLK 778
                                       68899999999********************************99987665899999************99876655 PP

                         WD40_like  81 .ieedistvkvi 91 
                                            +s v v+
  gi|386001327|ref|YP_005919626.1| 779 gHSASVSAVAVT 790
                                       144556666665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.2
                         WD40_like   6 idiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillslleneeeven 78 
                                       + + ++g   +  + d++++v +le +e++  +++ + Sv  v +  d  + +  + D t+   +le +ee ++
  gi|386001327|ref|YP_005919626.1| 787 VAVTPDGRKAVSASGDQTLKVWDLEKGEEIRTLKGHSASVRAVAVTPDGrKAVSSSGDQTLKVWDLERGEELRT 860
                                       666677777777899*************************9998886654777778888888888888887766 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.093
                         WD40_like   6 idiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillslleneeeveneki 81 
                                       + + ++g   +  + d++++v +le +e+ + +++ + Sv  v l  d  + +  + D t+   +le++ee+++ k 
  gi|386001327|ref|YP_005919626.1| 871 VAVTPDGRKAVSSSGDKTLKVWDLERGEELQTLKGHSASVSAVALTPDGrKAVSSSGDKTLKVWDLEKGEEIRTLKG 947
                                       556666777777789999***********************999987764788888999**999******9998775 PP

                         WD40_like  82 e.edistvkvi 91 
                                       +   +s v v+
  gi|386001327|ref|YP_005919626.1| 948 HsASVSAVAVT 958
                                       41456766665 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.014
                         WD40_like    6 idiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkll.dddlilvvtlDGtillslleneeevene 79  
                                        + + ++g   +   +d +++v +le +e+   +++ +d v  v +  d+++ + ++ D t+   +l ++e++ + 
  gi|386001327|ref|YP_005919626.1|  955 VAVTPDGRKAISACDDRTLKVWDLERGEELRTLKGHSDWVNAVVVTpDGQKTVSASDDQTLKVWDLGKGEVIATF 1029
                                        556666666777788999**********************988776255699999999***************** PP

                         WD40_like   80 kieedistvkvidd..klliGtnkGsiyvfskd 110 
                                          +  i ++ +  d   ++ G + G i+++  +
  gi|386001327|ref|YP_005919626.1| 1030 TADGPILCCAIAPDgaTIVAGESSGRIHLLRLE 1062
                                        ******99987654227899********98765 PP

>> HIRA_B  HIRA B motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.22   2.5e+02       4      12 ..     745     753 ..     744     755 .. 0.91
   2 ?    2.0   0.0      0.17   1.9e+02       4      12 ..     787     795 ..     785     797 .. 0.89
   3 ?    1.7   0.0      0.22   2.5e+02       4      12 ..     829     837 ..     828     839 .. 0.91
   4 ?    1.7   0.0      0.22   2.5e+02       4      12 ..     871     879 ..     870     881 .. 0.91
   5 ?   -2.3   0.0       3.8   4.3e+03       7      12 ..     916     921 ..     913     921 .. 0.88
   6 ?    2.0   0.0      0.17   1.9e+02       4      12 ..     955     963 ..     953     965 .. 0.89
   7 ?   -2.7   0.1       5.2   5.8e+03       4      10 ..     997    1003 ..     997    1005 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG+K
  gi|386001327|ref|YP_005919626.1| 745 VAVTPDGRK 753
                                       789*****9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG+K
  gi|386001327|ref|YP_005919626.1| 787 VAVTPDGRK 795
                                       88******9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.22
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG+K
  gi|386001327|ref|YP_005919626.1| 829 VAVTPDGRK 837
                                       789*****9 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.22
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG+K
  gi|386001327|ref|YP_005919626.1| 871 VAVTPDGRK 879
                                       789*****9 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 3.8
                            HIRA_B   7 tKdGKK 12 
                                       t+dG+K
  gi|386001327|ref|YP_005919626.1| 916 TPDGRK 921
                                       99***9 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.17
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG+K
  gi|386001327|ref|YP_005919626.1| 955 VAVTPDGRK 963
                                       88******9 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 5.2
                            HIRA_B    4 vTitKdG 10  
                                        v++t+dG
  gi|386001327|ref|YP_005919626.1|  997 VVVTPDG 1003
                                        789***9 PP

>> DUF2378  Protein of unknown function (DUF2378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027       0.3      22      63 ..     342     383 ..     327     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                           DUF2378  22 eelaerlraagldldrplfsaYPlevflrllrvaarelapql 63 
                                         + erl++a l++ r +f++YP  ++l++++v +++l+p++
  gi|386001327|ref|YP_005919626.1| 342 TVALERLQNADLEKIREQFPDYPYPDLLKAIQVSVDALEPEF 383
                                       55789***********************************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00088      0.99      26      51 ..     161     186 ..     137     390 .. 0.87
   2 ?   -1.9   0.1       3.3   3.7e+03      92     149 ..     451     516 ..     419     529 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00088
                            AAA_16  26 lvllsGesGvGKsslvrellralekd 51 
                                        v l+G+ G+GKs ++ +++r  e++
  gi|386001327|ref|YP_005919626.1| 161 KVGLHGMGGIGKSVMAAAVARDEETQ 186
                                       5679****************977766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                            AAA_16  92 aeleawrekleeala.........avpelagaea..srllellkrllallsrderplvlvlDdlqwade 149
                                        +l   +++l+e+++         +++ ++g  +    ++++l+r+l+ + ++++   l++D + w+++
  gi|386001327|ref|YP_005919626.1| 451 GDLKTLHDQLLESYSakylnnsrsPSAWAEG--PkdGYFFQHLARHLKEAGQEDELRALLFD-FNWIKA 516
                                       4455555666666666665554332222222..13366888888888766665554666665.777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1065 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.79u 0.26s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 6736.95
//
Query:       gi|386001328|ref|YP_005919627.1|  [L=355]
Description: family 7 extracellular solute-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-39  134.5   0.0    5.5e-39  134.2   0.0    1.1  1  DctP      Bacterial extracellular solute-binding protein, fam


Domain annotation for each model (and alignments):
>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.0     3e-43   5.5e-39      16     283 ..      56     319 ..      40     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 3e-43
                                       HHHHHHHHHHTTTSEEEEEEETTTTTTHHHHHHHHHTTSSSEEEEEGGGGTTTSGGGGGGGSTTTSCSHHHHHHHHH CS
                              DctP  16 ekfaklveektnGkvkievypssqLggdeeviealknGtvdivatssakleglvpeigvldlPFlfedeealkkvle 92 
                                           +++ee+++G++++++++ + Lg+  +  e + +G+ d++++ ++ + g +p   vl+lP  +e +e ++++  
  gi|386001328|ref|YP_005919627.1|  56 LPVLQALEERSGGRISCNLFDVGALGSGPDHYEIVASGRSDMGYATLTWTPGRFPLSDVLSLPATIEGKETATEIGR 132
                                       5667899********************************************************************** PP

                                       SHHHHHHHHHHHHHTEEEEEEEEEEEEEEEESSS--SSGGGGTTEEEEETSSHHHHHHHHHHTSEEEE-TGGGHHHH CS
                              DctP  93 gevgekllkslekkglkvLafwenGfrqftsnkkpinspeDlkglklRvpessvllevfkalGanptpipfgevyta 169
                                         +g++l+ +++  g+kvL++      ++ +n  p++++eD+ gl++R+p  +++ ++++alGa+p+ ip+  v  a
  gi|386001328|ref|YP_005919627.1| 133 AVYGRALRGEFA--GVKVLEVNPCVNSHLWTN-EPVETIEDVAGLRIRTP-GGLQTRCIEALGAVPVFIPLDAVRVA 205
                                       ********9986..67*****88888888886.9****************.9************************* PP

                                       HHTTSSSEEEEEHHHHHHTTGGGG-SEEEEEEEEEEEEEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              DctP 170 LqtgvvDGqenplsniysqklyevqkyltltnhgyldllvlvnkktwdsLpedlqaileeaakeatelqrklveele 246
                                       +++g++DG  +  s+i+  +l+ v+++ tl   g  +  +++n++ w++ pedl+ i+ee +++  +      + + 
  gi|386001328|ref|YP_005919627.1| 206 MENGTIDGIVTCPSMIQPFGLDGVARHCTLVTFGCVGEGLFMNQDAWERTPEDLKGIIEEVCENPYRTTGGMTKGTY 282
                                       ***************************************************************************** PP

                                       HHHHHHHHHTTSEEEEGEHHHHHHHHHHHHHHHHHHH CS
                              DctP 247 eealqklkeagvevieltpedlaafrealkpvykeif 283
                                       ++++++l e+gv++++l pe+ a + +a+ +v++e +
  gi|386001328|ref|YP_005919627.1| 283 DSIIAELNESGVVFTSLPPEEEARWHAAFSNVTREWV 319
                                       *********************************9955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2341.44
//
Query:       gi|386001329|ref|YP_005919628.1|  [L=559]
Description: hypothetical protein Mhar_0627 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 4152.08
//
Query:       gi|386001330|ref|YP_005919629.1|  [L=441]
Description: xanthine/uracil/vitamin C permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  110.0  27.0    1.4e-31  109.6  27.0    1.0  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
       0.91    8.5   8.7          2    7.4   8.7    1.6  1  FUSC-like        FUSC-like inner membrane protein yccS


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6  27.0   1.5e-35   1.4e-31       3     386 ..      21     397 ..      19     399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.5e-35
                                       HHHHHHHHHHHHHHHHHHHHHTTTS-.........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHGGG CS
                   Xan_ur_permease   3 llllglQhllamfaalvvvPllvgdalglaeelrqlisatllasGiatllqllifgirlpillgssfafvtalmial 79 
                                       + l+g + +la ++ ++v+P ++++a gl  +   + +at ++s+ +++l+ ++++ ++ ++ g+s +++ a++++ 
  gi|386001330|ref|YP_005919629.1|  21 EALAGATAFLATMYIILVNPAVLSEA-GL--PYGAVLTATVVVSAFSSILMGVYAKNPIVVAPGMSINYLFAYTVVE 94 
                                       6799**********************.44..5669************************************898888 PP

                                       -....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BTT.B-- CS
                   Xan_ur_permease  80 GsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaavegltvv 156
                                        +     +  +++lg+++ ag +f+l+ l+  ++ + ++ pP+  +++  +iGl++a+ +++++g +    +g  v+
  gi|386001330|ref|YP_005919629.1|  95 VE----AVPWETALGCVFWAGAIFLLLTLLDRKKLILEAVPPMLRYGFAGGIGLFIASLGFQSAGFVLPLESG--VM 165
                                       85....77788889***************************************************99644555..77 PP

                                       -HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHH.HTTSSHH.HHS-SS-----------HH... CS
                   Xan_ur_permease 157 slkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmg.ivnlspe.vseapwfqlpsplkfgtpl... 228
                                           + +a  + l++++++ +l+   +++++ +gi a++lla+ m   + + p  + + +w+++++ l +   l   
  gi|386001330|ref|YP_005919629.1| 166 GWGKINAATLTFLAGFIFTAVLMVRRVRGSLILGIGATALLAWGMEaALGMGPPsIASGWWASPDFSLLLRLDLwgp 242
                                       778889999999**********************************9888887558888999988766666665778 PP

                                       ..H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TII..IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHH CS
                   Xan_ur_permease 229 fnlgliltvlavalvavvesvGdiravakvvgrslkp..kpdlrralladGlatllsgllGalpvttyaeniGvval 303
                                       + ++l +++++++   +++s+++  +v +  ++ +++  + +l+r+l a+ l+++ s++lG++p+t+y+e++++v+ 
  gi|386001330|ref|YP_005919629.1| 243 LRIALWPIIFVFLSSCLFDSLATCVGVCEAGNLIDEEgdPRNLGRSLKANALGVIASAFLGTSPATCYVESAAGVQE 319
                                       7777777777777778899999999998888877766779************************************* PP

                                       HTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHHHHH CS
                   Xan_ur_permease 304 tkvasrrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavslvlG 380
                                       +    +r+++ a v  +l+  + +l++ll+++P  + +++ lv++g+ ++  +  + +++ld+a   ++  + + l+
  gi|386001330|ref|YP_005919629.1| 320 G----GRTGLSAVVAGLLFLPFLFLSPLLALVPPLA-TAPVLVLVGVFMLRPLVRVRWERLDDAIPFFLAMFLMPLT 391
                                       *....****************************888.**************************************** PP

                                       HH---- CS
                   Xan_ur_permease 381 lgvatv 386
                                        +++++
  gi|386001330|ref|YP_005919629.1| 392 YSITQG 397
                                       999876 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   8.7   0.00022         2      13      84 ..      41     114 ..      29     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00022
                         FUSC-like  13 slivqlllpypwlfvlglllstflftmlgalGqryatiafatLlvaiytmlgasqepeiwqqpllll..lGalw 84 
                                       +++ +  lpy+ ++++++++s+f+ +++g++ ++   +a+++ +  +++   ++ e + w+ +l ++  +Ga++
  gi|386001330|ref|YP_005919629.1|  41 AVLSEAGLPYGAVLTATVVVSAFSSILMGVYAKNPIVVAPGMSINYLFAYTVVEVEAVPWETALGCVfwAGAIF 114
                                       56678889************************************999999999977888999885541156665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 3031.01
//
Query:       gi|386001331|ref|YP_005919630.1|  [L=580]
Description: adenine deaminase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-67  226.0   0.4      1e-66  223.5   0.3    2.2  3  Adenine_deam_C  Adenine deaminase C-terminal domain
    1.4e-21   77.2   0.2    1.2e-19   70.9   0.2    2.4  1  Amidohydro_1    Amidohydrolase family
    3.2e-11   43.4   2.8    6.6e-06   25.9   0.2    2.3  2  Amidohydro_3    Amidohydrolase family


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.81   4.8e+03     136     163 ..     295     322 ..     281     323 .. 0.76
   2 ?   -0.9   0.0      0.16   9.3e+02      87     105 ..     345     361 ..     339     372 .. 0.80
   3 !  223.5   0.3   1.7e-70     1e-66       1     168 [.     400     567 ..     400     568 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.81
                                       TTTBSGGGGGSTT-TTSSSEEEETTSEE CS
                    Adenine_deam_C 136 kledpfmtlsflalpviPelkltdkGlv 163
                                          dp++++s+ +l    ++ l+d+G v
  gi|386001331|ref|YP_005919630.1| 295 AGLDPVVAISIGSLNAAEYFGLSDRGAV 322
                                       4678999999999999999999999976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.16
                                       TTSEEEEEETTEEEEEEE- CS
                    Adenine_deam_C  87 lgGGivvvedgkvlaelpL 105
                                       l+GG vv+e+g+++   pL
  gi|386001331|ref|YP_005919630.1| 345 LKGGAVVAEGGRMIV--PL 361
                                       79******9998654..44 PP

  == domain 3  score: 223.5 bits;  conditional E-value: 1.7e-70
                                       .SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHH CS
                    Adenine_deam_C   1 qliTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedm 77 
                                       q+iT++l ++ +v+ g+vv+dl++dll++avveRh++tgnvg+g+v+gfgl +gAiA+svahDshni +vG++ e++
  gi|386001331|ref|YP_005919630.1| 400 QIITRSLLARPKVEGGKVVCDLDSDLLEMAVVERHRGTGNVGLGLVSGFGLLRGAIATSVAHDSHNIAAVGVSSEEI 476
                                       79*************************************************************************** PP

                                       HHHHHHHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSS CS
                    Adenine_deam_C  78 alAvnrvielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPe 154
                                       ++Av +v+++gGG+vvv++g v a+l+LpiaGl+Sd+++eevaek+ee++ a+k+lg+ l+dpfmtlsfl+lpviPe
  gi|386001331|ref|YP_005919630.1| 477 FAAVSAVAKMGGGLVVVDGGIVAASLSLPIAGLLSDRSMEEVAEKIEEVTGAAKSLGSALDDPFMTLSFLCLPVIPE 553
                                       **************************************************88888********************** PP

                                       EEEETTSEEETTTT CS
                    Adenine_deam_C 155 lkltdkGlvdvkkf 168
                                       lkltd+Glvdv++f
  gi|386001331|ref|YP_005919630.1| 554 LKLTDRGLVDVTRF 567
                                       ***********998 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.2     2e-23   1.2e-19       2     344 .]      64     351 ..      63     351 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 2e-23
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEE CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglr 78 
                                       + PG+ID HvHle+ ++         + pe+a++++ +g+++ + +++++++  ga    gi+ ++ + ++ pl ++
  gi|386001331|ref|YP_005919630.1|  64 LAPGFIDGHVHLESAMV---------TVPEYARAVVPRGTTAIVADPHEIANVLGAE---GIRYIIASGRSSPLSVY 128
                                       78***********8887.........99****************************7...88888888888999*** PP

                                       EEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHH.....HHHHHTTEEE CS
                      Amidohydro_1  79 ilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealk.....eakkrdlpva 149
                                       ++++++++++    + ++s   l+ag a +++++++gv+   +++ ++ + f d  + + +        + +   ++
  gi|386001331|ref|YP_005919630.1| 129 VMLPSCVPAT----HLETSGSSLDAG-ALSELIDEEGVLGiGEVMNYPGVIFRDPSVLAKIClagmrRKDGHRPRID 200
                                       ********84....444555555555.456677888889999999999999988844443331233245555678** PP

                                       EEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHH CS
                      Amidohydro_1 150 iHa..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsi 224
                                        H   l+ +   +++  ++g+++e+++  e           k  l  g+ ++                      +  
  gi|386001331|ref|YP_005919630.1| 201 GHSplLSGRDLAAYVAVGIGSDHECTSSEEA----------KEKLRLGMRIMIR--------------------EGT 247
                                       *****9999999*************999999..........4459999999966....................344 PP

                                       SEHHHHHHHHHHHH.TSC.EEEEEECT........TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTH CS
                      Amidohydro_1 225 lrsgrealrkalde.Gvk.vglgtDga........asgnslnlleelrlalklqrgllyedeegglslkealrmaTi 291
                                        ++++++l ++++e +++ + +++D+         ++++s+     +r a+            +gl++  a+++ ++
  gi|386001331|ref|YP_005919630.1| 248 AAKNLDDLLPLVTEaNARrFLFVSDDRhpsdilrqGHIDSM-----VRRAV-----------GAGLDPVVAISIGSL 308
                                       79************99999******7767777665555555.....77777...........899************ PP

                                       HHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 292 ngAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                       n+A+++gl+ + G++++G++AD+vv+          + +  nv+kv ++G +v
  gi|386001331|ref|YP_005919630.1| 309 NAAEYFGLS-DRGAVAPGRRADIVVL---------DDLDGLNVQKVLKGGAVV 351
                                       ********7.99**************.........999999999999999776 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   1.1e-09   6.6e-06       1      27 [.      55      81 ..      55     102 .. 0.82
   2 !   17.6   0.2   3.6e-07    0.0021     418     453 ..     307     342 ..     296     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-09
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvn 27
                                      e+iD++Gr+++PGF+D H Hl ++ v 
  gi|386001331|ref|YP_005919630.1| 55 ETIDLSGRVLAPGFIDGHVHLESAMVT 81
                                      79******************7766544 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.6e-07
                      Amidohydro_3 418 TrgpAkalgledrkGtLevGadADlvvld.adpldvd 453
                                       + ++A+ +gl+dr G +++G +AD+vvld  d l v+
  gi|386001331|ref|YP_005919630.1| 307 SLNAAEYFGLSDR-GAVAPGRRADIVVLDdLDGLNVQ 342
                                       6799********9.**************944444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3487.24
//
Query:       gi|386001332|ref|YP_005919631.1|  [L=382]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-20   73.1   0.1    2.8e-19   70.1   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
    1.4e-10   41.2   0.2    3.5e-10   40.0   0.1    1.7  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.011   15.9   0.1      0.022   14.9   0.1    1.5  1  DUF2802      Protein of unknown function (DUF2802)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.094   5.6e+02      30      73 ..      56      96 ..      44     142 .. 0.75
   2 !   70.1   0.0   4.7e-23   2.8e-19       2     163 ..     156     320 ..     155     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.094
                                      HHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 30 sveeileevkelkaekgvkevilgggepllypdfvellerlakl 73
                                      + ee+ +ev   k    + + + gg +p+++p+++   + ++ +
  gi|386001332|ref|YP_005919631.1| 56 QAEEVYREVAGSK--V-KAVYVAGGPHPSARPEEALRHFDYVVI 96
                                      5667777775554..2.556666677888888887777766555 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 4.7e-23
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +++rgC+ +C +C++p     ++r r++s+  il+ ++ ++  +    + +  g++ +  + d+ve l+++      
  gi|386001332|ref|YP_005919631.1| 156 EISRGCPWGCAYCQTPCL--FGRRMRHRSIPVILRYARCYSdLRFTsPNALAYGSDGVHPRIDKVERLLAALSD--L 228
                                       689*************97..********************9666666667777766677778888888888887..4 PP

                                       TEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEE CS
                                       xxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvd 147
                                       g  i + t +  ++     ee +e+l++     ++s+g ++++d+ +lk+++rgh++e+v +a+++  +ag+ ++vd
  gi|386001332|ref|YP_005919631.1| 229 GKPIYFGTFPSEVRpdfvtEEAVELLARHCtNRTISIGGQSGSDR-ILKMVGRGHDVEAVRRACDLSLAAGLVPNVD 304
                                       6666666665555555************88999************.*************************999*** PP

                                       EEEEBTTTSHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 148 rivglpGendeeleel 163
                                        ivglpGe+ e+   +
  gi|386001332|ref|YP_005919631.1| 305 LIVGLPGETAEDQALT 320
                                       ***********95555 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   5.8e-14   3.5e-10      61     120 ..      50     106 ..      44     107 .. 0.89
   2 ?   -3.0   0.0       1.2   7.1e+03      66      89 ..     285     310 ..     281     332 .. 0.61

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.8e-14
                       B12-binding  61 ltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       ++   ++++e+ +++++ + ++  v+GG+hps+ pee l+   ++d+vv+gege++l++l
  gi|386001332|ref|YP_005919631.1|  50 YSFATAQAEEVYREVAGSKVKAVYVAGGPHPSARPEEALR---HFDYVVIGEGEETLPEL 106
                                       5666778999999999999******************887...59*************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                       B12-binding  66 eavkelvel..lkrirprvkvvvGGa 89 
                                       eav++ ++l  +++  p+v ++vG +
  gi|386001332|ref|YP_005919631.1| 285 EAVRRACDLslAAGLVPNVDLIVGLP 310
                                       55666666666777777777777644 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.7e-06     0.022      34      58 ..     272     296 ..     248     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                           DUF2802  34 sqAiklvrqGasveelaeecgLsra 58 
                                       ++ +k+v++G +ve + ++c+Ls a
  gi|386001332|ref|YP_005919631.1| 272 DRILKMVGRGHDVEAVRRACDLSLA 296
                                       5789*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2463.96
//
Query:       gi|386001333|ref|YP_005919632.1|  [L=112]
Description: hypothetical protein Mhar_0631 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 693.55
//
Query:       gi|386001334|ref|YP_005919633.1|  [L=215]
Description: Nitrogen-fixing NifU domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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  154.7   0.1    1.9e-45  154.2   0.1    1.3  1  NifU_N          NifU-like N terminal domain
    1.1e-06   28.8   1.8    2.7e-06   27.4   1.0    2.1  2  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.1   2.1e-49   1.9e-45       2     126 ..       6     127 ..       5     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 2.1e-49
                                       SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHT CS
                            NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvk 78 
                                       y++kvldh+knPrn G +e++d   +++ vg+ acGD+v+L++kv+ et++ied+kF++fGC++ iAs+s+ tel k
  gi|386001334|ref|YP_005919633.1|   6 YTEKVLDHFKNPRNPGRIEDAD---VTARVGSAACGDMVQLYMKVNPETEVIEDIKFESFGCAANIASTSATTELAK 79 
                                       9*********************...5*************************************************** PP

                                       TSBHHHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                            NifU_N  79 gktleealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                       gktleea+ i+ k+++eelgglpk+k+hc++la++ lkaa+ kY+a+k
  gi|386001334|ref|YP_005919633.1|  80 GKTLEEARGIHFKDVVEELGGLPKQKVHCAQLATSGLKAAIMKYEAIK 127
                                       ********************************************9987 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.33     3e+03      36      48 ..      26      38 ..      22      59 .. 0.73
   2 !   27.4   1.0   3.1e-10   2.7e-06       4      72 ..     137     202 ..     134     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.33
                                      EEEEE--SSTT-T CS
                    FeS_assembly_P 36 Vsvditltypacs 48
                                      + v+ +++++ac 
  gi|386001334|ref|YP_005919633.1| 26 ADVTARVGSAACG 38
                                      5677788888887 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 3.1e-10
                                       HHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P   4 vlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgvevveV 72 
                                       v++++  V DP  g+++v+++ v +i++eg +V+v ++ +       + +++d+  al  l    +v+V
  gi|386001334|ref|YP_005919633.1| 137 VRRMMTGVLDPAKGLNIVAAKRVDGIEVEGRRVRVVLSQD-LDPETRATMAQDVVGALSGLDL--EVSV 202
                                       999**********************************999.3333677888888888888887..6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1361.71
//
Query:       gi|386001335|ref|YP_005919634.1|  [L=740]
Description: Phosphoesterase, RecJ domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   33.5   0.1      2e-07   30.9   0.3    2.4  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    7.1e-08   32.7  11.8    7.1e-08   32.7  11.8    2.3  2  DnaJ_CXXCXGXG    DnaJ central domain
    2.8e-05   24.4   0.2    2.8e-05   24.4   0.2    1.9  2  S1               S1 RNA binding domain
     0.0004   20.6   0.3    0.00085   19.5   0.3    1.5  1  DHH              DHH family
     0.0013   18.9   0.0     0.0077   16.4   0.0    2.3  2  tRNA_anti_2      OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
       0.02   14.3   1.0       0.02   14.3   1.0    4.2  5  zf-ribbon_3      zinc-ribbon domain
      0.073   13.1   0.0       0.17   11.9   0.0    1.7  1  S1_2             S1 domain
       0.09   12.8  21.3       0.98    9.5   2.7    3.2  3  DZR              Double zinc ribbon
       0.75   10.0  11.3       0.33   11.2   7.3    2.3  2  PHF5             PHF5-like protein
          5    7.7  13.9       0.81   10.2   5.4    3.0  3  zf-CHY           CHY zinc finger


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.3   1.1e-10     2e-07       1      73 [.     229     298 ..     229     301 .. 0.96
   2 ?   -2.6   0.0       3.1   5.5e+03      11      31 ..     398     417 ..     393     430 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.1e-10
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                       V+++G+v+++  +++g+   +++ D++g + + +f  +  + + +++ +++vr+ G+v+ r+g+ +++ + ++
  gi|386001335|ref|YP_005919634.1| 229 VSIEGEVIQV--KQTGGPTIFTVADDSGLVFCAAFERAGVRAYPEVDTEMIVRAIGEVSVRNGQ-IQIEIRSM 298
                                       89********..**************************************************99.99998876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                                       EEEEETTEEEEEEEETTEEEE CS
                   tRNA_anti-codon  11 sdrsggkvifidlrDgtgriq 31 
                                       + r+ +k+ f++l+D t  + 
  gi|386001335|ref|YP_005919634.1| 398 R-RAPSKAPFYELEDVTKDLS 417
                                       4.8889999******998765 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  11.8   3.9e-11   7.1e-08       1      66 [.      25      95 ..      25      96 .. 0.78
   2 ?   -1.2   1.7       1.6   2.8e+03      43      64 ..     100     119 ..      96     122 .. 0.62

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.9e-11
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvree.....qkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGk 66
                                      C++C G+g + + +k C++CkG+G++++      + + +  +v++  ++C+ C+G+Gk+   +++C++C G 
  gi|386001335|ref|YP_005919634.1| 25 CDRCGGKGYSVTGEKACPNCKGTGRIESVslgeaSASeIDELVTKGATRCTVCKGEGKIP-VTETCEACGGL 95
                                      ********86666899********64433355432224777899999***********77.6679****995 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                     DnaJ_CXXCXGXG  43 tCpeCeGtGkvikekdkCkkCk 64 
                                       +C  C+ + ++   ++ C +C+
  gi|386001335|ref|YP_005919634.1| 100 SCAICGAKLSTR--SELCANCS 119
                                       566666665544..55677776 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.2   1.6e-08   2.8e-05       4      54 ..     138     179 ..     136     197 .. 0.82
   2 ?   -3.0   0.2       5.3   9.5e+03       8      18 ..     231     241 ..     226     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                                       TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTE CS
                                S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGd 54 
                                       +g+++ G+V+ + ++GafV+l  +v+g+ + + l+r            vG+
  gi|386001335|ref|YP_005919634.1| 138 IGDIYRGKVSGIANFGAFVDLNDHVRGLAHNKFLKRT---------PEVGE 179
                                       69********************************976.........33333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                                       EEEEEEEEETT CS
                                S1   8 veGeVtsvtkg 18 
                                       +eGeV++v + 
  gi|386001335|ref|YP_005919634.1| 231 IEGEVIQVKQT 241
                                       67888888765 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   4.7e-07   0.00085       3      61 ..     360     473 ..     358     512 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.7e-07
                                       EEE-ECSSSHHHHHHHHHHHH.......................................................C CS
                                       xxxxxxxxxxxxxxxxxxxxx.......................................................x RF
                               DHH   3 livghknpDtDsigSaialan.......................................................l 24 
                                       ++   ++ D+D++ +a+a+++                                                       +
  gi|386001335|ref|YP_005919634.1| 360 VV--RHHADADGMSAAVAIEAailplirevggadaeyynyrrapskapfyeledvtkdlsyaledhsrhdqkmpliV 434
                                       44..7899*************88888888888888888888888888888877777777777777777777777777 PP

                                       ECS--TCGGCGCCH..HCCCSEEEEEEE-S---SS---S CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  25 lvDhneksqavege..akeeaedviiiDHHrlgeefetl 61 
                                       l+D+++++++v +   a+  + +++++DHH + e ++++
  gi|386001335|ref|YP_005919634.1| 435 LMDNGSTEEDVPAMkqAQIYGLEMLVVDHHHPDEAVDKY 473
                                       *******99998744466667899********9755555 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.3   4.1e+03      60      77 ..     169     186 ..     131     195 .. 0.74
   2 !   16.4   0.0   4.3e-06    0.0077      20      94 ..     227     298 ..     214     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                       tRNA_anti_2  60 aklkftledGmkVlvkgr 77 
                                       + lk t+e G++++v++r
  gi|386001335|ref|YP_005919634.1| 169 KFLKRTPEVGEEMVVRVR 186
                                       345677999999999876 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.3e-06
                       tRNA_anti_2  20 kavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyqlivedi 94 
                                       k v ++Ge+ ++k ++ g + ft  D++  + ++ f+++   +++ +e +++++v++  +v  ++G++q+ ++++
  gi|386001335|ref|YP_005919634.1| 227 KIVSIEGEVIQVK-QTGGPTIFTVADDSGLVFCAAFERA--GVRAYPEVDTEMIVRAIGEVSVRNGQIQIEIRSM 298
                                       5689********5.4689**********99******954..4667799999999999999999*********998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.21   3.8e+02      15      24 ..      21      30 ..      17      31 .. 0.71
   2 ?    3.9   0.6     0.021        38      16      22 ..      38      44 ..      36      46 .. 0.52
   3 ?   -2.2   0.0       1.8   3.2e+03      12      23 ..      67      78 ..      65      80 .. 0.76
   4 ?   -2.0   0.4       1.6   2.8e+03      18      23 ..      88      93 ..      86      94 .. 0.61
   5 ?   14.3   1.0   1.1e-05      0.02       2      22 ..      98     118 ..      97     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.21
                       zf-ribbon_3 15 ddnvCpyCGt 24
                                       ++ C  CG+
  gi|386001335|ref|YP_005919634.1| 21 AMKLCDRCGG 30
                                      5678888887 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.021
                       zf-ribbon_3 16 dnvCpyC 22
                                       ++Cp+C
  gi|386001335|ref|YP_005919634.1| 38 EKACPNC 44
                                      4455555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                       zf-ribbon_3 12 lssddnvCpyCG 23
                                      ++++++ C+ C 
  gi|386001335|ref|YP_005919634.1| 67 VTKGATRCTVCK 78
                                      688899998886 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.6
                       zf-ribbon_3 18 vCpyCG 23
                                      +C  CG
  gi|386001335|ref|YP_005919634.1| 88 TCEACG 93
                                      466666 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 1.1e-05
                       zf-ribbon_3   2 tvrCPnCGaplssddnvCpyC 22 
                                       +++C  CGa+ls++   C++C
  gi|386001335|ref|YP_005919634.1|  98 EYSCAICGAKLSTRSELCANC 118
                                       789******88********** PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.7e-05      0.17       1      45 [.     138     182 ..     138     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                              S1_2   1 iGkintlkvlretdfgyfLqkdesgevlLpkkevpeeleiGdeve 45 
                                       iG i + kv  + +fg+f++ ++ +  l ++k ++++ e+G+e  
  gi|386001335|ref|YP_005919634.1| 138 IGDIYRGKVSGIANFGAFVDLNDHVRGLAHNKFLKRTPEVGEEMV 182
                                       89999***************9999******************975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  11.2     0.079   1.4e+02       1      49 []      25      93 ..      15      93 .. 0.57
   2 ?    6.6  10.8    0.0045       8.1      12      48 ..      86     118 ..      64     119 .. 0.80
   3 ?    9.5   2.7   0.00055      0.98      15      43 ..     101     129 ..      96     133 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.079
                               DZR  1 CpqCgee..lppdarfCseCgtklkavaa....................edrCpsCgek.vdpearfCpeCG 49
                                      C +Cg +     + + C++C+ + +                        ++rC  C+ +   p +++C +CG
  gi|386001335|ref|YP_005919634.1| 25 CDRCGGKgySVTGEKACPNCKGTGR---IesvslgeasaseidelvtkgATRCTVCKGEgKIPVTETCEACG 93
                                      4444444444445555555555522...02234555666777777777777777777666677777777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0045
                               DZR  12 arfCseCgtklkavaaedrCpsCgekvdpearfCpeC 48 
                                        ++C++Cg   +    e+ C  Cg+k++ +++ C +C
  gi|386001335|ref|YP_005919634.1|  86 TETCEACGGLGR----EYSCAICGAKLSTRSELCANC 118
                                       467888888877....9******************** PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00055
                               DZR  15 CseCgtklkavaaedrCpsCgek..vdpear 43 
                                       C  Cg+kl+  ++++ C +C++k  v+  +r
  gi|386001335|ref|YP_005919634.1| 101 CAICGAKLS--TRSELCANCSKKpvVHVLER 129
                                       666777776..55667777766544444444 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.3   0.00018      0.33      15      77 ..      59     120 ..      49     125 .. 0.87
   2 ?   -1.7   0.0       1.9   3.3e+03      13      32 ..     635     654 ..     626     658 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                              PHF5  15 pGtaigklcekcdgkcpicdslvkpatkvricdecsfgkleekciicgskgvsdayyclecvr 77 
                                       + ++i +l +k   +c++c    k +   + c+ c     e +c icg+k  +++  c++c++
  gi|386001335|ref|YP_005919634.1|  59 SASEIDELVTKGATRCTVCKGEGK-IPVTETCEACGGLGREYSCAICGAKLSTRSELCANCSK 120
                                       56789999999********99854.556789******************************87 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                              PHF5  13 kqpGtaigklcekcdgkcpi 32 
                                       k++G     lc++ +gk ++
  gi|386001335|ref|YP_005919634.1| 635 KTSGEVHDLLCKRYEGKPVV 654
                                       6778888899******9776 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.9      0.16   2.8e+02      52      73 ..      20      45 ..      15      47 .. 0.75
   2 ?   10.2   5.4   0.00045      0.81      22      74 ..      41     106 ..      40     107 .. 0.67
   3 ?   -0.4   0.2       0.9   1.6e+03      53      63 ..     111     121 ..     105     136 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                            zf-CHY 52 ekavlCkkCkk....efaeyfCpiCk 73
                                      ++ +lC +C+      ++e  Cp+Ck
  gi|386001335|ref|YP_005919634.1| 20 PAMKLCDRCGGkgysVTGEKACPNCK 45
                                      56789****775665566778****8 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00045
                            zf-CHY  22 CreCH..........eeledhelerl.evkevlcllCeteq..ekavlCkkCkkefaeyfCpiCkl 74 
                                       C +C            e ++ e+++l ++  + c++C+ e   +++++C++C+   +ey+C iC +
  gi|386001335|ref|YP_005919634.1|  41 CPNCKgtgriesvslGEASASEIDELvTKGATRCTVCKGEGkiPVTETCEACGGLGREYSCAICGA 106
                                       666666666666655233334444431344567999998875578889****************75 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.9
                            zf-CHY  53 kavlCkkCkke 63 
                                        ++lC +C+k+
  gi|386001335|ref|YP_005919634.1| 111 RSELCANCSKK 121
                                       44556666542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 5221.35
//
Query:       gi|386001336|ref|YP_005919635.1|  [L=173]
Description: tRNA (cytidine(56)-2'-O)-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-48  163.9   0.0    1.5e-48  163.6   0.0    1.1  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.6   0.0   8.6e-53   1.5e-48       1     119 []      49     165 ..      49     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.6 bits;  conditional E-value: 8.6e-53
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnq 77 
                                       wGgef+v+   s++   +++k++gg +vhltmyGe+i+e ++ei+++ + l+vvvGaekvp+e+ye+ad+nv+vgnq
  gi|386001336|ref|YP_005919635.1|  49 WGGEFRVRSVGSWRGEARRWKEAGGRIVHLTMYGEPISEKMDEIRSSGD-LMVVVGAEKVPAEIYEMADWNVGVGNQ 124
                                       ********************************************99865.*************************** PP

                                       ---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  78 PhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       Phsevaala+f+drl+eg+el +ef+ +k++v+Ps r k+v+
  gi|386001336|ref|YP_005919635.1| 125 PHSEVAALAVFMDRLWEGEELAREFS-GKIEVVPSPRYKTVI 165
                                       *************************9.9***********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1153.43
//
Query:       gi|386001337|ref|YP_005919636.1|  [L=376]
Description: hypothetical protein Mhar_0635 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  127.7   0.0    5.5e-37  127.3   0.0    1.2  1  ATP-grasp_3      ATP-grasp domain
    5.2e-09   36.0   0.0    1.4e-07   31.3   0.0    2.2  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    3.3e-06   26.7   0.0     0.0057   16.2   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    0.00063   19.3   0.0      0.098   12.2   0.0    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0013   18.0   0.0     0.0024   17.2   0.0    1.3  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.021   14.4   0.0    1.3  1  Ins134_P3_kin    Inositol 1,3,4-trisphosphate 5/6-kinase ATP-
      0.034   13.7   0.0       0.14   11.7   0.0    1.8  2  ATP-grasp        ATP-grasp domain
       0.05   13.2   0.0        0.2   11.2   0.0    2.0  1  RimK             RimK-like ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.0   2.5e-40   5.5e-37       1     161 []     108     271 ..     108     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 2.5e-40
                                       HTSHHHHHHHHTTT.S.---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEE CS
                       ATP-grasp_3   1 asdKlktykkLkeagv.kvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplS 76 
                                       asdKl+++++L+e+g+  vP + +   +  ++ +l vKpr+Gagg ++r+v ++ee+   +e + +vqef++G+p+S
  gi|386001337|ref|YP_005919636.1| 108 ASDKLRLARWLEEEGFaAVP-TWRVGDAPTADFPLMVKPRRGAGGGENRLVYAEEELA-LLEGDLIVQEFVRGTPAS 182
                                       79************762689.89999999999********************996666.777788************ PP

                                       EEEEE.SSSEEEEEEEEEEEET.......TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS.S CS
                       ATP-grasp_3  77 vsllsdgekvlvlavnrqliekaeke...fvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkdee 148
                                       vs+++dge+++ ++ n+qli++++++   ++y+Gn+tp       + e++++aee+ ++l +l+G++GvD++l+ ++
  gi|386001337|ref|YP_005919636.1| 183 VSVIADGERAVAISANEQLIGTEWLGgagYRYCGNITPLALPPdaSAEMMRIAEEIASRL-QLVGSNGVDFILAASG 258
                                       **********************9999999*********9987766899************.**************** PP

                                       EEEEEEESS--GG CS
                       ATP-grasp_3 149 pyviEvNPRltts 161
                                       p v+EvNPR+++s
  gi|386001337|ref|YP_005919636.1| 259 PLVLEVNPRFQGS 271
                                       ***********97 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.069   1.5e+02       4      31 ..     169     195 ..     167     207 .. 0.84
   2 !   31.3   0.0   6.2e-11   1.4e-07      46     116 ..     228     299 ..     213     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.069
                      ATPgrasp_Ter   4 allvmeyLegpEySvDvlaekgevlaav 31 
                                       +l+v+e+  g+  Sv v+a+ ge  +a+
  gi|386001337|ref|YP_005919636.1| 169 DLIVQEFVRGTPASVSVIAD-GERAVAI 195
                                       79*****************7.5555444 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 6.2e-11
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysala.Gvnlpylalklllgleteev 116
                                       ++e++ +ae++a +++l g ++v +   ++gp +LE+NpR++G l+    + G+nl ++ l  + gl ++ +
  gi|386001337|ref|YP_005919636.1| 228 SAEMMRIAEEIASRLQLVGSNGVDFILAASGPLVLEVNPRFQGSLDAVEIStGLNLFQAHLLSFDGLLPKRP 299
                                       6899*****************************************9765544*******9999998743333 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0007       1.6      35      64 ..     135     164 ..     130     172 .. 0.90
   2 !   16.2   0.0   2.6e-06    0.0057     133     198 ..     223     286 ..     219     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0007
                                       HHH-SSEEEEETTCCTTTTEEEESSHHHHH CS
                       CPSase_L_D2  35 keigyPviikaafglGGkGmrvarneeela 64 
                                        +  +P ++k+  g GG   r+++ eeela
  gi|386001337|ref|YP_005919636.1| 135 PTADFPLMVKPRRGAGGGENRLVYAEEELA 164
                                       5678***********************996 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.6e-06
                                       --HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHH CS
                       CPSase_L_D2 133 LtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvke 198
                                       L +++  ++ + a ++++ +++vg   v+f+l +  +   v+EvN+R + +    e  TGl+l ++
  gi|386001337|ref|YP_005919636.1| 223 LPPDASAEMMRIAEEIASRLQLVGSNGVDFILAA--SGPLVLEVNPRFQGSLDAVEISTGLNLFQA 286
                                       55666778889999*******************6..66789********************99876 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0094        21      67      96 ..      59      88 ..      45     107 .. 0.80
   2 !   12.2   0.0   4.4e-05     0.098      61     174 ..     156     266 ..     134     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0094
                                      HHHTT-SCEEEEE--ESEEEEEEEEETSSC CS
                   Dala_Dala_lig_C 67 eafkydekvlvEeaiegreievavlgnekl 96
                                      ea+ + ++ ++E+ai++  i++ vlg ++ 
  gi|386001337|ref|YP_005919636.1| 59 EALPRKARAVIEAAIDAGSIDCLVLGPGAE 88
                                      677888999****************95543 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEE.EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHH CS
                   Dala_Dala_lig_C  61 lkeaieeafkydekvlvEeaiegreievavlgneklevs.evgeivvkkgfydyeakysddkaqlevpaklekevee 136
                                       l  a ee +  + + +v e+++g    v+v+ +++  v+ +++e    +++    a y         p +l+++ ++
  gi|386001337|ref|YP_005919636.1| 156 LVYAEEELALLEGDLIVQEFVRGTPASVSVIADGERAVAiSANEQLIGTEWLG-GAGY--RYCGNITPLALPPDASA 229
                                       4444455556678899***************9887555404444444444443.4444..23455678999999999 PP

                                       HHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 137 kiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       ++  +a ++ + l+l G+  vDf+l ++g +vl EvN+
  gi|386001337|ref|YP_005919636.1| 230 EMMRIAEEIASRLQLVGSNGVDFILAASGPLVL-EVNP 266
                                       99999*********************8887665.8885 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0024     227     276 ..     230     280 ..     226     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNar..pglaivqiang 276
                                       e++ +a ++a +l  +g  G+D+ l++++ pl+lE+N r   +l+ v+i  g
  gi|386001337|ref|YP_005919636.1| 230 EMMRIAEEIASRLQLVGSNGVDFILAASG-PLVLEVNPRfqGSLDAVEISTG 280
                                       7899*************************.********97334666666554 PP

>> Ins134_P3_kin  Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.2e-06     0.021      31      74 ..     137     177 ..     124     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.2e-06
                                       --SSEEEEESB-SST.TTTEEEEE-SGGGGTT--SSEEEEE--- CS
                     Ins134_P3_kin  31 LklPliakplvadGtakshelslvydqeglkklkpPlvlqefvn 74 
                                         +Pl+ kp+   G     e  lvy +e l  l+  l++qefv 
  gi|386001337|ref|YP_005919636.1| 137 ADFPLMVKPRRGAGG---GENRLVYAEEELALLEGDLIVQEFVR 177
                                       579*******98888...6789********************96 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.48   1.1e+03      28      54 ..     138     163 ..     129     195 .. 0.70
   2 ?   11.7   0.0   6.5e-05      0.14     108     159 ..     217     267 ..     209     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.48
                                       -SCEEEEESSS-CTTTTEEEECTCCGH CS
                         ATP-grasp  28 glpvvvKarrlgydGkGqsvvrseedl 54 
                                       ++p++vK rr g  G  + +v  ee+l
  gi|386001337|ref|YP_005919636.1| 138 DFPLMVKPRR-GAGGGENRLVYAEEEL 163
                                       8999999555.5444445555555544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.5e-05
                                       EEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
                         ATP-grasp 108 svapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                                       ++ p +++ +a ++  +ia++i+++L+ vG  +v + + + g  lv E+ pR
  gi|386001337|ref|YP_005919636.1| 217 NITPLALPPDASAEMMRIAEEIASRLQLVGSNGVDFILAASGP-LVLEVNPR 267
                                       6789999****************************99997775.56699998 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.9e-05       0.2     126     179 ..     226     282 ..     133     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.9e-05
                                       ---HHHHHHHHHHHHHCT-S.EEEEEEEEETTEEEEEEEESS--..SHHHHHHHT-- CS
                              RimK 126 qlseeekelAikaakamelv.vaGvDllrakrgllvlEvnsspg..lekiektlgid 179
                                       + s e  ++A ++a  ++lv   GvD + a  g+lvlEvn   +  l+ +e  +g++
  gi|386001337|ref|YP_005919636.1| 226 DASAEMMRIAEEIASRLQLVgSNGVDFILAASGPLVLEVNPRFQgsLDAVEISTGLN 282
                                       56788999999999999998457***999***********86542356666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 2379.74
//
Query:       gi|386001338|ref|YP_005919637.1|  [L=371]
Description: hypothetical protein Mhar_0636 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-25   88.1  10.9    1.9e-13   50.5   0.6    2.5  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      9e-15   54.5   0.8    3.2e-06   27.0   0.0    2.7  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    1.3e-05   25.3   2.3      0.001   19.3   0.6    2.2  2  SdrD_B           SdrD B-like domain
      4e-05   23.5   3.7      0.058   13.4   0.2    2.8  2  Big_1            Bacterial Ig-like domain (group 1)
    0.00014   21.6   0.0       0.15   12.0   0.0    2.7  2  PEGA             PEGA domain
    0.00029   21.1   0.6       0.31   11.4   0.3    2.4  2  Invasin_D3       Invasin, domain 3
     0.0019   18.4   2.7       0.32   11.3   0.1    2.5  2  MetallophosN     N terminal of Calcineurin-like phosphoestera
     0.0093   15.4   0.2        4.1    6.8   0.0    2.4  2  Dioxygenase_C    Dioxygenase
  ------ inclusion threshold ------
      0.014   15.4   0.0        7.7    6.6   0.0    2.3  2  CooC_C           CS1-pili formation C-terminal
      0.014   15.4   0.1       0.81    9.7   0.0    2.4  2  phage_tail_N     Prophage tail fibre N-terminal
      0.016   15.4   0.0       0.94    9.6   0.0    2.5  3  DUF2012          Protein of unknown function (DUF2012)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   3.8   8.1e-14   1.3e-10       2      60 ..     194     250 ..     193     269 .. 0.91
   2 !   50.5   0.6   1.2e-16   1.9e-13       2      79 ..     290     360 ..     290     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 8.1e-14
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGya 60 
                                       + GrV+d+ g++i+ga V+ t  + g   +t td +G++ ++ +p g+y+vt++++G+ 
  gi|386001338|ref|YP_005919637.1| 194 LVGRVVDTRGNGIPGALVRMT-GSAGGIFTTATDLQGYYGMD-VPSGSYTVTAEKEGFT 250
                                       78*******************.68999*************97.**************96 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 1.2e-16
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttld 78 
                                       ++G Vtd sgap++gatV++         ++ttd+dG +  + l+pg +s+ v a+Gy+ ++  +v++++gq ++ld
  gi|386001338|ref|YP_005919637.1| 290 VEGVVTDRSGAPVPGATVRID-----GIFTVTTDRDGGYGAS-LAPGWHSISVYAAGYKFSSA-SVQIRPGQGSRLD 359
                                       78*******************.....8*************75.****************9997.5**********99 PP

                   CarboxypepD_reg  79 i 79 
                                       +
  gi|386001338|ref|YP_005919637.1| 360 L 360
                                       7 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 ?   -2.6   0.0       3.4   5.6e+03      44      57 ..     177     190 ..     167     191 .. 0.71
   2 !   25.0   0.2   8.7e-09   1.4e-05       3      55 ..     196     249 ..     194     258 .. 0.86
   3 !   27.0   0.0     2e-09   3.2e-06       1      70 [.     290     356 ..     290     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.4
                   CarbopepD_reg_2  44 gkytLvvsyvGykt 57 
                                       + + L vs+ Gy t
  gi|386001338|ref|YP_005919637.1| 177 NPVPLAVSSAGYPT 190
                                       56789999999976 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 8.7e-09
                   CarbopepD_reg_2   3 GtVvdketkeplpgatVyvkgtk...kgtvTdenGnFelknlpagkytLvvsyvGy 55 
                                       G+Vvd+ + + +pga V ++g+    + t+Td +G++ ++ +p+g yt++++  G+
  gi|386001338|ref|YP_005919637.1| 196 GRVVDTRG-NGIPGALVRMTGSAggiFTTATDLQGYYGMD-VPSGSYTVTAEKEGF 249
                                       9****975.8*********99853448899*********5.********9988777 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 2e-09
                   CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektl 70 
                                       ++G V+d + + p+pgatV + g  + ++Td +G +  + l +g + + v + Gyk  + +v++  ++  
  gi|386001338|ref|YP_005919637.1| 290 VEGVVTDRS-GAPVPGATVRIDGI-FTVTTDRDGGYGAS-LAPGWHSISVYAAGYKFSSASVQIRPGQGS 356
                                       689999976.69*********886.6688********96.999*******************99866544 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.6   6.4e-07     0.001      18      76 ..     200     255 ..     196     274 .. 0.85
   2 ?    5.5   0.0     0.012        19      18      75 ..     296     346 ..     290     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.4e-07
                            SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakk 76 
                                       d+  +gi g  V+++ ++g +  tt Td +G+Y  + + +G+Y+V+ +  +g+t+++++
  gi|386001338|ref|YP_005919637.1| 200 DTRGNGIPGALVRMTGSAGGIF-TTATDLQGYYGMD-VPSGSYTVTAE-KEGFTFSPST 255
                                       78889*********99999987.***********87.9*******985.5788888775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                            SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                       d   + + g tV++     + + t+tTd +G Y   +l+pG  ++++ + agy+++++
  gi|386001338|ref|YP_005919637.1| 296 DRSGAPVPGATVRI-----DGIFTVTTDRDGGYG-ASLAPGWHSISV-YAAGYKFSSA 346
                                       66678888999988.....34459*********9.569999999998.5567777655 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   3.6e-05     0.058      12      64 .]     197     244 ..     194     244 .. 0.84
   2 !   10.3   0.3   0.00033      0.54      12      28 ..     293     309 ..     290     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                             Big_1  12 tvkDangnpvagatVtfsvsggalsassgtTdanGkatvtltstkagtvtvtA 64 
                                       +v+D  gn ++ga V  + s+g ++  ++ Td +G + + +    +g++tvtA
  gi|386001338|ref|YP_005919637.1| 197 RVVDTRGNGIPGALVRMTGSAGGIF--TTATDLQGYYGMDVP---SGSYTVTA 244
                                       79*******************9995..688999999888776...57777766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00033
                             Big_1  12 tvkDangnpvagatVtf 28 
                                       +v+D++g pv+gatV +
  gi|386001338|ref|YP_005919637.1| 293 VVTDRSGAPVPGATVRI 309
                                       7**************76 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0041       6.6      31      46 ..     235     250 ..     231     258 .. 0.88
   2 !   12.0   0.0   9.3e-05      0.15      11      64 ..     303     360 ..     299     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0041
                              PEGA  31 leaGnyslrvekeGYe 46 
                                       +++G+y+++ ekeG++
  gi|386001338|ref|YP_005919637.1| 235 VPSGSYTVTAEKEGFT 250
                                       99************95 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.3e-05
                              PEGA  11 eGatVyidGkylGkTPvt....lsleaGnyslrvekeGYedlektvtvtagetvklnl 64 
                                       +GatV idG  +  T  +     sl++G +s+ v + GY+  ++ v++++g+  +l+l
  gi|386001338|ref|YP_005919637.1| 303 PGATVRIDGIFTVTTDRDggygASLAPGWHSISVYAAGYKFSSASVQIRPGQGSRLDL 360
                                       789999999888877643332278*************************999888775 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   0.00019      0.31      28      91 ..     198     258 ..     195     262 .. 0.87
   2 !    7.4   0.0    0.0033       5.3      28      82 ..     294     340 ..     289     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                        Invasin_D3  28 lkDangnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptvnG.vaiaatatv 91 
                                       + D+ gn + g+ v ++ ++ g ++++td + G y   +    +g++t+t++ +G + + +ta+v
  gi|386001338|ref|YP_005919637.1| 198 VVDTRGNGIPGALVRMTGSAGGIFTTATDLQ-GYYGMDV---PSGSYTVTAEKEGfTFSPSTARV 258
                                       78****************9566888887766.******9...779**********9888888887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0033
                        Invasin_D3  28 lkDangnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptvnG 82 
                                       ++D +g pv g+tv +     g + +vt++ dG y a L   + g  +i++   G
  gi|386001338|ref|YP_005919637.1| 294 VTDRSGAPVPGATVRID----G-IFTVTTDRDGGYGASL---APGWHSISVYAAG 340
                                       78************999....4.356999999***9999...5666666666666 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 !    7.0   0.4    0.0043         7       1      36 [.     196     237 ..     196     245 .. 0.76
   2 !   11.3   0.1    0.0002      0.32       1      36 [.     292     329 ..     292     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                      MetallophosN   1 GkVt.skgkgvagVvV.....sDGvnvtkTdakGrYeLksdk 36 
                                       G+V  + g+g++g  V       G+ +t+Td +G Y ++  +
  gi|386001338|ref|YP_005919637.1| 196 GRVVdTRGNGIPGALVrmtgsAGGIFTTATDLQGYYGMDVPS 237
                                       667669999999988855443469999*********998655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0002
                      MetallophosN   1 GkVt.skgkgvagVvVs.DGvnvtkTdakGrYeLksdk 36 
                                       G Vt ++g +v+g +V  DG+ +++Td++G Y  + + 
  gi|386001338|ref|YP_005919637.1| 292 GVVTdRSGAPVPGATVRiDGIFTVTTDRDGGYGASLAP 329
                                       789999********9966**************655554 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0025       4.1      32      51 ..     194     213 ..     177     248 .. 0.85
   2 !    6.3   0.0    0.0036       5.9      32      51 ..     290     309 ..     279     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                                       EEEEEE-TTSSB-TT-EEEE CS
                     Dioxygenase_C  32 lsGrvldeaGkplagalvel 51 
                                       l Grv+d+ G++++galv +
  gi|386001338|ref|YP_005919637.1| 194 LVGRVVDTRGNGIPGALVRM 213
                                       57****************88 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0036
                                       EEEEEE-TTSSB-TT-EEEE CS
                     Dioxygenase_C  32 lsGrvldeaGkplagalvel 51 
                                       ++G v+d+ G p++ga+v +
  gi|386001338|ref|YP_005919637.1| 290 VEGVVTDRSGAPVPGATVRI 309
                                       89***************976 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 ?    6.4   0.0    0.0056       9.1      17      67 ..     192     247 ..     181     264 .. 0.78
   2 ?    6.6   0.0    0.0047       7.7      19      64 ..     290     336 ..     279     353 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0056
                            CooC_C  17 vtviGrlvdedgqplanaki.....lnhagvavteedGvFtlevdakapsltveng 67 
                                       +  +Gr+vd  g+ + +a +     ++++ ++ t+ +G++ ++v +++ + t e++
  gi|386001338|ref|YP_005919637.1| 192 YGLVGRVVDTRGNGIPGALVrmtgsAGGIFTTATDLQGYYGMDVPSGSYTVTAEKE 247
                                       67899999999999998865333334667789999*********999877776655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0047
                            CooC_C  19 viGrlvdedgqplanakilnhagvavte.edGvFtlevdakapsltv 64 
                                       v G + d  g+p+ +a++  ++ ++vt   dG++ ++++ +  s+ v
  gi|386001338|ref|YP_005919637.1| 290 VEGVVTDRSGAPVPGATVRIDGIFTVTTdRDGGYGASLAPGWHSISV 336
                                       668999************999999998889****9998777666655 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 ?    9.7   0.0    0.0005      0.81      41      68 ..     223     250 ..     213     270 .. 0.85
   2 ?    3.3   0.0     0.045        74       5      31 ..     290     316 ..     287     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                      phage_tail_N  41 enpdeaGrysldvetGkysvilkvdgfp 68 
                                         +d +G y +dv  G y+v+ +++gf 
  gi|386001338|ref|YP_005919637.1| 223 TATDLQGYYGMDVPSGSYTVTAEKEGFT 250
                                       568899****************999986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.045
                      phage_tail_N   5 isGvlkdGtGkPvqnctiqlkarrtst 31 
                                       + Gv++d +G Pv + t+ +    t t
  gi|386001338|ref|YP_005919637.1| 290 VEGVVTDRSGAPVPGATVRIDGIFTVT 316
                                       578999999999999988877666555 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.8   1.1e+04     107     119 ..      27      39 ..      25      40 .. 0.85
   2 ?    9.6   0.0   0.00058      0.94      36      61 ..     234     259 ..     206     278 .. 0.83
   3 ?    2.9   0.0     0.067   1.1e+02      23      62 ..     314     352 ..     300     367 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.8
                           DUF2012 107 rekfsilsLlknP 119
                                       + ++++l++l nP
  gi|386001338|ref|YP_005919637.1|  27 ADEMTMLDFLPNP 39 
                                       67899******99 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00058
                           DUF2012  36 dlpegsYlLevespeyvFepyrVdvk 61 
                                       d+p+gsY++ +e+ +++F+p   +v 
  gi|386001338|ref|YP_005919637.1| 234 DVPSGSYTVTAEKEGFTFSPSTARVW 259
                                       9******************9776665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.067
                           DUF2012  23 kalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkd 62 
                                       ++ + rDG +    l +g + + v +++y F+   V++++
  gi|386001338|ref|YP_005919637.1| 314 TVTTDRDGGYG-ASLAPGWHSISVYAAGYKFSSASVQIRP 352
                                       34444444443.3567779******************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 2247.10
//
Query:       gi|386001339|ref|YP_005919638.1|  [L=1008]
Description: S-layer protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-193  639.7   6.1    3.2e-96  321.4   0.6    2.2  2  S-layer          S-layer protein
    4.6e-06   26.6   0.1      0.096   12.7   0.0    3.5  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    5.4e-06   26.5  13.8     0.0007   19.7   2.4    4.6  4  Big_3_5          Bacterial Ig-like domain (group 3)
    3.5e-05   23.6   3.5        1.6    8.6   0.2    4.6  5  PEGA             PEGA domain
      7e-05   23.0  14.6      0.025   14.8   1.2    4.7  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00032   20.9   0.7     0.0026   18.0   0.1    2.9  2  CARDB            CARDB
     0.0016   19.1  11.7     0.0019   19.0   0.2    4.6  4  Big_7            Bacterial Ig domain
  ------ inclusion threshold ------
      0.011   16.1   1.4         12    6.2   0.0    3.4  3  DUF4198          Domain of unknown function (DUF4198)
      0.032   14.2   0.1       0.52   10.3   0.0    3.0  2  Y_Y_Y            Y_Y_Y domain
      0.064   13.1   0.2         19    5.2   0.1    2.5  2  A2M              Alpha-2-macroglobulin family
      0.067   13.7   1.0        4.1    8.0   0.1    3.4  3  DUF4179          Domain of unknown function (DUF4179)
       0.11   13.0   0.2         22    5.6   0.0    3.5  3  DUF4981          Domain of unknown function(DUF4981)
       0.11   12.5   1.0       0.75    9.8   0.1    3.0  2  Cadherin_5       Cadherin-like domain
       0.21   11.7   2.3        8.1    6.7   0.1    3.3  3  PrcB_C           PrcB C-terminal


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 !  321.4   0.6   2.5e-99   3.2e-96       5     258 .]     168     426 ..     165     426 .. 0.96
   2 !  321.1   0.6   2.9e-99   3.7e-96       8     258 .]     454     702 ..     449     702 .. 0.98

  Alignments for each domain:
  == domain 1  score: 321.4 bits;  conditional E-value: 2.5e-99
                           S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlele...sksdrtieegelvYsttpvekefefeewgsYevigflaek 78 
                                       ++++++twt+++Fsgf+yd+dd++++E+lt++l+    + dr+i+e+el+Y t++ + ++ef++wg+Y+vigf+a+k
  gi|386001339|ref|YP_005919638.1| 168 KNPATYTWTPQTFSGFFYDLDDDVGTETLTVHLResgGSYDRSIREDELEYVTEADSITYEFSDWGQYQVIGFMAQK 244
                                       68899***************************99655349************************************* PP

                           S-layer  79 Yfagy..dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevds 153
                                       Yfagy   +sa++s+ +sll++e+L++vlid+d+e+t+ +gs+l L+egYel+ik+iD+dg+kvwl L+kdg+evds
  gi|386001339|ref|YP_005919638.1| 245 YFAGYegTDSAVVSKGISLLDEEELHEVLIDDDQEYTVDTGSVLPLGEGYELRIKEIDLDGNKVWLALAKDGSEVDS 321
                                       *****65555599**************************************************************** PP

                           S-layer 154 kvissska.dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsene 229
                                       +v+++++  +sty ye+dl + d++++++ hv+++frg+e+slv+i+g+fqisd+++++ +gd++g+mev+s+s n+
  gi|386001339|ref|YP_005919638.1| 322 RVVDPTSLgSSTYKYEADLRG-DKFPLVMAHVRSIFRGAETSLVTIDGLFQISDKFVTVASGDTYGSMEVDSISGNT 397
                                       *****8879***********9.89***************************************************** PP

                           S-layer 230 iemenddsitLsrdktieimddlkfkvaD 258
                                       i+m+nd++itL++++t+ +m+d++f vaD
  gi|386001339|ref|YP_005919638.1| 398 IRMANDRTITLRMGRTVPVMGDVSFLVAD 426
                                       ****************************8 PP

  == domain 2  score: 321.1 bits;  conditional E-value: 2.9e-99
                           S-layer   8 eeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagyd 84 
                                        e+twt+ nF+gfyydidd++++E+lt++    s+++i++g+l+Y t p+++ fe++ewgsY+vigflaekYfagy+
  gi|386001339|ref|YP_005919638.1| 454 GEFTWTPYNFEGFYYDIDDDVGTETLTARF---SGERIADGDLTYGTYPQSVPFEYAEWGSYNVIGFLAEKYFAGYN 527
                                       6899************************94...689***************************************** PP

                           S-layer  85 nsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska 161
                                       ++++ +++ sl+++++L+kvlid+d+++t++sg+++ L+egYel+ik++D+dg+k++l++tkdgeevdskv+++ ++
  gi|386001339|ref|YP_005919638.1| 528 SETVFTNEFSLINEGQLRKVLIDDDQSYTVRSGTTFPLKEGYELRIKEVDLDGNKIFLSITKDGEEVDSKVVEPGRT 604
                                       ***9**********************************************************************988 PP

                           S-layer 162 ..dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemendd 236
                                          st++ye+ + + + v+i+avhv++vfrg+e++l++iegifqisd++ ++eeg++++kme++svs++ i m+nd 
  gi|386001339|ref|YP_005919638.1| 605 vtGSTFTYEERISG-ERVPIVAVHVQSVFRGREEDLATIEGIFQISDKPRSVEEGETYDKMEIDSVSDSGIVMTNDG 680
                                       99**********99.67************************************************************ PP

                           S-layer 237 sitLsrdktieimddlkfkvaD 258
                                       si+L r++t++im+++ f++aD
  gi|386001339|ref|YP_005919638.1| 681 SISLGRGRTVSIMENIMFRIAD 702
                                       *********************8 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 ?   -2.5   0.0       4.1   5.2e+03      11      42 ..     618     652 ..     615     655 .. 0.66
   2 !    9.6   0.0   0.00071      0.92       7      65 ..     738     795 ..     735     818 .. 0.77
   3 !   12.7   0.0   7.5e-05     0.096      12      78 ..     828     892 ..     824     902 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                   CarbopepD_reg_2  11 keplpgatVyvkgtkkgtv...TdenGnFelknlp 42 
                                       +e +p + V+v++  +g     +  +G F+++++p
  gi|386001339|ref|YP_005919638.1| 618 GERVPIVAVHVQSVFRGREedlATIEGIFQISDKP 652
                                       67888888888876544432226678888888776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00071
                   CarbopepD_reg_2   7 dketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvs 65 
                                        ++++ p++ga +++ g ++gt+T ++G +  + + ag +++ ++   y++++  + vs
  gi|386001339|ref|YP_005919638.1| 738 ATSEGAPIIGAIITIDGEEVGTTT-ADGIYLYTPPAAGSFEISAKRDEYTEVKGVLVVS 795
                                       567889***************988.89**999988889999988877777766555555 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 7.5e-05
                   CarbopepD_reg_2  12 eplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillke 78 
                                       +p++ga + +++ + gt Td+ G+ +  +   g yt+++s  Gy++ ++++ v++  +++  i++ e
  gi|386001339|ref|YP_005919638.1| 828 RPVEGADIGFENVTIGT-TDSLGTLSYASDSVGSYTITASKEGYESGSRRIVVASPIRIT-GIEMPE 892
                                       58999*****9999997.9*********999*********************99877665.566655 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 ?    6.0   0.0      0.01        13      24      70 ..     416     486 ..     400     492 .. 0.59
   2 ?    1.0   0.2      0.39     5e+02       9      65 ..     733     780 ..     726     782 .. 0.61
   3 ?    4.2   0.1     0.037        47      46      66 ..     846     866 ..     825     872 .. 0.78
   4 !   19.7   2.4   5.5e-07    0.0007       1      65 [.     891     958 ..     891     959 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                                       S--EEEEEE...............TTEE-SS-EE--TTSEEEEEEE-SS.........-EEEEEEEEEE-T CS
                           Big_3_5  24 ptGtVtftd...............ggttlgtavllsanGtAtltvsala.........aGthsitAtYsGd 70 
                                       + G V+f +               g+ ++  +++  a+G  t+t  + +         +Gt ++tA++sG 
  gi|386001339|ref|YP_005919638.1| 416 VMGDVSFLVadaselrfaptvkrtGSYEIRGTIVDPAEGEFTWTPYNFEgfyydidddVGTETLTARFSGE 486
                                       5566666654333333333222223344433332334677777665544677777777************7 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.39
                                       EEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEE CS
                           Big_3_5   9 tvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitA 65 
                                       + ++ at  +a    p     +t++g ++gt+++   +G+  +t +a  aG+ +i A
  gi|386001339|ref|YP_005919638.1| 733 PAEIRATSEGA----PIIGAIITIDGEEVGTTTA---DGIYLYTPPA--AGSFEISA 780
                                       44444444444....4333457889999999773...5777666554..68888877 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.037
                                       TSEEEEEEE-SS-EEEEEEEE CS
                           Big_3_5  46 nGtAtltvsalaaGthsitAt 66 
                                       +   tl++++ ++G+++itA+
  gi|386001339|ref|YP_005919638.1| 846 DSLGTLSYASDSVGSYTITAS 866
                                       34558999999*********7 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 5.5e-07
                                       -S-EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS.-EE--..TTSEEEEEEE-SS-EEEEEEE CS
                           Big_3_5   1 ptsvtagqtvtltatVtaasggtptGtVtftdggttlgt.avlls..anGtAtltvsalaaGthsitA 65 
                                       p++v ag+tv++tat    ++ + t tV++ ++g++ gt  v++   ++G+A++ ++ l++G +++ +
  gi|386001339|ref|YP_005919638.1| 891 PETVRAGKTVEITATAENPGAVSDTTTVELRVNGVPEGTmEVTVGpgETGSAAFEYQPLEPGLYTVEV 958
                                       67999**************999***************996666655469****************975 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.3   6.8e+03      43      62 ..     292     310 ..     291     313 .. 0.78
   2 ?   -2.6   0.0         4   5.2e+03      42      57 ..     566     581 ..     565     587 .. 0.82
   3 ?    4.6   0.1     0.024        31      12      26 ..     747     761 ..     744     796 .. 0.79
   4 !    7.3   0.0    0.0034       4.4      32      54 ..     857     879 ..     830     885 .. 0.78
   5 !    8.6   0.2    0.0013       1.6       2      40 ..     918     958 ..     917     960 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.3
                              PEGA  43 eGYedlektvtvtagetvkl 62 
                                       eGYe   k+++++ g +v+l
  gi|386001339|ref|YP_005919638.1| 292 EGYELRIKEIDLD-GNKVWL 310
                                       8999999999999.666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4
                              PEGA  42 keGYedlektvtvtag 57 
                                       keGYe   k+v+++ +
  gi|386001339|ref|YP_005919638.1| 566 KEGYELRIKEVDLDGN 581
                                       8999999999999865 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.024
                              PEGA  12 GatVyidGkylGkTP 26 
                                       Ga ++idG+++G T 
  gi|386001339|ref|YP_005919638.1| 747 GAIITIDGEEVGTTT 761
                                       99**********985 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0034
                              PEGA  32 eaGnyslrvekeGYedlektvtv 54 
                                         G+y+++ +keGYe  ++++ v
  gi|386001339|ref|YP_005919638.1| 857 SVGSYTITASKEGYESGSRRIVV 879
                                       57*************99999877 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0013
                              PEGA   2 gtltirSnpeG.atVyidGkylGkTPvtls.leaGnyslrv 40 
                                       ++l+++  peG ++V+++  ++G++  ++  le+G y+++v
  gi|386001339|ref|YP_005919638.1| 918 VELRVNGVPEGtMEVTVGPGETGSAAFEYQpLEPGLYTVEV 958
                                       6799******9789*************************98 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.5   1.1e+04       2       9 ..     444     451 ..     435     457 .. 0.68
   2 !   12.5   0.3    0.0001      0.13       9      68 ..     740     793 ..     735     807 .. 0.78
   3 !   14.8   1.2     2e-05     0.025      12      70 ..     828     880 ..     822     907 .. 0.79
   4 ?    1.5   1.2      0.28   3.6e+02      41      59 ..     921     939 ..     892     975 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.5
                   CarboxypepD_reg   2 isGrVtda 9  
                                       i+G+++d+
  gi|386001339|ref|YP_005919638.1| 444 IRGTIVDP 451
                                       67777776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0001
                   CarboxypepD_reg   9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevt 68 
                                       + gapi ga +t+     g +   tt adG +  +  ++g++++ + ++ y ++    ++
  gi|386001339|ref|YP_005919638.1| 740 SEGAPIIGAIITID----G-EEVGTTTADGIYLYTPPAAGSFEISAKRDEYTEVKG-VLV 793
                                       47************....4.55556778******97777************99885.344 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2e-05
                   CarboxypepD_reg  12 apiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtlt 70 
                                       +p++ga + ++      v+  ttd+ G+ + ++   g+y++t+s++Gy++ +r+ ++++
  gi|386001339|ref|YP_005919638.1| 828 RPVEGADIGFE-----NVTIGTTDSLGTLSYASDSVGSYTITASKEGYESGSRR-IVVA 880
                                       68888888888.....366679**********999*****************95.3332 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.28
                   CarboxypepD_reg  41 rlrglppgtysvtvsapGy 59 
                                       r++g+p gt +vtv     
  gi|386001339|ref|YP_005919638.1| 921 RVNGVPEGTMEVTVGPGET 939
                                       5555555555555522222 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.9   7.5e+03      67      90 ..     766     788 ..     752     789 .. 0.74
   2 !   18.0   0.1     2e-06    0.0026       8      82 ..     887     958 ..     882     971 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.9
                                       EEEE-S-S-CEEEEEEEESTT-SS CS
                             CARDB  67 ftwtteategevtltvvvDpdnev 90 
                                       + +t++ ++g+ +++++ D++ ev
  gi|386001339|ref|YP_005919638.1| 766 YLYTPP-AAGSFEISAKRDEYTEV 788
                                       445666.99999999999999988 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltv 82 
                                        + +p+++ +g++++it+t +N G   s +t+v+l ++g   gt++v  + +ge+ +  f +++  ++g +t++v
  gi|386001339|ref|YP_005919638.1| 887 GIEMPETVRAGKTVEITATAENPGA-VSDTTTVELRVNGVPEGTMEV-TVGPGETGSAAFEYQPL-EPGLYTVEV 958
                                       56789999***************95.68899****************.89**************8.*****9998 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.29   3.8e+02      48      70 .]     167     198 ..     149     198 .. 0.79
   2 ?   -2.2   0.0       5.7   7.4e+03      53      69 ..     455     480 ..     435     481 .. 0.57
   3 ?    3.2   0.2      0.12   1.6e+02      16      70 .]     814     879 ..     802     879 .. 0.60
   4 !   19.0   0.2   1.4e-06    0.0019      12      70 .]     892     958 ..     883     967 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.29
                                       -SSSEEEEEE-...........-...SEEEEEEE CS
                             Big_7  48 tsapysltwtt...........taltagthtltV 70 
                                        ++p ++twt+           +  + gt tltV
  gi|386001339|ref|YP_005919638.1| 167 GKNPATYTWTPqtfsgffydldD--DVGTETLTV 198
                                       468999*****888888887643..578888887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                                       EEEEE-...........-...SEEEEEE CS
                             Big_7  53 sltwtt...........taltagthtlt 69 
                                       ++twt+           +  + gt tlt
  gi|386001339|ref|YP_005919638.1| 455 EFTWTPynfegfyydidD--DVGTETLT 480
                                       566666555555554422..35555555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.12
                                       TSEEEEEEEEE-S.S-E.......EEEEEEETTEE....EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  16 ggtvtisasAsdd.ggv.......skVefyvdgtl.g..lgtdtsapysltwtttaltagthtltV 70 
                                       g+++ i+a+   d   v       ++V++   ++l +  +++d+ + y++t + + +++g+  + V
  gi|386001339|ref|YP_005919638.1| 814 GESFVIKATIGVDlRPVegadigfENVTIGTTDSLgTlsYASDSVGSYTITASKEGYESGSRRIVV 879
                                       666666666654444442222233555555555553366788888999999999989999988765 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 1.4e-06
                                       --EB.TSEEEEEEEEE-SS-E...EEEEEEETTEE.......EEEE-SSSEEEEEE--...SEEEEEEE CS
                             Big_7  12 atvs.ggtvtisasAsddggv...skVefyvdgtl.g.....lgtdtsapysltwtttaltagthtltV 70 
                                       +tv  g+tv+i+a+A+++g+v   ++Ve++v+g++ g     +g   ++   +++++  l+ g +t+ V
  gi|386001339|ref|YP_005919638.1| 892 ETVRaGKTVEITATAENPGAVsdtTTVELRVNGVPeGtmevtVGPGETGSAAFEYQP--LEPGLYTVEV 958
                                       689999************9998889*********97799988777777777777777..5777777765 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0096        12     144     209 ..     726     780 ..     688     784 .. 0.78
   2 ?    3.6   0.0      0.06        76     138     203 ..     802     869 ..     799     870 .. 0.91
   3 ?    3.2   0.2     0.077        99     131     178 ..     895     941 ..     883     959 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0096
                           DUF4198 144 pydlkageelevqvlldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtftlpkaGlwllea 209
                                       p   ++g ++e++ + +G P  ga +++        ++     v +t adG+  +t+p+aG + ++a
  gi|386001339|ref|YP_005919638.1| 726 PQ-AVVGTPAEIRATSEGAPIIGAIITIDG------EE-----VgTTTADGIYLYTPPAAGSFEISA 780
                                       44.458999*************99999843......22.....237999999999999999887666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.06
                           DUF4198 138 ivPlthpydlkageelevqvl..ldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaG 203
                                       i ++t p ++ +ge++ ++ +  +d +P++ga++ +e    +  d+ ++  + +d+ G  t+t +k+G
  gi|386001339|ref|YP_005919638.1| 802 ILAVTAPQEVMKGESFVIKATigVDLRPVEGADIGFENVTIGTTDSLGTLSYASDSVGSYTITASKEG 869
                                       7889***********999988779999********999999999999999999999999999999988 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.077
                           DUF4198 131 pvglglEivP.lthpydlkageelevqvlldGkPlagaeveveyggtry 178
                                        +g+ +Ei +  ++p +  + ++ +v++ ++G P    ev+v +g+t++
  gi|386001339|ref|YP_005919638.1| 895 RAGKTVEITAtAENPGA--VSDTTTVELRVNGVPEGTMEVTVGPGETGS 941
                                       459999***94455554..59*********************9998843 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.3   1.6e+03      26      45 ..     846     865 ..     835     872 .. 0.74
   2 ?   10.3   0.0   0.00041      0.52      30      49 ..     943     962 ..     933     973 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                                       STS..EEEEES--SEEEEEEE CS
                             Y_Y_Y  26 dysq.easytnlppGdYtlkV 45 
                                       d+   ++sy   + G+Yt+++
  gi|386001339|ref|YP_005919638.1| 846 DS-LgTLSYASDSVGSYTITA 865
                                       33.24999999999****986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00041
                                       EEEEES--SEEEEEEEEEEE CS
                             Y_Y_Y  30 easytnlppGdYtlkVkakd 49 
                                        ++y +l+pG Yt++V+++ 
  gi|386001339|ref|YP_005919638.1| 943 AFEYQPLEPGLYTVEVRGIQ 962
                                       799*************9876 PP

>> A2M  Alpha-2-macroglobulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.015        19      51      78 ..     796     823 ..     776     825 .. 0.88
   2 ?    5.1   0.0     0.016        20      46      91 ..     874     919 ..     838     921 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                                       EE--SEEEEEE--SEEETTSEEEEEEEE CS
                               A2M  51 rvfkpffvdlnlPysvrrgeqveikavv 78 
                                       +v  + ++ ++ P+ v +ge++ ika++
  gi|386001339|ref|YP_005919638.1| 796 EVAEERILAVTAPQEVMKGESFVIKATI 823
                                       577888999*****************98 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                       EEEEEEE--SEEEE.EE--SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                               A2M  46 eplevrvfkpffvd.lnlPysvrrgeqveikavvfNyldkeikvrve 91 
                                       ++ +++v  p+ ++ +++P++vr g +vei+a+  N      + +ve
  gi|386001339|ref|YP_005919638.1| 874 SR-RIVVASPIRITgIEMPETVRAGKTVEITATAENPGAVSDTTTVE 919
                                       44.77788888776589*****************9987666666665 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.19   2.4e+02      65      84 ..     292     311 ..     243     313 .. 0.90
   2 ?    8.0   0.1    0.0032       4.1      28      86 ..     521     588 ..     513     590 .. 0.60
   3 ?   -2.2   0.0       4.7     6e+03      37      73 ..     641     680 ..     624     691 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                                       TTEEEEEEEEEE-SSEEEEE CS
                           DUF4179  65 nGitvtvnevvaDgnklivs 84 
                                        G+++ ++e+ +Dgnk++++
  gi|386001339|ref|YP_005919638.1| 292 EGYELRIKEIDLDGNKVWLA 311
                                       69**************9875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                                       XXXXXXX..--SS-HHHHT--SS-.......HHHHSEEEEEEE.EETTEEEEEEEEEE-SSEEEEEEE CS
                           DUF4179  28 palAsaln.pvigslfeklsdskg.......eqeyvkpvnksa.ednGitvtvnevvaDgnklivsys 86 
                                         +A + + +v+ + f+++++++         q y+   + +   + G+++ ++ev +Dgnk+++s++
  gi|386001339|ref|YP_005919638.1| 521 KYFAGYNSeTVFTNEFSLINEGQLrkvliddDQSYTVRSGTTFpLKEGYELRIKEVDLDGNKIFLSIT 588
                                       55555555455555555555443333444333333333333336689******************986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.7
                                       -SS-HHHHT--SS-...HHHHSEEEEEEEEETTEEEEEEE CS
                           DUF4179  37 vigslfeklsdskg...eqeyvkpvnksaednGitvtvne 73 
                                       +i+++f+ +++ ++    + y k    s++d Gi +t ++
  gi|386001339|ref|YP_005919638.1| 641 TIEGIFQISDKPRSveeGETYDKMEIDSVSDSGIVMTNDG 680
                                       5667777776666676544444444569999999998665 PP

>> DUF4981  Domain of unknown function(DUF4981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.6   7.1e+03      11      34 ..     302     325 ..     300     336 .. 0.78
   2 ?    5.6   0.0     0.017        22      11      44 ..     577     606 ..     573     636 .. 0.79
   3 ?    3.1   0.0       0.1   1.3e+02      18      63 ..     917     959 ..     883     974 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.6
                                       -GGGEEEEEEEEETTEEEEEEEEE CS
                           DUF4981  11 dlsdldlswellkdGkvvasgele 34 
                                       dl+  ++   l kdG++v+s  ++
  gi|386001339|ref|YP_005919638.1| 302 DLDGNKVWLALAKDGSEVDSRVVD 325
                                       7888888888999**999987665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                                       -GGGEEEEEEEEETTEEEEEEEEEE---TT-EEE CS
                           DUF4981  11 dlsdldlswellkdGkvvasgelelpvaPgesat 44 
                                       dl+  ++  +++kdG++v+s+     v+Pg ++t
  gi|386001339|ref|YP_005919638.1| 577 DLDGNKIFLSITKDGEEVDSKV----VEPGRTVT 606
                                       89999999***********974....55888776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.1
                                       EEEEEETTEEEEEEEEEE---TT-EEEEE--S.---TSSEEEEEEE CS
                           DUF4981  18 swellkdGkvvasgelelpvaPgesatvtlpetkeaeeseyfltvs 63 
                                       ++el  +G  v +g++e++v Pge+ +  ++++  +++  y+++v+
  gi|386001339|ref|YP_005919638.1| 917 TVELRVNG--VPEGTMEVTVGPGETGSAAFEYQPLEPG-LYTVEVR 959
                                       56788888..778999999*****99988765444333.4444443 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00058      0.75      50      91 ..     443     479 ..     423     484 .. 0.81
   2 ?   -3.2   0.0       6.6   8.4e+03      57      69 ..     760     772 ..     752     774 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00058
                        Cadherin_5  50 aenGtvvdngdGtftftpeanynGevtlsYtvsDgeggttta 91 
                                       +  Gt+vd ++G+ft+tp  n++G   + Y+++D+ g+ t  
  gi|386001339|ref|YP_005919638.1| 443 EIRGTIVDPAEGEFTWTPY-NFEG---FYYDIDDDVGTET-L 479
                                       457***************5.9999...99*****986543.3 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.6
                        Cadherin_5  57 dngdGtftftpea 69 
                                       + +dG + +tp a
  gi|386001339|ref|YP_005919638.1| 760 TTADGIYLYTPPA 772
                                       4579******976 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.072        93      13      32 ..     292     311 ..     290     324 .. 0.87
   2 ?    6.7   0.1    0.0063       8.1      13      45 ..     567     595 ..     565     608 .. 0.85
   3 ?   -3.3   0.2       8.5   1.1e+04      17      40 ..     883     911 ..     883     918 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.072
                            PrcB_C  13 gGYsievdkvyetenaiyvk 32 
                                       +GY ++++++ +++n++ + 
  gi|386001339|ref|YP_005919638.1| 292 EGYELRIKEIDLDGNKVWLA 311
                                       8**************99876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0063
                            PrcB_C  13 gGYsievdkvyetenaiyvkttllgPepgeevt 45 
                                       +GY +++++v +++n+i + +t    ++geev 
  gi|386001339|ref|YP_005919638.1| 567 EGYELRIKEVDLDGNKIFLSIT----KDGEEVD 595
                                       7******************999....6777765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.5
                            PrcB_C  17 ievdkvy.....etenaiyvkttllgPep 40 
                                       i++++++     + + ++ ++ t  +P++
  gi|386001339|ref|YP_005919638.1| 883 IRITGIEmpetvRAGKTVEITATAENPGA 911
                                       66777776655533334444444337753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1008 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.50
# Mc/sec: 6014.79
//
Query:       gi|386001340|ref|YP_005919639.1|  [L=432]
Description: Phenylacetate-coenzyme A ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-29  101.4   0.4    5.5e-29  100.3   0.4    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    1.4e-14   53.6   0.0    1.5e-13   50.2   0.0    2.0  1  AMP-binding      AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.4   6.1e-33   5.5e-29       1      96 []     333     430 ..     333     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 6.1e-33
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEET.TEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtreg.elDelevkvEvke.gfsdelkelealekkiakklksklgvsvkve 75 
                                       G+nvfPsqie+vl +i+e+++++q+vv+r+  +lDe+++kvE+++ +f+ el++l++l+kk++++lks+++++ k+e
  gi|386001340|ref|YP_005919639.1| 333 GINVFPSQIEDVLLKIPEIGDYFQVVVDRKRhGLDEISIKVEMSDrAFTGELADLARLQKKVEDELKSVMKIRSKIE 409
                                       99***************************9538************88999*************************** PP

                                       EE-TT-S---------EEE-S CS
                   AMP-binding_C_2  76 lvepgtlprsegKakrviDkR 96 
                                       lve+g+lpr+egK+k+++D R
  gi|386001340|ref|YP_005919639.1| 410 LVEKGSLPRTEGKSKKIVDLR 430
                                       *******************98 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.6e-17   1.5e-13     167     422 ..      91     331 ..      78     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.6e-17
                                       E--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                       AMP-binding 167 TSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                       +SGTTGkP  V ++ r + +    ++ ++    +++++dv+   + + + +g  l++ + + + +++ +++++  ++
  gi|386001340|ref|YP_005919639.1|  91 SSGTTGKPTVVGYTARDIETWSDMVA-RDLvmVGCTKEDVFQNAVNYGFFTGG-LGIHYGIERMGAMAVPSGTGSTR 165
                                       8****************954423322.22245668889**************8.66666666666677777777733 PP

                                       HHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEE CS
                       AMP-binding 242 pklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGl 317
                                         + +e + +++vt ++++P+ + +l+e   +     +  d  slr+  +g+ep s  + +++++ +  + +++YGl
  gi|386001340|ref|YP_005919639.1| 166 --RQIEIMIDFGVTALHCTPSYALYLAEtVTDMGL--A--DDLSLRVGCFGAEPWSDRARTELEEMLNIKAYDSYGL 236
                                       ..44899999****************885544442..2..4456***999*****************99******** PP

                                       GGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEET CS
                       AMP-binding 318 TEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdse 392
                                       +E+ g  + ++++e+       G  ++  +  v+i+D++ g p+++ge Gel++ +            +t+ea+   
  gi|386001340|ref|YP_005919639.1| 237 SEMFGPGVAFECQEQ------NGLHIWedHFLVEILDPD-GLPCAPGERGELVLTS------------LTKEAMP-L 293
                                       ******984554444......36666445899******9.99**********9864............5666663.2 PP

                                       CCEEEEEEEEEEETTS.........EEEEEEECCCEEEE CS
                       AMP-binding 393 grwlrTGDlgrldedG.........yleivgRkkdlikl 422
                                          ++TGD+ ++ ++            +++gR++d++++
  gi|386001340|ref|YP_005919639.1| 294 I-RYHTGDVTFMMAEEcpcgrtsvkLHRFLGRADDMLVV 331
                                       2.5777777776433334446665456677777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2805.59
//
Query:       gi|386001341|ref|YP_005919640.1|  [L=109]
Description: hypothetical protein Mhar_0639 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 813.03
//
Query:       gi|386001342|ref|YP_005919641.1|  [L=319]
Description: V8-like Glu-specific endopeptidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-10   42.1   0.1    2.5e-10   41.5   0.1    1.3  1  Trypsin_2     Trypsin-like peptidase domain
    5.3e-09   36.2   0.5    1.1e-07   31.9   0.5    2.1  1  Trypsin       Trypsin
     0.0024   17.8   0.1     0.0064   16.4   0.1    1.8  2  Peptidase_C3  3C cysteine protease (picornain 3C)


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.1   4.1e-14   2.5e-10       1     146 [.     125     285 ..     125     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.1e-14
                         Trypsin_2   1 GsGflvgsdglilTnaHvv.......................dsadgaav....kaikkkveeagadgrevpakvva 50 
                                       G+G ++g++  +lT+ H+v                              +     +     ++ +++++ v++ v  
  gi|386001342|ref|YP_005919641.1| 125 GTGAFIGPRV-VLTAGHCVylhadggwarkirvipgrnggssC------PssgtSSVCPYGYADATQYTSVKGWVNN 194
                                       9*********.********887666666666666555544321......0222233344455666677777777999 PP

                         Trypsin_2  51 adpelDlAllkv..ssderaglpplplgp.sealkggepvyvvGyplggeksg.svssGivsgvvesesaasgeges 123
                                       +d+++D+A++ +   ++ ++ ++++ l++ s  +  g +v   Gyp+ ++ ++ +++s+ + +v+           +
  gi|386001342|ref|YP_005919641.1| 195 KDSDYDYAVIILpaNQKLGNTVGWMGLANlSMGSLLGLNVNSSGYPGDKPYGTqWWNSNNILAVTG----------R 261
                                       99999********99999***********766888888*******876666669************..........9 PP

                         Trypsin_2 124 flqtdaatspGsSGGplfd.sdGr 146
                                       +l + ++t +G+SG+p+++ +dG+
  gi|386001342|ref|YP_005919641.1| 262 RLYYRIDTMGGQSGSPVWRyKDGQ 285
                                       9999999999********999987 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.5   1.8e-11   1.1e-07      23     199 ..     118     295 ..      97     316 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.8e-11
                                       C...EEEEEEEEEETTEEEEEGGGTTT......GGGEEE...EESESBTTSCTTT....EEEEEEEEEEEETTEBTT CS
                           Trypsin  23 g...khlCgGslisenwvlTAaHCvsn......asdvkv...vlgehnlkksegk....eqklkvekvivhpnynps 83 
                                       +    ++ +G+ i+++ vlTA+HCv+       a++++v   + g ++  +s ++    + +++  ++++ +++  +
  gi|386001342|ref|YP_005919641.1| 118 PngkAYIGTGAFIGPRVVLTAGHCVYLhadggwARKIRVipgRNGGSSCPSSGTSsvcpYGYADATQYTSVKGWVNN 194
                                       34567899******************999999988999955555554444444436666777788888888888888 PP

                                       T.TTTTEEEEEESSSSTSBSSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTT CS
                           Trypsin  84 t.ldnDiallklkepvklgdtvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgk 159
                                       +  d+D+a++ l ++ klg+tv ++ l+  s  +  g  +  sG++ +k  g     q  +  +     +       
  gi|386001342|ref|YP_005919641.1| 195 KdSDYDYAVIILPANQKLGNTVGWMGLANLSMGSLLGLNVNSSGYPGDKPYG----TQWWNSNN-----ILA----- 257
                                       867*************************966555777778888887776666....22222222.....222..... PP

                                       STTTEEEEESTTSSSBCTTTTTTSEEEETTT...EEEEEEEEE CS
                           Trypsin 160 vtenmlcagakeggkdacqGDSGGPlvcsdg...elvGivswg 199
                                       vt + l         d+  G SG+P+ + +     ++Gi++ g
  gi|386001342|ref|YP_005919641.1| 258 VTGRRLYYRI-----DTMGGQSGSPVWRYKDgqrHIIGIHTTG 295
                                       3334344444.....5556677777666655566666776666 PP

>> Peptidase_C3  3C cysteine protease (picornain 3C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.67     4e+03      97     123 ..      42      68 ..      35      78 .. 0.77
   2 !   16.4   0.1   1.1e-06    0.0064     137     172 ..     260     295 ..     180     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.67
                                       ---EEEEEEEE-SSSSTTEEEEEEEEE CS
                      Peptidase_C3  97 ikkgkpvvllinnneagrlivsveavt 123
                                       ++k++p++ l  +++++++iv+  +v+
  gi|386001342|ref|YP_005919641.1|  42 VDKMTPEMALAEAERFEEVIVEAADVS 68 
                                       678888999999999999999888775 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-06
                                       EEEEEESS---TT-TT-EEEE....TTEEEEEEEEE CS
                      Peptidase_C3 137 artlsYkaktkaGmCGgvviakeegngkilGiHvaG 172
                                        r l Y++ t  G+ G +v   ++g+  i+GiH  G
  gi|386001342|ref|YP_005919641.1| 260 GRRLYYRIDTMGGQSGSPVWRYKDGQRHIIGIHTTG 295
                                       56789****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2039.33
//
Query:       gi|386001343|ref|YP_005919642.1|  [L=556]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-43  142.6   0.8    4.9e-11   41.9   0.0    5.4  5  TPR_1            Tetratricopeptide repeat
    1.5e-38  127.8   6.9    7.9e-08   31.8   0.0    5.5  5  TPR_2            Tetratricopeptide repeat
    1.5e-34  117.4   0.6    1.4e-08   34.3   0.1    4.5  4  TPR_11           TPR repeat
    4.5e-27   92.0   0.5    9.4e-07   28.6   0.0    5.5  5  TPR_8            Tetratricopeptide repeat
    1.9e-22   79.6  10.6    3.1e-11   43.7   0.3    3.7  3  TPR_16           Tetratricopeptide repeat
    5.3e-20   71.5   5.5    1.4e-07   31.7   0.3    4.0  3  TPR_12           Tetratricopeptide repeat
    6.2e-20   70.2  11.8    4.9e-05   23.8   0.2    5.4  5  TPR_14           Tetratricopeptide repeat
    6.5e-20   70.0   1.2    3.1e-05   24.0   0.1    4.5  4  TPR_17           Tetratricopeptide repeat
    4.4e-16   59.1   2.3    3.9e-08   33.7   0.0    2.7  2  TPR_19           Tetratricopeptide repeat
    1.6e-14   53.8   4.3    2.1e-07   31.0   0.5    2.6  2  TPR_9            Tetratricopeptide repeat
    9.6e-14   50.3   3.0      0.003   17.5   0.0    4.9  5  TPR_7            Tetratricopeptide repeat
    3.9e-13   49.6   3.7    5.8e-13   49.0   3.7    1.2  1  Beta_helix       Right handed beta helix region
    2.9e-09   36.8   0.2      0.023   14.8   0.0    4.3  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    6.3e-09   35.5  12.7    3.5e-08   33.0  13.0    1.7  1  NosD             Periplasmic copper-binding protein (NosD)
      5e-08   33.1   0.7        3.9    8.3   0.0    5.4  5  TPR_6            Tetratricopeptide repeat
    5.4e-07   29.3   8.8       0.31   11.0   0.1    4.9  4  TPR_10           Tetratricopeptide repeat
    1.8e-06   27.5   1.1    0.00014   21.3   1.1    2.1  1  DUF1565          Protein of unknown function (DUF1565)
    3.3e-05   24.4   4.6      0.065   13.7   0.1    3.1  3  BTAD             Bacterial transcriptional activator domain
    4.3e-05   23.6   0.0       0.23   11.7   0.0    3.9  4  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    0.00023   21.1   0.4        7.6    6.7   0.0    4.4  4  MIT              MIT (microtubule interacting and transport) 
     0.0019   18.3   0.3        2.9    7.9   0.1    3.5  2  DUF3856          Domain of Unknown Function (DUF3856)
     0.0023   17.2   0.3        7.6    5.7   0.1    3.2  4  TPR_15           Tetratricopeptide repeat
     0.0037   17.1   0.0        1.5    8.6   0.0    3.1  3  DUF5113          Domain of unknown function (DUF5113)
     0.0067   15.4   0.3       0.11   11.4   0.0    2.4  3  NARP1            NMDA receptor-regulated protein 1
     0.0085   15.5   0.0        3.6    7.1   0.0    3.7  4  SHNi-TPR         SHNi-TPR
  ------ inclusion threshold ------
      0.027   13.7   0.1       0.36   10.0   0.0    2.5  2  FAT              FAT domain
      0.032   13.1   0.0       0.12   11.2   0.0    1.8  2  Chondroitinas_B  Chondroitinase B
      0.036   14.3   0.3        1.5    9.1   0.3    2.3  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      0.053   14.2   2.0         97    4.1   0.1    4.8  4  TPR_4            Tetratricopeptide repeat
       0.11   12.2   0.1        8.6    6.0   0.1    3.0  3  TPR_21           Tetratricopeptide repeat-like domain
       0.23   11.8   0.5         18    5.8   0.0    3.7  3  PPR              PPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   3.1e-09   1.8e-06       4      34 .]     393     423 ..     392     423 .. 0.93
   2 !   28.8   0.0   1.2e-09     7e-07       1      32 [.     424     455 ..     424     457 .. 0.96
   3 !   33.8   0.1   3.3e-11   1.9e-08       1      34 []     458     491 ..     458     491 .. 0.96
   4 !   41.9   0.0   8.5e-14   4.9e-11       1      32 [.     492     523 ..     492     525 .. 0.97
   5 ?    4.4   0.0     0.061        35       3      27 ..     528     552 ..     526     555 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.1e-09
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + + G  ++  g+y eA+ +ye+ALe++P n
  gi|386001343|ref|YP_005919642.1| 393 WTRWGDSLLGSGRYPEAITCYERALEIDPAN 423
                                       7888999999*******************65 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.2e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a a+ ++G  ++  g+yd+Al  ye+ALe++P
  gi|386001343|ref|YP_005919642.1| 424 AAAWAGKGDGLMMTGRYDKALRSYERALEIDP 455
                                       789****************************9 PP

  == domain 3  score: 33.8 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a  ++++Gna++ l ++++A ++y++AL+++P++
  gi|386001343|ref|YP_005919642.1| 458 AAGWCRKGNALQMLLRFEDAMACYNEALRIDPEF 491
                                       678*****************************86 PP

  == domain 4  score: 41.9 bits;  conditional E-value: 8.5e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a++++G ++ +lg+y eAle++++ALe++P
  gi|386001343|ref|YP_005919642.1| 492 AEAWNRRGSTLNRLGRYSEALECFDRALEIDP 523
                                       89****************************** PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                       a+  +  a++ lg+ + A e++++A
  gi|386001343|ref|YP_005919642.1| 528 AWSSKSWAHQMLGEDEAAKEAFDRA 552
                                       5555557999**************9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0     6e-10   3.4e-07       4      34 .]     393     423 ..     390     423 .. 0.94
   2 !   29.6   0.0   6.9e-10     4e-07       1      33 [.     424     456 ..     424     457 .. 0.95
   3 !   26.0   0.2     1e-08   6.1e-06       1      33 [.     458     490 ..     458     491 .. 0.95
   4 !   31.8   0.0   1.4e-10   7.9e-08       1      33 [.     492     524 ..     492     525 .. 0.97
   5 !   10.2   0.1    0.0012      0.68       1      27 [.     526     552 ..     526     554 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6e-10
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       + ++G++++ +g+y eA+ ++e+Ale+dP n
  gi|386001343|ref|YP_005919642.1| 393 WTRWGDSLLGSGRYPEAITCYERALEIDPAN 423
                                       889**************************86 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 6.9e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+   G+ ++  g+y++Al+ +e+Ale+dP 
  gi|386001343|ref|YP_005919642.1| 424 AAAWAGKGDGLMMTGRYDKALRSYERALEIDPA 456
                                       689*****************************5 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 1e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a ++++ G+a+  l ++e+A +++++Al++dP+
  gi|386001343|ref|YP_005919642.1| 458 AAGWCRKGNALQMLLRFEDAMACYNEALRIDPE 490
                                       678*****************************7 PP

  == domain 4  score: 31.8 bits;  conditional E-value: 1.4e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea++++G  + +lg+y eAle+f++Ale+dP+
  gi|386001343|ref|YP_005919642.1| 492 AEAWNRRGSTLNRLGRYSEALECFDRALEIDPG 524
                                       89******************************6 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0012
                             TPR_2   1 aealynlGlayyklgdyeeAleafekA 27 
                                       a a+    +a+  lg+ e A+eaf++A
  gi|386001343|ref|YP_005919642.1| 526 ASAWSSKSWAHQMLGEDEAAKEAFDRA 552
                                       579999********************9 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   2.4e-11   1.4e-08       1      35 [.     397     431 ..     397     436 .. 0.91
   2 !   30.4   0.0     4e-10   2.3e-07       5      40 ..     435     470 ..     431     471 .. 0.90
   3 !   29.0   0.0   1.1e-09   6.1e-07       9      42 .]     473     506 ..     473     506 .. 0.93
   4 !   22.1   0.0   1.5e-07   8.6e-05       1      33 [.     499     531 ..     499     540 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.4e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                       Gd +   G+y+eAi++Y++Al++dP na a+ + G
  gi|386001343|ref|YP_005919642.1| 397 GDSLLGSGRYPEAITCYERALEIDPANAAAWAGKG 431
                                       7788889***********************98766 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 4e-10
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       +  G+y++A+ +Y++Al++dP +a  ++  G+a+++
  gi|386001343|ref|YP_005919642.1| 435 MMTGRYDKALRSYERALEIDPASAAGWCRKGNALQM 470
                                       557******************************986 PP

  == domain 3  score: 29.0 bits;  conditional E-value: 1.1e-09
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++e+A+++Y++Al++dP++aea++ +G ++ ++G
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALRIDPEFAEAWNRRGSTLNRLG 506
                                       689************************9887776 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.5e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                                       G  +  +G+y eA+e++ +Al++dP  a+a++ 
  gi|386001343|ref|YP_005919642.1| 499 GSTLNRLGRYSEALECFDRALEIDPGLASAWSS 531
                                       5567789*******************9999975 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.4e-06    0.0025       8      34 .]     397     423 ..     393     423 .. 0.90
   2 !   16.7   0.0   1.1e-05    0.0062       3      33 ..     426     456 ..     424     457 .. 0.84
   3 !   16.2   0.0   1.5e-05    0.0088       3      33 ..     460     490 ..     458     491 .. 0.93
   4 !   28.6   0.0   1.6e-09   9.4e-07       1      32 [.     492     523 ..     492     524 .. 0.98
   5 ?    6.0   0.1     0.028        16       1      27 [.     526     552 ..     526     552 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.4e-06
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpdn 34 
                                       g+ +l  g+y eA+ +ye+ale+dp+n
  gi|386001343|ref|YP_005919642.1| 397 GDSLLGSGRYPEAITCYERALEIDPAN 423
                                       7888999******************86 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+  +g+ ++ +g+y++A  +ye+ale+dp+
  gi|386001343|ref|YP_005919642.1| 426 AWAGKGDGLMMTGRYDKALRSYERALEIDPA 456
                                       666677777779******************7 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        ++++g++++ l ++e A+++y++al++dp+
  gi|386001343|ref|YP_005919642.1| 460 GWCRKGNALQMLLRFEDAMACYNEALRIDPE 490
                                       69****************************7 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 1.6e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       aea+++ gs++  lg+y eA e++ +ale+dp
  gi|386001343|ref|YP_005919642.1| 492 AEAWNRRGSTLNRLGRYSEALECFDRALEIDP 523
                                       79*****************************9 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.028
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyeka 27 
                                       a+a+  ++++++ lg+ e+Ake++ +a
  gi|386001343|ref|YP_005919642.1| 526 ASAWSSKSWAHQMLGEDEAAKEAFDRA 552
                                       67899999****************987 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.3   5.4e-14   3.1e-11       3      67 ..     396     457 ..     394     458 .. 0.96
   2 !   37.8   0.3   3.7e-12   2.1e-09       3      66 ..     464     524 ..     462     526 .. 0.94
   3 !   20.0   0.6   1.4e-06   0.00081       9      62 ..     504     554 ..     504     556 .] 0.94

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 5.4e-14
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++++l +g+y++A+  +e+al+ d   P++a+A+ ++gd +   gr+++A+  y++al+ +p +
  gi|386001343|ref|YP_005919642.1| 396 WGDSLLGSGRYPEAITCYERALEID---PANAAAWAGKGDGLMMTGRYDKALRSYERALEIDPAS 457
                                       799**********************...**********************************987 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 3.7e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++a+  + +++dA a +++al+ d   P+ aeA++ +g  + r+gr+ eA++ +++al+ +p+
  gi|386001343|ref|YP_005919642.1| 464 KGNALQMLLRFEDAMACYNEALRID---PEFAEAWNRRGSTLNRLGRYSEALECFDRALEIDPG 524
                                       6777778889***************...**********************************97 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1.4e-06
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       r+g+y +A++ +++al+ d   P  a A+  + +a+  +g+ ++A +++++a +
  gi|386001343|ref|YP_005919642.1| 504 RLGRYSEALECFDRALEID---PGLASAWSSKSWAHQMLGEDEAAKEAFDRARG 554
                                       68*****************...*******************99999***99965 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   3.2e-10   1.9e-07       8      76 ..     395     455 ..     392     456 .. 0.91
   2 !   23.3   1.0   9.9e-08   5.7e-05       4      76 ..     425     489 ..     423     490 .. 0.89
   3 !   31.7   0.3   2.5e-10   1.4e-07       3      71 ..     492     552 ..     490     555 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.2e-10
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++++ l+  gry eA++++e+alei      p +   a++  + g+ + ++gry++Al+ +e+al+i++
  gi|386001343|ref|YP_005919642.1| 395 RWGDSLLGSGRYPEAITCYERALEID-----PAN---AAAWAGKGDGLMMTGRYDKALRSYERALEIDP 455
                                       68999999******************.....765...999999999999*****************975 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 9.9e-08
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a+   ++ l+  gryd+Al+ +e+alei      p     a+  +  g ++++l r+e+A + ++eal+i++
  gi|386001343|ref|YP_005919642.1| 425 AAWAGKGDGLMMTGRYDKALRSYERALEID-----PA---SAAGWCRKGNALQMLLRFEDAMACYNEALRIDP 489
                                       45546899999*******************.....75...58889999**********************986 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 2.5e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       a a+n+++++l+rlgry eAle++++alei      p   ++a++    ++++++lg+ e+A e++ +a
  gi|386001343|ref|YP_005919642.1| 492 AEAWNRRGSTLNRLGRYSEALECFDRALEID-----P---GLASAWSSKSWAHQMLGEDEAAKEAFDRA 552
                                       899*99*************************.....4...39************************998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   3.2e-07   0.00018       4      41 ..     393     430 ..     390     433 .. 0.90
   2 !   20.7   0.2   8.3e-07   0.00048       3      42 ..     426     465 ..     426     467 .. 0.90
   3 !   14.7   0.1     7e-05      0.04      16      41 ..     473     498 ..     465     500 .. 0.89
   4 !   23.8   0.2   8.5e-08   4.9e-05       1      38 [.     492     529 ..     492     532 .. 0.96
   5 ?    0.9   0.5       1.9   1.1e+03       9      27 ..     534     552 ..     526     555 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       + + ++ ll +G++ eAi++++ral+ +P++a+aw   
  gi|386001343|ref|YP_005919642.1| 393 WTRWGDSLLGSGRYPEAITCYERALEIDPANAAAWAGK 430
                                       6778999999*************************865 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 8.3e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a++  ++ l+  G++d+A++ ++ral+ +P++a+ w + +
  gi|386001343|ref|YP_005919642.1| 426 AWAGKGDGLMMTGRYDKALRSYERALEIDPASAAGWCRKG 465
                                       57777888999************************98865 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 7e-05
                            TPR_14  16 dpdeAiallrralalaPddaeawlll 41 
                                       ++++A+a++++al+ +P++aeaw + 
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALRIDPEFAEAWNRR 498
                                       79*********************765 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 8.5e-08
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +ea+ ++++ l +lG++ eA+++++ral+ +P+ a aw
  gi|386001343|ref|YP_005919642.1| 492 AEAWNRRGSTLNRLGRYSEALECFDRALEIDPGLASAW 529
                                       589******************************99998 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.9
                            TPR_14   9 eallalGdpdeAiallrra 27 
                                       +a+  lG+ ++A ++++ra
  gi|386001343|ref|YP_005919642.1| 534 WAHQMLGEDEAAKEAFDRA 552
                                       5666677777777777776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.2e-05     0.012       1      33 [.     412     444 ..     412     445 .. 0.92
   2 !   12.9   0.0    0.0002      0.12       2      26 ..     447     471 ..     446     479 .. 0.87
   3 !   24.0   0.1   5.4e-08   3.1e-05       1      34 []     480     513 ..     480     513 .. 0.96
   4 !   13.0   0.0   0.00019      0.11       1      34 []     514     547 ..     514     547 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y++ale+dP na a+  ++  l + G++++A+
  gi|386001343|ref|YP_005919642.1| 412 CYERALEIDPANAAAWAGKGDGLMMTGRYDKAL 444
                                       8****************9999999999999885 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0002
                            TPR_17   2 ylkaleldPnnadaynnLAelllkn 26 
                                       y++ale+dP +a  ++ ++++l ++
  gi|386001343|ref|YP_005919642.1| 447 YERALEIDPASAAGWCRKGNALQML 471
                                       9********************9865 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 5.4e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +al++dP  a+a+n ++ +l ++G++ +A++
  gi|386001343|ref|YP_005919642.1| 480 CYNEALRIDPEFAEAWNRRGSTLNRLGRYSEALE 513
                                       8****************************99975 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.00019
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ +ale+dP  a a+  + +++ ++G+ + A++
  gi|386001343|ref|YP_005919642.1| 514 CFDRALEIDPGLASAWSSKSWAHQMLGEDEAAKE 547
                                       799*************************999975 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   6.7e-11   3.9e-08       1      59 [.     400     458 ..     400     462 .. 0.95
   2 !   24.7   0.1   4.4e-08   2.6e-05       6      61 ..     473     528 ..     467     533 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6.7e-11
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       ll +g+y eA+  +e+al+ dp na+a+++  + l+ +g++d+A +  ++++e dp +a
  gi|386001343|ref|YP_005919642.1| 400 LLGSGRYPEAITCYERALEIDPANAAAWAGKGDGLMMTGRYDKALRSYERALEIDPASA 458
                                       7999***************************************************9965 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 4.4e-08
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       ++++A+a + +al  dp+ aea+ +    l  lg++ eA ++ d+++e dp  a +
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALRIDPEFAEAWNRRGSTLNRLGRYSEALECFDRALEIDPGLASA 528
                                       5899***********************************************96333 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   7.4e-08   4.3e-05       8      62 ..     403     457 ..     399     460 .. 0.93
   2 !   31.0   0.5   3.6e-10   2.1e-07      10      61 ..     473     524 ..     465     548 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.4e-08
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       + ++++a+ ++er l ++P  +  +   G  l+  G++ +Al+  e++l+++p+ 
  gi|386001343|ref|YP_005919642.1| 403 SGRYPEAITCYERALEIDPANAAAWAGKGDGLMMTGRYDKALRSYERALEIDPAS 457
                                       67899************************************************76 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 3.6e-10
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++e a+a+++  l ++P+ +e +  RG  l +lG++s+Al++++++l+++p 
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALRIDPEFAEAWNRRGSTLNRLGRYSEALECFDRALEIDPG 524
                                       6899**********************************************94 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-05     0.017      12      32 ..     403     421 ..     397     425 .. 0.78
   2 !   11.8   0.1   0.00034       0.2      13      29 ..     438     454 ..     436     459 .. 0.82
   3 ?    2.3   0.0      0.37   2.1e+02      14      33 ..     473     490 ..     461     493 .. 0.78
   4 !   17.5   0.0   5.2e-06     0.003       1      29 [.     494     522 ..     494     528 .. 0.85
   5 ?   -2.2   0.0       9.8   5.7e+03       8      24 ..     535     551 ..     524     552 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                             TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                        G+y eAi++ye++L+++  p
  gi|386001343|ref|YP_005919642.1| 403 SGRYPEAITCYERALEID--P 421
                                       69***********66554..4 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00034
                             TPR_7  13 GdyeeAielyeqsLalt 29 
                                       G+y++A++ ye++L+++
  gi|386001343|ref|YP_005919642.1| 438 GRYDKALRSYERALEID 454
                                       9***********66665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.37
                             TPR_7  14 dyeeAielyeqsLaltkdpe 33 
                                       ++e+A  +y +  al+ dpe
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNE--ALRIDPE 490
                                       79*********..6666655 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 5.2e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a+++ +++  rlG+y+eA+e++ ++L+++
  gi|386001343|ref|YP_005919642.1| 494 AWNRRGSTLNRLGRYSEALECFDRALEID 522
                                       688999******************66655 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 9.8
                             TPR_7   8 lysrlGdyeeAielyeq 24 
                                       +++ lG+ e A e + +
  gi|386001343|ref|YP_005919642.1| 535 AHQMLGEDEAAKEAFDR 551
                                       33338888888777765 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 !   49.0   3.7     1e-15   5.8e-13      22     114 ..      88     180 ..      73     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1e-15
                                       SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT..-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE CS
                        Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgs..snntisnntisdnngggialfgasnnlienneitdnggsGiy 96 
                                       gg++++l  ++  +ie+ +++n +g+G +  ++  ++n i++n i+dn  +gi+l+ga + +ie n i++n+  Gi+
  gi|386001343|ref|YP_005919642.1|  88 GGSAVTLLADGA-TIEGFVLEN-GGFGWAGIEVrsKENAIRGNLITDNRWYGIYLDGAEGCVIEENVIWNNKY-GIW 161
                                       677778888887.999999999.55544444444499999999999999999999999999999999999976.999 PP

                                       -T.T-S--EEES-EEESTT CS
                        Beta_helix  97 ln.yssnntienNiidnna 114
                                       +n +ss n +++N++ +n+
  gi|386001343|ref|YP_005919642.1| 162 INaGSSGNLVRKNVLQENE 180
                                       9988999999999999998 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.018        10      15      35 ..     404     424 ..     400     428 .. 0.90
   2 !    7.6   0.0    0.0066       3.8      14      33 ..     437     456 ..     433     458 .. 0.90
   3 ?    2.5   0.0      0.26   1.5e+02      16      37 ..     473     494 ..     470     496 .. 0.89
   4 !   14.8   0.0     4e-05     0.023      13      35 ..     504     526 ..     502     538 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.018
                                       T-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenr 35 
                                       g+Y eA  + ++ Lei+P n 
  gi|386001343|ref|YP_005919642.1| 404 GRYPEAITCYERALEIDPANA 424
                                       89*****************96 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0066
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                        g+Y++A+r  ++ Lei+P 
  gi|386001343|ref|YP_005919642.1| 437 TGRYDKALRSYERALEIDPA 456
                                       589***************96 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.26
                                       -HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenrQa 37 
                                       ++++A+ + +  L+i+Pe+  a
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALRIDPEFAEA 494
                                       6899**************9876 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 4e-05
                                       HHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                       +lg+YseA+++ d+ Lei+P+  
  gi|386001343|ref|YP_005919642.1| 504 RLGRYSEALECFDRALEIDPGLA 526
                                       9*******************865 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  13.0   6.1e-11   3.5e-08     112     212 ..     119     202 ..     108     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.1e-11
                              NosD 112 dssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWn 187
                                       +s++n i++N i+ n  +Gi+l+++++ +i++N i +n k+Gi++ ++s+gn++ +N + +n++  + d +  n W 
  gi|386001343|ref|YP_005919642.1| 119 RSKENAIRGNLITdNRWYGIYLDGAEGCVIEENVIWNN-KYGIWINAGSSGNLVRKNVLQENENRNAFDLG-TNLW- 192
                                       46778899999999999999999999999999999999.99999999999999999999777766665554.8999. PP

                              NosD 188 ttktsgtniiggpylgGNyWsdydg 212
                                                      +GN+++dydg
  gi|386001343|ref|YP_005919642.1| 193 ---------------EGNFYDDYDG 202
                                       ...............7999999998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.039        23       6      31 ..     396     421 ..     394     423 .. 0.83
   2 !    8.3   0.0    0.0068       3.9      13      33 .]     437     457 ..     426     457 .. 0.87
   3 ?    1.3   0.1       1.2   6.7e+02       7      31 ..     465     489 ..     463     490 .. 0.80
   4 ?    6.5   0.0     0.025        14       7      31 ..     499     523 ..     494     524 .. 0.84
   5 ?    4.0   0.1      0.16        91       8      26 ..     534     552 ..     532     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                        + s++  g++ +A++ +er ++  P
  gi|386001343|ref|YP_005919642.1| 396 WGDSLLGSGRYPEAITCYERALEIDP 421
                                       577777757************99887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0068
                                       HHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  13 lgdtdkAlealerlikeYPdS 33 
                                       +g++dkAl+ +er ++  P S
  gi|386001343|ref|YP_005919642.1| 437 TGRYDKALRSYERALEIDPAS 457
                                       58**************99976 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.2
                                       HHHHHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrk.lgdtdkAlealerlikeYP 31 
                                       + ++++ l + ++A++ +++ ++  P
  gi|386001343|ref|YP_005919642.1| 465 GNALQMlL-RFEDAMACYNEALRIDP 489
                                       55666657.99*********999877 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       +  + +lg++++Ale ++r ++  P
  gi|386001343|ref|YP_005919642.1| 499 GSTLNRLGRYSEALECFDRALEIDP 523
                                       55566789************99887 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerl 26 
                                       +++++lg+ ++A+ea++r 
  gi|386001343|ref|YP_005919642.1| 534 WAHQMLGEDEAAKEAFDRA 552
                                       7899999*********986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.012       6.8      15      31 ..     403     419 ..     398     420 .. 0.87
   2 !    8.2   0.0     0.004       2.3      13      31 ..     435     453 ..     431     453 .. 0.88
   3 ?    5.1   0.1     0.038        22       9      31 ..     465     487 ..     464     487 .. 0.94
   4 !   11.0   0.1   0.00053      0.31       9      31 ..     499     521 ..     492     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                            TPR_10  15 rgrydeAealleealai 31 
                                        gry eA   +e+al+i
  gi|386001343|ref|YP_005919642.1| 403 SGRYPEAITCYERALEI 419
                                       69999999999999987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.004
                            TPR_10  13 rqrgrydeAealleealai 31 
                                         +gryd+A++ +e+al+i
  gi|386001343|ref|YP_005919642.1| 435 MMTGRYDKALRSYERALEI 453
                                       568**************97 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.038
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +nal+ + r+++A+a + eal+i
  gi|386001343|ref|YP_005919642.1| 465 GNALQMLLRFEDAMACYNEALRI 487
                                       899*****************986 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00053
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + +l ++gry eA++ +++al+i
  gi|386001343|ref|YP_005919642.1| 499 GSTLNRLGRYSEALECFDRALEI 521
                                       8899*****************97 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.1   2.4e-07   0.00014      17     190 ..      38     180 ..      28     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.4e-07
                           DUF1565  17 tiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagkkvgplisgggddlsgvqnvt 93 
                                       +i  A+ +a++g+v+ + +GtY e      P+ +++     G+ + +           v     ggg+       vt
  gi|386001343|ref|YP_005919642.1|  38 SIQEAIDAARPGDVVSVQNGTYRETLVVDRPIALRDA----GDGTDRPI---------VD--AAGGGSA------VT 93 
                                       7889999999999999999999999999999999552....44333333.........33..2344444......44 PP

                           DUF1565  94 ivlaneatiaGvtitNpnilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiai 170
                                        +la+ ati G+ ++N       g+ ++s    i+ N it+n   Gi  +         g +i  n i ++k Gi i
  gi|386001343|ref|YP_005919642.1|  94 -LLADGATIEGFVLENGG-FGWAGIEVRSKENAIRGNLITDNRWYGIYLDGA------EGCVIEENVIWNNKYGIWI 162
                                       .46788999999999994.477889999999999999999999999866655......5889999999999999999 PP

                           DUF1565 171 sgasaavenkienNiivkNl 190
                                       +  s +  n +++N++ +N 
  gi|386001343|ref|YP_005919642.1| 163 NAGSSG--NLVRKNVLQENE 180
                                       998888..888999998885 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.6     9e+02      24      46 ..     180     202 ..     170     209 .. 0.81
   2 !   13.7   0.1   0.00011     0.065      72     123 ..     400     451 ..     393     459 .. 0.92
   3 !    9.8   0.8    0.0018         1      43     123 ..     473     553 ..     454     555 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHTT--SSTTGGGTT CS
                              BTAD  24 eaaelleaAlalwrGpaladlea 46 
                                       e +++++ + +lw+G +++d + 
  gi|386001343|ref|YP_005919642.1| 180 ENRNAFDLGTNLWEGNFYDDYDG 202
                                       566789999*********99765 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       +l  Gr+ ea++ +e++++ +P + ++++     l+ +Gr  +AL+ Yer+ 
  gi|386001343|ref|YP_005919642.1| 400 LLGSGRYPEAITCYERALEIDPANAAAWAGKGDGLMMTGRYDKALRSYERAL 451
                                       67789********************************************985 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0018
                                       GGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                              BTAD  43 dleagewleaererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevY 119
                                        +e+ + +  e+ r++ ++ ea  ++   + rlGr++eal+  +++++ +P    ++     A   +G+ ++A e++
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALRIDPEFAEAWNRRGSTLNRLGRYSEALECFDRALEIDPGLASAWSSKSWAHQMLGEDEAAKEAF 549
                                       45668889999999999***********************************9999999999999999999999999 PP

                                       HHHH CS
                              BTAD 120 erlr 123
                                       +r+r
  gi|386001343|ref|YP_005919642.1| 550 DRAR 553
                                       9987 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0004      0.23       7      36 ..     389     418 ..     384     425 .. 0.84
   2 ?    0.3   0.0       1.5   8.6e+02      13      35 ..     429     451 ..     420     460 .. 0.83
   3 ?    0.9   0.0      0.95   5.5e+02      13      34 ..     463     484 ..     452     489 .. 0.83
   4 ?    4.6   0.0     0.064        37       8      35 ..     492     519 ..     488     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0004
                         NRBF2_MIT   7 lahqqsrkadrllaaGkyeeaischkkaaa 36 
                                        a   +r  d ll +G+y eai+c+++a +
  gi|386001343|ref|YP_005919642.1| 389 TAGDWTRWGDSLLGSGRYPEAITCYERALE 418
                                       566678999****************99965 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.5
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkkaa 35 
                                        k d l+ +G+y++a+  +++a 
  gi|386001343|ref|YP_005919642.1| 429 GKGDGLMMTGRYDKALRSYERAL 451
                                       57899**********99988875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.95
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkka 34 
                                       rk + l    ++e+a++c++ a
  gi|386001343|ref|YP_005919642.1| 463 RKGNALQMLLRFEDAMACYNEA 484
                                       77778888889*******9887 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.064
                         NRBF2_MIT   8 ahqqsrkadrllaaGkyeeaischkkaa 35 
                                       a   +r+   l   G+y ea+ c  +a 
  gi|386001343|ref|YP_005919642.1| 492 AEAWNRRGSTLNRLGRYSEALECFDRAL 519
                                       6667999999*************99986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       7.6      18      32 ..     404     418 ..     401     419 .. 0.91
   2 ?    4.7   0.0     0.054        31      18      32 ..     438     452 ..     437     453 .. 0.91
   3 ?   -0.3   0.0         2   1.1e+03      20      32 ..     474     486 ..     471     487 .. 0.86
   4 ?    3.4   0.0      0.14        81      18      32 ..     506     520 ..     500     526 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                               MIT  18 gnyeeAlelYkeale 32 
                                       g y+eA+ +Y+ ale
  gi|386001343|ref|YP_005919642.1| 404 GRYPEAITCYERALE 418
                                       89***********98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.054
                               MIT  18 gnyeeAlelYkeale 32 
                                       g y++Al+ Y+ ale
  gi|386001343|ref|YP_005919642.1| 438 GRYDKALRSYERALE 452
                                       78***********98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2
                               MIT  20 yeeAlelYkeale 32 
                                       +e+A+ +Y eal+
  gi|386001343|ref|YP_005919642.1| 474 FEDAMACYNEALR 486
                                       799*******986 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.14
                               MIT  18 gnyeeAlelYkeale 32 
                                       g y+eAle++  ale
  gi|386001343|ref|YP_005919642.1| 506 GRYSEALECFDRALE 520
                                       789999999999887 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0051       2.9      45      83 ..     414     452 ..     406     490 .. 0.76
   2 ?    6.0   0.1      0.02        12     105     128 ..     497     520 ..     458     523 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0051
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalr 83 
                                       e a++ +  +a ++ag  + l+  gryd+al+s ++al+
  gi|386001343|ref|YP_005919642.1| 414 ERALEIDPANAAAWAGKGDGLMMTGRYDKALRSYERALE 452
                                       566777778899999999999999999999999999985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmage 128
                                       +r+ +l+ lGr++eal+ f  a e
  gi|386001343|ref|YP_005919642.1| 497 RRGSTLNRLGRYSEALECFDRALE 520
                                       566677777777777777766655 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.07        40     149     182 ..     393     426 ..     388     430 .. 0.83
   2 ?    4.5   0.1     0.029        17     158     180 ..     436     458 ..     424     462 .. 0.85
   3 ?   -1.8   0.0       2.5   1.4e+03     157     178 ..     469     490 ..     457     494 .. 0.72
   4 ?    5.7   0.1     0.013       7.6     147     200 ..     493     546 ..     468     553 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.07
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdssel 182
                                       + + + + +  g+  +A+++y++Al+ +p+++++
  gi|386001343|ref|YP_005919642.1| 393 WTRWGDSLLGSGRYPEAITCYERALEIDPANAAA 426
                                       666667778889999***************9876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.029
                            TPR_15 158 qegqtdaAlrdyreAlalapdss 180
                                        +g+ d+Alr y++Al+ +p+s+
  gi|386001343|ref|YP_005919642.1| 436 MTGRYDKALRSYERALEIDPASA 458
                                       68999***************975 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.5
                            TPR_15 157 rqegqtdaAlrdyreAlalapd 178
                                       +   + ++A+ +y eAl+ +p+
  gi|386001343|ref|YP_005919642.1| 469 QMLLRFEDAMACYNEALRIDPE 490
                                       555566899********99996 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.013
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLr 200
                                         + +r++   + g+  +Al+++ +Al+ +p+ +++ +   W+   lg+++ ++
  gi|386001343|ref|YP_005919642.1| 493 EAWNRRGSTLNRLGRYSEALECFDRALEIDPGLASAWSSKSWAHQMLGEDEAAK 546
                                       5699999***********************998877777666666666655555 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.27   1.6e+02       5      36 ..     387     418 ..     384     426 .. 0.91
   2 ?    2.3   0.0      0.22   1.3e+02       8      37 ..     424     453 ..     420     483 .. 0.81
   3 !    8.6   0.0    0.0025       1.5       7      36 ..     491     520 ..     481     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                           DUF5113   5 lqiandYanlayylnvegeyeeALeyldsale 36 
                                       l +a+d+  ++  l  +g+y eA+++ + ale
  gi|386001343|ref|YP_005919642.1| 387 LYTAGDWTRWGDSLLGSGRYPEAITCYERALE 418
                                       678999************************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaley 37 
                                       a ++a  +  l ++g+y++AL+  + ale+
  gi|386001343|ref|YP_005919642.1| 424 AAAWAGKGDGLMMTGRYDKALRSYERALEI 453
                                       56677778888899************9986 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0025
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        a+++   +++ln  g+y+eALe++d ale
  gi|386001343|ref|YP_005919642.1| 491 FAEAWNRRGSTLNRLGRYSEALECFDRALE 520
                                       4778888999******************97 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.47   2.7e+02     184     257 ..     379     455 ..     355     457 .. 0.76
   2 ?    0.5   0.0      0.37   2.1e+02     206     256 ..     438     488 ..     434     491 .. 0.88
   3 !   11.4   0.0   0.00019      0.11     203     255 ..     503     555 ..     499     556 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.47
                                       ----SSHHHHHHHHHHHHHHH...HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 184 ekepesallwvlyflAqhydk...lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                        +ep+++ l++      + d     g++ +A+++ ++a+e +p     +  K+  l  +G  +kA +  e+a ++D 
  gi|386001343|ref|YP_005919642.1| 379 VDEPPEVTLYTAGDWTRWGDSllgSGRYPEAITCYERALEIDPANAAAWAGKGDGLMMTGRYDKALRSYERALEIDP 455
                                       566666666666666666666322345669999999*******9999999999999999999999999999999885 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       g+++kAl+  ++a+e +p +   + +K++ l+    +++A+++ +ea ++D
  gi|386001343|ref|YP_005919642.1| 438 GRYDKALRSYERALEIDPASAAGWCRKGNALQMLLRFEDAMACYNEALRID 488
                                       789999999999999999999999999999999999999999999988777 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00019
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       ++lg++++Ale+ d+a+e +p l   +  K+  ++  G+ ++A e+ ++ar l
  gi|386001343|ref|YP_005919642.1| 503 NRLGRYSEALECFDRALEIDPGLASAWSSKSWAHQMLGEDEAAKEAFDRARGL 555
                                       8899**********************************************986 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0062       3.6      14      30 ..     403     419 ..     397     419 .. 0.92
   2 ?    1.2   0.0      0.44   2.6e+02      14      30 ..     437     453 ..     435     453 .. 0.90
   3 ?   -1.7   0.0       3.6   2.1e+03      16      29 ..     473     486 ..     473     487 .. 0.86
   4 ?    1.7   0.0      0.32   1.8e+02      16      30 ..     507     521 ..     506     521 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0062
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++p+A++ +++aLe+
  gi|386001343|ref|YP_005919642.1| 403 SGRYPEAITCYERALEI 419
                                       79*************98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.44
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       +++++ A+  +++aLe+
  gi|386001343|ref|YP_005919642.1| 437 TGRYDKALRSYERALEI 453
                                       579************98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.6
                          SHNi-TPR  16 nFpqAveDlrkaLe 29 
                                       +F++A   +++aL 
  gi|386001343|ref|YP_005919642.1| 473 RFEDAMACYNEALR 486
                                       79***999999996 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.32
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++++A+e +++aLe+
  gi|386001343|ref|YP_005919642.1| 507 RYSEALECFDRALEI 521
                                       8************98 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.67   3.9e+02     270     291 ..     408     429 ..     396     486 .. 0.63
   2 ?   10.0   0.0   0.00062      0.36     240     293 ..     487     535 ..     459     541 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.67
                                       SCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 270 eilqsysaateidpswykawht 291
                                       e+  +y +a eidp  + aw+ 
  gi|386001343|ref|YP_005919642.1| 408 EAITCYERALEIDPANAAAWAG 429
                                       5666677777777766666653 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00062
                                       ...HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC..CC CS
                               FAT 240 ftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawht..wa 293
                                       +  + a++ +++G+ +++l++        +e+l+++ +a eidp+++ aw +  wa
  gi|386001343|ref|YP_005919642.1| 487 IDPEFAEAWNRRGSTLNRLGR-------YSEALECFDRALEIDPGLASAWSSksWA 535
                                       55677999999***9999999.......89********************875576 PP

>> Chondroitinas_B  Chondroitinase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00021      0.12       5      49 ..      37      87 ..      34     103 .. 0.68
   2 ?   -1.0   0.0       1.1   6.3e+02     307     366 ..     147     208 ..     140     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                      HHHHHHHHH--TT-EEEE-SEEEET-.....EEEE-S--B.TTB-EEEEES CS
                   Chondroitinas_B  5 keleeavkeakpGdeivlknGvykdv.....qlkfkgeGt.eekPivlkae 49
                                      + ++ea+++a+pGd+++++nG+y++       + +   G   ++Piv +a 
  gi|386001343|ref|YP_005919642.1| 37 SSIQEAIDAARPGDVVSVQNGTYRETlvvdrPIALRDAGDgTDRPIVDAAG 87
                                      6799*******************9751111134455555423566665555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                       EEES-EEES-S.......SE..EEEHHHHHHHCT---B---SEEEES-EEE--SS----SEE CS
                   Chondroitinas_B 307 viaynsfidvksplqfsvGs..nidkkevlpaseirsarperiivannliykdkekkkpiva 366
                                       vi +n   ++k  +    Gs  n+ +k+vl+++e r a    + + +  +y+d + + p+ +
  gi|386001343|ref|YP_005919642.1| 147 VIEENVIWNNKYGIWINAGSsgNLVRKNVLQENENRNAFDLGTNLWEGNFYDDYDGSRPFYE 208
                                       67777777777777777776225559999999999999988888877778888887777765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3    0.0027       1.5       3      79 ..     404     481 ..     402     484 .. 0.80
   2 ?    8.6   0.2    0.0036       2.1       2      81 ..     437     517 ..     436     518 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                                       T-HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       ++y +Ai ++er+l  e + +++a +  ++  l  +g+y++A++ +++a ++++ s + +  ++ +l  L ++e+A 
  gi|386001343|ref|YP_005919642.1| 404 GRYPEAITCYERAL--EIDPANAAAWagKGDGLMMTGRYDKALRSYERAlEIDPASAAGWCRKGNALQMLLRFEDAM 478
                                       6899**********..6666666666447*******************99998888887777777777777777777 PP

                                       HHH CS
                            ANAPC3  77 aaL 79 
                                       a++
  gi|386001343|ref|YP_005919642.1| 479 ACY 481
                                       766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0036
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +++y++A+  +er+l+ ++ s+     ++ +l  + +++ A+  +++a +++++  +++   + +l  L++y eA+ 
  gi|386001343|ref|YP_005919642.1| 437 TGRYDKALRSYERALEIDPASAAGWCRKGNALQMLLRFEDAMACYNEAlRIDPEFAEAWNRRGSTLNRLGRYSEALE 513
                                       689************6666555555558************************************************* PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       ++++
  gi|386001343|ref|YP_005919642.1| 514 CFDR 517
                                       9986 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.89   5.2e+02       9      26 .]     398     415 ..     397     415 .. 0.82
   2 ?    4.1   0.1      0.17        97       2      26 .]     425     449 ..     424     449 .. 0.82
   3 ?    3.5   0.1      0.25   1.5e+02       8      26 .]     499     517 ..     492     517 .. 0.83
   4 ?   -0.8   0.1       6.1   3.5e+03       5      26 .]     530     551 ..     526     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.89
                             TPR_4   9 rallalGdldeAraller 26 
                                         ll  G+++eA +  er
  gi|386001343|ref|YP_005919642.1| 398 DSLLGSGRYPEAITCYER 415
                                       579999******887776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                       +a ++ +  l  +G++d A++  er
  gi|386001343|ref|YP_005919642.1| 425 AAWAGKGDGLMMTGRYDKALRSYER 449
                                       667777888999********98886 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.25
                             TPR_4   8 ArallalGdldeAraller 26 
                                       + +l +lG++ eA++ ++r
  gi|386001343|ref|YP_005919642.1| 499 GSTLNRLGRYSEALECFDR 517
                                       56799*********99876 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 6.1
                             TPR_4   5 laLArallalGdldeAraller 26 
                                       +   +a++ lG+ ++A ++++r
  gi|386001343|ref|YP_005919642.1| 530 SSKSWAHQMLGEDEAAKEAFDR 551
                                       5567999****99999887765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.21   1.2e+02     153     178 ..     397     422 ..     388     428 .. 0.87
   2 ?    6.0   0.1     0.015       8.6     152     185 ..     430     469 ..     422     479 .. 0.80
   3 ?   -1.9   0.0         4   2.3e+03     148     174 ..     494     520 ..     478     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.21
                            TPR_21 153 GDilvaqgkldeAraaYqaAlaalee 178
                                       GD l+  g+  eA + Y++Al+   +
  gi|386001343|ref|YP_005919642.1| 397 GDSLLGSGRYPEAITCYERALEIDPA 422
                                       9*******************986655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka......rellq 185
                                       +GD l+ +g+ d+A   Y++Al+   ++a       ++lq
  gi|386001343|ref|YP_005919642.1| 430 KGDGLMMTGRYDKALRSYERALEIDPASAagwcrkGNALQ 469
                                       9*********************988877666665545555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4
                            TPR_21 148 vaelrGDilvaqgkldeAraaYqaAla 174
                                       + ++rG  l + g+  eA + +++Al+
  gi|386001343|ref|YP_005919642.1| 494 AWNRRGSTLNRLGRYSEALECFDRALE 520
                                       45789999999*******999999986 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.5   2.6e+03      11      25 ..     401     415 ..     393     419 .. 0.78
   2 ?    0.7   0.0       1.4   7.9e+02       8      24 ..     432     448 ..     432     453 .. 0.81
   3 ?    5.8   0.0     0.032        18      12      26 ..     504     518 ..     495     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.5
                               PPR  11 cknGkleeAlelfke 25 
                                         +G++ eA+ ++++
  gi|386001343|ref|YP_005919642.1| 401 LGSGRYPEAITCYER 415
                                       5589999**999987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
                               PPR   8 sgycknGkleeAlelfk 24 
                                       +g+   G++++Al+ ++
  gi|386001343|ref|YP_005919642.1| 432 DGLMMTGRYDKALRSYE 448
                                       588899******98666 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.032
                               PPR  12 knGkleeAlelfkeM 26 
                                       + G+++eAle+f++ 
  gi|386001343|ref|YP_005919642.1| 504 RLGRYSEALECFDRA 518
                                       89**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3851.37
//
Query:       gi|386001344|ref|YP_005919643.1|  [L=226]
Description: hypothetical protein Mhar_0642 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1661.71
//
Query:       gi|386001345|ref|YP_005919644.1|  [L=2136]
Description: hypothetical protein Mhar_0643 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-83  272.5  11.0    1.3e-06   28.6   0.0   14.0 14  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    5.5e-72  239.1  32.3    5.4e-08   33.1   0.2   13.8 13  SdrD_B           SdrD B-like domain
    9.2e-47  157.3  45.5    7.1e-05   23.1   0.2   13.4 12  SpaA             Prealbumin-like fold domain
    2.7e-12   46.8   0.0    2.8e-06   27.5   0.0    8.7 10  DUF11            Domain of unknown function DUF11
    5.2e-11   42.5   4.2       0.18   11.8   0.0    9.5 13  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    2.4e-10   40.3  30.3        2.5    8.2   0.1   13.1 13  CarbopepD_reg_2  CarboxypepD_reg-like domain
    2.3e-07   30.4   4.1         28    4.1   0.0    9.4 10  Dioxygenase_C    Dioxygenase
    2.8e-05   24.1   9.5         13    6.0   0.1    8.4  9  HepII_C          Heparinase II C-terminal domain
  ------ inclusion threshold ------
       0.13   12.1   1.9         14    5.6   0.4    4.0  2  DUF824           Salmonella repeat of unknown function (DUF82


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0023       4.7       7      52 ..     209     255 ..     204     256 .. 0.87
   2 !   21.3   0.0   1.2e-07   0.00024       6      52 ..     301     347 ..     296     368 .. 0.91
   3 !   28.6   0.0   6.5e-10   1.3e-06       5      80 ..     389     466 ..     385     468 .. 0.85
   4 !   24.4   0.0   1.3e-08   2.6e-05      10      75 ..     483     550 ..     477     555 .. 0.75
   5 !   23.0   0.0   3.6e-08   7.2e-05      12      75 ..     574     639 ..     568     644 .. 0.79
   6 !   23.7   0.0   2.1e-08   4.2e-05      10      75 ..     661     728 ..     655     733 .. 0.79
   7 !   23.2   0.0     3e-08     6e-05      10      72 ..     750     814 ..     744     822 .. 0.78
   8 !   23.4   0.0   2.6e-08   5.2e-05       7      71 ..     835     901 ..     833     912 .. 0.77
   9 !   26.1   0.0   3.9e-09   7.7e-06       7      71 ..     925     991 ..     923    1002 .. 0.76
  10 !   15.4   0.1   8.4e-06     0.017       7      53 ..    1014    1061 ..    1009    1069 .. 0.89
  11 !   14.2   0.1     2e-05     0.039       7      53 ..    1107    1154 ..    1102    1163 .. 0.89
  12 !   11.3   0.0   0.00016      0.31       7      53 ..    1200    1247 ..    1195    1254 .. 0.88
  13 !   19.1   0.0   6.1e-07    0.0012       9      52 ..    1297    1341 ..    1289    1374 .. 0.88
  14 ?   -4.2   0.1         9   1.8e+04       5      19 ..    1403    1417 ..    1401    1418 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0023
                   CarboxypepD_reg   7 tda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysv 52 
                                        da +++p++g ++t+++ d+++     t+++G +++ gl+  ++sv
  gi|386001345|ref|YP_005919644.1| 209 LDAaNNQPLEGWNITLQDCDGKVIGWDITNETGFWKICGLQCCNFSV 255
                                       675599************99******************999887765 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.2e-07
                   CarboxypepD_reg   6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysv 52 
                                       V d  +  ++g ++t++n+ +    +ttt+++G++++ gl  g+y+v
  gi|386001345|ref|YP_005919644.1| 301 VIDCEDVDLSGWNITLYNETDVLIDTTTTNETGYYQFCGLDHGNYKV 347
                                       7777778899*******999999**********************98 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 6.5e-10
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysv.tvsapGyatatre..evtltagqtttld 78 
                                       +V d  g  +++ t+t+tn ++gtv +t t+a+G +r+ +l pg+y+v +  +pG+  +t +  +v lt++++t+ +
  gi|386001345|ref|YP_005919644.1| 389 KVIDCEGFDLSNWTITLTN-SSGTVGTTLTNATGWYRFCDLVPGSYTVcETLKPGFTNVTPTclDVPLTCDNATDKN 464
                                       588889999*********6.9**************************945589999999975446777777777777 PP

                   CarboxypepD_reg  79 it 80 
                                       +t
  gi|386001345|ref|YP_005919644.1| 465 FT 466
                                       65 PP

  == domain 4  score: 24.4 bits;  conditional E-value: 1.3e-08
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysv.tvsapGyatatre..evtltagqtt 75 
                                        ga  ++ t+t+tn ++gtv +t t+a+G +r+ +l pg+y+v +  +pG+  ++ +  +v lt+++ t
  gi|386001345|ref|YP_005919644.1| 483 EGADHSNWTITLTN-SSGTVGTTLTNATGWYRFCDLVPGSYTVcETLKPGFTNVSPTclDVPLTCDNVT 550
                                       57777899*****6.9**************************934467777766654334555555555 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 3.6e-08
                   CarboxypepD_reg  12 apiagatVtvtnadtgtvastttdadGafrlrglppgtysv.tvsapGyatatre..evtltagqtt 75 
                                       a  ++ t+t+tn ++gtv +t t+a+G +r+ +l pg y+v +  +pG+  +t +  +v lt+++ t
  gi|386001345|ref|YP_005919644.1| 574 ADHSNWTITLTN-SSGTVGTTLTNATGWYRFCDLVPGIYTVcETVKPGFTNVTPTciDVPLTCDNVT 639
                                       5567889****6.9**************************954579999999976334555555555 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 2.1e-08
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysv.tvsapGyatatre..evtltagqtt 75 
                                        ga  ++ t+t+tn ++gtv +t t+a+G +r+ +l pg y+v +  +pG+  +t +  +v lt+++ t
  gi|386001345|ref|YP_005919644.1| 661 EGADHSNWTITLTN-SSGTVGTTLTNATGWYRFCDLVPGIYTVcETVKPGFTNVTPTciDVPLTCDNVT 728
                                       57777899*****6.9**************************954579999999976334555555555 PP

  == domain 7  score: 23.2 bits;  conditional E-value: 3e-08
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysv.tvsapGyatatre..evtltag 72 
                                        ga  ++ t+t+tn ++gtv +t t+a+G +r+ +l pg y+v +  +pG+  +t +  +v lt++
  gi|386001345|ref|YP_005919644.1| 750 EGADHSNWTITLTN-SSGTVGTTLTNATGWYRFCDLVPGIYTVcETVKPGFTNVTPTclDVPLTCD 814
                                       57777899*****6.9**************************954578999988875334555555 PP

  == domain 8  score: 23.4 bits;  conditional E-value: 2.6e-08
                   CarboxypepD_reg   7 tdasgapiagatVtvtnadtgt.vastttdadGafrlrglppgtysvtv.sapGyatatreevtlta 71 
                                        d  g  +++ t+t++na t++   +ttt+a+G + + +l pg+y v+   +pGy  ++ + v +t 
  gi|386001345|ref|YP_005919644.1| 835 IDCEGSDLSNWTITLYNATTNQpINTTTTNATGWYIFCDLVPGDYAVEEtVKPGYVNFSAKRVPVTL 901
                                       56679999*********876653899*********************86568888877766555443 PP

  == domain 9  score: 26.1 bits;  conditional E-value: 3.9e-09
                   CarboxypepD_reg   7 tdasgapiagatVtvtnadtgt.vastttdadGafrlrglppgtysvtv.sapGyatatreevtlta 71 
                                        d  g  +++ t+t++na t++   +ttt+a+G +++ gl pg+y v+   +pGy  ++ + v +t 
  gi|386001345|ref|YP_005919644.1| 925 IDCEGSDLSNWTITLYNATTNQpINTTTTNATGWYSFCGLVPGDYAVEEtIKPGYVNFSAKRVPVTL 991
                                       56679999*********876653899*********************87557788777765444443 PP

  == domain 10  score: 15.4 bits;  conditional E-value: 8.4e-06
                   CarboxypepD_reg    7 tdasgapiagatVtvtnadtgt.vastttdadGafrlrglppgtysvt 53  
                                        t+ +ga ++g t++v+ ++t+t v + ttd++G++ + +l pgty+v+
  gi|386001345|ref|YP_005919644.1| 1014 TNDTGARLPGWTIEVYVNGTQTkVGENTTDSEGEWIVCDLLPGTYDVK 1061
                                        6789***********998888736889******************995 PP

  == domain 11  score: 14.2 bits;  conditional E-value: 2e-05
                   CarboxypepD_reg    7 tdasgapiagatVtvtnadtgt.vastttdadGafrlrglppgtysvt 53  
                                        t+ +ga ++g t++v+ ++t+t v + +td++G++ + +l pgty+v+
  gi|386001345|ref|YP_005919644.1| 1107 TNDTGARLPGWTIEVYVNGTQTkVGENVTDSKGEWIVCDLLPGTYDVK 1154
                                        7789***********998888736889******************995 PP

  == domain 12  score: 11.3 bits;  conditional E-value: 0.00016
                   CarboxypepD_reg    7 tdasgapiagatVtvtnadtgt.vastttdadGafrlrglppgtysvt 53  
                                        t+ +g  ++g +++v+ ++t+t v + ttd++G++ + +l pg y+v+
  gi|386001345|ref|YP_005919644.1| 1200 TNDTGVTLPGWKIEVYVNGTETkVGENTTDSEGEWIICDLLPGVYDVK 1247
                                        678999*********987776637899******************985 PP

  == domain 13  score: 19.1 bits;  conditional E-value: 6.1e-07
                   CarboxypepD_reg    9 asgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysv 52  
                                        ++++p++g ++tvt++++++v ++ttd++G++++ gl+   +y+v
  gi|386001345|ref|YP_005919644.1| 1297 SNKTPLEGWNITVTDSSGTVVGNATTDDEGYWKICGLAFgENYTV 1341
                                        6899***********9999****************9998666766 PP

  == domain 14  score: -4.2 bits;  conditional E-value: 9
                   CarboxypepD_reg    5 rVtdasgapiagatV 19  
                                        +V +  g p+ ++tV
  gi|386001345|ref|YP_005919644.1| 1403 TVCNNGGVPVRNVTV 1417
                                        67888999****999 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0058        11      19      70 ..     212     263 ..     205     292 .. 0.83
   2 !   33.1   0.2   2.7e-11   5.4e-08      18      71 ..     303     357 ..     298     383 .. 0.80
   3 !   24.2   0.0   1.6e-08   3.1e-05      26      75 ..     400     449 ..     391     470 .. 0.81
   4 !   22.8   0.0   4.3e-08   8.5e-05      28      71 ..     491     534 ..     481     554 .. 0.84
   5 !   21.8   0.1   8.5e-08   0.00017      28      74 ..     580     626 ..     573     642 .. 0.84
   6 !   21.9   0.1   7.9e-08   0.00016      28      74 ..     669     715 ..     659     731 .. 0.84
   7 !   21.8   0.1   8.4e-08   0.00017      28      74 ..     758     804 ..     748     817 .. 0.85
   8 !   28.0   0.1   9.7e-10   1.9e-06      24      76 ..     842     896 ..     833     914 .. 0.82
   9 !   29.6   0.2   3.1e-10   6.2e-07      24      77 ..     932     987 ..     924    1019 .. 0.79
  10 !   11.0   0.1   0.00019      0.37      25      90 ..    1022    1088 ..    1009    1112 .. 0.75
  11 !    9.1   0.1   0.00073       1.5      24      72 ..    1114    1163 ..    1093    1174 .. 0.77
  12 !    7.4   0.0    0.0025       4.9      19      66 ..    1200    1250 ..    1185    1263 .. 0.74
  13 !   12.3   0.0   7.6e-05      0.15      19      70 ..    1297    1349 ..    1289    1361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0058
                            SdrD_B  19 agekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy 70 
                                       a+++  +g ++tL+d +g+v+   +T+++G +k  +l+  +++V  +   g+
  gi|386001345|ref|YP_005919644.1| 212 ANNQPLEGWNITLQDCDGKVIGWDITNETGFWKICGLQCCNFSVCEILKPGW 263
                                       466999**********************************999987665555 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 2.7e-11
                            SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.t 71 
                                       d ++   sg ++tL+++++ +++tttT+++G+Y+F +l++G+YkV  +  +g+ +
  gi|386001345|ref|YP_005919644.1| 303 DCEDVDLSGWNITLYNETDVLIDTTTTNETGYYQFCGLDHGNYKVCEEVKDGWqN 357
                                       5566778999***********************************9988888743 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 1.6e-08
                            SdrD_B  26 gvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvtak 75 
                                       + t+tL++++g+v  tt+T+a+G Y+F +l pG+Y+V  t   g+ +vt++
  gi|386001345|ref|YP_005919644.1| 400 NWTITLTNSSGTV-GTTLTNATGWYRFCDLVPGSYTVCETLKPGFtNVTPT 449
                                       5689998777765.6**********************99997777466665 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 4.3e-08
                            SdrD_B  28 tVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.t 71 
                                       t+tL++++g+v  tt+T+a+G Y+F +l pG+Y+V  t   g+ +
  gi|386001345|ref|YP_005919644.1| 491 TITLTNSSGTV-GTTLTNATGWYRFCDLVPGSYTVCETLKPGFtN 534
                                       89997777765.6**********************9988777634 PP

  == domain 5  score: 21.8 bits;  conditional E-value: 8.5e-08
                            SdrD_B  28 tVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvta 74 
                                       t+tL++++g+v  tt+T+a+G Y+F +l pG Y+V  t   g+ +vt+
  gi|386001345|ref|YP_005919644.1| 580 TITLTNSSGTV-GTTLTNATGWYRFCDLVPGIYTVCETVKPGFtNVTP 626
                                       89997777765.6**********************9999777745665 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 7.9e-08
                            SdrD_B  28 tVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvta 74 
                                       t+tL++++g+v  tt+T+a+G Y+F +l pG Y+V  t   g+ +vt+
  gi|386001345|ref|YP_005919644.1| 669 TITLTNSSGTV-GTTLTNATGWYRFCDLVPGIYTVCETVKPGFtNVTP 715
                                       89997777765.6**********************9999777745665 PP

  == domain 7  score: 21.8 bits;  conditional E-value: 8.4e-08
                            SdrD_B  28 tVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvta 74 
                                       t+tL++++g+v  tt+T+a+G Y+F +l pG Y+V  t   g+ +vt+
  gi|386001345|ref|YP_005919644.1| 758 TITLTNSSGTV-GTTLTNATGWYRFCDLVPGIYTVCETVKPGFtNVTP 804
                                       89997777765.6**********************9999777745555 PP

  == domain 8  score: 28.0 bits;  conditional E-value: 9.7e-10
                            SdrD_B  24 isgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagy.tvtakk 76 
                                        s+ t+tL++a++++  +tttT+a+G Y F +l pG+Y Ve t   gy +++ak 
  gi|386001345|ref|YP_005919644.1| 842 LSNWTITLYNATTNQPiNTTTTNATGWYIFCDLVPGDYAVEETVKPGYvNFSAKR 896
                                       67789***9999988779************************9988885676654 PP

  == domain 9  score: 29.6 bits;  conditional E-value: 3.1e-10
                            SdrD_B  24 isgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapagy.tvtakka 77 
                                        s+ t+tL++a++++  +tttT+a+G Y+F +l pG+Y Ve t   gy +++ak  
  gi|386001345|ref|YP_005919644.1| 932 LSNWTITLYNATTNQPiNTTTTNATGWYSFCGLVPGDYAVEETIKPGYvNFSAKRV 987
                                       67789***9999988779************************99888857776654 PP

  == domain 10  score: 11.0 bits;  conditional E-value: 0.00019
                            SdrD_B   25 sgvtVtLk.dakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGsddaldSdadpa 90  
                                         g t++++ + ++++v + tTd++G++   +l pG+Y V+ +  ag+t      G  + +  d++++
  gi|386001345|ref|YP_005919644.1| 1022 PGWTIEVYvNGTQTKVGENTTDSEGEWIVCDLLPGTYDVKEVVDAGWTPIDPADGWHRGVVLDCEKT 1088
                                        56667774145566679************************99999988777777666666665555 PP

  == domain 11  score: 9.1 bits;  conditional E-value: 0.00073
                            SdrD_B   24 isgvtVtLk.dakgevvatttTdasGkYkFtnltpGeYkVeftapagytv 72  
                                          g t++++ + ++++v + +Td++G++   +l pG+Y V+ +  ag+t 
  gi|386001345|ref|YP_005919644.1| 1114 LPGWTIEVYvNGTQTKVGENVTDSKGEWIVCDLLPGTYDVKEVVDAGWTP 1163
                                        567777774145566669***********************999988865 PP

  == domain 12  score: 7.4 bits;  conditional E-value: 0.0025
                            SdrD_B   19 agekgi..sgvtVtL.kdakgevvatttTdasGkYkFtnltpGeYkVefta 66  
                                        ++++g+   g ++++  + ++++v + tTd++G++   +l pG Y V+ + 
  gi|386001345|ref|YP_005919644.1| 1200 TNDTGVtlPGWKIEVyVNGTETKVGENTTDSEGEWIICDLLPGVYDVKEVL 1250
                                        4454442257777773355666779**********************8665 PP

  == domain 13  score: 12.3 bits;  conditional E-value: 7.6e-05
                            SdrD_B   19 agekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGe.YkVeftapagy 70  
                                        ++++  +g ++t++d++g+vv + tTd +G++k  +l+ Ge Y+V  +  +g+
  gi|386001345|ref|YP_005919644.1| 1297 SNKTPLEGWNITVTDSSGTVVGNATTDDEGYWKICGLAFGEnYTVCEELKEGW 1349
                                        4558899*********************************99**987777666 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.3e-06     0.011      18      62 ..     307     351 ..     212     371 .. 0.65
   2 !   11.8   0.1   0.00011      0.23      28      64 ..     400     441 ..     351     459 .. 0.74
   3 !   11.4   0.1   0.00015       0.3      28      64 ..     489     530 ..     455     545 .. 0.80
   4 !   12.6   0.0   6.5e-05      0.13      29      71 ..     584     626 ..     552     637 .. 0.76
   5 !   12.6   0.1   6.4e-05      0.13      29      71 ..     673     715 ..     651     726 .. 0.73
   6 !   11.8   0.1   0.00011      0.22      29      64 ..     762     797 ..     740     813 .. 0.77
   7 !   21.9   0.2   8.1e-08   0.00016       5      79 ..     841     902 ..     837     905 .. 0.85
   8 !   23.1   0.2   3.5e-08   7.1e-05       5      79 ..     931     992 ..     927     995 .. 0.85
   9 !   16.0   0.3   5.6e-06     0.011       2      62 ..    1017    1064 ..    1010    1093 .. 0.82
  10 !   14.7   0.2   1.4e-05     0.028       2      61 ..    1110    1156 ..    1084    1160 .. 0.76
  11 !   13.2   0.2   4.3e-05     0.085       2      61 ..    1203    1249 ..    1185    1252 .. 0.77
  12 !   15.2   0.4   9.8e-06      0.02       2      60 ..    1298    1343 ..    1289    1348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                                       TSCCCHCHHTT.......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE CS
                              SpaA  18 tttdgkdalea......kktgtevttlttdenGkatfegLplGtYllvEtk 62 
                                       ++        +      ++t+  ++t tt+e+G+ +f gL+ G+Y++ E  
  gi|386001345|ref|YP_005919644.1| 307 VDLS------GwnitlyNETDVLIDTTTTNETGYYQFCGLDHGNYKVCEEV 351
                                       2233......13344446778888***********************9964 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                                       T......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-S CS
                              SpaA  28 a.....kktgtevttlttdenGkatfegLplGtYllvEtkaP 64 
                                       +     +++  +v+t  t+++G  +f +L +G+Y++ Et  P
  gi|386001345|ref|YP_005919644.1| 400 NwtitlTNSSGTVGTTLTNATGWYRFCDLVPGSYTVCETLKP 441
                                       144444556677899999*********************766 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00015
                                       T......TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-S CS
                              SpaA  28 a.....kktgtevttlttdenGkatfegLplGtYllvEtkaP 64 
                                       +     +++  +v+t  t+++G  +f +L +G+Y++ Et  P
  gi|386001345|ref|YP_005919644.1| 489 NwtitlTNSSGTVGTTLTNATGWYRFCDLVPGSYTVCETLKP 530
                                       134444556778899999********************9665 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 6.5e-05
                                       .TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-S CS
                              SpaA  29 kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvldk 71 
                                       +++  +v+t  t+++G  +f +L +G Y++ Et  P   + ++
  gi|386001345|ref|YP_005919644.1| 584 TNSSGTVGTTLTNATGWYRFCDLVPGIYTVCETVKPGFTNVTP 626
                                       556678899999*********************8884444344 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 6.4e-05
                                       .TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-S CS
                              SpaA  29 kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvldk 71 
                                       +++  +v+t  t+++G  +f +L +G Y++ Et  P   + ++
  gi|386001345|ref|YP_005919644.1| 673 TNSSGTVGTTLTNATGWYRFCDLVPGIYTVCETVKPGFTNVTP 715
                                       556778899999*********************8884444344 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00011
                                       .TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-S CS
                              SpaA  29 kktgtevttlttdenGkatfegLplGtYllvEtkaP 64 
                                       +++  +v+t  t+++G  +f +L +G Y++ Et  P
  gi|386001345|ref|YP_005919644.1| 762 TNSSGTVGTTLTNATGWYRFCDLVPGIYTVCETVKP 797
                                       556778899999*********************887 PP

  == domain 7  score: 21.9 bits;  conditional E-value: 8.1e-08
                                       B-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEEEEEC CS
                              SpaA   5 pLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllvEtkaPegYvldkepfevtvt 79 
                                        L++ + tly+++             t++ ++t tt+++G   f +L +G+Y ++Et  P  ++ +++ ++vt++
  gi|386001345|ref|YP_005919644.1| 841 DLSNWTITLYNAT-------------TNQPINTTTTNATGWYIFCDLVPGDYAVEETVKPGYVNFSAKRVPVTLD 902
                                       5666667777777.............7999***************************999777779999999986 PP

  == domain 8  score: 23.1 bits;  conditional E-value: 3.5e-08
                                       B-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEEEEEC CS
                              SpaA   5 pLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllvEtkaPegYvldkepfevtvt 79 
                                        L++ + tly+++             t++ ++t tt+++G  +f gL +G+Y ++Et  P  ++ +++ ++vt++
  gi|386001345|ref|YP_005919644.1| 931 DLSNWTITLYNAT-------------TNQPINTTTTNATGWYSFCGLVPGDYAVEETIKPGYVNFSAKRVPVTLD 992
                                       5666667777777.............7999***************************999777779999999986 PP

  == domain 9  score: 16.0 bits;  conditional E-value: 5.6e-06
                                        CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE CS
                              SpaA    2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYllvEtk 62  
                                        tg+ L+G + ++y +              t+t+v++ ttd++G+  + +L +GtY ++E+ 
  gi|386001345|ref|YP_005919644.1| 1017 TGARLPGWTIEVYVNG-------------TQTKVGENTTDSEGEWIVCDLLPGTYDVKEVV 1064
                                        5555666666666555.............7999**************************85 PP

  == domain 10  score: 14.7 bits;  conditional E-value: 1.4e-05
                                        CCCB-TS-EEEEEETTTSCCCHCHHTT........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEE CS
                              SpaA    2 tgkpLaGaeFtlykvdtttdgkdalea.......kktgtevttlttdenGkatfegLplGtYllvEt 61  
                                        tg+ L+                    +       + t+t+v++ +td++G+  + +L +GtY ++E+
  gi|386001345|ref|YP_005919644.1| 1110 TGARLP--------------------GwtievyvNGTQTKVGENVTDSKGEWIVCDLLPGTYDVKEV 1156
                                        333344....................2555555555899***************************7 PP

  == domain 11  score: 13.2 bits;  conditional E-value: 4.3e-05
                                        CCCB-TS-EEEEEETTTSCCCHCHHTT........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEE CS
                              SpaA    2 tgkpLaGaeFtlykvdtttdgkdalea.......kktgtevttlttdenGkatfegLplGtYllvEt 61  
                                        tg +L+                    +       + t t+v++ ttd++G+  + +L +G Y ++E+
  gi|386001345|ref|YP_005919644.1| 1203 TGVTLP--------------------GwkievyvNGTETKVGENTTDSEGEWIICDLLPGVYDVKEV 1249
                                        333333....................3555555555899**************************96 PP

  == domain 12  score: 15.2 bits;  conditional E-value: 9.8e-06
                                        CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESE.EEEEEE CS
                              SpaA    2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplG.tYllvE 60  
                                        +++pL+G   t+++++              gt+v+++ttd++G+ ++ gL+ G +Y++ E
  gi|386001345|ref|YP_005919644.1| 1298 NKTPLEGWNITVTDSS--------------GTVVGNATTDDEGYWKICGLAFGeNYTVCE 1343
                                        4566666666666666..............9**********************99***98 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.3   8.6e+03      66      81 ..     158     173 ..     118     181 .. 0.53
   2 ?   -1.9   1.3       2.1   4.3e+03      17      28 ..     400     411 ..     397     420 .. 0.80
   3 ?   -0.6   0.5      0.85   1.7e+03      16      28 ..     488     500 ..     484     511 .. 0.80
   4 ?   -1.1   1.0       1.2   2.3e+03      16      28 ..     577     589 ..     573     598 .. 0.79
   5 ?   -1.1   1.0       1.2   2.3e+03      16      28 ..     666     678 ..     662     687 .. 0.79
   6 ?   -1.1   1.0       1.2   2.3e+03      16      28 ..     755     767 ..     751     776 .. 0.79
   7 ?   -6.4   2.5         9   1.8e+04      17      32 ..     844     859 ..     841     864 .. 0.74
   8 !   27.5   0.0   1.4e-09   2.8e-06       1      79 [.    1383    1460 ..    1383    1466 .. 0.84
   9 !   16.9   0.0     3e-06    0.0059      16      80 ..    1864    1931 ..    1854    1941 .. 0.80
  10 !   18.8   0.0   7.7e-07    0.0015      13      90 ..    1986    2062 ..    1975    2063 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                             DUF11  66 agesatlsftvrvtrt 81 
                                       +ge++ +++++r+t+ 
  gi|386001345|ref|YP_005919644.1| 158 PGETKSFRTRARATVG 173
                                       5555555666665554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                             DUF11  17 tytltvtNtgpa 28 
                                       + t+t+tN++++
  gi|386001345|ref|YP_005919644.1| 400 NWTITLTNSSGT 411
                                       57******9986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.85
                             DUF11  16 vtytltvtNtgpa 28 
                                        + t+t+tN++++
  gi|386001345|ref|YP_005919644.1| 488 SNWTITLTNSSGT 500
                                       578******9986 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.2
                             DUF11  16 vtytltvtNtgpa 28 
                                        + t+t+tN++++
  gi|386001345|ref|YP_005919644.1| 577 SNWTITLTNSSGT 589
                                       578******9986 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.2
                             DUF11  16 vtytltvtNtgpa 28 
                                        + t+t+tN++++
  gi|386001345|ref|YP_005919644.1| 666 SNWTITLTNSSGT 678
                                       578******9986 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 1.2
                             DUF11  16 vtytltvtNtgpa 28 
                                        + t+t+tN++++
  gi|386001345|ref|YP_005919644.1| 755 SNWTITLTNSSGT 767
                                       578******9986 PP

  == domain 7  score: -6.4 bits;  conditional E-value: 9
                             DUF11  17 tytltvtNtgpasang 32 
                                       + t+t+ N  +++  +
  gi|386001345|ref|YP_005919644.1| 844 NWTITLYNATTNQPIN 859
                                       5799**9998887655 PP

  == domain 8  score: 27.5 bits;  conditional E-value: 1.4e-09
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsft 75  
                                        ++K  dk ev+  d+vtyt+tv N+g+++  +v+v D     +++ s + + +  + ++ + +++a    t++++
  gi|386001345|ref|YP_005919644.1| 1383 IKKVADKYEVQECDEVTYTITVCNNGGVPVRNVTVWDRFDKEVEILSMTPA-PGPDRKWHFDEIPARTCVTITIK 1456
                                        67999999******************************9999999999988.56667777777777777777777 PP

                             DUF11   76 vrvt 79  
                                        ++v+
  gi|386001345|ref|YP_005919644.1| 1457 IKVP 1460
                                        7766 PP

  == domain 9  score: 16.9 bits;  conditional E-value: 3e-06
                             DUF11   16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtr 80  
                                         tyt+   N g+++   v v+D+ P+g  + ++s +        a+++ + L  g  a +++++ v++
  gi|386001345|ref|YP_005919644.1| 1864 ATYTIRIENDGNRAFIPVNVQDLFPPGAVFLESSLRpteLTDSYANWNLTHLSIGDVAVITLKLDVAK 1931
                                        69*********************************955422223444448888888888888777765 PP

  == domain 10  score: 18.8 bits;  conditional E-value: 7.7e-07
                             DUF11   13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvtrtaas 84  
                                        G  v y +   N   +++  ++vtD lP+g+++  +s+  ++++    v    ++ + e++t+++++r+++ ++ 
  gi|386001345|ref|YP_005919644.1| 1986 GMVVLYRIDIENHDDVTR-VARVTDHLPEGMTFLDSSTPVASYDGVEVVwnlIDIGPFETRTIELSARASAPGR- 2058
                                        556789999999999999.9*******************5555544444444999**************99999. PP

                             DUF11   85 galtnv 90  
                                          +tnv
  gi|386001345|ref|YP_005919644.1| 2059 --YTNV 2062
                                        ..7887 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 !    6.8   0.0    0.0034       6.8      24      57 ..     213     246 ..     209     252 .. 0.90
   2 ?    3.5   0.0     0.036        72      29      59 ..     310     340 ..     308     353 .. 0.88
   3 ?   -3.2   0.0       4.3   8.6e+03      35      57 ..     405     426 ..     399     430 .. 0.75
   4 ?   -3.3   0.0       4.7   9.3e+03      35      56 ..     494     514 ..     488     518 .. 0.75
   5 ?   -3.4   0.0       5.1     1e+04      35      56 ..     583     603 ..     577     606 .. 0.74
   6 ?   -3.4   0.0       5.1     1e+04      35      56 ..     672     692 ..     666     695 .. 0.74
   7 ?   -3.4   0.0       5.1     1e+04      35      56 ..     761     781 ..     755     784 .. 0.74
   8 ?    1.9   0.0      0.11   2.3e+02      28      56 ..     842     871 ..     838     885 .. 0.85
   9 ?    3.4   0.0     0.038        76      28      58 ..     932     963 ..     928     976 .. 0.86
  10 ?    0.1   0.0      0.41   8.1e+02      25      53 ..    1018    1047 ..    1014    1058 .. 0.79
  11 ?   -0.9   0.0      0.84   1.7e+03      18      53 ..    1104    1140 ..    1088    1149 .. 0.71
  12 ?    2.5   0.0     0.074   1.5e+02      23      54 ..    1202    1234 ..    1180    1243 .. 0.75
  13 !   11.8   0.0   9.1e-05      0.18      25      57 ..    1299    1331 ..    1295    1342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0034
                              bMG3  24 sgkPvagaeVrlldkkgevlaegtTDaqGvarfa 57 
                                       +++P++g +++l d++g+v++   T+++G  ++ 
  gi|386001345|ref|YP_005919644.1| 213 NNQPLEGWNITLQDCDGKVIGWDITNETGFWKIC 246
                                       689**************************98875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                              bMG3  29 agaeVrlldkkgevlaegtTDaqGvarfaal 59 
                                       +g +++l+++++ ++ ++tT+++G+++f +l
  gi|386001345|ref|YP_005919644.1| 310 SGWNITLYNETDVLIDTTTTNETGYYQFCGL 340
                                       57789*********************99776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.3
                              bMG3  35 lldkkgevlaegtTDaqGvarfa 57 
                                       l + +g +++++ T+a+G +rf 
  gi|386001345|ref|YP_005919644.1| 405 LTNSSG-TVGTTLTNATGWYRFC 426
                                       444444.68999******99995 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4.7
                              bMG3  35 lldkkgevlaegtTDaqGvarf 56 
                                       l + +g +++++ T+a+G +rf
  gi|386001345|ref|YP_005919644.1| 494 LTNSSG-TVGTTLTNATGWYRF 514
                                       444444.689999*****9999 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 5.1
                              bMG3  35 lldkkgevlaegtTDaqGvarf 56 
                                       l + +g +++++ T+a+G +rf
  gi|386001345|ref|YP_005919644.1| 583 LTNSSG-TVGTTLTNATGWYRF 603
                                       444444.689999*****9998 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 5.1
                              bMG3  35 lldkkgevlaegtTDaqGvarf 56 
                                       l + +g +++++ T+a+G +rf
  gi|386001345|ref|YP_005919644.1| 672 LTNSSG-TVGTTLTNATGWYRF 692
                                       444444.689999*****9998 PP

  == domain 7  score: -3.4 bits;  conditional E-value: 5.1
                              bMG3  35 lldkkgevlaegtTDaqGvarf 56 
                                       l + +g +++++ T+a+G +rf
  gi|386001345|ref|YP_005919644.1| 761 LTNSSG-TVGTTLTNATGWYRF 781
                                       444444.689999*****9998 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.11
                              bMG3  28 vagaeVrlld.kkgevlaegtTDaqGvarf 56 
                                       +++ +++l++  +++ + ++tT+a+G + f
  gi|386001345|ref|YP_005919644.1| 842 LSNWTITLYNaTTNQPINTTTTNATGWYIF 871
                                       5677899999889*************9877 PP

  == domain 9  score: 3.4 bits;  conditional E-value: 0.038
                              bMG3  28 vagaeVrlld.kkgevlaegtTDaqGvarfaa 58 
                                       +++ +++l++  +++ + ++tT+a+G ++f +
  gi|386001345|ref|YP_005919644.1| 932 LSNWTITLYNaTTNQPINTTTTNATGWYSFCG 963
                                       5677899999889*************999965 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 0.41
                              bMG3   25 gkPvagaeVrlld.kkgevlaegtTDaqGv 53  
                                        g  ++g +++++   ++  ++e tTD++G 
  gi|386001345|ref|YP_005919644.1| 1018 GARLPGWTIEVYVnGTQTKVGENTTDSEGE 1047
                                        5566777788865488999*********97 PP

  == domain 11  score: -0.9 bits;  conditional E-value: 0.84
                              bMG3   18 wvtsLdsgkPvagaeVrlld.kkgevlaegtTDaqGv 53  
                                          ++ d+g  ++g +++++   ++  ++e  TD++G 
  gi|386001345|ref|YP_005919644.1| 1104 GKKTNDTGARLPGWTIEVYVnGTQTKVGENVTDSKGE 1140
                                        5555577777888888887548889999999999996 PP

  == domain 12  score: 2.5 bits;  conditional E-value: 0.074
                              bMG3   23 dsgkPvagaeVrlld.kkgevlaegtTDaqGva 54  
                                        d+g +++g +++++   ++  ++e tTD++G  
  gi|386001345|ref|YP_005919644.1| 1202 DTGVTLPGWKIEVYVnGTETKVGENTTDSEGEW 1234
                                        778888999999976488889999999999975 PP

  == domain 13  score: 11.8 bits;  conditional E-value: 9.1e-05
                              bMG3   25 gkPvagaeVrlldkkgevlaegtTDaqGvarfa 57  
                                          P++g ++++ d +g v++++tTD++G+ ++ 
  gi|386001345|ref|YP_005919644.1| 1299 KTPLEGWNITVTDSSGTVVGNATTDDEGYWKIC 1331
                                        579*************************99876 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.22   4.3e+02       1      38 [.     204     245 ..     204     250 .. 0.74
   2 !    6.7   0.1    0.0036       7.2      14      48 ..     309     347 ..     296     349 .. 0.71
   3 ?    2.2   0.0     0.089   1.8e+02      24      48 ..     410     435 ..     389     439 .. 0.73
   4 ?    1.5   0.1      0.15     3e+02      24      48 ..     500     524 ..     487     527 .. 0.79
   5 ?    0.0   0.1      0.44   8.8e+02      24      48 ..     589     613 ..     579     617 .. 0.78
   6 ?    0.1   0.1      0.42   8.4e+02      24      48 ..     678     702 ..     666     706 .. 0.78
   7 ?    0.1   0.1      0.42   8.4e+02      24      48 ..     767     791 ..     755     795 .. 0.78
   8 ?    4.3   0.0     0.021        41      20      74 ..     853     911 ..     834     915 .. 0.80
   9 ?    5.2   0.0     0.011        22      20      74 ..     943    1001 ..     924    1005 .. 0.81
  10 !    6.1   0.1    0.0054        11       8      48 ..    1015    1060 ..    1009    1062 .. 0.80
  11 !    6.8   0.1    0.0033       6.6       8      48 ..    1108    1153 ..    1103    1156 .. 0.80
  12 ?    3.9   0.1     0.026        52       9      48 ..    1202    1246 ..    1196    1255 .. 0.78
  13 !    8.2   0.1    0.0012       2.5       2      45 ..    1290    1337 ..    1289    1342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.22
                   CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtkkgtv....TdenGnFel 38 
                                       i+G  +d+ +++pl+g ++++++   +++    T+e G +++
  gi|386001345|ref|YP_005919644.1| 204 IEGYKLDAANNQPLEGWNITLQDCDGKVIgwdiTNETGFWKI 245
                                       56777899************9875544433345888887776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0036
                   CarbopepD_reg_2  14 lpgatVyvkgtk....kgtvTdenGnFelknlpagkytL 48 
                                       l g ++++ + +      t+T+e G++++  l++g+y++
  gi|386001345|ref|YP_005919644.1| 309 LSGWNITLYNETdvliDTTTTNETGYYQFCGLDHGNYKV 347
                                       56666666443323436799****************986 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.089
                   CarbopepD_reg_2  24 tkkgtv.TdenGnFelknlpagkytL 48 
                                        ++gt+ T++ G +++ +l +g yt+
  gi|386001345|ref|YP_005919644.1| 410 GTVGTTlTNATGWYRFCDLVPGSYTV 435
                                       2455545****************997 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.15
                   CarbopepD_reg_2  24 tkkgtvTdenGnFelknlpagkytL 48 
                                       t   t T++ G +++ +l +g yt+
  gi|386001345|ref|YP_005919644.1| 500 TVGTTLTNATGWYRFCDLVPGSYTV 524
                                       334456****************997 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.44
                   CarbopepD_reg_2  24 tkkgtvTdenGnFelknlpagkytL 48 
                                       t   t T++ G +++ +l +g yt+
  gi|386001345|ref|YP_005919644.1| 589 TVGTTLTNATGWYRFCDLVPGIYTV 613
                                       334456*********9999999986 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 0.42
                   CarbopepD_reg_2  24 tkkgtvTdenGnFelknlpagkytL 48 
                                       t   t T++ G +++ +l +g yt+
  gi|386001345|ref|YP_005919644.1| 678 TVGTTLTNATGWYRFCDLVPGIYTV 702
                                       334456*********9999999986 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 0.42
                   CarbopepD_reg_2  24 tkkgtvTdenGnFelknlpagkytL 48 
                                       t   t T++ G +++ +l +g yt+
  gi|386001345|ref|YP_005919644.1| 767 TVGTTLTNATGWYRFCDLVPGIYTV 791
                                       334456*********9999999986 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.021
                   CarbopepD_reg_2  20 yvkgtkkgtvTdenGnFelknlpagky....tLvvsyvGyktqekkvtvskektldvni 74 
                                       + ++  + t+T++ G + + +l +g+y    t++  yv +  + + vt++ ++ ld ++
  gi|386001345|ref|YP_005919644.1| 853 TTNQPINTTTTNATGWYIFCDLVPGDYaveeTVKPGYVNFSAKRVPVTLDCDNVLDKDF 911
                                       445556899****************9955557777899999999999998888888766 PP

  == domain 9  score: 5.2 bits;  conditional E-value: 0.011
                   CarbopepD_reg_2   20 yvkgtkkgtvTdenGnFelknlpagky....tLvvsyvGyktqekkvtvskektldvni 74  
                                        + ++  + t+T++ G +++  l +g+y    t++  yv +  + + vt++ ++ ld ++
  gi|386001345|ref|YP_005919644.1|  943 TTNQPINTTTTNATGWYSFCGLVPGDYaveeTIKPGYVNFSAKRVPVTLDCDNVLDKDF 1001
                                        45555689**************9999866667888899999999999999888888776 PP

  == domain 10  score: 6.1 bits;  conditional E-value: 0.0054
                   CarbopepD_reg_2    8 ketkeplpg..atVyvkgtkkgtv...TdenGnFelknlpagkytL 48  
                                        ++t+  lpg  + Vyv+gt++++    Td++G++ + +l +g+y +
  gi|386001345|ref|YP_005919644.1| 1015 NDTGARLPGwtIEVYVNGTQTKVGentTDSEGEWIVCDLLPGTYDV 1060
                                        5678899996678999**997764444*********9999999976 PP

  == domain 11  score: 6.8 bits;  conditional E-value: 0.0033
                   CarbopepD_reg_2    8 ketkeplpg..atVyvkgtkkgt...vTdenGnFelknlpagkytL 48  
                                        ++t+  lpg  + Vyv+gt++++   vTd++G++ + +l +g+y +
  gi|386001345|ref|YP_005919644.1| 1108 NDTGARLPGwtIEVYVNGTQTKVgenVTDSKGEWIVCDLLPGTYDV 1153
                                        5678899996678999*9987653337*********9999999976 PP

  == domain 12  score: 3.9 bits;  conditional E-value: 0.026
                   CarbopepD_reg_2    9 etkeplpg..atVyvkgtkkgtv...TdenGnFelknlpagkytL 48  
                                        +t+  lpg  + Vyv+gt++++    Td++G++ + +l +g y +
  gi|386001345|ref|YP_005919644.1| 1202 DTGVTLPGwkIEVYVNGTETKVGentTDSEGEWIICDLLPGVYDV 1246
                                        5667788866799**99987664444********99998888866 PP

  == domain 13  score: 8.2 bits;  conditional E-value: 0.0012
                   CarbopepD_reg_2    2 sGtVvdketkeplpgatVyvkgtk....kgtvTdenGnFelknlpagk 45  
                                         G+ +d ++k+pl+g +++v++++     +++Td++G++++  l  g+
  gi|386001345|ref|YP_005919644.1| 1290 DGHKYDYSNKTPLEGWNITVTDSSgtvvGNATTDDEGYWKICGLAFGE 1337
                                        677789999***********876533334567*********8888775 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.3   6.6e+03      77      98 ..     326     347 ..     320     351 .. 0.79
   2 ?    4.0   0.0     0.014        29      75      98 ..     412     435 ..     394     442 .. 0.85
   3 ?    4.1   0.0     0.014        28      75      98 ..     501     524 ..     485     531 .. 0.84
   4 ?    2.6   0.0     0.041        82      75      98 ..     590     613 ..     574     621 .. 0.83
   5 ?    2.6   0.0     0.041        82      75      98 ..     679     702 ..     663     710 .. 0.83
   6 ?    2.6   0.0     0.041        82      75      98 ..     768     791 ..     752     799 .. 0.83
   7 ?   -1.0   0.0      0.52     1e+03      77     100 ..     950     973 ..     908     979 .. 0.83
   8 ?    0.5   0.0      0.18   3.6e+02      76     100 ..    1038    1062 ..     993    1073 .. 0.88
   9 ?    1.2   0.0      0.11   2.2e+02      76     100 ..    1131    1155 ..    1120    1168 .. 0.86
  10 ?   -0.6   0.0      0.39   7.8e+02      76     100 ..    1224    1248 ..    1198    1253 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.3
                                       EEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  77 riltdeeGryrirtikPapYpi 98 
                                       ++ t+e G+y++  +  + Y++
  gi|386001345|ref|YP_005919644.1| 326 TTTTNETGYYQFCGLDHGNYKV 347
                                       5668899999999999888876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                                       EEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  75 rgriltdeeGryrirtikPapYpi 98 
                                        g++lt++ G yr+  + P++Y +
  gi|386001345|ref|YP_005919644.1| 412 VGTTLTNATGWYRFCDLVPGSYTV 435
                                       499*******************86 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.014
                                       EEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  75 rgriltdeeGryrirtikPapYpi 98 
                                        g++lt++ G yr+  + P++Y +
  gi|386001345|ref|YP_005919644.1| 501 VGTTLTNATGWYRFCDLVPGSYTV 524
                                       499*******************86 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.041
                                       EEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  75 rgriltdeeGryrirtikPapYpi 98 
                                        g++lt++ G yr+  + P+ Y +
  gi|386001345|ref|YP_005919644.1| 590 VGTTLTNATGWYRFCDLVPGIYTV 613
                                       499*******************86 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.041
                                       EEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  75 rgriltdeeGryrirtikPapYpi 98 
                                        g++lt++ G yr+  + P+ Y +
  gi|386001345|ref|YP_005919644.1| 679 VGTTLTNATGWYRFCDLVPGIYTV 702
                                       499*******************86 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.041
                                       EEEEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  75 rgriltdeeGryrirtikPapYpi 98 
                                        g++lt++ G yr+  + P+ Y +
  gi|386001345|ref|YP_005919644.1| 768 VGTTLTNATGWYRFCDLVPGIYTV 791
                                       499*******************86 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 0.52
                                       EEE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C  77 riltdeeGryrirtikPapYpipn 100
                                       ++ t++ G y++  + P+ Y +++
  gi|386001345|ref|YP_005919644.1| 950 TTTTNATGWYSFCGLVPGDYAVEE 973
                                       567888999999999999998765 PP

  == domain 8  score: 0.5 bits;  conditional E-value: 0.18
                                        EEEE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C   76 griltdeeGryrirtikPapYpipn 100 
                                        g   td+eG++ +  + P++Y++++
  gi|386001345|ref|YP_005919644.1| 1038 GENTTDSEGEWIVCDLLPGTYDVKE 1062
                                        6677999************999876 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.11
                                        EEEE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C   76 griltdeeGryrirtikPapYpipn 100 
                                        g  +td++G++ +  + P++Y++++
  gi|386001345|ref|YP_005919644.1| 1131 GENVTDSKGEWIVCDLLPGTYDVKE 1155
                                        7889*****************9986 PP

  == domain 10  score: -0.6 bits;  conditional E-value: 0.39
                                        EEEE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C   76 griltdeeGryrirtikPapYpipn 100 
                                        g   td+eG++ i  + P+ Y++++
  gi|386001345|ref|YP_005919644.1| 1224 GENTTDSEGEWIICDLLPGVYDVKE 1248
                                        66789****************9875 PP

>> HepII_C  Heparinase II C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.37   7.4e+02      42      55 ..     423     436 ..     406     444 .. 0.79
   2 ?    0.3   0.0      0.37   7.4e+02      42      55 ..     512     525 ..     495     533 .. 0.79
   3 ?   -0.7   0.0       0.8   1.6e+03      42      56 ..     601     615 ..     585     622 .. 0.79
   4 ?   -0.7   0.0       0.8   1.6e+03      42      56 ..     690     704 ..     674     711 .. 0.79
   5 ?   -0.7   0.0       0.8   1.6e+03      42      56 ..     779     793 ..     763     800 .. 0.79
   6 ?    1.8   0.0      0.13   2.5e+02      36      57 ..     863     884 ..     848     897 .. 0.77
   7 !    5.5   0.0    0.0091        18      37      55 ..    1043    1061 ..    1030    1067 .. 0.82
   8 !    6.0   0.1    0.0063        13      36      55 ..    1135    1154 ..    1123    1161 .. 0.78
   9 ?    3.3   0.0     0.044        88      37      55 ..    1229    1247 ..    1216    1253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
                                       EEE-SB-SEEEEEE CS
                           HepII_C  42 fvvtDlapGtwqVl 55 
                                       +   Dl+pG+++V 
  gi|386001345|ref|YP_005919644.1| 423 YRFCDLVPGSYTVC 436
                                       5678********97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                                       EEE-SB-SEEEEEE CS
                           HepII_C  42 fvvtDlapGtwqVl 55 
                                       +   Dl+pG+++V 
  gi|386001345|ref|YP_005919644.1| 512 YRFCDLVPGSYTVC 525
                                       5678********97 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.8
                                       EEE-SB-SEEEEEEE CS
                           HepII_C  42 fvvtDlapGtwqVlk 56 
                                       +   Dl+pG ++V  
  gi|386001345|ref|YP_005919644.1| 601 YRFCDLVPGIYTVCE 615
                                       5578********975 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.8
                                       EEE-SB-SEEEEEEE CS
                           HepII_C  42 fvvtDlapGtwqVlk 56 
                                       +   Dl+pG ++V  
  gi|386001345|ref|YP_005919644.1| 690 YRFCDLVPGIYTVCE 704
                                       5578********975 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.8
                                       EEE-SB-SEEEEEEE CS
                           HepII_C  42 fvvtDlapGtwqVlk 56 
                                       +   Dl+pG ++V  
  gi|386001345|ref|YP_005919644.1| 779 YRFCDLVPGIYTVCE 793
                                       5578********975 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.13
                                       SSS-EEEEE-SB-SEEEEEEET CS
                           HepII_C  36 gsqtlkfvvtDlapGtwqVlkd 57 
                                       +++t  ++  Dl+pG + V+  
  gi|386001345|ref|YP_005919644.1| 863 TNATGWYIFCDLVPGDYAVEET 884
                                       47777899***********875 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.0091
                                        SS-EEEEE-SB-SEEEEEE CS
                           HepII_C   37 sqtlkfvvtDlapGtwqVl 55  
                                        + + +++v Dl pGt++V+
  gi|386001345|ref|YP_005919644.1| 1043 DSEGEWIVCDLLPGTYDVK 1061
                                        556689************7 PP

  == domain 8  score: 6.0 bits;  conditional E-value: 0.0063
                                        SSS-EEEEE-SB-SEEEEEE CS
                           HepII_C   36 gsqtlkfvvtDlapGtwqVl 55  
                                        ++ + +++v Dl pGt++V+
  gi|386001345|ref|YP_005919644.1| 1135 TDSKGEWIVCDLLPGTYDVK 1154
                                        4556689************7 PP

  == domain 9  score: 3.3 bits;  conditional E-value: 0.044
                                        SS-EEEEE-SB-SEEEEEE CS
                           HepII_C   37 sqtlkfvvtDlapGtwqVl 55  
                                        + + ++++ Dl pG ++V+
  gi|386001345|ref|YP_005919644.1| 1229 DSEGEWIICDLLPGVYDVK 1247
                                        555689***********97 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.007        14      18      33 ..    1306    1321 ..    1305    1322 .. 0.93
   2 ?    2.7   0.1     0.056   1.1e+02      13      34 ..    1396    1417 ..    1391    1418 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.007
                            DUF824   18 titvkDasGnPvpnap 33  
                                        +itv+D+sG+ v+na+
  gi|386001345|ref|YP_005919644.1| 1306 NITVTDSSGTVVGNAT 1321
                                        8*************95 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.056
                            DUF824   13 EsipltitvkDasGnPvpnapf 34  
                                        ++++ titv +  G Pv n+++
  gi|386001345|ref|YP_005919644.1| 1396 DEVTYTITVCNNGGVPVRNVTV 1417
                                        67899**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.09u 0.32s 00:00:01.41 Elapsed: 00:00:00.53
# Mc/sec: 12145.36
//
Query:       gi|386001346|ref|YP_005919645.1|  [L=311]
Description: hypothetical protein Mhar_0644 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-06   26.7   0.2    2.1e-05   24.7   0.1    1.9  2  SdrD_B           SdrD B-like domain
  ------ inclusion threshold ------
      0.019   15.3   0.0      0.041   14.2   0.0    1.7  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      0.077   13.0   0.0       0.18   11.9   0.0    1.6  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
       0.11   12.8   0.0       0.24   11.7   0.0    1.6  1  SpaA             Prealbumin-like fold domain
       0.12   11.9   0.0       0.18   11.3   0.0    1.2  1  AsmA_2           AsmA-like C-terminal region


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 !   24.7   0.1   5.7e-09   2.1e-05       8      68 ..      15      73 ..      10      80 .. 0.86
   2 ?   -1.8   0.0         1   3.7e+03      53      71 ..      95     113 ..      79     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.7e-09
                            SdrD_B  8 weDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapa 68
                                      + D+n+nG  d +e   sg t+t+  ++++    t T+ +G++k  nl++G+Y+++   p 
  gi|386001346|ref|YP_005919645.1| 15 YWDKNQNGERDPEEGDLSGWTITVDGESTTW--WTATNIHGYWKICNLSAGTYYISERPPR 73
                                      67**********************5555544..69*******************9876665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                            SdrD_B  53 tnltpGeYkVeftapagyt 71 
                                       ++l++G+Y+    +p +y+
  gi|386001346|ref|YP_005919645.1|  95 KDLNSGNYRALHDEPRQYE 113
                                       5677788877777777763 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.041       8      53 ..      25      68 ..      24      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                   CarboxypepD_reg  8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvt 53
                                      d+    ++g t+tv   +++t+  t t+  G++++ +l +gty + 
  gi|386001346|ref|YP_005919645.1| 25 DPEEGDLSGWTITVD--GESTTWWTATNIHGYWKICNLSAGTYYIS 68
                                      6666678999*****..899***********************985 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.9e-05      0.18      13      48 ..      30      67 ..      24      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
                   CarbopepD_reg_2 13 plpgatVyv..kgtkkgtvTdenGnFelknlpagkytL 48
                                       l g t++v  ++t+  t+T+  G++++ nl ag+y +
  gi|386001346|ref|YP_005919645.1| 30 DLSGWTITVdgESTTWWTATNIHGYWKICNLSAGTYYI 67
                                      67888888833558999******************965 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.7e-05      0.24      28      60 ..      28      69 ..      11      93 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                                      T.........TTCCEESEEE..-BTTSEEEEEEEESEEEEEEE CS
                              SpaA 28 a........kktgtevttlt..tdenGkatfegLplGtYllvE 60
                                      +        + +g+ +tt+   t+  G+ ++ +L +GtY++ E
  gi|386001346|ref|YP_005919645.1| 28 EgdlsgwtiTVDGE-STTWWtaTNIHGYWKICNLSAGTYYISE 69
                                      24444455422222.33333147778***************99 PP

>> AsmA_2  AsmA-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.1e-05      0.18      59     119 ..     112     170 ..      85     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.1e-05
                            AsmA_2  59 lkrlglaevlgGkgslelnlswqgaplspdl.ssLsGdlsleledgqilgvsllrdlgllk.l 119
                                       ++++   + ++G+g l+++ s   ++l++d+ +++ G++++ le+ q+ +    ++++ l+  
  gi|386001346|ref|YP_005919645.1| 112 YEQFCESQLVTGSGYLDVKTSVLDKKLAMDYqNKIFGEGDIGLESAQVYS----QEPNKLRrP 170
                                       5777888899********************989*****************....666655441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2271.48
//
Query:       gi|386001347|ref|YP_005919646.1|  [L=409]
Description: hypothetical protein Mhar_0645 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00026   20.7   0.0     0.0013   18.4   0.0    2.3  2  PHP_C     PHP-associated
  ------ inclusion threshold ------
      0.035   14.4   0.0       0.07   13.4   0.0    1.6  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.5e-07    0.0013       7      52 ..     177     224 ..     173     227 .. 0.90
   2 ?   -3.0   0.0      0.74   6.6e+03      10      21 ..     261     272 ..     260     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-07
                             PHP_C   7 ArrfAeklglpgtgGSDAHrle..eVGrayTefeepiatpdelleair 52 
                                       A+r+Ae +   ++ +SDAH+++  ++Gr ++++e++  ++++l +ai 
  gi|386001347|ref|YP_005919646.1| 177 ADRIAELRVMTFLTNSDAHSPWpdKLGREFNQMEMKDLSFEDLRRAIG 224
                                       99*****************864449*********************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.74
                             PHP_C  10 fAeklglpgtgG 21 
                                        Ae++g + +gG
  gi|386001347|ref|YP_005919646.1| 261 MAERRGRCECGG 272
                                       799***999998 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.8e-06      0.07       1      37 [.       6      43 ..       6     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-06
                                      EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEE CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDh 37
                                      dlH+H+ ys +++g++ +  + ++a+++g+  +a  D 
  gi|386001347|ref|YP_005919646.1|  6 DLHIHSRYSaATSGNMDLPTIGREAAKKGIGVVATGDC 43
                                      89********999*****************99997775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2773.55
//
Query:       gi|386001348|ref|YP_005919647.1|  [L=283]
Description: Phosphoribosylaminoimidazole carboxylase related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.0   5.0      2e-14   53.4   5.0    1.3  1  AIRC      AIR carboxylase
     0.0012   18.7   0.1     0.0033   17.2   0.1    1.8  1  VbhA      Antitoxin VbhA


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   5.0   2.3e-18     2e-14       1     129 [.     149     276 ..     149     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.3e-18
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHH CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvva 73 
                                       kVg++ + + D++v+++a  + + +g     ey+v v+  hr    l+++ +      +++++++AG++  Lp vva
  gi|386001348|ref|YP_005919647.1| 149 KVGVLSAGTADIPVAEEARVTAEMMGCktavEYDVGVAGIHRLFPSLEKMHD------MDALVVAAGREGTLPAVVA 219
                                       69****************999998654333399999*****98777766544......789**************** PP

                                       HHSSS-EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTT CS
                              AIRC  74 slttlPVigvPvks...kalkgldsllSivqmPsgvpvatvaigkaknAallAaqilal 129
                                       +l++ PV+g Pv++       g  +llS++q +s + v++++   +  A+ +Aa+i  +
  gi|386001348|ref|YP_005919647.1| 220 GLMEAPVVGLPVSTgygAGGGGEAALLSMLQSCSVMVVVNID--AGFVAGAFAAKIAKM 276
                                       *************84433578899*********998776655..999999999999765 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.7e-07    0.0033      24      44 ..      30      50 ..      25      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-07
                              VbhA 24 vadleayvrGeIdadElvrrv 44
                                      +a le+++rGeI++dE++r+v
  gi|386001348|ref|YP_005919647.1| 30 RAVLERFARGEISLDEAIREV 50
                                      7889***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 2413.67
//
Query:       gi|386001349|ref|YP_005919648.1|  [L=453]
Description: Cobalt ABC transporter, ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-31  108.7   0.0      5e-31  108.0   0.0    1.3  1  ABC_tran    ABC transporter
    5.5e-15   56.0   0.4    5.5e-10   39.5   0.0    2.3  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    2.4e-07   30.4   0.0      2e-06   27.4   0.0    2.0  1  SMC_N       RecF/RecN/SMC N terminal domain
     0.0045   16.7   0.0     0.0091   15.7   0.0    1.5  1  AAA_29      P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0        1.1    8.9   0.0    2.2  2  IstB_IS21   IstB-like ATP binding protein
      0.074   13.5   0.0       0.13   12.7   0.0    1.3  1  AAA_23      AAA domain
       0.13   12.1   0.0         17    5.1   0.0    2.4  2  ATP_bind_1  Conserved hypothetical ATP binding protein
       0.14   10.7   0.0        4.6    5.8   0.0    2.0  2  AAA_13      AAA domain
       0.16   12.1   0.0        1.5    8.9   0.0    2.4  3  AAA_33      AAA domain
       0.18   12.1   0.0       0.94    9.7   0.0    2.1  2  AAA_22      AAA domain
       0.19   11.4   0.3        1.5    8.4   0.1    1.9  2  AAA_15      AAA ATPase domain
       0.27   11.5   1.9       0.36   11.1   0.1    2.2  2  SbcCD_C     Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0   3.4e-34     5e-31       2     136 ..      23     169 ..      22     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 3.4e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpel 74 
                                       + ++l ++ege++ +vG+nG+GKStL+ l+ g l+p +Ge+ll++++l++  ++l+++r+++g+++q+  +qlf  +
  gi|386001349|ref|YP_005919648.1|  23 RGINLRIEEGERISFVGPNGSGKSTLFLLFNGTLRPSAGEVLLRDRPLQYdpRSLRETRRRVGIVFQNsdDQLFAPT 99 
                                       579***********************************************999999************989999988 PP

                                       BHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        vr+              e ++++++al+ +g+++lk ++     ++LSgGqk+r a+a +++ +p++++lDEp 
  gi|386001349|ref|YP_005919648.1| 100 -VRQDvafgpanlglpkeEVERRVDTALEGVGIEGLKGRPP----HHLSGGQKKRAAIAGVMAMEPEVMILDEPL 169
                                       .89889**********9999999*****************9....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   1.7e-05     0.025       4      21 ..      37      54 ..      35      94 .. 0.82
   2 !   39.5   0.0   3.7e-13   5.5e-10     222     299 ..     127     201 ..      63     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                            AAA_21  4 liGpNgsGKSnLLdaldl 21
                                      ++GpNgsGKS+L+ ++ +
  gi|386001349|ref|YP_005919648.1| 37 FVGPNGSGKSTLFLLFNG 54
                                      79**********988854 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 3.7e-13
                            AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                         +  ++ + +p+++lS G+k+ +a++  ++  +    + ++DEp ++L+P+  ++++ell+el+++g+ +i++TH+
  gi|386001349|ref|YP_005919648.1| 127 EGVGIEGLKGRPPHHLSGGQKKRAAIAGVMAMEP---EVMILDEPLSNLDPAGSEEVMELLEELNQRGTTIIISTHD 200
                                       45556778899************99999999988...9**************************************9 PP

                            AAA_21 299 p 299
                                        
  gi|386001349|ref|YP_005919648.1| 201 V 201
                                       5 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.4e-09     2e-06      28     198 ..      36     199 ..      25     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.4e-09
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitfdnedkklkiekeevsi 99 
                                       + vGpNGSGKs l     F+L   +  +lr +  + l+         ++ + ++ +v i+f+n+d++l        +
  gi|386001349|ref|YP_005919648.1|  36 SFVGPNGSGKSTL-----FLLF--NG-TLRPSAGEVLLRDrplqyDPRSLRETRRRVGIVFQNSDDQLF-----APT 99 
                                       569********87.....5665..33.78999999998887774444555666779**********944.....344 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                        r+ +  g  +  + ++ev+ + v   le +gi+         LSgG+k+ +a+a ++A++   p+ +++lDe  ++
  gi|386001349|ref|YP_005919648.1| 100 VRQDVAFGPANLGLPKEEVE-RRVDTALEGVGIEGLkgrpphHLSGGQKKRAAIAGVMAME---PE-VMILDEPLSN 171
                                       56666677778889888886.468999999999854555555*************999975...54.679******* PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislr 198
                                       LD +  ++v ell+e +++   i+is +
  gi|386001349|ref|YP_005919648.1| 172 LDPAGSEEVMELLEELNQRGTTIIISTH 199
                                       *****************99877777765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06    0.0091      17      39 ..      27      49 ..      21      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      ++i++ + + ++Gp+GsGKSTl+
  gi|386001349|ref|YP_005919648.1| 27 LRIEEGERISFVGPNGSGKSTLF 49
                                      5666555899***********96 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.025        37      44      63 ..      29      48 ..      22      53 .. 0.90
   2 ?    8.9   0.0   0.00075       1.1     106     151 ..     157     201 ..     142     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                         IstB_IS21 44 iekkenivllGpsGvGKshl 63
                                      ie+ e i ++Gp G GKs l
  gi|386001349|ref|YP_005919648.1| 29 IEEGERISFVGPNGSGKSTL 48
                                      788999***********987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00075
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                        ++++++ilD+  l +ld a +e+++e++e+  +r ++ii s   +
  gi|386001349|ref|YP_005919648.1| 157 AMEPEVMILDE-PLSNLDPAGSEEVMELLEELNQRGTTIIISTHDV 201
                                       45679*****9.599**********************999887655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.8e-05      0.13      24      36 ..      37      49 ..      33      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                            AAA_23 24 ItGpNGaGKTTil 36
                                      ++GpNG+GK+T++
  gi|386001349|ref|YP_005919648.1| 37 FVGPNGSGKSTLF 49
                                      79*********98 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.02        30       1      13 [.      37      49 ..      37      60 .. 0.85
   2 ?    5.1   0.0     0.011        17      99     134 ..     309     343 ..     307     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.02
                        ATP_bind_1  1 vvGpaGsGKttfv 13
                                      +vGp GsGK+t+ 
  gi|386001349|ref|YP_005919648.1| 37 FVGPNGSGKSTLF 49
                                      58*********86 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                        ATP_bind_1  99 PGQielfthseslakiveeLesefalvvvyLvDsqr 134
                                       PG +++  h+e+++ +ve Le+  +++ v++ D+q+
  gi|386001349|ref|YP_005919648.1| 309 PGDMRV-IHLEDGRAVVEPLERPTRIGRVVIYDTQV 343
                                       677775.58899999*******************96 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.024        36      23      38 ..      39      54 ..      28      63 .. 0.83
   2 ?    5.8   0.0    0.0031       4.6     526     579 ..     159     209 ..     151     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.024
                            AAA_13 23 GwNGaGKTtLSrllrs 38
                                      G NG+GK+tL  l++ 
  gi|386001349|ref|YP_005919648.1| 39 GPNGSGKSTLFLLFNG 54
                                      99********877765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                       + ++ ++D P S LD   +  v+ l+++     +    ++i+TH +++   +++
  gi|386001349|ref|YP_005919648.1| 159 EPEVMILDEPLSNLDPAGSEEVMELLEELN---QRGTTIIISTHDVDLAYRWSD 209
                                       67899***********************97...99999********98777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.001       1.5       3      15 ..      36      48 ..      35      94 .. 0.90
   2 ?   -1.7   0.0         2   2.9e+03      73     108 ..     163     200 ..     147     210 .. 0.71
   3 ?   -0.8   0.0       1.1   1.6e+03      66     104 ..     393     431 ..     381     441 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                            AAA_33  3 llvGlpGsGKstl 15
                                       +vG++GsGKstl
  gi|386001349|ref|YP_005919648.1| 36 SFVGPNGSGKSTL 48
                                      59**********8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                            AAA_33  73 vildat..nlsrrerarflklarrlgvpvrivvvetde 108
                                       +ild +  nl+++  +++++l+++l+ + + ++++t +
  gi|386001349|ref|YP_005919648.1| 163 MILDEPlsNLDPAGSEEVMELLEELNQRGTTIIISTHD 200
                                       67788877778888888888888888776666666655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                            AAA_33  66 alsagrnvildatnlsrrerarflklarrlgvpvrivvv 104
                                       al  ++ +il ++   +++r+r+ +  r+ g+++++ vv
  gi|386001349|ref|YP_005919648.1| 393 ALCGEAVLILTNGGMVEHARRRIEEYCRQSGMKIEVSVV 431
                                       455555578888888999999999999999999988766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00063      0.94       9     125 ..      36     194 ..      30     207 .. 0.68
   2 ?   -3.3   0.0       6.7     1e+04      70      92 ..     404     426 ..     388     431 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka............. 70 
                                         +G+ G+GK+tl   +  +l  +++a e   r++ + +++ s+ + +     ++++ +++l a             
  gi|386001349|ref|YP_005919648.1|  36 SFVGPNGSGKSTLFLLFNGTL--RPSAGEvlLRDRPLQYDPRSLRETRRRVGIVFQNSDDQLFAptvrqdvafgpan 110
                                       569**************9999..566666886666677777777766666666666666666666677777777777 PP

                            AAA_22  71 ........................erlsseell.ealeqalrarav...ielliiDEaqh.lr...s...eealeeL 112
                                                               ++   ++l   +  +a+ a  +   +e++i+DE    l+   s   +e+leeL
  gi|386001349|ref|YP_005919648.1| 111 lglpkeeverrvdtalegvgieglKGRPPHHLSgGQKKRAAIAGVMamePEVMILDEPLSnLDpagSeevMELLEEL 187
                                       77777778888888888888888766666666665555555555556788888888855558776543344444444 PP

                            AAA_22 113 rsllnlsrkgvql 125
                                           n  + g+++
  gi|386001349|ref|YP_005919648.1| 188 ----N--QRGTTI 194
                                       ....4..444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.7
                            AAA_22  70 aerlsseellealeqalrarav.i 92 
                                       + ++  e+ ++++e+++r+ ++ i
  gi|386001349|ref|YP_005919648.1| 404 N-GGMVEHARRRIEEYCRQSGMkI 426
                                       4.5667788888888888888754 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1     0.001       1.5      26      40 ..      35      49 ..      22      59 .. 0.81
   2 ?    0.9   0.0       0.2   2.9e+02     326     365 ..     162     200 ..     157     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                            AAA_15 26 tvliGkNnsGKSsil 40
                                        ++G+N+sGKS++ 
  gi|386001349|ref|YP_005919648.1| 35 ISFVGPNGSGKSTLF 49
                                      679**********85 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       + +++EP  +L p   +++++ll el + +   +ii+TH 
  gi|386001349|ref|YP_005919648.1| 162 VMILDEPLSNLDPAGSEEVMELLEELNQRGT-TIIISTHD 200
                                       6678888888889999999999999999986.9******6 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00024      0.36      63      89 ..     159     185 ..     136     186 .. 0.84
   2 ?   -3.6   0.3       9.2   1.4e+04      31      38 ..     301     308 ..     288     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                        +++++LDE  s+lD+  +++++elle
  gi|386001349|ref|YP_005919648.1| 159 EPEVMILDEPLSNLDPAGSEEVMELLE 185
                                       4789*********************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.2
                           SbcCD_C  31 gtlSGGek 38 
                                       ++ SGGe+
  gi|386001349|ref|YP_005919648.1| 301 SGRSGGER 308
                                       56799996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3735.08
//
Query:       gi|386001350|ref|YP_005919649.1|  [L=261]
Description: Cobalt ABC transporter, inner membrane subunit CbiQ [Methanosaeta harundinacea 6Ac]
Scores for complete 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-42  144.2   9.5    5.7e-42  143.8   9.5    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.8   9.5   3.2e-46   5.7e-42       2     211 ..      12     222 ..      11     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 3.2e-46
                                       SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE... CS
                              CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqli 76 
                                       ks+l++ + r+kl+++ + ll+ + ++++v++l+i+  + ++    ++    ++a+ l+ pl f l+g+ ++l+++ 
  gi|386001350|ref|YP_005919649.1|  12 KSPLRHKNSRLKLAIVAAALLVGISSTSPVAPLFIALTMSFASIRLGEVpaGFYAKLLAPPLAFALFGTAVILLFFG 88 
                                       6899****************************9998887777655555578***************99999988899 PP

                                       ....EECTTEEE....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHH CS
                              CbiQ  77 ttegefvfaggg.qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfifl 152
                                       + ++ f f+ +g  ++ t eG   +ll++ R+++ +s+l++lalTTp+ el++ l+ l++P+ l+++ + +yR+if+
  gi|386001350|ref|YP_005919649.1|  89 SGPEIFSFSLLGqSLGATVEGAELSLLVLSRTVSGTSCLFFLALTTPMVELFALLKGLRIPDSLVELSMMIYRYIFV 165
                                       99**********99*************************************************************** PP

                                       HHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 153 LleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       Lle + ++++Aq++Rlg+   g+ rs+rs  +++++lf+r+++++er+ +Am+aR+Y+g
  gi|386001350|ref|YP_005919649.1| 166 LLEVAISMTHAQAMRLGYD--GFLRSIRSFSMMAGTLFIRSWEQGERLCTAMDARCYDG 222
                                       *******************..*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1787.19
//
Query:       gi|386001351|ref|YP_005919650.1|  [L=93]
Description: cobalt ABC transporter protein CbiN [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-27   92.8   1.4    1.2e-26   92.5   1.4    1.1  1  CbiN      Cobalt transport protein component CbiN
  ------ inclusion threshold ------
        1.7    8.6   6.0        1.1    9.2   0.6    2.4  2  PsbJ      PsbJ


Domain annotation for each model (and alignments):
>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   1.4   1.3e-30   1.2e-26       4      67 .]       6      74 ..       4      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.3e-30
                              CbiN  4 llllvvllavvplflv....kgaeFgGaDdqaeevIeei.apdyepwfeplweppsGEiESlLFalQAA 67
                                      ++ ++v+l+++ +++v    +gae+gGaD++ae vI e+ + +yepwf+plweppsGEiESlLF+lQAA
  gi|386001351|ref|YP_005919650.1|  6 IAGFAVILFFALFLYVsasnTGAEWGGADGEAEGVIAELtGGAYEPWFQPLWEPPSGEIESLLFSLQAA 74
                                      444556666666666689989999***************999**************************8 PP

>> PsbJ  PsbJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6   0.00012       1.1      14      31 ..       5      22 ..       4      28 .. 0.86
   2 ?    1.6   0.6     0.028   2.5e+02      23      34 ..      79      89 ..      68      92 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHHHHHHHT CS
                              PsbJ 14 tvaGlgvitvvglFfYGs 31
                                      ++aG +vi   +lF+Y s
  gi|386001351|ref|YP_005919650.1|  5 MIAGFAVILFFALFLYVS 22
                                      79**************76 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.028
                                      HHHHHHHHTTSS CS
                              PsbJ 23 vvglFfYGsYaG 34
                                      v+g +f+G Y G
  gi|386001351|ref|YP_005919650.1| 79 VIG-YFFGYYRG 89
                                      234.67898877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 686.72
//
Query:       gi|386001352|ref|YP_005919651.1|  [L=229]
Description: Cobalamin biosynthesis protein CbiM [Methanosaeta harundinacea 6Ac]
Scores for complete 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-52  177.8  19.2    2.8e-52  177.6  19.2    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
        3.4    7.4   9.5        0.1   12.4   2.2    2.1  3  DUF5381   Family of unknown function (DUF5381)


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.6  19.2   3.1e-56   2.8e-52       4     206 ..       2     207 ..       1     208 [. 0.95

  Alignments for each domain:
  == domain 1  score: 177.6 bits;  conditional E-value: 3.1e-56
                              CbiM   4 dgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaaiLlG 78 
                                       +g+L+ +++ a+ya++l++++++++r+++ ++e+r  +pllal++afif+++++++p  +g+++H++ga++ aiL+G
  gi|386001352|ref|YP_005919651.1|   2 EGFLPHPWWEAWYALSLPVVVYGIYRMNQLVKERRetLPLLALAGAFIFVLSSLKLPSVTGSCSHPTGAGMGAILFG 78 
                                       8******************************988889**************************************** PP

                              CbiM  79 pwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaall 155
                                       p+++++ ++vvl+ qal++++GG+t+LGaN+++m+++g+++ayl+yr   ++   k +  +++fla  ++ ++++++
  gi|386001352|ref|YP_005919651.1|  79 PAITAVLCLVVLVYQALFLAHGGLTTLGANLFSMGIAGPAVAYLIYRSA-GK--LKLNFYISIFLAVTVADLATYIV 152
                                       ***********************************************55.33..4799******************* PP

                              CbiM 156 valelalsgleas....lsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                       ++l+lal+   a+     s+ a+ a+++++++p++ilEgv+ a+i+k++ +v+ +
  gi|386001352|ref|YP_005919651.1| 153 TSLQLALAFPSATggvvGSFYAFGAIFAVTQIPLAILEGVVIALIFKYIIQVKGD 207
                                       ********6656689*9999999***************************99876 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.34     3e+03      24      53 ..      22      52 ..      10      57 .. 0.64
   2 ?   12.4   2.2   1.1e-05       0.1      11      64 ..      91     144 ..      82     156 .. 0.91
   3 ?   -1.7   0.2      0.23   2.1e+03      15      57 ..     159     201 ..     146     206 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.34
                           DUF5381 24 laglfllfeglkfes.kysllyiiigiigti 53
                                      + g++ + + +k    +  ll++++++i+++
  gi|386001352|ref|YP_005919651.1| 22 VYGIYRMNQLVKERReTLPLLALAGAFIFVL 52
                                      5566666666666554556677777777665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.1e-05
                           DUF5381  11 lrvllflatvglglaglfllfeglkfeskysllyiiigiigtifgliillmvlp 64 
                                       ++  lfla +gl+  g  l+++g+   ++ +l+y  +g + + f+++i+l v  
  gi|386001352|ref|YP_005919651.1|  91 VYQALFLAHGGLTTLGANLFSMGIAGPAVAYLIYRSAGKLKLNFYISIFLAVTV 144
                                       67789*********************************************9865 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.23
                           DUF5381  15 lflatvglglaglfllfeglkfeskysllyiiigiigtifgli 57 
                                       l + ++  g++g f  f ++   ++  l  + + +i +if  i
  gi|386001352|ref|YP_005919651.1| 159 LAFPSATGGVVGSFYAFGAIFAVTQIPLAILEGVVIALIFKYI 201
                                       4455555566666666666666666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1803.48
//
Query:       gi|386001353|ref|YP_005919652.1|  [L=128]
Description: sugar fermentation stimulation protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-39  135.0   0.0    1.8e-39  134.8   0.0    1.0  1  SfsA          Sugar fermentation stimulation protein RE domai
  ------ inclusion threshold ------
      0.089   12.4   0.0       0.11   12.1   0.0    1.1  1  PreAtp-grasp  Pre ATP-grasp domain
       0.17   11.8   0.1       0.22   11.4   0.1    1.2  1  GCSF          Granulocyte colony-stimulating factor


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0     3e-43   1.8e-39      25     134 ..       2     109 ..       1     112 [. 0.96

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 3e-43
                                       EES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHHTT-EEEEEEEE-SSS-- CS
                              SfsA  25 krevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLaelvkegyravvlfvvqredar 101
                                       + e + g+sr+Dfll +e  ++c++E Ks+tl+++g+alfPdapteRg++hl+eLa +v+eg ra+++fvv+r +a 
  gi|386001353|ref|YP_005919652.1|   2 RSEPARGKSRLDFLLAGE--RPCLLEAKSCTLVRDGVALFPDAPTERGRRHLQELAGAVREGCRAAIVFVVMRGGAP 76 
                                       678899**********95..**************99***************************************** PP

                                       EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE CS
                              SfsA 102 efkpnkeidpefaealreaaeaGVevlaydckv 134
                                       + +pn+e+dp+f++alreaa+ GVe +a+++++
  gi|386001353|ref|YP_005919652.1|  77 ALRPNDETDPAFGAALREAAAGGVEAMALAARY 109
                                       ****************************98876 PP

>> PreAtp-grasp  Pre ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.9e-05      0.11      36     121 ..      31     116 ..      25     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                      PreAtp-grasp  36 fardGDvlvlpvapeeeFlrYvtaltgvdreslrv.lvppagrlgsdlLsperlldpelverlraavaerpveellp 111
                                       ++rdG v + p ap+e+ +r++++l g  re  r  +v    r g+ +L p+  +dp++ ++lr+a a+      l+
  gi|386001353|ref|YP_005919652.1|  31 LVRDG-VALFPDAPTERGRRHLQELAGAVREGCRAaIVFVVMRGGAPALRPNDETDPAFGAALREAAAGGVEAMALA 106
                                       56777.6678*****************99888764256678899999*******************98866665555 PP

                      PreAtp-grasp 112 llpdasvarL 121
                                         +  + ++L
  gi|386001353|ref|YP_005919652.1| 107 ARYRDGWVEL 116
                                       5555555555 PP

>> GCSF  Granulocyte colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.6e-05      0.22     105     135 ..      73     104 ..      58     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                                       T-S-SS--SSS--S---SHHHHH.HHHHHHHH CS
                              GCSF 105 gvapavqptqgampaftsafqrr.aggvlvas 135
                                       g apa++p + + paf +a++   aggv +++
  gi|386001353|ref|YP_005919652.1|  73 GGAPALRPNDETDPAFGAALREAaAGGVEAMA 104
                                       88*****************9875267774433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 954.74
//
Query:       gi|386001354|ref|YP_005919653.1|  [L=78]
Description: sugar fermentation stimulation protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.1   0.0    1.3e-18   66.9   0.0    1.1  1  SfsA_N    SfsA N-terminal OB domain


Domain annotation for each model (and alignments):
>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0     7e-23   1.3e-18       1      56 [.      13      76 ..      13      78 .] 0.86

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 7e-23
                                      EEEEETTEEEEEEE..........EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEE CS
                            SfsA_N  1 lrRpnRFladveld.g....t...vHvpntGrlkelllpGarvllsksdnpkrKtkytleavek 56
                                      l+R  RF + +e+  g    +   +H+pn+Grl+ell+pGa++ll+++++p+rKtk+++ a+ +
  gi|386001354|ref|YP_005919653.1| 13 LSRTSRFSVTAEVAeGpadgEeqsCHLPNPGRLRELLVPGAEILLRPAKDPGRKTKFDVFAAVA 76
                                      79**********985244441456***********************************99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 536.65
//
Query:       gi|386001355|ref|YP_005919654.1|  [L=398]
Description: Exodeoxyribonuclease VII, large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-76  256.4   0.0    2.1e-67  227.9   0.2    2.2  2  Exonuc_VII_L     Exonuclease VII, large subunit
    1.8e-25   89.0   0.0    2.9e-25   88.3   0.0    1.3  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    1.3e-06   28.3   0.0    2.7e-06   27.3   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
        7.5    6.9   9.1          2    8.7   1.1    2.9  2  GGDEF_2          GGDEF-like domain


Domain annotation for each model (and alignments):
>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.9   0.2   4.6e-71   2.1e-67       1     209 [.     124     330 ..     124     339 .. 0.93
   2 !   27.7   0.0   4.2e-10   1.9e-06     247     302 ..     333     387 ..     323     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 227.9 bits;  conditional E-value: 4.6e-71
                      Exonuc_VII_L   1 lfdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvli 77 
                                       lfd+erk+p+p+ p  igvvtsp gaa+rD+lr+l    p ++i++ pa vQG++a+a+i++a+++++    aDv+i
  gi|386001355|ref|YP_005919654.1| 124 LFDAERKRPIPAHPACIGVVTSPDGAALRDVLRVLGAC-P-ARIVISPAVVQGDSAPASIASAISALQ--GIADVII 196
                                       8********************************99865.5.6**********************8887..5579*** PP

                      Exonuc_VII_L  78 iaRGGGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleeler 154
                                       ++RGGGS eDL++Fn+e +arai++s  Pv+savGHEtD+t+aDfvAdlrapTP+aaAe+v pd ++l+e l+ +e+
  gi|386001355|ref|YP_005919654.1| 197 VGRGGGSAEDLSPFNSELVARAIYQSAPPVVSAVGHETDVTVADFVADLRAPTPSAAAEMVRPDLERLREALAGAEA 273
                                       ***************************************************************************** PP

                      Exonuc_VII_L 155 rlekaikrlleekkqrleklasrl..kspeellerkrqrldeleerleralkkqlkk 209
                                       r+ ++++  le++++r  ++ + l  ++  ++++++rq+ld++++rl +a +++++ 
  gi|386001355|ref|YP_005919654.1| 274 RMVRSLAASLERRRARYLAFGRLLagRRMMAIVSEERQSLDRMTDRLVSAEDRRMEL 330
                                       ******************9*999965577789999************9988777665 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 4.2e-10
                      Exonuc_VII_L 247 erleeleeklealsplkvLkrGyaivrkedgkvvtsakdlkkgdeleirladgevk 302
                                        rle ++ kl++lspl++L+rGy+i    d  v+++a+dl++g+ +e+ +a+g++ 
  gi|386001355|ref|YP_005919654.1| 333 GRLEVAAGKLDSLSPLSTLRRGYSIALA-DSGVIRRASDLAPGELFELVFAEGRLL 387
                                       67888999*******************7.799********************9975 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.0   6.4e-29   2.9e-25       1      92 [.       5      97 ..       5     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 6.4e-29
                       tRNA_anti_2  1 lsVseltraikell..eaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgr 77
                                      ++V+el+++i+++l  + +l + +w rGe+sn+ +++sgh YftLkD +++i +v+fr++a++l+f+l dG++Vlv g 
  gi|386001355|ref|YP_005919654.1|  5 FTVTELNQRIRDRLtgDLRLCD-LWARGELSNVVNHRSGHRYFTLKDGESQIPCVLFRGNASRLDFDLADGQNVLVFGD 82
                                      79************66666645.**********8788****************************************** PP

                       tRNA_anti_2 78 lsvYeprGsyqlive 92
                                      +++Y p+G++q+ v+
  gi|386001355|ref|YP_005919654.1| 83 VEFYRPQGRVQILVK 97
                                      ************997 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     6e-10   2.7e-06       5      72 ..      31      98 ..      28     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6e-10
                                      EEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC..TTSSEEEEEEE CS
                   tRNA_anti-codon  5 GrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr..pggelelkvee 72
                                      G+++++   + +++ +++l+Dg+ +i +vlfr++a++l  +l  G+ v v+G v+++  +g+ +++ v+ 
  gi|386001355|ref|YP_005919654.1| 31 GELSNVV-NHRSGHRYFTLKDGESQIPCVLFRGNASRLDFDLADGQNVLVFGDVEFYrpQGR-VQILVKA 98
                                      6666664.6678999******************************************96665.*999875 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.1   0.00044         2      13     115 ..      65     189 ..      58     189 .. 0.60
   2 ?    1.5   1.5     0.077   3.4e+02      33      83 ..     271     323 ..     213     359 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00044
                           GGDEF_2  13 rrlgldldgpyvvvviel.......................eedaerllraleealralgpdalv.......avrgd 59 
                                       +rl++dl+  + v+v+                           +++r l++l+e l+a   + l+        + + 
  gi|386001355|ref|YP_005919654.1|  65 SRLDFDLADGQNVLVFGDvefyrpqgrvqilvkaarldvglG-EKHRELERLKERLAA---EGLFdaerkrpIPAHP 137
                                       566666666666666553255555555555554433332210.333334444444433...3333333333233334 PP

                           GGDEF_2  60 rlvlllpaedeedaeallerlarrlgglsvriGiGspveglaglrrSyreArrAlr 115
                                        ++ +++++d     a+l++++r lg++++ri i++ v + + ++ S   A  Al+
  gi|386001355|ref|YP_005919654.1| 138 ACIGVVTSPDG----AALRDVLRVLGACPARIVISPAVVQGDSAPASIASAISALQ 189
                                       55555555554....789999999****************************9996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.077
                           GGDEF_2  33 daerllraleealralgpdalvav...rgdrlvlllpaedeedaeallerlarr 83 
                                       ++ r++r l++ l++++ ++l++     g r  ++++ e +++++++ +rl ++
  gi|386001355|ref|YP_005919654.1| 271 AEARMVRSLAASLERRRARYLAFGrllAGRRMMAIVSEE-RQSLDRMTDRLVSA 323
                                       444578888888877777777753221444555555444.45777777776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2457.46
//
Query:       gi|386001356|ref|YP_005919655.1|  [L=81]
Description: Exodeoxyribonuclease VII, small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   71.2   3.7    7.4e-20   70.8   3.7    1.3  1  Exonuc_VII_S  Exonuclease VII small subunit


Domain annotation for each model (and alignments):
>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   3.7   4.1e-24   7.4e-20       2      52 .]      20      70 ..      15      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 4.1e-24
                      Exonuc_VII_S  2 EealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkvek 52
                                      E++laeLe Iv+ LE+gel+Leeslk +e+Gv L+++C++ Ld aeq++e+
  gi|386001356|ref|YP_005919655.1| 20 EASLAELEGIVRSLEEGELTLEESLKAFERGVSLIRRCNSLLDGAEQRIEI 70
                                      899**********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 611.86
//
Query:       gi|386001357|ref|YP_005919656.1|  [L=211]
Description: Lipolytic enzyme, G-D-S-L family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-25   88.5   0.0    8.2e-25   88.2   0.0    1.1  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
    3.3e-14   53.3   0.0    9.8e-14   51.8   0.0    1.7  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase
  ------ inclusion threshold ------
      0.091   11.9   0.0        2.3    7.3   0.0    2.0  2  DUF3965        Protein of unknown function (DUF3965)


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.0   1.4e-28   8.2e-25       1     179 []      28     202 ..      28     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 1.4e-28
                                       EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT-EEEEE...EEHCCH-H..HHHHHHHH.CTGGG-TSEEEEE--CCC CS
                     Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarlgldvvnn..lgvsGattallrllerlr.dllrlkpdlvtiliGtND 74 
                                       ++GDSiTaG+   +  r++++++ ++l+++++++ +     g  Gat+   + l rl+ ++ +++pdlvt+++G+ND
  gi|386001357|ref|YP_005919656.1|  28 LFGDSITAGF---AVRRGFDHFWLSMLKEKYPRAGIAMqnQGACGATS--FDGLARLDwSVVAHNPDLVTVNFGIND 99 
                                       59********...678888888899999999554444444********..9999999999***************** PP

                                       CCTT--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-HH CS
                     Lipase_GDSL_2  75 lgrgvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDlh 151
                                       ++ g   +++++n  l e+++++ +  pg      + l   ++++ +++ +++++  y ++l++va+e gv fvD++
  gi|386001357|ref|YP_005919656.1| 100 MYMGIRLGEFKGN--LIEIVERILEG-PGSG--SGPELLLLSSEPLMTPKFDRIVLSYYQVLEDVAEEMGVGFVDVY 171
                                       *************..**********9.4442..5666777777888888889************************6 PP

                                       HHH...HHCCCCCGGBBTTS.SSB-HHHHHH CS
                     Lipase_GDSL_2 152 dal...adsgerladlladdglHPnaaGyrl 179
                                       +a+    ++g +l+ l  ++  HPn+ Gyr+
  gi|386001357|ref|YP_005919656.1| 172 GAWmrrVGEGVPLDSLILPGLDHPNELGYRI 202
                                       6662214555566666666669*******96 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.6e-17   9.8e-14       1     200 []      26     207 ..      26     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.6e-17
                                       EEEEESHHHHTT....THHHHHHHCCCCEECCCTTC.GCEEEEEEECTTHHHHHHHCCHECTTTECHHHHHCTTSEE CS
                                       xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL   1 ivafGDSltdGd....gaatlntiqlktpknlnefdlaldrianignkgasdnelqqllnkyplkseqlkalhpdlv 73 
                                       iv+fGDS+t+G+    g+  ++ + lk    + ++      ++n+g+ ga ++    +l       +   a  pdlv
  gi|386001357|ref|YP_005919656.1|  26 IVLFGDSITAGFavrrGFDHFWLSMLKEKYPRAGI-----AMQNQGACGATSFDGLARL------DWSVVAHNPDLV 91 
                                       89**************************9999887.....6899999999999999999......999********* PP

                                       EEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL  74 iislGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegapkaivvlvsppglgpqeekdakklgekgnefvgey 150
                                       ++++G ND+        + ++ + ++i+ ++  ++    +g    + +l+s p  +p           k  ++v +y
  gi|386001357|ref|YP_005919656.1|  92 TVNFGINDM----YMGIRLGEFKGNLIEIVERILEGPG-SGSGPELLLLSSEPLMTP-----------KFDRIVLSY 152
                                       *********....5555566666666666666666555.443444555666667777...........899****** PP

                                       HHHHHHHHHHCTEEEECHHHHHHHTHCCGCHCHTSS......SB-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
                       Lipase_GDSL 151 nqrlndlaekdgfavvDlydelqglsgieqlkaDgl......Hpsekgyeklaell 200
                                        q+l+d+ae++g+ +vD+y  + ++ g + +  D l      Hp+e gy+++ae+l
  gi|386001357|ref|YP_005919656.1| 153 YQVLEDVAEEMGVGFVDVYGAWMRRVGEGVPL-DSLilpgldHPNELGYRIIAEEL 207
                                       *************************9988888.777888888***********975 PP

>> DUF3965  Protein of unknown function (DUF3965)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.011        65      27      63 ..      84     120 ..      66     123 .. 0.84
   2 ?    7.3   0.0   0.00039       2.3     168     207 ..     149     188 ..     134     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.011
                           DUF3965  27 eyetwdlltqavalnyliikyrigeltdrdveiwdrv 63 
                                            dl+t +  +n + +  r+ge+  + +ei +r+
  gi|386001357|ref|YP_005919656.1|  84 VAHNPDLVTVNFGINDMYMGIRLGEFKGNLIEIVERI 120
                                       445679***************************9997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00039
                           DUF3965 168 vddylyvmkemmehmtigvmdrydhfigkllsyvpffemi 207
                                       v  y  v++++ e m +g +d y+ ++ ++   vp+  +i
  gi|386001357|ref|YP_005919656.1| 149 VLSYYQVLEDVAEEMGVGFVDVYGAWMRRVGEGVPLDSLI 188
                                       557999********************99998888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1520.52
//
Query:       gi|386001358|ref|YP_005919657.1|  [L=185]
Description: hypothetical protein Mhar_0656 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1354.99
//
Query:       gi|386001359|ref|YP_005919658.1|  [L=1172]
Description: Helicase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-19   68.5   0.0    1.6e-18   67.1   0.0    1.9  1  Helicase_C     Helicase conserved C-terminal domain
      1e-17   63.9   0.1    2.7e-17   62.6   0.1    1.8  1  DUF3883        Domain of unknown function (DUF3883)
    5.2e-16   58.3   0.0    9.8e-16   57.4   0.0    1.4  1  SNF2_N         SNF2 family N-terminal domain
    4.5e-10   39.8   0.0    8.3e-10   38.9   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
    2.8e-05   24.0   0.0    5.4e-05   23.0   0.0    1.4  1  DEAD           DEAD/DEAH box helicase
    0.00061   19.1   0.0     0.0012   18.2   0.0    1.4  1  DUF2075        Uncharacterized conserved protein (DUF2075)
      0.003   18.0   0.0      0.082   13.3   0.0    2.7  1  AAA            ATPase family associated with various cellular
  ------ inclusion threshold ------
      0.013   14.4   0.0       0.14   11.0   0.0    2.1  1  AAA_34         P-loop containing NTP hydrolase pore-1
      0.041   13.7   0.0       0.12   12.2   0.0    1.8  1  Helicase_RecD  Helicase
      0.051   13.3   0.0       0.11   12.2   0.0    1.5  1  AAA_30         AAA domain
       0.25   12.2   2.0        1.6    9.6   2.0    2.5  1  Histone_HNS    H-NS histone family


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   9.6e-22   1.6e-18      10     111 .]     509     619 ..     500     619 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 9.6e-22
                                       H....HHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHH......HHHHHHHTTSSSEEEES CS
                        Helicase_C  10 l....kleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnere......eileqfnkgesdvLiat 73 
                                       +     ++  + k lif++ +d+l   ++l+ek    g++++ +hg +++ +r+       + ++f +++++v++at
  gi|386001359|ref|YP_005919658.1| 509 ItqegIFSDPKMKLLIFTEHKDTL---DYLTEKLrgwGLSITQIHGGMKAGSRDepgtrlSAEREF-REDCQVMVAT 581
                                       4444457788999***********...67766667799****************888877888888.5699****** PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        +a++Gi+++ + ++in+d+p+n+ ++ qr+GR++R+g
  gi|386001359|ref|YP_005919658.1| 582 EAAGEGINLQYCWFMINYDIPWNPVRLEQRMGRIHRYG 619
                                       ************************************86 PP

>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   1.7e-20   2.7e-17       2      90 ..    1048    1140 ..    1047    1142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.7e-20
                           DUF3883    2 Eklvlealkekekeegvewvnedve.dglgYDiesvd......kedgeerfIEVKttakgkkdfelsrnElefaq 69  
                                        E+++++a+ ++e+++g  w +e+ve ++ g+D+ s++      k+  e rfIEVK++a +  ++ l+ nE+++a+
  gi|386001359|ref|YP_005919658.1| 1048 ERIAVDAVIAREEARG--WKVESVEsENRGFDLISRRlhledpKTALEVRFIEVKGRA-TVGEVALTENEYKTAA 1119
                                        99*************9..******9999********887754434445**********.9*************** PP

                           DUF3883   70 ekgdkYwlyrVfnagkepkvk 90  
                                        + +++Ywly Vfn+ +ep+vk
  gi|386001359|ref|YP_005919658.1| 1120 RLKEDYWLYAVFNCASEPEVK 1140
                                        *****************9987 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0     6e-19   9.8e-16      59     247 ..     150     323 ..     146     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 6e-19
                                       EE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  59 iLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkm 135
                                       +LaD++G+GKT+++  l+++++            + l   +Liv Pa+l  qW++e+++   +   +  v  g    
  gi|386001359|ref|YP_005919658.1| 150 LLADDPGAGKTIMAGLLVKELKM-----------RGLIMRILIVTPANLTFQWQREMREKFGER-FE--VIRGV--- 209
                                       7*************999994444...........345566*****************9999877.33..33443... PP

                                       ----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH--......-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx RF
                            SNF2_N 136 kkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLs......ts 206
                                          + +   +  ++ d vit+   ++r       ++ l   +w+ v++DE+h++    s+ ++ + +L       t+
  gi|386001359|ref|YP_005919658.1| 210 -VLRANYGTNPWQERDQVITSMPWVARIE---DAKESLLHSHWDLVIVDEAHKMSAYSSEKKTLAYQLGealsemTD 282
                                       .2335566788899999******999777...577888889*************98855444444444444447899 PP

                                       -EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 207 nrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqr 247
                                       + +++t+TP + + +++   l +L e+++g+ ++ ++ + r
  gi|386001359|ref|YP_005919658.1| 283 HYLLMTATPHKGDPQNFCLFLRLLDEDVYGDVKSLEEAMRR 323
                                       *******************************9888777666 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   5.1e-13   8.3e-10       3     170 ..     128     292 ..     126     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.1e-13
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       ++ ++Q ea+ +   kl    + r+l++   G+GKT++a  l+++l+  g + ++l++ p  +l+ q+++e+++ + 
  gi|386001359|ref|YP_005919658.1| 128 DPLPHQLEAVYDYFLKL---PRIRFLLADDPGAGKTIMAGLLVKELKMRGLIMRILIVTPA-NLTFQWQREMREKFG 200
                                       56799999999999888...488*************************9999999888885.79************* PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T......TT CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk......sw 150
                                       e ++ i ++v   ++    +  ++++ ++t+   + +++     ++e+ll+++ d++i+DEaH+++a +      ++
  gi|386001359|ref|YP_005919658.1| 201 ERFEVIRGVVLRANYGT--NPWQERDQVITSMPWVARIE----DAKESLLHSHWDLVIVDEAHKMSAYSsekktlAY 271
                                       *9988888877777777..56778888888888888888....899********************98434445533 PP

                                       HHHHHT---..SEEEEEESS-S CS
                            ResIII 151 reilekfke..avllglTATpe 170
                                       +   e+++e     l +TATp 
  gi|386001359|ref|YP_005919658.1| 272 QL-GEALSEmtDHYLLMTATPH 292
                                       32.33333333556668***96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.3e-08   5.4e-05      18     174 ..     150     297 ..     133     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.3e-08
                                       EEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  18 lvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl 94 
                                       l+a + G+GKT ++ + v +  ++  g    ++liv+P   L+ q  +++++ + +   r + +i gv  r ++ + 
  gi|386001359|ref|YP_005919658.1| 150 LLADDPGAGKTIMAGLLVKELKMR--GL-IMRILIVTPA-NLTFQWQREMREKFGE---RFE-VIRGVVLRANYGTN 218
                                       677788*******99988855432..33.4478888885.7999999998777774...444.45556665555555 PP

                                       H.TTCSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSB CS
                                       x.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  95 d.ngvdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATl 169
                                         ++ d v++    ++++   +++l  s+  ++++DEa++++   +s + ++++ ql ++ ++   +   ++++AT+
  gi|386001359|ref|YP_005919658.1| 219 PwQERDQVITSMPWVARIEdAKESLLHSHWDLVIVDEAHKMSA--YSSEKKTLAYQLGEALSEMTDH--YLLMTATP 291
                                       325566666666555554435667889**************99..5777777778887777776644..******** PP

                                       S.HHHH CS
                                       x.xxxx RF
                              DEAD 170 p.kdvk 174
                                       +  d++
  gi|386001359|ref|YP_005919658.1| 292 HkGDPQ 297
                                       *66665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   7.3e-07    0.0012       9     106 ..     154     265 ..     149     285 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.3e-07
                           DUF2075   9 vaGtGKtvvllnllaeleddeeerta.vylsvNhplvlvlrealakke............ekkkkkeafeklssfin 72 
                                       ++G+GKt+++  l+ el  + ++    ++++   +l    ++++++k             + +  ++  ++ +++i+
  gi|386001359|ref|YP_005919658.1| 154 DPGAGKTIMAGLLVKEL--KMRGLIMrILIVTPANLTFQWQREMREKFgerfevirgvvlRANYGTNPWQERDQVIT 228
                                       79***************..4455444044444444555555555555555447776666555555566677777777 PP

                           DUF2075  73 nlsef...kkaeekkeepkedvvivDEAhrlltksdq 106
                                       ++      ++a+e+  + + d+vivDEAh++   s+ 
  gi|386001359|ref|YP_005919658.1| 229 SMPWVariEDAKESLLHSHWDLVIVDEAHKMSAYSSE 265
                                       777558888**********************983333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     5e-05     0.082       2     109 ..     150     290 ..     149     308 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                       EEESSTTSSHHHHHHHHHHHHTHE...............EEEEETTTCSSS.......................... CS
                               AAA   2 llyGppGtGKTllakavakelgve...............fleisgsellsk.......................... 37 
                                       ll   pG GKT++a  ++kel+++               f          +                          
  gi|386001359|ref|YP_005919658.1| 150 LLADDPGAGKTIMAGLLVKELKMRglimrilivtpanltF----------Qwqremrekfgerfevirgvvlranyg 216
                                       56668***************99664444433333333330..........234444444555555555555555567 PP

                                       ........STTHHHHHHHHHHHHHHHTS..TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTE CS
                               AAA  38 ........yvgesekkirelfkeakeka..kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskv 103
                                                v  s+    + +++ake+   ++   +++DE++++   +     +e+++++ qL ++l++++++    
  gi|386001359|ref|YP_005919658.1| 217 tnpwqerdQVITSMP-WVARIEDAKESLlhSHwDLVIVDEAHKMSAYS-----SEKKTLAYQLGEALSEMTDH---Y 284
                                       774444432222222.22233444444477555888888888885555.....67777788888888877772...4 PP

                                       EEEEEE CS
                               AAA 104 ivigat 109
                                       ++++at
  gi|386001359|ref|YP_005919658.1| 285 LLMTAT 290
                                       444444 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.8e-05      0.14      36     206 ..      76     281 ..      66     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                            AAA_34  36 lSalQleavvyacqrheellpdgk..............................................RaGfllG 66 
                                       lS+ Ql ++    ++ e++  d +                                              R  fll 
  gi|386001359|ref|YP_005919658.1|  76 LSSEQLKTLRNIGSNMESFDGDAFnfrlgieamrlgmaheydpffslsiarvdplphqleavydyflklpRIRFLLA 152
                                       6666666666666666666666656666666666666666666666677777777777777777777777999**** PP

                            AAA_34  67 DgaGvGkgrqiagiilenllqgrkkavwvsvsedLkeDaerDlkdigaseievvalnklkegkkikeseelkeGvlF 143
                                       D+ G Gk+   + ++ e  ++g    + + + ++L+   +r++++   ++ ev++   l+++  ++  +e ++ v+ 
  gi|386001359|ref|YP_005919658.1| 153 DDPGAGKTIMAGLLVKELKMRGLIMRILIVTPANLTFQWQREMREKFGERFEVIRGVVLRANYGTNPWQERDQ-VI- 227
                                       ********999999999999***********************998788777775444433322211223333.32. PP

                            AAA_34 144 vtYstliseskkkkksrleqlveWlgedfdGvivfDEchkaknlakseekkatktgkavlelq 206
                                        t    +++ ++ k+s    l   l +++d +++ DE+hk+    +++++ a + g+a  e+ 
  gi|386001359|ref|YP_005919658.1| 228 -TSMPWVARIEDAKES----L---LHSHWD-LVIVDEAHKMSAYSSEKKTLAYQLGEALSEMT 281
                                       .333333333333312....2...335566.77789999999888888888888888887776 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05      0.12       4     101 ..     153     258 ..     150     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                     Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke..........eekkkkaekael 69 
                                        d+G GK+ ++Gl++++l  +g  ++il++ p + + +   e+ +k  e+ ++ +          +    +++++ +
  gi|386001359|ref|YP_005919658.1| 153 DDPGAGKTIMAGLLVKELKMRGLiMRILIVTPANLTFQWQREMREKFGERFEVIRgvvlranygtN--PWQERDQVI 227
                                       589*****************99999********999998888887777777766676666555322..222222223 PP

                     Helicase_RecD  70 rvrkqrieyiapdellklkeqadllvvDEAAa 101
                                       ++     +    +e l  ++++dl++vDEA  
  gi|386001359|ref|YP_005919658.1| 228 TSMPWVARIEDAKESLL-HSHWDLVIVDEAHK 258
                                       33333333333333333.3367*******965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.6e-05      0.11      23     102 ..     151     261 ..     131     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-05
                            AAA_30  23 ltGpAGtGKttalkalreaweaag..grviglAptg...kaAkvLaeelgieastiakllkrlk............. 81 
                                       l   +G+GKt + + l++ ++ +g  +r+++++p +   +  ++++e++g + + i  ++ r +             
  gi|386001359|ref|YP_005919658.1| 151 LADDPGAGKTIMAGLLVKELKMRGliMRILIVTPANltfQWQREMREKFGERFEVIRGVVLRANygtnpwqerdqvi 227
                                       44579***********9999999999888888876522266778******9999999999777789999999999** PP

                            AAA_30  82 ............grarlepg.tllivDEagmvdt 102
                                                   ++  l+++ +l+ivDEa  +++
  gi|386001359|ref|YP_005919658.1| 228 tsmpwvariedaKESLLHSHwDLVIVDEAHKMSA 261
                                       ***********9556777888********98875 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.0   0.00099       1.6       2      37 ..     476     514 ..     475     564 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00099
                                       XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXX- CS
                       Histone_HNS   2 Lkalieelekqeea...leaeerkealaeirelaaeyGl 37 
                                       Lka+i+el++ +++   le++e++ +la++re++ ++G+
  gi|386001359|ref|YP_005919658.1| 476 LKAEIKELARLIDQaraLEEREIETKLAKLREVITQEGI 514
                                       8899999999888877679*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 7772.10
//
Query:       gi|386001360|ref|YP_005919659.1|  [L=565]
Description: Divergent AAA domain family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-17   61.2   0.0    1.8e-16   60.0   0.0    1.7  1  HATPase_c_4  Putative ATP-dependent DNA helicase recG C-termi
    6.4e-15   55.6   0.0    1.2e-14   54.7   0.0    1.4  1  AlbA_2       Putative DNA-binding domain
    0.00042   20.0   0.2    0.00087   18.9   0.2    1.5  1  HTH_42       Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.027   14.4   0.2       0.15   12.0   0.0    2.4  2  MarR_2       MarR family
      0.039   13.5   0.0       0.15   11.7   0.0    2.1  1  HTH_24       Winged helix-turn-helix DNA-binding
      0.074   13.4   0.2       0.19   12.1   0.2    1.7  1  TPR_12       Tetratricopeptide repeat
       0.49   10.4   2.3         11    6.0   0.0    3.6  4  HTH_Crp_2    Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HATPase_c_4  Putative ATP-dependent DNA helicase recG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0     7e-20   1.8e-16       3      88 .]     311     396 ..     310     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 7e-20
                       HATPase_c_4   3 kvqieifdDRleItspGglpggvtveskllegrssaRNelLasllerlrlmeergsGiqrilealeeaglpepefr. 78 
                                        v ++   D++  t+pGg+p g+tve+ +l ++++ RN++La++++r++++e+ g+G+++i+    ++g p+p++  
  gi|386001360|ref|YP_005919659.1| 311 AVYVQWHHDHILMTNPGGFPAGITVEN-ILVHEPKPRNSRLAEAFKRIGIIEQTGRGVDKIYMGQLRYGRPAPDYTr 386
                                       5889999*******************9.8**********************************************75 PP

                       HATPase_c_4  79 edgssftvtl 88 
                                       +d +s++++l
  gi|386001360|ref|YP_005919659.1| 387 SDADSVRIVL 396
                                       7889999986 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   4.8e-18   1.2e-14       1     113 [.      15     124 ..      15     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 4.8e-18
                            AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNsegGtlliGVeDdgkvvGvecsdqeedqlrlelksiikrfkpkvlp 77 
                                       E  ++EfK++ +  ++++   i ++++A+aN++gG+lliGVeDdg+v+G + ++ +  +  +++++i +++ p+++ 
  gi|386001360|ref|YP_005919659.1|  15 EALDIEFKSDRRRISDRE---IYEEVVAMANTRGGVLLIGVEDDGRVTGASPRHGKTTDPLKLQSAIFNNTVPNINT 88 
                                       6789*******9999965...*****************************8888888888888888*********** PP

                            AlbA_2  78 diervelkgk..kvlvvkvekskkkplyeneegvvyiR 113
                                       +i+ v   +   +vl+++v+  +++    + eg++ +R
  gi|386001360|ref|YP_005919659.1|  89 RISLVADADPegEVLAIEVDSYPEPC--ATTEGKALHR 124
                                       **99876655669******9999887..6666666666 PP

>> HTH_42  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   3.4e-07   0.00087     118     229 ..     445     562 ..     428     565 .] 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.4e-07
                            HTH_42 118 wkkpgkaskralellrlegelvvarrergfekvydlaerv.....lPravrs.........eaealreLvrrylray 180
                                       ++k  ++++r le+l+  g +   +  rg  +vy l ++            +         +  +++++v +y++a+
  gi|386001360|ref|YP_005919659.1| 445 IQKGATEARRTLEHLHEIGLVEGKGEARG--RVYHLSADMyrrlgQ-----PesyvrthgiAPIRQEAMVMEYVQAH 514
                                       44556789999999999998877775555..899999999555442.....13344445656666999********* PP

                            HTH_42 181 Gpatvadlaawsgltkarlraalaelvaegelvevrvergrerlfdlpe 229
                                       G    +++  ++glt+ ++ + l+++v++g+l +     + + +++ +e
  gi|386001360|ref|YP_005919659.1| 515 GRIERKHVMELCGLTSPQAGRILKKMVQNGKLKRRGTPPRWT-YYVIAE 562
                                       *******************************99877774355.777666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.7   4.4e+03      39      53 ..     453     467 ..     443     474 .. 0.78
   2 ?   12.0   0.0   5.7e-05      0.15       5      54 ..     502     549 ..     496     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHTTSEEE CS
                            MarR_2  39 srilkrLvaaGLver 53 
                                        r+l+ L + GLve 
  gi|386001360|ref|YP_005919659.1| 453 RRTLEHLHEIGLVEG 467
                                       588999999999985 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       +++a+v+ ++ ++++  +  + + + +gl+ + + rilk++v+ G + rr
  gi|386001360|ref|YP_005919659.1| 502 RQEAMVMEYVQAHGR--IERKHVMELCGLTSPQAGRILKKMVQNGKLKRR 549
                                       579999999999998..999************************988887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.15       8      47 ..     507     546 ..     504     547 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                            HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       ++e++q+++ri  + + e +gl+++   r lk+++++G +
  gi|386001360|ref|YP_005919659.1| 507 VMEYVQAHGRIERKHVMELCGLTSPQAGRILKKMVQNGKL 546
                                       5799*********************************976 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   7.3e-05      0.19      16      62 ..     446     490 ..     440     491 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.3e-05
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgrye 62 
                                       ++  +eA++ le+ +ei     +++ ++  ++++  +++yr+lg++e
  gi|386001360|ref|YP_005919659.1| 446 QKGATEARRTLEHLHEIGLV--EGKGEARGRVYHLSADMYRRLGQPE 490
                                       55578*************44..48899*****************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.49   1.3e+03      17      31 ..     187     200 ..     173     204 .. 0.60
   2 ?    0.8   0.1       0.2     5e+02      39      56 ..     348     366 ..     346     376 .. 0.80
   3 ?   -1.9   0.0       1.3   3.4e+03      40      54 ..     454     469 ..     450     480 .. 0.77
   4 ?    6.0   0.0    0.0045        11      22      54 ..     517     549 ..     504     558 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.49
                                       EEEEEHHHHHHHHHT CS
                         HTH_Crp_2  17 eielpltqeelAsml 31 
                                        + l l+ ee+A  l
  gi|386001360|ref|YP_005919659.1| 187 NL-LELSDEEIAKAL 200
                                       34.788899998876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                                       HHHHHHHHHTTSEE.ETEE CS
                         HTH_Crp_2  39 srilseLkreglis.rgrr 56 
                                       sr+  ++kr g+i+ +gr+
  gi|386001360|ref|YP_005919659.1| 348 SRLAEAFKRIGIIEqTGRG 366
                                       899999********76754 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                       HHHHHHHHTTSEE.ET CS
                         HTH_Crp_2  40 rilseLkreglis.rg 54 
                                       r+l +L + gl++ +g
  gi|386001360|ref|YP_005919659.1| 454 RTLEHLHEIGLVEgKG 469
                                       9999********9654 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglisrg 54 
                                       + ++   +++Glt  +  ril+++ + g ++r+
  gi|386001360|ref|YP_005919659.1| 517 IERKHVMELCGLTSPQAGRILKKMVQNGKLKRR 549
                                       566777799*******************99954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 3972.95
//
Query:       gi|386001361|ref|YP_005919660.1|  [L=1008]
Description: hypothetical protein Mhar_0659 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-23   81.1   1.3    1.1e-22   79.9   1.3    1.7  1  DUF1156          Protein of unknown function (DUF1156)
    0.00017   21.3   0.0     0.0065   16.2   0.0    2.1  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.062   13.0   0.0       0.51   10.0   0.0    2.2  2  UPF0020          Putative RNA methylase family UPF0020
      0.081   12.8   0.1        2.9    7.7   0.1    2.7  3  FdhE             Protein involved in formate dehydrogenase fo
      0.087   12.5   0.3          2    8.1   0.0    2.3  2  Cons_hypoth95    Conserved hypothetical protein 95
        7.3    6.7   5.5         30    4.7   0.1    2.6  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1156  Protein of unknown function (DUF1156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   1.3   3.8e-26   1.1e-22       2      52 ..      17      69 ..      16      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 3.8e-26
                           DUF1156  2 lPldkinaesakEksirhghlstLhlWWaRrPLaaaRAvifaqLvpdpss..e 52
                                      lP+++i++ + +Eksirhgh+stLh+WWaRrPLaa+RAv+ a+L pdp+    
  gi|386001361|ref|YP_005919660.1| 17 LPIKRISEHARREKSIRHGHISTLHIWWARRPLAACRAVVCASLWPDPADplC 69
                                      8**********************************************987432 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06    0.0065      24      64 ..     152     192 ..     145     225 .. 0.82
   2 ?    2.6   0.1      0.03        89     164     188 ..     529     552 ..     510     561 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                                       EEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH CS
                   MethyltransfD12  24 fvepFaGggaVffeakkqgkkvlinDinedlinlykalikn 64 
                                       +v+pFaGgga+ +ea++ g ++ ++D+n+  + l+k +++ 
  gi|386001361|ref|YP_005919660.1| 152 VVDPFAGGGAIPLEALRVGADAFASDLNPVAVLLNKVVLEY 192
                                       79****************************99999966654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.03
                                       EC-CHHHHTT--TTE.EEEE--S-T CS
                   MethyltransfD12 164 cgdfdavllkakieddivYlDPPYn 188
                                        +++++++l  ++ ++i++ DPPY 
  gi|386001361|ref|YP_005919660.1| 529 SKSANKNDLP-DEFAQILFTDPPYY 552
                                       3444444444.58999********5 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.51      27      54 ..     146     174 ..     133     214 .. 0.82
   2 ?   -0.3   0.0      0.25   7.4e+02     105     135 ..     527     555 ..     522     579 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                                       -TTS-E.EETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020  27 kpgepl.lDPmCGsGtilIEaallgania 54 
                                         ++pl +DP+ G+G+i++Ea  +ga++ 
  gi|386001361|ref|YP_005919660.1| 146 SGTRPLvVDPFAGGGAIPLEALRVGADAF 174
                                       45555527*************87777665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.25
                                       EEEEE--GGG--STTS---EEEE-------- CS
                           UPF0020 105 iefsqadaakLrlkegevdvivtnpPYGerl 135
                                        e ++a+  +L+ +e    ++ t+pPY +++
  gi|386001361|ref|YP_005919660.1| 527 AESKSANKNDLP-DE-FAQILFTDPPYYDAV 555
                                       566778888999.44.467899*****8766 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00097       2.9     166     187 ..     301     323 ..     286     328 .. 0.76
   2 ?    1.4   0.0     0.079   2.4e+02      66     149 ..     401     487 ..     385     491 .. 0.67
   3 ?   -2.3   0.0       1.1   3.3e+03      80     119 ..     633     674 ..     622     683 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00097
                                       TT-SS-TTT-.--EEEEEEE--- CS
                              FdhE 166 eekglCPvCg.saPvasvvrigg 187
                                       + +++CPvCg ++Pvasv r+ +
  gi|386001361|ref|YP_005919660.1| 301 RGSATCPVCGyTTPVASVRRQLK 323
                                       45689*****889****976655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.079
                                       HHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-SSHHHH.HHHHHHHH--HHHHHHHHHHH..HTT-GGGS-GGGHH CS
                              FdhE  66 qehgmpplaakalerdeawqelLqallealkeelpealr.ealerlrkadaeelealadal..lageleavdaakav 139
                                       ++ gm +++   + r++   ++L++l+ ++ e++ e+ +  + ++++++ + ++++ ad+l  la   ++ ++ + +
  gi|386001361|ref|YP_005919660.1| 401 RNYGMDLFEDLFTPRQALALTTLARLVREAGEKVAEEQEnGLAAAVQTCLSLAIDRSADKLssLARWDTSRENPQGT 477
                                       55666666666677777788899999996666555544404445566666666666666662233333455666789 PP

                                       HHHHHHHHHH CS
                              FdhE 140 fvaaAlqvvw 149
                                       f  +Alq+vw
  gi|386001361|ref|YP_005919660.1| 478 FSRQALQIVW 487
                                       9999999999 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.1
                                       HH-TTHHHHHHHHH.T--S-SSHHH.HHHHHHHHH--HHHHH CS
                              FdhE  80 rdeawqelLqalle.alkeelpeal.realerlrkadaeele 119
                                        ++ w+++Lqall+     +++ ++ +e+ +rlr++++++l 
  gi|386001361|ref|YP_005919660.1| 633 TTTGWEAMLQALLDaGWVITASWPIdTEMGTRLRAMNSAALA 674
                                       4578*********96333333333313455667777666665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00065         2      42      65 ..     149     172 ..     133     190 .. 0.80
   2 ?    1.8   0.1     0.053   1.6e+02     109     126 ..     537     554 ..     511     568 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00065
                                       C-EEEETT-TTSHHHHHHHHTT-S CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgak 65 
                                       +  v+D faG Ga+ lEAl  ga+
  gi|386001361|ref|YP_005919660.1| 149 RPLVVDPFAGGGAIPLEALRVGAD 172
                                       56699*************976654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.053
                                       -SS-EEEEEEE--SSSTT CS
                     Cons_hypoth95 109 kkkeefdivflDPPyake 126
                                         +e  +i f DPPy + 
  gi|386001361|ref|YP_005919660.1| 537 LPDEFAQILFTDPPYYDA 554
                                       344556799******875 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.7     0.044   1.3e+02       5      22 ..      51      70 ..      50      71 .. 0.92
   2 ?    4.7   0.1      0.01        30      19      33 ..     304     319 ..     291     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.044
                     Zn_Tnp_IS1595  5 earalLealrWpng..fvCP 22
                                      ++ra+++a  Wp+   + CP
  gi|386001361|ref|YP_005919660.1| 51 ACRAVVCASLWPDPadPLCP 70
                                      8*************999999 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayrik 33 
                                        +CP Cg++  + +++
  gi|386001361|ref|YP_005919660.1| 304 ATCPVCGYTtPVASVR 319
                                       78*****994334443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1008 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.81
# Mc/sec: 3777.65
//
Query:       gi|386001362|ref|YP_005919661.1|  [L=205]
Description: hypothetical protein Mhar_0660 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1323.93
//
Query:       gi|386001363|ref|YP_005919662.1|  [L=74]
Description: hypothetical protein Mhar_0661 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-17   61.5   0.0    8.5e-17   61.4   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.056   13.8   0.1        1.4    9.3   0.0    2.2  2  Jag_N            Jag N-terminus


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   9.5e-21   8.5e-17       1      61 [.       3      63 ..       3      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 9.5e-21
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssi 61
                                      y ++++++ +  y+v+vP lpGc + gdt+eea+++a eaiel+le+l edgeeip+ ++ 
  gi|386001363|ref|YP_005919662.1|  3 YRVLLKREPEGGYTVTVPSLPGCVTYGDTIEEAVKMAIEAIELYLESLREDGEEIPTEEDA 63
                                      7788999999**********************************************76554 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00015       1.4       2      18 ..      28      44 ..      27      51 .. 0.84
   2 ?    2.5   0.0     0.021   1.9e+02       5      14 ..      59      68 ..      58      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                             Jag_N  2 eGkTveeAiekAlkeLg 18
                                       G+T+eeA++ A++  +
  gi|386001363|ref|YP_005919662.1| 28 YGDTIEEAVKMAIEAIE 44
                                      69**********99766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.021
                             Jag_N  5 TveeAiekAl 14
                                      T e+A+e Al
  gi|386001363|ref|YP_005919662.1| 59 TEEDALEYAL 68
                                      99******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 517.33
//
Query:       gi|386001364|ref|YP_005919663.1|  [L=1010]
Description: ATPase (AAA+ superfamily)-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-21   76.1   0.0      2e-19   69.0   0.0    2.3  2  DUF499          Protein of unknown function (DUF499)
  ------ inclusion threshold ------
      0.041   12.3   0.0      0.073   11.4   0.0    1.3  1  BcsB            Bacterial cellulose synthase subunit
      0.062   13.2   0.0       0.13   12.2   0.0    1.4  1  Ribosomal_S24e  Ribosomal protein S24e
      0.071   13.1   0.8       0.17   11.9   0.8    1.6  1  Big_1           Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> DUF499  Protein of unknown function (DUF499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   4.4e-23     2e-19      51     263 ..     178     398 ..     172     409 .. 0.78
   2 !    4.6   0.0    0.0012       5.4     483     637 ..     589     741 ..     556     794 .. 0.75

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 4.4e-23
                            DUF499  51 kTlWGylayeLg...rYeiveksDrnetaPdieelrkllqgek.vliLiDEIadyvdnllrSgledkkdYaeevsaF 123
                                       kT WG +a++Lg    ++ v ++Dr   aP  +++r+ l   +  liL+DE+++yv    r     k d   ++ +F
  gi|386001364|ref|YP_005919663.1| 178 KTPWGEIAFQLGgeeAFATVAEHDRLMRAPAGDVIRQFLPKGRpCLILMDELMNYVS---RN---RKTDLPSQLYNF 248
                                       899********95545899******************9965555************9...43...23346699**** PP

                            DUF499 124 ldnLakAle.vsevalvitipaekreGeakaeeeYkrevvrailealrrvageiykPvrrneelvevlkkRiFsevd 199
                                       ++nL++ +   ++++lv+++pa   e +++ +  Y+    +++l+ l++    ++   ++++e+ e++++R+F+   
  gi|386001364|ref|YP_005919663.1| 249 IQNLSETVRgEDRMVLVVSVPASATEMNPEDHSDYD--RLKKLLDRLSK---AVIL--STETEISEIIRRRLFEF-- 316
                                       *********999**********99999999999994..46777776666...4554..569************99.. PP

                            DUF499 200 edekkkelk.kl......retaevreifgdesdlekelee.................tYPFHPeylevLreiierl. 251
                                        d k   l+ k+      r       + ++ + +  +  +                 +YPFHP+  +v ++  + l 
  gi|386001364|ref|YP_005919663.1| 317 -DSKSLDLNgKIvlpdeaR------AVCEEYARWVLDHRQqvpswfpvdnaraafeaAYPFHPMVYSVFERKWQTLp 386
                                       .555555541554444442......55555555544444444445555666677777************99999999 PP

                            DUF499 252 dlqrTRdlirIt 263
                                         qrTR ++r+ 
  gi|386001364|ref|YP_005919663.1| 387 RFQRTRGVLRLL 398
                                       *******99975 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0012
                            DUF499 483 pkEllDnkeykLvvlvkkdvskee......leklifkegggeRtyaNtvvvvapvkeklesllel.larlvAaeeik 552
                                        ++++D  ++ L+vl  +   ++       +  +  ++g++ Rt++  ++  a      +s l      l A eei+
  gi|386001364|ref|YP_005919663.1| 589 SNDIPDRASLTLIVLPPDRSMQDReavlrsIDSMTAEHGTSGRTFKSALIWSAAES---DSHLDHvARDLLALEEIQ 662
                                       567888888888888655432321122111444556669999****9877433322...34444404567899**** PP

                            DUF499 553 ee.lrelygeYakevlkiqknkveskkekaledllnqilslfrkVaYpvlgkereeveeveateSd.ksivekVesa 627
                                       +e l+  +        + qk ++++  ++ + dl + + +++r Va    ++  e+++ +    S   s+v+++ s 
  gi|386001364|ref|YP_005919663.1| 663 DEeLKLQL-------DDSQKLQLKDNLRRSERDLREAVWRTYRYVALL-GRENVEIIDLGLVHSSAaSSMVDLIISK 731
                                       98676555.......588889999999*******************98.4444557777766655425788999999 PP

                            DUF499 628 Lkekekivee 637
                                       Lk  ++++ +
  gi|386001364|ref|YP_005919663.1| 732 LKRDDLVADS 741
                                       9988877655 PP

>> BcsB  Bacterial cellulose synthase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.6e-05     0.073     471     564 ..     597     695 ..     593     730 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
                              BcsB 471 seTavvlpdrptaaelsallnllgrmGaqtgy......palrvtvadaadaesladkdlLvigslesqpllarleks 541
                                       s T++vlp+  + ++ +a+l  +  m+a+ g+      +al  ++a+ ++  ++  +dlL++ ++++ +l+ +l++s
  gi|386001364|ref|YP_005919663.1| 597 SLTLIVLPPDRSMQDREAVLRSIDSMTAEHGTsgrtfkSALIWSAAESDSHLDHVARDLLALEEIQDEELKLQLDDS 673
                                       5699***************************977666666666667777777788********************** PP

                              BcsB 542 lpllldqrrlelkdrseelkelk 564
                                       + l+l++ +l+ ++r  +++ ++
  gi|386001364|ref|YP_005919663.1| 674 QKLQLKD-NLRRSERDLREAVWR 695
                                       ******5.555555555554444 PP

>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.13      30      55 ..      99     124 ..      86     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                                       TTEEEEEEEE-SSSSEEEEEEEEES- CS
                    Ribosomal_S24e  30 dlvvvfgfrthfGggkttGfakiYds 55 
                                       +   vf+++t+fGggkt++  + Y  
  gi|386001364|ref|YP_005919663.1|  99 EASAVFNLNTQFGGGKTHALTLLYHL 124
                                       6678***************9999965 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 ?   11.9   0.8   3.9e-05      0.17      15      55 ..     872     914 ..     863     924 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                             Big_1  15 DangnpvagatVtfsvsggals..assgtTdanGkatvtltst 55 
                                       D+ gn  +  +V ++++gg++    + +  d++G++tvt++s+
  gi|386001364|ref|YP_005919663.1| 872 DQRGNDYPLDQVAWTATGGVIGdrGNFQAGDDDGRFTVTVSSK 914
                                       8899999999**************999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1010 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 6546.51
//
Query:       gi|386001365|ref|YP_005919664.1|  [L=59]
Description: hypothetical protein Mhar_0663 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-10   38.7   0.0      1e-09   38.5   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   5.8e-14     1e-09       3      50 ..       5      52 ..       3      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.8e-14
                   HicB_lk_antitox  3 iaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhleglie 50
                                      +++e+ e+  y v+ P lpGc+s gdt  ea++n++eaie  le+  e
  gi|386001365|ref|YP_005919664.1|  5 VTLEEAEEGGYIVSCPALPGCHSQGDTAVEALENIREAIEGCLESFSE 52
                                      6789999*************************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 433.95
//
Query:       gi|386001366|ref|YP_005919665.1|  [L=164]
Description: hypothetical protein Mhar_0664 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-17   61.9   4.0    9.1e-17   61.6   4.0    1.1  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   4.0   5.1e-21   9.1e-17       2     124 ..      14     129 ..      13     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 5.1e-21
                               RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvl..llvllvyqllllskkgqTlGk 76 
                                       as+ rR++A+liD++l+ i+  lla++++ ++ ++ ++    +  +++ + l +  +l+l++y+++l+ ++gq+lGk
  gi|386001366|ref|YP_005919665.1|  14 ASWRRRVGAWLIDIILVGILWDLLAGAAGPIT-QFHFWLPPGPIFSAWFVHLGSgdALILFAYWTVLEGTRGQSLGK 89 
                                       9*****************************55.7777777777666666666552268******************* PP

                               RDD  77 lllglkvvdedgrklglaqaliRalllllllvlglslvlllllligfl 124
                                       ++lglkv+d+ g  ++l +a i ++ +++ll         +  lig++
  gi|386001366|ref|YP_005919665.1|  90 MALGLKVTDRRGDAIDLSRAAIQSFGKAFLL--------PVDVLIGWI 129
                                       ************************9544433........333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1263.00
//
Query:       gi|386001367|ref|YP_005919666.1|  [L=460]
Description: Histone deacetylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-63  215.1   0.1    2.7e-63  214.3   0.1    1.3  1  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
       0.02   15.4   0.1      0.038   14.5   0.1    1.3  1  Evr1_Alr       Erv1 / Alr family


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   0.1     3e-67   2.7e-63      83     295 ..      78     285 ..      31     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 3e-67
                                       CTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-B..TTBSS-HHHHHHHHHHHCC-SS-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  83 vspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseas..GFClvNnvaiaikylqakhelkrvail 157
                                       v+  + +a l+a+g++l ++da ++g++++af+lvrPpgHH+++ + +  GFC vNn ai ++y+++k++++rvai+
  gi|386001367|ref|YP_005919666.1|  78 VEALVTEAHLIAAGSTLVLADAYMKGEINNAFALVRPPGHHSMRVAHGnrGFCNVNNEAIMVEYIRRKYGIRRVAII 154
                                       44556788899*******************************87776667*************************** PP

                                       E-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 158 DvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvl 234
                                       D DvHhG+Gt+e+fy+dpdvl++S+H+ ++++yPg+g +++ g  k++g ++n+pl+++t de +++v+ee++ p+l
  gi|386001367|ref|YP_005919666.1| 155 DTDVHHGDGTQEIFYHDPDVLFISFHQDGRTLYPGSGFVDEQGGPKAMGRTINIPLPPETPDEGIHYVLEELVLPIL 231
                                       *******************************************9********************************* PP

                                       CCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 235 eefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlea 295
                                       eef+P+l++ saG D + +dpl++++ s++gy++l ++la         +++leGGY +e+
  gi|386001367|ref|YP_005919666.1| 232 EEFRPQLVVNSAGQDNHYTDPLANMRFSAQGYARLNEMLAP-------DIAVLEGGYAIES 285
                                       *********************************99998853.......378******9854 PP

>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.2e-06     0.038      33      78 ..     405     457 ..     396     458 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-06
                                       HHHHHHHSSCHHHHHHHHHHHHHCH.C.......CCGSSHHHHHHHHHHHHHH CS
                          Evr1_Alr  33 lkliakfypCeeCaehfekvlaenppe.......kevesrdelvlWlweaHNe 78 
                                       + ++  ++ C++C+e+ ++ +++++++        + ++rde +l+  ++HNe
  gi|386001367|ref|YP_005919666.1| 405 FGVFVPLFACKSCREEAREEYEAHKTDsrynyifFQEKNRDEYRLYSTRMHNE 457
                                       5667779************777777444555555445999************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 3427.36
//
Query:       gi|386001368|ref|YP_005919667.1|  [L=560]
Description: hydantoinase/oxoprolinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-47  161.1  16.6      3e-45  154.7   4.0    2.9  3  Hydantoinase_A  Hydantoinase/oxoprolinase
    3.5e-30  105.0   7.5    5.6e-27   94.6   4.9    3.3  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.2e-06   28.2   0.0    0.00013   21.6   0.0    3.0  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
    5.5e-06   25.2   1.8      0.012   14.3   0.3    2.3  2  MutL            MutL protein
    0.00027   21.3   6.7      0.037   14.5   0.5    3.2  3  FtsA            Cell division protein FtsA
     0.0026   17.3   0.7     0.0076   15.8   0.1    2.1  2  ROK             ROK family
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.019   14.8   0.0    1.4  1  DEDD_Tnp_IS110  Transposase
      0.014   14.9   2.9       0.24   10.8   0.1    2.7  3  Ppx-GppA        Ppx/GppA phosphatase family
       0.03   13.2   1.3        1.1    8.0   0.2    2.2  2  EutA            Ethanolamine utilisation protein EutA
       0.15   10.8   7.7       0.38    9.5   0.4    2.9  3  MreB_Mbl        MreB/Mbl protein
        0.3   10.3   2.2        2.6    7.2   0.2    2.2  2  StbA            StbA protein
        1.1    9.2   5.8        1.1    9.2   0.4    2.8  3  TetR_C_14       MftR C-terminal domain


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.6   1.2e-05     0.018      81     105 ..       2      26 ..       1     141 [. 0.85
   2 !  154.7   4.0     2e-48     3e-45       1     288 [.     180     460 ..     180     462 .. 0.95
   3 ?   -4.0   0.1       4.5   6.7e+03     197     223 ..     493     525 ..     482     531 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                    Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsl 105
                                       +I++D+GGT+tD+ li++g+v  ++
  gi|386001368|ref|YP_005919667.1|   2 LIGIDVGGTTTDAVLIDEGKVIKTS 26 
                                       79******************94333 PP

  == domain 2  score: 154.7 bits;  conditional E-value: 2e-48
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r+ t+++ A+ ++ +r+++e+v k+++ r+++a+++++++dGg++++++   +pveti SGPaa+ +g+ a   ++ 
  gi|386001368|ref|YP_005919667.1| 180 RAATTALKAAAMDEYRKFAEEVAKAVAGRKIEAPVYILKADGGTLPLATSVDHPVETIFSGPAASTMGVLA--LTPA 254
                                       789********************************************************************..5556 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei.agvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgp 153
                                        +  +++D+GGT+tD++li dg++ +s+e      + ++++a ++++v++gG+s++ + egg++ +gp+ ag +   
  gi|386001368|ref|YP_005919667.1| 255 GQTSVVVDIGGTTTDLALILDGSPLISSEGARvNSYLTHIRAFAVKSVALGGDSRV-RAEGGRVAIGPDRAGPAFCL 330
                                       667999**********************987559**********************.************99977777 PP

                    Hydantoinase_A 154 acyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavr 230
                                            Gg e+t TDa+ +L+ +               ++  a++a+++l+ e++ ++ e+A+ ++++ave +  +++
  gi|386001368|ref|YP_005919667.1| 331 -----GGPEPTPTDAMRLLNLISIG------------ERGRAEEAMAKLGREIGCSAGEAAQMVVDAAVEMLLGEIE 390
                                       .....999**************987............5779************************************ PP

                    Hydantoinase_A 231 kl.............svergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvr 288
                                        +             +  ++ +++  ++v++GG++  +++ +ae+lg + +i +++  v++a+G+a+A+ +
  gi|386001368|ref|YP_005919667.1| 391 GMflaweeepayrvwEILQKEKIRPQNVVGVGGGSLGLVPLVAERLGARGIIPENA-TVANAIGAAVARPT 460
                                       ***************99999******************************999998.***********976 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4.5
                    Hydantoinase_A 197 rafeelakelnlk......veevAegilsvave 223
                                       +++ee+ak+l  +      +ee A++++ +a+e
  gi|386001368|ref|YP_005919667.1| 493 KEAEEMAKRLIIDragrmgIEEYAAEAVLTASE 525
                                       445555555555566666677777777766655 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   4.9   3.8e-30   5.6e-27       2     174 ..       3     156 ..       2     160 .. 0.93
   2 !    7.4   0.0    0.0022       3.3       2      17 ..     259     274 ..     258     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 3.8e-30
                        Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkger 78 
                                       igIDvGGT TDav++de+ +++++ K+++  d   e +++al+e  +     +++i+ v+++TT+ tN + e+k ++
  gi|386001368|ref|YP_005919667.1|   3 IGIDVGGTTTDAVLIDEG-KVIKTSKVPTDHDHLLECLLTALDEIVRG--VPPERIERVVLSTTLITNLIAEGKTDP 76 
                                       8***************98.*************************9654..449************************ PP

                        Hydant_A_N  79 vaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiav 155
                                       vaLi+  g           +p+ ++        l  ev  v++ ++++g+++++lde++v++a++++ ++g++ +av
  gi|386001368|ref|YP_005919667.1|  77 VALIIEPGPG--------MNPEGYS--------LGGEVQIVRGAIDYRGREIEALDEDQVQRAAAKIAERGYRKVAV 137
                                       ****988754........3455566........7889999************************************* PP

                        Hydant_A_N 156 vllhSylnpehElrvaeia 174
                                       ++ +  +n +hE+r +eia
  gi|386001368|ref|YP_005919667.1| 138 ASKFGQRNHAHEERMREIA 156
                                       ******************8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                        Hydant_A_N   2 igIDvGGTfTDavald 17 
                                       + +D+GGT TD+ ++ 
  gi|386001368|ref|YP_005919667.1| 259 VVVDIGGTTTDLALIL 274
                                       78*********98775 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   8.6e-08   0.00013       1     115 [.       3     268 ..       3     279 .. 0.66
   2 ?    2.6   0.0     0.052        78     203     265 ..     401     456 ..     395     457 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.6e-08
                                       EEEEE-SSEEEEEEEETTTEEEEEEEE--................................................ CS
                       BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitns................................................ 29 
                                       +GiD+G+Ttt avl+de + + +  + +                                                 
  gi|386001368|ref|YP_005919667.1|   3 IGIDVGGTTTDAVLIDEGKVIKTSKVPTDhdhlleclltaldeivrgvpperiervvlsttlitnliaegktdpval 79 
                                       7***************9988666666666999999999999999999999999999999999999999999999999 PP

                                       ..................................................TTS-HHH.........HHHHHHHHHHT CS
                       BcrAD_BadFG  30 ..................................................anlesvrfeaaekvleealtealerag 56 
                                                                                         +                 ++++  +++
  gi|386001368|ref|YP_005919667.1|  80 iiepgpgmnpegyslggevqivrgaidyrgreiealdedqvqraaakiaeR----------------GYRKVAVASK 140
                                       999999999999999999999999999988777755554444444444440................4444444444 PP

                                       --GGG......................................................................EC CS
                       BcrAD_BadFG  57 eeead......................................................................ie 63 
                                       + + +                                                                      i 
  gi|386001368|ref|YP_005919667.1| 141 FGQRNhaheermreialgtipgvhvemghqasgrlnfprraattalkaaamdeyrkfaeevakavagrkieapvyIL 217
                                       44444555555555555555555555555555555555555555555555555555555555555555533222222 PP

                                       EE..EEESTTCCCTCTTBSEEE-..HHHHHHHHHHHH-TT--..EEEEEETTEE CS
                       BcrAD_BadFG  64 etylvgtgyGratlpekfekeiirseilvhgdGavalypgtr..tvldigGqds 115
                                       +   +gt    ++++   + e+i s   + ++G+ al p+ +   v+digG+ +
  gi|386001368|ref|YP_005919667.1| 218 KA-DGGTLPLATSVD--HPVETIFSGPAASTMGVLALTPAGQtsVVVDIGGTTT 268
                                       22.233333333333..4555666678888889888888777668999999876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.052
                                       HHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHH CS
                       BcrAD_BadFG 203 alrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAal 265
                                       a rv+++ ++++ ++++v+ +GG +        l +lv e+ g     i+  + ++ a+GAa+
  gi|386001368|ref|YP_005919667.1| 401 AYRVWEILQKEKIRPQNVVGVGGGSLG------LVPLVAERLGA-RGIIPENATVANAIGAAV 456
                                       5699********************999......999******99.5889999*********95 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1   0.00015      0.23       3      63 ..       4      58 ..       2      63 .. 0.79
   2 !   14.3   0.3   7.7e-06     0.012     224     273 ..     237     282 ..     226     293 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                              MutL  3 viDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgktevdev 63
                                       iD+G ttT ++l+d+    ++++ +++ pT    +++le+l +al+e+ +    +++++v
  gi|386001368|ref|YP_005919667.1|  4 GIDVGGTTTDAVLIDE----GKVIKTSKVPTDH--DHLLECLLTALDEIVRGVPPERIERV 58
                                      5899999999999999....6799999999998..58999999999998777665555555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.7e-06
                              MutL 224 impTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                       i   PaA   +v +l  +  +     +vvD+GG+TTd+  +++gsp +++
  gi|386001368|ref|YP_005919667.1| 237 IFSGPAASTMGVLALTPA-GQ---TSVVVDIGGTTTDLALILDGSPLISS 282
                                       666777777777777773.23...58*****************9998765 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.5   2.5e-05     0.037       1      37 [.       3      39 ..       3     216 .. 0.87
   2 !    9.4   0.1   0.00089       1.3       1      20 [.     259     278 ..     259     307 .. 0.81
   3 ?   -3.5   0.1       9.3   1.4e+04      46      53 ..     493     500 ..     489     525 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                      EEEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvhlrvigvggngitkdi 37
                                      +++D+G+++td++++++g++++++ +++  +++ + +
  gi|386001368|ref|YP_005919667.1|  3 IGIDVGGTTTDAVLIDEGKVIKTSKVPTDHDHLLECL 39
                                      58************************99888876654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00089
                                       EEEEE-SSSEEEEEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgal 20 
                                       ++vDiG+++td+a++ dg++
  gi|386001368|ref|YP_005919667.1| 259 VVVDIGGTTTDLALILDGSP 278
                                       79***********9999874 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.3
                                       HHHHHHHH CS
                                       xxxxxxxx RF
                              FtsA  46 eeAeriki 53 
                                       +eAe++++
  gi|386001368|ref|YP_005919667.1| 493 KEAEEMAK 500
                                       67888873 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   5.1e-06    0.0076       2      53 ..       3      53 ..       2      75 .. 0.85
   2 ?   -2.5   0.0       1.8   2.7e+03       4      17 ..     261     274 ..     259     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.1e-06
                                      EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCC CS
                               ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerk 53
                                      igid+Ggt + + l+d eg++ ++ kv+t ++ + e l  a++e+v   + +
  gi|386001368|ref|YP_005919667.1|  3 IGIDVGGTTTDAVLID-EGKVIKTSKVPTDHDHLLECLLTALDEIVRGVPPE 53
                                      8***************.9**************************99887653 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                                       EEE-SSEEEEEEEE CS
                               ROK   4 idiGgtkialalvd 17 
                                       +diGgt + lal+ 
  gi|386001368|ref|YP_005919667.1| 261 VDIGGTTTDLALIL 274
                                       9*******999975 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.019       1      38 [.       3      39 ..       3      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                    DEDD_Tnp_IS110  1 vGiDvakdkhdacvidaegkvllservpndeegleall 38
                                      +GiDv+ ++ da++id egkv+++ +vp+d++ l ++l
  gi|386001368|ref|YP_005919667.1|  3 IGIDVGGTTTDAVLID-EGKVIKTSKVPTDHDHLLECL 39
                                      7**************8.*************98776644 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.026        38     115     137 ..       3      25 ..       1      36 [. 0.89
   2 ?   10.8   0.1   0.00016      0.24     101     133 ..     245     277 ..     229     283 .. 0.87
   3 ?   -2.8   0.0       2.2   3.3e+03     116     127 ..     418     429 ..     407     434 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.026
                                       EEEEEETTEEEEEEEETTEEEEE CS
                          Ppx-GppA 115 lviDiGGGStElvlgeekevskl 137
                                       + iD+GG  t+ vl++e +v k 
  gi|386001368|ref|YP_005919667.1|   3 IGIDVGGTTTDAVLIDEGKVIKT 25 
                                       569**************999875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHT---SSEEEEEEETTEEEEEEEETTE CS
                          Ppx-GppA 101 ylgvvssllekgrglviDiGGGStElvlgeeke 133
                                        +gv + +++ +  +v+DiGG  t+l+l+ +  
  gi|386001368|ref|YP_005919667.1| 245 TMGVLALTPAGQTSVVVDIGGTTTDLALILDGS 277
                                       589999999******************997765 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.2
                                       EEEEETTEEEEE CS
                          Ppx-GppA 116 viDiGGGStElv 127
                                       v+ +GGGS+ lv
  gi|386001368|ref|YP_005919667.1| 418 VVGVGGGSLGLV 429
                                       7889****9887 PP

>> EutA  Ethanolamine utilisation protein EutA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00074       1.1     146     169 ..       3      26 ..       1      30 [. 0.90
   2 ?    4.0   0.1     0.012        18     141     165 ..     255     278 ..     219     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00074
                              EutA 146 lniDiGGGtsnlalfkeGevidta 169
                                       + iD+GG t+ ++l++eG+vi+t+
  gi|386001368|ref|YP_005919667.1|   3 IGIDVGGTTTDAVLIDEGKVIKTS 26 
                                       679******************997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
                              EutA 141 kstrvlniDiGGGtsnlalfkeGev 165
                                        +t+ + +DiGG t+ lal+ +G+ 
  gi|386001368|ref|YP_005919667.1| 255 GQTS-VVVDIGGTTTDLALILDGSP 278
                                       4444.45999999999999998864 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0069        10     150     182 ..       5      37 ..       1      45 [. 0.87
   2 ?    9.5   0.4   0.00025      0.38     143     166 ..     254     277 ..     234     289 .. 0.73
   3 ?   -1.2   0.3      0.45   6.8e+02     115     139 ..     432     456 ..     419     462 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0069
                                       EEE-SS-EEEEEEETTEEEEEEEES-SHHHHHH CS
                          MreB_Mbl 150 vdiGggttevavislggivtsksvrvaGdelde 182
                                       +d+Gg tt+ ++i  g +++++ v +  d+l e
  gi|386001368|ref|YP_005919667.1|   5 IDVGGTTTDAVLIDEGKVIKTSKVPTDHDHLLE 37 
                                       8********************999988887755 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00025
                                       SSS-EEEEEE-SS-EEEEEEETTE CS
                          MreB_Mbl 143 epsgnmvvdiGggttevavislgg 166
                                       + + ++vvdiGg tt++a+i  g+
  gi|386001368|ref|YP_005919667.1| 254 AGQTSVVVDIGGTTTDLALILDGS 277
                                       55789*************996665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.45
                                       HHHHTT-SEEEEEEHHHHHHHHTT- CS
                          MreB_Mbl 115 aakkaGarevllieeplaAAiGagl 139
                                       +a+++Gar ++ ++ ++a AiGa +
  gi|386001368|ref|YP_005919667.1| 432 VAERLGARGIIPENATVANAIGAAV 456
                                       57899*****999999******975 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.041        61     168     194 ..       5      32 ..       1      72 [. 0.84
   2 ?    7.2   0.2    0.0018       2.6     163     181 ..     256     274 ..     239     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.041
                              StbA 168 iDlGGttLDvakv.rgklegiskvkgds 194
                                       iD+GGtt D   + +gk+ + skv +d 
  gi|386001368|ref|YP_005919667.1|   5 IDVGGTTTDAVLIdEGKVIKTSKVPTDH 32 
                                       9********9999458999999987765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                              StbA 163 eslLiiDlGGttLDvakvr 181
                                       + ++++D+GGtt D+a + 
  gi|386001368|ref|YP_005919667.1| 256 QTSVVVDIGGTTTDLALIL 274
                                       5789***********9986 PP

>> TetR_C_14  MftR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.1   6.1e+03      92     111 ..      31      50 ..      28      51 .. 0.81
   2 ?    9.2   0.4   0.00076       1.1      35      61 ..     183     209 ..     180     217 .. 0.89
   3 ?    1.5   0.3      0.18   2.7e+02      56      81 ..     431     456 ..     425     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                                       TTS-HHHHHHHHHHHHHH-S CS
                         TetR_C_14  92 edadlaelLdealdllaagl 111
                                       ++  l e+L  ald++++g+
  gi|386001368|ref|YP_005919667.1|  31 DHDHLLECLLTALDEIVRGV 50 
                                       45679999999999999987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00076
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TetR_C_14  35 vPaLqAhstlryaawrevvAefvAeRt 61 
                                       + aL+A+++ +y++  e vA++vA R 
  gi|386001368|ref|YP_005919667.1| 183 TTALKAAAMDEYRKFAEEVAKAVAGRK 209
                                       679*********************996 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.18
                                       HHHHHHTS-TTSHHHHHHHHHHHHHH CS
                         TetR_C_14  56 fvAeRtgtdaddlvprtvaaavlaaa 81 
                                       +vAeR+g++   +   tva a+ aa+
  gi|386001368|ref|YP_005919667.1| 431 LVAERLGARGIIPENATVANAIGAAV 456
                                       79999999998888889998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3892.01
//
Query:       gi|386001369|ref|YP_005919668.1|  [L=177]
Description: hypothetical protein Mhar_0667 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-33  114.2   0.0    5.9e-33  113.8   0.0    1.1  1  Fasciclin  Fasciclin domain


Domain annotation for each model (and alignments):
>> Fasciclin  Fasciclin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.0   3.3e-37   5.9e-33       2     128 .]      39     156 ..      38     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 3.3e-37
                                       GGHHHHHHHHTTTCCCCCTCSSSSEEEEEE-HHHHCCCHHHHHHHHHTCHHHHHHHHHTTEEESSS-HHHHHHHHEE CS
                         Fasciclin   2 dlstfvsllekaglaeeLnkkdgglTvFaPtneAfaklppellakllndkkklkeiLkyHvvpetvsssalkkaset 78 
                                       d++t+v+++e+agl ++L +++g++TvFaPt+eAfa++  e l++l  d + l+eiL+yHv+++++++++  ++  t
  gi|386001369|ref|YP_005919668.1|  39 DFNTLVAAVEAAGLLDTL-NGEGPFTVFAPTDEAFAAV--EGLDEL--DAETLAEILTYHVASGAIMAADALNM-AT 109
                                       79****************.677*************999..778888..9******************9999999.9* PP

                                       EECCTTSSEEEEEEEGGTTEEEETTEEEEEEEEEEESSEEEEEESS-TSX CS
                         Fasciclin  79 latllegaklrvniekgngtvtvngkarvvrsdieatngvihvidkvLlp 128
                                       ++t l+g +l+v+ +  ++ v vn+ a+v+++di ++ngvihvid vL+p
  gi|386001369|ref|YP_005919668.1| 110 IPT-LQGRNLTVEAT--DEGVLVNNGAKVTTADIFCSNGVIHVIDAVLMP 156
                                       ***.***********..777777777**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1088.49
//
Query:       gi|386001370|ref|YP_005919669.1|  [L=213]
Description: SOUL heme-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-44  151.3   0.0    3.1e-44  151.1   0.0    1.1  1  SOUL       SOUL heme-binding protein
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.19   12.0   0.0    1.3  1  GyrI-like  GyrI-like small molecule binding domain


Domain annotation for each model (and alignments):
>> SOUL  SOUL heme-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.0   3.5e-48   3.1e-44       2     167 ..      52     210 ..      51     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 3.5e-48
                              SOUL   2 etpkYevlke.ekkyEvRryepavwaettvseasleearssgfrrLarYifgkNekeekiamtaPvvtkvkekevtm 77 
                                       ++p+Y+v+++ e+++E+R+y++ +wa t  +      ++++gf+ L+rYi+g+N++++ki+mtaPvvt v e +  +
  gi|386001370|ref|YP_005919669.1|  52 KEPPYQVIQTlENDVEIREYADQIWAVTLAD------DQDRGFGLLFRYISGANDEGRKIEMTAPVVTGVAEGRPFI 122
                                       79******889888**************953......44479**************************9999999** PP

                              SOUL  78 sfvlpskyqaeepPkPtddsrVkleevpertvavrrFsGfateeevkeeaeeLreaLekdg..geekkdsyvlaqYn 152
                                       +fv+p+ ++ e +P+P +d+rVk+e v++r++a++rFsG+atee+ k++ ++L e+L+++g  +   + + vl+qYn
  gi|386001370|ref|YP_005919669.1| 123 AFVIPEGFDLEGTPRP-QDERVKIEVVEGRRMAAVRFSGYATEESQKRHLSALNETLKAHGmmA---RGEPVLMQYN 195
                                       ****************.777*******************99****************8888642...3344****** PP

                              SOUL 153 ppftppflrrNEvwi 167
                                       +p+tppf rrNEv++
  gi|386001370|ref|YP_005919669.1| 196 DPWTPPFIRRNEVAM 210
                                       *************98 PP

>> GyrI-like  GyrI-like small molecule binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.1e-05      0.19      79     141 ..     117     199 ..      56     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                                       C....................CGBTTSEEEEE-SEEEEEEEEECEG.GGHHHHHHHHHHTHHHHTT-EEEESEEEEE CS
                         GyrI-like  79 v....................egpeglefleipageyAvfrhkGpy.ddlqatyaklygewlpesgyerrdgpsiEi 134
                                                            + +e++++ ++++ ++A +r+ G + ++ q+      +e l+++g+  r++p++ +
  gi|386001370|ref|YP_005919669.1| 117 EgrpfiafvipegfdlegtprPQDERVKIEVVEGRRMAAVRFSGYAtEESQKRHLSALNETLKAHGMMARGEPVLMQ 193
                                       24455555666666888888899*********************9998888888888888*******9999999999 PP

                                       EECCCTS CS
                         GyrI-like 135 Ylsdpre 141
                                       Y +dp++
  gi|386001370|ref|YP_005919669.1| 194 Y-NDPWT 199
                                       9.88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1276.29
//
Query:       gi|386001371|ref|YP_005919670.1|  [L=146]
Description: hypothetical protein Mhar_0669 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.0   1.2      0.022   15.0   1.2    1.6  1  TctB      Tripartite tricarboxylate transporter TctB family


Domain annotation for each model (and alignments):
>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   1.2e-06     0.022      81     127 ..      64     134 ..      27     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                              TctB  81 alllep...........lGfilatalflllll.g............reerkwlkalilavvlallvyllFt 127
                                       ++l +            lG++++ +l l+l+  g            r++r++l++l ++++ +++v+ll +
  gi|386001371|ref|YP_005919670.1|  64 GALAGLvseelflpamvLGYWITNVLGLFLMHrGledllskdgrsgRRRRRILTDLSVSAAYTIVVVLLVE 134
                                       222222222233333336*******6664444535677889999**999****************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 950.93
//
Query:       gi|386001372|ref|YP_005919671.1|  [L=50]
Description: hypothetical protein Mhar_0670 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 388.02
//
Query:       gi|386001373|ref|YP_005919672.1|  [L=176]
Description: Archaemetzincin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-22   80.0   0.0    2.8e-22   79.6   0.0    1.1  1  Peptidase_M54  Peptidase family M54
     0.0018   16.9   0.2     0.0023   16.6   0.2    1.1  1  Metallopep     Putative peptidase family
     0.0023   17.8   0.0     0.0032   17.3   0.0    1.1  1  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
      0.018   14.0   0.0      0.024   13.6   0.0    1.1  1  Peptidase_M66  Peptidase M66
      0.069   13.7   0.0      0.088   13.3   0.0    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
       0.13   12.3   0.0       0.13   12.3   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   9.5e-26   2.8e-22      98     194 .]      70     169 ..      66     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 9.5e-26
                                       EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T..--.......SHHHHHHHHHHHHHHHHHHHTT----S-.TSTTS CS
                     Peptidase_M54  98 lplgsrdqyidiykkvlGievsiGnyavlals..ikefyte..dkeLflervvkevlhelGhlyGLshCke.dCvmn 169
                                       l++ ++d  +  +++v+G+++  G+ a+++l+   +efy    d+ +f er  ke +helGh++GL+hC++ +Cvm 
  gi|386001373|ref|YP_005919672.1|  70 LGVIEEDLSVANLDFVFGLAL--GRKAMISLArlSQEFYGLppDRGIFRERAEKEAVHELGHVFGLPHCRNaGCVMR 144
                                       677889999999******975..7*******988899**8556********************************** PP

                                       --SSHHHHHHS-SS--HHHHHHHHH CS
                     Peptidase_M54 170 fsndlkdvDrkapkyCksCleklkr 194
                                        s+++ ++D k++++C  C + l+r
  gi|386001373|ref|YP_005919672.1| 145 LSSSIAEIDFKSSRFCGGCRKVLER 169
                                       *******************999986 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   7.8e-07    0.0023     319     336 ..     124     143 ..     122     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.8e-07
                        Metallopep 319 lHEiGHllglpHqed..Gvm 336
                                       +HE+GH++glpH+ +   vm
  gi|386001373|ref|YP_005919672.1| 124 VHELGHVFGLPHCRNagCVM 143
                                       7************9974455 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-06    0.0032     113     134 ..     123     144 ..     114     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHTTBESXSSTTSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 113 aaHEiGHalGLeHssdkdalmy 134
                                       a+HE+GH+ GL H ++ + +m 
  gi|386001373|ref|YP_005919672.1| 123 AVHELGHVFGLPHCRNAGCVMR 144
                                       89****************9996 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.9e-06     0.024     190     209 ..     117     136 ..     102     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-06
                     Peptidase_M66 190 atltgefiHEqGHalGLpHy 209
                                       ++ ++e +HE+GH +GLpH 
  gi|386001373|ref|YP_005919672.1| 117 ERAEKEAVHELGHVFGLPHC 136
                                       5677899************4 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.088     105     123 ..     117     135 ..      67     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                      Reprolysin_3 105 kvgadtvaHEiGHnfganH 123
                                       +   + + HE+GH fg++H
  gi|386001373|ref|YP_005919672.1| 117 ERAEKEAVHELGHVFGLPH 135
                                       44457789*********** PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.5e-05      0.13     147     164 ..     124     141 ..      58     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                      Reprolysin_5 147 aHElGHnfGavHDcdsss 164
                                        HElGH fG +H  ++ +
  gi|386001373|ref|YP_005919672.1| 124 VHELGHVFGLPHCRNAGC 141
                                       6***********777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1321.68
//
Query:       gi|386001374|ref|YP_005919673.1|  [L=139]
Description: hypothetical protein Mhar_0672 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-25   85.5   4.1    3.1e-09   36.2   0.2    3.4  3  TPR_2       Tetratricopeptide repeat
    3.8e-24   83.5   0.8    4.7e-08   32.5   0.1    3.2  3  TPR_1       Tetratricopeptide repeat
    1.5e-18   65.4   0.1    9.6e-05   22.3   0.0    3.2  3  TPR_8       Tetratricopeptide repeat
    2.1e-15   57.1   7.8    3.6e-10   40.3   0.6    2.4  2  TPR_16      Tetratricopeptide repeat
    1.8e-14   53.8   9.9    1.6e-08   34.7   1.1    3.1  2  TPR_12      Tetratricopeptide repeat
      9e-14   50.9   0.5    2.6e-09   36.6   0.1    2.7  3  TPR_11      TPR repeat
    6.6e-12   45.0   0.2     0.0031   17.8   0.1    3.4  3  TPR_17      Tetratricopeptide repeat
    1.4e-11   44.3   3.5    8.9e-09   35.4   1.1    2.4  2  TPR_9       Tetratricopeptide repeat
    2.4e-09   36.8   8.1     0.0091   15.8   0.3    3.3  3  TPR_10      Tetratricopeptide repeat
    5.4e-09   36.1  13.4     0.0023   18.6   0.1    3.8  4  TPR_14      Tetratricopeptide repeat
    1.3e-07   31.1   3.6       0.19   11.8   0.1    3.3  3  TPR_7       Tetratricopeptide repeat
    2.6e-07   31.0   2.4    4.6e-05   23.9   0.3    2.4  2  TPR_19      Tetratricopeptide repeat
    3.4e-07   30.5   2.7      0.081   13.6   0.0    3.6  3  TPR_6       Tetratricopeptide repeat
    2.3e-06   27.7   6.4     0.0013   18.9   0.6    2.1  2  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    2.9e-05   23.9   0.0       0.37   10.8   0.0    3.3  3  TPR_3       Tetratricopeptide repeat
    0.00088   19.3   0.3       0.26   11.4   0.0    2.3  2  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
     0.0016   17.4   0.0     0.0023   16.9   0.0    1.3  1  NARP1       NMDA receptor-regulated protein 1
     0.0045   17.1   0.4      0.024   14.7   0.2    2.2  1  DUF3856     Domain of Unknown Function (DUF3856)
      0.009   16.5   1.0       0.03   14.8   0.7    1.8  2  BTAD        Bacterial transcriptional activator domain
  ------ inclusion threshold ------
      0.012   16.2   2.3       0.29   11.9   0.3    4.3  3  TPR_4       Tetratricopeptide repeat
      0.015   15.2   0.7      0.055   13.4   0.1    2.2  3  Wzy_C_2     Virulence factor membrane-bound polymerase, C-ter
      0.017   15.4   1.5          8    7.0   0.1    2.9  3  PPR         PPR repeat
      0.022   14.0   0.1       0.23   10.6   0.2    2.0  2  TPR_15      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   2.9e-09   2.2e-06       2      32 ..      40      70 ..      39      72 .. 0.94
   2 !   36.2   0.2     4e-12   3.1e-09       3      33 ..      75     105 ..      73     106 .. 0.96
   3 !   22.2   0.1   1.3e-07   9.9e-05       2      27 ..     108     133 ..     107     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.9e-09
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldP 32
                                      + ++++Gl+++ +++y++A++++e+A++++P
  gi|386001374|ref|YP_005919673.1| 40 DFWMAMGLILADRKRYDKAARCCERAVRIYP 70
                                      679***************************9 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 4e-12
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++n+Gl++y+lg+yeeAle +++Al l+P+
  gi|386001374|ref|YP_005919673.1|  75 AWNNWGLSLYQLGRYEEALERLDEALTLNPD 105
                                       9*****************************8 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 1.3e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                       e+++n Gl+++ lg+ eeA+eafe+A
  gi|386001374|ref|YP_005919673.1| 108 EGWHNKGLVLEGLGRVEEAEEAFERA 133
                                       79***********************8 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   3.1e-09   2.4e-06       2      33 ..      40      71 ..      39      72 .. 0.93
   2 !   32.5   0.1     6e-11   4.7e-08       3      33 ..      75     105 ..      73     106 .. 0.97
   3 !   21.3   0.0   2.1e-07   0.00017       2      27 ..     108     133 ..     107     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.1e-09
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPn 33
                                      + +  +G+++   ++yd+A  ++e+A++++P 
  gi|386001374|ref|YP_005919673.1| 40 DFWMAMGLILADRKRYDKAARCCERAVRIYPF 71
                                      67999*************************95 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 6e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++n G+ +++lg+y+eAle  ++AL+lnP+
  gi|386001374|ref|YP_005919673.1|  75 AWNNWGLSLYQLGRYEEALERLDEALTLNPD 105
                                       9*****************************8 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekA 27 
                                       + + n+G+++  lg+ +eA+e++e+A
  gi|386001374|ref|YP_005919673.1| 108 EGWHNKGLVLEGLGRVEEAEEAFERA 133
                                       67***********************9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00093       2      33 ..      40      71 ..      39      72 .. 0.94
   2 !   20.6   0.0   4.3e-07   0.00034       2      33 ..      74     105 ..      73     106 .. 0.96
   3 !   22.3   0.0   1.2e-07   9.6e-05       2      29 ..     108     135 ..     107     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      + ++ +g+i+ + ++y++A  ++e+a+++ p 
  gi|386001374|ref|YP_005919673.1| 40 DFWMAMGLILADRKRYDKAARCCERAVRIYPF 71
                                      689**************************995 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.3e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n g+ + +lg+yeeA e + +al+l+pd
  gi|386001374|ref|YP_005919673.1|  74 HAWNNWGLSLYQLGRYEEALERLDEALTLNPD 105
                                       79*****************************8 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.2e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       e ++n+g++++ lg+ eeA+e++e+a +
  gi|386001374|ref|YP_005919673.1| 108 EGWHNKGLVLEGLGRVEEAEEAFERADR 135
                                       67***********************965 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.1   7.4e-07   0.00058      16      66 ..      23      71 ..      19      73 .. 0.86
   2 !   40.3   0.6   4.6e-13   3.6e-10       2      62 ..      78     135 ..      77     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.4e-07
                            TPR_16 16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                      Aaa++ a+ kr+    d+ +++++ g++++ ++r+++Aa  +++a+r +p+
  gi|386001374|ref|YP_005919673.1| 23 AAAVAAALAKRFI--LDNSDFWMAMGLILADRKRYDKAARCCERAVRIYPF 71
                                      6777777777774..55778*****************************97 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 4.6e-13
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +++++++++g+y++A+++l++al ++   Pd  e + ++g+++  +gr++eA++++++a r
  gi|386001374|ref|YP_005919673.1|  78 NWGLSLYQLGRYEEALERLDEALTLN---PDLGEGWHNKGLVLEGLGRVEEAEEAFERADR 135
                                       5799**********************...****************************9955 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   2.0   5.9e-10   4.6e-07       7      72 ..      43     100 ..      39     100 .. 0.94
   2 !   34.7   1.1   2.1e-11   1.6e-08       4      71 ..      74     133 ..      71     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.9e-10
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                         ++++l+ ++ryd+A +++e+a++i+     p    ++ + +n g  +++lgryeeAle+l eal
  gi|386001374|ref|YP_005919673.1|  43 MAMGLILADRKRYDKAARCCERAVRIY-----PF---YVHAWNNWGLSLYQLGRYEEALERLDEAL 100
                                       469************************.....87...599************************98 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2.1e-11
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                        a+nn+++ l++lgry+eAle l++al +      pd   + +  +n g +++ lgr eeA+e++e+a
  gi|386001374|ref|YP_005919673.1|  74 HAWNNWGLSLYQLGRYEEALERLDEALTLN-----PD---LGEGWHNKGLVLEGLGRVEEAEEAFERA 133
                                       5899**********************9999.....65...6777889999999999999999999987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.1e-06   0.00085       1      42 []      46      87 ..      46      87 .. 0.98
   2 !   36.6   0.1   3.3e-12   2.6e-09       1      42 []      80     121 ..      80     121 .. 0.96
   3 ?   -0.1   0.0      0.98   7.7e+02       7      20 ..     120     133 ..     119     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      G ++ ++ +y++A  + ++A+++ P ++ a++n Gl +y++G
  gi|386001374|ref|YP_005919673.1| 46 GLILADRKRYDKAARCCERAVRIYPFYVHAWNNWGLSLYQLG 87
                                      8899************************************99 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 3.3e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G  +y++G+yeeA+e++ +Al l+Pd  e ++n Gl++  +G
  gi|386001374|ref|YP_005919673.1|  80 GLSLYQLGRYEEALERLDEALTLNPDLGEGWHNKGLVLEGLG 121
                                       7789*********************************99887 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.98
                            TPR_11   7 qGkyeeAieaYkkA 20 
                                       +G+ eeA ea+++A
  gi|386001374|ref|YP_005919673.1| 120 LGRVEEAEEAFERA 133
                                       6999***9999988 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0039         3      11      32 ..      37      58 ..      37      60 .. 0.95
   2 !   17.8   0.1   3.9e-06    0.0031       1      34 []      61      94 ..      61      94 .. 0.97
   3 !   15.2   0.0   2.6e-05      0.02       3      34 .]      97     128 ..      96     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0039
                            TPR_17 11 nnadaynnLAelllknGdlmtA 32
                                      +n+d++  ++ +l+ ++++++A
  gi|386001374|ref|YP_005919673.1| 37 DNSDFWMAMGLILADRKRYDKA 58
                                      79******************98 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.9e-06
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      ++++a++++P ++ a+nn +  l+++G++++A++
  gi|386001374|ref|YP_005919673.1| 61 CCERAVRIYPFYVHAWNNWGLSLYQLGRYEEALE 94
                                      89******************************85 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.6e-05
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                        +al l+P+  + ++n++ +l+ +G+ ++A++
  gi|386001374|ref|YP_005919673.1|  97 DEALTLNPDLGEGWHNKGLVLEGLGRVEEAEE 128
                                       589**************************986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   1.1   1.1e-11   8.9e-09       4      61 ..      48     105 ..      46     108 .. 0.96
   2 !   12.6   0.1   0.00014      0.11      22      55 ..     100     133 ..      99     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.1e-11
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       i++ ++++++a +++er + + P  ++ +   Gl l+qlG++++Al+ L+ +l l+pd
  gi|386001374|ref|YP_005919673.1|  48 ILADRKRYDKAARCCERAVRIYPFYVHAWNNWGLSLYQLGRYEEALERLDEALTLNPD 105
                                       78899*************************************************9998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                             TPR_9  22 lllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                       l l+Pd  e +   Gl+l+ lG++++A +++e++
  gi|386001374|ref|YP_005919673.1| 100 LTLNPDLGEGWHNKGLVLEGLGRVEEAEEAFERA 133
                                       67999999***********************985 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.3e-05      0.01       8      32 ..      45      69 ..      43      69 .. 0.95
   2 !   15.8   0.3   1.2e-05    0.0091       6      30 ..      77     101 ..      76     103 .. 0.91
   3 !    9.1   0.1    0.0015       1.2       6      28 ..     111     133 ..     111     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                            TPR_10  8 LanalrqrgrydeAealleealair 32
                                      ++ +l +r+ryd+A + +e+a++i+
  gi|386001374|ref|YP_005919673.1| 45 MGLILADRKRYDKAARCCERAVRIY 69
                                      6999*******************98 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.2e-05
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN +  l+q+gry+eA++ l+eal 
  gi|386001374|ref|YP_005919673.1|  77 NNWGLSLYQLGRYEEALERLDEALT 101
                                       677899*****************97 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0015
                            TPR_10   6 nNLanalrqrgrydeAealleea 28 
                                       +N + +l  +gr +eAe+ +e+a
  gi|386001374|ref|YP_005919673.1| 111 HNKGLVLEGLGRVEEAEEAFERA 133
                                       678999999************98 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.6       7.6   5.9e+03       7       8 ..      23      24 ..      13      34 .. 0.49
   2 !   18.6   0.1   2.9e-06    0.0023       3      40 ..      41      78 ..      39      82 .. 0.89
   3 !   17.6   0.2   6.2e-06    0.0048       3      39 ..      75     111 ..      73     115 .. 0.86
   4 !   10.1   0.2    0.0016       1.2       8      29 ..     114     135 ..     108     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.6
                            TPR_14  7 la 8 
                                      +a
  gi|386001374|ref|YP_005919673.1| 23 AA 24
                                      22 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.9e-06
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawll 40
                                       ++a++ +l+ + ++d+A+++++ra++ +P    aw  
  gi|386001374|ref|YP_005919673.1| 41 FWMAMGLILADRKRYDKAARCCERAVRIYPFYVHAWNN 78
                                      79****************************88877755 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 6.2e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a+   +  l++lG+++eA++ l++al l+Pd  e w 
  gi|386001374|ref|YP_005919673.1|  75 AWNNWGLSLYQLGRYEEALERLDEALTLNPDLGEGWH 111
                                       5666778899*********************988886 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0016
                            TPR_14   8 aeallalGdpdeAiallrrala 29 
                                       + +l+ lG+ +eA+++++ra +
  gi|386001374|ref|YP_005919673.1| 114 GLVLEGLGRVEEAEEAFERADR 135
                                       678999*************965 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00026      0.21       4      28 ..      44      66 ..      42      69 .. 0.88
   2 !   11.8   0.1   0.00024      0.19       6      31 ..      80     105 ..      75     108 .. 0.74
   3 !    7.2   0.0    0.0071       5.5       3      24 ..     111     132 ..     110     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLal 28
                                      +++ +  ++ +y++A++++e+  a+
  gi|386001374|ref|YP_005919673.1| 44 AMGLILADRKRYDKAARCCER--AV 66
                                      7999999**************..65 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00024
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       +    +lG+yeeA+e + ++L l  d
  gi|386001374|ref|YP_005919673.1|  80 GLSLYQLGRYEEALERLDEALTLNPD 105
                                       5566789************6666555 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0071
                             TPR_7   3 lnLarlysrlGdyeeAielyeq 24 
                                       +n + + + lG+ eeA+e +e+
  gi|386001374|ref|YP_005919673.1| 111 HNKGLVLEGLGRVEEAEEAFER 132
                                       788889999************9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.011       8.8      23      56 ..      37      70 ..      19      76 .. 0.79
   2 !   23.9   0.3   5.8e-08   4.6e-05       1      51 [.      83     133 ..      83     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                            TPR_19 23 knaearllLAeallalgqldeAealLdalpeedp 56
                                      +n++ ++++  +l   +++d+A ++++++ + +p
  gi|386001374|ref|YP_005919673.1| 37 DNSDFWMAMGLILADRKRYDKAARCCERAVRIYP 70
                                      5999999999999999*******99999988776 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 5.8e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       l++ g+y+eAl++l +al+ +p+ +e + +   +l  lg+++eAe++ +++
  gi|386001374|ref|YP_005919673.1|  83 LYQLGRYEEALERLDEALTLNPDLGEGWHNKGLVLEGLGRVEEAEEAFERA 133
                                       6788******************************************99886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0     0.001      0.81       6      31 ..      45      70 ..      38      71 .. 0.81
   2 !   13.6   0.0    0.0001     0.081       6      32 ..      79     105 ..      78     106 .. 0.93
   3 ?    4.9   0.0     0.061        48       6      25 ..     113     132 ..     108     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                                      HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  6 lalsyrklgdtdkAlealerlikeYP 31
                                      ++l +   +++dkA +  er ++ YP
  gi|386001374|ref|YP_005919673.1| 45 MGLILADRKRYDKAARCCERAVRIYP 70
                                      455555568****************9 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                        +ls+++lg++++Ale l++ ++  Pd
  gi|386001374|ref|YP_005919673.1|  79 WGLSLYQLGRYEEALERLDEALTLNPD 105
                                       699****99*************99998 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealer 25 
                                        +l ++ lg+ ++A ea+er
  gi|386001374|ref|YP_005919673.1| 113 KGLVLEGLGRVEEAEEAFER 132
                                       577888899**********9 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.7   2.8e-06    0.0022      24      81 ..      38      98 ..      19      99 .. 0.83
   2 !   18.9   0.6   1.6e-06    0.0013       2      81 ..      52     132 ..      51     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                                      HHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 24 edayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      ++ ++   +l l  +++y++A + +++a ++++    ++  ++ +l++L++yeeA+  L++
  gi|386001374|ref|YP_005919673.1| 38 NSDFWMamGLILADRKRYDKAARCCERAvRIYPFYVHAWNNWGLSLYQLGRYEEALERLDE 98
                                      4455543499999*******************************************98876 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-06
                                       TT-HHHHHHHHHHHH..HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   2 qnnyknAiflaerlla.aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       +++y++A  ++er++  +  + +    + +l+ly++g+y++A+e l++a  ln+   + +  ++ +l  L+++eeA+
  gi|386001374|ref|YP_005919673.1|  52 RKRYDKAARCCERAVRiYPFYVHAWNNW-GLSLYQLGRYEEALERLDEAlTLNPDLGEGWHNKGLVLEGLGRVEEAE 127
                                       6899999999999994333444444455.9*******************9999998899****************** PP

                                       HHH-S CS
                            ANAPC3  77 aaLek 81 
                                        a+e+
  gi|386001374|ref|YP_005919673.1| 128 EAFER 132
                                       *9997 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00047      0.37       1      21 [.      39      59 ..      39      61 .. 0.95
   2 !    9.1   0.0    0.0017       1.3       8      22 ..      80      94 ..      72     103 .. 0.85
   3 ?   -1.1   0.0       2.6     2e+03      15      24 ..     121     130 ..     120     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                                      HHHHHHHHHHHHHTT-HHHHH CS
                             TPR_3  1 ldylysyAaefynkkkyqeAr 21
                                      +d++++ +  + + k+y++A+
  gi|386001374|ref|YP_005919673.1| 39 SDFWMAMGLILADRKRYDKAA 59
                                      79******************7 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                                      HHHHHHTT-HHHHHH CS
                             TPR_3  8 AaefynkkkyqeAre 22
                                      + ++y+ ++y+eA+e
  gi|386001374|ref|YP_005919673.1| 80 GLSLYQLGRYEEALE 94
                                      789**********98 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.6
                                       T-HHHHHHH. CS
                             TPR_3  15 kkyqeArelf 24 
                                       ++ +eA+e+f
  gi|386001374|ref|YP_005919673.1| 121 GRVEEAEEAF 130
                                       67789***95 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.018        14      15      32 ..      53      70 ..      50      75 .. 0.90
   2 !   11.4   0.0   0.00033      0.26      11      33 ..      83     105 ..      79     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                                      T-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C 15 geYseArryvdalLeiEP 32
                                      ++Y++A r++++  +i P
  gi|386001374|ref|YP_005919673.1| 53 KRYDKAARCCERAVRIYP 70
                                      79**********999877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                                       HHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPe 33 
                                        y lg+Y+eA++ +d  L + P+
  gi|386001374|ref|YP_005919673.1|  83 LYQLGRYEEALERLDEALTLNPD 105
                                       699****************9997 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0023     204     255 ..      85     136 ..      56     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       +lg++e+Ale +d+a+  +p l e + +K+ +l+  G +++A e+ e+a +l
  gi|386001374|ref|YP_005919673.1|  85 QLGRYEEALERLDEALTLNPDLGEGWHNKGLVLEGLGRVEEAEEAFERADRL 136
                                       5899*****************************************9999765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   3.1e-05     0.024      64     127 ..      82     134 ..      69     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       +l +lgry+eale  d+al        l+ d G+ W     +++  le+lGr +ea +af+ a+
  gi|386001374|ref|YP_005919673.1|  82 SLYQLGRYEEALERLDEALT-------LNPDLGEGW----HNKGLVLEGLGRVEEAEEAFERAD 134
                                       5789***************6.......899999999....69******************9886 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.6   1.2e+03      19      36 ..      52      69 ..      40      77 .. 0.76
   2 !   14.8   0.7   3.8e-05      0.03      71     124 ..      82     135 ..      55     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.6
                                      TT-HHHHHHHHHHHHTT- CS
                              BTAD 19 agdpeeaaelleaAlalw 36
                                      + + ++aa+++e+A++++
  gi|386001374|ref|YP_005919673.1| 52 RKRYDKAARCCERAVRIY 69
                                      456677888888888776 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.8e-05
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        + +lGr+eeal++l+++++++P   + +    + l  +Gr +eA e++er+ r
  gi|386001374|ref|YP_005919673.1|  82 SLYQLGRYEEALERLDEALTLNPDLGEGWHNKGLVLEGLGRVEEAEEAFERADR 135
                                       5679*******************99999999999****************9865 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.4   3.1e+02       6      26 .]      44      64 ..      41      64 .. 0.84
   2 ?   11.9   0.3   0.00038      0.29       9      26 .]      81      98 ..      74     100 .. 0.91
   3 ?   10.5   0.1     0.001      0.78       5      26 .]     111     132 ..     107     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.4
                             TPR_4  6 aLArallalGdldeAraller 26
                                      a++  l+++ ++d A++  er
  gi|386001374|ref|YP_005919673.1| 44 AMGLILADRKRYDKAARCCER 64
                                      6788899999*******9887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00038
                             TPR_4  9 rallalGdldeAraller 26
                                        l++lG+++eA++ l++
  gi|386001374|ref|YP_005919673.1| 81 LSLYQLGRYEEALERLDE 98
                                      6799***********986 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.001
                             TPR_4   5 laLArallalGdldeAraller 26 
                                       ++ + +l  lG+ +eA++++er
  gi|386001374|ref|YP_005919673.1| 111 HNKGLVLEGLGRVEEAEEAFER 132
                                       67789999***********997 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.72   5.6e+02      44      68 ..       5      29 ..       2      32 .. 0.73
   2 ?   13.4   0.1     7e-05     0.055      99     180 ..      28     110 ..      18     118 .. 0.88
   3 ?   -1.1   0.0         2   1.6e+03     153     170 ..     117     134 ..     111     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.72
                           Wzy_C_2 44 rlrlrpklvlrvvalvlallglall 68
                                      +lrl + ++l++++++l+++++a+ 
  gi|386001374|ref|YP_005919673.1|  5 PLRLDMDPILLALFALLLAAAVAAA 29
                                      6788888888888888887777765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7e-05
                           Wzy_C_2  99 kvwkdrflfrayadllelgllplspenlaaklalarklihlsP.epavierlilslallGdedeAeqilararalfp 174
                                        + ++rf +++ +  +++gl+ ++++ +++     +++++ +P +    +++ lsl +lG+ +eA+  l++a  l p
  gi|386001374|ref|YP_005919673.1|  28 AALAKRFILDNSDFWMAMGLILADRKRYDKAARCCERAVRIYPfYVHAWNNWGLSLYQLGRYEEALERLDEALTLNP 104
                                       455677999**********************************778999**********************999888 PP

                           Wzy_C_2 175 eedakw 180
                                       +  + w
  gi|386001374|ref|YP_005919673.1| 105 DLGEGW 110
                                       877777 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                           Wzy_C_2 153 lallGdedeAeqilarar 170
                                       l +lG+ +eAe   +ra 
  gi|386001374|ref|YP_005919673.1| 117 LEGLGRVEEAEEAFERAD 134
                                       568999*****9999986 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       7.5   5.8e+03      13      23 ..      52      62 ..      42      68 .. 0.66
   2 ?    6.7   0.0     0.012       9.5       3      25 ..      76      98 ..      74     103 .. 0.81
   3 ?    7.0   0.1      0.01         8      14      31 .]     121     138 ..     117     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.5
                               PPR 13 nGkleeAlelf 23
                                        ++++A ++ 
  gi|386001374|ref|YP_005919673.1| 52 RKRYDKAARCC 62
                                      56777776655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                               PPR  3 ynslIsgycknGkleeAlelfke 25
                                      +n +  ++ + G++eeAle ++e
  gi|386001374|ref|YP_005919673.1| 76 WNNWGLSLYQLGRYEEALERLDE 98
                                      6666678899********97776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.01
                               PPR  14 GkleeAlelfkeMkekGi 31 
                                       G++eeA+e f++  + G+
  gi|386001374|ref|YP_005919673.1| 121 GRVEEAEEAFERADRLGV 138
                                       9**********9888775 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2    0.0003      0.23     138     197 ..      31      90 ..      16     101 .. 0.73
   2 ?    2.6   0.0     0.086        67     157     178 ..      84     105 ..      73     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                            TPR_15 138 eeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrra 197
                                       ++    +++ f++a++ +  ++ + d+A r+ ++A++  p    + +++   l  lgr++
  gi|386001374|ref|YP_005919673.1|  31 AKRFILDNSDFWMAMGLILADRKRYDKAARCCERAVRIYPFYVHAWNNWGLSLYQLGRYE 90 
                                       3334559999**************************998866666666555555555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.086
                            TPR_15 157 rqegqtdaAlrdyreAlalapd 178
                                        q g+ ++Al+ + eAl+l+pd
  gi|386001374|ref|YP_005919673.1|  84 YQLGRYEEALERLDEALTLNPD 105
                                       4667777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1060.42
//
Query:       gi|386001375|ref|YP_005919674.1|  [L=339]
Description: Cation efflux family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-43  148.1   6.7    3.1e-43  147.8   6.7    1.1  1  Cation_efflux  Cation efflux family
    4.2e-17   62.1   1.8    6.4e-17   61.5   1.8    1.3  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.77   10.0   5.0        1.9    8.8   0.6    2.8  3  DUF2104        Predicted membrane protein (DUF2104)


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   6.7   5.2e-47   3.1e-43       2     199 .]      43     235 ..      42     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 5.2e-47
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                        +s++a l+ alv+++ +ll++S+allad +h+l d+++ + l+la++l ++pp+ rf++Gygr+e l++l   l++
  gi|386001375|ref|YP_005919674.1|  43 KVSFIALLATALVQVAIVLLSGSVALLADTVHNLGDAATAIPLWLAFRLGQRPPTDRFTYGYGRAEDLAGLAIVLVI 119
                                       6899************************************************************************* PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlv 155
                                       ++ a+f  +ea  +l+ ++ ++ h + +++ +l++++ n a++l+ +r+gr+++saal a+ lh++ D+ltsl+vl+
  gi|386001375|ref|YP_005919674.1| 120 VVSALFTGYEAAMRLF-NPRPVGHLEAVILASLIGFAGNEAVALYRMRVGREINSAALVADGLHARADGLTSLAVLF 195
                                       ****************.************************************************************ PP

                     Cation_efflux 156 salvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       +a++++ + ++    aDp+++lli+ +il  ++k  +  l  Ll
  gi|386001375|ref|YP_005919674.1| 196 GAFGVMAG-HPR---ADPLVGLLIAGVILQIGWKSGRVVLTRLL 235
                                       *******9.554...******************98887777765 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   1.8   1.1e-20   6.4e-17       2      78 ..     239     315 ..     238     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.1e-20
                                       ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       d+e+  e+re+++  pgv++v ++r+r  G ++++++ ++vd+d++v+++H++a+ev +++++++p v++ ++Hv+P
  gi|386001375|ref|YP_005919674.1| 239 DPEVAIEVREAAAGAPGVEEVAEVRVRWLGMRLHAEINVVVDPDMTVERGHQVAEEVGHQLHHALPYVSRATVHVDP 315
                                       67788899********************************************************************9 PP

>> DUF2104  Predicted membrane protein (DUF2104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.18   1.1e+03      46      72 ..      38      63 ..      29      71 .. 0.67
   2 ?    8.8   0.6   0.00032       1.9      43      97 ..      62     120 ..      51     123 .. 0.65
   3 ?    1.8   0.1     0.048   2.9e+02      71      97 ..     194     220 ..     171     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.18
                           DUF2104 46 wllllnvsllvlvpsyilitiglllig 72
                                      ++l+++vs++ l+    l+ ++++l++
  gi|386001375|ref|YP_005919674.1| 38 GILAVKVSFIALLA-TALVQVAIVLLS 63
                                      46668889988888.444666666664 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00032
                           DUF2104  43 viGwllllnvsllvlvpsyilitigllliglvlgmRp.......GYGrietviGiivallvy 97 
                                       + G++ ll+ ++ +l +   +++i  l +++ lg+Rp       GYGr e + G+ ++l++ 
  gi|386001375|ref|YP_005919674.1|  62 LSGSVALLADTVHNLGD--AATAI-PLWLAFRLGQRPptdrftyGYGRAEDLAGLAIVLVIV 120
                                       45555544444333333..22222.3457899999988888888***********8877765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.048
                           DUF2104  71 iglvlgmRpGYGrietviGiivallvy 97 
                                       +  ++g  +G  r + ++G+++a ++ 
  gi|386001375|ref|YP_005919674.1| 194 LFGAFGVMAGHPRADPLVGLLIAGVIL 220
                                       344678899**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2427.14
//
Query:       gi|386001376|ref|YP_005919675.1|  [L=141]
Description: OsmC family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-14   52.4   0.0    7.7e-14   52.0   0.0    1.1  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   4.3e-18   7.7e-14       4      99 ..      42     136 ..      39     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4.3e-18
                                       SSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEE..EEECCECTCEEEEEEEEEEE-SS-H..HHHHHHH CS
                              OsmC   4 sgpsPeelllaalasCfaitlravakkkgikledlevevea..erdpegakgiteirlkvevkipgadseeklkkll 78 
                                       + psPe+l++aa  +C+ +t  ava +++++l++++ e+e+  er  +g + +t+i++kv+v +++++    l ++ 
  gi|386001376|ref|YP_005919675.1|  42 GFPSPEDLFVAAANACVFTTTLAVAGRRNVRLRSYTSEAEGvlERLGDGRE-VTRIDIKVRVAADEDP--SVLTEIF 115
                                       569*************************************86666666666.**********766666..9****** PP

                                       HHHHHHSHHHHHHCT-SSSEE CS
                              OsmC  79 ekaekrCpvsntlkngvkvel 99 
                                        ++++r pv ++++++v++++
  gi|386001376|ref|YP_005919675.1| 116 SEVADRVPVIRSMTSSVSIDF 136
                                       *****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 869.41
//
Query:       gi|386001377|ref|YP_005919676.1|  [L=190]
Description: hypothetical protein Mhar_0675 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  101.6   0.0      5e-29  101.3   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   2.8e-33     5e-29       3     132 .]      54     188 ..      50     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 2.8e-33
                                       -GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC...........EE-B CS
                               PBP   3 pkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega...........vqgk 66 
                                       p++y  +ge++sPp+++s++     s a++++DpDap ++  f+Hw+++n+   + s+peg             qg+
  gi|386001377|ref|YP_005919676.1|  54 PERYtcDGEDLSPPVEISGLEGSVASIAMILEDPDAP-RGP-FVHWLIWNLA-PPVSIPEGIspleevaapeaLQGR 127
                                       7777889*************99**************9.555.*********6.88999**999999999******** PP

                                       -TTSSCCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  67 nslgeesesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                       n +g+   +gY+gpcPp+gd +HrYv+ ++ald e ldl++g  r+el+aa++g vl++ + a++Y
  gi|386001377|ref|YP_005919676.1| 128 NGFGS---IGYRGPCPPPGD-PHRYVLRVFALDSE-LDLPPGSGRSELEAAMEGRVLQSGKAAATY 188
                                       *****...************.7***********99.59999*999*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 1320.85
//
Query:       gi|386001378|ref|YP_005919677.1|  [L=213]
Description: hypothetical protein Mhar_0676 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-05   25.1   1.0    2.3e-05   24.7   0.1    1.7  2  PEMT      Phospholipid methyltransferase
    0.00049   19.7   4.4    0.00049   19.7   4.4    1.6  2  NnrU      NnrU protein


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.57   5.1e+03      10      15 ..      22      27 ..       5      54 .. 0.53
   2 !   24.7   0.1   2.6e-09   2.3e-05      34     105 ..     105     177 ..      80     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                              PEMT 10 ialgll 15
                                      +++ l+
  gi|386001378|ref|YP_005919677.1| 22 LLASLW 27
                                      222223 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.6e-09
                              PEMT  34 fFlelmd....klvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvylialkfvEephlakiYgkr 105
                                       f ++  d    kl+ +G+Y  ++nP  ++ +l+++ + ++t++++   ++ l+++vy+i+ ++ Ee+ la+++g++
  gi|386001378|ref|YP_005919677.1| 105 FLGIRPDdggsKLIVRGLYCRTRNPLFLFALLVLWLTPIMTDNLL---VLYLIATVYFILGSVHEERILAEKFGAA 177
                                       444444467779******************************988...6667778899999999*********986 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   4.4   5.5e-08   0.00049       1     116 [.       8     131 ..       8     139 .. 0.74
   2 ?   -0.4   0.1     0.076   6.8e+02      62      94 ..     138     169 ..     133     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.5e-08
                              NnrU   1 vlilglllFlgaHsvraapalRarliarlGerg...ykilyslvsllglvlliigfgaaryevllWeppawlrhlal 74 
                                       +l+l l+ F+++Hs+ a   +++r+ ++lG+ +   y+++++lv++++l  l+  f   + e  l+++pa  r+ ++
  gi|386001378|ref|YP_005919677.1|   8 ILALYLVGFAALHSLLASLWAKGRARRALGDGAmrwYRLFFTLVAVATLLPLLRLFYLNPGE-VLYSVPAPWRWGMV 83 
                                       58899**********99777888888888875444499************************.99999955555555 PP

                              NnrU  75 llmlvafillaaallpgnplsvglka......dlaetgivritrHPml 116
                                       +   +a + +a ++l++ pl++ + +      +l  +g++  tr P+ 
  gi|386001378|ref|YP_005919677.1|  84 AGQGIAALAFAKTFLAAGPLQFLGIRpddggsKLIVRGLYCRTRNPLF 131
                                       555555555555555555555544333567778888888888888875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.076
                              NnrU  62 lWeppawlrhlalllmlvafillaaallpgnpl 94 
                                       lW  p ++  l l+l l+a++ ++ + +  +++
  gi|386001378|ref|YP_005919677.1| 138 LWLTPIMTDNL-LVLYLIATVYFILGSVHEERI 169
                                       55555444444.556666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1532.15
//
Query:       gi|386001379|ref|YP_005919678.1|  [L=204]
Description: hypothetical protein Mhar_0677 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-09   36.9   6.6    3.6e-09   36.4   6.6    1.1  1  NnrU      NnrU protein
     0.0025   18.2   1.6     0.0029   18.0   0.1    2.0  2  PEMT      Phospholipid methyltransferase


Domain annotation for each model (and alignments):
>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   6.6     4e-13   3.6e-09       2     172 ..      10     190 ..       9     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4e-13
                              NnrU   2 lilglllFlgaHsvraapalRarliarlGerg...ykilyslvsllglvlliigfgaaryevllWeppawlrhlall 75 
                                       l+l l++F+++Hs++a  ++++r+++ lG+r    y +++s+ +l++++ l++ +   + +  l+ +p   r+++++
  gi|386001379|ref|YP_005919678.1|  10 LVLYLACFAAVHSLMASLPFKRRAAKILGRRMdpwYPAIFSASALVMIAPLVYLVYLFPGK-ILYIVPSPWRWAMVA 85 
                                       899*************999999*******98555599************************.777777555555556 PP

                              NnrU  76 lmlvafillaaallpg.nplsvglka.........dlaetgivritrHPmllg..vaiWAlaHllanGdlasvllfg 140
                                         l+a +l + a++ + +++ v l+           l+++g++r++r P+ll+  ++iW    l +  +++ ++l +
  gi|386001379|ref|YP_005919678.1|  86 GQLLAGLLSVRAFVDApHRFKVPLQLlgpgaaggeGLEPRGVYRWIRDPFLLSgfLIIW----LTPFMTTNILILYV 158
                                       6666666666666654155555444478889999999************9987444667....88999999****** PP

                              NnrU 141 glllwalvgviaidrrkrrrlgeewealaart 172
                                       +  l+ ++g ++ +rr+ +++g+e + +++r+
  gi|386001379|ref|YP_005919678.1| 159 AVTLYLYLGSLHWERRLLAQFGDEYRSYQRRV 190
                                       ************************99888875 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.57   5.1e+03      72      88 ..      51      67 ..      46      73 .. 0.61
   2 !   18.0   0.1   3.2e-07    0.0029      43     100 ..     123     178 ..      81     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                              PEMT 72 saaglllallvllvyli 88
                                        a +++a lv+lvyl+
  gi|386001379|ref|YP_005919678.1| 51 ASALVMIAPLVYLVYLF 67
                                      33346666677766654 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.2e-07
                              PEMT  43 vtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvylialkfvEephlak 100
                                         +G+Yr++++P  + ++l+++ + ++t +++ +l++++ l++yl  l  +E++ la+
  gi|386001379|ref|YP_005919678.1| 123 EPRGVYRWIRDPFLLSGFLIIWLTPFMTTNIL-ILYVAVTLYLYLGSLH-WERRLLAQ 178
                                       568****************************9.5555556666666666.88888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1553.28
//
Query:       gi|386001380|ref|YP_005919679.1|  [L=321]
Description: hypothetical protein Mhar_0678 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0021   17.5   0.6        1.2    8.5   0.0    2.1  2  Neur_chan_LBD  Neurotransmitter-gated ion-channel ligand bind
  ------ inclusion threshold ------
        9.5    5.8   8.5          1    9.0   2.1    2.0  2  DUF4131        Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Neur_chan_LBD  Neurotransmitter-gated ion-channel ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00013       1.2      16      58 ..      17      61 ..       7      66 .. 0.86
   2 !    7.5   0.1   0.00028       2.5     105     193 ..      84     168 ..      74     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00013
                                      S-TTSTSSS-..EEEEEEEEEEEEEEEETTTTEEEEEEEEEEEEE CS
                     Neur_chan_LBD 16 vrPveneskp..vkVkvelslsqiidvdeknqvlttnvwlkqqWt 58
                                      + Pv+++++p  ++V ++ ++++i++++ k++++ +++++  +W+
  gi|386001380|ref|YP_005919679.1| 17 LVPVSSNDTPlhTDVLFGAYITKISRLSMKESNFDVDFYVWFKWK 61
                                      66887777754489******************************7 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00028
                                       EEEEETTSEEEEEEEEEEEEE-----SSTTT-EEEEEEEEEESSS-TTTEEEEESSSSSEEE.TC-BBTTEEEESCE CS
                     Neur_chan_LBD 105 nlrvssdGtvlwsppailkssCsidvkyFPfDeqnCslkfgSwtyngeeidlkwkeeekvveeeeidlsdflengew 181
                                       ++ ++++ t + +++++ ++  + dv  +PfD+++  +k++    +   +++  ++ +++   eei ++ + +++  
  gi|386001380|ref|YP_005919679.1|  84 QAELHENDTNYEQYQISASIIQPFDVMLYPFDNHKLIIKIEDCISSIYWLQYIPENLQNTSCSEEIYIPGYKSKSLP 160
                                       566677777777788888888899*******************9999999999999999999999999999999998 PP

                                       EEEEEEEEEEEC CS
                     Neur_chan_LBD 182 dleeveakrrek 193
                                       +++e    ++++
  gi|386001380|ref|YP_005919679.1| 161 TIVE----NHKY 168
                                       8888....2222 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.1   0.00012         1      11      59 ..     207     256 ..     198     269 .. 0.78
   2 ?    0.5   0.6     0.046   4.1e+02       9      50 ..     271     318 ..     261     321 .] 0.55

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00012
                           DUF4131  11 alllllllllllllrr.rprrrvllllllllllallgfalrapqpnandl 59 
                                       +l+++++++ + + +r +  +r+++++++l+++++ ++ + a+qp++n l
  gi|386001380|ref|YP_005919679.1| 207 GLFVAVAVAMITFTLRpNFAPRFIVGVGALFAAVANYYNVLALQPAVNYL 256
                                       4444444444444444599***************************9977 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.046
                           DUF4131   9 llalllllllllllllrr......rprrrvllllllllllallgfalr 50 
                                       +l +++  + + l+ +++      r  +   ++++++++++ l++ + 
  gi|386001380|ref|YP_005919679.1| 271 FLSMVGSSISYYLYSFKNninlsrRFDKYSVITFIFCFIFINLWIGWF 318
                                       344444444444444444787776555555666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2113.06
//
Query:       gi|386001381|ref|YP_005919680.1|  [L=285]
Description: Cobalt chelatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-59  201.7   0.0    3.4e-59  200.3   0.0    1.6  1  CbiK      Cobalt chelatase (CbiK)
    1.4e-06   28.6   0.1    1.3e-05   25.4   0.0    2.4  3  CbiX      CbiX
  ------ inclusion threshold ------
        0.1   13.3   0.3         23    5.7   0.0    2.3  2  Imm1      Immunity protein Imm1


Domain annotation for each model (and alignments):
>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.3   0.0   5.6e-63   3.4e-59       2     261 ..       8     278 ..       7     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 200.3 bits;  conditional E-value: 5.6e-63
                                       EEEEEE---S-HHHHHHHHHHHHHHHHHC-TTSEEEEEES-HHHHHHHHHHH------HHHHHHHHHHCT--EEEEE CS
                              CbiK   2 aillvsFGtsykdarektiekiekkvaaefpdyevfraftSsiiikklkerdeievdtpeealeklkeegykevivq 78 
                                       ai+lv +G+   +ar+ t+e+i+   + ef    v  aft+  i+++l+  ++  v++p +al kl++ gy++v+vq
  gi|386001381|ref|YP_005919680.1|   8 AIVLVAYGSLDLEARK-TYERIRAVYRREFEAPAVDIAFTAGFIRRRLAGGEGTAVHSPLTALAKLHDAGYQDVVVQ 83 
                                       89*************9.************************************************************ PP

                                       E--SCSSHHHHHHHHHH.....HHHGGGSSEEEEE--SCS......SHHHHHHHHHHHHTTS---............ CS
                              CbiK  79 plhiipGeeyeklkreV.....kkfkkkfekiklgrPlldykGvedsteDykevvealkdeiera............ 138
                                       +lh+ pG+e+ +l + V      + k  f+++ +g Pll          Dy  v +al+ e++r+            
  gi|386001381|ref|YP_005919680.1|  84 SLHVAPGSEFHELAALVsalgtVRGKLGFRSLSMGMPLLAS------GPDYDAVSKALAPEFDRTtaggegegaask 154
                                       *****************66655556778***********94......445555555544444322111111111111 PP

                                       -..TTEEEEEEE---SCHHHHHHHHHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS--HHH CS
                              CbiK 139 r..kdealvfvgHGtehesnavyaeldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAGdHa 213
                                       r  ++ a+v+vgHGt+h++ a+y+++ +vlk  + ++v++gt++g+P++e+v++e k +++++v+l+P++lvAG Ha
  gi|386001381|ref|YP_005919680.1| 155 RnpEETAVVLVGHGTAHPADAAYSRMARVLKRDH-RNVFLGTIDGFPGLEDVMAEAKAADVRRVRLLPFLLVAGGHA 230
                                       2257889***********************9875.89**************************************** PP

                                       HCCCCSSSTTSHHHHHHHTT--EEE----GGGSHHHHHHHHHHHHHHH CS
                              CbiK 214 knDmasdeedswkealeaaGikveiilkgLGeieeirsifikhikeai 261
                                       ++D+a+d+ +swk+a+e+aG++v+ +l+g+G+++++ +i i+h ++a+
  gi|386001381|ref|YP_005919680.1| 231 TKDLAGDDPESWKSAFEEAGFEVDLNLHGMGDTPRVVEILIEHTRQAL 278
                                       *******************************************99987 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.58   3.5e+03       2      32 ..      15      45 ..      15      48 .. 0.82
   2 ?   -0.4   0.0      0.24   1.4e+03      42      65 ..      67      90 ..      61     121 .. 0.75
   3 !   25.4   0.0   2.3e-09   1.3e-05       9     106 ..     174     271 ..     167     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.58
                                      STSSCCHHHHHHHHHHHHHHHCCSCCCEECE CS
                              CbiX  2 GSrdpesneeveklaeelrekgpfkpvelgf 32
                                      GS d e++++ e + + +r++ + + v ++f
  gi|386001381|ref|YP_005919680.1| 15 GSLDLEARKTYERIRAVYRREFEAPAVDIAF 45
                                      7778888888899999999999989999988 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                                      CSSHHHHC-SBSEEEEEEESSSSS CS
                              CbiX 42 ealrelaeqgvkrivvvPlflfaG 65
                                      +al++l + g++++vv  l +++G
  gi|386001381|ref|YP_005919680.1| 67 TALAKLHDAGYQDVVVQSLHVAPG 90
                                      578899999999999976666666 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHH....HHHCT--SS CS
                              CbiX   9 neeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDI....peeleeaee 81 
                                        ++   +a+ l++ ++   v+lg ++   p le++++e+ +  v+r+ ++P++l aG+h+++D+    pe  + a e
  gi|386001381|ref|YP_005919680.1| 174 DAAYSRMARVLKRDHR--NVFLGTID-GFPGLEDVMAEAKAADVRRVRLLPFLLVAGGHATKDLagddPESWKSAFE 247
                                       4555666777777555..99999998.88***********************************7666555555555 PP

                                       SS-TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  82 ahpkdveieytepLGthplvaevlk 106
                                       + + +v++ +   +G+ p+v+e+l+
  gi|386001381|ref|YP_005919680.1| 248 EAGFEVDLNL-HGMGDTPRVVEILI 271
                                       5554444443.45899999999986 PP

>> Imm1  Immunity protein Imm1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2    0.0039        24      65      99 ..     138     176 ..      52     179 .. 0.73
   2 ?    5.7   0.0    0.0038        23      51     110 ..     215     279 ..     182     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0039
                              Imm1  65 e....ddgpvsssngdppdseevvydyvggqtefPadse 99 
                                       e     +g+ + +++ ++++ee ++ +vg++t  Pad++
  gi|386001381|ref|YP_005919680.1| 138 EfdrtTAGGEGEGAASKRNPEETAVVLVGHGTAHPADAA 176
                                       1666677888899999999*****************986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0038
                              Imm1  51 ggdaglgglvylsge...ddgpvsssngdppdseev..vydyvggqt.efPadsevpleqvraAlk 110
                                       ++ + l+ +++++g+   +d    +++++++ +ee+  ++d++ ++  + P+ +e+ +e+ r+Al+
  gi|386001381|ref|YP_005919680.1| 215 RRVR-LLPFLLVAGGhatKDLAGDDPESWKSAFEEAgfEVDLNLHGMgDTPRVVEILIEHTRQALE 279
                                       5555.677888888888777777788888888888833456788999899**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1672.06
//
Query:       gi|386001382|ref|YP_005919681.1|  [L=204]
Description: hypothetical protein Mhar_0680 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1261.68
//
Query:       gi|386001383|ref|YP_005919682.1|  [L=462]
Description: hydroxymethylglutaryl-CoA synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-27   96.4   0.0      3e-27   96.0   0.0    1.1  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    8.5e-16   58.3   0.0    2.2e-15   57.0   0.0    1.6  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
  ------ inclusion threshold ------
       0.03   14.5   0.1        0.1   12.8   0.0    1.8  2  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


Domain annotation for each model (and alignments):
>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   5.1e-31     3e-27       7     229 ..     203     421 ..     198     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 5.1e-31
                                       --EEEE----SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHH..HHHHHHH------GGG-SEEEE--SSHH CS
                    HMG_CoA_synt_C   7 lrashmehayDFykPdlaseYPvvDGklslscYlkaldrcYksyskk..vkkitkdadkeftlddfdyvifhsPfck 81 
                                       + + + ++  DF++P +     vv+Gk+s +cYl a+d +++s++++  ++ + + ++     d++  +ifh P+ +
  gi|386001383|ref|YP_005919682.1| 203 VMGVYTRDENDFFRP-VGMRCAVVNGKYSNQCYLAAMDGAFSSFQRRalSRGMIRIGEGGCLSDHLRQIIFHIPYPR 278
                                       6788999999****9.445678************************964455555578888899************* PP

                                       HHHHHHHHHHHHHHHH.S-HH.HHHHH-GGGGGGTT--GGG.GGT-HHHHHHHHHHHH..HHHHHHTGGGGHHHHHH CS
                    HMG_CoA_synt_C  82 lvqkslarllynDflanassd.keeevkekleekddlklde.sltdkdlekallkiak..elfkkkvkpsllvptev 154
                                       + + + a ++  +++  ++ +  eee+ ++ ++  ++  +e +  + d ++ + k ak  e +++kvkps+l++  v
  gi|386001383|ref|YP_005919682.1| 279 MAEYAAASFFRREWRPLPRWQeVEEEIGAEPAAE-EVGGEEgAKESADYQRRFSKSAKflEAYERKVKPSTLISSAV 354
                                       *********9999998776430445555555554.666666145567888999998886689*************** PP

                                       ---GGGHHHHHHHHHHHHS-HHHHT.T-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTHHHHHHTSEEE CS
                    HMG_CoA_synt_C 155 GnmYtaslyaalasllskvsadela.gkriglfsYGsGlaaslfslrvkqdvsedsildiakvldlkkkLdsRkev 229
                                       Gn+Yt s+y  lasll   ++d l+ g rigl sYGsG +a++fs  v + v    ++d      + k+L++R e+
  gi|386001383|ref|YP_005919682.1| 355 GNIYTGSIYLGLASLL---AQDLLTpGARIGLGSYGSGCSAAFFSGVVGEGVRSL-ARD-----RILKRLEDRVEI 421
                                       ****************...56666537*********************9998882.222.....344556666555 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   3.7e-19   2.2e-15       4     170 ..       8     192 ..       5     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.7e-19
                    HMG_CoA_synt_N   4 dvgilaleiylpaqyvdqa.elekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrle 79 
                                        vgi  +   +p  ++  + e+ +  g+e  k + g+g  +m+  + +ed  +l+ +   +l+e+++l    +g++ 
  gi|386001383|ref|YP_005919682.1|   8 AVGIDDIAAAFPKLFISTTgEFARARGIEPAKLARGIGVEKMAVPDAHEDAATLAAASTLELMEKNDLRPAEVGKIY 84 
                                       699**********999865499******************************************************* PP

                    HMG_CoA_synt_N  80 vgtetiidksksvksvlmqlfee....sgntdiegidtlnacyggtaalfnavnwiessa......wd......gry 140
                                       +gte+ +d +k++ + ++ ++e        ++   ++   ac g t al   + w+++         d      gr 
  gi|386001383|ref|YP_005919682.1|  85 IGTESGVDEAKAIGTYVIGMLERvygpGTFSECSTVEFKAACIGATHALESVACWLKAGDdgggedADgpgrrrGRV 161
                                       ************999877655541111566788999999*****************874311111123332233789 PP

                    HMG_CoA_synt_N 141 alvvagdiaiydsgna.rptggagavallig 170
                                        +vva d+a y+ g++   t gag+valli 
  gi|386001383|ref|YP_005919682.1| 162 GIVVATDVARYELGSPgEYTQGAGSVALLIK 192
                                       9*************983579*********96 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.84     5e+03      27      57 ..      40      70 ..      35      76 .. 0.75
   2 ?   12.8   0.0   1.7e-05       0.1      42      83 ..     351     392 ..     328     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.84
                                      HHHHHT--GGGB--THHHH-B-GGGHHHHHH CS
                     ACP_syn_III_C 27 vakklglpeekvvvnldeyGntsaasiplaL 57
                                      +a+ +g+++  v+   ++ + ++aas + ++
  gi|386001383|ref|YP_005919682.1| 40 LARGIGVEKMAVPDAHEDAATLAAASTLELM 70
                                      6777788888888888888888888876555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.7e-05
                                       HHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTEE CS
                     ACP_syn_III_C  42 ldeyGntsaasiplaLdeaveegklkpgdlvllvgfGaGltw 83 
                                          +Gn+ + si l L+ ++++  l pg ++ l + G G + 
  gi|386001383|ref|YP_005919682.1| 351 SSAVGNIYTGSIYLGLASLLAQDLLTPGARIGLGSYGSGCSA 392
                                       4679***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2759.38
//
Query:       gi|386001384|ref|YP_005919683.1|  [L=118]
Description: hypothetical protein Mhar_0682 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0072   16.5   0.0     0.0082   16.3   0.0    1.2  1  P22_AR_C  P22AR C-terminal domain
  ------ inclusion threshold ------
       0.27   11.9   1.2        2.9    8.6   0.3    2.3  2  HTH_32    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> P22_AR_C  P22AR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.2e-07    0.0082       7      54 ..      18      65 ..      14      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.2e-07
                          P22_AR_C  7 lTekElqsLvWlWfalvrsvellrelepaLraigsnlapkaYsiakEY 54
                                      +++  + + v+ W +++r +e +++l + L+a+gs+   +a  + kEY
  gi|386001384|ref|YP_005919683.1| 18 FSARAISQEVSTWTEAFRLLEEIEQLAKRLDALGSKDRIEAAALLKEY 65
                                      5666677889*************************9887777778887 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.031   2.8e+02      35      69 ..      38      75 ..      19      82 .. 0.53
   2 ?    8.6   0.3   0.00032       2.9      16      43 ..      83     113 ..      77     118 .] 0.70

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.031
                            HTH_32 35 ariiallreep.rWsprqlaa..rlaere.gvkvShstv 69
                                      ++i +l+++     s +++ a   l +++ g+++S + v
  gi|386001384|ref|YP_005919683.1| 38 EEIEQLAKRLDaLGSKDRIEAaaLL-KEYaGGEMSLEEV 75
                                      4455555332212233333331133.5554555665555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00032
                            HTH_32  16 gLkdrprr.g...rprklsdevrariiallre 43 
                                       gL + p r     +p+ +++e +++++al+re
  gi|386001384|ref|YP_005919683.1|  83 GLIPMPARcTmrqKPP-ITPEAEEAVKALIRE 113
                                       6776666642323666.*************54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 716.71
//
Query:       gi|386001385|ref|YP_005919684.1|  [L=161]
Description: hypothetical protein Mhar_0683 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-22   77.5   0.0    1.2e-21   77.2   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    5.8e-05   23.2   0.0    7.4e-05   22.9   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   1.3e-25   1.2e-21       1     110 [.      10     113 ..      10     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 1.3e-25
                                       -HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGE CS
                      Pyridox_ox_2   1 dreeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfns 76 
                                       d+ e ++l++e++++r+af  d +p+i P+ y +dg+ +yf ++k++ +++ +r  p v+v+v++   + ++ s   
  gi|386001385|ref|YP_005919684.1|  10 DKGERDRLIEEEHLCRIAFRGDRYPHIAPFVYFFDGRFMYFLSTKYGSKIEFFRRDPhVSVEVER---YAPDLS--- 80 
                                       67899*************************************************77779999999...566777... PP

                                       EEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHST CS
                      Pyridox_ox_2  77 lnyrSVvvrGraeevtdeeekaealellvekivp 110
                                        +yr+V++rGr++ev+d +ek++++e++v+ i  
  gi|386001385|ref|YP_005919684.1|  81 -SYRFVTLRGRLAEVSDLQEKRRVREGFVDLIRR 113
                                       .7****************************9944 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   8.2e-09   7.4e-05       7      86 ..      16      96 ..       9      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.2e-09
                                      HHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT....GSEEEEEEEEE CS
                    Putative_PNPOx  7 eflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde....lgrgvrieGta 81
                                       +++e++++++A  + d +P++ p  +  +dgr  ++f + +   k +  +++p+v++ +  ++    ++r v+++G+ 
  gi|386001385|ref|YP_005919684.1| 16 RLIEEEHLCRIAF-RGDRYPHIAPFVYF-FDGR-FMYFLSTKYGSKIEFFRRDPHVSVEVERYApdlsSYRFVTLRGRL 91
                                      5789999999996.59************.7777.79999999999***************999999************9 PP

                                      EEESC CS
                    Putative_PNPOx 82 elvsd 86
                                      + vsd
  gi|386001385|ref|YP_005919684.1| 92 AEVSD 96
                                      99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 994.70
//
Query:       gi|386001386|ref|YP_005919685.1|  [L=532]
Description: Glutamate synthase (NADPH) GltB2 subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-13   48.2   0.0    3.2e-10   39.7   0.0    2.1  2  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0   0.00025       4.5      62     155 ..     118     239 ..     100     246 .. 0.67
   2 !   39.7   0.0   1.8e-14   3.2e-10     186     308 ..     287     415 ..     280     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00025
                                       HHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETT..S---GGGGS-----..................... CS
                      Glu_synthase  62 lkikkriltsamSyGalseeahealakamnrlgtksntGE..GGedeerlktakdv..................... 115
                                       +k+k +i t+a+    ++    e +a+++   g++  +GE   G+d+e +  ++                       
  gi|386001386|ref|YP_005919685.1| 118 VKMKVPIFTGALGSTDIAGANWEHFAIGAAISGITLVCGEnvCGVDPELVLDGRGKvsrspemdrrietykrfhegy 194
                                       56666666666666666666677777777777777777774446766665554444467777777777777777777 PP

                                       ..SEEE..E-TT-TT--HHHHH..H-SEEEEE---TTSTTS--EE- CS
                      Glu_synthase 116 ..aikQ..vasgrFGvteeyLn..nakaleikiaQGakpgeGgqlp 155
                                          ++Q  v   r G  e++ +  + + le+k +QGak   Gg+++
  gi|386001386|ref|YP_005919685.1| 195 geILVQmnVEDTRLGTAEYVSMrhELDTLELKWGQGAKCI-GGEIK 239
                                       7744441155788887766543125789**********87.88875 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.8e-14
                                       SHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHH..HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHH..H CS
                      Glu_synthase 186 siedlaqliedLkevnkeakvsvKlvaeagvetiaag..vakanadiilidGleGGTGAspkssikhaGlPlel..a 258
                                        +e + + +  L++++  ++++ K +a + +e   a    ++a+ d+++idG  GGTG sp+ ++++ G+P+    +
  gi|386001386|ref|YP_005919685.1| 287 TKESFLEEVDRLRDLG-FKRITLKTGAYSMAELAMALryGSEAKIDLLTIDGAPGGTGMSPWPMMNEWGIPTFYlqS 362
                                       5677888999999999.789******99999887765447899****************************965125 PP

                                       HH.HHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-S...EEE-SHHHHH CS
                      Glu_synthase 259 la.evdqtlkeeglrdrvsliadGglktgadvvkalalGAd...avgigtaali 308
                                       la e  ++l + g+r   +l ++Gg+ + + v+ka+a+GA    av +g+a +i
  gi|386001386|ref|YP_005919685.1| 363 LArEFAERLGKRGMRVP-DLAIAGGFSSEDGVFKAIAIGAPyfrAVCMGRALMI 415
                                       55245677777777754.8*********************72224556766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3419.67
//
Query:       gi|386001387|ref|YP_005919686.1|  [L=391]
Description: glutamate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-73  246.2   0.6    7.5e-73  245.2   0.3    1.6  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    5.4e-55  184.8   0.0    9.9e-55  183.9   0.0    1.5  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
  ------ inclusion threshold ------
      0.025   13.9   0.0      0.043   13.2   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.074   13.2   0.1       0.57   10.4   0.1    2.4  3  HTH_28           Helix-turn-helix domain
        0.1   12.9   0.1         23    5.4   0.0    2.7  2  NUMOD1           NUMOD1 domain


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.59   2.1e+03      65      83 ..      77      95 ..      75     100 .. 0.86
   2 !  245.2   0.3   2.1e-76   7.5e-73       1     243 []     151     386 ..     151     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.59
                                      SEEEEETTEE-HHHHHHHH CS
                     ELFV_dehydrog 65 sGviydpeGldieellelk 83
                                       Gvi++p+ l++ el +l 
  gi|386001387|ref|YP_005919686.1| 77 GGVICNPKELSMTELERLS 95
                                      599*******999998875 PP

  == domain 2  score: 245.2 bits;  conditional E-value: 2.1e-76
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-H CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldi 76 
                                       GGs +r++aT++G +++++e++k+l++d l+g++vai+G+Gn g +a  l+ el g +vva+sDs+G iy+++Gld+
  gi|386001387|ref|YP_005919686.1| 151 GGSCGRDDATARGGMFTIREAAKELGID-LSGATVAIQGYGNAGCHASFLCRELfGSRVVAISDSKGGIYNKDGLDL 226
                                       9***************************.**********************9999********************** PP

                                       HHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HH CS
                     ELFV_dehydrog  77 eellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqe 153
                                       e  +++k+e+ +v ++++   k++ +i+ne ellel+vdil+ +A++n+i++ena  +ik  +k+v+E AN+ptt+e
  gi|386001387|ref|YP_005919686.1| 227 ELACSVKKETCTVVNSPR---KTTVKITNE-ELLELDVDILIVAALENVITKENAP-RIK--AKIVAELANGPTTPE 296
                                       ************999993...456799997.*************************.***..*************** PP

                                       HHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHH CS
                     ELFV_dehydrog 154 AkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkgania 230
                                       A+eil ++gv v+pd+++NaGGVtvS++Em+qn+ r+ w+ eev+++l+++m++++++v+e+ ++y+ +++++a+++
  gi|386001387|ref|YP_005919686.1| 297 ADEILYKKGVHVIPDFLCNAGGVTVSYFEMVQNIDRYCWDVEEVRKRLDARMTRAYHSVLETSKDYNINMRQAAYVV 373
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++ +v+eamk +G
  gi|386001387|ref|YP_005919686.1| 374 AVGRVVEAMKIRG 386
                                       **********988 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.0   2.8e-58   9.9e-55       1     130 []       5     133 ..       5     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 2.8e-58
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p r l+v++pv++d+G+++v++g+r+q+++a gPakGGiRfhp+ ++d+v+aLaa+mt+K++l+dlp+GG+kggv++
  gi|386001387|ref|YP_005919686.1|   5 PMRELHVSIPVRMDDGSTKVFQGFRVQYNDAKGPAKGGIRFHPDETIDTVRALAAWMTWKCSLLDLPLGGGKGGVIC 81 
                                       67899************************************************************************ PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       +pk+ls +eler+ r +++++  +fiGp++DvpApDv+t+++ maw++dey+k
  gi|386001387|ref|YP_005919686.1|  82 NPKELSMTELERLSRGYIDRIW-QFIGPEKDVPAPDVYTTPQIMAWMMDEYSK 133
                                       **********************.****************************85 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.043      23      70 ..     166     216 ..     154     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       C..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHH CS
                      2-Hacid_dh_C  23 w..ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskk 70 
                                       +  ++ ++ lg +lsg tv+i G+G+ G ++  +++  fg +v+a++ sk 
  gi|386001387|ref|YP_005919686.1| 166 FtiREAAKELGIDLSGATVAIQGYGNAGCHASFLCReLFGSRVVAISDSKG 216
                                       455667789999**********************99889******998855 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00016      0.57      11      42 ..     163     195 ..     159     197 .. 0.85
   2 ?   -1.6   0.0      0.85     3e+03       2      12 ..     281     291 ..     281     297 .. 0.81
   3 ?   -3.6   0.0       3.7   1.3e+04      13      28 ..     353     368 ..     353     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                            HTH_28  11 aGh.svreaArelgisrrtvyrWikryeegGia 42 
                                        G+ ++reaA+elgi+ +   + i+ y   G++
  gi|386001387|ref|YP_005919686.1| 163 GGMfTIREAAKELGIDLSGATVAIQGYGNAGCH 195
                                       3569**************999999999998875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.85
                            HTH_28   2 RleiikllaaG 12 
                                       +++i+ +la+G
  gi|386001387|ref|YP_005919686.1| 281 KAKIVAELANG 291
                                       89*******99 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.7
                            HTH_28  13 hsvreaArelgisrrt 28 
                                       hsv e+++ ++i+ r+
  gi|386001387|ref|YP_005919686.1| 353 HSVLETSKDYNINMRQ 368
                                       6778999999997665 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0065        23      19      29 ..     168     178 ..     167     186 .. 0.86
   2 ?    4.6   0.0     0.011        40      15      31 ..     351     367 ..     344     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0065
                            NUMOD1  19 ireAakyLgis 29 
                                       ireAak Lgi+
  gi|386001387|ref|YP_005919686.1| 168 IREAAKELGID 178
                                       9*********7 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                            NUMOD1  15 kFsSireAakyLgishn 31 
                                        ++S+ e++k+ +i+++
  gi|386001387|ref|YP_005919686.1| 351 AYHSVLETSKDYNINMR 367
                                       59************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2413.56
//
Query:       gi|386001388|ref|YP_005919687.1|  [L=76]
Description: hypothetical protein Mhar_0686 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       135  (0.0075297); expected 358.6 (0.02)
Passed bias filter:                      123  (0.00686039); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 530.52
//
Query:       gi|386001389|ref|YP_005919688.1|  [L=77]
Description: hypothetical protein Mhar_0687 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 505.50
//
Query:       gi|386001390|ref|YP_005919689.1|  [L=305]
Description: Sulfide dehydrogenase (Flavoprotein) subunit SudB [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-12   46.4   3.9    5.7e-12   45.2   3.9    1.7  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.017   15.5   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
      0.098   12.7   0.0       0.17   11.9   0.0    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   3.9   9.5e-16   5.7e-12       3      41 ..     213     247 ..     211     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 9.5e-16
                                       --SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   3 rMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                        M++G+G+C++C+v++ g+    +k++C+dGP Fd+++v
  gi|386001390|ref|YP_005919689.1| 213 LMVDGTGMCGACRVEVGGE----TKFACVDGPDFDGHQV 247
                                       6***************764....8**************9 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.8e-06     0.017       3      96 ..       3      91 ..       1      93 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                                      EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHC CS
                     FAD_binding_6  3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLde 81
                                      +++eke + +++  ++++ p+ ++    ++Gq+v++r++ +ge+v  +  ++  + e+G++e++   y  G  ++ L  
  gi|386001390|ref|YP_005919689.1|  3 QIVEKEALVPNIIYLKIRAPKVAK--AARPGQFVIIRVDETGERV--PMGLAGWDAEEGTIEIV--FYVLGTSTMKLGT 75
                                      678999999999999999998888..7899*********888755..667779999*****988..6888********* PP

                                      S-TT-E.EEEEEEE-S CS
                     FAD_binding_6 82 lkigdt.leikGPlGk 96
                                      l++gd+ l++ GPlG+
  gi|386001390|ref|YP_005919689.1| 76 LRVGDSvLNLAGPLGT 91
                                      ****86269*****97 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05      0.17      54      73 ..     218     237 ..     211     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                            Fer2_3  54 egiCGscavainGkptlaCt 73 
                                        g+CG+c v++ G+++ aC 
  gi|386001390|ref|YP_005919689.1| 218 TGMCGACRVEVGGETKFACV 237
                                       79*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1977.50
//
Query:       gi|386001391|ref|YP_005919690.1|  [L=916]
Description: Formate dehydrogenase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-98  331.0   0.0    1.4e-98  330.7   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    8.7e-32  109.4   0.2    1.7e-30  105.3   0.0    2.8  3  Molydop_binding  Molydopterin dinucleotide binding domain
      7e-18   64.5   0.1      2e-17   63.0   0.1    1.9  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    7.6e-16   57.9   0.5    7.6e-16   57.9   0.5    2.6  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
      1e-08   34.6   9.1    0.00034   20.1   0.3    2.9  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    2.3e-07   30.4   1.2    2.3e-07   30.4   1.2    4.0  3  Fer4             4Fe-4S binding domain
    7.1e-07   29.7   6.8    7.1e-07   29.7   6.8    4.0  2  Fer4_7           4Fe-4S dicluster domain
    5.6e-06   26.4   5.1    5.6e-06   26.4   5.1    2.9  2  Fer4_21          4Fe-4S dicluster domain
    7.8e-05   22.8   8.8    7.8e-05   22.8   8.8    3.8  4  Fer4_9           4Fe-4S dicluster domain
    0.00065   19.8  10.3    0.00065   19.8  10.3    3.5  2  Fer4_10          4Fe-4S dicluster domain
     0.0033   17.4  23.0      0.011   15.8   1.2    4.2  4  Fer4_6           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   16.0   6.0      0.018   16.0   6.0    4.5  2  Fer4_3           4Fe-4S binding domain
       0.13   13.0   6.5        7.2    7.4   0.6    2.9  2  Fer4_15          4Fe-4S single cluster domain
        2.4    8.4  12.8       0.69   10.1   1.5    3.3  3  Fer4_18          4Fe-4S dicluster domain
        4.6    7.9  20.0        1.6    9.3   0.5    3.6  3  Fer4_17          4Fe-4S dicluster domain
        7.8    6.8  23.3       0.33   11.1   2.5    4.0  3  Fer4_2           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.7   0.0  1.3e-101   1.4e-98       1     431 [.     298     716 ..     298     717 .. 0.94

  Alignments for each domain:
  == domain 1  score: 330.7 bits;  conditional E-value: 1.3e-101
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rlk+P++R   +  G++v+++W+eAl ++ +++ +    +g+ r a+ ss + + +e+ ++++kl++l++   ++++
  gi|386001391|ref|YP_005919690.1| 298 RLKTPLIR---K-GGELVPATWEEALSVVVERFSR---AKGD-RFALLSSAKCT-NEENYLAQKLARLVME--TNNV 363
                                       9*******...6.9*********************...5555.67767776666.9***************..9*** PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+l++as++    +++gs+     +++n++e+l++++ i+++GsN  e +p+   ri  a ++ +ak+iv  pr
  gi|386001391|ref|YP_005919690.1| 364 DHCARLCHASTVaalaTAFGSG-----AMTNSIEELADAGCILIIGSNTTEQHPVIALRIKEAKRR-GAKIIVANPR 434
                                       ***********95555555554.....6788*************************7777776666.6********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                       + el kfad wl  +pgtd++l+la+++vil+e++ d+ef+  ++ g+ee+++ l +++ ee++++++v +  + e 
  gi|386001391|ref|YP_005919690.1| 435 WIELCKFADVWLRQTPGTDVPLVLALCKVILEEGLLDEEFIGERCEGFEEFRESLAGVTLEEAAAITGVEVGLIEEA 511
                                       ***************************************************************************** PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       ar +a++ + s i++ +g++++++g++++ a++ La+++gn g+p +g + l+Gq++++g a+++galp  l+ ++ 
  gi|386001391|ref|YP_005919690.1| 512 ARIYASNGP-SSIVYSMGITQHSHGTENILALADLAMMTGNLGKPSSGINPLRGQNNVQG-ACDMGALPNVLPGYQA 586
                                       *********.66677*********************************************.********99999888 PP

                                       TT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSH CS
                     Molybdopterin 305 ke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlts 378
                                       ++    + kf a +  +l++ p+ +++e  n+++ +g++vly++g+np ++++d  +v++alek d++vv +++l++
  gi|386001391|ref|YP_005919690.1| 587 VTnddLRRKFEARWDRELPKRPGLTLMEIFNAIHAGGVDVLYIIGENPQISDPDSTHVVEALEKVDFLVVQEIFLSE 663
                                       888999999******************************************************************** PP

                                       HHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 379 talyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       ta +aD++LPaa++ Ek++++tn+e+r+q+ ++av+ppgea++dw I++++ +
  gi|386001391|ref|YP_005919690.1| 664 TAMHADVVLPAASFAEKDGTFTNTERRVQRVRRAVPPPGEARPDWRIISEIGR 716
                                       **************************************************975 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.4   7.2e+03      52      65 ..      13      26 ..      12      30 .. 0.81
   2 ?    0.7   0.0      0.45     5e+02      42      59 ..     259     276 ..     256     283 .. 0.88
   3 !  105.3   0.0   1.6e-33   1.7e-30       1     111 []     801     907 ..     801     907 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.4
                                      EEETTEEEEEEEEE CS
                   Molydop_binding 52 vesrrGsvevrakv 65
                                      v++rrG+++++a+ 
  gi|386001391|ref|YP_005919690.1| 13 VRTRRGATVLEAAR 26
                                      99*****9999976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.45
                                       HT--TT-EEEEEETTEEE CS
                   Molydop_binding  42 lGikdGdlVevesrrGsv 59 
                                       lG+ dG +V+++ +rG++
  gi|386001391|ref|YP_005919690.1| 259 LGVLDGHIVTIRGKRGET 276
                                       899*************86 PP

  == domain 3  score: 105.3 bits;  conditional E-value: 1.6e-33
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       ++L+tgr+l ++h++t+tr+v  l+  ++ e veinp d + lGi dGdlVev+srrG+v+++a++te   pGvvfm
  gi|386001391|ref|YP_005919690.1| 801 FILTTGRVLCHFHTGTMTRKVAGLNYLRGeELVEINPGDGEVLGIGDGDLVEVSSRRGKVRAKARLTEKSSPGVVFM 877
                                       79*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksva 111
                                       +f++ e     +++N+lt++a+dp++++pe+k++a
  gi|386001391|ref|YP_005919690.1| 878 TFHFAE-----TPTNVLTNPALDPVAKIPELKVCA 907
                                       ****99.....*********************996 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.1   1.8e-20     2e-17       3      81 ..       3      78 ..       1      79 [. 0.96

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.8e-20
                            Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnv.racstpvedGlkvetq 80
                                      ++ lt+DG++v+ + G tv++A+  +g+++p++c +      l+++g+C+ C+Ve+ege     +c+t +e+G++v t 
  gi|386001391|ref|YP_005919690.1|  3 EIALTIDGRKVRTRRGATVLEAARGAGIYIPALCDH----PDLTPIGSCKLCIVEIEGESLRpTSCTTLAEEGMVVLTR 77
                                      799*********************************....89******************998*************997 PP

                            Fer2_4 81 t 81
                                      t
  gi|386001391|ref|YP_005919690.1| 78 T 78
                                      6 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       5.2   5.8e+03       6      12 ..     213     219 ..     211     220 .. 0.83
   2 !   57.9   0.5   6.8e-19   7.6e-16       2      54 ..     242     294 ..     241     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.2
                                       EE-SSBT CS
                    Molybdop_Fe4S4   6 taCpyCg 12 
                                       + C++Cg
  gi|386001391|ref|YP_005919690.1| 213 SECKFCG 219
                                       78****9 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 6.8e-19
                                       EEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCC CS
                    Molybdop_Fe4S4   2 kvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervy 54 
                                       ++v t+Cp+CgvgC +++ v dg iv+++g +    n+g+lCvKGr++l++v 
  gi|386001391|ref|YP_005919690.1| 242 ETVTTVCPFCGVGCVMDLGVLDGHIVTIRGKRGETPNRGQLCVKGRFGLDFVE 294
                                       799***********************************************996 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.1   2.8e-06    0.0031       1      25 [.      85     111 ..      85     120 .. 0.91
   2 !   20.1   0.3     3e-07   0.00034      16      40 .]     127     151 ..     124     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.8e-06
                   NADH-G_4Fe-4S_3   1 RktilellLa..nHpldCltCdknGnC 25 
                                       R+ +lel+La  +Hp  Cl Cd+  +C
  gi|386001391|ref|YP_005919690.1|  85 RRSALELILAltHHPTSCLFCDRKEEC 111
                                       999****986559************** PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3e-07
                   NADH-G_4Fe-4S_3  16 CltCdknGnCeLQdlayelgveesr 40 
                                       C +C++ G+CeLQd+++++g e++r
  gi|386001391|ref|YP_005919690.1| 127 CKYCPNDGRCELQDVVEYVGLERIR 151
                                       999*****************99876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       3.8   4.2e+03       9      14 ..     125     130 ..     125     133 .. 0.72
   2 !   12.7   1.1   7.7e-05     0.086       4      18 ..     170     184 ..     167     186 .. 0.91
   3 !   30.4   1.2     2e-10   2.3e-07       5      23 ..     212     230 ..     208     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                                       SS-THH CS
                              Fer4   9 igCGaC 14 
                                       +gC++C
  gi|386001391|ref|YP_005919690.1| 125 VGCKYC 130
                                       577777 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.7e-05
                                       ETTTSSS-THHHHHS CS
                              Fer4   4 deekCigCGaCvevC 18 
                                       d+++Ci C +Cv  C
  gi|386001391|ref|YP_005919690.1| 170 DYNLCILCSRCVRTC 184
                                       99************* PP

  == domain 3  score: 30.4 bits;  conditional E-value: 2e-10
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       e+ C +CGaCv+vCP+gA+
  gi|386001391|ref|YP_005919690.1| 212 ESECKFCGACVDVCPTGAL 230
                                       899***************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   6.8   6.3e-10   7.1e-07       2      52 .]     174     229 ..     173     229 .. 0.83
   2 ?    0.1   0.0       1.1   1.2e+03       5      13 ..     248     295 ..     244     374 .. 0.41

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.3e-10
                            Fer4_7   2 CigCgaCvaaCp....vkaield.eeenekgtekveidpekClgCgaCvavCPtga 52 
                                       Ci C +Cv++C      +++++d +++++ ++  v + +++C +CgaCv+vCPtga
  gi|386001391|ref|YP_005919690.1| 174 CILCSRCVRTCQevrgEGVLTFDvNYHHHHTIGPVSLFESECKFCGACVDVCPTGA 229
                                       ***********87777888888733345556677899999**************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                            Fer4_7   5 CgaCvaaC.......................................p 13 
                                       C +C + C                                       +
  gi|386001391|ref|YP_005919690.1| 248 CPFCGVGCvmdlgvldghivtirgkrgetpnrgqlcvkgrfgldfveS 295
                                       666666664444444444444444444444444444333333333330 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   5.1     5e-09   5.6e-06       5      53 ..     171     227 ..     168     231 .. 0.76
   2 ?   -1.8   0.2       3.2   3.6e+03      13      29 ..     365     381 ..     362     401 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5e-09
                           Fer4_21   5 edkCigCgkCliaCedtshqai.eidaktvl.......kvvedeCvGCnlCssvCPv 53 
                                        + Ci C +C+ +C++   + + ++d + ++        + e+eC  C  C++vCP+
  gi|386001391|ref|YP_005919690.1| 171 YNLCILCSRCVRTCQEVRGEGVlTFDVNYHHhhtigpvSLFESECKFCGACVDVCPT 227
                                       578************98777764555554444566644445***************6 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                           Fer4_21  13 kCliaCedtshqaieid 29 
                                       +C+  C+ +++ a+ ++
  gi|386001391|ref|YP_005919690.1| 365 HCARLCHASTVAALATA 381
                                       79999999998888533 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.8       3.6     4e+03      27      42 ..      83     111 ..      46     121 .. 0.61
   2 !   10.6   3.9   0.00044       0.5       4      48 ..     126     186 ..     124     189 .. 0.71
   3 !   22.8   8.8     7e-08   7.8e-05       2      50 ..     174     229 ..     173     230 .. 0.68
   4 ?   -2.9   0.2       7.2   8.1e+03      35      43 ..     247     256 ..     234     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.6
                            Fer4_9  27 rlraase............eaCigCga...C 42 
                                       ++r+               ++C++C +   C
  gi|386001391|ref|YP_005919690.1|  83 EMRR--SalelilalthhpTSCLFCDRkeeC 111
                                       3322..1335677777777789999765665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00044
                            Fer4_9   4 gCgaCvea..Cpagvvvedaaerkarlraase...............eaCigCgaCveaCpk 48 
                                       gC++C +   C+ + vve  + + +r++   +               + Ci C +Cv  C++
  gi|386001391|ref|YP_005919690.1| 126 GCKYCPNDgrCELQDVVEYVGLERIRYETS-YrnqpvlrepffdrdyNLCILCSRCVRTCQE 186
                                       899995543486655555555555554332.23589999999999999************85 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 7e-08
                            Fer4_9   2 CtgCgaCveaC.........pagvvvedaaerkarlraase........eaCigCgaCveaCpkga 50 
                                       C+ C +Cv+ C                      +++++           ++C +CgaCv++Cp+ga
  gi|386001391|ref|YP_005919690.1| 174 CILCSRCVRTCqevrgegvlT----------FDVNYHHHHTigpvslfeSECKFCGACVDVCPTGA 229
                                       ***********4444444333..........33333333334556666678*************97 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 7.2
                            Fer4_9  35 aCigCga.Cv 43 
                                        C +Cg  Cv
  gi|386001391|ref|YP_005919690.1| 247 VCPFCGVgCV 256
                                       4777776555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  10.3   5.8e-07   0.00065       5      56 .]     170     226 ..     167     226 .. 0.93
   2 !   13.0   7.0   7.7e-05     0.086       7      52 ..     213     256 ..     207     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.8e-07
                           Fer4_10   5 dddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       d + Ci C +Cv+ C  +        t ++++     +++v+   ++C +cgaCv++CP
  gi|386001391|ref|YP_005919690.1| 170 DYNLCILCSRCVRTC--QEvrgegvlTFDVNYHHHHTIGPVSLFESECKFCGACVDVCP 226
                                       7889***********..5559*****99******************************9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.7e-05
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg.aCv 52 
                                       + C  Cg+Cv++CP+   +     ++  + +++++   C++cg  Cv
  gi|386001391|ref|YP_005919690.1| 213 SECKFCGACVDVCPT---GALFARAERWGRPEETVTTVCPFCGvGCV 256
                                       68*************...55555555556667778889999997887 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.7   1.9e+03       6      16 ..      33      51 ..      31      53 .. 0.72
   2 !   15.8   1.2   9.7e-06     0.011       5      19 ..     170     184 ..     166     191 .. 0.92
   3 !   14.6   3.0   2.4e-05     0.026      12      24 .]     218     230 ..     212     230 .. 0.89
   4 ?   -3.2   0.4       9.9   1.1e+04      17      21 ..     246     250 ..     245     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                            Fer4_6  6 pdkCi........gCgdCv 16
                                      p +C+        +C  C+
  gi|386001391|ref|YP_005919690.1| 33 PALCDhpdltpigSCKLCI 51
                                      7899977666666699997 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.7e-06
                            Fer4_6   5 dpdkCigCgdCvrvC 19 
                                       d+++Ci C +Cvr C
  gi|386001391|ref|YP_005919690.1| 170 DYNLCILCSRCVRTC 184
                                       99************* PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.4e-05
                            Fer4_6  12 CgdCvrvCPegai 24 
                                       Cg+Cv+vCP+ga+
  gi|386001391|ref|YP_005919690.1| 218 CGACVDVCPTGAL 230
                                       ***********97 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 9.9
                            Fer4_6  17 rvCPe 21 
                                       +vCP+
  gi|386001391|ref|YP_005919690.1| 246 TVCPF 250
                                       79**6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.6     0.013        15       1      12 [.     174     185 ..     174     189 .. 0.92
   2 ?   16.0   6.0   1.6e-05     0.018       1      15 []     215     229 ..     215     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C++Cv+ C 
  gi|386001391|ref|YP_005919690.1| 174 CILCSRCVRTCQ 185
                                       ***********6 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.6e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  CgaCv+vCP+gA
  gi|386001391|ref|YP_005919690.1| 215 CKFCGACVDVCPTGA 229
                                       99************9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.7    0.0066       7.4       4      21 ..     170     187 ..     167     199 .. 0.88
   2 ?    7.4   0.6    0.0065       7.2       6      20 ..     213     227 ..     208     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0066
                           Fer4_15   4 DrdaCigcglCvaeapev 21 
                                       D ++Ci c +Cv+ ++ev
  gi|386001391|ref|YP_005919690.1| 170 DYNLCILCSRCVRTCQEV 187
                                       7789***********987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0065
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C  cg+Cv+++p+
  gi|386001391|ref|YP_005919690.1| 213 SECKFCGACVDVCPT 227
                                       78***********86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.3     0.058        65      85      99 ..     174     188 ..     168     201 .. 0.82
   2 ?   10.1   1.5   0.00061      0.69      58      74 ..     212     228 ..     188     233 .. 0.86
   3 ?   -0.8   0.0       1.5   1.7e+03       3      20 ..     241     258 ..     240     285 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.058
                           Fer4_18  85 ciscllcidacdkvm 99 
                                       ci c++c+ +c++v 
  gi|386001391|ref|YP_005919690.1| 174 CILCSRCVRTCQEVR 188
                                       899999999998886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00061
                           Fer4_18  58 agdcidcescvkvcPtg 74 
                                       +++c  c++cv+vcPtg
  gi|386001391|ref|YP_005919690.1| 212 ESECKFCGACVDVCPTG 228
                                       689************98 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                           Fer4_18   3 edvcvyvcPyarvqsvly 20 
                                       e+  + vcP+  v +v+ 
  gi|386001391|ref|YP_005919690.1| 241 EETVTTVCPFCGVGCVMD 258
                                       667789999999999884 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.7       4.1   4.6e+03      40      55 ..     101     120 ..      46     126 .. 0.54
   2 ?    1.8  11.4      0.31   3.5e+02       4      57 ..     126     185 ..     100     187 .. 0.56
   3 ?    9.3   0.5    0.0015       1.6       1      17 [.     214     230 ..     214     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                           Fer4_17  40 e....ekaslCieCgeCerk 55 
                                       +    ++ ++C+  +eC rk
  gi|386001391|ref|YP_005919690.1| 101 SclfcDRKEECSDLRECMRK 120
                                       13333455777777777766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                           Fer4_17   4 qCgyClp..eCpsyeaydn.epkkllraaklglleeaeke....ekaslCieCgeCerkCP 57 
                                       +C+yC +   C      +    +++++++++ +++ + +e    +  +lCi C +C+r C 
  gi|386001391|ref|YP_005919690.1| 126 GCKYCPNdgRCELQDVVEYvGLERIRYETSY-RNQPVLREpffdRDYNLCILCSRCVRTCQ 185
                                       3444444333333322111112233333322.12222222455489**************6 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0015
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       +C  Cg+C+++Cp+++ 
  gi|386001391|ref|YP_005919690.1| 214 ECKFCGACVDVCPTGAL 230
                                       59999999999998765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.6   0.00073      0.82       3      20 ..     165     184 ..     163     186 .. 0.81
   2 ?   11.1   2.5   0.00029      0.33      10      22 .]     215     227 ..     209     227 .. 0.83
   3 ?   -2.7   0.2       7.6   8.5e+03      17      21 ..     245     249 ..     245     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00073
                            Fer4_2   3 vvvdtd..rCigCgaCvsaC 20 
                                       +++d+d   Ci C+ Cv  C
  gi|386001391|ref|YP_005919690.1| 165 PFFDRDynLCILCSRCVRTC 184
                                       56666666***********9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C  CgaCv++CP+
  gi|386001391|ref|YP_005919690.1| 215 CKFCGACVDVCPT 227
                                       666*********7 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.6
                            Fer4_2  17 vsaCP 21 
                                       +++CP
  gi|386001391|ref|YP_005919690.1| 245 TTVCP 249
                                       69*** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (916 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5874.02
//
Query:       gi|386001392|ref|YP_005919691.1|  [L=496]
Description: Glutamate synthase (NADPH), homotetrameric [Methanosaeta harundinacea 6Ac]
Scores for 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-44  150.9   2.5    1.7e-44  150.2   2.5    1.3  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    1.4e-40  139.3   2.6    2.1e-40  138.8   2.6    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.8e-13   49.0   4.7      6e-06   26.7   0.3    3.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.3e-11   43.0   0.6      3e-05   23.4   0.2    3.2  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-07   31.0   4.8     0.0047   16.3   0.1    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    1.7e-07   31.4   0.4    1.7e-07   31.4   0.4    2.3  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.4e-06   27.1   2.5     0.0071   16.8   0.2    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    1.4e-05   24.6   7.0    1.8e-05   24.3   0.5    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    5.4e-05   22.5   0.3    5.4e-05   22.5   0.3    2.3  3  GIDA            Glucose inhibited division protein A
    5.8e-05   22.0   0.9    5.8e-05   22.0   0.9    1.7  2  HI0933_like     HI0933-like protein
    0.00011   21.5   0.2    0.00011   21.5   0.2    1.7  2  Thi4            Thi4 family
    0.00014   21.3   0.0       0.45    9.9   0.0    2.4  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00028   19.8   0.1     0.0059   15.4   0.0    2.3  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
    0.00028   20.2   1.8    0.00094   18.5   0.2    2.0  2  FAD_binding_3   FAD binding domain
    0.00037   19.7   1.9    0.00037   19.7   1.9    2.8  3  FAD_binding_2   FAD binding domain
    0.00049   19.3   0.0       0.51    9.4   0.0    2.8  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0013   18.6   0.1       0.46   10.2   0.0    2.2  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
     0.0016   18.1   1.9     0.0016   18.1   1.9    3.2  4  DAO             FAD dependent oxidoreductase
     0.0028   16.2   0.0        1.7    6.9   0.0    2.3  2  FMO-like        Flavin-binding monooxygenase-like
     0.0039   17.2   2.5      0.095   12.7   0.6    2.9  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0047   16.3   0.3     0.0047   16.3   0.3    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0057   17.2   0.4       0.56   10.7   0.0    2.7  2  XdhC_C          XdhC Rossmann domain
     0.0061   16.6   0.7        2.7    8.0   0.1    2.6  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0072   16.2   0.3       0.28   11.0   0.1    2.6  2  Rossmann-like   Rossmann-like domain
     0.0074   16.9   0.4     0.0074   16.9   0.4    2.6  2  Fer4_7          4Fe-4S dicluster domain
     0.0095   15.8   3.1       0.33   10.8   1.0    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.011   16.3   0.5        1.9    9.1   0.0    3.0  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.015   14.7   1.6        1.7    8.0   0.0    2.6  2  PALP            Pyridoxal-phosphate dependent enzyme
      0.021   15.0   0.7      0.021   15.0   0.7    1.9  2  Fer4_18         4Fe-4S dicluster domain
      0.021   14.2   0.0       0.51    9.7   0.0    2.3  2  ThiF            ThiF family
      0.046   13.8   0.0       0.55   10.3   0.0    2.3  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      0.053   13.4   0.1        3.3    7.6   0.1    2.3  2  YjeF_N          YjeF-related protein N-terminus
      0.092   12.3   0.1         13    5.2   0.0    2.3  2  DUF4147         Domain of unknown function (DUF4147)
      0.094   11.7   0.5       0.17   10.9   0.5    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      0.098   12.2   3.0       0.25   10.9   0.1    2.6  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.12   11.2   3.4      0.075   11.9   0.6    1.8  2  Trp_halogenase  Tryptophan halogenase
       0.16   12.1   9.4       0.45   10.7   9.4    1.8  1  Fer4_10         4Fe-4S dicluster domain
       0.17   11.6   0.0        4.2    7.0   0.0    2.6  3  MAF_flag10      Protein of unknown function DUF115
        0.3   11.6   7.2       0.21   12.1   2.1    2.2  2  Fer4_8          4Fe-4S dicluster domain
        1.3    9.7   8.6       0.18   12.4   0.8    2.5  2  Fer4_17         4Fe-4S dicluster domain
        4.3    7.7   8.7          1    9.6   3.1    2.5  2  Fer4_2          4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   2.5   3.8e-47   1.7e-44       1     111 [.      45     154 ..      45     156 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 3.8e-47
                                       HTTS-S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-G CS
                           Fer4_20   1 raknfkevalglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpq 77 
                                       r++nf+evalg+ e++a+eeA+RC+qCk++ c++gCPv idip fi+++++g++e+a++iik++nslp +cgrvCpq
  gi|386001392|ref|YP_005919691.1|  45 RRHNFSEVALGYAEDQAAEEADRCIQCKNPRCMEGCPVGIDIPAFIRAVRDGEMEDAVRIIKAKNSLPGICGRVCPQ 121
                                       689************************************************************************** PP

                                       GGTGCCS-GGGTTB.----HHHHHHHHHHHHHHT CS
                           Fer4_20  78 eelCegaCvlekkgkepvaigklerfvadaaree 111
                                       e +Ce++Cvlekkg +p+aig+lerfvad++ ++
  gi|386001392|ref|YP_005919691.1| 122 EVQCESRCVLEKKG-APIAIGRLERFVADWESKN 154
                                       **********9888.***************9886 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8   2.6   4.9e-43   2.1e-40       1     294 []     170     477 ..     170     477 .. 0.82

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 4.9e-43
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllgeevv 76 
                                       k+v+v+G+GpAG++aa +la+ g++vt++   ++++  g +l + + +++ ++ i++ ev      ++ + lg   v
  gi|386001392|ref|YP_005919691.1| 170 KRVAVVGAGPAGITAAADLARMGHQVTVF---EALHDAGGVLIYGIPEFRLPKAIVRsEV------EYVKSLG---V 234
                                       58***************************...8889999999999*****9999998543......3444444...3 PP

                                       EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.........TTBEECCSECHHHHHHCCSS-T.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx........xxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGv........aenvgklvrtldsaealklkllp.. 142
                                       +++ ++  v+ +  + ++  k  +d+++l +G+ + ++ g+pG+        +e+ ++   +l++a ++ +  +p  
  gi|386001392|ref|YP_005919691.1| 235 TFELDS--VVGRLVQVDELLKNGFDAVFLGIGAGAPRFlGVPGEnlngvysaNEYLTR--VNLMKAYRFPEYDTPir 307
                                       333333..222222226667889*********8655555*****76666643333333..366666666666666** PP

                                       ..SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.. CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2 143 ..krivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.. 214
                                         kr++vvGgG+++++ A  + +lg+e v++v++r++    ++ +l+++  e  ++eGv + + t+++++ ++++  
  gi|386001392|ref|YP_005919691.1| 308 qgKRVAVVGGGNVAMDAARCAVRLGAEeVHVVYRRSEAE--MPARLEEI--ENAKEEGVIFDFLTNPTRFVADDRgr 380
                                       ************************9988*********96..99999998..888999*****************9*9 PP

                                       .....EEEEEETTSCE...............EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTT CS
                                       .....xxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 .....klevvledgee...............idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpg 270
                                             +++vl++ +e               +d+d+v++avG +p++ l + ++ gle++++g ivv++++rt+ +g
  gi|386001392|ref|YP_005919691.1| 381 vagmeVVRMVLGEPDEsgrrrpvvekgseriVDVDTVIIAVGTTPNPLL-PgNTPGLETTRWGTIVVNDSGRTSREG 456
                                       9988666699999999999999999999999***************866.66************************* PP

                                       EEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 271 iyaiGDvaggkggpelaqaAvqqG 294
                                       ++a GD++   +g +++  A+ +G
  gi|386001392|ref|YP_005919691.1| 457 VWAGGDIT---TGGATVISAMGAG 477
                                       ********...7777777777665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.6   4.8e-07   0.00021       1      32 [.     171     202 ..     171     254 .. 0.77
   2 !   26.7   0.3   1.4e-08     6e-06       1      77 [.     311     385 ..     311     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.8e-07
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversd 32 
                                       +v+vvG+G  g+ +A+ la++g++Vtv+e+  
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMGHQVTVFEALH 202
                                       79**************************9865 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.4e-08
                                       EEEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSSTTSSHHHHHHH..HHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelg.kkVtvversdkllrllDeeaskil..qeklekngievllntkveeiegsedg.v 73 
                                       +v+vvGgG++++++A  + +lg  +V+vv r+++        + ++l   e+ +++g+ + + t++++++ +++g v
  gi|386001392|ref|YP_005919691.1| 311 RVAVVGGGNVAMDAARCAVRLGaEEVHVVYRRSEAE------MPARLeeIENAKEEGVIFDFLTNPTRFVADDRGrV 381
                                       79********************669**********9......44444225788999***************999988 PP

                                       EEEE CS
                         Pyr_redox  74 esvk 77 
                                        +++
  gi|386001392|ref|YP_005919691.1| 382 AGME 385
                                       8776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-05    0.0076     164     193 ..     169     198 ..     151     206 .. 0.71
   2 !   23.4   0.2   6.8e-08     3e-05     162     200 ..     307     346 ..     256     362 .. 0.80
   3 ?   -1.4   0.0       2.6   1.1e+03     254     292 ..     410     449 ..     394     461 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvv 193
                                       g++v+V+G++  ++ aA +l+r+g++Vtv+
  gi|386001392|ref|YP_005919691.1| 169 GKRVAVVGAGPAGITAAADLARMGHQVTVF 198
                                       667777777777777777777777777765 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.8e-08
                       Pyr_redox_3 162 yagqkvvViGgknSavDaAlelvrkga.eVtvvtrgseie 200
                                        +g++v+V+Gg+n a+DaA   vr ga eV+vv+r+se e
  gi|386001392|ref|YP_005919691.1| 307 RQGKRVAVVGGGNVAMDAARCAVRLGAeEVHVVYRRSEAE 346
                                       4699*********************9846*******9765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.6
                       Pyr_redox_3 254 kvevkddvvlatGykpdlsflkk.slfeldedgrpvltee 292
                                       ++   d v++a+G +p+  +  + +++e++++g++v++++
  gi|386001392|ref|YP_005919691.1| 410 RIVDVDTVIIAVGTTPNPLLPGNtPGLETTRWGTIVVNDS 449
                                       3444567788888888766655557777777777777765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.5   1.5e-05    0.0066      30      59 ..     171     200 ..     164     205 .. 0.90
   2 !   16.3   0.1   1.1e-05    0.0047      28      61 ..     309     343 ..     280     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                       +v v+G+G aG+ A+a  +++g +Vtv++ 
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMGHQVTVFEA 200
                                       79*************************986 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       --EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgak.VtvlDvrp 61 
                                         +v v+GgG + + A++ a++lga+ V v+  r+
  gi|386001392|ref|YP_005919691.1| 309 GKRVAVVGGGNVAMDAARCAVRLGAEeVHVVYRRS 343
                                       4479********************96366555443 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.4   3.9e-10   1.7e-07       1      33 [.     174     206 ..     174     215 .. 0.97
   2 ?    0.2   0.2       2.1   9.2e+02       1      25 [.     314     339 ..     314     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.9e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                                       +vGaG +G +aA+ La+ g++v+++e+ ++ GG
  gi|386001392|ref|YP_005919691.1| 174 VVGAGPAGITAAADLARMGHQVTVFEALHDAGG 206
                                       8*******************************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.1
                                       EE--SHHHHHHHHHHHCCTE.EEEEE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagf.dvlll 25 
                                       +vG+G  ++ aA+ + + g+ +v+++
  gi|386001392|ref|YP_005919691.1| 314 VVGGGNVAMDAARCAVRLGAeEVHVV 339
                                       8*******999999999887557765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2    0.0022      0.96       7      36 ..     169     198 ..     167     223 .. 0.94
   2 !   16.8   0.2   1.6e-05    0.0071       6      55 ..     308     387 ..     307     426 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0022
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvv 36 
                                       gk+v vvG+G+ + + +  l++ g +vtv 
  gi|386001392|ref|YP_005919691.1| 169 GKRVAVVGAGPAGITAAADLARMGHQVTVF 198
                                       89**************************96 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-05
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleaga.kvtvvapevkeele...elvklaeee........................ 54 
                                       +gk+v vvGgG+vA+  +r  ++ ga +v+vv  ++++e++   e ++ a+ee                        
  gi|386001392|ref|YP_005919691.1| 308 QGKRVAVVGGGNVAMDAARCAVRLGAeEVHVVYRRSEAEMParlEEIENAKEEgvifdfltnptrfvaddrgrvagm 384
                                       68*********************99626***9999655555433222222222455555555555433333333333 PP

                     NAD_binding_7  55 ..l 55 
                                         +
  gi|386001392|ref|YP_005919691.1| 385 evV 387
                                       330 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   4.1e-08   1.8e-05       2      41 ..     172     211 ..     171     219 .. 0.93
   2 ?    3.3   1.1     0.094        41       2      24 ..     312     334 ..     311     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.1e-08
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41 
                                       v VvG+gpaG++AA   ar+G +v + e     GG l  g
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADLARMGHQVTVFEALHDAGGVLIYG 211
                                       89*********************************98765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.094
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGak 24 
                                       v VvGGg   + AA  A r Ga+
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAE 334
                                       89*******************95 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   1.2e-07   5.4e-05       2      29 ..     172     199 ..     171     231 .. 0.88
   2 ?    0.6   0.3      0.53   2.3e+02       2      24 ..     312     334 ..     311     348 .. 0.89
   3 ?   -3.4   0.0         9   3.9e+03     132     150 ..     405     423 ..     397     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                       v V+G+G AG+ AA+ +ar+G++v+ + 
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADLARMGHQVTVFE 199
                                       89**********************9984 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.53
                                       EEEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGak 24 
                                       v V+GgG   + AA  a rlGa+
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAE 334
                                       89*****************9986 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9
                                       EETTS-EEEECEEEE--TT CS
                              GIDA 132 vtedgetikakavviatGt 150
                                        + +++++  ++v+ia Gt
  gi|386001392|ref|YP_005919691.1| 405 EKGSERIVDVDTVIIAVGT 423
                                       445667788889******9 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.9   1.3e-07   5.8e-05       2      36 ..     171     205 ..     170     210 .. 0.91
   2 ?   -3.4   0.6       6.6   2.9e+03       2      22 ..     311     331 ..     310     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +v+v+G+G+AG+ aA+ +a+ g++V+++e+ + +g
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMGHQVTVFEALHDAG 205
                                       79***************************977665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.6
                                       SEEEE--SHHHHHHHHHHHHT CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakr 22 
                                       +v+v+GgG   + aA  a + 
  gi|386001392|ref|YP_005919691.1| 311 RVAVVGGGNVAMDAARCAVRL 331
                                       699*****9988887766544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   2.6e-07   0.00011      19      83 ..     171     235 ..     162     246 .. 0.80
   2 ?   -2.8   0.2       6.9     3e+03      20      36 ..     312     328 ..     309     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.6e-07
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB..SEEEEETTTHHHHHHTT-- CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf..saivvrkpakelLdelgik 83 
                                        v++vGaG++G+taa  la+  + +v+++e+    GG    G   f   + +vr + +  ++ lg+ 
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARM-GHQVTVFEALHDAGGVLIYGIPEFrlPKAIVRSEVE-YVKSLGVT 235
                                       699******************.*********999999888887666224777777754.45556665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.9
                                       EEEE--SHHHHHHHHHH CS
                              Thi4  20 vvivGaGssGLtaayyl 36 
                                       v++vG+G   + aa+  
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCA 328
                                       8999***9999999864 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.002      0.86      34      67 ..     167     200 ..     141     224 .. 0.84
   2 !    9.9   0.0     0.001      0.45      35      72 ..     308     346 ..     283     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                       GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                        +gk+v+++G+G  G ++a  l+ +g +v++++ 
  gi|386001392|ref|YP_005919691.1| 167 QAGKRVAVVGAGPAGITAAADLARMGHQVTVFEA 200
                                       579**************************99876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                                       TTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHH CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgm.kviaydrskkke 72 
                                       +gk+v+++G G+++  +a+++  +g+ +v ++ r+ ++e
  gi|386001392|ref|YP_005919691.1| 308 QGKRVAVVGGGNVAMDAARCAVRLGAeEVHVVYRRSEAE 346
                                       79************************6565555543333 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.19        83     266     300 ..     163     197 ..     145     203 .. 0.83
   2 !   15.4   0.0   1.4e-05    0.0059     271     326 ..     308     363 ..     292     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                                       HHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEE CS
                    Oxidored_nitro 266 yheylagkrvaiygdpdrvvalarllkelGmevva 300
                                         e  agkrva++g +   +  a+ l+ +G +v +
  gi|386001392|ref|YP_005919691.1| 163 SAEFQAGKRVAVVGAGPAGITAAADLARMGHQVTV 197
                                       566778******************9999**99876 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       TT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEE CS
                    Oxidored_nitro 271 agkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepevi 326
                                       +gkrva++g++  ++  ar    lG+e v+++++ ++++  +rl+++  ++e+ vi
  gi|386001392|ref|YP_005919691.1| 308 QGKRVAVVGGGNVAMDAARCAVRLGAEEVHVVYRRSEAEMPARLEEIENAKEEGVI 363
                                       79**********************************88877777764444444555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   2.2e-06   0.00094       4      33 ..     172     201 ..     170     205 .. 0.91
   2 ?    0.7   0.1      0.56   2.5e+02       4      36 ..     312     345 ..     310     354 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       V++VGaGpaG+++a  L++ G +v++ e  
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADLARMGHQVTVFEAL 201
                                       99***********************99876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.56
                                       EEEE--SHHHHHHHHHHHHTTHH.EEEEESSSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvr.vvlvekrstt 36 
                                       V++VG+G + + +a+   + G + v++v +rs++
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAEeVHVVYRRSEA 345
                                       99*******************9878888888775 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.9   8.4e-07   0.00037       2      36 ..     172     206 ..     171     210 .. 0.91
   2 ?   -1.3   0.9         2   8.5e+02       2      29 ..     312     340 ..     311     349 .. 0.87
   3 ?    1.2   0.0      0.35   1.5e+02     149     239 ..     355     462 ..     346     471 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.4e-07
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       v V+G+G AG +AA+ +a+ G++v+v e  +  gg
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADLARMGHQVTVFEALHDAGG 206
                                       89**************************9887766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                       EEEE--SHHHHHHHHHHHHTTT.-EEEEE CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavve 29 
                                       v V+G+G   + AA  a + G+ +v vv 
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAeEVHVVY 340
                                       89************999999998999986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.35
                                       HHHHTCTEEEEESEEEEEEEECTT.EEEEEEEEET..............TTTCEEEEEES.EEEE-----GG..... CS
                     FAD_binding_2 149 esarkagvdfqerteadeLivedg.rvtGavvenp..............esgrevrirak.avvlatgGfgr.allk 208
                                       e+a++ gv f + t+ ++++ +d+ rv G++v  +               +++ +ri++   v++a g  ++  l+ 
  gi|386001392|ref|YP_005919691.1| 355 ENAKEEGVIFDFLTNPTRFVADDRgRVAGMEVVRMvlgepdesgrrrpvVEKGSERIVDVdTVIIAVGTTPNpLLPG 431
                                       56777778888999999999976669999999988888889666666663444447777779999999988865555 PP

                                       ......GSSSBSSGTT-S-HHHHHHHCTTSS CS
                     FAD_binding_2 209 ellgaaaeaettnapavtGdglalalragaa 239
                                        + g   +++ t ++  +G+  + +++ag++
  gi|386001392|ref|YP_005919691.1| 432 NTPGLETTRWGTIVVNDSGRTSREGVWAGGD 462
                                       5555556666666666666666666666665 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.012       5.1     185     218 ..     163     196 ..     149     202 .. 0.83
   2 !    9.4   0.0    0.0012      0.51     187     228 ..     298     345 ..     257     355 .. 0.74
   3 ?   -0.8   0.0       1.5   6.5e+02     141     168 ..     406     435 ..     384     489 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                       K_oxygenase 185 keellakkriaVvGsGqSaaeifedllrrqkkve 218
                                        +e +a+kr+aVvG+G  +   + dl+r  ++v+
  gi|386001392|ref|YP_005919691.1| 163 SAEFQAGKRVAVVGAGPAGITAAADLARMGHQVT 196
                                       4457899************999999999888655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                       K_oxygenase 187 e.......llakkriaVvGsGqSaaeifedllrrqkkvelklvtrseal 228
                                       +        +++kr+aVvG+G  a + ++ ++r   + e+++v r+++ 
  gi|386001392|ref|YP_005919691.1| 298 RfpeydtpIRQGKRVAVVGGGNVAMDAARCAVR-LGAEEVHVVYRRSEA 345
                                       04444445789**************98876555.556899999998865 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                       K_oxygenase 141 egeeeelearnlvlgvGtep..kiPevlek 168
                                       +g+e+ +   +++++vGt+p   +P  +  
  gi|386001392|ref|YP_005919691.1| 406 KGSERIVDVDTVIIAVGTTPnpLLPGNTPG 435
                                       567777777777777776541156665555 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.019       8.4      31      69 ..     168     209 ..     161     222 .. 0.86
   2 !   10.2   0.0     0.001      0.46      31      61 ..     308     338 ..     291     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                                       TTEEEEEE--SHHHHHHHHHHHHCT-EEE...EEEESSEEEE CS
                     ELFV_dehydrog  31 egkrvaisGsGnvgsyaallltelgakvv...avsDssGviy 69 
                                       +gkrva+ G G  g  aa  l+++g++v+   a+ D  Gv++
  gi|386001392|ref|YP_005919691.1| 168 AGKRVAVVGAGPAGITAAADLARMGHQVTvfeALHDAGGVLI 209
                                       799**********************99975567788888775 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                                       TTEEEEEE--SHHHHHHHHHHHHCT-EEEEE CS
                     ELFV_dehydrog  31 egkrvaisGsGnvgsyaallltelgakvvav 61 
                                       +gkrva+ G Gnv+  aa+++ +lga+ v v
  gi|386001392|ref|YP_005919691.1| 308 QGKRVAVVGGGNVAMDAARCAVRLGAEEVHV 338
                                       79***********************987766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.9   3.7e-06    0.0016       1      33 [.     171     205 ..     171     207 .. 0.91
   2 ?   -2.0   0.0       4.8   2.1e+03     148     207 ..     221     271 ..     218     306 .. 0.67
   3 ?    2.2   0.2      0.25   1.1e+02       1      32 [.     311     345 ..     311     349 .. 0.90
   4 ?   -0.8   0.1         2   8.8e+02     177     207 ..     398     429 ..     355     477 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       +v+++G+G +G+++A +Lar g  Vt++e+ ++ag
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMGhqVTVFEALHDAG 205
                                       59****************99999******988877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HH CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.ll 207
                                        +++  + +++lGv++ + + v +l +    v ++   ++g    +dav +  Ga++  +l
  gi|386001392|ref|YP_005919691.1| 221 IVRSEVEYVKSLGVTFELDSVVGRLVQ----VDEL--LKNG----FDAVFLGIGAGAPrFL 271
                                       555666778899999999965555632....6666..3436....5999999999988544 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.25
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSST CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdia 32 
                                       +v+++GGG + + +A+ + r g   V ++ ++++a
  gi|386001392|ref|YP_005919691.1| 311 RVAVVGGGNVAMDAARCAVRLGaeeVHVVYRRSEA 345
                                       59****************99999999999998765 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2
                                       TCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH CS
                               DAO 177 gkvwgverttp.gendaadavVnaaGawsd.ll 207
                                       g+   v +++  ++++ +d+v++a G   + ll
  gi|386001392|ref|YP_005919691.1| 398 GRRRPV-VEKGsERIVDVDTVIIAVGTTPNpLL 429
                                       555555.33332322355779999997665555 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0039       1.7       2      38 ..     170     206 ..     157     213 .. 0.64
   2 !    6.8   0.0    0.0045         2     173     211 ..     295     338 ..     251     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                          FMO-like   2 kkvaviGaGvsGlasikccleegleptcfersddiGG 38 
                                       k+vav+GaG +G+++       g + t fe  +d GG
  gi|386001392|ref|YP_005919691.1| 170 KRVAVVGAGPAGITAAADLARMGHQVTVFEALHDAGG 206
                                       5566666666666665555555666666666666555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0045
                          FMO-like 173 rdykepe....vfkgkrvlviGlGnsggdiavelsrt.aeqvll 211
                                       + y+ pe    + +gkrv v+G Gn + d a  + r  ae+v +
  gi|386001392|ref|YP_005919691.1| 295 KAYRFPEydtpIRQGKRVAVVGGGNVAMDAARCAVRLgAEEVHV 338
                                       555555522225699*************9997666642566655 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.6   0.00022     0.095       1      39 [.     173     206 ..     173     213 .. 0.87
   2 ?    2.8   0.0      0.24     1e+02     132     155 ..     399     423 ..     375     424 .. 0.74
   3 ?   -2.0   0.0       7.2   3.2e+03      37      76 ..     453     491 ..     438     493 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgag 39 
                                       a+vGaGp+G+++++ L++       +++t+f+  + +g g
  gi|386001392|ref|YP_005919691.1| 173 AVVGAGPAGITAAADLARM-----GHQVTVFEAlHDAG-G 206
                                       89***************99.....59999***988887.4 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                     NAD_binding_9 132 dgq.avlladgaslaadaVvLAlGh 155
                                       +++  v + +++ +++d V++A+G 
  gi|386001392|ref|YP_005919691.1| 399 RRRpVVEKGSERIVDVDTVIIAVGT 423
                                       33434555667788*********97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.2
                     NAD_binding_9  37 gagrvwrtdqseelllNvpasemslftddpptfaeWlrer 76 
                                        +++vw   +  +    ++ s+m + +   ++ ++Wlre 
  gi|386001392|ref|YP_005919691.1| 453 SREGVWAGGD-ITTGGATVISAMGAGKRSAEDIDRWLRED 491
                                       4566666664.33345577788888888889999999986 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.1e-05    0.0047       2      28 ..     180     206 ..     179     208 .. 0.96
   2 ?   -0.8   0.2       1.6   6.9e+02     421     451 ..     456     484 ..     443     485 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       aG++aA  L++ G++Vtv+Ea   +GG
  gi|386001392|ref|YP_005919691.1| 180 AGITAAADLARMGHQVTVFEALHDAGG 206
                                       9*********************99999 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                       TEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 421 rlffAGehtsreypgtvegAilSGlraAari 451
                                       ++   G+ t+    +tv  A+ +G+r+A++i
  gi|386001392|ref|YP_005919691.1| 456 GVWAGGDITT--GGATVISAMGAGKRSAEDI 484
                                       5555666666..6677************998 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.17        73       1      29 [.     172     200 ..     172     243 .. 0.91
   2 !   10.7   0.0    0.0013      0.56       1      45 [.     312     365 ..     312     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.17
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdp 29 
                                       ++++Gag+ +   a+ +a++g +vtv+++
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADLARMGHQVTVFEA 200
                                       579***********************986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0013
                                       EEEE--STTHHHHHHHHHHHTE.EEEEEES-GGGG-GGG-TT-SE........- CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgf.rvtvvdpreefatkerfpeade........t 45 
                                       ++++G+g+va   ar+a +lg  +v+vv  r+e++ ++r++e ++        +
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAeEVHVVYRRSEAEMPARLEEIENakeegvifD 365
                                       579******************636999999999887777776554444555551 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.024        10      11      42 ..     168     198 ..     161     201 .. 0.86
   2 !    8.0   0.1    0.0062       2.7      11      47 ..     308     344 ..     303     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.024
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                       ++k+v ++GaG  +  +a  L++ g + v+v+
  gi|386001392|ref|YP_005919691.1| 168 AGKRVAVVGAGPAGITAAADLARMGHQ-VTVF 198
                                       689******************999887.7775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0062
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47 
                                       ++k+v ++G G++a  +a+  ++ g+++v v+ R  e
  gi|386001392|ref|YP_005919691.1| 308 QGKRVAVVGGGNVAMDAARCAVRLGAEEVHVVYRRSE 344
                                       579****************************998765 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00065      0.28       8      45 ..     167     204 ..     157     229 .. 0.85
   2 ?    2.3   0.0      0.31   1.4e+02      72     106 ..     417     451 ..     402     468 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                     Rossmann-like   8 sarlsvGiisaGrvGtalgaaleraghvvvgisaisaa 45 
                                       +a   v +++aG  G + +a l+r gh+v+   a+ +a
  gi|386001392|ref|YP_005919691.1| 167 QAGKRVAVVGAGPAGITAAADLARMGHQVTVFEALHDA 204
                                       4556799***********************99998877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                     Rossmann-like  72 lllav...PdaelpglvkglaatgavraGtivahtsga 106
                                       +++av   P++ lpg   gl +t   r Gtiv+  sg 
  gi|386001392|ref|YP_005919691.1| 417 VIIAVgttPNPLLPGNTPGLETT---RWGTIVVNDSGR 451
                                       55555444889999999999887...9******99985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   1.7e-05    0.0074      29      52 .]      59      84 ..      25      84 .. 0.73
   2 ?    0.7   0.7       1.8     8e+02       7      16 ..     114     123 ..     112     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-05
                            Fer4_7 29 ekveidpekClgCga..CvavCPtga 52
                                      ++++ ++++C++C++  C++ CP+g+
  gi|386001392|ref|YP_005919691.1| 59 DQAAEEADRCIQCKNprCMEGCPVGI 84
                                      5668899*******999*******96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.8
                            Fer4_7   7 aCvaaCpvka 16 
                                        C ++Cp+++
  gi|386001392|ref|YP_005919691.1| 114 ICGRVCPQEV 123
                                       6777777654 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 !   10.8   1.0   0.00076      0.33       2      30 ..     172     200 ..     171     210 .. 0.91
   2 ?    4.7   0.0     0.058        26       2      44 ..     312     356 ..     311     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00076
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi 30 
                                       vav+GaG  G   aa +a+ g++V++++ 
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADLARMGHQVTVFEA 200
                                       9************************9986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.058
                                       EEEE--SCCHHHHHHHHHHTT-.EEEEE-S.-HHHHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagl.eVvlvdi.seealekalekiek 44 
                                       vav+G G +    a  +++ g  eV++v + se+ + + le+ie+
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAeEVHVVYRrSEAEMPARLEEIEN 356
                                       9******************99835888776244555555555555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.17        74       1      30 [.     171     197 ..     171     204 .. 0.92
   2 ?    9.1   0.0    0.0044       1.9       1      46 [.     311     354 ..     311     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.17
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEE CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivv 30 
                                       +++++GaG  g + a  l++ g   h+++v
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMG---HQVTV 197
                                       69********************...99996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0044
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeel 46 
                                       +++++G+Gn++   a+ +++ g  ++e+ v+ +r++ ++ +  ee+
  gi|386001392|ref|YP_005919691.1| 311 RVAVVGGGNVAMDAARCAVRLG--AEEVHVVYRRSEAEMPARLEEI 354
                                       69********************..8888888899887665555554 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6     0.032        14      53     101 ..     167     233 ..     136     261 .. 0.77
   2 ?    8.0   0.0    0.0039       1.7      53      90 ..     307     345 ..     282     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.032
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE..................EETTS-HHHHHHHHHTT CS
                              PALP  53 tgaktvveassGNhgralAaaaallGlkvtiv..................vpadaspekvallrllG 101
                                       +++k+v++ ++G +g+ +Aa  a++G +vt++                  +p+    + v+  ++lG
  gi|386001392|ref|YP_005919691.1| 167 QAGKRVAVVGAGPAGITAAADLARMGHQVTVFealhdaggvliygipefrLPKAIVRSEVEYVKSLG 233
                                       68999**************************977666666666666666666666666666666666 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0039
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-.EEEEEEETTS- CS
                              PALP  53 tgaktvveassGNhgralAaaaallGl.kvtivvpadas 90 
                                       +++k+v++ ++GN ++ +A +a +lG  +v++v  ++  
  gi|386001392|ref|YP_005919691.1| 307 RQGKRVAVVGGGNVAMDAARCAVRLGAeEVHVVYRRSEA 345
                                       46799*********************9799999766654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7   4.7e-05     0.021      44      78 ..      51      87 ..      23     114 .. 0.79
   2 ?   -1.9   0.2       8.2   3.6e+03      65      76 ..     113     124 ..      99     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.7e-05
                           Fer4_18 44 kkalkekeerkekgagdcidces..cvkvcPtgidir 78
                                      ++al   e++++++a  ci+c+   c++ cP+gidi 
  gi|386001392|ref|YP_005919691.1| 51 EVALGYAEDQAAEEADRCIQCKNprCMEGCPVGIDIP 87
                                      44555667778888999****9555**********95 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.2
                           Fer4_18  65 escvkvcPtgid 76 
                                       + c +vcP ++ 
  gi|386001392|ref|YP_005919691.1| 113 GICGRVCPQEVQ 124
                                       579999998875 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0012      0.51      18      42 ..     169     193 ..     154     199 .. 0.88
   2 ?    1.7   0.0      0.31   1.4e+02      18      48 ..     308     339 ..     294     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                                       TSEEEEE--SHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  18 dskvllvGaGglGsellknLalsGv 42 
                                        ++v++vGaG  G  ++ +La++G 
  gi|386001392|ref|YP_005919691.1| 169 GKRVAVVGAGPAGITAAADLARMGH 193
                                       489********************95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.31
                                       T.SEEEEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  18 d.skvllvGaGglGsellknLalsGvgkltlv 48 
                                       + ++v++vG G +   +++  +++G +++++v
  gi|386001392|ref|YP_005919691.1| 308 QgKRVAVVGGGNVAMDAARCAVRLGAEEVHVV 339
                                       4489***********************99997 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0013      0.55       6      53 ..     153     199 ..     149     203 .. 0.88
   2 ?    0.3   0.0       1.4   6.3e+02      22      48 ..     308     334 ..     287     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                                       CCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE- CS
                     AdoHcyase_NAD   6 reslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivte 53 
                                       +++l d  +r++++  aGk + v+G G  G  +aa l  +G +v+v e
  gi|386001392|ref|YP_005919691.1| 153 KNALPDRPRRSAEF-QAGKRVAVVGAGPAGITAAADLARMGHQVTVFE 199
                                       77888888888775.69***************************9987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                                       TTSEEEEE--SHHHHHHHHHHHHCT-E CS
                     AdoHcyase_NAD  22 aGkvavvaGyGdvGkGcaaslkglGar 48 
                                        Gk + v+G G+v   +a++   lGa 
  gi|386001392|ref|YP_005919691.1| 308 QGKRVAVVGGGNVAMDAARCAVRLGAE 334
                                       69************9999988888874 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0075       3.3      38      59 ..     177     198 ..     161     239 .. 0.88
   2 ?    3.3   0.0      0.15        66      30      69 ..     312     349 ..     295     374 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0075
                            YjeF_N  38 nGgdglaaArhLaqegakVtvl 59 
                                        G  g+ aA+ La++g++Vtv+
  gi|386001392|ref|YP_005919691.1| 177 AGPAGITAAADLARMGHQVTVF 198
                                       5899*****************5 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                            YjeF_N  30 lvlvGsgnnGgdglaaArhLaqegakVtvllleeeeklde 69 
                                       + +vG+gn   d+  +A  L  e+++V     ++e+++++
  gi|386001392|ref|YP_005919691.1| 312 VAVVGGGNVAMDAARCAVRLGAEEVHVVY--RRSEAEMPA 349
                                       56789999999998888888666655544..444445543 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.03        13      28      64 ..     161     196 ..     139     230 .. 0.70
   2 ?    4.7   0.0     0.044        19      29      72 ..     303     346 ..     280     395 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.03
                                       -........-SEEEEEESTTHHHHHHHHH.HHHGEEEE CS
                           DUF4147  28 e.eldlskkkrvvvvgaGKAaaamaaaleeealksgvv 64 
                                       + +++ ++ krv vvgaG A ++ aa l++  ++++v 
  gi|386001392|ref|YP_005919691.1| 161 RrSAEFQAGKRVAVVGAGPAGITAAADLAR--MGHQVT 196
                                       236677888************999988873..343333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                                       .......-SEEEEEESTTHHHHHHHHH.HHHG.EEE.EEEETT--- CS
                           DUF4147  29 eldlskkkrvvvvgaGKAaaamaaaleeealk.sgv.vvvkkghae 72 
                                        + +++ krv vvg G+ a+  a+++   +l+ + v vv ++ +ae
  gi|386001392|ref|YP_005919691.1| 303 DTPIRQGKRVAVVGGGNVAMDAARCAV--RLGaEEVhVVYRRSEAE 346
                                       4567799****************8877..34433331444433333 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00039      0.17       2      32 ..     172     200 ..     171     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvliea 32 
                                       v+v+GaGpAg+  Aa l  a++g +v++ ea
  gi|386001392|ref|YP_005919691.1| 172 VAVVGAGPAGITAAADL--ARMGHQVTVFEA 200
                                       89***************..999999999887 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00056      0.25       2      28 ..     171     197 ..     170     202 .. 0.94
   2 ?   -1.4   0.1       3.3   1.5e+03       2      25 ..     311     334 ..     310     399 .. 0.67
   3 ?    0.3   0.1         1   4.4e+02      69      87 ..     406     424 ..     395     437 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                                       EEEEE--STTHHHHHHHHHHCTSEEEE CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevig 28 
                                       +++v+G+G  G++ aa la++gh+v++
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMGHQVTV 197
                                       89***********************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                                       EEEEE--STTHHHHHHHHHHCTSE CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighe 25 
                                       +++v+G G v +  a +  ++g e
  gi|386001392|ref|YP_005919691.1| 311 RVAVVGGGNVAMDAARCAVRLGAE 334
                                       677777777776666665555532 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1
                                       -HHHHHHC-SEEEE----- CS
                    UDPG_MGDP_dh_N  69 dvekaveeadvifiaVgTP 87 
                                       + ++ + + d ++iaVgT 
  gi|386001392|ref|YP_005919691.1| 406 KGSERIVDVDTVIIAVGTT 424
                                       557788999*******984 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   0.00017     0.075       1      33 [.     171     200 ..     171     214 .. 0.92
   2 ?   -0.7   0.1       1.2     5e+02       1      28 [.     311     338 ..     311     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                       ++ +vG+G+aG +aAa la+++   ++vt+ e+
  gi|386001392|ref|YP_005919691.1| 171 RVAVVGAGPAGITAAADLARMG---HQVTVFEA 200
                                       689*******************...88998875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEE CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklev 28 
                                       ++ +vGGG  +  aA    + + ++++v
  gi|386001392|ref|YP_005919691.1| 311 RVAVVGGGNVAMDAARCAVRLGAEEVHV 338
                                       689*******999998888877665554 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   9.4     0.001      0.45       5      55 ..      64     129 ..      60     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                           Fer4_10   5 dddtCirCg..kCvkaCPadl............tsvgakgeaseeeavrkkvek.CtgcgaCveaC 55 
                                       ++d+Ci+C+  +C++ CP+ +            ++ +a  +++ ++   + +++ C++  +C + C
  gi|386001392|ref|YP_005919691.1|  64 EADRCIQCKnpRCMEGCPVGIdipafiravrdgEMEDAVRIIKAKNSLPGICGRvCPQEVQCESRC 129
                                       789******99********99999999887544444444444444444443332244445777777 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.79   3.5e+02      21      35 ..     165     179 ..     151     194 .. 0.82
   2 ?    7.0   0.0    0.0096       4.2     129     161 ..     306     338 ..     277     339 .. 0.74
   3 ?   -1.4   0.0       3.7   1.6e+03      50      64 ..     415     429 ..     410     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.79
                        MAF_flag10  21 kfkgnkpaiivgaGP 35 
                                       +f+  k + +vgaGP
  gi|386001392|ref|YP_005919691.1| 165 EFQAGKRVAVVGAGP 179
                                       5644699******** PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0096
                        MAF_flag10 129 leeekneilfgGgsvantaldlAvklgfkeIil 161
                                       +++ k++ + gGg+va  a  +Av+lg++e+++
  gi|386001392|ref|YP_005919691.1| 306 IRQGKRVAVVGGGNVAMDAARCAVRLGAEEVHV 338
                                       3344455899********************986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.7
                        MAF_flag10  50 kaviiaadtalkaLl 64 
                                       + viia++t+ ++Ll
  gi|386001392|ref|YP_005919691.1| 415 DTVIIAVGTTPNPLL 429
                                       579*******99997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.1   0.00048      0.21      44      65 .]      51      84 ..      16      84 .. 0.63
   2 ?    9.5   6.9    0.0031       1.3       2      63 ..      65     121 ..      64     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00048
                            Fer4_8 44 e..........eealwsCttcga..CtevCpvgi 65
                                      e          +e +++C +c++  C e Cpvgi
  gi|386001392|ref|YP_005919691.1| 51 EvalgyaedqaAEEADRCIQCKNprCMEGCPVGI 84
                                      0233333344468899999999888999999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0031
                            Fer4_8   2 lekCieCg..aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +++Ci+C   +C++ Cpv  +   ++   r++ +ed+++  +        + +  g C +vCp+
  gi|386001392|ref|YP_005919691.1|  65 ADRCIQCKnpRCMEGCPVGIDIPAFIRAVRDGEMEDAVRIIK-------AKNSLPGICGRVCPQ 121
                                       789****888*************9999999999995544433.......333444444444444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   0.00041      0.18      35      61 .]      57      85 ..      20      85 .. 0.68
   2 ?    0.6   1.6         2   8.6e+02      51      60 ..     114     123 ..     110     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00041
                           Fer4_17 35 eeaekeekaslCieCg..eCerkCPqgld 61
                                       e ++ e+a++Ci+C+  +C + CP g+d
  gi|386001392|ref|YP_005919691.1| 57 AEDQAAEEADRCIQCKnpRCMEGCPVGID 85
                                      22345589*******9556******9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2
                           Fer4_17  51 eCerkCPqgl 60 
                                        C r+CPq++
  gi|386001392|ref|YP_005919691.1| 114 ICGRVCPQEV 123
                                       6999999987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.1    0.0023         1       6      21 ..      64      81 ..      60      82 .. 0.89
   2 ?    0.1   0.3       2.5   1.1e+03      14      22 .]     113     121 ..     113     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0023
                            Fer4_2  6 dtdrCigCg..aCvsaCP 21
                                      ++drCi+C+   C   CP
  gi|386001392|ref|YP_005919691.1| 64 EADRCIQCKnpRCMEGCP 81
                                      579*****999******* PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.5
                            Fer4_2  14 gaCvsaCPa 22 
                                       g+C  +CP+
  gi|386001392|ref|YP_005919691.1| 113 GICGRVCPQ 121
                                       78999***5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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):              41  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3643.91
//
Query:       gi|386001393|ref|YP_005919692.1|  [L=259]
Description: Formate/nitrite family transporter [Methanosaeta harundinacea 6Ac]
Scores for complete 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-87  291.0  28.2    6.2e-87  290.8  28.2    1.0  1  Form_Nir_trans  Formate/nitrite transporter


Domain annotation for each model (and alignments):
>> Form_Nir_trans  Formate/nitrite transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.8  28.2   3.5e-91   6.2e-87       6     236 .]      13     255 ..       8     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 290.8 bits;  conditional E-value: 3.5e-91
                                       HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCT...TCHHHHHHHHHCCCHHHHHHHHHT---CCC CS
                    Form_Nir_trans   6 vvaagvkkaklsldklfllgilAGafigfgvllalvvaaalaes...npglakllgglvFpvGlilvvllgaeLfTg 79 
                                       v + g +k+ + +  l+ lg+lAGafi+fg+lla++v++++++    npgl+k+++g+vFpvGlilvv++gaeLfTg
  gi|386001393|ref|YP_005919692.1|  13 VDNIGCNKIGMAMGPLLALGFLAGAFIAFGGLLAVIVGGGVPDIklaNPGLQKFIFGAVFPVGLILVVVAGAELFTG 89 
                                       6678999**********************************988********************************* PP

                                       CCCHHHHHHCTTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTGG.....HHHHHHHHHCCCSS-HHHHHHHHH CS
                    Form_Nir_trans  80 ntllltlavlkkkvslkkllknwlvvllgNliGsllvalllvvlsgll.....aekllsiaeaklslsfleaflrGi 151
                                       nt+ ++ avl++k+s++ l++nw+++++gNliGsl+v+l+l++++gl+      + +  iaeak+s+ f+ +f++G+
  gi|386001393|ref|YP_005919692.1|  90 NTACCVPAVLSGKASWSGLARNWTFSYVGNLIGSLFVVLFLTYMTGLFasdpwLSSITGIAEAKVSQGFWPLFFKGV 166
                                       ***********************************************777777************************ PP

                                       HHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHH....SHHHHHHHCHHHHHHHHHH CS
                    Form_Nir_trans 152 lCNwlVclavwlalaakdvigkilaiflpifafvasgfeHsvanmfliplglll....tvadfilknlipvtlGNiv 224
                                       +CNwlVclavwla+a++dv++k++++++pi+afva+gfeHsvanmf+ip+g+++    t+adf++ nlipvtlGNiv
  gi|386001393|ref|YP_005919692.1| 167 GCNWLVCLAVWLAIASDDVASKVFGVWFPIMAFVAIGFEHSVANMFFIPAGIMYgaavTWADFFIANLIPVTLGNIV 243
                                       ****************************************************999999******************* PP

                                       HHHCCHHHHHHH CS
                    Form_Nir_trans 225 GGallvgllyly 236
                                       GGal+vg +y+y
  gi|386001393|ref|YP_005919692.1| 244 GGALFVGAIYWY 255
                                       ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1639.56
//
Query:       gi|386001394|ref|YP_005919693.1|  [L=108]
Description: hypothetical protein Mhar_0692 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00059   20.6   5.4    0.00093   20.0   5.4    1.3  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola
  ------ inclusion threshold ------
      0.019   14.9   0.2      0.023   14.6   0.2    1.2  1  DUF1065        Protein of unknown function (DUF1065)
       0.02   14.9   1.4       0.33   10.9   2.2    1.9  2  MetOD1         Metanogen output domain 1


Domain annotation for each model (and alignments):
>> 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 !   20.0   5.4   1.6e-07   0.00093      79     142 ..      36     101 ..      11     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.6e-07
                     ATC_hydrolase  79 leedkdeleidvtrCpyceawkkeGlp.elgkllC.eiDkavaeginpkvklertktlaeGgdcCd 142
                                         ++ +e+ +++t Cp+ + + + G +   +   C e+    +e++np++ +++tk + +G+dcC+
  gi|386001394|ref|YP_005919693.1|  36 SGSSGGEVVMKITGCPLLKEAMEIGADcGELSATCqEYVRSAVENLNPRCTFRYTKCMCSGDDCCE 101
                                       33478999***************9995467778899*****************************7 PP

>> DUF1065  Protein of unknown function (DUF1065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   3.9e-06     0.023      20      57 ..      20      57 ..      15      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-06
                           DUF1065 20 cvvvsmlyspffsndvkassyagavfkgsgcimdrnsf 57
                                      cvv  ++y p fs  v  ss    v+k +gc + ++++
  gi|386001394|ref|YP_005919693.1| 20 CVVSNVIYGPNFSWVVSGSSGGEVVMKITGCPLLKEAM 57
                                      9******************************8777665 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.015        91     104     130 ..       9      35 ..       5      40 .. 0.89
   2 ?   10.9   2.2   5.6e-05      0.33      82     149 ..      31     101 ..      15     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.015
                            MetOD1 104 WgeearknPifCllcraivsrsftwtg 130
                                       W+ +++   +fC+++  i    f+w+ 
  gi|386001394|ref|YP_005919693.1|   9 WDGDSEAGEVFCVVSNVIYGPNFSWVV 35 
                                       9999999************99999985 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.6e-05
                            MetOD1  82 fgiktekkedeknvlleftnCpWgeearknPi....fCllcraivsrsftwtglkgsveqkktlgngdekCv 149
                                       f   +   + + +v++++t Cp  +ea +       ++  c+  v   ++  + ++ ++ +k++ +gd++C+
  gi|386001394|ref|YP_005919693.1|  31 FSWVVS-GSSGGEVVMKITGCPLLKEAMEIGAdcgeLSATCQEYVRSAVENLNPRCTFRYTKCMCSGDDCCE 101
                                       555555.456667889999999999997655411227799*******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 818.06
//
Query:       gi|386001395|ref|YP_005919694.1|  [L=172]
Description: hypothetical protein Mhar_0693 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-19   71.3   0.0      7e-18   65.4   0.0    2.0  2  DUF45         Protein of unknown function DUF45
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.022   14.6   0.0    1.5  1  SprT-like     SprT-like family
      0.033   14.3   0.0      0.057   13.5   0.0    1.3  1  WLM           WLM domain
       0.16   12.1   0.0       0.21   11.7   0.0    1.2  1  Reprolysin_5  Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0091        41       2      53 ..      14      64 ..      13      84 .. 0.78
   2 !   65.4   0.0   1.6e-21     7e-18     137     193 ..      86     142 ..      75     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0091
                             DUF45  2 nlrlrvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleerakeaek 53
                                      +l+ r+ + g+++v aP  +s++e+ + v + ++ +  k+ + ++++ ++++
  gi|386001395|ref|YP_005919694.1| 14 TLQARMVE-GTLVVMAPAAISDRELAEHVSRFRARMALKMGERDDAHLARRA 64
                                      67778888.99******************99888888888777775444444 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 1.6e-21
                             DUF45 137 kdmktrWGsc.sskgkirlnwrLvkappevidYVvvHElaHlleknHskrFwalvekl 193
                                       + + +r+Gsc  ++g+ir++ rL  ap+ v dYVvvHElaHlle+ H krF +lv ++
  gi|386001395|ref|YP_005919694.1|  86 R-QMKRFGSCtIEDGTIRISSRLKDAPQWVEDYVVVHELAHLLEPSHDKRFRELVGRY 142
                                       3.4459*************************************************987 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.9e-06     0.022       6      76 ..      65     127 ..      60     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                         SprT-like   6 kklddavfggqaaggvkiiwskrlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHla 76 
                                       ++l++++f+g  +    i+ s+r  +  G ++++        +I++s++l d  ++     +++HEl+Hl+
  gi|386001395|ref|YP_005919694.1|  65 DHLNRKYFDGL-LRWRGISYSDRQMKRFGSCTIED------GTIRISSRLKDA-PQWVEDYVVVHELAHLL 127
                                       68999999999.7777889999999**********......***********9.7777788********97 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.3e-05     0.057      86     107 ..     118     139 ..     114     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                               WLM  86 tllHELaHnvygpHdakFyall 107
                                       + +HELaH +   Hd++F +l+
  gi|386001395|ref|YP_005919694.1| 118 VVVHELAHLLEPSHDKRFRELV 139
                                       679***************9886 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.7e-05      0.21     132     160 ..     101     133 ..      66     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                      Reprolysin_5 132 s....nsvvvstatevqvvaHElGHnfGavHDc 160
                                            + +   ++ e++vv HEl H +  +HD 
  gi|386001395|ref|YP_005919694.1| 101 IrissRLKDAPQWVEDYVVVHELAHLLEPSHDK 133
                                       23444566677999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1146.83
//
Query:       gi|386001396|ref|YP_005919695.1|  [L=69]
Description: Molybdenum-pterin-binding-protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-17   62.4   2.1    4.1e-17   62.2   2.1    1.0  1  TOBE      TOBE domain
    0.00014   22.0   0.4    0.00016   21.8   0.4    1.1  1  TOBE_2    TOBE domain


Domain annotation for each model (and alignments):
>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   2.1   4.5e-21   4.1e-17       2      64 .]       4      66 ..       3      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 4.5e-21
                              TOBE  2 sarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64
                                      sarN+l g+V+ v+ + +++eV v+l+gg+++++++t+rsaeeLgL+ G+eV +++ka++v++
  gi|386001396|ref|YP_005919695.1|  4 SARNVLSGRVKSVTYGVVSAEVVVELSGGEEIVSVITKRSAEELGLSEGKEVLVVVKATSVMI 66
                                      9************************************************************86 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.4   1.8e-08   0.00016       8      73 ..       1      64 [.       1      66 [. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-08
                            TOBE_2  8 lrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadr.dsalapGdtVelswdpdda 73
                                      +++   +++n lsG+V++v+y   s ++vvel gg+++v +   +++ +  l +G +V + +++ ++
  gi|386001396|ref|YP_005919695.1|  1 MQI---SARNVLSGRVKSVTYGVVSAEVVVELSGGEEIVSVITKRSAeELGLSEGKEVLVVVKATSV 64
                                      567...6779***************************99988888887899*******998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 505.84
//
Query:       gi|386001397|ref|YP_005919696.1|  [L=457]
Description: RNA-metabolising metallo-beta-lactamase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-27   95.9   0.0      3e-27   95.1   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    7.5e-16   57.8   0.0    1.7e-15   56.6   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    2.4e-08   34.2   2.6    3.4e-07   30.5   2.6    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    6.5e-06   25.8   0.1    2.1e-05   24.2   0.1    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00049   19.6   0.0    0.00086   18.8   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0   8.4e-31     3e-27       1     110 []     246     371 ..     246     371 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 8.4e-31
                                       HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG........................E-SHH....H CS
                         Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae........................veakslewme 53 
                                       +qe++y+L+++ ++++l    ++ ++dsp+a++ate+Y +++e                        v++++    e
  gi|386001397|ref|YP_005919696.1| 246 TQEIIYELNHYAERGRL--EGVKTFVDSPMAISATEIYSRHPEyfdeetlrllssgdnpldfpgieyVRSRE----E 316
                                       7***********99774..347****************************************9999988888....8 PP

                                       HHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  54 skkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       sk+  +n+ k+  +i+++sgm++gGr++++l+++++++++tv+++gyqaegT gr l
  gi|386001397|ref|YP_005919696.1| 317 SKA--INDMKDAHIIISASGMCTGGRVVHHLAQNIGRRESTVLFIGYQAEGTTGRML 371
                                       888..99999********************************************975 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   4.9e-19   1.7e-15       3      62 .]     386     448 ..     384     448 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 4.9e-19
                             RMMBL   3 pvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       +v+ar+e++d fS+H ++ +ll+++r++k  +  v+++HGe+ea +++a+++++e++ +v++P
  gi|386001397|ref|YP_005919696.1| 386 NVRARVEYLDaFSAHVGRTGLLNWLRSFKEFPrqVFINHGEPEASRSFAEAIRSEFDAEVVVP 448
                                       79***************************66666*************************9998 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   2.6   9.5e-11   3.4e-07      20     163 ..      28     197 ..      17     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 9.5e-11
                                       ES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCH CS
                       Lactamase_B  20 iDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgl 96 
                                       +D+G+ + ++  + +    g +p+ + a+ilTH+H+DH G  + lv++     ++   +++ l + +++d+a   + 
  gi|386001397|ref|YP_005919696.1|  28 VDAGLFQGRDSDR-NRGGFGHDPRSLGALILTHAHVDHSGRIPLLVKEGFSGEVYSTPATEDLCEIMLKDSAYLMKE 103
                                       5666666666655.45668999*********************************************9999888888 PP

                                       H.........................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEE CS
                       Lactamase_B  97 l.........................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlft 148
                                       +                          ++ +++kp+    ++d+++++ r+l    g+  g+  + ++ gg+++lft
  gi|386001397|ref|YP_005919696.1| 104 EadresrhpdqrngeprpplytdedvSYALRRFKPVDYYKVQDIGGASARFL--DAGHIIGSAMVELSVGGRRLLFT 178
                                       899*******************986544444444444433333333333333..356778899999999******** PP

                                       CTTTSSHHCCCCCC..... CS
                       Lactamase_B 149 GDallagetgridl....t 163
                                       GD++ +g   + d+    +
  gi|386001397|ref|YP_005919696.1| 179 GDMGRRGAPFLRDPdrveE 197
                                       *******999999944441 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   5.7e-09   2.1e-05      22     170 ..      43     211 ..      24     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.7e-09
                                       -SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEEHHHHH...HCCTTCGHHHCHTT..........T CS
                     Lactamase_B_2  22 velrdelppidaVllthaHyDHlaglltlre..lrpkklplyapkgvla...vleanfvylaleee..........p 83 
                                       +   ++++++ a++lthaH+DH   ++ l +  +++   ++y ++ + +   ++ + + yl++ee+           
  gi|386001397|ref|YP_005919696.1|  43 GGFGHDPRSLGALILTHAHVDHSGRIPLLVKegFSG---EVYSTPATEDlceIMLKDSAYLMKEEAdresrhpdqrN 116
                                       3478999****************99**999976555...46655444443336666667777777755555555665 PP

                                       TEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C.....TCCE-TTTSEEEEEE..CTTEEEEEESS-S---HHHH.. CS
                     Lactamase_B_2  84 avnvheldwgesfelgdggleitatparhksgr.....rldrnagdtlGlrie..gggkrvyyigDtgyipeeig.. 151
                                       ++++ +l ++e ++ +    +++++             r+ +    + + ++e   gg+r++++gD+g+  +     
  gi|386001397|ref|YP_005919696.1| 117 GEPRPPLYTDEDVSYAL--RRFKPVDYYKVQDIggasaRFLDAGHIIGSAMVElsVGGRRLLFTGDMGRRGAPFLrd 191
                                       66666666777777752..24555554444444444433333333444444557789***********777433335 PP

                                       .HHHCT-SEEEEE-S-SSTT CS
                     Lactamase_B_2 152 .erlggadllllditayedd 170
                                        +r++ ad l+++ t+ + d
  gi|386001397|ref|YP_005919696.1| 192 pDRVEEADWLVIESTYGNRD 211
                                       58999******999976654 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.4e-07   0.00086      34     158 ..      50     177 ..      18     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.4e-07
                     Lactamase_B_6  34 ptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpedseel......... 101
                                        ++ + +L+ha ++h G  +ll+++     + + +vy+t ++  L +++l d++   + ++  +s++          
  gi|386001397|ref|YP_005919696.1|  50 RSLGALILTHAHVDHSGRIPLLVKE-----GFSGEVYSTPATEDLCEIMLKDSAYLMKEEADRESRHPdqrngeprp 121
                                       567789***********99988875.....4578****************887643333333322222333444555 PP

                     Lactamase_B_6 102 ...eledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivY 158
                                          + ed++ a  ++k++ Y   +++ +  ++     + aGh +G ++ ++s +  ++++
  gi|386001397|ref|YP_005919696.1| 122 plyTDEDVSYALRRFKPVDYYKVQDIGGASAR----FLDAGHIIGSAMVELSVGGRRLLF 177
                                       55577******************999976544....468999999998887776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3348.70
//
Query:       gi|386001398|ref|YP_005919697.1|  [L=367]
Description: Aspartate aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-61  208.9   0.0    1.4e-61  208.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    4.1e-09   36.2   0.0    6.6e-09   35.5   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    4.1e-08   32.6   0.0    6.5e-08   31.9   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    1.2e-05   24.0   0.0    1.8e-05   23.4   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0039   16.5   0.4     0.0061   15.9   0.4    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0059   15.5   0.0      0.071   12.0   0.0    2.0  2  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.099   12.5   0.0    1.7  1  NIR_SIR_ferr     Nitrite/Sulfite reductase ferredoxin-like ha


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   0.0   5.4e-65   1.4e-61       4     362 ..      27     362 ..      24     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 5.4e-65
                                       EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                       inLg +++++d    t++++++a++e  +  ++++ y+ + g pel+ al + l+ +++l++ +  ++ v+sGa+++
  gi|386001398|ref|YP_005919697.1|  27 INLGLGQPDFD----TPDHIKQAAIE--AIEEGFTGYTMNLGIPELRAALSEKLRLENGLDYAPA-EIMVTSGASEA 96 
                                       9**********....**********9..999**********************************.*********** PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                       + ++i+   ++ gde+l+ dp + sy    r s+g  v++p++  e fhl++ea+ e ++       +t+ ++v+sp
  gi|386001398|ref|YP_005919697.1|  97 LFLAIASV-VEEGDEVLMGDPGFVSYAALTRVSQGRPVSVPMD--ERFHLTAEAVAERVTP------RTRALIVNSP 164
                                       ********.9*******************************88..***************9......********** PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEE CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyil 234
                                       +NPtG+v t+eel++l++la+ +++ l++De+Y+ f ++ + a    a+ +e  n+++ + +sK ++++G+R+Gy++
  gi|386001398|ref|YP_005919697.1| 165 NNPTGSVQTREELRALAELAEDHGFALISDEVYEQFIYEGEHAS--PALYSE--NVITINAVSKTYAMTGWRLGYLA 237
                                       ***************************************76332..344444..59********************* PP

                                       EEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEE CS
                     Aminotran_1_2 235 gnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfll 309
                                       +  + ++ + k+++ +    ss+ q+a++aa+s +++    +  mr+++ +rr++l+++L++ g ++  + ++++ +
  gi|386001398|ref|YP_005919697.1| 238 ARGEALENMLKVHQYVQAcaSSISQRAALAAVSGPQD---CVRMMREEFRRRRDVLVEGLRRMGAEMDVPAGAFYAF 311
                                       *************9887777****************7...9************************************ PP

                                       EEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 310 tdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                         +     +++s  L++  gv+ +pg+ f+   + ++Ri++ + + ++++ ++e+
  gi|386001398|ref|YP_005919697.1| 312 PKVGDG--DAVSARLIKA-GVVAVPGSAFGSaaRDHIRISY-AASMADIRTALER 362
                                       999977..89999*****.*************999******.8888999999887 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   2.6e-12   6.6e-09      43     144 ..      89     194 ..      59     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.6e-12
                                       EESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE... CS
                   DegT_DnrJ_EryC1  43 avssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl... 116
                                        +s +++Al la+    v++gdeV++   +Fv+ a+  + +  +pv v +d + + ++++a+++ +t+rt+a +   
  gi|386001398|ref|YP_005919697.1|  89 VTSGASEALFLAIAS-VVEEGDEVLMGDPGFVSYAALTRVSQGRPVSVPMD-ERFHLTAEAVAERVTPRTRALIvns 163
                                       345567899999865.5778*******************************.89******************98333 PP

                                       EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 117 pVhlyGqva...dmdalkaiaakhglkvieD 144
                                       p +  G v    ++ al ++a++hg  +i+D
  gi|386001398|ref|YP_005919697.1| 164 PNNPTGSVQtreELRALAELAEDHGFALISD 194
                                       3456777765669999*************99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.5e-11   6.5e-08      62     165 ..      85     181 ..      70     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.5e-11
                                       GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--T CS
                       Aminotran_5  62 eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllne 138
                                        ei++tsG++ea+ l++ s+   +++gde+++++ +  +   +  ++++ + +    +p+de+ +l+ +++++ +++
  gi|386001398|ref|YP_005919697.1|  85 AEIMVTSGASEALFLAIASV---VEEGDEVLMGDPGFVSYA-ALTRVSQGRPV---SVPMDERFHLTAEAVAERVTP 154
                                       69******************...**************9999.88888755444...56******************* PP

                                       TEEEEEEESBETTTTEB--HHHHHHHH CS
                       Aminotran_5 139 ktklvaithvsnvtGtiqpveeigkla 165
                                       +t++++++  +n tG +q  ee+ +la
  gi|386001398|ref|YP_005919697.1| 155 RTRALIVNSPNNPTGSVQTREELRALA 181
                                       ***************999877765544 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   7.2e-09   1.8e-05      64     175 ..      80     196 ..      64     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.2e-09
                                       HHT-SEEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTE CS
                   Cys_Met_Meta_PP  64 LeggeaalavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikent 138
                                       L+ + a ++v+sG + A+++ai +++++Gde+++ d  + +  +l +    + +++ ++      +e++++ ++++t
  gi|386001398|ref|YP_005919697.1|  80 LDYAPAEIMVTSGASeALFLAIASVVEEGDEVLMGDPGFVSYAALTRVSQGRpVSVPMDERFHLTAEAVAERVTPRT 156
                                       555667788889986699*********************876666665555555666666666899*********** PP

                                       EEEEEESS-TTTT---...-HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 139 klvylEtptnpllkvv...DiekiaklakkagvlvvvDnt 175
                                       +++ + +p np+ +v     ++++a+la ++g  ++ D +
  gi|386001398|ref|YP_005919697.1| 157 RALIVNSPNNPTGSVQtreELRALAELAEDHGFALISDEV 196
                                       ************9886333788899999999988888865 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   2.4e-06    0.0061      50     167 ..      86     194 ..      42     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                                       EEEES-HHHHHHHHH..HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TT CS
                   Beta_elim_lyase  50 alfvpqGtaAnsill..killqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgah 124
                                        + v++G a++++ l  + +++ g+ev++++p+ +      a+  +++ +++ ++ +e   +++e++++ +++    
  gi|386001398|ref|YP_005919697.1|  86 EIMVTSG-ASEALFLaiASVVEEGDEVLMGDPGFV---SYAALTRVSQGRPVSVPMDERFHLTAEAVAERVTP---- 154
                                       4446666.445443322777899999999999855...5577888888899*******999999999999988.... PP

                                       S-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 125 eekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                         +++++++   nn   G v + eelr++a++a+++g  l+ D
  gi|386001398|ref|YP_005919697.1| 155 --RTRALIVNSPNN-PTGSVQTREELRALAELAEDHGFALISD 194
                                       ..577777777777.58*********************99988 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   2.8e-05     0.071     127     237 ..     145     269 ..     137     297 .. 0.74
   2 ?    1.3   0.0      0.05   1.3e+02     309     362 ..     311     366 ..     298     367 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                                       STT-.--S..S-EEEEEESS-TTT----..----......-TT-EEEEEE-TT....-STTTS---S-B--SEEEEE CS
                       Alliinase_C 127 aaayvkkknpeefielvtsPnnPdgllr..eavv......kgseakviyDlay....YWPhytpitskadedimLft 191
                                       a+a +++ +p+    +v sPnnP g ++  e++       +++   +i D +y    Y  +++     +++ i + +
  gi|386001398|ref|YP_005919697.1| 145 AEAVAERVTPRTRALIVNSPNNPTGSVQtrEELRalaelaEDHGFALISDEVYeqfiYEGEHASPALYSENVITINA 221
                                       5556666667777779*********88522433233444445555678888875444666666666777888999** PP

                                       HHHHHS-GGG-EEEEEES-HHHHH..HHHHHHHHHHSS--HHHHHHHH CS
                       Alliinase_C 192 lskltGhaGsrlGWalvkdkevak..klveyieknsiGvskesqlrvl 237
                                       +sk+   +G rlG+   + +++ +  k+ +y++  +  +s+ + l ++
  gi|386001398|ref|YP_005919697.1| 222 VSKTYAMTGWRLGYLAARGEALENmlKVHQYVQACASSISQRAALAAV 269
                                       **************9999998866448899**9999999998877665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.05
                                       ESSSS..-.HHHHHHTTTEEEEEGGGGTS-TT.EEEEESSS-HHHHHHHHHHHHTS CS
                       Alliinase_C 309 cekeeded.caevlrekkiltrsGevfeaesr.yvrlsllkrdddfdvllerlkkl 362
                                         k +d d +++ l ++++++  G+ f++ +r ++r+s   + +d    ler++++
  gi|386001398|ref|YP_005919697.1| 311 FPKVGDGDaVSARLIKAGVVAVPGSAFGSAARdHIRISYAASMADIRTALERMREI 366
                                       444455441456788999*********9987658***********99999999876 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05     0.099      18      39 ..     165     190 ..     152     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                      NIR_SIR_ferr  18 n...Gri.taeqlraladiaekygsg 39 
                                       n   G + t e+lrala++ae++g+ 
  gi|386001398|ref|YP_005919697.1| 165 NnptGSVqTREELRALAELAEDHGFA 190
                                       44449999***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2600.54
//
Query:       gi|386001399|ref|YP_005919698.1|  [L=127]
Description: Translation initiation factor eIF-5A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-05   24.0   0.0    4.5e-05   23.4   0.0    1.3  1  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.059   13.1   0.1       0.59    9.9   0.0    2.2  2  DUF3945   Protein of unknown function (DUF3945)


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     5e-09   4.5e-05       2      33 ..       7      38 ..       6      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5e-09
                                      GGG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                             EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqa 33
                                      a elk G  + id++++v++++  +kpGk +a
  gi|386001399|ref|YP_005919698.1|  7 ARELKEGRYVIIDDEPCVIKSIAKSKPGKHGA 38
                                      88**************************9776 PP

>> DUF3945  Protein of unknown function (DUF3945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.058   5.2e+02      39      52 ..       6      19 ..       3      20 .. 0.83
   2 ?    9.9   0.0   6.6e-05      0.59      33      50 ..      97     114 ..      95     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.058
                           DUF3945 39 qkqdLreGkavlle 52
                                      + ++L+eG+ v ++
  gi|386001399|ref|YP_005919698.1|  6 EARELKEGRYVIID 19
                                      6689*****99987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.6e-05
                           DUF3945  33 vkLteeqkqdLreGkavl 50 
                                       v +tee++++L+eGk+v+
  gi|386001399|ref|YP_005919698.1|  97 VPITEEDREKLEEGKEVP 114
                                       779*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 907.09
//
Query:       gi|386001400|ref|YP_005919699.1|  [L=288]
Description: Agmatinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-73  246.8   0.0    3.2e-73  246.7   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.7   0.0   1.8e-77   3.2e-73       1     277 [.      17     279 ..      17     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 246.7 bits;  conditional E-value: 1.8e-77
                                       EEEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBT.HCHEETTTTESCCSEEEEEEEEE--SSCHHHHHHHHHHHH CS
                          Arginase   1 advallGvPfdaagsgrpGarfGPraireasarlee.aleynlelgvleelkivdlgdvavtpvdneevleqieeav 76 
                                       ad++++G+Pfda++ +r+G+r+GP+a+r+as ++e+   +y++  + +++l ++dlgd+ + + d+++++e+i e++
  gi|386001400|ref|YP_005919699.1|  17 ADFIIVGAPFDATTCFRSGTREGPEAVRRASYNFETyIHRYSI--D-FNDLLVADLGDLYLGA-DPADAMETIRESF 89 
                                       5899*******************************85555555..3.77**********9997.***********99 PP

                                       HHHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEE CS
                          Arginase  77 aeilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklv 153
                                          + +g++pi++GG+Hsi+ +i++ +a++ g ++gv+ +DAH+Dlr+++  g+++sh++  rr++e + +    ++
  gi|386001400|ref|YP_005919699.1|  90 GF-IPEGATPIFIGGEHSITPSIVAEVARRRG-EIGVVVLDAHLDLRDEY-GGTRYSHACASRRILEVEGVA--GYA 161
                                       65.7889***********************66.7****************.9**************777765..9** PP

                                       EEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B- CS
                          Arginase 154 qiGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGlt 230
                                        iGirs d +ey +a+e g+ +++ +e++e+g++av+ee+le vg  +d +ylS+D D++Dpa+aPG+Gtpep Gl+
  gi|386001400|ref|YP_005919699.1| 162 SIGIRSGDLKEYLYAEERGVSYHSSDEVRERGIEAVLEEALEEVG--CDEIYLSIDFDAIDPAFAPGVGTPEPFGLS 236
                                       ********************************************8..99**************************** PP

                                       HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 231 lrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       + +++++++++a   + vg+D  E++P++d  + qta+l+a+l+re+
  gi|386001400|ref|YP_005919699.1| 237 SWDVRHIVEKVAP--KAVGLDANEIAPQYDG-G-QTASLGAKLIREF 279
                                       ***********77..78*************9.5.9**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 2205.40
//
Query:       gi|386001401|ref|YP_005919700.1|  [L=127]
Description: hypothetical protein Mhar_0699 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   51.3   0.0    1.8e-13   51.1   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0     1e-17   1.8e-13       1     120 [.       2     117 ..       2     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1e-17
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaei 77 
                                       ivlDTs+li+l+rg+e+   +rk +   e+ +t+ ++ +E+ ++++     r  ++e+   +   s++ +l++  ++
  gi|386001401|ref|YP_005919700.1|   2 IVLDTSALIDLFRGSEE---IRKFVG--EDAATTMISCYEIFAGISH----RRSEREEQFFRRFFSGIDVLDFEMRA 69 
                                       79**********99995...588887..99*****************....777777777778899*********** PP

                                       HHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  78 aeeaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrrva 120
                                       ae+a++i+ ++      ++++D lia  A+ +g++ ++++D+df++++
  gi|386001401|ref|YP_005919700.1|  70 AEKAGAIMGQLLgqgtpVNALDVLIAGIAITNGAERLISRDRDFEKIS 117
                                       *********99999*********************888*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1027.57
//
Query:       gi|386001402|ref|YP_005919701.1|  [L=389]
Description: hypothetical protein Mhar_0700 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.11   11.4   0.1       0.18   10.7   0.1    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1     1e-05      0.18      92     138 ..      61     106 ..      55     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1e-05
                                       T-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BT CS
                   Transketolase_N  92 gsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkp 138
                                        s  +  Pe ++++ +e ttG  G G+++   +al e  +aat  kp
  gi|386001402|ref|YP_005919701.1|  61 YSVIASTPESEYSEKIEWTTGSTGHGLSQVDVVAL-EDGVAATNTKP 106
                                       5777889********************98766665.56677777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 3082.82
//
Query:       gi|386001403|ref|YP_005919702.1|  [L=304]
Description: Restriction endonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-37  127.2   0.0    5.6e-37  126.3   0.0    1.5  1  Mrr_cat    Restriction endonuclease
    3.7e-33  113.5   0.0    6.7e-33  112.7   0.0    1.5  1  Mrr_N      Mrr N-terminal domain
      2e-10   40.7   0.1      8e-10   38.7   0.0    1.8  2  Mrr_cat_2  Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   9.4e-41   5.6e-37       3     115 .]     159     278 ..     157     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 9.4e-41
                                       TT-TTCHHHHHHHHHHHHSSS.....EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCT CS
                           Mrr_cat   3 kmspkeFeklvaellealGyk.....eveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalk 74 
                                        +sp+ Fe+lv +ll a+Gy+       e++grsgDggiD+i+k+d+lg + +++qaKr++++vg+++Vq+++g+l+
  gi|386001403|ref|YP_005919702.1| 159 GCSPEFFERLVVDLLVAMGYGgsrrdAGEAVGRSGDGGIDGIIKEDKLGLDAVYIQAKRWEGTVGRPAVQAFAGSLM 235
                                       579******************99998779************************************************ PP

                                       TS..SEEEEEESS-B-HHHHHHHHTT-..-EEEE-HHHHHHHH CS
                           Mrr_cat  75 krgadkgifvttsdftkaAreeaeeln..kieLldgdeLaell 115
                                       +++a kg+f+tts+ftk+A +++++++  ki+L+dg++La+++
  gi|386001403|ref|YP_005919702.1| 236 GNRAGKGVFITTSQFTKEANDYVKGIQqpKIVLIDGEQLAQFM 278
                                       ************************965457**********976 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   1.1e-36   6.7e-33       1      86 [.       6      91 ..       6      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1.1e-36
                             Mrr_N  1 yqelmlplLealadgsehrlkeirervaerfglseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTe 79
                                      +q+lmlplL++l dg+eh+l e++e +a++f+l++eer+ellpsg+q ++ nrvgWarty+kkaglles+ rg+++i +
  gi|386001403|ref|YP_005919702.1|  6 FQRLMLPLLRVLGDGEEHSLHEVIESLADQFELTDEERRELLPSGRQAKLANRVGWARTYMKKAGLLESTGRGKFRIND 84
                                      89***************************************************************************** PP

                             Mrr_N 80 kGrevlk 86
                                      +G ++l+
  gi|386001403|ref|YP_005919702.1| 85 RGLSILR 91
                                      ***9997 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.24   1.4e+03      12      34 ..     101     123 ..      93     133 .. 0.76
   2 !   38.7   0.0   1.3e-13     8e-10      26     118 ..     191     282 ..     181     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                         Mrr_cat_2  12 eVwlwkewpeekrlgkkDtGIDl 34 
                                       ++  + e++e +r ++kD  IDl
  gi|386001403|ref|YP_005919702.1| 101 SLEQFPEFQEFHRRSSKDDDIDL 123
                                       55566677777888899999998 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.3e-13
                         Mrr_cat_2  26 gkkDtGIDlVake.rkegeywAIQcKfYaedekiqkedidsFlsasgkkkftkrliisTtdkwsknaeealkn.qki 100
                                        + D GID ++ke +   + + IQ+K+++   ++ ++ ++ F ++   ++  k+++i Tt++++k+a++ +k+ q++
  gi|386001403|ref|YP_005919702.1| 191 RSGDGGIDGIIKEdKLGLDAVYIQAKRWE--GTVGRPAVQAFAGSLMGNRAGKGVFI-TTSQFTKEANDYVKGiQQP 264
                                       478**********544457788****999..79***********************9.7778*********765899 PP

                         Mrr_cat_2 101 pvkridledLeeseidws 118
                                       ++ +id e+L++ +id +
  gi|386001403|ref|YP_005919702.1| 265 KIVLIDGEQLAQFMIDHD 282
                                       9***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2416.39
//
Query:       gi|386001404|ref|YP_005919703.1|  [L=207]
Description: hypothetical protein Mhar_0702 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-13   50.0   0.1      5e-13   49.6   0.1    1.1  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
    0.00021   21.4   0.0    0.00028   21.0   0.0    1.2  1  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   5.6e-17     5e-13      26     232 ..      16     195 ..       7     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.6e-17
                          PDDEXK_1  26 reeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeeilessarlrylaeklkevleklve 102
                                        eee le+ dlG+l H++le +       ++ le+l   a +   p +ll+ +++e++ r+ +   +  +  + +  
  gi|386001404|ref|YP_005919703.1|  16 DEEEPLEPKDLGRLAHQILESLGV----GGQTLEALG-SAERPRRPPHLLAGRFTEDELREVWTVLDGLKGHRLV-- 85 
                                       458899999***********9987....555777777.4444444444566666667777788888876666655.. PP

                          PDDEXK_1 103 rlaeeleakrgfrpvalelefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalae 179
                                       r+ e  +a++++++ ++   fgg   +L+Gr+D + ++ + + i+D+K  +    s      ++++Q+ +Yl++++e
  gi|386001404|ref|YP_005919703.1|  86 REIE--AAEKTRTEYQILRPFGG--HTLVGRVDKLVKTREGWHIVDFKFAD---SSAH--APAYEFQMKFYLYLARE 153
                                       4444..45555566666679997..56*******9955555*******777...5565..67799************ PP

                          PDDEXK_1 180 geelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeei 232
                                          ++     +ga ++ l      + + v+ + l++ee e +++el+ ++e++
  gi|386001404|ref|YP_005919703.1| 154 IF-RP----MLGARLFYL------KDGGVRDVRLEDEEVEGFEEELRGRIERL 195
                                       92.22....788888888......56666666677777766666666666554 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.2e-08   0.00028      54     130 ..     110     188 ..      70     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-08
                          Cas_Cas4  54 sikiDvvekekeklvvvEvK..kskkkeeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelek 128
                                        +++D + k++e++ +v++K   s++ ++a ++Q+++Yl+l ++    +  + l+y+k    ++v+l++e+ e  e+
  gi|386001404|ref|YP_005919703.1| 110 VGRVDKLVKTREGWHIVDFKfaDSSAHAPAYEFQMKFYLYLAREIFRPMLGARLFYLKDGGVRDVRLEDEEVEGFEE 186
                                       6899****9*******999933455567777***********9*99999999****************999888777 PP

                          Cas_Cas4 129 ai 130
                                        +
  gi|386001404|ref|YP_005919703.1| 187 EL 188
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1544.18
//
Query:       gi|386001405|ref|YP_005919704.1|  [L=838]
Description: exodeoxyribonuclease V [Methanosaeta harundinacea 6Ac]
Scores for complete 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-47  162.7   0.0    1.2e-23   84.2   0.0    2.1  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
      4e-31  108.7   0.0    2.3e-19   70.0   0.0    2.2  2  UvrD_C           UvrD-like helicase C-terminal domain
    3.8e-20   72.7   0.0      9e-20   71.5   0.0    1.7  1  AAA_19           AAA domain
    8.1e-11   41.6   0.6    1.1e-05   25.1   0.0    2.9  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    8.6e-07   28.9   0.1      0.053   13.2   0.1    2.7  3  AAA_30           AAA domain
    0.00096   18.8   0.0        5.2    6.6   0.0    3.3  3  AAA_12           AAA domain
     0.0015   18.3   0.4         17    5.0   0.1    4.0  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0032   16.9   0.1       0.33   10.4   0.0    2.3  2  PhoH             PhoH-like protein


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.1e-24   2.6e-21      13     140 ..       2     129 ..       1     139 [. 0.87
   2 !   84.2   0.0   5.2e-27   1.2e-23     204     313 ..     187     296 ..     173     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.1e-24
                                       SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS.....STGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHH CS
                     UvrD-helicase  13 ggpilveAsAGsGKTfvlaerilrlikeee.....iepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrl 84 
                                       +g+++++AsAG+GKT+++ +r+l+  +e+      i++ ++ ++TFT+kAa E+k Ri e ++++      d r + 
  gi|386001405|ref|YP_005919704.1|   2 KGDLFISASAGTGKTYTISKRYLEIFEEAFqageeISVGEVAAITFTRKAAGEMKRRIVEGIREKT-----DPRWTG 73 
                                       6899********************9987533333488888*********************99984.....66999* PP

                                       HHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHS CS
                     UvrD-helicase  85 alqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelle 140
                                        l ++  a+i+T++sf+ +il ++   +g+dp++r+ +   ++ l ++ +l ++ e
  gi|386001405|ref|YP_005919704.1|  74 LLYSIPFAWIGTIDSFAGRILAENGALAGIDPGLRVEAAAGSSALVRRVALRTVWE 129
                                       ***********************************999988776666666666555 PP

  == domain 2  score: 84.2 bits;  conditional E-value: 5.2e-27
                                       TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHH CS
                     UvrD-helicase 204 ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilklla 280
                                       e+++ + + ++ f+    +++++    Df   l+al  ll + + l+++l+ ++++i +DE+QDT++ Q +i+ ll 
  gi|386001405|ref|YP_005919704.1| 187 EANRAFLELFRRFDGARRREMDRLGQTDFLGVLLALRDLLLDSPALRARLSGQFRYIIVDEFQDTDHLQKEIVDLLR 263
                                       566677777778888888888888899************************************************** PP

                                       TTTTTEEEEE-GGG--GGGGTB-THHHHHHHHH CS
                     UvrD-helicase 281 sgheelfmvGDpkQsIYgFRgAdielflkkkkd 313
                                        ++  ++ vGD kQsIY+FRgA++e+f +++++
  gi|386001405|ref|YP_005919704.1| 264 GRKTRVVYVGDAKQSIYRFRGAEVEVFAEARRE 296
                                       ****************************99877 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.5e-12   3.4e-09       2     151 ..     306     488 ..     305     498 .. 0.91
   2 !   70.0   0.0     1e-22   2.3e-19     235     346 ..     584     729 ..     535     731 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.5e-12
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnr.rale.kek.......ktvekgekivvleaeteeeEaekiaatikall... 66 
                                        L +NyRS + +l+ an++++ i++    +  +e         + + g+  + +   + e+E +  a  i++++   
  gi|386001405|ref|YP_005919704.1| 306 ELSTNYRSHPGVLDFANRLFAGIFDGaGISGgPEYspviplpVAGKTGDLPRARILFHPEDEGKAAALFIRRMVgre 382
                                       589*********************99444435444789999999999**999999999******************* PP

                                       ...................xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  67 ...................ekneklediavLvRs..nkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkl 122
                                                           ++  + d a+L R+      d  +kaL+++gip+ vv+e  fF+ +e++ +  +lk+
  gi|386001405|ref|YP_005919704.1| 383 fdfldrkedgsggvnlvpeRRKVRYRDFALLLRKlrGGTGDRYAKALREMGIPCYVVGEAGFFDLPEVRGLVSILKV 459
                                       ******************99999**********96666889************************************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 123 lankqdkialkrilkrlvlgigkatveri 151
                                       la + d++a+   l ++ +g++ + ++r+
  gi|386001405|ref|YP_005919704.1| 460 LADPADDLAMTAALLSPAVGLDLQDLARL 488
                                       ******************99999988888 PP

  == domain 2  score: 70.0 bits;  conditional E-value: 1e-22
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx. RF
                            UvrD_C 235 eeklenlreLysllkelekkeeeeeveeklneileiatLseseleeskkk..ekipiiTiHqAKGlEFdvVflagl. 308
                                       +++  nlr+L++  k l+      + +e + e l  + L++ e+ +++ +  + ++++T+H+AKGlEF++V++a+  
  gi|386001405|ref|YP_005919704.1| 584 RRRTANLRKLMDSSKALDG--AGLSLRE-VIERLDGSGLEDVEPASVEGEetDAVKVMTVHKAKGLEFPIVIVAETs 657
                                       34899**************..8877776.88888889********9998889*********************9862 PP

                                       .xxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 309 .eegtfP.................................syrskkekrleEEkRlfYVaiTRAkkrLfisy 346
                                        ++  +P                                   ++++ ++ eEE R +YVa+TRA++ L i++
  gi|386001405|ref|YP_005919704.1| 658 wSDPATPppfllrrggdggsgpifsllpeekagegtflseMAEEERRREAEEEERSLYVAATRARDLLAITL 729
                                       25778889*************************999996534444477899*******************97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0     4e-23     9e-20      13     146 .]       5     283 ..       1     283 [. 0.87

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 4e-23
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvel.....ggvkpeeillvaftgrAakelrerlaalgae................ 68 
                                       l++ a +GtGKT+++ ++  ++ e+     +++++ e+++++ft++Aa e++ r+ +   +                
  gi|386001405|ref|YP_005919704.1|   5 LFISASAGTGKTYTISKRYLEIFEEafqagEEISVGEVAAITFTRKAAGEMKRRIVEGI-Rektdprwtgllysipf 80 
                                       789************9987555444011114556699*****************94333.25899999999999999 PP

                            AAA_19  69 ..atTiHrlal.................................................................. 77 
                                         + Ti ++a                                                                   
  gi|386001405|ref|YP_005919704.1|  81 awIGTIDSFAGrilaengalagidpglrveaaagssalvrrvalrtvwenealaepilrvaglddllgalavgvdgr 157
                                       999999999889***************************************************************** PP

                            AAA_19  78 ..............................................................ldfddlltealelle 92 
                                                                                                     l++ dll        
  gi|386001405|ref|YP_005919704.1| 158 gkviaarpagavegglplvedpasaaslaeanraflelfrrfdgarrremdrlgqtdflgvlLALRDLL-------L 227
                                       ******************************************999999988877766655554555544.......1 PP

                            AAA_19  93 .eaeeekklqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliyvfr 146
                                        + + +  l  ++ ++ivDEfqd+d lq+++++ l g+k++++ vGD++Q+iy fr
  gi|386001405|ref|YP_005919704.1| 228 dSPALRARLSGQFrYIIVDEFQDTDHLQKEIVDLLRGRKTRVVYVGDAKQSIYRFR 283
                                       33444567878889*************************99*************97 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   5.1e-09   1.1e-05       4      28 ..     637     661 ..     634     665 .. 0.88
   2 !   13.6   0.2   1.9e-05     0.043      30      51 ..     706     727 ..     693     728 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.1e-09
                          UvrD_C_2   4 altihkaQGsefpaVivfdpdlaaa 28 
                                       ++t+hka+G+efp+Viv++ +++++
  gi|386001405|ref|YP_005919704.1| 637 VMTVHKAKGLEFPIVIVAETSWSDP 661
                                       89***************99888765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.9e-05
                          UvrD_C_2  30 mgelrrrlLYtavTRAreklil 51 
                                       + e+  r LY+a+TRAr+ l +
  gi|386001405|ref|YP_005919704.1| 706 EAEEEERSLYVAATRARDLLAI 727
                                       3445899**********99976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   2.4e-05     0.053      22      76 ..       6      71 ..       2     101 .. 0.82
   2 !   12.5   0.0   4.1e-05     0.091      83     157 ..     233     313 ..     180     330 .. 0.73
   3 ?   -3.1   0.0       2.4   5.3e+03      90     111 ..     435     456 ..     411     458 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                            AAA_30 22 vltGpAGtGKttalkal.reaweaa.g.......grviglAptgkaAkvLaeel..gieastiakl 76
                                      ++ + AGtGKt+++++   e++e+a +       g+v++++ t kaA ++++ +  gi+ +t  ++
  gi|386001405|ref|YP_005919704.1|  6 FISASAGTGKTYTISKRyLEIFEEAfQageeisvGEVAAITFTRKAAGEMKRRIveGIREKTDPRW 71
                                      68899******9997654899988865889********************9854224666666555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.1e-05
                            AAA_30  83 rarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlvea.....agi.gtaeLt 152
                                       rarl+ + + +ivDE   +d  q +++++ ++ ++++v+ vGD +Q     +G+ ++  +ea     ag  ++ eL+
  gi|386001405|ref|YP_005919704.1| 233 RARLSGQfRYIIVDEFQDTDHLQ-KEIVDLLRGRKTRVVYVGDAKQSIYRFRGAEVEVFAEArreveAGSgTVLELS 308
                                       4677778899*****99888665.6899*****************97555556655555544322221113555666 PP

                            AAA_30 153 evvRq 157
                                       +++R 
  gi|386001405|ref|YP_005919704.1| 309 TNYRS 313
                                       66665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.4
                            AAA_30  90 tllivDEagmvdtkqlaallka 111
                                        +++v Eag  d  +++ l+++
  gi|386001405|ref|YP_005919704.1| 435 PCYVVGEAGFFDLPEVRGLVSI 456
                                       4789999999999999888765 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.15   3.4e+02      97     154 ..      25      92 ..      16      93 .. 0.81
   2 !    6.5   0.0    0.0025       5.5      14      38 ..     301     325 ..     292     327 .. 0.84
   3 !    6.6   0.0    0.0023       5.2     138     194 ..     630     727 ..     607     730 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                            AAA_12  97 klvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke..........ievntvdgfQGr 154
                                       ++ e+ +++g+e +  +++ it+ r+ +  +k+++ e  +ek++ +            ++t+d+f Gr
  gi|386001405|ref|YP_005919704.1|  25 EIFEEAFQAGEEISVGEVAAITFTRKAAGEMKRRIVEGIREKTDPRwtgllysipfAWIGTIDSFAGR 92 
                                       4445555555555889999****************99888887777999****99999*******997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
                            AAA_12  14 kekvvlLdtqYRmhpeIsrfpsklf 38 
                                       +  v  L+t+YR+hp +++f+++lf
  gi|386001405|ref|YP_005919704.1| 301 SGTVLELSTNYRSHPGVLDFANRLF 325
                                       567788****************987 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0023
                            AAA_12 138 ksekeievntvdgfQGrekdviilslVRsnekk.........................................eig 173
                                       +++ +++v tv +  G e  ++i+     ++                                           +  
  gi|386001405|ref|YP_005919704.1| 630 EETDAVKVMTVHKAKGLEFPIVIVAETSWSDPAtpppfllrrggdggsgpifsllpeekagegtflsemaeeerRRE 706
                                       33445999999999999999999887666533346667777777888888888888888888888888888877555 PP

                            AAA_12 174 flkderrlNValTRAksklii 194
                                         ++er l Va TRA++ l i
  gi|386001405|ref|YP_005919704.1| 707 AEEEERSLYVAATRARDLLAI 727
                                       7899999*********99987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.088     2e+02       3      21 ..       7      25 ..       5      63 .. 0.81
   2 ?    2.0   0.0     0.065   1.4e+02      57     106 ..     235     284 ..     227     296 .. 0.70
   3 ?    4.1   0.0     0.015        34     181     201 ..     634     653 ..     618     664 .. 0.78
   4 !    5.0   0.1    0.0076        17     210     232 ..     705     727 ..     698     728 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.088
                   Viral_helicase1  3 vhGvpGcGKStlirkllrt 21
                                      +++ +G GK+  i k + +
  gi|386001405|ref|YP_005919704.1|  7 ISASAGTGKTYTISKRYLE 25
                                      7889*********999887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.065
                   Viral_helicase1  57 lvkstkgkililDEylllhaGyill..laalskaklvilfGDplQipfhsrn 106
                                       ++ + +++++i+DE++  +  + +   l++  k   v+ +GD +Q+ +  r 
  gi|386001405|ref|YP_005919704.1| 235 RLSG-QFRYIIVDEFQDTDHLQKEIvdLLRGRKT-RVVYVGDAKQSIYRFRG 284
                                       4444.7999******9877544333224444444.79999*****9887665 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.015
                   Viral_helicase1 181 gvrevttvhevqGltfdkVtl 201
                                        v +v+tvh + Gl+f+ V++
  gi|386001405|ref|YP_005919704.1| 634 AV-KVMTVHKAKGLEFPIVIV 653
                                       44.49************9986 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0076
                   Viral_helicase1 210 elisesrenllvAlTRhrkslvi 232
                                        +++e++  l+vA TR+r+ l i
  gi|386001405|ref|YP_005919704.1| 705 REAEEEERSLYVAATRARDLLAI 727
                                       345567999*********99876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.012        28      23      35 ..       6      18 ..       2      37 .. 0.83
   2 !   10.4   0.0   0.00015      0.33     122     158 ..     242     278 ..     236     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                      EEE--TTSSTTHH CS
                              PhoH 23 faiGpaGtGKtyl 35
                                      f+ ++aGtGKty 
  gi|386001405|ref|YP_005919704.1|  6 FISASAGTGKTYT 18
                                      7899********6 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                       EEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                       ++i+DE Q+t + q +++    G++++vv +Gd +q 
  gi|386001405|ref|YP_005919704.1| 242 YIIVDEFQDTDHLQKEIVDLLRGRKTRVVYVGDAKQS 278
                                       8*************99998888*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 5995.83
//
Query:       gi|386001406|ref|YP_005919705.1|  [L=1003]
Description: ATP-dependent nuclease subunit B-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-26   93.2   0.0    4.7e-26   92.2   0.0    1.5  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
        2.8    8.7   9.5        1.3    9.8   5.1    2.6  2  KfrA_N    Plasmid replication region DNA-binding N-term


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   5.2e-30   4.7e-26       1     251 [.     700     987 ..     700     988 .. 0.74

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 5.2e-30
                          PDDEXK_1   1 rlSvsrletfleCplrfflryllglre....eeeleapdlGtlvHaaleefye....wkkldkedleelleeaveel 69 
                                       ++S+s+l+++++Cp+rffl++ lg+ e    + el++ ++Gt++Ha+l+++        +l+++  e+l++ +ve+ 
  gi|386001406|ref|YP_005919705.1| 700 SFSYSKLRDYRSCPFRFFLTRALGIEEpapgSLELTPLERGTAYHAVLRAVGGeappGADLREGGGEDLVRGEVERT 776
                                       58***********************4445779999999**********98888888766666669999999999999 PP

                          PDDEXK_1  70 wpellleeeilessarlrylaeklkevleklve.rlaeeleakrg.....frpvalelefg.............g.e 126
                                       +++ l +e++   +a  r + +++   l  +++ + +++ +a  g       p++l                  +  
  gi|386001406|ref|YP_005919705.1| 777 AARFLADEKVRRMEAVRRRIVSAVASDLLGYLRfEAEDPVRAAVGrrrmaEVPFSL----ElsrmgellprsaeSyG 849
                                       99955555553333333334333333333344434444444444464422333333....244666999****9556 PP

                          PDDEXK_1 127 kvrLkGriDrvd.....dkeg.elriiDyKtgsappkskelaelkegl.QlllYllalaegeelkeege..pagaly 194
                                       +++++GriDr+d     +k++ e+++ DyK+++      e       + Ql lY lal++    + +++    +al+
  gi|386001406|ref|YP_005919705.1| 850 DLTFRGRIDRIDlgapgKKGEiEVVLSDYKSST---SGAE-------WeQLQLYSLALLALGLPEVPARpgSMRALF 916
                                       8************9875444489999****877...4454.......33************5555555554444444 PP

                          PDDEXK_1 195 lrleepkvk........deevvkkmalteeeleallqeleelaeeilag.efparpskk.....CeyCpyk 251
                                         +++p ++        + + v++   ++  ++++  el+e ++ i++g ef+ + + +     C  Cp+ 
  gi|386001406|ref|YP_005919705.1| 917 RIVRRPGISrvlevhagEGRMVRQRSKPDPTFAEVDGELREALDGIFQGrEFRRAAEVEgstggCWGCPFE 987
                                       4555588889***999999999999999*******************9999999998778999******95 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.1   0.00014       1.3      63     110 ..     378     424 ..     354     426 .. 0.82
   2 ?   -0.8   0.1      0.27   2.4e+03       4      60 ..     772     829 ..     770     841 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                            KfrA_N  63 laeallaalwqaaleeaeeelaaaraelqaaraaleaeraeaearvee 110
                                         +  +++ w aal+e +++l++ ++ l+a++  le+e+a+a++r+e+
  gi|386001406|ref|YP_005919705.1| 378 DLAS-ARRSWIAALAEHQSALREMERVLAADETVLESEVAAAARRAES 424
                                       3334.59************************************99986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                            KfrA_N   4 qviaaadallaeGerpTveavrerlGgGspntisrvlkeweaelaaalaaraa..pelP 60 
                                       +v ++a ++la  +   +eavr+r+ +  ++ +  +l+ +eae+  ++a+  +  +e+P
  gi|386001406|ref|YP_005919705.1| 772 EVERTAARFLADEKVRRMEAVRRRIVSAVASDLLGYLR-FEAEDPVRAAVGRRrmAEVP 829
                                       57788888888888788999999998888888888875.55555555555544466666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1003 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 7157.70
//
Query:       gi|386001407|ref|YP_005919706.1|  [L=208]
Description: hypothetical protein Mhar_0705 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.37   11.3   1.6        8.9    6.8   0.1    2.3  2  DinB_2    DinB superfamily


Domain annotation for each model (and alignments):
>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.005        90      65     113 ..      16      64 ..       3      67 .. 0.84
   2 ?    6.8   0.1    0.0005       8.9      52      92 ..     119     159 ..     101     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.005
                            DinB_2  65 ppsaaealaylaevrarllallealtdadldrpltap.hpglgkltlgdv 113
                                       p s++ea+ + ++    +l  l++l +  l+r +t   ++++g+ t+ ++
  gi|386001407|ref|YP_005919706.1|  16 PRSLEEARGAVEARGLLFLRRLDRLEA-GLARVGTGReAERFGRATAMFL 64 
                                       46899999999999999*******999.8999999999999999998776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0005
                            DinB_2  52 geeaprpgldpltppsaaealaylaevrarllallealtda 92 
                                       ge + ++ +++ +  +++ea+++l+++ ar ++  e+l ++
  gi|386001407|ref|YP_005919706.1| 119 GEIHEIRDNPSTGAVDPEEAKKELEASIARSREAAERLLAE 159
                                       777778889999999***************99999998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1342.87
//
Query:       gi|386001408|ref|YP_005919707.1|  [L=1291]
Description: hypothetical protein Mhar_0706 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-54  184.0   0.0    7.8e-54  183.3   0.0    1.4  1  Peptidase_C25  Peptidase family C25
    0.00067   19.4   1.5       0.35   10.7   0.2    2.8  2  zinc_ribbon_5  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   8.7e-58   7.8e-54       1     378 []     331    1041 ..     331    1041 .. 0.87

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 8.7e-58
                                        EEEEE-GGG.............................HHHHHHHHHHHHHTTEEEEEEETTSTTT-S....... CS
                     Peptidase_C25    1 yliItddel.............................saaaerlaefrrskGldvkvvtveeiynefs...... 40  
                                        y+iItd+++                              + +erlae++ s+G++++vvtve+i ++        
  gi|386001408|ref|YP_005919707.1|  331 YVIITDNSTwpekgtdgngapekndprkkalnvngpgpVEHFERLAEWKTSRGMRTRVVTVESILAGDYgdfaha 405 
                                        899999999999999999************************************************877788887 PP

                                        .......SHHH.HHHHHHHHHHHHHTT--SEEEEES-T.........................TTS--EE-.... CS
                     Peptidase_C25   41 ...aGekdaaa.irnflkyayknwsasklkYllLvGdtsiv..........vkv..kspitksdliptyqiaks. 98  
                                           +  +d+++ irnf+k a +nw   +l+YllL+G  +iv            +  ++ ++ +    ++ i++s 
  gi|386001408|ref|YP_005919707.1|  406 nsaNPARDLQEvIRNFIKWAHNNW---GLEYLLLGGSLEIVpmrkllgyatC-KgkYPGWDFC--DYGEDIEASr 474 
                                        755444466668************...8***********9999999986541.1445666666..5555555557 PP

                                        ........................................................................... CS
                     Peptidase_C25   99 ........................................................................... 98  
                                                                                                                   
  gi|386001408|ref|YP_005919707.1|  475 tnppprgrvlvgnpkkarlchecrfftvnsltklcssrgkvikfkenrreigngelgwyftkrdyrplyednnqd 549 
                                        788999999999999999********************************************************* PP

                                        ............................................TTT-SEESHHHHS-T................ CS
                     Peptidase_C25   99 ..........................................lgnestiptDdyyasldgneds........... 120 
                                                                                  l++++ ip+D+yya++d++              
  gi|386001408|ref|YP_005919707.1|  550 lkgepepynsekgysetpkdtpvcnlivegpesdinddfywiLEKDRLIPSDLYYACMDSEPSDkhdfdlfdngy 624 
                                        ***********************************************************76555*********** PP

                                        .......................TSSS-SSEEEEE--SSHHHHHHHHHHHHHHHCT--S-G.............. CS
                     Peptidase_C25  121 .......................ddltpdlavGRipvtsaaeaaavvnKiiaYerntengsaagq.......... 162 
                                                               d   pd++vGR+pv++ ++a+++v++++ Yer+ ++    g+          
  gi|386001408|ref|YP_005919707.1|  625 ygqyrwvddetgehgeetpvdssDPSIPDIWVGRAPVRTGEDARSFVDRVLTYERLQTPV---GDnevpevvdpt 696 
                                        ********************************************************6653...223568999999 PP

                                        GGGEEEEEE--................................................................ CS
                     Peptidase_C25  163 wrnkvlliagd.vvgew......eaad................................................ 182 
                                        ++++v+++ +  +++++      +  +                                                
  gi|386001408|ref|YP_005919707.1|  697 YLKRVIMAVDLeEDTTNnlwqdpD--Riretpdsgkfiysvqddfvlihlqeklfqvlrdlwkesnfhvvarffe 769 
                                        *****9999996322224445551..05566667777777778888888999999999999999999******** PP

                                        ........................................................................... CS
                     Peptidase_C25  183 ........................................................................... 182 
                                                                                                                   
  gi|386001408|ref|YP_005919707.1|  770 adrefgtdisciyddgssvpitgflswrfverrvgmgrkyywgssstpteyvkltgsalkvapkriiwfygyprg 844 
                                        **************************************************************************9 PP

                                        .....HHTHHHHHHHHHHHTSSGGGT-SEEEEE-SS--..............TTTTHHHHH--SEEEEES-EETT CS
                     Peptidase_C25  183 .....gneiagttaettpseynvnklyadlaayeaetetevpaanqpl.lttqnllkalnqGvlfvnytGHGset 251 
                                               e+ ++  ++   e++  ++y++ +   + t+   +  +  + l+++n+++al++G+++  +  HG+++
  gi|386001408|ref|YP_005919707.1|  845 dtwtrQAEGMRNCLSGLFGEFDDYQRYYSDYKEVWGTA--SLPPA--QpLKVENIRAALDRGCHLAILQSHGNPS 915 
                                        99654237777777888888888888888666666666..34444..449************************* PP

                                        EETTTTE..EHHHHHT---TT--EEEEEE.SSSTT-TTSSS-..........-HHHHHHHSTTSSEEEEEEESS- CS
                     Peptidase_C25  252 awadesl..stndisaltntnklpiaita.aCltgafdeetkr.........sfgeklvlnangGavayigatrl 314 
                                        + a  +        ++++n n ++ia++  +C+t+ +d   ++         s+geklvl++ gGavayig+tr+
  gi|386001408|ref|YP_005919707.1|  916 RCAMVWCdeGHGARDDFKNHNEYFIAVAYsSCHTAEPDAYINDvhtpenrnqSLGEKLVLHPGGGAVAYIGNTRM 990 
                                        997777666788999***********98637******988877999***************************** PP

                                        --SS--SHHHHHHHHHHHHHHH...T-S-SS-HHHHHHH...............EEEEE-TT--- CS
                     Peptidase_C25  315 gysgvndrlsraffealfadaartlGealllaknelletglaqsiskgm.nkrtfnllGDPalrl 378 
                                        g+   nd  ++af+++l+++ +  lG a   a  + +        ++++ +  +  l+GDP++r+
  gi|386001408|ref|YP_005919707.1|  991 GF--GNDARHKAFWRSLYRNGR--LGPA---AGDQSWP-------DRDLwSVYERILYGDPEMRV 1041
                                        **..99************8888..6888...4444443.......3455566679********97 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1   0.00057       5.1      19      35 ..    1147    1163 ..    1145    1165 .. 0.90
   2 !   10.7   0.2   3.9e-05      0.35      22      37 .]    1200    1215 ..    1198    1215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00057
                     zinc_ribbon_5   19 lKksgkkVrCakCaevF 35  
                                        +K  + + rC kC   F
  gi|386001408|ref|YP_005919707.1| 1147 IKLQQSWRRCTKCHGLF 1163
                                        7999*********9888 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.9e-05
                     zinc_ribbon_5   22 sgkkVrCakCaevFda 37  
                                         +++ rC kC++ F a
  gi|386001408|ref|YP_005919707.1| 1200 QQGWRRCTKCRSLFFA 1215
                                        599**********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.85u 0.34s 00:00:01.19 Elapsed: 00:00:00.52
# Mc/sec: 7447.60
//
Query:       gi|386001409|ref|YP_005919708.1|  [L=157]
Description: hypothetical protein Mhar_0707 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1258.30
//
Query:       gi|386001410|ref|YP_005919709.1|  [L=220]
Description: Multiple antibiotic resistance (MarC)-related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-56  190.2   9.2    3.1e-56  190.0   9.2    1.0  1  MarC       MarC family integral membrane protein
  ------ inclusion threshold ------
      0.038   13.7  10.3       0.25   11.0   9.6    2.2  1  TerC       Integral membrane protein TerC family
        7.7    6.5  11.6        0.3   11.0   0.3    2.9  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.0   9.2   5.2e-60   3.1e-56       2     201 ..      13     211 ..      12     213 .. 0.97

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 5.2e-60
                              MarC   2 kaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgi 78 
                                        ++++a+ s+++i+np+ +  vf+sl+ e s+ er ri+l+a+ +a +i l+f+l+G+ +l++fg ++d+l++aGgi
  gi|386001410|ref|YP_005919709.1|  13 AYFFYALASVFIIVNPVEATMVFISLTPEASAGERARISLRAAAVAYVIALLFALSGDHVLRFFGATVDSLRVAGGI 89 
                                       6899************************************************************************* PP

                              MarC  79 llfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaal 155
                                       llf++ai+mlkak ++ k  + e +++ ++++++v+PLA+Pl++GPgaittv+vl+ +as   ek av+lai +  +
  gi|386001410|ref|YP_005919709.1|  90 LLFIMAIEMLKAKPRR-KVTEAELADASDREDVSVFPLATPLLTGPGAITTVIVLMGTASGPAEKGAVLLAITATFA 165
                                       ***************6.8888888889************************************************** PP

                              MarC 156 itllilllsslilrllgktginaleRlmGllLvalavqlivdGike 201
                                        t+lil++s+ + r lg tgi +++R+mGllL a+av+++  G  +
  gi|386001410|ref|YP_005919709.1| 166 ATYLILRSSEYVDRILGLTGIMVMTRIMGLLLGAIAVNFVAFGAWN 211
                                       ****************************************988765 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.6   4.2e-05      0.25      17      99 ..      34     120 ..      29     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
                              TerC  17 viallvkklpeeqqkkalllGilgAlvlRillillavallelf....dlilligglfLlytavkellekrle.nklv 88 
                                       v++ l+ +  + +++++ l   ++A+v+ +l+ l++ ++l++f    d + ++gg++L+++a+++l++k  + + ++
  gi|386001410|ref|YP_005919709.1|  34 VFISLTPEASAGERARISLRAAAVAYVIALLFALSGDHVLRFFgatvDSLRVAGGILLFIMAIEMLKAKP-RrKVTE 109
                                       5555555566778999999999********************77778*******************9765.313333 PP

                              TerC  89 keekkkkkktk 99 
                                        e ++ +++++
  gi|386001410|ref|YP_005919709.1| 110 AELADASDRED 120
                                       33333333333 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3     5e-05       0.3      63     117 ..      51     105 ..      44     113 .. 0.87
   2 ?   -2.3   5.7      0.66     4e+03      91     113 ..     151     173 ..     125     219 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                         RseC_MucC  63 llkaallvYllPllllilgallgsallgssellaalgallglvlgflivrllskr 117
                                        l+aa+++Y++ ll+ + g  +  +++++ + l ++g++l++++++ +++   +r
  gi|386001410|ref|YP_005919709.1|  51 SLRAAAVAYVIALLFALSGDHVLRFFGATVDSLRVAGGILLFIMAIEMLKAKPRR 105
                                       689***********************99999999999999999999988876665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.66
                         RseC_MucC  91 ssellaalgallglvlgflivrl 113
                                       +++++++l+  + +++++li+r 
  gi|386001410|ref|YP_005919709.1| 151 AEKGAVLLAITATFAATYLILRS 173
                                       45555555555555566666553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1770.28
//
Query:       gi|386001411|ref|YP_005919710.1|  [L=363]
Description: Iron-sulfur binding reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-29   99.8   4.9    2.4e-14   53.3   0.1    2.8  3  CCG       Cysteine-rich domain
    1.8e-10   41.1   4.5    1.8e-10   41.1   4.5    2.0  2  Fer4_8    4Fe-4S dicluster domain
    4.7e-10   39.8   3.3    4.7e-10   39.8   3.3    2.5  2  Fer4_17   4Fe-4S dicluster domain
    5.3e-07   30.1   9.2      6e-07   30.0   7.1    2.2  2  Fer4_7    4Fe-4S dicluster domain
    1.5e-06   28.2  22.4    4.8e-06   26.6  11.7    3.1  4  Fer4_10   4Fe-4S dicluster domain
    7.8e-06   25.5  17.2      0.013   15.2   4.6    3.0  2  Fer4      4Fe-4S binding domain
    9.1e-06   26.5  10.1     0.0001   23.2   8.7    2.9  3  Fer4_16   4Fe-4S double cluster binding domain
    1.3e-05   25.3  20.2      2e-05   24.7   9.9    3.0  3  Fer4_9    4Fe-4S dicluster domain
    7.5e-05   22.6  20.9    0.00022   21.1   3.2    3.2  3  Fer4_2    4Fe-4S binding domain
     0.0023   18.3   1.2     0.0023   18.3   1.2    3.6  3  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   15.3  14.7       0.19   11.8   3.7    3.0  2  Fer4_6    4Fe-4S binding domain
      0.042   14.0   5.9          3    8.1   1.6    2.7  2  Fer4_18   4Fe-4S dicluster domain
        0.1   12.8   0.6        0.1   12.8   0.6    3.7  4  Fer4_21   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       5.4   7.5e+03      70      81 ..      14      25 ..       5      27 .. 0.72
   2 !   48.3   0.0   6.4e-16   8.8e-13       2      85 .]     142     220 ..     141     220 .. 0.96
   3 !   53.3   0.1   1.8e-17   2.4e-14       1      83 [.     252     335 ..     252     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.4
                               CCG 70 adaivtacpgCl 81
                                      a  +++ c++C 
  gi|386001411|ref|YP_005919710.1| 14 ALEVCVRCGTCR 25
                                      555888999996 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 6.4e-16
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                       +yf+gC l  ++yp v  ++  +l++ gv l +   e+CCG++ +r+g+   a+++ ++n+++++e++a+ +vt c+
  gi|386001411|ref|YP_005919710.1| 142 VYFVGC-LDSYRYPVVAAKTFDILRRFGVALLPD--EKCCGSPLIRTGSS--ALKVIDENLRQIREMKAKTVVTGCA 213
                                       79****.************************966..*************9..8************************ PP

                               CCG  79 gCllqlk 85 
                                       gCl +lk
  gi|386001411|ref|YP_005919710.1| 214 GCLSTLK 220
                                       ***9985 PP

  == domain 3  score: 53.3 bits;  conditional E-value: 1.8e-17
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                       v+y+d+Chl+r+a   + +r+++k++    +ve+++  e++ CCG ggg++   + l++++akr+++ +   g+dai
  gi|386001411|ref|YP_005919710.1| 252 VTYHDPCHLGRHAgiFDPPREVIKAI--CRLVEMKRSrEDARCCGGGGGVRAGYPeLSLEIAKRRLQDVPA-GVDAI 325
                                       89************9999********..778*************998877655555*************99.9**** PP

                               CCG  74 vtacpgCllq 83 
                                       v+ cp C  +
  gi|386001411|ref|YP_005919710.1| 326 VSCCPLCIRN 335
                                       *******765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   4.5   1.3e-13   1.8e-10       2      64 ..      15      81 ..      14      82 .. 0.83
   2 ?   -2.4   0.0         5   6.9e+03      45      54 ..     206     215 ..     184     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.3e-13
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvlee.....eealwsCttcgaCtevCpvg 64
                                      le C++Cg C+s Cp+++  + +++++rg+++                 +      ++l++Cttcg C+ +Cp g
  gi|386001411|ref|YP_005919710.1| 15 LEVCVRCGTCRSVCPAFEVLGWESKNTRGRVMVakalgegL--------ApdasvLDSLNTCTTCGICAAKCPAG 81
                                      578******************999********944444330........345666778***************86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                            Fer4_8  45 eealwsCttc 54 
                                       ++ +  C +c
  gi|386001411|ref|YP_005919710.1| 206 KTVVTGCAGC 215
                                       6667777777 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   3.3   3.4e-13   4.7e-10       2      59 ..      18      81 ..      17      83 .. 0.84
   2 ?    0.2   0.1      0.82   1.1e+03      32      49 ..     198     215 ..     178     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 3.4e-13
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraakl..glleeaeke....ekaslCieCgeCerkCPqg 59
                                      C +Cg C+ +Cp +e  ++e k+++ ++++  +l e+   +    +  ++C++Cg C++kCP+g
  gi|386001411|ref|YP_005919710.1| 18 CVRCGTCRSVCPAFEVLGWESKNTRGRVMVakALGEGLAPDasvlDSLNTCTTCGICAAKCPAG 81
                                      **********************9999999975344554333556689***************87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.82
                           Fer4_17  32 glleeaekeekaslCieC 49 
                                        +++e+++++++  C++C
  gi|386001411|ref|YP_005919710.1| 198 RQIREMKAKTVVTGCAGC 215
                                       566777777889999998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   7.1   4.4e-10     6e-07       2      52 .]      18      82 ..      17      82 .. 0.73
   2 ?   -1.6   0.0       3.2   4.4e+03      30      41 ..     204     215 ..     187     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.4e-10
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt....ekv..........eid.pekClgCgaCvavCPtga 52
                                      C+ Cg C ++Cp+  +  +e++n +g+    + +          ++d  ++C++Cg C+a CP+ga
  gi|386001411|ref|YP_005919710.1| 18 CVRCGTCRSVCPAFEVLGWESKNTRGRvmvaK-AlgeglapdasVLDsLNTCTTCGICAAKCPAGA 82
                                      ************77777777778886544440.144445554444443789*************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                            Fer4_7  30 kveidpekClgC 41 
                                       k++ + + C gC
  gi|386001411|ref|YP_005919710.1| 204 KAKTVVTGCAGC 215
                                       445555666666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6  11.7   3.5e-09   4.8e-06       6      56 .]      15      79 ..      10      79 .. 0.88
   2 !   15.0   2.9   1.4e-05     0.019       6      29 ..      65      83 ..      60     111 .. 0.71
   3 ?   -1.3   0.0       1.8   2.5e+03      37      48 ..     204     215 ..     191     219 .. 0.64
   4 ?   -3.3   0.1       7.5     1e+04      18      23 ..     328     333 ..     326     348 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.5e-09
                           Fer4_10  6 ddtCirCgkCvkaCPadl..............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       + C+rCg+C+++CPa                 ++   +   +++ v + +  Ct+cg C+++CP
  gi|386001411|ref|YP_005919710.1| 15 LEVCVRCGTCRSVCPAFEvlgweskntrgrvmVAKALGEGLAPDASVLDSLNTCTTCGICAAKCP 79
                                      579*************77**********9987666677777788888899**************9 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-05
                           Fer4_10  6 ddtCirCgkCvkaCPadltsvgak 29
                                       +tC+ Cg C + CPa +     +
  gi|386001411|ref|YP_005919710.1| 65 LNTCTTCGICAAKCPAGA-----N 83
                                      689************944.....2 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                           Fer4_10  37 avrkkvekCtgc 48 
                                       + +++v  C gc
  gi|386001411|ref|YP_005919710.1| 204 KAKTVVTGCAGC 215
                                       444466667666 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 7.5
                           Fer4_10  18 aCPadl 23 
                                        CP ++
  gi|386001411|ref|YP_005919710.1| 328 CCPLCI 333
                                       577654 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   4.8   1.5e-05      0.02       6      19 ..      16      29 ..      15      30 .. 0.92
   2 !   15.2   4.6   9.8e-06     0.013       7      22 ..      67      82 ..      64      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                      TTSSS-THHHHHST CS
                              Fer4  6 ekCigCGaCvevCP 19
                                      e C++CG+C +vCP
  gi|386001411|ref|YP_005919710.1| 16 EVCVRCGTCRSVCP 29
                                      78************ PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.8e-06
                                      TSSS-THHHHHSTTTE CS
                              Fer4  7 kCigCGaCvevCPvgA 22
                                       C+ CG+C+  CP gA
  gi|386001411|ref|YP_005919710.1| 67 TCTTCGICAAKCPAGA 82
                                      7*************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   8.7   7.4e-08    0.0001       2      66 ..      18      80 ..      17      81 .. 0.86
   2 !   11.7   4.3   0.00029       0.4       1      16 [.      67      82 ..      67      98 .. 0.87
   3 ?    1.0   0.0       0.6   8.3e+02      47      61 ..     202     216 ..     180     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.4e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                      C++Cg C +vCP+  + +   ++ ++r  +  ++a  ++la+d+   ++ + +t C+iC++ CPa
  gi|386001411|ref|YP_005919710.1| 18 CVRCGTCRSVCPAFEVLGW--ESKNTRGRVMVAKALGEGLAPDASVLDSLNTCTTCGICAAKCPA 80
                                      *************999988..45555555555679999********999***************8 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                           Fer4_16  1 rCgtCgkCaevCPtna 16
                                      +C+tCg Ca  CP++a
  gi|386001411|ref|YP_005919710.1| 67 TCTTCGICAAKCPAGA 82
                                      5************998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.6
                           Fer4_16  47 kckkqeaitgCdiCq 61 
                                       ++k ++ +tgC+ C 
  gi|386001411|ref|YP_005919710.1| 202 EMKAKTVVTGCAGCL 216
                                       223345569999995 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.5   3.2e-05     0.044      23      48 ..       5      30 ..       1      34 [. 0.69
   2 !   24.7   9.9   1.4e-08     2e-05       2      50 ..      18      82 ..      17      83 .. 0.80
   3 ?   -1.3   0.2       1.9   2.6e+03      34      39 ..     210     215 ..     176     217 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                            Fer4_9 23 erkarlraaseeaCigCgaCveaCpk 48
                                      +++a+++++  e C+ Cg+C  +Cp 
  gi|386001411|ref|YP_005919710.1|  5 QQEAKIDQRALEVCVRCGTCRSVCPA 30
                                      3444444444467***********95 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.4e-08
                            Fer4_9  2 CtgCgaCveaCpagvv.vedaaerkarlraase...............eaCigCgaCveaCpkga 50
                                      C++Cg+C ++Cpa  v   +++++  r+  a++               + C++Cg C+++Cp ga
  gi|386001411|ref|YP_005919710.1| 18 CVRCGTCRSVCPAFEVlGWESKNTRGRVMVAKAlgeglapdasvldslNTCTTCGICAAKCPAGA 82
                                      ***********8754426555555555544445788************99************985 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                            Fer4_9  34 eaCigC 39 
                                       + C gC
  gi|386001411|ref|YP_005919710.1| 210 TGCAGC 215
                                       445555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.2   1.6e-07   0.00022       8      22 .]      16      30 ..       9      30 .. 0.92
   2 !   11.8   3.6   0.00014       0.2       8      22 .]      66      80 ..      60      80 .. 0.86
   3 ?   -2.8   0.4       6.8   9.3e+03      10      13 ..     212     215 ..     209     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                            Fer4_2  8 drCigCgaCvsaCPa 22
                                      + C++Cg+C+s+CPa
  gi|386001411|ref|YP_005919710.1| 16 EVCVRCGTCRSVCPA 30
                                      79************8 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                            Fer4_2  8 drCigCgaCvsaCPa 22
                                      ++C+ Cg+C   CPa
  gi|386001411|ref|YP_005919710.1| 66 NTCTTCGICAAKCPA 80
                                      79*******888**8 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.8
                            Fer4_2  10 CigC 13 
                                       C gC
  gi|386001411|ref|YP_005919710.1| 212 CAGC 215
                                       6666 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.2   1.7e-06    0.0023       2      15 ..      16      29 ..      15      41 .. 0.91
   2 !   11.7   1.7   0.00021      0.29       2      17 .]      66      81 ..      65      89 .. 0.92
   3 ?   -2.3   0.3       6.9   9.5e+03       6      10 ..     211     215 ..     210     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e C++Cg C+++CP
  gi|386001411|ref|YP_005919710.1| 16 EVCVRCGTCRSVCP 29
                                      78************ PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+ Cg C a CP g
  gi|386001411|ref|YP_005919710.1| 66 NTCTTCGICAAKCPAG 81
                                      79************65 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.9
                            Fer4_4   6 gCgsC 10 
                                       gC  C
  gi|386001411|ref|YP_005919710.1| 211 GCAGC 215
                                       56555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.2    0.0027       3.8       9      21 ..      18      30 ..      16      34 .. 0.89
   2 ?   11.8   3.7   0.00014      0.19       7      23 ..      66      82 ..      64      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0027
                            Fer4_6  9 CigCgdCvrvCPe 21
                                      C+ Cg C +vCP+
  gi|386001411|ref|YP_005919710.1| 18 CVRCGTCRSVCPA 30
                                      ************7 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                            Fer4_6  7 dkCigCgdCvrvCPega 23
                                      + C+ Cg C++ CP+ga
  gi|386001411|ref|YP_005919710.1| 66 NTCTTCGICAAKCPAGA 82
                                      78*************98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.6    0.0022         3      48      73 ..       5      30 ..       1      33 [. 0.77
   2 ?    7.2   0.2    0.0041       5.6      56      75 ..      63      82 ..      39      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                           Fer4_18 48 kekeerkekgagdcidcescvkvcPt 73
                                      +++ +  +++   c+ c++c +vcP 
  gi|386001411|ref|YP_005919710.1|  5 QQEAKIDQRALEVCVRCGTCRSVCPA 30
                                      4445556778889************6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0041
                           Fer4_18 56 kgagdcidcescvkvcPtgi 75
                                      ++ + c++c+ c + cP g 
  gi|386001411|ref|YP_005919710.1| 63 DSLNTCTTCGICAAKCPAGA 82
                                      56789************985 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   7.2e-05       0.1      38      53 ..      15      30 ..       2      36 .. 0.74
   2 ?   10.1   1.2    0.0005       0.7      39      53 ..      66      80 ..      53      87 .. 0.82
   3 ?    1.3   0.2      0.29   3.9e+02      11      48 ..     178     216 ..     170     219 .. 0.53
   4 ?   -2.5   0.5       4.2   5.8e+03      48      57 ..     326     333 ..     314     335 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                           Fer4_21 38 edeCvGCnlCssvCPv 53
                                       + Cv C  C svCP 
  gi|386001411|ref|YP_005919710.1| 15 LEVCVRCGTCRSVCPA 30
                                      5789999999999996 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0005
                           Fer4_21 39 deCvGCnlCssvCPv 53
                                      ++C+ C +C++ CP 
  gi|386001411|ref|YP_005919710.1| 66 NTCTTCGICAAKCPA 80
                                      579999999999994 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.29
                           Fer4_21  11 CgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCs 48 
                                       Cg+ li    ++ + i+ + +++ ++  +   +GC+ C+
  gi|386001411|ref|YP_005919710.1| 178 CGSPLIRTGSSALKVIDENLRQIREMKaKTVVTGCAGCL 216
                                       555555555555666644444444443234456666665 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4.2
                           Fer4_21  48 ssvCPvedci 57 
                                       +s CP+  ci
  gi|386001411|ref|YP_005919710.1| 326 VSCCPL--CI 333
                                       566775..55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2603.39
//
Query:       gi|386001412|ref|YP_005919711.1|  [L=485]
Description: FAD linked oxidase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-57  193.4   0.2    6.2e-57  193.1   0.2    1.1  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    2.8e-43  147.0   2.1    2.8e-43  147.0   2.1    1.9  2  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.1   0.2     7e-61   6.2e-57       1     250 []     211     459 ..     211     459 .. 0.93

  Alignments for each domain:
  == domain 1  score: 193.1 bits;  conditional E-value: 7e-61
                                       --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHH CS
                     FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeae 77 
                                       lp+ar+++ ++f+s e+a +av+++ +agi p+a+e++d+ ++ + ++ ++    l+ + + +ll+e++g++ ++ae
  gi|386001412|ref|YP_005919711.1| 211 LPKARRLVIASFNSAEEAGRAVAATFAAGIVPSACEILDRMTVAVLRRCDPS---LKLPDGDVLLFEVDGSEGAAAE 284
                                       599*************************************************...9999999**********87777 PP

                                       HHHHH.HHHHTTT-EEEEE...........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  78 eelea.lveaileatgaad.vlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikal 152
                                       +++e  +++++ ++++aa  v+v+    e+e++w+aR+ + + ++++  +++ +++ eD+ vP++++++l+r++ ++
  gi|386001412|ref|YP_005919711.1| 285 AAAEIaALCSASSGAAAAAsVAVVAGSGEMEEIWAARRLVGAAISRLDPAKSRIYVGEDVGVPIKEIPALIREVAEI 361
                                       777766555555444443337999999999************999998888999999******************** PP

                                       HHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THH CS
                     FAD-oxidase_C 153 ldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeegl 229
                                        d++g+ ++ +gH+gdgnlh+ + +d+ de+e++r++ ++d + ++a++lgG++s EHG+G +++ y+ +++g  +l
  gi|386001412|ref|YP_005919711.1| 362 SDRFGIPAMKYGHIGDGNLHVALFIDVLDEGEWARLAGAADAIHRAAIRLGGTVSSEHGIGAARSGYMMEQVGSGAL 438
                                       ***************************************************************************** PP

                                       HHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 230 almrriKaalDPkgiLNPgkv 250
                                        +mr+iK+alDP+gi+NPgk+
  gi|386001412|ref|YP_005919711.1| 439 SVMRAIKKALDPRGIMNPGKL 459
                                       *******************96 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   2.1   3.1e-47   2.8e-43       1     139 []      36     175 ..      36     175 .. 0.99
   2 ?   -3.0   0.3      0.61   5.5e+03     100     123 ..     411     433 ..     406     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 3.1e-47
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p++vvrp s++ev++++ la+++g+ v++rG+G++l+g+av  +gg+vldls +nri+e+d ++  ++ve+Gv+ ++
  gi|386001412|ref|YP_005919711.1|  36 PDYVVRPLSTAEVSDVVGLAAAEGVAVTARGAGTGLAGGAVpVRGGIVLDLSGMNRIVEMDLANLAVVVEPGVVQAR 112
                                       89***********************************999999********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                       l+e l+++g++++++pgs   +t+GG+ia+n++G++s kyG++r++vl levvladG+vvr++
  gi|386001412|ref|YP_005919711.1| 113 LNETLKPHGFFFPPDPGSAAFCTLGGLIANNGSGMRSVKYGTTRNYVLDLEVVLADGSVVRTG 175
                                       ************************************************************985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.61
                                       HHHTTTTT-EETTEEGG--HHGTE CS
                     FAD_binding_4 100 vGGaiatnagGygsekyGlirdnv 123
                                       +GG+++   +G g+ ++G + ++v
  gi|386001412|ref|YP_005919711.1| 411 LGGTVSS-EHGIGAARSGYMMEQV 433
                                       6888888.7899999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 3571.36
//
Query:       gi|386001413|ref|YP_005919712.1|  [L=1046]
Description: type II site-specific deoxyribonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-20   71.4   0.0    2.7e-19   69.6   0.0    2.0  1  Eco57I           Eco57I restriction-modification methylase
    3.3e-19   69.3   4.0    8.5e-09   35.1   0.0    3.6  4  N6_Mtase         N-6 DNA Methylase
    3.8e-13   49.5   0.1    1.3e-12   47.9   0.0    2.0  2  TaqI_C           TaqI-like C-terminal specificity domain
    0.00018   21.4   0.0    0.00073   19.5   0.0    2.0  2  HSDR_N_2         Type I restriction enzyme R protein N termin
    0.00026   20.7   0.0      0.045   13.4   0.0    2.9  2  UPF0020          Putative RNA methylase family UPF0020
     0.0015   18.5   0.0       0.27   11.2   0.0    2.6  2  HSDR_N           Type I restriction enzyme R protein N termin
  ------ inclusion threshold ------
      0.068   13.0   0.0          1    9.2   0.0    2.5  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0     1e-22   2.7e-19       3     102 ..     584     695 ..     581     699 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1e-22
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek............akdiyqkFvekalkle..dkylaliiparflasgkglkef 65 
                                       fd++iGNPPY++++ +ke+++ e +            ++d+y+ Fvek+l l    ++l++i+p++f+ ++++++ +
  gi|386001413|ref|YP_005919712.1| 584 FDAVIGNPPYIRIQMMKEWAPVEVEfykehytvakkgNYDVYVVFVEKGLALLneSGRLGFILPNKFF-NAQYGSPL 659
                                       9**********************99***************************977899**********.******** PP

                            Eco57I  66 rekllkdkklkklvefedskevFkdveikggilvflk 102
                                       r+ l + k+l ++v+f + + +F +v+++++++++ k
  gi|386001413|ref|YP_005919712.1| 660 RSLLSNGKNLDEIVNFGHGQ-IFCGVTTYTCLIFLNK 695
                                       ******************99.************9987 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       1.6     4e+03     125     155 ..      29      68 ..      19      80 .. 0.55
   2 !   35.1   0.0   3.3e-12   8.5e-09       4      68 ..     322     409 ..     320     419 .. 0.78
   3 ?    1.2   0.0      0.07   1.8e+02      76     108 ..     487     519 ..     475     539 .. 0.77
   4 !   31.7   0.0   3.5e-11     9e-08     122     236 ..     580     699 ..     558     727 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                          N6_Mtase 125 kfdvvvaNppfnqkew......kektlekderfrea...v 155
                                       ++ +   Np f + +w      ++   +++ rf+++    
  gi|386001413|ref|YP_005919712.1|  29 EIKIEFINPFFEALGWdvrnksNNPPDQREVRFEDTlrsE 68 
                                       4444456999999999665433333334444777774333 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 3.3e-12
                          N6_Mtase   4 dllGdvYEyllrkfae.............eegksgGeffTPrevsklivell..........epksgesvyDpacGs 57 
                                       d+lG+vYE++l+k  +             e  k gG ++TP+ ++  iv+ +          ++ s+  ++DpacGs
  gi|386001413|ref|YP_005919712.1| 322 DILGHVYEQFLGKVIQldeshkvsvvekpEVRKAGGVYYTPSYIVDYIVKNTvgkllegktpKEASDLRILDPACGS 398
                                       99*********998652222222222222346889**************98889999**9886667778******** PP

                          N6_Mtase  58 ggllvqaekvl 68 
                                       g++l+ a ++l
  gi|386001413|ref|YP_005919712.1| 399 GSFLIVAYQHL 409
                                       *******9987 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.07
                          N6_Mtase  76 kelsiyGqeknettyrLakmNlllhgieykkvk 108
                                          +iyG+++++++++++k+ lll+  e ++ +
  gi|386001413|ref|YP_005919712.1| 487 LLNNIYGVDIDTQAVEVTKLSLLLKVLEGENKA 519
                                       4568********************999988644 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 3.5e-11
                          N6_Mtase 122 kdkkfdvvvaNppfnqkewkektlekder.frea..vapksnadla..fllhiieslkpkGraavvlangvLfrggk 193
                                        +  fd+v+ Npp+   +  ++    +   ++e   va+k+n d+   f+   ++ l+++Gr +++l+n  +f+   
  gi|386001413|ref|YP_005919712.1| 580 AKGGFDAVIGNPPYIRIQMMKEWAPVEVEfYKEHytVAKKGNYDVYvvFVEKGLALLNESGRLGFILPN-KFFNAQY 655
                                       4688**********8766644444333330444467999999997667*******************97.5799999 PP

                          N6_Mtase 194 egkIrkalvekdlveavialpe.klFyntsiptcilvlkkekae 236
                                       +  +r+ l + ++++ ++++ + ++F +++  tc+++l+k  ++
  gi|386001413|ref|YP_005919712.1| 656 GSPLRSLLSNGKNLDEIVNFGHgQIFCGVTTYTCLIFLNKMPKD 699
                                       ********************8648****************8765 PP

>> 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 ?   -2.5   0.0       2.1   5.3e+03      40      64 ..     505     529 ..     449     533 .. 0.61
   2 !   47.9   0.0   4.9e-16   1.3e-12      17     120 .]     843     969 ..     803     969 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                            TaqI_C  40 kpKilvrdiskkldaaydekayyvl 64 
                                       k  +l++ ++++++a++ + ++y++
  gi|386001413|ref|YP_005919712.1| 505 KLSLLLKVLEGENKATITDLNMYSD 529
                                       4445666666667777776666665 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 4.9e-16
                            TaqI_C  17 k......gnYldlikkklkneka.....kelfe..........ekpKilvrdiskkldaaydekayyvlntl..yll 70 
                                       k        Yl+  ++ l+++ +      ++++          + pK+ ++++ ++l aayd +a ++l ++    +
  gi|386001413|ref|YP_005919712.1| 843 KqdfplaYDYLQKTRDLLDKRDRgsakgAQWYRyirtqniglqAYPKLAIPRLVHRLCAAYDANADFCLDNVdvGGV 919
                                       0444444678888888777777677778899999999999999**********************999886511569 PP

                            TaqI_C  71 iakdelevslkyllgiLNSklikfyykkiystlrggysrlkrkeleklPi 120
                                       i  ++++v + y+lg+LNSkl+++y+k  + + rgg+    r+++e+lPi
  gi|386001413|ref|YP_005919712.1| 920 ILSENSPVGYIYILGLLNSKLLNYYFKINSVHFRGGFFSANRQYIERLPI 969
                                       999**********************************************9 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.9e-07   0.00073      22     103 ..      57     139 ..      53     144 .. 0.88
   2 ?   -3.5   0.0       3.9     1e+04      14      43 ..    1013    1027 ..    1003    1041 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.9e-07
                          HSDR_N_2  22 eliavekelqlgskkkraDivvykkdkkpllivecKapsvki..seevleqlksYlealkaeylvvtNglehivykv 96 
                                        +++ e +l+++++++r+D+ ++ ++ +   ++++K+psv+i        q+k+Y+   + ++++vt+ +e+ vy++
  gi|386001413|ref|YP_005919712.1|  57 REVRFEDTLRSEGETQRPDYSFWLDR-ERKFFLDAKKPSVNIegGIIPAFQIKRYAYSSTLPLAIVTDFEEFAVYDC 132
                                       67999******************977.788899*********54446788**************************9 PP

                          HSDR_N_2  97 dkkkkkf 103
                                       + k+ kf
  gi|386001413|ref|YP_005919712.1| 133 RIKPFKF 139
                                       8877665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.9
                          HSDR_N_2   14 veelgypkeliavekelqlgskkkraDivv 43  
                                        ++++gy+ +               ++D++v
  gi|386001413|ref|YP_005919712.1| 1013 QNQIGYTDK---------------QIDALV 1027
                                        444555555...............555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.8e-05     0.045      29      93 ..     388     505 ..     383     526 .. 0.74
   2 ?    3.2   0.0     0.024        62     118     140 ..     580     601 ..     568     634 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                       TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS......................................... CS
                           UPF0020  29 gepllDPmCGsGtilIEaallganiapgllrefvle......................................... 64 
                                       + ++lDP CGsG++lI a +   +     ++ + +                                          
  gi|386001413|ref|YP_005919712.1| 388 DLRILDPACGSGSFLIVAYQHLLDWHLDWYKAHLVPlldagekptsngvqnllpspierpgknarsrskkiwerasv 464
                                       779*************9887777777444444444488888888888888888888888888888888888888888 PP

                                       ............HHHHHHHHHHHH--EEEEES-HHHHHHHH CS
                           UPF0020  65 ............lkaeaeeearaelklygsDldrrvvqgar 93 
                                                    +++ae++     ++yg+D+d ++v+ ++
  gi|386001413|ref|YP_005919712.1| 465 atlpieeragewHLKTAERKRILLNNIYGVDIDTQAVEVTK 505
                                       88888877766433344333334444888888888887776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.024
                                       TTS---EEEE----------HHH CS
                           UPF0020 118 kegevdvivtnpPYGerlgskka 140
                                       ++g +d++++npPY  r++  k+
  gi|386001413|ref|YP_005919712.1| 580 AKGGFDAVIGNPPYI-RIQMMKE 601
                                       56679*********4.5554444 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00011      0.27       2      35 ..      25      58 ..      24      68 .. 0.82
   2 !    5.9   0.0    0.0044        11     113     187 ..      58     131 ..      55     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      SSHHHHHH.HHHHHHHHTT-EE............ CS
                            HSDR_N  2 lsEaeleqelidellrelGyqvlskkdveiegrr 35
                                      + E+e++ e+i +++++lG++v +k++ ++++r+
  gi|386001413|ref|YP_005919712.1| 25 YKEEEIKIEFINPFFEALGWDVRNKSNNPPDQRE 58
                                      67999999*****************988877754 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0044
                                       ----S.....SSS---EEEEEEETTEEEEEEEE--TT.-HHHHHH...HHTSS---.---SSSGGGGG--EEEEE-S CS
                            HSDR_N 113 Qvtvt.....gnqkrrpDivlfvnglplvviElKrpg.tieeAin...QikryrkeksdvsipqlfrYlqfgvisng 180
                                       +v+++     +++++rpD++ + +    +++ +K+p+ +ie +i    Qikry   +          +l++ +++++
  gi|386001413|ref|YP_005919712.1|  58 EVRFEdtlrsEGETQRPDYSFWLDRERKFFLDAKKPSvNIEGGIIpafQIKRYAYSS----------TLPLAIVTDF 124
                                       5666677778999**********************9668888776666777776442..........4588888888 PP

                                       S-EEEEE CS
                            HSDR_N 181 ketrfya 187
                                       +e+ +y+
  gi|386001413|ref|YP_005919712.1| 125 EEFAVYD 131
                                       8877776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00039         1       3      24 ..     387     408 ..     385     422 .. 0.87
   2 ?    0.6   0.0      0.17   4.4e+02      30      44 ..     490     504 ..     474     508 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00039
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaee 24 
                                       ++lr+lD++CG+G +++++++ 
  gi|386001413|ref|YP_005919712.1| 387 SDLRILDPACGSGSFLIVAYQH 408
                                       789**************99974 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                   Methyltransf_31  30 evvGiDiseeaielA 44 
                                       +++G+Di+ +a+e+ 
  gi|386001413|ref|YP_005919712.1| 490 NIYGVDIDTQAVEVT 504
                                       49**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1046 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 7967.30
//
Query:       gi|386001414|ref|YP_005919713.1|  [L=407]
Description: Acyltransferase 3 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-24   85.3  39.6    2.9e-23   82.5  39.6    1.9  1  Acyl_transf_3  Acyltransferase family


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5  39.6   1.6e-27   2.9e-23       2     338 ..      14     392 ..      13     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.6e-27
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3   2 aylDllRgiAillVvflHaliayspdagrgspiqasqssqi........aflggfgvplFFllSGfflaamlyrrrg 70 
                                       +++D +R + i+ Vv+lHa++ ys  ++    ++a +   +         f+  +   l Fl+ G+f+    +rr+g
  gi|386001414|ref|YP_005919713.1|  14 YFIDNIRSFVIVQVVILHAAVTYSGLGMWYYREAAALEPLTtlsfgiiqSFIQAYSLGLLFLVAGYFVP-ASFRRKG 89 
                                       689******************9999998888888887766688889999*******************8.******* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3  71 lsklikrRilrlliplliwllliillial.vaghiqanasanvtlfdetkglmfllfefpatghlWfLwalfvlyll 146
                                         ++++ R+ rl +p li++l+i + i + v   + + +   +  f   +g    l++ ++ g++Wf  al++++++
  gi|386001414|ref|YP_005919713.1|  90 AGRFLRDRAVRLGVPALIYMLIINPAILYyVMSLSAVAPLPAPGGFY--LGYLLGLQFLGGSGPMWFAIALLIFSAA 164
                                       ***********************986655155666666666666663..688999********************** PP

                                       xxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 147 lpll................................lrllrkvrkshlllllilllllslvfirhelfgpatsvgll 191
                                       ++                                   + l ++r +++l+l+i++++++       +     +++l+
  gi|386001414|ref|YP_005919713.1| 165 YAAArllrgdpekrdeekaegaegvegaggaegageEATLPRHREVIALILVIAAAAFAIRLVQPIG-----TAVLN 236
                                       ******************************9886666666666666666666666666555555555.....56666 PP

                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                     Acyl_transf_3 192 plpsvla..llfflfGalladaddrdrnlsrglkislllsllllalillalfgqtdg.........gglvasvliqs 257
                                       +  s++a  ++ f++G+ +++ ++  r+     +++l ++l++  +++lalf+++ g         ggl + ++++ 
  gi|386001414|ref|YP_005919713.1| 237 MQLSFFAsyVALFVVGVAARRRRWLARIPYPFGIVWLKAALVGGTAFWLALFLVGIGpegeisminGGLRWQSAAYA 313
                                       666777778*********************************************************99999999999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 258 aslllvslgimllllllfalpsrsafkllrylgkiSygiYliHlpllmllqkllrdwglnlgevlllvlllvvsviv 334
                                          +++++g+ l ++  f+ + +s+ +l r+++++S+++Y +H+++l l++ +lr +   + ++  + ++  v+v +
  gi|386001414|ref|YP_005919713.1| 314 LWEAFFCVGACLGIVVIFRERFNSGGRLARFMADNSFAVYFFHPVILILVTAALRGF--AWHPLAKFAVAAAVAVPL 388
                                       9999999***999999********999******************************..445888888888888888 PP

                                       xxxx RF
                     Acyl_transf_3 335 svvl 338
                                       ++v 
  gi|386001414|ref|YP_005919713.1| 389 CFVA 392
                                       8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2636.55
//
Query:       gi|386001415|ref|YP_005919714.1|  [L=243]
Description: hypothetical protein Mhar_0713 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-44  151.3   0.0    3.1e-44  151.1   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.031   13.9   0.0      0.046   13.3   0.0    1.2  1  ThiI             Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.0   3.5e-48   3.1e-44       4     216 ..      20     232 ..      17     235 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 3.5e-48
                   Diphthami_syn_2   4 avlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkg 79 
                                       ++ + GGkD +la y+a++  ++v +L s  + ++e   +h v + l++++aes+G+pli++      e+e +++  
  gi|386001415|ref|YP_005919714.1|  20 VASWTGGKDGCLAAYRAMEAgVKVGYLLSFWNRGRE--GAHEVKAALLAAQAESMGLPLIRTGFF-SYEEEFKRIVR 93 
                                       5779***************99***************..9**********************9988.67888899999 PP

                   Diphthami_syn_2  80 tlkkld......veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldes 150
                                       +l++ +      + ++++G i++  +   + r+  +lG+ +++P+W  d+ee++ e ++ +fe+ +vav+   l+++
  gi|386001415|ref|YP_005919714.1|  94 QLDEAErgrgrrIGTAIFGHIKT--HDALVLRISADLGIEPMMPIWMMDSEEVIGELLASGFEAAIVAVRSDLLGDE 168
                                       99988777777788899999875..678899********************************************** PP

                   Diphthami_syn_2 151 lLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldier 216
                                       +LGrrid  ++ elk l    +id++ge+Ge++tlvlD+P+f+  l+++e+e+   +   +ldi+ 
  gi|386001415|ref|YP_005919714.1| 169 WLGRRIDGSFVSELKAL--DPSIDPCGENGEFHTLVLDGPIFENSLRIEEAEAVSRGMLRFLDIKE 232
                                       *****************..88******************************************997 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.2e-06     0.046       7      86 ..      20      98 ..      13     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-06
                              ThiI  7 laLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvke 85
                                      +a   gG D   aay++++ G++v ++  + + g + + + k   la   ae  ++  ++   ++++e  k i+++++e
  gi|386001415|ref|YP_005919714.1| 20 VASWTGGKDGCLAAYRAMEAGVKVGYLLSFWNRGREGAHEVKAALLA-AQAESMGLPLIRTGFFSYEEEFKRIVRQLDE 97
                                      344569******************98765544444444444444444.4455555788999999999999999999988 PP

                              ThiI 86 k 86
                                       
  gi|386001415|ref|YP_005919714.1| 98 A 98
                                      6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1768.14
//
Query:       gi|386001416|ref|YP_005919715.1|  [L=155]
Description: hypothetical protein Mhar_0714 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-06   27.2   0.0    7.7e-06   26.3   0.0    1.5  1  HTH_27    Winged helix DNA-binding domain
     0.0014   18.5   0.0       0.01   15.7   0.0    2.2  2  MarR      MarR family
  ------ inclusion threshold ------
      0.046   13.6   0.1       0.11   12.3   0.0    1.7  2  TrmB      Sugar-specific transcriptional regulator TrmB
      0.097   12.8   5.0       0.16   12.1   0.0    2.9  3  HTH_20    Helix-turn-helix domain
       0.16   12.0   0.5       0.16   12.0   0.5    2.7  2  ALF       Short repeats of unknown function


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   2.2e-09   7.7e-06       5      68 .]      14      73 ..      10      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.2e-09
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       a+ L  ir +++++  ++++++ + +  h+ ++l +++ +GLv   ++e ++r +r++lT+ G
  gi|386001416|ref|YP_005919715.1| 14 PAMALLAIR-ELDPAYVSAVAKAIDSTVPHTLKVLAAMEGMGLV---TSEPEGRIRRLALTPRG 73
                                      688999999.**********************************...777789*********98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.9e-06      0.01       8      51 ..      17      60 ..      15      66 .. 0.94
   2 ?    0.1   0.0      0.22   7.8e+02      25      43 ..      71      89 ..      60      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +L  ++e +p++vs  ak++  + +++ +vl ++e  Gl+++++
  gi|386001416|ref|YP_005919715.1| 17 ALLAIRELDPAYVSAVAKAIDSTVPHTLKVLAAMEGMGLVTSEP 60
                                      68889***********************************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                                      HHHTS-HHHHHHHHHHHHH CS
                              MarR 25 kklgvskstvtrvldrLek 43
                                       +     ++++ ++d+L +
  gi|386001416|ref|YP_005919715.1| 71 PRGDRAAAALSGLIDALQD 89
                                      5666778999*****9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.2e-05      0.11      11      58 ..      15      62 ..      10      72 .. 0.86
   2 ?   -2.4   0.0       1.3   4.6e+03      16      33 ..     127     144 ..     125     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                                      CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      a + la+ +l+pa ++ +a++++   +   +vL  +e +GlV+ e++ 
  gi|386001416|ref|YP_005919715.1| 15 AMALLAIRELDPAYVSAVAKAIDSTVPHTLKVLAAMEGMGLVTSEPEG 62
                                      5667777799*********************************99976 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                       HHHHHCCCHHCHHCCCTT CS
                              TrmB  16 aLlklgpatadeiaeelg 33 
                                       +Ll+ +  +++e a +l+
  gi|386001416|ref|YP_005919715.1| 127 KLLAAEGEEVREAAGALD 144
                                       677777777776665555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05      0.16      17      61 .]      22      63 ..      17      63 .. 0.92
   2 ?   -0.3   1.0      0.31   1.1e+03       9      18 ..      89      99 ..      77     132 .. 0.62
   3 ?    1.0   0.3      0.12   4.4e+02      10      35 ..     120     144 ..     114     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                                      HHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 17 raLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      r+L   +++ +s++a+++d +     + L+++e  gLv+++ egr
  gi|386001416|ref|YP_005919715.1| 22 REL---DPAYVSAVAKAIDSTVPHTLKVLAAMEGMGLVTSEPEGR 63
                                      445...9************************************97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                                      -.HHHHHHHHH CS
                            HTH_20  9 h.PvRrrilra 18
                                      + P Rrr+ r+
  gi|386001416|ref|YP_005919715.1| 89 DdPQRRRLARM 99
                                      44666665444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHSTCTTB-HHHHHHHHT CS
                            HTH_20  10 PvRrrilraLaraegltaselaerld 35 
                                       P Rr++ ++L  aeg  + e a +ld
  gi|386001416|ref|YP_005919715.1| 120 PLRRDLAKLL-AAEGEEVREAAGALD 144
                                       8899999999.777777777776665 PP

>> ALF  Short repeats of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.4      0.18   6.3e+02      18      32 ..      75      88 ..      74      89 .. 0.77
   2 ?   12.0   0.5   4.3e-05      0.16       1      21 [.     122     142 ..     122     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.18
                               ALF 18 AAqaALdaGtpaalr 32
                                       A+aAL+ G  +al+
  gi|386001416|ref|YP_005919715.1| 75 RAAAALS-GLIDALQ 88
                                      599***5.9888876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.3e-05
                               ALF   1 RvavarllatgGpaVraAAqa 21 
                                       R ++a lla+ G +Vr+AA a
  gi|386001416|ref|YP_005919715.1| 122 RRDLAKLLAAEGEEVREAAGA 142
                                       7889***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1113.01
//
Query:       gi|386001417|ref|YP_005919716.1|  [L=325]
Description: hypothetical protein Mhar_0715 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 2525.66
//
Query:       gi|386001418|ref|YP_005919717.1|  [L=304]
Description: Phosphoribosylaminoimidazole-succinocarboxamide synthase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-36  126.6   0.0    2.8e-36  125.4   0.0    1.5  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   1.6e-40   2.8e-36       2     246 ..       6     257 ..       5     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 1.6e-40
                                       EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSE CS
                       SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrs 76 
                                       l +G v++vY+l   ++l + ++Dris+fd v ++ ip+KG+ l++   +wf+  ++  i++h+ +      l  + 
  gi|386001418|ref|YP_005919717.1|   6 LRKGSVKEVYDL--GRELEFRFTDRISVFDKVIPTLIPHKGETLCREGVHWFNRAKRmgIKTHFEEF-----LPPNG 75 
                                       578********9..448***************************************667******66.....66788 PP

                                       EEEE-EEEESE..............EEEEEEE--HHH..........HH....HH..T--TT-EEEEEEEEEEE--C CS
                       SAICAR_synt  77 mlvkklkmlpv..............EvvvRgyltGslwkeykks...gkvcgirlpeglkegeklpepiftpstKae 136
                                       mlvkk+++++               Ev++R y++Gs++    ++    +  g    + ++ ge lp p +++stK e
  gi|386001418|ref|YP_005919717.1|  76 MLVKKVDVIQPedigpgsrnyliplEVICRWYAAGSIFDRLVTGkvgPEELGFPGGHKVEYGEPLPDPFIEVSTKLE 152
                                       8888888887778888888888888************8887665321122444444578899*************** PP

                                       CCT.S-EE-HHHHH.HTT.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTE CS
                       SAICAR_synt 137 egehDeniseeevvealg.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDss 212
                                           D  +++ e+++++g t++e+e i e+ l++ e +++ ++ rg+i vD K EF +d  d el+++D + t D  
  gi|386001418|ref|YP_005919717.1| 153 RV--DRLLDRGEALKLAGiTPQEYEAICETVLRIDEDIRREVEPRGLIHVDGKKEFAFDG-DRELMVIDVFGTADED 226
                                       96..9*********9999*****************************************6.9*************** PP

                                       EEEETTT.....GGGB-STHHHHTT-STHHHHHH CS
                       SAICAR_synt 213 RfwdaetyeegkeqeslDKqfvRdwleeveekwk 246
                                       Rfwd  +y+eg+    l K+ vR++ ++  +++k
  gi|386001418|ref|YP_005919717.1| 227 RFWDRAKYQEGE-FVDLSKEHVRQHYRR--TGYK 257
                                       *********776.67899*****99887..6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1924.14
//
Query:       gi|386001419|ref|YP_005919718.1|  [L=202]
Description: hypothetical protein Mhar_0717 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34    9.0   0.0       0.42    8.7   0.0    1.0  1  EFF-AFF   Type I membrane glycoproteins cell-cell fusogen


Domain annotation for each model (and alignments):
>> EFF-AFF  Type I membrane glycoproteins cell-cell fusogen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   2.3e-05      0.42     429     464 ..      75     110 ..      65     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 2.3e-05
                           EFF-AFF 429 siildsdsnrllnltvyevkGkvdgsvkmstgfgsd 464
                                       +i+l+ ++ r l+lt+y+++G++ g   m+tg+  +
  gi|386001419|ref|YP_005919718.1|  75 TITLEGEAPRRLDLTLYQAEGQIFGEGTMTTGVRLQ 110
                                       699999*************************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1292.44
//
Query:       gi|386001420|ref|YP_005919719.1|  [L=209]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 1507.68
//
Query:       gi|386001421|ref|YP_005919720.1|  [L=231]
Description: hypothetical protein Mhar_0719 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.14   11.8   0.2       0.28   10.8   0.0    1.6  2  EF_assoc_1  EF hand associated


Domain annotation for each model (and alignments):
>> EF_assoc_1  EF hand associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.6e-05      0.28      19      48 ..      24      52 ..      20      82 .. 0.85
   2 ?   -3.4   0.1      0.42   7.6e+03      26      39 ..     104     117 ..     100     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.6e-05
                        EF_assoc_1 19 tlqGwLaqWsltTlldvkttleyLaYlGyp 48
                                       lq wL  Ws+  + dv++t eyL   G +
  gi|386001421|ref|YP_005919720.1| 24 ALQDWLGGWSMS-IADVNNTAEYLEKAGSS 52
                                      5899******95.89*********988875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.42
                        EF_assoc_1  26 qWsltTlldvkttl 39 
                                        Wsl      ++tl
  gi|386001421|ref|YP_005919720.1| 104 RWSLAVTESTTRTL 117
                                       68888777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1778.46
//
Query:       gi|386001422|ref|YP_005919721.1|  [L=383]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for 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-15   55.5   0.0    1.5e-14   54.7   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    4.6e-09   36.7   0.0    9.3e-09   35.7   0.0    1.5  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.082   13.2   0.0       0.17   12.1   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   2.5e-18   1.5e-14       3     166 ..      94     245 ..      92     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.5e-18
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       + r+C+++C +C+ p+     + g++l   +i + + e+  e g   +++ ggep+l++d+ el++   ++    i+
  gi|386001422|ref|YP_005919721.1|  94 IIRACPNDCLHCSAPS-----RGGEVLASGDISRAIGEA-LELGSYLITFDGGEPMLRRDLPELVAGVDER---AIT 161
                                       5799***********7.....666666666666666666.5667**************************8...788 PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                       +t+++  +l  ee +++l+ +g+  v ++++++ +e++ +  +r + f++ l++++++ +ag+  v  ++v  p  n
  gi|386001422|ref|YP_005919721.1| 162 TTFSSGFGLT-EERARALKGAGLYAVRISIDSPRPEDHDRFRGREGAFSDALAGIRNALNAGLM-VDLFMVASP-MN 235
                                       8888888886.*************************9888888******************999.777777777.88 PP

                                       HHHHHHHHHH CS
                                       xxxxxxxxxx RF
                       Radical_SAM 157 deeleellel 166
                                        ++lee ++l
  gi|386001422|ref|YP_005919721.1| 236 IDQLEEAYSL 245
                                       8889998876 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.6e-12   9.3e-09       1      53 [.     311     358 ..     311     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.6e-12
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqe.fr 53 
                                       Cfa++r l +++ GdV pC ++      +  +Gn+r+ sl++Iw++    + +r
  gi|386001422|ref|YP_005919721.1| 311 CFAGRRWLHVDASGDVLPCAYM------PTPFGNVRDRSLRDIWRDMGRDRwLR 358
                                       9******************333......79**************9985555355 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05      0.17      22      99 ..     102     173 ..      93     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                           Fer4_12  22 CfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgytlee 98 
                                       C  +++ s  ++   + ++ + i e l +     +t+ GGEP+l   +++l elv  v e+++  + + ++g+ l e
  gi|386001422|ref|YP_005919721.1| 102 CLHCSAPSRGGEVLASGDISRAIGEAL-ELGSYLITFDGGEPML---RRDLPELVAGVDERAI--TTTFSSGFGLTE 172
                                       444445455555555555555555555.666789**********...99************99..567777776665 PP

                           Fer4_12  99 l 99 
                                        
  gi|386001422|ref|YP_005919721.1| 173 E 173
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 3024.84
//
Query:       gi|386001423|ref|YP_005919722.1|  [L=285]
Description: polyprenyl synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-45  154.3   0.0    3.4e-45  154.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.0   1.9e-49   3.4e-45       4     236 ..      27     240 ..      24     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 1.9e-49
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       l e+++y+++ +GKr+Rpl+++l++ea++ ++     + ++  ++el+haasLvhDDi D  + RRG+++a +++G+
  gi|386001423|ref|YP_005919722.1|  27 LGEVIRYVLNTPGKRVRPLILVLSSEAFGCDP---AYSVKASLALELVHAASLVHDDILDGGIERRGAESAFKRYGM 100
                                       67899************************666...55699999********************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHH CS
                   polyprenyl_synt  81 klAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfal 157
                                       ++A++ gd+l +r+  l++ +  ++  ++e fs++++++ eG++ldl ++    ++    e+y   + +KTa+l+++
  gi|386001423|ref|YP_005919722.1| 101 EAALLCGDYLISRSIGLISGY--RQ-PVIEAFSQACVEMSEGEMLDLASR----TT---PEDYYICICKKTASLISA 167
                                       *********************..66.9********************444....44...889999999********* PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHH CS
                   polyprenyl_synt 158 pvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkv 234
                                       + ++++++aga  e+++ ++++g++lGla+Qi DD+  + g +   gK      ++  +tlp+++  +++ ++  + 
  gi|386001423|ref|YP_005919722.1| 168 SSKIGCMIAGAGAEDVALFERYGRHLGLAYQIADDLNEFLGME--KGKS----SAKTSATLPVIYRRDHSAEATVRL 238
                                       ***********99***************************874..4677....778888888888888666555444 PP

                                       HH CS
                   polyprenyl_synt 235 lk 236
                                         
  gi|386001423|ref|YP_005919722.1| 239 CA 240
                                       44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1804.66
//
Query:       gi|386001424|ref|YP_005919723.1|  [L=515]
Description: hypothetical protein Mhar_0722 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   46.6   0.0    4.6e-07   29.8   0.0    2.9  3  Laminin_B  Laminin B (Domain IV)


Domain annotation for each model (and alignments):
>> Laminin_B  Laminin B (Domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.029   5.2e+02       5     101 ..      79     165 ..      75     183 .. 0.65
   2 !   29.8   0.0   2.6e-11   4.6e-07       1     118 [.     235     347 ..     235     354 .. 0.84
   3 !   12.3   0.0   6.3e-06      0.11       1     117 [.     400     507 ..     400     512 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.029
                         Laminin_B   5 PekflGnkltSYGgkLkytvryekeargesekep..dvileG.ngltlsyseseesspspsqettysvrLreenwrh 78 
                                       P++  G+     Gg ++y +r  ++ + e+   p   v +    g+ ls s      ps++  t+ +v L  +n+  
  gi|386001424|ref|YP_005919723.1|  79 PPSWAGDWSRYIGGVFSYDLRLIASGGAEP---PgvEVKILSsDGTVLSSSP----PPSERFWTREEVVLNASNF-- 146
                                       666667777777888899999885333333...2336655551555555553....4455446778899999888.. PP

                         Laminin_B  79 sdglpvsredfmrvLanltallI 101
                                         g  vs  d+ rv+ ++  +++
  gi|386001424|ref|YP_005919723.1| 147 --G--VSEADLRRVMRSVAGITV 165
                                       ..5..788888888887777665 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 2.6e-11
                         Laminin_B   1 ywsaPekflGnkltSYGgkLkytvryekeargesekepdvileGngltlsyseseesspsps.qettysvrLreenw 76 
                                       y+  P +  G+     Gg+L++ +++  + +g++ ++  v + G++ ++ +  s++s p+p+   t+ +v L++ ++
  gi|386001424|ref|YP_005919723.1| 235 YFASPRSWSGDWTPYVGGSLSFDLKVIDSGKGGPYEADLVRIVGADGSVVTVPSSPSGPNPEsGWTRLRVDLTPAAF 311
                                       7888999999999999***********76666663445999***76666665567888888647999********99 PP

                         Laminin_B  77 rhsdglpvsredfmrvLanltallIrasystgqsessLssvs 118
                                           g   + e f rv+ +++++ Ir+ ys++ +e  +++v 
  gi|386001424|ref|YP_005919723.1| 312 ----G--TTEEAFWRVMRSVDRVVIRGEYSDRGDEEGIDNVV 347
                                       ....5..689***********************999999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6.3e-06
                         Laminin_B   1 ywsaPekflGnkltSYGgkLkytvryekeargesekepdvileG.ngltlsyseseesspspsqettysvrLreenw 76 
                                       y+  P++  G+     Gg+L++++    + +g+s+    v + G  g  ls+s      p +s  t+ +v L+++++
  gi|386001424|ref|YP_005919723.1| 400 YYVSPPSWAGDWTGYIGGTLSFEIVEIDSGNGSSTFGDVVRIYGkDGSYLSWSC---DPPGKS-WTRRQVSLVPSSF 472
                                       7888999999999999*******877744444445556899***6699999998...456664.789********** PP

                         Laminin_B  77 rhsdglpvsredfmrvLanltallIrasystgqsessLssv 117
                                       r      +  + f  v+  + ++ Ir+ ys+  +   L++v
  gi|386001424|ref|YP_005919723.1| 473 R------AVGKSFEGVMEEVSEVWIRGEYSNMRDVGGLDNV 507
                                       4......34478*****************966666669888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 3664.05
//
Query:       gi|386001425|ref|YP_005919724.1|  [L=681]
Description: Peptidase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-19   69.2   2.4    4.4e-05   24.5   0.0    4.8  4  PPC       Bacterial pre-peptidase C-terminal domain
     0.0016   18.5   0.0         13    5.8   0.0    4.0  4  G8        G8 domain
  ------ inclusion threshold ------
      0.017   14.9   0.1        3.7    7.4   0.0    3.1  3  CDC48_2   Cell division protein 48 (CDC48), domain 2
      0.025   14.6   0.0         20    5.3   0.0    3.3  3  BiPBP_C   Penicillin-Binding Protein C-terminus Family
      0.063   13.3   0.0         74    3.4   0.0    3.6  4  U62_UL91  Functional domain of U62 and UL91 proteins


Domain annotation for each model (and alignments):
>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0083       1      67 [.      60     126 ..      60     128 .. 0.91
   2 !    6.0   0.3    0.0072        26       1      66 [.     179     261 ..     179     262 .. 0.74
   3 !   24.5   0.0   1.2e-08   4.4e-05       1      68 [.     303     370 ..     303     371 .. 0.82
   4 !   17.5   0.0   1.9e-06    0.0067       1      68 [.     422     489 ..     422     490 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                                       -EEEEEEEE-TT-EEEEEES-TT..SE..EEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEE CS
                               PPC   1 dvDvysfevpagdsltididggtidld..LylldsngtsvaaydansapsgsdeyieftapqaGtYyva 67 
                                       dvD++ fev++ + l++ ++ +  d+   + l+  n  +  +  ++s+p++    ++ +  ++G Yy++
  gi|386001425|ref|YP_005919724.1|  60 DVDFFGFEVESPGVLEVKLNALPHDMRarIDLYGKN-FNFITRKDASNPGDL-VALTLDLASPGRYYFG 126
                                       8***********************999778888888.999999999998887.88888899******87 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0072
                                       -EEEEEEEE-TT-EEEEEES-TT..SE..EEEE-TT..-SS-EE-STT-TT................S-TTS-EE-S CS
                               PPC   1 dvDvysfevpagdsltididggtidld..Lylldsngtsvaaydansapsg................sdeyieftap 59 
                                       d D y+ +v+ ++ l++  ++    ++  + l+  n  +  + +++s+p++                ++ y+ +t +
  gi|386001425|ref|YP_005919724.1| 179 DADIYKLNVTGSGILEVKAESVPEGMKtrIDLYGKN-FNFITRVDASNPGDlvtlkhdvvnpyswypVSYYVGITDL 254
                                       679999999999999999999999666334466666.7777777777777777777777666666666688888889 PP

                                       SSEEEEE CS
                               PPC  60 qaGtYyv 66 
                                       + G Y+v
  gi|386001425|ref|YP_005919724.1| 255 SGGSYHV 261
                                       9988876 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 1.2e-08
                                       -EEEEEEEE-TT-EEEEEES-TT..SE..EEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEEE CS
                               PPC   1 dvDvysfevpagdsltididggtidld..LylldsngtsvaaydansapsgsdeyieftapqaGtYyvaV 68 
                                       dvD+++fe+p+ + l++ + +    +   + l+  +  +  +  ++s+p++ + +++f+  ++G+Y+++V
  gi|386001425|ref|YP_005919724.1| 303 DVDFFKFEAPSPGILEVKTASVPEEMRtrIDLYGKS-FNFITRIDASNPGD-KTTLRFDVKSPGVYHIGV 370
                                       8*******************9999555334455555.77777777787666.5***************99 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 1.9e-06
                                       -EEEEEEEE-TT-EEEEEES-TT..SE..EEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEEE CS
                               PPC   1 dvDvysfevpagdsltididggtidld..LylldsngtsvaaydansapsgsdeyieftapqaGtYyvaV 68 
                                       dvD+y++++ + + l++ +++    +   + l+  n  +  + +++s+p++   ++++ ap +G Yy+++
  gi|386001425|ref|YP_005919724.1| 422 DVDFYKIWADSPGDLEVMLESVPDEMRarIDLYGKN-FNFITRADASNPGDL-ATLKYGAPGPGWYYIGI 489
                                       8**********************8555558888888.999999999998888.***************86 PP

>> G8  G8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.15   5.2e+02      62     115 ..      72     135 ..      65     140 .. 0.63
   2 ?    0.7   0.0      0.14   5.2e+02      57      90 ..     186     218 ..     175     234 .. 0.81
   3 !    5.8   0.0    0.0037        13      62     117 ..     315     380 ..     311     384 .. 0.83
   4 !    4.8   0.0    0.0078        28      55     115 ..     427     497 ..     415     502 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                                G8  62 GkleiGteeepfkgkatItLyGteewsstelpdlga.Kvlavsn..........gGtlelhGqpr 115
                                       G le+  +  p   +a+I LyG ++++     d ++   l++ +          +G ++l G+ +
  gi|386001425|ref|YP_005919724.1|  72 GVLEVKLNALPHDMRARIDLYG-KNFNFITRKDASNpGDLVALTldlaspgryyFGIVDLAGKSH 135
                                       677777778888899*******.666665555555534443333444445555566666666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                G8  57 lvqggGkleiGteeepfkgkatItLyGteewsst 90 
                                        v+g G le+  e+ p   k++I LyG ++++  
  gi|386001425|ref|YP_005919724.1| 186 NVTGSGILEVKAESVPEGMKTRIDLYG-KNFNFI 218
                                       588889999999999999*********.555544 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0037
                                G8  62 GkleiGteeepfkgkatItLyG..........teewsstelpdlgaKvlavsngGtlelhGqprkk 117
                                       G le+ t + p + +++I LyG          +++  ++ +  ++ K+ +v + G ++l G+ +k+
  gi|386001425|ref|YP_005919724.1| 315 GILEVKTASVPEEMRTRIDLYGksfnfitridASNPGDKTTLRFDVKSPGVYHIGVVDLAGRSHKV 380
                                       66888899999999********999998888766666666778888899************99875 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0078
                                G8  55 yilvqggGkleiGteeepfkgkatItLyG..........teewsstelpdlgaKvlavsngGtlelhGqpr 115
                                        i+  + G le+  e+ p + +a+I LyG          +++  +  + ++ga + +  + G ++l G+ +
  gi|386001425|ref|YP_005919724.1| 427 KIWADSPGDLEVMLESVPDEMRARIDLYGknfnfitradASNPGDLATLKYGAPGPGWYYIGIVDLAGRSH 497
                                       6888888**********************655555443322222233444444444555577777777666 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.001       3.7       4      24 ..     283     304 ..     282     325 .. 0.94
   2 ?   -2.6   0.0       1.3   4.8e+03      31      45 ..     611     625 ..     601     628 .. 0.82
   3 ?    3.7   0.0     0.015        53      18      45 ..     634     661 ..     633     667 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
                                       CCCCH.HHHCCCTTEEE-TTEE CS
                           CDC48_2   4 gdema.ylkrqFlgrpvtkGdl 24 
                                       gd +a ++ +q++g +++kGd+
  gi|386001425|ref|YP_005919724.1| 283 GDAVAiAFGDQIEGYIFSKGDV 304
                                       788999**************95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                                       CCCEEEEEEEECCCC CS
                           CDC48_2  31 gqeiklvVvstePkg 45 
                                       ++ ++l +v t P++
  gi|386001425|ref|YP_005919724.1| 611 MGSVDLEAVRTVPAE 625
                                       68899*******997 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.015
                                       EE-TTEEEEECCTCCCEEEEEEEECCCC CS
                           CDC48_2  18 pvtkGdlvvfefkgqeiklvVvstePkg 45 
                                       p+ +G ++v +   + +k+ V s++P  
  gi|386001425|ref|YP_005919724.1| 634 PLLEGHTIVARCNDGYVKFQVISVDPEA 661
                                       777888999999999***********86 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.088   3.1e+02      64      86 ..     113     136 ..     105     140 .. 0.84
   2 ?    5.3   0.0    0.0057        20      60      87 ..     352     380 ..     342     382 .. 0.78
   3 ?    3.2   0.0     0.025        91      68      86 ..     480     498 ..     467     503 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.088
                           BiPBP_C  64 lawqp.epGrhrLtvvDaaGrvdd 86 
                                       l++++ +pGr+   +vD aG++ d
  gi|386001425|ref|YP_005919724.1| 113 LTLDLaSPGRYYFGIVDLAGKSHD 136
                                       4566689*************9876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0057
                           BiPBP_C  60 rgrelawqp.epGrhrLtvvDaaGrvddv 87 
                                       ++ +l ++  +pG + + vvD aGr+ +v
  gi|386001425|ref|YP_005919724.1| 352 DKTTLRFDVkSPGVYHIGVVDLAGRSHKV 380
                                       44455555599**************9886 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.025
                           BiPBP_C  68 pepGrhrLtvvDaaGrvdd 86 
                                       p+pG + + +vD aGr+ +
  gi|386001425|ref|YP_005919724.1| 480 PGPGWYYIGIVDLAGRSHS 498
                                       69**************976 PP

>> U62_UL91  Functional domain of U62 and UL91 proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.021        74      23      44 ..      87     108 ..      79     117 .. 0.81
   2 ?    1.1   0.0      0.11     4e+02      25      43 ..     208     226 ..     198     231 .. 0.86
   3 ?   -1.9   0.0      0.98   3.5e+03      25      43 ..     332     350 ..     325     351 .. 0.79
   4 ?    3.2   0.0     0.024        85      25      43 ..     451     469 ..     442     475 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.021
                          U62_UL91  23 kiiDklsknfnFlveqvEslPR 44 
                                         iD   knfnF+  +  s P 
  gi|386001425|ref|YP_005919724.1|  87 ARIDLYGKNFNFITRKDASNPG 108
                                       5688899*********999995 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                          U62_UL91  25 iDklsknfnFlveqvEslP 43 
                                       iD   knfnF+     s P
  gi|386001425|ref|YP_005919724.1| 208 IDLYGKNFNFITRVDASNP 226
                                       77788******99988888 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.98
                          U62_UL91  25 iDklsknfnFlveqvEslP 43 
                                       iD   k fnF+     s P
  gi|386001425|ref|YP_005919724.1| 332 IDLYGKSFNFITRIDASNP 350
                                       6777899999998877776 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.024
                          U62_UL91  25 iDklsknfnFlveqvEslP 43 
                                       iD   knfnF+  +  s P
  gi|386001425|ref|YP_005919724.1| 451 IDLYGKNFNFITRADASNP 469
                                       78888**********9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 4841.51
//
Query:       gi|386001426|ref|YP_005919725.1|  [L=479]
Description: hypothetical protein Mhar_0724 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-63  213.0   0.0    5.6e-63  212.6   0.0    1.1  1  AAT       Acyl-coenzyme A:6-aminopenicillanic acid acyl-trans


Domain annotation for each model (and alignments):
>> AAT  Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.6   0.0   3.1e-67   5.6e-63       4     225 ..     170     434 ..     167     435 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 3.1e-67
                                       SE...EEEEEEE..E-S-S--EEEEE--S....SS--EEEESSSS-SEEEEEETTS-EEEE-TTS-TTT-------- CS
                               AAT   4 kdgk.llgrNeD..ldpetlsnrflvvased..sgfaslgyagslpGrtdGiNeaGLavtinllslkklrakGfpra 75 
                                       ++g+ ++g+NeD  ++p +l++r++vva +d   g+a+++y+g++ G+++G+NeaG+ ++++l s+++++++G+++a
  gi|386001426|ref|YP_005919725.1| 170 GEGElIFGKNEDnfNMPGQLDRRMMVVAAPDdgFGHAFMTYPGMI-GLDGGVNEAGFEMMTQLNSMRHESMAGCGIA 245
                                       56667**************************99999*********.******************************* PP

                                       -HHHHHHH.--SHHHHHHTHHHHTTTS-SEEEEEEETTEEEEEEE-SSS-EEEEEESS..EEEEE-SS-........ CS
                               AAT  76 fitRllLekcesveeAvellkeipraaginyivldaagnaavveveasskvcsirean..ealahtNHf........ 142
                                       ++tRllL++++sveeA+++++++pr+agi+y+v+da +  a v++++s++v ++r+ +  +al++tNH+        
  gi|386001426|ref|YP_005919725.1| 246 VFTRLLLAHARSVEEAINIFRDHPRCAGIAYHVADAGAREAAVVETSSKRVAVRRPPEgvDALWQTNHSncypgwmg 322
                                       **************************************************9*99999999***************** PP

                                       .................S-GGGSSS-......----HHHHHHHHHHHHHHCSSSSB...HHHHHHHT---STTTSSS CS
                               AAT 143 .................vnetleaen......qnilesSisRlerlqellsqkesa...eeaiellkDredepysvl 193
                                                        + +++e ++      +n+ ++++sR+er+ +l+++++ +   e a+++l+Dr+d py+++
  gi|386001426|ref|YP_005919725.1| 323 ycgynmvrdqapvndllDVSSVESWQkslkdpYNFSVQAPSRFERYSQLIHEHYGKitpEVAVKILSDRYD-PYTRM 398
                                       *****************777777777777777***************************************.***** PP

                                       S-....BSSSEEEE...EEE-TTS--EEEEEE--TT CS
                               AAT 194 rr.ksfkswenTil...talydlaarkaklvlgnpk 225
                                       +r + f+sw+n+il   +aly+++a++ak+++g++k
  gi|386001426|ref|YP_005919725.1| 399 TRpVGFPSWTNNILctiSALYPDFAYRAKEPVGSFK 434
                                       **************9999***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 3361.96
//
Query:       gi|386001427|ref|YP_005919726.1|  [L=319]
Description: Alpha/beta hydrolase fold protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-29  101.3   0.0    1.8e-27   96.6   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    1.7e-21   77.9   5.3    1.7e-21   77.9   5.3    1.5  2  Abhydrolase_6  Alpha/beta hydrolase family
    1.5e-19   70.3   0.0      2e-19   69.8   0.0    1.1  1  Hydrolase_4    Serine aminopeptidase, S33
    2.9e-06   27.6   0.0    5.1e-06   26.8   0.0    1.7  1  Thioesterase   Thioesterase domain
     0.0017   17.2   0.0     0.0021   16.8   0.0    1.3  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.014   15.1   0.0       0.02   14.6   0.0    1.2  1  Esterase       Putative esterase
      0.018   15.1   0.0       0.03   14.4   0.0    1.3  1  Abhydrolase_4  TAP-like protein
      0.045   13.2   0.0        1.3    8.4   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
      0.086   12.7   0.1       0.19   11.5   0.1    1.6  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.092   12.5   0.0        2.4    7.9   0.0    2.1  2  Abhydrolase_5  Alpha/beta hydrolase family
       0.14   11.2   0.0        7.4    5.6   0.1    2.1  2  DUF2048        Abhydrolase domain containing 18


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   1.1e-30   1.8e-27       2     254 ..      73     301 ..      72     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.1e-30
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +l+++ Gl+g     ++  l++ La+ g  vi++D rG g+S+ +p +    y++  +add   +ldalg+++  + 
  gi|386001427|ref|YP_005919726.1|  73 PLLLIMGLGGHIL-DWGWVLPERLAE-GRSVIAFDNRGAGRSEQPPGP----YSIEEMADDTVGLLDALGIEQTDVF 143
                                       89********776.455459999999.*******************75....************************* PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrh 155
                                       G SmGGmia ++aa++p+r+ +l+l ++    +  + a   + + ++ +++     +   +++++++ +++  + + 
  gi|386001427|ref|YP_005919726.1| 144 GVSMGGMIAQEMAARHPDRIGRLILGAT----SPGGAASVSAPPEVQAYLE--PRLDLTLHEALWWSAPAGYPQEFI 214
                                       ****************************....5555555555556665554..67788999***************9 PP

                                       HHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHH CS
                     Abhydrolase_1 156 rlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaled 232
                                       + +     p+ + r  + + + +ssla++++  +  + +   + ++ +      + aptlv++g+sD l+pp+++  
  gi|386001427|ref|YP_005919726.1| 215 DSH-----PEIVERKVQANMAHPSSLAAYEA-QLAAYRAFEIGDRISE------IRAPTLVMAGDSDVLIPPENGLI 279
                                       988.....*******************9993.3333444444444444......666******************** PP

                                       HHHCHTSEEEEEEETCSSSHHH CS
                     Abhydrolase_1 233 laqllpkkrlvvisdagHlafl 254
                                       la+++p+++ + i++agHl  +
  gi|386001427|ref|YP_005919726.1| 280 LAEKIPGAEFREIEGAGHLFWI 301
                                       ******************9765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.9       7.3   1.2e+04      79     101 ..      18      42 ..      13      59 .. 0.49
   2 !   77.9   5.3     1e-24   1.7e-21       1     220 []      74     310 ..      67     311 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.3
                                       HHHHHHCC....EEEEES-..---- CS
                     Abhydrolase_6  79 alaaapla..lvvgvlldppptalp 101
                                       a+a+++l+  l+  +ll++pp a++
  gi|386001427|ref|YP_005919726.1|  18 AAATLALLslLLLLLLLSAPPAAVG 42 
                                       3332222233333377777663333 PP

  == domain 2  score: 77.9 bits;  conditional E-value: 1e-24
                                       EEEE--GC.......GCHHHHHHHHCCTCEEEEE--TTSTS-..GGCS--HHHCHHH.HHHHCCTT..TTSEEEEEE CS
                     Abhydrolase_6   1 vlllHGagss..assWlvapLaallaagvhvlapDlpGhGrs..dpppldledladl.aalldelaagggpvvlvGH 72 
                                       +ll+ G+g++   ++W    L ++la+g  v+a+D +G Grs  +p p++ e+ ad+ + lld+l+    +  ++G 
  gi|386001427|ref|YP_005919726.1|  74 LLLIMGLGGHilDWGW---VLPERLAEGRSVIAFDNRGAGRSeqPPGPYSIEEMADDtVGLLDALG--IEQTDVFGV 145
                                       4566678888455556...999999***667*********88445555777887777799*****5..9999***** PP

                                       TCHHHHHHH.HHHCC..EE.EEES-..----TTT.S----TTHHHHHHTT-C.....CCCHCCH.S-HSCCCCHHHC CS
                     Abhydrolase_6  73 SlGGalala.aaplalvvg.vlldppptalpagl.laaalelllallallrl.....lawlsre.plprlfladeda 140
                                       S+GG++a++ aa++++++g ++l +   + p g     a++ ++a+l ++ +     + w s+   +p++f++  ++
  gi|386001427|ref|YP_005919726.1| 146 SMGGMIAQEmAARHPDRIGrLILGA---TSPGGAaSVSAPPEVQAYLEPRLDltlheALWWSAPaGYPQEFIDSHPE 219
                                       *********8777888888866666...3333332222222223333323321112333332224555677776662 PP

                                       ..CCCHCHCCCGHHHHCC...HHCHTT....CCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STTEEETCE...S CS
                     Abhydrolase_6 141 ..daawrarlarlaalla...glgllp....aaawadlpvpllvl.ggeDplvprllerlla..qagarlpvvlpga 205
                                         ++ ++a+ a+++ l+a   +l +++     +++  +++p+lv+ g++D l+p+    +la  ++ga++  +++ga
  gi|386001427|ref|YP_005919726.1| 220 ivERKVQANMAHPSSLAAyeaQLAAYRafeiGDRISEIRAPTLVMaGDSDVLIPPENGLILAekIPGAEF-REIEGA 295
                                       335777777777775555333333332344499*********999669999***7755555588899999.****** PP

                                       SS-HHHHSHHHHHHH CS
                     Abhydrolase_6 206 GHlphleepdevaea 220
                                       GHl+++++p+e+++a
  gi|386001427|ref|YP_005919726.1| 296 GHLFWISHPEETVAA 310
                                       *********777764 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   1.2e-22     2e-19       9     233 ..      76     298 ..      72     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.2e-22
                       Hydrolase_4   9 lvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                       l+ Gl+ h+     +  +  a+G +v+a+D+rG Grse   g   s++++ dD   +++++  e+      ++G Sm
  gi|386001427|ref|YP_005919726.1|  76 LIMGLGGHILDWGWVLPERLAEGRSVIAFDNRGAGRSEQPPG-PYSIEEMADDTVGLLDALGIEQ----TDVFGVSM 147
                                       5667777777777777777789***************99999.89**************999555....447***** PP

                       Hydrolase_4  86 GGliallyllrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqv...snnlkadslsrdpevvaay 158
                                       GG+ia+++++r+pd++ +lil a+  + +a+++ +p++++ l   l  +l +      +++   +++ ++pe v++ 
  gi|386001427|ref|YP_005919726.1| 148 GGMIAQEMAARHPDRIGRLILGATSPGGAASVSaPPEVQAYLEPRLDLTLHEALWwsaPAGYPQEFIDSHPEIVERK 224
                                       *******************************9877777777666666555544444559****************88 PP

                       Hydrolase_4 159 eadplvhgkitvrlllelld.amkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                        +  + h    +   ++l    + ++ +r ++i++P+l++ G++D +++pe+   l+e+++    +++ ++g+ H 
  gi|386001427|ref|YP_005919726.1| 225 VQANMAHPSSLAAYEAQLAAyRAFEIGDRISEIRAPTLVMAGDSDVLIPPENGLILAEKIP--GAEFREIEGAGHL 298
                                       8888887666666655555413457899999999***************************..6999999999996 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.1e-09   5.1e-06      30      90 ..     101     162 ..      90     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.1e-09
                                       EEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHC CS
                      Thioesterase  30 vlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesq 90 
                                       v+a   +g++  ++ p + siee+a+  +  l +   e  +++fG S+Gg++A+e+A++  ++
  gi|386001427|ref|YP_005919726.1| 101 VIAFDNRGAGrsEQPPGPYSIEEMADDTVGLLDALGIE-QTDVFGVSMGGMIAQEMAARHPDR 162
                                       5555555555325555578***************9999.9*****************986555 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06    0.0021      81     137 ..     120     176 ..     112     319 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                                       -HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S-- CS
                               Ndr  81 slddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaa 137
                                       s++++ad+ + +ld + +++   +Gv  G  i    a++hp+r+  l+L  + +  a
  gi|386001427|ref|YP_005919726.1| 120 SIEEMADDTVGLLDALGIEQTDVFGVSMGGMIAQEMAARHPDRIGRLILGATSPGGA 176
                                       89***********************************************87776554 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05      0.02     117     159 ..     140     204 ..     127     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                       EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC........................HCHHHC CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvssfSpivnps........................namWgq 159
                                       + v+G SmGG++A  +a++hpdr g+ +  +   +p                         +a+W+ 
  gi|386001427|ref|YP_005919726.1| 140 TDVFGVSMGGMIAQEMAARHPDRIGRLILGA--TSPGgaasvsappevqayleprldltlhEALWWS 204
                                       569********************99976655..2333555577777787777777777777777776 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05      0.03      34      93 ..     258     317 ..     245     319 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgala.agntCvdkavdaYLlt 93 
                                        ap+L++++  D   P+e +  la++++ga+    eg+GH +++  +++ v  av ++L+ 
  gi|386001427|ref|YP_005919726.1| 258 RAPTLVMAGDSDVLIPPENGLILAEKIPGAEFREIEGAGHLFWIsHPEETV-AAVVEFLEG 317
                                       479*****************************************7777777.777788875 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.055        90      68      88 ..     142     162 ..     132     170 .. 0.88
   2 ?    8.4   0.0   0.00081       1.3     133     188 ..     243     301 ..     213     316 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.055
                                       EEEETHHHHHHHHHHHH-GGG CS
                      Peptidase_S9  68 itGgSyGGyltgaalnqrpdl 88 
                                       ++G S GG+ +  +++++pd+
  gi|386001427|ref|YP_005919726.1| 142 VFGVSMGGMIAQEMAARHPDR 162
                                       79************9999996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00081
                                       HH-CGGG--.....---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S..ST CS
                      Peptidase_S9 133 pyspldnvk.....aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH..gv 188
                                       ++  + ++      + +p+L++ G+ D  +pp+++l l+++       ++++   ++gH  ++
  gi|386001427|ref|YP_005919726.1| 243 AAYRAFEIGdriseIRAPTLVMAGDSDVLIPPENGLILAEKIPG----AEFREIEGAGHlfWI 301
                                       33333333345556999*******************99987643....566666666665544 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.19      75     209 ..     142     299 ..     118     301 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                       EEEETHHHHHHHHHHHHHHHTT---................EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSC.. CS
                     Abhydrolase_3  75 laGdSaGGnlaaavalrardegepk................vagqvliyPvtdlertesesikkaeeladgpllt.. 133
                                       ++G S GG +a  +a r  d+ +                  ++ q+ + P +dl +  ++ + +a + + + ++   
  gi|386001427|ref|YP_005919726.1| 142 VFGVSMGGMIAQEMAARHPDRIGRLilgatspggaasvsapPEVQAYLEPRLDL-TLHEALWWSAPAGYPQEFIDsh 217
                                       89****************999433378999999999999999999999996666.3333333222222222222111 PP

                                       ....HHHHHHHHHH..HSS..GGGGGSTTTSGGGCS-.SST.---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEE CS
                     Abhydrolase_3 134 ....raaldlfwrl..ylp..eadrddplaspllaed.lsg.lpptlvvvaefDplrdegeayaerlraagveveli 200
                                            +++++ + +   l+  ea+++  +a  + + d +s+  +ptlv+ ++ D+l   +  +   l+++   +e++
  gi|386001427|ref|YP_005919726.1| 218 peivERKVQANMAHpsSLAayEAQLAAYRAFEI-G-DrISEiRAPTLVMAGDSDVLIPPENGLI--LAEKIPGAEFR 290
                                       111122222212110011112444444444433.2.2344425799999999999986554443..22223344567 PP

                                       EETTEETTG CS
                     Abhydrolase_3 201 eyegmvHgf 209
                                       e+eg+ H f
  gi|386001427|ref|YP_005919726.1| 291 EIEGAGHLF 299
                                       777777766 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0014       2.4      56      92 ..     137     174 ..     124     186 .. 0.82
   2 ?    2.3   0.0      0.08   1.3e+02      87     140 ..     242     297 ..     225     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                     Abhydrolase_5  56 lekfvvgGhslGGvvasrfaaee.ekiegvvflasYPe 92 
                                       +e+  v G s+GG++a ++aa++ ++i  +++ a+ P 
  gi|386001427|ref|YP_005919726.1| 137 IEQTDVFGVSMGGMIAQEMAARHpDRIGRLILGATSPG 174
                                       6677799**************99679999998888774 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.08
                     Abhydrolase_5  87 lasYPe...kdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnh 140
                                       la+Y +    d +se   ++l + g++D +++ ++    ++++p  +++ +ieG  h
  gi|386001427|ref|YP_005919726.1| 242 LAAYRAfeiGDRISEIRAPTLVMAGDSDVLIPPENGLILAEKIPG-AEFREIEGAGH 297
                                       66776554579999******************9999888888885.78888888877 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0045       7.4     177     201 ..     139     163 ..     120     179 .. 0.80
   2 ?    3.6   0.0     0.018        29     298     350 ..     263     315 ..     252     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0045
                           DUF2048 177 plgltGlSmGGhmaslaasnwpkpl 201
                                       +  + G+SmGG+ a+  a+ +p  +
  gi|386001427|ref|YP_005919726.1| 139 QTDVFGVSMGGMIAQEMAARHPDRI 163
                                       56688**********9999998766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.018
                           DUF2048 298 vvaAkdDayvpresvaslqeiwpgsevryldg.GHvsayllkkklfrkaiveal 350
                                       v+a ++D  +p e+   l e  pg+e r ++g GH+ +++++ +    a+ve l
  gi|386001427|ref|YP_005919726.1| 263 VMAGDSDVLIPPENGLILAEKIPGAEFREIEGaGHL-FWISHPEETVAAVVEFL 315
                                       455678999*999999999999*********999*8.56677666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1984.50
//
Query:       gi|386001428|ref|YP_005919727.1|  [L=717]
Description: parallel beta-helix repeat-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-40  137.6   1.4      7e-40  137.4   1.4    1.1  1  Peptidase_C25   Peptidase family C25
    3.9e-11   42.4   0.0    7.7e-11   41.5   0.0    1.5  1  Propeptide_C25  Propeptide_C25


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   1.4   7.8e-44     7e-40       1     378 []     291     689 ..     291     689 .. 0.80

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 7.8e-44
                                       EEEEE-GGG...HHHHHHHHHHHHHTTEEEEEEETTSTTT-S.....SHHH.HHHHHHHHHHHHHTT--SEEEEES- CS
                     Peptidase_C25   1 yliItddel...saaaerlaefrrskGldvkvvtveeiynefsaGekdaaa.irnflkyayknwsasklkYllLvGd 73 
                                       y+iIt+ +    s +++++++++++ G++v vvt ++    + ++ ++ a+ ir+ lk+ y++    + kY+lL+Gd
  gi|386001428|ref|YP_005919727.1| 291 YVIITTSAIvagSGKLADFIAHKERIGYRVLVVTESDFLPLTGQAPNNRAErIRQWLKNNYASL---GIKYVLLIGD 364
                                       99****99978888888888888888***********999876666555546**********99...89******** PP

                                       T.............TTS--EE-.......TTT-SEESHHHHS-T.........................TSSS-SSE CS
                     Peptidase_C25  74 tsivvkvkspitksdliptyqiaks..lgnestiptDdyyasldgneds....................ddltpdla 128
                                               +++++  +ip  +++    ++ + + ptD++ya+l+gn+d+                    +d+tp+++
  gi|386001428|ref|YP_005919727.1| 365 P------RPFESGEGEIPMKMCWPRyaETTYKEAPTDYFYADLTGNWDKngdgiygqwgskkdypvaggVDFTPEVY 435
                                       *......578888888888887766775566668******************************************* PP

                                       EEEE--SSHH..HHHHHHHHHHHHHCT--S-G....GGGEEEEEE--.............HH.THHHHHHHHHHHTS CS
                     Peptidase_C25 129 vGRipvtsaa..eaaavvnKiiaYerntengsaagqwrnkvlliagd.vvgew...eaadgn.eiagttaettpsey 198
                                       vGRipv +a+   + ++++K+i+Ye ++      ++wr+ +ll  +  + +++    +++ +  + +   ++  ++y
  gi|386001428|ref|YP_005919727.1| 436 VGRIPVYDADypALDSILEKTIRYELSAG-----TDWRRSALLPMAFsDSVTDgarLSEQMRdDYLNPGGYSSWRMY 507
                                       ********986679***********8833.....45*****776666322222233222222356666666666666 PP

                                       SGGGT-SEEEEE-SS--.............TTTTHHHHH.--SEEEEES-EETTEE.....TTTT....EEHHHHHT CS
                     Peptidase_C25 199 nvnklyadlaayeaetetevpaanqpllttqnllkalnq.GvlfvnytGHGsetaw.....ades....lstndisa 265
                                       ++ +++    a +++++     +++  +  + +++ +++  +++v + +HGs+t+      + +s    ++++ + +
  gi|386001428|ref|YP_005919727.1| 508 QQGTVGSC--ADSKYDS-----EEEL-HGGTVVRDRWSAgDYGIVCWWAHGSPTSAsigysG-CSggllFDSSYAAS 575
                                       66666655..4444444.....3333.6678899999984589***********99998852.3344435******* PP

                                       ---TT--EEEEEESSSTT-TTSSS-.-HHHHHHHSTTSSEEEEEEESS---SS-............-SHHHHHHHHH CS
                     Peptidase_C25 266 ltntnklpiaitaaCltgafdeetkrsfgeklvlnangGavayigatrlgysgv............ndrlsraffea 330
                                       l+ ++   +++  +Cl++++ e+t+ +++  ++   ++G ++ i+atr+++ +v            n  l  +++++
  gi|386001428|ref|YP_005919727.1| 576 LDDAH-PSFTYQCSCLNAQP-ETTD-NLAYSIL---KNGGIGTISATRVSWYYVnqlygnfdgspsNSGLGYEYVNR 646
                                       **977.9*************.6666.9******...9999***********77777777778888899999999999 PP

                                       HHHHHH...T-S-SS-HHHHHHH..............EEEEE-TT--- CS
                     Peptidase_C25 331 lfadaartlGealllaknelletglaqsiskgmnkrtfnllGDPalrl 378
                                       l+ + a   G+al +ak  ++     +s +++mn   +nl+GDP+++l
  gi|386001428|ref|YP_005919727.1| 647 LVDELA--AGDALYQAKGTVYPG--TYS-ETTMNWYVMNLYGDPSVSL 689
                                       998888..6********988853..334.66779999*******9975 PP

>> Propeptide_C25  Propeptide_C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   8.6e-15   7.7e-11     117     199 ..     183     268 ..      81     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 8.6e-15
                                       G.GG--S-BS--SEEE---EEETTEEEEEEEE--EEEETTTTEEEEEEEEEEEEE.....E...EEEE-SS------ CS
                    Propeptide_C25 117 slYsqnkslPseiatlsdpaylRdvrvqevnlaPlqYnPvtkelllykkikvaitfdrkae...taekrkeilnkva 190
                                        +Y+++  +P+  a+l +   +R  ++  v + PlqYnPv+k+l l k  +v+i++    e    a +   ++++va
  gi|386001428|ref|YP_005919727.1| 183 AVYERDANYPEPFAVLLPYSEMRKWKFARVDFFPLQYNPVSKRLTLIKSCVVEISYRSSPEpldEASAADLVMDEVA 259
                                       679****************************************************998877233344556799**** PP

                                       -----TTHH CS
                    Propeptide_C25 191 ksafinfEd 199
                                        + f n+E+
  gi|386001428|ref|YP_005919727.1| 260 PQIFDNYEE 268
                                       ********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 4295.68
//
Query:       gi|386001429|ref|YP_005919728.1|  [L=111]
Description: Nitrogen regulatory protein P-II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-37  126.9   0.8    4.4e-37  126.8   0.8    1.0  1  P-II      Nitrogen regulatory protein P-II
  ------ inclusion threshold ------
       0.04   14.4   1.0      0.073   13.5   1.0    1.4  1  P19Arf_N  Cyclin-dependent kinase inhibitor 2a p19Arf N-termi


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.8     5e-41   4.4e-37       1     102 []       6     107 ..       6     107 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 5e-41
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       +eaiirpe+l++vk+ Le+ g+ g+tv+ev+GrG+qkg +  yrg+++ v+llpkvk+e++v+de v++ + +i  a
  gi|386001429|ref|YP_005919728.1|   6 VEAIIRPERLDQVKKSLEEKGFVGMTVSEVTGRGEQKGIKLQYRGRTMDVDLLPKVKIELIVKDEAVDDLIATISAA 82 
                                       79*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg++GDG+iFv+pv + +r+rtg
  gi|386001429|ref|YP_005919728.1|  83 ARTGRPGDGRIFVIPVARSVRVRTG 107
                                       ************************8 PP

>> P19Arf_N  Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.0   8.2e-06     0.073      10      32 ..      84     106 ..      82     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-06
                                       HHS-STTHHHHHHHHHHT----- CS
                          P19Arf_N  10 RagrPprvRvFvvkivrparewa 32 
                                       R+grP   R+Fv+ ++r+ r ++
  gi|386001429|ref|YP_005919728.1|  84 RTGRPGDGRIFVIPVARSVRVRT 106
                                       9******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.55
# Mc/sec: 606.79
//
Query:       gi|386001430|ref|YP_005919729.1|  [L=400]
Description: Ammonium transporter [Methanosaeta harundinacea 6Ac]
Scores for 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-129  432.7  41.3   1.2e-129  432.6  41.3    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.6  41.3  6.5e-134  1.2e-129       1     399 []       9     399 ..       9     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 432.6 bits;  conditional E-value: 6.5e-134
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-.....TTT CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign.....lgl 72 
                                       a++l+s+a+v++m +g++l+++glvr+k+v++++  ++l+la+v++++vl+Gysl+fg +  v+gfig      l+ 
  gi|386001430|ref|YP_005919729.1|   9 AWVLVSTAMVMLMIPGVGLFYGGLVRKKDVVSMIGLSFLALALVSVQWVLVGYSLSFGAD--VGGFIGGldllgLKG 83 
                                       7**********************************************************9..*******99966444 PP

                                       TSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.- CS
                   Ammonium_transp  73 saagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliD 149
                                          ++ ++t++ +lf++fql+fa ++++i+++avaer+++ ++++f++l++tlvy p+ahw+wg ggw+ +lg+l D
  gi|386001430|ref|YP_005919729.1|  84 VGMDAGEGTIPGLLFMAFQLVFAGITLAIITSAVAERVRIGSFIVFGLLWTTLVYDPLAHWAWG-GGWAGQLGAL-D 158
                                       456778889999****************************************************.**********.* PP

                                       SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHH CS
                   Ammonium_transp 150 fAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavt 226
                                       fAg+tvVH+ +g+ +La+alv+gkr+g +   ++ +++hn+p++++G++lLwfgWfgFNaGsal+a++ a++ a+v+
  gi|386001430|ref|YP_005919729.1| 159 FAGGTVVHISSGFGALALALVIGKRIGFG---DHDMEPHNIPMTMIGAALLWFGWFGFNAGSALAADGLAAS-AFVV 231
                                       ***************************99...9***************************************.**** PP

                                       HHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-C CS
                   Ammonium_transp 227 TllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidD 303
                                       T+++a+agal++l++s+++ gk++ lg+++G++AGlVAiT+a+++v+p++Al+iG vAgvl++ ++ +++   ++d+
  gi|386001430|ref|YP_005919729.1| 232 TNVSASAGALAWLFASWVR-GKPSALGMVSGAIAGLVAITPAAGFVDPLSALVIGGVAGVLCYRAL-LFRVGRGLDE 306
                                       *******************.**********************************************.6********* PP

                                       TTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB- CS
                   Ammonium_transp 304 sldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLrv 380
                                       sld++avHgvgG+wG++a+gifa e v   + ++gll+g+  q+v+q+ig++++++yafvvt+ +++++++++gLrv
  gi|386001430|ref|YP_005919729.1| 307 SLDAWAVHGVGGLWGAVATGIFAVEAV---GGASGLLQGNVDQFVAQVIGAVAAVVYAFVVTYAIAKVVDATMGLRV 380
                                       *************************85...59999****************************************** PP

                                       -HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 381 seeeeevglDvaehgetay 399
                                       +e+ee+vglD+++hge+ay
  gi|386001430|ref|YP_005919729.1| 381 TEDEEYVGLDISQHGEKAY 399
                                       *****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2504.80
//
Query:       gi|386001431|ref|YP_005919730.1|  [L=192]
Description: Transcriptional regulator, CopG family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.024   14.6   0.0    1.6  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-06     0.024       2      36 ..      17      51 ..      16      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-06
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlrey 36
                                      v+i+ d+e +  ++e+++ +  S+Sel+R Al++y
  gi|386001431|ref|YP_005919730.1| 17 VTISFDRESAGIFREMKDGLVGSQSELLRTALKFY 51
                                      89******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1240.55
//
Query:       gi|386001432|ref|YP_005919731.1|  [L=94]
Description: hypothetical protein Mhar_0730 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 592.81
//
Query:       gi|386001433|ref|YP_005919732.1|  [L=344]
Description: sulfate transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-48  161.3  25.7    1.2e-28   99.7   9.5    3.4  4  MFS_MOT1         Molybdate transporter of MFS superfamily
    1.4e-08   33.9   2.7    1.4e-08   33.9   2.7    2.3  2  Sulfate_transp   Sulfate permease family
     0.0017   17.1  20.7      0.039   12.6   6.3    2.4  2  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   8.2   8.8e-25   5.3e-21       7     111 .]       1     109 [.       1     109 [. 0.98
   2 ?   -1.6   0.4      0.59   3.5e+03      67      82 ..     120     135 ..     112     158 .. 0.65
   3 !   99.7   9.5     2e-32   1.2e-28       3     111 .]     189     303 ..     187     303 .. 0.98
   4 ?   -1.1   0.5       0.4   2.4e+03      87     109 ..     320     342 ..     312     343 .. 0.69

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 8.8e-25
                          MFS_MOT1   7 lgdlglTllnlvialaalaslsltalllsvGlmnlltglfggvPmc.....hgAgglaaqyrfgartgaagillGlv 78 
                                       +g +g T+l+++++ a++++++l+ +ll++Gl+++++g+ +g+Pm+     +++++++a      +++a+g++lG+ 
  gi|386001433|ref|YP_005919732.1|   1 MGNFG-TVLPILLGAALVSEVDLGPALLFIGLWYIVMGIHYGIPMSvepmkAIGAIAIAGELTSGEIAASGLILGVG 76 
                                       699**.******************************************************777************** PP

                          MFS_MOT1  79 llllgltgllerllrliPksvlgglllgaGleL 111
                                       ll+lg ++ +erl+ liP+ v++g++lg+Gl L
  gi|386001433|ref|YP_005919732.1|  77 LLALGSFRGFERLQGLIPEGVVRGVQLGLGLIL 109
                                       ******************************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.59
                          MFS_MOT1  67 rtgaagillGlvllll 82 
                                        ++ a++ +G++ll+l
  gi|386001433|ref|YP_005919732.1| 120 DLIFAAAAVGIFLLFL 135
                                       4556666677776666 PP

  == domain 3  score: 99.7 bits;  conditional E-value: 2e-32
                          MFS_MOT1   3 lsgalgdlglTllnlvialaala......slsltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaagi 73 
                                       ++++l++++lTl+n+ +a+a++a      ++++++l++++G+mn+++++fgg+P+chgAgglaa++rfga +g + +
  gi|386001433|ref|YP_005919732.1| 189 WHLVLPQIPLTLTNATVATALIAedlfkkRIEPDRLCVTMGIMNIISAPFGGFPICHGAGGLAAHHRFGAVSGLSTV 265
                                       889******************999****999********************************************** PP

                          MFS_MOT1  74 llGlvllllgltgllerllrliPksvlgglllgaGleL 111
                                       + Glvll+++l+++  + l+++P  ++g+lll+++le+
  gi|386001433|ref|YP_005919732.1| 266 MGGLVLLVVALFFAGAEALAILPIGLFGALLLFVALEM 303
                                       ***********************************996 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.4
                          MFS_MOT1  87 llerllrliPksvlgglllgaGl 109
                                       +l +l   +  ++l g++l+a+l
  gi|386001433|ref|YP_005919732.1| 320 ALLALFTNVGLAFLFGIVLAAAL 342
                                       45666777888888888888876 PP

>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   5.0     0.012        69      86     133 ..      68     116 ..      43     125 .. 0.88
   2 !   33.9   2.7   2.3e-12   1.4e-08     258     356 ..     203     303 ..     189     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.012
                    Sulfate_transp  86 tltllaGviqvllGllR.LgflveflseavlsGfiaGaaivillsqikv 133
                                       ++ l+ Gv +++lG +R + +l  +++e v++G   G +++++ ++   
  gi|386001433|ref|YP_005919732.1|  68 ASGLILGVGLLALGSFRgFERLQGLIPEGVVRGVQLGLGLILIKTSAGM 116
                                       5678999*********999**********************99887665 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.3e-12
                    Sulfate_transp 258 eaiavsksldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGaktqlsglvsalvvllvllvlt 334
                                        ++a+++ ++   + ++++++  v +G++Ni+s+ fgg+p+  +    a   + Ga + ls+++ +lv+l+v l+++
  gi|386001433|ref|YP_005919732.1| 203 ATVATALIAEDLFKKRIEPDRLCVTMGIMNIISAPFGGFPICHGAGGLAAHHRFGAVSGLSTVMGGLVLLVVALFFA 279
                                       57899999999999************************************************************987 PP

                    Sulfate_transp 335 p..lleyiPkavLaaiiivagkgl 356
                                       +  +l+ +P+   +a+++++++++
  gi|386001433|ref|YP_005919732.1| 280 GaeALAILPIGLFGALLLFVALEM 303
                                       522799************999885 PP

>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   6.5   3.1e-05      0.19      66     146 ..      23     120 ..       5     144 .. 0.76
   2 !   12.6   6.3   6.6e-06     0.039     253     349 ..     205     301 ..     175     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.1e-05
                                       EE-GGGHHHHHGGG-.....................HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHH CS
                   Xan_ur_permease  66 gssfafvtalmialGsa.................edieialagllgallvagvlfilisltglrgrlarlipPvvtg 125
                                       g+++ f+++  i++G                      e + ++++ ++l+ gv  + ++ + + +rl+ lip  v+ 
  gi|386001433|ref|YP_005919732.1|  23 GPALLFIGLWYIVMGIHygipmsvepmkaigaiaIAGELTSGEIAASGLILGVGLLALGSFRGFERLQGLIPEGVVR 99 
                                       55555555555555544555555555555555565578888999999999999999998888889************ PP

                                       HHHHHHHHHHHHHHHHHTTSS CS
                   Xan_ur_permease 126 pvvlliGlslaqiavkkvggg 146
                                       +v l++Gl l+++ + ++   
  gi|386001433|ref|YP_005919732.1| 100 GVQLGLGLILIKTSAGMMVQD 120
                                       **************9999765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.6e-06
                                       HHHHHHHTS-TIIIIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHH CS
                   Xan_ur_permease 253 ravakvvgrslkpkpdlrralladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvtagvilillglipkla 329
                                        a+a +++  +k+ ++  r  ++ G++ ++s+ +G++p    a   +    ++  s+   v++g++l++++l+ + a
  gi|386001433|ref|YP_005919732.1| 205 VATALIAEDLFKKRIEPDRLCVTMGIMNIISAPFGGFPICHGAGGLAAHHRFGAVSGLSTVMGGLVLLVVALFFAGA 281
                                       68888999999999999999********************************************************* PP

                                       HHHTTS-HHHHHHHHHHHHH CS
                   Xan_ur_permease 330 allssIPepvlgGvllvvfg 349
                                       + l+++P    g+ ll v  
  gi|386001433|ref|YP_005919732.1| 282 EALAILPIGLFGALLLFVAL 301
                                       *******9997777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2323.50
//
Query:       gi|386001434|ref|YP_005919733.1|  [L=233]
Description: Glutamine amidotransferase class-I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-15   54.9   0.0    1.2e-14   54.5   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
      3e-05   23.9   0.2    0.00011   22.0   0.2    1.9  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.028   14.2   0.0      0.041   13.7   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
      0.092   12.3   0.0       0.12   11.9   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.14   11.1   0.0       0.17   10.7   0.0    1.1  1  HTS            Homoserine O-succinyltransferase


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   3.4e-18   1.2e-14      42     175 ..      44     179 ..      24     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3.4e-18
                                       STSEEEEEEESSCTT.......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETT CS
                            GATase  42 npdgilvsgGpgspg.......vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgdde 111
                                       ++dg++v gGp +++          +  +i++a+++++ +LGICLG Ql+a+ +g+ v k++++e   +  +l++++
  gi|386001434|ref|YP_005919733.1|  44 EFDGLIVMGGPMNVYeeerypwLAPEKVLIRRAIDEGKVVLGICLGAQLIADVLGGRVRKNEDREIGWHPVNLTSEG 120
                                       68*************99999*966666666777777999********************999888777777777776 PP

                                       T..CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTT CS
                            GATase 112 t..allyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEsts 175
                                       +  +l+  l++e+    +H+++++     p g + +a+s  ++    ++++ + ++g+QFH E+t 
  gi|386001434|ref|YP_005919733.1| 121 SksDLFGLLPEEFFPLSWHGDTFD----IPPGAVRMAES-GGC-ANQAFQLGR-AIGLQFHLEATA 179
                                       687999999***************....59999888888.564.455555554.8********986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   3.2e-08   0.00011      94     128 ..      69     103 ..      43     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-08
                     Peptidase_C26  94 elaLiraalergvPilgiCrGlqllnvalGGtlyq 128
                                       e  Lir+a+++g+ +lgiC+G ql++ +lGG++ +
  gi|386001434|ref|YP_005919733.1|  69 EKVLIRRAIDEGKVVLGICLGAQLIADVLGGRVRK 103
                                       678****************************9866 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.041      44     109 ..      24      95 ..      16     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                       TSEEEE-SEEGG.....GCTCCG-SEEEE--BHHHHHHHHTSH...HHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  44 rGlkvtvdasld.....dvkaaeyDalvlpGGragperlrene...kvvelvkefaekgklvaaICagpqlLaa 109
                                       rG++v+ ++ ++     d  ++e+D l++ GG  +  + ++ +       l++++ ++gk+v  IC g+ql a+
  gi|386001434|ref|YP_005919733.1|  24 RGHTVSWTRLFSgeglpD--PGEFDGLIVMGGPMNVYEEERYPwlaPEKVLIRRAIDEGKVVLGICLGAQLIAD 95 
                                       666666666665554333..889*********87554444444221335689*****************99864 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.5e-05      0.12      43      92 ..      48      97 ..      32     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                          GATase_3 43 lvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92
                                      l++++G  ++ ++  +      +  i++a+ +g+ vlgiC G q+  + +
  gi|386001434|ref|YP_005919733.1| 48 LIVMGGPMNVYEEERYPWLAPEKVLIRRAIDEGKVVLGICLGAQLIADVL 97
                                      6778888888888888888888899*******************976655 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.9e-05      0.17      98     156 ..      44     102 ..      39     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.9e-05
                                       -EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHHHHHHH---- CS
                               HTS  98 kfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaalyylygvek 156
                                       +fDgli+ G p++  e e   +    + ++  a ++ +  l iC++aq     l g  +
  gi|386001434|ref|YP_005919733.1|  44 EFDGLIVMGGPMNVYEEERYPWLAPEKVLIRRAIDEGKVVLGICLGAQLIADVLGGRVR 102
                                       7***********9988777777788888899****************976666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 1466.28
//
Query:       gi|386001435|ref|YP_005919734.1|  [L=350]
Description: hypothetical protein Mhar_0733 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-07   31.1   0.0    4.1e-07   29.9   0.0    1.6  1  YEATS       YEATS family
  ------ inclusion threshold ------
      0.067   13.7   1.1          7    7.3   0.0    3.3  3  RHS_repeat  RHS Repeat


Domain annotation for each model (and alignments):
>> YEATS  YEATS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   4.5e-11   4.1e-07      18      64 ..     273     321 ..     247     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.5e-11
                             YEATS  18 efikkVqFkLhetyanptrvvekp..PFevtetGwGeFeiqikiffkpe 64 
                                       + i++V ++Lh+t+++ ++++++p   Fe++   wG F+++i++++++ 
  gi|386001435|ref|YP_005919734.1| 273 YRIRSVHYQLHPTFSPSEQTMTNPrdNFELELWTWGAFNMPITVTMTDG 321
                                       6799***************99988889*****************99875 PP

>> RHS_repeat  RHS Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.2   1.8e+03       8      20 ..     164     177 ..     159     183 .. 0.84
   2 ?    7.3   0.0   0.00078         7       7      26 ..     238     257 ..     229     260 .. 0.78
   3 ?    2.7   0.1     0.021   1.9e+02      20      38 .]     305     323 ..     292     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                        RHS_repeat   8 tevtdpsGrv.ttY 20 
                                       +e+ +psG+v t+Y
  gi|386001435|ref|YP_005919734.1| 164 VEKRTPSGLVqTRY 177
                                       57889999997777 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00078
                        RHS_repeat   7 LtevtdpsGrvttYtYDaqG 26 
                                       +t+ +dp+++++ Y+Y++qG
  gi|386001435|ref|YP_005919734.1| 238 VTQAVDPQTNRVYYSYNPQG 257
                                       37779**7777669*****9 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.021
                        RHS_repeat  20 YtYDaqGrlttlTdpdGrt 38 
                                       +t+ a++ + t+T +dGr+
  gi|386001435|ref|YP_005919734.1| 305 WTWGAFNMPITVTMTDGRA 323
                                       6778888888888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 2696.52
//
Query:       gi|386001436|ref|YP_005919735.1|  [L=482]
Description: hypothetical protein Mhar_0734 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-19   69.4   1.1    7.9e-19   68.3   1.1    1.5  1  Laminin_G_3  Concanavalin A-like lectin/glucanases superfamil


Domain annotation for each model (and alignments):
>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   1.1   4.4e-23   7.9e-19       1     144 [.     177     329 ..     177     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 4.4e-23
                       Laminin_G_3   1 dggsdyvtlpd.aslptssf...TvsaWvkpdslpsaaqiiis...sssdg....rgfelgldgsg..rlrfsvnag 64 
                                       dg++dyv++ + ++ pt ++   ++++Wvk++s+p+++ +  s   +   g    +gf+lg  +s   +l f+++ag
  gi|386001436|ref|YP_005919735.1| 177 DGSGDYVRVGNvHQDPTRDLsqgSIEMWVKLESAPTNFVLAASgreY---GgsfdDGFYLGTHSSYskNLVFMIWAG 250
                                       6899*****995555455443339************99888867531...135677999999666556*******99 PP

                       Laminin_G_3  65 ngaeesvtsgasvpa..geWtHvavtydggtlrlYvNGvevgsatltggllsatsgplviGrdpggddpfdGlidev 139
                                       +  ++ ++sg + ++  geW Hv +t+    l ++v+G ++g++++tggl++++ +++ iG d++   + +Gli  v
  gi|386001436|ref|YP_005919735.1| 251 G--WKVADSGIPPEDliGEWRHVMGTWGPRGLEIWVDGILRGTKPHTGGLPNPNYATVLIGTDSW-RWDTHGLIGGV 324
                                       6..**********************************************9999***********9.56789****** PP

                       Laminin_G_3 140 riynr 144
                                       +iy+ 
  gi|386001436|ref|YP_005919735.1| 325 AIYDV 329
                                       ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 3067.04
//
Query:       gi|386001437|ref|YP_005919736.1|  [L=501]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-61  202.3   5.4    6.6e-10   38.4   0.2    8.5  8  TPR_1          Tetratricopeptide repeat
    2.4e-53  178.5  22.6    1.7e-23   82.8   3.0    5.2  5  HEAT_2         HEAT repeats
    2.5e-53  177.5  15.2    3.3e-09   36.3   0.9    7.5  7  TPR_11         TPR repeat
    9.5e-50  162.8  14.0    2.6e-07   30.2   0.3    9.0  8  TPR_2          Tetratricopeptide repeat
      1e-49  166.9  37.7    9.7e-11   42.1   0.9    8.2  8  TPR_16         Tetratricopeptide repeat
    4.3e-40  132.6   3.6    2.8e-05   24.0   0.1    8.4  8  TPR_8          Tetratricopeptide repeat
    3.6e-38  127.2   1.5    3.3e-05   24.0   0.0    8.1  7  TPR_17         Tetratricopeptide repeat
      2e-32  108.5  47.3    1.9e-06   28.0   0.6    9.2  8  HEAT_PBS       PBS lyase HEAT-like repeat
      3e-22   76.8   3.3     0.0024   18.0   0.0    8.2  8  HEAT           HEAT repeat
      2e-21   76.2  25.2    1.2e-05   25.7   0.3    7.1  8  TPR_19         Tetratricopeptide repeat
      6e-21   73.3  41.6    0.00075   20.1   0.1   11.8 13  TPR_14         Tetratricopeptide repeat
    1.6e-18   66.6  26.4    1.4e-05   25.1   0.0    7.2  7  TPR_9          Tetratricopeptide repeat
    6.9e-18   64.7  12.7      8e-06   26.1   0.4    6.6  5  TPR_12         Tetratricopeptide repeat
      1e-17   63.5   2.5    3.5e-05   23.7   0.0    6.4  6  Arm            Armadillo/beta-catenin-like repeat
    3.5e-17   61.1   7.1      0.022   14.7   0.0    7.4  8  TPR_7          Tetratricopeptide repeat
    3.4e-16   58.7   8.1      0.041   14.5   0.0    8.6  7  TPR_6          Tetratricopeptide repeat
    1.6e-12   46.9  21.9      0.028   14.3   0.3    8.5  8  TPR_10         Tetratricopeptide repeat
    4.2e-12   46.3  24.1     0.0075   16.8   3.4    7.7  7  HEAT_EZ        HEAT-like repeat
    2.7e-11   43.2   0.0        0.4   10.7   0.0    6.6  7  TPR_3          Tetratricopeptide repeat
    1.3e-08   35.1   4.7        1.6    8.8   0.0    6.4  6  DUF3856        Domain of Unknown Function (DUF3856)
    1.3e-07   30.9   0.0       0.03   13.3   0.1    4.0  4  NARP1          NMDA receptor-regulated protein 1
    3.2e-07   30.5   0.0       0.13   12.3   0.0    4.6  5  Cnd1           non-SMC mitotic condensation complex subunit 1
    9.4e-07   29.0   0.0      0.074   13.3   0.0    3.7  3  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
    1.5e-06   28.4   0.5        1.1    9.3   0.0    4.1  4  Aconitase_B_N  Aconitate B N-terminal domain
    6.2e-06   26.7  16.9       0.18   12.3   0.6    5.7  6  BTAD           Bacterial transcriptional activator domain
     0.0005   19.7   0.0     0.0029   17.2   0.0    2.1  2  ERAP1_C        ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.024   14.7   4.3        5.6    7.1   0.1    5.4  6  MIT            MIT (microtubule interacting and transport) do
      0.038   13.7   0.0        3.1    7.5   0.0    2.4  2  DSX_dimer      Doublesex dimerisation domain
      0.039   14.0   0.1         26    5.0   0.0    4.5  5  Fis1_TPR_C     Fis1 C-terminal tetratricopeptide repeat
      0.052   13.8   6.1        1.4    9.1   0.1    4.2  4  TPR_5          Tetratrico peptide repeat
      0.076   11.6   0.0        1.7    7.1   0.0    2.1  2  Adaptin_N      Adaptin N terminal region
       0.16   12.3   0.0    1.5e+02    2.8   0.0    4.2  5  RasGEF_N_2     Rapamycin-insensitive companion of mTOR RasGEF
        0.2   11.2   0.2         38    3.7   0.0    3.8  6  CLASP_N        CLASP N terminal
       0.27   11.1   0.9        6.4    6.7   0.1    3.7  4  BPS            BPS (Between PH and SH2)
       0.31   10.9   0.2         27    4.6   0.0    2.7  3  DUF3385        Domain of unknown function (DUF3385)
        4.3    7.0  13.9          4    7.1   0.3    5.5  7  TPR_21         Tetratricopeptide repeat-like domain
        9.9    6.0  12.4    1.1e+02    2.7   0.1    5.1  5  PPTA           Protein prenyltransferase alpha subunit repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.5   7.1e+02      24      32 ..     255     263 ..     253     264 .. 0.82
   2 !   23.5   0.0   6.7e-08   3.3e-05       2      34 .]     267     299 ..     266     299 .. 0.95
   3 !   28.6   0.0   1.7e-09   8.4e-07       2      34 .]     301     333 ..     300     333 .. 0.96
   4 !   35.1   0.0   1.5e-11   7.3e-09       3      34 .]     336     367 ..     334     367 .. 0.97
   5 !   30.1   0.0   5.6e-10   2.7e-07       1      34 []     368     401 ..     368     401 .. 0.96
   6 !   38.4   0.2   1.4e-12   6.6e-10       1      33 [.     402     434 ..     402     435 .. 0.96
   7 !   24.8   0.0   2.6e-08   1.3e-05       3      34 .]     438     469 ..     437     469 .. 0.96
   8 !   14.3   0.0   5.5e-05     0.027       2      28 ..     471     497 ..     470     499 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                                       HHHHHHHST CS
                             TPR_1  24 yekALelnP 32 
                                       y++A++++P
  gi|386001437|ref|YP_005919736.1| 255 YDEAISIDP 263
                                       788888888 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 6.7e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+ ++G+ ++  g++ eA+ +y+ AL+l+P++
  gi|386001437|ref|YP_005919736.1| 267 LAWGGKGLSLYDGGRLSEAVVAYDTALSLDPQD 299
                                       69*****************************86 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 1.7e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++++n+G+a++ lg++ eA+e+y+ A++l+P++
  gi|386001437|ref|YP_005919736.1| 301 YVWNNKGVALRDLGRLSEAVEAYDVAISLDPQY 333
                                       79*****************************86 PP

  == domain 4  score: 35.1 bits;  conditional E-value: 1.5e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+yn+G a+ ++g+ ++A+e+y+ A++l+P++
  gi|386001437|ref|YP_005919736.1| 336 AWYNKGIALDEMGEDEKAIEAYDMAISLDPED 367
                                       9*****************************86 PP

  == domain 5  score: 30.1 bits;  conditional E-value: 5.6e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++n+G+a+f +g++ eA+++y+ A+ l+P +
  gi|386001437|ref|YP_005919736.1| 368 ANAWNNKGVALFGQGQLSEAIKAYDVAIVLDPGY 401
                                       79*****************************975 PP

  == domain 6  score: 38.4 bits;  conditional E-value: 1.4e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a++n+G+a++ +g++ eA+e+y+ AL+l+P 
  gi|386001437|ref|YP_005919736.1| 402 AQAWNNKGVALYDQGRLSEAVEAYDMALSLDPA 434
                                       79******************************5 PP

  == domain 7  score: 24.8 bits;  conditional E-value: 2.6e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ n+G+a+++lg+y+eA+  y+++++ +P++
  gi|386001437|ref|YP_005919736.1| 438 AWMNKGLALRSLGRYEEAVLIYDEVIRQRPED 469
                                       8**************************99986 PP

  == domain 8  score: 14.3 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekAL 28 
                                       +a+ ++G+a++ lg+ +eA++++++  
  gi|386001437|ref|YP_005919736.1| 471 DAWVGRGAALQALGRGEEAEAAFSRGR 497
                                       79*********************9965 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   7.8e-05     0.038      45      73 ..      39      67 ..      24      68 .. 0.70
   2 !   82.8   3.0   3.6e-26   1.7e-23       1      88 []      58     144 ..      58     144 .. 0.98
   3 !   71.9   0.6   8.8e-23   4.3e-20       8      88 .]     128     207 ..     126     207 .. 0.98
   4 !   45.7   0.8   1.3e-14   6.2e-12       7      74 ..     190     256 ..     186     261 .. 0.92
   5 ?    0.9   0.1       1.2   5.9e+02      65      88 .]     461     484 ..     437     492 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-05
                            HEAT_2 45 pavRraaaeaLgaigdpealpaLkelldd 73
                                      ++vR+ aa+aLg+ g   a++ L  +l d
  gi|386001437|ref|YP_005919736.1| 39 ADVRAGAARALGEAGGAGAVDPLISALED 67
                                      56777777777777777777777777765 PP

  == domain 2  score: 82.8 bits;  conditional E-value: 3.6e-26
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                       +d+L++al +d+  evr +a+ aLg+ ++ +a+  L+ +l+d+dp vRr+aa+aLg+igdp+a++ L++l++ d+d 
  gi|386001437|ref|YP_005919736.1|  58 VDPLISAL-EDEASEVRCEAAAALGEVRDARAVGPLIAALKDPDPGVRREAARALGEIGDPQAIEPLAHLALKDPDG 133
                                       689*****.9******************************************************************* PP

                            HEAT_2  78 vvReaAaeaLa 88 
                                        vR +A+eaLa
  gi|386001437|ref|YP_005919736.1| 134 GVRGKAVEALA 144
                                       *********96 PP

  == domain 3  score: 71.9 bits;  conditional E-value: 8.8e-23
                            HEAT_2   8 lendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAa 84 
                                       l +dpd  vr +a++aL++ g+p a+  L+ +++de++ vR+ aa+aLg+igdp+a++ L+ l++ d+d  vR +A+
  gi|386001437|ref|YP_005919736.1| 128 L-KDPDGGVRGKAVEALAEAGDPAAVTPLIGAIKDENSSVRMRAARALGEIGDPQAIEPLAYLALKDPDGGVRGEAV 203
                                       6.9************************************************************************** PP

                            HEAT_2  85 eaLa 88 
                                       eaLa
  gi|386001437|ref|YP_005919736.1| 204 EALA 207
                                       **96 PP

  == domain 4  score: 45.7 bits;  conditional E-value: 1.3e-14
                            HEAT_2   7 alendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddd 74 
                                       al +dpd  vr +a++aL++ g p a+  L+ +l+d+dp v + a eaL+ igdp+a++ L e+ + d
  gi|386001437|ref|YP_005919736.1| 190 AL-KDPDGGVRGEAVEALAEAGGPAAVTPLIAALRDADPGVSEKASEALVIIGDPRAVAPLIEARRYD 256
                                       34.9**********************************************************987766 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.2
                            HEAT_2  65 paLkellddddddvvReaAaeaLa 88 
                                       ++ +++  d d +v R aA++aL+
  gi|386001437|ref|YP_005919736.1| 461 EVIRQRPEDGDAWVGRGAALQALG 484
                                       444555555555666666666654 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0039       1.9      16      31 ..     254     269 ..     252     275 .. 0.86
   2 !   35.2   0.0   1.5e-11   7.2e-09       1      38 [.     273     310 ..     273     310 .. 0.96
   3 !   31.8   0.1   1.7e-10   8.2e-08       3      42 .]     309     348 ..     307     348 .. 0.93
   4 !   36.3   0.1   6.8e-12   3.3e-09       6      42 .]     346     382 ..     343     382 .. 0.96
   5 !   36.3   0.9   6.8e-12   3.3e-09       3      42 .]     377     416 ..     377     416 .. 0.96
   6 !   28.8   0.1   1.4e-09     7e-07       3      38 ..     411     446 ..     409     446 .. 0.94
   7 !   27.2   0.0   4.8e-09   2.3e-06       1      42 []     443     484 ..     443     484 .. 0.98

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                            TPR_11  16 aYkkAlkldPdnaeay 31 
                                       +Y +A+ +dP ++ a+
  gi|386001437|ref|YP_005919736.1| 254 RYDEAISIDPASPLAW 269
                                       7************998 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 1.5e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G  +y+ G++ eA+ aY +Al ldP+++ +++n G+a+
  gi|386001437|ref|YP_005919736.1| 273 GLSLYDGGRLSEAVVAYDTALSLDPQDPYVWNNKGVAL 310
                                       7789*******************************985 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 1.7e-10
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a++++G++ eA+eaY  A+ ldP++  a+yn G a+ ++G
  gi|386001437|ref|YP_005919736.1| 309 ALRDLGRLSEAVEAYDVAISLDPQYSHAWYNKGIALDEMG 348
                                       89********************************997776 PP

  == domain 4  score: 36.3 bits;  conditional E-value: 6.8e-12
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       e G+ e+AieaY  A+ ldP++a+a++n G+a++ qG
  gi|386001437|ref|YP_005919736.1| 346 EMGEDEKAIEAYDMAISLDPEDANAWNNKGVALFGQG 382
                                       679*******************************998 PP

  == domain 5  score: 36.3 bits;  conditional E-value: 6.8e-12
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a++ qG++ eAi+aY  A+ ldP +a a++n G+a+y qG
  gi|386001437|ref|YP_005919736.1| 377 ALFGQGQLSEAIKAYDVAIVLDPGYAQAWNNKGVALYDQG 416
                                       5788***********************************9 PP

  == domain 6  score: 28.8 bits;  conditional E-value: 1.4e-09
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       a+y+qG++ eA+eaY  Al ldP +  a+ n Gla+
  gi|386001437|ref|YP_005919736.1| 411 ALYDQGRLSEAVEAYDMALSLDPAYHHAWMNKGLAL 446
                                       89*******************************995 PP

  == domain 7  score: 27.2 bits;  conditional E-value: 4.8e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a++++G+yeeA+  Y + ++ +P++ +a+ ++G+a++++G
  gi|386001437|ref|YP_005919736.1| 443 GLALRSLGRYEEAVLIYDEVIRQRPEDGDAWVGRGAALQALG 484
                                       889************************************998 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.7   8.4e+02      24      32 ..     255     263 ..     249     265 .. 0.61
   2 !   20.2   0.0   8.9e-07   0.00043       2      34 .]     267     299 ..     266     299 .. 0.94
   3 !   26.4   0.0   9.1e-09   4.4e-06       1      34 []     300     333 ..     300     333 .. 0.95
   4 !   26.1   0.0   1.1e-08   5.5e-06       3      34 .]     336     367 ..     334     367 .. 0.96
   5 !   27.0   0.0     6e-09   2.9e-06       1      33 [.     368     400 ..     368     401 .. 0.96
   6 !   30.2   0.3   5.4e-10   2.6e-07       1      33 [.     402     434 ..     402     435 .. 0.96
   7 !   21.4   0.0   3.6e-07   0.00017       3      34 .]     438     469 ..     436     469 .. 0.95
   8 !   11.7   0.2   0.00047      0.23       2      30 ..     471     499 ..     470     500 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.7
                             TPR_2  24 fekAleldP 32 
                                       +++A+++dP
  gi|386001437|ref|YP_005919736.1| 255 YDEAISIDP 263
                                       556666665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 8.9e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+   Gl++y  g++ eA+ a++ Al+ldP++
  gi|386001437|ref|YP_005919736.1| 267 LAWGGKGLSLYDGGRLSEAVVAYDTALSLDPQD 299
                                       68999**************************86 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 9.1e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++++n G a++ lg++ eA+ea++ A++ldP++
  gi|386001437|ref|YP_005919736.1| 300 PYVWNNKGVALRDLGRLSEAVEAYDVAISLDPQY 333
                                       579*****************************85 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 1.1e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+yn G a+ ++g+ e+A+ea++ A++ldP++
  gi|386001437|ref|YP_005919736.1| 336 AWYNKGIALDEMGEDEKAIEAYDMAISLDPED 367
                                       9*****************************86 PP

  == domain 5  score: 27.0 bits;  conditional E-value: 6e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++n G a++ +g++ eA++a++ A+ ldP+
  gi|386001437|ref|YP_005919736.1| 368 ANAWNNKGVALFGQGQLSEAIKAYDVAIVLDPG 400
                                       689*****************************7 PP

  == domain 6  score: 30.2 bits;  conditional E-value: 5.4e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a++n G a+y +g++ eA+ea++ Al+ldP 
  gi|386001437|ref|YP_005919736.1| 402 AQAWNNKGVALYDQGRLSEAVEAYDMALSLDPA 434
                                       789*****************************6 PP

  == domain 7  score: 21.4 bits;  conditional E-value: 3.6e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a++n Gla++ lg+yeeA+  ++++++  P++
  gi|386001437|ref|YP_005919736.1| 438 AWMNKGLALRSLGRYEEAVLIYDEVIRQRPED 469
                                       8**************************99986 PP

  == domain 8  score: 11.7 bits;  conditional E-value: 0.00047
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       +a+  +G a+ +lg+ eeA++af +  el
  gi|386001437|ref|YP_005919736.1| 471 DAWVGRGAALQALGRGEEAEAAFSRGREL 499
                                       69*********************997665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.8         1     5e+02       6      43 ..      76     114 ..      73     116 .. 0.80
   2 !   24.0   0.1   9.6e-08   4.7e-05      17      68 .]     252     300 ..     252     300 .. 0.95
   3 !   35.4   0.2   2.6e-11   1.2e-08       4      67 ..     273     333 ..     272     334 .. 0.96
   4 !   29.4   0.3     2e-09   9.6e-07       3      67 ..     306     367 ..     304     368 .. 0.95
   5 !   33.4   0.1   1.1e-10   5.3e-08       1      67 [.     338     401 ..     338     402 .. 0.94
   6 !   42.1   0.9     2e-13   9.7e-11       3      66 ..     374     434 ..     372     436 .. 0.95
   7 !   41.9   0.7   2.5e-13   1.2e-10       3      66 ..     408     468 ..     406     469 .. 0.95
   8 !   29.7   3.1   1.5e-09   7.2e-07       2      59 ..     441     495 ..     440     499 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                            TPR_16   6 aalragdyddAaaal.eaalkrdpssPdaaeAllllgda 43 
                                       aa+++g+ +dA+a+   +a  +dp++ +++eA+ +lg++
  gi|386001437|ref|YP_005919736.1|  76 AAAALGEVRDARAVGpLIAALKDPDPGVRREAARALGEI 114
                                       678888888888887777777777888899999999975 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 9.6e-08
                            TPR_16  17 aaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       a+++++a+  d   P+ + A+ ++g++++  grl eA+ +y+ al  +p++p
  gi|386001437|ref|YP_005919736.1| 252 ARRYDEAISID---PASPLAWGGKGLSLYDGGRLSEAVVAYDTALSLDPQDP 300
                                       688999*****...88888*******************************98 PP

  == domain 3  score: 35.4 bits;  conditional E-value: 2.6e-11
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++++ g+  +A+ a+++al +d   P+++  ++++g+a+  +grl eA+++y+ a+  +p++
  gi|386001437|ref|YP_005919736.1| 273 GLSLYDGGRLSEAVVAYDTALSLD---PQDPYVWNNKGVALRDLGRLSEAVEAYDVAISLDPQY 333
                                       789*********************...*******************************999986 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 2e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++ a++++g+  +A++a++ a+ +d   P+  +A++++g a+ + g+ ++A+++y+ a+  +p +
  gi|386001437|ref|YP_005919736.1| 306 KGVALRDLGRLSEAVEAYDVAISLD---PQYSHAWYNKGIALDEMGEDEKAIEAYDMAISLDPED 367
                                       67799********************...*******************************999987 PP

  == domain 5  score: 33.4 bits;  conditional E-value: 1.1e-10
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++ a+ + g+ ++A++a++ a+ +d   P++a A++++g+a++ qg l eA+ +y+ a+  +p++
  gi|386001437|ref|YP_005919736.1| 338 YNKGIALDEMGEDEKAIEAYDMAISLD---PEDANAWNNKGVALFGQGQLSEAIKAYDVAIVLDPGY 401
                                       67788888889999*************...*******************************999986 PP

  == domain 6  score: 42.1 bits;  conditional E-value: 2e-13
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ a++ +g+  +A++a++ a+ +d   P  a+A++++g+a++ qgrl eA+++y+ al  +p 
  gi|386001437|ref|YP_005919736.1| 374 KGVALFGQGQLSEAIKAYDVAIVLD---PGYAQAWNNKGVALYDQGRLSEAVEAYDMALSLDPA 434
                                       67799********************...*******************************99986 PP

  == domain 7  score: 41.9 bits;  conditional E-value: 2.5e-13
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ a++++g+  +A++a++ al +d   P+ ++A++++g+a+  +gr++eA+  y++ +r+ p 
  gi|386001437|ref|YP_005919736.1| 408 KGVALYDQGRLSEAVEAYDMALSLD---PAYHHAWMNKGLALRSLGRYEEAVLIYDEVIRQRPE 468
                                       6779*********************...*****************************9999996 PP

  == domain 8  score: 29.7 bits;  conditional E-value: 1.5e-09
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                       ++++a++ +g+y++A+  ++++++++   P++ +A+ ++g a+ ++gr +eA+a++ +
  gi|386001437|ref|YP_005919736.1| 441 NKGLALRSLGRYEEAVLIYDEVIRQR---PEDGDAWVGRGAALQALGRGEEAEAAFSR 495
                                       6899**********************...************************99987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.4   1.6e+03      24      33 ..     255     264 ..     254     265 .. 0.84
   2 !   12.7   0.0   0.00024      0.12       3      34 .]     268     299 ..     267     299 .. 0.94
   3 !   22.6   0.0   1.6e-07     8e-05       3      33 ..     302     332 ..     300     333 .. 0.95
   4 !   24.0   0.1   5.8e-08   2.8e-05       2      34 .]     335     367 ..     334     367 .. 0.96
   5 !   15.3   0.0   3.6e-05     0.017       1      32 [.     368     399 ..     368     401 .. 0.90
   6 !   23.0   0.1   1.2e-07   5.8e-05       1      33 [.     402     434 ..     402     435 .. 0.96
   7 !   22.4   0.0   1.8e-07   8.8e-05       2      33 ..     437     468 ..     436     469 .. 0.94
   8 ?    4.0   0.0      0.15        71       2      24 ..     471     493 ..     470     496 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.4
                                       HHHHHHHHHH CS
                             TPR_8  24 yekaleldpd 33 
                                       y +a+++dp+
  gi|386001437|ref|YP_005919736.1| 255 YDEAISIDPA 264
                                       7899999996 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+  +g+ + + g++ eA+ +y  al+ldp++
  gi|386001437|ref|YP_005919736.1| 268 AWGGKGLSLYDGGRLSEAVVAYDTALSLDPQD 299
                                       6888999***********************86 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++n+g ++++lg++ eA+e+y  a++ldp+
  gi|386001437|ref|YP_005919736.1| 302 VWNNKGVALRDLGRLSEAVEAYDVAISLDPQ 332
                                       8*****************************8 PP

  == domain 4  score: 24.0 bits;  conditional E-value: 5.8e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+yn+g +++++g+ e+A+e+y  a++ldp++
  gi|386001437|ref|YP_005919736.1| 335 HAWYNKGIALDEMGEDEKAIEAYDMAISLDPED 367
                                       79*****************************86 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 3.6e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a a++n+g +++ +g++ eA+++y  a+ ldp
  gi|386001437|ref|YP_005919736.1| 368 ANAWNNKGVALFGQGQLSEAIKAYDVAIVLDP 399
                                       679*********************88877776 PP

  == domain 6  score: 23.0 bits;  conditional E-value: 1.2e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a++n+g ++ ++g++ eA+e+y  al+ldp+
  gi|386001437|ref|YP_005919736.1| 402 AQAWNNKGVALYDQGRLSEAVEAYDMALSLDPA 434
                                       79******************************7 PP

  == domain 7  score: 22.4 bits;  conditional E-value: 1.8e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n+g+++++lg+yeeA+  y ++++ +p+
  gi|386001437|ref|YP_005919736.1| 437 HAWMNKGLALRSLGRYEEAVLIYDEVIRQRPE 468
                                       79*************************99987 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.15
                                       CHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyy 24 
                                       +a++  g +++ lg+ eeA++++
  gi|386001437|ref|YP_005919736.1| 471 DAWVGRGAALQALGRGEEAEAAF 493
                                       689999***************99 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.05        24       2      32 ..     255     285 ..     255     286 .. 0.89
   2 !   24.0   0.0   6.7e-08   3.3e-05       1      33 [.     288     320 ..     288     321 .. 0.94
   3 !   19.2   0.0   2.2e-06    0.0011       2      34 .]     323     355 ..     322     355 .. 0.94
   4 !   23.3   0.0   1.1e-07   5.4e-05       2      34 .]     357     389 ..     356     389 .. 0.94
   5 !   20.5   0.0   8.4e-07   0.00041       2      33 ..     391     422 ..     390     423 .. 0.92
   6 !   13.8   0.1   0.00012      0.06       2      32 ..     425     455 ..     424     456 .. 0.94
   7 !   11.2   0.0   0.00082       0.4       2      33 ..     459     490 ..     458     491 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y +a+ +dP ++ a+  ++  l+  G+l +A
  gi|386001437|ref|YP_005919736.1| 255 YDEAISIDPASPLAWGGKGLSLYDGGRLSEA 285
                                       89*************9999999988887766 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 6.7e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y  al ldP +++++nn++++l+ +G+l +A+
  gi|386001437|ref|YP_005919736.1| 288 AYDTALSLDPQDPYVWNNKGVALRDLGRLSEAV 320
                                       599*************************99997 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 2.2e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y  a+ ldP ++ a++n++ +l + G+ ++A++
  gi|386001437|ref|YP_005919736.1| 323 YDVAISLDPQYSHAWYNKGIALDEMGEDEKAIE 355
                                       8889**************************986 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 1.1e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y  a+ ldP +a+a+nn++++l  +G+l +A++
  gi|386001437|ref|YP_005919736.1| 357 YDMAISLDPEDANAWNNKGVALFGQGQLSEAIK 389
                                       888*************************99985 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 8.4e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y  a+ ldP +a a+nn++++l+ +G+l +A+
  gi|386001437|ref|YP_005919736.1| 391 YDVAIVLDPGYAQAWNNKGVALYDQGRLSEAV 422
                                       77899***********************9997 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 0.00012
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y  al ldP +  a+ n++ +l+++G++++A
  gi|386001437|ref|YP_005919736.1| 425 YDMALSLDPAYHHAWMNKGLALRSLGRYEEA 455
                                       8889*************************99 PP

  == domain 7  score: 11.2 bits;  conditional E-value: 0.00082
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +++++ P + da+  ++ +l  +G+ ++A+
  gi|386001437|ref|YP_005919736.1| 459 YDEVIRQRPEDGDAWVGRGAALQALGRGEEAE 490
                                       99************************988886 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 !   17.8   0.9   7.9e-06    0.0038       1      27 []      41      67 ..      41      67 .. 0.98
   2 !   22.5   1.7   2.3e-07   0.00011       1      27 []      72      98 ..      72      98 .. 0.98
   3 !   28.0   0.6   3.9e-09   1.9e-06       1      23 [.     103     125 ..     103     128 .. 0.93
   4 !   16.1   0.1   2.7e-05     0.013       1      27 []     135     161 ..     135     161 .. 0.94
   5 !   23.4   0.3   1.2e-07   5.9e-05       1      21 [.     166     186 ..     166     187 .. 0.97
   6 !   19.8   0.8   1.7e-06    0.0008       1      27 []     198     224 ..     198     224 .. 0.97
   7 !    9.9   0.1    0.0027       1.3       5      24 ..     233     252 ..     231     254 .. 0.91
   8 ?   -0.8   0.9       7.5   3.7e+03       2      11 ..     476     485 ..     476     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.9e-06
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR+ Aa+aLg+ g   a+++L+ aL+d
  gi|386001437|ref|YP_005919736.1| 41 VRAGAARALGEAGGAGAVDPLISALED 67
                                      8************************98 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.3e-07
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR++Aa aLg+++d +a+ +L++aL+d
  gi|386001437|ref|YP_005919736.1| 72 VRCEAAAALGEVRDARAVGPLIAALKD 98
                                      9************************98 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 3.9e-09
                                       HHHHHHHHHHHCTSGGGHHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLle 23 
                                       vRr+Aa+aLg++gd++ai++L  
  gi|386001437|ref|YP_005919736.1| 103 VRREAARALGEIGDPQAIEPLAH 125
                                       9********************76 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR  A++aL++ gd++a+ +L+ a +d
  gi|386001437|ref|YP_005919736.1| 135 VRGKAVEALAEAGDPAAVTPLIGAIKD 161
                                       89********************98876 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHHCTSGGGHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaL 21 
                                       vR +Aa+aLg++gd++ai++L
  gi|386001437|ref|YP_005919736.1| 166 VRMRAARALGEIGDPQAIEPL 186
                                       8*******************9 PP

  == domain 6  score: 19.8 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +A++aL++ g ++a+ +L++aL d
  gi|386001437|ref|YP_005919736.1| 198 VRGEAVEALAEAGGPAAVTPLIAALRD 224
                                       8************************87 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0027
                                       HHHHHHHCTSGGGHHHHHHH CS
                          HEAT_PBS   5 AakaLgqlgdeeaipaLlea 24 
                                       A +aL  +gd++a+++L+ea
  gi|386001437|ref|YP_005919736.1| 233 ASEALVIIGDPRAVAPLIEA 252
                                       56899*************98 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 7.5
                                       HHHHHHHHHH CS
                          HEAT_PBS   2 RraAakaLgq 11 
                                       R aA+ aLg+
  gi|386001437|ref|YP_005919736.1| 476 RGAALQALGR 485
                                       889*****96 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.22     1e+02      12      26 ..      37      51 ..      29      52 .. 0.81
   2 !   15.5   0.1     3e-05     0.015       3      26 ..      59      82 ..      57      83 .. 0.91
   3 !   18.0   0.0     5e-06    0.0024       4      27 ..      91     114 ..      89     116 .. 0.88
   4 ?    5.3   0.0     0.059        28       4      26 ..     122     145 ..     119     147 .. 0.84
   5 !   17.0   0.0     1e-05    0.0049       4      27 ..     154     177 ..     152     179 .. 0.90
   6 ?    3.4   0.0      0.25   1.2e+02       8      25 ..     190     207 ..     183     209 .. 0.85
   7 ?    3.6   0.0      0.21     1e+02       4      27 ..     217     240 ..     215     242 .. 0.84
   8 ?    1.4   0.0       1.1   5.2e+02      11      26 ..     469     485 ..     468     485 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.22
                                      SSHHHHHHHHHHHHH CS
                              HEAT 12 pspeVReaAakaLga 26
                                        ++VR+ Aa+aLg+
  gi|386001437|ref|YP_005919736.1| 37 GQADVRAGAARALGE 51
                                      5789*********96 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3e-05
                                      HHHHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT  3 PlllkllsDpspeVReaAakaLga 26
                                      ++l+++l+D+++eVR+ Aa aLg+
  gi|386001437|ref|YP_005919736.1| 59 DPLISALEDEASEVRCEAAAALGE 82
                                      679999****************97 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 5e-06
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+ +l+Dp+p VR+ Aa+aLg++
  gi|386001437|ref|YP_005919736.1|  91 PLIAALKDPDPGVRREAARALGEI 114
                                       467779****************99 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.059
                                       HHHHH.HT-SSHHHHHHHHHHHHH CS
                              HEAT   4 lllkl.lsDpspeVReaAakaLga 26 
                                       +l +l l+Dp+  VR  A++aL++
  gi|386001437|ref|YP_005919736.1| 122 PLAHLaLKDPDGGVRGKAVEALAE 145
                                       5666757**************985 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 1e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+ +++D++++VR+ Aa+aLg++
  gi|386001437|ref|YP_005919736.1| 154 PLIGAIKDENSSVRMRAARALGEI 177
                                       578899****************99 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.25
                                       HHT-SSHHHHHHHHHHHH CS
                              HEAT   8 llsDpspeVReaAakaLg 25 
                                       +l+Dp+  VR  A++aL+
  gi|386001437|ref|YP_005919736.1| 190 ALKDPDGGVRGEAVEALA 207
                                       58**************97 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.21
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+ +l+D +p V e A +aL+ +
  gi|386001437|ref|YP_005919736.1| 217 PLIAALRDADPGVSEKASEALVII 240
                                       466779**************9865 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 1.1
                                       -SSHHH.HHHHHHHHHH CS
                              HEAT  11 DpspeV.ReaAakaLga 26 
                                       D ++ V R aA++aLg+
  gi|386001437|ref|YP_005919736.1| 469 DGDAWVgRGAALQALGR 485
                                       65666779*******95 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       8.9   4.3e+03      20      35 ..      34      49 ..      31      54 .. 0.76
   2 ?   -0.9   0.1       4.9   2.4e+03      32      47 ..      74      89 ..      65     104 .. 0.86
   3 ?   -1.3   0.3       6.8   3.3e+03      24      29 ..     100     105 ..      75     140 .. 0.54
   4 ?    1.0   0.1       1.3   6.1e+02       2      41 ..     144     180 ..     137     200 .. 0.74
   5 !   15.7   0.0   3.3e-05     0.016      12      62 ..     253     303 ..     244     307 .. 0.94
   6 !   24.8   0.6   4.6e-08   2.2e-05       2      62 ..     311     371 ..     310     375 .. 0.94
   7 !   25.7   0.3   2.5e-08   1.2e-05       1      57 [.     378     434 ..     378     444 .. 0.93
   8 !   21.7   0.1   4.5e-07   0.00022       5      51 ..     450     496 ..     446     499 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.9
                            TPR_19 20 edpknaearllLAeal 35
                                       + ++a++r++ A+al
  gi|386001437|ref|YP_005919736.1| 34 LKYGQADVRAGAARAL 49
                                      5667999999999998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.9
                            TPR_19 32 AeallalgqldeAeal 47
                                      +ea  alg++ +A+a+
  gi|386001437|ref|YP_005919736.1| 74 CEAAAALGEVRDARAV 89
                                      7889999999999985 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.8
                            TPR_19  24 naearl 29 
                                       ++ +r 
  gi|386001437|ref|YP_005919736.1| 100 DPGVRR 105
                                       334444 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.3
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                        ++gd+a+  +l  ++   + +n+ +r++ A+al + g++
  gi|386001437|ref|YP_005919736.1| 144 AEAGDPAAVTPLIGAI---KDENSSVRMRAARALGEIGDP 180
                                       5677777777777777...888999999999998777775 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 3.3e-05
                            TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +++ +a++ dp ++ a+ +    l+  g+l eA  + d+++  dp+d++++
  gi|386001437|ref|YP_005919736.1| 253 RRYDEAISIDPASPLAWGGKGLSLYDGGRLSEAVVAYDTALSLDPQDPYVW 303
                                       68999********************************************98 PP

  == domain 6  score: 24.8 bits;  conditional E-value: 4.6e-08
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        + g++ eA++++  a++ dp+++ a+++  +al ++g+ ++A+++ d +   dp da+++
  gi|386001437|ref|YP_005919736.1| 311 RDLGRLSEAVEAYDVAISLDPQYSHAWYNKGIALDEMGEDEKAIEAYDMAISLDPEDANAW 371
                                       56799***************************************************98876 PP

  == domain 7  score: 25.7 bits;  conditional E-value: 2.5e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l+ +g++ eA++++  a+  dp++a a+ +   al+ +g+l eA ++ d ++  dp 
  gi|386001437|ref|YP_005919736.1| 378 LFGQGQLSEAIKAYDVAIVLDPGYAQAWNNKGVALYDQGRLSEAVEAYDMALSLDPA 434
                                       689************************************************999997 PP

  == domain 8  score: 21.7 bits;  conditional E-value: 4.5e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       g+y+eA+ ++ +++ + p++++a+ +   al alg+ +eAea+ ++ 
  gi|386001437|ref|YP_005919736.1| 450 GRYEEAVLIYDEVIRQRPEDGDAWVGRGAALQALGRGEEAEAAFSRG 496
                                       9*****************************************98875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.9       3.8   1.9e+03      10      36 ..      76     102 ..      72     114 .. 0.56
   2 ?    0.1   0.1       4.1     2e+03       3      31 ..     103     130 ..     101     136 .. 0.76
   3 ?    0.1   0.1       4.3   2.1e+03       7      19 ..     139     151 ..     134     177 .. 0.68
   4 ?   -0.2   0.2       5.4   2.6e+03       7      31 ..     170     193 ..     164     209 .. 0.55
   5 ?   -0.3   0.1       5.8   2.8e+03      10      34 ..     187     212 ..     186     222 .. 0.61
   6 ?    3.9   0.0      0.25   1.2e+02      23      39 ..     254     270 ..     235     275 .. 0.86
   7 !   12.0   0.0   0.00061       0.3      11      39 ..     276     304 ..     272     308 .. 0.89
   8 !   12.3   0.1   0.00049      0.24      10      40 ..     309     339 ..     306     341 .. 0.91
   9 !   20.1   0.1   1.6e-06   0.00075       3      40 ..     336     373 ..     334     377 .. 0.92
  10 !   12.8   0.0   0.00035      0.17      10      40 ..     377     407 ..     374     411 .. 0.90
  11 !   16.5   0.2   2.3e-05     0.011      10      41 ..     411     442 ..     408     445 .. 0.90
  12 !   17.2   0.2   1.3e-05    0.0064       3      41 ..     438     476 ..     436     479 .. 0.90
  13 ?    7.7   1.1     0.016       7.6       2      29 ..     471     498 ..     470     501 .] 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.8
                            TPR_14  10 allalGdpde..AiallrralalaPddae 36 
                                       a +alG+ ++  A+  l +al+ +Pd + 
  gi|386001437|ref|YP_005919736.1|  76 AAAALGEVRDarAVGPLIAALK-DPD-PG 102
                                       6677777555236667777776.555.33 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 4.1
                            TPR_14   3 allalaeallalGdpdeAiallrralala 31 
                                       +++++a+al + Gdp++ + l++ al+ +
  gi|386001437|ref|YP_005919736.1| 103 VRREAARALGEIGDPQAIEPLAHLALK-D 130
                                       567788888888899888888888877.4 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 4.3
                            TPR_14   7 laeallalGdpde 19 
                                       ++eal+++Gdp++
  gi|386001437|ref|YP_005919736.1| 139 AVEALAEAGDPAA 151
                                       6788999999884 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 5.4
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       +a+al + Gdp++ + l+  al+ +
  gi|386001437|ref|YP_005919736.1| 170 AARALGEIGDPQAIEPLAYLALK-D 193
                                       55555555556555555555554.2 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 5.8
                            TPR_14  10 allalGdpdeAia.llrralalaPdd 34 
                                       a+lal dpd+ ++  + +ala a ++
  gi|386001437|ref|YP_005919736.1| 187 AYLALKDPDGGVRgEAVEALAEAGGP 212
                                       68889999885544555555555555 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.25
                            TPR_14  23 llrralalaPddaeawl 39 
                                        +++a++ +P+++ aw 
  gi|386001437|ref|YP_005919736.1| 254 RYDEAISIDPASPLAWG 270
                                       489999**********6 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 0.00061
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawl 39 
                                       l+  G++ eA+ +++ al+l+P+d+ +w 
  gi|386001437|ref|YP_005919736.1| 276 LYDGGRLSEAVVAYDTALSLDPQDPYVWN 304
                                       6788*********************9995 PP

  == domain 8  score: 12.3 bits;  conditional E-value: 0.00049
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawll 40 
                                       al+ lG++ eA+++++ a++l+P+   aw+ 
  gi|386001437|ref|YP_005919736.1| 309 ALRDLGRLSEAVEAYDVAISLDPQYSHAWYN 339
                                       8999*********************999976 PP

  == domain 9  score: 20.1 bits;  conditional E-value: 1.6e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       a++  + al + G+ ++Ai++++ a++l+P+da aw  
  gi|386001437|ref|YP_005919736.1| 336 AWYNKGIALDEMGEDEKAIEAYDMAISLDPEDANAWNN 373
                                       89999******************************965 PP

  == domain 10  score: 12.8 bits;  conditional E-value: 0.00035
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawll 40 
                                       al+ +G++ eAi++++ a+ l+P+ a+aw  
  gi|386001437|ref|YP_005919736.1| 377 ALFGQGQLSEAIKAYDVAIVLDPGYAQAWNN 407
                                       78899***********************965 PP

  == domain 11  score: 16.5 bits;  conditional E-value: 2.3e-05
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlll 41 
                                       al+ +G++ eA+++++ al+l+P+   aw+  
  gi|386001437|ref|YP_005919736.1| 411 ALYDQGRLSEAVEAYDMALSLDPAYHHAWMNK 442
                                       7999*********************9999865 PP

  == domain 12  score: 17.2 bits;  conditional E-value: 1.3e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       a++  + al+ lG+++eA+ ++++++++ P+d +aw   
  gi|386001437|ref|YP_005919736.1| 438 AWMNKGLALRSLGRYEEAVLIYDEVIRQRPEDGDAWVGR 476
                                       7888899*****************************765 PP

  == domain 13  score: 7.7 bits;  conditional E-value: 0.016
                            TPR_14   2 eallalaeallalGdpdeAiallrrala 29 
                                       +a+  +++al alG+ +eA+a++ r  +
  gi|386001437|ref|YP_005919736.1| 471 DAWVGRGAALQALGRGEEAEAAFSRGRE 498
                                       58999******************99866 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.3     0.032        16      16      70 ..      88     141 ..      75     144 .. 0.83
   2 !   11.6   0.1   0.00048      0.23      20      63 ..     257     300 ..     252     301 .. 0.93
   3 !   22.1   0.2   2.6e-07   0.00013      12      62 ..     283     333 ..     280     344 .. 0.92
   4 !   25.1   0.0     3e-08   1.4e-05      12      61 ..     351     400 ..     340     404 .. 0.91
   5 !   21.7   0.3   3.4e-07   0.00016      13      63 ..     386     436 ..     385     438 .. 0.94
   6 !   22.9   1.2   1.4e-07   6.8e-05       9      65 ..     416     472 ..     414     474 .. 0.94
   7 ?    4.8   1.2     0.065        32      17      53 ..     458     494 ..     454     495 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.032
                             TPR_9  16 avverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeaira 70 
                                       av  ++ +l+  dp+ rr+ +++l + G+++ A++ L + + ++pd   +  + +
  gi|386001437|ref|YP_005919736.1|  88 AVGPLIAALKDPDPGVRREAARALGEIGDPQ-AIEPLAHLALKDPDGGVRGKAVE 141
                                       555678899999*****************96.89999999999999888776655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00048
                             TPR_9  20 rllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                         + ++P +p  +   Gl l+  G+ls+A+ + +++l+l+p++p
  gi|386001437|ref|YP_005919736.1| 257 EAISIDPASPLAWGGKGLSLYDGGRLSEAVVAYDTALSLDPQDP 300
                                       56789************************************997 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 2.6e-07
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++a  +++  l l+P+dp+ +   G++l  lG+ls+A+++ + +++l+p+ 
  gi|386001437|ref|YP_005919736.1| 283 SEAVVAYDTALSLDPQDPYVWNNKGVALRDLGRLSEAVEAYDVAISLDPQY 333
                                       67888999****************************************975 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 3e-08
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       e+a++++++ + l+P+d+  +   G++l+ +G+ls+A+++ + ++ l+p 
  gi|386001437|ref|YP_005919736.1| 351 EKAIEAYDMAISLDPEDANAWNNKGVALFGQGQLSEAIKAYDVAIVLDPG 400
                                       89***************************************999999885 PP

  == domain 5  score: 21.7 bits;  conditional E-value: 3.4e-07
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +a+++++  ++l+P  ++ +   G++l+ +G+ls+A+++ + +l+l+p+ +
  gi|386001437|ref|YP_005919736.1| 386 EAIKAYDVAIVLDPGYAQAWNNKGVALYDQGRLSEAVEAYDMALSLDPAYH 436
                                       699********************************************9755 PP

  == domain 6  score: 22.9 bits;  conditional E-value: 1.4e-07
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                        + ++a +++++ l l+P  ++ ++  Gl+l  lG++++A+   +  +++ p++ da
  gi|386001437|ref|YP_005919736.1| 416 GRLSEAVEAYDMALSLDPAYHHAWMNKGLALRSLGRYEEAVLIYDEVIRQRPEDGDA 472
                                       57789***********************************************99997 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.065
                             TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                       +++ ++   P+d + +  RG +l+ lG+ ++A a++ 
  gi|386001437|ref|YP_005919736.1| 458 IYDEVIRQRPEDGDAWVGRGAALQALGRGEEAEAAFS 494
                                       567777789***********************98876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0013      0.63       7      75 ..     270     330 ..     266     332 .. 0.79
   2 !   18.2   0.1   4.7e-06    0.0023       5      75 ..     302     364 ..     299     366 .. 0.89
   3 !   26.1   0.4   1.7e-08     8e-06       3      75 ..     368     432 ..     366     434 .. 0.88
   4 !   25.8   1.0   1.9e-08   9.4e-06       3      75 ..     402     466 ..     400     468 .. 0.90
   5 !    8.6   0.1    0.0046       2.2       5      30 ..     472     497 ..     468     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                          ++ l+  gr+ eA   +++al +      p+ p+   + +n g ++r lgr+ eA+e++  a+ ++
  gi|386001437|ref|YP_005919736.1| 270 GGKGLSLYDGGRLSEAVVAYDTALSLD-----PQDPY---VWNNKGVALRDLGRLSEAVEAYDVAISLD 330
                                       556777888888888888888888888.....88877...59999999999999999999998887765 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 4.7e-06
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       ++nn +++lr lgr+ eA e ++ a+ +      p+   ++ + +n g++++++g+ e+A+e++  a+ ++
  gi|386001437|ref|YP_005919736.1| 302 VWNNKGVALRDLGRLSEAVEAYDVAISLD-----PQ---YSHAWYNKGIALDEMGEDEKAIEAYDMAISLD 364
                                       5899***************9999997777.....65...69999********************9999876 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 1.7e-08
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+a+nn +++l+ +g++ eA++ ++ a+  +  l     p++a++ +n g +++ +gr+ eA+e++  al ++
  gi|386001437|ref|YP_005919736.1| 368 ANAWNNKGVALFGQGQLSEAIKAYDVAI--V--L----DPGYAQAWNNKGVALYDQGRLSEAVEAYDMALSLD 432
                                       89**************999998888773..3..3....4568****************************886 PP

  == domain 4  score: 25.8 bits;  conditional E-value: 1.9e-08
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a+a+nn +++l+ +gr+ eA e ++ al +    +  +h     +  n g ++r lgryeeA+ ++ e+++ +
  gi|386001437|ref|YP_005919736.1| 402 AQAWNNKGVALYDQGRLSEAVEAYDMALSLD---PAYHH-----AWMNKGLALRSLGRYEEAVLIYDEVIRQR 466
                                       889****************************...54566.....678*********************99866 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0046
                            TPR_12   5 alnnlaavlrrlgrydeAlellekal 30 
                                       a++ ++a+l++lgr +eA++ + + +
  gi|386001437|ref|YP_005919736.1| 472 AWVGRGAALQALGRGEEAEAAFSRGR 497
                                       7888999************9998755 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.5e-06   0.00071      11      37 ..      55      81 ..      51      83 .. 0.95
   2 !   23.7   0.0   7.2e-08   3.5e-05       7      39 ..      82     114 ..      81     116 .. 0.94
   3 ?    2.3   0.0      0.38   1.8e+02       8      36 ..     114     143 ..     113     145 .. 0.85
   4 !    8.5   0.0    0.0043       2.1      13      39 ..     151     177 ..     150     179 .. 0.93
   5 ?    1.1   0.0      0.95   4.6e+02       8      37 ..     177     207 ..     176     208 .. 0.88
   6 ?    3.0   0.1      0.24   1.1e+02      13      36 ..     214     237 ..     213     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                                      TTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm 11 aGavppLvrLLssedeevqeeAawALs 37
                                      aGav+pL++ L++e  ev++eAa+AL+
  gi|386001437|ref|YP_005919736.1| 55 AGAVDPLISALEDEASEVRCEAAAALG 81
                                      8*************************8 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 7.2e-08
                                       HHHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm   7 avieaGavppLvrLLssedeevqeeAawALsNL 39 
                                       +v++a av pL++ L+++d++v++eAa+AL+ +
  gi|386001437|ref|YP_005919736.1|  82 EVRDARAVGPLIAALKDPDPGVRREAARALGEI 114
                                       5899**************************987 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.38
                                       HHHTTHHHHHHHHTT.TSSHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLs.sedeevqeeAawAL 36 
                                       + +  a++pL +L   ++d +v+  A+ AL
  gi|386001437|ref|YP_005919736.1| 114 IGDPQAIEPLAHLALkDPDGGVRGKAVEAL 143
                                       66889*********9999999998888887 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0043
                                       HHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawALsNL 39 
                                       av pL+  +++e+ +v+  Aa+AL+ +
  gi|386001437|ref|YP_005919736.1| 151 AVTPLIGAIKDENSSVRMRAARALGEI 177
                                       688*********************987 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.95
                                       HHHTTHHHHHHHHTT.TSSHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLs.sedeevqeeAawALs 37 
                                       + +  a++pL  L   ++d +v+ eA+ AL+
  gi|386001437|ref|YP_005919736.1| 177 IGDPQAIEPLAYLALkDPDGGVRGEAVEALA 207
                                       5678899999999999**********99995 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHTTTSSHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawAL 36 
                                       av pL++ L++ d++v e A  AL
  gi|386001437|ref|YP_005919736.1| 214 AVTPLIAALRDADPGVSEKASEAL 237
                                       689*************99998877 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       4.9   2.4e+03      12      20 ..     252     260 ..     249     261 .. 0.82
   2 ?   -0.8   0.0       4.4   2.1e+03      13      35 ..     280     300 ..     276     301 .. 0.82
   3 !   10.6   0.0     0.001      0.49       2      32 ..     303     331 ..     302     332 .. 0.88
   4 !   14.7   0.0   4.6e-05     0.022       1      35 [.     336     368 ..     336     369 .. 0.93
   5 ?    7.0   0.0     0.014       6.7       1      32 [.     370     399 ..     370     400 .. 0.89
   6 !   10.8   0.1   0.00084      0.41       1      31 [.     404     432 ..     404     436 .. 0.87
   7 !   13.7   0.0   9.7e-05     0.047       2      34 ..     439     469 ..     438     471 .. 0.89
   8 ?   -1.6   0.1       7.5   3.6e+03       6      21 ..     477     492 ..     472     495 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.9
                             TPR_7  12 lGdyeeAie 20 
                                        ++y+eAi+
  gi|386001437|ref|YP_005919736.1| 252 ARRYDEAIS 260
                                       579****97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.4
                             TPR_7  13 GdyeeAielyeqsLaltkdpeda 35 
                                       G+ +eA+  y    al  dp+d+
  gi|386001437|ref|YP_005919736.1| 280 GRLSEAVVAYDT--ALSLDPQDP 300
                                       778899999999..888888875 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.001
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++n +++ ++lG+ +eA+e y    a+  dp
  gi|386001437|ref|YP_005919736.1| 303 WNNKGVALRDLGRLSEAVEAYDV--AISLDP 331
                                       799******************99..777666 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 4.6e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++n + +  ++G+ e+Aie y    a+  dpeda
  gi|386001437|ref|YP_005919736.1| 336 AWYNKGIALDEMGEDEKAIEAYDM--AISLDPEDA 368
                                       78999*******************..999999997 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.014
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n +++ + +G+ +eAi+ y    a+  dp
  gi|386001437|ref|YP_005919736.1| 370 AWNNKGVALFGQGQLSEAIKAYDV--AIVLDP 399
                                       799*******************99..777776 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00084
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n +++  ++G+ +eA+e y    al  d
  gi|386001437|ref|YP_005919736.1| 404 AWNNKGVALYDQGRLSEAVEAYDM--ALSLD 432
                                       799*********************..55554 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 9.7e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       + n + + ++lG+yeeA+ +y +  +++ +ped
  gi|386001437|ref|YP_005919736.1| 439 WMNKGLALRSLGRYEEAVLIYDE--VIRQRPED 469
                                       678899*****************..99988876 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 7.5
                             TPR_7   6 arlysrlGdyeeAiel 21 
                                       + + ++lG+ eeA+  
  gi|386001437|ref|YP_005919736.1| 477 GAALQALGRGEEAEAA 492
                                       7788999999999875 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.06        29       7      32 ..     273     298 ..     271     299 .. 0.91
   2 ?    7.2   0.0     0.019       9.1       7      32 ..     307     332 ..     305     333 .. 0.89
   3 !   13.1   0.0   0.00024      0.11       2      32 ..     336     366 ..     335     367 .. 0.93
   4 ?    6.1   0.0     0.042        20       7      31 ..     375     399 ..     373     401 .. 0.85
   5 ?    7.0   0.0     0.021        10       7      31 ..     409     433 ..     407     434 .. 0.87
   6 !   14.5   0.0   8.5e-05     0.041       2      32 ..     438     468 ..     437     469 .. 0.93
   7 ?    0.4   0.2       2.7   1.3e+03       1      25 [.     471     495 ..     471     495 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +ls++ +g+ ++A+ a++  ++  P+
  gi|386001437|ref|YP_005919736.1| 273 GLSLYDGGRLSEAVVAYDTALSLDPQ 298
                                       899***99**********99998886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++r lg+ ++A+ea++  i+  P+
  gi|386001437|ref|YP_005919736.1| 307 GVALRDLGRLSEAVEAYDVAISLDPQ 332
                                       78899999************998886 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A y+ + ++ ++g+ +kA+ea++  i+  P+
  gi|386001437|ref|YP_005919736.1| 336 AWYNKGIALDEMGEDEKAIEAYDMAISLDPE 366
                                       89***********************998885 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + +++ +g+ ++A++a++  i   P
  gi|386001437|ref|YP_005919736.1| 375 GVALFGQGQLSEAIKAYDVAIVLDP 399
                                       78999999*********99886665 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + +++ +g+ ++A+ea++  ++  P
  gi|386001437|ref|YP_005919736.1| 409 GVALYDQGRLSEAVEAYDMALSLDP 433
                                       78999999*********99987666 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 8.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A ++ +l++r+lg++++A+ +++++i++ P+
  gi|386001437|ref|YP_005919736.1| 438 AWMNKGLALRSLGRYEEAVLIYDEVIRQRPE 468
                                       77889******99***************996 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealer 25 
                                       dA   ++ ++++lg+ ++A +a+ r
  gi|386001437|ref|YP_005919736.1| 471 DAWVGRGAALQALGRGEEAEAAFSR 495
                                       67888999999999*****999965 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       6.7   3.2e+03      20      30 ..     251     260 ..     249     261 .. 0.57
   2 ?    2.0   0.0      0.42   2.1e+02      10      30 ..     274     294 ..     273     295 .. 0.87
   3 !   11.5   0.1   0.00044      0.21       6      30 ..     304     328 ..     304     329 .. 0.93
   4 ?    2.0   0.1      0.43   2.1e+02       7      30 ..     339     362 ..     338     363 .. 0.88
   5 ?    6.4   0.0     0.017       8.2       6      29 ..     372     395 ..     368     397 .. 0.86
   6 !   14.3   0.3   5.8e-05     0.028       6      30 ..     406     430 ..     402     431 .. 0.91
   7 !   12.8   0.1   0.00017     0.082       7      29 ..     441     463 ..     440     464 .. 0.91
   8 ?    6.2   0.5     0.021        10       9      24 ..     477     492 ..     476     495 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.7
                            TPR_10  20 eAealleeala 30 
                                       eA+++ +ea++
  gi|386001437|ref|YP_005919736.1| 251 EARRY-DEAIS 260
                                       66666.55554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.42
                            TPR_10  10 nalrqrgrydeAealleeala 30 
                                         l++ gr+ eA+  ++ al+
  gi|386001437|ref|YP_005919736.1| 274 LSLYDGGRLSEAVVAYDTALS 294
                                       568999************997 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00044
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN ++alr++gr+ eA++ ++ a++
  gi|386001437|ref|YP_005919736.1| 304 NNKGVALRDLGRLSEAVEAYDVAIS 328
                                       899****************998886 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.43
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++al ++g+ ++A + ++ a++
  gi|386001437|ref|YP_005919736.1| 339 NKGIALDEMGEDEKAIEAYDMAIS 362
                                       6699*************9998886 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.017
                            TPR_10   6 nNLanalrqrgrydeAealleeal 29 
                                       nN ++al+ +g++ eA + ++ a+
  gi|386001437|ref|YP_005919736.1| 372 NNKGVALFGQGQLSEAIKAYDVAI 395
                                       9***************99987665 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 5.8e-05
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN ++al+++gr+ eA++ ++ al+
  gi|386001437|ref|YP_005919736.1| 406 NNKGVALYDQGRLSEAVEAYDMALS 430
                                       999*****************99986 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.00017
                            TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                       N + alr++gry+eA+ +++e++
  gi|386001437|ref|YP_005919736.1| 441 NKGLALRSLGRYEEAVLIYDEVI 463
                                       6699*****************98 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.021
                            TPR_10   9 analrqrgrydeAeal 24 
                                       ++al+++gr++eAea 
  gi|386001437|ref|YP_005919736.1| 477 GAALQALGRGEEAEAA 492
                                       799***********85 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   3.4   1.6e-05    0.0075       2      54 ..      40      82 ..      39      83 .. 0.82
   2 !   14.8   0.1   6.5e-05     0.031      29      55 .]      88     114 ..      86     114 .. 0.93
   3 ?    3.2   0.0      0.27   1.3e+02      27      53 ..     117     144 ..     117     145 .. 0.74
   4 !   15.5   0.0   3.9e-05     0.019      27      55 .]     149     177 ..     148     177 .. 0.94
   5 ?    0.5   0.0       1.9   9.1e+02      28      53 ..     181     207 ..     180     209 .. 0.73
   6 ?    1.5   0.3      0.92   4.5e+02      27      52 ..     212     237 ..     197     237 .. 0.64
   7 ?    2.2   0.2      0.57   2.7e+02      45      54 ..     476     485 ..     468     500 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-05
                           HEAT_EZ  2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgn 54
                                       vR++Aa+aLG  +       +++v+ ++ aL      d++ eVR+ Aa aLg 
  gi|386001437|ref|YP_005919736.1| 40 DVRAGAARALG--E----AGGAGAVDPLISALE-----DEAsEVRCEAAAALGE 82
                                      59********8..3....346666678888999.....8888**********96 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.5e-05
                           HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       ++ +L+a+L+d+++ VR  Aa+aLg +
  gi|386001437|ref|YP_005919736.1|  88 AVGPLIAALKDPDPGVRREAARALGEI 114
                                       7899*********************86 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.27
                           HEAT_EZ  27 peilpaLl.alLnddsdeVRaaAagaLg 53 
                                       p+++ +L+  +L+d++  VR++A+ aL+
  gi|386001437|ref|YP_005919736.1| 117 PQAIEPLAhLALKDPDGGVRGKAVEALA 144
                                       67788888444566666*********96 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 3.9e-05
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       p+++ +L+ + +d++++VR  Aa+aLg +
  gi|386001437|ref|YP_005919736.1| 149 PAAVTPLIGAIKDENSSVRMRAARALGEI 177
                                       68899**********************86 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.9
                           HEAT_EZ  28 eilpaLl.alLnddsdeVRaaAagaLg 53 
                                       +++ +L+  +L+d++  VR+ A+ aL+
  gi|386001437|ref|YP_005919736.1| 181 QAIEPLAyLALKDPDGGVRGEAVEALA 207
                                       666777755567766699**9999996 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.92
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaL 52 
                                       p+++ +L+a+L+d ++ V ++A  aL
  gi|386001437|ref|YP_005919736.1| 212 PAAVTPLIAALRDADPGVSEKASEAL 237
                                       45667777777777767776666665 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.57
                           HEAT_EZ  45 RaaAagaLgn 54 
                                       R+aA+ aLg+
  gi|386001437|ref|YP_005919736.1| 476 RGAALQALGR 485
                                       4455555543 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0097       4.7       8      36 .]     273     299 ..     273     299 .. 0.86
   2 ?    4.7   0.0     0.063        30      15      34 ..     314     331 ..     312     332 .. 0.84
   3 ?    2.1   0.0       0.4   1.9e+02      18      36 .]     351     367 ..     346     367 .. 0.85
   4 !    8.2   0.0     0.005       2.4      10      34 ..     377     399 ..     375     399 .. 0.86
   5 !   10.7   0.0   0.00082       0.4      10      33 ..     411     432 ..     409     434 .. 0.84
   6 ?   -1.9   0.0       7.7   3.7e+03      15      24 ..     450     459 ..     448     460 .. 0.77
   7 ?   -1.0   0.0       3.8   1.8e+03       8      25 ..     477     494 ..     474     494 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0097
                                       HHHHHHTT-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3   8 AaefynkkkyqeArelfsYallaildken 36 
                                       + ++y+ ++++eA+ +++   +  ld+++
  gi|386001437|ref|YP_005919736.1| 273 GLSLYDGGRLSEAVVAYD--TALSLDPQD 299
                                       5789************77..888888776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.063
                                       T-HHHHHHH..HHHHHHH-T CS
                             TPR_3  15 kkyqeArelfsYallaildk 34 
                                       ++++eA+e+++  ++  ld+
  gi|386001437|ref|YP_005919736.1| 314 GRLSEAVEAYD--VAISLDP 331
                                       899******77..*988886 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.4
                                       HHHHHH..HHHHHHH-TT- CS
                             TPR_3  18 qeArelfsYallaildken 36 
                                       ++A+e+++   +  ld+e+
  gi|386001437|ref|YP_005919736.1| 351 EKAIEAYD--MAISLDPED 367
                                       79****77..999999997 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.005
                                       HHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3  10 efynkkkyqeArelfsYallaildk 34 
                                       +++ +++++eA+ +++  ++ +ld+
  gi|386001437|ref|YP_005919736.1| 377 ALFGQGQLSEAIKAYD--VAIVLDP 399
                                       56779*********77..***9985 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00082
                                       HHHHTT-HHHHHHH..HHHHHHH- CS
                             TPR_3  10 efynkkkyqeArelfsYallaild 33 
                                       ++y++++++eA+e+++   +  ld
  gi|386001437|ref|YP_005919736.1| 411 ALYDQGRLSEAVEAYD--MALSLD 432
                                       79************77..877666 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 7.7
                                       T-HHHHHHH. CS
                             TPR_3  15 kkyqeArelf 24 
                                       ++y+eA+  +
  gi|386001437|ref|YP_005919736.1| 450 GRYEEAVLIY 459
                                       99****8664 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 3.8
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       +a+++  ++ +eA+ +fs
  gi|386001437|ref|YP_005919736.1| 477 GAALQALGRGEEAEAAFS 494
                                       7999*****9****9998 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.04        19     105     127 ..     305     327 ..     301     332 .. 0.89
   2 !    8.8   0.0    0.0034       1.6     101     128 ..     335     362 ..     330     369 .. 0.88
   3 ?    2.6   0.0      0.28   1.3e+02     104     126 ..     372     394 ..     368     397 .. 0.88
   4 ?    5.1   0.0     0.046        23     102     127 ..     404     429 ..     400     432 .. 0.88
   5 ?    4.7   0.0      0.06        29     102     124 ..     438     460 ..     434     468 .. 0.84
   6 ?    3.9   0.1      0.11        53     104     128 ..     474     498 ..     464     499 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.04
                                       HHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmag 127
                                       +++val +lGr +ea++a+ +a 
  gi|386001437|ref|YP_005919736.1| 305 NKGVALRDLGRLSEAVEAYDVAI 327
                                       89*****************9885 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrmage 128
                                        a ++++ al+e+G  ++a++a+ ma  
  gi|386001437|ref|YP_005919736.1| 335 HAWYNKGIALDEMGEDEKAIEAYDMAIS 362
                                       6779*********************975 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.28
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                        +++val + G+ +ea+ka+ +a
  gi|386001437|ref|YP_005919736.1| 372 NNKGVALFGQGQLSEAIKAYDVA 394
                                       589*****************987 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a  +++val + Gr +ea++a+ ma 
  gi|386001437|ref|YP_005919736.1| 404 AWNNKGVALYDQGRLSEAVEAYDMAL 429
                                       55689******************995 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHTT-HHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafr 124
                                       a ++++ al +lGr++ea+  + 
  gi|386001437|ref|YP_005919736.1| 438 AWMNKGLALRSLGRYEEAVLIYD 460
                                       6689**************98876 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.11
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmage 128
                                       + r++al+ lGr +ea  af    e
  gi|386001437|ref|YP_005919736.1| 474 VGRGAALQALGRGEEAEAAFSRGRE 498
                                       579*************999987665 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.039        19     216     265 ..     256     306 ..     251     313 .. 0.88
   2 !   13.3   0.1   6.2e-05      0.03     205     259 ..     313     367 ..     308     377 .. 0.92
   3 !    6.7   0.0    0.0061       2.9     206     258 ..     382     434 ..     377     443 .. 0.93
   4 ?    1.4   0.0      0.23   1.1e+02      44      72 ..     442     470 ..     437     497 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.039
                                       HHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHH.HHH CS
                             NARP1 216 dkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyi.Nsk 265
                                       d+ai+ +p +   +  K+  l   G l++A+ + ++a +lD +D y+ N+k
  gi|386001437|ref|YP_005919736.1| 256 DEAISIDPASPLAWGGKGLSLYDGGRLSEAVVAYDTALSLDPQDPYVwNNK 306
                                       789999999999999999999999**********************95665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.2e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       lg+ ++A+e  d ai+ +p+    +++K+  l  +G+ +kA+e+ + a +lD +D
  gi|386001437|ref|YP_005919736.1| 313 LGRLSEAVEAYDVAISLDPQYSHAWYNKGIALDEMGEDEKAIEAYDMAISLDPED 367
                                       567789**********************************************998 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0061
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                       g+ ++A++  d ai  +p   + + +K+  l  +G l++A+e+ + a +lD a
  gi|386001437|ref|YP_005919736.1| 382 GQLSEAIKAYDVAIVLDPGYAQAWNNKGVALYDQGRLSEAVEAYDMALSLDPA 434
                                       56789*********************************************975 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.23
                                       HHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  44 kaelllkLgrkeeAeatyeaLlernpens 72 
                                       k+  l  Lgr+eeA  +y + +++ pe+ 
  gi|386001437|ref|YP_005919736.1| 442 KGLALRSLGRYEEAVLIYDEVIRQRPEDG 470
                                       56667789999999999999999988865 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.086        42      23      85 ..      58      83 ..      51      89 .. 0.58
   2 !   12.3   0.0   0.00027      0.13      23      84 ..      89     145 ..      86     149 .. 0.81
   3 ?    5.2   0.0      0.04        20      23      83 ..     152     175 ..     117     182 .. 0.64
   4 ?    7.1   0.0     0.011       5.1      23      82 ..     152     206 ..     149     210 .. 0.72
   5 ?    3.5   0.0      0.13        64       2      47 ..     166     208 ..     165     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.086
                              Cnd1 23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaaltei 85
                                      v+pL ++L+De + VR                                       a aal e+
  gi|386001437|ref|YP_005919736.1| 58 VDPLISALEDEASEVR-------------------------------------CEAAAALGEV 83
                                      4455555555555555.....................................5555555554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00027
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalte 84 
                                       v pL ++LkD+dp VR+ aa ++ ++ +++ ++          +l+D++  V+  a+ al e
  gi|386001437|ref|YP_005919736.1|  89 VGPLIAALKDPDPGVRREAARALGEIGDPQAIEPLA-----HLALKDPDGGVRGKAVEALAE 145
                                       78999******************9999999988655.....335777777777777777766 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.04
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalt 83 
                                       v+pL  ++kDe++ VR+ aa ++                                      
  gi|386001437|ref|YP_005919736.1| 152 VTPLIGAIKDENSSVRMRAARAL-------------------------------------G 175
                                       45555666666666666666544.....................................3 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaal 82 
                                       v+pL  ++kDe++ VR+ aa ++ ++ +++ ++        + +l+D++  V+  a+ al
  gi|386001437|ref|YP_005919736.1| 152 VTPLIGAIKDENSSVRMRAARALGEIGDPQAIEPLA-----YLALKDPDGGVRGEAVEAL 206
                                       678889999999999999999999888888877655.....4455666666666655555 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.13
                              Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvak 47 
                                       +R  a r+lg i  p+ +e+l    + +LkD+d  VR  a+ ++a+
  gi|386001437|ref|YP_005919736.1| 166 VRMRAARALGEIGDPQAIEPLA---YLALKDPDGGVRGEAVEALAE 208
                                       6777888888888888888876...789999999999999877764 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.68   3.3e+02      30      80 ..     273     324 ..     266     341 .. 0.77
   2 !   13.2   0.0   0.00017     0.081       6      80 ..     351     426 ..     346     428 .. 0.92
   3 !   13.3   0.0   0.00015     0.074       1      80 [.     414     494 ..     414     496 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.68
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +l+ly  g+  +A   +++a  l+++++ ++  ++ +l +L+++ eA+ a++
  gi|386001437|ref|YP_005919736.1| 273 GLSLYDGGRLSEAVVAYDTAlSLDPQDPYVWNNKGVALRDLGRLSEAVEAYD 324
                                       5677777777777777777777777777777777788888888888887765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++Ai  ++ + + ++e++++   ++ +l+ +gq  +A++ ++ a  l++   +++  ++ +l++++++ eA+ a++
  gi|386001437|ref|YP_005919736.1| 351 EKAIEAYDMAISLDPEDANAWNNKGVALFGQGQLSEAIKAYDVAiVLDPGYAQAWNNKGVALYDQGRLSEAVEAYD 426
                                       67888899999999999999999************************************************99876 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00015
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       dq+++ +A+  ++ +l+ ++  + + + ++l+l ++g+y++A  ++++  ++++++  +++  + +l +L++ eeA+
  gi|386001437|ref|YP_005919736.1| 414 DQGRLSEAVEAYDMALSLDPAYHHAWMNKGLALRSLGRYEEAVLIYDEViRQRPEDGDAWVGRGAALQALGRGEEAE 490
                                       68889999999999998888888888889************************************************ PP

                                       HHH- CS
                            ANAPC3  77 aaLe 80 
                                       aa++
  gi|386001437|ref|YP_005919736.1| 491 AAFS 494
                                       *986 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0049       2.4      81     119 ..      43      81 ..      24      84 .. 0.90
   2 ?    4.1   0.0     0.092        45      83     119 ..      76     112 ..      75     114 .. 0.90
   3 ?    4.3   0.0     0.082        40      82     119 ..     138     175 ..     135     177 .. 0.91
   4 !    9.3   0.0    0.0022       1.1      82     118 ..     201     237 ..     198     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0049
                     Aconitase_B_N  81 eeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       + A + Lg+  G  +v++Li++l+++ +e++ eaa+aL 
  gi|386001437|ref|YP_005919736.1|  43 AGAARALGEAGGAGAVDPLISALEDEASEVRCEAAAALG 81 
                                       568899***99999*********************9996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.092
                     Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       A   Lg+     +v +Li +lk+ d  +++eaa+aL 
  gi|386001437|ref|YP_005919736.1|  76 AAAALGEVRDARAVGPLIAALKDPDPGVRREAARALG 112
                                       778899999999**********************996 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.082
                     Aconitase_B_N  82 eAvelLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       +Ave L++    ++v++Li ++k+++++++  aa+aL 
  gi|386001437|ref|YP_005919736.1| 138 KAVEALAEAGDPAAVTPLIGAIKDENSSVRMRAARALG 175
                                       8999999999999*********************9996 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0022
                     Aconitase_B_N  82 eAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                       eAve L++  G ++v++Li +l+++d  + e+a eaL
  gi|386001437|ref|YP_005919736.1| 201 EAVEALAEAGGPAAVTPLIAALRDADPGVSEKASEAL 237
                                       8*********************************998 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4       1.7   8.3e+02      63     108 ..      68     113 ..      43     121 .. 0.71
   2 ?   -1.9   0.0       8.4   4.1e+03     104     109 ..     204     209 ..     164     257 .. 0.57
   3 ?    7.4   0.0     0.011       5.4      76     120 ..     280     324 ..     271     330 .. 0.92
   4 !   10.3   0.0    0.0015      0.71      74     120 ..     346     392 ..     335     399 .. 0.93
   5 ?    3.0   0.1      0.25   1.2e+02     104     121 ..     410     427 ..     397     432 .. 0.82
   6 !   12.3   0.6   0.00037      0.18      71     124 ..     445     498 ..     434     499 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH CS
                              BTAD  63 ealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlar 108
                                       ea e ++ea ++lG+ ++a a    ++a+++ +   +r+  rAl  
  gi|386001437|ref|YP_005919736.1|  68 EASEVRCEAAAALGEVRDARAVGPLIAALKDPDPGVRREAARALGE 113
                                       5678889999999988777666666666666666666666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.4
                                       HHHHHT CS
                              BTAD 104 rAlars 109
                                       +Ala  
  gi|386001437|ref|YP_005919736.1| 204 EALAEA 209
                                       222222 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.011
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                              BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                       Gr +ea+  ++ +++++P +   +     Al+ +Gr +eA e+Y+
  gi|386001437|ref|YP_005919736.1| 280 GRLSEAVVAYDTALSLDPQDPYVWNNKGVALRDLGRLSEAVEAYD 324
                                       8999****************************************8 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0015
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                       ++G+ e+a++ ++ +++++P + +++     Al+ +G+ +eA+++Y+
  gi|386001437|ref|YP_005919736.1| 346 EMGEDEKAIEAYDMAISLDPEDANAWNNKGVALFGQGQLSEAIKAYD 392
                                       7899******************************************7 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.25
                                       HHHHHTT-HHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYer 121
                                        Al+ +Gr +eA e+Y+ 
  gi|386001437|ref|YP_005919736.1| 410 VALYDQGRLSEAVEAYDM 427
                                       599999999999999975 PP

  == domain 6  score: 12.3 bits;  conditional E-value: 0.00037
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a+ +lGr+eea+  +++ +++ P + +++    +Al ++Gr +eA +++ r r+
  gi|386001437|ref|YP_005919736.1| 445 ALRSLGRYEEAVLIYDEVIRQRPEDGDAWVGRGAALQALGRGEEAEAAFSRGRE 498
                                       56789*********************************************9987 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.47   2.3e+02     164     234 ..      40     110 ..      37     114 .. 0.78
   2 !   17.2   0.0     6e-06    0.0029     123     235 ..      99     206 ..      85     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT.T..S-GGGHHH CS
                           ERAP1_C 164 dlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvle.sdevrnqdlra 234
                                       d+r  + +al  +gg+  +d l+   +d+ + + +  a++al+ ++d+ ++  l++ + + ++ vr + +ra
  gi|386001437|ref|YP_005919736.1|  40 DVRAGAARALGEAGGAGAVDPLISALEDEAS-EVRCEAAAALGEVRDARAVGPLIAALKDpDPGVRREAARA 110
                                       6777777788778899999999999877777.88**************999887777753577777766665 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6e-06
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHH CS
                           ERAP1_C 123 ldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykdtsapseke 199
                                        d  +r+++ +a++  gdp+++e ++ l  +        +  +r+ ++ ala +g++a +  l+   kd+++ s + 
  gi|386001437|ref|YP_005919736.1|  99 PDPGVRREAARALGEIGDPQAIEPLAHLALKD------PDGGVRGKAVEALAEAGDPAAVTPLIGAIKDENS-SVRM 168
                                       456799999**********9999999776555......4568**********************99999999.**** PP

                                       HHHHHHCC-S-HHHHHHHHHHCT.T.T..S-GGGHHHH CS
                           ERAP1_C 200 aalralaatpdpellerllnfvl.e.sdevrnqdlral 235
                                       +a+ral+ + dp+++e l  ++l + ++ vr + ++al
  gi|386001437|ref|YP_005919736.1| 169 RAARALGEIGDPQAIEPLAYLALkDpDGGVRGEAVEAL 206
                                       ****************9555557436777777666665 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.6   3.7e+03      18      32 ..     280     294 ..     278     295 .. 0.81
   2 ?    0.2   0.0       1.7   8.1e+02      17      32 ..     313     328 ..     305     329 .. 0.78
   3 ?    7.1   0.1     0.012       5.6       9      32 ..     339     362 ..     334     363 .. 0.89
   4 ?    0.7   0.0       1.2   5.6e+02      17      31 ..     381     395 ..     373     397 .. 0.84
   5 ?    1.2   0.1       0.8   3.9e+02      14      32 ..     412     430 ..     402     431 .. 0.78
   6 ?   -1.5   0.0       5.6   2.7e+03      17      29 ..     449     461 ..     441     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.6
                               MIT  18 gnyeeAlelYkeale 32 
                                       g  +eA+ +Y +al 
  gi|386001437|ref|YP_005919736.1| 280 GRLSEAVVAYDTALS 294
                                       678899999999985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                               MIT  17 agnyeeAlelYkeale 32 
                                        g  +eA+e+Y  a+ 
  gi|386001437|ref|YP_005919736.1| 313 LGRLSEAVEAYDVAIS 328
                                       57899******99985 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.012
                               MIT   9 kkAveeDnagnyeeAlelYkeale 32 
                                       +k + +D+ g+ e+A+e+Y  a+ 
  gi|386001437|ref|YP_005919736.1| 339 NKGIALDEMGEDEKAIEAYDMAIS 362
                                       78999**************99985 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.2
                               MIT  17 agnyeeAlelYkeal 31 
                                       +g+ +eA+++Y  a+
  gi|386001437|ref|YP_005919736.1| 381 QGQLSEAIKAYDVAI 395
                                       58999******9887 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.8
                               MIT  14 eDnagnyeeAlelYkeale 32 
                                       +  +g  +eA+e+Y  al 
  gi|386001437|ref|YP_005919736.1| 412 LYDQGRLSEAVEAYDMALS 430
                                       55679999******99985 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 5.6
                               MIT  17 agnyeeAlelYke 29 
                                        g yeeA+  Y e
  gi|386001437|ref|YP_005919736.1| 449 LGRYEEAVLIYDE 461
                                       5899***999976 PP

>> DSX_dimer  Doublesex dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        57      10      37 ..     109     136 ..     100     147 .. 0.82
   2 ?    7.5   0.0    0.0064       3.1       7      37 ..     169     199 ..     163     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                         DSX_dimer  10 WlleklGyPWemmPlmyvilksadGdvq 37 
                                         l  +G P  + Pl ++ lk  dG v+
  gi|386001437|ref|YP_005919736.1| 109 RALGEIGDPQAIEPLAHLALKDPDGGVR 136
                                       56778999*****************996 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0064
                         DSX_dimer   7 raqWlleklGyPWemmPlmyvilksadGdvq 37 
                                       ra   l  +G P  + Pl y+ lk  dG v+
  gi|386001437|ref|YP_005919736.1| 169 RAARALGEIGDPQAIEPLAYLALKDPDGGVR 199
                                       777889999*******************985 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.6   2.7e+03      14      35 ..     313     334 ..     308     338 .. 0.86
   2 ?   -1.2   0.0       4.7   2.3e+03      10      37 ..     343     370 ..     334     371 .. 0.79
   3 ?    1.4   0.0       0.7   3.4e+02       9      37 ..     376     404 ..     374     406 .. 0.92
   4 ?    5.0   0.0     0.053        26       9      36 ..     410     437 ..     408     439 .. 0.91
   5 ?   -0.3   0.0       2.3   1.1e+03      14      34 ..     449     469 ..     443     472 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.6
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       lg+ seA +  d  ++++P+ +
  gi|386001437|ref|YP_005919736.1| 313 LGRLSEAVEAYDVAISLDPQYS 334
                                       78999*******9999999875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.7
                                       HHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQa 37 
                                       +   +ge ++A +  d+ ++++Pe  +a
  gi|386001437|ref|YP_005919736.1| 343 ALDEMGEDEKAIEAYDMAISLDPEDANA 370
                                       555678889999999********98765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.7
                                       HHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQa 37 
                                       ++ + +g+ seA +  d  + ++P+  Qa
  gi|386001437|ref|YP_005919736.1| 376 VALFGQGQLSEAIKAYDVAIVLDPGYAQA 404
                                       788889********************998 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.053
                                       HHHHHHT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQ 36 
                                       ++ y +g+ seA +  d+ L+++P  + 
  gi|386001437|ref|YP_005919736.1| 410 VALYDQGRLSEAVEAYDMALSLDPAYHH 437
                                       789999******************9875 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.3
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       lg+Y+eA    d +++  Pe 
  gi|386001437|ref|YP_005919736.1| 449 LGRYEEAVLIYDEVIRQRPED 469
                                       89*****99999998888875 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       4.7   2.3e+03      46     106 ..      44     101 ..      28     112 .. 0.61
   2 ?   -1.7   0.0       6.8   3.3e+03      47      94 ..     309     320 ..     278     328 .. 0.65
   3 ?    4.5   0.0     0.082        40       2      28 ..     335     361 ..     334     372 .. 0.89
   4 ?    9.1   0.1     0.003       1.4      14      93 ..     415     491 ..     402     494 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.7
                             TPR_5  46 ssLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsivllalaehlp 106
                                        + R lGea  a a ++++++a +de ++ +++ +a +L +  r++ av  ++ al +  p
  gi|386001437|ref|YP_005919736.1|  44 GAARALGEAGGAGA-VDPLISALEDEASE-VRCEAAAALGE-VRDARAVGPLIAALKDPDP 101
                                       45566666654443.45566666666544.56666666654.4677777777777766555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.8
                             TPR_5  47 sLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereav 94 
                                       +LR lG++ e                                    av
  gi|386001437|ref|YP_005919736.1| 309 ALRDLGRLSE------------------------------------AV 320
                                       3444444444....................................44 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.082
                             TPR_5   2 vaaFeragarDstGhedkavplYrraL 28 
                                       +a ++++ a D +G+++ka++ Y  a+
  gi|386001437|ref|YP_005919736.1| 335 HAWYNKGIALDEMGEDEKAIEAYDMAI 361
                                       68899999***************9987 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.003
                             TPR_5  14 tGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgre 90 
                                        G+  +av+ Y  aL     +    +a +    +LR lG+ eea+ + ++ + +++++ d+ +   +aL     g e
  gi|386001437|ref|YP_005919736.1| 415 QGRLSEAVEAYDMALSL---DPAYHHAWMNKGLALRSLGRYEEAVLIYDEVIRQRPEDGDAWVGRGAALQALGRGEE 488
                                       57777888888888863...55667788888889***********99999999999998888888888887777777 PP

                             TPR_5  91 rea 93 
                                       +ea
  gi|386001437|ref|YP_005919736.1| 489 AEA 491
                                       776 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0035       1.7      86     179 ..      63     146 ..      57     157 .. 0.72
   2 ?    2.1   0.0      0.12        56      87     137 ..     158     205 ..     151     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0035
                                       HHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT CS
                         Adaptin_N  86 kDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikells 162
                                        +l+d  + +r+ A  +L+ +r+++ +  l     ++lkd++p vr++Aa a+  +   dp+++++      + +l+
  gi|386001437|ref|YP_005919736.1|  63 SALEDEASEVRCEAAAALGEVRDARAVGPL----IAALKDPDPGVRREAARALGEIG--DPQAIEPL----AHLALK 129
                                       567778888888888888888887766554....45678899999999998888774..67776553....555678 PP

                                       -SSHHHHHHHHHHHHHH CS
                         Adaptin_N 163 dkdpgvvlaAvalleei 179
                                       d d gv + Av +l e 
  gi|386001437|ref|YP_005919736.1| 130 DPDGGVRGKAVEALAEA 146
                                       88888888888888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                       HCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHH CS
                         Adaptin_N  87 DlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAala 137
                                       + kd n+ +r+ A r+L+ i++p+  e la     +lkd++  vr +A+ a
  gi|386001437|ref|YP_005919736.1| 158 AIKDENSSVRMRAARALGEIGDPQAIEPLAY---LALKDPDGGVRGEAVEA 205
                                       5688999999999999999999987666653...46666666666666655 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.41     2e+02       7      36 ..      58      87 ..      57      97 .. 0.84
   2 ?    2.8   0.0      0.32   1.5e+02       9      41 ..      91     122 ..      88     132 .. 0.79
   3 ?    1.2   0.0         1   4.9e+02       7      31 ..     152     176 ..     119     186 .. 0.62
   4 ?    1.0   0.0       1.1   5.3e+02       7      34 ..     152     179 ..     148     204 .. 0.82
   5 ?   -1.9   0.0       8.8   4.3e+03       7      29 ..     215     237 ..     213     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.41
                        RasGEF_N_2  7 iellvnqLydqsrevvaaaleiLeeacddk 36
                                      ++ l+  L+d+++ev+  a+ +L e+ d +
  gi|386001437|ref|YP_005919736.1| 58 VDPLISALEDEASEVRCEAAAALGEVRDAR 87
                                      67899******************9997665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.32
                        RasGEF_N_2   9 llvnqLydqsrevvaaaleiLeeacddkeslev 41 
                                        l+  L+d+++ v++ a+++L e+  d++ +e 
  gi|386001437|ref|YP_005919736.1|  91 PLIAALKDPDPGVRREAARALGEI-GDPQAIEP 122
                                       68999****************998.44455555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLee 31 
                                       ++ l+  ++d++++v++ a+++L e
  gi|386001437|ref|YP_005919736.1| 152 VTPLIGAIKDENSSVRMRAARALGE 176
                                       3445555566666666666666655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.1
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacd 34 
                                       ++ l+  ++d++++v++ a+++L e+ d
  gi|386001437|ref|YP_005919736.1| 152 VTPLIGAIKDENSSVRMRAARALGEIGD 179
                                       56788999***************99844 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 8.8
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiL 29 
                                       ++ l+  L d ++ v+++a e+L
  gi|386001437|ref|YP_005919736.1| 215 VTPLIAALRDADPGVSEKASEAL 237
                                       6789999************9988 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.8   1.3e+03     179     196 ..      59      76 ..      50      86 .. 0.82
   2 ?    3.7   0.0     0.079        38     181     196 ..      92     107 ..      86     113 .. 0.82
   3 ?   -1.6   0.0       3.4   1.7e+03     177     196 ..     120     139 ..     117     146 .. 0.80
   4 ?   -1.8   0.0       3.8   1.8e+03     179     196 ..     153     170 ..     136     175 .. 0.79
   5 ?   -2.6   0.0       6.6   3.2e+03     179     196 ..     185     202 ..     181     209 .. 0.76
   6 ?    1.4   0.0      0.39   1.9e+02     177     200 ..     214     237 ..     201     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                           CLASP_N 179 kslkkgleDanptVReta 196
                                       + l+++leD  ++VR +a
  gi|386001437|ref|YP_005919736.1|  59 DPLISALEDEASEVRCEA 76 
                                       56899**********776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.079
                           CLASP_N 181 lkkgleDanptVReta 196
                                       l+++l+D++p+VR++a
  gi|386001437|ref|YP_005919736.1|  92 LIAALKDPDPGVRREA 107
                                       7899********9765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.4
                           CLASP_N 177 iekslkkgleDanptVReta 196
                                       ie++ + +l+D++ +VR +a
  gi|386001437|ref|YP_005919736.1| 120 IEPLAHLALKDPDGGVRGKA 139
                                       67777779*********887 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.8
                           CLASP_N 179 kslkkgleDanptVReta 196
                                         l+ +++D n++VR  a
  gi|386001437|ref|YP_005919736.1| 153 TPLIGAIKDENSSVRMRA 170
                                       557788999999999654 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 6.6
                           CLASP_N 179 kslkkgleDanptVReta 196
                                       ++   +l+D++ +VR +a
  gi|386001437|ref|YP_005919736.1| 185 PLAYLALKDPDGGVRGEA 202
                                       5555689********876 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.39
                           CLASP_N 177 iekslkkgleDanptVRetaRstf 200
                                       ++  l+++l Da+p+V e+a +++
  gi|386001437|ref|YP_005919736.1| 214 AVTPLIAALRDADPGVSEKASEAL 237
                                       5667999*********99987665 PP

>> BPS  BPS (Between PH and SH2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.7   4.2e+03      26      38 ..     257     269 ..     254     273 .. 0.86
   2 ?   -1.0   0.0       3.3   1.6e+03      16      41 ..     315     340 ..     302     343 .. 0.77
   3 ?    6.7   0.1     0.013       6.4       9      42 ..     342     375 ..     338     378 .. 0.90
   4 ?   -2.1   0.0       7.3   3.5e+03      15      41 ..     416     442 ..     406     445 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.7
                               BPS  26 EalsaaleegqaW 38 
                                       Ea s+++   +aW
  gi|386001437|ref|YP_005919736.1| 257 EAISIDPASPLAW 269
                                       9******999999 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
                               BPS  16 qkgrvIeNptEalsaaleegqaWRkk 41 
                                       + +  +e    a s +++  +aW  k
  gi|386001437|ref|YP_005919736.1| 315 RLSEAVEAYDVAISLDPQYSHAWYNK 340
                                       5555666667789999999****777 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.013
                               BPS   9 VaMDFSGqkgrvIeNptEalsaaleegqaWRkks 42 
                                       +a+D  G+  + Ie    a s ++e++ aW  k 
  gi|386001437|ref|YP_005919736.1| 342 IALDEMGEDEKAIEAYDMAISLDPEDANAWNNKG 375
                                       688889999999******************9885 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 7.3
                               BPS  15 GqkgrvIeNptEalsaaleegqaWRkk 41 
                                       G+ +  +e    als ++   +aW  k
  gi|386001437|ref|YP_005919736.1| 416 GRLSEAVEAYDMALSLDPAYHHAWMNK 442
                                       666666777777999999999999776 PP

>> DUF3385  Domain of unknown function (DUF3385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.1   1.5e+03      25      46 ..      39      63 ..      31      84 .. 0.67
   2 ?    4.6   0.0     0.055        27      23      46 ..      99     125 ..      89     153 .. 0.77
   3 ?    2.8   0.0       0.2        96      15      46 ..     155     188 ..     148     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.1
                           DUF3385 25 qsirrevikllG...ilGALDPykh 46
                                       ++r  +++ lG     GA+DP   
  gi|386001437|ref|YP_005919736.1| 39 ADVRAGAARALGeagGAGAVDPLIS 63
                                      5677778888762225689999876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.055
                           DUF3385  23 qsqsirrevikllGilG...ALDPykh 46 
                                        +  +rre+++ lG +G   A+ P  h
  gi|386001437|ref|YP_005919736.1|  99 PDPGVRREAARALGEIGdpqAIEPLAH 125
                                       46789************8888888887 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                           DUF3385  15 LlnilkteqsqsirrevikllGilG...ALDPykh 46 
                                       L++ +k e + s+r  +++ lG +G   A+ P  +
  gi|386001437|ref|YP_005919736.1| 155 LIGAIKDE-NSSVRMRAARALGEIGdpqAIEPLAY 188
                                       77888866.789*************6666666655 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       9.9   4.8e+03     146     167 ..      67      88 ..      63      89 .. 0.83
   2 ?   -0.9   0.0       2.3   1.1e+03     153     176 ..     273     296 ..     229     303 .. 0.83
   3 ?    0.7   0.0      0.73   3.5e+02     151     174 ..     305     328 ..     295     336 .. 0.86
   4 ?    0.8   0.1      0.69   3.4e+02     152     178 ..     340     366 ..     335     373 .. 0.84
   5 ?    3.4   0.1      0.11        53     150     173 ..     372     395 ..     367     403 .. 0.86
   6 ?    7.1   0.3    0.0083         4     143     175 ..     400     431 ..     378     447 .. 0.74
   7 ?   -1.4   0.1       3.3   1.6e+03     152     172 ..     476     496 ..     473     499 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.9
                            TPR_21 146 alvaelrGDilvaqgkldeAra 167
                                        +++e+r ++++a g+  +Ara
  gi|386001437|ref|YP_005919736.1|  67 DEASEVRCEAAAALGEVRDARA 88 
                                       5778999999999999999996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.3
                            TPR_21 153 GDilvaqgkldeAraaYqaAlaal 176
                                       G  l+  g+l eA  aY+ Al+  
  gi|386001437|ref|YP_005919736.1| 273 GLSLYDGGRLSEAVVAYDTALSLD 296
                                       555677899999999999999755 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.73
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        +G +l   g+l eA +aY+ A++
  gi|386001437|ref|YP_005919736.1| 305 NKGVALRDLGRLSEAVEAYDVAIS 328
                                       58999999************9987 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.69
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaalee 178
                                       +G +l ++g+ ++A +aY+ A++   e
  gi|386001437|ref|YP_005919736.1| 340 KGIALDEMGEDEKAIEAYDMAISLDPE 366
                                       67778899*************986665 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.11
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAl 173
                                       + +G +l+ qg+l eA +aY+ A+
  gi|386001437|ref|YP_005919736.1| 372 NNKGVALFGQGQLSEAIKAYDVAI 395
                                       679999***************997 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0083
                            TPR_21 143 afaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       ++ a++ + +G +l+ qg+l eA +aY+ Al+ 
  gi|386001437|ref|YP_005919736.1| 400 GY-AQAWNNKGVALYDQGRLSEAVEAYDMALSL 431
                                       44.4566789********************975 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 3.3
                            TPR_21 152 rGDilvaqgkldeAraaYqaA 172
                                       rG +l a g+ +eA aa++++
  gi|386001437|ref|YP_005919736.1| 476 RGAALQALGRGEEAEAAFSRG 496
                                       8999*************9875 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.32   1.6e+02       8      20 ..     292     304 ..     290     306 .. 0.89
   2 ?    2.5   0.3      0.27   1.3e+02       8      20 ..     326     338 ..     324     339 .. 0.91
   3 ?    2.7   0.1      0.23   1.1e+02       7      20 ..     359     372 ..     358     374 .. 0.89
   4 ?    0.8   0.0       0.9   4.3e+02       8      20 ..     394     406 ..     392     408 .. 0.87
   5 ?    1.9   0.1      0.43   2.1e+02       8      19 ..     428     439 ..     426     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.32
                                       HHHH-TT-CHHHH CS
                              PPTA   8 liekdpkNYsaWn 20 
                                       ++++dp++  +Wn
  gi|386001437|ref|YP_005919736.1| 292 ALSLDPQDPYVWN 304
                                       899*********9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.27
                                       HHHH-TT-CHHHH CS
                              PPTA   8 liekdpkNYsaWn 20 
                                       +i++dp+  +aW+
  gi|386001437|ref|YP_005919736.1| 326 AISLDPQYSHAWY 338
                                       799*********8 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.23
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                        +i++dp +  aWn
  gi|386001437|ref|YP_005919736.1| 359 MAISLDPEDANAWN 372
                                       589**********9 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.9
                                       HHHH-TT-CHHHH CS
                              PPTA   8 liekdpkNYsaWn 20 
                                       +i +dp   +aWn
  gi|386001437|ref|YP_005919736.1| 394 AIVLDPGYAQAWN 406
                                       6889********9 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.43
                                       HHHH-TT-CHHH CS
                              PPTA   8 liekdpkNYsaW 19 
                                       ++++dp   +aW
  gi|386001437|ref|YP_005919736.1| 428 ALSLDPAYHHAW 439
                                       899********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.72u 0.26s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2955.29
//
Query:       gi|386001438|ref|YP_005919737.1|  [L=562]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-54  184.7  54.6    4.9e-28   98.0   5.1    4.0  4  NosD        Periplasmic copper-binding protein (NosD)
    1.3e-40  138.8  65.2      1e-17   64.5  27.7    3.4  3  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 !   46.6  15.6   2.9e-16   2.6e-12      38     148 ..     142     254 ..     116     257 .. 0.86
   2 !   12.4   0.2   7.8e-06      0.07      76     112 ..     258     293 ..     256     298 .. 0.87
   3 !   49.2  13.1   4.5e-17     4e-13      44     133 ..     307     398 ..     294     403 .. 0.89
   4 !   98.0   5.1   5.4e-32   4.9e-28      58     239 ..     390     558 ..     387     560 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.9e-16
                              NosD  38 rdgilldnssnntitgntienl.ryGihlensesntiedntlssne..sGialmsssnntlenNtisnnenyGills 111
                                       ++gi   +s+ n+i +nt+e +  ++i l n+++n i +nt+++ +  +Gi++++s +nt+e+N +++n+  Gi+l+
  gi|386001438|ref|YP_005919737.1| 142 HAGI-KVYSDFNKIVNNTFEGNdLTAIGLINASNNQILGNTIKDVSfgYGITMYNSPENTIEGNSLIHNNW-GISLQ 216
                                       4555.678999999999999997899999999999999999999999999999999999999999999988.99999 PP

                              NosD 112 dssnntisnNtis.nnnkGiflensssntitgNriesn 148
                                       +s++nt ++N+i  + n+Gi+  n++ + itgN i++n
  gi|386001438|ref|YP_005919737.1| 217 RSDSNTFRENEIReSVNDGIWAVNANFTFITGNIISRN 254
                                       99999999999998999999999999999999999998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.8e-06
                              NosD  76 ntlssnesGialmsssnntlenNtisnnenyGillsd 112
                                       +++++n++Gi l  s+   + nN+is n+++Gi+++ 
  gi|386001438|ref|YP_005919737.1| 258 SEFEGNGKGIHLVGST-GLIANNVISFNRDHGIYIQS 293
                                       5789999999999999.88889999999999999876 PP

  == domain 3  score: 49.2 bits;  conditional E-value: 4.5e-17
                              NosD  44 dnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnnti 118
                                       ++ss+n + gn+ie + r Gi+le++ +n+i dn ++sn+ +Gi++ +s+nnt + N++++++  Gi+l++s+++++
  gi|386001438|ref|YP_005919737.1| 307 EESSENLVIGNRIEGNgRDGIRLEKTWKNNIIDNNITSNHgNGISFLQSHNNTADLNNVTRSDH-GIFLDRSNYTKV 382
                                       7899**********999*********997777777777777*********************88.************ PP

                              NosD 119 snNtis.nnnkGifle 133
                                       +nNtis  +++Gi + 
  gi|386001438|ref|YP_005919737.1| 383 NNNTISeGEKTGILFW 398
                                       ******999***9875 PP

  == domain 4  score: 98.0 bits;  conditional E-value: 5.4e-32
                              NosD  58 nlryGihlensesntiedntlssnesGialmsssnn.tlenNtisnnenyGillsd.ssnntisnNtisnnnkGifl 132
                                        +++Gi ++++ +  +++nt++++  G+++++ss    ++ N+i+n ++ G+ +s+ s++n++++N++s+++ G+ l
  gi|386001438|ref|YP_005919737.1| 390 GEKTGILFWSTIGASAYNNTIFDSPVGVSVEESSSGlAITENRIKNATE-GMNISGgSRENQVTGNNVSSSDVGVIL 465
                                       4589******************************888************.998876266799*************** PP

                              NosD 133 ensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsd 209
                                        ++++n itgN i ++   Gi+   +s gn+iy+N++ +n e ++++g  +n W+  +            +GN W  
  gi|386001438|ref|YP_005919737.1| 466 VGATRNLITGNLIFDS-ILGIVADFASRGNSIYGNDLSGNGEAARDEG--DNLWDDGS------------RGNLWGP 527
                                       ****************.*****99999********************9..9*******............******9 PP

                              NosD 210 ydgeDadgDGigDtpYeindgv.iDylplvn 239
                                         ++DadgDG+++ p  i++g  +D++pl++
  gi|386001438|ref|YP_005919737.1| 528 DVCDDADGDGVCEGPRIIPGGKnTDRFPLAR 558
                                       999*************9996666******86 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 !   57.7  21.1   1.3e-19   1.2e-15       8     138 ..     113     255 ..     100     264 .. 0.90
   2 !   64.5  27.7   1.1e-21     1e-17       2     158 .]     235     410 ..     234     410 .. 0.97
   3 !   34.9  11.0   1.4e-12   1.2e-08       2     115 ..     394     506 ..     393     515 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.3e-19
                                       S-E.EEESEEEES-...............SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---. CS
                        Beta_helix   8 ssnvtiknntisns...............ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn. 68 
                                       +  vt++n+ i+++               g++Gi+++++ n  i nn++++n  + i++ ++snn+i +nti d   
  gi|386001438|ref|YP_005919737.1| 113 DF-VTVENFVITGAtwprpydtgehndviGHAGIKVYSDFN-KIVNNTFEGNDLTAIGLINASNNQILGNTIKDVSf 187
                                       33.599999999999999999999999999***********.8888*****************************99 PP

                                       SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-S CS
                        Beta_helix  69 gggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnk 138
                                       g+gi ++++  n+ie+n  ++n ++Gi+l+ s++nt+++N i++  ++Gi   + +  + +t+N+i+ n+
  gi|386001438|ref|YP_005919737.1| 188 GYGITMYNSPENTIEGNSLIHN-NWGISLQRSDSNTFRENEIRESVNDGIWAVNAN-FTFITGNIISRNG 255
                                       *********************9.67**************************99999.6668******998 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 1.1e-21
                                       SEEE-SS-E.EEESEEEES-........SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT...............- CS
                        Beta_helix   2 gisingssnvtiknntisns........ggyGiylrgssnvvienneiannsgsGiyilgs...............s 55 
                                       gi+  + + + i++n+is++        +g Gi+l gs++ +i nn+i+ n+++Giyi++                s
  gi|386001438|ref|YP_005919737.1| 235 GIWAVNANFTFITGNIISRNgfesefegNGKGIHLVGSTG-LIANNVISFNRDHGIYIQSIfweycseppcgaeesS 310
                                       89999999999*****************************.******************99**************** PP

                                       S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES- CS
                        Beta_helix  56 nntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnN 132
                                       +n + +n+i++n+ +gi l+++ +n i +n+it n g+Gi++ +s+nnt   N+++    +Gi++d s+  ++v+nN
  gi|386001438|ref|YP_005919737.1| 311 ENLVIGNRIEGNGRDGIRLEKTWKNNIIDNNITSNHGNGISFLQSHNNTADLNNVTRSD-HGIFLDRSN-YTKVNNN 385
                                       ********************************************************999.*********.8888*** PP

                                       EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix 133 titnnkgaGiavvgsssnvtvrnNti 158
                                       ti+   + Gi ++++ +    +nNti
  gi|386001438|ref|YP_005919737.1| 386 TISEGEKTGILFWSTIG-ASAYNNTI 410
                                       **********9999999.99999997 PP

  == domain 3  score: 34.9 bits;  conditional E-value: 1.4e-12
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT- CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssn.vvienneiannsgsGiyilgs.snntisnntisdnngggialfg 76 
                                       gi+++++ +++  nnti + +  G+ +++ss+   i++n+i n  ++G+ i+g+  +n++++n++s +  +g+ l g
  gi|386001438|ref|YP_005919737.1| 394 GILFWSTIGASAYNNTIFD-SPVGVSVEESSSgLAITENRIKN-ATEGMNISGGsRENQVTGNNVSSSD-VGVILVG 467
                                       89999999999********.7*********99877778*****.********9989**********999.******* PP

                                       -S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT- CS
                        Beta_helix  77 asnnlienneitdnggsGiyln.yssnntienNiidnnag 115
                                       a +nli +n i+d    Gi  +  s  n+i +N +++n++
  gi|386001438|ref|YP_005919737.1| 468 ATRNLITGNLIFDSIL-GIVADfASRGNSIYGNDLSGNGE 506
                                       **************99.**99988999******9999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 4266.72
//
Query:       gi|386001439|ref|YP_005919738.1|  [L=171]
Description: hypothetical protein Mhar_0737 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-09   37.0   0.1    6.4e-09   36.7   0.1    1.1  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola
     0.0049   16.8   0.2      0.014   15.4   0.2    1.7  1  MetOD1         Metanogen output domain 1
  ------ inclusion threshold ------
       0.15   12.0   0.0       0.33   10.9   0.0    1.5  1  YAcAr          YspA, cpYpsA-related SLOG family


Domain annotation for each model (and alignments):
>> 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 !   36.7   0.1   1.1e-12   6.4e-09       8     145 .]      19     162 ..      12     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.1e-12
                     ATC_hydrolase   8 il.valyealkkeigkeeakeiirkalerlgkergkklaekakakkdkadvekflalyseifek..enalkfevlee 81 
                                       ++ + ++ ++++  g eea e+ r+++  l k ++++l++++k    ++ +e++++    i +k   + ++fe + +
  gi|386001439|ref|YP_005919738.1|  19 AVdGLWFMKVEEMRGFEEALEADRRVWSVLPKIQARTLRTMLK---ADEGIEGLARC---ISAKhsAEGFDFEAEMD 89 
                                       4457889999998899***********9999**********99...55556666554...33332345566666666 PP

                     ATC_hydrolase  82 .dkdeleidvtrCpyceawkkeGlp....elgkllCeiDkav.aeginpk...vklertktlaeGgdcCdfrf 145
                                        d   l++ + +Cp++e+ ++ G +     +g ++C+ ++a  a ++++    + ++ ++++ +G+++C f+f
  gi|386001439|ref|YP_005919738.1|  90 eDGRLLRLIISKCPWHELLVRSGREplseRVGTTICNAEYAAwAAEFEGGdlkISFSLKSQICKGDQVCTFCF 162
                                       4455577****************8547778999***99997524444443666******************98 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.3e-06     0.014      81     153 ..      81     163 ..      54     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-06
                            MetOD1  81 nfgiktekkedeknvlleftnCpWge...earknPi.......fCllcraivsrsftwtglkgsveqkktlgngdek 147
                                       +f ++ e +ed+    l + +CpW e   ++ ++P        +C+   a     f+  +lk+s+  k+++ +gd+ 
  gi|386001439|ref|YP_005919738.1|  81 GFDFEAEMDEDGRLLRLIISKCPWHEllvRSGREPLservgttICNAEYAAWAAEFEGGDLKISFSLKSQICKGDQV 157
                                       5666666679**************988555556664222222256666677888899999***************** PP

                            MetOD1 148 CvFeik 153
                                       C+F ++
  gi|386001439|ref|YP_005919738.1| 158 CTFCFE 163
                                       ***997 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.5e-05      0.33      14      64 ..      41      88 ..      28      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.5e-05
                             YAcAr 14 leliwatLdklhaeapidmvlvhGgakGaDrlAarWAaergvelvrfpaDw 64
                                       +++w  L k++a+       +  +++G++ lA++ +a++  e  +f+a++
  gi|386001439|ref|YP_005919738.1| 41 DRRVWSVLPKIQARTLR---TMLKADEGIEGLARCISAKHSAEGFDFEAEM 88
                                      4599**********994...445788*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1118.12
//
Query:       gi|386001440|ref|YP_005919739.1|  [L=589]
Description: Archaeosine tRNA-ribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-49  167.2   0.0    3.5e-49  166.6   0.0    1.3  1  DUF5591   Domain of unknown function (DUF5591)
    4.2e-13   49.0   0.6      9e-13   48.0   0.1    1.8  2  PUA       PUA domain
    3.6e-08   33.0   0.0    4.9e-07   29.2   0.0    2.4  3  TGT       Queuine tRNA-ribosyltransferase
    2.1e-05   24.5   0.0    6.1e-05   23.1   0.0    1.8  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.6   0.0   7.8e-53   3.5e-49       1     153 [.     297     441 ..     297     442 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 7.8e-53
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       v+rf+ervlerY+ pe ++vl+LlPcsa+kPys+s+shr fa+a++++++++he+iltsPl++vPreleevYPaa+Y
  gi|386001440|ref|YP_005919739.1| 297 VTRFAERVLERYRAPE-SDVLLLLPCSARKPYSTSRSHRLFASALGEARRRLHELILTSPLALVPRELEEVYPAASY 372
                                       89*************7.************************************************************ PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkea 153
                                       d++vtg+w+  e+++++++l++yle+++y++++ah+e+e +e+v +     g+++++t      t+ e+l +L+ea
  gi|386001440|ref|YP_005919739.1| 373 DVPVTGRWDLLERKWLTRCLERYLERNRYRRIVAHIEGELEEAVVD----SGIDAVFTG---GGTDGEALGRLSEA 441
                                       ***************************************6665555....468888888...56888888888776 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.3     1e+04      16      24 ..     473     481 ..     470     486 .. 0.82
   2 !   48.0   0.1     2e-16     9e-13      18      73 ..     533     586 ..     524     586 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                                       T-EEEGGGE CS
                               PUA  16 gasLlapGv 24 
                                       g++Lla Gv
  gi|386001440|ref|YP_005919739.1| 473 GRDLLAGGV 481
                                       899***999 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 2e-16
                                       EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       ++lapGv ++++++++gd+V +  e   + +vG+a++s+ e+ ++++g++ve+++v
  gi|386001440|ref|YP_005919739.1| 533 DVLAPGVARADDQIRPGDEVIVTGE--AAFGVGRAKMSGWEMVEATRGIAVELRHV 586
                                       99******************77777..***************************97 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.075   3.4e+02       3      21 ..      23      40 ..      19      44 .. 0.87
   2 !   29.2   0.0   1.1e-10   4.9e-07     190     346 ..     116     253 ..     108     257 .. 0.86
   3 ?   -2.1   0.0      0.36   1.6e+03     153     183 ..     386     422 ..     385     449 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.075
                                      EEEEEEEETTEEEEESEEE CS
                               TGT  3 aRlGklelphgtietPafm 21
                                      aR+G+l+l+  ++etPa++
  gi|386001440|ref|YP_005919739.1| 23 ARMGRLRLAA-PVETPAIL 40
                                      9*******88.8****987 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.1e-10
                                       -SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEE CS
                               TGT 190 fdgyaigGlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsege 266
                                       +d+y++g+     + +el+  + +++e  p d   y     tP +l+ +v lGvD++d + +   +  gr+  ++g 
  gi|386001440|ref|YP_005919739.1| 116 ADVYVLGAAGSLRNPRELVASIVKIREMTPPDSALYAPALATPANLALLVYLGVDLVDGARIVVDGLLGRYHLRDGV 192
                                       4678889855444455555555699***************************************************9 PP

                                       EETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                               TGT 267 lnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefvee 343
                                       + ++    +e   p    C C+ C+         l +++    ++L+++HN   + e+++ +++ I++gt+ e++e+
  gi|386001440|ref|YP_005919739.1| 193 WPVE--ALKEL--P----CRCPFCR--------ALEEEQD---PKLVAEHNQLKLEEELSIVKTMIRSGTLREYAER 250
                                       9887..44444..8....******9........7776677...*******************************998 PP

                                       HHH CS
                               TGT 344 far 346
                                        +r
  gi|386001440|ref|YP_005919739.1| 251 QVR 253
                                       665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.36
                                       HHHHHHHHHH......SEEEEEE--TT-HHHHHHHHH CS
                               TGT 153 rwldrcleah......qalfgivqGglyedlreesae 183
                                       +wl rcle++        +++ ++G l+e +    ++
  gi|386001440|ref|YP_005919739.1| 386 KWLTRCLERYlernryRRIVAHIEGELEEAVVDSGID 422
                                       7999**9988888886668888888776665554444 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.4e-08   6.1e-05       3      65 ..     460     516 ..     458     518 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.4e-08
                            TGT_C2   3 lraiadYqFGagagdaLfpedvtitrsatgrirqvlv.dgerlatlraqdgrltLsleGarrlh 65 
                                        ra+adY FG gag++L  + v+++       r++   d + la++    g+  Ls eGarrl 
  gi|386001440|ref|YP_005919739.1| 460 FRALADYSFGLGAGRDLLAGGVRVR------GRELSSaDRKPLASF-TPHGTIALSPEGARRLL 516
                                       69****************9988887......78888879******9.567************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3581.52
//
Query:       gi|386001441|ref|YP_005919740.1|  [L=478]
Description: Archaeosine tRNA-ribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-77  259.2   0.0    7.5e-77  258.8   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.8   0.0   4.2e-81   7.5e-77       3     349 ..      14     336 ..      10     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 258.8 bits;  conditional E-value: 4.2e-81
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       +R+G+l++phg++etPa+mpv  +++++ ++p +l e lga+i+++n+y++++ p+ + +a+ +g+h++lg+++pi+
  gi|386001441|ref|YP_005919740.1|  14 GRIGRLRTPHGVVETPALMPV-VNPHLRLIEPADL-ERLGAEILITNSYIIHQDPELHDLAAKEGVHRLLGFEGPIM 88 
                                       8********************.999**********.699************************************** PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                       tdsg+fq   l           s + G+ + ++p e++++q+ + sDi+++ld ++p++  ++r+e ++  T+++l 
  gi|386001441|ref|YP_005919740.1|  89 TDSGAFQ---L-----------SVY-GN-IDVQPLEILDFQRLIASDICVPLDIPTPPDVPRSRAEAELAITEERLS 149
                                       *******...3...........336.99.************************************************ PP

                                       HHHHHH...SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEE CS
                               TGT 157 rcleah...qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpryl 226
                                       ++ e +   ++ l g++qG++y+dlr  + +++ +++fd  +ig+ ++++e  + ++l+evv+a+++ l    p++l
  gi|386001441|ref|YP_005919740.1| 150 EAREDWsegGSlLAGPIQGSTYPDLRFGAGRRVGEMGFDLCPIGAvVPLMEayRFRDLVEVVAASKQGLGPAAPVHL 226
                                       ***9999**555*********************************888***8888********************** PP

                                       TTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHH CS
                               TGT 227 mGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllk 303
                                       +G+g+P++++ a alG+D+fd++++++ ar+gr+lt++g+l+l++ ky     p    C C +C+   ra  + l +
  gi|386001441|ref|YP_005919740.1| 227 FGAGHPMMFALAAALGCDLFDSAAYALSARQGRYLTTSGTLHLEELKYL----P----CCCEVCR--DRA-AEDLAE 292
                                       ********************************************99999....9....*******..444.455655 PP

                                       TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 304 tkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                         e   + Ll+ HNl + l +++r+R++I eg+++e+ve++ar+++
  gi|386001441|ref|YP_005919740.1| 293 DPE--RTELLARHNLSVSLAEVRRVRQSIWEGSLWELVERRARSHP 336
                                       666..688**********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2937.74
//
Query:       gi|386001442|ref|YP_005919741.1|  [L=649]
Description: Aconitate hydratase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.2e-106  356.1   1.6   3.4e-104  349.4   1.6    2.3  1  Aconitase    Aconitase family (aconitate hydratase)
    3.7e-18   66.1   0.0    6.3e-18   65.4   0.0    1.3  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.012   14.3   0.0      0.018   13.8   0.0    1.2  1  DUF521       Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.4   1.6  5.7e-108  3.4e-104       1     461 []       7     407 ..       7     407 .. 0.90

  Alignments for each domain:
  == domain 1  score: 349.4 bits;  conditional E-value: 5.7e-108
                         Aconitase   1 ekiwdahlvee.....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       eki+++hl +      ++i    d+ l+qd+tg +a  ++++++ +          i++  +v+  +dh+       
  gi|386001442|ref|YP_005919741.1|   7 EKILRDHLLDGsyepgKEIGIRIDQTLTQDATGTMAYLQFESMGLSR---------IETELSVS-YVDHNT------ 67 
                                       68888887733333332255558**********************99.........55555555.444544...... PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgie 149
                                          ++  fe+ +   + L++ a+++gi++  pg+GI+Hqv lE  +  pg t++g+DSHT++ gglG++aiG Gg +
  gi|386001442|ref|YP_005919741.1|  68 ---VQVGFEN-ADDHRYLQTIAERYGIHFSRPGNGICHQVHLER-FGRPGRTLLGSDSHTPTCGGLGMIAIGAGGLD 139
                                       ...3333443.55668899*************************.******************************** PP

                         Aconitase 150 aeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaE 226
                                       ++ ++ g  ++l++p+v++v+l+G+l+e+vtakD++l+v ++l++kg vg++ E++Gegv+sL++ +raTi+NM+aE
  gi|386001442|ref|YP_005919741.1| 140 VAVAMGGGAYYLTCPRVIRVNLEGELPEWVTAKDVILKVLSELTTKGNVGCICEYVGEGVQSLTVPERATITNMGAE 216
                                       ***************************************************************************** PP

                         Aconitase 227 vGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                       +G tt+lfp de+t ++L+a++r        +++       laad++a+y+++l++dls+l+p +a p++P + vp+
  gi|386001442|ref|YP_005919741.1| 217 TGVTTSLFPSDEQTQKFLAAQDRG------GQWA------PLAADDGAKYHRELDVDLSDLVPLMAAPHSPGNIVPV 281
                                       *******************77773......3333......4788********************************* PP

                         Aconitase 304 selvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                                       s+l+                             ++vd+++igSCTNss  d++ +a++++     g++  ++v++ v
  gi|386001442|ref|YP_005919741.1| 282 SDLA----------------------------GTPVDQVMIGSCTNSSFADLMTVAEMVR-----GRRLPSSVSLGV 325
                                       4433............................45699***********************.....************ PP

                         Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrleegeaivsssNRNFegRqgpntra.yLaSPelvva 456
                                       aPGS++v   + ++G l +L + G+ +++++C+ Cigns   ++++ ++ +sNRNF+gR g+ + + yLaSP  ++a
  gi|386001442|ref|YP_005919741.1| 326 APGSRQVLMMIAENGSLADLIAFGARILESACGFCIGNSISPKTDSISIRTSNRNFKGRSGTASANvYLASPVAAAA 402
                                       *****************************************99999**************9766666********** PP

                         Aconitase 457 aAlaG 461
                                       aAl G
  gi|386001442|ref|YP_005919741.1| 403 AALRG 407
                                       ***98 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0     1e-21   6.3e-18      61     129 ..     512     580 ..     479     582 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1e-21
                                       EHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                       Aconitase_C  61 dvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                       ++ + a   ++ g+  +++ag  +G+GSSRehAA+ +  lG+kav+a+S erI+  nl++ g++p +f 
  gi|386001442|ref|YP_005919741.1| 512 EFSKRAAVRRDRGIANLIVAGVSYGQGSSREHAALCPMYLGVKAVMAKSMERIHAANLVNFGIIPFTFV 580
                                       666666666777888899999********************************************9985 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     3e-06     0.018     289     367 ..     287     369 ..     280     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-06
                            DUF521 289 ekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtCmvv..s 361
                                       ++vd v++G c   s+ +l+++ae+++g++  ++v l v   sr+v  ++ + g ++ l ++G+++l++ C ++  +
  gi|386001442|ref|YP_005919741.1| 287 TPVDQVMIGsCTNSSFADLMTVAEMVRGRRLPSSVSLGVApGSRQVLMMIAENGSLADLIAFGARILESACGFCigN 363
                                       678999998688999**********************88735899**************************776687 PP

                            DUF521 362 plikkk 367
                                        +++k+
  gi|386001442|ref|YP_005919741.1| 364 SISPKT 369
                                       777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3926.43
//
Query:       gi|386001443|ref|YP_005919742.1|  [L=335]
Description: Diphthamide biosynthesis protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-78  264.1   0.0    2.1e-78  263.8   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.8   0.0   1.2e-82   2.1e-78       2     297 ..      34     322 ..      33     326 .. 0.95

  Alignments for each domain:
  == domain 1  score: 263.8 bits;  conditional E-value: 1.2e-82
                   Diphthamide_syn   2 Pegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd..rlpvlYvfveield 75 
                                       Pegl++ + ++a+ + ee+ aev+ +gD++YGaC+vd   +++  adl++H Ghs++ + d  + +v+Yv ++++ d
  gi|386001443|ref|YP_005919742.1|  34 PEGLKRMASDLARDIqEETCAEVIFSGDPCYGACDVDLDLCRA--ADLVIHVGHSEMLEGDplHDKVVYVEARMRAD 108
                                       ***************9999************************..*************999999************* PP

                   Diphthamide_syn  76 vehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevdai 152
                                       v++ ve +++ + +++++++v+t+q+ h+l+ev e+l  +g+e +  p   ++++pg+vlgc+++++++  ++vd++
  gi|386001443|ref|YP_005919742.1| 109 VREAVEGAAELL-KTSRVGVVTTVQHIHKLPEVLELLGGRGIEGIVRPGG-RTRYPGQVLGCNYEAARN--ADVDEY 181
                                       ************.7889*********************999988855655.9***************95..59**** PP

                   Diphthamide_syn 153 lyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelver 229
                                       l++g+g+fh+l+++l++ k +v+++dp++++++    da+ +lrrRy ai++a da+++++iv+++ +q+r+el++r
  gi|386001443|ref|YP_005919742.1| 182 LFVGTGQFHPLGVALATGK-RVVAADPVTGNVS--VIDAAPMLRRRYGAIARAGDAERIAVIVSKKPGQRRMELARR 255
                                       *****************77.9********9777..5569************************************** PP

                   Diphthamide_syn 230 lkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgere 297
                                       + +l +e+gk+++lv++++++p+ L n+  +da V +aCpr+++dd+ +++ Pvltp E+ev+lg+r+
  gi|386001443|ref|YP_005919742.1| 256 MMSLGEEQGKRMILVYLDRMEPDALVNL-GVDAAVSTACPRIALDDQAKYPVPVLTPPEFEVLLGRRK 322
                                       ****************************.************************************554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2179.80
//
Query:       gi|386001444|ref|YP_005919743.1|  [L=336]
Description: FLAP endonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-25   88.9   0.0    3.7e-25   88.1   0.0    1.4  1  XPG_I         XPG I-region
    3.6e-17   62.7   0.0    5.8e-17   62.0   0.0    1.4  1  XPG_N         XPG N-terminal domain
    3.3e-05   24.4   0.0    7.4e-05   23.3   0.0    1.6  1  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold
     0.0047   17.0   0.1      0.019   15.1   0.1    1.9  2  HHH_2         Helix-hairpin-helix motif
     0.0088   16.6   0.3       0.72   10.5   0.0    3.1  3  HHH_5         Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.026   14.4   0.0    1.4  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
      0.091   12.2   0.0       0.18   11.3   0.0    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.43   10.7   2.0       0.43   10.7   0.3    1.8  2  BCL_N         BCL7, N-terminal conserver region


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   1.7e-28   3.7e-25       2      94 .]     139     234 ..     138     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.7e-28
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mgip v+Ap+E+EAq+a+++ kg+vd v s+D+D+llFGap+v+rn+  ++k+k    + ++++ +evi+l++ l 
  gi|386001444|ref|YP_005919743.1| 139 AMGIPAVQAPSEGEAQAAFMAIKGDVDLVGSQDYDALLFGAPRVVRNMAiTGKRKLPgkNVYVEVMPEVISLDEELL 215
                                       79**********************************************9655555547799999************* PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       +lg+ r ql+++ i++g+D
  gi|386001444|ref|YP_005919743.1| 216 RLGIARRQLVEIGIMCGTD 234
                                       ******************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   2.6e-20   5.8e-17      18     100 ..      13     100 ..       1     101 [. 0.92

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 2.6e-20
                                       EEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHH CS
                             XPG_N  18 svsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkke 89 
                                       ++++e+l gk +a+Da   ly+fl  +r+q+g+ l+      tshl g+++r+  ll+ g k +fVFdg++p +k+e
  gi|386001444|ref|YP_005919743.1|  13 KIELEELAGKLIAVDAFNTLYQFLSIIRQQDGTPLRDgsgrtTSHLSGILYRMTNLLEAGAKVVFVFDGEPPRFKRE 89 
                                       4899*******************************9999999*********************************** PP

                                       HHHHHHHHHHH CS
                             XPG_N  90 elekrserrqe 100
                                       +l +r e r+ 
  gi|386001444|ref|YP_005919743.1|  90 TLDQRAETRSR 100
                                       ******99976 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.3e-08   7.4e-05      18      49 ..     234     265 ..     220     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.3e-08
                        5_3_exonuc  18 DnipGvpgiGektAakLlkeygsleeilenld 49 
                                       D  +G + +G+ktA kL+ke+g+le++le+  
  gi|386001444|ref|YP_005919743.1| 234 DYNEGLKRVGPKTALKLIKEHGNLEGVLEARG 265
                                       55579***********************9653 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   4.3e+03       1      11 [.     135     145 ..     135     157 .. 0.87
   2 !   15.1   0.1   8.5e-06     0.019       7      43 ..     238     274 ..     236     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                             HHH_2   1 rllfaLGIrhV 11 
                                       rll a+GI+ V
  gi|386001444|ref|YP_005919743.1| 135 RLLEAMGIPAV 145
                                       688999**998 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.5e-06
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddi 43 
                                       G++ VG ktA +L k+ ++l+   +a  e++    +i
  gi|386001444|ref|YP_005919743.1| 238 GLKRVGPKTALKLIKEHGNLEGVLEARGETIEDAAEI 274
                                       8899***********************9999887776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.19   4.2e+02      13      31 ..     131     150 ..     130     165 .. 0.73
   2 !   10.5   0.0   0.00032      0.72       6      38 ..     238     269 ..     235     276 .. 0.75
   3 ?   -0.2   0.0      0.72   1.6e+03      31      51 ..     315     335 ..     307     336 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                                       HHHHHHHTT.T--SHHHHHH CS
                             HHH_5  13 ktAlallsa.Giesvedlaa 31 
                                       ++A++ll+a Gi  v++  +
  gi|386001444|ref|YP_005919743.1| 131 ADAMRLLEAmGIPAVQAPSE 150
                                       68*******99999987555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00032
                                       TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaadveeLa 38 
                                       +++ +GpktAl+l++   + +e +++a  e++ 
  gi|386001444|ref|YP_005919743.1| 238 GLKRVGPKTALKLIKE-HGNLEGVLEARGETIE 269
                                       5789********9999.6778877777555554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.72
                                       HS-HHHHHTSTTS-HHHHHHH CS
                             HHH_5  31 aadveeLakipGiGkktAeri 51 
                                       +++v++L ++  +G+ t +++
  gi|386001444|ref|YP_005919743.1| 315 EKAVKRLMEAVKVGQSTLDKW 335
                                       568999999999999999887 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.026       3     101 ..      24     148 ..      22     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                      5_3_exonuc_N   3 lLiDgsslifRayyal.......lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKanR 72 
                                       + +D+ + +++    +       l+  +g+ t+ + g+l  +++lle  +  ++++vfD +++ f++e +++  ++R
  gi|386001444|ref|YP_005919743.1|  24 IAVDAFNTLYQFLSIIrqqdgtpLRDGSGRTTSHLSGILYRMTNLLEAGA--KVVFVFDGEPPRFKRETLDQRAETR 98 
                                       566776666654443355666566666899****************9766..6******9999*********99999 PP

                      5_3_exonuc_N  73 ....................eetpeelk.eqlplikevlealgikvleve 101
                                                           +++   l+ e ++   ++lea+gi+ ++++
  gi|386001444|ref|YP_005919743.1|  99 sraeemwqrakeegldgfkyAQAASRLEdEMIADAMRLLEAMGIPAVQAP 148
                                       88888888888888888877445555542556778888888888888765 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.8e-05      0.18      25      92 ..      89     150 ..      66     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.8e-05
                                       C.......HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBC CS
                      AP_endonuc_2  25 l.......sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpG 92 
                                               ++++++e++++++e gl         +f y     r ++     + + +a++l +a+G+p ++ ++ 
  gi|386001444|ref|YP_005919743.1|  89 EtldqraeTRSRAEEMWQRAKEEGLD--------GFKYAQAASRLED-----EMIADAMRLLEAMGIPAVQAPSE 150
                                       234445567899**************........9999776655555.....9*****************98865 PP

>> BCL_N  BCL7, N-terminal conserver region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00019      0.43       4      20 ..      93     109 ..      90     112 .. 0.88
   2 ?   -2.6   0.1       2.6   5.9e+03      11      23 ..     313     325 ..     310     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                             BCL_N   4 lRaeTRsrakddlkrvi 20 
                                       +RaeTRsra++  +r++
  gi|386001444|ref|YP_005919743.1|  93 QRAETRSRAEEMWQRAK 109
                                       6**********999976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                             BCL_N  11 rakddlkrviksl 23 
                                       r ++ +kr+++++
  gi|386001444|ref|YP_005919743.1| 313 RVEKAVKRLMEAV 325
                                       6667778877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2042.18
//
Query:       gi|386001445|ref|YP_005919744.1|  [L=113]
Description: HesB/YadR/YfhF-family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-05   25.0   0.0    2.1e-05   24.7   0.0    1.2  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-09   2.1e-05       3     101 ..       4      93 ..       2     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-09
                                       EEE-HHHHHHHHHHHHCTTECEEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS CS
                       Fe-S_biosyn   3 itlteaAaeklkkllaedkkelrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvfl 79 
                                       i++t+ Aae lk  + ++   +r+ +            + g++y l + d + +e+d+v+esng+kv++ +++++ l
  gi|386001445|ref|YP_005919744.1|   4 IEITDVAAEVLKGNMIQGRV-VRMILAATD--------ATGANYVLAWGD-P-AEDDVVFESNGIKVHMAPEDAEIL 69 
                                       99***********9999988.555555554........45********88.5.7*********************** PP

                                       .TTEE.EEEEEE.TTEEEEEEETC CS
                       Fe-S_biosyn  80 deglv.ldfved.lgtlgLksdng 101
                                       ++  + +d+v++ + + g+  + +
  gi|386001445|ref|YP_005919744.1|  70 GDSPTiIDYVDTeDLGTGFIIEGP 93 
                                       988662688754144555655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 710.35
//
Query:       gi|386001446|ref|YP_005919745.1|  [L=662]
Description: acetyl-CoA synthetase [Methanosaeta harundinacea 6Ac]
Scores for 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-88  296.2   0.0    3.7e-88  295.9   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    5.4e-29  101.0   0.5    1.8e-28   99.3   0.4    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    7.8e-16   57.7   3.9    7.8e-16   57.7   3.9    2.6  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.9   0.0   6.2e-92   3.7e-88       7     422 ..     106     542 ..      99     543 .. 0.88

  Alignments for each domain:
  == domain 1  score: 295.9 bits;  conditional E-value: 6.2e-92
                                       HSTTSEEEEE.....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   7 ktpdkvalvd.....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                        + ++va+++     ++  + +TY+e +e vn+lA+gL+slGvkkgdr+ i++p+ pe v+a+la++k+Ga+++ + 
  gi|386001446|ref|YP_005919745.1| 106 GKGKRVAYHFipeatDQPERAYTYQEIYETVNKLANGLKSLGVKKGDRISIYMPMLPETVMAMLACAKIGAIHSLVF 182
                                       4557888888889988899********************************************************** PP

                                       TTS-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSC CS
                       AMP-binding  79 ptltaeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeesee 145
                                       ++++++     ++d+eakv++         +        ++++e  ++  +vk vivl++ +l+  +++  +    e
  gi|386001446|ref|YP_005919745.1| 183 SGFSSKGFGDRVQDCEAKVVFtadgfyrrgK---PMPlKPQADEGVKDAASVKNVIVLKRTGLEVPWTEGRDVWFHE 256
                                       *********************9988875331...3444566777777778999******999887766655554333 PP

                                       TTS.....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHH CS
                       AMP-binding 146 kae.....kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifg 216
                                                ++ +e  ++++ ++i+YTSGTTGkPKG+ + h ++ v  ++++k    f+l+edd +++++++ +i+g
  gi|386001446|ref|YP_005919745.1| 257 --LvdkqsADCATEVMDAEERLFILYTSGTTGKPKGIEHAHgGYCVGPAYTCK--WVFDLNEDDIYWCTADVGWITG 329
                                       ..13456667788899*************************667777777764..3488999*************** PP

                                       HHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEES CS
                       AMP-binding 217 lilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllgg 292
                                       +++  +++l+ G t v+++++++ +d +++++ i+++kvtv++++P+++++l+++g++    ++ d ss+rl+ ++g
  gi|386001446|ref|YP_005919745.1| 330 HSYVAYGPLCLGITSVMYEGSPDyPDFGRWYKIIQDYKVTVFYTAPTAVRMLMKQGNEW--PEKFDRSSVRLLGSVG 404
                                       ***********************888****************************86655..445599********** PP

                                       S-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEE CS
                       AMP-binding 293 eplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGe 366
                                       epl+pe+  ++r+ fg+   ++++++++TE +++v+  pl+    k+gsv  plpg    i Dee g++vp ge G 
  gi|386001446|ref|YP_005919745.1| 405 EPLNPEAYIWYRKYFGNeisPIMDTWWQTESGCHVI-SPLPMTPCKPGSVAYPLPGFNTTIYDEE-GNEVPLGEGGN 479
                                       ***********************************8.4555555799*****************9.*********** PP

                                       EEEEET..TS-SEBTT-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 367 llvrgp..gvmkgYlkkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       ++   p  ++ + ++k++ + ++ +++     +++ +  GD +++d+dGy ++ gR++d++ +
  gi|386001446|ref|YP_005919745.1| 480 IVNPTPwpSMLRAFYKDEVRYKKEYWDmywkvKPGTYLAGDKATRDKDGYWFVQGRIDDVLSV 542
                                       **8888668*****************999977457************************9865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.6   9.3e+03      42      53 ..      42      53 ..      30      64 .. 0.66
   2 !   99.3   0.4   3.1e-32   1.8e-28       1      76 []     551     629 ..     551     629 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHH CS
                     AMP-binding_C 42 leeeLkahvrke 53
                                      +e+e +a++ ++
  gi|386001446|ref|YP_005919745.1| 42 TEKEMRAWCGEH 53
                                      567777777664 PP

  == domain 2  score: 99.3 bits;  conditional E-value: 3.1e-32
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea..leeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                       evEs lv+h++VaeaaV+G+pde+kGea++afV+lk+g  + +  l+++Lk hvr+++gp+a p  v+fvd+lpktr
  gi|386001446|ref|YP_005919745.1| 551 EVESSLVAHKDVAEAAVIGKPDEIKGEAIIAFVILKEGvkT-SddLAKALKTHVRTTMGPLAIPAGVYFVDDLPKTR 626
                                       8***********************************99642.236******************************** PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                       sGK
  gi|386001446|ref|YP_005919745.1| 627 SGK 629
                                       **9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   3.9   1.3e-19   7.8e-16       2      55 .]      44      98 ..      43      98 .. 0.97
   2 ?    1.3   0.5     0.056   3.3e+02      22      49 ..     506     536 ..     490     537 .. 0.65

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.3e-19
                                      HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      ke+ ++  e++ +FW+e+ak   dW++p+++v+d+s++p++kWF GGk+N+ yN+
  gi|386001446|ref|YP_005919745.1| 44 KEMRAWCGEHYLEFWDEMAKTyADWYEPYTQVMDDSEKPYFKWFIGGKINMFYNA 98
                                      78999***************98********************************7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.056
                                       CS--SB--S-SECSTTTC...T-EESTT-EE CS
                            ACAS_N  22 eldWekpfdkvldgskgp...fikWFeGGkl 49 
                                       +++W+ ++ + l g+k+    +  WF+ G++
  gi|386001446|ref|YP_005919745.1| 506 DMYWKVKPGTYLAGDKATrdkDGYWFVQGRI 536
                                       4688888888887665333358999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 4951.05
//
Query:       gi|386001447|ref|YP_005919746.1|  [L=110]
Description: hypothetical protein Mhar_0750 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 770.43
//
Query:       gi|386001448|ref|YP_005919747.1|  [L=662]
Description: acetyl-CoA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-89  300.4   0.0    2.1e-89  300.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    5.8e-29  100.9   0.4    2.1e-28   99.1   0.3    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    2.3e-16   59.5   3.5    2.3e-16   59.5   3.5    2.6  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.1   0.0   3.5e-93   2.1e-89       8     422 ..     107     542 ..      99     543 .. 0.89

  Alignments for each domain:
  == domain 1  score: 300.1 bits;  conditional E-value: 3.5e-93
                                       STTSEEEEE.....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   8 tpdkvalvd.....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       +  kva+++     ++  + +TY+e +e vn+lA+gL+slGv kgdrV i++p+ pe v+a+la++k+Ga+++ + +
  gi|386001448|ref|YP_005919747.1| 107 KGAKVAYHFipeptDQAEKDYTYQEIYETVNKLANGLKSLGVVKGDRVSIYMPMLPETVMAMLACAKIGAIHSLVFS 183
                                       4578888888899878899********************************************************** PP

                                       TS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS CS
                       AMP-binding  80 tltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae 148
                                       +++++     ++d++akv++       +  +     ++++ea++  ++vk vivl++ +++  ++  ++    e   
  gi|386001448|ref|YP_005919747.1| 184 GFSSKGFGDRVDDCQAKVVFtsdgfyrR-GKPMPlKPQADEATKGIQSVKNVIVLKRTGIEVPWNDAKDVWFHE--L 257
                                       ********************99888752.2344557788888999999********999998866665554443..1 PP

                                       .....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHH CS
                       AMP-binding 149 .....kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilplahifgli 218
                                             ++++eel+++d ++i+YTSGTTGkPKG+ + h ++ v+ +++l+     f+lke+dv+++++++ +i+g++
  gi|386001448|ref|YP_005919747.1| 258 ikgqsAECKTEELDAEDRLFILYTSGTTGKPKGIEHAHgGYCVTPAQTLH---WvFDLKENDVWWCTADVGWITGHS 331
                                       34667788999***************************777777777763...2488999***************** PP

                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS- CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggep 294
                                       +  +++l+ Gat ++++++++ +d +++++ i++ kvtv++++P+++++l+++g++    +++dlss+rl+ ++gep
  gi|386001448|ref|YP_005919747.1| 332 YVAYGPLCLGATTIMYEGSPDfPDFGRWYKIIQEQKVTVFYTAPTAVRMLMKQGEEW--PAKYDLSSIRLLGSVGEP 406
                                       *********************888****************************87655..5566************** PP

                                       EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEE CS
                       AMP-binding 295 lspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGell 368
                                       l+pe+  ++r+ f     ++++++++TEt+++v+  pl+    k+gsv  plpg    i Dee g++vp ge G ++
  gi|386001448|ref|YP_005919747.1| 407 LNPEAYIWYRKNFAYdkaPIMDTWWQTETGCFVI-SPLPMTPCKPGSVAYPLPGFNTTIYDEE-GNEVPLGEGGNIV 481
                                       *************98999***************8.4555555799*****************9.************* PP

                                       EEET..TS-SEBTT-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 369 vrgp..gvmkgYlkkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                          p  ++ + ++k++ + ++ +++     +++ +  GD +++d+dGy ++ gR++d++ +
  gi|386001448|ref|YP_005919747.1| 482 NPTPwpSMLRAFYKDEVRYKKEYWDmywkvKPGTYLAGDKATRDKDGYWFVQGRIDDVLSV 542
                                       8888668*****************999977457************************9865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.6   9.3e+03      42      53 ..      42      53 ..      30      64 .. 0.66
   2 !   99.1   0.3   3.5e-32   2.1e-28       1      76 []     551     629 ..     551     629 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHH CS
                     AMP-binding_C 42 leeeLkahvrke 53
                                      +e+e +a++ ++
  gi|386001448|ref|YP_005919747.1| 42 TEKEMRAWCGEH 53
                                      567777777664 PP

  == domain 2  score: 99.1 bits;  conditional E-value: 3.5e-32
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea...leeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                       evEs lv+h++V+eaaV+G+pde+kGea++afV+lk++ + +   l++eLk hvr+++gp+a p  v+fvd+lpktr
  gi|386001448|ref|YP_005919747.1| 551 EVESSLVAHKDVSEAAVIGKPDEIKGEAIIAFVILKKDvK-PsddLAKELKTHVRTTMGPLAIPAGVYFVDDLPKTR 626
                                       8**********************************98842.2346******************************** PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                       sGK
  gi|386001448|ref|YP_005919747.1| 627 SGK 629
                                       **9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   3.5   3.8e-20   2.3e-16       2      55 .]      44      98 ..      43      98 .. 0.97
   2 ?    1.3   0.5     0.056   3.3e+02      22      49 ..     506     536 ..     490     537 .. 0.65

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.8e-20
                                      HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      ke+ ++  e++ +FW+e+ak   dW+kp++kv+d+s +p++kWF+GGk+N+ yN+
  gi|386001448|ref|YP_005919747.1| 44 KEMRAWCGEHYLEFWDEMAKTyADWYKPYTKVMDDSGMPYFKWFTGGKVNVFYNA 98
                                      78999***************98********************************7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.056
                                       CS--SB--S-SECSTTTC...T-EESTT-EE CS
                            ACAS_N  22 eldWekpfdkvldgskgp...fikWFeGGkl 49 
                                       +++W+ ++ + l g+k+    +  WF+ G++
  gi|386001448|ref|YP_005919747.1| 506 DMYWKVKPGTYLAGDKATrdkDGYWFVQGRI 536
                                       4688888888887665333358999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4715.94
//
Query:       gi|386001449|ref|YP_005919748.1|  [L=664]
Description: acetyl-CoA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-93  311.3   0.0    9.8e-93  311.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.3e-27   94.9   4.9    8.3e-27   94.0   1.1    2.9  3  AMP-binding_C  AMP-binding enzyme C-terminal domain
    5.8e-19   67.8   2.8    5.8e-19   67.8   2.8    2.4  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.14   12.0   0.5       0.37   10.6   0.5    1.7  1  DUF1391        Protein of unknown function (DUF1391)


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 !  311.0   0.0   2.2e-96   9.8e-93       3     422 ..     101     543 ..      99     544 .. 0.91

  Alignments for each domain:
  == domain 1  score: 311.0 bits;  conditional E-value: 2.2e-96
                                       HHHHHST.TSEEEEE.....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-E CS
                       AMP-binding   3 eqaaktp.dkvalvd.....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGav 73 
                                       ++a+  + dkva+++     ++  q++TY++l+++vn+lA+gL+slG+kkgdrV +++p+ p++ +++la++k+G++
  gi|386001449|ref|YP_005919748.1| 101 RHAKGAKkDKVAYIWvpeptDQPTQKITYGDLYKEVNKLANGLKSLGLKKGDRVSVYMPMIPQLPITVLACAKLGVI 177
                                       56655555************999****************************************************** PP

                                       EEEEETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCC CS
                       AMP-binding  74 vvplnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeee 142
                                       ++++ ++++++ l+   +d++++++i       +  +     ++++ea a  ++v++viv+++ +++  ++   +  
  gi|386001449|ref|YP_005919748.1| 178 HSVVFSGFSSKGLSDRAADCGSRAIIttdglyrR-GKPVPlKPNVDEALAGAPSVEHVIVYKRTGIEVPWKDGRDVW 253
                                       **************************99887642.34556689999999999***********99998877766665 PP

                                       CSCTTS....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTS CS
                       AMP-binding 143 seekae....kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilplah 213
                                       + +       +++e+e+l+p++ +yi+YTSGTTGkPKG+ + + +n+v  +++l+     f+lke+dv+++++++ +
  gi|386001449|ref|YP_005919748.1| 254 WHDL-VagksEECEPEKLDPEHRLYILYTSGTTGKPKGIEHAQgGNAVGPAQTLH---WvFDLKESDVWWCTADIGW 326
                                       5544.14667899999***************************9****9999974...3488999************ PP

                                       CHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEE CS
                       AMP-binding 214 ifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvl 289
                                       ++g+++ ++++l+ G+t v++++ ++ +d +++++ i++ kv+v++++P+++++++++ga+    +++dlsslrl+ 
  gi|386001449|ref|YP_005919748.1| 327 VTGHSYIVYGPLVLGMTGVMYEGAPDyPDFGRWWKIIQENKVSVLYTAPTAIRMFMKQGAEW--PDKYDLSSLRLLG 401
                                       **************************888****************************87665..5677********* PP

                                       EESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTS CS
                       AMP-binding 290 lggeplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdge 363
                                       ++gep++pe++ ++r++ g    ++++++++TEt++++   pl+    k+gs+ +plpg  + + Dee g++vp ge
  gi|386001449|ref|YP_005919748.1| 402 SVGEPINPEAWMWYREHIGAgklQIMDTWWQTETGTFLN-SPLPITPLKPGSCTFPLPGFNISVYDEE-GNEVPLGE 476
                                       *****************999******************8.6666666799*****************9.******** PP

                                       EEEEEEEET..TS-SEBTT-HHHHHHHEEE.....TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 364 eGellvrgp..gvmkgYlkkpeataeafds.....egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                        G ++ + p  ++ + +++++e+  + +++     ++r  +  GD +++d+dGy++i gR++d++ +
  gi|386001449|ref|YP_005919748.1| 477 GGNIVSQTPwpSMLRAFWGDKERFMKEYWQfywdtPKRgTYLAGDKATRDKDGYFWIQGRIDDVLSV 543
                                       *******99778*****************8899874444************************9865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.39   1.8e+03      42      53 ..      42      53 ..      24      64 .. 0.71
   2 ?   -0.2   0.1      0.47   2.1e+03       2      18 ..     221     237 ..     220     246 .. 0.83
   3 !   94.0   1.1   1.8e-30   8.3e-27       1      76 []     552     630 ..     552     630 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHHH CS
                     AMP-binding_C 42 leeeLkahvrke 53
                                      +e+eL++++ k+
  gi|386001449|ref|YP_005919748.1| 42 TEKELREWCSKN 53
                                      678999998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.47
                                       HHHHHHSSTTEEEEEEE CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVv 18 
                                       v +al+  p V+ + V+
  gi|386001449|ref|YP_005919748.1| 221 VDEALAGAPSVEHVIVY 237
                                       789*************9 PP

  == domain 3  score: 94.0 bits;  conditional E-value: 1.8e-30
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea.leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsalv+hp++aeaaVvG+pd+vkGe +vafV+l+ g  +++ l+++ + +vrk+lgp+a+p++v+fv++lpktrs
  gi|386001449|ref|YP_005919748.1| 552 EVESALVAHPKIAEAAVVGKPDAVKGESIVAFVILRVGndPTPeLAKDAINFVRKTLGPVAAPSEVHFVNDLPKTRS 628
                                       8**********************************866433226********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|386001449|ref|YP_005919748.1| 629 GK 630
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   2.8   1.3e-22   5.8e-19       2      55 .]      44      98 ..      43      98 .. 0.97
   2 ?   -0.8   1.0      0.33   1.5e+03      14      29 ..     492     513 ..     488     535 .. 0.65

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.3e-22
                                      HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      kel ++  +++ +FW+e+ake +dW+kp++kvld+s +p++kWF+GG++Ni+yN+
  gi|386001449|ref|YP_005919748.1| 44 KELREWCSKNYIEFWDEMAKEyIDWFKPYTKVLDDSGMPYFKWFTGGEVNITYNA 98
                                      68999***************99********************************7 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                                       HHHHHHHC......CS--SB-- CS
                            ACAS_N  14 aFWaeqak......eldWekpf 29 
                                       aFW++  +      +++W++p 
  gi|386001449|ref|YP_005919748.1| 492 AFWGDKERfmkeywQFYWDTPK 513
                                       7888877655444347777764 PP

>> DUF1391  Protein of unknown function (DUF1391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   8.3e-05      0.37      25      46 ..      31      52 ..      29      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-05
                           DUF1391 25 amtytksktfktetGarrWLek 46
                                       m y k k fkte   r W  k
  gi|386001449|ref|YP_005919748.1| 31 VMKYMKKKGFKTEKELREWCSK 52
                                      599****************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 4566.71
//
Query:       gi|386001450|ref|YP_005919749.1|  [L=430]
Description: MiaB-like tRNA modifying enzyme [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.4e-22   78.1   0.0    2.8e-21   76.6   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    1.6e-17   63.3   0.0      3e-17   62.5   0.0    1.4  1  UPF0004      Uncharacterized protein family UPF0004
    0.00021   21.2   0.0     0.0004   20.3   0.0    1.5  1  TRAM         TRAM domain
  ------ inclusion threshold ------
      0.059   13.3   0.1        3.6    7.6   0.0    2.7  2  TetR_C_36    Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   5.4e+03      28      67 ..      68     103 ..      63     110 .. 0.79
   2 !   76.6   0.0   6.3e-25   2.8e-21       1     166 [.     144     315 ..     144     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  28 slsveeileevkelkaekgvkevilgggepllypdfvell 67 
                                       +++ ++i + + el     ++ +i+ g  p++ p+ v++l
  gi|386001450|ref|YP_005919749.1|  68 ERTERDIRRRLSELQ----GERLIVAGCLPSAIPEAVRDL 103
                                       577788888888886....899999999999988888776 PP

  == domain 2  score: 76.6 bits;  conditional E-value: 6.3e-25
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfveller 69 
                                       v++++gC + Cs+C++++    +g+ rs++v+e++eev++   + g+ ev l +++  +y        p++++++++
  gi|386001450|ref|YP_005919749.1| 144 VNISEGCLGSCSYCIVRR---ARGPLRSRTVQEVAEEVRRR-LKEGAVEVQLASQDAAAYgldlgsslPELIDAVAE 216
                                       6899*************8...8*******************.7999*******************888888888888 PP

                                       HHHTCCCTEEEEEEECSSCHG..HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  70 laklavpgiritvetngtlpd..eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                       +       ir+ +  +g +    ee ++  ++      ++l++++++ e vl+ m+rg+t++++l    +lr+a ++
  gi|386001450|ref|YP_005919749.1| 217 IEGD--FRIRVGMMNPGQVKPilEELIRSYDDPKvYKFLHLPVQSGSAE-VLRSMRRGYTPQDFLSMAARLRAA-FP 289
                                       8887..6999999999999547777777777766***************.************************.** PP

                                       T...EEEEEEEBTTTSHHHHHHHHHH CS
                                       x...xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 r...vvdrivglpGendeeleellel 166
                                            +d+i g+pGe +e++ ++ el
  gi|386001450|ref|YP_005919749.1| 290 GltlYTDVIAGHPGEREEDFAATEEL 315
                                       ********************999776 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   6.7e-21     3e-17       1      88 [.      21     102 ..      21     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 6.7e-21
                                       XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEH CS
                           UPF0004   1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGC 77 
                                       +++iet+GC  N+ +se++as+L ++g+++ ++ eeAd+v+vnTCav+e++e++++++l+el+ ++     ++v+GC
  gi|386001450|ref|YP_005919749.1|  21 RFYIETYGCAANRGNSEAFASALVEAGHRRSSQ-EEADLVIVNTCAVTERTERDIRRRLSELQGER-----LIVAGC 91 
                                       799*************************99766.89*************************99877.....9***** PP

                                       HHHS-HHHHHH CS
                           UPF0004  78 maqrekeellk 88 
                                       ++++ +e + +
  gi|386001450|ref|YP_005919749.1|  92 LPSAIPEAVRD 102
                                       *9988887665 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     9e-08    0.0004       2      62 .]     369     427 ..     368     427 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9e-08
                                       XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       +y G+++   v++ + + g+ ++r  n++ ++v+ +lp +G +   kI +++++yL+Ge++
  gi|386001450|ref|YP_005919749.1| 369 RYLGEEIIAQVTEMG-RGGTVMARSANYRKIVVNEPLP-LGSVHRFKIVRTTPFYLKGEAI 427
                                       799************.********************99.********************85 PP

>> TetR_C_36  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00081       3.6      37      77 ..     158     198 ..     154     206 .. 0.90
   2 ?    2.7   0.0     0.026   1.2e+02      86     109 ..     292     315 ..     276     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00081
                         TetR_C_36  37 llttkagevqrrvvaavaelleeevaageleppldlddlAy 77 
                                       ++  ++g++++r+v+ vae +++  ++g++e +l+ +d A 
  gi|386001450|ref|YP_005919749.1| 158 IVRRARGPLRSRTVQEVAEEVRRRLKEGAVEVQLASQDAAA 198
                                       666789*************************9999999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.026
                         TetR_C_36  86 flYadliageepdidkaetavraL 109
                                       +lY+d+iag++ + ++  +a++ L
  gi|386001450|ref|YP_005919749.1| 292 TLYTDVIAGHPGEREEDFAATEEL 315
                                       58*********9888766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 3248.69
//
Query:       gi|386001451|ref|YP_005919750.1|  [L=391]
Description: hypothetical protein Mhar_0754 [Methanosaeta harundinacea 6Ac]
Scores for 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-40  136.8  35.5    1.2e-39  136.4  35.5    1.1  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4  35.5   6.5e-44   1.2e-39       3     323 ..      16     344 ..      14     347 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 6.5e-44
                   AI-2E_transport   3 lilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvplliaq 78 
                                       li+vl+llll+ y++++ l+  +++++v+ay+  p+++++ +++++   +a+++++l ++++l l ++ +v    +q
  gi|386001451|ref|YP_005919750.1|  16 LIPVLFLLLLITYFLFP-LMDGIILGVVFAYVGRPIKERFgRRERLGSAVATTAIVLPIALILGLGGVEVV----SQ 87 
                                       799**************.****************************************************9....99 PP

                   AI-2E_transport  79 ltqlvkslpayidslqnilnelpslleele.n.........liqalkqslskilsnilssilns.llsllasllgli 144
                                       l+ +v++   ++++  ++l el+  l                 ++l  sl ++++ +   + ++ + s+ +s++ + 
  gi|386001451|ref|YP_005919750.1|  88 LNWVVENQAEIVKRAGSFLAELETPLAGYDiLpaiyeippaIYDDLTGSLKTMIELLARILSSFpVFSYGMSIILIG 164
                                       9999999998888888888888876666643367777789866666666665555444333332245788899999* PP

                   AI-2E_transport 145 lslvlvllllffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpya 221
                                       l+l+ ++++++fll dg kl +gi  +lp +  + +k++  +++++lsg+++g + +++++g+l+  +++++g+p +
  gi|386001451|ref|YP_005919750.1| 165 LNLIASIYVCYFLLMDGGKLATGISTILPTEHLAIYKKYEARIDSILSGIFIGAIYTSILSGILSVLVFYAFGIPNP 241
                                       ***************************************************************************** PP

                   AI-2E_transport 222 lllailvglanliPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsl 297
                                       + la lv+++ +iP++ +++v+ipi++++++  + +  +l+++++ +++ +  + i++P++++ +  +hpl+++l++
  gi|386001451|ref|YP_005919750.1| 242 FALAALVFISGVIPILSSWLVIIPISAWMYIELSpFDGILFFVVSSAMIYIPSDLIIRPYIVSVKSTIHPLLVVLAF 318
                                       *******************************98889999************************************** PP

                   AI-2E_transport 298 laggklfGlvGlilavpltavikail 323
                                       ++g+ ++Gl G++la+ l++v+  ++
  gi|386001451|ref|YP_005919750.1| 319 VGGVLVAGLGGFFLAPALMGVVVGVY 344
                                       ********************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2939.26
//
Query:       gi|386001452|ref|YP_005919751.1|  [L=358]
Description: hypothetical protein Mhar_0755 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   21.3   1.6    0.00022   20.6   1.6    1.3  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.6   1.2e-08   0.00022     150     260 ..     153     262 ..     132     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-08
                                       TTECEEEEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH.....-TT..HHHHHHH CS
                           DBI_PRT 150 agadllalGemGigNttaaaallaallglepeevvGrGtglddeglarKiavieqalarh.....aek.dplevLak 220
                                       +  d++ +Ge   g tt+a a+++al    p +v    + l d+ la+K +++++al+r      + + dpl++L++
  gi|386001452|ref|YP_005919751.1| 153 SLSDCIFIGESIAGGTTTAMAVMQALGY--PGRV---SSSLLDHPLAKKQEIVDAALDRCgasfgSMRsDPLRALKE 224
                                       457899*****************99853..3333...46899******************886653345******** PP

                                       HS-HHHHHHHHHHHHHHHTT--EEE-SHHHHHHHHHHHHH CS
                           DBI_PRT 221 vGGleiaalaGailgAaarripvvlDGfistaAalvAvrl 260
                                       vG   i a+ G++ g    +  vvl G   +aA+l+A++ 
  gi|386001452|ref|YP_005919751.1| 225 VGDPMIPAVLGLLRGM--GGSKVVLAGGTQMAAVLCAADA 262
                                       ***********98875..4566899999999****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2375.99
//
Query:       gi|386001453|ref|YP_005919752.1|  [L=441]
Description: Molybdenum cofactor synthesis domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-36  124.6   0.6    5.1e-36  123.8   0.6    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)
    4.3e-22   78.3   0.0    8.9e-22   77.3   0.0    1.5  1  MoCF_biosynth  Probable molybdopterin binding domain
    1.6e-13   50.6   0.3      1e-12   48.0   0.1    2.5  2  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.6   8.5e-40   5.1e-36       3     157 .]      57     210 ..      55     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 8.5e-40
                                       HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S- CS
                            MoeA_N   3 veealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageeper 77 
                                        +e l+ +l+++ +++++e v+l a+a grvl  d+ +p+++P+f+++amDGYAvra++++ga++  p    e  + 
  gi|386001453|ref|YP_005919752.1|  57 ASESLKDLLERCrPVTRSEpVHL-ASARGRVLSGDLASPVNLPAFNRAAMDGYAVRAADTRGATPLAP-VYLE-VGD 130
                                       56888889999977788888***.88*************************************77666.3334.444 PP

                                       --TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTES--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHH CS
                            MoeA_N  78 llpgg.avrimTGaplPegadaVvpvEdte.eeeaketvevkavkpgenvrraGedikaGevllragtrltpaeigl 152
                                       +  +g +v + TG + P+gadaV+++Ed+  +   +e + +++v+p +n  r+Ged++  e++l++g+rl+p +i+l
  gi|386001453|ref|YP_005919752.1| 131 EAGEGrCVPVRTGMAAPPGADAVLMIEDALlR--GREVEATAEVHPYRNLARVGEDVALWETVLKEGHRLRPPDIAL 205
                                       445555**********************8653..233334599********************************** PP

                                       HHHCT CS
                            MoeA_N 153 lasvG 157
                                       las+G
  gi|386001453|ref|YP_005919752.1| 206 LASLG 210
                                       ***98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   1.5e-25   8.9e-22       2     142 ..     224     359 ..     223     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 1.5e-25
                                       EEEE-HHHH.........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSS CS
                     MoCF_biosynth   2 vitvGdell.........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGpt 69 
                                       +i +G el+         +g+++ +ng +   + +  g + +k+++v Dd+  i+ea++++l++ d+i+++GGt+++
  gi|386001453|ref|YP_005919752.1| 224 IIPTGGELVplfsdqkllPGQAREANGLICEMYAEIWGGSPQKTSIVEDDPRLIREAIARSLDA-DLILISGGTSIG 299
                                       677777777777777777*********888888888**********************999777.************ PP

                                       TT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth  70 pdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpal 142
                                       + D+ p ++++++e        ++++v+  p kp+ ++ +   ++   k++i+LPG+p+a+ +al ++ +p +
  gi|386001453|ref|YP_005919752.1| 300 EEDYAPPIIEEMGE-------LLVHGVRITPAKPTALGVI---DG---KPVICLPGYPVAALAALYIFARPLI 359
                                       **************.......8***********9888888...54...58******************99876 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.57   3.4e+03      17      34 ..     121     140 ..      99     145 .. 0.61
   2 !   48.0   0.1   1.7e-16     1e-12       2      71 ..     374     439 ..     373     440 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.57
                                       EEEEEEE..S-S-EEEEEE- CS
                            MoeA_C  17 flRvilt..eedgeyvaept 34 
                                       + +v l+  +e+ge  + p+
  gi|386001453|ref|YP_005919752.1| 121 LAPVYLEvgDEAGEGRCVPV 140
                                       44555555555566555555 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.7e-16
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                       a+la ++ s pg  +f Rv+l+    e va+p+ ++g g+Lss a+A+g++ +pe+ eg e+Ge Vev l
  gi|386001453|ref|YP_005919752.1| 374 AKLAGKIVSRPGYLTFARVSLK----EGVATPIMTTGAGILSSVARAEGYVLVPEELEGREKGEMVEVNL 439
                                       8999******************....78****************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2707.74
//
Query:       gi|386001454|ref|YP_005919753.1|  [L=756]
Description: phosphoenolpyruvate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-114  381.8   0.3   4.2e-114  381.2   0.3    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
      2e-85  286.5   0.1    2.8e-85  286.0   0.1    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    3.2e-25   87.6   2.3    8.1e-25   86.4   2.3    1.8  1  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.2   0.3  7.1e-118  4.2e-114       2     315 ..      16     321 ..      15     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 381.2 bits;  conditional E-value: 7.1e-118
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       ++vGGKga+L+e++n  g pvP gfa+ta+a+ref++++g++e+i e+lk +dv+d ++l+ a++++++l+l+a++P
  gi|386001454|ref|YP_005919753.1|  16 AVVGGKGASLGEMIN-VGAPVPGGFAVTAQAYREFITRSGIAEDIFEALK-VDVHDPEALSGAAERAKRLVLEAKVP 90 
                                       57***********77.**********************************.7************************* PP

                            PPDK_N  79 eeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYr 155
                                       +e+e+ai++ y e++k+ g+e ++vaVRSSataEDlp+asfaGqq+t+Ln+ ge++v+ea+++++aSl+ +rAi+Yr
  gi|386001454|ref|YP_005919753.1|  91 KEIEKAIRDRYLEMSKREGKE-VLVAVRSSATAEDLPDASFAGQQETFLNILGEDQVFEAVRKCWASLYGARAIFYR 166
                                       ****************99998.******************************************************* PP

                            PPDK_N 156 kekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilek 232
                                        e+g++he+v+++v+vqkm+ns+  +sGV+fs +p+tG +  v+i+a++GlGeaVV+G v+pd++vv++ ++ki+++
  gi|386001454|ref|YP_005919753.1| 167 VEQGFEHEKVNISVTVQKMINSE--KSGVMFSSHPSTG-EPHVIIEAAWGLGEAVVSGSVSPDNYVVDRADKKIVSR 240
                                       ***********************..*************.************************************** PP

                            PPDK_N 233 kigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpe 309
                                        +++kei+iv+d+k+ +t++ +vp ++rek +Lsdee+ +La  ++++e+hyg p+diE+a++   gk+y+lQ+Rp+
  gi|386001454|ref|YP_005919753.1| 241 FVAKKEIMIVRDKKTGKTVTKKVPADKREKVVLSDEEILQLAAQGEALEEHYGIPQDIEWAFE--GGKMYILQSRPI 315
                                       ***************99********************************************99..************ PP

                            PPDK_N 310 trtsek 315
                                       t+ s+ 
  gi|386001454|ref|YP_005919753.1| 316 TTISKG 321
                                       *99875 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.0   0.1   4.7e-89   2.8e-85      13     293 ..     457     745 ..     445     746 .. 0.93

  Alignments for each domain:
  == domain 1  score: 286.0 bits;  conditional E-value: 4.7e-89
                                       CHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC.HHHHHH..........HHHHHHHHHHHTTTS CS
                   PEP-utilizers_C  13 vtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmaree.lpteee..........qaeaykkvleamngr 78 
                                       v k+++++++ +N++++e+ae+a+++ a+G+GLlR+E++++   + + + ++          ++   ++v+ea++++
  gi|386001454|ref|YP_005919753.1| 457 VYKPITATEIKVNVSMAEAAEQAAATLADGVGLLRIEHMILGLGKtPRYYINagkedeyldeLVGGVRTVAEAFYPK 533
                                       66789999**********************************98835555557889999999*************** PP

                                       EEEEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC..EEEEEESSXXSHHHH CS
                   PEP-utilizers_C  79 pvvvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasaag..kleimlPmvasveel 151
                                       pv+vRtlD+++d  + ++ +++ep+e NPmlG+Rgir+ l+e + f+ ++rA+++  ++g  ++ imlP+v++v+e+
  gi|386001454|ref|YP_005919753.1| 534 PVWVRTLDAPTDefRGMEGGENEPHEHNPMLGWRGIRRDLTETDHFRLEMRAFKKLHEMGlsNVGIMLPLVQHVSEF 610
                                       ************8888******************************************6666*************** PP

                                       HHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHHHHSX CS
                   PEP-utilizers_C 152 eeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneevaklyd 227
                                       ++ak+++ e+  +le        k+ vGiM+E+p aal++d++++  +dF+S+GtNDLtQytlavdR+n++va+ly 
  gi|386001454|ref|YP_005919753.1| 611 QRAKALMVEEGLDLE--------KIDVGIMVETPGAALTIDDFIEDgIDFVSFGTNDLTQYTLAVDRNNQNVAYLYT 679
                                       *******99955554........78********************99****************************** PP

                                       TTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                   PEP-utilizers_C 228 plepavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                                       +l+pavl li++v++ ++++g++++iCG+++++p++++ lv++G+ ++S++ ++v+++r+++a++e
  gi|386001454|ref|YP_005919753.1| 680 ELHPAVLTLIEYVVERCNRAGVTTSICGQAGSYPEMAKRLVEIGITSISANIDAVATVRETVARAE 745
                                       *************************************************************99875 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   2.3   1.3e-28   8.1e-25       1      73 []     362     434 ..     362     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 1.3e-28
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       k++eg+ILv+ +t p++++++++a +ivt++GGmt+HaAiv+relg PaVvg++e t+ l eg +itvDg +G
  gi|386001454|ref|YP_005919753.1| 362 KIKEGDILVTVMTEPDMVPAMKRAGAIVTDEGGMTCHAAIVSRELGFPAVVGTKEGTKILTEGMIITVDGGKG 434
                                       5899*****************************************************999999*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (756 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 5361.58
//
Query:       gi|386001455|ref|YP_005919754.1|  [L=377]
Description: L-tyrosine decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for 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-32  110.3   0.0    6.8e-31  107.3   0.0    1.9  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    4.1e-06   26.0   0.0    7.4e-06   25.2   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
     0.0039   16.5   0.0      0.006   15.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.12   11.6   0.0       0.18   11.1   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.0   1.5e-34   6.8e-31      75     357 ..      59     307 ..      26     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 1.5e-34
                                       HHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEE CS
                     Pyridoxal_deC  75 PaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlyts 151
                                       P ++ele   + ++aellg p      e+ g l++g++es++ a+ Aar+ +      +             +++  
  gi|386001455|ref|YP_005919754.1|  59 PGSAELEAEAVRMMAELLGHP------EACGYLSTGGTESNIQAIRAARNSADF----R-----------DGNIVVP 114
                                       8999*****************......488******************976422....2...........2467778 PP

                                       TTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT CS
                     Pyridoxal_deC 152 dqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekyd 228
                                         ah s +k++ +l +++r   ld + k+ + + e++i e+          v ++Gtt  g+ d ++ lg +   ++
  gi|386001455|ref|YP_005919754.1| 115 RSAHFSFDKIGDLLSLEIRKADLDGDLKVEVGSVEELIDEKTVS------LVGIAGTTEFGQVDPIDRLGRLALDWG 185
                                       889**********************************9876655......5679*********************** PP

                                       -EEEEE-TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTT CS
                     Pyridoxal_deC 229 lwlHvDAAyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsd 302
                                       ++lHvDAA++G  f+ p+  +   +++ +e + Sit+ phK++++++  + l+++  e+l++     a YL      
  gi|386001455|ref|YP_005919754.1| 186 IPLHVDAAFGG--FVLPFLGGdwrWDFSVEGVTSITIDPHKMGMATIPGGGLLFRHPEDLERLA-AYAPYLT----- 254
                                       ***********..******99999************************************9977.6788**9..... PP

                                       TSEECCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                     Pyridoxal_deC 303 vaadlgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklirkde 357
                                            + ka+   r    ++ +w v+  lG+eg++++++ ++ l++ +++  ++ +
  gi|386001455|ref|YP_005919754.1| 255 ---VARPKALTGTRsGAAAAAIWAVMSHLGMEGFKEVVNGCMALSRRMASGAKEIG 307
                                       ...35789999999788999****************************99876654 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.6e-09   7.4e-06      68     177 ..      87     193 ..      63     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.6e-09
                                       SSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEE CS
                       Aminotran_5  68 sGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklv 143
                                        G+te++  +++++++s   ++ +ivv ++ h +      ++ +   ++++++ ld + ++++  +e+l++ekt  +
  gi|386001455|ref|YP_005919754.1|  87 TGGTESNIQAIRAARNSaDFRDGNIVVPRSAHFSFD----KIGDLLSLEIRKADLDGDLKVEVGSVEELIDEKTVSL 159
                                       588887777777777776445668999998888866....9999999****************************** PP

                                       EEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 144 aithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                          +  ++ G ++p++++g+la + g+ ++vDaa
  gi|386001455|ref|YP_005919754.1| 160 VGIAGTTEFGQVDPIDRLGRLALDWGIPLHVDAA 193
                                       *********************************8 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-06     0.006      36     169 ..      67     193 ..      42     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHTT-SEEE..EES-HHHHHHHHH....HHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBT CS
                   Beta_elim_lyase  36 rLedavaelfgkeaal..fvpqGtaAnsill....kill.qrgeevivtepahihfdetgaiaelagvklrdlknke 105
                                       +    +ael+g+  a     + Gt +n  ++    +  +  r  +++v + ah+ fd  g +  l+     dl+++ 
  gi|386001455|ref|YP_005919754.1|  67 EAVRMMAELLGHPEACgyLSTGGTESNIQAIraarN-SAdFRDGNIVVPRSAHFSFDKIGDLLSLEIR-KADLDGDL 141
                                       556678888888766642455688888888844431.22247889999***********999766544.56677777 PP

                                       TTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 106 aGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                         k+++ ++e++i+e     + ++l+ ++ T++   Gqv +++   ++  +a + giplh+D+A
  gi|386001455|ref|YP_005919754.1| 142 --KVEVGSVEELIDE-----KTVSLVGIAGTTEF--GQVDPID---RLGRLALDWGIPLHVDAA 193
                                       ..*************.....589**********9..9997765...567899***********9 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     4e-05      0.18      47     146 ..      89     193 ..      59     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                       HHHHHHHHHHHTTTT...TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE...EEEEE CS
                   DegT_DnrJ_EryC1  47 GtaAlhlaLralgvg...pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert...kaIlp 117
                                       Gt+++  a+ra   +   ++  ++vp    ++  +    l ++   +D d  ++ +++ ++e++i e+t    +I  
  gi|386001455|ref|YP_005919754.1|  89 GTESNIQAIRAARNSadfRDGNIVVPRSAHFSFDKIGDLLSLEIRKADLD-GDLKVEVGSVEELIDEKTvslVGIAG 164
                                       56666666666332223445556666666666666666666666777777.6789999***********98889999 PP

                                       B-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 118 VhlyGqvadmdalkaiaakhglkvieDaA 146
                                          +Gqv  +d+l ++a ++g+++  DaA
  gi|386001455|ref|YP_005919754.1| 165 TTEFGQVDPIDRLGRLALDWGIPLHVDAA 193
                                       999*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2976.58
//
Query:       gi|386001456|ref|YP_005919755.1|  [L=76]
Description: TRAM domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-13   50.3   1.5      2e-13   50.1   1.5    1.1  1  TRAM      TRAM domain
  ------ inclusion threshold ------
        0.1   12.3   0.2       0.26   11.1   0.2    1.6  1  Hexapep   Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   1.5   2.2e-17     2e-13       2      61 ..      20      75 ..      19      76 .] 0.96

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.2e-17
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                      ++vG++++V++e+ + ++g+gi+r++ g+v+fvp ++   Gd V++ +++v r+++ G+ 
  gi|386001456|ref|YP_005919755.1| 20 VEVGKEYDVEIEDIA-KQGDGIARVE-GFVIFVPETKV--GDHVTIAVDRVMRKFAIGHK 75
                                      78************9.**********.*********99..****************9986 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   2.9e-05      0.26      10      29 ..      43      62 ..      40      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.9e-05
                                      E-TTEEEETTEEE-TTEEEE CS
                           Hexapep 10 IgpfaviggnVkIGdnvkIg 29
                                      +  f+++ + +k+Gd+v+I+
  gi|386001456|ref|YP_005919755.1| 43 VEGFVIFVPETKVGDHVTIA 62
                                      6779**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 617.37
//
Query:       gi|386001457|ref|YP_005919756.1|  [L=76]
Description: TRAM domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.0   0.7    2.2e-12   46.8   0.7    1.1  1  TRAM      TRAM domain
  ------ inclusion threshold ------
      0.056   13.2   0.3      0.094   12.5   0.3    1.3  1  Hexapep   Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.7   2.4e-16   2.2e-12       3      60 ..      21      74 ..      19      76 .] 0.94

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.4e-16
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGe 60
                                      + G+++eV++e+++ ++g+gi+r++ g+v+fvp+++   Gd V+V I++v  +++ ++
  gi|386001457|ref|YP_005919756.1| 21 EAGKEYEVEIEDVA-KKGDGIARIE-GFVIFVPDTKV--GDHVTVVIDRVMQRFAIAH 74
                                      67***********9.**********.*********99..***********99999876 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3     1e-05     0.094       9      28 ..      42      61 ..      40      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                                      EE-TTEEEETTEEE-TTEEE CS
                           Hexapep  9 lIgpfaviggnVkIGdnvkI 28
                                       I  f+++ +++k+Gd+v++
  gi|386001457|ref|YP_005919756.1| 42 RIEGFVIFVPDTKVGDHVTV 61
                                      7999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 609.06
//
Query:       gi|386001458|ref|YP_005919757.1|  [L=358]
Description: NOL1/NOP2/sun family putative RNA methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-50  169.3   0.0    1.1e-49  168.9   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.5e-06   28.6   0.0    3.1e-06   27.6   0.0    1.5  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    9.3e-06   25.9   0.0    1.5e-05   25.2   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
     0.0014   19.3   0.3     0.0037   17.9   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
     0.0036   17.1   0.0     0.0053   16.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.024   14.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      0.038   14.3   0.0       0.17   12.1   0.0    1.8  2  DUF2431          Domain of unknown function (DUF2431)


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   0.0   4.2e-53   1.1e-49       2     199 ..     152     355 ..     151     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 4.2e-53
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       ++L p+++e++lDlcaaPG+KTt ia +m+n+g +vA+d  ++R+ ++ +n +r g  n+ v+++D+r++++     
  gi|386001458|ref|YP_005919757.1| 152 VVLSPEPGERVLDLCAAPGSKTTQIAMMMENRGLLVANDPANTRVASLRSNCERAGAVNVAVTRYDGRRFPDR---- 224
                                       689*******************************************************************653.... PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                        fDr+L+DaPC+g+g+ r+d  v  r + k    +++lq++ll  a++++++gG++vYsTC+ ++eEne v+  aL 
  gi|386001458|ref|YP_005919757.1| 225 GFDRVLVDAPCTGQGMARKDITVLGRWSLKRSLGIQRLQRALLRRALQVTRSGGTVVYSTCTFAPEENEGVVSWALG 301
                                       4**********************9999999999******************************************** PP

                                       H-TTEEEESSBSTTSTTSSECEEC...........TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 156 kredvelvetelsepkglklgeea...........gtlrllPhtenkdgffiakl 199
                                       +   v+l+e ++ +  g+     +              r++Ph+++  gff+akl
  gi|386001458|ref|YP_005919757.1| 302 QVSGVRLQEASVRGLAGSPGLA-EwagsrfgdemeLCTRYYPHQNDAGGFFVAKL 355
                                       *********9888755543222.236778888888899****************9 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.2e-09   3.1e-06       8      90 .]      66     148 ..      63     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                                       HHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTTS- CS
                   Methyltr_RsmF_N   8 kmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaGly 82 
                                       +++e+++ +++ f++a+++p ++  R+NtlK+++++l++  +  +++++p  w + G  le e +pg+  +  +G +
  gi|386001458|ref|YP_005919757.1|  66 RYREVIP-DFDLFVEAIRRPLPVTARINTLKADRDRLTSRLRrgKVAFTPFSWYPFGLRLEVE-KPGNLLESLMGQI 140
                                       5566554.7999************************998777799*****************9.9************ PP

                                       EE--TTTH CS
                   Methyltr_RsmF_N  83 YiQEpSam 90 
                                       +iQE  +m
  gi|386001458|ref|YP_005919757.1| 141 HIQEEISM 148
                                       ****8887 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.7e-09   1.5e-05      20     140 ..     157     289 ..     135     303 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.7e-09
                                       -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH.TTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE-- CS
                              FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl.pgvttiqgditdpetiekikealserkvdlvvsDg 95 
                                       +pg++v+Dl+aaPG+ +  ++  ++++g +va D  + +    + ++ ++   + ++ +   + + +r++d v+ D 
  gi|386001458|ref|YP_005919757.1| 157 EPGERVLDLCAAPGSKTTQIAMMMENRGLLVANDPANTRVAsLRSNCERAGAVNVAVTRYDGRRFPDRGFDRVLVDA 233
                                       37799******************9999*******98863222333333444444444444445677799*******8 PP

                                       S-..........SS-CHHHHHHHHH..........C.CCCHHHHCCHCCCCECCCEEEECCCHCCC CS
                              FtsJ  96 ap..........dvsgvhdldeylq..........s.qLllaalelalkllkpggtfvlkifrgee 140
                                                    v                     + +L +a l+ al++ + ggt+v  +++++ 
  gi|386001458|ref|YP_005919757.1| 234 PCtgqgmarkdiTV----------LgrwslkrslgIqRLQRALLRRALQVTRSGGTVVYSTCTFAP 289
                                       65444445554444..........34555555555549999*****************98888433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0037       1      70 [.     162     231 ..     162     246 .. 0.90
   2 ?   -2.0   0.1       2.4   6.1e+03      82      97 .]     263     278 ..     257     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLdl++ +G  t ++a  + +++ +++ D++ + ++  r+++e++g+ nv + + d +++p  d+ fD v++
  gi|386001458|ref|YP_005919757.1| 162 VLDLCAAPGSKTTQIAMMMeNRGLLVANDPANTRVASLRSNCERAGAvNVAVTRYDGRRFP--DRGFDRVLV 231
                                       9***************9996699********************999889999999998876..778999986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHEEEEE CS
                   Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                       ++++l+++ +v++ gG
  gi|386001458|ref|YP_005919757.1| 263 QRALLRRALQVTRSGG 278
                                       4789999*****9999 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-06    0.0053      72     135 ..     157     220 ..     138     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk 135
                                       ++g+rvL++ +  G +t  +a++++++g++v+ +  +  v++ + n ++ ++ nv+v+  DGr 
  gi|386001458|ref|YP_005919757.1| 157 EPGERVLDLCAAPGSKTTQIAMMMENRGLLVANDPANTRVASLRSNCERAGAVNVAVTRYDGRR 220
                                       799***********************************************************96 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.4e-06     0.024       3     113 ..     158     286 ..     156     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.4e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                        g rvlDl ++ G +t ++a  +  ++ +v  D   + + + r+n+++ g  nv + + d   ++    d+ fD +l
  gi|386001458|ref|YP_005919757.1| 158 PGERVLDLCAAPGSKTTQIAMMMENRGLLVANDPANTRVASLRSNCERAGAVNVAVTRYDGRRFP----DRGFDRVL 230
                                       6789****************66666888***********************************99....89****** PP

                   Methyltransf_31  80 snevl..naladpdkile....................eiervlkpggilliedpr 113
                                        ++++  + +a +d +                      ++ +v ++gg ++ +++ 
  gi|386001458|ref|YP_005919757.1| 231 VDAPCtgQGMARKDITVLgrwslkrslgiqrlqrallrRALQVTRSGGTVVYSTCT 286
                                       **666663333333333334444444444444444444999*******99999998 PP

>> DUF2431  Domain of unknown function (DUF2431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.42   1.1e+03     116     150 ..     153     187 ..     142     190 .. 0.85
   2 ?   12.1   0.0   6.7e-05      0.17      45     142 ..     196     298 ..     176     323 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.42
                           DUF2431 116 llsekpgeilvtlfegepytlwnikdlareaglkv 150
                                       +ls++pge ++ l+   + ++ +i  + ++ gl v
  gi|386001458|ref|YP_005919757.1| 153 VLSPEPGERVLDLCAAPGSKTTQIAMMMENRGLLV 187
                                       599999******************99999888866 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.7e-05
                           DUF2431  45 ieeLeee.gvkvlfgVDatkleksklqeklkkekfdriifnFPhvggkstdvnr.........qvranqeLlvsffk 111
                                       +++L+++ +   +++V +t+++      ++ +++fdr+++  P++g++++ ++          +    q+L +++++
  gi|386001458|ref|YP_005919757.1| 196 VASLRSNcERAGAVNVAVTRYD----GRRFPDRGFDRVLVDAPCTGQGMARKDItvlgrwslkRSLGIQRLQRALLR 268
                                       5555555333345567777777....35677888***************98877888888766666678******** PP

                           DUF2431 112 sakellsekpgeilvtlfegepytlwnikdl 142
                                       +a ++ + + g+++ + ++  p ++  +++ 
  gi|386001458|ref|YP_005919757.1| 269 RALQVTRSG-GTVVYSTCTFAPEENEGVVSW 298
                                       *********.****99999988666555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2899.83
//
Query:       gi|386001459|ref|YP_005919758.1|  [L=146]
Description: hypothetical protein Mhar_0762 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-11   44.4   0.0    1.9e-11   43.7   0.0    1.3  1  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe


Domain annotation for each model (and alignments):
>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.1e-15   1.9e-11       1      50 []      82     131 ..      82     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.1e-15
                   Methyltranf_PUA   1 alrYlkGetielepdlkkGwvlVcydgyplGwgKlvggrlKNkyPkglRr 50 
                                       alr+++Ge   ++ + ++G+v+V++++ +lG+g++++g+l++++Pk++R+
  gi|386001459|ref|YP_005919758.1|  82 ALRFAAGERQRIPAPVEEGYVVVSHGEDVLGCGQYLDGELISLLPKERRI 131
                                       89**********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1215.67
//
Query:       gi|386001460|ref|YP_005919759.1|  [L=323]
Description: FO synthase subunit 2 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-11   44.3   0.1    4.4e-11   43.5   0.0    1.5  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.4e-15   4.4e-11       1     164 [.      27     194 ..      27     197 .. 0.83
   2 ?   -4.0   0.0      0.93   1.7e+04     128     151 ..     226     248 ..     215     252 .. 0.60

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.4e-15
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.. 74 
                                       +++t+ C + CsfCa++     + +g+ l+ e ile v+++ ++   ++ +++gg  p l  + +  +++++k++  
  gi|386001460|ref|YP_005919759.1|  27 INFTNRCVGSCSFCAFR-----RADGYLLTEEAILERVEAA-ERSSaTEICLQGGLAPGLVLEDYCRILEAIKEDyp 97 
                                       689**************.....68*****************.89996777777777777766666666666666656 PP

                                       ........CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTT CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ........vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreag 141
                                                 ++    e++gt+p  e +++l ++g        +e++ d+ v+  ++  + +  ++ e + +++++g
  gi|386001460|ref|YP_005919759.1|  98 lmhlhaysPMEVLYMSESSGTTP-AESIRELQRAGlGSMPGTAAEILVDR-VRGEICpSKLSTAQWREIVTTAHRLG 172
                                       66666666555556666666666.***********999999999999999.999999899***************** PP

                                       SETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikrvvdrivglpGendeeleell 164
                                       ++ ++++i+ ++ e  e++ ++l
  gi|386001460|ref|YP_005919759.1| 173 VP-TTSTILYGHVERLEDRIAHL 194
                                       **.99999999999999877766 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 128 eevlealeklreagikrvvdrivg 151
                                        +++e le+l+ + +   v  +++
  gi|386001460|ref|YP_005919759.1| 226 ARRMEILENLKMHALA-RVALHPL 248
                                       5666666666665555.4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2435.78
//
Query:       gi|386001461|ref|YP_005919760.1|  [L=274]
Description: Phosphate ABC transporter substrate-binding protein, PhoT family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-32  113.0   0.9    1.3e-31  110.3   0.9    1.8  1  PBP_like_2  PBP superfamily domain
    3.8e-14   52.3   0.0    4.8e-14   51.9   0.0    1.3  1  PBP_like    PBP superfamily domain
      0.003   17.4   0.0     0.0085   15.9   0.0    1.9  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.9   2.2e-35   1.3e-31       5     282 .]      21     260 ..      18     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2.2e-35
                        PBP_like_2   5 eatsvgeifgaGsttpapalrkladafekaapgakvny.astGSgagikalrngdvdfagsdrplteseia.agwaa 79 
                                       +at+   ++++Gstt+ p+++  a+ f+  +  + v++   +GSg gik +++g  d+++s+r+++e+e++      
  gi|386001461|ref|YP_005919760.1|  21 GATET--VTVTGSTTVMPLVEVSAERFNLIQDRVMVTVsGVGGSGVGIKNVASGFSDIGMSSRMVREDEVElY---- 91 
                                       45555..************************9999***55568*************************99543.... PP

                        PBP_like_2  80 ngaggliqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfst 152
                                         + ++    ++++ai+++v+++    +++ +sr++L++I+ g++t+W d lg+p d++I vv+r  gsgt +lf +
  gi|386001461|ref|YP_005919760.1|  92 --GDNFSVYLIGYDAICIAVSEPiyeAGVTsISRQQLRAIYDGNLTSWRD-LGGP-DADIYVVARMVGSGTGDLFNE 164
                                       ..4889*****************99988889*******************.8888.********************* PP

                        PBP_like_2 153 alaeqgpwtasgigasg....segvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkva 224
                                       +++     +++++ga      ++++++a+ + + aigy+  +y ++ +  ++a                    ++  
  gi|386001461|ref|YP_005919760.1| 165 MVMGD--LQTETLGADTyaqnNGEMKTAItKSDKAIGYLGFNYVQDGPLRPIA--------------------YEG- 218
                                       ***55..6666777655666699999999777******999998844333333....................222. PP

                        PBP_like_2 225 kiasnplawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsde 282
                                                 + p+ e+i +++yPlsr++y+++ +++       a+ +aF+d+ll +e
  gi|386001461|ref|YP_005919760.1| 219 ----------VAPSAESIRADDYPLSRPLYVMTWNEP------DAGEEAFIDFLLGEE 260
                                       ..........8889999999***************99......9**********9875 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   8.1e-18   4.8e-14       3     154 ..      44     206 ..      42     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 8.1e-18
                                       HHHHH-TTCEEEEEES.-HHHHHHHHHTTS-SEEEESS---CCCH....HCCCCCEEEEEEEEEEE........E-C CS
                          PBP_like   3 elaeknpgvrvavanv.GsggGlkalrageadiagshlldketee....ynapalrkaldgievvl........vnl 66 
                                       +++  +  v v+v++v Gsg G+k+++ g  di++s+++ +e+e      n++ +   +d+i +++        v+ 
  gi|386001461|ref|YP_005919760.1|  44 RFNLIQDRVMVTVSGVgGSGVGIKNVASGFSDIGMSSRMVREDEVelygDNFSVYLIGYDAICIAVsepiyeagVTS 120
                                       555556678888776527999******************99888777666777666666776444455555566666 PP

                                       C-HCHCCCCHCCHHHS--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHC CS
                          PBP_like  67 arreqglvvakgnpkkitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVa 141
                                        +r+q   ++ g   ++t+w+dl  +da++ +v R  GSGt dlf+e++ +  ++ + +   +++a++++++++a+ 
  gi|386001461|ref|YP_005919760.1| 121 ISRQQLRAIYDG---NLTSWRDLggPDADIYVVARMVGSGTGDLFNEMVMG-DLQTETLGA-DTYAQNNGEMKTAIT 192
                                       777777777777...79********************************88.466666665.89************* PP

                                       CETTCCEC.CCGG- CS
                          PBP_like 142 agradvgv.gieav 154
                                       + + ++g+ g+  v
  gi|386001461|ref|YP_005919760.1| 193 KSDKAIGYlGFNYV 206
                                       *******6555444 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-06    0.0085      79     229 ..     103     270 ..      26     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                                       EEEEEEESTT-................TT.---SHHHHHHSS--.EEEE--T-TTTTHH.HHHHGGG--HHHHHHHH CS
                        SBP_bac_11  79 splviavpkgn................pk.kikgwadLlkpglk.lavadPttspsGlaalalleaagaqellkale 137
                                         ++iav ++                 ++ + ++w dL++p+    +va    s++G+   +++       l+++  
  gi|386001461|ref|YP_005919760.1| 103 DAICIAVSEPIyeagvtsisrqqlraiYDgNLTSWRDLGGPDADiYVVARMVGSGTGDLFNEMVMG-D---LQTETL 175
                                       556677777664444333333333433233788999999999962445555568999988877664.3...444444 PP

                                       HTEEEEESSHHHHHHHHHTTT-S...EEEEEHHHHH.....HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHH CS
                        SBP_bac_11 138 kkvvklgessrqlltaveagead...agivyeseakaa...engdkleavylpeglnldpldypaavlkkaakreaA 208
                                        ++ +++++ + + ta+   + +   +g+ y ++  ++    +g   +a  ++++ +  pl  p+ v++ +   +  
  gi|386001461|ref|YP_005919760.1| 176 -GADTYAQNNGEMKTAITKSDKAigyLGFNYVQDGPLRpiaYEGVAPSAESIRADDY--PLSRPLYVMTWNEPDAGE 249
                                       .34457888888888877666443338999999996652212333444446666666..677777777765445566 PP

                                       HHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 209 raFlafLrspeaqailrkyGf 229
                                       +aF++fL+++e+q ++++ Gf
  gi|386001461|ref|YP_005919760.1| 250 EAFIDFLLGEEGQSLVEEIGF 270
                                       9*****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2191.11
//
Query:       gi|386001462|ref|YP_005919761.1|  [L=366]
Description: hypothetical protein Mhar_0765 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2856.28
//
Query:       gi|386001463|ref|YP_005919762.1|  [L=295]
Description: hypothetical protein Mhar_0766 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 1826.44
//
Query:       gi|386001464|ref|YP_005919763.1|  [L=104]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-08   33.4   0.0    5.7e-08   32.7   0.0    1.3  1  HTH_20    Helix-turn-helix domain
    3.9e-05   23.4   0.1    0.00041   20.2   0.0    2.5  2  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.04   14.1   0.0      0.048   13.8   0.0    1.3  1  FUR       Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   9.5e-12   5.7e-08       6      56 ..      18      71 ..      13      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.5e-12
                                      HHS-HHHHHHHHHHSTCTTB-HHHHHHHHT....S-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  6 ALahPvRrrilraLaraegltaselaerld....lskntlsyHLrvLeeagLvev 56
                                      AL  P+R ri + + +ae+++  e+ e+l+    +s + l+yHL +L  ag+vev
  gi|386001464|ref|YP_005919763.1| 18 ALHCPTRWRIIQCI-GAEERSTREIFEELGlgeeISLAGLYYHLSALKGAGIVEV 71
                                      5555**********.**************55566*************99*****8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.8e-08   0.00041       1      46 [.      21      70 ..      21      71 .. 0.88
   2 ?   -1.5   0.0      0.41   2.5e+03       2      13 ..      89     100 ..      89     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.8e-08
                                      SHHHHHHHHHHTTSSEEHHHHHHHHT....S-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelg....lsqstvShHLkkLreaGLVe 46
                                      +ptR +I++    +e++  e+ eelg    +s + + +HL++L+ aG+Ve
  gi|386001464|ref|YP_005919763.1| 21 CPTRWRIIQCIGAEERSTREIFEELGlgeeISLAGLYYHLSALKGAGIVE 70
                                      59***********************8222257799**************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHTT CS
                             HTH_5   2 ptRlkILklLae 13 
                                       +tR+ ++ lL++
  gi|386001464|ref|YP_005919763.1|  89 KTRRIVIDLLED 100
                                       589999999986 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     8e-06     0.048      24      67 ..      36      78 ..      20     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8e-06
                                      BEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSE CS
                               FUR 24 lsaeevykelkeedpeislaTVYrtLklleeaglvkelefedge 67
                                       s  e+++el   ++eisla +Y  L  l+ ag+v+  ++++++
  gi|386001464|ref|YP_005919763.1| 36 RSTREIFEELG-LGEEISLAGLYYHLSALKGAGIVEVASYRESK 78
                                      46777887774.6899*******************998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 670.82
//
Query:       gi|386001465|ref|YP_005919764.1|  [L=89]
Description: hypothetical protein Mhar_0768 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.025   15.1   0.3      0.031   14.8   0.3    1.2  1  FoP_duplication  C-terminal duplication domain of Friend of P
        1.3   10.2  16.1          3    9.0  16.1    1.9  1  DUF5320          Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> FoP_duplication  C-terminal duplication domain of Friend of PRMT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   3.5e-06     0.031      10      63 ..      16      71 ..       8      84 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
                   FoP_duplication 10 ggggrggrrgrgrggrggrggrgrgrggrgg...rkkkkpltkeeLDaeLDaYmgkk 63
                                      +g+gr  + g ++ g  + g +g gr+g gg       +p+++ee+   L++Y g +
  gi|386001465|ref|YP_005919764.1| 16 RGAGRDEGCGCQGHGHDQAGHHGLGRSGEGGgccCGGHPPVSREEMISTLEEYRG-S 71
                                      33333333333333344456666666666667888899****************9.3 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  16.1   0.00033         3       9      99 .]      13      86 ..       2      86 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00033
                           DUF5320  9 pmGlGpmtGrglGyCagadapgyansagfGrgrggrglgrgfgrrrraggarlaaaetaeaskeeekelLeeqaeaLee 87
                                      p+G+G+    g G   g     +a ++g+Gr   g g g ++g+             + + s ee ++ Lee+  +L++
  gi|386001465|ref|YP_005919764.1| 13 PLGRGAGRDEGCGCQ-G-HGHDQAGHHGLGR--SGEGGGCCCGG-------------HPPVSREEMISTLEEYRGSLRR 74
                                      445554444444422.2.2222233356666..56666655565.............56789***************** PP

                           DUF5320 88 eleaikkrlkel 99
                                      ele ++++l+el
  gi|386001465|ref|YP_005919764.1| 75 ELERVEAKLREL 86
                                      *********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 556.53
//
Query:       gi|386001466|ref|YP_005919765.1|  [L=322]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-30  104.9   0.0    6.6e-30  104.4   0.0    1.2  1  ABC_tran      ABC transporter
    9.3e-15   55.2   2.5    1.1e-09   38.6   0.2    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
  ------ inclusion threshold ------
      0.011   16.3   0.1       0.02   15.4   0.1    1.3  1  AAA_23        AAA domain
      0.016   14.6   0.1        2.6    7.4   0.0    2.3  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.027   14.7   0.2       0.11   12.7   0.2    2.0  1  AAA_22        AAA domain
      0.031   14.0   0.0        3.2    7.4   0.0    2.1  2  AAA_15        AAA ATPase domain
      0.047   13.4   0.1       0.21   11.3   0.1    1.9  1  AAA_30        AAA domain
      0.058   13.1   0.1       0.11   12.2   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.15   11.4   0.1        4.3    6.7   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.16   12.4   0.1       0.58   10.6   0.1    2.1  1  AAA           ATPase family associated with various cellular 


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   3.7e-33   6.6e-30       2     136 ..      20     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 3.7e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +s++++ege+ +++G+nG+GK+t +++l gl++pt+G+ ++ g dl++  + +++++igv+p  ++l +elt+re
  gi|386001466|ref|YP_005919765.1|  20 DGISFDVEEGEVFGLLGPNGSGKTTTIRMLVGLSRPTAGTAKVLGYDLSS-GIVEAKRRIGVVPDSSNLYEELTARE 95 
                                       789***********************************************.99999********************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             ++++++e++l+ +gl++  d++      ++S G+k+ + +a+al+ +p ll+lDEpt
  gi|386001466|ref|YP_005919765.1|  96 NllfmaglygvpkaDREDRAEELLRAFGLSGRGDDRF----GTFSRGMKRALTIAAALIHDPHLLFLDEPT 162
                                       ************9888889************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   2.5e-06    0.0044       2      25 ..      32      55 ..      31      94 .. 0.82
   2 !   38.6   0.2   5.9e-13   1.1e-09     220     298 ..     118     193 ..      73     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                       +l GpNgsGK++ ++ l +l+r 
  gi|386001466|ref|YP_005919765.1| 32 FGLLGPNGSGKTTTIRMLVGLSRP 55
                                      689***************999874 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 5.9e-13
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        ++ +  +++++  +  +S G+kr+l +++al+ ++    ll++DEp  gL+  + r+l  l+++l+++g  ++ltT
  gi|386001466|ref|YP_005919765.1| 118 LLRAFGLSGRGDDRFGTFSRGMKRALTIAAALIHDP---HLLFLDEPTVGLDVVAARSLRSLISDLHDRGLTIVLTT 191
                                       34555556778888999****************999...89************************************ PP

                            AAA_21 297 HS 298
                                       H 
  gi|386001466|ref|YP_005919765.1| 192 HY 193
                                       *6 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   1.1e-05      0.02      16      37 ..      23      47 ..      11      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                            AAA_23 16 dF...skgltlItGpNGaGKTTild 37
                                       F   +  ++ + GpNG+GKTT ++
  gi|386001466|ref|YP_005919765.1| 23 SFdveEGEVFGLLGPNGSGKTTTIR 47
                                      4444556799************987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0086        15      27      47 ..      34      54 ..      28      78 .. 0.83
   2 ?    7.4   0.0    0.0015       2.6      11      52 ..     139     183 ..     135     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0086
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllp 47
                                      l+Gp GsGKt  ++ l +l  
  gi|386001466|ref|YP_005919765.1| 34 LLGPNGSGKTTTIRMLVGLSR 54
                                      79**********999998854 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                      Mg_chelatase  11 akraleiaaaGgH..nlllvGppGsGKtmlakr.lpsllpplsee 52 
                                        kral+iaaa  H  +ll++  p  G  ++a+r l sl+++l+++
  gi|386001466|ref|YP_005919765.1| 139 MKRALTIAAALIHdpHLLFLDEPTVGLDVVAARsLRSLISDLHDR 183
                                       69*********99777**********9988765389999998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   6.3e-05      0.11      10      81 ..      34     121 ..      27     201 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee...............................erpevvfvtlpsstsskd 55 
                                       + G+ G+GKTt++r+l+      a  ++                               +               ++
  gi|386001466|ref|YP_005919765.1|  34 LLGPNGSGKTTTIRMLVGLSRPTAGTAKvlgydlssgiveakrrigvvpdssnlyeeltA---------------RE 95 
                                       67**************99875554444488888888888666444444444444444432...............44 PP

                            AAA_22  56 llrellralglelkaerlsseellea 81 
                                        l  ++  +g+++ +++++ eell+a
  gi|386001466|ref|YP_005919765.1|  96 NLLFMAGLYGVPKADREDRAEELLRA 121
                                       44444444444444433333333333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0018       3.2      28      44 ..      34      50 ..      21      68 .. 0.85
   2 ?    4.5   0.0     0.013        24     322     364 ..     151     192 ..     136     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                            AAA_15 28 liGkNnsGKSsileald 44
                                      l G+N+sGK++ +++l 
  gi|386001466|ref|YP_005919765.1| 34 LLGPNGSGKTTTIRMLV 50
                                      78***********9985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        ++++l+++EP + L   a ++l  l+ +l + +   +++tTH
  gi|386001466|ref|YP_005919765.1| 151 HDPHLLFLDEPTVGLDVVAARSLRSLISDLHDRGL-TIVLTTH 192
                                       478*******************************7.9****** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.21      19      52 ..      30      65 ..      25     192 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.grvigl 52
                                       v  l Gp G+GKtt+++ l+ + +   g  +v+g+
  gi|386001466|ref|YP_005919765.1| 30 EVFGLLGPNGSGKTTTIRMLVGLSRPTaGtAKVLGY 65
                                      477899*************99888766444445544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.2e-05      0.11      15      39 ..      22      46 ..      17      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       ++++++ +++ l Gp+GsGK+T +
  gi|386001466|ref|YP_005919765.1| 22 ISFDVEEGEVFGLLGPNGSGKTTTI 46
                                      556676555999**********976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0024       4.3      28      41 ..      33      46 ..      21      54 .. 0.82
   2 ?    2.6   0.0     0.044        78     148     207 ..     142     199 ..     103     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                                      EEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnll 41
                                       ++GpNGSGK+  +
  gi|386001466|ref|YP_005919765.1| 33 GLLGPNGSGKTTTI 46
                                      689*******9765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.044
                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                       aL +A   ++   l +lDe    LD    + + +l+   +++   iv   +++ le+ad+
  gi|386001466|ref|YP_005919765.1| 142 ALTIAAALIHDPHLLFLDEPTVGLDVVAARSLRSLISDLHDRGLTIVL--TTHYLEEADH 199
                                       56666666666678899********************99977655554..4556666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00032      0.58       3      22 ..      34      53 ..      32     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      l Gp G GKT++++ ++  +
  gi|386001466|ref|YP_005919765.1| 34 LLGPNGSGKTTTIRMLVGLS 53
                                      78************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1814.37
//
Query:       gi|386001467|ref|YP_005919766.1|  [L=241]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for 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-30  105.2  13.4    4.1e-30  104.8  13.4    1.2  1  ABC2_membrane    ABC-2 type transporter
    6.3e-15   55.1  14.5      8e-15   54.8  14.5    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.5e-08   33.5  17.2    5.1e-08   32.5  17.0    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00094   18.7   6.7     0.0012   18.4   6.7    1.3  1  CcmB             CcmB protein
  ------ inclusion threshold ------
      0.011   15.5   9.7      0.014   15.1   8.2    1.8  2  ABC2_membrane_6  ABC-2 family transporter protein
        1.2    9.1  10.5        1.3    8.9   6.5    2.3  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8  13.4   1.4e-33   4.1e-30       3     210 .]       9     208 ..       7     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.4e-33
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr..pgllffsvlflafsaltsvapvfer 77 
                                       i+++  +++++++  p  +  w +++pl ++l f +         + ++   pgl+++++lf + +a+ +v+++fe 
  gi|386001467|ref|YP_005919766.1|   9 IWLIAAKDMRTYYLKPPAI-SWGIVFPLAWTLAFFLRSP------GDFEDlvPGLIAMTILFST-TAAEAVVINFEL 77 
                                       79999**************.**************99999......3442246************.9999999***** PP

                     ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisal 154
                                       + g+ler+l +p+ ++ a++l+kvl+ ++++ll++ +++l +++ + l+++  + +++++l+++l+ ss+g l+s+ 
  gi|386001467|ref|YP_005919766.1|  78 RIGSLERLLLAPV-RTDAVLLGKVLGGFLFGLLMTSVVTLSTVVGLRLRPD-LAALIPVVLISLLVYSSMGALFSVG 152
                                       *************.**************************88886688886.99*********************** PP

                     ABC2_membrane 155 apsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                       ++ +  a+++ +l  +++++l+G+++pi++mp+ lq +++++Plty+ve+lr ++f
  gi|386001467|ref|YP_005919766.1| 153 FKEVFEAQTFLNLPRFLMVFLCGVVYPISAMPEGLQLLSRVLPLTYTVEGLRTAFF 208
                                       *******************************99*******************9987 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 !   54.8  14.5   2.7e-18     8e-15     158     338 ..      48     227 ..      34     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.7e-18
                   ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afglgi 233
                                       ++++ + gli++ ++f t +  av i +E + + +e++l+++v++ + +l+k+lg fl +ll++ +++l  ++g  +
  gi|386001467|ref|YP_005919766.1|  48 DFEDLVPGLIAMTILFSTTAAEAVVINFELRIGSLERLLLAPVRTDAVLLGKVLGGFLFGLLMTSVVTLStVVG--L 122
                                       566777787777776666666666799*************************************99999669**..9 PP

                   ABC2_membrane_3 234 pfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffap 309
                                           +l +l+ ++l+ +l+y+++g+l+s+ fk   +aq+++ +  +l+ +++g+++p++++p++l+ +++++P+++ 
  gi|386001467|ref|YP_005919766.1| 123 RLRpDLAALIPVVLISLLVYSSMGALFSVGFKEVFEAQTFLNLPRFLMVFLCGVVYPISAMPEGLQLLSRVLPLTYT 199
                                       9999******************************************9****************************** PP

                   ABC2_membrane_3 310 glgllrlitgd.plweillsliilalfavv 338
                                        +gl +  +   +  +  ++ ++la+f ++
  gi|386001467|ref|YP_005919766.1| 200 VEGLRTAFFSGsSSPQ--TASLVLAGFLLI 227
                                       ****999865512223..233333333333 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5  17.0   1.7e-11   5.1e-08      77     274 ..      53     229 ..      12     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.7e-11
                   ABC2_membrane_2  77 vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalg 153
                                       v++++a+ i +  +++ a +i+ E   g+l++lL  Pv  d++llgK++gg++    +++++ ++   +l  +++l 
  gi|386001467|ref|YP_005919766.1|  53 VPGLIAMTILFSTTAAEAVVINFELRIGSLERLLLAPVRTDAVLLGKVLGGFLF---GLLMTSVV---TLSTVVGLR 123
                                       677888888888888889999*********************************...55555555...5666778** PP

                   ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                         ++l++l+ +v+ s+   l  v+ ++g+l+S+ ++  + +a+  l l  +l+++  +v+y++++++ g +      
  gi|386001467|ref|YP_005919766.1| 124 LRPDLAALIPVVLISL---L--VYSSMGALFSVGFK-EVFEAQTFLNLPRFLMVFLCGVVYPISAMPEGLQL----- 189
                                       ***********99999...3..467***********.99999**************************9999..... PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlnalgstatnllilllllav 274
                                         ls + p  +   +l++ + +++ + +++    +++ll+   +
  gi|386001467|ref|YP_005919766.1| 190 --LSRVLPLTYTVEGLRTAFFSGSSSPQTASLVLAGFLLI--FI 229
                                       ..88888888877777666655544444444444444444..33 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   6.7   3.9e-07    0.0012      43     134 ..      48     142 ..       9     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-07
                              CcmB  43 llsriapgilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglpl..vllapllalll 117
                                        ++++ pg++ +++l+++  +   + + +   GsLe lllapv  ++++l+K+l  +l+ +l    v l+++++l l
  gi|386001467|ref|YP_005919766.1|  48 DFEDLVPGLIAMTILFSTTAAEAVVINFELRIGSLERLLLAPVRTDAVLLGKVLGGFLFGLLMTsvVTLSTVVGLRL 124
                                       567899*************99999**********************************9988642155789999999 PP

                              CcmB 118 nleaaal.gllaltLllG 134
                                         + aal ++++++Ll+ 
  gi|386001467|ref|YP_005919766.1| 125 RPDLAALiPVVLISLLVY 142
                                       999877526777788764 PP

>> ABC2_membrane_6  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.46   1.4e+03     189     212 ..      20      43 ..      18      46 .. 0.87
   2 ?   15.1   8.2   4.8e-06     0.014      39     183 ..      59     200 ..      52     239 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                   ABC2_membrane_6 189 ivlgklsivfalvlqlilalvllv 212
                                       ++l+ + i + +v +l ++l++++
  gi|386001467|ref|YP_005919766.1|  20 YYLKPPAISWGIVFPLAWTLAFFL 43 
                                       889999999*****9999999986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.8e-06
                   ABC2_membrane_6  39 lqglaavffapalsrigesvrdGsldflLlkPinlllqillkrlnlrrvgrllvgiilliyavkkldikltaakill 115
                                       +  l++++ a+a+  i ++ r Gsl+ lLl P+++ + +l k l+ + +g l+ +++ l+++v +l +  +    l+
  gi|386001467|ref|YP_005919766.1|  59 MTILFSTTAAEAV-VINFELRIGSLERLLLAPVRTDAVLLGKVLGGFLFGLLMTSVVTLSTVV-GLRLRPD----LA 129
                                       5566777777777.89*******************************************9999.6666554....55 PP

                   ABC2_membrane_6 116 liislilglliltslffilgslsfw....fvkseeiieileglleaakyPltiyplilrklltfiiPvafls 183
                                       ++i ++l +l+++s + +l s+ f+    +++  +   +l  +l    yP+++ p+ l+ ll  ++P++ + 
  gi|386001467|ref|YP_005919766.1| 130 ALIPVVLISLLVYSSMGALFSVGFKevfeAQTFLNLPRFLMVFLCGVVYPISAMPEGLQ-LLSRVLPLTYTV 200
                                       55555555566666655555554441100333334444555557788899999999987.566678888765 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.5   0.00044       1.3      61     121 ..      62     122 ..      30     151 .. 0.77
   2 ?    0.2   2.8      0.21   6.2e+02     106     147 ..     134     177 ..     128     202 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00044
                   ABC2_membrane_4  61 plilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfa 121
                                        + ++   + +i+ E   + l  Ll+ Pv   ++ll+K++  +l+ +l++ v +l+tv+  
  gi|386001467|ref|YP_005919766.1|  62 LFSTTAAEAVVINFELRIGSLERLLLAPVRTDAVLLGKVLGGFLFGLLMTSVVTLSTVVGL 122
                                       33444455899999*********************************99999888887764 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.21
                   ABC2_membrane_4 106 svllmlvtf.litvlfallsgfvgfsvklvlel..lkkclelgll 147
                                       +vl++l+ +  + +lf  +  + +f+++++l+l  + +++++g++
  gi|386001467|ref|YP_005919766.1| 134 VVLISLLVYsSMGALF-SVGFKEVFEAQTFLNLprFLMVFLCGVV 177
                                       3333333220223333.3333355666655543112223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1365.07
//
Query:       gi|386001468|ref|YP_005919767.1|  [L=125]
Description: hypothetical protein Mhar_0771 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 791.50
//
Query:       gi|386001469|ref|YP_005919768.1|  [L=171]
Description: hypothetical protein Mhar_0772 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       156  (0.00870099); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1106.79
//
Query:       gi|386001470|ref|YP_005919769.1|  [L=384]
Description: Extracellular solute-binding protein family 3 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-34  117.0   0.0    1.8e-33  115.9   0.0    1.5  2  SBP_bac_3        Bacterial extracellular solute-binding prote
      3e-10   40.4   0.1    4.9e-10   39.7   0.1    1.3  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
    7.2e-06   25.8   0.0    1.2e-05   25.1   0.0    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.29   11.1   0.0    1.4  1  Pirin            Pirin


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0     4e-37   1.8e-33       1     224 [.      39     252 ..      39     253 .. 0.94
   2 ?   -2.3   0.0      0.54   2.4e+03     185     200 ..     314     329 ..     264     338 .. 0.51

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 4e-37
                                       EEEEE-S-BTTTBEE-TTS-EESHHHHHHHHHHHHCT-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3   1 lrvgvdadypPfsykdengeltGfdvdlakaiakrlgvkvefvpvswdelipalksgkvDiaiaaititpeReekvd 77 
                                       lr+ +d d++Pf+y++  g l Gf+ dl++ + ++ g+++  +p+ w+e+    + g +  +i+++  t+eR ++++
  gi|386001470|ref|YP_005919769.1|  39 LRFVFDRDFAPFTYEE-GGSLRGFELDLLRLLGEEVGFRLIPEPMVWTEAQRTFQRGVAE-VIGGLVKTEERLAEFN 113
                                       6788999*********.****************************************777.789************* PP

                                       EES.ESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSS CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  78 Fsq.pyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkkgaeivefdtleealqaLkngrv 153
                                       F+  p+ +  +  +vr+ d     ++ s + L+g+kv+vq+gs + +llk   ++g+e+  +++  ealqaLk g++
  gi|386001470|ref|YP_005919769.1| 114 FTArPHGTFDILTFVRD-DG----DVISADMLAGRKVAVQNGSISFDLLKD--RNGIEVLAYESEGEALQALKGGEA 183
                                       **98999999999**95.43....34456799******************9..459********************* PP

                                       SEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 154 davvadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelkadgtlakisekWfg 224
                                       da+v+  ++ + +++ ++d  +   + p +  +++++vr  d+eL+  i++a+ el +dg+++++++ Wf 
  gi|386001470|ref|YP_005919769.1| 184 DAFVGGGSTTRFWMRLHDDSGIRPLATPWEMHSLYFGVR--DPELLRSIDAAMVELLEDGRYDQLYRSWFV 252
                                       ***********************99************98..9****************************6 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.54
                                       CEEEEEEETTTHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                         SBP_bac_3 185 eeyaiavrkgdseLrk 200
                                         ++ a+ +gdse r+
  gi|386001470|ref|YP_005919769.1| 314 VAIYKAISEGDSEIRA 329
                                       3334444445555555 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1   1.1e-13   4.9e-10      43     109 ..     259     325 ..     224     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.1e-13
                                       .S-HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHHTT-- CS
                   dCMP_cyt_deam_2  43 kddelkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvlggke 109
                                       + ++l+ea  +a  ++yapys+ p G a+ t++g++y+G  +E+a +  + ++l++A+ +++ +g++
  gi|386001470|ref|YP_005919769.1| 259 EVSALAEASRKASLSAYAPYSRYPVGAAVLTSSGRIYTGCNVENALYGLTTSALKVAIYKAISEGDS 325
                                       2456888888899999********************************************9995543 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.7e-09   1.2e-05       6      69 ..     262     326 ..     257     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.7e-09
                                       HHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSC CS
                   dCMP_cyt_deam_1   6 kllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsk 69 
                                        l e + ka+  a+ ++s+ +VGa+++++  +i+tg+n e+a +  t  A  +Ai ka ++g s+
  gi|386001470|ref|YP_005919769.1| 262 ALAEASRKASLSAYaPYSRYPVGAAVLTSSGRIYTGCNVENALYGLTTSALKVAIYKAISEGDSE 326
                                       455666667777779*************99****************************9986434 PP

>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.5e-05      0.29      36      80 ..     106     153 ..      86     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.5e-05
                                       EEEE.T-EEEEEEEBSEEEEEEEE.CSEEEEEETT.S-EEEEETT-EE CS
                             Pirin  36 edvi.gagfpphphrgletvtyll.eGevehrDsl.GnkgvirpGdvq 80 
                                       e+++ + +f  +ph  ++++t++  +G v   D l G+k  +++G + 
  gi|386001470|ref|YP_005919769.1| 106 EERLaEFNFTARPHGTFDILTFVRdDGDVISADMLaGRKVAVQNGSIS 153
                                       67777899***************9459**9999854899999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2317.13
//
Query:       gi|386001471|ref|YP_005919770.1|  [L=194]
Description: hypothetical protein Mhar_0774 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-14   53.5   0.0    3.3e-14   53.2   0.0    1.1  1  NT5C      5' nucleotidase, deoxy (Pyrimidine), cytosolic type


Domain annotation for each model (and alignments):
>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.8e-18   3.3e-14       6     160 ..       1     155 [.       1     162 [. 0.87

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.8e-18
                              NT5C   6 vDlDgvladlygkmlevankrfeatllpeevsswdleefvkPeqreslyrfltepglFadlepipgarevLeelade 82 
                                       +D+Dgvlad +g++lev+++++++  ++ +v   d+  f       ++ r l  p++  +l  i+g++  +e+l d+
  gi|386001471|ref|YP_005919770.1|   1 MDIDGVLADQVGAVLEVIEREYGERYHKGDVDRADWT-FGGRRLWSEVGRLLADPEYTLNLPLIEGSQGGVERLKDH 76 
                                       69******************************99995.5566777888899************************** PP

                              NT5C  83 grlvvitaallqfydavkekveWldehlplipyrnlvlvkekdlvrgDvlidDapknl....eklrgrs.ilfdspt 154
                                        ++ v+ta+    +da + +  Wl+ h+p +       ++ k+ + +DvlidD   n+    + ++ r+ ilf +p 
  gi|386001471|ref|YP_005919770.1|  77 -EVFVVTARR---PDAEEATRRWLKAHFPCLRGYFTAGTGTKHKIPSDVLIDDLDLNIvefvRSHPHRRgILFVHPW 149
                                       .999999875...5699************************************999962111555655579999998 PP

                              NT5C 155 nrhied 160
                                        +  +d
  gi|386001471|ref|YP_005919770.1| 150 SINGTD 155
                                       776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1242.89
//
Query:       gi|386001472|ref|YP_005919771.1|  [L=123]
Description: hypothetical protein Mhar_0775 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   17.6   0.7     0.0042   16.9   0.1    1.7  2  MarR_2    MarR family
  ------ inclusion threshold ------
       0.01   15.7   0.1       0.02   14.7   0.0    1.6  2  TrmB      Sugar-specific transcriptional regulator TrmB
      0.052   13.5   0.2       0.21   11.5   0.0    2.1  2  MarR      MarR family


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   7.1e-07    0.0042       2      60 ..      24      80 ..      23      82 .. 0.87
   2 ?   -3.3   0.1       1.5     9e+03      41      47 ..      97     103 ..      96     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.1e-07
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                                      g+ +a a v+ ++  +++   t +e++++++l +s vs ++  L    ++ +r+++  +
  gi|386001472|ref|YP_005919771.1| 24 GIQRAMAVVITYISKAGE--ATSKEIEEATRLRQSEVSVAVHGLRGEDWIDERTAQPQG 80
                                      566666778888999998..9*******************************9987665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                                       HHHHHHH CS
                            MarR_2  41 ilkrLva 47 
                                       i++rL++
  gi|386001472|ref|YP_005919771.1|  97 IIRRLEE 103
                                       5666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.4e-06      0.02       1      63 [.      20      89 ..      20      93 .. 0.86
   2 ?   -3.2   0.1       1.3   7.9e+03      30      44 ..     103     117 ..      98     120 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                      Lq lG++   a v +++ k g+at +ei e++ + +s v  ++  L   ++++ +  +       p +Y+
  gi|386001472|ref|YP_005919771.1| 20 LQSLGIQRAMAVVITYISKAGEATSKEIEEATRLRQSEVSVAVHGLRGEDWIDERTAQpqgkgrpPAVYS 89
                                      6788888888888888999**********************************99988666666666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                                       CCTTSSCHCHHHHHH CS
                              TrmB  30 eelgvprskvYevLr 44 
                                       ee  ++++ v e +r
  gi|386001472|ref|YP_005919771.1| 103 EEKRREHAEVMEKIR 117
                                       444445555555444 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.5e-05      0.21       7      48 ..      31      72 ..      25      80 .. 0.90
   2 ?   -1.6   0.1      0.45   2.7e+03      37      43 ..      97     103 ..      94     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      v+++ ++  g+++ +e+ ++  + +s v+ +++ L  +++i+
  gi|386001472|ref|YP_005919771.1| 31 VVITYISKAGEATSKEIEEATRLRQSEVSVAVHGLRGEDWID 72
                                      6788899*********************************95 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                                       HHHHHHH CS
                              MarR  37 vldrLek 43 
                                       +++rLe+
  gi|386001472|ref|YP_005919771.1|  97 IIRRLEE 103
                                       6788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.58
# Mc/sec: 634.12
//
Query:       gi|386001473|ref|YP_005919772.1|  [L=97]
Description: hypothetical protein Mhar_0776 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-05   23.3   0.0    4.7e-05   22.9   0.0    1.1  1  Hfq       Hfq protein
     0.0012   18.5   0.0     0.0018   17.9   0.0    1.3  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.3e-09   4.7e-05      14      61 ..      40      88 ..      32      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.3e-09
                                      -EEEEEETTS-EEEEEEEEE-SSEEEEEETTEEE.EEEGGGEEEEEESS CS
                               Hfq 14 ipvtifLvnGiklkGviksfDnftvlLesdgkqq.lvYKhaistivpar 61
                                       p+++ +  G  +kGv++++ n+ +l++  +  + +++K ais i  ++
  gi|386001473|ref|YP_005919772.1| 40 RPIMVRMKDGRPIKGVLEAYNNYELLIDLGQSKRlIIFKGAISSIEAEE 88
                                      58899999*******************977765559*********8765 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-07    0.0018       2      31 ..      33      62 ..      32      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-07
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETT CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqf 31
                                      fl++l+++ + v++k+gr ++G+L+++ ++
  gi|386001473|ref|YP_005919772.1| 33 FLDSLLHRPIMVRMKDGRPIKGVLEAYNNY 62
                                      99***********************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 582.43
//
Query:       gi|386001474|ref|YP_005919773.1|  [L=183]
Description: hypothetical protein Mhar_0777 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1141.35
//
Query:       gi|386001475|ref|YP_005919774.1|  [L=96]
Description: hypothetical protein Mhar_0778 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 634.91
//
Query:       gi|386001476|ref|YP_005919775.1|  [L=158]
Description: hypothetical protein Mhar_0779 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00025   21.0   0.2    0.00058   19.9   0.2    1.6  1  HTH_20       Helix-turn-helix domain
  ------ inclusion threshold ------
        0.2   12.2   0.0       0.32   11.5   0.0    1.2  1  AAA_assoc_C  C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   6.4e-08   0.00058       2      57 ..      79     131 ..      78     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.4e-08
                                       HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20   2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                        +++AL +P Rrr+  +   +++l+++ +  ++   ++ l yHL+ Le agL+ev 
  gi|386001476|ref|YP_005919775.1|  79 LVHHALESPIRRRMIILM-VEGCLSVEGISGAV--GPKMLGYHLHRLELAGLIEVA 131
                                       5899********999888.9***********95..7888********99*****96 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.32      20      43 ..     121     144 ..     115     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                       AAA_assoc_C  20 aaelLglveveegdielTelGrkf 43 
                                        +el gl+ev++g i lTe+G+++
  gi|386001476|ref|YP_005919775.1| 121 RLELAGLIEVADGTIALTEAGEAY 144
                                       67899****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 983.33
//
Query:       gi|386001477|ref|YP_005919776.1|  [L=62]
Description: hypothetical protein Mhar_0780 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 416.44
//
Query:       gi|386001478|ref|YP_005919777.1|  [L=170]
Description: NADH dehydrogenase/NAD(P)H nitroreductase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-21   75.0   3.5    1.1e-12   48.4   0.5    2.5  3  Nitroreductase  Nitroreductase family
    1.6e-11   44.2   0.1     0.0089   15.6   0.5    3.3  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.5   1.2e-16   1.1e-12       1      53 [.       5      57 ..       5      63 .. 0.89
   2 !   28.1   0.0     2e-10   1.8e-06      79     170 .]      60     149 ..      51     149 .. 0.88
   3 ?   -2.3   0.1      0.45   4.1e+03      12      21 ..     154     163 ..     153     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.2e-16
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelrykl 53
                                      +rkRrS+Rk++de +++e++e + eaa r+P++ n +pwrfv v+d+ ++++l
  gi|386001478|ref|YP_005919777.1|  5 LRKRRSVRKYRDEDIEAEVVELLKEAALRSPTSRNFRPWRFVFVTDRGKLAAL 57
                                      59******************************************776666655 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2e-10
                                       HHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG.........GG CS
                    Nitroreductase  79 lklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd.........ea 146
                                       +k++  ++laga + +v+          a+e++ ++ + d+++a   l+La ++lGlgsc+i             e+
  gi|386001478|ref|YP_005919777.1|  60 AKESGSSFLAGARLGVVV---------CADEGESDVWIEDCSIASIILQLAGQSLGLGSCWIQIRLrmhtdsvtsEE 127
                                       467888999999999999.........89999999999****************************88888875444 PP

                                       HHHHHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 147 aeevrkllglpdeeeivvliavGy 170
                                          vr +l lp+  ++  +ia+Gy
  gi|386001478|ref|YP_005919777.1| 128 --YVRSILRLPEYIRVESMIAFGY 149
                                       ..6********999999******9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.45
                                       S----HHHHH CS
                    Nitroreductase  12 depvpkeele 21 
                                       +epvp+eele
  gi|386001478|ref|YP_005919777.1| 154 KEPVPAEELE 163
                                       789****998 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5     1e-06    0.0089       4      31 ..       3      30 ..       1      31 [. 0.90
   2 !   11.9   0.0   1.4e-05      0.12     165     209 ..      29      78 ..      26      79 .. 0.74
   3 !   14.5   0.0   2.1e-06     0.019      92     149 ..      99     168 ..      93     170 .] 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-06
                                      HHHHH--B---B--S---HHHHHHHHH- CS
                    TM1586_NiRdase  4 eaiekRhsvRkYkdealeeelleelkea 31
                                      + ++kR+svRkY+de +e e++e lkea
  gi|386001478|ref|YP_005919777.1|  3 DLLRKRRSVRKYRDEDIEAEVVELLKEA 30
                                      6789*******************99986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.4e-05
                                       HHHHTS--GGG----EEE.E-SS.EE.........EEE-S-HHHHHHHHH CS
                    TM1586_NiRdase 165 eaarlAPsAlNqqpwrfelkddd.eiki....kasvlgklskiDlGIall 209
                                       eaa+ +P++ N +pwrf +++d  ++++    k s  ++l    lG++++
  gi|386001478|ref|YP_005919777.1|  29 EAALRSPTSRNFRPWRFVFVTDRgKLAAlsraKESGSSFLAGARLGVVVC 78 
                                       799***************98864355556664445556777777777765 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.1e-06
                                       HHHHHHTT-EEEEES--SST.....................T-S-EEEEE-BS----...-----HHHHB CS
                    TM1586_NiRdase  92 vLkltalGlgtcWvggtykk..........kkakvelkkgeklvivIalGyaktklv..eakrkpleelc 149
                                        L  ++lGlg+cW+ +              +++ + l++  ++  +Ia+Gy+++++   +a++ ++e+++
  gi|386001478|ref|YP_005919777.1|  99 QLAGQSLGLGSCWIQIRLRMhtdsvtseeyVRSILRLPEYIRVESMIAFGYPDEEKEpvPAEELEAEKIL 168
                                       466789*******8754333222344443445556777888999*********99954477777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1251.96
//
Query:       gi|386001479|ref|YP_005919778.1|  [L=614]
Description: hypothetical protein Mhar_0782 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-22   78.3  69.2    2.9e-08   33.7   5.5    4.8  6  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.12   12.0   3.0       0.23   11.0   3.0    1.4  1  Ni_hydr_CYTB    Prokaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.7   5.8e-10   5.2e-06      13      47 ..     254     289 ..     231     290 .. 0.67
   2 !   30.7   5.0     3e-11   2.6e-07       2      45 ..     254     298 ..     253     300 .. 0.95
   3 !   17.7  10.4   3.2e-07    0.0029       1      44 [.     286     330 ..     286     330 .. 0.95
   4 !   18.9   9.2   1.3e-07    0.0012       1      44 [.     297     341 ..     297     341 .. 0.95
   5 !   33.7   5.5   3.3e-12   2.9e-08       1      47 [.     319     366 ..     319     367 .. 0.97
   6 !   20.1   0.9   5.9e-08   0.00053       1      44 [.     363     406 ..     363     410 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.8e-10
                    Pentapeptide_3  13 rgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       +++ F+g+++F+++ F ++++F g++F  dv F+++
  gi|386001479|ref|YP_005919778.1| 254 TNSIFEGDINFKRTKFnNNISFYGSHFLNDVHFEES 289
                                       366666666666666655666666666666666665 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 3e-11
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                       ++++F+g+ +F ++ F++ +sF +++F ++++F+++ F+++++F+
  gi|386001479|ref|YP_005919778.1| 254 TNSIFEGDINFKRTKFNNNISFYGSHFlNDVHFEESVFSRTATFT 298
                                       69*************************************99*997 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 3.2e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdF 44 
                                       F++++Fs++a+F+ + F+g a+F+n++F +++ F  a F+ d+ F
  gi|386001479|ref|YP_005919778.1| 286 FEESVFSRTATFTYVYFYGFAFFKNSQFnNDSYFNYADFSMDAYF 330
                                       99**************************88*********988776 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 1.3e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadFsgarFtgdvdF 44 
                                       F+ + F+g a+F ++ F+++ +F+ adF+ +a Fs + F+g ++F
  gi|386001479|ref|YP_005919778.1| 297 FTYVYFYGFAFFKNSQFNNDSYFNYADFSmDAYFSMCKFSGYASF 341
                                       88899***************99******66**********99999 PP

  == domain 5  score: 33.7 bits;  conditional E-value: 3.3e-12
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F+ a Fs +a+F+++ Fsg asF +++F g+++F+++ F + +dF+++
  gi|386001479|ref|YP_005919778.1| 319 FNYADFSMDAYFSMCKFSGYASFLRSQFlGDSNFDDTEFQKYADFKES 366
                                       999*******************************************98 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 5.9e-08
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdF 44 
                                       F+++nF g ad ++a F+ +a+F +++F ++  F ++ F+ ++ +
  gi|386001479|ref|YP_005919778.1| 363 FKESNFVGLADYSRAIFIVDADFIGSHFsDNLIFNESKFY-TLKL 406
                                       99**************************88*********9.7665 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.0   2.6e-05      0.23      20      64 ..     563     610 ..     561     614 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHS------S-GGG-...HHHHHHHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB  20 lllsgllianlhprlywgdsgk...aralHklaGlvllalllfrllwl 64 
                                       +++s l+++++hp+++w +sgk   ++ +  +aG+++la+++++l+ +
  gi|386001479|ref|YP_005919778.1| 563 IYFSTLIFFHTHPPAHWYPSGKwkfVVVIEDIAGWLFLAIFVVVLVNR 610
                                       689******************98877777*************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3749.15
//
Query:       gi|386001480|ref|YP_005919779.1|  [L=83]
Description: hypothetical protein Mhar_0783, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.3   0.0    1.6e-18   67.0   0.0    1.1  1  DUF763    Protein of unknown function (DUF763)
  ------ inclusion threshold ------
      0.061   13.4   0.0      0.098   12.7   0.0    1.4  1  EKAL      EMP3-KAHRP-like N-terminal domain


Domain annotation for each model (and alignments):
>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   1.7e-22   1.6e-18     270     312 .]       1      43 [.       1      43 [. 0.98

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.7e-22
                            DUF763 270 vGpktlraLalvaeliygekasfkDPvkysfavGgKdgvPypv 312
                                       +G++ +raLal++eliyg+++s++DP++ysfa+Gg dg+Pypv
  gi|386001480|ref|YP_005919779.1|   1 MGQRRVRALALISELIYGAETSWRDPARYSFAHGGEDGHPYPV 43 
                                       799***************************************8 PP

>> EKAL  EMP3-KAHRP-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.098      19      41 ..      51      73 ..      40      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                              EKAL 19 KhfklkEsvdngkkdCDEKYEaa 41
                                          lkE+v+ngk d  EKY+a 
  gi|386001480|ref|YP_005919779.1| 51 SISTLKEAVENGKLDRREKYDAI 73
                                      55679***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 618.07
//
Query:       gi|386001481|ref|YP_005919780.1|  [L=284]
Description: hypothetical protein Mhar_0784 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1956.49
//
Query:       gi|386001482|ref|YP_005919781.1|  [L=393]
Description: hypothetical protein Mhar_0785 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-05   26.2  10.1    0.00022   22.3   2.3    4.4  4  PPC       Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0035        63      51      69 ..     101     118 ..      60     119 .. 0.54
   2 ?   -1.5   0.0      0.32   5.8e+03      60      69 ..     123     132 ..     121     133 .. 0.82
   3 ?   -0.3   0.2      0.13   2.4e+03      52      66 ..     230     245 ..     153     249 .. 0.46
   4 !   22.3   2.3   1.2e-08   0.00022       1      70 []     303     370 ..     303     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0035
                                       -TTS-EE-SSSEEEEEEE. CS
                               PPC  51 deyieftapqaGtYyvaVs 69 
                                         ++++ta +aGtY ++V 
  gi|386001482|ref|YP_005919781.1| 101 EDLLRMTA-DAGTYLLRVD 118
                                       35788899.9999999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                                       SSEEEEEEE. CS
                               PPC  60 qaGtYyvaVs 69 
                                       q+G+Y v++s
  gi|386001482|ref|YP_005919781.1| 123 QTGNYTVSIS 132
                                       8999999987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.13
                                       TTS-EE-.SSSEEEEE CS
                               PPC  52 eyiefta.pqaGtYyv 66 
                                         +e++a ++aG Y +
  gi|386001482|ref|YP_005919781.1| 230 GDGEMAAdLSAGRYAL 245
                                       3344555566666655 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 1.2e-08
                                       -EEEEEEEE-TT-EEEEEES-TT...SEEEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEEE.. CS
                               PPC   1 dvDvysfevpagdsltididggti.dldLylldsngtsvaaydansapsgsdeyieftapqaGtYyvaVss 70 
                                       dvD+y  ++++  ++ ++++g    d+ Lyl+d+   +  +yd+ s +++  ++ie   ++aGtYy++V+s
  gi|386001482|ref|YP_005919781.1| 303 DVDYYLLVLEEAMEVVVETSGDDRgDSYLYLYDDL-EEEIDYDDDSGEDSW-SRIE-EELSAGTYYIKVAS 370
                                       8*****************9777644666*******.888888888877776.9***.999*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 3064.14
//
Query:       gi|386001483|ref|YP_005919782.1|  [L=330]
Description: Nucleoside recognition domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.2  15.5     0.0079   16.5   3.1    2.7  2  Gate      Nucleoside recognition


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.1   4.4e-07    0.0079       2      96 ..      20     105 ..      19     175 .. 0.91
   2 !    7.7   4.7   0.00023       4.1       2      96 ..     197     282 ..     196     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.4e-07
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                        k +p ++l++il +++  + +++ri++l +p+ +     l+  a +s+++ f++   + ++l+  y       + g
  gi|386001483|ref|YP_005919782.1|  20 SKSLPPMVLGLILAELIVVYDAAERIAFLAKPITRFSH--LSDAAGASFMMAFFSAASANSMLAGYY-------HDG 87 
                                       67899******************************977..**************9988999999999.......999 PP

                              Gate  79 fdtpksalafllfvllyt 96 
                                       +  +++ +++ l++++  
  gi|386001483|ref|YP_005919782.1|  88 IIEKRELFVASLVNSFPA 105
                                       999999999998888866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00023
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplg.qeldwkatvslltgfaakevvvgtlgtlytsalgellq 77 
                                       ++++++   +++l+++l + ++++ +++ l+ +   l        ++++ ++g++a  +v+g l           ++
  gi|386001483|ref|YP_005919782.1| 197 VRVVKMTTGIMFLVSVLIQVGAFDLLSQQLRGIGGLLPlPAAGISIIAAQFAGYVAAYTVAGGLL----------AA 263
                                       7899999**************************88877445555555566666666666666654..........45 PP

                              Gate  78 gfdtpksalafllfvllyt 96 
                                       g+ + k+++++l+++   t
  gi|386001483|ref|YP_005919782.1| 264 GELSGKDVVVTLMIGNVIT 282
                                       9999999888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2378.84
//
Query:       gi|386001484|ref|YP_005919783.1|  [L=374]
Description: 3-dehydroquinate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.7e-145  482.2   0.6   8.6e-145  482.1   0.6    1.0  1  DHQS      3-dehydroquinate synthase II
  ------ inclusion threshold ------
      0.011   15.8   0.1       0.44   10.7   0.0    2.8  3  OapA      Opacity-associated protein A LysM-like domain
       0.12   11.9   0.1          8    5.9   0.1    2.3  2  Hint      Hint module


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.1   0.6  1.4e-148  8.6e-145       1     352 []       2     374 .]       2     374 .] 0.98

  Alignments for each domain:
  == domain 1  score: 482.1 bits;  conditional E-value: 1.4e-148
                              DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed....davlvgkd........... 62 
                                       ke w++a++++wee k ++t+ale+g+d+v++++ed+e++++lg+i++ ++ ++    d+++vg+            
  gi|386001484|ref|YP_005919783.1|   2 KEKWMMASDGPWEEMKPRITTALESGFDCVVARQEDVERIRRLGDIRIGSFGTErggeDILIVGRGgegdgsvplpe 78 
                                       789********************************************99998655677999999999********** PP

                              DHQS  63 ......dleklkka.kkvaalveikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksae 132
                                             d++ +++a   va +vei+ k++ee+a+e++k++dy++v ++dw+vIPlEn+iA lqg+++kii++vk+ae
  gi|386001484|ref|YP_005919783.1|  79 dlgaslDISLARAAdGVVAGYVEIRGKRYEEFAVELGKSVDYLVVVGTDWKVIPLENMIAGLQGAKVKIISGVKTAE 155
                                       ****9999999988778999********************************************************* PP

                              DHQS 133 eAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvG 209
                                       eA++ + tLEkGadg+ll+t+d +eik++++l+e+a  ++l+L+ a++t+v++vgmgdRvcvDtc++m++geGmLvG
  gi|386001484|ref|YP_005919783.1| 156 EAEVDFATLEKGADGILLDTSDLSEIKRVQKLAEKAGMARLDLSIARITTVRPVGMGDRVCVDTCTMMRPGEGMLVG 232
                                       ***************************************************************************** PP

                              DHQS 210 sssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRP 286
                                       s+s++ fLv+sE++es+Yva+RPFRVNAGavhaYv+v g+kT+YLseLkaGdev++vd++G t++avvGRvKiEkRP
  gi|386001484|ref|YP_005919783.1| 233 SQSKAAFLVQSESEESSYVAARPFRVNAGAVHAYVKV-GEKTRYLSELKAGDEVTIVDAEGGTKTAVVGRVKIEKRP 308
                                       *************************************.*************************************** PP

                              DHQS 287 lllveaeaegkkvstilQnaetirlvtedgkaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                       l+l+eae++g+k+st+lQnaeti+lv+++g +++vt+L++Gdevlv++e kaRHfG++ieE+i+E+
  gi|386001484|ref|YP_005919783.1| 309 LMLIEAEVDGEKISTLLQNAETIKLVGKGGGPKAVTDLQPGDEVLVHFEGKARHFGMSIEESILER 374
                                       ****************************************************************97 PP

>> OapA  Opacity-associated protein A LysM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.89   5.3e+03      52      71 ..     152     171 ..     141     187 .. 0.67
   2 ?   10.7   0.0   7.3e-05      0.44      23      58 ..     259     294 ..     250     312 .. 0.81
   3 ?    1.7   0.0     0.048   2.9e+02      29      66 ..     332     369 ..     323     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.89
                              OapA  52 klnaqgkvdelqlekgaksv 71 
                                       k +++ +vd  +lekga+ +
  gi|386001484|ref|YP_005919783.1| 152 KTAEEAEVDFATLEKGADGI 171
                                       55666667777777666544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.3e-05
                              OapA  23 plsdvnalakveGadkplSnlksGqkvriklnaqgk 58 
                                       +   v+a +kv  + + lS+lk+G++v+i  ++ g+
  gi|386001484|ref|YP_005919783.1| 259 NAGAVHAYVKVGEKTRYLSELKAGDEVTIVDAEGGT 294
                                       566799**********************97666554 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.048
                              OapA  29 alakveGadkplSnlksGqkvriklnaqgkvdelqlek 66 
                                       +l+   G  k++ +l+ G++v ++ + + +   +++e+
  gi|386001484|ref|YP_005919783.1| 332 KLVGKGGGPKAVTDLQPGDEVLVHFEGKARHFGMSIEE 369
                                       5555667889************9999998888888876 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0013         8      20      47 ..     268     294 ..     260     307 .. 0.78
   2 ?    3.6   0.0     0.007        42      22      40 ..     336     354 ..     329     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  20 tvedgeqkslseLepGdkVlavdesgev 47 
                                       +v  ++++ lseL+ Gd+V  vd++g +
  gi|386001484|ref|YP_005919783.1| 268 KVG-EKTRYLSELKAGDEVTIVDAEGGT 294
                                       443.45889**************87754 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.007
                                       XXXXXXXXXXXXXXXXXXX CS
                              Hint  22 edgeqkslseLepGdkVla 40 
                                       ++g+ k++ +L+pGd+Vl 
  gi|386001484|ref|YP_005919783.1| 336 KGGGPKAVTDLQPGDEVLV 354
                                       57889************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2475.34
//
Query:       gi|386001485|ref|YP_005919784.1|  [L=264]
Description: 3-dehydroquinate dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-39  134.9   0.0    6.2e-39  134.6   0.0    1.1  1  DHquinase_I  Type I 3-dehydroquinase


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   3.5e-43   6.2e-39      21     229 .]      69     258 ..      62     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 3.5e-43
                                       T.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-SEEEEE CS
                       DHquinase_I  21 e.kaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgadyvDvE 96 
                                         +aDlvE+RlDl++ +       + l+e+r+ ++lp+i+t r + egg f r+ e+e++e+l +a ++ ad+vDvE
  gi|386001485|ref|YP_005919784.1|  69 GlGADLVEVRLDLIPGD-----GMKILREVRQATTLPIIATNRWAVEGGAF-RGGEDERIEILAEASAW-ADLVDVE 138
                                       358***********755.....46899***9999*****************.9**************98.9****** PP

                                       GG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHH CS
                       DHquinase_I  97 lteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltseak 173
                                       ++ a+    +rl e         I+Syhdf+g p  ee  ++l+ +++ ga i+K+a +++s e+ l+llsl     
  gi|386001485|ref|YP_005919784.1| 139 VM-AE--GRDRLLEMV---DRPAILSYHDFSGVPGIEEAGSILRVAFEAGAGIAKLALTPASLEECLALLSLLL--- 206
                                       *7.33..345888887...6678*************************************************83... PP

                                       HHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHHH CS
                       DHquinase_I 174 eekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelreil 229
                                         +++ p+  + mG+ G+  R l++++Gs++t++ ++++  +apGq+++++lr +l
  gi|386001485|ref|YP_005919784.1| 207 --SAPGPTSLLGMGDVGRHLRALAPIYGSVLTYGYITAP--AAPGQIPVKDLRGVL 258
                                       ..5689*****************************9999..***********9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1833.52
//
Query:       gi|386001486|ref|YP_005919785.1|  [L=809]
Description: Acetyl-CoA decarbonylase/synthase alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-87  294.5   3.8    3.4e-73  247.1   0.0    2.1  2  Prismane  Prismane/CO dehydrogenase family
    1.1e-06   28.7   9.1    1.1e-06   28.7   9.1    3.2  1  Fer4_9    4Fe-4S dicluster domain
    1.6e-06   28.1  20.4      2e-05   24.6  11.2    3.6  3  Fer4_10   4Fe-4S dicluster domain
    1.9e-06   28.7   8.4     0.0025   18.7   0.5    3.5  3  Fer4_16   4Fe-4S double cluster binding domain
    2.7e-06   27.8  13.2     0.0042   17.6   0.8    3.8  3  Fer4_17   4Fe-4S dicluster domain
    2.8e-05   24.5   1.0     0.0023   18.3   0.2    4.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00053   19.7  21.2      0.001   18.8   3.5    3.4  3  Fer4      4Fe-4S binding domain
     0.0014   18.8   7.4     0.0067   16.6   0.5    2.9  2  Fer4_18   4Fe-4S dicluster domain
     0.0025   17.8  26.5      0.023   14.8   4.1    4.2  4  Fer4_2    4Fe-4S binding domain
     0.0081   16.7  13.8     0.0081   16.7  13.8    4.3  4  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.02   14.9   2.8       0.02   14.9   2.8    4.3  4  Fer4_6    4Fe-4S binding domain
        4.8    7.0  17.3        3.1    7.6   9.9    3.0  3  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
        7.9    6.7  24.3       0.45   10.7   1.6    3.6  4  Fer4_21   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   3.6   2.9e-15   3.9e-12       3      55 ..      67     119 ..      65     136 .. 0.90
   2 !  247.1   0.0   2.5e-76   3.4e-73     115     510 ..     142     694 ..     137     695 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.9e-15
                                       E-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   3 CrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladtl 55 
                                       C +C++gpC++t++krG+CG d+++++ r +l+avl+g+ ah+ah+r+l++  
  gi|386001486|ref|YP_005919785.1|  67 CTLCTYGPCDLTGDKRGACGLDQAAQQGRIVLLAVLMGCTAHCAHGRHLYHWT 119
                                       ************************************************95543 PP

  == domain 2  score: 247.1 bits;  conditional E-value: 2.5e-76
                                       HHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          Prismane 115 rslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGtP. 190
                                       r++++++pk+lk+     + vl+y++e+v+++la t++g+e+++ d++skal++G+ld  g e++d +++++++ P 
  gi|386001486|ref|YP_005919785.1| 142 RTITGTKPKTLKEF----GPVLSYVEEQVAQLLACTHTGQEGNYRDFESKALHAGMLDSLGKEVSDMIQIIAYDMPr 214
                                       67888888888888....*********************************************************** PP

                                       ...--EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCC......... CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx......... RF
                          Prismane 191 ...eppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrh......... 254
                                           +pl+e+++g+ldk+k  ++  GH+la ++e + ++e+++l ++++   + g+ccta + +++ +         
  gi|386001486|ref|YP_005919785.1| 215 gdeDAPLVECGMGTLDKEKAILITYGHNLAGSAEAMFYAEDNKLWDKVD---IGGVCCTAIDnTRIGEglgypeein 288
                                       **9888************8778888************************...**********777777********* PP

                                       ........EEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE-.-CTTCH.. CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.. RF
                          Prismane 255 ........lvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhie.eeekad.. 320
                                                ++++G + + +k++ ++++d+++vd++C++++  ++ ++ k +li+t+e+++ g+ +   ++ + +  
  gi|386001486|ref|YP_005919785.1| 289 tkyrmvgtKAKIAGAMGWWRKMVEADVMDCVMVDEQCVYTNALQECQEKKVPLIATNEKIMLGLPDRTnDPVD-Eiv 364
                                       ******************************************999999*************888888732333.133 PP

                                       .................HHHHHHHHHHHCCHCCTTCGG.-..................................... CS
                                       .................xxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                          Prismane 321 .................kdaseiiekAielakareekkve..................................... 343
                                                        k+ +  +++Ai+++++r++++ +                                     
  gi|386001486|ref|YP_005919785.1| 365 ddlvnfrmpgvaiidpiKAGEVGVRTAIAVKPKRADERKKafiteeefkkyaesctychscqfvcpphikigdvvqe 441
                                       45677788888899998999999***********8866667899999999999999998888888888888777777 PP

                                       ...........................HHH........................................HHTTSS- CS
                                       ...........................xxx........................................xxxxxxx RF
                          Prismane 344 ...........................ida........................................iksGtIk 353
                                                                                                             ++ GtI+
  gi|386001486|ref|YP_005919785.1| 442 aakgnleplsstyeicvgcrrceqacpQ-DipilslyayanqeyiknqkfkmragrgpvkdteirrvgapLVLGTIP 517
                                       6666666666666666555555555550.05555556666666666677888888888888888999999******* PP

                                       EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHC...CCTTTTEC...GHHHHSTHCEESEEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 354 gvvlvvGCdnakkgrdyytelakelikrdvlvltaGCakyal...nklglgti...eaaelagegiPrvLdvGsCvd 424
                                       gv++++GC n+++g++  +++a+e++ r  +v t+GC+++++    +++++ti    +  ++g +   + ++GsCv+
  gi|386001486|ref|YP_005919785.1| 518 GVIAIIGCANYPNGTKECYDIAREFVDRGFIVTTTGCMAMDMslyTDADGKTIweqFPGGFDGRN---ICNIGSCVS 591
                                       *****************************************9999********877778899988...********* PP

                                       HHHHHHHHHHHHHHT.......TS.SGGGSSE...EEEECC-..-SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHH CS
                                       xxxxxxxxxxxxxxx.......xx.xxxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 425 nyrivvialklaeal.......gv.dindLpl...aalalew..yeqKAvailltllalGinihlgptlpafgspnv 488
                                       n++i+++a+k+a ++       ++ di+d++l   +a+ ++w  ++qKA++i++++++lG+++++ p+  +++++++
  gi|386001486|ref|YP_005919785.1| 592 NAHIHGAAIKVATIFagrneraNYdDIADYILskvGACGVAWgaMSQKAASIATGFNRLGVPAVVQPHSVMYRRAFL 668
                                       *********************9999*********9****************************************99 PP

                                       HHHHHCH....HHHHHCEEEECHCHH CS
                                       xxxxxxx....xxxxxxxxxxxxxxx RF
                          Prismane 489 lkvlved....fedriggivtveedp 510
                                        ++  ++    +++r g+ v  e++p
  gi|386001486|ref|YP_005919785.1| 669 GRTDKKEdweiIDARDGSRVYCEPAP 694
                                       99887777777777777777777776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   9.1   8.1e-10   1.1e-06       2      49 ..     419     470 ..     418     471 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.1e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                       Ct C++C+ +Cp ++ ++d +++ a+ + +      e C+gC++C++aCp++
  gi|386001486|ref|YP_005919785.1| 419 CTYCHSCQFVCPPHIKIGDVVQEAAKGNLEPLsstyEICVGCRRCEQACPQD 470
                                       *************************998877699**99************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   3.5       1.4     2e+03       8      22 ..      63      76 ..      58     111 .. 0.66
   2 !   24.6  11.2   1.5e-08     2e-05       6      56 .]     416     468 ..     412     468 .. 0.83
   3 !   17.8   1.7     2e-06    0.0027       6      24 ..     454     483 ..     449     500 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                           Fer4_10  8 tCirCgkCvka.CPad 22
                                       C rC+ C+   C  d
  gi|386001486|ref|YP_005919785.1| 63 ICDRCTLCTYGpC--D 76
                                      5888888876555..4 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.5e-08
                           Fer4_10   6 ddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++C+ C  C+ +CP ++    v++++++ + e+ +  +e C gc  C +aCP
  gi|386001486|ref|YP_005919785.1| 416 AESCTYCHSCQFVCPPHIkiGDVVQEAAKGNLEPLSSTYEICVGCRRCEQACP 468
                                       589*************998545555556666677777***************9 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadl...........t 24 
                                        + C++C++C +aCP+d+           +
  gi|386001486|ref|YP_005919785.1| 454 YEICVGCRRCEQACPQDIpilslyayanqE 483
                                       579*************99777664332221 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.4   4.7e+03       2       8 ..      64      70 ..      41      72 .. 0.76
   2 !   18.7   0.5   1.8e-06    0.0025      33      65 ..     398     430 ..     375     432 .. 0.73
   3 !   13.0   0.3   0.00011      0.15       2      16 ..     457     471 ..     456     505 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                           Fer4_16  2 CgtCgkC 8 
                                      C +C+ C
  gi|386001486|ref|YP_005919785.1| 64 CDRCTLC 70
                                      6666666 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.8e-06
                           Fer4_16  33 yntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                        +++ kk ++++ee +k +e +t+C  Cq vCP
  gi|386001486|ref|YP_005919785.1| 398 RADERKKAFITEEEFKKYAESCTYCHSCQFVCP 430
                                       345666777666666666999***********9 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00011
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++C++C ++CP++ 
  gi|386001486|ref|YP_005919785.1| 457 CVGCRRCEQACPQDI 471
                                       ************875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.8       2.8   3.8e+03       2       9 ..      64      71 ..      55      83 .. 0.77
   2 !   17.0   0.3   4.8e-06    0.0066      36      60 ..     409     433 ..     386     434 .. 0.74
   3 !   17.6   0.8     3e-06    0.0042      41      61 .]     452     472 ..     437     472 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                           Fer4_17  2 CiqCgyCl 9 
                                      C +C  C+
  gi|386001486|ref|YP_005919785.1| 64 CDRCTLCT 71
                                      66666664 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.8e-06
                           Fer4_17  36 eaekeekaslCieCgeCerkCPqgl 60 
                                       e+e +++a++C+ C+ C+ +CP ++
  gi|386001486|ref|YP_005919785.1| 409 EEEFKKYAESCTYCHSCQFVCPPHI 433
                                       334458****************997 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 3e-06
                           Fer4_17  41 ekaslCieCgeCerkCPqgld 61 
                                       ++ + C++C++Ce++CPq+++
  gi|386001486|ref|YP_005919785.1| 452 STYEICVGCRRCEQACPQDIP 472
                                       57789*************985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.7e-06    0.0023      44      65 .]     405     433 ..     380     433 .. 0.71
   2 !   13.7   0.0   4.7e-05     0.065       5      65 .]     457     471 ..     439     522 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                            Fer4_8  44 e.......eealwsCttcgaCtevCpvgi 65 
                                       +       +++++sCt c++C+ vCp +i
  gi|386001486|ref|YP_005919785.1| 405 AfiteeefKKYAESCTYCHSCQFVCPPHI 433
                                       12223455899***************886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.7e-05
                            Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       C++C +C++aCp                                              ++i
  gi|386001486|ref|YP_005919785.1| 457 CVGCRRCEQACP----------------------------------------------QDI 471
                                       666666666665..............................................433 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   2.2       5.7   7.9e+03       9      14 ..      65      70 ..      63      71 .. 0.56
   2 !   13.1   1.0   4.8e-05     0.066       5      19 ..     416     430 ..     412     433 .. 0.89
   3 !   18.8   3.5   7.3e-07     0.001       5      22 ..     454     471 ..     453     473 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.7
                                      SS-THH CS
                              Fer4  9 igCGaC 14
                                       +C +C
  gi|386001486|ref|YP_005919785.1| 65 DRCTLC 70
                                      555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.8e-05
                                       TTTSSS-THHHHHST CS
                              Fer4   5 eekCigCGaCvevCP 19 
                                        e C++C  C  vCP
  gi|386001486|ref|YP_005919785.1| 416 AESCTYCHSCQFVCP 430
                                       799************ PP

  == domain 3  score: 18.8 bits;  conditional E-value: 7.3e-07
                                       TTTSSS-THHHHHSTTTE CS
                              Fer4   5 eekCigCGaCvevCPvgA 22 
                                       +e C+gC +C+++CP + 
  gi|386001486|ref|YP_005919785.1| 454 YEICVGCRRCEQACPQDI 471
                                       689************986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   4.8e-06    0.0067      43      82 ..     401     440 ..     391     447 .. 0.76
   2 ?    4.1   1.8     0.036        50      59      77 ..     455     473 ..     439     479 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.8e-06
                           Fer4_18  43 ekkalkekeerkekgagdcidcescvkvcPtgidirkGlq 82 
                                       e+k+   +ee+ +k a  c+ c+sc  vcP +i i + +q
  gi|386001486|ref|YP_005919785.1| 401 ERKKAFITEEEFKKYAESCTYCHSCQFVCPPHIKIGDVVQ 440
                                       333333445556788899*****************98877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.036
                           Fer4_18  59 gdcidcescvkvcPtgidi 77 
                                         c+ c+ c + cP +i i
  gi|386001486|ref|YP_005919785.1| 455 EICVGCRRCEQACPQDIPI 473
                                       56************99977 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.6     0.043        59       9      18 ..      63      72 ..      55      77 .. 0.60
   2 !   12.8   1.6   7.1e-05     0.098       7      21 ..     416     430 ..     410     431 .. 0.89
   3 !   14.8   4.1   1.6e-05     0.023       8      22 .]     455     469 ..     453     469 .. 0.92
   4 ?   -2.4   0.1       4.9   6.8e+03       9      18 ..     583     591 ..     578     592 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.043
                            Fer4_2  9 rCigCgaCvs 18
                                      +C +C  C+ 
  gi|386001486|ref|YP_005919785.1| 63 ICDRCTLCTY 72
                                      5666666653 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.1e-05
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +++C+ C +C+ +CP
  gi|386001486|ref|YP_005919785.1| 416 AESCTYCHSCQFVCP 430
                                       689***********9 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.6e-05
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       ++C+gC+ C +aCP+
  gi|386001486|ref|YP_005919785.1| 455 EICVGCRRCEQACPQ 469
                                       89************6 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.9
                            Fer4_2   9 rCigCgaCvs 18 
                                       +C + g+Cvs
  gi|386001486|ref|YP_005919785.1| 583 IC-NIGSCVS 591
                                       55.5589987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3       1.1   1.5e+03      19      45 ..     306     335 ..     288     337 .. 0.70
   2 !   12.4   2.8   0.00013      0.18      28      49 ..     406     430 ..     388     433 .. 0.67
   3 !   16.7  13.8   5.8e-06    0.0081       1      51 [.     418     470 ..     418     471 .. 0.73
   4 !   12.4   3.6   0.00013      0.18       2      15 ..     457     470 ..     456     493 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                            Fer4_7  19 ldeeenekgtekveidpekClgCga...Cv 45 
                                       ++ + +e+ +++++++ e+C++++a   C+
  gi|386001486|ref|YP_005919785.1| 306 WWRKMVEADVMDCVMVDEQCVYTNAlqeCQ 335
                                       445555556677788888888876555576 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00013
                            Fer4_7  28 t...ekveidpekClgCgaCvavCP 49 
                                       +   e+ +  +e+C++C++C+ vCP
  gi|386001486|ref|YP_005919785.1| 406 FiteEEFKKYAESCTYCHSCQFVCP 430
                                       1333556777899************ PP

  == domain 3  score: 16.7 bits;  conditional E-value: 5.8e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.gt.ekveidpekClgCgaCvavCPtg 51 
                                       +C+ C+ C+ +Cp +    d +++++ g+ e +   +e C+gC++C+++CP +
  gi|386001486|ref|YP_005919785.1| 418 SCTYCHSCQFVCPPHIKIGDVVQEAAkGNlEPLSSTYEICVGCRRCEQACPQD 470
                                       5************76555554433321433455667899************87 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00013
                            Fer4_7   2 CigCgaCvaaCpvk 15 
                                       C+gC++C++aCp++
  gi|386001486|ref|YP_005919785.1| 457 CVGCRRCEQACPQD 470
                                       88888888888865 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   3.7       3.6   4.9e+03       8      16 ..      63      71 ..      61      75 .. 0.78
   2 ?   -1.9   0.2         3   4.2e+03      15      22 ..     105     112 ..     103     113 .. 0.79
   3 ?   -0.1   2.2      0.83   1.1e+03       7      20 ..     417     430 ..     416     435 .. 0.86
   4 ?   14.9   2.8   1.5e-05      0.02       7      20 ..     455     468 ..     453     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                            Fer4_6  8 kCigCgdCv 16
                                       C+ C  C+
  gi|386001486|ref|YP_005919785.1| 63 ICDRCTLCT 71
                                      588888885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                            Fer4_6  15 CvrvCPeg 22 
                                       C+++C +g
  gi|386001486|ref|YP_005919785.1| 105 CTAHCAHG 112
                                       99999886 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.83
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                       ++C+ C  C  vCP
  gi|386001486|ref|YP_005919785.1| 417 ESCTYCHSCQFVCP 430
                                       68999999*****9 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 1.5e-05
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                       + C+gC++C+ +CP
  gi|386001486|ref|YP_005919785.1| 455 EICVGCRRCEQACP 468
                                       78************ PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.1       3.6   4.9e+03      22      33 ..      65      76 ..      63      79 .. 0.87
   2 ?    7.6   9.9    0.0022       3.1      10      56 ..     405     449 ..     396     469 .. 0.75
   3 ?    2.4   1.8     0.092   1.3e+02      24      44 ..     457     475 ..     451     492 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.6
                                      TT----TT-HHH CS
                           Fer4_20 22 sRClqCkkapcv 33
                                      +RC  C+  pc 
  gi|386001486|ref|YP_005919785.1| 65 DRCTLCTYGPCD 76
                                      7*****999995 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                                       ----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHH CS
                           Fer4_20  10 lglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnlee 56 
                                         +teee ++ A+ C +C  + c+  CP +i+i + +++ a+gnle 
  gi|386001486|ref|YP_005919785.1| 405 AFITEEEFKKYAESCTYC--HSCQFVCPPHIKIGDVVQEAAKGNLEP 449
                                       4568889999********..89*********************9764 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.092
                                       ----TT-HHHHCSTT---HHH CS
                           Fer4_20  24 ClqCkkapcvkgCPveidipe 44 
                                       C+ C  + c+++CP +i i +
  gi|386001486|ref|YP_005919785.1| 457 CVGC--RRCEQACPQDIPILS 475
                                       9999..88******9998865 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.6         2   2.8e+03      41      48 ..      64      71 ..      54      79 .. 0.67
   2 ?   -3.4   0.3       8.1   1.1e+04       6      10 ..     323     327 ..     314     347 .. 0.52
   3 ?   10.7   1.6   0.00033      0.45      31      52 ..     409     430 ..     389     436 .. 0.83
   4 ?   10.3  13.1   0.00043      0.59       6      53 ..     417     469 ..     416     473 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2
                           Fer4_21 41 CvGCnlCs 48
                                      C  C+lC+
  gi|386001486|ref|YP_005919785.1| 64 CDRCTLCT 71
                                      66666664 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.1
                           Fer4_21   6 dkCig 10 
                                       ++C+ 
  gi|386001486|ref|YP_005919785.1| 323 EQCVY 327
                                       23332 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00033
                           Fer4_21  31 ktvlkvvedeCvGCnlCssvCP 52 
                                       ++ +k  +++C+ C+ C  vCP
  gi|386001486|ref|YP_005919785.1| 409 EEEFKKYAESCTYCHSCQFVCP 430
                                       55667889************** PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00043
                           Fer4_21   6 dkCigCgkCliaCedtshqai....eidaktvl...kvvedeCvGCnlCssvCPv 53 
                                       ++C  C +C  +C+   h  i    + +ak  l     + + CvGC  C + CP 
  gi|386001486|ref|YP_005919785.1| 417 ESCTYCHSCQFVCPP--HIKIgdvvQEAAKGNLeplSSTYEICVGCRRCEQACPQ 469
                                       68***********95..4444432244444333322556899************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (809 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 5717.78
//
Query:       gi|386001487|ref|YP_005919786.1|  [L=181]
Description: Acetyl-CoA decarbonylase/synthase complex subunit epsilon [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-36  124.5   0.0    3.9e-36  124.3   0.0    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    0.00021   21.1   0.0    0.00055   19.7   0.0    1.7  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3   0.0   4.4e-40   3.9e-36       4     167 ..       8     175 ..       5     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 4.4e-40
                                       XXXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET.....HHHTT CS
                             CO_dh   4 ekiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata.....lkeag 75 
                                       + +Pf+ a+i+++++a++ +   v+  +ikkakrPll+vG ++ ++ +++ k+ +i +  ++++ata     + e+g
  gi|386001487|ref|YP_005919786.1|   8 NAVPFEMAQIPGPEMAKAYNT-AVIGAIIKKAKRPLLVVGAELFEDPVMFDKAIAIGKTGVPIAATAhsikgFVERG 83 
                                       578*****************9.9********************************************9999999999 PP

                                       -G..GGSE-HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEEE-- CS
                             CO_dh  76 lkdyekknklveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvslan 152
                                         +   +  l+ lt+ l  ++++g dg+g+yd+v+f+G+ y  as + s lk+f   i+ ++id+yyh +Ad++++n
  gi|386001487|ref|YP_005919786.1|  84 YTENVTMIGLHPLTNYLRFKDWQGLDGKGQYDVVIFTGIFYKFASAMFSTLKNFNRDIKRVSIDRYYHVNADMTFGN 160
                                       998888889******************************************************************** PP

                                       -GGGHHHHHHHHHHH CS
                             CO_dh 153 lskeeeeylemleel 167
                                       l  + e+y e ++e+
  gi|386001487|ref|YP_005919786.1| 161 LAFDPEKYHEAVDEV 175
                                       *********999997 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.1e-08   0.00055       6     110 ..      33     147 ..      29     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.1e-08
                                       HHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGG.TTSS-TTSTTEEEESGGGS........CHHHHH CS
                      TPP_enzyme_M   6 ellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmg.kgvipedhplylgmlglhg........skaane 73 
                                       +++k+akrp+++vG +   + +  + +  + k+g+P++ t +  kg++++    ++ m+glh         + ++ +
  gi|386001487|ref|YP_005919786.1|  33 AIIKKAKRPLLVVGAELFEDPVMFDKAIAIGKTGVPIAATAHSiKGFVERGYTENVTMIGLHPltnylrfkDWQGLD 109
                                       68****************9988888888899******9999998******************654333332222223 PP

                                       HHHH-SEEEEES-SSSTCCCTT.TTT.TTTTT-EEEEEE CS
                      TPP_enzyme_M  74 aleeaDlvlalGarfddirttg.sep.efapeakiihid 110
                                          + D+v++ G  +++  ++  s   +f+++ k + id
  gi|386001487|ref|YP_005919786.1| 110 GKGQYDVVIFTGIFYKF-ASAMfSTLkNFNRDIKRVSID 147
                                       33347777777755544.444433332444443555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1419.24
//
Query:       gi|386001488|ref|YP_005919787.1|  [L=490]
Description: Acetyl-CoA decarbonylase/synthase complex subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-56  188.7   0.1    9.2e-56  188.0   0.1    1.4  1  CdhC           CO dehydrogenase/acetyl-CoA synthase complex b
  ------ inclusion threshold ------
      0.026   15.2   0.0      0.064   13.9   0.0    1.6  1  RPA_C          Replication protein A C terminal
       0.12   11.7   0.0       0.21   10.9   0.0    1.2  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.0   0.1   1.5e-59   9.2e-56       1     155 []      27     181 ..      27     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 1.5e-59
                              CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkle 77 
                                       i++++sp++eGeriRk d++ve+gg k+kafEl  + +++ev+dgk++v+Gpdi+++ egs++p++++++vaG+ +e
  gi|386001488|ref|YP_005919787.1|  27 IELDMSPMYEGERIRKGDIWVEMGGPKAKAFELSVAGSMNEVQDGKVTVVGPDISAIPEGSTIPFGMIFKVAGELIE 103
                                       6789*********************99************************************************** PP

                              CdhC  78 edlEpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdee 153
                                       +dlE+++ERr+H++l+y++G+mHl+qRd+iw+R + + +++G+ +++++ + +++++k+e+ ++++k+evt++td++
  gi|386001488|ref|YP_005919787.1| 104 KDLESIIERRNHALLSYVHGLMHLNQRDAIWMRAGLDLKKAGVtSFEQVFKNVMNLYKAEM-PFIEKMEVTVLTDPA 179
                                       *******************************************99****************.*************98 PP

                              CdhC 154 kv 155
                                       +v
  gi|386001488|ref|YP_005919787.1| 180 AV 181
                                       76 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.064      48      97 ..     443     489 ..     423     489 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       XHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  48 talaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97 
                                       ++ ++qv+ +i + + ++  + vd i++kl++s+ +  q++++L+neGi+
  gi|386001488|ref|YP_005919787.1| 443 SEYEEQVIAFIEE-TGGD--IDVDAIKAKLNMSEGQFMQVIEYLQNEGIL 489
                                       5566777777777.3333..89**************************85 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.5e-05      0.21      77     130 ..     435     487 ..     426     489 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                                       CHHHHHTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTT CS
                     RNA_pol_Rpc34  77 eAkkktslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskk 130
                                       e  k++  se e+ V ++Iee+G + I+  +ik+kln+ + +  +++ +L  ++
  gi|386001488|ref|YP_005919787.1| 435 EGWKVEDPSEYEEQVIAFIEETGGD-IDVDAIKAKLNMSEGQFMQVIEYLQNEG 487
                                       55677888899999*********98.***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 3088.71
//
Query:       gi|386001489|ref|YP_005919788.1|  [L=250]
Description: CoB-CoM heterodisulfide reductase, subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-05   22.0  17.7      0.005   16.4  15.5    2.7  1  Nitrate_red_gam  Nitrate reductase gamma subunit
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.16   11.8   0.0    1.2  1  HeLo             Prion-inhibition and propagation


Domain annotation for each model (and alignments):
>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  15.5   5.6e-07     0.005      74     209 ..     121     244 ..      79     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-07
                   Nitrate_red_gam  74 ealgvseelyqllalva..GliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldy 148
                                       ++lg+ +e+  + +++a    i+g l+l+G+++ ++RR++ ++vr++tsa D+v+l  ++l +++G+++ ++     
  gi|386001489|ref|YP_005919788.1| 121 NLLGLAHEAEMVKEMMAlpFDIFGYLLLFGATIGVARRIFLREVRSRTSAYDVVLLGGVFLITITGFYAQWM----- 192
                                       45555555555544443114689******************************9999999999988876555..... PP

                   Nitrate_red_gam 149 gseretispwlrslltlqpd.aellaevplifklHvllglllfa.lfPFtrLvHvlsapleYl 209
                                                  r+  +l  d  ++   +p +  +H++l+l+lf+ ++P+++ +H+++ap++ l
  gi|386001489|ref|YP_005919788.1| 193 -----------RGNSFLVGDvFAYPIYAPHFALVHTILALALFVvILPWSKYMHIIAAPMTIL 244
                                       ...........444445555456667788888899999999986268************9876 PP

>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.16       3      57 ..     103     156 ..     102     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                                       HHS---HHHHHHHHHHTTTTEEEBGGGGGGHHHHHHHHHHHHHHHHHHHHHHTTT CS
                              HeLo   3 alGvvslaqlFsgcvkgfellsaarnlgkdyellrlkLdieqlRLlqWgeavgll 57 
                                       al+++s ++lF + ++ f+ll  a++ ++  e + l +di  ++Ll +g ++g++
  gi|386001489|ref|YP_005919788.1| 103 ALAAMSGFALFMDIIEHFNLLGLAHEAEMVKEMMALPFDIFGYLLL-FGATIGVA 156
                                       899*************************************998776.88888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1550.74
//
Query:       gi|386001490|ref|YP_005919789.1|  [L=458]
Description: CoB-CoM heterodisulfide reductase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-23   83.3  11.3    2.6e-12   46.8   0.1    2.9  3  CCG       Cysteine-rich domain
    1.4e-08   35.1   2.8    1.4e-08   35.1   2.8    3.0  3  Fer4_8    4Fe-4S dicluster domain
    2.8e-07   31.0   3.7    2.8e-07   31.0   3.7    3.4  4  Fer4_17   4Fe-4S dicluster domain
    6.2e-05   23.9   3.7    6.2e-05   23.9   3.7    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00025   21.1   7.6    0.00025   21.1   7.6    3.8  4  Fer4_9    4Fe-4S dicluster domain
     0.0014   18.8   1.5        1.6    9.0   0.1    2.8  2  Fer4_18   4Fe-4S dicluster domain
     0.0036   17.9  11.7     0.0036   17.9  11.7    3.6  4  Fer4_7    4Fe-4S dicluster domain
     0.0048   17.0  12.7     0.0048   17.0  12.7    3.8  4  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.017   15.2   9.4       0.84    9.8   0.5    3.7  3  Fer4_21   4Fe-4S dicluster domain
      0.059   14.2  13.5        9.1    7.2   0.1    4.2  4  Fer4_22   4Fe-4S dicluster domain
       0.52   11.4  16.3       0.35   11.9   3.5    3.5  2  Fer4_3    4Fe-4S binding domain
        2.3    8.5  16.8        0.7   10.1   1.4    3.5  3  Fer4_2    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.4       3.4     5e+03      68      82 ..      87     101 ..      76     103 .. 0.69
   2 !   43.1   1.5   2.5e-14   3.7e-11       1      82 [.     168     249 ..     168     252 .. 0.97
   3 !   46.8   0.1   1.7e-15   2.6e-12       1      83 [.     293     386 ..     293     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.4
                               CCG  68 tgadaivtacpgCll 82 
                                       t++ + +t+c+ C +
  gi|386001490|ref|YP_005919789.1|  87 TEDTYYCTTCGVCGT 101
                                       347788999999975 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 2.5e-14
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                       +ayf gC  + ++++++  a  +l++al + +  l ++e+CC ++ +r+g+ +++++ a +nv+++++ g++ ++ a
  gi|386001490|ref|YP_005919789.1| 168 IAYFAGC-TAAYRQQALAVASVRLMNALEIPFCMLgKDEWCCSSALVRTGQRNIMKEHAVHNVDALKDRGVRTVLYA 243
                                       69*****.9******************************************************************** PP

                               CCG  77 cpgCll 82 
                                       c+gC+ 
  gi|386001490|ref|YP_005919789.1| 244 CAGCQR 249
                                       ****85 PP

  == domain 3  score: 46.8 bits;  conditional E-value: 1.7e-15
                               CCG   1 vayfdgChllraa.........ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetae 66 
                                       v+y+d+Ch +r+           +++r +lk ++++++ ++ +  e + CCGaggg++   + la++ ak ++  a+
  gi|386001490|ref|YP_005919789.1| 293 VTYHDPCHNGRHLmhvngrdvaFEAPRDILKSIPGVQFEDMARSrEFQRCCGAGGGVKAGIPdLALDCAKARMGDAQ 369
                                       89******999999******************************************9999777************** PP

                               CCG  67 etgadaivtacpgCllq 83 
                                          ad+i ++cp+C  +
  gi|386001490|ref|YP_005919789.1| 370 LIAADVITSTCPFCRRN 386
                                       **************876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   2.8   9.3e-12   1.4e-08       2      65 .]      24     107 ..      23     107 .. 0.76
   2 ?    0.8   0.6      0.46   6.8e+02      44      55 ..     231     248 ..     198     250 .. 0.58
   3 ?   -1.5   0.0       2.4   3.6e+03      13      24 ..     378     389 ..     364     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.3e-12
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvlee.....................eealwsCttcgaC 57 
                                       l+ C++C+ C++ Cp++  +++++  ++  +++ + +e   ++                      e  ++Cttcg C
  gi|386001490|ref|YP_005919789.1|  24 LDGCTRCQECMKWCPTFDVRQDRPEITPMYKIA-KFRELLGSQhglraklfgpkplnedeinrfTEDTYYCTTCGVC 99 
                                       678****************99555555555555.333333333466677778888888888888999********** PP

                            Fer4_8  58 tevCpvgi 65 
                                        +vC  gi
  gi|386001490|ref|YP_005919789.1| 100 GTVCESGI 107
                                       ****9887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                            Fer4_8  44 e......eealwsCttcg 55 
                                       +      ++ l++C +c+
  gi|386001490|ref|YP_005919789.1| 231 AlkdrgvRTVLYACAGCQ 248
                                       022244578899999998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                            Fer4_8  13 saCpvlrrtkkh 24 
                                       s+Cp++rr  ++
  gi|386001490|ref|YP_005919789.1| 378 STCPFCRRNIMD 389
                                       679998886544 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   3.7   1.9e-10   2.8e-07       2      61 .]      27     108 ..      26     108 .. 0.80
   2 ?    1.3   0.6      0.36   5.3e+02      12      50 ..     207     248 ..     198     251 .. 0.76
   3 ?   -1.3   0.0       2.3   3.4e+03      32      50 ..     328     346 ..     308     347 .. 0.74
   4 ?   -3.1   0.1       8.3   1.2e+04      12      17 ..     380     385 ..     377     401 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.9e-10
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepk.kllraakl...................glleeaeke..ekaslCieCgeCerkC 56 
                                       C++C+ C++ Cp++  ++++p+ +++++++                     l+e+++++  e    C++Cg C ++C
  gi|386001490|ref|YP_005919789.1|  27 CTRCQECMKWCPTFDVRQDRPEiTPMYKIAKfrellgsqhglraklfgpkPLNEDEINRftEDTYYCTTCGVCGTVC 103
                                       ****************999988679999977788898888777777776423333333366899************* PP

                           Fer4_17  57 Pqgld 61 
                                        +g++
  gi|386001490|ref|YP_005919789.1| 104 ESGIN 108
                                       *9985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                           Fer4_17  12 Cpsyeaydnepkkllraaklglleeaeke...ekaslCieCg 50 
                                       C s +  ++ +++++++ +++ +++ +++   ++   C++C+
  gi|386001490|ref|YP_005919789.1| 207 CCSSALVRTGQRNIMKEHAVHNVDALKDRgvrTVLYACAGCQ 248
                                       5555555666788999988888888877677679999*9998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                           Fer4_17  32 glleeaekeekaslCieCg 50 
                                        ++e++ +++++++C++ g
  gi|386001490|ref|YP_005919789.1| 328 VQFEDMARSREFQRCCGAG 346
                                       4678888999999**9865 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.3
                           Fer4_17  12 Cpsyea 17 
                                       Cp++++
  gi|386001490|ref|YP_005919789.1| 380 CPFCRR 385
                                       666665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   3.7   4.1e-08   6.2e-05       2      64 ..      27     103 ..      26     106 .. 0.84
   2 ?   -0.5   0.2       1.7   2.5e+03      52      61 ..     239     248 ..     205     250 .. 0.51

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.1e-08
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.............ntaekkdlaedeekck..kqeaitgCdiCqdv 63 
                                       C++C++C++ CPt  ++++ ++ei +  +i++             +  + k l+ede ++     + +t C++C +v
  gi|386001490|ref|YP_005919789.1|  27 CTRCQECMKWCPTFDVRQD-RPEITPMYKIAKfrellgsqhglraKLFGPKPLNEDEINRFteDTYYCTTCGVCGTV 102
                                       *******************.788888888777888999999999988888888888876552235778********* PP

                           Fer4_16  64 C 64 
                                       C
  gi|386001490|ref|YP_005919789.1| 103 C 103
                                       * PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                           Fer4_16  52 eaitgCdiCq 61 
                                       + ++ C+ Cq
  gi|386001490|ref|YP_005919789.1| 239 TVLYACAGCQ 248
                                       2236666666 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   7.6   1.7e-07   0.00025       2      49 ..      27     106 ..      26     108 .. 0.93
   2 ?   -0.2   0.3      0.79   1.2e+03      33      40 ..     237     248 ..     205     250 .. 0.58
   3 ?   -2.4   0.3       3.8   5.7e+03      35      40 ..     379     384 ..     359     398 .. 0.64
   4 ?   -2.3   0.0       3.5   5.2e+03       9      22 ..     436     449 ..     432     455 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase................................eaCigCgaCveaC 46 
                                       Ct+C++C++ Cp+  v++d+ e +  +++a+                                   C++Cg C  +C
  gi|386001490|ref|YP_005919789.1|  27 CTRCQECMKWCPTFDVRQDRPEITPMYKIAKFrellgsqhglraklfgpkplnedeinrftedtYYCTTCGVCGTVC 103
                                       ***********99999999999999888887799****************************9988*********** PP

                            Fer4_9  47 pkg 49 
                                       ++g
  gi|386001490|ref|YP_005919789.1| 104 ESG 106
                                       998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.79
                            Fer4_9  33 e....eaCigCg 40 
                                             aC gC+
  gi|386001490|ref|YP_005919789.1| 237 VrtvlYACAGCQ 248
                                       355556677775 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.8
                            Fer4_9  35 aCigCg 40 
                                        C +C+
  gi|386001490|ref|YP_005919789.1| 379 TCPFCR 384
                                       344443 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3.5
                            Fer4_9   9 veaCpagvvvedaa 22 
                                       +++C+ ++++++a 
  gi|386001490|ref|YP_005919789.1| 436 EDVCKVETIERKAE 449
                                       45566666665554 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1     0.001       1.6      57      78 ..      23      43 ..       5      46 .. 0.82
   2 !    7.7   0.1    0.0025       3.8      54      76 ..      86     108 ..      71     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                           Fer4_18 57 gagdcidcescvkvcPtgidir 78
                                      +   c+ c+ c+k cPt  d+r
  gi|386001490|ref|YP_005919789.1| 23 ELDGCTRCQECMKWCPT-FDVR 43
                                      5678************9.5777 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                           Fer4_18  54 kekgagdcidcescvkvcPtgid 76 
                                        ++++  c++c++c +vc  gi+
  gi|386001490|ref|YP_005919789.1|  86 FTEDTYYCTTCGVCGTVCESGIN 108
                                       4566778************9996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   4.1     0.001       1.5      33      50 ..      22      39 ..       6      40 .. 0.87
   2 !   17.9  11.7   2.4e-06    0.0036       2      52 .]      27     107 ..      26     107 .. 0.60
   3 ?   -1.4   0.3       2.5   3.7e+03      31      43 ..     237     249 ..     207     254 .. 0.59
   4 ?   -3.2   0.0       9.4   1.4e+04      10      19 ..     437     446 ..     432     451 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                            Fer4_7 33 idpekClgCgaCvavCPt 50
                                      ++ + C+ C++C++ CPt
  gi|386001490|ref|YP_005919789.1| 22 MELDGCTRCQECMKWCPT 39
                                      56789************7 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.4e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..............................gtekveidpekClgCgaCvavC 48 
                                       C+ C+ C++ Cp+  ++ d  e  +                              ++ + + d  +C++Cg+C +vC
  gi|386001490|ref|YP_005919789.1|  27 CTRCQECMKWCPTFDVRQDRPEITPmykiakfrellgsqhglraklfgpkplnedEINRFTEDTYYCTTCGVCGTVC 103
                                       ***********87666665322222222223333333333333333333333322778889999************* PP

                            Fer4_7  49 Ptga 52 
                                        +g+
  gi|386001490|ref|YP_005919789.1| 104 ESGI 107
                                       9885 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.5
                            Fer4_7  31 veidpekClgCga 43 
                                       v+ +   C gC++
  gi|386001490|ref|YP_005919789.1| 237 VRTVLYACAGCQR 249
                                       3455556777764 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 9.4
                            Fer4_7  10 aaCpvkaiel 19 
                                       ++C+v++ie 
  gi|386001490|ref|YP_005919789.1| 437 DVCKVETIER 446
                                       6788887775 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  12.7   3.2e-06    0.0048       5      55 ..      23     103 ..      20     104 .. 0.85
   2 ?    5.7   3.1      0.01        16       7      19 ..      91     103 ..      86     119 .. 0.74
   3 ?   -0.4   0.4      0.84   1.2e+03      32      49 ..     231     248 ..     199     252 .. 0.77
   4 ?   -1.1   1.2       1.4   2.1e+03      30      49 ..     365     384 ..     340     398 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadl.............................tsvgakgeaseeeavrk.kvekCtgcgaC 51 
                                       + d C+rC++C+k CP+                               +  g k+ +++e    + + + Ct+cg C
  gi|386001490|ref|YP_005919789.1|  23 ELDGCTRCQECMKWCPTFDvrqdrpeitpmykiakfrellgsqhglraKLFGPKPLNEDEINRFTeDTYYCTTCGVC 99 
                                       5689*************55************************9999866666666555555554599********* PP

                           Fer4_10  52 veaC 55 
                                         +C
  gi|386001490|ref|YP_005919789.1| 100 GTVC 103
                                       ***9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                           Fer4_10   7 dtCirCgkCvkaC 19 
                                         C+ Cg C ++C
  gi|386001490|ref|YP_005919789.1|  91 YYCTTCGVCGTVC 103
                                       4577777777777 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.84
                           Fer4_10  32 aseeeavrkkvekCtgcg 49 
                                       a ++  vr+++++C gc 
  gi|386001490|ref|YP_005919789.1| 231 ALKDRGVRTVLYACAGCQ 248
                                       556667788889999885 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.4
                           Fer4_10  30 geaseeeavrkkvekCtgcg 49 
                                         + +  a ++  + C++c 
  gi|386001490|ref|YP_005919789.1| 365 MGDAQLIAADVITSTCPFCR 384
                                       55556666777788899984 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00056      0.84      39      54 ..      25      40 ..      16      43 .. 0.80
   2 ?    7.9   0.5    0.0023       3.4      38      51 ..      90     103 ..      78     116 .. 0.69
   3 ?    0.5   0.1      0.46   6.9e+02      23      46 ..     226     249 ..     219     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                           Fer4_21 39 deCvGCnlCssvCPve 54
                                      d C+ C+ C++ CP+ 
  gi|386001490|ref|YP_005919789.1| 25 DGCTRCQECMKWCPTF 40
                                      7899999999999975 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0023
                           Fer4_21  38 edeCvGCnlCssvC 51 
                                       +  C+ C +C +vC
  gi|386001490|ref|YP_005919789.1|  90 TYYCTTCGVCGTVC 103
                                       44677777777777 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.46
                           Fer4_21  23 hqaieidaktvlkvvedeCvGCnl 46 
                                       +  ++  +++ +++v   C GC+ 
  gi|386001490|ref|YP_005919789.1| 226 VHNVDALKDRGVRTVLYACAGCQR 249
                                       555566667777888889****86 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0061       9.1      78      94 ..      23      39 ..       5      59 .. 0.77
   2 ?    7.0   0.7    0.0073        11      78      96 .]      89     107 ..      76     107 .. 0.78
   3 ?    6.1   0.6     0.014        21      39      89 ..     198     251 ..     172     255 .. 0.80
   4 ?   -0.4   0.0       1.4   2.1e+03      34      86 ..     293     346 ..     282     352 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0061
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      +  gC+ C  C+++cp+
  gi|386001490|ref|YP_005919789.1| 23 ELDGCTRCQECMKWCPT 39
                                      55667777777777764 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0073
                           Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                       +++ C+ Cg C ++c ++i
  gi|386001490|ref|YP_005919789.1|  89 DTYYCTTCGVCGTVCESGI 107
                                       6788999999999998765 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.014
                           Fer4_22  39 sClleeftkvaggenvrkekkerlrqrllhklsefkekf...gesgCvGCgRCi 89 
                                        C+l + +   +++ vr+ +++ ++++ +h +  +k++      ++C GC R  
  gi|386001490|ref|YP_005919789.1| 198 FCMLGKDEWCCSSALVRTGQRNIMKEHAVHNVDALKDRGvrtVLYACAGCQRTA 251
                                       57777777778888899999************9999987444678999999976 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.4
                           Fer4_22  34 vrvwdsClleeftkvaggenvr.kekkerlrqrllhklsefkekfgesgCvGCg 86 
                                       v  +d C+  ++ ++ +g++v  +  ++ l++    ++++++++ + + C+G g
  gi|386001490|ref|YP_005919789.1| 293 VTYHDPCHNGRHLMHVNGRDVAfEAPRDILKSIPGVQFEDMARSREFQRCCGAG 346
                                       556777888777766655554415556666777778899999999999999987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.5   0.00023      0.35       1      13 [.      27      39 ..      27      41 .. 0.95
   2 ?    3.2   5.1      0.14   2.1e+02       1      14 [.      93     106 ..      93     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      Ct C+ C+++CP+
  gi|386001490|ref|YP_005919789.1| 27 CTRCQECMKWCPT 39
                                      ************6 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct Cg C  vC +g
  gi|386001490|ref|YP_005919789.1|  93 CTTCGVCGTVCESG 106
                                       ***********665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4   0.00047       0.7       7      22 .]      24      39 ..      21      39 .. 0.89
   2 ?    6.0   3.4    0.0098        15       7      20 ..      90     103 ..      85     105 .. 0.84
   3 ?   -2.1   0.1       3.7   5.5e+03       9      14 ..     243     248 ..     240     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00047
                            Fer4_2  7 tdrCigCgaCvsaCPa 22
                                       d C++C  C + CP+
  gi|386001490|ref|YP_005919789.1| 24 LDGCTRCQECMKWCPT 39
                                      577************7 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0098
                            Fer4_2   7 tdrCigCgaCvsaC 20 
                                       t  C+ Cg C ++C
  gi|386001490|ref|YP_005919789.1|  90 TYYCTTCGVCGTVC 103
                                       556*********** PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                            Fer4_2   9 rCigCg 14 
                                       +C gC 
  gi|386001490|ref|YP_005919789.1| 243 ACAGCQ 248
                                       699995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 3131.47
//
Query:       gi|386001491|ref|YP_005919790.1|  [L=218]
Description: Iron sulfur flavoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-29  100.6   0.0    9.9e-29  100.1   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
      9e-15   54.9   0.0    1.4e-14   54.3   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.0   1.1e-32   9.9e-29       1     145 [.       1     147 [.       1     153 [. 0.92

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.1e-32
                                       -EEEEEES--S.TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHT.CGGSHHHHHHHHHHHH-S CS
                           FMN_red   1 mkilvisGSlr.kgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlese.gqtsddvaellekiaaad 74 
                                       mki++i++S+r ++s t +l+++++e ++e gae+el+dl +l i+ c++c   + +  ++ +dd+ el++ki  +d
  gi|386001491|ref|YP_005919790.1|   1 MKIIGINASPRgSKSQTLRLVKAVLEGAREGGAETELVDLCKLdIKYCNACATCFATGrCVYDDDFDELYQKILGCD 77 
                                       9**********889**************999*****************445444433359***************** PP

                                       CEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEEC CS
                           FMN_red  75 aliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpr 145
                                       +l++++P Y+ ++++++K++ Dr+    + + l+gK++  va++g+ + g +++  l ++l  +ga vv++
  gi|386001491|ref|YP_005919790.1|  78 GLVLGSPNYFQTVTAQMKTLVDRMADAVHCQLLTGKYGCSVATAGSPASG-EVTGYLNKILIGFGANVVGE 147
                                       ************************999999**************998877.8999999999999**99998 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   1.5e-18   1.4e-14       1     144 [.       1     130 [.       1     147 [. 0.85

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.5e-18
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT.C.HHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek.p.adveseq.iek 74 
                                       mki  ina+pr++ks++ +l +a++e++++ g +e + +dL ++ +  +++ +++     +++ + +d + ++  +k
  gi|386001491|ref|YP_005919790.1|   1 MKIIGINASPRGSKSQTLRLVKAVLEGAREGG-AETELVDLCKLDIKYCNA-CAT---CFATGrCvYDDDFDElYQK 72 
                                       9*******************************.9*********85555443.232...3444447799999999*** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTT CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpeesyqer 144
                                       +l +d +vl++P ++ +v a++K  +Dr + a +++           +L+gk    ++t+G+p +s +  
  gi|386001491|ref|YP_005919790.1|  73 ILGCDGLVLGSPNYFQTVTAQMKTLVDRMADAVHCQ-----------LLTGKYGCSVATAGSP-ASGEVT 130
                                       ****************************98887755...........8999999999999999.555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1665.97
//
Query:       gi|386001492|ref|YP_005919791.1|  [L=111]
Description: hypothetical protein Mhar_0795 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 929.90
//
Query:       gi|386001493|ref|YP_005919792.1|  [L=82]
Description: transglycosylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-10   40.0  12.5    3.6e-10   40.0  12.5    2.2  2  Transgly_assoc   Transglycosylase associated protein
  ------ inclusion threshold ------
       0.17   10.7   3.6       0.22   10.3   3.6    1.1  1  DUF2254          Predicted membrane protein (DUF2254)
        1.6    8.8  21.8        1.4    9.0  12.1    2.2  2  Gly-zipper_Omp   Glycine zipper
        3.1    7.6   9.7        4.2    7.2   0.0    2.8  3  DUF4118          Domain of unknown function (DUF4118)
        4.8    7.3   8.7         21    5.3   0.1    3.0  3  DUF4235          Protein of unknown function (DUF4235)
        5.6    7.5  14.2       0.71   10.4   8.7    2.0  2  SNARE_assoc      SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> Transgly_assoc  Transglycosylase associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   4.0     0.073   2.2e+02       2      28 ..       9      31 ..       8      35 .. 0.51
   2 !   40.0  12.5   1.2e-13   3.6e-10       1      48 [.      33      79 ..      33      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.073
                    Transgly_assoc  2 ilGivGAfvGgfllgllgigvgggela 28
                                      i+Gi+  +++g + +  g+    g ++
  gi|386001493|ref|YP_005919792.1|  9 IIGIIAGWLAGRITRGKGF----GLVG 31
                                      6666666666666443333....4444 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 1.2e-13
                    Transgly_assoc  1 IilGivGAfvGgfllgllgigvgggelaslivaiiGAiILLfivrlvr 48
                                      +++G++GAfvGgfl+gl+g+  ++g+++s+i+a++GA+ ++ + r ++
  gi|386001493|ref|YP_005919792.1| 33 MVMGVIGAFVGGFLFGLVGL-SAHGFVGSIIAATVGAVAFIYLTRYLK 79
                                      69******************.*****************9999988776 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.6   7.3e-05      0.22      92     144 ..      34      77 ..      31      82 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.3e-05
                           DUF2254  92 tqvvLGtfigtfvYsllvlrairteeevpqlsvlvalllaivsvllLiyFihh 144
                                       +  v+G+f+g+f++ l++l a +         ++ +++ a v ++++iy  + 
  gi|386001493|ref|YP_005919792.1|  34 VMGVIGAFVGGFLFGLVGLSAHG---------FVGSIIAATVGAVAFIYLTRY 77 
                                       5679*****************99.........778888888888888886555 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.7    0.0049        15       5      39 ..      10      43 ..       8      44 .. 0.75
   2 ?    9.0  12.1   0.00047       1.4       3      33 ..      36      69 ..      34      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0049
                    Gly-zipper_Omp  5 iGAaaGaliGgavggrgtGaliGAavGaavGgliG 39
                                      iG +aG+l G ++ g g G l+G  v +++G+ +G
  gi|386001493|ref|YP_005919792.1| 10 IGIIAGWLAGRITRGKGFG-LVGNMVMGVIGAFVG 43
                                      7889*********988777.777666666666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00047
                    Gly-zipper_Omp  3 aaiGAaaGaliGgavg...grgtGaliGAavGaa 33
                                      ++iGA++G+ + g vg   +  +G++i+A vGa+
  gi|386001493|ref|YP_005919792.1| 36 GVIGAFVGGFLFGLVGlsaHGFVGSIIAATVGAV 69
                                      589************9655445666666666666 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0014       4.2      78      99 ..       2      23 ..       1      25 [. 0.89
   2 ?    1.8   0.6     0.067     2e+02      40      58 ..      29      47 ..      26      52 .. 0.76
   3 ?    2.3   3.4     0.048   1.4e+02      34      61 ..      48      74 ..      45      77 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                           DUF4118 78 ltlvvflvvallvstlvararr 99
                                      ++++ fl++++++++l+ r+ r
  gi|386001493|ref|YP_005919792.1|  2 FSWLWFLIIGIIAGWLAGRITR 23
                                      67899*************9876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.067
                           DUF4118 40 llgglgpgllaallsvllf 58
                                      l+g +++g++ a+++ +lf
  gi|386001493|ref|YP_005919792.1| 29 LVGNMVMGVIGAFVGGFLF 47
                                      6778888888888888877 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.048
                           DUF4118 34 avllvallgglgpgllaallsvllfnyf 61
                                      + +  + + g++ +++aa +++++f y+
  gi|386001493|ref|YP_005919792.1| 48 GLVGLSAH-GFVGSIIAATVGAVAFIYL 74
                                      55555444.6777788888888888775 PP

>> DUF4235  Protein of unknown function (DUF4235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0069        21       6      20 ..       8      22 ..       5      30 .. 0.86
   2 ?    4.6   1.0     0.011        33       5      22 ..      32      49 ..      29      50 .. 0.87
   3 ?    1.8   0.1     0.087   2.6e+02       5      20 ..      56      71 ..      52      80 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0069
                           DUF4235  6 lvlglvaGavagkaf 20
                                      l++g++aG++ag++ 
  gi|386001493|ref|YP_005919792.1|  8 LIIGIIAGWLAGRIT 22
                                      5789*******9986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                           DUF4235  5 glvlglvaGavagkafaa 22
                                      ++v+g+++++v+g +f  
  gi|386001493|ref|YP_005919792.1| 32 NMVMGVIGAFVGGFLFGL 49
                                      599**********99976 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.087
                           DUF4235  5 glvlglvaGavagkaf 20
                                      g+v +++a+ v+  af
  gi|386001493|ref|YP_005919792.1| 56 GFVGSIIAATVGAVAF 71
                                      4555555555555444 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   3.1      0.16   4.9e+02      13      30 ..      26      43 ..       1      45 [. 0.58
   2 ?   10.4   8.7   0.00024      0.71       7      42 ..      40      79 ..      31      82 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                       SNARE_assoc 13 lfglllgtlvtslgallG 30
                                       fgl+  +++ ++ga++G
  gi|386001493|ref|YP_005919792.1| 26 GFGLVGNMVMGVIGAFVG 43
                                      235555777777777777 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00024
                       SNARE_assoc  7 lvaaGvlfglll....gtlvtslgallGaslayllgrylg 42
                                      ++++G+lfgl+     g++ ++++a++Ga+   +l ryl 
  gi|386001493|ref|YP_005919792.1| 40 AFVGGFLFGLVGlsahGFVGSIIAATVGAVAFIYLTRYLK 79
                                      589999999999999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 675.34
//
Query:       gi|386001494|ref|YP_005919793.1|  [L=118]
Description: hypothetical protein Mhar_0797 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 994.41
//
Query:       gi|386001495|ref|YP_005919794.1|  [L=445]
Description: Putative Tungsten formylmethanofuran dehydrogenase, subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-32  110.4   0.0    1.3e-31  109.4   0.0    1.6  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
    4.8e-14   52.1   0.0    1.1e-13   50.9   0.0    1.7  1  PadR          Transcriptional regulator PadR-like family
    1.6e-06   27.9   2.2    3.6e-06   26.8   2.2    1.6  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
    0.00059   20.0   0.0     0.0014   18.7   0.0    1.6  1  FUR           Ferric uptake regulator family
     0.0047   17.0   0.3      0.011   15.8   0.3    1.6  1  DUF2129       Uncharacterized protein conserved in bacteria (
  ------ inclusion threshold ------
      0.043   13.6   0.0      0.072   12.8   0.0    1.3  1  DUF4364       Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   4.4e-35   1.3e-31       1     131 [.     236     379 ..     236     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 4.4e-35
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT..SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg..deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkk 75 
                                       +HGH+Cpg +lG++++ + l++lg++  ++   e+l+a+ve+++C++D++q++ gctlG+++l+++d+g+ a+tf  
  gi|386001495|ref|YP_005919794.1| 236 IHGHFCPGSALGVMASAYGLNRLGMESISSdgLENLMAVVEINACFADGVQAVSGCTLGNNALVYRDLGRLAVTFAV 312
                                       5***********************988777999******************************************** PP

                                       TTT-EEEEEEE-...........CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  76 rktgkavrlklk...........eelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                       r++ ++vr+++            +e+  l+ek++k++a ++k+ + ++e+ +ea+ +++++p eelf
  gi|386001495|ref|YP_005919794.1| 313 RGRDTGVRVRVLpdfrekvaeaaPEFYPLMEKVIKDRAGDKKDAASFRETGREAAFALIELPFEELF 379
                                       *7777777777777************************9999************************9 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   3.8e-17   1.1e-13       2      74 ..      72     137 ..      71     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.8e-17
                                       HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR   2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74 
                                       L+ ++e++  Gy+i+k++e l+ g +++s Gs+Yp+Lk++e+eg+++++ ++      + +Y lT+ G++ +a
  gi|386001495|ref|YP_005919794.1|  72 LHFMKEGEVSGYDIMKKVESLT-G-EKPSTGSVYPLLKKMEREGWISGRTKD-----GKTCYSLTEVGKEHVA 137
                                       8999*****************5.6.7***********************998.....699*********9875 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   2.2   1.2e-09   3.6e-06       3      36 .]     395     431 ..     393     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                      zf-dskA_traR   3 ygs..CeeCGEpIpeaRlral.PgarlCveCqekaer 36 
                                       ++s  C +CGE+I+  ++ a  +g+ lC++C+++++r
  gi|386001495|ref|YP_005919794.1| 395 TESviCPGCGEMIMATKVIAEgDGRGLCFSCAGGEYR 431
                                       55567************888867***********997 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.7e-07    0.0014      27      95 ..      83     153 ..      67     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHH.HTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS..SSSEEEEEETTT--EEEE--H CS
                               FUR  27 eevykelk.eedpeislaTVYrtLklleeaglvkelefedgesryelak..kehhdhlicekCgkviefkdd 95 
                                        +++k+++  ++++ s  +VY  Lk +e++g ++  + +dg++ y l++  keh + + + kCg ++++ + 
  gi|386001495|ref|YP_005919794.1|  83 YDIMKKVEsLTGEKPSTGSVYPLLKKMEREGWISGRT-KDGKTCYSLTEvgKEHVAQIKEAKCGFIKNIYQS 153
                                       57777777446788999****************9865.55********998899999*********999765 PP

>> DUF2129  Uncharacterized protein conserved in bacteria (DUF2129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   3.6e-06     0.011      24      64 ..      44      84 ..      30      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-06
                           DUF2129 24 hYvSkkmkYvvlYvneedveeiveklkklkfVkkVerSerp 64
                                       Y Skk  Y+  Yv+++ + + + k+++l+f k+ e+S ++
  gi|386001495|ref|YP_005919794.1| 44 EYQSKKYMYLHRYVDADIMAAGILKMMTLHFMKEGEVSGYD 84
                                      7********************************99999766 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05     0.072      39      75 ..     105     141 ..     101     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlelfen 75 
                                        l++++ +g i+ ++k++kt+y++Te Gke + ++++
  gi|386001495|ref|YP_005919794.1| 105 LLKKMEREGWISGRTKDGKTCYSLTEVGKEHVAQIKE 141
                                       6899**************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2886.86
//
Query:       gi|386001496|ref|YP_005919795.1|  [L=144]
Description: Methyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-14   53.9   0.0    2.9e-14   53.5   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
      2e-12   47.2   0.0    2.4e-12   46.9   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.9e-11   44.5   0.0    2.9e-11   43.9   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    9.1e-11   41.5   0.0    1.1e-10   41.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.1e-06   27.8   0.0    4.2e-06   27.4   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    1.7e-05   24.8   0.0    1.8e-05   24.7   0.0    1.1  1  Methyltransf_8   Hypothetical methyltransferase
    0.00075   18.9   0.0    0.00092   18.6   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.064   13.8   0.0       0.12   13.0   0.0    1.4  1  POTRA            Surface antigen variable number repeat


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.3e-17   2.9e-14      19      96 .]      11      93 ..       2      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.3e-17
                                      SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.TSS-TT-EEEEEEES-CCC-...CCHHHHHHHHHHHEEEEE CS
                   Methyltransf_11 19 arvvgvDlskemlklakekaseegl.kvefvvadaek.lpfednsfDlvvssevlhhv...edpekalkeiaRvLkpgG 92
                                      + v+ +D ++ +++   eka+ +g+ +++ vv+d+++ lp+ d+s+Dl+++s vlh +   +   +++ ei+RvLkpgG
  gi|386001496|ref|YP_005919795.1| 11 GAVYSLDRWQDVIDDLAEKARSRGFrNIRAVVSDISEhLPVDDESVDLCFISTVLHSLdlaDVETSLFGEIRRVLKPGG 89
                                      589**********9999*******999********9658*******************996677889************ PP

                                      EEEE CS
                   Methyltransf_11 93 llvi 96
                                      +++i
  gi|386001496|ref|YP_005919795.1| 90 RVAI 93
                                      9875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0     1e-15   2.4e-12      25     119 ..       7     103 ..       2     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1e-15
                   Methyltransf_31  25 lgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevl...naladpdkileei 97 
                                       +g+ + v+++D+ +++i    e+a++ g+ n++  ++di e l+  + de++Dl +   vl   ++     + ++ei
  gi|386001496|ref|YP_005919795.1|   7 VGDSGAVYSLDRWQDVIDDLAEKARSRGFRNIRAVVSDISEhLP--VDDESVDLCFISTVLhslDLADVETSLFGEI 81 
                                       688899**************************************..99*********999977333334456678** PP

                   Methyltransf_31  98 ervlkpggilliedprllaelp 119
                                        rvlkpgg+++i +++ ++++ 
  gi|386001496|ref|YP_005919795.1|  82 RRVLKPGGRVAIIECKKEEQQF 103
                                       ****************666555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.3e-14   2.9e-11      21      97 .]      10      89 ..       2      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.3e-14
                                      SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSSSTTTEEEEEEESTGGGSSHHHHHH.HHHHHHHHEEEE CS
                   Methyltransf_25 21 kakvtgvDiseemleaareraeeegl.nvefvqgda.edlpfedgsfDlvvssgalhhlsdedlek.alkeiarvLkpg 96
                                      ++ v+ +D  ++ ++  +e+a+++g+ n++ v+ d+ e+lp +d+s+Dl+++s +lh l+ +d+e+ ++ ei+rvLkpg
  gi|386001496|ref|YP_005919795.1| 10 SGAVYSLDRWQDVIDDLAEKARSRGFrNIRAVVSDIsEHLPVDDESVDLCFISTVLHSLDLADVETsLFGEIRRVLKPG 88
                                      67899*******************************777*************988***99999874399********** PP

                                      E CS
                   Methyltransf_25 97 G 97
                                      G
  gi|386001496|ref|YP_005919795.1| 89 G 89
                                      9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0     5e-14   1.1e-10      65     158 ..       3     100 ..       1     108 [. 0.89

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5e-14
                                       HHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--.TTT-TTS-T-EEEEEEES-GG..G-S-HHHHH.H CS
                   Ubie_methyltran  65 lsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan.aeeLpfeddsfDvvtvsfGlr..nvtDklkaL.k 137
                                        s+ vg++g v  lD  +++++   +k++ +g+ ni+ ++++ +e+Lp +d+s D+  +s  l   +++D +++L  
  gi|386001496|ref|YP_005919795.1|   3 ASEIVGDSGAVYSLDRWQDVIDDLAEKARSRGFRNIRAVVSDiSEHLPVDDESVDLCFISTVLHslDLADVETSLfG 79 
                                       57889********************************999974789***********999999833578*9999846 PP

                                       HHHHHEEEEEEEEEEEE---- CS
                   Ubie_methyltran 138 eayrvlkpGGrlvvlefskve 158
                                       e++rvlkpGGr+ ++e  k e
  gi|386001496|ref|YP_005919795.1|  80 EIRRVLKPGGRVAIIECKKEE 100
                                       9***************98866 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.9e-09   4.2e-06      23      99 .]      13      91 ..       3      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                   Methyltransf_12 23 ytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnvlhhl..kdir.evldnirklLkpg 96
                                      ++ +D  +++i+d +ek ++r+     n++  + d++++ +   +s+Dl ++s vlh l  +d++ +++ +ir++Lkpg
  gi|386001496|ref|YP_005919795.1| 13 VYSLDRWQDVIDDLAEKARSRGF---RNIRAVVSDISEHLPVddESVDLCFISTVLHSLdlADVEtSLFGEIRRVLKPG 88
                                      66778888899888888888886...5566666666655555668****************999979999********* PP

                   Methyltransf_12 97 Grl 99
                                      Gr+
  gi|386001496|ref|YP_005919795.1| 89 GRV 91
                                      *85 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   8.2e-09   1.8e-05     107     161 ..      39      98 ..      30     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.2e-09
                                       TEEES-T.TS-S--TT-EEEEEEES---SS-HHH....HHHHHHHHEEEEEEEEEEEEGG CS
                    Methyltransf_8 107 rvvacdl.akvPledesvdvavfclslmgtnlad....flkeanrvlkvGGllkvaevks 161
                                       r v+ d+  ++P++desvd+  +   l + +lad       e++rvlk+GG + + e k 
  gi|386001496|ref|YP_005919795.1|  39 RAVVSDIsEHLPVDDESVDLCFISTVLHSLDLADvetsLFGEIRRVLKPGGRVAIIECKK 98 
                                       6678899779*********9988777766666541112568**************99875 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.1e-07   0.00092     111     173 ..      36     102 ..      19     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-07
                                       TTEEEEES-TTTS---....--SEEEEESSGGGS-HHHHH.HHHHHHHHH--TT-EEEEEE----TTS CS
                    Methyltransf_2 111 ervefvgGdffkdslP....eaDaillkrvlhDwsdekcv.klLkrvkkalpagGkvivveavlgadp 173
                                       ++++ v  d+  ++lP    + D+ +++ vlh  + +++   l  ++++ l++gG+v ++e+  ++++
  gi|386001496|ref|YP_005919795.1|  36 RNIRAVVSDIS-EHLPvddeSVDLCFISTVLHSLDLADVEtSLFGEIRRVLKPGGRVAIIECKKEEQQ 102
                                       56677777777.77886554579*********9998888625899*****************887765 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.3e-05      0.12      28      69 ..      11      57 ..       4      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                                      TSBHCHHHHHHHHHHHHHHHHCTT-EE.EEEEEE.....HSSTTSEE CS
                             POTRA 28 gdvynpekleadkealksryanlGyfdasVqvel.....peddedkn 69
                                      g vy+ +++++ +++l+++ +++G+ + + +v+      p dde ++
  gi|386001496|ref|YP_005919795.1| 11 GAVYSLDRWQDVIDDLAEKARSRGFRNIRAVVSDisehlPVDDESVD 57
                                      89***********************9988866555536655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1051.48
//
Query:       gi|386001497|ref|YP_005919796.1|  [L=199]
Description: hypothetical protein Mhar_0800 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-26   92.3   0.0    3.6e-26   91.7   0.0    1.2  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0     2e-30   3.6e-26       5     117 ..      60     171 ..      57     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 2e-30
                                       SGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E..-TT-.SS-E.EGGGS--S-SSS- CS
                              TrmO   5 qpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvr..pprlggnervGvfatRsphRpnp 79 
                                       q + +++a +ei++++++  +  l+g+ee+shl++l++ h+  e++ +++v+  p   ++  +vG+f+t sp Rpnp
  gi|386001497|ref|YP_005919796.1|  60 QVREVRQAISEIVIDETL--TGILDGIEEYSHLVVLYWAHKVPEEG-RSLVKvhPMGRKDIPEVGIFSTCSPARPNP 133
                                       6677889999******99..99******************997777.6666631333345589************** PP

                                       EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HH CS
                              TrmO  80 iglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpy 117
                                       +  +vv+l  ++gnvlev+g+D++dg+pv+DiKPYv++
  gi|386001497|ref|YP_005919796.1| 134 VLTTVVRLCGLRGNVLEVAGLDAVDGSPVVDIKPYVKD 171
                                       ***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1536.09
//
Query:       gi|386001498|ref|YP_005919797.1|  [L=516]
Description: Extracellular solute-binding protein, family 5 [Methanosaeta harundinacea 6Ac]
Scores for 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-76  258.4   0.0    1.4e-76  257.9   0.0    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.9   0.0   7.9e-81   1.4e-76       3     363 ..      81     418 ..      80     431 .. 0.93

  Alignments for each domain:
  == domain 1  score: 257.9 bits;  conditional E-value: 7.9e-81
                                       EESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEE CS
                         SBP_bac_5   3 vpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvr 79 
                                       vpaLAes we ++   ++ f+LR+gv+++DG+p+ A+Dvvf+ e+ ++++++   +  +      +++e+vddy+vr
  gi|386001498|ref|YP_005919797.1|  81 VPALAES-WE-MEGDDVFLFRLREGVTWHDGEPFGADDVVFTVEYNKEHPYPLVDNGII------DRAEKVDDYKVR 149
                                       7******.57.888889**********************************99997765......8*********** PP

                                       EEESSETTTTTTHCHHHHHHHGC.CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSSE CS
                         SBP_bac_5  80 ftlkkpnalfltllaavpasiak.kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkldr 154
                                       ++l++p+a+fl  +a + + +++  +++ +d ++  ++e+++gtGPY+l+++++ q +  +++ +dY+  g+p++++
  gi|386001498|ref|YP_005919797.1| 150 IYLSEPYAPFLDQVAGTLPILPEhIWKDVSDPTSFLEDEALIGTGPYTLADYDKVQgTYQYRAYDDYY-LGAPRVKE 225
                                       *******************999966666677777788999**************775788*******9.******** PP

                                       EEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS CS
                         SBP_bac_5 155 iefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAi 231
                                       i++  i +s+ +aa+l +G++  +++++p++i+ql   + l++      ++v+ l++N++k+p++dkr+RqAl+yAi
  gi|386001498|ref|YP_005919797.1| 226 IRYVKI-SSAIAAASLMQGDV-EAVDIQPGMIDQLSGFEILEM---PEHASVYKLMINHQKEPMSDKRFRQALAYAI 297
                                       ******.**************.8889*****************...999999************************* PP

                                       -HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTS CS
                         SBP_bac_5 232 Dreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgs 307
                                       Dr+e+v++v +gy+ ++    +pp  +++++e++  y+ +dp+ A++lL++ Gy +            + ll+++g+
  gi|386001498|ref|YP_005919797.1| 298 DRDELVEIVVQGYGLAGSPGfIPPDNDWYNPEMEGLYP-HDPARAEELLEDMGYGGET----------VELLINGGD 363
                                       **************8887766*************9885.7****************96..........999999999 PP

                                       HHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTH CS
                         SBP_bac_5 308 paekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpd 363
                                       + + +i eli+++l+++Gi v+++++d+ +t +++v+ ++fd+ + + g+  +dp+
  gi|386001498|ref|YP_005919797.1| 364 TRAGRIGELIKEDLEAVGIGVDLRAMDS-KTIDSKVQGWEFDLTVNSHGGLIGDPS 418
                                       9999************************.******************999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 4277.64
//
Query:       gi|386001499|ref|YP_005919798.1|  [L=389]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-23   81.6   0.0    9.1e-23   81.1   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.072   12.2   0.0        0.1   11.6   0.0    1.2  1  MCR_C         Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0     1e-26   9.1e-23      44     236 ..     117     324 ..      50     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1e-26
                                       SBESSSB-HHHHHHH--SEEEE-GGG.......GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHHHHHTT-H CS
                      Peripla_BP_2  44 vgadgeidvEklaalkPDlvilskgl....gltdedeellksgiptvivessntg.....eslkeqiralgellgle 111
                                        g +g+++vE++a l PDl+il   +    ++++  e  ++++iptv+  +         + ++e++r lge+++++
  gi|386001499|ref|YP_005919798.1| 117 GGPYGTVNVETIASLEPDLLILRDLGnddeAVQKFLESMEQLNIPTVVLKYPDCYddidvSTIYEEVRLLGEVFDRQ 193
                                       6789*****************988887777777888999*************98899******************** PP

                                       HHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE........EEEE-TTSTTTHHHHT.S--EESTTT--ST CS
                      Peripla_BP_2 112 deaeklvaeidsklaaaksaidse..kpkpvlvfggade......ggyvvagsnsyigdllda.lgieniaaeskks 179
                                       +eae +v ++d  ++ ++++++    +++p +++ ga++      g  + +g+ +  + +l++ ++++n+++     
  gi|386001499|ref|YP_005919798.1| 194 EEAERIVDHMDAQVQLIRERTADVdeDETPRVLYFGAPSqaadsgGVGYAFGTETIESIFLEDiVNAKNAYDG---T 267
                                       **********************997766666666666667888888888888888888888877888888665...6 PP

                                       T-EEE-HHHHHHH--SEEEEEEH...HHHT-S--HHHHT-S.HHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 180 eyeeisaEqilasdpdvifvsgr...aeadnktgleflken.pllaelpAvkngrVyalds 236
                                       + + is E++la dpdvi+ s+    +      +    +e+   +++l A k+g+Vy l +
  gi|386001499|ref|YP_005919798.1| 268 GTDIISTEHLLALDPDVIILSTYsgyH----PPREMYEAERfGKVQDLRALKEGKVYSLSA 324
                                       9**********************4442....333222222234457889********9865 PP

>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.2e-05       0.1     135     219 ..     140     220 ..     115     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                             MCR_C 135 vlGnfkdCikkkkeklfedievPvvvtggPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldk 211
                                        lGn ++ ++k   + +e++++P vv   P+  +  +v+++ + v  lG +  r  ++e i  +d++  +v +++ +
  gi|386001499|ref|YP_005919798.1| 140 DLGNDDEAVQK-FLESMEQLNIPTVVLKYPDCYDDIDVSTIYEEVRLLGEVFDRQEEAERI--VDHMDAQV-QLIRE 212
                                       58999999998.666778*************99999***************9997666644..55555555.56677 PP

                             MCR_C 212 kreelakD 219
                                       + +++++D
  gi|386001499|ref|YP_005919798.1| 213 RTADVDED 220
                                       77777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2865.96
//
Query:       gi|386001500|ref|YP_005919799.1|  [L=365]
Description: ABC transporter substrate-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-19   70.9   0.0    2.2e-19   69.9   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   1.3e-23   2.2e-19      13     235 ..      46     295 ..      43     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.3e-23
                                       HHTT-GGGEEEB-GGG--GGGGGGT........TS-BSBESSSB-HHHHHHH--SEEEE-GGG.............G CS
                      Peripla_BP_2  13 lalGatdkvvgvdtttsdpldadklee......aivevgadgeidvEklaalkPDlvilskgl..........gltd 73 
                                       +alG+ d++vg++++ s  + +  +        + +++g + ++++E+ aal+PD++il  ++          +   
  gi|386001500|ref|YP_005919799.1|  46 AALGVGDRIVGTGGAISALTNETIATYlvpqikELPDLGRGYNLNFESAAALDPDVIILERDGagqgtglteyDKLI 122
                                       69**************9999997544488888888****************************99988666665555 PP

                                       GGHHHHHHHS-EEE----TTS.....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEE CS
                      Peripla_BP_2  74 edeellksgiptvivessntg.....eslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvf 143
                                       e  el +   ptv+ ++         +s++++i  lgel++ ed+a ++v +++ +++ ++++++ +   +kp +++
  gi|386001500|ref|YP_005919799.1| 123 EKLELFEDSFPTVVLNNPACYappdvSSIYREIGILGELFDMEDRATEIVDHLEAEVQLIRDRTADIddEEKPRVLY 199
                                       6666667777888877776559*********************************************8855555555 PP

                                       EETTE.........EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHH CS
                      Peripla_BP_2 144 ggade.......ggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktglef 213
                                       +g  +       +  +   ++  ++ + d+ +i+n++ e   ++++ +s Eqila dpd+i+   +      ++ + 
  gi|386001500|ref|YP_005919799.1| 200 MGLMGgvdsgkgAVALALPDYDCGTLYPDITKIKNAYTE---ESRGYLSTEQILAVDPDLIILVRS--PGGYEVRQL 271
                                       555555888873344444455555555566999999777...59999*************999999..555555555 PP

                                       HT-S..HHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 214 lken..pllaelpAvkngrVyald 235
                                        +e+  ++l+el A+k++rVy ++
  gi|386001500|ref|YP_005919799.1| 272 YEEDyyTGLSELRAIKERRVYSTG 295
                                       555577899************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2658.84
//
Query:       gi|386001501|ref|YP_005919800.1|  [L=360]
Description: iron chelate uptake ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-93  312.7  29.3    2.7e-93  312.4  29.3    1.0  1  FecCD     FecCD transport family
    6.6e-08   32.4  13.7    6.6e-08   32.4  13.7    2.3  3  ABC-3     ABC 3 transport family
     0.0076   16.0   0.5     0.0076   16.0   0.5    3.3  4  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.4  29.3   4.5e-97   2.7e-93       2     311 ..      38     352 ..      34     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 312.4 bits;  conditional E-value: 4.5e-97
                             FecCD   2 lllllllslllgavkispsevfeallgka.........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrN 69 
                                       ++++ +++++ g ++is+ +v+ + l++          ++l+++iv++lr+pr+l+a+ vG+aLa++Ga++Q+ +rN
  gi|386001501|ref|YP_005919800.1|  38 MIVTAAIAISRGVYEISVVDVYTITLAHLspivdvstvNKLQNTIVWDLRIPRILLAITVGVALATSGAVFQGCFRN 114
                                       67888899999999*******9999988899999999999************************************* PP

                             FecCD  70 pLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsa 146
                                       pL++P+ilG+ssgaa+ga l++++    + + ++ + af+++ +a++l +llar r ++  ++liLaG+++++++sa
  gi|386001501|ref|YP_005919800.1| 115 PLVEPYILGVSSGAAFGASLGIVY---PQFFLSIQVSAFIFGSVAVALAYLLARTRDETPIVTLILAGVIIGSVFSA 188
                                       ***********************8...4677799******************************************* PP

                             FecCD 147 ltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrll 223
                                       l+s+l++++n++al++i+fwl+G +++asw++v+l+++++++++l+l+++  kl++l++gde+A++lGvn+e++++l
  gi|386001501|ref|YP_005919800.1| 189 LVSILKYISNDSALREIVFWLMGGFYYASWKDVALVSPVVIASFLVLWFFGWKLNILSMGDEEARTLGVNPEKYKFL 265
                                       ***************************************************************************** PP

                             FecCD 224 llllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtal 300
                                       l+ +++l+t++av+ vG+i++vGL++Ph arl++g+dhr ++p++a+lG++ l+++d+lar+l+ ++e+pvgi+t++
  gi|386001501|ref|YP_005919800.1| 266 LISIATLITSLAVSTVGIIAWVGLMMPHAARLILGPDHRFVIPAAAMLGGTYLIVCDTLARTLT-SAEIPVGIITSI 341
                                       ***************************************************************7.6*********** PP

                             FecCD 301 iGapffiylll 311
                                       +Gap+++yll+
  gi|386001501|ref|YP_005919800.1| 342 LGAPYLFYLLR 352
                                       *********97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.8      0.23   1.4e+03     187     205 ..      28      47 ..      26      75 .. 0.69
   2 ?   -1.4   0.2      0.23   1.4e+03     174     190 ..      91     107 ..      86     109 .. 0.86
   3 !   32.4  13.7   1.1e-11   6.6e-08      42     241 ..     132     334 ..     120     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.23
                             ABC-3 187 vGviL.vialliiPaatArr 205
                                       vGv++ + +l+i+ aa+A+ 
  gi|386001501|ref|YP_005919800.1|  28 VGVLIsLLSLMIVTAAIAIS 47 
                                       77766467888888888864 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.23
                             ABC-3 174 alialavvvalqavGvi 190
                                       +l+a++v val + G++
  gi|386001501|ref|YP_005919800.1|  91 ILLAITVGVALATSGAV 107
                                       78999999999999986 PP

  == domain 3  score: 32.4 bits;  conditional E-value: 1.1e-11
                             ABC-3  42 alpGvala.yllgvnlllgailvgliaavalellkrktklked....taigivlsvflalglvlvslikk..skvdl 111
                                       a  G++   ++l+++  ++a+++g + aval++l ++t+ ++     ++ g+++ ++++  + ++++i++  +  ++
  gi|386001501|ref|YP_005919800.1| 132 ASLGIVYPqFFLSIQ--VSAFIFGSV-AVALAYLLARTRDETPivtlILAGVIIGSVFSALVSILKYISNdsALREI 205
                                       334444431444444..455555533.45555555555544441111567999999999888899999877666788 PP

                             ABC-3 112 dsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavG 188
                                         +L+G     s +d+ l++ +++  +l+l +f  +l ++++  e A++ g++++ +k+ll+ +  l  ++a+ +vG
  gi|386001501|ref|YP_005919800.1| 206 VFWLMGGFYYASWKDVALVSPVVIASFLVLWFFGWKLNILSMGDEEARTLGVNPEKYKFLLISIATLITSLAVSTVG 282
                                       88899*****************99999999999999***************************************** PP

                             ABC-3 189 viLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatGa 241
                                       +i  + l+ +P a+ + l+ + + ++  A++lg   +++  +l  +l  a  +
  gi|386001501|ref|YP_005919800.1| 283 IIAWVGLM-MPHAARLILGPDHRFVIPAAAMLGGTYLIVCDTLARTLTSAEIP 334
                                       **999976.69888899999999999999999988887776666666555544 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.6       1.7     1e+04      36      41 ..      35      36 ..      28      46 .. 0.43
   2 ?   -4.1   1.6       2.5   1.5e+04      23      34 ..      91     102 ..      91     108 .. 0.71
   3 !   16.0   0.5   1.3e-06    0.0076       5      51 ..     156     204 ..     149     205 .. 0.90
   4 ?   -1.4   0.5      0.36   2.1e+03      28      44 ..     229     241 ..     220     247 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                          LapA_dom 36 llslws 41
                                      l    s
  gi|386001501|ref|YP_005919800.1| 35 L----S 36
                                      2....2 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.5
                          LapA_dom  23 llvafgiGallg 34 
                                       +l+a+ +G+ l+
  gi|386001501|ref|YP_005919800.1|  91 ILLAITVGVALA 102
                                       677778888776 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.3e-06
                          LapA_dom   5 pVtvnflfaq.v.elpLsllllvafgiGallgwllslwsylrlrrelrr 51 
                                       +V + +l+a+   e p+++l+l+ ++iG ++  l+s+++y+ + ++lr+
  gi|386001501|ref|YP_005919800.1| 156 AVALAYLLARtRdETPIVTLILAGVIIGSVFSALVSILKYISNDSALRE 204
                                       6888999888437****************************99999985 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.36
                          LapA_dom  28 giGallgwllslwsylr 44 
                                       ++ +l+ w+++    ++
  gi|386001501|ref|YP_005919800.1| 229 IASFLVLWFFG----WK 241
                                       33344444444....34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2233.63
//
Query:       gi|386001502|ref|YP_005919801.1|  [L=281]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-29  103.6   0.0    1.5e-29  103.2   0.0    1.2  1  ABC_tran  ABC transporter
    2.3e-13   50.7   0.0    1.5e-08   34.8   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    7.3e-07   28.8   0.0    2.3e-05   23.9   0.0    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
    6.5e-05   23.5   0.1    9.9e-05   22.9   0.1    1.5  1  AAA_23    AAA domain
    0.00011   22.7   0.0     0.0013   19.1   0.0    2.2  1  AAA       ATPase family associated with various cellular acti
     0.0014   18.4   0.0        1.6    8.4   0.0    2.1  2  AAA_15    AAA ATPase domain
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.016   15.6   0.0    1.4  1  AAA_16    AAA ATPase domain
       0.02   14.5   0.0       0.57    9.7   0.0    2.3  2  AAA_25    AAA domain
      0.022   14.8   0.0       0.62   10.1   0.0    2.2  2  AAA_14    AAA domain
      0.035   14.0   0.0      0.054   13.4   0.0    1.3  1  ATPase_2  ATPase domain predominantly from Archaea
      0.042   13.6   0.0      0.086   12.6   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.21   11.5   0.0       0.49   10.3   0.0    1.5  2  Rad17     Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0     1e-32   1.5e-29       2     137 .]      18     166 ..      17     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       + vs+++ ege+ +++G+nG+GK+tL+k+ ++ lk   G++ ++g d++++++e + + ++++pqe +  fp l v+
  gi|386001502|ref|YP_005919801.1|  18 EGVSFDVDEGELCGLFGPNGCGKTTLFKCCLKFLKYHRGSVVMNGIDITDHRIENMARLVAYVPQEhKPPFPYL-VK 93 
                                       689***************************************************************77777887.99 PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e                  +++e++ +al++l++ +l+d++     ++LSgGq+q+v +ara++++ k+++lDEpt+
  gi|386001502|ref|YP_005919801.1|  94 EVvlmgrtphlrgvfgisrKDKERALTALETLDIAHLADQPY----NQLSGGQRQMVLMARAIAQDTKIMFLDEPTS 166
                                       99999*************999999*****************9....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.9e-05     0.028       3      18 ..      31      46 ..      29      69 .. 0.85
   2 !   34.8   0.0     1e-11   1.5e-08     222     300 ..     123     198 ..      65     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                            AAA_21  3 vliGpNgsGKSnLLda 18
                                      +l GpNg+GK++L+++
  gi|386001502|ref|YP_005919801.1| 31 GLFGPNGCGKTTLFKC 46
                                      699***********96 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1e-11
                            AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        +l+  +  + p+++lS G++++  ++ a++++    ++ ++DEp + L+ + + r++ ++++ +++g+ +++ +H+
  gi|386001502|ref|YP_005919801.1| 123 ETLDIAHLADQPYNQLSGGQRQMVLMARAIAQDT---KIMFLDEPTSALDFSNQIRIWNIMRRVAEEGVTILACSHD 196
                                       455555667889***********66666666544...9***********************999999********** PP

                            AAA_21 299 pl 300
                                       p 
  gi|386001502|ref|YP_005919801.1| 197 PN 198
                                       96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.6e-08   2.3e-05      28     205 ..      31     203 ..      17     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.6e-08
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSC.EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekee.vsisrr 102
                                        + GpNG+GK+ l+   l  L        r + + + i    +++  + a++  ++ +e k  ++   +e v + r+
  gi|386001502|ref|YP_005919801.1|  31 GLFGPNGCGKTTLFKCCLKFLK-----YHRGSVVMNGIDI-TDHRIENMARLVAYVPQEHKPpFPYLVKEvVLMGRT 101
                                       5789999999999988733332.....2344444444554.667777777777766555554555555551556677 PP

                                       EETTSEEEEEETTEEE-HH..HHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkk..evsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                           g   +  ++ke   +  e  ++ + a+   ++LSgG++++v +a  +    ++ + +++lDe  +aLD++n  
  gi|386001502|ref|YP_005919801.1| 102 PHLRGVFGISRKDKERALTalETLDIAHLADQPYNQLSGGQRQMVLMARAI----AQDTKIMFLDEPTSALDFSNQI 174
                                       77777755544444444440033344444555567*********9776554....5778899*************** PP

                                       HHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkekskn.aQfivislreemleka 205
                                       ++ +++++  ++ + ++  s++ ++++  
  gi|386001502|ref|YP_005919801.1| 175 RIWNIMRRVAEEgVTILACSHDPNHVSWF 203
                                       ******98877757777788888777655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   6.6e-08   9.9e-05      10      46 ..      17      55 ..      14     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.6e-08
                            AAA_23 10 frdqeidF.skgltlItGpNGaGKTTil.dAiklaLyge 46
                                      f+++++d  +  l  ++GpNG+GKTT++ +++k+  y++
  gi|386001502|ref|YP_005919801.1| 17 FEGVSFDVdEGELCGLFGPNGCGKTTLFkCCLKFLKYHR 55
                                      5666677744468899************77777777884 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 !   19.1   0.0   8.9e-07    0.0013       3      53 ..      32      84 ..      30     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.9e-07
                                      EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgve..fleisgsellskyvgesekkirelfkea 53
                                      l+Gp G+GKT+l k   k l+ +   + ++g +++++ ++++++ ++ + +e 
  gi|386001502|ref|YP_005919801.1| 32 LFGPNGCGKTTLFKCCLKFLKYHrgSVVMNGIDITDHRIENMARLVAYVPQEH 84
                                      89*****************9855337999999999888888777777776664 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0011       1.6      25      48 ..      29      52 ..      16      78 .. 0.73
   2 !    8.2   0.0    0.0012       1.8     291     367 ..     132     198 ..     103     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                            AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                      l  l G+N++GK+++ +   +Fl+
  gi|386001502|ref|YP_005919801.1| 29 LCGLFGPNGCGKTTLFKCCLKFLK 52
                                      66688**********999888888 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                            AAA_15 291 elplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       ++p+n+ + G+++++l++  ++ a+       +++i +++EP   L  ++q  +++ ++++a+++   ++ ++H p 
  gi|386001502|ref|YP_005919801.1| 132 DQPYNQLSGGQRQMVLMA--RAIAQ-------DTKIMFLDEPTSALDFSNQIRIWNIMRRVAEEGV-TILACSHDPN 198
                                       678888888888887765..33333.......4699*****************************7.999****985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.1e-05     0.016      24      56 ..      27      59 ..      16     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggifl 56
                                      +el+ l G+ G+GK++l +++l+ l+ ++g ++
  gi|386001502|ref|YP_005919801.1| 27 GELCGLFGPNGCGKTTLFKCCLKFLKYHRGSVV 59
                                      4788899****************9999964442 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00038      0.57      31      49 ..      25      43 ..      19      88 .. 0.93
   2 ?    2.5   0.0     0.064        95       4      39 ..     157     192 ..     154     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00038
                            AAA_25 31 pagelallaGapgtGKttl 49
                                       +gel+ l+G+ g+GKttl
  gi|386001502|ref|YP_005919801.1| 25 DEGELCGLFGPNGCGKTTL 43
                                      789***************8 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.064
                            AAA_25   4 plelsavsvadlaapppprrwlvkgllpagelalla 39 
                                       ++++ + ++++l+ + + r w +++ ++++++++la
  gi|386001502|ref|YP_005919801.1| 157 KIMFLDEPTSALDFSNQIRIWNIMRRVAEEGVTILA 192
                                       56888999999***********************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00042      0.62       5      54 ..      30      78 ..      26      95 .. 0.72
   2 ?    2.5   0.0     0.094   1.4e+02      56      84 ..     147     175 ..     114     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpeklle 54
                                      + + G+  +GKTtl k ++k l   ++  + +n  d +d ++++ ++l  
  gi|386001502|ref|YP_005919801.1| 30 CGLFGPNGCGKTTLFKCCLKFLK-YHRGSVVMNGIDITDHRIENMARLVA 78
                                      6789**********988876655.55677777777777776666555544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.094
                            AAA_14  56 ilek.lkeekktylflDEiqevpewekalk 84 
                                       ++++ +  ++++++flDE   + ++++ ++
  gi|386001502|ref|YP_005919801.1| 147 LMARaIA-QDTKIMFLDEPTSALDFSNQIR 175
                                       3333244.48999*****999988888876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.6e-05     0.054      25      67 ..      32      75 ..      24     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                          ATPase_2 25 iYGpegsGKtaLlkeiienledkdk.yviyyialreesisklde 67
                                      ++Gp g+GKt+L+k  ++ l+ +    v+  i++ +++i+++ +
  gi|386001502|ref|YP_005919801.1| 32 LFGPNGCGKTTLFKCCLKFLKYHRGsVVMNGIDITDHRIENMAR 75
                                      79************999988544331445556666666666555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.8e-05     0.086      12      39 ..      17      44 ..      10      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      f+g ++++d+ + + l Gp+G GK+Tl+
  gi|386001502|ref|YP_005919801.1| 17 FEGVSFDVDEGELCGLFGPNGCGKTTLF 44
                                      888999999777999***********97 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00033      0.49      50      72 ..      32      54 ..      16      75 .. 0.79
   2 ?   -2.5   0.0       2.7   4.1e+03     125     148 ..     148     171 ..     117     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                             Rad17 50 isGPsGCgkstvvkvLskelgik 72
                                      + GP GCgk+t  k   k l ++
  gi|386001502|ref|YP_005919801.1| 32 LFGPNGCGKTTLFKCCLKFLKYH 54
                                      78***********9998888775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                             Rad17 125 lGddlrtdkklilvedlPnkfyrd 148
                                       +   +  d k++++++  +    +
  gi|386001502|ref|YP_005919801.1| 148 MARAIAQDTKIMFLDEPTSALDFS 171
                                       455566777888888755555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1800.85
//
Query:       gi|386001503|ref|YP_005919802.1|  [L=393]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-17   62.5   0.0    8.4e-17   61.5   0.0    1.7  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   4.7e-21   8.4e-17      41     235 ..     110     324 ..      57     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 4.7e-21
                                       S-BSBESSSB-HHHHHHH--SEEEE-GGG...........GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHH CS
                      Peripla_BP_2  41 ivevgadgeidvEklaalkPDlvilskgl........gltdedeellksgiptvivessntg.....eslkeqiral 104
                                       + ++++++ +++E+l+ l+PDlvi   g+        g ++++  ++++gip ++    nt      + + e+ir +
  gi|386001503|ref|YP_005919802.1| 110 PLVASYGMPPNYEMLVSLDPDLVIIRGGDctfwtdedGMQQAINTIDSLGIPLIVTYGPNTYdepnmSIISEEIRII 186
                                       5788999*****************988888888***999*************88777777779999999******** PP

                                       HHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE.......EEEE-TTSTTTHHHHT.S--EES CS
                      Peripla_BP_2 105 gellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggade.....ggyvvagsnsyigdllda.lgieni 172
                                       g+++g e+ea +l+  ++++++ ++++++ +    ++ vl+fg +++     g+  + g ++  + +l++ ++++n+
  gi|386001503|ref|YP_005919802.1| 187 GQIFGIEEEAIELADYLEREVEFVRERTEDIpddEKPRVLLFGLSPRsrdggGAGDIEGIDTIESFFLEEiVNAKNA 263
                                       ******************************99977777888888888999999999********************* PP

                                       TTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHH...HHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 173 aaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpl...laelpAvkngrVyald 235
                                       ++e    ++  +saE++la dpdvi+  +   +     + +l e p    l+el+Avkn+rV+al+
  gi|386001503|ref|YP_005919802.1| 264 FQE--PAHFRLVSAEHVLALDPDVIVLPTD--WGYH-PPRELYEAPYyqnLQELTAVKNRRVIALP 324
                                       999..79*********************99..4444.45555555550115567*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2976.73
//
Query:       gi|386001504|ref|YP_005919803.1|  [L=287]
Description: Methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   44.9   0.0    3.1e-11   43.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    6.9e-08   33.1   0.0    1.2e-07   32.4   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.2e-07   31.8   0.0    1.7e-07   31.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    2.1e-07   30.3   0.0      4e-07   29.4   0.0    1.4  2  RrnaAD           Ribosomal RNA adenine dimethylase
    9.3e-07   29.4   0.0    2.1e-06   28.3   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      6e-06   26.1   0.0    9.2e-06   25.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.4e-05   24.7   0.0    2.3e-05   24.0   0.0    1.3  1  MTS              Methyltransferase small domain
    2.1e-05   23.9   0.0    3.4e-05   23.3   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
    0.00098   18.5   0.0     0.0014   18.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0014   17.8   0.0      0.002   17.3   0.0    1.3  1  DREV             DREV methyltransferase
     0.0014   18.4   0.0       0.18   11.5   0.0    2.5  3  Met_10           Met-10+ like-protein
      0.002   17.6   0.0     0.0062   16.0   0.0    1.7  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0021   17.8   0.0     0.0032   17.3   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0044   16.7   0.0     0.0066   16.1   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.028   14.2   0.0      0.043   13.5   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
       0.12   11.7   0.0       0.21   11.0   0.0    1.3  1  TehB             Tellurite resistance protein TehB
       0.16   11.6   0.0       0.24   11.0   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.16   10.9   0.0       0.23   10.4   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   3.2e-14   3.1e-11       1      92 [.      68     158 ..      68     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.2e-14
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT...TEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg...sfDlvvssga 73 
                                       vLd+G+G+G+l++ ++k    a+vt+v++s++m +  +e++ee+++ nv+++q+  e+++ e +    +Dlvv+s++
  gi|386001504|ref|YP_005919803.1|  68 VLDIGAGPGTLAIPFSKVT--AHVTAVEPSASMARVLQENLEERRIgNVDCIQKRWEEVDVERDlkpPYDLVVASFS 142
                                       9***************996..**********************999************9965444559******988 PP

                                       GGGSSHHHHHHHHHHHHHH CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarv 92 
                                       l +    d+++a++++ +v
  gi|386001504|ref|YP_005919803.1| 143 LGM---TDIKAAVQKMTKV 158
                                       776...4688999998876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.2e-10   1.2e-07       1      92 [.      69     158 ..      69     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.2e-10
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnve..lealdlldldggssfDlvvasnv 75 
                                       L+iG+G G+l+ ++ +   ++++t+v++s+s+    +e l +r+  n+++++  +e+ d++ +  +  +Dlvvas+ 
  gi|386001504|ref|YP_005919803.1|  69 LDIGAGPGTLAIPFSKV--TAHVTAVEPSASMARVLQENLEERRIGNVDCIQkrWEEVDVERD-LKPPYDLVVASFS 142
                                       8****************..**************888888888888887776511666665444.446********** PP

                   Methyltransf_12  76 lhhlkdirevldnirkl 92 
                                       l  + di+++++++ k+
  gi|386001504|ref|YP_005919803.1| 143 LGMT-DIKAAVQKMTKV 158
                                       **96.999999999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.7e-10   1.7e-07      20      96 ..      62     147 ..      32     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.7e-10
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                        ++  rvLdiG+G G+l+  +++  ++vt+v++s  +   ++         + ++ qk  +  + +++ +  +dl+v
  gi|386001504|ref|YP_005919803.1|  62 IKSTYRVLDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQenleerrigNVDCIQKRWEEVDVERDLKPPYDLVV 138
                                       355559****************************99888888*******************99999*********** PP

                   Methyltransf_23  88 lrevlehvp 96 
                                       ++++l+  +
  gi|386001504|ref|YP_005919803.1| 139 ASFSLGMTD 147
                                       ****99765 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.1e-10     4e-07      21      78 ..      55     111 ..      50     139 .. 0.86
   2 ?   -3.5   0.0       4.2   4.2e+03      59      87 ..     241     272 ..     239     277 .. 0.58

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.1e-10
                                       HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCE CS
                            RrnaAD  21 eIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdekl 78 
                                         ldk+ ++ +  vl+ig+G+G l  ++ k   +v+++E   ++a +lq++l+ ++++
  gi|386001504|ref|YP_005919803.1|  55 VLLDKITIKSTYRVLDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQENLE-ERRI 111
                                       5799**********************************************998.3333 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                                       -S-HHHHHH...HHCHTTTCCCEEEE-S-CCG CS
                            RrnaAD  59 ElderLakl...lqkklskdeklkvvhqDflk 87 
                                       E d ++akl   l++ +++d+ + v++ Dfl+
  gi|386001504|ref|YP_005919803.1| 241 ETDDQMAKLsgyLSQVVEEDGESWVLKYDFLN 272
                                       56666555422245555577777777777766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   2.1e-09   2.1e-06       1      87 [.      69     158 ..      69     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT...-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn...sfDlvvssevlhh 73 
                                       Ld+G+G G la ++ k  a+v++v++s+ m ++ +e+ +e+++ +v++++ + e++ +e +    +Dlvv+s++l  
  gi|386001504|ref|YP_005919803.1|  69 LDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQENLEERRIgNVDCIQKRWEEVDVERDlkpPYDLVVASFSLGM 145
                                       8**************999*********************************99999888766669*******99987 PP

                                       -CCHHHHHHHHHHH CS
                   Methyltransf_11  74 vedpekalkeiaRv 87 
                                         d ++a++++ +v
  gi|386001504|ref|YP_005919803.1| 146 T-DIKAAVQKMTKV 158
                                       7.577777777665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   9.2e-09   9.2e-06       2     102 ..      63     160 ..      62     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.2e-09
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...ekf 75 
                                       ++++rvlD+G+G G+l++ +  ++   a+v+ ++ s+ + ++ +en+++  + nv   q  +ee +  +e+    ++
  gi|386001504|ref|YP_005919803.1|  63 KSTYRVLDIGAGPGTLAIPFS-KV--TAHVTAVEPSASMARVLQENLEERRIGNVDCIQKRWEEVD--VERdlkPPY 134
                                       7899****************9.55..69************************************88..66656689* PP

                   Methyltransf_31  76 Dlilsnevlnaladpdkileeiervlk 102
                                       Dl+++      ++d +++ +++++v +
  gi|386001504|ref|YP_005919803.1| 135 DLVVASFS-LGMTDIKAAVQKMTKVSS 160
                                       ****9644.599999999999999865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.3e-08   2.3e-05      21     103 ..      54     139 ..      48     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-08
                                       HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTS CS
                               MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleev 93 
                                       k+Ll++++ + + +vlD+G+G G l++ + k + +  vt+v+ +a   ++ +enle+ ++     ++ ++++v  e 
  gi|386001504|ref|YP_005919803.1|  54 KVLLDKITIKSTYRVLDIGAGPGTLAIPFSKVTAH--VTAVEPSASMARVLQENLEERRIGnvdcIQKRWEEVDVER 128
                                       68999999999999*****************9888..9*******************99877667666665554444 PP

                                       T.TS-EEEEEE CS
                               MTS  94 e.ekkfdlivs 103
                                       + +  +dl+v 
  gi|386001504|ref|YP_005919803.1| 129 DlKPPYDLVVA 139
                                       33377888875 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.4e-08   3.4e-05      47     139 ..      64     157 ..      40     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.4e-08
                                       CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC....TTTTT-EEEE CS
                              GidB  47 ekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee....kqeeekydvv 119
                                       +   +v+D+G+G+G  +ip +  + + ++t +e++   ++ L+e  ee ++ nv  +++r ee    ++ + +yd+v
  gi|386001504|ref|YP_005919803.1|  64 STY-RVLDIGAGPGTLAIPFS--KVTAHVTAVEPSASMARVLQENLEERRIGNVDCIQKRWEEvdveRDLKPPYDLV 137
                                       222.6*********9999977..5566788*********************************88877888999999 PP

                                       EEC-SSSHHHHHHHHCCCEE CS
                              GidB 120 tsRAlaslnelteillkllk 139
                                       ++     + ++++ ++k+ k
  gi|386001504|ref|YP_005919803.1| 138 VASFSLGMTDIKAAVQKMTK 157
                                       87555555556666555555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-06    0.0014      43     132 ..      45     138 ..      25     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES CS
                              CMAS  43 LeeAqlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevkll 119
                                       +e    + ++++l+k+++k   ++LdiG+G G+l++   +   ++v ++  S+  a++ +++++e+ + +   +  +
  gi|386001504|ref|YP_005919803.1|  45 IERDGGEYVKVLLDKITIKSTYRVLDIGAGPGTLAIPFSKV-TAHVTAVEPSASMARVLQENLEERRIGNVDCI-QK 119
                                       55555567899**********************99987665.9**********999999999998876654444.45 PP

                                       -GGG---......--SEEE CS
                              CMAS 120 dyedlde......kvdrvv 132
                                        +e++d       ++d vv
  gi|386001504|ref|YP_005919803.1| 120 RWEEVDVerdlkpPYDLVV 138
                                       6766654333444777776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     2e-06     0.002      94     159 ..      64     135 ..      51     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkk.kkynvlsale.....lqetdvkldlilcln 159
                                        + ++ld+GaG G ++   ++   +v a e s  m   l+  ++ + +++++     ++e dv+ dl   ++
  gi|386001504|ref|YP_005919803.1|  64 STYRVLDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQEnLEERRIGNVDciqkrWEEVDVERDLKPPYD 135
                                       5889*******************************9888742333444433321136777777777655555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00018      0.18      98     151 ..      62     113 ..      46     130 .. 0.85
   2 ?    4.4   0.0     0.028        28      16      72 ..     128     183 ..     123     191 .. 0.79
   3 ?   -2.5   0.0       3.7   3.7e+03      53      90 ..     245     283 ..     235     285 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                       ++   +V+d+ AG G +aip +k      v a++   +  + l+en++  ++ +
  gi|386001504|ref|YP_005919803.1|  62 IKSTYRVLDIGAGPGTLAIPFSK--VTAHVTAVEPSASMARVLQENLEERRIGN 113
                                       566678*****************..77789******99********99887765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.028
                                       TTSSH.HHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTE CS
                            Met_10  16 eelke.ykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngc 72 
                                        +lk+ y+ v++   l +t++k+ ++k+++v++ f    l   aG+ s  ++ +E + 
  gi|386001504|ref|YP_005919803.1| 128 RDLKPpYDLVVASFSLGMTDIKAAVQKMTKVSSGF--VYLAWFAGDTSWDVQAREVSA 183
                                       455544************************99987..456778888888888888655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.7
                                       -EEEEEES-.SEEEEEETTEEEEEETTTS-.--GGGHHH CS
                            Met_10  53 elevlaGsdstetihkEngcrfklDvskvy.fsskleaE 90 
                                       ++  l G  s ++++  ++  +k D+ +++ + ++++ E
  gi|386001504|ref|YP_005919803.1| 245 QMAKLSGYLSQVVEEDGESWVLKYDFLNMMvWWNNNHRE 283
                                       566777777677777777778888886654344445554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   1.2e+03      44      77 ..      14      47 ..       6      61 .. 0.76
   2 !   16.0   0.0   6.2e-06    0.0062     155     232 ..      57     139 ..      53     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                              PrmA 44 epaleeeelkeevkvkalfkeeteakeliaqlke 77
                                      ++ ++++e++  ++  a++++e+ea + ++ ++ 
  gi|386001504|ref|YP_005919803.1| 14 DQMKRHNEMNGGMDCAAYWDSEEEARNYWRMIER 47
                                      5556666777888999999999999999988876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.2e-06
                              PrmA 155 lekl.vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.....ee 225
                                       l+k+ +k++ +vlD+G+G G Lai  +k+ a +v+av       +v +eN+e  ++ +   ++   e ++     + 
  gi|386001504|ref|YP_005919803.1|  57 LDKItIKSTYRVLDIGAGPGTLAIPFSKVTA-HVTAVEPSASMARVLQENLEERRIGNVDCIQKRWEEVDverdlKP 132
                                       55553667779*****************987.799**9999999*******99988874435444444422334557 PP

                              PrmA 226 kadviva 232
                                       ++d++va
  gi|386001504|ref|YP_005919803.1| 133 PYDLVVA 139
                                       8899988 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.2e-06    0.0032      65     128 ..      56     116 ..      50     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEE CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenviv 128
                                       +l+ +++k   rvL++G+G G l+  ++++  +++   ++e ++++++  ++nl++  + nv  
  gi|386001504|ref|YP_005919803.1|  56 LLDKITIKSTYRVLDIGAGPGTLAIPFSKVTAHVT---AVEPSASMARVLQENLEERRIGNVDC 116
                                       5677889**********************998877...9****************999998865 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.7e-06    0.0066      43     117 ..      66     137 ..      56     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.7e-06
                                       -EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  43 arvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                        rvLD+ aG G+l++   S   +++++ve +++++++l+enlee ++ +    +++++ e+++ +   k+++d+v
  gi|386001504|ref|YP_005919803.1|  66 YRVLDIGAGPGTLAI-PFSKVTAHVTAVEPSASMARVLQENLEERRIGN--VDCIQKRWEEVDVERDLKPPYDLV 137
                                       689************.59**************************99997..555556666666555566667766 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.4e-05     0.043      21     127 ..      31     140 ..      14     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                   Methyltransf_16  21 vWdaavvlvkylekklake........lganelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkkn 88 
                                        Wd+   +  y  +   ++        ++ +  s+ +vl++G+G G   + + +    a+v+    +  +  +l++n
  gi|386001504|ref|YP_005919803.1|  31 YWDSEEEARNYWRMIERDGgeyvkvllDKITIKSTYRVLDIGAGPGTLAIPFSKV--TAHVTAVEPSAsMARVLQEN 105
                                       588888888887775444477888876566677899****************999..77777665554499****** PP

                   Methyltransf_16  89 ielnknalkskvkvevLdWge.eleedllekeevDlilaa 127
                                       +e        +v   +  W+e ++e+dl  k ++Dl++a+
  gi|386001504|ref|YP_005919803.1| 106 LEER---RIGNVDCIQKRWEEvDVERDL--KPPYDLVVAS 140
                                       **94...47889999999*874555555..5689***997 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.21      24     106 ..      58     144 ..      48     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                       HHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHT...T-TTEEEEE--GG.G----S-E CS
                              TehB  24 eavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikeke...nlknistalydin.eakldery 96 
                                       + + i +  +vld+g g g  ++ +s +  +vta++  ++    l+e  e     n++ i+ +  +++ e +l+  y
  gi|386001504|ref|YP_005919803.1|  58 DKITIKSTYRVLDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQENLEERrigNVDCIQKRWEEVDvERDLKPPY 134
                                       6677778899***************************9999999998877651116666666666665345677779 PP

                                       EEEEEESSGG CS
                              TehB  97 dfilstvvlm 106
                                       d+++++  l 
  gi|386001504|ref|YP_005919803.1| 135 DLVVASFSLG 144
                                       9888776554 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.24       3      82 ..      67     144 ..      65     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                        +lD+ +G G  +i f +v  +v a+e + +   + q+N e   +  ++++++  ++e+  +  l+   +dlv++S 
  gi|386001504|ref|YP_005919803.1|  67 RVLDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQENLEERRI-GNVDCIQKRWEEVDVERDLKPP-YDLVVASF 141
                                       589*************************************98855.5788888888886666555554.89999987 PP

                   Methyltransf_15  80 PwG 82 
                                         G
  gi|386001504|ref|YP_005919803.1| 142 SLG 144
                                       666 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.23     198     261 ..      61     124 ..      53     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                   tRNA_U5-meth_tr 198 tqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeel 261
                                       t +s+  +l++  G G +++++++   +v a e + s   + q n+++ +i nv+ i+   ee+
  gi|386001504|ref|YP_005919803.1|  61 TIKSTYRVLDIGAGPGTLAIPFSKVTAHVTAVEPSASMARVLQENLEERRIGNVDCIQKRWEEV 124
                                       5566667899999******************************************998877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2067.14
//
Query:       gi|386001505|ref|YP_005919804.1|  [L=364]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   72.2   0.0    7.3e-20   71.5   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
        0.1   13.1   0.0        0.2   12.1   0.0    1.4  1  ZapA          Cell division protein ZapA


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   8.1e-24   7.3e-20      42     235 ..      81     295 ..      26     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 8.1e-24
                                       -BSBESSSB-HHHHHHH--SEEEE-GGG............GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHH CS
                      Peripla_BP_2  42 vevgadgeidvEklaalkPDlvilskgl.........gltdedeellksgiptvivessntg.....eslkeqiral 104
                                       v v + + +++E+l+ l+PD+v+l +g          + ++ +e ++++gip vi    +       + + ++ir +
  gi|386001505|ref|YP_005919804.1|  81 VLVEGATAVNYEMLVYLDPDVVFLREGSwafsagsdeKIQKTIESIESLGIPLVILVGPPYQeqpsvDYIGDEIRLV 157
                                       77889999*****************9989****999999999************9654443345555********** PP

                                       HHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.....-EEEEEEEETTE........EEEE-TTSTTTHHHHT.S--E CS
                      Peripla_BP_2 105 gellgledeaeklvaeidsklaaaksaidse....kpkpvlvfggade......ggyvvagsnsyigdllda.lgie 170
                                       ge++ +e+ ae+l++ ++s +++++s+++      kp+++ +  +  +      g+ +  g ++  ++++++ ++++
  gi|386001505|ref|YP_005919804.1| 158 GEVFSREEDAEALASYLESQIEEIRSRTKDVpedeKPSMMQLGLS--PrardggGAGMAWGLDTIESYFIEDiANAK 232
                                       ***************************999977444444444443..2469999*****************99**** PP

                                       ESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTS...HHHHTT-EEEE- CS
                      Peripla_BP_2 171 niaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllael...pAvkngrVyald 235
                                       n+++    +++  +s E+il++dpdvi+  +    +    + +l + p +++l   +Avkn rVyal+
  gi|386001505|ref|YP_005919804.1| 233 NVYDG--MGAFVVVSTEHILKMDPDVIVLPTA---QGYHPARELYTAPYYQNLqelTAVKNERVYALP 295
                                       **999..7************************...444455555555555443333*********997 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05       0.2      18      54 ..     163     199 ..     150     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                              ZapA  18 eeeylreaaklvdekikeireaggnlseerllvmaaL 54 
                                        ee  +++a +++++i+eir++++ ++e++   m+ L
  gi|386001505|ref|YP_005919804.1| 163 REEDAEALASYLESQIEEIRSRTKDVPEDEKPSMMQL 199
                                       599*********************9998887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2796.47
//
Query:       gi|386001506|ref|YP_005919805.1|  [L=266]
Description: DNA-directed RNA polymerase subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete 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-23   82.5   0.0    4.7e-23   81.7   0.0    1.4  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    3.1e-17   61.8   0.0    3.8e-17   61.5   0.0    1.1  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    5.3e-09   35.5  13.3    4.8e-06   26.2   3.4    2.8  2  Fer4           4Fe-4S binding domain
    4.8e-07   29.8   7.9    4.8e-07   29.8   7.9    2.2  2  Fer4_9         4Fe-4S dicluster domain
    7.4e-07   29.7   8.6    7.4e-07   29.7   8.6    2.1  2  Fer4_7         4Fe-4S dicluster domain
    5.4e-06   26.4   7.6    5.4e-06   26.4   7.6    2.2  2  Fer4_10        4Fe-4S dicluster domain
    0.00014   21.8  12.8    0.00026   20.9   2.7    2.8  2  Fer4_6         4Fe-4S binding domain
    0.00037   20.4   3.3    0.00037   20.4   3.3    3.6  3  Fer4_2         4Fe-4S binding domain
     0.0004   21.3  12.2     0.0016   19.3   0.9    3.0  3  Fer4_16        4Fe-4S double cluster binding domain
     0.0098   16.3   3.7     0.0098   16.3   3.7    3.4  3  Fer4_4         4Fe-4S binding domain
  ------ inclusion threshold ------
      0.017   15.6   0.7      0.017   15.6   0.7    2.8  2  Fer4_17        4Fe-4S dicluster domain
       0.02   15.3  14.2       0.46   11.0   8.8    2.6  2  Fer4_8         4Fe-4S dicluster domain
      0.032   15.2   5.8      0.032   15.2   5.8    3.4  2  Fer4_3         4Fe-4S binding domain
      0.034   14.3   4.4      0.034   14.3   4.4    2.8  4  Fer4_21        4Fe-4S dicluster domain
       0.64   10.6   7.2        3.2    8.3   7.2    2.2  1  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
        1.3    9.3  10.0          3    8.1  10.0    1.6  1  Fer4_18        4Fe-4S dicluster domain
        1.5    9.6  11.9       0.15   12.8   2.2    2.6  2  Fer4_15        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   4.4e-26   4.7e-23       1     112 []      44     153 ..      44     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 4.4e-26
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadve 77 
                                       + i++ntsvl DE ++ rlgl+p++++d    +   +e+ e    g++ ++v ++L+++gp +v +gdl ++d+ v+
  gi|386001506|ref|YP_005919805.1|  44 ISIYDNTSVLFDEQLSLRLGLVPIKADDLSL-FRVPEEC-ECGGAGCPACQVGMTLSAEGPCTVHSGDLRFSDPGVK 118
                                       68***********************877766.*******.44579******************************** PP

                                       ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +v ++i+Ia L +g++l le +v  ++G +hak++
  gi|386001506|ref|YP_005919805.1| 119 VVFEKIPIAILGEGEKLMLEGIVTLNRGTVHAKWQ 153
                                       **********************************6 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   3.6e-20   3.8e-17       1      66 [.      14     252 ..      14     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 3.6e-20
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                         RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea............................................... 30 
                                       +fllrgv+++++Na+Rr +l+evp++ai++                                               
  gi|386001506|ref|YP_005919805.1|  14 RFLLRGVTPAFANAIRRACLAEVPSLAIDEisiydntsvlfdeqlslrlglvpikaddlslfrvpeececggagcpa 90 
                                       59**************************************************9999999999999999999999999 PP

                                       ............................................................................. RF
                         RNA_pol_L  31 ............................................................................. 30 
                                                                                                                    
  gi|386001506|ref|YP_005919805.1|  91 cqvgmtlsaegpctvhsgdlrfsdpgvkvvfekipiailgegeklmlegivtlnrgtvhakwqagtqcgyknlpeit 167
                                       99999998888888888888888888888888887777777776666666666666666666666666666666665 PP

                                       ...............xx..................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  31 ...............pv..................................vkvntdkdklilevetdgslkPeeal 58 
                                                      p                                   ++v++++d +++++ tdgs+++++++
  gi|386001506|ref|YP_005919805.1| 168 isdrcegcgkcvevcPRkvlvigegegkvrvhdpiscslcklcigecdvgaINVSAVEDVFVMKIDTDGSMPAKDLV 244
                                       5555555555555550055555666666566666677777777788787888999********************** PP

                                       xxxxxxxx RF
                         RNA_pol_L  59 keAlkiLk 66 
                                       + A+  ++
  gi|386001506|ref|YP_005919805.1| 245 TGAAGEIR 252
                                       ***98876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.4   4.5e-09   4.8e-06       5      22 ..     169     186 ..     166     188 .. 0.87
   2 !   14.0   2.3   3.1e-05     0.033       3      23 ..     199     219 ..     197     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.5e-09
                                       TTTSSS-THHHHHSTTTE CS
                              Fer4   5 eekCigCGaCvevCPvgA 22 
                                        ++C gCG+CvevCP  +
  gi|386001506|ref|YP_005919805.1| 169 SDRCEGCGKCVEVCPRKV 186
                                       79*************876 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.1e-05
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                        d+  C  C++C+  C vgAI
  gi|386001506|ref|YP_005919805.1| 199 HDPISCSLCKLCIGECDVGAI 219
                                       68889***************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.3       3.1   3.3e+03      11      16 ..      87      92 ..      68     104 .. 0.68
   2 !   29.8   7.9   4.6e-10   4.8e-07       1      51 []     171     219 ..     171     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.1
                            Fer4_9 11 aCpagv 16
                                       Cpa+ 
  gi|386001506|ref|YP_005919805.1| 87 GCPACQ 92
                                      344443 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 4.6e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C gCg+Cve+Cp +v v  ++e+k+r++     +C  C+ C+  C  gai
  gi|386001506|ref|YP_005919805.1| 171 RCEGCGKCVEVCPRKVLVIGEGEGKVRVHDP--ISCSLCKLCIGECDVGAI 219
                                       5***************************887..57************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.8       8.2   8.7e+03      40      45 ..      87      92 ..      75      94 .. 0.57
   2 !   29.7   8.6   7.1e-10   7.4e-07       1      52 []     171     218 ..     171     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.2
                            Fer4_7 40 gCgaCv 45
                                      gC aC+
  gi|386001506|ref|YP_005919805.1| 87 GCPACQ 92
                                      455554 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 7.1e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekv.eidpekClgCgaCvavCPtga 52 
                                       rC gCg+Cv++Cp k++ + e e      kv ++dp +C+ C+ C+ +C +ga
  gi|386001506|ref|YP_005919805.1| 171 RCEGCGKCVEVCPRKVLVIGEGE-----GKVrVHDPISCSLCKLCIGECDVGA 218
                                       8******************9963.....4450567**************9997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   2.4       7.1   7.5e+03      18      21 ..      86      90 ..      76     106 .. 0.66
   2 !   26.4   7.6   5.1e-09   5.4e-06       6      55 ..     169     214 ..     165     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.1
                           Fer4_10 18 a.CPa 21
                                      a CPa
  gi|386001506|ref|YP_005919805.1| 86 AgCPA 90
                                      33555 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.1e-09
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                       +d+C +CgkCv++CP      ++  + ++e++vr+ ++ +C  c  C+ +C
  gi|386001506|ref|YP_005919805.1| 169 SDRCEGCGKCVEVCPR-----KVLVIGEGEGKVRVhDPISCSLCKLCIGEC 214
                                       69**************.....66666666666665589**********999 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.7   2.5e-07   0.00026       6      22 ..     169     185 ..     166     187 .. 0.88
   2 ?    5.1   2.6     0.024        25       4      24 .]     199     219 ..     198     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.5e-07
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                        d+C gCg+Cv vCP +
  gi|386001506|ref|YP_005919805.1| 169 SDRCEGCGKCVEVCPRK 185
                                       69*************66 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       +dp +C  C  C+  C  gai
  gi|386001506|ref|YP_005919805.1| 199 HDPISCSLCKLCIGECDVGAI 219
                                       56668***********99998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   3.0       7.1   7.5e+03      12      16 ..      87      91 ..      75      94 .. 0.53
   2 !   20.4   3.3   3.5e-07   0.00037       7      21 ..     169     183 ..     165     184 .. 0.93
   3 ?    2.6   2.0      0.17   1.8e+02       5      20 ..     199     214 ..     195     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.1
                            Fer4_2 12 gCgaC 16
                                      gC aC
  gi|386001506|ref|YP_005919805.1| 87 GCPAC 91
                                      23355 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.5e-07
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +drC gCg+Cv +CP
  gi|386001506|ref|YP_005919805.1| 169 SDRCEGCGKCVEVCP 183
                                       79************* PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.17
                            Fer4_2   5 vdtdrCigCgaCvsaC 20 
                                        d+ +C  C+ C+  C
  gi|386001506|ref|YP_005919805.1| 199 HDPISCSLCKLCIGEC 214
                                       56668*******8777 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.7       5.7     6e+03      54      61 ..      83      92 ..      71      93 .. 0.74
   2 !   19.3   0.9   1.6e-06    0.0016       1      18 [.     171     188 ..     171     201 .. 0.84
   3 !    9.4   0.2    0.0019       2.1       2      20 ..     204     222 ..     203     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.7
                           Fer4_16 54 i..tgCdiCq 61
                                      +  +gC +Cq
  gi|386001506|ref|YP_005919805.1| 83 CggAGCPACQ 92
                                      3448999997 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.6e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       rC +CgkC+evCP +++ 
  gi|386001506|ref|YP_005919805.1| 171 RCEGCGKCVEVCPRKVLV 188
                                       6************99975 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0019
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C  C+ C+  C ++ai+  
  gi|386001506|ref|YP_005919805.1| 204 CSLCKLCIGECDVGAINVS 222
                                       99**************976 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.6       3.5   3.7e+03       4      10 ..      81      91 ..      78      93 .. 0.69
   2 !   16.3   3.7   9.3e-06    0.0098       1      16 [.     169     184 ..     169     187 .. 0.92
   3 ?    0.1   3.4       1.4   1.5e+03       3      14 ..     203     214 ..     203     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.5
                            Fer4_4  4 C....igCgsC 10
                                      C     gC++C
  gi|386001506|ref|YP_005919805.1| 81 CecggAGCPAC 91
                                      5445569**** PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.3e-06
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       ++rC gCg+Cv +CP 
  gi|386001506|ref|YP_005919805.1| 169 SDRCEGCGKCVEVCPR 184
                                       69*************5 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                            Fer4_4   3 rCigCgsCvaaC 14 
                                       +C  C+ C+  C
  gi|386001506|ref|YP_005919805.1| 203 SCSLCKLCIGEC 214
                                       5999****9877 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.7   1.6e-05     0.017      41      59 ..     167     185 ..     138     187 .. 0.67
   2 ?    7.2   0.1     0.007       7.4       2      17 ..     204     219 ..     200     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                       +  ++C +Cg+C+++CP +
  gi|386001506|ref|YP_005919805.1| 167 TISDRCEGCGKCVEVCPRK 185
                                       3558999999999999976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.007
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C+ C+ C+ eC  +++
  gi|386001506|ref|YP_005919805.1| 204 CSLCKLCIGECDVGAI 219
                                       8888888888887665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.8   0.00044      0.46      44      65 .]     157     186 ..      80     186 .. 0.63
   2 ?    6.8   0.2    0.0087       9.2      50      64 ..     203     217 ..     192     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                            Fer4_8  44 e........eealwsCttcgaCtevCpvgi 65 
                                       +         ++ ++C +cg+C+evCp ++
  gi|386001506|ref|YP_005919805.1| 157 QcgyknlpeITISDRCEGCGKCVEVCPRKV 186
                                       24455566688999*************986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0087
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                       sC+ c+ C  +C vg
  gi|386001506|ref|YP_005919805.1| 203 SCSLCKLCIGECDVG 217
                                       788899888888775 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   5.8     3e-05     0.032       1      14 [.     172     185 ..     172     186 .. 0.93
   2 ?    0.9   3.1       1.1   1.1e+03       1      15 []     204     218 ..     204     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C gCg CvevCP +
  gi|386001506|ref|YP_005919805.1| 172 CEGCGKCVEVCPRK 185
                                       99**********76 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  C +C   C vgA
  gi|386001506|ref|YP_005919805.1| 204 CSLCKLCIGECDVGA 218
                                       89999**99998887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.6       5.1   5.4e+03      40      47 ..      82      91 ..      67      94 .. 0.58
   2 ?   14.3   4.4   3.2e-05     0.034      36      52 ..     167     183 ..     154     189 .. 0.84
   3 ?   10.0  14.2   0.00068      0.71       6      58 ..     170     220 ..     169     221 .. 0.75
   4 ?    4.7   2.6     0.032        34      40      58 ..     203     220 ..     197     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                           Fer4_21 40 eC..vGCnlC 47
                                      eC   GC  C
  gi|386001506|ref|YP_005919805.1| 82 ECggAGCPAC 91
                                      3422356666 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.2e-05
                           Fer4_21  36 vvedeCvGCnlCssvCP 52 
                                       +++d+C GC  C++vCP
  gi|386001506|ref|YP_005919805.1| 167 TISDRCEGCGKCVEVCP 183
                                       4699************* PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00068
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58 
                                       d+C gCgkC+ +C+      + ++++ +++v    +C  C+lC+  C v ++i+
  gi|386001506|ref|YP_005919805.1| 170 DRCEGCGKCVEVCPR--KVLVIGEGEGKVRVHdPISCSLCKLCIGECDV-GAIN 220
                                       79************5..3334445555556651569***********99.8886 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.032
                           Fer4_21  40 eCvGCnlCssvCPvedcie 58 
                                       +C  C+lC+  C v ++i+
  gi|386001506|ref|YP_005919805.1| 203 SCSLCKLCIGECDV-GAIN 220
                                       35555555555555.4443 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.2    0.0031       3.2       4      33 ..     170     200 ..     168     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                           Fer4_13   4 dtCiacgaCvelaP.dvFeeddeggasvvae 33 
                                       d+C +cg+Cve++P +v  + + +g+++v++
  gi|386001506|ref|YP_005919805.1| 170 DRCEGCGKCVEVCPrKVLVIGEGEGKVRVHD 200
                                       89************55999999999999976 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  10.0    0.0029         3      55      96 ..     166     215 ..     137     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                           Fer4_18  55 ekgagdcidcescvkvcPtgi........dirkGlqleciscllcidacd 96 
                                        + +  c  c++cv+vcP ++         +r    ++c  c lci  cd
  gi|386001506|ref|YP_005919805.1| 166 ITISDRCEGCGKCVEVCPRKVlvigegegKVRVHDPISCSLCKLCIGECD 215
                                       455678************99732222222234444688999999999998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.2   0.00014      0.15       6      20 ..     170     184 ..     169     203 .. 0.74
   2 ?    1.8   2.2      0.38     4e+02       6      22 ..     202     228 ..     196     245 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                           Fer4_15   6 daCigcglCvaeape 20 
                                       d+C+gcg Cv+++p+
  gi|386001506|ref|YP_005919805.1| 170 DRCEGCGKCVEVCPR 184
                                       9************75 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.38
                           Fer4_15   6 daCigcglCvaea..........pevf 22 
                                         C  c lC+ e+          ++vf
  gi|386001506|ref|YP_005919805.1| 202 ISCSLCKLCIGECdvgainvsavEDVF 228
                                       57*********9955555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1769.91
//
Query:       gi|386001507|ref|YP_005919806.1|  [L=129]
Description: 30S ribosomal protein S11 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-45  153.4   7.0    3.9e-45  152.8   7.0    1.3  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8   7.0   2.2e-49   3.9e-45       1     110 []       7     125 ..       7     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 2.2e-49
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       Gvahi+asfnntiititdl+Gae+++k +Gg++vka+r +ssPy+a+++a ++ae+++ +Gi  v+v+v++      
  gi|386001507|ref|YP_005919806.1|   7 GVAHIYASFNNTIITITDLTGAETIAKVSGGMVVKAARdESSPYTAMQMAGQIAEQAMTNGIIGVHVRVRApggnrq 83 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ralaraGlkigriedvtPiPhdg+++ ++rr
  gi|386001507|ref|YP_005919806.1|  84 rsPGPGAQAAIRALARAGLKIGRIEDVTPIPHDGTKPSGGRR 125
                                       ***************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 944.41
//
Query:       gi|386001508|ref|YP_005919807.1|  [L=158]
Description: 30S ribosomal protein S4 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-13   50.3   1.4    1.7e-13   50.0   0.1    1.9  2  S4        S4 domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.27   4.9e+03       9      17 ..      35      43 ..      30      46 .. 0.52
   2 !   50.0   0.1   9.6e-18   1.7e-13       1      47 [.      84     130 ..      84     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.27
                                      HTTSSSSHH CS
                                S4  9 rlglassrr 17
                                      +l+ a +r 
  gi|386001508|ref|YP_005919807.1| 35 QLLAATTRG 43
                                      344455555 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 9.6e-18
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                       rRL++ ++r+gla++ r+Arq+I hG++++ G++v+ p+y Vk g++
  gi|386001508|ref|YP_005919807.1|  84 RRLQTQVYRQGLAKTLRQARQFITHGHIQITGRKVTVPGYYVKRGEE 130
                                       8******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1198.14
//
Query:       gi|386001509|ref|YP_005919808.1|  [L=151]
Description: 30S ribosomal protein S13 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-38  129.9   4.4      8e-38  129.7   4.4    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   4.4   4.5e-42     8e-38       1     128 []      13     140 ..      13     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 4.5e-42
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       Ri++td++g++ v++alt i+G+Grr+a+ +++ka+++ +  +g+l++e i++++eive  aq++ p w+ nr+kd+
  gi|386001509|ref|YP_005919808.1|  13 RIMNTDLNGHQPVQMALTGITGMGRRNARLLAQKAEIEPTETLGKLSDEAISRLREIVES-AQEHLPVWMkNRRKDL 88 
                                       9**********************************************************9.8999999999****** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                        +G+d hv+ +dl + lre+++  +k rsyrG+RH+rGl+vRGQ+T++tgR+
  gi|386001509|ref|YP_005919808.1|  89 LTGEDRHVMGTDLVMALREEMDIIRKTRSYRGIRHERGLRVRGQKTRSTGRR 140
                                       ***************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1139.73
//
Query:       gi|386001510|ref|YP_005919809.1|  [L=423]
Description: putative 3-phosphoshikimate 1-carboxyvinyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.8e-109  364.5   0.2     7e-109  364.3   0.2    1.0  1  EPSP_synthase   EPSP synthase (3-phosphoshikimate 1-carboxyvi
  ------ inclusion threshold ------
        7.1    6.9   6.7       0.84    9.9   0.2    2.6  3  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.3   0.2  7.8e-113    7e-109       4     417 .]       7     411 ..       5     411 .. 0.94

  Alignments for each domain:
  == domain 1  score: 364.3 bits;  conditional E-value: 7.8e-113
                                       SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE CS
                     EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfea 80 
                                       +++++gev vp+sks+++ra+ ++aL+ g s ++ +L s+D+r+++ a  ++gaei+    e+e++ v+g gg  ++
  gi|386001510|ref|YP_005919809.1|   7 RSQVSGEVSVPPSKSYTHRAITISALGPGGS-VKRPLLSADTRATIRAAEAFGAEIAI---EGETLAVAGVGGGPKT 79 
                                       5789************************997.899******************87744...58999999999***** PP

                                       -HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BE CS
                     EPSP_synthase  81 peelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkg 156
                                       p e+v+d+ nsgt+lr+++a++al     vLtGd+sir RP  +ll++L  lGae  + +++ +apl v+g  k+++
  gi|386001510|ref|YP_005919809.1|  80 P-ENVIDVENSGTTLRIMAAVAALT-DGAVLTGDASIRRRPNGPLLRSLGDLGAEAFSIRKNDCAPLVVRGrIKGGR 154
                                       9.6********************97.6799*********************************************** PP

                                       EEEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SS..B--EE CS
                     EPSP_synthase 157 veikaevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkek..lpgte 229
                                       + ++++vsSq++++ll++ +l  e+ ++e+++ l+s+p+ ++tl+ml+++g+ iet  + +++  +G+++  l    
  gi|386001510|ref|YP_005919809.1| 155 TVLDGSVSSQFLSALLISCPLAEEDsEIEIKGeLKSRPYAEITLEMLEEAGAVIET--DFQRFSLRGGQSydLG--G 227
                                       ********************77777*******************************..8888********7444..6 PP

                                       EE--B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEET.TS--BEEEEEB CS
                     EPSP_synthase 230 yvvegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgps.glklkdvdiet 305
                                       y+v+gD ssA+y+l+aAa+tg++ tv++++++  qGd +++  il++mga+i++  ++   + +   l++++vd + 
  gi|386001510|ref|YP_005919809.1| 228 YTVPGDFSSASYLLAAAAVTGSRLTVRGLRPS-NQGDSAIVS-ILQEMGAKISWDRSEGVLEIEGrDLSGVEVDASL 302
                                       ****************************9985.689977777.**********99988777666669********** PP

                                       GSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTT CS
                     EPSP_synthase 306 lpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhR 382
                                        pd++pt+avl a+aeg+tv+++++++r ketdrl ama eL+k+Ga++ e++dgl i+++   l+ga+v+ ++DhR
  gi|386001510|ref|YP_005919809.1| 303 TPDLVPTIAVLGAVAEGRTVVRNAEHVRHKETDRLRAMAVELSKMGAKISERPDGLVIEGGG--LRGARVNGHHDHR 377
                                       *********************************************************88885..8************ PP

                                       TTHHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 383 iamalalaglvaegeveiddiectdksfpefeekL 417
                                       i ma+++agl ++g++ ++ +e++++s+p+f+e++
  gi|386001510|ref|YP_005919809.1| 378 IVMAMTVAGL-VAGDTMVETAEAVSVSYPGFFEEM 411
                                       *********5.5666*****************986 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   9.3e-05      0.84      18      56 ..      44      76 ..      44      77 .. 0.92
   2 ?   -0.6   0.3      0.18   1.6e+03      16      28 ..     235     247 ..     235     272 .. 0.82
   3 ?   -2.9   0.1      0.92   8.3e+03      19      29 ..     381     391 ..     381     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.3e-05
                                      HHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHS CS
                    GHMP_kinases_N 18 AAlavalvaAllallglsleeaklaleaerlaqggngsg 56
                                      +A++ a+++A+ a+       a++a+e+e la+ g+g+g
  gi|386001510|ref|YP_005919809.1| 44 SADTRATIRAAEAFG------AEIAIEGETLAVAGVGGG 76
                                      79999*****98888......9**********9999988 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHH CS
                    GHMP_kinases_N  16 SSAAlavalvaAl 28 
                                       SSA++ +a++a  
  gi|386001510|ref|YP_005919809.1| 235 SSASYLLAAAAVT 247
                                       8999999988865 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.92
                                       HHHHHHHHHHH CS
                    GHMP_kinases_N  19 AlavalvaAll 29 
                                       A++va+++A  
  gi|386001510|ref|YP_005919809.1| 381 AMTVAGLVAGD 391
                                       78999998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 3186.93
//
Query:       gi|386001511|ref|YP_005919810.1|  [L=244]
Description: putative ribosomal RNA small subunit methyltransferase A [Methanosaeta harundinacea 6Ac]
Scores for complete 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-50  171.1   0.0    2.5e-50  171.0   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
      7e-06   26.7   0.0    1.2e-05   25.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00044   20.8   0.0    0.00079   20.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0013   18.6   0.0     0.0018   18.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0075   16.0   0.0      0.048   13.4   0.0    1.9  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.037   13.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      0.046   13.7   0.0      0.072   13.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.085   13.0   0.0       0.12   12.5   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
       0.11   13.2   0.0       0.17   12.6   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
        0.2   10.7   0.0       0.26   10.4   0.0    1.2  1  DREV             DREV methyltransferase


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0   0.0   1.4e-53   2.5e-50       6     228 ..       2     207 ..       1     241 [. 0.93

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 1.4e-53
                                       XGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE- CS
                            RrnaAD   6 ksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvh 82 
                                       k++gq+fl+++ v+ +I d + l  ++ vle+gpG+G+lT+ L +ra +v ++E d++La +l+ +++   ++ ++ 
  gi|386001511|ref|YP_005919810.1|   2 KKLGQHFLIDRRVLSRIGDYASLGRSDAVLEVGPGTGNLTRVLSERAGSVYAIEVDPALASSLEGRFE---NVSIIR 75 
                                       689**************************************************************888...****** PP

                                       S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHH CS
                            RrnaAD  83 qDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsv 159
                                        D+l   +pe            ++v+nlPy+is+++ ++ll   r+ +  ++l+ q+efa+r++a+pg ++r+rls+
  gi|386001511|ref|YP_005919810.1|  76 GDALRVPLPE----------YNKIVSNLPYQISSKITFRLLA--RP-FDLAVLMYQREFAERMVAPPGTRERGRLSL 139
                                       **********..........349******************6..44.5799************************** PP

                                       HHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCT CS
                            RrnaAD 160 lreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksl 228
                                       ++ ++++++++++v++ +fsP p+v+sa+v+l++++++   +d++ +e+++r l+  +rk+++ +l  +
  gi|386001511|ref|YP_005919810.1| 140 NVAFWAEAEVLETVPRGAFSPRPQVESAIVRLRPRKTP-APVDWAGFEALTRGLFSMRRKKIKRALAAM 207
                                       *************************************9.599*********************998754 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   6.6e-09   1.2e-05       1      71 [.      30      92 ..      30     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.6e-09
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71
                                      vL++G GtG+lt+ l++r   ++v+++++++++    + r+e    nv++++gda ++p+++  ++ +vs+
  gi|386001511|ref|YP_005919810.1| 30 VLEVGPGTGNLTRVLSERA--GSVYAIEVDPALASSLEGRFE----NVSIIRGDALRVPLPE--YNKIVSN 92
                                      9*****************7..9*******************4....9************997..8888874 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.4e-07   0.00079       1      59 [.      31      85 ..      31      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.4e-07
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfed 59
                                      L+vG GtG l++ l +r+++v+++++++++    + + ++    v+++++da ++p+++
  gi|386001511|ref|YP_005919810.1| 31 LEVGPGTGNLTRVLSERAGSVYAIEVDPALASSLEGRFEN----VSIIRGDALRVPLPE 85
                                      89***************************99655444444....779*********997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     1e-06    0.0018      15      62 ..      17      76 ..       6     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                   Methyltransf_23 15 rllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........k 62
                                      r++++  l ++  vL++G+GtG+l++vl+e+  sv++++ +p++ + +e          +
  gi|386001511|ref|YP_005919810.1| 17 RIGDYasLGRSDAVLEVGPGTGNLTRVLSERAGSVYAIEVDPALASSLEgrfenvsiirG 76
                                      4554443678889******************99******999877766555555555551 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.7e-05     0.048      64     116 ..      17      66 ..       7      80 .. 0.78
   2 ?   -0.0   0.0      0.34   6.2e+02      22      37 ..     147     162 ..     143     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                                       ++ ++ +l + + vLevG G+G lt vl++  g++    +ie  + l+++ + 
  gi|386001511|ref|YP_005919810.1|  17 RIGDYASLGRSDAVLEVGPGTGNLTRVLSERAGSV---YAIEVDPALASSLEG 66 
                                       5668889999******************9866555...488887777766555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.34
                                       HHHHHHS-GGGGSSCG CS
                              PCMT  22 aealeevdReefvpes 37 
                                       ae+le+v+R+ f+p++
  gi|386001511|ref|YP_005919810.1| 147 AEVLETVPRGAFSPRP 162
                                       689**********985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.037       5      82 ..      28      93 ..      24     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                   Methyltransf_31  5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82
                                        vl++G GtG+lt +l e++g+   v+ i+ ++   ++ + +     ++nv+  +gd+   +  l    ++ i+sn 
  gi|386001511|ref|YP_005919810.1| 28 DAVLEVGPGTGNLTRVLSERAGS---VYAIEVDPALASSLEGR-----FENVSIIRGDALRVP--LP--EYNKIVSNL 93
                                      579***************99877...********998888887.....99***********99..55..488888874 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     4e-05     0.072      24      73 ..      25      70 ..      12      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                   Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraek 73
                                       ++  v++vG G g L++vl+        +v++i++  +l+++ e r e+
  gi|386001511|ref|YP_005919810.1| 25 GRSDAVLEVGPGTGNLTRVLSE----RAGSVYAIEVDPALASSLEGRFEN 70
                                      567899****************....489*********999988877665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.6e-05      0.12      20      72 ..      25      80 ..      11     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                                      -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEECS-CCC CS
                              FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditd 72
                                       + ++v+++g ++G+ + vl++r    g v+a+ + p         +++v++i+gd ++
  gi|386001511|ref|YP_005919810.1| 25 GRSDAVLEVGPGTGNLTRVLSERA---GSVYAIEVDPAlassleGRFENVSIIRGDALR 80
                                      46678******************4...78********99976644559********865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.7e-05      0.17       1      40 [.      31      68 ..      31     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakekl 40
                                      Le+G GtG+l+r+l e+    ++++++++p+     + ++
  gi|386001511|ref|YP_005919810.1| 31 LEVGPGTGNLTRVLSER--AGSVYAIEVDPALASSLEGRF 68
                                      8****************..99999***9999885444444 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014      0.26      89     133 ..      21      65 ..       1      78 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                              DREV  89 pasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlk 133
                                       +as  ++  +l++G G G++t+ +++    vya e+   +   l+
  gi|386001511|ref|YP_005919810.1|  21 YASLGRSDAVLEVGPGTGNLTRVLSERAGSVYAIEVDPALASSLE 65 
                                       556567789**************************9888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1530.18
//
Query:       gi|386001512|ref|YP_005919811.1|  [L=179]
Description: hypothetical protein Mhar_0816 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-60  201.9   0.0    8.9e-60  201.7   0.0    1.0  1  DUF655    Protein of unknown function (DUF655)
    9.4e-06   25.8   0.0    1.7e-05   24.9   0.0    1.4  1  HHH_6     Helix-hairpin-helix motif
    2.5e-05   24.5   0.0    7.1e-05   23.0   0.0    1.7  1  HHH_3     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.7   0.0   1.5e-63   8.9e-60       8     180 ..       1     173 [.       1     174 [. 0.97

  Alignments for each domain:
  == domain 1  score: 201.7 bits;  conditional E-value: 1.5e-63
                                       EEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-HHHHH CS
                            DUF655   8 LDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtdvara 84 
                                       +Dylp+G+ +d +  ++++p++q++ger++ L+e+ p++ +  ++  +  +  + +  +++++r+i ye+L+++ar+
  gi|386001512|ref|YP_005919811.1|   1 MDYLPYGHVSDSMGRFQKRPLIQGVGERDFVLMEMAPKEGAVPEIGVRAVLVGKDRPIVDRVNRRIGYEELSQGARV 77 
                                       6****************************************99999887777778999******************* PP

                                       HHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHH CS
                            DUF655  85 eLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeil 161
                                       eLp++++kiv +kE  + +ffnea p+t+R+HaLelLpg+gkkl+++il+eR++ +F+sFed+++rvkg+ +p+++l
  gi|386001512|ref|YP_005919811.1|  78 ELPYAIQKIVLDKEAYYLRFFNEAGPLTTRMHALELLPGIGKKLMWAILNERKKGPFKSFEDLSERVKGIYNPEKLL 154
                                       ***************************************************************************** PP

                                       HHHHHHHHH-TTSS--SS- CS
                            DUF655 162 verileEiedktekYylFv 180
                                       ++ri +Ei d++ kY++F+
  gi|386001512|ref|YP_005919811.1| 155 AKRIEDEIADDRIKYRIFT 173
                                       ******************8 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.9e-09   1.7e-05      28      66 ..     110     148 ..     104     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.9e-09
                             HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvds.l 66 
                                       +L+ + g+g++ + +i++eR+ +gpfks+edl++rv+   
  gi|386001512|ref|YP_005919811.1| 110 ALELLPGIGKKLMWAILNERK-KGPFKSFEDLSERVKGiY 148
                                       678889**************9.8*************9654 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.2e-08   7.1e-05      14      52 ..     109     147 ..     105     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.2e-08
                             HHH_3  14 eeLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                         L+ lpG+g+kl  +I++ R k+Gpfks+e+L  +vkg+
  gi|386001512|ref|YP_005919811.1| 109 HALELLPGIGKKLMWAILNER-KKGPFKSFEDLSeRVKGI 147
                                       67999****************.99*********9678887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1205.82
//
Query:       gi|386001513|ref|YP_005919812.1|  [L=115]
Description: DNA-directed RNA polymerase subunit F [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-08   33.4   1.8    6.7e-08   32.9   1.8    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4
  ------ inclusion threshold ------
       0.16   12.2   0.3       0.32   11.1   0.2    1.6  1  DUF3567       Protein of unknown function (DUF3567)
       0.16   11.2   0.9        2.5    7.3   0.2    2.0  2  COOH-NH2_lig  Phage phiEco32-like COOH.NH2 ligase-type 2


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   1.8   1.1e-11   6.7e-08       2     119 ..      12     112 ..       8     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.1e-11
                                       E-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTST CS
                      RNA_pol_Rpb4   2 LsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLt 78 
                                       +++ Ev++ l+ e+  r               + e +++l ++l++++++ +  fs+ + +e+ + + el+   ++t
  gi|386001513|ref|YP_005919812.1|  12 MTLAEVKEALE-EIRLR---------------RAEEPEELGYELRRAIKHAEI-FSKGEAAESRKMVEELMGLEKMT 71 
                                       56666666666.44444...............234689***************.*****7777666666666777** PP

                                       HHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHH CS
                      RNA_pol_Rpb4  79 kaEklqlvnlkPesavelktlieeleerfedeqleeiLdel 119
                                       +  ++++ +++P++ +e+++l ++++  + de+l++iLd +
  gi|386001513|ref|YP_005919812.1|  72 NEIAIKIADIRPKTKDEIRALYAKERFTLLDEDLDAILDVV 112
                                       **************************************976 PP

>> DUF3567  Protein of unknown function (DUF3567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   5.4e-05      0.32      25      71 ..      29      74 ..       8      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                           DUF3567 25 aekaargGyEivDKrakkeiyldGslAesfrkevkalieeepseeev 71
                                      ae+ ++ GyE+     + ei+ +G++Aes rk v++l+  e+ ++e+
  gi|386001513|ref|YP_005919812.1| 29 AEEPEELGYELRRAIKHAEIFSKGEAAES-RKMVEELMGLEKMTNEI 74
                                      2333889*******************998.88999999888877776 PP

>> COOH-NH2_lig  Phage phiEco32-like COOH.NH2 ligase-type 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2   0.00041       2.5      39      71 ..      15      47 ..       7      66 .. 0.87
   2 ?    3.2   0.0    0.0073        44      38      62 ..      71      95 ..      54     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00041
                      COOH-NH2_lig 39 eekelplaElRPapaedpaelleelrkllqeaa 71
                                      +e + +l E+R + ae+p+el  elr+++++a+
  gi|386001513|ref|YP_005919812.1| 15 AEVKEALEEIRLRRAEEPEELGYELRRAIKHAE 47
                                      5667899***********************997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0073
                      COOH-NH2_lig 38 reekelplaElRPapaedpaellee 62
                                      ++e ++ +a++RP+ + + ++l ++
  gi|386001513|ref|YP_005919812.1| 71 TNEIAIKIADIRPKTKDEIRALYAK 95
                                      45667889********999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 815.05
//
Query:       gi|386001514|ref|YP_005919813.1|  [L=96]
Description: 50S ribosomal protein L21e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-34  116.2   0.4    5.3e-34  116.1   0.4    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.4   2.9e-38   5.3e-34       1     100 [.       1      96 []       1      96 [] 0.99

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 2.9e-38
                                       X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEE CS
                    Ribosomal_L21e   1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivn 77 
                                       m++s+g r++tr+ +sk++r++g++p+s+++++++ G++V+i+ dps+++gmp + +hGktg+v   ++r+++++++
  gi|386001514|ref|YP_005919813.1|   1 MPKSHGIRKRTRDRLSKSVRERGISPVSRAIQDFDDGQMVHIVLDPSIHRGMPNPKFHGKTGKV--LGRRGRAYVLE 75 
                                       89**************************************************************..*********** PP

                                       EEETTE..EEEEEE-GGGEEE-- CS
                    Ribosomal_L21e  78 kkvggkileKriivriehlkksk 100
                                       +++g+   +K+++  +ehlk+++
  gi|386001514|ref|YP_005919813.1|  76 VRDGNA--KKTVVSLPEHLKPQN 96 
                                       ******..************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 745.95
//
Query:       gi|386001515|ref|YP_005919814.1|  [L=451]
Description: tRNA pseudouridine synthase Pus10 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-10   39.9   0.0    7.1e-09   35.9   0.0    2.3  2  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   3.9e-13   7.1e-09      58     142 ..      98     194 ..      82     196 .. 0.93
   2 ?    1.1   0.1     0.021   3.7e+02      31      77 ..     317     359 ..     291     373 .. 0.60

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.9e-13
                                       EEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-E CS
                             THUMP  58 evceadledileaakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglk 119
                                       e  +a+l++  eaa+   ++  +e   tF V+++  g  +               e  + e+nrevGk+i e+tg+ 
  gi|386001515|ref|YP_005919814.1|  98 EMEPARLDRWAEAAERELRHLEHE---TFLVGTRMSGLLAeneeliladggsrhaEPMKSELNREVGKRIAERTGKA 171
                                       667889999999999999999888...**********99999*********************************** PP

                                       E-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP 120 VdlenPdivvrveiikdkayisi 142
                                        ++++Pd++  +++ + ++++++
  gi|386001515|ref|YP_005919814.1| 172 TSFTSPDVLAVLDLEEGAVEVQV 194
                                       *********************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.021
                                       EEEEETHHHHHHHHHTSTTECEEEEE....EEEEESSHHHHHHHHHHHHHH CS
                             THUMP  31 ekpeedeellkealekargiqrvipv....cevceadledileaakeivkk 77 
                                       e++e+ +++l        + ++ ++v    +ev+e++l+++l++ + +v+ 
  gi|386001515|ref|YP_005919814.1| 317 ETVEGLKKAL--------FEKSYSMVvelgEEVPEEKLKSVLDKLVGLVEQ 359
                                       3333333333........222222223366888888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2675.42
//
Query:       gi|386001516|ref|YP_005919815.1|  [L=204]
Description: hypothetical protein Mhar_0820 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-51  172.3   0.0    1.1e-50  172.1   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
      0.092   12.1   0.4       0.21   10.9   0.4    1.6  1  SAMP             SAMP Motif


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.1   0.0   1.2e-54   1.1e-50       7     196 ..       2     186 ..       1     188 [. 0.94

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 1.2e-54
                                       EESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHHHH CS
                   Methyltrn_RNA_2   7 lankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspderni 83 
                                       ++n a+T++d++l+dlpG++gr+d+l+rc++ a+ +shgiR+dv++yl+L g+   p+t+++++  +++ +pder  
  gi|386001516|ref|YP_005919815.1|   2 VGNLATTTPDFSLEDLPGTSGRIDILCRCINSAFVLSHGIRRDVQIYLILRGGG-APKTVRLQGRDLRHLNPDERTT 77 
                                       7899***********************************************775.689******************* PP

                                       HHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCTSEEEEESTTSEEGGGS---SSEEEEEE-TT-SHHH CS
                   Methyltrn_RNA_2  84 ailikkalkaveeikkqekkvrpgltVrkegfealleelsekksiillkekGedisnakielnPvFilgdHidlpee 160
                                       a l+kkal a  e    + k++pg+ Vr   + +l     +    ++l e+G d +   +  + +F+lgdHi+l+ee
  gi|386001516|ref|YP_005919815.1|  78 AALLKKAL-AL-EADFAWTKSTPGISVRAGDLADLPIRAEG--RTYYLREDGSDHRGLPLAGDGTFVLGDHIGLSEE 150
                                       ********.55.69999************999999655555..89*******9999999999*************** PP

                                       HHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 161 eekllerlkakrvslgPlsLhadhcvtlihneldkk 196
                                       +e +l+ l+a+ vs+gP+sLhadhc++l  neld+ 
  gi|386001516|ref|YP_005919815.1| 151 DEAFLAGLGAEIVSVGPKSLHADHCIVLLNNELDRR 186
                                       **********************************86 PP

>> SAMP  SAMP Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   2.3e-05      0.21       6      16 ..      24      34 ..      24      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.3e-05
                              SAMP  6 ddlLqeCIgSA 16
                                      +d+L +CI+SA
  gi|386001516|ref|YP_005919815.1| 24 IDILCRCINSA 34
                                      6*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1452.21
//
Query:       gi|386001517|ref|YP_005919816.1|  [L=489]
Description: hypothetical protein Mhar_0821 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-21   74.3   0.0    9.1e-18   64.5   0.0    2.3  2  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00011         2      42     167 ..     140     244 ..      57     261 .. 0.72
   2 !   64.5   0.0   5.1e-22   9.1e-18     174     298 .]     366     478 ..     346     478 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00011
                                       GEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  42 ngadsettstnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkvldtsggsmetgteliraieeaa 118
                                       n +  + ++++++ +d++    HG     ia+a       ++ +apg+ki+ v v+ t+       ++++ra+e+ +
  gi|386001517|ref|YP_005919816.1| 140 NADIVTLYDDESYGKDEV----HG-----IACAE-----LISSIAPGVKIYLVDVGITE-------EGVARAVERLL 195
                                       444444455555555544....55.....55555.....67788999999988888443.......67889999987 PP

                                       H..CT-SEEEE-EE...SCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T CS
                                       x..xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 119 e..dkvdvinmslg...estslpktgrsiealainravnkkgvlvviSaGNngk 167
                                       e  +++d++++s     ++++ ++ +  ++   +++++ ++g+l + +aGN+  
  gi|386001517|ref|YP_005919816.1| 196 EleERIDIVSCSSDfpfGGFDGEDAV--CQ--DVEKMT-SNGTLWINAAGNEAL 244
                                       7668999*****99444344444333..33..567777.78**********974 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 5.1e-22
                                       -TTCEECTTTSTTCEEEEEES.TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 174 agspvgtpstsknvitvgayt.tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSm 249
                                       ++ ++g  + ++nv+tvga++ +  +i p+SsrGp+ dg+ kpd++ap     s++ +++           + GTS+
  gi|386001517|ref|YP_005919816.1| 366 QNTSIGILGCCRNVVTVGAINiSTLEIQPYSSRGPTEDGRQKPDLMAPDNVTTSSYATEG-----------FVGTSA 431
                                       66777888899**********88889**********************888666666666...........89**** PP

                                       CHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 250 AsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                       A+P++ag+aAl+l+ +++  + +vr++ll +A+dlg +  + ++++G+G
  gi|386001517|ref|YP_005919816.1| 432 AAPFVAGCAALVLELFKDDPDLDVRRVLLESATDLGPP--GPDEICGWG 478
                                       ***********************************666..********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 3678.62
//
Query:       gi|386001518|ref|YP_005919817.1|  [L=590]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-33  113.6  31.9    1.7e-08   34.9   2.2    7.6  8  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
    2.1e-18   66.1  61.8    0.00021   21.3   1.5   10.1  9  FG-GAP           FG-GAP repeat
    2.6e-18   66.0   1.0      0.026   14.6   0.0    7.5  7  BBS2_Mid         Ciliary BBSome complex subunit 2, middle reg
    2.4e-12   46.5  17.1      0.041   12.9   0.0    7.5  8  Itfg2            Integrin-alpha FG-GAP repeat-containing prot
    1.1e-08   35.3  21.7      0.062   13.8   0.0    7.3  7  PQQ_3            PQQ-like domain
    9.1e-05   22.2   9.2        2.6    8.1   0.0    6.3  6  PQQ              PQQ enzyme repeat
    0.00078   19.2   0.6       0.54   10.0   0.0    4.2  5  PliI             Periplasmic lysozyme inhibitor of I-type lys
  ------ inclusion threshold ------
      0.048   14.5   7.4        1.8    9.6   0.1    4.8  4  WD40             WD domain, G-beta repeat
      0.062   12.7  23.1        2.5    7.4   0.1    7.2  8  TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal reg
        3.3    7.5  21.6         58    3.6   0.0    7.2  7  EF-hand_1        EF hand


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1     2e+03      35      53 ..      87     105 ..      71     105 .. 0.76
   2 !   17.6   0.0   2.4e-06    0.0042       1      26 [.     190     216 ..     160     235 .. 0.80
   3 !   34.9   2.2   9.6e-12   1.7e-08       1      61 []     237     295 ..     237     295 .. 0.80
   4 !   23.6   3.1   3.3e-08     6e-05       1      59 [.     284     340 ..     284     342 .. 0.79
   5 !   27.2   1.1   2.5e-09   4.5e-06       1      61 []     331     413 ..     331     413 .. 0.63
   6 !   32.2   2.3   6.9e-11   1.2e-07       1      60 [.     449     505 ..     449     506 .. 0.89
   7 !   28.0   2.4   1.4e-09   2.5e-06       1      60 [.     495     552 ..     495     553 .. 0.83
   8 !   12.9   0.3   7.4e-05      0.13       1      30 [.     542     570 ..     542     585 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                              VCBS  35 tslggsgggtgvavgDlDg 53 
                                       +++++++  +  a+gDl+g
  gi|386001518|ref|YP_005919817.1|  87 QESSENFEVMKSAAGDLNG 105
                                       577778888999******8 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.4e-06
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngd 26 
                                       D+dgDG l++vv++ +g+l+v+  +g+
  gi|386001518|ref|YP_005919817.1| 190 DIDGDGELEIVVGTnEGRLYVFNRDGS 216
                                       788888888888864677777777765 PP

  == domain 3  score: 34.9 bits;  conditional E-value: 9.6e-12
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       DldgDG+lD+vv++ dg+l+ + ++g    + ++ + l+++  + ++a+gDlDgD  l+++v
  gi|386001518|ref|YP_005919817.1| 237 DLDGDGLLDIVVGSdDGRLYAWNGRGE---ELSGFPRLTSNSVWSSPAIGDLDGDSGLEVVV 295
                                       9************85787777766654...233335788888899**********9999987 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 3.3e-08
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtkt.slggsgggtgvavgDlDgDGdlDl 59 
                                       DldgD  l++vv++ d g++ + ++g    ++v  +  ++++  + ++a+gDlDgDG lD 
  gi|386001518|ref|YP_005919817.1| 284 DLDGDSGLEVVVGStDRGIYAFNGDG----SPVCGYpLITSNSVWSSPAIGDLDGDGLLDS 340
                                       9************8788888887764....46655515666777779************95 PP

  == domain 5  score: 27.2 bits;  conditional E-value: 2.5e-09
                              VCBS   1 DldgDGrlDlvvan..dgg...........lrvyrnngdGtft........dvtktslgg.sgggtgvavgDlDgDG 55 
                                       DldgDG+lD v+++  +g+            +vy  +g G++         +++ t+l+g + g+ ++ ++DlDgDG
  gi|386001518|ref|YP_005919817.1| 331 DLDGDGLLDSVIGSskMGTdilaiflglytGQVYAVDGLGSLLpgypvdlsSPSLTDLSGsAIGYSSPILADLDGDG 407
                                       9************532477665555444444555555555433444442224444555554555668********** PP

                              VCBS  56 dlDllv 61 
                                        l++++
  gi|386001518|ref|YP_005919817.1| 408 SLEIVI 413
                                       ***985 PP

  == domain 6  score: 32.2 bits;  conditional E-value: 6.9e-11
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D+dgDG  ++v +  dg+l+++r +g+         ++ ++g+  ++a++D+DgDG+ +++
  gi|386001518|ref|YP_005919817.1| 449 DVDGDGEVEIVGGAtDGRLYLWRSDGSD----HPGFPIQTGGYVKNIALADIDGDGQQEII 505
                                       9***********966*********9764....4566899999999************9997 PP

  == domain 7  score: 28.0 bits;  conditional E-value: 1.4e-09
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D+dgDG ++++ ++ d++++ +r +g+        ++++ ++  t++a++Dl gDG lD++
  gi|386001518|ref|YP_005919817.1| 495 DIDGDGQQEIIGGSlDNRVHAWRLDGTE-VDGF--PKVTLGNVDTTPAIADLEGDGVLDMV 552
                                       9***********************9753.2222..34555677899*************98 PP

  == domain 8  score: 12.9 bits;  conditional E-value: 7.4e-05
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtft 30 
                                       Dl gDG lD+v+++ dg++++++ +  G f 
  gi|386001518|ref|YP_005919817.1| 542 DLEGDGVLDMVAGSdDGRIYIWEIS--GAFG 570
                                       899**********868999999887..4554 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.48   8.5e+02       6      12 ..      99     105 ..      97     105 .. 0.89
   2 !   18.5   0.2     9e-07    0.0016       3      31 ..     184     205 ..     182     215 .. 0.82
   3 !   21.3   1.5   1.2e-07   0.00021       3      32 ..     231     260 ..     229     262 .. 0.82
   4 ?    3.4   5.5     0.048        86       3      21 ..     278     296 ..     276     310 .. 0.81
   5 !    9.8   3.4   0.00047      0.84       3      19 ..     325     341 ..     323     366 .. 0.86
   6 !   14.1   0.7   2.1e-05     0.038       4      24 ..     397     417 ..     394     431 .. 0.78
   7 !   13.0   0.8   4.9e-05     0.087       5      23 ..     445     465 ..     443     485 .. 0.80
   8 !   11.9   0.3    0.0001      0.18       5      21 ..     491     507 ..     490     515 .. 0.89
   9 !    7.3   0.5     0.003       5.3       4      36 ..     537     562 ..     536     563 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.48
                                       EEESTSS CS
                            FG-GAP   6 avgDvNG 12 
                                       a+gD+NG
  gi|386001518|ref|YP_005919817.1|  99 AAGDLNG 105
                                       89****9 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 9e-07
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTT CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggayg 31 
                                       +s a++D++GDG  +++vG       +++
  gi|386001518|ref|YP_005919817.1| 184 SSPALADIDGDGELEIVVG-------TNE 205
                                       899****************.......333 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 1.2e-07
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTT..B CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggayg..G 32 
                                       +s av D++GDG+ D++vG  +++g+ y+  G
  gi|386001518|ref|YP_005919817.1| 231 SSPAVEDLDGDGLLDIVVG--SDDGRLYAwnG 260
                                       7999***************..65777666655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.048
                                       SSEEEESTSSSSS-EEEEE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavG 21 
                                       +s a gD++GD   +++vG
  gi|386001518|ref|YP_005919817.1| 278 SSPAIGDLDGDSGLEVVVG 296
                                       899********99999999 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00047
                                       SSEEEESTSSSSS-EEE CS
                            FG-GAP   3 yslavgDvNGDGyaDLa 19 
                                       +s a gD++GDG+ D +
  gi|386001518|ref|YP_005919817.1| 325 SSPAIGDLDGDGLLDSV 341
                                       899**********9955 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 2.1e-05
                                       SEEEESTSSSSS-EEEEEETT CS
                            FG-GAP   4 slavgDvNGDGyaDLavGApe 24 
                                       s  ++D++GDG  ++++GA+ 
  gi|386001518|ref|YP_005919817.1| 397 SPILADLDGDGSLEIVIGASD 417
                                       55579*************843 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 4.9e-05
                                       EEEESTSSSSS-EEEEEE..T CS
                            FG-GAP   5 lavgDvNGDGyaDLavGA..p 23 
                                       +a+gDv+GDG  +++ GA  +
  gi|386001518|ref|YP_005919817.1| 445 IAAGDVDGDGEVEIVGGAtdG 465
                                       79*************998551 PP

  == domain 8  score: 11.9 bits;  conditional E-value: 0.0001
                                       EEEESTSSSSS-EEEEE CS
                            FG-GAP   5 lavgDvNGDGyaDLavG 21 
                                       +a++D++GDG ++++ G
  gi|386001518|ref|YP_005919817.1| 491 IALADIDGDGQQEIIGG 507
                                       699***********988 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.003
                                       SEEEESTSSSSS-EEEEEETT-ETCSTTBEEEE CS
                            FG-GAP   4 slavgDvNGDGyaDLavGApeskggaygGaVyv 36 
                                       + a +D+ GDG+ D + G       +++G++y+
  gi|386001518|ref|YP_005919817.1| 537 TPAIADLEGDGVLDMVAG-------SDDGRIYI 562
                                       67899************9.......55566666 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.026       3      31 ..     187     215 ..     185     224 .. 0.90
   2 !    6.5   0.0    0.0047       8.4       3      27 ..     234     258 ..     232     265 .. 0.85
   3 !    8.6   0.0     0.001       1.8       3      30 ..     281     308 ..     279     312 .. 0.91
   4 ?    5.0   0.0     0.014        25       4      21 ..     400     417 ..     397     425 .. 0.84
   5 ?    4.5   0.0     0.019        34       3      30 ..     446     473 ..     444     477 .. 0.84
   6 !   11.1   0.0   0.00017       0.3       2      28 ..     491     517 ..     490     524 .. 0.89
   7 !    5.8   0.0    0.0077        14       3      27 ..     539     563 ..     538     569 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                          BBS2_Mid   3 aladvdgdgeneLvvgsddfeirvfkeee 31 
                                       alad+dgdge e+vvg+++ ++ vf+++ 
  gi|386001518|ref|YP_005919817.1| 187 ALADIDGDGELEIVVGTNEGRLYVFNRDG 215
                                       799**********************9985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0047
                          BBS2_Mid   3 aladvdgdgeneLvvgsddfeirvf 27 
                                       a+ d+dgdg  ++vvgsdd ++  +
  gi|386001518|ref|YP_005919817.1| 234 AVEDLDGDGLLDIVVGSDDGRLYAW 258
                                       57899**************987655 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.001
                          BBS2_Mid   3 aladvdgdgeneLvvgsddfeirvfkee 30 
                                       a+ d+dgd   e+vvgs+d  i  f+++
  gi|386001518|ref|YP_005919817.1| 281 AIGDLDGDSGLEVVVGSTDRGIYAFNGD 308
                                       5789*********************987 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.014
                          BBS2_Mid   4 ladvdgdgeneLvvgsdd 21 
                                       lad+dgdg+ e+v+g+ d
  gi|386001518|ref|YP_005919817.1| 400 LADLDGDGSLEIVIGASD 417
                                       789999999999999888 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.019
                          BBS2_Mid   3 aladvdgdgeneLvvgsddfeirvfkee 30 
                                       a  dvdgdge e+v g++d ++ +++ +
  gi|386001518|ref|YP_005919817.1| 446 AAGDVDGDGEVEIVGGATDGRLYLWRSD 473
                                       667999**********999998887765 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00017
                          BBS2_Mid   2 laladvdgdgeneLvvgsddfeirvfk 28 
                                       +alad+dgdg++e++ gs d+++  ++
  gi|386001518|ref|YP_005919817.1| 491 IALADIDGDGQQEIIGGSLDNRVHAWR 517
                                       799*******************99877 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.0077
                          BBS2_Mid   3 aladvdgdgeneLvvgsddfeirvf 27 
                                       a+ad++gdg  ++v+gsdd +i ++
  gi|386001518|ref|YP_005919817.1| 539 AIADLEGDGVLDMVAGSDDGRIYIW 563
                                       58999**************999876 PP

>> Itfg2  Integrin-alpha FG-GAP repeat-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0022       3.9      84     107 ..     188     211 ..     183     220 .. 0.82
   2 !    5.5   0.2    0.0042       7.6      84     109 ..     235     258 ..     233     278 .. 0.80
   3 !   10.4   0.0   0.00013      0.23      84     108 ..     282     306 ..     270     312 .. 0.90
   4 ?   -2.7   0.0       1.3   2.4e+03      84      99 ..     329     344 ..     326     346 .. 0.88
   5 !    7.3   0.0    0.0012       2.1      83     102 ..     399     418 ..     395     430 .. 0.89
   6 !    6.6   0.1    0.0019       3.5      85     109 ..     448     470 ..     441     480 .. 0.77
   7 !   12.9   0.0   2.3e-05     0.041      79     109 ..     488     518 ..     477     531 .. 0.88
   8 ?    2.8   0.1     0.028        50      84     109 ..     540     563 ..     528     575 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                             Itfg2  84 iaDidgDgkvElvvgytDrvvray 107
                                       +aDidgDg++E+vvg  +   +++
  gi|386001518|ref|YP_005919817.1| 188 LADIDGDGELEIVVGTNEGRLYVF 211
                                       68************9877655555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0042
                             Itfg2  84 iaDidgDgkvElvvgytDrvvrayrW 109
                                       ++D+dgDg++++vvg  D   r y W
  gi|386001518|ref|YP_005919817.1| 235 VEDLDGDGLLDIVVGSDDG--RLYAW 258
                                       89*************9997..55666 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00013
                             Itfg2  84 iaDidgDgkvElvvgytDrvvrayr 108
                                       i D+dgD  +E+vvg tDr ++a++
  gi|386001518|ref|YP_005919817.1| 282 IGDLDGDSGLEVVVGSTDRGIYAFN 306
                                       88********************996 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.3
                             Itfg2  84 iaDidgDgkvElvvgy 99 
                                       i D+dgDg+++ v+g 
  gi|386001518|ref|YP_005919817.1| 329 IGDLDGDGLLDSVIGS 344
                                       78*********99996 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0012
                             Itfg2  83 liaDidgDgkvElvvgytDr 102
                                       ++aD+dgDg +E+v+g +D 
  gi|386001518|ref|YP_005919817.1| 399 ILADLDGDGSLEIVIGASDG 418
                                       689**************995 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.0019
                             Itfg2  85 aDidgDgkvElvvgytDrvvrayrW 109
                                        D+dgDg+vE+v g tD     y W
  gi|386001518|ref|YP_005919817.1| 448 GDVDGDGEVEIVGGATDGR--LYLW 470
                                       69***************74..4555 PP

  == domain 7  score: 12.9 bits;  conditional E-value: 2.3e-05
                             Itfg2  79 tkvvliaDidgDgkvElvvgytDrvvrayrW 109
                                        k++ +aDidgDg+ E++ g  D  v+a+r 
  gi|386001518|ref|YP_005919817.1| 488 VKNIALADIDGDGQQEIIGGSLDNRVHAWRL 518
                                       58899**********************9997 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.028
                             Itfg2  84 iaDidgDgkvElvvgytDrvvrayrW 109
                                       iaD++gDg +++v+g  D   r y W
  gi|386001518|ref|YP_005919817.1| 540 IADLEGDGVLDMVAGSDDG--RIYIW 563
                                       8999*********999986..44556 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.5e-05     0.062       8      38 ..     177     213 ..     174     214 .. 0.80
   2 !   13.1   0.1   5.9e-05      0.11      11      37 ..     227     259 ..     222     261 .. 0.80
   3 !   10.9   0.2   0.00029      0.51      11      37 ..     274     306 ..     270     308 .. 0.77
   4 ?    4.0   1.0     0.043        76      12      37 ..     322     367 ..     318     368 .. 0.75
   5 ?   -1.6   0.1       2.4   4.4e+03      22      36 ..     407     422 ..     387     423 .. 0.56
   6 ?    0.5   0.1      0.54   9.6e+02      23      34 ..     450     468 ..     431     475 .. 0.67
   7 ?    1.5   0.1      0.26   4.7e+02      14      34 ..     535     561 ..     526     565 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                             PQQ_3   8 qlpgpvnsspavd...ggl....vyvgtgdGtlyAlDa 38 
                                       q+ +pv+sspa++   g      ++vgt  G+ly ++ 
  gi|386001518|ref|YP_005919817.1| 177 QTSSPVWSSPALAdidG-DgeleIVVGTNEGRLYVFNR 213
                                       7899******9985542.23458************986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.9e-05
                             PQQ_3  11 gpvnsspavd....ggl..vyvgtgdGtlyAlD 37 
                                       +++ sspav     +gl  ++vg++dG+lyA +
  gi|386001518|ref|YP_005919817.1| 227 DYIRSSPAVEdldgDGLldIVVGSDDGRLYAWN 259
                                       6899***995454468789************75 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00029
                             PQQ_3  11 gpvnsspavd...ggl...vyvgtgdGtlyAlD 37 
                                         v+sspa++   g+    v+vg++d ++yA++
  gi|386001518|ref|YP_005919817.1| 274 NSVWSSPAIGdldGDSgleVVVGSTDRGIYAFN 306
                                       479****997442333559************97 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.043
                             PQQ_3  12 pvnsspavd....ggl................vyvgtgdGtlyAlD 37 
                                        v+sspa++    +gl                ++ g + G +yA+D
  gi|386001518|ref|YP_005919817.1| 322 SVWSSPAIGdldgDGLldsvigsskmgtdilaIFLGLYTGQVYAVD 367
                                       68888888655445666777777777778888999999******99 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.4
                             PQQ_3  22 gl..vyvgtgdGtlyAl 36 
                                       g   +++g++  +lyAl
  gi|386001518|ref|YP_005919817.1| 407 GSleIVIGAS-DGLYAL 422
                                       2235777777.777776 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.54
                             PQQ_3  23 l.......vyvgtgdGtly 34 
                                       +       ++ g++dG+ly
  gi|386001518|ref|YP_005919817.1| 450 VdgdgeveIVGGATDGRLY 468
                                       3444444567777799998 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.26
                             PQQ_3  14 nsspavd....ggl..vyvgtgdGtly 34 
                                        ++pa++    +g+   ++g++dG++y
  gi|386001518|ref|YP_005919817.1| 535 DTTPAIAdlegDGVldMVAGSDDGRIY 561
                                       556666544434555578899999999 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.6   4.6e+03      27      37 ..     177     187 ..     177     188 .. 0.83
   2 !    8.1   0.0    0.0015       2.6       3      27 ..     199     222 ..     199     233 .. 0.88
   3 !    5.9   0.0    0.0071        13       3      14 ..     246     257 ..     245     261 .. 0.89
   4 ?    0.6   0.1      0.35   6.2e+02       3      17 ..     293     307 ..     293     312 .. 0.84
   5 ?    4.2   0.2     0.026        46       3      16 ..     354     367 ..     353     368 .. 0.92
   6 ?    2.6   0.0     0.081   1.4e+02       3      13 ..     551     561 ..     550     562 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                                       ESSSCGSSESE CS
                               PQQ  27 ktggpvlslpi 37 
                                       +t++pv+s+p+
  gi|386001518|ref|YP_005919817.1| 177 QTSSPVWSSPA 187
                                       58999***996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                                       EEEEETTSEEEEEETTTCCEEEEEE CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfk 27 
                                       +++g++ G+ly ++ ++G ++  f+
  gi|386001518|ref|YP_005919817.1| 199 IVVGTNEGRLYVFN-RDGSKVTGFP 222
                                       6899**********.****999886 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0071
                                       EEEEETTSEEEE CS
                               PQQ   3 vylgsadGylyA 14 
                                       +++gs+dG+lyA
  gi|386001518|ref|YP_005919817.1| 246 IVVGSDDGRLYA 257
                                       89*********9 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.35
                                       EEEEETTSEEEEEET CS
                               PQQ   3 vylgsadGylyAlDa 17 
                                       v++gs d  +yA++ 
  gi|386001518|ref|YP_005919817.1| 293 VVVGSTDRGIYAFNG 307
                                       78999999*****93 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.026
                                       EEEEETTSEEEEEE CS
                               PQQ   3 vylgsadGylyAlD 16 
                                       ++lg + G++yA+D
  gi|386001518|ref|YP_005919817.1| 354 IFLGLYTGQVYAVD 367
                                       89999********9 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.081
                                       EEEEETTSEEE CS
                               PQQ   3 vylgsadGyly 13 
                                       +++gs+dG++y
  gi|386001518|ref|YP_005919817.1| 551 MVAGSDDGRIY 561
                                       899*******9 PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.04        72      63      79 ..     187     203 ..     166     207 .. 0.84
   2 ?   -3.1   0.0       3.4     6e+03      62      77 ..     233     248 ..     209     250 .. 0.60
   3 ?   -0.9   0.0      0.73   1.3e+03      64      77 ..     400     413 ..     396     418 .. 0.87
   4 ?   -0.9   0.0      0.74   1.3e+03      56      76 ..     437     459 ..     430     463 .. 0.82
   5 !   10.0   0.0    0.0003      0.54      56      76 ..     485     505 ..     479     542 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.04
                                       EEE-SSSSSS-EEEEEE CS
                              PliI  63 kladvngdkkkelvvlk 79 
                                        lad++gd++ e+vv +
  gi|386001518|ref|YP_005919817.1| 187 ALADIDGDGELEIVVGT 203
                                       69************976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.4
                                       EEEE-SSSSSS-EEEE CS
                              PliI  62 vkladvngdkkkelvv 77 
                                         + d++gd+  ++vv
  gi|386001518|ref|YP_005919817.1| 233 PAVEDLDGDGLLDIVV 248
                                       4567888888888887 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.73
                                       EE-SSSSSS-EEEE CS
                              PliI  64 ladvngdkkkelvv 77 
                                       lad++gd++ e+v+
  gi|386001518|ref|YP_005919817.1| 400 LADLDGDGSLEIVI 413
                                       79*********998 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.74
                                       SSEEEE..EEEE-SSSSSS-EEE CS
                              PliI  56 dGsvee..vkladvngdkkkelv 76 
                                        Gs+++  +   dv+gd++ e+v
  gi|386001518|ref|YP_005919817.1| 437 TGSLQDsfIAAGDVDGDGEVEIV 459
                                       488888778888*******9998 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0003
                                       SSEEEEEEEE-SSSSSS-EEE CS
                              PliI  56 dGsveevkladvngdkkkelv 76 
                                        G v+++ lad++gd+++e++
  gi|386001518|ref|YP_005919817.1| 485 GGYVKNIALADIDGDGQQEII 505
                                       599*****************9 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.058     1e+02      15      38 .]     237     259 ..     227     259 .. 0.71
   2 ?    1.4   0.1      0.38   6.9e+02      21      37 ..     453     470 ..     437     471 .. 0.63
   3 ?   -2.0   0.0       4.4     8e+03      19      37 ..     497     516 ..     484     517 .. 0.71
   4 ?    9.6   0.1     0.001       1.8      16      37 ..     551     563 ..     534     564 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.058
                                       EEEEETTSSE.EEEEETTSEEEEEE CS
                              WD40  15 slafspdgaw.lasGsdDgtvriWd 38 
                                       +l  + dg + ++ GsdDg ++ W+
  gi|386001518|ref|YP_005919817.1| 237 DL--DGDGLLdIVVGSDDGRLYAWN 259
                                       55..3344445456*******9998 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                                       TSSE.EEEEETTSEEEEE CS
                              WD40  21 dgaw.lasGsdDgtvriW 37 
                                       dg   ++ G  Dg +++W
  gi|386001518|ref|YP_005919817.1| 453 DGEVeIVGGATDGRLYLW 470
                                       333334444459999999 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.4
                                       ETTSSE.EEEEETTSEEEEE CS
                              WD40  19 spdgaw.lasGsdDgtvriW 37 
                                       + dg+  ++ Gs D+ v+ W
  gi|386001518|ref|YP_005919817.1| 497 DGDGQQeIIGGSLDNRVHAW 516
                                       45555556667899999988 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.001
                                       EEEETTSSEEEEEETTSEEEEE CS
                              WD40  16 lafspdgawlasGsdDgtvriW 37 
                                       +        + +GsdDg ++iW
  gi|386001518|ref|YP_005919817.1| 551 M--------V-AGSDDGRIYIW 563
                                       3........5.6********** PP

>> TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.052        94      32      47 ..     187     202 ..     172     220 .. 0.79
   2 ?    3.2   0.4     0.028        50      33      47 ..     235     249 ..     219     261 .. 0.85
   3 ?   -2.9   0.1       2.1   3.7e+03      33      52 ..     282     301 ..     279     313 .. 0.73
   4 ?    7.4   0.1    0.0014       2.5      32      53 ..     328     349 ..     314     368 .. 0.81
   5 ?    2.4   0.1     0.048        86      33      51 ..     400     418 ..     389     431 .. 0.81
   6 ?    1.3   0.1       0.1   1.9e+02      21      45 ..     435     459 ..     426     466 .. 0.83
   7 ?    2.0   0.0     0.063   1.1e+02      26      44 ..     488     504 ..     477     515 .. 0.78
   8 ?    4.7   0.1    0.0099        18      28      46 ..     535     553 ..     527     568 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.052
                   TcdB_toxin_midN  32 slaDldGdGladlvlt 47 
                                        laD+dGdG +++v+ 
  gi|386001518|ref|YP_005919817.1| 187 ALADIDGDGELEIVVG 202
                                       589*********9875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                   TcdB_toxin_midN  33 laDldGdGladlvlt 47 
                                       + DldGdGl+d+v+ 
  gi|386001518|ref|YP_005919817.1| 235 VEDLDGDGLLDIVVG 249
                                       67*********9875 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
                   TcdB_toxin_midN  33 laDldGdGladlvltipsag 52 
                                       ++DldGd  +++v+ +   g
  gi|386001518|ref|YP_005919817.1| 282 IGDLDGDSGLEVVVGSTDRG 301
                                       78999999999877666555 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0014
                   TcdB_toxin_midN  32 slaDldGdGladlvltipsagt 53 
                                        ++DldGdGl+d v+ ++++gt
  gi|386001518|ref|YP_005919817.1| 328 AIGDLDGDGLLDSVIGSSKMGT 349
                                       589****************993 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.048
                   TcdB_toxin_midN  33 laDldGdGladlvltipsa 51 
                                       laDldGdG +++v+  +  
  gi|386001518|ref|YP_005919817.1| 400 LADLDGDGSLEIVIGASDG 418
                                       79*********99877654 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.1
                   TcdB_toxin_midN  21 gtstsvedtnlslaDldGdGladlv 45 
                                       +t +s +d  + ++D+dGdG  ++v
  gi|386001518|ref|YP_005919817.1| 435 KTTGSLQDSFIAAGDVDGDGEVEIV 459
                                       566888899999********99876 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.063
                   TcdB_toxin_midN  26 vedtnlslaDldGdGladl 44 
                                       v+  n+ laD+dGdG  ++
  gi|386001518|ref|YP_005919817.1| 488 VK--NIALADIDGDGQQEI 504
                                       44..4589*******9886 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.0099
                   TcdB_toxin_midN  28 dtnlslaDldGdGladlvl 46 
                                       dt   +aDl+GdG +d+v 
  gi|386001518|ref|YP_005919817.1| 535 DTTPAIADLEGDGVLDMVA 553
                                       555789**********875 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.032        58       8      18 ..     188     198 ..     187     199 .. 0.85
   2 ?    1.8   0.3      0.12   2.2e+02      10      18 ..     237     245 ..     235     246 .. 0.90
   3 ?    1.8   0.4      0.12   2.2e+02      10      18 ..     331     339 ..     328     340 .. 0.87
   4 ?    2.7   0.1      0.06   1.1e+02       9      18 ..     401     410 ..     400     411 .. 0.84
   5 ?    3.3   0.2     0.039        70       6      18 ..     445     457 ..     442     458 .. 0.79
   6 ?    2.8   0.1     0.057     1e+02       6      16 ..     491     501 ..     489     501 .. 0.87
   7 ?    0.5   0.0      0.32   5.7e+02       8      18 ..     540     550 ..     539     551 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.032
                                       HHTTTSSSEEE CS
                         EF-hand_1   8 efDkDgdGkId 18 
                                       ++D DgdG ++
  gi|386001518|ref|YP_005919817.1| 188 LADIDGDGELE 198
                                       69******986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                                       TTTSSSEEE CS
                         EF-hand_1  10 DkDgdGkId 18 
                                       D DgdG +d
  gi|386001518|ref|YP_005919817.1| 237 DLDGDGLLD 245
                                       99****998 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                                       TTTSSSEEE CS
                         EF-hand_1  10 DkDgdGkId 18 
                                       D DgdG +d
  gi|386001518|ref|YP_005919817.1| 331 DLDGDGLLD 339
                                       9*****998 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.06
                                       HTTTSSSEEE CS
                         EF-hand_1   9 fDkDgdGkId 18 
                                       +D DgdG ++
  gi|386001518|ref|YP_005919817.1| 401 ADLDGDGSLE 410
                                       8******875 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.039
                                       HHHHTTTSSSEEE CS
                         EF-hand_1   6 FrefDkDgdGkId 18 
                                       ++  D+DgdG ++
  gi|386001518|ref|YP_005919817.1| 445 IAAGDVDGDGEVE 457
                                       6677******986 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.057
                                       HHHHTTTSSSE CS
                         EF-hand_1   6 FrefDkDgdGk 16 
                                       ++++D DgdG+
  gi|386001518|ref|YP_005919817.1| 491 IALADIDGDGQ 501
                                       5789******6 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 0.32
                                       HHTTTSSSEEE CS
                         EF-hand_1   8 efDkDgdGkId 18 
                                       ++D  gdG +d
  gi|386001518|ref|YP_005919817.1| 540 IADLEGDGVLD 550
                                       68******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 3523.61
//
Query:       gi|386001519|ref|YP_005919818.1|  [L=197]
Description: hypothetical protein Mhar_0823 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1333.53
//
Query:       gi|386001520|ref|YP_005919819.1|  [L=233]
Description: hypothetical protein Mhar_0824 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-28  100.3   0.1    1.7e-28  100.1   0.1    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.1   9.7e-33   1.7e-28       2     198 ..      12     203 ..      11     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 9.7e-33
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEETTT.SEEEEEEE... CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyakdsgsrdllvlqg... 74 
                                       i G+pgiG+Vg++a+d++++ le   +    s++ +p     p+v ve+g  +  +++l a+ +g  dl++l g   
  gi|386001520|ref|YP_005919819.1|  12 IGGMPGIGSVGKVAADYIAAALESITFQLMVSTG-FP-----PEVPVEDGlARALQVELKAP-EGRDDLIILCGdaq 81 
                                       679*******************************.**.....********988888888766.34679999999777 PP

                                       .E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEH CS
                              PAC2  75 .repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivg 145
                                          p+ +y+ +a ++l+++ +++v+  v+L+++          t ++ v+g+atd++l+  le       + g+++g
  gi|386001520|ref|YP_005919819.1|  82 pLKPPHMYN-LAGEILKVLASYEVTDLVTLAAYV----G----TSEDTVYGVATDPDLALALEGGgvtllRSGIVGG 149
                                       777777777.***********************9....4....55669***********88873356789******* PP

                                       HHHHHHHHHHHTT-EEEEEEEEEECCC.--HHHHHHHHHHHHHHHT---HCHHH CS
                              PAC2 146 itglLlsaakergipavgllaevphyl.pdPkaaaalleflskllglevdtedL 198
                                       ++g+L+++a  +gi +v+l++ ++++  +d +aa  l+ + s+llgle++te L
  gi|386001520|ref|YP_005919819.1| 150 LNGILVGLAPLYGIRGVCLMGKTDGEKaVDLAAAENLIGATSDLLGLEISTEVL 203
                                       *************************8758*********************9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1594.03
//
Query:       gi|386001521|ref|YP_005919820.1|  [L=285]
Description: hypothetical protein Mhar_0825 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-34  118.3   0.2    7.1e-33  114.0   0.2    2.0  1  DUF89      Protein of unknown function DUF89
  ------ inclusion threshold ------
       0.11   11.2   0.1       0.15   10.7   0.1    1.1  1  EVC2_like  Ellis van Creveld protein 2 like protein


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.2     8e-37   7.1e-33       5     350 ..       7     278 ..       4     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 8e-37
                                       HHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHHHHT CS
                             DUF89   5 rlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrllelfg 81 
                                       ++ cil ++  +++   ++  +e+ +++eel ++   + ++++++ +                + ++  r +++  +
  gi|386001521|ref|YP_005919820.1|   7 CYSCILDRAKFEADLLFSD-DAEKMEAMEELLDFI--VCHKREVPSV----------------VGTERERIMKRRSK 64 
                                       8888888888888885555.578888888888877..7788888888................88888888888888 PP

                                       HSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHHHHH CS
                             DUF89  82 lskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeeeark 158
                                             n Dp++e+K esn+ a ++++  ++ ++ +e++   +++l++i+ + N + +++++  +d+  d+ ee+  
  gi|386001521|ref|YP_005919820.1|  65 ------NPDPYREMKAESNRVATALLPLTERFYDLSEEK---LEALIRIAAAANSMEWGVKG--HDFDVDSFEEVFF 130
                                       ......*******************99999999999998...********************..8888888888777 PP

                                       HHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHHHHH CS
                             DUF89 159 aleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeDfew 235
                                       ++ k+ l  dle++ +++   + +rv++++DNaG E+vfDl+++ +L e  +++ Vv+ +k  P +++Dvt ++++ 
  gi|386001521|ref|YP_005919820.1| 131 DTLKENLDGDLEEARRRI--DRFSRVLYLTDNAG-EVVFDLFVIGKLEE--MGKAVVIGPKTEP-ILNDVTSDELR- 200
                                       777778899*********..**************.**************..*************.***********. PP

                                       HHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHH.C-SEEEEEHHHHHHHHTTS CS
                             DUF89 236 lleqladsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeele.kadLvifKGdlNyrkLtgd 311
                                                            +    ++l l+++    +gls++e+   pel++ l  +  Lvi+KG++N++++t+ 
  gi|386001521|ref|YP_005919820.1| 201 ---------------------S---MTTLPLEPTG-PVIGLSLEEA--RPELLDLLMdEGVLVIAKGMGNFETMTEF 250
                                       .....................3...4456666666.589*******..*****9998799**************988 PP

                                       CTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH.STTT CS
                             DUF89 312 rkwppttpfttalgfspvpvlaLrtvKadvvagll.egeg 350
                                        +                ++++ +++K+d+va  l +++g
  gi|386001521|ref|YP_005919820.1| 251 DDML------------AGRLIYVMRAKCDPVADALgVPRG 278
                                       7776............578*************99877666 PP

>> EVC2_like  Ellis van Creveld protein 2 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   1.7e-05      0.15     327     411 ..      18     102 ..      14     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.7e-05
                         EVC2_like 327 aAkrllqeyskiqeeieellDfvqankryhLeerlaqRkyLvkslqsletrvsallntaatqlasliqkleragkld 403
                                       +A  l ++  + +e +eellDf++ +kr + +    +R+ ++k+  +  +  +++     +  + l+  +er   l+
  gi|386001521|ref|YP_005919820.1|  18 EADLLFSDDAEKMEAMEELLDFIVCHKREVPSVVGTERERIMKRRSKNPDPYREMKAESNRVATALLPLTERFYDLS 94 
                                       5778999999******************9999999999999988887777777776666667777788888888888 PP

                         EVC2_like 404 eeqlelll 411
                                       ee+le+l 
  gi|386001521|ref|YP_005919820.1|  95 EEKLEALI 102
                                       88888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1737.80
//
Query:       gi|386001522|ref|YP_005919821.1|  [L=282]
Description: Histone deacetylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-34  117.4   0.4    1.6e-32  113.2   0.6    2.4  2  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.027   4.8e+02       7      53 ..      22      68 ..      17      74 .. 0.75
   2 !  113.2   0.6     9e-37   1.6e-32      82     307 .]      70     279 ..      49     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.027
                                      HHHHHHHHHHHT.THHHHCCE..EE-----HHHHTTTS-HHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  7 Rlsaileslaesvglldelel.liqpseatkeellkvHskeYlelles 53
                                      R++   e+l++s gll+   + ++++++a  + ++ +H++e++e++++
  gi|386001522|ref|YP_005919821.1| 22 RIRPSFEALKRS-GLLEGSDVqVFEAEPAPLSLVEGAHTPEHMERMRT 68
                                      666677888887.66644333478888999999999*******99875 PP

  == domain 2  score: 113.2 bits;  conditional E-value: 9e-37
                                       HCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  82 pvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailD 158
                                       p +   +++all++g+vl+a++ v++g++++ f++   +gHHa ++ + GFC++N+vai i +l++  +l r++i+D
  gi|386001522|ref|YP_005919821.1|  70 PSERMYYDVALLSAGSVLKAAEMVARGEARHSFAFTGTAGHHASPGSCWGFCYFNDVAISILRLRE-MGLARFLIVD 145
                                       55667899**********************************************************.99******** PP

                                       -SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 159 vDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvle 235
                                       vD H+G+Gt ++f  dp+v+++ + + + + +             g+ +n  + +    +de++l+ +   + ++++
  gi|386001522|ref|YP_005919821.1| 146 VDPHFGDGTRNFFGGDPNVYHINFNHQQSSNFD------------GELNNYDIGIGFDAEDEQFLRELAGSM-EMAK 209
                                       ***********************9885554443............334566677777889999999999888.788* PP

                                       CH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 236 efkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlealaravtavlsal 307
                                       +f+ ++  v  G D++++d +g+++l+v  y ++ + ++e   +   +v++l GG  +e +ara+ +v+++l
  gi|386001522|ref|YP_005919821.1| 210 DFDFEICFVVFGHDSHADD-YGGFELTVAAYPKMARIIKEAVGER-SIVFVLSGGSVPEVAARAIPEVIAVL 279
                                       ***************9866.799*****************99976.*****************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1712.15
//
Query:       gi|386001523|ref|YP_005919822.1|  [L=511]
Description: Putative thymidine phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-15   56.1   0.2    1.4e-14   53.4   0.0    2.3  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    7.3e-15   54.6   0.1    2.3e-14   52.9   0.0    1.9  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    2.6e-11   43.6   0.3    9.1e-11   41.8   0.3    1.8  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    7.8e-05   21.7   0.0    0.00013   21.0   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
    9.7e-05   22.4   0.1     0.0002   21.3   0.1    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   9.1e+02      19      31 ..     293     305 ..     289     315 .. 0.83
   2 !   53.4   0.0     4e-18   1.4e-14       1      73 [.     429     494 ..     429     496 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                                       TSBSSTTS---TT CS
                            PYNP_C  19 AGRakkeDpidla 31 
                                       AGR+ ++D idl+
  gi|386001523|ref|YP_005919822.1| 293 AGRSMAKDLIDLG 305
                                       9*********975 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 4e-18
                                       EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHHHEE CS
                            PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkkaik 73 
                                       yv ++++++i  +a+++GA       p d+++G+++hkk+G+ VkkGepl+ti+++k +++e+a +++   + 
  gi|386001523|ref|YP_005919822.1| 429 YVISFNNKRIVEIARNAGA-------PADKQAGVRIHKKMGEVVKKGEPLFTIHSSKDWEVERASNDALRDMP 494
                                       78899**************.......**************************************998877665 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   6.5e-18   2.3e-14       2      63 .]      88     149 ..      87     149 .. 0.97
   2 ?   -2.9   0.0       1.8   6.6e+03      12      22 ..     213     223 ..     208     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 6.5e-18
                                       HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       ++ik+++d+e Lt+++ir ++++i++++++d++i+A L+ l+++  + +E+  l++Am++ g
  gi|386001523|ref|YP_005919822.1|  88 SYIKRIMDHERLTEDQIRTIVQDIVDNNLSDVEISAYLTTLYIRNFDSQETEWLTRAMIDTG 149
                                       69********************************************************9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                       ---HHHHHHHH CS
                   Glycos_trans_3N  12 eLtaeeirfai 22 
                                       e++a+ei+++ 
  gi|386001523|ref|YP_005919822.1| 213 EFSADEIKEIA 223
                                       78899998875 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.3   2.5e-14   9.1e-11       3     252 ..     158     391 ..     156     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.5e-14
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHS..EE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevg..vg 77 
                                       ++vD+++ GG+  n   +S+   ++vAaaG+ ++k + r+++  +G++D++e l   +e +++e++++ e+vg  ++
  gi|386001523|ref|YP_005919822.1| 158 PVVDKHSIGGVPGNK--VSLLVVPIVAAAGLLIPKTSSRAITGAGGTSDLMEIL-APVEFSADEIKEIAENVGgiLA 231
                                       79***********99..9**********************************98.5899*********999983334 PP

                                       EEEHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHH CS
                   Glycos_transf_3  78 flfapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGlde 154
                                         +a++  +a ++ +++  +l+i            p   ++ l +++sk+ a ++++v+++++v+ +  +++  +d 
  gi|386001523|ref|YP_005919822.1| 232 WGGATNIAPADDKLIKAEYALTI-----------DP--YSQMLASIMSKKGAVGADSVVMDMPVGPGTKLPT--VDA 293
                                       45789999999999999999988...........44..4566889***********************9999..999 PP

                                       HHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHT CS
                   Glycos_transf_3 155 vsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvla 230
                                        + +ak ++   +  g + e +++    +++r  + ale+   ke++ +l++  +g++s   r+  l +ag +l + 
  gi|386001523|ref|YP_005919822.1| 294 GRSMAKDLIDLGDrLGIRVECAMTFGGSPVGRTVGPALEV---KEALTMLESG-QGPNSL--REKSLSLAGILLEIG 364
                                       999***9999999999999999999999999999999999...9999999987.777776..566666666666544 PP

                                       TSSSS.....HHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 231 gkads.....lkegvakaeevidsGkA 252
                                         a         eg a ae +++sGkA
  gi|386001523|ref|YP_005919822.1| 365 CSAGMgcvaaRGEGKAMAERILTSGKA 391
                                       333222232277888889999999988 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.5e-08   0.00013     186     255 ..     413     487 ..     380     494 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.5e-08
                           DUF2254 186 eseeeeatpiraersGylqaidveaLvklaeehd......lvielevrpGdfvvkgeplakvwgeeddeelaeklr 255
                                        +  e ++ i a+++Gy+ + + +++v++a++++      + +++++++G+ v kgepl+++++ + d e++++ +
  gi|386001523|ref|YP_005919822.1| 413 IEIGEHSRDILAPTTGYVISFNNKRIVEIARNAGapadkqAGVRIHKKMGEVVKKGEPLFTIHSSK-DWEVERASN 487
                                       455678899*********************976522222278*********************988.344444444 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   5.6e-08    0.0002      31      82 ..      16      68 ..      11      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.6e-08
                                      EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEEEESSHCC CS
                   Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvfmpfgwwe 82
                                       v++n +dA+ +G + Gd+V+v+ +  s+++   vt + v pG v + + + +
  gi|386001523|ref|YP_005919822.1| 16 KVMLNLADARDMGMNAGDRVRVKAKGASITAILDVTTQmVEPGKVGIFTEAHR 68
                                      599******************************77766599**9988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 3595.70
//
Query:       gi|386001524|ref|YP_005919823.1|  [L=249]
Description: hypothetical protein Mhar_0828 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1994.27
//
Query:       gi|386001525|ref|YP_005919824.1|  [L=317]
Description: hypothetical protein Mhar_0829 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-05   24.0   0.0    7.7e-05   22.9   0.0    1.6  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.3e-09   7.7e-05       3      61 ..     100     155 ..      98     192 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-09
                                       HHHHHHHHHTT....TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCC CS
                      NTP_transf_2   3 klleelkelep....vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiik 61 
                                       +++e++  l++      k+ ++GS   G+ ++gSDiD+lv+++++       +++++ + + k
  gi|386001525|ref|YP_005919824.1| 100 RIAEIVAVLDKggvpREKMGITGSILVGLEGPGSDIDFLVYGRDW-------WRARAAISEAK 155
                                       56666666666668899*************************999.......33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2322.41
//
Query:       gi|386001526|ref|YP_005919825.1|  [L=193]
Description: Translation factor (SUA5 family) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-47  158.9   0.0    9.8e-47  158.7   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.0   5.5e-51   9.8e-47       1     179 []      11     183 ..      11     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 5.5e-51
                                       HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGp 77 
                                       e+l +Gg v++ptetvYg+++++  ++aver++eiKgrp+  pl+v vas+e++ ++a+  +++  l ll+r++PGp
  gi|386001526|ref|YP_005919825.1|  11 EVLARGGTVVYPTETVYGIGASVFIPRAVERVFEIKGRPRGMPLSVAVASFEMMGEIAR--IDDGDLPLLRRVLPGP 85 
                                       5899******************************************************8..**************** PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildg 154
                                       +t+l++r  + lp+ v++g++ vG+r Pd+p a++L+   g p+++TSanlsg p++ + +e++ e++++vdl+ldg
  gi|386001526|ref|YP_005919825.1|  86 VTFLVERGPK-LPDLVTAGSELVGIRFPDHPAALELIALSG-PITSTSANLSGLPPPASLAELDGEIRKNVDLVLDG 160
                                       ******8666.***************************976.*********************************** PP

                                       ---SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 155 geiavgvdstVvdltegkpkilRrG 179
                                       g+ + g +st vdl e   k++R+G
  gi|386001526|ref|YP_005919825.1| 161 GRSRYGLPSTLVDLAE--RKVIRKG 183
                                       **************96..9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1265.94
//
Query:       gi|386001527|ref|YP_005919826.1|  [L=161]
Description: XRE family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-05   23.6   0.3    5.9e-05   23.0   0.3    1.3  1  HTH_3     Helix-turn-helix
    0.00027   20.9   0.2    0.00097   19.1   0.2    1.8  2  HTH_19    Helix-turn-helix domain
     0.0022   18.3   0.0     0.0045   17.3   0.0    1.5  1  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.035   14.0   0.2       0.11   12.3   0.2    1.8  2  HTH_25    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   1.3e-08   5.9e-05       1      53 [.      81     133 ..      81     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                       +ke+R+  gl+ eeL  k+  + s i++iE+ e  P  ++ +kl++ Lgv+l+
  gi|386001527|ref|YP_005919826.1|  81 VKEAREGMGLTPEELGLKIKEKASLIRKIERHEIVPEDSVRVKLERELGVKLT 133
                                       69************************************************997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   2.2e-07   0.00097       1      56 [.      78     132 ..      78     134 .. 0.90
   2 ?   -1.5   0.0      0.57   2.6e+03      11      20 ..     148     157 ..     146     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.2e-07
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56 
                                       G+ +keaRe  glt eel  +++   s i++iE  ++ vp+ ++  k+ ++lg+ l
  gi|386001527|ref|YP_005919826.1|  78 GQIVKEAREGMGLTPEELGLKIKEKASLIRKIERHEI-VPEDSVRVKLERELGVKL 132
                                       899******************************9988.988888888888888765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.57
                            HTH_19  11 lgltqeelae 20 
                                       +glt+ ++a+
  gi|386001527|ref|YP_005919826.1| 148 RGLTLGDIAS 157
                                       89******97 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     1e-06    0.0045       3      56 ..      78     130 ..      76     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-06
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                       G+ ++++Re  GL+ ee++  +   +s ++++E+ ++ +p  +v  +l r lg+
  gi|386001527|ref|YP_005919826.1|  78 GQIVKEAREGMGLTPEELGLKIKEKASLIRKIERHEI-VPEDSVRVKLERELGV 130
                                       88999********************************.7*****9999999998 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.5e-05      0.11       3      33 ..      82     112 ..      80     117 .. 0.94
   2 ?   -2.0   0.0      0.75   3.4e+03       9      18 ..     148     157 ..     147     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                       HHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                            HTH_25   3 raaRearglsleevaketkIrkdylealEed 33 
                                       ++aRe +gl+ ee+  ++k ++++++++E+ 
  gi|386001527|ref|YP_005919826.1|  82 KEAREGMGLTPEELGLKIKEKASLIRKIERH 112
                                       79***************************86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.75
                                       TT--HHHHHH CS
                            HTH_25   9 rglsleevak 18 
                                       rgl+l ++a 
  gi|386001527|ref|YP_005919826.1| 148 RGLTLGDIAS 157
                                       89****9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1114.46
//
Query:       gi|386001528|ref|YP_005919827.1|  [L=406]
Description: proteasome-activating nucleotidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-43  146.3   0.0    1.3e-42  145.4   0.0    1.5  1  AAA              ATPase family associated with various cellul
    6.6e-12   45.2   0.2      2e-11   43.7   0.1    1.9  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.6e-11   43.1   1.2    6.3e-11   41.9   1.2    1.7  1  AAA_lid_3        AAA+ lid domain
      6e-06   26.3   1.0    4.5e-05   23.5   0.1    3.0  2  AAA_5            AAA domain (dynein-related subfamily)
    6.2e-06   26.7   2.5    0.00078   19.9   0.1    3.0  3  AAA_16           AAA ATPase domain
    1.3e-05   25.3   0.0    2.7e-05   24.3   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    8.1e-05   22.2   2.8    0.00024   20.7   0.2    2.8  3  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    9.3e-05   22.2   0.0    0.00022   21.0   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00012   21.3   0.0     0.0002   20.6   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
    0.00032   21.0   0.3      0.019   15.2   0.1    2.6  2  AAA_22           AAA domain
     0.0045   16.2   0.0     0.0087   15.3   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0051   16.2   0.0      0.013   14.9   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0053   17.3   0.1      0.019   15.5   0.0    2.1  2  AAA_18           AAA domain
     0.0063   16.3   0.0      0.013   15.3   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0067   16.0   1.8      0.012   15.3   1.8    1.2  1  Filament         Intermediate filament protein
     0.0095   16.2   0.8      0.014   15.7   0.0    1.7  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.026   14.7   0.0    1.6  1  AAA_33           AAA domain
      0.012   16.0   0.0      0.021   15.2   0.0    1.4  1  RNA_helicase     RNA helicase
      0.012   15.5   0.0      0.026   14.4   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.014   15.0   0.0      0.026   14.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.019   14.7   0.0      0.036   13.8   0.0    1.5  1  AAA_24           AAA domain
      0.029   14.1   0.2      0.087   12.5   0.2    1.7  1  AAA_30           AAA domain
      0.035   13.4   0.1        0.1   11.9   0.0    1.8  2  ATPase           KaiC
      0.036   14.0   0.1       0.15   12.0   0.0    2.0  2  NTPase_1         NTPase
       0.04   14.4   0.1       0.55   10.7   0.0    2.2  2  ABC_tran         ABC transporter
      0.043   13.6   0.5       0.87    9.3   0.0    2.2  2  AAA_11           AAA domain
      0.052   13.5   0.3       0.73    9.7   0.0    2.6  3  NACHT            NACHT domain
      0.076   12.7   0.0       0.28   10.9   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
      0.087   12.8   0.0        0.2   11.7   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.088   11.9   0.0        0.2   10.7   0.0    1.5  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.11   11.9   0.1        0.2   11.1   0.1    1.4  1  PhoH             PhoH-like protein
       0.12   12.3   0.0          2    8.3   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
       0.22   11.1   2.7       0.22   11.1   0.2    2.1  2  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0   2.4e-45   1.3e-42       1     132 []     182     315 ..     182     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 2.4e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppGtGKTllakava++++++fl++ gsel++ky+ge+++ +relf+ a++ka p i+f+DE+da++++r   
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEATFLRVVGSELVQKYIGEGARMVRELFELAQNKA-PAIIFVDELDAIGSRRmdg 257
                                       79******************************************************9.*****************87 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                        +s ++e +r++ qLl+e+dg++ + ++v +i+atnr d+ldpallr gRfdr i+++l
  gi|386001528|ref|YP_005919827.1| 258 ATSGDREVQRTLMQLLAEMDGFDPR-GEVKLIAATNRLDMLDPALLRpGRFDRLIYVPL 315
                                       777889999***************7.66****************************985 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.1   3.6e-14     2e-11       1      57 []      70     124 ..      70     124 .. 0.96
   2 ?   -2.6   0.0        10   5.4e+03      18      30 ..     200     212 ..     154     213 .. 0.53

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3.6e-14
                                       EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       V+t+ +vldd +r++Vk+s++  +vv+++  +  e Lrpg++Va++++++ ++ +LP
  gi|386001528|ref|YP_005919827.1|  70 VGTIQDVLDD-NRVVVKSSTGPRFVVNVSQFIEGE-LRPGTRVALNQQSFSVMFVLP 124
                                       9*********.**********************66.***************999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 10
                                       -TTS-EEEEEE-G CS
                    Prot_ATP_ID_OB  18 tssdeevvvslag 30 
                                        ss e  ++++ g
  gi|386001528|ref|YP_005919827.1| 200 ASSTEATFLRVVG 212
                                       2666666777665 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   1.2   1.2e-13   6.3e-11       1      44 [.     337     380 ..     337     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.2e-13
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       dvdl ++A   eG SGADl+al  eA++ A+r+ ++ +  +dfe
  gi|386001528|ref|YP_005919827.1| 337 DVDLRRIADGAEGASGADLKALATEAGMFAIREERDIVCHQDFE 380
                                       9******************************************8 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.8   2.6e+03      79      97 ..      67      85 ..      18     121 .. 0.68
   2 !   23.5   0.1   8.2e-08   4.5e-05       1     135 [.     181     302 ..     181     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.8
                                      HHHHHHHHHHHHSSEEE.. CS
                             AAA_5 79 sevlnsLlslleerrllle 97
                                      + ++++ + +l+++r+ + 
  gi|386001528|ref|YP_005919827.1| 67 PLIVGTIQDVLDDNRVVVK 85
                                      3444555555555555555 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 8.2e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK+ la+ +a+ ++++++ v +++      l++++  ++ + +++  +l  + + ++i+++DE++ +
  gi|386001528|ref|YP_005919827.1| 181 GVLLYGPPGTGKTLLAKAVASSTEATFLRVVGSE------LVQKYIGEGARMVRELFELA-QNKAPAIIFVDELDAI 250
                                       59****************************9987......88888843333344444444.4558999999999999 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalr 135
                                        s  ++   s   e ++ l+++  +++     + +r  + +ia++n+ld     l+pal+
  gi|386001528|ref|YP_005919827.1| 251 GSRRMDGATSGDREVQRTLMQLLAEMDG----FDPRgeVKLIAATNRLD----MLDPALL 302
                                       8665555544443434444444333322....22334488888888888....6677765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       4.2   2.3e+03       6      22 ..      50      66 ..      17      72 .. 0.88
   2 !   19.9   0.1   1.4e-06   0.00078      24      51 ..     179     206 ..     149     219 .. 0.78
   3 ?    5.2   0.0     0.046        25     124     146 ..     228     257 ..     222     278 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.2
                            AAA_16  6 eeeleqLlsalervrsg 22
                                      e+e+++L+s ler+r+g
  gi|386001528|ref|YP_005919827.1| 50 EREVRKLRSELERLRTG 66
                                      68999999999999887 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.4e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                       p  vll+G++G+GK+ l+++++ + e++
  gi|386001528|ref|YP_005919827.1| 179 PKGVLLYGPPGTGKTLLAKAVASSTEAT 206
                                       489******************9655544 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.046
                            AAA_16 124 krllallsrderplvlvlDdlq........w 146
                                       ++l++l+++ + p ++++D+l+         
  gi|386001528|ref|YP_005919827.1| 228 RELFELAQN-KAPAIIFVDELDaigsrrmdG 257
                                       567799999.778*********555554442 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     5e-08   2.7e-05       6     103 ..     182     273 ..     178     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++ r+  sel +    + + +     ++    a+++   i+++DE+d i
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEA----TFLRVVGSELVQ----KYIGEGARMVRELFELAQNKApaIIFVDELDAI 250
                                       6889****************9985....************....66666666666666666666688********** PP

                                       ------------HHHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLLqil 103
                                        +++  ga     +Vqr L+q+l
  gi|386001528|ref|YP_005919827.1| 251 GSRRMDGATSGDREVQRTLMQLL 273
                                       **99999999999********98 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   4.5e-07   0.00024       3      49 ..      71     116 ..      69     127 .. 0.86
   2 ?   -2.2   0.0         6   3.2e+03       2      14 ..     204     215 ..     203     227 .. 0.68
   3 ?   -0.1   0.0       1.4   7.4e+02      27      42 ..     333     348 ..     331     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.5e-07
                     Prot_ATP_OB_N   3 GtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEal 49 
                                       Gt+  v ++ + +  ++ g r++V+vs  ++  eLrpG++V Ln+++
  gi|386001528|ref|YP_005919827.1|  71 GTIQDVLDDNRVVVKSSTGPRFVVNVSQFIE-GELRPGTRVALNQQS 116
                                       77777887888888899**************.************875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6
                     Prot_ATP_OB_N   2 yGtflavnsqdgt 14 
                                        +tfl+v+   + 
  gi|386001528|ref|YP_005919827.1| 204 EATFLRVVG-SEL 215
                                       599**9994.444 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.4
                     Prot_ATP_OB_N  27 avsPlvdaeeLrpGqe 42 
                                       +++P+vd+ ++  G+e
  gi|386001528|ref|YP_005919827.1| 333 NLHPDVDLRRIADGAE 348
                                       78********999975 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.1e-07   0.00022      34      94 ..     180     248 ..     172     256 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.1e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvleka.gd...laalltnleek...dvlfideih 94 
                                         vllyGpPG Gkt lak +a+  ++++ ++  +  ++k  g+   ++  l +l ++    ++f+de+ 
  gi|386001528|ref|YP_005919827.1| 180 KGVLLYGPPGTGKTLLAKAVASSTEATFlRVVGSELVQKYiGEgarMVRELFELAQNkapAIIFVDELD 248
                                       579*******************99998615555555555334411144444555444222589999876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.7e-07    0.0002      52     116 ..     178     247 ..     136     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       p + vLL+G  GtGK  l ka+ ++++++ Lr++  e+ ++ + e  ++v++l    +++   i+fvD L
  gi|386001528|ref|YP_005919827.1| 178 PPKGVLLYGPPGTGKTLLAKAVASSTEATFLRVVgsELVQKYIGEGARMVRELFelaQNKAPAIIFVDEL 247
                                       6678******************************88899999999999988765222677789*****98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.5e-05     0.019       8      29 ..     182     203 ..     177     210 .. 0.86
   2 ?    4.4   0.0     0.075        41      51     104 ..     202     251 ..     199     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++GtGKT+l++ ++++ 
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASST 203
                                       689**************99876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.075
                            AAA_22  51 tsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlr 104
                                       ++ +++lr + ++l ++  +   +  ++++ l + ++++a  +++ +DE + + 
  gi|386001528|ref|YP_005919827.1| 202 STEATFLRVVGSELVQKYIG---EGARMVRELFELAQNKAP-AIIFVDELDAIG 251
                                       56778888888888887777...888999999999999999.9********996 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05    0.0087      51      90 ..     180     217 ..     171     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       ++vLl Gp+gtGkt la a++ +  ++  f  ++gse+ +
  gi|386001528|ref|YP_005919827.1| 180 KGVLLYGPPGTGKTLLAKAVASS--TEATFLRVVGSELVQ 217
                                       89******************986..56899******9865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.3e-05     0.013      24      43 ..     181     200 ..     170     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                        +ll+GppG+GKt+lak+++
  gi|386001528|ref|YP_005919827.1| 181 GVLLYGPPGTGKTLLAKAVA 200
                                       589**************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       5.5     3e+03      70      86 ..      33      49 ..       9      83 .. 0.59
   2 !   15.5   0.0   3.5e-05     0.019       1      25 [.     182     219 ..     182     345 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.5
                            AAA_18 70 aleegknlvidghlael 86
                                      ++ eg+  +++ +  ++
  gi|386001528|ref|YP_005919827.1| 33 DRVEGEKRIMENQKLKF 49
                                      33333333444444333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.............g 25 
                                       +ll G+pG+GKt lak+++++++               
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEAtflrvvgselvqkY 219
                                       799***************99874346765654443330 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.3e-05     0.013      47      71 ..     179     203 ..     169     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                        ++++l Gp+G+GK+ la a++ ++
  gi|386001528|ref|YP_005919827.1| 179 PKGVLLYGPPGTGKTLLAKAVASST 203
                                       57899***************99765 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.8   2.1e-05     0.012      17      67 ..      15      64 ..       9      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX CS
                          Filament 17 idkVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldelt 67
                                      +d+ r+LE+ n +L+ +  + e + ++  ++ k  +e+e+++lr++l++l 
  gi|386001528|ref|YP_005919827.1| 15 MDRMRQLEERNLALREQKDRVEGE-KRIMENQKLKFEREVRKLRSELERLR 64
                                      6**************999999888.78888899**************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-05     0.014       2      40 ..     182     225 ..     181     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileekla 40 
                                       + + G+++tGKT l++a a    a+  +vv  E + +++ e+++
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVAssteATFLRVVgSELVQKYIGEGAR 225
                                       6799***************5443336667777777777766653 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.8e-05     0.026       2      29 ..     182     209 ..     182     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                       vll G+pG+GK+ la+ ++  + a++l+
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEATFLR 209
                                       7899**************9988855544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.9e-05     0.021       1      61 [.     182     233 ..     182     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqv 61 
                                       ++lyGp+g+GK++lak +a          +++ ++ r + ++ +++Y g+ + ++ ++ + 
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVA---------SSTEATFLRVVGSELVQKYIGEGARMVRELFEL 233
                                       689**************44.........344566667777777777777776666666555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.7e-05     0.026       2      30 ..     182     210 ..     181     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktll+ka+a++ +++f r+
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEATFLRV 210
                                       7999**********************998 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05     0.026      24      58 ..     170     204 ..     164     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkld 58 
                                        +++  ++  k vll+Gp GtGKt+++k + ++ +
  gi|386001528|ref|YP_005919827.1| 170 LFVKVGIEPPKGVLLYGPPGTGKTLLAKAVASSTE 204
                                       566677778899****************9988877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.6e-05     0.036       5      22 ..     182     199 ..     179     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-05
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g+GKT lak  
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAV 199
                                       89*************987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00016     0.087      21      51 ..     182     212 ..     176     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                       ++l Gp+GtGKt + ka++   ea   rv+g
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEATFLRVVG 212
                                       5789****************99999888887 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         7   3.8e+03     135     154 ..      44      63 ..      14      80 .. 0.57
   2 ?   11.9   0.0   0.00019       0.1      11      37 ..     171     197 ..     159     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7
                            ATPase 135 ekeavaReilrqlvrvlkkl 154
                                       +++ ++ +++r+l ++l+ l
  gi|386001528|ref|YP_005919827.1|  44 NQKLKFEREVRKLRSELERL 63 
                                       22333334444444444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00019
                            ATPase  11 ilkgGipegrvvlitGepGtGKtifal 37 
                                       ++k Gi   + vl++G pGtGKt++a+
  gi|386001528|ref|YP_005919827.1| 171 FVKVGIEPPKGVLLYGPPGTGKTLLAK 197
                                       44789999999**************97 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.5   1.4e+03     106     136 ..      48      77 ..      41      98 .. 0.59
   2 ?   12.0   0.0   0.00027      0.15       2      63 ..     182     244 ..     181     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                                       TTGGG-HHHHHHHHHHHTTTSEEEEE--SS- CS
                          NTPase_1 106 kmElkskkfkeaveevLksekpvlavihrrk 136
                                       k+E +++k+++++e+ L++++ ++++i+   
  gi|386001528|ref|YP_005919827.1|  48 KFEREVRKLRSELER-LRTGPLIVGTIQDVL 77 
                                       344444444444443.566777777777665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00027
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--EEEEEET CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgeegiLarv 63 
                                       v++ GppG+GKt l k v++  +   ++v G  +++++  +g r+  ++ +la+++   +  v
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASSTEATFLRVVGSeLVQKYIGEGARMVRELFELAQNKAPAIIFV 244
                                       6788************************99974688888************999987666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.83   4.5e+02      52      95 ..      17      63 ..       2      97 .. 0.76
   2 ?   10.7   0.0     0.001      0.55       4      37 ..     172     205 ..     171     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.83
                                      B-HHHCCHCEEEE-SS--S-TTSBHHHH...HHHTCHHHHHHHSTTG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                          ABC_tran 52 qeleslrkeigvlpqepqlfpeltvren...esdeeiekalsklglk 95
                                      + ++  +++++  +q++++  e+++ en   + ++e+ k++s+l+  
  gi|386001528|ref|YP_005919827.1| 17 RMRQLEERNLALREQKDRVEGEKRIMENqklKFEREVRKLRSELERL 63
                                      56777888999999999999999999999998888888888877754 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.001
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkp 37 
                                       v++ +++ + v + G+ G+GK+ L+k++a  ++ 
  gi|386001528|ref|YP_005919827.1| 172 VKVGIEPPKGVLLYGPPGTGKTLLAKAVASSTEA 205
                                       56788999999****************9987765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.24   1.3e+02     150     199 ..      29      83 ..       6      87 .. 0.59
   2 ?    9.3   0.0    0.0016      0.87      19      38 ..     181     200 ..     170     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.24
                            AAA_11 150 eklkkskekskskleqerrklkkerkelskeleeaeesle.....eevldeaeiv 199
                                       +++k   e +k+ +e+++ k ++e+++l++ele+ +         ++vld+ ++v
  gi|386001528|ref|YP_005919827.1|  29 REQKDRVEGEKRIMENQKLKFEREVRKLRSELERLRTGPLivgtiQDVLDDNRVV 83 
                                       4455556666666677777777777777777766665433555556666666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                            AAA_11  19 itliqGPPGtgKTktivell 38 
                                        +l+ GPPGtgKT    ++ 
  gi|386001528|ref|YP_005919827.1| 181 GVLLYGPPGTGKTLLAKAVA 200
                                       4799*********5544444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.6     2e+03      29      46 ..     112     129 ..     109     137 .. 0.86
   2 ?    9.7   0.0    0.0013      0.73       3      23 ..     182     202 ..     180     208 .. 0.89
   3 ?    0.2   0.0       1.2   6.3e+02      66     114 ..     224     274 ..     201     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.6
                                       SCCCC-SEEEEEETTTTT CS
                             NACHT  29 lpqgafklvFflslrels 46 
                                       l+q+ f+++F+l++++++
  gi|386001528|ref|YP_005919827.1| 112 LNQQSFSVMFVLPSSRDP 129
                                       67888********99876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT L++ +a+ 
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASS 202
                                       799*************99975 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                                       -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                       a+ v+e   +l++++  + + +D lD + +       ++ ++v++ L +l+ 
  gi|386001528|ref|YP_005919827.1| 224 ARMVRE-LFELAQNKAPAIIFVDELDAIGSRRMDgatSGDREVQRTLMQLLA 274
                                       344555.666788888888889999999987666778888888888888876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00051      0.28      22      46 ..     179     203 ..     165     218 .. 0.83
   2 ?   -2.0   0.0       4.6   2.5e+03     134     143 ..     284     293 ..     262     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                                       SS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                       +  vl+ G  GtGK+lla+a+ +++
  gi|386001528|ref|YP_005919827.1| 179 PKGVLLYGPPGTGKTLLAKAVASST 203
                                       5679***************997654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.6
                                       -EEEEEEESS CS
                   Sigma54_activat 134 dvriiaatne 143
                                       +v++iaatn+
  gi|386001528|ref|YP_005919827.1| 284 EVKLIAATNR 293
                                       6889999986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00037       0.2      21      47 ..     181     209 ..     149     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                                       EEEEEESTTSSHHHHHHHHHHHTT--..- CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..e 47 
                                        +lL+G+ G+GKT l++++a++ + +  +
  gi|386001528|ref|YP_005919827.1| 181 GVLLYGPPGTGKTLLAKAVASSTEATflR 209
                                       49******************998876553 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00036       0.2     117     137 ..     182     202 ..     176     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt la+a a  
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASS 202
                                       89***************9976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00037       0.2      22      41 ..     182     201 ..     173     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt+la a+a 
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVAS 201
                                       6789***********99885 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 ?    8.3   0.0    0.0036         2      19      45 ..     178     204 ..     172     220 .. 0.83
   2 ?    1.2   0.0      0.52   2.8e+02     113     138 ..     233     258 ..     206     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienle 45 
                                       p + +++YGp g GKt L k +++  e
  gi|386001528|ref|YP_005919827.1| 178 PPKGVLLYGPPGTGKTLLAKAVASSTE 204
                                       5566899***********999987764 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.52
                          ATPase_2 113 ikkkgkkiiiiiDelqklidlglnga 138
                                       + +++   ii++Del  +++  ++ga
  gi|386001528|ref|YP_005919827.1| 233 LAQNKAPAIIFVDELDAIGSRRMDGA 258
                                       33333447888999999887666654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.2   1.7e+03     103     154 ..      32      76 ..       9      84 .. 0.58
   2 ?   11.1   0.2   0.00041      0.22      36      56 ..     182     202 ..     155     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.2
                            AAA_25 103 llvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsra 154
                                        + + ++     +   ++++  + +++v++l+ ++e+  + + +++ +++ +
  gi|386001528|ref|YP_005919827.1|  32 KDRVEGE----KR--IMENQKLKFEREVRKLRSELERL-RTGPLIVGTIQDV 76 
                                       3333322....22..34455555888888888888885.4666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00041
                            AAA_25  36 allaGapgtGKttlaldlala 56 
                                       +ll+G+pgtGKt la  +a +
  gi|386001528|ref|YP_005919827.1| 182 VLLYGPPGTGKTLLAKAVASS 202
                                       79************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                       150  (0.00836633); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2906.71
//
Query:       gi|386001529|ref|YP_005919828.1|  [L=134]
Description: hypothetical protein Mhar_0833 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-38  129.4   0.0    8.1e-38  129.2   0.0    1.0  1  CTP-dep_RFKase  Domain of unknown function DUF120
  ------ inclusion threshold ------
      0.013   15.4   2.0      0.026   14.5   0.4    2.1  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.0     9e-42   8.1e-38       1     120 [.       7     123 ..       7     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 9e-42
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       V sGlg G+yy+s+egy++qf+e+lg++p pGTLN+kld++ +  +   ++ ++i+iegf +e+r+fga+ + p++i
  gi|386001529|ref|YP_005919828.1|   7 VASGLGVGRYYISREGYRRQFSERLGLDPIPGTLNLKLDRPFVLDD---SDPDSIRIEGFIEEGRSFGACICRPVRI 80 
                                       78***************************************66544...457889********************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdeveve 120
                                        +i++a+v+pert+y+ ++lE++ap++LRe+l+l+dgdevev 
  gi|386001529|ref|YP_005919828.1|  81 GGIRGAIVRPERTSYSATLLELVAPVNLREALGLSDGDEVEVV 123
                                       *****************************************95 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.16   1.4e+03      14      24 ..      57      67 ..      55      69 .. 0.83
   2 ?   14.5   0.4   2.9e-06     0.026      12      34 ..     105     127 ..     105     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.16
                                      CCHHHCCEECT CS
                    MazE_antitoxin 14 evrfelgireG 24
                                       +r e++i+eG
  gi|386001529|ref|YP_005919828.1| 57 SIRIEGFIEEG 67
                                      589999***99 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.9e-06
                                       -CCCHHHCCEECTCEEEEEECTT CS
                    MazE_antitoxin  12 PkevrfelgireGdevelevdgd 34 
                                       P  +r++lg++ Gdeve++ +g 
  gi|386001529|ref|YP_005919828.1| 105 PVNLREALGLSDGDEVEVVLEGP 127
                                       7889**************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 967.41
//
Query:       gi|386001530|ref|YP_005919829.1|  [L=1145]
Description: hypothetical protein Mhar_0834 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); 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):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 8553.80
//
Query:       gi|386001531|ref|YP_005919830.1|  [L=277]
Description: hypothetical protein Mhar_0835 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1788.65
//
Query:       gi|386001532|ref|YP_005919831.1|  [L=3371]
Description: peptidoglycan-binding lysin domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-20   70.9   0.0     0.0048   16.9   0.0    8.3  8  LysM          LysM domain
  ------ inclusion threshold ------
      0.041   13.3   0.1        0.1   12.0   0.1    1.6  1  DUF2093       Uncharacterized protein conserved in bacteria (
       0.13   11.9   0.4        2.2    8.0   0.4    2.7  2  Phage_tail_X  Phage Tail Protein X
       0.22   11.9   0.3       0.42   11.0   0.3    1.4  1  RPN6_N        26S proteasome regulatory subunit RPN6 N-termin


Domain annotation for each model (and alignments):
>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0011         5       1      27 [.    1372    1398 ..    1372    1409 .. 0.85
   2 ?    3.6   0.0     0.015        69       1      24 [.    1418    1442 ..    1418    1450 .. 0.79
   3 !   16.5   0.0   1.5e-06    0.0067       1      36 [.    1467    1502 ..    1467    1503 .. 0.93
   4 !    5.3   0.0    0.0047        21       9      27 ..    2003    2021 ..    1999    2028 .. 0.93
   5 !   16.9   0.0   1.1e-06    0.0048       5      27 ..    2032    2054 ..    2031    2068 .. 0.89
   6 !    8.0   0.0   0.00066         3       9      44 .]    2085    2122 ..    2079    2122 .. 0.90
   7 ?   -0.7   0.0      0.36   1.6e+03       8      29 ..    2134    2159 ..    2133    2167 .. 0.75
   8 ?    0.0   0.0       0.2     9e+02       8      27 ..    2192    2211 ..    2190    2219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                                        EEE-TT--HHHHHHHCTCHHHHHHHHC CS
                              LysM    1 YtVkkGDTLwsIAkrygitveklleaN 27  
                                        +++ + DTL+sIA +  + v kl+eaN
  gi|386001532|ref|YP_005919831.1| 1372 HRIGPSDTLSSIAEKGPVEVIKLAEAN 1398
                                        567788********************* PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.015
                                        EEE-TT--HHHHHHHC.TCHHHHHH CS
                              LysM    1 YtVkkGDTLwsIAkry.gitvekll 24  
                                        Y+++  DTL+sI+k     ++++ll
  gi|386001532|ref|YP_005919831.1| 1418 YVIRDEDTLESISKDLfAGSMKDLL 1442
                                        999**********987655666665 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.5e-06
                                        EEE-TT--HHHHHHHCTCHHHHHHHHC.TCSSCGG-- CS
                              LysM    1 YtVkkGDTLwsIAkrygitveklleaN.nlsspdkif 36  
                                        +t k+G++L+++A+ ygi+v++l+ea  nl+ p+ +f
  gi|386001532|ref|YP_005919831.1| 1467 HTTKEGESLERVAAEYGIPVRRLAEAEaNLKVPG-LF 1502
                                        799***********************99999998.76 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0047
                                        HHHHHHHCTCHHHHHHHHC CS
                              LysM    9 LwsIAkrygitveklleaN 27  
                                        L +IA+ +++t+e+++eaN
  gi|386001532|ref|YP_005919831.1| 2003 LADIASYFNTTEEAIKEAN 2021
                                        78***************** PP

  == domain 5  score: 16.9 bits;  conditional E-value: 1.1e-06
                                        TT--HHHHHHHCTCHHHHHHHHC CS
                              LysM    5 kGDTLwsIAkrygitveklleaN 27  
                                        + D+L +IA+ry+it ++l+eaN
  gi|386001532|ref|YP_005919831.1| 2032 PEDSLATIADRYQITPSQLAEAN 2054
                                        57********************* PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.00066
                                        HHHHHHHCTCHHHHHHHHC.TCSSCG.G--TTEEEEEE CS
                              LysM    9 LwsIAkrygitveklleaN.nlsspd.kifpGqkLkiP 44  
                                        L++IA+ ++++ e++++aN ++++   +++pG +++iP
  gi|386001532|ref|YP_005919831.1| 2085 LEDIASYFNTPGEEIIKANpEIDPWPeLLEPGLVIRIP 2122
                                        89******************99884448*********9 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 0.36
                                        -HHHHHHHCTCHHHHHHHHC....TC CS
                              LysM    8 TLwsIAkrygitveklleaN....nl 29  
                                        T  ++ + yg+t+ +++e N    +l
  gi|386001532|ref|YP_005919831.1| 2134 TFADLTSFYGTTIADFAEINrstkGL 2159
                                        556666669***********666555 PP

  == domain 8  score: 0.0 bits;  conditional E-value: 0.2
                                        -HHHHHHHCTCHHHHHHHHC CS
                              LysM    8 TLwsIAkrygitveklleaN 27  
                                        T  ++A+ yg +  +l+e N
  gi|386001532|ref|YP_005919831.1| 2192 TFADLAAFYGCSAADLAEDN 2211
                                        8899**************99 PP

>> DUF2093  Uncharacterized protein conserved in bacteria (DUF2093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.3e-05       0.1       5      18 ..    1916    1929 ..    1914    1930 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                           DUF2093    5 GsfVlCAvtgkkIp 18  
                                        Gs+V CAvtg++I+
  gi|386001532|ref|YP_005919831.1| 1916 GSYVNCAVTGDPID 1929
                                        9***********96 PP

>> Phage_tail_X  Phage Tail Protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.14   6.4e+02       9      27 ..    1952    1970 ..    1948    1972 .. 0.85
   2 ?    8.0   0.4    0.0005       2.2      27      56 ..    2097    2126 ..    2093    2128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                        -SHHHHHHHTTS--TTTHH CS
                      Phage_tail_X    9 dtlDalcwryYGrtlgvve 27  
                                        + lD +++ryY     +ve
  gi|386001532|ref|YP_005919831.1| 1952 ESLDEMARRYYTTPIELVE 1970
                                        789********98888887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0005
                                        HHHHHHSTTTTTT-S---TTEEEE-TT--S CS
                      Phage_tail_X   27 eavleaNPgLAelgpvLphGtavelPdist 56  
                                        e++++aNP +  +   L  G+++ +P+i++
  gi|386001532|ref|YP_005919831.1| 2097 EEIIKANPEIDPWPELLEPGLVIRIPEIEV 2126
                                        89***********99************986 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   9.4e-05      0.42       5      74 ..    2453    2522 ..    2449    2525 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.4e-05
                            RPN6_N    5 aksdpkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrsflssiaKaKta 74  
                                        a++d +  ++ly ++l+++ +++e+   + e++lle ++l  ++++ ++L+  i+++ +fls +a+ ++a
  gi|386001532|ref|YP_005919831.1| 2453 ASQDLRVYRQLYYQLLNTTGSDEETIKISIEASLLEEASLELAKDQIQGLRGWIEDIYQFLSDLAQGRAA 2522
                                        566888899**********98888888899***********************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (3371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.96u 0.25s 00:00:01.21 Elapsed: 00:00:00.46
# Mc/sec: 21957.19
//
Query:       gi|386001533|ref|YP_005919832.1|  [L=523]
Description: D-3-phosphoglycerate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-64  217.1   0.2    2.3e-64  216.0   0.0    1.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.3e-43  147.0   0.9    4.8e-43  146.0   0.8    1.6  2  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    3.2e-06   27.4   0.6    9.5e-06   25.9   0.0    2.1  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      2e-05   24.7   0.6    0.00035   20.7   0.0    2.4  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    0.00075   19.1   0.0     0.0045   16.6   0.0    2.1  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
      0.027   14.9   0.0       0.15   12.5   0.0    2.2  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      0.042   13.8   0.4       0.84    9.7   0.3    2.5  2  DUF5608         Domain of unknown function (DUF5608)


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.2   5.5e+03     116     132 ..      81      97 ..      80      99 .. 0.81
   2 !  216.0   0.0     9e-68   2.3e-64       1     178 []     104     278 ..     104     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                       CSTTTEEEEESS-GGGB CS
                      2-Hacid_dh_C 116 kmkkgailiNtaRGglv 132
                                       + kkg i++Nt  G+++
  gi|386001533|ref|YP_005919832.1|  81 ATKKGIIVVNTPGGNTI 97 
                                       6799******9888766 PP

  == domain 2  score: 216.0 bits;  conditional E-value: 9e-68
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +a++l+l+r+++ a++++++gew ++k+++g e+++kt+Gi+GlGrIG ++a r+kafgm+++ayd++ ++e+ +++
  gi|386001533|ref|YP_005919832.1| 104 IAMMLSLARNIPLANASLKAGEW-NRKKYTGVEVYNKTLGIVGLGRIGAEIASRMKAFGMRILAYDPFVTAER-AAD 178
                                       68*********************.9*******************************************99887.9** PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       lg++l++l+e+++esD++++h+plt+etr+li++++++ mk+g+ liN+aRGg+++eeaL++a+ +g++agaa+Dvf
  gi|386001533|ref|YP_005919832.1| 179 LGIRLATLDEIFRESDFITVHTPLTKETRNLIDEDQFKIMKPGVRLINCARGGIINEEALAKAVAEGRVAGAAIDVF 255
                                       ***************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                        +ep+   +pll+   vi+tPH++
  gi|386001533|ref|YP_005919832.1| 256 TKEPPA-GNPLLDQAGVIVTPHLG 278
                                       ****99.55*************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.0   0.8   1.9e-46   4.8e-43       1     134 []       3     310 ..       3     310 .. 0.99
   2 ?   -2.8   0.0       1.7   4.4e+03      42      63 ..     492     513 ..     485     518 .. 0.72

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 1.9e-46
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl+++pl+ee+++ l+  ++ev+v ++l+ eel+e++kd+dal +rs tkvtaev++a++kLkvi+ragvGvDnvD+
  gi|386001533|ref|YP_005919832.1|   3 VLVSDPLSEEGVRKLET-EMEVDVITNLSPEELVERIKDYDALAIRSGTKVTAEVIAAADKLKVIGRAGVGVDNVDI 78 
                                       7999*************.67********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       daa+++Gi+V+n+pg +t+s+AE+t                                                    
  gi|386001533|ref|YP_005919832.1|  79 DAATKKGIIVVNTPGGNTISAAEHTiammlslarniplanaslkagewnrkkytgvevynktlgivglgrigaeias 155
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|386001533|ref|YP_005919832.1| 156 rmkafgmrilaydpfvtaeraadlgirlatldeifresdfitvhtpltketrnlidedqfkimkpgvrlincarggi 232
                                       ***************************************************************************** PP

                                       ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     a+T eaq n+a  +ae+++a+++ge p+na+
  gi|386001533|ref|YP_005919832.1| 233 ineealakavaegrvagaaidvftkeppagnplldqagvivtphlgASTAEAQVNVAVAVAEQILAVARGELPPNAL 309
                                       ***************************************************************************98 PP

                                       S CS
                                       x RF
                        2-Hacid_dh 134 n 134
                                       n
  gi|386001533|ref|YP_005919832.1| 310 N 310
                                       7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                                       EEEE-TTS-BSHHHHHHHTT-- CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh  42 alivrsntkvtaevlealpkLk 63 
                                       ++++++  +v++e+l +l ++ 
  gi|386001533|ref|YP_005919832.1| 492 IMVLNVDHPVSEETLGRLTSVS 513
                                       5666667799999999887665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.2     3e+03     103     115 ..      80      92 ..      13     112 .. 0.59
   2 !   25.9   0.0   3.7e-09   9.5e-06       2     107 ..     141     245 ..     140     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                       HHHHTT-EEEEEE CS
                     NAD_binding_2 103 elkekglkfldaP 115
                                       ++++kg+ ++++P
  gi|386001533|ref|YP_005919832.1|  80 AATKKGIIVVNTP 92 
                                       2334444444444 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.7e-09
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g++GlG +G+++a+++++ g+++ +y+     +e++++ g+  ++++ e++++ d++ +  + +k+++++i++  +
  gi|386001533|ref|YP_005919832.1| 141 LGIVGLGRIGAEIASRMKAFGMRILAYDPF-VTAERAADLGI-RLATLDEIFRESDFITVHTPLTKETRNLIDEdQF 215
                                       79**************************65.45566666666.6778999************************99* PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHT CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkek 107
                                       + +k+g  li+++   + + + lak+++e 
  gi|386001533|ref|YP_005919832.1| 216 KIMKPGVRLINCARGGIINEEALAKAVAEG 245
                                       ************999999999999998875 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.11   2.8e+02      52     100 ..      58     106 ..      43     122 .. 0.79
   2 !   20.7   0.0   1.4e-07   0.00035      16     108 ..     131     226 ..     120     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.11
                                       E-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS CS
                     AdoHcyase_NAD  52 tevdPicalqaameGfevvtleevvkkadivvtttGnkdiitlehlkkm 100
                                       +  d +  +  a  G + v ++ ++kk+ ivv t G + i  +eh  +m
  gi|386001533|ref|YP_005919832.1|  58 AAADKLKVIGRAGVGVDNVDIDAATKKGIIVVNTPGGNTISAAEHTIAM 106
                                       45566666666667888889999999999***99999999999997776 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.4e-07
                                       HH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-H.HHHHHHHCTT-EE--HHHCTTT-SEEEE-S....S CS
                     AdoHcyase_NAD  16 atdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdP.icalqaameGfevvtleevvkkadivvttt....G 87 
                                        t v +  k+  ++G G +G   a+ +k++G r++    dP ++a +aa  G +++tl+e+ +++d++   t     
  gi|386001533|ref|YP_005919832.1| 131 YTGVEVYNKTLGIVGLGRIGAEIASRMKAFGMRILA--YDPfVTAERAADLGIRLATLDEIFRESDFITVHTpltkE 205
                                       566777789999********************9875..6894578889999***************88665422225 PP

                                       SSSSB-HHHHCCS-TTEEEEE CS
                     AdoHcyase_NAD  88 nkdiitlehlkkmkddaivcn 108
                                       ++++i  +++k mk  + + n
  gi|386001533|ref|YP_005919832.1| 206 TRNLIDEDQFKIMKPGVRLIN 226
                                       789**********98664444 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.31     8e+02      79     113 ..      32      66 ..      16     108 .. 0.75
   2 !   16.6   0.0   1.7e-06    0.0045       3      89 ..     137     222 ..     135     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                                       HHTGGG--TT-EEEESSSHHHHTTSS---TTSEEE CS
                              IlvN  79 eeiepnlkegkalafahGfnihfglikppkdvdvv 113
                                       ee+ + +k+ +ala  +G ++  + i + ++++v+
  gi|386001533|ref|YP_005919832.1|  32 EELVERIKDYDALAIRSGTKVTAEVIAAADKLKVI 66 
                                       45556666667777777777777777766666665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.7e-06
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH.HHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel.qkevye 78 
                                        +k++ ++G G  G   a  ++  g+ +    ++   ++++A + g++ +t++e+ +++d++++ +P +   +++++
  gi|386001533|ref|YP_005919832.1| 137 YNKTLGIVGLGRIGAEIASRMKAFGMRILA--YDPFVTAERAADLGIRLATLDEIFRESDFITVHTPLTKeTRNLID 211
                                       589**********************99763..4455589****************************6541566777 PP

                                       HHTGGG--TT- CS
                              IlvN  79 eeiepnlkegk 89 
                                       e+  + +k g 
  gi|386001533|ref|YP_005919832.1| 212 EDQFKIMKPGV 222
                                       77777777665 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.99   2.5e+03      33      72 ..       3      46 ..       1      69 [. 0.63
   2 ?   12.5   0.0     6e-05      0.15      21      81 ..     152     208 ..     150     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.99
                                      EEEE-SSTHHCCCCHHGG.....BTCCEEES-CHHHHTT-SEEEE CS
                    UDPG_MGDP_dh_C 33 vkiyDPkvkeeaveaele.....ekgvevvdsleealkgadaivi 72
                                      v + DP  +e  ++ e+e      +++ + ++l e++k++da+ i
  gi|386001533|ref|YP_005919832.1|  3 VLVSDPLSEEGVRKLETEmevdvITNL-SPEELVERIKDYDALAI 46
                                      666777777666666554433321122.23345677777777766 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6e-05
                                       HHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--.GGGGG CS
                    UDPG_MGDP_dh_C  21 diieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh.defke 81 
                                       +i+ ++++ g+++ +yDP v++e+++      g++++ +l+e ++++d i ++t+  +e ++
  gi|386001533|ref|YP_005919832.1| 152 EIASRMKAFGMRILAYDPFVTAERAAD----LGIRLA-TLDEIFRESDFITVHTPLtKETRN 208
                                       68999******************9987....478888.79************9986355555 PP

>> DUF5608  Domain of unknown function (DUF5608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.16   4.2e+02      16      28 ..     242     254 ..     238     258 .. 0.86
   2 ?    9.7   0.3   0.00033      0.84       7      47 ..     417     458 ..     412     463 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                                       ETTEEEEEEEEEE CS
                           DUF5608  16 lanGrvqGrlidi 28 
                                       +a+Grv G  id+
  gi|386001533|ref|YP_005919832.1| 242 VAEGRVAGAAIDV 254
                                       699********98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00033
                                       -TTSEEEEE.ETTEEEEEEEEEE-SSEEEEXETTEEE.EEEGG CS
                           DUF5608   7 PkGiGvtvy.lanGrvqGrlidiGvyevlvevGGdii.yihkd 47 
                                       PkG  v+vy    G+  Gr++ i  y v v   G +i  ih d
  gi|386001533|ref|YP_005919832.1| 417 PKG-SVSVYgTVYGKNEGRIVQINEYRVYVPTEGYMImAIHED 458
                                       666.4778834579****************9988655169988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 4045.46
//
Query:       gi|386001534|ref|YP_005919833.1|  [L=233]
Description: hypothetical protein Mhar_0838 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-88  296.7   0.2    1.3e-88  296.5   0.2    1.0  1  4HFCP_synth  4-HFC-P synthase


Domain annotation for each model (and alignments):
>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5   0.2   7.5e-93   1.3e-88       1     227 [.       3     228 ..       3     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 7.5e-93
                                       EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TTSEEEEEEEEE-S-HHHHHHHHHHHHHT CS
                       4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgsvpvSaaiGdlpekpgtvslaalgaaaa 77 
                                       LLvS++n+ Eae+a+aggadi+DvKnP+eGsLGa+fp+vir+++ev++g+vpvSa+iGd+++kpgt+slaalgaa +
  gi|386001534|ref|YP_005919833.1|   3 LLVSPINAVEAEAAMAGGADILDVKNPREGSLGANFPWVIRSVAEVAAGRVPVSATIGDFDFKPGTASLAALGAAFS 79 
                                       8**************************************************************************** PP

                                       T-SEEEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS-S CS
                       4HFCP_synth  78 gvdyvKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadKd 154
                                       g+dy+KvGl ++++++ea+e+l+++v++vke d++k++va++y+Da+rv+s+sp++l+e+aae+ga++vm+DTa+Kd
  gi|386001534|ref|YP_005919833.1|  80 GADYIKVGLLKIRDRDEAAEMLRPLVRSVKEFDANKRLVAAAYSDASRVGSISPMDLPEVAAECGADVVMVDTAIKD 156
                                       ***************************************************************************** PP

                                       S--HHHHS-HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTTSSB-HHHHHHH CS
                       4HFCP_synth 155 gkslldflseeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRngkidaelvekl 227
                                       g+++++f++e+e+++f++  +++g+++a+AG++k+ dl+ Lk+++p+i+GvRgavC +gdR g+i++elv+++
  gi|386001534|ref|YP_005919833.1| 157 GRTTFEFMTESEISDFIALGHDLGMEVAIAGTIKFGDLALLKRVGPEIIGVRGAVC-GGDRAGEIKEELVRRM 228
                                       ********************************************************.*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1771.97
//
Query:       gi|386001535|ref|YP_005919834.1|  [L=230]
Description: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-26   92.0   0.0    4.8e-26   91.6   0.0    1.2  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.16   11.3   0.0    1.2  1  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   5.3e-30   4.8e-26       3     228 ..       5     223 ..       3     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 5.3e-30
                                       EEEEEEETTEEEEECTTCSTCEEEETTSHHH......HHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S CS
                      His_biosynth   3 ipalDlkdGkvVrlvkGdrfqelryagdpve......lakryeeegadelhvvDldaakegreanldlveeiaeevf 73 
                                       +++lDl +G +V+ v+G+r+++  +++   +       ++ ++    +e++v+Dld ++ g ++nldl+ eia++  
  gi|386001535|ref|YP_005919834.1|   5 VFVLDLFNGSAVHAVRGERKKYRPIQEM-SKivgtssPLSILDLLRPKEVYVADLDRIM-GAGENLDLIGEIARR-- 77 
                                       689****************554444332.221222223466788899*********996.***************.. PP

                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHH CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldav 150
                                       ++ + + GI+s ++++ l  +   k ++gt++   + l++e++++     +vv+iD   g +v+ +    +  + ++
  gi|386001535|ref|YP_005919834.1|  78 AETMADIGISSKDELDLLPPS--VKPVLGTETGFIS-LLEEASSR---RDVVVSIDLFGG-EVLSRDPALK--IPPL 145
                                       99***********77655554..5777899887654.78888884...689*********.9999888777..**** PP

                                       HHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTS CS
                      His_biosynth 151 elakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyege 227
                                       +l++kl+ l ++e++l + dr+Gt +G d  ++++ a+  ++p++ +GGv+++ dl++l++ g ++++v++a + g+
  gi|386001535|ref|YP_005919834.1| 146 DLIRKLNPLPIREVILLSLDRVGTSKGLDERFLRAAADLSDHPLLLGGGVRDVRDLERLEDLGLAGALVATAVHRGK 222
                                       ***************************************************************************98 PP

                                       S CS
                      His_biosynth 228 l 228
                                       +
  gi|386001535|ref|YP_005919834.1| 223 V 223
                                       6 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.8e-05      0.16     154     213 ..     166     224 ..     147     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                                       STTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                              ThiG 154 piGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                        +G+++Gl +  +l+   +  + P+++  G++   d     +lG+ + l++tav + k p
  gi|386001535|ref|YP_005919834.1| 166 RVGTSKGLDE-RFLRAAADLSDHPLLLGGGVRDVRDLERLEDLGLAGALVATAVHRGKVP 224
                                       5899999975.6899999999*********************************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1650.73
//
Query:       gi|386001536|ref|YP_005919835.1|  [L=571]
Description: Iron transport protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-50  170.9   0.1    1.9e-50  170.4   0.1    1.2  1  FeoB_N    Ferrous iron transport protein B
    1.4e-25   89.7  16.5    8.7e-13   48.5   7.5    2.9  2  Gate      Nucleoside recognition
    3.4e-16   59.3   0.0    5.9e-16   58.6   0.0    1.4  1  MMR_HSR1  50S ribosome-binding GTPase
      8e-12   44.7   0.3      8e-12   44.7   0.3    3.0  2  FeoB_C    Ferrous iron transport protein B C terminus
    1.5e-05   24.4   0.0    2.5e-05   23.7   0.0    1.3  1  AIG1      AIG1 family
     0.0036   16.7   0.0     0.0059   16.1   0.0    1.2  1  SRPRB     Signal recognition particle receptor beta subunit
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.92    9.7   0.0    2.2  2  Roc       Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4   0.1   7.6e-54   1.9e-50       2     156 .]       7     160 ..       6     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 7.6e-54
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       +++l+GnpnvGk+++f +ltg +   +N+pG+tve + g+++++g+++e++D PG+Ysl++  + e+v+r+++ ee 
  gi|386001536|ref|YP_005919835.1|   7 KIILMGNPNVGKSVVFSRLTGIEVISSNYPGTTVEYTLGRTSIAGESAEVIDPPGVYSLEPSCRAEEVTREIF-EEG 82 
                                       799*******************************************************************976.688 PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                       +dvvv+vvdatnlernL Ltlq+le g+p+v++ln++d+a+++gieidl++L+e+Lgvpvv+++a +++gi+el +a
  gi|386001536|ref|YP_005919835.1|  83 ADVVVDVVDATNLERNLNLTLQILERGLPTVVVLNLWDVATRTGIEIDLAALEEELGVPVVPAVAVSGQGIRELAEA 159
                                       9*************************************************************************998 PP

                                       H CS
                            FeoB_N 156 i 156
                                       i
  gi|386001536|ref|YP_005919835.1| 160 I 160
                                       6 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   1.6   2.8e-15   7.1e-12       4     111 ..     291     384 ..     288     385 .. 0.96
   2 !   48.5   7.5   3.4e-16   8.7e-13       1     111 [.     446     544 ..     446     545 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.8e-15
                              Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80 
                                       ++p+++++ i++++l++ ++l ri+ l++ ++++ g  l++ a+v++++g++   ++v+ ++ ++           +
  gi|386001536|ref|YP_005919835.1| 291 VLPFVIPFYIVLGVLEDVGYLPRISVLVDALMHRVG--LHGAAVVPCILGLG---CNVPGVMATR---------VLE 353
                                       79**********************************..**************...*********9.........*** PP

                              Gate  81 tpksalafllfvllytpcvatlavivrelgs 111
                                       ++k+++ +  +++ ++pc a+ a+i + lg 
  gi|386001536|ref|YP_005919835.1| 354 SEKQRYLAATLMAVSVPCAAQNAMIWGLLGP 384
                                       ***********************99998885 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 3.4e-16
                              Gate   1 llkagpiillasiliwflssssllgrigkllepvfap.lgqeldwkatvslltgfaakevvvgtlgtlytsalgell 76 
                                       l+ a+p++ll+++l+++l   ++++ +g l ep++   +g  l+  a++++++gf+ k v+vg+l+ l         
  gi|386001536|ref|YP_005919835.1| 446 LKEAVPYVLLGVFLMNVLFIAGVVDLVGGLAEPIITGlFG--LPKDAAATMIVGFLRKDVAVGMLAPL--------- 511
                                       6889******************************555499..***********************888......... PP

                              Gate  77 qgfdtpksalafllfvllytpcvatlavivrelgs 111
                                           t  + +++ +++++y+pcvat+av+++elg 
  gi|386001536|ref|YP_005919835.1| 512 --GMTAGQLVVASVVLAMYFPCVATFAVFMKELGL 544
                                       ..68889999***********************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   2.3e-19   5.9e-16       1     113 [.       7     117 ..       7     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.3e-19
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee 75 
                                       +++++G+pNvGKS ++++ltg ++i s++pgtT + + gr ++ g++ e++D pG+++   + + +++++++ + e 
  gi|386001536|ref|YP_005919835.1|   7 KIILMGNPNVGKSVVFSRLTGIEVISSNYPGTTVEYTLGRTSIAGESAEVIDPPGVYSlePSCRAEEVTREIFE-EG 82 
                                       589****************************************************8854222223356666664.44 PP

                                       TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  76 adlillvvdaseeklkpldeeleelleeakkplilvln 113
                                       ad+++ vvda+ + l+++ +   ++l e++ p+++vln
  gi|386001536|ref|YP_005919835.1|  83 ADVVVDVVDAT-N-LERNLNLTLQIL-ERGLPTVVVLN 117
                                       9********77.4.555544444554.46778888887 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.3   3.1e-15     8e-12       3      53 .]     392     441 ..     390     441 .. 0.96
   2 ?    0.0   0.8      0.27   6.9e+02       6      21 ..     552     567 ..     548     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.1e-15
                            FeoB_C   3 slYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                       ++Y + +lv++ ++++l+++   ge++  ++E+PpYr+P+ + +++ktw+R
  gi|386001536|ref|YP_005919835.1| 392 VVYGTLFLVFISAGFILSRI-VGGESPEIFLEIPPYRVPDGRALFKKTWMR 441
                                       6899***************9.****************************98 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.27
                            FeoB_C   6 llgilvallvalllkk 21 
                                       l+++l+a +v+ +l+ 
  gi|386001536|ref|YP_005919835.1| 552 LIMVLAATIVGTILNA 567
                                       78999999*****987 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   9.7e-09   2.5e-05       2     106 ..       7     105 ..       6     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 9.7e-09
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       +i+l+G   +GkS     + g ++ +s++   + t + +  +++ +g++ +ViD Pg+ +l+ s     +e++r  +
  gi|386001536|ref|YP_005919835.1|   7 KIILMGNPNVGKSVVFSRLTGIEVISSNY--PGTTVEYTLGRTSIAGESAEVIDPPGVYSLEPSCR--AEEVTR--E 77 
                                       8***************************6..777888999999***************99998754..445554..5 PP

                                       HCTT-ESEEEEEEETTB-SHHHHHHHHH CS
                              AIG1  79 lseegihalllvlslgrfteedekalkt 106
                                       + eeg ++++ v+++++++++ + +l+ 
  gi|386001536|ref|YP_005919835.1|  78 IFEEGADVVVDVVDATNLERNLNLTLQI 105
                                       557*******999998888776666665 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-06    0.0059       5      95 ..       7     102 ..       5     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCC....SHHHHHHHHHHGGE CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhekl....rqklleklkakssl 76 
                                       +++l+G  + GK  +f rLt  +v ++       + +l  +s  g++ ++iD PG  +l    r + +++ + ++ +
  gi|386001536|ref|YP_005919835.1|   7 KIILMGNPNVGKSVVFSRLTGIEVISSNYPGtTVEYTLGRTSIAGESAEVIDPPGVYSLepscRAEEVTREIFEEGA 83 
                                       69******************9877666554436677777799*************9888444466777777888899 PP

                                       EEEEEEEETTS-HHHHHHH CS
                             SRPRB  77 kglvfvvDStidpkevkev 95 
                                         +v vvD+t  +++++ +
  gi|386001536|ref|YP_005919835.1|  84 DVVVDVVDATNLERNLNLT 102
                                       99999***99999988765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00036      0.92       1      27 [.       7      33 ..       7      57 .. 0.76
   2 ?    0.1   0.0      0.36   9.2e+02      55      65 ..     113     123 ..      72     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                                      EEEEESSTTSSHHHHHHCHCT-CCC-E CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfsek 27
                                      K++l+G+ +vGK+  ++r++  ++ ++
  gi|386001536|ref|YP_005919835.1|  7 KIILMGNPNVGKSVVFSRLTGIEVISS 33
                                      9*****************997665444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                                       CEEEEEEEE-S CS
                               Roc  55 kvklniWDtaG 65 
                                        v ln+WD+a 
  gi|386001536|ref|YP_005919835.1| 113 VVVLNLWDVAT 123
                                       46789999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 4171.82
//
Query:       gi|386001537|ref|YP_005919836.1|  [L=262]
Description: hypothetical protein Mhar_0841 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.5   0.0    1.9e-12   46.9   0.0    1.1  1  RsmJ      Ribosomal RNA large subunit methyltransferase D, Rl


Domain annotation for each model (and alignments):
>> RsmJ  Ribosomal RNA large subunit methyltransferase D, RlmJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   1.1e-16   1.9e-12       5     143 ..      35     167 ..      32     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.1e-16
                                       EEEESS--SSEEETTSHHHHHHSGGGGTGGGTTT-TT--GGGHHHHHHHHHTTTTSS--EEE-HHHHHHHHS-TT-E CS
                              RsmJ   5 avlDthaGvGrYdLsseeaektgeaeeGiaRliaqadlpaeleryldvvrklnkgeklryYpGspllarrllReqDr 81 
                                       +++++haG+  Y+L        ge+e Gi+Rl+  + ++   ++y +++ +ln++  l++YpGs+ ++ +l R++  
  gi|386001537|ref|YP_005919836.1|  35 VYVESHAGRPGYRLR-----PGGEWEGGIGRLWPIP-VGMAARPYFQILAALNPQ-GLELYPGSASIVLHLARKRGF 104
                                       699***********6.....57***********986.566679**********95.69******************* PP

                                       EEEE---TTHHHHHHHHTTT.-TTEEEESS-HHHHHHHS-S-TTS-EEEEE----SSCCHHHH CS
                              RsmJ  82 lvlteLhpkdaalLkaelak.dkrvrvkkadGfaalkaklppkekRglvliDPPyeakdeydr 143
                                        + +eL +   ++  a +++ ++ vr + +dGf+ +   + + ++ +l+l+D P+    + d 
  gi|386001537|ref|YP_005919836.1| 105 SLRAELWDTSPEVEAAWFSSrQEGVRFHLGDGFSGAGRLARELKEPALLLVDSPWTDPRDADL 167
                                       *********999999999761567*************99999999**********98877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 2068.26
//
Query:       gi|386001538|ref|YP_005919837.1|  [L=653]
Description: Acetyl-CoA hydrolase/N-acetyltransferase GNAT family fusion protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-60  201.9   0.0    7.7e-60  201.3   0.0    1.3  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    1.3e-46  159.1   0.0    3.6e-46  157.6   0.0    1.7  2  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    7.4e-11   42.3   0.0    3.5e-10   40.1   0.0    2.1  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.5e-09   37.4   0.0    7.1e-09   36.5   0.0    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    3.3e-07   30.6   0.0    7.1e-07   29.5   0.0    1.5  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    4.2e-06   27.1   0.0    9.4e-06   26.0   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.9e-05   24.0   0.1    5.7e-05   23.1   0.1    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00017   21.1   0.0       0.37   10.1   0.0    2.4  2  CoA_trans        Coenzyme A transferase
      0.001   19.0   0.0     0.0025   17.8   0.0    1.6  1  FR47             FR47-like protein
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.074   13.0   0.0    2.3  3  DeoRC            DeoR C terminal sensor domain
      0.018   13.4   0.1        2.1    6.6   0.0    2.2  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans
       0.09   12.9   0.1        0.3   11.3   0.1    1.9  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.3   0.0   5.1e-63   7.7e-60       1     154 []     304     457 ..     304     457 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 5.1e-63
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHST CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalsk 77 
                                       G  + y++ld+np++e++ ++y+n+p +i++ k++++insa+e+dltGq+++eslg++++sG+Ggq dF+rga l++
  gi|386001538|ref|YP_005919837.1| 304 GRAETYEYLDDNPSVEFKTIDYTNNPLIISKIKRMTAINSAMEIDLTGQATAESLGSTFYSGIGGQADFMRGALLAP 380
                                       78899************************************************************************ PP

                                       T-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                   AcetylCoA_hyd_C  78 ggksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                       ggksi+alpSta  g++SrIvp+l +g++vt tr dv+yvvTE Gia+L+gk++rera+ li+iAhpdf+++L+eea
  gi|386001538|ref|YP_005919837.1| 381 GGKSILALPSTALGGKVSRIVPALLPGSGVTLTRGDVQYVVTERGIAYLQGKNIRERAMDLISIAHPDFQPWLIEEA 457
                                       **************************************************************************997 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6   0.0   2.4e-49   3.6e-46       3     190 ..      26     212 ..      24     217 .. 0.96
   2 ?   -2.6   0.0       3.1   4.6e+03     109     127 ..     526     544 ..     508     547 .. 0.78

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 2.4e-49
                   AcetylCoA_hydro   3 eeyekklke.peeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevlee 78 
                                       ++y + +   pe++a++  ++  i+ ++++++gt +++p+ l k  ve+++ ++k +++++v  v+s+g  +++ +e
  gi|386001538|ref|YP_005919837.1|  26 QDYRREREIwPEKFASVGAIFRKIHPGDRIFIGTGCGEPQHLLKALVEYVKSNPKAFFEAEVIHVWSLG-VAPYADE 101
                                       5688877767***********************************************************.******* PP

                   AcetylCoA_hydro  79 kdavlyrpapkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiE 155
                                       k a ++r  ++++g+ +r a+n g++++++++ls+vp+++ ++ +piDval++++++de+Gy+ lGv+v+++K++ E
  gi|386001538|ref|YP_005919837.1| 102 KLAENFRLDSFFIGDSTRDAVNRGAADYTPIFLSQVPDLFRREITPIDVALVQTSPPDEHGYMSLGVSVDIVKAALE 178
                                       ***************************************************************************** PP

                   AcetylCoA_hydro 156 vaelvvivvkknpPrvngydelialdkvdyivvdp 190
                                       +a lv+++v+  +Pr++g d++  ++ vdy+v  +
  gi|386001538|ref|YP_005919837.1| 179 MAPLVIAQVNRFMPRIHG-DGFLSVEDVDYLVPYD 212
                                       ******************.***********88655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                   AcetylCoA_hydro 109 khlsevpqklekgfvpiDv 127
                                          ++vp ++ ++fv++D+
  gi|386001538|ref|YP_005919837.1| 526 SARRNVPREVRQEFVAVDY 544
                                       556789999*******998 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.5   2.3e+03      80      92 ..      66      78 ..      22      97 .. 0.70
   2 !   40.1   0.0   2.4e-13   3.5e-10      34     117 .]     550     633 ..     511     633 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHHHT CS
                    Acetyltransf_1 80 aLlealeeraree 92
                                      +Ll+al+e+++++
  gi|386001538|ref|YP_005919837.1| 66 HLLKALVEYVKSN 78
                                      5677777777666 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 2.4e-13
                                       EEEEEEET...TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHH CS
                    Acetyltransf_1  34 gllvaeed...geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednda 107
                                        l v+ee+   ++ +G  +++ +pd    +++   l+V+ +++gkG+Gs+Ll +l   a+++g+    ++v ++n++
  gi|386001538|ref|YP_005919837.1| 550 ILAVVEEEreqETAVGVGQYSLNPD---MHTAEVALVVRDDFQGKGVGSELLHYLTYLAKRQGLLGFSAEVLVTNRP 623
                                       3334555566688************...677777******************************66688******** PP

                                       HHHHHHHTTE CS
                    Acetyltransf_1 108 airlYeklGF 117
                                       +++l+e +GF
  gi|386001538|ref|YP_005919837.1| 624 MMALFEGMGF 633
                                       *****77*99 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.7e-12   7.1e-09       2     138 .]     495     634 ..     494     634 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.7e-12
                    Acetyltransf_3   2 LlLrplteeDlealfel...rsdpe.vmrylpe.pltleeaeewlerawaeeseeegygwaivl..kdtgv.iGsvg 70 
                                       +lLrp++ +D + + e+   +sd+    r+++     + e ++ +    a ++ ++ + +a+v+  ++++  +G+  
  gi|386001538|ref|YP_005919837.1| 495 ILLRPVRISDEPLIKEFfysLSDESlYSRFISArRNVPREVRQEFV---AVDYSRDMVILAVVEeeREQETaVGVGQ 568
                                       79********444446444588999788885542222333333333...3344446677888775655544488777 PP

                    Acetyltransf_3  71 lrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +   + + ++ae+ ++++++f+gkG+++e ++ l+ +a +++gl  + a++  +N+ + +++e +Gfe
  gi|386001538|ref|YP_005919837.1| 569 YSLNP-DMHTAEVALVVRDDFQGKGVGSELLHYLTYLA-KRQGLLGFSAEVLVTNRPMMALFEGMGFE 634
                                       76544.4555*********************9988777.8888************************7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   4.8e-10   7.1e-07      56     141 ..     559     640 ..     543     647 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.8e-10
                    Acetyltransf_4  56 esdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkal 132
                                       e+++ vG  +++ +++    + ae+   +   d + +g+g+el+ +l   +k+q+++ + ae+ ++n + +++++ +
  gi|386001538|ref|YP_005919837.1| 559 EQETAVGVGQYS-LNP--DMHTAEVALVVR-DDFQGKGVGSELLHYLTYLAKRQGLLGFSAEVLVTNRPMMALFEGM 631
                                       499999999999.777..77******9995.799**************999************************** PP

                    Acetyltransf_4 133 GFelvgifk 141
                                       GFe++++ +
  gi|386001538|ref|YP_005919837.1| 632 GFEIEKRRE 640
                                       ***998755 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   6.3e-09   9.4e-06       7      75 ..     553     634 ..     538     635 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.3e-09
                                       EEEET...TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH....TT.SEEEEE...EEEETHHHHHHHH CS
                    Acetyltransf_7   7 Vaedd...gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea....ae.kgiile...qlelnaekaikfY 69 
                                       V+e++   +  vG   +sl+    + +  l+V+ +++gkG+G++Ll +    a+ +g+      ++ +++++  +++
  gi|386001538|ref|YP_005919837.1| 553 VVEEEreqETAVGVGQYSLNPdmhTAEVALVVRDDFQGKGVGSELLHYltylAKrQGLL-GfsaEVLVTNRPMMALF 628
                                       555556664444544444444434444449****************9756652255633.222222233335566** PP

                                       HHTTEE CS
                    Acetyltransf_7  70 eklGFe 75 
                                       e +GFe
  gi|386001538|ref|YP_005919837.1| 629 EGMGFE 634
                                       *****8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   3.8e-08   5.7e-05      38     113 ..     559     640 ..     522     650 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.8e-08
                   Acetyltransf_10  38 eggkivGviel.rdgs.hisll..fVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFka 108
                                       e+++ vGv+++  + + h + +  +V+++++g+G+g++Ll+++   a+++g+   + +v  ++    +++e +GF+ 
  gi|386001538|ref|YP_005919837.1| 559 EQETAVGVGQYsLNPDmHTAEValVVRDDFQGKGVGSELLHYLTYLAKRQGLLGfSAEVLVTNrPMMALFEGMGFEI 635
                                       3466778886644443566554339**********************9999999*9999999999**********98 PP

                   Acetyltransf_10 109 vgeeq 113
                                        ++ +
  gi|386001538|ref|YP_005919837.1| 636 EKRRE 640
                                       75543 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00085       1.3       7      44 ..      44      80 ..      41     113 .. 0.74
   2 !   10.1   0.0   0.00025      0.37       4      69 ..     230     289 ..     227     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00085
                                      HHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHT.TTSE CS
                         CoA_trans  7 avakeikdGmtvavGGFgligiPealiaalarsg.vkdl 44
                                      a+ ++i+ G+ +++G  +++g+P++l +al++    +++
  gi|386001538|ref|YP_005919837.1| 44 AIFRKIHPGDRIFIG--TGCGEPQHLLKALVEYVkSNPK 80
                                      56679**********..************9986533444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                                       HHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEE CS
                         CoA_trans   4 aaeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllngsvkkvi 69 
                                       +a  va+ i+dG+tv vG     g  P+al   l ++   ++  i+ e  + g+  l+++g v++  
  gi|386001538|ref|YP_005919837.1| 230 IASYVARIIEDGSTVQVG----YGyAPNALLSHLHKK---KHLGIHTELLTDGIVELMKSGVVDNSR 289
                                       6778999***********....8889*8888888876...999999999999999999999998765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0025      25      80 ..     580     636 ..     569     641 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                       EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  25 galqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                        al v+++++++G gs l + l++   ++g    ++ v  +N p  +l+e +Gfe  
  gi|386001538|ref|YP_005919837.1| 580 VALVVRDDFQGKGVGSELLHYLTYLAKRQGLLgFSAEVLVTNRPMMALFEGMGFEIE 636
                                       6899********************999999752679999***************976 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4   2.1e+03      14      29 ..      46      61 ..      40      73 .. 0.80
   2 ?   -2.8   0.0       3.6   5.4e+03      83     100 ..      99     116 ..      91     125 .. 0.78
   3 ?   13.0   0.0     5e-05     0.074       7      49 ..     228     270 ..     224     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                             DeoRC 14 aeliedgdtifldaGt 29
                                       + i++gd if+++G 
  gi|386001538|ref|YP_005919837.1| 46 FRKIHPGDRIFIGTGC 61
                                      56799*******9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                             DeoRC  83 laeealrqfnvdkaflga 100
                                       + e+  ++f++d +f+g 
  gi|386001538|ref|YP_005919837.1|  99 ADEKLAENFRLDSFFIGD 116
                                       45667899*******995 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 5e-05
                             DeoRC   7 rrIAkaAaeliedgdtifldaGtTtlelaraLaekknltvvTn 49 
                                       +rIA+++a++iedg+t+ ++ G    +l ++L++kk+l + T 
  gi|386001538|ref|YP_005919837.1| 228 ARIASYVARIIEDGSTVQVGYGYAPNALLSHLHKKKHLGIHTE 270
                                       69***********************************999986 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0058       8.6     137     207 ..     146     214 ..     132     253 .. 0.77
   2 ?    6.6   0.0    0.0014       2.1     447     482 ..     411     445 ..     402     448 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0058
                   Mal_decarbox_Al 137 iP.nvalvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdklprvd.iPadwvdfvveadkp 207
                                       +P +valv ++  d++G +  G++ +    iv a+     +viaqvn+ + ++     +  + vd++v  d+p
  gi|386001538|ref|YP_005919837.1| 146 TPiDVALVQTSPPDEHGYMSLGVSVD----IVKAALEMAPLVIAQVNRFMPRIHGDGfLSVEDVDYLVPYDEP 214
                                       55369*****************9986....8888888899*******99766543322455666666665544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                   Mal_decarbox_Al 447 miygddvthvvteeGiayllkaesleereqairava 482
                                        +   dv +vvte Giayl   +++ er   + ++a
  gi|386001538|ref|YP_005919837.1| 411 TLTRGDVQYVVTERGIAYLQ-GKNIRERAMDLISIA 445
                                       566679************96.567777776666665 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0002       0.3       8      58 ..     560     610 ..     553     611 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                   Acetyltransf_CG   8 egeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       +++ v++ +Y+ +++ + +    +V + ++GkG++++L  +    a+++gl
  gi|386001538|ref|YP_005919837.1| 560 QETAVGVGQYSLNPDMHTAEVALVVRDDFQGKGVGSELLHYLTYLAKRQGL 610
                                       45578888999888888888899****************999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 4988.41
//
Query:       gi|386001539|ref|YP_005919838.1|  [L=334]
Description: hypothetical protein Mhar_0843 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1631  (0.0909699); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1944.19
//
Query:       gi|386001540|ref|YP_005919839.1|  [L=148]
Description: glyoxalase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-11   42.6   0.0    1.6e-10   41.3   0.0    1.6  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    5.1e-08   33.7   0.0    1.7e-07   32.0   0.0    1.7  1  Glyoxalase_6  Glyoxalase-like domain
     0.0011   18.9   0.0     0.0063   16.4   0.0    1.9  1  Glyoxalase_2  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   2.6e-14   1.6e-10       2     128 .]      12     131 ..      11     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.6e-14
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC....TS CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee....tv 74 
                                       ++ v+l v dle++++FY++ LG+ l+  ++        ++a f  ++g +  +  +    +++ v+   +    ++
  gi|386001540|ref|YP_005919839.1|  12 LNIVTLGVEDLERAVSFYKDGLGWPLSSISG-------GDYAIFKTSTGTALALFPRRLLAEDACVQ---DrggfGG 78 
                                       67899**************************.......56666666655555555555555555552...2345678 PP

                                       EEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  75 hhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                         +a  + + e+v+ al ++ +ag+   +   ++ +g+  + yf DpdG+ +e+
  gi|386001540|ref|YP_005919839.1|  79 ITLAQNVPSREEVDGALSQAVSAGGTLLKRASDTDWGGYSG-YFADPDGHPWEV 131
                                       89**********************************99997.7*********96 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.9e-11   1.7e-07       2     107 .]      15     132 ..      14     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.9e-11
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree...aaledpegvgpaaedaatllfqrvpe.............paknrvHl 62 
                                       v+l ++d ++++ F+++ lgw++++ +   +a+ + +++++ a    +                          + l
  gi|386001540|ref|YP_005919839.1|  15 VTLGVEDLERAVSFYKDGLGWPLSSISggdYAIFKTSTGTALALFPRR-------LlaedacvqdrggfG---GITL 81 
                                       678899*******************99555333333333332222223.......223445434432220...3555 PP

                      Glyoxalase_6  63 dlav...edldaevarlvalGArvlreprdgthgr...vlaDPeGneFcvv 107
                                         +v   e++d +  ++v++G++ l++  d ++g+    +aDP+G+++ v+
  gi|386001540|ref|YP_005919839.1|  82 AQNVpsrEEVDGALSQAVSAGGTLLKRASDTDWGGysgYFADPDGHPWEVA 132
                                       55555579999**********************99************9985 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     1e-06    0.0063       3     114 ..      14     132 ..      12     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-06
                                       ----EES-HHHHHHHHHHTT---EEE.E-SSEEEETTS-..EEEEHHHHHH-------S..--SS-EEEE...EES- CS
                      Glyoxalase_2   3 lillvvkdieeskkFYedvlelkikl.dfGenvsfetgf..alkedlkelinldesiae..qsnnfeLyF...eved 71 
                                       ++ l v+d+e++ +FY+d l  ++     G++  f+t +  al    ++l+  d+ ++       + L       e+
  gi|386001540|ref|YP_005919839.1|  14 IVTLGVEDLERAVSFYKDGLGWPLSSiSGGDYAIFKTSTgtALALFPRRLLAEDACVQDrgGFGGITLAQnvpSREE 90 
                                       566889*****************975277899999865522665444555555554443113334455441115689 PP

                                       HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEE CS
                      Glyoxalase_2  72 vdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEig 114
                                       vd +l++  +a+   ll++     Wg    +f+DpD+h  E++
  gi|386001540|ref|YP_005919839.1|  91 VDGALSQAVSAG-GTLLKRASDTDWGGYSGYFADPDGHPWEVA 132
                                       999999987777.689**********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 1058.59
//
Query:       gi|386001541|ref|YP_005919840.1|  [L=109]
Description: Mitomycin resistance protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-35  119.9   0.0    4.5e-35  119.7   0.0    1.0  1  Cdd1      Pathogenicity locus
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.24   11.5   0.0    1.5  2  TfoX_C    TfoX C-terminal domain
       0.15   12.7   0.0        0.2   12.3   0.0    1.2  1  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   7.5e-39   4.5e-35       2      86 .]       3      86 ..       2      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 7.5e-39
                              Cdd1  2 rkalkelqdiPniGkalaedlvelGirsveelkgedpeelyeklekltgarhDpCvldvfrsvvkfaegdeeakkWwsf 80
                                      r+++++l++iPn+G+++aedl+ +G++++++l g+dp+++ye+l+ +tg++hDpCv+dvf+s+v+f+eg e++++Ww +
  gi|386001541|ref|YP_005919840.1|  3 REKFTRLEEIPNVGPSIAEDLRLVGVSHPQDLIGRDPYQMYEELCLKTGEQHDPCVIDVFISAVRFMEG-EPQRPWWAY 80
                                      68899****************************************************************.********* PP

                              Cdd1 81 tderka 86
                                      t erk+
  gi|386001541|ref|YP_005919840.1| 81 TPERKE 86
                                      ****96 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     4e-05      0.24       3      31 ..       7      35 ..       5      56 .. 0.85
   2 ?   -2.4   0.0      0.91   5.5e+03      64      77 ..      75      88 ..      74      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                            TfoX_C  3 nrLkdLpNlglklerlLkkaGIktveeLr 31
                                      +rL+++pN g+ +++ L+ +G+   ++L 
  gi|386001541|ref|YP_005919840.1|  7 TRLEEIPNVGPSIAEDLRLVGVSHPQDLI 35
                                      69*********************999985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                            TfoX_C 64 vhwndlpeeekeeL 77
                                      ++w + + e+ke+L
  gi|386001541|ref|YP_005919840.1| 75 RPWWAYTPERKERL 88
                                      57888889999998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2       1      34 [.       6      39 ..       6      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                      -HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-H CS
                             HHH_5  1 feeLlsvsGiGpktAlallsaGiesvedlaaadv 34
                                      f  L +++ +Gp++A  l   G++ ++dl+  d+
  gi|386001541|ref|YP_005919840.1|  6 FTRLEEIPNVGPSIAEDLRLVGVSHPQDLIGRDP 39
                                      67899************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:01.56
# Mc/sec: 211.26
//
Query:       gi|386001542|ref|YP_005919841.1|  [L=216]
Description: DNA-(Apurinic or apyrimidinic site) lyase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.15   11.3   0.0    1.3  1  AGOG      N-glycosylase/DNA lyase


Domain annotation for each model (and alignments):
>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.6e-06      0.15     197     227 ..     179     207 ..     135     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-06
                                       HCCHCS.HHHHHHHHHHHHT--HHHHHHHHH CS
                              AGOG 197 kelvqeevieaWkevsreseiPplhlDsllW 227
                                       k+ ++  + +  +e s++++iP  hlD llW
  gi|386001542|ref|YP_005919841.1| 179 KRYLE--IERRMMEFSQKTGIPMGHLDLLLW 207
                                       44444..45556788**************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1494.59
//
Query:       gi|386001543|ref|YP_005919842.1|  [L=229]
Description: hypothetical protein Mhar_0847 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-15   54.9   0.0    1.3e-14   54.5   0.0    1.1  1  DUF4130   Domain of unknown function (DUF4130


Domain annotation for each model (and alignments):
>> DUF4130  Domain of unknown function (DUF4130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   7.1e-19   1.3e-14      18     122 ..      28     190 ..      17     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 7.1e-19
                           DUF4130  18 gkkvledladpdvlrleelarkvsreahrmkgfvRFreledgiyvakiePkhnvlellaehFadRfadekwlIldek 94 
                                        ++ +e  +dp+vlr++++a +v+ e  rm+gf+R   l d+++ ++i+P+h+v   ++++Fa+Rf+ +  ++ d +
  gi|386001543|ref|YP_005919842.1|  28 SPEEMEGSTDPEVLRIRRMALAVRGEVCRMRGFIRLAPLGDRVLWGRISPHHDVGFEVSDFFARRFPGKLIVLGDGR 104
                                       566678899******************************************************************** PP

                           DUF4130  95 rklalvyd..........................................................lseeedefeel 113
                                       r+   +y                                                           +++   +  +l
  gi|386001543|ref|YP_005919842.1| 105 RSWSSLYAgglllhqeggglaatlseisgimdllaqegeeegrqrseekggkdqaetkvepqhigaVERPGTAAADL 181
                                       *****************************************************9999999999998888899***** PP

                           DUF4130 114 Wktyfksia 122
                                       W  y++s+ 
  gi|386001543|ref|YP_005919842.1| 182 WTVYYQSLD 190
                                       *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1471.25
//
Query:       gi|386001544|ref|YP_005919843.1|  [L=403]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-10   41.3   0.0    3.1e-10   40.7   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    5.8e-08   32.9   0.0    1.6e-07   31.5   0.0    1.7  1  HHH_3        Helix-hairpin-helix motif
    1.1e-06   28.2   0.0      5e-06   26.1   0.0    2.2  1  HHH          Helix-hairpin-helix motif
    0.00027   21.5   0.0     0.0011   19.5   0.0    2.0  2  HHH_5        Helix-hairpin-helix domain
    0.00048   20.4   0.0     0.0007   19.9   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.29   11.3   0.0    1.6  1  HHH_2        Helix-hairpin-helix motif
        3.3    8.3   5.3       0.57   10.8   1.0    1.9  3  ShK          ShK domain-like


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.2e-13   3.1e-10       4     160 ..      84     247 ..      81     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.2e-13
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                       t++C+++C +C++ +t +  +r  s s+ee++++   l++e+++++++l++g  + +++ +   e++ +   + +r+
  gi|386001544|ref|YP_005919843.1|  84 TNACPHDCGYCPNAST-SAKKRIFSYSPEELARITLDLYQENRIEGLFLSSG--IGRDENETMEEMIEAV--RLLRT 155
                                       89*************9.*********************97777*******99..5544444444444443..45666 PP

                                       EEEECSSCHG.......HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...... CS
                                       xxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       Radical_SAM  81 tvetngtlpd.......eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...... 144
                                       +    g+++        +e+++   el  drvs++le ++  +  +l+  ++   ++l+  +++r++  ++      
  gi|386001544|ref|YP_005919843.1| 156 AHHFRGYVHLkilpgssKEHVRQAMELA-DRVSVNLEGPSAARMAELCPSKEYENDILARQRYIRDL-SRDlalpag 230
                                       666666666566667779**********.*************99999977788899***********.677799999 PP

                                       .EEEEEEEBTTTSHHHH CS
                                       .xxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 .vvdrivglpGendeel 160
                                        ++ ++vg  Ge+d+e+
  gi|386001544|ref|YP_005919843.1| 231 qTTQMVVGAAGETDREI 247
                                       9*************997 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   6.1e-11   1.6e-07       3      48 ..     332     376 ..     330     378 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.1e-11
                             HHH_3   3 avgvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlk 48 
                                       +++vd N As +eL ++pG+gpk+A++I+  R kn +++++ +L k
  gi|386001544|ref|YP_005919843.1| 332 EEPVDPNGASFAELIRVPGIGPKTARRILICR-KNSRIERMGDLAK 376
                                       579*****************************.8889999999976 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.9e-09     5e-06       8      28 ..     340     360 ..     339     362 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.9e-09
                                       SSHHHHHTSTT-SHHHHHHHH CS
                               HHH   8 asreeLlalPGVGpktAeaIl 28 
                                       as++eL  +PG+GpktA++Il
  gi|386001544|ref|YP_005919843.1| 340 ASFAELIRVPGIGPKTARRIL 360
                                       89******************8 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         7   1.8e+04      30      40 ..     106     116 ..     103     117 .. 0.70
   2 !   19.5   0.0   4.4e-07    0.0011       1      19 [.     342     360 ..     338     365 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7
                                       HHS-HHHHHTS CS
                             HHH_5  30 aaadveeLaki 40 
                                        + ++eeLa+i
  gi|386001544|ref|YP_005919843.1| 106 FSYSPEELARI 116
                                       56678888887 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.4e-07
                                       -HHHHTSTT--HHHHHHHH CS
                             HHH_5   1 feeLlsvsGiGpktAlall 19 
                                       f eL++v+GiGpktA+++l
  gi|386001544|ref|YP_005919843.1| 342 FAELIRVPGIGPKTARRIL 360
                                       4556666666666666654 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.7e-07    0.0007       8      61 ..      80     134 ..      69     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.7e-07
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeii.edlkkesiegltllGG 61 
                                        +l+++ C++ C +C n +t   k+   ++ e l++i  +  ++++iegl l+ G
  gi|386001544|ref|YP_005919843.1|  80 KTLYTNACPHDCGYCPNASTSAKKRIFSYSPEELARITlDLYQENRIEGLFLSSG 134
                                       3899*************************96666666505555688999999877 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.29      32      52 ..     340     360 ..     338     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                             HHH_2  32 asleeLlevddiGeeiAqsiv 52 
                                       as+ eL+ v++iG+++A+ i 
  gi|386001544|ref|YP_005919843.1| 340 ASFAELIRVPGIGPKTARRIL 360
                                       99****************996 PP

>> ShK  ShK domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.8   1.5e+04      15      22 ..      41      48 ..      39      51 .. 0.69
   2 ?   10.8   1.0   0.00022      0.57       8      38 .]      65      94 ..      61      94 .. 0.90
   3 ?   -2.9   0.1       4.2   1.1e+04      27      33 ..     198     204 ..     194     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.8
                               ShK 15 lgfCtnpt 22
                                      ++ Ct+++
  gi|386001544|ref|YP_005919843.1| 41 YDLCTSSA 48
                                      56799876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00022
                               ShK  8 dCaswaalgfCtnptyrdlmkeqCpktCgfC 38
                                       C s++  g C + + ++l++  Cp  Cg+C
  gi|386001544|ref|YP_005919843.1| 65 LCHSFTGSGRCVSLF-KTLYTNACPHDCGYC 94
                                      599999*****7765.*************** PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.2
                               ShK  27 mkeqCpk 33 
                                       m+e Cp+
  gi|386001544|ref|YP_005919843.1| 198 MAELCPS 204
                                       8999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2876.89
//
Query:       gi|386001545|ref|YP_005919844.1|  [L=836]
Description: subtilase family peptidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-38  130.7   0.0      2e-18   66.2   0.0    2.4  2  P_proprotein  Proprotein convertase P-domain
    4.2e-29  101.8   0.0    6.4e-29  101.1   0.0    1.2  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> P_proprotein  Proprotein convertase P-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   3.6e-21   3.2e-17       3      85 ..     618     703 ..     616     704 .. 0.91
   2 !   66.2   0.0   2.3e-22     2e-18       2      86 .]     743     830 ..     742     830 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 3.6e-21
                                       EEEEEEEEEESSGGGEEEEEE-TTS-EEEEE---TT---SS-EEEEEEE......ESTTTTS---EEEEEEEEESST CS
                      P_proprotein   3 hvqvsvnithtrrgdlritLvsPsGtrsvLlnrrgkdksrsgfldwtfm......sthlwgeraeGeWkLevkdsee 73 
                                       + +v+v+i+h+ +gdlr+tL++PsG+ +v+++r+g     s++ + tf       +  l g+ ++G+W+L v+d ++
  gi|386001545|ref|YP_005919844.1| 618 RARVTVDISHSFIGDLRLTLIAPSGKFVVIHERNGG---GSDDIRATFDpmttpaLASLAGQFVQGDWTLLVQDLAA 691
                                       678*********************************...77777777777778889999****************** PP

                                       T--EEEEEEEEE CS
                      P_proprotein  74 edtgtlkswkLr 85 
                                       +dtg+l++w+L 
  gi|386001545|ref|YP_005919844.1| 692 RDTGRLNRWELE 703
                                       **********97 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 2.3e-22
                                       EEEEEEEEEEESSGGGEEEEEE-TTS-EEEEE---TT---SS-EEEEEEE......ESTTTTS---EEEEEEEEESS CS
                      P_proprotein   2 ehvqvsvnithtrrgdlritLvsPsGtrsvLlnrrgkdksrsgfldwtfm......sthlwgeraeGeWkLevkdse 72 
                                        +++v+v+ith  +gdl++tL+sP+Gt + L+ r+g     +++  + ++      +++l+g++++G W+L+v d +
  gi|386001545|ref|YP_005919844.1| 743 RDLEVYVDITHGFIGDLEVTLISPAGTAVPLHLREGM---ATDNIIKSYTsattpdLQKLRGQQVRGAWRLKVADLA 816
                                       5789*********************************...77777777777888999******************** PP

                                       TT--EEEEEEEEEE CS
                      P_proprotein  73 eedtgtlkswkLrl 86 
                                       ++d+g+l++w+Lr+
  gi|386001545|ref|YP_005919844.1| 817 RSDVGKLNRWGLRI 830
                                       ************85 PP

>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   7.2e-33   6.4e-29       3     282 ..     211     511 ..     209     527 .. 0.73

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 7.2e-33
                                       T-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS.......HHHHHHHHHH-B. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                      Peptidase_S8   3 gvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsie...HGthvAGiaaana 76 
                                        v+v+v D+G+  +h d+     ++ k+      +g++++++ +   ++++     +  ++   HGt ++G++aa  
  gi|386001545|ref|YP_005919844.1| 211 SVVVGVTDDGCRLDHADFD----SPEKFAGWGYFRGTTLVKEINIGADPSE-----M-YTRgddHGTSCCGVIAAE- 276
                                       599**************88....5566654444444444444443333332.....2.222345************. PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH...HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHH...HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetg.teliraieeaaedkvdvinmslgestslpktgrsieal...ainr 149
                                       +++   +g apg+++l +k   +++g    + ++++ a+++ a  kvdv+++s+g s  l+    +++ +       
  gi|386001545|ref|YP_005919844.1| 277 ADSALTVGAAPGCRLLPIKWEVDDSGYLLISdDKVMTALSYLAD-KVDVLSNSWGSSPTLDFAPAVVRLIgdlSRAG 352
                                       9******************9877777776666888888888777.**********6555544444444335434444 PP

                                       HH.CCT-EEEEE--SS-....................T-HH.........EEE-TTCEECTTTSTTCEEEEEESTTS CS
                                       xxxxxxxxxxxxxxxxx....................xxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 150 avnkkgvlvviSaGNng....................ktgs.........slqagspvgtpstsknvitvgaytteg 197
                                       ++  +g+++v++aGN +                    ++gs             ++ vg p    +v+ v+a ++ +
  gi|386001545|ref|YP_005919844.1| 353 GRRGRGIVFVWAAGNANcpvnhtgsmevpftdgwvirPDGSplwvgvdtaRRFENQLVGIP----GVMIVAALSSMA 425
                                       55577************77776665555555555444333355333322223344444444....69********** PP

                                       SB-TT--B-TT.......-EEEE-S-..CCCCCCCCCHHHTTTHH........EEEE-SHHHCHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 198 kiapfSsrGpssdgklkpdivapGgn..ivstwsrqsnnsaglss........yqsmsGTSmAsPnaagaaAlllsa 264
                                       + + +S++G+ +      +i+ap +n  ++   + q+   +            ++ + GTS A+P++ag+aAl++sa
  gi|386001545|ref|YP_005919844.1| 426 QRSHYSNYGSGI------SITAPTSNlhSYYRLTLQGLGIT---TasgeripvTEEFGGTSSAAPLVAGIAALVISA 493
                                       **********88......8*******555555555554444...3556***************************** PP

                                       HTT--HHHHHHHHHCCS- CS
                                       xxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 265 lpkltpetvraallntAq 282
                                       +p+l++ +v ++l +tA+
  gi|386001545|ref|YP_005919844.1| 494 NPDLSALEVVSILKRTAS 511
                                       *****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (836 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 6009.73
//
Query:       gi|386001546|ref|YP_005919845.1|  [L=627]
Description: Acetyl-CoA hydrolase/N-acetyltransferase GNAT family fusion protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-53  180.3   0.0    3.2e-53  179.8   0.0    1.3  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    2.9e-31  109.0   0.0    5.4e-31  108.1   0.0    1.4  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    1.1e-10   41.8   0.1      2e-10   40.9   0.1    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.8e-09   37.0   0.0    8.1e-09   36.3   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    7.7e-06   26.1   0.0    1.3e-05   25.4   0.0    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.3e-05   23.8   0.0    6.2e-05   22.9   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.9e-05   23.0   0.1    0.00017   21.9   0.1    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00032   20.6   0.0    0.00072   19.5   0.0    1.5  1  FR47             FR47-like protein
     0.0017   17.8   0.0        1.7    8.0   0.0    2.5  2  CoA_trans        Coenzyme A transferase
  ------ inclusion threshold ------
       0.21   11.6   0.0       0.38   10.8   0.0    1.3  1  DUF480           Protein of unknown function, DUF480


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   1.8e-56   3.2e-53       1     154 []     282     435 ..     282     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 1.8e-56
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHST CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalsk 77 
                                       G ++ yd ld+np++ +rp++ + + +via  +++++in+ale+dltGq+++eslggr++sGvG + +F+rgaal++
  gi|386001546|ref|YP_005919845.1| 282 GRRETYDLLDKNPAVLFRPIDRTASLAVIASMRNLTAINTALEIDLTGQATAESLGGRFYSGVGAEAEFMRGAALAP 358
                                       8899************************************************************************* PP

                                       T-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                   AcetylCoA_hyd_C  78 ggksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                       gg+si+alpS +++g+ SrIvp+l++ga  t +r dv+yvvTEyGia+Lrg+s+rera+ li i+hp fr++L+e+a
  gi|386001546|ref|YP_005919845.1| 359 GGRSILALPSLSPDGRASRIVPRLAPGASATFHRGDVQYVVTEYGIANLRGRSVRERAMSLIGISHPMFRPRLMEAA 435
                                       **************************************************************************986 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0     3e-34   5.4e-31       9     191 ..      11     191 ..       7     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 3e-34
                   AcetylCoA_hydro   9 lkepeeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekdavlyr 85 
                                       +  pe+++++ +++  +  + +++vgta+++p++l++   +   +    l+dl+ + +  +g  +++ ee    + r
  gi|386001546|ref|YP_005919845.1|  11 RRFPEKFVPMEEIFGVLRSGARIFVGTACGEPQALVRGLLDHLRASSTELFDLEILSIYGLG-SAPYAEEGLKESLR 86 
                                       44599*********************************************************.************** PP

                   AcetylCoA_hydro  86 papkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEvaelvvi 162
                                        +++ +ge  r  +n+g +++++++ls vp+++ ++ +piD+al++++ +d+ G + lG++v+a+ +++E  ++v +
  gi|386001546|ref|YP_005919845.1|  87 INSFAIGEAARDSVNDGSADYTPVFLSAVPDLIRQEVIPIDLALVQTSLPDKAGNVSLGISVDAVLAAVEGSKIVAA 163
                                       ***************************************************************************** PP

                   AcetylCoA_hydro 163 vvkknpPrvngydelialdkvdyivvdpe 191
                                       + +  +P+v g d++  l  +dy+vv++e
  gi|386001546|ref|YP_005919845.1| 164 QANPRMPYVLG-DGIVSLRDLDYVVVHDE 191
                                       ***********.***************98 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   1.1e-13     2e-10      41     117 .]     530     605 ..     480     605 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.1e-13
                                       T..TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHT CS
                    Acetyltransf_1  41 d..geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYekl 115
                                       +  + +iG  +++       g+ +   ++V+ +y+++G+G++L ++l ++a+++g+    ++v edn +a +l +k+
  gi|386001546|ref|YP_005919845.1| 530 GerEVVIGIGQYSRGGR---GELAELAVVVRDDYQRRGVGTLLHTYLTDIAKRRGLVGFTAEVLEDNLPALKLIKKM 603
                                       23355999999999988...6666669*****************************66677*************88* PP

                                       TE CS
                    Acetyltransf_1 116 GF 117
                                       GF
  gi|386001546|ref|YP_005919845.1| 604 GF 605
                                       *9 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   4.5e-12   8.1e-09       3     138 .]     469     606 ..     468     606 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.5e-12
                    Acetyltransf_3   3 lLrplteeDlealf.el...rsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtg.v.iGsvglr 72 
                                        Lrp++ +D e+l+ e+   +sd++  +r+   ++ +e+ +++++++ a ++ ++ + +a+ l++++ v iG+  + 
  gi|386001546|ref|YP_005919845.1| 469 FLRPVKISD-EPLVkEFfysLSDKTlYRRFA--SARREMHHSRIQDFVAVDYSRDMVILALLLRGEReVvIGIGQYS 542
                                       79*******.555425434478988555664..5688*********9887777777778887777765559999887 PP

                    Acetyltransf_3  73 dleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +  +  e ael  +++++++++G++t     l+++a ++ gl  + a++ ++N    ++++k+Gfe
  gi|386001546|ref|YP_005919845.1| 543 RGGRG-ELAELAVVVRDDYQRRGVGTLLHTYLTDIA-KRRGLVGFTAEVLEDNLPALKLIKKMGFE 606
                                       54444.45****************************.7777************************7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   7.4e-09   1.3e-05      58     138 ..     533     609 ..     513     616 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.4e-09
                    Acetyltransf_4  58 drivGyaylgqfkkr.akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalG 133
                                       + ++G+ +++    r ++ + ael v +   d + +g+g  l+++l +++k+ ++  ++ae+  +n ++ ++ k++G
  gi|386001546|ref|YP_005919845.1| 533 EVVIGIGQYS----RgGRGELAELAVVVR-DDYQRRGVGTLLHTYLTDIAKRRGLVGFTAEVLEDNLPALKLIKKMG 604
                                       5566777776....558999********6.79********************************************* PP

                    Acetyltransf_4 134 Felvg 138
                                       Fe v+
  gi|386001546|ref|YP_005919845.1| 605 FERVA 609
                                       *9875 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.5e-08   6.2e-05      39     112 ..     532     611 ..     499     620 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.5e-08
                   Acetyltransf_10  39 ggkivGvielrdgs..hisll..fVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkav 109
                                        + ++G++++++g+  +++ l  +V+++y+++G+g+ L  ++ + a+++g+   + +v +++  a ++ +k+GF++v
  gi|386001546|ref|YP_005919845.1| 532 REVVIGIGQYSRGGrgELAELavVVRDDYQRRGVGTLLHTYLTDIAKRRGLVGfTAEVLEDNlPALKLIKKMGFERV 608
                                       4556688888555557777765689*********************9998888**********************99 PP

                   Acetyltransf_10 110 gee 112
                                          
  gi|386001546|ref|YP_005919845.1| 609 AVD 611
                                       655 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   9.6e-08   0.00017      14      76 .]     535     607 ..     512     607 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.6e-08
                                       EEEEEEEEEES.TCTEE..EEE-GGGTTSSHHHHHHHH....TT.SEEEEE.EEEE.THH.HHHHHHHHTTEEE CS
                    Acetyltransf_7  14 ivGfialslld.aeitr..laVdpeyrgkGiGraLlea....ae.kgiile.qlel.nae.kaikfYeklGFee 76 
                                       ++G   +s+ + +e+ +  ++V+ +y+++G+G+ L ++    a+ +g+    ++e+ +++ +a+k+ +k+GFe+
  gi|386001546|ref|YP_005919845.1| 535 VIGIGQYSRGGrGELAElaVVVRDDYQRRGVGTLLHTYltdiAKrRGLV-GfTAEVlEDNlPALKLIKKMGFER 607
                                       356555455446444445699**************99766542256632.232333333359**********95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     4e-07   0.00072      26      79 ..     553     607 ..     541     612 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4e-07
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfek 79 
                                       a+ v+++ +rrG g++l   l+    +rg    ++ v ++N p+ +l +k+Gfe 
  gi|386001546|ref|YP_005919845.1| 553 AVVVRDDYQRRGVGTLLHTYLTDIAKRRGLVgFTAEVLEDNLPALKLIKKMGFER 607
                                       789***************99986555588652679999***************97 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0018       3.3      12      39 ..      27      52 ..      19      80 .. 0.88
   2 !    8.0   0.0   0.00093       1.7       3      67 ..     207     265 ..     205     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                                      --TTEEEEE-SBTTBTHHHHHHHHHHHH CS
                         CoA_trans 12 ikdGmtvavGGFgligiPealiaalars 39
                                      +++G+ ++vG  +++g+P+al++ l++ 
  gi|386001546|ref|YP_005919845.1| 27 LRSGARIFVG--TACGEPQALVRGLLDH 52
                                      89********..***********99986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00093
                                       HHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEE CS
                         CoA_trans   3 taaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagvlglgplllngsvkk 67 
                                       ++ e va+ ++dG+t+ vG     g+P  ++ + +    k++  ++s+  + g+  ll++g +++
  gi|386001546|ref|YP_005919845.1| 207 RIGENVARIVEDGATLQVG---FGGLP-DAVLSHLSE--KRHLGLHSDLFTDGAAELLRSGAIDN 265
                                       677899*************...5669*.777777777..89999999998899999999988876 PP

>> DUF480  Protein of unknown function, DUF480
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.38      42     103 ..     472     531 ..     470     535 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                       S-----HHHHHHHHHHHHHTTSEEEE..--SS--EEEE-HHHHHT--HHHHHHHHHHHHH-S CS
                            DUF480  42 PvmelsesevqealdeLkkkklvseaseagsRvekyehrleealklseaelavlalllLRGp 103
                                       Pv   +e  v+e   +L++k+l ++   a++R e ++ r+++ + ++ ++ +v+  llLRG 
  gi|386001546|ref|YP_005919845.1| 472 PVKISDEPLVKEFFYSLSDKTLYRRF--ASARREMHHSRIQDFVAVDYSRDMVILALLLRGE 531
                                       7777889999***************9..99*******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 4686.13
//
Query:       gi|386001547|ref|YP_005919846.1|  [L=374]
Description: Histone deacetylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-78  263.2   0.0    6.1e-78  262.4   0.0    1.4  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.4   0.0   3.4e-82   6.1e-78       1     306 [.      19     307 ..      19     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 262.4 bits;  conditional E-value: 3.4e-82
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hp +p R+s + ++l+e +gl+de +++ +p++at+eel  vH+ eYle++++ + +l                 l 
  gi|386001547|ref|YP_005919846.1|  19 HPLSPIRVS-LAHKLIEDSGLIDERTRVLRPEPATEEELSLVHTLEYLEAVREEAPDLAFG--------------LG 80 
                                       788999999.777777777********************************9755554333..............46 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrv 154
                                       +ddtpv+p++++a+   +g+++ea++++l++  ++a     ++ HHa +++a GFC++N++a+ai +l++  +++rv
  gi|386001547|ref|YP_005919846.1|  81 SDDTPVFPGIFEASCSMAGGSIEAAKKILEE--DCAAFNLAGGLHHAFPTQAAGFCVFNDAALAISVLKR--RFSRV 153
                                       899**************************99..88888889***************************99..688** PP

                                       EEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 155 ailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                       +++D+D+HhG+G++++fy+dp+vlt+SiH++++ ++Pgtg +++ g+g g g+++nvp++ + gd+++l +fee+  
  gi|386001547|ref|YP_005919846.1| 154 LYIDIDAHHGDGVQQIFYEDPEVLTFSIHESGKYLFPGTGFVDEAGAGPGLGYSVNVPMPMNAGDRDFLLAFEEVGP 230
                                       ***************************************************************************** PP

                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlealaravtavlsa 306
                                       +++  f+P++++ ++G+D++ +dpl +ln++ +gy  +++++++l +++ k ++++l++GGYnl+ +++a+t++l++
  gi|386001547|ref|YP_005919846.1| 231 KLFDWFRPEAVVAQLGVDTHYSDPLTSLNVTLRGYVAAVRRIVDLTNRYaKgRLLALGGGGYNLAVVPTAWTSALAI 307
                                       **************************************************99********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2570.22
//
Query:       gi|386001548|ref|YP_005919847.1|  [L=192]
Description: hypothetical protein Mhar_0852 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1397.81
//
Query:       gi|386001549|ref|YP_005919848.1|  [L=113]
Description: Nucleic acid binding, OB-fold, tRNA/helicase-type [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.007   16.3   0.0     0.0099   15.9   0.0    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.5e-07    0.0099       6      71 ..      43     105 ..      36     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-07
                                       EEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEE CS
                   tRNA_anti-codon   6 rvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkve 71 
                                          s+ +r +g+++ i l      i v+ ++ +a+ la ++ +Gd +r++G++  ++g+  e+ v+
  gi|386001549|ref|YP_005919848.1|  43 TAASV-QRTEGGHLIIRLYSSQMPIFVSQDS-GADLLAGRIARGDRIRAKGEIAWYEGR-REIAVQ 105
                                       44445.4889999999998888888888888.*************************99.888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 871.97
//
Query:       gi|386001550|ref|YP_005919849.1|  [L=58]
Description: F420H2 dehydrogenase subunit O [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-15   55.8   0.6    5.2e-15   55.7   0.6    1.0  1  FpoO      F420H2 dehydrogenase subunit FpoO


Domain annotation for each model (and alignments):
>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.6   2.9e-19   5.2e-15       1      55 [.       1      53 [.       1      58 [] 0.88

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.9e-19
                              FpoO  1 madcdlcgvsiPtviPvrvfkPrlelsyPeGvwkGlcekclkaakktydelskee 55
                                      madc+lcg + Pt++Pv+v    l  + PeG +kGlc++cl++ + +y+++  e+
  gi|386001550|ref|YP_005919849.1|  1 MADCELCGLAKPTLVPVKVQVHTL--ANPEGAYKGLCQDCLASCEAAYQQHFGEK 53
                                      9******************98776..67********************9986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 453.17
//
Query:       gi|386001551|ref|YP_005919850.1|  [L=257]
Description: hypothetical protein Mhar_0855 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-74  249.7   0.0    2.7e-74  249.5   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   0.0   1.5e-78   2.7e-74       1     234 [.      10     248 ..      10     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 1.5e-78
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       itLl+DFG  + y++ mkg+ils+  da +vDi+Hd+pp+dvr++af+L+aa+ +fpkgtvhlavVDpgvgt+r  +
  gi|386001551|ref|YP_005919850.1|  10 ITLLSDFG--SLYPAEMKGAILSRIGDAILVDIAHDVPPQDVRAGAFALMAAAGHFPKGTVHLAVVDPGVGTDRLGI 84 
                                       9*******..******************************************************************* PP

                                       EEEETTSEEEEESSSTTHHHH...SEEEEEEGSSCC...--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS-S CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal...lleeaveieeee...ssatFhgrDvFapvaarlaagvsleelgeeldpeelvr 148
                                       vv ++g++fvgPDNGll +a+   +  +a+ i  +    ++ tF grDvFap+aa la+g ++ ++g+++dp+ l  
  gi|386001551|ref|YP_005919850.1|  85 VVASGGHLFVGPDNGLLIPAAksaGEPAAWMIGPSFfegAAPTFAGRDVFAPAAAVLASGGDPGSFGPAVDPAGLDF 161
                                       *********************766338899998444888779******************************76633 PP

                                       SS.E..CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE..EEEEESSGGGSTTTSEEEEE-TTSEEEEEETTC CS
                   SAM_adeno_trans 149 le.e..derlegevlyvDrFGNvitniskelleelekerkva..klkkvetyaevaegellalvnssglleiavnkg 220
                                        + +  de +e+ev+yvD FGNv++n  +   +++e        +l++++tyae+ + e+l++++s+g+ eiavn g
  gi|386001551|ref|YP_005919850.1| 162 GRaRilDEGIEAEVIYVDGFGNVVLNSAAIPWDRVEL----MgrRLRRARTYAEAGADEPLITLGSHGFAEIAVNGG 234
                                       224356899*****************99444444433....13366778**************************** PP

                                       -HHHHHT--TT-EE CS
                   SAM_adeno_trans 221 saaellglkvgdev 234
                                       sa++l+gl++gd++
  gi|386001551|ref|YP_005919850.1| 235 SAKDLFGLAPGDRI 248
                                       ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1973.15
//
Query:       gi|386001552|ref|YP_005919851.1|  [L=319]
Description: 5,10-methylenetetrahydromethanopterin reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-61  207.3   3.3    4.5e-61  207.0   3.3    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.0   3.3   2.5e-65   4.5e-61      28     314 .]      18     296 ..       9     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 2.5e-65
                    Bac_luciferase  28 laraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglg 104
                                       +a++aE++Gfd++w+++h+++    +d +++la la aT+r+rlgt+vt++ytr+ av+A ++a+++++sgGR++lg
  gi|386001552|ref|YP_005919851.1|  18 MAKLAEDAGFDTIWITDHYNN----RDVYSTLAILALATSRVRLGTGVTNPYTRNVAVTASSIASINEISGGRAILG 90 
                                       79******************9....**************************************************** PP

                    Bac_luciferase 105 lgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglel 181
                                       +g g  a+  +++G+ +++++   r+ v +lr+l+++++v+ +G      ga+l      + iP+y++a +p++le+
  gi|386001552|ref|YP_005919851.1|  91 IGPGDKATF-DAMGIAWEKPLSAVRDSVAALRELLAKKRVEGHGMA----GAQLAFSA-GK-IPIYIGAQGPKMLEM 160
                                       ****99888.999**********************99999999977....55555544.44.9************** PP

                    Bac_luciferase 182 aarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagldfyalds 255
                                       a+ +adg+l++ ++p++ + +++ +r+ga++agrdp ++++ + +++++++++++A  ea    a+i  +      s
  gi|386001552|ref|YP_005919851.1| 161 AGMIADGVLVNASHPDDFKYAVPLVRQGAEKAGRDPKEVEISAYTSFSADKNPDKAANEAkivVAFIVAGSPETVLS 237
                                       ************************************************************99989998888999999 PP

                    Bac_luciferase 256 egagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                       ++   ++eaa+ +++ +++++ +a +av+  +++ + + Gtp ++++r++++ ++gv++
  gi|386001552|ref|YP_005919851.1| 238 RHGIEAEEAAAVSRAIAKGDFGSALAAVTSTMIDVFSVSGTPVECRARVDELLATGVTQ 296
                                       9999999999******************************************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2279.71
//
Query:       gi|386001553|ref|YP_005919852.1|  [L=171]
Description: nicotinamide-nucleotide adenylyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-15   56.3   0.0    6.7e-15   55.5   0.0    1.4  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.01   15.7   0.1      0.017   15.0   0.1    1.3  1  FAD_syn          FAD synthetase
      0.067   12.4   0.0        6.5    5.8   0.0    2.0  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   1.1e-18   6.7e-15       1     142 [.       5     132 ..       5     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.1e-18
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       l+ G+F+p HlGH ++l+++ ++++e ++vg+ s++ ++ + +++++a eR+ m+  a +  +    + +++ + v 
  gi|386001553|ref|YP_005919852.1|   5 LYIGRFQPYHLGHQAVLQKIVEEVDE-VVVGLGSAQASHTT-ENPFTAGERISMIWPALRGLD----ATCYVIPLVD 75 
                                       689***********************.************99.****************44444....5888888666 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                        ++++   ++v+  ++++      +++ +++n++lvv+ + e   +v  ++++r++ +S+t ir+
  gi|386001553|ref|YP_005919852.1|  76 MERNA---VWVAHVEAMTP-----KFDVVYSNNPLVVQLFVEAGMEVRRPPMYRREVYSGTAIRR 132
                                       66655...78888888877.....89**************************************7 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.8e-06     0.017      11      34 ..       6      29 ..       2      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-06
                           FAD_syn 11 tlGnFDGvHlGHqallkkaveaak 34
                                       +G F   HlGHqa+l+k+ve+ +
  gi|386001553|ref|YP_005919852.1|  6 YIGRFQPYHLGHQAVLQKIVEEVD 29
                                      69*****************99765 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0011       6.5      10      30 ..      10      30 ..       6      37 .. 0.83
   2 ?    4.6   0.0    0.0027        16     201     236 ..     122     155 ..     111     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0011
                       HIGH_NTase1 10 YNPfHnGHlyhlekakeltga 30
                                      + P+H GH+  l+k+ e++++
  gi|386001553|ref|YP_005919852.1| 10 FQPYHLGHQAVLQKIVEEVDE 30
                                      78*************998654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0027
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilke 236
                                       +e+ S taiR+++      e  ++lvP s++++++e
  gi|386001553|ref|YP_005919852.1| 122 REVYSGTAIRRMILAG--DEGWRRLVPPSVASAIEE 155
                                       4789*********666..478********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1390.57
//
Query:       gi|386001554|ref|YP_005919853.1|  [L=463]
Description: putative membrane protein, containing TPR repeats [Methanosaeta harundinacea 6Ac]
Scores for 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-121  390.8  31.6    3.7e-11   42.4   0.2   11.1 11  TPR_1          Tetratricopeptide repeat
    1.3e-95  306.0  38.9    8.3e-09   34.9   0.1   11.2 11  TPR_2          Tetratricopeptide repeat
      1e-92  303.5  49.2      3e-10   39.6   0.1   12.0 12  TPR_11         TPR repeat
    8.3e-85  272.1  22.3    6.6e-08   32.2   0.2   11.1 11  TPR_8          Tetratricopeptide repeat
      3e-76  246.5  30.4    6.7e-07   29.3   0.0   11.7 11  TPR_17         Tetratricopeptide repeat
      2e-71  236.4  60.0    2.1e-11   44.2   1.0    8.2  9  TPR_16         Tetratricopeptide repeat
    4.6e-61  203.0  55.1    6.2e-11   42.4   2.5    8.6  8  TPR_12         Tetratricopeptide repeat
    3.2e-51  167.6  24.5    1.5e-05   24.7   0.1   11.1 11  TPR_7          Tetratricopeptide repeat
      6e-48  157.4  36.9    0.00024   21.7   0.2   11.2 11  TPR_14         Tetratricopeptide repeat
    1.1e-36  125.1  24.9    5.3e-08   33.3   1.7    6.8  7  TPR_19         Tetratricopeptide repeat
    3.3e-35  120.1  27.8    1.4e-08   34.8   0.9    7.2  7  TPR_9          Tetratricopeptide repeat
    1.8e-31  107.1  45.3    0.00027   20.7   0.2   11.2 11  TPR_10         Tetratricopeptide repeat
    7.6e-25   85.9  22.0      0.031   14.9   0.1   11.2 11  TPR_6          Tetratricopeptide repeat
    2.1e-22   79.7   5.4      0.046   13.8   0.1    9.7  9  DUF3856        Domain of Unknown Function (DUF3856)
    2.8e-19   67.7  24.5       0.32   11.7   0.3   10.6 10  TPR_4          Tetratricopeptide repeat
    7.3e-18   65.4  23.3    0.00032   21.2   0.3    6.0  6  BTAD           Bacterial transcriptional activator domain
    7.5e-10   39.1  11.6       0.32   11.3   0.0    8.3  8  TPR_5          Tetratrico peptide repeat
    8.6e-10   38.5  22.3        2.1    8.5   0.0   10.1 11  Fis1_TPR_C     Fis1 C-terminal tetratricopeptide repeat
      1e-09   38.3  27.6        1.8    8.7   0.2   10.2 11  MIT            MIT (microtubule interacting and transport) do
    1.8e-08   33.8   0.3       0.27   10.1   0.0    5.3  6  NARP1          NMDA receptor-regulated protein 1
    2.9e-08   33.3  12.5       0.07   12.3   0.0    5.4  5  TPR_15         Tetratricopeptide repeat
    2.9e-08   33.8  11.4      0.038   14.2   0.0    4.9  4  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
    1.1e-07   31.6   0.3       0.46    9.9   0.0    4.1  4  Coatomer_E     Coatomer epsilon subunit
      5e-07   29.2   3.4        1.8    7.7   0.4    6.1  7  FAT            FAT domain
    3.2e-05   24.2   2.8         14    6.2   0.1    6.3  7  DUF2799        Protein of unknown function (DUF2799)
    0.00047   19.8   3.6        9.3    6.1   0.0    6.2  6  PPTA           Protein prenyltransferase alpha subunit repeat
     0.0009   19.0   3.5         16    5.2   0.1    5.8  7  RPN7           26S proteasome subunit RPN7
     0.0018   18.4  11.2        2.1    8.6   0.1    7.1  7  NRBF2_MIT      MIT domain of nuclear receptor-binding factor 
     0.0025   18.1   3.0         32    4.9   0.1    4.9  4  TPR_20         Tetratricopeptide repeat
      0.003   17.1   3.0        1.5    8.2   0.0    3.7  3  EST1_DNA_bind  Est1 DNA/RNA binding domain
     0.0049   17.0   6.8         56    4.3   0.0    7.4  7  PPR            PPR repeat
     0.0084   16.4   0.0         12    6.2   0.0    5.2  6  YnfE           Uncharacterized YnfE-like
     0.0087   15.9   9.2         14    5.5   0.1    6.8  8  DUF5113        Domain of unknown function (DUF5113)
  ------ inclusion threshold ------
      0.021   15.5   3.0        3.6    8.4   0.2    4.4  2  Sel1           Sel1 repeat
      0.023   14.5   7.4         36    4.1   0.0    6.5  7  PvlArgDC       Pyruvoyl-dependent arginine decarboxylase (Pvl
      0.048   13.4  14.1         16    5.2   0.1    6.6  6  TPR_21         Tetratricopeptide repeat-like domain
      0.052   13.6   0.1         93    3.1   0.0    4.3  4  DUF627         Protein of unknown function (DUF627)
       0.06   13.0   0.0        8.2    6.1   0.0    4.0  4  APP_E2         E2 domain of amyloid precursor protein
       0.21   11.5  13.1         39    4.1   3.2    5.8  7  Wzy_C_2        Virulence factor membrane-bound polymerase, C-
       0.28   11.2   7.6         41    4.3   0.0    6.2  5  DUF3775        Protein of unknown function (DUF3775)
        1.9    8.3  10.8         46    3.8   0.1    6.2  6  Sda            Sporulation inhibitor A
        5.1    5.4   8.1         39    2.4   0.2    5.3  7  SMG1           Serine/threonine-protein kinase smg-1


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.2   8.6e-14   3.7e-11       2      34 .]      33      65 ..      32      65 .. 0.96
   2 !   39.8   0.5   5.5e-13   2.4e-10       1      34 []      66      99 ..      66      99 .. 0.97
   3 !   36.2   0.0   7.4e-12   3.2e-09       1      33 [.     100     132 ..     100     133 .. 0.95
   4 !   34.8   0.0   2.1e-11   9.1e-09       1      33 [.     134     166 ..     134     167 .. 0.96
   5 !   28.3   0.1   2.4e-09     1e-06       2      32 ..     169     199 ..     169     201 .. 0.98
   6 !   40.4   0.0   3.5e-13   1.5e-10       1      34 []     202     235 ..     202     235 .. 0.96
   7 !   30.9   0.0   3.7e-10   1.6e-07       3      34 .]     238     269 ..     236     269 .. 0.96
   8 !   33.4   0.1   5.6e-11   2.4e-08       2      34 .]     271     303 ..     270     303 .. 0.95
   9 !   39.6   0.2   6.5e-13   2.8e-10       1      33 [.     304     336 ..     304     337 .. 0.96
  10 !   41.6   0.0   1.5e-13   6.6e-11       2      33 ..     339     370 ..     338     371 .. 0.96
  11 !   38.7   0.1   1.2e-12   5.3e-10       2      30 ..     373     401 ..     372     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 8.6e-14
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                       a+yn+G+a+ +lg+y+eA++ y+ ALel+P++
  gi|386001554|ref|YP_005919853.1| 33 LAWYNKGVALSELGRYEEAVASYDNALELDPEY 65
                                      69*****************************86 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 5.5e-13
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a a++n+G a+  lg+ +eAl++y++ Le++P++
  gi|386001554|ref|YP_005919853.1| 66 ALAWNNKGIALSALGRNEEALACYNRSLEIDPDY 99
                                      68******************************97 PP

  == domain 3  score: 36.2 bits;  conditional E-value: 7.4e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a++n+G+++  lg+ deAle y++ALe++P 
  gi|386001554|ref|YP_005919853.1| 100 APAWNNRGVVLEALGRGDEALESYDRALEVDPA 132
                                       68******************************5 PP

  == domain 4  score: 34.8 bits;  conditional E-value: 2.1e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a+ n G ++++ g+y+  +e+ye+ALe++P 
  gi|386001554|ref|YP_005919853.1| 134 ALAWSNQGGVFYSRGDYNRSIECYERALEIDPR 166
                                       68******************************6 PP

  == domain 5  score: 28.3 bits;  conditional E-value: 2.4e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a++nlG  +f  g+y+  +e y++AL+++P
  gi|386001554|ref|YP_005919853.1| 169 EAWNNLGRSLFAAGEYERSIEGYDEALKIDP 199
                                       69****************************9 PP

  == domain 6  score: 40.4 bits;  conditional E-value: 3.5e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a++n+G a+  lg+++eAl++ye+AL+++P++
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNKGIALGTLGRHQEALDCYEEALKIEPSH 235
                                       679*****************************86 PP

  == domain 7  score: 30.9 bits;  conditional E-value: 3.7e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       alyn+G a+  lg+ +eA+e+y+ +L+++P++
  gi|386001554|ref|YP_005919853.1| 238 ALYNKGIALGLLGRQEEAVECYDAVLKVDPSY 269
                                       9*****************************97 PP

  == domain 8  score: 33.4 bits;  conditional E-value: 5.6e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+yn+G+a+  lg+ ++A + y++AL+l+P +
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASYDEALKLDPGY 303
                                       69*****************************76 PP

  == domain 9  score: 39.6 bits;  conditional E-value: 6.5e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a++n+G a+ +lg+ +eAl+ y++ALe++P 
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEIDPA 336
                                       79******************************5 PP

  == domain 10  score: 41.6 bits;  conditional E-value: 1.5e-13
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+yn G+a+  lg+y+eA+  y++ALel+P+
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALELDPE 370
                                       79*****************************7 PP

  == domain 11  score: 38.7 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                       +a++n+G a+  lg+++eA+e+ye+ALe+
  gi|386001554|ref|YP_005919853.1| 373 EAWNNKGIALSALGRHQEAIECYERALEV 401
                                       8**************************95 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   2.2e-11   9.5e-09       2      34 .]      33      65 ..      32      65 .. 0.95
   2 !   30.9   0.4   3.8e-10   1.6e-07       1      34 []      66      99 ..      66      99 .. 0.96
   3 !   28.2   0.0   2.7e-09   1.2e-06       1      33 [.     100     132 ..     100     133 .. 0.95
   4 !   29.4   0.0   1.1e-09   4.6e-07       1      33 [.     134     166 ..     134     167 .. 0.96
   5 !   28.6   0.2     2e-09   8.7e-07       2      32 ..     169     199 ..     168     201 .. 0.96
   6 !   30.5   0.0     5e-10   2.1e-07       1      34 []     202     235 ..     202     235 .. 0.95
   7 !   22.4   0.0   1.9e-07   8.1e-05       3      33 ..     238     268 ..     236     269 .. 0.95
   8 !   28.5   0.2   2.1e-09     9e-07       2      33 ..     271     302 ..     270     303 .. 0.95
   9 !   30.2   0.3     6e-10   2.6e-07       1      33 [.     304     336 ..     304     337 .. 0.96
  10 !   34.9   0.1   1.9e-11   8.3e-09       2      33 ..     339     370 ..     338     371 .. 0.96
  11 !   29.6   0.2   9.8e-10   4.2e-07       2      29 ..     373     400 ..     372     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.2e-11
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                       a+yn G a+ +lg+yeeA++ ++ AleldP++
  gi|386001554|ref|YP_005919853.1| 33 LAWYNKGVALSELGRYEEAVASYDNALELDPEY 65
                                      79*****************************85 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 3.8e-10
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a a++n G a+ +lg+ eeAl++++++le+dP++
  gi|386001554|ref|YP_005919853.1| 66 ALAWNNKGIALSALGRNEEALACYNRSLEIDPDY 99
                                      689*****************************96 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 2.7e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++n+G ++++lg+ +eAle +++Ale dP 
  gi|386001554|ref|YP_005919853.1| 100 APAWNNRGVVLEALGRGDEALESYDRALEVDPA 132
                                       569****************************96 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 1.1e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+ n+G + y +gdy++ +e++e+Ale+dP+
  gi|386001554|ref|YP_005919853.1| 134 ALAWSNQGGVFYSRGDYNRSIECYERALEIDPR 166
                                       689*****************************7 PP

  == domain 5  score: 28.6 bits;  conditional E-value: 2e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea++nlG++++++g+ye+ +e +++Al++dP
  gi|386001554|ref|YP_005919853.1| 169 EAWNNLGRSLFAAGEYERSIEGYDEALKIDP 199
                                       89****************************9 PP

  == domain 6  score: 30.5 bits;  conditional E-value: 5e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a++n G a+  lg+++eAl+++e+Al+++P +
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNKGIALGTLGRHQEALDCYEEALKIEPSH 235
                                       679*****************************86 PP

  == domain 7  score: 22.4 bits;  conditional E-value: 1.9e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       alyn G a+  lg+ eeA+e+++++l+ dP 
  gi|386001554|ref|YP_005919853.1| 238 ALYNKGIALGLLGRQEEAVECYDAVLKVDPS 268
                                       89****************************7 PP

  == domain 8  score: 28.5 bits;  conditional E-value: 2.1e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        a+yn+G a+  lg+ e+A++ +++Al+ldP+
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASYDEALKLDPG 302
                                       59*****************************7 PP

  == domain 9  score: 30.2 bits;  conditional E-value: 6e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a++n+G a+  lg+ eeAl+ +++Ale+dP 
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEIDPA 336
                                       789*****************************6 PP

  == domain 10  score: 34.9 bits;  conditional E-value: 1.9e-11
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a+yn+G a  +lg+y+eA+  +++AleldP+
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALELDPE 370
                                       69*****************************7 PP

  == domain 11  score: 29.6 bits;  conditional E-value: 9.8e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                       ea++n G a+ +lg+++eA+e++e+Ale
  gi|386001554|ref|YP_005919853.1| 373 EAWNNKGIALSALGRHQEAIECYERALE 400
                                       8**************************8 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.041        17      24      42 .]      28      46 ..      27      46 .. 0.90
   2 !   39.4   1.9   8.4e-13   3.6e-10       6      42 .]      44      80 ..      41      80 .. 0.94
   3 !   39.6   0.1   6.9e-13     3e-10       6      42 .]      78     114 ..      75     114 .. 0.95
   4 !   24.8   0.6     3e-08   1.3e-05       7      39 ..     113     145 ..     112     145 .. 0.92
   5 !   38.5   0.0   1.6e-12   6.8e-10       3      38 ..     143     178 ..     141     181 .. 0.92
   6 !   34.4   0.3   2.9e-11   1.2e-08       1      42 []     175     216 ..     175     216 .. 0.96
   7 !   25.2   0.0   2.3e-08   9.7e-06       7      42 .]     215     250 ..     214     250 .. 0.95
   8 !   35.0   0.0     2e-11   8.5e-09       7      42 .]     249     284 ..     248     284 .. 0.95
   9 !   31.8   1.1     2e-10   8.5e-08       7      42 .]     283     318 ..     281     318 .. 0.95
  10 !   36.5   0.8   6.7e-12   2.9e-09       6      42 .]     316     352 ..     313     352 .. 0.95
  11 !   33.4   0.1   6.3e-11   2.7e-08       3      42 .]     347     386 ..     345     386 .. 0.93
  12 !   13.1   0.1   0.00013     0.057       6      22 ..     384     400 ..     382     401 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.041
                            TPR_11 24 dPdnaeayynLGlayykqG 42
                                      +P ++ a+yn G+a+ ++G
  gi|386001554|ref|YP_005919853.1| 28 NPLYPLAWYNKGVALSELG 46
                                      5779**********99988 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 8.4e-13
                            TPR_11  6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      e+G+yeeA+++Y +Al+ldP++a a++n G a+ ++G
  gi|386001554|ref|YP_005919853.1| 44 ELGRYEEAVASYDNALELDPEYALAWNNKGIALSALG 80
                                      89******************************99887 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 6.9e-13
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++G++eeA+++Y++ l++dPd+a a++n+G+++ ++G
  gi|386001554|ref|YP_005919853.1|  78 ALGRNEEALACYNRSLEIDPDYAPAWNNRGVVLEALG 114
                                       79*******************************9998 PP

  == domain 4  score: 24.8 bits;  conditional E-value: 3e-08
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       +G+ +eA+e+Y +Al+ dP +a a++n G ++y
  gi|386001554|ref|YP_005919853.1| 113 LGRGDEALESYDRALEVDPAYALAWSNQGGVFY 145
                                       7889***********************998876 PP

  == domain 5  score: 38.5 bits;  conditional E-value: 1.6e-12
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       ++y++G+y+ +ie+Y++Al++dP + ea++nLG  +
  gi|386001554|ref|YP_005919853.1| 143 VFYSRGDYNRSIECYERALEIDPRSREAWNNLGRSL 178
                                       89*******************************766 PP

  == domain 6  score: 34.4 bits;  conditional E-value: 2.9e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+ +++ G+ye +ie Y +Alk+dP +a+a++n G a+  +G
  gi|386001554|ref|YP_005919853.1| 175 GRSLFAAGEYERSIEGYDEALKIDPLYATAWNNKGIALGTLG 216
                                       889**********************************98887 PP

  == domain 7  score: 25.2 bits;  conditional E-value: 2.3e-08
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+  eA+ +Y++Alk+ P+ + a+yn G a+  +G
  gi|386001554|ref|YP_005919853.1| 215 LGRHQEALDCYEEALKIEPSHVMALYNKGIALGLLG 250
                                       699****************************98877 PP

  == domain 8  score: 35.0 bits;  conditional E-value: 2e-11
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+ eeA+e+Y + lk dP+++ a+yn+G+a+  +G
  gi|386001554|ref|YP_005919853.1| 249 LGRQEEAVECYDAVLKVDPSYPPAWYNRGVALGLLG 284
                                       69*****************************98877 PP

  == domain 9  score: 31.8 bits;  conditional E-value: 2e-10
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+ e+A ++Y +AlkldP +a a++n+G a+  +G
  gi|386001554|ref|YP_005919853.1| 283 LGRQEQAAASYDEALKLDPGYAQAWNNRGIALGSLG 318
                                       69*****************************98887 PP

  == domain 10  score: 36.5 bits;  conditional E-value: 6.7e-12
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++G+ eeA+++Y++Al++dP +  a+yn G+a+ ++G
  gi|386001554|ref|YP_005919853.1| 316 SLGRQEEALQSYQRALEIDPAYSQAWYNQGVAFSALG 352
                                       68*******************************9887 PP

  == domain 11  score: 33.4 bits;  conditional E-value: 6.3e-11
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+ ++G+y eAi +Y +Al+ldP+  ea++n G a+ ++G
  gi|386001554|ref|YP_005919853.1| 347 AFSALGRYQEAISSYDRALELDPELSEAWNNKGIALSALG 386
                                       66789******************************99887 PP

  == domain 12  score: 13.1 bits;  conditional E-value: 0.00013
                            TPR_11   6 eqGkyeeAieaYkkAlk 22 
                                       ++G+  eAie+Y++Al+
  gi|386001554|ref|YP_005919853.1| 384 ALGRHQEAIECYERALE 400
                                       68*************98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.2   1.5e-10   6.6e-08       3      33 ..      34      64 ..      33      65 .. 0.97
   2 !   26.6   0.1   9.5e-09   4.1e-06       3      34 .]      68      99 ..      66      99 .. 0.96
   3 !   22.1   0.0   2.6e-07   0.00011       1      33 [.     100     132 ..     100     133 .. 0.96
   4 !   20.5   0.0   8.3e-07   0.00036       3      32 ..     136     165 ..     134     167 .. 0.91
   5 !   19.2   0.0   2.2e-06   0.00095       2      32 ..     169     199 ..     169     199 .. 0.98
   6 !   27.2   0.0   6.3e-09   2.7e-06       1      34 []     202     235 ..     202     235 .. 0.96
   7 !   20.6   0.0     8e-07   0.00034       3      33 ..     238     268 ..     238     269 .. 0.96
   8 !   24.7   0.0   3.9e-08   1.7e-05       2      32 ..     271     301 ..     270     303 .. 0.95
   9 !   28.0   0.1   3.3e-09   1.4e-06       1      33 [.     304     336 ..     304     337 .. 0.96
  10 !   30.6   0.1   5.1e-10   2.2e-07       2      33 ..     339     370 ..     338     371 .. 0.96
  11 !   26.7   0.1   8.7e-09   3.7e-06       2      29 ..     373     400 ..     372     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.5e-10
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+yn+g ++++lg+yeeA+++y  aleldp+
  gi|386001554|ref|YP_005919853.1| 34 AWYNKGVALSELGRYEEAVASYDNALELDPE 64
                                      8*****************************8 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 9.5e-09
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      a++n+g +++ lg+ eeA ++y++ le+dpd+
  gi|386001554|ref|YP_005919853.1| 68 AWNNKGIALSALGRNEEALACYNRSLEIDPDY 99
                                      8*****************************85 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 2.6e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a++n g +++ lg+ +eA e+y +ale dp+
  gi|386001554|ref|YP_005919853.1| 100 APAWNNRGVVLEALGRGDEALESYDRALEVDPA 132
                                       79******************************7 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+ n g +  + gdy+ ++e+ye+ale+dp
  gi|386001554|ref|YP_005919853.1| 136 AWSNQGGVFYSRGDYNRSIECYERALEIDP 165
                                       788889999999*****************9 PP

  == domain 5  score: 19.2 bits;  conditional E-value: 2.2e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ea++nlg+ ++  g+ye ++e y +al++dp
  gi|386001554|ref|YP_005919853.1| 169 EAWNNLGRSLFAAGEYERSIEGYDEALKIDP 199
                                       79****************************9 PP

  == domain 6  score: 27.2 bits;  conditional E-value: 6.3e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a a++n+g ++ +lg+++eA  +ye+al+++p++
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNKGIALGTLGRHQEALDCYEEALKIEPSH 235
                                       679*****************************86 PP

  == domain 7  score: 20.6 bits;  conditional E-value: 8e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+yn+g ++  lg+ eeA+e+y  +l+ dp+
  gi|386001554|ref|YP_005919853.1| 238 ALYNKGIALGLLGRQEEAVECYDAVLKVDPS 268
                                       69****************************7 PP

  == domain 8  score: 24.7 bits;  conditional E-value: 3.9e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +a+yn g ++  lg+ e+A ++y +al+ldp
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASYDEALKLDP 301
                                       79****************************9 PP

  == domain 9  score: 28.0 bits;  conditional E-value: 3.3e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a++n g ++ +lg+ eeA ++y++ale+dp+
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEIDPA 336
                                       79******************************7 PP

  == domain 10  score: 30.6 bits;  conditional E-value: 5.1e-10
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+yn g + + lg+y+eA+++y +aleldp+
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALELDPE 370
                                       89*****************************6 PP

  == domain 11  score: 26.7 bits;  conditional E-value: 8.7e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                       ea++n+g +++ lg+++eA+e+ye+ale
  gi|386001554|ref|YP_005919853.1| 373 EAWNNKGIALSALGRHQEAIECYERALE 400
                                       89*************************8 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   3.8e-06    0.0016       7      33 ..      26      52 ..      24      53 .. 0.93
   2 !   25.5   0.7   2.4e-08     1e-05       2      33 ..      55      86 ..      54      87 .. 0.96
   3 !   29.3   0.0   1.6e-09   6.7e-07       1      33 [.      88     120 ..      88     121 .. 0.94
   4 !   14.1   0.0   0.00011     0.048       2      33 ..     123     154 ..     122     155 .. 0.94
   5 !   23.4   0.0   1.2e-07   4.9e-05       1      33 [.     156     188 ..     156     189 .. 0.95
   6 !   23.0   0.1   1.6e-07   6.9e-05       2      33 ..     191     222 ..     191     223 .. 0.97
   7 !   21.8   0.0   3.8e-07   0.00016       1      34 []     224     257 ..     224     257 .. 0.96
   8 !   22.2   0.0   2.9e-07   0.00012       1      32 [.     258     289 ..     258     291 .. 0.96
   9 !   25.2   0.1     3e-08   1.3e-05       2      34 .]     293     325 ..     292     325 .. 0.97
  10 !   27.5   0.1   5.5e-09   2.4e-06       2      33 ..     327     358 ..     326     359 .. 0.97
  11 !   29.0   0.0     2e-09   8.4e-07       2      34 .]     361     393 ..     360     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.8e-06
                            TPR_17  7 eldPnnadaynnLAelllknGdlmtAr 33
                                      e +P ++ a++n++++l+++G++++A+
  gi|386001554|ref|YP_005919853.1| 26 EENPLYPLAWYNKGVALSELGRYEEAV 52
                                      88***********************97 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 2.4e-08
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      y +aleldP +a a+nn++ +l+ +G+ ++A+
  gi|386001554|ref|YP_005919853.1| 55 YDNALELDPEYALAWNNKGIALSALGRNEEAL 86
                                      99***************************997 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 1.6e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y ++le+dP++a+a+nn++++l+ +G+ ++A+
  gi|386001554|ref|YP_005919853.1|  88 CYNRSLEIDPDYAPAWNNRGVVLEALGRGDEAL 120
                                       8**************************988886 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 0.00011
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +ale dP +a a+ n + +++++Gd+ + +
  gi|386001554|ref|YP_005919853.1| 123 YDRALEVDPAYALAWSNQGGVFYSRGDYNRSI 154
                                       99**************************9876 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 1.2e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y++ale+dP + +a+nnL++ l  +G++++ +
  gi|386001554|ref|YP_005919853.1| 156 CYERALEIDPRSREAWNNLGRSLFAAGEYERSI 188
                                       8****************************9976 PP

  == domain 6  score: 23.0 bits;  conditional E-value: 1.6e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +al++dP +a a+nn++ +l  +G++++A+
  gi|386001554|ref|YP_005919853.1| 191 YDEALKIDPLYATAWNNKGIALGTLGRHQEAL 222
                                       89****************************96 PP

  == domain 7  score: 21.8 bits;  conditional E-value: 3.8e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y++al+++P+++ a++n++ +l  +G+ ++A++
  gi|386001554|ref|YP_005919853.1| 224 CYEEALKIEPSHVMALYNKGIALGLLGRQEEAVE 257
                                       8******************************975 PP

  == domain 8  score: 22.2 bits;  conditional E-value: 2.9e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y  +l+ dP++++a++n++++l  +G+ ++A
  gi|386001554|ref|YP_005919853.1| 258 CYDAVLKVDPSYPPAWYNRGVALGLLGRQEQA 289
                                       89*************************99998 PP

  == domain 9  score: 25.2 bits;  conditional E-value: 3e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +al+ldP +a a+nn++ +l ++G+ ++A+q
  gi|386001554|ref|YP_005919853.1| 293 YDEALKLDPGYAQAWNNRGIALGSLGRQEEALQ 325
                                       99*****************************97 PP

  == domain 10  score: 27.5 bits;  conditional E-value: 5.5e-09
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y++ale+dP ++ a++n +++++ +G++++A+
  gi|386001554|ref|YP_005919853.1| 327 YQRALEIDPAYSQAWYNQGVAFSALGRYQEAI 358
                                       9******************************7 PP

  == domain 11  score: 29.0 bits;  conditional E-value: 2e-09
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +aleldP  ++a+nn++ +l+ +G++++A++
  gi|386001554|ref|YP_005919853.1| 361 YDRALELDPELSEAWNNKGIALSALGRHQEAIE 393
                                       99*****************************86 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.0   8.9e-08   3.8e-05      25      66 ..      26      64 ..      22      66 .. 0.89
   2 !   42.4   2.3   1.9e-13     8e-11       1      67 [.      36      99 ..      36     100 .. 0.96
   3 !   38.7   1.5   2.7e-12   1.2e-09       3      67 ..      72     133 ..      70     134 .. 0.95
   4 !   43.2   0.0   1.1e-13   4.6e-11       2      65 ..     139     199 ..     138     202 .. 0.95
   5 !   31.7   0.0   4.1e-10   1.8e-07       3      68 .]     208     270 ..     206     270 .. 0.95
   6 !   31.4   1.6   5.2e-10   2.2e-07      11      67 ..     250     303 ..     249     304 .. 0.95
   7 !   32.6   4.5   2.1e-10     9e-08      11      67 ..     284     337 ..     283     338 .. 0.94
   8 !   42.1   1.8   2.3e-13     1e-10       3      65 ..     310     369 ..     308     370 .. 0.95
   9 !   44.2   1.0     5e-14   2.1e-11       1      62 [.     342     400 ..     342     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8.9e-08
                            TPR_16 25 krdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                      + +   P+ + A++++g+a+ ++gr++eA+a y+ al+ +p 
  gi|386001554|ref|YP_005919853.1| 26 EEN---PLYPLAWYNKGVALSELGRYEEAVASYDNALELDPE 64
                                      455...*******************************99996 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 1.9e-13
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      ++++ a+ ++g+y++A+a ++ al++d   P+ a A++++g a+ ++gr +eA+a y++ l+ +pd+
  gi|386001554|ref|YP_005919853.1| 36 YNKGVALSELGRYEEAVASYDNALELD---PEYALAWNNKGIALSALGRNEEALACYNRSLEIDPDY 99
                                      67888999*******************...***********************************97 PP

  == domain 3  score: 38.7 bits;  conditional E-value: 2.7e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++ a+ ++g+ ++A+a +++ l+ d   Pd a A++++g+++ ++gr +eA++ y++al+ +p +
  gi|386001554|ref|YP_005919853.1|  72 KGIALSALGRNEEALACYNRSLEID---PDYAPAWNNRGVVLEALGRGDEALESYDRALEVDPAY 133
                                       6889999******************...*******************************999975 PP

  == domain 4  score: 43.2 bits;  conditional E-value: 1.1e-13
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++  ++ +gdy + ++ +e+al+ d   P+ +eA+++lg++++++g++++ ++ y++al+ +p
  gi|386001554|ref|YP_005919853.1| 139 NQGGVFYSRGDYNRSIECYERALEID---PRSREAWNNLGRSLFAAGEYERSIEGYDEALKIDP 199
                                       68999*********************...*******************************9999 PP

  == domain 5  score: 31.7 bits;  conditional E-value: 4.1e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++ a+  +g+ ++A+  +e+alk     P ++ Al+++g a+  +gr +eA++ y+a l+ +p++p
  gi|386001554|ref|YP_005919853.1| 208 KGIALGTLGRHQEALDCYEEALKIE---PSHVMALYNKGIALGLLGRQEEAVECYDAVLKVDPSYP 270
                                       6888999******************...********************************999887 PP

  == domain 6  score: 31.4 bits;  conditional E-value: 5.2e-10
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       g+ ++A++ ++a+lk d   P  + A++++g+a+  +gr + Aaa y++al+ +p++
  gi|386001554|ref|YP_005919853.1| 250 GRQEEAVECYDAVLKVD---PSYPPAWYNRGVALGLLGRQEQAAASYDEALKLDPGY 303
                                       55689************...***********************************97 PP

  == domain 7  score: 32.6 bits;  conditional E-value: 2.1e-10
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       g+ ++Aaa +++alk+d   P  a+A++++g a+  +gr +eA++ y++al+ +p +
  gi|386001554|ref|YP_005919853.1| 284 GRQEQAAASYDEALKLD---PGYAQAWNNRGIALGSLGRQEEALQSYQRALEIDPAY 337
                                       5668*************...**********************************976 PP

  == domain 8  score: 42.1 bits;  conditional E-value: 2.3e-13
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++ a+  +g+ ++A+  +++al+ d   P+  +A+++ g+a+ ++gr++eA+  y++al+ +p
  gi|386001554|ref|YP_005919853.1| 310 RGIALGSLGRQEEALQSYQRALEID---PAYSQAWYNQGVAFSALGRYQEAISSYDRALELDP 369
                                       67788899999**************...*******************************9998 PP

  == domain 9  score: 44.2 bits;  conditional E-value: 5e-14
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++++ a+ ++g+y++A+  +++al++d   P+  eA++++g a+ ++gr++eA++ y++al+
  gi|386001554|ref|YP_005919853.1| 342 YNQGVAFSALGRYQEAISSYDRALELD---PELSEAWNNKGIALSALGRHQEAIECYERALE 400
                                       78999999*******************...*****************************994 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   1.4   6.1e-13   2.6e-10       5      76 ..      34      97 ..      31      98 .. 0.94
   2 !   39.3   0.1   1.4e-12   5.9e-10       3      76 ..     100     165 ..      98     166 .. 0.93
   3 !   30.3   0.1   8.9e-10   3.8e-07       3      74 ..     134     197 ..     132     199 .. 0.78
   4 !   39.1   0.5   1.6e-12   6.9e-10       4      74 ..     169     231 ..     166     234 .. 0.95
   5 !   36.6   0.4   9.7e-12   4.1e-09       3      75 ..     202     266 ..     200     268 .. 0.94
   6 !   25.9   4.6   2.1e-08   8.8e-06       5      76 ..     272     335 ..     271     336 .. 0.91
   7 !   33.8   2.6   7.4e-11   3.1e-08       3      76 ..     304     369 ..     304     370 .. 0.94
   8 !   42.4   2.5   1.5e-13   6.2e-11       4      74 ..     339     401 ..     336     404 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.1e-13
                            TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                                      a++n +++l +lgry+eA + ++ ale+      p++   a + +n g++++algr eeAl+ ++++l+i++
  gi|386001554|ref|YP_005919853.1| 34 AWYNKGVALSELGRYEEAVASYDNALELD-----PEY---ALAWNNKGIALSALGRNEEALACYNRSLEIDP 97
                                      788**************************.....885...99***************************975 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 1.4e-12
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a+nn+++vl +lgr deAle +++ale+      p   ++a +  n g +++ +g+y   +e +e+al+i++
  gi|386001554|ref|YP_005919853.1| 100 APAWNNRGVVLEALGRGDEALESYDRALEVD-----P---AYALAWSNQGGVFYSRGDYNRSIECYERALEIDP 165
                                       66999*************************9.....6...4799***************************975 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 8.9e-10
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a a++n + v + +g+y  ++e++e+alei      p +    ++ +nLgr ++a+g+ye  +e + eal+i
  gi|386001554|ref|YP_005919853.1| 134 ALAWSNQGGVFYSRGDYNRSIECYERALEID-----PRS---REAWNNLGRSLFAAGEYERSIEGYDEALKI 197
                                       67999**************************.....543...556666666666666666666666666665 PP

  == domain 4  score: 39.1 bits;  conditional E-value: 1.6e-12
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a+nnl+  l+++g+y+ ++e +++al i      p   l+at+ +n g+++  lgr++eAl+ +eeal+i
  gi|386001554|ref|YP_005919853.1| 169 EAWNNLGRSLFAAGEYERSIEGYDEALKID-----P---LYATAWNNKGIALGTLGRHQEALDCYEEALKI 231
                                       6999**********************9999.....5...68****************************97 PP

  == domain 5  score: 36.6 bits;  conditional E-value: 9.7e-12
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       ata+nn + +l  lgr++eAl+++e+al i      p h   + +l+n g+++ +lgr+eeA+e +  +l+++
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNKGIALGTLGRHQEALDCYEEALKIE-----PSH---VMALYNKGIALGLLGRQEEAVECYDAVLKVD 266
                                       89*****************************.....988...99**********************9999876 PP

  == domain 6  score: 25.9 bits;  conditional E-value: 2.1e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a++n++++l  lgr ++A + +++al +      p   ++a++ +n g+++  lgr+eeAl+ +++al+i++
  gi|386001554|ref|YP_005919853.1| 272 AWYNRGVALGLLGRQEQAAASYDEALKLD-----P---GYAQAWNNRGIALGSLGRQEEALQSYQRALEIDP 335
                                       57899999999999999999999998888.....5...38*****************************975 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 7.4e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+a+nn++ +l  lgr +eAl+ +++alei      p   +++++ +n g +++algry+eA++ + +al++++
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEID-----P---AYSQAWYNQGVAFSALGRYQEAISSYDRALELDP 369
                                       6799***************************.....6...4799***************************976 PP

  == domain 8  score: 42.4 bits;  conditional E-value: 1.5e-13
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a++n +++  +lgry+eA++ +++ale+      p+   ++++ +n g++++algr++eA+e +e+al++
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALELD-----PE---LSEAWNNKGIALSALGRHQEAIECYERALEV 401
                                       6899**************************.....76...89***************************96 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     2e-06   0.00084       1      32 [.      34      63 ..      34      65 .. 0.86
   2 !   15.8   0.1   2.4e-05      0.01       1      31 [.      68      98 ..      68     100 .. 0.94
   3 !   14.0   0.0   9.4e-05      0.04       1      32 [.     102     131 ..     102     132 .. 0.91
   4 !   18.5   0.0   3.4e-06    0.0015       1      32 [.     136     165 ..     136     169 .. 0.79
   5 !   12.3   0.0   0.00032      0.14       1      28 [.     170     197 ..     170     200 .. 0.86
   6 !   14.6   0.0     6e-05     0.026       1      31 [.     204     232 ..     204     236 .. 0.83
   7 !   11.7   0.0    0.0005      0.21       1      32 [.     238     267 ..     238     268 .. 0.89
   8 !    8.4   0.1    0.0056       2.4       1      32 [.     272     301 ..     272     302 .. 0.89
   9 !   12.9   0.1   0.00021     0.088       1      29 [.     306     334 ..     306     339 .. 0.90
  10 !   24.7   0.1   3.5e-08   1.5e-05       1      31 [.     340     370 ..     340     373 .. 0.85
  11 !   23.8   0.1   6.8e-08   2.9e-05       1      27 [.     374     400 ..     374     415 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-06
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32
                                      a++n +++ s+lG+yeeA+  y    al+ dp
  gi|386001554|ref|YP_005919853.1| 34 AWYNKGVALSELGRYEEAVASYDN--ALELDP 63
                                      789*********************..555554 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.4e-05
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31
                                      a++n + + s+lG+ eeA+ +y +sL+++ d
  gi|386001554|ref|YP_005919853.1| 68 AWNNKGIALSALGRNEEALACYNRSLEIDPD 98
                                      799***********************99876 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 9.4e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n +++ ++lG+ +eA+e y +  al+ dp
  gi|386001554|ref|YP_005919853.1| 102 AWNNRGVVLEALGRGDEALESYDR--ALEVDP 131
                                       799*********************..777776 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 3.4e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n + ++ ++Gdy + ie+ye++L+++  p
  gi|386001554|ref|YP_005919853.1| 136 AWSNQGGVFYSRGDYNRSIECYERALEID--P 165
                                       577888888899************66655..3 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00032
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++nL+r  ++ G+ye+ ie y ++L +
  gi|386001554|ref|YP_005919853.1| 170 AWNNLGRSLFAAGEYERSIEGYDEALKI 197
                                       79******************99995543 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 6e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n + +   lG+++eA+++ye++L +  +
  gi|386001554|ref|YP_005919853.1| 204 AWNNKGIALGTLGRHQEALDCYEEALKI--E 232
                                       68999999999*************5544..4 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 0.0005
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       aL+n + +   lG+ eeA+e+y +  +l  dp
  gi|386001554|ref|YP_005919853.1| 238 ALYNKGIALGLLGRQEEAVECYDA--VLKVDP 267
                                       79999999999*************..777776 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.0056
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n +++   lG+ e+A+  y +  al  dp
  gi|386001554|ref|YP_005919853.1| 272 AWYNRGVALGLLGRQEQAAASYDE--ALKLDP 301
                                       689999******************..777776 PP

  == domain 9  score: 12.9 bits;  conditional E-value: 0.00021
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++n + +  +lG+ eeA++ y+++L+++
  gi|386001554|ref|YP_005919853.1| 306 AWNNRGIALGSLGRQEEALQSYQRALEID 334
                                       7899********************88876 PP

  == domain 10  score: 24.7 bits;  conditional E-value: 3.5e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n ++++s+lG+y+eAi+ y ++L+l+ +
  gi|386001554|ref|YP_005919853.1| 340 AWYNQGVAFSALGRYQEAISSYDRALELDPE 370
                                       789*********************6666544 PP

  == domain 11  score: 23.8 bits;  conditional E-value: 6.8e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                       a++n + + s+lG+++eAie+ye++L+
  gi|386001554|ref|YP_005919853.1| 374 AWNNKGIALSALGRHQEAIECYERALE 400
                                       799*********************664 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   8.7e-07   0.00037       3      39 ..      34      70 ..      32      74 .. 0.92
   2 !   18.9   0.1   4.4e-06    0.0019       8      39 ..      73     104 ..      72     108 .. 0.92
   3 !   19.4   0.9   3.1e-06    0.0013       6      38 ..     105     137 ..     102     141 .. 0.91
   4 !   21.0   0.0   8.8e-07   0.00038       6      43 ..     139     176 ..     136     177 .. 0.90
   5 !   17.5   0.2   1.2e-05     0.005       2      39 ..     169     206 ..     168     211 .. 0.93
   6 !   14.5   0.0   0.00012     0.049      10      40 ..     211     241 ..     207     245 .. 0.87
   7 !   13.1   0.0   0.00032      0.14      10      42 ..     245     277 ..     238     280 .. 0.85
   8 !   15.2   0.8   6.6e-05     0.028       2      39 ..     271     308 ..     270     315 .. 0.91
   9 !   17.2   0.6   1.5e-05    0.0065       3      40 ..     306     343 ..     305     347 .. 0.89
  10 !   21.7   0.2   5.6e-07   0.00024       2      39 ..     339     376 ..     338     380 .. 0.93
  11 !   15.7   0.2   4.5e-05     0.019       2      31 ..     373     402 ..     372     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.7e-07
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawl 39
                                      a++  + al +lG+++eA+a ++ al+l+P+ a aw 
  gi|386001554|ref|YP_005919853.1| 34 AWYNKGVALSELGRYEEAVASYDNALELDPEYALAWN 70
                                      8999999****************************95 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.4e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       + al alG+ +eA+a+++r l+ +Pd a aw 
  gi|386001554|ref|YP_005919853.1|  73 GIALSALGRNEEALACYNRSLEIDPDYAPAWN 104
                                       5799************************9995 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 3.1e-06
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeaw 38 
                                        ++ +l+alG+ deA++ ++ral+ +P+ a aw
  gi|386001554|ref|YP_005919853.1| 105 NRGVVLEALGRGDEALESYDRALEVDPAYALAW 137
                                       57889***************************9 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 8.8e-07
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                         + +++ +Gd+ ++i++++ral+ +P ++eaw  l++
  gi|386001554|ref|YP_005919853.1| 139 NQGGVFYSRGDYNRSIECYERALEIDPRSREAWNNLGR 176
                                       5678999**************************99987 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 1.2e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ea+  l++ l+a+G+++++i+ +++al+ +P  a+aw 
  gi|386001554|ref|YP_005919853.1| 169 EAWNNLGRSLFAAGEYERSIEGYDEALKIDPLYATAWN 206
                                       89999*******************************95 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 0.00012
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawll 40 
                                       al +lG+++eA++++++al+  P++  a++ 
  gi|386001554|ref|YP_005919853.1| 211 ALGTLGRHQEALDCYEEALKIEPSHVMALYN 241
                                       56679********************999875 PP

  == domain 7  score: 13.1 bits;  conditional E-value: 0.00032
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                                       al  lG+ +eA+++++++l+ +P+ + aw+  +
  gi|386001554|ref|YP_005919853.1| 245 ALGLLGRQEEAVECYDAVLKVDPSYPPAWYNRG 277
                                       555689***********************8765 PP

  == domain 8  score: 15.2 bits;  conditional E-value: 6.6e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                        a++ ++ al  lG+ ++A+a +++al+l+P+ a+aw 
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASYDEALKLDPGYAQAWN 308
                                       589999999999************************95 PP

  == domain 9  score: 17.2 bits;  conditional E-value: 1.5e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       a+  ++ al  lG+ +eA++ ++ral+ +P+  +aw+ 
  gi|386001554|ref|YP_005919853.1| 306 AWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQAWYN 343
                                       66678899999*************************75 PP

  == domain 10  score: 21.7 bits;  conditional E-value: 5.6e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +a++  + a+ alG+++eAi  ++ral+l+P+  eaw 
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALELDPELSEAWN 376
                                       699999******************************95 PP

  == domain 11  score: 15.7 bits;  conditional E-value: 4.5e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                       ea+   + al alG+++eAi++++ral+ +
  gi|386001554|ref|YP_005919853.1| 373 EAWNNKGIALSALGRHQEAIECYERALEVG 402
                                       56667789*******************965 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   4.4e-05     0.019      19      59 ..      26      66 ..      22      70 .. 0.87
   2 !   33.3   1.7   1.2e-10   5.3e-08       4      59 ..      45     101 ..      42     105 .. 0.93
   3 !   25.4   0.8   3.5e-08   1.5e-05       5      61 ..      80     136 ..      76     140 .. 0.92
   4 !   24.2   0.0   8.1e-08   3.5e-05       3      59 ..     146     202 ..     144     207 .. 0.92
   5 !   20.9   0.0   8.8e-07   0.00037       5      59 ..     216     271 ..     215     275 .. 0.94
   6 !   18.9   3.3   3.8e-06    0.0016       5      62 ..     284     341 ..     283     345 .. 0.93
   7 !   27.7   0.1   6.7e-09   2.9e-06       5      53 ..     352     400 ..     348     402 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-05
                            TPR_19 19 qedpknaearllLAeallalgqldeAealLdalpeedpdda 59
                                      +e+p ++ a+++   al +lg+++eA a  d ++e dp  a
  gi|386001554|ref|YP_005919853.1| 26 EENPLYPLAWYNKGVALSELGRYEEAVASYDNALELDPEYA 66
                                      789999****************************9999854 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.2e-10
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.a 59 
                                        g+y+eA+a + +al+ dp++a a+ +  +al alg+ +eA a+ ++ +e dpd  +
  gi|386001554|ref|YP_005919853.1|  45 LGRYEEAVASYDNALELDPEYALAWNNKGIALSALGRNEEALACYNRSLEIDPDYaP 101
                                       59****************************************************744 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 3.5e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       g+ +eAla + + l+ dp++a a+ +   +l alg+ deA +  d+++e dp  a +
  gi|386001554|ref|YP_005919853.1|  80 GRNEEALACYNRSLEIDPDYAPAWNNRGVVLEALGRGDEALESYDRALEVDPAYALA 136
                                       8889***********************************************986555 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 8.1e-08
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                        +gdy + ++ +e+al+ dp + ea+ +L + l+a+g+++  ++  d++++ dp  a
  gi|386001554|ref|YP_005919853.1| 146 SRGDYNRSIECYERALEIDPRSREAWNNLGRSLFAAGEYERSIEGYDEALKIDPLYA 202
                                       68************************************************9999854 PP

  == domain 5  score: 20.9 bits;  conditional E-value: 8.8e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.a 59 
                                       g+++eAl+ +e+al+ +p +  a+++  +al  lg+ +eA ++ da+++ dp   +
  gi|386001554|ref|YP_005919853.1| 216 GRHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVLKVDPSYpP 271
                                       89*************************************************99634 PP

  == domain 6  score: 18.9 bits;  conditional E-value: 3.8e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       g+ ++A+a + +al+ dp++a a+ +  +al +lg+ +eA +  ++++e dp  ++++
  gi|386001554|ref|YP_005919853.1| 284 GRQEQAAASYDEALKLDPGYAQAWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQAW 341
                                       56689***********************************************977665 PP

  == domain 7  score: 27.7 bits;  conditional E-value: 6.7e-09
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       g+y+eA++ + +al+ dp+ +ea+ +  +al alg+ +eA+++ ++++e
  gi|386001554|ref|YP_005919853.1| 352 GRYQEAISSYDRALELDPELSEAWNNKGIALSALGRHQEAIECYERALE 400
                                       9******************************************999876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.4e-05     0.014      29      61 ..      32      64 ..      27      69 .. 0.91
   2 !   34.8   0.9   3.2e-11   1.4e-08       8      61 ..      79     132 ..      72     138 .. 0.92
   3 !   15.4   0.1   3.7e-05     0.016       7      60 ..     146     199 ..     141     211 .. 0.92
   4 !   20.3   0.0     1e-06   0.00044      10      60 ..     217     267 ..     208     268 .. 0.95
   5 !   23.4   0.7   1.1e-07   4.9e-05      12      63 ..     253     304 ..     250     306 .. 0.92
   6 !   21.9   1.6   3.5e-07   0.00015      12      64 ..     287     339 ..     285     341 .. 0.93
   7 !   22.5   0.4   2.2e-07   9.2e-05      10      58 ..     353     401 ..     346     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-05
                             TPR_9 29 peerrdRGlllaqlGclsaAladLeaylalapd 61
                                      p  ++  G++l +lG++++A+a  + +l+l+p+
  gi|386001554|ref|YP_005919853.1| 32 PLAWYNKGVALSELGRYEEAVASYDNALELDPE 64
                                      789*****************************7 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3.2e-11
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                         ++e+ala+++r l ++Pd +  +  RG++l+ lG+  +Al+  +++l+++p+
  gi|386001554|ref|YP_005919853.1|  79 LGRNEEALACYNRSLEIDPDYAPAWNNRGVVLEALGRGDEALESYDRALEVDPA 132
                                       5789************************************************96 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.7e-05
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ++ d+ r ++++er l ++P++ e +   G+ l+  G ++  ++  + +l ++p
  gi|386001554|ref|YP_005919853.1| 146 SRGDYNRSIECYERALEIDPRSREAWNNLGRSLFAAGEYERSIEGYDEALKIDP 199
                                       57899**************************************99999999988 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 1e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ++++al ++e  l + P ++  ++  G++l  lG+ ++A+++ +a l ++p
  gi|386001554|ref|YP_005919853.1| 217 RHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVLKVDP 267
                                       899********************************************9999 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 1.1e-07
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       e+a ++++ +l ++P  p  ++ RG++l  lG+ ++A+a  + +l l+p  +
  gi|386001554|ref|YP_005919853.1| 253 EEAVECYDAVLKVDPSYPPAWYNRGVALGLLGRQEQAAASYDEALKLDPGYA 304
                                       789*********************************************9654 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 3.5e-07
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       e+a a ++  l l+P  ++ +  RG++l  lG+ ++Al+  +++l+++p+  +
  gi|386001554|ref|YP_005919853.1| 287 EQAAASYDEALKLDPGYAQAWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQ 339
                                       789999*******************************************7555 PP

  == domain 7  score: 22.5 bits;  conditional E-value: 2.2e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                       ++++a+  ++r l l+P+  e +   G++l  lG+ ++A+++ e++l++
  gi|386001554|ref|YP_005919853.1| 353 RYQEAISSYDRALELDPELSEAWNNKGIALSALGRHQEAIECYERALEV 401
                                       7999******************************************986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.3   0.00034      0.15       7      30 ..      37      60 ..      36      61 .. 0.91
   2 !   13.2   0.6   0.00015     0.062       6      31 ..      70      95 ..      66      95 .. 0.94
   3 !   13.3   0.2   0.00013     0.057       6      30 ..     104     128 ..     104     129 .. 0.96
   4 ?    7.2   0.0     0.012       4.9      11      31 ..     143     163 ..     138     165 .. 0.84
   5 !   10.5   0.1    0.0011      0.45       6      31 ..     172     197 ..     170     197 .. 0.96
   6 !   20.1   0.1   9.7e-07   0.00041       3      31 ..     203     231 ..     202     232 .. 0.91
   7 !    9.5   0.0    0.0021      0.89       3      30 ..     237     264 ..     236     265 .. 0.92
   8 ?    4.1   0.6       0.1        44       7      30 ..     275     298 ..     274     299 .. 0.92
   9 !   14.8   0.8   4.6e-05      0.02       6      31 ..     308     333 ..     304     333 .. 0.94
  10 !    7.5   0.1     0.009       3.9       9      30 ..     345     366 ..     343     367 .. 0.90
  11 !   20.7   0.2   6.3e-07   0.00027       6      31 ..     376     401 ..     374     407 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                            TPR_10  7 NLanalrqrgrydeAealleeala 30
                                      N ++al+++gry+eA+a ++ al+
  gi|386001554|ref|YP_005919853.1| 37 NKGVALSELGRYEEAVASYDNALE 60
                                      6699***************99997 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00015
                            TPR_10  6 nNLanalrqrgrydeAealleealai 31
                                      nN ++al+++gr +eA+a + ++l+i
  gi|386001554|ref|YP_005919853.1| 70 NNKGIALSALGRNEEALACYNRSLEI 95
                                      999******************99987 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00013
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN +++l ++gr+deA++ +++al+
  gi|386001554|ref|YP_005919853.1| 104 NNRGVVLEALGRGDEALESYDRALE 128
                                       999********************98 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.012
                            TPR_10  11 alrqrgrydeAealleealai 31 
                                       + ++rg+y+++ + +e+al+i
  gi|386001554|ref|YP_005919853.1| 143 VFYSRGDYNRSIECYERALEI 163
                                       568999999999999999987 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.0011
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nNL++ l++ g+y+++ + ++eal i
  gi|386001554|ref|YP_005919853.1| 172 NNLGRSLFAAGEYERSIEGYDEALKI 197
                                       9**********************976 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 9.7e-07
                            TPR_10   3 sslnNLanalrqrgrydeAealleealai 31 
                                       ++ nN ++al  +gr++eA++ +eeal i
  gi|386001554|ref|YP_005919853.1| 203 TAWNNKGIALGTLGRHQEALDCYEEALKI 231
                                       5569***********************86 PP

  == domain 7  score: 9.5 bits;  conditional E-value: 0.0021
                            TPR_10   3 sslnNLanalrqrgrydeAealleeala 30 
                                       ++l N ++al  +gr +eA++ ++ +l 
  gi|386001554|ref|YP_005919853.1| 237 MALYNKGIALGLLGRQEEAVECYDAVLK 264
                                       7999******************999986 PP

  == domain 8  score: 4.1 bits;  conditional E-value: 0.1
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++al  +gr ++A a ++eal 
  gi|386001554|ref|YP_005919853.1| 275 NRGVALGLLGRQEQAAASYDEALK 298
                                       77999*****************96 PP

  == domain 9  score: 14.8 bits;  conditional E-value: 4.6e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++al ++gr +eA++ +++al+i
  gi|386001554|ref|YP_005919853.1| 308 NNRGIALGSLGRQEEALQSYQRALEI 333
                                       9***********************97 PP

  == domain 10  score: 7.5 bits;  conditional E-value: 0.009
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       ++a +++gry+eA   +++al+
  gi|386001554|ref|YP_005919853.1| 345 GVAFSALGRYQEAISSYDRALE 366
                                       678899**************98 PP

  == domain 11  score: 20.7 bits;  conditional E-value: 6.3e-07
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++al+++gr++eA + +e+al++
  gi|386001554|ref|YP_005919853.1| 376 NNKGIALSALGRHQEAIECYERALEV 401
                                       899*********************96 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00087      0.37       2      32 ..      34      64 ..      33      65 .. 0.93
   2 ?    3.9   0.0      0.24     1e+02       7      32 ..      73      98 ..      71      99 .. 0.85
   3 ?    4.8   0.0      0.12        51       6      31 ..     106     131 ..     105     133 .. 0.85
   4 !    9.3   0.0    0.0044       1.9      10      33 .]     139     167 ..     132     167 .. 0.76
   5 !    8.3   0.0    0.0091       3.9       5      31 ..     173     199 ..     173     201 .. 0.92
   6 ?    5.1   0.0     0.094        40      12      32 ..     214     234 ..     200     235 .. 0.80
   7 !   11.0   0.0    0.0012      0.53       2      31 ..     238     267 ..     237     269 .. 0.93
   8 !    9.0   0.2    0.0054       2.3       2      31 ..     272     301 ..     271     303 .. 0.93
   9 ?    7.2   0.1      0.02       8.5       6      31 ..     310     335 ..     305     337 .. 0.87
  10 !   14.9   0.1   7.3e-05     0.031       1      31 [.     339     369 ..     339     370 .. 0.94
  11 ?    6.3   0.0     0.039        17       7      27 ..     379     399 ..     377     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00087
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYPd 32
                                      A y+ + ++ +lg++++A++ +++ ++  P+
  gi|386001554|ref|YP_005919853.1| 34 AWYNKGVALSELGRYEEAVASYDNALELDPE 64
                                      89*********9************9998885 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.24
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                      + ++ +lg+ ++Al+ ++r ++  Pd
  gi|386001554|ref|YP_005919853.1| 73 GIALSALGRNEEALACYNRSLEIDPD 98
                                      56677789***********9998887 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       ++  +++lg+ d+Ale ++r ++  P
  gi|386001554|ref|YP_005919853.1| 106 RGVVLEALGRGDEALESYDRALEVDP 131
                                       688899999***********998655 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0044
                                       HHHH.....HHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  10 yrkl.....gdtdkAlealerlikeYPdS 33 
                                        + +     gd+ +++e +er ++  P S
  gi|386001554|ref|YP_005919853.1| 139 NQGGvfysrGDYNRSIECYERALEIDPRS 167
                                       4444555559**************99987 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0091
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYP 31 
                                       +l++s++++g++++++e +++ +k  P
  gi|386001554|ref|YP_005919853.1| 173 NLGRSLFAAGEYERSIEGYDEALKIDP 199
                                       69******99**********9999777 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                        lg++++Al+ +e+ +k  P 
  gi|386001554|ref|YP_005919853.1| 214 TLGRHQEALDCYEEALKIEPS 234
                                       459*************99886 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       Aly+ + ++  lg+ ++A+e ++ ++k  P
  gi|386001554|ref|YP_005919853.1| 238 ALYNKGIALGLLGRQEEAVECYDAVLKVDP 267
                                       9**********99************99766 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       A y+++ ++  lg+ ++A + +++ +k  P
  gi|386001554|ref|YP_005919853.1| 272 AWYNRGVALGLLGRQEQAAASYDEALKLDP 301
                                       89*********99************99888 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       ++ ++ +lg+ ++Al+ ++r ++  P
  gi|386001554|ref|YP_005919853.1| 310 RGIALGSLGRQEEALQSYQRALEIDP 335
                                       577788889************99877 PP

  == domain 10  score: 14.9 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +A y+++ ++ +lg++++A+  ++r ++  P
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALELDP 369
                                       699*********9*************99888 PP

  == domain 11  score: 6.3 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerli 27 
                                       + ++ +lg++++A+e +er +
  gi|386001554|ref|YP_005919853.1| 379 GIALSALGRHQEAIECYERAL 399
                                       56777889***********87 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00034      0.14      94     129 ..      26      61 ..      19      66 .. 0.83
   2 !   13.8   0.1   0.00011     0.046      74     128 ..      78     128 ..      66     132 .. 0.89
   3 ?    0.1   0.0       1.9   7.9e+02      55      88 ..     134     167 ..     129     188 .. 0.77
   4 ?    5.7   0.0     0.033        14      99     126 ..     201     228 ..     170     234 .. 0.79
   5 ?    6.4   0.0     0.021       8.9     100     125 ..     236     261 ..     232     265 .. 0.88
   6 ?    3.4   0.0      0.17        74     103     126 ..     273     296 ..     269     300 .. 0.88
   7 !   11.3   0.0   0.00062      0.26     102     129 ..     306     333 ..     301     337 .. 0.90
   8 !    8.3   0.0    0.0054       2.3     102     129 ..     340     367 ..     334     374 .. 0.84
   9 !   12.3   0.1    0.0003      0.13      64     136 ..     347     408 ..     346     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                                       THHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  94 deGklWiaavfsravaleelGrkdealkafrmagem 129
                                       +e  l+  a ++++val+elGr++ea+ ++  a e+
  gi|386001554|ref|YP_005919853.1|  26 EENPLYPLAWYNKGVALSELGRYEEAVASYDNALEL 61 
                                       55666677889*******************999986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  74 alesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       al   ++al  +nr  e++ d    W     +r+v le lGr deal+++  a e
  gi|386001554|ref|YP_005919853.1|  78 ALGRNEEALACYNRSLEIDPDYAPAW----NNRGVVLEALGRGDEALESYDRALE 128
                                       6777899*************999888....69******************99988 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalryfnrr 88 
                                       al+++   + +   g+y+ ++e+ ++al+   r 
  gi|386001554|ref|YP_005919853.1| 134 ALAWSNQGGVFYSRGDYNRSIECYERALEIDPRS 167
                                       6777777888889999999999999999866655 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrma 126
                                       + +a  +++ al  lGr++eal+ ++ a
  gi|386001554|ref|YP_005919853.1| 201 YATAWNNKGIALGTLGRHQEALDCYEEA 228
                                       4556678888888888888888888776 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrm 125
                                       + a+++++ al  lGr++ea++ +  
  gi|386001554|ref|YP_005919853.1| 236 VMALYNKGIALGLLGRQEEAVECYDA 261
                                       6799*****************99976 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrma 126
                                        ++r+val  lGr+++a  ++  a
  gi|386001554|ref|YP_005919853.1| 273 WYNRGVALGLLGRQEQAAASYDEA 296
                                       589***************999877 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                       a  +r+ al +lGr++eal++++ a e+
  gi|386001554|ref|YP_005919853.1| 306 AWNNRGIALGSLGRQEEALQSYQRALEI 333
                                       5579********************9985 PP

  == domain 8  score: 8.3 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                       a ++++va++ lGr++ea+ ++  a e+
  gi|386001554|ref|YP_005919853.1| 340 AWYNQGVAFSALGRYQEAISSYDRALEL 367
                                       6688999999999999999999998886 PP

  == domain 9  score: 12.3 bits;  conditional E-value: 0.0003
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S- CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemiaerkGe 136
                                       a+  lgry+ea++s d+al       el+ +  + W     +++ al+ lGr++ea++ ++ a e+     G+
  gi|386001554|ref|YP_005919853.1| 347 AFSALGRYQEAISSYDRAL-------ELDPELSEAW----NNKGIALSALGRHQEAIECYERALEVGLASAGN 408
                                       6788999999999988888.......6777767777....68*********************9976555555 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0029       1.2       1      22 [.      32      53 ..      32      56 .. 0.89
   2 ?    7.5   0.1     0.017       7.4       5      23 ..      70      88 ..      66      91 .. 0.83
   3 !    9.4   0.1    0.0044       1.9       3      25 ..     102     124 ..     100     125 .. 0.84
   4 ?    4.3   0.0      0.19        79       4      18 ..     171     185 ..     169     187 .. 0.86
   5 ?    7.2   0.0     0.022       9.4       6      26 .]     207     227 ..     202     227 .. 0.85
   6 !    9.9   0.0     0.003       1.3       2      24 ..     237     259 ..     236     261 .. 0.89
   7 !   11.7   0.3   0.00076      0.32       2      24 ..     271     293 ..     270     295 .. 0.88
   8 ?    6.5   0.4     0.036        15       2      23 ..     305     326 ..     304     329 .. 0.86
   9 ?    3.9   0.0      0.25   1.1e+02       2      20 ..     339     357 ..     338     363 .. 0.90
  10 ?    6.2   0.0     0.047        20       6      26 .]     377     397 ..     373     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0029
                             TPR_4  1 arallaLArallalGdldeAra 22
                                      + a ++ + al +lG+++eA a
  gi|386001554|ref|YP_005919853.1| 32 PLAWYNKGVALSELGRYEEAVA 53
                                      568999**************98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.017
                             TPR_4  5 laLArallalGdldeAral 23
                                       + + al alG+ +eA+a 
  gi|386001554|ref|YP_005919853.1| 70 NNKGIALSALGRNEEALAC 88
                                      57799************97 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0044
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       a  +++ +l alG+ deA++  +
  gi|386001554|ref|YP_005919853.1| 102 AWNNRGVVLEALGRGDEALESYD 124
                                       56699*************98665 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.19
                             TPR_4   4 llaLArallalGdld 18 
                                         +L+r l+a+G+++
  gi|386001554|ref|YP_005919853.1| 171 WNNLGRSLFAAGEYE 185
                                       569**********98 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.022
                             TPR_4   6 aLArallalGdldeAraller 26 
                                       + + al  lG++ eA++  e+
  gi|386001554|ref|YP_005919853.1| 207 NKGIALGTLGRHQEALDCYEE 227
                                       6789************99886 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.003
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                        al++ + al +lG+ +eA +  
  gi|386001554|ref|YP_005919853.1| 237 MALYNKGIALGLLGRQEEAVECY 259
                                       699****************9876 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 0.00076
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                        a ++++ al +lG+ ++A+a  
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASY 293
                                       6899***************9965 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.036
                             TPR_4   2 rallaLArallalGdldeAral 23 
                                       +a  +++ al  lG+ +eA++ 
  gi|386001554|ref|YP_005919853.1| 305 QAWNNRGIALGSLGRQEEALQS 326
                                       67889**************985 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.25
                             TPR_4   2 rallaLArallalGdldeA 20 
                                       +a ++++ a  alG++ eA
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEA 357
                                       68899*************9 PP

  == domain 10  score: 6.2 bits;  conditional E-value: 0.047
                             TPR_4   6 aLArallalGdldeAraller 26 
                                       + + al alG++ eA +  er
  gi|386001554|ref|YP_005919853.1| 377 NKGIALSALGRHQEAIECYER 397
                                       6689***********887776 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   3.1e-06    0.0013      71     121 ..      41      91 ..      33      98 .. 0.93
   2 ?    2.0   0.1      0.62   2.6e+02     106     123 ..     110     127 ..      94     140 .. 0.86
   3 !   14.1   0.1   0.00011     0.047      64     123 ..     170     229 ..     161     235 .. 0.92
   4 !   10.8   0.2    0.0012      0.51      74     123 ..     214     263 ..     203     266 .. 0.91
   5 !   19.9   0.7   1.8e-06   0.00078      74     122 ..     282     330 ..     272     333 .. 0.92
   6 !   21.2   0.3   7.4e-07   0.00032      73     123 ..     349     399 ..     341     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-06
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       a+++lGr+eea+a ++++++++P    ++     Al ++Gr++eAL+ Y+r
  gi|386001554|ref|YP_005919853.1|  41 ALSELGRYEEAVASYDNALELDPEYALAWNNKGIALSALGRNEEALACYNR 91 
                                       6789*********************************************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.62
                                       HHHTT-HHHHHHHHHHHH CS
                              BTAD 106 larsGrqaeALevYerlr 123
                                       l ++Gr  eALe Y+r+ 
  gi|386001554|ref|YP_005919853.1| 110 LEALGRGDEALESYDRAL 127
                                       667899999999999975 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       a   l + +++ G++e+ ++ ++++++ +Pl  +++     Al  +Gr +eAL  Ye++ 
  gi|386001554|ref|YP_005919853.1| 170 AWNNLGRSLFAAGEYERSIEGYDEALKIDPLYATAWNNKGIALGTLGRHQEALDCYEEAL 229
                                       56677788999**********************************************985 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.0012
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       +lGr++eal+ +e++++ +P +  +      Al  +Grq+eA e Y+ + 
  gi|386001554|ref|YP_005919853.1| 214 TLGRHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVL 263
                                       799*******************************************9875 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 1.8e-06
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        lGr e+a+a ++++++++P   +++     Al  +Grq+eAL+ Y+r+
  gi|386001554|ref|YP_005919853.1| 282 LLGRQEQAAASYDEALKLDPGYAQAWNNRGIALGSLGRQEEALQSYQRA 330
                                       589********************************************98 PP

  == domain 6  score: 21.2 bits;  conditional E-value: 7.4e-07
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++lGr++ea++ ++++++++P   +++     Al ++Gr +eA+e Yer+ 
  gi|386001554|ref|YP_005919853.1| 349 SALGRYQEAISSYDRALELDPELSEAWNNKGIALSALGRHQEAIECYERAL 399
                                       689*********************************************986 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.18        75      10      60 ..      41      88 ..      32     120 .. 0.52
   2 ?    2.2   0.0      0.47     2e+02       6      29 ..     105     128 ..     100     130 .. 0.87
   3 !   11.3   0.0   0.00074      0.32       6     100 ..     139     228 ..     134     245 .. 0.84
   4 ?   -0.8   0.0       4.2   1.8e+03       4      27 ..     239     262 ..     236     265 .. 0.67
   5 ?    3.3   0.1      0.22        96       3      29 ..     272     298 ..     270     310 .. 0.86
   6 ?    5.7   0.0     0.038        16       6      29 ..     309     332 ..     304     335 .. 0.87
   7 ?    3.6   0.0      0.18        77       2      29 ..     339     366 ..     338     380 .. 0.86
   8 !    8.6   0.0     0.005       2.1       9      34 ..     380     405 ..     372     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.18
                             TPR_5 10 arDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaL 60
                                      a    G+ ++av  Y +aL+          a      +L  lG+ eeala 
  gi|386001554|ref|YP_005919853.1| 41 ALSELGRYEEAVASYDNALELD---PEYALAWNNKGIALSALGRNEEALAC 88
                                      4555555555555555555532...22222222223333344444444444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.47
                             TPR_5   6 eragarDstGhedkavplYrraLa 29 
                                       +r+ + +  G+ d+a + Y raL+
  gi|386001554|ref|YP_005919853.1| 105 NRGVVLEALGRGDEALESYDRALE 128
                                       578888999*************97 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00074
                             TPR_5   6 eragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaL 82 
                                       +++g++ s G+ +++++ Y+raL+    + r r a   L  sL   Ge e++++  ++ l+   d l +       +
  gi|386001554|ref|YP_005919853.1| 139 NQGGVFYSRGDYNRSIECYERALE---IDPRSREAWNNLGRSLFAAGEYERSIEGYDEALK--IDPLYATAWNNKGI 210
                                       57899******************9...59***********************988777665..56677777788889 PP

                             TPR_5  83 vLsdlgrereavsivlla 100
                                       +L  lgr++ea+    +a
  gi|386001554|ref|YP_005919853.1| 211 ALGTLGRHQEALDCYEEA 228
                                       999999999998766555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 4.2
                             TPR_5   4 aFeragarDstGhedkavplYrra 27 
                                       +++++ a    G++++av+ Y   
  gi|386001554|ref|YP_005919853.1| 239 LYNKGIALGLLGRQEEAVECYDAV 262
                                       566666667777888888877665 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.22
                             TPR_5   3 aaFeragarDstGhedkavplYrraLa 29 
                                       a ++r+ a    G++++a+  Y +aL+
  gi|386001554|ref|YP_005919853.1| 272 AWYNRGVALGLLGRQEQAAASYDEALK 298
                                       67899999999**************95 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.038
                             TPR_5   6 eragarDstGhedkavplYrraLa 29 
                                       +r+ a  s G++++a + Y+raL+
  gi|386001554|ref|YP_005919853.1| 309 NRGIALGSLGRQEEALQSYQRALE 332
                                       6888999***************97 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.18
                             TPR_5   2 vaaFeragarDstGhedkavplYrraLa 29 
                                       +a ++++ a+   G+ ++a+  Y raL+
  gi|386001554|ref|YP_005919853.1| 339 QAWYNQGVAFSALGRYQEAISSYDRALE 366
                                       6778889999999999999999999996 PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.005
                             TPR_5   9 garDstGhedkavplYrraLaeGLag 34 
                                        a    G++++a++ Y+raL+ GLa 
  gi|386001554|ref|YP_005919853.1| 380 IALSALGRHQEAIECYERALEVGLAS 405
                                       566778******************86 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.012       5.3       5      33 ..      36      64 ..      34      68 .. 0.89
   2 ?    1.4   0.0      0.79   3.4e+02      14      34 ..      79      99 ..      73     102 .. 0.84
   3 ?    0.2   0.0       1.9   8.1e+02      18      33 ..     117     132 ..     113     135 .. 0.86
   4 !    8.5   0.0    0.0049       2.1      15      37 ..     148     170 ..     145     172 .. 0.91
   5 ?    2.3   0.0      0.42   1.8e+02      15      33 ..     182     200 ..     179     204 .. 0.91
   6 ?    6.0   0.0     0.029        12      14      33 ..     215     234 ..     209     236 .. 0.88
   7 ?    4.5   0.0     0.088        38       4      33 ..     239     268 ..     237     273 .. 0.84
   8 ?    0.8   0.1       1.2   5.2e+02      14      37 ..     283     306 ..     272     308 .. 0.77
   9 ?    6.0   0.1      0.03        13      14      37 ..     317     340 ..     311     341 .. 0.87
  10 ?    6.8   0.0     0.017       7.1       5      37 ..     342     374 ..     340     376 .. 0.85
  11 ?   -1.6   0.0       7.2   3.1e+03      13      30 ..     384     401 ..     379     402 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  5 YylAlGhyklgeYseArryvdalLeiEPe 33
                                      Y   ++   lg+Y+eA    d  Le++Pe
  gi|386001554|ref|YP_005919853.1| 36 YNKGVALSELGRYEEAVASYDNALELDPE 64
                                      666788999*******************8 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.79
                                      HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPen 34
                                      lg+ +eA+ + ++ Lei+P+ 
  gi|386001554|ref|YP_005919853.1| 79 LGRNEEALACYNRSLEIDPDY 99
                                      777799*************85 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  18 seArryvdalLeiEPe 33 
                                       +eA++  d+ Le++P 
  gi|386001554|ref|YP_005919853.1| 117 DEALESYDRALEVDPA 132
                                       6899999*******96 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0049
                                       T-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQa 37 
                                       g+Y+++ ++ ++ Lei+P+ r a
  gi|386001554|ref|YP_005919853.1| 148 GDYNRSIECYERALEIDPRSREA 170
                                       8*****************99887 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.42
                                       T-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPe 33 
                                       geY+++ +  d  L+i+P 
  gi|386001554|ref|YP_005919853.1| 182 GEYERSIEGYDEALKIDPL 200
                                       8****************95 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.029
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+++eA+ + +  L+iEP+
  gi|386001554|ref|YP_005919853.1| 215 LGRHQEALDCYEEALKIEPS 234
                                       89*****************6 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPe 33 
                                       lY   ++   lg+ +eA ++ da+L+++P+
  gi|386001554|ref|YP_005919853.1| 239 LYNKGIALGLLGRQEEAVECYDAVLKVDPS 268
                                       666667777788899**************7 PP

  == domain 8  score: 0.8 bits;  conditional E-value: 1.2
                                       HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                       lg+ ++A    d  L+++P+  Qa
  gi|386001554|ref|YP_005919853.1| 283 LGRQEQAAASYDEALKLDPGYAQA 306
                                       66667888888999*******998 PP

  == domain 9  score: 6.0 bits;  conditional E-value: 0.03
                                       HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                       lg+ +eA++  ++ Lei+P  +Qa
  gi|386001554|ref|YP_005919853.1| 317 LGRQEEALQSYQRALEIDPAYSQA 340
                                       566789*****************8 PP

  == domain 10  score: 6.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                       Y   ++   lg+Y+eA    d+ Le++Pe + a
  gi|386001554|ref|YP_005919853.1| 342 YNQGVAFSALGRYQEAISSYDRALELDPELSEA 374
                                       5666777789******************97765 PP

  == domain 11  score: -1.6 bits;  conditional E-value: 7.2
                                       HHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLei 30 
                                        lg+++eA ++ ++ Le+
  gi|386001554|ref|YP_005919853.1| 384 ALGRHQEAIECYERALEV 401
                                       589999999999999986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0042       1.8       9      33 ..      37      61 ..      33      61 .. 0.88
   2 ?    1.6   0.1      0.68   2.9e+02       9      32 ..      71      94 ..      64      95 .. 0.77
   3 ?    5.0   0.0      0.06        26      10      32 ..     106     128 ..     102     129 .. 0.88
   4 ?    3.2   0.0      0.22        95      17      32 ..     147     162 ..     138     163 .. 0.93
   5 ?    2.0   0.2      0.51   2.2e+02      17      32 ..     181     196 ..     180     197 .. 0.91
   6 ?    6.5   0.0     0.021       8.8      16      32 ..     214     230 ..     202     231 .. 0.80
   7 ?   -0.5   0.0       3.2   1.4e+03      18      28 ..     250     260 ..     238     264 .. 0.76
   8 ?   -1.7   0.0       7.5   3.2e+03      21      32 ..     287     298 ..     277     299 .. 0.65
   9 ?    5.9   0.0     0.032        14      17      32 ..     317     332 ..     308     333 .. 0.84
  10 !    8.4   0.1    0.0051       2.2      14      33 ..     348     367 ..     340     373 .. 0.85
  11 !    7.5   0.1    0.0097       4.2      16      33 ..     384     401 ..     374     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0042
                               MIT  9 kkAveeDnagnyeeAlelYkealel 33
                                      +k v + + g yeeA+  Y +alel
  gi|386001554|ref|YP_005919853.1| 37 NKGVALSELGRYEEAVASYDNALEL 61
                                      678888899**************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.68
                               MIT  9 kkAveeDnagnyeeAlelYkeale 32
                                      +k + +   g  eeAl +Y  +le
  gi|386001554|ref|YP_005919853.1| 71 NKGIALSALGRNEEALACYNRSLE 94
                                      566666667888*********998 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.06
                               MIT  10 kAveeDnagnyeeAlelYkeale 32 
                                       + v ++  g  +eAle Y  ale
  gi|386001554|ref|YP_005919853.1| 106 RGVVLEALGRGDEALESYDRALE 128
                                       67888999999**********98 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.22
                               MIT  17 agnyeeAlelYkeale 32 
                                       +g+y   +e+Y+ ale
  gi|386001554|ref|YP_005919853.1| 147 RGDYNRSIECYERALE 162
                                       699***********98 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.51
                               MIT  17 agnyeeAlelYkeale 32 
                                       ag+ye  +e Y eal+
  gi|386001554|ref|YP_005919853.1| 181 AGEYERSIEGYDEALK 196
                                       89************96 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.021
                               MIT  16 nagnyeeAlelYkeale 32 
                                         g  +eAl++Y+eal+
  gi|386001554|ref|YP_005919853.1| 214 TLGRHQEALDCYEEALK 230
                                       66899**********96 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 3.2
                               MIT  18 gnyeeAlelYk 28 
                                       g  eeA+e+Y 
  gi|386001554|ref|YP_005919853.1| 250 GRQEEAVECYD 260
                                       77899999996 PP

  == domain 8  score: -1.7 bits;  conditional E-value: 7.5
                               MIT  21 eeAlelYkeale 32 
                                       e A   Y eal+
  gi|386001554|ref|YP_005919853.1| 287 EQAAASYDEALK 298
                                       555566666654 PP

  == domain 9  score: 5.9 bits;  conditional E-value: 0.032
                               MIT  17 agnyeeAlelYkeale 32 
                                        g  eeAl+ Y+ ale
  gi|386001554|ref|YP_005919853.1| 317 LGRQEEALQSYQRALE 332
                                       57889*********98 PP

  == domain 10  score: 8.4 bits;  conditional E-value: 0.0051
                               MIT  14 eDnagnyeeAlelYkealel 33 
                                           g y+eA++ Y  alel
  gi|386001554|ref|YP_005919853.1| 348 FSALGRYQEAISSYDRALEL 367
                                       556799************96 PP

  == domain 11  score: 7.5 bits;  conditional E-value: 0.0097
                               MIT  16 nagnyeeAlelYkealel 33 
                                         g  +eA+e+Y+ ale+
  gi|386001554|ref|YP_005919853.1| 384 ALGRHQEAIECYERALEV 401
                                       56889***********95 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.017       7.2      15      72 ..      43     100 ..      33     132 .. 0.61
   2 ?    5.0   0.0     0.023       9.7     204     277 ..     112     185 ..     107     189 .. 0.85
   3 ?    3.6   0.0     0.057        24     205     256 ..     215     266 ..     212     268 .. 0.77
   4 ?    2.3   0.0      0.15        62     206     256 ..     250     300 ..     246     304 .. 0.91
   5 ?    0.2   0.1      0.62   2.7e+02      42      72 ..     308     338 ..     284     351 .. 0.73
   6 !   10.1   0.0   0.00062      0.27     202     253 ..     348     399 ..     332     404 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                                       HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                       +e g++eeA++  +++ +   +     ++k+  l +Lgr+eeA a y++ le  p+  
  gi|386001554|ref|YP_005919853.1|  43 SELGRYEEAVASYDNALELDPEYALAWNNKGIALSALGRNEEALACYNRSLEIDPDYA 100
                                       4555556665555554444444444445666777777777777777777777766654 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.023
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHTT-HH CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcakymLradeve 277
                                        lg+ ++Ale  d+a+e +p     + + + ++   Gd ++ +e+ e+a ++D + R   ++  + ++ a+e+e
  gi|386001554|ref|YP_005919853.1| 112 ALGRGDEALESYDRALEVDPAYALAWSNQGGVFYSRGDYNRSIECYERALEIDPRSREAWNNLGRSLFAAGEYE 185
                                       5677899**********************************************998866666666666666655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.057
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       lg+ ++Al++ ++a++ +p+ v   ++K+  l   G  ++A+e+ +   k+D
  gi|386001554|ref|YP_005919853.1| 215 LGRHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVLKVD 266
                                       5667788888888888888888888888888888888888888877766665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.15
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       g++e+A+e+ d+ ++ +p+    +++++  l   G  ++Aa+  +ea klD
  gi|386001554|ref|YP_005919853.1| 250 GRQEEAVECYDAVLKVDPSYPPAWYNRGVALGLLGRQEQAAASYDEALKLD 300
                                       678899999999999999999999999999999999999999999999999 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.62
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                             NARP1  42 etkaelllkLgrkeeAeatyeaLlernpens 72 
                                       ++++  l  Lgr+eeA + y++ le  p  s
  gi|386001554|ref|YP_005919853.1| 308 NNRGIALGSLGRQEEALQSYQRALEIDPAYS 338
                                       4566677788888888888888888777654 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.00062
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                       +  lg++++A++  d+a+e +p+l e + +K+  l   G  ++A+e+ e+a 
  gi|386001554|ref|YP_005919853.1| 348 FSALGRYQEAISSYDRALELDPELSEAWNNKGIALSALGRHQEAIECYERAL 399
                                       667999****************************************999985 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.022       9.2     191     242 ..      43      94 ..      40      99 .. 0.74
   2 ?    4.6   0.0     0.037        16     147     178 ..     101     132 ..      94     138 .. 0.89
   3 !   12.3   0.0   0.00016      0.07     149     268 ..     137     256 ..     133     264 .. 0.79
   4 ?    1.6   0.1       0.3   1.3e+02     147     180 ..     271     304 ..     248     309 .. 0.81
   5 !   12.2   3.2   0.00018     0.076     146     241 ..     304     399 ..     287     402 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                            TPR_15 191 iDlgrraeLrellkawkaraesdasLwgpl...aaAlllLgrpkkALeylrkqak 242
                                        +lgr++e   +++ + ++ e d+++ ++    + Al++Lgr+++AL+ +++ ++
  gi|386001554|ref|YP_005919853.1|  43 SELGRYEE---AVASYDNALELDPEYALAWnnkGIALSALGRNEEALACYNRSLE 94 
                                       57777775...888888888777666554422278999*********99999876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.037
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapd 178
                                         +  r+ + ++ g+ d+Al+ y +Al+++p+
  gi|386001554|ref|YP_005919853.1| 101 PAWNNRGVVLEALGRGDEALESYDRALEVDPA 132
                                       56888999999*******************98 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00016
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaa 222
                                       ++  + +   +g+ ++++++y++Al+ +p s e+ ++l   l  +g+++     ++ + ++       a+ w+  + 
  gi|386001554|ref|YP_005919853.1| 137 WSNQGGVFYSRGDYNRSIECYERALEIDPRSREAWNNLGRSLFAAGEYER---SIEGYDEALkidPLYATAWNNKGI 210
                                       555555666789999*********************99888888887774...677777666333555667888899 PP

                            TPR_15 223 AlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAw 268
                                       Al +Lgr ++AL+ ++  +k +++ ++ l     al   gr++eA 
  gi|386001554|ref|YP_005919853.1| 211 ALGTLGRHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAV 256
                                       ********************99999888777777777777777775 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.3
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdss 180
                                         ++ r+ +    g++++A   y eAl+l+p+ +
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASYDEALKLDPGYA 304
                                       5677777777778999999999999999999865 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00018
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdssel..raallWlliDlgrraeLrellkawkaraesdasLwgpl 220
                                       a+ +  r+ +    g++++Al+ y++Al+ +p+ s++   ++  +  +  gr++e   +++ + ++ e d++L ++ 
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQAwyNQGVAFSAL--GRYQE---AISSYDRALELDPELSEAW 375
                                       66788888888899*******************999833455666655..99996...9*****9998888887776 PP

                            TPR_15 221 ...aaAlllLgrpkkALeylrkqa 241
                                          + Al++Lgr ++A e +++ +
  gi|386001554|ref|YP_005919853.1| 376 nnkGIALSALGRHQEAIECYERAL 399
                                       44479*************999865 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.036        15      29      78 ..      38      88 ..      20      92 .. 0.60
   2 !   14.2   0.0   8.9e-05     0.038      11      76 ..     122     188 ..     111     197 .. 0.76
   3 ?    6.1   0.1      0.03        13      36      80 ..     215     260 ..     204     262 .. 0.90
   4 !   11.4   0.6   0.00065      0.28      11      81 ..     326     397 ..     316     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                                      HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3 29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78
                                      ++ +l ++g+y++A   +++a +l+++   ++  ++ +l +L++ eeA+a+
  gi|386001554|ref|YP_005919853.1| 38 KGVALSELGRYEEAVASYDNAlELDPEYALAWNNKGIALSALGRNEEALAC 88
                                      255555666666666666666666666666666666666666666666665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.9e-05
                                       HHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3  11 laerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                        ++r+l  e + ++++ +   + ++y++g+y+r +e +++a +++++s +++  ++++l++ ++ye  i
  gi|386001554|ref|YP_005919853.1| 122 SYDRAL--EVDPAYALAWsnQGGVFYSRGDYNRSIECYERAlEIDPRSREAWNNLGRSLFAAGEYERSI 188
                                       555555..4444444445334789999999999999999999999999999999999999999998655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.03
                                       TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +g++++A++ +++a k+++++  ++y ++ +l  L++ eeA+ +++
  gi|386001554|ref|YP_005919853.1| 215 LGRHQEALDCYEEAlKIEPSHVMALYNKGIALGLLGRQEEAVECYD 260
                                       689999********************99999999999999998876 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00065
                                       HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        + r+l+ ++  +++ y  + ++  +g+y++A+  +++a +l+++  +++  ++ +l +L++++eAi ++e+
  gi|386001554|ref|YP_005919853.1| 326 SYQRALEIDPAYSQAWYNQGVAFSALGRYQEAISSYDRAlELDPELSEAWNNKGIALSALGRHQEAIECYER 397
                                       55555644444444555558888899******************************************9986 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.012         5     207     256 ..      38      87 ..      25      98 .. 0.86
   2 ?   -1.6   0.0       3.3   1.4e+03     207     240 ..     106     139 ..      95     161 .. 0.84
   3 !    9.7   0.0    0.0012      0.51     170     261 ..     202     296 ..     186     301 .. 0.86
   4 !    9.9   0.0    0.0011      0.46     170     256 ..     304     393 ..     301     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                                       HHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 207 kAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       k v+   lgryeeA  +  +aL+ d++++ +  N  +a   lg+++e+ +
  gi|386001554|ref|YP_005919853.1|  38 KGVALSELGRYEEAVASYDNALELDPEYALAWNNKGIALSALGRNEEALA 87 
                                       55666789***********************************9998865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                                       HHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHH CS
                        Coatomer_E 207 kAvvslllgryeeAeslLkeaLdkdakdeetLiN 240
                                       + vv  +lgr +eA ++   aL+ d+ ++ + +N
  gi|386001554|ref|YP_005919853.1| 106 RGVVLEALGRGDEALESYDRALEVDPAYALAWSN 139
                                       566777889999**********999998877666 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0012
                                       HHHHHH..HHH-T.THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                        Coatomer_E 170 Aqawvk..lavgg.ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvv 243
                                       A+aw +  +a g+ ++ q+A+  ++e     +s  + l  k ++  llgr eeA +     L+ d+ ++ +  N  v
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNkgIALGTlGRHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVLKVDPSYPPAWYNRGV 278
                                       677765447889999999999999999998899999999999999999999****9999999999999999999999 PP

                                       HHHHTT--HHHHHHHHHH CS
                        Coatomer_E 244 aaqhlgkdaevsernlsq 261
                                       a  +lg+++++ + + + 
  gi|386001554|ref|YP_005919853.1| 279 ALGLLGRQEQAAASYDEA 296
                                       999999998887766555 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0011
                                       HHHHHH..HHH-T.THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                        Coatomer_E 170 Aqawvk..lavgg.ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvv 243
                                       Aqaw +  +a g+ ++ ++A+  +q   e  +  +     + v+  +lgry+eA s+   aL+ d++  e+  N  +
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNrgIALGSlGRQEEALQSYQRALEIDPAYSQAWYNQGVAFSALGRYQEAISSYDRALELDPELSEAWNNKGI 380
                                       66665433677777777788888887777767777777888899999999999999999999999999999999999 PP

                                       HHHHTT--HHHHH CS
                        Coatomer_E 244 aaqhlgkdaevse 256
                                       a   lg+ +e++e
  gi|386001554|ref|YP_005919853.1| 381 ALSALGRHQEAIE 393
                                       9999999988876 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.018       7.8     234     291 ..      55     105 ..      36     112 .. 0.82
   2 ?    1.1   0.0      0.44   1.9e+02     251     291 ..     106     139 ..     104     142 .. 0.86
   3 ?    5.4   0.0     0.021       8.8     272     303 ..     154     185 ..     145     204 .. 0.86
   4 ?   -2.6   0.0       5.8   2.5e+03     250     284 ..     207     234 ..     195     254 .. 0.74
   5 ?   -2.0   0.0       3.7   1.6e+03     268     291 ..     252     275 ..     248     288 .. 0.88
   6 !    7.7   0.4    0.0042       1.8     245     291 ..     304     343 ..     283     351 .. 0.82
   7 ?    3.0   0.0      0.11        48     256     291 ..     349     377 ..     343     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                                       .........HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 234 ptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                        +n  e+  + a + + kG  ++al++       +ee+l++y ++ eidp+ + aw++
  gi|386001554|ref|YP_005919853.1|  55 YDNALELDPEYALAWNNKGIALSALGR-------NEEALACYNRSLEIDPDYAPAWNN 105
                                       556666666667777889999999999.......9*********************86 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.44
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       +G  +eal++        +e+l+sy +a e+dp  + aw +
  gi|386001554|ref|YP_005919853.1| 106 RGVVLEALGR-------GDEALESYDRALEVDPAYALAWSN 139
                                       5677788888.......79**************99999975 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.021
                                       CHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHH CS
                               FAT 272 lqsysaateidpswykawhtwalfnfevvske 303
                                        ++y +a eidp++ +aw+++++  f + + e
  gi|386001554|ref|YP_005919853.1| 154 IECYERALEIDPRSREAWNNLGRSLFAAGEYE 185
                                       689*******************9999876655 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.8
                                       TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCC CS
                               FAT 250 kkGewqealqkldwseekieeilqsysaateidps 284
                                        kG  +  l++        +e+l++y +a +i ps
  gi|386001554|ref|YP_005919853.1| 207 NKGIALGTLGR-------HQEALDCYEEALKIEPS 234
                                       55555555666.......78999999999988876 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.7
                                       -SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 268 ieeilqsysaateidpswykawht 291
                                       +ee++++y a  ++dps   aw++
  gi|386001554|ref|YP_005919853.1| 252 QEEAVECYDAVLKVDPSYPPAWYN 275
                                       7999************99999986 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0042
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       a++ + +G  + +l++       +ee+lqsy++a eidp   +aw++
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGR-------QEEALQSYQRALEIDPAYSQAWYN 343
                                       5555666666667777.......9*********************87 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.11
                                       CCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 256 ealqkldwseekieeilqsysaateidpswykawht 291
                                       +al++        +e+ +sy +a e+dp++ +aw++
  gi|386001554|ref|YP_005919853.1| 349 SALGR-------YQEAISSYDRALELDPELSEAWNN 377
                                       55555.......789*******************87 PP

>> DUF2799  Protein of unknown function (DUF2799)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         4   1.7e+03       2      25 ..      35      58 ..      34      64 .. 0.87
   2 ?   -1.0   0.0       5.9   2.5e+03       2      26 ..     171     195 ..     170     200 .. 0.87
   3 ?    5.3   0.0     0.062        27       2      45 ..     205     247 ..     204     251 .. 0.83
   4 ?    4.8   0.0     0.087        37       2      26 ..     273     297 ..     272     302 .. 0.92
   5 ?    6.2   0.1     0.032        14       2      41 ..     307     345 ..     306     350 .. 0.78
   6 ?    0.3   0.0       2.3   9.9e+02       2      25 ..     341     364 ..     340     368 .. 0.89
   7 ?   -1.1   0.0         6   2.6e+03       2      25 ..     375     398 ..     374     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 4
                           DUF2799  2 WqqiGyedgaaGktasrleelaka 25
                                      W++ G++    G+ ++ ++++ +a
  gi|386001554|ref|YP_005919853.1| 35 WYNKGVALSELGRYEEAVASYDNA 58
                                      999****99999999999999887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.9
                           DUF2799   2 WqqiGyedgaaGktasrleelakac 26 
                                       W+++G +  aaG+ ++++e + +a 
  gi|386001554|ref|YP_005919853.1| 171 WNNLGRSLFAAGEYERSIEGYDEAL 195
                                       9999999999999999999998876 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.062
                           DUF2799   2 WqqiGyedgaaGktasrleelakacakagvkpdaaaYekGykeG 45 
                                       W++ G++ g+ G++++ l+ + +a + +  +  +a Y+kG + G
  gi|386001554|ref|YP_005919853.1| 205 WNNKGIALGTLGRHQEALDCYEEALKIE-PSHVMALYNKGIALG 247
                                       *********************9998754.346678888887766 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.087
                           DUF2799   2 WqqiGyedgaaGktasrleelakac 26 
                                       W+++G++ g  G++++ ++++ +a 
  gi|386001554|ref|YP_005919853.1| 273 WYNRGVALGLLGRQEQAAASYDEAL 297
                                       ******************9999876 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.032
                           DUF2799   2 WqqiGyedgaaGktasrleelakacakagvkpdaaaYekG 41 
                                       W+++G++ g+ G++++ l+++++a +       +a Y++G
  gi|386001554|ref|YP_005919853.1| 307 WNNRGIALGSLGRQEEALQSYQRALEIDPA-YSQAWYNQG 345
                                       *********************998764332.444555555 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 2.3
                           DUF2799   2 WqqiGyedgaaGktasrleelaka 25 
                                       W++ G++  a G+ ++ ++++ +a
  gi|386001554|ref|YP_005919853.1| 341 WYNQGVAFSALGRYQEAISSYDRA 364
                                       ***************999999876 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 6
                           DUF2799   2 WqqiGyedgaaGktasrleelaka 25 
                                       W++ G++  a G++++ +e + +a
  gi|386001554|ref|YP_005919853.1| 375 WNNKGIALSALGRHQEAIECYERA 398
                                       9999**99999*999999888765 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       0.6   2.6e+02       9      27 ..      93     111 ..      90     112 .. 0.80
   2 ?    3.2   0.0      0.18        76       6      21 ..     158     173 ..     158     174 .. 0.89
   3 ?    0.3   0.1       1.5   6.5e+02       7      20 ..     193     206 ..     192     207 .. 0.88
   4 ?    0.4   0.0       1.4   6.1e+02       8      22 ..     262     276 ..     260     278 .. 0.89
   5 ?    6.1   0.0     0.022       9.3       7      22 ..     295     310 ..     294     310 .. 0.93
   6 ?    1.1   0.1      0.84   3.6e+02       7      20 ..     329     342 ..     328     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.6
                                       HHH-TT-CHHHHHHHHHHC CS
                              PPTA   9 iekdpkNYsaWnyRrwlle 27 
                                       +e dp+   aWn R  +le
  gi|386001554|ref|YP_005919853.1|  93 LEIDPDYAPAWNNRGVVLE 111
                                       677888888*****87776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                                       HHHHHH-TT-CHHHHH CS
                              PPTA   6 ekliekdpkNYsaWny 21 
                                       e ++e dp++  aWn 
  gi|386001554|ref|YP_005919853.1| 158 ERALEIDPRSREAWNN 173
                                       5799**********96 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.5
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                       ++++ dp   +aWn
  gi|386001554|ref|YP_005919853.1| 193 EALKIDPLYATAWN 206
                                       78999**999***9 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.4
                                       HHHH-TT-CHHHHHH CS
                              PPTA   8 liekdpkNYsaWnyR 22 
                                       +++ dp+   aW+ R
  gi|386001554|ref|YP_005919853.1| 262 VLKVDPSYPPAWYNR 276
                                       68999********98 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.022
                                       HHHHH-TT-CHHHHHH CS
                              PPTA   7 kliekdpkNYsaWnyR 22 
                                       +++++dp   +aWn R
  gi|386001554|ref|YP_005919853.1| 295 EALKLDPGYAQAWNNR 310
                                       799***********99 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.84
                                       HHHHH-TT-CHHHH CS
                              PPTA   7 kliekdpkNYsaWn 20 
                                        ++e dp   +aW+
  gi|386001554|ref|YP_005919853.1| 329 RALEIDPAYSQAWY 342
                                       6899*********8 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.81   3.5e+02      31      63 ..      61      93 ..      35      99 .. 0.73
   2 ?   -1.6   0.0       4.4   1.9e+03      31      64 ..      95     128 ..      89     132 .. 0.82
   3 ?    3.1   0.0      0.16        67      31      64 ..     129     162 ..     104     164 .. 0.80
   4 ?    0.4   0.0       1.1   4.6e+02      33      63 ..     165     195 ..     161     198 .. 0.88
   5 ?    3.2   0.0      0.15        64      35      85 ..     201     249 ..     180     264 .. 0.74
   6 ?    1.8   0.0      0.41   1.8e+02      23      64 ..     324     366 ..     316     368 .. 0.80
   7 ?    5.2   0.1     0.037        16      20      64 ..     355     400 ..     339     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.81
                                      -HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7 31 gkeeirrakldlaehYlkigdleeAlkaysrir 63
                                       + e + a+++++      g  eeAl++y+r +
  gi|386001554|ref|YP_005919853.1| 61 LDPEYALAWNNKGIALSALGRNEEALACYNRSL 93
                                      455667777788888888899999999999865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                                       -HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  31 gkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       ++ + + a+++++      g  +eAl+ y r++e
  gi|386001554|ref|YP_005919853.1|  95 IDPDYAPAWNNRGVVLEALGRGDEALESYDRALE 128
                                       6667777888888888999999********9986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                                       -HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  31 gkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       ++   + a+ + +  +++ gd++ ++++y+r++e
  gi|386001554|ref|YP_005919853.1| 129 VDPAYALAWSNQGGVFYSRGDYNRSIECYERALE 162
                                       5556667778888899***************986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysrir 63 
                                          r+a+++l++  + +g++e +++ y +++
  gi|386001554|ref|YP_005919853.1| 165 PRSREAWNNLGRSLFAAGEYERSIEGYDEAL 195
                                       567999*******************999976 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHH CS
                              RPN7  35 irrakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaif 85 
                                        + a+++++    + g ++eAl +y+++++  + ++h++ ++ + i +++ 
  gi|386001554|ref|YP_005919853.1| 201 YATAWNNKGIALGTLGRHQEALDCYEEALK--IEPSHVMALYNKGIALGLL 249
                                       5677777888888999***********975..6677888888777777765 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.41
                                       HHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  23 lkdak.enlgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       l+ ++   +++    +a+++ +  +   g ++eA+  y r++e
  gi|386001554|ref|YP_005919853.1| 324 LQSYQrALEIDPAYSQAWYNQGVAFSALGRYQEAISSYDRALE 366
                                       55555456677788899999999999999*******9999876 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.037
                                       HHHHHHHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  20 daelkdak.enlgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       ++ +  +    + + e  +a+++++      g ++eA+++y+r++e
  gi|386001554|ref|YP_005919853.1| 355 QEAISSYDrALELDPELSEAWNNKGIALSALGRHQEAIECYERALE 400
                                       5555555545566778889999999999999************987 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.2   4.9e+02      21      35 ..      45      59 ..      36      65 .. 0.81
   2 ?    3.2   0.0      0.25   1.1e+02      16      34 ..      74      92 ..      64      98 .. 0.81
   3 ?   -1.2   0.0       5.8   2.5e+03      20      35 ..     146     161 ..     134     164 .. 0.83
   4 ?    1.1   0.0       1.1   4.6e+02      17      33 ..     177     193 ..     167     198 .. 0.82
   5 ?    0.0   0.0       2.4     1e+03      20      36 ..     214     230 ..     199     245 .. 0.71
   6 ?    2.9   0.0      0.29   1.2e+02      20      36 ..     350     366 ..     343     376 .. 0.82
   7 !    8.6   0.1    0.0049       2.1      14      48 ..     378     413 ..     369     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                         NRBF2_MIT 21 aGkyeeaischkkaa 35
                                       G+yeea++ +  a 
  gi|386001554|ref|YP_005919853.1| 45 LGRYEEAVASYDNAL 59
                                      69******9988775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.25
                         NRBF2_MIT 16 drllaaGkyeeaischkka 34
                                        l a G+ eea++c++++
  gi|386001554|ref|YP_005919853.1| 74 IALSALGRNEEALACYNRS 92
                                      567899*********9876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.8
                         NRBF2_MIT  20 aaGkyeeaischkkaa 35 
                                       + G y+ +i c+++a 
  gi|386001554|ref|YP_005919853.1| 146 SRGDYNRSIECYERAL 161
                                       6799********9986 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.1
                         NRBF2_MIT  17 rllaaGkyeeaischkk 33 
                                        l+aaG ye +i  +  
  gi|386001554|ref|YP_005919853.1| 177 SLFAAGEYERSIEGYDE 193
                                       589*******9987665 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 2.4
                         NRBF2_MIT  20 aaGkyeeaischkkaaa 36 
                                       + G+++ea+ c++ a +
  gi|386001554|ref|YP_005919853.1| 214 TLGRHQEALDCYEEALK 230
                                       45777777777776643 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.29
                         NRBF2_MIT  20 aaGkyeeaischkkaaa 36 
                                       a G+y+eais + +a +
  gi|386001554|ref|YP_005919853.1| 350 ALGRYQEAISSYDRALE 366
                                       78*********999876 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0049
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaaay.lseamkltkse 48 
                                       k   l a G+++eai c+++a ++ l+ a +ltk++
  gi|386001554|ref|YP_005919853.1| 378 KGIALSALGRHQEAIECYERALEVgLASAGNLTKAD 413
                                       55668899*************886599999999975 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.62   2.6e+02      27      85 ..      71     127 ..      40     128 .. 0.64
   2 ?    4.5   0.0       0.1        43       7      52 ..     153     198 ..     149     208 .. 0.86
   3 ?    2.2   0.0      0.53   2.2e+02       6      52 ..     220     266 ..     216     279 .. 0.84
   4 ?    4.9   0.1     0.075        32       5      43 ..     321     359 ..     317     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.62
                            TPR_20  27 dlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyRrkL 85 
                                       +   al a gr+eeAl+   + l+ d ++    a +    ++ealg +d++ + y r L
  gi|386001554|ref|YP_005919853.1|  71 NKGIALSALGRNEEALACYNRSLEIDPDY--APAWNNRGVVLEALGRGDEALESYDRAL 127
                                       44456677778888887777777777777..4445555557888888888877776665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.1
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       +++  e+al+ +p   +a  +l + l+aag+ye ++e   e lk d
  gi|386001554|ref|YP_005919853.1| 153 SIECYERALEIDPRSREAWNNLGRSLFAAGEYERSIEGYDEALKID 198
                                       67778999**************************999766666665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.53
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       + l+  e+al+ +p+ + a ++   al   gr+eeA+e   ++lk d
  gi|386001554|ref|YP_005919853.1| 220 EALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVLKVD 266
                                       567778999***************************99766666655 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.075
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       ++ l++ ++al+ +p+  +a ++   a  a gry+eA++
  gi|386001554|ref|YP_005919853.1| 321 EEALQSYQRALEIDPAYSQAWYNQGVAFSALGRYQEAIS 359
                                       5778999******************************97 PP

>> EST1_DNA_bind  Est1 DNA/RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.14        58       3      55 ..      87     139 ..      85     182 .. 0.48
   2 ?    3.5   0.5     0.097        41       1      55 [.     289     343 ..     289     351 .. 0.90
   3 !    8.2   0.0    0.0036       1.5       1      43 [.     357     399 ..     357     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                                       HHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHHHHHHHBSB--TTHHHH CS
                     EST1_DNA_bind   3 rYYllAaellPsnGepyNQlgviaiysedkldavYyylRSllssnpfptAkeN 55 
                                        +Y++  e+ P++  + N  gv+  + ++  +a   y R+l ++  +  A++N
  gi|386001554|ref|YP_005919853.1|  87 ACYNRSLEIDPDYAPAWNNRGVVLEALGRGDEALESYDRALEVDPAYALAWSN 139
                                       55555555555555555555555555544444444444444333333333333 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHHHHHHHBSB--TTHHHH CS
                     EST1_DNA_bind   1 AlrYYllAaellPsnGepyNQlgviaiysedkldavYyylRSllssnpfptAkeN 55 
                                       A+  Y++A +l P++ ++ N  g+   + +++ +a   y R+l  +  +++A+ N
  gi|386001554|ref|YP_005919853.1| 289 AAASYDEALKLDPGYAQAWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQAWYN 343
                                       6778***************************************998888999888 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                     EST1_DNA_bind   1 AlrYYllAaellPsnGepyNQlgviaiysedkldavYyylRSl 43 
                                       A++ Y++A el P++ e+ N  g+   + +++ +a+ +y R+l
  gi|386001554|ref|YP_005919853.1| 357 AISSYDRALELDPELSEAWNNKGIALSALGRHQEAIECYERAL 399
                                       7899*************************************99 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.8   1.2e+03       9      20 ..      41      52 ..      41      59 .. 0.84
   2 ?    0.9   0.0       1.6   6.9e+02       9      25 ..      75      91 ..      74      95 .. 0.84
   3 ?   -1.0   0.0       6.7   2.8e+03      13      25 ..     113     125 ..     110     128 .. 0.81
   4 ?    1.5   0.0         1   4.3e+02       2      25 ..     170     193 ..     169     197 .. 0.87
   5 ?    3.3   0.0      0.27   1.2e+02      10      25 ..     212     227 ..     210     231 .. 0.83
   6 ?    0.4   0.0       2.3     1e+03       9      25 ..     347     363 ..     347     368 .. 0.80
   7 ?    4.3   0.0      0.13        56       9      30 ..     381     402 ..     380     412 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.8
                               PPR  9 gycknGkleeAl 20
                                      +++  G++eeA+
  gi|386001554|ref|YP_005919853.1| 41 ALSELGRYEEAV 52
                                      57889******8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.6
                               PPR  9 gycknGkleeAlelfke 25
                                      +++  G+ eeAl ++++
  gi|386001554|ref|YP_005919853.1| 75 ALSALGRNEEALACYNR 91
                                      6788999*****99987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 6.7
                               PPR  13 nGkleeAlelfke 25 
                                        G+ +eAle +++
  gi|386001554|ref|YP_005919853.1| 113 LGRGDEALESYDR 125
                                       5999***997765 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1
                               PPR   2 tynslIsgycknGkleeAlelfke 25 
                                       ++n l +++  +G++e  +e ++e
  gi|386001554|ref|YP_005919853.1| 170 AWNNLGRSLFAAGEYERSIEGYDE 193
                                       69**************99987777 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.27
                               PPR  10 ycknGkleeAlelfke 25 
                                       ++  G+++eAl++++e
  gi|386001554|ref|YP_005919853.1| 212 LGTLGRHQEALDCYEE 227
                                       6678**********99 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 2.3
                               PPR   9 gycknGkleeAlelfke 25 
                                       +++  G+++eA++ +++
  gi|386001554|ref|YP_005919853.1| 347 AFSALGRYQEAISSYDR 363
                                       67889******997776 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.13
                               PPR   9 gycknGkleeAlelfkeMkekG 30 
                                       +++  G+++eA+e++++ +e G
  gi|386001554|ref|YP_005919853.1| 381 ALSALGRHQEAIECYERALEVG 402
                                       67889**********9977766 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       7.7   3.3e+03      31      44 ..     115     128 ..     111     134 .. 0.78
   2 ?   -0.4   0.0       3.5   1.5e+03      35      55 ..     153     173 ..     149     183 .. 0.82
   3 ?    0.3   0.0       2.1   8.8e+02      30      46 ..     216     232 ..     213     238 .. 0.85
   4 ?   -0.4   0.0       3.5   1.5e+03      30      46 ..     250     266 ..     248     274 .. 0.83
   5 ?   -1.1   0.1       5.7   2.4e+03      30      45 ..     318     333 ..     316     346 .. 0.79
   6 ?    6.2   0.0     0.029        12      29      51 ..     385     407 ..     382     422 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7.7
                              YnfE  31 kqkeqlelYekqLk 44 
                                       +  e le Y++ L+
  gi|386001554|ref|YP_005919853.1| 115 RGDEALESYDRALE 128
                                       56789999999986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.5
                              YnfE  35 qlelYekqLkqesssdedfDe 55 
                                        +e Ye+ L+ +  s e +++
  gi|386001554|ref|YP_005919853.1| 153 SIECYERALEIDPRSREAWNN 173
                                       69*******998888887766 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.1
                              YnfE  30 ekqkeqlelYekqLkqe 46 
                                        +++e l+ Ye  Lk e
  gi|386001554|ref|YP_005919853.1| 216 GRHQEALDCYEEALKIE 232
                                       6899**********976 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.5
                              YnfE  30 ekqkeqlelYekqLkqe 46 
                                        +q+e +e Y+  Lk +
  gi|386001554|ref|YP_005919853.1| 250 GRQEEAVECYDAVLKVD 266
                                       58999******999965 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 5.7
                              YnfE  30 ekqkeqlelYekqLkq 45 
                                        +q+e l  Y++ L+ 
  gi|386001554|ref|YP_005919853.1| 318 GRQEEALQSYQRALEI 333
                                       689999****999975 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.029
                              YnfE  29 lekqkeqlelYekqLkqesssde 51 
                                       l +++e +e Ye+ L+ + +s+ 
  gi|386001554|ref|YP_005919853.1| 385 LGRHQEAIECYERALEVGLASAG 407
                                       5689***********99988764 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.85   3.6e+02      13      37 ..      37      61 ..      33      79 .. 0.82
   2 ?   -0.9   0.1         3   1.3e+03      17      40 ..      68      91 ..      55     107 .. 0.61
   3 ?   -0.7   0.0       2.6   1.1e+03      10      36 ..     136     162 ..     123     164 .. 0.74
   4 ?    2.5   0.0      0.26   1.1e+02       9      36 ..     169     196 ..     165     201 .. 0.91
   5 ?    5.5   0.1     0.032        14       8      48 ..     202     242 ..     191     261 .. 0.80
   6 ?    1.8   0.1      0.44   1.9e+02       8      48 ..     304     344 ..     293     356 .. 0.80
   7 ?    2.3   0.1       0.3   1.3e+02       8      36 ..     338     366 ..     327     370 .. 0.79
   8 ?    0.9   0.0      0.81   3.5e+02       8      36 ..     372     400 ..     361     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.85
                           DUF5113 13 nlayylnvegeyeeALeyldsaley 37
                                      n + +l   g+yeeA++  d+ale+
  gi|386001554|ref|YP_005919853.1| 37 NKGVALSELGRYEEAVASYDNALEL 61
                                      5667777889************985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                           DUF5113 17 ylnvegeyeeALeyldsaleylNa 40
                                      + n +g   +AL   ++al + N+
  gi|386001554|ref|YP_005919853.1| 68 AWNNKGIALSALGRNEEALACYNR 91
                                      345555555555555555555554 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.6
                           DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                       ++ n +   + +g+y++++e+ + ale
  gi|386001554|ref|YP_005919853.1| 136 AWSNQGGVFYSRGDYNRSIECYERALE 162
                                       455777778889999999999999987 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.26
                           DUF5113   9 ndYanlayylnvegeyeeALeyldsale 36 
                                       +++ nl+  l++ geye+++e  d+al+
  gi|386001554|ref|YP_005919853.1| 169 EAWNNLGRSLFAAGEYERSIEGYDEALK 196
                                       578899********************97 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.032
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakk 48 
                                       a ++ n + +l + g+++eAL++ ++al++   h +  ++k
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNKGIALGTLGRHQEALDCYEEALKIEPSHVMALYNK 242
                                       56677888899999***************988888776665 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.44
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakk 48 
                                       a+++ n + +l   g+ eeAL+  + ale+  a+ + ++++
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQAWYNQ 344
                                       66777788888889999**********99887777777765 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.3
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       ++++ n + +  + g+y+eA++  d ale
  gi|386001554|ref|YP_005919853.1| 338 SQAWYNQGVAFSALGRYQEAISSYDRALE 366
                                       45566777778889999999999999997 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.81
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       ++++ n + +l + g+++eA+e+ + ale
  gi|386001554|ref|YP_005919853.1| 372 SEAWNNKGIALSALGRHQEAIECYERALE 400
                                       67888999999999***********9997 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0084       3.6       4      35 ..     132     162 ..     132     164 .. 0.82
   2 ?    4.1   0.0       0.2        84      24      35 ..     389     400 ..     385     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0084
                              Sel1   4 myrLGmfylylnGlgvpk.DpekAiewyekAAe 35 
                                       +y+L+     + G    + D+++ ie+ye+A e
  gi|386001554|ref|YP_005919853.1| 132 AYALA--WSNQGGVFYSRgDYNRSIECYERALE 162
                                       58888..877777776678************65 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.2
                              Sel1  24 ekAiewyekAAe 35 
                                       ++Aie+ye+A e
  gi|386001554|ref|YP_005919853.1| 389 QEAIECYERALE 400
                                       79********76 PP

>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.5   6.3e+02      12      25 ..      46      59 ..      38      61 .. 0.85
   2 ?    4.1   0.0     0.085        36       7      25 ..     109     127 ..     105     129 .. 0.87
   3 ?    1.7   0.0      0.45   1.9e+02      11      25 ..     215     229 ..     207     231 .. 0.87
   4 ?   -0.7   0.1       2.5   1.1e+03      12      25 ..     284     297 ..     281     299 .. 0.89
   5 ?   -0.6   0.0       2.5   1.1e+03      11      25 ..     317     331 ..     312     333 .. 0.87
   6 ?   -0.4   0.0       2.1   8.9e+02       9      25 ..     349     365 ..     345     367 .. 0.87
   7 ?    3.5   0.1      0.13        55       8      35 ..     382     409 ..     377     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                          PvlArgDC 12 geskeelasFdlAL 25
                                      g+ +e++as+d+AL
  gi|386001554|ref|YP_005919853.1| 46 GRYEEAVASYDNAL 59
                                      788899*******9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.085
                          PvlArgDC   7 ltkGvgeskeelasFdlAL 25 
                                       + ++ g+++e+l+s+d AL
  gi|386001554|ref|YP_005919853.1| 109 VLEALGRGDEALESYDRAL 127
                                       56789*************9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.45
                          PvlArgDC  11 vgeskeelasFdlAL 25 
                                        g+++e+l ++++AL
  gi|386001554|ref|YP_005919853.1| 215 LGRHQEALDCYEEAL 229
                                       69************9 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.5
                          PvlArgDC  12 geskeelasFdlAL 25 
                                       g+++++ as+d+AL
  gi|386001554|ref|YP_005919853.1| 284 GRQEQAAASYDEAL 297
                                       889999*******9 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.5
                          PvlArgDC  11 vgeskeelasFdlAL 25 
                                        g+++e+l+s+  AL
  gi|386001554|ref|YP_005919853.1| 317 LGRQEEALQSYQRAL 331
                                       6999**********9 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 2.1
                          PvlArgDC   9 kGvgeskeelasFdlAL 25 
                                       ++ g+ +e++ s+d AL
  gi|386001554|ref|YP_005919853.1| 349 SALGRYQEAISSYDRAL 365
                                       57899999********9 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.13
                          PvlArgDC   8 tkGvgeskeelasFdlALldAgIenfNL 35 
                                        ++ g+++e++++++ AL  +  +  NL
  gi|386001554|ref|YP_005919853.1| 382 LSALGRHQEAIECYERALEVGLASAGNL 409
                                       5789**************8665555555 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.33   1.4e+02     127     174 ..      46      94 ..      40     102 .. 0.65
   2 ?    3.3   0.1      0.14        60     150     175 ..     104     129 ..      76     140 .. 0.86
   3 ?   -0.2   0.0       1.6   6.9e+02     158     175 ..     112     129 ..     109     178 .. 0.61
   4 ?    0.7   0.0      0.83   3.6e+02     146     175 ..     202     231 ..     170     241 .. 0.77
   5 ?    3.7   1.1       0.1        43     146     175 ..     304     333 ..     278     346 .. 0.74
   6 ?    5.2   0.1     0.037        16     140     180 ..     371     406 ..     343     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                            TPR_21 127 kkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       + y+eA++  +++ e +   al+ + +G +l+a g+++eA a Y+++l+
  gi|386001554|ref|YP_005919853.1|  46 GRYEEAVASYDNALElDPEYALAWNNKGIALSALGRNEEALACYNRSLE 94 
                                       4555555555443321222355566788899999999999999988876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaa 175
                                       + rG +l a g+ deA + Y++Al+ 
  gi|386001554|ref|YP_005919853.1| 104 NNRGVVLEALGRGDEALESYDRALEV 129
                                       46999******************985 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.6
                            TPR_21 158 aqgkldeAraaYqaAlaa 175
                                       a g+ deA + Y++Al+ 
  gi|386001554|ref|YP_005919853.1| 112 ALGRGDEALESYDRALEV 129
                                       555556666666666543 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.83
                            TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       a + + +G +l   g+ +eA + Y++Al+ 
  gi|386001554|ref|YP_005919853.1| 202 ATAWNNKGIALGTLGRHQEALDCYEEALKI 231
                                       55667789999999*************975 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.1
                            TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       a++ + rG +l + g+++eA + Yq+Al+ 
  gi|386001554|ref|YP_005919853.1| 304 AQAWNNRGIALGSLGRQEEALQSYQRALEI 333
                                       34446799999****************985 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.037
                            TPR_21 140 keeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                        +ea+     + +G +l+a g+ +eA + Y++Al+ + ++a
  gi|386001554|ref|YP_005919853.1| 371 LSEAW-----NNKGIALSALGRHQEAIECYERALEVGLASA 406
                                       44444.....4589999****************98776665 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.22        93      62     105 ..     153     196 ..     118     198 .. 0.73
   2 ?    2.3   0.0      0.39   1.7e+02      61      96 ..     220     255 ..     217     270 .. 0.79
   3 ?    1.8   0.0      0.54   2.3e+02      62     104 ..     323     365 ..     279     368 .. 0.65
   4 ?   -0.5   0.0       2.8   1.2e+03      61      83 ..     390     412 ..     387     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.22
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLs 105
                                       s+ec+++a e+   + +   +l++ l    +Y+ +++   +aL+
  gi|386001554|ref|YP_005919853.1| 153 SIECYERALEIDPRSREAWNNLGRSLFAAGEYERSIEGYDEALK 196
                                       89999999999955555555555555555555555555555554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.39
                            DUF627  61 asvecfseavelsrfyArsLfelasqlgsklyYkka 96 
                                        +++c++ea ++   + + L++ +  lg     ++a
  gi|386001554|ref|YP_005919853.1| 220 EALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEA 255
                                       699**********99999999988777765555555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.54
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraL 104
                                       +++++++a e+   y +  ++ +  +     Y++a+++  raL
  gi|386001554|ref|YP_005919853.1| 323 ALQSYQRALEIDPAYSQAWYNQGVAFSALGRYQEAISSYDRAL 365
                                       5566666666666666666666666666666666666666665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.8
                            DUF627  61 asvecfseavelsrfyArsLfel 83 
                                        ++ec+++a e+   +A  L ++
  gi|386001554|ref|YP_005919853.1| 390 EAIECYERALEVGLASAGNLTKA 412
                                       69*******99998888888765 PP

>> APP_E2  E2 domain of amyloid precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.6   2.8e+03     110     126 ..      81      97 ..      74     102 .. 0.84
   2 ?   -0.7   0.0       2.3   9.6e+02     113     162 ..     152     199 ..     149     211 .. 0.72
   3 ?    6.1   0.0     0.019       8.2      76     127 ..     217     268 ..     189     275 .. 0.91
   4 ?    0.4   0.0       1.1   4.7e+02     106     124 ..     383     401 ..     321     412 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.6
                            APP_E2 110 krrkalekylqalqeep 126
                                       ++++al +y ++l+ +p
  gi|386001554|ref|YP_005919853.1|  81 RNEEALACYNRSLEIDP 97 
                                       7899********98776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                            APP_E2 113 kalekylqalqeeppnaerilkaLkkllraeqkdrvhtlrhykhllksdp 162
                                        ++e+y +al+ +p + e   +  + l +a + +r  +++ y ++lk+dp
  gi|386001554|ref|YP_005919853.1| 152 RSIECYERALEIDPRSREAWNNLGRSLFAAGEYER--SIEGYDEALKIDP 199
                                       6899******9999988877777677766666665..3566666666655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.019
                            APP_E2  76 rFqetvealEeeaaaerqqLvetHqqrveaalnekrrkalekylqalqeepp 127
                                       r qe ++  Ee  + e   ++++ ++ ++  l  ++++a+e+y + l+ +p 
  gi|386001554|ref|YP_005919853.1| 217 RHQEALDCYEEALKIEPSHVMALYNKGIALGLLGRQEEAVECYDAVLKVDPS 268
                                       889999***************************************9998886 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.1
                            APP_E2 106 alnekrrkalekylqalqe 124
                                       +   ++++a+e+y +al+ 
  gi|386001554|ref|YP_005919853.1| 383 SALGRHQEAIECYERALEV 401
                                       4445777888888888875 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.23        99     127     181 ..      49     104 ..      40     109 .. 0.82
   2 ?   -0.8   0.1       2.8   1.2e+03     153     180 ..     110     137 ..      99     141 .. 0.84
   3 ?    0.5   0.0       1.2   5.1e+02     148     170 ..     207     229 ..     181     242 .. 0.83
   4 ?    2.2   0.0      0.35   1.5e+02     127     180 ..     219     273 ..     209     278 .. 0.70
   5 ?    3.9   0.3       0.1        45     144     181 ..     271     308 ..     250     311 .. 0.82
   6 ?    4.1   3.2     0.091        39     135     180 ..     295     341 ..     286     347 .. 0.77
   7 ?    1.2   0.1      0.71     3e+02     127     169 ..     355     398 ..     349     401 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.23
                           Wzy_C_2 127 aaklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakwv 181
                                       ++ +a + ++++l Pe a+  ++  ++l +lG+ +eA+  + r   + p+++ +w+
  gi|386001554|ref|YP_005919853.1|  49 EEAVASYDNALELDPEYALaWNNKGIALSALGRNEEALACYNRSLEIDPDYAPAWN 104
                                       5667778888888888776257788999**************99999999999995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
                           Wzy_C_2 153 lallGdedeAeqilararalfpeedakw 180
                                       l +lG+ deA+  ++ra  + p+++ +w
  gi|386001554|ref|YP_005919853.1| 110 LEALGRGDEALESYDRALEVDPAYALAW 137
                                       6789*************99988888888 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                           Wzy_C_2 148 rlilslallGdedeAeqilarar 170
                                       +  ++l  lG+++eA++ +++a 
  gi|386001554|ref|YP_005919853.1| 207 NKGIALGTLGRHQEALDCYEEAL 229
                                       55678999**********99986 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.35
                           Wzy_C_2 127 aaklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakw 180
                                       ++ l+ ++++++  P   + +++  ++l llG+++eA   ++ + ++ p +  +w
  gi|386001554|ref|YP_005919853.1| 219 QEALDCYEEALKIEPSHVMaLYNKGIALGLLGRQEEAVECYDAVLKVDPSYPPAW 273
                                       5667777777777776544267777888899999998887777666666666655 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.1
                           Wzy_C_2 144 avierlilslallGdedeAeqilararalfpeedakwv 181
                                          ++  ++l llG++++A+  +++a +l p ++++w+
  gi|386001554|ref|YP_005919853.1| 271 PAWYNRGVALGLLGRQEQAAASYDEALKLDPGYAQAWN 308
                                       5556667899*************************995 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.091
                           Wzy_C_2 135 klihlsPe.pavierlilslallGdedeAeqilararalfpeedakw 180
                                       ++++l P+ ++  ++  ++l  lG+++eA+q ++ra  + p++ ++w
  gi|386001554|ref|YP_005919853.1| 295 EALKLDPGyAQAWNNRGIALGSLGRQEEALQSYQRALEIDPAYSQAW 341
                                       5666666413455677789999*****************99999999 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.71
                           Wzy_C_2 127 aaklalarklihlsPepa.vierlilslallGdedeAeqilara 169
                                       ++ ++ + ++++l Pe     ++  ++l +lG+++eA   ++ra
  gi|386001554|ref|YP_005919853.1| 355 QEAISSYDRALELDPELSeAWNNKGIALSALGRHQEAIECYERA 398
                                       66666677777777774314567778899999999999999887 PP

>> DUF3775  Protein of unknown function (DUF3775)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.4   5.9e+02      20      40 ..      40      60 ..      38      62 .. 0.92
   2 ?    4.3   0.0     0.097        41      20      40 ..     108     128 ..     107     131 .. 0.90
   3 ?    1.9   0.0      0.54   2.3e+02      20      40 ..     278     298 ..     277     310 .. 0.89
   4 ?   -1.1   0.0       4.5   1.9e+03      20      40 ..     346     366 ..     344     378 .. 0.85
   5 ?    1.1   0.0      0.96   4.1e+02      20      43 ..     380     403 ..     369     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.4
                           DUF3775 20 vALmwiGRgdfeaeewdeave 40
                                      vAL  +GR ++++  +d+a+e
  gi|386001554|ref|YP_005919853.1| 40 VALSELGRYEEAVASYDNALE 60
                                      89999**********999986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.097
                           DUF3775  20 vALmwiGRgdfeaeewdeave 40 
                                       v+L  +GRgd++ e +d+a+e
  gi|386001554|ref|YP_005919853.1| 108 VVLEALGRGDEALESYDRALE 128
                                       67889************9986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.54
                           DUF3775  20 vALmwiGRgdfeaeewdeave 40 
                                       vAL  +GR + +a  +dea++
  gi|386001554|ref|YP_005919853.1| 278 VALGLLGRQEQAAASYDEALK 298
                                       8999***********999975 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.5
                           DUF3775  20 vALmwiGRgdfeaeewdeave 40 
                                       vA   +GR +++ + +d+a+e
  gi|386001554|ref|YP_005919853.1| 346 VAFSALGRYQEAISSYDRALE 366
                                       678889***999999999876 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.96
                           DUF3775  20 vALmwiGRgdfeaeewdeaveeAr 43 
                                       +AL  +GR +++ e +++a+e + 
  gi|386001554|ref|YP_005919853.1| 380 IALSALGRHQEAIECYERALEVGL 403
                                       79*********9999999998765 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.8     2e+03      12      20 ..      54      62 ..      53      64 .. 0.88
   2 ?    1.3   0.0       0.7     3e+02      10      20 ..     120     130 ..     117     131 .. 0.87
   3 ?    2.5   0.0      0.28   1.2e+02      10      20 ..     154     164 ..     154     165 .. 0.90
   4 ?   -1.0   0.0       3.5   1.5e+03      10      20 ..     324     334 ..     323     334 .. 0.87
   5 ?    0.3   0.0       1.4   5.8e+02      10      20 ..     358     368 ..     358     371 .. 0.88
   6 ?    3.8   0.1      0.11        46      10      21 ..     392     403 ..     391     406 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.8
                               Sda 12 aYekAleln 20
                                      +Y++Alel+
  gi|386001554|ref|YP_005919853.1| 54 SYDNALELD 62
                                      79****997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.7
                               Sda  10 ieaYekAleln 20 
                                       +e+Y++Ale++
  gi|386001554|ref|YP_005919853.1| 120 LESYDRALEVD 130
                                       7*******975 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.28
                               Sda  10 ieaYekAleln 20 
                                       ie+Ye+Ale +
  gi|386001554|ref|YP_005919853.1| 154 IECYERALEID 164
                                       8*******975 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.5
                               Sda  10 ieaYekAleln 20 
                                       +++Y++Ale +
  gi|386001554|ref|YP_005919853.1| 324 LQSYQRALEID 334
                                       689*****975 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.4
                               Sda  10 ieaYekAleln 20 
                                       i +Y++Alel+
  gi|386001554|ref|YP_005919853.1| 358 ISSYDRALELD 368
                                       679******97 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.11
                               Sda  10 ieaYekAlelnL 21 
                                       ie+Ye+Ale+ L
  gi|386001554|ref|YP_005919853.1| 392 IECYERALEVGL 403
                                       8********987 PP

>> SMG1  Serine/threonine-protein kinase smg-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.091        39     505     527 ..      40      62 ..      24      98 .. 0.73
   2 ?    0.0   0.0      0.49   2.1e+02     505     526 ..     108     129 ..     102     140 .. 0.88
   3 ?   -3.7   0.0       6.5   2.8e+03     511     526 ..     250     265 ..     244     268 .. 0.86
   4 ?   -1.8   0.0       1.7   7.4e+02     511     526 ..     284     299 ..     276     309 .. 0.84
   5 ?   -0.1   0.1      0.53   2.3e+02     509     526 ..     316     333 ..     307     347 .. 0.85
   6 ?    0.9   0.1      0.26   1.1e+02     504     529 ..     345     370 ..     336     397 .. 0.80
   7 ?   -1.8   0.0       1.7   7.4e+02     505     526 ..     380     401 ..     370     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.091
                              SMG1 505 vaeqAaGkfekAaeeykelLkek 527
                                       va    G++e+A+++y + L+ +
  gi|386001554|ref|YP_005919853.1|  40 VALSELGRYEEAVASYDNALELD 62 
                                       66666799999999999988764 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.49
                              SMG1 505 vaeqAaGkfekAaeeykelLke 526
                                       v+ +A G+ ++A+e+y + L+ 
  gi|386001554|ref|YP_005919853.1| 108 VVLEALGRGDEALESYDRALEV 129
                                       7899**************9986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.5
                              SMG1 511 GkfekAaeeykelLke 526
                                       G+ e+A+e y  +Lk 
  gi|386001554|ref|YP_005919853.1| 250 GRQEEAVECYDAVLKV 265
                                       999*****99999986 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.7
                              SMG1 511 GkfekAaeeykelLke 526
                                       G+ e+Aa++y e Lk 
  gi|386001554|ref|YP_005919853.1| 284 GRQEQAAASYDEALKL 299
                                       9***********9985 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.53
                              SMG1 509 AaGkfekAaeeykelLke 526
                                         G+ e+A+++y++ L+ 
  gi|386001554|ref|YP_005919853.1| 316 SLGRQEEALQSYQRALEI 333
                                       57************9985 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.26
                              SMG1 504 avaeqAaGkfekAaeeykelLkekte 529
                                        va  A G++++A+++y + L+ + e
  gi|386001554|ref|YP_005919853.1| 345 GVAFSALGRYQEAISSYDRALELDPE 370
                                       578899*************9987655 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 1.7
                              SMG1 505 vaeqAaGkfekAaeeykelLke 526
                                       +a  A G+ ++A+e y++ L+ 
  gi|386001554|ref|YP_005919853.1| 380 IALSALGRHQEAIECYERALEV 401
                                       78899************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.99u 0.30s 00:00:01.29 Elapsed: 00:00:00.66
# Mc/sec: 2109.62
//
Query:       gi|386001555|ref|YP_005919854.1|  [L=155]
Description: Cytidylyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-17   61.6   0.0    1.1e-16   61.4   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
    0.00022   21.2   0.1    0.00038   20.4   0.0    1.5  2  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
      0.036   14.8   0.0      0.067   13.9   0.0    1.4  1  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   1.8e-20   1.1e-16       2     140 ..       7     142 ..       6     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.8e-20
                                       EEE--TT--HHHHHHHHHHHHHSSES..EEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH. CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleed..livgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltr. 74 
                                       +gGtFDpiH GH++ll++a++  eed  ++++++sd  +k++  +p+ + ++R+++l++a +++     +++e+++ 
  gi|386001555|ref|YP_005919854.1|   7 VGGTFDPIHDGHIALLRKAFEVAEEDgeVVIALTSDGMAKSQRtRPVRNFDTRVRNLRAALKENL--GREDFEIEMl 81 
                                       69****************************************55****************55555..6677777776 PP

                                       .....HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHH CS
                   CTP_transf_like  75 .....evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstki 140
                                            + ++  + d  ++v++ ++   + + +e+++  g  +l +v ++       +  +++   iSst+i
  gi|386001555|ref|YP_005919854.1|  82 htfygSAIE-EDYD--FIVVSPETEPMACNINEIRRENGLSPLKIVMID-------YQLAEDDVRISSTRI 142
                                       577753332.3348..9999999999998999**************999.......888899999****98 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.4e-08   0.00038       9      44 ..       5      40 ..       2      84 .. 0.85
   2 ?   -3.2   0.0       1.2   7.1e+03     146     158 .]     129     141 ..     123     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.4e-08
                           FAD_syn  9 vvtlGnFDGvHlGHqallkkaveaakekglpsvvvt 44
                                      v + G FD +H GH all+ka e a+e+g  ++ +t
  gi|386001555|ref|YP_005919854.1|  5 VAVGGTFDPIHDGHIALLRKAFEVAEEDGEVVIALT 40
                                      556699*********************998877776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                           FAD_syn 146 kveleeekissta 158
                                       ++ +++++isst+
  gi|386001555|ref|YP_005919854.1| 129 QLAEDDVRISSTR 141
                                       4578899999985 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.067      19      76 ..      62     127 ..      59     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHCT....EEEEETTEEGGGHHHHHHT-SEEEEEESSGG.....CTHHHHTT.SEEEEECTT CS
                           PTS_IIB  19 klekaakelg....ieaegeagveleaeeiaddaDlvllapqvrv.....kdlarfag.kpvavinik 76 
                                       +l+ a+ke+     +e+e+ +++    ++i++d+D+++++p+++      +++ r +g  p++++ i+
  gi|386001555|ref|YP_005919854.1|  62 NLRAALKENLgredFEIEMLHTF--YGSAIEEDYDFIVVSPETEPmacniNEIRRENGlSPLKIVMID 127
                                       67888888777888999999999..899999**********999556777788888775466666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1148.18
//
Query:       gi|386001556|ref|YP_005919855.1|  [L=152]
Description: FAD synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-19   70.9   0.0    1.5e-19   70.6   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   8.2e-24   1.5e-19       1     141 [.       5     131 ..       5     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 8.2e-24
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       la GtFD++H GHl +leq k+l++e l+v+v+ d ++++k +p+++ e+Rl m+ ++k v++++  +++++ +  +
  gi|386001556|ref|YP_005919855.1|   5 LATGTFDLLHPGHLMYLEQSKALGDE-LVVIVARDANVQHKPRPIIPQEQRLLMVSALKMVERAVLGSERDMFQ-PI 79 
                                       689***********************.************999*******************************8.** PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                       ++l+pd  ++ +g d++ d+     l+e l+ +++  ++++       l ++ +++ +Ss ki 
  gi|386001556|ref|YP_005919855.1|  80 EELRPD--VITLGYDQHFDA---LLLQEELATRGIGARVVR-------LEEHDPCPLCSSRKIV 131
                                       ******..*******99996...789999999999999888.......9999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1180.18
//
Query:       gi|386001557|ref|YP_005919856.1|  [L=151]
Description: hypothetical protein Mhar_0861 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-07   29.2   0.0    8.8e-07   28.7   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
      0.082   12.9   0.0       0.13   12.3   0.0    1.3  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   9.8e-11   8.8e-07       9     116 ..      32     124 ..      25     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 9.8e-11
                          Prok-JAB   9 vaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkf.earerglevvgiwHSHpggsarP 84 
                                       +++ r++ p E +Gll  +     +++v+ l            +e+s +++     +  ++++ g +HSHp +  rP
  gi|386001557|ref|YP_005919856.1|  32 LEASRSTLPVEFAGLLRAED--GVITEVIMLP----------GTEASSKSALIrLYMLPNMRIAGSVHSHPSPDIRP 96 
                                       56777888889999888876..5555555533..........333333333333788999***************** PP

                          Prok-JAB  85 SetDrrdaaalarvkalliivgdkaeelrawr 116
                                       S++D+  ++++   +  +ii+g  + ++ +w 
  gi|386001557|ref|YP_005919856.1|  97 SQADLIFFSKT---GDYHIIAGM-PFDMDSWI 124
                                       **********9...566677664.66666775 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05      0.13      70      89 ..      86     105 ..      79     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                                       EEE-TTS--S--HHHHHHHH CS
                              RadC  70 aHnhPsgdlepSeeDieltk 89 
                                       +H hPs d++pS++D+ +  
  gi|386001557|ref|YP_005919856.1|  86 VHSHPSPDIRPSQADLIFFS 105
                                       8**************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1151.05
//
Query:       gi|386001558|ref|YP_005919857.1|  [L=323]
Description: Biotin/acetyl-CoA-carboxylase ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-21   75.2   0.1    1.7e-20   73.3   0.0    1.9  2  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
    7.1e-12   45.1   0.6    1.6e-11   44.0   0.1    1.8  2  HTH_11           HTH domain
    1.1e-09   38.0   0.2    2.4e-09   36.9   0.2    1.6  1  BPL_C            Biotin protein ligase C terminal domain
    9.7e-05   22.0   0.1    0.00015   21.4   0.1    1.4  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
    0.00023   20.6   0.0    0.00088   18.8   0.0    2.0  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0054   16.6   1.1       0.12   12.3   0.0    2.6  2  MarR_2           MarR family
  ------ inclusion threshold ------
      0.012   15.3   3.4      0.069   12.8   0.0    3.0  3  GntR             Bacterial regulatory proteins, gntR family
      0.018   15.0   0.3      0.074   13.0   0.0    2.3  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.035   13.9   0.8       0.16   11.8   0.1    2.6  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
       0.11   12.3   0.2       0.11   12.3   0.2    3.5  3  VbhA             Antitoxin VbhA
       0.15   12.3   0.0        0.3   11.3   0.0    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3     2e+03      34      53 ..      12      30 ..      10      46 .. 0.85
   2 !   73.3   0.0     1e-23   1.7e-20       7     131 .]      90     207 ..      83     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                      S-B-B--B-TTSEEEEEEEE CS
                     BPL_LplA_LipB 34 gGrnvwhspkgeltysllls 53
                                      gG   w+s ++el+ sl +s
  gi|386001558|ref|YP_005919857.1| 12 GGLGSWIS-GQELAASLGIS 30
                                      788899**.99***999776 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 1e-23
                                       -HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH CS
                     BPL_LplA_LipB   7 stntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavleal 79 
                                       st   + e  +++  e g++v+++ qt+Gr    + whsp g++++s++l+p+    +++ + ++    ++av++al
  gi|386001558|ref|YP_005919857.1|  90 ST---NAEAKRFAASEEGTVVIAEVQTAGRgrmdRSWHSPRGGVWMSIILKPQI---PPAQAFRVNIAAAVAVARAL 160
                                       54...33455788899***********************************776...76678888888888899999 PP

                                       ......HHTT-TTEEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  80 gyrdskpgiegipvfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                              g  g  v+ikwpnDl+v+grK++Gi+++    + +l + v+g+g+n
  gi|386001558|ref|YP_005919857.1| 161 ------EGLYGLEVKIKWPNDLMVGGRKVSGILTEIGAdMDRLDYAVVGIGIN 207
                                       ......6889************************9988999999999999998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   9.7e-15   1.6e-11      16      55 .]      18      56 ..      14      56 .. 0.96
   2 ?   -2.6   0.0       3.4   5.6e+03      16      21 ..     254     259 ..     238     281 .. 0.52

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 9.7e-15
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                      isg+eLA  L++Sr++v++ +++L++ g++Ie++++ GYr
  gi|386001558|ref|YP_005919857.1| 18 ISGQELAASLGISRAAVWKAVASLRAEGYEIEASKR-GYR 56
                                      9***********************************.**8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                            HTH_11  16 isgeeL 21 
                                        s+ +L
  gi|386001558|ref|YP_005919857.1| 254 ASSGRL 259
                                       344444 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.2   1.5e-12   2.4e-09       1      47 [.     269     315 ..     269     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                       ++G++V+++ +dg++eG a+ +++dG L ++ d+gl++ + +Gd+++
  gi|386001558|ref|YP_005919857.1| 269 TLGRRVRILARDGEFEGLAEALEADGSLAVRRDGGLLERVIAGDCVH 315
                                       69*******************************************98 PP

>> BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   9.1e-08   0.00015      35     154 ..     123     238 ..      86     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.1e-08
                   BPL_LplA_LipB_2  35 yslaadlleaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngarvGgvrlaaseadeee 111
                                       ++  +  + ++++l+P+ p a+A ++  +++va++ Al+ l    + v+++wp++++v g +v g+  ++    + +
  gi|386001558|ref|YP_005919857.1| 123 WHSPRGGVWMSIILKPQIPPAQAFRVNIAAAVAVARALEGLYG--LEVKIKWPNDLMVGGRKVSGILTEIGA--DMD 195
                                       55556667899******************************98..88999********99999887776665..445 PP

                   BPL_LplA_LipB_2 112 vPdwlvvglelalekeseepGetpdetaLeeEGcaeveavall 154
                                         d+ vvg+ ++++ +  +     ++t++++E   +v +++l+
  gi|386001558|ref|YP_005919857.1| 196 RLDYAVVGIGINANLDPGDLAGGWKATSISSEIGRKVLRAELV 238
                                       5689999999988777665544556777777766666666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.4e-07   0.00088      18      46 ..      18      46 ..      16      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.4e-07
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGl 46
                                      is +eLA  lg+S+++v++ +  L  eG+
  gi|386001558|ref|YP_005919857.1| 18 ISGQELAASLGISRAAVWKAVASLRAEGY 46
                                      6779************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   7.4e-05      0.12      23      50 ..      19      46 ..       8      46 .. 0.90
   2 ?    2.0   0.2      0.12     2e+02       8      49 ..     239     281 ..     237     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTS CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGL 50
                                      + +ela+ lg+s++av ++++ L a G+
  gi|386001558|ref|YP_005919857.1| 19 SGQELAASLGISRAAVWKAVASLRAEGY 46
                                      678**********************997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHCTTTS.EEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2   8 arvLaaLgrrpgr.dltvgelarrlglsksavsrilkrLvaaG 49 
                                       +rvL +L  +  + + + g l +++ +   ++ r+++ L + G
  gi|386001558|ref|YP_005919857.1| 239 RRVLEELEGASQEmEASSGRLQEEWSIRSETLGRRVRILARDG 281
                                       7999999999987877********************9988766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.2e-05     0.069      24      53 ..      18      46 ..      10      56 .. 0.85
   2 ?    2.1   0.1     0.091   1.5e+02       5      37 ..      69     101 ..      65     105 .. 0.87
   3 ?   -3.3   0.2       4.5   7.3e+03      41      49 ..     238     246 ..     235     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                                      ---HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              GntR 24 LPsereLaaefgVsrttvReALrrLeaegl 53
                                      + s +eLaa +g+sr  v +A   L aeg+
  gi|386001558|ref|YP_005919857.1| 18 I-SGQELAASLGISRAAVWKAVASLRAEGY 46
                                      5.669***********************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHTTSS-TTSB---HHHHHHHHTS- CS
                              GntR   5 vyerLredIlsgelrpGdkLPsereLaaefgVs 37 
                                       + e Lr ++l  ++ + ++LPs ++ a++f+ s
  gi|386001558|ref|YP_005919857.1|  69 IREGLRTELLGRRIIASEALPSTNAEAKRFAAS 101
                                       67889*****************99988888776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.5
                                       HHHHHHHHH CS
                              GntR  41 vReALrrLe 49 
                                       vR++L +Le
  gi|386001558|ref|YP_005919857.1| 238 VRRVLEELE 246
                                       899999997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-05     0.074      22      53 ..      18      51 ..       1      64 [. 0.83
   2 ?   -2.0   0.1       2.3   3.7e+03      45      63 ..     259     280 ..     257     281 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTS.EE.E CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkregl.is.r 53
                                      ++ +elA+ lG++r  v ++ + L+ eg+ i+  
  gi|386001558|ref|YP_005919857.1| 18 ISGQELAASLGISRAAVWKAVASLRAEGYeIEaS 51
                                      6779************************966652 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                                       HHHTTSEE..E.TEEEEES-HH CS
                         HTH_Crp_2  45 Lkreglis..r.grririldle 63 
                                       L++e  i+  + grr+ril ++
  gi|386001558|ref|YP_005919857.1| 259 LQEEWSIRseTlGRRVRILARD 280
                                       5556566654235558888776 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0001      0.16      18      42 .]      18      42 ..      17      42 .. 0.89
   2 ?   -2.7   0.1       3.3   5.4e+03      10      21 ..     288     299 ..     286     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                     HTH_AsnC-type 18 isyaeLAervGlSestvlrRvrrLe 42
                                      is +eLA+ +G+S+++v++ v+ L+
  gi|386001558|ref|YP_005919857.1| 18 ISGQELAASLGISRAAVWKAVASLR 42
                                      5779**************9988775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                     HTH_AsnC-type  10 eaLqedaRisya 21 
                                       eaL++d+++ ++
  gi|386001558|ref|YP_005919857.1| 288 EALEADGSLAVR 299
                                       689999987665 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.9e-05      0.11       2      21 ..      31      50 ..      31      53 .. 0.92
   2 ?    0.7   0.2       0.3   4.9e+02       3      19 ..     152     168 ..     151     169 .. 0.87
   3 ?   -1.1   0.3       1.1   1.8e+03      38      45 ..     235     242 ..     234     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                              VbhA  2 rraVrqAlAsnelEGlepsa 21
                                      r+aV+ A+As + EG+e  a
  gi|386001558|ref|YP_005919857.1| 31 RAAVWKAVASLRAEGYEIEA 50
                                      89**************9865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.3
                              VbhA   3 raVrqAlAsnelEGlep 19 
                                       +aV+ A+A   l Gle+
  gi|386001558|ref|YP_005919857.1| 152 AAVAVARALEGLYGLEV 168
                                       89******999999887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                              VbhA  38 dElvrrvr 45 
                                       +Elvrrv+
  gi|386001558|ref|YP_005919857.1| 235 AELVRRVL 242
                                       8*****97 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019       0.3      23      59 ..      18      54 ..      12      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                      ++ ++la  L++s + V + +  L+ +Gy + + ++g
  gi|386001558|ref|YP_005919857.1| 18 ISGQELAASLGISRAAVWKAVASLRAEGYEIEASKRG 54
                                      77899************************88887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 2163.83
//
Query:       gi|386001559|ref|YP_005919858.1|  [L=495]
Description: Pyruvate carboxylase subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-74  250.6   0.0    2.1e-74  249.6   0.0    1.5  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.7e-48  163.7   0.1    7.1e-48  161.7   0.1    2.1  2  Biotin_carb_N    Biotin carboxylase, N-terminal domain
      2e-42  143.7   0.0    4.1e-42  142.7   0.0    1.6  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    8.1e-13   48.4   0.0      2e-12   47.1   0.0    1.7  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    4.1e-07   30.2   0.0    8.2e-07   29.2   0.0    1.6  1  ATP-grasp_3      ATP-grasp domain
    2.5e-05   23.9   0.0    5.5e-05   22.8   0.0    1.5  1  ATP-grasp        ATP-grasp domain
      8e-05   22.3   0.1     0.0091   15.6   0.0    2.6  3  RimK             RimK-like ATP-grasp domain
  ------ inclusion threshold ------
      0.024   14.1   0.0       0.11   12.0   0.0    1.9  2  ATP-grasp_5      ATP-grasp domain
       0.03   14.9   0.7      0.055   14.1   0.7    1.4  1  OAD_gamma        Oxaloacetate decarboxylase, gamma chain
      0.031   14.0   0.0       0.19   11.5   0.0    2.0  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.058   13.0   0.0       0.13   11.8   0.0    1.6  1  ATP-grasp_4      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.6   0.0   1.3e-77   2.1e-74       2     209 ..     116     321 ..     115     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 1.3e-77
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       k +a++++k ++vp+vp+s++ +++  ea+++++ igyPv++k+a+g+GG Gm+++++e++la ++ +a++ a++af
  gi|386001559|ref|YP_005919858.1| 116 KIAARDIMKSAGVPIVPGSEGGISNPAEAMDLVEAIGYPVMLKPAAGGGGIGMKIVWEEKDLAPALDSARSIARSAF 192
                                       67899************************************************************************ PP

                                       STS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                       ++++v++ek+l++p++iE+++l+D+kg +i+v +re+s+q+r+qk+ie+ Ps+ +t+e r+++++ av+++++++++
  gi|386001559|ref|YP_005919858.1| 193 SDETVYIEKYLTEPRHIEFQILADSKGKTIYVSDRECSIQRRHQKLIEESPSPIMTPELREEMGSIAVRAAEAIDYR 269
                                       ***************************************************************************** PP

                                       EEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 156 gagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +agtvef+++  ++eyy++E+NtRl+ve++++e++T +dl+ke+++ia+ge+L 
  gi|386001559|ref|YP_005919858.1| 270 SAGTVEFMYS--KGEYYFLEMNTRLQVEHPITEMVTSVDLAKEQIRIAAGEPLA 321
                                       *********9..5**************************************996 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.7   0.1   4.4e-51   7.1e-48       1     110 []       1     110 [.       1     110 [. 0.98
   2 ?   -2.1   0.0       3.4   5.6e+03      11      30 ..     256     275 ..     254     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 161.7 bits;  conditional E-value: 4.4e-51
                                       ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SE CS
                     Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgada 77 
                                       +++k+lianrGeiA+ri+ra+relgi+tvavyse+d+n+l++++adeav +gp++as+sYl+i++i++aa+e+ga+a
  gi|386001559|ref|YP_005919858.1|   1 MFQKILIANRGEIAIRIMRACRELGISTVAVYSEADRNALFAKYADEAVFVGPSPASQSYLRIDRILEAAEETGAEA 77 
                                       799************************************************************************** PP

                                       EE--SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                     Biotin_carb_N  78 vhpGyGflsEnaefaeaveeagivfiGPsaeal 110
                                       +hpGyGflsEn++fa+a+ee+g+vfiGP+++++
  gi|386001559|ref|YP_005919858.1|  78 IHPGYGFLSENPKFARACEEKGVVFIGPTSSSI 110
                                       ****************************99875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHTT-EEEE CS
                     Biotin_carb_N  11 GeiAvriiravrelgietva 30 
                                       G iAvr ++a+   +  tv 
  gi|386001559|ref|YP_005919858.1| 256 GSIAVRAAEAIDYRSAGTVE 275
                                       89999999999888777775 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   0.0   2.5e-45   4.1e-42       1     107 [.     335     441 ..     335     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 2.5e-45
                                       EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EE CS
                     Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelri 77 
                                       e+R+naEdp ++f+ps+G++++++ p+gpg+Rvdsgv++g  ++pyyDs+++K+++ g++r+ea+ar++raL e+ +
  gi|386001559|ref|YP_005919858.1| 335 ECRVNAEDPLNDFAPSPGRIKRYRSPGGPGIRVDSGVYAGFLIPPYYDSMISKVVAMGRDRNEAIARMERALYEYIV 411
                                       8**************************************************************************** PP

                                       ESS-BSHHHHHHHHH-HHHHHT---TTTCC CS
                     Biotin_carb_C  78 eGvktnieflrailedeefakgeldtkfle 107
                                       +Gvktni+f+ a+l++e+f++g+++t+fl+
  gi|386001559|ref|YP_005919858.1| 412 TGVKTNINFHLAVLRHERFRRGDINTNFLK 441
                                       ****************************97 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.2e-15     2e-12      29     174 ..     145     290 ..     122     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.2e-15
                                       HHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT......T-SCEEEEE--.ESEEEEEEEEETSSCEE CS
                   Dala_Dala_lig_C  29 ekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk......ydekvlvEeai.egreievavlgneklev 98 
                                        +++e++gypv+ Kpa  G  +G++ v  e++l+ a+++a +       de+v +E+++ e r ie  +l + k ++
  gi|386001559|ref|YP_005919858.1| 145 MDLVEAIGYPVMLKPAAGGGGIGMKIVWEEKDLAPALDSARSiarsafSDETVYIEKYLtEPRHIEFQILADSKGKT 221
                                       468999******************************99887633333369*********9***********888877 PP

                                       EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                         v ++    ++ + ++k ++++        +++e +e++  +a++a +a+d r  + v f+++ +ge ++ E+Nt
  gi|386001559|ref|YP_005919858.1| 222 IYVSDREC--SIQRRHQKLIEESP----SPIMTPELREEMGSIAVRAAEAIDYRSAGTVEFMYS-KGEYYFLEMNT 290
                                       77766554..45567777764332....233577899999**********************98.9*********9 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.1e-10   8.2e-07      16     159 ..     138     293 ..     113     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.1e-10
                                       S---....-EESS--SSSEEEEESS-------B--SS--TTE....................EEEE---SEEEEEEE CS
                       ATP-grasp_3  16 vkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.............lvqefieGkplSvsl 79 
                                       + +P    ++ +e   +++ +Kp+ G+gg ++ +v e++++  a+++               + +   e +++  ++
  gi|386001559|ref|YP_005919858.1| 138 ISNP-AEAMDLVEAIGYPVMLKPAAGGGGIGMKIVWEEKDLAPALDSARsiarsafsdetvyIEKYLTEPRHIEFQI 213
                                       3444.33334455669*************************99999988999********988888889******** PP

                                       EE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEE CS
                       ATP-grasp_3  80 lsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkdeepyviEvN 155
                                       l+d +   + +  r+   +++++     + +pi t + +ee+ ++a ++ e++ + ++   v+++++++e y++E N
  gi|386001559|ref|YP_005919858.1| 214 LADSKGKTIYVSDRECSIQRRHQKLIEESPSPIMTPElREEMGSIAVRAAEAI-DYRSAGTVEFMYSKGEYYFLEMN 289
                                       **998888877778877777777888899999999877***************.*********************** PP

                                       SS-- CS
                       ATP-grasp_3 156 PRlt 159
                                        Rl+
  gi|386001559|ref|YP_005919858.1| 290 TRLQ 293
                                       **97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.4e-08   5.5e-05      15     159 ..     139     291 ..     126     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.4e-08
                                       CCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEE CS
                         ATP-grasp  15 eskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvv 83 
                                       ++ +e+ +++e++g+pv++K +  g  G G ++v +e+dl  al+ +        ++e+v++E++    + +   + 
  gi|386001559|ref|YP_005919858.1| 139 SNPAEAMDLVEAIGYPVMLK-PAAGGGGIGMKIVWEEKDLAPALDSArsiarsafSDETVYIEKYLTEPRHIEFQIL 214
                                       5667888999**********.99999*****************9999999****99********************* PP

                                       EETTC-EEE--EEE.EEE..ETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEE CS
                         ATP-grasp  84 rsaeGetafypvve.tvq..edgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEla 157
                                        + +G+t  +   e  +q  +++ +++s  p  ++ +  ++  +ia +++e++++    +vE+ +  +ge ++ E+ 
  gi|386001559|ref|YP_005919858.1| 215 ADSKGKTIYVSDREcSIQrrHQKLIEESPSPI-MTPELREEMGSIAVRAAEAIDYRSAGTVEFMYS-KGEYYFLEMN 289
                                       *****976665433244410445566666666.67789999*********************8777.7887777766 PP

                                       SS CS
                         ATP-grasp 158 pR 159
                                        R
  gi|386001559|ref|YP_005919858.1| 290 TR 291
                                       55 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.023        37      24      71 ..     138     183 ..     117     215 .. 0.78
   2 !   15.6   0.0   5.6e-06    0.0091     126     186 ..     250     313 ..     245     315 .. 0.88
   3 ?   -3.0   0.1       2.8   4.6e+03     108     145 ..     431     470 ..     425     484 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.023
                                       ESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH CS
                              RimK  24 ardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea 71 
                                       + ++ +a +l+e i  + Pv++K   g  Gi++ +  +e++l   l++
  gi|386001559|ref|YP_005919858.1| 138 ISNPAEAMDLVEAI--GYPVMLKPAAGGGGIGMKIVWEEKDLAPALDS 183
                                       567889999****9..69*********999998777777666666554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.6e-06
                                       ---HHHHHHHHHHHHHCT-SEEE.EEEEEETTEEEEEEEESS--SHH..HHHHHT--HHHHHHH CS
                              RimK 126 qlseeekelAikaakamelvvaG.vDllrakrgllvlEvnsspglek..iektlgidiakklie 186
                                       +l ee   +A++aa+a++   aG v+ + +k ++++lE+n+  ++e+   e+ + +d+ak+ i+
  gi|386001559|ref|YP_005919858.1| 250 ELREEMGSIAVRAAEAIDYRSAGtVEFMYSKGEYYFLEMNTRLQVEHpiTEMVTSVDLAKEQIR 313
                                       57899999**************9677****************9999644799999999998775 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.8
                                       -SSS----TTTT-E..EEE----HHHHHHHHHHHHHCT-S CS
                              RimK 108 keGdFRsnlhrGgv..aeklqlseeekelAikaakamelv 145
                                       + Gd  +n  +  +   e+ +++e e+e  +  a a++++
  gi|386001559|ref|YP_005919858.1| 431 RRGDINTNFLKEEAimEEVKKVTEAEREKELSLASALGAD 470
                                       6788888866654311355667777777777777776665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.5e-05      0.11      12      52 ..     116     158 ..     107     163 .. 0.90
   2 ?   -1.2   0.1      0.69   1.1e+03      35      90 ..     395     458 ..     388     465 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                       ATP-grasp_5  12 eaeakelleaygipvvetrl..assaeeaveaaeeigypvvlK 52 
                                       +  a+++++  g+p+v+     +s+++ea++++e+igypv lK
  gi|386001559|ref|YP_005919858.1| 116 KIAARDIMKSAGVPIVPGSEggISNPAEAMDLVEAIGYPVMLK 158
                                       66899************99888********************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.69
                       ATP-grasp_5  35 aeeaveaaeeigypvvlKivspdil........hKtdvgGvrlnlkdaeevraaaeeilervke 90 
                                        +ea++ +e+  y + +  v  +i          + + g +  n+ ++e++ +++++++e+ +e
  gi|386001559|ref|YP_005919858.1| 395 RNEAIARMERALYEYIVTGVKTNINfhlavlrhERFRRGDINTNFLKEEAIMEEVKKVTEAERE 458
                                       5666666666666666666666655444444434777888999999999999999998887655 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   3.4e-05     0.055      43      76 ..     447     484 ..     433     485 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                         OAD_gamma  43 akaaaaaaaaaaaaa......eldddeelvAvIaaAiaay 76 
                                       ++ ++  +a+ +  +      +l  d++ vA+I+aA+ ay
  gi|386001559|ref|YP_005919858.1| 447 EEVKKVTEAERE--KelslasALGADTRKVAAISAAVGAY 484
                                       333322222222..234677799**************998 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.19      42     112 ..     248     319 ..     213     336 .. 0.78
   2 ?   -0.5   0.1      0.59   9.7e+02      21      59 ..     414     455 ..     406     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                      ATPgrasp_Ter  42 elekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgle 112
                                       + e +ee+ ++a r ae++       v + + +++++ LE+N+R +    ++ +++ v+l++  ++ + g++
  gi|386001559|ref|YP_005919858.1| 248 TPELREEMGSIAVRAAEAIDYRSAGTVEFMYSKGEYYFLEMNTRLQVEHPITeMVTSVDLAKEQIRIAAGEP 319
                                       55678899999***********************************99888734568999999999888853 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.59
                      ATPgrasp_Ter  21 laekgevlaavpRrKe..kgglq.elekdeelielaerlaee 59 
                                       ++++ + + av R     +g+++ ++ k+e+++e +++++e+
  gi|386001559|ref|YP_005919858.1| 414 VKTNINFHLAVLRHERfrRGDINtNFLKEEAIMEEVKKVTEA 455
                                       55666777888887776668887899999****999999876 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.1e-05      0.13       1      58 [.     151     205 ..     151     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                       ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvE 58 
                                       i +Pv +KP+ g + +G+ ++ +e+++  a+++ ++    a++ + +e+v  e++l E
  gi|386001559|ref|YP_005919858.1| 151 IGYPVMLKPAAGGGGIGMKIVWEEKDLAPALDSARSI---ARSAFSDETVYIEKYLTE 205
                                       579****************************999965...455566666656666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3565.62
//
Query:       gi|386001560|ref|YP_005919859.1|  [L=142]
Description: Pyridoxamine 5'-phosphate oxidase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-23   81.9   0.0    4.9e-23   81.7   0.0    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    4.9e-08   33.0   0.0    6.3e-08   32.7   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   5.4e-27   4.9e-23       1     140 [.       7     138 ..       7     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 5.4e-27
                                       -HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGE CS
                      Pyridox_ox_2   1 dreeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfns 76 
                                       +r+e+++lL+++++gr++++++++p++lP++yv+ g+ +++h+  ++++++ +r++p v+++v  v+g     +   
  gi|386001560|ref|YP_005919859.1|   7 SRDECEELLAKSRFGRIGLSTGDRPYVLPMSYVYAGGVILLHSGLAGKKLDMARENPfVSFEVDSVEG----GR--- 76 
                                       69****************************************************77788888888888....55... PP

                                       EEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT.GGCSB---CCCCCT..EEEEEEEEEEEEEE CS
                      Pyridox_ox_2  77 lnyrSVvvrGraeevtdeeekaealellvekivpgr.wenlrpptrkelka..tsvlrlkieevsgr 140
                                         +rSV++ Gr+++ +d+  k+++++l+++  + g+  +  r   r+++ +    +++++iee+ gr
  gi|386001560|ref|YP_005919859.1|  77 --WRSVIASGRVRLSSDAGAKERLFDLFTRGEMGGHaGKAFR---REDMVKmpMVIWEIEIEELAGR 138
                                       ..****************************999999444444...55555556799********998 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     7e-12   6.3e-08       2      87 ..       8      92 ..       7      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7e-12
                                      HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEEEE CS
                    Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..lgrgvrie 78
                                      ++e++e+la+s++++++  + d  P+v p+++++  g   i++++    +kl   +enp v++ +++ e    r+v  +
  gi|386001560|ref|YP_005919859.1|  8 RDECEELLAKSRFGRIGLSTGDR-PYVLPMSYVYAGGV--ILLHSGLAGKKLDMARENPFVSFEVDSVEggRWRSVIAS 83
                                      589****************9998.*********99999..*****************************877777777* PP

                                      EEEEEESCH CS
                    Putative_PNPOx 79 Gtaelvsdg 87
                                      G+++l sd+
  gi|386001560|ref|YP_005919859.1| 84 GRVRLSSDA 92
                                      ****99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       187  (0.01043); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1065.90
//
Query:       gi|386001561|ref|YP_005919860.1|  [L=509]
Description: replication factor C large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-11   45.4   0.0    1.9e-11   44.5   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.1e-06   26.6   0.0    1.9e-05   24.4   0.0    2.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.8e-06   26.6   0.4     0.0015   18.9   0.0    3.4  4  AAA_16           AAA ATPase domain
    3.8e-05   24.0   0.0      0.078   13.3   0.0    3.0  2  AAA_22           AAA domain
      6e-05   23.1   0.0    9.7e-05   22.4   0.0    1.4  1  Rad17            Rad17 P-loop domain
    0.00017   21.4   3.3    0.00084   19.1   3.2    2.1  1  AAA_30           AAA domain
     0.0002   21.1   0.0     0.0004   20.2   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0011   18.6   4.3      0.017   14.7   0.1    3.2  3  AAA_25           AAA domain
     0.0024   17.9   0.0      0.005   16.9   0.0    1.5  1  AAA_14           AAA domain
     0.0032   17.8   0.1     0.0092   16.3   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
     0.0061   16.8   0.1       0.77   10.0   0.0    2.6  2  AAA_28           AAA domain
     0.0063   16.5   0.1      0.096   12.7   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.013   15.3   0.0        4.8    6.9   0.0    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.013   16.0   0.0      0.044   14.3   0.0    2.0  2  AAA_18           AAA domain
      0.032   13.6   0.0       0.06   12.7   0.0    1.4  1  IPT              Isopentenyl transferase
      0.035   13.1   0.0      0.081   11.9   0.0    1.5  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.053   13.2   0.0      0.092   12.5   0.0    1.4  1  AAA_24           AAA domain
      0.059   12.6   0.0        0.1   11.8   0.0    1.3  1  TIP49            TIP49 P-loop domain
      0.072   12.5   0.3       0.92    8.9   0.1    2.3  2  PhoH             PhoH-like protein
      0.075   13.4   0.0       0.17   12.3   0.0    1.6  1  RNA_helicase     RNA helicase
      0.089   12.6   0.0         16    5.3   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
       0.13   12.3   0.0       0.25   11.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   11.8   0.0       0.22   11.0   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
       0.13   12.7   0.0        1.1    9.8   0.0    2.2  2  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   2.6e-14   1.9e-11       1     120 [.      45     150 ..      45     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.6e-14
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaks 73 
                                       v+lyGp G+GKT++a a+a+e+g + +e+++s+ +      +++ i+++  +a ++     k+  +++DE+d+l +s
  gi|386001561|ref|YP_005919860.1|  45 VVLYGPAGVGKTSAALALAEEMGWDQIEMNASDSR------TAAAISKVAGAAARMMtfsgKKRLVILDEADNLYGS 115
                                       68*********************************......66666666666544444666679************* PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                               ++   +++l+ +++ ++      v++++n++  l+++l+
  gi|386001561|ref|YP_005919860.1| 116 A-------DRGGSAAMLRLVKEADQ-----PVVLIANDYYGLSKPLR 150
                                       9.......77778888888888877.....46666677777766666 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.6e-08   1.9e-05       2      95 ..      11     111 ..      10     124 .. 0.74
   2 ?   -0.8   0.0       1.5   1.2e+03      67      88 ..     267     288 ..     259     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.6e-08
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk.lki.....tsgPvleka 72 
                                       rP++l+e +g  k  ++l+   ++ ++   +   v+lyGp G+Gkt+ a  +a+e+g + +++      ++ +++k 
  gi|386001561|ref|YP_005919860.1|  11 RPRRLKEVLGNGKAVSELEAWARSWERGIPEKRAVVLYGPAGVGKTSAALALAEEMGWDqIEMnasdsRTAAAISKV 87 
                                       9******************999988877788889**********************853133311111345567666 PP

                            RuvB_N  73 gdlaalltnl.eekdvlfideihr 95 
                                       +  aa ++++  +k ++ +de   
  gi|386001561|ref|YP_005919860.1|  88 AGAAARMMTFsGKKRLVILDEADN 111
                                       555554444404556666777655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                            RuvB_N  67 Pvlekagdlaalltnleekdvl 88 
                                       P + k++dlaa   +l++ dv+
  gi|386001561|ref|YP_005919860.1| 267 PLVYKPADLAAGYERLSRADVF 288
                                       8999**************9985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-06    0.0015       7      49 ..      23      67 ..      17      94 .. 0.76
   2 ?    1.6   0.0      0.43   3.2e+02     117     170 .]      85     138 ..      68     138 .. 0.67
   3 ?    2.2   0.0      0.28   2.1e+02      35     129 ..     161     238 ..     158     268 .. 0.55
   4 ?   -2.4   0.0       7.4   5.5e+03      34      63 ..     334     359 ..     333     422 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                            AAA_16  7 eeleqLlsalervrsgrp..elvllsGesGvGKsslvrellrale 49
                                      + +++L++  +++ +g p  ++v+l+G++GvGK+s + +l++++ 
  gi|386001561|ref|YP_005919860.1| 23 KAVSELEAWARSWERGIPekRAVVLYGPAGVGKTSAALALAEEMG 67
                                      56778888888899999999****************999998654 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.43
                            AAA_16 117 srllellkrllallsrderplvlvlDdlq....wadeaslqllaaLlrlleskpllvv 170
                                       s ++ + +r++ ++ +   + +++lD+++     ad +  +++  L++++++ p++++
  gi|386001561|ref|YP_005919860.1|  85 SKVAGAAARMMTFSGK---KRLVILDEADnlygSADRGGSAAMLRLVKEADQ-PVVLI 138
                                       5555555555555554...4799******99998888888887777777776.66665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.28
                            AAA_16  35 vGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpel 111
                                       + Ks+++ +l++ +++++g + + + ++         +a+++ + + lr   +++++ +le +re  e      + +
  gi|386001561|ref|YP_005919860.1| 161 ITKSTVLSALRE-ICRAEGAACTPELVEE--------IADMA-N-GDLRSGINDLQA-ALEGAREVGEV-----ATA 220
                                       568999988885.5555433333333333........56666.4.444444444344.34444443333.....233 PP

                            AAA_16 112 agaeasrllellkrllal 129
                                        ++++ ++++ ++++l+ 
  gi|386001561|ref|YP_005919860.1| 221 VRDAKASIFDGVAKILRG 238
                                       444445666666666654 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 7.4
                            AAA_16  34 GvGKsslvrellralekdggiflrgkcdql 63 
                                        +G ++ +r++++++ k+    +  +c+ +
  gi|386001561|ref|YP_005919860.1| 334 RMGQTKGARQVRESAAKK----IGRHCHIS 359
                                       578888888888888888....66666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0    0.0001     0.078       5      53 ..      42      81 ..      40      90 .. 0.79
   2 !    7.4   0.0    0.0067         5      91     112 ..      96     128 ..      75     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstss 53
                                      ++ +v++G++G+GKT  +  l+e+          + ++++++++ s + 
  gi|386001561|ref|YP_005919860.1| 42 KRAVVLYGPAGVGKTSAALALAEEM---------GWDQIEMNASDSRTA 81
                                      6789*****************9997.........666666666666555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0067
                            AAA_22  91 v....ielliiDEaqhlr....s...eealeeL 112
                                       +    ++l+i+DEa++l     +   +++l+ +
  gi|386001561|ref|YP_005919860.1|  96 TfsgkKRLVILDEADNLYgsadRggsAAMLRLV 128
                                       3666679**********8754413335555444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-07   9.7e-05       8      76 ..       5      73 ..       2     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-07
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                      +W eky+P  ++e+    k ++e++ w ++      +kr +++ GP+G gk+ +   L+ e+g + +e 
  gi|386001561|ref|YP_005919860.1|  5 KWTEKYRPRRLKEVLGNGKAVSELEAWARSWERGIPEKRAVVLYGPAGVGKTSAALALAEEMGWDQIEM 73
                                      7**************************9988777788999***********************988875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   3.2   1.1e-06   0.00084      18     128 ..      42     145 ..      37     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlliv 94 
                                       +r +vl GpAG GKt a  al+e +     ++ + A+ ++ A+++++ +g++a ++  +     g     +++l+i 
  gi|386001561|ref|YP_005919860.1|  42 KRAVVLYGPAGVGKTSAALALAEEMGW--DQIEMNASDSRTAAAISKVAGAAA-RMMTFS----G-----KKRLVIL 106
                                       56899**********987777665553..5799*************8777444.444455....3.....569**** PP

                            AAA_30  95 DEagmv....dtkqlaallkaaekagakvilvG.DerQl 128
                                       DEa  +    d    aa+l+ +++a+  v+l+  D   l
  gi|386001561|ref|YP_005919860.1| 107 DEADNLygsaDRGGSAAMLRLVKEADQPVVLIAnDYYGL 145
                                       **9665555577788888888888876776664144444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.4e-07    0.0004      44     136 ..      39     130 ..      22     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-07
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlg.. 118
                                       i +k ++vl Gp+GvGK+  a al+ e    g+  + + ++d  +  ++ +  g +ar+++   k +l+ilD+    
  gi|386001561|ref|YP_005919860.1|  39 IPEKRAVVLYGPAGVGKTSAALALAEEM---GWDQIEMNASDSRTAAAISKVAGAAARMMTFSGKKRLVILDEADnl 112
                                       567899******************9876...666666788999999999999********************98622 PP

                         IstB_IS21 119 llpldqaeaellfeviek 136
                                       +   d+  ++ +++++++
  gi|386001561|ref|YP_005919860.1| 113 YGSADRGGSAAMLRLVKE 130
                                       455666667777777765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.3e-05     0.017      26      54 ..      35      63 ..      11      67 .. 0.81
   2 ?    3.7   0.1     0.054        41     118     174 ..      75     133 ..      64     135 .. 0.68
   3 ?   -0.6   0.1       1.2   8.6e+02     110     158 ..     191     239 ..     167     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                            AAA_25 26 vkgllpagelallaGapgtGKttlaldla 54
                                      +++ +p++  ++l+G+ g+GKt +al la
  gi|386001561|ref|YP_005919860.1| 35 WERGIPEKRAVVLYGPAGVGKTSAALALA 63
                                      45557**********************98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.054
                            AAA_25 118 akdrggtlltadvdaleaaieeveg.vrlvviDplsralgg.densnsdvgalvealer 174
                                       a+d++ +++ ++v+  +a++    g  rlv++D  + ++g  d   ++++ +lv+ +++
  gi|386001561|ref|YP_005919860.1|  75 ASDSRTAAAISKVAGAAARMMTFSGkKRLVILDEADNLYGSaDRGGSAAMLRLVKEADQ 133
                                       4444444433444444444444444799*************898888989999998875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_25 110 gveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggd 158
                                       ++ + +L++ +++ +++ +  +++ +++++v +++  ++D ++++l+g+
  gi|386001561|ref|YP_005919860.1| 191 DMANGDLRSGINDLQAALEGAREVGEVATAVRDAKASIFDGVAKILRGS 239
                                       3344455556666666445557888888888888888888888888875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.7e-06     0.005       2      76 ..      42     112 ..      41     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-06
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek..lkeekktylflDEiqev 76 
                                       ++++v+ G+  vGKT  +  l++e      + +++n  d r++++  +  +  +  ++  +++ kk++++lDE+ ++
  gi|386001561|ref|YP_005919860.1|  42 KRAVVLYGPAGVGKTSAALALAEEMG---WDQIEMNASDSRTAAAISK--VAGAAARMmtFSG-KKRLVILDEADNL 112
                                       6899******************9888...7888999999888654433..4444444322455.99*******9886 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.2e-05    0.0092       6      43 ..     180     216 ..     176     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                       AAA_assoc_2   6 kleddalealaeladGDaRkaLnlLElaaeaaeakegk 43 
                                       +++++ +e +a++a+GD R+ +n L++a+e a++  g+
  gi|386001561|ref|YP_005919860.1| 180 ACTPELVEEIADMANGDLRSGINDLQAALEGARE-VGE 216
                                       567899***********************99986.333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.001      0.77       2      25 ..      45      69 ..      44      97 .. 0.87
   2 ?    4.0   0.0      0.07        52      12      58 ..     163     213 ..     162     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                            AAA_28  2 ivitGgestGKTtlleaLaar.gyp 25
                                      +v+ G+ + GKT+ + aLa++ g+ 
  gi|386001561|ref|YP_005919860.1| 45 VVLYGPAGVGKTSAALALAEEmGWD 69
                                      9******************876775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.07
                            AAA_28  12 KTtlleaLa....argypvvpEaareileeklakgedalpwvedllafaer 58 
                                       K+t+l+aL     a+g  + pE + ei +    + +  +++ + +l+ a++
  gi|386001561|ref|YP_005919860.1| 163 KSTVLSALReicrAEGAACTPELVEEIADMANGDLRSGINDLQAALEGARE 213
                                       9********555444************998886655555443333444443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00013     0.096       2      41 ..      45      84 ..      44     115 .. 0.81
   2 ?    0.7   0.0      0.65   4.9e+02      49      77 ..     207     235 ..     162     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHH CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedl 41
                                      v+L Gp G+gK++ a  la+ +++   +++ +++ t++ +
  gi|386001561|ref|YP_005919860.1| 45 VVLYGPAGVGKTSAALALAEEMGWDQIEMNASDSRTAAAI 84
                                      89********************999988888887777665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.65
                                       ........--------G-SEEEEESGGG- CS
                             AAA_5  49 ngttslvdsplvraaregeilvlDEvera 77 
                                         + +++ +++ +a+r ++  ++D+v ++
  gi|386001561|ref|YP_005919860.1| 207 ALEGAREVGEVATAVRDAKASIFDGVAKI 235
                                       5556677799999************9987 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0097       7.3      20      47 ..      43      70 ..      28      87 .. 0.84
   2 ?    6.9   0.0    0.0065       4.8      96     161 ..      93     160 ..      73     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0097
                   DNA_pol3_delta2 20 hayLfeGdegigkkelalnlakallcee 47
                                       a +++G++g+gk ++al+la+++  ++
  gi|386001561|ref|YP_005919860.1| 43 RAVVLYGPAGVGKTSAALALAEEMGWDQ 70
                                      6999*****************9876555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0065
                   DNA_pol3_delta2  96 srkpreskkkiiiiedaekmtksA....aNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfsp 161
                                         +++ +kk+++i+++a+++  sA    + a+L+++ E ++   ++Li++d   l k++r  +  ++f++
  gi|386001561|ref|YP_005919860.1|  93 RMMTFSGKKRLVILDEADNLYGSAdrggSAAMLRLVKEADQ--PVVLIANDYYGLSKPLREGTLGIQFRR 160
                                       456788**************98883333579******9955..556889998888888887777777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.8e-05     0.044       1      24 [.      45      68 ..      45     141 .. 0.79
   2 ?   -2.3   0.0       8.3   6.2e+03      11      25 ..     163     186 ..     163     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf 24
                                      ++l G++GvGKt+ a +L++++g 
  gi|386001561|ref|YP_005919860.1| 45 VVLYGPAGVGKTSAALALAEEMGW 68
                                      789****************99754 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.3
                            AAA_18  11 KttlakeLskrlgf.........g 25 
                                       K+t+  +L++ +           +
  gi|386001561|ref|YP_005919860.1| 163 KSTVLSALREICRAegaactpelV 186
                                       788888887664223333333333 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.1e-05      0.06       4      31 ..      45      72 ..      42     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                               IPT  4 ylifGatttGKtaeaiklaketgapviv 31
                                       +++G+ ++GKt+ a +la+e g+  i 
  gi|386001561|ref|YP_005919860.1| 45 VVLYGPAGVGKTSAALALAEEMGWDQIE 72
                                      579*********************8775 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011     0.081      36      77 ..      46      87 ..      38      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                             AAA_6 36 apaGpagtGKtEtvkdLakalakqvvvfncsdqldykslgki 77
                                       ++Gpag GKt +   La++++   + +n sd+ ++ +++k+
  gi|386001561|ref|YP_005919860.1| 46 VLYGPAGVGKTSAALALAEEMGWDQIEMNASDSRTAAAISKV 87
                                      578******************************999999886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.092       2      22 ..      42      62 ..      41     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      k+ +++yGp+g+GKT+ a+ l
  gi|386001561|ref|YP_005919860.1| 42 KRAVVLYGPAGVGKTSAALAL 62
                                      5679************99887 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.1      51      78 ..      43      71 ..      38      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                      XXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                             TIP49 51 ravLlaGpsgtGktalaiaiskelg.edv 78
                                      rav+l Gp+g Gkt+ a+a+++e+g +++
  gi|386001561|ref|YP_005919860.1| 43 RAVVLYGPAGVGKTSAALALAEEMGwDQI 71
                                      89**********************94444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0012      0.92      17      42 ..      40      65 ..      32      75 .. 0.86
   2 ?    1.0   0.0      0.33   2.5e+02     119     131 ..     100     112 ..      69     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                                      HH-SEEEEE--TTSSTTHHHHHHHHH CS
                              PhoH 17 kkndivfaiGpaGtGKtylavalave 42
                                       ++  v+  GpaG GKt  a+ala e
  gi|386001561|ref|YP_005919860.1| 40 PEKRAVVLYGPAGVGKTSAALALAEE 65
                                      5678899**************99865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.33
                                       -SEEEEE-SGGG- CS
                              PhoH 119 ndafvilDEAQnt 131
                                       ++ +vilDEA n+
  gi|386001561|ref|YP_005919860.1| 100 KKRLVILDEADNL 112
                                       3679******997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.17       1      28 [.      45      73 ..      45     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall.kklkl 28
                                      ++lyGp+g+GK+++a  La+++  +++++
  gi|386001561|ref|YP_005919860.1| 45 VVLYGPAGVGKTSAALALAEEMGwDQIEM 73
                                      689****************9998555544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.035        26      13      34 ..      41      62 ..      32      84 .. 0.82
   2 ?    5.3   0.0     0.021        16     122     149 ..     101     128 ..      86     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.035
                                      TTCEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTlaflip 34
                                      +++ v++ ++ G GKT a+l  
  gi|386001561|ref|YP_005919860.1| 41 EKRAVVLYGPAGVGKTSAALAL 62
                                      77899*************8765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnql 149
                                        r+++lDEad+l  +  +    ++l+ +
  gi|386001561|ref|YP_005919860.1| 101 KRLVILDEADNLYGSADRGGSAAMLRLV 128
                                       589********99886666666666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.25       6      48 ..      27      71 ..      22      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                                      HHHHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT---- CS
                              TsaE  6 etealgkklakal..gdvilLeGdLGaGKTtlvrglakalgveev 48
                                      e+ea +++  + +  +++++L+G+ G+GKT  + +la+++g +++
  gi|386001561|ref|YP_005919860.1| 27 ELEAWARSWERGIpeKRAVVLYGPAGVGKTSAALALAEEMGWDQI 71
                                      566677777776676778**********************98754 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.22      31      78 ..      40      84 ..      33      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanql 78
                                       +k+ v+l+Gp+G+GKt+ +  l +++    +  + +n s + +a+ +
  gi|386001561|ref|YP_005919860.1| 40 PEKRAVVLYGPAGVGKTSAALALAEEMG---WDQIEMNASDSRTAAAI 84
                                      67899***************99999998...77777777777666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0014       1.1       8      46 ..      39      75 ..      34      96 .. 0.79
   2 ?   -0.4   0.0         2   1.5e+03     122     136 ..      96     110 ..      90     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                                      EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGeilldg 46
                                      + e + v++ G+ G GK++ + +la+++ +++  i+++ 
  gi|386001561|ref|YP_005919860.1| 39 IPEKRAVVLYGPAGVGKTSAALALAEEMGWDQ--IEMNA 75
                                      678899*******************9998854..44444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                                       HHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxx RF
                          ABC_tran 122 allkkpkllllDEpt 136
                                       ++  k++l++lDE+ 
  gi|386001561|ref|YP_005919860.1|  96 TFSGKKRLVILDEAD 110
                                       677899*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 3620.84
//
Query:       gi|386001562|ref|YP_005919861.1|  [L=369]
Description: hypothetical protein Mhar_0866 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   47.0   0.0    0.00086   18.2   0.0    3.1  3  Sortilin-Vps10  Sortilin, neurotensin receptor 3,
    1.2e-07   30.7  15.8       0.95    9.7   0.1    6.0  5  BNR             BNR/Asp-box repeat
    5.6e-05   22.6   4.3       0.68    9.1   0.4    4.2  4  PSII_BNR        Photosynthesis system II assembly factor YCF4
  ------ inclusion threshold ------
       0.09   13.0   0.0        1.2    9.3   0.0    2.7  2  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


Domain annotation for each model (and alignments):
>> Sortilin-Vps10  Sortilin, neurotensin receptor 3,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.4e-06      0.02       3      60 ..      75     133 ..      73     136 .. 0.87
   2 !   10.9   0.0   3.2e-05      0.14       3      83 ..     165     256 ..     163     263 .. 0.78
   3 !   18.2   0.0   1.9e-07   0.00086       2      84 ..     264     351 ..     263     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-06
                                       EEEESSTTSS-EE-GGGGTTEEBE-EEE-STTS--EEEEEE.S-EEEEESSTTSSEEEE CS
                    Sortilin-Vps10   3 vyiSeDeGktwkkvkeklkgeaiqeivvhpfdkkkaylltd.skklyvttDrGktwkkf 60 
                                       vy SeD+G tw+  ++ l  e+++++ vh+ +++   +     + ++ ++D +++w+k+
  gi|386001562|ref|YP_005919861.1|  75 VYKSEDAGLTWNLASSGLPTEDVSALAVHHGNSDILHADVGvRGDIFASEDGANSWRKV 133
                                       89*********************99999999888666533379*************986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.2e-05
                                       EEEESSTTSS-EE-GGGGTTEEBE.......-EEE-STTS--EEEEEE.....S-EEEEESSTTSSEEEEE-SS-BS CS
                    Sortilin-Vps10   3 vyiSeDeGktwkkvkeklkgeaiq.......eivvhpfdkkkaylltd.....skklyvttDrGktwkkfklpfkps 67 
                                       + +S++ G +w+  +  l +++ +       ++ ++p +++ +y+ t      +  +y t D G++w++ +      
  gi|386001562|ref|YP_005919861.1| 165 LIRSTNGGMSWQACDGGLPKSDDErigayviSLAIDPLNSRVIYAGTGgwvgqGHGVYKTVDGGDSWTSANRGILDY 241
                                       689*********9998444333333448889999*******999988899998999************987666655 PP

                                       ...S--EEESSETTEE CS
                    Sortilin-Vps10  68 lsaeplsfhakdkdwl 83 
                                        + + l+ +++d++++
  gi|386001562|ref|YP_005919861.1| 242 -RITALAADPTDSQTI 256
                                       .567777777777665 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.9e-07
                                       EEEEESSTTSS-EE-GGGGTTEEBE.....-EEE-STTS--EEEEEES-EEEEESSTTSSEEEEE-SS-BS....S- CS
                    Sortilin-Vps10   2 evyiSeDeGktwkkvkeklkgeaiq.....eivvhpfdkkkaylltdskklyvttDrGktwkkfklpfkpsl.saep 72 
                                       e+++S D G+tw +++++l + +++     +i ++p d +++y+l d   l+ ++D G +w+++  p+ p+  + ++
  gi|386001562|ref|YP_005919861.1| 264 EFFRSVDGGATWVDLTDRLPRASYSlptfqAIEIDPAD-STVYVLMDRVGLLSSSDGGLSWESYGRPDAPEDlRFTD 339
                                       789**************999998888999777778877.6788889999*********************9878888 PP

                                       -EEESSETTEEE CS
                    Sortilin-Vps10  73 lsfhakdkdwli 84 
                                       +++ +  + + +
  gi|386001562|ref|YP_005919861.1| 340 MAISPGPPTRAV 351
                                       877777666555 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0019       8.6       1      11 [.      76      86 ..      76      87 .. 0.87
   2 !    9.7   0.1   0.00021      0.95       2      11 ..     167     176 ..     166     177 .. 0.88
   3 !    5.7   1.0    0.0045        20       1      11 [.     222     232 ..     222     233 .. 0.86
   4 !    8.4   0.1   0.00059       2.6       1      10 [.     266     275 ..     266     277 .. 0.90
   5 !    6.8   0.4    0.0019       8.7       3      11 ..     316     324 ..     314     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                                      EEESSTTSS-E CS
                               BNR  1 yyStDgGktWs 11
                                      y S D G tW+
  gi|386001562|ref|YP_005919861.1| 76 YKSEDAGLTWN 86
                                      6799******8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                                       EESSTTSS-E CS
                               BNR   2 yStDgGktWs 11 
                                        St+gG++W+
  gi|386001562|ref|YP_005919861.1| 167 RSTNGGMSWQ 176
                                       6********8 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0045
                                       EEESSTTSS-E CS
                               BNR   1 yyStDgGktWs 11 
                                       y + DgG +W+
  gi|386001562|ref|YP_005919861.1| 222 YKTVDGGDSWT 232
                                       5689******7 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00059
                                       EEESSTTSS- CS
                               BNR   1 yyStDgGktW 10 
                                       + S DgG tW
  gi|386001562|ref|YP_005919861.1| 266 FRSVDGGATW 275
                                       68******** PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0019
                                       ESSTTSS-E CS
                               BNR   3 StDgGktWs 11 
                                       S DgG +W+
  gi|386001562|ref|YP_005919861.1| 316 SSDGGLSWE 324
                                       99******8 PP

>> PSII_BNR  Photosynthesis system II assembly factor YCF48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.1    0.0026        12      84     139 ..      75     132 ..      65     149 .. 0.71
   2 !    5.0   0.9    0.0027        12      71      95 ..     209     232 ..     150     238 .. 0.62
   3 !    9.1   0.4   0.00015      0.68      31     104 ..     213     283 ..     195     289 .. 0.65
   4 !    8.9   0.0   0.00018      0.79      35      96 ..     260     325 ..     239     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0026
                                       EEEESSTTSS-EE----TT-SS-EEEEEEEETTEEEEE.ETT...--EEEESSTTSSEEE CS
                          PSII_BNR  84 llhttdgGksWerikLsekLPGePllitalgkkkaelv.tdv...gaiYrtedagknWka 139
                                       +  ++d+G +W+    s+ LP e +   a+ + ++++  +dv   g i+ +ed++++W+ 
  gi|386001562|ref|YP_005919861.1|  75 VYKSEDAGLTWNLA--SSGLPTEDVSALAVHHGNSDILhADVgvrGDIFASEDGANSWRK 132
                                       55678888888754..55688888888888888777641444444778888888888864 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0027
                                       ETTEEEEEEETTEEEEESSTTSS-E CS
                          PSII_BNR  71 kgdegwivGkPslllhttdgGksWe 95 
                                       +g  gw vG+   +  t dgG+sW+
  gi|386001562|ref|YP_005919861.1| 209 AGTGGW-VGQGHGVYKTVDGGDSWT 232
                                       444444.255555555555555554 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00015
                                       EEEEETTTEEEEESSTTSS-EE-----S--.--EEEEE..EEETTEEEEEE.ETTEEEEESSTTSS-EE----TT-S CS
                          PSII_BNR  31 GflvGtkatlletlDGGktWeersldleeevnyrlesv..sfkgdegwivG.kPslllhttdgGksWerikLsekLP 104
                                       G  vG+ + ++ t+DGG++W + +  + +    r++++  + +++    +G +   ++ + dgG +W  ++L ++LP
  gi|386001562|ref|YP_005919861.1| 213 G-WVGQGHGVYKTVDGGDSWTSANRGILDY---RITALaaDPTDSQTIYAGsDKGEFFRSVDGGATW--VDLTDRLP 283
                                       3.4788888889999999998776555544...3333300334444444441455677888888888..56777777 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00018
                                       ETTTEEEEESSTTSS-EE--..---S--...--EEEEEEEETTEEEEEEETTEEEEESSTTSS-EE CS
                          PSII_BNR  35 GtkatlletlDGGktWeers..ldleeev..nyrlesvsfkgdegwivGkPslllhttdgGksWer 96 
                                        +k  ++ ++DGG+tW   +  l  ++    +++  +++ +++  +++ +   ll ++dgG sWe 
  gi|386001562|ref|YP_005919861.1| 260 SDKGEFFRSVDGGATWVDLTdrLPRASYSlpTFQAIEIDPADSTVYVLMDRVGLLSSSDGGLSWES 325
                                       456789999*******98886655444441145555566678889999999999**********85 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00028       1.2       1      49 [.      87     137 ..      87     178 .. 0.84
   2 ?    0.2   0.0       0.2   8.9e+02      72      85 ..     312     325 ..     293     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                                       HHHTT--GGG-SEEEE-SSSHHHHHH.HHHHHT-.-GGGB--THHHH-B-G CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriida.vakklgl.peekvvvnldeyGnts 49 
                                       L+ +gl +ed++al  h+ n  i++a v  + ++ + e  +++++++Gn++
  gi|386001562|ref|YP_005919861.1|  87 LASSGLPTEDVSALAVHHGNSDILHAdVGVRGDIfASEDGANSWRKVGNCG 137
                                       6889*********************98776666515668889999999986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                                       EEEEEEETTTEEEE CS
                     ACP_syn_III_C  72 vllvgfGaGltwga 85 
                                        ll++  +Gl+w +
  gi|386001562|ref|YP_005919861.1| 312 GLLSSSDGGLSWES 325
                                       57888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2757.88
//
Query:       gi|386001563|ref|YP_005919862.1|  [L=321]
Description: S-layer protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   26.0   3.5    2.8e-05   24.9   2.2    2.1  2  CAP       Cysteine-rich secretory protein family


Domain annotation for each model (and alignments):
>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   2.2   1.6e-09   2.8e-05       2      84 ..      42     157 ..      41     174 .. 0.74
   2 ?   -1.6   0.0      0.26   4.6e+03      38      59 ..     256     282 ..     245     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-09
                                       HHHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH.............T---S-GGG--HHHHHHTT-T........ CS
                               CAP   2 eahNeyRaaaglppLkwdatLekaAqdhardcaash............sdsssspeggdllkyaenagk........ 58 
                                       +++NeyR ++gl ++ + ++L k+A++h++d+ a+h            ++s ss   +++++y  +a +        
  gi|386001563|ref|YP_005919862.1|  42 RLVNEYREESGLGAVLVTNSLTKVARAHVADLNAHHpdtatygtgecnRHSWSSFGDWTAVCYTGSAQAsamwnkpr 118
                                       689*****************************999967666666666544445555555555555555588998888 PP

                                       .............EEEEEES--CCCHHHHHHTSHH.... CS
                               CAP  59 .............eniaaaseaaedavdsWysepgtynk 84 
                                                    ++ + +  ++ +a+  W++++++++ 
  gi|386001563|ref|YP_005919862.1| 119 eitesytgngyevAYWSGQGATPSSAMGEWKNSAAHSDT 157
                                       888877776665446666666699*********995443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.26
                                       T---S-GGG--HHHHHHTT-T.....E CS
                               CAP  38 sdsssspeggdllkyaenagk.....e 59 
                                       s+ ++sp+++++ ++++++g      +
  gi|386001563|ref|YP_005919862.1| 256 SYYRTSPDNWRFKTPVIEFGGvakaiQ 282
                                       567889999999999999994333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2381.48
//
Query:       gi|386001564|ref|YP_005919863.1|  [L=396]
Description: S-adenosylmethionine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     5e-173  575.4   4.5   5.7e-173  575.2   4.5    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.097   13.4   0.1       0.55   11.0   0.0    2.4  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  575.2   4.5  6.4e-177  5.7e-173       1     396 []       3     392 ..       3     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 575.2 bits;  conditional E-value: 6.4e-177
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni+ve+l+++pveeq +E+vErKGiGHPDsiaDg+ae++sral++ey +++ga+lhhn+D++++vaG+s p+fgGG
  gi|386001564|ref|YP_005919863.1|   3 RNIKVEKLSQQPVEEQMIELVERKGIGHPDSIADGLAESISRALCHEYKSRVGAVLHHNTDETQVVAGRSCPAFGGG 79 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BE CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevpla 154
                                       e+i+pi++llsgrat+ +e+++ipv+ ia ++akey+++ l ++d++++vi+d+++g+gs+dL+dvf+r   +vp a
  gi|386001564|ref|YP_005919863.1|  80 EIIQPIYVLLSGRATRFFEEQEIPVDVIARRTAKEYIRSVLCNIDVSDHVILDCRIGTGSSDLQDVFKR---KVPGA 153
                                       *********************************************************************...69*** PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtSfgvgyap+se+e++v++ter+l +  lkk++p++GeD+Kvm++R+++ i++Tva+a+v r+++dl++Y+e+ke
  gi|386001564|ref|YP_005919863.1| 154 NDTSFGVGYAPFSETETVVYNTERFLMD--LKKRIPAIGEDVKVMAMRSGDIINITVACAMVGRHLDDLADYMETKE 228
                                       **************************95..9********************************************** PP

                                       HHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-T CS
                   AdoMet_Synthase 232 eikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNP 308
                                        i +e+ee++ ++++ r+v+v++N aD++e++svyltv+GtsaE+gDdGsvGRGNR+nGlit+nrpms+EA++GKNP
  gi|386001564|ref|YP_005919863.1| 229 VIVREIEENVCSCAQ-RKVKVQLNVADDPESGSVYLTVSGTSAEMGDDGSVGRGNRANGLITLNRPMSMEATSGKNP 304
                                       ***********9999.************************************************************* PP

                                       TT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-H CS
                   AdoMet_Synthase 309 vsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideeleki 385
                                       + HvGKiYn+l+++ia++iv+ev++v evyvr+lsqiGkpideP+++s+q ++++g++ ++v++e+e+i++++l++i
  gi|386001564|ref|YP_005919863.1| 305 IRHVGKIYNLLSTQIANKIVSEVDEVGEVYVRILSQIGKPIDEPHMLSIQTTVKEGANYSQVQAEAEQIANQWLDDI 381
                                       ***************************************************************************** PP

                                       HHHHHHHTTT- CS
                   AdoMet_Synthase 386 eeiteeliegk 396
                                         i+e+l++g+
  gi|386001564|ref|YP_005919863.1| 382 LVIQEKLMKGE 392
                                       ********986 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.1e-05      0.55      11      54 ..      28      71 ..      20     134 .. 0.74
   2 ?   -2.1   0.0      0.72   6.5e+03      18      30 ..     370     382 ..     351     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.1e-05
                   S-AdoMet_synt_N 11 eGHPDkvadqisdaildailkedpkarvacetlvttg.lvvvage 54
                                       GHPD +ad ++++i  a l ++ k+rv +    +t+ + vvag+
  gi|386001564|ref|YP_005919863.1| 28 IGHPDSIADGLAESISRA-LCHEYKSRVGAVLHHNTDeTQVVAGR 71
                                      6***********998766.66777888866555444415566665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.72
                   S-AdoMet_synt_N  18 adqisdaildail 30 
                                       a+qi+++ ld il
  gi|386001564|ref|YP_005919863.1| 370 AEQIANQWLDDIL 382
                                       6788888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2923.21
//
Query:       gi|386001565|ref|YP_005919864.1|  [L=300]
Description: Putative arsenical pump-driving ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-67  227.8   0.0    1.9e-67  227.6   0.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    6.7e-08   32.7   0.0    1.3e-07   31.8   0.0    1.6  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      2e-06   27.9   0.0    8.2e-06   25.9   0.0    2.0  2  AAA_31       AAA domain
    1.4e-05   24.7   0.5      0.031   13.7   0.1    2.2  2  ParA         NUBPL iron-transfer P-loop NTPase
     0.0017   17.9   0.1     0.0091   15.5   0.0    2.0  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.6   0.0   5.2e-71   1.9e-67       1     304 [.       1     293 [.       1     294 [. 0.92

  Alignments for each domain:
  == domain 1  score: 227.6 bits;  conditional E-value: 5.2e-71
                                       -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHH CS
                       ArsA_ATPase   1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeak 77 
                                       ++++ ++GKGGVGK+ +saat+++ se+gkk+l  s DPAhslsD+++ ++g +pt + eNL+avE d   e+e+  
  gi|386001565|ref|YP_005919864.1|   1 MRLVYMAGKGGVGKSVCSAATGLWASEQGKKTLAFSMDPAHSLSDILEADIGDQPTPIAENLYAVEPDLAAEAEKFY 77 
                                       799************************************************************************99 PP

                                       CCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHH CS
                       ArsA_ATPase  78 qevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlekllek 154
                                        +  +  +al++   + +v       lPG+ e++ +++l + + e +y+vvv+D+aPT   l ll+lpev   ++++
  gi|386001565|ref|YP_005919864.1|  78 AAYRSLFRALFE-MFQFEVRPADFGVLPGVGELIFMDRLYDVYMEGDYEVVVIDSAPTALVLPLLKLPEVTTGVVTR 153
                                       999999999998.56667777888999************************************************** PP

                                       HHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLk 231
                                       l+ +k   + + ++l    g+g++ ++  + +l++   + +++++ l+dpe+t++ +V+ipEk ++ E+eR+ik ++
  gi|386001565|ref|YP_005919864.1| 154 LLGMKSRWTGIFNMLEP--GFGDSVVK-EVRRLRT---KAETMRNALIDPEITTISVVMIPEKAAVLESERLIKTVE 224
                                       ******99999998833..66666555.4455555...5556669******************************** PP

                                       HTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHHC CS
                       ArsA_ATPase 232 kygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklselly 304
                                         g++vd++ivN++++   +  C+++ +r + qk y++ei+ +f +++++ lp + eEv+G+  l ++++ ly
  gi|386001565|ref|YP_005919864.1| 225 AHGVTVDSIIVNHVMAP--C-GCDYCSRRVASQKGYIEEIKTKFANKQIALLPSYGEEVKGA-GLAQVARDLY 293
                                       **************974..5.489*************************************7.5788888887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   3.5e-11   1.3e-07       4      55 ..       6     250 ..       3     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.5e-11
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                       +++kGGvGK++ +a+ +   +++g+++l++ +Dp  +++ ile + +d+ +                          
  gi|386001565|ref|YP_005919864.1|   6 MAGKGGVGKSVCSAATGLWASEQGKKTLAFSMDPAHSLSDILEADIGDQPTpiaenlyavepdlaaeaekfyaayrs 82 
                                       789*************************************9888888888899999********************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386001565|ref|YP_005919864.1|  83 lfralfemfqfevrpadfgvlpgvgelifmdrlydvymegdyevvvidsaptalvlpllklpevttgvvtrllgmks 159
                                       *************************************************************************9999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386001565|ref|YP_005919864.1| 160 rwtgifnmlepgfgdsvvkevrrlrtkaetmrnalidpeittisvvmipekaavleserliktveahgvtvdsiivn 236
                                       99999999999999999999999999999999999999999999999999999995555555555555555555555 PP

                                       .............C CS
                                       .............x RF
                              CbiA  55 .............d 55 
                                                     
  gi|386001565|ref|YP_005919864.1| 237 hvmapcgcdycsrR 250
                                       55555555555553 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.3e-09   8.2e-06       8     128 ..       7     134 ..       2     143 .. 0.70
   2 ?   -1.8   0.0       0.7   2.5e+03     144     144 ..     239     239 ..     190     277 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.3e-09
                            AAA_31   8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne....iektlyevlieeknikeaiiktkven 80 
                                         KGGvGK+  s + + + +++gkk+L   +Dp  +++  l+ +  +    i ++ly v     +++  + k     
  gi|386001565|ref|YP_005919864.1|   7 AGKGGVGKSVCSAATGLWASEQGKKTLAFSMDPAHSLSDILEADIGDqptpIAENLYAVE---PDLAAEAEKFYAAY 80 
                                       56*************************************999887773334444555552...23322222222333 PP

                            AAA_31  81 ldlipssidLaeaeielvelekk....eeilkellekv..kdeYDyiiiDcpPs 128
                                        +l  +  ++ ++e++ +++       e i+ + l +v  + +Y +++iD  P+
  gi|386001565|ref|YP_005919864.1|  81 RSLFRALFEMFQFEVRPADFGVLpgvgELIFMDRLYDVymEGDYEVVVIDSAPT 134
                                       366666666666666665555547777888877776652256699999999997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.7
                            AAA_31 144 i 144
                                       +
  gi|386001565|ref|YP_005919864.1| 239 M 239
                                       3 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   8.8e-06     0.031       8      36 ..       5      33 ..       2      56 .. 0.85
   2 !    9.3   0.0   0.00019      0.69     135     204 ..     198     268 ..     168     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.8e-06
                              ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvg 36
                                       ++gKGGVGKS +++   l  +++g+k+ 
  gi|386001565|ref|YP_005919864.1|  5 YMAGKGGVGKSVCSAATGLWASEQGKKTL 33
                                      589*************9999999999875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
                              ParA 135 plagaviVttpqevaladvkkaiemfkkvkvkvlGvveN..msgfvcpkcgekteifgkgggeklaeelgvp 204
                                       +++ + +V  p+++a+ + ++ i+ ++   v+v +++ N  m+ + c+ c+++++  +kg  e++ +++  +
  gi|386001565|ref|YP_005919864.1| 198 EITTISVVMIPEKAAVLESERLIKTVEAHGVTVDSIIVNhvMAPCGCDYCSRRVA-SQKGYIEEIKTKFANK 268
                                       55677899*****************************994455555555655533.2455566666655555 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-06    0.0091       4      41 ..       5      42 ..       2      59 .. 0.87
   2 ?   -0.0   0.0      0.14   4.9e+02     177     210 ..     242     275 ..     195     291 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                         Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaD 41
                                       + GkGG+Gks+ s+ +    +e+gkk l    DP + 
  gi|386001565|ref|YP_005919864.1|  5 YMAGKGGVGKSVCSAATGLWASEQGKKTLAFSMDPAHS 42
                                      567********************************875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.14
                         Fer4_NifH 177 gGliinsrkvddereliekfaeelgtkvlevvPr 210
                                        G  + sr+v+++++ ie++ ++ + k ++ +P 
  gi|386001565|ref|YP_005919864.1| 242 CGCDYCSRRVASQKGYIEEIKTKFANKQIALLPS 275
                                       3444557888888888888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2211.30
//
Query:       gi|386001566|ref|YP_005919865.1|  [L=104]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 820.03
//
Query:       gi|386001567|ref|YP_005919866.1|  [L=675]
Description: hypothetical protein Mhar_0871 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-09   35.6   0.0    1.5e-08   34.4   0.0    1.6  1  PEGA      PEGA domain


Domain annotation for each model (and alignments):
>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   8.6e-13   1.5e-08       2      48 ..     593     640 ..     592     644 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 8.6e-13
                              PEGA   2 gtltirSnpeGatVyidGkylG.kTPvtlsleaGnyslrvekeGYedl 48 
                                       g++  +S+p+Ga++ i+Gk +   TP++l l++G +++ + keGY++ 
  gi|386001567|ref|YP_005919866.1| 593 GNVKLTSKPSGAKIWINGKFTYqMTPIKLILPKGIHRISLRKEGYQEC 640
                                       7899**************987769*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4381.02
//
Query:       gi|386001568|ref|YP_005919867.1|  [L=796]
Description: hypothetical protein Mhar_0872 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-07   32.0   0.6        0.3   11.9   0.0    4.7  4  Big_7         Bacterial Ig domain
    0.00061   19.7  18.5    0.00061   19.7  18.5    2.5  2  Beta_helix    Right handed beta helix region
  ------ inclusion threshold ------
       0.01   15.5   0.1       0.44   10.2   0.0    2.8  2  ChitinaseA_N  Chitinase A, N-terminal domain
      0.019   14.9   2.7       0.35   10.8   0.1    3.7  4  Y_Y_Y         Y_Y_Y domain


Domain annotation for each model (and alignments):
>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.048   2.1e+02      17      66 ..     107     162 ..     101     165 .. 0.58
   2 ?   -1.0   0.0      0.71   3.2e+03       1      19 [.     194     213 ..     194     259 .. 0.71
   3 !   11.3   0.2    0.0001      0.46       1      68 [.     386     458 ..     386     460 .. 0.78
   4 !   11.9   0.0   6.7e-05       0.3       1      58 [.     485     556 ..     485     574 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.048
                                       SEEEEEEEEE-SS-EEEEEEEETTEE...EEEE-S..SSEEEEEE--.....SEEE CS
                             Big_7  17 gtvtisasAsddggvskVefyvdgtl.g.lgtdts..apysltwttta..ltagth 66 
                                       g+v++s +   +    ++ fy+dg+  g l ++ +    + + +t ++   ++g+h
  gi|386001568|ref|YP_005919867.1| 107 GPVNVSFWWKLSEDGGSIFFYIDGNYiGaLRENDQnsREWDYYITDQNnrIPNGSH 162
                                       5666666665554445788******9667333333124444444433345888888 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.71
                                       XEEEEEE--TT--EB.TSEE CS
                             Big_7   1 PtvtitsPangatvs.ggtv 19 
                                       P v+++sP ++a++   + v
  gi|386001568|ref|YP_005919867.1| 194 PKVKLVSPDDQAVYYlWDRV 213
                                       9999****999987655555 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0001
                                       XEEEEEE--TT--EB..TSEEEEEEEEE-SS-EEEEEEEETTEE........EEEE-SSSEEEEEE--...SEEEEE CS
                             Big_7   1 PtvtitsPangatvs..ggtvtisasAsddggvskVefyvdgtl.g......lgtdtsapysltwtttaltagthtl 68 
                                       Ptv ++sP +g++ s  ++ v +    sdd  ++   + +d +  g      +    ++++++t++t+    g ht 
  gi|386001568|ref|YP_005919867.1| 386 PTVVLISPDDGDNSSyvNKAVHFVYRPSDDKKIEYCALLIDENDtGlksespVIGVEDTTFNWTFNTS----GLHTW 458
                                       9********9995554569**********************999667777775555566777777775....66665 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 6.7e-05
                                       XEEEEEE--TT--EB.TSEEEEEEEEE-SS-EEEEEEEETTEE..............EEEE-SSSEEEEEE- CS
                             Big_7   1 PtvtitsPangatvs.ggtvtisasAsddggvskVefyvdgtl.g............lgtdtsapysltwtt 58 
                                       P vti +P++g+    ++t+++     dd   ++ +fy++g++              l +    p  ++w++
  gi|386001568|ref|YP_005919867.1| 485 PLVTILYPQDGDLCFvNQTIEFVYIPADDRRLDRCVFYINGSEeDrdgspingseslLRAEVPQPGKYAWNI 556
                                       89**********88888*************************944777775554444333333555555555 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 ?   -1.8   0.5      0.56   2.5e+03      60      89 ..     315     343 ..     300     368 .. 0.51
   2 !   19.7  18.5   1.4e-07   0.00061       9      92 ..     657     761 ..     650     792 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.56
                                       ES-EEE---SEEE-TT--S--EEES-EEES CS
                        Beta_helix  60 snntisdnngggialfgasnnlienneitd 89 
                                       ++n+ ++++   i+ + ++n+ i+  + + 
  gi|386001568|ref|YP_005919867.1| 315 TDNNLRNCT-LFINESRTDNVKINPENGSV 343
                                       333333333.33333333333333333333 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.4e-07
                                       -E.EEESEEEES-.......SS-SEEE-SSS-......EEES-EEES-SS-SEEE-TT-S-EEES-EEE---..... CS
                        Beta_helix   9 snvtiknntisns.......ggyGiylrgssn.....vvienneiannsgsGiyilgssnntisnntisdnn..... 68 
                                       +nvti+++ ++++       + +Giy+ gs+n     ++i nn+i+  + +Gi ilg+++ +i nn+isd++     
  gi|386001568|ref|YP_005919867.1| 657 NNVTIDGFYVTGTsndgpadHPSGIYASGSENnyldnIIIYNNDISARTRYGILILGVNYPIIINNNISDFTnngdh 733
                                       56799999999999999999999999999999888877777899999999999999999999999999999977777 PP

                                       ...SEEE-TT.--S--EEES-EEES-SS CS
                        Beta_helix  69 ...gggialf.gasnnlienneitdngg 92 
                                          + gi+l   a+n  i++n i+  +g
  gi|386001568|ref|YP_005919867.1| 734 shsSAGIYLCnCAGNGHIYDNYIRCVDG 761
                                       7777777766456666666666654432 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.038   1.7e+02      74     109 ..     250     286 ..     231     289 .. 0.79
   2 ?   10.2   0.0   9.8e-05      0.44      71     102 ..     342     374 ..     323     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.038
                      ChitinaseA_N  74 satfkvkkgGryqlevelCdaeG.CsksapkeivvaD 109
                                       +   +++++G +  ++  C++   C+ +    i++ D
  gi|386001568|ref|YP_005919867.1| 250 TLYHTFNNTGDFVWKIVCCNNVSkCTPARERRITIKD 286
                                       445678999**********98555*********9988 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.8e-05
                      ChitinaseA_N  71 akesatfkvkkgGryqlevelCdaeG.Csksap 102
                                       + ++ +++++ +G y  +ve Cd+eG C  s+ 
  gi|386001568|ref|YP_005919867.1| 342 SVNTFEYQFNDTGIYTWSVECCDEEGqCNPSQE 374
                                       45677999******************9988865 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   1.1e+03      29      63 ..     247     284 ..     234     285 .. 0.72
   2 ?   10.8   0.1   7.9e-05      0.35      27      65 ..     340     380 ..     328     381 .. 0.84
   3 ?    0.5   0.0      0.14   6.1e+02      30      55 ..     445     470 ..     417     479 .. 0.85
   4 ?   -1.5   0.0      0.55   2.5e+03      38      63 ..     549     574 ..     548     575 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                                       ...EEEEES--SEEEEEEEEEEETTS-B-SS-.EEEEE CS
                             Y_Y_Y  29 q..easytnlppGdYtlkVkakdndgqwnydi.tslsf 63 
                                       +  ++  t ++ Gd++ k+ +++n ++  +   +++++
  gi|386001568|ref|YP_005919867.1| 247 RnyTLYHTFNNTGDFVWKIVCCNNVSKCTPAReRRITI 284
                                       33488889999*************99988776666655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.9e-05
                                       TS...EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  27 ysq..easytnlppGdYtlkVkakdndgqwnyditslsfti 65 
                                       +++  +++y  +  G Yt  V+++d++gq n+ +  +s++i
  gi|386001568|ref|YP_005919867.1| 340 NGSvnTFEYQFNDTGIYTWSVECCDEEGQCNPSQEVWSVEI 380
                                       333459**************************999999998 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.14
                                       EEEEES--SEEEEEEEEEEETTS-B- CS
                             Y_Y_Y  30 easytnlppGdYtlkVkakdndgqwn 55 
                                       ++++t + +G  t kV + dn++ +n
  gi|386001568|ref|YP_005919867.1| 445 TFNWTFNTSGLHTWKVICYDNESASN 470
                                       899*****************999776 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.55
                                       SEEEEEEEEEEETTS-B-SS-EEEEE CS
                             Y_Y_Y  38 pGdYtlkVkakdndgqwnyditslsf 63 
                                       pG+Y   + + d+  ++n+ + s+s+
  gi|386001568|ref|YP_005919867.1| 549 PGKYAWNITCWDDGDNSNFSEGSISV 574
                                       9***9999999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (796 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 5575.20
//
Query:       gi|386001569|ref|YP_005919868.1|  [L=290]
Description: ATP phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-45  152.8   0.0    9.8e-45  152.4   0.0    1.2  1  HisG      ATP phosphoribosyltransferase
    1.1e-24   86.3   0.5    1.1e-23   83.1   0.1    2.4  3  HisG_C    HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.0   1.1e-48   9.8e-45       1     156 [.      49     207 ..      49     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.1e-48
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESE.....EEEEEEEETTSS--SGCGG.TT-.EEEEE CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgk.....cklvvavpeesevkslkdlvedkgkriaT 72 
                                       r+++iptyV++g +dlGi G D+v Es++   v+++ +L++gk     +k+vvavpe ++  s+kd     g ri T
  gi|386001569|ref|YP_005919868.1|  49 RPQEIPTYVAKGYFDLGISGTDWVVESGA--VVVTVAELDYGKqgpgkVKVVVAVPEAQRAASAKDIL--PGSRIST 121
                                       89************************864..6*********9999999*********88888888752..567**** PP

                                       S-HHHHHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHS.. CS
                              HisG  73 sypnlakkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkk.. 147
                                       +ypnl++k+f+++g+ ve+ ++ G++Ea+++  laDa+vDl+etG+TL +ngLk+++ iles++ Liank+s+++  
  gi|386001569|ref|YP_005919868.1| 122 EYPNLTRKFFADLGIPVEVENSFGATEAKVPE-LADAVVDLTETGSTLVKNGLKIVDVILESTSELIANKNSWADpe 197
                                       *******************************9.9***************************************9734 PP

                                       .HHHHHHHHH CS
                              HisG 148 .kekieelle 156
                                        +e+ie + +
  gi|386001569|ref|YP_005919868.1| 198 kREEIEAIET 207
                                       4447777665 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.078     7e+02      30      50 ..      81     105 ..      75     114 .. 0.78
   2 ?   -1.1   0.1      0.25   2.2e+03      14      27 ..     105     118 ..      93     121 .. 0.60
   3 !   83.1   0.1   1.3e-27   1.1e-23       1      73 []     215     287 ..     215     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.078
                                       EEEE-.....SS-EEEEEEEEECCC CS
                            HisG_C  30 Tvspla....degwvaVsavveeke 50 
                                       Tv++l+     +g v V + v+e +
  gi|386001569|ref|YP_005919868.1|  81 TVAELDygkqGPGKVKVVVAVPEAQ 105
                                       8999977767788888888888876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.25
                                       GGHHHHHHH---SS CS
                            HisG_C  14 esleevlkilPGlr 27 
                                       ++++ +++ilPG r
  gi|386001569|ref|YP_005919868.1| 105 QRAASAKDILPGSR 118
                                       45666777788765 PP

  == domain 3  score: 83.1 bits;  conditional E-value: 1.3e-27
                                       TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                            HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                       Ar++vl+ +nvp++++eev+++lP+++ PTvs+l+++g++aV++vv+++ ++ +i+ Lk+aGA+dI+++ i+k
  gi|386001569|ref|YP_005919868.1| 215 ARGKVLIALNVPEDRIEEVIALLPSMKRPTVSKLYNSGFYAVQSVVDRSGINLLIPLLKKAGAEDIIEVAISK 287
                                       89*******************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 2138.42
//
Query:       gi|386001570|ref|YP_005919869.1|  [L=210]
Description: NADH dehydrogenase/NAD(P)H nitroreductase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  101.7   0.2    9.6e-26   90.8   0.2    2.1  1  Nitroreductase  Nitroreductase family
    3.3e-05   23.5   0.0       0.46   10.0   0.2    2.7  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.2   1.1e-29   9.6e-26       2     170 .]      46     188 ..      45     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.1e-29
                                       HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGH CS
                    Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkee 78 
                                        +RrS+R + d+pv ++ +++++eaa +aPsagnl+  +++vv        l++ ++ +l +a              
  gi|386001570|ref|YP_005919869.1|  46 TGRRSVRRYADRPVGRDLIASLIEAAETAPSAGNLRAREYYVV--------LRPELKHALAAAA------------- 101
                                       68*****************************************........4444444444442............. PP

                                       HHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT CS
                    Nitroreductase  79 lklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllg 155
                                            q+ +a apv+iv+ a++++s r++++r+  y+++da+ a + llLaA ++Gl+sc++g+fde    vr++l 
  gi|386001570|ref|YP_005919869.1| 102 ---FSQEQVASAPVVIVVCADPSRSGRRYGDRGGLYSIQDAASATTCLLLAAFDMGLASCWTGAFDESM--VREILS 173
                                       ...33456678**********************************************************..****** PP

                                       -S..SEEEEEEEEE- CS
                    Nitroreductase 156 lpdeeeivvliavGy 170
                                       lp    ++++++vG+
  gi|386001570|ref|YP_005919869.1| 174 LPRRLVPTAIVPVGW 188
                                       **999999******8 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   5.1e-05      0.46       1      35 [.      40      74 ..      40      83 .. 0.82
   2 !    4.7   0.1    0.0022        20     160     177 ..      64      81 ..      61     107 .. 0.85
   3 !    9.0   0.0   0.00011      0.97      90     136 ..     145     192 ..     142     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.1e-05
                                      -HHHHHHH--B---B--S---HHHHHHHHH----- CS
                    TM1586_NiRdase  1 nlyeaiekRhsvRkYkdealeeelleelkeaieei 35
                                      n ++a++ R+svR+Y d+++  +l+  l ea+e+ 
  gi|386001570|ref|YP_005919869.1| 40 NFKDALTGRRSVRRYADRPVGRDLIASLIEAAETA 74
                                      56789999*************99999998887765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHTS--GGG-- CS
                    TM1586_NiRdase 160 fkeileaarlAPsAlNqq 177
                                       + +++eaa+ APsA N +
  gi|386001570|ref|YP_005919869.1|  64 IASLIEAAETAPSAGNLR 81 
                                       5689**********9965 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS-- CS
                    TM1586_NiRdase  90 qlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktk 136
                                       +l+L +   Gl++cW g+  ++ +++ ++l++     +++ +G ++++
  gi|386001570|ref|YP_005919869.1| 145 CLLLAAFDMGLASCWTGAFDESmVREILSLPRRLVPTAIVPVGWPAER 192
                                       689999***********8666567777788888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1591.99
//
Query:       gi|386001571|ref|YP_005919870.1|  [L=533]
Description: Histone acetyltransferase, ELP3 family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-25   86.8   0.0    1.2e-24   86.1   0.0    1.4  1  Radical_SAM_C    Radical_SAM C-terminal domain
    1.2e-18   68.0   0.0    2.2e-18   67.2   0.0    1.3  1  Radical_SAM      Radical SAM superfamily
    1.3e-07   31.8   0.2    2.8e-07   30.8   0.2    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.5e-06   28.2   0.0    4.7e-06   26.6   0.0    1.8  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.011   16.1   0.2      0.021   15.2   0.2    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0   3.5e-28   1.2e-24       1      80 [.     316     395 ..     316     397 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 3.5e-28
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd +K+yp lv++gTeL++ly +gey+pl   e+ +l+ +i+el+pp +r++R+++dip + + ag++++nlr+l++
  gi|386001571|ref|YP_005919870.1| 316 PDYLKIYPALVVEGTELYDLYLRGEYEPLGDGEAAELISRIKELIPPYTRLQRVQRDIPAPAIAAGVKKSNLRQLAK 392
                                       89**************************************************************************9 PP

                     Radical_SAM_C  78 krl 80 
                                       +rl
  gi|386001571|ref|YP_005919870.1| 393 ARL 395
                                       997 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   6.1e-22   2.2e-18       7     158 ..      95     299 ..      90     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 6.1e-22
                                       ESS-.-TTTSCCTT..................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHH CS
                                       xxxx.xxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   7 Cnlr.CsfCarpet..................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfv 64 
                                       C+++ C+ C+ +                      + g+  +l+v+  l+++ e+ +  ++  +i++gg+ + +p  +
  gi|386001571|ref|YP_005919870.1|  95 CPHGvCVPCPGGIGlssptpqsytgrepaamrAIQQGYDPYLQVRARLRQLSEIGHPLDKVDLIIMGGTITSRPLGY 171
                                       77777999999988999999999999999999889999999999999999999999999**************9999 PP

                                       HHHHHHHHTC................................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxx................................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                       Radical_SAM  65 ellerlakla................................vpgiritvetngtlpd...eeklerllelgvdrvs 106
                                         ++  + l+                                ++ +r++ +t +t+pd   +  ++ +l lg + v+
  gi|386001571|ref|YP_005919870.1| 172 ASWFVKRCLEamndhpqrgpgpggsslqearksfqevaleneSSRVRNVGTTFETRPDwcgPASIRSILHLGGTKVE 248
                                       9998888888899999999999999999999999999999**8888888888888888888**************** PP

                                       EEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 107 lgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       lg++++dde  l +m+rght+ e++ea ++lreag+k+ +++++glpG   +
  gi|386001571|ref|YP_005919870.1| 249 LGVQSTDDE-LLLRMRRGHTVRETIEANRALREAGLKVGFHMMPGLPGSDPQ 299
                                       *********.999999********************************8876 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.2   7.9e-11   2.8e-07      32     117 .]     434     521 ..     407     521 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.9e-11
                                       TCEEEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEE.........SGGGTTSSHHHHHHHHHHHHHHHTTESEEE CS
                    Acetyltransf_1  32 aegllv.aeedgeliGfisllkipdekggvayieslaV.........speyrgkGlGsaLlealeerareegikkiv 98 
                                       +e++l+   edg+l+Gf++l+         a++++l+V         +  ++++G+Gs+Ll ++ee+   +g++ + 
  gi|386001571|ref|YP_005919870.1| 434 EERFLSfEAEDGTLAGFLRLRLSEG-----AHVRELHVygpmtplgkRGGWQHRGIGSTLLAEAEEISSYRGYESLR 505
                                       23444468899**************.....9999999999999999999*****************99999999986 PP

                                       EEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  99 laveedndaairlYeklGF 117
                                       +    +  +a+++Y++ G+
  gi|386001571|ref|YP_005919870.1| 506 V---TSGIGARPYYRRQGY 521
                                       6...689*******88998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.3e-09   4.7e-06      38     111 ..     443     526 ..     421     531 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-09
                   Acetyltransf_10  38 eggkivGviel..rdgshisllfV.........dpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYek 103
                                       e+g+++G+++l  ++g h+  l V         +  ++++Gig+ Ll ++ee  + +g++ +l v +   a+p+Y++
  gi|386001571|ref|YP_005919870.1| 443 EDGTLAGFLRLrlSEGAHVRELHVygpmtplgkRGGWQHRGIGSTLLAEAEEISSYRGYE-SLRVTSGIGARPYYRR 518
                                       5567777776631333366666553333344444579*****************9****9.**************** PP

                   Acetyltransf_10 104 lGFkavge 111
                                       +G++  g+
  gi|386001571|ref|YP_005919870.1| 519 QGYQLQGP 526
                                       ***98776 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   5.9e-06     0.021      36      75 ..     479     522 ..     437     523 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.9e-06
                                       GTTSSHHHHHHH.HTT....SEEEEEEEEE.THH..HHHHHHHHTTEE CS
                    Acetyltransf_7  36 yrgkGiGraLle.aae....kgiileqlel.nae..kaikfYeklGFe 75 
                                       ++ +GiG+ Ll+ a+e    +g++     l +++   a+++Y++ G++
  gi|386001571|ref|YP_005919870.1| 479 WQHRGIGSTLLAeAEEissyRGYE----SLrVTSgiGARPYYRRQGYQ 522
                                       89*********8343255566643....332222469999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 4015.97
//
Query:       gi|386001572|ref|YP_005919871.1|  [L=122]
Description: hypothetical protein Mhar_0877 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34   11.5   4.0         12    6.6   0.3    2.6  3  DUF2627   Protein of unknown function (DUF2627)


Domain annotation for each model (and alignments):
>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0015        28      46      68 ..       7      28 ..       6      34 .. 0.89
   2 ?   -1.8   0.0      0.28     5e+03       7      21 ..      65      79 ..      60      84 .. 0.78
   3 ?    6.6   0.3   0.00065        12      42      66 ..      87     111 ..      79     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0015
                           DUF2627 46 lllfaiglgfiaGfilhrdrKrn 68
                                      lll++ g+ f+a f+++ d K++
  gi|386001572|ref|YP_005919871.1|  7 LLLIMEGIPFLA-FVYYLDHKKK 28
                                      78999******9.******9985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.28
                           DUF2627  7 liLvipgllaayGik 21
                                       i++ p l+   Gi 
  gi|386001572|ref|YP_005919871.1| 65 AIIIAPNLARHAGIE 79
                                      578888888888886 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00065
                           DUF2627  42 flaGlllfaiglgfiaGfilhrdrK 66 
                                       +l+G++++  gl+++ G+   r rK
  gi|386001572|ref|YP_005919871.1|  87 LLLGIVVLCSGLAMLLGYGIMRGRK 111
                                       589*******************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 911.11
//
Query:       gi|386001573|ref|YP_005919872.1|  [L=561]
Description: Thermosome subunit gamma [Methanosaeta harundinacea 6Ac]
Scores for complete 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-166  553.5  18.8   4.5e-166  553.3  18.8    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.095   13.0   0.0        0.3   11.4   0.0    1.8  1  HA2             Helicase associated domain (HA2)
        0.1   12.9   0.8        0.7   10.3   0.1    2.6  2  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
       0.17   12.1   2.3        8.6    6.6   0.3    3.5  3  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
        1.5    8.4   8.9       0.37   10.4   0.6    3.5  4  PrpR_N          Propionate catabolism activator


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.3  18.8  1.2e-169  4.5e-166       1     490 [.      35     526 ..      35     527 .. 0.98

  Alignments for each domain:
  == domain 1  score: 553.3 bits;  conditional E-value: 1.2e-169
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++tlGP+GmdK+lv+ +g+v++TnDG+til+e+e+ehPaak+lveaa++q++ vGDGTttv+iL+geLl++a
  gi|386001573|ref|YP_005919872.1|  35 VAKAVRSTLGPRGMDKLLVDTIGDVTITNDGVTILREMEVEHPAAKMLVEAAKAQNDAVGDGTTTVAILTGELLKRA 111
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l++ gvhpt i++gy +a++ka+e L+ +a+++s  ekdr+ L k+a t++++kl  +   ++sk +vd v++++
  gi|386001573|ref|YP_005919872.1| 112 EELVDLGVHPTMIVQGYSMAADKAIEVLEGMARKVS--EKDRNLLEKIALTAMTGKLAGTPDVQISKDAVDMVLAVT 186
                                       *******************************77777..569******************************995554 PP

                                       CCS....EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                        Cpn60_TCP1 155 ene....keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsda 227
                                       e +    k + l+++ v+k+ g+s++ds+l++G+++dk+ ++p+mpkk+ena++++l +++e   tetk+++ +++ 
  gi|386001573|ref|YP_005919872.1| 187 EVTeegkKVVSLKNVIVEKKAGESMDDSQLFHGIIIDKERVHPNMPKKVENARIAILGTPIEARDTETKAEISITSS 263
                                       444599999******************************************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGG CS
                        Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledl 304
                                       ++++ ++++e++ +++++ek+i++g+nvv+cqkgiddla+++lak+gi+a rr++k+dl++la+a G+++v++l+++
  gi|386001573|ref|YP_005919872.1| 264 DQFKIFANQEKEAIKKVVEKVIATGANVVFCQKGIDDLAQSILAKAGIMAFRRIRKTDLKKLARASGGNIVTNLDEM 340
                                       ***************************************************************************** PP

                                       GCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHH CS
                        Cpn60_TCP1 305 tpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatel 381
                                       tp +lG a+ vee+k+g   + ++++ + ++++++llrg t++v+d +era++dAl++v++a+ed+ +v+GGGa e+
  gi|386001573|ref|YP_005919872.1| 341 TPADLGRAELVEEKKVGGAPMAFVTGLAREGTVSLLLRGGTQQVVDSLERALDDALHAVAAAVEDGTLVAGGGAPEV 417
                                       ***************************************************************************** PP

                                       HHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCT CS
                        Cpn60_TCP1 382 elakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveag 458
                                       el+ kl+ey+++ +g+eqla+ +fa+A  +ipk+LaeNaG+d+i+ l++++++h++g k+ g+++ +g+++d++e g
  gi|386001573|ref|YP_005919872.1| 418 ELYLKLREYSSNFKGREQLAVAKFAEAVAEIPKALAENAGFDAITKLTEMKSSHEAGMKTGGLNTSDGKVVDMWEMG 494
                                       ***************************************************************************** PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiikak 490
                                       vv+pl+vk+qa+ksAt+aa++iLrid++i  k
  gi|386001573|ref|YP_005919872.1| 495 VVEPLRVKTQAIKSATDAANLILRIDDVIASK 526
                                       *****************************987 PP

>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.3e-05       0.3      16      67 ..      60     111 ..      50     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.3e-05
                               HA2  16 nlTelGrk.maelPlsprlakmLlaaaeleegcldevitivAalsveeiflee 67 
                                        +T+ G + + e+ ++   akmL+ aa+ +++ + +  t vA+l+ +e++ + 
  gi|386001573|ref|YP_005919872.1|  60 TITNDGVTiLREMEVEHPAAKMLVEAAKAQNDAVGDGTTTVAILT-GELLKRA 111
                                       567777651456999*****************************9.5555444 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.67   2.4e+03      16      38 ..     184     209 ..     181     225 .. 0.68
   2 ?   10.3   0.1   0.00019       0.7      24      87 ..     257     323 ..     251     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.67
                                       EEEEESSSCEEEEEEE...E.GCCCT CS
                     Nitro_FeMo-Co  16 aiyeveegevkivenr...veeaada 38 
                                       a+ ev+e+++k+v+ +   ve+ a++
  gi|386001573|ref|YP_005919872.1| 184 AVTEVTEEGKKVVSLKnviVEKKAGE 209
                                       78899999999999985444444333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                                       CEEEEEEE.E.GCCCTSSCSSTHHHHHHHHTT-SEEEES.SSCHHHHHHHCTTTSEEEES.-SSBHH CS
                     Nitro_FeMo-Co  24 evkivenr.veeaadaegggggklaqllaeegvdvvivg.kiGpralakleaagievykg.aggtve 87 
                                       e++i + + ++ +a++e+++ +k+++ + + g++vv+++ +i   a+  l++agi +++  ++++++
  gi|386001573|ref|YP_005919872.1| 257 EISITSSDqFKIFANQEKEAIKKVVEKVIATGANVVFCQkGIDDLAQSILAKAGIMAFRRiRKTDLK 323
                                       5556666688889999**********************73699************999976666665 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.11   3.9e+02      59      94 ..      16      53 ..       4      63 .. 0.75
   2 ?    6.6   0.3    0.0024       8.6      79     119 ..     363     403 ..     358     426 .. 0.79
   3 ?    1.1   0.0      0.12   4.4e+02      59      92 ..     428     461 ..     409     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                    baeRF_family10 59 drfqrreeeqaer..hlkevAellaklleergverlvl 94
                                      +r++r +e++a    ++++vA+++++ l +rg++ l++
  gi|386001573|ref|YP_005919872.1| 16 ARRERGREAMANNimAARAVAKAVRSTLGPRGMDKLLV 53
                                      5666666666665226789***************9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
                    baeRF_family10  79 llaklleergverlvlgGdeeetaalldrlpkalrarvvgt 119
                                       +++ l++e  v  l+ gG++++ + l+ +l  al+a+ ++ 
  gi|386001573|ref|YP_005919872.1| 363 FVTGLAREGTVSLLLRGGTQQVVDSLERALDDALHAVAAAV 403
                                       6788999999*************************887754 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.12
                    baeRF_family10  59 drfqrreeeqaerhlkevAellaklleergverl 92 
                                        +f+ re+  + +++++vAe+ ++l+e+ g++++
  gi|386001573|ref|YP_005919872.1| 428 SNFKGREQLAVAKFAEAVAEIPKALAENAGFDAI 461
                                       578889999999****************999987 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.091   3.3e+02      48      85 ..     169     204 ..     161     218 .. 0.82
   2 ?   10.4   0.6    0.0001      0.37      72     135 ..     238     304 ..     230     314 .. 0.74
   3 ?   -1.6   0.0      0.49   1.8e+03     148     159 ..     386     397 ..     364     410 .. 0.55
   4 ?   -2.3   0.0      0.79   2.8e+03      11      32 ..     438     461 ..     435     472 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.091
                            PrpR_N  48 vPVveikvsgyDilralkqakklgekialvgfeniikg 85 
                                       +P v+i+  + D++ a++++ ++g+   +v+ +n+i +
  gi|386001573|ref|YP_005919872.1| 169 TPDVQISKDAVDMVLAVTEVTEEGK--KVVSLKNVIVE 204
                                       577999999***************8..56777776665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
                            PrpR_N  72 ekialvgfeniikglktlsel...ldldieiytinseeeaeaavkelkaegvevvvGdgvvadlAek 135
                                        +ia++g +   ++++t +e+    + + +i++ ++ e ++++v+++ a g +vv + + + dlA++
  gi|386001573|ref|YP_005919872.1| 238 ARIAILGTPIEARDTETKAEIsitSSDQFKIFANQEKEAIKKVVEKVIATGANVVFCQKGIDDLAQS 304
                                       577777776555555554444111466777788888888*************************987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.49
                            PrpR_N 148 esvrqAieeAle 159
                                       +s+++A+++Al 
  gi|386001573|ref|YP_005919872.1| 386 DSLERALDDALH 397
                                       333444444443 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.79
                            PrpR_N  11 egdleeavelakel..eaegvdvi 32 
                                       ++++ eav+++ ++  e+ g+d+i
  gi|386001573|ref|YP_005919872.1| 438 VAKFAEAVAEIPKAlaENAGFDAI 461
                                       567777777777665556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3974.43
//
Query:       gi|386001574|ref|YP_005919873.1|  [L=329]
Description: hypothetical protein Mhar_0879 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2315.19
//
Query:       gi|386001575|ref|YP_005919874.1|  [L=1208]
Description: hypothetical protein Mhar_0880 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   44.6   0.1    4.2e-11   42.8   0.1    1.9  1  CHAT      CHAT domain
    2.9e-05   24.3  14.7        0.2   12.0   0.1    6.6  7  TPR_12    Tetratricopeptide repeat
     0.0001   22.7   0.0    0.00093   19.6   0.1    2.7  1  AAA_16    AAA ATPase domain
     0.0018   17.5   0.0      0.005   16.1   0.0    1.7  1  NB-ARC    NB-ARC domain
     0.0048   17.1   1.1        6.1    7.2   0.2    4.4  4  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0065   16.3   9.6        1.3    9.0   0.2    5.8  5  TPR_10    Tetratricopeptide repeat
     0.0067   16.7   0.0      0.034   14.4   0.0    2.2  2  AAA_22    AAA domain
      0.007   16.8  12.0      0.094   13.2   1.1    5.0  5  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.026   15.1   2.3      0.026   15.1   2.3    7.0  5  TPR_4     Tetratricopeptide repeat
      0.033   15.0   0.2      0.033   15.0   0.2    6.1  5  TPR_14    Tetratricopeptide repeat
      0.067   12.6   0.0       0.13   11.7   0.0    1.4  1  PhoH      PhoH-like protein
      0.076   13.4   0.0       0.19   12.2   0.0    1.7  1  AAA       ATPase family associated with various cellular acti
       0.18   12.5   0.1       0.18   12.5   0.1    5.3  4  TPR_16    Tetratricopeptide repeat
       0.26   11.4   9.8         21    5.4   0.0    5.8  6  TPR_7     Tetratricopeptide repeat
       0.37   11.0   9.6        5.2    7.4   0.0    5.2  5  TPR_2     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   3.5e-14   4.2e-11       4     267 ..      55     337 ..      52     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.5e-14
                                       xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT   4 araLydlliaPleaeldgqsvr.....qlvivpdg.eLqliPfealvdpdgrylleryavsyapsarllselrkaaa 74 
                                       +r++  +++  +++ l   ++r     ++v+ p++ ++ ++P+e+   +  ++ + r ++s++++++  + ++ +  
  gi|386001575|ref|YP_005919874.1|  55 SRWIGSKVFGEVAESL--SKLRtpvtvRVVFPPEArAVAHLPLELAEVGG-KPAALR-DLSLVFEVKGSEPVEHEGV 127
                                       5666666666666666..22222344678888887888888888744443.455555.6777777777777766666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx..xxxxxxxx.xxxxxxxxx.x.xx RF
                              CHAT  75 saasalqlvvgdpkfdaaellrklvfpelpgteaE....aeaiakllaegel..kvllgeaa.tesalksal.s.rr 142
                                       +++ +  ++ + p++  a          l ++++     ++ ia++++   l  ++ + + + t+++l++al + + 
  gi|386001575|ref|YP_005919874.1| 128 GERLRMLAIYSLPTDVSA--------LALRRERYQqmrlIRSIAQTHN---LgvELRVLQYGvTRDNLQEALeEgEG 193
                                       666665466667765544........4444444444003555555554...433555555555*********559** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxx............... RF
                              CHAT 143 yrvvHfatHgvfnanpplqsglvlsaenseedglLtaeeile.lnldg..aelVvLsACqtg............... 201
                                       ++++H+++Hg         +++vl++ +   +++++ e++++ l+l +  ++ V+Ls+C ++               
  gi|386001575|ref|YP_005919874.1| 194 WDLIHISGHGRQ-------GAIVLENPDG-TMDEVSSEDLADlLSLARgrLKFVTLSSCLSAaatleetlnwlkipv 262
                                       **********65.......5****99888.999*********77888899*************************** PP

                                       .......xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                              CHAT 202 .......lgevi....dgegvlgLaralllaGarsviaslwpVddeatalLmkrfyqnlla.glskaeALreaqlkl 266
                                                  +    dg  +  La+ l+     +v+a+++pV d+ +++L+ ++y++l + g+++ +AL+   +++
  gi|386001575|ref|YP_005919874.1| 263 peevkkaT---ScfeaDGGPMPALAQELVDRLDCAVLAMRYPVGDDFAIKLASELYERLFGkGQPLPRALQLSLREA 336
                                       88865541...134457777888**************************************9666666666544444 PP

                                       x RF
                              CHAT 267 l 267
                                       l
  gi|386001575|ref|YP_005919874.1| 337 L 337
                                       4 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0039       4.7      13      45 ..     804     834 ..     800     850 .. 0.76
   2 !    7.4   0.7    0.0043       5.2      32      70 ..     840     876 ..     830     879 .. 0.72
   3 ?   -2.0   0.0       3.8   4.5e+03       9      27 ..     897     915 ..     888     916 .. 0.76
   4 ?   -2.3   0.0       4.7   5.6e+03      12      21 ..     941     950 ..     939     958 .. 0.64
   5 ?   -0.2   0.2         1   1.2e+03      16      48 ..     995    1026 ..     985    1028 .. 0.62
   6 !   12.0   0.1   0.00016       0.2      13      73 ..    1033    1091 ..    1033    1093 .. 0.94
   7 ?    1.0   0.0      0.46   5.4e+02      35      59 ..    1093    1117 ..    1089    1125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                            TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhplta 45 
                                       l+rlgr+deA +ll++a+ + ++l  ++ ++++
  gi|386001575|ref|YP_005919874.1| 804 LMRLGRWDEASTLLDQAIYRDKSL--GTAAAVL 834
                                       789**************8887666..4455555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0043
                            TPR_12  32 iarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                       ia+++ G+d+  + +    L+ +++a+gr++eA+++l+ 
  gi|386001575|ref|YP_005919874.1| 840 IAEATEGTDR--EPIDTAVLAKALLAAGRWQEAEAMLRS 876
                                       5566666666..555556788888888888888888875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.8
                            TPR_12   9 laavlrrlgrydeAlelle 27 
                                       l ++l+  gr++e l + e
  gi|386001575|ref|YP_005919874.1| 897 LIQILLTTGRFEEGLHIAE 915
                                       88899999****9998776 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.7
                            TPR_12  12 vlrrlgryde 21 
                                       +l++lgryde
  gi|386001575|ref|YP_005919874.1| 941 ALNKLGRYDE 950
                                       4667777776 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1
                            TPR_12   16 lgrydeAlellekaleiarrllGpdhpltattl 48  
                                         g+++ Alel  + l +  ++ G + +++a++ 
  gi|386001575|ref|YP_005919874.1|  995 SGDFQLALELNAEELKAK-EVRGATDLNLANAA 1026
                                        466666666666666666.56666666776665 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00016
                            TPR_12   13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73  
                                        l+rl+ry+eA +ll  +  ++++   +d +    +  +L++l +++g++++A ++ e+al+
  gi|386001575|ref|YP_005919874.1| 1033 LLRLERYEEAGSLLWNCKVVFEKE--KDIEMIGKVFSALADLKDEMGQTDQAARFEEDALR 1091
                                        57899****************999..88889****************************97 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.46
                            TPR_12   35 rllGpdhpltattlrnLgrlyralg 59  
                                        ++l +d + ++ + +nLg ++r++g
  gi|386001575|ref|YP_005919874.1| 1093 EYLTGDTESVSVSHNNLGYYHRKMG 1117
                                        556678999999********99998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.8e-07   0.00093       1     146 [.     395     516 ..     395     542 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.8e-07
                            AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd.g.giflrgkcdqlesaipysalaqa 75 
                                       r+vGR   + +  sal    +++ + vl++G++G GK++ + el+ + +++ +   f++ k+ +l            
  gi|386001575|ref|YP_005919874.1| 395 RFVGRSGPMIRASSALA--VESDKRGVLFHGMAGAGKTACALELAYHHSRSpRfQGFVWYKAPDL------------ 457
                                       57888888878888886..455569****************999988887733233455565555............ PP

                            AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqw 146
                                          +e+  +lld a++ e++    k   a++        +a ++++ l +l   l++  + +++vlD+l+ 
  gi|386001575|ref|YP_005919874.1| 458 --GKEIGGALLDLATEMERQLPGFKMVHAVG--------DADSFRDFLPQLRGVLEN-NS-ILVVLDNLES 516
                                       ..22333333333333344444444444444........457888888888888888.66.8888888883 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.2e-06     0.005      17     139 ..     416     550 ..     403     553 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE..............EEESXXHHHHHHHXXHHHHHCC CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdevegrFdsvawv..............vvsktdkseeiletilkeLsls 79 
                                       +     v ++Gm+G GKt  a +   + ++   rF +++w                             ++ e++++
  gi|386001575|ref|YP_005919874.1| 416 K---RGVLFHGMAGAGKTACALELAYH-HSRSPRFQGFVWYkapdlgkeiggallD-------------LATEMERQ 475
                                       3...35889*************99988.67778********666555555444332.............33333333 PP

                                       CTTSSSS-STTS...............HHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEEEES CS
                            NB-ARC  80 eddleekeeves...............lkrklvrlLltkrfllvlDDVweeedwdkigvvlparenrlrvllTTR 139
                                           +  + v +                ++ +  +L +  +ll  D  w  e w  +  +l +++  +r ++T+R
  gi|386001575|ref|YP_005919874.1| 476 LPGFKMVHAVGDadsfrdflpqlrgvlENNSILVVLDNLESLLTSDGSWRDERWGILAKTLLDQDGFSRTIFTSR 550
                                       322222222222333333222344455556666666666666666777999999999999999999999999999 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.62   7.4e+02      66      81 ..     804     819 ..     800     820 .. 0.77
   2 !    7.2   0.2    0.0051       6.1      60      80 ..     855     875 ..     811     885 .. 0.75
   3 ?    3.6   0.0     0.063        75      29      81 ..     897     957 ..     886     958 .. 0.69
   4 ?   -2.3   0.0       4.5   5.4e+03      66      79 ..    1033    1046 ..    1033    1049 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.62
                                       HHHTT-HHHHHHHH-S CS
                            ANAPC3  66 llkLkkyeeAiaaLek 81 
                                       l  L++++eA ++L+ 
  gi|386001575|ref|YP_005919874.1| 804 LMRLGRWDEASTLLDQ 819
                                       4578999999999875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  60 ylfAqcllkLkkyeeAiaaLe 80 
                                        ++A++ll+ ++++eA+a L 
  gi|386001575|ref|YP_005919874.1| 855 AVLAKALLAAGRWQEAEAMLR 875
                                       478999999999999998886 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.063
                                       HHHHHHHTT-HHHHHHHHHCTSHHHC-H..HHHHHHH......HHHHHTT-HHHHHHHH-S CS
                            ANAPC3  29 lAlclylngqykrAyellrkaklnsksl..gcrylfA......qcllkLkkyeeAiaaLek 81 
                                       l + l+ +g++++ +++++++k +s+    g +  +       q+l kL++y+e ++a e+
  gi|386001575|ref|YP_005919874.1| 897 LIQILLTTGRFEEGLHIAEEMKGYSRKAglGPWTQLSdeasrlQALNKLGRYDEVLTAVEE 957
                                       5777778888888888888776666555444555554555556788899999999999886 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.5
                                        HHHTT-HHHHHHHH CS
                            ANAPC3   66 llkLkkyeeAiaaL 79  
                                        ll L++yeeA ++L
  gi|386001575|ref|YP_005919874.1| 1033 LLRLERYEEAGSLL 1046
                                        5889*****97766 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.4   2.9e+03      30      41 ..     313     324 ..     310     325 .. 0.87
   2 !    6.3   0.0    0.0077       9.2      12      29 ..     804     821 ..     803     828 .. 0.89
   3 !    9.0   0.2    0.0011       1.3       8      26 ..     857     875 ..     855     881 .. 0.88
   4 ?    1.1   0.1      0.32   3.9e+02       9      30 ..    1070    1091 ..    1066    1092 .. 0.83
   5 ?   -0.8   0.2       1.3   1.5e+03       6      16 ..    1107    1117 ..    1106    1118 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                            TPR_10  30 airrrllGpdHP 41 
                                       ++++rl+G  +P
  gi|386001575|ref|YP_005919874.1| 313 ELYERLFGKGQP 324
                                       78******9887 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0077
                            TPR_10  12 lrqrgrydeAealleeal 29 
                                       l ++gr+deA  ll++a+
  gi|386001575|ref|YP_005919874.1| 804 LMRLGRWDEASTLLDQAI 821
                                       7899*************8 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0011
                            TPR_10   8 LanalrqrgrydeAealle 26 
                                       La al + gr++eAea+l+
  gi|386001575|ref|YP_005919874.1| 857 LAKALLAAGRWQEAEAMLR 875
                                       999**************87 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.32
                            TPR_10    9 analrqrgrydeAealleeala 30  
                                        a +  ++g+ d+A ++ e+al+
  gi|386001575|ref|YP_005919874.1| 1070 ADLKDEMGQTDQAARFEEDALR 1091
                                        5555689*************96 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 1.3
                            TPR_10    6 nNLanalrqrg 16  
                                        nNL+ ++r++g
  gi|386001575|ref|YP_005919874.1| 1107 NNLGYYHRKMG 1117
                                        9*******998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.8e-05     0.034       4     125 ..     415     544 ..     412     554 .. 0.80
   2 ?   -2.5   0.0       4.6   5.5e+03      25      68 ..    1085    1134 ..    1076    1153 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka........e 71 
                                       +++ ++ +G +G+GKT ++ +l++ + +      +  ++v +++p ++ +    l +l+ +++++l +         
  gi|386001575|ref|YP_005919874.1| 415 DKRGVLFHGMAGAGKTACALELAYHHSRS----PRFQGFVWYKAPDLGkEIGGALLDLATEMERQLPGfkmvhavgD 487
                                       5666789*****************99532....2456667999999998888889999999999999999**99999 PP

                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlr....s..eealeeL.rsllnlsrkgvql 125
                                        +s +++l +l+  l++ +   l+++D+ + l     s  +e +  L ++ll+  ++g++ 
  gi|386001575|ref|YP_005919874.1| 488 ADSFRDFLPQLRGVLENNSI--LVVLDNLESLLtsdgSwrDERWGILaKTLLD--QDGFSR 544
                                       99999999*****9999999..*********6555542557777777677777..766665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.6
                            AAA_22   25 lleqldeeakaee..erpevv....fvtlpsstsskdllrellralglel 68  
                                        + e + ++++ +   e+++v      ++  + +ssk+l+++l++a+ + l
  gi|386001575|ref|YP_005919874.1| 1085 FEEDALRYEYLTGdtESVSVShnnlGYYHRKMGSSKSLAHHLASAVIRLL 1134
                                        55555555555555533333333336666777799999999999887544 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.016        19      35      56 ..     804     825 ..     794     834 .. 0.84
   2 !   13.2   1.1   7.9e-05     0.094      30      52 ..     856     878 ..     827     884 .. 0.78
   3 !   11.1   0.1   0.00035      0.42       1      43 [.     861     909 ..     861     916 .. 0.90
   4 ?   -2.7   0.4       7.5   8.9e+03       1      34 [.     992    1025 ..     992    1028 .. 0.71
   5 ?    0.6   0.1      0.71   8.5e+02      30      45 ..    1068    1083 ..    1063    1093 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                            TPR_19  35 llalgqldeAealLdalpeedp 56 
                                       l+ lg++deA  lLd++   d+
  gi|386001575|ref|YP_005919874.1| 804 LMRLGRWDEASTLLDQAIYRDK 825
                                       789************9977665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.9e-05
                            TPR_19  30 lLAeallalgqldeAealLdalp 52 
                                        LA+alla+g+++eAea+L  l+
  gi|386001575|ref|YP_005919874.1| 856 VLAKALLAAGRWQEAEAMLRSLL 878
                                       39*****************9875 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00035
                            TPR_19   1 llaegdyaeAlalleqal...qedpknaearl...lLAeallalgqlde 43 
                                       lla+g+ +eA a+l+++l   +++ k +ea +   +L+++ll +g+++e
  gi|386001575|ref|YP_005919874.1| 861 LLAAGRWQEAEAMLRSLLikcSDEGKFWEASAfstYLIQILLTTGRFEE 909
                                       79**************998888899988888888899**********98 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 7.5
                            TPR_19    1 llaegdyaeAlalleqalqedpknaearllLAea 34  
                                        +l +gd++ Al+l ++ l+++   ++  l+LA+a
  gi|386001575|ref|YP_005919874.1|  992 ALGSGDFQLALELNAEELKAKEVRGATDLNLANA 1025
                                        5889999999998777666666666666666666 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.71
                            TPR_19   30 lLAeallalgqldeAe 45  
                                        +LA++  ++gq+d+A 
  gi|386001575|ref|YP_005919874.1| 1068 ALADLKDEMGQTDQAA 1083
                                        6999999999999996 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.032        38      11      26 .]     804     819 ..     803     819 .. 0.90
   2 ?   15.1   2.3   2.1e-05     0.026       5      25 ..     855     875 ..     854     876 .. 0.94
   3 ?   -0.5   0.0       2.4   2.8e+03       8      25 ..     898     915 ..     895     916 .. 0.78
   4 ?    1.0   0.0       0.8   9.6e+02       9      26 .]     940     957 ..     940     957 .. 0.87
   5 ?   -0.2   0.0       1.9   2.3e+03       6      22 ..    1068    1084 ..    1065    1085 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.032
                             TPR_4  11 llalGdldeAraller 26 
                                       l +lG++deA +ll++
  gi|386001575|ref|YP_005919874.1| 804 LMRLGRWDEASTLLDQ 819
                                       679**********997 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.1e-05
                             TPR_4   5 laLArallalGdldeAralle 25 
                                       ++LA alla+G++ eA+a+l+
  gi|386001575|ref|YP_005919874.1| 855 AVLAKALLAAGRWQEAEAMLR 875
                                       78******************9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.4
                             TPR_4   8 ArallalGdldeAralle 25 
                                        + ll +G+++e + ++e
  gi|386001575|ref|YP_005919874.1| 898 IQILLTTGRFEEGLHIAE 915
                                       57899******9876655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.8
                             TPR_4   9 rallalGdldeAraller 26 
                                       +al  lG++de ++++e+
  gi|386001575|ref|YP_005919874.1| 940 QALNKLGRYDEVLTAVEE 957
                                       58999******9999886 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.9
                             TPR_4    6 aLArallalGdldeAra 22  
                                        aLA +  + G+ d+A++
  gi|386001575|ref|YP_005919874.1| 1068 ALADLKDEMGQTDQAAR 1084
                                        788888899******98 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.9       3.2   3.8e+03      12      33 ..     622     643 ..     615     647 .. 0.73
   2 ?    6.2   0.2     0.019        23      10      28 ..     803     821 ..     795     843 .. 0.90
   3 ?   15.0   0.2   2.8e-05     0.033       5      42 ..     855     892 ..     851     894 .. 0.87
   4 ?    0.2   0.1       1.6   1.9e+03       7      26 ..     938     957 ..     935     963 .. 0.85
   5 ?   -1.1   0.1         4   4.8e+03       5      22 ..    1067    1084 ..    1064    1091 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.2
                            TPR_14  12 lalGdpdeAiallrralalaPd 33 
                                       +++ dp++ +++l ra a++ d
  gi|386001575|ref|YP_005919874.1| 622 AQAKDPAALERHLGRAAAAWGD 643
                                       6788899999999999776655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                            TPR_14  10 allalGdpdeAiallrral 28 
                                       +l++lG++deA +ll++a+
  gi|386001575|ref|YP_005919874.1| 803 YLMRLGRWDEASTLLDQAI 821
                                       79**************996 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.8e-05
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + la+alla+G+++eA+a+lr +l ++ d+  +w + a
  gi|386001575|ref|YP_005919874.1| 855 AVLAKALLAAGRWQEAEAMLRSLLIKCSDEGKFWEASA 892
                                       679********************999998888887655 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.6
                            TPR_14   7 laeallalGdpdeAiallrr 26 
                                       +++al  lG++de +++ ++
  gi|386001575|ref|YP_005919874.1| 938 RLQALNKLGRYDEVLTAVEE 957
                                       6799*********8888776 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 4
                            TPR_14    5 lalaeallalGdpdeAia 22  
                                         ala++  + G++d+A++
  gi|386001575|ref|YP_005919874.1| 1067 SALADLKDEMGQTDQAAR 1084
                                        5889999999****9987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.13      20      78 ..     417     474 ..     405     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------T CS
                              PhoH  20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdp 78 
                                         v   G aG+GKt  a+ la +  ++ +++ ++  ++  + g+e+G    dl++ ++ 
  gi|386001575|ref|YP_005919874.1| 417 RGVLFHGMAGAGKTACALELAYHHSRSPRFQGFVWYKAP-DLGKEIGGALLDLATEMER 474
                                       457789****************************99864.7799999888888887765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.19       1      81 [.     419     527 ..     419     567 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       EEEESSTTSSHHHHHHHHHHHHTHE.....EEEEETTTCSSS.......................STTHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgve.....fleisgsellsk.......................yvgesekkirel 49 
                                       vl++G  G GKT++a  +a + +++     f+  ++++l ++                        v   ++++r++
  gi|386001575|ref|YP_005919874.1| 419 VLFHGMAGAGKTACALELAYHHSRSprfqgFVWYKAPDLGKEiggalldlatemerqlpgfkmvhAV-GDADSFRDF 494
                                       79******************98633344559999999999668999999999999999999988533.334555555 PP

                                       HHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHH CS
                               AAA  50 fkeakeka..kpsilfiDEidalaksrsgsesee 81 
                                       + +++     +   +++D++++l +s+ gs ++e
  gi|386001575|ref|YP_005919874.1| 495 LPQLRGVLenNSILVVLDNLESLLTSD-GSWRDE 527
                                       555544444335889999999999998.333333 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4       0.7   8.4e+02      22      50 ..     618     647 ..     611     654 .. 0.79
   2 ?    5.8   0.2     0.018        21       4      29 ..     801     826 ..     798     834 .. 0.80
   3 ?   12.5   0.1   0.00015      0.18       3      54 ..     857     911 ..     855     920 .. 0.84
   4 ?   -0.1   0.8       1.3   1.5e+03       6      27 ..     991    1012 ..     988    1045 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.7
                            TPR_16  22 aalkrdpssPdaaeAllllgdaal.rqgrl 50 
                                       ++ ++++++P+a e +l+++ aa+   grl
  gi|386001575|ref|YP_005919874.1| 618 ELADAQAKDPAALERHLGRAAAAWgDEGRL 647
                                       567777788999999999999998666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                            TPR_16   4 araalragdyddAaaaleaalkrdps 29 
                                       a +++r+g++d+A  +l++a+ rd+s
  gi|386001575|ref|YP_005919874.1| 801 APYLMRLGRWDEASTLLDQAIYRDKS 826
                                       889**************999877754 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00015
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAa 54 
                                       la+a+l+ag++++A+a+l+ +l + +++     a +++ +l +++l  gr++e +
  gi|386001575|ref|YP_005919874.1| 857 LAKALLAAGRWQEAEAMLRSLLIKCSDEGKfweASAFSTYLIQILLTTGRFEEGL 911
                                       89********************999555558889999999999999999998876 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.3
                            TPR_16    6 aalragdyddAaaaleaalkrd 27  
                                        aal +gd++ A+++  + lk+ 
  gi|386001575|ref|YP_005919874.1|  991 AALGSGDFQLALELNAEELKAK 1012
                                        4556666666666555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.018        21      10      31 ..     805     824 ..     803     828 .. 0.87
   2 ?    3.4   0.1     0.079        95       5      26 ..     857     878 ..     855     886 .. 0.84
   3 ?   -3.2   0.0       9.8   1.2e+04      11      20 ..     944     953 ..     941     958 .. 0.77
   4 ?   -0.9   0.0       1.8   2.2e+03      12      28 ..     995    1009 ..     990    1016 .. 0.82
   5 ?    3.4   0.2     0.079        94       3      28 ..    1067    1090 ..    1065    1095 .. 0.83
   6 ?   -2.3   0.0       5.2   6.2e+03       1      13 [.    1105    1117 ..    1105    1118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                             TPR_7  10 srlGdyeeAielyeqsLaltkd 31 
                                        rlG+++eA +l+ q  a+ +d
  gi|386001575|ref|YP_005919874.1| 805 MRLGRWDEASTLLDQ--AIYRD 824
                                       69*************..88777 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.079
                             TPR_7   5 LarlysrlGdyeeAielyeqsL 26 
                                       La +  + G+++eA+  ++ +L
  gi|386001575|ref|YP_005919874.1| 857 LAKALLAAGRWQEAEAMLRSLL 878
                                       89999**********9988755 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.8
                             TPR_7  11 rlGdyeeAie 20 
                                       +lG+y+e ++
  gi|386001575|ref|YP_005919874.1| 944 KLGRYDEVLT 953
                                       6999999876 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.8
                             TPR_7   12 lGdyeeAielyeqsLal 28  
                                         Gd++ A+el+ +  +l
  gi|386001575|ref|YP_005919874.1|  995 SGDFQLALELNAE--EL 1009
                                        69********998..44 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.079
                             TPR_7    3 lnLarlysrlGdyeeAielyeqsLal 28  
                                        ++La+l  ++G++++A+++ e   al
  gi|386001575|ref|YP_005919874.1| 1067 SALADLKDEMGQTDQAARFEED--AL 1090
                                        79***************98666..55 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 5.2
                             TPR_7    1 aLlnLarlysrlG 13  
                                        +++nL+  ++++G
  gi|386001575|ref|YP_005919874.1| 1105 SHNNLGYYHRKMG 1117
                                        5799**9999987 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0044       5.2      11      30 ..     804     823 ..     803     826 .. 0.88
   2 ?    5.1   0.1     0.024        29       7      25 ..     857     875 ..     855     882 .. 0.86
   3 ?   -2.4   0.0       6.3   7.6e+03      13      26 ..     944     957 ..     944     958 .. 0.79
   4 ?   -2.4   0.1       6.2   7.4e+03      11      20 ..    1033    1042 ..    1033    1042 .. 0.87
   5 ?   -0.6   0.0       1.6     2e+03       4      15 ..    1106    1117 ..    1104    1119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0044
                             TPR_2  11 yyklgdyeeAleafekAlel 30 
                                       +++lg+++eA  ++++A+  
  gi|386001575|ref|YP_005919874.1| 804 LMRLGRWDEASTLLDQAIYR 823
                                       79***************965 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                             TPR_2   7 lGlayyklgdyeeAleafe 25 
                                       l++a++++g+++eA++ ++
  gi|386001575|ref|YP_005919874.1| 857 LAKALLAAGRWQEAEAMLR 875
                                       899***********98665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.3
                             TPR_2  13 klgdyeeAleafek 26 
                                       klg+y+e l a e+
  gi|386001575|ref|YP_005919874.1| 944 KLGRYDEVLTAVEE 957
                                       69****98877665 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 6.2
                             TPR_2   11 yyklgdyeeA 20  
                                        +++l +yeeA
  gi|386001575|ref|YP_005919874.1| 1033 LLRLERYEEA 1042
                                        57999****9 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.6
                             TPR_2    4 lynlGlayyklg 15  
                                        ++nlG+ ++k+g
  gi|386001575|ref|YP_005919874.1| 1106 HNNLGYYHRKMG 1117
                                        89*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 7165.08
//
Query:       gi|386001576|ref|YP_005919875.1|  [L=254]
Description: hypothetical protein Mhar_0881 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1822.66
//
Query:       gi|386001577|ref|YP_005919876.1|  [L=409]
Description: Efflux ABC transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-29  102.5   0.1    3.6e-29  102.5   0.1    1.9  2  MacB_PCD  MacB-like periplasmic core domain
    1.3e-09   38.4   5.0    1.3e-09   38.4   5.0    2.6  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
        0.1   12.6   0.9        1.5    8.9   0.0    2.7  2  DUF3042   Protein of unknown function (DUF3042)


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.1     6e-33   3.6e-29       2     194 ..      22     252 ..      21     253 .. 0.79
   2 ?   -5.2   4.7         3   1.8e+04      11      37 ..     291     317 ..     285     391 .. 0.60

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 6e-33
                          MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdl.gnlvtvtpgk..................gsgeslsdpdvea 59 
                                       +++ LGi+iGv +++a++s+g+gl   v++q+ d+  +l+ v+pg+                  g++++++d+dv++
  gi|386001577|ref|YP_005919876.1|  22 FMSSLGIIIGVISIVALLSVGQGLYGGVSEQFGDMdMDLISVRPGSgmgmgmgpgpggrpastpGEPAEFDDRDVKI 98 
                                       8999*****************************99546899999988999888877766666665555599999966 PP

                          MacB_PCD  60 lrrevpveavapvv.....tvrgggsgeeevtvvgvdp.dyfkvfglklaeGrffteadlrggpnvvvigeelaerl 130
                                       +   ++v+a+ p       + +++g+ + +vtvvg +p +  ++++  la Grf+ e+d r    ++v+++e+ae+l
  gi|386001577|ref|YP_005919876.1|  99 IGNVLGVDAAYPLKnsralL-SFRGD-NASVTVVGISPaNHEDMRDS-LARGRFLAESDYR----AAVVSHEVAEEL 168
                                       54345599999965566543.33332.55599***664288889999.999****998766....8*********** PP

                          MacB_PCD 131 f....pvGdtirl........kpftVvGvled.pp.gsgsalgddavylp.........lttlqrrsitvrlkdgad 184
                                       f      G +ir+         +++VvGvle+ ++ + +s+     +y+          +++++++si+vr++d+a 
  gi|386001577|ref|YP_005919876.1| 169 FrmkiSPGNQIRIysdeksryMDLKVVGVLEEdEDpSYASG---GGIYIAhramkelldAENYNYDSIIVRARDSAE 242
                                       ***9989*********9999888******977543232333...35999866766665566668999********** PP

                          MacB_PCD 185 leaaaaelek 194
                                       +e++a++++k
  gi|386001577|ref|YP_005919876.1| 243 VEEVAEKVDK 252
                                       ******9987 PP

  == domain 2  score: -5.2 bits;  conditional E-value: 3
                          MacB_PCD  11 Gvaaviaivslgeglqasvlsqisdlg 37 
                                       Gv  +++ +++ + +  +v+++ s+ g
  gi|386001577|ref|YP_005919876.1| 291 GVSLIVGAIGISNVMMLTVKERTSEIG 317
                                       677777777777777777766666444 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.027   1.6e+02      28      60 ..      26      58 ..      19      73 .. 0.69
   2 ?   -3.3   0.4       2.2   1.3e+04      28      37 ..     289     299 ..     277     307 .. 0.52
   3 !   38.4   5.0   2.2e-13   1.3e-09       2      95 ..     314     400 ..     313     401 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.027
                              FtsX 28 itlvalviGlglgllaaqllsdvllssvfssel 60
                                      ++++  vi+++++l + q l+ +++++++ + +
  gi|386001577|ref|YP_005919876.1| 26 LGIIIGVISIVALLSVGQGLYGGVSEQFGDMDM 58
                                      556666667777777777777777777654333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                              FtsX  28 itlvalviG.l 37 
                                       i+ v+l++G +
  gi|386001577|ref|YP_005919876.1| 289 IGGVSLIVGaI 299
                                       34444444422 PP

  == domain 3  score: 38.4 bits;  conditional E-value: 2.2e-13
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       +eig+++a+G++ ++v+ l+l+ + +++l ++++G++lg+l+++l+  v        +++  + + +v++++++++l
  gi|386001577|ref|YP_005919876.1| 314 SEIGVMKAIGATAWDVRALYLLDAGMLGLASSIVGIILGALVSKLVGGV-------AMIPTEVTVQSVALGLLFGVL 383
                                       7**********************************99999999995555.......7899***************** PP

                              FtsX  79 lallagllsiskilkke 95 
                                       ++++ag++++ +++  +
  gi|386001577|ref|YP_005919876.1| 384 ITTAAGIYPANRAAILD 400
                                       **********9987665 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3     0.091   5.5e+02       6      19 ..      26      39 ..      23      42 .. 0.88
   2 ?    8.9   0.0   0.00025       1.5       6      35 ..     376     403 ..     372     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.091
                           DUF3042  6 kGflvGvlatiaav 19
                                       G+++Gv++ +a +
  gi|386001577|ref|YP_005919876.1| 26 LGIIIGVISIVALL 39
                                      59*******99976 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00025
                           DUF3042   6 kGflvGvlatiaavagavfvfKkkviePiE 35 
                                        G+l+Gvl+t a  ag   + +  +++PiE
  gi|386001577|ref|YP_005919876.1| 376 LGLLFGVLITTA--AGIYPANRAAILDPIE 403
                                       79*****98765..7999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2744.26
//
Query:       gi|386001578|ref|YP_005919877.1|  [L=315]
Description: hypothetical protein Mhar_0883 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 2298.40
//
Query:       gi|386001579|ref|YP_005919878.1|  [L=225]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-30  107.0   0.0    1.4e-30  106.6   0.0    1.2  1  ABC_tran      ABC transporter
      5e-10   39.7   0.0    4.9e-06   26.6   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.8e-07   30.9   0.0    0.00017   21.1   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0023   17.9   0.0     0.0041   17.0   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0055   16.4   0.0     0.0096   15.6   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
     0.0082   16.3   0.3       0.12   12.6   0.3    2.2  1  AAA_33        AAA domain
     0.0082   16.5   0.0      0.013   15.8   0.0    1.3  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.036   14.0   0.0    1.7  2  Rad17         Rad17 P-loop domain
      0.025   14.1   0.0      0.064   12.8   0.0    1.6  2  AAA_25        AAA domain
      0.031   14.6   0.0       0.19   12.0   0.0    2.1  2  AAA_22        AAA domain
      0.037   13.7   0.0       0.37   10.5   0.0    1.9  2  AAA_15        AAA ATPase domain
      0.038   14.5   0.0       0.66   10.5   0.0    2.3  2  AAA_18        AAA domain
      0.042   14.2   0.0      0.085   13.3   0.0    1.5  1  RNA_helicase  RNA helicase
      0.049   13.4   0.0        0.9    9.2   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.051   13.3   0.0       0.32   10.7   0.0    1.9  2  AAA_24        AAA domain
      0.056   13.4   0.0        9.2    6.1   0.0    2.4  2  NTPase_1      NTPase
       0.11   12.7   0.0        1.3    9.3   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.12   12.5   0.0       0.38   10.8   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   1.4e-33   1.4e-30       1     136 [.      23     171 ..      23     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.4e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ ++l+++eg  va++G++G+GKSt++++l  l +p  G+ill+g+dl +    +  ++ r eig+++q  +l  +
  gi|386001579|ref|YP_005919878.1|  23 LRGIDLEIEEGDFVALMGPSGCGKSTFMNILGCLDRPSDGTILLQGRDLGRlsdrDLARIRRDEIGFVFQRFHLIGR 99 
                                       67899********************************************99999777888999************** PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +++  n             e++++++++l+ +gl +    +++ sp++LSgG++qrva+aral+++p+++l+DEpt
  gi|386001579|ref|YP_005919878.1| 100 ISNLMNvelpmtfkelpkeERRDRAKELLEAVGLGG----RLGFSPTNLSGGERQRVAIARALANDPSVILADEPT 171
                                       **99999*********98888888999999999999....555667*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00029      0.29       1      23 [.      35      57 ..      35      85 .. 0.79
   2 !   26.6   0.0   4.9e-09   4.9e-06     227     300 ..     134     204 ..      93     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +l Gp g+GKS+++ +l +l 
  gi|386001579|ref|YP_005919878.1| 35 FVALMGPSGCGKSTFMNILGCLD 57
                                      57899**************9983 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.9e-09
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       g++  +++++lS G ++  a++ al+ ++   s++l DEp  +L+ k  r+++e++k l+r+g  +i++TH+ +
  gi|386001579|ref|YP_005919878.1| 134 GGRLGFSPTNLSGGERQRVAIARALANDP---SVILADEPTGNLDQKSRREIIEIMKGLNREGRTIIMVTHDAE 204
                                       677889999********999999999988...***************************************976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0021         2      25      42 ..      34      51 ..      24      57 .. 0.84
   2 !   21.1   0.0   1.7e-07   0.00017     129     211 ..     136     215 ..     113     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                       f a++Gp G+GKs +++
  gi|386001579|ref|YP_005919878.1| 34 DFVALMGPSGCGKSTFMN 51
                                      599***********9986 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.7e-07
                                       CTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 129 sagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                       + g+s+++LSgGe++ va+a  +A    +  ++ l De   +LD+k ++++ e++k  + +   +i++++++e++e 
  gi|386001579|ref|YP_005919878.1| 136 RLGFSPTNLSGGERQRVAIARALA----NDPSVILADEPTGNLDQKSRREIIEIMKGLNREgRTIIMVTHDAETTES 208
                                       5678899***********998877....34467789********************766653788999********9 PP

                                       -SCEEEE CS
                                       xxxxxxx RF
                             SMC_N 205 adklvgv 211
                                       +++++ +
  gi|386001579|ref|YP_005919878.1| 209 CSRVIWM 215
                                       9998755 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.1e-06    0.0041      99     119 ..      32      53 ..      14      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                                       T.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinal 119
                                       + ++++l+G+SG GKSt++n l
  gi|386001579|ref|YP_005919878.1|  32 EgDFVALMGPSGCGKSTFMNIL 53 
                                       44899***************88 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.6e-06    0.0096      16      39 ..      27      50 ..      22      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.6e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      ++ei++ +++ l+GpsG GKST++
  gi|386001579|ref|YP_005919878.1| 27 DLEIEEGDFVALMGPSGCGKSTFM 50
                                      567876669*************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.3   0.00012      0.12       2     109 ..      36     203 ..      35     211 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                            AAA_33   2 vllvGlpGsGKstlaerl..lkklg...avllssdt......................................... 32 
                                       v l G++G+GKst+   l  l + +   ++ll   +                                         
  gi|386001579|ref|YP_005919878.1|  36 VALMGPSGCGKSTFMNILgcLDR-PsdgTILLQGRDlgrlsdrdlarirrdeigfvfqrfhligrisnlmnvelpmt 111
                                       6689**********998765222.23544444444456666666666666667777777776665555555544442 PP

                            AAA_33  33 .......lrrrlfgtdqqskt...................dytrvldrlyqilnelarkalsagrnvil.dat..nl 80 
                                              +            +                    +t+++   +q++ ++ar al+   +vil d +  nl
  gi|386001579|ref|YP_005919878.1| 112 fkelpkeE------------RrdrakelleavglggrlgfSPTNLSGGERQRV-AIAR-ALANDPSVILaDEPtgNL 174
                                       22222221............033345556666666666666666777777776.5664.444444455555555588 PP

                            AAA_33  81 srrerarflklarrlgvpvrivvvetdee 109
                                       +++ r++++++ + l+ + r +++ t ++
  gi|386001579|ref|YP_005919878.1| 175 DQKSRREIIEIMKGLNREGRTIIMVTHDA 203
                                       88888888888888877755544444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.4e-05     0.013      25     140 ..      34     199 ..      27     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                            AAA_16  25 elvllsGesGvGKsslv...rellralekdggiflrgkcdql..esa...ipysalaqalareellrqllde..... 88 
                                         v l G+sG+GKs+ +    +l r+    g i+l+g+      +++   i+++ +  ++ r +l+  + +      
  gi|386001579|ref|YP_005919878.1|  34 DFVALMGPSGCGKSTFMnilGCLDRPSD--GTILLQGRDLGRlsDRDlarIRRDEIGFVFQRFHLIGRISNLmnvel 108
                                       5799***********9933344444333..44556665555544444444555779999999999999999988888 PP

                            AAA_16  89 .......aesaeleawrekleeala................................avpelagaea.........s 117
                                              + + e+++ +++l+ea++                                +                  +
  gi|386001579|ref|YP_005919878.1| 109 pmtfkelP-KEERRDRAKELLEAVGlggrlgfsptnlsggerqrvaiaralandpsvI--------LadeptgnldQ 176
                                       87776633.3345555555555555888888877777666665555444444333330........13334444446 PP

                            AAA_16 118 rllellkrllallsrderplvlv 140
                                         ++++ ++++ l r++r++++v
  gi|386001579|ref|YP_005919878.1| 177 KSRREIIEIMKGLNREGRTIIMV 199
                                       66666666665555556655555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.036      45      65 ..      33      53 ..      19      59 .. 0.82
   2 ?   -2.0   0.0       2.8   2.8e+03     130     176 ..     159     204 ..     138     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                             Rad17 45 kriLLisGPsGCgkstvvkvL 65
                                         + + GPsGCgkst +++L
  gi|386001579|ref|YP_005919878.1| 33 GDFVALMGPSGCGKSTFMNIL 53
                                      5567799***********998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                             Rad17 130 rtdkklilvedlPnkfyrds.dalrevirkylrssealplilviteie 176
                                         d ++il ++   +  + s + + e+++   r +++  +i+v  + e
  gi|386001579|ref|YP_005919878.1| 159 ANDPSVILADEPTGNLDQKSrREIIEIMKGLNREGRT--IIMVTHDAE 204
                                       4556667666655444443325566666555555555..677665555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.4e-05     0.064      30      50 ..      30      50 ..      21      55 .. 0.90
   2 ?   -2.4   0.0         3     3e+03     107     107 ..     141     141 ..     114     197 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +g++++l+G++g+GK+t+ 
  gi|386001579|ref|YP_005919878.1| 30 IEEGDFVALMGPSGCGKSTFM 50
                                      679****************95 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                            AAA_25 107 d 107
                                        
  gi|386001579|ref|YP_005919878.1| 141 P 141
                                       1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.19       4      23 ..      32      51 ..      29      81 .. 0.89
   2 ?    0.2   0.0      0.84   8.3e+02      81      99 ..     153     169 ..     101     207 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_22  4 tagilvvtGesGtGKTtllr 23
                                      +  +++++G+sG+GK+t ++
  gi|386001579|ref|YP_005919878.1| 32 EGDFVALMGPSGCGKSTFMN 51
                                      567899***********987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.84
                            AAA_22  81 aleqalraravielliiDE 99 
                                       a+++al +   +++++ DE
  gi|386001579|ref|YP_005919878.1| 153 AIARALAND--PSVILADE 169
                                       222222222..23555544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00037      0.37      18      50 ..      27      60 ..      23     130 .. 0.68
   2 ?    1.3   0.0      0.22   2.2e+02     322     365 ..     160     202 ..     149     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +++++e  +  l G+ ++GKS+++++l  +   +
  gi|386001579|ref|YP_005919878.1| 27 DLEIEEGdFVALMGPSGCGKSTFMNILGCLDRPS 60
                                      34444446******************97766555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++ ++l +EP  +L  +  +++i+ +k l ++++  +i+ TH 
  gi|386001579|ref|YP_005919878.1| 160 NDPSVILADEPTGNLDQKSRREIIEIMKGLNREGR-TIIMVTHD 202
                                       67889999**************************9.9******6 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00066      0.66       1      18 [.      36      53 ..      36     101 .. 0.86
   2 ?    1.7   0.0      0.35   3.5e+02      47      85 ..     169     204 ..     136     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      ++l+G++G+GK+t+ + L
  gi|386001579|ref|YP_005919878.1| 36 VALMGPSGCGKSTFMNIL 53
                                      689***********9988 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.35
                            AAA_18  47 deskrldedkldklldaleenssaleegknlvidghlae 85 
                                       +++  ld++ + ++++++++ ++   eg ++++  h ae
  gi|386001579|ref|YP_005919878.1| 169 EPTGNLDQKSRREIIEIMKGLNR---EGRTIIMVTHDAE 204
                                       45788999999999999999975...9999999999876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.5e-05     0.085       2      18 ..      37      53 ..      36      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeL 18
                                       l Gpsg+GKSt+++ L
  gi|386001579|ref|YP_005919878.1| 37 ALMGPSGCGKSTFMNIL 53
                                      689***********986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00091       0.9      44      68 ..      30      54 ..      11      60 .. 0.83
   2 ?    1.9   0.0      0.16   1.6e+02     110     149 ..     162     203 ..     145     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00091
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      ie+ + ++l+GpsG GKs +   lg
  gi|386001579|ref|YP_005919878.1| 30 IEEGDFVALMGPSGCGKSTFMNILG 54
                                      788899************8876666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                         IstB_IS21 110 dllilDdlgllpldqaeaellfevie..kryerrsiiitsnl 149
                                         +il d  + +ldq++++++ e+++  +r +r+ i++t + 
  gi|386001579|ref|YP_005919878.1| 162 PSVILADEPTGNLDQKSRREIIEIMKglNREGRTIIMVTHDA 203
                                       456777788999*************94446777778888665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.32       5      22 ..      36      53 ..      34      92 .. 0.86
   2 ?    0.1   0.0      0.58   5.8e+02     108     135 ..     179     206 ..     172     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gpsg GK+t+++ l
  gi|386001579|ref|YP_005919878.1| 36 VALMGPSGCGKSTFMNIL 53
                                      689***********9877 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                            AAA_24 108 aeefrrllkklqelrknvifiahektrk 135
                                       ++e+++++k l+  + ++i++ h  + +
  gi|386001579|ref|YP_005919878.1| 179 RREIIEIMKGLNREGRTIIMVTHDAETT 206
                                       6899999999999999*****9988766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.019        19       2      17 ..      36      51 ..      35      94 .. 0.75
   2 ?    6.1   0.0    0.0093       9.2      85     141 ..     151     209 ..     124     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                                      EEEE--TTSSHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvk 17
                                      v++ Gp+G GK+T+++
  gi|386001579|ref|YP_005919878.1| 36 VALMGPSGCGKSTFMN 51
                                      6789*********985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHH CS
                          NTPase_1  85 alealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrkdlalv 141
                                        +++ r   +++ vi+ DE  G++  ks++ + ++ + L+ +++ +++v h +++ +  
  gi|386001579|ref|YP_005919878.1| 151 RVAIARALANDPSVILADEpTGNLDQKSRREIIEIMKGLNrEGRTIIMVTHDAETTESC 209
                                       4444555558999******88*******99999999999989999****9999754444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0013       1.3      62      89 ..     160     187 ..     135     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       +++++++ DE  ++lD++s+++++e+++
  gi|386001579|ref|YP_005919878.1| 160 NDPSVILADEPTGNLDQKSRREIIEIMK 187
                                       45889999****************9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00038      0.38       2      19 ..      36      53 ..      35      62 .. 0.92
   2 ?   -1.7   0.0       3.1   3.1e+03      70      70 ..     186     186 ..     147     217 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      va++G +  GKSt++n l
  gi|386001579|ref|YP_005919878.1| 36 VALMGPSGCGKSTFMNIL 53
                                      89**************77 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                       H CS
                          MMR_HSR1  70 f 70 
                                       +
  gi|386001579|ref|YP_005919878.1| 186 M 186
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1670.11
//
Query:       gi|386001580|ref|YP_005919879.1|  [L=223]
Description: hypothetical protein Mhar_0885 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1701.11
//
Query:       gi|386001581|ref|YP_005919880.1|  [L=177]
Description: hypothetical protein Mhar_0886 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 1403.58
//
Query:       gi|386001582|ref|YP_005919881.1|  [L=311]
Description: hypothetical protein Mhar_0887 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.22   11.3   0.3       0.22   11.3   0.3    6.0  6  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
       0.73    9.8  12.8        2.1    8.3   0.8    2.4  2  GnsAB_toxin      GnsA/GnsB toxin of bacterial toxin-antitoxin
        2.2    8.5   4.5         56    3.9   2.9    3.6  3  Phage_TAC_7      Phage tail assembly chaperone proteins, E, o
        2.5    8.7   9.4        1.1    9.8   0.6    3.2  3  DUF2482          Hypothetical protein of unknown function (DU
        4.5    7.8   9.5         11    6.6   1.6    3.3  3  bZIP_Maf         bZIP Maf transcription factor


Domain annotation for each model (and alignments):
>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.33   1.2e+03       7      17 ..      44      54 ..      44      56 .. 0.85
   2 ?   11.3   0.3   6.1e-05      0.22       7      20 ..     119     132 ..     119     136 .. 0.92
   3 ?    0.9   0.4       0.1   3.7e+02       9      19 ..     159     169 ..     158     169 .. 0.87
   4 ?    3.9   0.7     0.012        44       6      20 ..     190     204 ..     187     207 .. 0.87
   5 ?    5.3   0.7    0.0044        16       6      23 ..     209     226 ..     205     230 .. 0.86
   6 ?    3.2   0.5     0.021        75       8      19 ..     230     241 ..     228     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                                      HHHHTSBHHHH CS
                   Ribosomal_L12_N  7 eaikeltvLEl 17
                                      e+ +++t+ El
  gi|386001582|ref|YP_005919881.1| 44 EEMENMTLGEL 54
                                      6889****998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.1e-05
                                       HHHHTSBHHHHHHH CS
                   Ribosomal_L12_N   7 eaikeltvLElseL 20 
                                       e+ik++t+ Els+L
  gi|386001582|ref|YP_005919881.1| 119 EEIKNMTLAELSDL 132
                                       79***********9 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.1
                                       HHTSBHHHHHH CS
                   Ribosomal_L12_N   9 ikeltvLElse 19 
                                        +++t+ El e
  gi|386001582|ref|YP_005919881.1| 159 MENMTLAELRE 169
                                       68******987 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.012
                                       HHHHHTSBHHHHHHH CS
                   Ribosomal_L12_N   6 ieaikeltvLElseL 20 
                                       +e+++++t+ E+  L
  gi|386001582|ref|YP_005919881.1| 190 LEELEGMTLAEIEAL 204
                                       79*********9887 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.0044
                                       HHHHHTSBHHHHHHHHHH CS
                   Ribosomal_L12_N   6 ieaikeltvLElseLvka 23 
                                       i +++++t+ El eL++a
  gi|386001582|ref|YP_005919881.1| 209 IGELEKMTIGELEELNEA 226
                                       6689***********987 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.021
                                       HHHTSBHHHHHH CS
                   Ribosomal_L12_N   8 aikeltvLElse 19 
                                       + +++t+ Else
  gi|386001582|ref|YP_005919881.1| 230 EMENMTLAELSE 241
                                       579********8 PP

>> GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.8   0.00059       2.1       4      35 ..     119     150 ..     116     163 .. 0.86
   2 ?    5.8   5.3    0.0036        13       3      45 ..     190     232 ..     188     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00059
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEE CS
                       GnsAB_toxin   4 EeLkkkAEeeiaeliakKiaELkKkTGkEVse 35 
                                       Ee+k+   +e+++l a K+aEL   T  E+  
  gi|386001582|ref|YP_005919881.1| 119 EEIKNMTLAELSDLRAEKMAELGNMTSEEIEA 150
                                       99999999******************999865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEEEEEEEEEETT CS
                       GnsAB_toxin   3 iEeLkkkAEeeiaeliakKiaELkKkTGkEVseieFtaREkmt 45 
                                        EeL     +ei +l   Ki EL+K T  E  e++ + R  m 
  gi|386001582|ref|YP_005919881.1| 190 LEELEGMTLAEIEALREEKIGELEKMTIGELEELNEARRTEME 232
                                       589999999******************9999999888887775 PP

>> Phage_TAC_7  Phage tail assembly chaperone proteins, E, or 41 or 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.33   1.2e+03      58      76 ..      41      59 ..      35      79 .. 0.64
   2 ?    0.5   0.0      0.19   6.8e+02      58      76 ..     116     134 ..      88     141 .. 0.85
   3 ?    3.9   2.9     0.016        56      55      77 ..     184     207 ..     117     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.33
                       Phage_TAC_7 58 lppedlekLdlaDlarlqe 76
                                      l++e++e+++l  l++ ++
  gi|386001582|ref|YP_005919881.1| 41 LTEEEMENMTLGELRAHRQ 59
                                      4555555555544444333 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                       Phage_TAC_7  58 lppedlekLdlaDlarlqe 76 
                                       l+ e++++++la l  l++
  gi|386001582|ref|YP_005919881.1| 116 LTDEEIKNMTLAELSDLRA 134
                                       7889999999998887765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.016
                       Phage_TAC_7  55 lsg.lppedlekLdlaDlarlqer 77 
                                       l++ +++e+le+++la +++l+e+
  gi|386001582|ref|YP_005919881.1| 184 LATdITLEELEGMTLAEIEALREE 207
                                       3336999*********99999985 PP

>> DUF2482  Hypothetical protein of unknown function (DUF2482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6   0.00032       1.1       2      26 ..     120     144 ..     119     150 .. 0.86
   2 ?    5.3   0.2     0.008        29       2      24 ..     139     161 ..     138     171 .. 0.86
   3 ?    1.1   0.9      0.15   5.6e+02       2      25 ..     192     215 ..     191     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00032
                           DUF2482   2 efKdmtqeeikdllaeKskeLyeli 26 
                                       e+K+mt  e+ dl aeK  eL ++ 
  gi|386001582|ref|YP_005919881.1| 120 EIKNMTLAELSDLRAEKMAELGNMT 144
                                       89*******************8765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.008
                           DUF2482   2 efKdmtqeeikdllaeKskeLye 24 
                                       e+ +mt eei  l +eK  e+ +
  gi|386001582|ref|YP_005919881.1| 139 ELGNMTSEEIEALWQEKRLEMEN 161
                                       678**************988765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.15
                           DUF2482   2 efKdmtqeeikdllaeKskeLyel 25 
                                       e+  mt  ei  l +eK +eL ++
  gi|386001582|ref|YP_005919881.1| 192 ELEGMTLAEIEALREEKIGELEKM 215
                                       6778999*************9764 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.29     1e+03       2      18 ..      42      58 ..      41      68 .. 0.80
   2 ?    6.6   1.6    0.0032        11       1      34 [.     116     156 ..     116     174 .. 0.78
   3 ?    4.2   0.1     0.018        64       4      48 ..     191     243 ..     188     251 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                          bZIP_Maf  2 sdeellslsvrEfnrfl 18
                                      ++ee+ ++++ E++ + 
  gi|386001582|ref|YP_005919881.1| 42 TEEEMENMTLGELRAHR 58
                                      78999999999998765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0032
                          bZIP_Maf   1 lsdeellslsvrEfnrfl.......rglteeeverLKqrRR 34 
                                       l+dee+ +++++E+            ++t+ee+e L q  R
  gi|386001582|ref|YP_005919881.1| 116 LTDEEIKNMTLAELSDLRaekmaelGNMTSEEIEALWQEKR 156
                                       689**********9654356666778999999999998776 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.018
                          bZIP_Maf   4 eellslsvrEfnrfl........rglteeeverLKqrRRr.lKNrgyakscrkr 48 
                                       eel  ++++E    l        +++t  e+e+L ++RR+ + N   a  + +r
  gi|386001582|ref|YP_005919881.1| 191 EELEGMTLAEIEA-LreekigelEKMTIGELEELNEARRTeMENMTLAELSEQR 243
                                       6666677776632.224445666999*********9999834566666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2089.87
//
Query:       gi|386001583|ref|YP_005919882.1|  [L=314]
Description: Cation diffusion facilitator family transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-45  155.3   6.0    1.9e-45  155.0   6.0    1.1  1  Cation_efflux  Cation efflux family
    1.5e-24   85.9   3.8    2.4e-24   85.3   3.8    1.3  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
      0.067   12.8   0.0       0.15   11.6   0.0    1.6  1  SUR7           SUR7/PalI family
       0.16   11.9   2.7        1.2    9.0   0.1    2.5  2  DUF418         Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   6.0   4.3e-49   1.9e-45       2     199 .]      28     222 ..      27     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 4.3e-49
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       ++++++nl+l+++e+++g++ nS+a++ada+hslsd+v+ + +l+++++ ++ppde +p G+ r+e+l++++ gl+l
  gi|386001583|ref|YP_005919882.1|  28 LIGVVINLALTFMEFVAGIVGNSQAVVADAVHSLSDTVTGVAVLVGVRFWSRPPDECHPHGHRRIEFLVTIFIGLIL 104
                                       689************************************************************************** PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlv 155
                                        ++a+ + ++a+  l   ++r  + ++a++ a+v+++ + +l+  ++ +g+++rs+al a+a+h+++Dal+s+ ++ 
  gi|386001583|ref|YP_005919882.1| 105 AAVALGIGYNALATLH-DPQRKPPGAVAFFAAVVMIFTKEFLYQWTISVGKEIRSPALIASAWHHRSDALSSIPAAA 180
                                       ************8887.************************************************************ PP

                     Cation_efflux 156 salvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                       ++ ++ +++  s   +D++++++i+++il  a+k+++ sl +L+
  gi|386001583|ref|YP_005919882.1| 181 AVAGAAIVPGLS--FLDHLGAIVISAFILQVAWKIIRPSLEQLV 222
                                       *******96665..**************************9996 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   3.8   5.3e-28   2.4e-24       2      79 .]     227     304 ..     226     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 5.3e-28
                                       ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       +ee+++ i+++++++pgv++vh +rtr++Gs i vdlh+ vd++l+v+e+Hei++ev++r+ e + +v dv++H+eP
  gi|386001583|ref|YP_005919882.1| 227 PEEIRRGIEQLASATPGVEEVHAIRTRHIGSGIEVDLHVLVDPRLTVEEGHEISEEVKRRLIEYVSDVVDVVVHLEP 303
                                       79999************************************************************************ PP

                                       . CS
                          ZT_dimer  79 e 79 
                                       +
  gi|386001583|ref|YP_005919882.1| 304 Y 304
                                       7 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.4e-05      0.15      97     168 ..      12     113 ..       3     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                              SUR7  97 lPsnlrktlsklnnltkalfilhiialvlsfislvvgllaic..................................v 139
                                       l s+ r   s+   + +  +i  +i l+l+f+++v g+++++                                  +
  gi|386001583|ref|YP_005919882.1|  12 LESENRRHAST---VRRLTLIGVVINLALTFMEFVAGIVGNSqavvadavhslsdtvtgvavlvgvrfwsrppdecH 85 
                                       66666666666...8999***********************999************************998888844 PP

                              SUR7 140 spdnsrllsflnlllsvlsflatllaall 168
                                        + ++ ++ fl++++  l++ a++l+ + 
  gi|386001583|ref|YP_005919882.1|  86 PHGHR-RIEFLVTIFIGLILAAVALGIGY 113
                                       44444.59999999999999888888765 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00027       1.2       9      66 ..      15      73 ..       9      78 .. 0.79
   2 ?    2.5   0.2     0.027   1.2e+02      53      89 ..      99     135 ..      85     163 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00027
                            DUF418  9 dpeehkrllrrllligllvglplnllla.vlaeaaeesallelllsvlrylaglllalg 66
                                      ++ +h + +rrl lig+++ l+l+++ + + +  +++++++  + s+ + ++g+++ +g
  gi|386001583|ref|YP_005919882.1| 15 ENRRHASTVRRLTLIGVVINLALTFMEFvAGIVGNSQAVVADAVHSLSDTVTGVAVLVG 73
                                      67899**********************96666666667777777777777777776655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.027
                            DUF418  53 svlrylaglllalgyvalillllakekrrrllralaa 89 
                                       ++   la+++l++gy al +l  +++k   ++  +aa
  gi|386001583|ref|YP_005919882.1|  99 FIGLILAAVALGIGYNALATLHDPQRKPPGAVAFFAA 135
                                       2333344444444444444444444444443443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1938.13
//
Query:       gi|386001584|ref|YP_005919883.1|  [L=355]
Description: hypothetical protein Mhar_0889 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-31  107.2  14.9    6.8e-31  107.2  14.9    2.7  3  DUF389    Domain of unknown function (DUF389)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.2    0.0056     1e+02      71     100 ..     137     166 ..     116     167 .. 0.82
   2 !  107.2  14.9   3.8e-35   6.8e-31       1     141 [.     168     302 ..     168     303 .. 0.97
   3 ?   -1.5   0.1      0.13   2.3e+03      21      47 ..     318     345 ..     307     353 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0056
                            DUF389  71 pnlvdllvAlasGaagalallsgnssslvG 100
                                       ++ v++++ ++s +++a+ +l++n ++++G
  gi|386001584|ref|YP_005919883.1| 137 VSRVYVFMVILSSIVAAFGVLKNNVAVIIG 166
                                       446889999******************999 PP

  == domain 2  score: 107.2 bits;  conditional E-value: 3.8e-35
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeelptsemlsrtepnlvdll 77 
                                       M+i+Pl+ p +++++++++gdr l+ r+lk+ ++g+ +a+++++l+g++lp++       + +e++srt + l +++
  gi|386001584|ref|YP_005919883.1| 168 MVIAPLLLPNVSFSLATILGDRGLAVRALKANVVGVGTAIAFSYLLGTFLPVD------PEIPEIASRTGVGLGEVA 238
                                       ***********************************************888885......5668************** PP

                            DUF389  78 vAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIv 141
                                       +AlasG agala+++g s++l+Gv++a+aLlPP+v++Gl+++ g+ +la+g++ll++ N++ ++
  gi|386001584|ref|YP_005919883.1| 239 LALASGSAGALAFTTGVSATLIGVMVAVALLPPLVAFGLLMGSGHESLAWGAMLLFIANFISVN 302
                                       *************************************************************987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.13
                            DUF389  21 drkllrrglknlliglllall.vgflfg 47 
                                       +++ +rr+ ++ +++++l l+ +++l+ 
  gi|386001584|ref|YP_005919883.1| 318 KWSEARRAKRASIVAMVLWLImLAALLI 345
                                       5666666666666665554430344433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2110.35
//
Query:       gi|386001585|ref|YP_005919884.1|  [L=357]
Description: Magnesium and cobalt transport protein CorA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-81  272.8   0.2    4.2e-81  272.5   0.2    1.0  1  CorA           CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
       0.14   11.7   0.1       0.23   11.0   0.1    1.3  1  Hormone_recep  Ligand-binding domain of nuclear hormone recep
        5.2    7.0   6.6        0.3   11.0   0.6    2.1  2  T2SSF          Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.5   0.2   7.1e-85   4.2e-81       3     292 .]      61     353 ..      59     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.5 bits;  conditional E-value: 7.1e-85
                              CorA   3 gfvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeev...plsill 75 
                                       +++W+ +  ++++  +ee+ + + +++l+led++ +++rp++edydd  ++vl+ + + ++e  + e+   +ls+++
  gi|386001585|ref|YP_005919884.1|  61 TVTWIKVVGVHTPeVIEEIGRSFEIHPLVLEDIVHTDQRPKMEDYDDRVFIVLRLLSRVEGEGGRGEIrseQLSLIV 137
                                       689*******99979*************************************************9999********* PP

                              CorA  76 gdnflitvrreplealdevikrlk..deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeil 150
                                       g+ +li++++ ++++++ +++r++  + + ++  +  l y l+d++vd++f +le++ eel+ le+el    + e +
  gi|386001585|ref|YP_005919884.1| 138 GRGLLISFQETDMDVFEPARDRIRksKGKIRRLGADYLAYSLIDAVVDSYFLILEEVGEELEVLEEELLGGPTPEAA 214
                                       ************************9999999********************************************** PP

                              CorA 151 relaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtysslls 227
                                       +e+ +l+r+++ lrr+++p+rev+ ++l++++ + +++  + ylrd++d++ +++e +e+ re+l+ + ++y s +s
  gi|386001585|ref|YP_005919884.1| 215 QEIHRLKRDMIFLRRSIWPLREVI-SRLSRGESEIFTEPTEIYLRDVYDHTVQAIEAIETFREVLSGMLEIYLSSIS 290
                                       ************************.6666699999999999************************************ PP

                              CorA 228 erlNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                                       +r+N+vmkvLT++++if+PlT+++GiyGmNf+++Pel w++gyp+v  l++m+++ +++l++f+r
  gi|386001585|ref|YP_005919884.1| 291 NRMNEVMKVLTIIATIFIPLTFVAGIYGMNFDYMPELRWQWGYPAV--LLFMLISGVIMLLYFRR 353
                                       **********************************************..***************98 PP

>> Hormone_recep  Ligand-binding domain of nuclear hormone receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.8e-05      0.23     152     192 ..     266     305 ..     255     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.8e-05
                                       H..HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHCCC CS
                     Hormone_recep 152 etqeiveklqeklsneLheYysseyssRlakllkilpelrs 192
                                       +  e++e ++e+ls  L  Y+ss  s+R+++ +k+l+ + +
  gi|386001585|ref|YP_005919884.1| 266 QAIEAIETFREVLSGMLEIYLSSI-SNRMNEVMKVLTIIAT 305
                                       3449*****************766.89*********99876 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6     5e-05       0.3      36     120 ..     235     317 ..     189     319 .. 0.85
   2 ?   -3.1   0.8       1.2   7.1e+03     105     120 ..     334     349 ..     329     351 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                                       HHHHHHHHTTSSHHHHHCT-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXX CS
                             T2SSF  36 kriarrlraGgslsealertpssefpelvvqlirageeggnLaevLerlaeyleeerelrrkllaallepllllvva 112
                                       ++++ rl+ G+  se + + ++  ++++++  ++a+e+  +  evL+ + e +     +r ++  + l  ++++++ 
  gi|386001585|ref|YP_005919884.1| 235 REVISRLSRGE--SEIFTEPTEIYLRDVYDHTVQAIEAIETFREVLSGMLEIYLSSISNRMNEVMKVLTIIATIFIP 309
                                       56677777777..677776555666*******************************************999999987 PP

                                       XXXXXXXX CS
                             T2SSF 113 llvllill 120
                                       l +++ + 
  gi|386001585|ref|YP_005919884.1| 310 LTFVAGIY 317
                                       77776665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                                       TXXXXXXXXXXXXXXX CS
                             T2SSF 105 pllllvvallvllill 120
                                       p++ll++++  +++ll
  gi|386001585|ref|YP_005919884.1| 334 PAVLLFMLISGVIMLL 349
                                       5555555544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2185.56
//
Query:       gi|386001586|ref|YP_005919885.1|  [L=318]
Description: Transporter, small conductance mechanosensitive ion channel (MscS) family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-30  104.8   5.8    4.2e-30  104.8   5.8    1.9  2  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.048   14.0   1.8       0.13   12.6   0.8    2.1  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3      0.51   4.6e+03      27      50 ..      29      55 ..       8      60 .. 0.45
   2 !  104.8   5.8   4.7e-34   4.2e-30       4     199 ..      72     288 ..      69     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHHHH...HHCHHHHHHH CS
                        MS_channel 27 llavlGalglalgl...alkdlisnlv 50
                                      ll  + ++++a+gl    +k l+++l+
  gi|386001586|ref|YP_005919885.1| 29 LLQKAFLTAVAVGLihiLFKHLFEDLL 55
                                      333333344444431114666666665 PP

  == domain 2  score: 104.8 bits;  conditional E-value: 4.7e-34
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                       ++i+ +vv   +vl  +   +++ll++ G+++++l+ al+d+++n+++G+++ ++  +++GD+ve+    G V+di 
  gi|386001586|ref|YP_005919885.1|  72 VSIIYLVVLAAVVLNIWIETTQSLLVSYGIIAAGLAVALQDIFKNFFGGVVIFVTGIYRVGDRVEMDSRMGDVIDID 148
                                       55555666666666666666********************************************************* PP

                                       SSEEEE.........EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-T CS
                        MS_channel  81 lrttki.........rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekp 148
                                        + t++          + +gr+++iPn ++++  + N+++ ++  ++++si +ty+sd   +++++ +++ +++++ 
  gi|386001586|ref|YP_005919885.1| 149 VLYTTLmemgewmsgDQATGRLTMIPNGYVLSGLVNNYTKDHPFLWDEISIPITYDSD---WREAVTTILSVVRRET 222
                                       *****93333333333568***************************************...********99999999 PP

                                       TB-T..................TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHH CS
                        MS_channel 149 evlk..................dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkil 199
                                       ++                    + + ++v+ +++d+ +nf +r+++     +e+  +++ + +ri + +
  gi|386001586|ref|YP_005919885.1| 223 DDVGreaetsissleekyylprKVTEPAVFVTMTDNWINFNIRYVTVV---RERRMTKDRLSRRILEQI 288
                                       99989****************999999*****************9877...788888888888776554 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.27   2.4e+03      28      60 ..      12      43 ..       3      50 .. 0.58
   2 ?   12.6   0.8   1.4e-05      0.13      22      74 ..      73     116 ..      60     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.27
                   Phage_holin_5_2 28 giiGiilgvvivft.adfqaedilifgaiiqGil 60
                                      +++ ++lg++  +  + + ++++l+  a+++G++
  gi|386001586|ref|YP_005919885.1| 12 TALAAALGALHHLHpNPLLQKAFLT--AVAVGLI 43
                                      4556666655555433555555555..7777766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.4e-05
                   Phage_holin_5_2  22 yIPlilgiiGiilgvvivftadfqaedilifg....aiiqGilsggastglnQliKQ 74 
                                        I++++++  ++l+             i+i +     +  Gi+++g+++ l++++K+
  gi|386001586|ref|YP_005919885.1|  73 SIIYLVVLAAVVLN-------------IWIETtqslLVSYGIIAAGLAVALQDIFKN 116
                                       46666667777777.............8987788888999****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1775.33
//
Query:       gi|386001587|ref|YP_005919886.1|  [L=325]
Description: CaCA family Na+/Ca+ antiporter [Methanosaeta harundinacea 6Ac]
Scores for complete 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-48  164.8  40.9    4.1e-25   88.5  15.8    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein
  ------ inclusion threshold ------
       0.34   11.0   5.4        1.3    9.1   0.1    3.4  4  DUF3593   Protein of unknown function (DUF3593)


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5  15.8   4.6e-29   4.1e-25       4     149 ..       9     147 ..       6     150 .. 0.83
   2 !   82.4  17.2   3.5e-27   3.2e-23       6     146 ..     186     318 ..     182     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 4.6e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       ++f+ sl++++ ++d++++sae i+  +gis+ ++G+t++A g+s pEl+ss+ a+++g+++++ gnv+Gsn+ n++
  gi|386001587|ref|YP_005919886.1|   9 LIFVGSLAVLVKASDVFTDSAERIGVGFGISPFIIGVTIVAVGTSTPELVSSVLAVIKGSPEIVAGNVMGSNVTNIF 85 
                                       6899************************************************************************* PP

                                       THHHHHHHHHH.BTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigs.lkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                       l++G++a++g+ ++   e  ++dl+l++  alll+l  ++       +g  t+ e+l++l+  ++yl+++
  gi|386001587|ref|YP_005919886.1|  86 LILGISAIVGKkMVTSYELANVDLPLFVGSALLLSL--MVG------DGAFTLPEALLCLACLLVYLLYA 147
                                       *********995444444557777888887777733..332......36666666666666666666554 PP

  == domain 2  score: 82.4 bits;  conditional E-value: 3.5e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTH CS
                          Na_Ca_ex   6 filslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllv 82 
                                       ++ls+++++++a++ v s+ ++++++gi  ++++   +Alg+slpEl++s+ aa+ ++++laign++Gsnifn l++
  gi|386001587|ref|YP_005919886.1| 186 LFLSVVFLYIGANYTVVSVVKLSEIVGIGTEIIAASAVALGTSLPELVVSVKAAAMNKPELAIGNIIGSNIFNALGI 262
                                       68999************************************************************************ PP

                                       HHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  83 iGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                       +G++al+g++++ +  +++   ++ +++++ ll+++++      ++++t +eg +l+++Ya++l
  gi|386001587|ref|YP_005919886.1| 263 MGISALFGTVVIPETITAF---VMPMMIVATLLYFVVIW-----EKEMTHWEGWMLVIFYAFFL 318
                                       *********5444434333...34444444433344433.....49****************98 PP

>> DUF3593  Protein of unknown function (DUF3593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.36   3.2e+03      29      48 ..      32      51 ..       9      66 .. 0.64
   2 ?    9.1   0.1   0.00015       1.3      16      70 ..      62     117 ..      57     123 .. 0.81
   3 ?    3.0   0.0     0.011     1e+02      26      58 ..     130     162 ..     116     168 .. 0.76
   4 ?   -2.0   0.2      0.41   3.7e+03      36      40 ..     291     295 ..     272     318 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.36
                           DUF3593 29 tlvGfallLlFvavtipagi 48
                                      + vGf +  + + vti+a  
  gi|386001587|ref|YP_005919886.1| 32 IGVGFGISPFIIGVTIVAVG 51
                                      44677777777888888755 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00015
                           DUF3593  16 LvllkkskelpkltlvGfallLlFvavtipagivakevygesLanvDl.LHGlaes 70 
                                       L ++k s+e+    ++G  ++ +F ++ i a +  k v  ++LanvDl L  ++  
  gi|386001587|ref|YP_005919886.1|  62 LAVIKGSPEIVAGNVMGSNVTNIFLILGISAIVGKKMVTSYELANVDLpLFVGSAL 117
                                       667788888889999***************99999999999******734444444 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.011
                           DUF3593  26 pkltlvGfallLlFvavtipagivakevygesL 58 
                                        +++l+  a+lL++ + ++ ++ va+e++++++
  gi|386001587|ref|YP_005919886.1| 130 LPEALLCLACLLVYLLYAVSVERVAEEARDRTM 162
                                       566788888999999999999999999888776 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.41
                           DUF3593  36 lLlFv 40 
                                       lL Fv
  gi|386001587|ref|YP_005919886.1| 291 LLYFV 295
                                       22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2400.05
//
Query:       gi|386001588|ref|YP_005919887.1|  [L=256]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for complete 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-39  135.3  21.3    2.4e-39  134.9  21.3    1.1  1  ABC2_membrane    ABC-2 type transporter
    9.9e-15   54.5  22.2    9.9e-15   54.5  22.2    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.6e-08   34.2  16.1    2.1e-08   33.8  16.1    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9  21.3   4.1e-43   2.4e-39       2     209 ..       8     220 ..       7     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 4.1e-43
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.....nsedglnr.....pgllffsvlflafsal 68 
                                        i+ l+ re+++++r +s   + +l+ p++++ ++g+ f ++      +  d   +     pg++++++lf +  ++
  gi|386001588|ref|YP_005919887.1|   8 AIYSLWLREMIRFFRLKSRV-FGSLAPPFFFLAFLGFGFRSAAmpaipEGVD---YisflaPGIIGMTLLFSS--TF 78 
                                       6899*************888.*******************944443334444...355599************..** PP

                     ABC2_membrane  69 tsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltal 142
                                        +++++++re g+l + +v+p+ s+ ++v++++++ ++ ++lq+li+l+  + + gl++s     +l+l++++l+a 
  gi|386001588|ref|YP_005919887.1|  79 GGLSMLWDREFGFLREIMVAPV-SRLSIVIGRTAGGVTTAVLQGLIILVPGVAM-GLEISglpGLLLALVFMVLIAT 153
                                       **********************.*******************************.****977444************ PP

                     ABC2_membrane 143 aasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       ++ slgl++++ ++++  +s++++++++pl+llsG+++pi+++p wl+ ++yl Plty+v++lr++l
  gi|386001588|ref|YP_005919887.1| 154 TFNSLGLAFASRMKDMSGFSLIMNFMVFPLFLLSGALFPISNLPPWLRTLSYLDPLTYGVDGLRGSL 220
                                       *******************************************77*******************986 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 !   54.5  22.2   1.7e-18   9.9e-15     157     345 .]      57     248 ..      46     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.7e-18
                   ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafgl 231
                                        ++ sfl++ i+ + ++++++f   s++ ++e + +  ++v++vs+l++++++  g ++ ++lq l+il+  +a gl
  gi|386001588|ref|YP_005919887.1|  57 VDYISFLAPGIIGMTLLFSSTFGGLSMLWDREFGFLREIMVAPVSRLSIVIGRTAGGVTTAVLQGLIILVpgVAMGL 133
                                       57889999966666666777778889**********99*******************************98889994 PP

                   ABC2_membrane_3 232 gipfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPff 307
                                       +i+   +l+l+l++++l + ++ +lg+++ s +k+++  ++++ ++ ++l++++g+lfp+++lp +l++++++ P++
  gi|386001588|ref|YP_005919887.1| 134 EISGLpGLLLALVFMVLIATTFNSLGLAFASRMKDMSGFSLIMNFMVFPLFLLSGALFPISNLPPWLRTLSYLDPLT 210
                                       444446778888999999999999999999999999999999999999***************************** PP

                   ABC2_membrane_3 308 apglgllrlitgdplweillsliilalfavvylllall 345
                                       +  +gl   + g++ ++++ +l+il + +++ l l+++
  gi|386001588|ref|YP_005919887.1| 211 YGVDGLRGSLVGASSFSLAFDLAILTACSIAALGLGAY 248
                                       ******************************99999875 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8  16.1   3.5e-12   2.1e-08      97     288 .]      83     255 ..      35     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.5e-12
                   ABC2_membrane_2  97 iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvllll 173
                                          ++e g l+  +  PvsR +i++g   gg++       a+l + l+ l++ +a g ++++     l++a v+++l
  gi|386001588|ref|YP_005919887.1|  83 MLWDREFGFLREIMVAPVSRLSIVIGRTAGGVTT------AVLQG-LIILVPGVAMGLEISGL--PGLLLALVFMVL 150
                                       555677788888999****************999......66666.33355555556555554..444444444455 PP

                   ABC2_membrane_2 174 lv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllnei 249
                                       +  +f++lgl+++s +++ +   +++ ++++  ++l +++l+++++l+        +  +ls+l+p  +   +l+  
  gi|386001588|ref|YP_005919887.1| 151 IAtTFNSLGLAFASRMKDMSGFSLIMNFMVF-PLFLLSGALFPISNLPP-------WLRTLSYLDPLTYGVDGLRGS 219
                                       44489************66666666655555.559999******99999.......555588888887755444444 PP

                   ABC2_membrane_2 250 lagsdlnalgstatnllilllllavllvlgyvlFkrkDl 288
                                       l g++   ++s a+ l+il +  ++ l+lg++lF+r D+
  gi|386001588|ref|YP_005919887.1| 220 LVGAS---SFSLAFDLAILTACSIAALGLGAYLFERSDV 255
                                       44442...69***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1575.82
//
Query:       gi|386001589|ref|YP_005919888.1|  [L=335]
Description: daunorubicin resistance ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-33  115.4   0.0    4.2e-33  114.8   0.0    1.3  1  ABC_tran  ABC transporter
    6.1e-13   49.2   0.9    8.6e-07   29.0   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.9e-09   37.5   0.0    5.6e-09   36.6   0.0    1.5  1  DUF4162   Domain of unknown function (DUF4162)
    1.4e-05   25.7   0.0    2.1e-05   25.1   0.0    1.4  1  AAA_23    AAA domain
    0.00018   21.2   0.1    0.00035   20.3   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
    0.00032   20.5   0.0     0.0087   15.8   0.0    2.0  2  AAA_15    AAA ATPase domain
     0.0014   18.1   0.0     0.0066   15.9   0.0    1.9  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0045   17.4   0.1      0.061   13.7   0.1    2.5  1  AAA       ATPase family associated with various cellular acti
     0.0047   16.6   0.0        1.9    8.1   0.0    2.2  2  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.07   13.0   0.0      0.094   12.6   0.0    1.2  1  Rad17     Rad17 P-loop domain
      0.094   12.2   0.2       0.19   11.2   0.2    1.4  1  iPGM_N    BPG-independent PGAM N-terminus (iPGM_N)
      0.098   13.0   0.2        0.3   11.5   0.1    1.9  2  AAA_16    AAA ATPase domain
       0.14   12.3   0.0       0.35   11.0   0.0    1.6  1  IGR       IGR protein motif
       0.14   11.8   0.0        0.4   10.3   0.0    1.7  2  AAA_27    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   0.0   3.3e-36   4.2e-33       2     136 ..      22     164 ..      21     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 3.3e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++v+l++++ge+ +++G+nGaGKSt++k+l+ +l+p +G+  + g d+k+ e+  +r++igv++q+p+++++l+ re
  gi|386001589|ref|YP_005919888.1|  22 DDVDLEIERGELFGLLGPNGAGKSTIIKILTTMLRPSAGSAAVWGYDIKR-ERDAVRSSIGVVFQDPSVDSQLSGRE 97 
                                       89************************************************.************************** PP

                                       H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n          +++ +++++++ l+l++  +++++  ++ +SgG+++r+++ar l+ +p++l+lDEpt
  gi|386001589|ref|YP_005919888.1|  98 NldfhgrmygmDRKTRADRIAEVLELVD-LNDKADVLMEDYSGGMQRRLEIARGLMHHPSVLFLDEPT 164
                                       *********9966666666666666666.444456667*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4     8e-07     0.001       2      24 ..      34      56 ..      33      98 .. 0.78
   2 !   29.0   0.0   6.7e-10   8.6e-07     207     298 ..      92     196 ..      72     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +l GpNg+GKS+++++l  + r
  gi|386001589|ref|YP_005919888.1| 34 FGLLGPNGAGKSTIIKILTTMLR 56
                                      689***************87754 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 6.7e-10
                            AAA_21 207 eliasvderlrer...............gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                                       +l+ +++++  +r                + +++ +d  ++ + + S G++r l ++  l   +   s+l++DEp +
  gi|386001589|ref|YP_005919888.1|  92 QLSGRENLDFHGRmygmdrktradriaeVLELVDLNDKADVLMEDYSGGMQRRLEIARGLMHHP---SVLFLDEPTL 165
                                       4444444444444555555566666666777888889999999999999999988888888766...********** PP

                            AAA_21 269 gLHPkllrrllell.kelsrngaQviltTHS 298
                                       gL+ +  r +++ + + ++++g+ v+ltTH 
  gi|386001589|ref|YP_005919888.1| 166 GLDAQTRRYIWRYIeRMNEEEGVTVVLTTHY 196
                                       ***********99964444479********5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   4.4e-12   5.6e-09       3      80 ..     221     307 ..     220     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.4e-12
                                       HHHHHTTS-SSEEEEE.......-------..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE- CS
                           DUF4162   3 leeiKrsygknrieve.......adaeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeee 70 
                                       +e +K+ +g +++++e       +++++l +++gve v+++g++l+l ++  e+  +e+  a+ ++g+ irs++ +e
  gi|386001589|ref|YP_005919888.1| 221 PERLKDLIGADIVNLEvddsvtdEQVGALSDLEGVEAVDRAGSTLRLSVDRsEARIPEIVLAAsRAGLLIRSVTMHE 297
                                       68899**********99888865558889999******************889999***999977************ PP

                                       --HHHHHHHH CS
                           DUF4162  71 PsLndIFiek 80 
                                       P+L+d+F++ 
  gi|386001589|ref|YP_005919888.1| 298 PTLEDVFLKF 307
                                       *******985 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.7e-08   2.1e-05       3      43 ..      14      55 ..      12     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.7e-08
                            AAA_23  3 kienfrsfrdqeidFsk.gltlItGpNGaGKTTildAiklaL 43
                                      + ++f   +d++++ ++  l+ + GpNGaGK+Ti+  ++ +L
  gi|386001589|ref|YP_005919888.1| 14 RFNGFLAVDDVDLEIERgELFGLLGPNGAGKSTIIKILTTML 55
                                      6778888899999997736*****************999887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.7e-07   0.00035      13      50 ..      22      59 ..      17      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.7e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      d+ ++ei++ + + l Gp+G+GKST++  ++++L p+ 
  gi|386001589|ref|YP_005919888.1| 22 DDVDLEIERGELFGLLGPNGAGKSTIIKILTTMLRPSA 59
                                      567788886669999************99999999976 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.8e-06    0.0087      15      50 ..      22      58 ..      13     101 .. 0.82
   2 ?    2.4   0.0     0.082     1e+02     324     364 ..     155     195 ..     141     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.8e-06
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +dv+++++   l  l G+N++GKS+i+++l  +l  +
  gi|386001589|ref|YP_005919888.1| 22 DDVDLEIERGeLFGLLGPNGAGKSTIIKILTTMLRPS 58
                                      565666665569999****************999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.082
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       + +l+++EP + L  q  + +++++ ++ +++   v++tTH
  gi|386001589|ref|YP_005919888.1| 155 PSVLFLDEPTLGLDAQTRRYIWRYIERMNEEEGVTVVLTTH 195
                                       6789****************************99******* PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.2e-06    0.0066      27     209 ..      34     204 ..      13     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.2e-06
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSS.SSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklki.ekeevsis 100
                                         ++GpNG+GKs ++  +         + lr +  s+ +     k+++ + + ++ ++f++++ +++   +e++   
  gi|386001589|ref|YP_005919888.1|  34 FGLLGPNGAGKSTIIKIL----T----TMLRPSAGSAAVWGydIKRERDAVRSSIGVVFQDPSVDSQLsGRENLDFH 102
                                       4689***********987....2....35888888877776677889999999******998887333033334444 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                        r++  ++ +    ++ ++  e+ +l  +a++ +e  SgG +  + +a       ++  ++ +lDe    LD++ ++
  gi|386001589|ref|YP_005919888.1| 103 GRMYGMDR-KT-RADRIAEVLELVDLNDKADVLMEDYSGGMQRRLEIA----RGLMHHPSVLFLDEPTLGLDAQTRR 173
                                       44444433.22.234556666777777888888889****87755554....444444556679************* PP

                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemlekadklv 209
                                        + +++++ +++  + v+ l+++ +e+ad+l+
  gi|386001589|ref|YP_005919888.1| 174 YIWRYIERMNEEEGVTVV-LTTHYMEEADHLC 204
                                       *******99987776665.6666777777664 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   4.8e-05     0.061       3     120 ..      36     205 ..      34     215 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                                       EESSTTSSHHHHHHHHHHHH.....THE......................EEEEETTTCSSS............... CS
                               AAA   3 lyGppGtGKTllakavakel.....gve......................fleisgsellsk............... 37 
                                       l Gp G GK++++k + + l     +                                   +               
  gi|386001589|ref|YP_005919888.1|  36 LLGPNGAGKSTIIKILTTMLrpsagS-AavwgydikrerdavrssigvvfQ----------Dpsvdsqlsgrenldf 101
                                       78*****************8444431.133333344444433344433330..........2555555666666666 PP

                                       ...............................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHH CS
                               AAA  38 ...............................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseee 82 
                                                                      ++++ +  ++  ++ a+    +ps+lf+DE      ++        
  gi|386001589|ref|YP_005919888.1| 102 hgrmygmdrktradriaevlelvdlndkadvLMEDYSGGMQRRLEIARGLMhHPSVLFLDEPTLGLDAQ-------- 170
                                       6666666666666677777777777777777666666666666666665556689******87776666........ PP

                                       HHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  83 ervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                         +   + + +++++++e+ v+v+++t+++++ d    
  gi|386001589|ref|YP_005919888.1| 171 --TRRYIWRYIERMNEEEG-VTVVLTTHYMEEADHLCE 205
                                       ..55667777777766544.999999999998887655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0015       1.9       6      41 ..      36      71 ..      32      76 .. 0.90
   2 !    6.4   0.0    0.0049       6.3      67     149 ..     115     195 ..      93     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                      l+G++GaGK t +  L  +l+ ++ ++++   D+ R
  gi|386001589|ref|YP_005919888.1| 36 LLGPNGAGKSTIIKILTTMLRPSAGSAAVWGYDIKR 71
                                      79******************9999999999999887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0049
                                       CHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCS CS
                             SRP54  67 dpaavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgit 143
                                       d +a + e v+   ++k+dv++ D +G +q   e+ + l +  +v+  de  l lda t +   + +++ +e+ g+t
  gi|386001589|ref|YP_005919888.1| 115 DRIAEVLELVDL--NDKADVLMEDYSGGMQRRLEIARGLMHHPSVLFLDEPTLGLDAQTRRYIWRYIERMNEEEGVT 189
                                       444444444443..3459*********************************************************99 PP

                                       EEEEES CS
                             SRP54 144 gviltk 149
                                        v  t 
  gi|386001589|ref|YP_005919888.1| 190 VVLTTH 195
                                       888776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.3e-05     0.094      40      72 ..      26      58 ..      19     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.3e-05
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                      Le ++ ++  + GP G gkst++k+L+  l ++
  gi|386001589|ref|YP_005919888.1| 26 LEIERGELFGLLGPNGAGKSTIIKILTTMLRPS 58
                                      555556678899**************9888765 PP

>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00015      0.19     102     125 ..     102     125 ..      91     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                       EEHHHHT--SS-HHHHHHHHHHHC CS
                            iPGM_N 102 sGRyyaMDRdkrwervekaydalv 125
                                        GR+y MDR +r +r+ +  +++ 
  gi|386001589|ref|YP_005919888.1| 102 HGRMYGMDRKTRADRIAEVLELVD 125
                                       7***************99988764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00023       0.3      24     142 ..      31     161 ..      24     173 .. 0.56
   2 ?   -1.7   0.0       2.6   3.4e+03      81     116 ..     223     257 ..     179     290 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysalaqalareellrqllde........aes 91 
                                       +el  l G+ G GKs++++ l + l+ + g  +++g   + e+++ +s +  ++   ++  ql  +           
  gi|386001589|ref|YP_005919888.1|  31 GELFGLLGPNGAGKSTIIKILTTMLRPSaGSAAVWGYDIKRERDAVRSSIGVVFQDPSVDSQLSGRenldfhgrMYG 107
                                       4677799***********99998888874345577777777666555444444433333333333344444444223 PP

                            AAA_16  92 aeleawrekleeala..avpelagaea...srllellkrll.allsrderplvlvlD 142
                                        ++   ++++ e+l+  + ++ a       ++    ++r l       ++p vl+lD
  gi|386001589|ref|YP_005919888.1| 108 MDRKTRADRIAEVLElvDLNDKA---DvlmEDYSGGMQRRLeIARGLMHHPSVLFLD 161
                                       33444444444444422222222...2344666666666663222223556777777 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                            AAA_16  81 llrqlldeaesaeleawrekleealaavpelagaea 116
                                        l++l  + +  +le ++   +e+++a ++l+g ea
  gi|386001589|ref|YP_005919888.1| 223 RLKDLIGA-DIVNLEVDDSVTDEQVGALSDLEGVEA 257
                                       33333333.233555555555555555666666555 PP

>> IGR  IGR protein motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.35      35      52 ..     165     182 ..     158     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                               IGR  35 lGipvrqRRYiLrwreky 52 
                                       lG+++++RRYi r+ e+ 
  gi|386001589|ref|YP_005919888.1| 165 LGLDAQTRRYIWRYIERM 182
                                       89************9985 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031       0.4      18      49 ..      23      54 ..       9      56 .. 0.75
   2 ?   -2.0   0.0       1.8   2.3e+03     102     129 ..      84     112 ..      69     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       +d++ e+ +l  ++GpN AGKst+++ ++ +
  gi|386001589|ref|YP_005919888.1| 23 DVDLEIERGELFGLLGPNGAGKSTIIKILTTM 54
                                      455666678888899**********9887766 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                            AAA_27 102 lpeevlaallggldretF.ealFgLdher 129
                                        ++  +++ l g +   F  +++g+d ++
  gi|386001589|ref|YP_005919888.1|  84 FQDPSVDSQLSGRENLDFhGRMYGMDRKT 112
                                       55555555555555544415788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2404.09
//
Query:       gi|386001590|ref|YP_005919889.1|  [L=462]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-12   46.9   1.8    2.1e-11   44.5   1.8    2.2  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   1.8   1.2e-15   2.1e-11       3     165 ..     168     338 ..     166     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-15
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..... 74 
                                       +trgC  +C+fC++p+      r++ +++e++++ + ++k e+ +++v++   +  ++++ ++ +  l  +      
  gi|386001590|ref|YP_005919889.1| 168 TTRGCGVGCKFCQTPK---FCNRPHPVPLESLERVISYYK-EHEINVVLIEDENFGANRRHADRVVDLLDEYgmvwg 240
                                       79*************8...8*******************7.555**************9999999999999888888 PP

                                       ............CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ............vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklre 139
                                                    ++++++    + +       r+++ g+   ++g+e ++ e  l+ +n++++ e+vle++++l +
  gi|386001590|ref|YP_005919889.1| 241 cmaradylrkkiPEWVEMRAKPDPATG---RKPRMVK-GFAGAAIGIENLHQE-KLDDINKKEGTEDVLETVRLLQK 312
                                       888888888777666666666666664...3356666.678999*********.67777799*************** PP

                                       TTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 140 agikrvvdrivglpGendeeleelle 165
                                       +g+  v + ++g+p  ++e l++ + 
  gi|386001590|ref|YP_005919889.1| 313 YGLGTVGYYMIGFPDDTKESLRKDIA 338
                                       *******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3185.76
//
Query:       gi|386001591|ref|YP_005919890.1|  [L=485]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-15   56.9   0.1    3.5e-13   50.3   0.0    3.6  3  Radical_SAM  Radical SAM superfamily
    2.5e-13   50.1   0.0      5e-13   49.2   0.0    1.4  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.12   1.1e+03      91     108 ..      51      68 ..       5     108 .. 0.61
   2 ?   -1.8   0.0      0.41   3.7e+03      31      86 ..     126     180 ..     115     182 .. 0.56
   3 !   50.3   0.0   3.9e-17   3.5e-13       1     159 [.     191     347 ..     191     387 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                                       HHHHHHHHHTT-SEEEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelgvdrvslg 108
                                       +e+le +l+ g d v l+
  gi|386001591|ref|YP_005919890.1|  51 REYLEGILRNGYDLVGLS 68 
                                       444444444444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTCCCTEEEEEEECS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  31 veeileevkelkaekgvkevilgggeplly.pdfvellerlaklavpgiritvetng 86 
                                        +e++e ++ ++   gv+++   gg+ +++ p+  +l    ++l  p++ ++++t g
  gi|386001591|ref|YP_005919890.1| 126 FRELIEAIDDGRDLAGVRGLSYWGGDKMVHnPPRPVLDVSDIEL--PNRDCRLITKG 180
                                       44555566666544455555555555555435555555555555..66666666665 PP

  == domain 3  score: 50.3 bits;  conditional E-value: 3.9e-17
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla... 74 
                                       v+++rgC+++C+fC++ ++   ++  r  + ++il+ ++ + + +g++ +++  ++ +l+ +  e l  ++ +a   
  gi|386001591|ref|YP_005919890.1| 191 VETSRGCTNGCKFCSIQQM--YGRSFRRYPFDRILDDIRDA-EAHGARSIFFPDDNMTLDVKRMERLCDAIVEAgls 264
                                       5789**************7..********************.9999**************98888888888888999 PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                       + ++++  ++ g+  +++ +++++  g+d v lg+e ++ +  l+ +++g+  +   +a+e+++++ i  v+ +++g
  gi|386001591|ref|YP_005919890.1| 265 HLKYKVQASARGIGSSRRLVQKMAASGFDGVFLGIENTSRD-NLRFLGKGKMSDNADKAIEYMHDNEII-VSAGLIG 339
                                       99************99*************************.999999999999999999999999999.8888888 PP

                                       BTTTSHHH CS
                                       xxxxxxxx RF
                       Radical_SAM 152 lpGendee 159
                                       +  e d+e
  gi|386001591|ref|YP_005919890.1| 340 GNPEDDAE 347
                                       88777743 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   5.5e-17     5e-13      12     121 .]      21     130 ..      19     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.5e-17
                       B12-binding  12 lhplGlavlaaalrd.agfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvG 87 
                                       ++++Gl ++a+ + d   ++V +l     + + ++ i ++ +d+vglS+ ++ q+ av  l++++k+   ++ +v+G
  gi|386001591|ref|YP_005919890.1|  21 IPNYGLVSIAGNVDDlCTVDVADLHGVKRPREYLEGILRNGYDLVGLSC-MSFQYHAVLPLAKMAKES--GAATVFG 94 
                                       68999*********955999998855555788889999***********.****************98..669**** PP

                       B12-binding  88 Gahpsldpeetleak...lgiddvvvgegedaleala 121
                                       G hp+l ++e+ e     l  d++v+gege ++++l+
  gi|386001591|ref|YP_005919890.1|  95 GYHPTLNYDEIGESPegrLS-DYIVRGEGEATFRELI 130
                                       **********9887689666.************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 3360.39
//
Query:       gi|386001592|ref|YP_005919891.1|  [L=357]
Description: glucokinase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-75  253.5   0.0    2.7e-75  253.3   0.0    1.0  1  Glucokinase  Glucokinase


Domain annotation for each model (and alignments):
>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.3   0.0   1.5e-79   2.7e-75       1     313 [.      32     352 ..      32     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 253.3 bits;  conditional E-value: 1.5e-79
                       Glucokinase   1 LagDiGGTkarlalveaeeeelelleiekyasadyasleealqaflaeaeaevk.rpksavlAvAgpveg.develt 75 
                                       L gD+GGT++++a++ ++e++ +ll+ ++++s+  +sl  a+++ l+  + +   ++ ++v++vAgpv++  +++ t
  gi|386001592|ref|YP_005919891.1|  32 LGGDVGGTNTNIAVAGVREGKATLLYSAHFESRRLTSLAPAIREALDYGRVKYGiEVVRGVVGVAGPVTDpRKAKPT 108
                                       679*******************************************9664443314566*********98346788* PP

                       Glucokinase  76 NlpWviseeelakelgleaveliNDfeavayaiplleaedlvqlgggkkdaeapiavlGaGTGLGvallipekerrv 152
                                       NlpW++++ee+++e+g+e++++ NDf+ ++ +i++l+++dl   +gg++   + +av+GaGTGLG+a+l++++e++ 
  gi|386001592|ref|YP_005919891.1| 109 NLPWTVDAEEMRREFGFEEFRIENDFQIIGRGIESLKETDLFSAKGGDPAFGDGRAVIGAGTGLGKAILVYDGEKYR 185
                                       ***************************************************************************** PP

                       Glucokinase 153 vlasEGGhvdfapeseeevelleilrkkl.grvsaErvlSGpGLvnlyealaaad.......kleeellepaeitea 221
                                       +++sEGGh+df+ +++ +  l++++r    +  s+E++lSG+G++ +y++l+ ++       ++ee+++++a+i+++
  gi|386001592|ref|YP_005919891.1| 186 PVPSEGGHADFPIQDHFDLDLADFIRGGRdTPASYEDLLSGRGIEVIYDFLKGRRgrtdltaEIEEAEDKAAAISKQ 262
                                       **************************999899**********************98888888888888*******99 PP

                       Glucokinase 222 alegedplarealelFlailGsvagdlaLkllargGvyiaGGiapkilellkaseFreafedkgrlsellekipvyv 298
                                          ++dpl+re+  ++++++G+ a + +L+ +a+gG+yiaGGia+k+ e++++ eF  +f +  + ++lle+ pv+v
  gi|386001592|ref|YP_005919891.1| 263 R--KTDPLCRETFAVYARCFGRCAKNFVLEAVATGGLYIAGGIAAKNREVFASTEFSTEFLNAEKQRHLLERTPVSV 337
                                       8..699*********************************************************************** PP

                       Glucokinase 299 vlneeagLlGaaaaa 313
                                       ++n +++L Ga+ aa
  gi|386001592|ref|YP_005919891.1| 338 ITNYDVSLYGACNAA 352
                                       ***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2478.84
//
Query:       gi|386001593|ref|YP_005919892.1|  [L=649]
Description: PBS lyase HEAT domain-containing protein repeat-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-127  415.0  67.9    3.6e-19   68.9   3.7   10.2 10  HEAT_2         HEAT repeats
    1.7e-88  282.4  79.1    1.3e-07   31.6   0.1   19.7 20  HEAT_PBS       PBS lyase HEAT-like repeat
    1.4e-75  242.6  15.4    0.00014   21.9   0.0   18.9 19  HEAT           HEAT repeat
    8.6e-40  134.7  56.1    0.00034   21.0   0.0   17.6 16  HEAT_EZ        HEAT-like repeat
      6e-34  117.4   0.0      0.013   15.5   0.0   12.8 12  Cnd1           non-SMC mitotic condensation complex subunit 1
    4.6e-31  105.9  13.7      0.012   15.7   0.0   13.9 15  Arm            Armadillo/beta-catenin-like repeat
    2.1e-08   34.4   7.6         25    4.9   0.0   10.0 11  Aconitase_B_N  Aconitate B N-terminal domain
    3.6e-08   32.4   0.0        2.1    6.8   0.0    6.5  7  Adaptin_N      Adaptin N terminal region
    3.8e-08   33.8   0.0         21    5.8   0.1   10.7 11  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
    2.2e-05   24.8   0.0        6.2    7.3   0.0    7.0 10  RasGEF_N_2     Rapamycin-insensitive companion of mTOR RasGEF
    0.00055   19.1   8.6        4.1    6.4   0.1    6.4  7  IFRD           Interferon-related developmental regulator (IF
  ------ inclusion threshold ------
      0.028   14.1   0.3         38    3.9   0.0    5.0  6  DUF4042        Domain of unknown function (DUF4042)
      0.048   13.2   0.7         12    5.4   0.1    5.0  6  CLASP_N        CLASP N terminal
       0.12   12.6  10.9         36    4.8   0.0    7.6  9  Cohesin_HEAT   HEAT repeat associated with sister chromatid c
       0.29   11.5   2.1         18    5.8   0.1    3.5  3  Gag_p12        Gag polyprotein, inner coat protein p12
        3.2    6.5   3.3         58    2.3   0.0    4.0  6  API5           Apoptosis inhibitory protein 5 (API5)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   1.9e-13   2.1e-10       2      67 ..      25      89 ..      24      95 .. 0.91
   2 !   41.8   0.1   9.4e-14   1.1e-10       4      58 ..      89     142 ..      86     154 .. 0.88
   3 !   55.8   2.2   4.1e-18   4.6e-15       4      88 .]     173     255 ..     170     255 .. 0.92
   4 !   50.1   0.8   2.4e-16   2.7e-13       3      72 ..     203     271 ..     202     273 .. 0.96
   5 !   46.1   1.3   4.3e-15   4.8e-12      11      74 ..     241     321 ..     241     322 .. 0.93
   6 !   63.5   0.3   1.5e-20   1.7e-17       3      78 ..     313     388 ..     311     389 .. 0.95
   7 !   50.2   0.1   2.3e-16   2.6e-13       1      73 [.     374     445 ..     374     446 .. 0.96
   8 !   62.3   2.1   3.7e-20   4.1e-17       3      88 .]     438     521 ..     437     521 .. 0.95
   9 !   68.9   3.7   3.3e-22   3.6e-19       1      88 []     528     613 ..     528     613 .. 0.96
  10 !   47.6   3.4   1.5e-15   1.7e-12       2      58 ..     591     646 ..     590     648 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.9e-13
                            HEAT_2  2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaL 67
                                      d  +++l +dp++ +r+  + +Lg++g+p+a++ L+e+l+de ++vR +aa +L+++g+pe l+  
  gi|386001593|ref|YP_005919892.1| 25 DDAIAYL-KDPEWGLRAGGAASLGNLGDPRAIDPLIEALSDEVSMVRVHAASSLVKLGRPEYLDRV 89
                                      567899*.9**************************************************9987765 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 9.4e-14
                            HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgai 58 
                                        + al +d+d+ vr  a+  Lg+ig+p+a+  L+e+l+dedp+vR  a +aLg+i
  gi|386001593|ref|YP_005919892.1|  89 VILAL-EDEDKWVRGWAATHLGDIGDPRAIVPLREALRDEDPWVRSKASDALGKI 142
                                       56678.9**********************************************98 PP

  == domain 3  score: 55.8 bits;  conditional E-value: 4.1e-18
                            HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                                       Ll  l ++ dpe r aa+ +Lg++g+ +a+  L+e+l+d +++vR aa+ aL+ igd++a++    +l+d+ d+ vR
  gi|386001593|ref|YP_005919892.1| 173 LLYDL-EHGDPEERVAAALSLGEMGDARAVGPLIEALKDVEWEVRGAAVIALAGIGDDRAVDPVIGALLDE-DPAVR 247
                                       66778.8*************************************************************975.66679 PP

                            HEAT_2  81 eaAaeaLa 88 
                                       + Aa aL+
  gi|386001593|ref|YP_005919892.1| 248 TLAAAALG 255
                                       99999986 PP

  == domain 4  score: 50.1 bits;  conditional E-value: 2.4e-16
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelld 72 
                                       +L++al +d ++evr aa++aL+ ig+++a++ ++ +l dedpavR  aa aLg+++dp+  + L+++l+
  gi|386001593|ref|YP_005919892.1| 203 PLIEAL-KDVEWEVRGAAVIALAGIGDDRAVDPVIGALLDEDPAVRTLAAAALGRLADPRGFEPLTDALL 271
                                       69****.9****************************************************9999999986 PP

  == domain 5  score: 46.1 bits;  conditional E-value: 4.3e-15
                            HEAT_2  11 dpdpevrraairaLgrignp.................ealpaLvellededpavRraaaeaLgaigdpealpaLkel 70 
                                       d+dp+vr  a+ aLgr+++p                  a++ L e+l d ++ vR++aaeaLg+igdp+al  L ++
  gi|386001593|ref|YP_005919892.1| 241 DEDPAVRTLAAAALGRLADPrgfepltdallgeiggaGAVDHLAEALGDGNWSVRAMAAEALGRIGDPRALGPLIAA 317
                                       89*****************99999999888888888888*************************************9 PP

                            HEAT_2  71 lddd 74 
                                       l d+
  gi|386001593|ref|YP_005919892.1| 318 LGDE 321
                                       9886 PP

  == domain 6  score: 63.5 bits;  conditional E-value: 1.5e-20
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigd.pealpaLkellddddddv 78 
                                       +L++al  d++  vr  a+ +Lg  g+pea++ L+e+l+d +pavR+aa+ aLg++gd p+a++ L  +l+ddd ++
  gi|386001593|ref|YP_005919892.1| 313 PLIAAL-GDENATVRLIAAGVLGGSGSPEAIDPLIEALKDGEPAVRAAAVYALGEMGDdPRAIDGLISSLKDDDPAL 388
                                       79****.*************************************************966************998775 PP

  == domain 7  score: 50.2 bits;  conditional E-value: 2.3e-16
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldd 73 
                                       +d L++ l +d dp++r+  ++ Lg +g+++a+  L++ll+d++p+vR++a  aLg ig+++a+  L +ll d
  gi|386001593|ref|YP_005919892.1| 374 IDGLISSL-KDDDPALRIYGAMILGGLGDERAVSPLIDLLKDDEPEVRAMAGVALGDIGSEKAAGPLIDLLED 445
                                       578999**.9***********************************************************9987 PP

  == domain 8  score: 62.3 bits;  conditional E-value: 3.7e-20
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvv 79 
                                       +L+ +l +d+ pevr+ a++aL++ g+++a + L+e+l de++ vR  a  aLg ig pea++ L + l  d+d+ v
  gi|386001593|ref|YP_005919892.1| 438 PLIDLL-EDEAPEVRAGAAQALATVGDERATRPLIEALGDEEASVRSWASLALGSIGGPEAVDPLIAGLG-DEDEGV 512
                                       699999.9************************************************************96.678888 PP

                            HEAT_2  80 ReaAaeaLa 88 
                                       R+ Aa aLa
  gi|386001593|ref|YP_005919892.1| 513 RTVAAAALA 521
                                       *****9996 PP

  == domain 9  score: 68.9 bits;  conditional E-value: 3.3e-22
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddddd 77 
                                       +d+L++al + +dp v++ a++aLg+ig+p+a++ L+e+l++ed avR +a+  L+ ++d++ ++ L ++l+ d+d+
  gi|386001593|ref|YP_005919892.1| 528 VDPLIKAL-EEEDPSVQIWAAWALGEIGDPKAVDPLIEALKNEDQAVRLMAVVGLAGFDDDRRAEPLIAALA-DEDE 602
                                       689*****.9***********************************************************996.6899 PP

                            HEAT_2  78 vvReaAaeaLa 88 
                                       vvR aAa aLa
  gi|386001593|ref|YP_005919892.1| 603 VVRFAAAAALA 613
                                       *********96 PP

  == domain 10  score: 47.6 bits;  conditional E-value: 1.5e-15
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgai 58 
                                       ++L++al  d+d+ vr aa+ aL++ig+p+a + L ++lededp+vRr aaeaL ++
  gi|386001593|ref|YP_005919892.1| 591 EPLIAAL-ADEDEVVRFAAAAALAEIGDPRAEEPLKKALEDEDPDVRRKAAEALDRL 646
                                       789****.9********************************************9875 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 !   23.0   0.1   6.7e-08   7.6e-05       2      27 .]      39      64 ..      38      64 .. 0.91
   2 !    9.9   0.0    0.0011       1.3       1      27 []      69      95 ..      69      95 .. 0.97
   3 !   22.6   0.1   9.5e-08   0.00011       1      27 []     100     126 ..     100     126 .. 0.97
   4 ?   -2.1   0.0       8.7   9.7e+03       1      12 [.     131     142 ..     131     142 .. 0.89
   5 !   22.6   0.2   9.1e-08    0.0001       2      27 .]     185     210 ..     184     210 .. 0.97
   6 !   16.9   0.4   6.7e-06    0.0075       1      27 []     215     241 ..     215     241 .. 0.94
   7 !   13.7   0.3   6.7e-05     0.075       1      25 [.     246     270 ..     246     272 .. 0.92
   8 ?    3.6   0.1      0.12   1.4e+02       9      27 .]     271     289 ..     270     289 .. 0.93
   9 !   23.7   0.8   4.1e-08   4.6e-05       1      27 []     294     320 ..     294     320 .. 0.96
  10 !   20.3   0.0   5.2e-07   0.00058       1      27 []     325     351 ..     325     351 .. 0.97
  11 !   25.3   0.0   1.3e-08   1.4e-05       1      27 []     356     383 ..     356     383 .. 0.97
  12 !   15.4   0.0   1.9e-05     0.022       2      27 .]     389     414 ..     388     414 .. 0.93
  13 !   10.1   0.1   0.00099       1.1       1      27 []     419     445 ..     419     445 .. 0.96
  14 !   18.6   0.7   1.8e-06     0.002       1      27 []     450     476 ..     450     476 .. 0.96
  15 !   20.0   0.0   6.6e-07   0.00073       1      27 []     481     507 ..     481     507 .. 0.95
  16 !   16.4   0.4   9.6e-06     0.011       1      26 [.     512     536 ..     512     537 .. 0.94
  17 !   31.6   0.1   1.2e-10   1.3e-07       1      27 []     542     568 ..     542     568 .. 0.96
  18 !    7.6   0.3    0.0064       7.2       1      27 []     573     599 ..     573     599 .. 0.96
  19 !   25.8   0.4   8.3e-09   9.4e-06       1      27 []     604     630 ..     604     630 .. 0.98
  20 ?    3.0   0.1       0.2   2.2e+02       1      12 [.     635     646 ..     635     648 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.7e-08
                                      HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  2 RraAakaLgqlgdeeaipaLleaLqd 27
                                      R+  a +Lg+lgd++ai++L+eaL d
  gi|386001593|ref|YP_005919892.1| 39 RAGGAASLGNLGDPRAIDPLIEALSD 64
                                      667799******************97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR  Aa +L +lg +e++++ + aL+d
  gi|386001593|ref|YP_005919892.1| 69 VRVHAASSLVKLGRPEYLDRVILALED 95
                                      899**********************98 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 9.5e-08
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +Aa  Lg +gd++ai +L+eaL d
  gi|386001593|ref|YP_005919892.1| 100 VRGWAATHLGDIGDPRAIVPLREALRD 126
                                       9************************87 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgql 12 
                                       vR  A  aLg++
  gi|386001593|ref|YP_005919892.1| 131 VRSKASDALGKI 142
                                       8999999***97 PP

  == domain 5  score: 22.6 bits;  conditional E-value: 9.1e-08
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       R aAa +Lg++gd +a+ +L+eaL+d
  gi|386001593|ref|YP_005919892.1| 185 RVAAALSLGEMGDARAVGPLIEALKD 210
                                       89**********************98 PP

  == domain 6  score: 16.9 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR aA+ aL+ +gd++a+++ + aL d
  gi|386001593|ref|YP_005919892.1| 215 VRGAAVIALAGIGDDRAVDPVIGALLD 241
                                       9*******************9988876 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR  Aa aLg+l d++  ++L  aL
  gi|386001593|ref|YP_005919892.1| 246 VRTLAAAALGRLADPRGFEPLTDAL 270
                                       7788******************999 PP

  == domain 8  score: 3.6 bits;  conditional E-value: 0.12
                                       HHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   9 LgqlgdeeaipaLleaLqd 27 
                                       Lg++g   a+++L eaL d
  gi|386001593|ref|YP_005919892.1| 271 LGEIGGAGAVDHLAEALGD 289
                                       9***************976 PP

  == domain 9  score: 23.7 bits;  conditional E-value: 4.1e-08
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR+ Aa+aLg++gd++a+ +L++aL d
  gi|386001593|ref|YP_005919892.1| 294 VRAMAAEALGRIGDPRALGPLIAALGD 320
                                       8***********************976 PP

  == domain 10  score: 20.3 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR  Aa  Lg  g++eai++L+eaL+d
  gi|386001593|ref|YP_005919892.1| 325 VRLIAAGVLGGSGSPEAIDPLIEALKD 351
                                       8999*********************98 PP

  == domain 11  score: 25.3 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHCTS.GGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgd.eeaipaLleaLqd 27 
                                       vR+aA++aLg++gd ++ai+ L+  L+d
  gi|386001593|ref|YP_005919892.1| 356 VRAAAVYALGEMGDdPRAIDGLISSLKD 383
                                       9***********************9997 PP

  == domain 12  score: 15.4 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                       R + a  Lg lgde+a+ +L+ +L+d
  gi|386001593|ref|YP_005919892.1| 389 RIYGAMILGGLGDERAVSPLIDLLKD 414
                                       7788999*****************98 PP

  == domain 13  score: 10.1 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR+ A  aLg +g+e a+ +L+ +L+d
  gi|386001593|ref|YP_005919892.1| 419 VRAMAGVALGDIGSEKAAGPLIDLLED 445
                                       899999*******************98 PP

  == domain 14  score: 18.6 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR+ Aa aL+++gde+a  +L+eaL d
  gi|386001593|ref|YP_005919892.1| 450 VRAGAAQALATVGDERATRPLIEALGD 476
                                       8***********************976 PP

  == domain 15  score: 20.0 bits;  conditional E-value: 6.6e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +A  aLg +g +ea+++L++ L d
  gi|386001593|ref|YP_005919892.1| 481 VRSWASLALGSIGGPEAVDPLIAGLGD 507
                                       8**********************9965 PP

  == domain 16  score: 16.4 bits;  conditional E-value: 9.6e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR  Aa aL+++g  +a+++L++aL+
  gi|386001593|ref|YP_005919892.1| 512 VRTVAAAALAEIGG-DAVDPLIKALE 536
                                       7889**********.**********8 PP

  == domain 17  score: 31.6 bits;  conditional E-value: 1.2e-10
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       v+ +Aa+aLg++gd+ a+++L+eaL++
  gi|386001593|ref|YP_005919892.1| 542 VQIWAAWALGEIGDPKAVDPLIEALKN 568
                                       899**********************85 PP

  == domain 18  score: 7.6 bits;  conditional E-value: 0.0064
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR  A+ +L+ + d++ +++L++aL+d
  gi|386001593|ref|YP_005919892.1| 573 VRLMAVVGLAGFDDDRRAEPLIAALAD 599
                                       8999*********************97 PP

  == domain 19  score: 25.8 bits;  conditional E-value: 8.3e-09
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR aAa aL+++gd++a ++L++aL+d
  gi|386001593|ref|YP_005919892.1| 604 VRFAAAAALAEIGDPRAEEPLKKALED 630
                                       8************************98 PP

  == domain 20  score: 3.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgql 12 
                                       vRr Aa+aL +l
  gi|386001593|ref|YP_005919892.1| 635 VRRKAAEALDRL 646
                                       9********877 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.28   3.2e+02       8      27 ..      30      49 ..      27      51 .. 0.88
   2 !   10.9   0.0   0.00039      0.44       2      27 ..      55      80 ..      54      82 .. 0.90
   3 !    7.0   0.0    0.0073       8.2       5      27 ..      89     111 ..      86     113 .. 0.85
   4 !   16.7   0.0   5.4e-06    0.0061       5      29 ..     120     144 ..     117     146 .. 0.90
   5 ?    1.6   0.0       0.4   4.5e+02      12      27 ..     180     195 ..     171     198 .. 0.78
   6 !   15.3   0.0   1.5e-05     0.017       4      27 ..     203     226 ..     201     229 .. 0.89
   7 !   16.2   0.1   7.9e-06    0.0088       4      28 ..     234     258 ..     231     259 .. 0.89
   8 !   21.9   0.0   1.2e-07   0.00014       3      27 ..     281     305 ..     279     307 .. 0.92
   9 !    9.8   0.0   0.00088      0.99       4      25 ..     313     334 ..     310     335 .. 0.87
  10 !   20.2   0.0   4.2e-07   0.00047       2      27 ..     342     367 ..     341     370 .. 0.91
  11 ?    2.0   0.0       0.3   3.4e+02       4      27 ..     376     399 ..     373     401 .. 0.84
  12 !   15.0   0.0   1.9e-05     0.021       3      28 ..     406     431 ..     404     433 .. 0.91
  13 !   15.0   0.0     2e-05     0.022       5      26 ..     439     460 ..     437     463 .. 0.90
  14 !   14.4   0.0   3.1e-05     0.034       4      27 ..     469     492 ..     468     493 .. 0.91
  15 !   11.5   0.0   0.00025      0.28       4      27 ..     500     523 ..     497     525 .. 0.89
  16 !   13.1   0.0   7.9e-05     0.089       3      27 ..     529     553 ..     527     555 .. 0.91
  17 ?    5.4   0.0     0.024        27       3      25 ..     560     582 ..     558     584 .. 0.86
  18 !   15.0   0.1   1.9e-05     0.021       5      27 ..     593     615 ..     591     617 .. 0.88
  19 !   15.7   0.0   1.2e-05     0.013       5      27 ..     624     646 ..     622     646 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                                      HHT-SSHHHHHHHHHHHHHH CS
                              HEAT  8 llsDpspeVReaAakaLgal 27
                                       l+Dp++  R+  a +Lg+l
  gi|386001593|ref|YP_005919892.1| 30 YLKDPEWGLRAGGAASLGNL 49
                                      699**************998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00039
                                      HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  2 lPlllkllsDpspeVReaAakaLgal 27
                                      +++l+++lsD+ + VR  Aa +L++l
  gi|386001593|ref|YP_005919892.1| 55 IDPLIEALSDEVSMVRVHAASSLVKL 80
                                      568999*****************987 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0073
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       ++ +l+D++  VR  Aa  Lg++
  gi|386001593|ref|YP_005919892.1|  89 VILALEDEDKWVRGWAATHLGDI 111
                                       55569****************99 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 5.4e-06
                                       HHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgalae 29 
                                       l ++l+D++p VR+ A  aLg+++e
  gi|386001593|ref|YP_005919892.1| 120 LREALRDEDPWVRSKASDALGKIIE 144
                                       5899*******************87 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.4
                                       SSHHHHHHHHHHHHHH CS
                              HEAT  12 pspeVReaAakaLgal 27 
                                        +pe R aAa++Lg++
  gi|386001593|ref|YP_005919892.1| 180 GDPEERVAAALSLGEM 195
                                       5666699*******98 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 1.5e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+++l+D ++eVR aA+ aL+ +
  gi|386001593|ref|YP_005919892.1| 203 PLIEALKDVEWEVRGAAVIALAGI 226
                                       57899****************987 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 7.9e-06
                                       HHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                       +++ +l D++p VR  Aa aLg+la
  gi|386001593|ref|YP_005919892.1| 234 PVIGALLDEDPAVRTLAAAALGRLA 258
                                       6788899****************98 PP

  == domain 8  score: 21.9 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       ++l ++l D +++VR++Aa+aLg++
  gi|386001593|ref|YP_005919892.1| 281 DHLAEALGDGNWSVRAMAAEALGRI 305
                                       7899*******************99 PP

  == domain 9  score: 9.8 bits;  conditional E-value: 0.00088
                                       HHHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLg 25 
                                       +l+ +l D+++ VR  Aa  Lg
  gi|386001593|ref|YP_005919892.1| 313 PLIAALGDENATVRLIAAGVLG 334
                                       577889************9998 PP

  == domain 10  score: 20.2 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                       +++l+++l+D +p VR+aA++aLg++
  gi|386001593|ref|YP_005919892.1| 342 IDPLIEALKDGEPAVRAAAVYALGEM 367
                                       568999******************98 PP

  == domain 11  score: 2.0 bits;  conditional E-value: 0.3
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                        l++ l+D++p  R   a  Lg l
  gi|386001593|ref|YP_005919892.1| 376 GLISSLKDDDPALRIYGAMILGGL 399
                                       68999*********9988888876 PP

  == domain 12  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgala 28 
                                        +l+ ll+D++peVR++A  aLg++ 
  gi|386001593|ref|YP_005919892.1| 406 SPLIDLLKDDEPEVRAMAGVALGDIG 431
                                       57999*******************96 PP

  == domain 13  score: 15.0 bits;  conditional E-value: 2e-05
                                       HHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLga 26 
                                       l+ ll+D++peVR+ Aa+aL++
  gi|386001593|ref|YP_005919892.1| 439 LIDLLEDEAPEVRAGAAQALAT 460
                                       7899****************87 PP

  == domain 14  score: 14.4 bits;  conditional E-value: 3.1e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+++l D++++VR+ A +aLg +
  gi|386001593|ref|YP_005919892.1| 469 PLIEALGDEEASVRSWASLALGSI 492
                                       47899*****************98 PP

  == domain 15  score: 11.5 bits;  conditional E-value: 0.00025
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l+  l D++  VR  Aa aL+++
  gi|386001593|ref|YP_005919892.1| 500 PLIAGLGDEDEGVRTVAAAALAEI 523
                                       678889***************998 PP

  == domain 16  score: 13.1 bits;  conditional E-value: 7.9e-05
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       ++l+k+l+ ++p+V   Aa+aLg++
  gi|386001593|ref|YP_005919892.1| 529 DPLIKALEEEDPSVQIWAAWALGEI 553
                                       6799*******************99 PP

  == domain 17  score: 5.4 bits;  conditional E-value: 0.024
                                       HHHHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLg 25 
                                       ++l+++l+ ++  VR +A+  L+
  gi|386001593|ref|YP_005919892.1| 560 DPLIEALKNEDQAVRLMAVVGLA 582
                                       679999************97765 PP

  == domain 18  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       l+ +l D++  VR aAa aL+++
  gi|386001593|ref|YP_005919892.1| 593 LIAALADEDEVVRFAAAAALAEI 615
                                       67779****************98 PP

  == domain 19  score: 15.7 bits;  conditional E-value: 1.2e-05
                                       HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                       l k+l+D++p+VR+ Aa+aL +l
  gi|386001593|ref|YP_005919892.1| 624 LKKALEDEDPDVRRKAAEALDRL 646
                                       7799***************9765 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.7    0.0024       2.7       3      53 ..      69     109 ..      36     111 .. 0.60
   2 ?    5.7   0.0      0.02        22      28      55 .]     115     142 ..     114     142 .. 0.91
   3 !    7.7   1.1    0.0047       5.2       2      52 ..     183     223 ..     182     224 .. 0.73
   4 !   17.7   2.3   3.3e-06    0.0037       1      55 []     213     257 ..     213     257 .. 0.82
   5 !    8.6   0.0    0.0025       2.8      30      55 .]     280     305 ..     275     305 .. 0.71
   6 !   11.1   0.1    0.0004      0.45      27      53 ..     308     334 ..     307     334 .. 0.94
   7 !   21.0   0.0   3.1e-07   0.00034      27      55 .]     339     367 ..     337     367 .. 0.96
   8 ?    4.7   0.0     0.039        44      27      49 ..     371     393 ..     370     397 .. 0.83
   9 !   14.3   0.0   3.8e-05     0.043      28      54 ..     403     429 ..     401     430 .. 0.91
  10 !   11.3   0.1   0.00033      0.37      32      53 ..     438     459 ..     433     461 .. 0.88
  11 !    8.0   0.0    0.0036       4.1      31      55 .]     468     492 ..     464     492 .. 0.88
  12 ?    6.2   0.1     0.014        15      27      55 .]     495     523 ..     495     523 .. 0.91
  13 !   14.9   0.0   2.6e-05      0.03      29      55 .]     527     553 ..     525     553 .. 0.89
  14 ?    4.8   0.1     0.037        41      27      50 ..     556     579 ..     556     582 .. 0.88
  15 ?    6.1   0.8     0.014        16      28      55 .]     592     615 ..     579     615 .. 0.79
  16 !   12.3   2.0   0.00016      0.18       3      52 ..     604     643 ..     603     646 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0024
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLg 53 
                                       vR +Aa+ L     g+pe+l     +++ aL      d+d  VR+ Aa +Lg
  gi|386001593|ref|YP_005919892.1|  69 VRVHAASSLV--KLGRPEYLD----RVILALE-----DEDkWVRGWAATHLG 109
                                       5555555552..344555555....6666666.....666455777777776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       +++ +L  +L+d+++ VR +A  aLg++
  gi|386001593|ref|YP_005919892.1| 115 RAIVPLREALRDEDPWVRSKASDALGKI 142
                                       67778999******************97 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0047
                           HEAT_EZ   2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaL 52 
                                       ++R aAa+ LG+     + + +     ++ +L+ +L+d    eVR+aA++aL
  gi|386001593|ref|YP_005919892.1| 183 EERVAAALSLGE-----MGDAR-----AVGPLIEALKD-VEwEVRGAAVIAL 223
                                       678888888873.....33555.....77888888865.556*********9 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 3.3e-06
                           HEAT_EZ   1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       w+vR aA+ aL+   g +++    +v+ ++ aLl     d+d +VR+ Aa aLg+l
  gi|386001593|ref|YP_005919892.1| 213 WEVRGAAVIALA---GIGDDR---AVDPVIGALL-----DEDpAVRTLAAAALGRL 257
                                       99*********6...443333...4589999999.....8888***********97 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0025
                           HEAT_EZ  30 lpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       ++ L+ +L  d   +VRa Aa aLg++
  gi|386001593|ref|YP_005919892.1| 280 VDHLAEALG-DGNwSVRAMAAEALGRI 305
                                       444555555.5555***********97 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.0004
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLg 53 
                                       p++l +L+a+L d++++VR  Aag Lg
  gi|386001593|ref|YP_005919892.1| 308 PRALGPLIAALGDENATVRLIAAGVLG 334
                                       678999******************998 PP

  == domain 7  score: 21.0 bits;  conditional E-value: 3.1e-07
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       pe++++L+ +L+d +++VRaaA++aLg +
  gi|386001593|ref|YP_005919892.1| 339 PEAIDPLIEALKDGEPAVRAAAVYALGEM 367
                                       899************************86 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.039
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAa 49 
                                       p++++ L++ L+dd+++ R + a
  gi|386001593|ref|YP_005919892.1| 371 PRAIDGLISSLKDDDPALRIYGA 393
                                       6899************9997655 PP

  == domain 9  score: 14.3 bits;  conditional E-value: 3.8e-05
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgn 54 
                                       +++ +L+ lL+dd++eVRa A  aLg 
  gi|386001593|ref|YP_005919892.1| 403 RAVSPLIDLLKDDEPEVRAMAGVALGD 429
                                       57899********************95 PP

  == domain 10  score: 11.3 bits;  conditional E-value: 0.00033
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLg 53 
                                       +L+ lL+d+ +eVRa Aa aL+
  gi|386001593|ref|YP_005919892.1| 438 PLIDLLEDEAPEVRAGAAQALA 459
                                       79999***************97 PP

  == domain 11  score: 8.0 bits;  conditional E-value: 0.0036
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaLgnl 55 
                                       ++L+ +L d++++VR  A  aLg +
  gi|386001593|ref|YP_005919892.1| 468 RPLIEALGDEEASVRSWASLALGSI 492
                                       679999999999***********86 PP

  == domain 12  score: 6.2 bits;  conditional E-value: 0.014
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       pe++++L+a+L d++  VR+ Aa aL+ +
  gi|386001593|ref|YP_005919892.1| 495 PEAVDPLIAGLGDEDEGVRTVAAAALAEI 523
                                       78999******************999875 PP

  == domain 13  score: 14.9 bits;  conditional E-value: 2.6e-05
                           HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       ++++L+++L+ ++++V+  Aa+aLg +
  gi|386001593|ref|YP_005919892.1| 527 AVDPLIKALEEEDPSVQIWAAWALGEI 553
                                       68889999999999***********86 PP

  == domain 14  score: 4.8 bits;  conditional E-value: 0.037
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAag 50 
                                       p+++++L+ +L++++++VR  A+ 
  gi|386001593|ref|YP_005919892.1| 556 PKAVDPLIEALKNEDQAVRLMAVV 579
                                       6899**************999885 PP

  == domain 15  score: 6.1 bits;  conditional E-value: 0.014
                           HEAT_EZ  28 eilpaLlalLnddsdeV.RaaAagaLgnl 55 
                                        +++aL+     d+deV R aAa aL+ +
  gi|386001593|ref|YP_005919892.1| 592 PLIAALA-----DEDEVvRFAAAAALAEI 615
                                       4899999.....99999999999999865 PP

  == domain 16  score: 12.3 bits;  conditional E-value: 0.00016
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaL 52 
                                       vR+aAa+aL+   + +++  +   + + +aL      d+d +VR +Aa aL
  gi|386001593|ref|YP_005919892.1| 604 VRFAAAAALA---EIGDPRAE---EPLKKALE-----DEDpDVRRKAAEAL 643
                                       8********9...66666666...46778888.....7777*********9 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00014      0.16      23      85 ..      55     111 ..      51     116 .. 0.86
   2 !    8.9   0.0    0.0013       1.5      23      50 ..     117     144 ..     113     154 .. 0.88
   3 ?    3.0   0.0     0.087        97      23      46 ..     201     224 ..     198     232 .. 0.89
   4 !   15.5   0.0   1.2e-05     0.013      22      85 ..     231     305 ..     228     311 .. 0.82
   5 ?    1.1   0.0      0.31   3.5e+02      23      44 ..     311     332 ..     308     335 .. 0.84
   6 !    7.8   0.0    0.0028       3.2      23      47 ..     342     366 ..     338     375 .. 0.79
   7 !   11.8   0.0   0.00016      0.18      24      88 ..     375     433 ..     371     437 .. 0.85
   8 !    7.4   0.0    0.0038       4.2      21      85 ..     434     492 ..     432     494 .. 0.78
   9 !    7.3   0.0    0.0039       4.4       3      47 ..     482     522 ..     463     523 .. 0.63
  10 !   10.4   0.0   0.00045       0.5       3      86 ..     482     554 ..     480     558 .. 0.74
  11 !    7.6   0.1    0.0033       3.7      23      85 ..     559     615 ..     556     617 .. 0.66
  12 !   11.7   0.1   0.00017      0.19      23      46 ..     621     644 ..     619     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaaltei 85 
                                       ++pL ++L+De ++VR +aa  + kL ++++      l+++  +leDe++ V+  a + l +i
  gi|386001593|ref|YP_005919892.1|  55 IDPLIEALSDEVSMVRVHAASSLVKLGRPEY------LDRVILALEDEDKWVRGWAATHLGDI 111
                                       799***********************99987......56888888999988888888888777 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLil 50 
                                       + pLr++L+Dedp VR  a  ++ k+i+
  gi|386001593|ref|YP_005919892.1| 117 IVPLREALRDEDPWVRSKASDALGKIIE 144
                                       579***************9988888876 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.087
                              Cnd1  23 vepLrkrLkDedpyVRktaaivva 46 
                                       v pL ++LkD +  VR  a+i++a
  gi|386001593|ref|YP_005919892.1| 201 VGPLIEALKDVEWEVRGAAVIALA 224
                                       78999****************998 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 1.2e-05
                              Cnd1  22 lvepLrkrLkDedpyVRktaaivvakL........ilndm...vkekgflselaklleDenprVvanalaaltei 85 
                                        v+p+  +L Dedp VR  aa ++ +L        ++  +   +   g +++la++l D n +V+a+a  al  i
  gi|386001593|ref|YP_005919892.1| 231 AVDPVIGALLDEDPAVRTLAAAALGRLadprgfepLTDALlgeIGGAGAVDHLAEALGDGNWSVRAMAAEALGRI 305
                                       68899999*******************888887653333322244566*********************999877 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.31
                              Cnd1  23 vepLrkrLkDedpyVRktaaiv 44 
                                       + pL ++L De+++VR  aa v
  gi|386001593|ref|YP_005919892.1| 311 LGPLIAALGDENATVRLIAAGV 332
                                       5689999*********998865 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0028
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvak 47 
                                       ++pL ++LkD +p VR  a++++ +
  gi|386001593|ref|YP_005919892.1| 342 IDPLIEALKDGEPAVRAAAVYALGE 366
                                       7888889999999999999887765 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.00016
                              Cnd1  24 epLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                       + L ++LkD+dp  R   a+++  L ++        +s l +ll+D++p+V+a+a  al +i ++
  gi|386001593|ref|YP_005919892.1| 375 DGLISSLKDDDPALRIYGAMILGGLGDER------AVSPLIDLLKDDEPEVRAMAGVALGDIGSE 433
                                       55778999999999999999999886654......567899******************999765 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0038
                              Cnd1  21 ylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaaltei 85 
                                       +   pL   L+De p VR  aa ++a + +      +     l ++l De+++V++ a +al  i
  gi|386001593|ref|YP_005919892.1| 434 KAAGPLIDLLEDEAPEVRAGAAQALATVGD------ERATRPLIEALGDEEASVRSWASLALGSI 492
                                       566789999999999999999999997544......44556788888899999999888888765 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.0039
                              Cnd1   3 RalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvak 47 
                                       R+ a  +lg+i  p+     v+pL ++L Ded+ VR  aa ++a+
  gi|386001593|ref|YP_005919892.1| 482 RSWASLALGSIGGPEA----VDPLIAGLGDEDEGVRTVAAAALAE 522
                                       4444444444444444....4455667778888888888777764 PP

  == domain 10  score: 10.4 bits;  conditional E-value: 0.00045
                              Cnd1   3 RalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanal 79 
                                       R+ a  +lg+i  p+     v+pL ++L Ded+ VR  aa ++a++         + ++ l k+le+e+p+V+  a 
  gi|386001593|ref|YP_005919892.1| 482 RSWASLALGSIGGPEA----VDPLIAGLGDEDEGVRTVAAAALAEI-------GGDAVDPLIKALEEEDPSVQIWAA 547
                                       5555555555555555....55677899*************99975.......233778888889999999988888 PP

                              Cnd1  80 aalteis 86 
                                        al ei 
  gi|386001593|ref|YP_005919892.1| 548 WALGEIG 554
                                       8888885 PP

  == domain 11  score: 7.6 bits;  conditional E-value: 0.0033
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaaltei 85 
                                       v+pL ++Lk ed+ VR  a++++a         +    + l  +l De++ V+  a aal ei
  gi|386001593|ref|YP_005919892.1| 559 VDPLIEALKNEDQAVRLMAVVGLAGF------DDDRRAEPLIAALADEDEVVRFAAAAALAEI 615
                                       67777777778888887777777653......4444556666677777777777777777776 PP

  == domain 12  score: 11.7 bits;  conditional E-value: 0.00017
                              Cnd1  23 vepLrkrLkDedpyVRktaaivva 46 
                                        epL+k+L+Dedp VR+ aa ++ 
  gi|386001593|ref|YP_005919892.1| 621 EEPLKKALEDEDPDVRRKAAEALD 644
                                       68*****************97765 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.03        34      10      36 ..      51      77 ..      48      81 .. 0.88
   2 ?   -1.9   0.0       3.7   4.1e+03      11      37 ..     114     140 ..     111     142 .. 0.81
   3 ?   -1.9   0.0       3.7   4.1e+03       9      22 ..     196     209 ..     194     219 .. 0.83
   4 !    8.1   0.0    0.0026       2.9      10      40 ..     228     258 ..     226     259 .. 0.90
   5 ?    5.6   0.0     0.016        18       8      39 ..     274     305 ..     272     306 .. 0.91
   6 ?    4.6   0.1     0.031        34      10      37 ..     307     334 ..     304     334 .. 0.90
   7 !    8.1   0.0    0.0024       2.7      13      38 ..     341     366 ..     338     368 .. 0.92
   8 !   12.7   0.0   8.7e-05     0.098      10      37 ..     401     428 ..     399     432 .. 0.90
   9 !    7.0   0.1    0.0055       6.1      16      36 ..     438     458 ..     434     460 .. 0.94
  10 ?   -0.7   0.0       1.5   1.7e+03       8      30 ..     461     483 ..     459     493 .. 0.78
  11 !   10.5   0.0   0.00044      0.49      12      39 ..     496     523 ..     491     524 .. 0.91
  12 !   15.7   0.0     1e-05     0.012      13      39 ..     527     553 ..     526     555 .. 0.94
  13 !    9.6   0.0   0.00084      0.94       8      36 ..     553     581 ..     552     582 .. 0.90
  14 !    8.9   0.0    0.0014       1.6      15      39 ..     591     615 ..     591     617 .. 0.93
  15 ?    3.1   0.0     0.092     1e+02      16      36 ..     623     643 ..     622     643 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                                      HTTHHHHHHHHTTTSSHHHHHHHHHHH CS
                               Arm 10 eaGavppLvrLLssedeevqeeAawAL 36
                                      +  a++pL++ Ls+e  +v+  Aa+ L
  gi|386001593|ref|YP_005919892.1| 51 DPRAIDPLIEALSDEVSMVRVHAASSL 77
                                      6679******************99877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.7
                                       TTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  11 aGavppLvrLLssedeevqeeAawALs 37 
                                         a+ pL + L++ed+ v+  A  AL+
  gi|386001593|ref|YP_005919892.1| 114 PRAIVPLREALRDEDPWVRSKASDALG 140
                                       567889999999999999999988887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.7
                                       HHTTHHHHHHHHTT CS
                               Arm   9 ieaGavppLvrLLs 22 
                                        +a av pL++ L+
  gi|386001593|ref|YP_005919892.1| 196 GDARAVGPLIEALK 209
                                       68899*****9998 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0026
                                       HTTHHHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                               Arm  10 eaGavppLvrLLssedeevqeeAawALsNLa 40 
                                       +  av+p +  L +ed+ v++ Aa+AL+ La
  gi|386001593|ref|YP_005919892.1| 228 DDRAVDPVIGALLDEDPAVRTLAAAALGRLA 258
                                       56699***********************998 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.016
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawALsNL 39 
                                       +  aGav++L + L +++ +v+  Aa AL+ +
  gi|386001593|ref|YP_005919892.1| 274 IGGAGAVDHLAEALGDGNWSVRAMAAEALGRI 305
                                       5679*************************965 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.031
                                       HTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLssedeevqeeAawALs 37 
                                       +  a+ pL++ L +e+ +v+  Aa+ L+
  gi|386001593|ref|YP_005919892.1| 307 DPRALGPLIAALGDENATVRLIAAGVLG 334
                                       667899*******************996 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0024
                                       HHHHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawALsN 38 
                                       a++pL++ L+++ + v+ +A+ AL+ 
  gi|386001593|ref|YP_005919892.1| 341 AIDPLIEALKDGEPAVRAAAVYALGE 366
                                       8***********************85 PP

  == domain 8  score: 12.7 bits;  conditional E-value: 8.7e-05
                                       HTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLssedeevqeeAawALs 37 
                                       +  av pL++LL+++ +ev+  A  AL+
  gi|386001593|ref|YP_005919892.1| 401 DERAVSPLIDLLKDDEPEVRAMAGVALG 428
                                       5679*******************99998 PP

  == domain 9  score: 7.0 bits;  conditional E-value: 0.0055
                                       HHHHHTTTSSHHHHHHHHHHH CS
                               Arm  16 pLvrLLssedeevqeeAawAL 36 
                                       pL++LL++e +ev+  Aa AL
  gi|386001593|ref|YP_005919892.1| 438 PLIDLLEDEAPEVRAGAAQAL 458
                                       9*****************999 PP

  == domain 10  score: -0.7 bits;  conditional E-value: 1.5
                                       HHHTTHHHHHHHHTTTSSHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqe 30 
                                       v +  a +pL++ L +e  +v+ 
  gi|386001593|ref|YP_005919892.1| 461 VGDERATRPLIEALGDEEASVRS 483
                                       67788899*******99999986 PP

  == domain 11  score: 10.5 bits;  conditional E-value: 0.00044
                                       THHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLssedeevqeeAawALsNL 39 
                                        av+pL++ L +ede+v+++Aa+AL+ +
  gi|386001593|ref|YP_005919892.1| 496 EAVDPLIAGLGDEDEGVRTVAAAALAEI 523
                                       58***********************876 PP

  == domain 12  score: 15.7 bits;  conditional E-value: 1e-05
                                       HHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeAawALsNL 39 
                                       av+pL++ L+ ed++vq  AawAL+ +
  gi|386001593|ref|YP_005919892.1| 527 AVDPLIKALEEEDPSVQIWAAWALGEI 553
                                       7***********************987 PP

  == domain 13  score: 9.6 bits;  conditional E-value: 0.00084
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawAL 36 
                                       + +  av+pL++ L++ed+ v+  A+  L
  gi|386001593|ref|YP_005919892.1| 553 IGDPKAVDPLIEALKNEDQAVRLMAVVGL 581
                                       66889******************999876 PP

  == domain 14  score: 8.9 bits;  conditional E-value: 0.0014
                                       HHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  15 ppLvrLLssedeevqeeAawALsNL 39 
                                       +pL++ L +ede v+++Aa+AL+ +
  gi|386001593|ref|YP_005919892.1| 591 EPLIAALADEDEVVRFAAAAALAEI 615
                                       59********************876 PP

  == domain 15  score: 3.1 bits;  conditional E-value: 0.092
                                       HHHHHTTTSSHHHHHHHHHHH CS
                               Arm  16 pLvrLLssedeevqeeAawAL 36 
                                       pL + L++ed++v++ Aa AL
  gi|386001593|ref|YP_005919892.1| 623 PLKKALEDEDPDVRRKAAEAL 643
                                       7888899***********998 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.4e+03      94     119 ..      53      78 ..      42      80 .. 0.80
   2 ?    1.3   0.0      0.28   3.2e+02      64     137 ..      85     158 ..      82     165 .. 0.79
   3 ?    3.3   0.0      0.07        78      82     118 ..     187     223 ..     180     226 .. 0.85
   4 ?    1.5   0.1      0.24   2.7e+02      86     119 ..     270     303 ..     266     305 .. 0.92
   5 ?    1.7   0.0      0.22   2.5e+02      94     119 ..     340     365 ..     316     367 .. 0.78
   6 ?    4.9   0.0     0.022        25      82     118 ..     386     427 ..     376     431 .. 0.76
   7 ?    2.4   0.0      0.13   1.4e+02      95     120 ..     435     460 ..     423     462 .. 0.84
   8 ?    4.0   0.0     0.042        47      83     120 ..     485     522 ..     473     523 .. 0.88
   9 ?    4.3   0.0     0.036        40      91     118 ..     523     550 ..     522     554 .. 0.89
  10 ?    1.0   0.0      0.36     4e+02      93     115 ..     556     578 ..     546     584 .. 0.76
  11 ?   -0.9   0.1       1.4   1.6e+03      85     118 ..     610     643 ..     591     646 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                     Aconitase_B_N  94 ynvksLidllkekdeelaeeaaeaLk 119
                                        ++++Li++l+++ + ++ +aa+ L 
  gi|386001593|ref|YP_005919892.1|  53 RAIDPLIEALSDEVSMVRVHAASSLV 78 
                                       6899*******999999999998875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.28
                     Aconitase_B_N  64 fLaaiakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkktllvydafedveelake 137
                                       +L++++   +  +   +  A + Lg++    ++ +L ++l+++d  ++++a +aL k++  +   e vee  +e
  gi|386001593|ref|YP_005919892.1|  85 YLDRVILALEDEDKWVRGWAATHLGDIGDPRAIVPLREALRDEDPWVRSKASDALGKIIEATGDDEGVEEEKEE 158
                                       66666666666666666778888999999999************************999888777777776665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.07
                     Aconitase_B_N  82 eAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                        A   Lg+M    +v +Li++lk+ + e++ +a+ aL
  gi|386001593|ref|YP_005919892.1| 187 AAALSLGEMGDARAVGPLIEALKDVEWEVRGAAVIAL 223
                                       566779*****************98888888888777 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.24
                     Aconitase_B_N  86 lLgtMlGGynvksLidllkekdeelaeeaaeaLk 119
                                       lLg++ G  +v++L ++l + + ++++ aaeaL 
  gi|386001593|ref|YP_005919892.1| 270 LLGEIGGAGAVDHLAEALGDGNWSVRAMAAEALG 303
                                       899999999**********************996 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.22
                     Aconitase_B_N  94 ynvksLidllkekdeelaeeaaeaLk 119
                                        ++++Li++lk+ + +++++a+ aL 
  gi|386001593|ref|YP_005919892.1| 340 EAIDPLIEALKDGEPAVRAAAVYALG 365
                                       5799*******999999999998885 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.022
                     Aconitase_B_N  82 eAvelLgtM.lGG....ynvksLidllkekdeelaeeaaeaL 118
                                        A+++ g M lGG     +v++Lidllk+++ e+++ a  aL
  gi|386001593|ref|YP_005919892.1| 386 PALRIYGAMiLGGlgdeRAVSPLIDLLKDDEPEVRAMAGVAL 427
                                       5777888773476333358*********99999999988777 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.13
                     Aconitase_B_N  95 nvksLidllkekdeelaeeaaeaLkk 120
                                       +  +Lidll+++  e+++ aa+aL +
  gi|386001593|ref|YP_005919892.1| 435 AAGPLIDLLEDEAPEVRAGAAQALAT 460
                                       6789*******************975 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.042
                     Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                       A   Lg + G  +v++Li  l ++de +++ aa+aL +
  gi|386001593|ref|YP_005919892.1| 485 ASLALGSIGGPEAVDPLIAGLGDEDEGVRTVAAAALAE 522
                                       555799999999**********************9975 PP

  == domain 9  score: 4.3 bits;  conditional E-value: 0.036
                     Aconitase_B_N  91 lGGynvksLidllkekdeelaeeaaeaL 118
                                       +GG +v++Li++l+e+d +++  aa aL
  gi|386001593|ref|YP_005919892.1| 523 IGGDAVDPLIKALEEEDPSVQIWAAWAL 550
                                       59***************99998888877 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 0.36
                     Aconitase_B_N  93 GynvksLidllkekdeelaeeaa 115
                                         +v++Li++lk++d++++  a+
  gi|386001593|ref|YP_005919892.1| 556 PKAVDPLIEALKNEDQAVRLMAV 578
                                       56899*******99999887776 PP

  == domain 11  score: -0.9 bits;  conditional E-value: 1.4
                     Aconitase_B_N  85 elLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                         L+++    + ++L ++l+++d +++++aaeaL
  gi|386001593|ref|YP_005919892.1| 610 AALAEIGDPRAEEPLKKALEDEDPDVRRKAAEAL 643
                                       3333333333344555566666666666666666 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.55   6.1e+02     117     141 ..      56      80 ..      50      91 .. 0.78
   2 !    5.4   0.0    0.0049       5.5      87     147 ..      92     148 ..      86     231 .. 0.87
   3 ?   -1.7   0.0      0.71     8e+02      87     138 ..     207     254 ..     200     261 .. 0.61
   4 !    4.7   0.0     0.008       8.9      87     197 ..     286     381 ..     279     391 .. 0.63
   5 ?    3.2   0.0     0.024        27      88     142 ..     412     462 ..     404     498 .. 0.77
   6 ?    1.8   0.0     0.061        68     148     194 ..     527     563 ..     470     578 .. 0.69
   7 !    6.8   0.0    0.0019       2.1      87     138 ..     596     643 ..     591     647 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.55
                                       HHHHHHHT-SSHHHHHHHHHHHHHC CS
                         Adaptin_N 117 paikkllkdrspyvrkkAalailkl 141
                                       + + ++l+d+ ++vr  Aa +++kl
  gi|386001593|ref|YP_005919892.1|  56 DPLIEALSDEVSMVRVHAASSLVKL 80 
                                       5667788888888888888888887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0049
                                       HCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHH CS
                         Adaptin_N  87 DlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpd 147
                                       +l+d ++ +rg A + L++i++p+        ++++l+d++p vr+kA  a+ k+++++ d
  gi|386001593|ref|YP_005919892.1|  92 ALEDEDKWVRGWAATHLGDIGDPR----AIVPLREALRDEDPWVRSKASDALGKIIEATGD 148
                                       5889999999999999***99986....445699**************9999999988544 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.71
                                       HCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHH CS
                         Adaptin_N  87 DlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalai 138
                                       +lkd +  +rg A+ +L+ i++++ +    + +  +l d++p vr  Aa a+
  gi|386001593|ref|YP_005919892.1| 207 ALKDVEWEVRGAAVIALAGIGDDRAV----DPVIGALLDEDPAVRTLAAAAL 254
                                       55555666666666666666665544....4445556677777777777665 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.008
                                       HCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT- CS
                         Adaptin_N  87 DlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsd 163
                                       +l d n  +r++A  +L++i++p+ +      + ++l d+++ vr  Aa  +    + +p++     ++ ++e+l+d
  gi|386001593|ref|YP_005919892.1| 286 ALGDGNWSVRAMAAEALGRIGDPRALGP----LIAALGDENATVRLIAAGVLGG--SGSPEA-----IDPLIEALKD 351
                                       5666666666666666666666654433....3445566666666555444332..334444.....6788999999 PP

                                       SSHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCH CS
                         Adaptin_N 164 kdpgvvlaAvalleeikkndrlllkllpklvrrL 197
                                        +p v +aAv +l e+   d+   +++  l++ L
  gi|386001593|ref|YP_005919892.1| 352 GEPAVRAAAVYALGEM--GDDP--RAIDGLISSL 381
                                       9999999999999999..5555..5666666655 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.024
                                       CCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCC CS
                         Adaptin_N  88 lkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailkly 142
                                       lkd ++ +r++A  +L++i++++ a      + +ll+d+ p vr  Aa+a++++ 
  gi|386001593|ref|YP_005919892.1| 412 LKDDEPEVRAMAGVALGDIGSEKAA----GPLIDLLEDEAPEVRAGAAQALATVG 462
                                       7889999999999999999987655....55678999999999999999998774 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.061
                                       CCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCCHHHHHHH CS
                         Adaptin_N 148 llrkqlveeikellsdkdpgvvlaAvalleeikkndrlllkllpklv 194
                                       +     v+ ++++l+++dp+v+  A  +l ei   +    k++  l+
  gi|386001593|ref|YP_005919892.1| 527 A-----VDPLIKALEEEDPSVQIWAAWALGEI-GDP----KAVDPLI 563
                                       3.....56678888888888888888888888.222....2233333 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.0019
                                       HCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHH CS
                         Adaptin_N  87 DlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalai 138
                                       +l d ++++r  A  +L+ i++p+     ++ +kk+l+d++p vr+kAa a+
  gi|386001593|ref|YP_005919892.1| 596 ALADEDEVVRFAAAAALAEIGDPR----AEEPLKKALEDEDPDVRRKAAEAL 643
                                       688999999999999999999986....78899***************9775 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.39   4.3e+02      29      52 ..      55      78 ..      51      83 .. 0.89
   2 ?    0.0   0.0       1.2   1.3e+03      28      50 ..      85     107 ..      78     112 .. 0.83
   3 ?   -0.9   0.0       2.3   2.6e+03      31      56 ..     119     144 ..     115     149 .. 0.80
   4 ?    1.2   0.0      0.49   5.5e+02      27      51 ..     230     254 ..     219     259 .. 0.87
   5 ?   -1.4   0.0       3.4   3.8e+03      29      48 ..     311     330 ..     308     333 .. 0.84
   6 ?   -1.4   0.0       3.3   3.7e+03      28      48 ..     341     361 ..     338     366 .. 0.79
   7 ?    0.4   0.0      0.91     1e+03      29      51 ..     405     427 ..     401     458 .. 0.75
   8 ?   -0.5   0.0       1.7   1.9e+03      30      50 ..     468     488 ..     454     492 .. 0.82
   9 ?    1.4   0.0      0.44   4.9e+02      28      54 ..     497     523 ..     494     538 .. 0.81
  10 ?    0.1   0.0       1.1   1.3e+03      28      48 ..     558     578 ..     555     582 .. 0.88
  11 ?    5.8   0.1     0.019        21      30      57 ..     591     618 ..     587     647 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.39
                     Vac14_Fab1_bd 29 vkpvlkcfsDkdsrvRyyacEsly 52
                                      ++p+++++sD+ s vR +a+ sl 
  gi|386001593|ref|YP_005919892.1| 55 IDPLIEALSDEVSMVRVHAASSLV 78
                                      899****************99986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyacEs 50 
                                        ++ v+ +++D+d+ vR +a+  
  gi|386001593|ref|YP_005919892.1|  85 YLDRVILALEDEDKWVRGWAATH 107
                                       57789999*********888765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                     Vac14_Fab1_bd  31 pvlkcfsDkdsrvRyyacEslyniak 56 
                                       p+ ++++D+d  vR  a+++l  i+ 
  gi|386001593|ref|YP_005919892.1| 119 PLREALRDEDPWVRSKASDALGKIIE 144
                                       6668899*******999999987765 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.49
                     Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEsl 51 
                                       + v+pv+ ++ D+d  vR  a+ +l
  gi|386001593|ref|YP_005919892.1| 230 RAVDPVIGALLDEDPAVRTLAAAAL 254
                                       5689**************9998776 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 3.4
                     Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyac 48 
                                       + p+++++ D+++ vR  a+
  gi|386001593|ref|YP_005919892.1| 311 LGPLIAALGDENATVRLIAA 330
                                       568999**********9886 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.3
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyac 48 
                                        ++p++++++D +  vR  a+
  gi|386001593|ref|YP_005919892.1| 341 AIDPLIEALKDGEPAVRAAAV 361
                                       588999999999999997765 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.91
                     Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEsl 51 
                                       v+p+++ ++D++ +vR  a  +l
  gi|386001593|ref|YP_005919892.1| 405 VSPLIDLLKDDEPEVRAMAGVAL 427
                                       77888888888888887765554 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 1.7
                     Vac14_Fab1_bd  30 kpvlkcfsDkdsrvRyyacEs 50 
                                       +p+++++ D+++ vR +a+ +
  gi|386001593|ref|YP_005919892.1| 468 RPLIEALGDEEASVRSWASLA 488
                                       689999999999999988755 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.44
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyacEslyni 54 
                                        v+p+++ + D+d+ vR  a+ +l  i
  gi|386001593|ref|YP_005919892.1| 497 AVDPLIAGLGDEDEGVRTVAAAALAEI 523
                                       589999************999998776 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 1.1
                     Vac14_Fab1_bd  28 ivkpvlkcfsDkdsrvRyyac 48 
                                        v+p++++++ +d+ vR  a+
  gi|386001593|ref|YP_005919892.1| 558 AVDPLIEALKNEDQAVRLMAV 578
                                       5899*************9886 PP

  == domain 11  score: 5.8 bits;  conditional E-value: 0.019
                     Vac14_Fab1_bd  30 kpvlkcfsDkdsrvRyyacEslyniakv 57 
                                       +p+++++ D+d+ vR+ a+ +l  i   
  gi|386001593|ref|YP_005919892.1| 591 EPLIAALADEDEVVRFAAAAALAEIGDP 618
                                       5778888888888888888877666544 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.3   9.3e+03       7      30 ..      55      78 ..      54      92 .. 0.79
   2 ?   -1.7   0.0       3.4   3.9e+03      10      34 ..     120     144 ..     116     149 .. 0.82
   3 ?   -2.8   0.0       7.5   8.4e+03       8      30 ..     233     255 ..     231     260 .. 0.81
   4 !    7.3   0.0    0.0055       6.2       7      44 ..     342     379 ..     341     396 .. 0.86
   5 ?    0.2   0.0      0.87   9.7e+02       7      32 ..     405     430 ..     402     439 .. 0.83
   6 ?    2.9   0.0      0.12   1.4e+02      10      36 ..     439     465 ..     435     476 .. 0.85
   7 ?   -1.0   0.0         2   2.3e+03       8      32 ..     499     523 ..     497     556 .. 0.68
   8 ?   -0.9   0.0       1.9   2.2e+03       7      36 ..     559     588 ..     558     602 .. 0.78
   9 ?   -1.3   0.0       2.5   2.8e+03       8      32 ..     591     615 ..     589     626 .. 0.86
  10 ?    2.0   0.0      0.23   2.6e+02      10      31 ..     624     645 ..     620     647 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.3
                        RasGEF_N_2  7 iellvnqLydqsrevvaaaleiLe 30
                                      i+ l++ L+d+ + v+ +a++ L 
  gi|386001593|ref|YP_005919892.1| 55 IDPLIEALSDEVSMVRVHAASSLV 78
                                      788999999999988888887775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                        RasGEF_N_2  10 lvnqLydqsrevvaaaleiLeeacd 34 
                                       l + L d+++ v+++a ++L ++++
  gi|386001593|ref|YP_005919892.1| 120 LREALRDEDPWVRSKASDALGKIIE 144
                                       667899************9988765 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.5
                        RasGEF_N_2   8 ellvnqLydqsrevvaaaleiLe 30 
                                       +  +  L d++++v+  a+ +L 
  gi|386001593|ref|YP_005919892.1| 233 DPVIGALLDEDPAVRTLAAAALG 255
                                       56678899********9999886 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0055
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacddkeslevlve 44 
                                       i+ l++ L+d +++v+aaa+ +L e+ dd++ +  l++
  gi|386001593|ref|YP_005919892.1| 342 IDPLIEALKDGEPAVRAAAVYALGEMGDDPRAIDGLIS 379
                                       899***********************999987776665 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.87
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeea 32 
                                       ++ l++ L+d+++ev+a+a  +L ++
  gi|386001593|ref|YP_005919892.1| 405 VSPLIDLLKDDEPEVRAMAGVALGDI 430
                                       678999************99888766 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.12
                        RasGEF_N_2  10 lvnqLydqsrevvaaaleiLeeacddk 36 
                                       l++ L+d+++ev+a a+++L  + d++
  gi|386001593|ref|YP_005919892.1| 439 LIDLLEDEAPEVRAGAAQALATVGDER 465
                                       7899****************9987766 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 2
                        RasGEF_N_2   8 ellvnqLydqsrevvaaaleiLeea 32 
                                       + l+  L d+++ v+ +a+ +L e+
  gi|386001593|ref|YP_005919892.1| 499 DPLIAGLGDEDEGVRTVAAAALAEI 523
                                       6677788888888888888888776 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 1.9
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacddk 36 
                                       ++ l++ L++++++v+ +a+  L  + dd+
  gi|386001593|ref|YP_005919892.1| 559 VDPLIEALKNEDQAVRLMAVVGLAGFDDDR 588
                                       678999*************99988774444 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 2.5
                        RasGEF_N_2   8 ellvnqLydqsrevvaaaleiLeea 32 
                                       e l+  L d+++ v+ aa+ +L e+
  gi|386001593|ref|YP_005919892.1| 591 EPLIAALADEDEVVRFAAAAALAEI 615
                                       578999**************99997 PP

  == domain 10  score: 2.0 bits;  conditional E-value: 0.23
                        RasGEF_N_2  10 lvnqLydqsrevvaaaleiLee 31 
                                       l + L+d++++v+++a+e+L++
  gi|386001593|ref|YP_005919892.1| 624 LKKALEDEDPDVRRKAAEALDR 645
                                       66889***************86 PP

>> IFRD  Interferon-related developmental regulator (IFRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0036       4.1     223     277 ..     116     176 ..     103     185 .. 0.76
   2 ?   -3.9   0.0       5.2   5.8e+03     223     247 ..     279     303 ..     266     304 .. 0.78
   3 ?   -1.3   0.0      0.81     9e+02     127     151 ..     343     365 ..     324     368 .. 0.70
   4 !    5.4   0.0    0.0075       8.4     221     247 ..     402     428 ..     377     430 .. 0.88
   5 ?    3.9   0.2     0.022        25     221     248 ..     433     460 ..     426     492 .. 0.87
   6 ?    0.8   0.0      0.19   2.1e+02     221     246 ..     525     550 ..     478     555 .. 0.77
   7 ?    0.6   0.3      0.22   2.4e+02     224     249 ..     590     615 ..     571     643 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0036
                              IFRD 223 alealvelLdssdvevriAAGeaiALlfElsreedeefeeeeee......dteelleqlre 277
                                       a+  l e L ++d  vr  A+ a++ + E   +++  +ee+eee      +++el + l +
  gi|386001593|ref|YP_005919892.1| 116 AIVPLREALRDEDPWVRSKASDALGKIIEATGDDEGVEEEKEEEkdgaseEDDELSRLLYD 176
                                       67778899*********************66555544444444467888877777766655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.2
                              IFRD 223 alealvelLdssdvevriAAGeaiA 247
                                       a+++l e L + + +vr  A ea++
  gi|386001593|ref|YP_005919892.1| 279 AVDHLAEALGDGNWSVRAMAAEALG 303
                                       5777888888888888888888875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.81
                              IFRD 127 pvLkriikdssvslsakaaaieaLg 151
                                       ++L +++kd++  ++++aaa++aLg
  gi|386001593|ref|YP_005919892.1| 343 DPLIEALKDGE--PAVRAAAVYALG 365
                                       45556666666..677777777776 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0075
                              IFRD 221 eealealvelLdssdvevriAAGeaiA 247
                                       e+a++ l++lL++++ evr  AG a++
  gi|386001593|ref|YP_005919892.1| 402 ERAVSPLIDLLKDDEPEVRAMAGVALG 428
                                       789********************9985 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.022
                              IFRD 221 eealealvelLdssdvevriAAGeaiAL 248
                                       e+a+  l++lL+++  evr  A +a+A 
  gi|386001593|ref|YP_005919892.1| 433 EKAAGPLIDLLEDEAPEVRAGAAQALAT 460
                                       5678889*******************96 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.19
                              IFRD 221 eealealvelLdssdvevriAAGeai 246
                                        +a++ l++ L+ +d +v+i A  a+
  gi|386001593|ref|YP_005919892.1| 525 GDAVDPLIKALEEEDPSVQIWAAWAL 550
                                       56789999999999999999887766 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.22
                              IFRD 224 lealvelLdssdvevriAAGeaiALl 249
                                       +e l++ L ++d  vr+AA  a+A +
  gi|386001593|ref|YP_005919892.1| 590 AEPLIAALADEDEVVRFAAAAALAEI 615
                                       67788899999999999999888855 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.9   7.7e+03      49      67 ..     239     257 ..     238     259 .. 0.80
   2 ?   -1.3   0.0       1.3   1.5e+03      48      66 ..     286     304 ..     276     308 .. 0.85
   3 ?    3.1   0.0     0.062        69      48      72 ..     348     372 ..     317     385 .. 0.87
   4 ?    3.9   0.0     0.033        38      48      70 ..     442     464 ..     427     493 .. 0.76
   5 ?   -2.0   0.0       2.2   2.4e+03      47      71 ..     503     527 ..     482     545 .. 0.73
   6 ?   -1.9   0.0       2.1   2.4e+03      47      67 ..     595     615 ..     586     643 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.9
                           DUF4042  49 lkDpspkvRaaalqvlaal 67 
                                       l D  p vR++a+ +l  l
  gi|386001593|ref|YP_005919892.1| 239 LLDEDPAVRTLAAAALGRL 257
                                       5688899999999998776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                           DUF4042  48 llkDpspkvRaaalqvlaa 66 
                                       +l D++  vRa+a+++l  
  gi|386001593|ref|YP_005919892.1| 286 ALGDGNWSVRAMAAEALGR 304
                                       5789***********9976 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.062
                           DUF4042  48 llkDpspkvRaaalqvlaalLdgsk 72 
                                       +lkD++p vRaaa+ +l ++ d+++
  gi|386001593|ref|YP_005919892.1| 348 ALKDGEPAVRAAAVYALGEMGDDPR 372
                                       699***************9977765 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.033
                           DUF4042  48 llkDpspkvRaaalqvlaalLdg 70 
                                       ll+D  p vRa a+q+la++ d+
  gi|386001593|ref|YP_005919892.1| 442 LLEDEAPEVRAGAAQALATVGDE 464
                                       689***************98665 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 2.2
                           DUF4042  47 illkDpspkvRaaalqvlaalLdgs 71 
                                        +l D    vR++a+ +la++  + 
  gi|386001593|ref|YP_005919892.1| 503 AGLGDEDEGVRTVAAAALAEIGGDA 527
                                       5677888899999999999985555 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 2.1
                           DUF4042  47 illkDpspkvRaaalqvlaal 67 
                                        +l D    vR aa+ +la++
  gi|386001593|ref|YP_005919892.1| 595 AALADEDEVVRFAAAAALAEI 615
                                       567788888888888888876 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   2.3e+03     181     198 ..     120     137 ..     118     144 .. 0.85
   2 ?   -1.7   0.0       1.6   1.8e+03     181     196 ..     345     360 ..     337     363 .. 0.86
   3 ?   -2.2   0.0       2.2   2.5e+03     179     195 ..     406     422 ..     399     424 .. 0.82
   4 ?   -0.8   0.0       0.8     9e+02     181     199 ..     439     457 ..     430     485 .. 0.82
   5 ?   -0.4   0.0      0.62   6.9e+02     178     199 ..     498     519 ..     491     530 .. 0.84
   6 ?    5.4   0.1      0.01        12     177     197 ..     620     640 ..     593     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                           CLASP_N 181 lkkgleDanptVRetaRs 198
                                       l+++l D +p VR++a +
  gi|386001593|ref|YP_005919892.1| 120 LREALRDEDPWVRSKASD 137
                                       7899*********99865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                           CLASP_N 181 lkkgleDanptVReta 196
                                       l+++l+D +p+VR +a
  gi|386001593|ref|YP_005919892.1| 345 LIEALKDGEPAVRAAA 360
                                       8899*********876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.2
                           CLASP_N 179 kslkkgleDanptVRet 195
                                         l+ +l+D +p+VR  
  gi|386001593|ref|YP_005919892.1| 406 SPLIDLLKDDEPEVRAM 422
                                       568999*********75 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.8
                           CLASP_N 181 lkkgleDanptVRetaRst 199
                                       l+ +leD  p+VR  a ++
  gi|386001593|ref|YP_005919892.1| 439 LIDLLEDEAPEVRAGAAQA 457
                                       7788999999999887555 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.62
                           CLASP_N 178 ekslkkgleDanptVRetaRst 199
                                       ++ l++gl D + +VR +a ++
  gi|386001593|ref|YP_005919892.1| 498 VDPLIAGLGDEDEGVRTVAAAA 519
                                       566899**********998665 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.01
                           CLASP_N 177 iekslkkgleDanptVRetaR 197
                                       +e+ lkk+leD +p VR++a 
  gi|386001593|ref|YP_005919892.1| 620 AEEPLKKALEDEDPDVRRKAA 640
                                       6888*************9985 PP

>> Cohesin_HEAT  HEAT repeat associated with sister chromatid cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         7   7.9e+03      10      30 ..      15      34 ..       9      35 .. 0.67
   2 ?   -1.4   0.1       2.8   3.2e+03      23      35 ..      58      70 ..      56      73 .. 0.86
   3 ?   -2.5   0.0         6   6.7e+03      26      35 ..     123     132 ..     122     133 .. 0.87
   4 ?    2.5   0.0      0.17   1.9e+02      23      37 ..     235     249 ..     233     250 .. 0.87
   5 ?    4.8   0.0     0.032        36      23      39 ..     345     361 ..     337     364 .. 0.89
   6 ?   -1.4   0.0       2.8   3.2e+03      27      36 ..     412     421 ..     407     423 .. 0.87
   7 ?   -1.0   0.0       2.1   2.4e+03      27      36 ..     443     452 ..     442     454 .. 0.91
   8 ?    2.8   0.0      0.13   1.4e+02      24      38 ..     471     485 ..     469     485 .. 0.85
   9 ?    0.3   0.1       0.8   8.9e+02      23      35 ..     624     636 ..     624     639 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7
                                      -GGGGGSHHHHHHHHHHHHSS CS
                      Cohesin_HEAT 10 dpsiLsapevldtiarrltDs 30
                                         +++a++v d+ia+ l D+
  gi|386001593|ref|YP_005919892.1| 15 LAGLVAADQVDDAIAY-LKDP 34
                                      4456667777788887.7777 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                                      HHHHHHSS-HHHH CS
                      Cohesin_HEAT 23 iarrltDsspsVR 35
                                      +++ l+D+ ++VR
  gi|386001593|ref|YP_005919892.1| 58 LIEALSDEVSMVR 70
                                      5778********9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6
                                       HHHSS-HHHH CS
                      Cohesin_HEAT  26 rltDsspsVR 35 
                                        l+D++p VR
  gi|386001593|ref|YP_005919892.1| 123 ALRDEDPWVR 132
                                       699****999 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.17
                                       HHHHHHSS-HHHHHH CS
                      Cohesin_HEAT  23 iarrltDsspsVRdA 37 
                                       ++  l+D++p VR  
  gi|386001593|ref|YP_005919892.1| 235 VIGALLDEDPAVRTL 249
                                       6889*********75 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.032
                                       HHHHHHSS-HHHHHHHH CS
                      Cohesin_HEAT  23 iarrltDsspsVRdAaL 39 
                                       +++ l D +p VR+Aa+
  gi|386001593|ref|YP_005919892.1| 345 LIEALKDGEPAVRAAAV 361
                                       6788************8 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 2.8
                                       HHSS-HHHHH CS
                      Cohesin_HEAT  27 ltDsspsVRd 36 
                                       l D +p VR+
  gi|386001593|ref|YP_005919892.1| 412 LKDDEPEVRA 421
                                       78*******7 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 2.1
                                       HHSS-HHHHH CS
                      Cohesin_HEAT  27 ltDsspsVRd 36 
                                       l+D++p VR+
  gi|386001593|ref|YP_005919892.1| 443 LEDEAPEVRA 452
                                       79*******6 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.13
                                       HHHHHSS-HHHHHHH CS
                      Cohesin_HEAT  24 arrltDsspsVRdAa 38 
                                       ++ l D+++sVR +a
  gi|386001593|ref|YP_005919892.1| 471 IEALGDEEASVRSWA 485
                                       56688*******997 PP

  == domain 9  score: 0.3 bits;  conditional E-value: 0.8
                                       HHHHHHSS-HHHH CS
                      Cohesin_HEAT  23 iarrltDsspsVR 35 
                                       +++ l+D++p VR
  gi|386001593|ref|YP_005919892.1| 624 LKKALEDEDPDVR 636
                                       6899********9 PP

>> Gag_p12  Gag polyprotein, inner coat protein p12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.1   1.1e+02      22      36 ..     406     420 ..     399     426 .. 0.85
   2 ?    5.8   0.1     0.016        18      20      40 ..     435     455 ..     430     475 .. 0.76
   3 ?   -3.0   0.0       8.9     1e+04      19      33 ..     526     540 ..     521     543 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                           Gag_p12  22 Gplidlltedpppyr 36 
                                        plidll +d p  r
  gi|386001593|ref|YP_005919892.1| 406 SPLIDLLKDDEPEVR 420
                                       6*********99876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                           Gag_p12  20 sGGplidlltedpppyrdarp 40 
                                       + Gplidll ++ p  r    
  gi|386001593|ref|YP_005919892.1| 435 AAGPLIDLLEDEAPEVRAGAA 455
                                       67*******999998876544 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.9
                           Gag_p12  19 dsGGplidlltedpp 33 
                                       d+  pli  l e+ p
  gi|386001593|ref|YP_005919892.1| 526 DAVDPLIKALEEEDP 540
                                       777899999987766 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.43   4.8e+02      59      98 ..      53      90 ..      51      94 .. 0.86
   2 ?   -0.0   0.0      0.26   2.9e+02      58      89 ..     339     370 ..     336     380 .. 0.90
   3 ?   -0.5   0.0      0.36   4.1e+02      58      86 ..     402     430 ..     401     436 .. 0.80
   4 ?    2.3   0.0     0.051        58      58      88 ..     433     463 ..     430     471 .. 0.87
   5 ?   -3.2   0.0       2.4   2.7e+03      60      96 ..     497     533 ..     496     536 .. 0.82
   6 ?   -3.4   0.1       2.7   3.1e+03      59      88 ..     557     586 ..     556     591 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.43
                              API5 59 kaidaqlDLiedddlgirkqAikdLpslckdtkeyvskia 98
                                      +aid +++ + d+  ++r+ A  +L++l +  +ey+ +++
  gi|386001593|ref|YP_005919892.1| 53 RAIDPLIEALSDEVSMVRVHAASSLVKLGR--PEYLDRVI 90
                                      689999**********************86..77887776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.26
                              API5  58 ekaidaqlDLiedddlgirkqAikdLpslckd 89 
                                        +aid +++ + d + ++r +A+ +L ++  d
  gi|386001593|ref|YP_005919892.1| 339 PEAIDPLIEALKDGEPAVRAAAVYALGEMGDD 370
                                       589***********************999877 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.36
                              API5  58 ekaidaqlDLiedddlgirkqAikdLpsl 86 
                                       e+a+  ++DL+ dd+ ++r  A  +L  +
  gi|386001593|ref|YP_005919892.1| 402 ERAVSPLIDLLKDDEPEVRAMAGVALGDI 430
                                       5788899************9886666555 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.051
                              API5  58 ekaidaqlDLiedddlgirkqAikdLpslck 88 
                                       eka   ++DL+ed+  ++r  A ++L+++  
  gi|386001593|ref|YP_005919892.1| 433 EKAAGPLIDLLEDEAPEVRAGAAQALATVGD 463
                                       6777789*******************99875 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 2.4
                              API5  60 aidaqlDLiedddlgirkqAikdLpslckdtkeyvsk 96 
                                       a+d ++  + d+d g+r  A  +L+++  d+ + + k
  gi|386001593|ref|YP_005919892.1| 497 AVDPLIAGLGDEDEGVRTVAAAALAEIGGDAVDPLIK 533
                                       56666777789****************9999887666 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 2.7
                              API5  59 kaidaqlDLiedddlgirkqAikdLpslck 88 
                                       ka+d +++ + ++d ++r  A+ +L+ +  
  gi|386001593|ref|YP_005919892.1| 557 KAVDPLIEALKNEDQAVRLMAVVGLAGFDD 586
                                       68999999999**********999987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3923.24
//
Query:       gi|386001594|ref|YP_005919893.1|  [L=388]
Description: Putative transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-13   51.1   0.0    2.2e-13   50.6   0.0    1.2  1  AlbA_2    Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.2e-17   2.2e-13       1     121 [.      26     152 ..      26     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.2e-17
                            AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNsegGtlliGVeD.dgk...vvGvecsdqeedqlrlelksiikrfkp 73 
                                       E++ +++K+ l   ++ ++r++++++ +faN++gG+l++GV++ +g    + G+   d +e  lrl +  +++ + p
  gi|386001594|ref|YP_005919893.1|  26 ESKVIDYKRRLPGPSDLEKREFIRDVTSFANASGGHLVYGVAEeNGVpvrIPGLPGIDPDEAILRLDSM-VQTGIAP 101
                                       8999**************************************954446666677778888888888888.******* PP

                            AlbA_2  74 k.vlpdiervelkgk.kvlvvkvekskkkp.lyeneegvvyiRrggsskrl 121
                                       + + ++++ v lkgk  v+vv+++ks   p + ++ ++++y R+ + +++l
  gi|386001594|ref|YP_005919893.1| 102 RiPGISMRAVPLKGKrFVIVVRIPKSWASPhMITKGSSKFYSRNSAGKYPL 152
                                       *7789*********97899***********9999999*******9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2682.89
//
Query:       gi|386001595|ref|YP_005919894.1|  [L=53]
Description: hypothetical protein Mhar_0900 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 388.25
//
Query:       gi|386001596|ref|YP_005919895.1|  [L=72]
Description: hypothetical protein Mhar_0901 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-17   62.6   0.1      3e-17   62.5   0.1    1.0  1  DUF2582   Winged helix-turn-helix domain (DUF2582)
    6.8e-05   22.9   0.0    7.7e-05   22.7   0.0    1.1  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
     0.0066   16.3   0.0     0.0086   15.9   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.16   10.7   0.0       0.16   10.7   0.0    1.0  1  GNT-I     GNT-I family


Domain annotation for each model (and alignments):
>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.1   6.6e-21     3e-17       4      63 ..       8      67 ..       1      69 [. 0.90

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 6.6e-21
                                      HHHHHHHHHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETTEEEE CS
                           DUF2582  4 eiiGenAGkvwhlLnengeislkelkrktglsdkelalAiGWLaREdKivierkekelfv 63
                                      +i G +AG vw +Lneng  ++ e+ ++t+l +++++ A+GWL RE+Ki++e + +  ++
  gi|386001596|ref|YP_005919895.1|  8 SIFGSKAGLVWDALNENGPSTITEIMKATSLRREDVYGALGWLGRENKIAVEMRGRARVF 67
                                      457*************************************************98877665 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.7e-08   7.7e-05       6      48 ..       5      47 ..       1      54 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.7e-08
                                      HHHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHH CS
                             HTH_9  6 iieehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksL 48
                                       +e++FG+ +  V + L ++g +t++e+ k+t+L +  V  +L
  gi|386001596|ref|YP_005919895.1|  5 TVESIFGSKAGLVWDALNENGPSTITEIMKATSLRREDVYGAL 47
                                      69*********************************99997776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.9e-06    0.0086      16      55 ..      20      59 ..      16      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      aL ++gp+t++ei +++ + r  vY +L  L +   + +e
  gi|386001596|ref|YP_005919895.1| 20 ALNENGPSTITEIMKATSLRREDVYGALGWLGRENKIAVE 59
                                      6779************************999887766665 PP

>> GNT-I  GNT-I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.7e-05      0.16     229     262 ..      19      52 ..       7      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                             GNT-I 229 saWndnGkkqfvdasapealyrsdffpGlGWlls 262
                                        a n+nG   + +  +++ l r d +  lGWl +
  gi|386001596|ref|YP_005919895.1|  19 DALNENGPSTITEIMKATSLRREDVYGALGWLGR 52 
                                       578****************************955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 524.55
//
Query:       gi|386001597|ref|YP_005919896.1|  [L=271]
Description: 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-64  215.8   0.0    8.1e-64  215.4   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    3.2e-55  186.6   0.1    3.8e-55  186.4   0.1    1.0  1  adh_short     short chain dehydrogenase
    2.7e-14   53.5   0.0    3.6e-14   53.1   0.0    1.1  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.4   0.0   1.4e-67   8.1e-64       3     234 .]      26     269 ..      24     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 215.4 bits;  conditional E-value: 1.4e-67
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnna 77 
                                         gIG+aiAk la eGa  ++t ++e++  + vee+ + +ga+ ++ +DVt+e+ ve+++++v e +g++Dilvnna
  gi|386001597|ref|YP_005919896.1|  26 TYGIGEAIAKILAGEGAISIVTGRSEDEgGRVVEEIRSGGGAAeYYSLDVTSEKRVEEVARAVYEGYGRIDILVNNA 102
                                       57**************************88888999988886668******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       gi  + ++p++e +r e++r++dvn++++fl++k+++p+mk+g  g+iv +ss+ + ++ +++ ay+a+Kaa   ++
  gi|386001597|ref|YP_005919896.1| 103 GIGGP-SKPTHEYTRREWERVFDVNVTGAFLCTKHVIPYMKRGggGNIVYISSIYGIVGSQDNPAYHATKAANRIMA 178
                                       *****.***********************************9999******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGS..TT.......HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgi..kg.......fdelleelearaplgrlgtpeevaeaalfLasdeas 220
                                       ++ A  +++++iRvN+v+pg+i T++++++  ++        ++l++el ar+p+g+lg+pe+++  +l+L+sdea+
  gi|386001597|ref|YP_005919896.1| 179 KTGALIYAKDNIRVNSVHPGFIWTPMVEEFliEQskelgvpLEDLKRELGARHPIGHLGEPEDIGYGVLYLVSDEAK 255
                                       **************************88752233333444456699******************************* PP

                                       T--SEEEEESTTGG CS
                      adh_short_C2 221 yitGqtlvvDgGlt 234
                                       ++tG++l++DgG+t
  gi|386001597|ref|YP_005919896.1| 256 FVTGSELIIDGGYT 269
                                       *************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.4   0.1   6.3e-59   3.8e-55       2     189 ..      19     207 ..      18     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.4 bits;  conditional E-value: 6.3e-59
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       +++vtG + GIG aiak la eGa  +v++rse++  +v++e+++ g  a ++++Dvt++++ve++ +++ + +g++
  gi|386001597|ref|YP_005919896.1|  19 TAIVTGSTYGIGEAIAKILAGEGAISIVTGRSEDEGGRVVEEIRSGGGAAEYYSLDVTSEKRVEEVARAVYEGYGRI 95 
                                       79*************************************************************************** PP

                                       SEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  79 dvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       d+LvnNAGi   s+p++e++ +ewerv++vN+tg+fl+t++v+p+m+++ +G+Iv +sS+ g v++   +aY A+Ka
  gi|386001597|ref|YP_005919896.1|  96 DILVNNAGIgGPSKPTHEYTRREWERVFDVNVTGAFLCTKHVIPYMKRGGGGNIVYISSIYGIVGSQDNPAYHATKA 172
                                       *********9899**************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmake 189
                                       a + ++++ a  +a+++irvn+v+PG++ T+m++e
  gi|386001597|ref|YP_005919896.1| 173 ANRIMAKTGALIYAKDNIRVNSVHPGFIWTPMVEE 207
                                       ********************************987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   6.1e-18   3.6e-14       3     154 ..      20     172 ..      18     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 6.1e-18
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        ++tG + g+G ++a+ la +ga ++v ++Rs  +de   + ++e+++ g   e++++Dv++++ ve++ +++ +  
  gi|386001597|ref|YP_005919896.1|  20 AIVTGSTYGIGEAIAKILAGEGAISIV-TGRS--EDE-GGRVVEEIRSGGGAAEYYSLDVTSEKRVEEVARAVYEGY 92 
                                       69**********************986.8***..444.4559********************************999 PP

                                       S---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  80 ppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                       ++i   ++ Ag+    k+  e t  ++e+v+   v+Ga    + + +         +v++SSi g++gs+   +Y a
  gi|386001597|ref|YP_005919896.1|  93 GRIDILVNNAGIGGpSKPTHEYTRREWERVFDVNVTGAFLCTKHVIPymkrGGGGNIVYISSIYGIVGSQDNPAYHA 169
                                       ************9867899******************8766554433343388899*******************98 PP

                                       HHH CS
                                KR 152 aNa 154
                                       + a
  gi|386001597|ref|YP_005919896.1| 170 TKA 172
                                       755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 2030.46
//
Query:       gi|386001598|ref|YP_005919897.1|  [L=330]
Description: hypothetical protein Mhar_0903 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.057   13.7   0.0       0.14   12.5   0.0    1.6  1  B5              tRNA synthetase B5 domain
      0.061   12.5   0.1      0.096   11.8   0.1    1.2  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
       0.11   12.8   0.0       0.22   11.8   0.0    1.6  1  AAA_22          AAA domain


Domain annotation for each model (and alignments):
>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05      0.14       3      54 ..     273     323 ..     272     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                                       EEHHHHHHHHT.S---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   3 lrvekinkllG.idlseeeiikiLkrlgceriekdkdlllVtvPswRsDlere 54 
                                       l++++++++lG +dls+e ++ iL++ g+   + d++ ++ ++ + + D+e+e
  gi|386001598|ref|YP_005919897.1| 273 LELDELSEVLGpVDLSAEMMAAILEEKGLV--SIDGEAVTLKPEALKIDIEHE 323
                                       78999******77****************6..8******************98 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.6e-05     0.096     239     271 ..      91     121 ..      90     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHH--SEEEESSTTTTHHHHHH CS
                    DNA_pol_B_exo1 239 kelLqaflefikqydPdvitgYNidnFDlpYil 271
                                       ++l+++fl+f+ +++  +it++N  +F ++Y++
  gi|386001598|ref|YP_005919897.1|  91 FDLMNRFLSFVTSEERLFITTWN--SFSWRYLE 121
                                       589********************..******98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05      0.22      91     116 ..      69     101 ..      17     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                            AAA_22  91 v..ielliiDEaqhlr.s....eealeeLrsll 116
                                       +  +++l++DEa++l+ +     ++++ + s++
  gi|386001598|ref|YP_005919897.1|  69 RapQRILVVDEAHRLSlRriggFDLMNRFLSFV 101
                                       23358**********552566788888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2436.13
//
Query:       gi|386001599|ref|YP_005919898.1|  [L=305]
Description: hypothetical protein Mhar_0904 [Methanosaeta harundinacea 6Ac]
Scores for complete 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  126.1   0.0    1.3e-36  126.1   0.0    1.6  2  MS_channel     Mechanosensitive ion channel
     0.0019   18.1   0.8     0.0019   18.1   0.8    1.9  3  PhageMin_Tail  Phage-related minor tail protein
  ------ inclusion threshold ------
       0.26   11.3   2.0        1.8    8.6   0.4    2.8  3  TM_helix       Conserved TM helix


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.0      0.69   4.1e+03      15      46 ..      36      65 ..      32      70 .. 0.60
   2 !  126.1   0.0   2.2e-40   1.3e-36       7     205 ..      93     288 ..      89     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.69
                                      HHHHTTT--SCCHHHHHHHHHHHHHHHHCHHH CS
                        MS_channel 15 ivlsllgvnvsallavlGalglalglalkdli 46
                                       +l+ +g++ s+++ v  +l l+l++++  ++
  gi|386001599|ref|YP_005919898.1| 36 SALQAFGIDSSTIVHV--ILVLVLAYVATRIV 65
                                      5677777776666654..45555555555555 PP

  == domain 2  score: 126.1 bits;  conditional E-value: 2.2e-40
                                       HHHHHHHHHHH.HTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SS CS
                        MS_channel   7 liivvgilivl.sllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglr 82 
                                        i+ ++++ +l s++  +++ lla  G++g+a+g++lkdl++++v+Gi+++++kp++iGD v++ ++ G+V+diglr
  gi|386001599|ref|YP_005919898.1|  93 AIYGFAVYHILgSVFQLSTNQLLAFSGLIGAAVGFGLKDLVAEVVGGIVIVLDKPYQIGDKVRVDGHYGEVTDIGLR 169
                                       555566665551566777*********************************************************** PP

                                       EEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB.-TTS-EEE CS
                        MS_channel  83 ttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpev.lkdkellv 158
                                       +t++ ++d +++++ n+ +++++ +N + +s +++++++  ++ ssd   +++++++l++a+  +++v +++k +  
  gi|386001599|ref|YP_005919898.1| 170 ATRLVSPDDSLIVVSNQRMISQALANANAGSLEMQVVIDLFIDSSSD---ASRAMKILRDAAVTSRYVyISSKRPVT 243
                                       ***********************************************...**********99888876367999999 PP

                                       EEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT-- CS
                        MS_channel 159 vldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegie 205
                                       +l++    +  ++ rv+v++  ++  ++++s++++r ++++ e+gie
  gi|386001599|ref|YP_005919898.1| 244 ILLKDRPFYRRVRARVYVND--LRYEFKFESDVTKRAWDAFLEAGIE 288
                                       ********************..9**********************97 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.8   3.1e-07    0.0019      32      79 ..       4      52 ..       2      62 .. 0.87
   2 ?   -3.6   0.0       1.4   8.2e+03      33      56 ..     112     135 ..     108     166 .. 0.62
   3 ?   -2.0   0.1      0.46   2.7e+03     108     128 ..     194     214 ..     179     230 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-07
                     PhageMin_Tail 32 teeilnll.egaaklataggaddleeaaeilstalnafglsaadaeeaa 79
                                      +ee+ +++ e++ +l++ + ++ ++ea+e++s+al+afg++++ + ++ 
  gi|386001599|ref|YP_005919898.1|  4 GEEMAAVAqESSSNLSASSPSEGVGEASEAISSALQAFGIDSSTIVHVI 52
                                      589999999***********888******************76777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                     PhageMin_Tail  33 eeilnllegaaklataggadd.lee 56 
                                       +++l++  g   +a+ +g  d ++e
  gi|386001599|ref|YP_005919898.1| 112 NQLLAF-SGLIGAAVGFGLKDlVAE 135
                                       555555.555555666664445333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.46
                     PhageMin_Tail 108 kaaGlsfeetaaalallaaag 128
                                       ++a+    e+  ++ l++++ 
  gi|386001599|ref|YP_005919898.1| 194 ANANAGSLEMQVVIDLFIDSS 214
                                       333333333333333333322 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.33   1.9e+03      35      49 ..      31      45 ..      30      46 .. 0.85
   2 ?    8.6   0.4   0.00029       1.8      17      44 ..      48      75 ..      47      78 .. 0.87
   3 ?   -0.4   0.1      0.19   1.2e+03       8      21 ..     112     125 ..     106     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.33
                                      HHHHHHHHHHHTS-H CS
                          TM_helix 35 srlvtkllaktgidd 49
                                      s +++  l+++gid 
  gi|386001599|ref|YP_005919898.1| 31 SEAISSALQAFGIDS 45
                                      6778999******95 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00029
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix 17 LvgAilILlvGwiiAkfvsrlvtkllak 44
                                      +v  il+L+++++  ++v+ l+t+  ++
  gi|386001599|ref|YP_005919898.1| 48 IVHVILVLVLAYVATRIVAFLLTRFSER 75
                                      6678*******************98776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.19
                                       HHHHTTHSHHHHHH CS
                          TM_helix   8 nellsflPnLvgAi 21 
                                       n+ll+f + + +A+
  gi|386001599|ref|YP_005919898.1| 112 NQLLAFSGLIGAAV 125
                                       89999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2219.86
//
Query:       gi|386001600|ref|YP_005919899.1|  [L=327]
Description: hypothetical protein Mhar_0905 [Methanosaeta harundinacea 6Ac]
Scores for 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-29  101.7   0.9    1.1e-28   99.8   0.2    2.0  2  DUF4268   Domain of unknown function (DUF4268)
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.35   10.9   0.0    1.8  2  NRho      Rhomboid N-terminal domain


Domain annotation for each model (and alignments):
>> DUF4268  Domain of unknown function (DUF4268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.073   6.6e+02      57      88 ..     104     135 ..      92     168 .. 0.57
   2 !   99.8   0.2   1.2e-32   1.1e-28       1     139 [.     173     306 ..     173     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.073
                           DUF4268  57 IskkdeeenkeifekLkeqkeeieeelgeele 88 
                                       I    ++e k++ ++L ++ +e  + +g++le
  gi|386001600|ref|YP_005919899.1| 104 IASDFTDEHKKALDWLNDHTSEELSFYGVKLE 135
                                       54444455555555555555554444555554 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 1.2e-32
                           DUF4268   1 lrleFWtafleylkekekefsnrkpsprhWlnystgisgvslklvas..kkkarvelyIskkdeeenkeifekLkeq 75 
                                       l+leFWt+f+++l + ++  s ++p+p+ W+++s g sg++l+ va+  ++k+ v +yIs+        +  +L+e 
  gi|386001600|ref|YP_005919899.1| 173 LQLEFWTKFRDRLMKCKEIPSVQTPRPQYWYDVSLGKSGINLSNVANtyDNKIGVRVYISN---RIADIVLPQLMEI 246
                                       69*************8899999*************************************66...9************ PP

                           DUF4268  76 keeieeelgeeleWerleekkasrisriyvlkedvdikdkedwpeiiswliekmeklekafkky 139
                                       +++ieee+ge+l W+ ++e++++ i  +     d+++ +ke+w+e+ +wl+e+ +k++ +f+ +
  gi|386001600|ref|YP_005919899.1| 247 RQKIEEEIGETLLWDPHPENRDKVIGLYR----DANLAQKENWDEYLDWLTETTIKFRVIFSRV 306
                                       *************************7666....899************************9876 PP

>> NRho  Rhomboid N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.5   1.3e+04      22      45 ..       8      31 ..       7      34 .. 0.73
   2 ?   10.9   0.0     4e-05      0.35      25      57 ..     244     276 ..     239     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.5
                                      HHTTT--SEEEEETTEEEEE---S CS
                              NRho 22 LqrlkVphRvsEeegeQvLwvpde 45
                                      L+ l+V ++ + e +e   w+++e
  gi|386001600|ref|YP_005919899.1|  8 LKLLNVRFKWTNEATEFTPWLAEE 31
                                      566788888888888877787765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4e-05
                                       TT--SEEEEETTEEEEE---SSHHHHHHHHHTT CS
                              NRho  25 lkVphRvsEeegeQvLwvpderlaeqvreLyer 57 
                                       +++  ++ Ee ge +Lw p+++ +++v +Ly++
  gi|386001600|ref|YP_005919899.1| 244 MEIRQKIEEEIGETLLWDPHPENRDKVIGLYRD 276
                                       5788899************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2392.01
//
Query:       gi|386001601|ref|YP_005919900.1|  [L=219]
Description: HAD-superfamily hydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-13   49.5   0.0    1.1e-12   48.5   0.0    1.5  1  HAD_2           Haloacid dehalogenase-like hydrolase
    7.1e-12   46.1   0.0    2.5e-10   41.0   0.0    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    5.4e-05   23.7   0.4    9.5e-05   22.9   0.4    1.5  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.025   13.5   0.1       0.91    8.3   0.0    2.1  2  5_nucleotid     5' nucleotidase family
      0.047   13.4   0.0        6.1    6.5   0.0    2.3  2  Hydrolase_3     haloacid dehalogenase-like hydrolase
      0.048   13.7   0.0       0.13   12.3   0.0    1.7  1  T2SSG           Type II secretion system (T2SS), protein G
       0.14   12.2   0.0       0.42   10.7   0.0    1.8  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   4.1e-16   1.1e-12       3     175 ..      15     191 ..      13     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.1e-16
                             HAD_2   3 FDlDgTlldt...eeliiqafnelleey...glselseeelrkliglslrellrklgeseeeee..kieellrkyne 71 
                                       FD+DgTl+ +   e ++++ + +l+++    g++e  +  +++++   +r+l ++  +        +i+   +  n 
  gi|386001601|ref|YP_005919900.1|  15 FDMDGTLVTSryvERVWLEGVPTLYAQRhgiGMEEARKLVYDEYMSVGTRDLRWYDLSHWLGRFdlDIPHA-DLLNM 90 
                                       9*******762223556666666666557777778888889999999999998888886554444444444.44444 PP

                             HAD_2  72 ekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk.KPdpeviekalek 147
                                         +   v++y++ +e+L  L ++++ l +++++ +e ve +l+ l   ++F  i++ + +++k K  pe+++ ++++
  gi|386001601|ref|YP_005919900.1|  91 YRQ--DVELYPETEEVLALL-SEDFDLVVASNGATEFVEFELDGLR--HHFREILSVTSTFGKvKDYPETFLDLCRH 162
                                       444..6**************.99***************99888665..9999999877666555************* PP

                             HAD_2 148 lklkkeeviyvGDsp.tDieaakkagikv 175
                                       l++k+eevi +GD+  +D e  k+ag+ +
  gi|386001601|ref|YP_005919900.1| 163 LGAKPEEVIHIGDHRyFDYEVPKEAGLAA 191
                                       **************************876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   9.7e-14   2.5e-10       1     210 []      10     188 ..      10     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 9.7e-14
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHH.HHHHHHH....HHHHHHHHHETTTEHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkal.vaaakar....sgaltgfatfigrgayaig 72 
                                       ik v fD+dGTL+t++  ve+v+ +                    + + +a+ +    ++a + +       +y+  
  gi|386001601|ref|YP_005919900.1|  10 IKIVSFDMDGTLVTSR-YVERVWLEG-------------------VpTLYAQRHgigmEEARKLVYD-----EYMSV 61 
                                       799**********888.9********...................3233333332233222222222.....33333 PP

                                       HHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  73 kpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae 149
                                         + l++        +  + + + + +      ++l ++    +  ++pe++e++a L +  +++v+++++  e++e
  gi|386001601|ref|YP_005919900.1|  62 GTRDLRWY-------DLSHWLGRFDLDIPHA--DLLNMYRQDVE--LYPETEEVLALLSED-FDLVVASNGATEFVE 126
                                       33333333.......2336666666666666..88899998888..************966.9************** PP

                                       HHHHHTTGGGE.SEEEEHHCESSTTT..SHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 150 raanqlGddyf.daviasdietvakp..spegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                         ++ l  ++f ++     ++t++k+   pe ++ ++r L++kpeev+++GD    D +  ++Ag
  gi|386001601|ref|YP_005919900.1| 127 FELDGLR-HHFrEILS--VTSTFGKVkdYPETFLDLCRHLGAKPEEVIHIGDHRYfDYEVPKEAG 188
                                       5555555.56633333..34446666559***********************9887877777776 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.4   3.7e-08   9.5e-05       3     128 ..      15     140 ..      13     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.7e-08
                               HAD   3 fDfDgTLldgdslelllrfllrrgaprlwralrek.lllalfrellrldraglaellea....llagls.eelaael 73 
                                       fD+DgTL+++     +++++  +g p l++  +    ++a+   + +++  g++ l ++     l++++ +  +a+l
  gi|386001601|ref|YP_005919900.1|  15 FDMDGTLVTS----RYVERVWLEGVPTLYAQRHGIgMEEARKLVYDEYMSVGTRDLRWYdlshWLGRFDlDIPHADL 87 
                                       9*********....55553333455555555555543333333333333334444444455559999999999**** PP

                               HAD  74 erfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg..adevl 128
                                         ++++ ++   l+p+  e+la  +++ + +vv S+g  ++ve  l+ l   + e+l
  gi|386001601|ref|YP_005919900.1|  88 LNMYRQDVE---LYPETEEVLA-LLSEDFDLVVASNGATEFVEFELDGLRhhFREIL 140
                                       ****66665...55********.77*****************988876554444444 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        28      10      25 ..       8      23 ..       4      59 .. 0.87
   2 ?    8.3   0.0   0.00036      0.91     290     319 ..     156     185 ..     108     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                                      TT--EEEE-TBTTTBE CS
                       5_nucleotid 10 kkIkvvGFDmDYTLaq 25
                                      k Ik+v FDmD TL++
  gi|386001601|ref|YP_005919900.1|  8 KMIKIVSFDMDGTLVT 23
                                      679***********95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00036
                                       HHHHHHHTT--GGGEEEEESS--S-HHHHH CS
                       5_nucleotid 290 lkelekllgvkgkevLYvGDhiygDilksk 319
                                       + +l++ lg+k +ev+ +GDh y D   +k
  gi|386001601|ref|YP_005919900.1| 156 FLDLCRHLGAKPEEVIHIGDHRYFDYEVPK 185
                                       557999*****************9976665 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.01        26       2      12 ..      14      24 ..      13      27 .. 0.86
   2 ?    6.5   0.0    0.0024       6.1     194     212 ..     158     176 ..     154     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.01
                                      EEEIIIIIS-T CS
                       Hydrolase_3  2 alDlDGTLlns 12
                                       +D+DGTL++s
  gi|386001601|ref|YP_005919900.1| 14 SFDMDGTLVTS 24
                                      69******987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0024
                                       HHHHHCT--GGGEEEEESS CS
                       Hydrolase_3 194 klakelnisleeviafGDg 212
                                       +l+ +l+ ++eevi++GD 
  gi|386001601|ref|YP_005919900.1| 158 DLCRHLGAKPEEVIHIGDH 176
                                       79****************6 PP

>> T2SSG  Type II secretion system (T2SS), protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.13      24      48 ..      87     111 ..      82     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHTSS---TTHHHHHHHS- CS
                             T2SSG  24 aldlYkldvgryPtteqgLeaLvek 48 
                                        l++Y+ dv+ yP+te+ L+ L e 
  gi|386001601|ref|YP_005919900.1|  87 LLNMYRQDVELYPETEEVLALLSED 111
                                       599****************999875 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.42       6      45 ..     152     191 ..     149     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                       SSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EE CS
                    Hydrolase_like   6 epemydfalevlgsdpeevlmiGDrlatDiagAnnaGwks 45 
                                        pe++    ++lg++peev+ iGD  + D +  ++aG+  
  gi|386001601|ref|YP_005919900.1| 152 YPETFLDLCRHLGAKPEEVIHIGDHRYFDYEVPKEAGLAA 191
                                       6899999******************999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1564.07
//
Query:       gi|386001602|ref|YP_005919901.1|  [L=251]
Description: Zinc/iron ZIP family permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-26   92.2  20.9    1.2e-21   77.3   7.8    2.0  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
        5.7    7.0   8.1         18    5.4   0.9    2.7  2  TOM13     Outer membrane protein TOM13


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   4.2   5.8e-09   5.2e-05       6      99 ..      11      91 ..       6     100 .. 0.87
   2 !   77.3   7.8   1.4e-25   1.2e-21     175     331 ..      97     245 ..      89     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.8e-09
                               Zip  6 laiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvll 84
                                      ++ ++  +++ +g+l++++vp    +++ + ls+ l fa Gv++  af++L+  a ea++          + a l++l 
  gi|386001602|ref|YP_005919901.1| 11 ILTFLAGLATGVGGLIAYFVP----RPDMRYLSVSLGFATGVMIFVAFVDLFCSAKEAIGM---------VRADLFFLA 76
                                      445555667778889999999....578899*****************************9.........88******* PP

                               Zip 85 Gflllllveklltmi 99
                                      G+l++++++k++ ++
  gi|386001602|ref|YP_005919901.1| 77 GMLVVYFLDKVVPHA 91
                                      ***********9875 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 1.4e-25
                               Zip 175 dkeklaslkvraiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavlln 249
                                        ++++ +l   +i+++lg+ +H++++GLA++  + ++   gi++ iA+ +H++pe+++  ++L+ a  +r+k   ++
  gi|386001602|ref|YP_005919901.1|  97 ADPHCDRLYRGGIMMTLGIAIHNLPEGLAVAlvALADLRLGIPIAIAIAIHNIPEGVACSVPLYCATGDRRKSCFYS 173
                                       456777777789********************999****************************************** PP

                               Zip 250 llfaltaplGiliGilvrs.isessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllG 325
                                       +l +++ plG++i+ilv        ga ++s+   a+ aG+++ + + el+p  ++n+      + ++l +lgl++G
  gi|386001602|ref|YP_005919901.1| 174 FLAGMAEPLGAIIAILVLLpF--LNGAVLASS--IAFVAGVMVFICFDELIP--IANSY-----GDEHLTNLGLIAG 239
                                       ****************55442..334444444..59****************..66655.....689********** PP

                               Zip 326 falmll 331
                                       + +m++
  gi|386001602|ref|YP_005919901.1| 240 ISVMMI 245
                                       ****86 PP

>> TOM13  Outer membrane protein TOM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.6    0.0025        22      48      66 ..      10      28 ..       5      31 .. 0.92
   2 ?    5.4   0.9     0.002        18      45      58 ..     187     200 ..     181     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0025
                             TOM13 48 lvLPFinGlmLGfGellAh 66
                                      l+L F+ Gl  G G l+A+
  gi|386001602|ref|YP_005919901.1| 10 LILTFLAGLATGVGGLIAY 28
                                      89***************96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.002
                             TOM13  45 ainlvLPFinGlmL 58 
                                       ai ++LPF+nG +L
  gi|386001602|ref|YP_005919901.1| 187 AILVLLPFLNGAVL 200
                                       8899*******877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1860.91
//
Query:       gi|386001603|ref|YP_005919902.1|  [L=760]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-96  318.6   0.0    3.8e-48  163.3   0.0    2.4  2  AAA              ATPase family associated with various cellul
    1.3e-29  101.7   1.3    1.5e-15   56.7   0.3    3.1  2  AAA_lid_3        AAA+ lid domain
    4.7e-22   78.0   0.3      3e-21   75.4   0.5    2.3  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      2e-15   56.9   0.0    1.8e-06   27.8   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.7e-15   57.2   0.2    1.8e-06   28.5   0.0    3.6  2  AAA_16           AAA ATPase domain
    3.8e-13   49.0   0.1      1e-12   47.6   0.1    1.7  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.6e-12   47.6   1.4    0.00011   22.3   0.0    3.9  2  AAA_5            AAA domain (dynein-related subfamily)
    4.7e-12   46.3   0.6    0.00039   20.7   0.1    4.1  3  AAA_22           AAA domain
    1.3e-11   44.9   0.0    5.2e-05   23.4   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.5e-11   44.1   0.0    0.00015   21.1   0.0    2.5  2  TIP49            TIP49 P-loop domain
    1.5e-09   38.2   0.0    0.00067   19.8   0.0    2.7  2  AAA_33           AAA domain
    3.5e-09   36.8   0.0    0.00021   21.3   0.0    2.4  2  AAA_14           AAA domain
    7.3e-08   32.3   0.0      0.015   15.1   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    1.3e-07   31.5   0.2      0.051   13.3   0.1    3.7  2  Sigma54_activat  Sigma-54 interaction domain
    1.6e-07   31.7   0.0      0.035   14.5   0.0    2.7  2  RNA_helicase     RNA helicase
    1.6e-07   30.9   0.6      0.016   14.6   0.1    2.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.6e-07   31.2   0.0      0.059   13.9   0.0    3.1  2  AAA_18           AAA domain
    3.1e-07   30.8   0.1      0.038   14.2   0.0    2.8  2  AAA_28           AAA domain
    4.6e-07   29.9   0.0      0.073   13.0   0.0    3.7  4  NACHT            NACHT domain
    6.3e-07   29.2   2.1       0.43   10.1   0.2    4.0  3  AAA_25           AAA domain
    2.2e-06   28.3   0.0      0.058   13.9   0.0    2.4  2  ABC_tran         ABC transporter
    2.3e-06   27.3   0.0      0.041   13.4   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    3.1e-06   27.0   0.0      0.018   14.7   0.0    2.5  2  AAA_24           AAA domain
    7.1e-06   26.0   0.0       0.13   12.3   0.0    3.0  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.6e-05   24.2   0.0       0.16   11.1   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    1.8e-05   24.2   0.0       0.31   10.4   0.0    3.1  3  ATPase           KaiC
    3.9e-05   23.0   0.0       0.15   11.2   0.0    2.7  2  NB-ARC           NB-ARC domain
    4.1e-05   23.5   0.0       0.19   11.5   0.0    2.4  2  AAA_11           AAA domain
    9.4e-05   22.3   0.0       0.28   11.1   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00011   21.8   0.3       0.34   10.3   0.1    2.4  2  PhoH             PhoH-like protein
    0.00013   21.2   0.0       0.36    9.9   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00013   21.3   0.1       0.29   10.4   0.0    2.5  2  Zeta_toxin       Zeta toxin
    0.00018   21.3   1.1       0.34   10.6   0.0    3.0  2  AAA_30           AAA domain
    0.00019   20.8   0.0       0.36   10.0   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00023   21.5   0.1        2.1    8.6   0.0    3.4  3  AAA_19           AAA domain
    0.00038   20.6   0.0        1.1    9.4   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00054   19.7   0.3        6.2    6.5   0.0    4.4  4  Guanylate_kin    Guanylate kinase
    0.00064   19.7   0.0        2.9    7.8   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0024   17.7   0.0          2    8.2   0.0    2.4  2  Bac_DnaA         Bacterial dnaA  protein
     0.0027   17.4   0.0       0.95    9.1   0.0    2.7  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0028   16.6   0.0       0.45    9.4   0.0    2.3  2  AFG1_ATPase      AFG1-like ATPase
     0.0034   17.1   0.2        1.8    8.2   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
     0.0037   17.7   0.0        1.7    9.1   0.0    2.6  2  AAA_17           AAA domain
     0.0049   16.3   0.0        1.5    8.2   0.0    2.9  2  TniB             Bacterial TniB protein
      0.008   15.9   0.0        3.5    7.3   0.0    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
       0.01   15.8   0.0        5.1    7.0   0.0    2.9  2  NTPase_1         NTPase
      0.031   14.4   0.1         11    6.1   0.0    2.8  2  SKI              Shikimate kinase
      0.038   14.0   0.0        5.4    7.0   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
      0.045   13.5   0.0         19    5.1   0.0    2.8  2  AAA_29           P-loop containing region of AAA domain
      0.047   13.8   0.0        7.9    6.6   0.0    2.9  3  Torsin           Torsin
      0.051   13.6   0.0        1.4    9.0   0.0    2.5  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.052   12.6   0.0        9.3    5.3   0.0    3.1  4  MCM              MCM P-loop domain
       0.08   12.3   0.2         37    3.6   0.0    3.2  3  IPT              Isopentenyl transferase
       0.09   11.8   0.0         14    4.7   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
       0.12   12.6   0.0         22    5.3   0.0    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.13   12.0   0.0         18    5.0   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.15   12.3   0.2         10    6.3   0.0    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.21   11.2   0.3         17    4.9   0.0    2.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   0.0   1.2e-50   3.8e-48       1     131 [.     245     374 ..     245     375 .. 0.97
   2 !  153.1   0.0   1.7e-47   5.3e-45       1     131 [.     518     649 ..     518     650 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 1.2e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKT+lakava+e++++f +i+g+e++sky gesek+ire+f+e +++a p i+f+DE+d++a++r++ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFASINGPEIVSKYYGESEKRIREVFEESERNA-PAIIFLDELDSIAPKREEV 320
                                       79**************************************************99999.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e e+r+v+qLl+ +dg+k++ ++vivigatnrpd +dpal+r gRfdr+ie++
  gi|386001603|ref|YP_005919902.1| 321 AGEMERRMVAQLLSLMDGQKER-ANVIVIGATNRPDAVDPALRRpGRFDREIELG 374
                                       *********************7.66**************************9975 PP

  == domain 2  score: 153.1 bits;  conditional E-value: 1.7e-47
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vllyGppGtGKTllakava+e++++fl+++gse+lsk+ gese++i+e+f++a++ a p i+f+DE+d+la+ r   
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNANFLTTKGSEILSKWYGESERHIAEIFRKARQVA-PAIVFLDELDSLAPVRggG 593
                                       79******************************************************9.****************987 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++e  ++er+vnqLl+e+dg+++ ++ v+vi+atnrpd +dpal+r gRfd+ i ++
  gi|386001603|ref|YP_005919902.1| 594 TGEPHVTERIVNQLLSEIDGMEELRG-VVVIAATNRPDIIDPALIRpGRFDELIMVP 649
                                       789********************866.*************************99876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.5e-13   4.7e-11       1      39 [.     397     435 ..     397     441 .. 0.93
   2 !   56.7   0.3   4.9e-18   1.5e-15       1      43 [.     672     716 ..     672     718 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.5e-13
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeit 39 
                                       dvdl+e A +T G++GAD+aa  reAa++Alrr+++ i+
  gi|386001603|ref|YP_005919902.1| 397 DVDLEEFATLTYGFVGADIAAFSREAAMNALRRVLPRID 435
                                       9********************************998776 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 4.9e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedf 43 
                                       dvdl++L+erT+ y+GAD+a++cr+A++lAlr+++   e+ +++f
  gi|386001603|ref|YP_005919902.1| 672 DVDLDRLVERTDQYTGADIASICRKAGRLALREDMNavEVRKSHF 716
                                       9***********************************655889998 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.5   9.6e-24     3e-21       1      84 [.       8      91 ..       8      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 9.6e-24
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      rL++ ea q+dvg+givri+   m++lg+   d vei+g++ T a+++ a+p de+ ++ r+dg++R+n+g++iG+ V+
  gi|386001603|ref|YP_005919902.1|  8 RLKIIEADQRDVGKGIVRISGRQMADLGVADYDLVEIRGTKATSALAVKAYPTDEDMDVARVDGLIRSNVGAGIGQYVE 86
                                      69999************************************************************************** PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      ++kae
  gi|386001603|ref|YP_005919902.1| 87 ISKAE 91
                                      ***97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   5.8e-09   1.8e-06      35     115 ..     244     331 ..     234     371 .. 0.71
   2 !   26.3   0.0   1.7e-08   5.2e-06      32      97 ..     514     587 ..     507     591 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.8e-09
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                        vll+GpPG Gkt lak +a+e  +++ +  gP +      e ++ +  ++ + e++   ++f+de+  ++++ eev
  gi|386001603|ref|YP_005919902.1| 244 GVLLHGPPGTGKTMLAKAVANESSAHFASINGPEIvskyygESEKRIREVFEESERNapAIIFLDELDSIAPKREEV 320
                                       59*******************************9844333334556777776665542269************9998 PP

                            RuvB_N 104 lysamedfrldi 115
                                           me  ++  
  gi|386001603|ref|YP_005919902.1| 321 A-GEMERRMVAQ 331
                                       5.3456555443 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.7e-08
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrls 97 
                                       a   vllyGpPG Gkt lak +a+e ++++ +t g  +      e ++ +a ++ + ++    ++f+de+  l+
  gi|386001603|ref|YP_005919902.1| 514 APKGVLLYGPPGTGKTLLAKAVANESNANFLTTKGSEIlskwygESERHIAEIFRKARQVapAIVFLDELDSLA 587
                                       56679****************************99877444444456788888887765422688999887775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   5.7e-09   1.8e-06      15     140 ..     233     347 ..     231     356 .. 0.69
   2 !   23.8   0.1   1.6e-07   4.8e-05      16      76 ..     507     559 ..     505     623 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.7e-09
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeae 90 
                                       ++er+  + p+ vll+G++G+GK+ l+++++++ +   ++f++ +  +      y+          + +r++ +e+e
  gi|386001603|ref|YP_005919902.1| 233 LFERLGIDPPRGVLLHGPPGTGKTMLAKAVANESS---AHFASINGPEI--VSKYYGeSE------KRIREVFEESE 298
                                       5677777778*********************8555...56888877777..223333233......44555555533 PP

                            AAA_16  91 s.aeleawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                         a +  + ++l++ +    e+ag+ ++r+ ++l +l++  ++++   v+v
  gi|386001603|ref|YP_005919902.1| 299 RnAPAIIFLDELDSIAPKREEVAGEMERRMVAQLLSLMDGQKERAN--VIV 347
                                       303444455555555558889999999******9999966665454..444 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.6e-07
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                       ++r+    p  vll+G++G+GK+ l+++++++ +++   fl++k  +      +s +    
  gi|386001603|ref|YP_005919902.1| 507 FRRLGIEAPKGVLLYGPPGTGKTLLAKAVANESNAN---FLTTKGSEI-----LSKWYGES 559
                                       5667777899********************988888...777777777.....22222222 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   3.4e-15     1e-12       8      62 ..     113     197 ..     107     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 3.4e-15
                                       H.HHHCCCTTEEE-TTEEE..................EECCT..............CCCEEEEEEEECCCCSCEEEC CS
                           CDC48_2   8 a.ylkrqFlgrpvtkGdlv..................vfefk..............gqeiklvVvstePkgpvgite 51 
                                       + +l+++Flgrpv+kGd++                  +   +              ++e+k +Vvst P+g+v+i e
  gi|386001603|ref|YP_005919902.1| 113 SeALRKVFLGRPVSKGDVIstttlrrppgdlatgkdtM---FdeifkrsdkgsafgLGEVKMRVVSTVPSGTVRIGE 186
                                       449****************7777777777766666663...044466777888899********************* PP

                                       TSCCEEESTTC CS
                           CDC48_2  52 tTeielgtkpv 62 
                                       +Te el  ++v
  gi|386001603|ref|YP_005919902.1| 187 ETELELLSRAV 197
                                       *****998776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.7   2.8e-06   0.00086       1     136 [.     244     363 ..     244     365 .. 0.77
   2 !   22.3   0.0   3.4e-07   0.00011       1      79 [.     517     588 ..     517     638 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK++la+ +a    + +  +++++      ++ ++   ++ +++   ++ ++ r  ++i++lDE++ 
  gi|386001603|ref|YP_005919902.1| 244 GVLLHGPPGTGKTMLAKAVANESSAHFASINGPE------IVSKYY--GESEKRIREVFEESERnAPAIIFLDELDS 312
                                       59******************99999999998887......555555..33344444444444445899********9 PP

                                       --...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  77 ae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                       +     ev++++ + +  + l+l++g+++   +n      + vi+++n++d     ++palr+
  gi|386001603|ref|YP_005919902.1| 313 IApkrEEVAGEMERRMVAQLLSLMDGQKER--AN------VIVIGATNRPD----AVDPALRR 363
                                       974345799999888888888888888887..44......99*******99....77888886 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.4e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a   n+++++  +++      ++ ++    g+ +++  ++ r+ar   ++i++lDE++
  gi|386001603|ref|YP_005919902.1| 517 GVLLYGPPGTGKTLLAKAVANESNANFLTTKGSE------ILSKWY---GESERHIAEIFRKARqvAPAIVFLDELD 584
                                       59**************************988876......666666...5666666888888888999999999999 PP

                                       G--H CS
                             AAA_5  76 raes 79 
                                        + +
  gi|386001603|ref|YP_005919902.1| 585 SLAP 588
                                       7665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.3e-06   0.00039       8      58 ..     245     295 ..     240     357 .. 0.66
   2 !   15.9   0.0   3.8e-05     0.012       8      31 ..     518     541 ..     513     569 .. 0.80
   3 ?   -0.0   0.0       3.1   9.7e+02      81     105 ..     562     590 ..     557     626 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllr 58 
                                       ++++G++GtGKT+l++ ++++  ++ +   ++pe+v +++  s++  +++++
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFASI-NGPEIVsKYYGESEKRIREVFE 295
                                       689******************86554444.4555554555555444444433 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                                       ++++G++GtGKT+l++ ++++ ++
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNA 541
                                       689****************99743 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 3.1
                            AAA_22  81 aleqalrarav..ielliiDEaqhlr..s 105
                                       ++++ +r+++   ++++ +DE + l   +
  gi|386001603|ref|YP_005919902.1| 562 HIAEIFRKARQvaPAIVFLDELDSLApvR 590
                                       556666666667789999*****996551 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.7e-07   5.2e-05       6     105 ..     245     338 ..     240     343 .. 0.85
   2 !   18.9   0.0     4e-06    0.0013       6     103 ..     518     611 ..     515     615 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.7e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    +++ ++  e+      + + ++++  ++   + e +   i++lDE+d i
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSA----HFASINGPEIVS----KYYGESEKRIREVFEESERNApaIIFLDELDSI 313
                                       6899*****************996....************....88888888888888888888888********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+   ++ r  V + LL +++g
  gi|386001603|ref|YP_005919902.1| 314 APKrEEVAGEMERRMVAQ-LLSLMDG 338
                                       **9666666666666655.6677776 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++ +   se+l     + + +++ + ++   +a +    iv+lDE+d  
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNA----NFLTTKGSEILS----KWYGESERHIAEIFRKARQVApaIVFLDELDSL 586
                                       5789******************96....************....99999999999999999999888********** PP

                                       ---..---------HHHHHHHHHHH CS
                             AAA_2  81 hpk..essgadvSregVqrdLLqil 103
                                       +p   + +g+    e +++ LL  +
  gi|386001603|ref|YP_005919902.1| 587 APVrgGGTGEPHVTERIVNQLLSEI 611
                                       *987644444445566666666555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.3e-07   0.00026      51      97 ..     243     287 ..     237     329 .. 0.87
   2 !   21.1   0.0   4.7e-07   0.00015      50     108 ..     515     572 ..     509     575 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       r+vLl Gp+gtGkt la a+++e +   +f++++g e+ s     +e
  gi|386001603|ref|YP_005919902.1| 243 RGVLLHGPPGTGKTMLAKAVANESS--AHFASINGPEIVSKYYGESE 287
                                       89********************966..89*********887554444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.7e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksig 108
                                        ++vLl Gp+gtGkt la a+++e +    f + +gse+ s     +e  + + +rk+ +
  gi|386001603|ref|YP_005919902.1| 515 PKGVLLYGPPGTGKTLLAKAVANESN--ANFLTTKGSEILSKWYGESErHIAEIFRKARQ 572
                                       599********************966..78************999988458899999865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.2e-06   0.00067       2      48 ..     245     293 ..     245     367 .. 0.80
   2 !   15.6   0.0   4.4e-05     0.013       2      79 ..     518     627 ..     518     684 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.2e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdy 48 
                                       vll+G+pG+GK+ la+ ++++    +  ++ +++ ++++g+ ++++++ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSahFASINGPEIVSKYYGESEKRIREV 293
                                       799****************999988999*****9999999888877743 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.4e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdt.........................lrrrlfgtdqqskt....... 46 
                                       vll G+pG+GK+ la+ ++++  a +l++                           +                    
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNANFLTTKGseilskwygeserhiaeifrkarqvA------------Paivflde 582
                                       7899*****************999888876555444444444444444333333330............03333333 PP

                            AAA_33  47 ............dytrvldrlyqilnelarkalsagrnvildatn 79 
                                                     ++v++r+ ++l   ++ + + ++ v++ atn
  gi|386001603|ref|YP_005919902.1| 583 ldslapvrgggtGEPHVTERIVNQLLSEIDGMEELRGVVVIAATN 627
                                       333333333333556666666666666666666666666666664 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   6.9e-07   0.00021       5     102 ..     245     352 ..     242     374 .. 0.82
   2 !   13.2   0.0   0.00022     0.069       4      76 ..     517     586 ..     514     649 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.9e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT+l+k +++e+     ++  in  +   k + ++ek +++++e+ +++   ++flDE   +     
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESS---AHFASINGPEIVSKYYGESEKRIREVFEESERNAPAIIFLDELDSIapkre 318
                                       7899***************9999...9******99998888777665555555543445999**********99999 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSns 102
                                              +++   l sl+d ++++ +viv G  +
  gi|386001603|ref|YP_005919902.1| 319 evagemeRRMVAQLLSLMDgQKERANVIVIGATN 352
                                       9999999889999999999544788999998765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00022
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev 76 
                                        +++ G+  +GKT l+k +++e+     ++l  +  +   k + ++e ++ e++++  ++    ++flDE   +
  gi|386001603|ref|YP_005919902.1| 517 GVLLYGPPGTGKTLLAKAVANESN---ANFLTTKGSEILSKWYGESErHIAEIFRKA-RQVAPAIVFLDELDSL 586
                                       57899***************9988...9******99999988887773455555554.4447899*****8765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.2e-05     0.025      48      72 ..     243     267 ..     231     278 .. 0.85
   2 !   15.1   0.0   4.7e-05     0.015      44      71 ..     512     539 ..     510     584 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveav 72 
                                        +++l Gp+G+GK+ la a++ e  
  gi|386001603|ref|YP_005919902.1| 243 RGVLLHGPPGTGKTMLAKAVANESS 267
                                       6799****************98865 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.7e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       ie+ ++++l Gp+G+GK+ la a++ e 
  gi|386001603|ref|YP_005919902.1| 512 IEAPKGVLLYGPPGTGKTLLAKAVANES 539
                                       5677899****************99875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00017     0.051      24      60 ..     244     277 ..     232     358 .. 0.74
   2 !   11.7   0.0   0.00051      0.16      21      48 ..     514     541 ..     506     551 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTT CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaa 60 
                                        vl++G  GtGK++la+a+ ++s+   ++f ++n  +
  gi|386001603|ref|YP_005919902.1| 244 GVLLHGPPGTGKTMLAKAVANESS---AHFASINGPE 277
                                       69*****************98876...5666666554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00051
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskr 48 
                                        +  vl+ G  GtGK+lla+a+ ++s+ 
  gi|386001603|ref|YP_005919902.1| 514 APKGVLLYGPPGTGKTLLAKAVANESNA 541
                                       56679*****************998874 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00013     0.042       1      36 [.     245     280 ..     245     298 .. 0.85
   2 !   14.5   0.0   0.00011     0.035       1      36 [.     518     553 ..     518     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00013
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++l+Gp+g+GK++lak +a++ + ++ +++ ++++s
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFASINGPEIVS 280
                                       689******************999997777666655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++lyGp+g+GK++lak +a++   ++ ++k +++ s
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNANFLTTKGSEILS 553
                                       689**************9999888887776666654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     5e-05     0.016      25      42 ..     245     262 ..     242     268 .. 0.91
   2 !   13.5   0.0   0.00011     0.035      25      43 ..     518     536 ..     510     561 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll GppG+GKtmlak++
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAV 262
                                       79*************987 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00011
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVA 536
                                       89*************9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0    0.0002     0.062       1      34 [.     245     281 ..     245     350 .. 0.68
   2 !   13.9   0.0   0.00019     0.059       1      25 [.     518     548 ..     518     581 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0002
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvake 34 
                                       +ll G+pG+GKt lak+++++  +    ++n  +++++
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANES-SahfaSINGPEIVSK 281
                                       7899**************8874.224464444444433 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00019
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.....g 25 
                                       +ll G+pG+GKt lak+++++  ++     g
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESnANflttkG 548
                                       799***************8774222454441 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00019     0.059       2      45 ..     245     293 ..     244     337 .. 0.72
   2 !   14.2   0.0   0.00012     0.038       2      53 ..     518     571 ..     517     582 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00019
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgeda 45 
                                       + + G+++tGKT l++a a++    +  +  pE++ +++ e  ++ ++ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANEssaHFASIngPEIVSKYYGESEKRIREV 293
                                       6799***************765544444457777777776655444444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00012
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv.edll 53 
                                       + + G+++tGKT l++a a++ + + ++  + eil++ + + e+++++  +++ 
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANEsNANFLTTKGSEILSKWYGESERHIAEIfRKAR 571
                                       6799***************88789999999999999999888888887755554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00023     0.073       3      23 ..     245     265 ..     243     270 .. 0.89
   2 ?    3.4   0.0      0.21        64      59     134 ..     280     359 ..     274     385 .. 0.69
   3 !    8.8   0.0    0.0047       1.4       3      23 ..     518     538 ..     516     548 .. 0.88
   4 ?   -1.9   0.0       8.9   2.8e+03      57     100 ..     551     595 ..     539     629 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00023
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G++G GKT+L++ +a +
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANE 265
                                       89**************99875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.21
                                       CCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT--EEEE..EEEC CS
                             NACHT  59 fsqlpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllpeaslll..tvrp 129
                                        + + e++++++ev+++  +++  + + lD lD ++ + ++    +e++ v +lL +l+ ++  + + +++  t rp
  gi|386001603|ref|YP_005919902.1| 280 SKYYGESEKRIREVFEESERNAPAIIF-LDELDSIAPKREEvageMERRMVAQLL-SLMDGQKERANVIVIgaTNRP 354
                                       566788999999988887666666655.8*******9888899977788888877.888876666666665336677 PP

                                       CCHHH CS
                             NACHT 130 ralrd 134
                                       +a+  
  gi|386001603|ref|YP_005919902.1| 355 DAVDP 359
                                       77644 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0047
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT L++ +a +
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANE 538
                                       799*************99976 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 8.9
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH... CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq..k 100
                                       +l + + e+++++ e++    +++  +   lD lD l+   g    
  gi|386001603|ref|YP_005919902.1| 551 ILSKWYGESERHIAEIFRKARQVAPAI-VFLDELDSLAPVRGGgtG 595
                                       566666677777777444444444444.446888888776655542 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0049       1.5      36      53 ..     245     262 ..     241     268 .. 0.87
   2 ?    6.9   0.0     0.014       4.3     130     177 ..     290     337 ..     281     353 .. 0.81
   3 !   10.1   0.2    0.0014      0.43      36      97 ..     518     577 ..     512     623 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0049
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt+la  +
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAV 262
                                       689***********9655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                            AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       ++++ ++ e+ + ++ + +D l+++ +  e+ + ++ +++v++l ++ +
  gi|386001603|ref|YP_005919902.1| 290 IREVFEESER-NAPAIIFLDELDSIAPKREEVAGEMeRRMVAQLLSLMD 337
                                       6677778788.66**********************99******998865 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0014
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       +ll+G+pgtGKt la  +a +     ++l    +e    +y   E   +e+ r++r+v  a+
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESN--ANFLTTKGSEILSKWYGESERHIAEIFRKARQVAPAI 577
                                       69**********99876654433..3444433346666666666666666666666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00019     0.058      10      75 ..     241     305 ..     236     353 .. 0.71
   2 !   11.8   0.0   0.00086      0.27       7      71 ..     511     574 ..     508     625 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00019
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpelt 75 
                                       + + v + G+ G+GK+ L+k++a++++    +i  +g ++ ++   +++k+i+ +++e ++  p + 
  gi|386001603|ref|YP_005919902.1| 241 PPRGVLLHGPPGTGKTMLAKAVANESSAHFASI--NGPEIVSKYYGESEKRIREVFEEsERNAPAII 305
                                       5566889*******************9988888..88888888899999999999999444445443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00086
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlf 71 
                                        +++ + v + G+ G+GK+ L+k++a++++     ++ +g ++ ++   +++++i+ ++ +  q+ 
  gi|386001603|ref|YP_005919902.1| 511 GIEAPKGVLLYGPPGTGKTLLAKAVANESNA--NFLTTKGSEILSKWYGESERHIAEIFRKaRQVA 574
                                       677778899******************9975..566667777777777777777777766644555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00068      0.21      34      60 ..     243     268 ..     233     320 .. 0.87
   2 !   13.4   0.0   0.00013     0.041      28      61 ..     510     542 ..     489     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00068
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldke 60 
                                       + vll Gp GtGKt+++k + ++ +  
  gi|386001603|ref|YP_005919902.1| 243 RGVLLHGPPGTGKTMLAKAVANESS-A 268
                                       679***************9988876.3 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00013
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkek 61 
                                       l +++ k vll+Gp GtGKt+++k + ++ +  +
  gi|386001603|ref|YP_005919902.1| 510 LGIEAPKGVLLYGPPGTGKTLLAKAVANESN-AN 542
                                       55778899****************9999887.44 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0017      0.54       5      22 ..     245     262 ..     242     351 .. 0.82
   2 !   14.7   0.0   5.9e-05     0.018       4      45 ..     517     559 ..     514     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0017
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+ Gp+g+GKT+lak  
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAV 262
                                       799************987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.9e-05
                            AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpd 45 
                                        +l+yGp+g+GKT lak    ++ + + t kG+  l  + +++
  gi|386001603|ref|YP_005919902.1| 517 GVLLYGPPGTGKTLLAKAVaNESNANFLTTKGSEILSKWYGES 559
                                       589**************99855555555556676666666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       9.5   2.9e+03      26      41 ..     141     156 ..     137     161 .. 0.86
   2 !   12.3   0.0   0.00041      0.13      20      59 ..     243     282 ..     213     292 .. 0.75
   3 !   10.0   0.0    0.0021      0.66      19      44 ..     515     540 ..     492     560 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9.5
                                       ESTTSSHHHHHHHHHH CS
                              TsaE  26 GdLGaGKTtlvrglak 41 
                                       GdL +GK t+  ++ k
  gi|386001603|ref|YP_005919902.1| 141 GDLATGKDTMFDEIFK 156
                                       9******999988876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00041
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                       + +lL+G+ G+GKT+l++++a++   +  +++ P   +v++Y
  gi|386001603|ref|YP_005919902.1| 243 RGVLLHGPPGTGKTMLAKAVANESSAHfaSINGP--EIVSKY 282
                                       349******************9987766677777..455555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0021
                                       TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                        + +lL+G+ G+GKT l++++a++ +
  gi|386001603|ref|YP_005919902.1| 515 PKGVLLYGPPGTGKTLLAKAVANESN 540
                                       4459*****************99865 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00053      0.16      54     151 ..     243     353 ..     235     363 .. 0.67
   2 !   10.6   0.0   0.00073      0.23      54      82 ..     516     544 ..     466     584 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDDL.sFeeeeee 124
                                       + vLL G  GtGK  l ka+ ne +++   +   e+  +   e +k ++++    er+   i+f+D L s   + ee
  gi|386001603|ref|YP_005919902.1| 243 RGVLLHGPPGTGKTMLAKAVANESSAHFasINGPEIVSKYYGESEKRIREVFeesERNAPAIIFLDELdSIAPKREE 319
                                       579********************998874455567766666555544444431224556689999998544433333 PP

                            DUF815 125 y.........ksLksvLeGsleakpenvliyaTsNr 151
                                                  +L s+++G+  ++ +nv++   +Nr
  gi|386001603|ref|YP_005919902.1| 320 VagemerrmvAQLLSLMDGQ--KERANVIVIGATNR 353
                                       33344444446677888885..45567777777777 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00073
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeegL 82 
                                       + vLL+G  GtGK  l ka+ ne +++ L
  gi|386001603|ref|YP_005919902.1| 516 KGVLLYGPPGTGKTLLAKAVANESNANFL 544
                                       679********************998876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0035       1.1      15      38 ..     238     261 ..     231     271 .. 0.82
   2 ?    0.9   0.0      0.76   2.3e+02     125     162 ..     310     348 ..     283     358 .. 0.82
   3 !   10.4   0.0   0.00099      0.31      15      38 ..     511     534 ..     488     543 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   r vl+ G pGtGKt++a+ 
  gi|386001603|ref|YP_005919902.1| 238 GIDPPRGVLLHGPPGTGKTMLAKA 261
                                       77777889*************975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.76
                            ATPase 125 iDsitglayeekeavaReilrqlvrvl.kklgvTailvs 162
                                       +Dsi++  +e   ++ R+ + ql++ +  +++  +++v 
  gi|386001603|ref|YP_005919902.1| 310 LDSIAPKREEVAGEMERRMVAQLLSLMdGQKERANVIVI 348
                                       6899999888899999***********766677777765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00099
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   + vl++G pGtGKt++a+ 
  gi|386001603|ref|YP_005919902.1| 511 GIEAPKGVLLYGPPGTGKTLLAKA 534
                                       7888889**************975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0005      0.15      23      45 ..     245     267 ..     232     290 .. 0.86
   2 !    8.7   0.0    0.0028      0.88      23      44 ..     518     539 ..     510     545 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l+G +G GKt lak + n+s+
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESS 267
                                       789****************9954 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt lak + n+s
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANES 539
                                       779***************9995 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00061      0.19      20      42 ..     245     267 ..     221     306 .. 0.77
   2 !    9.4   0.0    0.0027      0.85      17      42 ..     515     540 ..     506     572 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00061
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                       +l++GPPGtgKT    ++ ++  
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESS 267
                                       69**********88777777764 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0027
                            AAA_11  17 seitliqGPPGtgKTktivellsqll 42 
                                       ++ +l+ GPPGtgKT    ++ ++ +
  gi|386001603|ref|YP_005919902.1| 515 PKGVLLYGPPGTGKTLLAKAVANESN 540
                                       555799*********88777777764 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00089      0.28       2      30 ..     245     273 ..     244     285 .. 0.92
   2 !    8.6   0.0    0.0052       1.6       2      27 ..     518     543 ..     517     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00089
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++kt+l+ka+a+  +++f  i
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFASI 273
                                       89******************999999877 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0052
                             AAA_3   2 vllegvPGlaktllvkalakaldlef 27 
                                       vll g PG++ktll+ka+a+  +++f
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNANF 543
                                       7999***************9988877 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.003      0.92      22      42 ..     245     265 ..     239     273 .. 0.86
   2 !   10.3   0.1    0.0011      0.34      22      42 ..     518     538 ..     510     548 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt+la a+a e
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANE 265
                                       5678***********999865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt+la a+a e
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANE 538
                                       7889***********999865 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0024      0.74     117     137 ..     245     265 ..     240     271 .. 0.89
   2 !    9.9   0.0    0.0012      0.36     117     137 ..     518     538 ..     515     542 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0024
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v+++Gp+ tGkt+la+a a+ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANE 265
                                       789**************9986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt la+a a+ 
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANE 538
                                       899**************9985 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0047       1.5      16      41 ..     242     267 ..     233     278 .. 0.85
   2 !   10.4   0.0   0.00094      0.29      14      46 ..     513     543 ..     505     551 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0047
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdele 41 
                                       P  +ll G pG GK+ la+++++e  
  gi|386001603|ref|YP_005919902.1| 242 PRGVLLHGPPGTGKTMLAKAVANESS 267
                                       7789******************9973 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00094
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnv 46 
                                       e Pk +ll G pG GK+ la+++++e   + n+
  gi|386001603|ref|YP_005919902.1| 513 EAPKGVLLYGPPGTGKTLLAKAVANES--NANF 543
                                       78***********************98..5655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0011      0.34      20      40 ..     244     264 ..     232     276 .. 0.82
   2 !    7.9   0.1    0.0076       2.3      21      40 ..     518     537 ..     509     548 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                            AAA_30  20 vavltGpAGtGKttalkalre 40 
                                        ++l+Gp+GtGKt++ ka+++
  gi|386001603|ref|YP_005919902.1| 244 GVLLHGPPGTGKTMLAKAVAN 264
                                       5789************99976 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0076
                            AAA_30  21 avltGpAGtGKttalkalre 40 
                                       ++l Gp+GtGKt + ka+++
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVAN 537
                                       5789**********999976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0012      0.36       4      45 ..     245     279 ..     242     327 .. 0.74
   2 !    8.6   0.0    0.0032         1       4      25 ..     518     539 ..     515     572 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl 45 
                                       vl +G +GtGKt+++ ++++e        +a+++s N+p++ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANES-------SAHFASINGPEIV 279
                                       6889************999998.......6777777777643 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0032
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +GtGKt+++ ++++e 
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANES 539
                                       6789*************99997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0069       2.1      13      34 ..     245     266 ..     240     349 .. 0.78
   2 ?    7.7   0.1     0.013       4.1      12      32 ..     517     537 ..     511     552 .. 0.82
   3 ?    0.3   0.0       2.7   8.2e+02      18      53 ..     591     628 ..     584     630 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0069
                            AAA_19  13 llvtaGpGtGKTrvlkhivall 34 
                                       +l+ ++pGtGKT + k++ ++ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANES 266
                                       799*********9888776554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.013
                            AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                        +l+ ++pGtGKT + k++ +
  gi|386001603|ref|YP_005919902.1| 517 GVLLYGPPGTGKTLLAKAVAN 537
                                       5899*********98777655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.7
                            AAA_19  18 GpGtGKTrvlkhivallvel..ggvkpeeillvaftgr 53 
                                       G GtG  +v++ iv+ l+++  g ++++ ++++a t+r
  gi|386001603|ref|YP_005919902.1| 591 GGGTGEPHVTERIVNQLLSEidGMEELRGVVVIAATNR 628
                                       78***********9987765223345689999999988 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0072       2.2      24      49 ..     245     270 ..     241     353 .. 0.75
   2 !    9.4   0.0    0.0035       1.1      23      53 ..     517     547 ..     512     589 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0072
                                       EEEEEETT--HHHHHHCC--TTS-EE CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwl 49 
                                       v+l G++G+gk++ A++ +++s+   
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHF 270
                                       99****************99988654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0035
                                       -EEEEEETT--HHHHHHCC--TTS-EE--SS CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwleifv 53 
                                        v+l G++G+gk+l A++ +++s  +   ++
  gi|386001603|ref|YP_005919902.1| 517 GVLLYGPPGTGKTLLAKAVANESNANFLTTK 547
                                       59******************99987655433 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.02       6.2       3      31 ..     243     271 ..     241     278 .. 0.89
   2 ?    2.8   0.0      0.27        82      75      95 ..     279     299 ..     273     313 .. 0.79
   3 ?    2.7   0.0      0.28        87       3      30 ..     516     543 ..     514     549 .. 0.87
   4 ?    2.4   0.0      0.35   1.1e+02      73      96 ..     549     578 ..     533     584 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                       r v l gp g+Gk +l ka+ +e + +f+
  gi|386001603|ref|YP_005919902.1| 243 RGVLLHGPPGTGKTMLAKAVANESSAHFA 271
                                       67899*****************9999996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.27
                                       TTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                        +++yg+s + i+ev+e+   
  gi|386001603|ref|YP_005919902.1| 279 VSKYYGESEKRIREVFEESER 299
                                       579*************98654 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.28
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + v l gp g+Gk  l ka+ +e + +f
  gi|386001603|ref|YP_005919902.1| 516 KGVLLYGPPGTGKTLLAKAVANESNANF 543
                                       66899**************999988777 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.35
                                       E.ETTEEEEEEHHHHHHHHHTTSE.....E CS
                     Guanylate_kin  73 e.fsgnlygtsveaieevlekgki.....v 96 
                                       +   ++ yg+s   i e++ k+++     v
  gi|386001603|ref|YP_005919902.1| 549 SeILSKWYGESERHIAEIFRKARQvapaiV 578
                                       4477899****************9555444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.016       4.9      19      49 ..     241     270 ..     231     348 .. 0.61
   2 !    7.8   0.0    0.0093       2.9      23      44 ..     518     539 ..     510     547 .. 0.86
   3 ?   -2.0   0.0       8.9   2.8e+03     109     131 ..     562     587 ..     542     626 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdk 49 
                                       p + +++ Gp g GKt L k ++++++  ++
  gi|386001603|ref|YP_005919902.1| 241 PPRGVLLHGPPGTGKTMLAKAVANESSA-HF 270
                                       55567899************99999844.22 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0093
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       +++YGp g GKt L k +++++
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANES 539
                                       689*************999987 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.9
                          ATPase_2 109 llekikkkgkk...iiiiiDelqkli 131
                                        +++i +k+++    i+++Del  l 
  gi|386001603|ref|YP_005919902.1| 562 HIAEIFRKARQvapAIVFLDELDSLA 587
                                       45566666666665678889998876 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.014       4.2      37      63 ..     245     271 ..     241     398 .. 0.79
   2 !    8.2   0.0    0.0066         2      37      66 ..     518     547 ..     512     572 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                       ++++g+ G Gkt L ka++ne  +++ 
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFA 271
                                       79*****************99877665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0066
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                       +++yg+ G Gkt L ka++ne  +n+  ++
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNANFLTTK 547
                                       79******************9988876655 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0031      0.95      18      66 ..     246     308 ..     243     350 .. 0.76
   2 ?    5.2   0.0     0.048        15      18      64 ..     519     571 ..     514     595 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0031
                                       EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHH........S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxx........x RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpe........g 66 
                                       l+ g  g+Gkt+++++++++s+++        i+    Ge ++ ++ev+ee ++        +
  gi|386001603|ref|YP_005919902.1| 246 LLHGPPGTGKTMLAKAVANESSAHfasinGpEIVSKYYGESEKRIREVFEESERnapaiiflD 308
                                       577999**************9887999973599999**************9988544444441 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.048
                                       EEEESTTSSHHHHHHHHHHHSSTS......SEEEEEEESEEHHHHHHHHHHCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd......daiiyvgiGergnevaevleefp 64 
                                       l+ g  g+Gkt ++++++++sn++      + i     Ge ++ +ae++++ +
  gi|386001603|ref|YP_005919902.1| 519 LLYGPPGTGKTLLAKAVANESNANflttkgSEILSKWYGESERHIAEIFRKAR 571
                                       678999***************99988886447777888999999999887765 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0014      0.45      51      79 ..     233     259 ..     188     268 .. 0.71
   2 ?    4.7   0.0     0.038        12      58      79 ..     511     532 ..     494     540 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                       AFG1_ATPase  51 lfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                       lf r      p+rg+ l+G+ G GKt+l 
  gi|386001603|ref|YP_005919902.1| 233 LFERL--GIDPPRGVLLHGPPGTGKTMLA 259
                                       44433..578*****************96 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.038
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         e+++g+ l+G+ G GKt l 
  gi|386001603|ref|YP_005919902.1| 511 GIEAPKGVLLYGPPGTGKTLLA 532
                                       5689***************985 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.02       6.3       3      26 ..     247     270 ..     245     274 .. 0.89
   2 !    8.2   0.0    0.0059       1.8       4      29 ..     521     546 ..     518     549 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                                       EE-STTSSHHHHHHHHHHHHT-EE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                       + GP g+GK  +a+a+a++ ++++
  gi|386001603|ref|YP_005919902.1| 247 LHGPPGTGKTMLAKAVANESSAHF 270
                                       68****************999887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0059
                                       E-STTSSHHHHHHHHHHHHT-EEEEH CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyldt 29 
                                        GP g+GK  +a+a+a++ ++++l t
  gi|386001603|ref|YP_005919902.1| 521 YGPPGTGKTLLAKAVANESNANFLTT 546
                                       6**********************988 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.057        18       2      21 ..     249     268 ..     248     305 .. 0.76
   2 !    9.1   0.0    0.0054       1.7       1      31 [.     521     552 ..     521     578 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.057
                                       E-TTSSHHHHHHHHHHHHTE CS
                            AAA_17   2 GgPGsGKgtqceklvekygf 21 
                                       G+PG GK+ +++ ++ +   
  gi|386001603|ref|YP_005919902.1| 249 GPPGTGKTMLAKAVANESSA 268
                                       9**********999877633 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0054
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllr 31 
                                       +G+PG GK+ +++ ++ + +  +l++ G+ + 
  gi|386001603|ref|YP_005919902.1| 521 YGPPGTGKTLLAKAVANESNANFLTTkGSEIL 552
                                       7****************999999887655554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0048       1.5      26      61 ..     233     268 ..     216     281 .. 0.82
   2 ?    4.6   0.0     0.059        18      35      62 ..     515     542 ..     507     555 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0048
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61 
                                       L+e+   + ++ +ll+G++ +GKtm+++  a++ ++
  gi|386001603|ref|YP_005919902.1| 233 LFERLGIDPPRGVLLHGPPGTGKTMLAKAVANESSA 268
                                       566666667789***************998887665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.059
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhppe 62 
                                       ++ +ll+G++ +GKt +++  a++ +++
  gi|386001603|ref|YP_005919902.1| 515 PKGVLLYGPPGTGKTLLAKAVANESNAN 542
                                       5789**************9988877665 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       3.5       2      70 ..     246     309 ..     245     313 .. 0.63
   2 ?    6.0   0.0     0.029         9       5      71 ..     522     583 ..     518     588 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       + hG pG GK+ l + ++++s  ++ +++   e++++   +++++  + +++ + ++       i++lDE
  gi|386001603|ref|YP_005919902.1| 246 LLHGPPGTGKTMLAKAVANESsAHFASING-PEIVSKYYGESEKRIREVFEESERNA-----PAIIFLDE 309
                                       68******************8855555554.46666555444444444444322222.....24666666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.029
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + ++++s  ++ + +   e+l+++  +++++  + ++++ + +       i++lDE 
  gi|386001603|ref|YP_005919902.1| 522 GPPGTGKTLLAKAVANESnANFLTTKG-SEILSKWYGESERHIAEIFRKARQVA-----PAIVFLDEL 583
                                       78***************8866666666.68888888888888888877666533.....358999985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.016       5.1       2      32 ..     245     275 ..     244     313 .. 0.84
   2 ?    5.5   0.0     0.046        14       2      26 ..     518     542 ..     517     552 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+++ + +  +++G
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFASING 275
                                       6789**************9987666555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.046
                                       EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                       v++ GppG+GKt l k v+++ + +
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNAN 542
                                       6788**********99999886555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.066        20       1      41 [.     251     296 ..     251     301 .. 0.68
   2 ?    6.1   0.0     0.035        11       1      32 [.     524     557 ..     524     573 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.066
                                       TTSSHHHHHHHHHHHHTSEEEEHH..HHHHHHHT...S-HHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD..eliekrtg...ksiaeifee 41 
                                       +G+GK+ ++k++A++ + +f  +   e+++k  g   k+i+e+fee
  gi|386001603|ref|YP_005919902.1| 251 PGTGKTMLAKAVANESSAHFASINgpEIVSKYYGeseKRIREVFEE 296
                                       69*************9999976541145566555333556666655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.035
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg 32 
                                       +G+GK+ ++k++A++ + +f+ +   e+++k  g
  gi|386001603|ref|YP_005919902.1| 524 PGTGKTLLAKAVANESNANFLTTkgSEILSKWYG 557
                                       69******************98842334444444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.017       5.4      11      47 ..     216     265 ..     212     309 .. 0.78
   2 ?    4.6   0.0     0.093        29      22      48 ..     513     539 ..     460     571 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.017
                                       HHHHHT...................TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII  11 aienlleklks.............krdkrglikmaTGtGKTlvaaklier 47 
                                       ai++++e ++              +  + +l++ + GtGKT++a +++ +
  gi|386001603|ref|YP_005919902.1| 216 AIQRVREMIELplkhpelferlgiDPPRGVLLHGPPGTGKTMLAKAVANE 265
                                       5555555554455556666666657778899***********99766654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.093
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierl 48 
                                       +  k +l+  + GtGKTl+a +++ + 
  gi|386001603|ref|YP_005919902.1| 513 EAPKGVLLYGPPGTGKTLLAKAVANES 539
                                       6778899999********997766654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.062        19      21      41 ..     242     261 ..     233     264 .. 0.77
   2 ?    5.1   0.0     0.063        19      21      39 ..     515     532 ..     494     537 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.062
                            AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                       ++g +ll Gp G+GK+ l  A
  gi|386001603|ref|YP_005919902.1| 242 PRG-VLLHGPPGTGKTMLAKA 261
                                       355.9**********988655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.063
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|386001603|ref|YP_005919902.1| 515 PKG-VLLYGPPGTGKTLLA 532
                                       466.9**********8765 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.026       7.9      57      76 ..     246     265 ..     240     285 .. 0.88
   2 ?    3.3   0.0      0.26        80      56      76 ..     518     538 ..     489     557 .. 0.86
   3 ?   -1.2   0.0       6.7   2.1e+03      62      79 ..     592     609 ..     589     629 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                                       EEEE-TTSSHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaen 76 
                                        +hG +GtGk  +a+ +a++
  gi|386001603|ref|YP_005919902.1| 246 LLHGPPGTGKTMLAKAVANE 265
                                       58**************9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.26
                                       EEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaen 76 
                                       + ++G +GtGk  +a+ +a++
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANE 538
                                       5589*************9986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 6.7
                                       TTSSHHHHHHHHHHHHST CS
                            Torsin  62 tGtGknfvaeiiaenlyr 79 
                                        GtG  +v+e i+++l  
  gi|386001603|ref|YP_005919902.1| 592 GGTGEPHVTERIVNQLLS 609
                                       59***********99865 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0         1   3.1e+02      19      44 ..     441     466 ..     434     472 .. 0.84
   2 ?    9.0   0.0    0.0045       1.4      26      54 ..     708     736 ..     701     740 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                       ip + l e  vt+ D+++a++++ p+
  gi|386001603|ref|YP_005919902.1| 441 IPREILEELVVTRGDLEAAMHEVSPS 466
                                       6666677779***********99998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0045
                            Vps4_C  26 ePpvtlkDflkalkkarptVskeDLekhe 54 
                                       + +v+ ++fl+al+++ p+V+++ ++ + 
  gi|386001603|ref|YP_005919902.1| 708 AVEVRKSHFLAALEEVGPSVTPDTMKYYA 736
                                       56899*****************9999886 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.16        51      60      88 ..     245     272 ..     240     281 .. 0.81
   2 ?   -2.9   0.0       9.6     3e+03     124     150 ..     304     329 ..     301     330 .. 0.85
   3 ?    5.3   0.0      0.03       9.3      59      91 ..     517     548 ..     491     552 .. 0.81
   4 ?   -1.2   0.0       2.9   8.8e+02      11      38 ..     596     623 ..     594     628 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravyts 88 
                                       vll g pgt+K+ l k+v++  + a ++s
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANE-SSAHFAS 272
                                       89************9999854.4555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.6
                                       EEEEESGGGSTCHHHHHHHHHHHHSEE CS
                               MCM 124 vcciDefdkmkeedrsalhEamEqqti 150
                                       ++ +De+d +   +r+ +   mE+ ++
  gi|386001603|ref|YP_005919902.1| 304 IIFLDELDSIAP-KREEVAGEMERRMV 329
                                       7899*****999.88889999998766 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.03
                                       EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSS CS
                               MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgkg 91 
                                        vll g pgt+K+ l k+v++ ++  ++ + kg
  gi|386001603|ref|YP_005919902.1| 517 GVLLYGPPGTGKTLLAKAVANESNA-NFLTTKG 548
                                       59***********999999966555.5555555 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.9
                                       SSTHHHHHHHHSSTTSSS-HHHHHHHHH CS
                               MCM  11 ekdiieklvksiapsiyghedvkkaill 38 
                                       e++++e++v+++  +i g+e+ +  +++
  gi|386001603|ref|YP_005919902.1| 596 EPHVTERIVNQLLSEIDGMEELRGVVVI 623
                                       678999***************9987776 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.96     3e+02     132     155 ..     213     236 ..     205     238 .. 0.88
   2 ?    3.4   0.0      0.14        44       5      27 ..     246     268 ..     243     274 .. 0.88
   3 ?    3.6   0.0      0.12        37       5      27 ..     519     541 ..     516     546 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.96
                               IPT 132 lakakkRvrqmlrpeeegaslldE 155
                                       +++a++Rvr+m++   +++ l++ 
  gi|386001603|ref|YP_005919902.1| 213 MKHAIQRVREMIELPLKHPELFER 236
                                       789**********99999888775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                               IPT   5 lifGatttGKtaeaiklaketga 27 
                                       l++G+ +tGKt  a ++a+e +a
  gi|386001603|ref|YP_005919902.1| 246 LLHGPPGTGKTMLAKAVANESSA 268
                                       899***************99887 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.12
                               IPT   5 lifGatttGKtaeaiklaketga 27 
                                       l++G+ +tGKt  a ++a+e  a
  gi|386001603|ref|YP_005919902.1| 519 LLYGPPGTGKTLLAKAVANESNA 541
                                       89****************98765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.059        18     132     154 ..     245     267 ..     196     275 .. 0.86
   2 ?    4.7   0.0     0.044        14     127     155 ..     513     541 ..     503     547 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.059
                             T2SSE 132 ilvsGgTgsGKttllyallkein 154
                                       +l+ G+ g+GKt l+ a+ +e  
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESS 267
                                       7999***********99988765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeink 155
                                       ++ + +l+ G+ g+GKt l+ a+ +e n+
  gi|386001603|ref|YP_005919902.1| 513 EAPKGVLLYGPPGTGKTLLAKAVANESNA 541
                                       55677999************999988765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.11        35       2      39 ..     245     281 ..     244     295 .. 0.73
   2 ?    5.3   0.0      0.07        22       2      39 ..     518     554 ..     517     569 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.11
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltk 39 
                                       v+l G  g+GKt l+k + ++  s +  s+ g ++++k
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANE-SSAHFASINGPEIVSK 281
                                       6788**********9998855.4455566666666555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.07
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltk 39 
                                       v+l G  g+GKt l+k +  ++ + +  +t g ++l+k
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVA-NESNANFLTTKGSEILSK 554
                                       6899********9988877.666777888888888776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0       0.1        31       4      25 ..     245     266 ..     243     272 .. 0.89
   2 ?    5.0   0.0     0.059        18       2      25 ..     516     539 ..     515     553 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                         PduV-EutP   4 illiGkvgsGKttLtqalkgee 25 
                                       +ll G+ g+GKt L++a+ +e+
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANES 266
                                       8999*************99875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.059
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkgee 25 
                                       k +ll G+ g+GKt L++a+ +e+
  gi|386001603|ref|YP_005919902.1| 516 KGVLLYGPPGTGKTLLAKAVANES 539
                                       5699***************99874 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.033        10       2      30 ..     245     273 ..     244     292 .. 0.87
   2 ?    3.8   0.1       0.2        61       2      29 ..     518     545 ..     517     549 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.033
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++hG+P +GKt  a ++a +  a + +i
  gi|386001603|ref|YP_005919902.1| 245 VLLHGPPGTGKTMLAKAVANESSAHFASI 273
                                       689***************99888776666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.2
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllt 29 
                                       +++ G+P +GKt  a ++a + +a +lt
  gi|386001603|ref|YP_005919902.1| 518 VLLYGPPGTGKTLLAKAVANESNANFLT 545
                                       5789*******************99998 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.056        17       4      23 ..     246     265 ..     244     276 .. 0.76
   2 ?    3.4   0.1      0.17        52       4      23 ..     519     538 ..     517     545 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.056
                                       EEEESTTCCHHHHHHHHHCT CS
                              cobW   4 vltGflGsGKTtLlnhllen 23 
                                       +l G++G+GKT+L +++ ++
  gi|386001603|ref|YP_005919902.1| 246 LLHGPPGTGKTMLAKAVANE 265
                                       689********998877644 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.17
                                       EEEESTTCCHHHHHHHHHCT CS
                              cobW   4 vltGflGsGKTtLlnhllen 23 
                                       +l G++G+GKT L +++ ++
  gi|386001603|ref|YP_005919902.1| 519 LLYGPPGTGKTLLAKAVANE 538
                                       688*******9888777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        58  (0.00323498); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              58  [number of targets reported over threshold]
# CPU time: 0.85u 0.31s 00:00:01.15 Elapsed: 00:00:00.51
# Mc/sec: 4519.78
//
Query:       gi|386001604|ref|YP_005919903.1|  [L=385]
Description: L-sorbosone dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-15   55.2   0.0    3.3e-14   53.0   0.0    2.1  2  GSDH      Glucose / Sorbosone dehydrogenase
     0.0015   18.2   0.0       0.01   15.5   0.0    2.2  2  SGL       SMP-30/Gluconolactonase/LRE-like region
     0.0016   18.3   0.7        3.5    7.8   0.0    4.1  4  NHL       NHL repeat


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.66   3.9e+03      11      28 ..      60      78 ..      53      90 .. 0.53
   2 !   53.0   0.0   5.5e-18   3.3e-14     112     331 ..     146     367 ..     134     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.66
                                      TTS-EEEEET.TTEEEEEE CS
                              GSDH 11 pdgrlLvter.sGrlrlvk 28
                                       +g+++v  r +Gr+  ++
  gi|386001604|ref|YP_005919903.1| 60 SEGTVFVGTRsEGRVYAIR 78
                                      3444555444445555544 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 5.5e-18
                                       -------EEE-TTS-EEEE---TT-GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE CS
                              GSDH 112 gahfGsrlafgpdgtLfvtvGdrskreeaqdlsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlal 188
                                       + h    +afgpdg+L+v +G      +  d+ ++  +i r+ +dGs      f        ei++ G+Rn+ G+ +
  gi|386001604|ref|YP_005919903.1| 146 RSHGWKFIAFGPDGKLYVPIGAP---CNVCDPGDPYASITRMDPDGSN-----F--------EIFARGVRNTVGFDW 206
                                       44555569************975...56788999999*********94.....4........8************** PP

                                       -TTT--EEEEEE--SSS......EEEEE.E-TT-B--TTT-S......S-.....-S-TTS---SEEETT---EEEE CS
                              GSDH 189 dpdtgeLwesEhGprgg......Delnl.ieaGknYGWplvsygeeYsgkkigesetreglekpvlvwtpsiapsgl 258
                                       +pdt eLw ++ G          Deln+ + aG  +G+p  + g       +g s+   ++++p +   p +a  g+
  gi|386001604|ref|YP_005919903.1| 207 HPDTAELWFTDNGRDWLgddeppDELNRaPVAGLHFGFPFCHAGIPDP--VFGGSRGCGEFTDPEMNLGPHVAALGM 281
                                       *************8743457888****84689**********988644..5667788999***************** PP

                                       EEE.........TTEEEEEETT........TTEEEEEEEEEEEEEEEEEEEE.ESS-.-E...E..EEEE-TTS-EE CS
                              GSDH 259 afytgdaf.pewkgdllvggLk........sqsllrleldegekvveeerll.eelgeri...R..dVeqgpdGaly 320
                                        fy+g af p+++g ++++             +++ ++++ ++++++ e +    lg r+   R  dV + pdGal 
  gi|386001604|ref|YP_005919903.1| 282 RFYSGAAFpPAYRGGIFIAEHGswnradpiGYRVTFVRFE-DGRATDYEIFAeGWLGGRVawgRpvDVLVMPDGALL 357
                                       *******9679******98654444666666778888888.446555555444445666644434478889999998 PP

                                       EEE-TTTTT.. CS
                              GSDH 321 vltdeedgkll 331
                                       v  d + g+++
  gi|386001604|ref|YP_005919903.1| 358 VSDD-RAGAVY 367
                                       8877.677666 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06      0.01      42     152 ..     101     217 ..      70     223 .. 0.79
   2 ?   -1.3   0.0      0.22   1.3e+03      71     103 ..     327     360 ..     280     378 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                               SGL  42 svGaiaprkdgrlvvasksglalldlasgeletladeee.........dekpllrfNDgvvdpdGrlwf..Gtmgde 107
                                       ++G++++  dg l+va+ s+++++d    ++e ++de++           ++++ +  +++ pdG+l++  G +++ 
  gi|386001604|ref|YP_005919903.1| 101 PNGVAFR--DGSLYVAEVSRILRYD----AIESHLDEPPdpvvvkddlPSQRSHGWKFIAFGPDGKLYVpiGAPCNV 171
                                       6777777..9999999999999998....455555553334445544444467777778999****99544999999 PP

                               SGL 108 eakgeevgalyrldpd.gklervlddltipNGlawspdgktlYlaD 152
                                        ++g+ ++++ r+dpd +  e  ++++  + G  w pd+  l ++D
  gi|386001604|ref|YP_005919903.1| 172 CDPGDPYASITRMDPDgSNFEIFARGVRNTVGFDWHPDTAELWFTD 217
                                       9999888*********999*************************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                               SGL  71 eletladeee.dekpllrfNDgvvdpdGrlwfGt 103
                                       ++e +a+ +  ++++  r+ D+ v pdG+l + +
  gi|386001604|ref|YP_005919903.1| 327 DYEIFAEGWLgGRVAWGRPVDVLVMPDGALLVSD 360
                                       4444444433345555566777777777776655 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.27   1.6e+03       4      17 ..      53      66 ..      50      67 .. 0.84
   2 !    7.8   0.0   0.00059       3.5       2      19 ..      99     115 ..      98     118 .. 0.86
   3 ?   -0.1   0.0      0.19   1.1e+03       7      17 ..     153     163 ..     152     163 .. 0.90
   4 !    4.6   0.1    0.0064        38       3      19 ..     344     360 ..     343     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                                      EEEEEEETTTEEEE CS
                               NHL  4 PhGvavdsnGdiyV 17
                                      ++++a+ s G ++V
  gi|386001604|ref|YP_005919903.1| 53 ARSLALGSEGTVFV 66
                                      6789********99 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00059
                                       SSEEEEEEETTTEEEEEE CS
                               NHL   2 nyPhGvavdsnGdiyVaD 19 
                                         P+Gva   +G +yVa+
  gi|386001604|ref|YP_005919903.1|  99 DLPNGVAF-RDGSLYVAE 115
                                       67******.********8 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.19
                                       EEEETTTEEEE CS
                               NHL   7 vavdsnGdiyV 17 
                                       +a  ++G +yV
  gi|386001604|ref|YP_005919903.1| 153 IAFGPDGKLYV 163
                                       7899******9 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0064
                                       SEEEEEEETTTEEEEEE CS
                               NHL   3 yPhGvavdsnGdiyVaD 19 
                                       +P +v v+++G ++V+D
  gi|386001604|ref|YP_005919903.1| 344 RPVDVLVMPDGALLVSD 360
                                       799999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2733.25
//
Query:       gi|386001605|ref|YP_005919904.1|  [L=157]
Description: hypothetical protein Mhar_0910 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1103.48
//
Query:       gi|386001606|ref|YP_005919905.1|  [L=99]
Description: Thioredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-12   47.3   0.0    1.8e-12   47.1   0.0    1.0  1  Thioredoxin    Thioredoxin
     0.0064   16.4   0.2     0.0079   16.1   0.2    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
  ------ inclusion threshold ------
      0.026   15.0   0.1       0.14   12.6   0.1    1.8  1  Thioredoxin_2  Thioredoxin-like domain
      0.053   13.3   0.0       0.06   13.2   0.0    1.2  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0     4e-16   1.8e-12      19     102 ..      12      95 ..       4      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4e-16
                                       SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHH CS
                       Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegareke 95 
                                       + vl eFy + Cg C++ a  le+lae ++ kv + ++d++ +  la++  v ++Ptl+l ++g+ v++++g    e
  gi|386001606|ref|YP_005919905.1|  12 EVVLTEFYTEACGFCREEAMILEELAEVFARKVEFRRIDAQVEGRLAEEQVVFNVPTLILERDGELVERFNGFVAGE 88 
                                       57999*******************************************************************99999 PP

                                       HHHHHHH CS
                       Thioredoxin  96 klaaflk 102
                                       +l++ ++
  gi|386001606|ref|YP_005919905.1|  89 RLERAIR 95 
                                       9998876 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.8e-06    0.0079      44     100 ..      27      82 ..       9      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                                       S-HCHHHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEE CS
                              HyaE  44 sDvaVvlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvla 100
                                        + a +l El ++F    +   +   + e +lae+  v+ +P+l++ rdge++   +
  gi|386001606|ref|YP_005919905.1|  27 REEAMILEELAEVFARKVEFRRID-AQVEGRLAEEQVVFNVPTLILERDGELVERFN 82 
                                       56799************9999998.999**********************9987665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.1e-05      0.14       8     108 ..      14      93 ..      11      94 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                     Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPti 84 
                                       vl+ f+++ C++C+     l+el +v        + ++   ++++i+ + e             la++  v+ +Pt+
  gi|386001606|ref|YP_005919905.1|  14 VLTEFYTEACGFCREEAMILEELAEV--------FARK--VEFRRIDAQVEGR-----------LAEEQVVFNVPTL 69 
                                       56668888888888855555555444........5444..7777777777775...........99**********8 PP

                     Thioredoxin_2  85 v.fldgkeivarlpGyvpaeeleal 108
                                       +   dg+  v+r  G+v  e+le +
  gi|386001606|ref|YP_005919905.1|  70 IlERDGE-LVERFNGFVAGERLERA 93 
                                       8345666.999******99999875 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05      0.06     132     175 ..      14      57 ..       7      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                              TraF 132 gLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpel 175
                                        L  Fy + c++c+++a il+++a+ +  +v +  +d ++  +l
  gi|386001606|ref|YP_005919905.1|  14 VLTEFYTEACGFCREEAMILEELAEVFARKVEFRRIDAQVEGRL 57 
                                       6777********************98887777766666665545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 668.17
//
Query:       gi|386001607|ref|YP_005919906.1|  [L=499]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-23   81.7   0.0      1e-21   78.0   0.0    2.5  3  Radical_SAM      Radical SAM superfamily
    5.3e-21   74.6   0.2    1.6e-20   73.1   0.0    1.9  2  AsnC_trans_reg2  AsnC-like ligand binding domain
      1e-09   38.0   0.3    3.2e-09   36.5   0.3    1.9  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    8.5e-09   35.8   0.4    1.9e-08   34.7   0.4    1.7  1  SPASM            Iron-sulfur cluster-binding domain
    2.6e-08   34.2   0.0    7.8e-08   32.7   0.0    1.8  1  Fer4_12          4Fe-4S single cluster domain
      9e-06   25.8   0.0    2.9e-05   24.2   0.0    1.9  2  Fer4_14          4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.19   11.9   3.0        4.5    7.5   0.8    2.6  2  cwf21            cwf21 domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0     4e-25     1e-21       2     140 ..       7     137 ..       6     161 .. 0.92
   2 ?   -1.1   0.0      0.85   2.2e+03      31     144 ..     383     400 ..     347     434 .. 0.67
   3 ?    0.2   0.1      0.34   8.7e+02      77      99 ..     453     474 ..     381     491 .. 0.58

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 4e-25
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +vt +Cnl+C +C  + +    ++g++ls+ee +  ++++ a      +il+ggepll+pd+  l+e ++ +   gi
  gi|386001607|ref|YP_005919906.1|   7 EVTAACNLACEYCRASAS--ASPDGAELSTEEAEGFIDQV-APL-RPMLILSGGEPLLRPDIFHLAEYARSR---GI 76 
                                       6899************97..********************.688.9****************9999999987...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklrea 140
                                       r ++ tngtl+++e +er++++g+ rvs++l+ + +e v++  +++++f+  ++++ +lr  
  gi|386001607|ref|YP_005919906.1|  77 RASLATNGTLLTPEAVERIKRAGIMRVSISLDGPGPE-VHDASRGPGSFDLAVRGIGNLRGE 137
                                       *************************************.******99*********9999865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  31 veeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvsl 107
                                                                                                                    
  gi|386001607|ref|YP_005919906.1| 383 E---------------------------------------------------------------------------- 383
                                       3............................................................................ PP

                                       EEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 108 gleaaddekvlklmnrghtfeevlealeklreagikr 144
                                                           ee +e  ++l + gi r
  gi|386001607|ref|YP_005919906.1| 384 --------------------EEAMERAKRLQDWGIIR 400
                                       ....................44444444444444433 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.34
                                       TEEEEEEECSSCHGHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerlle 99 
                                       ++ +t+++++ ++ ee+l +++e
  gi|386001607|ref|YP_005919906.1| 453 NMWFTISASEERI-EEILSEMKE 474
                                       3444555555555.666666655 PP

>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.1   5.5e+03       8      33 ..     143     168 ..     140     170 .. 0.78
   2 !   73.1   0.0   6.1e-24   1.6e-20       2      82 .]     411     490 ..     410     490 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.1
                   AsnC_trans_reg2   8 alvawkvpeerveevaevvaelpevt 33 
                                        +++ ++++++v ++    +el +v+
  gi|386001607|ref|YP_005919906.1| 143 NMTVTRANQNQVSATMDLAEELGAVA 168
                                       58899999999988888888877775 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 6.1e-24
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR..ewpynlyfmvharseeeveevlaeiaaatgledyevLp 76 
                                       lG +  +lva+ v ++r+eevaevv++++e++H+Y+R  e ++n++f+++a see++ee+l+e++++tgl+   vLp
  gi|386001607|ref|YP_005919906.1| 411 LGCS-GVLVALPVSDDRMEEVAEVVNSYQEISHNYLRpnETEFNMWFTISA-SEERIEEILSEMKEKTGLH-QLVLP 484
                                       7888.99******************************8778********98.689****************.99*** PP

                   AsnC_trans_reg2  77 strefK 82 
                                       ++r fK
  gi|386001607|ref|YP_005919906.1| 485 TKRIFK 490
                                       *****9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.3   1.3e-12   3.2e-09       1      42 []     350     394 ..     350     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.3e-12
                     HTH_AsnC-type   1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42 
                                       LDe+Dr++Le+ qe      +++ +L+e++G Se+++++R +rL+
  gi|386001607|ref|YP_005919906.1| 350 LDELDRRLLEIVQEEfplTARPFLALGEALGTSEEEAMERAKRLQ 394
                                       8******************************************96 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.4   7.6e-12   1.9e-08       1      67 [.     238     296 ..     238     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 7.6e-12
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskkfplielCrnC 67 
                                       C a+++ +f++  GdV+pC     +   +++ Gn+rees+ eIw+s+  + ++r   +++l   C  C
  gi|386001607|ref|YP_005919906.1| 238 CLAGTSFVFVSRTGDVSPC----GYL--PIVAGNVREESFPEIWESSpVFLDLR---RRELLGRCGGC 296
                                       8889999************....233..7***************7777****99...44444557666 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     3e-11   7.8e-08      12      97 ..       9      88 ..       2     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3e-11
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90
                                      ++ Cnl+C++C + +  s+++ +  t+e++   i+++  + ++ l+l+GGEPll   ++++  l+++ +++++    ++
  gi|386001607|ref|YP_005919906.1|  9 TAACNLACEYCRASASASPDGAELSTEEAE-GFIDQV-APLRPMLILSGGEPLL---RPDIFHLAEYARSRGI-RASLA 81
                                      568*****************9999999886.566777.799*************...****************.57999 PP

                           Fer4_12 91 ytgytle 97
                                      ++g+ l 
  gi|386001607|ref|YP_005919906.1| 82 TNGTLLT 88
                                      9998775 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.1e-08   2.9e-05       5      92 ..       9      87 ..       6     110 .. 0.81
   2 ?   -2.5   0.0       2.1   5.3e+03      18      46 ..     449     477 ..     445     483 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.1e-08
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83
                                      ++ Cnl+C  C  +++ + +  + +tee +   ++++   +     l l+GGePL+    +++++l ++ + ++  ++ 
  gi|386001607|ref|YP_005919906.1|  9 TAACNLACEYCRASASASPDGAELSTEEAE-GFIDQVAPLRP--M-LILSGGEPLLR---PDIFHLAEYARSRG--IRA 78
                                      789***********************9999.77745544444..5.*********55...9*************..999 PP

                           Fer4_14 84 wletngtle 92
                                       l tngtl 
  gi|386001607|ref|YP_005919906.1| 79 SLATNGTLL 87
                                      9****9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                           Fer4_14  18 ketwkselgkpqteelleqilkdlkksei 46 
                                       ++++++  +   +ee +e+il+++k++  
  gi|386001607|ref|YP_005919906.1| 449 ETEFNMWFTISASEERIEEILSEMKEKTG 477
                                       56677777777888888899877666554 PP

>> cwf21  cwf21 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8    0.0018       4.5       5      13 ..     203     211 ..     201     213 .. 0.90
   2 ?    3.8   0.1     0.026        66      18      40 ..     425     475 ..     381     476 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                             cwf21   5 rrReIEvkv 13 
                                       rrR+IEvkv
  gi|386001607|ref|YP_005919906.1| 203 RRRKIEVKV 211
                                       9*******9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                             cwf21  18 deLEeeg...........................l.seeeIeervdelRek 40 
                                       d++Ee                             + see Iee ++e +ek
  gi|386001607|ref|YP_005919906.1| 425 DRMEEVAevvnsyqeishnylrpnetefnmwftiSaSEERIEEILSEMKEK 475
                                       5555521345555666777777777777788888559*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3815.79
//
Query:       gi|386001608|ref|YP_005919907.1|  [L=328]
Description: Aspartate-semialdehyde dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-37  127.2   0.0    1.5e-36  126.2   0.0    1.5  2  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    1.7e-25   89.8   0.0    2.6e-25   89.2   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.55   4.9e+03     119     134 ..      71      85 ..      43     104 .. 0.62
   2 !  126.2   0.0   1.7e-40   1.5e-36       1     175 [.     144     300 ..     144     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHHHCSTT CS
                   Semialdhyde_dhC 119 dveveeveellaaape 134
                                       ++e++++e+++a+a +
  gi|386001608|ref|YP_005919907.1|  71 ADEAKKAEAEFAKA-G 85 
                                       44455555555554.3 PP

  == domain 2  score: 126.2 bits;  conditional E-value: 1.7e-40
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       LkPL+   +e++rviva++qavSGaG+                    +gv++++i+gN+ip+i +ee+k e e +++
  gi|386001608|ref|YP_005919907.1| 144 LKPLMP--MEIQRVIVASMQAVSGAGY--------------------EGVPSMAILGNIIPFISGEEEKVEREAQKI 198
                                       89****..69*****************....................6***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.......TTEEEEESSHCHH CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.......pevkvvvneeedr 145
                                       l+  + ++   + + +vsa+c+rVPv++Gh+eav+++++  ++++ev+e++ ++          p+  ++v++e dr
  gi|386001608|ref|YP_005919907.1| 199 LGTFDGDRIVDAPF-DVSASCHRVPVMDGHTEAVWVEMAknPTPAEVREAFLNFNPGlsdlptePKRPIIVRDEVDR 274
                                       ****9966555544.6**********************9899999999999999999******************** PP

                                       SSHHHHTTC..SSSEEEEEEEEETTCTTEEEE CS
                   Semialdhyde_dhC 146 Ptpaavagg..tnsvsVGRirkdemgdeglkl 175
                                       P+p+++++   +++vsVGRir+         +
  gi|386001608|ref|YP_005919907.1| 275 PQPRLDRNAgkGMAVSVGRIREGI------RF 300
                                       *******9889**********865......34 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.0   2.9e-29   2.6e-25      12     118 ..       2     113 ..       1     116 [. 0.98

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 2.9e-29
                                       HHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHH CS
                    Semialdhyde_dh  12 GqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivflalpagvskel 82 
                                       Gq++++ L +hp++el+ l++s+rsaGkk++ea++       ++e+ d+kv +vd++e+ ++d+vf+alpa+ +k+ 
  gi|386001608|ref|YP_005919907.1|   2 GQRFIEQLWDHPWFELSSLAASERSAGKKYREAARwrleneLPAEVGDMKVVNVDPKEV-QADVVFSALPADEAKKA 77 
                                       9*********************************9****99999***************.9**************** PP

                                       HHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGG CS
                    Semialdhyde_dh  83 apklaeagvkviDlssdfRlkddavyvlpevnreai 118
                                       ++++a+ag+ v +++s++R+++d+++++pe n++++
  gi|386001608|ref|YP_005919907.1|  78 EAEFAKAGFAVASNASAYRFDPDVPLMIPECNADHL 113
                                       *********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 2298.62
//
Query:       gi|386001609|ref|YP_005919908.1|  [L=182]
Description: hypothetical protein Mhar_0914 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 1619.52
//
Query:       gi|386001610|ref|YP_005919909.1|  [L=575]
Description: Chloride transporter, chloride channel (ClC) family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-73  248.0  41.1    1.6e-73  248.0  41.1    2.0  2  Voltage_CLC  Voltage gated chloride channel
    6.8e-25   87.3   5.2    1.8e-12   47.5   0.1    2.9  3  CBS          CBS domain


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.7     0.018   1.6e+02     166     192 ..      16      42 ..       9      59 .. 0.88
   2 !  248.0  41.1   1.8e-77   1.6e-73       1     353 [.      61     413 ..      61     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC 166 lfvllGilgGllgalfvrlllkverlf 192
                                       l+v  G+lgGl +++f +l   v+ lf
  gi|386001610|ref|YP_005919909.1|  16 LAVGTGLLGGLGAVVFRWLAGEVQGLF 42 
                                       57889*************998888654 PP

  == domain 2  score: 248.0 bits;  conditional E-value: 1.8e-77
                                       HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsr 77 
                                       lggl++gll+ ++apea+g Gip  + al+++ g+++ r+ ++ ++as++t+gsG+s+Gre+p+ qiGA++gs+l++
  gi|386001610|ref|YP_005919909.1|  61 LGGLAVGLLILRFAPEARGEGIPALMVALHKRGGRVRRRTGPAILIASAITIGSGGSAGRESPIAQIGASFGSLLGQ 137
                                       589************************************************************************** PP

                                       HTT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T-- CS
                       Voltage_CLC  78 llklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrlllgeepafgeve 154
                                       +l+l+  d  ++l ++G  AG+A +FnaPlg ++f++E+v+r+f++  ++p+++++vv+a +++++lg+ paf   +
  gi|386001610|ref|YP_005919909.1| 138 RLRLDVAD-VQILAVSGFVAGLAGTFNAPLGSAIFGMEVVMRRFRMVDAVPILLSAVVGAATASAFLGQSPAFT--P 211
                                       ****9999.999*************************************************************8..5 PP

                                       -...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC..CSSSSCC CS
                       Voltage_CLC 155 slfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpa.svlgggye 230
                                         ++++l el+l +l+G+++G l++l++ ll ++erlf  l   ++k  l+p l+gl+ g+ g+ +    v+g gy+
  gi|386001610|ref|YP_005919909.1| 212 VWTEITLPELLLCFLMGLTFGGLAILWAGLLSRAERLFLWL---PLKEGLKPGLGGLVAGAAGVYFIGyGVMGVGYD 285
                                       5779**********************************887...88999**************9999779******* PP

                                       HHHHHC......TT-S-...HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSS CS
                       Voltage_CLC 231 liasll......egstl...llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaa 298
                                        ++ +l      +          +l+ll l+ +k lata tlgsg +gG++ P+LviGA++G+ +gl++++l+p a 
  gi|386001610|ref|YP_005919909.1| 286 GVDRILaiasdpA---GsdgSRLVLFLLALAAAKALATASTLGSGGCGGTIGPTLVIGAVAGASFGLLFGHLVPAAG 359
                                       *999996654443...1666777788999*******************************************99544 PP

                                       C...HHHHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                       Voltage_CLC 299 ssdpgafalvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkavad 353
                                         +  a+al+G+aa+lag ++apl+++v++ E+ +d++ll+ lm++++ ++ava+
  gi|386001610|ref|YP_005919909.1| 360 G-HAPAYALLGAAALLAGSAGAPLASVVLISEMAADYSLLPALMITSAASYAVAS 413
                                       4.4579***********************************************86 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.4   3.6e+03      19      44 ..     174     195 ..     171     203 .. 0.69
   2 !   47.5   0.1     2e-16   1.8e-12       1      54 [.     445     497 ..     445     500 .. 0.94
   3 !   41.2   0.2   1.8e-14   1.6e-10       1      54 [.     507     562 ..     507     564 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHTSSEEEEEETTTBEEE CS
                               CBS  19 eealelmrekgvsrlPVVdedgklvG 44 
                                       e +++++  + v+++P++  +  +vG
  gi|386001610|ref|YP_005919909.1| 174 EVVMRRF--RMVDAVPIL-LSA-VVG 195
                                       6678888..449999996.345.555 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 2e-16
                                       HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+d mtr+vv + p+tt++ea+ + + e++v+++PVV e g+l Givt  Dl r+
  gi|386001610|ref|YP_005919909.1| 445 VRDAMTREVVALGPETTVREAMARiF-EENVRGFPVV-EGGRLAGIVTFDDLRRV 497
                                       8999******************8868.999*******.89************986 PP

  == domain 3  score: 41.2 bits;  conditional E-value: 1.8e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllra 54 
                                       Vg++  +dv+++ pd++++ +++++ +++v+rlPV+  ++ +k+vGivt++D + a
  gi|386001610|ref|YP_005919909.1| 507 VGEVAVKDVIVAFPDENMKNVMDRLYRNNVGRLPVMerEDPKKVVGIVTRTDAIAA 562
                                       7899999*****************99**********6555559*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3627.88
//
Query:       gi|386001611|ref|YP_005919910.1|  [L=579]
Description: Chloride transporter, chloride channel (ClC) family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-79  265.5  40.4    7.2e-78  262.3  35.3    2.0  2  Voltage_CLC  Voltage gated chloride channel
      4e-24   84.8   4.0    2.6e-11   43.8   0.2    2.8  3  CBS          CBS domain
  ------ inclusion threshold ------
        1.6    9.1  10.4        1.1    9.6   4.9    3.1  2  DUF3021      Protein of unknown function (DUF3021)


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.2   4.1e-06     0.024     160     220 ..      22      85 ..       5      86 .. 0.82
   2 !  262.3  35.3   1.2e-81   7.2e-78       1     353 [.      73     423 ..      73     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-06
                                       -GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH.CHHHH..HHH.HHHHHHHHHHHHCCCS CS
                       Voltage_CLC 160 sllelilfvllGilgGllgalfvrlllkverlfrkle.klkik..krl.epalvgllvgllglll 220
                                        + +l l++l+G++gG+ +++f r    v+r+f +    ++ +   ++ +p+++gl+vg ++++l
  gi|386001611|ref|YP_005919910.1|  22 AYIDL-LAILIGVVGGVGAIVFDRAIDLVSRIFFSGIdPASGPgvSVIlYPIIGGLIVGPIVFIL 85 
                                       55554.499*********************9777777677777785556************9986 PP

  == domain 2  score: 262.3 bits;  conditional E-value: 1.2e-81
                                       HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsr 77 
                                       +ggl++g +v  +apea+g+G++ +++ +    g+++ r  ++ +l+s++t+gsG+s+GreGp+ qiG+++gs++++
  gi|386001611|ref|YP_005919910.1|  73 IGGLIVGPIVFILAPEAKGQGVSRIIESVLVGGGRIRRRAGFLLILSSAVTIGSGGSAGREGPIAQIGGSFGSLVGQ 149
                                       689************************************************************************** PP

                                       HTT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTTTSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T-- CS
                       Voltage_CLC  78 llklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEevsrefslrallpvfvasvvaalvlrlllgeepafgeve 154
                                       +++l + d  + l ++G+AAG+A  F+aP+gG++f++E+v+r+fs+   +p+++++vv++ v+++l+g   a++  +
  gi|386001611|ref|YP_005919910.1| 150 IFRLGPTD-LKLLTVCGVAAGVAGSFGAPMGGAIFSMEVVARRFSPYDSVPILLSAVVGTAVASALIGPVEALK-NP 224
                                       ****9999.999********************************************************999999.45 PP

                                       -...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC..CSSSSCC CS
                       Voltage_CLC 155 slfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpa.svlgggye 230
                                       + fa+s  +++l +llG l+G+++ l+vr +++ve+lf++l   +++ +l+pal+g++ g+ g+ll    ++g gy+
  gi|386001611|ref|YP_005919910.1| 225 Q-FAFSGIDIALCFLLGPLFGAIAFLWVRFFYTVEELFDDL---SVPEMLKPALGGAVAGVGGYLLYGyGIMGVGYD 297
                                       4.89999*********************************9...999999****************988******** PP

                                       HHHHHCTT-S-...HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HH CS
                       Voltage_CLC 231 liasllegstl...llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpga 304
                                        i+ ++e + l     ++++l++l l+k++at++++gsg +gGifaPsL+iG ++G ++gl+++++lpg  + +p++
  gi|386001611|ref|YP_005919910.1| 298 GITRIFEMQDLsasADMVIFLIVLGLVKIAATSFSVGSGGSGGIFAPSLYIGFMFGVAFGLLADMALPGLGAASPEV 374
                                       ******66655666667778899*********************************************7666689** PP

                                       HHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                       Voltage_CLC 305 falvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkavad 353
                                       + l+Gmaa++ag+ raplt+iv++ E+  +++ l+p+++a+++++a+++
  gi|386001611|ref|YP_005919910.1| 375 YGLLGMAALFAGAGRAPLTCIVMIPEMASSYDRLPPVIIACVLSYATTQ 423
                                       *********************************************9976 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.8   1.6e+04      18      36 ..     185     201 ..     184     207 .. 0.75
   2 !   43.8   0.2   4.3e-15   2.6e-11       1      53 [.     455     506 ..     455     509 .. 0.95
   3 !   41.7   0.1   1.9e-14   1.1e-10       2      54 ..     518     572 ..     517     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHTSSEEEEE CS
                               CBS  18 leealelmrekgvsrlPVV 36 
                                       +e +++++  + ++++P++
  gi|386001611|ref|YP_005919910.1| 185 MEVVARRF--SPYDSVPIL 201
                                       77888899..778999985 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 4.3e-15
                                       HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       Vg+ m+rdvv v  +++l+e+ +l + +++++++PVV edgklvGivt  Dl +
  gi|386001611|ref|YP_005919910.1| 455 VGEAMNRDVVAVGSEMPLRELRDLiF-RTNHTGFPVV-EDGKLVGIVTFDDLRN 506
                                       8999********************88.99999*****.9************986 PP

  == domain 3  score: 41.7 bits;  conditional E-value: 1.9e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllra 54 
                                       gd+    vvtv+pd++ + a++lm ++ ++rlPVV  d+ ++l G++t++D++ra
  gi|386001611|ref|YP_005919910.1| 518 GDVAEGAVVTVRPDQSTKYAMDLMYQHQIGRLPVVrsDDPKRLEGMITRTDVIRA 572
                                       66655568****************9999*******988888************98 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.12   7.2e+02      42      61 ..      26      45 ..      17      57 .. 0.81
   2 ?    9.6   4.9   0.00018       1.1       6      86 ..     235     330 ..     231     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                           DUF3021 42 llsaliGvlfalaslifese 61
                                      ll++liGv+ +++ ++f+  
  gi|386001611|ref|YP_005919910.1| 26 LLAILIGVVGGVGAIVFDRA 45
                                      67899****99999999865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00018
                           DUF3021   6 lgiliGiligliislvislfsgettll................estavlkqvllsaliGvlfalaslifeserlsll 66 
                                       l +l+G l+g+i +l + +f++ + l+                 +      +++++++Gv++ +++ ife+++ls +
  gi|386001611|ref|YP_005919910.1| 235 LCFLLGPLFGAIAFLWVRFFYTVEELFddlsvpemlkpalggaVAGVGGYLLYGYGIMGVGYDGITRIFEMQDLSAS 311
                                       6789999999999999999999999999999999999987764333334445566********************** PP

                           DUF3021  67 kqtlihflvvlllvlllall 86 
                                         ++i fl+vl lv ++a+ 
  gi|386001611|ref|YP_005919910.1| 312 ADMVI-FLIVLGLVKIAATS 330
                                       ***99.66666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 3359.37
//
Query:       gi|386001612|ref|YP_005919911.1|  [L=309]
Description: hypothetical protein Mhar_0917 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-24   84.5  33.4    5.9e-07   30.0   2.1    4.8  5  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
    9.3e-19   67.2  15.6      0.021   15.0   0.1    5.9  5  FG-GAP           FG-GAP repeat
    9.8e-07   28.7   2.5         14    5.2   0.0    5.0  5  DUF1926          Domain of unknown function (DUF1926)
    1.5e-06   28.2   0.5         30    4.7   0.0    5.1  5  BBS2_Mid         Ciliary BBSome complex subunit 2, middle reg
    2.2e-05   24.6   0.0         33    4.5   0.0    4.8  5  LolB             Outer membrane lipoprotein LolB
    0.00026   20.4  10.9         13    5.1   0.1    5.1  5  TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal reg
     0.0081   16.3   0.1         25    5.1   0.0    5.1  5  Trp_ring         Trimeric autotransporter adhesin Trp ring do
  ------ inclusion threshold ------
      0.011   16.3   0.5         16    6.1   0.0    4.6  5  DUF2627          Protein of unknown function (DUF2627)
      0.081   13.0  11.9         40    4.4   0.1    4.7  5  CagY_I           CagY type 1 repeat
       0.11   11.0   2.1         37    2.7   0.0    3.6  4  Agro_virD5       Agrobacterium VirD5 protein
       0.15   12.0  13.2         28    4.8   0.2    4.3  4  UBA              UBA/TS-N domain
        0.9    9.8  16.5         34    4.7   0.2    4.7  5  Dockerin_1       Dockerin type I domain


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.4   2.1e-09   3.1e-06       1      61 []      28      96 ..      28      96 .. 0.70
   2 !   30.0   2.1   3.9e-10   5.9e-07       1      61 []      85     153 ..      85     153 .. 0.72
   3 !   29.8   2.3   4.4e-10   6.6e-07       1      61 []     142     210 ..     142     210 .. 0.72
   4 !   29.2   2.9   7.1e-10   1.1e-06       1      61 []     199     267 ..     199     267 .. 0.72
   5 !   15.0   0.1   1.9e-05     0.028       1      30 [.     256     284 ..     256     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.1e-09
                              VCBS  1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslgg........sgggtgva.....vgDlDgDGdlDllv 61
                                      D+dgDG++++++++++g+ ++  +g G ++ + + + g+        +    +++     ++D+DgDG+ ++lv
  gi|386001612|ref|YP_005919911.1| 28 DFDGDGKAEILISSPWGIGILKMEG-GALRAPVMAANGAtftggylvN----TADnnfemAADFDGDGQDEILV 96
                                      9**********************97.6777555542222233222322....3323333599**********98 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.9e-10
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslgg........sgggtgva.....vgDlDgDGdlDllv 61 
                                       D+dgDG ++++v++++g+ ++  +gd t++ + + + g+        +    +++     ++D+DgDG+ ++lv
  gi|386001612|ref|YP_005919911.1|  85 DFDGDGQDEILVSSPWGIGILKMTGD-TLSAPVMAANGAtftggylvN----TADnnfemAADFDGDGQDEILV 153
                                       9***********************99.777665543222243233322....3323333599**********98 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 4.4e-10
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslgg........sgggtgva.....vgDlDgDGdlDllv 61 
                                       D+dgDG ++++v++++g+ ++  +gd t++ + + + g+        +    +++     ++D+DgDG+ ++lv
  gi|386001612|ref|YP_005919911.1| 142 DFDGDGQDEILVSSPWGIGILKMTGD-TLSAPVMAANGAtftggylvN----TADnnfemAADFDGDGQDEILV 210
                                       9***********************99.777665543222243233322....3323333599**********98 PP

  == domain 4  score: 29.2 bits;  conditional E-value: 7.1e-10
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslgg........sgggtgva.....vgDlDgDGdlDllv 61 
                                       D+dgDG ++++v++++g+ ++  +gd t++ + + + g+        +    +++     ++D+DgDG+ ++lv
  gi|386001612|ref|YP_005919911.1| 199 DFDGDGQDEILVSSPWGIGILKMTGD-TLSAPVMAANGAtftggylvN----TADnnfemAADFDGDGQDEILV 267
                                       9***********************99.777665543222243233322....3323333599**********98 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 1.9e-05
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtft 30 
                                       D+dgDG ++++v++++g+ ++  +gd t++
  gi|386001612|ref|YP_005919911.1| 256 DFDGDGQDEILVSSPWGIGILKMTGD-TLS 284
                                       9******************9999998.555 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.4e-05     0.021       7      21 ..      26      40 ..      24      47 .. 0.86
   2 !   14.8   0.2   1.6e-05     0.024       7      21 ..      83      97 ..      82     103 .. 0.89
   3 !   14.8   0.2   1.6e-05     0.024       7      21 ..     140     154 ..     139     160 .. 0.89
   4 !   14.8   0.2   1.6e-05     0.024       7      21 ..     197     211 ..     196     217 .. 0.89
   5 !   14.8   0.2   1.6e-05     0.024       7      21 ..     254     268 ..     253     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                      EESTSSSSS-EEEEE CS
                            FG-GAP  7 vgDvNGDGyaDLavG 21
                                        D++GDG+a++++ 
  gi|386001612|ref|YP_005919911.1| 26 GSDFDGDGKAEILIS 40
                                      56***********98 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      EESTSSSSS-EEEEE CS
                            FG-GAP  7 vgDvNGDGyaDLavG 21
                                      ++D++GDG ++++v 
  gi|386001612|ref|YP_005919911.1| 83 AADFDGDGQDEILVS 97
                                      79***********98 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.6e-05
                                       EESTSSSSS-EEEEE CS
                            FG-GAP   7 vgDvNGDGyaDLavG 21 
                                       ++D++GDG ++++v 
  gi|386001612|ref|YP_005919911.1| 140 AADFDGDGQDEILVS 154
                                       79***********98 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 1.6e-05
                                       EESTSSSSS-EEEEE CS
                            FG-GAP   7 vgDvNGDGyaDLavG 21 
                                       ++D++GDG ++++v 
  gi|386001612|ref|YP_005919911.1| 197 AADFDGDGQDEILVS 211
                                       79***********98 PP

  == domain 5  score: 14.8 bits;  conditional E-value: 1.6e-05
                                       EESTSSSSS-EEEEE CS
                            FG-GAP   7 vgDvNGDGyaDLavG 21 
                                       ++D++GDG ++++v 
  gi|386001612|ref|YP_005919911.1| 254 AADFDGDGQDEILVS 268
                                       79***********98 PP

>> DUF1926  Domain of unknown function (DUF1926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0096        14       1      28 [.      28      54 ..      28      56 .. 0.88
   2 ?    4.8   0.0     0.012        19       1      20 [.      85     104 ..      85     110 .. 0.82
   3 ?    4.8   0.0     0.012        19       1      20 [.     142     161 ..     142     167 .. 0.82
   4 ?    4.8   0.0     0.012        19       1      20 [.     199     218 ..     199     224 .. 0.82
   5 ?    4.8   0.0     0.012        19       1      20 [.     256     275 ..     256     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0096
                           DUF1926  1 DfdlDgreEvlleseklvavlkpaqGGs 28
                                      Dfd Dg+ E+l++s+  + +lk  +GG+
  gi|386001612|ref|YP_005919911.1| 28 DFDGDGKAEILISSPWGIGILKM-EGGA 54
                                      9**************99999999.5554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                           DUF1926   1 DfdlDgreEvlleseklvav 20 
                                       Dfd Dg++E+l++s+  + +
  gi|386001612|ref|YP_005919911.1|  85 DFDGDGQDEILVSSPWGIGI 104
                                       9***********99765555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.012
                           DUF1926   1 DfdlDgreEvlleseklvav 20 
                                       Dfd Dg++E+l++s+  + +
  gi|386001612|ref|YP_005919911.1| 142 DFDGDGQDEILVSSPWGIGI 161
                                       9***********99765555 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.012
                           DUF1926   1 DfdlDgreEvlleseklvav 20 
                                       Dfd Dg++E+l++s+  + +
  gi|386001612|ref|YP_005919911.1| 199 DFDGDGQDEILVSSPWGIGI 218
                                       9***********99765555 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.012
                           DUF1926   1 DfdlDgreEvlleseklvav 20 
                                       Dfd Dg++E+l++s+  + +
  gi|386001612|ref|YP_005919911.1| 256 DFDGDGQDEILVSSPWGIGI 275
                                       9***********99765555 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.099   1.5e+02       5      19 ..      27      41 ..      26      50 .. 0.92
   2 ?    4.7   0.0      0.02        30       5      19 ..      84      98 ..      82     113 .. 0.90
   3 ?    4.7   0.0      0.02        30       5      19 ..     141     155 ..     139     170 .. 0.90
   4 ?    4.7   0.0      0.02        30       5      19 ..     198     212 ..     196     227 .. 0.90
   5 ?    4.7   0.0      0.02        30       5      19 ..     255     269 ..     253     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.099
                          BBS2_Mid  5 advdgdgeneLvvgs 19
                                      +d+dgdg++e++++s
  gi|386001612|ref|YP_005919911.1| 27 SDFDGDGKAEILISS 41
                                      59***********98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                          BBS2_Mid  5 advdgdgeneLvvgs 19
                                      ad+dgdg++e++v+s
  gi|386001612|ref|YP_005919911.1| 84 ADFDGDGQDEILVSS 98
                                      79***********98 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.02
                          BBS2_Mid   5 advdgdgeneLvvgs 19 
                                       ad+dgdg++e++v+s
  gi|386001612|ref|YP_005919911.1| 141 ADFDGDGQDEILVSS 155
                                       79***********98 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.02
                          BBS2_Mid   5 advdgdgeneLvvgs 19 
                                       ad+dgdg++e++v+s
  gi|386001612|ref|YP_005919911.1| 198 ADFDGDGQDEILVSS 212
                                       79***********98 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.02
                          BBS2_Mid   5 advdgdgeneLvvgs 19 
                                       ad+dgdg++e++v+s
  gi|386001612|ref|YP_005919911.1| 255 ADFDGDGQDEILVSS 269
                                       79***********98 PP

>> LolB  Outer membrane lipoprotein LolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.22   3.3e+02      30      65 ..      34      69 ..      29      76 .. 0.89
   2 ?    4.4   0.0     0.023        34      29      65 ..      90     126 ..      73     133 .. 0.86
   3 ?    4.4   0.0     0.023        34      29      65 ..     147     183 ..     130     190 .. 0.86
   4 ?    4.5   0.0     0.022        33      29      65 ..     204     240 ..     187     249 .. 0.87
   5 ?    3.2   0.0     0.054        81      29      64 ..     261     296 ..     244     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                              LolB 30 ryeleLtspLGqtvlelevdpegatledsdgqayta 65
                                      + e+ ++sp G + l++e+ + +a +  ++g ++t+
  gi|386001612|ref|YP_005919911.1| 34 KAEILISSPWGIGILKMEGGALRAPVMAANGATFTG 69
                                      47899******************9999999999876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                              LolB  29 dryeleLtspLGqtvlelevdpegatledsdgqayta 65 
                                        ++e+ ++sp G + l++++d  +a +  ++g ++t+
  gi|386001612|ref|YP_005919911.1|  90 GQDEILVSSPWGIGILKMTGDTLSAPVMAANGATFTG 126
                                       4699***********************9999999886 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.023
                              LolB  29 dryeleLtspLGqtvlelevdpegatledsdgqayta 65 
                                        ++e+ ++sp G + l++++d  +a +  ++g ++t+
  gi|386001612|ref|YP_005919911.1| 147 GQDEILVSSPWGIGILKMTGDTLSAPVMAANGATFTG 183
                                       4699***********************9999999886 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.022
                              LolB  29 dryeleLtspLGqtvlelevdpegatledsdgqayta 65 
                                        ++e+ ++sp G + l++++d  +a +  ++g ++t+
  gi|386001612|ref|YP_005919911.1| 204 GQDEILVSSPWGIGILKMTGDTLSAPVMAANGATFTG 240
                                       4699***********************9999999886 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.054
                              LolB  29 dryeleLtspLGqtvlelevdpegatledsdgqayt 64 
                                        ++e+ ++sp G + l++++d  +a +  ++g ++t
  gi|386001612|ref|YP_005919911.1| 261 GQDEILVSSPWGIGILKMTGDTLSAPVMAANGVRFT 296
                                       4699******************99999999988776 PP

>> TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.018        26      34      49 ..      27      42 ..      23      57 .. 0.89
   2 !    5.1   0.1    0.0086        13      27      49 ..      76      99 ..      56     117 .. 0.79
   3 ?    4.9   0.1      0.01        15      27      49 ..     133     156 ..     117     168 .. 0.79
   4 !    5.0   0.1    0.0092        14      27      49 ..     190     213 ..     169     225 .. 0.79
   5 !    5.0   0.1     0.009        14      27      49 ..     247     270 ..     224     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.018
                   TcdB_toxin_midN 34 aDldGdGladlvltip 49
                                       D+dGdG+a++++ +p
  gi|386001612|ref|YP_005919911.1| 27 SDFDGDGKAEILISSP 42
                                      6*********998887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0086
                   TcdB_toxin_midN 27 edtnlsl.aDldGdGladlvltip 49
                                      +d n+++ aD+dGdG  ++++ +p
  gi|386001612|ref|YP_005919911.1| 76 ADNNFEMaADFDGDGQDEILVSSP 99
                                      566666527********9998877 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.01
                   TcdB_toxin_midN  27 edtnlsl.aDldGdGladlvltip 49 
                                       +d n+++ aD+dGdG  ++++ +p
  gi|386001612|ref|YP_005919911.1| 133 ADNNFEMaADFDGDGQDEILVSSP 156
                                       556666527********9998877 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0092
                   TcdB_toxin_midN  27 edtnlsl.aDldGdGladlvltip 49 
                                       +d n+++ aD+dGdG  ++++ +p
  gi|386001612|ref|YP_005919911.1| 190 ADNNFEMaADFDGDGQDEILVSSP 213
                                       566666527********9998877 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.009
                   TcdB_toxin_midN  27 edtnlsl.aDldGdGladlvltip 49 
                                       +d n+++ aD+dGdG  ++++ +p
  gi|386001612|ref|YP_005919911.1| 247 ADNNFEMaADFDGDGQDEILVSSP 270
                                       566666527********9998877 PP

>> Trp_ring  Trimeric autotransporter adhesin Trp ring domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   2.4e+03      19      30 ..      62      73 ..      47      82 .. 0.59
   2 ?    1.0   0.0      0.32   4.8e+02       6      30 ..     106     130 ..      95     138 .. 0.77
   3 ?    1.0   0.0      0.32   4.8e+02       6      30 ..     163     187 ..     152     195 .. 0.77
   4 ?    1.0   0.0      0.32   4.8e+02       6      30 ..     220     244 ..     209     252 .. 0.77
   5 ?    5.1   0.0     0.017        25       5      27 ..     276     298 ..     266     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                          Trp_ring 19 AneVkFvGegga 30
                                      An   F+G  ++
  gi|386001612|ref|YP_005919911.1| 62 ANGATFTGGYLV 73
                                      555555554444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.32
                          Trp_ring   6 sadgnaYsaaVkNAneVkFvGegga 30 
                                       + +g++ sa V  An   F+G  ++
  gi|386001612|ref|YP_005919911.1| 106 KMTGDTLSAPVMAANGATFTGGYLV 130
                                       4488888999999999999998776 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.32
                          Trp_ring   6 sadgnaYsaaVkNAneVkFvGegga 30 
                                       + +g++ sa V  An   F+G  ++
  gi|386001612|ref|YP_005919911.1| 163 KMTGDTLSAPVMAANGATFTGGYLV 187
                                       4488888999999999999998776 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.32
                          Trp_ring   6 sadgnaYsaaVkNAneVkFvGegga 30 
                                       + +g++ sa V  An   F+G  ++
  gi|386001612|ref|YP_005919911.1| 220 KMTGDTLSAPVMAANGATFTGGYLV 244
                                       4488888999999999999998776 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.017
                          Trp_ring   5 VsadgnaYsaaVkNAneVkFvGe 27 
                                       ++ +g++ sa V  An V+F+G 
  gi|386001612|ref|YP_005919911.1| 276 LKMTGDTLSAPVMAANGVRFTGG 298
                                       44489999*************96 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         1   1.5e+03      47      61 ..      59      73 ..      41      79 .. 0.85
   2 ?    0.6   0.0      0.56   8.4e+02      42      61 ..     111     130 ..      98     136 .. 0.81
   3 ?    0.6   0.0      0.56   8.4e+02      42      61 ..     168     187 ..     155     193 .. 0.81
   4 ?    0.7   0.0      0.56   8.3e+02      42      61 ..     225     244 ..     212     251 .. 0.81
   5 ?    6.1   0.0     0.011        16      42      64 ..     282     304 ..     268     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                           DUF2627 47 llfaiglgfiaGfil 61
                                      +++a g +f +G++ 
  gi|386001612|ref|YP_005919911.1| 59 VMAANGATFTGGYLV 73
                                      67889999****986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.56
                           DUF2627  42 flaGlllfaiglgfiaGfil 61 
                                       +l+  +++a g +f +G++ 
  gi|386001612|ref|YP_005919911.1| 111 TLSAPVMAANGATFTGGYLV 130
                                       55566889999******986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.56
                           DUF2627  42 flaGlllfaiglgfiaGfil 61 
                                       +l+  +++a g +f +G++ 
  gi|386001612|ref|YP_005919911.1| 168 TLSAPVMAANGATFTGGYLV 187
                                       55566889999******986 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.56
                           DUF2627  42 flaGlllfaiglgfiaGfil 61 
                                       +l+  +++a g +f +G++ 
  gi|386001612|ref|YP_005919911.1| 225 TLSAPVMAANGATFTGGYLV 244
                                       55566889999******986 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.011
                           DUF2627  42 flaGlllfaiglgfiaGfilhrd 64 
                                       +l+  +++a g+ f +G++l+ +
  gi|386001612|ref|YP_005919911.1| 282 TLSAPVMAANGVRFTGGWLLNTE 304
                                       556668999**********9865 PP

>> CagY_I  CagY type 1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7   2.6e+03      48      58 ..      27      37 ..      24      41 .. 0.78
   2 ?    4.4   0.1     0.027        40      41      58 ..      77      94 ..      74      98 .. 0.88
   3 ?    4.4   0.1     0.027        40      41      58 ..     134     151 ..     131     155 .. 0.88
   4 ?    4.4   0.1     0.027        40      41      58 ..     191     208 ..     188     212 .. 0.88
   5 ?    4.4   0.1     0.027        40      41      58 ..     248     265 ..     245     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                            CagY_I 48 tnfdGdkseei 58
                                       +fdGd   ei
  gi|386001612|ref|YP_005919911.1| 27 SDFDGDGKAEI 37
                                      58****87776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
                            CagY_I 41 dnPtetqtnfdGdkseei 58
                                      dn  e  ++fdGd  +ei
  gi|386001612|ref|YP_005919911.1| 77 DNNFEMAADFDGDGQDEI 94
                                      9999*********99998 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.027
                            CagY_I  41 dnPtetqtnfdGdkseei 58 
                                       dn  e  ++fdGd  +ei
  gi|386001612|ref|YP_005919911.1| 134 DNNFEMAADFDGDGQDEI 151
                                       9999*********99998 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.027
                            CagY_I  41 dnPtetqtnfdGdkseei 58 
                                       dn  e  ++fdGd  +ei
  gi|386001612|ref|YP_005919911.1| 191 DNNFEMAADFDGDGQDEI 208
                                       9999*********99998 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.027
                            CagY_I  41 dnPtetqtnfdGdkseei 58 
                                       dn  e  ++fdGd  +ei
  gi|386001612|ref|YP_005919911.1| 248 DNNFEMAADFDGDGQDEI 265
                                       9999*********99998 PP

>> Agro_virD5  Agrobacterium VirD5 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.62   9.3e+02     491     520 ..      55      84 ..      52      92 .. 0.84
   2 ?    2.7   0.0     0.025        37     490     520 ..     111     141 ..     106     153 .. 0.87
   3 ?    2.7   0.0     0.025        37     490     520 ..     168     198 ..     163     210 .. 0.87
   4 ?    2.7   0.0     0.025        37     490     520 ..     225     255 ..     220     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.62
                        Agro_virD5 491 lsdpvasaesvtasngyqlnqlgyahqlat 520
                                       l  pv +a+++t + gy +n      ++a+
  gi|386001612|ref|YP_005919911.1|  55 LRAPVMAANGATFTGGYLVNTADNNFEMAA 84 
                                       778***************998877777665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                        Agro_virD5 490 tlsdpvasaesvtasngyqlnqlgyahqlat 520
                                       tls pv +a+++t + gy +n      ++a+
  gi|386001612|ref|YP_005919911.1| 111 TLSAPVMAANGATFTGGYLVNTADNNFEMAA 141
                                       9*******************99877777776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.025
                        Agro_virD5 490 tlsdpvasaesvtasngyqlnqlgyahqlat 520
                                       tls pv +a+++t + gy +n      ++a+
  gi|386001612|ref|YP_005919911.1| 168 TLSAPVMAANGATFTGGYLVNTADNNFEMAA 198
                                       9*******************99877777776 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.025
                        Agro_virD5 490 tlsdpvasaesvtasngyqlnqlgyahqlat 520
                                       tls pv +a+++t + gy +n      ++a+
  gi|386001612|ref|YP_005919911.1| 225 TLSAPVMAANGATFTGGYLVNTADNNFEMAA 255
                                       9*******************99877777776 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.019        28      26      36 ..      76      86 ..      75      86 .. 0.92
   2 ?    4.8   0.2     0.019        28      26      36 ..     133     143 ..     132     143 .. 0.92
   3 ?    4.8   0.2     0.019        28      26      36 ..     190     200 ..     189     200 .. 0.92
   4 ?    4.8   0.2     0.019        28      26      36 ..     247     257 ..     246     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                                      TTTSHHHHHHH CS
                               UBA 26 tgnNeErAvey 36
                                      ++nN E+A+++
  gi|386001612|ref|YP_005919911.1| 76 ADNNFEMAADF 86
                                      79*******97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                                       TTTSHHHHHHH CS
                               UBA  26 tgnNeErAvey 36 
                                       ++nN E+A+++
  gi|386001612|ref|YP_005919911.1| 133 ADNNFEMAADF 143
                                       79*******97 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.019
                                       TTTSHHHHHHH CS
                               UBA  26 tgnNeErAvey 36 
                                       ++nN E+A+++
  gi|386001612|ref|YP_005919911.1| 190 ADNNFEMAADF 200
                                       79*******97 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.019
                                       TTTSHHHHHHH CS
                               UBA  26 tgnNeErAvey 36 
                                       ++nN E+A+++
  gi|386001612|ref|YP_005919911.1| 247 ADNNFEMAADF 257
                                       79*******97 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.7   2.5e+03      38      44 ..      28      34 ..      23      38 .. 0.73
   2 ?    4.7   0.2     0.023        34      27      45 ..      74      92 ..      70      95 .. 0.85
   3 ?    4.7   0.2     0.023        34      27      45 ..     131     149 ..     127     152 .. 0.85
   4 ?    4.7   0.2     0.023        34      27      45 ..     188     206 ..     184     209 .. 0.85
   5 ?    4.7   0.2     0.023        34      27      45 ..     245     263 ..     241     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                                      STT-SSC CS
                        Dockerin_1 38 DvNgDGr 44
                                      D +gDG+
  gi|386001612|ref|YP_005919911.1| 28 DFDGDGK 34
                                      7777777 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.023
                                      BTTSCCCHGGGSTT-SSCE CS
                        Dockerin_1 27 gqssssngkaaDvNgDGrv 45
                                      ++ +++ + aaD +gDG+ 
  gi|386001612|ref|YP_005919911.1| 74 NTADNNFEMAADFDGDGQD 92
                                      7889999**********85 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.023
                                       BTTSCCCHGGGSTT-SSCE CS
                        Dockerin_1  27 gqssssngkaaDvNgDGrv 45 
                                       ++ +++ + aaD +gDG+ 
  gi|386001612|ref|YP_005919911.1| 131 NTADNNFEMAADFDGDGQD 149
                                       7889999**********85 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.023
                                       BTTSCCCHGGGSTT-SSCE CS
                        Dockerin_1  27 gqssssngkaaDvNgDGrv 45 
                                       ++ +++ + aaD +gDG+ 
  gi|386001612|ref|YP_005919911.1| 188 NTADNNFEMAADFDGDGQD 206
                                       7889999**********85 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.023
                                       BTTSCCCHGGGSTT-SSCE CS
                        Dockerin_1  27 gqssssngkaaDvNgDGrv 45 
                                       ++ +++ + aaD +gDG+ 
  gi|386001612|ref|YP_005919911.1| 245 NTADNNFEMAADFDGDGQD 263
                                       7889999**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2192.10
//
Query:       gi|386001613|ref|YP_005919912.1|  [L=569]
Description: AMP-dependent acyl-CoA synthetase and ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.5e-111  371.8   0.0   4.1e-111  371.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      1e-17   64.9   0.0    2.4e-17   63.7   0.0    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.11   11.3   0.0        2.4    6.9   0.0    2.3  2  PhnI           Bacterial phosphonate metabolism protein (PhnI
       0.63    9.9   2.3        8.2    6.3   0.0    3.2  3  YL1_C          YL1 nuclear protein C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.6   0.0  9.2e-115  4.1e-111       1     422 [.      27     460 ..      27     461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 371.6 bits;  conditional E-value: 9.2e-115
                                       HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                       AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                       ++e a+++p+  a+v+ ++g ++TYrel+++vnr+A+gL +lG+kkgdr ai++ n +ew++  +a++k+G++ v +
  gi|386001613|ref|YP_005919912.1|  27 FDEIAERYPENDAIVSIHQGLRYTYRELQQEVNRAAKGLHALGLKKGDRLAIWATNIAEWIICQFATAKVGIIMVNI 103
                                       67899****99999998899********************************************************* PP

                                       ETTS-HHHHHHHHHHHTESEEE...................ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCH CS
                       AMP-binding  78 nptltaeelayiledseakvli...................atvdselleklleaaakleavklvivldadellkee 135
                                       np+++ +el y+l++se ++l+                   ++ ++e  + ++e     +  k+ +++  ++ +   
  gi|386001613|ref|YP_005919912.1| 104 NPAYRTHELLYALKQSETEALFlidrfktsdyvgmffeicpEAAEAEPGKISCESL---PYLKTAVLIRGERQP--G 175
                                       ************************99988877776664433111122222223333...333333333322221..1 PP

                                       CCCHCCCCSCTTS.................-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHH CS
                       AMP-binding 136 elkeeeeseekae.................kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslklet 195
                                       +           +                 +  e+e+l+ dd+++i+YTSGTTG PKGV+l+h n+++n + +   +
  gi|386001613|ref|YP_005919912.1| 176 M-----------YtweevlkmgdevhddvlRA-EQESLDFDDPINIQYTSGTTGFPKGVVLTHHNILNNGYFI--GE 238
                                       1...........01222222334455567533.5568999*****************************7775..78 PP

                                       CSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCC CS
                       AMP-binding 196 rfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesga 272
                                       + k++++d+++  +p++h+fg++l+ ++++++Ga++vl+   + +dp+  l+++e++++t ++gvP+++ a le+++
  gi|386001613|ref|YP_005919912.1| 239 CMKFTDQDRLCIPVPFYHCFGMVLSNMACMTHGAAMVLPA--EYFDPASTLAAVERERCTALHGVPTMFVAELEHPD 313
                                       899999********************************77..44789999*************************98 PP

                                       HHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEE CS
                       AMP-binding 273 lkaakkakdlsslrlvllggeplspellrffralfge.evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgve 347
                                       ++    ++dlsslr+ +++g+p++ e ++++++l+   ev+ +YG+TE+++ +t+  + +  ++++++vGkp+p++e
  gi|386001613|ref|YP_005919912.1| 314 FD----KYDLSSLRTGIMAGSPCPTEYMKKVSSLMNMrEVVITYGQTEASPGITMsSTSDSLDRRVSTVGKPMPHTE 386
                                       88....67***************************9999**************87744455567899********** PP

                                       EEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 348 vkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       vki D++tg+ +++ge+Ge++ rg  +m++Y+++p at++a+d +++wl+TGDlg ld++ y +i+gR+kd++++
  gi|386001613|ref|YP_005919912.1| 387 VKITDPKTGKIMHRGETGEICARGYAIMRCYYNNPGATEKAID-KEGWLHTGDLGILDDEDYCKITGRLKDMVIR 460
                                       ******************************************9.647***********99*************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   5.3e-21   2.4e-17       1      76 []     469     544 ..     469     544 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 5.3e-21
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       e+E+ l +hp+++++ V+Gvpd++ Ge l+a + lk+g ++++ee+ a++r ++++++ p++++fvd +p+t +GK
  gi|386001613|ref|YP_005919912.1| 469 EIEEFLYTHPDISDVQVIGVPDARYGEELMAWIKLKEGRTLTAEEVLAFCRGRIAHFKIPRYIKFVDGFPMTVTGK 544
                                       8**********************************99976799********************************9 PP

>> PhnI  Bacterial phosphonate metabolism protein (PhnI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00054       2.4     198     220 ..     397     419 ..     335     426 .. 0.92
   2 ?    1.8   0.0     0.019        87     326     340 ..     520     534 ..     512     545 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00054
                              PhnI 198 alaRgdegallalaYstlRgyge 220
                                        + Rg++g + a +Y+ +R y +
  gi|386001613|ref|YP_005919912.1| 397 IMHRGETGEICARGYAIMRCYYN 419
                                       699*****************976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.019
                              PhnI 326 GfveHlKlPHYvtFq 340
                                       G + H+K+P Y+ F 
  gi|386001613|ref|YP_005919912.1| 520 GRIAHFKIPRYIKFV 534
                                       889**********95 PP

>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0018       8.2       7      18 ..     276     287 ..     276     288 .. 0.88
   2 ?    0.5   0.1      0.12   5.4e+02      12      17 ..     390     395 ..     385     396 .. 0.88
   3 ?    0.3   0.1      0.14   6.2e+02       1       7 [.     447     453 ..     447     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0018
                             YL1_C   7 lpAkYrDPkTgL 18 
                                       lpA Y+DP + L
  gi|386001613|ref|YP_005919912.1| 276 LPAEYFDPASTL 287
                                       8*******9876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                             YL1_C  12 rDPkTg 17 
                                       +DPkTg
  gi|386001613|ref|YP_005919912.1| 390 TDPKTG 395
                                       8****9 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.14
                             YL1_C   1 yCdITGl 7  
                                       yC ITG+
  gi|386001613|ref|YP_005919912.1| 447 YCKITGR 453
                                       9*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 3947.52
//
Query:       gi|386001614|ref|YP_005919913.1|  [L=315]
Description: Iron-sulfur cluster-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.2  13.9    5.6e-06   25.9   1.4    2.5  2  Fer4      4Fe-4S binding domain
    3.4e-07   30.0   9.7    0.00012   22.0   1.7    2.4  2  Fer4_6    4Fe-4S binding domain
    3.9e-06   26.9   9.0    7.4e-05   22.8  10.6    2.1  2  Fer4_10   4Fe-4S dicluster domain
    2.4e-05   24.8  20.7    0.00069   20.2  10.5    2.2  2  Fer4_7    4Fe-4S dicluster domain
    4.8e-05   23.2  12.7     0.0015   18.5   3.8    2.7  2  Fer4_2    4Fe-4S binding domain
    6.4e-05   23.8   9.7    0.00083   20.2   9.7    2.2  1  Fer4_16   4Fe-4S double cluster binding domain
    0.00027   21.3   2.8       0.11   12.9   1.0    2.5  2  Fer4_8    4Fe-4S dicluster domain
    0.00028   21.0   9.9     0.0048   17.0  10.5    2.4  2  Fer4_9    4Fe-4S dicluster domain
    0.00029   21.3   2.6       0.17   12.4   0.6    2.4  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.7  13.2      0.053   14.0   1.6    2.8  2  Fer4_4    4Fe-4S binding domain
      0.038   14.9  17.6       0.29   12.2   5.9    2.7  2  Fer4_3    4Fe-4S binding domain
      0.063   13.4  12.5       0.21   11.7   2.1    2.1  2  Fer4_21   4Fe-4S dicluster domain
       0.29   11.9   3.7       0.47   11.2   1.5    2.2  2  Fer4_15   4Fe-4S single cluster domain
       0.72   10.1  10.2        2.2    8.5   2.0    2.2  2  Fer4_18   4Fe-4S dicluster domain
        1.1   10.1   5.0        3.2    8.7   0.2    2.2  2  Fer4_22   4Fe-4S dicluster domain
        1.2    9.7   8.0       0.97   10.0   2.0    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.4     5e-09   5.6e-06       3      23 ..     219     239 ..     217     240 .. 0.90
   2 !   10.1   5.2   0.00049      0.55      11      21 ..     269     279 ..     269     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5e-09
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                         e++C++C++Cv+ CP gA+
  gi|386001614|ref|YP_005919913.1| 219 MEEDLCTRCMRCVQLCPAGAL 239
                                       569*****************8 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00049
                                       -THHHHHSTTT CS
                              Fer4  11 CGaCvevCPvg 21 
                                       CG C++vCPvg
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCPVG 279
                                       *********97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.7   1.1e-07   0.00012       2      24 .]     217     239 ..     217     239 .. 0.92
   2 !   12.4   1.3   0.00011      0.13       5      22 ..     250     279 ..     249     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       ++  +d+C+ C++Cv  CP+ga+
  gi|386001614|ref|YP_005919913.1| 217 PVMEEDLCTRCMRCVQLCPAGAL 239
                                       57789****************97 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                            Fer4_6   5 dpdkCi............gCgdCvrvCPeg 22 
                                       d+++C+             Cg C++vCP g
  gi|386001614|ref|YP_005919913.1| 250 DKSACTaysaslakrgvsPCGVCIKVCPVG 279
                                       6778887777777776656*********76 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8  10.6   6.6e-08   7.4e-05       3      56 .]     218     277 ..     216     277 .. 0.79
   2 !   10.0   0.5   0.00066      0.74      11      21 ..     268     278 ..     263     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.6e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtg............cgaCveaCP 56 
                                       v ++d C+rC +Cv+ CPa        + ++++ +  + + ++Ct+            cg C+++CP
  gi|386001614|ref|YP_005919913.1| 218 VMEEDLCTRCMRCVQLCPA-------GALDDRDYPAGItDKSACTAysaslakrgvspCGVCIKVCP 277
                                       67899**************.......33333333333334589999999999**************9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00066
                           Fer4_10  11 rCgkCvkaCPa 21 
                                        Cg C k+CP+
  gi|386001614|ref|YP_005919913.1| 268 PCGVCIKVCPV 278
                                       5*********9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.5   3.4e-06    0.0038      29      52 .]     215     238 ..     197     238 .. 0.84
   2 !   20.2  10.5   6.2e-07   0.00069       2      51 ..     224     279 ..     223     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                            Fer4_7  29 ekveidpekClgCgaCvavCPtga 52 
                                       ++++++++ C+ C +Cv+ CP+ga
  gi|386001614|ref|YP_005919913.1| 215 PDPVMEEDLCTRCMRCVQLCPAGA 238
                                       5678999**************997 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 6.2e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClg............CgaCvavCPtg 51 
                                       C+ C +Cv+ Cp++a++ +++  ++g      d + C+             Cg+C++vCP+g
  gi|386001614|ref|YP_005919913.1| 224 CTRCMRCVQLCPAGALDDRDY--PAG----ITDKSACTAysaslakrgvspCGVCIKVCPVG 279
                                       ***************997665..444....556777775556666667777*********97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.8   1.3e-06    0.0015       3      22 .]     217     236 ..     214     236 .. 0.91
   2 !    9.2   1.6    0.0012       1.3      13      21 ..     269     277 ..     247     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       +v ++d C++C  Cv+ CPa
  gi|386001614|ref|YP_005919913.1| 217 PVMEEDLCTRCMRCVQLCPA 236
                                       8999***************8 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                            Fer4_2  13 CgaCvsaCP 21 
                                       Cg C+++CP
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCP 277
                                       ********* PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   9.7   7.4e-07   0.00083       2      66 ..     224     278 ..     223     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.4e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C++C +C++ CP++a++ +     ++++ i   +  +  ++ + +    +  +  C++C +vCP+
  gi|386001614|ref|YP_005919913.1| 224 CTRCMRCVQLCPAGALDDR-----DYPAGITD-KSACTAYSASLA----KRGVSPCGVCIKVCPV 278
                                       ******************9.....55555443.122222333333....44589**********8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.0    0.0001      0.11      49      64 ..     222     237 ..     210     238 .. 0.89
   2 !    7.6   0.0    0.0046       5.2       8      22 ..     269     283 ..     267     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       + Ct c++C++ Cp g
  gi|386001614|ref|YP_005919913.1| 222 DLCTRCMRCVQLCPAG 237
                                       57***********986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                            Fer4_8   8 CgaCqsaCpvlrrtk 22 
                                       Cg C + Cpv +++ 
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCPVGEDRE 283
                                       999999999777643 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.3   6.1e-06    0.0068      34      50 ..     222     238 ..     204     239 .. 0.77
   2 !   17.0  10.5   4.3e-06    0.0048       2      49 ..     224     279 ..     223     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-06
                            Fer4_9  34 eaCigCgaCveaCpkga 50 
                                       + C+ C++Cv+ Cp ga
  gi|386001614|ref|YP_005919913.1| 222 DLCTRCMRCVQLCPAGA 238
                                       57999999999999986 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.3e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkg 49 
                                       Ct+C +Cv+ Cpag+  +++ +  +  + a               Cg C+++Cp g
  gi|386001614|ref|YP_005919913.1| 224 CTRCMRCVQLCPAGALDDRDYPAGITDKSACTaysaslakRGVSPCGVCIKVCPVG 279
                                       ***************977666555554333224588999522356*********76 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.6   0.00015      0.17      45      59 ..     223     237 ..     208     261 .. 0.77
   2 !    8.3   0.1     0.003       3.3       5      21 ..     269     285 ..     267     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                           Fer4_17  45 lCieCgeCerkCPqg 59 
                                       lC+ C +C++ CP+g
  gi|386001614|ref|YP_005919913.1| 223 LCTRCMRCVQLCPAG 237
                                       566666666666654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                           Fer4_17   5 CgyClpeCpsyeaydne 21 
                                       Cg C+++Cp +e+++ +
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCPVGEDRELY 285
                                       *********99986654 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.6   4.8e-05     0.053       2      16 ..     222     236 ..     221     242 .. 0.91
   2 ?    8.4   1.6     0.003       3.3       7      17 .]     269     279 ..     269     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C++C++Cv  CP 
  gi|386001614|ref|YP_005919913.1| 222 DLCTRCMRCVQLCPA 236
                                       78************6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.003
                            Fer4_4   7 CgsCvaaCPqg 17 
                                       Cg+C+ +CP+g
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCPVG 279
                                       *********75 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.9   0.00026      0.29       1      15 []     224     238 ..     224     238 .. 0.97
   2 ?    7.8   3.8    0.0066       7.4       4      14 ..     269     279 ..     267     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C++Cv+ CP gA
  gi|386001614|ref|YP_005919913.1| 224 CTRCMRCVQLCPAGA 238
                                       ************998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0066
                            Fer4_3   4 CgaCvevCPvg 14 
                                       Cg C +vCPvg
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCPVG 279
                                       99*******98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.1   0.00019      0.21      37      53 ..     220     236 ..     210     240 .. 0.74
   2 ?   10.5  12.5   0.00047      0.53       3      53 ..     219     278 ..     217     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                           Fer4_21  37 vedeCvGCnlCssvCPv 53 
                                        ed C+ C  C++ CP 
  gi|386001614|ref|YP_005919913.1| 220 EEDLCTRCMRCVQLCPA 236
                                       36788888888888884 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00047
                           Fer4_21   3 idedkCigCgkCliaCedtshqai........eidaktvl.kvvedeCvGCnlCssvCPv 53 
                                       ++ed C  C +C++ C+ ++ +          + +  ++   + +     C +C++vCPv
  gi|386001614|ref|YP_005919913.1| 219 MEEDLCTRCMRCVQLCPAGALDDRdypagitdKSACTAYSaSLAKRGVSPCGVCIKVCPV 278
                                       7899*************988886655554332111122331344566667*********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.5   0.00042      0.47       3      30 ..     219     245 ..     218     259 .. 0.79
   2 ?   -0.1   0.0       1.5   1.6e+03      11      19 ..     269     277 ..     267     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedgla 30 
                                        ++d+C+ c +Cv+++p    ld+++++
  gi|386001614|ref|YP_005919913.1| 219 MEEDLCTRCMRCVQLCP-AGALDDRDYP 245
                                       689*************9.5566666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                           Fer4_15  11 cglCvaeap 19 
                                       cg+C++++p
  gi|386001614|ref|YP_005919913.1| 269 CGVCIKVCP 277
                                       999999998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.0     0.002       2.2      59      74 ..     222     237 ..     214     256 .. 0.84
   2 ?    5.7   1.9     0.015        17      62      76 ..     267     281 ..     248     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                           Fer4_18  59 gdcidcescvkvcPtg 74 
                                         c+ c  cv++cP g
  gi|386001614|ref|YP_005919913.1| 222 DLCTRCMRCVQLCPAG 237
                                       55************97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                           Fer4_18  62 idcescvkvcPtgid 76 
                                         c++c+kvcP+g d
  gi|386001614|ref|YP_005919913.1| 267 SPCGVCIKVCPVGED 281
                                       56*********9976 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0028       3.2      77      94 ..     219     236 ..     199     238 .. 0.85
   2 ?    3.3   0.7      0.14   1.5e+02      79      94 ..     263     278 ..     248     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++e  C+ C RC++ cp+
  gi|386001614|ref|YP_005919913.1| 219 MEEDLCTRCMRCVQLCPA 236
                                       47889***********97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                       + g   Cg Ci++cpv
  gi|386001614|ref|YP_005919913.1| 263 KRGVSPCGVCIKVCPV 278
                                       5555668888888886 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.0   0.00086      0.97       3      18 ..     221     236 ..     219     237 .. 0.90
   2 ?    2.4   0.4       0.2   2.3e+02       8      17 ..     268     277 ..     265     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00086
                           Fer4_13   3 rdtCiacgaCvelaPd 18 
                                       +d C+ c+ Cv+l+P 
  gi|386001614|ref|YP_005919913.1| 221 EDLCTRCMRCVQLCPA 236
                                       689************5 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.2
                           Fer4_13   8 acgaCvelaP 17 
                                        cg+C +++P
  gi|386001614|ref|YP_005919913.1| 268 PCGVCIKVCP 277
                                       5********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2380.75
//
Query:       gi|386001615|ref|YP_005919914.1|  [L=267]
Description: 3-oxoacyl-ACP reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-59  200.2   0.0    4.2e-59  199.9   0.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.3e-51  174.9   0.0    1.5e-51  174.7   0.0    1.0  1  adh_short        short chain dehydrogenase
      6e-11   42.6   0.0    8.9e-11   42.0   0.0    1.2  1  KR               KR domain
    0.00063   19.3   0.0     0.0018   17.8   0.0    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00079   18.9   0.0     0.0014   18.1   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
  ------ inclusion threshold ------
      0.029   13.4   0.0      0.037   13.0   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.057   12.7   0.0       0.13   11.6   0.0    1.5  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.063   12.4   0.0      0.094   11.8   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.069   13.6   0.0       0.11   13.0   0.0    1.3  1  NAD_binding_7    Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9   0.0   2.1e-62   4.2e-59       4     233 ..      24     263 ..      20     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 2.1e-62
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSE...E..EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgae...v..lecDVtdeeqvealveevvekfgklDil 73 
                                        gIG+ iA  l++eGa v +  ++ e+  +++ e+  ++ +++   +   ecDV+d   v+++++ +++ +g   +l
  gi|386001615|ref|YP_005919914.1|  24 TGIGKRIALDLHAEGAYVHILGRRGERllEAKREASSRSAPSDgerFfcHECDVSDHHRVDEVFDSIRDLTGLASGL 100
                                       69****************9999888776555555555555443334468**************************** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHH CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaal 148
                                       v +a+i p+ ++ ++et  ++++++l+vnl+++f+++kaa+  +++ g gsivn+ssvg+ +++   + y+a+K ++
  gi|386001615|ref|YP_005919914.1| 101 VTCAAINPS-RKGITETALDDWRKTLEVNLTGVFNCCKAAVLqMLAGGgGSIVNISSVGGLKAFRTRTSYNASKFGV 176
                                       ********9.******************************995555558**************************** PP

                                       HHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT..HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT-- CS
                      adh_short_C2 149 ealtrylAvelgpkgiRvNavspgpikTlaasgikg..fdelleelearaplgrlgtpeevaeaalfLasdeasyit 223
                                       ++lt ++A ++++++iR Nav+pg+++T++++ + +   +e  ++l   + +grlg+pee+ +a+lfL+s+eas+it
  gi|386001615|ref|YP_005919914.1| 177 VGLTESIALDYAREKIRANAVCPGYVATELTAPLFEkmGEEGFAALVGAHAMGRLGRPEEISRAVLFLLSEEASFIT 253
                                       ******************************9998665577899999******************************* PP

                                       SEEEEESTTG CS
                      adh_short_C2 224 GqtlvvDgGl 233
                                       G  l vDgG+
  gi|386001615|ref|YP_005919914.1| 254 GVALPVDGGY 263
                                       *********9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   0.0   7.4e-55   1.5e-51       1     193 [.      15     213 ..      15     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 7.4e-55
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.....TSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.....gakalaiqvDvtdreevealvekav 72 
                                       k+v+vtG++ GIG+ ia  l +eGa v +++r+ e+l e++ e  +      g+++++ ++Dv+d+++v+++++ ++
  gi|386001615|ref|YP_005919914.1|  15 KTVVVTGGGTGIGKRIALDLHAEGAYVHILGRRGERLLEAKREASSRsapsdGERFFCHECDVSDHHRVDEVFDSIR 91 
                                       79***************************************99988777888899********************** PP

                                       HHHSSESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHH CS
                         adh_short  73 kklgkldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaa 148
                                       + +g    Lv++A+i   ++ + e+  ++w++++evNltgvf++++a++ +ml++ +G+Ivn+sSv g++++   ++
  gi|386001615|ref|YP_005919914.1|  92 DLTGLASGLVTCAAInPSRKGITETALDDWRKTLEVNLTGVFNCCKAAVLQMLAGGGGSIVNISSVGGLKAFRTRTS 168
                                       ***************8778899******************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 149 YsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       Y AsK++v+glt+s+a ++a+++ir nav+PG+v+T+++++l ek
  gi|386001615|ref|YP_005919914.1| 169 YNASKFGVVGLTESIALDYAREKIRANAVCPGYVATELTAPLFEK 213
                                       ***************************************998876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   4.5e-14   8.9e-11       2     151 ..      16     171 ..      15     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 4.5e-14
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS....--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsa..aadedskaliaelealgaevevvaaDvsdkdavealleeik 76 
                                       t+++tGG  g+G+ +a  l ++ga  + +l+R++    +++ +a  ++  + g +  + ++Dvsd++ v +++++i+
  gi|386001615|ref|YP_005919914.1|  16 TVVVTGGGTGIGKRIALDLHAEGA-YVHILGRRGerLLEAKREASSRSAPSDGERFFCHECDVSDHHRVDEVFDSIR 91 
                                       689********************8.578889997443344555567777888************************* PP

                                       HHSS---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HH CS
                                KR  77 aeeppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqan 148
                                       + ++  +G + +A +    k ++e+  +d+++ l+  ++G+ n  ++            +v +SS++gl   +++++
  gi|386001615|ref|YP_005919914.1|  92 DLTGLASGLVTCAAINPsRKGITETALDDWRKTLEVNLTGVFNCCKAAVLqmlaGGGGSIVNISSVGGLKAFRTRTS 168
                                       99999******99998637789*******************998877655233344568999999999999999999 PP

                                       HHH CS
                                KR 149 Yaa 151
                                       Y a
  gi|386001615|ref|YP_005919914.1| 169 YNA 171
                                       987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.1e-07    0.0018       1      96 [.      17     129 ..      17     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.1e-07
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...........EEEE--TT-HHHHHHHHHHH.T. CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...........elveldltdrsalerlfkee.q. 64 
                                       ++VtG+   iG+ ++  l ++g  v+ l r+ ++  +a++e               +e+d+ d+ +++++f++  + 
  gi|386001615|ref|YP_005919914.1|  17 VVVTGGGTGIGKRIALDLHAEGAYVHILGRRGERLLEAKREASsrsapsdgerfFCHECDVSDHHRVDEVFDSIrDl 93 
                                       68*****************************665555555544999******9999***************975222 PP

                                       ...-SEEEE--S.---HHHHHHSHHHHHHHHTHHHH CS
                         Epimerase  65 ...pdavihlAa.vggvaassedpadfieknlqgtl 96 
                                          +   + +Aa   + +   e++ d ++k+l+++l
  gi|386001615|ref|YP_005919914.1|  94 tglASGLVTCAAiNPSRKGITETALDDWRKTLEVNL 129
                                       222233455555444444444444444554444444 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 !   18.1   0.0     7e-07    0.0014       2      75 ..      19      91 ..      18      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7e-07
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-.TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssf.ntgriehlakdpkeeleenlklhkgDltDssslerllaevq 75
                                      +TG+   iG  +a  L ++g  vh++ rr + + +++r ++ ++ p  +  e+++ h++D++D++++++++++++
  gi|386001615|ref|YP_005919914.1| 19 VTGGGTGIGKRIALDLHAEGAYVHILGRRGERLlEAKREASSRSAP--SDGERFFCHECDVSDHHRVDEVFDSIR 91
                                      8888777*******************99886651555555555555..4578*******************9875 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 ?   13.0   0.0   1.9e-05     0.037       1      69 [.      18      92 ..      18     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlD......lrespelleelskvnvkk........viegDvtdkdkleeale 65
                                      vvtGg+  +G+++   L  ++    v++l       l+ +    e +s++            ++e+Dv d+++++e+ +
  gi|386001615|ref|YP_005919914.1| 18 VVTGGGTGIGKRIALDLHAEGA--YVHILGrrgerlLEAKR---EASSRS---ApsdgerffCHECDVSDHHRVDEVFD 88
                                      89***************99995..89999844433322222...333333...133366689***************99 PP

                         3Beta_HSD 66 gvdv 69
                                      ++  
  gi|386001615|ref|YP_005919914.1| 89 SIRD 92
                                      8754 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.13      31      80 ..       9      58 ..       3      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                                      T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCS CS
                     THF_DHG_CYH_C 31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitrea 80
                                      +   + k+vvv G ++ +gk +al L++++a V ++ ++ + l e  rea
  gi|386001615|ref|YP_005919914.1|  9 RCRFTSKTVVVTGGGTGIGKRIALDLHAEGAYVHILGRRGERLLEAKREA 58
                                      556789*********************************99999888877 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05     0.094       1      76 [.      17      90 ..      17     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH.......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeieke.leeelkkkklkveivpvigdvrdkerlekaleel 76
                                      v+vtG+g  iG+++   + ++ +  + +l r   +l e ++e  ++++ ++  +++  +  +dv d++r++++++++
  gi|386001615|ref|YP_005919914.1| 17 VVVTGGGTGIGKRIALDLHAEGAY-VHILGRRGERLLEAKREaSSRSAPSDGERFF--CHECDVSDHHRVDEVFDSI 90
                                      79************9998877665.5556655556666666625556666666555..7889***********9854 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.3e-05      0.11       4      77 ..      11      85 ..       9     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                     NAD_binding_7  4 dlkgkkvlvvGgGe.vAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelner 77
                                      +++ k+v+v GgG+ ++ r +  l ++ga+v+++  + ++ le + +++++ +++d e++++  + ++d++  ++
  gi|386001615|ref|YP_005919914.1| 11 RFTSKTVVVTGGGTgIGKRIALDLHAEGAYVHILGRRGERLLEAKREASSRSAPSDGERFFCHECDVSDHHRVDE 85
                                      6899********976999999****************88888888888888888887777665555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1890.32
//
Query:       gi|386001616|ref|YP_005919915.1|  [L=359]
Description: hypothetical protein Mhar_0921 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-15   57.2   0.7    7.7e-15   55.2   0.1    2.2  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    8.6e-07   28.9   0.0    1.5e-06   28.2   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-06   28.4   0.0    2.2e-06   27.5   0.0    1.4  1  FR47             FR47-like protein
    2.9e-06   27.6   0.2      4e-05   24.0   0.1    2.3  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.7e-06   27.0   0.0    3.7e-05   23.8   0.1    2.5  3  Acetyltransf_9   Acetyltransferase (GNAT) domain
      9e-05   22.5   0.1    0.00017   21.7   0.1    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.001   19.2   0.0     0.0036   17.4   0.0    1.9  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.013   16.2   0.1       0.03   15.0   0.1    1.7  1  Acetyltransf_3   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1   3.4e-18   7.7e-15      34     117 .]      49     134 ..      12     134 .. 0.88
   2 ?    0.3   0.0      0.36     8e+02      34      55 ..     206     233 ..     169     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.4e-18
                                       EEEEEEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHH CS
                    Acetyltransf_1  34 gllvaeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaa 108
                                          vae dg+++G+++ + +    e ++ +y+ ++ Vspe+r++G++++L e++ee ar+ g++ i++ +  +nda+
  gi|386001616|ref|YP_005919915.1|  49 KVAVAEVDGRVAGWAGWTVKEMagEGKRSVYLAEVIVSPEFRRMGVAKRLAEEAEEDARKSGADHIYCFIYGPNDAS 125
                                       56679**********8888888******************************************************* PP

                                       HHHHHH.TTE CS
                    Acetyltransf_1 109 irlYek.lGF 117
                                        rl+ k lG+
  gi|386001616|ref|YP_005919915.1| 126 KRLF-KgLGY 134
                                       ****.88998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                                       EEEEEEET......TEEEEEEEEEEEET CS
                    Acetyltransf_1  34 gllvaeed......geliGfisllkipd 55 
                                        ++va+e       g ++++++l+    
  gi|386001616|ref|YP_005919915.1| 206 NFWVAKEKgddegeGDIVACAGLWDCST 233
                                       4566555555555455888887665544 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   6.5e-10   1.5e-06      30     115 ..      47     143 ..      22     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 6.5e-10
                   Acetyltransf_10  30 ealllvaeeggkivGvi.....elrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvna 93 
                                       + ++ vae++g+++G +     e+           +++ ++V+pe+r+ G++k+L e++ee a+k g  +    +  
  gi|386001616|ref|YP_005919915.1|  47 RWKVAVAEVDGRVAGWAgwtvkEM---AgegkrsvYLAEVIVSPEFRRMGVAKRLAEEAEEDARKSGADHiYCFIYG 120
                                       556889999999999995544433...15556999*******************************99999888888 PP

                   Acetyltransf_10  94 sp.yavpfYeklGFkavgeeqee 115
                                        + + +++++ lG+ +v++ ++ 
  gi|386001616|ref|YP_005919915.1| 121 PNdASKRLFKGLGYSNVSDIKNV 143
                                       8879999*******999887765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   9.8e-10   2.2e-06      22      80 ..      78     137 ..      57     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.8e-10
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                        +l  + v pe+rr+G ++rl+++  ++ ++ g +++   +   N++s rl++ lG+   
  gi|386001616|ref|YP_005919915.1|  78 VYLAEVIVSPEFRRMGVAKRLAEEAEEDARKSGaDHIYCFIYGPNDASKRLFKGLGYSNV 137
                                       57899**************************6626788899999*************865 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.8e-08     4e-05       4      74 ..      49     134 ..      42     136 .. 0.68
   2 ?    1.1   0.0      0.24   5.4e+02       3      23 ..     205     231 ..     203     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.8e-08
                                       EEEEEEETTEEEEEEEEEEES........TCTEEEEE-GGGTTSSHHHHHHHH.TT....SE...EEEEEEEE.... CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld........aeitrlaVdpeyrgkGiGraLlea.ae....kg...iileqlel.... 60 
                                       +v Vae dg++ G ++ ++ +         ++ ++ V+pe+r+ G++++L e  +e    +g   i     +     
  gi|386001616|ref|YP_005919915.1|  49 KVAVAEVDGRVAGWAGWTVKEmagegkrsVYLAEVIVSPEFRRMGVAKRLAEEaEEdarkSGadhI-----YCfiyg 120
                                       5789********988877777987776666666699***************953224444452221.....112232 PP

                                       .THHHHHHHHHHTTE CS
                    Acetyltransf_7  61 .naekaikfYeklGF 74 
                                        n+ ++ ++++ lG+
  gi|386001616|ref|YP_005919915.1| 121 pND-ASKRLFKGLGY 134
                                       322.56668888887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                                       EEEEEEEET......TEEEEEEEEEEE CS
                    Acetyltransf_7   3 gevfVaedd......gkivGfialsll 23 
                                       ++++Va+++      g iv +++l+ +
  gi|386001616|ref|YP_005919915.1| 205 ENFWVAKEKgddegeGDIVACAGLWDC 231
                                       579***999777777777776666654 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   1.6e-08   3.7e-05      28     125 ..      30     134 ..       3     137 .. 0.72
   2 ?   -3.2   0.0       3.9   8.6e+03      38      59 ..     201     228 ..     181     232 .. 0.70
   3 ?   -0.1   0.0       0.4   8.9e+02       4      52 ..     265     307 ..     263     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                                       ......HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHH CS
                    Acetyltransf_9  28 l....eeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlarale 100
                                       +    +e   +  +++++ +v +ae +g+++g ++++  e++  Gk+    +++ V v pe r+ gv+++L ++a e
  gi|386001616|ref|YP_005919915.1|  30 AmgvrKEDVIARYRMYDRWKVAVAEVDGRVAGWAGWTVKEMAGEGKR--SVYLAEVIVSPEFRRMGVAKRLAEEAEE 104
                                       3455323334456899999**********************988874..6799************************ PP

                                       HHHHTT--EEEE--.....SSHHHHHTTT- CS
                    Acetyltransf_9 101 emreegqplsllfP.....ssipiYrrfGy 125
                                       ++r+ g+  ++ f      +s ++++ +Gy
  gi|386001616|ref|YP_005919915.1| 105 DARKSGADHIYCFIygpndASKRLFKGLGY 134
                                       *****8876654421155555666666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                                       HHTTSEEEEEEE......TTEEEEEEEE CS
                    Acetyltransf_9  38 lleesrvlgaed......ngelvgqlal 59 
                                        ++ +++++a +      +g++v++++l
  gi|386001616|ref|YP_005919915.1| 201 GYGLENFWVAKEkgddegEGDIVACAGL 228
                                       5666777777775555555557776665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.4
                                       EE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTE CS
                    Acetyltransf_9   4 elteedldevlellkyaFqdeespleeireyfrklleesrvlgaednge 52 
                                       +++e ++  ++ l +yaF ++++    +    ++ll++ + +++e++ge
  gi|386001616|ref|YP_005919915.1| 265 TVREGEYFTFHYLTDYAFDRKNPGG--M----ENLLSHLNSVLLEEGGE 307
                                       577888888999999***9999985..3....67777777777777665 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   7.4e-08   0.00017      11      58 ..      59     111 ..      47     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.4e-08
                   Acetyltransf_CG  11 evafleYe.....vrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                        ++ + ++      +++  + +  ++V++e+r+ G+Ak+L+++a +dar+ g 
  gi|386001616|ref|YP_005919915.1|  59 VAGWAGWTvkemaGEGKRSVYLAEVIVSPEFRRMGVAKRLAEEAEEDARKSGA 111
                                       555555553333223444889999*************************9985 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0036      51     142 ..      49     142 ..       4     146 .. 0.77
   2 ?   -1.6   0.0       1.2   2.6e+03      90     118 ..     285     313 ..     264     316 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                    Acetyltransf_4  51 vflvae.sdrivGyaylg..qfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnen 124
                                          vae ++r++G a     ++   +k+   + +v +     + +g+++ l +  e+ +++ +   ++  i+ pn++
  gi|386001616|ref|YP_005919915.1|  49 KVAVAEvDGRVAGWAGWTvkEMAGEGKRSVYLAEVIVS-PEFRRMGVAKRLAEEAEEDARKSGADHIYCFIYGPNDA 124
                                       446888899**999965422777767777777778786.6799********************************** PP

                    Acetyltransf_4 125 siqfhkalGFelvgifkk 142
                                       s+ ++k lG+++v + k+
  gi|386001616|ref|YP_005919915.1| 125 SKRLFKGLGYSNVSDIKN 142
                                       *************99887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                    Acetyltransf_4  90 nkeglgrelidaleqvlkeqnienllaei 118
                                       ++ g   +l+ +l  vl e + e+++a++
  gi|386001616|ref|YP_005919915.1| 285 KNPGGMENLLSHLNSVLLEEGGEYFVACL 313
                                       33344457999999999999999999996 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.3e-05      0.03       4     137 ..       4     134 ..       2     135 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                    Acetyltransf_3   4 LrplteeDlealfel.....rsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdle 75 
                                       +rp++e D+e+l ++       d+++   ++  ++++   ++    +      + +  a+ + d++v G++g +  e
  gi|386001616|ref|YP_005919915.1|   4 IRPYEEGDAEKLQKIealspQGDERCA--MGV-RKEDVIARYRM--Y------DRWKVAVAEVDGRVAGWAGWTVKE 69 
                                       677777777777544221111222211..122.21222211111..2......346667766666579999877444 PP

                    Acetyltransf_3  76 eedee....aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                          e        + ++ p+f++ G+a+  ++ + e a ++ g++++++ i   N aS r+++ lG+
  gi|386001616|ref|YP_005919915.1|  70 MAGEGkrsvYLAEVIVSPEFRRMGVAKRLAEEAEEDA-RKSGADHIYCFIYGPNDASKRLFKGLGY 134
                                       3333245865556778899******************.8888**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2410.99
//
Query:       gi|386001617|ref|YP_005919916.1|  [L=111]
Description: AbrB family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0036   17.3   0.1       0.01   15.8   0.1    1.7  1  MraZ            MraZ protein, putative antitoxin-like
     0.0051   16.7   1.8     0.0056   16.6   0.2    1.9  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.043   13.9   0.0       0.14   12.2   0.0    1.7  2  AbrB-like       AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.7e-06      0.01       9      29 ..      29      49 ..      27      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                                      EB-TTSEEE--CHHHHHTTSC CS
                              MraZ  9 elDakGRlllPaklreeakle 29
                                      ++D+ GR+ lP++lr+++kl+
  gi|386001617|ref|YP_005919916.1| 29 KIDDRGRVQLPSNLRRKMKLK 49
                                      79****************998 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.92   5.5e+03      33      42 ..       9      18 ..       6      18 .. 0.73
   2 !   16.6   0.2   9.3e-07    0.0056       2      39 ..      29      67 ..      28      73 .. 0.88
   3 ?   -3.1   0.0       1.3     8e+03      27      34 ..      92      99 ..      88     109 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.92
                                      TTCCCCCCCH CS
                    MazE_antitoxin 33 gdkiilrplk 42
                                      g+ i+++++k
  gi|386001617|ref|YP_005919916.1|  9 GGVIWDKWVK 18
                                      5689998875 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.3e-07
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilr 39
                                      k++  g+v +P  +r+++ ++eGde  +e  g+  iil+
  gi|386001617|ref|YP_005919916.1| 29 KIDDRGRVQLPSNLRRKMKLKEGDEFAVEDLGEdTIILK 67
                                      778899999*******************99999877776 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.3
                                      EEEEECTT CS
                    MazE_antitoxin 27 velevdgd 34
                                       e+e++++
  gi|386001617|ref|YP_005919916.1| 92 REIEEESN 99
                                      56666665 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.14      38      70 .]      33      66 ..      28      66 .. 0.78
   2 ?   -1.0   0.0      0.33     2e+03       4      20 ..      77      93 ..      75     109 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                         AbrB-like 38 nGnLliGsaYTkklgLkpGdefeIk.lgrkhihL 70
                                       G++ + s+  +k+ Lk Gdef ++ lg+++i L
  gi|386001617|ref|YP_005919916.1| 33 RGRVQLPSNLRRKMKLKEGDEFAVEdLGEDTIIL 66
                                      566667777889***********96588888865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.33
                         AbrB-like  4 nAlleAkGikldseakk 20
                                      +A+ +A+ ++ld+ +++
  gi|386001617|ref|YP_005919916.1| 77 DAIEKARSVDLDELERE 93
                                      67778888888876542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 752.36
//
Query:       gi|386001618|ref|YP_005919917.1|  [L=96]
Description: Addiction module toxin, RelE/StbE family, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-08   33.5   0.9    5.5e-08   33.3   0.9    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    1.2e-06   28.3   0.0    1.7e-06   27.9   0.0    1.1  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
    7.8e-06   25.8   0.3      1e-05   25.4   0.3    1.1  1  YoeB_toxin       YoeB-like toxin of bacterial type II toxin-a
  ------ inclusion threshold ------
      0.022   15.2   0.1      0.032   14.6   0.1    1.4  1  HigB-like_toxin  RelE-like toxin of type II toxin-antitoxin s
       0.04   14.2   4.3       0.13   12.6   4.3    1.8  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s


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 !   33.3   0.9   1.5e-11   5.5e-08      13      87 ..      22      89 ..       8      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.5e-11
                                      HHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC...CTTEEEEEEC.TEEEEEEEETSTTEEEEEEEEEHH CS
                        ParE_toxin 13 kiadyiardgpaakrfldaleealellaenpalgrprrelg...lkglrririg.dyriiYriddeelvvvilrvlhrs 87
                                      ++ +         k + ++++++++++ e+p++g+p    +   l g ++i++  +y+i+Y++  ee+vv+ l v h++
  gi|386001618|ref|YP_005919917.1| 22 RLTKK-------DKVLAERIKRKIRDICEYPERGEP----LsgnLAGKWSIHVAdHYVILYEVIHEEKVVRLLSVHHHD 89
                                      44332.......566778888888888899999999....44666799*****99*******977999999******97 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 !   27.9   0.0   4.7e-10   1.7e-06       6      83 ..      19      92 ..      12      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.7e-10
                   ParE-like_toxin  6 rfkkalkklkeklkadldkavkeiiedPelGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGtheNfY 83
                                      +f++  kk  + l++++++++++i+e Pe Ge+  G L+g ++   ++++ ++ + Ye+ ++++v+ ll+v  h+  Y
  gi|386001618|ref|YP_005919917.1| 19 SFRRLTKK-DKVLAERIKRKIRDICEYPERGEPLSGNLAGKWSI--HVAD-HYVILYEVIHEEKVVRLLSVHHHDYAY 92
                                      34444444.3348899************************9975..5555.56677***************9998666 PP

>> YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   2.9e-09     1e-05       5      79 ..      15      88 ..      12      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-09
                                      HHHH.HHHHHCC-HHHHHHHHHHHHHHHHSTTSSTT--EE-SGGGTTEEEEESSSSEEEEEEE..ESSEEEEEESSST CS
                        YoeB_toxin  5 aweD.ylywqeadkkilkkineLikeikRdpfeGiGkPepLkedlsglwsRRideehRlvYlv..eddeltilsaryH 79
                                      +++D +   +++dk ++++i++ i++i+  p +G    epL ++l+g ws  + +   ++Y v  e++ + +ls+++H
  gi|386001618|ref|YP_005919917.1| 15 TFDDsFRRLTKKDKVLAERIKRKIRDICEYPERG----EPLSGNLAGKWSIHVADHYVILYEVihEEKVVRLLSVHHH 88
                                      566647788999******************9888....9**********************97334778899999988 PP

>> HigB-like_toxin  RelE-like toxin of type II toxin-antitoxin system HigB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     9e-06     0.032      52      90 ..      47      85 ..       7      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9e-06
                   HigB-like_toxin 52 klekLkgdlkglySirvNkqyrlifkfkaeeaevvdlyl 90
                                      + e L g+l g +Si+v + y + ++   ee++v+ l +
  gi|386001618|ref|YP_005919917.1| 47 RGEPLSGNLAGKWSIHVADHYVILYEVIHEEKVVRLLSV 85
                                      55889******************9999887777765555 PP

>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.3   3.5e-05      0.13      45      84 ..      48      89 ..       8      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                      -EE-SSS-TTEEEEEEETTEEEEEEE-SS..EEEEEEEE-HH CS
                        YafQ_toxin 45 dHaLkgnwkgyrecHikpDllLiYrledd..elvlvrlGsHs 84
                                        +L+gn++g + +H+++  +++Y++ ++  +++l+++  H+
  gi|386001618|ref|YP_005919917.1| 48 GEPLSGNLAGKWSIHVADHYVILYEVIHEekVVRLLSVHHHD 89
                                      448*********************976654599999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 628.29
//
Query:       gi|386001619|ref|YP_005919918.1|  [L=653]
Description: putative membrane protein, ion channel family [Methanosaeta harundinacea 6Ac]
Scores for complete 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-58  192.7 145.4    4.4e-08   33.2   3.4   10.9 13  Pentapeptide_3  Pentapeptide repeats (9 copies)
      3e-07   29.9  29.8        2.3    7.9   0.7   14.4 13  Pentapeptide    Pentapeptide repeats (8 copies)
    7.4e-06   25.8   9.4    1.4e-05   24.9   9.4    1.5  1  Ion_trans_2     Ion channel


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2   0.00014      0.85      13      44 ..      67      99 ..      63     102 .. 0.80
   2 !   24.5   8.9   3.6e-09   2.2e-05       1      47 [.      88     137 ..      88     138 .. 0.94
   3 !   31.2   4.8   3.1e-11   1.9e-07       3      47 ..     101     148 ..      99     149 .. 0.94
   4 !   31.8   3.8   1.9e-11   1.1e-07       1      47 [.     122     170 ..     122     171 .. 0.97
   5 !   27.6   5.2   3.9e-10   2.4e-06       1      47 [.     167     215 ..     167     216 .. 0.94
   6 !   30.5   3.0     5e-11     3e-07       1      41 [.     212     254 ..     212     258 .. 0.94
   7 !   18.3   1.6   3.1e-07    0.0019       8      36 ..     254     284 ..     253     289 .. 0.86
   8 !   33.1   7.7   7.8e-12   4.7e-08       3      47 ..     283     330 ..     281     331 .. 0.93
   9 !   31.8   5.4   1.9e-11   1.1e-07       1      47 [.     327     375 ..     327     376 .. 0.97
  10 !   33.2   3.4   7.3e-12   4.4e-08       1      46 [.     349     397 ..     349     398 .. 0.96
  11 !   31.6   4.1   2.2e-11   1.3e-07       1      47 [.     372     420 ..     372     421 .. 0.96
  12 !   29.8   6.3   7.9e-11   4.7e-07       1      47 [.     395     443 ..     395     444 .. 0.97
  13 !   27.1   4.6   5.6e-10   3.4e-06       1      47 [.     429     476 ..     429     477 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                    Pentapeptide_3 13 rgatFsgaasFsnadF.gsadFsgarFtgdvdF 44
                                      +++  ++ + F n  F + ++F g++F+  ++F
  gi|386001619|ref|YP_005919918.1| 67 TNSEIRSEVKFYNVKFqEQITFLGTNFDVSTNF 99
                                      677788888899999988999999999866777 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.6e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF..gsadFsgarFtgd.vdFsga 47 
                                       F g+nF+ +++F +a F+g+a F+ a F  g  +F ga Ftg+ ++F+ga
  gi|386001619|ref|YP_005919918.1|  88 FLGTNFDVSTNFMRAKFNGDAKFDKAKFtgGITNFWGAEFTGAnCRFKGA 137
                                       6699*************************66****************998 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 3.1e-11
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaa.sFsnadF.g.sadFsgarFtgdvdFsga 47 
                                       +a F g+a F++a F+g++ +F +a F g +++F ga F + +dF+ a
  gi|386001619|ref|YP_005919918.1| 101 RAKFNGDAKFDKAKFTGGItNFWGAEFtGaNCRFKGAEFGKYADFRYA 148
                                       799****************99*******88**********99***976 PP

  == domain 4  score: 31.8 bits;  conditional E-value: 1.9e-11
                    Pentapeptide_3   1 FsganFsga.adFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F ga+F+ga ++F ga F + a+F+ a F g  +F ga F gd+ F+g+
  gi|386001619|ref|YP_005919918.1| 122 FWGAEFTGAnCRFKGAEFGKYADFRYAKFaGYGNFKGAKFGGDAKFEGS 170
                                       889********************************************98 PP

  == domain 5  score: 27.6 bits;  conditional E-value: 3.9e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaa.sFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F+g++F+  a+F +a F g++  F++a+F ++a F +a F   ++F ga
  gi|386001619|ref|YP_005919918.1| 167 FEGSEFEEIANFMEAKFAGGIaGFRGANFgRDALFGRAEFREYCSFVGA 215
                                       99*******************99******55**********88***998 PP

  == domain 6  score: 30.5 bits;  conditional E-value: 5e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaa.sFsnadF.gsadFsgarFtgd 41 
                                       F+ga+F g a F ++ F+g + +F+na F g a+F++a Ft +
  gi|386001619|ref|YP_005919918.1| 212 FVGAEFGGIAIFKETKFTGKIaDFRNAKFiGYANFRRAKFTSG 254
                                       99**************************************966 PP

  == domain 7  score: 18.3 bits;  conditional E-value: 3.1e-07
                    Pentapeptide_3   8 gaadFrgatFsgaa.sFsnadF.gsadFsga 36 
                                       g a+F +a F++++ +F+++ F g+a+F ga
  gi|386001619|ref|YP_005919918.1| 254 GRAYFVEAKFISGTaDFRESEFgGNATFMGA 284
                                       7789999999999999999999779999998 PP

  == domain 8  score: 33.1 bits;  conditional E-value: 7.8e-12
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaa.sFsnadF.gsadFsgarFtgd.vdFsga 47 
                                       ga+++ +a+Frga F+g++ +Fs+a F g a+F garFtg+ + F+ a
  gi|386001619|ref|YP_005919918.1| 283 GAELRSTANFRGAKFTGGTaDFSGAEFgGKATFIGARFTGGdAYFGKA 330
                                       8999***********************88***********99999876 PP

  == domain 9  score: 31.8 bits;  conditional E-value: 1.9e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgd.vdFsga 47 
                                       F  a F g+++F +a F  +asF +a + ++a+F +a Ftg+ +dFsga
  gi|386001619|ref|YP_005919918.1| 327 FGKAKFGGDVHFGRAEFGEDASFVEAELlSTANFGEAKFTGGtADFSGA 375
                                       7899*******************************************98 PP

  == domain 10  score: 33.2 bits;  conditional E-value: 7.3e-12
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaa.sFsnadF.gsadFsgarFtgd.vdFsg 46 
                                       F++a++  +a+F +a F+g++ +Fs+a F g a F++a Ftg+ + F+g
  gi|386001619|ref|YP_005919918.1| 349 FVEAELLSTANFGEAKFTGGTaDFSGAEFgGKAYFREAKFTGGdAKFEG 397
                                       899**************************88************999998 PP

  == domain 11  score: 31.6 bits;  conditional E-value: 2.2e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaas..FsnadFg.sadFsgarFtgd.vdFsga 47 
                                       Fsga+F g a+Fr+a F+g+ +  F++  F+ sa+F ga F+ + ++Fsga
  gi|386001619|ref|YP_005919918.1| 372 FSGAEFGGKAYFREAKFTGG-DakFEGVEFSwSATFMGAKFN-WyANFSGA 420
                                       9*******************.888******99**********.99****98 PP

  == domain 12  score: 29.8 bits;  conditional E-value: 7.9e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF..gsadFsgarFtgdvdFsga 47 
                                       F+g++Fs +a+F ga F+  a+Fs+a F  g+adF++a F g ++F+++
  gi|386001619|ref|YP_005919918.1| 395 FEGVEFSWSATFMGAKFNWYANFSGAKFtaGTADFRKAEFGGVANFGRV 443
                                       99***************************99**********99***987 PP

  == domain 13  score: 27.1 bits;  conditional E-value: 5.6e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F+ a+F g a+F ++ F  +a F++a F g+a+F   +F+++v+F++a
  gi|386001619|ref|YP_005919918.1| 429 FRKAEFGGVANFGRVEFGEDAIFEEAEFgGNAHFNQDQFHKWVSFKDA 476
                                       899*************************88****************98 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.3    0.0017        10      16      37 ..     108     131 ..      96     131 .. 0.63
   2 !    6.9   0.1   0.00082       4.9      16      28 ..     120     132 ..     106     139 .. 0.67
   3 ?    0.7   0.0     0.071   4.3e+02       7      15 ..     144     152 ..     141     174 .. 0.59
   4 ?    0.2   0.0       0.1   6.3e+02      21      21 ..     176     176 ..     155     187 .. 0.53
   5 ?   -1.8   0.0      0.44   2.6e+03      23      28 ..     190     195 ..     188     197 .. 0.44
   6 ?   -2.7   0.0      0.84     5e+03      11      16 ..     210     215 ..     198     219 .. 0.57
   7 ?   -3.0   0.0         1   6.1e+03      32      40 .]     222     230 ..     221     230 .. 0.31
   8 !    6.6   0.1     0.001         6       6      24 ..     233     252 ..     233     262 .. 0.63
   9 !    7.9   0.7   0.00039       2.3      15      35 ..     278     299 ..     268     311 .. 0.83
  10 !    6.8   0.4   0.00089       5.3       6      35 ..     290     322 ..     290     325 .. 0.46
  11 ?    2.7   0.1     0.017     1e+02      16      25 ..     358     367 ..     345     379 .. 0.53
  12 !    3.7   1.6    0.0085        51      18      18 ..     400     400 ..     354     424 .. 0.58
  13 !    4.2   0.2    0.0055        33      16      24 ..     415     423 ..     403     437 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0017
                                       CCCESEEECT..-B-TT-EECCEE CS
                      Pentapeptide  16 anlsgAnLtg..AnlsgAdLsgan 37 
                                       a +  A++tg  +n+ gA ++gan
  gi|386001619|ref|YP_005919918.1| 108 AKFDKAKFTGgiTNFWGAEFTGAN 131
                                       556666666633477777777776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00082
                                       CCCESEEECT-B- CS
                      Pentapeptide  16 anlsgAnLtgAnl 28 
                                       +n+ gA +tgAn+
  gi|386001619|ref|YP_005919918.1| 120 TNFWGAEFTGANC 132
                                       5666666666666 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.071
                                       B-CCSCCEE CS
                      Pentapeptide   7 nLsganLsg 15 
                                       +++ a++ g
  gi|386001619|ref|YP_005919918.1| 144 DFRYAKFAG 152
                                       333333332 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.1
                                       E CS
                      Pentapeptide  21 A 21 
                                       A
  gi|386001619|ref|YP_005919918.1| 176 A 176
                                       2 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 0.44
                                       ECT-B- CS
                      Pentapeptide  23 LtgAnl 28 
                                       ++gAn+
  gi|386001619|ref|YP_005919918.1| 190 FRGANF 195
                                       222222 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 0.84
                                       SCCEEC CS
                      Pentapeptide  11 anLsga 16 
                                       +++ ga
  gi|386001619|ref|YP_005919918.1| 210 CSFVGA 215
                                       333333 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 1
                                       EECCEEECT CS
                      Pentapeptide  32 dLsganLsg 40 
                                        +++++++g
  gi|386001619|ref|YP_005919918.1| 222 IFKETKFTG 230
                                       333333333 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.001
                                       -B-CCSCCEE.CCCESEEEC CS
                      Pentapeptide   6 AnLsganLsg.anlsgAnLt 24 
                                       A++++a++ g an+++A++t
  gi|386001619|ref|YP_005919918.1| 233 ADFRNAKFIGyANFRRAKFT 252
                                       45555555544555555555 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.00039
                                       ECCCESEEECT-.B-TT-EECC CS
                      Pentapeptide  15 ganlsgAnLtgA.nlsgAdLsg 35 
                                       +a + gA L+++ n++gA+++g
  gi|386001619|ref|YP_005919918.1| 278 NATFMGAELRSTaNFRGAKFTG 299
                                       6788888888888888888887 PP

  == domain 10  score: 6.8 bits;  conditional E-value: 0.00089
                                       -B-CCSCCEE..CCCESEEECT.-B-TT-EECC CS
                      Pentapeptide   6 AnLsganLsg..anlsgAnLtg.AnlsgAdLsg 35 
                                       An++ga+++g  a++sgA + g A+++gA+++g
  gi|386001619|ref|YP_005919918.1| 290 ANFRGAKFTGgtADFSGAEFGGkATFIGARFTG 322
                                       455555555544555555553224555555544 PP

  == domain 11  score: 2.7 bits;  conditional E-value: 0.017
                                       CCCESEEECT CS
                      Pentapeptide  16 anlsgAnLtg 25 
                                       an+ +A++tg
  gi|386001619|ref|YP_005919918.1| 358 ANFGEAKFTG 367
                                       3333333333 PP

  == domain 12  score: 3.7 bits;  conditional E-value: 0.0085
                                       C CS
                      Pentapeptide  18 l 18 
                                       +
  gi|386001619|ref|YP_005919918.1| 400 F 400
                                       1 PP

  == domain 13  score: 4.2 bits;  conditional E-value: 0.0055
                                       CCCESEEEC CS
                      Pentapeptide  16 anlsgAnLt 24 
                                       an+sgA++t
  gi|386001619|ref|YP_005919918.1| 415 ANFSGAKFT 423
                                       444444444 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   9.4   2.4e-09   1.4e-05       2      76 ..     577     650 ..     576     653 .] 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.4e-09
                                       HHHHTCHHHHHHHHT....T.---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   2 vlllvlifgaviysleegwe.kwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkv 76 
                                       ++l+v++f++ + ++ + +e +  ++d ++fs+ t  T GY  + p++++ +++t + +++G ++ a+f+a++++ 
  gi|386001619|ref|YP_005919918.1| 577 WILMVFLFASYYWYF-DAVEgTSAWFDYIWFSIATSATPGYALYNPIGHY-KIVTGIQAIIGTFMWAAFIATFARK 650
                                       567777777777777.444446799*************************.*********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4736.38
//
Query:       gi|386001620|ref|YP_005919919.1|  [L=491]
Description: hypothetical protein Mhar_0925 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-26   90.7  81.7    1.1e-09   38.3   3.2    7.2  7  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.22   11.2   1.7        0.4   10.3   1.7    1.4  1  Prok-E2_D       Prokaryotic E2 family D
       0.25   11.4  16.3          2    8.4  14.8    2.8  2  Ion_trans_2     Ion channel
          6    6.6  35.0        2.3    7.9   0.6    9.8  9  Pentapeptide    Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   3.2   2.4e-13   1.1e-09       2      47 ..      68     114 ..      67     115 .. 0.94
   2 !   17.0   5.7   1.1e-06    0.0049       1      33 [.     111     144 ..     111     145 .. 0.94
   3 !   18.8  11.5     3e-07    0.0013       5      47 ..     148     193 ..     147     193 .. 0.93
   4 !   22.8   6.8   1.7e-08   7.6e-05       8      44 ..     186     225 ..     185     226 .. 0.93
   5 !   18.1   8.8   4.8e-07    0.0022       1      45 [.     237     282 ..     237     283 .. 0.95
   6 !   21.9   4.3   3.3e-08   0.00015       4      39 ..     279     315 ..     277     322 .. 0.90
   7 ?   -2.6   0.4       1.5   6.7e+03      30      41 ..     434     445 ..     429     451 .. 0.45

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.4e-13
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       ++++ +g ++F++a+F+ +++F++a F g+a+F ga Ftg+++F++a
  gi|386001620|ref|YP_005919919.1|  68 TNSEIKGKVNFSNARFQEPINFNGAYFgGDASFIGAKFTGNASFTEA 114
                                       689999*********************88***************998 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.1e-06
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadF 33 
                                       F++anF g++ F +a Fsg+a+F +a Fg +a F
  gi|386001620|ref|YP_005919919.1| 111 FTEANFAGSVCFGEAEFSGDAYFFRAKFGwDAKF 144
                                       99**************************978766 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 3e-07
                    Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadF..gsadFsgarFtgd.vdFsga 47 
                                        F g+a+F  a F + a+F +a+F  g+a+F +a Ftg+ ++F ga
  gi|386001620|ref|YP_005919919.1| 148 KFCGCANFNAAKFGKNADFASAVFsdGGAHFTDAKFTGGdARFQGA 193
                                       5779*********************88************9***986 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 1.7e-08
                    Pentapeptide_3   8 gaadFrgatFsgaasFsnadF..gsadFsgarFtgd.vdF 44 
                                       g+a+F ga F g a+F  a F  g+a+F+ a F+g+ ++F
  gi|386001620|ref|YP_005919919.1| 186 GDARFQGAKFAGNANFVKAEFagGDANFAYAVFSGGnANF 225
                                       789*******************66***********98888 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 4.8e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                       F +a+F g+a F g+tF + a+F +a F g+a+F  a+  g+++F+
  gi|386001620|ref|YP_005919919.1| 237 FIDAEFGGNALFMGSTFGRIAFFIDAKFrGDATFGAANLGGAATFG 282
                                       6689************************99**********99*997 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 3.3e-08
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFg.sadFsgarFt 39 
                                       a+F  +adF ga Fsg a Fs+a Fg  a+F +a F+
  gi|386001620|ref|YP_005919919.1| 279 ATFGADADFGGAKFSGEAGFSGAKFGaYANFMKAEFD 315
                                       79999********************77*********9 PP

  == domain 7  score: -2.6 bits;  conditional E-value: 1.5
                    Pentapeptide_3  30 sadFsgarFtgd 41 
                                       s  Fs  +Ftg+
  gi|386001620|ref|YP_005919919.1| 434 SFYFSIMTFTGG 445
                                       444444444443 PP

>> Prok-E2_D  Prokaryotic E2 family D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7     9e-05       0.4     100     152 ..     117     170 ..     108     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9e-05
                         Prok-E2_D 100 sgsiClGnaekPkasaake.leaweelFfsSeFthpN.lvkykggakpealwkdl 152
                                        gs+C+G+ae + +  + + +  w++ F+ ++F         k g+ ++++ +++
  gi|386001620|ref|YP_005919919.1| 117 AGSVCFGEAEFSGDAYFFRaKFGWDAKFWITKFCGCAnFNAAKFGK-NADFASAV 170
                                       69********9999988885889**********9854144444444.66666665 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   4.7      0.14   6.1e+02      30      70 ..     391     429 ..     377     432 .. 0.68
   2 ?    8.4  14.8   0.00045         2       5      78 ..     416     490 ..     409     491 .] 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.14
                                       HHHHHHHTTS----SSTT.-----HHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  30 YfsfvtltTiGYGdivpe.tdagrlftivyillGlalfalfl 70 
                                       ++ +++  + GYG + p  t +   +  v+ ++G++++++f 
  gi|386001620|ref|YP_005919919.1| 391 FMDIISWISCGYG-VRPLhTVL--SIFGVVFIIGIIFLGYFD 429
                                       5567888999***.99996666..334444456777766665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00045
                                       HTCHHHHHHHHT....T---HHHHHHHHHHHHT......TS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   5 lvlifgaviysleegwekwsfldalYfsfvtlt......TiGYGdivpetdagrlftivyillGlalfalflavlgk 75 
                                       +v+i+g+++  +  +    s+++++Yfs++t+t      T G  di  e+ + r +++++++lG++l+alf+ vl++
  gi|386001620|ref|YP_005919919.1| 416 VVFIIGIIFLGY--F---DSIFESFYFSIMTFTgglitfTGGEADILIEERWLRSLAMIEAILGYLLMALFVVVLAR 487
                                       334444444433..3...59************966666677888888888888**********************99 PP

                                       HHH CS
                       Ion_trans_2  76 vlt 78 
                                        ++
  gi|386001620|ref|YP_005919919.1| 488 KFI 490
                                       875 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.004        18      16      33 ..      76      94 ..      74      96 .. 0.83
   2 ?    7.9   0.6   0.00052       2.3       5      34 ..      97     128 ..      96     129 .. 0.67
   3 ?    2.3   3.0      0.03   1.3e+02      15      25 ..     175     185 ..     150     197 .. 0.63
   4 ?    2.4   3.5     0.028   1.3e+02      16      31 ..     188     204 ..     175     224 .. 0.52
   5 ?   -0.7   0.0      0.27   1.2e+03      25      36 ..     222     233 ..     221     234 .. 0.77
   6 ?   -2.6   0.0         1   4.6e+03      18      24 ..     259     265 ..     257     266 .. 0.32
   7 ?   -1.6   0.2      0.51   2.3e+03       6      16 ..     268     278 ..     267     279 .. 0.64
   8 ?    2.2   0.0     0.032   1.4e+02       6      15 ..     285     294 ..     283     303 .. 0.61
   9 ?   -2.3   0.0      0.82   3.7e+03      21      28 ..     307     314 ..     306     316 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.004
                                      CCCESEEECT-.B-TT-EE CS
                      Pentapeptide 16 anlsgAnLtgA.nlsgAdL 33
                                      +n+s+A +++  n++gA +
  gi|386001620|ref|YP_005919919.1| 76 VNFSNARFQEPiNFNGAYF 94
                                      7999999999999999876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00052
                                       T-B-CCSCCE.ECCCESEEECT-.B-TT-EEC CS
                      Pentapeptide   5 gAnLsganLs.ganlsgAnLtgA.nlsgAdLs 34 
                                       +A + ga+++ +a++++An+ g+  +  A +s
  gi|386001620|ref|YP_005919919.1|  97 DASFIGAKFTgNASFTEANFAGSvCFGEAEFS 128
                                       56777777763488888888887666666666 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.03
                                       ECCCESEEECT CS
                      Pentapeptide  15 ganlsgAnLtg 25 
                                       ga++++A++tg
  gi|386001620|ref|YP_005919919.1| 175 GAHFTDAKFTG 185
                                       45555555554 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.028
                                       CCCESEEECT-.B-TT- CS
                      Pentapeptide  16 anlsgAnLtgA.nlsgA 31 
                                       a + gA++ g  n+ +A
  gi|386001620|ref|YP_005919919.1| 188 ARFQGAKFAGNaNFVKA 204
                                       33333333333333333 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.27
                                       T-B-TT-EECCE CS
                      Pentapeptide  25 gAnlsgAdLsga 36 
                                       +An+ ++ ++g 
  gi|386001620|ref|YP_005919919.1| 222 NANFLWTEFNGG 233
                                       688988888875 PP

  == domain 6  score: -2.6 bits;  conditional E-value: 1
                                       CESEEEC CS
                      Pentapeptide  18 lsgAnLt 24 
                                       + +A+++
  gi|386001620|ref|YP_005919919.1| 259 FIDAKFR 265
                                       3333333 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 0.51
                                       -B-CCSCCEEC CS
                      Pentapeptide   6 AnLsganLsga 16 
                                       A +  anL ga
  gi|386001620|ref|YP_005919919.1| 268 ATFGAANLGGA 278
                                       66677777665 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.032
                                       -B-CCSCCEE CS
                      Pentapeptide   6 AnLsganLsg 15 
                                       A++ ga++sg
  gi|386001620|ref|YP_005919919.1| 285 ADFGGAKFSG 294
                                       4444444433 PP

  == domain 9  score: -2.3 bits;  conditional E-value: 0.82
                                       EEECT-B- CS
                      Pentapeptide  21 AnLtgAnl 28 
                                       An+ +A++
  gi|386001620|ref|YP_005919919.1| 307 ANFMKAEF 314
                                       34444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 3761.03
//
Query:       gi|386001621|ref|YP_005919920.1|  [L=340]
Description: Methylthioribose-1-phosphate isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-81  271.4   0.0    8.9e-81  271.2   0.0    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.2   0.0     5e-85   8.9e-81       2     282 .]      45     333 ..      44     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 5e-85
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       vrG+pa++ a+ ++++ ++ ++ +++ a L +++r+a+ ++++arPtav+l++ ++r+ k++ e+  s+ v+e++++
  gi|386001621|ref|YP_005919920.1|  45 VRGAPALGAAGGYGVALAAARSAATNPAALLHDVREAAGVIRAARPTAVNLSWGVDRAVKAVDEMGGSAGVEEIRAA 121
                                       8**************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG 147
                                       ++ +++ ++ e++ ++++ gd +a l++dgd++lT+cn++         +l+v+r+a+ e+kk++V+ +E+rP  qG
  gi|386001621|ref|YP_005919920.1| 122 ALAAAELIAGEDVSINRALGDRGARLLEDGDVVLTHCNAGRlacvgwgtALGVIRSAVAEGKKISVYSCETRPLHQG 198
                                       ***************************************************************************** PP

                                       .HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGB CS
                             IF-2B 148 .rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkf 222
                                        rlta+eL++++ipvtli ds++++vm++ ++dkvivGAdri+++  ++nkiGT++ AvlA+++ ip++v+a+ ++f
  gi|386001621|ref|YP_005919920.1| 199 sRLTAWELSEDNIPVTLICDSMAGMVMRQgKIDKVIVGADRITRDA-VFNKIGTYTHAVLARAHGIPFYVAAPISTF 274
                                       *********************************************9.****************************** PP

                                       ESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 223 servqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       +   + ++++ ieerd++e+ +  +++ a+  ++v+npafD tP +l+t+iITe G++ p
  gi|386001621|ref|YP_005919920.1| 275 DLA-HSEKEVEIEERDADEIRRLGERQLAPPGVEVYNPAFDATPLDLVTAIITERGIFRP 333
                                       *99.89999999*********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2417.84
//
Query:       gi|386001622|ref|YP_005919921.1|  [L=230]
Description: Ribose 5-phosphate isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-61  206.7   0.0    2.4e-61  206.3   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    6.5e-07   29.4   0.4    5.8e-05   23.1   0.0    2.3  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.081   12.0   0.1       0.12   11.5   0.1    1.2  1  Sugar-bind      Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.3   0.0   4.1e-65   2.4e-61       2     168 ..      56     219 ..      55     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 4.1e-65
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       gvptS+q++ela ++gipl+sld+ + +dlaiDGaDe+++dl++iKGgG+a+ rEK+vaa+a+ f+++ad+sK+v++
  gi|386001622|ref|YP_005919921.1|  56 GVPTSYQAQELAIAAGIPLTSLDQDPVLDLAIDGADEIAKDLTAIKGGGAAHAREKVVAASARWFVIVADSSKYVDS 132
                                       8**************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l  +pvPveVlp a +   r++e+l gg+p++R+ak+kdgpv+Tdngn+++D++f ++iedp  l+++l++ipGVve
  gi|386001622|ref|YP_005919921.1| 133 LS-HPVPVEVLPIAGRLASRRIEEL-GGSPQIRQAKMKDGPVITDNGNFVIDADF-GRIEDPGGLAARLSEIPGVVE 206
                                       *6.9*******************75.*****************************.6788***************** PP

                                       ESEE-S--SEEEE CS
                    Rib_5-P_isom_A 156 tGlFlgladkvlv 168
                                       +G+F ++ + v+v
  gi|386001622|ref|YP_005919921.1| 207 HGIFENVNELVVV 219
                                       ******9998876 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   9.7e-09   5.8e-05       2      40 ..       8      46 ..       7      55 .. 0.93
   2 !    4.5   0.1     0.005        30     117     139 ..     107     129 ..      47     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.7e-09
                             DeoRC  2 naeeKrrIAkaAaeliedgdtifldaGtTtlelaraLae 40
                                      na eKr+ ++aAa +++dg+++ l++G+T+++ ++++ e
  gi|386001622|ref|YP_005919921.1|  8 NAGEKRAAGEAAAGMVRDGMVLGLGTGSTVAWTIKKIGE 46
                                      788******************************999865 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.005
                             DeoRC 117 aevkralieaarrvillaDssKf 139
                                        + ++ ++++ar  +++aDssK+
  gi|386001622|ref|YP_005919921.1| 107 HAREKVVAASARWFVIVADSSKY 129
                                       4456677888889999******8 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     2e-05      0.12      40      79 ..      13      52 ..       2      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                                      HHHHHHHHHH--TTEEEEE-SSHHHHHHHHHTHHCCHTCE CS
                        Sugar-bind 40 raaaqllesllkdgdvvgvgwGrtlsavaealtpkslrdv 79
                                      raa++    +++dg+v+g+g+G t++ +++++ ++  +++
  gi|386001622|ref|YP_005919921.1| 13 RAAGEAAAGMVRDGMVLGLGTGSTVAWTIKKIGEMVEEGM 52
                                      456666667899******************9988666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1717.26
//
Query:       gi|386001623|ref|YP_005919922.1|  [L=537]
Description: O-phosphoseryl-tRNA(Cys) synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-51  173.9   0.0    1.4e-48  165.5   0.0    2.2  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    6.9e-14   51.6   0.3    1.4e-13   50.6   0.3    1.6  1  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
      4e-07   29.7   0.0    7.1e-05   22.4   0.0    2.3  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
       0.12   12.4   0.1        0.3   11.1   0.1    1.6  1  Lambda_Bor       Bor protein
       0.15   11.1   0.0         11    5.0   0.0    2.1  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
       0.17   11.9   0.0       0.38   10.7   0.0    1.6  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0021       6.3       5      47 ..      35      77 ..      31      88 .. 0.85
   2 !  165.5   0.0   4.7e-52   1.4e-48      14     237 ..     119     352 ..     104     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0021
                                      SSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHH CS
                      tRNA-synt_2d  5 tlpgkrieagklhpltkvleeikeiflelgfeevegpevesef 47
                                       +p +  + g+ hp+ +v+ +++e +l+lgf e+ +p + ++ 
  gi|386001623|ref|YP_005919922.1| 35 RYPRRVSSYGRPHPIFDVIGRLREAYLRLGFDEAINPLIVEDS 77
                                      566677788999**********************999987665 PP

  == domain 2  score: 165.5 bits;  conditional E-value: 4.7e-52
                                       SB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHH CS
                      tRNA-synt_2d  14 gklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttav 90 
                                        +++  ++ ++ +++i++ +++  veg+++   + +  aL  ++      ++++F+  +   +++++++LR+h+t+ 
  gi|386001623|ref|YP_005919922.1| 119 LGRDLSAEEVDAVRRILHGYKKGTVEGDDL--VHEISAALGASDALVSTLLAEVFPEFEALAPAATTKTLRSHMTSG 193
                                       566777788999**************8887..688999*************************************** PP

                                       HHHHH....TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEE. CS
                      tRNA-synt_2d  91 qirtl....ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrf. 161
                                       +++tl     + ++p+k++si+r+fRr++ +Da +l+++h+++++++de++s++d k+v++ ll ++ g++ k+rf 
  gi|386001623|ref|YP_005919922.1| 194 WFITLgslaGRASLPTKLFSIDRCFRREQsEDAARLMTYHSASCVIMDEDLSVEDGKVVADGLLAQF-GFQ-KFRFl 268
                                       *****99988999****************99************************************.**9.77772 PP

                                       .EECEETTEEEEEEEEEEE.........CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT- CS
                      tRNA-synt_2d 162 .rpsyfpftePsaevdvyl.........vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygi 228
                                        + + ++++ P+++++vy+         ++ +++w+E++++G+++p++l+++++   ++++++GlGveRlam+ yg 
  gi|386001623|ref|YP_005919922.1| 269 pDDKRSKYYVPDTQIEVYAyhpglvgssTKYSTGWVEVATFGIYSPTALSMYDV--PYPVMNLGLGVERLAMILYGA 343
                                       25589*************9*********9*************************..********************* PP

                                       SSGHHHHTT CS
                      tRNA-synt_2d 229 eDiRelven 237
                                       +D+R+l ++
  gi|386001623|ref|YP_005919922.1| 344 KDLRALTYP 352
                                       ******987 PP

>> SepRS_C  O-phosphoseryl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.3   4.8e-17   1.4e-13       1      30 [.     435     464 ..     435     465 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.8e-17
                                       EEEEEETTEEEEEES-TTTCCHHHHSEEEE CS
                           SepRS_C   1 NEvyVYdGnIlGvPdtekwkearenGvsTG 30 
                                       NEv VY+ nIlGvP+t+kw++a+enGv TG
  gi|386001623|ref|YP_005919922.1| 435 NEVLVYKENILGVPKTSKWEDAFENGVTTG 464
                                       *****************************9 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0052        16       4      50 ..      35      81 ..      32      91 .. 0.87
   2 !   22.4   0.0   2.4e-08   7.1e-05      71     208 ..     183     327 ..     176     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0052
                   tRNA_synthFbeta  4 tlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldk 50
                                      + P+ +   g++++ +++  +lr++   +G+ E+i+   v ++e++k
  gi|386001623|ref|YP_005919922.1| 35 RYPRRVSSYGRPHPIFDVIGRLREAYLRLGFDEAINPLIVEDSEVKK 81
                                      67999999999*************************88888887766 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.4e-08
                   tRNA_synthFbeta  71 qsvlRtsLlpglLevlarNlargnedvrlFEigkvflkdseeel..peeerhlaivltgkreeeswsekaravdfyd 145
                                       +++lR+ +++g   +l++   r     +lF i ++f+ +++e+       +  ++v++ ++            +++d
  gi|386001623|ref|YP_005919922.1| 183 TKTLRSHMTSGWFITLGSLAGRASLPTKLFSIDRCFRREQSEDAarLMTYHSASCVIMDED-----------LSVED 248
                                       7899****************999999*************3333311444444555555555...........***** PP

                   tRNA_synthFbeta 146 lkgivealleslgiekvefep..aehpalhpgrsAeikvdgk..............evGvlGelhpevleafdlkqr 206
                                        k +++ ll+++g++k++f p  +  +++ p  + e+++                 ev  +G  +p  l  +d++++
  gi|386001623|ref|YP_005919922.1| 249 GKVVADGLLAQFGFQKFRFLPddKRSKYYVPDTQIEVYAYHPglvgsstkystgwvEVATFGIYSPTALSMYDVPYP 325
                                       *******************9955557888888888885533334444555555666********************9 PP

                   tRNA_synthFbeta 207 vy 208
                                       v+
  gi|386001623|ref|YP_005919922.1| 326 VM 327
                                       86 PP

>> Lambda_Bor  Bor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0001       0.3      56      74 ..     302     320 ..     292     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                        Lambda_Bor  56 gLlgvvTlGIYtPrttkvy 74 
                                       g ++v T+GIY+P+   +y
  gi|386001623|ref|YP_005919922.1| 302 GWVEVATFGIYSPTALSMY 320
                                       66899*********88766 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0037        11      92     112 ..     209     229 ..     205     241 .. 0.83
   2 ?    3.7   0.0    0.0093        28     287     308 ..     329     350 ..     319     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0037
                                       SEEEEEEEEE--S--BTTB-S CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  92 drvfqiaraFRaEdsrtdrhl 112
                                       ++ f+i r+FR E+s+    l
  gi|386001623|ref|YP_005919922.1| 209 TKLFSIDRCFRREQSEDAARL 229
                                       589***********9876555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0093
                                       EEEEHHHHHHHHCT-SSGGGCS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdvi 308
                                       lglG++Rl m+l g+++ r ++
  gi|386001623|ref|YP_005919922.1| 329 LGLGVERLAMILYGAKDLRALT 350
                                       79***************99875 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013      0.38      34      70 ..     206     240 ..     194     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                       GSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  34 rLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvf 70 
                                        LP kl+ i +++R+E+s+     R+  +h   ++++
  gi|386001623|ref|YP_005919922.1| 206 SLPTKLFSIDRCFRREQSEDAA--RLMTYHSASCVIM 240
                                       5****************93333..6666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3609.23
//
Query:       gi|386001624|ref|YP_005919923.1|  [L=426]
Description: hypothetical protein Mhar_0929 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.5   1.0     0.0012   18.5   1.0    2.7  2  MscS_porin       Mechanosensitive ion channel porin domain
     0.0069   15.3  12.3      0.029   13.2   1.3    2.7  3  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.011   15.6   2.6      0.011   15.6   2.6    2.6  3  JAKMIP_CC3       JAKMIP CC3 domain
      0.016   14.3  13.2       0.06   12.4   3.0    2.4  2  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.023   14.7   1.3       0.79    9.7   0.0    3.0  2  FlxA             FlxA-like protein
       0.19   10.3   3.9        1.4    7.4   0.6    2.1  2  AAA_13           AAA domain
       0.67   10.4  17.0       0.78   10.2   3.3    2.7  3  Fez1             Fez1
       0.96    9.3  11.7          1    9.2   1.4    3.6  3  DivIC            Septum formation initiator
        1.1    9.5  19.2       0.46   10.7   3.7    3.0  3  ATG16            Autophagy protein 16 (ATG16)
          2    8.5   9.1       0.59   10.2   0.8    2.7  2  ADIP             Afadin- and alpha -actinin-Binding
        2.6    8.1   9.5        8.3    6.5   1.8    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        5.7    7.0  16.2       0.41   10.7   3.8    3.4  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        7.8    5.8   7.7       0.25   10.7   0.9    1.9  2  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M


Domain annotation for each model (and alignments):
>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.2     0.085   1.2e+02      81     135 ..     161     214 ..     109     251 .. 0.71
   2 !   18.5   1.0   8.5e-07    0.0012     152     201 ..     339     388 ..     326     395 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.085
                        MscS_porin  81 eeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnr 135
                                       +eL   l++++ + + + ++ a++ ++++e + ++e +++++++    l+ +r++
  gi|386001624|ref|YP_005919923.1| 161 SELGDLLQERE-ESLGAHREAASAAARVREGRGQIEALRAEISDGEALLSRLRDE 214
                                       44444444444.4444556667777888888888888888888877777777664 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 8.5e-07
                        MscS_porin 152 talqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelq 201
                                        +l+a+ +al+a+ieele +l      ++ lk++rdl ++ri  le+el+
  gi|386001624|ref|YP_005919923.1| 339 HLLKARHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELE 388
                                       689********************************************997 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   1.0    0.0019       2.6     179     256 ..     124     207 ..      87     224 .. 0.59
   2 !    6.5   3.2    0.0024       3.4     170     239 ..     158     225 ..     115     272 .. 0.54
   3 !   13.2   1.3   2.1e-05     0.029     196     279 ..     333     416 ..     298     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                              Spc7 179 leeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleelee......kieelkeqkseleee 249
                                       l+++++k  +a++  +++ + e+e+++++l +++  ++e+ + l+e++e l + +e      ++ e + q++ l++e
  gi|386001624|ref|YP_005919923.1| 124 LQNTVQKFGRAQRYTAALFPGEVEAIKSDLGAISRHLSELGDLLQEREESLGAHREaasaaaRVREGRGQIEALRAE 200
                                       55555555555556666667777777777777777777777777777766544443000000344444444444444 PP

                              Spc7 250 iaeaerv 256
                                       i+  e +
  gi|386001624|ref|YP_005919923.1| 201 ISDGEAL 207
                                       4444444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0024
                              Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                         l+e  + l+e+ e+l +  +  +++  ++++e r ++++l aei+  ++ l++l+++ +  +e+ie+ 
  gi|386001624|ref|YP_005919923.1| 158 RHLSELGDLLQEREESLGA--HREAASAAARVREGRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAW 225
                                       2222222222222222222..1123345555555555555555555555555555555555555555554 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 2.1e-05
                              Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlk 272
                                       ++   L+ l+ + ++l aeiee+++ l+++  + ++l++k + +++++s+le+e++  +r l   ++  + ++s lk
  gi|386001624|ref|YP_005919923.1| 333 LEDRPLHLLKARHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELEDRRRSLALLEDRLSGDLSDLK 409
                                       44667999999999999999999999999999999999999999999999999999999999999999999999999 PP

                              Spc7 273 eevkale 279
                                        +++++ 
  gi|386001624|ref|YP_005919923.1| 410 GRLEEIA 416
                                       9998875 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   5.2       2.9   4.1e+03      92     167 ..     169     254 ..     152     262 .. 0.71
   2 ?   -0.3   0.4      0.64   8.9e+02     104     143 ..     242     282 ..     233     286 .. 0.75
   3 ?   15.6   2.6   8.3e-06     0.011     105     176 ..     333     409 ..     318     415 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.9
                        JAKMIP_CC3  92 lLreklggeldaere.lkareqleselrktkskikdLeeaLaqkGqdskwveekQalikrnqe..........Lvek 157
                                       +  e+lg++++a +  ++ re  + +++  +++i+d e+ L++   +  + +e      r  e          L ek
  gi|386001624|ref|YP_005919923.1| 169 EREESLGAHREAASAaARVRE-GRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWSRSDEgrrgreekryLEEK 244
                                       446789999988765156777.7889999999999999999988666666666655555555566777777777777 PP

                        JAKMIP_CC3 158 ikkleeeesk 167
                                       +++ ++ e+ 
  gi|386001624|ref|YP_005919923.1| 245 MRERDQIEMS 254
                                       7776666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                        JAKMIP_CC3 104 erelkareqleselrktkskikd.LeeaLaqkGqdskwvee 143
                                       e+++++r+q+e+ +r   + +++ L +a +q  +d   ++ 
  gi|386001624|ref|YP_005919923.1| 242 EEKMRERDQIEMSMRDLVAPLAKaLSRAVKQDDSDRIALQH 282
                                       78999999999999999887644377777777777666665 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 8.3e-06
                        JAKMIP_CC3 105 relkareqleselrktkskikdLeeaLaqkGqdskwveekQalikrnqe.....LvekikkleeeeskLkqeiqdlr 176
                                        e +    l++  +  +++i++Lee+L+++G d+  ++ k  l+++        L ++ ++l   e +L  +++dl+
  gi|386001624|ref|YP_005919923.1| 333 LEDRPLHLLKARHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISsleaeLEDRRRSLALLEDRLSGDLSDLK 409
                                       5556666678888899****************************9987667777*********************98 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.6    0.0018       2.4      47     139 ..     165     257 ..     144     293 .. 0.73
   2 ?   12.4   3.0   4.4e-05      0.06      49     127 ..     333     414 ..     301     421 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                             Atg14  47 kalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqn 123
                                       ++l+++ee+  + +++ + +a+++e + +i+ lr++++  ++ ls+l++e +  ++++++ s++   Rr + e+ + 
  gi|386001624|ref|YP_005919923.1| 165 DLLQEREESLGAHREAASAAARVREGRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWSRSDEGRRGREEKRYL 241
                                       34444445555566888899999999999999999999999999999999999999999999998888888788888 PP

                             Atg14 124 eleerrkkqiaklqda 139
                                       e + r+++qi++  ++
  gi|386001624|ref|YP_005919923.1| 242 EEKMRERDQIEMSMRD 257
                                       8888888888765554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.4e-05
                             Atg14  49 legke......eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdle 119
                                       le +       + + l+++i+ + ++l++   ++a+l+++  ++++++s+l +e+e++++ la l d l+    dl+
  gi|386001624|ref|YP_005919923.1| 333 LEDRPlhllkaRHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELEDRRRSLALLEDRLS---GDLS 406
                                       3333344444444777888888888888888888888888888888888888888888888888888886...4444 PP

                             Atg14 120 slqnelee 127
                                        l+ +lee
  gi|386001624|ref|YP_005919923.1| 407 DLKGRLEE 414
                                       45555444 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.17   2.3e+02      18      46 ..     193     221 ..     176     284 .. 0.60
   2 ?    9.7   0.0   0.00057      0.79      20      67 ..     346     389 ..     338     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                              FlxA  18 qiasLqkQiknlqkqLkelsesdeltkee 46 
                                       qi++L+ +i++ +  L+ l ++++  +ee
  gi|386001624|ref|YP_005919923.1| 193 QIEALRAEISDGEALLSRLRDEEAGHQEE 221
                                       44445544444444444444444433333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00057
                              FlxA  20 asLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaq 67 
                                       ++L+ +i++l+++L++ + +    +   k++++l+ + I++l+a+++ 
  gi|386001624|ref|YP_005919923.1| 346 SALTAEIEELEESLSKRGGD----TARLKAKRDLVRQRISSLEAELED 389
                                       45555666666655555555....444779**************9975 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6     0.001       1.4     292     404 ..     113     227 ..     107     285 .. 0.72
   2 ?    4.1   0.2      0.01        14     409     466 ..     343     400 ..     303     416 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
                            AAA_13 292 iekveskkselleklkavsde...asensa..feedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkak 363
                                       +e++ s++   l+ l++ +++   a+++ a  f  ++e +k+ + a++  L +l + l+++ + + ++ e  s++a+
  gi|386001624|ref|YP_005919923.1| 113 AEEYHSTI---LKLLQNTVQKfgrAQRYTAalFPGEVEAIKSDLGAISRHLSELGDLLQEREESLGAHREAASAAAR 186
                                       44444444...45555555543223333332345559**************************************** PP

                            AAA_13 364 iesikklvaeineliakhNekvanleeekeeakkklelhlv 404
                                       + ++  +++++ + i++  +  ++l +e++  ++++e+   
  gi|386001624|ref|YP_005919923.1| 187 VREGRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWSR 227
                                       *****************999999999999988888887655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.01
                            AAA_13 409 seldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                       +  ++++ ++++le++++k   + +  +a+   ++++i+ Le++l+d +++ + +++ 
  gi|386001624|ref|YP_005919923.1| 343 ARHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELEDRRRSLALLEDR 400
                                       2222333333333333333333333344444444444666666666666666665555 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9     4e+03     116     116 ..     125     125 ..      52     174 .. 0.53
   2 ?    6.0   5.5     0.011        15      36     127 ..     190     291 ..     176     330 .. 0.71
   3 ?   10.2   3.3   0.00057      0.78      32     106 ..     313     397 ..     304     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                              Fez1 116 e 116
                                       +
  gi|386001624|ref|YP_005919923.1| 125 Q 125
                                       2 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                              Fez1  36 lkaqlrelrakleekeeeikeleesleektlelevc..enelqrkkseaellrekvekleeelkelreelselslee 110
                                        ++q+  lra++++ e+ +++l+++   +++e+e     +e +r ++e+  l+ek+++ ++  +++r+ ++ l++  
  gi|386001624|ref|YP_005919923.1| 190 GRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWsrSDEGRRGREEKRYLEEKMRERDQIEMSMRDLVAPLAKAL 266
                                       58999999**************999999999999762257889999************9999999999777766665 PP

                              Fez1 111 eeaalesdeakaqrqe........a 127
                                       ++a+++ d+ +   q+         
  gi|386001624|ref|YP_005919923.1| 267 SRAVKQDDSDRIALQHrevfelliV 291
                                       5555555554444333334555550 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00057
                              Fez1  32 eivalkaqlrel.raklee..keeeikeleesleektlelevcenelqrk.......kseaellrekvekleeelke 98 
                                       +++ l+ ++re   +++++  +++ ++ l+++ +  t+e+e++e+ l+++       k++ +l+r+++++le+el++
  gi|386001624|ref|YP_005919923.1| 313 DLLGLRDKMRERvMEHIDHllEDRPLHLLKARHSALTAEIEELEESLSKRggdtarlKAKRDLVRQRISSLEAELED 389
                                       567778888775134454422355666778888889999999999999999999999999****************9 PP

                              Fez1  99 lreelsel 106
                                        r++l+ l
  gi|386001624|ref|YP_005919923.1| 390 RRRSLALL 397
                                       99988764 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.4   0.00075         1      15      60 ..     190     244 ..     181     254 .. 0.80
   2 ?    1.2   0.1      0.23   3.2e+02      36      51 ..     341     356 ..     338     363 .. 0.67
   3 ?    3.6   0.7     0.041        57      26      52 ..     366     392 ..     359     400 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00075
                                       XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX.........XXXXXXXX CS
                             DivIC  15 gllaykqlkqeiaalqaelaklkaeneeLeaevkdLks.........dedyieer 60 
                                       g  ++ +l++ei + +a l +l++e++  ++e++ ++          ++ y+ee+
  gi|386001624|ref|YP_005919923.1| 190 GRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWSRsdegrrgreEKRYLEEK 244
                                       6678999*****************************6565555555555555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHCC-X CS
                             DivIC  36 lkaeneeLeaevkdLk 51 
                                       lka+  +L+ae+++L+
  gi|386001624|ref|YP_005919923.1| 341 LKARHSALTAEIEELE 356
                                       5667777777777763 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  26 iaalqaelaklkaeneeLeaevkdLks 52 
                                        a+l+a+ + +++++ +Leae++d + 
  gi|386001624|ref|YP_005919923.1| 366 TARLKAKRDLVRQRISSLEAELEDRRR 392
                                       6889999999***********998765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.8    0.0025       3.4      88     159 ..     151     221 ..      66     228 .. 0.65
   2 ?   -1.4   0.5       1.7   2.3e+03     124     141 ..     240     257 ..     219     282 .. 0.58
   3 ?   10.7   3.7   0.00033      0.46     105     158 ..     346     399 ..     339     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0025
                             ATG16  88 eelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                       ++l +  +  +el + l+e +e+l + +e + + ++r++e + +++al+ +++d e+ l  ++      q+E
  gi|386001624|ref|YP_005919923.1| 151 SDLGAISRHLSELGDLLQEREESLGAHRE-AASAAARVREGRGQIEALRAEISDGEALLSRLRDEEAGHQEE 221
                                       45555555555555555555544444433.233344455555555555555555544444444433333333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                             ATG16 124 rlaeleaeraaletklkd 141
                                        l+e  +er ++e  ++d
  gi|386001624|ref|YP_005919923.1| 240 YLEEKMRERDQIEMSMRD 257
                                       333333333333333333 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00033
                             ATG16 105 lelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqD 158
                                        +l++e+++lee+l+++    a+l+a+r  ++++++++e+el+++++ +  l D
  gi|386001624|ref|YP_005919923.1| 346 SALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELEDRRRSLALLED 399
                                       67999**************************************99999888877 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   2.0      0.19   2.6e+02      44      97 ..     166     222 ..     155     281 .. 0.67
   2 ?   10.2   0.8   0.00043      0.59      57     118 ..     340     401 ..     333     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                              ADIP  44 Llqardrdle.qre..slnetirkleaeierlqskierlktqleqlerelalvqake 97 
                                       Llq r++ l  +re  s ++++r+ +  ie l+++i+  ++ l++l+ e a +q++ 
  gi|386001624|ref|YP_005919923.1| 166 LLQEREESLGaHREaaSAAARVREGRGQIEALRAEISDGEALLSRLRDEEAGHQEEI 222
                                       666666666413331133455666666666666666666666666666666555543 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                              ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeel 118
                                       +l+++++ l+aeie l+ + ++    +++l+ + +lv ++  +le++l++  + l  + + l
  gi|386001624|ref|YP_005919923.1| 340 LLKARHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELEDRRRSLALLEDRL 401
                                       57889999999999999999999999999999999999999999999999999988887766 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.8     0.006       8.3      72     153 ..     162     250 ..     145     271 .. 0.76
   2 ?    5.9   1.1    0.0089        12      90     166 ..     337     413 ..     302     419 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                           UPF0242  72 ekeaklteldeglktkee......aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae.....dfeelk 137
                                       e   +l+e +e+l  ++e       ++e + + e L+ e++  e +l rl+ e++  qe+ ea ++        e k
  gi|386001624|ref|YP_005919923.1| 162 ELGDLLQEREESLGAHREaasaaaRVREGRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWSRsdegrRGREEK 238
                                       55567788888888888888888899999**********************************99974444344444 PP

                           UPF0242 138 leleeqLaekqellqe 153
                                       + lee+++e+    ++
  gi|386001624|ref|YP_005919923.1| 239 RYLEEKMRER----DQ 250
                                       4455555444....33 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0089
                           UPF0242  90 aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvle 166
                                        l  l++++  L  e+++ ee l ++  + + L+ k   + + ++ l  ele++ +   +l + +   +++++  le
  gi|386001624|ref|YP_005919923.1| 337 PLHLLKARHSALTAEIEELEESLSKRGGDTARLKAKRDLVRQRISSLEAELEDRRRSLALLEDRLSGDLSDLKGRLE 413
                                       55566777777777778888888888888888887777777777777777777766666666666666666666665 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   4.7      0.68   9.4e+02      43      95 ..     178     230 ..     145     252 .. 0.61
   2 ?    0.9   0.1      0.33   4.5e+02      61      80 ..     340     359 ..     326     363 .. 0.66
   3 ?   10.7   3.8    0.0003      0.41      51     116 ..     344     416 ..     342     418 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.68
                        TPR_MLP1_2  43 qkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswe 95 
                                       +  ++      e   +++alr+e+++ +a ++ l++e    ++e+e+   s e
  gi|386001624|ref|YP_005919923.1| 178 REAASAAARVREGRGQIEALRAEISDGEALLSRLRDEEAGHQEEIEAWSRSDE 230
                                       44444444444445566677777777777777777776666666666555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.33
                        TPR_MLP1_2  61 alreelnelkaeiaelkaea 80 
                                        l+++++ l+aei+el++++
  gi|386001624|ref|YP_005919923.1| 340 LLKARHSALTAEIEELEESL 359
                                       45666666666666666554 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0003
                        TPR_MLP1_2  51 khaedvkelqalreel.......nelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                        h++ + e+++l e l       ++lka++  ++++  s++aele  + s++  +++l  +ls+l+ r+e++ 
  gi|386001624|ref|YP_005919923.1| 344 RHSALTAEIEELEESLskrggdtARLKAKRDLVRQRISSLEAELEDRRRSLALLEDRLSGDLSDLKGRLEEIA 416
                                       5888888888888888666666678888888888888899999999999999999999999999999999986 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.9       1.5     2e+03     207     207 ..     229     229 ..     167     283 .. 0.57
   2 ?   10.7   0.9   0.00018      0.25     168     232 ..     343     408 ..     305     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                   Phlebovirus_NSM 207 s 207
                                        
  gi|386001624|ref|YP_005919923.1| 229 D 229
                                       1 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                   Phlebovirus_NSM 168 iknqvlhseieqlknelqkkRndikrgqekrd.akklveesmArvkdlkeelkiltdelsqiksei 232
                                        +   l  eie l++ l+k+  d  r + krd ++++++ ++A  +d +  l  l d ls   s++
  gi|386001624|ref|YP_005919923.1| 343 ARHSALTAEIEELEESLSKRGGDTARLKAKRDlVRQRISSLEAELEDRRRSLALLEDRLSGDLSDL 408
                                       56777899***********************94589********************9988655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 2998.30
//
Query:       gi|386001625|ref|YP_005919924.1|  [L=560]
Description: Glycogen phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-25   90.2   0.0    5.3e-19   68.0   0.0    3.1  3  Phosphorylase   Carbohydrate phosphorylase
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.036   13.7   0.0    1.5  2  Glyco_transf_5  Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.2e-07    0.0011      23      72 ..      34      84 ..      28     101 .. 0.92
   2 !   68.0   0.0   5.9e-23   5.3e-19     318     581 ..     244     479 ..     205     484 .. 0.87
   3 ?    0.2   0.3     0.019   1.7e+02     673     707 ..     522     557 ..     506     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-07
                                      SHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEEET.TEEEEEEEBTT CS
                     Phosphorylase 23 GGLGRLAacfldslatlelpavGygirYeyGlFkQkied.gaqveepdeWl 72
                                      GGLG LA   + s a l++p v +++  + G F+Q++++ g+q+e+p eW 
  gi|386001625|ref|YP_005919924.1| 34 GGLGTLAGDTVRSSADLGIPLVAVTLASRKGSFRQELDEiGRQIEHPAEWD 84
                                      9************************************6549*********6 PP

  == domain 2  score: 68.0 bits;  conditional E-value: 5.9e-23
                                       TSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGGEEE----B-CHHHCCCTSHHHHHHHHHHCSSGG CS
                     Phosphorylase 318 eekkvrmanlaivgshsvngvaalhsellkkevlkdfyelypekfnnktnGitprrwlllanpelaelitekigeew 394
                                        +++++m  +a+  s+ vngva+ h e   ++++  +       ++ +tnG+    w + + +el    ++    +w
  gi|386001625|ref|YP_005919924.1| 244 GRDRLNMTLFALNLSMYVNGVAKRHRETS-RSMFPGY------EIHSVTNGVHSHSWTCPSFREL---YDRY-LPGW 309
                                       567899*******************9975.4566554......5789**********87665555...4444.479* PP

                                       CCSGGGGGGGGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHH CS
                     Phosphorylase 395 vkdleeLkkLekladdkefleelaeikqenKerlaelikekegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYn 471
                                        ++ e L k+  +  d++++    e++ + K +l +++++++g ++dpe l     +R  eYkR +L +++ +++ +
  gi|386001625|ref|YP_005919924.1| 310 ANEPEMLVKVGIV-PDEKIV----EAHAAAKGELIDYVNRSTGAAMDPEVLTLGFARRSTEYKRPTL-LFSDLDRLR 380
                                       *********9865.555554....556678999*********************************9.577788888 PP

                                       HHHHSTTS----EEEEEE----TT-HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE CS
                     Phosphorylase 472 eikenpekkvvprtvifggkaapgYalAkkiiklinsvaevvnndpevkdklkvvflenynvslaekiipaadlseq 548
                                       +i ++      +  v+++gka p   + k++i+ i +va+ ++ d      ++v++l ny++ la k+i++ d+  +
  gi|386001625|ref|YP_005919924.1| 381 RISSRG-----EVQVVMAGKAHPRDLQGKRLIEEIFRVARALKGD------IEVAYLANYDMILASKMISGVDVWLN 446
                                       888885.....667899**********************987766......7789********************** PP

                                       ---TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                     Phosphorylase 549 istagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                         +   eASGT+ mk + nG +  + lDG  +E
  gi|386001625|ref|YP_005919924.1| 447 TPLRPLEASGTSGMKAAHNGVINFSVLDGWWIE 479
                                       *****************************8776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.019
                                       HHHCSHHHHHHHHHHHHHC.GGGGBHHHHHHHHHHH CS
                     Phosphorylase 673 eaYkdkkewakksilniak.sgkFssDrtikeYaee 707
                                       + Y+ k++w +++  +i   + +F s r ++ Y +e
  gi|386001625|ref|YP_005919924.1| 522 TFYHRKDDWVRMMNNSIGMlAYYFNSHRMMRRYVTE 557
                                       468999********9998725689*********987 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 ?   13.7   0.0     4e-06     0.036      14     227 ..      32     270 ..      15     286 .. 0.68
   2 ?   -3.4   0.0       0.7   6.3e+03      35      88 ..     387     445 ..     383     447 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-06
                    Glyco_transf_5  14 ktGGLadvvgaLpkaLaklghdvrvilPry..gaikeek............keleevae....lskaaed.evevev 71 
                                        +GGL+  +g+  +  a lg     ++ +   g++++e                    +    ++  +e+  v+v+ 
  gi|386001625|ref|YP_005919924.1|  32 YAGGLGTLAGDTVRSSADLGIPLVAVTLASrkGSFRQELdeigrqiehpaeW------DpselCDLLPERaMVRVRG 102
                                       5789999999999999999986655555542455555555555443333221......0222222233334455553 PP

                    Glyco_transf_5  72 ekvkvaklkk.......dgvdvyfldnpeffd....reg....lYgdkgedyednaerfalfsraalelleklgwkp 133
                                         v va  ++         v+v+fld   + +    r g    lYg    d  +  ++ ++++ + +++le lg+  
  gi|386001625|ref|YP_005919924.1| 103 RPVAVAAWEQilksptgGSVPVLFLDTNLVENspedR-GitdvLYGG---DDRYRLKQEIVLGVGGMRILEALGFSI 175
                                       3333333333556777779********9988756552.135679966...55566777778999********98888 PP

                    Glyco_transf_5 134 dvihahDWhtalvpallkelykerglfkkiktvftiHN..layqgrfpkdel.aalglpaedfekldglefygkvnf 207
                                          h++  h++l+++ l e    ++   + ++vft H    a + +f+++ + ++lg    + e+l+ +   +++n+
  gi|386001625|ref|YP_005919924.1| 176 RKYHMNEGHSSLLALELLERSGGDPEGVRKRCVFTTHTpvQAGHDQFSYEIVrEILGGG--AIEMLRRFGGRDRLNM 250
                                       888****************9888888889********7654444567788886778888..5667889999999999 PP

                    Glyco_transf_5 208 lkagivyadavttVSptyak 227
                                          +++++  v+ V + + +
  gi|386001625|ref|YP_005919924.1| 251 TLFALNLSMYVNGVAKRHRE 270
                                       99999999999998877755 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.7
                    Glyco_transf_5  35 dvrvilPrygaikeek..keleevaelskaaedevevev...ekvkvaklkkdgvdvyf 88 
                                       +v+v++ +  + ++ +  + +ee++++  a+++++ev +   +++ +a+   +gvdv++
  gi|386001625|ref|YP_005919924.1| 387 EVQVVMAGKAHPRDLQgkRLIEEIFRVARALKGDIEVAYlanYDMILASKMISGVDVWL 445
                                       67777766533333333356677777766676677777434454555555557888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3996.48
//
Query:       gi|386001626|ref|YP_005919925.1|  [L=287]
Description: Met10+ like methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-43  148.5   0.0    2.9e-43  147.9   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00052   19.6   0.0    0.00092   18.8   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.016   14.2   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.064   12.9   0.0        0.1   12.2   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.11   13.2   0.0       0.34   11.6   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
       0.14   12.9   0.0       0.32   11.7   0.0    1.6  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9   0.0   9.8e-47   2.9e-43       2     199 .]      21     240 ..      20     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 9.8e-47
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +f  +Gdv+++ ++   +   + ige+i+  + +v+tvl+k s+vege R++e+evlaG + t t h+E+g++++lD
  gi|386001626|ref|YP_005919925.1|  21 SFYLVGDVAVVSISPARQGEGRRIGEAIISSHkNVRTVLNKISKVEGERRVAEFEVLAGGG-TLTCHREYGYSYRLD 96 
                                       6899**************************999****************************.*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       v++v+f+++l+ Er+r+a++v +ge+ +  fAG+Gpfaip+a    a rvla ++ Pe  ++l en klN v + ++
  gi|386001626|ref|YP_005919925.1|  97 VARVFFNPRLAGERMRVASKVLPGERAIVPFAGVGPFAIPLAA--AAARVLALEISPEGCRWLAENAKLNGVGDGIE 171
                                       ******************************************7..8889**************************** PP

                                       EEES-GGG---TT-EE........................EEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevireqlad........................rvvmnlpksaieFldkvlaalkdggvihy 199
                                        +++D+  + r  +                          r v + p+   + l+++   +k gg ih+
  gi|386001626|ref|YP_005919925.1| 172 IVNADAFAFCRALTGRapeegettgsggggearpperrfdRAVVPTPYGRDDILEAISPLVKAGGAIHF 240
                                       *********985554466888999999999999999999999999999999999999999999998887 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.1e-07   0.00092       5      65 ..     124     184 ..     121     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.1e-07
                   Methyltransf_15   5 lDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellakl 65 
                                       + +f+G G  +i +a    +v a+ei++e +   ++Na++ gv d i +v +d f   + l
  gi|386001626|ref|YP_005919925.1| 124 IVPFAGVGPFAIPLAAAAARVLALEISPEGCRWLAENAKLNGVGDGIEIVNADAFAFCRAL 184
                                       558***************************************************9977765 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.4e-06     0.016     209     267 ..     127     186 ..     119     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-06
                   tRNA_U5-meth_tr 209 ycGnGnfslalarnfekvlateiakssveaaqyniaanki.dnvqiirlsaeeltealkk 267
                                       + G G f+++la    +vla ei+         n + n + d ++i+   a  + +al++
  gi|386001626|ref|YP_005919925.1| 127 FAGVGPFAIPLAAAAARVLALEISPEGCRWLAENAKLNGVgDGIEIVNADAFAFCRALTG 186
                                       6799**********************************99567*****999999999987 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.4e-05       0.1      32      81 ..     114     163 ..     106     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                                       T.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT CS
                              TPMT  32 alkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl 81 
                                       a+k+ +g+r++vP  G +  ++ lA+   +v+++e+s+ + +  +e+a+l
  gi|386001626|ref|YP_005919925.1| 114 ASKVLPGERAIVPFAGVGPFAIPLAAAAARVLALEISPEGCRWLAENAKL 163
                                       467899*********************************99987666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.34       6      52 ..     129     177 ..     128     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                       TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEEC CS
                   Methyltransf_11   6 GtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvada 52 
                                       G G +a +la ++arv+++++s+e  ++  e+a+ +g+   +e+v ada
  gi|386001626|ref|YP_005919925.1| 129 GVGPFAIPLAAAAARVLALEISPEGCRWLAENAKLNGVgdGIEIVNADA 177
                                       8899999***999*************99988888888777789999987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.32       6      56 ..     128     178 ..     127     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       -TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCC CS
                   Methyltransf_25   6 cGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdae 56 
                                       +G G +++ la++   a+v++++is+e ++  +e+a+ +g+   +e+v++da 
  gi|386001626|ref|YP_005919925.1| 128 AGVGPFAIPLAAAA--ARVLALEISPEGCRWLAENAKLNGVgdGIEIVNADAF 178
                                       58999******996..********************99999999****99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 1928.85
//
Query:       gi|386001627|ref|YP_005919926.1|  [L=201]
Description: DJ-1 family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      6e-48  162.8   0.2    7.6e-48  162.4   0.2    1.1  1  DJ-1_PfpI  DJ-1/PfpI family
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.041   13.5   0.0    1.3  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.2   8.5e-52   7.6e-48       1     163 [.       1     179 [.       1     181 [. 0.98

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 8.5e-52
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESS..................TSEEEETTSEEEE-SEEGGGCTC CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvd..................keevkgsrGlkvtvdaslddvka 59 
                                       +kv+v +a+g+e++E+++ vd+l+ra+++v+++s++                   + v+gs+G ++++das+d++++
  gi|386001627|ref|YP_005919926.1|   1 MKVVVPMAEGFEEIEFVTIVDILRRAEVEVVTASLGkrngdgsagrggaadedeVGAVRGSHGIRIVPDASIDEIDP 77 
                                       69*************************************************9988999******************* PP

                                       CG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE- CS
                         DJ-1_PfpI  60 aeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyv 136
                                       +++Da+vlpGG  g  +l e+e+v++lv+++ e gk vaaIC +p +L++agv++grr+T +pa +++l  +  +yv
  gi|386001627|ref|YP_005919926.1|  78 EDFDAVVLPGGYPGFVHLGEDERVLDLVRRMDELGKYVAAICGAPSVLIKAGVVEGRRATIHPAGRKDL--SDDQYV 152
                                       *********************************************************************..99**** PP

                                       SSSEEEETTEEEESSGGGHHHHHHHHH CS
                         DJ-1_PfpI 137 dkrvvvdgnlvTsrgpgaaiefalell 163
                                       d+rvvv+g+lvTs+++g+a+efal l+
  gi|386001627|ref|YP_005919926.1| 153 DDRVVVSGKLVTSKAAGTAMEFALRLV 179
                                       ************************987 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.5e-06     0.041      37      85 ..      72     122 ..      57     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-06
                          GATase_3  37 lg....edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGl 85 
                                       ++    ed d+v+lpGg++    l    ++++ + ++++ e g+ v +iCG  
  gi|386001627|ref|YP_005919926.1|  72 IDeidpEDFDAVVLPGGYPGFVHLGE--DERVLDLVRRMDELGKYVAAICGAP 122
                                       33333588***********9877654..4569999****************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1545.43
//
Query:       gi|386001628|ref|YP_005919927.1|  [L=640]
Description: hypothetical protein Mhar_0933 [Methanosaeta harundinacea 6Ac]
Scores for complete 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   35.9   0.0    8.2e-09   35.2   0.0    1.3  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
      0.054   13.6   0.2          2    8.6   0.0    2.7  2  T3SchapCesA   Type III secretion system filament chaperone Ce


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   9.1e-13   8.2e-09       1     159 [.     407     551 ..     407     559 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 9.1e-13
                                       EEEEEEBB-.............STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHH CS
                      CN_hydrolase   1 rvAvvQlpq.............kaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetl 64 
                                       r+A+vQ+++                 le+nl+   +++++A++k+ad+i++PE+f +                  +l
  gi|386001628|ref|YP_005919927.1| 407 RIALVQPKIsfdecytkddyalNRIGLEQNLKIFDDMLDQAVQKDADVIIFPEIFFPA----------------SEL 467
                                       5788888888888887777666445689****************************93................489 PP

                                       HHHHHHHHHHTEEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EE CS
                      CN_hydrolase  65 allaalarkngiavvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvf 141
                                       + l++ ++kn+i++++gl +++  ++ + + n+  +  +dg +  ++ K  Lf       +++ ++ + +gd++ vf
  gi|386001628|ref|YP_005919927.1| 468 DHLKMKSKKNNIIIITGLDYEK-ISPEY-FVNSCAVALPDGRV-IRQKK--LF------KSKYDSPRMVEGDELFVF 533
                                       9*******************98.66666.59999999999994.55555..55......79999999999***99** PP

                                       EETTEEEEEEEGGGGGSH CS
                      CN_hydrolase 142 dtpvgkiGaaiCyeigfp 159
                                       +t +g++++ iCy+    
  gi|386001628|ref|YP_005919927.1| 534 KTHFGNFSVFICYDYLSA 551
                                       *************97655 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.021   1.9e+02      34      59 ..     290     318 ..     282     342 .. 0.72
   2 ?    8.6   0.0   0.00022         2      46      86 ..     341     384 ..     328     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.021
                       T3SchapCesA  34 vkesvnilsekaktdpqaa...eklnkli 59 
                                       vke++ i+sek k   +a+   ++l+ li
  gi|386001628|ref|YP_005919927.1| 290 VKEALTIVSEKLKITKKACanpDQLEDLI 318
                                       79**********99888761223455555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00022
                       T3SchapCesA  46 ktdpqaaeklnkliegytygee...rklydsalskieklietlk 86 
                                         dp+aa ++ +l + y   +e    k y   ls i  lietlk
  gi|386001628|ref|YP_005919927.1| 341 TRDPDAARTIVRLFDIYRKPDEidsSKDYSNLLSEISDLIETLK 384
                                       469**************99887444689**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4672.21
//
Query:       gi|386001629|ref|YP_005919928.1|  [L=215]
Description: hypothetical protein Mhar_0934 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.059   12.4   0.1      0.076   12.1   0.1    1.2  1  DUF4831       Domain of unknown function (DUF4831)
        0.5   10.5   2.5       0.69   10.0   2.5    1.3  1  MnmE_helical  MnmE helical domain


Domain annotation for each model (and alignments):
>> DUF4831  Domain of unknown function (DUF4831)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.4e-06     0.076     108     155 ..     124     169 ..      65     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-06
                           DUF4831 108 kkkkslkklnprdylteeilsagstakmaelaakeiyeiResrndLlr 155
                                       +++  ++ +++r+++++ei  a+ + k a+++   i++ R +rn L++
  gi|386001629|ref|YP_005919928.1| 124 HAA--NEDIKKREFYSNEIQEAKHKGKPADVVWLYIFNERRHRNYLAA 169
                                       222..68999**********************************9987 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.5   7.7e-05      0.69      46      97 ..      28      82 ..      17     173 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.7e-05
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                      MnmE_helical 46 aeleaaiDFpeedleelseeelaekleelkeelekllatakrgellreGik.....D 97
                                       ++  aiD+pee+++++ +  + +k++e k++ +++ ++ + g+l r+ i+     D
  gi|386001629|ref|YP_005919928.1| 28 ERISLAIDYPEEEIDDIRQT-VLTKIKEEKRRASRYGKK-DYGSLERQNISqdlesD 82
                                      67899********9998777.888898888888776554.55777777666644442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 1207.72
//
Query:       gi|386001630|ref|YP_005919929.1|  [L=1020]
Description: Multi-sensor signal transduction histidine kinase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-54  183.0   9.9    4.8e-13   49.3   0.0    6.7  7  PAS_4         PAS fold
      1e-39  134.7   2.6    3.2e-22   78.6   0.1    6.9  5  PAS_3         PAS fold
    1.6e-38  131.1   0.0    2.9e-09   37.1   0.0    5.9  5  PAS_9         PAS domain
    6.9e-38  129.1   0.4      3e-10   40.1   0.0    7.2  6  PAS           PAS fold
    5.4e-28   96.5   0.8    3.3e-05   23.8   0.0    6.0  6  PAS_8         PAS domain
      1e-23   83.6   0.0    2.3e-23   82.5   0.0    1.7  1  Response_reg  Response regulator receiver domain
    3.2e-11   43.7   0.2    1.3e-10   41.8   0.1    2.1  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    3.6e-07   30.3   1.1       0.55   10.4   0.0    6.7  6  PAS_7         PAS fold
    1.1e-06   28.8   0.0       0.58   10.3   0.0    4.0  3  MLTR_LBD      MmyB-like transcription regulator ligand bindin
    5.2e-05   23.8   0.0        4.5    7.9   0.0    4.3  3  PAS_10        PAS domain
    0.00045   20.2   0.3     0.0046   17.0   0.1    2.9  2  HisKA         His Kinase A (phospho-acceptor) domain
     0.0071   16.2   0.1          5    6.8   0.0    2.9  3  dCache_1      Cache domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.056   13.6   0.0    1.8  1  PAS_11        PAS domain
      0.025   14.3   0.1      0.081   12.6   0.1    1.9  1  SPOB_a        Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   2.4e+03      44      65 ..     106     127 ..      97     142 .. 0.78
   2 !   30.7   0.0   2.2e-10   2.9e-07      13     110 .]     163     252 ..     161     252 .. 0.93
   3 !   43.1   0.0   3.2e-14     4e-11       4     110 .]     271     393 ..     268     393 .. 0.83
   4 !   44.4   0.0   1.3e-14   1.6e-11       5     109 ..     413     519 ..     409     520 .. 0.91
   5 !   49.3   0.0   3.8e-16   4.8e-13       4     107 ..     539     658 ..     536     661 .. 0.95
   6 !   15.4   0.5   1.3e-05     0.016      21     110 .]     697     791 ..     684     791 .. 0.90
   7 ?   -3.4   0.1       8.7   1.1e+04      50      83 ..     873     906 ..     867     913 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                             PAS_4  44 lpeedaarleralrrvlegeep 65 
                                        p+ + a+l +++r+++e  ++
  gi|386001630|ref|YP_005919929.1| 106 NPKVLYAELTHQIRQAAERMRT 127
                                       5777899999999999998766 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.2e-10
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlr 89 
                                       +d+ v++aN++++   g++++e++G++  e++p    +++ +++ rv e++ p++f+ +      +rh++++++ + 
  gi|386001630|ref|YP_005919929.1| 163 TDYLVRDANPQIELFTGWRAQEAIGRRASEIFPS-EVPPFLEIYSRVDETGCPAKFEGCFPE--TGRHFSISAFSI- 235
                                       58889****************************9.9**********************7766..************. PP

                             PAS_4  90 desGevigvlvisrDiTerrr 110
                                         +G+   +  i+ +iTe++r
  gi|386001630|ref|YP_005919929.1| 236 -GRGR---FATIFSEITEQKR 252
                                       .4566...9*********986 PP

  == domain 3  score: 43.1 bits;  conditional E-value: 3.2e-14
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...............daarleralrrvlegeep 65 
                                       lpda++v+d+  +v+++N+a++e+ g++  e++G+ ++++  +                d + + +++    +g+++
  gi|386001630|ref|YP_005919929.1| 271 LPDATFVIDEKRTVIAWNRAIEEMTGVSKGEIVGRGPYSYGEPFygfetpvlidsifseDSGIVKEYDHLSRRGDAV 347
                                       8*************************************754444777888999999*96666666666666666555 PP

                             PAS_4  66 iefleelll.pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         ++ +++l +g++ ++   ++Pl+d++G+++g+++ +rD+T+r+r
  gi|386001630|ref|YP_005919929.1| 348 FAEVYVPHLyGGRGAYIWAIASPLFDDDGRIVGAIESIRDVTDRKR 393
                                       555555555888888888888***********************97 PP

  == domain 4  score: 44.4 bits;  conditional E-value: 1.3e-14
                             PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeer 79 
                                       ++++av++p++++++ N+a+++l g+++ee++Gk    llp+e +++  + ++ +lege  +e++e++ +  +g  r
  gi|386001630|ref|YP_005919929.1| 413 NAPIAVWGPNMKFIRFNRAFERLTGYAAEEVIGKEATILLPDEEREEALAKMAYALEGE-GWESVEIPIRcrDGTVR 488
                                       789*******************************************************5.77777777777****** PP

                             PAS_4  80 hyelrllPlr.desGevigvlvisrDiTerr 109
                                       +++++   +r + +G+v+++++ +++iTer+
  gi|386001630|ref|YP_005919929.1| 489 IVLWNSANIRsEKDGTVVATIIQGQEITERK 519
                                       ******5555156888*************97 PP

  == domain 5  score: 49.3 bits;  conditional E-value: 3.8e-16
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktla...ellpee...........daarleralrrvlegeepi 66 
                                       lpd+++v+d + rv+++N+a++e+ g+p +e++Gk ++   e++                ++le+ +  v ++++++
  gi|386001630|ref|YP_005919929.1| 539 LPDPTFVIDGERRVIAWNRAIEEMSGVPKDEIVGKGDYaygEVFYGTkrpilidmifsKDEDLESLYHYVKREGDTL 615
                                       8*************************************9999888889***************************** PP

                             PAS_4  67 efleelll..pgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                       + + ++++   g++ ++  +++Pl+d++G + g+++ +rD+Te
  gi|386001630|ref|YP_005919929.1| 616 FAEAYVTPprTGRGSYVWGTASPLFDRDGNIAGAIESIRDVTE 658
                                       ********9999999999999*********************9 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 1.3e-05
                             PAS_4  21 NaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll..pgeerhyelrl.lPlrdes 92 
                                       N++  e++g++  +l+G   +  e+  ++d +++++al+   +g+ p+++ +++l+  +g++ ++  r  +  rd  
  gi|386001630|ref|YP_005919929.1| 697 NRRLVEILGCSEGDLVGNVREreEMIHPDDFEGVMAALDDHFAGRSPHYEIDYRLRrkDGRWIWVHDRGqVMARDGA 773
                                       77778899999999999888888899999***************************77777777776668999**** PP

                             PAS_4  93 GevigvlvisrDiTerrr 110
                                       G+++   +i++DiTe rr
  gi|386001630|ref|YP_005919929.1| 774 GRPLRMTGITQDITEIRR 791
                                       **************9765 PP

  == domain 7  score: -3.4 bits;  conditional E-value: 8.7
                             PAS_4  50 arleralrrvlegeepiefleelllpgeerhyel 83 
                                       +r+++a+rr+++   + ++   ++l+ e++++e+
  gi|386001630|ref|YP_005919929.1| 873 QRVSEAVRRAAAASPAEISRGQVRLEVETETVEV 906
                                       6788888888876555555554554555555555 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.68   8.7e+02       4      22 ..     170     188 ..     167     218 .. 0.83
   2 !    7.9   0.0    0.0028       3.6       2      26 ..     285     307 ..     284     384 .. 0.83
   3 !   32.5   0.0   5.9e-11   7.6e-08       2      83 ..     426     506 ..     425     510 .. 0.87
   4 !    6.5   0.0    0.0078        10       2      25 ..     553     576 ..     552     636 .. 0.63
   5 !   78.6   0.1   2.5e-25   3.2e-22       4      88 ..     696     782 ..     693     783 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.68
                             PAS_3   4 vserveeilGyspeellgk 22 
                                       +++++e  +G++++e +g+
  gi|386001630|ref|YP_005919929.1| 170 ANPQIELFTGWRAQEAIGR 188
                                       89*************9999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                             PAS_3   2 iyvserveeilGyspeellgkvesw 26 
                                       i +++++ee++G+s+ e+ g+    
  gi|386001630|ref|YP_005919929.1| 285 IAWNRAIEEMTGVSKGEIVGR--GP 307
                                       89****************999..44 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 5.9e-11
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvi.r 76 
                                       i  ++++e+++Gy +ee++gk  +   l+  e+re++ ++++ al++ + + ++e+ ir++dG++r v +    i  
  gi|386001630|ref|YP_005919929.1| 426 IRFNRAFERLTGYAAEEVIGK--EATILLPDEEREEALAKMAYALEGEG-WeSVEIPIRCRDGTVRIVLWNSANIrS 499
                                       7899*****************..8888888888*********9996666.779***************999999957 PP

                             PAS_3  77 dengkpv 83 
                                        ++g +v
  gi|386001630|ref|YP_005919929.1| 500 EKDGTVV 506
                                       7777765 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0078
                             PAS_3   2 iyvserveeilGyspeellgkves 25 
                                       i +++++ee+ G+ ++e+ gk + 
  gi|386001630|ref|YP_005919929.1| 553 IAWNRAIEEMSGVPKDEIVGKGDY 576
                                       89******************9443 PP

  == domain 5  score: 78.6 bits;  conditional E-value: 2.5e-25
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvi.rde 78 
                                        ++r  eilG s+ +l g+v++  +++hp+D e v++al++++++++ +ye++yR+rrkdG ++wv++r++v+ rd 
  gi|386001630|ref|YP_005919929.1| 696 RNRRLVEILGCSEGDLVGNVREREEMIHPDDFEGVMAALDDHFAGRSpHYEIDYRLRRKDGRWIWVHDRGQVMaRDG 772
                                       588999*********************************************************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                        g+p+r+ g+
  gi|386001630|ref|YP_005919929.1| 773 AGRPLRMTGI 782
                                       ********98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.013        16      13      45 ..     166     197 ..     147     248 .. 0.82
   2 !   37.1   0.0   2.3e-12   2.9e-09       1     104 []     272     390 ..     272     390 .. 0.81
   3 !   34.7   0.0   1.2e-11   1.6e-08       8     104 .]     420     517 ..     413     517 .. 0.85
   4 !   33.7   0.0   2.6e-11   3.3e-08       1     104 []     540     658 ..     540     658 .. 0.75
   5 !   12.2   0.0   0.00013      0.17      17     104 .]     697     788 ..     689     788 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                             PAS_9  13 il.yaNeaalrllGyspeevlgksitdlfvtdpe 45 
                                       ++ +aN++ + ++G  ++e +g++ +++f  ++e
  gi|386001630|ref|YP_005919929.1| 166 LVrDANPQIELFTGWRAQEAIGRRASEIF--PSE 197
                                       6779*************************..333 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.3e-12
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgks...itdlf.............vtdpeanerlraaleqgrk.k 60 
                                       pd++++++++ +++ +N+a ++++G s+ e++g+    + + f             ++d+   ++ +++ ++g+   
  gi|386001630|ref|YP_005919929.1| 272 PDATFVIDEKRTVIAWNRAIEEMTGVSKGEIVGRGpysYGEPFygfetpvlidsifSEDSGIVKEYDHLSRRGDAvF 348
                                       678888889999**********************9777444445666666777766999999999999999999554 PP

                             PAS_9  61 erevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       ++ +  +l+   g ++w  + asp++dddg++vg+i  +rD+t+
  gi|386001630|ref|YP_005919929.1| 349 AEVYVPHLYGGRGAYIW--AIASPLFDDDGRIVGAIESIRDVTD 390
                                       44444455666679999..***********************96 PP

  == domain 3  score: 34.7 bits;  conditional E-value: 1.2e-11
                             PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                        p+ + +++N+a++rl+Gy +eev+gk  t l+  ++ +ea  +++ ale      ++ve+ ++ ++g+   vl + 
  gi|386001630|ref|YP_005919929.1| 420 GPNMKFIRFNRAFERLTGYAAEEVIGKEATILLpdEEREEALAKMAYALEGEG--WESVEIPIRCRDGTVRIVLWNS 494
                                       4788899**************************66666666666666666666..9********************* PP

                             PAS_9  83 spvkdd.dgelvgiivilrDite 104
                                       + ++++ dg++v+ i+  + ite
  gi|386001630|ref|YP_005919929.1| 495 ANIRSEkDGTVVATIIQGQEITE 517
                                       ******99999998888777776 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 2.6e-11
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgks...itdlf.............vtdpeanerlraaleqgrkke 61 
                                       pd++++++ + r++ +N+a +++ G  ++e++gk    + ++f             ++d++ ++  + + ++g++  
  gi|386001630|ref|YP_005919929.1| 540 PDPTFVIDGERRVIAWNRAIEEMSGVPKDEIVGKGdyaYGEVFygtkrpilidmifSKDEDLESLYHYVKREGDT-L 615
                                       677888778889***********************9995555555555555555546666666666666666665.4 PP

                             PAS_9  62 revevvlirkng..etfwvlltaspvkdddgelvgiivilrDite 104
                                       +++ +v   ++g  +++w   tasp++d dg++ g+i  +rD+te
  gi|386001630|ref|YP_005919929.1| 616 FAEAYVTPPRTGrgSYVW--GTASPLFDRDGNIAGAIESIRDVTE 658
                                       444444444444248888..************************8 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00013
                             PAS_9  17 NeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk...kerevevvlirkngetfwvlltaspv.kdd 88 
                                       N+ + ++lG s+ +++g ++++     +p++ e + aal+++     + +e ++ l+rk+g+ +wv+ +   + +d+
  gi|386001630|ref|YP_005919929.1| 697 NRRLVEILGCSEGDLVG-NVREREeMIHPDDFEGVMAALDDHFAgrsPHYEIDYRLRRKDGRWIWVHDRGQVMaRDG 772
                                       66666777777777777.3333333235666666666666666678899******************9999997888 PP

                             PAS_9  89 dgelvgiivilrDite 104
                                        g+  ++ +i +Dite
  gi|386001630|ref|YP_005919929.1| 773 AGRPLRMTGITQDITE 788
                                       9999999********8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0014       1.9      22      53 ..     166     197 ..     136     230 .. 0.83
   2 !   30.0   0.0   3.1e-10     4e-07       2      44 ..     263     305 ..     262     313 .. 0.94
   3 ?   -0.4   0.0      0.88   1.1e+03      84     113 .]     359     388 ..     348     388 .. 0.85
   4 !   40.1   0.0   2.3e-13     3e-10       3     101 ..     405     502 ..     403     511 .. 0.88
   5 !   29.1   0.0   6.2e-10   7.9e-07       5      44 ..     534     573 ..     530     656 .. 0.63
   6 !   10.2   0.1   0.00046      0.59       4     113 .]     674     786 ..     671     786 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                                       BEEEECHHHHHHHSSTHHHCTTSBGGGGBSTT CS
                               PAS  22 rilyvNaaaeellGlsreevlgkslldlihee 53 
                                        +  +N+ +e ++G++++e++g+  ++ ++ e
  gi|386001630|ref|YP_005919929.1| 166 LVRDANPQIELFTGWRAQEAIGRRASEIFPSE 197
                                       67889******************988666554 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.1e-10
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgk 44 
                                       +l++i++ lpd++fv+De+  ++ +N+a+ee++G s  e++g+
  gi|386001630|ref|YP_005919929.1| 263 QLQEIIDILPDATFVIDEKRTVIAWNRAIEEMTGVSKGEIVGR 305
                                       5899*************************************98 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.88
                                       SSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  84 grpihlevraspvrdaggeilgflgvlrdi 113
                                       gr  ++   asp++d +g+i g++  +rd+
  gi|386001630|ref|YP_005919929.1| 359 GRGAYIWAIASPLFDDDGRIVGAIESIRDV 388
                                       56666677899***********99988886 PP

  == domain 4  score: 40.1 bits;  conditional E-value: 2.3e-13
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       l+++l+ + +pi v+  + +++ +N+a+e+l+G+++eev+gk   +l++ e++ e a +   ++++ge ++++ei +
  gi|386001630|ref|YP_005919929.1| 405 LESLLHYANAPIAVWGPNMKFIRFNRAFERLTGYAAEEVIGKEATILLPDEER-EEALAKMAYALEGEGWESVEIPI 480
                                       689999******************************************98765.56666667888999*******99 PP

                                       ECTTSSEEEEEEEEEEEEETTE CS
                               PAS  80 klrdgrpihlevraspvrdagg 101
                                       + rdg+++ ++ + + +r++++
  gi|386001630|ref|YP_005919929.1| 481 RCRDGTVRIVLWNSANIRSEKD 502
                                       99********999999999877 PP

  == domain 5  score: 29.1 bits;  conditional E-value: 6.2e-10
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgk 44 
                                       +i++ lpdp+fv+D   r++ +N+a+ee+ G + +e++gk
  gi|386001630|ref|YP_005919929.1| 534 EIIDFLPDPTFVIDGERRVIAWNRAIEEMSGVPKDEIVGK 573
                                       78999*********************************98 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00046
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS..BGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgk..slldliheeddaelaelleqlleqgeesrageis 78 
                                       + ++e +  +i+ ++  +  +  N+   e+lG s+ +++g      + ih++d + + ++l  + + +++    + +
  gi|386001630|ref|YP_005919929.1| 674 KLVIEGANLGIWDRNVETGEVVRNRRLVEILGCSEGDLVGNvrEREEMIHPDDFEGVMAALDDHFAGRSPHYEIDYR 750
                                       678999999******9999999*****************9631444445555556999999999************* PP

                                       EECTTSSEEEEEEEEEEE.EETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspv.rdaggeilgflgvlrdi 113
                                       ++++dgr i+++ r   + rd+ g++l   g+ +di
  gi|386001630|ref|YP_005919929.1| 751 LRRKDGRWIWVHDRGQVMaRDGAGRPLRMTGITQDI 786
                                       *************97654388888888888888876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.6e-08   3.3e-05       1      56 [.     136     201 ..     136     210 .. 0.77
   2 !   21.7   0.0   1.2e-07   0.00015       2      42 ..     263     304 ..     262     322 .. 0.81
   3 !   21.0   0.0     2e-07   0.00025       2      57 ..     404     460 ..     403     471 .. 0.83
   4 ?   -2.8   0.0       5.7   7.3e+03       8      29 ..     474     495 ..     473     495 .. 0.68
   5 !   20.7   0.0   2.4e-07   0.00031       6      43 ..     535     573 ..     527     593 .. 0.84
   6 ?    1.5   0.0      0.24   3.1e+02       4      42 ..     674     713 ..     673     738 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.6e-08
                             PAS_8   1 erlralfesspdgiav....vdlgd........rivdvNqaalellGys.adlkgellgqllpvlrpll 56 
                                       er+ralfe++++g ++        +        +++d+N++ + ++G++ ++ +g    +++p   p++
  gi|386001630|ref|YP_005919929.1| 136 ERYRALFENMNEGFVLyeilR---NpvgratdyLVRDANPQIELFTGWRaQEAIGRRASEIFPSEVPPF 201
                                       7**************955441...2345344456***************99998888887777766655 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.2e-07
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkg 42 
                                       +l+ +++ +pd+ +v+d+ ++++ +N+a +e++G+s  ++ g
  gi|386001630|ref|YP_005919929.1| 263 QLQEIIDILPDATFVIDEKRTVIAWNRAIEEMTGVSkGEIVG 304
                                       5899*************5556*************99544443 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2e-07
                             PAS_8   2 rlralfesspdgiavvdlgd...rivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                       +l++l++ ++ +iav+   +   +++  N+a+++l+Gy  ++++g++  +llp+ + +++
  gi|386001630|ref|YP_005919929.1| 404 YLESLLHYANAPIAVW---GpnmKFIRFNRAFERLTGYAaEEVIGKEATILLPDEEREEA 460
                                       899***********99...34557***************999999999877777776665 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.7
                             PAS_8   8 esspdgiavvdlgd.rivdvNqa 29 
                                       es+  +i   d g+ riv +N a
  gi|386001630|ref|YP_005919929.1| 474 ESVEIPIRCRD-GTvRIVLWNSA 495
                                       56666777444.4489*****86 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 2.4e-07
                             PAS_8   6 lfesspdgiavvdlgdrivdvNqaalellGys.adlkge 43 
                                       +++ +pd+ +v+d+ +r++ +N+a +e+ G++ +++ g+
  gi|386001630|ref|YP_005919929.1| 535 IIDFLPDPTFVIDGERRVIAWNRAIEEMSGVPkDEIVGK 573
                                       6899*********6679***************9988874 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.24
                             PAS_8   4 ralfesspdgiavvdlgdrivd....vNqaalellGys.adlkg 42 
                                       + ++e ++ gi+ +   + +       N++  e+lG s  dl g
  gi|386001630|ref|YP_005919929.1| 674 KLVIEGANLGIW-DR--N-VETgevvRNRRLVEILGCSeGDLVG 713
                                       678999999999.64..4.66677778999999**977444333 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   1.8e-26   2.3e-23       1     110 [.       4     113 ..       4     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.8e-26
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl vdDdp+++e+ r +l ++g  +v+ ++++ ea++ lk  ++d+i+ D  mp+mdGl +lk +r +dpe+p i++
  gi|386001630|ref|YP_005919929.1|   4 VLMVDDDPVILEIARIFLGRSGDIQVDGVASAVEAVARLKDGRYDVIVSDYVMPEMDGLSFLKWVRSRDPEVPFILF 80 
                                       89*****************66655***************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlka 110
                                       t+++ ee+++eal+ gad +l+K+ +p+ L + 
  gi|386001630|ref|YP_005919929.1|  81 TGKGREEVVIEALNNGADYYLQKDANPKVLYAE 113
                                       **************************9999876 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 !   41.8   0.1     1e-13   1.3e-10       6     111 ..     912    1013 ..     909    1014 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1e-13
                                        HHHHHHHHHHHHHHHHSTTTEEEEEEEE..EE....TEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTS CS
                         HATPase_c    6 LrqiisnlvdNavkfatkageieveika..se....ddlvisveDnGiGipkedlkklfe.kfsqddstkrgggg 73  
                                        L++++ nl++N++++   +g   v+++   +e     + vi veD+G Gip  +  ++f+ +f +          
  gi|386001630|ref|YP_005919929.1|  912 LEKVFCNLLENSLRH--GGGVTGVRVSFfeRErgveAEGVIAVEDDGLGIPAGMKARIFDqAFGR---------H 975 
                                        78999*********9..45555666665442255668***********************9****.........* PP

                                        SSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c   74 tGlGlsivkklvelmgGeiwvesepgrGttftftlple 111 
                                        tG+Gl +++++    g +i+ + e+grG +f +++p e
  gi|386001630|ref|YP_005919929.1|  976 TGYGLFLSQEILGITGMTITETGEEGRGARFEISVPRE 1013
                                        **********9998999****************99976 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.22   2.9e+02      84     114 ..     224     254 ..     211     255 .. 0.86
   2 !    7.2   0.0    0.0042       5.3       6      33 ..     273     300 ..     268     307 .. 0.84
   3 ?    0.7   0.0      0.46   5.8e+02      99     114 ..     380     395 ..     374     396 .. 0.90
   4 !   10.4   0.0   0.00043      0.55       9      35 ..     544     570 ..     537     577 .. 0.89
   5 ?    0.3   0.0      0.57   7.3e+02      43      91 ..     710     762 ..     690     794 .. 0.56
   6 ?   -3.4   0.1         8     1e+04      40      77 ..     851     889 ..     841     911 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.22
                             PAS_7  84 dgrvievrgnplpdgGfVttytDiTerrrae 114
                                       +gr  ++ +  +  g f t++++iTe++r +
  gi|386001630|ref|YP_005919929.1| 224 TGRHFSISAFSIGRGRFATIFSEITEQKRMN 254
                                       6777888888888999***********9965 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0042
                             PAS_7   6 qGisvfDadlrLvawNrrylelldlpee 33 
                                       ++  v+D++  ++awNr + e+ +++++
  gi|386001630|ref|YP_005919929.1| 273 DATFVIDEKRTVIAWNRAIEEMTGVSKG 300
                                       56689*****************998875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.46
                             PAS_7  99 GfVttytDiTerrrae 114
                                       G + +  D+T+r+rae
  gi|386001630|ref|YP_005919929.1| 380 GAIESIRDVTDRKRAE 395
                                       888999********98 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00043
                             PAS_7   9 svfDadlrLvawNrrylelldlpeelv 35 
                                        v+D + r++awNr + e+ ++p++ +
  gi|386001630|ref|YP_005919929.1| 544 FVIDGERRVIAWNRAIEEMSGVPKDEI 570
                                       599********************9865 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.57
                             PAS_7  43 ellrynaergefg.agdveaeverrlaaaragkphs...fererpdgrvievr 91 
                                       +l+   +er+e+  ++d e  +++  ++ + ++ph+   +  +r+dgr+i v+
  gi|386001630|ref|YP_005919929.1| 710 DLVGNVREREEMIhPDDFEGVMAALDDHFAGRSPHYeidYRLRRKDGRWIWVH 762
                                       44444455555443566666666666666666666433356677888888774 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 8
                             PAS_7  40 pleellrynaergefgagdve.aeverrlaaaragkphs 77 
                                       +++  l++ ++ +e+g +++e + v + +++a+a +p  
  gi|386001630|ref|YP_005919929.1| 851 TIKRQLAFARDYQEMGVKAPEwQRVSEAVRRAAAASPAE 889
                                       444445555555555533322133444444444444433 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0012       1.6       4      39 ..     263     297 ..     260     307 .. 0.86
   2 ?    4.5   0.0     0.027        34      11      40 ..     410     439 ..     401     459 .. 0.84
   3 !   10.3   0.0   0.00045      0.58       5      41 ..     532     567 ..     527     596 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                          MLTR_LBD   4 alrrlLdalepvPAlVldrrwdvlaaNraaraLlgd 39 
                                       +l+ ++d l p + +V+d + +v+a+Nra + + g 
  gi|386001630|ref|YP_005919929.1| 263 QLQEIIDIL-PDATFVIDEKRTVIAWNRAIEEMTGV 297
                                       688888888.7889****************999875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                          MLTR_LBD  11 alepvPAlVldrrwdvlaaNraaraLlgdp 40 
                                       ++ ++P +V ++++  ++ Nra+++L g  
  gi|386001630|ref|YP_005919929.1| 410 HYANAPIAVWGPNMKFIRFNRAFERLTGYA 439
                                       56799**********************983 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00045
                          MLTR_LBD   5 lrrlLdalepvPAlVldrrwdvlaaNraaraLlgdpa 41 
                                       l  ++d l p P +V+d+   v+a+Nra + + g p+
  gi|386001630|ref|YP_005919929.1| 532 LLEIIDFL-PDPTFVIDGERRVIAWNRAIEEMSGVPK 567
                                       44555555.88*******************9998765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0035       4.5      55     106 .]     334     389 ..     264     389 .. 0.76
   2 ?    3.4   0.0     0.089   1.1e+02       2      75 ..     406     481 ..     405     509 .. 0.72
   3 !    7.2   0.0    0.0058       7.4      70     106 .]     617     657 ..     596     657 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                            PAS_10  55 veeviealrtgekdevevvvp....kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       v+e  +  r+g  +  ev+vp     +g ++    +p+ d+dg+i G++e + D+t
  gi|386001630|ref|YP_005919929.1| 334 VKEYDHLSRRGDAVFAEVYVPhlygGRGAYIWAIASPLFDDDGRIVGAIESIRDVT 389
                                       4556677788889999999998888889999999********************96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.089
                            PAS_10   2 nnlLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknveeviealrtgekdevevvvp 75 
                                       + lL  ++  +     n++++rF++a ++l  + +++ +G + + + p+ ++++ + ++  al  +  + ve+++ 
  gi|386001630|ref|YP_005919929.1| 406 ESLLHYANAPIAVWGPNMKFIRFNRAFERLTGYAAEEvIGKEATILLPDeEREEALAKMAYALEGEGWESVEIPIR 481
                                       5677777788888889**********99999987765268888888888667777777777776666677776665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0058
                            PAS_10  70 vevvvp....kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                        e +v+     +g +v  + +p+ d dg+iaG++e + D+t
  gi|386001630|ref|YP_005919929.1| 617 AEAYVTpprtGRGSYVWGTASPLFDRDGNIAGAIESIRDVT 657
                                       4444433444779999999********************96 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.6   3.3e+03      38      52 ..     112     126 ..      97     146 .. 0.67
   2 !   17.0   0.1   3.6e-06    0.0046       8      55 ..     809     856 ..     802     866 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHH CS
                             HisKA  38 keyletiesearrld 52 
                                       +e+ ++i++ a+r++
  gi|386001630|ref|YP_005919929.1| 112 AELTHQIRQAAERMR 126
                                       455555666666554 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHH CS
                             HisKA   8 gvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlv 55 
                                          H++ + ++a++g++++L++ ++ ++  ++y+++i + a+ + +++
  gi|386001630|ref|YP_005919929.1| 809 ITRHDIQNQITALSGYVHLLREGIPRDPAAERYIDRIGEVAETIKRQL 856
                                       568*****************9998889999999999999888887766 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0078        10     119     153 ..     344     381 ..     261     383 .. 0.82
   2 !    6.8   0.0    0.0039         5      57     153 ..     522     649 ..     501     653 .. 0.68
   3 ?   -2.1   0.0       2.1   2.7e+03       4      30 ..     796     822 ..     736     864 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0078
                          dCache_1 119 gkpvisdpyvdqt...ggkpvitiavpiyddsgkfiGv 153
                                       g+ v+ ++yv+      g ++ +ia+p++dd+g+++G+
  gi|386001630|ref|YP_005919929.1| 344 GDAVFAEVYVPHLyggRGAYIWAIASPLFDDDGRIVGA 381
                                       3778888884443434677*****************97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
                          dCache_1  57 reslqallksilksnpdi.sgvylvdadGqviassdpssppnleg...............................t 101
                                       +e+l ++ k++l+  +++ +  +++d + +via ++++ +    g                                
  gi|386001630|ref|YP_005919929.1| 522 EERLIQAHKQLLEIIDFLpDPTFVIDGERRVIA-WNRAIE-EMSGvpkdeivgkgdyaygevfygtkrpilidmifS 596
                                       566666666666666555666666666666655.444333.222245655555555566666666666677777776 PP

                          dCache_1 102 ddpadrdwykealaggggkpvisdpyvdqt...ggkpvitiavpiyddsgkfiGv 153
                                       +d   +++y+ ++ +g  ++++ ++yv ++    g +v   a+p++d++g++ G+
  gi|386001630|ref|YP_005919929.1| 597 KDEDLESLYHYVKREG--DTLFAEAYVTPPrtgRGSYVWGTASPLFDRDGNIAGA 649
                                       6777888899999999..899999994444456788***********99**9997 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.1
                          dCache_1   4 eeqaeeqllglaeqlanniedvldsle 30 
                                        ++a++ l+ l+  + ++i+++++ l 
  gi|386001630|ref|YP_005919929.1| 796 LQEANRKLKLLSSITRHDIQNQITALS 822
                                       345555555555555555555555544 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.4e-05     0.056      42      90 ..     720     768 ..     706     775 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                            PAS_11  42 dLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklf 90 
                                       +++hp+d++ ++ +l + +  +  + +  yRLr +++++++v+ ++++ 
  gi|386001630|ref|YP_005919929.1| 720 EMIHPDDFEGVMAALDDHFAGRSPHYEIDYRLRRKDGRWIWVHDRGQVM 768
                                       789****************7777777888**************888875 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 ?   12.6   0.1   6.4e-05     0.081       6      39 ..     796     830 ..     792     856 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                            SPOB_a   6 ikelkeliklL.rsqRHDflNhLQvIsGylqLgky 39 
                                       ++e++  +klL +  RHD  N++  +sGy++L + 
  gi|386001630|ref|YP_005919929.1| 796 LQEANRKLKLLsSITRHDIQNQITALSGYVHLLRE 830
                                       567777788886779****************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1020 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 7137.34
//
Query:       gi|386001631|ref|YP_005919930.1|  [L=405]
Description: hypothetical protein Mhar_0936 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.2  18.9        4.4    7.2   0.0    5.9  6  DUF2064   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2   0.00034       6.2      93     108 ..      39      54 ..      33      62 .. 0.85
   2 ?    5.4   0.3   0.00083        15      95     108 ..      93     106 ..      86     118 .. 0.85
   3 ?    0.6   0.1     0.026   4.7e+02      96     108 ..     146     158 ..     138     167 .. 0.84
   4 ?    2.5   0.1    0.0069   1.2e+02      91     108 ..     193     210 ..     189     218 .. 0.80
   5 ?    7.2   0.0   0.00024       4.4      95     110 ..     300     315 ..     291     326 .. 0.81
   6 ?    1.6   0.3     0.013   2.4e+02      95     108 ..     354     367 ..     347     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00034
                                       EEEBTTSSEEEEEEEG CS
                           DUF2064  93 lgpaeDGGYyllGlkk 108
                                       +  a+DGGY++ G+++
  gi|386001631|ref|YP_005919930.1|  39 ISRAQDGGYVMTGMTE 54 
                                       5679**********95 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.00083
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                       +a DGGY++ G+++
  gi|386001631|ref|YP_005919930.1|  93 AARDGGYVVAGYTT 106
                                       799********996 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.026
                                       BTTSSEEEEEEEG CS
                           DUF2064  96 aeDGGYyllGlkk 108
                                       a  GGY+++G + 
  gi|386001631|ref|YP_005919930.1| 146 APSGGYVVVGWTD 158
                                       667*******984 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.0069
                                       EEEEEBTTSSEEEEEEEG CS
                           DUF2064  91 aVlgpaeDGGYyllGlkk 108
                                       + + ++ DGGY++ G ++
  gi|386001631|ref|YP_005919930.1| 193 LAVVATRDGGYAIAGRTT 210
                                       5677899******99875 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.00024
                                       EBTTSSEEEEEEEG-G CS
                           DUF2064  95 paeDGGYyllGlkkrl 110
                                        a+DGGY+++G ++r+
  gi|386001631|ref|YP_005919930.1| 300 VASDGGYAVVGSTSRA 315
                                       799********99743 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.013
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        ae+GGY++ G+++
  gi|386001631|ref|YP_005919930.1| 354 VAEEGGYIVGGFTN 367
                                       69*********994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 3015.52
//
Query:       gi|386001632|ref|YP_005919931.1|  [L=412]
Description: hypothetical protein Mhar_0937 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00064   19.6   0.2        6.6    6.5   0.1    3.4  3  DUF4166   Domain of unknown function (DUF4166)


Domain annotation for each model (and alignments):
>> DUF4166  Domain of unknown function (DUF4166)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0023        41      64      83 ..     102     119 ..      98     140 .. 0.82
   2 !    6.5   0.1   0.00037       6.6      64      82 ..     154     170 ..     149     181 .. 0.87
   3 !    4.9   0.0    0.0012        21      64      81 ..     205     220 ..     202     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0023
                           DUF4166  64 rdesgretltwtRtfefpgk 83 
                                       +d++gre   w+Rt+++pg 
  gi|386001632|ref|YP_005919931.1| 102 TDSKGRE--LWNRTIGGPGD 119
                                       5899***..********953 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00037
                           DUF4166  64 rdesgretltwtRtfefpg 82 
                                       +d++gre  +w+Rtf++pg
  gi|386001632|ref|YP_005919931.1| 154 TDPQGRE--VWNRTFGGPG 170
                                       589****..*******995 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0012
                           DUF4166  64 rdesgretltwtRtfefp 81 
                                        d++gre  +w+Rtf++ 
  gi|386001632|ref|YP_005919931.1| 205 ADPQGRE--VWNRTFGGT 220
                                       5899***..******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 3074.63
//
Query:       gi|386001633|ref|YP_005919932.1|  [L=84]
Description: XRE family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-16   60.1   0.0    1.9e-16   59.9   0.0    1.1  1  HTH_3           Helix-turn-helix
    5.4e-10   39.2   0.1    6.1e-10   39.0   0.1    1.1  1  HTH_19          Helix-turn-helix domain
    8.3e-06   26.1   0.0    1.2e-05   25.6   0.0    1.2  1  HTH_31          Helix-turn-helix domain
    1.2e-05   25.7   0.0    1.3e-05   25.5   0.0    1.1  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00035   20.0   0.0     0.0007   19.1   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
    0.00061   19.7   0.0    0.00098   19.0   0.0    1.3  1  HTH_11          HTH domain
    0.00097   19.1   0.0     0.0018   18.2   0.0    1.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0019   17.8   0.0      0.043   13.5   0.0    2.1  2  Sigma70_r4_2    Sigma-70, region 4
     0.0037   17.0   0.0        0.5   10.2   0.0    2.2  2  MerR            MerR family regulatory protein
      0.004   17.2   0.0        1.8    8.7   0.0    2.2  2  MerR_1          MerR HTH family regulatory protein
     0.0067   16.3   0.0     0.0098   15.7   0.0    1.3  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.033   14.0   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.024   14.2   0.0      0.034   13.7   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.036   13.9   0.0      0.056   13.3   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.066   13.3   0.0      0.087   12.9   0.0    1.1  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
      0.097   12.6   0.0       0.13   12.2   0.0    1.2  1  MarR_2          MarR family
       0.14   12.3   0.0       0.35   11.1   0.0    1.6  1  HTH_17          Helix-turn-helix domain
       0.16   11.8   0.1       0.35   10.7   0.1    1.6  2  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   1.9e-19   1.9e-16       4      54 ..       8      58 ..       5      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.9e-19
                                      HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                      +R   +l+qeeLA+klGv+r+ti +iE+++ nPsl+ ++k+a+ +gv++++
  gi|386001633|ref|YP_005919932.1|  8 YRAIFDLTQEELAKKLGVTRQTIIAIEKDKYNPSLDLAFKMARIFGVKIED 58
                                      666679******************************************987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   6.1e-13   6.1e-10       4      60 ..       5      60 ..       3      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.1e-13
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      +k +R  + ltqeela++lg++r  i+aiE++k+ +ps +l  k a+++g+ +e ++
  gi|386001633|ref|YP_005919932.1|  5 IKVYRAIFDLTQEELAKKLGVTRQTIIAIEKDKY-NPSLDLAFKMARIFGVKIEDIF 60
                                      677788899***********************99.*****************99766 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.2e-08   1.2e-05      14      57 ..      13      55 ..       2      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                            HTH_31 14 GLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                       L+qee+A+ lgv++ t+  +E  +  +ps++   ++ar++g+ 
  gi|386001633|ref|YP_005919932.1| 13 DLTQEELAKKLGVTRQTIIAIEKDKY-NPSLDLAFKMARIFGVK 55
                                      69************************.6*************995 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.3e-08   1.3e-05      10      61 ..      13      63 ..       4      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-08
                            HTH_26 10 gitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleye 61
                                      ++t+ eLa+++g++++t+  + k+k  ++sld   k ++++g++++D+++y 
  gi|386001633|ref|YP_005919932.1| 13 DLTQEELAKKLGVTRQTIIAIEKDK-YNPSLDLAFKMARIFGVKIEDIFVYD 63
                                      6799********************9.6***********************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     7e-07    0.0007      20      42 ..      13      35 ..       5      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7e-07
                                      T--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 20 glTleEIgerlgiSrerVrqiek 42
                                      +lT+eE++++lg++r ++  iek
  gi|386001633|ref|YP_005919932.1| 13 DLTQEELAKKLGVTRQTIIAIEK 35
                                      89****************99987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.9e-07   0.00098      15      33 ..      13      31 ..       5      32 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.9e-07
                            HTH_11 15 pisgeeLAeeLnvSrrtvr 33
                                      +++ eeLA++L+v+r+t+ 
  gi|386001633|ref|YP_005919932.1| 13 DLTQEELAKKLGVTRQTII 31
                                      5899*************95 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-06    0.0018      20      39 ..      12      31 ..       2      36 .. 0.86
   2 ?   -3.2   0.0       8.4   8.4e+03      27      36 ..      48      57 ..      47      59 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                      EEHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvs 39
                                      ++ltqeelA  lG+tr+t+ 
  gi|386001633|ref|YP_005919932.1| 12 FDLTQEELAKKLGVTRQTII 31
                                      79****************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.4
                                      HHHHTTSSHH CS
                         HTH_Crp_2 27 lAsmlGltre 36
                                      +A++ G+  e
  gi|386001633|ref|YP_005919932.1| 48 MARIFGVKIE 57
                                      7888888776 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.3e-05     0.043      21      43 ..       8      30 ..       6      30 .. 0.92
   2 ?    2.1   0.0      0.15   1.5e+02      18      32 ..      45      59 ..      44      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                                      HHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtV 43
                                       r++++l+++E A++lg++ +t+
  gi|386001633|ref|YP_005919932.1|  8 YRAIFDLTQEELAKKLGVTRQTI 30
                                      5899***************9996 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                                      HHHHHHTS---HHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEI 32
                                      +f + +++g ++++I
  gi|386001633|ref|YP_005919932.1| 45 AFKMARIFGVKIEDI 59
                                      799********9998 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0005       0.5       4      17 ..      18      31 ..      17      38 .. 0.88
   2 ?    4.8   0.0     0.024        24       5      35 ..      48      77 ..      47      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                                      HHHHHHTTTHHHHH CS
                              MerR  4 evAeltGvsprtLR 17
                                      e+A+++Gv+ +t+ 
  gi|386001633|ref|YP_005919932.1| 18 ELAKKLGVTRQTII 31
                                      9***********96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                                      HHHHHTTTHHHHHHHHHTTSSTSEEETTTSS CS
                              MerR  5 vAeltGvsprtLRyYEreGLipppeRtegGy 35
                                      +A+++Gv +  +  Y++e L+ p eR  +G+
  gi|386001633|ref|YP_005919932.1| 48 MARIFGVKIEDIFVYDEE-LLDPEERGGTGR 77
                                      69999****99999***9.999999988886 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1     0.008         8       4      17 ..      17      30 ..      14      35 .. 0.90
   2 !    8.7   0.0    0.0018       1.8       6      35 ..      48      77 ..      47      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.008
                                      HHHHHHHTS-HHHH CS
                            MerR_1  4 gevakilgvtthtl 17
                                       e+ak+lgvt  t+
  gi|386001633|ref|YP_005919932.1| 17 EELAKKLGVTRQTI 30
                                      69**********98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                                      HHHHHTS-HHHHHHHHHHTT-S-EE-TTS- CS
                            MerR_1  6 vakilgvtthtlrywekegllkpkrteggr 35
                                       a+i+gv+   +  +++e l + +r ++gr
  gi|386001633|ref|YP_005919932.1| 48 MARIFGVKIEDIFVYDEELLDPEERGGTGR 77
                                      69****************999999977776 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.9e-06    0.0098      11      36 ..      14      39 ..       9      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.9e-06
                                      --HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25 11 lsleevaketkIrkdylealEeddfd 36
                                      l+ ee+ak++ +  +++ a+E+d+++
  gi|386001633|ref|YP_005919932.1| 14 LTQEELAKKLGVTRQTIIAIEKDKYN 39
                                      89*********************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.033      17      37 ..      13      33 ..       2      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                            HTH_23 17 GlsvreIAreLgvsrrTvyrw 37
                                       l+++e A++Lgv+r+T+  +
  gi|386001633|ref|YP_005919932.1| 13 DLTQEELAKKLGVTRQTIIAI 33
                                      5799*************9765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.4e-05     0.034      18      34 ..      14      30 ..       3      33 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                            HTH_24 18 isqreLAerlglSpstv 34
                                      ++q eLA++lg++++t+
  gi|386001633|ref|YP_005919932.1| 14 LTQEELAKKLGVTRQTI 30
                                      8**************98 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.7e-05     0.056      10      27 ..      15      32 ..      14      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsq 27
                                      +q +LA++lgv++q++  
  gi|386001633|ref|YP_005919932.1| 15 TQEELAKKLGVTRQTIIA 32
                                      599************965 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.7e-05     0.087      14      61 ..      15      63 ..       9      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                                      SCHHHHCCTT--HHHHHHHHHSSS--.HHHHHHHHHHH---HHHHHC-S CS
                     Phage_CI_repr 14 mqkeLAdlLgiakssvstwvrRdffP.gdvvvtcaletdtsLewLatGk 61
                                      +q+eLA+ Lg+ ++++    +  ++P  d+  ++a   ++++e++ + +
  gi|386001633|ref|YP_005919932.1| 15 TQEELAKKLGVTRQTIIAIEKDKYNPsLDLAFKMARIFGVKIEDIFVYD 63
                                      589*************888887888889***999999999999987655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.13      21      38 ..      13      30 ..       2      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      EEEHHHHHHHHTSSHHHH CS
                            MarR_2 21 dltvgelarrlglsksav 38
                                      dlt+ ela++lg++++++
  gi|386001633|ref|YP_005919932.1| 13 DLTQEELAKKLGVTRQTI 30
                                      79**************97 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00035      0.35       2      18 ..      14      30 ..      14      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                            HTH_17  2 ltveEaAelLgvsrstv 18
                                      lt eE+A+ Lgv r+t+
  gi|386001633|ref|YP_005919932.1| 14 LTQEELAKKLGVTRQTI 30
                                      799*************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00035      0.35      10      37 ..       2      30 ..       2      31 .. 0.83
   2 ?   -3.1   0.0       7.1   7.1e+03      25      32 ..      47      54 ..      47      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                            HTH_38 10 ReeIerlla.eGlslreIArrLgrspsTI 37
                                      R++I   +a  +l++ e A++Lg+ ++TI
  gi|386001633|ref|YP_005919932.1|  2 RNKIKVYRAiFDLTQEELAKKLGVTRQTI 30
                                      67777777644699**************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.1
                            HTH_38 25 eIArrLgr 32
                                      ++Ar+ g+
  gi|386001633|ref|YP_005919932.1| 47 KMARIFGV 54
                                      68999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 550.47
//
Query:       gi|386001634|ref|YP_005919933.1|  [L=123]
Description: hypothetical protein Mhar_0939 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-28   99.0   4.4    1.7e-28   98.9   4.4    1.0  1  DUF2178   Predicted membrane protein (DUF2178)
  ------ inclusion threshold ------
      0.033   14.6   0.2       0.04   14.3   0.2    1.2  1  DUF3796   Protein of unknown function (DUF3796)


Domain annotation for each model (and alignments):
>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   4.4   1.9e-32   1.7e-28       1     106 []       1     104 [.       1     104 [. 0.98

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.9e-32
                           DUF2178   1 lliivavialvglgiwaaignvllaviavaaGvllaillkkkveevveDERlariaekAsrktlqillfliallgvv 77 
                                       +++iva++a+ g+++   i++v l++i+ a+G +l++l+++++eevv DER++r++e+A++++++ ++++ al+gv+
  gi|386001634|ref|YP_005919933.1|   1 MVVIVATVAVAGWSA--VIAEVPLVLISAATGGFLFYLCRSRMEEVVVDERDERVSERAAKVAVEAFAAASALVGVL 75 
                                       689***********9..999********************************************************* PP

                           DUF2178  78 livlksdfpeytrvgfllafsallllilY 106
                                       +i++++++p+ ++vgf+lafsa++l+ilY
  gi|386001634|ref|YP_005919933.1|  76 FIAARDEHPGLMNVGFALAFSASALMILY 104
                                       ****************************9 PP

>> DUF3796  Protein of unknown function (DUF3796)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.5e-06      0.04      15      93 ..      14      89 ..       5     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-06
                           DUF3796 15 lglfyflleeealllffaFfaffsfffvaklstvllDErfeenvkraaaiafkvaileiiiavlislilsrvelsevll 93
                                      +     + e + +l+  a  +f+ +   +++++v+ DEr e   +raa +a +    +++++ ++ +++++ +   + +
  gi|386001634|ref|YP_005919933.1| 14 SA---VIAEVPLVLISAATGGFLFYLCRSRMEEVVVDERDERVSERAAKVAVEAFAAASALVGVLFIAARDEHPGLMNV 89
                                      44...45566777777777789999999***************999999999988888888888877777664333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 925.01
//
Query:       gi|386001635|ref|YP_005919934.1|  [L=354]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-25   87.2  18.5    1.8e-06   27.5   0.5    7.2  7  TPR_11           TPR repeat
    4.3e-23   81.7  51.2    2.1e-06   28.3   1.3    6.6  6  TPR_16           Tetratricopeptide repeat
    2.6e-21   74.5  22.6     0.0016   18.2   0.1    8.9  9  TPR_1            Tetratricopeptide repeat
    2.2e-20   71.1  14.2    0.00056   19.9   0.1    8.2  8  TPR_8            Tetratricopeptide repeat
    2.4e-19   67.8  33.8    0.00014   21.7   0.1    9.5 10  TPR_2            Tetratricopeptide repeat
    1.6e-17   62.7  39.0    0.00079   20.1   0.9    7.8  7  TPR_14           Tetratricopeptide repeat
    1.6e-16   59.4   2.4      0.086   13.3   0.0    7.5  7  TPR_17           Tetratricopeptide repeat
    9.5e-13   48.5  32.5     0.0005   20.5   5.5    5.5  7  TPR_19           Tetratricopeptide repeat
    1.6e-12   47.5  29.1    0.00035   20.8   1.0    5.5  5  TPR_12           Tetratricopeptide repeat
    1.2e-06   29.1   1.5      0.012   16.1   0.0    3.2  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    1.8e-05   25.0  14.9        2.5    8.9   0.2    6.4  6  TPR_6            Tetratricopeptide repeat
    0.00019   21.5  26.8     0.0012   19.0   3.1    5.7  5  TPR_9            Tetratricopeptide repeat
    0.00021   21.0   0.6    0.00021   21.0   0.6    6.1  6  TPR_10           Tetratricopeptide repeat
     0.0013   18.6  24.2       0.38   10.9   0.2    6.9  7  TPR_7            Tetratricopeptide repeat
     0.0016   17.5   0.4        2.5    6.9   0.0    3.8  4  NARP1            NMDA receptor-regulated protein 1
     0.0041   16.6   9.3       0.33   10.3   2.7    3.1  3  SNAP             Soluble NSF attachment protein, SNAP
  ------ inclusion threshold ------
       0.08   13.6   2.2       0.08   13.6   2.2    6.9  5  TPR_4            Tetratricopeptide repeat
      0.096   12.8   4.1        2.4    8.3   0.1    4.1  4  Exonuc_VII_S     Exonuclease VII small subunit
        0.4   10.7  10.5        1.9    8.6   2.8    3.7  5  DUF3856          Domain of Unknown Function (DUF3856)
        1.7    8.5   5.5         11    5.9   0.2    3.5  3  Wzy_C_2          Virulence factor membrane-bound polymerase, 


Domain annotation for each model (and alignments):
>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.5     2e-09   1.8e-06       1      40 [.      39      78 ..      39      79 .. 0.93
   2 !   23.4   0.1   3.8e-08   3.4e-05      10      37 ..      90     117 ..      89     120 .. 0.90
   3 ?    2.4   0.0      0.14   1.3e+02      20      35 ..     144     159 ..     135     163 .. 0.84
   4 ?    4.6   0.0      0.03        26      10      25 ..     175     190 ..     171     190 .. 0.90
   5 !   20.9   0.3   2.4e-07   0.00022      10      39 ..     228     259 ..     219     262 .. 0.80
   6 !    9.9   0.8   0.00063      0.57       7      26 ..     261     280 ..     255     288 .. 0.79
   7 !    6.3   0.0    0.0083       7.5       4      42 .]     297     335 ..     296     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2e-09
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                      G  + e G ye+A +aY +A+  dP+n ++++  G+a+y+
  gi|386001635|ref|YP_005919934.1| 39 GEDLLEAGSYEDAAAAYDEAISMDPENGTLHLSKGDALYA 78
                                      5668899*******************************97 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 3.8e-08
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGla 37 
                                       +eeAi+aY++A++ldP +a a ++ G a
  gi|386001635|ref|YP_005919934.1|  90 LEEAIAAYEEAIRLDPASAMARLGKGRA 117
                                       79*****************999888866 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.14
                            TPR_11  20 AlkldPdnaeayynLG 35 
                                       A++ldP + +a+  +G
  gi|386001635|ref|YP_005919934.1| 144 AIDLDPVFFDAWVLRG 159
                                       9**********99888 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.03
                            TPR_11  10 yeeAieaYkkAlkldP 25 
                                       y++++ aY++A++l P
  gi|386001635|ref|YP_005919934.1| 175 YNQSLSAYERAIDLAP 190
                                       999**********966 PP

  == domain 5  score: 20.9 bits;  conditional E-value: 2.4e-07
                            TPR_11  10 yeeAieaYkkAlkldPdna..eayynLGlayy 39 
                                       ye A++aY +A++ldPd+a  ea +n++ +++
  gi|386001635|ref|YP_005919934.1| 228 YERAVAAYDEAIELDPDFAglEARLNRASVLA 259
                                       9****************995556666666665 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.00063
                            TPR_11   7 qGkyeeAieaYkkAlkldPd 26 
                                       +G+ye +ieaY +A +  P 
  gi|386001635|ref|YP_005919934.1| 261 LGRYERSIEAYDQAAEAAPG 280
                                       7*************886665 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.0083
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + e G+ e A+e++ +A   dP na a+   G+++ ++G
  gi|386001635|ref|YP_005919934.1| 297 LLEMGEEELALESLDAATFADPGNAAAWTRKGDLLSALG 335
                                       56889999*********************9999988777 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.3   2.3e-09   2.1e-06       4      50 ..      39      82 ..      36      85 .. 0.92
   2 !   18.7   1.6   2.3e-06    0.0021      14      48 ..      91     122 ..      88     125 .. 0.91
   3 ?    5.7   0.2     0.027        24      15      52 ..     136     170 ..     134     193 .. 0.70
   4 ?    1.8   3.0      0.44   3.9e+02      10      33 ..     172     195 ..     164     219 .. 0.76
   5 !   26.2  12.7   1.1e-08   9.4e-06       2      67 ..     217     281 ..     209     281 .. 0.83
   6 !   21.7   4.4   2.6e-07   0.00023       3      57 ..     293     344 ..     291     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.3e-09
                            TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrl 50
                                      + ++l+ag y+dAaaa+++a+ +d   P++   +l +gda++++ r 
  gi|386001635|ref|YP_005919934.1| 39 GEDLLEAGSYEDAAAAYDEAISMD---PENGTLHLSKGDALYALARA 82
                                      789*********************...***************98765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.3e-06
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqg 48 
                                       ++A+aa+e+a+++d   P+ a A+l++g+a+  ++
  gi|386001635|ref|YP_005919934.1|  91 EEAIAAYEEAIRLD---PASAMARLGKGRALSLAS 122
                                       89************...*************98665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.027
                            TPR_16  15 dAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52 
                                       +A+ a e a+++d   P+  +A+ l+g ++ ++  l++
  gi|386001635|ref|YP_005919934.1| 136 EALSAVEMAIDLD---PVFFDAWVLRGTLLDELAALTG 170
                                       6888888889999...9999999999988877754444 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.44
                            TPR_16  10 agdyddAaaaleaalkrdpssPd...a 33 
                                       +  y + + a+e+a++++   P+   +
  gi|386001635|ref|YP_005919934.1| 172 LSGYNQSLSAYERAIDLA---PFgdaR 195
                                       5679999**********9...874332 PP

  == domain 5  score: 26.2 bits;  conditional E-value: 1.1e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       a++++  +a  y++A+aa+++a+++d   Pd    eA+l+++ +++ +gr+++ +++y+ a++aap++
  gi|386001635|ref|YP_005919934.1| 217 AAGDSEGAAEMYERAVAAYDEAIELD---PDfaGLEARLNRASVLAGLGRYERSIEAYDQAAEAAPGD 281
                                       45666666666788888888888888...55779********************************97 PP

  == domain 6  score: 21.7 bits;  conditional E-value: 2.6e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaaly 57 
                                       +a  +l+ g+ + A++ l+aa+ +d   P +a+A+  +gd++ ++gr  eA+a+ 
  gi|386001635|ref|YP_005919934.1| 293 KAGVLLEMGEEELALESLDAATFAD---PGNAAAWTRKGDLLSALGRGSEAEAAR 344
                                       6899*********************...***********************9764 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.8e-06    0.0052       4      34 .]      35      65 ..      32      65 .. 0.89
   2 !   14.3   0.5   2.9e-05     0.026      18      32 ..      91     105 ..      90     107 .. 0.93
   3 ?    1.7   0.0      0.29   2.6e+02      18      32 ..     135     149 ..     134     151 .. 0.92
   4 !    6.4   0.1    0.0093       8.4      17      32 ..     175     190 ..     175     191 .. 0.93
   5 !    7.7   0.1    0.0038       3.4       1      28 [.     205     232 ..     205     233 .. 0.94
   6 !   18.1   0.9   1.8e-06    0.0016      15      34 .]     226     245 ..     212     245 .. 0.92
   7 !   18.2   0.1   1.7e-06    0.0016       2      33 ..     249     280 ..     248     281 .. 0.91
   8 ?    0.9   0.0      0.52   4.6e+02      10      28 ..     296     314 ..     289     320 .. 0.78
   9 ?    6.2   0.1     0.011       9.8       1      22 [.     321     342 ..     321     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                                      ++  G  +++ g y++A ++y++A++ +P+n
  gi|386001635|ref|YP_005919934.1| 35 WFLVGEDLLEAGSYEDAAAAYDEAISMDPEN 65
                                      66667778999******************97 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHHST CS
                             TPR_1  18 deAleyyekALelnP 32 
                                       +eA+++ye+A++l+P
  gi|386001635|ref|YP_005919934.1|  91 EEAIAAYEEAIRLDP 105
                                       9*************9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHST CS
                             TPR_1  18 deAleyyekALelnP 32 
                                       +eAl + e A+ l+P
  gi|386001635|ref|YP_005919934.1| 135 KEALSAVEMAIDLDP 149
                                       6999999*******9 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHHHHHHST CS
                             TPR_1  17 ydeAleyyekALelnP 32 
                                       y++ l +ye+A+ l P
  gi|386001635|ref|YP_005919934.1| 175 YNQSLSAYERAIDLAP 190
                                       88999*********99 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0038
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekAL 28 
                                       a al  l+n +   g+ + A e ye+A+
  gi|386001635|ref|YP_005919934.1| 205 AAALSTLANGLAAAGDSEGAAEMYERAV 232
                                       679999*********************7 PP

  == domain 6  score: 18.1 bits;  conditional E-value: 1.8e-06
                                       T-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  15 gkydeAleyyekALelnPnn 34 
                                       ++y+ A+++y++A+el+P++
  gi|386001635|ref|YP_005919934.1| 226 EMYERAVAAYDEAIELDPDF 245
                                       68****************97 PP

  == domain 7  score: 18.2 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a  n++ ++  lg+y+  +e+y++A e  P 
  gi|386001635|ref|YP_005919934.1| 249 EARLNRASVLAGLGRYERSIEAYDQAAEAAPG 280
                                       5789**********************998886 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.52
                                       HHHHTT-HHHHHHHHHHHH CS
                             TPR_1  10 ayfklgkydeAleyyekAL 28 
                                       +++++g+ + Ale  + A 
  gi|386001635|ref|YP_005919934.1| 296 VLLEMGEEELALESLDAAT 314
                                       7899*********998886 PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHTT-HHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAle 22 
                                       a a+ ++G ++  lg+  eA++
  gi|386001635|ref|YP_005919934.1| 321 AAAWTRKGDLLSALGRGSEAEA 342
                                       78**************999986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00014      0.13      11      34 .]      42      65 ..      35      65 .. 0.86
   2 !   15.3   0.1   1.9e-05     0.017       4      33 ..      76     106 ..      73     107 .. 0.76
   3 ?   -1.9   0.0       6.3   5.6e+03      18      32 ..     135     149 ..     134     150 .. 0.84
   4 ?    4.9   0.0     0.041        37      17      32 ..     175     190 ..     171     191 .. 0.91
   5 !   13.5   0.1   6.9e-05     0.062      15      33 ..     226     244 ..     212     245 .. 0.86
   6 !   19.9   0.1   6.3e-07   0.00056       2      33 ..     249     280 ..     248     281 .. 0.93
   7 ?    2.3   0.0      0.27   2.4e+02       7      28 ..     293     314 ..     289     320 .. 0.81
   8 ?    5.0   0.0     0.038        34       1      22 [.     321     342 ..     321     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                      HHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 11 ylklgdyeeAkeyyekaleldpdn 34
                                      +l+ g ye A ++y +a+++dp+n
  gi|386001635|ref|YP_005919934.1| 42 LLEAGSYEDAAAAYDEAISMDPEN 65
                                      56789*****************86 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiy.lklgdyeeAkeyyekaleldpd 33 
                                       +y l+++  ++   +eeA+++ye+a++ldp+
  gi|386001635|ref|YP_005919934.1|  76 LYALARAQgFDPRTLEEAIAAYEEAIRLDPA 106
                                       555555555555668***************7 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.3
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekaleldp 32 
                                       +eA ++ e a++ldp
  gi|386001635|ref|YP_005919934.1| 135 KEALSAVEMAIDLDP 149
                                       688888999999998 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekaleldp 32 
                                       y+++ ++ye+a++l+p
  gi|386001635|ref|YP_005919934.1| 175 YNQSLSAYERAIDLAP 190
                                       788999********99 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 6.9e-05
                                       T-HHHHHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekaleldpd 33 
                                       + ye A+++y +a+eldpd
  gi|386001635|ref|YP_005919934.1| 226 EMYERAVAAYDEAIELDPD 244
                                       679***************8 PP

  == domain 6  score: 19.9 bits;  conditional E-value: 6.3e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea +n +s++  lg+ye ++e+y +a e++p 
  gi|386001635|ref|YP_005919934.1| 249 EARLNRASVLAGLGRYERSIEAYDQAAEAAPG 280
                                       7889************************9995 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.27
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekal 28 
                                       ++ ++l++g+ e A e++  a+
  gi|386001635|ref|YP_005919934.1| 293 KAGVLLEMGEEELALESLDAAT 314
                                       6678999**********99987 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.038
                                       CCHHHHHHHHHHHTT-HHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAke 22 
                                       a a+ ++g++++ lg+  eA++
  gi|386001635|ref|YP_005919934.1| 321 AAAWTRKGDLLSALGRGSEAEA 342
                                       579************9888876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.6e-07   0.00014       3      34 .]      34      65 ..      32      65 .. 0.94
   2 ?   -2.4   0.1       8.1   7.2e+03       2      10 ..      74      82 ..      72      83 .. 0.70
   3 !   14.1   0.5   4.4e-05     0.039      18      33 ..      91     106 ..      90     107 .. 0.92
   4 ?    0.9   0.0      0.71   6.4e+02      18      32 ..     135     149 ..     134     149 .. 0.93
   5 ?    5.5   0.1     0.023        21      17      32 ..     175     190 ..     175     191 .. 0.92
   6 !   12.0   0.6    0.0002      0.18       1      29 [.     205     233 ..     205     234 .. 0.94
   7 !   15.3   2.1   1.8e-05     0.016       4      33 ..     215     244 ..     212     245 .. 0.83
   8 !   19.5   0.4   7.8e-07    0.0007       3      34 .]     250     281 ..     248     281 .. 0.92
   9 ?    2.0   0.0      0.31   2.8e+02       8      34 .]     294     320 ..     288     320 .. 0.85
  10 ?    3.1   0.2      0.14   1.2e+02       1      22 [.     321     342 ..     321     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                       ++  G+ ++++g ye+A++a+++A++ dP+n
  gi|386001635|ref|YP_005919934.1| 34 DWFLVGEDLLEAGSYEDAAAAYDEAISMDPEN 65
                                      599***************************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.1
                             TPR_2  2 ealynlGla 10
                                      +aly+l++a
  gi|386001635|ref|YP_005919934.1| 74 DALYALARA 82
                                      577777765 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.4e-05
                             TPR_2  18 eeAleafekAleldPn 33 
                                       eeA++a+e+A++ldP 
  gi|386001635|ref|YP_005919934.1|  91 EEAIAAYEEAIRLDPA 106
                                       9**************5 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.71
                             TPR_2  18 eeAleafekAleldP 32 
                                       +eAl a e A+ ldP
  gi|386001635|ref|YP_005919934.1| 135 KEALSAVEMAIDLDP 149
                                       79************9 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.023
                             TPR_2  17 yeeAleafekAleldP 32 
                                       y++ l a+e+A+ l+P
  gi|386001635|ref|YP_005919934.1| 175 YNQSLSAYERAIDLAP 190
                                       78899*********99 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.0002
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       a al  l++ ++++gd e A+e +e+A++
  gi|386001635|ref|YP_005919934.1| 205 AAALSTLANGLAAAGDSEGAAEMYERAVA 233
                                       6899***********************86 PP

  == domain 7  score: 15.3 bits;  conditional E-value: 1.8e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       l + G++  ++  ye+A++a+++A+eldP+
  gi|386001635|ref|YP_005919934.1| 215 LAAAGDSEGAAEMYERAVAAYDEAIELDPD 244
                                       5566777777889****************8 PP

  == domain 8  score: 19.5 bits;  conditional E-value: 7.8e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a  n++ +++ lg+ye+ +ea+++A e +P++
  gi|386001635|ref|YP_005919934.1| 250 ARLNRASVLAGLGRYERSIEAYDQAAEAAPGD 281
                                       66799************************986 PP

  == domain 9  score: 2.0 bits;  conditional E-value: 0.31
                             TPR_2   8 GlayyklgdyeeAleafekAleldPnn 34 
                                       + +++++g+ e Ale +++A   dP+n
  gi|386001635|ref|YP_005919934.1| 294 AGVLLEMGEEELALESLDAATFADPGN 320
                                       567899*************99888876 PP

  == domain 10  score: 3.1 bits;  conditional E-value: 0.14
                             TPR_2   1 aealynlGlayyklgdyeeAle 22 
                                       a a+ + G+++ +lg+  eA++
  gi|386001635|ref|YP_005919934.1| 321 AAAWTRKGDLLSALGRGSEAEA 342
                                       689*************999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.9e-05     0.035       4      39 ..      35      70 ..      32      75 .. 0.87
   2 !   17.5   2.7   5.7e-06    0.0051       3      43 ..      75     116 ..      73     117 .. 0.90
   3 ?    0.6   0.0       1.6   1.4e+03      18      42 ..     135     159 ..     134     163 .. 0.82
   4 ?    1.2   0.2         1   8.9e+02      19      33 ..     177     192 ..     152     202 .. 0.68
   5 !   13.7   4.4   9.4e-05     0.084       2      33 ..     206     237 ..     205     252 .. 0.75
   6 !   20.1   0.9   8.8e-07   0.00079       2      41 ..     249     288 ..     248     291 .. 0.92
   7 !   14.5   0.2   5.3e-05     0.048       8      44 .]     294     330 ..     289     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-05
                            TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawl 39
                                      + + +e ll++G +++A+a++++a++ +P++ +++l
  gi|386001635|ref|YP_005919934.1| 35 WFLVGEDLLEAGSYEDAAAAYDEAISMDPENGTLHL 70
                                      66678889**********************998887 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.7e-06
                            TPR_14   3 allalaeal.lalGdpdeAiallrralalaPddaeawlllaq 43 
                                       al+ala+a  +  + ++eAia++++a++l+P++a a+l  ++
  gi|386001635|ref|YP_005919934.1|  75 ALYALARAQgFDPRTLEEAIAAYEEAIRLDPASAMARLGKGR 116
                                       889999998688889**********************98887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.6
                            TPR_14  18 deAiallrralalaPddaeawllla 42 
                                       +eA+ + + a++l+P + +aw l +
  gi|386001635|ref|YP_005919934.1| 135 KEALSAVEMAIDLDPVFFDAWVLRG 159
                                       5899999********8888887655 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1
                            TPR_14  19 eAiallrralalaP.d 33 
                                       +++ +++ra++laP +
  gi|386001635|ref|YP_005919934.1| 177 QSLSAYERAIDLAPfG 192
                                       4778999999999963 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 9.4e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPd 33 
                                       +al  la  l+a+Gd ++A+++++ra+a++ +
  gi|386001635|ref|YP_005919934.1| 206 AALSTLANGLAAAGDSEGAAEMYERAVAAYDE 237
                                       6888999********99999999998885543 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 8.8e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       ea+l +a++l+ lG+++++i+++++a ++aP+d+ a+  l
  gi|386001635|ref|YP_005919934.1| 249 EARLNRASVLAGLGRYERSIEAYDQAAEAAPGDLKAYVSL 288
                                       79999*****************************999766 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 5.3e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                       a +ll+ G+ + A++ l++a  ++P++a+aw++ ++l
  gi|386001635|ref|YP_005919934.1| 294 AGVLLEMGEEELALESLDAATFADPGNAAAWTRKGDL 330
                                       789*****************************99875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0028       2.5       1      26 [.      54      79 ..      54      91 .. 0.84
   2 !    9.9   0.0    0.0011      0.98       1      26 [.      96     121 ..      96     135 .. 0.89
   3 !    7.1   0.0    0.0089       7.9       5      25 ..     144     164 ..     141     173 .. 0.89
   4 ?    0.8   0.1       0.9   8.1e+02       2      11 ..     182     191 ..     181     226 .. 0.58
   5 !   13.3   0.0   9.6e-05     0.086       1      33 [.     234     268 ..     234     269 .. 0.94
   6 ?    1.8   0.0      0.42   3.8e+02       1      19 [.     270     288 ..     270     308 .. 0.78
   7 !    9.2   0.0    0.0019       1.7       9      31 ..     317     339 ..     305     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                            TPR_17  1 lylkaleldPnnadaynnLAelllkn 26
                                      +y +a+  dP n  ++  ++ +l+ +
  gi|386001635|ref|YP_005919934.1| 54 AYDEAISMDPENGTLHLSKGDALYAL 79
                                      599*********99999999988754 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                            TPR_17   1 lylkaleldPnnadaynnLAelllkn 26 
                                       +y++a++ldP +a a   ++++l+ +
  gi|386001635|ref|YP_005919934.1|  96 AYEEAIRLDPASAMARLGKGRALSLA 121
                                       5********************99854 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0089
                            TPR_17   5 aleldPnnadaynnLAelllk 25 
                                       a++ldP  +da+ ++++ll +
  gi|386001635|ref|YP_005919934.1| 144 AIDLDPVFFDAWVLRGTLLDE 164
                                       89****************974 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.9
                            TPR_17   2 ylkaleldPn 11 
                                       y++a++l P 
  gi|386001635|ref|YP_005919934.1| 182 YERAIDLAPF 191
                                       8888888775 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 9.6e-05
                            TPR_17   1 lylkaleldPnn..adaynnLAelllknGdlmtAr 33 
                                       +y +a+eldP+    +a  n+A +l+ +G++++ +
  gi|386001635|ref|YP_005919934.1| 234 AYDEAIELDPDFagLEARLNRASVLAGLGRYERSI 268
                                       59**********99*****************9976 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.42
                            TPR_17   1 lylkaleldPnnadaynnL 19 
                                       +y +a+e  P + +ay  L
  gi|386001635|ref|YP_005919934.1| 270 AYDQAAEAAPGDLKAYVSL 288
                                       599*********8888766 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.0019
                            TPR_17   9 dPnnadaynnLAelllknGdlmt 31 
                                       dP na a++ ++ ll+ +G+  +
  gi|386001635|ref|YP_005919934.1| 317 DPGNAAAWTRKGDLLSALGRGSE 339
                                       9****************996433 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.2   1.7e-06    0.0015       1      40 [.      42      81 ..      42      84 .. 0.91
   2 !   11.0   1.0   0.00051      0.46       6      36 ..      89     119 ..      80     124 .. 0.86
   3 ?   -2.4   0.0         8   7.2e+03       9      29 ..     136     156 ..     135     164 .. 0.77
   4 ?   -0.7   0.2       2.3     2e+03      26      42 ..     206     222 ..     175     227 .. 0.54
   5 !   20.5   5.5   5.6e-07    0.0005       4      64 ..     225     288 ..     215     291 .. 0.81
   6 !   15.1   3.2   2.8e-05     0.025       5      59 ..     262     321 ..     260     323 .. 0.92
   7 !   14.3   1.2   4.7e-05     0.042       1      47 [.     297     343 ..     297     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgq 40
                                      ll++g y++A+a++ +a++ dp+n+ + l   +al+al +
  gi|386001635|ref|YP_005919934.1| 42 LLEAGSYEDAAAAYDEAISMDPENGTLHLSKGDALYALAR 81
                                      79*********************99999999999988865 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00051
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeall 36 
                                        ++eA+a++e+a+  dp +a arl+  +al 
  gi|386001635|ref|YP_005919934.1|  89 TLEEAIAAYEEAIRLDPASAMARLGKGRALS 119
                                       789**********************999986 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8
                            TPR_19   9 eAlalleqalqedpknaearl 29 
                                       eAl++ e a++ dp   +a+ 
  gi|386001635|ref|YP_005919934.1| 136 EALSAVEMAIDLDPVFFDAWV 156
                                       799999999999997666665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.3
                            TPR_19  26 earllLAeallalgqld 42 
                                       +a+  LA+ l a+g+ +
  gi|386001635|ref|YP_005919934.1| 206 AALSTLANGLAAAGDSE 222
                                       22223444444444444 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 5.6e-07
                            TPR_19   4 egdyaeAlalleqalqedpk..naearllLAeallalgqldeAealLdalpeedpdd.aryasL 64 
                                       ++ y++A+a++ +a++ dp+   +earl+ A +l  lg+++  +++ d++ e++p d  +y sL
  gi|386001635|ref|YP_005919934.1| 225 AEMYERAVAAYDEAIELDPDfaGLEARLNRASVLAGLGRYERSIEAYDQAAEAAPGDlKAYVSL 288
                                       44566777777778888***6666777777**************************99888877 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 2.8e-05
                            TPR_19   5 gdyaeAlalleqalqedpknaearllL.....AeallalgqldeAealLdalpeedpdda 59 
                                       g+y++ ++++ qa +++p+++ a   L     A +ll++g+ + A + Lda+  +dp +a
  gi|386001635|ref|YP_005919934.1| 262 GRYERSIEAYDQAAEAAPGDLKAYVSLvfvekAGVLLEMGEEELALESLDAATFADPGNA 321
                                       899****************9999998888888*********************9999854 PP

  == domain 7  score: 14.3 bits;  conditional E-value: 4.7e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       ll++g  + Al+ l +a  +dp+na+a+ +  ++l alg+  eAea+
  gi|386001635|ref|YP_005919934.1| 297 LLEMGEEELALESLDAATFADPGNAAAWTRKGDLLSALGRGSEAEAA 343
                                       6899999999999***9999*************************86 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.4   2.4e-06    0.0022       8      75 ..      37     104 ..      29     106 .. 0.91
   2 ?    6.5   0.1     0.011       9.9      21      75 ..     136     189 ..     117     190 .. 0.83
   3 !   14.4   2.6   3.8e-05     0.034      41      76 ..     201     236 ..     193     237 .. 0.88
   4 !   20.8   1.0   3.9e-07   0.00035       6      69 ..     251     311 ..     248     314 .. 0.92
   5 ?    2.6   0.2      0.18   1.6e+02       3      29 ..     321     347 ..     319     352 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrly.ralgryeeAlelleealaia 75 
                                        +++ l+++g y++A + +++a+ +     G+ h+    +l++L+r++ +    +eeA++++eea++++
  gi|386001635|ref|YP_005919934.1|  37 LVGEDLLEAGSYEDAAAAYDEAISMD-PENGTLHLSKGDALYALARAQgFDPRTLEEAIAAYEEAIRLD 104
                                       579999********************.6679*****************6688**************987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                            TPR_12  21 eAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       eAl+  e a+++   ++ + + l  t l  L+ l   l  y + l+++e+a+++a
  gi|386001635|ref|YP_005919934.1| 136 EALSAVEMAIDLD-PVFFDAWVLRGTLLDELAALTGDLSGYNQSLSAYERAIDLA 189
                                       7777777777777.6677788899999999999999999************9987 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.8e-05
                            TPR_12  41 hpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +++ a++l +L+  + a+g+ e A e++e+a+a++ 
  gi|386001635|ref|YP_005919934.1| 201 WDGKAAALSTLANGLAAAGDSEGAAEMYERAVAAYD 236
                                       56799***************************9986 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 3.9e-07
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                         n+a+vl+ lgry+ ++e +++a e+a   +G+ +++++ +    + +++++g+ e Ale l 
  gi|386001635|ref|YP_005919934.1| 251 RLNRASVLAGLGRYERSIEAYDQAAEAA---PGDLKAYVSLVFVEKAGVLLEMGEEELALESLD 311
                                       569*********************9999...*****************************9876 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.18
                            TPR_12   3 atalnnlaavlrrlgrydeAlelleka 29 
                                       a+a+++ +++l +lgr  eA++   +a
  gi|386001635|ref|YP_005919934.1| 321 AAAWTRKGDLLSALGRGSEAEAARARA 347
                                       566777888888888888887766665 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.12     1e+02      77     120 ..      40      83 ..      30      87 .. 0.90
   2 !    6.9   0.2    0.0091       8.1      67     124 ..     203     269 ..     187     278 .. 0.76
   3 !   16.1   0.0   1.3e-05     0.012      73     126 ..     291     344 ..     286     347 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH- CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqa 120
                                       ++ l++g y+ aa   + ++  dpen + +  k dal +l++++
  gi|386001635|ref|YP_005919934.1|  40 EDLLEAGSYEDAAAAYDEAISMDPENGTLHLSKGDALYALARAQ 83 
                                       577899********************999999999999998875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0091
                                       TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-.........HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  67 Ggaekvlekakealkegdyrwaaellnhlvfadpen.........aeakelkadaleqlgyqaesat 124
                                       G a+++ + a+  +++gd + aae+ + +v+a +e           ea+  +a++l  lg+ ++s  
  gi|386001635|ref|YP_005919934.1| 203 GKAAALSTLANGLAAAGDSEGAAEMYERAVAAYDEAieldpdfagLEARLNRASVLAGLGRYERSIE 269
                                       67788888899999****99999999999998444223333344369999999*9999999988865 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHH CS
                   Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwR 126
                                       +eka   l+ g+ ++a+e l+ + fadp na+a + k d l +lg+++e+ ++R
  gi|386001635|ref|YP_005919934.1| 291 VEKAGVLLEMGEEELALESLDAATFADPGNAAAWTRKGDLLSALGRGSEAEAAR 344
                                       6788888999***************************************99988 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13   1.1e+02       5      31 ..      37      63 ..      35      65 .. 0.79
   2 !    7.9   0.5    0.0058       5.2       1      33 []      74     107 ..      74     107 .. 0.82
   3 ?    2.2   0.0       0.4   3.6e+02      14      31 ..     173     190 ..     153     191 .. 0.67
   4 !    7.6   0.1    0.0074       6.6      13      30 ..     218     235 ..     206     244 .. 0.59
   5 !    8.9   0.2    0.0028       2.5       1      31 [.     249     279 ..     249     281 .. 0.91
   6 ?   -1.7   0.0       6.8   6.1e+03       9      24 ..     297     311 ..     293     313 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  5 klalsyrklgdtdkAlealerlikeYP 31
                                      + ++ ++++g +++A +a+++ i+  P
  gi|386001635|ref|YP_005919934.1| 37 LVGEDLLEAGSYEDAAAAYDEAISMDP 63
                                      5566678888**********9998666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHHH.HHHHHHHHHHHHHHH-TT- CS
                             TPR_6   1 dAlyklalsyrklg.dtdkAlealerlikeYPdS 33 
                                       dAly la+++       ++A++a+e+ i+  P S
  gi|386001635|ref|YP_005919934.1|  74 DALYALARAQGFDPrTLEEAIAAYEEAIRLDPAS 107
                                       799999999996532677***********99976 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHH-T CS
                             TPR_6  14 gdtdkAlealerlikeYP 31 
                                         + ++l a+er i+  P
  gi|386001635|ref|YP_005919934.1| 173 SGYNQSLSAYERAIDLAP 190
                                       5577999******99877 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHHHHHH- CS
                             TPR_6  13 lgdtdkAlealerlikeY 30 
                                       +gd++ A e++er +  Y
  gi|386001635|ref|YP_005919934.1| 218 AGDSEGAAEMYERAVAAY 235
                                       455555555555555544 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       +A +++a  +  lg++++++ea+++  +  P
  gi|386001635|ref|YP_005919934.1| 249 EARLNRASVLAGLGRYERSIEAYDQAAEAAP 279
                                       699999*99**999***********999888 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAleale 24 
                                       ++ ++g+ + Ale l+
  gi|386001635|ref|YP_005919934.1| 297 LL-EMGEEELALESLD 311
                                       44.4669999999875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.018        16      29      66 ..      32      69 ..      12      83 .. 0.84
   2 ?    3.7   0.3     0.077        69       9      38 ..      88     117 ..      80     120 .. 0.83
   3 ?    4.4   0.5     0.046        41      13      45 ..     136     168 ..     133     201 .. 0.67
   4 !   19.0   3.1   1.3e-06    0.0012       9      65 ..     226     284 ..     224     287 .. 0.89
   5 ?    3.0   0.5      0.13   1.2e+02      12      48 ..     304     340 ..     292     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                             TPR_9 29 peerrdRGlllaqlGclsaAladLeaylalapdapdae 66
                                      +++++  G  l + G ++ A+a+ + +++++p++ + +
  gi|386001635|ref|YP_005919934.1| 32 ASDWFLVGEDLLEAGSYEDAAAAYDEAISMDPENGTLH 69
                                      67888899999999******************887765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.077
                             TPR_9   9 edweralavverllllaPddpeerrdRGll 38 
                                       +  e+a+a++e  + l+P ++  r+  G++
  gi|386001635|ref|YP_005919934.1|  88 RTLEEAIAAYEEAIRLDPASAMARLGKGRA 117
                                       567899999999999999999998887776 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.046
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGcl 45 
                                       +al +ve+ + l+P   + +  RG ll +l +l
  gi|386001635|ref|YP_005919934.1| 136 EALSAVEMAIDLDPVFFDAWVLRGTLLDELAAL 168
                                       69999*********9999999999998776553 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 1.3e-06
                             TPR_9   9 edweralavverllllaPddp..eerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       e +era a+++  + l+Pd +  e r+ R+ +la lG+++  +++ +++++ ap +  a
  gi|386001635|ref|YP_005919934.1| 226 EMYERAVAAYDEAIELDPDFAglEARLNRASVLAGLGRYERSIEAYDQAAEAAPGDLKA 284
                                       679***************9872267*****************************88666 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.13
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                       e al+ ++     +P  +  +   G ll  lG+ s+A
  gi|386001635|ref|YP_005919934.1| 304 ELALESLDAATFADPGNAAAWTRKGDLLSALGRGSEA 340
                                       5688888888888899999999999999988888877 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.07        62      11      31 ..      41      61 ..      38      61 .. 0.86
   2 ?    2.8   0.2      0.13   1.2e+02      26      35 ..      91     100 ..      76     103 .. 0.74
   3 ?   -0.2   0.1       1.1   9.9e+02       5      30 ..     162     187 ..     160     189 .. 0.74
   4 !   21.0   0.6   2.4e-07   0.00021       2      37 ..     205     240 ..     205     245 .. 0.92
   5 ?    4.1   2.0     0.049        44       4      30 ..     250     276 ..     248     278 .. 0.88
   6 ?    2.1   0.1      0.21   1.9e+02      11      23 ..     330     342 ..     328     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.07
                            TPR_10 11 alrqrgrydeAealleealai 31
                                       l + g y++A a ++ea+++
  gi|386001635|ref|YP_005919934.1| 41 DLLEAGSYEDAAAAYDEAISM 61
                                      5778899***********986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                            TPR_10  26 eealairrrl 35 
                                       eea+a+++++
  gi|386001635|ref|YP_005919934.1|  91 EEAIAAYEEA 100
                                       5666666554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.1
                            TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                                       l  La++  ++  y++++  +e+a++
  gi|386001635|ref|YP_005919934.1| 162 LDELAALTGDLSGYNQSLSAYERAID 187
                                       56677777777778888888999886 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 2.4e-07
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrllG 37 
                                       A++l+ Lan l + g+ ++A +++e+a+a++ ++ +
  gi|386001635|ref|YP_005919934.1| 205 AAALSTLANGLAAAGDSEGAAEMYERAVAAYDEAIE 240
                                       89*****************************99876 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.049
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                       ++ N a +l  +gry+++ + +++a +
  gi|386001635|ref|YP_005919934.1| 250 ARLNRASVLAGLGRYERSIEAYDQAAE 276
                                       67799*******************987 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.21
                            TPR_10  11 alrqrgrydeAea 23 
                                       +l+++gr+ eAea
  gi|386001635|ref|YP_005919934.1| 330 LLSALGRGSEAEA 342
                                       699********97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.12   1.1e+02      13      33 ..      46      64 ..      39      67 .. 0.83
   2 ?   -2.4   0.1       7.4   6.6e+03       1       9 [.      75      83 ..      75      84 .. 0.84
   3 ?    5.1   0.2     0.031        28      16      33 ..      91     106 ..      90     109 .. 0.87
   4 ?    2.1   0.0      0.26   2.4e+02      15      34 ..     175     192 ..     161     194 .. 0.79
   5 !   10.2   0.5   0.00073      0.65       1      29 [.     207     233 ..     207     245 .. 0.82
   6 !   10.9   0.2   0.00043      0.38       3      34 ..     252     281 ..     250     284 .. 0.83
   7 ?   -0.5   0.1       1.8   1.7e+03       2      21 ..     324     343 ..     323     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                             TPR_7 13 GdyeeAielyeqsLaltkdpe 33
                                      G ye+A+  y +  a+  dpe
  gi|386001635|ref|YP_005919934.1| 46 GSYEDAAAAYDE--AISMDPE 64
                                      679*********..8888887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.4
                             TPR_7  1 aLlnLarly 9 
                                      aL++Lar++
  gi|386001635|ref|YP_005919934.1| 75 ALYALARAQ 83
                                      799999985 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.031
                             TPR_7  16 eeAielyeqsLaltkdpe 33 
                                       eeAi  ye+  a++ dp 
  gi|386001635|ref|YP_005919934.1|  91 EEAIAAYEE--AIRLDPA 106
                                       89*******..9999986 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.26
                             TPR_7  15 yeeAielyeqsLaltkdped 34 
                                       y + ++ ye+  a++ +p++
  gi|386001635|ref|YP_005919934.1| 175 YNQSLSAYER--AIDLAPFG 192
                                       7788999999..99888876 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00073
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       aL+ La+   + Gd e A+e ye+  a++
  gi|386001635|ref|YP_005919934.1| 207 ALSTLANGLAAAGDSEGAAEMYER--AVA 233
                                       6889999999**************..554 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00043
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ln a++   lG+ye+ ie y q  a + +p+d
  gi|386001635|ref|YP_005919934.1| 252 LNRASVLAGLGRYERSIEAYDQ--AAEAAPGD 281
                                       688999999*************..66666655 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 1.8
                             TPR_7   2 LlnLarlysrlGdyeeAiel 21 
                                       + + ++l s+lG+ +eA+  
  gi|386001635|ref|YP_005919934.1| 324 WTRKGDLLSALGRGSEAEAA 343
                                       56679999999999999875 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.075        67      46     109 ..      40     110 ..      16     114 .. 0.73
   2 ?    1.9   0.0     0.094        85     205     237 ..     131     163 ..     124     187 .. 0.84
   3 ?    1.3   0.0      0.14   1.3e+02     206     253 ..     226     275 ..     208     283 .. 0.79
   4 !    6.9   0.0    0.0028       2.5      11      60 ..     294     343 ..     284     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.075
                                       HHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT.........SSS-HHHHHHHHHHTTTS-TT-SHH CS
                             NARP1  46 elllkLgrkeeAeatyeaLlernpenskYyeglekak.......klskedeeallalydelaekyprsdap 109
                                       e ll+ g +e+A+a+y + +++ pen + + +   a+       +++  + e+  a+y+e+ +  p s+++
  gi|386001635|ref|YP_005919934.1|  40 EDLLEAGSYEDAAAAYDEAISMDPENGTLHLSKGDALyalaraqGFDPRTLEEAIAAYEEAIRLDPASAMA 110
                                       55777889999999999999999999887765555544444444677778888888888877766666555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.094
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilk 237
                                       +  +++Al+ ++ ai+ +p + + ++ ++++l 
  gi|386001635|ref|YP_005919934.1| 131 VSGKKEALSAVEMAIDLDPVFFDAWVLRGTLLD 163
                                       455679*******************99998775 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.14
                                       T-SHHHHHHHHHHHHH-TT-..HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptl..velyltKarilkhaGdlkkAaevmeear 253
                                       + +e+A+   d+aie +p +  +e  l++a +l   G  ++ +e+ ++a 
  gi|386001635|ref|YP_005919934.1| 226 EMYERAVAAYDEAIELDPDFagLEARLNRASVLAGLGRYERSIEAYDQAA 275
                                       45789999999999999987335778889999988888888888888775 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0028
                                       HHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHH CS
                             NARP1  11 nqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeat 60 
                                       + ++ e g++e Ale L+++      + a  + k++ll +Lgr +eAea+
  gi|386001635|ref|YP_005919934.1| 294 AGVLLEMGEEELALESLDAATFADPGNAAAWTRKGDLLSALGRGSEAEAA 343
                                       66899**************999999999*******************986 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.4    0.0058       5.2      74     143 ..      32     102 ..      17     111 .. 0.81
   2 ?    4.1   0.0      0.03        27     119     174 ..     164     218 ..     132     221 .. 0.83
   3 !   10.3   2.7   0.00037      0.33     120     185 ..     211     278 ..     204     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHH.HHHHHHHHHHHHHTT--HHHHHHHHHHHHH CS
                              SNAP  74 aanayveAakcykkvspeeAvealekAieiytekgrfrra.AklkkeiaelyekelgdlekAieaYekAae 143
                                       a++ ++     ++  s e+A++a+++Ai++  e+g ++ + ++    +a     +   le+Ai+aYe+A  
  gi|386001635|ref|YP_005919934.1|  32 ASDWFLVGEDLLEAGSYEDAAAAYDEAISMDPENGTLHLSkGDALYALARAQGFDPRTLEEAIAAYEEAIR 102
                                       55555555666777789999999999999999999998765788889999999999999999999999975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.03
                                       HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHH CS
                              SNAP 119 eiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekA 174
                                       e+a l   +l+ ++++++aYe+A +l    +a +la     k+A ls+  + +++A
  gi|386001635|ref|YP_005919934.1| 164 ELAALTG-DLSGYNQSLSAYERAIDLAPFGDARSLALAWDGKAAALSTLANGLAAA 218
                                       5555544.4588999***********99999**************99987766655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00037
                                       HHHHHHHTT--HHHHHHHHHHHHHHHHHTT...-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT CS
                              SNAP 120 iaelyekelgdlekAieaYekAaelyeqee...akalankcllkvAelsaelekyekAieiyekvakks 185
                                       +a+ +  + gd e A e+Ye+A   y++        +  +++l+ A++ a l++ye++ie+y++ a+++
  gi|386001635|ref|YP_005919934.1| 211 LANGLAAA-GDSEGAAEMYERAVAAYDEAIeldPDFAGLEARLNRASVLAGLGRYERSIEAYDQAAEAA 278
                                       56666666.899999999999999998764212455667889999*******************99875 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6      0.38   3.4e+02       8      25 ..      39      56 ..      39      57 .. 0.86
   2 ?    0.8   0.2       1.2   1.1e+03       3      11 ..      75      83 ..      73      85 .. 0.86
   3 ?   13.6   2.2     9e-05      0.08       1      26 []     205     230 ..     205     230 .. 0.95
   4 ?    7.1   0.8     0.011       9.9       2      19 ..     249     266 ..     248     277 .. 0.90
   5 ?   -0.5   4.2       3.1   2.8e+03       8      23 ..     328     343 ..     321     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.38
                             TPR_4  8 ArallalGdldeAralle 25
                                      ++ ll++G +++A+a+ +
  gi|386001635|ref|YP_005919934.1| 39 GEDLLEAGSYEDAAAAYD 56
                                      5789**********9987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                             TPR_4  3 allaLAral 11
                                      al+aLAra+
  gi|386001635|ref|YP_005919934.1| 75 ALYALARAQ 83
                                      899****97 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 9e-05
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       a+al+ LA  l+a+Gd++ A+++ er
  gi|386001635|ref|YP_005919934.1| 205 AAALSTLANGLAAAGDSEGAAEMYER 230
                                       689********************997 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                             TPR_4   2 rallaLArallalGdlde 19 
                                        a+l++A +l+ lG++++
  gi|386001635|ref|YP_005919934.1| 249 EARLNRASVLAGLGRYER 266
                                       69*************986 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 3.1
                             TPR_4   8 ArallalGdldeAral 23 
                                       + +l alG+  eA+a+
  gi|386001635|ref|YP_005919934.1| 328 GDLLSALGRGSEAEAA 343
                                       7789999999999986 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0026       2.4      21      35 ..      89     103 ..      88     103 .. 0.94
   2 ?    1.4   0.0      0.37   3.3e+02      24      36 ..     177     189 ..     176     193 .. 0.89
   3 ?    0.5   0.1      0.73   6.5e+02      27      38 ..     226     237 ..     222     241 .. 0.54
   4 ?   -2.0   0.1       4.3   3.9e+03      23      34 ..     265     276 ..     264     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                      Exonuc_VII_S  21 sLeeslklyeeGvkL 35 
                                       +Lee+++ yee+++L
  gi|386001635|ref|YP_005919934.1|  89 TLEEAIAAYEEAIRL 103
                                       7***********987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.37
                      Exonuc_VII_S  24 eslklyeeGvkLl 36 
                                       +sl  ye+++ L+
  gi|386001635|ref|YP_005919934.1| 177 QSLSAYERAIDLA 189
                                       799*******997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.73
                      Exonuc_VII_S  27 klyeeGvkLlke 38 
                                       ++ye++v+ + e
  gi|386001635|ref|YP_005919934.1| 226 EMYERAVAAYDE 237
                                       566666655443 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.3
                      Exonuc_VII_S  23 eeslklyeeGvk 34 
                                       e s++ y ++++
  gi|386001635|ref|YP_005919934.1| 265 ERSIEAYDQAAE 276
                                       678999999887 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.043        38      16      38 ..      39      61 ..      29     104 .. 0.75
   2 ?    0.8   1.3      0.52   4.6e+02      61     127 ..     165     232 ..     116     239 .. 0.61
   3 ?    8.6   2.8    0.0021       1.9      25     128 ..     175     276 ..     171     282 .. 0.80
   4 ?    5.7   3.2     0.016        15      61     128 ..     211     276 ..     206     331 .. 0.67
   5 ?    0.3   0.1      0.74   6.7e+02      55      81 ..     287     313 ..     278     353 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.043
                                      HHHHHHHT-HHHHHHHHHHHHHH CS
                           DUF3856 16 aekqleegayeeaaasyrkalev 38
                                      +e  le+g+ye+aaa y +a+ +
  gi|386001635|ref|YP_005919934.1| 39 GEDLLEAGSYEDAAAAYDEAISM 61
                                      67778888999999988888876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.52
                                       HHHHHHHTT-HHHHHHHHHHHHHH..HHHH--TT.STHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  61 lsealaklgrydealesadkalry..fnrrGele.qdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       l+     l  y+++l++ ++a+    f     l    +Gk   aa+ + a +l+  G ++ a ++++ a+
  gi|386001635|ref|YP_005919934.1| 165 LAALTGDLSGYNQSLSAYERAIDLapFGDARSLAlAWDGK--AAALSTLANGLAAAGDSEGAAEMYERAV 232
                                       4545556777888888888875431143333333133455..3677777778888888888888887776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHTTS.-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHH CS
                           DUF3856  25 yeeaaasyrkalevsrti.paeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWi 100
                                       y+++   y++a++++    +   a+ ++G  a + ++l++ la  g+ + a e  ++a+  ++   el+ d     +
  gi|386001635|ref|YP_005919934.1| 175 YNQSLSAYERAIDLAPFGdARSLALAWDGK-AAALSTLANGLAAAGDSEGAAEMYERAVAAYDEAIELDPDFAG--L 248
                                       556666666777766543133446677774.667899999***********************99999999765..5 PP

                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrmage 128
                                        a ++ra  l++lGr++ +++a+ +a+e
  gi|386001635|ref|YP_005919934.1| 249 EARLNRASVLAGLGRYERSIEAYDQAAE 276
                                       7889*******************99998 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.016
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  61 lsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       l++ la  g+ + a e  ++a+  ++   el+ d     + a ++ra  l++lGr++ +++a+ +a+e
  gi|386001635|ref|YP_005919934.1| 211 LANGLAAAGDSEGAAEMYERAVAAYDEAIELDPDFAG--LEARLNRASVLAGLGRYERSIEAYDQAAE 276
                                       5555555555555555555555555555555555443..35556666666666666666666666665 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadka 81 
                                       +l++   ++ l+++g+ + ales d a
  gi|386001635|ref|YP_005919934.1| 287 SLVFVEKAGVLLEMGEEELALESLDAA 313
                                       555555566666666666666665554 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.27   2.5e+02     113     145 ..      77     109 ..      70     113 .. 0.86
   2 ?    5.9   0.2     0.012        11     144     175 ..     206     237 ..     194     244 .. 0.88
   3 ?    0.9   0.1       0.4   3.6e+02     151     170 ..     329     348 ..     303     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.27
                           Wzy_C_2 113 llelgllplspenlaaklalarklihlsPepav 145
                                       ++ ++ +  +p +l++ +a+++++i+l P  a+
  gi|386001635|ref|YP_005919934.1|  77 YALARAQGFDPRTLEEAIAAYEEAIRLDPASAM 109
                                       6777888899*******************9887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                           Wzy_C_2 144 avierlilslallGdedeAeqilararalfpe 175
                                       a ++ l+  la++Gd ++A+ +++ra a++ e
  gi|386001635|ref|YP_005919934.1| 206 AALSTLANGLAAAGDSEGAAEMYERAVAAYDE 237
                                       5667888999********************76 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.4
                           Wzy_C_2 151 lslallGdedeAeqilarar 170
                                       ++l +lG+ +eAe  +arar
  gi|386001635|ref|YP_005919934.1| 329 DLLSALGRGSEAEAARARAR 348
                                       67889999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2024.43
//
Query:       gi|386001636|ref|YP_005919935.1|  [L=463]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-42  138.0  25.4    1.8e-05   24.5   0.1   11.1 11  TPR_2            Tetratricopeptide repeat
    4.5e-39  130.7  22.1    7.1e-05   22.5   0.0   10.9 11  TPR_1            Tetratricopeptide repeat
    5.5e-35  119.7  32.2    2.2e-11   44.2   0.1    8.1  8  TPR_16           Tetratricopeptide repeat
    1.8e-34  117.1  19.2    7.3e-08   32.0   0.0   10.1 10  TPR_11           TPR repeat
    5.3e-27   91.7  11.4    0.00076   19.5   0.0   10.9 11  TPR_8            Tetratricopeptide repeat
    2.1e-22   79.2  28.0    1.5e-08   34.8   0.3    8.2  9  TPR_12           Tetratricopeptide repeat
    5.4e-21   74.9  22.2    7.3e-06   26.4   0.0    6.9  7  TPR_19           Tetratricopeptide repeat
    8.1e-21   73.0  34.4     0.0029   18.3   0.0   11.0 11  TPR_14           Tetratricopeptide repeat
      7e-16   57.4   9.1     0.0051   17.1   0.1    9.2  8  TPR_17           Tetratricopeptide repeat
    2.8e-15   56.2  18.9    1.7e-06   28.1   0.0    6.4  7  TPR_9            Tetratricopeptide repeat
    2.1e-09   37.5   2.2       0.21   11.8   0.0    5.4  5  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    7.8e-08   31.8  18.8       0.15   12.1   0.0    9.0  9  TPR_7            Tetratricopeptide repeat
    3.4e-07   30.2   7.0        2.4    8.3   0.0    6.2  6  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
      4e-07   30.3  26.0          2    9.2   0.0    9.5 10  TPR_6            Tetratricopeptide repeat
    1.3e-05   25.3  10.7      0.012   15.7   0.2    6.6  6  DUF3856          Domain of Unknown Function (DUF3856)
    0.00089   19.0  16.3        2.4    7.9   0.0    6.0  5  TPR_21           Tetratricopeptide repeat-like domain
     0.0011   18.9   0.2        1.8    8.7   0.0    3.0  2  TAD2             Transactivation domain 2
     0.0013   18.7  10.5       0.56   10.3   0.0    5.8  5  TPR_3            Tetratricopeptide repeat
      0.005   16.9  12.0        1.2    9.2   0.3    5.8  6  MIT              MIT (microtubule interacting and transport) 
     0.0051   16.2   0.5       0.38   10.1   0.0    3.2  4  TPR_MalT         MalT-like TPR region
     0.0059   17.1  17.4       0.76   10.2   0.0    5.8  5  BTAD             Bacterial transcriptional activator domain
     0.0086   15.0   0.0        4.9    5.9   0.0    3.8  4  NARP1            NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.011   15.6  28.4       0.15   12.0   0.0    8.2  8  TPR_10           Tetratricopeptide repeat
      0.037   14.3   8.8          3    8.3   0.0    4.8  5  TPR_20           Tetratricopeptide repeat
      0.061   14.0  24.6        1.7    9.5   0.3    6.2  5  TPR_4            Tetratricopeptide repeat
      0.071   13.3   0.2         93    3.3   0.0    3.9  4  DUF1510          Domain of unknown function (DUF1510)
       0.13   12.7   2.5        6.4    7.2   0.1    3.0  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
        0.2   10.6   0.1        2.1    7.3   0.0    2.3  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   2.5e-07   0.00016       1      34 []      52      85 ..      52      85 .. 0.93
   2 !   16.6   0.0   9.4e-06     0.006       2      34 .]      87     119 ..      86     119 .. 0.96
   3 !   15.3   0.0   2.5e-05     0.016       1      33 [.     120     152 ..     120     153 .. 0.95
   4 ?    5.0   0.1     0.048        31       2      23 ..     155     176 ..     154     181 .. 0.89
   5 ?    0.2   0.0       1.7   1.1e+03      21      34 .]     213     226 ..     195     226 .. 0.74
   6 !   12.2   0.1   0.00024      0.15       2      28 ..     228     254 ..     227     256 .. 0.91
   7 !   15.9   0.0   1.6e-05      0.01       2      31 ..     267     296 ..     266     298 .. 0.91
   8 !   18.6   0.1   2.2e-06    0.0014       7      33 ..     314     340 ..     305     341 .. 0.92
   9 !   24.5   0.1   2.9e-08   1.8e-05       2      33 ..     344     375 ..     343     376 .. 0.96
  10 !    7.4   0.1    0.0081       5.2       3      27 ..     384     408 ..     382     410 .. 0.92
  11 !    8.2   0.9    0.0046         3       2      29 ..     431     458 ..     430     461 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-07
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ae l  +Gl +y++  y+eAl+a+++Al l P++
  gi|386001636|ref|YP_005919935.1| 52 AEDLIDMGLELYQNRSYQEALKAYDQALFLSPDD 85
                                      5678899*************************96 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.4e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a++  G++  +lgdy++ + a++ A ++ P++
  gi|386001636|ref|YP_005919935.1|  87 RAWMGKGKVFSALGDYNQSILAYQNATRISPDD 119
                                       79*****************************96 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.5e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +ea++  Gl  + l+d+++ l+a+++Ale d n
  gi|386001636|ref|YP_005919935.1| 120 PEAWFGVGLNRFLLQDLNDSLKALDRALEMDGN 152
                                       69***************************9977 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.048
                             TPR_2   2 ealynlGlayyklgdyeeAlea 23 
                                       +a+     +++++g+ +eAlea
  gi|386001636|ref|YP_005919935.1| 155 RAWELKSAVLAQMGKNDEALEA 176
                                       58999999************97 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.7
                             TPR_2  21 leafekAleldPnn 34 
                                       l+a+e A  ldP+n
  gi|386001636|ref|YP_005919935.1| 213 LAALENATTLDPQN 226
                                       789999******97 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00024
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                       +a+  lG+a+  +g+y++ l+af+  l
  gi|386001636|ref|YP_005919935.1| 228 DAWILLGEALQGRGEYDRSLAAFDSLL 254
                                       79*********************8666 PP

  == domain 7  score: 15.9 bits;  conditional E-value: 1.6e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                        +l   G +++ +g+yeeA+ ++++ + ld
  gi|386001636|ref|YP_005919935.1| 267 LVLIDKGSVLIDMGRYEEARGLYQQTIDLD 296
                                       678899*******************99997 PP

  == domain 8  score: 18.6 bits;  conditional E-value: 2.2e-06
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                        G ++++lgdy eAleaf+++ e +P+
  gi|386001636|ref|YP_005919935.1| 314 EGVSLLRLGDYGEALEAFNRSMEAEPR 340
                                       699******************999985 PP

  == domain 9  score: 24.5 bits;  conditional E-value: 2.9e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a+  +G+a + lg ye+Al+a++ Ale++P+
  gi|386001636|ref|YP_005919935.1| 344 DAWRGIGDARMGLGFYEKALQAYDTALEIYPE 375
                                       69*****************************7 PP

  == domain 10  score: 7.4 bits;  conditional E-value: 0.0081
                             TPR_2   3 alynlGlayyklgdyeeAleafekA 27 
                                       a+   G+a+++ g+ ++Al a++ A
  gi|386001636|ref|YP_005919935.1| 384 AWKGNGDALMAIGRDDDALLAYQNA 408
                                       78889*****************988 PP

  == domain 11  score: 8.2 bits;  conditional E-value: 0.0046
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                       e + n+G ++++lg  ++A+ea+ kA e
  gi|386001636|ref|YP_005919935.1| 431 EFWLNRGAVLEALGLGAQAEEAYGKARE 458
                                       78***********************976 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.4   5.5e-07   0.00035       5      34 .]      56      85 ..      52      85 .. 0.91
   2 !   22.5   0.0   1.1e-07   7.1e-05       2      34 .]      87     119 ..      86     119 .. 0.96
   3 !   12.2   0.0   0.00019      0.12       1      34 []     120     153 ..     120     153 .. 0.94
   4 ?    3.7   0.1     0.096        62      10      23 ..     163     176 ..     162     180 .. 0.86
   5 ?   -0.8   0.0       2.4   1.6e+03      21      34 .]     213     226 ..     213     226 .. 0.87
   6 !   10.5   0.1   0.00068      0.44       2      25 ..     228     251 ..     227     254 .. 0.94
   7 !   12.8   0.0   0.00012     0.077       2      31 ..     267     296 ..     266     298 .. 0.91
   8 !   15.3   0.0     2e-05     0.013       7      32 ..     314     339 ..     309     341 .. 0.87
   9 !   20.6   0.0   4.3e-07   0.00027       2      33 ..     344     375 ..     343     376 .. 0.95
  10 ?    6.3   0.2     0.014       9.2       3      27 ..     384     408 ..     383     408 .. 0.95
  11 !   11.9   0.2   0.00024      0.16       3      29 ..     432     458 ..     430     459 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.5e-07
                                      HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  5 ynlGnayfklgkydeAleyyekALelnPnn 34
                                        +G+ ++++  y+eAl++y++AL l P++
  gi|386001636|ref|YP_005919935.1| 56 IDMGLELYQNRSYQEALKAYDQALFLSPDD 85
                                      568*************************96 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+ ++G ++  lg+y++ + +y+ A ++ P++
  gi|386001636|ref|YP_005919935.1|  87 RAWMGKGKVFSALGDYNQSILAYQNATRISPDD 119
                                       8******************************96 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++a+++ G+  f l+++++ l++ ++ALe + n+
  gi|386001636|ref|YP_005919935.1| 120 PEAWFGVGLNRFLLQDLNDSLKALDRALEMDGNY 153
                                       589***************************9886 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.096
                                       HHHHTT-HHHHHHH CS
                             TPR_1  10 ayfklgkydeAley 23 
                                       ++ ++gk deAle+
  gi|386001636|ref|YP_005919935.1| 163 VLAQMGKNDEALEA 176
                                       6789********97 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHSTTH CS
                             TPR_1  21 leyyekALelnPnn 34 
                                       l++ e A +l+P+n
  gi|386001636|ref|YP_005919935.1| 213 LAALENATTLDPQN 226
                                       578999******97 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyye 25 
                                       +a+  lG a++  g+yd  l++++
  gi|386001636|ref|YP_005919935.1| 228 DAWILLGEALQGRGEYDRSLAAFD 251
                                       8*******************9996 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                        +l  +G ++  +g+y+eA   y++ + l+
  gi|386001636|ref|YP_005919935.1| 267 LVLIDKGSVLIDMGRYEEARGLYQQTIDLD 296
                                       567789********************9998 PP

  == domain 8  score: 15.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnP 32 
                                        G+ +++lg+y eAle++++  e +P
  gi|386001636|ref|YP_005919935.1| 314 EGVSLLRLGDYGEALEAFNRSMEAEP 339
                                       5999****************988777 PP

  == domain 9  score: 20.6 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+ ++G a + lg y++Al++y+ ALe++P+
  gi|386001636|ref|YP_005919935.1| 344 DAWRGIGDARMGLGFYEKALQAYDTALEIYPE 375
                                       6999***************************7 PP

  == domain 10  score: 6.3 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                       a+++ G a++  g+ d+Al +y+ A
  gi|386001636|ref|YP_005919935.1| 384 AWKGNGDALMAIGRDDDALLAYQNA 408
                                       79999******************98 PP

  == domain 11  score: 11.9 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                        + n+G+++  lg   +A+e+y kA e
  gi|386001636|ref|YP_005919935.1| 432 FWLNRGAVLEALGLGAQAEEAYGKARE 458
                                       6***********************965 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   3.4e-14   2.2e-11       2      68 .]      57     120 ..      56     120 .. 0.96
   2 !   25.6   0.0   2.2e-08   1.4e-05       8      64 ..      97     150 ..      93     153 .. 0.91
   3 !   10.9   0.3   0.00086      0.55      11      61 ..     134     181 ..     133     188 .. 0.88
   4 !   20.9   0.2   6.5e-07   0.00041      17      65 ..     213     259 ..     213     262 .. 0.89
   5 !   24.5   0.2   4.8e-08     3e-05       2      59 ..     271     333 ..     270     334 .. 0.88
   6 !   32.8   1.5   1.3e-10   8.2e-08       3      66 ..     314     375 ..     312     377 .. 0.92
   7 !   19.0   3.1   2.5e-06    0.0016       4      59 ..     350     408 ..     350     415 .. 0.89
   8 !    9.6   0.7    0.0023       1.5      14      57 ..     413     453 ..     411     460 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.4e-14
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++++++++++ y++A++a+++al +    Pd+++A++++g ++ ++g++   + +y+ a r +pd+p
  gi|386001636|ref|YP_005919935.1|  57 DMGLELYQNRSYQEALKAYDQALFLS---PDDVRAWMGKGKVFSALGDYNQSILAYQNATRISPDDP 120
                                       6899**********************...************************9999999*****98 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.2e-08
                            TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                        ++gdy + + a++ a++     Pd++eA+++ g+ ++ +++l + + ++++al+ +
  gi|386001636|ref|YP_005919935.1|  97 SALGDYNQSILAYQNATRIS---PDDPEAWFGVGLNRFLLQDLNDSLKALDRALEMD 150
                                       579*****************...99999*******************9999999765 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00086
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +d  d ++al++al++d       +A+ l+  ++++ g  +eA+++ ++a 
  gi|386001636|ref|YP_005919935.1| 134 QDLNDSLKALDRALEMD---GNYTRAWELKSAVLAQMGKNDEALEASKRAR 181
                                       57899************...9***********************8877765 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 6.5e-07
                            TPR_16  17 aaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal.raap 65 
                                       +aale a+ +d   P++++A+ llg+a+  +g++++ +a+++++l   ap
  gi|386001636|ref|YP_005919935.1| 213 LAALENATTLD---PQNYDAWILLGEALQGRGEYDRSLAAFDSLLsNIAP 259
                                       5899*******...****************************99865555 PP

  == domain 5  score: 24.5 bits;  conditional E-value: 4.8e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrd.pssPd....aaeAllllgdaalrqgrlaeAaalyra 59 
                                       +++  +++ g+y++A+ ++++++++d + +P+      +A l+ g+++lr+g++ eA++++++
  gi|386001636|ref|YP_005919935.1| 271 DKGSVLIDMGRYEEARGLYQQTIDLDfSLDPLdqyyLGRAELGEGVSLLRLGDYGEALEAFNR 333
                                       678899*****************987255555**************************99887 PP

  == domain 6  score: 32.8 bits;  conditional E-value: 1.3e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ ++lr+gdy +A++a+++  ++ p   + a +A+ + gda+  +g +++A+++y+ al+ +p 
  gi|386001636|ref|YP_005919935.1| 314 EGVSLLRLGDYGEALEAFNRSMEAEP---RlADDAWRGIGDARMGLGFYEKALQAYDTALEIYPE 375
                                       67799********************5...4499******************************96 PP

  == domain 7  score: 19.0 bits;  conditional E-value: 2.5e-06
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAa.alyra 59 
                                       ++a++ +g y++A+ a+++al+ +   P+     + +A+ + gda+ + gr ++A+ a+ +a
  gi|386001636|ref|YP_005919935.1| 350 GDARMGLGFYEKALQAYDTALEIY---PEsvnaeRGHAWKGNGDALMAIGRDDDALlAYQNA 408
                                       689999******************...6666699**********************666555 PP

  == domain 8  score: 9.6 bits;  conditional E-value: 0.0023
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaaly 57 
                                       d A+++ ++ + ++   P++ e++l++g ++ ++g  a A+++y
  gi|386001636|ref|YP_005919935.1| 413 DLAIEMPDQGRQSY---PLNGEFWLNRGAVLEALGLGAQAEEAY 453
                                       55666666667788...************************555 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   2.4e-09   1.5e-06       1      42 []      59     100 ..      59     100 .. 0.96
   2 !   32.0   0.0   1.1e-10   7.3e-08       1      36 [.      93     128 ..      93     132 .. 0.95
   3 ?    6.3   0.0     0.012       7.5       5      42 .]     131     168 ..     127     168 .. 0.83
   4 ?    2.8   0.1      0.14        92       4      16 ..     164     176 ..     162     180 .. 0.82
   5 !   16.0   0.1   1.1e-05     0.007       3      39 ..     202     238 ..     202     241 .. 0.90
   6 !   11.2   0.0   0.00036      0.23       1      24 [.     273     296 ..     273     299 .. 0.94
   7 !    7.1   0.0    0.0069       4.4       5      40 ..     319     355 ..     315     357 .. 0.79
   8 !   17.3   0.2   4.5e-06    0.0029       1      30 [.     350     379 ..     350     380 .. 0.93
   9 !    8.5   0.1    0.0024       1.5       1      20 [.     389     408 ..     389     409 .. 0.97
  10 ?    0.3   0.0      0.87   5.6e+02      29      42 .]     431     444 ..     427     444 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.4e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G ++y+   y eA++aY +Al l+Pd+++a+ + G+++ ++G
  gi|386001636|ref|YP_005919935.1|  59 GLELYQNRSYQEALKAYDQALFLSPDDVRAWMGKGKVFSALG 100
                                       78899999*****************************99887 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.1e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+++ ++G+y+++i aY++A +++Pd++ea+++ Gl
  gi|386001636|ref|YP_005919935.1|  93 GKVFSALGDYNQSILAYQNATRISPDDPEAWFGVGL 128
                                       889999**************************9885 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.012
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + +++++++++a+ +Al+ d ++ +a+    ++++++G
  gi|386001636|ref|YP_005919935.1| 131 FLLQDLNDSLKALDRALEMDGNYTRAWELKSAVLAQMG 168
                                       67899***************999999877777776666 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.14
                            TPR_11   4 yyeqGkyeeAiea 16 
                                       + + Gk++eA+ea
  gi|386001636|ref|YP_005919935.1| 164 LAQMGKNDEALEA 176
                                       6799*******97 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 1.1e-05
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       ++++ G+  e ++a+++A  ldP+n +a+  LG+a++
  gi|386001636|ref|YP_005919935.1| 202 ILRQMGRDGELLAALENATTLDPQNYDAWILLGEALQ 238
                                       578888888889***********************97 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.00036
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       G ++ + G+yeeA   Y++ ++ld
  gi|386001636|ref|YP_005919935.1| 273 GSVLIDMGRYEEARGLYQQTIDLD 296
                                       78999****************998 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.0069
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnae.ayynLGlayyk 40 
                                         +G+y eA+ea+++  +  P  a+ a+ ++G+a + 
  gi|386001636|ref|YP_005919935.1| 319 LRLGDYGEALEAFNRSMEAEPRLADdAWRGIGDARMG 355
                                       579************9999999884377777777665 PP

  == domain 8  score: 17.3 bits;  conditional E-value: 4.5e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30 
                                       Gda + +G ye+A++aY +Al++ P++++a
  gi|386001636|ref|YP_005919935.1| 350 GDARMGLGFYEKALQAYDTALEIYPESVNA 379
                                       8999999******************99886 PP

  == domain 9  score: 8.5 bits;  conditional E-value: 0.0024
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       Gda+++ G+ ++A+ aY++A
  gi|386001636|ref|YP_005919935.1| 389 GDALMAIGRDDDALLAYQNA 408
                                       9******************9 PP

  == domain 10  score: 0.3 bits;  conditional E-value: 0.87
                            TPR_11  29 eayynLGlayykqG 42 
                                       e+++n+G+++ ++G
  gi|386001636|ref|YP_005919935.1| 431 EFWLNRGAVLEALG 444
                                       789*******9998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0088       5.6       7      34 .]      58      85 ..      55      85 .. 0.88
   2 !   19.5   0.0   1.2e-06   0.00076       2      34 .]      87     119 ..      86     119 .. 0.96
   3 ?    5.6   0.0     0.033        21       2      33 ..     121     152 ..     120     153 .. 0.91
   4 ?    5.7   0.1     0.032        20       2      27 ..     155     180 ..     154     180 .. 0.90
   5 ?    5.2   0.0     0.045        29       3      34 .]     195     226 ..     193     226 .. 0.89
   6 ?    7.1   0.1     0.011         7       2      27 ..     228     253 ..     227     256 .. 0.89
   7 !   11.0   0.0   0.00062       0.4       4      31 ..     269     296 ..     266     298 .. 0.85
   8 !   10.2   0.0    0.0011      0.72      10      32 ..     317     339 ..     314     340 .. 0.89
   9 !   11.5   0.0   0.00043      0.28       7      33 ..     349     375 ..     344     376 .. 0.90
  10 ?   -0.8   0.0       3.8   2.4e+03      17      29 ..     405     417 ..     389     419 .. 0.69
  11 ?    3.5   0.1      0.16     1e+02       2      27 ..     431     456 ..     430     459 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0088
                                      HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  7 lgsiylklgdyeeAkeyyekaleldpdn 34
                                      +g+ + +   y+eA ++y +al l+pd+
  gi|386001636|ref|YP_005919935.1| 58 MGLELYQNRSYQEALKAYDQALFLSPDD 85
                                      688889999*************999985 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.2e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a++ +g++ + lgdy++++ +y+ a++++pd+
  gi|386001636|ref|YP_005919935.1|  87 RAWMGKGKVFSALGDYNQSILAYQNATRISPDD 119
                                       89*****************************96 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.033
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea++  g+  + l+d++ + +++ +ale+d +
  gi|386001636|ref|YP_005919935.1| 121 EAWFGVGLNRFLLQDLNDSLKALDRALEMDGN 152
                                       789999999999*****************976 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.032
                                       CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                       +a+ +++ ++ ++g+ +eA e+ ++a
  gi|386001636|ref|YP_005919935.1| 155 RAWELKSAVLAQMGKNDEALEASKRA 180
                                       7999999*************998776 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++  + i++++g+  e  +++e a++ldp+n
  gi|386001636|ref|YP_005919935.1| 195 SWVSESFILRQMGRDGELLAALENATTLDPQN 226
                                       677777899*********************96 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.011
                                       CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                       +a+ +lg +++  g+y+ + +++   
  gi|386001636|ref|YP_005919935.1| 228 DAWILLGEALQGRGEYDRSLAAFDSL 253
                                       89******************999765 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       +  +gs+++++g+yeeA   y++ ++ld
  gi|386001636|ref|YP_005919935.1| 269 LIDKGSVLIDMGRYEEARGLYQQTIDLD 296
                                       6789*************98888877776 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.0011
                                       HHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleldp 32 
                                        +l lgdy eA e++++  e++p
  gi|386001636|ref|YP_005919935.1| 317 SLLRLGDYGEALEAFNRSMEAEP 339
                                       6789**************99988 PP

  == domain 9  score: 11.5 bits;  conditional E-value: 0.00043
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                       +g++ + lg ye+A ++y  ale+ p+
  gi|386001636|ref|YP_005919935.1| 349 IGDARMGLGFYEKALQAYDTALEIYPE 375
                                       89999*******************996 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekale 29 
                                       y++A  +y  a+e
  gi|386001636|ref|YP_005919935.1| 405 YQNASIAYDLAIE 417
                                       5667777777776 PP

  == domain 11  score: 3.5 bits;  conditional E-value: 0.16
                                       CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                       e ++n g +++ lg   +A+e+y ka
  gi|386001636|ref|YP_005919935.1| 431 EFWLNRGAVLEALGLGAQAEEAYGKA 456
                                       689********************998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.1    0.0025       1.6      42      72 ..      49      79 ..      32      84 .. 0.86
   2 ?    5.6   0.0      0.03        19      45      75 ..      86     116 ..      81     118 .. 0.77
   3 !    9.5   0.4    0.0018       1.2       9      71 ..     126     180 ..     118     184 .. 0.77
   4 ?    6.9   0.2     0.012       7.6       6      29 ..     157     180 ..     152     225 .. 0.81
   5 ?    5.9   0.2     0.025        16       5      27 ..     229     251 ..     195     254 .. 0.83
   6 !   26.8   0.1   7.6e-09   4.9e-06       5      74 ..     229     295 ..     225     296 .. 0.91
   7 !   34.8   0.3   2.3e-11   1.5e-08       3      73 ..     266     336 ..     264     338 .. 0.94
   8 !   18.9   0.6   2.2e-06    0.0014       5      69 ..     345     406 ..     341     409 .. 0.87
   9 ?    6.8   0.2     0.013       8.1       6      32 ..     433     459 ..     430     462 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                            TPR_12 42 pltattlrnLgrlyralgryeeAlelleeal 72
                                      ++ta+ l+++g  +++   y+eAl+++ +al
  gi|386001636|ref|YP_005919935.1| 49 EDTAEDLIDMGLELYQNRSYQEALKAYDQAL 79
                                      579999***********************98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.03
                            TPR_12  45 attlrnLgrlyralgryeeAlelleealaia 75 
                                       +++  + g +++alg+y + + +++ a++i 
  gi|386001636|ref|YP_005919935.1|  86 VRAWMGKGKVFSALGDYNQSILAYQNATRIS 116
                                       5566667889999999999999999888875 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0018
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       +++  + l+++ ++l+ l++ale+      +++    ++    + ++ ++g+ +eAle+ ++a
  gi|386001636|ref|YP_005919935.1| 126 VGLNRFLLQDLNDSLKALDRALEMD-----GNY---TRAWELKSAVLAQMGKNDEALEASKRA 180
                                       6667788889999999999999999.....665...467777777778999999999998887 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.012
                            TPR_12   6 lnnlaavlrrlgrydeAlelleka 29 
                                       +    avl+++g+ deAle  ++a
  gi|386001636|ref|YP_005919935.1| 157 WELKSAVLAQMGKNDEALEASKRA 180
                                       556778999999999999988888 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.025
                            TPR_12   5 alnnlaavlrrlgrydeAlelle 27 
                                       a+  l+++l+ +g+yd +l+ ++
  gi|386001636|ref|YP_005919935.1| 229 AWILLGEALQGRGEYDRSLAAFD 251
                                       45568888888888888888776 PP

  == domain 6  score: 26.8 bits;  conditional E-value: 7.6e-09
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdh.pltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+  l+++l+ +g+yd +l+ ++  l  +  +    + p +a +l++ g ++  +gryeeA+ l+++++++
  gi|386001636|ref|YP_005919935.1| 229 AWILLGEALQGRGEYDRSLAAFDSLLSNIAPT----SpPFLALVLIDKGSVLIDMGRYEEARGLYQQTIDL 295
                                       5667*************************555....4478***************************9986 PP

  == domain 7  score: 34.8 bits;  conditional E-value: 2.3e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       a +l   ++vl  +gry+eA+ l+++ +++  +l   d +++ ++  + g  +++lg+y eAle+++++++
  gi|386001636|ref|YP_005919935.1| 266 ALVLIDKGSVLIDMGRYEEARGLYQQTIDLDFSLDPLDQYYLGRAELGEGVSLLRLGDYGEALEAFNRSME 336
                                       6677789************************888889999*****************************98 PP

  == domain 8  score: 18.9 bits;  conditional E-value: 2.2e-06
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                       a++ ++++ + lg y++Al+ +++alei+   ++  +++   +  + g+++ a gr ++Al +++
  gi|386001636|ref|YP_005919935.1| 345 AWRGIGDARMGLGFYEKALQAYDTALEIY---PESVNAERGHAWKGNGDALMAIGRDDDALLAYQ 406
                                       78789************************...555577889999999999999999999999987 PP

  == domain 9  score: 6.8 bits;  conditional E-value: 0.013
                            TPR_12   6 lnnlaavlrrlgrydeAlellekalei 32 
                                       + n++avl +lg  ++A+e + ka+e+
  gi|386001636|ref|YP_005919935.1| 433 WLNRGAVLEALGLGAQAEEAYGKAREM 459
                                       459999*************99999985 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.1e-08   7.3e-06       1      62 [.      62     123 ..      62     126 .. 0.96
   2 !   12.1   0.2   0.00034      0.21       5      51 ..     134     180 ..     131     190 .. 0.90
   3 !   18.0   0.2   4.7e-06     0.003      11      52 ..     213     254 ..     210     267 .. 0.92
   4 ?    5.8   0.0     0.031        20       1      19 [.     276     294 ..     276     301 .. 0.79
   5 !   19.4   0.5   1.7e-06    0.0011       1      57 [.     318     375 ..     318     384 .. 0.94
   6 !    9.5   0.2    0.0021       1.4       7      45 ..     359     402 ..     354     409 .. 0.81
   7 ?    2.8   0.2      0.27   1.7e+02       7      50 ..     412     455 ..     403     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l+++  y+eAl+++ qal  +p++ +a+++  ++  alg++++ + + + + +  pdd++++
  gi|386001636|ref|YP_005919935.1|  62 LYQNRSYQEALKAYDQALFLSPDDVRAWMGKGKVFSALGDYNQSILAYQNATRISPDDPEAW 123
                                       68999*****************************************************8865 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00034
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       +d+ + l++l +al+ d ++ +a+ l   +l ++g  deA ++ +++
  gi|386001636|ref|YP_005919935.1| 134 QDLNDSLKALDRALEMDGNYTRAWELKSAVLAQMGKNDEALEASKRA 180
                                       6889999*********************************9986665 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 4.7e-06
                            TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                       la+le+a + dp+n +a++lL eal   g++d   a+ d l+
  gi|386001636|ref|YP_005919935.1| 213 LAALENATTLDPQNYDAWILLGEALQGRGEYDRSLAAFDSLL 254
                                       6899*******************************9999987 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.031
                            TPR_19   1 llaegdyaeAlalleqalq 19 
                                       l+++g+y+eA  l++q ++
  gi|386001636|ref|YP_005919935.1| 276 LIDMGRYEEARGLYQQTID 294
                                       6788999999999988765 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 1.7e-06
                            TPR_19   1 llaegdyaeAlalleqalqedpk.naearllLAeallalgqldeAealLdalpeedpd 57 
                                       ll  gdy eAl+++ + ++++p   ++a+ +  +a + lg +++A ++ d+++e +p 
  gi|386001636|ref|YP_005919935.1| 318 LLRLGDYGEALEAFNRSMEAEPRlADDAWRGIGDARMGLGFYEKALQAYDTALEIYPE 375
                                       5778**************************************************9997 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0021
                            TPR_19   7 yaeAlalleqalqedpk.....naearllLAeallalgqldeAe 45 
                                       y+ Al+++  al+ +p+      + a+ +  +al+a g+ d+A 
  gi|386001636|ref|YP_005919935.1| 359 YEKALQAYDTALEIYPEsvnaeRGHAWKGNGDALMAIGRDDDAL 402
                                       899*********99999555556666667799999999999996 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.27
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       y+ A+++  q  q +p n+e +l+   +l alg  ++Ae++  +
  gi|386001636|ref|YP_005919935.1| 412 YDLAIEMPDQGRQSYPLNGEFWLNRGAVLEALGLGAQAEEAYGK 455
                                       66677777788888999**********************98665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   6.3e-06     0.004       4      43 ..      55      94 ..      52      95 .. 0.88
   2 !   18.3   0.0   4.5e-06    0.0029       2      39 ..      87     124 ..      86     128 .. 0.95
   3 ?    6.1   0.1     0.036        23      14      41 ..     133     160 ..     130     163 .. 0.88
   4 ?    4.2   0.2      0.15        99       3      30 ..     156     183 ..     155     193 .. 0.77
   5 !   12.5   0.2   0.00033      0.21      11      43 ..     203     235 ..     200     236 .. 0.94
   6 !   11.9   0.0   0.00052      0.33       2      37 ..     228     264 ..     228     271 .. 0.86
   7 ?    6.8   0.0     0.022        14       6      30 ..     271     295 ..     265     314 .. 0.76
   8 !   10.9   0.2    0.0011       0.7      10      39 ..     317     347 ..     307     351 .. 0.81
   9 !   13.9   0.1   0.00012     0.076       2      35 ..     344     377 ..     343     385 .. 0.91
  10 ?   -0.3   0.2       4.4   2.8e+03       9      27 ..     390     408 ..     389     413 .. 0.85
  11 ?    4.1   0.5      0.16     1e+02       3      27 ..     432     456 ..     431     460 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.3e-06
                            TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43
                                      l +++  l++++ ++eA++++++al l Pdd +aw+  ++
  gi|386001636|ref|YP_005919935.1| 55 LIDMGLELYQNRSYQEALKAYDQALFLSPDDVRAWMGKGK 94
                                      5677888999*************************98765 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.5e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +a++  ++++ alGd+ ++i +++ a +  Pdd+eaw+
  gi|386001636|ref|YP_005919935.1|  87 RAWMGKGKVFSALGDYNQSILAYQNATRISPDDPEAWF 124
                                       79999********************************7 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.036
                            TPR_14  14 lGdpdeAiallrralalaPddaeawlll 41 
                                       l+d+ +++++l+ral+ + +  +aw l 
  gi|386001636|ref|YP_005919935.1| 133 LQDLNDSLKALDRALEMDGNYTRAWELK 160
                                       6788899******************875 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.15
                            TPR_14   3 allalaeallalGdpdeAiallrralal 30 
                                       a+ +  ++l++ G+ deA+++ +ra  +
  gi|386001636|ref|YP_005919935.1| 156 AWELKSAVLAQMGKNDEALEASKRARMT 183
                                       66667789************99998655 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00033
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                                       l++ G+  e +a+l+ a  l+P++ +aw+ll++
  gi|386001636|ref|YP_005919935.1| 203 LRQMGRDGELLAALENATTLDPQNYDAWILLGE 235
                                       7899***************************97 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00052
                            TPR_14   2 eallalaeallalGdpdeAiallrrala.laPddaea 37 
                                       +a+ +l+eal  +G++d+++a+++ +l+  aP+++ +
  gi|386001636|ref|YP_005919935.1| 228 DAWILLGEALQGRGEYDRSLAAFDSLLSnIAPTSPPF 264
                                       599************************9668988754 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.022
                            TPR_14   6 alaeallalGdpdeAiallrralal 30 
                                       + +++l   G+++eA+ l+++ ++l
  gi|386001636|ref|YP_005919935.1| 271 DKGSVLIDMGRYEEARGLYQQTIDL 295
                                       56899***************98774 PP

  == domain 8  score: 10.9 bits;  conditional E-value: 0.0011
                            TPR_14  10 allalGdpdeAiallrralalaPdda.eawl 39 
                                        ll+lGd+ eA+++++r  ++ P  a +aw+
  gi|386001636|ref|YP_005919935.1| 317 SLLRLGDYGEALEAFNRSMEAEPRLAdDAWR 347
                                       489*****************99975436776 PP

  == domain 9  score: 13.9 bits;  conditional E-value: 0.00012
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                       +a++ +++a + lG +++A+++++ al+ +P++ 
  gi|386001636|ref|YP_005919935.1| 344 DAWRGIGDARMGLGFYEKALQAYDTALEIYPESV 377
                                       69999**************************986 PP

  == domain 10  score: -0.3 bits;  conditional E-value: 4.4
                            TPR_14   9 eallalGdpdeAiallrra 27 
                                       +al+a G+ d+A+ +++ a
  gi|386001636|ref|YP_005919935.1| 390 DALMAIGRDDDALLAYQNA 408
                                       789999******9998876 PP

  == domain 11  score: 4.1 bits;  conditional E-value: 0.16
                            TPR_14   3 allalaeallalGdpdeAiallrra 27 
                                        +l ++++l+alG  ++A++++ +a
  gi|386001636|ref|YP_005919935.1| 432 FWLNRGAVLEALGLGAQAEEAYGKA 456
                                       6999****************99877 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0     0.005       3.2       2      31 ..      75     104 ..      68     106 .. 0.88
   2 ?    6.8   0.0     0.016        10       1      17 [.     108     124 ..     108     128 .. 0.93
   3 !    8.0   0.1    0.0065       4.2       2      34 .]     143     175 ..     142     175 .. 0.94
   4 !   17.1   0.1     8e-06    0.0051       2      32 ..     216     246 ..     215     248 .. 0.91
   5 ?    1.4   0.0      0.82   5.2e+02      12      33 ..     265     286 ..     258     287 .. 0.88
   6 ?    2.2   0.0      0.45   2.9e+02      16      34 .]     304     329 ..     288     329 .. 0.68
   7 ?    2.5   0.0      0.38   2.4e+02       2      15 ..     366     379 ..     365     396 .. 0.84
   8 ?    6.0   0.1     0.028        18       9      27 ..     426     444 ..     424     453 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.005
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       y +al l P+++ a+  ++++++ +Gd+ +
  gi|386001636|ref|YP_005919935.1|  75 YDQALFLSPDDVRAWMGKGKVFSALGDYNQ 104
                                       77777789*******************987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                            TPR_17   1 lylkaleldPnnadayn 17 
                                       +y++a ++ P++++a++
  gi|386001636|ref|YP_005919935.1| 108 AYQNATRISPDDPEAWF 124
                                       59**************8 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0065
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +ale d n+  a+ ++  +l++ G+ ++A++
  gi|386001636|ref|YP_005919935.1| 143 LDRALEMDGNYTRAWELKSAVLAQMGKNDEALE 175
                                       579***************************985 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 8e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +++a  ldP n da+ +L+e+l  +G++++ 
  gi|386001636|ref|YP_005919935.1| 216 LENATTLDPQNYDAWILLGEALQGRGEYDRS 246
                                       688999**********************986 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.82
                            TPR_17  12 nadaynnLAelllknGdlmtAr 33 
                                        a ++  ++ +l   G++++Ar
  gi|386001636|ref|YP_005919935.1| 265 LALVLIDKGSVLIDMGRYEEAR 286
                                       58899999************98 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.45
                            TPR_17  16 ynnLAelll.......knGdlmtArq 34 
                                        ++L+++ l       ++Gd+++A++
  gi|386001636|ref|YP_005919935.1| 304 QYYLGRAELgegvsllRLGDYGEALE 329
                                       5777777777777777*******975 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.38
                            TPR_17   2 ylkaleldPnnada 15 
                                       y  ale++P +++a
  gi|386001636|ref|YP_005919935.1| 366 YDTALEIYPESVNA 379
                                       999******99876 PP

  == domain 8  score: 6.0 bits;  conditional E-value: 0.028
                            TPR_17   9 dPnnadaynnLAelllknG 27 
                                       +P n +++ n++ +l+ +G
  gi|386001636|ref|YP_005919935.1| 426 YPLNGEFWLNRGAVLEALG 444
                                       799************9999 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.7e-09   1.7e-06       7      65 ..      64     122 ..      61     123 .. 0.97
   2 !   12.1   0.1   0.00026      0.17      19      61 ..     110     152 ..     104     163 .. 0.86
   3 ?    2.4   0.2      0.27   1.7e+02      10      50 ..     135     175 ..     132     179 .. 0.87
   4 !   10.3   0.4    0.0009      0.58      12      56 ..     210     254 ..     201     267 .. 0.87
   5 ?    3.9   0.0     0.095        61      33      57 ..     270     294 ..     262     301 .. 0.85
   6 !   18.5   0.7   2.6e-06    0.0017       5      67 ..     318     381 ..     315     384 .. 0.92
   7 ?   -1.7   0.1       5.1   3.3e+03      32      49 ..     433     450 ..     429     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.7e-09
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       +++ +++al++++  l l Pdd++ ++  G +   lG++++ + + + + +++pd+p+a
  gi|386001636|ref|YP_005919935.1|  64 QNRSYQEALKAYDQALFLSPDDVRAWMGKGKVFSALGDYNQSILAYQNATRISPDDPEA 122
                                       7899****************************************************987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00026
                             TPR_9  19 erllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +    + Pddpe ++  Gl ++ l +l+  l++L+++l+++++
  gi|386001636|ref|YP_005919935.1| 110 QNATRISPDDPEAWFGVGLNRFLLQDLNDSLKALDRALEMDGN 152
                                       5667899********************************9975 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.27
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                       d    l++++r l ++ +  + +     +laq+G   +Al+
  gi|386001636|ref|YP_005919935.1| 135 DLNDSLKALDRALEMDGNYTRAWELKSAVLAQMGKNDEALE 175
                                       66667999999999999999999999999999999888886 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0009
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                        ++la++e    l+P+  + +   G +l+ +G +   la+++  l
  gi|386001636|ref|YP_005919935.1| 210 GELLAALENATTLDPQNYDAWILLGEALQGRGEYDRSLAAFDSLL 254
                                       5789***********************************999877 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.095
                             TPR_9  33 rdRGlllaqlGclsaAladLeayla 57 
                                        d G +l  +G++++A+   ++ ++
  gi|386001636|ref|YP_005919935.1| 270 IDKGSVLIDMGRYEEARGLYQQTID 294
                                       69**************987777665 PP

  == domain 6  score: 18.5 bits;  conditional E-value: 2.6e-06
                             TPR_9   5 aireedweralavverllllaPddpee.rrdRGlllaqlGclsaAladLeaylalapdapdaea 67 
                                       ++r  d+ +al++ +r +   P+ +++ +r  G +++ lG +++Al++ +++l++ p+   ae+
  gi|386001636|ref|YP_005919935.1| 318 LLRLGDYGEALEAFNRSMEAEPRLADDaWRGIGDARMGLGFYEKALQAYDTALEIYPESVNAER 381
                                       5788999****************99755*****************************9988886 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 5.1
                             TPR_9  32 rrdRGlllaqlGclsaAl 49 
                                       ++ RG +l+ lG  ++A 
  gi|386001636|ref|YP_005919935.1| 433 WLNRGAVLEALGLGAQAE 450
                                       899*****9999877775 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.2   0.00056      0.36      18      81 ..      47     111 ..      28     112 .. 0.84
   2 ?    5.7   0.0     0.028        18      20      78 ..     117     176 ..     108     180 .. 0.83
   3 !   11.8   0.0   0.00033      0.21      13      80 ..     217     290 ..     210     292 .. 0.80
   4 ?    3.6   0.0      0.12        79      31      49 ..     316     334 ..     300     369 .. 0.72
   5 ?   -0.5   0.0       2.3   1.5e+03       4      37 ..     404     437 ..     402     459 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       a  + +ed+   +l ly+n  y++A++ +++a  l + + ++++ ++++  +L+ y++ i a+++
  gi|386001636|ref|YP_005919935.1|  47 AVEDTAEDLIDMGLELYQNRSYQEALKAYDQAlFLSPDDVRAWMGKGKVFSALGDYNQSILAYQN 111
                                       556667777778899*******************************************9988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.028
                                       H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++pe+ +  +l  +l+++ +  ++ l++a + +++  +++ l+  +l +++k +eA+ a
  gi|386001636|ref|YP_005919935.1| 117 PDDPEAWFGVGLNRFLLQDLNDSLKALDRAlEMDGNYTRAWELKSAVLAQMGKNDEALEA 176
                                       67777777777778888888888999999988899999*******************987 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00033
                                       HHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT..SHHHC-H....HHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  13 erllaaetespedayllAlclylngqykrAyellrka..klnsksl....gcrylfAqcllkLkkyeeAiaaLe 80 
                                       e + + +++++++  ll+++l  +g+y+r +  ++++  +++++s+     +++ ++ +l+++++yeeA+ +++
  gi|386001636|ref|YP_005919935.1| 217 ENATTLDPQNYDAWILLGEALQGRGEYDRSLAAFDSLlsNIAPTSPpflaLVLIDKGSVLIDMGRYEEARGLYQ 290
                                       55556899*********************9999999986777777777333333345999*********99876 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.12
                                       HHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  31 lclylngqykrAyellrka 49 
                                        +l+++g+y +A+e ++++
  gi|386001636|ref|YP_005919935.1| 316 VSLLRLGDYGEALEAFNRS 334
                                       4667777777777777766 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.3
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylng 37 
                                       +y+nA + ++++ ++  +  ++  l ++  +++g
  gi|386001636|ref|YP_005919935.1| 404 AYQNASIAYDLAIEMPDQGRQSYPLNGEFWLNRG 437
                                       6999999999999533333333333344444444 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.12        76      15      35 ..      68      86 ..      62      87 .. 0.86
   2 !    7.6   0.0    0.0069       4.4       6      36 .]      93     121 ..      88     121 .. 0.89
   3 ?   -0.2   0.0       2.1   1.3e+03       8      33 ..     202     225 ..     202     227 .. 0.88
   4 ?    3.8   0.0      0.11        72       1      23 [.     229     251 ..     229     260 .. 0.83
   5 !   12.1   0.0   0.00024      0.15       6      31 ..     273     296 ..     268     305 .. 0.78
   6 ?    5.5   0.0     0.032        21       8      28 ..     317     337 ..     315     344 .. 0.79
   7 ?    3.4   0.0      0.15        96       5      28 ..     349     372 ..     345     378 .. 0.80
   8 ?   -1.0   0.1       3.6   2.3e+03       6      24 ..     389     407 ..     389     418 .. 0.79
   9 ?   -1.5   0.2       5.3   3.4e+03       3      24 ..     434     455 ..     433     458 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                             TPR_7 15 yeeAielyeqsLaltkdpeda 35
                                      y+eA++ y q  al  +p+d+
  gi|386001636|ref|YP_005919935.1| 68 YQEALKAYDQ--ALFLSPDDV 86
                                      9*********..998888876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0069
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpedae 36 
                                       + ++s+lGdy + i  y+   a++ +p+d+e
  gi|386001636|ref|YP_005919935.1|  93 GKVFSALGDYNQSILAYQN--ATRISPDDPE 121
                                       7899***************..9999998875 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.1
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpe 33 
                                       + +++G+  e++  +e   a+t dp+
  gi|386001636|ref|YP_005919935.1| 202 ILRQMGRDGELLAALEN--ATTLDPQ 225
                                       5789999999*******..***9997 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.11
                             TPR_7   1 aLlnLarlysrlGdyeeAielye 23 
                                       a+  L+++ + +G+y++ +  + 
  gi|386001636|ref|YP_005919935.1| 229 AWILLGEALQGRGEYDRSLAAFD 251
                                       5778*************988775 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00024
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       +++  ++G+yeeA +ly+q   ++ d
  gi|386001636|ref|YP_005919935.1| 273 GSVLIDMGRYEEARGLYQQ--TIDLD 296
                                       788899*************..66544 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.032
                             TPR_7   8 lysrlGdyeeAielyeqsLal 28 
                                          rlGdy eA+e + +s++ 
  gi|386001636|ref|YP_005919935.1| 317 SLLRLGDYGEALEAFNRSMEA 337
                                       5789***********996654 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.15
                             TPR_7   5 LarlysrlGdyeeAielyeqsLal 28 
                                       +++++  lG ye+A++ y  +L++
  gi|386001636|ref|YP_005919935.1| 349 IGDARMGLGFYEKALQAYDTALEI 372
                                       688888888899999999997765 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 3.6
                             TPR_7   6 arlysrlGdyeeAielyeq 24 
                                       +++  + G+ ++A+  y+ 
  gi|386001636|ref|YP_005919935.1| 389 GDALMAIGRDDDALLAYQN 407
                                       6788889999999988887 PP

  == domain 9  score: -1.5 bits;  conditional E-value: 5.3
                             TPR_7   3 lnLarlysrlGdyeeAielyeq 24 
                                       ln + + ++lG  ++A+e y +
  gi|386001636|ref|YP_005919935.1| 434 LNRGAVLEALGLGAQAEEAYGK 455
                                       6788889999999999999987 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.27   1.7e+02      12      33 ..      63      84 ..      60      88 .. 0.88
   2 !    7.9   0.0    0.0048       3.1      14      50 ..     133     169 ..     127     172 .. 0.92
   3 ?    0.8   0.0      0.82   5.3e+02      15      29 ..     241     255 ..     232     258 .. 0.87
   4 ?   -0.4   0.0         2   1.3e+03      14      26 ..     279     291 ..     277     296 .. 0.81
   5 !    8.3   0.0    0.0038       2.4      11      33 ..     318     340 ..     315     343 .. 0.91
   6 !    7.4   0.0     0.007       4.5      12      36 ..     354     378 ..     348     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.27
                                      HHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 12 yklgeYseArryvdalLeiEPe 33
                                      y  + Y+eA++  d+ L + P+
  gi|386001636|ref|YP_005919935.1| 63 YQNRSYQEALKAYDQALFLSPD 84
                                      77899***********999887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0048
                                       HT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLkeliedkikk 50 
                                       l++ +++++ +d+ Le++ +   a +Lk+++  ++ k
  gi|386001636|ref|YP_005919935.1| 133 LQDLNDSLKALDRALEMDGNYTRAWELKSAVLAQMGK 169
                                       78999*************************9998866 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.82
                                       T-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLe 29 
                                       geY++++   d lL+
  gi|386001636|ref|YP_005919935.1| 241 GEYDRSLAAFDSLLS 255
                                       9***********996 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2
                                       HT-HHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvda 26 
                                       +g+Y+eAr + ++
  gi|386001636|ref|YP_005919935.1| 279 MGRYEEARGLYQQ 291
                                       89******87665 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0038
                                       HHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPe 33 
                                        ++lg+Y eA++  ++ +e EP+
  gi|386001636|ref|YP_005919935.1| 318 LLRLGDYGEALEAFNRSMEAEPR 340
                                       58********************7 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.007
                                       HHHT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQ 36 
                                       + lg Y++A++  d+ Lei Pe  +
  gi|386001636|ref|YP_005919935.1| 354 MGLGFYEKALQAYDTALEIYPESVN 378
                                       45788**************998655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   2.0       3.1     2e+03      10      26 ..      63      78 ..      31      79 .. 0.75
   2 ?    5.3   0.0     0.056        36       4      32 ..      90     118 ..      87     119 .. 0.85
   3 ?    3.0   0.0      0.31     2e+02       1      27 [.     121     147 ..     121     149 .. 0.90
   4 ?   -0.4   0.1       3.5   2.3e+03       8      22 ..     163     176 ..     157     181 .. 0.70
   5 !    9.1   0.0    0.0035       2.2       1      32 [.     228     260 ..     228     261 .. 0.86
   6 ?    5.9   0.0     0.035        23      10      28 ..     276     294 ..     268     296 .. 0.85
   7 ?    6.7   0.1     0.019        12       4      25 ..     312     333 ..     304     340 .. 0.80
   8 !    9.2   0.0    0.0031         2      16      33 .]     359     376 ..     344     376 .. 0.82
   9 ?   -1.3   0.1       6.9   4.4e+03       9      25 ..     391     407 ..     389     409 .. 0.76
  10 ?   -1.1   0.2       6.1   3.9e+03       5      26 ..     435     456 ..     433     458 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.1
                                      HHHHHHHHHHHHHHHHH CS
                             TPR_6 10 yrklgdtdkAlealerl 26
                                      y++   +++Al+a+++ 
  gi|386001636|ref|YP_005919935.1| 63 YQNR-SYQEALKAYDQA 78
                                      3334.788888888775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       +  ++ + +lgd+ +++ a+++  +  Pd
  gi|386001636|ref|YP_005919935.1|  90 MGKGKVFSALGDYNQSILAYQNATRISPD 118
                                       55678888999************999998 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerli 27 
                                       +A +  +l ++ l+d  ++l+al+r +
  gi|386001636|ref|YP_005919935.1| 121 EAWFGVGLNRFLLQDLNDSLKALDRAL 147
                                       79999*******77*********9987 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlea 22 
                                        + + +g+ d+Alea
  gi|386001636|ref|YP_005919935.1| 163 VLAQ-MGKNDEALEA 176
                                       4444.6699***998 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlike.YPd 32 
                                       dA  +l+++++  g++d++l+a+++l+++  P+
  gi|386001636|ref|YP_005919935.1| 228 DAWILLGEALQGRGEYDRSLAAFDSLLSNiAPT 260
                                       677789*****988************9986665 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                       ++ +g++++A+ ++++ i+
  gi|386001636|ref|YP_005919935.1| 276 LIDMGRYEEARGLYQQTID 294
                                       56789**********9886 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealer 25 
                                       +  + s+++lgd+ +Alea++r
  gi|386001636|ref|YP_005919935.1| 312 LGEGVSLLRLGDYGEALEAFNR 333
                                       4457788888**********98 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHH-TT- CS
                             TPR_6  16 tdkAlealerlikeYPdS 33 
                                       ++kAl+a++  ++ YP+S
  gi|386001636|ref|YP_005919935.1| 359 YEKALQAYDTALEIYPES 376
                                       89**************98 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealer 25 
                                       ++ + g+ d+Al a+++
  gi|386001636|ref|YP_005919935.1| 391 ALMAIGRDDDALLAYQN 407
                                       56666799999999996 PP

  == domain 10  score: -1.1 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerl 26 
                                       +++  +++lg  ++A ea+ + 
  gi|386001636|ref|YP_005919935.1| 435 NRGAVLEALGLGAQAEEAYGKA 456
                                       6677778888889999999886 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.3   8.3e+02      71      83 ..      68      80 ..      57     115 .. 0.55
   2 ?    1.8   0.0      0.36   2.3e+02     105     126 ..     159     180 ..     121     186 .. 0.66
   3 ?    4.0   0.0     0.074        48      46      83 ..     220     255 ..     208     295 .. 0.70
   4 ?    2.5   0.0      0.22   1.4e+02      64      81 ..     317     334 ..     266     343 .. 0.61
   5 !   15.7   0.2   1.9e-05     0.012      59     127 ..     347     409 ..     342     421 .. 0.90
   6 ?    0.9   0.0      0.66   4.2e+02     104     129 ..     434     459 ..     428     461 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHH CS
                           DUF3856 71 ydealesadkalr 83
                                      y+eal++ d+al 
  gi|386001636|ref|YP_005919935.1| 68 YQEALKAYDQALF 80
                                      4455555444442 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.36
                                       HHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrma 126
                                        +++ l+++G++deal+a + a
  gi|386001636|ref|YP_005919935.1| 159 LKSAVLAQMGKNDEALEASKRA 180
                                       4566677777777777766554 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.074
                                       S---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  46 eafdheGfdalchaglsealaklgrydealesadkalr 83 
                                        ++d + +da +   l eal + g+yd +l + d+ l 
  gi|386001636|ref|YP_005919935.1| 220 TTLDPQNYDAWI--LLGEALQGRGEYDRSLAAFDSLLS 255
                                       566777788754..688999999999999998887664 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.22
                                       HHHHTT-HHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadka 81 
                                       +l++lg+y eale+ +++
  gi|386001636|ref|YP_005919935.1| 317 SLLRLGDYGEALEAFNRS 334
                                       456666777766665554 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  59 aglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                        g+ +a+++lg y++al++ d+al+ +     ++ + G+ W       + al  +Gr d+al a++ a+
  gi|386001636|ref|YP_005919935.1| 347 RGIGDARMGLGFYEKALQAYDTALEIYPE--SVNAERGHAWK----GNGDALMAIGRDDDALLAYQNAS 409
                                       67899********************9975..689999****6....589***************99875 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.66
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                       ++r++ le lG  ++a +a+ +a em
  gi|386001636|ref|YP_005919935.1| 434 LNRGAVLEALGLGAQAEEAYGKAREM 459
                                       5899********************99 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.11        72     101     174 ..      42     114 ..      37     137 .. 0.70
   2 ?    4.3   0.2     0.046        30     131     184 ..     138     192 ..     128     195 .. 0.75
   3 !    7.9   0.0    0.0037       2.4     140     174 ..     260     294 ..     233     305 .. 0.82
   4 ?    6.3   2.8     0.011       6.9     124     173 ..     361     409 ..     303     416 .. 0.68
   5 ?    1.2   0.2       0.4   2.6e+02     151     174 ..     435     458 ..     411     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                            TPR_21 101 wvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeaf.aalvaelrGDilvaqgkldeAraaYqaAla 174
                                       w+ ++a +++ ++l+ + L   l ++  y+eAlk+ +++   +  ++++   +G +++a g+ ++   aYq+A +
  gi|386001636|ref|YP_005919935.1|  42 WATASAVEDTAEDLIDMGLE--LYQNRSYQEALKAYDQALFLSPdDVRAWMGKGKVFSALGDYNQSILAYQNATR 114
                                       55555555556666666554..55666777777777665443330334445599999999999999999999976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.046
                            TPR_21 131 eAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaaleekarell 184
                                       + lk+L+++ + ++   ++ el+  +l+++gk+deA +a ++A  + +++++e+l
  gi|386001636|ref|YP_005919935.1| 138 DSLKALDRAlEMDGNYTRAWELKSAVLAQMGKNDEALEASKRARMTSGPSDTEML 192
                                       5666665441334555677799999**************9999988888777766 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0037
                            TPR_21 140 keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       ++  f alv   +G +l+ +g+ +eAr  Yq+ ++
  gi|386001636|ref|YP_005919935.1| 260 TSPPFLALVLIDKGSVLIDMGRYEEARGLYQQTID 294
                                       566799999999*******************9886 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.011
                            TPR_21 124 laekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAl 173
                                        a ++yd Al+   ++ ++  ++++    GD+l+a g+ d+A  aYq+A 
  gi|386001636|ref|YP_005919935.1| 361 KALQAYDTALEIYPESVNA-ERGHAWKGNGDALMAIGRDDDALLAYQNAS 409
                                       4566777777655433333.355566668******************996 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.4
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        rG +l a g  ++A +aY +A +
  gi|386001636|ref|YP_005919935.1| 435 NRGAVLEALGLGAQAEEAYGKARE 458
                                       69******************9965 PP

>> TAD2  Transactivation domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0028       1.8       9      20 ..      79      90 ..      73      92 .. 0.83
   2 ?    6.8   0.1     0.011         7      11      20 ..     115     124 ..     113     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                              TAD2  9 LmLsPDDiEqWF 20
                                      L LsPDD+  W 
  gi|386001636|ref|YP_005919935.1| 79 LFLSPDDVRAWM 90
                                      89********96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                              TAD2  11 LsPDDiEqWF 20 
                                       +sPDD E WF
  gi|386001636|ref|YP_005919935.1| 115 ISPDDPEAWF 124
                                       6********* PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0043       2.7       8      35 ..      59      84 ..      53      85 .. 0.84
   2 ?    0.8   0.0      0.78     5e+02       9      22 ..     162     175 ..     149     177 .. 0.68
   3 !   10.3   0.0   0.00088      0.56      13      34 ..     278     297 ..     273     299 .. 0.82
   4 ?   -1.1   0.0       3.2   2.1e+03      15      24 ..     322     331 ..     321     332 .. 0.87
   5 ?    0.3   0.2       1.1   7.2e+02      17      25 ..     359     367 ..     357     375 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0043
                                      HHHHHHTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3  8 AaefynkkkyqeArelfsYallaildke 35
                                      + e+y+   yqeA+ +++  ++ +l ++
  gi|386001636|ref|YP_005919935.1| 59 GLELYQNRSYQEALKAYD--QALFLSPD 84
                                      789999999*******77..**999776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.78
                                       HHHHHTT-HHHHHH CS
                             TPR_3   9 aefynkkkyqeAre 22 
                                       a++ +++k +eA+e
  gi|386001636|ref|YP_005919935.1| 162 AVLAQMGKNDEALE 175
                                       56667777777766 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00088
                                       HTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3  13 nkkkyqeArelfsYallaildk 34 
                                       ++++y+eAr+l++  ++  ld+
  gi|386001636|ref|YP_005919935.1| 278 DMGRYEEARGLYQ--QTIDLDF 297
                                       69*********88..8776665 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.2
                                       T-HHHHHHH. CS
                             TPR_3  15 kkyqeArelf 24 
                                       ++y eA+e+f
  gi|386001636|ref|YP_005919935.1| 322 GDYGEALEAF 331
                                       89******96 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.1
                                       HHHHHHH.. CS
                             TPR_3  17 yqeArelfs 25 
                                       y++A+++++
  gi|386001636|ref|YP_005919935.1| 359 YEKALQAYD 367
                                       899999977 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3    0.0019       1.2       3      31 ..      51      79 ..      49      81 .. 0.88
   2 ?   -2.0   0.1       5.9   3.8e+03      27      38 ..     153     164 ..     137     181 .. 0.54
   3 ?    4.4   0.0     0.062        39      18      33 ..     280     295 ..     266     295 .. 0.86
   4 ?    1.3   0.0      0.56   3.6e+02      11      32 ..     315     336 ..     308     337 .. 0.82
   5 ?    4.3   0.1     0.064        41      20      33 ..     359     372 ..     356     383 .. 0.84
   6 ?   -0.5   0.0       2.1   1.3e+03      21      39 ..     399     417 ..     396     441 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                               MIT  3 kAlelvkkAveeDnagnyeeAlelYkeal 31
                                      +A +l+ +  e+ ++  y+eAl++Y +al
  gi|386001636|ref|YP_005919935.1| 51 TAEDLIDMGLELYQNRSYQEALKAYDQAL 79
                                      67788999999999**************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                               MIT  27 YkealelLlqal 38 
                                       Y+ a el + +l
  gi|386001636|ref|YP_005919935.1| 153 YTRAWELKSAVL 164
                                       444444444444 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.062
                               MIT  18 gnyeeAlelYkealel 33 
                                       g yeeA  lY++ ++l
  gi|386001636|ref|YP_005919935.1| 280 GRYEEARGLYQQTIDL 295
                                       89**********9985 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.56
                               MIT  11 AveeDnagnyeeAlelYkeale 32 
                                        v + + g+y eAle++  ++e
  gi|386001636|ref|YP_005919935.1| 315 GVSLLRLGDYGEALEAFNRSME 336
                                       56777889*******9988776 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.064
                               MIT  20 yeeAlelYkealel 33 
                                       ye+Al++Y +ale+
  gi|386001636|ref|YP_005919935.1| 359 YEKALQAYDTALEI 372
                                       99999999999985 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 2.1
                               MIT  21 eeAlelYkealelLlqalk 39 
                                       ++Al +Y++a     +a+ 
  gi|386001636|ref|YP_005919935.1| 399 DDALLAYQNASIAYDLAIE 417
                                       4566666666555555543 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.8   2.4e+03      97     107 ..      69      79 ..      37     118 .. 0.65
   2 ?    1.2   0.2      0.29   1.9e+02     264     302 ..     138     176 ..     131     181 .. 0.80
   3 !   10.1   0.0   0.00059      0.38      43     109 ..     230     295 ..     224     296 .. 0.92
   4 ?   -1.3   0.0       1.7   1.1e+03      86     113 ..     349     376 ..     326     409 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.8
                          TPR_MalT  97 heAletyeqal 107
                                       +eAl+ y qal
  gi|386001636|ref|YP_005919935.1|  69 QEALKAYDQAL 79 
                                       23333333333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                          TPR_MalT 264 erLlkaaeelgrvrslieiliLqalalqaqgreeeAlaa 302
                                       ++L +  ++l++ +   +++ L + +l ++g+++eAl+a
  gi|386001636|ref|YP_005919935.1| 138 DSLKALDRALEMDGNYTRAWELKSAVLAQMGKNDEALEA 176
                                       5666777777777888899999999*********99986 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00059
                          TPR_MalT  43 tavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalql 109
                                         +lGea + +G+ +++l+a+ ++ + + + +s+++ +l l++ + +l+  Gr +eA  +y+q + l
  gi|386001636|ref|YP_005919935.1| 230 WILLGEALQGRGEYDRSLAAFDSLLSNI-APTSPPFLALVLIDKGSVLIDMGRYEEARGLYQQTIDL 295
                                       5689********************9877.68999999999***********************9975 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.7
                          TPR_MalT  86 qaeilvaqGrLheAletyeqalqlateq 113
                                       +++ ++  G+ ++Al+ y  al+ ++e+
  gi|386001636|ref|YP_005919935.1| 349 IGDARMGLGFYEKALQAYDTALEIYPES 376
                                       5666666777777777777777766654 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.6       0.2   1.3e+02      72     123 ..     130     181 ..      39     185 .. 0.78
   2 !   10.2   0.0    0.0012      0.76      74     122 ..     205     253 ..     189     258 .. 0.92
   3 !    7.3   0.2    0.0093         6      72     125 ..     318     372 ..     309     386 .. 0.88
   4 ?    5.1   0.2     0.045        29      71     122 ..     352     408 ..     349     418 .. 0.69
   5 ?   -0.5   0.0       2.4   1.6e+03      91     124 ..     425     458 ..     413     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ++ l + ++ l+ l+++++++    r++++  + la++G++ eALe+ +r+r
  gi|386001636|ref|YP_005919935.1| 130 RFLLQDLNDSLKALDRALEMDGNYTRAWELKSAVLAQMGKNDEALEASKRAR 181
                                       5556666777888888888888888999999999999999999999988877 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0012
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++Gr  e+la le++++++P + +++ +l +Al   G+    L+++++l
  gi|386001636|ref|YP_005919935.1| 205 QMGRDGELLAALENATTLDPQNYDAWILLGEALQGRGEYDRSLAAFDSL 253
                                       789*****************************************99887 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0093
                                       HHHTT-HHHHHHHHHHHHHHST.T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehP.lrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       +lrlG++ eal+  ++ ++++P l ++++r +  A + +G  ++AL++Y+++ ++
  gi|386001636|ref|YP_005919935.1| 318 LLRLGDYGEALEAFNRSMEAEPrLADDAWRGIGDARMGLGFYEKALQAYDTALEI 372
                                       689*******************6689***********************998765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.045
                                       HHHHTT-HHHHHHHHHHHHHHSTT.....-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPl.....rErlhrqlmrAlarsGrqaeALevYerl 122
                                       a++ lG +e+al+ ++ +++ +P      r  +++    Al++ Gr  +AL +Y+++
  gi|386001636|ref|YP_005919935.1| 352 ARMGLGFYEKALQAYDTALEIYPEsvnaeRGHAWKGNGDALMAIGRDDDALLAYQNA 408
                                       5566677777777777777777752221133445555689**************986 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.4
                                       HSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  91 ehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        +Pl+ +++    + l ++G  a+A e+Y ++r+
  gi|386001636|ref|YP_005919935.1| 425 SYPLNGEFWLNRGAVLEALGLGAQAEEAYGKARE 458
                                       5788888888888999999999999999998886 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0076       4.9     205     252 ..      65     112 ..      59     119 .. 0.87
   2 ?    2.7   0.0     0.076        48     206     253 ..     134     181 ..     129     184 .. 0.91
   3 ?    1.0   0.0      0.25   1.6e+02      43      66 ..     271     294 ..     236     381 .. 0.76
   4 ?   -1.8   0.0       1.7   1.1e+03     207     245 ..     358     394 ..     347     403 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0076
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                        +s+++Al+  d+a+  +p  v  ++ K++++   Gd ++ + + ++a
  gi|386001636|ref|YP_005919935.1|  65 NRSYQEALKAYDQALFLSPDDVRAWMGKGKVFSALGDYNQSILAYQNA 112
                                       47899*********************************9987766666 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.076
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                       ++ + +l+ +d+a+e + + +  +  K+ +l ++G  ++A e+ ++ar
  gi|386001636|ref|YP_005919935.1| 134 QDLNDSLKALDRALEMDGNYTRAWELKSAVLAQMGKNDEALEASKRAR 181
                                       56778999**********************************999998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.25
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1  43 tkaelllkLgrkeeAeatyeaLle 66 
                                        k+++l+ +gr+eeA+ +y++ ++
  gi|386001636|ref|YP_005919935.1| 271 DKGSVLIDMGRYEEARGLYQQTID 294
                                       578888888888888888887665 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.7
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkA 245
                                        +ekAl+  d+a+e  p++v+    +++ +k  Gd   A
  gi|386001636|ref|YP_005919935.1| 358 FYEKALQAYDTALEIYPESVNA--ERGHAWKGNGDALMA 394
                                       4678888888888888887764..556667777776555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.023        14       7      29 ..      57      79 ..      55      79 .. 0.89
   2 ?    3.0   0.1      0.16     1e+02      10      24 ..     162     176 ..     161     180 .. 0.83
   3 ?    3.7   0.1     0.096        61       8      25 ..     233     250 ..     232     255 .. 0.88
   4 ?   12.0   0.0   0.00023      0.15       9      30 ..     273     294 ..     265     295 .. 0.85
   5 ?    1.7   0.0       0.4   2.5e+02      10      29 ..     316     335 ..     315     337 .. 0.81
   6 ?    3.3   0.0      0.13        81      16      32 ..     357     373 ..     351     382 .. 0.73
   7 ?   -2.2   0.0       6.7   4.3e+03      11      26 ..     391     406 ..     389     410 .. 0.77
   8 ?    0.4   0.6         1   6.5e+02       7      30 ..     435     458 ..     434     460 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                            TPR_10  7 NLanalrqrgrydeAealleeal 29
                                      +++  l+q + y+eA++ +++al
  gi|386001636|ref|YP_005919935.1| 57 DMGLELYQNRSYQEALKAYDQAL 79
                                      578889***************98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.16
                            TPR_10  10 nalrqrgrydeAeal 24 
                                       ++l q+g+ deA++ 
  gi|386001636|ref|YP_005919935.1| 162 AVLAQMGKNDEALEA 176
                                       6899********985 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.096
                            TPR_10   8 LanalrqrgrydeAeall 25 
                                       L+ al+ rg+yd+++a +
  gi|386001636|ref|YP_005919935.1| 233 LGEALQGRGEYDRSLAAF 250
                                       89***********99866 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00023
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + +l ++gry+eA+ l++++++
  gi|386001636|ref|YP_005919935.1| 273 GSVLIDMGRYEEARGLYQQTID 294
                                       88999**************986 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.4
                            TPR_10  10 nalrqrgrydeAealleeal 29 
                                       + l ++g+y eA++ + +++
  gi|386001636|ref|YP_005919935.1| 316 VSLLRLGDYGEALEAFNRSM 335
                                       668899*******9887776 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.13
                            TPR_10  16 grydeAealleealair 32 
                                       g y++A++ ++ al+i+
  gi|386001636|ref|YP_005919935.1| 357 GFYEKALQAYDTALEIY 373
                                       55677777777777776 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 6.7
                            TPR_10  11 alrqrgrydeAealle 26 
                                       al + gr d+A+  ++
  gi|386001636|ref|YP_005919935.1| 391 ALMAIGRDDDALLAYQ 406
                                       6788899999987665 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 1
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N +++l ++g +++Ae+ + +a +
  gi|386001636|ref|YP_005919935.1| 435 NRGAVLEALGLGAQAEEAYGKARE 458
                                       67999999*********9999976 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3       1.2   7.5e+02      17      43 ..      47      73 ..      35      88 .. 0.75
   2 ?    4.9   0.1     0.052        34       7      82 ..     105     178 ..      94     184 .. 0.79
   3 ?    8.3   0.0    0.0046         3       7      45 ..     212     250 ..     207     260 .. 0.83
   4 ?   -2.1   0.0       7.7   4.9e+03      34      61 ..     320     347 ..     315     349 .. 0.79
   5 ?    1.8   0.1      0.49   3.1e+02      40      82 ..     364     406 ..     326     408 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.2
                            TPR_20 17 anpddldarldlAlallaagryeeAle 43
                                      a  d  +  +d+ l l+++  y+eAl+
  gi|386001636|ref|YP_005919935.1| 47 AVEDTAEDLIDMGLELYQNRSYQEALK 73
                                      444555667888888999999999886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.052
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyR 82 
                                       ++ + ++a   +pdd +a + + l  +  ++  ++l++L + l+ d ++   +a +   ++++ +g++d++ ++++
  gi|386001636|ref|YP_005919935.1| 105 SILAYQNATRISPDDPEAWFGVGLNRFLLQDLNDSLKALDRALEMDGNY--TRAWELKSAVLAQMGKNDEALEASK 178
                                       5667788888999999999999999999999999999999999999999..4555555666777777777666554 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0046
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqL 45 
                                        la+le+a + +p+++da + l +al  +g+y+ +l+++
  gi|386001636|ref|YP_005919935.1| 212 LLAALENATTLDPQNYDAWILLGEALQGRGEYDRSLAAF 250
                                       5899****************************9766554 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 7.7
                            TPR_20  34 aagryeeAleqLleilkrdrkweddaar 61 
                                         g+y eAle++ + ++++   +dda r
  gi|386001636|ref|YP_005919935.1| 320 RLGDYGEALEAFNRSMEAEPRLADDAWR 347
                                       5688999999999999888888888766 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.49
                            TPR_20  40 eAleqLleilkrdrkweddaarkqllkifealgsqdplvakyR 82 
                                       +A +  lei  +  ++e+++a k   + + a+g +d++  +y+
  gi|386001636|ref|YP_005919935.1| 364 QAYDTALEIYPESVNAERGHAWKGNGDALMAIGRDDDALLAYQ 406
                                       4667899999999999999999999999999999998887775 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       4.9   3.1e+03       9      22 ..     162     175 ..     155     176 .. 0.83
   2 ?    9.3   0.3     0.003         2       3      24 ..     229     250 ..     228     252 .. 0.89
   3 ?    5.8   0.0     0.043        28       3      25 ..     268     290 ..     266     291 .. 0.81
   4 ?    9.5   0.3    0.0026       1.7       2      24 ..     309     331 ..     308     333 .. 0.85
   5 ?    4.2   0.5      0.13        86       4      23 ..     433     452 ..     430     455 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4.9
                             TPR_4   9 rallalGdldeAra 22 
                                        +l++ G  deA++
  gi|386001636|ref|YP_005919935.1| 162 AVLAQMGKNDEALE 175
                                       689999*99***97 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.003
                             TPR_4   3 allaLArallalGdldeArall 24 
                                       a ++L++al+ +G++d+ +a++
  gi|386001636|ref|YP_005919935.1| 229 AWILLGEALQGRGEYDRSLAAF 250
                                       6799************999976 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.043
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       +l++ + +l + G+++eAr l +
  gi|386001636|ref|YP_005919935.1| 268 VLIDKGSVLIDMGRYEEARGLYQ 290
                                       5677788999*********8766 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0026
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                       ra l+ +  ll+lGd+ eA++++
  gi|386001636|ref|YP_005919935.1| 309 RAELGEGVSLLRLGDYGEALEAF 331
                                       66778899************976 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.13
                             TPR_4   4 llaLArallalGdldeAral 23 
                                        l+++ +l alG  ++A+++
  gi|386001636|ref|YP_005919935.1| 433 WLNRGAVLEALGLGAQAEEA 452
                                       689**************986 PP

>> DUF1510  Domain of unknown function (DUF1510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.37   2.3e+02      27      51 ..      67      91 ..      62     106 .. 0.86
   2 ?    1.9   0.0      0.38   2.4e+02      27      50 ..     101     124 ..      94     127 .. 0.91
   3 ?   -0.1   0.1       1.6     1e+03      26      53 ..     134     161 ..     133     173 .. 0.86
   4 ?    3.3   0.0      0.14        93      30      51 ..     211     232 ..     206     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.37
                           DUF1510 27 DwnEmekavskatglsednmivwwl 51
                                       ++E +ka  +a  ls d++  w+ 
  gi|386001636|ref|YP_005919935.1| 67 SYQEALKAYDQALFLSPDDVRAWMG 91
                                      599*****************99974 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.38
                           DUF1510  27 DwnEmekavskatglsednmivww 50 
                                       D+n    a ++at +s d+   w+
  gi|386001636|ref|YP_005919935.1| 101 DYNQSILAYQNATRISPDDPEAWF 124
                                       9999**************998885 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
                           DUF1510  26 vDwnEmekavskatglsednmivwwlgn 53 
                                       +D n+ +ka+ +a +++ +    w l++
  gi|386001636|ref|YP_005919935.1| 134 QDLNDSLKALDRALEMDGNYTRAWELKS 161
                                       7999************998888888765 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.14
                           DUF1510  30 Emekavskatglsednmivwwl 51 
                                       E + a+++at l+ +n+  w l
  gi|386001636|ref|YP_005919935.1| 211 ELLAALENATTLDPQNYDAWIL 232
                                       7789****************87 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0099       6.4      69     123 ..      52     106 ..      20     112 .. 0.88
   2 ?    3.9   0.1      0.11        67      84     124 ..     135     175 ..     129     184 .. 0.86
   3 ?   -2.2   0.0       7.9     5e+03      92     130 ..     216     254 ..     211     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ae ++++  e +++  y+ a++  ++++f  p++ +a   k +++ +lg  ++s 
  gi|386001636|ref|YP_005919935.1|  52 AEDLIDMGLELYQNRSYQEALKAYDQALFLSPDDVRAWMGKGKVFSALGDYNQSI 106
                                       68899999****************************************9888775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                                       -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  84 dyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       d++ +++ l+ +++ d + ++a elk ++l q+g+  e+  
  gi|386001636|ref|YP_005919935.1| 135 DLNDSLKALDRALEMDGNYTRAWELKSAVLAQMGKNDEALE 175
                                       5666788899999999999***************9998765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.9
                                       HHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHH CS
                   Alkyl_sulf_dimr  92 lnhlvfadpenaeakelkadaleqlgyqaesatwRniYl 130
                                       l+++ + dp+n +a  l+ +al+ +g+  +s ++    l
  gi|386001636|ref|YP_005919935.1| 216 LENATTLDPQNYDAWILLGEALQGRGEYDRSLAAFDSLL 254
                                       556667799999999999999999999888887766655 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0032       2.1     245     290 ..      63     108 ..      44     123 .. 0.86
   2 ?   -0.1   0.0      0.55   3.5e+02     241     293 ..     199     252 ..     169     255 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                                       HHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             ChAPs 245 lskkkeelAlevakravksaPsefktWalLvkvYikledienALlt 290
                                        ++++++ Al++ ++a  ++P + + W+   kv+ +l+d+++ +l+
  gi|386001636|ref|YP_005919935.1|  63 YQNRSYQEALKAYDQALFLSPDDVRAWMGKGKVFSALGDYNQSILA 108
                                       45567788*********************************99886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.55
                                       HHHHHHSS--.HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                             ChAPs 241 aefllskkke.elAlevakravksaPsefktWalLvkvYikledienALltLNs 293
                                         f+l +       l++ ++a+++ P ++  W+lL +     ++++  L +  s
  gi|386001636|ref|YP_005919935.1| 199 ESFILRQMGRdGELLAALENATTLDPQNYDAWILLGEALQGRGEYDRSLAAFDS 252
                                       45665554441333445578999************9998888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.60
# Mc/sec: 2337.37
//
Query:       gi|386001637|ref|YP_005919936.1|  [L=619]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-70  230.3  16.4    1.3e-06   28.0   0.0   14.2 14  TPR_1         Tetratricopeptide repeat
    8.1e-66  212.9  21.8    1.9e-06   27.6   0.1   13.6 13  TPR_2         Tetratricopeptide repeat
    2.8e-54  176.8  10.9      0.001   19.1   0.0   13.0 13  TPR_8         Tetratricopeptide repeat
    1.1e-50  169.1  21.8    5.1e-07   29.3   0.3   11.4 11  TPR_11        TPR repeat
    1.9e-45  150.0   4.4    0.00029   21.0   0.0   13.0 13  TPR_17        Tetratricopeptide repeat
    2.3e-44  149.8  26.0    2.5e-10   40.8   0.4    8.0  8  TPR_16        Tetratricopeptide repeat
      1e-39  131.8  37.5    0.00038   21.0   0.2   12.4 12  TPR_14        Tetratricopeptide repeat
    3.9e-39  132.8  25.3    4.4e-09   36.5   0.5    9.1  8  TPR_12        Tetratricopeptide repeat
    3.8e-33  113.8  18.9    1.3e-05   25.6   0.0    8.4  9  TPR_19        Tetratricopeptide repeat
    2.4e-27   94.9  25.1      4e-08   33.3   0.4    8.3  8  TPR_9         Tetratricopeptide repeat
    4.4e-17   60.8  20.4       0.54   10.4   0.0   11.2 10  TPR_7         Tetratricopeptide repeat
    7.5e-17   60.6  32.7       0.54   10.2   0.1   11.1 11  TPR_10        Tetratricopeptide repeat
    4.5e-15   55.2  19.7       0.37   11.5   0.0   11.5 11  TPR_6         Tetratricopeptide repeat
    2.5e-12   46.8   0.8      0.003   17.8   0.0    5.5  6  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    4.9e-12   46.1  16.0       0.01   15.9   0.1    8.5  7  DUF3856       Domain of Unknown Function (DUF3856)
    6.3e-12   45.2   3.3     0.0021   17.1   0.0    6.3  7  NARP1         NMDA receptor-regulated protein 1
    1.3e-11   44.4   1.4      0.035   14.2   0.0    5.8  5  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    6.8e-10   39.6  20.7     0.0038   17.7   0.0    7.0  5  BTAD          Bacterial transcriptional activator domain
    6.7e-09   35.6   2.2    4.7e-06   26.2   0.4    3.8  4  TPR_MalT      MalT-like TPR region
    4.9e-07   29.7  14.8        0.4   10.4   0.1    6.2  6  TPR_21        Tetratricopeptide repeat-like domain
    9.5e-07   28.5   0.1        0.1   12.0   0.0    4.2  4  Coatomer_E    Coatomer epsilon subunit
    2.5e-06   27.0   1.9         14    5.3   0.0    7.4  7  HTH_Bact      Helix-turn-helix bacterial domain
    0.00012   22.1   0.1         22    5.1   0.0    4.8  3  SRP_TPR_like  Putative TPR-like repeat
     0.0014   19.0  23.6        3.1    8.7   0.0    9.2  9  TPR_4         Tetratricopeptide repeat
     0.0035   16.6   2.8        1.5    8.0   0.1    3.8  4  FAT           FAT domain
  ------ inclusion threshold ------
      0.012   15.6  10.4         66    3.7   0.0    7.8  9  ANAPC5        Anaphase-promoting complex subunit 5
      0.017   15.1   0.0      0.069   13.2   0.0    2.0  1  RNR_N         Ribonucleotide reductase N-terminal
      0.017   15.1  15.9         31    4.7   0.1    7.5  8  MIT           MIT (microtubule interacting and transport) dom
       0.02   14.9   1.3        1.8    8.6   0.0    4.1  3  TPR_3         Tetratricopeptide repeat
      0.049   14.0   4.0        9.2    6.7   0.1    4.7  4  TPR_20        Tetratricopeptide repeat
      0.077   11.9   0.0         15    4.3   0.0    3.0  4  DUF5588       Family of unknown function (DUF5588)
       0.16   11.8   0.8         33    4.2   0.0    4.5  5  DUF5113       Domain of unknown function (DUF5113)
       0.16   11.7   4.9         30    4.3   0.0    4.8  6  RPN7          26S proteasome subunit RPN7
        1.2    9.2   2.9         72    3.5   0.0    3.8  3  DUF1896       Domain of unknown function (DUF1896)


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.4e-07   7.6e-05       3      33 ..     150     180 ..     148     181 .. 0.93
   2 ?   -0.6   0.0       2.6   1.4e+03       1      10 [.     182     191 ..     182     195 .. 0.86
   3 !   10.3   0.1   0.00091      0.48      17      33 ..     205     221 ..     205     222 .. 0.93
   4 !   26.1   0.0   9.3e-09   4.9e-06       3      32 ..     225     254 ..     223     254 .. 0.97
   5 ?    6.5   0.0     0.015         8       3      23 ..     259     279 ..     257     285 .. 0.86
   6 !   18.4   0.0   2.5e-06    0.0013       1      34 []     294     327 ..     294     327 .. 0.96
   7 !   19.5   0.1   1.2e-06   0.00062      13      34 .]     341     362 ..     338     362 .. 0.94
   8 !   20.5   0.0   5.5e-07   0.00029      14      34 .]     377     397 ..     376     397 .. 0.94
   9 !   22.8   0.0     1e-07   5.4e-05       2      34 .]     399     431 ..     398     431 .. 0.95
  10 !   18.0   0.0   3.4e-06    0.0018       4      33 ..     435     464 ..     434     465 .. 0.88
  11 !   13.8   0.0   7.4e-05     0.039       1      32 [.     471     502 ..     471     509 .. 0.95
  12 !   14.6   0.0   4.1e-05     0.021       7      31 ..     518     542 ..     513     544 .. 0.89
  13 !   28.0   0.0   2.4e-09   1.3e-06       3      32 ..     554     583 ..     552     584 .. 0.95
  14 ?    4.7   0.1     0.056        29       2      18 ..     587     603 ..     586     606 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++ +G  +  +g  +eAl++ye+A+el+P+
  gi|386001637|ref|YP_005919936.1| 150 DWFEKGEELSMNGSTEEALAAYERAVELDPK 180
                                       5999**************************7 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                                       HHHHHHHHHH CS
                             TPR_1   1 akalynlGna 10 
                                       a+a+ ++G+a
  gi|386001637|ref|YP_005919936.1| 182 AEAWTGRGYA 191
                                       89******98 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00091
                                       HHHHHHHHHHHHHHSTT CS
                             TPR_1  17 ydeAleyyekALelnPn 33 
                                       y+eAl  +e+A+eln +
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRS 221
                                       99*************75 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 9.3e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a+++++ ++  +g+ydeA+++y+  Le +P
  gi|386001637|ref|YP_005919936.1| 225 AWNGKATLLSMMGRYDEAVDAYDASLEMDP 254
                                       9****************************9 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAley 23 
                                       +l +++na+ klg+++e +++
  gi|386001637|ref|YP_005919936.1| 259 VLVGKANALWKLGRHNESIAA 279
                                       67899************9986 PP

  == domain 6  score: 18.4 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a +++ +++++ + g+y+  +e+ ++A+el P++
  gi|386001637|ref|YP_005919936.1| 294 AFVWFERAHLFAEDGDYNGTVEALNRAIELAPDY 327
                                       568*****************************97 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 1.2e-06
                                       HTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  13 klgkydeAleyyekALelnPnn 34 
                                       +lg+y+eAl y ++ALe++P++
  gi|386001637|ref|YP_005919936.1| 341 HLGRYEEALIYIDRALEIDPEY 362
                                       69******************86 PP

  == domain 8  score: 20.5 bits;  conditional E-value: 5.5e-07
                                       TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  14 lgkydeAleyyekALelnPnn 34 
                                       lg+yde le++e+A+ ++P++
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDIDPED 397
                                       9******************86 PP

  == domain 9  score: 22.8 bits;  conditional E-value: 1e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +++  +G+++++lg+  eAl+++++A++ nP++
  gi|386001637|ref|YP_005919936.1| 399 DTWRLKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       7899***************************86 PP

  == domain 10  score: 18.0 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +  ++ ++ ++++yde le+y++AL l P+
  gi|386001637|ref|YP_005919936.1| 435 WQWKASLLVEMNRYDESLEAYDEALDLIPE 464
                                       5567889999*****************996 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+++  +G a+ k gk +eA e++ + L l++
  gi|386001637|ref|YP_005919936.1| 471 AQTWLSKGTALKKTGKQEEATEAFARSLALYE 502
                                       789*************************9976 PP

  == domain 12  score: 14.6 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   7 lGnayfklgkydeAleyyekALeln 31 
                                       +G a+++lg+yde le y++ Le  
  gi|386001637|ref|YP_005919936.1| 518 RGRALYELGRYDESLEVYDQILESS 542
                                       89******************99955 PP

  == domain 13  score: 28.0 bits;  conditional E-value: 2.4e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a+ ++G a++ lg+ +eAle+y++A+el P
  gi|386001637|ref|YP_005919936.1| 554 AWIGRGDALRALGRNQEALEAYNRAIELGP 583
                                       9**************************987 PP

  == domain 14  score: 4.7 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHTT-HH CS
                             TPR_1   2 kalynlGnayfklgkyd 18 
                                       +a+y++G   + lg+  
  gi|386001637|ref|YP_005919936.1| 587 NAWYGRGESQRALGQVY 603
                                       79************965 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.4e-07   0.00023       2      33 ..     149     180 ..     148     181 .. 0.94
   2 !    8.0   0.1    0.0067       3.5      17      32 ..     205     220 ..     205     221 .. 0.93
   3 !   19.4   0.0   1.5e-06   0.00077       3      32 ..     225     254 ..     223     255 .. 0.96
   4 !    8.2   0.0    0.0057         3       4      29 ..     260     285 ..     257     288 .. 0.89
   5 !   13.8   0.1   8.8e-05     0.046       1      34 []     294     327 ..     294     327 .. 0.96
   6 !   19.8   0.1   1.1e-06   0.00056      12      34 .]     340     362 ..     337     362 .. 0.91
   7 !   16.5   0.0   1.2e-05    0.0064      14      34 .]     377     397 ..     376     397 .. 0.95
   8 !   25.6   0.0   1.5e-08   7.8e-06       2      34 .]     399     431 ..     398     431 .. 0.95
   9 !   17.7   0.0   5.2e-06    0.0027       4      33 ..     435     464 ..     433     465 .. 0.92
  10 !   13.2   0.0   0.00014     0.075       2      33 ..     472     503 ..     471     511 .. 0.92
  11 !   21.5   0.0     3e-07   0.00016       4      32 ..     515     543 ..     512     545 .. 0.92
  12 !   27.6   0.1   3.5e-09   1.9e-06       3      33 ..     554     584 ..     552     585 .. 0.95
  13 ?    2.4   0.2      0.41   2.2e+02       2      17 ..     587     602 ..     586     605 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.4e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       + +++ G+ +  +g  eeAl+a+e+A+eldP+
  gi|386001637|ref|YP_005919936.1| 149 RDWFEKGEELSMNGSTEEALAAYERAVELDPK 180
                                       679****************************6 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0067
                             TPR_2  17 yeeAleafekAleldP 32 
                                       y+eAl  fe+A+el+ 
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNR 220
                                       99************95 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.5e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       a++  + ++  +g+y+eA++a++++le dP
  gi|386001637|ref|YP_005919936.1| 225 AWNGKATLLSMMGRYDEAVDAYDASLEMDP 254
                                       899**************************9 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0057
                             TPR_2   4 lynlGlayyklgdyeeAleafekAle 29 
                                       l   ++a++klg+++e ++a ++A+ 
  gi|386001637|ref|YP_005919936.1| 260 LVGKANALWKLGRHNESIAAGDEAID 285
                                       66789****************99985 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 8.8e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a ++++++ + ++ gdy+  +ea+++A+el+P++
  gi|386001637|ref|YP_005919936.1| 294 AFVWFERAHLFAEDGDYNGTVEALNRAIELAPDY 327
                                       679*****************************85 PP

  == domain 6  score: 19.8 bits;  conditional E-value: 1.1e-06
                             TPR_2  12 yklgdyeeAleafekAleldPnn 34 
                                       ++lg+yeeAl + ++Ale+dP++
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEIDPEY 362
                                       689******************85 PP

  == domain 7  score: 16.5 bits;  conditional E-value: 1.2e-05
                             TPR_2  14 lgdyeeAleafekAleldPnn 34 
                                       lg+y+e lea+e+A+ +dP++
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDIDPED 397
                                       8******************86 PP

  == domain 8  score: 25.6 bits;  conditional E-value: 1.5e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       + +   Gl++++lg+ +eAl+af++A++ +P++
  gi|386001637|ref|YP_005919936.1| 399 DTWRLKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       6899***************************86 PP

  == domain 9  score: 17.7 bits;  conditional E-value: 5.2e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       + + + ++ ++++y+e lea+++Al l P+
  gi|386001637|ref|YP_005919936.1| 435 WQWKASLLVEMNRYDESLEAYDEALDLIPE 464
                                       8889999********************997 PP

  == domain 10  score: 13.2 bits;  conditional E-value: 0.00014
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       + +   G a+ k g+ eeA eaf ++l+l+++
  gi|386001637|ref|YP_005919936.1| 472 QTWLSKGTALKKTGKQEEATEAFARSLALYEE 503
                                       678899***********************975 PP

  == domain 11  score: 21.5 bits;  conditional E-value: 3e-07
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       l  +G+a+y+lg+y+e le +++ le  P
  gi|386001637|ref|YP_005919936.1| 515 LQTRGRALYELGRYDESLEVYDQILESSP 543
                                       778**********************9888 PP

  == domain 12  score: 27.6 bits;  conditional E-value: 3.5e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+  +G+a+++lg+ +eAlea+++A+el P+
  gi|386001637|ref|YP_005919936.1| 554 AWIGRGDALRALGRNQEALEAYNRAIELGPH 584
                                       8***************************997 PP

  == domain 13  score: 2.4 bits;  conditional E-value: 0.41
                             TPR_2   2 ealynlGlayyklgdy 17 
                                        a+y +G++ ++lg+ 
  gi|386001637|ref|YP_005919936.1| 587 NAWYGRGESQRALGQV 602
                                       59***********985 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-05     0.011       4      33 ..     151     180 ..     149     181 .. 0.92
   2 ?    4.7   0.1     0.082        43      17      33 ..     205     221 ..     205     222 .. 0.91
   3 !   14.7   0.0   4.9e-05     0.026       3      32 ..     225     254 ..     225     254 .. 0.96
   4 !    7.6   0.0    0.0093       4.9       5      29 ..     261     285 ..     259     289 .. 0.83
   5 !   12.5   0.0   0.00025      0.13       3      34 .]     296     327 ..     296     327 .. 0.96
   6 !   16.3   0.0   1.6e-05    0.0083      12      33 ..     340     361 ..     330     362 .. 0.88
   7 !   18.6   0.0   2.8e-06    0.0015       2      34 .]     364     397 ..     363     397 .. 0.92
   8 !   15.5   0.0   2.8e-05     0.015       6      34 .]     403     431 ..     398     431 .. 0.91
   9 !   19.1   0.0     2e-06     0.001       3      33 ..     434     464 ..     432     465 .. 0.94
  10 !   12.7   0.2   0.00022      0.11       1      31 [.     471     501 ..     471     504 .. 0.92
  11 !   13.2   0.0   0.00015      0.08       5      32 ..     516     543 ..     513     544 .. 0.91
  12 !   17.6   0.0   5.9e-06    0.0031       3      30 ..     554     581 ..     552     584 .. 0.93
  13 ?   -1.1   0.0       5.8   3.1e+03       2      20 ..     587     605 ..     586     610 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++ +g  ++  g  eeA ++ye+a+eldp+
  gi|386001637|ref|YP_005919936.1| 151 WFEKGEELSMNGSTEEALAAYERAVELDPK 180
                                       78888888889******************7 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekaleldpd 33 
                                       y+eA  ++e+a+el+++
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRS 221
                                       799***********985 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a++ ++ +++ +g+y+eA+ +y   le+dp
  gi|386001637|ref|YP_005919936.1| 225 AWNGKATLLSMMGRYDEAVDAYDASLEMDP 254
                                       7999999**********************9 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekale 29 
                                       + ++++++klg+++e++++  +a++
  gi|386001637|ref|YP_005919936.1| 261 VGKANALWKLGRHNESIAAGDEAID 285
                                       5689*************98666665 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +++  +++  + gdy+  +e++++a+el+pd+
  gi|386001637|ref|YP_005919936.1| 296 VWFERAHLFAEDGDYNGTVEALNRAIELAPDY 327
                                       699***************************85 PP

  == domain 6  score: 16.3 bits;  conditional E-value: 1.6e-05
                                       HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  12 lklgdyeeAkeyyekaleldpd 33 
                                         lg+yeeA  y+ +ale+dp+
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEIDPE 361
                                       579******************8 PP

  == domain 7  score: 18.6 bits;  conditional E-value: 2.8e-06
                                       CHHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiy.lklgdyeeAkeyyekaleldpdn 34 
                                       +a+  +++i+  +lg+y+e+ e++e+a+++dp++
  gi|386001637|ref|YP_005919936.1| 364 DAWISKAQILgPSLGRYDESLEACERAIDIDPED 397
                                       7899999999999*******************86 PP

  == domain 8  score: 15.5 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++g+i+++lg+  eA +++ +a++ +p++
  gi|386001637|ref|YP_005919936.1| 403 LKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       79**********************99985 PP

  == domain 9  score: 19.1 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++++++s++ ++++y+e+ e+y +al+l p+
  gi|386001637|ref|YP_005919936.1| 434 SWQWKASLLVEMNRYDESLEAYDEALDLIPE 464
                                       79**************************986 PP

  == domain 10  score: 12.7 bits;  conditional E-value: 0.00022
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+ ++ +g +++k+g+ eeA e++ + l l 
  gi|386001637|ref|YP_005919936.1| 471 AQTWLSKGTALKKTGKQEEATEAFARSLALY 501
                                       689*********************9999876 PP

  == domain 11  score: 13.2 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +  g+++ +lg+y+e+ e+y + le +p
  gi|386001637|ref|YP_005919936.1| 516 QTRGRALYELGRYDESLEVYDQILESSP 543
                                       6789********************9988 PP

  == domain 12  score: 17.6 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+   g++++ lg+ +eA e+y++a+el
  gi|386001637|ref|YP_005919936.1| 554 AWIGRGDALRALGRNQEALEAYNRAIEL 581
                                       8999**********************98 PP

  == domain 13  score: -1.1 bits;  conditional E-value: 5.8
                                       CHHHHHHHHHHHTT-HHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeA 20 
                                        a+y  g   + lg+  +A
  gi|386001637|ref|YP_005919936.1| 587 NAWYGRGESQRALGQVYNA 605
                                       5899999999999998777 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.5e-09   7.8e-07       7      37 ..     161     191 ..     155     195 .. 0.91
   2 ?    5.2   0.0     0.031        16      10      27 ..     205     222 ..     205     233 .. 0.87
   3 !   19.7   0.0   9.3e-07   0.00049       8      42 .]     237     271 ..     235     271 .. 0.98
   4 !   15.3   0.1   2.3e-05     0.012       2      37 ..     302     337 ..     301     341 .. 0.88
   5 !   12.8   0.2   0.00014     0.072       7      34 ..     342     369 ..     339     374 .. 0.88
   6 !   24.4   0.0   3.2e-08   1.7e-05       6      42 .]     376     412 ..     376     412 .. 0.96
   7 !   12.6   0.0   0.00016     0.084       1      28 [.     405     432 ..     405     437 .. 0.92
   8 !   14.6   0.1   3.7e-05     0.019       3      26 ..     441     464 ..     439     467 .. 0.89
   9 ?    0.9   0.1      0.68   3.6e+02       1      23 [.     478     500 ..     478     506 .. 0.78
  10 !   15.0   0.0   2.7e-05     0.014       1      19 [.     519     537 ..     519     543 .. 0.91
  11 !   29.3   0.3   9.7e-10   5.1e-07       1      41 [.     559     599 ..     559     600 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.5e-09
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                        G  eeA++aY++A++ldP+ aea+ ++G+a
  gi|386001637|ref|YP_005919936.1| 161 NGSTEEALAAYERAVELDPKMAEAWTGRGYA 191
                                       5999*************************88 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.031
                            TPR_11  10 yeeAieaYkkAlkldPdn 27 
                                       y+eA+ ++++A++l+ ++
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRSQ 222
                                       89************9875 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 9.3e-07
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+y+eA+ aY + l+ dP +++++ + ++a++k+G
  gi|386001637|ref|YP_005919936.1| 237 GRYDEAVDAYDASLEMDPLQPWVLVGKANALWKLG 271
                                       9********************************99 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.3e-05
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       +++ e G+y++ +ea+++A++l Pd+ +++ n G++
  gi|386001637|ref|YP_005919936.1| 302 HLFAEDGDYNGTVEALNRAIELAPDYKNFWINGGVL 337
                                       578899********************9999887765 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 0.00014
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynL 34 
                                       +G+yeeA+    +Al++dP++++a+   
  gi|386001637|ref|YP_005919936.1| 342 LGRYEEALIYIDRALEIDPEYVDAWISK 369
                                       79**********************9665 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 3.2e-08
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++G+y+e++ea ++A+++dP++++ +   Gl+++++G
  gi|386001637|ref|YP_005919936.1| 376 SLGRYDESLEACERAIDIDPEDPDTWRLKGLILMNLG 412
                                       58*******************************9998 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00016
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                       G +++ +G+  eA++a+ +A++ +P++ 
  gi|386001637|ref|YP_005919936.1| 405 GLILMNLGRDAEALAAFDEAIRQNPEDF 432
                                       789999*******************985 PP

  == domain 8  score: 14.6 bits;  conditional E-value: 3.7e-05
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPd 26 
                                       +++e ++y+e++eaY +Al+l P+
  gi|386001637|ref|YP_005919936.1| 441 LLVEMNRYDESLEAYDEALDLIPE 464
                                       58999***************9886 PP

  == domain 9  score: 0.9 bits;  conditional E-value: 0.68
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G a+ + Gk eeA ea+ + l+l
  gi|386001637|ref|YP_005919936.1| 478 GTALKKTGKQEEATEAFARSLAL 500
                                       55788899999999988777765 PP

  == domain 10  score: 15.0 bits;  conditional E-value: 2.7e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkk 19 
                                       G+a+ye+G+y+e++e+Y +
  gi|386001637|ref|YP_005919936.1| 519 GRALYELGRYDESLEVYDQ 537
                                       99***************98 PP

  == domain 11  score: 29.3 bits;  conditional E-value: 9.7e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       Gda++++G++ eA+eaY++A++l P   +a+y++G+ + ++
  gi|386001637|ref|YP_005919936.1| 559 GDALRALGRNQEALEAYNRAIELGPHWSNAWYGRGESQRAL 599
                                       9**********************************977555 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.9   2.1e+03      16      33 ..     151     168 ..     144     169 .. 0.91
   2 !    9.5   0.0    0.0026       1.4       1      22 [.     170     191 ..     170     201 .. 0.92
   3 !   19.4   0.0   1.8e-06   0.00096       2      33 ..     212     243 ..     211     244 .. 0.96
   4 ?    6.3   0.0     0.028        15       1      30 [.     245     274 ..     245     278 .. 0.85
   5 ?    3.6   0.0       0.2   1.1e+02      13      29 ..     294     310 ..     292     315 .. 0.89
   6 !   12.4   0.0    0.0003      0.16       2      33 ..     317     349 ..     316     350 .. 0.91
   7 !   16.7   0.0   1.3e-05    0.0067       3      32 ..     353     383 ..     351     385 .. 0.89
   8 !   21.0   0.0   5.5e-07   0.00029       2      33 ..     387     418 ..     386     419 .. 0.95
   9 !   14.4   0.0   7.1e-05     0.037       2      33 ..     421     452 ..     420     453 .. 0.92
  10 ?    4.0   0.0      0.15        79       2      32 ..     455     490 ..     454     492 .. 0.78
  11 !   14.6   0.0   6.3e-05     0.033       1      33 [.     500     532 ..     500     533 .. 0.94
  12 ?    2.2   0.0      0.55   2.9e+02      14      34 .]     553     573 ..     551     573 .. 0.89
  13 !   10.7   0.0     0.001      0.55       1      28 [.     574     601 ..     574     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.9
                            TPR_17  16 ynnLAelllknGdlmtAr 33 
                                       +++++e l++nG +++A+
  gi|386001637|ref|YP_005919936.1| 151 WFEKGEELSMNGSTEEAL 168
                                       9999999*******9997 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0026
                            TPR_17   1 lylkaleldPnnadaynnLAel 22 
                                       +y++a+eldP+ a+a++ ++++
  gi|386001637|ref|YP_005919936.1| 170 AYERAVELDPKMAEAWTGRGYA 191
                                       5****************99987 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.8e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +++a+el+ + + a+n +A+ll++ G++++A+
  gi|386001637|ref|YP_005919936.1| 212 FERAIELNRSQSMAWNGKATLLSMMGRYDEAV 243
                                       89****************************96 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.028
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                       +y  +le dP  ++++  +A++l k+G++ 
  gi|386001637|ref|YP_005919936.1| 245 AYDASLEMDPLQPWVLVGKANALWKLGRHN 274
                                       599******************997777665 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.2
                            TPR_17  13 adaynnLAelllknGdl 29 
                                       a +++++A l+++ Gd+
  gi|386001637|ref|YP_005919936.1| 294 AFVWFERAHLFAEDGDY 310
                                       669************98 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.0003
                            TPR_17   2 ylkaleldPnnadaynnLAelll.knGdlmtAr 33 
                                       + +a+el P++ +++ n ++ll+ ++G++++A+
  gi|386001637|ref|YP_005919936.1| 317 LNRAIELAPDYKNFWINGGVLLSaHLGRYEEAL 349
                                       579*******************6699****995 PP

  == domain 7  score: 16.7 bits;  conditional E-value: 1.3e-05
                            TPR_17   3 lkaleldPnnadaynnLAelll.knGdlmtA 32 
                                        +ale+dP ++da+  +A++l  ++G++++ 
  gi|386001637|ref|YP_005919936.1| 353 DRALEIDPEYVDAWISKAQILGpSLGRYDES 383
                                       79*******************8799999986 PP

  == domain 8  score: 21.0 bits;  conditional E-value: 5.5e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +++a+++dP ++d + +++ +l ++G+ ++A+
  gi|386001637|ref|YP_005919936.1| 387 CERAIDIDPEDPDTWRLKGLILMNLGRDAEAL 418
                                       89**************************9997 PP

  == domain 9  score: 14.4 bits;  conditional E-value: 7.1e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +a++++P ++ +++ +A ll + +++++ +
  gi|386001637|ref|YP_005919936.1| 421 FDEAIRQNPEDFGSWQWKASLLVEMNRYDESL 452
                                       889************************99865 PP

  == domain 10  score: 4.0 bits;  conditional E-value: 0.15
                            TPR_17   2 ylkaleldPnn.....adaynnLAelllknGdlmtA 32 
                                       y +al+l P +     a  +  ++++l+k G+ ++A
  gi|386001637|ref|YP_005919936.1| 455 YDEALDLIPESdaetlAQTWLSKGTALKKTGKQEEA 490
                                       6666666666556666999*************9998 PP

  == domain 11  score: 14.6 bits;  conditional E-value: 6.3e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ly++a+  dP ++++++ ++++l+++G++++ +
  gi|386001637|ref|YP_005919936.1| 500 LYEEAIMEDPGDVVLLQTRGRALYELGRYDESL 532
                                       7****************************9875 PP

  == domain 12  score: 2.2 bits;  conditional E-value: 0.55
                            TPR_17  14 daynnLAelllknGdlmtArq 34 
                                        a+  ++ +l+ +G+ ++A++
  gi|386001637|ref|YP_005919936.1| 553 TAWIGRGDALRALGRNQEALE 573
                                       68999*************985 PP

  == domain 13  score: 10.7 bits;  conditional E-value: 0.001
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGd 28 
                                       +y +a+el P  ++a++ ++e ++ +G+
  gi|386001637|ref|YP_005919936.1| 574 AYNRAIELGPHWSNAWYGRGESQRALGQ 601
                                       59********************999998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   7.7e-06    0.0041      10      43 ..     161     191 ..     152     195 .. 0.90
   2 !   21.7   0.1   4.4e-07   0.00023      13      67 ..     205     256 ..     204     257 .. 0.91
   3 !   24.0   0.3   8.4e-08   4.4e-05      11      63 ..     237     286 ..     236     289 .. 0.95
   4 !   26.0   0.1     2e-08   1.1e-05       2      66 ..     299     361 ..     298     363 .. 0.96
   5 !   32.4   0.0     2e-10   1.1e-07      10      67 ..     377     431 ..     376     432 .. 0.95
   6 !   17.0   0.6   1.3e-05    0.0068       4      64 ..     439     501 ..     438     505 .. 0.90
   7 !   40.8   0.4   4.7e-13   2.5e-10       3      65 ..     518     583 ..     517     586 .. 0.94
   8 !   22.1   1.5   3.4e-07   0.00018       3      49 ..     558     601 ..     556     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.7e-06
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgda 43 
                                       +g  ++A+aa+e+a+++d   P  aeA+ ++g a
  gi|386001637|ref|YP_005919936.1| 161 NGSTEEALAAYERAVELD---PKMAEAWTGRGYA 191
                                       67789*************...***********87 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 4.4e-07
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       y +A+  +e+a++++        A+++++ ++   gr++eA+++y+a l+ +p  
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELN---RSQSMAWNGKATLLSMMGRYDEAVDAYDASLEMDPLQ 256
                                       779999*********...55566***************************99966 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 8.4e-08
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       g+yd+A+ a++a l++d   P+ +  l ++++a++++gr+ e +a+ ++a++a
  gi|386001637|ref|YP_005919936.1| 237 GRYDEAVDAYDASLEMD---PLQPWVLVGKANALWKLGRHNESIAAGDEAIDA 286
                                       9****************...99999************************9987 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 2e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyraalraapd 66 
                                       ++a+++++ gdy   ++al++a++++   Pd   ++ + g+++  ++gr++eA+ ++++al+ +p 
  gi|386001637|ref|YP_005919936.1| 299 ERAHLFAEDGDYNGTVEALNRAIELA---PDYKNFWINGGVLLSaHLGRYEEALIYIDRALEIDPE 361
                                       689***********************...***************899***************9996 PP

  == domain 5  score: 32.4 bits;  conditional E-value: 2e-10
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +g+yd+ ++a e+a++ d   P++++ + l+g+++  +gr aeA+a++++a+r+ p +
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDID---PEDPDTWRLKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       69****************...88888***************************99975 PP

  == domain 6  score: 17.0 bits;  conditional E-value: 1.3e-05
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       a ++++ ++yd+ ++a+++al++ p+s +   a+ +l +g a+ + g  +eA +++++ l+ +
  gi|386001637|ref|YP_005919936.1| 439 ASLLVEMNRYDESLEAYDEALDLIPESDAetLAQTWLSKGTALKKTGKQEEATEAFARSLALY 501
                                       7899********************77777************************9999888765 PP

  == domain 7  score: 40.8 bits;  conditional E-value: 4.7e-13
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++ra++++g+yd+ ++++++ l++    P       +  A+ ++gda+ ++gr +eA+++y++a++ +p
  gi|386001637|ref|YP_005919936.1| 518 RGRALYELGRYDESLEVYDQILESS---PGvephlvDTTAWIGRGDALRALGRNQEALEAYNRAIELGP 583
                                       79****************9999999...888888*******************************9988 PP

  == domain 8  score: 22.1 bits;  conditional E-value: 3.4e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49 
                                       +++a++++g+ ++A++a+++a++++   P    A++++g++  ++g 
  gi|386001637|ref|YP_005919936.1| 558 RGDALRALGRNQEALEAYNRAIELG---PHWSNAWYGRGESQRALGQ 601
                                       799**********************...************9998885 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   7.2e-07   0.00038       4      42 ..     151     189 ..     148     192 .. 0.86
   2 ?    2.3   0.0      0.73   3.8e+02      18      42 ..     206     230 ..     201     232 .. 0.87
   3 !   13.0   0.1   0.00027      0.14       7      41 ..     229     263 ..     223     266 .. 0.84
   4 ?    2.9   0.0      0.48   2.5e+02       4      30 ..     260     286 ..     257     292 .. 0.81
   5 !   14.5   0.0   9.2e-05     0.048       3      39 ..     296     332 ..     294     337 .. 0.92
   6 !   16.7   0.1   1.8e-05    0.0093      12      44 .]     340     372 ..     334     372 .. 0.91
   7 !   17.6   0.0   8.9e-06    0.0047      14      42 ..     377     405 ..     376     407 .. 0.93
   8 !   19.6   0.4   2.1e-06    0.0011       1      41 [.     398     438 ..     398     441 .. 0.88
   9 !   10.0   0.2    0.0025       1.3       4      35 ..     435     466 ..     432     477 .. 0.84
  10 ?    7.2   0.2      0.02        11       4      36 ..     481     513 ..     471     516 .. 0.64
  11 !   13.9   0.0   0.00015     0.077       3      33 ..     514     544 ..     512     549 .. 0.90
  12 !   20.5   0.4     1e-06   0.00055       3      41 ..     554     592 ..     553     595 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.2e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + + +e l  +G ++eA+a+++ra++l+P+ aeaw+  +
  gi|386001637|ref|YP_005919936.1| 151 WFEKGEELSMNGSTEEALAAYERAVELDPKMAEAWTGRG 189
                                       66777888899************************7654 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.73
                            TPR_14  18 deAiallrralalaPddaeawllla 42 
                                       +eA+  ++ra++l+ ++  aw   a
  gi|386001637|ref|YP_005919936.1| 206 KEALLSFERAIELNRSQSMAWNGKA 230
                                       789999***********99997666 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00027
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlll 41 
                                        a +l   G++deA++++++ l+ +P +++++   
  gi|386001637|ref|YP_005919936.1| 229 KATLLSMMGRYDEAVDAYDASLEMDPLQPWVLVGK 263
                                       57788889******************999988765 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.48
                            TPR_14   4 llalaeallalGdpdeAiallrralal 30 
                                       l   a al+ lG++ e+ia+ ++a+++
  gi|386001637|ref|YP_005919936.1| 260 LVGKANALWKLGRHNESIAAGDEAIDA 286
                                       555699************998888765 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 9.2e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ++ ++a+++++ Gd+ + +++l+ra++laPd   +w+
  gi|386001637|ref|YP_005919936.1| 296 VWFERAHLFAEDGDYNGTVEALNRAIELAPDYKNFWI 332
                                       5999***************************988886 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 1.8e-05
                            TPR_14  12 lalGdpdeAiallrralalaPddaeawlllaql 44 
                                       ++lG+++eA+ + +ral+ +P+  +aw+  aq+
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEIDPEYVDAWISKAQI 372
                                       589************************999985 PP

  == domain 7  score: 17.6 bits;  conditional E-value: 8.9e-06
                            TPR_14  14 lGdpdeAiallrralalaPddaeawllla 42 
                                       lG++de++++++ra++ +P+d+++w+l +
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDIDPEDPDTWRLKG 405
                                       7************************9876 PP

  == domain 8  score: 19.6 bits;  conditional E-value: 2.1e-06
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       p+ +++ + +l++lG+ +eA+a++++a++++P+d   w   
  gi|386001637|ref|YP_005919936.1| 398 PDTWRLKGLILMNLGRDAEALAAFDEAIRQNPEDFGSWQWK 438
                                       6789999**************************98777655 PP

  == domain 9  score: 10.0 bits;  conditional E-value: 0.0025
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPdda 35 
                                       ++  a++l +  ++de+++++++al+l P+++
  gi|386001637|ref|YP_005919936.1| 435 WQWKASLLVEMNRYDESLEAYDEALDLIPESD 466
                                       788899********************999764 PP

  == domain 10  score: 7.2 bits;  conditional E-value: 0.02
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddae 36 
                                       l++ ++ ++a + +++++al+++a+  +P+d +
  gi|386001637|ref|YP_005919936.1| 481 LKKTGKQEEATEAFARSLALYEEAIMEDPGDVV 513
                                       444455666666677777777777777777765 PP

  == domain 11  score: 13.9 bits;  conditional E-value: 0.00015
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPd 33 
                                       +l+ +++al++lG++de++++++++l+  P+
  gi|386001637|ref|YP_005919936.1| 514 LLQTRGRALYELGRYDESLEVYDQILESSPG 544
                                       57889*********************98886 PP

  == domain 12  score: 20.5 bits;  conditional E-value: 1e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       a+  +++al+alG+ +eA+++++ra++l+P    aw+  
  gi|386001637|ref|YP_005919936.1| 554 AWIGRGDALRALGRNQEALEAYNRAIELGPHWSNAWYGR 592
                                       78899*************************988888765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0026       1.4      44      76 ..     147     179 ..     144     180 .. 0.83
   2 !   17.2   0.4   8.8e-06    0.0046      26      75 ..     205     253 ..     203     254 .. 0.76
   3 !   15.2   0.0   3.6e-05     0.019       5      76 ..     259     325 ..     255     326 .. 0.91
   4 !   18.6   0.4   3.3e-06    0.0017      14      76 ..     340     395 ..     331     396 .. 0.90
   5 !   16.5   0.2   1.5e-05    0.0077      16      66 ..     377     426 ..     364     428 .. 0.88
   6 !   36.5   0.5   8.3e-12   4.4e-09       9      77 .]     438     503 ..     431     503 .. 0.95
   7 !   35.6   0.4   1.6e-11   8.5e-09       8      74 ..     517     581 ..     511     584 .. 0.93
   8 !   19.0   0.4   2.5e-06    0.0013       4      56 ..     553     604 ..     550     606 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                            TPR_12  44 tattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ta+  +  g+ +++ g +eeAl+++e+a+++++
  gi|386001637|ref|YP_005919936.1| 147 TARDWFEKGEELSMNGSTEEALAAYERAVELDP 179
                                       566666678889999**************9976 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 8.8e-06
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++al  ++r+ + ++   + + ++ ++l++++gry+eA++++  +l+++
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNR-SQSMAWNGKATLLSMMGRYDEAVDAYDASLEMD 253
                                       5566666666655555.688899999999999999999999999999985 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3.6e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +l+  a++l++lgr+ e+++  ++a+++       +  + a + +  + l+ + g+y   +e+l++a+++a+
  gi|386001637|ref|YP_005919936.1| 259 VLVGKANALWKLGRHNESIAAGDEAIDAT-----SETVEKAFVWFERAHLFAEDGDYNGTVEALNRAIELAP 325
                                       67889************************.....556679****************************9986 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 3.3e-06
                            TPR_12  14 rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyr.algryeeAlelleealaiae 76 
                                       ++lgry+eAl + ++alei      p++   + + +  ++++   lgry+e le+ e+a++i++
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEID-----PEY---VDAWISKAQILGpSLGRYDESLEACERAIDIDP 395
                                       79******************.....885...889********98****************9976 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 1.5e-05
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                       lgryde+le +e+a++i      +++ l   +l nLgr  +al  ++eA++
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDID-PEDPDTWRLKGLILMNLGRDAEALAAFDEAIR 426
                                       8*****************.444577899999*******9999999999986 PP

  == domain 6  score: 36.5 bits;  conditional E-value: 8.3e-12
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        a++l ++ ryde+le +++al+++   ++ d + +a+t    g+++ ++g++eeA e++ ++la++e+
  gi|386001637|ref|YP_005919936.1| 438 KASLLVEMNRYDESLEAYDEALDLI---PESDAETLAQTWLSKGTALKKTGKQEEATEAFARSLALYEE 503
                                       6899999******************...8899999********************************96 PP

  == domain 7  score: 35.6 bits;  conditional E-value: 1.6e-11
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        ++ +l++lgryde+le +++ le    +  + h+   t+ ++ g+++ralgr +eAle++++a+++
  gi|386001637|ref|YP_005919936.1| 517 TRGRALYELGRYDESLEVYDQILESSPGV--EPHLVDTTAWIGRGDALRALGRNQEALEAYNRAIEL 581
                                       48999*********************989..779999***************************997 PP

  == domain 8  score: 19.0 bits;  conditional E-value: 2.5e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyr 56 
                                       ta+  ++++lr+lgr +eAle +++a+e+   + +  +++  +++r+Lg++y 
  gi|386001637|ref|YP_005919936.1| 553 TAWIGRGDALRALGRNQEALEAYNRAIELGPHWSNA-WYGRGESQRALGQVYN 604
                                       467788999999999999999999999998778654.8888888888888885 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   9.5e-05      0.05       3      30 ..     160     187 ..     158     196 .. 0.88
   2 !   19.0   0.0   2.9e-06    0.0015       7      57 ..     205     255 ..     204     259 .. 0.96
   3 !   23.0   0.0   1.6e-07   8.6e-05       3      47 ..     235     279 ..     233     289 .. 0.91
   4 !   14.7   0.1   6.2e-05     0.033       3      59 ..     306     363 ..     304     372 .. 0.84
   5 !   20.6   0.0   8.9e-07   0.00047       5      66 ..     343     405 ..     337     407 .. 0.92
   6 !   24.3   0.0   6.2e-08   3.3e-05       5      58 ..     378     431 ..     376     436 .. 0.96
   7 !   18.6   1.0   3.7e-06     0.002       8      61 ..     415     467 ..     408     475 .. 0.90
   8 !   25.6   0.0   2.5e-08   1.3e-05       9      57 ..     492     544 ..     485     554 .. 0.88
   9 !   10.4   0.1    0.0013       0.7       2      41 ..     563     602 ..     562     606 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.5e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearll 30 
                                       ++g  +eAla++e+a + dpk+aea+ +
  gi|386001637|ref|YP_005919936.1| 160 MNGSTEEALAAYERAVELDPKMAEAWTG 187
                                       5899*********************975 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.9e-06
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       y eAl  +e+a++ +  ++ a+ + A +l  +g++deA ++ da +e+dp 
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRSQSMAWNGKATLLSMMGRYDEAVDAYDASLEMDPL 255
                                       789*********************************************997 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 1.6e-07
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       ++g+y+eA++++ + l+ dp +++++ + A+al++lg+ +e +a+
  gi|386001637|ref|YP_005919936.1| 235 MMGRYDEAVDAYDASLEMDPLQPWVLVGKANALWKLGRHNESIAA 279
                                       69*************************************998876 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 6.2e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallal.gqldeAealLdalpeedpdda 59 
                                       ++gdy   +++l +a++ +p++ + +++   +l a  g+++eA   +d+++e dp   
  gi|386001637|ref|YP_005919936.1| 306 EDGDYNGTVEALNRAIELAPDYKNFWINGGVLLSAHlGRYEEALIYIDRALEIDPEYV 363
                                       79*************************7777777667*****************9843 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 8.9e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeall.algqldeAealLdalpeedpddaryasLlA 66 
                                       g+y+eAl +  +al+ dp++ +a++  A++l  +lg++de  ++++++ + dp d++ ++L++
  gi|386001637|ref|YP_005919936.1| 343 GRYEEALIYIDRALEIDPEYVDAWISKAQILGpSLGRYDESLEACERAIDIDPEDPDTWRLKG 405
                                       89***********************8888886356*********************9999986 PP

  == domain 6  score: 24.3 bits;  conditional E-value: 6.2e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       g+y+e l++ e+a++ dp++++ + l   +l++lg+ +eA a+ d++ +++p d
  gi|386001637|ref|YP_005919936.1| 378 GRYDESLEACERAIDIDPEDPDTWRLKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       89*************************************************986 PP

  == domain 7  score: 18.6 bits;  conditional E-value: 3.7e-06
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       aeAla++ +a+ ++p++   + + A +l++++++de  ++ d++++  p  +++
  gi|386001637|ref|YP_005919936.1| 415 AEALAAFDEAIRQNPEDFGSWQWKASLLVEMNRYDESLEAYDEALDLIPE-SDA 467
                                       89****************************************99998887.544 PP

  == domain 8  score: 25.6 bits;  conditional E-value: 2.5e-08
                            TPR_19   9 eA....lalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       eA    lal+e+a+ edp++  ++    +al++lg++de  ++ d+++e+ p 
  gi|386001637|ref|YP_005919936.1| 492 EAfarsLALYEEAIMEDPGDVVLLQTRGRALYELGRYDESLEVYDQILESSPG 544
                                       445555*******************************************9986 PP

  == domain 9  score: 10.4 bits;  conditional E-value: 0.0013
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                        a g+ +eAl+++ +a++  p+ ++a+++  e + algq+
  gi|386001637|ref|YP_005919936.1| 563 RALGRNQEALEAYNRAIELGPHWSNAWYGRGESQRALGQV 602
                                       577999*******************************996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00037      0.19      10      39 ..     163     192 ..     158     196 .. 0.88
   2 ?    6.9   0.1     0.013       7.1      13      60 ..     207     254 ..     203     266 .. 0.90
   3 !   13.9   0.0   8.6e-05     0.045      32      61 ..     297     326 ..     292     329 .. 0.95
   4 !   10.2   0.1    0.0012      0.64      39      65 ..     339     365 ..     337     373 .. 0.52
   5 !   33.3   0.4   7.6e-11     4e-08      10      62 ..     379     431 ..     376     434 .. 0.95
   6 ?    7.2   0.1     0.011       5.6      25      63 ..     428     466 ..     427     474 .. 0.86
   7 !   17.0   0.4   8.9e-06    0.0047       9      61 ..     492     546 ..     488     564 .. 0.88
   8 !    9.3   0.2    0.0023       1.2       9      52 ..     566     609 ..     560     610 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                             TPR_9  10 dweralavverllllaPddpeerrdRGlll 39 
                                         e+ala++er + l+P+ +e +  RG + 
  gi|386001637|ref|YP_005919936.1| 163 STEEALAAYERAVELDPKMAEAWTGRGYAK 192
                                       5799*********************99876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +al   er + l+  +   +   + ll  +G++ +A+++ +a l+++p
  gi|386001637|ref|YP_005919936.1| 207 EALLSFERAIELNRSQSMAWNGKATLLSMMGRYDEAVDAYDASLEMDP 254
                                       6778889999999999999**************************999 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 8.6e-05
                             TPR_9  32 rrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +++R+ l a+ G++++ +++L+++++lapd
  gi|386001637|ref|YP_005919936.1| 297 WFERAHLFAEDGDYNGTVEALNRAIELAPD 326
                                       99***************************8 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0012
                             TPR_9  39 laqlGclsaAladLeaylalapdapda 65 
                                        a+lG++++Al   +++l+++p+  da
  gi|386001637|ref|YP_005919936.1| 339 SAHLGRYEEALIYIDRALEIDPEYVDA 365
                                       556666666666666666666654444 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 7.6e-11
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++++ l+++er + ++P+dp+ +r  Gl+l+ lG+ ++Ala+++ +++++p++
  gi|386001637|ref|YP_005919936.1| 379 RYDESLEACERAIDIDPEDPDTWRLKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       67889**********************************************86 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.011
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +P+d + +   + ll++++++ + l++ + +l+l p+ +
  gi|386001637|ref|YP_005919936.1| 428 NPEDFGSWQWKASLLVEMNRYDESLEAYDEALDLIPESD 466
                                       599999999*************************99543 PP

  == domain 7  score: 17.0 bits;  conditional E-value: 8.9e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap..d 61 
                                       e ++r la +e  ++ +P d+ ++  RG++l++lG++ + l+  ++ l+ +p  +
  gi|386001637|ref|YP_005919936.1| 492 EAFARSLALYEEAIMEDPGDVVLLQTRGRALYELGRYDESLEVYDQILESSPgvE 546
                                       7789999999999999******************************999999553 PP

  == domain 8  score: 9.3 bits;  conditional E-value: 0.0023
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladL 52 
                                        ++++al++++r + l P+    ++ RG  +  lG++  A + L
  gi|386001637|ref|YP_005919936.1| 566 GRNQEALEAYNRAIELGPHWSNAWYGRGESQRALGQVYNATMSL 609
                                       6899************************9999999988887665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.28   1.5e+02      15      32 ..     164     179 ..     161     183 .. 0.84
   2 ?    0.4   0.1       1.6   8.4e+02      15      31 ..     205     221 ..     205     223 .. 0.73
   3 !    9.6   0.0    0.0018      0.97       9      29 ..     233     253 ..     225     257 .. 0.79
   4 !    7.4   0.0    0.0096       5.1       9      29 ..     338     359 ..     334     362 .. 0.78
   5 !    8.9   0.0     0.003       1.6      11      35 ..     376     398 ..     376     399 .. 0.90
   6 ?    4.0   0.0      0.12        61       6      34 ..     405     431 ..     400     431 .. 0.86
   7 !    7.6   0.1    0.0082       4.3       6      31 ..     439     462 ..     438     467 .. 0.83
   8 ?    4.5   0.0     0.077        41      10      33 ..     482     510 ..     473     512 .. 0.53
   9 !   10.4   0.0     0.001      0.54       6      33 ..     519     544 ..     514     547 .. 0.84
  10 !    7.6   0.1     0.008       4.2       6      30 ..     559     581 ..     554     584 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                             TPR_7  15 yeeAielyeqsLaltkdp 32 
                                       +eeA+  ye+  a++ dp
  gi|386001637|ref|YP_005919936.1| 164 TEEALAAYER--AVELDP 179
                                       699*******..777776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                             TPR_7  15 yeeAielyeqsLaltkd 31 
                                       y+eA+  +e++++l ++
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRS 221
                                       78888889997777666 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0018
                             TPR_7   9 ysrlGdyeeAielyeqsLalt 29 
                                        s +G+y+eA++ y +sL+++
  gi|386001637|ref|YP_005919936.1| 233 LSMMGRYDEAVDAYDASLEMD 253
                                       5558************88876 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0096
                             TPR_7   9 ysr.lGdyeeAielyeqsLalt 29 
                                        s+ lG+yeeA+ +  ++L+++
  gi|386001637|ref|YP_005919936.1| 338 LSAhLGRYEEALIYIDRALEID 359
                                       55559************77765 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.003
                             TPR_7  11 rlGdyeeAielyeqsLaltkdpeda 35 
                                       +lG+y+e +e +e+  a++ dped+
  gi|386001637|ref|YP_005919936.1| 376 SLGRYDESLEACER--AIDIDPEDP 398
                                       59************..999999886 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.12
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       + +  +lG+ +eA+  + +  a++  ped
  gi|386001637|ref|YP_005919936.1| 405 GLILMNLGRDAEALAAFDE--AIRQNPED 431
                                       678999*************..99988875 PP

  == domain 7  score: 7.6 bits;  conditional E-value: 0.0082
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       a+l +++++y+e +e y +  al+  
  gi|386001637|ref|YP_005919936.1| 439 ASLLVEMNRYDESLEAYDE--ALDLI 462
                                       78999**************..66554 PP

  == domain 8  score: 4.5 bits;  conditional E-value: 0.077
                             TPR_7  10 srlGdyeeAielyeqsLalt.....kdpe 33 
                                        + G+ eeA e + +sLal      +dp+
  gi|386001637|ref|YP_005919936.1| 482 KKTGKQEEATEAFARSLALYeeaimEDPG 510
                                       55566666666666666554222226666 PP

  == domain 9  score: 10.4 bits;  conditional E-value: 0.001
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +r+  +lG+y+e +e+y q   l+++p+
  gi|386001637|ref|YP_005919936.1| 519 GRALYELGRYDESLEVYDQ--ILESSPG 544
                                       889999*************..7766665 PP

  == domain 10  score: 7.6 bits;  conditional E-value: 0.008
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltk 30 
                                       +++ ++lG+ +eA+e y +  a++ 
  gi|386001637|ref|YP_005919936.1| 559 GDALRALGRNQEALEAYNR--AIEL 581
                                       899****************..5554 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.088        46      19      30 ..     165     176 ..     156     179 .. 0.63
   2 ?   -2.0   0.1       7.1   3.8e+03      18      32 ..     205     219 ..     205     220 .. 0.83
   3 !    9.2   0.0    0.0021       1.1       9      31 ..     230     252 ..     227     252 .. 0.91
   4 !    7.8   0.0    0.0057         3       9      37 ..     264     292 ..     263     296 .. 0.89
   5 ?    6.3   0.1     0.017       8.9      13      31 ..     340     358 ..     333     358 .. 0.86
   6 ?    5.9   0.0     0.023        12      15      31 ..     377     393 ..     376     393 .. 0.92
   7 ?    7.0   0.1      0.01       5.4       9      30 ..     405     426 ..     405     426 .. 0.92
   8 !    7.4   0.1    0.0077         4      10      30 ..     440     460 ..     438     462 .. 0.88
   9 !    9.3   0.0     0.002         1       9      35 ..     478     504 ..     477     509 .. 0.94
  10 !   10.2   0.1     0.001      0.54       9      30 ..     519     540 ..     515     542 .. 0.91
  11 !    7.8   0.9    0.0057         3      10      31 ..     560     581 ..     558     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.088
                            TPR_10  19 deAealleeala 30 
                                       +eA+a +e+a++
  gi|386001637|ref|YP_005919936.1| 165 EEALAAYERAVE 176
                                       555555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.1
                            TPR_10  18 ydeAealleealair 32 
                                       y+eA+  +e+a+++ 
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELN 219
                                       67999999***9975 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0021
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a +l+ +grydeA++ ++ +l++
  gi|386001637|ref|YP_005919936.1| 230 ATLLSMMGRYDEAVDAYDASLEM 252
                                       67899*************99986 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0057
                            TPR_10   9 analrqrgrydeAealleealairrrllG 37 
                                       anal+++gr++e+ a  +ea+++  ++++
  gi|386001637|ref|YP_005919936.1| 264 ANALWKLGRHNESIAAGDEAIDATSETVE 292
                                       89*******************99877765 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.017
                            TPR_10  13 rqrgrydeAealleealai 31 
                                        ++gry+eA+ + ++al+i
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEI 358
                                       689**************97 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.023
                            TPR_10  15 rgrydeAealleealai 31 
                                       +gryde+++ +e+a++i
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDI 393
                                       7*************986 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.01
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + +l ++gr +eA+a ++ea++
  gi|386001637|ref|YP_005919936.1| 405 GLILMNLGRDAEALAAFDEAIR 426
                                       67899***************95 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0077
                            TPR_10  10 nalrqrgrydeAealleeala 30 
                                        +l +++ryde+++ ++eal+
  gi|386001637|ref|YP_005919936.1| 440 SLLVEMNRYDESLEAYDEALD 460
                                       56889**************97 PP

  == domain 9  score: 9.3 bits;  conditional E-value: 0.002
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       + al ++g+ +eA + + ++la+++++
  gi|386001637|ref|YP_005919936.1| 478 GTALKKTGKQEEATEAFARSLALYEEA 504
                                       78999********************97 PP

  == domain 10  score: 10.2 bits;  conditional E-value: 0.001
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       ++al+++gryde+++ +++ l+
  gi|386001637|ref|YP_005919936.1| 519 GRALYELGRYDESLEVYDQILE 540
                                       89***************99987 PP

  == domain 11  score: 7.8 bits;  conditional E-value: 0.0057
                            TPR_10  10 nalrqrgrydeAealleealai 31 
                                        alr++gr +eA++ + +a+++
  gi|386001637|ref|YP_005919936.1| 560 DALRALGRNQEALEAYNRAIEL 581
                                       689****************985 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0      0.04        21      14      32 ..     162     180 ..     148     180 .. 0.83
   2 ?    4.0   0.0      0.18        94       9      24 ..     232     247 ..     222     252 .. 0.85
   3 ?    7.1   0.0     0.018       9.7       3      32 ..     297     326 ..     295     327 .. 0.89
   4 ?    1.3   0.0       1.2   6.5e+02      12      32 ..     340     361 ..     334     362 .. 0.81
   5 ?    4.1   0.0      0.17        89      13      32 ..     377     396 ..     365     397 .. 0.79
   6 ?    7.4   0.0     0.014       7.6       7      32 ..     405     430 ..     403     431 .. 0.89
   7 ?    3.2   0.0      0.31   1.6e+02       7      28 ..     439     460 ..     437     465 .. 0.81
   8 ?    0.6   0.1       2.2   1.2e+03       7      26 ..     478     497 ..     474     503 .. 0.83
   9 !   11.5   0.0    0.0007      0.37       6      31 ..     518     543 ..     517     544 .. 0.93
  10 !    9.0   0.2    0.0044       2.3       6      28 ..     558     580 ..     553     581 .. 0.89
  11 ?    1.6   0.1      0.99   5.2e+02       2      16 ..     588     602 ..     587     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHH-TT CS
                             TPR_6  14 gdtdkAlealerlikeYPd 32 
                                       g t++Al+a+er ++  P+
  gi|386001637|ref|YP_005919936.1| 162 GSTEEALAAYERAVELDPK 180
                                       689***********99885 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAleale 24 
                                       ++ ++g++d+A++a++
  gi|386001637|ref|YP_005919936.1| 232 LLSMMGRYDEAVDAYD 247
                                       555689********97 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                        + +a ++ + gd+   +eal+r i+  Pd
  gi|386001637|ref|YP_005919936.1| 297 WFERAHLFAEDGDYNGTVEALNRAIELAPD 326
                                       578888999977***************998 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.2
                                       H.HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  12 k.lgdtdkAlealerlikeYPd 32 
                                       + lg++++Al + +r ++  P+
  gi|386001637|ref|YP_005919936.1| 340 AhLGRYEEALIYIDRALEIDPE 361
                                       4489********9999998885 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  13 lgdtdkAlealerlikeYPd 32 
                                       lg++d++lea er i+  P+
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDIDPE 396
                                       39*************99886 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +l + +lg+ ++Al+a+++ i++ P+
  gi|386001637|ref|YP_005919936.1| 405 GLILMNLGRDAEALAAFDEAIRQNPE 430
                                       67788899***************996 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       a ++ +++++d++lea+++ ++
  gi|386001637|ref|YP_005919936.1| 439 ASLLVEMNRYDESLEAYDEALD 460
                                       55677899*********99987 PP

  == domain 8  score: 0.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerl 26 
                                       + +++k+g+ ++A ea+ r 
  gi|386001637|ref|YP_005919936.1| 478 GTALKKTGKQEEATEAFARS 497
                                       78899999*******99885 PP

  == domain 9  score: 11.5 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       +++++++lg++d++le +++++++ P
  gi|386001637|ref|YP_005919936.1| 518 RGRALYELGRYDESLEVYDQILESSP 543
                                       599****99*************9988 PP

  == domain 10  score: 9.0 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       ++ ++r+lg+ ++Alea++r i+
  gi|386001637|ref|YP_005919936.1| 558 RGDALRALGRNQEALEAYNRAIE 580
                                       7999***99***********997 PP

  == domain 11  score: 1.6 bits;  conditional E-value: 0.99
                                       HHHHHHHHHHHHHHH CS
                             TPR_6   2 Alyklalsyrklgdt 16 
                                       A y +++s+r+lg+ 
  gi|386001637|ref|YP_005919936.1| 588 AWYGRGESQRALGQV 602
                                       89*********8875 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00034      0.18       1      80 [.     160     247 ..     160     249 .. 0.94
   2 !    9.4   0.0    0.0023       1.2       5      78 ..     205     279 ..     201     283 .. 0.75
   3 ?    3.9   0.0      0.12        64       7      80 ..     275     353 ..     269     355 .. 0.71
   4 ?    6.3   0.1     0.021        11      35      80 ..     341     388 ..     288     390 .. 0.83
   5 !   17.8   0.0   5.7e-06     0.003       3      81 ..     378     457 ..     376     458 .. 0.96
   6 ?    6.1   0.0     0.025        13      18      49 ..     504     538 ..     483     578 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                                       HTT-HHHHHHHHHHHH.HHH--HHH....HHHHHHHHHHTT-...HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHT CS
                            ANAPC3   1 dqnnyknAiflaerllaaetesped....ayllAlclylngq...ykrAyellrka.klnskslgcrylfAqcllkL 69 
                                       +++ +++A+  +er+++ +++++e+     y+++   + +++   yk+A+  +++a +ln +   ++  +A  l  +
  gi|386001637|ref|YP_005919936.1| 160 MNGSTEEALAAYERAVELDPKMAEAwtgrGYAKSRLAFIDKDpagYKEALLSFERAiELNRSQSMAWNGKATLLSMM 236
                                       578899*******************99999999******************************************** PP

                                       T-HHHHHHHH- CS
                            ANAPC3  70 kkyeeAiaaLe 80 
                                       ++y+eA++a++
  gi|386001637|ref|YP_005919936.1| 237 GRYDEAVDAYD 247
                                       ********986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   5 yknAiflaerllaaetespedayl..lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       yk+A++ +er+   e +++++  +  +A  l  +g+y++A + ++ + + ++  + +++ +A +l kL++++e iaa
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAI--ELNRSQSMAWngKATLLSMMGRYDEAVDAYDASlEMDPLQPWVLVGKANALWKLGRHNESIAA 279
                                       899999999999..555555555534799999999999999999999555555555555566777899999999886 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHH.HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-HHHHHHH CS
                            ANAPC3   7 nAiflaerllaaetespedayll...AlclylngqykrAyellrka.klnskslgcrylfAqcll.kLkkyeeAiaa 78 
                                       + i  ++ +  a +e  e a+     A  + ++g+y+   e l++a +l++  ++ ++  +  l   L++yeeA+  
  gi|386001637|ref|YP_005919936.1| 275 ESIAAGDEAIDATSETVEKAFVWferAHLFAEDGDYNGTVEALNRAiELAPDYKNFWINGGVLLSaHLGRYEEALIY 351
                                       55556666666666666666653366999999999999999999997777777777776665553489******976 PP

                                       H- CS
                            ANAPC3  79 Le 80 
                                       ++
  gi|386001637|ref|YP_005919936.1| 352 ID 353
                                       65 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.021
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-HHHHHHHH- CS
                            ANAPC3  35 lngqykrAyellrka.klnskslgcrylfAqcll.kLkkyeeAiaaLe 80 
                                       ++g+y++A+ ++++a +++++   +++ +Aq l   L++y+e + a e
  gi|386001637|ref|YP_005919936.1| 341 HLGRYEEALIYIDRAlEIDPEYVDAWISKAQILGpSLGRYDESLEACE 388
                                       578999999999999999999999999999999669999999888765 PP

  == domain 5  score: 17.8 bits;  conditional E-value: 5.7e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++y++ +  +er+   ++e+p+   l++l l ++g+  +A+  +++a ++n+++ g++  +A  l+++++y+e + a
  gi|386001637|ref|YP_005919936.1| 378 GRYDESLEACERAIDIDPEDPDTWRLKGLILMNLGRDAEALAAFDEAiRQNPEDFGSWQWKASLLVEMNRYDESLEA 454
                                       689999********999**********************************************************99 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       +++
  gi|386001637|ref|YP_005919936.1| 455 YDE 457
                                       876 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.025
                                       HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  18 aetespedayll...AlclylngqykrAyellrka 49 
                                       a  e+p d+ ll   + +ly++g+y++ +e++++ 
  gi|386001637|ref|YP_005919936.1| 504 AIMEDPGDVVLLqtrGRALYELGRYDESLEVYDQI 538
                                       55677777777666777777777777777777766 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.31   1.6e+02     104     129 ..     152     177 ..     147     189 .. 0.87
   2 !    8.4   0.2    0.0041       2.2      72     129 ..     199     252 ..     181     256 .. 0.82
   3 ?    4.6   0.0      0.06        32      59      82 ..     261     284 ..     253     329 .. 0.84
   4 ?    4.2   0.1     0.077        41      90      94 ..     357     361 ..     290     393 .. 0.63
   5 ?    3.3   0.0      0.15        78      67      82 ..     376     391 ..     358     438 .. 0.75
   6 !   12.8   0.2   0.00018     0.095      62     131 ..     439     502 ..     431     514 .. 0.78
   7 !   15.9   0.1     2e-05      0.01      45     129 ..     502     581 ..     495     583 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmagem 129
                                       f+++  l+  G+++eal a++ a+e+
  gi|386001637|ref|YP_005919936.1| 152 FEKGEELSMNGSTEEALAAYERAVEL 177
                                       7889999999**********999996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  72 dealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       d+     ++al  f+r  el++ +   W      +a+ l+ +Gr+dea++a+  + em
  gi|386001637|ref|YP_005919936.1| 199 DKDPAGYKEALLSFERAIELNRSQSMAWN----GKATLLSMMGRYDEAVDAYDASLEM 252
                                       5555566889999*********9999995....6999****************99998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.06
                                       HHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  59 aglsealaklgrydealesadkal 82 
                                        g ++al+klgr++e++ + d+a+
  gi|386001637|ref|YP_005919936.1| 261 VGKANALWKLGRHNESIAAGDEAI 284
                                       567899999999999999999987 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.077
                                       -TTST CS
                           DUF3856  90 eleqd 94 
                                       e++ +
  gi|386001637|ref|YP_005919936.1| 357 EIDPE 361
                                       33333 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.15
                                       HTT-HHHHHHHHHHHH CS
                           DUF3856  67 klgrydealesadkal 82 
                                        lgryde+le+ ++a+
  gi|386001637|ref|YP_005919936.1| 376 SLGRYDESLEACERAI 391
                                       5888888888888876 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 0.00018
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemia 131
                                       ++ l+++ ryde+le+ d+al          + + +   ++ +s+++al+++G+++ea +af  +  + +
  gi|386001637|ref|YP_005919936.1| 439 ASLLVEMNRYDESLEAYDEALDLIP------ESDAETLAQTWLSKGTALKKTGKQEEATEAFARSLALYE 502
                                       5668999**************9865......4444555566679*****************987655444 PP

  == domain 7  score: 15.9 bits;  conditional E-value: 2e-05
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealk 121
                                       eea   +  d +   +   al +lgryde+le  d+ l+      e +  +   Wi     r+ al  lGr++eal+
  gi|386001637|ref|YP_005919936.1| 502 EEAIMEDPGDVVLLQTRGRALYELGRYDESLEVYDQILESS-PGVEPHLVDTTAWI----GRGDALRALGRNQEALE 573
                                       6677777778888888899******************9965.45688888999998....59*************** PP

                                       HHHHHHHH CS
                           DUF3856 122 afrmagem 129
                                       a++ a e+
  gi|386001637|ref|YP_005919936.1| 574 AYNRAIEL 581
                                       ****9985 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.8   1.5e+03     206     230 ..     162     186 ..     157     200 .. 0.86
   2 ?    1.9   0.0      0.16        83     208     256 ..     205     253 ..     171     259 .. 0.76
   3 ?    2.1   0.0      0.14        74     204     263 ..     269     333 ..     257     337 .. 0.71
   4 !   17.1   0.0   3.9e-06    0.0021     204     259 ..     341     397 ..     336     398 .. 0.89
   5 !    8.8   0.0    0.0013      0.68      44     108 ..     404     467 ..     399     471 .. 0.71
   6 !    7.2   0.0     0.004       2.1      11      69 ..     478     543 ..     471     547 .. 0.75
   7 ?    1.6   0.0      0.19     1e+02      32      69 ..     547     583 ..     544     599 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.8
                                       T-SHHHHHHHHHHHHH-TT-HHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyl 230
                                       gs+e+Al   ++a+e +p++ e ++
  gi|386001637|ref|YP_005919936.1| 162 GSTEEALAAYERAVELDPKMAEAWT 186
                                       6889999999********9999875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                                       SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       +++Al   ++aie + +    +  Ka++l  +G  ++A+++ + + ++D
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRSQSMAWNGKATLLSMMGRYDEAVDAYDASLEMD 253
                                       4566666677777777777777777777777777777777777766666 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                                       HHT-SHHHHHHHHHHHHH-TT-HH...HHHHHHHHHHHTT-HHHHHHHHHHHHHC..TTT-HHHH CS
                             NARP1 204 klgsrekAleyidkaiehtptlve...lyltKarilkhaGdlkkAaevmeearkl..DlaDRyiN 263
                                       klg+ ++++   d+ai+ t + ve   ++  +a+++   Gd ++ +e++++a +l  D +  +iN
  gi|386001637|ref|YP_005919936.1| 269 KLGRHNESIAAGDEAIDATSETVEkafVWFERAHLFAEDGDYNGTVEALNRAIELapDYKNFWIN 333
                                       56677777888888888888888844445678888888888888888888887774555555555 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 3.9e-06
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHH.HTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilk.haGdlkkAaevmeearklDlaD 259
                                       +lg++e+Al yid+a+e +p+ v+ ++ Ka+il    G  ++  e+ e+a  +D +D
  gi|386001637|ref|YP_005919936.1| 341 HLGRYEEALIYIDRALEIDPEYVDAWISKAQILGpSLGRYDESLEACERAIDIDPED 397
                                       7899****************************9635799999999999999998777 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0013
                                       HHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SH CS
                             NARP1  44 kaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydelaekyprsda 108
                                       k+ +l++Lgr +eA a++ + +++npe+   ++  ++++ ++ +  ++ l++yde+ + +p+sda
  gi|386001637|ref|YP_005919936.1| 404 KGLILMNLGRDAEALAAFDEAIRQNPEDFGSWQ-WKASLLVEMNRYDESLEAYDEALDLIPESDA 467
                                       677888888888888888888888888876664.3444445666677778888888777777776 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.004
                                       HHHHHHHTHHHHHHHHHHH....HGGG---...HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  11 nqiieeagkleeAlehLee....kekqivD...klavketkaelllkLgrkeeAeatyeaLlernp 69 
                                        + ++++gk eeA e + +    +e+ i++    + +++t+++ l +Lgr++e+ ++y ++le  p
  gi|386001637|ref|YP_005919936.1| 478 GTALKKTGKQEEATEAFARslalYEEAIMEdpgDVVLLQTRGRALYELGRYDESLEVYDQILESSP 543
                                       55677778888777654443334888888623347899***********************99876 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.19
                                       GG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  32 kqivDklavketkaelllkLgrkeeAeatyeaLlernp 69 
                                        ++vD+ a+   +++ l +Lgr++eA ++y++ +e  p
  gi|386001637|ref|YP_005919936.1| 547 PHLVDTTAWI-GRGDALRALGRNQEALEAYNRAIELGP 583
                                       5677887776.589****************99887655 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0       0.1        55      14      32 ..     236     254 ..     234     256 .. 0.94
   2 !   14.2   0.0   6.6e-05     0.035      12      34 ..     340     362 ..     339     365 .. 0.90
   3 !   10.9   0.0   0.00069      0.36      14      44 ..     377     407 ..     376     415 .. 0.89
   4 ?   -0.7   0.0       2.9   1.5e+03      14      33 ..     445     464 ..     443     473 .. 0.81
   5 !    8.0   0.0    0.0056         3      10      33 ..     521     544 ..     519     546 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                                       HT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                       +g+Y+eA    da Le++P
  gi|386001637|ref|YP_005919936.1| 236 MGRYDEAVDAYDASLEMDP 254
                                       89****************9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.6e-05
                                       HHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                       + lg+Y+eA+ y+d+ Lei+Pe 
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEIDPEY 362
                                       569******************96 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00069
                                       HT-HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLkeli 44 
                                       lg+Y+e+++ +++ + i+Pe      Lk li
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDIDPEDPDTWRLKGLI 407
                                       79*******************9999999988 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.9
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       + +Y+e+++  d  L + Pe
  gi|386001637|ref|YP_005919936.1| 445 MNRYDESLEAYDEALDLIPE 464
                                       67899999999999988776 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0056
                                       HHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPe 33 
                                       + y lg+Y+e+++  d++Le  P+
  gi|386001637|ref|YP_005919936.1| 521 ALYELGRYDESLEVYDQILESSPG 544
                                       6799****************9996 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.0   0.00082      0.43      13     118 ..     155     279 ..     148     289 .. 0.77
   2 ?   -1.0   0.0         4   2.1e+03      73      94 ..     340     361 ..     336     368 .. 0.81
   3 !   17.7   0.0   7.3e-06    0.0038      74     131 ..     376     433 ..     368     441 .. 0.93
   4 ?    5.9   0.1      0.03        16      10      43 ..     475     508 ..     465     519 .. 0.80
   5 !   11.7   1.4   0.00049      0.26      64     123 ..     514     579 ..     511     581 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00082
                                       HHHHHHTT-HHHHHHHHHHHHTT.......--SSTTGGGTT..........STTHHHHHHHHHHHHHHHHHHHHH.. CS
                              BTAD  13 graalaagdpeeaaelleaAlal.......wrGpaladlea..........gewleaererleelrlealealae.. 70 
                                       g++++ +g +eea++++e+A++l       w G+ +a+ +           +e l ++ +++e  r + +++  +  
  gi|386001637|ref|YP_005919936.1| 155 GEELSMNGSTEEALAAYERAVELdpkmaeaWTGRGYAKSRLafidkdpagyKEALLSFERAIELNRSQSMAWNGKat 231
                                       55556666666666666666654444444477777777555777778888878888888888888888888877622 PP

                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                       +++ +Gr++ea++ ++a ++++Pl+ +       Al ++Gr +e +++
  gi|386001637|ref|YP_005919936.1| 232 LLSMMGRYDEAVDAYDASLEMDPLQPWVLVGKANALWKLGRHNESIAA 279
                                       56799*************************************998875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4
                                       HHTT-HHHHHHHHHHHHHHSTT CS
                              BTAD  73 lrlGraeealaelealvaehPl 94 
                                       ++lGr+eeal + +++++ +P 
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEALIYIDRALEIDPE 361
                                       6789999999999998888885 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 7.3e-06
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLg 131
                                       +lGr++e l+  e++++ +P + +++r+  + l+ +Gr aeAL++++++ r+  e++g
  gi|386001637|ref|YP_005919936.1| 376 SLGRYDESLEACERAIDIDPEDPDTWRLKGLILMNLGRDAEALAAFDEAIRQNPEDFG 433
                                       69**********************************************9998877777 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.03
                                       HHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGG CS
                              BTAD  10 vaagraalaagdpeeaaelleaAlalwrGpalad 43 
                                        ++g+a+ + g++eea e++ + lal+++  ++d
  gi|386001637|ref|YP_005919936.1| 475 LSKGTALKKTGKQEEATEAFARSLALYEEAIMED 508
                                       567899999999***************9999988 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHH......HHHHTT-HHHHHHHHHHHH CS
                              BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmr......AlarsGrqaeALevYerlr 123
                                        l+++ +a+ +lGr++e l+ ++++++  P  E       +      Al+++Gr++eALe+Y+r+ 
  gi|386001637|ref|YP_005919936.1| 514 LLQTRGRALYELGRYDESLEVYDQILESSPGVEPHLVDTTAwigrgdALRALGRNQEALEAYNRAI 579
                                       578999999*******************9998876554442222333****************985 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.84   4.4e+02      49     115 ..     157     224 ..     152     252 .. 0.73
   2 ?    1.2   0.0      0.36   1.9e+02     123     189 ..     295     357 ..     257     373 .. 0.73
   3 ?    3.9   0.0     0.055        29      13      59 ..     376     424 ..     364     430 .. 0.77
   4 !   26.2   0.4   8.8e-09   4.7e-06       7     159 ..     438     589 ..     437     605 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.84
                          TPR_MalT  49 asllqGdleaAlqalqeaekla.rqadslhvallallqqaeilvaqGrLheAletyeqalqlateqgl 115
                                          ++G +e+Al+a++ a++l  ++a++++   +a  ++a i       +eAl  +e+a++l + q++
  gi|386001637|ref|YP_005919936.1| 157 ELSMNGSTEEALAAYERAVELDpKMAEAWTGRGYAKSRLAFIDKDPAGYKEALLSFERAIELNRSQSM 224
                                       55677778888888887777633777777777777777777777777777777777777777776665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.36
                          TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllekaee 189
                                       f+  ++a+l+ E +d  +  ++l+++iel+ ++++ ++    +l a+     G+ eeA+ ++++a e
  gi|386001637|ref|YP_005919936.1| 295 FVWFERAHLFAEDGDYNGTVEALNRAIELAPDYKNFWINGGVLLSAH----LGRYEEALIYIDRALE 357
                                       55567888888888888888888888888888866665554444444....5777777777777765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.055
                          TPR_MalT  13 asgdaeralelArqALallpeddllar..iaatavlGeasllqGdleaA 59 
                                       + g+ +++le +++A+++ ped   +r  ++++++lG+ +     +++A
  gi|386001637|ref|YP_005919936.1| 376 SLGRYDESLEACERAIDIDPEDPDTWRlkGLILMNLGRDAEALAAFDEA 424
                                       6689999*************99888886689999999766665555555 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 8.8e-09
                          TPR_MalT   7 rAllaiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaekl...arqadslhval 80 
                                       +A l + +++ +++le   +AL+l+pe+d  + +++ ++ G+a   +G+ e+A++a++   +l   a ++d  +v+l
  gi|386001637|ref|YP_005919936.1| 438 KASLLVEMNRYDESLEAYDEALDLIPESDAETLAQTWLSKGTALKKTGKQEEATEAFARSLALyeeAIMEDPGDVVL 514
                                       678889999999**********************************************6665544489999999999 PP

                          TPR_MalT  81 lallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlep 157
                                       l+++  +  l + Gr +e+le+y q+l+  +  + + + +  ++  +++d l+  ++ +eA ++ +++iel+ ++++
  gi|386001637|ref|YP_005919936.1| 515 LQTR--GRALYELGRYDESLEVYDQILESSPGVEPHLVDTTAWI--GRGDALRALGRNQEALEAYNRAIELGPHWSN 587
                                       9999..9999999***************6666666655666666..99***************************98 PP

                          TPR_MalT 158 ea 159
                                       ++
  gi|386001637|ref|YP_005919936.1| 588 AW 589
                                       77 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.051        27     152     176 ..     154     178 ..     147     187 .. 0.88
   2 ?    3.4   0.2       0.1        53     115     175 ..     191     252 ..     180     268 .. 0.77
   3 ?    1.9   0.0       0.3   1.6e+02      60     108 ..     278     326 ..     263     349 .. 0.87
   4 ?    4.9   0.0     0.035        19     151     179 ..     403     431 ..     379     446 .. 0.89
   5 !    9.5   0.7    0.0014      0.72     126     177 ..     452     502 ..     439     522 .. 0.83
   6 !   10.4   0.1   0.00076       0.4     152     174 ..     558     580 ..     544     588 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.051
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaal 176
                                       +G+ l+ +g ++eA aaY++A++  
  gi|386001637|ref|YP_005919936.1| 154 KGEELSMNGSTEEALAAYERAVELD 178
                                       899999***************9865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                            TPR_21 115 arlRLarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       a+ RLa +  +   y+eAl   e++ e +  ++++ + +  +l+ +g+ deA +aY+a+l+ 
  gi|386001637|ref|YP_005919936.1| 191 AKSRLAFIDKDPAGYKEALLSFERAIElNRSQSMAWNGKATLLSMMGRYDEAVDAYDASLEM 252
                                       67788888888888888888876544314555556677778999*************99976 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.3
                            TPR_21  60 eaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakd 108
                                       +a +e +d+ ++t   a+  +  A+  +e gd++   ++L++++e a+d
  gi|386001637|ref|YP_005919936.1| 278 AAGDEAIDATSETVEKAFVWFERAHLFAEDGDYNGTVEALNRAIELAPD 326
                                       55667788889999999999***********************998776 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.035
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleek 179
                                       l+G il++ g+ +eA aa+++A++++ e+
  gi|386001637|ref|YP_005919936.1| 403 LKGLILMNLGRDAEALAAFDEAIRQNPED 431
                                       799********************998765 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0014
                            TPR_21 126 ekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaale 177
                                        ++ydeAl ++ ++++e+  a+    +G +l ++gk++eA +a+ ++la  e
  gi|386001637|ref|YP_005919936.1| 452 LEAYDEALDLIPESDAETL-AQTWLSKGTALKKTGKQEEATEAFARSLALYE 502
                                       5789999999987776665.666679******************99997655 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00076
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       rGD+l a g+++eA +aY++A++
  gi|386001637|ref|YP_005919936.1| 558 RGDALRALGRNQEALEAYNRAIE 580
                                       9********************97 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00019       0.1     183     255 ..     205     277 ..     190     289 .. 0.90
   2 ?    4.3   0.0     0.044        23     205     239 ..     333     367 ..     322     385 .. 0.85
   3 ?    1.9   0.0      0.23   1.2e+02     214     256 ..     377     419 ..     371     432 .. 0.81
   4 ?    5.0   0.1     0.027        14     207     261 ..     438     497 ..     416     505 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                       +++A++ f+   e   s ++  ngkA    ++gry+eA      +L+ d+ ++ +L+    a  +lg+ +e++
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELNRSQSMAWNGKATLLSMMGRYDEAVDAYDASLEMDPLQPWVLVGKANALWKLGRHNESI 277
                                       89************9***********************************99999998888888888777765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.044
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHH CS
                        Coatomer_E 205 ngkAvvslllgryeeAeslLkeaLdkdakdeetLi 239
                                       ng    s +lgryeeA   +  aL+ d+++ ++ i
  gi|386001637|ref|YP_005919936.1| 333 NGGVLLSAHLGRYEEALIYIDRALEIDPEYVDAWI 367
                                       666777889*********************99865 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.23
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       lgry+e  +  + a+d d++d++t         +lg+dae+ +
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACERAIDIDPEDPDTWRLKGLILMNLGRDAEALA 419
                                       799********************97666666667787777665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.027
                                       HHHHHHHTT-HHHHHHHHHHHHHH.-TT-HHHHHHHH....HHHHHTT--HHHHHHHHHH CS
                        Coatomer_E 207 kAvvslllgryeeAeslLkeaLdk.dakdeetLiNlv....vaaqhlgkdaevsernlsq 261
                                       kA   + ++ry+e  +   eaLd   + d+etL+       +a +++gk++e++e +  +
  gi|386001637|ref|YP_005919936.1| 438 KASLLVEMNRYDESLEAYDEALDLiPESDAETLAQTWlskgTALKKTGKQEEATEAFARS 497
                                       7888899***************97256799***987622225667888888887766555 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.21   1.1e+02       2      23 ..     205     225 ..     204     229 .. 0.83
   2 ?   -2.0   0.0       5.1   2.7e+03       2      16 ..     310     324 ..     309     330 .. 0.81
   3 ?    5.3   0.0     0.027        14       1      15 [.     344     358 ..     344     361 .. 0.94
   4 ?    5.2   0.0      0.03        16       1      15 [.     379     393 ..     379     396 .. 0.93
   5 ?    1.1   0.0      0.56   2.9e+02       1      40 [.     447     485 ..     447     493 .. 0.63
   6 ?    2.6   0.0      0.19        99       1      16 [.     527     542 ..     527     544 .. 0.92
   7 ?    0.1   0.0       1.2   6.3e+02       3      15 ..     569     581 ..     567     587 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHTTB-T CS
                          HTH_Bact   2 YeeaLeqvnkAieiSirinsMs 23 
                                       Y eaL   ++Aie+  r +sM+
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIELN-RSQSMA 225
                                       99***********86.666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.1
                                       HHHHHHHHHHHHHHH CS
                          HTH_Bact   2 YeeaLeqvnkAieiS 16 
                                       Y+   e  n+Aie+ 
  gi|386001637|ref|YP_005919936.1| 310 YNGTVEALNRAIELA 324
                                       88889999****986 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.027
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rYeeaL ++++A+ei
  gi|386001637|ref|YP_005919936.1| 344 RYEEALIYIDRALEI 358
                                       7************97 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.03
                                       -HHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                       rY+e+Le  ++Ai i
  gi|386001637|ref|YP_005919936.1| 379 RYDESLEACERAIDI 393
                                       7************87 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.56
                                       -HHHHHHHHHHHHHHHHHTTB-TTHHHHHHHHHHHHHHTT CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSirinsMsLlGQLyYqkgecleklg 40 
                                       rY+e+Le  + A+ + i  +    l Q +  kg  l+k g
  gi|386001637|ref|YP_005919936.1| 447 RYDESLEAYDEALDL-IPESDAETLAQTWLSKGTALKKTG 485
                                       799999999999876.333334444555555666665555 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.19
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rY+e+Le+ ++ +e+S
  gi|386001637|ref|YP_005919936.1| 527 RYDESLEVYDQILESS 542
                                       7**********99887 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       +eaLe  n+Aie+
  gi|386001637|ref|YP_005919936.1| 569 QEALEAYNRAIEL 581
                                       68*********96 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.042        22       9      65 ..     216     277 ..     207     305 .. 0.72
   2 ?    5.0   0.0     0.044        23      21      41 ..     336     356 ..     314     393 .. 0.78
   3 ?    4.7   0.1     0.057        30      19      60 ..     437     486 ..     418     549 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.042
                      SRP_TPR_like   9 lrlegkelkkf..kvvaliklekyeeaLkllk...kgsalsedvrfEkaYvlYklkkykkal 65 
                                       ++l+ ++   +  k++ l  +++y+ea+ + +   +++ l+  v + ka +l+kl + +++ 
  gi|386001637|ref|YP_005919936.1| 216 IELNRSQSMAWngKATLLSMMGRYDEAVDAYDaslEMDPLQPWVLVGKANALWKLGRHNESI 277
                                       45554444444668888889999999998776222455778889999999999999988875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
                      SRP_TPR_like  21 vvaliklekyeeaLkllkkgs 41 
                                       v+   +l++yeeaL++++ + 
  gi|386001637|ref|YP_005919936.1| 336 VLLSAHLGRYEEALIYIDRAL 356
                                       555679**********99765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.057
                      SRP_TPR_like  19 fkvvaliklekyeeaLkllkkgs........alsedvrfEkaYvlYklkk 60 
                                       +k+  l+++++y+e+L++ +++         ++  ++   k  +l k+ k
  gi|386001637|ref|YP_005919936.1| 437 WKASLLVEMNRYDESLEAYDEALdlipesdaETLAQTWLSKGTALKKTGK 486
                                       47777888888888888777665455544452223333333333333333 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       5.6   2.9e+03      15      26 .]     162     173 ..     156     173 .. 0.85
   2 ?    3.2   0.0      0.34   1.8e+02       8      24 ..     230     246 ..     224     248 .. 0.82
   3 ?    5.2   0.0      0.08        42       1      17 [.     257     273 ..     257     276 .. 0.93
   4 ?    1.8   0.0      0.96   5.1e+02      12      21 ..     340     349 ..     337     349 .. 0.88
   5 ?   -0.8   0.0         7   3.7e+03      14      26 .]     377     389 ..     377     389 .. 0.88
   6 ?    0.1   0.1       3.6   1.9e+03      10      25 ..     407     422 ..     400     423 .. 0.77
   7 !    8.7   0.0     0.006       3.1       7      26 .]     518     537 ..     517     537 .. 0.90
   8 ?    6.5   1.2      0.03        16       3      23 ..     554     574 ..     553     577 .. 0.88
   9 ?   -0.8   0.1         7   3.7e+03       3      16 ..     588     601 ..     587     602 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5.6
                             TPR_4  15 GdldeAraller 26 
                                       G  +eA+a+ er
  gi|386001637|ref|YP_005919936.1| 162 GSTEEALAAYER 173
                                       7789****9997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.34
                             TPR_4   8 ArallalGdldeArall 24 
                                       A +l   G++deA ++ 
  gi|386001637|ref|YP_005919936.1| 230 ATLLSMMGRYDEAVDAY 246
                                       7888999******9876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.08
                             TPR_4   1 arallaLArallalGdl 17 
                                       +++l++ A al+ lG++
  gi|386001637|ref|YP_005919936.1| 257 PWVLVGKANALWKLGRH 273
                                       799*************8 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.96
                             TPR_4  12 lalGdldeAr 21 
                                       ++lG+++eA+
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEAL 349
                                       79*******6 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 7
                             TPR_4  14 lGdldeAraller 26 
                                       lG++de +++ er
  gi|386001637|ref|YP_005919936.1| 377 LGRYDESLEACER 389
                                       7*****9999886 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 3.6
                             TPR_4  10 allalGdldeAralle 25 
                                        l  lG+ +eA+a+++
  gi|386001637|ref|YP_005919936.1| 407 ILMNLGRDAEALAAFD 422
                                       6677899999999887 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.006
                             TPR_4   7 LArallalGdldeAraller 26 
                                       ++ral++lG++de +++ ++
  gi|386001637|ref|YP_005919936.1| 518 RGRALYELGRYDESLEVYDQ 537
                                       79***********9999876 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.03
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       a ++++ al alG+  eA+++
  gi|386001637|ref|YP_005919936.1| 554 AWIGRGDALRALGRNQEALEA 574
                                       6789**************987 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 7
                             TPR_4   3 allaLArallalGd 16 
                                       a +++++ + alG+
  gi|386001637|ref|YP_005919936.1| 588 AWYGRGESQRALGQ 601
                                       45677777777775 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0028       1.5     245     290 ..     148     186 ..     119     196 .. 0.81
   2 ?   -1.6   0.0       2.3   1.2e+03     265     290 ..     202     227 ..     188     251 .. 0.79
   3 ?    0.2   0.0      0.65   3.4e+02     242     278 ..     468     504 ..     407     510 .. 0.77
   4 ?    5.2   0.0     0.019        10     252     290 ..     559     590 ..     553     601 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                       ar  ++kGe ++  +       + ee+l++y +a+e+dp++++aw 
  gi|386001637|ref|YP_005919936.1| 148 ARDWFEKGEELSMNG-------STEEALAAYERAVELDPKMAEAWT 186
                                       555555565444444.......49*********************5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                       ...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 265 eekieeilqsysaateidpswykawh 290
                                        +  +e+l s+ +a e+++s+  aw+
  gi|386001637|ref|YP_005919936.1| 202 PAGYKEALLSFERAIELNRSQSMAWN 227
                                       556789999***********999997 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.65
                                       .HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCC CS
                               FAT 242 kllarcylkkGewqealqkldwseekieeilqsysaa 278
                                       + la++ l kG  +++++k ++++e +   l+ y +a
  gi|386001637|ref|YP_005919936.1| 468 ETLAQTWLSKGTALKKTGKQEEATEAFARSLALYEEA 504
                                       4458888889998888888777777777777777666 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.019
                                       CCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 252 Gewqealqkldwseekieeilqsysaateidpswykawh 290
                                       G+ ++al++       ++e+l++y +a e+ p+w +aw+
  gi|386001637|ref|YP_005919936.1| 559 GDALRALGR-------NQEALEAYNRAIELGPHWSNAWY 590
                                       667778888.......9*********************6 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.7   1.4e+03      56      74 ..     204     222 ..     189     237 .. 0.82
   2 ?   -1.0   0.0       3.6   1.9e+03      47      64 ..     229     246 ..     219     252 .. 0.81
   3 ?    1.1   0.1      0.81   4.3e+02      52      80 ..     268     296 ..     256     305 .. 0.77
   4 ?    0.5   0.0       1.2   6.3e+02      45      72 ..     298     325 ..     287     330 .. 0.80
   5 ?    0.4   0.0       1.3     7e+02      48      70 ..     336     358 ..     326     366 .. 0.81
   6 ?    1.9   0.0      0.46   2.4e+02      50      79 ..     373     402 ..     360     407 .. 0.82
   7 ?    3.7   0.0      0.13        66      52      69 ..     409     426 ..     404     431 .. 0.87
   8 ?    3.6   0.1      0.13        69      49      80 ..     440     471 ..     437     504 .. 0.56
   9 ?   -1.0   0.0       3.7   1.9e+03      53      70 ..     564     581 ..     561     584 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.7
                            ANAPC5  56 hneeAvkaleeairlAren 74 
                                        ++eA+ ++e ai+l r +
  gi|386001637|ref|YP_005919936.1| 204 GYKEALLSFERAIELNRSQ 222
                                       689***********99876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                            ANAPC5  47 laslhadfghneeAvkal 64 
                                        a+l + +g ++eAv+a 
  gi|386001637|ref|YP_005919936.1| 229 KATLLSMMGRYDEAVDAY 246
                                       68899999******9985 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.81
                            ANAPC5  52 adfghneeAvkaleeairlArenkDkscL 80 
                                        ++g ++e+++a  eai    e+ +k+++
  gi|386001637|ref|YP_005919936.1| 268 WKLGRHNESIAAGDEAIDATSETVEKAFV 296
                                       57899999999999999988887776665 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.2
                            ANAPC5  45 LnlaslhadfghneeAvkaleeairlAr 72 
                                       ++ a l a+ g+++  v+al+ ai+lA 
  gi|386001637|ref|YP_005919936.1| 298 FERAHLFAEDGDYNGTVEALNRAIELAP 325
                                       5677788888999999999999999985 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1.3
                            ANAPC5  48 aslhadfghneeAvkaleeairl 70 
                                       + l+a++g +eeA+  +  a ++
  gi|386001637|ref|YP_005919936.1| 336 VLLSAHLGRYEEALIYIDRALEI 358
                                       5689*********9988888766 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.46
                            ANAPC5  50 lhadfghneeAvkaleeairlArenkDksc 79 
                                       l  ++g ++e+++a e ai +  e  D+  
  gi|386001637|ref|YP_005919936.1| 373 LGPSLGRYDESLEACERAIDIDPEDPDTWR 402
                                       566899**************9988888765 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.13
                            ANAPC5  52 adfghneeAvkaleeair 69 
                                       +++g ++eA++a+ eair
  gi|386001637|ref|YP_005919936.1| 409 MNLGRDAEALAAFDEAIR 426
                                       57899************8 PP

  == domain 8  score: 3.6 bits;  conditional E-value: 0.13
                            ANAPC5  49 slhadfghneeAvkaleeairlArenkDkscL 80 
                                       sl  +++ ++e+++a  ea  l  e+  ++  
  gi|386001637|ref|YP_005919936.1| 440 SLLVEMNRYDESLEAYDEALDLIPESDAETLA 471
                                       55556666666666666666655544333222 PP

  == domain 9  score: -1.0 bits;  conditional E-value: 3.7
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                       ++g n+eA++a + ai+l
  gi|386001637|ref|YP_005919936.1| 564 ALGRNQEALEAYNRAIEL 581
                                       5799*********99987 PP

>> RNR_N  Ribonucleotide reductase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.069      18      67 ..     410     457 ..     405     460 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                             RNR_N  18 qlekDkeAleaYlkehvnpntvkfesleekldyLvendYyeeevlekYsk 67 
                                       +l  D eAl+a+  e +++n   f s + k + Lve + y+e++ e Y++
  gi|386001637|ref|YP_005919936.1| 410 NLGRDAEALAAF-DEAIRQNPEDFGSWQWKASLLVEMNRYDESL-EAYDE 457
                                       6789********.889************************9876.99986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.11        60       9      33 ..     153     177 ..     146     177 .. 0.79
   2 ?   -1.4   0.0       4.9   2.6e+03      20      33 ..     205     218 ..     200     223 .. 0.73
   3 ?    3.3   0.0      0.17        89      18      32 ..     237     251 ..     228     252 .. 0.85
   4 ?   -2.0   0.0       7.7     4e+03      19      38 ..     344     356 ..     341     362 .. 0.55
   5 ?    4.7   0.1     0.059        31      18      34 ..     446     462 ..     438     464 .. 0.89
   6 ?    3.2   0.3      0.18        95       1      31 [.     475     505 ..     475     507 .. 0.92
   7 ?   -2.3   0.0       9.4   4.9e+03      18      29 ..     526     537 ..     524     540 .. 0.81
   8 ?    3.7   0.1      0.12        63      19      33 ..     567     581 ..     564     582 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                               MIT   9 kkAveeDnagnyeeAlelYkealel 33 
                                       +k  e+  +g  eeAl +Y+ a+el
  gi|386001637|ref|YP_005919936.1| 153 EKGEELSMNGSTEEALAAYERAVEL 177
                                       566666678999**********996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                               MIT  20 yeeAlelYkealel 33 
                                       y+eAl  ++ a+el
  gi|386001637|ref|YP_005919936.1| 205 YKEALLSFERAIEL 218
                                       66777777777664 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.17
                               MIT  18 gnyeeAlelYkeale 32 
                                       g y+eA+++Y  +le
  gi|386001637|ref|YP_005919936.1| 237 GRYDEAVDAYDASLE 251
                                       89*********9997 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.7
                               MIT  19 nyeeAlelYkealelLlqal 38 
                                               Y+eal ++  al
  gi|386001637|ref|YP_005919936.1| 344 R-------YEEALIYIDRAL 356
                                       4.......444444444444 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.059
                               MIT  18 gnyeeAlelYkealelL 34 
                                       + y+e le+Y eal+l+
  gi|386001637|ref|YP_005919936.1| 446 NRYDESLEAYDEALDLI 462
                                       68************985 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.18
                               MIT   1 ldkAlelvkkAveeDnagnyeeAlelYkeal 31 
                                       l+k+ +l k+  +e+  + ++  l lY+ea+
  gi|386001637|ref|YP_005919936.1| 475 LSKGTALKKTGKQEEATEAFARSLALYEEAI 505
                                       7899999999*******************98 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 9.4
                               MIT  18 gnyeeAlelYke 29 
                                       g y+e le Y +
  gi|386001637|ref|YP_005919936.1| 526 GRYDESLEVYDQ 537
                                       789999999976 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.12
                               MIT  19 nyeeAlelYkealel 33 
                                         +eAle+Y  a+el
  gi|386001637|ref|YP_005919936.1| 567 RNQEALEAYNRAIEL 581
                                       569**********96 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0035       1.8      13      32 ..     235     252 ..     232     254 .. 0.82
   2 ?   -1.0   0.0       3.6   1.9e+03      15      23 ..     343     351 ..     341     361 .. 0.79
   3 ?    1.4   0.0      0.64   3.4e+02      10      25 ..     521     536 ..     519     537 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                                       HTT-HHHHHHH..HHHHHHH CS
                             TPR_3  13 nkkkyqeArelfsYallail 32 
                                       ++++y+eA+++++   +  +
  gi|386001637|ref|YP_005919936.1| 235 MMGRYDEAVDAYD--ASLEM 252
                                       79*********77..66655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       ++y+eA+ +
  gi|386001637|ref|YP_005919936.1| 343 GRYEEALIY 351
                                       89****998 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.64
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++y  ++y+e +e+++
  gi|386001637|ref|YP_005919936.1| 521 ALYELGRYDESLEVYD 536
                                       68********999976 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.03        16       6      53 ..     382     429 ..     379     442 .. 0.89
   2 ?    6.7   0.1     0.017       9.2       4      44 ..     414     454 ..     411     469 .. 0.88
   3 ?    3.7   0.0      0.15        79       7      50 ..     497     540 ..     491     569 .. 0.84
   4 ?   -0.9   0.0       4.1   2.2e+03      29      46 ..     559     576 ..     539     605 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       ++l++ e+a+  +p+d d+     l l+  gr +eAl+++ e ++++ 
  gi|386001637|ref|YP_005919936.1| 382 ESLEACERAIDIDPEDPDTWRLKGLILMNLGRDAEALAAFDEAIRQNP 429
                                       6789999******************************99999999875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       da+ la++++a+ +np+d       A +l++ +ry+e+le+
  gi|386001637|ref|YP_005919936.1| 414 DAEALAAFDEAIRQNPEDFGSWQWKASLLVEMNRYDESLEA 454
                                       78899**************999999999******9998875 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.15
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       +la  e+a+ ++p d+ +     +al++ gry+e+le   +il+
  gi|386001637|ref|YP_005919936.1| 497 SLALYEEAIMEDPGDVVLLQTRGRALYELGRYDESLEVYDQILE 540
                                       6777899****************************986655555 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4.1
                            TPR_20  29 AlallaagryeeAleqLl 46 
                                        +al a gr++eAle+  
  gi|386001637|ref|YP_005919936.1| 559 GDALRALGRNQEALEAYN 576
                                       566666677777776544 PP

>> DUF5588  Family of unknown function (DUF5588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.6   1.9e+03      92     115 ..     227     251 ..     222     256 .. 0.80
   2 ?    4.3   0.0     0.029        15      92     157 ..     261     326 ..     254     348 .. 0.80
   3 ?   -1.5   0.0       1.6   8.6e+02      98     109 ..     339     350 ..     328     403 .. 0.83
   4 ?    3.5   0.0     0.052        28      37     110 ..     501     574 ..     490     583 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
                           DUF5588  92 egqarclahlgrhaealei.aadle 115
                                       +g+a  l+ +gr+ ea++   a le
  gi|386001637|ref|YP_005919936.1| 227 NGKATLLSMMGRYDEAVDAyDASLE 251
                                       699*************974246666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.029
                           DUF5588  92 egqarclahlgrhaealeiaadlenkatntdhlttvlylqlaicsslqnlektilclqklislhpf 157
                                        g+a  l +lgrh+e+++   +    +++t   + v + +  +++   + + t+  l++ i l p 
  gi|386001637|ref|YP_005919936.1| 261 VGKANALWKLGRHNESIAAGDEAIDATSETVEKAFVWFERAHLFAEDGDYNGTVEALNRAIELAPD 326
                                       699************998777666666778888888888888999999999999999999999884 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.6
                           DUF5588  98 lahlgrhaeale 109
                                        ahlgr++eal 
  gi|386001637|ref|YP_005919936.1| 339 SAHLGRYEEALI 350
                                       58*******984 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.052
                           DUF5588  37 yeetessddvealtikkfkgdlayrrqeyqkalqeyssiseklsstnfa.mkrdvqegqarclahlgrhaealei 110
                                       yee+  +d  +++ + + +g   y    y+ +l+ y  i e  +  +   +      g+   l  lgr +eale 
  gi|386001637|ref|YP_005919936.1| 501 YEEAIMEDPGDVVLL-QTRGRALYELGRYDESLEVYDQILESSPGVEPHlVDTTAWIGRGDALRALGRNQEALEA 574
                                       666666665555544.4689999999999999999999999999876541566677899999999*****99985 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.3   1.7e+03       7      36 ..     147     176 ..     145     187 .. 0.88
   2 ?   -1.8   0.0       4.4   2.3e+03      13      36 ..     228     251 ..     205     253 .. 0.76
   3 ?    4.2   0.0     0.062        33      20      44 ..     341     365 ..     306     390 .. 0.83
   4 ?   -0.5   0.0       1.7   9.2e+02     116     131 ..     444     459 ..     434     495 .. 0.71
   5 ?    1.0   0.0       0.6   3.2e+02     113     134 ..     521     542 ..     520     550 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.3
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                       +a d+ + + +l ++g+ eeAL+  + a+e
  gi|386001637|ref|YP_005919936.1| 147 TARDWFEKGEELSMNGSTEEALAAYERAVE 176
                                       5778889999999*********99999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.4
                           DUF5113  13 nlayylnvegeyeeALeyldsale 36 
                                         a+ l + g+y+eA++  d  le
  gi|386001637|ref|YP_005919936.1| 228 GKATLLSMMGRYDEAVDAYDASLE 251
                                       456667788888888888887775 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.062
                           DUF5113  20 vegeyeeALeyldsaleylNahyek 44 
                                         g+yeeAL y+d ale+  ++ + 
  gi|386001637|ref|YP_005919936.1| 341 HLGRYEEALIYIDRALEIDPEYVDA 365
                                       459*************976655555 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.7
                           DUF5113 116 kllrqDksLesycrql 131
                                       ++ r D+sLe+y ++l
  gi|386001637|ref|YP_005919936.1| 444 EMNRYDESLEAYDEAL 459
                                       4444455555554444 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.6
                           DUF5113 113 dllkllrqDksLesycrqlers 134
                                       +l++l r D+sLe y + le+s
  gi|386001637|ref|YP_005919936.1| 521 ALYELGRYDESLEVYDQILESS 542
                                       699999********99999876 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.056        30      33      64 ..     145     176 ..     135     209 .. 0.92
   2 ?    0.1   0.0       1.1   5.8e+02      34      63 ..     221     250 ..     207     253 .. 0.85
   3 ?    1.6   0.0      0.38     2e+02      47     133 ..     268     349 ..     261     371 .. 0.64
   4 ?    2.5   0.1       0.2     1e+02     107     142 ..     465     500 ..     435     517 .. 0.59
   5 ?   -2.9   0.0         9   4.8e+03      44      65 ..     520     541 ..     513     546 .. 0.81
   6 ?   -2.1   0.0       5.3   2.8e+03      49      64 ..     565     580 ..     558     581 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysrire 64 
                                       e+++r + +++e   + g +eeAl+ay+r++e
  gi|386001637|ref|YP_005919936.1| 145 EKTARDWFEKGEELSMNGSTEEALAAYERAVE 176
                                       788999999********************987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  34 eirrakldlaehYlkigdleeAlkaysrir 63 
                                       +  +a++ +a    ++g ++eA+ ay + +
  gi|386001637|ref|YP_005919936.1| 221 SQSMAWNGKATLLSMMGRYDEAVDAYDASL 250
                                       5678899999999************98765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.38
                                       HHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHHHHHHHHHHHH CS
                              RPN7  47 lkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskylekakellekggdwerknrlkvyeGlal 123
                                        k g ++e+++a  ++++ ++ +  k+ ++++  +  +f++d   ++  +e +++ +e +   ++kn      +l++
  gi|386001637|ref|YP_005919936.1| 268 WKLGRHNESIAAGDEAIDATSETVEKAFVWFERAH--LFAEDG-DYNGTVEALNRAIELA--PDYKNFWINGGVLLS 339
                                       56677777777777777777777777777777444..344442.3445555555555553..446666666666666 PP

                                       HHTT-HHHHH CS
                              RPN7 124 lairkfkeAa 133
                                       ++ ++++eA 
  gi|386001637|ref|YP_005919936.1| 340 AHLGRYEEAL 349
                                       6666666665 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.2
                                       -.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GG CS
                              RPN7 107 gdwerknrlkvyeGlallairkfkeAaellldilst 142
                                        d e+ ++   ++G+al +++k +eA+e +  +l+ 
  gi|386001637|ref|YP_005919936.1| 465 SDAETLAQTWLSKGTALKKTGKQEEATEAFARSLAL 500
                                       235555555566666666666666666666655554 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 9
                                       HHHHHCT-HHHHHHHHHTCCCC CS
                              RPN7  44 ehYlkigdleeAlkaysrirey 65 
                                       +  ++ g ++e+l+ y +i+e 
  gi|386001637|ref|YP_005919936.1| 520 RALYELGRYDESLEVYDQILES 541
                                       556789999*******999986 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 5.3
                                       CT-HHHHHHHHHTCCC CS
                              RPN7  49 igdleeAlkaysrire 64 
                                        g  +eAl+ay+r++e
  gi|386001637|ref|YP_005919936.1| 565 LGRNQEALEAYNRAIE 580
                                       57789********876 PP

>> DUF1896  Domain of unknown function (DUF1896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.41   2.2e+02      34      55 ..     163     184 ..     150     189 .. 0.84
   2 ?    0.1   0.0       1.5     8e+02      33      66 ..     446     478 ..     436     483 .. 0.83
   3 ?    3.5   0.0      0.14        72      34      55 ..     567     588 ..     558     591 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHT--HHHH CS
                           DUF1896  34 RadeAaeayeeaveeGlsvaea 55 
                                        ++eA+ aye+ave + ++aea
  gi|386001637|ref|YP_005919936.1| 163 STEEALAAYERAVELDPKMAEA 184
                                       589***********99888887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHT--HHHHHHHHHHHHHTT CS
                           DUF1896  33 eRadeAaeayeeaveeGlsvaeaeelanevLyqg 66 
                                       +R de +eay ea++   + ++ae+la+  L +g
  gi|386001637|ref|YP_005919936.1| 446 NRYDESLEAYDEALDL-IPESDAETLAQTWLSKG 478
                                       69999*******9876.78888999999999887 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHT--HHHH CS
                           DUF1896  34 RadeAaeayeeaveeGlsvaea 55 
                                       R +eA+eay +a+e G  +++a
  gi|386001637|ref|YP_005919936.1| 567 RNQEALEAYNRAIELGPHWSNA 588
                                       999*************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.88u 0.33s 00:00:01.21 Elapsed: 00:00:00.57
# Mc/sec: 3276.37
//
Query:       gi|386001638|ref|YP_005919937.1|  [L=302]
Description: TPR-repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-36  120.8  20.8    1.9e-10   40.1   0.3    7.7  8  TPR_1            Tetratricopeptide repeat
    8.2e-33  109.9  30.1    1.3e-09   37.4   0.4    8.1  8  TPR_2            Tetratricopeptide repeat
    4.2e-26   88.9  18.8    2.4e-06   27.3   0.2    7.9  8  TPR_8            Tetratricopeptide repeat
    2.5e-25   88.8  35.6    7.8e-11   42.4   0.1    6.0  6  TPR_16           Tetratricopeptide repeat
    2.9e-24   83.7  32.8    0.00012   22.6   0.1    8.1  8  TPR_14           Tetratricopeptide repeat
    1.4e-23   82.9  41.6    1.1e-06   28.8   0.4    6.3  6  TPR_12           Tetratricopeptide repeat
    1.6e-22   78.9  21.6    3.4e-07   29.8   0.3    7.3  7  TPR_11           TPR repeat
    7.2e-17   61.7  24.0    2.7e-08   34.2   0.5    5.3  5  TPR_19           Tetratricopeptide repeat
    7.6e-17   60.4   5.2    1.8e-07   31.1   0.1    7.0  6  TPR_17           Tetratricopeptide repeat
    3.7e-11   42.2  18.9      0.008   16.1   0.1    7.5  8  TPR_7            Tetratricopeptide repeat
    3.3e-10   39.5  28.1     0.0083   16.0   0.0    7.5  7  TPR_10           Tetratricopeptide repeat
    3.4e-10   40.0   2.7    1.5e-06   28.3   0.0    3.7  3  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.1e-09   37.0  13.8    0.00058   19.9   0.1    4.8  5  DUF3856          Domain of Unknown Function (DUF3856)
    5.4e-09   36.1  21.1      0.053   14.2   0.1    7.9  8  TPR_6            Tetratricopeptide repeat
      1e-07   31.3   7.9      4e-05   22.7   0.2    4.2  5  NARP1            NMDA receptor-regulated protein 1
    2.2e-07   31.4  18.2      0.008   16.6   0.1    4.3  3  BTAD             Bacterial transcriptional activator domain
    2.7e-07   30.6  18.3    4.4e-05   23.5   0.2    5.1  4  TPR_9            Tetratricopeptide repeat
    2.2e-05   23.8  10.6     0.0017   17.6   0.7    3.2  3  TPR_15           Tetratricopeptide repeat
    0.00076   19.5   0.4        3.2    7.9   0.1    3.5  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0012   19.3   3.9       0.87   10.0   0.0    3.8  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0013   19.0   7.3       0.06   13.7   0.1    3.8  4  TPR_20           Tetratricopeptide repeat
     0.0038   17.7  23.2        2.7    8.9   0.0    6.7  6  TPR_4            Tetratricopeptide repeat
     0.0043   17.1   0.7        2.1    8.4   0.0    4.1  5  MAS20            MAS20 protein import receptor
  ------ inclusion threshold ------
      0.011   15.5  19.2       0.13   12.0   0.6    5.4  5  TPR_21           Tetratricopeptide repeat-like domain
      0.011   16.0   4.9       0.24   11.6   0.0    4.0  3  TPR_5            Tetratrico peptide repeat
      0.014   14.7   1.3        1.5    8.0   1.2    2.7  2  FAT              FAT domain
      0.019   14.7   1.4        6.3    6.6   0.1    3.3  4  DUF5113          Domain of unknown function (DUF5113)
       0.02   15.1   4.3         16    5.8   0.3    3.9  4  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
      0.055   14.0   3.3        4.3    7.9   0.1    4.5  5  DUF4810          Domain of unknown function (DUF4810)
      0.095   12.3   0.1         24    4.6   0.0    4.4  5  HTH_Bact         Helix-turn-helix bacterial domain
       0.11   12.6   0.1       0.34   11.0   0.0    1.8  1  DUF1447          Protein of unknown function (DUF1447)
       0.83    9.8   3.1         10    6.2   0.2    3.7  4  ANAPC5           Anaphase-promoting complex subunit 5
       0.94    9.5   5.7        8.9    6.4   0.1    3.9  3  TPR_3            Tetratricopeptide repeat
        3.6    7.5  13.0         23    4.8   0.1    4.0  4  Wzy_C_2          Virulence factor membrane-bound polymerase, 


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.1e-05     0.048      16      34 .]      10      28 ..       1      28 [. 0.83
   2 !   40.1   0.3   3.6e-13   1.9e-10       1      34 []      29      62 ..      29      62 .. 0.97
   3 ?   -1.5   0.0       5.1   2.7e+03       7      24 ..      69      86 ..      65      88 .. 0.78
   4 !   18.9   0.0   1.8e-06   0.00097       2      30 ..     105     133 ..     104     136 .. 0.95
   5 !   21.7   0.3   2.3e-07   0.00012       5      28 ..     146     169 ..     142     171 .. 0.92
   6 !    9.4   0.1    0.0017      0.92       4      27 ..     188     211 ..     186     213 .. 0.93
   7 !   18.9   0.7   1.8e-06   0.00093       1      29 [.     226     254 ..     226     258 .. 0.95
   8 ?    6.8   0.1     0.012       6.2       6      30 ..     274     298 ..     270     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-05
                                      -HHHHHHHHHHHHHHSTTH CS
                             TPR_1 16 kydeAleyyekALelnPnn 34
                                       ++e +e+++kA+e++P+n
  gi|386001638|ref|YP_005919937.1| 10 SLEESVEAFDKAIEVDPQN 28
                                      5799*************97 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 3.6e-13
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      a+a+  ++++++ +g+ydeA+++++kA+e++P++
  gi|386001638|ref|YP_005919937.1| 29 AEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQD 62
                                      89******************************86 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.1
                                      HHHHHHHTT-HHHHHHHH CS
                             TPR_1  7 lGnayfklgkydeAleyy 24
                                      ++ ++  +g+  eAl+ +
  gi|386001638|ref|YP_005919937.1| 69 KASLLIIMGRQAEALAIF 86
                                      677788899999999766 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        a+  +Gn++ ++g ++e l +y++A+el
  gi|386001638|ref|YP_005919937.1| 105 SAWRSKGNVFAEQGLWNESLRAYDRAIEL 133
                                       599*************************8 PP

  == domain 5  score: 21.7 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekAL 28 
                                        n+G ++ klg+y+eA+e+++ AL
  gi|386001638|ref|YP_005919937.1| 146 SNKGRVLNKLGRYEEAVEACDMAL 169
                                       7**********************9 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekA 27 
                                       +  +G a+   g++deA  +ye+A
  gi|386001638|ref|YP_005919937.1| 188 WLWKGEALEGIGRLDEAALAYEQA 211
                                       8889*******************9 PP

  == domain 7  score: 18.9 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                       ak ++ ++ a+  +g+++eA + ye+A+e
  gi|386001638|ref|YP_005919937.1| 226 AKFWKYKADALEGMGRHEEAAASYERAVE 254
                                       789************************98 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.012
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALel 30 
                                        +G a+  lg+  eA++++ +A el
  gi|386001638|ref|YP_005919937.1| 274 WMGEALEALGRDSEAEAAFARAREL 298
                                       589******************9876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00063      0.33      14      34 .]       8      28 ..       1      28 [. 0.83
   2 !   37.4   0.4   2.5e-12   1.3e-09       1      34 []      29      62 ..      29      62 .. 0.97
   3 ?    3.9   0.0      0.14        72       8      33 ..      70      95 ..      67      96 .. 0.84
   4 !   15.7   0.0   2.3e-05     0.012       3      30 ..     106     133 ..     104     137 .. 0.93
   5 !   11.6   0.2   0.00045      0.24       6      30 ..     147     171 ..     143     174 .. 0.85
   6 !   13.7   0.8    0.0001     0.053       3      29 ..     187     213 ..     185     216 .. 0.91
   7 !   19.3   1.3   1.6e-06   0.00084       1      31 [.     226     256 ..     226     259 .. 0.92
   8 !   12.5   1.0   0.00024      0.13       4      30 ..     272     298 ..     271     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                             TPR_2 14 lgdyeeAleafekAleldPnn 34
                                      ++ +ee +eaf+kA+e dP+n
  gi|386001638|ref|YP_005919937.1|  8 NDSLEESVEAFDKAIEVDPQN 28
                                      56689**************97 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 2.5e-12
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      aea+ + +l+++ +g+y+eA++af+kA+e+dP++
  gi|386001638|ref|YP_005919937.1| 29 AEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQD 62
                                      89******************************86 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.14
                             TPR_2  8 GlayyklgdyeeAleafekAleldPn 33
                                      + +++ +g+ +eAl+ f++  +  P+
  gi|386001638|ref|YP_005919937.1| 70 ASLLIIMGRQAEALAIFDELTAEVPE 95
                                      6678889************9988887 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 2.3e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       a+   G++ +++g ++e l+a+++A+el
  gi|386001638|ref|YP_005919937.1| 106 AWRSKGNVFAEQGLWNESLRAYDRAIEL 133
                                       8999***********************9 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00045
                             TPR_2   6 nlGlayyklgdyeeAleafekAlel 30 
                                       n G+++ klg+yeeA+ea++ Al  
  gi|386001638|ref|YP_005919937.1| 147 NKGRVLNKLGRYEEAVEACDMALNA 171
                                       77888889***********999975 PP

  == domain 6  score: 13.7 bits;  conditional E-value: 0.0001
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                        + + G+a++  g+++eA+ a+e+A +
  gi|386001638|ref|YP_005919937.1| 187 PWLWKGEALEGIGRLDEAALAYEQAAA 213
                                       6999*********************86 PP

  == domain 7  score: 19.3 bits;  conditional E-value: 1.6e-06
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+ + + ++a++ +g++eeA++ +e+A+e  
  gi|386001638|ref|YP_005919937.1| 226 AKFWKYKADALEGMGRHEEAAASYERAVEAF 256
                                       689************************9976 PP

  == domain 8  score: 12.5 bits;  conditional E-value: 0.00024
                             TPR_2   4 lynlGlayyklgdyeeAleafekAlel 30 
                                       + ++G+a+++lg+  eA++af +A el
  gi|386001638|ref|YP_005919937.1| 272 YQWMGEALEALGRDSEAEAAFARAREL 298
                                       6789********************987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00017      0.09      11      34 .]       5      28 ..       1      28 [. 0.85
   2 !   27.3   0.2   4.5e-09   2.4e-06       7      34 .]      35      62 ..      29      62 .. 0.92
   3 ?    6.5   0.0     0.022        12       4      26 ..      66      88 ..      63      91 .. 0.87
   4 ?   -0.6   0.0         4   2.1e+03       8      30 ..     111     133 ..     105     133 .. 0.72
   5 !   14.2   0.1   7.3e-05     0.039       6      28 ..     147     169 ..     143     174 .. 0.87
   6 !   11.1   0.1    0.0007      0.37       3      27 ..     187     211 ..     185     214 .. 0.92
   7 !   16.4   0.2   1.4e-05    0.0073       7      30 ..     232     255 ..     232     259 .. 0.90
   8 ?    7.2   0.1     0.013       6.7       4      27 ..     272     295 ..     271     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                                      HHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 11 ylklgdyeeAkeyyekaleldpdn 34
                                      +l    +ee++e++ ka+e dp+n
  gi|386001638|ref|YP_005919937.1|  5 LLFNDSLEESVEAFDKAIEVDPQN 28
                                      6667789***************96 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 4.5e-09
                                      HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  7 lgsiylklgdyeeAkeyyekaleldpdn 34
                                      +++i++++g+y+eA++++ ka+e+dp++
  gi|386001638|ref|YP_005919937.1| 35 KALILRDQGEYDEAIAAFDKAIEIDPQD 62
                                      799***********************86 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.022
                                      HHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyek 26
                                       ++++s+++ +g+  eA + + +
  gi|386001638|ref|YP_005919937.1| 66 RVQKASLLIIMGRQAEALAIFDE 88
                                      5789**************99976 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 4
                                       HHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekalel 30 
                                       g++  ++g  +e+  +y +a+el
  gi|386001638|ref|YP_005919937.1| 111 GNVFAEQGLWNESLRAYDRAIEL 133
                                       66666666667888889999986 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekal 28 
                                       n+g+++ klg+yeeA+e++  al
  gi|386001638|ref|YP_005919937.1| 147 NKGRVLNKLGRYEEAVEACDMAL 169
                                       89***************987655 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                        ++++g +++  g+++eA  +ye+a
  gi|386001638|ref|YP_005919937.1| 187 PWLWKGEALEGIGRLDEAALAYEQA 211
                                       599*********************9 PP

  == domain 7  score: 16.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekalel 30 
                                       ++++++ +g++eeA ++ye+a+e+
  gi|386001638|ref|YP_005919937.1| 232 KADALEGMGRHEEAAASYERAVEA 255
                                       6899******************97 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyeka 27 
                                       y+++g +++ lg+  eA++++ +a
  gi|386001638|ref|YP_005919937.1| 272 YQWMGEALEALGRDSEAEAAFARA 295
                                       8899*****************887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.1   1.5e-13   7.8e-11       6      67 ..       4      62 ..       1      63 [. 0.92
   2 !   21.5   0.2   5.3e-07   0.00028      11      68 .]      77     138 ..      68     138 .. 0.93
   3 !   32.5   0.3   1.9e-10     1e-07       3      63 ..     110     171 ..     108     176 .. 0.94
   4 !    9.4   3.8    0.0031       1.6      37      63 ..     188     214 ..     186     221 .. 0.83
   5 !   15.9   6.1   2.9e-05     0.016      13      66 ..     208     258 ..     207     260 .. 0.93
   6 !   11.7  10.0   0.00058      0.31       4      61 ..     233     296 ..     232     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.5e-13
                            TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      ++l +   ++ ++a++ a++ d   P++aeA+ ++++++  qg+++eA+a++++a++ +p++
  gi|386001638|ref|YP_005919937.1|  4 ELLFNDSLEESVEAFDKAIEVD---PQNAEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQD 62
                                      56666778999***********...***********************************97 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.3e-07
                            TPR_16  11 gdyddAaaaleaalkrdpssPd....aaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       g+ ++A+a ++++++  p++P+       A+  +g+++++qg + e + +y++a++ ++++p
  gi|386001638|ref|YP_005919937.1|  77 GRQAEALAIFDELTAEVPEDPEerlwQSSAWRSKGNVFAEQGLWNESLRAYDRAIELGSGDP 138
                                       66689****************************************************99998 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 1.9e-10
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPd.aaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       +++ ++++g + + ++a+++a+++++++P+ +++A+ ++g+++ ++gr++eA+++++ al a
  gi|386001638|ref|YP_005919937.1| 110 KGNVFAEQGLWNESLRAYDRAIELGSGDPLaTYAASSNKGRVLNKLGRYEEAVEACDMALNA 171
                                       68999****************************************************99855 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0031
                            TPR_16  37 llllgdaalrqgrlaeAaalyraalra 63 
                                       +l++g+a+   grl+eAa +y+ a++a
  gi|386001638|ref|YP_005919937.1| 188 WLWKGEALEGIGRLDEAALAYEQAAAA 214
                                       899***************666665544 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 2.9e-05
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       y++Aaaa+e  + ++   P+ a ++ +++da+   gr++eAaa y++a++a  d
  gi|386001638|ref|YP_005919937.1| 208 YEQAAAAFELETSAY---PEIAKFWKYKADALEGMGRHEEAAASYERAVEAFKD 258
                                       99******9999999...******************************988755 PP

  == domain 6  score: 11.7 bits;  conditional E-value: 0.00058
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPd.aaeAll.....llgdaalrqgrlaeAaalyraal 61 
                                       a+a+   g+ ++Aaa +e+a+++++++ + +aeA++     + g+a+ ++gr  eA+a++++a 
  gi|386001638|ref|YP_005919937.1| 233 ADALEGMGRHEEAAASYERAVEAFKDEIEtHAEASNiwryqWMGEALEALGRDSEAEAAFARAR 296
                                       8999********************66655*7777664444668**************9999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.8e-05    0.0094      12      42 ..       6      36 ..       1      38 [. 0.86
   2 !   22.6   0.1   2.3e-07   0.00012       8      43 ..      36      71 ..      33      72 .. 0.90
   3 !    8.8   0.1    0.0063       3.3       5      36 ..      67      98 ..      64     103 .. 0.86
   4 !   12.4   0.0   0.00042      0.22       3      40 ..     106     143 ..     104     146 .. 0.91
   5 !    8.6   0.0    0.0074       3.9       8      31 ..     149     172 ..     148     180 .. 0.86
   6 ?    7.6   2.6     0.015       8.1       4      40 ..     188     224 ..     186     233 .. 0.81
   7 !   18.2   0.4   6.1e-06    0.0032       3      40 ..     228     265 ..     226     269 .. 0.90
   8 !    9.8   2.1    0.0029       1.5       4      29 ..     272     297 ..     268     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-05
                            TPR_14 12 lalGdpdeAiallrralalaPddaeawllla 42
                                      l ++ ++e+++++++a++ +P++aeaw++ a
  gi|386001638|ref|YP_005919937.1|  6 LFNDSLEESVEAFDKAIEVDPQNAEAWRYKA 36
                                      5567799*********************988 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.3e-07
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawlllaq 43
                                      a +l+ +G++deAia++++a++ +P+d  ++ + a 
  gi|386001638|ref|YP_005919937.1| 36 ALILRDQGEYDEAIAAFDKAIEIDPQDTKTRVQKAS 71
                                      67899**********************999988875 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0063
                            TPR_14  5 lalaeallalGdpdeAiallrralalaPddae 36
                                       + a++l   G+ +eA+a+++++ a  P+d+e
  gi|386001638|ref|YP_005919937.1| 67 VQKASLLIIMGRQAEALAIFDELTAEVPEDPE 98
                                      56799999********************9985 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00042
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       a++  + +++++G + e++++++ra++l+ +d+ a ++
  gi|386001638|ref|YP_005919937.1| 106 AWRSKGNVFAEQGLWNESLRAYDRAIELGSGDPLATYA 143
                                       899999***********************999988765 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0074
                            TPR_14   8 aeallalGdpdeAiallrralala 31 
                                       +++l  lG+++eA+++++ al ++
  gi|386001638|ref|YP_005919937.1| 149 GRVLNKLGRYEEAVEACDMALNAY 172
                                       6899***************99765 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.015
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       +l  +eal+  G++deA+ ++++a a++  +  a+ +
  gi|386001638|ref|YP_005919937.1| 188 WLWKGEALEGIGRLDEAALAYEQAAAAFELETSAYPE 224
                                       88999*******************9987766665544 PP

  == domain 7  score: 18.2 bits;  conditional E-value: 6.1e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                        ++  a+al+  G+++eA+a ++ra++++ d+ e++ +
  gi|386001638|ref|YP_005919937.1| 228 FWKYKADALEGMGRHEEAAASYERAVEAFKDEIETHAE 265
                                       68889**************************9998765 PP

  == domain 8  score: 9.8 bits;  conditional E-value: 0.0029
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       ++ ++eal+alG+  eA+a++ ra +
  gi|386001638|ref|YP_005919937.1| 272 YQWMGEALEALGRDSEAEAAFARARE 297
                                       56789******************977 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   1.1e-06   0.00056       3      32 ..      29      58 ..       5      61 .. 0.62
   2 !   23.6   0.5   8.9e-08   4.7e-05       3      70 ..      29      88 ..      27      95 .. 0.83
   3 !   28.8   0.4   2.1e-09   1.1e-06       3      76 ..     104     173 ..     102     174 .. 0.91
   4 !   21.3   0.0   4.6e-07   0.00024       5      39 ..     144     178 ..     139     184 .. 0.87
   5 !   22.3   6.0   2.2e-07   0.00012       9      76 ..     191     257 ..     185     258 .. 0.91
   6 !   22.2   5.8   2.4e-07   0.00013       6      74 ..     229     298 ..     224     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-06
                            TPR_12  3 atalnnlaavlrrlgrydeAlellekalei 32
                                      a a++  a++lr +g+ydeA++ ++ka+ei
  gi|386001638|ref|YP_005919937.1| 29 AEAWRYKALILRDQGEYDEAIAAFDKAIEI 58
                                      445555666666666666666666666665 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 8.9e-08
                            TPR_12  3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70
                                      a a++  a++lr +g+ydeA++ ++ka+ei      p+      t+   + l+  +gr++eAl+++ e
  gi|386001638|ref|YP_005919937.1| 29 AEAWRYKALILRDQGEYDEAIAAFDKAIEID-----PQDT---KTRVQKASLLIIMGRQAEALAIFDE 88
                                      6788889************************.....6653...4678888888888888888888876 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 2.1e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++a++  ++v +++g + e+l+ +++a+e+   +  +d ++t ++  n gr++ +lgryeeA+e+   al+++ 
  gi|386001638|ref|YP_005919937.1| 104 SSAWRSKGNVFAEQGLWNESLRAYDRAIELG--S--GDPLATYAASSNKGRVLNKLGRYEEAVEACDMALNAYN 173
                                       5688789************************..3..56679***********************9999999986 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 4.6e-07
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGp 39 
                                       a +n + vl++lgry+eA e ++ al+++++++G 
  gi|386001638|ref|YP_005919937.1| 144 ASSNKGRVLNKLGRYEEAVEACDMALNAYNETPGL 178
                                       4459*************************999885 PP

  == domain 5  score: 22.3 bits;  conditional E-value: 2.2e-07
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        +++l   gr+deA   +e+a ++++      +p+ a      +++++ +gr+eeA + +e+a+++++
  gi|386001638|ref|YP_005919937.1| 191 KGEALEGIGRLDEAALAYEQAAAAFEL-ETSAYPEIAKFWKYKADALEGMGRHEEAAASYERAVEAFK 257
                                       78999999*****************54.45789********************************987 PP

  == domain 6  score: 22.2 bits;  conditional E-value: 2.4e-07
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdh.pltattlrnLgrlyralgryeeAlelleealai 74 
                                       +   a++l  +gr++eA + +e+a+e+++   +++  +  ++ ++ +g++++algr  eA++++ +a ++
  gi|386001638|ref|YP_005919937.1| 229 WKYKADALEGMGRHEEAAASYERAVEAFKDEIETHAeASNIWRYQWMGEALEALGRDSEAEAAFARAREL 298
                                       5558999*********************666554445888899999*********************986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   4.4e-07   0.00023      10      33 ..      11      34 ..       8      39 .. 0.88
   2 !   29.8   0.3   6.5e-10   3.4e-07       3      27 ..      38      62 ..      36      64 .. 0.94
   3 !   16.5   0.0   9.2e-06    0.0049       1      30 [.     111     140 ..     111     143 .. 0.88
   4 !    8.8   0.1    0.0024       1.2       1      16 [.     149     164 ..     149     174 .. 0.92
   5 ?    4.2   1.0     0.065        34       8      21 ..     199     212 ..     193     213 .. 0.93
   6 !    8.9   0.1    0.0022       1.2       8      22 ..     240     254 ..     234     264 .. 0.88
   7 ?   -1.5   0.0       4.1   2.2e+03      27      42 .]     268     283 ..     265     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.4e-07
                            TPR_11 10 yeeAieaYkkAlkldPdnaeayyn 33
                                      +ee++ea+ kA++ dP+naea+  
  gi|386001638|ref|YP_005919937.1| 11 LEESVEAFDKAIEVDPQNAEAWRY 34
                                      8********************976 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 6.5e-10
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdn 27
                                      ++++qG+y+eAi+a+ kA+++dP++
  gi|386001638|ref|YP_005919937.1| 38 ILRDQGEYDEAIAAFDKAIEIDPQD 62
                                      89*********************97 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 9.2e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30 
                                       G+++ eqG ++e++ aY +A++l + ++ a
  gi|386001638|ref|YP_005919937.1| 111 GNVFAEQGLWNESLRAYDRAIELGSGDPLA 140
                                       9*********************97766665 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0024
                            TPR_11   1 GdayyeqGkyeeAiea 16 
                                       G+++ ++G+yeeA+ea
  gi|386001638|ref|YP_005919937.1| 149 GRVLNKLGRYEEAVEA 164
                                       8999**********96 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.065
                            TPR_11   8 GkyeeAieaYkkAl 21 
                                       G+++eA  aY++A 
  gi|386001638|ref|YP_005919937.1| 199 GRLDEAALAYEQAA 212
                                       9***********95 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0022
                            TPR_11   8 GkyeeAieaYkkAlk 22 
                                       G+ eeA ++Y++A++
  gi|386001638|ref|YP_005919937.1| 240 GRHEEAAASYERAVE 254
                                       9************97 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 4.1
                            TPR_11  27 naeayynLGlayykqG 42 
                                       n + y ++G+a+ ++G
  gi|386001638|ref|YP_005919937.1| 268 NIWRYQWMGEALEALG 283
                                       6677889999999887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.5   1.3e-09   6.6e-07       7      58 ..      11      62 ..       5      64 .. 0.92
   2 !   34.2   0.5   5.1e-11   2.7e-08       1      60 [.      39      98 ..      39     102 .. 0.96
   3 !   12.5   0.1   0.00029      0.15       3      57 ..     116     174 ..     114     180 .. 0.84
   4 !   12.2   4.6   0.00038       0.2       5      58 ..     199     259 ..     195     269 .. 0.84
   5 !   15.8   1.0   2.8e-05     0.015       4      53 ..     239     297 ..     238     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.3e-09
                            TPR_19  7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                                      ++e ++++ +a++ dp+naea+ + A +l  +g++deA+a+ d++ e dp+d
  gi|386001638|ref|YP_005919937.1| 11 LEESVEAFDKAIEVDPQNAEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQD 62
                                      6677899******************************************996 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 5.1e-11
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60
                                      l ++g y+eA+a++ +a++ dp++   r + A +l+ +g+ +eA a+ d+l +e p d++
  gi|386001638|ref|YP_005919937.1| 39 LRDQGEYDEAIAAFDKAIEIDPQDTKTRVQKASLLIIMGRQAEALAIFDELTAEVPEDPE 98
                                      679***************************************************999875 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00029
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllL....AeallalgqldeAealLdalpeedpd 57 
                                       ++g   e l+++ +a++   +++ a ++      ++l +lg+++eA +++d +++++  
  gi|386001638|ref|YP_005919937.1| 116 EQGLWNESLRAYDRAIELGSGDPLATYAAssnkGRVLNKLGRYEEAVEACDMALNAYNE 174
                                       667777788999999999999999999666666********************998866 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00038
                            TPR_19   5 gdyaeAlalleqalqe.......dpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       g+++eA+ ++eqa ++       +p+ a  + + A+al  +g+ +eA a  +++ e+++d+
  gi|386001638|ref|YP_005919937.1| 199 GRLDEAALAYEQAAAAfeletsaYPEIAKFWKYKADALEGMGRHEEAAASYERAVEAFKDE 259
                                       68888888888887555555555999999999*************************9995 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 2.8e-05
                            TPR_19   4 egdyaeAlalleqalqedpk.........naearl..lLAeallalgqldeAealLdalpe 53 
                                       +g+++eA+a +e+a ++  +         n +     ++ eal alg+  eAea+ +++ e
  gi|386001638|ref|YP_005919937.1| 239 MGRHEEAAASYERAVEAFKDeiethaeasNIW--RyqWMGEALEALGRDSEAEAAFARARE 297
                                       899999*9999999988555555533322444..356******************999876 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   3.4e-10   1.8e-07       2      33 ..      18      49 ..      17      50 .. 0.95
   2 !   15.3   0.0   3.6e-05     0.019       2      33 ..      52      83 ..      51      84 .. 0.94
   3 ?    4.1   0.0      0.14        72      17      34 .]     146     163 ..     126     163 .. 0.74
   4 ?    0.9   0.0       1.5   7.7e+02      14      32 ..     186     204 ..     185     205 .. 0.91
   5 ?    2.6   0.1      0.41   2.1e+02       9      32 ..     222     245 ..     208     247 .. 0.89
   6 ?    1.0   0.0       1.4   7.2e+02      16      33 ..     272     289 ..     249     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.4e-10
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      + ka+e dP na+a+ ++A +l+ +G++++A+
  gi|386001638|ref|YP_005919937.1| 18 FDKAIEVDPQNAEAWRYKALILRDQGEYDEAI 49
                                      89*****************************8 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.6e-05
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      + ka+e+dP + +   ++A ll   G+ ++A+
  gi|386001638|ref|YP_005919937.1| 52 FDKAIEIDPQDTKTRVQKASLLIIMGRQAEAL 83
                                      89**************************9997 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.14
                            TPR_17  17 nnLAelllknGdlmtArq 34 
                                        n++++l k+G++++A++
  gi|386001638|ref|YP_005919937.1| 146 SNKGRVLNKLGRYEEAVE 163
                                       589999********9975 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.5
                            TPR_17  14 daynnLAelllknGdlmtA 32 
                                       +++  ++e+l+ +G+l++A
  gi|386001638|ref|YP_005919937.1| 186 EPWLWKGEALEGIGRLDEA 204
                                       68999***********998 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.41
                            TPR_17   9 dPnnadaynnLAelllknGdlmtA 32 
                                       +P  a+++ ++A +l+  G++++A
  gi|386001638|ref|YP_005919937.1| 222 YPEIAKFWKYKADALEGMGRHEEA 245
                                       7999*************9999998 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 1.4
                            TPR_17  16 ynnLAelllknGdlmtAr 33 
                                       y+ ++e+l+ +G+  +A+
  gi|386001638|ref|YP_005919937.1| 272 YQWMGEALEALGRDSEAE 289
                                       788899999999888886 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.2   6.4e+02      16      35 ..      12      29 ..      11      30 .. 0.82
   2 !   16.1   0.1   1.5e-05     0.008       4      34 ..      34      62 ..      31      65 .. 0.80
   3 ?   -1.4   0.0       6.1   3.2e+03      12      35 ..      76      97 ..      70     100 .. 0.73
   4 ?    4.4   0.0     0.083        44       6      28 ..     111     133 ..     106     139 .. 0.79
   5 !   10.8   0.0   0.00076       0.4       3      27 ..     146     171 ..     144     180 .. 0.81
   6 ?    4.3   0.3     0.092        49       7      28 ..     193     215 ..     191     220 .. 0.77
   7 !   10.2   0.1    0.0012      0.62       6      27 ..     233     255 ..     229     262 .. 0.80
   8 ?    2.4   0.2      0.37   1.9e+02       5      24 ..     275     294 ..     275     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.2
                             TPR_7 16 eeAielyeqsLaltkdpeda 35
                                      ee +e + +  a++ dp++a
  gi|386001638|ref|YP_005919937.1| 12 EESVEAFDK--AIEVDPQNA 29
                                      688999999..999999887 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-05
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdped 34
                                      + a + +++G+y+eAi  + +  a++ dp+d
  gi|386001638|ref|YP_005919937.1| 34 YKALILRDQGEYDEAIAAFDK--AIEIDPQD 62
                                      56889****************..66655554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 6.1
                             TPR_7 12 lGdyeeAielyeqsLaltkdpeda 35
                                      +G+ +eA+ ++ +   +++ ped+
  gi|386001638|ref|YP_005919937.1| 76 MGRQAEALAIFDE--LTAEVPEDP 97
                                      5888899999988..555555544 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.083
                             TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                       ++++ ++G + e ++ y ++++l
  gi|386001638|ref|YP_005919937.1| 111 GNVFAEQGLWNESLRAYDRAIEL 133
                                       899999***********995544 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00076
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsL.a 27 
                                       +n +r+  +lG+yeeA+e +  +L a
  gi|386001638|ref|YP_005919937.1| 146 SNKGRVLNKLGRYEEAVEACDMALnA 171
                                       58899999***********9997755 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.092
                             TPR_7   7 rlysrlGdyeeAielyeqsL.al 28 
                                       ++ +  G+ +eA+  yeq+  a+
  gi|386001638|ref|YP_005919937.1| 193 EALEGIGRLDEAALAYEQAAaAF 215
                                       56666899**********77555 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0012
                             TPR_7   6 arlysrlGdyeeAielyeqsL.a 27 
                                       a++ + +G++eeA+  ye++  a
  gi|386001638|ref|YP_005919937.1| 233 ADALEGMGRHEEAAASYERAVeA 255
                                       889999*************6544 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.37
                             TPR_7   5 LarlysrlGdyeeAielyeq 24 
                                       ++++ ++lG+ +eA+  + +
  gi|386001638|ref|YP_005919937.1| 275 MGEALEALGRDSEAEAAFAR 294
                                       79999*********999887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.8e-05     0.025       9      31 ..      36      58 ..      35      58 .. 0.95
   2 ?    2.0   0.0      0.38     2e+02      13      27 ..      74      88 ..      70      89 .. 0.82
   3 ?    4.2   0.0     0.081        43       9      31 ..     111     133 ..     110     134 .. 0.91
   4 !   16.0   0.0   1.6e-05    0.0083       6      39 ..     146     179 ..     141     182 .. 0.88
   5 ?    2.8   1.1      0.22   1.2e+02      15      30 ..     198     213 ..     192     216 .. 0.82
   6 !    9.2   0.4    0.0022       1.2      11      31 ..     235     255 ..     233     262 .. 0.86
   7 ?    5.9   0.7     0.024        13       5      30 ..     272     297 ..     269     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                            TPR_10  9 analrqrgrydeAealleealai 31
                                      a +lr++g+ydeA a +++a++i
  gi|386001638|ref|YP_005919937.1| 36 ALILRDQGEYDEAIAAFDKAIEI 58
                                      789******************97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.38
                            TPR_10 13 rqrgrydeAeallee 27
                                        +gr +eA+a+++e
  gi|386001638|ref|YP_005919937.1| 74 IIMGRQAEALAIFDE 88
                                      568*********986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.081
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       +n+  ++g ++e+++ +++a+++
  gi|386001638|ref|YP_005919937.1| 111 GNVFAEQGLWNESLRAYDRAIEL 133
                                       788899**************985 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.6e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealairrrllGpd 39 
                                       +N +++l ++gry+eA++ ++ al+++ ++ G  
  gi|386001638|ref|YP_005919937.1| 146 SNKGRVLNKLGRYEEAVEACDMALNAYNETPGLA 179
                                       688************************9987755 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.22
                            TPR_10  15 rgrydeAealleeala 30 
                                        gr+deA   +e+a a
  gi|386001638|ref|YP_005919937.1| 198 IGRLDEAALAYEQAAA 213
                                       69***********987 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0022
                            TPR_10  11 alrqrgrydeAealleealai 31 
                                       al  +gr++eA a +e+a+++
  gi|386001638|ref|YP_005919937.1| 235 ALEGMGRHEEAAASYERAVEA 255
                                       56679*************986 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.024
                            TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                                       +  ++ al ++gr  eAea + +a +
  gi|386001638|ref|YP_005919937.1| 272 YQWMGEALEALGRDSEAEAAFARARE 297
                                       567899**************999976 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   2.9e-09   1.5e-06       7      81 ..      13      88 ..       8      89 .. 0.93
   2 !    7.6   0.0    0.0085       4.5      20      78 ..      94     164 ..      86     168 .. 0.73
   3 ?    1.7   0.3      0.56     3e+02      41      81 ..     213     251 ..     200     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.9e-09
                                      HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      + +  ++++ + +++++e+  ++Al l  +g+y++A+  ++ka ++++++ + r+ +A  l+ +++  eA+a++++
  gi|386001638|ref|YP_005919937.1| 13 ESVEAFDKAIEVDPQNAEAWRYKALILRDQGEYDEAIAAFDKAiEIDPQDTKTRVQKASLLIIMGRQAEALAIFDE 88
                                      55667899999*************************************************************9986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0085
                                       H--HHHHHHH.......HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHH....HHHHHTT-HHHHHHH CS
                            ANAPC3  20 tespedayll.......AlclylngqykrAyellrka.klnskslgcrylfA....qcllkLkkyeeAiaa 78 
                                       +e+pe +++        + ++ ++g +++ ++ +++a +l s ++ + y +     ++l kL++yeeA+ a
  gi|386001638|ref|YP_005919937.1|  94 PEDPEERLWQssawrskGNVFAEQGLWNESLRAYDRAiELGSGDPLATYAASsnkgRVLNKLGRYEEAVEA 164
                                       5666666663333333377777888899999999999888888888888776777799**********976 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.56
                                       HHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  41 rAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        A+el  +   +++  + +  +A +l  ++++eeA a +e+
  gi|386001638|ref|YP_005919937.1| 213 AAFELETS--AYPEIAKFWKYKADALEGMGRHEEAAASYER 251
                                       33333333..4777788999999999999999999998876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.06        32     105     129 ..      34      58 ..       7      68 .. 0.78
   2 ?    1.2   0.1      0.64   3.4e+02     128     128 ..      57      57 ..      41     103 .. 0.59
   3 ?    2.1   0.1      0.35   1.8e+02      94     129 ..      97     133 ..      79     135 .. 0.77
   4 !   19.9   0.1   1.1e-06   0.00058      64     127 ..     151     212 ..     136     223 .. 0.87
   5 !   14.5   2.4   5.1e-05     0.027      62     129 ..     233     298 ..     226     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.06
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmagem 129
                                        +a  l + G +dea+ af +a e+
  gi|386001638|ref|YP_005919937.1|  34 YKALILRDQGEYDEAIAAFDKAIEI 58 
                                       5788899999999999999999885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.64
                                       H CS
                           DUF3856 128 e 128
                                       e
  gi|386001638|ref|YP_005919937.1|  57 E 57 
                                       2 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.35
                                       THHHHHHH.HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  94 deGklWia.avfsravaleelGrkdealkafrmagem 129
                                        e +lW + a  s++  ++e G  +e+l+a+  a e+
  gi|386001638|ref|YP_005919937.1|  97 PEERLWQSsAWRSKGNVFAEQGLWNESLRAYDRAIEL 133
                                       4778897615568999999999999999999999885 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 1.1e-06
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTST..HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqd..eGklWiaavfsravaleelGrkdealkafrmag 127
                                        l klgry+ea+e+ d al+ +n    l +    G+ W+     ++ ale++Gr dea  a+++a+
  gi|386001638|ref|YP_005919937.1| 151 VLNKLGRYEEAVEACDMALNAYNETPGLASPflMGEPWL----WKGEALEGIGRLDEAALAYEQAA 212
                                       5789************************98633688886....69**************9999886 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 5.1e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                       ++al ++gr++ea  s ++a++ f    e + +  ++W       + ale lGr +ea  af  a e+
  gi|386001638|ref|YP_005919937.1| 233 ADALEGMGRHEEAAASYERAVEAFKDEIETHAEASNIWRYQW--MGEALEALGRDSEAEAAFARAREL 298
                                       7899****************************9999998765..5899**************999885 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.9   9.9e+02      17      32 ..      12      27 ..       4      28 .. 0.84
   2 !   14.2   0.1    0.0001     0.053       6      32 ..      35      61 ..      30      62 .. 0.88
   3 ?    3.9   0.0      0.19     1e+02      13      32 ..      76      95 ..      67      96 .. 0.86
   4 ?    2.9   0.0       0.4   2.1e+02       9      28 ..     113     132 ..     110     133 .. 0.83
   5 ?    5.6   0.0     0.055        29       7      30 ..     149     172 ..     146     172 .. 0.86
   6 ?    3.4   0.4      0.26   1.4e+02       5      27 ..     190     212 ..     188     217 .. 0.64
   7 ?    7.4   0.2     0.015       7.8       7      30 ..     233     256 ..     231     258 .. 0.85
   8 ?    5.9   0.5     0.043        22       5      27 ..     274     296 ..     272     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHH-TT CS
                             TPR_6 17 dkAlealerlikeYPd 32
                                      ++++ea+++ i+  P+
  gi|386001638|ref|YP_005919937.1| 12 EESVEAFDKAIEVDPQ 27
                                      7999******998886 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  6 lalsyrklgdtdkAlealerlikeYPd 32
                                       al +r +g++d+A++a+++ i+  P+
  gi|386001638|ref|YP_005919937.1| 35 KALILRDQGEYDEAIAAFDKAIEIDPQ 61
                                      68899999***************9996 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 13 lgdtdkAlealerlikeYPd 32
                                      +g+ ++Al+++++l  e P+
  gi|386001638|ref|YP_005919937.1| 76 MGRQAEALAIFDELTAEVPE 95
                                      47999*********999885 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealerlik 28 
                                        + ++g + ++l+a++r i+
  gi|386001638|ref|YP_005919937.1| 113 VFAEQGLWNESLRAYDRAIE 132
                                       5778999999*****99986 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                       ++ + klg++++A+ea +  ++ Y
  gi|386001638|ref|YP_005919937.1| 149 GRVLNKLGRYEEAVEACDMALNAY 172
                                       77888999********99988877 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       + +++++  g+ d+A  a+e+  
  gi|386001638|ref|YP_005919937.1| 190 WKGEALEGIGRLDEAALAYEQAA 212
                                       55666666567777777777754 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                       a +++ +g++++A + +er ++ +
  gi|386001638|ref|YP_005919937.1| 233 ADALEGMGRHEEAAASYERAVEAF 256
                                       67778899***********99977 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       ++++++++lg+ ++A +a+ r +
  gi|386001638|ref|YP_005919937.1| 274 WMGEALEALGRDSEAEAAFARAR 296
                                       79******99*********9986 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   7.5e-08     4e-05     207     259 ..      10      62 ..       6      64 .. 0.95
   2 ?    3.5   0.0     0.053        28      42      71 ..      67      96 ..      63     132 .. 0.86
   3 ?    2.6   0.0     0.095        50      34      64 ..     138     168 ..     101     176 .. 0.69
   4 ?    4.0   0.4     0.037        19      19      74 ..     207     262 ..     200     273 .. 0.82
   5 ?   -1.1   0.1       1.3   6.7e+02      39      62 ..     270     293 ..     248     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.5e-08
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       s e+++e  dkaie +p+  e +  Ka il+ +G+ ++A+++ ++a ++D +D
  gi|386001638|ref|YP_005919937.1|  10 SLEESVEAFDKAIEVDPQNAEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQD 62 
                                       568999********************************************999 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.053
                                      HHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                             NARP1 42 etkaelllkLgrkeeAeatyeaLlernpen 71
                                       +ka+ll+ +gr++eA a++ +L    pe+
  gi|386001638|ref|YP_005919937.1| 67 VQKASLLIIMGRQAEALAIFDELTAEVPED 96
                                      589********************9999886 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.095
                                       ---HHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1  34 ivDklavketkaelllkLgrkeeAeatyeaL 64 
                                        + + a + +k+++l kLgr+eeA ++    
  gi|386001638|ref|YP_005919937.1| 138 PLATYAASSNKGRVLNKLGRYEEAVEACDMA 168
                                       4456677889999999999999999876655 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHH CS
                             NARP1  19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskY 74 
                                        +e+A + +e + +   +  ++ + ka+ l  +gr+eeA+a ye+ +e  +++ + 
  gi|386001638|ref|YP_005919937.1| 207 AYEQAAAAFELETSAYPEIAKFWKYKADALEGMGRHEEAAASYERAVEAFKDEIET 262
                                       5677888888888888888889999******************9999988887765 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHTT-HHHHHHHHH CS
                             NARP1  39 avketkaelllkLgrkeeAeatye 62 
                                          + ++e l +Lgr +eAea++ 
  gi|386001638|ref|YP_005919937.1| 270 WRYQWMGEALEALGRDSEAEAAFA 293
                                       446789999999*******99985 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.5e-05     0.008      69     124 ..      36      91 ..       6     103 .. 0.84
   2 !   14.6   7.9   6.4e-05     0.034       8     135 ..     144     265 ..     101     269 .. 0.90
   3 ?    4.1   0.9      0.11        59     104     124 ..     277     297 ..     262     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-05
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a  +   G+++ea+a  +++++ +P + +++ q    l  +GrqaeAL+ +++l +
  gi|386001638|ref|YP_005919937.1|  36 ALILRDQGEYDEAIAAFDKAIEIDPQDTKTRVQKASLLIIMGRQAEALAIFDELTA 91 
                                       44456789*******************************************99865 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                              BTAD   8 alvaagraalaagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealae 84 
                                       a  ++gr + + g+ eea+e+++ Al+ +++++      +++l +e   ++ ++le + +l ea l+++   +a+a 
  gi|386001638|ref|YP_005919937.1| 144 ASSNKGRVLNKLGRYEEAVEACDMALNAYNETPGLA---SPFLMGEPWLWKGEALEGIGRLDEAALAYE---QAAAA 214
                                       5567889999999*****************999887...699999999999999999999999888765...55666 PP

                                       HHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS---- CS
                              BTAD  85 lealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepg 135
                                        e  ++++P   ++++    Al  +Gr +eA + Yer+++  ++e+ + ++
  gi|386001638|ref|YP_005919937.1| 215 FELETSAYPEIAKFWKYKADALEGMGRHEEAAASYERAVEAFKDEIETHAE 265
                                       6777899**************************************988776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.11
                                       HHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlrr 124
                                       +Al ++Gr +eA +++ r+r+
  gi|386001638|ref|YP_005919937.1| 277 EALEALGRDSEAEAAFARARE 297
                                       79999************9997 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   8.4e-08   4.4e-05      12      66 ..      12      66 ..       6      73 .. 0.87
   2 !    8.6   0.3     0.004       2.1      13      66 ..      81     141 ..      69     146 .. 0.75
   3 !    9.5   0.2    0.0021       1.1       6      51 ..     115     164 ..     112     176 .. 0.83
   4 ?    5.3   0.7     0.042        22      11      57 ..     208     254 ..     203     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.4e-08
                             TPR_9 12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66
                                      e+  ++ +  + ++P+ +e +r  +l+l  +G + +A+a+++ +++++p++   +
  gi|386001638|ref|YP_005919937.1| 12 EESVEAFDKAIEVDPQNAEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQDTKTR 66
                                      555677888999*************************************997655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.004
                             TPR_9  13 ralavverllllaPddpee.......rrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       +ala+ + l +  P+dpee       +r  G + a++G +++ l++ +++++l   +p a 
  gi|386001638|ref|YP_005919937.1|  81 EALAIFDELTAEVPEDPEErlwqssaWRSKGNVFAEQGLWNESLRAYDRAIELGSGDPLAT 141
                                       5666666666666666655333333389***********************9988887765 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0021
                             TPR_9   6 ireedweralavverllllaPddpeerr....dRGlllaqlGclsaAlad 51 
                                       +++  w + l++++r + l + dp   +      G++l +lG++++A+++
  gi|386001638|ref|YP_005919937.1| 115 AEQGLWNESLRAYDRAIELGSGDPLATYaassNKGRVLNKLGRYEEAVEA 164
                                       67888999***************99998333358*************987 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.042
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                       +e+a a+ e+     P+ +  +   + +l+ +G+ ++A+a  e++++
  gi|386001638|ref|YP_005919937.1| 208 YEQAAAAFELETSAYPEIAKFWKYKADALEGMGRHEEAAASYERAVE 254
                                       5777788888888888899999999*******************996 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   3.2e-06    0.0017     141     218 ..      21     103 ..       7     109 .. 0.75
   2 ?   -1.4   0.0         2   1.1e+03     149     179 ..     107     137 ..     103     145 .. 0.78
   3 !    9.0   3.2    0.0014      0.72     134     188 ..     216     270 ..     123     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-06
                            TPR_15 141 aae...qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara..es 212
                                       a e   q+a  + + a + r++g+ d+A+ ++ +A++ +p++++ r +   lli +gr+ae+ ++  ++ a+   + 
  gi|386001638|ref|YP_005919937.1|  21 AIEvdpQNAEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQDTKTRVQKASLLIIMGRQAEALAIFDELTAEVpeDP 97 
                                       33333678889999999999999999999999999999999999999999999999999998888888888875455 PP

                            TPR_15 213 dasLwg 218
                                       +++Lw+
  gi|386001638|ref|YP_005919937.1|  98 EERLWQ 103
                                       556665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapds 179
                                       +   +++  ++g ++++lr+y +A++l  ++
  gi|386001638|ref|YP_005919937.1| 107 WRSKGNVFAEQGLWNESLRAYDRAIELGSGD 137
                                       6666677788999999999999999987765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0014
                            TPR_15 134 ksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapds..selraallW 188
                                       +   e++a+ + a f+ + a + +  g++++A   y++A++++ d+  + + a  +W
  gi|386001638|ref|YP_005919937.1| 216 EL--ETSAYPEIAKFWKYKADALEGMGRHEEAAASYERAVEAFKDEieTHAEASNIW 270
                                       22..4555668899***************************9999722445555566 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.3   1.6e+02      18      39 ..      12      33 ..       9      41 .. 0.82
   2 ?    5.0   0.0     0.049        26      14      34 ..      42      62 ..      39      66 .. 0.92
   3 !    7.9   0.1    0.0061       3.2      13      29 ..     154     170 ..     152     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.3
                                      HHHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C 18 seArryvdalLeiEPenrQaqs 39
                                      +e+ +  d  +e++P+n  a  
  gi|386001638|ref|YP_005919937.1| 12 EESVEAFDKAIEVDPQNAEAWR 33
                                      67889999*********99865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.049
                                      HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPen 34
                                      +geY+eA    d  +ei+P+ 
  gi|386001638|ref|YP_005919937.1| 42 QGEYDEAIAAFDKAIEIDPQD 62
                                      59*****************86 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0061
                                       HHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLe 29 
                                       klg+Y+eA + +d+ L+
  gi|386001638|ref|YP_005919937.1| 154 KLGRYEEAVEACDMALN 170
                                       9*************996 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0043       2.3      80     122 ..       6      48 ..       1      51 [. 0.86
   2 !   10.0   0.0    0.0017      0.87      80     123 ..      40      83 ..      34      87 .. 0.92
   3 ?    4.1   0.3      0.11        59      85     124 ..     208     247 ..     141     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0043
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       l ++ ++ ++e  +++++ dp+naea + ka +l+  g+  e+
  gi|386001638|ref|YP_005919937.1|   6 LFNDSLEESVEAFDKAIEVDPQNAEAWRYKALILRDQGEYDEA 48 
                                       5567788899*************************99998776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       +++g+y  a+   +++++ dp++++++  ka+ l  +g+qae+ 
  gi|386001638|ref|YP_005919937.1|  40 RDQGEYDEAIAAFDKAIEIDPQDTKTRVQKASLLIIMGRQAEAL 83 
                                       589**************************************975 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
                   Alkyl_sulf_dimr  85 yrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                       y+ aa   +    a pe a+  + kadale +g+++e+a+
  gi|386001638|ref|YP_005919937.1| 208 YEQAAAAFELETSAYPEIAKFWKYKADALEGMGRHEEAAA 247
                                       333334444444467778999999**********999875 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0054       2.8       6      44 ..      13      51 ..       9      52 .. 0.93
   2 !   13.7   0.1   0.00011      0.06       8      43 ..      49      84 ..      48      93 .. 0.92
   3 ?   -1.0   0.0       4.4   2.3e+03      29      43 ..     149     163 ..     123     169 .. 0.77
   4 ?   -0.1   0.2       2.3   1.2e+03      34      74 ..     245     285 ..     232     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0054
                            TPR_20  6 pelaeleaalaanpddldarldlAlallaagryeeAleq 44
                                      ++++++++a++ +p++ +a    Al l  +g+y+eA+++
  gi|386001638|ref|YP_005919937.1| 13 ESVEAFDKAIEVDPQNAEAWRYKALILRDQGEYDEAIAA 51
                                      57899*******************************975 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                            TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAle 43
                                      +a++++a++ +p+d ++r++ A +l+  gr++eAl+
  gi|386001638|ref|YP_005919937.1| 49 IAAFDKAIEIDPQDTKTRVQKASLLIIMGRQAEALA 84
                                      78999*****************************96 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.4
                            TPR_20  29 AlallaagryeeAle 43 
                                        ++l++ gryeeA+e
  gi|386001638|ref|YP_005919937.1| 149 GRVLNKLGRYEEAVE 163
                                       456777889999987 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2.3
                            TPR_20  34 aagryeeAleqLleilkrdrkweddaarkqllkifealgsq 74 
                                       aa  ye A+e++ + ++++ ++++    + + + +ealg +
  gi|386001638|ref|YP_005919937.1| 245 AAASYERAVEAFKDEIETHAEASNIWRYQWMGEALEALGRD 285
                                       55566666666666666666665555555555666666655 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.018       9.6       4      24 ..      32      52 ..      29      54 .. 0.80
   2 ?    3.9   0.0      0.21   1.1e+02      10      26 .]      72      88 ..      65      88 .. 0.77
   3 !    8.9   0.0    0.0051       2.7       3      23 ..     144     164 ..     142     166 .. 0.86
   4 ?    1.2   0.4       1.6   8.4e+02       5      21 ..     189     205 ..     186     210 .. 0.79
   5 ?    6.1   0.5     0.039        21       8      26 .]     233     251 ..     232     251 .. 0.88
   6 ?    1.1   2.0       1.7   8.9e+02       6      25 ..     274     293 ..     274     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                             TPR_4  4 llaLArallalGdldeArall 24
                                          A  l ++G++deA a++
  gi|386001638|ref|YP_005919937.1| 32 WRYKALILRDQGEYDEAIAAF 52
                                      5566999**********8876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.21
                             TPR_4 10 allalGdldeAraller 26
                                      +l   G+ +eA+a++++
  gi|386001638|ref|YP_005919937.1| 72 LLIIMGRQAEALAIFDE 88
                                      56667********9875 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0051
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       a ++ +r+l  lG+++eA ++
  gi|386001638|ref|YP_005919937.1| 144 ASSNKGRVLNKLGRYEEAVEA 164
                                       667899************986 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.6
                             TPR_4   5 laLArallalGdldeAr 21 
                                       l+ ++al   G+ldeA+
  gi|386001638|ref|YP_005919937.1| 189 LWKGEALEGIGRLDEAA 205
                                       5667788888*****96 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.039
                             TPR_4   8 ArallalGdldeAraller 26 
                                       A al   G+++eA+a  er
  gi|386001638|ref|YP_005919937.1| 233 ADALEGMGRHEEAAASYER 251
                                       7899999*******98886 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 1.7
                             TPR_4   6 aLArallalGdldeAralle 25 
                                       ++++al alG+  eA+a+++
  gi|386001638|ref|YP_005919937.1| 274 WMGEALEALGRDSEAEAAFA 293
                                       5799*******999999876 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0     0.004       2.1      81     110 ..       1      30 [.       1      33 [. 0.94
   2 ?    1.7   0.0      0.48   2.5e+02      87     109 ..      41      63 ..      35      65 .. 0.84
   3 ?   -2.1   0.0       7.3   3.9e+03      85     107 ..     152     174 ..     146     182 .. 0.76
   4 ?    1.2   0.0      0.69   3.7e+02      81     110 ..     184     213 ..     178     225 .. 0.86
   5 ?   -1.2   0.1       3.8     2e+03      80     101 ..     274     295 ..     231     298 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.004
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpqPqe 110
                                       +GEell +++ ee++e++ +A+ v pq +e
  gi|386001638|ref|YP_005919937.1|   1 MGEELLFNDSLEESVEAFDKAIEVDPQNAE 30 
                                       7***********************999865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.48
                             MAS20  87 aqgeeeeaaehlynAlkvcpqPq 109
                                        qge++ea+ ++ +A+ + pq +
  gi|386001638|ref|YP_005919937.1|  41 DQGEYDEAIAAFDKAIEIDPQDT 63 
                                       459*************9998865 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.3
                             MAS20  85 llaqgeeeeaaehlynAlkvcpq 107
                                       l + g++eea+e+   Al  +++
  gi|386001638|ref|YP_005919937.1| 152 LNKLGRYEEAVEACDMALNAYNE 174
                                       44449999999999999999876 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.69
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpqPqe 110
                                       +GE +l +ge  e++  l  A   ++q ++
  gi|386001638|ref|YP_005919937.1| 184 MGEPWLWKGEALEGIGRLDEAALAYEQAAA 213
                                       8*********************99999875 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 3.8
                             MAS20  80 qlGEellaqgeeeeaaehlynA 101
                                        +GE l a g+  ea  ++++A
  gi|386001638|ref|YP_005919937.1| 274 WMGEALEALGRDSEAEAAFARA 295
                                       3566666666666666666555 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00024      0.13      83     176 ..      36     134 ..       8     145 .. 0.75
   2 ?    3.6   0.1      0.09        48     129     178 ..     127     174 ..     126     183 .. 0.79
   3 ?    6.7   0.9      0.01       5.3     152     191 ..     191     236 ..     189     238 .. 0.84
   4 ?    4.9   0.6     0.037        20     150     179 ..     230     259 ..     225     269 .. 0.84
   5 ?    0.8   0.3      0.66   3.5e+02     151     173 ..     274     296 ..     261     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            TPR_21  83 AkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktL.....eakkeeafaalvaelrGD 154
                                       A    ++g++++A a++++++e  ++++ +++ +  L  ++  + ++ +   +L     e+ +e  +++++   +G+
  gi|386001638|ref|YP_005919937.1|  36 ALILRDQGEYDEAIAAFDKAIEIDPQDTKTRVQKASLLIIMGRQAEALAIFDELtaevpEDPEERLWQSSAWRSKGN 112
                                       55566899***************99998888877666666655555444444444333445556679********** PP

                            TPR_21 155 ilvaqgkldeAraaYqaAlaal 176
                                       ++++qg  +e   aY++A++ +
  gi|386001638|ref|YP_005919937.1| 113 VFAEQGLWNESLRAYDRAIELG 134
                                       ******************9865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.09
                            TPR_21 129 ydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       yd+A+++ ++++ +++aa+    +G +l + g+ +eA +a + Al+a +e
  gi|386001638|ref|YP_005919937.1| 127 YDRAIELGSGDPLATYAASS--NKGRVLNKLGRYEEAVEACDMALNAYNE 174
                                       56666666666666776665..59*********************99776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.01
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka......rellqlKlddL 191
                                       +G++l   g+ldeA  aY++A aa e ++       ++ + K d+L
  gi|386001638|ref|YP_005919937.1| 191 KGEALEGIGRLDEAALAYEQAAAAFELETsaypeiAKFWKYKADAL 236
                                       8999******************998877777777777777787777 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.037
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaaleek 179
                                         + D+l  +g+ +eA a Y++A++a +++
  gi|386001638|ref|YP_005919937.1| 230 KYKADALEGMGRHEEAAASYERAVEAFKDE 259
                                       567899999***************998765 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.66
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAl 173
                                         G++l a g+  eA aa+ +A 
  gi|386001638|ref|YP_005919937.1| 274 WMGEALEALGRDSEAEAAFARAR 296
                                       56999**************9996 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00046      0.24      14      70 ..      42      95 ..      31     108 .. 0.82
   2 ?   -1.4   0.0       4.9   2.6e+03      83      97 ..     151     165 ..     140     174 .. 0.63
   3 ?    2.8   0.1      0.25   1.3e+02       8      31 ..     233     256 ..     225     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                             TPR_5 14 tGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsd 70
                                       G+ d+a+  + +a++    + +  +  +q as L  +G+ +eala+ ++++++ ++
  gi|386001638|ref|YP_005919937.1| 42 QGEYDEAIAAFDKAIEI---DPQDTKTRVQKASLLIIMGRQAEALAIFDELTAEVPE 95
                                      58889999999999986...67777778******************99988776443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                             TPR_5  83 vLsdlgrereavsiv 97 
                                       vL +lgr +eav   
  gi|386001638|ref|YP_005919937.1| 151 VLNKLGRYEEAVEAC 165
                                       555666666666544 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.25
                             TPR_5   8 agarDstGhedkavplYrraLaeG 31 
                                       a a + +G++++a+  Y+ra+++ 
  gi|386001638|ref|YP_005919937.1| 233 ADALEGMGRHEEAAASYERAVEAF 256
                                       555667788888888888888764 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.27   1.4e+02     267     291 ..      10      34 ..       7      38 .. 0.87
   2 ?    8.0   1.2    0.0028       1.5     147     310 ..      29     250 ..      17     272 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.27
                                       .-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 267 kieeilqsysaateidpswykawht 291
                                       + ee ++++ +a e+dp+ ++aw +
  gi|386001638|ref|YP_005919937.1|  10 SLEESVEAFDKAIEVDPQNAEAWRY 34 
                                       5789999****************86 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                                       TTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCC. CS
                               FAT 147 aemwlkfanlarksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLreftsellekke. 222
                                       ae+w   a + r++g+++ A+ a  +++e dp++ +        ++++ +l+  g+q eal    e t e+ e++e 
  gi|386001638|ref|YP_005919937.1|  29 AEAWRYKALILRDQGEYDEAIAAFDKAIEIDPQDTK------TRVQKASLLIIMGRQAEALAIFDELTAEVPEDPEe 99 
                                       566666666677777777777777777777773333......34556666677777777777777777777776664 PP

                                       ...............SS-SS---...................................................... CS
                               FAT 223 ...............elqsgleaq..................................................... 231
                                                      +       +                                                     
  gi|386001638|ref|YP_005919937.1| 100 rlwqssawrskgnvfA-------Eqglwneslraydraielgsgdplatyaassnkgrvlnklgryeeaveacdmal 169
                                       4444444432222220.......123333333333344444432222222222222222222222222222223333 PP

                                       .............HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHH CS
                               FAT 232 ..keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeq 306
                                          + t       l+++  l kGe +e +++ld++    e++ +++ + t+  p+++k w + a++ + + ++ee  
  gi|386001638|ref|YP_005919937.1| 170 naYNETPGLASPFLMGEPWLWKGEALEGIGRLDEAALAYEQAAAAFELETSAYPEIAKFWKYKADALEGMGRHEEAA 246
                                       22222222222223344445555578888888888888888888888888888888888888888877777777666 PP

                                       SSSS CS
                               FAT 307 keee 310
                                       ++ e
  gi|386001638|ref|YP_005919937.1| 247 ASYE 250
                                       5544 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.037        19       7      37 ..      28      58 ..      26      83 .. 0.91
   2 ?   -0.7   0.0       2.1   1.1e+03       5      36 ..     101     132 ..      98     133 .. 0.86
   3 ?    6.6   0.1     0.012       6.3      12      40 ..     146     174 ..     136     175 .. 0.85
   4 ?   -2.5   0.1       7.4   3.9e+03      19      42 ..     237     260 ..     221     278 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.037
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsaley 37
                                       a++++  a  l  +gey+eA++ +d+a+e+
  gi|386001638|ref|YP_005919937.1| 28 NAEAWRYKALILRDQGEYDEAIAAFDKAIEI 58
                                      68899999999999**************985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.1
                           DUF5113   5 lqiandYanlayylnvegeyeeALeyldsale 36 
                                       l  ++++++ ++    +g ++e+L+  d a+e
  gi|386001638|ref|YP_005919937.1| 101 LWQSSAWRSKGNVFAEQGLWNESLRAYDRAIE 132
                                       556889999999*************9999986 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                           DUF5113  12 anlayylnvegeyeeALeyldsaleylNa 40 
                                        n +  ln  g+yeeA+e  d al+  N+
  gi|386001638|ref|YP_005919937.1| 146 SNKGRVLNKLGRYEEAVEACDMALNAYNE 174
                                       5778899*****************99886 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.4
                           DUF5113  19 nvegeyeeALeyldsaleylNahy 42 
                                          g++eeA +  + a+e      
  gi|386001638|ref|YP_005919937.1| 237 EGMGRHEEAAASYERAVEAFKDEI 260
                                       444444555444444444444333 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.034        18      15      52 ..      36      72 ..      25      88 .. 0.73
   2 ?    2.5   0.0      0.32   1.7e+02      12      32 ..     146     167 ..     136     177 .. 0.66
   3 ?   -2.2   0.0       9.4     5e+03      21      37 ..     198     214 ..     191     222 .. 0.61
   4 ?    5.8   0.3      0.03        16      11      42 ..     229     260 ..     217     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.034
                         NRBF2_MIT 15 adrllaaGkyeeaischkkaaaylseamkltkseqaql 52
                                      a  l   G y+eai+   ka ++  +  k t+ ++a l
  gi|386001638|ref|YP_005919937.1| 36 ALILRDQGEYDEAIAAFDKAIEIDPQDTK-TRVQKASL 72
                                      5556678*************987665554.55555555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.32
                         NRBF2_MIT  12 srkadrllaaGkyeeai.schk 32 
                                       s k   l   G+yeea+ +c  
  gi|386001638|ref|YP_005919937.1| 146 SNKGRVLNKLGRYEEAVeACDM 167
                                       5555556678******944544 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.4
                         NRBF2_MIT  21 aGkyeeaischkkaaay 37 
                                        G+ +ea   +++aaa 
  gi|386001638|ref|YP_005919937.1| 198 IGRLDEAALAYEQAAAA 214
                                       56666666555555543 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.03
                         NRBF2_MIT  11 qsrkadrllaaGkyeeaischkkaaaylseam 42 
                                        + kad l   G++eea + +++a + + + +
  gi|386001638|ref|YP_005919937.1| 229 WKYKADALEGMGRHEEAAASYERAVEAFKDEI 260
                                       5679*******************999887755 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         2     1e+03      52      70 ..      36      54 ..       9      61 .. 0.86
   2 ?   -1.9   0.0       9.5     5e+03      52      77 ..      70      95 ..      65      96 .. 0.77
   3 ?   -0.6   0.0       3.8     2e+03      52      77 ..     149     174 ..     144     179 .. 0.83
   4 ?    7.9   0.1    0.0082       4.3      61      82 ..     208     229 ..     198     231 .. 0.87
   5 ?    1.3   0.1      0.98   5.2e+02      60      79 ..     248     267 ..     239     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2
                           DUF4810 52 Gllylkegkkeeaieafek 70
                                      +l++ ++g+ +eai+af+k
  gi|386001638|ref|YP_005919937.1| 36 ALILRDQGEYDEAIAAFDK 54
                                      5778899999999999987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9.5
                           DUF4810 52 GllylkegkkeeaieafekEkelfPE 77
                                      + l++ +g+++ea + f++ ++  PE
  gi|386001638|ref|YP_005919937.1| 70 ASLLIIMGRQAEALAIFDELTAEVPE 95
                                      66888899999999999876666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.8
                           DUF4810  52 GllylkegkkeeaieafekEkelfPE 77 
                                       G ++ k g+ eea+ea +   ++++E
  gi|386001638|ref|YP_005919937.1| 149 GRVLNKLGRYEEAVEACDMALNAYNE 174
                                       77889999999999999988888888 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0082
                           DUF4810  61 keeaieafekEkelfPESatfm 82 
                                        e+a +afe E++++PE a+f 
  gi|386001638|ref|YP_005919937.1| 208 YEQAAAAFELETSAYPEIAKFW 229
                                       689**************99985 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.98
                           DUF4810  60 kkeeaieafekEkelfPESa 79 
                                         e a+eaf+ E e++ E++
  gi|386001638|ref|YP_005919937.1| 248 SYERAVEAFKDEIETHAEAS 267
                                       57889999999999999976 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.9     1e+03       3      15 ..      12      24 ..      11      29 .. 0.86
   2 ?    4.6   0.0     0.046        24       1      15 [.      44      58 ..      44      63 .. 0.92
   3 ?   -0.7   0.0         2   1.1e+03       3      15 ..     121     133 ..     120     134 .. 0.87
   4 ?   -1.5   0.0       3.6   1.9e+03      32      46 ..     148     162 ..     147     167 .. 0.72
   5 ?   -0.0   0.0       1.3   6.6e+02       1      38 [.     157     197 ..     157     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHH CS
                          HTH_Bact  3 eeaLeqvnkAiei 15
                                      ee+ e  +kAie+
  gi|386001638|ref|YP_005919937.1| 12 EESVEAFDKAIEV 24
                                      799999*****97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.046
                                      -HHHHHHHHHHHHHH CS
                          HTH_Bact  1 rYeeaLeqvnkAiei 15
                                      +Y+ea+   +kAiei
  gi|386001638|ref|YP_005919937.1| 44 EYDEAIAAFDKAIEI 58
                                      6************98 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHH CS
                          HTH_Bact   3 eeaLeqvnkAiei 15 
                                       +e+L   ++Aie+
  gi|386001638|ref|YP_005919937.1| 121 NESLRAYDRAIEL 133
                                       799********86 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.6
                                       HHHHHHHTT--HHHH CS
                          HTH_Bact  32 kgecleklgfseeeI 46 
                                       kg  l klg  ee +
  gi|386001638|ref|YP_005919937.1| 148 KGRVLNKLGRYEEAV 162
                                       788888888766654 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 1.3
                                       -HHHHHHHHHHHHHHHHHT...TB-TTHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiSiri...nsMsLlGQLyYqkgeclek 38 
                                       rYeea e  + A++   ++   +s  L+G  +  kge le 
  gi|386001638|ref|YP_005919937.1| 157 RYEEAVEACDMALNAYNETpglASPFLMGEPWLWKGEALEG 197
                                       57777777777765433321114455666666667777765 PP

>> DUF1447  Protein of unknown function (DUF1447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00065      0.34      45      67 ..     196     218 ..     193     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                           DUF1447  45 EfieelsgkaLeYEkesedfklt 67 
                                       E i  l+++aL+YE+  ++f+l+
  gi|386001638|ref|YP_005919937.1| 196 EGIGRLDEAALAYEQAAAAFELE 218
                                       77999****************97 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2      0.02        10      15      70 ..       8      58 ..       4      76 .. 0.76
   2 ?   -1.1   0.0       3.7     2e+03      46      68 ..      68      90 ..      63      96 .. 0.84
   3 ?    0.4   0.0       1.3   6.8e+02      44      67 ..     145     168 ..     120     175 .. 0.71
   4 ?   -0.6   0.1       2.8   1.5e+03      56      73 ..     248     265 ..     237     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.02
                            ANAPC5 15 qqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairl 70
                                      +++l++  + FD +++ + ++ ++ ++y +L l     d g+++eA++a+  ai++
  gi|386001638|ref|YP_005919937.1|  8 NDSLEESVEAFDKAIEVDPQN-AEAWRYKALIL----RDQGEYDEAIAAFDKAIEI 58
                                      566777777788877777777.66677666544....5789*************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.7
                            ANAPC5 46 nlaslhadfghneeAvkaleeai 68
                                      + asl   +g ++eA++ + e +
  gi|386001638|ref|YP_005919937.1| 68 QKASLLIIMGRQAEALAIFDELT 90
                                      678899999******99999865 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.3
                            ANAPC5  44 lLnlaslhadfghneeAvkaleea 67 
                                         n  ++  ++g +eeAv+a   a
  gi|386001638|ref|YP_005919937.1| 145 SSNKGRVLNKLGRYEEAVEACDMA 168
                                       456777788999999999997655 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.8
                            ANAPC5  56 hneeAvkaleeairlAre 73 
                                        +e Av+a+++ i++  e
  gi|386001638|ref|YP_005919937.1| 248 SYERAVEAFKDEIETHAE 265
                                       466777777777766555 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.017       8.9      13      35 ..      41      61 ..      36      62 .. 0.82
   2 ?    0.6   0.0       1.1   5.8e+02      15      23 ..     156     164 ..     154     172 .. 0.86
   3 ?    1.6   0.7      0.54   2.8e+02      15      33 ..     199     215 ..     199     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                                      HTT-HHHHHHH..HHHHHHH-TT CS
                             TPR_3 13 nkkkyqeArelfsYallaildke 35
                                      ++++y+eA+ +f+   +  +d++
  gi|386001638|ref|YP_005919937.1| 41 DQGEYDEAIAAFD--KAIEIDPQ 61
                                      69*********98..77777766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       ++y+eA+e+
  gi|386001638|ref|YP_005919937.1| 156 GRYEEAVEA 164
                                       89****997 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.54
                                       T-HHHHHHH..HHHHHHH- CS
                             TPR_3  15 kkyqeArelfsYallaild 33 
                                       ++++eA+ +  Y+++a+ +
  gi|386001638|ref|YP_005919937.1| 199 GRLDEAALA--YEQAAAAF 215
                                       7899*****..99*99876 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.044        23     122     179 ..      41      99 ..       9     108 .. 0.78
   2 ?    0.3   0.2       1.1   5.7e+02     152     175 ..     194     217 ..     192     229 .. 0.83
   3 ?    4.2   1.6     0.069        37     145     180 ..     228     263 ..     208     268 .. 0.79
   4 ?    3.1   0.3      0.15        80     151     171 ..     277     297 ..     271     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.044
                           Wzy_C_2 122 spenlaaklalarklihlsPepavierl.ilslallGdedeAeqilararalfpeedak 179
                                       ++  +++ +a+  k+i+  P+ + ++ + + +l + G+++eA+ i +++ a  pe+ ++
  gi|386001638|ref|YP_005919937.1|  41 DQGEYDEAIAAFDKAIEIDPQDTKTRVQkASLLIIMGRQAEALAIFDELTAEVPEDPEE 99 
                                       56777888888888888888888777552566778899999999999988887777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                           Wzy_C_2 152 slallGdedeAeqilararalfpe 175
                                       +l + G+ deA+  +++a a+f  
  gi|386001638|ref|YP_005919937.1| 194 ALEGIGRLDEAALAYEQAAAAFEL 217
                                       677889**************9964 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.069
                           Wzy_C_2 145 vierlilslallGdedeAeqilararalfpeedakw 180
                                       + +  +++l + G+++eA+  ++ra  +f +e ++ 
  gi|386001638|ref|YP_005919937.1| 228 FWKYKADALEGMGRHEEAAASYERAVEAFKDEIETH 263
                                       4555689999*******************9987765 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.15
                           Wzy_C_2 151 lslallGdedeAeqilarara 171
                                       ++l +lG+++eAe   arar 
  gi|386001638|ref|YP_005919937.1| 277 EALEALGRDSEAEAAFARARE 297
                                       68999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.61
# Mc/sec: 1503.12
//
Query:       gi|386001639|ref|YP_005919938.1|  [L=194]
Description: hypothetical protein Mhar_0944 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1226.82
//
Query:       gi|386001640|ref|YP_005919939.1|  [L=310]
Description: hypothetical protein Mhar_0945 [Methanosaeta harundinacea 6Ac]
Scores for 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-85  284.9   0.0    8.1e-85  284.7   0.0    1.0  1  DUF1848   Domain of unknown function (DUF1848)
  ------ inclusion threshold ------
      0.014   15.1   0.3      0.031   14.1   0.3    1.5  1  GAGA      GAGA factor


Domain annotation for each model (and alignments):
>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.7   0.0   9.1e-89   8.1e-85       1     265 []       2     269 ..       2     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 284.7 bits;  conditional E-value: 9.1e-89
                           DUF1848   1 iisaSrrtDipafyseWflnrlkegyvlvrnPfnkkqvsrvslspedvdlivFwtknpkpllkkleelkergiklyf 77 
                                       iisaS rtDipafy eWf +rl++gy+ v+nP+n++qv+rvsl pedvd +vFwt+n  p++ +l+++ + g ++++
  gi|386001640|ref|YP_005919939.1|   2 IISASYRTDIPAFYGEWFEKRLEAGYCSVSNPYNNRQVRRVSLLPEDVDGFVFWTRNLGPFMGRLTRVAQFGRPFVV 78 
                                       9**************************************************************************** PP

                           DUF1848  78 qfTltdyekelepnvpsleerietfkelseklgkerviwRyDPilltekltvelhlekfeklaeelkgytekvviSf 154
                                       q T+t+y+++lep     + +++++++++e +g+++ +wRyDPi++++ +++e+hle+fe+la++l+g +++vviSf
  gi|386001640|ref|YP_005919939.1|  79 QQTVTGYPRALEPAAVGAAVAVRQIRAVAEAYGPKAAVWRYDPIIFSSLTPAEFHLENFESLASALEGSVDEVVISF 155
                                       ***************************************************************************** PP

                           DUF1848 155 vdlykkvkrnlkk...k..lelrelseeekeelaeelaeiakklglelatCaekedlselgieknkCidkellerll 226
                                       +++y+k++rnl+    +  +++ ++ ++ k +la++l e+a+++g++l+ C++++ +   g ++++C+d++ l+ + 
  gi|386001640|ref|YP_005919939.1| 156 AQVYRKAARNLDLaarNfgFTWMDPPDDVKLDLASKLVEVARRHGMSLSVCSQRKYI-VPGAAAARCVDARRLAAVG 231
                                       ***********73444357999*******************************9965.56***************** PP

                           DUF1848 227 gkklkakkdkgqrkeCgCveskDiGayntClhgCvYCYA 265
                                       g++++ ++ kg+r+eCgC+e++DiG+y+tC+ gC++CYA
  gi|386001640|ref|YP_005919939.1| 232 GRRIR-ARLKGKRPECGCYEAVDIGEYDTCPAGCAFCYA 269
                                       99986.899*****************************9 PP

>> GAGA  GAGA factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   3.5e-06     0.031      24      42 ..     261     279 ..     257     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                                       -EE-TTT--EESSHHHHHH CS
                              GAGA  24 PAtCPiCqAviRqsRnLRR 42 
                                       PA C  C+Av+R    LRR
  gi|386001640|ref|YP_005919939.1| 261 PAGCAFCYAVLRREMALRR 279
                                       9*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1851.34
//
Query:       gi|386001641|ref|YP_005919940.1|  [L=90]
Description: hypothetical protein Mhar_0946 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 557.39
//
Query:       gi|386001642|ref|YP_005919941.1|  [L=80]
Description: hypothetical protein Mhar_0947 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.6   0.1    2.9e-06   27.4   0.1    1.0  1  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
     0.0002   21.1   1.3      0.097   12.6   0.0    2.3  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
     0.0006   19.6   0.4     0.0028   17.4   0.1    2.0  2  Rad50_zn_hook    Rad50 zinc hook motif
    0.00094   19.2   3.5     0.0034   17.4   3.5    2.0  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
     0.0054   16.5   1.7      0.018   14.8   0.3    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.017   15.2   1.1       0.29   11.2   0.2    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.023   14.1   0.2        2.4    7.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.025   14.7   0.5        0.4   10.8   0.2    2.2  2  DUF1272          Protein of unknown function (DUF1272)
      0.052   12.9   3.6       0.31   10.4   3.6    2.0  1  zf-TFIIB         Transcription factor zinc-finger
      0.057   12.8   0.1       0.78    9.2   0.0    2.1  2  zf_Rg            Reverse gyrase zinc finger
      0.066   13.3   2.7       0.84    9.8   0.1    2.8  3  Zn-ribbon_8      Zinc ribbon domain
      0.075   13.4   0.2       0.13   12.6   0.2    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.9   0.8       0.32   11.4   0.9    1.7  2  DnaJ_CXXCXGXG    DnaJ central domain
       0.13   11.8   1.7        1.4    8.5   0.3    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.17   12.2   1.1        5.8    7.3   0.5    2.2  2  zinc_ribbon_9    zinc-ribbon
       0.22   11.3   0.5       0.65    9.7   0.0    1.7  2  MafB19-deam      MafB19-like deaminase
       0.25   11.4   2.9        1.7    8.7   0.1    2.3  2  ADK_lid          Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   2.7e-09   2.9e-06       2      66 ..       6      68 ..       5      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                    MqsA_antitoxin  2 kCpvCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseellefrkkvna 66
                                      kCpvCg+  + +++    +   g +t + +v+++ C rCG  v+++e  +r+ e   ++r++  a
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVEKEVEK--LLRGGAHTALLKVRAEVCLRCGGRVYSQETVRRFEEIRSKLRRQDTA 68
                                      8****97655555543..45689999999*****************************9998555 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   9.2e-05     0.097       2      14 ..       5      18 ..       4      31 .. 0.75
   2 !    7.8   0.2    0.0029       3.1       2      10 ..      37      45 ..      36      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-05
                                      SB-TTT--B.BEEE CS
                      zf-FPG_IleRS  2 epCpRCwry.ierv 14
                                      e+Cp+C++  +e++
  gi|386001642|ref|YP_005919941.1|  5 EKCPVCGGElVEKE 18
                                      9******9944444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                                      SB-TTT--B CS
                      zf-FPG_IleRS  2 epCpRCwry 10
                                      e+C RC++ 
  gi|386001642|ref|YP_005919941.1| 37 EVCLRCGGR 45
                                      89*****85 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.7e-06    0.0028      21      39 ..       6      24 ..       4      29 .. 0.93
   2 ?   -0.0   0.0      0.77   8.1e+02      50      52 .]      56      58 ..      45      68 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                                      E-TTT--EE-HHHHHHHHH CS
                     Rad50_zn_hook 21 cCPlCgReldeehrseLik 39
                                      +CP+Cg el e++ ++L++
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVEKEVEKLLR 24
                                      9****************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.77
                                      ... CS
                     Rad50_zn_hook 50 eel 52
                                      ee+
  gi|386001642|ref|YP_005919941.1| 56 EEI 58
                                      332 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 !   17.4   3.5   3.3e-06    0.0034       1      21 [.       6      43 ..       6      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-06
                    DNA_ligase_ZBD  1 hCPvCGsavvRee.................geaiyRCt 21
                                      +CPvCG ++v +e                  e+ +RC 
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVEKEvekllrggahtallkvrAEVCLRCG 43
                                      6*********9886777776555555555448888885 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   1.7e-05     0.018       2      15 ..       5      18 ..       4      21 .. 0.90
   2 ?    0.9   0.1      0.39   4.1e+02       2      16 ..      37      51 ..      36      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      EE-SSS--EEEEEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkr 15
                                      ekCP Cgg+Lv+k+
  gi|386001642|ref|YP_005919941.1|  5 EKCPVCGGELVEKE 18
                                      79*********996 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                                      EE-SSS--EEEEEE- CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkrg 16
                                      e C  Cgg +  +++
  gi|386001642|ref|YP_005919941.1| 37 EVCLRCGGRVYSQET 51
                                      57999**99887766 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00027      0.29       3      18 ..       6      21 ..       4      24 .. 0.93
   2 ?    3.0   0.0       0.1   1.1e+02       4      15 ..      39      50 ..      36      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                            zf-ACC  3 KCpsCgemlykkeLer 18
                                      KCp Cg  l  ke+e+
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVEKEVEK 21
                                      9**************8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.1
                            zf-ACC  4 CpsCgemlykke 15
                                      C +Cg  +y +e
  gi|386001642|ref|YP_005919941.1| 39 CLRCGGRVYSQE 50
                                      667888888776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0022       2.4       4      13 ..       6      16 ..       3      21 .. 0.68
   2 ?    4.7   0.0      0.02        21      11      25 ..      31      45 ..      29      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                       zf-ribbon_3  4 rCPnCGa.pls 13
                                      +CP CG  +++
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGeLVE 16
                                      68888865655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                       zf-ribbon_3 11 plssddnvCpyCGtk 25
                                      +l+ ++ vC  CG++
  gi|386001642|ref|YP_005919941.1| 31 LLKVRAEVCLRCGGR 45
                                      67999********85 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00038       0.4      43      54 ..       6      17 ..       3      19 .. 0.87
   2 ?    1.9   0.0      0.22   2.4e+02      41      51 ..      36      46 ..      29      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                           DUF1272 43 vCPncgGelvkR 54
                                       CP cgGelv++
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVEK 17
                                      7********975 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                           DUF1272 41 envCPncgGel 51
                                      ++vC  cgG +
  gi|386001642|ref|YP_005919941.1| 36 AEVCLRCGGRV 46
                                      57999999976 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.6   0.00029      0.31       1      27 [.       6      44 ..       6      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                          zf-TFIIB  1 kCPkCqdele..eser............ggveidyCpqCrG 27
                                      kCP+C+ el+  e  +             +v  ++C +C+G
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVekE--VekllrggahtalLKVRAEVCLRCGG 44
                                      8*********662..43355566666568899999999999 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00074      0.78       9      24 ..       6      21 ..       4      25 .. 0.74
   2 ?    1.5   0.0      0.18   1.9e+02       7      19 ..      36      48 ..      31      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00074
                             zf_Rg  9 lCPNCgGdisdeRlek 24
                                       CP CgG++ ++ +ek
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVEKEVEK 21
                                      6*******97665554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
                             zf_Rg  7 eklCPNCgGdisd 19
                                       + C  CgG + +
  gi|386001642|ref|YP_005919941.1| 36 AEVCLRCGGRVYS 48
                                      5679999998865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0008      0.84      25      38 ..       3      17 ..       1      19 [. 0.76
   2 ?    2.9   0.1      0.11   1.2e+02      27      36 ..      37      46 ..      25      49 .. 0.74
   3 ?    1.5   0.4      0.31   3.2e+02       8      14 ..      39      45 ..      38      68 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0008
                       Zn-ribbon_8 25 pltaCPeCgs.evrr 38
                                      p ++CP Cg+  v++
  gi|386001642|ref|YP_005919941.1|  3 PFEKCPVCGGeLVEK 17
                                      5678******66666 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                       Zn-ribbon_8 27 taCPeCgsev 36
                                      ++C +Cg++v
  gi|386001642|ref|YP_005919941.1| 37 EVCLRCGGRV 46
                                      4588888865 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.31
                       Zn-ribbon_8  8 CeeCghe 14
                                      C +Cg +
  gi|386001642|ref|YP_005919941.1| 39 CLRCGGR 45
                                      4444433 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00013      0.13       4      37 ..       5      48 ..       3      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigq.......cvyCadCga...s 37
                                      + CP Cgg+ v ++ ++   ++++          C  Cg    s
  gi|386001642|ref|YP_005919941.1|  5 EKCPVCGGELVEKEVEKLLRGGAHtallkvrAEVCLRCGGrvyS 48
                                      57*******99999988887666689999887778888875443 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9    0.0003      0.32      15      51 ..       5      46 ..       2      54 .. 0.68
   2 ?    5.6   0.1      0.02        21      14      28 ..      36      50 ..      24      69 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                     DnaJ_CXXCXGXG 15 ktCktCkGsGvvreeqk..t..lgp.fvqqsqstCpeCeGtG 51
                                      ++C+ C+G+ v++e +k  +   ++ + +   + C +C+G+ 
  gi|386001642|ref|YP_005919941.1|  5 EKCPVCGGELVEKEVEKllRggAHTaLLKVRAEVCLRCGGRV 46
                                      68*******9644433222234344467777889*****975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                     DnaJ_CXXCXGXG 14 kktCktCkGsG.vvre 28
                                      ++ C +C+G+  + +e
  gi|386001642|ref|YP_005919941.1| 36 AEVCLRCGGRVyS-QE 50
                                      5679999998732.22 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0013       1.4       2      10 ..       6      14 ..       5      21 .. 0.77
   2 ?    2.7   0.1     0.086        90       2       9 ..      38      45 ..      37      58 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      kCP+Cg++ 
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGEL 14
                                      899999974 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.086
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      +C  Cg++
  gi|386001642|ref|YP_005919941.1| 38 VCLRCGGR 45
                                      45555553 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5    0.0055       5.8      22      33 ..       6      16 ..       2      19 .. 0.86
   2 ?    3.4   0.0     0.091        96      20      29 ..      36      44 ..      29      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0055
                     zinc_ribbon_9 22 vlCPhCgggFVE 33
                                      + CP Cgg  VE
  gi|386001642|ref|YP_005919941.1|  6 K-CPVCGGELVE 16
                                      5.*******999 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.091
                     zinc_ribbon_9 20 sdvlCPhCgg 29
                                      ++v C +Cgg
  gi|386001642|ref|YP_005919941.1| 36 AEV-CLRCGG 44
                                      467.****98 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00062      0.65      80     103 ..       5      28 ..       4      38 .. 0.83
   2 ?    1.0   0.1      0.32   3.3e+02      73      89 ..      30      46 ..      27      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00062
                       MafB19-deam  80 epCdmCagaivqaglkklvygagn 103
                                       e C++C+g +v+ ++ kl++g++ 
  gi|386001642|ref|YP_005919941.1|   5 EKCPVCGGELVEKEVEKLLRGGAH 28 
                                       68******************9984 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.32
                       MafB19-deam 73 atlyvtlepCdmCagai 89
                                      a l v  e+C  C+g +
  gi|386001642|ref|YP_005919941.1| 30 ALLKVRAEVCLRCGGRV 46
                                      6778999******8754 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0016       1.7      23      33 ..       6      16 ..       3      18 .. 0.87
   2 ?    2.9   0.3       0.1   1.1e+02       3      12 ..      38      48 ..      37      61 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                                      B-TTT--.-B- CS
                           ADK_lid 23 lCDkCGepLvq 33
                                      +C +CG++Lv 
  gi|386001642|ref|YP_005919941.1|  6 KCPVCGGELVE 16
                                      9********95 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
                                      E-TTT-.-EEE CS
                           ADK_lid  3 vCpkCG.rsYh 12
                                      vC  CG r+Y+
  gi|386001642|ref|YP_005919941.1| 38 VCLRCGgRVYS 48
                                      78888536887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 493.96
//
Query:       gi|386001643|ref|YP_005919942.1|  [L=395]
Description: hypothetical protein Mhar_0948 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-05   24.0   0.0    7.3e-05   23.1   0.0    1.5  1  DUF4062   Domain of unknown function (DUF4062)
  ------ inclusion threshold ------
       0.16   11.8   0.2       0.43   10.4   0.2    1.7  1  PPI_Ypi1  Protein phosphatase inhibitor


Domain annotation for each model (and alignments):
>> DUF4062  Domain of unknown function (DUF4062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   8.2e-09   7.3e-05       1      83 []       9     103 ..       9     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.2e-09
                           DUF4062   1 rvFiSStfrdlkeeRealieallelglep..........vgmee..faardqsqlelcleevdecd..ifililger 63 
                                       rvF++S   d+ +eR++l + + el+ +           +++e+   +   +++ +++ +++d+ +  ifi+i+ +r
  gi|386001643|ref|YP_005919942.1|   9 RVFVASP-GDVTKERRKLDDVVDELNRTWsdklgthldlITWERdvCPGVGEDPQDVINKQIDNYNydIFIGIIWKR 84 
                                       8*****9.8*********999996666657777777776666658878889999********765444********* PP

                           DUF4062  64 YGsipeksgiSyteeEyetA 83 
                                        G+  +++  S t eEye+A
  gi|386001643|ref|YP_005919942.1|  85 LGTA-TTRADSGTVEEYERA 103
                                       ****.************998 PP

>> PPI_Ypi1  Protein phosphatase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   4.8e-05      0.43      29      50 ..     136     162 ..     129     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.8e-05
                          PPI_Ypi1  29 NEgmnkkksK.....iCCIyhkprefd 50 
                                        +++nk k K      CCIy+  +ef+
  gi|386001643|ref|YP_005919942.1| 136 LDKINKFKAKlrlhnLCCIYEDIDEFG 162
                                       5789******99999******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 3027.51
//
Query:       gi|386001644|ref|YP_005919943.1|  [L=330]
Description: Putative methanogenesis marker protein 12 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1988.22
//
Query:       gi|386001645|ref|YP_005919944.1|  [L=265]
Description: LPPG:Fo 2-phospho-L-lactate transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-27   93.9   0.0    1.3e-26   93.6   0.0    1.1  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.0   7.1e-31   1.3e-26      76     256 ..      33     221 ..      13     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 7.1e-31
                                       SSSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEE.STTTGGGG-S.. CS
                           UPF0052  76 gdgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledGeeit.geskisearklk 150
                                       gd d + h+++  lL++     g sl+ea++ l+++lkv g+v+P+tddpv++++ + +Ge i+ +e ++ +++  +
  gi|386001645|ref|YP_005919944.1|  33 GDLDRSIHIFRSELLRE-----GlSLSEATARLCRALKVAGKVVPMTDDPVSTMISTPEGE-IHlQEFWVGRSG--R 101
                                       3778889**********.....99*************************************.666*****5554..5 PP

                                       .-EEE.EEEESTT----HHHHHHHHH-SE....EEE-SS-IIIIIHHHHTSCCHHHHHHH........-SSEEEEE- CS
                           UPF0052 151 apikr.vflepegaeaapevleaikeAdl....ivlgpGslytSiiPiLlvpgiaealre........skakkvlvs 214
                                       +++    f + e+a +  e l+a+++A      i++gp+++++Si+PiL+++g+++ l++        ++ +++++s
  gi|386001645|ref|YP_005919944.1| 102 PDVMGvRFRGIEDALPSLEFLAALERAAEvgepILIGPSNPVSSIGPILALRGVRDLLSKkgcgserrRRSRVIAIS 178
                                       8999989*****************9984335559************************54244444336889***** PP

                                       -SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S..-SEEEEE-S CS
                           UPF0052 215 nimtqkGetdgfsvsdhvkaieravg.....kgvakay..vdavlvnts 256
                                       +++       g +vs+++++ +ra g     +gva+ +  vd ++v  +
  gi|386001645|ref|YP_005919944.1| 179 PLVD------GRPVSGPAAKFMRAWGfpvtdQGVAEILgcVDLMVVSPG 221
                                       ***5......****************98887666665577888887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 1866.38
//
Query:       gi|386001646|ref|YP_005919945.1|  [L=192]
Description: ZPR1-related zinc finger protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-35  120.4   0.0      8e-35  120.0   0.0    1.1  1  zf-ZPR1     ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.027   14.6   0.1      0.062   13.5   0.1    1.6  1  zf-piccolo  Piccolo Zn-finger


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0   8.9e-39     8e-35       1     158 [.       7     163 ..       7     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 8.9e-39
                           zf-ZPR1   1 slCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetat 77 
                                       s+Cp C+ ++      + +iP+f+e +i++ +C++Cg+k +++  +++ ++  +r+ +++e+ +dln +v++S+++t
  gi|386001646|ref|YP_005919945.1|   7 SSCPICS-AEIAFDWETKEIPHFGEALIIAGVCDACGFKLSDTILLSQGDP--VRYAITIEEVADLNARVIRSTSGT 80 
                                       58****6.7788888888*********************************..************************ PP

                           zf-ZPR1  78 veipeleleippg.tlegrlttvEGlLeqikeele.keegdqaer..edeekekieeflekleeliegeepftlild 150
                                       +++pel+++++pg ++e+++++vEG+L+++++ +     + +a++  ++e+  + e ++e++++++eg  p+tlil+
  gi|386001646|ref|YP_005919945.1|  81 IRLPELGIDVEPGpASEAYISNVEGVLQRVRDIVLfA--TRSARDagAEENVCRGEWIIERIDRAMEGVGPLTLILE 155
                                       *********************************9642..3333334333789999********************** PP

                           zf-ZPR1 151 DpagnSfi 158
                                       Dp+gnS+i
  gi|386001646|ref|YP_005919945.1| 156 DPLGNSAI 163
                                       ******98 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.9e-06     0.062       2      40 ..       8      47 ..       7      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-06
                        zf-piccolo  2 lCplCktelnvgs..keppnyntCteCkkqvCnlCGFnptp 40
                                      +Cp+C +e+ +    ke p + +       vC +CGF  ++
  gi|386001646|ref|YP_005919945.1|  8 SCPICSAEIAFDWetKEIPHFGEALI-IAGVCDACGFKLSD 47
                                      7*****88876543288899988765.678*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1279.82
//
Query:       gi|386001647|ref|YP_005919946.1|  [L=120]
Description: hypothetical protein Mhar_0952 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-11   42.8   0.1    6.9e-11   42.3   0.1    1.2  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1   3.9e-15   6.9e-11       1      72 []      37     110 ..      37     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 3.9e-15
                                       EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                              SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                       v+++e++++e  +ei+ +++ g+ V+++++ + +  + +  ++ +l+  v +l+Gdi+ +g++ ++++P+ ++i
  gi|386001647|ref|YP_005919946.1|  37 VKMAELNDLEVLPEIKTEIERGNLVLVDISPMRRekDLLDEAIGELKASVEDLRGDIAGLGDNLVIVVPRRMRI 110
                                       78999****************************999**********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 885.63
//
Query:       gi|386001648|ref|YP_005919947.1|  [L=61]
Description: hypothetical protein Mhar_0953 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   15.7   0.7      0.014   15.5   0.7    1.1  1  SirB      Invasion gene expression up-regulator, SirB


Domain annotation for each model (and alignments):
>> SirB  Invasion gene expression up-regulator, SirB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.7   7.8e-07     0.014      76     115 ..      13      52 ..       8      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-07
                              SirB  76 llvvyivlgvvalkrakskklrllafvlAlvvflyivslA 115
                                       +lv+  +l ++ ++++  + +r ++fv+A+++f++++ lA
  gi|386001648|ref|YP_005919947.1|  13 GLVLLMILLLILVQTEAPEPMRPAGFVVAVLAFMILMGLA 52 
                                       56666667777777999********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 504.35
//
Query:       gi|386001649|ref|YP_005919948.1|  [L=333]
Description: FO synthase subunit 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-12   48.1   0.0    4.1e-12   46.8   0.0    1.7  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   2.3e-16   4.1e-12       1     165 [.      13     180 ..      13     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.3e-16
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.............TTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.............pdfv 64 
                                       ++vt  C++rC +C+++     ++rgr++  +e +++++++ a+ g  e +++ ge                 +d++
  gi|386001649|ref|YP_005919948.1|  13 IPVTDVCRNRCGYCSFR-----RDRGRIIGRREAIDLLDRG-ASAGSSEALFSLGEAPWEvsgfaeilkgagyDDLI 83 
                                       67999************.....69*****************.8***7776666444444445555555555558888 PP

                                       HHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  65 ellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                        +l +l++la  ++ +   tn++l+++e ++rl +++   + l le++ + + ++   +g+ +  +l+a+ ++ e+ 
  gi|386001649|ref|YP_005919948.1|  84 GYLIELSELA-LERGLLPHTNAGLLSKEEMRRLMPYN-ASMGLMLETTAEVEAHRSS-PGKRPLLRLAAMAAAGELK 157
                                       8888888887.**************************.************9999999.******************* PP

                                       SETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 142 ikrvvdrivglpGendeeleelle 165
                                       i+  +++i+++ Ge+++++   ++
  gi|386001649|ref|YP_005919948.1| 158 IP-FTTGILVGIGETEADRLRSID 180
                                       **.**************9887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2366.50
//
Query:       gi|386001650|ref|YP_005919949.1|  [L=149]
Description: hypothetical protein Mhar_0955 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-53  179.9   0.7    2.6e-53  179.7   0.7    1.0  1  UPF0179   Uncharacterised protein family (UPF0179)


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.7   0.7   1.4e-57   2.6e-53       1     140 []       7     147 ..       7     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 1.4e-57
                           UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapieali 77 
                                       +itLig+klA+ G+eFi+  +++eCe+Ckl+++C+nLe+gr+Yri ++r + +h+C++he gv+avev+e+pi+a+i
  gi|386001650|ref|YP_005919949.1|   7 QITLIGTKLATIGMEFIFNAPSPECETCKLRNTCTNLESGRRYRILGIRGELVHDCPIHEAGVRAVEVTESPIIAAI 83 
                                       59*************************************************************************** PP

                           UPF0179  78 eskkavegskitleseeCdevecesyelcepeglkegekvkivevlgeiee.ckkgrslkkvel 140
                                       +++ka++gsk  le+++C+++ec++yelc+p glkeg++++iv+ +ge++e c+ g++lk+vel
  gi|386001650|ref|YP_005919949.1|  84 DARKAFAGSKTVLEPPRCERYECTMYELCHPVGLKEGDRCTIVDLVGEAPEeCEIGNKLKLVEL 147
                                       **************************************************99**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 940.73
//
Query:       gi|386001651|ref|YP_005919950.1|  [L=343]
Description: Glycerol-1-phosphate dehydrogenase [NAD(P)] [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-69  234.0   1.8    2.9e-69  233.6   1.8    1.2  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    2.7e-23   82.4   5.8    4.6e-22   78.3   5.8    2.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.2e-06   27.9   1.2    4.3e-06   26.1   1.2    1.8  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.6   1.8   4.8e-73   2.9e-69       2     250 .]       9     266 ..       8     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: 233.6 bits;  conditional E-value: 4.8e-73
                          Fe-ADH_2   2 igegaleklgellkelelk.kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       +g+g+ ++++e+ ++l+l   +l+v++  t +++g ++++ l+e g +++++   ++ +++eeve+  + ++  ++ 
  gi|386001651|ref|YP_005919950.1|   9 VGSGVAREVAEISRDLKLAgGALIVTGPRTCELVGGEISRRLEEGGFETALM--ITKFSKIEEVERAERMAADMGAG 83 
                                       899*************9865999***********************999855..466777888888888888889** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrll 154
                                       ++v+vGgG+ iD+ak++s + +vp+vs+pTaaS+DG++s +asl+ dg++++v +a+aP++++aD+ ++++AP+rll
  gi|386001651|ref|YP_005919950.1|  84 FLVGVGGGRSIDVAKLASVRVGVPFVSIPTAASHDGICSAQASLTIDGETTSV-SAQAPFGIVADTAIISQAPKRLL 159
                                       **************************************************999.9********************** PP

                          Fe-ADH_2 155 asGvGDllgkytaladwklan........evseplaklsaamvqeaaeklve...dkketealeellealalsgigi 220
                                       a+G+GD+++++ta+ dwkla+        e++  l++++a+m++e+ ++l     + +++ + + + +++a+s++g+
  gi|386001651|ref|YP_005919950.1| 160 AAGCGDIISNITAVRDWKLAHrlrgeeysEYASALSEMTARMIVETSSELKPgleESARIVVKALISSGVAMSIAGS 236
                                       *********************9999977777889999999999999999865331333444444455557******* PP

                          Fe-ADH_2 221 srpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       srpaSGsEH+++Ha++++++ +alHGe +G
  gi|386001651|ref|YP_005919950.1| 237 SRPASGSEHKFAHAINRIEPGKALHGELCG 266
                                       ***************************987 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   5.8   7.7e-26   4.6e-22       1     278 [.       4     269 ..       4     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 7.7e-26
                                       -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEE.E.EEE-S---HHHHHHHHT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgak.ralivtdkgslkksglldkvlesleeagievt.vfdgvepnptleeveeaaa 75 
                                       P+ +v g+g+++e++e  ++l++   alivt++++  ++ +  ++ + lee g+e + +++++    ++eeve+a +
  gi|386001651|ref|YP_005919950.1|   4 PRLVVVGSGVAREVAEISRDLKLAgGALIVTGPRTC-EL-VGGEISRRLEEGGFETAlMITKF---SKIEEVERAER 75 
                                       667899**********9999984449********87.55.889**************665555...9********** PP

                                       TS-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSE CS
                            Fe-ADH  76 lareegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeege 152
                                       +a + ga ++++vGGG +iD+AK++++ ++                  +p++ iPT a+ +  +++ a +t +   e
  gi|386001651|ref|YP_005919950.1|  76 MAADMGAGFLVGVGGGRSIDVAKLASVRVG------------------VPFVSIPTAASHDGICSAQASLTIDG--E 132
                                       ******************************..................***********************544..5 PP

                                       EEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH........T---TTSSB--HHHHHHHHHHH CS
                            Fe-ADH 153 klsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvsk........kanplsdalaleairliaknle 221
                                        +s++     P  ++ D++++ ++Pkr++aa+ +D+++        k        + +++  al++  +r+i++   
  gi|386001651|ref|YP_005919950.1| 133 TTSVS--AQAPFGIVADTAIISQAPKRLLAAGCGDIISNITAVRDWKlahrlrgeEYSEYASALSEMTARMIVETSS 207
                                       67777..668999**************************99987666344444445555555555555555555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.C.GGG.GGS-HHHHH CS
                            Fe-ADH 222 ravadgedleareqmllastlaglafsnaglg.....avHalahalgalf.gip.hglanaill 278
                                       ++   ++  e  + ++ a + +g+a+s ag +       H +aha+  +  g + hg+++++  
  gi|386001651|ref|YP_005919950.1| 208 ELK--PGLEESARIVVKALISSGVAMSIAGSSrpasgSEHKFAHAINRIEpGKAlHGELCGLGT 269
                                       543..3333555555555555999999999988888899*****99994332224777776533 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.2   7.2e-10   4.3e-06      33     253 ..      84     308 ..      60     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.2e-10
                                       EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS- CS
                      DHQ_synthase  33 llialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktLp 109
                                        l+ +GGG   D+a +++  ++ Gv fv +Pt+  a  D    +  ++ ++     + a   P  +++d+++++  p
  gi|386001651|ref|YP_005919950.1|  84 FLVGVGGGRSIDVAKLAS--VRVGVPFVSIPTA--ASHDGICSAQASLTIDGETTSVSA-QAPFGIVADTAIISQAP 155
                                       689***********9864..677*********7..889999999999999888888866.78*************** PP

                                       HHHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHH.......HHHHHHHHHHHHHCCTTTTGGGG CS
                      DHQ_synthase 110 erelraGlaEviK.yalikdeelfelleenaeallkeeeeealeeli.......arsievkaevveeDekekglral 178
                                       +r l+aG++++i  +++++d +l ++l+ ++ +  ++  +e ++++i       +  +e  a++v +    +g+ + 
  gi|386001651|ref|YP_005919950.1| 156 KRLLAAGCGDIISnITAVRDWKLAHRLRGEEYSEYASALSEMTARMIvetsselKPGLEESARIVVKALISSGVAMS 232
                                       ***********9627899*********99998888855555555555444444422333334555555544444433 PP

                                       ........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT.. CS
                      DHQ_synthase 179 ........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkel.l 246
                                                   H ++Hai ++    k lHGe   +G ++ ++l          + + +++ l+k+g p+s  +  l
  gi|386001651|ref|YP_005919950.1| 233 iagssrpaSGSEHKFAHAINRIEPG-KALHGELCGLGTIVMMYLH-------GGDWRMIREALEKVGAPTSAADIgL 301
                                       122222117788********99876.************9999887.......2345678888888888888777644 PP

                                       -HHHHHH CS
                      DHQ_synthase 247 eveelle 253
                                       + e+++e
  gi|386001651|ref|YP_005919950.1| 302 AEETVIE 308
                                       4455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2094.92
//
Query:       gi|386001652|ref|YP_005919951.1|  [L=252]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-30  106.7   0.0    2.1e-30  106.0   0.0    1.4  1  ABC_tran      ABC transporter
    1.1e-06   28.7   0.0     0.0069   16.2   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.5e-05   23.4   0.4      0.001   19.5   0.4    2.2  1  AAA           ATPase family associated with various cellular 
    0.00084   19.6   0.1     0.0029   17.9   0.1    2.0  1  AAA_22        AAA domain
     0.0013   19.0   0.3      0.016   15.5   0.1    2.2  2  AAA_28        AAA domain
     0.0013   19.1   0.0     0.0023   18.4   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0038   16.7   0.0        1.7    8.0   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0056   16.6   0.0     0.0092   15.9   0.0    1.3  1  Rad17         Rad17 P-loop domain
     0.0064   17.0   0.0       0.01   16.3   0.0    1.3  1  AAA_23        AAA domain
     0.0065   16.4   0.0      0.012   15.5   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0078   15.6   0.0       0.26   10.6   0.0    2.4  3  Mg_chelatase  Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.012   15.6   0.4      0.034   14.1   0.1    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.013   15.2   0.0       0.45   10.2   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.018   15.0   0.0      0.042   13.8   0.0    1.6  1  NACHT         NACHT domain
      0.021   15.4   0.3      0.056   14.0   0.3    1.9  1  AAA_18        AAA domain
      0.022   14.5   0.1       0.14   11.9   0.0    2.0  2  AAA_24        AAA domain
       0.03   14.2   0.0       0.17   11.8   0.0    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
      0.031   14.0   0.0      0.052   13.3   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
      0.043   14.0   0.0      0.099   12.8   0.0    1.7  1  AAA_33        AAA domain
       0.06   13.6   0.1       0.21   11.8   0.1    1.9  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.077   12.8   0.0       0.16   11.7   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.098   12.4   0.0       0.18   11.5   0.0    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.13   12.2   0.0       0.23   11.5   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
        0.2   12.0   0.0       0.43   11.0   0.0    1.5  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   2.8e-33   2.1e-30       1     136 [.      24     163 ..      24     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 2.8e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++v+l+++  e + ++G++G+GK+tLl+++agl++pt+G +lldg++++         + g+++qe +lfp  t+ 
  gi|386001652|ref|YP_005919951.1|  24 LRDVNLSVYDKEFICLLGPSGCGKTTLLRIMAGLERPTSGAVLLDGEPIEG-----PGPQRGMVFQEYSLFPWRTIL 95 
                                       689*******************************************99998.....99999**************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e+ e++ ++++ +gl +++++      ++LSgG+kqrva++ral+++p+ l++DEp+
  gi|386001652|ref|YP_005919951.1|  96 DNvafglelkgvskaERHEKARRYITAVGLAGFENSYP----HELSGGMKQRVAIVRALVNNPRALFMDEPF 163
                                       ************98888888999999999999999998....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.3e-06    0.0069       1      24 [.      36      59 ..      36     121 .. 0.81
   2 !   10.7   0.0   0.00046      0.34     234     298 ..     133     195 ..     111     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      + +l Gp g+GK++LL+++ +l r
  gi|386001652|ref|YP_005919951.1| 36 FICLLGPSGCGKTTLLRIMAGLER 59
                                      5789***************99844 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00046
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll..ellkelsrngaQviltTHS 298
                                       ++elS G+k+  a++ al   +   + l+ DEp   L+   +r ++  ell++ ++    vi++THS
  gi|386001652|ref|YP_005919951.1| 133 PHELSGGMKQRVAIVRALVNNP---RALFMDEPFGALDA-QTRNVMqaELLRIWQEQQKTVIFVTHS 195
                                       6899*******99999999999...89************.6666666666655555556*******9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   1.4e-06     0.001       1     113 [.      37     197 ..      37     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
                                       EEEESSTTSSHHHHHHHHHHH.........HTHE..........................................E CS
                               AAA   1 vllyGppGtGKTllakavake.........lgve..........................................f 26 
                                       ++l Gp G+GKT+l + +a           l  +                                           
  gi|386001652|ref|YP_005919951.1|  37 ICLLGPSGCGKTTLLRIMAGLerptsgavlL--DgepiegpgpqrgmvfqeyslfpwrtildnvafglelkgvskaE 111
                                       689****************985555444431..04444455555555555666666666666666544444444440 PP

                                       EEEETTTCSSS...................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  27 leisgsellsk...................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                                                     y  e +  +++ ++ +++   +p  lf+DE      ++       ++
  gi|386001652|ref|YP_005919951.1| 112 ----------RhekarryitavglagfensYPHELSGGMKQRVAIVRALVnNPRALFMDEPFGALDAQ------TRN 172
                                       ..........244455555555555555558888888888888777766667999***9966666666......688 PP

                                       HHHHHHHHHHHHTTTSSSTEEEEEEESSGG CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnrpd 113
                                        ++++Ll+ +++++k     +vi +t+++d
  gi|386001652|ref|YP_005919951.1| 173 VMQAELLRIWQEQQK-----TVIFVTHSVD 197
                                       999999999999999.....4666666544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.9e-06    0.0029       4      70 ..      33     108 ..      30     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.9e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralgl 66 
                                       ++ ++++ G+sG+GKTtllr ++      +                  ++++ + ++  s+  ++++l +++  l+l
  gi|386001652|ref|YP_005919951.1|  33 DKEFICLLGPSGCGKTTLLRIMAGLER--PT--SgavlldgepiegpgPQRG-MVFQEYSLFPWRTILDNVAFGLEL 104
                                       5789***************98887652..22..1335577777766633333.344445555577777777777777 PP

                            AAA_22  67 elka 70 
                                       ++ +
  gi|386001652|ref|YP_005919951.1| 105 KGVS 108
                                       6666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.1e-05     0.016       2      22 ..      37      57 ..      36     116 .. 0.89
   2 ?    1.6   0.0      0.38   2.8e+02      67      89 ..     177     202 ..     146     244 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      i+++G++++GKTtll+ +a  
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRIMAGL 57
                                      99**************99843 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.38
                            AAA_28  67 eaaa...aankvlfcDrglldtlaYa 89 
                                       e  +   +++k++++ + ++d+++Y+
  gi|386001652|ref|YP_005919951.1| 177 ELLRiwqEQQKTVIFVTHSVDEAIYL 202
                                       11113334556666666666666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     3e-06    0.0023      25     107 ..      35     162 ..      19     199 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdql...esa...ipy..salaqalareellrqlldeaes 91 
                                       e + l G+sG+GK++l+r  +  le+   g+++l g+  +    +++    +y   ++ ++l++   +  +l   ++
  gi|386001652|ref|YP_005919951.1|  35 EFICLLGPSGCGKTTLLRIMA-GLERPtsGAVLLDGEPIEGpgpQRGmvfQEYslFPWRTILDN-VAFGLELKGVSK 109
                                       7899*************8887.566664445555555555544433444544433445555544.555555544333 PP

                            AAA_16  92 aeleawrekleeala.....................................a 107
                                       ae+ + +++  +a++                                     +
  gi|386001652|ref|YP_005919951.1| 110 AERHEKARRYITAVGlagfensyphelsggmkqrvaivralvnnpralfmdeP 162
                                       33333333333333345555554444444444444444444444444433333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0053       3.9      21      41 ..      31      51 ..      15      55 .. 0.80
   2 !    8.0   0.0    0.0023       1.7     135     213 ..     134     211 ..      92     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0053
                                      ETTSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 21 pfsksftaivGpNGSGKsnll 41
                                       ++k+f +++Gp G+GK+ ll
  gi|386001652|ref|YP_005919951.1| 31 VYDKEFICLLGPSGCGKTTLL 51
                                      46899*************987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0023
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH.HHHHH..HHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv.aellk..eksknaQfivislreemlekadkl 208
                                       ++LSgG k+ v  a++ A+ + +p++l+ +De   aLD++ ++ + aell+  ++++++ ++v+   +e +  ad++
  gi|386001652|ref|YP_005919951.1| 134 HELSGGMKQRV--AIVRALVN-NPRALF-MDEPFGALDAQTRNVMqAELLRiwQEQQKTVIFVTHSVDEAIYLADRV 206
                                       57999999855..55666654.666665.8*********99987736677654444444455555556777777887 PP

                                       EEEEE CS
                                       xxxxx RF
                             SMC_N 209 vgvtk 213
                                       v ++ 
  gi|386001652|ref|YP_005919951.1| 207 VIMSA 211
                                       77666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0092      39      66 ..      28      55 ..      15      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLs 66
                                       L    k+ + + GPsGCgk+t +++++
  gi|386001652|ref|YP_005919951.1| 28 NLSVYDKEFICLLGPSGCGKTTLLRIMA 55
                                      5666677888899************987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-05      0.01       5      37 ..      19      52 ..      15      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                            AAA_23  5 enfrsfrdqeidF.skgltlItGpNGaGKTTild 37
                                      + f  +rd+++   +k + ++ Gp G+GKTT+l+
  gi|386001652|ref|YP_005919951.1| 19 KRFEALRDVNLSVyDKEFICLLGPSGCGKTTLLR 52
                                      6677788888888899****************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-05     0.012      88     121 ..      22      56 ..       7      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       e+l++++  + d ++++l+G+SG GK+tL+  +++
  gi|386001652|ref|YP_005919951.1|  22 EALRDVNLSVYDkEFICLLGPSGCGKTTLLRIMAG 56 
                                       555555544444499***************98876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00035      0.26      10      49 ..      22      61 ..      13      74 .. 0.79
   2 ?   -2.4   0.0       3.5   2.6e+03     179     196 ..     130     147 ..     124     155 .. 0.82
   3 ?    2.0   0.0      0.15   1.1e+02     124     185 ..     177     242 ..     153     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                      Mg_chelatase 10 eakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                      ea r +++++  +  + l+Gp+G+GKt l + +++l  p 
  gi|386001652|ref|YP_005919951.1| 22 EALRDVNLSVYDKEFICLLGPSGCGKTTLLRIMAGLERPT 61
                                      56677888888888999*************9999886665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                      Mg_chelatase 179 erYlsklsgplldRidlq 196
                                       ++Y + lsg +  R+ + 
  gi|386001652|ref|YP_005919951.1| 130 NSYPHELSGGMKQRVAIV 147
                                       679999999999999886 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.15
                      Mg_chelatase 124 evLRePledge..vtisrakakvefparfqlvaamNpcpcgklkdke..kectcsekeierYlskl 185
                                       e LR   e+++  + ++ +  ++ + a+  +++++ p + +++ d e  +  +++++e++rY++++
  gi|386001652|ref|YP_005919951.1| 177 ELLRIWQEQQKtvIFVTHSVDEAIYLADRVVIMSARPGQISEIIDVEipRPRVRTSAEVNRYREQV 242
                                       557766666542266788888999*************99999877552245566788889998876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.5e-05     0.034       2      21 ..      37      56 ..      36      67 .. 0.89
   2 ?   -1.4   0.0       2.8   2.1e+03      63      64 ..     211     212 ..     167     249 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-05
                                      EEEE--SSSSHHHHHHHGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaa 21
                                      ++L+Gp+G+gK++l + +a 
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRIMAG 56
                                      69*************99886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                                       -- CS
                             AAA_5  63 ar 64 
                                       ar
  gi|386001652|ref|YP_005919951.1| 211 AR 212
                                       33 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0006      0.45      11      43 ..      21      54 ..      15      65 .. 0.84
   2 ?    3.2   0.0      0.08        60     300     365 ..     139     195 ..      96     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0006
                            AAA_15 11 FRslkdveidlsee.ltvliGkNnsGKSsileal 43
                                      F +l+dv +++ ++ + +l G+ ++GK+++l+++
  gi|386001652|ref|YP_005919951.1| 21 FEALRDVNLSVYDKeFICLLGPSGCGKTTLLRIM 54
                                      567788777776667****************987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.08
                            AAA_15 300 GvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       G+++ + ++  ++++ +          l+++EP   L  q  +v+   l+++ ++ ++ vi+ THS
  gi|386001652|ref|YP_005919951.1| 139 GMKQRVAIVRALVNNPRA---------LFMDEPFGALDAQTRNVMQAELLRIWQEQQKTVIFVTHS 195
                                       555555555555555555.........999999999999**************************9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05     0.042       3      19 ..      37      53 ..      35      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                                      EEEEC-TTTCHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqk 19
                                      ++l G++G+GKTtLl+ 
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRI 53
                                      89*************74 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   7.5e-05     0.056       1      19 [.      37      55 ..      37     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                            AAA_18  1 IlltGtpGvGKttlakeLs 19
                                      I+l G++G+GKttl +  +
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRIMA 55
                                      9*************99775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.14       5      23 ..      37      57 ..      33      81 .. 0.83
   2 ?    0.3   0.0      0.67     5e+02     113     134 ..     177     198 ..     162     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                            AAA_24  5 iliyGpsgiGKTtlakel..g 23
                                      i++ Gpsg GKTtl++ +   
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRIMagL 57
                                      89************9988662 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.67
                            AAA_24 113 rllkklqelrknvifiahektr 134
                                       +ll+  qe +k+vif+ h+  +
  gi|386001652|ref|YP_005919951.1| 177 ELLRIWQEQQKTVIFVTHSVDE 198
                                       4555566777799999998655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.17      20      40 ..      34      54 ..      19      64 .. 0.79
   2 ?    0.1   0.0      0.83   6.2e+02      45      65 ..     183     203 ..     140     251 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                          ATPase_2 20 neiyfiYGpegsGKtaLlkei 40
                                      +e++ + Gp g+GKt+Ll+ +
  gi|386001652|ref|YP_005919951.1| 34 KEFICLLGPSGCGKTTLLRIM 54
                                      6788999***********965 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.83
                          ATPase_2  45 edkdkyviyyialreesiskl 65 
                                       ++++k vi+++   +e+i  +
  gi|386001652|ref|YP_005919951.1| 183 QEQQKTVIFVTHSVDEAIYLA 203
                                       333444455544444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.9e-05     0.052      21      63 ..       7      50 ..       1      59 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                         IstB_IS21 21 didfraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshl 63
                                        d +++ s++ +++++L+  +  + +ke i+llGpsG GK+ l
  gi|386001652|ref|YP_005919951.1|  7 IRDLSKSFSVKGKRFEALRDVNLsVYDKEFICLLGPSGCGKTTL 50
                                      5566677778888889998777548899**************87 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.099       3      33 ..      38     103 ..      36     208 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt...............................l 33 
                                        l G++G+GK+tl++ ++  +     avll+                                  +
  gi|386001652|ref|YP_005919951.1|  38 CLLGPSGCGKTTLLRIMAGLERptsgAVLLDGEPiegpgpqrgmvfqeyslfpwrtildnvafglE 103
                                       578***********9874322234677777655556666666666666666666666555555552 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00028      0.21      62      84 ..     152     174 ..     131     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatl 84 
                                       +++r +f+DE F+ lD+++++ +
  gi|386001652|ref|YP_005919951.1| 152 NNPRALFMDEPFGALDAQTRNVM 174
                                       679**************998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.16      21      39 ..      33      51 ..      19      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                            AAA_29 21 lkgatlltGpsGsGKSTll 39
                                       k+++ l GpsG GK+Tll
  gi|386001652|ref|YP_005919951.1| 33 DKEFICLLGPSGCGKTTLL 51
                                      3448899***********8 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.18       4      24 ..      37      57 ..      34      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      i l+G++g+GKttL + + g 
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRIMAGL 57
                                      789***********9988775 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.23      18      40 ..      31      55 ..      11      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                      H..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgla 40
                                      +  +++i+L G+ G+GKTtl r +a
  gi|386001652|ref|YP_005919951.1| 31 VydKEFICLLGPSGCGKTTLLRIMA 55
                                      134667***************9875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00057      0.43       1      18 [.      37      54 ..      37      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00057
                      RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                      i+l Gpsg+GK+tl + +
  gi|386001652|ref|YP_005919951.1| 37 ICLLGPSGCGKTTLLRIM 54
                                      799***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1514.34
//
Query:       gi|386001653|ref|YP_005919952.1|  [L=264]
Description: Iron-sulfur cluster-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-13   49.3  10.5    4.1e-08   32.7   5.0    2.5  2  Fer4      4Fe-4S binding domain
    2.6e-10   39.9   9.2    4.2e-08   32.9   4.1    2.7  2  Fer4_6    4Fe-4S binding domain
    2.2e-07   30.9   5.6      4e-07   30.1   5.6    1.4  1  Fer4_21   4Fe-4S dicluster domain
    2.7e-07   30.6   4.8    1.3e-06   28.4   5.3    1.9  2  Fer4_10   4Fe-4S dicluster domain
    6.1e-07   29.5   3.9    1.5e-06   28.3   3.9    1.7  1  Fer4_9    4Fe-4S dicluster domain
    7.3e-07   29.7   5.9    3.1e-06   27.7   5.7    2.1  2  Fer4_7    4Fe-4S dicluster domain
    8.2e-07   29.9   5.3     0.0024   18.7   1.0    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    2.5e-05   24.1   1.4    2.5e-05   24.1   1.4    2.6  2  Fer4_2    4Fe-4S binding domain
    0.00064   20.4   9.1      0.018   15.8   9.1    2.7  1  Fer4_15   4Fe-4S single cluster domain
     0.0045   17.8   5.8     0.0045   17.8   5.8    3.0  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.017   15.6   2.2       0.79   10.3   1.0    2.5  2  Fer4_17   4Fe-4S dicluster domain
      0.085   13.4   1.3      0.085   13.4   1.3    3.1  2  Fer4_4    4Fe-4S binding domain
       0.11   12.9   4.3        1.7    9.2   1.5    2.5  2  Fer4_8    4Fe-4S dicluster domain
        0.8   10.6   6.6       0.62   10.9   0.7    2.3  2  Fer4_22   4Fe-4S dicluster domain
        2.6    8.2   7.3        7.3    6.8   4.9    2.7  2  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   5.0   3.5e-11   4.1e-08       1      24 []       9      32 ..       9      32 .. 0.95
   2 !   19.6   0.2   4.9e-07   0.00058       2      23 ..      40      61 ..      39      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.5e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++ide +C gCG+Cv +CP +AI+
  gi|386001653|ref|YP_005919952.1|  9 IKIDEALCDGCGNCVLACPENAIE 32
                                      68*********************6 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 4.9e-07
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      v+ e++C g GaC+  CP+gA+
  gi|386001653|ref|YP_005919952.1| 40 VVRESLCDGLGACIGDCPTGAL 61
                                      6889*****************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   4.1   3.5e-11   4.2e-08       1      24 []       8      31 ..       8      31 .. 0.96
   2 !    9.1   0.2    0.0012       1.4       4      24 .]      41      61 ..      39      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.5e-11
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++ id+ +C+gCg+Cv +CPe+ai
  gi|386001653|ref|YP_005919952.1|  8 IIKIDEALCDGCGNCVLACPENAI 31
                                      689********************8 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      + +++C+g g+C+  CP+ga+
  gi|386001653|ref|YP_005919952.1| 41 VRESLCDGLGACIGDCPTGAL 61
                                      6789***************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   5.6   3.3e-10     4e-07       2      59 .]      10      63 ..       9      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.3e-10
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      +ide+ C gCg+C++aC++   +aiei + +   v+e+ C G   C+  CP+ ++++m
  gi|386001653|ref|YP_005919952.1| 10 KIDEALCDGCGNCVLACPE---NAIEIVGGKAKVVRESLCDGLGACIGDCPT-GALSM 63
                                      69****************7...88888888898999***************6.88877 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   5.3   1.1e-09   1.3e-06       2      56 .]       9      57 ..       8      57 .. 0.92
   2 ?   -2.8   0.0       5.9   7.1e+03      19      24 ..     108     113 ..     106     132 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.1e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      ++id+  C +Cg+Cv aCP       +  e+ +++a+ +  + C+g gaC+  CP
  gi|386001653|ref|YP_005919952.1|  9 IKIDEALCDGCGNCVLACPE------NAIEIVGGKAKVVRESLCDGLGACIGDCP 57
                                      789*****************......88888888889999999***********9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.9
                           Fer4_10  19 CPadlt 24 
                                       CP+ l+
  gi|386001653|ref|YP_005919952.1| 108 CPMALR 113
                                       999553 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   3.9   1.2e-09   1.5e-06       2      50 ..      16      60 ..      15      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.2e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      C gCg+Cv aCp ++++   ++ k+  +      C g gaC+  Cp+ga
  gi|386001653|ref|YP_005919952.1| 16 CDGCGNCVLACPENAIEIVGGKAKVVRES----LCDGLGACIGDCPTGA 60
                                      ****************9999999988754....6*************97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   5.7   2.6e-09   3.1e-06       2      52 .]      16      60 ..      15      60 .. 0.88
   2 !   10.3   0.2   0.00069      0.82       2      26 ..      46      70 ..      45      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.6e-09
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C gCg+Cv aCp +aie+         +  +++++ C g gaC+  CPtga
  gi|386001653|ref|YP_005919952.1| 16 CDGCGNCVLACPENAIEIVGG------KAKVVRESLCDGLGACIGDCPTGA 60
                                      ******************764......233567899*************98 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00069
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek 26
                                      C g gaC   Cp++a++++e+e e+
  gi|386001653|ref|YP_005919952.1| 46 CDGLGACIGDCPTGALSMEEREAEE 70
                                      8888999999999999999985543 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.0     2e-06    0.0024       2      18 ..      16      32 ..      15      44 .. 0.84
   2 !   13.0   0.2   0.00013      0.16       2      30 ..      46      73 ..      45      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C +Cg+C+ +CP+nai+
  gi|386001653|ref|YP_005919952.1| 16 CDGCGNCVLACPENAIE 32
                                      ***************98 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearec 30
                                      C + g+C+  CPt+a++++ e+e+e  ++
  gi|386001653|ref|YP_005919952.1| 46 CDGLGACIGDCPTGALSME-EREAEEFDE 73
                                      88889************99.444443333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   1.4   2.1e-08   2.5e-05       3      22 .]       9      28 ..       6      28 .. 0.91
   2 ?    1.5   0.4      0.32   3.8e+02      10      22 .]      46      58 ..      38      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.1e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +++d++ C gCg Cv aCP+
  gi|386001653|ref|YP_005919952.1|  9 IKIDEALCDGCGNCVLACPE 28
                                      899****************5 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.32
                            Fer4_2 10 CigCgaCvsaCPa 22
                                      C g gaC+  CP+
  gi|386001653|ref|YP_005919952.1| 46 CDGLGACIGDCPT 58
                                      4433899999997 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   9.1   1.5e-05     0.018       1      49 [.       9      76 ..       9      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvl...................lddgeiaegevpddee 49
                                      +++D+ +C+gcg+Cv ++pe   +   g+a+v+                   l+ +e++ +e+++   
  gi|386001653|ref|YP_005919952.1|  9 IKIDEALCDGCGNCVLACPENAIEIVGGKAKVVreslcdglgacigdcptgaLSMEEREAEEFDELAA 76
                                      79****************99888888999999988888888888888777765555555555554444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   5.8   3.8e-06    0.0045       1      15 []      16      30 ..      16      30 .. 0.98
   2 ?    1.9   1.3      0.46   5.5e+02       1      15 []      46      60 ..      46      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv +CP++A
  gi|386001653|ref|YP_005919952.1| 16 CDGCGNCVLACPENA 30
                                      *************98 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.46
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+g gaC   CP+gA
  gi|386001653|ref|YP_005919952.1| 46 CDGLGACIGDCPTGA 60
                                      777788988899998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   0.00066      0.79      45      59 ..      15      29 ..       6      32 .. 0.84
   2 ?    3.8   0.0     0.072        86       2      17 ..      46      61 ..      36      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                           Fer4_17 45 lCieCgeCerkCPqg 59
                                      lC +Cg+C+ +CP++
  gi|386001653|ref|YP_005919952.1| 15 LCDGCGNCVLACPEN 29
                                      799999999999986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.072
                           Fer4_17  2 CiqCgyClpeCpsyea 17
                                      C + g+C+  Cp+++ 
  gi|386001653|ref|YP_005919952.1| 46 CDGLGACIGDCPTGAL 61
                                      6666777777776555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.3   7.1e-05     0.085       4      16 ..      16      28 ..      13      35 .. 0.91
   2 ?    0.9   0.4      0.71   8.4e+02       8      17 .]      50      59 ..      44      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-05
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C gCg Cv aCP 
  gi|386001653|ref|YP_005919952.1| 16 CDGCGNCVLACPE 28
                                      9***********5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.71
                            Fer4_4  8 gsCvaaCPqg 17
                                      g+C+  CP+g
  gi|386001653|ref|YP_005919952.1| 50 GACIGDCPTG 59
                                      5899999985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.5    0.0014       1.7      50      64 ..      15      29 ..      10      30 .. 0.87
   2 ?    3.8   0.1     0.066        79      50      64 ..      45      59 ..      35      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                       C +cg+C+ +Cp++
  gi|386001653|ref|YP_005919952.1| 15 LCDGCGNCVLACPEN 29
                                      699999999999986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.066
                            Fer4_8 50 sCttcgaCtevCpvg 64
                                       C + gaC   Cp+g
  gi|386001653|ref|YP_005919952.1| 45 LCDGLGACIGDCPTG 59
                                      699999999999986 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00052      0.62      76      95 ..      10      29 ..       2      30 .. 0.84
   2 ?    2.3   0.7      0.25     3e+02      77      94 ..      41      58 ..      34      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                      k++e  C GCg C+ acp++
  gi|386001653|ref|YP_005919952.1| 10 KIDEALCDGCGNCVLACPEN 29
                                      568999***********986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      + es C G g Ci  cp+
  gi|386001653|ref|YP_005919952.1| 41 VRESLCDGLGACIGDCPT 58
                                      56789***********97 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.9    0.0061       7.3       8      61 ..       9      63 ..       6      66 .. 0.75
   2 ?   -3.2   0.0       7.6   9.1e+03      34      40 ..     179     185 ..     178     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0061
                           Fer4_19  8 iednrelCihsgnCvk....glpevFdpkrkpwikpdeasteeiievverCPSGALsy 61
                                      i  +++lC++ gnCv     ++ e+   k+k     +e+  + + + +  CP GALs+
  gi|386001653|ref|YP_005919952.1|  9 IKIDEALCDGCGNCVLacpeNAIEIVGGKAK---VVRESLCDGLGACIGDCPTGALSM 63
                                      677899*********9443344445555555...56677789999***********97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.6
                           Fer4_19  34 kpwikpd 40 
                                        pw+++d
  gi|386001653|ref|YP_005919952.1| 179 TPWVHQD 185
                                       69**987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1643.09
//
Query:       gi|386001654|ref|YP_005919953.1|  [L=117]
Description: cupin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-15   56.7   0.1    2.1e-15   56.2   0.1    1.2  1  Cupin_2          Cupin domain
     0.0014   18.6   0.0     0.0017   18.2   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
     0.0015   18.5   0.0     0.0018   18.2   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
       0.01   16.2   0.0      0.013   15.9   0.0    1.2  1  Pirin_C          Pirin C-terminal cupin domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.019   14.6   0.0    1.3  1  Cupin_1          Cupin
      0.075   12.7   0.0       0.16   11.6   0.0    1.6  1  Auxin_BP         Auxin binding protein
      0.084   12.8   0.0       0.11   12.5   0.0    1.2  1  Cupin_7          ChrR Cupin-like domain
       0.11   12.2   0.0       0.17   11.6   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
       0.13   12.5   0.0       0.15   12.3   0.0    1.2  1  CENP-C_C         Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.1   1.1e-18   2.1e-15       2      70 ..      38     105 ..      37     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.1e-18
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       + +l+pGes + h+ p    +fyVleG+g +++++e+ e++a+ +v  pa+ pHr+ N+gd  +r+lvv
  gi|386001654|ref|YP_005919953.1|  38 HLTLAPGESLKKHVTPVD-VVFYVLEGRGIVEIGDEKREVTADSLVESPAKIPHRWTNPGDRRLRVLVV 105
                                       5799*************8.************************************************98 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.7e-07    0.0017      11      72 ..      42     103 ..      33     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.7e-07
                                       STT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEE CS
                      AraC_binding  11 ypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyr 72 
                                       +p++s ++hv +  v+ yv+eG+g+++++++  ++++++l+  p   pH+    ++ +++  
  gi|386001654|ref|YP_005919953.1|  42 APGESLKKHVTPVDVVFYVLEGRGIVEIGDEKREVTADSLVESPAKIPHRWTNPGDRRLRVL 103
                                       688889999999999**********************************9988886555554 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.8e-07    0.0018      55     137 ..      26     107 ..       4     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.8e-07
                   MannoseP_isomer  55 evldegeryqvkritvkPgeklslqkhhhrae.hWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkipl 130
                                       + ++ +e+ qv ++t+ Pge  sl+kh    +  + v++G   v+++de+ +++++  +  p+   hr  npG   l
  gi|386001654|ref|YP_005919953.1|  26 RMISDTESAQVVHLTLAPGE--SLKKHVTPVDvVFYVLEGRGIVEIGDEKREVTADSLVESPAKIPHRWTNPGDRRL 100
                                       57889999***********9..5688888776257799*************************************** PP

                   MannoseP_isomer 131 elievqs 137
                                       +++ v++
  gi|386001654|ref|YP_005919953.1| 101 RVLVVKT 107
                                       9998875 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.3e-06     0.013       2      68 ..      37     105 ..      36     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.3e-06
                                       EEEEE-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-.SSSEEEEE--SS-EEEEEE CS
                           Pirin_C   2 ldltleagaelelplpegleaavyvleGel..evggerseieeeqlavlg.dgdslvvkaeekgarvlLl 68 
                                       ++ltl++g++l+      ++++ yvleG++  e+g+e++e+++++l+    +  + + + +++++rvl++
  gi|386001654|ref|YP_005919953.1|  37 VHLTLAPGESLKKH-VTPVDVVFYVLEGRGivEIGDEKREVTADSLVESPaKIPHRWTNPGDRRLRVLVV 105
                                       899*********99.78899*******996448889999***9999876644444455555577777776 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.4e-06     0.019      34     121 ..      35     113 ..      21     117 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                                       EEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEE CS
                           Cupin_1  34 saarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavai 110
                                        ++ + l+pg  l  h++     ++yvl+G+g v++  ++       +++++  ++  Pa ++h + n g +  + +
  gi|386001654|ref|YP_005919953.1|  35 QVVHLTLAPGESLKKHVT-PVDVVFYVLEGRGIVEIGDEK-------REVTADSLVESPAKIPHRWTNPG-DRRLRV 102
                                       566677788888888888.8899**********7776555.......5899999999************9.788888 PP

                                       EEEESSSTT-E CS
                           Cupin_1 111 vvfdtnnpgnq 121
                                        v++t  p +q
  gi|386001654|ref|YP_005919953.1| 103 LVVKTPRPTEQ 113
                                       88888888777 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.1e-05      0.16      45      85 ..      35      75 ..      22     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                                      EEEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSSS CS
                          Auxin_BP 45 evwlqtlapgsrtpihrhsceevfvvlkgkgtlylassssk 85
                                      +v   tlapg+    h   ++ vf vl g+g + +++ + +
  gi|386001654|ref|YP_005919953.1| 35 QVVHLTLAPGESLKKHVTPVDVVFYVLEGRGIVEIGDEKRE 75
                                      566779**************************999976654 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-05      0.11       8      76 ..      21      90 ..      17     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                                      TTEEEEEEEEESSSS-EEEEEEEE-TTEE---EE-TT-EEEEEEEE....EEEETTEEEETTEEEEE-TT-EE CS
                           Cupin_7  8 egvevkpLerdgeekaratslvryapgsafsahkHpggeeilVLeG....vfsdeegdypaGsylrnppgssh 76
                                      +gv+ ++++++++    ++  + +apg+++++h  p  + ++VLeG    +  de+++  a s + +p +  h
  gi|386001654|ref|YP_005919953.1| 21 HGVDARMISDTESA---QVVHLTLAPGESLKKHVTPVDVVFYVLEGrgivEIGDEKREVTADSLVESPAKIPH 90
                                      57888888855544...5555679**********************333334455556666666666666555 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.17      26      65 ..      55      93 ..      31      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                      EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEECCC CS
                           Cupin_3 26 dEfcyileGevkvtpeggetvelraGDlvvlpkglsgtwd 65
                                      d  +y+leG+  v+  g e++e+ a +lv  p++    w+
  gi|386001654|ref|YP_005919953.1| 55 DVVFYVLEGRGIVEI-GDEKREVTADSLVESPAKIPHRWT 93
                                      5678***********.*************99999887775 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.7e-05      0.15      21      73 ..      43      94 ..      29     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                                      TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE CS
                          CENP-C_C 21 pgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieN 73
                                      p +e  kk++    +vFyV++Gr  v++ +++  ++  s    Pa      +N
  gi|386001654|ref|YP_005919953.1| 43 P-GESLKKHVTPVDVVFYVLEGRGIVEIGDEKREVTADSLVESPAKIPHRWTN 94
                                      3.44567899999****************999988888887777766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 727.41
//
Query:       gi|386001655|ref|YP_005919954.1|  [L=305]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-22   79.5   0.2    5.7e-22   78.9   0.2    1.3  1  Radical_SAM  Radical SAM superfamily
    0.00015   21.9   1.0     0.0003   20.9   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain
     0.0016   18.7   0.0      0.004   17.4   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.2   9.5e-26   5.7e-22       3     165 ..      49     228 ..      47     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 9.5e-26
                                       EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlakl 73 
                                       v + Cn +C++C+r ++     r+++++++l++ e l+ v+e+  + +  + + + g gepl++ + +++++rl+ +
  gi|386001655|ref|YP_005919954.1|  49 VAPRCNIQCNYCIRDFDcvneTRPGVTSQVLTPAEALQRVDEVMeKLHYiKVVAVAGPGEPLYN-EATFETFRLVGE 124
                                       6799***************************************966666566677778999985.588999999999 PP

                                       CCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH................HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxx RF
                       Radical_SAM  74 avpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf................eevleal 134
                                       + p++ ++v+tng+l+ ++ +erl+ lgv  v+++l+a+d+  + k +   h +                +++l++l
  gi|386001655|ref|YP_005919954.1| 125 KYPKLILCVSTNGLLL-PDEIERLDSLGVSNVTVTLNAVDPN-IGKEI-YEHVIyagkkytgleaaelllDHQLRGL 198
                                       99**************.*************************.*****.999999********************** PP

                                       HHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 135 eklreagikrvvdrivglpGendeeleelle 165
                                       e + ++ +  v++++v++p  nd ++ ++ +
  gi|386001655|ref|YP_005919954.1| 199 EEAVRRKMI-VKVNTVLIPTINDGHIMDITK 228
                                       ******999.***************998765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.1e-08    0.0003       7      92 ..      52     140 ..      48     161 .. 0.75
   2 ?   -1.9   0.4      0.59   3.5e+03      11      25 ..     279     300 ..     272     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.1e-08
                           Fer4_14   7 gCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlke 76 
                                       +Cn++C  C       n++    +++     e l q+++++ ++   i+ + + G GePL  +n+ + ++  + + e
  gi|386001655|ref|YP_005919954.1|  52 RCNIQCNYCIrdfdcvNETRPGVTSQVLTPAEAL-QRVDEVMEKLHYIKVVAVAGpGEPL--YNEAT-FETFRLVGE 124
                                       8******888655555666555566666666666.6666666666668889*********..45555.566699999 PP

                           Fer4_14  77 eypekkiwletngtle 92 
                                       +yp++   + tng+l 
  gi|386001655|ref|YP_005919954.1| 125 KYPKLILCVSTNGLLL 140
                                       ************9874 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.59
                           Fer4_14  11 sCk.......gCdnketwksel 25 
                                       +C+       gCd +++++++ 
  gi|386001655|ref|YP_005919954.1| 279 QCRsdaigklGCDVQQEFDKSE 300
                                       3447777777999888887764 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.8e-07     0.004      13      98 ..      51     142 ..      40     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.8e-07
                           Fer4_12  13 sgCnlsCkgCfnketwsfk......sgkeft.kelleeiiedlkk.esiegltllG.GEPllpenaeallelvkevk 80 
                                        +Cn++C++C+ ++  +++      +++  t  e+l+++ e ++k ++i+ + + G GEPl    +ea  e ++ v 
  gi|386001655|ref|YP_005919954.1|  51 PRCNIQCNYCI-RDFDCVNetrpgvTSQVLTpAEALQRVDEVMEKlHYIKVVAVAGpGEPLY---NEATFETFRLVG 123
                                       58*******98.333333344444455555447776666555555699**************...667777778888 PP

                           Fer4_12  81 eekp.ekdiwlytgytlee 98 
                                       e++p    +++++g  l +
  gi|386001655|ref|YP_005919954.1| 124 EKYPkLILCVSTNGLLLPD 142
                                       8888455677778876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1876.13
//
Query:       gi|386001656|ref|YP_005919955.1|  [L=95]
Description: signal recognition particle protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-23   83.6   0.1    1.8e-23   83.3   0.1    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.1     1e-27   1.8e-23       1      92 [.       9      91 ..       9      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1e-27
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekik 78
                                      vi+P+Y+d+ ++r +GR v+++ ave+Pt++ei  a+ ++gl++++e++k+yP++w+++ GrVrv++k           
  gi|386001656|ref|YP_005919955.1|  9 VIWPAYIDAGRSRGQGRAVSRRDAVEEPTVDEILVAALEMGLQAEAERDKHYPKEWWEKsGRVRVQKK----------G 77
                                      7******************************************************77555******85..........5 PP

                                      -CHHHHHHHHHHHH CS
                             SRP19 79 nkkellkkiaellk 92
                                       k +l+++ia++++
  gi|386001656|ref|YP_005919955.1| 78 PKAALVREIATRIR 91
                                      67777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 591.68
//
Query:       gi|386001657|ref|YP_005919956.1|  [L=97]
Description: hypothetical protein Mhar_0962 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-38  130.0   2.9      3e-38  129.9   2.9    1.0  1  DUF211    Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   2.9   1.6e-42     3e-38       2      88 ..       5      91 ..       4      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.6e-42
                                      EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEE CS
                            DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevva 80
                                      irrlvLDvlkph p+i+ela++l++l g++gvn++++evD++te++kiti+G++idy ++e++ie++ggvihSiDevva
  gi|386001657|ref|YP_005919956.1|  5 IRRLVLDVLKPHVPTILELAEALSKLGGITGVNLSLSEVDQQTETIKITIKGDKIDYLAVESVIEDFGGVIHSIDEVVA 83
                                      9****************************************************************************** PP

                                      ESS----- CS
                            DUF211 81 Gkkiveev 88
                                      Gk+ive v
  gi|386001657|ref|YP_005919956.1| 84 GKEIVEGV 91
                                      ******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 713.23
//
Query:       gi|386001658|ref|YP_005919957.1|  [L=230]
Description: Putative phosphatase, PHP family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-08   34.7   0.0      3e-08   34.2   0.0    1.3  1  PHP          PHP domain
     0.0013   18.3   0.0     0.0037   16.8   0.0    1.9  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
      0.031   14.1   0.1      0.062   13.1   0.1    1.4  1  TetR_C_1     Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0     5e-12     3e-08       1      73 [.      22      96 ..      22     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5e-12
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT......HHHHHHHHHHHHTTTTSEEEEEEE........ CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf......gyvefykaakkkykagikpiiGleayvaddse 73
                                      dlH+Ht +s     l ++elv++a+ +g+ a++iTDh+++       + v  +ka+  ++  +++++ G+e++ ++  +
  gi|386001658|ref|YP_005919957.1| 22 DLHTHTVFSDG--ELIPSELVRRAEMKGCRALGITDHVDFTnvefviSQVSKVKAL--EDVLEMRILAGVELTHVPPAK 96
                                      7999*999944..3337************************888666666666666..344689*******88777665 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.2e-07    0.0037      13     145 ..      34     163 ..      21     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.2e-07
                                       .....HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.HHHHHHHHH CS
                       RNase_P_p30  13 kkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpsklqrlskvrqk 89 
                                         +s+++++++  g ++  i+ +v+  ++++  ++    +++k+l++ l+ +++l +v+l+   p+k++rl++++++
  gi|386001658|ref|YP_005919957.1|  34 LIPSELVRRAEMKGCRALGITDHVDFTNVEFVISQV---SKVKALEDVLE-MRILAGVELTHVPPAKMERLATLARR 106
                                       456678888889999999999999999999999999...67777777777.9****************999999997 PP

                                       -..-EEEEE......--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                       RNase_P_p30  90 f..dllavr......PttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                          dl++v+      P+    +r a+e   vDi+ ++       +++ +++ +A+++gv +E++
  gi|386001658|ref|YP_005919957.1| 107 IgaDLVVVHgetavePVAPGTNRRAIEI-GVDILAHPG------FITPEEVDLARDNGVCLELT 163
                                       5338997761111115556789999955.9******99......79***************986 PP

>> TetR_C_1  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     1e-05     0.062      24      68 ..     178     222 ..     168     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                       HTSTTHHHHHHT-SS--HHHHHHHHHHHHHHHHTT--HHHHHHHH CS
                          TetR_C_1  24 lrhrdlarlfagtprlspnelrgmErlLrllrdaGlsdedavyal 68 
                                       l+  ++ar++++t+   p+ l   Er +++ r aGl++e a+ ++
  gi|386001658|ref|YP_005919957.1| 178 LALEAGARIVVDTDAHAPEDLIDRERAIEIARGAGLTLERATAVV 222
                                       67789***********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1426.21
//
Query:       gi|386001659|ref|YP_005919958.1|  [L=132]
Description: hypothetical protein Mhar_0964 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-42  144.5   0.2      2e-42  144.3   0.2    1.0  1  DUF2209   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.3   0.2   1.1e-46     2e-42       1     120 [.       4     119 ..       4     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 1.1e-46
                           DUF2209   1 vavDiSGRHkekdgeylmvcaaVslevsadriekveqvkilvvaseeepkledvvklieeaveelkeegtivaEkGe 77 
                                       vavDiSGRH+++ g+y+mv+a+V++++s++ +e++++++ lv +++e++++e v+ l+ee+v++l  +g+++aE+G+
  gi|386001659|ref|YP_005919958.1|   4 VAVDISGRHAVA-GRYIMVSASVAARISPEGVERTRRMR-LVPRVAESVDMEVVIGLMEESVRGL--SGVVLAERGD 76 
                                       8***********.99************************.9999*********************..********** PP

                           DUF2209  78 lynepewlveailkkefkyqeslgEreaielAHhvslsarkll 120
                                       lyn ++w+ve+il++efky+es+gEr+a+elAHh+s++ r+l 
  gi|386001659|ref|YP_005919958.1|  77 LYNLERWRVESILGREFKYPESRGERRAVELAHHASFAGRRLA 119
                                       ****************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 784.96
//
Query:       gi|386001660|ref|YP_005919959.1|  [L=443]
Description: GTP-binding protein HflX [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-20   71.5   0.0      9e-20   70.9   0.0    1.3  1  MMR_HSR1      50S ribosome-binding GTPase
      4e-17   62.7   0.0    8.4e-17   61.6   0.0    1.6  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    1.1e-14   54.8   3.0    1.9e-14   54.0   3.0    1.4  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    4.3e-07   29.9   0.0    7.4e-07   29.2   0.0    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    3.1e-06   27.2   0.0      0.067   13.1   0.0    2.3  2  RsgA_GTPase   RsgA GTPase
    3.8e-06   26.5   0.0    1.2e-05   24.9   0.0    1.8  1  FeoB_N        Ferrous iron transport protein B
    0.00016   21.3   0.0      0.022   14.3   0.0    2.6  1  GTP_EFTU      Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.027   14.1   0.0          2    7.9   0.0    2.3  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.03   14.4   0.0      0.055   13.5   0.0    1.4  1  Dynamin_N     Dynamin family
       0.11   11.9   0.0       0.31   10.5   0.0    1.8  1  Arf           ADP-ribosylation factor family
       0.42   10.2   1.8        3.3    7.3   0.1    2.5  2  AAA_25        AAA domain
       0.96   10.0   2.6          1    9.9   0.0    2.4  1  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0     6e-23     9e-20       2     101 ..     190     290 ..     189     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 6e-23
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH....HHHHHHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek....glgkaflale 74 
                                       va++G++N+GKStL+n+l +e++ ++d+p+tT+ ++++ v+ +++++ l+Dt+G+i+  +        ++ +++++ 
  gi|386001660|ref|YP_005919959.1| 190 VALAGYTNAGKSTLFNRLAEEAVAAKDQPFTTLSPTTRAVAARDRRFLLTDTVGFID--DLPLflikAFRSTLAEIV 264
                                       89***************************************999**********887..334411324555555688 PP

                                       CTSEEEEEEETTTTCSHHHHHHHHHHH CS
                          MMR_HSR1  75 eadlillvvdaseeklkpldeeleell 101
                                       eadl+llvvd+s +  + l+e+++++ 
  gi|386001660|ref|YP_005919959.1| 265 EADLVLLVVDLS-DPPEVLRERVASCH 290
                                       9*********98.54555566666554 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   5.6e-20   8.4e-17       2      89 .]      22     104 ..      21     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 5.6e-20
                         GTP-bdg_N   2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkVi 78 
                                       e+++El+ La++ag++v++ev+q+r   d+++ +G+Gkv e ++l      d +if++ Lsp q+ n+ ke+e+  +
  gi|386001660|ref|YP_005919959.1|  22 EEVTELRGLAEAAGYTVLAEVFQRR-GRDRRFQLGRGKVVEAASLGP----DKLIFNEPLSPGQIFNIGKEFEIPPM 93 
                                       6789*******************97.78*************998764....569*********************** PP

                         GTP-bdg_N  79 DRtqLILdIFA 89 
                                       DR +LIL+IFA
  gi|386001660|ref|YP_005919959.1|  94 DRFNLILEIFA 104
                                       **********8 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   3.0   1.3e-17   1.9e-14       1      79 []     106     182 ..     106     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.3e-17
                                       H--SHHHHHHHHHHHHHHHHHHHC..XXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLe..glgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelq 75 
                                       rA+t+eaklQVelA+l y+ p ++  +  k+ls+     g rG+G + + ++ r i+ r+ak++ eL++v+++   +
  gi|386001660|ref|YP_005919959.1| 106 RASTREAKLQVELARLSYEAPFVRtiESLKKLSER---PGYRGSGSYDVSMY-RDIKGRMAKIRAELRAVEETGVRR 178
                                       9**********************435444444444...458*******9987.89*******************999 PP

                                       ...T CS
                         GTP-bdg_M  76 rkkR 79 
                                       r++R
  gi|386001660|ref|YP_005919959.1| 179 RERR 182
                                       9998 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.9e-10   7.4e-07      54     104 ..     298     353 ..     291     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.9e-10
                      MMR_HSR1_Xtn  54 vYipclyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiweeL 104
                                        Y p + vlNK+Dli+ ee +e +r      p  v +Sa+++l+l++L+++i e+L
  gi|386001660|ref|YP_005919959.1| 298 CYAPLVSVLNKVDLITPEEAEERCRLledlaPTPVLVSAREGLGLEALLDAILEKL 353
                                       69********************999666787899******************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   4.5e-05     0.067      87     126 ..     175     214 ..     149     249 .. 0.70
   2 !   11.9   0.0    0.0001      0.15      17      98 ..     267     350 ..     253     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                                       HTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLinallpelelk 126
                                       +   +e +++l  ++++l+G + +GKStL n+l++e+ ++
  gi|386001660|ref|YP_005919959.1| 175 GVRRRERRRKLGFDLVALAGYTNAGKSTLFNRLAEEAVAA 214
                                       4455555667777899******************985443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0001
                                       -EEEEEEESTT.TT--HHHHHHHHHHHHHTT-..EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  17 dqllivvslke.pelslnlldrfLvlaeekgi..epvivlnKiDlleeeeeleelkeelealgyevllvsaktkegl 90 
                                       d +l+vv l++ pe+  +++  +  ++++ g   ++v vlnK+Dl++ ee +ee    le+l  +++lvsa+++ gl
  gi|386001660|ref|YP_005919959.1| 267 DLVLLVVDLSDpPEVLRERVASCHGALWDCGCyaPLVSVLNKVDLITPEE-AEERCRLLEDLAPTPVLVSAREGLGL 342
                                       555555555441344555555555566665554256679***********.************************** PP

                                       HHHHHHCT CS
                       RsgA_GTPase  91 eelkellk 98 
                                       e+l +++ 
  gi|386001660|ref|YP_005919959.1| 343 EALLDAIL 350
                                       *9987765 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   7.7e-09   1.2e-05       3     156 .]     190     349 ..     188     349 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.7e-09
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSS CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeep 79 
                                       val+G  n+Gk+tlfn+l++        p +t   ++ ++  +++++ ++D  G  +  +    +    ++    e+
  gi|386001660|ref|YP_005919959.1| 190 VALAGYTNAGKSTLFNRLAEEAVAAKDQPFTTLSPTTRAVAARDRRFLLTDTVGFIDDLPLFLIKAFRSTLAEIVEA 266
                                       89****************************************************97766655555554444445567 PP

                                       SEEEEEEEGGG...H..HHHHHHHHHHHHTT..SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTH CS
                            FeoB_N  80 dvvvnvvdatn...l..ernLyLtlqllelg..vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegi 149
                                       d+v+ vvd +    +  er       l + g  +p+v +ln++d ++ ++ e   + L++   +pv  +sa+++ g+
  gi|386001660|ref|YP_005919959.1| 267 DLVLLVVDLSDppeVlrERVASCHGALWDCGcyAPLVSVLNKVDLITPEEAEERCRLLEDLAPTPV-LVSAREGLGL 342
                                       777777776541114224445566678898866799**************9988888877766765.689******* PP

                                       HHHHHHH CS
                            FeoB_N 150 eellkai 156
                                       e+ll+ai
  gi|386001660|ref|YP_005919959.1| 343 EALLDAI 349
                                       **99886 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.5e-05     0.022      63     193 ..     229     354 ..     188     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                                       EETTCSSEEEEEEEESSSGG....GHHHHHHH....HHT-SEEEEEEETTTBSTHHHHHHHH...HHHHTTTE..EE CS
                          GTP_EFTU  63 leketkkylinliDtPGHvd....Fskevirg....lrvlDgavlvvdaveGvepqteevlr...lalkegvp..ii 126
                                       +    +++++ l Dt G +d    F  +  r+    +  +D+++lvvd ++ +e+  e+v+     +++ g+   ++
  gi|386001660|ref|YP_005919959.1| 229 V--AARDRRFLLTDTVGFIDdlplFLIKAFRStlaeIVEADLVLLVVDLSDPPEVLRERVASchgALWDCGCYapLV 303
                                       3..3778889999999998888888888777765556789**********99888888877611146666665669* PP

                                       EEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 127 vfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                        ++NK+D +  e  e    + ++l                  + v +Sa +g g+++ll+a+ e+lp
  gi|386001660|ref|YP_005919959.1| 304 SVLNKVDLITPEEAEERCRLLEDL------------A----PTPVLVSAREGLGLEALLDAILEKLP 354
                                       *********776666555555566............1....235789***************99988 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.026        39       3      23 ..     190     210 ..     188     218 .. 0.83
   2 ?    7.9   0.0    0.0014         2      83     163 ..     234     322 ..     220     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.026
                                       EEEEESTTCCHHHHHHHHHCT CS
                              cobW   3 tvltGflGsGKTtLlnhllen 23 
                                       + l+G+  +GK+tL n+l e+
  gi|386001660|ref|YP_005919959.1| 190 VALAGYTNAGKSTLFNRLAEE 210
                                       5789*************9855 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                                       -SEEEEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHHHHHTSSEE.EEE-HH CS
                              cobW  83 ldviliEttGlaePapv.aft..eeelksdltldavvavvDaknl....eaeeekieekaedqlaaadll.vlnKtD 151
                                          +l  t+G  +  p+ +++   ++l++ +++d v+ vvD +       ++  + +  + d   +a l+ vlnK+D
  gi|386001660|ref|YP_005919959.1| 234 RRFLLTDTVGFIDDLPLfLIKafRSTLAEIVEADLVLLVVDLSDPpevlRERVASCHGALWDCGCYAPLVsVLNKVD 310
                                       467888899988777774333579999999999*******99877777655666666677777777777669***** PP

                                       HHCHC..HHHHH CS
                              cobW 152 lldeeallekle 163
                                       l++ e+  e+++
  gi|386001660|ref|YP_005919959.1| 311 LITPEEAEERCR 322
                                       ***997756554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.7e-05     0.055       1      36 [.     190     225 ..     190     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-E CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrpl 36 
                                       +a+ G +++GKS++ n L +e++  +++  tT  p+
  gi|386001660|ref|YP_005919959.1| 190 VALAGYTNAGKSTLFNRLAEEAVAAKDQPFTTLSPT 225
                                       6889*******************9999999998877 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00021      0.31      19      65 ..     192     241 ..     183     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                                       EEESTTSSHHHHHHHHHHSSCEE.CSS..SSSEEEEEEEETTEEEEEEEE CS
                               Arf  19 llGLDnaGKtTilkklkleelvt.tvP..TigfnveeleiknlkftvwDv 65 
                                       l G  naGK+T+ ++l +e ++   +P  T+ ++++ ++ ++ +f + D 
  gi|386001660|ref|YP_005919959.1| 192 LAGYTNAGKSTLFNRLAEEAVAAkDQPftTLSPTTRAVAARDRRFLLTDT 241
                                       45889*************99876444544999999999999999988775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0022       3.3      35      73 ..     189     228 ..     165     231 .. 0.81
   2 ?    2.1   0.4     0.082   1.2e+02      98     149 ..     231     274 ..     221     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                            AAA_25  35 lallaGapgtGKttlaldlalava..tGkpwlgpvapeqgk 73 
                                       l++laG + +GK+tl   la + +  +++p++  + p+ ++
  gi|386001660|ref|YP_005919959.1| 189 LVALAGYTNAGKSTLFNRLAEEAVaaKDQPFTT-LSPTTRA 228
                                       789************999997655468888877.5555555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.082
                            AAA_25  98 rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviD 149
                                       ++d+r l++d +g+ ++lpLf        ++a+   l++ +e+  +++l+v+D
  gi|386001660|ref|YP_005919959.1| 231 ARDRRFLLTDTVGFiDDLPLFL-------IKAFRSTLAEIVEA--DLVLLVVD 274
                                       4567777888889999999985.......67776666666666..8*****99 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0007         1       1      22 [.     190     211 ..     190     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0007
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       ++l+G+  +GK+tl ++L+++ 
  gi|386001660|ref|YP_005919959.1| 190 VALAGYTNAGKSTLFNRLAEEA 211
                                       689***************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3209.11
//
Query:       gi|386001661|ref|YP_005919960.1|  [L=243]
Description: hypothetical protein Mhar_0966 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.24   11.3   1.0       0.65    9.9   1.0    1.7  1  Peptidase_C25_C  Peptidase family C25, C terminal ig-like dom
       0.53    9.8   0.0       0.53    9.8   0.0    2.2  2  ApbE             ApbE family


Domain annotation for each model (and alignments):
>> Peptidase_C25_C  Peptidase family C25, C terminal ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   7.2e-05      0.65      20      58 ..     162     200 ..     149     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.2e-05
                                       EEEESSTT-EEEEEETTEEEEEEE-BTTEEEEE-S--TT CS
                   Peptidase_C25_C  20 evscdvdgalvalSannkllGsaivasGqatlnitpite 58 
                                        +s + + a va+S++  l + a +a G+a+ + +++++
  gi|386001661|ref|YP_005919960.1| 162 SISFGSADAAVAISDDVSLADAAATALGNAVGSASQLAD 200
                                       57778889**********************987777765 PP

>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   5.9e-05      0.53     111     189 ..      74     156 ..      15     160 .. 0.69
   2 ?   -1.2   2.0      0.13   1.1e+03     220     235 ..     172     188 ..     162     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.9e-05
                                       EESTT..-----TTTHHHHHHHHHHHHHHH.TT-EEEEEETTEEEEEC-ECT-EEEEEE-TT...S.SEEEEEEESS CS
                              ApbE 111 lakkgpgmkLDlggiaKGyavdrvaellka.giksalvnlGGdiralGpdgkpwrvgiedPr...a.ellavlslsd 182
                                       +a++g+++ +   +   G ++  +  ++ + g + a+v+ GGd++++  d +p+  gi       +  ++++   + 
  gi|386001661|ref|YP_005919960.1|  74 MARAGRAVGIGPMSAVAGTIARFALGAMMEaGATYAIVDNGGDVALIA-D-RPVLMGIYAGPsplKdLAFEIAPRT- 147
                                       6666667777777777788888888888888**************998.4.6888888743323222122233333. PP

                                       S..EEEEEE CS
                              ApbE 183 d..avaTSG 189
                                       +  +++TS+
  gi|386001661|ref|YP_005919960.1| 148 EplGICTSS 156
                                       346777775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.13
                                       EEEESC.HHHHHHHHHH CS
                              ApbE 220 tViads.alADalaTal 235
                                         i+d+  lADa+aTal
  gi|386001661|ref|YP_005919960.1| 172 VAISDDvSLADAAATAL 188
                                       334555599******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1647.68
//
Query:       gi|386001662|ref|YP_005919961.1|  [L=145]
Description: hypothetical protein Mhar_0967 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-07   31.1   1.5    3.8e-07   30.7   1.5    1.2  1  PIN       PIN domain
     0.0044   17.5   0.0     0.0095   16.4   0.0    1.5  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.5   4.2e-11   3.8e-07       1     118 [.       2     120 ..       2     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.2e-11
                                       EEE-HHHHHHHH..TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEE CS
                               PIN   1 ivlDTsvliall..rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkil 71 
                                       iv+D+sv+++l+   ++++++ a  l+  +      ++ +++  +E++  l r   +  k+++  +++++ s+++++
  gi|386001662|ref|YP_005919961.1|   2 IVVDASVFLDLIfdYRSDRTAIADGLFTLMeedgVPIFEPDAFKIEMIGQLVR---RLTKEEATALAEEIFSNINFI 75 
                                       79***********97788888888888777888999999**************...66666666666666******* PP

                                       EBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  72 pidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                       +  +e++++a+ +a   g +++D + +A Ak + + l+ ++D++  +
  gi|386001662|ref|YP_005919961.1|  76 E-ASELFDMAYSVAVLTGSRAIDSFYVAAAKLEEAFLV-SNDKHQVE 120
                                       *.*********************************888.****9766 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-06    0.0095       1      69 [.       2      75 ..       2      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                            PIN_12  1 ifiDTnifld..effrlseeealkklleliesgkiklivpdivldEflknrekkiees..kklekalks.lskl 69
                                      i++D ++fld  + +r++  ++ + l++l e+ ++ ++ pd  + E++ ++ +++ +   + l ++++s ++ +
  gi|386001662|ref|YP_005919961.1|  2 IVVDASVFLDliFDYRSDRTAIADGLFTLMEEDGVPIFEPDAFKIEMIGQLVRRLTKEeaTALAEEIFSnINFI 75
                                      89********9999999999*******************************88888774444445555543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1069.67
//
Query:       gi|386001663|ref|YP_005919962.1|  [L=69]
Description: Putative antitoxin PYRAB11980 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-15   56.6   3.9    3.1e-15   56.3   3.9    1.1  1  DUF104    Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.091   12.6   0.0       0.12   12.2   0.0    1.2  1  TrkA_C    TrkA-C domain


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   3.9   3.5e-19   3.1e-15       3      59 .]      11      66 ..      10      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 3.5e-19
                            DUF104  3 kvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleelle 59
                                      k Ie+vYE+Gv++PL++v+LkEG+e  ++I+    il+  +   k+++e+ l+e++e
  gi|386001663|ref|YP_005919962.1| 11 KKIEVVYEGGVFRPLGDVKLKEGTEAFVVIKP-GGILEAARRHRKKVEEDLLKEFVE 66
                                      88******************************.555555555555999******986 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.12      36      67 ..      19      50 ..      13      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                      -EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C 36 geliipsgdtvLeeGDvllvvgspsdlaelre 67
                                      g ++ p gd +L+eG + +vv +p ++ e+++
  gi|386001663|ref|YP_005919962.1| 19 GGVFRPLGDVKLKEGTEAFVVIKPGGILEAAR 50
                                      46899*********************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 544.29
//
Query:       gi|386001664|ref|YP_005919963.1|  [L=99]
Description: hypothetical protein Mhar_0969 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-05   24.4   0.1      3e-05   24.2   0.1    1.4  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family
    7.4e-05   22.5   0.6     0.0044   16.9   0.0    2.3  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   3.3e-09     3e-05      14      45 ..       9      40 ..       4      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.3e-09
                             RHH_8 14 DLgqiDlLveeGfYsnRtDlirtairaqLakh 45
                                      +  qi  Lve G Y n +D++r air++La+ 
  gi|386001664|ref|YP_005919963.1|  9 EFEQIQRLVEAGVYLNTSDFVRDAIRDKLASI 40
                                      567999***********************875 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.9e-07    0.0044      10      37 ..       9      37 ..       4      38 .. 0.88
   2 !    3.4   0.4    0.0086        77       5      23 ..      77      95 ..      76      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.9e-07
                                      HHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1 10 llerLdelarrrg.rSrSelIReAlreyl 37
                                      + e++++l++++   + S+++R+A+r+ l
  gi|386001664|ref|YP_005919963.1|  9 EFEQIQRLVEAGVyLNTSDFVRDAIRDKL 37
                                      6699**********************987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0086
                                      EEEHHHHHHHHHHHHHHTS CS
                             RHH_1  5 rldeellerLdelarrrgr 23
                                       ld +l++++ e  rr+gr
  gi|386001664|ref|YP_005919963.1| 77 ELDYDLVAEITEELRREGR 95
                                      5899********9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 711.87
//
Query:       gi|386001665|ref|YP_005919964.1|  [L=57]
Description: hypothetical protein Mhar_0970 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.2   0.3       0.12   12.1   0.3    1.1  1  Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain


Domain annotation for each model (and alignments):
>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   6.9e-06      0.12      71      98 ..      12      40 ..       4      53 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-06
                      Succ_CoA_lig 71 flsaarraark.kpvvvlksGrseagara 98
                                       +++  +a++   pvv++k Gr++a++  
  gi|386001665|ref|YP_005919964.1| 12 GARIYAEARKIsDPVVIVKTGRHKAQRVI 40
                                      4445555555559*********9887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 422.83
//
Query:       gi|386001666|ref|YP_005919965.1|  [L=399]
Description: McrBC 5-methylcytosine restriction system component-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-33  115.3   0.0    3.5e-33  115.1   0.0    1.1  1  McrBC     McrBC 5-methylcytosine restriction system component


Domain annotation for each model (and alignments):
>> McrBC  McrBC 5-methylcytosine restriction system component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.0     2e-37   3.5e-33       2     320 .]      56     357 ..      55     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 2e-37
                             McrBC   2 kagnyvGviqlksgaileIlPKlfendeskelarklLlkmLsylknlrfkesslaalesakl.pLseilillflqel 77 
                                       +a+ + G i l  ++++  lPK+  ++         L+ mL+y+  l+  + +    +   l +++e l++lf+ ++
  gi|386001666|ref|YP_005919965.1|  56 TANGWAGHIPLTPEFQIALLPKVEIRN---------LFGMLEYAYRLESLKFPEGLTDCDSLeEFYETLARLFALRV 123
                                       577888999999999999999998774.........699***9999999999988888777779************* PP

                             McrBC  78 qrllkkglyseYqsveenlsalkGrllvkeqlkknlaqkhkfeveydefsednaenRilksalelllkllrssetlk 154
                                           +kg  ++Yq  ++  ++++Gr +v++  +k+ + k   e+ y+e + d  +n+il  +l+++l++   +e++ 
  gi|386001666|ref|YP_005919965.1| 124 LDRGRKGFFRSYQPRKDRIPYVRGRFDVRKSCQKPWMVKP--ECCYEEHTSDVEDNQILAWTLRRILQSGVCTERSL 198
                                       *******************************999988766..79***********************9998888888 PP

                             McrBC 155 .elrellsilkev.arskisekdlqkvqlnrlfarykkvlqlaevilknqsplakqgkqkalglLfdmeklFEeyva 229
                                        ++r++ ++l+ + ++ ++  +d +    +rl+++y+ + +l++ +l++  p++  g +  + +L+dm+ l+E +va
  gi|386001666|ref|YP_005919965.1| 199 pQVRRAYQSLRGLtTPIPCDPQDCAGRLYSRLNEDYQPMHALCRFFLEQSGPSHRIGGRTMIPFLVDMARLYELFVA 275
                                       8999999999766257899999999999************************************************* PP

                             McrBC 230 klLrkelskdakvktqeqskyllkaegeaefklkpDl..likkkkeesivlDtKwKklekekakkkgisqsDlYQll 304
                                       ++L++++ +d  v+ +e+  +++ + g+ +f +  Dl  + + +++  +vlDtK+K+ ++         + D+ Q++
  gi|386001666|ref|YP_005919965.1| 276 EWLKAKMPPDFVVRPHEE--VVIGRGGRVRFDI--DLvvYDRDSQKALFVLDTKYKAPDHP-------GNDDISQVV 341
                                       ****99999999998865..6777777766666..5632666666667*********9754.......679****** PP

                             McrBC 305 aYaqayqaeqgkLvYP 320
                                       +Ya+a  + ++ L+YP
  gi|386001666|ref|YP_005919965.1| 342 TYAAAKDCDEAVLIYP 357
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2347.96
//
Query:       gi|386001667|ref|YP_005919966.1|  [L=849]
Description: ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-21   75.7   0.0      6e-21   74.9   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
    2.7e-09   37.5   0.0    9.1e-09   35.8   0.0    1.9  1  AAA           ATPase family associated with various cellular 
    4.6e-06   26.5   0.0    2.2e-05   24.3   0.0    2.0  2  AAA_24        AAA domain
      3e-05   24.5   0.0    0.00091   19.6   0.0    2.9  1  AAA_16        AAA ATPase domain
    5.9e-05   23.4   0.0    0.00031   21.0   0.0    2.1  1  AAA_22        AAA domain
     0.0014   19.2   0.0     0.0056   17.2   0.0    2.0  1  AAA_18        AAA domain
     0.0017   18.1   0.0     0.0086   15.8   0.0    1.9  2  IstB_IS21     IstB-like ATP binding protein
     0.0023   17.6   0.0      0.018   14.6   0.0    2.1  2  AAA_25        AAA domain
     0.0046   16.7   0.1       0.77    9.5   0.0    3.0  4  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.006   16.9   0.0      0.025   14.9   0.0    1.9  2  AAA_19        AAA domain
     0.0074   16.7   0.1      0.033   14.6   0.0    2.1  2  RNA_helicase  RNA helicase
      0.009   15.5   0.0      0.017   14.6   0.0    1.3  1  PhoH          PhoH-like protein
     0.0093   16.2   0.1      0.064   13.5   0.0    2.4  2  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.028   13.2   0.0      0.044   12.6   0.0    1.1  1  PPV_E1_C      Papillomavirus helicase
      0.044   13.5   0.0       0.16   11.7   0.0    1.9  2  AAA_30        AAA domain
      0.059   13.2   0.0       0.11   12.3   0.0    1.4  1  AAA_11        AAA domain
      0.061   13.5   0.1       0.13   12.4   0.1    1.6  1  AAA_33        AAA domain
      0.076   12.1   0.0       0.13   11.3   0.0    1.3  1  Parvo_NS1     Parvovirus non-structural protein NS1
      0.076   12.9   0.0        1.3    8.9   0.0    2.2  1  AAA_3         ATPase family associated with various cellular 
      0.076   12.4   0.0       0.52    9.7   0.0    2.1  2  TniB          Bacterial TniB protein
      0.079   13.0   0.0       0.34   10.9   0.0    2.1  1  AAA_14        AAA domain
       0.17   11.9   0.0       0.47   10.4   0.0    1.7  1  ResIII        Type III restriction enzyme, res subunit
       0.18   11.3   0.0       0.42   10.1   0.0    1.5  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   7.7e-24     6e-21       3     138 .]     605     752 ..     603     752 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 7.7e-24
                                       EEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT--HHHHH--B--..............--------...... CS
                             AAA_5   3 lLvGppGtgKselaerlaaal....nreveyvqltrdtteedlkgrreik.....ngttslvdsplvraar...... 64 
                                       +L GppGtgK+ +ae+la+ l          vq++  + +ed++++++++     + ++  v++ + + ++      
  gi|386001667|ref|YP_005919966.1| 605 VLYGPPGTGKTYVAEHLAKHLiggtDGFSDLVQFHPAYAYEDFIQGIRPQsdddgGLRYPIVPGRFLEFCEraesrh 681
                                       79*********************87777889*******************9986556667799999999999*9998 PP

                                       G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE...-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  65 egeilvlDEverae.sevlnsLlslleerrllle.eggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                         ++l++DE++ra+ s+v+++L+ lle r ++++  gg++ + +++     + +i+t+n++drs + ++ alr+Rf
  gi|386001667|ref|YP_005919966.1| 682 GTCVLIIDEINRANlSQVFGELMYLLEYRSRSIPlAGGRRLRIPEN-----VLIIGTMNTADRSIALVDHALRRRF 752
                                       889****************************988355556666665.....************************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   1.2e-11   9.1e-09       2     125 ..     605     753 ..     604     760 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.2e-11
                                       EEESSTTSSHHHHHHHHHHHH.....T.HEEEEEETTTCSSS...............STTHHHHHHHHHHHHHHHTS CS
                               AAA   2 llyGppGtGKTllakavakel.....g.vefleisgsellsk...............yvgesekkirelfkeakeka 57 
                                       +lyGppGtGKT++a+ +ak+l     g ++++++  +   ++                    + ++ e+ ++a++  
  gi|386001667|ref|YP_005919966.1| 605 VLYGPPGTGKTYVAEHLAKHLiggtdGfSDLVQFHPAYAYEDfiqgirpqsdddgglRYPIVPGRFLEFCERAESRH 681
                                       69******************876555133344444333333344455666667788866778999999999999988 PP

                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESS....GGGSTHHH CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk...........eskvivigatnr....pdkldpal 119
                                       ++++l+iDEi + + s+          v  +L+  l+  +++            ++v++ig+ n+    +  +d al
  gi|386001667|ref|YP_005919966.1| 682 GTCVLIIDEINRANLSQ----------VFGELMYLLEYRSRSiplaggrrlriPENVLIIGTMNTadrsIALVDHAL 748
                                       77***********9999..........9***********999***********777********9666666789999 PP

                                       HSTTSS CS
                               AAA 120 lrgRfd 125
                                       + +Rf 
  gi|386001667|ref|YP_005919966.1| 749 R-RRFA 753
                                       9.6886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   1.4e+03      91     119 ..      94     121 ..      87     126 .. 0.75
   2 !   24.3   0.0   2.8e-08   2.2e-05       2      77 ..     601     694 ..     600     700 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                            AAA_24  91 kaeskedkgdgkGygelaeefrrllkklq 119
                                       k+es  +  d+  + ++a+e+ r++++ +
  gi|386001667|ref|YP_005919966.1|  94 KFES-AGWTDQESWPQVADEILRFVRRCY 121
                                       4444.35566778************9876 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.8e-08
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel................... 59 
                                       k++ ++yGp+g+GKT++a +l  k l+  t++ ++ ++++      ++edf++ +                      
  gi|386001667|ref|YP_005919966.1| 601 KRQAVLYGPPGTGKTYVAEHL-AKHLIGGTDGFSDLVQFHPAY---AYEDFIQGIRPQsdddgglrypivpgrflef 673
                                       67789****************.**********77777777765...9999999999888999*************** PP

                            AAA_24  60 ...aaeladyktlviDtidel 77 
                                          a+  ++  +l+iD i+ +
  gi|386001667|ref|YP_005919966.1| 674 cerAESRHGTCVLIIDEINRA 694
                                       **999999999*****99976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00091       9      51 ..     588     628 ..     586     717 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                            AAA_16   9 leqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       le+L++ ++++r+   +  +l+G++G+GK+ ++++l+++l + 
  gi|386001667|ref|YP_005919966.1| 588 LETLERWVRAIRRK--RQAVLYGPPGTGKTYVAEHLAKHLIGG 628
                                       56777778877777..5688*****************999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.9e-07   0.00031       4     116 ..     600     707 ..     596     733 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.9e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka.erlsseel 78 
                                       +++  v++G++GtGKT++++ l++ l          +++  +v+       +d+ + +  + ++++   ++    ++
  gi|386001667|ref|YP_005919966.1| 600 RKRQAVLYGPPGTGKTYVAEHLAKHLIGG------TDGFSdLVQFHPAYAYEDFIQGIRPQSDDDGGLrYPIVPGRF 670
                                       567789*******************9432......555557888888889999999999999976555667777777 PP

                            AAA_22  79 lealeqalraravielliiDEaqhlr.seealeeLrsll 116
                                       le +e+a +++++  +liiDE+ + + s +++ eL  ll
  gi|386001667|ref|YP_005919966.1| 671 LEFCERAESRHGT-CVLIIDEINRANlS-QVFGELMYLL 707
                                       7888888888888.********998543.3333333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.2e-06    0.0056       3      23 ..     606     627 ..     605     663 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrl.g 23 
                                       l G+pG+GKt +a++L+k+l g
  gi|386001667|ref|YP_005919966.1| 606 LYGPPGTGKTYVAEHLAKHLiG 627
                                       89*****************843 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05    0.0086      44      72 ..     598     626 ..     584     641 .. 0.86
   2 ?   -0.9   0.0       1.5   1.2e+03     109     131 ..     683     705 ..     672     717 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveav 72 
                                       i++k   vl Gp+G+GK+++a  l+++ +
  gi|386001667|ref|YP_005919966.1| 598 IRRKRQAVLYGPPGTGKTYVAEHLAKHLI 626
                                       789999******************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                         IstB_IS21 109 vdllilDdlgllpldqaeaellf 131
                                       + +li+D++   +l+q   el++
  gi|386001667|ref|YP_005919966.1| 683 TCVLIIDEINRANLSQVFGELMY 705
                                       569**********9998777766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.3e-05     0.018      22      62 ..     591     630 ..     571     643 .. 0.80
   2 ?    0.1   0.0      0.67   5.2e+02     123     154 ..     660     694 ..     636     699 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalavatGkp 62 
                                       ++ +v+ + +++  a+l+G+pgtGKt +a +la ++  G  
  gi|386001667|ref|YP_005919966.1| 591 LERWVRAI-RRKRQAVLYGPPGTGKTYVAEHLAKHLIGGTD 630
                                       55555555.689999******************99988765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.67
                            AAA_25 123 gtl...ltadvdaleaaieevegvrlvviDplsra 154
                                       g +   +++ + +  +++e+++g  +++iD ++ra
  gi|386001667|ref|YP_005919966.1| 660 GLRypiVPGRFLEFCERAESRHGTCVLIIDEINRA 694
                                       444554677788889999999*********99998 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.1   4.7e+03      14      39 ..      39      64 ..      30      70 .. 0.82
   2 ?   -3.4   0.0       9.4   7.3e+03      72      92 ..     145     165 ..     144     169 .. 0.84
   3 !    9.5   0.0   0.00098      0.77      36      57 ..     604     625 ..     588     631 .. 0.81
   4 ?    3.5   0.0     0.068        53      87     156 ..     685     755 ..     678     758 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.1
                            RuvB_N 14 kvkeklkifieaakkreealdhvlly 39
                                      + + +++ ++ea ++ e+  d vl+ 
  gi|386001667|ref|YP_005919966.1| 39 EGRRNFETILEAERQGEDVTDEVLMK 64
                                      5577899999*************997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.4
                            RuvB_N  72 agdlaalltnleekdvlfide 92 
                                       +g l+ +l  l+++d ++i++
  gi|386001667|ref|YP_005919966.1| 145 SGTLTPILHALRPEDFILINN 165
                                       578999*********999976 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00098
                            RuvB_N  36 vllyGpPGlGkttlakiiakel 57 
                                        +lyGpPG Gkt +a+ +ak l
  gi|386001667|ref|YP_005919966.1| 604 AVLYGPPGTGKTYVAEHLAKHL 625
                                       579*************999876 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.068
                            RuvB_N  87 vlfideihr..lsraveevlysamedfrldivigkGpsarsikldlpkftlvgattragllssPlrdrfgiv 156
                                       vl idei r  ls++  e++y  +e  +  i +  G+  r  +  l   t+ +a    +l+ + lr rf++ 
  gi|386001667|ref|YP_005919966.1| 685 VLIIDEINRanLSQVFGELMYL-LEYRSRSIPLAGGRRLRIPENVLIIGTMNTADRSIALVDHALRRRFAFL 755
                                       89******96677889999996.7888888999999888888888888888888888999999999999875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-05     0.025       8      35 ..     599     626 ..     592     634 .. 0.85
   2 ?   -1.4   0.0       3.4   2.7e+03     100     115 ..     679     695 ..     666     713 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallv 35 
                                        +++  ++ ++pGtGKT+v +h  ++l+
  gi|386001667|ref|YP_005919966.1| 599 RRKRQAVLYGPPGTGKTYVAEHLAKHLI 626
                                       56788999*****************997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                            AAA_19 100 lqeee.llivDEfqdvd 115
                                        ++++ +li+DE+   +
  gi|386001667|ref|YP_005919966.1| 679 SRHGTcVLIIDEINRAN 695
                                       3466669*****98766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       5.1     4e+03      38      72 ..     355     391 ..     351     401 .. 0.71
   2 !   14.6   0.0   4.3e-05     0.033       2      24 ..     605     627 ..     604     650 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.1
                      RNA_helicase  38 npeddfwdgYtgqevvvidDfgqvkdee.nps.dlae 72 
                                       ++ d+++d Y++    +   f+ +k +    + ++ +
  gi|386001667|ref|YP_005919966.1| 355 SSGDEIFDAYEDALNYIANKFKDWKRSPwRNKhQERF 391
                                       578999999*999999988888888665544435544 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.3e-05
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallk 24 
                                       +lyGp+g+GK+++a++Lak+l +
  gi|386001667|ref|YP_005919966.1| 605 VLYGPPGTGKTYVAEHLAKHLIG 627
                                       79*****************9974 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.2e-05     0.017      11      57 ..     593     640 ..     589     651 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT.TS-SEEEEEE- CS
                              PhoH  11 eylealkkndivfaiGpaGtGKtylavalavealkk.kkvkriiltrp 57 
                                       + ++a++++   +  Gp GtGKty+a  la +++   + ++ ++ + p
  gi|386001667|ref|YP_005919966.1| 593 RWVRAIRRKRQAVLYGPPGTGKTYVAEHLAKHLIGGtDGFSDLVQFHP 640
                                       67899**9******************9999887754344555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9     3e+03     133     155 ..     253     275 ..     251     280 .. 0.86
   2 !   13.5   0.0   8.2e-05     0.064       3      23 ..     605     628 ..     603     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                            AAA_28 133 ereaiderlrealrelgipviiv 155
                                       e+e+  ++++ +l++lgi+ +++
  gi|386001667|ref|YP_005919966.1| 253 EAEWAFDLFKTTLERLGIESLDD 275
                                       789999************98776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.2e-05
                            AAA_28   3 vitGgestGKTtlleaLaar...g 23 
                                       v+ G+++tGKT ++e+La++   g
  gi|386001667|ref|YP_005919966.1| 605 VLYGPPGTGKTYVAEHLAKHligG 628
                                       89****************997754 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05     0.044     249     288 ..     588     627 ..     578     634 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                          PPV_E1_C 249 ltalkefLkgvPkknclvllGppntGkslfamslikfLkG 288
                                       l +l ++++ + +k   vl+Gpp tGk++ a  l k L G
  gi|386001667|ref|YP_005919966.1| 588 LETLERWVRAIRRKRQAVLYGPPGTGKTYVAEHLAKHLIG 627
                                       66899*****************************999877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0002      0.16      11      41 ..     596     624 ..     579     637 .. 0.85
   2 ?   -1.7   0.0       2.5     2e+03      86     122 ..     679     717 ..     640     721 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                            AAA_30  11 ealltsgdrvavltGpAGtGKttalkalrea 41 
                                       +a+  ++   avl Gp+GtGKt++ ++l+++
  gi|386001667|ref|YP_005919966.1| 596 RAIRRKR--QAVLYGPPGTGKTYVAEHLAKH 624
                                       5555444..599************9999775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                            AAA_30  86 lepg.tllivDEagmvdtkq.laallkaaekagakvilv 122
                                        ++g  +li+DE+  ++ +q + +l+  +e ++ ++ l+
  gi|386001667|ref|YP_005919966.1| 679 SRHGtCVLIIDEINRANLSQvFGELMYLLEYRSRSIPLA 717
                                       4455478999**998876551456666665555555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.11      12      42 ..     596     626 ..     587     696 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_11  12 salseseitliqGPPGtgKTktivellsqll 42 
                                       +a++++  +++ GPPGtgKT +  +l ++l+
  gi|386001667|ref|YP_005919966.1| 596 RAIRRKRQAVLYGPPGTGKTYVAEHLAKHLI 626
                                       455555569***********99888888886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017      0.13       3      23 ..     605     625 ..     604     629 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            AAA_33   3 llvGlpGsGKstlaerllkkl 23 
                                       +l G+pG+GK+++ae+l+k+l
  gi|386001667|ref|YP_005919966.1| 605 VLYGPPGTGKTYVAEHLAKHL 625
                                       578**************9876 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.13      79     136 ..     571     623 ..     548     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                         Parvo_NS1  79 dieenriykllslngynpvevgqvllawlskqlgkrntvwfyGpantGktnlaeaIak 136
                                       + +e ++ykl++++g++   +     +w++    kr +v +yGp+ tGkt++ae +ak
  gi|386001667|ref|YP_005919966.1| 571 PPSEYPLYKLAEDTGFDLETLE----RWVRAIRRKRQAV-LYGPPGTGKTYVAEHLAK 623
                                       6667788888888888877777....7777766667776.79*************998 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0017       1.3       3     114 ..     605     738 ..     603     753 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                             AAA_3   3 llegvPGlaktllvkalakal....dlefkriqftpdllPsdil.Gtevfeeke............kefef.kkGpv 61 
                                       +l g PG++kt ++++lak+l    d   + +qf p     d + G++  ++++             ef    +   
  gi|386001667|ref|YP_005919966.1| 605 VLYGPPGTGKTYVAEHLAKHLiggtDGFSDLVQFHPAYAYEDFIqGIRPQSDDDgglrypivpgrfLEFCErAESRH 681
                                       57788999999999999998733212223568888888888854266655555556555555543312211022223 PP

                             AAA_3  62 fanllladeinrap.pktqsalleameerqvtv...egethklpepflvlatqnPie 114
                                        + +l+ deinra+ +++   l+  +e r  ++   +g++ ++pe+ l++ t n  +
  gi|386001667|ref|YP_005919966.1| 682 GTCVLIIDEINRANlSQVFGELMYLLEYRSRSIplaGGRRLRIPENVLIIGTMNTAD 738
                                       355888999999974577777777766554443222577889999999999999776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00067      0.52      13      57 ..     578     623 ..     573     630 .. 0.80
   2 ?   -0.5   0.0      0.91   7.1e+02     119     131 ..     682     694 ..     677     700 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00067
                              TniB  13 yprakeilerLeeLleypk.rkrmpnlllvGdsnnGKtmivekFar 57 
                                       y+ a++    Le L ++ +   r ++++l+G++ +GKt ++e+ a+
  gi|386001667|ref|YP_005919966.1| 578 YKLAEDTGFDLETLERWVRaIRRKRQAVLYGPPGTGKTYVAEHLAK 623
                                       66677777788889998873445589***************99776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.91
                              TniB 119 kvrvLiiDEihnl 131
                                       ++ vLiiDEi+++
  gi|386001667|ref|YP_005919966.1| 682 GTCVLIIDEINRA 694
                                       5679******975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00044      0.34       5      76 ..     604     694 ..     600     718 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..........vkkesilyinldderdkkladpe..........kllelileklk 61 
                                        v+ G+  +GKT+++++l+k+l+            +  + y ++ +     ++d +          ++le++ +  +
  gi|386001667|ref|YP_005919966.1| 604 AVLYGPPGTGKTYVAEHLAKHLIggtdgfsdlvQFHPAYAYEDFIQGIRP-QSDDDgglrypivpgRFLEFCERAES 679
                                       6899****************999998777666422233444444442111.11111344444344455555555444 PP

                            AAA_14  62 eekktylflDEiqev 76 
                                       ++++ +l++DEi ++
  gi|386001667|ref|YP_005919966.1| 680 RHGTCVLIIDEINRA 694
                                       47888899***9886 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0006      0.47      10      49 ..     589     626 ..     585     632 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
                                       HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierll 49 
                                       e +e+++ ++  +r++++++  + GtGKT+va +l+++l 
  gi|386001667|ref|YP_005919966.1| 589 ETLERWVRAI--RRKRQAVLYGPPGTGKTYVAEHLAKHLI 626
                                       5677888777..69999****************9999986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00054      0.42      30      57 ..     598     625 ..     590     634 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkl 57 
                                       +++k++ +l+Gp GtGKt ++++l k+l
  gi|386001667|ref|YP_005919966.1| 598 IRRKRQAVLYGPPGTGKTYVAEHLAKHL 625
                                       7889999*************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (849 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 4954.43
//
Query:       gi|386001668|ref|YP_005919967.1|  [L=933]
Description: cation-transporting ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-50  170.0   2.2    3.7e-50  170.0   2.2    2.8  4  E1-E2_ATPase     E1-E2 ATPase
    5.7e-46  156.5   9.5    5.7e-46  156.5   9.5    1.9  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.7e-23   84.0   6.9      3e-22   79.9   6.9    2.6  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.6e-18   65.4   0.0    5.3e-18   64.5   0.0    1.6  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    5.3e-18   64.9   0.0      1e-17   64.0   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    3.2e-08   33.6   0.8    0.00019   21.3   0.4    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    3.4e-06   27.6   0.1    7.6e-06   26.5   0.1    1.6  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.33   10.7   1.1        1.5    8.5   0.4    2.5  2  Phage_holin_2_2  Phage holin T7 family, holin superfamily II


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   1.3         3   6.8e+03     124     155 ..      64      94 ..      58      98 .. 0.61
   2 !  170.0   2.2   1.7e-53   3.7e-50      14     181 .]     149     336 ..     143     336 .. 0.98
   3 ?   -2.7   0.2       1.6   3.6e+03      94     138 ..     707     751 ..     689     771 .. 0.60
   4 ?   -2.3   0.0       1.2   2.7e+03     126     150 ..     806     832 ..     787     844 .. 0.42

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase 124 pvvlliallvflialllgkslaeallralall 155
                                       p+++++++++++  ll +k +  a+++a+ +l
  gi|386001668|ref|YP_005919967.1|  64 PIIIVLGIAAVIS-LLAEKRIDAAVIFAVIVL 94 
                                       4555555555555.455666667777777766 PP

  == domain 2  score: 170.0 bits;  conditional E-value: 1.7e-53
                                       S-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-...................G-TTEE CS
                      E1-E2_ATPase  14 teeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek...................ekgdmv 70 
                                       + ++++a+e+v+GDi+l++ag++vpaD+ri+e  + e+des+LTGEs+p++k                   e  +++
  gi|386001668|ref|YP_005919967.1| 149 RKVRVKAREIVVGDIILVEAGSKVPADARIIEAANlEIDESMLTGESVPAKKcvdseicrnppamgtlsemEIDNTI 225
                                       66789*****************************************************************99***** PP

                                       -TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHH CS
                      E1-E2_ATPase  71 fsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaea 147
                                       f+Gt+v++g+akavV atg+ t +gkia+++ ++k++ tpl+k    lg+ ++++++l++ l+f++ l++g +l++a
  gi|386001668|ref|YP_005919967.1| 226 FAGTIVTRGRAKAVVFATGMATDMGKIADMLTKTKKSATPLKKRTLDLGRKIMFLAILAGGLTFAVGLYRGFDLIDA 302
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 148 llralallvaaiPcaLplavplalalgarrlakk 181
                                       +l++la+ v+aiP aLp+a+++ala+g++r+ak+
  gi|386001668|ref|YP_005919967.1| 303 FLFTLAMTVSAIPAALPAAITVALAVGVSRMAKR 336
                                       ********************************96 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                                       TTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-S CS
                      E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvvlliallvflial 138
                                       ++ i+++vee +    ++ k ++ l+++ +  vl+i++ ++++al
  gi|386001668|ref|YP_005919967.1| 707 FQSIVNAVEEGRVIFQNIRKVVRYLINTSAGEVLAITASLLFLAL 751
                                       566666666666555555555555555544444444444444443 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHS-ST..TTSSTTHHHHH CS
                      E1-E2_ATPase 126 vlliallvfliall..lgkslaeallr 150
                                        l+ial++++ +l+  ++++ +  l+r
  gi|386001668|ref|YP_005919967.1| 806 TLFIALIMAVGTLFvfTREWNNGDLIR 832
                                       222222222222220033333344444 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.91     2e+03      50      69 ..     273     292 ..     235     330 .. 0.56
   2 !  156.5   9.5   2.5e-49   5.7e-46       2     181 ..     754     923 ..     753     924 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.91
                   Cation_ATPase_C  50 mlrriliqgllqalvtllvf 69 
                                       + r+i++ ++l + +t++v 
  gi|386001668|ref|YP_005919967.1| 273 LGRKIMFLAILAGGLTFAVG 292
                                       33444444444444444332 PP

  == domain 2  score: 156.5 bits;  conditional E-value: 2.5e-49
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       l+++++qiLw+nLvtD+++ + La+ep+e+d+m++pPr++ e++i++ +++++l+++l++a+ tl+vf  t  +++ 
  gi|386001668|ref|YP_005919967.1| 754 LIFTPVQILWVNLVTDGILVVNLAMEPKERDVMDQPPRDPAEKIINRDIVLNTLFIALIMAVGTLFVF--TREWNNG 828
                                       68******************************************************************..4444466 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                       +  +       aqtm Fit++++q+fnaln+rsr++s+f+  glfsn+ l +ai++s++lq+l +   ++na++g +
  gi|386001668|ref|YP_005919967.1| 829 DLIR-------AQTMGFITMAMFQVFNALNCRSRTQSVFS-LGLFSNRNLMVAIFASVVLQLLATELSFFNAALGSV 897
                                       6665.......*****************************.************************************ PP

                   Cation_ATPase_C 156 plsleewlialllalvvllvdelvKl 181
                                       +lsl++w++++++a+ vl+  e++K+
  gi|386001668|ref|YP_005919967.1| 898 SLSLTDWITMVAVAATVLIGEEIRKM 923
                                       *************************8 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   6.9   1.4e-25     3e-22       2     209 ..     353     680 ..     352     681 .. 0.68

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.4e-25
                                       SEEEEESBTTTBCHHHHHHHHHHHH...........................CHHHHHHHHHH.............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxx.............. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa...........................alalaaaletg.............. 37 
                                       ++++ Dk+GTLtt ++ v +++                              + +la  l+++              
  gi|386001668|ref|YP_005919967.1| 353 TAICTDKTGTLTTNQMTVQRIYLPDrivsvtgagfkpegsfevegseldpkeDGSLATFLRIAalcndsslsskegd 429
                                       799************99999777775555566666666666666666666664444444444433433444444555 PP

                                       .......HHCHHHHHH.HHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHH......HCHHHHHHHHHHHHHHCHHH CS
                                       .......xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  38 .......sehpigkal.vaaakarsgaltgfatfigrgayaigkpewltal......dippdlgaaigsaqsqgrtv 100
                                                 p   al vaaa                 ++   k+++ ++       ++ pd +   +  +++gr +
  gi|386001668|ref|YP_005919967.1| 430 dgerweiQGDPTEGALvVAAA-----------------KAGLAKEDLEASFprideiPFDPDKRYMATFNERDGRVE 489
                                       555555544444444433333.................333333333333344454455555555555555555555 PP

                                       HHH...................................................................TTHHHHH CS
                                       xxx...................................................................xxxxxxx RF
                         Hydrolase 101 all...................................................................qaralav 110
                                       + l                                                                        ++
  gi|386001668|ref|YP_005919967.1| 490 VCLkgapetvlgissaiavdgeprdlteadkerildmssqmaadalrvlgfatktigkeevagfkeagpsGLIFSGL 566
                                       55555555555555555555555555555555555566666666666888999999999999999765543344455 PP

                                       HHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.....GGGE.SEEEEHHCES........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx.xxxxxxxxxx........... RF
                         Hydrolase 111 ftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.....ddyf.daviasdiet........... 170
                                         + dp  ++pea ea+a  k+agi+vv++tgd++ tae++a+++G      ++f    +++ ++            
  gi|386001668|ref|YP_005919967.1| 567 SGMMDP--PRPEAIEAIALAKKAGIKVVMATGDHKITAEAIAREMGivegdSRAFaGSDLDGMDDSeldaamedaav 641
                                       555599..****************************************999666655555555555688899999** PP

                                       STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       +a +spe+k+++++ L+ k++ vam GDgvnDa+al+ A
  gi|386001668|ref|YP_005919967.1| 642 FARVSPEHKHRIVESLRRKGHIVAMTGDGVNDAPALKVA 680
                                       *******************999**************987 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   2.4e-21   5.3e-18       1      69 []       9      76 ..       9      76 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 2.4e-21
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      +++ls+e+v+e+L+ + e GLt+ ea +rl+ +GpNel+e k  ++ ++l++q++np++i+L +aa++s
  gi|386001668|ref|YP_005919967.1|  9 WYSLSIEDVFERLG-SGEGGLTTPEATRRLQDHGPNELEEGKGATWPEILISQIKNPIIIVLGIAAVIS 76
                                      899**********9.9***************************************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   4.5e-21     1e-17       1      86 [.     416     501 ..     416     506 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 4.5e-21
                     Cation_ATPase   1 ilcNsaaf..sensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrl 75 
                                       +lcN++++  +e ++ +++++ G++tE AL+v+a+k+gl +e+l+++++++ eipF+ ++++m++  +   +++v +
  gi|386001668|ref|YP_005919967.1| 416 ALCNDSSLssKEGDDGERWEIQGDPTEGALVVAAAKAGLAKEDLEASFPRIDEIPFDPDKRYMATFNE--RDGRVEV 490
                                       69**9999889999****************************************************99..57***** PP

                     Cation_ATPase  76 yvKGApeiilk 86 
                                         KGApe +l 
  gi|386001668|ref|YP_005919967.1| 491 CLKGAPETVLG 501
                                       *********96 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00016      0.37      18      54 ..     575     611 ..     571     621 .. 0.91
   2 !   21.3   0.4   8.5e-08   0.00019     196     254 ..     654     713 ..     650     714 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgl 54 
                                       ++++eai+ +k++gikvv ATG +  +++ +++e+g+
  gi|386001668|ref|YP_005919967.1| 575 PEAIEAIALAKKAGIKVVMATGDHKITAEAIAREMGI 611
                                       6899*********************999999999986 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 8.5e-08
                                       HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGVaka 254
                                       ++ l+ +   v+  GDg ND + L++a++g+Amg  +++  k+ Ad++ ++ n  ++++a
  gi|386001668|ref|YP_005919967.1| 654 VESLRRKGHIVAMTGDGVNDAPALKVAEIGIAMGiTGTDVTKETADMILTDDNFQSIVNA 713
                                       56666677778899*******************9789*************9999998876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   3.4e-09   7.6e-06      87     188 .]     574     678 ..     511     678 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.4e-09
                               HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelg.....adevlatelevddrltgelglegkpvrgegkvaal 158
                                       +p+a e++a +++aG++vv+ +g +++ +e++++e+g     + ++ ++      +l+g    +  + +  +++a+ 
  gi|386001668|ref|YP_005919967.1| 574 RPEAIEAIALAKKAGIKVVMATGDHKITAEAIAREMGivegdSRAFAGS------DLDGM--DDSELDAAMEDAAVF 642
                                       36***********************************333333333333......66666..333333333344444 PP

                               HAD 159 rewlaaegegidlee.....vvay.GDspsDlpllr 188
                                       ++   ++++ i ++      +va  GD+++D p+l+
  gi|386001668|ref|YP_005919967.1| 643 ARVSPEHKHRIVESLrrkghIVAMtGDGVNDAPALK 678
                                       4433344444433334455477778*********96 PP

>> Phage_holin_2_2  Phage holin T7 family, holin superfamily II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.8   1.8e+03      20      42 ..     860     882 ..     855     887 .. 0.85
   2 ?    8.5   0.4   0.00069       1.5      18      49 ..     893     923 ..     881     928 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.8
                   Phage_holin_2_2  20 ysaGlsldeWvlvatllYtVlQI 42 
                                        s+Gl  +  ++va ++ +VlQ+
  gi|386001668|ref|YP_005919967.1| 860 FSLGLFSNRNLMVAIFASVVLQL 882
                                       57899999999**********96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                   Phage_holin_2_2  18 aaysaGlsldeWvlvatllYtVlQIGakvvdk 49 
                                       a+ s  lsl +W+++++++ tVl IG+ + + 
  gi|386001668|ref|YP_005919967.1| 893 ALGSVSLSLTDWITMVAVAATVL-IGEEIRKM 923
                                       4447789***************9.89887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 6301.29
//
Query:       gi|386001669|ref|YP_005919968.1|  [L=326]
Description: hypothetical protein Mhar_0974 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00029   20.4   0.1     0.0021   17.6   0.1    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00032   20.7   2.5    0.00076   19.5   2.1    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.08   12.9   0.1       0.19   11.7   0.1    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
       0.17   11.8   0.0       0.38   10.6   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.7e-07    0.0021      29     169 ..      49     161 ..      37     187 .. 0.81
   2 ?   -0.4   0.0      0.15   6.9e+02     178     200 ..     274     296 ..     258     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.7e-07
                                       .SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEE CS
                     Lactamase_B_2  29 ppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdgglei 105
                                        + da l+thaH DH+    ++ +      + +a++++++ le +          + + +++  g+s+ ++  +le+
  gi|386001669|ref|YP_005919968.1|  49 VQPDAYLITHAHSDHYGKSAMISP------EAVASRETARALEIRHG-------RRYEGRTFPVGGSILVD--DLEV 110
                                       477999**********77777777......4689********99933.......2466788*********9..5788 PP

                                       EEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SST CS
                     Lactamase_B_2 106 tatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayed 169
                                        +    h+ g         ++G+  +  g rv+ +gD++ ++      l ++dll+ ++++ ++
  gi|386001669|ref|YP_005919968.1| 111 VTYSTGHTIGS-------VAFGWETD-LGVRVLVTGDVKNYE-----NLPKCDLLVTEANYGDP 161
                                       88888888888.......99999988.899********9766.....67889999999885544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.15
                                       ---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 178 HltpeeaveaaadlgakrlvliH 200
                                       Hl+ ++ +++++++++k +++ H
  gi|386001669|ref|YP_005919968.1| 274 HLDFKGLMRMVERISPKAALVYH 296
                                       89999999999999999998888 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.1   1.7e-07   0.00076      44     162 ..      50     151 ..      42     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-07
                                       GEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTE CS
                       Lactamase_B  44 dvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggr 120
                                       ++da ++TH+H+DH+G  + +  ++ +     ++ +  + ++++++                  ++  +  + ++  
  gi|386001669|ref|YP_005919968.1|  50 QPDAYLITHAHSDHYGKSAMISPEAVASRETARALEIRHGRRYEGR-----------------TFPVGGSILVDDLE 109
                                       688889****************999999888888888888877744.................38888888888888 PP

                                       EEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 121 ralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                       + +y tg+   +   g  ++ g +vl+tGD+   ++ ++ dl
  gi|386001669|ref|YP_005919968.1| 110 VVTYSTGHTIGSVAFGWETDLGVRVLVTGDVKNYENLPKCDL 151
                                       99999999999999999999**********998888888887 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.2e-05      0.19      10      56 ..     268     313 ..     266     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                             RMMBL  10 eidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeeg 56 
                                       +i  S H d+ +l++++++++p+   + H e + +  +a +l +e g
  gi|386001669|ref|YP_005919968.1| 268 QIRISDHLDFKGLMRMVERISPKAALVYHPEGRRANMMAHHL-RELG 313
                                       7889********************999998888877777777.6665 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.5e-05      0.38      34      82 ..      46     114 ..      12     155 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.5e-05
                     Lactamase_B_3  34 a..eeaDlvlisqaledHahletlkqlaenvkvlee......................geslevggleirava 82 
                                       +  +++D+ li++a++dH+   ++ +    ++ +++                      g+s+ v++le+ + +
  gi|386001669|ref|YP_005919968.1|  46 KgsVQPDAYLITHAHSDHYGKSAMIS----PEAVASretaraleirhgrryegrtfpvGGSILVDDLEVVTYS 114
                                       15589**************9887776....4444442333333334444444333333444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2278.06
//
Query:       gi|386001670|ref|YP_005919969.1|  [L=420]
Description: hypothetical protein Mhar_0975 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-67  227.3  37.0    3.2e-67  227.0  37.0    1.0  1  TctA      Tripartite tricarboxylate transporter TctA family
  ------ inclusion threshold ------
       0.21   11.3   8.9      0.054   13.2   1.5    2.7  3  HlyIII    Haemolysin-III related


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0  37.0   3.6e-71   3.2e-67       2     408 ..       8     408 ..       7     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 3.6e-71
                              TctA   2 llvllGvllGtliGllPGlhatlavalllpltf.....gldpeaalilllgiyvgaifggsipaillgvPGtpssva 73 
                                        +v++G l+G+++Gl PG+h+++++alll+l++     gl+p+ ++ ++l+++v+++f++++p+i++g+P ++++++
  gi|386001670|ref|YP_005919969.1|   8 SSVFFGLLFGIFSGLTPGIHSNNFAALLLALSPaflslGLEPLDLATAILAASVAHTFLDIVPSIFIGAP-DADTAL 83 
                                       579*******************************************************************.****** PP

                              TctA  74 tvldgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse...... 144
                                       +vl+g++++++G++ eA+rl+a+gS+ ++lv++ll+++l++l+ ++   f   +++ l+ll++++++il+e      
  gi|386001670|ref|YP_005919969.1|  84 AVLPGHEMMLEGKGIEAIRLSALGSASSILVALLLIVPLSLLFGRFYETF--MDHVGLVLLAIAAVTILTErgevie 158
                                       ********************************************777777..9************************ PP

                              TctA 145 ........ksllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.. 211
                                               k  l +l+++l ++llgt+++  +  ++     s+  +    l+p+l GlFg+s ll sl s+++ p  
  gi|386001670|ref|YP_005919969.1| 159 gqgslaplKYKLIALVLFLTSGLLGTFAFAHQDLAQ-----SPLGFRPEVLMPLLGGLFGASILLISLGSRAEVPdq 230
                                       ********************************9776.....788899*********************998888765 PP

                              TctA 212 .......lslkdlkkslptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaa 281
                                              +     + ++++++ g l+G++v+++Pgv++++a++++ + +  +           +e++++++++n+a+
  gi|386001670|ref|YP_005919969.1| 231 retgfgmP----ARTITKAAFFGGLAGSVVAWVPGVTPAVATVATRFGSD-W---------SGREFLVSVSGVNTAN 293
                                       54443321....12355678899*******************99998854.3.........679************* PP

                              TctA 282 aggaliplltlgipgsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.ki 357
                                       a  ++++ll+ g p+sg+a+++ +++            + +  l+++++ ++++ ++l+++ +l++++ +ak++ ++
  gi|386001670|ref|YP_005919969.1| 294 ALLTMVALLVVGRPRSGAAVAIQELV------------ELDRRLLLFMVTVAVFVSILSYLATLAAGRAAAKVVrRL 358
                                       *******************9999965............33667888899***********************888** PP

                              TctA 358 pkelLlpiilvllvigayalnnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                       ++  L+++il+ll++++ya+++  f+++++l+++v+Gl+    gv++ +++
  gi|386001670|ref|YP_005919969.1| 359 DYGRLCIAILALLTALTYAFTGP-FGLFIYLVSTVVGLVAPFAGVRKTHAM 408
                                       ***********************.************************998 PP

>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.34   3.1e+03     110     140 ..       6      36 ..       3      67 .. 0.66
   2 ?    2.1   0.1     0.015   1.3e+02      79      96 ..     134     151 ..     104     214 .. 0.53
   3 ?   13.2   1.5     6e-06     0.054      47     122 ..     326     398 ..     290     418 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.34
                            HlyIII 110 ylslilalgvlgiisklvplfsrpearplra 140
                                       ++s++    ++gi+s l+p  +++++  l  
  gi|386001670|ref|YP_005919969.1|   6 LISSVFFGLLFGIFSGLTPGIHSNNFAALLL 36 
                                       5566666667888888888777766655544 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.015
                            HlyIII  79 lDysgIslliagsylpli 96 
                                       +D++g++ll ++ ++ l+
  gi|386001670|ref|YP_005919969.1| 134 MDHVGLVLLAIAAVTILT 151
                                       344444333333333222 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 6e-06
                            HlyIII  47 fllgallcllcSalyHtlsihseeklrkffaklDysgIslliagsylplilyalakapkagllylslilalgvlgi 122
                                        l+ + + +++S l+ + +    + + k++++lDy  +++ i++  ++l++      + +gl++  +++++g+++ 
  gi|386001670|ref|YP_005919969.1| 326 LLFMVTVAVFVSILSYLATLAAGRAAAKVVRRLDYGRLCIAILALLTALTYAFT---GPFGLFIYLVSTVVGLVAP 398
                                       45556666778888888888888899*******************999988766...5688888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2628.64
//
Query:       gi|386001671|ref|YP_005919970.1|  [L=120]
Description: 50S ribosomal protein L18e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-16   60.5   0.0    1.5e-16   60.3   0.0    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    3.1e-09   37.6   0.3    1.4e-08   35.5   0.3    1.9  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   1.7e-20   1.5e-16      15     139 ..       2     120 .]       1     120 [] 0.91

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.7e-20
                     Ribosomal_L18  15 kapksenvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrl 91 
                                       k++k +n+ l  L+   +  +r  +s   + v krL + r+n +++ +s++ +++      + ++ v g+v+    l
  gi|386001671|ref|YP_005919970.1|   2 KKVKKTNPGLVTLIDDLKAATRNDGSAIWRDVAKRLEKPRRNYAAVNVSKINRHTAP----DDLVLVAGKVLGTGDL 74 
                                       567778888888888888889999999999**********************99985....589999****999888 PP

                     Ribosomal_L18  92 levPklsvaALrftetararilkaGGeiltlDqLalraPtGkntvLlr 139
                                        +  k++vaAL+f+e+a ++i  aGGe+l +D+La ++P+G+  ++lr
  gi|386001671|ref|YP_005919970.1|  75 DH--KVTVAALQFSEQAASKIKSAGGECLRIDELADKHPKGSGIIILR 120
                                       75..9****************************************998 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.3   1.5e-12   1.4e-08      72     126 ..      44     100 ..      18     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.5e-12
                                       --EEEGGGTTTTSSS......SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  72 aeeidleelaeaglikk..kdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                        + ++++++ ++   +        Kvlg+g+l +k++v a +fS++A +kI++aGG++
  gi|386001671|ref|YP_005919970.1|  44 YAAVNVSKINRHTAPDDlvL-VAgKVLGTGDLDHKVTVAALQFSEQAASKIKSAGGEC 100
                                       34555555533333333422.235*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 887.28
//
Query:       gi|386001672|ref|YP_005919971.1|  [L=138]
Description: 50S ribosomal protein L13 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-11   44.7   0.7    2.3e-09   37.6   0.7    2.1  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.7   1.3e-13   2.3e-09       4     114 ..       2      98 ..       1     106 [. 0.80

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-13
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHH CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakell 80 
                                       +iDA+g++lgrlas +a+ L             +G+ + ++naek  ++g++  + +y+++ +   +  +++     
  gi|386001672|ref|YP_005919971.1|   2 IIDASGMILGRLASLAASEL------------LAGEEIAIVNAEKAIISGRR--ETIYREYEEMKNK-GSTEKGPHY 63 
                                       78999999999999988766............479999************96..5577776665444.445555667 PP

                                       CCSHHHHHHHHHHCCS-S.SHHHHHHGCTEEEESS CS
                     Ribosomal_L13  81 ekkpeeilekaVkgmLpk.nklgrrrlkrLkvyag 114
                                        k+pe+il+++V+gmLp+ +k gr+ ++rL++y g
  gi|386001672|ref|YP_005919971.1|  64 PKRPERILKRTVRGMLPHkTKRGRDAMSRLRIYVG 98 
                                       788**************7256899999******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.43
# Mc/sec: 970.60
//
Query:       gi|386001673|ref|YP_005919972.1|  [L=132]
Description: 30S ribosomal protein S9 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-34  119.7   0.9    1.1e-34  119.5   0.9    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.9   6.4e-39   1.1e-34       1     121 []       8     132 .]       8     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 6.4e-39
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+ ++++Ar++++egkg++++n+k+le  f+ e  r+k++ep+ +++++ + +d+ vkv+gGG++gqa+A+r++iar
  gi|386001673|ref|YP_005919972.1|   8 GKNRTAIARATLTEGKGRVRINSKPLEI-FEPELVRQKIMEPVMIAQEKASgLDIDVKVRGGGFMGQAAAVRTAIAR 83 
                                       899*************************.877**************999988************************* PP

                                       HHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       ++v+++    ++Lk      +++ll++D R++ErkK+g ++AR+kyq+s+R
  gi|386001673|ref|YP_005919972.1|  84 GIVEWTG--DTALKeaymeyDRSLLVNDHRQKERKKVGGPGARAKYQKSYR 132
                                       *****88..578887777789****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 948.07
//
Query:       gi|386001674|ref|YP_005919973.1|  [L=39]
Description: hypothetical protein Mhar_0980, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.019   14.9   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     1e-06     0.019      32      49 .]      12      29 ..       2      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-06
                                      -SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6 32 qkpvviAlrEiaegkipi 49
                                       +p+ iAl+E+  g +pi
  gi|386001674|ref|YP_005919973.1| 12 IDPLEIALEEMRLGFVPI 29
                                      49************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       187  (0.01043); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.40
# Mc/sec: 295.60
//
Query:       gi|386001675|ref|YP_005919974.1|  [L=208]
Description: 30S ribosomal protein S2P [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-26   90.6   1.3    1.4e-15   57.1   0.6    2.0  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
      0.027   14.0   0.5      0.056   13.0   0.5    1.5  1  Peripla_BP_4  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   5.4e-12   4.8e-08       2      95 ..      25     115 ..      24     122 .. 0.92
   2 !   57.1   0.6   1.5e-19   1.4e-15     148     213 ..     123     188 ..     119     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.4e-12
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L+ag+h+G q++  +++m  yIy +r +g +++d++ t + +r a+k++ +   + +kil v+ ++  ++  +  +k
  gi|386001675|ref|YP_005919974.1|  25 LAAGIHIGTQQK--TKSMMDYIYRVRtDGLYVLDVQATDKRIRLAAKFLAKY--DPSKILVVSARQYGQRPATMFSK 97 
                                       89******6665..89*******999569********************975..7899******************* PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                        +++  +  r+++ t+TN
  gi|386001675|ref|YP_005919974.1|  98 AVGSKAIVGRFIPNTMTN 115
                                       ****************** PP

  == domain 2  score: 57.1 bits;  conditional E-value: 1.5e-19
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                        Pd+vvv+dp  ++ a++Ea  +gipv+a++Dtn  +++vd +Ip N++  ++++li+ +la+ + 
  gi|386001675|ref|YP_005919974.1| 123 EPDVVVVTDPAGDSQAINEAIDVGIPVVALCDTNNLTSNVDLVIPTNNKGRKALTLIYWLLAKEVL 188
                                       59***********************************************************99875 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   6.2e-06     0.056      58     105 ..     126     171 ..     110     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-06
                                       EEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HH CS
                      Peripla_BP_4  58 giivapvdstalapalkkakaaGIpVvafdsddapsgerlayvgfdne 105
                                       +  v ++d+++ ++a+++a + GIpVva    ++ +++++ ++ ++n+
  gi|386001675|ref|YP_005919974.1| 126 V--VVVTDPAGDSQAINEAIDVGIPVVALCDTNNLTSNVDLVIPTNNK 171
                                       4..4455988889***************54444889999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1376.83
//
Query:       gi|386001676|ref|YP_005919975.1|  [L=260]
Description: hypothetical protein Mhar_0982 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-74  249.1   0.0    4.8e-74  248.9   0.0    1.0  1  Memo      Memo-like protein
     0.0019   17.3   0.0     0.0028   16.8   0.0    1.3  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.9   0.0   5.4e-78   4.8e-74       4     270 ..       1     257 [.       1     258 [. 0.98

  Alignments for each domain:
  == domain 1  score: 248.9 bits;  conditional E-value: 5.4e-78
                              Memo   4 vAGsfYpedeeelkkqleeflekntgkkei.arviisPHagyvysgevaakayaelesskvervvilGpsHtilgsk 79 
                                       +AG+fYp ++++l + l++ +   +g ++   r  ++PHagy+ysg vaa++y +l ++  e++v++Gp+H++lg +
  gi|386001676|ref|YP_005919975.1|   1 MAGQFYPLQPQKLLEELKAAFSGASGGEPLpIRGAVVPHAGYIYSGAVAAEVYGRLPER--ETFVLIGPNHHGLGLP 75 
                                       59*******************99999998899************************999..9*************** PP

                              Memo  80 vsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseeta 156
                                       v++++ + + TPlG+++ D el+ +L    +i ++de a+l+EHSlEvq+pfL+ ++    fki+Pi ++ q+eeta
  gi|386001676|ref|YP_005919975.1|  76 VAISR-DSWMTPLGTVESDVELADALAG--SILEVDESAHLYEHSLEVQIPFLQARFSG--FKILPIAMGLQDEETA 147
                                       *****.********************99..59***************************..**************** PP

                              Memo 157 kevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGekpi 231
                                        evgea+ +++k       +i+SsD++Hy+     pqe+a+++ D+++i+a+ +++   ++ +++++n t cG++pi
  gi|386001676|ref|YP_005919975.1| 148 VEVGEAVGEAAKSLGrdCTIIASSDFTHYE-----PQEEARRK-DAQAIEAILRMDVPSVYRAVYGQNLTACGYGPI 218
                                       *************99889************.....********.********************************* PP

                              Memo 232 avilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                       ++++ a++ lga+ +kll+Y++s+dv +d+++vV+y+++
  gi|386001676|ref|YP_005919975.1| 219 SATITAARILGAETGKLLRYSTSGDVLGDYSQVVGYGAI 257
                                       ************************************875 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.1e-07    0.0028     141     196 ..     134     189 ..     115     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-07
                              LigB 141 lntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaqt 196
                                       + ++a++l + e   ++GeA+++a ++l +   i++s +++H+ +++ea  +daq 
  gi|386001676|ref|YP_005919975.1| 134 ILPIAMGLQDEETAVEVGEAVGEAAKSLGRDCTIIASSDFTHYEPQEEARRKDAQA 189
                                       45566889999********************************9999999999863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1797.67
//
Query:       gi|386001677|ref|YP_005919976.1|  [L=319]
Description: Mevalonate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-17   61.4   1.3    2.3e-16   59.8   0.3    2.2  2  GHMP_kinases_N  GHMP kinases N terminal domain
    8.4e-12   45.3   0.6    2.2e-11   44.0   0.6    1.7  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.19   1.7e+03      21      35 ..       9      23 ..       8      45 .. 0.66
   2 !   59.8   0.3   2.5e-20   2.3e-16       1      66 []      86     154 ..      86     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHHTTEH CS
                    GHMP_kinases_N 21 avalvaAllallgls 35
                                      +v+++aAl a+ +l+
  gi|386001677|ref|YP_005919976.1|  9 VVSGAAALGAAVDLR 23
                                      788888888887643 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 2.5e-20
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       +++++seiP+++GLGSSA+++va++ Al ++l l++  ee a+ a+++er +q g gs+ D a +++Gg
  gi|386001677|ref|YP_005919976.1|  86 RVTVESEIPPASGLGSSASVVVATLGALSRHLALDMstEEiAMEAFRIERTVQEGLGSPTDTALAAFGG 154
                                       589*****************************888744448999************************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.6   2.4e-15   2.2e-11       3      79 ..     217     290 ..     215     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.4e-15
                    GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselG.algaklsGaGgGptvfalfkdkdeaeqvara 78 
                                       e++++g+le+lgel+n ++   l++ vg+ ++el el+ a +  G a+gakl+GaGgG++ +al   +++   v+ra
  gi|386001677|ref|YP_005919976.1| 217 ELIREGRLEELGELMNTNHG--LLEAVGVGTRELSELVYASRGGGqAFGAKLTGAGGGGCMIALP--RPGPGGVLRA 289
                                       67899***************..899***************99999*******************9..5555566666 PP

                    GHMP_kinases_C  79 l 79 
                                       +
  gi|386001677|ref|YP_005919976.1| 290 M 290
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 2294.03
//
Query:       gi|386001678|ref|YP_005919977.1|  [L=252]
Description: Isopentenyl phosphate kinase [Methanosaeta harundinacea 6Ac]
Scores for 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-33  114.2   0.7    8.1e-33  114.0   0.7    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.076   13.4   0.0       0.21   12.0   0.0    1.7  2  RAMA       Restriction Enzyme Adenine Methylase Associated


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.7   9.1e-37   8.1e-33       2     241 .]       4     228 ..       3     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 9.1e-37
                                       EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HH CS
                         AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstlee 72 
                                       + ++K+GGs+ltdk +      + ++r+a+++a     g+ l++VhG+gsf+++++++ + l +++ a         
  gi|386001678|ref|YP_005919977.1|   4 IRILKVGGSVLTDKTRlesartEEIERIAAEVAGC---GEGLILVHGAGSFGHFHAER-YRLAERFDA--------- 67 
                                       579************9*****999***********...888*****************.********9......... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEE CS
                         AA_kinase  73 agevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigl 149
                                       +g ++t+++++ l+  +v+ l +ag + v++++  + + ++gr       +   +   i e++ +g vpvl+g++++
  gi|386001678|ref|YP_005919977.1|  68 EGVLETHRSVVRLNDLVVEGLRRAGSSPVPVHPLGSSLLKDGR-------IVGMEVGPILEMVRRGLVPVLHGDVAM 137
                                       8*********************************999998888.......*************************** PP

                                       ETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.......CSSS.TTTHH CS
                         AA_kinase 150 deegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.......saselatgGm 219
                                       d   + +++s+D++ ++lA ++++  + + t  dGV ++        ++lp+++   +         sa+ ++tgGm
  gi|386001678|ref|YP_005919977.1| 138 DLVRGAAIVSGDQLVSHLARLVKPTIVALGTAADGVISDG-------EVLPQLRRAGVSGiwselgpSAGVDVTGGM 207
                                       ************************************9775.......44555544444444449999********** PP

                                       HHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 220 kvkhpaalaaarrggipvvItn 241
                                       + k+++ l++a +g +  vI+n
  gi|386001678|ref|YP_005919977.1| 208 RGKVEELLDLADEG-VSSVIFN 228
                                       **************.8888887 PP

>> RAMA  Restriction Enzyme Adenine Methylase Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05      0.21      16      65 ..      72     115 ..      56     128 .. 0.81
   2 ?   -2.6   0.0      0.82   7.3e+03      35      49 ..     144     157 ..     136     186 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                              RAMA  16 ktapsrrarvtlkdLleagllepGekll.ieykgrthkAdlladGkIkgqe 65 
                                       +   + r+ v+l dL+ +gl ++G   + ++ +g     +ll+dG+I+g e
  gi|386001678|ref|YP_005919977.1|  72 E---THRSVVRLNDLVVEGLRRAGSSPVpVHPLGS----SLLKDGRIVGME 115
                                       2...23555************************98....9*******9765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.82
                              RAMA  35 llepGekllieykgr 49 
                                        +  G++l+ + + r
  gi|386001678|ref|YP_005919977.1| 144 AIVSGDQLV-SHLAR 157
                                       555555555.33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1781.95
//
Query:       gi|386001679|ref|YP_005919978.1|  [L=362]
Description: Isopentenyl-diphosphate delta-isomerase, type 2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-21   74.3   5.8    4.7e-12   45.6   4.2    2.2  2  FMN_dh        FMN-dependent dehydrogenase
     0.0093   15.0   0.7     0.0093   15.0   0.7    2.3  2  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
        0.8    8.8   4.7        1.2    8.1   2.4    2.3  2  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.7e-10     1e-06      28     103 ..      24     100 ..      16     128 .. 0.85
   2 !   45.6   4.2   7.8e-16   4.7e-12     208     343 ..     171     331 ..     136     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.7e-10
                                       HGGGGEEE---SSSS-SS-..B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HH CS
                            FMN_dh  28 aaferirlrprvlrdvskv..dlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvastsle 102
                                       + fe+++l++r+l ++  +  d ++++lG++l++P++i  +       ++ +++la aa++ g+ ++++++ +++le
  gi|386001679|ref|YP_005919978.1|  24 QPFEDVALVHRALPEIDAAeiDSRCRFLGKELAFPFMITGMTGGHPETKEINVNLALAAQEVGVAMGVGSQ-RAALE 99 
                                       679**********9876554499******************99999999*****************99987.55555 PP

                                       H CS
                            FMN_dh 103 e 103
                                       +
  gi|386001679|ref|YP_005919978.1| 100 N 100
                                       4 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 7.8e-16
                                       HHHHHHHHS..SEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG............TSSTT---HHHCH...... CS
                            FMN_dh 208 ikwlreqtk..lplvvKGv...ltaedakraveaGvdgivvSNHGG............RqldgapatidvL...... 261
                                       ++ +r++ +  +p++ K+    ++ eda  ++eaGv+ i v+  GG               dg  a +  L      
  gi|386001679|ref|YP_005919978.1| 171 MAAIRAASDgrVPIIAKETgagICREDALALLEAGVEVIDVAGMGGtswsgveayraeERGDGESAVMGRLfwswgv 247
                                       566666666337999999888999*******************************8886678888888888888888 PP

                                       ...HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                            FMN_dh 262 ...peiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGv 335
                                           ++ve +   +ev+ +gG+r+G Dv+k +alGA++ + + pfl   a++G   v  +l+  ++ ++++m l+  
  gi|386001679|ref|YP_005919978.1| 248 ptpVSVVECASAGAEVISSGGVRSGIDVAKSIALGARLGGAALPFLRP-ATEGSSEVVGALRAYERAFRTAMFLTAS 323
                                       7766778888889********************************887.89*************************9 PP

                                       SBHHHHHC CS
                            FMN_dh 336 ksvaeldr 343
                                       ++++ l++
  gi|386001679|ref|YP_005919978.1| 324 RDLSALES 331
                                       99998865 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.8     0.028   1.6e+02     133     177 ..     168     217 ..      26     222 .. 0.71
   2 !   15.0   0.7   1.6e-06    0.0093     181     231 ..     238     284 ..     230     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHTTT.SEEEE...EEE-SHHHHHHHHHTT-SEEEE.-SS-S CS
                                       xxxxxxxxxxxxx.xxxxx...xxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             IMPDH 133 leavkeikkkvee.vevia...GnvataegakaLieagadavkv.GiGpG 177
                                         a+++i+++ +  v +ia   G    +e a aL+eag++++ v G+G  
  gi|386001679|ref|YP_005919978.1| 168 RGAMAAIRAASDGrVPIIAketGAGICREDALALLEAGVEVIDVaGMGGT 217
                                       34556666666545777753336667789999999999999988778865 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-06
                                       HHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 181 ttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGad 231
                                       + r   + Gvp   +v+e+a+a    g +vi+ GG+++  d++k++a+Ga 
  gi|386001679|ref|YP_005919978.1| 238 MGRLFWSWGVPTPVSVVECASA----GAEVISSGGVRSGIDVAKSIALGAR 284
                                       5677778899999999998875....778********************96 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.13   7.8e+02      64     100 ..      55      92 ..      44     115 .. 0.77
   2 ?    8.1   2.4   0.00021       1.2     276     297 ..     262     283 ..     170     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.13
                                       HHTTEE---B-TTTS.-HHHHHHHHHHHHHHT-B-EET CS
                      Glu_synthase  64 ikkriltsamSyGal.seeahealakamnrlgtksntG 100
                                       ++ ++++++m  G    +e +  la a++++g ++  G
  gi|386001679|ref|YP_005919978.1|  55 LAFPFMITGMTGGHPeTKEINVNLALAAQEVGVAMGVG 92 
                                       66678888888886425677788888888888888776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00021
                                       EEEEESS--SHHHHHHHHHHT- CS
                      Glu_synthase 276 sliadGglktgadvvkalalGA 297
                                       ++i +Gg+++g dv+k++alGA
  gi|386001679|ref|YP_005919978.1| 262 EVISSGGVRSGIDVAKSIALGA 283
                                       5789*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2396.62
//
Query:       gi|386001680|ref|YP_005919979.1|  [L=446]
Description: RNA-metabolising metallo-beta-lactamase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-09   37.7   0.3    6.8e-08   32.3   0.1    2.4  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.4e-08   34.5   0.3    3.4e-07   30.1   0.1    2.6  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    6.2e-06   26.4   0.8    1.5e-05   25.1   0.7    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.075   12.1   0.0       0.12   11.5   0.0    1.2  1  PDEase_II      cAMP phosphodiesterases class-II


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   1.5e-11   6.8e-08      30     144 ..      74     176 ..      61     190 .. 0.86
   2 ?    3.1   0.0     0.013        60     165     200 ..     378     410 ..     336     411 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.5e-11
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleit 106
                                       +++ +  th+H DH+  +  l++ +  k+p+++++ +++ +++++ ++ l+   + +v+++++g+++++  +++e++
  gi|386001680|ref|YP_005919979.1|  74 KVKTIACTHGHLDHIGAISKLAHKY--KAPIVGTPFTADLIKQEIEAEKLQGT-KNEVVTMNAGKKMQVS-SDVELE 146
                                       789999*********9999999954..38*****************9999999.***************7.69**** PP

                                       EEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2 107 atparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                       ++ ++h+           ++  +i +++  ++y+ D +
  gi|386001680|ref|YP_005919979.1| 147 FIRVQHSIVD--------CVFAAIHTPRGVILYANDFK 176
                                       ******8777........77777777777777777765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                                       S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 165 tayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                        +y++       gH+ +e+ +e++++++++ +++ H
  gi|386001680|ref|YP_005919979.1| 378 RVYDNVH---VSGHACVEDHWELLRMINPEHVIPSH 410
                                       4555544...689*********************99 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.068     3e+02      32      55 ..      76      98 ..      72     115 .. 0.85
   2 !   30.1   0.1   7.5e-11   3.4e-07       9      45 ..     381     417 ..     374     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.068
                             RMMBL 32 rnvilvHGeeeatsalarllkeee 55
                                      + ++  HG+ +++ a  +l+  ++
  gi|386001680|ref|YP_005919979.1| 76 KTIACTHGHLDHIGAISKLA-HKY 98
                                      77999*********999998.655 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 7.5e-11
                             RMMBL   9 eeidfSgHadknellelirklkprnvilvHGeeeats 45 
                                       +++++SgHa  +++ el+r+++p++vi+ HG  e   
  gi|386001680|ref|YP_005919979.1| 381 DNVHVSGHACVEDHWELLRMINPEHVIPSHGTFETHG 417
                                       4566***************************987555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.7   3.4e-09   1.5e-05      43      82 ..      73     112 ..      13     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.4e-09
                                       GGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B  43 kdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        +v+++  TH+HlDHiG+  +l++++++p++  + +a   
  gi|386001680|ref|YP_005919979.1|  73 GKVKTIACTHGHLDHIGAISKLAHKYKAPIVGTPFTADLI 112
                                       579**************************99877666555 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05      0.12      77     128 ..      71     116 ..      52     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                                       HHHTEEEEE-S---GGGTHHHHHHGGGGGS-S.--EEEEE-HHHHHHHHHHT CS
                         PDEase_II  77 iknniksylItHsHLDHvsglvinSaefykaqlkkktivGlpytInalqkhl 128
                                       +  ++k+   tH HLDH++ ++   a+ yka      ivG p+t + +++++
  gi|386001680|ref|YP_005919979.1|  71 VDGKVKTIACTHGHLDHIG-AISKLAHKYKA-----PIVGTPFTADLIKQEI 116
                                       6678999999*******95.66777777776.....69********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 3152.98
//
Query:       gi|386001681|ref|YP_005919980.1|  [L=322]
Description: Farnesyl-diphosphate synthase/ geranylgeranyl-diphosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-70  235.9   0.0    4.3e-70  235.7   0.0    1.0  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.072   13.3   0.4        3.7    7.8   0.0    3.2  3  TetR_C_30        Tetracyclin repressor-like, C-terminal domai


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.0   4.8e-74   4.3e-70       2     254 ..      29     272 ..      28     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 4.8e-74
                                       HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCT CS
                   polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlv 78 
                                       ++l++a ++lv+agGKrlRp ++l+aaea++    +l+ +  +a+ +el+h+++L+hDDimD++etRRG+p++h ++
  gi|386001681|ref|YP_005919980.1|  29 RELYAAGRHLVDAGGKRLRPSMLLMAAEAVG---GDLRAVVPAAVSIELVHNFTLIHDDIMDNAETRRGRPAVHVKW 102
                                       5789999************************...4689*************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHH...STTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTH CS
                   polyprenyl_synt  79 GnklAindgdfllarafellaklf...ekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTa 152
                                       +++ Ai++gd l+++afe+l+      e+ +  +++++++++ ++eGq ld+e e++d+++   ++eyle++++KT+
  gi|386001681|ref|YP_005919980.1| 103 DEAGAILAGDTLYSKAFEILTVAEarpEEMVASVKMLAKTCAAICEGQWLDMEFERRDEVT---EAEYLEMIEKKTG 176
                                       ********************98877655559*********************999999999...************* PP

                                       HHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-H CS
                   polyprenyl_synt 153 ylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelasp 229
                                       +l+ +++ ++a l+ga+++e++ l+++g+ +G+aFQiqDD+lDl++ ++vlgKp g D++egk tl++++a+ +   
  gi|386001681|ref|YP_005919980.1| 177 VLYGAAAWMGARLSGAAEKEADGLERFGRLVGMAFQIQDDVLDLTAPAKVLGKPRGGDLAEGKKTLIMIHAMARGA- 252
                                       ****************9999*****************************************************333. PP

                                       HHHHHHHHHTTSSHHHHHHHHHHHH CS
                   polyprenyl_synt 230 eqrkvlkeilgkkaekeedvkeale 254
                                              ei+gkk++++e++++al+
  gi|386001681|ref|YP_005919980.1| 253 -----RIEIFGKKNASQEEIEAALD 272
                                       .....36899999999999999886 PP

>> TetR_C_30  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.073   6.5e+02      52      70 ..      16      34 ..       3      42 .. 0.77
   2 ?    0.2   0.0     0.095   8.5e+02      12      30 ..     194     212 ..     183     223 .. 0.77
   3 ?    7.8   0.0   0.00041       3.7      77     108 ..     243     274 ..     241     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.073
                         TetR_C_30 52 iaalrralPdlpeeelfwr 70
                                        a+ ++lP +p++el+ +
  gi|386001681|ref|YP_005919980.1| 16 SGAIEELLPVVPPRELYAA 34
                                      579999**********986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.095
                         TetR_C_30  12 eeggeggrafarllarvys 30 
                                       e + +g+ +f rl+++++ 
  gi|386001681|ref|YP_005919980.1| 194 EKEADGLERFGRLVGMAFQ 212
                                       45568999*******9987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00041
                         TetR_C_30  77 allftladtgrldilsggecssadlealierl 108
                                        +++++a+  r++i +++ +s++++ea+++ l
  gi|386001681|ref|YP_005919980.1| 243 IMIHAMARGARIEIFGKKNASQEEIEAALDAL 274
                                       599*************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2364.01
//
Query:       gi|386001682|ref|YP_005919981.1|  [L=80]
Description: hypothetical protein Mhar_0988 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0046   16.8   3.5     0.0051   16.6   3.5    1.3  1  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.025   14.7   0.9      0.026   14.7   0.9    1.1  1  DUF2407_C      DUF2407 C-terminal domain
       0.33   10.5   1.3       0.52    9.9   1.3    1.4  1  Phage_fiber_2  Phage tail fibre repeat


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.5   8.6e-07    0.0051      69     104 ..      20      53 ..       5      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.6e-07
                         SprT-like  69 aHElcHlalfvisgvrnnpHGaeFkawaakvekala 104
                                       aHE+ Hl+ + i++  n+ H ++F+a a+++e a+ 
  gi|386001682|ref|YP_005919981.1|  20 AHEIEHLLDHWIEH--NKSHSESFRARAREMEAASP 53 
                                       8*************..***************99874 PP

>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   4.4e-06     0.026      27      79 ..       2      54 ..       1      76 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
                         DUF2407_C 27 ygseetpdtmpsdleeeeeeelreLEerWidstanaeeaaeaeeegeaakeee 79
                                      +++++ +dt++s+ +e + +e+ +L ++Wi+++++++e+ +a++++++a++ +
  gi|386001682|ref|YP_005919981.1|  2 HEHKHGSDTHGSHEHELNAHEIEHLLDHWIEHNKSHSESFRARAREMEAASPK 54
                                      5678889999999888888**************97777666444444443333 PP

>> Phage_fiber_2  Phage tail fibre repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   8.7e-05      0.52      18      33 ..      46      64 ..      45      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.7e-05
                     Phage_fiber_2 18 setlAATpkA...VKtayD 33
                                      +e +AA+pkA   V++a +
  gi|386001682|ref|YP_005919981.1| 46 REMEAASPKAaarVREAAE 64
                                      89********999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1245  (0.0694406); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 599.10
//
Query:       gi|386001683|ref|YP_005919982.1|  [L=244]
Description: transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-25   88.4   0.1    3.5e-25   87.7   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      1e-05   24.8   0.0    1.7e-05   24.1   0.0    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0024   17.6   0.0     0.0057   16.4   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.066   13.0   0.0       0.17   11.8   0.0    1.6  1  HTH_23          Homeodomain-like domain
       0.09   12.7   0.0       0.29   11.1   0.0    1.9  2  MarR_2          MarR family
      0.095   13.1   0.0       0.18   12.2   0.0    1.5  1  Rrf2            Transcriptional regulator


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 !   87.7   0.1   1.2e-28   3.5e-25       1      68 []       9      76 ..       9      76 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.2e-28
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      L+klGL+eyEa+ Y+aL+ lg+ata+e++e++gvpr++vY++L+ L +kG+ e ++g+p++Yra++pe
  gi|386001683|ref|YP_005919982.1|  9 LRKLGLTEYEARSYTALVGLGEATAREVHEMSGVPRTRVYDILKDLTEKGFAEFVQGSPTYYRAIEPE 76
                                      78****************************************************************97 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.8e-09   1.7e-05       2      97 ..     110     217 ..     109     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.8e-09
                                       EEEESSHHHHHHHHHHHHHH-SSEEEE.EE-GGGHHHHHHHHHHHHHTT-EEEEEESS.........----GGGSSS CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAeneliv.slpselLeelreeliaaaergvtVllliyp.........dedleeldle 68 
                                       vw v+++  +++r+++l + A+ el++ + ++ +L+e r++l +  ++g++ ++++           d  +     +
  gi|386001683|ref|YP_005919982.1| 110 VWCVRNEWGIKNRVRDLMKRADGELLIfCRSPDFLREHRSDLSSELKEGCKLVMIVDRkdkfedlglDLREIWGGAA 186
                                       8***********************987356889**********************9998888844333333333445 PP

                                       SEEEEEE-S---S...EEEEETTTEEEEE-S CS
                    Regulator_TrmB  69 evatevrvrrsga..pllvivDrkrgvvapr 97 
                                       e+++++rv   +     ++i+D+k+++v++r
  gi|386001683|ref|YP_005919982.1| 187 EIYKDIRVDGVNYslDCMMIADGKESIVITR 217
                                       6667778776666345689999999999987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.9e-06    0.0057      18      49 ..      30      61 ..      25      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyve 49
                                      e t +e+++ +g+p++ v+ +L+ L+e G+ e
  gi|386001683|ref|YP_005919982.1| 30 EATAREVHEMSGVPRTRVYDILKDLTEKGFAE 61
                                      56899*************************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.5e-05      0.17      19      47 ..      32      60 ..      26      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                            HTH_23 19 svreIAreLgvsrrTvyrwlkryreeGle 47
                                      + re+ ++ gv+r  vy +lk   e+G++
  gi|386001683|ref|YP_005919982.1| 32 TAREVHEMSGVPRTRVYDILKDLTEKGFA 60
                                      789********************999975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   3.3e+03      41      54 ..       5      18 ..       4      25 .. 0.83
   2 ?   11.1   0.0   9.6e-05      0.29      21      56 ..      30      65 ..      12      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                      HHHHHHHTTSEEEE CS
                            MarR_2 41 ilkrLvaaGLverr 54
                                      i++ L + GL e++
  gi|386001683|ref|YP_005919982.1|  5 IVDGLRKLGLTEYE 18
                                      78999999999987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.6e-05
                                      EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 21 dltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      + t++e+ +  g+++ +v  ilk+L ++G+ e + g
  gi|386001683|ref|YP_005919982.1| 30 EATAREVHEMSGVPRTRVYDILKDLTEKGFAEFVQG 65
                                      379****************************98866 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.9e-05      0.18      26      62 ..      31      67 ..      11      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                      ++++e++e+ +++++ +  il+ L+++g+ + v+G  
  gi|386001683|ref|YP_005919982.1| 31 ATAREVHEMSGVPRTRVYDILKDLTEKGFAEFVQGSP 67
                                      799****************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1713.37
//
Query:       gi|386001684|ref|YP_005919983.1|  [L=327]
Description: hypothetical protein Mhar_0990 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-05   24.1   0.1       0.39   11.0   0.0    3.6  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    0.00013   22.2   0.0      0.029   14.6   0.0    2.8  2  CARDB        CARDB
    0.00033   20.9   0.3       0.06   13.7   0.1    2.6  3  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.018   14.5   0.0       0.22   10.9   0.0    2.2  2  TRAP_beta    Translocon-associated protein beta (TRAPB)
      0.026   15.4   0.5        8.1    7.4   0.3    3.8  3  DUF756       Domain of unknown function (DUF756)
       0.13   11.9   1.6         52    3.4   0.1    3.5  4  DUF4131      Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.069   2.1e+02       3      24 ..      34      55 ..      32      65 .. 0.84
   2 !    6.5   0.1    0.0032       9.6      16      79 .]      77     145 ..      68     145 .. 0.77
   3 !   11.0   0.0   0.00013      0.39       6      69 ..     205     267 ..     202     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.069
                       NPCBM_assoc  3 pGetvtltltvtndgtaaatnv 24
                                      +Ge+++l lt+tn g+ +  +v
  gi|386001684|ref|YP_005919983.1| 34 QGEETSLYLTLTNRGRVTSIRV 55
                                      8**************8766555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0032
                       NPCBM_assoc  16 dgtaaatnvslslslPeGWt....vvevspasaaslapGe.tveatvkVtppagaaaGdyevtakarlt 79 
                                       + ++aa++vs+sl +P+  +     v+ ++a a +l+ G+ + + ++ + + +++ +Gdy++ a++++t
  gi|386001684|ref|YP_005919983.1|  77 NARTAAQDVSVSLLVPQTGEevplEVKRQVAYAGTLREGQvSSRLEFPIEVYERTPPGDYDLLAVVNYT 145
                                       45678999********988754443556666666999998456899999999********999999875 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00013
                       NPCBM_assoc   6 tvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd 69 
                                       ++ +++t+ n g++ a+++  +l+  +G   v+v+   ++ l+pGet+e   k+ ++++a++ +
  gi|386001684|ref|YP_005919983.1| 205 DNVVKMTIENVGDDYARDLVARLRPESGIY-VSVDESPIPLLRPGETAELVYKLDVSKDAVPEK 267
                                       567899*****************9999999.9****************************9844 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.014        41      10      70 ..      27      58 ..      20     144 .. 0.73
   2 !   14.6   0.0   9.8e-06     0.029      16      85 ..     201     276 ..     187     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                                      EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE CS
                             CARDB 10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwt 70
                                      l  + +++gee ++++t++N G  +s  ++                             ++
  gi|386001684|ref|YP_005919983.1| 27 LDREMVYQGEETSLYLTLTNRGRVTSIRVN-----------------------------DP 58
                                      444555666666666666666665554444.............................33 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.8e-06
                                       ETTSEEEEEEEEEE-SSS-EEEEEEEEEETT.EEE..EEEEESEE-CTEEEEEEEEEE-S...-S-CEEEEEEEES CS
                             CARDB  16 fvgeentitvtvkNqGtaasgatkvalyldg.elv..gtvtvpsLaagesttvsftwtte...ategevtltvvvD 85 
                                       +  ++n +++t++N G++++++  ++l  +    v  +++++p L +ge+++  ++  ++     e+++ l+v  +
  gi|386001684|ref|YP_005919983.1| 201 VGSRDNVVKMTIENVGDDYARDLVARLRPESgIYVsvDESPIPLLRPGETAELVYKLDVSkdaVPEKTYSLKVLFE 276
                                       34567999*******************9765144477**************9999888776644445555777665 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1     2e-05      0.06       4      47 ..      26      65 ..      23     130 .. 0.67
   2 ?   -2.6   0.0       2.4   7.2e+03      67      83 ..     170     186 ..     165     195 .. 0.72
   3 ?    4.6   0.0     0.013        40      19      84 ..     209     265 ..     188     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                             DUF11  4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtl...Paglayvs 47
                                      + d++ v  G++++  lt+tN+g +++  ++v+D++   P      +
  gi|386001684|ref|YP_005919983.1| 26 SLDREMVYQGEETSLYLTLTNRGRVTS--IRVNDPPstsP-----EE 65
                                      568889999*****************9..*****664441.....22 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                             DUF11  67 gesatlsftvrvtrtaa 83 
                                       ++s t+ +t+rv r++ 
  gi|386001684|ref|YP_005919983.1| 170 SKSETVPLTLRVVRESG 186
                                       56788888888888765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.013
                             DUF11  19 tltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaas 84 
                                         t  N g + a ++v + + P++  yvsv  s         ++ L +ge+a l +++ v++ a  
  gi|386001684|ref|YP_005919983.1| 209 KMTIENVGDDYARDLVAR-LRPESGIYVSVDES--------PIPLLRPGETAELVYKLDVSKDAVP 265
                                       566777777777554444.45777778888888........45899*************9998875 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 ?    0.7   0.0     0.096   2.9e+02      29      54 ..      30      55 ..      24      67 .. 0.85
   2 ?   10.9   0.0   7.4e-05      0.22      21      54 ..     190     223 ..     175     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.096
                         TRAP_beta 29 rllvegedltveytiyNvGssaAldV 54
                                      +++ +ge+ ++++t++N G  + + V
  gi|386001684|ref|YP_005919983.1| 30 EMVYQGEETSLYLTLTNRGRVTSIRV 55
                                      5677899************9887766 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.4e-05
                         TRAP_beta  21 lvkKkilnrllvegedltveytiyNvGssaAldV 54 
                                        vk  + ++l v+ +d++v++ti NvG+  A+d+
  gi|386001684|ref|YP_005919983.1| 190 RVKEVAPSDLIVGSRDNVVKMTIENVGDDYARDL 223
                                       45666678999********************996 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3    0.0027       8.1       3      25 ..      29      51 ..      21     156 .. 0.85
   2 ?    2.6   0.0     0.086   2.6e+02       4      38 ..     165     197 ..     162     226 .. 0.78
   3 ?   -3.3   0.0         6   1.8e+04      44      58 ..     247     261 ..     244     275 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                            DUF756  3 valpYdlaagnlrltlrNtgkaa 25
                                      + + Y+++ ++l+ltl+N+g+ +
  gi|386001684|ref|YP_005919983.1| 29 REMVYQGEETSLYLTLTNRGRVT 51
                                      566788888***********943 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.086
                            DUF756   4 alpYdlaagnlrltlrNtgkaaarftVydnakapw 38 
                                       +  Y+ ++ ++ ltlr   +++a f V++   ap 
  gi|386001684|ref|YP_005919983.1| 165 FYLYESKSETVPLTLRVVRESGAEFRVKEV--APS 197
                                       5669999999*****************874..444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6
                            DUF756  44 agdqledhwklassg 58 
                                       +g++ e++ kl+ s+
  gi|386001684|ref|YP_005919983.1| 247 PGETAELVYKLDVSK 261
                                       566666555555443 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3     4e+03     119     132 ..       8      21 ..       3      24 .. 0.80
   2 ?    2.9   0.3     0.025        76      67     133 ..      47     113 ..      30     118 .. 0.65
   3 ?    2.2   0.0     0.042   1.3e+02     106     132 ..     231     257 ..     203     262 .. 0.87
   4 ?    3.4   0.1     0.017        52       5      28 ..     300     323 ..     297     327 .] 0.65

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                           DUF4131 119 glrpGdrlrltgrl 132
                                       ++ pGd+ +++g++
  gi|386001684|ref|YP_005919983.1|   8 EIFPGDFYKVEGSP 21 
                                       789*******9986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.025
                           DUF4131  67 qeviveGvvaslpeltgsgt...rfvlevervlsagktkpvsgrvlvtvpkspae.glrpGdrlrltgrlk 133
                                       +  +   +v + p ++++ +   r++le e    + +t+    +v + vp+  +e  l+   +++  g+l+
  gi|386001684|ref|YP_005919983.1|  47 RGRVTSIRVNDPPSTSPEERyaaRVELELE----NARTAAQDVSVSLLVPQTGEEvPLEVKRQVAYAGTLR 113
                                       444446688999999988777778888855....5566666666666666666665577777777666665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.042
                           DUF4131 106 grvlvtvpkspaeglrpGdrlrltgrl 132
                                         ++v+v++sp + lrpG++  l  +l
  gi|386001684|ref|YP_005919983.1| 231 SGIYVSVDESPIPLLRPGETAELVYKL 257
                                       569****************98877666 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.017
                           DUF4131   5 lalvllalllllllllllllrrrp 28 
                                       ++ ++ +++l++l++++ll +rr+
  gi|386001684|ref|YP_005919983.1| 300 PWGLISGAVLAALAAAGLLIHRRR 323
                                       677777778888887777754333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2460.69
//
Query:       gi|386001685|ref|YP_005919984.1|  [L=312]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-29  102.0   0.0    5.8e-29  101.4   0.0    1.3  1  ABC_tran    ABC transporter
    9.6e-14   51.9   0.0    2.1e-06   27.8   0.1    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0006   19.5   0.0     0.0012   18.6   0.0    1.3  1  AAA_29      P-loop containing region of AAA domain
     0.0011   18.8   0.0      0.056   13.2   0.0    2.1  2  AAA_24      AAA domain
     0.0011   19.5   0.0     0.0019   18.7   0.0    1.3  1  AAA_23      AAA domain
     0.0031   17.3   0.0       0.18   11.5   0.0    2.0  2  AAA_15      AAA ATPase domain
     0.0033   17.8   0.2     0.0056   17.1   0.0    1.6  1  AAA_16      AAA ATPase domain
     0.0078   16.6   0.0      0.019   15.4   0.0    1.7  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.018   15.0   0.0    1.4  1  MutS_V      MutS domain V
      0.033   14.2   0.0       0.05   13.6   0.0    1.4  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
      0.037   14.0   0.0      0.059   13.4   0.0    1.3  1  AAA_5       AAA domain (dynein-related subfamily)
      0.041   13.8   0.0      0.069   13.1   0.0    1.3  1  NACHT       NACHT domain
      0.042   13.3   0.0      0.086   12.3   0.0    1.5  2  SMC_N       RecF/RecN/SMC N terminal domain
      0.044   13.7   0.0        1.6    8.7   0.0    2.3  2  MobB        Molybdopterin guanine dinucleotide synthesis prot
      0.068   13.3   0.0       0.11   12.7   0.0    1.6  1  AAA_33      AAA domain
      0.068   12.9   0.0       0.16   11.7   0.0    1.6  1  AAA_30      AAA domain
       0.12   12.0   0.2       0.73    9.4   0.0    2.2  2  AAA_25      AAA domain
       0.15   11.8   0.0       0.24   11.1   0.0    1.3  1  ATP_bind_1  Conserved hypothetical ATP binding protein
       0.25   11.2   0.0       0.46   10.4   0.0    1.4  1  ATPase_2    ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   6.1e-32   5.8e-29       1     136 [.      32     174 ..      32     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 6.1e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++s+ + +g+++ ++G+nG+GK+t+++++agll+ + G + + g+++++    ++  +ig+++q++ l p+lt+r
  gi|386001685|ref|YP_005919984.1|  32 LNDLSVRIPRGTTYCLLGPNGSGKTTFIRAVAGLLRLDGGYLSVLGEPVHT--VDRVYPRIGYMTQHKALYPDLTLR 106
                                       799***********************************************9..9999999***************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e+de+i+++l+ ++l +  d++       LSgG+ qr++la++l+ +p+llllDEpt
  gi|386001685|ref|YP_005919984.1| 107 ENmefyaglygieggERDERISELLEMVDLADHIDRIT----GDLSGGMYQRLSLACTLIHDPDLLLLDEPT 174
                                       *************9999999*********999888888....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.2e-07   0.00012       3      25 ..      46      68 ..      45      97 .. 0.79
   2 !   27.8   0.1   2.3e-09   2.1e-06     237     297 ..     147     204 ..     113     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                      +l GpNgsGK+++++a  +l rl
  gi|386001685|ref|YP_005919984.1| 46 CLLGPNGSGKTTFIRAVAGLLRL 68
                                      699*****************986 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.3e-09
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       lS G+ + l l+  l+ ++   +lll+DEp  g +P l + ++++++ l+++ga +++tTH
  gi|386001685|ref|YP_005919984.1| 147 LSGGMYQRLSLACTLIHDP---DLLLLDEPTVGVDPILREAFWRFFDGLAEGGATILITTH 204
                                       6666655444444444444...9***********************999999********* PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-06    0.0012      17      46 ..      37      66 ..      31      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalL 46
                                      ++i  +g ++ l Gp+GsGK+T++ A++ lL
  gi|386001685|ref|YP_005919984.1| 37 VRIP-RGtTYCLLGPNGSGKTTFIRAVAGLL 66
                                      6665.555999*************9999887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     6e-05     0.056       3      39 ..      43      76 ..      41     113 .. 0.79
   2 ?    3.6   0.0      0.05        47     107     161 ..     181     233 ..     180     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksld 39
                                        +++ Gp+g+GKTt+++     + ++ +++G+ s+ 
  gi|386001685|ref|YP_005919984.1| 43 TTYCLLGPNGSGKTTFIRAV---AGLLRLDGGYLSVL 76
                                      6789*************998...55666666666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.05
                            AAA_24 107 laeefrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelk 161
                                       l+e f+r+ + l e + ++ ++ h+  +    ++ +  y+r   +l +++ +elk
  gi|386001685|ref|YP_005919984.1| 181 LREAFWRFFDGLAEGGATILITTHLMDEAERCKTVG--YMRGGRMLAEGSPEELK 233
                                       5789**********************9999988888..77888888877777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     2e-06    0.0019      21      40 ..      44      63 ..      23      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                       +++ GpNG+GKTT+++A+ 
  gi|386001685|ref|YP_005919984.1| 44 TYCLLGPNGSGKTTFIRAVA 63
                                      5699*************986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00019      0.18      21      43 ..      39      62 ..      26      91 .. 0.81
   2 ?    3.8   0.0      0.04        38     323     364 ..     164     204 ..     155     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                            AAA_15 21 lsee.ltvliGkNnsGKSsileal 43
                                      +    + +l G+N+sGK+++++a 
  gi|386001685|ref|YP_005919984.1| 39 IPRGtTYCLLGPNGSGKTTFIRAV 62
                                      44443559*************986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.04
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++++ll++EP +   p + + +++ +  la+ +   ++itTH
  gi|386001685|ref|YP_005919984.1| 164 DPDLLLLDEPTVGVDPILREAFWRFFDGLAEGGA-TILITTH 204
                                       789******************************8.9****** PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.9e-06    0.0056      18      76 ..      36      96 ..      26     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.9e-06
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql.esaipysalaqal 76
                                      +vr +r+    l G+ G+GK++ +r+++  l+ dgg++ + g+ ++  ++  p++ + ++ 
  gi|386001685|ref|YP_005919984.1| 36 SVRIPRGTTYCLLGPNGSGKTTFIRAVAGLLRLDGGYLsVLGEPVHTvDRVYPRIGYMTQH 96
                                      466667778889****************999999999888887777655555555555555 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 !   15.4   0.0     2e-05     0.019       2      22 ..      46      66 ..      45      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                      +l Gp G GKT++++ava  l
  gi|386001685|ref|YP_005919984.1| 46 CLLGPNGSGKTTFIRAVAGLL 66
                                      899***************876 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.9e-05     0.018       3      50 ..      47      92 ..      45     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                      EE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE-- CS
                            MutS_V  3 itGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvga 50
                                      + Gpn +Gk t++r va   ll   G ++      +  vd+++ R+g 
  gi|386001685|ref|YP_005919984.1| 47 LLGPNGSGKTTFIRAVA--GLLRLDGGYLSVLGEPVHTVDRVYPRIGY 92
                                      57************765..788889*********************95 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.3e-05      0.05      19      45 ..      42      68 ..      22     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
                                      TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakalgv 45
                                      g++ +L G+ G+GKTt++r++a  l +
  gi|386001685|ref|YP_005919984.1| 42 GTTYCLLGPNGSGKTTFIRAVAGLLRL 68
                                      6789****************9987765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.2e-05     0.059       3      47 ..      46      92 ..      44     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                                      EEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B-- CS
                             AAA_5  3 lLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrrei 47
                                      +L+Gp G+gK+++++ +a +l     ++ v++    t + +  r+ +
  gi|386001685|ref|YP_005919984.1| 46 CLLGPNGSGKTTFIRAVAGLLrlDGGYLSVLGEPVHTVDRVYPRIGY 92
                                      9******************9988777777777776666666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-05     0.069       2      25 ..      44      67 ..      43      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      + +l G++GsGKTt+++ +a +++
  gi|386001685|ref|YP_005919984.1| 44 TYCLLGPNGSGKTTFIRAVAGLLR 67
                                      6799*************9997765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.1e-05     0.086      27      45 ..      45      63 ..      23      69 .. 0.82
   2 ?   -3.0   0.0       4.2   3.9e+03     137     179 ..     147     185 ..     122     216 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.1e-05
                                      EEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAil 45
                                       +++GpNGSGK+ ++ A+ 
  gi|386001685|ref|YP_005919984.1| 45 YCLLGPNGSGKTTFIRAVA 63
                                      5799***********9985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       LSgG  + ++l    A   ++   l llDe     D   ++++
  gi|386001685|ref|YP_005919984.1| 147 LSGGMYQRLSL----ACTLIHDPDLLLLDEPTVGVDPILREAF 185
                                       55554333332....3333333345555555555555555555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0016       1.6       3      41 ..      46      84 ..      44      89 .. 0.86
   2 ?    2.5   0.0      0.13   1.2e+02      76      97 ..     275     296 ..     265     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                              MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhahhgfd 41
                                      ++ g +gsGKTt++  +   l+  g  ++++   +h +d
  gi|386001685|ref|YP_005919984.1| 46 CLLGPNGSGKTTFIRAVAGLLRLDGGYLSVLGEPVHTVD 84
                                      678999***************999999998887777765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                              MobB  76 eaelsleellarlsevDlvlvE 97 
                                       e++ +l+e+l+r+++ Dl lvE
  gi|386001685|ref|YP_005919984.1| 275 EDTRRLKEILERVEPSDLRLVE 296
                                       34789****************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.11       4      25 ..      47      73 ..      45     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                            AAA_33  4 lvGlpGsGKstlaerllkklg.....a 25
                                      l G++GsGK+t+++ ++  l       
  gi|386001685|ref|YP_005919984.1| 47 LLGPNGSGKTTFIRAVAGLLRldggyL 73
                                      57************9975444444544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.16      21      49 ..      45      73 ..      39     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrv 49
                                       +l Gp G+GKtt ++a++ +++ +gg +
  gi|386001685|ref|YP_005919984.1| 45 YCLLGPNGSGKTTFIRAVAGLLRLDGGYL 73
                                      5789***************9998886544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00078      0.73      29      50 ..      38      59 ..      16      65 .. 0.86
   2 ?   -0.9   0.0       1.1     1e+03      70      99 ..     265     288 ..     252     302 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00078
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                       +p+g++  l G+ g+GKtt+ 
  gi|386001685|ref|YP_005919984.1| 38 RIPRGTTYCLLGPNGSGKTTFI 59
                                      57******************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                            AAA_25  70 eqgkVlyvsaEdsedelrrRlravgealrd 99 
                                         g Vl v  Ed++     Rl++++e + +
  gi|386001685|ref|YP_005919984.1| 265 VVGGVLQVRIEDTR-----RLKEILERV-E 288
                                       56889999999999.....555555554.3 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.24       2      23 ..      48      69 ..      47      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelr 23
                                      +Gp GsGKttf++a++ +l+l 
  gi|386001685|ref|YP_005919984.1| 48 LGPNGSGKTTFIRAVAGLLRLD 69
                                      7*************99887765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00049      0.46      10      45 ..      34      67 ..      26      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                          ATPase_2 10 eleeilerepneiyfiYGpegsGKtaLlkeiienle 45
                                      +l   + r   + y + Gp gsGKt++++ ++  l+
  gi|386001685|ref|YP_005919984.1| 34 DLSVRIPR--GTTYCLLGPNGSGKTTFIRAVAGLLR 67
                                      55555555..4568889************9988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2301.32
//
Query:       gi|386001686|ref|YP_005919985.1|  [L=380]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-31  110.0  11.3    1.3e-23   83.7  16.8    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    4.7e-30  104.6  11.7    4.7e-30  104.6  11.7    2.4  3  ABC2_membrane    ABC-2 type transporter
    1.6e-11   44.1   1.1    3.5e-11   42.9   1.1    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
    6.6e-05   22.5   2.7    0.00012   21.7   2.7    1.4  1  CcmB             CcmB protein
    0.00041   20.3   5.1    0.00041   20.3   5.1    2.1  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-07   0.00059       2     105 ..      27     122 ..      26     142 .. 0.82
   2 !   83.7  16.8   3.5e-27   1.3e-23     165     344 ..     188     372 ..     171     373 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-07
                   ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngd 78 
                                       +++ ++++ P++l++l+g+++s +      ++++vvd+        l e l++ ++++   ++ se++a++++ +g 
  gi|386001686|ref|YP_005919985.1|  27 RTIGLITFAPVFLMILFGYALSGEM---AGINLGVVDLG---GQDALREHLASVDDFD-LLHLGSESDAERLIVEGR 96 
                                       577788999*******999988666...89********8...46779**********9.****************** PP

                   ABC2_membrane_3  79 idgilvipkgfskdllkgesatvtvli 105
                                       + g++vi +     ll+g+s+++t+ i
  gi|386001686|ref|YP_005919985.1|  97 LHGAVVIGEEVR-VLLDGSSPQITASI 122
                                       *******87773.45566666666544 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 3.5e-27
                   ABC2_membrane_3 165 g.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...lafglgipfg. 236
                                       + ++ ++++f+t++ +a s+++E++++ +e  +vs++s+ +++ + +lg  l +llq++ +ll   lafg  +p++ 
  gi|386001686|ref|YP_005919985.1| 188 PaVLGLVVFFFTFITAAISFLRERTQGSLEKFMVSPLSRPEMVAGYLLGFSLFALLQSATTLLvvvLAFG--VPMNg 262
                                       33666777888888888999**************************************988874335888..****8 PP

                   ABC2_membrane_3 237 nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgl 313
                                       n + ++ ++ll g   ++lg +ls + k++  + ++i+ivil+  +++g+ +ple++p++++ i++i+P+++ +++l
  gi|386001686|ref|YP_005919985.1| 263 NPLTAFGVILLLGAGGLVLGGFLSNFAKTEFQVVQFIPIVILPQVVLSGVWWPLESIPDFIRPISYILPLTYSSDAL 339
                                       889999************************************999999999************************** PP

                   ABC2_membrane_3 314 lrli.tgdplweil.lsliilalfavvylllal 344
                                         ++ +g+  +eil ++l++l++f+v+ + +a 
  gi|386001686|ref|YP_005919985.1| 340 RAVMlKGAGVSEILvPDLLFLVGFFVIAFGAAT 372
                                       ***86666889*****************99886 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0011       3.9       3      42 ..      11      49 ..       9      63 .. 0.85
   2 !  104.6  11.7   1.3e-33   4.7e-30      53     210 .]     188     344 ..     160     344 .. 0.90
   3 ?   -4.5   1.3       3.3   1.2e+04     132     143 ..     358     369 ..     353     375 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                     ABC2_membrane  3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn 42
                                      ++++ +r ++q +rd+ ++  + ++ p++l+++fg++ ++
  gi|386001686|ref|YP_005919985.1| 11 VLVVARRVVRQLKRDRRTI-GLITFAPVFLMILFGYALSG 49
                                      578999**********888.99**************9884 PP

  == domain 2  score: 104.6 bits;  conditional E-value: 1.3e-33
                     ABC2_membrane  53 pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls. 128
                                       p +l+  v+f+++++++++++++er++g+le+ +vspl s++++v++++l++ +++llq++  ll+v++ +g++++ 
  gi|386001686|ref|YP_005919985.1| 188 PAVLGL-VVFFFTFITAAISFLRERTQGSLEKFMVSPL-SRPEMVAGYLLGFSLFALLQSATTLLVVVLAFGVPMNg 262
                                       444444.4444448889999******************.*************************************7 PP

                     ABC2_membrane 129 rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyaveal 205
                                       + + ++ ++ll++  ++ lg ++s +a+++ +++q++++v+lp ++lsG+ +p++s+p +++ i+y++Plty  +al
  gi|386001686|ref|YP_005919985.1| 263 NPLTAFGVILLLGAGGLVLGGFLSNFAKTEFQVVQFIPIVILPQVVLSGVWWPLESIPDFIRPISYILPLTYSSDAL 339
                                       77********************************************************9****************** PP

                     ABC2_membrane 206 rsnlf 210
                                       r++++
  gi|386001686|ref|YP_005919985.1| 340 RAVML 344
                                       **985 PP

  == domain 3  score: -4.5 bits;  conditional E-value: 3.3
                     ABC2_membrane 132 lflllllltala 143
                                       lfl+ ++++a+ 
  gi|386001686|ref|YP_005919985.1| 358 LFLVGFFVIAFG 369
                                       333333333333 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   1.1   9.8e-15   3.5e-11       2     286 ..      13     378 ..      12     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 9.8e-15
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli.............dvalaylkdlgss..lqseakaikeatlaleyveaasa 63 
                                       ++a++ +r+l r+rr+++l  + p++              ++   + dlg++  l +  +++++ +l    +e ++ 
  gi|386001686|ref|YP_005919985.1|  13 VVARRVVRQLKRDRRTIGLITFAPVFlmilfgyalsgemAGINLGVVDLGGQdaLREHLASVDDFDLLHLGSESDAE 89 
                                       56777789999*****9999999999777666666665522222222222220023333444444444433333333 PP

                   ABC2_membrane_2  64 sdeaedtdqdlkv................................................................ 76 
                                                   +                                                                
  gi|386001686|ref|YP_005919985.1|  90 ------------Rlivegrlhgavvigeevrvlldgsspqitasimtevkngllpreglqnggrmgvggelgalngg 154
                                       ............133344444445799999999999999999999999999************************** PP

                   ABC2_membrane_2  77 ...................................vstimavlipviaalfgadaiagEkergTlkllLskPvsRde 118
                                                                          v +++ +++++i a   a ++ +E+++g+l+  + +P sR e
  gi|386001686|ref|YP_005919985.1| 155 wpggdgilggvggpevvqryirgydlemmdsvgpaVLGLVVFFFTFITA---AISFLRERTQGSLEKFMVSPLSRPE 228
                                       ******************************9955555555555555555...55678******************** PP

                   ABC2_membrane_2 119 illgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssrea 194
                                        ++g ++g ++ +l+  a +ll+       ++la+g+++++  l+ + v  + l++    l lg +lS +a+ ++ +
  gi|386001686|ref|YP_005919985.1| 229 MVAGYLLGFSLFALLqSATTLLV-------VVLAFGVPMNGNPLTAFGVILL-LGA--GGLVLGGFLSNFAK-TEFQ 294
                                       ************55555555555.......5666888888888777766555.444..357799999****9.6677 PP

                   ABC2_membrane_2 195 aalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllillll 271
                                           + ++++ +++ ++v  +   l++ p +   i+++  +l+ t + ++l++ +l+g++++   + +  ll+l++ 
  gi|386001686|ref|YP_005919985.1| 295 VVQFIPIVILPQVVLSGVWWP---LESIPDF---IRPISYILPLTYSSDALRAVMLKGAGVS--EILVPDLLFLVGF 363
                                       777777777777777777755...4444445...6666666666666777777777777766..89999******** PP

                   ABC2_membrane_2 272 lavllvlgyvlFkrk 286
                                        ++ ++ ++ ++kr+
  gi|386001686|ref|YP_005919985.1| 364 FVIAFGAATLMLKRE 378
                                       *******99999985 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.7   3.2e-08   0.00012      38     142 ..     177     283 ..     170     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.2e-08
                              CcmB  38 GPdtallsriapgilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglplvllaplla 114
                                       G d++++  ++p++l + + + +++++   f  ++ +GsLe+++++p++ + +v++  l   l+++l    +  ++ 
  gi|386001686|ref|YP_005919985.1| 177 GYDLEMMDSVGPAVLGLVVFFFTFITAAISFLRERTQGSLEKFMVSPLSRPEMVAGYLLGFSLFALLQSATTLLVVV 253
                                       7799***************************************************************9887777777 PP

                              CcmB 115 lllnleaaalglla..ltLllGtpalsllg 142
                                       l +++++++ +l+a  + LllG+ +l l g
  gi|386001686|ref|YP_005919985.1| 254 LAFGVPMNGNPLTAfgVILLLGAGGLVLGG 283
                                       777777777665542278999999986544 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.53   1.9e+03      15      31 ..      30      46 ..      22      59 .. 0.43
   2 !   20.3   5.1   1.2e-07   0.00041      56     171 ..     191     303 ..     170     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.53
                   ABC2_membrane_4 15 vwllvlaallvpllall 31
                                       +++++ ++l+ l++ +
  gi|386001686|ref|YP_005919985.1| 30 GLITFAPVFLMILFGYA 46
                                      23333322222222222 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.2e-07
                   ABC2_membrane_4  56 lllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvk 132
                                       l l++ + + i a++++ rE++++ l + ++ P sr +++++ l+    +s+ + l++ + t+l+ +l+ +v+++++
  gi|386001686|ref|YP_005919985.1| 191 LGLVVFFFTFITAAISFLRERTQGSLEKFMVSPLSRPEMVAGYLLG---FSL-FALLQSATTLLVVVLAFGVPMNGN 263
                                       3355556666789**************************9985444...433.44556667888888899999**99 PP

                   ABC2_membrane_4 133 lvlellkkcl.elgllvffavlpiialvllkksyvlplil 171
                                       +++ + +++l   g lv+  +l  +a + ++  +++p+++
  gi|386001686|ref|YP_005919985.1| 264 PLTAFGVILLlGAGGLVLGGFLSNFAKTEFQVVQFIPIVI 303
                                       9776655444255555555566666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2609.65
//
Query:       gi|386001687|ref|YP_005919986.1|  [L=290]
Description: hypothetical protein Mhar_0993 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-42  140.2  36.6    1.2e-05   25.4   0.6   10.2 10  LRV           Leucine rich repeat variant
    1.1e-05   25.1  20.2       0.18   11.3   0.1    4.4  5  DUF2336       Uncharacterised protein conserved in bacteria (
     0.0054   16.9  24.4       0.82   10.1   0.2    8.6  9  HEAT          HEAT repeat
  ------ inclusion threshold ------
       0.01   16.2  25.5        4.6    7.7   4.3    7.0  5  HEAT_2        HEAT repeats
      0.071   13.2   0.2          1    9.4   0.1    2.7  2  DUF1743       Domain of unknown function (DUF1743)
          9    6.1   5.5    1.5e+02    2.2   0.0    4.4  5  PHF12_MRG_bd  PHD finger protein 12 MRG binding domain


Domain annotation for each model (and alignments):
>> LRV  Leucine rich repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0026       7.7       8      24 ..      10      26 ..      10      28 .. 0.90
   2 !   25.4   0.6     4e-09   1.2e-05       1      24 [.      29      52 ..      29      54 .. 0.97
   3 !   17.7   0.1   1.1e-06    0.0034       3      26 .]      57      80 ..      56      80 .. 0.94
   4 !   22.1   0.2   4.3e-08   0.00013       3      25 ..      83     105 ..      81     105 .. 0.94
   5 !   13.9   0.0   1.9e-05     0.056       5      26 .]     122     143 ..     120     143 .. 0.93
   6 !   11.9   0.2   7.7e-05      0.23       2      18 ..     145     161 ..     144     168 .. 0.93
   7 !    8.2   0.7    0.0012       3.6       1      24 [.     170     193 ..     170     194 .. 0.90
   8 !   14.9   0.1     9e-06     0.027       2      26 .]     197     221 ..     197     221 .. 0.97
   9 !   16.5   0.1   2.7e-06    0.0081       2      24 ..     223     245 ..     222     245 .. 0.96
  10 !   23.0   0.0   2.4e-08     7e-05       1      26 []     248     273 ..     248     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                               LRV  8 ArrPdlPpeaLerLahD 24
                                      A+ P  ++e LerLa+D
  gi|386001687|ref|YP_005919986.1| 10 ASDPEIDGEELERLARD 26
                                      678999**********9 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 4e-09
                               LRV  1 reVRaaVArrPdlPpeaLerLahD 24
                                      ++VR+aVA +P++P e L++La+D
  gi|386001687|ref|YP_005919986.1| 29 WHVRRAVANNPAAPMEILGELARD 52
                                      99*********************9 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 1.1e-06
                               LRV  3 VRaaVArrPdlPpeaLerLahDPd 26
                                      VR+aVA+ P++++e L  La D d
  gi|386001687|ref|YP_005919986.1| 57 VREAVAASPQADGEILDLLAEDGD 80
                                      9********************966 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 4.3e-08
                               LRV   3 VRaaVArrPdlPpeaLerLahDP 25 
                                       VRaaVA++P+++pe+L  La D+
  gi|386001687|ref|YP_005919986.1|  83 VRAAVALNPRTSPEVLSDLAEDE 105
                                       9*******************995 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 1.9e-05
                               LRV   5 aaVArrPdlPpeaLerLahDPd 26 
                                       +a+A +P +P e++++La+D d
  gi|386001687|ref|YP_005919986.1| 122 EAAAKNPKTPEEVIRALADDGD 143
                                       599*****************76 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 7.7e-05
                               LRV   2 eVRaaVArrPdlPpeaL 18 
                                        VRaaV+++P  P ++L
  gi|386001687|ref|YP_005919986.1| 145 GVRAAVVSNPTVPEDVL 161
                                       5**************99 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.0012
                               LRV   1 reVRaaVArrPdlPpeaLerLahD 24 
                                       + VR a+Ar P++ +e L  La+D
  gi|386001687|ref|YP_005919986.1| 170 WSVRTAAARSPQATVELLAYLAAD 193
                                       569**********99999999999 PP

  == domain 8  score: 14.9 bits;  conditional E-value: 9e-06
                               LRV   2 eVRaaVArrPdlPpeaLerLahDPd 26 
                                       +VRaaVA +  +++ +L +La+D d
  gi|386001687|ref|YP_005919986.1| 197 DVRAAVAMNKKTSASTLASLAADRD 221
                                       7**********************98 PP

  == domain 9  score: 16.5 bits;  conditional E-value: 2.7e-06
                               LRV   2 eVRaaVArrPdlPpeaLerLahD 24 
                                       e+RaaVA++P ++p++L++L+ D
  gi|386001687|ref|YP_005919986.1| 223 EIRAAVASNPIADPATLVALSGD 245
                                       89******************998 PP

  == domain 10  score: 23.0 bits;  conditional E-value: 2.4e-08
                               LRV   1 reVRaaVArrPdlPpeaLerLahDPd 26 
                                       + VR+ VA++P++P e++++L+ D d
  gi|386001687|ref|YP_005919986.1| 248 WKVREKVAQNPSTPEEVVRALVGDGD 273
                                       89*********************966 PP

>> DUF2336  Uncharacterised protein conserved in bacteria (DUF2336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.59   1.8e+03      46      65 ..      23      42 ..      13      44 .. 0.75
   2 !    8.4   0.2   0.00044       1.3      17      63 ..      46      92 ..      42     104 .. 0.93
   3 !   11.3   0.1   5.9e-05      0.18      31      63 ..     123     155 ..     116     157 .. 0.92
   4 !    9.4   8.0   0.00022      0.67       8      65 ..     178     235 ..     176     269 .. 0.88
   5 ?    2.2   0.0     0.034     1e+02      29      56 ..     251     278 ..     235     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.59
                           DUF2336 46 laergdeevvrallaNpgAe 65
                                      la+  d +v ra+++Np A 
  gi|386001687|ref|YP_005919986.1| 23 LARDWDWHVRRAVANNPAAP 42
                                      56666777888888888885 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00044
                           DUF2336 17 LvdiartgsqahllaIAsRpdlsaaVadalaergdeevvrallaNpg 63
                                      L ++ar++ q  + a+A  p+ + ++ d lae gd  v +a++ Np+
  gi|386001687|ref|YP_005919986.1| 46 LGELARDRVQWVREAVAASPQADGEILDLLAEDGDGFVRAAVALNPR 92
                                      5589*****************************************96 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 5.9e-05
                           DUF2336  31 aIAsRpdlsaaVadalaergdeevvrallaNpg 63 
                                       a A+ p+ +++V  ala+ gde v +a+++Np+
  gi|386001687|ref|YP_005919986.1| 123 AAAKNPKTPEEVIRALADDGDEGVRAAVVSNPT 155
                                       66888999***********************97 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00022
                           DUF2336   8 rSpvLtdedLvdiartgsqahllaIAsRpdlsaaVadalaergdeevvrallaNpgAe 65 
                                       rSp  t e L+ +a+++ q+ ++a+A  ++ sa+  + la+ +d e  +a+++Np A 
  gi|386001687|ref|YP_005919986.1| 178 RSPQATVELLAYLAADRIQDVRAAVAMNKKTSASTLASLAADRDVEIRAAVASNPIAD 235
                                       788888999*********************************************9875 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.034
                           DUF2336  29 llaIAsRpdlsaaVadalaergdeevvr 56 
                                       +  +A+ p+ +++V+ al+  gd++v  
  gi|386001687|ref|YP_005919986.1| 251 REKVAQNPSTPEEVVRALVGDGDQSVKK 278
                                       6668999999999999999999998865 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.039   1.2e+02      10      22 ..      25      37 ..      19      38 .. 0.77
   2 ?    2.6   0.1     0.068     2e+02       5      22 ..      46      63 ..      43      64 .. 0.80
   3 ?    3.2   0.0     0.045   1.3e+02       5      22 ..      71      89 ..      70      90 .. 0.84
   4 ?    1.6   0.0      0.15   4.4e+02       6      22 ..     136     152 ..     133     153 .. 0.75
   5 !   10.1   0.2   0.00027      0.82      11      22 ..     167     178 ..     160     179 .. 0.87
   6 ?    0.7   0.1      0.28   8.3e+02       9      22 ..     190     204 ..     184     205 .. 0.73
   7 ?    2.7   0.2     0.066     2e+02       5      22 ..     213     230 ..     211     231 .. 0.85
   8 ?    2.2   0.1     0.097   2.9e+02      13      22 ..     247     256 ..     237     257 .. 0.78
   9 ?   -0.9   0.0      0.91   2.7e+03       7      20 ..     267     280 ..     263     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.039
                                      T-SSHHHHHHHHH CS
                              HEAT 10 sDpspeVReaAak 22
                                      +D +++VR+a+a+
  gi|386001687|ref|YP_005919986.1| 25 RDWDWHVRRAVAN 37
                                      5669******997 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.068
                                      HHHHHT-SSHHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAak 22
                                      l +l +D    VRea+a 
  gi|386001687|ref|YP_005919986.1| 46 LGELARDRVQWVREAVAA 63
                                      55778999*******996 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.045
                                      HHHHH.T-SSHHHHHHHHH CS
                              HEAT  5 llkll.sDpspeVReaAak 22
                                      +l ll +D + +VR+a+a+
  gi|386001687|ref|YP_005919986.1| 71 ILDLLaEDGDGFVRAAVAL 89
                                      5677779*********997 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.15
                                       HHHHT-SSHHHHHHHHH CS
                              HEAT   6 lkllsDpspeVReaAak 22 
                                         l  D +  VR+a++ 
  gi|386001687|ref|YP_005919986.1| 136 RALADDGDEGVRAAVVS 152
                                       3445999*******986 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00027
                                       -SSHHHHHHHHH CS
                              HEAT  11 DpspeVReaAak 22 
                                       Dps++VR aAa+
  gi|386001687|ref|YP_005919986.1| 167 DPSWSVRTAAAR 178
                                       9*********97 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.28
                                       H.T-SSHHHHHHHHH CS
                              HEAT   9 l.sDpspeVReaAak 22 
                                       l  D   +VR+a+a 
  gi|386001687|ref|YP_005919986.1| 190 LaADRIQDVRAAVAM 204
                                       43788899****996 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.066
                                       HHHHHT-SSHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAak 22 
                                       l +l  D + e+R+a+a 
  gi|386001687|ref|YP_005919986.1| 213 LASLAADRDVEIRAAVAS 230
                                       677889*********997 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.097
                                       SHHHHHHHHH CS
                              HEAT  13 speVReaAak 22 
                                       +++VRe +a+
  gi|386001687|ref|YP_005919986.1| 247 AWKVREKVAQ 256
                                       7******998 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 0.91
                                       HHHT-SSHHHHHHH CS
                              HEAT   7 kllsDpspeVReaA 20 
                                        l  D + +V +aA
  gi|386001687|ref|YP_005919986.1| 267 ALVGDGDQSVKKAA 280
                                       34499999**9998 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.6    0.0018       5.5      35      84 ..      19      88 ..      11      92 .. 0.68
   2 ?    2.2   0.0     0.078   2.3e+02      67      84 ..      71      88 ..      63     109 .. 0.70
   3 ?    7.7   4.3    0.0015       4.6      13      85 ..     127     204 ..     108     207 .. 0.55
   4 ?    2.0   6.6     0.095   2.8e+02      64      84 ..     183     203 ..     158     231 .. 0.45
   5 ?    0.9   6.6      0.21   6.2e+02       6      52 ..     188     229 ..     183     285 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                            HEAT_2 35 aLvellededpavRraaae.......aLgai.............gdpealpaLkellddddddvvReaAa 84
                                       L +l++d d++vRra+a+        Lg++             ++p+a    ++ll++d d +vR+a+a
  gi|386001687|ref|YP_005919986.1| 19 ELERLARDWDWHVRRAVANnpaapmeILGELardrvqwvreavaASPQADGEILDLLAEDGDGFVRAAVA 88
                                      5888999999999999996443222255655433333333333336888888888888888999998766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.078
                            HEAT_2 67 LkellddddddvvReaAa 84
                                       ++ll++d d +vR+a+a
  gi|386001687|ref|YP_005919986.1| 71 ILDLLAEDGDGFVRAAVA 88
                                      455666666666665544 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0015
                            HEAT_2  13 dpevrraairaLgrignpea...........lpaLvellededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                       +p++  ++iraL++ g++ +            + L++   d+++ vR aaa      ++p+a   L+++l+ d+ ++
  gi|386001687|ref|YP_005919986.1| 127 NPKTPEEVIRALADDGDEGVraavvsnptvpEDVLFDRRIDPSWSVRTAAA------RSPQATVELLAYLAADRIQD 197
                                       333333444444433333111112222222344444444444444444444......46888888888899999999 PP

                            HEAT_2  79 vReaAae 85 
                                       vR+a+a 
  gi|386001687|ref|YP_005919986.1| 198 VRAAVAM 204
                                       9998765 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.095
                            HEAT_2  64 lpaLkellddddddvvReaAa 84 
                                          L+++l+ d+ ++vR+a+a
  gi|386001687|ref|YP_005919986.1| 183 TVELLAYLAADRIQDVRAAVA 203
                                       333333333333333333332 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.21
                            HEAT_2   6 qalendpdpevrraairaLgrignpealpaLvellededpavRraaa 52 
                                       ++l+ d  ++vr+a+++     + +++  +L +l+ d d ++R+a+a
  gi|386001687|ref|YP_005919986.1| 188 AYLAADRIQDVRAAVAM-----NKKTSASTLASLAADRDVEIRAAVA 229
                                       55554555555555544.....4445556788888777777777776 PP

>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.78   2.3e+03      66      90 ..     125     149 ..     103     162 .. 0.69
   2 ?    9.4   0.1   0.00034         1       9      91 ..     170     254 ..     168     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.78
                                       CCS-STTSSEEEEEEES-HHHHHHH CS
                           DUF1743  66 vlvPhtpdpvlfGirgedpeallka 90 
                                       + +P+tp+ v+ +  ++  e +++a
  gi|386001687|ref|YP_005919986.1| 125 AKNPKTPEEVIRALADDGDEGVRAA 149
                                       4456666667777766666666554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00034
                                       HHHH-..-TT.S-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSS.....EEEEE CS
                           DUF1743   9 aalganiale.dstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdp.....vlfGi 79 
                                       +++    a++ ++t EllaY   +r+     d    +++++kt  +t  ++  ++++ + +  +++p      l + 
  gi|386001687|ref|YP_005919986.1| 170 WSVRTAAARSpQATVELLAYLAADRI----QDVRAAVAMNKKTSASTLASLAADRDVEIRAAVASNPiadpaTLVAL 242
                                       5555555666679*********9988....78888899999999988887654443333333333333344655566 PP

                                       EES-HHHHHHHH CS
                           DUF1743  80 rgedpeallkaa 91 
                                        g+ + ++++ +
  gi|386001687|ref|YP_005919986.1| 243 SGDWAWKVREKV 254
                                       665555555555 PP

>> PHF12_MRG_bd  PHD finger protein 12 MRG binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.051   1.5e+02      13      22 ..      83      92 ..      80      93 .. 0.86
   2 ?   -1.7   0.0      0.86   2.6e+03      15      22 ..     122     129 ..     118     130 .. 0.74
   3 ?    1.0   0.0      0.12   3.5e+02      13      22 ..     146     155 ..     146     156 .. 0.92
   4 ?   -1.3   0.1      0.61   1.8e+03      13      20 ..     198     205 ..     198     208 .. 0.84
   5 ?    1.0   0.1      0.12   3.5e+02      13      21 ..     224     232 ..     221     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.051
                      PHF12_MRG_bd 13 irAAslmNPk 22
                                      +rAA  +NP+
  gi|386001687|ref|YP_005919986.1| 83 VRAAVALNPR 92
                                      8********7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.86
                      PHF12_MRG_bd  15 AAslmNPk 22 
                                        A  +NPk
  gi|386001687|ref|YP_005919986.1| 122 EAAAKNPK 129
                                       57889**9 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.12
                      PHF12_MRG_bd  13 irAAslmNPk 22 
                                       +rAA  +NP+
  gi|386001687|ref|YP_005919986.1| 146 VRAAVVSNPT 155
                                       79*******7 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.61
                      PHF12_MRG_bd  13 irAAslmN 20 
                                       +rAA  mN
  gi|386001687|ref|YP_005919986.1| 198 VRAAVAMN 205
                                       79****** PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.12
                      PHF12_MRG_bd  13 irAAslmNP 21 
                                       irAA  +NP
  gi|386001687|ref|YP_005919986.1| 224 IRAAVASNP 232
                                       9*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1863.56
//
Query:       gi|386001688|ref|YP_005919987.1|  [L=312]
Description: hypothetical protein Mhar_0994 [Methanosaeta harundinacea 6Ac]
Scores for 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-19   68.1   0.4    8.5e-19   68.1   0.4    1.9  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    2.1e-07   31.2   0.5    2.1e-07   31.2   0.5    1.8  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    5.7e-06   26.5   0.3    5.7e-06   26.5   0.3    2.2  2  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
    5.1e-05   23.6   0.0    9.6e-05   22.7   0.0    1.5  1  eRF1_2          eRF1 domain 2
     0.0095   16.0   4.6     0.0095   16.0   4.6    1.9  2  bZIP_1          bZIP transcription factor
  ------ inclusion threshold ------
      0.033   14.5  10.6      0.033   14.5  10.6    2.3  3  DUF4164         Domain of unknown function (DUF4164)
       0.23   11.3   3.6        0.4   10.5   3.6    1.3  1  DUF724          Protein of unknown function (DUF724)
        1.2    9.1   6.4        1.2    9.0   0.6    3.2  3  PKcGMP_CC       Coiled-coil N-terminus of cGMP-dependent prot


Domain annotation for each model (and alignments):
>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       1.4   3.1e+03      51     121 ..      38      60 ..      13      70 .. 0.46
   2 !   68.1   0.4   3.8e-22   8.5e-19       2     121 ..     185     305 ..     184     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                           acVLRF1  51 renqadalleavaeaaarllaeesaevvlgGdrslvaevledarlaplatlareelldvpdprravLedav 121
                                       r+++++                                                ++ ++++  + +L+ a 
  gi|386001688|ref|YP_005919987.1|  38 RDEKIR------------------------------------------------KMTAAQQEASLALKAAE 60 
                                       222222................................................22233333333444443 PP

  == domain 2  score: 68.1 bits;  conditional E-value: 3.8e-22
                           acVLRF1   2 rlgvllvrrggfavgvve.ggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae. 76 
                                       +++v+  ++g   +g++   +   ++ v ++ v++++ +GGwSq+Rf+R re+ ++++++ vae+++ ll+ +++  
  gi|386001688|ref|YP_005919987.1| 185 PVLVVAAHAGETLLGLALgREGFIEEAVVKSTVKEKHTKGGWSQRRFERLREEDIRQHAALVAERLESLLEGRRSIp 261
                                       689999************445578999*******************************************5555559 PP

                           acVLRF1  77 ..vvlgGdrslvaevledarlaplatlareelldvpdprravLedav 121
                                          v+gG+ +lv+ ++   ++  l++   +  +d +dp  +vLe++ 
  gi|386001688|ref|YP_005919987.1| 262 vyAVVGGESALVRMIRPAIEMPILEAKFGR--IDRKDP-AEVLEEVY 305
                                       999*************99997778888888..899999.99999875 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       1.1   2.4e+03      21      48 ..      35      62 ..      17     107 .. 0.44
   2 !   31.2   0.5   9.5e-11   2.1e-07      36     134 ..     207     303 ..     175     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                    baeRF_family10 21 vdreraRlfevylgeleeveevegevpg 48
                                      ++r++ ++  +   + e +  +++++++
  gi|386001688|ref|YP_005919987.1| 35 IERRDEKIRKMTAAQQEASLALKAAEQR 62
                                      4444443333333333333333333332 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 9.5e-11
                    baeRF_family10  36 leeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklleerg..verlvlgGdeeetaalldrlpk 110
                                       + e+ +v++ v++++ +ggw sq+rf+r +ee +++h+  vAe l++lle r+      v+gG  +   +++ +   
  gi|386001688|ref|YP_005919987.1| 207 FIEEAVVKSTVKEKHTKGGW-SQRRFERLREEDIRQHAALVAERLESLLEGRRsiPVYAVVGGESALVRMIRPAIEM 282
                                       56789999************.*****************************999643444667777777777777666 PP

                    baeRF_family10 111 alrarvvgtlplpvdasaaaVlek 134
                                       ++ +  +g+++ ++   +a+Vle+
  gi|386001688|ref|YP_005919987.1| 283 PILEAKFGRIDRKD---PAEVLEE 303
                                       66666666643333...6666665 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.32   7.2e+02      15      70 ..      43     102 ..      29     108 .. 0.53
   2 !   26.5   0.3   2.5e-09   5.7e-06       3      92 ..     186     277 ..     184     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.32
                     baeRF_family2  15 tlvdaggeeeeetveGghdpvhkvragg....wshrryqrraeeswerNaeavAeevdrl 70 
                                       + ++a+++e +   ++ ++ +   ++gg     +++   +  e+sw    ++vA+ +drl
  gi|386001688|ref|YP_005919987.1|  43 RKMTAAQQEASLALKAAEQRIAALQEGGsedgGEEKGRPKPEEKSWTLKPREVARLLDRL 102
                                       555544455555555555555555444433322222223335667777777777777765 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.5e-09
                     baeRF_family2   3 lvvevDrtGadltlvdaggeeeeetveGghdpvhkvraggwshrryqrraeeswerNaeavAeevdrlvresg..ae 77 
                                       ++v++ ++G  l   + g+e+  e++  ++   +k  +ggws+rr++r  ee +++ a+ vAe++++l + ++  + 
  gi|386001688|ref|YP_005919987.1| 186 VLVVAAHAGETLLGLALGREGFIEEAVVKSTVKEKHTKGGWSQRRFERLREEDIRQHAALVAERLESLLEGRRsiPV 262
                                       78888899999999998988888888888888888899******************************976652255 PP

                     baeRF_family2  78 lVvlaGDvrarsllr 92 
                                         v+ G+   ++++r
  gi|386001688|ref|YP_005919987.1| 263 YAVVGGESALVRMIR 277
                                       557777776666665 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.3e-08   9.6e-05      27      68 ..     212     253 ..     187     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.3e-08
                                       EEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                            eRF1_2  27 kievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaanka 68 
                                        ++++v  Kh +Gg s+rrfeRlree +++    vae +++ 
  gi|386001688|ref|YP_005919987.1| 212 VVKSTVKEKHTKGGWSQRRFERLREEDIRQHAALVAERLESL 253
                                       56788999**********************999999988765 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.6   4.2e-06    0.0095      21      60 ..       7      46 ..       6      50 .. 0.95
   2 ?   -2.3   0.0       2.2   4.9e+03      27      47 ..      94     114 ..      91     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 21 RqRKqaeieeLerrvkaLekeNksLkseleelkkevekLk 60
                                      R+R+++ei eL ++v+ Le+e  sL+ ++e+  +++ k+ 
  gi|386001688|ref|YP_005919987.1|  7 RKRREEEIGELRSKVALLEEERDSLALQIERRDEKIRKMT 46
                                      9*********************************999985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLks 47 
                                       e+++L +r +++ ++  +L s
  gi|386001688|ref|YP_005919987.1|  94 EVARLLDRLDEIRSKDDDLLS 114
                                       667777777777777666655 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  10.6   1.5e-05     0.033      27      85 ..       7      65 ..       3      68 .. 0.93
   2 ?   -2.4   0.0       2.7   6.2e+03      69      81 ..      92     104 ..      84     108 .. 0.63
   3 ?   -1.3   0.1       1.2   2.7e+03      29      50 ..     232     240 ..     210     259 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                           DUF4164 27 rleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietira 85
                                      r ++e++ +el++++++l+e+r  La ++  +  + +++ ++++E+s +Lkaa + i a
  gi|386001688|ref|YP_005919987.1|  7 RKRREEEIGELRSKVALLEEERDSLALQIERRDEKIRKMTAAQQEASLALKAAEQRIAA 65
                                      66789999***********************************************9976 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                           DUF4164  69 nrEvsrrLkaaie 81 
                                        rEv+r L++++e
  gi|386001688|ref|YP_005919987.1|  92 PREVARLLDRLDE 104
                                       5677776666654 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                           DUF4164  29 eaerkrdeleaeiealgedrsR 50 
                                       e+ r++               R
  gi|386001688|ref|YP_005919987.1| 232 ERLREE-------------DIR 240
                                       333333.............222 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.6   0.00018       0.4     126     183 ..       8      65 ..       5      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                            DUF724 126 rkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFea 183
                                       ++ eeei el +k++ le+++++l  + e+ d++i ++ + +++++ +l+++eq+  a
  gi|386001688|ref|YP_005919987.1|   8 KRREEEIGELRSKVALLEEERDSLALQIERRDEKIRKMTAAQQEASLALKAAEQRIAA 65 
                                       56799***********************************************998765 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6   0.00055       1.2      19      30 ..       9      20 ..       8      21 .. 0.92
   2 ?    1.4   0.2      0.13   2.9e+02       6      13 ..      38      45 ..      31      52 .. 0.71
   3 ?   -2.9   0.0       2.9   6.5e+03       3      14 ..      56      67 ..      54      68 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00055
                         PKcGMP_CC 19 ekdeEIqELrsk 30
                                      +++eEI ELrsk
  gi|386001688|ref|YP_005919987.1|  9 RREEEIGELRSK 20
                                      79*********9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                         PKcGMP_CC  6 KDERIREL 13
                                       DE+IR +
  gi|386001688|ref|YP_005919987.1| 38 RDEKIRKM 45
                                      57777765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.9
                         PKcGMP_CC  3 lllKDERIRELE 14
                                      l++ + RI+ L+
  gi|386001688|ref|YP_005919987.1| 56 LKAAEQRIAALQ 67
                                      556688998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1821.99
//
Query:       gi|386001689|ref|YP_005919988.1|  [L=310]
Description: Sulfide dehydrogenase (Flavoprotein) subunit SudB [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-11   42.2   2.6    9.7e-11   41.3   2.6    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
      0.029   14.4   0.8      0.055   13.5   0.8    1.3  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   2.6   1.1e-14   9.7e-11       3      42 .]     226     261 ..     225     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.1e-14
                                       --SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB. CS
                   DHODB_Fe-S_bind   3 rMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadevd 42 
                                       +M +G+G+C++C+v ++g+    +k +C++GP+F + +vd
  gi|386001689|ref|YP_005919988.1| 226 IMIDGTGMCGACRVNVAGE----TKLACVEGPEFAGRDVD 261
                                       7***************986....8************9985 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   6.1e-06     0.055      54      73 ..     231     250 ..     227     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-06
                            Fer2_3  54 egiCGscavainGkptlaCt 73 
                                        g+CG+c v++ G+++laC 
  gi|386001689|ref|YP_005919988.1| 231 TGMCGACRVNVAGETKLACV 250
                                       69*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2082.87
//
Query:       gi|386001690|ref|YP_005919989.1|  [L=535]
Description: hypothetical protein Mhar_0997 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0002   21.6   0.1     0.0006   20.1   0.1    1.8  1  DUF11     Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   3.3e-08    0.0006      29      89 ..     438     511 ..     421     513 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.3e-08
                             DUF11  29 sangvvvtDtlPaglayvsvsas...........qgtasaltsvgsLeagesatlsftvrvtrtaasga..ltn 89 
                                       ++++v vtD+lP g+ y ++ ++           + + s ++++++Le  e+++++++ +  ++a++++  l+n
  gi|386001690|ref|YP_005919989.1| 438 NLTNVNVTDLLPKGFGYTRGNSTkmdgeifeptnKTSSSLTWTITRLEHDETLYINVAFSIENSADTKTrlLDN 511
                                       789***************************88877777788888*****************9999998776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3836.99
//
Query:       gi|386001691|ref|YP_005919990.1|  [L=364]
Description: hypothetical protein Mhar_0998 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-06   25.8   0.0      2e-05   24.8   0.0    1.5  1  DUF11     Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.1e-09     2e-05      15      69 ..     247     314 ..     231     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-09
                             DUF11  15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas.............qgtasaltsvgsLeages 69 
                                        v+y +t++Ntg + +++v++ DtlP g+ +  v  s                +++++s g L  ges
  gi|386001691|ref|YP_005919990.1| 247 IVVYKITASNTGETRLKNVTLDDTLPLGMDFDNVYYSeggspdfllgeeaGKPCDVTMSLGYLDTGES 314
                                       589**************************998877775555566665543223334444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2560.79
//
Query:       gi|386001692|ref|YP_005919991.1|  [L=529]
Description: cobyric acid synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-51  174.8   0.0    2.1e-51  174.3   0.0    1.2  1  GATase_3     CobB/CobQ-like glutamine amidotransferase domain
    8.1e-21   74.7   0.0    6.2e-20   71.9   0.0    2.0  1  AAA_26       AAA domain
    1.4e-19   70.4   0.0    2.5e-19   69.6   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00044   20.1   0.0      0.001   18.8   0.0    1.6  1  GATase       Glutamine amidotransferase class-I
    0.00099   18.4   0.2       0.14   11.4   0.0    2.8  3  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
     0.0015   18.5   0.0     0.0079   16.1   0.0    1.9  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
  ------ inclusion threshold ------
      0.021   13.8   0.0        0.7    8.8   0.0    2.4  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.17   11.7   0.0       0.28   11.0   0.0    1.3  1  SNO          SNO glutamine amidotransferase family
       0.18   12.2   0.0       0.32   11.4   0.0    1.3  1  DUF3280      Protein of unknown function (DUF2380)
       0.19   11.0   0.0       0.37   10.1   0.0    1.4  1  CTP_synth_N  CTP synthase N-terminus


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.3   0.0   1.2e-54   2.1e-51       1     196 []     288     472 ..     288     472 .. 0.93

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 1.2e-54
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +iav+rlp+isn+td++pLe+e+  rvr+v  ++e lg+ +d+vi+pG+k+t++dl+ +r +g+d++i ++ +ag+p
  gi|386001692|ref|YP_005919991.1| 288 EIAVVRLPRISNFTDFEPLEREA--RVRYVA-PGEPLGS-PDAVIIPGTKNTVADLEEMRVRGTDREILALRRAGVP 360
                                       69*****************9976..999***.*****88.************************************* PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeageveglglLdietefek.ekltgqvegevel......aaegeevkGyEiHsG 147
                                       +lgiCGG+q+LG++i+d  g+e+++ e++glglLd+ t+f + ek+t qve+ v           ge+v GyEiH+G
  gi|386001692|ref|YP_005919991.1| 361 ILGICGGYQILGKRIVD-LGIENATVEMPGLGLLDLVTRFDRyEKRTVQVEKPVTGggpilgRIMGERVWGYEIHMG 436
                                       ****************9.69**********************9****9999997779*99987788*********** PP

                          GATase_3 148 rtilkekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrna 196
                                        t +++   p++         ++dGav    dg v+GtYlHg+f n+n+
  gi|386001692|ref|YP_005919991.1| 437 VTASRD--PPAF---------GDDGAV--ADDGLVIGTYLHGIFNNQNF 472
                                       877655..5666.........56****..66***************986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   3.5e-23   6.2e-20       3     191 ..      41     263 ..      39     266 .. 0.74

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 3.5e-23
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....................ededselikellgld 58 
                                       i+v gt  ++GK+++ ++L+r+l+++g kv+ fK  +  ++                       e sel+  +l  +
  gi|386001692|ref|YP_005919991.1|  41 IVVLGTCSHSGKSTIVAALCRILRNRGLKVAPFKSQNMSLNswvtsegkemgiaqavqawaaGVEPSELMNPILLKP 117
                                       89*********************************988888888866654444444444332233555555555444 PP

                            AAA_26  59 qtyelpeplalsaplspelaarqegedid.lekiv....kelekdadivvVEGagglgvp.itee.llnadiaknlg 128
                                       +     + +++  p++++ a +   ++id l+ +v    +el++++d +vVEGagg  +  +++    n+++a++lg
  gi|386001692|ref|YP_005919991.1| 118 KGDRTSQVIVFGVPVADRSAEEY-YREIDgLKGVVdraiDELSQEYDYIVVEGAGGAAEInLFDRdIANIYVARKLG 193
                                       44444555555556555554444.345555555558888*******************7624444588********* PP

                            AAA_26 129 apvilVargglg.tinqllltiealrqknvr..vlGvilNkvrnp....e.nvetlekksgipvlGvvPyl 191
                                       ap+ilV+ +++g  ++ l+ t+++l   ++r  v+G+++Nk+r +    e  + +le+ +g+pvlGv+Pyl
  gi|386001692|ref|YP_005919991.1| 194 APIILVGDIERGgVFASLYGTAALLPP-EIRplVKGLVINKFRGDpailEpGLGMLEELTGVPVLGVMPYL 263
                                       **********97256666666666666.56558*********9886555269*****************97 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   1.4e-22   2.5e-19       1     116 [.      41     264 ..      41     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.4e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       i++ +t + +GK+t++a+L+r+l +rgl+V++++ ++++ n+ +  eg+e+ i++                      
  gi|386001692|ref|YP_005919991.1|  41 IVVLGTCSHSGKSTIVAALCRILRNRGLKVAPFKSQNMSLNSWVtSEGKEMGIAQavqawaagvepselmnpillkp 117
                                       7899**************************************99********************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386001692|ref|YP_005919991.1| 118 kgdrtsqvivfgvpvadrsaeeyyreidglkgvvdraidelsqeydyivvegaggaaeinlfdrdianiyvarklga 194
                                       ***************************************************************************** PP

                                       ......CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                       ......xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                             d++r ++++++l+++ all      +++g+v+n+++g+   + l+ +l  l++ +gvpvlgv+p+ +
  gi|386001692|ref|YP_005919991.1| 195 piilvgDIER-GGVFASLYGTAALLppeirPLVKGLVINKFRGD--PAILEPGLGMLEELTGVPVLGVMPYLD 264
                                       **********.**********9999*******************..999999999999888*********965 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.8e-07     0.001      40      88 ..     321     375 ..     298     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.8e-07
                                       HHSTSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHT CS
                            GATase  40 lknpdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaief 88 
                                       l +pd+++++g  ++++      v g+ + i  +r +++PiLGIC G Q+l++ +
  gi|386001692|ref|YP_005919991.1| 321 LGSPDAVIIPGTKNTVAdleemrVRGTDREILALRRAGVPILGICGGYQILGKRI 375
                                       5689999999999999998888888888888888889*************98865 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   7.9e-05      0.14      11      53 ..      37      79 ..      25      99 .. 0.86
   2 ?    3.5   0.1     0.021        37      71      98 ..     147     172 ..     143     177 .. 0.84
   3 ?   -1.1   0.0      0.55   9.9e+02     116     152 ..     323     357 ..     321     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                           DUF1611 11 kakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtg 53
                                       ++ ++v+GT +  GK t   +l + l++rGlk+a +    ++
  gi|386001692|ref|YP_005919991.1| 37 MTRFIVVLGTCSHSGKSTIVAALCRILRNRGLKVAPFKSQNMS 79
                                      56789****************************9877666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                           DUF1611  71 vaGaveglvkkaaeeeepdlilveGQgs 98 
                                         G v ++++++ + e  d+i+veG g+
  gi|386001692|ref|YP_005919991.1| 147 LKGVVDRAIDELSQ-EY-DYIVVEGAGG 172
                                       569999*******6.44.9******986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.55
                           DUF1611 116 qPdalvLchrpgrkhirglpeialppleeeielieal 152
                                       +Pda+++   +  +++ +l+e+++++  +ei +++++
  gi|386001692|ref|YP_005919991.1| 323 SPDAVIIPGTK--NTVADLEEMRVRGTDREILALRRA 357
                                       68999988766..889999999999999999888765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.4e-06    0.0079       3      47 ..      43      89 ..      41     109 .. 0.83
   2 ?   -0.8   0.0      0.75   1.4e+03      82      98 ..     152     169 ..     132     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.4e-06
                              MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhahhgfd..vdkpgk 47
                                       +  +s sGK t++  l ++l++rgl+v+  K ++ +++  v ++gk
  gi|386001692|ref|YP_005919991.1| 43 VLGTCSHSGKSTIVAALCRILRNRGLKVAPFKSQNMSLNswVTSEGK 89
                                      455689**************************998776655555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.75
                              MobB  82 eellarl.sevDlvlvEG 98 
                                       ++ ++ l +e+D ++vEG
  gi|386001692|ref|YP_005919991.1| 152 DRAIDELsQEYDYIVVEG 169
                                       56666774569******9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00039       0.7      38      61 ..      48      71 ..      37      75 .. 0.86
   2 ?    2.0   0.0     0.047        84     206     232 ..     485     511 ..     478     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00039
                                      TTSSHHHHHHHHHHHHHCTT--EE CS
                              MeaB 38 PGaGkstlvealglelrrrGkrva 61
                                        +Gkst+v al   lr+rG +va
  gi|386001692|ref|YP_005919991.1| 48 SHSGKSTIVAALCRILRNRGLKVA 71
                                      458********************8 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.047
                                       EEEEEBCCCTBSHHHHHHHHHHHHHHH CS
                              MeaB 206 kvlktsavegeGidelvdaieehrevl 232
                                       ++++ sa++g+G del++a e++ +  
  gi|386001692|ref|YP_005919991.1| 485 NLVRGSALRGDGYDELASAAEKFLDLE 511
                                       68999****************998765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.28      28     107 ..     318     404 ..     304     414 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                       GGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEE...TTB....SS-SS--CC CS
                               SNO  28 kedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskel...ene....lvktlellk 97 
                                        e l   da+iiPG   t   +   r    +     ++++  ++lG C G  +l k++   ++e    +++ l+ll+
  gi|386001692|ref|YP_005919991.1| 318 GEPLGSPDAVIIPGTKNTVADLEEMRVRGTDREILALRRAGVPILGICGGYQILGKRIvdlGIEnatvEMPGLGLLD 394
                                       5778889*********9988876666655666555667777*************99762222334456667788898 PP

                                       EEEETTTT-S CS
                               SNO  98 vkvkrnafGr 107
                                       ++ + + + +
  gi|386001692|ref|YP_005919991.1| 395 LVTRFDRYEK 404
                                       8877776655 PP

>> DUF3280  Protein of unknown function (DUF2380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.32       2      89 ..     124     204 ..     123     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                           DUF3280   2 kvavldfeliDtsaepadqtaeearRlaavteqlreaLaesgryevvdlapaaaeiekesnlrkCngceadiArklg 78 
                                       +v v+++ + D sae       e   l+ v ++  ++L+++ +y vv+ a  aaei    nl++ + ++  +Arklg
  gi|386001692|ref|YP_005919991.1| 124 QVIVFGVPVADRSAEEY---YREIDGLKGVVDRAIDELSQEYDYIVVEGAGGAAEI----NLFDRDIANIYVARKLG 193
                                       5899999999*999999...5788899*********************99999988....899999999******** PP

                           DUF3280  79 AdlvlvgevqK 89 
                                       A ++lvg +++
  gi|386001692|ref|YP_005919991.1| 194 APIILVGDIER 204
                                       *******9876 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0002      0.37       2      37 ..      40      74 ..      39      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                                      EEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEE CS
                       CTP_synth_N  2 yilvtGGvvSglGkGiiaaslgallksrglkvtlik 37
                                      +i+v G  +S  Gk  i+a+l+++l++rglkv+  k
  gi|386001692|ref|YP_005919991.1| 40 FIVVLG-TCSHSGKSTIVAALCRILRNRGLKVAPFK 74
                                      777775.68999********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3404.82
//
Query:       gi|386001693|ref|YP_005919992.1|  [L=287]
Description: Putative signal transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-39  133.2  12.1    9.7e-15   54.8   1.7    4.2  4  CBS       CBS domain
     0.0062   17.2   0.5        3.5    8.3   0.1    2.4  2  GAF       GAF domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.6   1.1e-12   9.8e-09       1      53 [.       6      57 ..       6      60 .. 0.95
   2 !   54.8   1.7   1.1e-18   9.7e-15       4      56 ..      67     118 ..      64     119 .. 0.94
   3 !   22.7   0.0   1.1e-08    0.0001      12      54 ..     137     179 ..     123     181 .. 0.81
   4 !   24.9   0.0   2.3e-09   2.1e-05      10      55 ..     233     278 ..     215     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.1e-12
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      V+++m rdv +v+   +   +l+ + e++vs++PVV + g+lvG+vt++Dllr
  gi|386001693|ref|YP_005919992.1|  6 VKEVMVRDVAYVTVPGSRDMVLKALQERHVSGVPVV-KGGELVGMVTRTDLLR 57
                                      89***********************7777*******.899************8 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 1.1e-18
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +mtrd+++v+pd+++ ea++ ++e++++rlPVV edg lvGiv+  D++r+++
  gi|386001693|ref|YP_005919992.1|  67 LMTRDPLVVHPDDDVVEAARHLAENDIRRLPVV-EDGALVGIVSVADVIRVVA 118
                                       5*********************9999*******.8***************986 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 1.1e-08
                                       EETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  12 vppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +  +++l  a   m+ ++v + PV+d++ klvGiv++rDl++a
  gi|386001693|ref|YP_005919992.1| 137 LWDEMPLPVAGAVMEYANVQASPVIDSELKLVGIVSDRDLINA 179
                                       5667888888888944559778***8777************97 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 2.3e-09
                                       EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       vt+  ++ ++e+++ m +kg+++lPVV    kl G++ ++Dll al
  gi|386001693|ref|YP_005919992.1| 233 VTAIKTSEVSECARVMMRKGIDQLPVVTAHQKLAGMLKDSDLLWAL 278
                                       47777777*******88**********77779**********9776 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1   0.00065       5.9      79     106 ..      24      51 ..       7      68 .. 0.81
   2 !    8.3   0.1   0.00039       3.5      54     109 ..      65     112 ..      50     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00065
                                       HHHHHHTTESEEEEEEEEETTEEEEEEE CS
                               GAF  79 rdllenmgirsslvvPlvndgelwGllv 106
                                        ++l++ + r + +vP+v +gel+G+++
  gi|386001693|ref|YP_005919992.1|  24 DMVLKALQERHVSGVPVVKGGELVGMVT 51 
                                       567888999999*************997 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00039
                                       HHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE CS
                               GAF  54 qvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn 109
                                       + l t++plv++   pd++  +    ++l++  ir    +P+v dg l+G++++ +
  gi|386001693|ref|YP_005919992.1|  65 ALLMTRDPLVVH---PDDDVVE--AARHLAENDIR---RLPVVEDGALVGIVSVAD 112
                                       56789*******...9999999..55677777777...99************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1723.22
//
Query:       gi|386001694|ref|YP_005919993.1|  [L=147]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-33  114.4   0.5    6.2e-33  114.3   0.5    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.5   3.5e-37   6.2e-33       1     141 []       1     141 [.       1     141 [. 0.98

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 3.5e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m++rI++a+Dgs++s++A+  ++ela+ +g+ +++++v d+ + ++ ++ +  a    l  +e e++ +   ++ae 
  gi|386001694|ref|YP_005919993.1|   1 MFERIMIATDGSKHSERAAAVGIELARLSGGSVTIVYVADTGRLSHLPEDMALASIRDLLIKEGENATAFIGEMAER 77 
                                       99**************************************************9999999999999988889****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        gv+ +  v+eg+p+ee+++vaee +++ iV+Gs grsgl+++llGSv+e+v+r +++pV+ V+
  gi|386001694|ref|YP_005919993.1|  78 SGVASTKMVVEGNPGEELVRVAEEVGVNAIVIGSCGRSGLEKFLLGSVAEKVVRTSTVPVITVP 141
                                       *************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 881.39
//
Query:       gi|386001695|ref|YP_005919994.1|  [L=352]
Description: amidohydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-34  118.9   0.2    2.4e-32  112.6   0.2    2.8  1  Amidohydro_1  Amidohydrolase family
    1.7e-07   31.1   0.2    1.7e-07   31.1   0.2    2.0  2  Amidohydro_3  Amidohydrolase family
    1.2e-06   28.1   0.0    1.7e-06   27.6   0.0    1.1  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.6   0.2     4e-36   2.4e-32       1     329 [.      49     343 ..      49     352 .] 0.80

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 4e-36
                                       EEEE-EEEEEEECETTECSSS...GHHHHH............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwl............vppetaaealesgiktalksGtttvadmgattstg 62 
                                       i+ P+l++ HvHl +s+++++   +l d++            +p +++ e++++ +  + +sGt  +ad+++  s+g
  gi|386001695|ref|YP_005919994.1|  49 IIAPALVNGHVHLGDSFFKDPpylPLRDLVgpgglkhralasAPRREVVEGMRRSLLYMARSGTAAFADFREGGSDG 125
                                       689**************9999999999999*********************************************** PP

                                       HHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHH CS
                      Amidohydro_1  63 iealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealk 139
                                       +e llea+e + l  ri+g            +    +++++ +              +++ ++    ++++++e+++
  gi|386001695|ref|YP_005919994.1| 126 VEMLLEAMEGTGLAGRIFGR-----------PDPGSVRIHEKC-------------WGVGISSTKDHPRSWVEEVAE 178
                                       **********8445555544...........333446666666.............56666677777899******* PP

                                       HHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEE CS
                      Amidohydro_1 140 eakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagva 216
                                       +a++++++va Ha+e + +  d+e+a      +    +              l+h +  +p ++++++e+  ++ v+
  gi|386001695|ref|YP_005919994.1| 179 AARREGKKVALHAGEADRD--DIEDALS---LE---PDL-------------LVHLTRAEPRDLRMVAEA--GVPVV 232
                                       *************664443..4555555...22...233.............444444446677777777..66667 PP

                                       HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHH.HHHHHHHTHH CS
                      Amidohydro_1 217 hcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglsl.kealrmaTin 292
                                        cp+sn++ + g+++++++l+ G+ vglgtD + + ns+nl+ e+ la            ++ l    +++ m+T+n
  gi|386001695|ref|YP_005919994.1| 233 VCPRSNLVTGVGLPDVARMLEMGITVGLGTD-NVMLNSPNLFSEMELAS-----------KALLHNdRQVFMMCTLN 297
                                       89*****************************.*****************...........3334330569******* PP

                                       HHHHTT-TTTSSSS-TTSB--EEEECC.........CTCGGGTTTC CS
                      Amidohydro_1 293 gAkalglddkvGsievGkdADlvvvdl.........dilaafvglk 329
                                       gA++lg dd++G+i vGk+  + v+d          d+la++v  +
  gi|386001695|ref|YP_005919994.1| 298 GARILGADDEAGAIRVGKECRIMVIDRrsenmagsrDPLASLVRRA 343
                                       *************************986554443333355555554 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3      0.42   2.5e+03      10      21 ..      50      61 ..      48      65 .. 0.87
   2 !   31.1   0.2   2.9e-11   1.7e-07     256     448 ..     164     325 ..     150     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.42
                      Amidohydro_3 10 vlPGFvDsHtHl 21
                                       +P++v  H Hl
  gi|386001695|ref|YP_005919994.1| 50 IAPALVNGHVHL 61
                                      79*********6 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.9e-11
                      Amidohydro_3 256 gwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaa 332
                                       +++d+++  ++e+++aa+  g  va+ha +++  d          ++++++    l h +   +++++ va+ +v  
  gi|386001695|ref|YP_005919994.1| 164 STKDHPRSWVEEVAEAARREGKKVALHAGEADRDD--------IEDALSLEPD-LLVHLTRAEPRDLRMVAEAGVPV 231
                                       56777777799999999999999999995555544........3455677766.89999999*************** PP

                      Amidohydro_3 333 gvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeels 409
                                        v+p++n              + g++ v+++l++g++v lg+D   +++ + p + +          e++     + 
  gi|386001695|ref|YP_005919994.1| 232 VVCPRSNL-----------VTGVGLPDVARMLEMGITVGLGTD---NVMLNSPNLFSEM--------ELASKALLHN 286
                                       ******99...........456788******************...4444444443333........6666777778 PP

                      Amidohydro_3 410 leealalyTrgpAkalgledrkGtLevGadADlvvldad 448
                                        ++++ ++T ++A++lg++d++G ++vG++  ++v+d+ 
  gi|386001695|ref|YP_005919994.1| 287 DRQVFMMCTLNGARILGADDEAGAIRVGKECRIMVIDRR 325
                                       89******************************9999954 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.8e-10   1.7e-06     172     302 ..     166     289 ..     153     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.8e-10
                                       TSTTGGGHHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHH CS
                       A_deaminase 172 kiepaslflklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSN 248
                                       k +p s   ++ ++a+ ++ +++ HaGEa + + + +Al l + + + H  ++r +p+ +   a+a +p+ vcP SN
  gi|386001695|ref|YP_005919994.1| 166 KDHPRSWVEEVAEAARREGKKVALHAGEA-DRDDIEDALSL-EPDLLVH--LTRAEPRDLRMVAEAGVPVVVCPRSN 238
                                       4455555778889999************8.7899*****99.9******..666778888999************** PP

                                       CCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHH.T--HH CS
                       A_deaminase 249 valgafleyaenPlkeflerglnvslntDDPlqfgttLieeYaiaaqvf.klsee 302
                                         +g+ l++    + + le g+ v l+tD+ ++ + +L  e++ a++++ + +++
  gi|386001695|ref|YP_005919994.1| 239 LVTGVGLPD----VARMLEMGITVGLGTDNVMLNSPNLFSEMELASKALlHNDRQ 289
                                       ***887776....789******************************998444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2141.74
//
Query:       gi|386001696|ref|YP_005919995.1|  [L=221]
Description: Diaminohydroxyphosphoribosylaminopyrimidine reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-52  176.5   0.0    6.1e-52  176.4   0.0    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0   3.4e-56   6.1e-52       1     200 []       4     215 ..       4     215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 3.4e-56
                                       -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS CS
                            RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearq 76 
                                       p+v +++a+S+DGk++   +++ +i+g+e+  +v+ lrae+da++vG+gtvlad+p l v+ ++ r  + + ++ ++
  gi|386001696|ref|YP_005919995.1|   4 PFVFINSAMSADGKISSFLRQQVRISGPEDMGRVGLLRAESDAVMVGVGTVLADDPGLRVKSPDHRGMRsKLGKPED 80 
                                       89***************************************************************9888777777** PP

                                       -EEEEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC.....E.....SE-HHHHHHHHHHTT--EEEEEET CS
                            RibD_C  77 pvrvVvdstlrvpldakvltddaptlvatteeadkekveklk.....v.....rvdlkelleeLkergirsllveGG 143
                                       p+rvVvds+ ++p++akvl d+   ++a++++a++e+++ l      v     rvdl+ell+ L++rg+r+l+veGG
  gi|386001696|ref|YP_005919995.1|  81 PLRVVVDSQGKTPPSAKVLGDG--CILAVSRAAPEERLRLLGdrcevVafgeeRVDLPELLSFLYKRGVRRLMVEGG 155
                                       *********************9..99999999999999988899885388999************************ PP

                                       HHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS..EEEEEEEEEEETTEEEE CS
                            RibD_C 144 atLagsllraglvDelrlyiaPkllGg.agktlfdgegfka..lklklvksealgegvvl 200
                                       atL++sl++ glvDe+  yi P+++Gg  ++tl+dg gf+   ++l+l  +eal+ gv+l
  gi|386001696|ref|YP_005919995.1| 156 ATLNWSLVEGGLVDEISTYIGPIIIGGaRAPTLVDGPGFSGgyPELELSAAEALDGGVLL 215
                                       ***************************************99************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1429.81
//
Query:       gi|386001697|ref|YP_005919996.1|  [L=233]
Description: hypothetical protein Mhar_1004 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-56  190.3   0.0    4.3e-56  190.1   0.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.1   0.0   2.4e-60   4.3e-56       2     204 ..      10     217 ..       9     218 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 2.4e-60
                            DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklks 78 
                                       L  +l+l+t+PV+vk+++ ++e+p++++ i+ + r+C mv+ ar +g+t +++ + ++C+gGaa+lG++e pe++ s
  gi|386001697|ref|YP_005919996.1|  10 LVATLHLETNPVGVKLIRGEEEIPPEMKMIPGPLRYCEMVQAARLRGETTLANSDLHSCKGGAAGLGLMEFPENISS 86 
                                       7899************************************************************************* PP

                            DUF169  79 g......egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnv 149
                                       g      ++++++ ea  k+v+s p  +ag++ +++vapLek++ +Pdvv+f+++p q++r vq+al+++gg r+ +
  gi|386001697|ref|YP_005919996.1|  87 GnlyfskLNKVETKEAGSKIVSSFPAQKAGSTVATLVAPLEKMKLKPDVVIFVGKPFQARRVVQAALFAEGG-RVDF 162
                                       *************************99*******************************************99.**** PP

                            DUF169 150 sfpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                       +++g+++ C d+++ p+ +g+ n++lg+ ga k+a+l+dd +++giP++++e++v
  gi|386001697|ref|YP_005919996.1| 163 DTSGIQSFCVDATSSPILKGDVNVSLGCDGAAKNAGLEDDFVVVGIPFDMAEKVV 217
                                       ****************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1393.46
//
Query:       gi|386001698|ref|YP_005919997.1|  [L=48]
Description: hypothetical protein Mhar_1005 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.046   13.5   0.5      0.046   13.5   0.5    2.4  3  RelB_N          RelB Antitoxin alpha helical domain
      0.083   12.6   0.0      0.097   12.3   0.0    1.0  1  DUF188          Uncharacterized BCR, YaiI/YqxD family COG1671
       0.21   11.7   3.4        3.8    7.7   0.5    2.1  2  Bac_small_YrzI  Probable sporulation protein (Bac_small_yrzI)


Domain annotation for each model (and alignments):
>> RelB_N  RelB Antitoxin alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.017     1e+02      29      38 ..       9      18 ..       4      19 .. 0.75
   2 ?   13.5   0.5   7.7e-06     0.046       8      19 ..      18      29 ..      15      30 .. 0.90
   3 ?   -2.3   0.4       0.7   4.2e+03      38      45 ..      39      46 ..      37      47 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.017
                                      TTT--EEECC CS
                            RelB_N 29 vkdeepLsie 38
                                        d+epLs e
  gi|386001698|ref|YP_005919997.1|  9 ETDDEPLSEE 18
                                      5799***976 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.7e-06
                                      HHHHHHHHHH.H CS
                            RelB_N  8 eeyekIeEiLED 19
                                      e++++IeE+LED
  gi|386001698|ref|YP_005919997.1| 18 ETFKRIEEALED 29
                                      89*********9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.7
                                      CCHH-XXX CS
                            RelB_N 38 eeAleyye 45
                                      ee+++++e
  gi|386001698|ref|YP_005919997.1| 39 EEIEAELE 46
                                      55555554 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05     0.097      57      91 ..      10      46 ..       6      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                            DUF188 57 TqDipLAarvlekgaaals..prGevyteenIdella 91
                                      T D pL ++  ++   al+  +rG+ ytee+I++ l+
  gi|386001698|ref|YP_005919997.1| 10 TDDEPLSEETFKRIEEALEdlKRGRYYTEEEIEAELE 46
                                      899***************9446***********9986 PP

>> Bac_small_YrzI  Probable sporulation protein (Bac_small_yrzI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0035        21      18      39 ..      10      31 ..       8      33 .. 0.87
   2 ?    7.7   0.5   0.00064       3.8      15      25 ..      34      44 ..      31      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0035
                    Bac_small_YrzI 18 seeEiereqqiekieeemkdrq 39
                                      +++E ++e+  ++iee ++d +
  gi|386001698|ref|YP_005919997.1| 10 TDDEPLSEETFKRIEEALEDLK 31
                                      6789999*********998865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00064
                    Bac_small_YrzI 15 RkyseeEiere 25
                                      R+y+eeEie+e
  gi|386001698|ref|YP_005919997.1| 34 RYYTEEEIEAE 44
                                      88*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 293.31
//
Query:       gi|386001699|ref|YP_005919998.1|  [L=167]
Description: Appr-1-p processing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-44  150.9   0.0    1.7e-44  150.6   0.0    1.1  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   9.8e-49   1.7e-44       1     118 []      21     133 ..      21     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 9.8e-49
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       VnAaN +llggggv+gaihraag++l+eec++l    ggc++Gea +t++y+lpak+vihtvgp+++ +++++ee+l
  gi|386001699|ref|YP_005919998.1|  21 VNAANPTLLGGGGVDGAIHRAAGPRLLEECRTL----GGCPTGEARITKGYDLPAKFVIHTVGPIWH-GGGRGEEDL 92 
                                       9********************************....99***************************6.9******** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       lakay+++lela e+gik++afPais+G +g+p+e+a ++a
  gi|386001699|ref|YP_005919998.1|  93 LAKAYRSSLELAGENGIKTIAFPAISAGAYGFPMERASKIA 133
                                       *************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1000.47
//
Query:       gi|386001700|ref|YP_005919999.1|  [L=522]
Description: D-alanine--D-alanine ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-25   89.2   0.0    3.9e-25   88.6   0.0    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.5e-18   67.8   0.0    5.2e-18   66.0   0.0    1.8  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.6e-11   43.8   0.0    1.2e-10   41.7   0.0    2.1  2  Acetyltransf_1   Acetyltransferase (GNAT) family
      2e-10   41.0   0.0    5.2e-10   39.6   0.0    1.7  1  ATP-grasp_3      ATP-grasp domain
    6.2e-10   38.9   0.0    2.9e-09   36.8   0.0    1.9  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    9.8e-07   28.5   0.0    3.6e-05   23.4   0.0    2.3  1  ATP-grasp_4      ATP-grasp domain
    1.3e-05   25.3   0.0    2.1e-05   24.7   0.0    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    6.4e-05   22.5   0.0     0.0021   17.6   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    0.00025   20.9   0.0    0.00056   19.8   0.0    1.6  1  FR47             FR47-like protein
     0.0018   18.7   0.0     0.0039   17.6   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0021   18.0   0.0     0.0037   17.2   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0028   17.3   0.0       0.12   12.0   0.0    2.2  2  RimK             RimK-like ATP-grasp domain
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.35   10.6   0.0    1.5  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
        0.2   10.9   0.0        1.3    8.2   0.0    2.0  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0     3e-28   3.9e-25      34     202 ..     134     319 ..     111     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 3e-28
                                       HC-SSEEEEESSSSTTTTE...EEESSGGGHHHHHHHHHT.T-SCEEEEE--ESEEEEEEE.EETSSCEEEEEEEEE CS
                   Dala_Dala_lig_C  34 elgypvfVKpareGSSvGv...skveseeelkeaieeafk.ydekvlvEeaiegreievav.lgneklevsevgeiv 105
                                       +l +pv++Kpa e  S+G+   s ++ e el++ +++ ++ y +  l Ee+i gre++ a+ +g + +ev+++ eiv
  gi|386001700|ref|YP_005919999.1| 134 SLDFPVIIKPALEDASIGItfdSIAKDEVELRAKVSQVIEtYCQAALAEEYIGGREVNAALfIGPGGFEVLPISEIV 210
                                       589****************4444788999******9987538999***************8468999********** PP

                                       -SS.....SSS-HHHHH...C...TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEE CS
                   Dala_Dala_lig_C 106 vkk.....gfydyeaky...sd..dkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnE 171
                                        +      ++  +eak+   s   +++   +pa le+e +e+i++la++a +al+++G aRvDf + +e+ge+++ E
  gi|386001700|ref|YP_005919999.1| 211 FDLpdgtpKILGFEAKWieeSPlyQNTIPLCPAPLEPELRERIEDLAKRACSALGVEGYARVDFRIrEEDGEPFVIE 287
                                       98888899*********65533345777789***********************************8899******* PP

                                       EESS---STT.SHHHHHHHCTT--HHHHHHHH CS
                   Dala_Dala_lig_C 172 vNtlPGfTei.SlfpklakasGlefkkLvdql 202
                                       vN+ P +  + S f+++a+a+G+e+++L+ ++
  gi|386001700|ref|YP_005919999.1| 288 VNPNPCINPTgSGFARAAAAAGMEYPELILRI 319
                                       *******865499***************9876 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.1     4e+03      90     107 ..     297     312 ..     264     324 .. 0.78
   2 !   66.0   0.0   4.1e-21   5.2e-18       4     138 .]     358     485 ..     356     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.1
                    Acetyltransf_3  90 sfwgkGyateavralley 107
                                          g G+a+ a++a +ey
  gi|386001700|ref|YP_005919999.1| 297 T--GSGFARAAAAAGMEY 312
                                       3..889999999998888 PP

  == domain 2  score: 66.0 bits;  conditional E-value: 4.1e-21
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmrylpe..pltleeaeewlerawaeeseeegygwaivlkdtgv.iGsvglrdleee 77 
                                       +r++++eD++ lf++++d+e+++y+ +  +lt ++  + +      +s  ++  ++i++ ++   iG+++l+++ + 
  gi|386001700|ref|YP_005919999.1| 358 FRRVRAEDAPLLFRWFEDQELTKYMEPsmSLTIDQLVASIL-----CS--KDEDFVIFE-GD-LpIGFASLYERTPC 425
                                       799********************944324666666655555.....33..45569**74.44.55*******99998 PP

                    Acetyltransf_3  78 deeaelgymla.psfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +  +e++y+++ p+++g G++   v+a++e+ f++lgl+ ++a +  eN  Sir le +Gf+
  gi|386001700|ref|YP_005919999.1| 426 T--GEISYLIGdPDHRGVGLGNAIVEAIVEHGFSRLGLNSIYASATVENISSIRALEAAGFR 485
                                       7..9*******777***********************************************6 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.1   3.9e+03      44      55 ..      81      92 ..      46     116 .. 0.63
   2 !   41.7   0.0     9e-14   1.2e-10      34     117 .]     403     484 ..     363     484 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                                      EEEEEEEEEEET CS
                    Acetyltransf_1 44 liGfisllkipd 55
                                      ++Gfi ll ip+
  gi|386001700|ref|YP_005919999.1| 81 VAGFIELLGIPF 92
                                      555555555554 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 9e-14
                                       EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHH CS
                    Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveedndaai 109
                                       + +v+ e++ +iGf+sl+ +++    +++i  l  +p++rg GlG a +ea++e+ +++ g++ i++  ++ n  +i
  gi|386001700|ref|YP_005919999.1| 403 EDFVIFEGDLPIGFASLYERTP---CTGEISYLIGDPDHRGVGLGNAIVEAIVEHGFSRlGLNSIYASATVENISSI 476
                                       4566777788************...89****************************************8889****** PP

                                       HHHHHTTE CS
                    Acetyltransf_1 110 rlYeklGF 117
                                       r +e  GF
  gi|386001700|ref|YP_005919999.1| 477 RALEAAGF 484
                                       ***99*99 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   4.1e-13   5.2e-10       2     156 ..     104     290 ..     103     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.1e-13
                                       TSHHHHHHHHTTT.S---.......-EESS--SSSEEEEESS-------B--SS--TTE.................E CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP...tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..........l 65 
                                        dK  +   L+++g+++P      + ee+ + + ++++Kp+   ++ ++++    +++ +  ++v+          l
  gi|386001700|ref|YP_005919999.1| 104 RDKGLSKLVLEREGIPTPrfsIFRNGEEPFSLDFPVIIKPALEDASIGITFDSIAKDEVELRAKVSqvietycqaaL 180
                                       689999999*********6532333455556699*******99999999987766555444444445678999**** PP

                                       EEE---SEEEEEEEEE.SSSEEEEEEEEEEEET......................TEEEEEEES----HHHHHHHHH CS
                       ATP-grasp_3  66 vqefieGkplSvsllsdgekvlvlavnrqliekaeke..................fvyaGnvtpietelkeevvela 124
                                       + e+i G+++ + l      + vl +++ + +                       +    + +p e el+e++++la
  gi|386001700|ref|YP_005919999.1| 181 AEEYIGGREVNAALFIGPGGFEVLPISEIVFDLPDGTpkilgfeakwieesplyqNTIPLCPAPLEPELRERIEDLA 257
                                       **********999988899*************9777799************886655555667888889******** PP

                                       HHHHTTSTT--EEEEEEEEESS...SEEEEEEES CS
                       ATP-grasp_3 125 eevvekleglaGyvGvDlvlkd..eepyviEvNP 156
                                       ++++++l g+ Gy+ vD+ +++  +ep viEvNP
  gi|386001700|ref|YP_005919999.1| 258 KRACSAL-GVEGYARVDFRIREedGEPFVIEVNP 290
                                       *******.**********9887679********* PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.2e-12   2.9e-09       4     142 ..     364     489 ..     362     492 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.2e-12
                                       GGHHHHHHHCTSCCCHHHH-----HHHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-E CS
                    Acetyltransf_8   4 aDlellhrWmnrprvaewweeagtleevrellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdr 80 
                                       +D++ll rW+++ ++ +++e + +l+            ++  + i++ ++e++  fe   +     a  y+  p + 
  gi|386001700|ref|YP_005919999.1| 364 EDAPLLFRWFEDQELTKYMEPSMSLT-----------IDQLVASILCSKDEDFVIFEGDLPIGF--ASLYERTPCTG 427
                                       78899999999999988888888632...........234456677777777777777666666..67778889999 PP

                                       EEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEE CS
                    Acetyltransf_8  81 GiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekeke 142
                                        i +lig++++rg gl++a+++a+v+  f++ + +++ +   v+N  +ir+le+aGf++ ++
  gi|386001700|ref|YP_005919999.1| 428 EISYLIGDPDHRGVGLGNAIVEAIVEHGFSRLGLNSIYASATVENISSIRALEAAGFRRIGT 489
                                       **********************************************************9876 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.8e-08   3.6e-05       2     151 ..     136     291 ..     135     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.8e-08
                       ATP-grasp_4   2 slPvviKPsvgffSlGVyk...inneeewkaavaaieeeleqakeeykeevveeesflvEeyie..GeEf..avday 71 
                                       ++Pv+iKP+ + +S+G+++   +++e e++a v+++ e    +++  +ee++ ++++    +i   G+E+    ++ 
  gi|386001700|ref|YP_005919999.1| 136 DFPVIIKPALEDASIGITFdsiAKDEVELRAKVSQVIETY--CQAALAEEYIGGREVNAALFIGpgGFEVlpISEIV 210
                                       69***************86222566667777776666553..44455666666666655556632255542223667 PP

                       ATP-grasp_4  72 fd.eeGepvilnilkkefaseedvsdrlyvtsakvieetlealeellkevnallglknfpvHiElrvse.dgkiipi 146
                                       fd  +G+p il +  k   +++  ++++ + +a +  e  e++e+l k++ ++lg++ + + + +r++e dg+ ++i
  gi|386001700|ref|YP_005919999.1| 211 FDlPDGTPKILGFEAKWIEESPLYQNTIPLCPAPLEPELRERIEDLAKRACSALGVE-GYARVDFRIREeDGEPFVI 286
                                       77469********9999999999********************************97.5568999987526799*** PP

                       ATP-grasp_4 147 Evnpl 151
                                       Evnp 
  gi|386001700|ref|YP_005919999.1| 287 EVNPN 291
                                       ***96 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.6e-08   2.1e-05       2     147 ..     359     497 ..     358     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                    Acetyltransf_4   2 raateeDakeilaiyaeyvvntaitfeyevssve.efekflealdsekeyvflvaesdrivGyaylgqfkkrakdwk 77 
                                       r ++ eDa  + ++ +++++    t +  ++s+   ++++ +++   k   f ++e d  +G a l +  +      
  gi|386001700|ref|YP_005919999.1| 359 RRVRAEDAPLLFRWFEDQEL----TKY-MEPSMSlTIDQLVASILCSKDEDFVIFEGDLPIGFASLYERTP----CT 426
                                       67899999999999998555....444.455555145577777777788899**************98777....89 PP

                    Acetyltransf_4  78 aelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkn 147
                                       +e+s+++ + d +  glg ++++a+++   ++ ++++++a+  ++n++si  ++a GF+  g  +  +  +
  gi|386001700|ref|YP_005919999.1| 427 GEISYLIGDPDHRGVGLGNAIVEAIVEHGfSRLGLNSIYASATVENISSIRALEAAGFRRIGTRRASSLLG 497
                                       9******9999999999*********6555*****************************999887666555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.065        83      37      72 ..     135     173 ..     128     189 .. 0.72
   2 !   17.6   0.0   1.7e-06    0.0021     122     178 ..     235     290 ..     228     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.065
                                       H-SSEEEEETT...CCTTTTEEEESSHHHHHHHHHHHHH CS
                       CPSase_L_D2  37 igyPviikaaf...glGGkGmrvarneeelaelvkkala 72 
                                       + +Pviik+a    ++G +   +a++e el++ v++ ++
  gi|386001700|ref|YP_005919999.1| 135 LDFPVIIKPALedaSIGITFDSIAKDEVELRAKVSQVIE 173
                                       679*******72214455556788888888887777655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.7e-06
                                       CCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEES CS
                       CPSase_L_D2 122 qkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNt 178
                                       q+ i   P++ L++e r++++  a ++++++gv+g + v+f + ++++e +viEvN+
  gi|386001700|ref|YP_005919999.1| 235 QNTIPLCPAP-LEPELRERIEDLAKRACSALGVEGYARVDFRIREEDGEPFVIEVNP 290
                                       6677778887.89*******************************************8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.4e-07   0.00056      18      80 ..     422     487 ..     407     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                                       E-TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  18 rkdg.gelgalqvlpehrrrGlgsrlvkalakeiae.rg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       r +  ge++ l  +p+hr+ Glg  +v+a+ ++     g + + + +  +N  sir +e+ Gf+ i
  gi|386001700|ref|YP_005919999.1| 422 RTPCtGEISYLIGDPDHRGVGLGNAIVEAIVEHGFSrLGlNSIYASATVENISSIRALEAAGFRRI 487
                                       555569***********************99875553663567788999**************998 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     3e-06    0.0039       6      53 ..     405     456 ..     400     486 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                                       EEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH..TTSEE CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea..aekgi 53 
                                       fV+ +++ ++Gf++l+++    +ei +l  dp++rg G+G a++ea  + +g+
  gi|386001700|ref|YP_005919999.1| 405 FVIFEGDLPIGFASLYERTpctGEISYLIGDPDHRGVGLGNAIVEAivE-HGF 456
                                       77899999*********9999888888******************8431.442 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.9e-06    0.0037      34     111 ..     405     489 ..     372     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                   Acetyltransf_10  34 lvaeeggkivGvielrdgs....hisllfVdpeyrgqGigkaLleaveee.aekdgikleltvnasp...yavpfYe 102
                                       +v +eg+ ++G+++l+++     +is l+ dp++rg G+g+a++ea+ e+ +++ g++ ++ + a+      ++  e
  gi|386001700|ref|YP_005919999.1| 405 FVIFEGDLPIGFASLYERTpctgEISYLIGDPDHRGVGLGNAIVEAIVEHgFSRLGLN-SIYASATVeniSSIRALE 480
                                       6788999******9955555999**************************988888888.555555441156677778 PP

                   Acetyltransf_10 103 klGFkavge 111
                                         GF+++g 
  gi|386001700|ref|YP_005919999.1| 481 AAGFRRIGT 489
                                       888887765 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   9.3e-05      0.12       1      85 [.     103     188 ..     103     196 .. 0.76
   2 ?    3.1   0.0      0.05        64     127     169 ..     249     294 ..     245     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEE...EE-SHHHHH....HHHH CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvv...lakkeqklk....qvle 70 
                                       ardK +s  +L +++i++p++ + r+ e+       + l fPv++K       i++    +ak+e +l+    qv+e
  gi|386001700|ref|YP_005919999.1| 103 ARDKGLSKLVLEREGIPTPRFSIFRNGEE------PFSLDFPVIIKPALEDASIGITfdsIAKDEVELRakvsQVIE 173
                                       79***********************9985......56789******8866555555322379998766522227777 PP

                                       HGGG--EEEEE--SS CS
                              RimK  71 alkeailvqeyieea 85 
                                       +  +a l  eyi   
  gi|386001700|ref|YP_005919999.1| 174 TYCQAALAEEYIGGR 188
                                       778888999999655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.05
                                       --HHHHHHHHHHHHHCT-S.EEEEE..EEEETTEEEEEEEESS--S CS
                              RimK 127 lseeekelAikaakamelv.vaGvD..llrakrgllvlEvnsspgl 169
                                       l e  ++lA +a  a+++  +a vD  + +++ +++v+Evn +p +
  gi|386001700|ref|YP_005919999.1| 249 LRERIEDLAKRACSALGVEgYARVDfrIREEDGEPFVIEVNPNPCI 294
                                       566777888888888877548999*8555666779*******9976 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.35      46     106 ..     250     318 ..     246     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededg..pkLLEiNpRa......sGGlgysalaGvnlpylalk 106
                                       +e++ +la+r   ++g++g+  v +r +e+   p ++E+Np +      sG  + +a+aG++ p+l l+
  gi|386001700|ref|YP_005919999.1| 250 RERIEDLAKRACSALGVEGYARVDFRIREEDgePFVIEVNPNPcinptgSGFARAAAAAGMEYPELILR 318
                                       5678899*************9998886654336******997644444456667777889999988876 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.31   3.9e+02      15      78 ..      99     154 ..      95     185 .. 0.68
   2 ?    8.2   0.0     0.001       1.3     228     270 ..     253     296 ..     247     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
                       ATPgrasp_ST  15 efplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilv 78 
                                       ++++  dK + k +++r+g+++p+ + ++++++     e f  ++ + v+iKpa   +  Gi++
  gi|386001700|ref|YP_005919999.1|  99 ALEVARDKGLSKLVLEREGIPTPR-FSIFRNGE-----EPFSLDF-P-VIIKPALEDASIGITF 154
                                       567778999999999999999999.77776664.....3455555.4.6666666666556555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                       ATPgrasp_ST 228 vlelaakaaeklpglgylGwDivldee.kgplllElNarpglai 270
                                       + +la++a   l   gy  +D+ + ee ++p ++E+N +p++++
  gi|386001700|ref|YP_005919999.1| 253 IEDLAKRACSALGVEGYARVDFRIREEdGEPFVIEVNPNPCINP 296
                                       5679999999888889********876267***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3793.31
//
Query:       gi|386001701|ref|YP_005920000.1|  [L=335]
Description: D-alanine--D-alanine ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-30  105.1   0.0    4.5e-30  104.7   0.0    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0011   19.1   0.0     0.0084   16.2   0.0    2.0  1  ATP-grasp_3      ATP-grasp domain
     0.0059   16.2   0.0      0.015   14.9   0.0    1.7  2  ATP-grasp_4      ATP-grasp domain
      0.007   16.2   0.0      0.012   15.4   0.0    1.4  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
      0.077   13.5   0.0       0.12   12.8   0.0    1.3  1  Dala_Dala_lig_N  D-ala D-ala ligase N-terminus
        0.1   12.1   0.0       0.27   10.8   0.0    1.7  2  ATP-grasp        ATP-grasp domain
       0.13   12.0   0.0        4.2    7.1   0.0    2.5  3  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T


Domain annotation for each model (and alignments):
>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   1.7e-33   4.5e-30       6     202 ..     119     323 ..     114     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 1.7e-33
                                       T--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEE...ESSGGGHHHHH.HHHHTT-SCEEEE CS
                   Dala_Dala_lig_C   6 GlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvsk...veseeelkeai.eeafkydekvlvE 78 
                                       G++++ ++ l++++  +            l +p+f Kp  eGSS G+++   v+ +eel++   e  +ky + vlvE
  gi|386001701|ref|YP_005920000.1| 119 GIRTPRFQLLRRADELR----------PDLDFPLFLKPNGEGSSRGITArslVREVEELEAVAgEMMAKYRQPVLVE 185
                                       66666666666555444..........459*****************75455999****99772556799******* PP

                                       E--ESEEEEEEEEETSSCEEEEEEEEE-SS......SSS-HHHHH....C..TT-EEESS----HHHHHHHHHHHHH CS
                   Dala_Dala_lig_C  79 eaiegreievavlgneklevsevgeivvkk......gfydyeaky....sd.dkaqlevpaklekeveekiqelalk 144
                                       e++ gre++v++lg + +ev++v+e+  ++       f  ye k+     +    + ++pa+l+++ +++i+ +a +
  gi|386001701|ref|YP_005920000.1| 186 EYLTGREFTVGLLG-NPPEVLPVVEVGFEGlpagapRFDCYEVKWiydsLEaGFDTTVCPADLDEDLRSRIERAATE 261
                                       **************.789********999999999966667777753442224456799****************** PP

                                       HHHHTT--SEEEEEEEEETTTEEEEEEEESS---....STTSHHHHHHHCTT--HHHHHHHH CS
                   Dala_Dala_lig_C 145 aykaldlrGlaRvDfflteegeivlnEvNtlPGf....TeiSlfpklakasGlefkkLvdql 202
                                        ++al++r+l+R+D+ l+++ge+ + +vN lPG+     e S+fpk+a a+G +++ L+ ++
  gi|386001701|ref|YP_005920000.1| 262 SFEALEVRDLCRLDLRLDADGEPSVFDVNALPGLipdpAENSRFPKAAYAAGYSYEGLIGKI 323
                                       *********************************95555689*****************9887 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.3e-06    0.0084       3     155 ..     107     290 ..     105     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                                       SHHHHHHHHTTT.S---.......-EESS--.SSSEEEEESS-------B...--SS--TTE..............E CS
                       ATP-grasp_3   3 dKlktykkLkeagvkvP..tkl.eaeeleee.ekklvvKprdGaggesvr...vveekeeaeaaieeve.......l 65 
                                       dK++t + L ++g+++P  + l +a+el++  + +l +Kp   + + +++   +v+e ee+ea   e+        l
  gi|386001701|ref|YP_005920000.1| 107 DKRRTKEVLLANGIRTPrfQLLrRADELRPDlDFPLFLKPNGEGSSRGITarsLVREVEELEAVAGEMMakyrqpvL 183
                                       9****************7644313444444467899****877777666522256777777766655558999**** PP

                                       EEE---SEEEEEEEEE.SSSEEEEE.EEEEEEET..................TEEEEEEES----H..HHHHHHHHH CS
                       ATP-grasp_3  66 vqefieGkplSvsllsdgekvlvla.vnrqliekaeke..............fvyaGnvtpietel..keevvelae 125
                                       v e++ G++++v ll++  +vl+++ v  + +  +  +                +   v p++ ++  +++++++a 
  gi|386001701|ref|YP_005920000.1| 184 VEEYLTGREFTVGLLGNPPEVLPVVeVGFEGLPAGAPRfdcyevkwiydsleAGFDTTVCPADLDEdlRSRIERAAT 260
                                       ****************9988887652444444444444777777777777774444444444443333778888888 PP

                                       HHHTTSTT--EEEEEEEEESS..SEEEEEEE CS
                       ATP-grasp_3 126 evvekleglaGyvGvDlvlkd.eepyviEvN 155
                                       e  e+l +++ +   Dl l   +ep v +vN
  gi|386001701|ref|YP_005920000.1| 261 ESFEAL-EVRDLCRLDLRLDAdGEPSVFDVN 290
                                       888888.788888888766544778888877 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     6e-06     0.015       2      70 ..     139     197 ..     138     203 .. 0.76
   2 ?   -3.1   0.0         2   5.2e+03     105     149 ..     247     290 ..     242     293 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                       ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavda 70 
                                       ++P+ +KP+ + +S+G+++ +  +e ++ ++a+  e   + ++y      ++ +lvEey+ G Ef v +
  gi|386001701|ref|YP_005920000.1| 139 DFPLFLKPNGEGSSRGITARSLVREVEE-LEAVAGE---MMAKY------RQPVLVEEYLTGREFTVGL 197
                                       6899*************98777777666.4444444...33444......46789**********9965 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                       ATP-grasp_4 105 vieetlealeellkevnallglknfpvHiElrvsedgkiipiEvn 149
                                       + e+  +++e++ +e  ++l++++  +   lr+++dg+  + +vn
  gi|386001701|ref|YP_005920000.1| 247 LDEDLRSRIERAATESFEALEVRDL-CRLDLRLDADGEPSVFDVN 290
                                       5555566666666666666666664.3456666666655555555 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.8e-06     0.012       2     100 ..     107     199 ..     106     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.8e-06
                                       BHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE...SSHHHHHHHHHHHCTS-T CS
                            GARS_A   2 sKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgviva...kseeealkavkeilekkk 75 
                                       +K+ +k++l + gi+t++++ +  ++e++    +++++   +K++g  + +g++     +++ee  +++ e++    
  gi|386001701|ref|YP_005920000.1| 107 DKRRTKEVLLANGIRTPRFQLLRRADELR---PDLDFPL-FLKPNGEGSSRGITARslvREVEELEAVAGEMMA--- 176
                                       5778999**********999987766666...5778998.99**********9865332777777777778886... PP

                                       TCCCCSSEEEEE---SEEEEEEEEE CS
                            GARS_A  76 fGeagekvviEelleGeEvsllalv 100
                                         +  + v++Ee+l+G E+++  l 
  gi|386001701|ref|YP_005920000.1| 177 --KYRQPVLVEEYLTGREFTVGLLG 199
                                       ..55699************997665 PP

>> Dala_Dala_lig_N  D-ala D-ala ligase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.8e-05      0.12      67     103 .]      59      97 ..      15      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-05
                                       CTCE--SEEEEE-TTTTTT..SSHHHHHHHHTT--BSS- CS
                   Dala_Dala_lig_N  67 ekkaeldvvfpvlhGkngE..DGtlqgllellgipyvGs 103
                                           ++d++f++  G  gE  + ++ ++le+lgipy Gs
  gi|386001701|ref|YP_005920000.1|  59 LRRGDFDFAFNIAEGIRGEarEAQIPAMLEMLGIPYSGS 97 
                                       4566899***********95557888***********97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.27       4      72 ..     118     188 ..     115     195 .. 0.80
   2 ?   -3.5   0.0       2.5   6.5e+03     108     135 ..     241     268 ..     238     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                       TT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTT...EEEECTCCGHHCHHHHC...GTTCEEEEE-- CS
                         ATP-grasp   4 lglpvprflaveskeeleeaaeelglpvvvKarrlgydGkG...qsvvrseedleqaleal...keekvivEefv 72 
                                       +g+++prf+++++++el+    +l++p+ +K + +  + +G    s+vr+ e+le ++ ++    +++v+vEe+ 
  gi|386001701|ref|YP_005920000.1| 118 NGIRTPRFQLLRRADELRP---DLDFPLFLK-PNGEGSSRGitaRSLVREVEELEAVAGEMmakYRQPVLVEEYL 188
                                       799*********9977765...6********.5554455773335799******99998888878899****986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
                                       EEECEE-SCHHHHHHHHHHHHHHHHHTS CS
                         ATP-grasp 108 svapaevsekaqkkaeeiakkiveeLgg 135
                                        v pa+++e+   ++e+ a +  e+L++
  gi|386001701|ref|YP_005920000.1| 241 TVCPADLDEDLRSRIERAATESFEALEV 268
                                       6788889999888888888888888776 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.9   4.8e+03      41      82 ..      47      89 ..      44     103 .. 0.70
   2 ?    7.1   0.0    0.0016       4.2       3      28 ..     180     205 ..     178     209 .. 0.82
   3 ?    1.8   0.0     0.073   1.9e+02      49      84 ..     255     291 ..     249     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.9
                      ATPgrasp_Ter 41 qelekdeelielaerlaeefgldglvnvQvrededg.pkLLEi 82
                                      + +e+dee+ e  +r    f+++   ++    +e++ p++LE+
  gi|386001701|ref|YP_005920000.1| 47 EVVEADEEAYERLRRGDFDFAFNIAEGIRGEAREAQiPAMLEM 89
                                      5667777777777777777777777777777777777888886 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0016
                      ATPgrasp_Ter   3 pallvmeyLegpEySvDvlaekgevl 28 
                                       +++lv eyL g E++v  l +  evl
  gi|386001701|ref|YP_005920000.1| 180 QPVLVEEYLTGREFTVGLLGNPPEVL 205
                                       689*************9988766665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.073
                      ATPgrasp_Ter  49 lielaerlaeefgldglvnvQvrededg.pkLLEiNp 84 
                                       +  +a++  e++++  l  + +r d+dg p + ++N+
  gi|386001701|ref|YP_005920000.1| 255 IERAATESFEALEVRDLCRLDLRLDADGePSVFDVNA 291
                                       56789999****************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2524.97
//
Query:       gi|386001702|ref|YP_005920001.1|  [L=362]
Description: L-lysine 2,3-aminomutase [Methanosaeta harundinacea 6Ac]
Scores for 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-15   55.5   0.0    2.2e-14   54.2   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
    1.6e-14   54.1   0.1    2.6e-14   53.5   0.1    1.3  1  LAM_C        Lysine-2,3-aminomutase
     0.0003   21.1   0.0    0.00057   20.2   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    0.00047   20.3   0.0     0.0012   18.9   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   4.9e-18   2.2e-14       3     159 ..     114     261 ..     112     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 4.9e-18
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlakla...v 75 
                                       v+  C++ C+fC+r++   + gr++  ++++i + +++++ +   v+ v+l+gg+pll+++ + ++  +  +    v
  gi|386001702|ref|YP_005920001.1| 114 VSSKCAMYCRFCTRKR---SVGRVEQTPMQQIFQGIDYIRgHPE-VRDVLLSGGDPLLRSNRELDIILRELRSiphV 186
                                       5778***********8...7*******************95555.*************9877666655555557799 PP

                                       CTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                       + iri   ++ ++p+   ++ ++ l+++++ +++l+ e++ +       n+     +  +al++l++agi+   + +
  gi|386001702|ref|YP_005920001.1| 187 EIIRIGSRVPSVMPErvtPRLVKVLKKYHPLYMNLHFEHPREI------NP-----DSERALKLLADAGIP-LGSQT 251
                                       999999999999999***************************7......44.....5667799999*****.9**** PP

                                       EEBTTTSHHH CS
                                       xxxxxxxxxx RF
                       Radical_SAM 150 vglpGendee 159
                                       v+l+G nd+ 
  gi|386001702|ref|YP_005920001.1| 252 VLLRGINDDP 261
                                       *****99985 PP

>> LAM_C  Lysine-2,3-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1   5.8e-18   2.6e-14       2      57 ..     305     360 ..     304     362 .] 0.91

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 5.8e-18
                             LAM_C   2 eglrGhtsGyavPtfvvdaPgGGGkialq.PnyllsqsedkvvlrnfeGvitsypeP 57 
                                        +l+GhtsG++vP  ++d+Pg GGki++  P+yll+  e+k v+ n+ G +  yp+P
  gi|386001702|ref|YP_005920001.1| 305 CHLQGHTSGLCVPHLIIDSPG-GGKIPILpPDYLLATDEEKAVISNYKGEVYEYPNP 360
                                       689*****************6.6899975279***********************99 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.3e-07   0.00057      10      73 ..     112     174 ..     103     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                           Fer4_12  10 lf.vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlk.kesiegltllGGEPllpenaeall 73 
                                       l   s C + C++C  k  +s+ + ++++ + + + i+ +  +++++++ l+GG+Pll++n+e l 
  gi|386001702|ref|YP_005920001.1| 112 LMvSSKCAMYCRFCTRK--RSVGRVEQTPMQQIFQGIDYIRgHPEVRDVLLSGGDPLLRSNRE-LD 174
                                       442689********955..556666666666777777877746999************77765.44 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.7e-07    0.0012       4      76 ..     114     182 ..     111     195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.7e-07
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlke 76 
                                         s+C + C++C +k +     ++p  +++  q ++    +  +++ + l+GG+PL+  +++el+ ++++l+ 
  gi|386001702|ref|YP_005920001.1| 114 VSSKCAMYCRFCTRKRSVGRVEQTPM-QQIF-QGIDYIRGHPEVRD-VLLSGGDPLLR-SNRELDIILRELRS 182
                                       469**********9995443333332.2333.45555555555556.*********65.66777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 2824.96
//
Query:       gi|386001703|ref|YP_005920002.1|  [L=290]
Description: Ion transport protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-18   66.0  14.8    3.6e-18   65.7  14.8    1.0  1  Ion_trans       Ion transport protein
    6.9e-18   64.4   4.1    6.9e-18   64.4   4.1    2.9  3  Ion_trans_2     Ion channel
  ------ inclusion threshold ------
      0.034   14.1   0.5      0.062   13.2   0.5    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.057   13.6   3.7      0.085   13.0   1.6    2.0  2  Ribosomal_L37e  Ribosomal protein L37e
      0.077   13.4   1.6       0.13   12.6   1.6    1.4  1  zf-RING_2       Ring finger domain
      0.096   12.4   1.0        1.2    8.9   1.3    2.1  2  zinc_ribbon_2   zinc-ribbon domain
       0.13   12.3   0.8       0.24   11.5   0.8    1.3  1  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7  14.8   1.4e-21   3.6e-18       6     226 ..      34     232 ..      30     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.4e-21
                                       HHHHHHHHHHHHHHHCCCSSSSHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHHHHHH CS
                         Ion_trans   6 lfilllillncvflaletyfpedelektileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvvlpsl 82 
                                       + i++l ll c+++ l+ty  ++ ++ ++l  le++++++f+le l +++a++   ++r ++ +  ++D++++lp+l
  gi|386001703|ref|YP_005920002.1|  34 VSIIFLNLLVCAIFVLDTYEISEATR-SFLWRLEVAVVGLFVLEYLARLYAAPD--RRRQISGIYSVIDLVAILPTL 107
                                       56778888888888889999998888.***************************..9******************** PP

                                       HHHHHHH....HHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS CS
                         Ion_trans  83 lslvlse....esllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgk 155
                                       + +vl       ++  ++ +r+f+vlr++++++ +         ++ +  +l++++ l+  +l++f++ +  +f   
  gi|386001703|ref|YP_005920002.1| 108 FQAVLPLfgltLNIAFVKTIRVFKVLRIFRFLRFIAAPHL---FFGSISLELVKLVRLVTTILILFFIGSGIFF--- 178
                                       *995444544446777888888888888888888888677...5666677777777777777777776666666... PP

                                       CCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 156 lreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflll 226
                                                  e+p   n+ ++nf++a++++++ +tt+g+gd+++ t  ++      ++ i++il++++l+
  gi|386001703|ref|YP_005920002.1| 179 ------H---VESP--ANPGVTNFGDAFYFTVVALTTVGFGDVTPSTDAGR------LVTILMILSGIILI 232
                                       ......2...2233..3446668****************************......***********997 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.22   5.7e+02      48      72 ..      26      50 ..      23      57 .. 0.81
   2 ?   -0.5   0.2      0.49   1.3e+03      55      74 ..     109     128 ..      99     131 .. 0.77
   3 !   64.4   4.1   2.7e-21   6.9e-18       2      74 ..     166     240 ..     165     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                                      -----HHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 48 tdagrlftivyillGlalfalflav 72
                                      t++g+ + + +i+l l+++a+f+ +
  gi|386001703|ref|YP_005920002.1| 26 TPLGKGIDVSIIFLNLLVCAIFVLD 50
                                      6678888899999999999999876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  55 tivyillGlalfalflavlg 74 
                                         v+ l+Gl+l ++f++++ 
  gi|386001703|ref|YP_005920002.1| 109 QAVLPLFGLTLNIAFVKTIR 128
                                       56777899999999998875 PP

  == domain 3  score: 64.4 bits;  conditional E-value: 2.7e-21
                                       HHHHTCHHHHHHHHT......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   2 vlllvlifgaviysl..eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlg 74 
                                       +l+l++i + +++++   ++    +f da+Yf++v ltT+G+Gd++p tdagrl+ti+ il G++l+ +  ++++
  gi|386001703|ref|YP_005920002.1| 166 ILILFFIGSGIFFHVesPANPGVTNFGDAFYFTVVALTTVGFGDVTPSTDAGRLVTILMILSGIILIPWEASKIV 240
                                       789999999999999552334489******************************************998776665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.4e-05     0.062      25      56 ..     248     277 ..     241     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                    OrfB_Zn_ribbon  25 ayTSktCseCgsknkealsgrtfkCpnCgfe.a 56 
                                       + TS+ C+ Cg +  e    +  +C++Cg++ +
  gi|386001703|ref|YP_005920002.1| 248 RKTSTLCPLCGLEEHE---VDASYCRRCGHRlY 277
                                       56*********99999...9999******9855 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.6     0.001       2.7      13      40 ..     248     275 ..     246     275 .. 0.92
   2 ?   13.0   1.6   3.3e-05     0.085      12      33 ..     262     283 ..     255     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                    Ribosomal_L37e  13 kktHilCrrCgkrsyhvqkktCascGyp 40 
                                       +kt +lC  Cg +   v  ++C  cG++
  gi|386001703|ref|YP_005920002.1| 248 RKTSTLCPLCGLEEHEVDASYCRRCGHR 275
                                       6899**********************85 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.3e-05
                    Ribosomal_L37e  12 kkktHilCrrCgkrsyhvqkkt 33 
                                       ++     CrrCg+r yh q ++
  gi|386001703|ref|YP_005920002.1| 262 HEVDASYCRRCGHRLYHQQISE 283
                                       5555568**********99776 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6   5.2e-05      0.13       3      28 ..     254     280 ..     252     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                         zf-RING_2   3 CpIC.leelssadsvlllpCgHv.fhre 28 
                                       Cp+C lee + + s+++  CgH  +h++
  gi|386001703|ref|YP_005920002.1| 254 CPLCgLEEHEVDASYCRR-CGHRlYHQQ 280
                                       ***********9999999.***989985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.049   1.3e+02      12      20 ..     250     258 ..     248     260 .. 0.80
   2 ?    8.9   1.3   0.00048       1.2       2      23 .]     254     276 ..     253     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.049
                     zinc_ribbon_2  12 nakFCpyCG 20 
                                       +++ Cp CG
  gi|386001703|ref|YP_005920002.1| 250 TSTLCPLCG 258
                                       678899998 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00048
                     zinc_ribbon_2   2 CpnCG.aelqdnakFCpyCGtpl 23 
                                       Cp CG +e++ +a +C +CG+ l
  gi|386001703|ref|YP_005920002.1| 254 CPLCGlEEHEVDASYCRRCGHRL 276
                                       777774566779********976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   9.3e-05      0.24       1      23 [.     254     277 ..     247     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                               DZR   1 CpqCgee.lppdarfCseCgtklk 23 
                                       Cp Cg e ++ da +C +Cg++l 
  gi|386001703|ref|YP_005920002.1| 254 CPLCGLEeHEVDASYCRRCGHRLY 277
                                       899986547788999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2231.07
//
Query:       gi|386001704|ref|YP_005920003.1|  [L=526]
Description: Cation transport protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-50  170.6  24.4    4.5e-30  104.6   7.3    3.1  2  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   9.1   1.3e-22   2.3e-18      31     283 ..      64     330 ..      38     332 .. 0.92
   2 !  104.6   7.3   2.5e-34   4.5e-30     321     497 ..     347     521 ..     338     526 .] 0.94

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.3e-22
                              TrkH  31 alkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveeslprsgltlraqlq....... 100
                                         kd+f iv   ++   v g+l+ +     ++f+d+lfe++sg+tttg++  ++++  ++++ +  a          
  gi|386001704|ref|YP_005920003.1|  64 GHKDAFLIVTFGWLLAAVFGALPFV--LMGVGFIDSLFESMSGFTTTGATILTEYDANGYWIINSTASSGclasgiv 138
                                       5677888888888888888888865..567899****************************998887777999**** PP

                              TrkH 101 ......................................qiGglgvvvlaylslptlgrgsaflylseaqkeelggke 139
                                                                              +Gglg++ l  +++p lg  + +ly   +   ++ +  
  gi|386001704|ref|YP_005920003.1| 139 tglshqlaggpttnaaliggdiadptyygllfwrsftqLLGGLGIILLFIAIFPHLGVAGRQLYYVDS-ARLKKETL 214
                                       *************************************999*****************99999999988.6799999* PP

                              TrkH 140 lrslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnkn 216
                                       ++++++++ki + +y+++  l  ++l         y +++      p+++ + +++ +++++G+s  ++ ++ + + 
  gi|386001704|ref|YP_005920003.1| 215 TPRVKDTAKIFWGIYLLMVGLETFML---------YLAGM------PIYDSILTAFATLSTAGYSPQASGIVAYSS- 275
                                       ************99999999999999.........9****......******************************. PP

                              TrkH 217 ivillvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwlll 283
                                         i++++++f+ilG++++ +++ ++ +  +++            +++d ++r+ +L++as++v++ll
  gi|386001704|ref|YP_005920003.1| 276 LPIEAIVVFFMILGATSYNLHYILLYKGSISV------------YVRDSEFRFYLLIMASAIVMILL 330
                                       *************************9999988............679******************97 PP

  == domain 2  score: 104.6 bits;  conditional E-value: 2.5e-34
                              TrkH 321 Fqsvstrta.GFs.vvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksid 395
                                       Fq+v+t t+ GF+  +++  ++ a  +++v  m igg+ gSt ggI+  +++ + + g++e+ +  +p+av++++i 
  gi|386001704|ref|YP_005920003.1| 347 FQVVTTMTTtGFTnNFEYNTWPVASSMIIVALMLIGGCVGSTGGGIKVARILLILKYGRRELIELIHPRAVKPIKIT 423
                                       9***999999**8469************************************************************* PP

                              TrkH 396 gkhlerqllvdlwslflvlliililegl..klsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttiskl 470
                                       g+++++++l+++ +++l++l+++++ +l  +l++ ++p f+++    +++ ++g vG++lG + a  +  +t ++k+
  gi|386001704|ref|YP_005920003.1| 424 GATVQEEVLRSILFFALLYLLVFFVASLamALTEAGNPVFDLISTVSAIATCMGAVGPGLG-AVAYDFSGVTAAGKM 499
                                       **********************99998622689999*************************.88889999******* PP

                              TrkH 471 vlialmirGrlrglpvlldraillpsd 497
                                       + ++ m++Gr+++lpv+++++     +
  gi|386001704|ref|YP_005920003.1| 500 IGVICMFVGRMEILPVMVLFM-----P 521
                                       *******************98.....4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 3436.30
//
Query:       gi|386001705|ref|YP_005920004.1|  [L=426]
Description: Amino acid/polyamine/organocation transporter, APC superfamily [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-41  142.6  39.9    1.9e-41  142.3  39.9    1.0  1  AA_permease_2   Amino acid permease
    3.1e-37  128.3  39.1    4.1e-37  127.9  39.1    1.1  1  AA_permease     Amino acid permease
    2.5e-09   36.4  16.7    2.5e-09   36.4  16.7    2.2  2  Spore_permease  Spore germination protein
     0.0024   17.9   0.7     0.0024   17.9   0.7    5.2  5  AA_permease_C   C-terminus of AA_permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3  39.9   4.3e-45   1.9e-41       1     399 [.      11     396 ..      11     418 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 4.3e-45
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+l+ +++  +g+++g+gi++    +a+ +g ++++ + +a+li  +  +l yaElss +pr   +y yt +afgk+
  gi|386001705|ref|YP_005920004.1|  11 LGLFEVTLSGVGIILGAGIYALIgkAAELAGNSVWIAFALAALIA-IFTGLSYAELSSIFPRASAEYEYTDRAFGKR 86 
                                       7899999*************997877777***************9.7999*************************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       +af+++w+  f+ v+++++++  +++y+  ++g         ++  a+++++l+ ++ + g+k sa+++ + +++ +
  gi|386001705|ref|YP_005920004.1|  87 LAFVVGWLIIFSGVIGASTVALGFGGYFEALTGAP-------ILPSAVLLILLLSVVLLWGVKLSAWFAIVFTLIET 156
                                       *****************999999999998887733.......444567778888888889***************** PP

                     AA_permease_2 153 llpliiliilglitvdg.ggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifig 226
                                          l+i+i +g+  ++  ++           +p+g +gv+ + + +++++ Gfe  +  see  ++++++p+a++ +
  gi|386001705|ref|YP_005920004.1| 157 A-GLLIVIYVGIPHLGSvDYL---------QMPGGLTGVFEAAALIFFAYMGFEEMVKLSEEtrDPERNMPLALIAA 223
                                       6.5566665666665331233.........399*****************************77777********** PP

                     AA_permease_2 227 llivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvleala 303
                                       l+i+++ly+lv+++++ vvp++ +a +s    +a++ +ea+g + +++++++++ ++ +  ++  ++++sr+++ +a
  gi|386001705|ref|YP_005920004.1| 224 LAITIILYILVALSVVSVVPWEVLAASSA--PFAEVAAEALG-PEAFVVISAIALFATANTVLLMLLAASRIAYGMA 297
                                       ************************98776..47999999988.999999999999999999999************* PP

                     AA_permease_2 304 rdgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl 379
                                       +   lP+++ +v+  + +p++ai+ + ++s+    +f++  s  + f++s+  + l++ ++++  +++ lr++ p++
  gi|386001705|ref|YP_005920004.1| 298 EAASLPTVLGRVHpGRRTPMAAIVAVTLLSI----AFAF--SGEIAFVASANDFILFLTFIVINGSLIALRRRDPDR 368
                                       *************88**************93....3455..468********************************* PP

                     AA_permease_2 380 krpgk........ilvaiigalfllfll 399
                                       +rp +        +++  +g+l++lfl+
  gi|386001705|ref|YP_005920004.1| 369 PRPFRvplavgwvPVLPVLGILTCLFLI 396
                                       **77745555543345555577777776 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9  39.1   9.1e-41   4.1e-37       2     431 ..      16     399 ..      15     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 9.1e-41
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       v++  +g + G+g++  +g+++  aG  ++++a++la ++ ++++ls +e+++++p++++ y y  r  g++l+fv+
  gi|386001705|ref|YP_005920004.1|  16 VTLSGVGIILGAGIYALIGKAAELAGN-SVWIAFALAALIAIFTGLSYAELSSIFPRASAEYEYTDRAFGKRLAFVV 91 
                                       5667789999************99999.************************************************* PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafii 155
                                       G++  fs+++++     + + ++   e +t +p +   +++++++l+++ l gvk+++ + ++++li    ++++i 
  gi|386001705|ref|YP_005920004.1|  92 GWLIIFSGVIGASTVALGFGGYF---EALTGAP-ILPSAVLLILLLSVVLLWGVKLSAWFAIVFTLIETAGLLIVIY 164
                                       ***99999888776655555444...4447777.5556888999999999*************************** PP

                       AA_permease 156 vgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksi 232
                                       vg i++ g     +                +p+g        +++++ +++ ++fa++G+e  + +++E++dPe+++
  gi|386001705|ref|YP_005920004.1| 165 VG-IPHLGSVDYLQ----------------MPGG--------LTGVFEAAALIFFAYMGFEEMVKLSEETRDPERNM 216
                                       **.78988886666................7778........99********************************* PP

                       AA_permease 233 PkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanssly 309
                                       P a + ++ +++i+Y+l++l+++++vp+  l   +       pf  +  e+  + + ++i a+ l a+ ++++ +l 
  gi|386001705|ref|YP_005920004.1| 217 PLALIAALAITIILYILVALSVVSVVPWEVLAASS------APFAEVAAEALGPEAFVVISAIALFATANTVLLMLL 287
                                       ******************************66666......366666666666666677888888889999999*** PP

                       AA_permease 310 sasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliil 385
                                       +asR+ y +a+   +P   ++++  r+ P++ai++++++s ++     ++ +    ++f+ +++ +i ++++++i+ 
  gi|386001705|ref|YP_005920004.1| 288 AASRIAYGMAEAASLPtVLGRVHPGRRTPMAAIVAVTLLSIAFA----FSGE----IAFVASANDFILFLTFIVING 356
                                       ****************445566789*****************99....6666....67779**************** PP

                       AA_permease 386 sylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilal 431
                                       s++ +R+       + + +++ +a++   v  vl +l+ ++lil l
  gi|386001705|ref|YP_005920004.1| 357 SLIALRRR---DPDRPRPFRVPLAVGWVPVLPVLGILTCLFLILHL 399
                                       *******9...55555566666666666666666666666666655 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4  16.7   5.6e-13   2.5e-09      12     238 ..      21     246 ..      13     293 .. 0.84
   2 !    3.9   1.5    0.0045        20     111     152 ..     314     355 ..     286     397 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 5.6e-13
                    Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektl.iellkkilgkwLGsllsilfil 87 
                                       v ++lG+gi  l + +ae a+ + Wi+  la++i+++  l + +l++ fp  +  +e+ +  +gk L+++ + l+i 
  gi|386001705|ref|YP_005920004.1|  21 VGIILGAGIYALIGKAAELAGNSVWIAFALAALIAIFTGLSYAELSSIFPRASAeYEYTDRAFGKRLAFVVGWLIIF 97 
                                       6789****************99****************************987659********************* PP

                    Spore_permease  88 yFlllaafelRefseliqvfl.ledtplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklae 163
                                         ++ a++++  f+  ++     + +p++++++lll v+l+  vk    +a  ++f ++ +   l++i + +  l  
  gi|386001705|ref|YP_005920004.1|  98 SGVIGASTVALGFGGYFEALTgAPILPSAVLLILLLSVVLLWGVKLSAWFA--IVFTLIETAGLLIVIYVGIPHLGS 172
                                       *************99998654267788888877777777776666555555..666666666666666677777777 PP

                    Spore_permease 164 iknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaall.gvlistllyllttlivilvlsveq 238
                                       +++l+  +  g+  v++++  + ++++g+e ++ l +  +d+++    al+ +++i+++ly+l+ l v++v   e 
  gi|386001705|ref|YP_005920004.1| 173 VDYLQ--MPGGLTGVFEAAALIFFAYMGFEEMVKLSEETRDPERNMPLALIaALAITIILYILVALSVVSVVPWEV 246
                                       77776..78*********************************9988877661567899999999999988876555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0045
                    Spore_permease 111 dtplwiiilllllvilYlvvkGieslareflfiivilliill 152
                                       +tp+++i+++ ll i+++ ++ i  +a  + fi++ ++i++ 
  gi|386001705|ref|YP_005920004.1| 314 RTPMAAIVAVTLLSIAFAFSGEIAFVASANDFILFLTFIVIN 355
                                       8**************************844444444444332 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       0.2   9.1e+02      29      48 ..      16      35 ..      10      37 .. 0.77
   2 ?   -2.0   0.2      0.85   3.8e+03      29      41 ..      45      57 ..      41      63 .. 0.69
   3 ?   -1.2   5.3      0.48   2.2e+03       7      49 ..     121     168 ..     119     170 .. 0.59
   4 ?   -1.0   1.1      0.43   1.9e+03      11      27 ..     223     239 ..     218     247 .. 0.72
   5 !   17.9   0.7   5.3e-07    0.0024       3      32 ..     378     407 ..     372     419 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.2
                     AA_permease_C 29 wirfgvwmliglliYflYgi 48
                                        + gv +++g  iY l g+
  gi|386001705|ref|YP_005920004.1| 16 VTLSGVGIILGAGIYALIGK 35
                                      5667899********98775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.85
                     AA_permease_C 29 wirfgvwmligll 41
                                      wi f+   li ++
  gi|386001705|ref|YP_005920004.1| 45 WIAFALAALIAIF 57
                                      8888877777664 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.48
                     AA_permease_C   7 PflPa...lsIlvNiyLmlqLdsltwirfgvwmli...glliYflYgir 49 
                                       P+lP+   l +l+ + L+   +  +w  ++  + i   glli +++gi 
  gi|386001705|ref|YP_005920004.1| 121 PILPSavlLILLLSVVLLWGVKLSAWFAIVFTL-IetaGLLIVIYVGIP 168
                                       666651114556799999988888887544433.334476666666665 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.43
                     AA_permease_C  11 alsIlvNiyLmlqLdsl 27 
                                       al+I + +y+++ L++ 
  gi|386001705|ref|YP_005920004.1| 223 ALAITIILYILVALSVV 239
                                       67777777777777765 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 5.3e-07
                     AA_permease_C   3 vPlvPflPalsIlvNiyLmlqLdsltwirf 32 
                                       v +vP+lP+l+Il+ ++L+l+Ld ++ ++ 
  gi|386001705|ref|YP_005920004.1| 378 VGWVPVLPVLGILTCLFLILHLDGAAILLG 407
                                       337********************9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2869.70
//
Query:       gi|386001706|ref|YP_005920005.1|  [L=535]
Description: hypothetical protein Mhar_1013 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 4033.96
//
Query:       gi|386001707|ref|YP_005920006.1|  [L=246]
Description: Metallo-beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-27   96.2   0.1    2.2e-27   95.9   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.3e-21   75.8   0.2    5.9e-21   75.4   0.2    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00078   19.4   0.0     0.0013   18.7   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.1   3.7e-31   2.2e-27       3     201 .]      49     221 ..      48     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 3.7e-31
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       +LiD++pdlr q+ r+         ++++d+V++thaHyDH+ag+ ++ + ++ ++p y+ k++++++ + + y+++
  gi|386001707|ref|YP_005920006.1|  49 VLIDTSPDLRWQLIRT--------GISRVDGVIWTHAHYDHYAGFGDFHRVQN-RVPAYGLKETMDYILNYL-YFMR 115
                                       8*********994444........588***********************877.5***********999995.4444 PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHHC CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerlg 155
                                       ++     ++ ++ g +fe++  g+e+t+++++h           +++G+++++g+k+++ +gDt  +ipe+  ++++
  gi|386001707|ref|YP_005920006.1| 116 PR-----RNVVEMGVPFEVA--GMEFTLFEVNHPPIC-------EAAGVVVREGNKKLVVTGDTTlQIPEASLDLMR 178
                                       44.....5788889*****9..899********9999.......********************97899999***** PP

                                       T-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 156 gadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       +adll+ d+   ++  +     H++ eeav + ++l ak +vl+Hi
  gi|386001707|ref|YP_005920006.1| 179 NADLLVADAI--TPPGYA-LTKHMNSEEAVGLGRELAAKEVVLTHI 221
                                       ******9955..555544.699***********************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.2   9.9e-25   5.9e-21       6     183 ..      37     209 ..      33     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 9.9e-25
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        +s+l+e++ g +LiDt  + +++++       + ++ +vd vi TH+H+DH++g g++ +  + ++++  +e+  +
  gi|386001707|ref|YP_005920006.1|  37 RFSILVENGSGKVLIDTSPDLRWQLI-------RTGISRVDGVIWTHAHYDHYAGFGDFHRVQNRVPAYGLKETMDY 106
                                       6899*********************5.......8******************************************* PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                       + +++++ ++r          ++++++  + ++ +++  +++v + p   + ++vv+ g++k+++tGD++l+ ++++
  gi|386001707|ref|YP_005920006.1| 107 ILNYLYFMRPR----------RNVVEMGVPFEVAGMEFTLFEVNHPPICEAAGVVVREGNKKLVVTGDTTLQIPEAS 173
                                       *****876665..........689***************************************************** PP

                                       CCC.............TTCEEE-SHCHHHHHHHHHH CS
                       Lactamase_B 160 idl............tlrgaevrdpsdaekyldsll 183
                                       +dl            t+ g +  ++   e++    +
  gi|386001707|ref|YP_005920006.1| 174 LDLmrnadllvadaiTPPGYALTKHMNSEEAVGLGR 209
                                       ***888888777777666666666666666555555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.1e-07    0.0013       9     163 .]      39     220 ..      38     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-07
                     Lactamase_B_3   9 sflletagarilvDPfkanlgyeppa...eeaDlvlisqaledHahletlkql........................ 58 
                                       s+l+e +  ++l+D   + l ++  +    ++D v+ ++a+ dH++   +                           
  gi|386001707|ref|YP_005920006.1|  39 SILVENGSGKVLIDTS-PDLRWQLIRtgiSRVDGVIWTHAHYDHYAGFGDFHRvqnrvpayglketmdyilnylyfm 114
                                       6788888899999954.46666666667799**************97655443488899999999999999999998 PP

                     Lactamase_B_3  59 aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltP 135
                                         + +v+e g  +ev+g+e++ ++ +h     ++  e  g ++++++ +++  G++  ++ +++l+ + ++D++++ 
  gi|386001707|ref|YP_005920006.1| 115 RPRRNVVEMGVPFEVAGMEFTLFEVNH-----PPICEAAGVVVREGNKKLVVTGDTTLQIPEASLDLMRNADLLVAD 186
                                       777789999999999999999999999.....5667778899**********************************9 PP

                     Lactamase_B_3 136 vgg......pltlgqeealelakrLkpklvlPmh 163
                                        +       ++ ++ eea+ l ++L +k v+ +h
  gi|386001707|ref|YP_005920006.1| 187 AITppgyalTKHMNSEEAVGLGRELAAKEVVLTH 220
                                       999999999999****************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1558.55
//
Query:       gi|386001708|ref|YP_005920007.1|  [L=439]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-35  122.2   0.0    3.7e-35  121.2   0.0    1.6  1  AAA           ATPase family associated with various cellular 
      2e-12   46.7   0.0    4.6e-12   45.5   0.0    1.6  1  AAA_lid_3     AAA+ lid domain
    0.00011   22.2   0.1    0.00052   20.0   0.1    2.2  1  AAA_5         AAA domain (dynein-related subfamily)
    0.00015   22.3   0.0    0.00086   19.8   0.0    2.4  1  AAA_18        AAA domain
     0.0037   17.4   0.1      0.023   14.9   0.1    2.3  1  AAA_33        AAA domain
     0.0046   17.4   0.2       0.46   10.9   0.0    2.8  2  AAA_16        AAA ATPase domain
      0.005   17.1   0.4      0.028   14.7   0.0    2.4  3  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.062   13.0   0.0    1.6  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.035   14.4   0.7        2.6    8.3   0.2    2.7  2  AAA_22        AAA domain
      0.035   13.8   0.2       0.28   10.9   0.1    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.037   13.2   0.0      0.076   12.2   0.0    1.6  1  TIP49         TIP49 P-loop domain
      0.039   13.1   0.0      0.057   12.6   0.0    1.3  1  DUF815        Protein of unknown function (DUF815)
      0.074   12.8   0.3       0.21   11.3   0.1    1.7  1  AAA_11        AAA domain
      0.081   12.4   0.2       0.17   11.3   0.2    1.6  1  AAA_7         P-loop containing dynein motor region
      0.098   12.0   0.0       0.23   10.8   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.098   12.1   2.3       0.14   11.6   0.6    2.1  2  DegS          Sensor protein DegS
       0.14   12.1   0.0       0.22   11.4   0.0    1.3  1  Rad17         Rad17 P-loop domain
       0.16   12.9   0.1        0.4   11.6   0.1    1.7  1  CSN5_C        Cop9 signalosome subunit 5 C-terminal domain
       0.23   11.5   1.5       0.88    9.7   0.0    2.6  2  AAA_2         AAA domain (Cdc48 subfamily)
       0.29   11.6   2.9       0.44   11.0   0.2    2.7  2  AAA_17        AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   4.2e-38   3.7e-35       1     131 [.     228     356 ..     228     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 4.2e-38
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +l++GppGtGKT++a a+  ++g +++e+ +s ++s+y+ge++k+i ++f+ ak+ + p+ilfiDE+d +ak+r+++
  gi|386001708|ref|YP_005920007.1| 228 LLFVGPPGTGKTSTAMALSGKFGLPLVEVRLSMVTSQYLGETSKNIDKVFDLAKTLS-PCILFIDEFDFVAKTRTSD 303
                                       69******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       e++  +r+vn+Ll+++d+v+  e+ v++i+atn+p+ ld a   +Rfd+++ ++
  gi|386001708|ref|YP_005920007.1| 304 EHGAIKRAVNTLLKAIDDVSLVEDGVLLIAATNHPQLLDYAAW-RRFDKVVSFP 356
                                       *******************************************.7*****9987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   5.1e-15   4.6e-12       2      43 ..     378     419 ..     377     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 5.1e-15
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       vd + LAerTeGySG D+  ++reA+l+Al  ++ +i++ed+
  gi|386001708|ref|YP_005920007.1| 378 VDPEVLAERTEGYSGSDIRLVVREAVLNALLADRRSIDQEDM 419
                                       89999***********************************98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   5.8e-07   0.00052       2     137 ..     228     348 ..     227     349 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.8e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +l vGppGtgK++ a+ l+  ++ ++++v l+  t  ++ +g+++      +  d+++   a+  +++il++DE++ 
  gi|386001708|ref|YP_005920007.1| 228 LLFVGPPGTGKTSTAMALSGKFGLPLVEVRLSMVT--SQYLGETS------KNIDKVFD-LAKtlSPCILFIDEFDF 295
                                       799*************************9998644..34444444......22333333.22234888888888886 PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                       + +  ++  +  + +    l +    v+  +d+    + +ia++n ++     l+ a ++R
  gi|386001708|ref|YP_005920007.1| 296 VAKTRTSDEHGAIKRAVNTLLKAIDDVSLVEDG----VLLIAATNHPQ----LLDYAAWRR 348
                                       665555555555555555555555555554544....66666666666....555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.6e-07   0.00086       3     110 ..     230     366 ..     228     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.6e-07
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskr 51 
                                         G+pG+GKt+ a +Ls + g+                      +++ d+ak   +++ + +e           s++
  gi|386001708|ref|YP_005920007.1| 230 FVGPPGTGKTSTAMALSGKFGLplvevrlsmvtsqylgetsknIDKVFDLAKTLSPCILFIDEfdfvaktR--TSDE 304
                                       68**************999888999999999999***999999999*************999988776332..2222 PP

                            AAA_18  52 ldedkldklldaleenss..aleegknlvidghlaele.seaakdikk..vvLtaspeelleRl 110
                                           k  +++++l ++++  +l e ++l+i       + ++aa+++    v   +++ee+++R+
  gi|386001708|ref|YP_005920007.1| 305 HGAIK--RAVNTLLKAIDdvSLVEDGVLLIAATNHPQLlDYAAWRRFDkvVSFPLPDEEMRRRI 366
                                       22222..233333333334766777777777766655525555555558888888888888887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.5e-05     0.023       3     136 ..     229     386 ..     228     409 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.....................dytrvldrly 56 
                                       l+vG+pG+GK+  a  l  k g   v ++   + +++ g+  +++                                
  gi|386001708|ref|YP_005920007.1| 229 LFVGPPGTGKTSTAMALSGKFGlpLVEVRLSMVTSQYLGETSKNIDkvfdlaktlspcilfidefdfV--------- 296
                                       89***************999997755555555555555544444442332222222222222222220......... PP

                            AAA_33  57 qilnelarkalsagrnvil..datnlsr.rer....arflklarrlgvp...........vrivvvetdeetlkeRl 115
                                             a+ + s + ++i    +t+l++ ++     + +l +a   + p           +++v +  ++e++++R+
  gi|386001708|ref|YP_005920007.1| 297 ------AKTRTSDEHGAIKraVNTLLKAiDDVslveDGVLLIA-ATNHPqlldyaawrrfDKVVSFPLPDEEMRRRI 366
                                       ......2222233333333233333333222222211111111.122223333333333345666666666666666 PP

                            AAA_33 116 akRaangddrsevpeealdrq 136
                                         +   g+ +++v+ e+l + 
  gi|386001708|ref|YP_005920007.1| 367 FGKVL-GRMDARVDPEVLAER 386
                                       66666.444455666666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00051      0.46      14      44 ..     215     245 ..     203     251 .. 0.82
   2 ?    3.6   0.1     0.089        80     125     146 ..     275     301 ..     268     332 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrel 44 
                                       ++l+ v   + + +l++G++G+GK+s + +l
  gi|386001708|ref|YP_005920007.1| 215 DYLREVGLYDIGKLLFVGPPGTGKTSTAMAL 245
                                       56666666666779************98776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                            AAA_16 125 rllallsrderplvlvlDdlq......w 146
                                       + ++l+++  +p +l++D+++       
  gi|386001708|ref|YP_005920007.1| 275 KVFDLAKT-LSPCILFIDEFDfvaktrT 301
                                       55688888.778*********7554441 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.4   3.1e+03      51      63 ..     154     166 ..     127     209 .. 0.66
   2 !   14.7   0.0   3.1e-05     0.028       3      51 ..     229     278 ..     227     287 .. 0.79
   3 ?   -2.7   0.0       6.8   6.1e+03      96     121 ..     336     362 ..     331     365 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.4
                            AAA_28  51 dllafaervleeq 63 
                                       d+ ++++++ e++
  gi|386001708|ref|YP_005920007.1| 154 DREWIQSKIREME 166
                                       3333333333333 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.1e-05
                            AAA_28   3 vitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwved 51 
                                        ++G+++tGKT+++ aL+ + g p v+    +++++ l ++ +++++v+d
  gi|386001708|ref|YP_005920007.1| 229 LFVGPPGTGKTSTAMALSGKfGLPLVEVRLSMVTSQYLGETSKNIDKVFD 278
                                       699***************88899999877777777777666666666655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.8
                            AAA_28  96 aeaeleaaarekrydlvfllp.papei 121
                                        +++l + a+ +r d+v+ +p p++e+
  gi|386001708|ref|YP_005920007.1| 336 NHPQLLDYAAWRRFDKVVSFPlPDEEM 362
                                       467888888899999999998667777 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-05     0.062      35      94 ..     227     294 ..     201     310 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelg.....vklki.tsgPvlekagdlaal..ltnleekdvlfideih 94 
                                        +l++GpPG Gkt+ a+ ++ ++g     v+l + ts    e ++++  +  l++  +  +lfide  
  gi|386001708|ref|YP_005920007.1| 227 KLLFVGPPGTGKTSTAMALSGKFGlplveVRLSMvTSQYLGETSKNIDKVfdLAKTLSPCILFIDEFD 294
                                       689****************9987622211334431343333444444333113333344688888865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2     0.003       2.6       8      26 ..     228     246 ..     225     264 .. 0.82
   2 ?    3.5   0.0     0.091        82      84     117 ..     278     321 ..     249     343 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                            AAA_22   8 lvvtGesGtGKTtllrrll 26 
                                       l+ +G++GtGKT ++  l 
  gi|386001708|ref|YP_005920007.1| 228 LLFVGPPGTGKTSTAMALS 246
                                       6789********9997765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.091
                            AAA_22  84 qalraravielliiDEaqhlr....s......eealeeL.rslln 117
                                       + +++ +   +l iDE++++     s      ++a+++L + + +
  gi|386001708|ref|YP_005920007.1| 278 DLAKTLSP-CILFIDEFDFVAktrtSdehgaiKRAVNTLlKAIDD 321
                                       45555555.9*********98765426677787777777444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00032      0.28      49      68 ..     227     246 ..     188     251 .. 0.80
   2 ?    0.1   0.0      0.64   5.8e+02      78     111 ..     287     322 ..     278     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                         IstB_IS21  49 nivllGpsGvGKshlaialg 68 
                                        ++++Gp+G+GK+  a+al+
  gi|386001708|ref|YP_005920007.1| 227 KLLFVGPPGTGKTSTAMALS 246
                                       6899**************96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.64
                         IstB_IS21  78 vlfvrvedLveelkrarrdgklaralkrllkv..dl 111
                                       +lf+   d+v++ ++ +++g ++ra+++llk+  d+
  gi|386001708|ref|YP_005920007.1| 287 ILFIDEFDFVAKTRTSDEHGAIKRAVNTLLKAidDV 322
                                       788888999999999999****99999998864444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.5e-05     0.076      53      90 ..     228     263 ..     218     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  53 vLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       +L++Gp+gtGkt+ a+a+s ++g  +p v +  s v s
  gi|386001708|ref|YP_005920007.1| 228 LLFVGPPGTGKTSTAMALSGKFG--LPLVEVRLSMVTS 263
                                       799****************9999..6666666555544 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.057      30     124 ..     201     301 ..     176     361 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                            DUF815  30 Lvgidkqkealve.nteqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr 103
                                       +++i+k  +al + +  + +  +   ++L++G  GtGK s+  al  ++      +rl  v+ + l e +k ++++ 
  gi|386001708|ref|YP_005920007.1| 201 VTEIEKAAKALEHrDYLREVGLYDIGKLLFVGPPGTGKTSTAMALSGKFGLPLveVRLSMVTSQYLGETSKNIDKVF 277
                                       555555555554313333344445567899*****************998776668888889999988777777665 PP

                            DUF815 104 ...erperfilfvDDLsFeeeeee 124
                                          ++   +ilf+D   F ++ ++
  gi|386001708|ref|YP_005920007.1| 278 dlaKTLSPCILFIDEFDFVAKTRT 301
                                       111455679******999765443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00024      0.21      18      37 ..     215     245 ..     196     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                            AAA_11  18 e...........itliqGPPGtgKTktivel 37 
                                       +             l+ GPPGtgKT+t ++l
  gi|386001708|ref|YP_005920007.1| 215 DylrevglydigKLLFVGPPGTGKTSTAMAL 245
                                       45555555555567999*********99877 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00019      0.17      35      58 ..     227     250 ..     214     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                             AAA_7  35 pvllvGptGtGKtviikdllkkld 58 
                                       ++l+vGp GtGKt++++ l  k+ 
  gi|386001708|ref|YP_005920007.1| 227 KLLFVGPPGTGKTSTAMALSGKFG 250
                                       689************999887776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.23      24      44 ..     227     247 ..     207     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlps 44 
                                       +ll+vGppG+GKt  a +l++
  gi|386001708|ref|YP_005920007.1| 227 KLLFVGPPGTGKTSTAMALSG 247
                                       79***********99998865 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00016      0.14      80     132 ..     128     180 ..     120     184 .. 0.91
   2 ?   -2.0   0.0       2.5   2.2e+03      37      61 ..     185     209 ..     182     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                              DegS  80 keaYeeakelqvelallrekEkqlrerRdelerrLkklketierAeklvsqvg 132
                                          Ye+ ++l v+ a +r++ + l + R+ ++ +++++++ +e A+++++ v 
  gi|386001708|ref|YP_005920007.1| 128 AYFYENYDSLDVSYAEARKRNQPLLTDREWIQSKIREMEAKVEEADEILKLVR 180
                                       567********************************************998775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                              DegS  37 eelkeevsevikevdklekkerkar 61 
                                       e++++++++++ + d++++ e+ a+
  gi|386001708|ref|YP_005920007.1| 185 EDVRDRIEDLVLTKDQVTEIEKAAK 209
                                       6788888888888888888888876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.22      18      76 ..     191     256 ..     187     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                             Rad17  18 aeelavhkkkieevkewlkadvLesrkkr.........iLLisGPsGCgkstvvkvLskelgiklrew 76 
                                        e+l + k ++ e++++ ka  Le+r             LL  GP+G gk+ +   Ls ++g  l e 
  gi|386001708|ref|YP_005920007.1| 191 IEDLVLTKDQVTEIEKAAKA--LEHRDYLrevglydigKLLFVGPPGTGKTSTAMALSGKFGLPLVEV 256
                                       67899999999999998665..555543234777786669******************9999877765 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00045       0.4       4      43 ..     150     189 ..     148     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                            CSN5_C   4 pLltNrdYatkqisDLaeKlekaessvsrsrsaagtlsee 43 
                                       pLlt r++++++i+++++K+e+a++ ++  r +a++  ++
  gi|386001708|ref|YP_005920007.1| 150 PLLTDREWIQSKIREMEAKVEEADEILKLVRIKAPEDVRD 189
                                       9**********************99988877666655543 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       2.8   2.5e+03      48      82 ..     171     209 ..     153     219 .. 0.58
   2 ?    9.7   0.0   0.00098      0.88       3     107 ..     225     323 ..     223     337 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                                       --THHHHHHHHHTTT-HHHHTTSEEE....EETGGG--- CS
                             AAA_2  48 evehlvsrligappgyvgaeegGivl....lDEidKihp 82 
                                       e++++++   +++p +v+   +  vl    + Ei+K+++
  gi|386001708|ref|YP_005920007.1| 171 EADEILKLVRIKAPEDVRDRIEDLVLtkdqVTEIEKAAK 209
                                       555555555555555555554444442222458888887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00098
                                       ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG CS
                             AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidK 79 
                                       i+++l++gp g+Gkt +a al+    +      +r+ + + +   e ++ +++    ++         i+++DE d 
  gi|386001708|ref|YP_005920007.1| 225 IGKLLFVGPPGTGKTSTAMALSGKFGL--PLVEVRLSMVTSQYLGETSKNIDKVFDLAKTL----SPCILFIDEFDF 295
                                       68899************9999999886..22222333333333224555555555544444....4669*******9 PP

                                       -------------HHHHHHHHHHHH--E CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqileggt 107
                                       ++++++s +    +  ++ LL+ +++  
  gi|386001708|ref|YP_005920007.1| 296 VAKTRTSDEHGAIKRAVNTLLKAIDDVS 323
                                       9998444444444555577777777755 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       3.8   3.5e+03      70      91 ..     170     190 ..     141     212 .. 0.49
   2 ?   11.0   0.2    0.0005      0.44       1      49 [.     231     276 ..     231     384 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.8
                                       HSSEEEEEE-SEEEETTEEEES CS
                            AAA_17  70 kkkgvlvdghprikeqagfldg 91 
                                       ++ + ++ +  rik++++ +d+
  gi|386001708|ref|YP_005920007.1| 170 EEADEIL-KLVRIKAPEDVRDR 190
                                       2222222.22222333333322 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0005
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHH.HHHHTTTSHSSHHHHCTS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllr.eeakrgglakardemrkl 49 
                                       +G+PG GK+  +  l  k+g++ ++    +r ++++++ l+++ ++++k+
  gi|386001708|ref|YP_005920007.1| 231 VGPPGTGKTSTAMALSGKFGLPLVE----VRlSMVTSQYLGETSKNIDKV 276
                                       7**********************99....444666777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 2573.04
//
Query:       gi|386001709|ref|YP_005920008.1|  [L=500]
Description: (R)-citramalate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-73  247.1   0.5    4.2e-73  246.2   0.5    1.5  1  HMGL-like   HMGL-like
    2.6e-33  114.8   1.5    5.4e-33  113.7   1.5    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.081   12.9   0.0       0.21   11.6   0.0    1.7  1  DUF4974     Domain of unknown function (DUF4974)


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.2   0.5     7e-77   4.2e-73       1     264 []       9     266 ..       9     266 .. 0.99

  Alignments for each domain:
  == domain 1  score: 246.2 bits;  conditional E-value: 7e-77
                                       B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHH CS
                         HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekd 77 
                                       +v+++dttLRDGeq+++++l++eek+ ia++Ld++g+d+iE+g ++ se+++ +++a+a+++  a+++++vrar  d
  gi|386001709|ref|YP_005920008.1|   9 RVRLLDTTLRDGEQTPGVSLTLEEKVSIARQLDALGLDVIEAGSAVTSEGERRAMKAVAEEGLRAEVCSYVRARTGD 85 
                                       5899************************************************************************* PP

                                       HHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHH CS
                         HMGL-like  78 ikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevvea 154
                                       ++ a +    + ++++h+++++s+lh++ kl+ dre v++ a+e++++a+ +g  vels edasr+d  +l+ ++ a
  gi|386001709|ref|YP_005920008.1|  86 VDLALN----CDVDSIHLVVPVSDLHIRCKLRSDREGVMRAAVEVTEYAKGHGLIVELSGEDASRADEGYLTALYRA 158
                                       ******....******************************************************************* PP

                                       HHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSB CS
                         HMGL-like 155 aeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGera 231
                                        ++aGa+r+   DtvGvl  ++a+e++s+l++ ++  v++svHcH+d+GlA+ant+aA++ Ga+   +tvnG+Ger 
  gi|386001709|ref|YP_005920008.1| 159 GIDAGADRLCYCDTVGVLVAEKAFEVFSRLSK-LP--VPVSVHCHDDFGLATANTVAALRGGASMAHVTVNGIGERG 232
                                       ******************************75.89..9*************************************** PP

                                       BB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 232 Gnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                       Gn++lee+v++le l  ++t+++ q+l+s+++lv
  gi|386001709|ref|YP_005920008.1| 233 GNTSLEEVVMTLESLYgIKTEIQCQELYSLSRLV 266
                                       *************9977**************997 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   1.5   9.1e-37   5.4e-33       2     132 ..     362     493 ..     361     494 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 9.1e-37
                                       XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T CS
                        LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..d 75 
                                       vtd+dl+++++ +l  ++  ++kl++++++sg++  +ta+v++ v +g+e  ++++G+GpvdA++nA+r+a++   d
  gi|386001709|ref|YP_005920008.1| 362 VTDADLQTIAEIVLSIQKePKVKLNEFTIVSGNHAIPTASVRIIV-NGSEILEAGTGVGPVDAAINAIRRAISGvrD 437
                                       9*************99888**************************.*************************99889* PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       ++L++Y+v+a+t+gt+a++ev V++   ++++++++G+ +di++AS++A+++++nrl
  gi|386001709|ref|YP_005920008.1| 438 VRLEEYHVDAVTGGTNALVEVWVTMA-MGDRTITARGAGADIIMASVEAVLEGINRL 493
                                       **************************.55556***********************98 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.5e-05      0.21       6      31 ..     234     259 ..     233     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                                       EEEHHHHHHHHHHHHT--EEE-TTS- CS
                           DUF4974   6 nesLeeilkkLerwYnveivieneel 31 
                                       n+sLee++ +Le  Y+++ +i+ +el
  gi|386001709|ref|YP_005920008.1| 234 NTSLEEVVMTLESLYGIKTEIQCQEL 259
                                       89******************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3305.96
//
Query:       gi|386001710|ref|YP_005920009.1|  [L=580]
Description: Acetolactate synthase, large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-59  200.1   0.1    4.9e-59  198.8   0.1    1.7  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    9.3e-56  187.4   0.1    1.5e-55  186.6   0.1    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    3.4e-52  176.3   0.1    5.3e-51  172.4   0.1    2.6  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.033   13.7   0.0       0.09   12.4   0.0    1.7  1  HTH_47        winged helix-turn-helix
      0.039   13.7   0.3      0.077   12.7   0.3    1.4  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.8   0.1   1.4e-62   4.9e-59       1     169 [.       4     170 ..       4     172 .. 0.99
   2 ?   -3.7   0.0       2.2     8e+03     111     145 ..     487     521 ..     480     522 .. 0.76

  Alignments for each domain:
  == domain 1  score: 198.8 bits;  conditional E-value: 1.4e-62
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++aea++++Lk +gve +fg+pG+ +lpl+da+ +++ ir++l+rhEq+aa+aAdgyaratg++gv+l+tsgpGat
  gi|386001710|ref|YP_005920009.1|   4 MSGAEAILECLKLEGVEIIFGLPGGVLLPLYDAIYDSD-IRHILVRHEQAAAHAADGYARATGRVGVCLATSGPGAT 79 
                                       789**********************************6.************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t++a+A+ d++P+++++g++pt l+g++++q e d++++  pvtk+++ v++++e+p+++r+A+ +a +grpgP
  gi|386001710|ref|YP_005920009.1|  80 NLVTGIATAYMDSVPMVAMTGQVPTNLIGKDAFQ-EADITGITMPVTKHSYLVKDAKEIPRVFREAFYIARTGRPGP 155
                                       **********************************.****************************************** PP

                                       EEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 155 vylelpkdvlleevd 169
                                       v+++lp+dv  +ev+
  gi|386001710|ref|YP_005920009.1| 156 VLIDLPRDVTADEVE 170
                                       **********99986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.2
                                       C--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHH CS
                      TPP_enzyme_N 111 qqeldqlalfrpvtkyaervtspeelpealrrAir 145
                                       + + d +++++ +     r t+p+el+ +l++Ai+
  gi|386001710|ref|YP_005920009.1| 487 HRVPDFVKVAEAYGALGLRATKPSELEGVLKEAID 521
                                       54557777777777778889999999999999986 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.6   0.1   4.3e-59   1.5e-55       1     137 []     192     327 ..     192     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.6 bits;  conditional E-value: 4.3e-59
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       i+kaa++l +a+rpvi+vGggv++s+ ++el +lae++++Pv+ttlmg g++pedhpl+lgmlg+hg+k+an a++e
  gi|386001710|ref|YP_005920009.1| 192 IRKAAKALMEAERPVIYVGGGVKYSDGHRELLRLAERIKAPVTTTLMGIGCFPEDHPLSLGMLGMHGTKYANYAVQE 268
                                       789************************************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       aDl+la+Garfdd r+tg+   fap+a++ih+d+dpaeigkn++vd+++vgd+k +l++L
  gi|386001710|ref|YP_005920009.1| 269 ADLILAVGARFDD-RVTGKVASFAPQARVIHVDVDPAEIGKNVRVDIPVVGDAKSALTEL 327
                                       *************.*******************************************987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.1   3.8e+02     124     152 ..     128     159 ..      92     160 .. 0.71
   2 ?   -3.6   0.0       2.3   8.3e+03      41      78 ..     197     236 ..     195     238 .. 0.65
   3 !  172.4   0.1   1.5e-54   5.3e-51       2     153 .]     383     530 ..     382     530 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                                       EEEESSH.HHHHHHHHHHHH.....CSSSEEEEE CS
                      TPP_enzyme_C 124 garvekadveeleealkeal.....ekkgpalie 152
                                        + v++a  +e+ ++++ea+      + gp+li+
  gi|386001710|ref|YP_005920009.1| 128 SYLVKDA--KEIPRVFREAFyiartGRPGPVLID 159
                                       4555666..9*********999999999999998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.3
                                       HHH.STTSEEEEEEEHHHHHHTGGGHHHHHHT.T-SEEEE CS
                      TPP_enzyme_C  41 kla.kpdrevvaivGDGgflmilqelatavrr.nlpitvv 78 
                                       k++ + +r+v+ + G   + + + el   ++r ++p+t+ 
  gi|386001710|ref|YP_005920009.1| 197 KALmEAERPVIYVGGGVKYSDGHRELLRLAERiKAPVTTT 236
                                       4431347888888887777777888888888733477765 PP

  == domain 3  score: 172.4 bits;  conditional E-value: 1.5e-54
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvv 78 
                                       +G++++waa+++  k pr++++sgglgtmGyg+paAiGakl  pd++v+ i+GDG+f+m++qelatav + + ++v+
  gi|386001710|ref|YP_005920009.1| 383 VGQNQMWAAQFFTHKDPRRFISSGGLGTMGYGFPAAIGAKLGCPDADVFDIAGDGSFQMNIQELATAVVNEVAVKVI 459
                                       9**************************************************************************** PP

                                       EEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  79 vlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       +lnN+++gm++++q+ f++kr+s+++    + +df+k+aea+Ga g+r +k+  +ele +lkea++++ +++++v
  gi|386001710|ref|YP_005920009.1| 460 ILNNGVLGMVRQWQDLFYEKRFSSTT--LHRVPDFVKVAEAYGALGLRATKP--SELEGVLKEAIDSEVVTVVDV 530
                                       ************************99..57888***************7788..*******************98 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.09      41      62 ..     214     235 ..     212     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                       HH-EEEEEHHHHHHHHT--HHH CS
                            HTH_47  41 nlaDGkrsLldiAeriglpfdr 62 
                                        ++DG+r+Ll +Aeri++p+ +
  gi|386001710|ref|YP_005920009.1| 214 KYSDGHRELLRLAERIKAPVTT 235
                                       69*****************976 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   2.1e-05     0.077      37      94 ..      41     100 ..      32     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                       E.EEEE-SSHHHHHHHHHH.HHCTT-EE.EEEEECCHHHHCCCCHHHHHHTT--EEEEEE CS
                             POR_N  37 dvevvqmesEigaisaviG.AaaaGara.aTaTSgqGllLmienlglaageelPvvivvv 94 
                                       d++ + +  E +a+ a+ G A a+G  +   aTSg+G    +  +  a ++ +P+v +  
  gi|386001710|ref|YP_005920009.1|  41 DIRHILVRHEQAAAHAADGyARATGRVGvCLATSGPGATNLVTGIATAYMDSVPMVAMTG 100
                                       567788999*********96667787651469************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 4294.78
//
Query:       gi|386001711|ref|YP_005920010.1|  [L=163]
Description: Acetolactate synthase, small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-30  103.7   3.1    4.4e-30  103.7   3.1    2.0  2  ALS_ss_C        Small subunit of acetolactate synthase
    6.7e-20   70.7   1.0    1.8e-19   69.3   0.1    2.1  2  ACT_5           ACT domain
    2.5e-16   59.1   0.5    7.6e-16   57.6   0.1    1.9  2  ACT             ACT domain
    6.1e-06   26.7   1.6    1.4e-05   25.6   0.2    2.0  2  ACT_4           ACT domain
      0.001   18.9   0.2       0.58   10.1   0.0    2.5  2  NIL             NIL domain
  ------ inclusion threshold ------
      0.022   14.7   0.3         10    6.2   0.0    2.8  3  ACT_6           ACT domain
      0.032   14.1   1.1      0.094   12.5   1.0    1.6  1  SLS             Mitochondrial inner-membrane-bound regulator
      0.078   13.1   1.9       0.18   11.9   1.7    1.6  1  DUF2096         Uncharacterized protein conserved in archaea 
       0.11   12.9   0.2       0.56   10.6   0.1    2.0  2  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.76   1.5e+03      39      57 ..      48      66 ..      41      76 .. 0.48
   2 !  103.7   3.1   2.2e-33   4.4e-30       1      74 []      84     157 ..      84     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.76
                                      EEEEE-HHHHHHHHHHS-G CS
                          ALS_ss_C 39 ieltgteekidaliellkp 57
                                      i + g+e  ++++ + l++
  gi|386001711|ref|YP_005920010.1| 48 ITVDGDEVVLEQVTKQLNK 66
                                      4444444444444444432 PP

  == domain 2  score: 103.7 bits;  conditional E-value: 2.2e-33
                                       EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                          ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                       REla+iKV+a+ke+rsei++i+++fraki+dvsp s+iie+tg+++k++a+++ll++fgi+e++RtG+v + RG
  gi|386001711|ref|YP_005920010.1|  84 RELAMIKVAAKKEDRSEIMQIVSVFRAKIIDVSPRSMIIEVTGSQDKVEAMVRLLRQFGIKEMARTGKVSMIRG 157
                                       9***********************************************************************98 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.1   8.9e-23   1.8e-19       1      62 []      11      73 ..      11      73 .. 0.98
   2 ?   -1.0   0.1      0.82   1.6e+03      36      48 ..     120     133 ..     108     142 .. 0.64

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 8.9e-23
                             ACT_5  1 dapgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                      ++pgvL+R+ ++++rrgF+++sl++ +t++ +++r+++tV++ e  +e++++Ql+KLi+V++V
  gi|386001711|ref|YP_005920010.1| 11 NRPGVLVRIAGLFSRRGFNIDSLTVGATDNPDYSRMTITVDGdEVVLEQVTKQLNKLINVIRV 73
                                      58**********************************************************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.82
                             ACT_5  36 ieltVes.ersvel 48 
                                       + ++V++ ++ ve 
  gi|386001711|ref|YP_005920010.1| 120 MIIEVTGsQDKVEA 133
                                       56677776666666 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.1   3.8e-19   7.6e-16       2      66 ..       4      68 ..       3      69 .. 0.96
   2 ?   -1.0   0.0      0.79   1.6e+03      43      63 ..     119     139 ..     105     142 .. 0.64

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 3.8e-19
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                      ++ + v++rPG+L r++g++++rg+Nids++++ ++    +++++++ +de +le+v ++l+kl+
  gi|386001711|ref|YP_005920010.1|  4 TIALIVENRPGVLVRIAGLFSRRGFNIDSLTVGATDNPDYSRMTITVDGDEVVLEQVTKQLNKLI 68
                                      67789**********************************************************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.79
                                       EEEEEEEEEHHHHHHHHHHHH CS
                               ACT  43 ivfvvivvdeedleevlealk 63 
                                        +++ ++++++ +e++++ l+
  gi|386001711|ref|YP_005920010.1| 119 SMIIEVTGSQDKVEAMVRLLR 139
                                       566666666777777666666 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   6.8e-09   1.4e-05       8      78 ..       4      73 ..       2      74 .. 0.88
   2 ?   -0.1   0.1      0.73   1.5e+03      21      38 ..      99     116 ..      86     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.8e-09
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78
                                      ++ +++e+r+g+L +i+ ++s  + ni s+++ ++++  + +++itv   d   L++v ++L+++ +Vi+V
  gi|386001711|ref|YP_005920010.1|  4 TIALIVENRPGVLVRIAGLFSRRGFNIDSLTVGATDNPDYSRMTITVD-GDEVVLEQVTKQLNKLINVIRV 73
                                      6899******************************87755777777777.56778***************99 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.73
                             ACT_4  21 aditqviseekanivsvn 38 
                                       ++i+q++s  +a+i +v+
  gi|386001711|ref|YP_005920010.1|  99 SEIMQIVSVFRAKIIDVS 116
                                       467777777777777665 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0037       7.5      35      67 ..      35      67 ..      27      73 .. 0.81
   2 !   10.1   0.0   0.00029      0.58      45      69 ..     119     143 ..     105     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0037
                                      EEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT CS
                               NIL 35 veriqgtpfGqlvielsgsqesiaaalqylrkr 67
                                      v+  ++  + +++i++ g++  ++++ + l+k 
  gi|386001711|ref|YP_005920010.1| 35 VGATDNPDYSRMTITVDGDEVVLEQVTKQLNKL 67
                                      5566677899**********99***99999986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00029
                                       EEEEEEES-HHHHHHHHHHHHHTT- CS
                               NIL  45 qlvielsgsqesiaaalqylrkrnv 69 
                                       +++ie++gsq++++a+++ lr+ ++
  gi|386001711|ref|YP_005920010.1| 119 SMIIEVTGSQDKVEAMVRLLRQFGI 143
                                       6*******************99876 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0093        19      10      64 ..      10      66 ..       5      72 .. 0.81
   2 ?    6.2   0.0     0.005        10      17      33 ..      99     115 ..      97     117 .. 0.93
   3 ?   -1.6   0.0       1.4   2.7e+03       4      56 ..     121     132 ..     118     144 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0093
                             ACT_6 10 pdrpGltasLtsvlaefgvni..lDieqavihgrlsLgllvsgpedalarlekaLlf 64
                                      ++rpG++ +++++ ++ g ni  l+++     +    ++ v+g+e  l+++ k+L +
  gi|386001711|ref|YP_005920010.1| 10 ENRPGVLVRIAGLFSRRGFNIdsLTVGATDNPDYSRMTITVDGDEVVLEQVTKQLNK 66
                                      68************9977776558888888888888888888888888888888876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.005
                             ACT_6  17 asLtsvlaefgvnilDi 33 
                                       +++++++++f+++i+D+
  gi|386001711|ref|YP_005920010.1|  99 SEIMQIVSVFRAKIIDV 115
                                       689*************8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                             ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedala 56 
                                       +i vtG                                         ++d+++
  gi|386001711|ref|YP_005920010.1| 121 IIEVTG-----------------------------------------SQDKVE 132
                                       444444.........................................444443 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   4.7e-05     0.094      62     162 ..      42     138 ..      17     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                               SLS  62 nrsenklritAtkstaeyieasineilknittetvd.lsellklskvdklkdl.lseelleelgrltntvie....v 132
                                       + s+ ++ + +++ + e++ +++n++++ i++ ++d ++     ++   + ++  ++e+ +e++++ +++      v
  gi|386001711|ref|YP_005920010.1|  42 DYSRMTITVDGDEVVLEQVTKQLNKLINVIRVSELDpAESV---ERELAMIKVaAKKEDRSEIMQIVSVFRAkiidV 115
                                       5567789999**************************43322...333344445568899999999999988732221 PP

                               SLS 133 seddnnknskselkisal.gedradlakRlL 162
                                               s   + i+ + ++d+++   RlL
  gi|386001711|ref|YP_005920010.1| 116 --------SPRSMIIEVTgSQDKVEAMVRLL 138
                                       ........11222233220333555555555 PP

>> DUF2096  Uncharacterized protein conserved in archaea (DUF2096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.7   9.1e-05      0.18     108     166 ..      81     140 ..      58     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.1e-05
                           DUF2096 108 evprgfetirvklkkpleeerlqeiaEyegvIiefeeddv.vvvyGdkedikkaLkelse 166
                                        v r+ ++i+v  kk+ ++e++q ++ +   Ii+++  ++ ++v G ++++++ ++ l++
  gi|386001711|ref|YP_005920010.1|  81 SVERELAMIKVAAKKEDRSEIMQIVSVFRAKIIDVSPRSMiIEVTGSQDKVEAMVRLLRQ 140
                                       5678999*****************************999989*********988876665 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00028      0.56      30      73 ..      28      71 ..      18      95 .. 0.72
   2 ?    0.5   0.1      0.41   8.2e+02      46      73 ..      86     112 ..      68     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                      EEEEEEEXXSSTT.SXEEEEEEEEESSHHHHHHHHHHHHHHHHHS CS
                    Saccharop_dh_N 30 fevlefevGkkkk.dtSyaelevsaedeevLeeileeltelgael 73
                                      f++ +++vG++ + d S  +++v ++ e vLe++ ++l++l + +
  gi|386001711|ref|YP_005920010.1| 28 FNIDSLTVGATDNpDYSRMTITVDGD-EVVLEQVTKQLNKLINVI 71
                                      99*******87542666666666664.589*******99984433 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.41
                                       EEEEEEEESSHHHHHHHHHHHHHHHHHS CS
                    Saccharop_dh_N  46 yaelevsaedeevLeeileeltelgael 73 
                                        a ++v a++e+  +ei++ ++ + a++
  gi|386001711|ref|YP_005920010.1|  86 LAMIKVAAKKED-RSEIMQIVSVFRAKI 112
                                       456666666543.355655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1138.81
//
Query:       gi|386001712|ref|YP_005920011.1|  [L=331]
Description: ketol-acid reductoisomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-75  250.1   0.1      9e-75  249.8   0.1    1.1  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    1.7e-61  206.7   0.4    2.3e-61  206.3   0.4    1.2  1  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    6.4e-08   32.2   0.0    1.1e-07   31.4   0.0    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.7e-06   28.5   0.0      3e-06   27.7   0.0    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    5.1e-06   26.7   0.0    8.7e-06   26.0   0.0    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      2e-05   24.7   0.0    3.5e-05   23.9   0.0    1.3  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      0.008   15.0   0.0     0.0093   14.7   0.0    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.022   15.6   0.0      0.037   14.8   0.0    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.047   14.0   0.2       0.27   11.6   0.2    2.2  1  Mur_ligase      Mur ligase family, catalytic domain
       0.07   13.0   0.0       0.13   12.1   0.0    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.12   12.7   0.1       0.29   11.5   0.1    1.6  1  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.8   0.1   5.5e-78     9e-75       1     165 []      14     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.8 bits;  conditional E-value: 5.5e-78
                                       HHHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHH CS
                              IlvN   1 llkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevy 77 
                                       +lkgk+ia+iGyGsqGhaqa+nlrdsgl+vv +   gsk +k+A+++g++v+t+ ea+k+ad+++il+PDel+ ++y
  gi|386001712|ref|YP_005920011.1|  14 VLKGKTIAIIGYGSQGHAQAQNLRDSGLEVVAADVPGSKAWKRAEADGIRVTTTPEAAKEADLIHILLPDELHPKIY 90 
                                       59*************************************************************************** PP

                                       HHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHH CS
                              IlvN  78 eeeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelala 154
                                       +++iep+l+eg+al f+hGfnihf++i pp++vdv++vAPkgpG+lvr++y eg G+p+l+a++qd +g+a+++a+a
  gi|386001712|ref|YP_005920011.1|  91 KKDIEPHLEEGNALGFSHGFNIHFSQIIPPENVDVYMVAPKGPGDLVRRTYVEGIGTPCLVAIQQDFTGTAFDKAMA 167
                                       ***************************************************************************** PP

                                       HHHHTTHHHH- CS
                              IlvN 155 yakgiGatraG 165
                                       yakgiG+traG
  gi|386001712|ref|YP_005920011.1| 168 YAKGIGGTRAG 178
                                       **********9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.3   0.4   1.4e-64   2.3e-61       1     144 []     184     327 ..     184     327 .. 1.00

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 1.4e-64
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       F+eEtetDlfgEq+ LcGgv+el++a Fetl++aGy+pe+Ayfe++helklivdliyegG+ +m++++S+taeyg+l
  gi|386001712|ref|YP_005920011.1| 184 FQEETETDLFGEQVDLCGGVTELIKASFETLIRAGYQPEIAYFETCHELKLIVDLIYEGGLMRMWDNVSNTAEYGGL 260
                                       9**************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                       t+g+r+i+e+++e+m eil+eiq+Gefa+e+i+e +ag p  ++l++ e+eh ie+vg++lra+mpw
  gi|386001712|ref|YP_005920011.1| 261 TRGDRIINEQSREAMWEILTEIQTGEFAREWILESQAGLPVKRALERMESEHLIEEVGAELRAMMPW 327
                                       *****************************************************************98 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   6.5e-11   1.1e-07      34     100 ..      15      82 ..       5      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 6.5e-11
                                       GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlp 100
                                       l+gkt++iiG+G+ G+a a+ l+  g++v+a d+  +k   ++e+ g+++++  e+ +e+D + + lp
  gi|386001712|ref|YP_005920011.1|  15 LKGKTIAIIGYGSQGHAQAQNLRDSGLEVVAADVPGSKAWkRAEADGIRVTTTPEAAKEADLIHILLP 82 
                                       89********************************999766789999******************9999 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.8e-09     3e-06       1      77 [.      19      89 ..      19     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.8e-09
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveev 77
                                      +i+iiG+G++g+a a++l  +g    e+v a++   +ka + ae+ g++vt+  + eaa+ead + + ++ e ++++
  gi|386001712|ref|YP_005920011.1| 19 TIAIIGYGSQGHAQAQNLRDSG---LEVV-AADVPGSKAWKRAEADGIRVTT--TPEAAKEADLIHILLPDELHPKI 89
                                      69********************...****.6588888999999999*9*999..99********9988887776666 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.3e-09   8.7e-06       1      85 [.      19     103 ..      19     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.3e-09
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHC CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegll 77 
                                       +i++iG G  G+  a+nl ++g +v++ ++  +k+ + +++    +++  e+++++d++ ++++++ + +   +++ 
  gi|386001712|ref|YP_005920011.1|  19 TIAIIGYGSQGHAQAQNLRDSGLEVVAADVPGSKAWKRAEADGIRVTTTPEAAKEADLIHILLPDELHPKIYKKDIE 95 
                                       59***************************99888877777766666666679*************999888877899 PP

                                       CC--TT-E CS
                     NAD_binding_2  78 ealkkgdi 85 
                                       ++l++g+ 
  gi|386001712|ref|YP_005920011.1|  96 PHLEEGNA 103
                                       99998875 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.2e-08   3.5e-05      20      82 ..      14      77 ..       8      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                                      --TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHH.HHCTT-EE--HHHCTTT-SEE CS
                     AdoHcyase_NAD 20 llaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalq.aameGfevvtleevvkkadiv 82
                                      +l Gk++ ++GyG  G   a+ l+  G  v+ ++v    a + a  +G +v+t  e++k+ad++
  gi|386001712|ref|YP_005920011.1| 14 VLKGKTIAIIGYGSQGHAQAQNLRDSGLEVVAADVPGSKAWKrAEADGIRVTTTPEAAKEADLI 77
                                      689*********************************9999753889***************986 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.7e-06    0.0093     269     316 ..      14      59 ..       4     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                                       HHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHH CS
                    Oxidored_nitro 269 ylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlka 316
                                       +l+gk++ai+g++++ +a a+ l++ G evvaa ++ + ++++ r++a
  gi|386001712|ref|YP_005920011.1|  14 VLKGKTIAIIGYGSQGHAQAQNLRDSGLEVVAADVPGS-KAWK-RAEA 59 
                                       689*****************************998877.4433.3333 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-05     0.037       2      81 ..      19      92 ..      18      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHH CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelak 80
                                       +aiiG+G  g  ++++l++s  ++evva+  p++++ ++ ae+ g+ + +  e+ ++   +d++ +  p ++h ++ k
  gi|386001712|ref|YP_005920011.1| 19 TIAIIGYGSQGHAQAQNLRDS--GLEVVAADVPGSKAWKR-AEADGIRVTTTPEAAKE---ADLIHILLPDELHPKIYK 91
                                      589****98887777666666..99999887777777776.7******9999998888...9************99987 PP

                                      H CS
                      GFO_IDH_MocA 81 a 81
                                      +
  gi|386001712|ref|YP_005920011.1| 92 K 92
                                      6 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00017      0.27      19      80 ..      20      71 ..      17     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                      HHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHHH CS
                        Mur_ligase 19 lalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesraeaL 80
                                      +a+ Gy  +G+  +++l+++G ++v ++ ++           +  ++a + gi+v  ++ea 
  gi|386001712|ref|YP_005920011.1| 20 IAIIGYGSQGHAQAQNLRDSGLEVVAADVPG----------SKAWKRAEADGIRVTTTPEAA 71
                                      6788999*********************999..........888999999999998888875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     8e-05      0.13       1      37 [.      19      55 ..      19      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealek 37
                                      ++a+iG G  G+  a+ +  +gleVv  d+  +++ k
  gi|386001712|ref|YP_005920011.1| 19 TIAIIGYGSQGHAQAQNLRDSGLEVVAADVPGSKAWK 55
                                      69***************************95544333 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.29      40      82 ..      26      69 ..      16      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                      SCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES.- CS
                     Nitro_FeMo-Co 40 gggggklaqllaeegvdvvivgkiGpralakleaagievykg.a 82
                                      g++g + aq l ++g +vv +   G +a+++ ea gi+v ++ +
  gi|386001712|ref|YP_005920011.1| 26 GSQGHAQAQNLRDSGLEVVAADVPGSKAWKRAEADGIRVTTTpE 69
                                      5678888999*****************************99743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2445.21
//
Query:       gi|386001713|ref|YP_005920012.1|  [L=115]
Description: hypothetical protein Mhar_1020 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.5   0.4    2.5e-12   46.8   0.4    1.3  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.4   1.4e-16   2.5e-12       1      48 [.      58     105 ..      58     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.4e-16
                           DUF2283   1 kitYDpeaDalYIyl.segpveeseevdddiilDfDedGrlvGIEiLnA 48 
                                       +++YD+eaD+lY+++  +++  +se  ddd+i++  e+G++vG+++Ln+
  gi|386001713|ref|YP_005920012.1|  58 WVDYDEEADVLYVNFkRPSRADDSELTDDDVIIRR-EKGEVVGMTFLNV 105
                                       79*************999999999999********.***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 908.18
//
Query:       gi|386001714|ref|YP_005920013.1|  [L=334]
Description: S-layer protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-90  302.6   1.9      1e-44  152.5   0.5    2.0  2  S-layer   S-layer protein
     0.0086   16.2   0.1        4.2    7.6   0.1    2.6  2  PrcB_C    PrcB C-terminal
  ------ inclusion threshold ------
       0.13   12.4   0.0        1.1    9.4   0.0    2.0  2  CIF       Cycle inhibiting factor (CIF)
       0.15   12.5   0.0        1.7    9.2   0.0    2.6  2  DUF4981   Domain of unknown function(DUF4981)


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 !  149.8   0.0   1.6e-47   7.1e-44      60     215 ..       3     167 ..       1     170 [. 0.94
   2 !  152.5   0.5   2.3e-48     1e-44      57     211 ..     172     334 .]     168     334 .] 0.94

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 1.6e-47
                           S-layer  60 efefeewgsYevigflaekYfagy.dnsa...etsddvsllsdekLskvlidedeektlksgssleLeegYeleikq 132
                                        f++eewgs+ ++ + +e+ fa y +      e+s d++l +++ Ls+vlide e+++++sg  leLeegYel i++
  gi|386001714|ref|YP_005920013.1|   3 PFQLEEWGSFWTVDLQGERLFAAYaE-VGhlwESSIDTDLTKSGRLSRVLIDEVEDRVFTSGMPLELEEGYELAIQS 78 
                                       6999********************53.4346788999**************************************** PP

                           S-layer 133 iDvdgdkvwleLtkdgeevdskvissska.....dstyvyekdlgd.eddvviiavhvdevfrgtedslvviegifq 203
                                       iD+dg+kv+++L++ g+ vds+v+++s++     d+ty+y+ dlg+ e+dvviiavh+++ frg++ +l++++gi+q
  gi|386001714|ref|YP_005920013.1|  79 IDLDGNKVFVQLMRGGAVVDSAVVEPSREgadldDRTYTYSVDLGGaEEDVVIIAVHFKNSFRGADRDLATVDGIWQ 155
                                       **************************99899*************97368**************************** PP

                           S-layer 204 isddvleieegd 215
                                       isd+++ei eg+
  gi|386001714|ref|YP_005920013.1| 156 ISDTPIEIGEGE 167
                                       ********9986 PP

  == domain 2  score: 152.5 bits;  conditional E-value: 2.3e-48
                           S-layer  57 vekefefeewgsYevigflaekYfagydnsa...etsddvsllsdekLskvlidedeektlksgssleLeegYelei 130
                                       +  +fe ++wg++ ++   +e Yfa y ++     +s++ +l++++ Ls+++ d+ +e+t++sg+sleLeegYel i
  gi|386001714|ref|YP_005920013.1| 172 QWRNFERDDWGHFYTLESDGEDYFAAYADDGclyDVSKEPDLVNHNLLSRIIYDDGQERTFTSGTSLELEEGYELAI 248
                                       5678***********************66555788999*************************************** PP

                           S-layer 131 kqiDvdgdkvwleLtkdgeevdskvissska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegif 202
                                       ++iD+dg+kv++eL kdg+ vd ++i++        ++ty+y++d+g+++dvv+iavh++  frg++++l++i+gi+
  gi|386001714|ref|YP_005920013.1| 249 ESIDLDGNKVYVELLKDGRVVDAEIINAGVLgaaaeEKTYTYTRDMGEAEDVVTIAVHFERSFRGADQDLATIDGIW 325
                                       ***************************965588899***************************************** PP

                           S-layer 203 qisddvlei 211
                                       qis++++++
  gi|386001714|ref|YP_005920013.1| 326 QISETPISV 334
                                       ****99876 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0037        16      13      33 ..      70      90 ..      67     104 .. 0.90
   2 !    7.6   0.1   0.00093       4.2      13      33 ..     242     262 ..     240     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0037
                            PrcB_C 13 gGYsievdkvyetenaiyvkt 33
                                      +GY + ++++ +++n++ v++
  gi|386001714|ref|YP_005920013.1| 70 EGYELAIQSIDLDGNKVFVQL 90
                                      7******************97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00093
                            PrcB_C  13 gGYsievdkvyetenaiyvkt 33 
                                       +GY + ++++ +++n++yv++
  gi|386001714|ref|YP_005920013.1| 242 EGYELAIESIDLDGNKVYVEL 262
                                       7******************86 PP

>> CIF  Cycle inhibiting factor (CIF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.14   6.1e+02      64     117 ..      75     130 ..      58     145 .. 0.56
   2 ?    9.4   0.0   0.00024       1.1      60     112 ..     243     297 ..     231     318 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                                       HHHHCCS-TTSEEEEEEEETTTTEEEEEEE---TT...--EEEEE--B-SSSSS--B CS
                               CIF  64 aesvdtldsaknyvvlvndrrlghkflidlpaldq...ervayiiqsdlgqgalpal 117
                                       a +  +ld +k +v l+  + +    +++ p+ +    +  +y +  dlg+     +
  gi|386001714|ref|YP_005920013.1|  75 AIQSIDLDGNKVFVQLMRGGAVVDSAVVE-PSREGadlDDRTYTYSVDLGGAEEDVV 130
                                       44444555566666666555555555554.222211225556666677766544443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00024
                                       CCHHHHHHCCS-TTSEEEEEEEETTTTEEEEEEE---TT..--EEEEE--B-SSS CS
                               CIF  60 ntefaesvdtldsaknyvvlvndrrlghkflidlpaldq..ervayiiqsdlgqg 112
                                       + e+a +  +ld +k yv l++d+r+    +i+   l    e  +y +  d+g+ 
  gi|386001714|ref|YP_005920013.1| 243 GYELAIESIDLDGNKVYVELLKDGRVVDAEIINAGVLGAaaEEKTYTYTRDMGEA 297
                                       55667666679*******************999776654448999*******975 PP

>> DUF4981  Domain of unknown function(DUF4981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.3   1.4e+03      10      39 ..      79     104 ..      69     131 .. 0.78
   2 ?    9.2   0.0   0.00038       1.7      10      53 ..     251     296 ..     241     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                                       --GGGEEEEEEEEETTEEEEEEEEEE---T CS
                           DUF4981  10 tdlsdldlswellkdGkvvasgelelpvaP 39 
                                       +dl+  ++ ++l++ G vv+s  +e    P
  gi|386001714|ref|YP_005920013.1|  79 IDLDGNKVFVQLMRGGAVVDSAVVE----P 104
                                       6888888889999999888875443....4 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00038
                                       --GGGEEEEEEEEETTEEEEEEEEEE-..--TT-EEEEE--S.--- CS
                           DUF4981  10 tdlsdldlswellkdGkvvasgelelp..vaPgesatvtlpetkea 53 
                                       +dl+  ++ +ellkdG+vv+ + ++     a+ e++t+t   +  +
  gi|386001714|ref|YP_005920013.1| 251 IDLDGNKVYVELLKDGRVVDAEIINAGvlGAAAEEKTYTYTRDMGE 296
                                       699999**************99999888656688888886543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2509.69
//
Query:       gi|386001715|ref|YP_005920014.1|  [L=95]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-16   57.6   0.1    1.1e-15   57.5   0.1    1.0  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    3.5e-14   52.9   0.3      4e-14   52.7   0.3    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.13   12.1   0.1    1.3  1  LpxI_N        LpxI N-terminal domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1   1.8e-19   1.1e-15       1      86 [.      10      93 ..      10      95 .] 0.96

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.8e-19
                                      -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHH CS
                           Polbeta  1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllye 79
                                      ek+ ++l+++ +++ a  FGS+++g+++eeSD+D+ v ++ +++l +   l+ ele++ + ++vD++++ + +pll+++
  gi|386001715|ref|YP_005920014.1| 10 EKVLAVLRRN-DVKRAAFFGSIVRGEMTEESDVDILVEFEGRKSLMDLSGLKIELEEA-IDREVDVLTYASLHPLLKER 86
                                      789999****.***********************************************.99****************** PP

                                      HHHS-EE CS
                           Polbeta 80 ilkegkl 86
                                      il+e   
  gi|386001715|ref|YP_005920014.1| 87 ILNEQVP 93
                                      **98765 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.3   6.7e-18     4e-14       3      91 ..      11      90 ..       5      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 6.7e-18
                                      HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                      NTP_transf_2  3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled 81
                                      k+l  l++++ v++++ fGS +rG+++++SD+D+lv ++         ++l +l+    +lee   +evd++t+++l+ 
  gi|386001715|ref|YP_005920014.1| 11 KVLAVLRRND-VKRAAFFGSIVRGEMTEESDVDILVEFEGR-------KSLMDLSGLKIELEEAIDREVDVLTYASLH- 80
                                      4455555555.******************************.......66899*************************. PP

                                      CTEEEEEECE CS
                      NTP_transf_2 82 pllvksilee 91
                                      pll++ il+e
  gi|386001715|ref|YP_005920014.1| 81 PLLKERILNE 90
                                      ***9999987 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.2e-05      0.13      55      92 ..      10      52 ..       4      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                            LpxI_N 55 gklikaLkregvtevvmaGkvekpkll.....dlrpDlralkl 92
                                      +k+++ L+r++v+++ + G++ + ++      d++ ++++ k 
  gi|386001715|ref|YP_005920014.1| 10 EKVLAVLRRNDVKRAAFFGSIVRGEMTeesdvDILVEFEGRKS 52
                                      6899*********************995544444444454444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 728.11
//
Query:       gi|386001716|ref|YP_005920015.1|  [L=113]
Description: hypothetical protein Mhar_1023 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-27   93.5   0.2    8.9e-27   93.3   0.2    1.0  1  DUF86     Protein of unknown function DUF86
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.02   14.8   0.0    1.2  1  DUF1706   Protein of unknown function (DUF1706)
      0.067   12.6   0.0      0.067   12.6   0.0    1.0  1  A_deamin  Adenosine-deaminase (editase) domain


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.2   1.5e-30   8.9e-27       1     119 []      12     108 ..      12     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 1.5e-30
                                       HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHH CS
                             DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepee 77 
                                       i+e++++++ + +++++eef +++  +da++r +++igEa+++++++                      ++ ++pe+
  gi|386001716|ref|YP_005920015.1|  12 ILESIDLIEGYSAGKTREEFVESRQLQDAIIRRIEIIGEAVKNLPED----------------------FKRNHPEI 66 
                                       6899*******************************************......................******** PP

                                       HHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHHH CS
                             DUF86  78 pwrkmiglRNrLvHgYlgidpeivwsiikenlpdleeflesi 119
                                        w+k++g+R++L+H+Y+g+d+   w++i+ ++pdl++++ +i
  gi|386001716|ref|YP_005920015.1|  67 AWQKVAGMRDVLIHQYFGVDLALTWDVIQSDIPDLKRYISRI 108
                                       *************************************99875 PP

>> DUF1706  Protein of unknown function (DUF1706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.3e-06      0.02       8      65 ..      35      92 ..      29     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-06
                                      HHHHHHHHHHHHHHHHTTTTS-GGGT...T--BTTCSS-HHHHHHHHHHHHHHHHHHH CS
                           DUF1706  8 eeLleaieknfekLiklidsipeeekkapeeavkgrdktvadvlayllgWhklllkWl 65
                                       +L +ai +++e + + ++++pe+ k+++ e +++    ++dvl++++   +l l+W 
  gi|386001716|ref|YP_005920015.1| 35 RQLQDAIIRRIEIIGEAVKNLPEDFKRNHPEIAWQKVAGMRDVLIHQYFGVDLALTWD 92
                                      5899999999999*************99989*****************9999999996 PP

>> A_deamin  Adenosine-deaminase (editase) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.067     181     219 ..      29      71 ..       7     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                          A_deamin 181 kslysqealeravykRl....alvsklpkpyrvnkpllsllse 219
                                       +++ ++++l+ a+++R+    + v++lp+ +++n+p++   + 
  gi|386001716|ref|YP_005920015.1|  29 EEFVESRQLQDAIIRRIeiigEAVKNLPEDFKRNHPEIAWQKV 71 
                                       3456679*********9999999***************55443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 861.49
//
Query:       gi|386001717|ref|YP_005920016.1|  [L=82]
Description: hypothetical protein Mhar_1024 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-13   49.9   0.4    3.6e-13   49.5   0.4    1.1  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.4     2e-17   3.6e-13       1      48 [.      25      72 ..      25      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2e-17
                           DUF2283  1 kitYDpeaDalYIyl.segpveeseevdddiilDfDedGrlvGIEiLnA 48
                                      +++YD+eaD+lY+++  +++  +se  dddii++  e+G++vG+++Ln+
  gi|386001717|ref|YP_005920016.1| 25 WVEYDEEADVLYVNFkRPSRADDSELTDDDIIIRR-EKGEVVGMTFLNV 72
                                      89*************999999999999********.***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 616.79
//
Query:       gi|386001718|ref|YP_005920017.1|  [L=103]
Description: hypothetical protein Mhar_1025 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.8   0.1    0.00021   21.6   0.1    1.1  1  PBECR2    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
     0.0061   16.9   0.2      0.014   15.8   0.1    1.6  2  DUF4258   Domain of unknown function (DUF4258)
  ------ inclusion threshold ------
      0.049   14.3   0.0      0.067   13.9   0.0    1.2  1  PBECR1    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1


Domain annotation for each model (and alignments):
>> PBECR2  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   3.4e-08   0.00021      25     111 ..      12      95 ..       2     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.4e-08
                            PBECR2  25 vviseelfehlaegekrgrerylplLaetledPdeIwldeeeskklrrrylkrfkd.rglfavfelgedggwsgita 100
                                       + + +e+  h+ e +  + + +++ + et+edPd I+++e  +    +   k+++  ++l++v++  +++g ++ita
  gi|386001718|ref|YP_005920017.1|  12 IRLPDERWLHIIESH-TEMAGLYSDVLETVEDPDAIYEAESGE----LLATKEVQSdKYLVVVYKEVSREGGFVITA 83 
                                       555666666776566.566777788889************994....899999966577777777666767777777 PP

                            PBECR2 101 f.pkdenylekq 111
                                       f + ++++le++
  gi|386001718|ref|YP_005920017.1|  84 FlTRRSKQLERR 95 
                                       757799999996 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.8   4.8e+03      39      48 ..      14      23 ..       6      26 .. 0.74
   2 !   15.8   0.1   2.3e-06     0.014      17      62 ..      34      84 ..      32      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.8
                           DUF4258 39 tsegrplhvv 48
                                       +++r+lh++
  gi|386001718|ref|YP_005920017.1| 14 LPDERWLHII 23
                                      5678888875 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.3e-06
                           DUF4258 17 edieevlenGe.iieeys..lvlgktsegrplhvvvapdedpv..vviTvy 62
                                      +d++e++e ++ i e+ s  l++ k+   +   vvv+ + +    +viT++
  gi|386001718|ref|YP_005920017.1| 34 SDVLETVEDPDaIYEAESgeLLATKEVQSDKYLVVVYKEVSREggFVITAF 84
                                      79*********7777777**777777777666666666666666*****97 PP

>> PBECR1  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.067      30     106 ..      21      89 ..      16      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                            PBECR1  30 hilekhledfkefkekaeklinkleeiiekgk.vkeeeevntielkkee.eeykvglskgfkgkgdnkwvitayekk 104
                                       hi+e+h+        +++ l +++ e++e+   + e e+ + +++k+ + ++y v++ k+ +   +  +vita+ ++
  gi|386001718|ref|YP_005920017.1|  21 HIIESHT--------EMAGLYSDVLETVEDPDaIYEAESGELLATKEVQsDKYLVVVYKEVS--REGGFVITAFLTR 87 
                                       7888884........6689999999****99988888888888877754499*******755..5789******887 PP

                            PBECR1 105 ke 106
                                       ++
  gi|386001718|ref|YP_005920017.1|  88 RS 89 
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 666.63
//
Query:       gi|386001719|ref|YP_005920018.1|  [L=115]
Description: hypothetical protein Mhar_1026 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-25   87.3   0.1    7.6e-25   87.1   0.1    1.0  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.1   4.3e-29   7.6e-25       2     118 ..      13     107 ..      12     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 4.3e-29
                                       HHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHH CS
                             DUF86   2 kealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeep 78 
                                       + +++kl +++e+ld++ f sde+  dav +nl v+gEaa++++ h                      +++++pe++
  gi|386001719|ref|YP_005920018.1|  13 QISCRKLLRYAENLDFDLFASDEVFHDAVVYNLVVLGEAAKQVPPH----------------------IRKRYPEVQ 67 
                                       66799*****************************************......................********* PP

                                       HHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                             DUF86  79 wrkmiglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                       wrk++glR++ vH+Y+++d ei+w+i++++++ l++ l +
  gi|386001719|ref|YP_005920018.1|  68 WRKIAGLRDISVHRYFSLDEEIIWDILQNEVRPLLDKLDQ 107
                                       *******************************999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 744.77
//
Query:       gi|386001720|ref|YP_005920019.1|  [L=83]
Description: hypothetical protein Mhar_1027 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-15   57.7   0.0    1.2e-15   57.5   0.0    1.0  1  NTP_transf_2  Nucleotidyltransferase domain
    1.1e-11   44.6   0.0    1.3e-11   44.5   0.0    1.0  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   1.3e-19   1.2e-15      14      94 ..       3      75 ..       1      76 [. 0.94

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.3e-19
                                      TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEEEEEECEE CS
                      NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpllvksileer 92
                                      v+++++fGS+ar++a+++SD+D+lv ++ +        + + ++   +fle llg++vdlvtr +++ p+l+  i++e+
  gi|386001720|ref|YP_005920019.1|  3 VKSLAIFGSTARDEAGPESDVDVLVEFSGP-------ATFNGYMDLKFFLEDLLGRPVDLVTRRSIR-PGLKARIESEA 73
                                      7899**************************.......56799*************************.*****999999 PP

                                      EH CS
                      NTP_transf_2 93 pl 94
                                      ++
  gi|386001720|ref|YP_005920019.1| 74 RY 75
                                      87 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   1.4e-15   1.3e-11      13      84 ..       3      73 ..       1      78 [. 0.94

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.4e-15
                                      HHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS- CS
                           Polbeta 13 ielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkeg 84
                                      ++ + +FGS a+++a +eSD+D+ v ++   +++ +++l+  led+ lg+ vDlv+ ++ +p l+++i +e 
  gi|386001720|ref|YP_005920019.1|  3 VKSLAIFGSTARDEAGPESDVDVLVEFSGPATFNGYMDLKFFLEDL-LGRPVDLVTRRSIRPGLKARIESEA 73
                                      78899*****************************************.9***********99*****998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       130  (0.00725082); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 505.85
//
Query:       gi|386001721|ref|YP_005920020.1|  [L=91]
Description: Toxin-antitoxin system, antitoxin component, HicB family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-05   25.2   0.0    1.6e-05   25.0   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     9e-10   1.6e-05       9      57 ..      20      68 ..      15      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9e-10
                   HicB_lk_antitox  9 edsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      +d+ y  +vP+lpG++  g t+ee  ++  e+ie ++ + +++g  ip 
  gi|386001721|ref|YP_005920020.1| 20 DDDPYFASVPELPGVWASGRTVEECRKELIEVIEEWIVARLQRGLPIPP 68
                                      45678899***********************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 701.37
//
Query:       gi|386001722|ref|YP_005920021.1|  [L=69]
Description: hypothetical protein Mhar_1029 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 479.41
//
Query:       gi|386001723|ref|YP_005920022.1|  [L=252]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-16   60.0   0.0    4.6e-16   59.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.4e-13   51.3   0.0    2.1e-13   50.7   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.1e-10   39.7   0.0    1.1e-09   38.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.4e-08   34.7   0.0    1.9e-08   34.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      1e-06   28.6   0.0    1.4e-06   28.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.9e-05   24.1   0.0    2.7e-05   23.6   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00029   20.4   0.0    0.00053   19.6   0.0    1.4  1  MTS              Methyltransferase small domain
    0.00036   20.2   0.0    0.00052   19.7   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    0.00063   19.2   0.0    0.00091   18.7   0.0    1.2  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.017   14.6   0.0        3.8    6.9   0.0    2.3  2  CheR             CheR methyltransferase, SAM binding domain
       0.19   11.3   0.0        0.3   10.7   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   2.8e-19   4.6e-16       2      97 .]      48     136 ..      47     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.8e-19
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG.S CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh.l 77 
                                       L lGcG G + + + +++    vtgvDise+mle+ar+ +    ++v++++g+++dl++e+ +fD+vv+  ++ + +
  gi|386001723|ref|YP_005920022.1|  48 LHLGCGAGMNDFTFKREF---YVTGVDISEGMLEIARKLN----PEVRYIRGEMRDLSLEE-TFDAVVIPDSIGYmT 116
                                       789************996...9****************99....9*************986.*******98899978 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +++dle+a++ +  +LkpgG
  gi|386001723|ref|YP_005920022.1| 117 TERDLERAISTANGHLKPGG 136
                                       899****************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.3e-16   2.1e-13       1      96 []      48     140 ..      48     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.3e-16
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-... CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv... 74 
                                       L++GcG+G +   +++ +  v+gvD+s+ ml++a++ ++e    v+++++++++l +e+ +fD+vv+  ++ ++   
  gi|386001723|ref|YP_005920022.1|  48 LHLGCGAGMNDFTFKREF-YVTGVDISEGMLEIARKLNPE----VRYIRGEMRDLSLEE-TFDAVVIPDSIGYMtte 118
                                       789************888.9**************999888....669**********98.***********999888 PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                        d+e+a++ +   LkpgG+l+i
  gi|386001723|ref|YP_005920022.1| 119 RDLERAISTANGHLKPGGVLLI 140
                                       8******************986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   6.8e-13   1.1e-09       1      99 []      48     138 ..      48     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 6.8e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG G + + + ++     +tgvDis+ ++e a++   + +      ++ e +dl   + +++fD+vv+ + + 
  gi|386001723|ref|YP_005920022.1|  48 LHLGCGAGMNDFTFKRE---FYVTGVDISEGMLEIARKLNPEVR-----YIRGEMRDL---SLEETFDAVVIPDSIG 113
                                       789*******9999999...8999*********44444433333.....455555554...4446************ PP

                   Methyltransf_12  78 hl...kdirevldnirklLkpgGrl 99 
                                       ++   +d++++++ +  +LkpgG+l
  gi|386001723|ref|YP_005920022.1| 114 YMtteRDLERAISTANGHLKPGGVL 138
                                       ***********************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.2e-11   1.9e-08       3     162 ..      26     222 ..      24     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-11
                   Methyltransf_23   3 aqreeelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae....kakkaqkdqfdeqe 75 
                                       +q+ e++++++   +  + + + +L +GcG G +   ++++ f vtgvD+s+ + eia+    + +  +     e+ 
  gi|386001723|ref|YP_005920022.1|  26 RQETEYFCELIRSNS--RIEVKTLLHLGCGAGMNDFTFKRE-FYVTGVDISEGMLEIARklnpEVRYIRG----EMR 95 
                                       566788888888888..89999**********777777666.78*************9744332232222....334 PP

                   Methyltransf_23  76 aaepqgkfdlIvlrevlehvp...dppellrqiatllkpgGylllseplaslkedrllld................. 132
                                       +   +++fd +v  ++++ +    d+++++++++ +lkpgG+ll+    +++  ++ + +                 
  gi|386001723|ref|YP_005920022.1|  96 DLSLEETFDAVVIPDSIGYMTterDLERAISTANGHLKPGGVLLIVALVSEDFMENNFAYagsagdlevtifennqr 172
                                       666889**************98889*********************9999987776666644444444444444444 PP

                   Methyltransf_23 133 ...................wlylvpagrhi.sffsarslkelleeaGlev 162
                                                           +++v+ +rh   +f ++++  ll + Glev
  gi|386001723|ref|YP_005920022.1| 173 cwsnpamyeavlvylirrqGELEVITDRHEqGLFPSTAWFSLLADLGLEV 222
                                       43333333333333333333334555555545555566666666666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   8.4e-10   1.4e-06       6     113 ..      46     144 ..      43     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.4e-10
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       ++l lGCG+G   f + +e +    v+G+Dise ++e Ar+     +  +v+  +g++ +l+  le e+fD ++  +
  gi|386001723|ref|YP_005920022.1|  46 TLLHLGCGAGMNDFTFKREFY----VTGVDISEGMLEIARKL----NP-EVRYIRGEMRDLS--LE-ETFDAVVIPD 110
                                       6789******99999997765....***************94....44.69999********..78.9*******99 PP

                   Methyltransf_31  83 vl...naladpdkileeiervlkpggilliedpr 113
                                        +    +  d++ ++  +   lkpgg+lli    
  gi|386001723|ref|YP_005920022.1| 111 SIgymTTERDLERAISTANGHLKPGGVLLIVALV 144
                                       998989999*******************998776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.7e-08   2.7e-05      47     166 ..      43     155 ..      30     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.7e-08
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE. CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv. 122
                                       + +++l + +G+g   f++     +++ v+++Di+e mL++++k        +++++ ++  +L  e ++fD v + 
  gi|386001723|ref|YP_005920022.1|  43 EVKTLLHLGCGAGMNDFTFK----REFYVTGVDISEGMLEIARKL-----NPEVRYIRGEMRDLSLE-ETFDAVVIp 109
                                       55678899999987777664....57899************9864.....3479**********986.69****994 PP

                                       .ES-GG.G-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHH CS
                   Ubie_methyltran 123 .sfGlr.nvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqay 166
                                        s G      D ++a+ +a   lkpGG l+++ +        ++ay
  gi|386001723|ref|YP_005920022.1| 110 dSIGYMtTERDLERAISTANGHLKPGGVLLIVALVSEDFMENNFAY 155
                                       4455430345999****************99987666666666666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.2e-07   0.00053      31     139 ..      43     142 ..      20     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                       + +++l lGcGaG+   ++++   e  vt vd++   le+a++     + ev+++  ++ +   e+ fd++v   P 
  gi|386001723|ref|YP_005920022.1|  43 EVKTLLHLGCGAGMNDFTFKR---EFYVTGVDISEGMLEIARK----LNPEVRYIRGEMRDLSLEETFDAVVI--PD 110
                                       4467899******99888877...5668************986....4667889999999988899******9..88 PP

                                       TTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEE CS
                               MTS 108 hagkatelavaeeliaeAkeaLkegGeLliVa 139
                                         g  t+++  e+ i +A+ +Lk+gG LliVa
  gi|386001723|ref|YP_005920022.1| 111 SIGYMTTERDLERAISTANGHLKPGGVLLIVA 142
                                       8899999999*********************8 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.2e-07   0.00052      38     143 ..      38     139 ..      11     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.2e-07
                              NodS  38 slaqgsiadalevGcaaGa..lterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivv 112
                                       s +  ++   l +Gc aG   +t +   y   +t vd+ e  ++ ar+     +++ +i  +++ +s++e fd +v+
  gi|386001723|ref|YP_005920022.1|  38 SNSRIEVKTLLHLGCGAGMndFTFKREFY---VTGVDISEGMLEIARKL---NPEVRYIRGEMRDLSLEETFDAVVI 108
                                       3445567899*******963366666665...68999999999998864...368********************** PP

                              NodS 113 aevlyyiedvaelraavrnlvsllapdgqlv 143
                                        + + y++   +l  a+      l+p+g l+
  gi|386001723|ref|YP_005920022.1| 109 PDSIGYMTTERDLERAISTANGHLKPGGVLL 139
                                       ******************9999999999876 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.6e-07   0.00091      17     141 ..      30     149 ..      23     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                                       ---HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---- CS
                              TehB  17 athsevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakld 93 
                                       +   e++ +   ++    l lgcg g n + ++   + vt +d  e  ++    i+ k n + ++    ++ +++l+
  gi|386001723|ref|YP_005920022.1|  30 EYFCELIRSNSRIEVKTLLHLGCGAGMNDFTFK-REFYVTGVDISEGMLE----IARKLNPE-VRYIRGEMRDLSLE 100
                                       5566777777777778889*********97776.5688*****9887554....55555555.666667888899** PP

                                       S-EEEEEEESSGGGS-GGG.HHHHHHHHHHTEEEEEEEEEEEEB--SSS CS
                              TehB  94 erydfilstvvlmfleaer.ipsiienmqectkvggynlivaamstddv 141
                                       e +d ++    + ++ +er + + i+  + + k+gg  liva +s d +
  gi|386001723|ref|YP_005920022.1| 101 ETFDAVVIPDSIGYMTTERdLERAISTANGHLKPGGVLLIVALVSEDFM 149
                                       ****99876666665554438999****************998876644 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0069        11      63      83 ..      63      83 ..      30      92 .. 0.88
   2 ?    6.9   0.0    0.0023       3.8     131     173 ..      97     140 ..      85     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0069
                                      S-EEEEEEESSCHHHHHHHHT CS
                              CheR 63 lkvkilAtDidlkvlekAkag 83
                                       ++ ++++Di++ +le A+++
  gi|386001723|ref|YP_005920022.1| 63 REFYVTGVDISEGMLEIARKL 83
                                      3899**************987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0023
                                       SGGG--EEEEEE-SSGGGC-CH.HHHHHHHHHHCCEEEEEEEEE CS
                              CheR 131 ksvlgklDvifcrnvliYfdee.tqekvlerfaeklkpgglLll 173
                                        s+++ +D ++  + + Y++ e + e+ ++  + +lkpgg+Ll+
  gi|386001723|ref|YP_005920022.1|  97 LSLEETFDAVVIPDSIGYMTTErDLERAISTANGHLKPGGVLLI 140
                                       678899*************876156899**************98 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018       0.3       3      40 ..      46      82 ..      44     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                   Methyltransf_15  3 vilDlfsGaGGnviqfalvfekviaieinleklacaqh 40
                                      ++l l +GaG n  +f+++f  v +++i++  l++a +
  gi|386001723|ref|YP_005920022.1| 46 TLLHLGCGAGMNDFTFKREF-YVTGVDISEGMLEIARK 82
                                      688999**************.9*******999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1855.26
//
Query:       gi|386001724|ref|YP_005920023.1|  [L=250]
Description: Putative carbon monoxide dehydrogenase maturation factor [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.6   0.0    1.7e-14   54.0   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      1e-07   31.7   0.3    2.6e-07   30.3   0.5    1.5  2  ParA             NUBPL iron-transfer P-loop NTPase
    8.5e-07   29.0   0.2    1.7e-06   28.0   0.1    1.6  2  AAA_31           AAA domain
    1.2e-05   25.3   0.1    2.2e-05   24.4   0.1    1.4  1  APS_kinase       Adenylylsulphate kinase
    1.3e-05   24.6   0.0    7.8e-05   22.1   0.0    1.9  2  MipZ             ATPase MipZ
    2.7e-05   23.5   0.5      6e-05   22.4   0.5    1.6  1  ArsA_ATPase      Anion-transporting ATPase
    3.8e-05   23.3   0.0     0.0055   16.2   0.1    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    4.9e-05   22.9   0.1    9.1e-05   22.0   0.1    1.4  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    6.8e-05   23.1   0.2    0.00012   22.3   0.1    1.5  1  DUF87            Helicase HerA, central domain
    0.00022   20.9   0.2     0.0011   18.6   0.1    2.0  2  SRP54            SRP54-type protein, GTPase domain
    0.00022   20.5   0.1    0.00037   19.8   0.1    1.3  1  Zeta_toxin       Zeta toxin
    0.00023   20.7   0.0    0.00045   19.8   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
     0.0003   20.7   0.0     0.0022   17.8   0.0    2.0  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    0.00064   19.4   0.0     0.0021   17.7   0.0    1.7  2  AAA_25           AAA domain
     0.0015   19.0   0.0     0.0033   18.0   0.0    1.6  1  AAA_18           AAA domain
     0.0024   18.3   0.0     0.0069   16.8   0.0    1.7  2  AAA_16           AAA ATPase domain
     0.0029   17.8   0.0     0.0045   17.1   0.0    1.3  1  AAA_33           AAA domain
     0.0044   16.0   0.4       0.13   11.2   0.0    2.5  3  AAA_10           AAA-like domain
     0.0059   16.4   0.0      0.023   14.4   0.0    1.9  2  AAA_24           AAA domain
     0.0071   16.5   0.1        1.9    8.6   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0075   16.5   0.0       0.51   10.6   0.0    2.4  2  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
       0.02   15.0   0.1        5.8    7.0   0.0    2.3  2  MMR_HSR1         50S ribosome-binding GTPase
      0.022   14.1   0.0      0.036   13.4   0.0    1.3  1  ATPase           KaiC
      0.026   14.3   0.2       0.08   12.7   0.1    1.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.03   14.1   0.8        6.4    6.5   0.3    2.2  2  AAA_26           AAA domain
      0.036   13.0   0.0       0.27   10.1   0.0    2.0  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.041   13.6   0.0       0.37   10.4   0.0    2.0  2  CoaE             Dephospho-CoA kinase
      0.046   13.4   0.1        0.3   10.7   0.0    2.2  3  Thymidylate_kin  Thymidylate kinase
      0.062   13.7   0.0       0.15   12.5   0.0    1.7  1  RNA_helicase     RNA helicase
      0.082   13.2   0.0       0.17   12.2   0.0    1.5  1  AAA_22           AAA domain
      0.095   12.5   0.7        0.4   10.5   0.2    2.2  2  AAA_29           P-loop containing region of AAA domain
       0.11   12.2   0.0       0.22   11.2   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
       0.11   13.0   0.1       0.18   12.3   0.1    1.5  1  ABC_tran         ABC transporter
       0.12   12.1   0.3       0.22   11.2   0.3    1.7  1  AAA_30           AAA domain
       0.13   12.7   0.0       0.24   11.8   0.0    1.5  1  AAA              ATPase family associated with various cellul
       0.13   11.2   0.1       0.23   10.4   0.1    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
        0.2   10.7   0.1       0.85    8.6   0.1    1.9  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.29   10.2   0.3        0.7    9.0   0.0    1.7  2  G-alpha          G-protein alpha subunit


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   3.6e-17   1.7e-14       4     124 ..       5     230 ..       2     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.6e-17
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                       + +kGG+GK+t+aa La+++a+rg++Vl+vD D     l+      + + p                          
  gi|386001724|ref|YP_005920023.1|   5 VCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLH---RQLGMELPstlmdhfggkkemmgkmrrsfaggee 78 
                                       669****************************999965555...333333335779999999999************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386001724|ref|YP_005920023.1|  79 aslfdekwtfasipaeattekdgirllaigkihdfgegcacpmgalsrkfldnlavgnkemvivdteagiehfgrgi 155
                                       ***************************************************************************** PP

                                       ...............CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...............dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                                          l++ +++++kk +   k++ +vlnrvd+e +++++ e+le++      +v + ip+++
  gi|386001724|ref|YP_005920023.1| 156 eagcdailavldpsyESLLLSKKIAEISKKIN---KPLYFVLNRVDEE-RKAAMLEFLEKE------RVAAAIPEKK 222
                                       **999999999888855566888888888875...9**********99.577777888775......7999999999 PP

                                       CHCCCCHH CS
                                       xxxxxxxx RF
                              CbiA 117 avaeapar 124
                                       ++ +a   
  gi|386001724|ref|YP_005920023.1| 223 EIFRAGLA 230
                                       99888765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.5   5.5e-10   2.6e-07       8      54 ..       4      50 ..       1      68 [. 0.86
   2 ?   -2.5   0.0       5.7   2.7e+03     102     122 ..     127     147 ..     119     196 .. 0.54

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.5e-10
                              ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgve 54
                                       + gKGG GKStva+ lA ++ak+g++v ++D D   + + r lg+e
  gi|386001724|ref|YP_005920023.1|  4 LVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLHRQLGME 50
                                      568*******************************7777777666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                              ParA 102 qllkdvewgelDyLiiDlPPG 122
                                       ++l + + g+ +++i+D+  G
  gi|386001724|ref|YP_005920023.1| 127 KFLDNLAVGNKEMVIVDTEAG 147
                                       566666666666666666444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   3.7e-09   1.7e-06       9      40 ..       7      38 ..       1      69 [. 0.90
   2 ?   -2.4   0.0         8   3.8e+03     138     172 ..     157     187 ..     131     192 .. 0.53

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.7e-09
                            AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                       KGG GK+T +  la+++ak+g  vL+vD D 
  gi|386001724|ref|YP_005920023.1|  7 GKGGSGKSTVAALLAKSMAKRGFNVLVVDSDE 38
                                      6*****************************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                            AAA_31 138 vasdsviipvqaeayaleGleqllktieevkkkln 172
                                       +  d ++ ++++++ +l     l k+i e+ kk+n
  gi|386001724|ref|YP_005920023.1| 157 AGCDAILAVLDPSYESL----LLSKKIAEISKKIN 187
                                       44555555555543333....24455555555555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   4.6e-08   2.2e-05       5      52 ..       3      50 ..       1      54 [. 0.95

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.6e-08
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SS CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfs 52
                                      v++ G  gsGKst+a  l+k++ ++g +v ++d d+   gL ++Lg++
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLHRQLGME 50
                                      7889*****************************************975 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.6e-07   7.8e-05       4      48 ..       3      47 ..       1      56 [. 0.90
   2 ?    0.1   0.0      0.85     4e+02      99     157 ..     136     194 ..     124     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-07
                                      EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH CS
                              MipZ  4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl 48
                                      vl   kGGsGkst+a  +a +++k+G++v ++d d     l+r l
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLHRQL 47
                                      56667******************************9998888866 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.85
                                       H-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHCCCEEE-SSS--EEEE-HHHH CS
                              MipZ  99 eldfividtPGsdsalsrlahsladtlvtPlndsfvdfdllgkvdpetlkvkrpslyae 157
                                       + +++++dt    ++  r   +  d++++ l+ s+  + l  k+   + k+++p ++  
  gi|386001724|ref|YP_005920023.1| 136 NKEMVIVDTEAGIEHFGRGIEAGCDAILAVLDPSYESLLLSKKIAEISKKINKPLYFVL 194
                                       56789999999999999999999999999999999999999999999999999876654 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.5   1.3e-07     6e-05       4      38 ..       3      37 ..       1      40 [. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-07
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +lv GKGG GK+tv+a +a  +++ g +vl++  D
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSD 37
                                      789*****************************887 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-05    0.0055      10      42 ..       8      40 ..       1      57 [. 0.87
   2 ?    5.2   0.0     0.026        12     106     154 ..     126     175 ..      84     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdn 42
                                      +GG G+++++a La+++ + g +vlv+D   +n
  gi|386001724|ref|YP_005920023.1|  8 KGGSGKSTVAALLAKSMAKRGFNVLVVDSDESN 40
                                      7***************************98887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.026
                          CBP_BcsQ 106 laalkelk.eqyrwillDlpagasaltrellaladlvllvvepdanchvr 154
                                        ++l++l+ ++ +++++D  ag ++  r + a +d  l+v+ p   + ++
  gi|386001724|ref|YP_005920023.1| 126 RKFLDNLAvGNKEMVIVDTEAGIEHFGRGIEAGCDAILAVLDPSYESLLL 175
                                       5677888889999*****************************98877544 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.9e-07   9.1e-05       1      63 [.       1      63 [.       1      72 [. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-07
                         Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekg 63
                                      +k+ + GkGG+Gkst ++ l++++a++g  vl+v  D  +   +  lg  + +t++d +  k+
  gi|386001724|ref|YP_005920023.1|  1 MKVLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLHRQLGMELPSTLMDHFGGKK 63
                                      578999*******************************99988888888888888888876655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   2.5e-07   0.00012      26      61 ..       3      37 ..       1      60 [. 0.92

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-07
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDpH 61
                                      +++ g+ GsGKS+ +a+L ++++ k+g ++l++D +
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMA-KRGFNVLVVDSD 37
                                      7899*******************.**********65 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.4e-06    0.0011       4      49 ..       3      48 ..       1      72 [. 0.87
   2 ?   -0.1   0.0       1.3   6.2e+02      83     122 ..     136     176 ..     122     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLk 49
                                      +l++G  G+GK t +a La+ + k+g +vl+v  D    +   QL 
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLHRQLG 48
                                      799******************************9998888877775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                                       TSSEEEEEE.--SSTTHHHHHHHHHHHHHHHSSSEEEEEEE CS
                             SRP54  83 kidvvlvDT.aGrlqndkelmeelkkikkvvkpdevllvld 122
                                       + ++v+vDT aG  +  + + +  ++i  v++p    l l+
  gi|386001724|ref|YP_005920023.1| 136 NKEMVIVDTeAGIEHFGRGIEAGCDAILAVLDPSYESLLLS 176
                                       67889999967777776666666666666666665555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   7.8e-07   0.00037      19      53 ..       3      38 ..       1      41 [. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.8e-07
                        Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                      +l+ G  G+GKs++a+ll+++++ r+ nv+++d D+
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAkRGFNVLVVDSDE 38
                                      799********************7888******997 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.6e-07   0.00045       4      41 ..       3      40 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.6e-07
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                      v+++G   sGKst+a+ Lak +++++ +v v+d++  +
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESN 40
                                      89******************************977654 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.6e-06    0.0022       1      31 [.       7      37 ..       7      64 .. 0.92
   2 ?    0.6   0.0      0.89   4.2e+02     102     133 ..     136     170 ..     121     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.6e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                      G+  sGKST+a+lL+  ++++g ++++vD D
  gi|386001724|ref|YP_005920023.1|  7 GKGGSGKSTVAALLAKSMAKRGFNVLVVDSD 37
                                      6778*************************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.89
                            CLP1_P 102 kasgliIntpGwvkglgaell...leliealepdv 133
                                       +++ +i++t   ++ +g+ +     +++++l p++
  gi|386001724|ref|YP_005920023.1| 136 NKEMVIVDTEAGIEHFGRGIEagcDAILAVLDPSY 170
                                       67788888888888776543211234555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.4e-06    0.0021      36      90 ..       3      47 ..       2      59 .. 0.90
   2 ?   -2.2   0.0       5.5   2.6e+03      74      82 ..     139     147 ..     123     183 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.4e-06
                            AAA_25 36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRl 90
                                      +l++G +g+GK+t+a  la ++a+          +  +Vl+v+ ++s+ +l+r l
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAK----------RGFNVLVVDSDESNYGLHRQL 47
                                      6899*******************5..........3459**********9999976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.5
                            AAA_25  74 VlyvsaEds 82 
                                        ++v++E +
  gi|386001724|ref|YP_005920023.1| 139 MVIVDTEAG 147
                                       333333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     7e-06    0.0033       1      28 [.       3      31 ..       3      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gfgvnl 28
                                      +l++G+ G+GK+t+a  L+k++ + g+n+
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMaKRGFNV 31
                                      79****************99974545554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-05    0.0069      27      63 ..       3      39 ..       2      86 .. 0.83
   2 ?   -1.5   0.0       6.1   2.9e+03     128     145 ..     181     198 ..     155     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      vl+ G  G+GKs+++  l++++ k+g+ +l  + d++
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDES 39
                                      89***********************877766666666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.1
                            AAA_16 128 allsrderplvlvlDdlq 145
                                       + +++  +pl++vl  ++
  gi|386001724|ref|YP_005920023.1| 181 EISKKINKPLYFVLNRVD 198
                                       444455556666665555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.6e-06    0.0045       2      36 ..       3      46 ..       3      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdt....lrrr 36
                                      vl++G  GsGKst+a  l+k  +     + +++sd+    l+r+
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAkrgfnVLVVDSDEsnygLHRQ 46
                                      799*************9966655566777777777766664444 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00027      0.13      24      68 ..       3      47 ..       1      59 [. 0.86
   2 ?    2.2   0.0      0.14        67     241     259 ..      77      95 ..      63     104 .. 0.73
   3 ?   -1.8   0.0       2.4   1.1e+03     292     313 ..     185     206 ..     134     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                            AAA_10 24 sliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl 68
                                      +l+ G+ G GKS +a ll   ++ +g  +l++D  + ++   ++l
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDESNYGLHRQL 47
                                      6899*****************************998887777766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                            AAA_10 241 fkvvifDEawiftssaeGk 259
                                       +++  fDE w+f+s++  +
  gi|386001724|ref|YP_005920023.1|  77 EEASLFDEKWTFASIPAEA 95 
                                       56689********998655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.4
                            AAA_10 292 knniglklaFretdkeeikkvL 313
                                       k n +l ++ + +d+e +  +L
  gi|386001724|ref|YP_005920023.1| 185 KINKPLYFVLNRVDEERKAAML 206
                                       2222333333333333334444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.8e-05     0.023       4      39 ..       2      44 ..       1     119 [. 0.77
   2 ?   -0.2   0.0       1.5   7.2e+02      23      37 ..     136     150 ..     125     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksld 39
                                      k+l+ G+ g+GK+t+a+ l       g ++l++d +++   l 
  gi|386001724|ref|YP_005920023.1|  2 KVLVCGKGGSGKSTVAALLaksmakrGFNVLVVDSDESNYGLH 44
                                      89***************999999999999*****999765554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.5
                            AAA_24  23 gpkplfidtekGlks 37 
                                        ++ +++dte+G  +
  gi|386001724|ref|YP_005920023.1| 136 NKEMVIVDTEAGIEH 150
                                       477899999999865 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0039       1.9      23      47 ..       2      26 ..       1      46 [. 0.87
   2 ?    5.8   0.0      0.03        14      62      99 ..     163     200 ..     125     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0039
                                      -EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2 23 pvfltGekGsgkelvArlLhknsgp 47
                                       v++ G  Gsgk++vA lL+k+ ++
  gi|386001724|ref|YP_005920023.1|  2 KVLVCGKGGSGKSTVAALLAKSMAK 26
                                      59*****************997655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.03
                                       HHHHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHTTT CS
                   Sigma54_activ_2  62 ldlleqakggtLylkdiadlskaeqkeLlellakaeks 99 
                                       l +l+ + + +L+ k ia++sk+  k L+++l++ +++
  gi|386001724|ref|YP_005920023.1| 163 LAVLDPSYESLLLSKKIAEISKKINKPLYFVLNRVDEE 200
                                       67788889999*********************997644 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0011      0.51       1      41 [.       3      48 ..       3      54 .. 0.83
   2 ?    3.3   0.0      0.21        97       6      62 ..     121     181 ..     118     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                                      EEEES-SHHHHHHHHHHHHTT......EEEEEEESSHHHHHHHHHTT CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg......kdvvvidkdeerveelreeg 41
                                      ++++G G  G+s +  L +++      + v+v+d+de++   +r+ g
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSmakrgfN-VLVVDSDESNYGLHRQLG 48
                                      689*******999999999766999966.********9877766665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
                                       -SHHHHHHHHHHHHTTEEEEEEESSH..HHHHHHHHTTSE..EEES-TTSHHHHHHTTGGG CS
                            TrkA_N   6 lGrvGrslaeeLseggkdvvvidkde..erveelreegle..vvvgdatdeevLeeagiek 62 
                                       +G + r+ +++L  g+k++v++d++   e++ +  e g++    v d++ e++L + +i++
  gi|386001724|ref|YP_005920023.1| 121 MGALSRKFLDNLAVGNKEMVIVDTEAgiEHFGRGIEAGCDaiLAVLDPSYESLLLSKKIAE 181
                                       7888899999999977679999997644445555666666223346777777777766665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.027        13       1      24 [.       2      25 ..       2      82 .. 0.79
   2 ?    7.0   0.0     0.012       5.8      45     114 .]     136     196 ..     123     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                                      EEEEEESTTSSHHHHHHHHHTSTE CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltgeka 24
                                      +v++ G+  +GKSt+   l ++ a
  gi|386001724|ref|YP_005920023.1|  2 KVLVCGKGGSGKSTVAALLAKSMA 25
                                      5899***********999988744 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                                       TEEEEEEEC.GGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  45 gkeielvDt.pGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +ke+++vDt +G ie       +g+ ++a   +d+il v+d s e    l ++++e+ ++ +kpl +vln+
  gi|386001724|ref|YP_005920023.1| 136 NKEMVIVDTeAG-IE------HFGRGIEA--GCDAILAVLDPSYE-SLLLSKKIAEISKKINKPLYFVLNR 196
                                       566777777555.66......45666554..59********7744.2345688888888899**9999995 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.6e-05     0.036      22      66 ..       3      46 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                            ATPase 22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlren 66
                                      vl++G+ G+GK+++a+  + + a++ g +++ v  +e++  l+++
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKR-GFNVLVVDSDESNYGLHRQ 46
                                      89************99888777777.************9999876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00017      0.08       1      33 [.       5      37 ..       5      46 .. 0.91
   2 ?   -1.4   0.0       3.5   1.7e+03     154     194 ..     185     222 ..     171     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                      v+G  GsGK+t    l++ + +rg +v vv  D
  gi|386001724|ref|YP_005920023.1|  5 VCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSD 37
                                      89***************************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                        ATP_bind_1 154 rlelPhvvvlnkfDllkeklekeleffedvealslllekee 194
                                       +++ P   vln++D  +   + ++  f + e++ +++ +++
  gi|386001724|ref|YP_005920023.1| 185 KINKPLYFVLNRVDEER---KAAMLEFLEKERVAAAIPEKK 222
                                       56667777888888744...666666666777766666555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3     0.014       6.4      11      32 ..      10      31 ..       3      34 .. 0.89
   2 ?    6.0   0.0      0.02       9.7     144     193 ..     172     223 ..     162     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                            AAA_26 11 gvGKTvvslgLvralkrkgvkv 32
                                      g+GK++v+++L++++ ++g++v
  gi|386001724|ref|YP_005920023.1| 10 GSGKSTVAALLAKSMAKRGFNV 31
                                      89*************9999987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                            AAA_26 144 qllltiealr.qknvr.vlGvilNkvrnpenvetlekksgipvlGvvPylpd 193
                                        lll+ +++  +k+++  l  +lN+v ++++ ++le   + +v +++P +++
  gi|386001724|ref|YP_005920023.1| 172 SLLLSKKIAEiSKKINkPLYFVLNRVDEERKAAMLEFLEKERVAAAIPEKKE 223
                                       566666666555666558889*****999*******************9886 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00057      0.27      17      51 ..       2      36 ..       1      42 [. 0.93
   2 ?    0.6   0.0      0.43     2e+02      33      72 ..     126     167 ..      87     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                     TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDl 51
                                      ++l+ G  GsGK++++  l +++ +rg  ++v+D 
  gi|386001724|ref|YP_005920023.1|  2 KVLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDS 36
                                      57899****************************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                     TrwB_AAD_bind  33 ekllrairargdraivlDltGafvsrfyd...egkdillnPlD 72 
                                       +k+l+++   ++ ++++D++   +++f +   +g+d +l+ lD
  gi|386001724|ref|YP_005920023.1| 126 RKFLDNLAVGNKEMVIVDTEAG-IEHFGRgieAGCDAILAVLD 167
                                       7899999999********9975.67777666588888887666 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00079      0.37       5      65 ..       5      71 ..       1      78 [. 0.70
   2 ?    0.7   0.0      0.77   3.6e+02      35      77 ..      94     138 ..      89     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00079
                                      EEESTTSSHHHHHHHHHH......TT-EEEEHHHHHHHTTCC.THHHHHHHHHHHGGGCB.TTSSE-H CS
                              CoaE  5 ltGgiasGKstvanlfad......lgvpivDaDlvArqvvep.gsealkkiveeFgeeildedGeLdR 65
                                      + G  +sGKstva+l+a+      ++v +vD D     +  + g e  + ++++Fg +  +  G+++R
  gi|386001724|ref|YP_005920023.1|  5 VCGKGGSGKSTVAALLAKsmakrgFNVLVVDSDESNYGLHRQlGMELPSTLMDHFGGKK-EMMGKMRR 71
                                      567889*******99975321123468899***99988865516666678999999654.44566666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.77
                                       HHTTCCTHHHHHHH..HHHHGGGCB.TTSSE-HHHHHHHHHTSHH CS
                              CoaE  35 rqvvepgsealkki..veeFgeeildedGeLdReaLrkkvFadpe 77 
                                          +e++   l +i   + Fge      G+L R+ L ++   ++e
  gi|386001724|ref|YP_005920023.1|  94 EATTEKDGIRLLAIgkIHDFGEGCACPMGALSRKFLDNLAVGNKE 138
                                       55566677777776223579****99**********998777765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00064       0.3       5      29 ..       9      33 ..       7      49 .. 0.80
   2 ?   -0.9   0.0       2.5   1.2e+03     157     180 ..     126     150 ..     123     155 .. 0.78
   3 ?   -2.1   0.0       5.5   2.6e+03     107     133 ..     179     204 ..     169     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00064
                                      TTSSHHHHHHHHHHHHHHTTE.EEE CS
                   Thymidylate_kin  5 DGaGKttqaellkerlkeegikvvl 29
                                       G+GK+t+a+ll++ + ++g +v++
  gi|386001724|ref|YP_005920023.1|  9 GGSGKSTVAALLAKSMAKRGFNVLV 33
                                      59******************99443 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                                       HHHHHHHH.TTSTEEEEETTS-HHH CS
                   Thymidylate_kin 157 erylelak.ederiliidasksiee 180
                                       +++l+ ++  +++++i+d++  ie 
  gi|386001724|ref|YP_005920023.1| 126 RKFLDNLAvGNKEMVIVDTEAGIEH 150
                                       456666676999*******999886 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.5
                                       HHHHGGGTTSE-SEEEEEESSHHHHHT CS
                   Thymidylate_kin 107 vlslnedvllkPdltflldvdpevalk 133
                                       + ++++++  kP +++l  vd+e +++
  gi|386001724|ref|YP_005920023.1| 179 IAEISKKIN-KPLYFVLNRVDEERKAA 204
                                       556666655.77777777776666554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00032      0.15       1      25 [.       3      27 ..       3      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00032
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      ++++G+ g GKSt+a  Lak+++k+
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKR 27
                                      679*****************99975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00036      0.17       9      67 ..       4      54 ..       2      84 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00036
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgle 67
                                      +v+G  G+GK+t+++ l+++          ++++    + s++s   l r+l  +l + 
  gi|386001724|ref|YP_005920023.1|  4 LVCGKGGSGKSTVAALLAKSMA--------KRGFNVLVVDSDESNYGLHRQLGMELPST 54
                                      89***************99974........44444444444444555555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00085       0.4      25      39 ..       3      17 ..       1      31 [. 0.77
   2 ?   -1.0   0.0       3.2   1.5e+03      40      49 ..     160     169 ..     159     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00085
                            AAA_29 25 tlltGpsGsGKSTll 39
                                      +l+ G+ GsGKST+ 
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVA 17
                                      699**********75 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.2
                            AAA_29  40 DAiqalLvpa 49 
                                       DAi a+L p+
  gi|386001724|ref|YP_005920023.1| 160 DAILAVLDPS 169
                                       9******997 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00047      0.22      50      81 ..       3      34 ..       1      47 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfv 81
                                      ++++G  G GKs +a+ l+++ +++g++vl v
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVV 34
                                      799*************************9866 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00038      0.18      13      37 ..       2      26 ..       1      79 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00038
                                      EEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                      kv + G+ G+GKSt+++lla+ + +
  gi|386001724|ref|YP_005920023.1|  2 KVLVCGKGGSGKSTVAALLAKSMAK 26
                                      57789**************998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00047      0.22      22      52 ..       4      34 ..       1     148 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrvigl 52
                                      ++ G  G+GK+t+ + l++ ++++g++v+++
  gi|386001724|ref|YP_005920023.1|  4 LVCGKGGSGKSTVAALLAKSMAKRGFNVLVV 34
                                      678999*********************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00051      0.24       1      29 [.       3      34 ..       3      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00051
                                      EEEESSTTSSHHHHHHHHHHHH...THEEEEE CS
                               AAA  1 vllyGppGtGKTllakavakel...gveflei 29
                                      vl++G  G GK+++a  +ak++   g+++l +
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMakrGFNVLVV 34
                                      799******************94443444444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00048      0.23      32      68 ..       3      39 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                      v + G  G+Gkst+   l+ ++++rG  v v+  D s
  gi|386001724|ref|YP_005920023.1|  3 VLVCGKGGSGKSTVAALLAKSMAKRGFNVLVVDSDES 39
                                      558899**********************999877755 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0018      0.85      46      71 ..       9      34 ..       1      36 [. 0.91
   2 ?   -1.0   0.0       1.6   7.5e+02     286     299 ..      96     109 ..      86     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                                      S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                      GG+GK  +++ l+k +++rg++v v+
  gi|386001724|ref|YP_005920023.1|  9 GGSGKSTVAALLAKSMAKRGFNVLVV 34
                                      9**********************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                       E-HHHHTTSTT... CS
                              LpxK 286 tTeKDavklaalak 299
                                       tTeKD ++l a+ k
  gi|386001724|ref|YP_005920023.1|  96 TTEKDGIRLLAIGK 109
                                       89999999987555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0015       0.7      24      41 ..       1      18 [.       1      35 [. 0.82
   2 ?   -1.7   0.0       2.6   1.2e+03     253     280 ..     171     198 ..     169     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                      EEEEEEESTTSSHHHHHH CS
                           G-alpha 24 vkllllGqseSGKsTilk 41
                                      +k+l++G+++SGKsT+  
  gi|386001724|ref|YP_005920023.1|  1 MKVLVCGKGGSGKSTVAA 18
                                      69*************965 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                       HHHHHHHCCCC-GGGTTSEEEEEEE-HH CS
                           G-alpha 253 eslklFkeicnnkllkntpiiLflnKlD 280
                                       esl l k+i + +   n+p++++ln +D
  gi|386001724|ref|YP_005920023.1| 171 ESLLLSKKIAEISKKINKPLYFVLNRVD 198
                                       7899999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                       153  (0.00853366); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1701.71
//
Query:       gi|386001725|ref|YP_005920024.1|  [L=276]
Description: Iron(III) ABC transporter, ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-30  104.2   0.0    9.8e-30  103.8   0.0    1.2  1  ABC_tran      ABC transporter
    2.8e-12   47.1   0.6    1.2e-05   25.3   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    8.9e-07   28.6   0.0    0.00014   21.4   0.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.1e-05   25.4   0.0    0.00085   19.1   0.0    2.0  2  AAA_15        AAA ATPase domain
    0.00042   20.8   0.1     0.0007   20.0   0.1    1.5  1  AAA_16        AAA ATPase domain
    0.00056   19.6   0.2     0.0012   18.6   0.2    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0037   17.2   0.1      0.017   15.1   0.0    2.0  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0074   16.3   0.0       0.19   11.7   0.0    2.1  2  AAA_14        AAA domain
     0.0076   16.7   0.1      0.033   14.6   0.1    1.9  2  AAA           ATPase family associated with various cellular 
     0.0083   16.1   0.1      0.014   15.3   0.1    1.3  1  NACHT         NACHT domain
      0.009   16.5   0.2      0.016   15.7   0.2    1.3  1  AAA_23        AAA domain
     0.0095   15.7   0.1      0.019   14.7   0.1    1.7  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.012   15.9   0.1      0.085   13.1   0.1    1.9  2  AAA_22        AAA domain
      0.013   14.9   0.0      0.024   14.0   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.02   14.6   0.5       0.11   12.2   0.3    2.0  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.022   14.7   0.2      0.092   12.7   0.1    1.9  2  NTPase_1      NTPase
      0.024   14.2   0.0      0.037   13.5   0.0    1.2  1  AAA_7         P-loop containing dynein motor region
      0.025   13.8   0.0      0.034   13.3   0.0    1.1  1  G-alpha       G-protein alpha subunit
      0.033   13.4   0.0       0.09   11.9   0.0    1.7  1  NB-ARC        NB-ARC domain
      0.037   14.6   0.0        0.2   12.2   0.1    2.0  2  AAA_18        AAA domain
      0.038   13.7   0.1      0.069   12.9   0.1    1.4  1  AAA_24        AAA domain
      0.057   13.7   0.0       0.89    9.8   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.064   12.9   0.1      0.073   12.7   0.1    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.073   13.2   0.0       0.15   12.2   0.0    1.6  1  AAA_33        AAA domain
      0.076   13.3   0.1       0.15   12.3   0.1    1.5  1  AAA_28        AAA domain
      0.086   12.7   0.0       0.13   12.2   0.0    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
       0.12   12.3   0.4       0.25   11.3   0.2    1.6  2  Rad17         Rad17 P-loop domain
       0.14   12.5   0.0       0.25   11.7   0.0    1.4  1  RNA_helicase  RNA helicase
       0.15   12.4   0.1        0.7   10.2   0.1    1.8  2  AAA_19        AAA domain
       0.16   11.6   0.1       0.64    9.6   0.1    1.9  2  AAA_25        AAA domain
       0.25   11.3   0.6          1    9.2   0.1    1.9  2  RsgA_GTPase   RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0   1.7e-32   9.8e-30       2     137 .]      20     168 ..      19     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 1.7e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                         ++l++ +g+kv ++G+nG+GK+tLlk++ +llkp++G++ +dgk  ++   ++l + ig++pq   + fp ++  
  gi|386001725|ref|YP_005920024.1|  20 AGIDLSIDRGSKVTLLGPNGCGKTTLLKTINRLLKPASGSVVIDGKIASQMGARELAQVIGYVPQGhRSSFPFTS-F 95 
                                       5799****************************************9999999**************9666677664.4 PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e                   + e + +al+ +g  +l d++     +++SgG++q+v++ar+l+++p++lllDEpt+
  gi|386001725|ref|YP_005920024.1|  96 EIvltgrlphisnfsspgaRDFEVARRALELVGAGHLSDRPY----TQISGGERQMVMIARSLAQEPRFLLLDEPTS 168
                                       555899****99999877666666899999999999999998....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   7.5e-07   0.00043       4      23 ..      34      53 ..      32      84 .. 0.80
   2 !   25.3   0.0   2.1e-08   1.2e-05     221     299 ..     124     200 ..      93     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.5e-07
                            AAA_21  4 liGpNgsGKSnLLdaldlla 23
                                      l GpNg+GK++LL+++  l 
  gi|386001725|ref|YP_005920024.1| 34 LLGPNGCGKTTLLKTINRLL 53
                                      89**************9995 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.1e-08
                            AAA_21 221 vvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltT 296
                                       + ++  g+  ++p++++S G +++   + +  ++++++++ll+DEp + L+ k + r+l+ + ++++++g+ vi+t 
  gi|386001725|ref|YP_005920024.1| 124 LELVGAGHLSDRPYTQISGGERQM---VMIARSLAQEPRFLLLDEPTSYLDFKNQVRVLKTVtSIAATEGVTVIMTL 197
                                       5555667778899***********...55555555666*********************88856666689******9 PP

                            AAA_21 297 HSp 299
                                       H+p
  gi|386001725|ref|YP_005920024.1| 198 HDP 200
                                       998 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.3e-07   0.00014      28     195 ..      33     196 ..      21     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-07
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                        ++GpNG+GK+ ll  i        ++ l+ ++ s +i     ++  + + a+v  +   ++++++   ++++i  +
  gi|386001725|ref|YP_005920024.1|  33 TLLGPNGCGKTTLLKTI--------NRLLKPASGSVVIDGkiASQMGARELAQVIGY-VPQGHRSSFPFTSFEIVLT 100
                                       57899999999999999........45677888888888766566777788888775.4555555666666666666 PP

                                       EETTSEEEEEETTEE.E-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingke.vtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                             s++   g +  +  +   el+   ++s     ++SgGe+++v++a  +A        + llDe  + LD+k
  gi|386001725|ref|YP_005920024.1| 101 GRLPHISNFSSPGARdFEVaRRALELVGAGHLSDRpytQISGGERQMVMIARSLAQ----EPRFLLLDEPTSYLDFK 173
                                       666666666554432122212223333333343324449***********988774....44599************ PP

                                       HHHHHHHHHHHHCTT..SEEEEE CS
                                       xxxxxxxxxxxxxxx..xxxxxx RF
                             SMC_N 175 nvkkvaellkekskn..aQfivi 195
                                       n  +v + + +   +  + +i++
  gi|386001725|ref|YP_005920024.1| 174 NQVRVLKTVTSIAATegVTVIMT 196
                                       ******99996544411333333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-06   0.00085      21      68 ..      24      70 ..      20      79 .. 0.76
   2 ?    4.3   0.0     0.046        27     321     366 ..     155     200 ..     141     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                            AAA_15 21 lsee...ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleif 68
                                      ls +     +l G+N++GK+++l+ ++ +l+      +  ++i+ +  +++
  gi|386001725|ref|YP_005920024.1| 24 LSIDrgsKVTLLGPNGCGKTTLLKTINRLLKPA----SGSVVIDGKIASQM 70
                                      444444588999*******************88....56677777766665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.046
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                        +++ +ll++EP  +L  ++q  + k+  ++a ++   vi+t H p
  gi|386001725|ref|YP_005920024.1| 155 AQEPRFLLLDEPTSYLDFKNQVRVLKTVTSIAATEGVTVIMTLHDP 200
                                       567889************************************9998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.2e-06    0.0007      23      63 ..      28      69 ..      22     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      r++ v l G+ G+GK++l++++ r l+ + g +++ gk  + 
  gi|386001725|ref|YP_005920024.1| 28 RGSKVTLLGPNGCGKTTLLKTINRLLKPAsGSVVIDGKIASQ 69
                                      5566899****************9888885577899998877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2     2e-06    0.0012      17      50 ..      24      57 ..      19      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++id+ + + l Gp+G GK+Tll  i+ lL pa+
  gi|386001725|ref|YP_005920024.1| 24 LSIDRGSKVTLLGPNGCGKTTLLKTINRLLKPAS 57
                                      677755589999******************9986 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 !   15.1   0.0     3e-05     0.017       2      24 ..      32      58 ..      31      89 .. 0.73
   2 ?   -0.5   0.0       1.9   1.1e+03      96     123 ..     163     200 ..     138     215 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                                      EEEE--SSSSHHHHHHHGGGGB....S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal....n 24
                                      v L+Gp G+gK++l + + ++l    +
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINRLLkpasG 58
                                      78*******************975433 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                                       ..-SSSEEE---................-EEEEEESS- CS
                             AAA_5  96 leeggelvkakndd.ller.........frviatanpl 123
                                       l+e + + ++kn+   l++         ++vi+t +++
  gi|386001725|ref|YP_005920024.1| 163 LDEPTSYLDFKNQVrVLKTvtsiaategVTVIMTLHDP 200
                                       33333344444433333334444444556666665555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00033      0.19       5      27 ..      32      53 ..      29      83 .. 0.77
   2 ?    2.3   0.0      0.27   1.6e+02      55      87 ..     149     180 ..     131     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                            AAA_14  5 lvitGaRrvGKTtllkqlikell 27
                                      +++ G+  +GKTtllk++ + ll
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINR-LL 53
                                      6899**********988754.33 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                            AAA_14  55 lileklkeekktylflDEiqevpewekalkslv 87 
                                       +i ++l + + ++l+lDE   + ++++ ++ l 
  gi|386001725|ref|YP_005920024.1| 149 MIARSLAQ-EPRFLLLDEPTSYLDFKNQVRVLK 180
                                       44444444.8899********999998888765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   5.7e-05     0.033       2      23 ..      33      54 ..      32      90 .. 0.78
   2 ?   -0.6   0.0       2.9   1.7e+03      48      66 ..     146     165 ..     118     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-05
                                      EEESSTTSSHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelg 23
                                       l Gp G+GKT+l k + + l+
  gi|386001725|ref|YP_005920024.1| 33 TLLGPNGCGKTTLLKTINRLLK 54
                                      699************9988775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
                                       HHHHHHHHTS.TSEEEEEET CS
                               AAA  48 elfkeakeka.kpsilfiDE 66 
                                       +++  a++ a +p  l++DE
  gi|386001725|ref|YP_005920024.1| 146 QMVMIARSLAqEPRFLLLDE 165
                                       44445555555677888887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.5e-05     0.014       3      25 ..      32      54 ..      30      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                      v l G++G+GKTtLl+ + ++++
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINRLLK 54
                                      7899*************988876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   2.8e-05     0.016      21      40 ..      32      50 ..      19      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-05
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                      +t + GpNG+GKTT+l  i 
  gi|386001725|ref|YP_005920024.1| 32 VT-LLGPNGCGKTTLLKTIN 50
                                      44.46***********9886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.3e-05     0.019      21      62 ..      32      75 ..      24     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrvi..glAptgkaAkvL 62
                                      ++l Gp G GKtt+lk+++++++ a g+v+  g   ++  A++L
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINRLLKPASGSVVidGKIASQMGAREL 75
                                      5788******************9996566513333344444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00015     0.085       8      30 ..      32      54 ..      26      82 .. 0.74
   2 ?    0.4   0.0       1.2   7.2e+02      85     127 ..     150     195 ..     106     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      +++ G+ G+GKTtll+++ + l+
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINRLLK 54
                                      5789*************999885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                            AAA_22  85 alrarav.ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                        +r+ a  +++l++DE    l+   + ++l+++ s++   + gv++i+
  gi|386001725|ref|YP_005920024.1| 150 IARSLAQePRFLLLDEPTSyLDfknQVRVLKTVTSIAA--TEGVTVIM 195
                                       23333335679999998887877544777777777777..88887776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.1e-05     0.024      23      62 ..      30      68 ..      20      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllpplseeealevakias 62
                                       ++ l+Gp G+GKt l k ++ ll p s + +++  kias
  gi|386001725|ref|YP_005920024.1| 30 SKVTLLGPNGCGKTTLLKTINRLLKPASGSVVIDG-KIAS 68
                                      57899*******************99987766653.4444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3    0.0002      0.11       2      22 ..      30      50 ..      29      54 .. 0.90
   2 ?   -0.3   0.0       1.4   8.2e+02      41      64 ..     163     187 ..     154     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                         PduV-EutP  2 kkilliGkvgsGKttLtqalk 22
                                      +k+ l+G+ g+GKttL ++++
  gi|386001725|ref|YP_005920024.1| 30 SKVTLLGPNGCGKTTLLKTIN 50
                                      5899*************9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                         PduV-EutP  41 iDtPGeylenrklysalivt.saea 64 
                                       +D P  yl+ ++  ++l+++ s+ a
  gi|386001725|ref|YP_005920024.1| 163 LDEPTSYLDFKNQVRVLKTVtSIAA 187
                                       7999999999998888865413332 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00016     0.092       2      37 ..      32      69 ..      31      81 .. 0.77
   2 ?   -0.5   0.0       1.7     1e+03     114     138 ..     178     202 ..     131     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfytee 37
                                      v + Gp G GKtTl+k + +llk     v ++G ++++
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINRLLKPAsgSVVIDGKIASQ 69
                                      7788******************8653256667766655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHT.TTSEEEEE--SS--S CS
                          NTPase_1 114 fkeaveevLk.sekpvlavihrrkdl 138
                                       + ++v+ + + +++ v++++h ++ +
  gi|386001725|ref|YP_005920024.1| 178 VLKTVTSIAAtEGVTVIMTLHDPN-H 202
                                       446677777768889999999884.3 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.4e-05     0.037      26      78 ..      22      75 ..      18      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkld.kekylsltinfsaqtsanql 78
                                      ++l ++++ +v l Gp G+GKt+++k++ + l+  +  +++  ++ +q+ a++l
  gi|386001725|ref|YP_005920024.1| 22 IDLSIDRGSKVTLLGPNGCGKTTLLKTINRLLKpASGSVVIDGKIASQMGAREL 75
                                      57789999******************9998888233444455555555555555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05     0.034      24      50 ..      30      56 ..      23      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                                      EEEEEEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha 24 vkllllGqseSGKsTilkqlkllykkg 50
                                       k+ llG +++GK+T+lk + +l k++
  gi|386001725|ref|YP_005920024.1| 30 SKVTLLGPNGCGKTTLLKTINRLLKPA 56
                                      6899*****************998875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.09      23      42 ..      32      51 ..      23      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                      EEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 23 valvGmgGvGKttlakqiln 42
                                      v+l G  G+GKttl+k i++
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINR 51
                                      89***************997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00034       0.2       1      25 [.      32      60 ..      32      84 .. 0.77
   2 ?   -0.3   0.0       2.5   1.4e+03      30      89 ..     153     205 ..     131     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf....g 25
                                      + l G+ G+GKttl k ++++l+     +
  gi|386001725|ref|YP_005920024.1| 32 VTLLGPNGCGKTTLLKTINRLLKPasgsV 60
                                      6799**************99983234332 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.5
                            AAA_18  30 dvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaelese 89 
                                       ++a+e + ll ++p        ld +++ ++l+++  +++  +eg ++++  h  ++  +
  gi|386001725|ref|YP_005920024.1| 153 SLAQEPRFLLLDEPT-----SYLDFKNQVRVLKTVTSIAA--TEGVTVIMTLHDPNHALA 205
                                       555555555555555.....77888888888888888876..888888888887776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.069       3      26 ..      30      52 ..      28      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkp 26
                                       k+ + Gp+g GKTtl+k++ ++ 
  gi|386001725|ref|YP_005920024.1| 30 SKVTLLGPNGCGKTTLLKTI-NRL 52
                                      6999***************9.554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0015      0.89      27      88 ..     134     182 ..     114     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       +r +++ SGGe+q++   ++a    +l        + +r+++LDE  s lD +++ ++l+++
  gi|386001725|ref|YP_005920024.1| 134 DRPYTQISGGERQMV---MIAR---SL-------AQEPRFLLLDEPTSYLDFKNQVRVLKTV 182
                                       566777777777432...2231...22.......345999***********99999988875 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00013     0.073      10      45 ..      25      62 ..      21     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                      -EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS..EEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                       ATP-synt_ab 10 pivqGqrtlipgafgvGktvisqslskqsnsdd..aii 45
                                      +i +G ++ ++g +g+Gkt++++++ +  + ++  ++i
  gi|386001725|ref|YP_005920024.1| 25 SIDRGSKVTLLGPNGCGKTTLLKTINRLLKPASgsVVI 62
                                      5779******************9998876555331333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.15       3      78 ..      33     166 ..      32     208 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt........................................... 32 
                                        l G++G+GK+tl++ + + l+     v+++  +                                           
  gi|386001725|ref|YP_005920024.1|  33 TLLGPNGCGKTTLLKTINRLLKpasgSVVIDGKIasqmgarelaqvigyvpqghrssfpftsfeivltgrlphisnf 109
                                       578**********9986444444446777777776666666666666666666666666666666666666666666 PP

                            AAA_33  33 ..........lrr..rlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat 78 
                                                 +rr   l+g +  s++ yt+++   +q++  +ar+ +++ r ++ld +
  gi|386001725|ref|YP_005920024.1| 110 sspgardfevARRalELVGAGHLSDRPYTQISGGERQMV-MIARSLAQEPRFLLLDEP 166
                                       666666666544422333355555556666666666655.666666666666666666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00025      0.15       1      21 [.      31      51 ..      31      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                            AAA_28  1 kivitGgestGKTtlleaLaa 21
                                      k+ ++G+ ++GKTtll+ +++
  gi|386001725|ref|YP_005920024.1| 31 KVTLLGPNGCGKTTLLKTINR 51
                                      6889************98874 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.13      25      45 ..      34      54 ..      24      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                          ATPase_2 25 iYGpegsGKtaLlkeiienle 45
                                      + Gp g+GKt+Llk i   l+
  gi|386001725|ref|YP_005920024.1| 34 LLGPNGCGKTTLLKTINRLLK 54
                                      67***********98866554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00043      0.25      50      69 ..      34      53 ..      24      61 .. 0.83
   2 ?   -2.8   0.0       8.5   4.9e+03     128     153 ..     153     180 ..     144     201 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                             Rad17 50 isGPsGCgkstvvkvLskel 69
                                      + GP GCgk+t +k + + l
  gi|386001725|ref|YP_005920024.1| 34 LLGPNGCGKTTLLKTINRLL 53
                                      56************988766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.5
                             Rad17 128 dlrtdkklilvedlP..nkfyrdsdalr 153
                                        l  + +++l+++      f+ +++ l+
  gi|386001725|ref|YP_005920024.1| 153 SLAQEPRFLLLDEPTsyLDFKNQVRVLK 180
                                       4444555555555331122333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00043      0.25       2      24 ..      33      54 ..      32      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallk 24
                                       l Gp+g+GK+tl k+ +++llk
  gi|386001725|ref|YP_005920024.1| 33 TLLGPNGCGKTTLLKT-INRLLK 54
                                      689*************.555553 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0012       0.7      12      37 ..      31      56 ..      25      80 .. 0.86
   2 ?   -0.2   0.0         2   1.2e+03     101     127 ..     156     184 ..     113     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                            AAA_19 12 vllvtaGpGtGKTrvlkhivallvel 37
                                       + ++++ G+GKT++lk+i +ll+ +
  gi|386001725|ref|YP_005920024.1| 31 KVTLLGPNGCGKTTLLKTINRLLKPA 56
                                      67899*************99998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                            AAA_19 101 qeeellivDE.fqdvd.elqyrLlkallg 127
                                       qe   l+ DE ++ +d + q+r+lk+++ 
  gi|386001725|ref|YP_005920024.1| 156 QEPRFLLLDEpTSYLDfKNQVRVLKTVTS 184
                                       34448888996678888999999998874 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0011      0.64      30      50 ..      26      46 ..      21      58 .. 0.92
   2 ?   -0.9   0.0       1.7     1e+03     167     188 ..     177     198 ..     121     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +g+ + l G+ g+GKttl+
  gi|386001725|ref|YP_005920024.1| 26 IDRGSKVTLLGPNGCGKTTLL 46
                                      7899***************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                            AAA_25 167 alvealeriarrtgaavllvhH 188
                                       ++++ + +ia+  g++v+++ H
  gi|386001725|ref|YP_005920024.1| 177 RVLKTVTSIAATEGVTVIMTLH 198
                                       6777788888888888888877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0018         1     100     121 ..      30      51 ..      20      65 .. 0.82
   2 ?   -0.2   0.0       1.4   8.3e+02      12      39 ..     184     211 ..     159     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                                       SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                       + ++l+G+ G GK+tL+++++ 
  gi|386001725|ref|YP_005920024.1|  30 SKVTLLGPNGCGKTTLLKTINR 51 
                                       56789***********999875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                                       TEES--EEEEEEESTTTT--HHHHHHHH CS
                       RsgA_GTPase  12 kvaNvdqllivvslkepelslnlldrfL 39 
                                       ++a  + + ++++l++p+  l   dr++
  gi|386001725|ref|YP_005920024.1| 184 SIAATEGVTVIMTLHDPNHALAYSDRVV 211
                                       3888899999999999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1770.86
//
Query:       gi|386001726|ref|YP_005920025.1|  [L=350]
Description: Iron(III) ABC transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-87  291.5  29.3    7.5e-87  291.2  29.3    1.0  1  FecCD           FecCD transport family
      0.009   16.2   5.0        1.1    9.6   0.1    2.8  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.2  29.3   8.4e-91   7.5e-87       5     312 .]      35     343 ..      26     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 291.2 bits;  conditional E-value: 8.4e-91
                             FecCD   5 llllslllgavkispsevfeallgka......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPs 75 
                                       ++l+s+++g+++i++ e+  +++++        s  +++++++rlprvl+ ++vG aL+++Ga +Q+++rNpL+dP+
  gi|386001726|ref|YP_005920025.1|  35 AFLISMTIGTFPITTGEIAGVIVSRIgmdmghPSVYETVIFQVRLPRVLLSMMVGSALSASGAAFQGIFRNPLVDPY 111
                                       799*******************9998999999999999*************************************** PP

                             FecCD  76 ilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslll 152
                                       ilG+ssgaa+ga+l+l +     s++ + l af+++lla+++   +ar ++++  ++l+L+G++vsa++s+l ++++
  gi|386001726|ref|YP_005920025.1| 112 ILGLSSGAAFGAALSLGV----VSWIPVQLSAFIFSLLAVAVACSMARTEGRTPVVSLVLSGVIVSAVFSSLLAIVQ 184
                                       **************9866....599999************************************************* PP

                             FecCD 153 lllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllva 229
                                       + ++e+al+si++w++Gs+++aswsk+  +++l+ll++l +l l+ +l++lalgde+A+s+G+++er++ ++++ +a
  gi|386001726|ref|YP_005920025.1| 185 IAVDERALQSIVYWMMGSMNTASWSKLESSFPLALLGCLGILSLRWRLNVLALGDEEARSVGMDPERYKGIFVISAA 261
                                       ***************************************************************************** PP

                             FecCD 230 lltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapff 306
                                       l++++ava++G+ig++GLivPhi+r+++g+dhr+l+pls+ +Ga++++l+d lar +l  +e+pvgi+t+liGapff
  gi|386001726|ref|YP_005920025.1| 262 LASSSAVAVAGIIGLLGLIVPHILRMIFGPDHRTLIPLSITFGATFMVLVDDLARAAL-GFEVPVGIITTLIGAPFF 337
                                       *********************************************************9.7***************** PP

                             FecCD 307 iylllr 312
                                       +yll+r
  gi|386001726|ref|YP_005920025.1| 338 AYLLRR 343
                                       ****97 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   1.3   0.00069       6.2      13      39 ..     114     142 ..     110     160 .. 0.75
   2 !    9.6   0.1   0.00012       1.1      14      32 ..     262     280 ..     255     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00069
                                       SSCHHHHHHHHHHHHHHHHTTEHHHH..H CS
                    GHMP_kinases_N  13 GLGSSAAlavalvaAllallglslee..a 39 
                                       GL+S+AA+ +al + + ++  ++l+   +
  gi|386001726|ref|YP_005920025.1| 114 GLSSGAAFGAALSLGVVSWIPVQLSAfiF 142
                                       9***************9999877755452 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00012
                                       SCHHHHHHHHHHHHHHHHT CS
                    GHMP_kinases_N  14 LGSSAAlavalvaAllall 32 
                                       L+SS+A+ava++  ll l 
  gi|386001726|ref|YP_005920025.1| 262 LASSSAVAVAGIIGLLGLI 280
                                       99**********9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2167.07
//
Query:       gi|386001727|ref|YP_005920026.1|  [L=344]
Description: Iron(III) ABC transporter, solute-binding protein HemV2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-21   76.9   0.1    2.2e-21   76.5   0.1    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.1   1.3e-25   2.2e-21      46     235 ..      97     289 ..      55     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.3e-25
                                       ESSSB-HHHHHHH--SEEEE-GGG....GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                      Peripla_BP_2  46 adgeidvEklaalkPDlvilskgl.gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaei 121
                                        +g +++E+laa  PDlv+l ++  ++      ++ +gip+++v  ++  e+ ++q+r+ g++ g+ d+a ++ a +
  gi|386001727|ref|YP_005920026.1|  97 DSGLVSLETLAAEGPDLVVLWATSpEDENLKAITETLGIPVYAVFITSI-EDMYKQVREMGTISGRADRAAEVEAIM 172
                                       457799****************998888888899*************97.*************************** PP

                                       HHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH CS
                      Peripla_BP_2 122 dsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilas 192
                                       +s ++++ sa++ +   ++p ++++++d      ag+ s++ dl+ ++g+ n+           e  +++ E++ + 
  gi|386001727|ref|YP_005920026.1| 173 KSYVEEVTSATEGIsdEDRPKVYWMWSDV--LGTAGRESGFDDLIYQAGGINVMNFWEndasRMEHPTVPLETLISL 247
                                       **************999999999999988..8899***************99966655678999************* PP

                                       --SEEEEEEHHHHT-S--HHHHT-S...HHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 193 dpdvifvsgraeadnktgleflken...pllaelpAvkngrVyald 235
                                       +pdvi++  +     k ++e++++     ++++++AvkngrVy++ 
  gi|386001727|ref|YP_005920026.1| 248 NPDVIYMWYN----EKLDPEDVISGtefAGWKDINAVKNGRVYEIE 289
                                       ***9976555....899999999873446899***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2413.49
//
Query:       gi|386001728|ref|YP_005920027.1|  [L=425]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-25   87.7   0.0    1.4e-24   87.0   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.032   14.4   2.2      0.087   13.0   2.2    1.7  1  Dockerin_1    Dockerin type I domain
       0.15   12.5   0.3       0.64   10.5   0.1    2.0  2  EF-hand_7     EF-hand domain pair


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   2.3e-28   1.4e-24       1     235 [.     105     366 ..     105     368 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 2.3e-28
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskglgltded 75 
                                       i+ ++   +eil+ l a d+v+gv  t  +++ +++ ++  +++++g++ ++d+E+++ ++PDl+i+ +++ + ++ 
  gi|386001728|ref|YP_005920027.1| 105 IVIYNHQCAEILQILNADDRVAGVRDT--FETQENRFPQisKKKNIGSGVDLDIEAIISVDPDLIIAYTFYPTKEDL 179
                                       899999999******999*99998543..3444444444559*****************************888888 PP

                                       HHHHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEET CS
                      Peripla_BP_2  76 eellksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfgga 146
                                       e +l s+ip +  +    g    +s+ + +  lg ll+  dea  +++++d+ +  ++++++ +  +++  +++ + 
  gi|386001728|ref|YP_005920027.1| 180 EAELPSKIPILRIDCAGGGpcgiDSIRDGVSILGYLLDARDEAARYQEWHDRYVGPVEARTSAIpeGERVRVYLEST 256
                                       8899999999999888766999******************************************7555555555555 PP

                                       TE.......EEEE-TTSTTTHHHHTS--EESTTT--......STT-EEE-HHHHHHH--SEEEEEEH.......... CS
                      Peripla_BP_2 147 de.....ggyvvagsnsyigdlldalgieniaaesk......kseyeeisaEqilasdpdvifvsgr.......... 202
                                       +e     ++ + +g n+  g l++ +g+ niaa +        +ey+ei  E++l+++p+vi+ + +          
  gi|386001728|ref|YP_005920027.1| 257 PEgsetiSSRTAIGKNHPAGNLIELAGGVNIAAGHLplymdtDNEYGEIETEWVLEENPEVIVGRAMgagvrpyene 333
                                       5599999999************************99**************************************998 PP

                                       HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 203 aeadnktgleflkenpllaelpAvkngrVyald 235
                                       +++   +  +++k  p++ ++ Avkn rVy + 
  gi|386001728|ref|YP_005920027.1| 334 DDSLLRAYSDQIKGLPGFDGVDAVKNDRVYIIT 366
                                       777888889*********************986 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.2   1.4e-05     0.087       7      50 ..      34      72 ..      28      79 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                      SSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHH CS
                        Dockerin_1  7 DgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDa 50
                                      D +++  D+   +     ++ ++++ +++ aDvNgDG+v+  D+
  gi|386001728|ref|YP_005920027.1| 34 DDVIDERDIEYAR-----GIIDGTERMTDLADVNGDGNVDEEDI 72
                                      5555555544333.....34458889999999****99999887 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.29   1.7e+03      14      38 ..      32      55 ..      31      59 .. 0.81
   2 ?   10.5   0.1   0.00011      0.64      10      36 ..      58      91 ..      52     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                         EF-hand_7 14 dgdgyldkeellrllrkifqgageg 38
                                      + d  +d+++++ + r i++g++++
  gi|386001728|ref|YP_005920027.1| 32 NMDDVIDERDIE-YARGIIDGTERM 55
                                      568889******.***999987665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                         EF-hand_7 10 elDtdgdgyldkeellrllrkifqga........g 36
                                      + D++gdg +d+e+++ l + i++g+        +
  gi|386001728|ref|YP_005920027.1| 58 LADVNGDGNVDEEDIR-LTEEIIDGTaaeikvidS 91
                                      78**************.****99998776666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 2932.96
//
Query:       gi|386001729|ref|YP_005920028.1|  [L=457]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-21   74.9   0.0    1.3e-20   74.0   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.076   13.2   3.1       0.18   12.0   3.1    1.6  1  Dockerin_1    Dockerin type I domain
       0.11   12.0   0.5       0.57    9.8   0.5    2.3  1  EF-hand_5     EF hand


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   2.2e-24   1.3e-20       1     233 [.     108     373 ..     108     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 2.2e-24
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       i++ + +++e++  l   dkvvgvd ++  ++++  +++  ++vg+ +e+d+E+++  +PDl++  + +   +++++
  gi|386001729|ref|YP_005920028.1| 108 IVVEYLDNAELVSILNSKDKVVGVDYAVAKSEAQFPDLARRKNVGQMNEPDYEAVLSTDPDLLLTFSPMNIKTKADN 184
                                       77888999*****************99999999977777******************************55666666 PP

                                       HHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETT CS
                      Peripla_BP_2  78 llksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggad 147
                                       l  +++ ++   +        +++ + +r lg +l++e++ae+++ +  + +++++s+++      +++vl+ ++ +
  gi|386001729|ref|YP_005920028.1| 185 LPGVDVVFLGLYFPDISdpagSKYVDGVRKLGYILDEEERAEEFIRWNLGWVEEIRSRAAGVpeeERPKVLISAYPY 261
                                       655555555555444448888***********************************998877766788888887777 PP

                                       E......EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH--SEEEEEEH.............. CS
                      Peripla_BP_2 148 e....ggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilasdpdvifvsgr.............. 202
                                       +    g++   ++    ++++   g++ +a++ +    +s+++++++E++ +sdpd i+ +                
  gi|386001729|ref|YP_005920028.1| 262 AhldtGTFRTYSMIDTLTQMAVLTGVRVMAEDLPeffgSSYNIQVDPEWVIESDPDFIYLHLVahtysglslepang 338
                                       7888888888888888899999999999999999************************99888889*********** PP

                                       ....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 203 ....aeadnktgleflkenpllaelpAvkngrVya 233
                                           + a   +  +++ ++p+lae+ Avk grVy 
  gi|386001729|ref|YP_005920028.1| 339 ydatDPAGIRAARDAFTSRPELAEMRAVKDGRVYL 373
                                       **999999999***********************7 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.1     3e-05      0.18       5      53 ..      35      78 ..      32      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallv 53
                                      N D +++ lD+  ++  +      ++ ++++ aD N+DG ++  D++++
  gi|386001729|ref|YP_005920028.1| 35 NMDDTIDQLDIEHVRGIID-----GRYEKTDLADANRDGAIDEEDIAQI 78
                                      8899999999999998888.....99999*****************997 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   9.5e-05      0.57       8      20 ..      62      74 ..      60      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.5e-05
                                      H-SS-SSCE-HHH CS
                         EF-hand_5  8 iDlNgDGkIskeE 20
                                      +D+N+DG I+ e 
  gi|386001729|ref|YP_005920028.1| 62 ADANRDGAIDEED 74
                                      8*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 2876.37
//
Query:       gi|386001730|ref|YP_005920029.1|  [L=241]
Description: oligopeptide ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for 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-35  120.1   0.0    1.2e-34  119.8   0.0    1.2  1  ABC_tran      ABC transporter
    5.2e-10   39.6   3.0    4.2e-06   26.8   0.5    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.2e-06   27.1   0.2    1.4e-05   25.4   0.2    1.8  1  AAA_22        AAA domain
      2e-05   25.1   0.8    3.3e-05   24.4   0.8    1.3  1  AAA_16        AAA ATPase domain
    4.6e-05   23.0   0.0    9.3e-05   22.0   0.0    1.4  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00036   21.0   0.1     0.0038   17.7   0.1    2.2  1  AAA           ATPase family associated with various cellular 
     0.0077   16.2   0.9       0.17   11.9   0.1    2.4  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0097   15.3   0.3        1.3    8.4   0.1    2.6  3  TniB          Bacterial TniB protein
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.021   15.0   0.0    1.6  1  AAA_33        AAA domain
      0.015   15.0   1.3       0.51   10.0   0.3    2.1  2  AAA_30        AAA domain
      0.021   13.5   0.0        2.7    6.5   0.0    2.0  2  AAA_13        AAA domain
      0.026   15.1   0.0      0.071   13.7   0.0    1.8  2  AAA_18        AAA domain
      0.028   14.2   0.1      0.052   13.3   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.065   13.5   0.0        1.2    9.5   0.0    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.073   12.8   0.1       0.84    9.3   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.087   12.2   0.0       0.15   11.4   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.095   12.3   1.5       0.36   10.4   1.5    1.9  1  AAA_25        AAA domain
        0.1   12.5   1.7       0.17   11.8   0.2    2.0  2  NACHT         NACHT domain
       0.11   12.2   0.0       0.24   11.1   0.0    1.6  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.11   11.6   0.1       0.19   10.9   0.1    1.4  1  NB-ARC        NB-ARC domain
       0.12   12.2   0.0        0.2   11.5   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
       0.15   11.8   0.1       0.23   11.2   0.1    1.3  1  AAA_24        AAA domain
       0.37   10.5   1.3        3.9    7.2   1.3    2.0  1  DEAD          DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.0   1.6e-37   1.2e-34       1     137 []      28     178 ..      28     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 1.6e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfp 72 
                                       l++v+l++ eg+++++vG++G+GK+tL++++agl++pt+G++l++g+dl++    e++ +r+++++++q+   +l+p
  gi|386001730|ref|YP_005920029.1|  28 LEDVTLEIGEGRTLGLVGPSGSGKTTLARIVAGLETPTAGRVLYRGRDLRDlrgGERKAFRRRVQMIFQDpeGSLNP 104
                                       689**************************************************9****************7778*** PP

                                       TSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++t+r++                  +++++ l+ ++++++v+++ ps+LSgGq qr+alaral+ +p++l+lDEpt+
  gi|386001730|ref|YP_005920029.1| 105 RKTIRRSleevldlrgvqgGG---RQEVREVLEVVGMEAEVLDRLPSQLSGGQNQRIALARALILEPEVLVLDEPTS 178
                                       *****9999988877643333...666666666666777999999******************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   9.4e-05     0.073       3      22 ..      42      61 ..      41      99 .. 0.85
   2 !   26.8   0.5   5.4e-09   4.2e-06     234     302 ..     147     213 ..     132     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.4e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +l+Gp gsGK++L ++  +l
  gi|386001730|ref|YP_005920029.1| 42 GLVGPSGSGKTTLARIVAGL 61
                                      69**************9888 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.4e-09
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       +++lS G+ + +al+ al+  +    +l++DEp + L+ ++++ +l ll++l+r +g+  +l +H p+++
  gi|386001730|ref|YP_005920029.1| 147 PSQLSGGQNQRIALARALILEP---EVLVLDEPTSALDVSVQAQILHLLRDLQReRGIGYLLISHHPEVV 213
                                       5788999988889999999988...9***********************999999************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   1.8e-08   1.4e-05      10     129 ..      43     207 ..      36     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.8e-08
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsst.sskdllrellralg 65 
                                       ++G+sG+GKTtl+r ++   +  + a +                    +r++ +f ++ +s   +k+++r l + l+
  gi|386001730|ref|YP_005920029.1|  43 LVGPSGSGKTTLARIVAGLET--PTAGRvlyrgrdlrdlrggerkafrRRVQMIFQDPEGSLnPRKTIRRSLEEVLD 117
                                       89*************999874..344447899999999999999998555555555555444677778999999999 PP

                            AAA_22  66 lelka.....................erlsseellealeqalrarav...ielliiDEaqh.lr...seealeeLrs 114
                                       l++                        rl s+    + ++ + ara    +e+l++DE    l+   ++++l  Lr+
  gi|386001730|ref|YP_005920029.1| 118 LRGVQgggrqevrevlevvgmeaevlDRLPSQLSGGQNQRIALARALilePEVLVLDEPTSaLDvsvQAQILHLLRD 194
                                       88888999*****999999999998777777777788888888888899***********99989655********* PP

                            AAA_22 115 llnlsrkgvqliLvG 129
                                       l+   + g+  +L+ 
  gi|386001730|ref|YP_005920029.1| 195 LQR--ERGIGYLLIS 207
                                       ***..9999999985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.8   4.2e-08   3.3e-05      19     165 ..      33     200 ..      17     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.2e-08
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysa.laqalareellrqlldeaesae 93 
                                       +  g+++ + l+G+sG+GK++l+r ++  le+   g +l+   d       +     +a+ r + ++ + +++e  +
  gi|386001730|ref|YP_005920029.1|  33 LEIGEGRTLGLVGPSGSGKTTLARIVA-GLETPTaGRVLYRGRDLR----DLRGgERKAF-R-RRVQMIFQDPEG-S 101
                                       5668889999*****************.566663266644444444....2223234555.4.666666666444.4 PP

                            AAA_16  94 leawrekleeala.................avpelagaea.......srllellkrllallsrder..........p 136
                                       l++ ++ ++++l+                 +                  +l+ l + l+  ++ +r          p
  gi|386001730|ref|YP_005920029.1| 102 LNPRKT-IRRSLEevldlrgvqgggrqevrE--------VlevvgmeAEVLDRLPSQLSGGQN-QRialaralileP 168
                                       444333.444455333366666665555552........033333333333333333333333.3344444555557 PP

                            AAA_16 137 lvlvlDdlqwadeaslql.laaLlrlles..k 165
                                        vlvlD+   a + s q+ + +Llr+l++  +
  gi|386001730|ref|YP_005920029.1| 169 EVLVLDEPTSALDVSVQAqILHLLRDLQRerG 200
                                       8********99999999999999999998541 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.2e-07   9.3e-05      28     202 ..      42     213 ..      28     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                        +vGp GSGK+ l   +  +   ++ + l r ++l+dl   +  ++++ + +v+++f++++ +    +++ +i+r++
  gi|386001730|ref|YP_005920029.1|  42 GLVGPSGSGKTTLARIVAGLETPTAGRVLyRGRDLRDL---RGGERKAFRRRVQMIFQDPEGS---LNPRKTIRRSL 112
                                       59*********998766333333344433355555555...5678888999********9999...34444555555 PP

                                       ETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtk.kevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                           e    + g +    +ev+e+le +g++ e       +LSgG+ + +ala  +     +p+ + +lDe  +aLD
  gi|386001730|ref|YP_005920029.1| 113 ----EEVLDLRGVQGGGrQEVREVLEVVGMEAEvldrlpsQLSGGQNQRIALARALI---LEPE-VLVLDEPTSALD 181
                                       ....555557776654449999999999999999999999*******9999886543...4566.5689******** PP

                                       HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkekskn..aQfivislreeml 202
                                        +  +++ +ll+  + +    ++ is++ e++
  gi|386001730|ref|YP_005920029.1| 182 VSVQAQILHLLRDLQRErgIGYLLISHHPEVV 213
                                       ************66554347889999888776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.9e-06    0.0038       3      22 ..      43      66 ..      41     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.9e-06
                                      EESSTTSSHHHHHHHHHHH....H CS
                               AAA  3 lyGppGtGKTllakavake....l 22
                                      l+Gp G GKT+la+ va      +
  gi|386001730|ref|YP_005920029.1| 43 LVGPSGSGKTTLARIVAGLetptA 66
                                      89***************8733331 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00021      0.17       4      21 ..      43      60 ..      40      79 .. 0.89
   2 ?    2.8   0.1      0.14   1.1e+02      58      93 ..     159     196 ..     118     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                      EE--SSSSHHHHHHHGGG CS
                             AAA_5  4 LvGppGtgKselaerlaa 21
                                      LvGp+G+gK++la+ +a 
  gi|386001730|ref|YP_005920029.1| 43 LVGPSGSGKTTLARIVAG 60
                                      9************98875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                                       -------.G-SEEEEESGGG--.HHHHHHHHHHHHSSE CS
                             AAA_5  58 plvraar.egeilvlDEverae.sevlnsLlslleerr 93 
                                       +l ra   e+e+lvlDE + a   +v++  l ll + +
  gi|386001730|ref|YP_005920029.1| 159 ALARALIlEPEVLVLDEPTSALdVSVQAQILHLLRDLQ 196
                                       4555555799*******999987899999988887655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.035        28      37      54 ..      40      57 ..      28      68 .. 0.81
   2 ?   -0.7   0.0         1   7.8e+02     108     142 ..     126     160 ..     108     165 .. 0.82
   3 !    8.4   0.1    0.0016       1.3     118     157 ..     166     203 ..     131     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.035
                              TniB 37 nlllvGdsnnGKtmivek 54
                                       l lvG+s  GKt++++ 
  gi|386001730|ref|YP_005920029.1| 40 TLGLVGPSGSGKTTLARI 57
                                      6779**********9875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
                              TniB 108 eqqvlrllrelkvrvLiiDEihnllagsarkqref 142
                                       +q+v ++l+ ++++  ++D + + l+g ++++ ++
  gi|386001730|ref|YP_005920029.1| 126 RQEVREVLEVVGMEAEVLDRLPSQLSGGQNQRIAL 160
                                       68899999999999999999999999998887665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0016
                              TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipi 157
                                       l+++vL++DE  ++l   ++ q ++l +l+ L++e  i  
  gi|386001730|ref|YP_005920029.1| 166 LEPEVLVLDEPTSAL--DVSVQAQILHLLRDLQRERGIGY 203
                                       5789***********..6677889*********9988865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.7e-05     0.021       4      20 ..      43      59 ..      41     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      lvG++GsGK+tla+ ++
  gi|386001730|ref|YP_005920029.1| 43 LVGPSGSGKTTLARIVA 59
                                      79***********9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00065      0.51      19      46 ..      39      66 ..      31      74 .. 0.78
   2 ?    3.7   0.0     0.055        43      61     114 ..     131     194 ..     118     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00065
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaag 46
                                      r+  l+Gp G+GKtt+ + ++ + +   
  gi|386001730|ref|YP_005920029.1| 39 RTLGLVGPSGSGKTTLARIVAGLETPTA 66
                                      57789**********9998887666554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.055
                            AAA_30  61 vLaeelgieastiakllkrlk.........grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                       ++ e +g+ea+ +++l ++l          +ra + + ++l+ DE ++ +d +  a++l  +++
  gi|386001730|ref|YP_005920029.1| 131 EVLEVVGMEAEVLDRLPSQLSggqnqrialARALILEPEVLVLDEpTSALDVSVQAQILHLLRD 194
                                       44567899********9999999999999876777777*******4556688888888877765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0035       2.7      23      41 ..      45      63 ..      43      72 .. 0.87
   2 ?    5.0   0.0      0.01       7.8     524     569 ..     165     209 ..     156     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0035
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G  G+GKTtL+r+ + le+
  gi|386001730|ref|YP_005920029.1| 45 GPSGSGKTTLARIVAGLET 63
                                      677************9986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.01
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTH 569
                                       i + ++ v+D P S LD  ++  +  l+++   ++  +  l+i+ H
  gi|386001730|ref|YP_005920029.1| 165 ILEPEVLVLDEPTSALDVSVQAQILHLLRDLQ-RERGIGYLLISHH 209
                                       67899************************997.7888888888877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.1e-05     0.071       3      21 ..      43      61 ..      41      98 .. 0.79
   2 ?   -1.3   0.0       3.9   3.1e+03      80      80 ..     174     174 ..     107     219 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-05
                            AAA_18  3 ltGtpGvGKttlakeLskr 21
                                      l G++G+GKttla+ ++ +
  gi|386001730|ref|YP_005920029.1| 43 LVGPSGSGKTTLARIVAGL 61
                                      89************98755 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.9
                            AAA_18  80 d 80 
                                       d
  gi|386001730|ref|YP_005920029.1| 174 D 174
                                       1 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.6e-05     0.052      16      38 ..      32      54 ..      27      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-05
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTl 38
                                      t+ei + g +  l+GpsGsGK+Tl
  gi|386001730|ref|YP_005920029.1| 32 TLEIGE-GrTLGLVGPSGSGKTTL 54
                                      566663.436679**********8 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0015       1.2      26      89 ..     143     193 ..     113     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       l+r  ++lSGG++q +       ala ++         +++++LDE  s lD   +a++l ll+
  gi|386001730|ref|YP_005920029.1| 143 LDRLPSQLSGGQNQRI-------ALARALIL------EPEVLVLDEPTSALDVSVQAQILHLLR 193
                                       5555666666666332.......22333333......3789*****************999987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011      0.84      45      68 ..      36      59 ..      14      79 .. 0.74
   2 ?    1.4   0.1       0.3   2.3e+02      96     136 ..     155     194 ..     125     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialg 68
                                       +   + l+GpsG GK+ la  ++
  gi|386001730|ref|YP_005920029.1| 36 GEGRTLGLVGPSGSGKTTLARIVA 59
                                      55667889***********97654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                         IstB_IS21  96 dgklaralkrllkvdllilDdlgllpldqaeaellfeviek 136
                                       ++++a a + +l++++l+lD+     ld   ++++++++ +
  gi|386001730|ref|YP_005920029.1| 155 NQRIALARALILEPEVLVLDEPT-SALDVSVQAQILHLLRD 194
                                       45666666778899******964.45555555566666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.15      24      48 ..      40      64 ..      29     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpp 48
                                       l lvGp+GsGKt la+ +++l +p
  gi|386001730|ref|YP_005920029.1| 40 TLGLVGPSGSGKTTLARIVAGLETP 64
                                      5779*************99988665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.5   0.00046      0.36      31     188 ..      36     208 ..      22     212 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00046
                            AAA_25  31 pagelallaGapgtGKttlaldlalava........tGkpwlg....pvap..eqgkVlyvsaEdsedelrrRlrav 93 
                                        +g +  l+G++g+GKttla  +a   +        +G+ + +    +++   +++  ++ + E+s  + r+ +r+ 
  gi|386001730|ref|YP_005920029.1|  36 GEGRTLGLVGPSGSGKTTLARIVAGLETptagrvlyRGRDLRDlrggERKAfrRRVQMIFQDPEGSL-NPRKTIRRS 111
                                       56777889***********954443322232333366666666777744333366677777777765.444555555 PP

                            AAA_25  94 geal.........rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieev.egvrlvviDplsralggde 159
                                       +e++          +++   vl ++g+  ++    +dr  ++l +  ++ +a +++   +++++v+D  ++al+ + 
  gi|386001730|ref|YP_005920029.1| 112 LEEVldlrgvqggGRQEVREVLEVVGMeAEV----LDRLPSQLSGGQNQRIALARALiLEPEVLVLDEPTSALDVSV 184
                                       5444444566777555555566665553222....123333333333333333333213488888888888887777 PP

                            AAA_25 160 nsnsdvgalvealeriarrtgaavllvhH 188
                                       +     ++++  l++++r+ g+  ll+ H
  gi|386001730|ref|YP_005920029.1| 185 Q-----AQILHLLRDLQRERGIGYLLISH 208
                                       7.....66666677776677766555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00022      0.17       1      21 [.      39      59 ..      39      69 .. 0.84
   2 ?   -0.4   0.1       1.2   9.7e+02     102     113 ..     185     196 ..     100     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      SCEEEEC-TTTCHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqkla 21
                                      r++ l G++GsGKTtL++ +a
  gi|386001730|ref|YP_005920029.1| 39 RTLGLVGPSGSGKTTLARIVA 59
                                      677899**********97554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                       .......HHHHH CS
                             NACHT 102 kqpvrtlLseli 113
                                       ++++ +lL++l 
  gi|386001730|ref|YP_005920029.1| 185 QAQILHLLRDLQ 196
                                       333333333333 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0003      0.24      38      55 ..      43      60 ..      20      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                            RuvB_N 38 lyGpPGlGkttlakiiak 55
                                      l+Gp G Gkttla+i+a 
  gi|386001730|ref|YP_005920029.1| 43 LVGPSGSGKTTLARIVAG 60
                                      89**************94 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00025      0.19      22      40 ..      40      58 ..      21      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                      EEEEEESTTSSHHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqi 40
                                       ++lvG  G+GKttla+ +
  gi|386001730|ref|YP_005920029.1| 40 TLGLVGPSGSGKTTLARIV 58
                                      689************9855 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026       0.2      90     121 ..      28      60 ..      17      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       le+++ ++ + +t  lvG+SG GK+tL   +++
  gi|386001730|ref|YP_005920029.1|  28 LEDVTLEIGEgRTLGLVGPSGSGKTTLARIVAG 60 
                                       555655555559999************987766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.23       4      21 ..      40      57 ..      37      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                            AAA_24  4 kiliyGpsgiGKTtlake 21
                                       + ++Gpsg+GKTtla+ 
  gi|386001730|ref|YP_005920029.1| 40 TLGLVGPSGSGKTTLARI 57
                                      6789***********986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.3    0.0051       3.9      13     149 ..      37     195 ..      27     205 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0051
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHS................TTSTS.........-EEEEEESSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxx.........xxxxxxxxxxxxxxxxx RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyet................kgktg.........pkalivePtreLaeqtl 64 
                                       +g+ + + ++ GsGKT+ + i +    +et                +   g          ++++  P  +L     
  gi|386001730|ref|YP_005920029.1|  37 EGRTLGLVGPSGSGKTTLARIVAG---LETptagrvlyrgrdlrdlR---GgerkafrrrVQMIFQDPEGSLNPR-- 105
                                       677777889999999999888776...34333344444444444330...0344444444555555555555433.. PP

                                       HHHHHHTTT.STSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH.....CTTEEEEEEETHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                              DEAD  65 nnlkkfkky.idlrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln.....lsqvrflVlDEadrlld 135
                                       +++++++++ +dlr +   g ++ r+ l+++  +++++   p++l     ++++      + + ++lVlDE    ld
  gi|386001730|ref|YP_005920029.1| 106 KTIRRSLEEvLDLRGVQGGGRQEVREVLEVVGMEAEVLDRLPSQLSGGQ-NQRIAlaralILEPEVLVLDEPTSALD 181
                                       2333333332344444333444444444444444555555554444422.223231122233346666666666666 PP

                                       TTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxx RF
                              DEAD 136 qgfsdfinrilnql 149
                                        + + +i ++l+ l
  gi|386001730|ref|YP_005920029.1| 182 VSVQAQILHLLRDL 195
                                       66666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.78
# Mc/sec: 934.31
//
Query:       gi|386001731|ref|YP_005920030.1|  [L=347]
Description: oligopeptide ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-20   73.7   0.0    2.7e-20   73.3   0.0    1.2  1  ABC_tran      ABC transporter
    8.4e-15   55.0   0.1    1.7e-14   54.1   0.1    1.5  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    0.00057   20.2   0.0     0.0021   18.3   0.0    1.9  1  AAA_22        AAA domain
     0.0019   17.6   0.0      0.078   12.4   0.0    2.3  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.01   16.3   0.1      0.016   15.6   0.1    1.4  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.023   14.2   0.0    1.2  1  AAA_7         P-loop containing dynein motor region
       0.08   12.9   0.0       0.39   10.7   0.0    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.082   13.0   0.0       0.12   12.4   0.0    1.2  1  DUF87         Helicase HerA, central domain
       0.11   11.7   0.0        0.4    9.8   0.0    1.7  2  NB-ARC        NB-ARC domain
       0.15   11.5   0.0          1    8.8   0.0    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
       0.21   11.4   0.0       0.39   10.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   1.6e-23   2.7e-20       3     136 ..      63     215 ..      61     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.6e-23
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pql 70 
                                       +vsl++++ e++a+vGe+G+GKS +++ +++ll      +Gei + g+dl      +  ++  +ei++++q+   +l
  gi|386001731|ref|YP_005920030.1|  63 DVSLDIRREETLALVGETGCGKSVVAASVLQLLPSyaeVKGEIFFGGRDLLGlgerEMARVRGREISMIFQNpsLSL 139
                                       79*************************9999877666699***********9999888888999********87788 PP

                                       -TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       +p +t++ +               +++ ++ +ls+lgl +      +  p +LSgG+ qr ++a+a +  p+l+++D
  gi|386001731|ref|YP_005920030.1| 140 NPVYTIGHQvaesaliggraspaGARSMADSILSRLGLAGRG----GMYPFQLSGGMNQRAMIAAAGVAGPRLIIAD 212
                                       9999999999999999998887666666*********99933....3457*************************** PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ept
  gi|386001731|ref|YP_005920030.1| 213 EPT 215
                                       **9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1     1e-17   1.7e-14       1      65 []     267     326 ..     267     326 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1e-17
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+gp+++++++p+HPY+ aLl+s+p    +      i+g+ ps+ r++ GC+F+pRC  a + C
  gi|386001731|ref|YP_005920030.1| 267 VETGPVADVLERPRHPYSLALLKSLPGQGFH-----PIPGSSPSAVRRPPGCLFHPRCSWAEPGC 326
                                       8*************************98555.....56**************************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0021       5      38 ..      71     140 ..      68     254 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee....................................e 38 
                                       +  l+++Ge+G+GK+++++ +l+ l+ +a+ +                                     +
  gi|386001731|ref|YP_005920030.1|  71 EETLALVGETGCGKSVVAASVLQLLPSYAEVKGeiffggrdllglgeremarvrgreismifqnpslslN 140
                                       56689*********************99998877777776666666666666655555555555555550 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   4.8e-05     0.078      22      50 ..      71      99 ..      54     106 .. 0.83
   2 ?    2.7   0.0     0.042        69      69      98 ..     133     162 ..     111     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllppls 50
                                      +  l lvG  G+GK+++a+ + +llp+  
  gi|386001731|ref|YP_005920030.1| 71 EETLALVGETGCGKSVVAASVLQLLPSYA 99
                                      56789*********************876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.042
                      Mg_chelatase  69 eekllkrrpfraphhsaskaalvGggskpk 98 
                                       ++  l+  p  +  h ++++al+Gg ++p 
  gi|386001731|ref|YP_005920030.1| 133 QNPSLSLNPVYTIGHQVAESALIGGRASPA 162
                                       56677888999999***********98764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   9.8e-06     0.016      12      51 ..      58      97 ..      53     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.8e-06
                            AAA_16 12 Llsale.rvrsgrpelvllsGesGvGKsslvrellralekd 51
                                      +++a++ ++   r+e + l+Ge G+GKs ++ ++l +l  +
  gi|386001731|ref|YP_005920030.1| 58 VHAAVDvSLDIRREETLALVGETGCGKSVVAASVL-QLLPS 97
                                      5666665556667799******************9.56555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.023      27      58 ..      65      96 ..      52     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkld 58
                                      +l ++++  + lvG+tG+GK+v++ ++l+ l+
  gi|386001731|ref|YP_005920030.1| 65 SLDIRREETLALVGETGCGKSVVAASVLQLLP 96
                                      55678889999***************999887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.39       3      25 ..      75      97 ..      73     111 .. 0.86
   2 ?   -0.8   0.0      0.87   1.4e+03      33      62 ..     146     175 ..     138     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                      EEE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnr 25
                                       LvG++G+gKs +a +++++l +
  gi|386001731|ref|YP_005920030.1| 75 ALVGETGCGKSVVAASVLQLLPS 97
                                      69****************99954 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.87
                                       -TT--HHHHH--B--.........------ CS
                             AAA_5  33 trdtteedlkgrreikngttslvdsplvra 62 
                                         +  e+ l+g+r    g +s+ ds+l r 
  gi|386001731|ref|YP_005920030.1| 146 GHQVAESALIGGRASPAGARSMADSILSRL 175
                                       45578999999999889*******999875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.5e-05      0.12      10      47 ..      60      95 ..      53     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-05
                             DUF87 10 sevpvyldlnklvtrHlAilgsTGsGKSntvavLleel 47
                                        v+v+ld+ +  ++ lA +g+TG GKS  +a+ l+ l
  gi|386001731|ref|YP_005920030.1| 60 AAVDVSLDIRR--EETLALVGETGCGKSVVAASVLQLL 95
                                      45889999944..699***************9988866 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00025       0.4      22      42 ..      73      93 ..      60     103 .. 0.86
   2 ?   -1.2   0.0      0.56   9.2e+02     128     150 ..     235     257 ..     220     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                                      EEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqiln 42
                                       +alvG  G+GK+++a+++l+
  gi|386001731|ref|YP_005920030.1| 73 TLALVGETGCGKSVVAASVLQ 93
                                      689**************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.56
                                       CHTTSEEEEEESBCCCCCCS-S- CS
                            NB-ARC 128 renrlrvllTTRdeevanavsat 150
                                         nr+++ll T d eva + +++
  gi|386001731|ref|YP_005920030.1| 235 DLNRSSMLLITHDLEVARRTADR 257
                                       468999**********9998876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00062         1      25      89 ..      72     138 ..      62     268 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00062
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedkk 89 
                                       +  a+vG+ G+GKs +  ++l +L   s+ +++ e +   +dl+   ++e a+v   e++++f+n++ +
  gi|386001731|ref|YP_005920030.1|  72 ETLALVGETGCGKSVVAASVLQLLP--SYAEVKGEIFfggRDLLGLgEREMARVRGREISMIFQNPSLS 138
                                       45689**************999888..555677775433356666555666677777777777777666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00024      0.39      16      40 ..      65      89 ..      56     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllD 40
                                      +++i+++++  l+G++G GKS +  
  gi|386001731|ref|YP_005920030.1| 65 SLDIRREETLALVGETGCGKSVVAA 89
                                      56777777999**********8764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2043.95
//
Query:       gi|386001732|ref|YP_005920031.1|  [L=281]
Description: Oligopeptide ABC transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for 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-22   77.7  15.4    9.1e-22   77.7  15.4    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.016   15.2   1.2      0.016   15.2   1.2    2.8  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4      0.31   2.8e+03      31      61 ..      16      36 ..      12      45 .. 0.55
   2 !   77.7  15.4     1e-25   9.1e-22       1     172 [.      94     263 ..      94     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.31
                      BPD_transp_1 31 Psfvlaillvlvfvilsilghlilpviilll 61
                                      P+ ++++ll+          +++l+++il+ 
  gi|386001732|ref|YP_005920031.1| 16 PMRWIGVLLL----------TGFLAAAILAP 36
                                      5555555555..........33444444444 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 1e-25
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g+++G++a+ +++++ d++l++l++v+l++P + l+i l         l  ++++ +++++ll ++ ++r++r++a+
  gi|386001732|ref|YP_005920031.1|  94 GTMVGLVAG-YYRGWADEVLMGLTDVVLMIPQIPLIITLA------AFLRPSFWMiALLMGLLWWPSMARVVRSRAI 163
                                       7899*****.999*************************99......88998888879******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +++++++veaar lG ++++i+ + vlPn++ +i++ ++l++++++ + + ++flg    l +++   ++g  +s++
  gi|386001732|ref|YP_005920031.1| 164 QVREMSFVEAARCLGFPHRHIILTDVLPNTVHVILPKFMLTVASAMIAEASISFLG----LVDPT-ARSWGTTISFA 235
                                       ********************************************************....77554.56777777777 PP

                      BPD_transp_1 154 s.........nggvlalviavlllnlva 172
                                                 ++ +l  +i++ l++l++
  gi|386001732|ref|YP_005920031.1| 236 FarggfingyWWWYLPPGICITLFVLSL 263
                                       7888889888444445555554444443 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.2   1.8e-06     0.016      14      51 .]      16      53 ..      13      53 .. 0.86
   2 ?   -1.1   1.1      0.21   1.9e+03      24      36 ..     127     139 ..     125     150 .. 0.80
   3 ?   -4.0   0.8       1.7   1.5e+04      26      31 ..     258     263 ..     254     267 .. 0.42

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                            OppC_N 14 klAvvglvilllllliaifaPliaPydp...qdliqnllpP 51
                                      ++ ++g  +l  +l++ai+aP+i+P dp    d+   ++pP
  gi|386001732|ref|YP_005920031.1| 16 PMRWIGVLLLTGFLAAAILAPVISPADPrarFDP---YQPP 53
                                      667899999999*************998876666...9999 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.21
                            OppC_N  24 llllliaifaPli 36 
                                       l+++l+a++ P +
  gi|386001732|ref|YP_005920031.1| 127 LIITLAAFLRPSF 139
                                       6788999988877 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.7
                            OppC_N  26 llliai 31 
                                       l+++++
  gi|386001732|ref|YP_005920031.1| 258 LFVLSL 263
                                       333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1833.94
//
Query:       gi|386001733|ref|YP_005920032.1|  [L=319]
Description: Oligopeptide ABC transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-30  104.7  18.0    1.3e-29  103.3  18.0    1.8  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3  18.0   7.1e-34   1.3e-29       1     184 [.     114     312 ..      85     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 7.1e-34
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpl.iivllslPsfvlaillvlvf................vilsilghlilpviill 60 
                                       g+ lG+la+    +++++ l++l  i+++s P++ + ++ v+++                  l++l+hl+lpv+i++
  gi|386001733|ref|YP_005920032.1| 114 GTYLGALAG-WDEGRGSRRLQTLaAIAIYSSPPYFISLVAVYILgfklgwfplkgvyltgDPLNVLHHLFLPVFIMT 189
                                       567888888.555555555555416778899***999999999999**************9999************* PP

                      BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGl 137
                                       l+ a   ++++r +++++  + +v +ara+G+ r +i++  v++na+ piit+++l fg+++ ga+++e+++s +G+
  gi|386001733|ref|YP_005920032.1| 190 LFAASRNFMIMRGSVIQEKRSLYVSYARAKGLYRDEILFASVFKNAILPIITLIALDFGFIFSGALFIEIVFSMNGM 266
                                       ***************************************************************************** PP

                      BPD_transp_1 138 gtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       g+l+ +a l +dy+  + g++l+++++v++ n++ad+++ ++dprvr
  gi|386001733|ref|YP_005920032.1| 267 GLLIYDAVLCRDYPVLQ-GAMLIITVMVIIANILADLIYGVVDPRVR 312
                                       *****************.****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2256.32
//
Query:       gi|386001734|ref|YP_005920033.1|  [L=271]
Description: hypothetical protein Mhar_1041 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   35.6   0.0    3.3e-08   34.1   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    2.9e-08   34.2   0.0    2.1e-06   28.3   0.0    2.2  2  Methyltransf_11  Methyltransferase domain
    6.3e-07   29.3   0.0    8.3e-06   25.7   0.0    2.1  1  Methyltransf_31  Methyltransferase domain
    0.00024   21.0   0.0    0.00061   19.7   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
    0.00036   19.9   0.0    0.00052   19.4   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
    0.00095   19.0   0.0     0.0012   18.6   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0011   19.7   0.0     0.0028   18.4   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
      0.003   16.9   0.0     0.0049   16.2   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.041   13.8   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.023   13.7   0.0      0.034   13.1   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.03   14.1   0.0        6.3    6.5   0.0    2.2  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.054   12.8   0.0      0.078   12.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.056   13.2   0.0      0.087   12.6   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
       0.16   11.5   0.0       0.26   10.8   0.0    1.3  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.6e-11   3.3e-08       2      92 ..      67     154 ..      66     158 .. 0.88
   2 ?   -1.5   0.0       3.3   4.3e+03      66      97 .]     206     236 ..     186     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.6e-11
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       Ld+G+GtG +++ la r+   +v+++D+s  +l+  +e+a+++g+ n+e++     +++ + + +Dl +s  a++++
  gi|386001734|ref|YP_005920033.1|  67 LDVGAGTGAFAIPLAPRM--RRVLALDPSTHQLRVLEEKARSRGIyNIEIISSRWGEVD-PRQLVDLDFSLAAYSIF 140
                                       9****************8..9**********************************9998.45688888886567777 PP

                                       SHHHHHHHHHHHHHH CS
                   Methyltransf_25  78 sdedlekalkeiarv 92 
                                       + ed+  +lk++ +v
  gi|386001734|ref|YP_005920033.1| 141 E-EDVYSFLKKMIDV 154
                                       6.7888999999877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                                       EEEEEEST.GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  66 Dlvvssga.lhhlsdedlekalkeiarvLkpgG 97 
                                       D+v+  ++ lh l     ++  +ei r L++gG
  gi|386001734|ref|YP_005920033.1| 206 DYVLPLHCiLHGLCS--SARSPEEIMRYLEDGG 236
                                       566665664554432..2355689999999998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.6e-09   2.1e-06       1      95 [.      67     162 ..      67     163 .. 0.89
   2 ?    4.0   0.0     0.063        80      63      95 ..     206     239 ..     177     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.6e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-.C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv.e 75 
                                       LdvG+GtG++a +la r +rv+++D+s+ +l++ +eka+ +g+ ++e++ ++  ++  + + +Dl +s  +   + e
  gi|386001734|ref|YP_005920033.1|  67 LDVGAGTGAFAIPLAPRMRRVLALDPSTHQLRVLEEKARSRGIyNIEIISSRWGEVD-PRQLVDLDFSLAAYSIFeE 142
                                       8**************999**************************9999999999985.4557888888888888888 PP

                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                       d+ ++lk++  v   g llv
  gi|386001734|ref|YP_005920033.1| 143 DVYSFLKKMIDVSSRGVLLV 162
                                       99999999988887777766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.063
                                       EEEEEES.-CCC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  63 Dlvvsse.vlhhvedpekalkeiaRvLkpgGllv 95 
                                       D v+  +  lh +   ++  +ei+R L+ gG+++
  gi|386001734|ref|YP_005920033.1| 206 DYVLPLHcILHGLCSSARSPEEIMRYLEDGGRIA 239
                                       555544425566678899999**********986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.5e-09   8.3e-06       4     113 ..      63     167 ..      60     243 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.5e-09
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g ++lD+G+GtG++++ la +++   +v  +D s + +++ +e+a++ g+ n+e   + + e +     + +Dl +s
  gi|386001734|ref|YP_005920033.1|  63 GSSLLDVGAGTGAFAIPLAPRMR---RVLALDPSTHQLRVLEEKARSRGIYNIEIISSRWGEVDPR---QLVDLDFS 133
                                       5689***************8876...5***********************************6643...45555333 PP

                   Methyltransf_31  81 nevl.naladpdkileeiervlkpggilliedpr 113
                                        ++      d  ++l+++++v + g  l+ +  r
  gi|386001734|ref|YP_005920033.1| 134 LAAYsIFEEDVYSFLKKMIDVSSRGVLLVFRAGR 167
                                       2222334555556666777777766666666555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   2.8e+03     145     163 ..      11      29 ..       6      30 .. 0.81
   2 !   19.7   0.0   4.8e-07   0.00061       9      61 ..      49     101 ..      38     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                   Methyltransf_23 145 ffsarslkelleeaGlevv 163
                                       +  ++s+ ++l+e G +++
  gi|386001734|ref|YP_005920033.1|  11 YVKSTSYQRILQERGITND 29 
                                       5678999*******99875 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.8e-07
                   Methyltransf_23   9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae 61 
                                       + + ler++   ++g+++Ld+G+GtG ++  l+++   v + D+s ++   +e
  gi|386001734|ref|YP_005920033.1|  49 PGEILERVSSLIPPGSSLLDVGAGTGAFAIPLAPRMRRVLALDPSTHQLRVLE 101
                                       567888888878999******************************98776655 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.1e-07   0.00052      46     120 ..      61     132 ..      51     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.1e-07
                                       -CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEE CS
                              GidB  46 kekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvt 120
                                            +++DvG+G G  +ipLa      ++  l+++  + + Lee  +  ++ n+ei+ +r  e ++++ +d+  
  gi|386001734|ref|YP_005920033.1|  61 PPGS-SLLDVGAGTGAFAIPLAPR--MRRVLALDPSTHQLRVLEEKARSRGIYNIEIISSRWGEVDPRQLVDLDF 132
                                       4445.69*************9854..445778********************************99999888755 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.7e-07    0.0012      92     145 ..      54     105 ..      39     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.7e-07
                                       HHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHH CS
                            Met_10  92 erlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenik 145
                                       er+ +l+ +g   +dv AG G faip+a   + +rvla d   +  + l+e  +
  gi|386001734|ref|YP_005920033.1|  54 ERVSSLIPPGSSLLDVGAGTGAFAIPLAP--RMRRVLALDPSTHQLRVLEEKAR 105
                                       7999999*********************8..********999999999988765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.2e-06    0.0028       1      47 [.      67     111 ..      67     156 .. 0.85
   2 ?   -2.3   0.0       6.1   7.9e+03      68      99 .]     206     238 ..     199     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.2e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennn 47 
                                       L++G+GtG+++ +l+++    +++++D+s++++   +ek ++r+ +n
  gi|386001734|ref|YP_005920033.1|  67 LDVGAGTGAFAIPLAPR--MRRVLALDPSTHQLRVLEEKARSRGIYN 111
                                       8****************..**************77777777766555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.1
                   Methyltransf_12  68 Dlvv.asnvlhhlkdirevldnirklLkpgGrl 99 
                                       D+v+ +++ lh l   +++ ++i + L +gGr+
  gi|386001734|ref|YP_005920033.1| 206 DYVLpLHCILHGLCSSARSPEEIMRYLEDGGRI 238
                                       566633355666666666777888899999975 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.9e-06    0.0049      47     106 ..      62     118 ..      52     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                       +g+++lDv +Gtg +a+ l+  ++   +v  lD + + L+v e+k++ +g +nie + + 
  gi|386001734|ref|YP_005920033.1|  62 PGSSLLDVGAGTGAFAIPLAPRMR---RVLALDPSTHQLRVLEEKARSRGIYNIEIISSR 118
                                       6899***************98876...6999************************99876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.2e-05     0.041       5      67 ..      53     112 ..      51     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                   Methyltransf_18   5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledki 67 
                                       L+++ sl+++gs+++D+G+  g  +i l+   ++++v+a D +++ l+  +e++++ g+  +i
  gi|386001734|ref|YP_005920033.1|  53 LERVSSLIPPGSSLLDVGAGTGAFAIPLA--PRMRRVLALDPSTHQLRVLEEKARSRGIY-NI 112
                                       899*************************9..67899****************99998874.34 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.034     204     254 ..      65     115 ..      56     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                   tRNA_U5-meth_tr 204 dllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqii 254
                                        ll++  G G f+++la ++++vla + +  ++ +      +  i n++ii
  gi|386001734|ref|YP_005920033.1|  65 SLLDVGAGTGAFAIPLAPRMRRVLALDPSTHQLRVLEEKARSRGIYNIEII 115
                                       699999*********************999999999999999999999998 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.005       6.3      68      96 ..      55      85 ..      43     117 .. 0.77
   2 ?    5.5   0.0    0.0095        12     145     173 ..     213     242 ..     207     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.005
                                      HTT..--TT-EEEEES-TTSHHHHHHHHHHC CS
                              PCMT 68 lle..lkkgarvLevGsGsGyltavlarlvg 96
                                       ++  + +g++ L+vG+G+G  +  la  ++
  gi|386001734|ref|YP_005920033.1| 55 RVSslIPPGSSLLDVGAGTGAFAIPLAPRMR 85
                                      45566789************98877765555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0095
                                       EEEESSBB.SS--HHHHHTEEEEEEEEEEE CS
                              PCMT 145 aihvgaaa.peiPealidQLkeGGrlvvPv 173
                                        i+ g ++    Pe++++ L++GGr+ +P 
  gi|386001734|ref|YP_005920033.1| 213 CILHGLCSsARSPEEIMRYLEDGGRIAAPQ 242
                                       566665541568**************9995 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.1e-05     0.078      61     154 ..      61     153 ..      52     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                                       -TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SEEEEES CS
                              CMAS  61 kpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdrvvsvg 135
                                        pG+ lLd+G+G G+ ++  + r   +v++l  S+ q ++ +++  ++++  + e+  + + ++d    vd   s+ 
  gi|386001734|ref|YP_005920033.1|  61 PPGSSLLDVGAGTGAFAIPLAPR-MRRVLALDPSTHQLRVLEEKARSRGIY-NIEIISSRWGEVDPrqLVDLDFSLA 135
                                       69*******************99.789********************9976.5678888999998654678778888 PP

                                       -GGGTSGGGHHHHHHHHHH CS
                              CMAS 136 afehvgkenydtffkklkk 154
                                       a   + ++ y  f kk+ +
  gi|386001734|ref|YP_005920033.1| 136 AYSIFEEDVYS-FLKKMID 153
                                       88877777764.5555554 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.8e-05     0.087      14      77 ..      52     112 ..      47     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-05
                            DUF938  14 ilevLksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnl 77 
                                       ile + s ++  ++ +L++++GtG  A+ +Ap++ ++  ++ d+  ++   ++  a++ ++ n+
  gi|386001734|ref|YP_005920033.1|  52 ILERVSSLIPPGSS-LLDVGAGTGAFAIPLAPRMRRV--LALDPSTHQLRVLEEKARSRGIYNI 112
                                       66666777777776.******************9764..5666666666667777777777776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.26      33      85 ..      64     115 ..      52     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEE CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevv 85 
                                        ++lD+G+G+G+ ++ la +  +  v ++d +++ l++ +e +++ ++  +e++
  gi|386001734|ref|YP_005920033.1|  64 SSLLDVGAGTGAFAIPLAPRMRR--VLALDPSTHQLRVLEEKARSRGIYnIEII 115
                                       568***************99888..99999999999999999988877655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2015.36
//
Query:       gi|386001735|ref|YP_005920034.1|  [L=525]
Description: Oligopeptide ABC transporter, solute-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-67  227.8   1.3    2.8e-67  227.3   1.3    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   1.3   1.6e-71   2.8e-67       2     366 ..      72     430 ..      72     440 .. 0.89

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 1.6e-71
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       vv++ Aes +evs+Dgkt++f +R+++++sDG++lt eDv f+fe+l ++ +++g+ ++       ++  av    v
  gi|386001735|ref|YP_005920034.1|  72 VVGQTAES-YEVSEDGKTWRFQIRDDLYWSDGEKLTPEDVRFTFEYLGEKYPPAGWIKD------TVEEIAVEGDAV 141
                                       68899***.8****************************************999999555......58999999999* PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEE.EEE-TTSTTTSCSSSSE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkiv.lernpdYwgggkpkldr 154
                                       +f l+kp++ +   +a +++ + +++++ ed        ++vg GP+++ + +    +  +e+np+ w g+++k+  
  gi|386001735|ref|YP_005920034.1| 142 VFALNKPYSRLNLEFATYNILPEHVWKDVEDPMVHVDEGPVVGFGPFVISRTDLAAGVLyFEKNPY-WEGEAAKIGG 217
                                       *********7777777777777777888888888888888889**********98855559****9.789******* PP

                                       EEEEE-.SHHHHHHHHHTTSSSEE....ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHH CS
                         SBP_bac_5 155 iefkvipdsdaraaalqsGeiddv....aepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAl 227
                                       +e+ ++++ d+   al +G++d +       p +++++l+ a g +v +e+ ++g  +l++N + +p++d+++R+Al
  gi|386001735|ref|YP_005920034.1| 218 VEIHMYANMDVLSMALMKGDVDAYykyaGTYPYANLAALDSAGGFDV-VETDNTGLIFLGLNLREAPMSDPAFREAL 293
                                       *********************87655556677888888899999999.***************************** PP

                                       HHHS-HHHHHHHCTTTSS.EEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC.EEEEEEE CS
                         SBP_bac_5 228 syAiDreeivkavlegya.tpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek.klkltll 302
                                       + AiD++ei+k     y+ +p  +++pps+ +++e+ k     yd e+A++lL+eaGy+d++g+g+ e    +++ l
  gi|386001735|ref|YP_005920034.1| 294 ASAIDYQEILKLDALDYGsVPNRGFVPPSMGYFKETEKL---IYDAEEARRLLEEAGYTDVNGDGFLETpDGEMIDL 367
                                       ***********87766653788888***99999887665...489*************************99***** PP

                                       EETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHH CS
                         SBP_bac_5 303 lasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnfl 366
                                       +  + ++ ++i el+q++l++iGik+ +kt d+ +t+ + ++d ++d+ +++ +++    ++  
  gi|386001735|ref|YP_005920034.1| 368 TFLTRADYQRITELLQEYLADIGIKTGIKTADQ-STWITMKDDYQYDLTVTRTTPWGMMMHANW 430
                                       *******************************99.999999999999999999999877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3246.39
//
Query:       gi|386001736|ref|YP_005920035.1|  [L=293]
Description: ABC transporter substrate binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.1   0.1    2.4e-12   46.8   0.1    1.1  1  ZnuA      Zinc-uptake complex component A periplasmic
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.29   11.3   0.0    1.5  1  VP9       VP9 protein


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.1   2.7e-16   2.4e-12       1     218 [.      33     254 ..      33     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.7e-16
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT-.---HHHHHH....HHHSSEEEESSTTTSGTHH.HHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx....xxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsy.eptprdvrk....laeAdllvynglelEtwld.kllasssq 71 
                                       +vatts+l d +  ++G+rve  ++ +p   pH    + p+ ++     + +Ad+++    + ++ ++  +++++ +
  gi|386001736|ref|YP_005920035.1|  33 IVATTSVLMDPATFIGGERVEAISIADPTLCPHLQaDIIPNRIQLnmafIRDADVFMAYNDNNDKNFNiPAVENFMA 109
                                       8********************************8757888887655666**********999996655333444432 PP

                                       CCCEEEEETTTTCCSEBCSSEST.GGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  72 atrvevidlsegveeeeeeeDpH.iWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireela 147
                                       a++   ++ +  v      +Dp   W  p  a+ ++ ++   L+e dpa++++y+ ++++y    ++++   +e+  
  gi|386001736|ref|YP_005920035.1| 110 ANNFGAVKWK-KV------SDPSrGWNTPTTAKLLAAEVLGWLIEEDPAGEAYYQGRYDEYLMTFDAVEPTETERSR 179
                                       2222222111.22......266547*******************************************988888877 PP

                                       TSSGTEGEEEESSSTTHHHHHHTT-EEEEEE..SSSSS.....HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 148 eipeekrklvtthdafgylarayglevagia..giste.....aaqiaalieeikeagvkaifveplaspklaetla 217
                                         + +  ++++++++++ +    g+ev++++  ++  +      + + ++i + ++ +  a ++e+++s +la+ + 
  gi|386001736|ref|YP_005920035.1| 180 LQETKVIVMLWQREPVENW---LGMEVVNFFapEFAMNgtktaDKIVDEIIATPEKYQDVAYVIENMQSGELAKGIE 253
                                       4555677788899999988...8*****9976666666966654445555555566666666777777888877777 PP

                                       H CS
                                       x RF
                              ZnuA 218 e 218
                                       e
  gi|386001736|ref|YP_005920035.1| 254 E 254
                                       6 PP

>> VP9  VP9 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.3e-05      0.29      15      49 ..     158     194 ..     151     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                               VP9  15 ekYEevlltfeave..svrkSelrdgvfiVrlkdkkv 49 
                                        +Y+e l tf+ave     +S l++   iV l + + 
  gi|386001736|ref|YP_005920035.1| 158 GRYDEYLMTFDAVEptETERSRLQETKVIVMLWQREP 194
                                       69***********9444689***********988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1851.94
//
Query:       gi|386001737|ref|YP_005920036.1|  [L=276]
Description: ABC-3 transport family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-48  165.4  37.0      2e-48  165.1  37.0    1.0  1  ABC-3     ABC 3 transport family
    0.00082   18.5  36.4     0.0016   17.5  36.5    1.6  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1  37.0   2.2e-52     2e-48       3     257 ..       9     265 ..       7     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 2.2e-52
                             ABC-3   3 eflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktk 79 
                                       +++ ra+ a ++ s+ac++lg+ +     s +g ++sHaa++G a++++l++n+ ++ai++++ +a  ++ ++ k+k
  gi|386001737|ref|YP_005920036.1|   9 NVVCRAVEAMVFASVACSILGVIISRMNLSSIGFTMSHAAFAGAAIGMFLEINPQMAAIIFSVGVAALIGPVSDKAK 85 
                                       5678999*****************999************************************************** PP

                             ABC-3  80 lkedtaigivlsvflalglvlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfd 154
                                       ++ d+ +g+++++++a++++lvs ++      +  + LfGn++++ +ed++ +a+++a++++ +l f+ke+++i+f+
  gi|386001737|ref|YP_005920036.1|  86 MAADATLGVLFAMSMAVAIFLVSFMQYsgRGLSAGNLLFGNVISLYREDIYALAAVSALTIIFVLAFYKEITAIMFN 162
                                       **************************9444455669***************************************** PP

                             ABC-3 155 eelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlll 231
                                        + A+++g++vkl++++ll ++a++v+++l++vG +L++ ll++Pa+tA +++ +++s+++ A l++l  +++G++ 
  gi|386001737|ref|YP_005920036.1| 163 MKIAEAAGVRVKLVYYILLFIVAISVSLTLNIVGGLLIFVLLVTPASTAGQFCFNVRSMFVAAPLVALSISAFGVWA 239
                                       ***************************************************************************** PP

                             ABC-3 232 SyyldlatGavivlvatllfllallv 257
                                        + + l+  ++++l++t++f +++lv
  gi|386001737|ref|YP_005920036.1| 240 GFEYTLPIAPLVALLLTSAFGVSVLV 265
                                       ********************988875 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  36.5   1.8e-07    0.0016      80     305 ..      45     263 ..      17     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-07
                             FecCD  80 ssgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslllllln 156
                                       s++a +ga+++++l      ++   +aa+++++ +++l+  ++ k k a  ++l   G+ +++ ++ ++ l+ ++  
  gi|386001737|ref|YP_005920036.1|  45 SHAAFAGAAIGMFL------EINPQMAAIIFSVGVAALIGPVSDKAKMAADATL---GVLFAMSMAVAIFLVSFMQY 112
                                       44445555555544......5566677777777777777777744444444444...44433333222222222224 PP

                             FecCD 157 eealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallta 233
                                       + +  s+ + l+G++ +   ++++ l+++++l+++++l++++++++++++ ++A++ Gv+v+ v ++ll++va+ ++
  gi|386001737|ref|YP_005920036.1| 113 SGRGLSAGNLLFGNVISLYREDIYALAAVSALTIIFVLAFYKEITAIMFNMKIAEAAGVRVKLVYYILLFIVAISVS 189
                                       457788999******************************************************************** PP

                             FecCD 234 vavalv.GpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllspte.lpvgivtaliGapf 305
                                       ++  +v G + Fv L+ P      +  + r++ +++ l++  + ++  +++  ++ p+  l + ++t+++G+ +
  gi|386001737|ref|YP_005920036.1| 190 LTLNIVgGLLIFVLLVTPASTAGQFCFNVRSMFVAAPLVALSISAFGVWAGFEYTLPIApLVALLLTSAFGVSV 263
                                       *9976626789*******99987777778887777777777776666666554444444233345555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2025.29
//
Query:       gi|386001738|ref|YP_005920037.1|  [L=248]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-24   85.2   0.0    7.6e-24   84.8   0.0    1.1  1  ABC_tran    ABC transporter
    6.7e-08   32.7   0.1     0.0038   17.1   0.1    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0011   19.1   0.8       0.11   12.8   0.8    2.6  1  SbcCD_C     Putative exonuclease SbcCD, C subunit
     0.0032   18.0   0.1     0.0054   17.3   0.1    1.2  1  AAA_23      AAA domain
     0.0094   15.6   0.0      0.017   14.7   0.0    1.3  1  AAA_27      AAA domain
  ------ inclusion threshold ------
      0.012   15.0   0.1        2.7    7.3   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
      0.015   15.0   0.1      0.028   14.2   0.1    1.4  1  AAA_29      P-loop containing region of AAA domain
      0.072   11.9   0.1       0.52    9.0   0.1    1.9  2  ABC_ATPase  Predicted ATPase of the ABC class
      0.082   12.0   0.2       0.12   11.4   0.2    1.2  1  T2SSE       Type II/IV secretion system protein
       0.11   12.3   0.0        2.4    8.0   0.0    2.0  2  ATPase_2    ATPase domain predominantly from Archaea
       0.17   12.2   0.1       0.28   11.6   0.1    1.6  1  AAA_16      AAA ATPase domain
       0.18   11.5   0.0       0.26   11.0   0.0    1.2  1  AAA_15      AAA ATPase domain
       0.21   11.8   0.1       0.36   11.0   0.1    1.4  1  AAA_28      AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.0   5.5e-27   7.6e-24       2     136 ..      22     170 ..      21     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 5.5e-27
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltv 76 
                                       + +sl++k ge ++i G+n aGK+tLl+ +  l++ t G+ ++ g dl++   +++r+++g++ q+     f   tv
  gi|386001738|ref|YP_005920037.1|  22 RGLSLSVKSGEYLVIGGPNSAGKTTLLESINALVRITHGSATVCGLDLRR-YGNEVRRKVGYVIQNfyFDPFTPFTV 97 
                                       579**********************************************9.7888999********55444444457 PP

                                       HHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +e                   ++e +++a++ lg+++l+ +++     +LSgGq+q+ ++a  ++k+p++l+lDEp+
  gi|386001738|ref|YP_005920037.1|  98 EEVvmmgrygkmgllkrpsrSDREAASEAIRLLGIEDLASKTI----GTLSGGQQQKTMIAHNIAKEPEVLMLDEPF 170
                                       777*************99855555599***************9....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.8e-06    0.0038       3      46 ..      35      86 ..      33      95 .. 0.73
   2 !   13.7   0.0     3e-05     0.041     233     297 ..     139     200 ..     104     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl........drdvegltdelsggggirkip 46
                                      v+ GpN++GK++LL+ +  l r+          d+++ ++e ++++g+ ++ 
  gi|386001738|ref|YP_005920037.1| 35 VIGGPNSAGKTTLLESINALVRIthgsatvcGLDLRRYGNEVRRKVGYVIQN 86
                                      899**************99988777777776666666666666666665555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-05
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++  lS G+++   +++  ++  +   +l +DEp ++L+ ++ + l +++k+ +++g+ ++l++H
  gi|386001738|ref|YP_005920037.1| 139 TIGTLSGGQQQK-TMIAHNIAKEP--EVLMLDEPFSNLDFSAREYLQGVFKSVAKKGTPILLVSH 200
                                       456679999999.77777776665..9*************************************9 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.8   7.8e-05      0.11      27      88 ..     137     185 ..     117     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       s+ +gtlSGG++q+++         + +       + +++++LDE Fs+lD   ++ l +++
  gi|386001738|ref|YP_005920037.1| 137 SKTIGTLSGGQQQKTMIA-------HNI------AKEPEVLMLDEPFSNLDFSAREYLQGVF 185
                                       667788888888665432.......222......34699************98888776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   3.9e-06    0.0054      23      40 ..      35      52 ..      23      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                            AAA_23 23 lItGpNGaGKTTildAik 40
                                      +I GpN aGKTT+l+ i 
  gi|386001738|ref|YP_005920037.1| 35 VIGGPNSAGKTTLLESIN 52
                                      8**************997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.017      19      49 ..      24      54 ..      21      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      l++s ++ +  +i GpN AGK+t+l++i++l
  gi|386001738|ref|YP_005920037.1| 24 LSLSVKSGEYLVIGGPNSAGKTTLLESINAL 54
                                      677777888899****************988 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0053       7.3      27      45 ..      34      52 ..      25      62 .. 0.86
   2 ?    7.3   0.0     0.002       2.7     136     197 ..     142     200 ..      83     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0053
                                      EEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAil 45
                                       +i GpN +GK+ ll++i 
  gi|386001738|ref|YP_005920037.1| 34 LVIGGPNSAGKTTLLESIN 52
                                      5899*************95 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivisl 197
                                       +LSgG+++ +++a  +A    k   + +lDe  ++LD++ ++ +  ++k+  k+ + ++ +s+
  gi|386001738|ref|YP_005920037.1| 142 TLSGGQQQKTMIAHNIA----KEPEVLMLDEPFSNLDFSAREYLQGVFKSVAKKgTPILLVSH 200
                                       79*****9999986654....34446789***************9999987766466777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-05     0.028      17      46 ..      26      55 ..      20      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      ++++  +  ++ Gp+ +GK+Tll +i+al 
  gi|386001738|ref|YP_005920037.1| 26 LSVKSGEYLVIGGPNSAGKTTLLESINALV 55
                                      5566444777889************99985 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00038      0.52     240     266 ..      26      53 ..      14      56 .. 0.77
   2 ?    0.4   0.0      0.16   2.2e+02     320     358 ..     140     178 ..     128     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00038
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                       + ++ G   +I G++  GK+TLLe++++
  gi|386001738|ref|YP_005920037.1|  26 LSVKSGeYLVIGGPNSAGKTTLLESINA 53 
                                       357889667778889*********9975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.16
                                       ESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH-- CS
                        ABC_ATPase 320 tedASGStsqAanimealeagakllLiDEDtsAtNlmir 358
                                         + SG   q   i+  +  + ++l++DE  s   +  r
  gi|386001738|ref|YP_005920037.1| 140 IGTLSGGQQQKTMIAHNIAKEPEVLMLDEPFSNLDFSAR 178
                                       56679999999******************8877666555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2     9e-05      0.12     120     153 ..      22      55 ..       9      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                             T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallkei 153
                                       + l+ +v++   +++ G+ + GKttll ++ + +
  gi|386001738|ref|YP_005920037.1|  22 RGLSLSVKSGEYLVIGGPNSAGKTTLLESINALV 55 
                                       66888999999****************7665544 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 ?    8.0   0.0    0.0017       2.4      20      41 ..      31      52 ..      24      86 .. 0.79
   2 ?    2.5   0.0     0.086   1.2e+02      72     124 ..     147     198 ..     104     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeii 41
                                       e ++i Gp + GKt+Ll  i 
  gi|386001738|ref|YP_005920037.1| 31 GEYLVIGGPNSAGKTTLLESIN 52
                                      567899***********98764 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.086
                          ATPase_2  72 eeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiii 124
                                       +++k+ ++  ++++ +   l+e +++    + ++++ +++++ kkg+ i + +
  gi|386001738|ref|YP_005920037.1| 147 QQQKTMIAHNIAKEPEVLMLDEPFSNLDFSAREYLQGVFKSVAKKGTPILL-V 198
                                       55566666666677777778888889999999*************995544.3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0002      0.28      21      48 ..      30      55 ..      22     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellral 48
                                      sg  e++++ G+   GK++l++++   +
  gi|386001738|ref|YP_005920037.1| 30 SG--EYLVIGGPNSAGKTTLLESINALV 55
                                      44..89***************9998533 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.26      25      48 ..      33      56 ..      22      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                            AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                      + v+ G+N++GK+++le ++ +  
  gi|386001738|ref|YP_005920037.1| 33 YLVIGGPNSAGKTTLLESINALVR 56
                                      678889*************99876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00026      0.36       3      21 ..      35      53 ..      33      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                            AAA_28  3 vitGgestGKTtlleaLaa 21
                                      vi G+ s+GKTtlle ++a
  gi|386001738|ref|YP_005920037.1| 35 VIGGPNSAGKTTLLESINA 53
                                      788999********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2029.90
//
Query:       gi|386001739|ref|YP_005920038.1|  [L=64]
Description: hypothetical protein Mhar_1046 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.4   0.0      0.067   13.2   0.0    1.1  1  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.7e-06     0.067      56     104 ..       1      45 [.       1      62 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-06
                                       TTTTSEEE--SS-SEEEEEETTT-EEEEEEE-CCTHHHHHHHCCT--.GG CS
                              FmdE  56 lGkgnlivmdygkkaltfkkrktgkavrlklkeelpelreklakgka.ke 104
                                       +Gkgn+  +d+g+ ++tf     g+ v+lk+k   + +++++++g   + 
  gi|386001739|ref|YP_005920038.1|   1 MGKGNIETVDLGRAEATFSA--GGERVTLKVK---DGVMAEIKAGGYaSL 45 
                                       6*****************95..6899999999...777777776654333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.50
# Mc/sec: 386.70
//
Query:       gi|386001740|ref|YP_005920039.1|  [L=311]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-19   69.1   0.3    7.8e-19   68.2   0.3    1.5  1  DDE_Tnp_1    Transposase DDE domain
    1.1e-18   67.0   0.0    2.3e-18   66.0   0.0    1.5  1  DUF772       Transposase domain (DUF772)
     0.0015   18.2   0.0     0.0023   17.6   0.0    1.4  1  DDE_Tnp_4    DDE superfamily endonuclease
     0.0016   18.7   0.0     0.0029   17.8   0.0    1.4  1  DDE_Tnp_1_6  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.3   1.7e-22   7.8e-19       3     214 .]     133     299 ..     131     299 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.7e-22
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w++kg+++++gyklh  vd    li  +++t+++vhds++ 
  gi|386001740|ref|YP_005920039.1| 133 VKRGTIQDATFIEADPGSskkpredqaktrrsRDGTWTKKGDEFHFGYKLHSKVDIDYALIREIDTTTAKVHDSRVD 209
                                       6789999*******88889*************9*****************************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                                  g +vl+D+GY+  ++  ++                              ++++ ++++l   +++r
  gi|386001740|ref|YP_005920039.1| 210 LS-----V--PGEVVLRDKGYFgVPARGEDFT----------------------------MKRRTTERPLDDLENER 251
                                       54.....2..9***********5566666666............................***************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       n+                          +++lR+  Er F+ +kr+fg +r+ + +l rv  +++  ++++nl
  gi|386001740|ref|YP_005920039.1| 252 NR-------------------------LISKLRSPGERPFAVIKRVFGAGRVLVTTLKRVYGKMIVAAISYNL 299
                                       **.........................*********************************************8 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   5.1e-22   2.3e-18       1      72 [.      50     121 ..      50     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 5.1e-22
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp+ ++ +m+++l+l ++ygl d e+++++++++sf+ flg+    ++vpd st++ f +r++e    +r+++e
  gi|386001740|ref|YP_005920039.1|  50 GRPNCDVLMMFRILILEEWYGLNDLEVVRQIKDRVSFMGFLGFP---EQVPDSSTIWLFKERMIEtgtHDRVWDE 121
                                       9*****************************************95...99**************999988887776 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.2e-07    0.0023      73     134 ..     212     276 ..     176     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.2e-07
                         DDE_Tnp_4  73 kpgdvilaDkgFklsekl...lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfril 134
                                        pg+v+l Dkg+ + +      ++++++++ +l+  e e+nr i++ r   Er ++ +k+ f   
  gi|386001740|ref|YP_005920039.1| 212 VPGEVVLRDKGYFGVPARgedFTMKRRTTERPLDDLENERNRLISKLRSPGERPFAVIKRVFGAG 276
                                       4799********8655222327888889*******************************998765 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.4e-07    0.0029      68     124 ..     247     302 ..     229     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.4e-07
                       DDE_Tnp_1_6  68 ikseegkaeykkRaitvEgvfaqikrnlglrrfrlrGlkkvklqfllvalalNlkkl 124
                                       ++ e+ +   k R+   E+ fa ikr  g+ r+ ++ lk+v  ++++ a+ +Nl +l
  gi|386001740|ref|YP_005920039.1| 247 LENERNRLISKLRS-PGERPFAVIKRVFGAGRVLVTTLKRVYGKMIVAAISYNLYQL 302
                                       55565666667776.99*************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.65 Elapsed: 00:00:00.81
# Mc/sec: 1154.77
//
Query:       gi|386001741|ref|YP_005920040.1|  [L=170]
Description: hypothetical protein Mhar_1048 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00093   19.3   0.8     0.0014   18.6   0.8    1.4  1  CoA_binding_3  CoA-binding domain
  ------ inclusion threshold ------
       0.19   12.0   6.3        2.5    8.4   0.5    2.4  2  Orf78          Orf78 (ac78)
          8    6.7   6.0       0.85    9.9   0.2    2.0  2  Glycophorin_A  Glycophorin A


Domain annotation for each model (and alignments):
>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.8   2.4e-07    0.0014      17      77 ..      35      96 ..      24     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
                     CoA_binding_3 17 lllrvlsawllvllllallsfs.lkdafSRlwlaywavvglvllivsrllvravlrrlrrng 77
                                      +l+  + ++ l+++++ ++  s l+d +S +w+ ++av+ l+  i+s++++++++++  r++
  gi|386001741|ref|YP_005920040.1| 35 ELTICAISVYLSWGIFYMTTPSrLTDKLSIIWFSSFAVILLLYFILSQYIIHRMMTKAKRDN 96
                                      455555566666666666555546799***************************99987764 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00042       2.5      64      96 ..      60      93 ..      33     101 .. 0.76
   2 ?    6.8   0.8    0.0014       8.3      60      88 ..     141     169 ..     102     170 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00042
                             Orf78 64 nillisllavvcvlvlly.viyYfvilrerqkss 96
                                      + l i   + ++v++lly +++ ++i r  +k +
  gi|386001741|ref|YP_005920040.1| 60 DKLSIIWFSSFAVILLLYfILSQYIIHRMMTKAK 93
                                      5566666777888888761667899999877665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0014
                             Orf78  60 aqalnillisllavvcvlvllyviyYfvi 88 
                                        ++++il i+l++++ ++v+l  i++ v+
  gi|386001741|ref|YP_005920040.1| 141 FGIYEILHIVLIVIIPLVVVLLEIIFEVV 169
                                       567899*********99999999988665 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00014      0.85      61      92 ..      63      95 ..      58     101 .. 0.83
   2 ?   -1.0   1.3      0.33     2e+03      58      79 ..     144     165 ..     116     170 .] 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHHHHHHHHH.HHHHTHSXXXXXX CS
                     Glycophorin_A 61 tliifgvmAgvigtillis.YlirRliKKssvd 92
                                        i f+  A++++  +++s Y+i R++ K++ d
  gi|386001741|ref|YP_005920040.1| 63 SIIWFSSFAVILLLYFILSqYIIHRMMTKAKRD 95
                                      56889999999998887766*******999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.33
                                       TTHHHHHHHHHHHHHHHHHHHH CS
                     Glycophorin_A  58 lvitliifgvmAgvigtillis 79 
                                        +i  i++ v+  ++ ++l i 
  gi|386001741|ref|YP_005920040.1| 144 YEILHIVLIVIIPLVVVLLEII 165
                                       5555555555544444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1096.26
//
Query:       gi|386001742|ref|YP_005920041.1|  [L=109]
Description: hypothetical protein Mhar_1049 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-28   98.3   6.0    4.8e-28   98.1   6.0    1.0  1  DUF5320    Family of unknown function (DUF5320)
  ------ inclusion threshold ------
      0.044   14.2   0.3      0.057   13.8   0.3    1.1  1  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   6.0   5.4e-32   4.8e-28       1      99 []       1     105 [.       1     105 [. 0.87

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 5.4e-32
                           DUF5320   1 MPrgdgtGpmGlGpmtGrglGyCagadapgyansagfGr....grg...grglgrgfgrrrraggarlaaaetaeas 70 
                                       MP+gdgtGp G Gp+tGrg+GyC+g++apgya+  g+Gr    grg   grg+g +f++r+ ++ a+l+ +++ ++s
  gi|386001742|ref|YP_005920041.1|   1 MPGGDGTGPAGFGPRTGRGMGYCSGFEAPGYAR-GGYGRpfgsGRGgirGRGRGLCFWYRMPTPLASLGPYPPGAPS 76 
                                       *******************************98.666665555555545777777788888888888879******* PP

                           DUF5320  71 keeekelLeeqaeaLeeeleaikkrlkel 99 
                                       +e e + Le  ae+Le++l+ ik+r++el
  gi|386001742|ref|YP_005920041.1|  77 PEVEMADLEVMAESLEAQLKSIKARIEEL 105
                                       ***************************97 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   6.4e-06     0.057       6      34 ..      78     106 ..      77     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                         FlaC_arch   6 Enklsklsteletvkkeneelsksveelk 34 
                                       E ++ +l+++ e++++++++++  +eelk
  gi|386001742|ref|YP_005920041.1|  78 EVEMADLEVMAESLEAQLKSIKARIEELK 106
                                       779************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 725.59
//
Query:       gi|386001743|ref|YP_005920042.1|  [L=115]
Description: hypothetical protein Mhar_1050 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-19   70.6   0.3    2.9e-19   69.4   0.1    1.6  2  DUF134        Protein of unknown function  DUF134
  ------ inclusion threshold ------
      0.013   15.1   1.0       0.02   14.6   0.0    1.8  2  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.1   3.3e-23   2.9e-19      34      96 ..       2      64 ..       1      66 [. 0.96
   2 ?   -1.1   0.0      0.32   2.9e+03      36      47 ..      87      98 ..      75     114 .. 0.54

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 3.3e-23
                            DUF134 34 aisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiakalveGraiilkGGeyk 96
                                      +++l+eleairlvd+ dl+q+ea+  +G+s+++lw+ l ++rkk+a+al+ G  i+++GG y 
  gi|386001743|ref|YP_005920042.1|  2 KVTLEELEAIRLVDFLDLQQQEASLYVGVSRKALWNDLRSGRKKVASALICGLGIVIEGGSYL 64
                                      589*********************************************************995 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                            DUF134 36 sldeleairlvd 47
                                       l ele i l +
  gi|386001743|ref|YP_005920042.1| 87 RLLELEMIALEE 98
                                      344444443332 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-06      0.02      17      53 ..       9      45 ..       4      46 .. 0.94
   2 ?   -2.6   0.3       0.5   4.5e+03      46      51 ..     101     106 ..      99     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-06
                                      HHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2 17 eifllryleglsykEIAellgisegtVksrlsRArkk 53
                                      e++ l ++ +l ++E++ + g+s ++  + l+ +rkk
  gi|386001743|ref|YP_005920042.1|  9 EAIRLVDFLDLQQQEASLYVGVSRKALWNDLRSGRKK 45
                                      7999********************************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.5
                                       HHHHHH CS
                      Sigma70_r4_2  46 rlsRAr 51 
                                       rl+RAr
  gi|386001743|ref|YP_005920042.1| 101 RLMRAR 106
                                       899999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 795.20
//
Query:       gi|386001744|ref|YP_005920043.1|  [L=140]
Description: hypothetical protein Mhar_1051 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1064.03
//
Query:       gi|386001745|ref|YP_005920044.1|  [L=295]
Description: hypothetical protein Mhar_1052 [Methanosaeta harundinacea 6Ac]
Scores for 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-26   90.8  16.4    1.1e-25   90.3  16.4    1.1  1  UbiA          UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3  16.4   6.4e-30   1.1e-25       6     233 ..      22     248 ..      18     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 6.4e-30
                              UbiA   6 lvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme...rtpnRPlvsGrispkealifaivllil 79 
                                       l+g++la+gg       ll+l++ l+++++a ++N++fD++iD++++      + Pl++Gr+  + +++++++l+ +
  gi|386001745|ref|YP_005920044.1|  22 LAGALLAGGGADRV---LLVLIAYLFLISYAFVVNNFFDADIDRQHRlkvASGKNPLAAGRVEERRVILMMLLLISI 95 
                                       78999998887666...7888888899999*****************99866778********************** PP

                              UbiA  80 gllllalllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafg.lppllgwaavtgslsllalllalavf 153
                                        lll+ l l+   a+++l++l++ ++Y+   +rlK r l++    g+ fg lp+l+g+ +++g++s  ++l+++++f
  gi|386001745|ref|YP_005920044.1|  96 PLLLS-LRLSTAGAVFVLINLVVMTAYStSrIRLKERYLWDAASHGLMFGaLPFLAGFLLCGGEVSRGIILISILLF 171
                                       *****.**********************989*************9999885888888888***************** PP

                              UbiA 154 lltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallra 230
                                       ++    ++a ++ d+ +D+     t++++ G+k+ + +l  l a+ +  +++l +  l  + l++a+++a++++++ 
  gi|386001745|ref|YP_005920044.1| 172 IVGCEALIAHQIVDYAEDLGS-TTTTVTRVGQKNGLLMLGGLAALSV--VFALAASRLYQPSLAVAAASALYLVAYP 245
                                       *********999999999544.4666677799999984333333332..3566677777777777777777777665 PP

                              UbiA 231 arl 233
                                        + 
  gi|386001745|ref|YP_005920044.1| 246 TYS 248
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 2248.24
//
Query:       gi|386001746|ref|YP_005920045.1|  [L=225]
Description: Glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-15   57.2   0.1    3.4e-15   56.3   0.0    1.5  2  Glycos_transf_2  Glycosyl transferase family 2
    6.8e-11   42.5   0.8    6.9e-10   39.2   0.8    2.0  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    5.1e-05   23.3   0.1    6.7e-05   22.9   0.1    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    7.3e-05   22.3   0.0    0.00016   21.2   0.0    1.6  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   7.6e-19   3.4e-15      33     167 ..       2     120 ..       1     123 [. 0.87
   2 ?   -3.1   0.0       1.3   5.8e+03     109     132 ..     145     168 ..     140     194 .. 0.52

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 7.6e-19
                                       EEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TT CS
                   Glycos_transf_2  33 vvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdga 109
                                       vvD gS D tvei+e++a+     rvi +++  G +ga++ g++aatg  ++f DaD+++++ wle + + le  ++
  gi|386001746|ref|YP_005920045.1|   2 VVDGGSDDATVEIAEKYAD-----RVISQTHP-GIGGARRDGAQAATGGALAFTDADTAFPKVWLEVVSRNLEV-RE 71 
                                       8****************98.....99999988.*****************************************.66 PP

                                       CEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHH CS
                   Glycos_transf_2 110 dvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrreale 167
                                       +    + p+if+++d ++         r ++  +k  +  n  ++igs++++rre ++
  gi|386001746|ref|YP_005920045.1|  72 A---STGPVIFQDRDLRTEI------LRAWRSSYKLLKAFNFCYMIGSNMAMRRETYQ 120
                                       4...4445555555555544......34689***********************9765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                       TCEEEEEEEEEECCCCCCCHC-SS CS
                   Glycos_transf_2 109 advvlgqrprifgetdeiernkrv 132
                                       ad+v+  r +   ++++ ++ +++
  gi|386001746|ref|YP_005920045.1| 145 ADAVYDPRQAVYTSSRRAHKLLTY 168
                                       444555555544444444444443 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 !   39.2   0.8   1.5e-13   6.9e-10      36     216 ..       2     162 ..       1     168 [. 0.81

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.5e-13
                   Glyco_tranf_2_3  36 vvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvvePdtlkrllqff 112
                                       vv+ +sd++t+e ae    ++ d   rv+ +++ +g++g++r   ++ +a+++  +++ D+Dt   +  l+++ + +
  gi|386001746|ref|YP_005920045.1|   2 VVDGGSDDATVEIAE----KYAD---RVISQTH-PGIGGARR---DGAQAATGGALAFTDADTAFPKVWLEVVSRNL 67 
                                       666678888888665....6999...6999999.9*****99...***************************99999 PP

                   Glyco_tranf_2_3 113 ..ltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgvltlnGsgslirrevlkelegldplflltdD 187
                                         +    +a ++pv ++ r+  +  l a +      +  ++ +a+++ ++ Gs +++rre +++ +g++   +l dD
  gi|386001746|ref|YP_005920045.1|  68 evR----EASTGPVIFQDRDLRTEILRAWR------SSYKLLKAFNFCYMIGSNMAMRRETYQRAGGHRD-ISLLDD 133
                                       321....44446665554443333333322......23346789*********************99999.9***** PP

                   Glyco_tranf_2_3 188 yelglrlrragfrtayvpgaavrevfpss 216
                                       y+l++rl r g + +y p+ av++++++ 
  gi|386001746|ref|YP_005920045.1| 134 YDLSVRLFRIGADAVYDPRQAVYTSSRRA 162
                                       ************************99865 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.5e-08   6.7e-05      69     127 ..     104     160 ..      46     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                   Glyco_trans_2_3  69 vvpsvGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeksp 127
                                       ++ + Gs+++ rr+  q++gg +  + s+ +D+d+++rl+r G + ++ p  +v+++s+
  gi|386001746|ref|YP_005920045.1| 104 FCYMIGSNMAMRRETYQRAGGHR--DISLLDDYDLSVRLFRIGADAVYDPRQAVYTSSR 160
                                       45689******************..9********************9999999999886 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.6e-08   0.00016      35     157 ..      47     161 ..      36     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.6e-08
                   Glyco_transf_21  35 visDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqaklsglgfavGksmalrre 111
                                        + D+d+++++  Le + ++le    +  t++ v  + + l +++ +a     +++l+a +  +  ++G+ ma+rre
  gi|386001746|ref|YP_005920045.1|  47 AFTDADTAFPKVWLEVVSRNLEV--REASTGP-VIFQDRDLRTEILRAWR-SSYKLLKA-F-NFCYMIGSNMAMRRE 117
                                       56666666666666666666663..2333443.33444445555544443.33444555.2.445579********* PP

                   Glyco_transf_21 112 aLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvpr 157
                                       + +++GG + +   L +Dy l+ +l + G   v  p+ ++ ts +r
  gi|386001746|ref|YP_005920045.1| 118 TYQRAGGHRDI--SLLDDYDLSVRLFRIGADAVYDPRQAVYTSSRR 161
                                       **********5..7*******************9999988888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1492.48
//
Query:       gi|386001747|ref|YP_005920046.1|  [L=205]
Description: lysine exporter protein LysE/YggA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-30  103.6  11.8    1.1e-29  103.3  11.8    1.0  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3  11.8   6.1e-34   1.1e-29       2     188 ..      17     197 ..      16     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 6.1e-34
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       +++l+pGp ++++++++++rg+  g  va g++++++v +ll+++Gla + +     ++++  +Gg  L+ +g+++l
  gi|386001747|ref|YP_005920046.1|  17 TGALAPGPTLVATINTSLQRGWTMGPKVATGHALAEVVVFLLIVVGLASVAE---RHTAVVAAVGGTALILFGLMTL 90 
                                       689***********************************************99...557788999************* PP

                              LysE  79 rdakekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfslla 155
                                       r + + ++e + +     ++p+l+g+l+s++NP++ ++wlsv+sal+ +   +g    +i+++g++ a+  w+++++
  gi|386001747|ref|YP_005920046.1|  91 RGSRTATMEFSPEGA--SSNPYLAGALTSVANPYFWVWWLSVGSALVLAELREGILLAMIFMIGHWGADYGWYTFVS 165
                                       *******98888886..9******************************77889999999****************** PP

                              LysE 156 flaarlsrrlsskkvlriinvvvgvlligfavk 188
                                       ++  r ++ ls+  ++    +++g++l++f++ 
  gi|386001747|ref|YP_005920046.1| 166 TSLHRGRNFLSEVNYR-RTLALCGAFLVLFGAS 197
                                       *************988.56689********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1640.49
//
Query:       gi|386001748|ref|YP_005920047.1|  [L=207]
Description: hypothetical protein Mhar_1056 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-30  105.1  16.9    4.5e-30  104.8  16.9    1.2  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8  16.9   2.5e-34   4.5e-30       2     156 .]      21     187 ..       7     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.5e-34
                            SpoIIM   2 lllflvgillgallaasnfa...eqis......seskensalslflaifanNlrvalllfllGllllgiptilvlli 69 
                                       + lf+ +++lg++++a +++    ++       +   + s+++++laif+nNl  ++l++llG+  +gi++++v+++
  gi|386001748|ref|YP_005920047.1|  21 VSLFFGAAVLGFAVSARDPTlgaAYVGevadklEWILDLSPAKMMLAIFLNNLFASALALLLGV-GFGIVPAVVVVL 96 
                                       568999999999999944444442333455677788999999*********************7.************ PP

                            SpoIIM  70 nGfvlGav.aalvaefgglllflllilPhgilelpaiiiagaaglrlgkal....rsrrkalkeakrellklllllv 141
                                       nG+v+G+v +  v+  gg  ++l++i+Phgi+elp +++a+++g+rlg  +      rr +l+ +  + ++ll +++
  gi|386001748|ref|YP_005920047.1|  97 NGAVVGLVvHQAVMA-GGATFVLVAIIPHGIIELPTVLVAIGVGFRLGHLMiltlLGRRVDLEGELLAGIRLLRWVA 172
                                       ******663666666.56*************************************9999****************** PP

                            SpoIIM 142 pllliAaliEafvtp 156
                                       +ll+iAa iEaf+tp
  gi|386001748|ref|YP_005920047.1| 173 LLLFIAAAIEAFITP 187
                                       **************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1571.73
//
Query:       gi|386001749|ref|YP_005920048.1|  [L=473]
Description: prolyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-26   90.8   0.0    1.4e-25   90.3   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.1e-18   67.2   0.0    3.9e-18   65.4   0.1    2.0  2  HGTP_anticodon  Anticodon binding domain
    2.8e-12   46.6   1.2    2.8e-12   46.6   1.2    2.3  3  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
        0.1   12.8   0.3          1    9.6   0.0    2.5  3  DUF3006         Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   3.1e-29   1.4e-25      10     178 ..     103     271 ..      90     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.1e-29
                                       EEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxx RF
                      tRNA-synt_2b  10 eyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslrdl 83 
                                       +++L+Pt+e++++ +++ + +rs  +LPlk+yqi   +R+E++ +r+L+R+re++  k+++ +ha  +++ ++++  
  gi|386001749|ref|YP_005920048.1| 103 KLALRPTSETAIYPIFKLW-VRShADLPLKIYQIVNTFRYETKHTRPLIRLREITSfKEAHTVHAtWDEAAEQVEAA 178
                                       789**************88.9**778*****************9**********8659*******7799******** PP

                                       HHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksv 159
                                       ++ ++++++rl ++f   ++  +++  +  +++  ++ v++  +++++igt++ lgt+++ + g+t+ +e +++++ 
  gi|386001749|ref|YP_005920048.1| 179 LNIYAEFYRRLAIPFLFARRPsWDK-FPGSDYSIALDTVMP-DGRTLQIGTAHLLGTNFATTYGITFENEGGEQEFA 253
                                       *************996666654775.489999*********.9********************************** PP

                                       EEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 160 imicaaigveRllsaileq 178
                                         +c++++ eR ++a++++
  gi|386001749|ref|YP_005920048.1| 254 NQTCYGVS-ERCIAALISV 271
                                       ********.******9875 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.1   8.6e-22   3.9e-18       1      93 [.     288     380 ..     288     381 .. 0.89
   2 ?   -3.5   0.0       2.8   1.2e+04      48      64 ..     448     464 ..     447     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 8.6e-22
                                       SEEEEESSSS.HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                    HGTP_anticodon   1 qvvviplnek.aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                       qvv++p+  k +e+ +e+ ++++++L aagir+ +d+s+e++g k+ +++++g+p+++++G++++e+g+  + +r +
  gi|386001749|ref|YP_005920048.1| 288 QVVIVPILFKdKERTLEVSREIKARLAAAGIRAAIDESDERPGAKFYKWEMKGVPIRIEIGPRDIENGVAVLARR-D 363
                                       8******999888899*************************************************6665555555.6 PP

                                       CEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  77 reqervsldelveklke 93 
                                       +++ +v+ld l++ ++e
  gi|386001749|ref|YP_005920048.1| 364 GKKLTVPLDGLLASIEE 380
                                       7778***9999988876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                       HHHTT-SEEEEE-HHHH CS
                    HGTP_anticodon  48 adllgipfavvvGekel 64 
                                       + ++g + ++v G+++ 
  gi|386001749|ref|YP_005920048.1| 448 SSEKGERSCIVCGARTE 464
                                       578899999****9986 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4   6.4e+03      10      24 ..     160     174 ..     156     180 .. 0.70
   2 ?   -3.3   0.0       2.5   1.1e+04      20      34 ..     301     315 ..     275     327 .. 0.62
   3 !   46.6   1.2   6.3e-16   2.8e-12      11      69 .]     416     473 .]     407     473 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                       TT-EEEEEESSGHHH CS
                         ProRS-C_1  10 kkgfvlapWcgeeec 24 
                                       + + v a W++ +e 
  gi|386001749|ref|YP_005920048.1| 160 EAHTVHATWDEAAEQ 174
                                       556889999986654 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                       SGHHHHHHHHHHHS- CS
                         ProRS-C_1  20 geeecEekIkeetga 34 
                                        + e  ++Ik + +a
  gi|386001749|ref|YP_005920048.1| 301 RTLEVSREIKARLAA 315
                                       344566677777643 PP

  == domain 3  score: 46.6 bits;  conditional E-value: 6.3e-16
                                       T-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1  11 kgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                        g++++ Wcg+eec  +I+ee+ga +l+ p+ +  ++++  Civcg  ++k +l +r+Y
  gi|386001749|ref|YP_005920048.1| 416 AGVARVAWCGSEECGHRIEEEVGAAVLGEPWRS-SEKGERSCIVCGARTEKCALLARQY 473
                                       4699***************************96.789*********************9 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.3   1.5e+04      19      34 ..      48      63 ..      46      64 .. 0.72
   2 ?   -0.2   0.0      0.26   1.2e+03      47      63 ..     297     313 ..     283     315 .. 0.85
   3 ?    9.6   0.0   0.00023         1       6      34 ..     352     380 ..     351     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.3
                           DUF3006 19 etidiprsdLpegake 34
                                      +++d+ r++L ++ +e
  gi|386001749|ref|YP_005920048.1| 48 NVYDLMRELLDPDHQE 63
                                      6788888888877655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                           DUF3006  47 ldpeetekrkeriqell 63 
                                        d+e t +  ++i+++l
  gi|386001749|ref|YP_005920048.1| 297 KDKERTLEVSREIKARL 313
                                       69999999999999997 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00023
                           DUF3006   6 fEgdlAVleledgetidiprsdLpegake 34 
                                       +E+++AVl  +dg+++++p++ L ++++e
  gi|386001749|ref|YP_005920048.1| 352 IENGVAVLARRDGKKLTVPLDGLLASIEE 380
                                       8********************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 3704.43
//
Query:       gi|386001750|ref|YP_005920049.1|  [L=304]
Description: hypothetical protein Mhar_1058 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-33  115.8   0.0    2.5e-33  115.4   0.0    1.1  1  ATP-grasp_3     ATP-grasp domain
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.059   13.6   0.0    1.5  1  preATP-grasp_3  pre ATP-grasp 3 domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.0   2.7e-37   2.5e-33       2     161 .]     111     261 ..     110     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 2.7e-37
                                       TSHHHHHHHHTTT.S---....-EESS--.SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleee.ekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSv 77 
                                       +dKl+++++L+e++v+v    e + ++     ++v+Kpr G+g+e + +v+e +e+      + ++ +f +G+ lSv
  gi|386001750|ref|YP_005920049.1| 111 ADKLACTRRLQEEAVPVV---EIADPDDPgTGPFVLKPRFGCGSERMELVDELPEDL----GDRIATRFCQGEALSV 180
                                       7************55554...66666655488*********************8888....456************* PP

                                       EEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEE CS
                       ATP-grasp_3  78 sllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEv 154
                                       sl+++g +vl+l+vn+ql+   e +f y+G+++p++ +++ee+ ++a+ + ++l +l Gy+G+Dlv+ d  p v++v
  gi|386001750|ref|YP_005920049.1| 181 SLIASGDRVLPLTVNKQLVSV-EAGFEYRGGIVPYRSDREEEILKAAKMAARAL-DLSGYAGIDLVVGD-LPRVVDV 254
                                       *******************86.888*****************************.**************.******* PP

                                       ESS--GG CS
                       ATP-grasp_3 155 NPRltts 161
                                       NPR+tts
  gi|386001750|ref|YP_005920049.1| 255 NPRPTTS 261
                                       *****97 PP

>> preATP-grasp_3  pre ATP-grasp 3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.6e-06     0.059      28      76 ..      59     106 ..      47     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-06
                    preATP-grasp_3  28 edvdetfrrlaa..eaDaVlvIAPEtdgiLarltrlveaagkrlLGssskA 76 
                                       ++ de+f++ +a  +aDa lvIAP  d++L  + +++e+    +LG+s++A
  gi|386001750|ref|YP_005920049.1|  59 GKSDEHFEDFLAgsGADAGLVIAP--DELLPGFLEILEKG-TANLGCSPAA 106
                                       5677888888642279********..9********99987.9*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2263.33
//
Query:       gi|386001751|ref|YP_005920050.1|  [L=77]
Description: hypothetical protein Mhar_1059 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-15   55.0   0.2    6.1e-15   55.0   0.2    1.3  2  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.2   3.4e-19   6.1e-15       2      58 .]       6      61 ..       5      61 .. 0.96
   2 ?   -2.9   0.1       0.4   7.2e+03      13      21 ..      67      75 ..      67      77 .] 0.66

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.4e-19
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      ++ +k+ +klGf+++rqkG H r+khpd+r ++t+p H + e++ +    Ilkq+G+
  gi|386001751|ref|YP_005920050.1|  6 KDREKAAAKLGFQKIRQKGGHARWKHPDGR-ATTIPIHANSEIGGWPFYEILKQLGI 61
                                      67799************************9.78**********************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.4
                                      -EEEEEETT CS
                        HicA_toxin 13 fevvrqkGS 21
                                      +++vr  G 
  gi|386001751|ref|YP_005920050.1| 67 WKLVRGDGG 75
                                      788887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 511.69
//
Query:       gi|386001752|ref|YP_005920051.1|  [L=75]
Description: hypothetical protein Mhar_1060 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-09   35.6   0.0    9.3e-09   35.5   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   5.2e-13   9.3e-09       1      64 [.       7      70 ..       7      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 5.2e-13
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssieel 64
                                      y i++ +d++ ++   vP +pGc+ +g+t eea a++ ++ e+  e+  e+g+++p+  ++e++
  gi|386001752|ref|YP_005920051.1|  7 YTIVLRPDDNGTFVAYVPAIPGCHAWGETPEEAQAEIVNVFEMIKEEYREEGRQLPQDVDLESV 70
                                      89******************************************************99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 487.48
//
Query:       gi|386001753|ref|YP_005920052.1|  [L=104]
Description: hypothetical protein Mhar_1061 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.022   14.8   0.0    1.2  1  ATP-grasp_3  ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-06     0.022     137     161 .]      28      51 ..      19      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
                                       EEEEEEEESS.SEEEEEEESS--GG CS
                       ATP-grasp_3 137 yvGvDlvlkdeepyviEvNPRltts 161
                                        +G+Dlv+ d  + v++ NPR+tts
  gi|386001753|ref|YP_005920052.1|  28 PAGIDLVVGD-LLRVVDANPRPTTS 51 
                                       57********.9***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 635.92
//
Query:       gi|386001754|ref|YP_005920053.1|  [L=123]
Description: hypothetical protein Mhar_1062 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 764.32
//
Query:       gi|386001755|ref|YP_005920054.1|  [L=119]
Description: hypothetical protein Mhar_1063 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.1   0.1        1.5    8.7   0.1    2.0  2  CHASE3    CHASE3 domain


Domain annotation for each model (and alignments):
>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.001        19      78     123 ..       4      48 ..       1      66 [. 0.52
   2 ?    8.7   0.1   8.3e-05       1.5      78     117 ..      49      91 ..      34      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.001
                            CHASE3  78 lieqklaeleetialrreggleaalalvrsdegkelmdeiraliae 123
                                       l+ + ++ + et+++ re  +e    lvr +  k   d++r+l+ +
  gi|386001755|ref|YP_005920054.1|   4 LFSRSVKMMSETVEVSRE-VFEPISMLVRDGLFKDEKDALRSLVLD 48 
                                       555555666666666666.555555556655555555555555543 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 8.3e-05
                            CHASE3  78 lieqklaeleetialrre...ggleaalalvrsdegkelmdei 117
                                       ++ +k+ +++ +i+ +r+    ++e+ ++++rs++g e +de 
  gi|386001755|ref|YP_005920054.1|  49 QAGSKIRHFDSLIEEMRAkydMSFEEFEERIRSRKGDESFDEW 91 
                                       4455555666666666653334888999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 771.11
//
Query:       gi|386001756|ref|YP_005920055.1|  [L=74]
Description: hypothetical protein Mhar_1064 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-14   52.0   0.0    7.8e-14   51.8   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.061   13.3   0.0      0.073   13.1   0.0    1.1  1  PHD_like         Antitoxin of toxin-antitoxin, RelE / RelB, T


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   8.7e-18   7.8e-14       1      61 [.       6      65 ..       6      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 8.7e-18
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssi 61
                                      + ++iekd d  y  + P+l+Gc++ gdt eea++n ++ai+lh+++++e+gee+pe++ i
  gi|386001756|ref|YP_005920055.1|  6 FSVVIEKDRD-GYFAFCPELQGCYTQGDTYEEALENVEDAISLHVKDILEAGEELPEVEFI 65
                                      6799**9998.677899***************************************98766 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.2e-06     0.073      53     105 ..       2      53 ..       1      57 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-06
                                       ..TT--EEEEEEEETTEEEEEECCGT.EEEEESSHHHHHHHHHHHHHHHHHHHH CS
                          PHD_like  53 rgyklepeieeekdgevytltldele.vyvegstkeeaaedLvedlldYaqdYl 105
                                       ++y++ ++ie+++dg    +  +el+  y++g+t eea+e+  + +    +d l
  gi|386001756|ref|YP_005920055.1|   2 KNYRFSVVIEKDRDGYF--AFCPELQgCYTQGDTYEEALENVEDAISLHVKDIL 53 
                                       68999999999999976..777777449*************9999988888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 543.05
//
Query:       gi|386001757|ref|YP_005920056.1|  [L=76]
Description: Ssr1766 protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-18   65.3   0.0    4.5e-18   65.0   0.0    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   2.5e-22   4.5e-18       2      58 .]      11      66 ..      10      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.5e-22
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      +++i++Le++Gf++ rq+GSH +fk++ ++ ++t+p  +gk l+p+ lksIlk+a+l
  gi|386001757|ref|YP_005920056.1| 11 DDAIRALERAGFYLARQSGSHKIFKNEAGT-RITIPYRSGKILHPKILKSILKDADL 66
                                      89************************7666.89*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 489.58
//
Query:       gi|386001758|ref|YP_005920057.1|  [L=50]
Description: hypothetical protein Mhar_1066 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 336.40
//
Query:       gi|386001759|ref|YP_005920058.1|  [L=64]
Description: putative periplasmic or secreted lipoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-15   55.6   0.3    4.6e-15   55.4   0.3    1.0  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.3   2.5e-19   4.6e-15       2      58 .]       5      57 ..       4      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 2.5e-19
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC- CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaGl 58
                                      +++i++L++ Gf v+r+ GSHv++++   +++  vp H  +elk+ tlk+Il q Gl
  gi|386001759|ref|YP_005920058.1|  5 ERLIRILARKGFSVKRRAGSHVVLQKG--EIVSSVPLH--DELKKVTLKAILSQSGL 57
                                      689***********************4..4566*****..**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 414.20
//
Query:       gi|386001760|ref|YP_005920059.1|  [L=70]
Description: hypothetical protein Mhar_1068 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-07   31.5   0.0    1.6e-07   31.4   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   9.2e-12   1.6e-07       1      49 [.       3      51 ..       3      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 9.2e-12
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegli 49
                                      y +++e++e+  y+v   +lpG++s g+t eea+ ++keai l +e l 
  gi|386001760|ref|YP_005920059.1|  3 YTVVLEPQEEGGYTVRCLELPGAISQGETKEEALMKIKEAIGLVFEVLR 51
                                      899******************************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 438.84
//
Query:       gi|386001761|ref|YP_005920060.1|  [L=78]
Description: hypothetical protein Mhar_1069 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-09   36.0   0.1    6.6e-09   35.9   0.1    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   3.7e-13   6.6e-09       2      48 ..       7      53 ..       6      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.7e-13
                   HicB_lk_antitox  2 piaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegl 48
                                      pi++e ded  y v+ P l+ c++ g+t+eea++++ke+ie+ le++
  gi|386001761|ref|YP_005920060.1|  7 PIIVEIDEDGYYIVSCPLLKACHTFGETIEEAMEKIKEVIEMCLEDT 53
                                      89******************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      863  (0.0481343); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.67
# Mc/sec: 349.76
//
Query:       gi|386001762|ref|YP_005920061.1|  [L=81]
Description: hypothetical protein Mhar_1070 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-16   59.0   0.1    4.5e-16   58.6   0.1    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.1   2.5e-20   4.5e-16       1      55 [.       9      62 ..       9      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.5e-20
                                      -HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHH CS
                        HicA_toxin  1 wreviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkq 55
                                      ++e++k L +lGf+vvr++GSH +++ +d+r  +t+p H ++e+++g+l++I+++
  gi|386001762|ref|YP_005920061.1|  9 GQELLKFLSSLGFVVVRTRGSHLQLRAEDGR-STTIPLHAKREVPKGLLRKIIRD 62
                                      589*************************999.68******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 515.22
//
Query:       gi|386001763|ref|YP_005920062.1|  [L=158]
Description: hypothetical protein Mhar_1071 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 973.42
//
Query:       gi|386001764|ref|YP_005920063.1|  [L=451]
Description: Threonine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-27   95.5   0.0    1.2e-26   93.8   0.0    1.6  1  PALP         Pyridoxal-phosphate dependent enzyme
    5.1e-25   87.5   0.0    2.3e-24   85.4   0.0    2.1  2  Thr_synth_N  Threonine synthase N terminus


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   1.4e-30   1.2e-26      25     288 ..      97     392 ..      91     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.4e-30
                                       EEEEGGGSTTSBTTHHHHH...HHHHH....HHTTTTTSEEEEEBSSHHHHHHHHHHHHH.T-EEEEEEETTS-H.H CS
                              PALP  25 flKlEslnptgSfKdRgae...yllar....lkegtgaktvveassGNhgralAaaaall.Glkvtivvpadasp.e 92 
                                       ++ + +  pt SfKd +a             lke+ + +++++a+sG++g a+A+a   l +++v++++p++  +  
  gi|386001764|ref|YP_005920063.1|  97 YVMRLDRGPTFSFKDFAARlmgR---LmqhfLKEEGRSMVILTATSGDTGSAVAHAFYGLdNIRVVVLFPEGEVTgR 170
                                       56677899***********4432...2446866667************************99**********99737 PP

                                       HHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTT.SHH..HHHH.HHTHHHHHHHHTTTTEE...E CS
                              PALP  93 kvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfd.npt..vieg.ygtiglEileqlggkpd...a 160
                                       +++++  lG +v++   +g +d+++a+++e+  + +++  ++ ++ n+   + +  ++   +  ++++  +pd   +
  gi|386001764|ref|YP_005920063.1| 171 QRKQMTTLGKNVHVMavDGKFDDCQAMVKEAFVD-PDFADLNLSSaNSIniGRLIpQSIYYFYAWSRTA-APDrevV 245
                                       7899*****98888777*****************.9999999888766623334457777778887774.6664455 PP

                                       EEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B........................S CS
                              PALP 161 vvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs.......................d 214
                                       + vp+G+ g++++   +++ + p  r++++ ++++d + r+l +g++ ++ +s                        
  gi|386001764|ref|YP_005920063.1| 246 FSVPCGNFGNVMAGLLAMRMDLPVHRFVIA-TNENDEFPRFLSTGDYRPIRPSvkcisnamnvghpsnlarifwlyG 321
                                       88*********************7666666.667*******************977777777777777666654442 PP

                                       SS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEE CS
                              PALP 215 tiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrv 288
                                         +d  +   + +  +e+++r +  +v+v+d+e+ e++ + ++r  +++ep++a++ a+l +r  +e++++ + 
  gi|386001764|ref|YP_005920063.1| 322 GEMDETGRV-VRAPQIEAMRRDI-FAVSVTDAETRETISEAYNRYDVLLEPHGAVGWAGL-ARYLKEVEDWRPS 392
                                       223332222.4444555555555.59**********************************.9999888887655 PP

>> Thr_synth_N  Threonine synthase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   2.5e-28   2.3e-24       1      79 []       5      83 ..       5      83 .. 0.99
   2 ?   -2.5   0.0      0.68   6.1e+03      47      66 ..     106     124 ..      99     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.5e-28
                       Thr_synth_N  1 kYiSTRgeaeklsfeeallkGlAeDgGLyvPeeiPklsaeeleelrklsYaelafevlklfiedeipeedLkeliekaY 79
                                      +Y+ST g+ e+l+f+eall+G A+D GLyvP++iP++ +eel+++++++Y+e+a+ v++++i+d ipe+dL +++++aY
  gi|386001764|ref|YP_005920063.1|  5 QYYSTNGHPERLDFKEALLRGQAPDKGLYVPDSIPRIPKEELARFSGMEYPEIALSVMRRYIGDLIPEDDLVAILKDAY 83
                                      6*****************************************************************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.68
                       Thr_synth_N  47 klsYaelafevlklfiedei 66 
                                       ++s+++ a++++ + + +++
  gi|386001764|ref|YP_005920063.1| 106 TFSFKDFAARLMGRLM-QHF 124
                                       6789999999888777.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2820.49
//
Query:       gi|386001765|ref|YP_005920064.1|  [L=336]
Description: 5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2107.29
//
Query:       gi|386001766|ref|YP_005920065.1|  [L=146]
Description: hypothetical protein Mhar_1074 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-59  199.5   0.3    1.5e-59  199.3   0.3    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.3   8.3e-64   1.5e-59       1     130 []      12     141 ..      12     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 8.3e-64
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       m++rvvsskeei +ln+ne+++Hlafrpsn+d+++l+++cp+++++q p+Sy++t+sk+a++fleiqg+ell+gdvw
  gi|386001766|ref|YP_005920065.1|  12 MRLRVVSSKEEIPELNPNEQMIHLAFRPSNMDVMTLIQRCPRIRTVQTPPSYYRTMSKAARQFLEIQGVELLRGDVW 88 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdi+eyye++e vieri++l+seg + +e+++ +++etkls+d+ik++lk
  gi|386001766|ref|YP_005920065.1|  89 GHRKDIDEYYEIDEGVIERISKLISEGRKIDEVVTLVKRETKLSEDMIKYILK 141
                                       ***************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1123.65
//
Query:       gi|386001767|ref|YP_005920066.1|  [L=262]
Description: Triose-phosphate isomerase [Methanosaeta harundinacea 6Ac]
Scores for 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-12   45.2   0.0    9.7e-12   44.8   0.0    1.2  1  TIM       Triosephosphate isomerase
    0.00061   19.3   1.3    0.00061   19.3   1.3    1.9  2  NMO       Nitronate monooxygenase
    0.00081   18.8   0.2    0.00081   18.8   0.2    2.0  3  ThiG      Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.039   13.0   1.6      0.079   12.0   0.7    1.8  2  FMN_dh    FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   2.2e-15   9.7e-12       3     132 ..      44     168 ..      42     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.2e-15
                                       EEEE-TBTS-HHHHHHHHHH..HHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHH CS
                               TIM   3 iagNwKmnktleeakellkk..lkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsae 77 
                                       ++ N+K++ + + a++l  +  +++++++ +ve+++a+++  ++ +++ +   ++ ++aq v+    G fTG+++a+
  gi|386001767|ref|YP_005920066.1|  44 VVLNFKTYSEATGAEALKLSriCEEAKDQYDVEIAVAVQAPDIRLISENV---SIPVYAQHVDGVGFGGFTGSITAA 117
                                       6679****98877777765552555555599**********999988777...5*********************** PP

                                       HHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHHT CS
                               TIM  78 mlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleerea 132
                                        +k +g++ ++i HsErr  + E     ++ ++a+ ++g+++i+C  +  ++r a
  gi|386001767|ref|YP_005920066.1| 118 AVKAAGATGTLINHSERRLRLAEI----EASISACRAAGISAIVCTNNVPTTRAA 168
                                       *******************99885....56678999999999*999877666655 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.13   5.7e+02      18      39 ..     106     127 ..      56     132 .. 0.70
   2 !   19.3   1.3   1.4e-07   0.00061     128     233 ..     144     251 ..     137     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.13
                               NMO  18 gmggiskarLaaavsnaGgLGv 39 
                                       g gg ++   aaav  aG+ G 
  gi|386001767|ref|YP_005920066.1| 106 GFGGFTGSITAAAVKAAGATGT 127
                                       3444555555555555555554 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.4e-07
                               NMO 128 vvarlkeagvvliptissvkearkvearGaDalivqGpeaGGh.qGtpevgdkglfaLvpqvldavd.....iPviA 198
                                        + +  +ag+ +i+ +  v   r+++++ +D + v+ pe  G  ++ ++++d g   +v   ++av+     + v+ 
  gi|386001767|ref|YP_005920066.1| 144 SISACRAAGISAIVCTNNVPTTRAAASLKPDYVAVEPPELIGSgIP-VSKADPG---IVTGSVEAVKriepsVGVLC 216
                                       566778999****************************997664144.5555533...33334444444447799*** PP

                               NMO 199 aGGiidrrgvaaaLalGAsgvqigtrfLltkesda 233
                                         Gi +++++ aaL lG +gv +++  + +k+ +a
  gi|386001767|ref|YP_005920066.1| 217 GAGISRGEDLRAALDLGSEGVLLASGIVKAKDQKA 251
                                       **************************999999877 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.39   1.7e+03      75      98 ..      56      79 ..      40     111 .. 0.63
   2 ?   -1.2   0.4      0.22   9.8e+02     167     205 ..      86     131 ..      77     170 .. 0.58
   3 !   18.8   0.2   1.8e-07   0.00081     173     214 ..     209     250 ..     184     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHHHHTTS-SEEEE-- CS
                              ThiG 75 aeeAvriarlarevletdliklEv 98
                                       +eA++++r+  e+ ++  + + v
  gi|386001767|ref|YP_005920066.1| 56 GAEALKLSRICEEAKDQYDVEIAV 79
                                      556666666666655444333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.22
                                       HHHHHHH-SS-BE...EE.S---...SHHHHHHHHHTT-SEEEESH CS
                              ThiG 167 lkiiieeakvPvi...vD.AGig...spsdaaqamelGadavllnt 205
                                       +++i e++++Pv    vD  G g    +  aa++   Ga++ l+n 
  gi|386001767|ref|YP_005920066.1|  86 IRLISENVSIPVYaqhVDgVGFGgftGSITAAAVKAAGATGTLINH 131
                                       6777777777775222442222222123344445556666666664 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1.8e-07
                                       H-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                              ThiG 173 eakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                       e +v v+  AGi + +d  +a++lG ++vll++ + +akd  
  gi|386001767|ref|YP_005920066.1| 209 EPSVGVLCGAGISRGEDLRAALDLGSEGVLLASGIVKAKDQK 250
                                       448999*********************************975 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.16     7e+02     125     147 ..     141     163 ..     106     174 .. 0.75
   2 ?   12.0   0.7   1.8e-05     0.079     263     303 ..     203     243 ..     193     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHCTESEEEEESSTS CS
                            FMN_dh 125 teellkraeaagykalvltvDtp 147
                                       +e+ +  ++aag++a+v t  +p
  gi|386001767|ref|YP_005920066.1| 141 IEASISACRAAGISAIVCTNNVP 163
                                       45556667777777777776555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.8e-05
                                       HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       e v++++ ++ vl+  Gi+rG+D   Al lG ++vll+  +
  gi|386001767|ref|YP_005920066.1| 203 EAVKRIEPSVGVLCGAGISRGEDLRAALDLGSEGVLLASGI 243
                                       34555556888*************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1917.18
//
Query:       gi|386001768|ref|YP_005920067.1|  [L=89]
Description: acylphosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   80.0   0.1    1.4e-22   79.9   0.1    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.1   7.8e-27   1.4e-22       1      83 [.       4      85 ..       4      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 7.8e-27
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeee 79
                                      vr++v+GrVQgv +R+f+r++A elg+kG+v+Nl+ g Ve++++ge++kv ++l+ +k+gp  a v+ +ev+e++ +e 
  gi|386001768|ref|YP_005920067.1|  4 VRVRVSGRVQGVSYRNFTRSHAAELGVKGWVQNLPGGGVEALLQGERKKVGELLSLMKEGPAGALVSGMEVSEVPCREI 82
                                      5899********************************************************************9988876 PP

                   Acylphosphatase 80 fkdF 83
                                       ++F
  gi|386001768|ref|YP_005920067.1| 83 -EEF 85
                                      .566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 678.09
//
Query:       gi|386001769|ref|YP_005920068.1|  [L=60]
Description: Ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      7e-13   47.8  13.6    3.4e-07   29.8   2.7    2.1  2  Fer4        4Fe-4S binding domain
    1.4e-10   41.6  20.1    9.5e-07   29.3  12.3    2.0  2  Fer4_7      4Fe-4S dicluster domain
    1.7e-10   41.7   9.4    7.6e-05   23.6   2.4    2.0  2  Fer4_16     4Fe-4S double cluster binding domain
    6.2e-09   35.9  24.7    1.6e-05   24.9  14.2    2.0  2  Fer4_10     4Fe-4S dicluster domain
    1.5e-07   31.1  12.5    0.00095   19.1   2.3    2.1  2  Fer4_2      4Fe-4S binding domain
    4.2e-07   29.8  12.3     0.0023   17.9   3.0    2.1  2  Fer4_6      4Fe-4S binding domain
    9.4e-07   28.9  12.7    2.2e-05   24.5  13.2    2.0  2  Fer4_9      4Fe-4S dicluster domain
    1.8e-06   28.0  10.1    0.00017   21.8   1.3    2.3  2  Fer4_4      4Fe-4S binding domain
    3.7e-06   27.3  23.5     0.0024   18.3   2.2    2.1  3  Fer4_8      4Fe-4S dicluster domain
    1.3e-05   25.2  12.0    9.6e-05   22.4  12.0    1.9  1  Fer4_21     4Fe-4S dicluster domain
    0.00046   20.9  19.6     0.0053   17.6   3.8    2.3  2  Fer4_3      4Fe-4S binding domain
     0.0017   18.9  13.0      0.015   15.8   2.3    2.1  2  Fer4_17     4Fe-4S dicluster domain
     0.0075   16.5  11.6      0.044   14.0   1.6    2.0  2  Fer4_18     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.1  10.9       0.49   11.0   2.5    2.1  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
      0.083   13.6   9.0        1.9    9.3   1.9    2.4  2  Fer4_15     4Fe-4S single cluster domain
        0.7   10.8  15.4       0.47   11.3   3.6    2.1  3  Fer4_22     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   2.7     3e-10   3.4e-07       3      24 .]       4      25 ..       2      25 .. 0.91
   2 !   24.0   3.3   2.1e-08   2.3e-05       6      24 .]      35      53 ..      33      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3e-10
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      ++  kC +CGaCv vCPv A++
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCPVAALE 25
                                      7899***************985 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.1e-08
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                      ++C+ CG+C ++CP gA++
  gi|386001769|ref|YP_005920068.1| 35 DDCTECGRCTKICPLGALE 53
                                      89***************85 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3  12.3   8.5e-10   9.5e-07       1      52 []       8      51 ..       8      51 .. 0.93
   2 !   22.3   0.9   1.3e-07   0.00014       2      23 ..      37      58 ..      36      60 .] 0.89

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.5e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C  CgaCv +Cpv a+el e         +  + ++C+ Cg+C + CP ga
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVAALELVET--------WIEVGDDCTECGRCTKICPLGA 51
                                      7******************886........88888**************987 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                            Fer4_7  2 CigCgaCvaaCpvkaieldeee 23
                                      C++Cg+C++ Cp +a+el++e+
  gi|386001769|ref|YP_005920068.1| 37 CTECGRCTKICPLGALELKKEA 58
                                      *****************99875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.7   1.1e-07   0.00012       1      20 [.       8      27 ..       8      34 .. 0.88
   2 !   23.6   2.4   6.8e-08   7.6e-05       2      23 ..      37      58 ..      36      60 .] 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +Cg Cg+C+ vCP++a++  
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVAALELV 27
                                      6***************9976 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 6.8e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekkek 23
                                      C++Cg+C+++CP +a++ kke+
  gi|386001769|ref|YP_005920068.1| 37 CTECGRCTKICPLGALELKKEA 58
                                      *****************99765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  14.2   1.5e-08   1.6e-05       4      56 .]       4      48 ..       1      48 [. 0.77
   2 !   21.9   2.8   1.3e-07   0.00014       5      21 ..      33      49 ..      29      60 .] 0.75

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.5e-08
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +++ +C  Cg+Cv +CP+        ++ +  e+  ++ ++Ct+cg C+++CP
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCPV--------AALELVETWIEVGDDCTECGRCTKICP 48
                                      67889*************........333333444444588***********9 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.3e-07
                           Fer4_10  5 dddtCirCgkCvkaCPa 21
                                        d C++Cg+C+k CP 
  gi|386001769|ref|YP_005920068.1| 33 VGDDCTECGRCTKICPL 49
                                      5689************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.8   2.6e-06    0.0029       5      21 ..       4      20 ..       2      21 .. 0.91
   2 !   19.1   2.3   8.5e-07   0.00095       8      21 ..      35      48 ..      30      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      v++ +C  CgaCv +CP
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCP 20
                                      7899************* PP

  == domain 2  score: 19.1 bits;  conditional E-value: 8.5e-07
                            Fer4_2  8 drCigCgaCvsaCP 21
                                      d C++Cg C++ CP
  gi|386001769|ref|YP_005920068.1| 35 DDCTECGRCTKICP 48
                                      56***********9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.0   3.2e-06    0.0036       4      24 .]       4      24 ..       2      24 .. 0.90
   2 !   17.9   3.0     2e-06    0.0023       8      22 ..      36      50 ..      35      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      +++ kC  Cg+Cv vCP +a+
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCPVAAL 24
                                      78889999*********9996 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2e-06
                            Fer4_6  8 kCigCgdCvrvCPeg 22
                                       C+ Cg+C+++CP g
  gi|386001769|ref|YP_005920068.1| 36 DCTECGRCTKICPLG 50
                                      5************55 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.8   3.6e-05      0.04      35      50 ..       8      23 ..       2      24 .. 0.81
   2 !   24.5  13.2     2e-08   2.2e-05       1      50 [.       8      51 ..       8      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                            Fer4_9 35 aCigCgaCveaCpkga 50
                                      +C  CgaCv +Cp  a
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVAA 23
                                      7999********9875 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 2e-08
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      kC  CgaCv +Cp  + +    e+ +++      +C++Cg+C+++Cp ga
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVAALELV--ETWIEVGD----DCTECGRCTKICPLGA 51
                                      7999*********8887665..55555544....6************986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.0    0.0004      0.45       7      16 ..      12      21 ..       7      29 .. 0.91
   2 !   21.8   1.3   1.5e-07   0.00017       2      16 ..      35      49 ..      30      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                            Fer4_4  7 CgsCvaaCPq 16
                                      Cg+Cv +CP+
  gi|386001769|ref|YP_005920068.1| 12 CGACVGVCPV 21
                                      *********6 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C++Cg+C+ +CP 
  gi|386001769|ref|YP_005920068.1| 35 DDCTECGRCTKICPL 49
                                      56************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.1   5.3e-05      0.06       4      18 ..       8      22 ..       5      29 .. 0.76
   2 !   18.3   2.2   2.2e-06    0.0024      47      63 ..      33      49 ..      21      51 .. 0.72
   3 !   16.8   3.0   6.4e-06    0.0072       4      18 ..      36      50 ..      34      59 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                            Fer4_8  4 kCieCgaCqsaCpvl 18
                                      kC+ CgaC   Cpv+
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVA 22
                                      788888888888875 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
                            Fer4_8 47 alwsCttcgaCtevCpv 63
                                        + Ct+cg+Ct+ Cp 
  gi|386001769|ref|YP_005920068.1| 33 VGDDCTECGRCTKICPL 49
                                      56778888888888886 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 6.4e-06
                            Fer4_8  4 kCieCgaCqsaCpvl 18
                                      +C+eCg+C++ Cp+ 
  gi|386001769|ref|YP_005920068.1| 36 DCTECGRCTKICPLG 50
                                      566666666666654 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4  12.0   8.5e-08   9.6e-05       3      57 ..       4      52 ..       2      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.5e-08
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      +++ kC  Cg C+ +C+ ++ + +e     ++  v d+C+ C  C+++CP+ +++
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCPVAALELVE-----TWIEVGDDCTECGRCTKICPL-GAL 52
                                      78899************66665555.....3456789*************7.666 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   8.0    0.0021       2.4       3      14 ..      11      22 ..       9      23 .. 0.81
   2 !   17.6   3.8   4.7e-06    0.0053       1      15 []      37      51 ..      37      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                            Fer4_3  3 gCgaCvevCPvg 14
                                       CgaCv vCPv 
  gi|386001769|ref|YP_005920068.1| 11 YCGACVGVCPVA 22
                                      4*********85 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.7e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg+C + CP gA
  gi|386001769|ref|YP_005920068.1| 37 CTECGRCTKICPLGA 51
                                      ************998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   2.5    0.0011       1.2       1      15 [.       8      22 ..       8      30 .. 0.80
   2 !   15.8   2.3   1.3e-05     0.015      44      58 ..      35      49 ..      22      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C  Cg+C+ +Cp  
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVA 22
                                      588999999999975 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++C+eCg+C++ CP 
  gi|386001769|ref|YP_005920068.1| 35 DDCTECGRCTKICPL 49
                                      789999999999995 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   2.7    0.0019       2.1      59      74 ..       7      22 ..       2      28 .. 0.86
   2 !   14.0   1.6   3.9e-05     0.044      58      74 ..      34      50 ..      23      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                       +c  c++cv vcP+ 
  gi|386001769|ref|YP_005920068.1|  7 YKCGYCGACVGVCPVA 22
                                      57999*********85 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.9e-05
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                        dc++c+ c k+cP g
  gi|386001769|ref|YP_005920068.1| 34 GDDCTECGRCTKICPLG 50
                                      469************97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00065      0.73       1      17 [.       4      20 ..       4      22 .. 0.95
   2 ?   11.0   2.5   0.00044      0.49       4      17 ..      35      48 ..      31      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00065
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      V+r +C  cgaCv ++P
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCP 20
                                      8999************9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00044
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d C++cg C +++P
  gi|386001769|ref|YP_005920068.1| 35 DDCTECGRCTKICP 48
                                      89***********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.9    0.0017       1.9       3      19 ..       4      20 ..       2      26 .. 0.88
   2 ?    8.7   0.8    0.0026       2.9       6      19 ..      35      48 ..      30      60 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      v+r +C  cg+Cv ++p
  gi|386001769|ref|YP_005920068.1|  4 VNRYKCGYCGACVGVCP 20
                                      8999***********98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                           Fer4_15  6 daCigcglCvaeap 19
                                      d C+ cg+C + +p
  gi|386001769|ref|YP_005920068.1| 35 DDCTECGRCTKICP 48
                                      89**********98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.1     0.033        37       1      14 [.       8      21 ..       3      23 .. 0.59
   2 ?    6.0   3.4     0.019        21       1      15 [.       8      22 ..       8      36 .. 0.83
   3 ?   11.3   3.6   0.00042      0.47      81      93 ..      36      48 ..      25      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.033
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C  CgaC  vCp 
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPV 21
                                      45556666666653 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      +C  CgaC  vCp  
  gi|386001769|ref|YP_005920068.1|  8 KCGYCGACVGVCPVA 22
                                      688999999999975 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00042
                           Fer4_22 81 gCvGCgRCieacp 93
                                       C+ CgRC++ cp
  gi|386001769|ref|YP_005920068.1| 36 DCTECGRCTKICP 48
                                      5888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 423.47
//
Query:       gi|386001770|ref|YP_005920069.1|  [L=391]
Description: digeranylgeranylglycerophospholipid reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-18   66.3   0.7    2.7e-13   49.9   0.5    3.0  2  FAD_binding_3   FAD binding domain
    4.5e-09   35.8   0.3    7.9e-06   25.2   0.5    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    9.3e-09   34.8   1.1    2.3e-07   30.3   0.2    2.2  2  FAD_binding_2   FAD binding domain
    1.1e-07   31.6   4.8    2.3e-07   30.5   4.8    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    1.2e-07   31.9   0.0    1.3e-06   28.5   0.0    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.5e-07   30.5   0.3    2.5e-07   29.8   0.3    1.3  1  HI0933_like     HI0933-like protein
    2.8e-07   30.5   5.3    7.5e-05   22.5   0.3    2.3  2  DAO             FAD dependent oxidoreductase
    6.4e-06   25.3   0.0      0.019   13.8   0.1    2.2  2  Trp_halogenase  Tryptophan halogenase
      6e-05   22.4   0.9    0.00016   21.0   0.4    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00018   20.7   0.1    0.00029   20.0   0.1    1.3  1  GIDA            Glucose inhibited division protein A
    0.00051   19.4   0.3     0.0019   17.5   0.1    2.0  2  Thi4            Thi4 family
    0.00077   19.4   0.1      0.018   15.0   0.0    2.6  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0012   18.2   0.1     0.0021   17.4   0.1    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.012   16.2   0.2      0.012   16.2   0.2    2.2  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.012   16.1   0.2      0.049   14.1   0.2    2.3  1  XdhC_C          XdhC Rossmann domain
      0.036   13.4   0.1      0.073   12.4   0.1    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.075   12.1   0.1       0.13   11.3   0.1    1.4  1  SE              Squalene epoxidase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.5   2.6e-16   2.7e-13       2     179 ..       3     171 ..       2     200 .. 0.82
   2 !    9.9   0.0   0.00038       0.4     283     337 ..     269     324 ..     232     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.6e-16
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       +d ++VGaGpaG m+a+  +eaG +vvl+ekr++  +  r a+g+++  +  l +   + + +    + e+ g   +
  gi|386001770|ref|YP_005920069.1|   3 CDLVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIGDPVRcAEGVSKAALKKLVDP--DPTWI----SAEVKGARIR 73 
                                       8999****************************999888864788888887766553..22222....2345556666 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                       ++  d  ++ +  + ++++e  +v+  + ++r+L+++a+e+g++v  kt+ + l+  e gv a v+ +  ge  +++
  gi|386001770|ref|YP_005920069.1|  74 GP--DGTEIVISED-RAGAEVGYVLERKVFDRALAQEAAEAGAKVMVKTRALDLLW-EGGVPAGVTAQFIGESLRIE 146
                                       66..4456777777.7999999****************************997765.5799**************** PP

                                       EEEEEE--GTT-HHHHHHTGGEEEE CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgiefege 179
                                       a  +vGaDG+ S+v + +gi+   +
  gi|386001770|ref|YP_005920069.1| 147 APLVVGADGVESKVGRWAGIDTALK 171
                                       *******************985544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                                       ETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHH.HHHTTSS-GGGGHHHHHH CS
                     FAD_binding_3 283 kgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLa.avlkGeAkeelLdtYeee 337
                                        + v l+GDAa    P +G G+  +++  v  +   a +v kGe +++ L+ Ye+ 
  gi|386001770|ref|YP_005920069.1| 269 ADGVILVGDAARQSDPITGGGIINGMRAGVMAGEIAAdLVPKGEVDKRSLQVYEKG 324
                                       689*******************99*9999888877663466899999999999875 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.5   7.5e-09   7.9e-06       1     148 [.       4     162 ..       4     180 .. 0.76
   2 !    8.5   0.0   0.00084      0.88     233     312 ..     248     329 ..     234     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.5e-09
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecve..hsW.....sgtivyld 70 
                                       D+vv+GaGpAg   A+    a++gl vvl+e  +++   ++ v + e+    al+++v+   +W     +g++++ +
  gi|386001770|ref|YP_005920069.1|   4 DLVVVGAGPAGSMTAKAA--AEAGLDVVLLEKRQEI---GDPVRCAEGVSKAALKKLVDpdPTWisaevKGARIRGP 75 
                                       9**********9999988..************9999...77788888888888888875224673333366778899 PP

                     Lycopene_cycl  71 dgkkillg.......raYgrvsskrlkeellerlvengvkl.leakvesveeeea..geslvvleggr.kirarlvv 136
                                       dg +i ++         Y  +++k + + l+++ +e+g+k  ++ ++     e    + +++   g+  +i+a+lvv
  gi|386001770|ref|YP_005920069.1|  76 DGTEIVISedragaeVGY-VLERKVFDRALAQEAAEAGAKVmVKTRALDLLWEGGvpAGVTAQFIGESlRIEAPLVV 151
                                       999999988866643444.4699************99887526788877765544356777777777779******* PP

                     Lycopene_cycl 137 darglaslkkar 148
                                        a g  ++k +r
  gi|386001770|ref|YP_005920069.1| 152 GADG-VESKVGR 162
                                       **99.4554444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00084
                     Lycopene_cycl 233 kevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....slsaraw 304
                                        +v e   g +Pv   g+++++ +  v+ +G aa    P TG  + + +++   +a  iaa l  +    ++s ++ 
  gi|386001770|ref|YP_005920069.1| 248 GKVLEMMAGGVPV--SGPIEATVADgVILVGDAARQSDPITGGGIINGMRAGV-MAGEIAADLVPKgevdKRSLQVY 321
                                       56777788999**..99999999988***********************9654.88888888876677776666666 PP

                     Lycopene_cycl 305 atlwprer 312
                                       ++ w++++
  gi|386001770|ref|YP_005920069.1| 322 EKGWRETI 329
                                       66666554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2   2.2e-10   2.3e-07       1      50 [.       4      53 ..       4      65 .. 0.92
   2 ?    3.3   0.0     0.034        36     146     198 ..     103     153 ..      94     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.2e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT. CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavls 50
                                      D++V+G+G AG + A +aaeaGl+v+++ek qe g    +++G   a+l+
  gi|386001770|ref|YP_005920069.1|  4 DLVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIGDPVRCAEGVSKAALK 53
                                      89*********************************9*******9999884 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE- CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvla 198
                                       +l+++a +ag +++ +t+a++L+ e+g   G++++    g+  ri+a  vv a
  gi|386001770|ref|YP_005920069.1| 103 ALAQEAAEAGAKVMVKTRALDLLWEGGVPAGVTAQ--FIGESLRIEAPLVVGA 153
                                       688999999****************9999999998..5566666666666655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   4.8   2.2e-10   2.3e-07       1     157 [.       4     169 ..       4     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.2e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll.tsglvatdignkaeeqvvtgiarefl.erlrqrgga.. 73 
                                       D+vVvG+gpaG + A aAa+aG  v+L+e+r+ +G  +  +++v+    +k  +   t i  e+  +r+r  +g   
  gi|386001770|ref|YP_005920069.1|   4 DLVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIGDPVrCAEGVSKAALKKLVDPDPTWISAEVKgARIRGPDGTei 80 
                                       99*********************************754255666666666666656666666664256655333335 PP

                      FAD_oxidored  74 ...rlkkrskwn...tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                          +  +r++ +   + e +v+ ++l +  aeag +v+ +tr+ +   eg+   +vt++   +  +i+A++++ A g
  gi|386001770|ref|YP_005920069.1|  81 visE--DRAGAEvgyVLERKVFDRALAQEAAEAGAKVMVKTRALDLLWEGGVPAGVTAQFIGESLRIEAPLVVGADG 155
                                       4321..2222213459*********************************9778889886444599999999998866 PP

                      FAD_oxidored 145 .dGdlaalaGvpyr 157
                                        + +++ +aG+ + 
  gi|386001770|ref|YP_005920069.1| 156 vESKVGRWAGIDTA 169
                                       56777777777665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.2e-09   1.3e-06       1      32 [.       7      38 ..       7      65 .. 0.89
   2 ?    0.2   0.0      0.88   9.3e+02      18      30 ..     314     326 ..     296     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G+ +A ++a+ag+dv+llekr+ +G
  gi|386001770|ref|YP_005920069.1|  7 VVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIG 38
                                      8******************************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.88
                                       CTEEEEEE-SSSS CS
                     NAD_binding_8  18 agfdvlllekrdr 30 
                                       ++++ +++ek++r
  gi|386001770|ref|YP_005920069.1| 314 DKRSLQVYEKGWR 326
                                       377899****998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3   2.4e-10   2.5e-07       2      40 ..       4      42 ..       3      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.4e-10
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      d++v+G+G+AG m+A +aa++g +V+llek +++g  ++
  gi|386001770|ref|YP_005920069.1|  4 DLVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIGDPVR 42
                                      89********************************98766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   7.1e-08   7.5e-05       1      33 [.       4      38 ..       4      55 .. 0.90
   2 !   10.0   0.9   0.00043      0.45     144     352 .]      96     307 ..      44     307 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.1e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      d+v++G+G +G+ tA ++a++g  V+llek+ ++g
  gi|386001770|ref|YP_005920069.1|  4 DLVVVGAGPAGSMTAKAAAEAGldVVLLEKRQEIG 38
                                      89*****************************8877 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00043
                                       EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT..EEE.EEEEE..EEE--GGGHH..HHHTT.CT CS
                               DAO 144 dpakltaalaraaealGveilegtevtgleeedgkvwgverttp..gen.daada..vVnaaGawsd..llgll.ke 212
                                       +   + +ala++a+++G+++  +t++ +l  e+g  +gv  t++  ge  + ++a  vV a G+ s+   ++++   
  gi|386001770|ref|YP_005920069.1|  96 ERKVFDRALAQEAAEAGAKVMVKTRALDLLWEGGVPAGV--TAQfiGESlR-IEAplVVGADGVESKvgRWAGIdTA 169
                                       5666789*********************97888888888..3333455433.4667699999999875544333333 PP

                                       TTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHH CS
                               DAO 213 ldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidell 289
                                       l+++   + +q lv    ++k +  + ++ +   + +g++v  +p       vG      +++ d +     i+ l+
  gi|386001770|ref|YP_005920069.1| 170 LKPKDIETCAQFLVQ---DDKIDDDYCVFYLGNEIAPGGYVWSFPKGPSLANVGIGV--LGSKAD-S--GTPIRLLR 238
                                       333334455555555...222333454444444666666666666432222233322..333333.2..23477899 PP

                                       HHHHHHSGGGCGEEEEEEEEEE.......E.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 290 ealrklfPqlgdvlrkwaGlrp.......l.pdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       e ++k fP+ g+vl+  aG  p       +  dg  l+g + + ++ +   G+  +G+  + ++G+++a+l
  gi|386001770|ref|YP_005920069.1| 239 EFMKKNFPD-GKVLEMMAGGVPvsgpieaTvADGVILVGDAARQSDPITGGGI-INGMRAGVMAGEIAADL 307
                                       999999999.8899888986665444433345888888886544444444444.88888888888888886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.8e-05     0.019       2      35 ..       5      35 ..       4      46 .. 0.90
   2 !    9.1   0.0    0.0005      0.53     143     382 ..      87     342 ..      76     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      +v+vG+G+aG+++A a a+a+   l+v l+e+ +
  gi|386001770|ref|YP_005920069.1|  5 LVVVGAGPAGSMTAKAAAEAG---LDVVLLEKRQ 35
                                      79*****************99...9*****9864 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0005
                                       B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-II... CS
                    Trp_halogenase 143 salsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgll... 213
                                       ++ + +y l+++ +++ L + a ++G +++  + +   l e g  ++++ +      ++ea l++ + G ++++   
  gi|386001770|ref|YP_005920069.1|  87 AGAEVGYVLERKVFDRALAQEAAEAGAKVMVKTRALDLLWEGGVPAGVTAQFigeSLRIEAPLVVGADGVESKVgrw 163
                                       56778999*******************99876664444444555455555436325568999********9986444 PP

                                       ..IIIIT-.--EEE-TTT----EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHH CS
                    Trp_halogenase 214 ..ieqaLk.tgfedwsdvLltdrAlavqveseelvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAla 286
                                         i+ aLk + +e+ +++L+ d  +      ++    y +      G +W  P   +l n G+ +  + ad  + ++
  gi|386001770|ref|YP_005920069.1| 164 agIDTALKpKDIETCAQFLVQDDKID-----DDYCVFYLGNEIAPGGYVWSFPKGPSLANvGIGVLGSKADSGTPIR 235
                                       44888998445777888887776654.....668888999999999*********999999*999999999999999 PP

                                       HHHHHCT--TTTS-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BT CS
                    Trp_halogenase 287 ellaeldgkleaeprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdk 353
                                        l++ ++++   + + +++ +G        + +   +v+++G+a+   +P+ + +i   ++    a +  + l p++
  gi|386001770|ref|YP_005920069.1| 236 LLREFMKKNF-PDGKVLEMMAGGvpvsgpIEATVADGVILVGDAARQSDPITGGGIINGMRagvmAGEIAADLVPKG 311
                                       8888777553.344788888777788888999999******************999876654443334456789999 PP

                                       T--HHHHHHHHHHHHHHHHH..HHHHHHHHH CS
                    Trp_halogenase 354 sdepaaiaefnrevareler..vrdfiilhY 382
                                        +++ +++ +++  ++++++  +r+f++  +
  gi|386001770|ref|YP_005920069.1| 312 EVDKRSLQVYEKGWRETIGKsiTRNFAVKEF 342
                                       9999999999999998887633567766655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   1.5e-07   0.00016       2      33 ..       4      35 ..       3      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      d+vv+G+GpAG  +a+ +a+ag++v+l+e+++
  gi|386001770|ref|YP_005920069.1|  4 DLVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQ 35
                                      68999999999999999999999999996443 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.8e-07   0.00029       1      37 [.       4      39 ..       4      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                      d++V+G+G AG+  A aaa++G++v+L+ +k ++i+ 
  gi|386001770|ref|YP_005920069.1|  4 DLVVVGAGPAGSMTAKAAAEAGLDVVLL-EKRQEIGD 39
                                      689************************9.55555554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.8e-06    0.0019      17      54 ..       2      38 ..       1      45 [. 0.91
   2 ?   -1.3   0.0         1   1.1e+03     111     124 ..     111     124 ..      77     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                        D+v+vGaG++G  +a+  a++ +l v++le++  +G
  gi|386001770|ref|YP_005920069.1|  2 RCDLVVVGAGPAGSMTAKAAAEA-GLDVVLLEKRQEIG 38
                                      57*****************9999.********998777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                                       TTEEEEESEEEEEE CS
                              Thi4 111 anvkllnavaveDl 124
                                       a++k++  + + Dl
  gi|386001770|ref|YP_005920069.1| 111 AGAKVMVKTRALDL 124
                                       33333333333333 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.018       3      35 ..       6      38 ..       4      68 .. 0.83
   2 ?   -3.3   0.0       6.7   7.1e+03      14      30 ..     104     120 ..     101     125 .. 0.78
   3 ?    1.3   0.0      0.27   2.8e+02       9      42 ..     328     361 ..     327     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                                      EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHH CS
                           3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseeal 35
                                       v+GaG  G+  a+++a+agl+Vvl++ ++e+ 
  gi|386001770|ref|YP_005920069.1|  6 VVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIG 38
                                      69*************************998864 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.7
                                       HHHHHHHTT-EEEEE-S CS
                           3HCDH_N  14 iaavfasagleVvlvdi 30 
                                       +a+ +a+ag +V +  +
  gi|386001770|ref|YP_005920069.1| 104 LAQEAAEAGAKVMVKTR 120
                                       78899999999988765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.27
                                       CCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N   9 tmGagiaavfasagleVvlvdiseealekaleki 42 
                                       t+G++i+  fa +++ V l+d + ++l ++l+ i
  gi|386001770|ref|YP_005920069.1| 328 TIGKSITRNFAVKEFFVDLTDDDLNRLIHSLDGI 361
                                       79******************99888776666655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     2e-06    0.0021       1      33 [.       6      38 ..       6      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                      +++GaGPaG  +a ++ +agl d++ lEk  +ig
  gi|386001770|ref|YP_005920069.1|  6 VVVGAGPAGSMTAKAAAEAGL-DVVLLEKRqEIG 38
                                      79*******************.8*****985666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.2   0.2   1.1e-05     0.012       2      35 ..       5      38 ..       4      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +vvvG+G  g + A+a+ae g +V ++e + ++ 
  gi|386001770|ref|YP_005920069.1|  5 LVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIG 38
                                      79*****************************998 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   4.7e-05     0.049       1      41 [.       5      45 ..       5     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpe 41
                                      lv++Gag+ +   a+ aa++g++v+++++r+e+ ++ r +e
  gi|386001770|ref|YP_005920069.1|  5 LVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEIGDPVRCAE 45
                                      79*****************************9886666553 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.9e-05     0.073      29      63 ..       3      37 ..       1      68 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                      +  +v+G+G aG   +++a++ g +V++l++r++ 
  gi|386001770|ref|YP_005920069.1|  3 CDLVVVGAGPAGSMTAKAAAEAGLDVVLLEKRQEI 37
                                      6789***************************9875 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00013      0.13     127     155 ..     267     295 ..     234     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                SE 127 nekkGlillGDalnmRHPltggGmtvaln 155
                                       +   G+il+GDa     P+tggG++ +++
  gi|386001770|ref|YP_005920069.1| 267 TVADGVILVGDAARQSDPITGGGIINGMR 295
                                       4458*******************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2840.34
//
Query:       gi|386001771|ref|YP_005920070.1|  [L=171]
Description: hypothetical protein Mhar_1079 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1075.67
//
Query:       gi|386001772|ref|YP_005920071.1|  [L=349]
Description: Type I restriction-modification system DNA methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-40  139.9   0.0    5.1e-36  124.5   0.0    2.3  2  N6_Mtase         N-6 DNA Methylase
    0.00066   20.3   0.5     0.0013   19.3   0.0    1.8  2  HsdM_N           HsdM N-terminal domain
  ------ inclusion threshold ------
      0.027   14.3   0.0       0.15   11.9   0.0    2.0  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   8.6e-40   5.1e-36       2     198 ..      81     256 ..      80     263 .. 0.91
   2 !   13.1   0.0   7.2e-06     0.043     278     312 .]     276     310 ..     265     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 8.6e-40
                          N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee.dgktke 77 
                                       s d++G++YE++l +fa +++ +gGeffTP ++++li++         v+Dpa Gsgg++vq+++ ++e+ ++ t +
  gi|386001772|ref|YP_005920071.1|  81 SGDIFGRIYEFFLTQFADQKAHDGGEFFTPISLVSLIAH---------VLDPATGSGGMFVQSARIVEEQgQNPTDR 148
                                       579**********************************98.........679*****************994445666 PP

                          N6_Mtase  78 lsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNp..pfnqkewkektlekderfr 152
                                       l++ G+ekn+tt+rLakmNl++hg e +   i+ + t+ ++ +e+  k+d v + p  pf+  +     ++kd+   
  gi|386001772|ref|YP_005920071.1| 149 LTFRGLEKNATTIRLAKMNLAVHGLEGD---IQRAITYYEDPHEQVGKADKVKTDPrlPFGLPG----VNKKDK--- 215
                                       7777************************...99999****99999**********977999993....344444... PP

                          N6_Mtase 153 eavapksnadlafllhiieslkpkGraavvlangvLfrggkegkIr 198
                                             sn ++ ++ ++ ++l+++Gra++v+ + + ++gg e+k+r
  gi|386001772|ref|YP_005920071.1| 216 -----VSNGNYIWISYFYSYLNEGGRAGFVMSSRASSAGGGEAKVR 256
                                       .....6899***********************************99 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.2e-06
                          N6_Mtase 278 evdkfskvveleeiaendynlnvgryveteeeeed 312
                                       +v++  k+v+  eia+nd+ l++gryv+ + eeed
  gi|386001772|ref|YP_005920071.1| 276 DVEGLGKLVDRAEIAANDWSLTPGRYVGVAPEEED 310
                                       788999**********************9999885 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.2e-07    0.0013       1      34 [.      10      45 ..      10      95 .. 0.88
   2 ?   -2.6   0.2       1.3   7.7e+03      87     111 ..     315     342 ..     308     347 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-07
                                      HHHHHHHHHHHHHHS..-SHHHHHHHHHHHHHHHHH CS
                            HsdM_N  1 lesklwkaadiLRgk..vdaseykeyilgLlFlKrl 34
                                      +e+ lw+aad+LR +  +   ey   + gL+Fl+  
  gi|386001772|ref|YP_005920071.1| 10 IEKRLWNAADTLRANsnYASNEYFLPVMGLVFLRHA 45
                                      6899*********99999****************86 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                                       HHHHHHHCHHHHCT--ST...HHHHHHH CS
                            HsdM_N  87 lgenlnkafpaleelnks...lkgvfmk 111
                                       ++e+l+++  +le+ln +   l++++++
  gi|386001772|ref|YP_005920071.1| 315 FEEALREIHVELEDLNAEavkLAATIKN 342
                                       4566666666677776633447777753 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.15       6      64 ..     119     178 ..     118     235 .. 0.84
   2 ?   -0.4   0.0      0.15   8.7e+02      27      51 ..     320     342 ..     313     348 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                   Methyltransf_31   6 rvlDlGCGtGeltfelae...elgpkae....vvGiDiseeaielArenaqklgldnveFeqgdie 64 
                                       +vlD+++G+G    + a+   e g++ +    + G++ +++ i+lA+ n++ +gl+      gdi+
  gi|386001772|ref|YP_005920071.1| 119 HVLDPATGSGGMFVQSARiveEQGQNPTdrltFRGLEKNATTIRLAKMNLAVHGLE------GDIQ 178
                                       69***************966655554448888**********************98......4444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.15
                   Methyltransf_31  27 pkaevvGiDiseeaielArenaqkl 51 
                                        +++v + D ++ea++lA ++   +
  gi|386001772|ref|YP_005920071.1| 320 REIHVELEDLNAEAVKLAATIK--N 342
                                       5566777799********9973..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2102.51
//
Query:       gi|386001773|ref|YP_005920072.1|  [L=342]
Description: hypothetical protein Mhar_1081 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-64  215.2   0.1    7.1e-64  214.3   0.1    1.4  1  YhcG_C     YhcG PDDEXK nuclease domain
    4.9e-49  166.0   1.0    8.5e-49  165.2   1.0    1.4  1  DUF1016_N  DUF1016 N-terminal domain


Domain annotation for each model (and alignments):
>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   0.1     8e-68   7.1e-64       3     155 .]     177     329 ..     175     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 8e-68
                            YhcG_C   3 ilkdpyvldflelkeeykErelekalieklkkfllelGkgFafvgrqyrleveekefyidLlfYhlklkcyvvieLK 79 
                                       +++d+y++df+e+ ee++Erele+ali ++++fl  +G  Fafvg+q rlev++ke++idLl+Yh++lkc+v+ieLK
  gi|386001773|ref|YP_005920072.1| 177 AVRDEYTFDFIEMGEEHSERELERALIARIEDFLRAMGGLFAFVGSQFRLEVDDKEYFIDLLLYHRRLKCLVAIELK 253
                                       79*************************************************************************** PP

                            YhcG_C  80 vgefkpedagklnlYlsaldeelkkeednptiGiilckekdktvveyalkeinkpigvseYelpkelpeelkeklp 155
                                       +gef+pe++gk+++Yl+ald+++++e++np+iGiilckek++tvveyal++++kpigvs+Y++ k+lp+elk +lp
  gi|386001773|ref|YP_005920072.1| 254 IGEFQPEFVGKMQFYLTALDRQVREEGENPSIGIILCKEKSRTVVEYALHDARKPIGVSTYRMVKRLPKELKGQLP 329
                                       ************************************************************************9996 PP

>> DUF1016_N  DUF1016 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.2   1.0   9.5e-53   8.5e-49       1     137 []      18     154 ..      18     154 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 9.5e-53
                         DUF1016_N   1 eikelieqarqkaakavnselvelyweiGkrivekqeraeyGkkvikkLsedLkkefpevkGFsernlknmrqfyea 77 
                                       e+ke++ +a+ +a+kavn+elv lyw+iGk i  +qer+++G++v+++L++dL++efp+v+GFs++nl++mrqfy +
  gi|386001773|ref|YP_005920072.1|  18 EVKERVYSAQYEALKAVNRELVALYWDIGKLIAGRQEREGWGRSVVERLADDLQNEFPGVRGFSVQNLWYMRQFYLE 94 
                                       699************************************************************************** PP

                         DUF1016_N  78 ykeeeilqqlvaqlsWshnllllekvkdeeerefYleeaieegWsrreLerqiksklyer 137
                                       y+ +e+lq+lv ++sWs+nl+++ + kd+ erefY++++ + gWs+++L +qi+++ ye+
  gi|386001773|ref|YP_005920072.1|  95 YRGDEKLQPLVGEISWSKNLIIMARSKDPLEREFYIRMTRKFGWSKNVLIHQIENQSYEK 154
                                       **********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2258.25
//
Query:       gi|386001774|ref|YP_005920073.1|  [L=413]
Description: Drug resistance transporter, Bcr/CflA subfamily [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-38  130.8  48.3    5.5e-38  130.8  48.3    1.5  1  MFS_1     Major Facilitator Superfamily
    3.4e-09   36.1  10.1    3.4e-09   36.1  10.1    2.3  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8  48.3   6.1e-42   5.5e-38       2     353 .]      23     360 ..      22     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 6.1e-42
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        ++ +++ l+ ++++palp  +a  +g+s++ ++l l l+++++++++l++G+lsdr+Grr+vll++l ++ +++l 
  gi|386001774|ref|YP_005920073.1|  23 TFLSAFVPLSTDLYLPALP-GMALYFGVSADLANLTLILFFVFFGAGTLFWGPLSDRYGRRPVLLAALSIYTAASLG 98 
                                       577889999**********.******************************************************888 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       +++ s+    l+++r++q++ga+++f+++ a++ d++  ++r   ++++++++ ++++ +p+lg++l+  ++Wr++f
  gi|386001774|ref|YP_005920073.1|  99 CAL-SGDIhQLIAFRIFQAVGASGAFAVATAMVKDVYESKRREPILAMVQSMVLISPVAAPVLGAILLRFVSWRGAF 174
                                       887.787879******************************************************************* PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..lltl 229
                                       ++la+++lla++ ++l l+e+  er+  s            l  +++  +++  + + l+ l++   + s+  + + 
  gi|386001774|ref|YP_005920073.1| 175 WALALIGLLALL-GGLALVETIGERSGGSLLGA--------LGRIFRVAKNPG-F-STLLLLFSLPGISSMafIAAS 240
                                       *********955.77777777777777766666........333344444444.4.355555555544444346666 PP

                             MFS_1 230 lplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll 305
                                       + +y    +g s  +++ +++  ++++++    ++  r+s+rl r  r ++a +++++a  gl++  + + a++ll+
  gi|386001774|ref|YP_005920073.1| 241 SYIY-INGFGVSpQVYSYYFAANAVGMISG--PMIYMRVSRRLRR--RSIIAASFGAIAGSGLLISIFGERAPWLLA 312
                                       6667.8999999765555544444444444..4488888899665..777888888888888888888888999999 PP

                             MFS_1 306 vlvl.iGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       + +l +++ +++v++++++l+ +   +  +g+a++l++++g ++g+lg+
  gi|386001774|ref|YP_005920073.1| 313 AALLpATISASLVRTPATNLMLEQQ-RGDTGSAAALMSFFGIFAGSLGM 360
                                       77775777*************9998.59*************99999996 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1  10.1   3.8e-13   3.4e-09      54     194 ..      60     194 ..      20     195 .. 0.93
   2 !    3.4   5.5    0.0032        28      52     155 ..     259     357 ..     232     383 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.8e-13
                                       THHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTT CS
                          Sugar_tr  54 iflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEi 130
                                       +f+v   +G lf g+l+dr+GR+++ll+a  ++ ++++ +a++     + +li+ R++  +g+ +a ++++  ++ +
  gi|386001774|ref|YP_005920073.1|  60 LFFVFFGAGTLFWGPLSDRYGRRPVLLAALSIYTAASLGCALSG---DIHQLIAFRIFQAVGASGAFAVATAMVKDV 133
                                       3444444799**********************************...9***************************** PP

                                       S-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 131 ApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                          k R  +  + q+++ +  + a ++g++l ++ +   wr  ++  +++ ll l+++l l E+
  gi|386001774|ref|YP_005920073.1| 134 YESKRREPILAMVQSMVLISPVAAPVLGAILLRFVS---WRGAFWALALIGLLALLGGLALVET 194
                                       ************************************...******************9998776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0032
                                       HHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  52 vsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                       +++  vG i G ++ + ++ r  R+ s+++a++ +++g+ l + + g+++ ++l+++ + + i++     lv + + 
  gi|386001774|ref|YP_005920073.1| 259 FAANAVGMISGPMIYMRVS-RRLRRRSIIAASFGAIAGSGLLISIFGERAPWLLAAALLPATISA----SLVRTPAT 330
                                       3444444444444444444.4447899*******************99*****998754333333....33333334 PP

                                       TTS-SCCHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaa 155
                                        +  ++ Rg  +s   l+  fGi+ ++
  gi|386001774|ref|YP_005920073.1| 331 NLMLEQQRGDTGSAAALMSFFGIFAGS 357
                                       444446677777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2358.64
//
Query:       gi|386001775|ref|YP_005920074.1|  [L=71]
Description: hypothetical protein Mhar_1083 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 438.14
//
Query:       gi|386001776|ref|YP_005920075.1|  [L=156]
Description: hypothetical protein Mhar_1084 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.17   11.9   0.0    1.2  1  DUF5051   3' exoribonuclease, RNase T-like


Domain annotation for each model (and alignments):
>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.4e-06      0.17      14      65 ..      11      69 ..       4      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.4e-06
                           DUF5051 14 etaelvsIGaVff..petG......eFyae.idlesdeeagidaetieWWlkqskearael 65
                                      +++e+++IG V+f   + G       F  +   +++ ++ g   + + WWl+q+   +a +
  gi|386001776|ref|YP_005920075.1| 11 AEVEIIQIGEVVFgrGTSGgagappAFLPVeAGPRPTRDEG--IKSMVWWLHQDPPPAAGA 69
                                      5789*********9955556999998875414565665444..689*******98776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1171.79
//
Query:       gi|386001777|ref|YP_005920076.1|  [L=287]
Description: hypothetical protein Mhar_1085 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-109  364.1   0.2   4.6e-109  363.8   0.2    1.0  1  SDH_sah        Serine dehydrogenase proteinase
     0.0074   16.2   0.0      0.013   15.3   0.0    1.4  1  CLP_protease   Clp protease
  ------ inclusion threshold ------
      0.071   13.2   0.4         55    4.0   0.0    3.2  3  DUF3906        Protein of unknown function (DUF3906)
      0.099   11.9   0.0       0.14   11.5   0.0    1.2  1  ECH_1          Enoyl-CoA hydratase/isomerase
        0.1   12.6   0.0       0.21   11.5   0.0    1.5  1  Peptidase_S49  Peptidase family S49


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.8   0.2  1.3e-112  4.6e-109       9     275 ..      13     285 ..       6     287 .] 0.96

  Alignments for each domain:
  == domain 1  score: 363.8 bits;  conditional E-value: 1.3e-112
                           SDH_sah   9 slssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevlrai 85 
                                       sl+s +w+llfl+l+l p l+r+ l ++r+++l k++++r+s v+t+ihrqe ++flGip+ ++i+i+dse+vlrai
  gi|386001777|ref|YP_005920076.1|  13 SLFSNVWVLLFLFLFLVPMLQRRFLEQSRRRLLVKMGKRRRSVVVTLIHRQEVLTFLGIPLARYIDIDDSEQVLRAI 89 
                                       68999************************************************************************ PP

                           SDH_sah  86 rltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgq. 161
                                       r+tpkd pidli+htpGGl+laatqia alk+h+a+ +vi+phyamsGGtliala deii+d++a lGpvdpqlg+ 
  gi|386001777|ref|YP_005920076.1|  90 RTTPKDVPIDLILHTPGGLALAATQIALALKAHPARKTVIIPHYAMSGGTLIALAVDEIIMDPHAALGPVDPQLGDh 166
                                       *************************************************************************9744 PP

                           SDH_sah 162 ...ypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypltve 235
                                          ypa+s++k +ekk+ +++ddkt++lad a+ka++q+  +v  +l  + d ek   i +++ +G++thd+p+  e
  gi|386001777|ref|YP_005920076.1| 167 tgsYPATSLVKLLEKKKIDEVDDKTIVLADQAEKALRQMDGLVRTILDGRCDGEKVDLIIEEFVSGKYTHDHPFIAE 243
                                       4449************************************************************************9 PP

                           SDH_sah 236 elke.lGlevntnvpeevyellelyeqplgqrps.veyipvp 275
                                       ++++ lG  vnt+vp evy+l++ly+  + +r + vey+pv 
  gi|386001777|ref|YP_005920076.1| 244 DARRlLGECVNTDVPPEVYDLMKLYRMEVARRRPgVEYVPVT 285
                                       998736999*******************9998888*****96 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.7e-06     0.013      38      98 ..      87     147 ..      57     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                                       HHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                      CLP_protease  38 llLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                        ++ ++ +d +i l++++pGG   a++ I+ +++ + ++ ++i    a+S g+l+++a ++
  gi|386001777|ref|YP_005920076.1|  87 RAIRTTPKDVPIDLILHTPGGLALAATQIALALKAHPARKTVIIPHYAMSGGTLIALAVDE 147
                                       45556678999*****************************99999************9876 PP

>> DUF3906  Protein of unknown function (DUF3906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.015        55      27      57 ..     155     185 ..     148     189 .. 0.80
   2 ?    3.6   0.0      0.02        72      17      33 ..     191     207 ..     185     213 .. 0.86
   3 ?    2.0   0.1     0.062   2.2e+02       1       9 [.     265     273 ..     265     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.015
                           DUF3906  27 AFrqleielekhylklPevkevallEkKrir 57 
                                       A   ++ +l  h    P    v llEkK+i 
  gi|386001777|ref|YP_005920076.1| 155 ALGPVDPQLGDHTGSYPATSLVKLLEKKKID 185
                                       566677777778888899999********96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.02
                           DUF3906  17 vvvvAendeqAFrqlei 33 
                                        +v+A++ e+A rq++ 
  gi|386001777|ref|YP_005920076.1| 191 TIVLADQAEKALRQMDG 207
                                       69************995 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.062
                           DUF3906   1 mnlYrfeve 9  
                                       m+lYr+ev 
  gi|386001777|ref|YP_005920076.1| 265 MKLYRMEVA 273
                                       99*****97 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.9e-05      0.14      98     152 ..     133     187 ..     121     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                                       EEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHH CS
                             ECH_1  98 aaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeei 152
                                       +a+ GG ++ala D +i++ +a+ g    +lG   g++    l++ + k+k  e+
  gi|386001777|ref|YP_005920076.1| 133 YAMSGGTLIALAVDEIIMDPHAALGPVDPQLGDHTGSYPATSLVKLLEKKKIDEV 187
                                       899****************************999999999999888888887765 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.8e-05      0.21      11      40 ..     128     157 ..     120     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.8e-05
                                       EEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49  11 asaenvaaSggYylasaadkivanpstivg 40 
                                       +++  +a Sgg ++a a d+i+++p++  g
  gi|386001777|ref|YP_005920076.1| 128 VIIPHYAMSGGTLIALAVDEIIMDPHAALG 157
                                       677899********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2000.77
//
Query:       gi|386001778|ref|YP_005920077.1|  [L=376]
Description: Transposase, IS605 OrfB family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-22   79.8   0.0    4.3e-22   78.6   0.0    1.6  1  OrfB_IS605      Probable transposase
    5.9e-22   77.4   0.0    1.3e-21   76.3   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    6.3e-17   60.8   2.9    1.4e-16   59.6   2.9    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
    0.00082   19.0   0.3     0.0013   18.3   0.3    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0016   17.9   0.3       0.46   10.0   0.0    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0019   18.2   0.4     0.0033   17.4   0.4    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.024   14.2   0.8          1    9.0   0.1    3.0  3  RecR            RecR protein
      0.035   14.7   1.3        3.7    8.1   0.2    2.9  3  FeoB_Cyto       FeoB cytosolic helical domain
       0.05   13.3   0.5        4.3    7.2   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.088   12.4   0.3        1.1    9.0   0.1    2.6  2  GATA            GATA zinc finger


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 !   78.6   0.0   2.4e-25   4.3e-22       3     117 ..     165     277 ..     163     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2.4e-25
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve++++ +p+ k + +agiD+G++ +at+++++   ++ ++r+++s++k+lak++++l++  k++  + ka + ++
  gi|386001778|ref|YP_005920077.1| 165 SVEIDDPqKPPWKDGLMAGIDVGLESFATLSNGE---KIDNPRFFRSEEKALAKAQRRLSKYEKGTPERWKALKVVQ 238
                                       678777746777999*******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r h+++++rr +++h+++++l+++   ++ e+L + nm 
  gi|386001778|ref|YP_005920077.1| 239 RTHERIANRRYDFAHQVSHNLVERFGLIAFEDLSITNML 277
                                       *************************************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   7.3e-25   1.3e-21       5      68 ..     295     358 ..     291     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 7.3e-25
                    OrfB_Zn_ribbon   5 keqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                           +yka+ +G  v++v+p++TS+ Cs+Cg k++++ls+r+++Cp+Cg+++drD nAaiNil+
  gi|386001778|ref|YP_005920077.1| 295 VITTSYKAESAGSMVVLVDPRNTSQLCSRCGLKVNKSLSDRVHECPQCGLVMDRDENAAINILR 358
                                       55568*********************************************************97 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 !   59.6   2.9   8.1e-20   1.4e-16       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 8.1e-20
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lka+kyr+yPT+ Q+ k+++t++ +R+ YN  La+rk+  e+egk
  gi|386001778|ref|YP_005920077.1|  1 M-LKAFKYRIYPTKAQRSKMEQTLELCRWTYNETLAYRKNSFEQEGK 46
                                      8.*******************************************98 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   7.4e-07    0.0013       2      30 ..     317     345 ..     316     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.4e-07
                     zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                       t++ C+rCG ++ ++  ++   Cp+Cgl 
  gi|386001778|ref|YP_005920077.1| 317 TSQLCSRCGLKVNKSLSDRVHECPQCGLV 345
                                       789************************85 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00026      0.46      11      30 ..     310     329 ..     305     335 .. 0.85
   2 !    5.6   0.1    0.0063        11      22      31 ..     339     348 ..     337     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00026
                                       CHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCGlVle 30 
                                       +++Dp ++  +C++CGl + 
  gi|386001778|ref|YP_005920077.1| 310 VLVDPRNTSQLCSRCGLKVN 329
                                       689**************986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0063
                                       ESSSSBEEEE CS
                      TF_Zn_Ribbon  22 CtdCGlVled 31 
                                       C+ CGlV++ 
  gi|386001778|ref|YP_005920077.1| 339 CPQCGLVMDR 348
                                       *******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   1.8e-06    0.0033      10      44 ..     316     352 ..     312     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + ++ Cs+Cg k+++  +   + Cp+Cg  +d +++ 
  gi|386001778|ref|YP_005920077.1| 316 NTSQLCSRCGLKVNKSLSdrVHECPQCGLVMDRDENA 352
                                       6789*********9877799********999999875 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.73   1.3e+03       5      16 ..      71      82 ..      69      84 .. 0.87
   2 ?    1.8   0.1     0.099   1.8e+02      13      23 ..     315     325 ..     310     326 .. 0.75
   3 ?    9.0   0.1   0.00058         1      12      29 ..     332     349 ..     330     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.73
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq++ e+v
  gi|386001778|ref|YP_005920077.1| 71 FSQTLQNVQERV 82
                                      89*******998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.099
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +++ + CsrCg
  gi|386001778|ref|YP_005920077.1| 315 RNTSQLCSRCG 325
                                       666789****8 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00058
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + ++v+ C++Cg + ++d
  gi|386001778|ref|YP_005920077.1| 332 LSDRVHECPQCGLVMDRD 349
                                       679*********998886 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.9     7e+03      46      67 ..      62      83 ..      50      91 .. 0.66
   2 ?    8.1   0.2    0.0021       3.7       6      35 ..     210     237 ..     209     242 .. 0.93
   3 ?    4.7   0.0     0.025        44      70      90 ..     240     260 ..     237     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.9
                         FeoB_Cyto 46 kedpelraeveearkeleaelg 67
                                      k++pel++   ++ ++++++ +
  gi|386001778|ref|YP_005920077.1| 62 KNKPELKEVFSQTLQNVQERVD 83
                                      3446777777777777777655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                         FeoB_Cyto   6 EkaiekleellkesnlkaklppRwlAlklL 35 
                                       Eka++k ++ l+++  ++  p+Rw Alk+ 
  gi|386001778|ref|YP_005920077.1| 210 EKALAKAQRRLSKY--EKGTPERWKALKVV 237
                                       89***********9..************86 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
                         FeoB_Cyto  70 ledvIvdarykfiegilrevv 90 
                                       + + I++ ry+f+++++   v
  gi|386001778|ref|YP_005920077.1| 240 THERIANRRYDFAHQVSHNLV 260
                                       5678************98766 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.024        44      11      20 ..     316     325 ..     315     328 .. 0.77
   2 ?    7.2   0.1    0.0024       4.3       7      20 ..     330     343 ..     329     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                     zinc_ribbon_2  11 dnakFCpyCG 20 
                                       ++++ C++CG
  gi|386001778|ref|YP_005920077.1| 316 NTSQLCSRCG 325
                                       5678899998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2   7 aelqdnakFCpyCG 20 
                                       + l+d++  Cp+CG
  gi|386001778|ref|YP_005920077.1| 330 KSLSDRVHECPQCG 343
                                       679999*******9 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00059       1.1      16      31 ..     314     329 ..     312     333 .. 0.86
   2 ?   -0.1   0.0      0.41   7.4e+02      21      28 ..     337     344 ..     334     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00059
                              GATA  16 pdgnksLCnaCGlyyk 31 
                                       p+++ +LC  CGl+  
  gi|386001778|ref|YP_005920077.1| 314 PRNTSQLCSRCGLKVN 329
                                       89999********865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                              GATA  21 sLCnaCGl 28 
                                       + C +CGl
  gi|386001778|ref|YP_005920077.1| 337 HECPQCGL 344
                                       57999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2732.31
//
Query:       gi|386001779|ref|YP_005920078.1|  [L=175]
Description: peroxiredoxin family protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  126.7   0.0    5.6e-37  126.4   0.0    1.1  1  AhpC-TSA  AhpC/TSA family
    8.6e-18   64.5   0.0      1e-17   64.2   0.0    1.1  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.0   6.2e-41   5.6e-37       2     122 ..      23     149 ..      22     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 6.2e-41
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                       gd+ap f+l+++d ++v l++++g++vvl+fypkd++ +Ct+e+ ++ +++++f+++g+ev+gvs+dsp+sh++f e
  gi|386001779|ref|YP_005920078.1|  23 GDAAPGFCLPDQDEQEVCLAELSGRWVVLYFYPKDNTSGCTREALDFTERLKDFRDLGAEVFGVSPDSPKSHRSFRE 99 
                                       89*************************************************************************** PP

                                       H-H.SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEE CS
                          AhpC-TSA  79 keslnfpllsDeegkvakaygvlkee......kglalratfvidkegkir 122
                                       k++l+++llsD+++ v +ayg++ ++      + + lr+t ++d++gk++
  gi|386001779|ref|YP_005920078.1| 100 KHRLEVTLLSDPDHGVLEAYGAWGKKkmygkeYDGVLRSTAIVDPDGKVA 149
                                       ***********************999*****99***************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   1.2e-21     1e-17       3     130 ..      23     151 ..      21     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.2e-21
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvke 78 
                                       gd+aP f lp+  +d ++v l+e+ g+ vv++f+p   +  C++e++ + e l+++ ++ g +v++v+ d+    ++
  gi|386001779|ref|YP_005920078.1|  23 GDAAPGFCLPD--QDEQEVCLAELSGRWVVLYFYPKDNTSGCTREALdFTERLKDF-RDLGAEVFGVSPDSPKSHRS 96 
                                       899******99..**********************************888888888.******************** PP

                                       HHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEE CS
                           Redoxin  79 fwgkeglkfpvlsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvyl 130
                                       f +k+ l +++lsD+++ + +a+G ++ +++  g      ++++a++d dgkv  +
  gi|386001779|ref|YP_005920078.1|  97 FREKHRLEVTLLSDPDHGVLEAYG-AWGKKKMYGkeydGVLRSTAIVDPDGKVARI 151
                                       ************************.666666656899999*************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1337.89
//
Query:       gi|386001780|ref|YP_005920079.1|  [L=505]
Description: hypothetical protein Mhar_1088 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-10   41.5   0.0    2.6e-10   40.8   0.0    1.3  1  VWA            von Willebrand factor type A domain
    1.2e-05   25.1   0.0    6.7e-05   22.7   0.0    1.9  1  Integrin_beta  Integrin beta chain VWA domain
    0.00062   20.4   0.0       0.12   13.1   0.0    2.2  2  VWA_2          von Willebrand factor type A domain


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 !   40.8   0.0   4.3e-14   2.6e-10       1     166 [.      89     272 ..      89     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 4.3e-14
                                       EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS...........EEEEEETTSHC......H CS
                               VWA   1 DivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfsse...........vktefslndys......s 60 
                                       Divfv D+ gsm +++++++k+++k+++++l+++  + r+gl  + ++             + f+++ y+      +
  gi|386001780|ref|YP_005920079.1|  89 DIVFVFDTTGSM-GGEIDEMKSIAKEFADRLTSSGIDYRLGLTEYRDYdldcggdsacgGSEDFPYKVYNegvltgN 164
                                       9***********.999******************************6666666667887777777777777777788 PP

                                       HHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSST.TSEEEEEEEES......S--CSS.......HTHHH CS
                               VWA  61 keellsalnnlkysgggttntgkalkyaleklfkssagaRe.nakkviilltd......Gksndg.......dpkea 123
                                        ++++ +++ l    gg+    +a+ +a+ +  + +++ R  +a kvi+l+td      G    +        +  a
  gi|386001780|ref|YP_005920079.1| 165 SATFKAWIDGLGLGWGGDE--PEAVLAAMIHTVDDQQW-RGgDAAKVIVLITDapahpdG----DccnqegeTLGGA 234
                                       8**********99999999..66777777778888888.677***********7766664....1444445789999 PP

                                       HHHHHGCTEEEEEEEESSSHHHHHHHHHSSSSCHHCEEEESSH CS
                               VWA 124 aneakeqgikvfavGvgnadekelLnkiasepgeghvftvtdf 166
                                       +  + ++g+kv+a+G     e++ ++k+a e+g g+++  ++ 
  gi|386001780|ref|YP_005920079.1| 235 ISYLAANGVKVYAIGP---EEES-IQKMAFETG-GKFYLIRSG 272
                                       99999**********6...4445.889999999.888877665 PP

>> Integrin_beta  Integrin beta chain VWA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.1e-08   6.7e-05       7     153 ..      89     223 ..      85     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-08
                     Integrin_beta   7 DLYyLmDlSySmkddlenlkklgkklaeelkkitsnlrlGfgsfvdktvlpfvsttpeklknpcsekkeeCqppfgf 83 
                                       D+ ++ D + Sm  +++++k+++k+ a++l++   ++rlG+ ++ d  +    +       + c  ++   + p++ 
  gi|386001780|ref|YP_005920079.1|  89 DIVFVFDTTGSMGGEIDEMKSIAKEFADRLTSSGIDYRLGLTEYRDYDLDCGGD-------SACGGSE---DFPYKV 155
                                       78899***************************************9988765554.......6788764...899999 PP

                     Integrin_beta  84 khvlsLtedveeFeeevkkqkisgnlDapEGglDAllQaavCkekigwrk.earrllvfstdaafhlagdg 153
                                        +   Lt ++++F++ ++   +    D+pE+ l A++ ++   ++ +wr  +a +++v+ tda  h  gd 
  gi|386001780|ref|YP_005920079.1| 156 YNEGVLTGNSATFKAWIDGLGLGWGGDEPEAVLAAMIHTV---DDQQWRGgDAAKVIVLITDAPAHPDGDC 223
                                       9***********************************9887...4557886689*************99986 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 !   13.1   0.0     2e-05      0.12       1      47 [.      90     134 ..      90     140 .. 0.85
   2 !    5.1   0.0    0.0061        36      55     106 ..     161     215 ..     148     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl...pgd.rvglvtfsd 47 
                                       +vfv Dt+gSm+++      ++ +k++++++ ++l     d r+gl  ++d
  gi|386001780|ref|YP_005920079.1|  90 IVFVFDTTGSMGGE------IDEMKSIAKEFADRLtssGIDyRLGLTEYRD 134
                                       79***********8......9999999999999885534458999998876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0061
                             VWA_2  55 ltkdkakilnalrnleakgggtnlaaaLqlarkalkkrr...kgekrvivlitDg 106
                                       lt + a++++ +++l    gg   +a L  +  ++++++     + +vivlitD+
  gi|386001780|ref|YP_005920079.1| 161 LTGNSATFKAWIDGLGLGWGGDEPEAVLAAMIHTVDDQQwrgGDAAKVIVLITDA 215
                                       57788888888888887777777777777777777777777789**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3994.35
//
Query:       gi|386001781|ref|YP_005920080.1|  [L=184]
Description: Adenine phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-21   75.9   1.0      3e-21   75.6   1.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    4.4e-06   26.3   0.0    7.4e-06   25.6   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
     0.0013   18.2   0.0     0.0019   17.7   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase
  ------ inclusion threshold ------
       0.22   11.0   0.0       0.29   10.6   0.0    1.1  1  DUF4846       Domain of unknown function (4846)


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   1.0   6.6e-25     3e-21      14     140 ..      38     167 ..      33     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 6.6e-25
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----TT CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpag 87 
                                        +++    i++++n   d +v+i+  G+ ++++l+   ++pl+++rk++y  +g  e++++   +     l ++  g
  gi|386001781|ref|YP_005920080.1|  38 LIREVVTHIIRTANLDVDKIVTIEAMGIHIGTALSLSTDIPLVIIRKRRYGLPGEIEVSQVTGYSKgqlYLNGISPG 114
                                       789999999*************************************************98776555999999***** PP

                                       SEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS CS
                      Pribosyltran  88 kkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrv 140
                                        +V++VDD+++tGgT la+le+Lk++g+++v +++++++++++e+ +   + +
  gi|386001781|ref|YP_005920080.1| 115 DRVIVVDDVISTGGTALATLEALKAAGAQVVDVVAVIERGSGAERLKGQGYQI 167
                                       ******************************************99877665555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.6e-09   7.4e-06     121     180 ..     114     171 ..      86     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-09
                           UPRTase 121 ertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvvt 180
                                        ++v+++D vi+TGg+a a ++ Lk +g+  + + v++v+   +g++rl  +  ++k ++
  gi|386001781|ref|YP_005920080.1| 114 GDRVIVVDDVISTGGTALATLEALKAAGA--QVVDVVAVIERGSGAERLKGQGYQIKTML 171
                                       578***********************666..578999***********998877777655 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.2e-07    0.0019     122     159 ..     115     151 ..     105     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-07
                          PRTase_2 122 kelvLvDDEistGktalnliralqeklprkryvvvslv 159
                                       +++++vDD istG tal++++al+++  +  + vv+++
  gi|386001781|ref|YP_005920080.1| 115 DRVIVVDDVISTGGTALATLEALKAAGAQ-VVDVVAVI 151
                                       689********************998765.34444444 PP

>> DUF4846  Domain of unknown function (4846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.5e-05      0.29     149     203 ..      91     146 ..      80     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.5e-05
                           DUF4846 149 kelkkvkledlqiGdvfikggspghavivvDvaenekgekvfLL.aqsymPaqeih 203
                                        e++  +++  + G ++++g spg+ vivvD    + g  ++ L a     aq ++
  gi|386001781|ref|YP_005920080.1|  91 GEIEVSQVTGYSKGQLYLNGISPGDRVIVVDDVISTGGTALATLeALKAAGAQVVD 146
                                       5667777888899******************9998887766544144555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1236.88
//
Query:       gi|386001782|ref|YP_005920081.1|  [L=85]
Description: hypothetical protein Mhar_1090 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-17   61.1   0.1    9.2e-17   60.9   0.1    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   5.1e-21   9.2e-17       1      73 []      13      78 ..       9      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 5.1e-21
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                      ++++++eea e+v+       p ge++e +  ++e+Yl+D++yfle+gdl++ + ++ +a++w++ gar+g+l
  gi|386001782|ref|YP_005920081.1| 13 KWLKRAEEARERVS-------PRGEEGEGFSANIEAYLSDCRYFLERGDLIRGFEAVIWAWAWIEIGARVGVL 78
                                      45666666666666.......**************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 559.24
//
Query:       gi|386001783|ref|YP_005920082.1|  [L=739]
Description: Oligosaccharyl transferase, STT3 subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-21   74.3  18.1    5.4e-20   71.8  18.1    2.0  1  STT3      Oligosaccharyl transferase STT3 subunit
    1.8e-15   57.0   0.1    2.9e-15   56.3   0.1    1.4  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
    2.3e-07   31.2  13.1    2.3e-07   31.2  13.1    2.9  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8  18.1     9e-24   5.4e-20      30     485 ..      48     524 ..      40     526 .. 0.72

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 9e-24
                                       --SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHCHHHHHHHHCC CS
                              STT3  30 lsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsldvsirevclwl 106
                                       ++  D++Y  R + ++++n       ++++ wfd +  +P+G++++++pl   + ++ +a++    +  + +++ ++
  gi|386001783|ref|YP_005920082.1|  48 FYGYDSFYHARRILYTAEN-------FPHTLWFDSYLHHPLGHPITWPPLFDQM-VAGAALLLGGSPGAVEAAAAAF 116
                                       5678***************.......8************************999.6666666666679********* PP

                                       HHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTCHH CS
                              STT3 107 pallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnkisl 183
                                       p+llg  +  + y+l+++l++ + +ll+A+llai    ++rt  G+ D+d +e++l+l v+ ++  a+   ++   +
  gi|386001783|ref|YP_005920082.1| 117 PPLLGTSMILILYLLTKKLFGMRVALLSAFLLAIDSKHIARTLFGLPDHDPLELLLMLGVILLLAHALTDRDRWAWY 193
                                       ************************************************************************999** PP

                                       HHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT...............S-CCHHHHH............... CS
                              STT3 184 aviaaliiflivlaWggyailiyallllfilalLiigr...............felklkiav............... 230
                                        ++a+++++ + ++W+g     + ++ + i a++ i+                                        
  gi|386001783|ref|YP_005920082.1| 194 GAAAGVMMAAVAYSWLGA---PIYMIGVLIYATIQITLdlregadvcetiaplA-------Aafgaalllilpfrne 260
                                       *****************8...566777777777777777778999955555540.......4444444555566666 PP

                                       ..HHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC.....CHHTT.HHH CS
                              STT3 231 ..tfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfis.....lfqpgilse 300
                                         +++  i++l + + + +f g+  +    ++    +++++ ++ + +  ++ +  +  ++ s     + +++  s 
  gi|386001783|ref|YP_005920082.1| 261 awLIPSFIGALGSLVALGVFYGLFLLFAARRLPWQAFVPTVAFLSYFGAILSSSTEEGRKVGSllaegIRYFF-GSD 336
                                       6688888888887777788888887778899999999999888888888888666666666664444333333.344 PP

                                       HTT--GGGHHHHHHHHHHHHC.........CCCCCTS---.........--TTHHHHHHHHHS---S--CCHHHCCS CS
                              STT3 301 vlgligevvtalavlglialw.........lgilyslldl.........eyaklkikiiilvsvwlpvgllaltkgl 359
                                       +  +++e  +++  +  ia+          +       +l         e   ++++++     w  ++ ++++   
  gi|386001783|ref|YP_005920082.1| 337 LARVGVEETMPIFRVYEIASLpvlglvfalA-------GLwililrmreEGWRRDHLLF---LLWALLSTALMISQA 403
                                       4555577777776666666667744444442.......444444422324445555444...558888999999999 PP

                                       SST.TTTCCCHH.HCHHCCHHCTCHHHHHHH...HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHH CS
                              STT3 360 rfl.iftvPlgi.ifvgllleflavfvkiys...vsqilfsgvvvillmltllpvlallaavkiskifstykdekea 431
                                       rfl +f+v  ++ +++ ++ + +++     +      + ++g+ ++ll+l+l +++ l a    +       +e++ 
  gi|386001783|ref|YP_005920082.1| 404 RFLfLFSVIGSVlVSLLFFWGTERIGPSQLPlraDPGLARAGTAAFLLLLLLPAAVNLPAVARYQ-------PEISG 473
                                       99988888888775555555666655555552213456666666665544444444444444444.......44444 PP

                                       HHHHHHHHHHHHHCT.TTTTHHHTTHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              STT3 432 kikvaakavaptksnglkeslewkantnrdsvvitwwdyghilaveadrpVtfd 485
                                       +++ + +   ++++     + +       +  + +wwdyg  + + ++rpV+++
  gi|386001783|ref|YP_005920082.1| 474 DWSDSLEW--VGEKTPPTAGFDR-PVEAAEYGILSWWDYGNWILYKSKRPVVAN 524
                                       44432222..2333334445555.344567789999999999999999999876 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1   4.9e-19   2.9e-15       1      92 []     646     735 ..     646     735 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 4.9e-19
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEE..... CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevta..... 72 
                                       GA+i G+++ ++ v + +el++nqgr f+Y  +a +  dG++e++vPYsteg        +v+  gpY v       
  gi|386001783|ref|YP_005920082.1| 646 GAKIAGTTPYDEPVGVILELTSNQGRRFQYFASA-TPVDGRYEIVVPYSTEG------REGVHSIGPYLVGPlkdvp 715
                                       9*********************************.6***************7......5688888999887744444 PP

                                       TTEEEEE---HHHHHHT-EE CS
                           AglB_L1  73 gnvtaeveVpEeaVlsgetv 92 
                                       g  ++eveV E++Vl+g t+
  gi|386001783|ref|YP_005920082.1| 716 GGDSREVEVREAEVLEGMTI 735
                                       66***************987 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2  13.1   3.8e-11   2.3e-07       3     133 ..      88     232 ..      86     258 .. 0.75
   2 ?   -1.3   1.6      0.39   2.3e+03     104     114 ..     390     400 ..     342     428 .. 0.50

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.8e-11
                             PMT_2   3 PPliawllalftklf....gfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftp. 74 
                                       PPl+  + a  + l+    g  e a+  ++ l+g  +il+lyll ++lfg r+all+a+lla+    +a ++ + p 
  gi|386001783|ref|YP_005920082.1|  88 PPLFDQMVAGAALLLggspGAVEAAAAAFPPLLGTSMILILYLLTKKLFGMRVALLSAFLLAIDSKHIARTLFGLPd 164
                                       5555555555555553333567888999999********************************88888888855553 PP

                             PMT_2  75 .daplvllwalalylllrale.knklkyw.llagvlfGlgflsKytaallliaallyllis......a 133
                                        d + +ll++ +++ll+ al+ ++++ ++ ++agv++++  +s   a +++i++l+y+ i+      +
  gi|386001783|ref|YP_005920082.1| 165 hDPLELLLMLGVILLLAHALTdRDRWAWYgAAAGVMMAAVAYSWLGAPIYMIGVLIYATIQitldlrE 232
                                       388999999999999999999455599999999**********9999999999999998875555442 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                             PMT_2 104 agvlfGlgfls 114
                                       + +l+  ++++
  gi|386001783|ref|YP_005920082.1| 390 LWALLSTALMI 400
                                       11111222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 5143.99
//
Query:       gi|386001784|ref|YP_005920083.1|  [L=373]
Description: Transposase, IS605 OrfB family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-24   86.3   0.0    3.7e-24   85.2   0.0    1.5  1  OrfB_IS605      Probable transposase
    5.2e-23   80.8   0.1    1.2e-22   79.5   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.7e-18   65.2   1.4    5.3e-18   64.2   1.4    1.5  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0027   17.2   0.3       0.78    9.3   0.0    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0073   16.3   0.5      0.014   15.4   0.5    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.024   14.3   0.5      0.062   13.0   0.5    1.7  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.08   12.1   0.1       0.46    9.6   0.1    1.9  1  RuvC_1          RuvC nuclease domain
      0.093   11.9   0.0       0.14   11.3   0.0    1.2  1  NB-ARC          NB-ARC domain
       0.29   10.9   1.2         23    4.9   1.4    2.5  2  zinc_ribbon_2   zinc-ribbon domain
       0.44   10.6   3.3       0.33   10.9   1.3    1.8  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.84    9.3   4.7        2.1    8.0   0.1    3.0  3  RecR            RecR protein


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 !   85.2   0.0   2.3e-27   3.7e-24       3     117 ..     165     277 ..     163     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 2.3e-27
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve++++ +p+ k +  +giD+G++ +at ++++   ++ ++r+++sd+ +lak++++l++++k++ ++++a + ++
  gi|386001784|ref|YP_005920083.1| 165 TVEIDDPpKPPWKDGLSVGIDVGLESFATISNGE---KIGNPRFFRSDETALAKAQRRLSKCAKGTSQRRAAVKVVQ 238
                                       577777646677999*******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h+++++rr +++h+++++l+ ++  ++ e+Ln++nm 
  gi|386001784|ref|YP_005920083.1| 239 RVHERIANRRYNFAHQMSNQLVSKYGLIVFEDLNIKNML 277
                                       **************************************7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.1   7.7e-26   1.2e-22       1      68 [.     291     358 ..     291     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 7.7e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       +r l +  +yka+ +G kv++v+p++TS+ Cs+Cg k+ ++ls+r+++C++Cg+++drD nAaiNil+
  gi|386001784|ref|YP_005920083.1| 291 WRMLVTTTSYKAESAGSKVVLVDPRNTSQLCSRCGVKVPKSLSDRVHECTQCGLVMDRDENAAINILR 358
                                       777888889*********************************************************97 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 !   64.2   1.4   3.2e-21   5.3e-18       1      46 [.       1      45 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 3.2e-21
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeeg 46
                                      M lkayk+rl PT++Q+ k++rt++ +R+VYN+ La+rk+a+e+eg
  gi|386001784|ref|YP_005920083.1|  1 M-LKAYKFRLFPTKTQRSKMERTLDLCRWVYNQTLAYRKDAWEKEG 45
                                      8.******************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00048      0.78       8      29 ..     307     328 ..     305     335 .. 0.84
   2 !    5.6   0.1    0.0067        11      22      32 ..     339     349 ..     337     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00048
                                       CEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon   8 stnlveDpergelvCtdCGlVl 29 
                                       s+ +++Dp ++  +C++CG+ +
  gi|386001784|ref|YP_005920083.1| 307 SKVVLVDPRNTSQLCSRCGVKV 328
                                       444799*************987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0067
                                       ESSSSBEEEEC CS
                      TF_Zn_Ribbon  22 CtdCGlVledn 32 
                                       Ct CGlV++ +
  gi|386001784|ref|YP_005920083.1| 339 CTQCGLVMDRD 349
                                       *******9855 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   8.5e-06     0.014      10      44 ..     316     352 ..     312     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.5e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + ++ Cs+Cg k+++  +   + C +Cg  +d +++ 
  gi|386001784|ref|YP_005920083.1| 316 NTSQLCSRCGVKVPKSLSdrVHECTQCGLVMDRDENA 352
                                       6789********99777699********999998875 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   3.8e-05     0.062       2      30 ..     317     345 ..     316     346 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                     zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                       t++ C+rCG ++ ++  ++   C +Cgl 
  gi|386001784|ref|YP_005920083.1| 317 TSQLCSRCGVKVPKSLSDRVHECTQCGLV 345
                                       789************************85 PP

>> RuvC_1  RuvC nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00028      0.46      93     167 ..     250     324 ..     211     371 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RuvC_1  93 qvvhkiaklaikynaivvlEdLnlgFkrgrqkvekqvyqkfEkaLidklnylvdkkkkeeeaggllkayqltakv 167
                                       +  h++++ ++ +  ++v+EdLn++ + + + v k++  +  ++L+   +y ++   ++      +++ ql ++ 
  gi|386001784|ref|YP_005920083.1| 250 NFAHQMSNQLVSKYGLIVFEDLNIKNMLKNHCVAKSISDAAWRMLVTTTSYKAESAGSKVVLVDPRNTSQLCSRC 324
                                       567999999999999*******************************99999888877777777777777777665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.6e-05      0.14      83     141 ..     242     300 ..     220     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                                       SSSS-STTSHHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEEEESBC CS
                            NB-ARC  83 leekeeveslkrklvrlLltkrfllvlDDVweeedwdkigvvlparenrlrvllTTRde 141
                                         + + +++ ++++ + L +k  l+v+ D   ++ +++ +v+ +  +  +r+l+TT + 
  gi|386001784|ref|YP_005920083.1| 242 ERIANRRYNFAHQMSNQLVSKYGLIVFEDLNIKNMLKNHCVAKSISDAAWRMLVTTTSY 300
                                       345566677999********************************************775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.021        33      11      20 ..     316     325 ..     315     328 .. 0.72
   2 ?    4.9   1.4     0.014        23       2      20 ..     321     343 ..     320     343 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                     zinc_ribbon_2  11 dnakFCpyCG 20 
                                       ++++ C++CG
  gi|386001784|ref|YP_005920083.1| 316 NTSQLCSRCG 325
                                       5677888888 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                     zinc_ribbon_2   2 CpnCGae....lqdnakFCpyCG 20 
                                       C++CG +    l+d++  C++CG
  gi|386001784|ref|YP_005920083.1| 321 CSRCGVKvpksLSDRVHECTQCG 343
                                       77777551111455555577777 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.6   1.1e+04      34      41 ..     217     224 ..     209     225 .. 0.67
   2 ?   10.9   1.3    0.0002      0.33      19      44 ..     319     343 ..     314     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.6
                     Zn_Tnp_IS1595  34 trglfqCk 41 
                                       +r+l +C+
  gi|386001784|ref|YP_005920083.1| 217 QRRLSKCA 224
                                       37888887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                     Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCr 44 
                                       + C +Cg++ + ++++ ++++C  C+
  gi|386001784|ref|YP_005920083.1| 319 QLCSRCGVKVPKSLSD-RVHECTQCG 343
                                       56*************9.********7 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.3   2.2e+03       8      20 ..     212     224 ..     211     225 .. 0.87
   2 ?    1.8   0.1      0.11   1.7e+02      13      23 ..     315     325 ..     310     326 .. 0.75
   3 ?    8.0   0.1    0.0013       2.1      12      29 ..     332     349 ..     330     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                       HHHHHHHH-EE-T CS
                              RecR   8 aLqeakekvrhCs 20 
                                       aL +a ++++ C 
  gi|386001784|ref|YP_005920083.1| 212 ALAKAQRRLSKCA 224
                                       89999****9996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +++ + CsrCg
  gi|386001784|ref|YP_005920083.1| 315 RNTSQLCSRCG 325
                                       666789****8 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0013
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + ++v+ C +Cg + ++d
  gi|386001784|ref|YP_005920083.1| 332 LSDRVHECTQCGLVMDRD 349
                                       679*********998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2622.92
//
Query:       gi|386001785|ref|YP_005920084.1|  [L=366]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-22   78.0   0.0    1.1e-21   77.4   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00012   22.0   0.0    0.00016   21.6   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.077   12.5   0.0       0.13   11.7   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
        1.1    8.6   9.3        0.5    9.8   2.4    2.2  2  DUF2162          Predicted transporter (DUF2162)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   2.5e-25   1.1e-21       9     168 ..       3     156 ..       1     157 [. 0.93

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.5e-25
                                       -TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEE CS
                   Glycos_transf_2   9 eektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyil 84 
                                       ee+t+ e++++++a  ++      ++v D+S+Det+ei+++l     +  v+r e + G+++a+ ag+++a+g+yi+
  gi|386001785|ref|YP_005920084.1|   3 EEETIGECIRRARAVfEEMGIEGEVIVADSSRDETPEIARSL-----GAEVVRPE-KLGYGNAYLAGFSRARGRYIV 73 
                                       89*************75555555788899999**********.....89999988.66******************* PP

                                       EEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEE CS
                   Glycos_transf_2  85 flDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaall 161
                                       ++D D+++dp  ++++++ le ++ad+v+g+r + + e++ ++  +r +  ++l + + +   + ++s+ +++++++
  gi|386001785|ref|YP_005920084.1|  74 IMDGDLTYDPLEIPEFIRVLESGRADLVIGTRLKGRIEEGAMPALHR-YLGNPLLTGILNLLFGAGISDAHSGMRAI 149
                                       *******************************************9988.7**************************** PP

                                       EEHHHHH CS
                   Glycos_transf_2 162 rrealee 168
                                        real++
  gi|386001785|ref|YP_005920084.1| 150 TREALDR 156
                                       ****976 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.6e-08   0.00016      13     122 ..       3     103 ..       1     178 [. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.6e-08
                   Glyco_tranf_2_3  13 eedvlgevlesllaq.eyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravk 87 
                                       ee+++ge+++ + a  e++ +e  v+v d s++et e a+     l++    vv++++ lg   + +a+  ++++++
  gi|386001785|ref|YP_005920084.1|   3 EEETIGECIRRARAVfEEMGIEGEVIVaDSSRDETPEIARS----LGA---EVVRPEK-LG---YGNAYLAGFSRAR 68 
                                       67788888888886645677777677768899999998876....666...4776666.55...78899******** PP

                   Glyco_tranf_2_3  88 sdlvllvDdDtvvePdtlkrllqffltpkvgavgt 122
                                       +++++++D+D   +P  ++ + +++++ +++ v +
  gi|386001785|ref|YP_005920084.1|  69 GRYIVIMDGDLTYDPLEIPEFIRVLESGRADLVIG 103
                                       ******************99999997777777654 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05      0.13      21     116 ..      59     157 ..      49     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                   Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaaflntl.agvlqa.k 94 
                                       + l ++++a+ +++vi D d + +p  + e+ + le+ ++ lV ++ +  + + g+  al++ + n+l  g+l   +
  gi|386001785|ref|YP_005920084.1|  59 AYLAGFSRARGRYIVIMDGDLTYDPLEIPEFIRVLESGRADLVIGTRLKGRIEeGAMPALHRYLGNPLlTGILNLlF 135
                                       56788999****************************************66555388888888888866477777765 PP

                   Glyco_transf_21  95 lsglgfavGksmalrreaLeai 116
                                        +g++ a   + a++reaL+++
  gi|386001785|ref|YP_005920084.1| 136 GAGISDAHSGMRAITREALDRL 157
                                       5777555544556777778765 PP

>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.4   0.00011       0.5     131     189 ..     221     278 ..     213     313 .. 0.73
   2 ?    2.2   1.5     0.022     1e+02      68      85 ..     334     351 ..     289     356 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                           DUF2162 131 glvlglvflilvlvtyllsrkivkltktnypiiLGnlmlfiGlyfLlsaliipniaqak 189
                                       g ++++++l l+l + +l+++ ++    +   iLG+++l++G  +Lls + i+++ +a 
  gi|386001785|ref|YP_005920084.1| 221 GPGAVALLLGLALTLFVLMQEPSR-DLRAHSLILGSMLLIMGYQTLLSGFYIAAFGKAY 278
                                       555555555555555555553333.33446779*********************99875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.022
                           DUF2162  68 hllmAlllialGlytlkk 85 
                                         +mA++l+++G++t+++
  gi|386001785|ref|YP_005920084.1| 334 ESVMAMILVVIGVQTIFS 351
                                       458999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 2714.36
//
Query:       gi|386001786|ref|YP_005920085.1|  [L=375]
Description: group 1 glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-35  120.6   0.0    6.7e-35  120.2   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    3.4e-28   98.8   0.4    4.6e-28   98.3   0.4    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
      5e-28   98.2   0.1    9.5e-28   97.3   0.1    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.9e-23   81.5   3.6    1.9e-22   80.4   3.6    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.2e-06   27.4   0.0    5.9e-06   26.6   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.018   15.1   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0   2.2e-38   6.7e-35      14     164 ..     197     347 ..     187     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 2.2e-38
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleel 89 
                                         + +++vgrl+ +K+vdlli+a+ ll+++  p +++ i+Gng+e + l++l++ ++l+ +v+flg+++ ++++ + 
  gi|386001786|ref|YP_005920085.1| 197 ALYDLIYVGRLSAHKRVDLLIEAVGLLREE-VPGIRCGIVGNGPEMAALSRLVQDRGLEGRVEFLGFLDgEDEVVAK 272
                                       55679**********************997.********************************************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                       +k+a ifvlps++EgfG+++lEA a+glp+++++   + +a+++++g++G+l+ p  a ++a +++ ll  + ++er
  gi|386001786|ref|YP_005920085.1| 273 FKAARIFVLPSTREGFGMSVLEANACGLPAVVVDakRSAAADLITEGKNGVLCRPS-ASSIASKVAGLLAGG-SYER 347
                                       *********************************9877899***************9.9*******9999988.4444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.4   1.6e-31   4.6e-28       2     170 .]      16     188 ..      15     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.6e-31
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv...tpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkre...k 72 
                                       GG+er v+e++r+La+ GheV+++     ++d+ +e+e  +v  ++++   l+ + +rs++++ r+ ++l      +
  gi|386001786|ref|YP_005920085.1|  16 GGAERRVWEVSRRLAKGGHEVHIFgmkHWEGDDLIERE-GVVLHGVSPAGSLYSGGRRSISAAVRFSARLLPKlrgD 91 
                                       9***********************96433333333333.5666666666777778888887777766655544467* PP

                    Glyco_transf_4  73 pDvvHahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                       +Dv+ a+++++l +  ++l + r+g+plV+t H  +   +++ +l++  ++    er +lr   r+i vSe ++++l
  gi|386001786|ref|YP_005920085.1|  92 FDVIDAQQFPYLPCFSAKLHAlRRGAPLVITWHEVW-GEYWREYLGRMAPFGILAERGALRLPERIIPVSERVRADL 167
                                       ****99998776443333222569************.8*************************************** PP

                    Glyco_transf_4 149 rerygvppekitVipnGvDler 170
                                       +  +gv +++++V+ nGvDl+r
  gi|386001786|ref|YP_005920085.1| 168 LG-MGVGADRMEVVNNGVDLDR 188
                                       **.*****************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 !   97.3   0.1   3.2e-31   9.5e-28       3     133 ..     200     341 ..     199     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 3.2e-31
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---...THHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv...edlaella 71 
                                       ++++vGrl++ +k+vdll+eav llr++ + +r+ ivG+gp + ++l +l++  gle rvef+Gf+   +++ + ++
  gi|386001786|ref|YP_005920085.1| 200 DLIYVGRLSA-HKRVDLLIEAVGLLREEvPgIRCGIVGNGPeM-AALSRLVQdrGLEGRVEFLGFLdgeDEVVAKFK 274
                                       589*****55.5**************88758*********966.5999888779**999*******99555****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGG..GTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvg..giaevv..gengllvppgdpealaeailrLle 133
                                       aa++fv+Ps  egfg+++lEa a+glp V+ d++  ++a+++  g+ng+l+ p +++++a +++ Ll+
  gi|386001786|ref|YP_005920085.1| 275 AARIFVLPStrEGFGMSVLEANACGLPAVVVDAKrsAAADLIteGKNGVLCRP-SASSIASKVAGLLA 341
                                       **********99*******************99533579999999******86.699******99985 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 !   80.4   3.6   6.3e-26   1.9e-22       1     160 []      16     183 ..      16     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 6.3e-26
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrl.pvprr.pspladlaalralrrll.rqrrerp 74 
                                       gG++r+v e++r+La+ GheV+++  +  +g++ +e++gv +h++ p++   ++++++ +a+ ++ + l    r  +
  gi|386001786|ref|YP_005920085.1|  16 GGAERRVWEVSRRLAKGGHEVHIFGMKHWEGDDLIEREGVVLHGVsPAGSLySGGRRSISAAVRFSARLlPKLRGDF 92 
                                       8************************999999998*********985666553358888888888855554779**** PP

                   Glyco_trans_4_4  75 dvvhahs.pt.aglaarlarrrrgiplvvtlhgll...lrrgsgavrrlyralerrllrradavlvvseaeaeelra 146
                                       dv+ a++ p+   + a+l ++rrg+plv+t+h+ +   +r++ g+ +++   +er +lr   +++ vse ++++l  
  gi|386001786|ref|YP_005920085.1|  93 DVIDAQQfPYlPCFSAKLHALRRGAPLVITWHEVWgeyWREYLGRMAPFGILAERGALRLPERIIPVSERVRADLLG 169
                                       *******65544566666666***********8774446666888888889************************** PP

                   Glyco_trans_4_4 147 lgvpadrvvvvpng 160
                                       +gv adr++vv ng
  gi|386001786|ref|YP_005920085.1| 170 MGVGADRMEVVNNG 183
                                       ************98 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     2e-09   5.9e-06       1      82 [.     278     360 ..     278     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2e-09
                   Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltdda..egleelftpgkevilfe.dleelaekiryllanpeerraiaeaar 74 
                                       i++ ps +e++ + ++Ea acG +a++ da  ++ ++l+t+gk ++l + +  ++a k++ lla  + ++++a  a+
  gi|386001786|ref|YP_005920085.1| 278 IFVLPSTREGFGMSVLEANACGLPAVVVDAkrSAAADLITEGKNGVLCRpSASSIASKVAGLLA-GGSYERMAGPAK 353
                                       57789*********************99999*****************************9875.666677777666 PP

                   Glyco_trans_1_2  75 ervlaeht 82 
                                       e+  + ++
  gi|386001786|ref|YP_005920085.1| 354 EF-AKGYD 360
                                       66.45555 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     6e-06     0.018       1     108 [.       2     125 ..       2     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6e-06
                   Glyco_trans_4_2   1 killlanlssvht.....lrl...akeLakrgyeVhvitpkkga.kdeleaegihvhrlkvd....rkgpleylk.a 63 
                                       ki++++++ ++++     +r+    + Lak g+eVh++ +k  + +d  e+eg+ +h +  +     +g    ++ a
  gi|386001786|ref|YP_005920085.1|   2 KIAYVHDVIYPYVkggaeRRVwevSRRLAKGGHEVHIFGMKHWEgDDLIEREGVVLHGVS-PagslYSGGRRSISaA 77 
                                       799999999999644443333233667*************99986777779999999995.4456655566667635 PP

                   Glyco_trans_4_2  64 fkl.kklikki..kPDvvhahyakpy.gllgslaarlsgvipvvlsvwG 108
                                        ++ ++l+ k+   +Dv+ a++ + +  + ++l a++ g  p+v++ ++
  gi|386001786|ref|YP_005920085.1|  78 VRFsARLLPKLrgDFDVIDAQQFPYLpCFSAKLHALRRG-APLVITWHE 125
                                       588889998873359*******87667999********9.999988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2877.24
//
Query:       gi|386001787|ref|YP_005920086.1|  [L=372]
Description: group 1 glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-37  126.2   0.0    1.6e-36  125.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
      2e-32  112.4   0.1    5.4e-32  111.0   0.0    1.8  2  Glyco_trans_1_4  Glycosyl transferases group 1
    4.9e-21   75.5   0.1    1.3e-20   74.1   0.1    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.1e-18   66.3   0.2    2.6e-17   63.7   0.0    2.1  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      5e-13   49.3   0.0    1.1e-12   48.2   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    2.6e-06   27.5   0.0    4.2e-06   26.8   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.026   14.2   0.0    1.5  1  Glyco_transf_5   Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.0   6.1e-40   1.6e-36      21     171 ..     196     348 ..     177     349 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 6.1e-40
                                       ESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEE CS
                   Glycos_transf_1  21 vgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifv 97 
                                       + r  ++Kg+++l+ a+a +k++  ++v+l++ G+ge ++ +++ ++ l+l++nv+flg+v++e + + ++++dif+
  gi|386001787|ref|YP_005920086.1| 196 LDRHHRYKGLEVLLSALAVVKEE-VSDVQLLVGGGGELLDHYRRASARLGLEENVQFLGFVPEEMVAKHYNRCDIFI 271
                                       4577788***********99987.***************************************************** PP

                                       EEESS...BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1  98 lpsis...EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                       lps+s   EgfG+v+lEA+a+g pvi++ + g+ae v+    Gl+v+pn++e la+ai++ll+++++++r+g ++r+
  gi|386001787|ref|YP_005920086.1| 272 LPSTSrsqEGFGMVALEALACGRPVICTRIVGVAEDVERVGAGLVVEPNDPEGLARAIARLLQSGPEARRMGAAGRR 348
                                       *****************************8888888888888*******************************9985 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 ?   -3.3   0.0       4.6   1.2e+04     114     130 ..      37      52 ..      21      68 .. 0.59
   2 !  111.0   0.0   2.1e-35   5.4e-32       3     133 ..     189     334 ..     187     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.6
                                       EE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4 114 llvppgdpealaeailr 130
                                       +l++ ++p++ ae+il+
  gi|386001787|ref|YP_005920086.1|  37 VLCA-NEPKSAAEEILQ 52 
                                       3333.345555555554 PP

  == domain 2  score: 111.0 bits;  conditional E-value: 2.1e-35
                                       EEEEES--.-G.G.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---.TH.HHHHH CS
                   Glyco_trans_1_4   3 vilfvGrl.ee.nvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv.ed.laell 70 
                                       ++ f++ l ++ ++kg+++ll a++ ++++  dv+l++ G+g+  + ++++  a  glee+v+f+Gfv e+ +a+++
  gi|386001787|ref|YP_005920086.1| 189 TLFFLSLLdRHhRYKGLEVLLSALAVVKEEvsDVQLLVGGGGElLD-HYRRASArlGLEENVQFLGFVpEEmVAKHY 264
                                       56677766533599**************88755*******999875.666433358************7447***** PP

                                       HH-SEEEE--.....---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  71 aaadvfvaPs.....egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       +++d+f++Ps     egfg+++lEa+a+g+pv++t++ g+ae v    +gl+v+p+dpe la+ai+rLl+
  gi|386001787|ref|YP_005920086.1| 265 NRCDIFILPStsrsqEGFGMVALEALACGRPVICTRIVGVAEDVerVGAGLVVEPNDPEGLARAIARLLQ 334
                                       ***********99888*********************9*99988542367******************98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.1     5e-24   1.3e-20       1     170 []      14     177 ..      14     177 .. 0.73
   2 ?   -2.6   0.0       1.8   4.7e+03     133     142 ..     266     275 ..     253     299 .. 0.54

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 5e-24
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                       vGGve++v+ L+ +L ++GheVtv++ + ++ ++ee   +v v+rvp   + +   +    + l  ++ re++D++H
  gi|386001787|ref|YP_005920086.1|  14 VGGVENYVRSLSGELVKLGHEVTVLCANEPKSAAEEILQGVKVRRVP---YVGKVANTNITPGLPIAILREEFDLLH 87 
                                       7***********************************54444444444...444444455556677778889****** PP

                    Glyco_transf_4  78 ahspaalga..allalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviav.Seatadelrer 151
                                       +h p ++ a  +++a+++ +++plVlt+ +       ++  + ++ ++   +r llr a r++ +  e+++  +++ 
  gi|386001787|ref|YP_005920086.1|  88 THLPTPWSAdvSGFAAAA-KRKPLVLTYYNEIV--GEGSAGRIARLYNGTGLRLLLRLAARITIIqPEYLKSPHLR- 160
                                       **9988876224444444.8************4..44444455555555556666776766666515556666666. PP

                    Glyco_transf_4 152 ygvppekitVipnGvDler 170
                                        g++ ek++Vip GvDl+r
  gi|386001787|ref|YP_005920086.1| 161 -GFE-EKVEVIPVGVDLAR 177
                                       .999.8**********987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                    Glyco_transf_4 133 radrviavSe 142
                                       r+d +i +S 
  gi|386001787|ref|YP_005920086.1| 266 RCDIFILPST 275
                                       4444444443 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0     1e-20   2.6e-17       1     160 []      15     172 ..      15     172 .. 0.87
   2 ?   -0.2   0.0      0.47   1.2e+03     102     105 ..     318     330 ..     259     363 .. 0.46

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1e-20
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG++ yv+ l+ +L+++GheVtvl+++++ +a e+   gv v+r+p   +   +a+   +++l  ++   re +d++
  gi|386001787|ref|YP_005920086.1|  15 GGVENYVRSLSGELVKLGHEVTVLCANEPKSAAEEILQGVKVRRVPYVGK---VANTNITPGLPIAI--LREEFDLL 86 
                                       8************************99988888766679*****998866...68999*****9999..9******* PP

                   Glyco_trans_4_4  78 hahspt...aglaarlarrrrgiplvvtlhglllrrg.sgavrrly.ralerrllrradavlvvseaeaeelralgv 149
                                       h+h pt   a   + +a+ +++ plv+t+++  + +g +g+ +rly  +  r+llr a++++ + ++  +  + +g+
  gi|386001787|ref|YP_005920086.1|  87 HTHLPTpwsADVSGFAAA-AKRKPLVLTYYNEIVGEGsAGRIARLYnGTGLRLLLRLAARITIIQPEYLKSPHLRGF 162
                                       ***988564556666666.99*********988777768888889966669************99999999888888 PP

                   Glyco_trans_4_4 150 padrvvvvpng 160
                                         ++v+v+p g
  gi|386001787|ref|YP_005920086.1| 163 E-EKVEVIPVG 172
                                       7.899999987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.47
                   Glyco_trans_4_4 102 tlh.........g 105
                                       ++          +
  gi|386001787|ref|YP_005920086.1| 318 EPNdpeglaraiA 330
                                       2222222211111 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 !   48.2   0.0   4.1e-16   1.1e-12       5      91 ..     275     364 ..     265     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.1e-16
                   Glyco_trans_1_2   5 psrs.espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervl 78 
                                       +srs e++ ++ +Ea+acG++++++++ g++e ++    ++++e  d+e la++i++ll++  e+r++++a+r+ ++
  gi|386001787|ref|YP_005920086.1| 275 TSRSqEGFGMVALEALACGRPVICTRIVGVAEDVERVGAGLVVEpnDPEGLARAIARLLQSGPEARRMGAAGRRLAE 351
                                       4455788********************888888888889999999******************************** PP

                   Glyco_trans_1_2  79 aehtydhraeqll 91 
                                       +++ +++ ae++ 
  gi|386001787|ref|YP_005920086.1| 352 ERYGWRKVAERFE 364
                                       **********985 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 !   26.8   0.0   1.6e-09   4.2e-06      12     106 ..      20     114 ..      14     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.6e-09
                   Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkgpleylkaf.klkklikkikPDvvhahyakpy 86 
                                       +++ l  eL k g+eV+v++ ++++   e++ +g++v r++    g++ + ++   l   i ++++D++h+h ++p 
  gi|386001787|ref|YP_005920086.1|  20 YVRSLSGELVKLGHEVTVLCANEPKsAAEEILQGVKVRRVP--YVGKVANTNITpGLPIAILREEFDLLHTHLPTPW 94 
                                       56778889*************99999999***********9..6667777777668844455678*******99887 PP

                   Glyco_trans_4_2  87 .gllgslaarlsgvipvvlsv 106
                                        + + ++aa  ++ +p+vl+ 
  gi|386001787|ref|YP_005920086.1|  95 sADVSGFAAAAKR-KPLVLTY 114
                                       5555667777777.9999875 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05     0.026       2      53 ..       3      53 ..       2     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                    Glyco_transf_5  2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry.gaikeekkel 53
                                      il+  + ++p   +GG+   v++L+ +L klgh+v+v+  +  ++  ee  + 
  gi|386001787|ref|YP_005920086.1|  3 ILHTPPRYPP--AVGGVENYVRSLSGELVKLGHEVTVLCANEpKSAAEEILQG 53
                                      5555555666..89************************999844444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2304.13
//
Query:       gi|386001788|ref|YP_005920087.1|  [L=412]
Description: GDP-mannose 4,6-dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-68  231.8   0.0    7.4e-33  114.3   0.0    3.0  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.8e-53  179.2   0.0    1.8e-52  178.2   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.5e-08   33.4   0.0    3.9e-08   32.8   0.0    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.2e-07   30.2   0.0    4.2e-07   29.2   0.0    1.4  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-07   30.1   0.0    8.2e-06   25.1   0.0    2.1  2  RmlD_sub_bind    RmlD substrate binding domain
    0.00028   20.2   0.0     0.0011   18.2   0.0    1.9  1  NAD_binding_4    Male sterility protein
    0.00058   19.4   0.0      0.018   14.5   0.0    2.2  2  adh_short        short chain dehydrogenase
     0.0026   17.7   0.0     0.0059   16.5   0.0    1.6  1  KR               KR domain
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.045   13.7   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
        0.2   11.2   0.0       0.32   10.5   0.0    1.3  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   4.8e-35   8.6e-32       1     137 [.       9     138 ..       9     154 .. 0.89
   2 !  114.3   0.0   4.1e-36   7.4e-33     136     331 ..     161     397 ..     149     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 4.8e-35
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TGi+Gf+Gs l ++L+++g ev+g+ rr +      + h  k++   + ++++l +gDl + ssl  +l   +pd
  gi|386001788|ref|YP_005920087.1|   9 LVTGISGFVGSKLGKRLVDEGAEVFGLLRRRADGI---LPHNLKRE--GVGPQVRLLEGDLAEISSLGAALTASDPD 80 
                                       9*****************************99965...55555443..5789************************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq 137
                                        v++LAAqs+V++sf +P +tae+n lGt++LLeair+ +++    f++a++sE YG v 
  gi|386001788|ref|YP_005920087.1|  81 LVFHLAAQSFVPRSFASPLETAEANCLGTANLLEAIRIKEVD--PVFVFAGSSEEYGLVI 138
                                       **************************************8875..68999********984 PP

  == domain 2  score: 114.3 bits;  conditional E-value: 4.1e-36
                                       -SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-E CS
                     GDP_Man_Dehyd 136 vqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevl 212
                                       v e p++Et+p++P sPYaa+K+y d++++ny ++ygl +v+++ fnhe+  rg  fvt  +t +v+   +g+ +++
  gi|386001788|ref|YP_005920087.1| 161 VPELPIKETNPLRPMSPYAASKVYGDFLTRNYCHSYGLKTVVSRAFNHEGAGRGGIFVTSVVTSQVMSLVMGEADKI 237
                                       56899************************************************************************ PP

                                       ECTTTT-EEEEEEHHHHHHHHHHHHHCSS---.EEE-TT-EEECHHCHHCCHHCCCHHHHHH............... CS
                     GDP_Man_Dehyd 213 ylGnldakRdwghvkDyveamwlmlqqdkped.yviatgethsvrefvelaflelgktiewegkgeeevg....... 281
                                       ++Gn +a Rdw hv+D+++++ l+  +++  d y+ ++ +t sv + + l+++++g  i+  ++   e++       
  gi|386001788|ref|YP_005920087.1| 238 RIGNVNAFRDWSHVDDVIDGYLLLADKGRFGDvYNQGSMRTNSVLSYLLLSLERAGYPIDGIETFRGEKAvaspteq 314
                                       ***************************99876367789999***************887765554444433367777 PP

                                       ......................................TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS- CS
                     GDP_Man_Dehyd 282 ..................................rakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvs 324
                                                                         + +   +v +e+dp++frp+ev  l+ +++k+   Lg+ ++ s
  gi|386001788|ref|YP_005920087.1| 315 dpseifgskfektkvdgmllrgevefgaedggvvALSGADRVPIEFDPERFRPAEVPILFSETAKIS-GLGFVARRS 390
                                       77777777777777777766666666655555433346778889999*******************8.899999999 PP

                                       HHHHHHH CS
                     GDP_Man_Dehyd 325 feelvre 331
                                       + +++++
  gi|386001788|ref|YP_005920087.1| 391 LGDIIED 397
                                       9998876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   0.0   9.9e-56   1.8e-52       1     239 [.       8     272 ..       8     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 9.9e-56
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..........EEEE--TT-HHHHHHHHHHHT-SE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..........elveldltdrsalerlfkeeqpda 67 
                                       +lVtG++Gf+Gs l k+l ++g ev gl r++ ++   +              +l e+dl + s+l +++   +pd 
  gi|386001788|ref|YP_005920087.1|   8 VLVTGISGFVGSKLGKRLVDEGAEVFGLLRRRADGILPH---NlkregvgpqvRLLEGDLAEISSLGAALTASDPDL 81 
                                       79*************************999955544333...23447899*************************** PP

                                       EEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGT....................... CS
                         Epimerase  68 vihlAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYG....................... 120
                                       v+hlAa++ v++s+ +p +++e+n+ gt nllea+r ++v+  ++f++Sse YG                       
  gi|386001788|ref|YP_005920087.1|  82 VFHLAAQSFVPRSFASPLETAEANCLGTANLLEAIRIKEVDpVFVFAGSSEEYGlvisseeqlqrardkygtvfpep 158
                                       ****************************************99********************************955 PP

                                       .SCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
                         Epimerase 121 .kdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkileg 196
                                        +++e p +et    pl+p spYaa+K++g+ l+++y ++ygl++++ r fn++G+++g  +v++v++  + ++  g
  gi|386001788|ref|YP_005920087.1| 159 aEVPELPIKETN---PLRPMSPYAASKVYGDFLTRNYCHSYGLKTVVSRAFNHEGAGRGGIFVTSVVTSQVMSLVMG 232
                                       444445677777...************************************************************** PP

                                       SSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEE CS
                         Epimerase 197 kqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyn 239
                                       + + + +g+ +a Rd+ +v+Dv++++ll++++ ++g   ++yn
  gi|386001788|ref|YP_005920087.1| 233 EADKIRIGNVNAFRDWSHVDDVIDGYLLLADKGRFG---DVYN 272
                                       *999999*************************6665...5566 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   2.2e-11   3.9e-08       1     123 [.       8     124 ..       8     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.2e-11
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG +G +Gs+l ++++++ ++   ll r    +   +  l++e    ++++    + gd+++ ++l  al++ +
  gi|386001788|ref|YP_005920087.1|   8 VLVTGISGFVGSKLGKRLVDEGAEVFGLLRRRADGILPHN--LKREGVGPQVRL----LEGDLAEISSLGAALTASD 78 
                                       89**********************9999999887775444..433444444543....47***************** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv 123
                                       +d+vfh AA   VP     ple+ + N lgt n++ea   ++v+ v
  gi|386001788|ref|YP_005920087.1|  79 PDLVFHLAAQSFVPRSFASPLETAEANCLGTANLLEAIRIKEVDPV 124
                                       *************************************999888765 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.4e-10   4.2e-07       1     122 [.       9     136 ..       9     176 .. 0.74
   2 ?   -3.6   0.0       2.4   4.3e+03     200     225 ..     233     258 ..     221     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.4e-10
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkev.....rvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvv 70 
                                       +vtG +GF+G++l k+Lv+++   ev     r +D    ++l+ e    +v+ ++egD+ + ++l +al  +  d+v
  gi|386001788|ref|YP_005920087.1|   9 LVTGISGFVGSKLGKRLVDEGA--EVfgllrRRADGILPHNLKREGVGPQVR-LLEGDLAEISSLGAALTASdpDLV 82 
                                       69******************96..5422233445555555555555555555.***************98663379* PP

                         3Beta_HSD  71 ihlaslvdvag.kltedeimkvnvkGTrnvleacvkagv.rvlvYtSsaevvgp 122
                                       +hla+ + v     +  e  ++n  GT n+lea + ++v +v+v+  s e  g 
  gi|386001788|ref|YP_005920087.1|  83 FHLAAQSFVPRsFASPLETAEANCLGTANLLEAIRIKEVdPVFVFAGSSEEYGL 136
                                       *****99997736677899********************558999988775554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.4
                         3Beta_HSD 200 glalfkigdeevlsdrvYvgNvawah 225
                                       +  +++ig+ +++ d+  v+ v + +
  gi|386001788|ref|YP_005920087.1| 233 EADKIRIGNVNAFRDWSHVDDVIDGY 258
                                       45678888899999998888887655 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   4.6e-09   8.2e-06       2      94 ..       7     121 ..       6     135 .. 0.93
   2 ?    2.9   0.0     0.027        49     112     142 ..     165     195 ..     152     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.6e-09
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHHH--SEEE CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellkeakpdvvv 56 
                                       ++lvtG +G +Gs+L k+l  eg+ev +l r+                      e dl++ +++ ++l + +pd+v 
  gi|386001788|ref|YP_005920087.1|   7 RVLVTGISGFVGSKLGKRLVDEGAEVFGLLRRradgilphnlkregvgpqvrllEGDLAEISSLGAALTASDPDLVF 83 
                                       79***************************77779******************************************* PP

                                       E------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT- CS
                     RmlD_sub_bind  57 naAAytavDkaEseeeaayavnaeavealAeaaaavga 94 
                                       ++AA   v +    + + +++n  ++++l ea +  ++
  gi|386001788|ref|YP_005920087.1|  84 HLAAQSFVPRSFASPLETAEANCLGTANLLEAIRIKEV 121
                                       ****************************9988765554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.027
                                       -B-TTS----SSHHHHHHHHHHHHHHHH-SS CS
                     RmlD_sub_bind 112 pYeeddetsPlnvYGrtKlaGEqavlaagkk 142
                                       p +e+++  P++ Y+++K+ G    +++++ 
  gi|386001788|ref|YP_005920087.1| 165 PIKETNPLRPMSPYAASKVYGDFLTRNYCHS 195
                                       6899*****************9999987764 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.1e-07    0.0011       1     208 [.      10     210 ..      10     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.1e-07
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG +GF+G+ L ++L+++ +  +++ l+R + +    + l    ++ ++          +++ +eGDl+e    +s
  gi|386001788|ref|YP_005920087.1|  10 VTGISGFVGSKLGKRLVDEGA--EVFGLLRRRADGILPHNL----KREGV--------GPQVRLLEGDLAE----IS 68 
                                       7******************98..899999988553333333....33333........67789******98....56 PP

                                       HHHHHHHHHH--EEEE--SS-....S.STTSSEEHHHHHHHHHHHHHHHTSSS--..-EEEEEE..GGGTTS-TTT- CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtv....nfdepykellrvNveGtrevlelakklkkl.kvllhvST..ayvngeregev 147
                                       +  +   a+  d+++h aA+     +f +p++   ++N +Gt ++le  + +k+   v+++  +   y    +++e 
  gi|386001788|ref|YP_005920087.1|  69 SLGAALTASDPDLVFHLAAQSfvprSFASPLE-TAEANCLGTANLLEAIR-IKEVdPVFVFAGSseEYGLVISSEE- 142
                                       6667788999*********9722224444554.5689**********877.5444235555544363333222222. PP

                                       -SSS-H...............HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 148 eekvyeege.........keekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                         ++ ++ +          e+ +   ++++       Y  sK+ ++ l r++ ++ gl++v+ R  +  g
  gi|386001788|ref|YP_005920087.1| 143 --QLQRARDkygtvfpepAEVPELPIKETNPLRPMSPYAASKVYGDFLTRNYCHSYGLKTVVSRAFNHEG 210
                                       ..2222222444677855556666666666666677*************************999755555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   9.8e-06     0.018       1      68 [.       6      74 ..       6      79 .. 0.85
   2 ?    2.5   0.0      0.05        89     142     170 ..     171     199 ..     167     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-06
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealv 68
                                      k vlvtG s+ +G ++ k+l+ eGa+v+ + r+ ++   +  +lk+e  g ++  +++D+++ +++ a++
  gi|386001788|ref|YP_005920087.1|  6 KRVLVTGISGFVGSKLGKRLVDEGAEVFGLLRRRADG-ILPHNLKREgvGPQVRLLEGDLAEISSLGAAL 74
                                      679*************************955555555.48889999989999*******99988877665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.05
                                       B-TTBHHHHHHHHHHHHHHHHHHHHHGGG CS
                         adh_short 142 pvagvaaYsAsKaavagltrslakelapt 170
                                       p+  +++Y+AsK   + ltr+  + +  +
  gi|386001788|ref|YP_005920087.1| 171 PLRPMSPYAASKVYGDFLTRNYCHSYGLK 199
                                       666789*************9999888765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.3e-06    0.0059       3     138 ..       8     131 ..       7     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-..EEEE----TT-HHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga..evevvaaDvsdkdavealleeika 77 
                                       +l+tG  G +G +l + l+++ga+   ll R+a  d     l ++l++ g+  +v++++ D+++ +++ a+l++ + 
  gi|386001788|ref|YP_005920087.1|   8 VLVTGISGFVGSKLGKRLVDEGAEVFGLLRRRA--DGI---LPHNLKREGVgpQVRLLEGDLAEISSLGAALTASDP 79 
                                       69******************************2..333...556777776666*******************99996 PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHH CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSia 138
                                       +      v+h A     + +   + ++  +  ++ + G+ nL e+++ +++d + +f+  +
  gi|386001788|ref|YP_005920087.1|  80 DL-----VFHLAA----QSFVPRSFASPLETAEANCLGTANLLEAIRIKEVDPVFVFAGSS 131
                                       66.....999885....56666777777778889999999999999999999766665444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.045       2      90 ..      13     121 ..      12     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                                       TTSHHHHHHHHHHHHC-T-EEEEEETT......HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S.EEEES---T CS
                    NAD_binding_10   2 AtGkvGrllvkellargghevtalvRn......peklaeleaeeglevvegdvtdvedlaealkgad.aVvsalggg 71 
                                        +G vG++l k+l+++g  ev  l R+      p+ l++    ++++++egd+ + ++l +al+  d   v+ l+++
  gi|386001788|ref|YP_005920087.1|  13 ISGFVGSKLGKRLVDEG-AEVFGLLRRradgilPHNLKREGVGPQVRLLEGDLAEISSLGAALTASDpDLVFHLAAQ 88 
                                       58**************5.999888877444444444443334499******************98885355555444 PP

                                       CC........HHHH........HHHHHHHHHHCT- CS
                    NAD_binding_10  72 gk........deeg........aknivdaakeagv 90 
                                       +                     ++n+++a + ++v
  gi|386001788|ref|YP_005920087.1|  89 SFvprsfaspL--EtaeanclgTANLLEAIRIKEV 121
                                       43233333332..0335567778888888776666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00018      0.32       1      66 [.       8      78 ..       8      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.-SHHHHHHHHSTT....EEEES-TT-HHHHHHHHTT-S CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt.kselakslkeaGv....elvkgdlddkeslvealkgvd 66
                                      +lv+G +G  G+ + + l+++g +v+ l+R   ++ l ++lk +Gv     l++gdl + +sl +al  +d
  gi|386001788|ref|YP_005920087.1|  8 VLVTGISGFVGSKLGKRLVDEGAEVFGLLRRRaDGILPHNLKREGVgpqvRLLEGDLAEISSLGAALTASD 78
                                      79**************************998868888899****964443799************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 3108.16
//
Query:       gi|386001789|ref|YP_005920088.1|  [L=185]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-68  230.0   0.0    1.4e-68  229.8   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.8   0.0   7.8e-73   1.4e-68       2     168 ..       8     176 ..       7     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 229.8 bits;  conditional E-value: 7.8e-73
                                       -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEE CS
                   dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevld 78 
                                       + ++gvlli+p++f+D+RG+fle++++e++a+ag+e efvqdn+s+s+ gvlRG+Hfq+ep aqak+v++vrG v+d
  gi|386001789|ref|YP_005920088.1|   8 LGLPGVLLIKPRIFRDDRGYFLETYKKEDLARAGIEGEFVQDNCSRSAYGVLRGMHFQREPCAQAKIVQCVRGVVYD 84 
                                       5799************************************************************************* PP

                                       EEEE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..S CS
                   dTDP_sugar_isom  79 vaVDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..e 153
                                       vaVDlR+gSptfg + ++ Ls+ n+rqly+p+g+ahGflvlsd  ev+Ykv++ y+pe+e+g+ w+Dp++++ w  +
  gi|386001789|ref|YP_005920088.1|  85 VAVDLRRGSPTFGAYAACILSEGNRRQLYVPRGLAHGFLVLSDVGEVMYKVDSPYSPECEGGLIWDDPDVDVPWpvD 161
                                       ****************************************************************************9 PP

                                       S.B--HHHHT-B-HH CS
                   dTDP_sugar_isom 154 elilSekDkaapsla 168
                                       ++il+e+D+++p l+
  gi|386001789|ref|YP_005920088.1| 162 DPILAERDRRWPDLK 176
                                       9***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 1496.08
//
Query:       gi|386001790|ref|YP_005920089.1|  [L=366]
Description: Glucose-1-phosphate thymidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-53  179.8   0.0      8e-53  179.6   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.6e-08   35.1   0.0    2.4e-08   34.5   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    9.4e-06   25.2   8.2      0.021   14.5   1.8    4.4  4  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00011   21.3   0.0    0.00015   20.8   0.0    1.2  1  Fucokinase       L-fucokinase
     0.0025   17.8   0.0     0.0038   17.2   0.0    1.2  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.074   11.2   1.6       0.28    9.3   1.6    1.7  1  DUF4954          Domain of unknown function (DUF4954)
       0.08   12.7   0.7       0.08   12.7   0.7    4.4  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
       0.29   10.2   0.1       0.48    9.4   0.1    1.3  1  DUF3516          Domain of unknown function (DUF3516)


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 !  179.6   0.0   3.6e-56     8e-53       1     246 [.      17     249 ..      17     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 3.6e-56
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       ka+IL+GG+GtRL+P+t++++k+l+p+++k +++ + ++ ++++g ee+ ++    +++ v e +++++ +g ev++
  gi|386001790|ref|YP_005920089.1|  17 KALILSGGRGTRLRPITHSQQKQLIPIANK-PVLFYAIEDVIEAGAEEVGII-VGPNKEQVIETVRSKA-WGAEVEF 90 
                                       799***************************.*****************5555.5566677777777765.999**** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++ e+kg+A+ +++a+e+l+d++    +++Lg++++ +  + +  +k++e++   + ++++++ve+++++Gv+  d
  gi|386001790|ref|YP_005920089.1|  91 IFQGEPKGLAHTILVAEEFLGDDDF---IMYLGDNVIKG-GILKHSEKFRESGP--DSLVLLTEVEDPQRFGVADLD 161
                                       ************************6...88888776555.88888899999999..89999**************** PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       eegrv+r+vEKPk ++ s++a  GiY+f +++++   k +++++r e eitd+++ +l++g++  a + +++  W+D
  gi|386001790|ref|YP_005920089.1| 162 EEGRVRRLVEKPKVPP-SNYALVGIYFFRPSIVEAC-KRIKPSWRNELEITDAIQWLLDSGRRVEASIVDGW--WKD 234
                                       ****************.*****************99.88********************************6..*** PP

                                       XSSHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekla 246
                                       +G+ +++lean+ ++
  gi|386001790|ref|YP_005920089.1| 235 TGKAEDILEANRLIL 249
                                       ***********9776 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 !   34.5   0.0     1e-11   2.4e-08       1      97 [.      18     123 ..      18     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1e-11
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC....TS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl....gvrvvede 66 
                                       a+iL GGr++R+      + K+l+p+++kp+l ++++ + +ag++ev +++g+  e+v + ++++    +v+++ + 
  gi|386001790|ref|YP_005920089.1|  18 ALILSGGRGTRLRpithsQQKQLIPIANKPVLFYAIEDVIEAGAEEVGIIVGPnkEQVIETVRSKawgaEVEFIFQG 94 
                                       79**********6554436****************************999877555555555444333379999997 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-T CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmP 97 
                                       +  kg +++++ a + + ++d +++ ++D +
  gi|386001790|ref|YP_005920089.1|  95 E-PKGLAHTILVAEEFL-GDDDFIMYLGDNV 123
                                       5.59**********999.8888888888875 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.8   9.4e-06     0.021       2      29 ..     269     295 ..     268     301 .. 0.92
   2 !   13.7   0.2   1.7e-05     0.039       2      30 ..     286     313 ..     285     314 .. 0.91
   3 !    7.7   0.1    0.0013       2.9       9      22 ..     298     311 ..     295     329 .. 0.53
   4 ?    3.2   0.0     0.034        77      10      17 ..     338     345 ..     335     347 .. 0.43

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.4e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29 
                                       +v+G++++I  ++ i g++++G n+ I 
  gi|386001790|ref|YP_005920089.1| 269 AVVGKGCVIE-NSEIKGPCILGANCAIR 295
                                       79********.**************995 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.7e-05
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +++G n+ I+  ++ig+ + I d+++I+ 
  gi|386001790|ref|YP_005920089.1| 286 CILGANCAIR-DSYIGPYTSINDGCTIEG 313
                                       78999*****.**************9985 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0013
                                       EE-TTEEEETTEEE CS
                           Hexapep   9 lIgpfaviggnVkI 22 
                                       +Igp++ i ++++I
  gi|386001790|ref|YP_005920089.1| 298 YIGPYTSINDGCTI 311
                                       45555555555554 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.034
                                       E-TTEEEE CS
                           Hexapep  10 Igpfavig 17 
                                       Ig+++vi+
  gi|386001790|ref|YP_005920089.1| 338 IGKNVVIR 345
                                       44444443 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   6.7e-08   0.00015     270     337 ..     247     318 ..     213     345 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.7e-08
                        Fucokinase 270 k.......kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlslkl 337
                                               k+++v  +S + +++ vg+g+vie+s++kg++  g+n+ + + ++   ++   + d + + ++++++
  gi|386001790|ref|YP_005920089.1| 247 LildemrpKNEGVLRSSRIFGRAVVGKGCVIENSEIKGPCILGANCAIRDSYIGPYTS---INDGCTIEGTEVED 318
                                       145555568899999999*********************************9999877...55555555555544 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.7e-06    0.0038      15      92 ..      37     115 ..      34     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                                       TGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHHHHHHHTTT. CS
                      CTP_transf_3  15 gKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakefg..asvlvtrsslesdterflevvkaflmse 88 
                                       +K l+++++kp ++y +e +++++a e  +iv   +e++ +++ +    a+v ++ + ++++++ +  v ++fl + 
  gi|386001790|ref|YP_005920089.1|  37 QKQLIPIANKPVLFYAIEDVIEAGAEEVgIIVGPNKEQVIETVRSKAwgAEVEFIFQGEPKGLAHTILVAEEFLGD- 112
                                       79***********************8889**********9999665555************************999. PP

                                       TTSE CS
                      CTP_transf_3  89 neei 92 
                                        ++ 
  gi|386001790|ref|YP_005920089.1| 113 -DDF 115
                                       .333 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.6   0.00013      0.28     176     255 ..     271     345 ..     255     351 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
                           DUF4954 176 igekvkilnaglikNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqav 252
                                       +g+ ++i+n+++     +g+ + i+ +     ++in       +i eg ++ed++i++G++i+ +  i+++++G++v
  gi|386001790|ref|YP_005920089.1| 271 VGKGCVIENSEIKGPCILGANCAIRDSYIGPYTSIND----GCTI-EGTEVEDSVIMEGCTISRAGRIVESLIGKNV 342
                                       4444444444444444444444444444333333332....2222.4445567777777777777777777777777 PP

                           DUF4954 253 klk 255
                                        + 
  gi|386001790|ref|YP_005920089.1| 343 VIR 345
                                       665 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       0.6   1.3e+03      12      22 ..      59      70 ..      57      71 .. 0.73
   2 ?   -2.8   0.1       2.5   5.6e+03      20      25 ..     119     124 ..     119     124 .. 0.77
   3 ?    2.4   0.1     0.061   1.4e+02      20      28 ..     271     279 ..     262     279 .. 0.80
   4 ?   12.7   0.7   3.6e-05      0.08       8      27 ..     286     312 ..     285     313 .. 0.86
   5 ?    0.4   0.0      0.26   5.8e+02      10      16 ..     338     344 ..     335     348 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.6
                                      TT-E.ESEEE-T CS
                         Hexapep_2 12 anag.iGvslGd 22
                                      a a+ +G+++G 
  gi|386001790|ref|YP_005920089.1| 59 AGAEeVGIIVGP 70
                                      456657999995 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                       E-TT-E CS
                         Hexapep_2  20 lGdncv 25 
                                       lGdn++
  gi|386001790|ref|YP_005920089.1| 119 LGDNVI 124
                                       789986 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.061
                                       E-TT-EE-T CS
                         Hexapep_2  20 lGdncvvga 28 
                                       +G++cv+++
  gi|386001790|ref|YP_005920089.1| 271 VGKGCVIEN 279
                                       788888886 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 3.6e-05
                                       -EE-TT-EE.....S..EEE-TT-EE- CS
                         Hexapep_2   8 CliGanagi.....G..vslGdncvvg 27 
                                       C++Gan+ i     G  +s+ d+c+++
  gi|386001790|ref|YP_005920089.1| 286 CILGANCAIrdsyiGpyTSINDGCTIE 312
                                       9*****9866666689*********97 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.26
                                       E-TT-EE CS
                         Hexapep_2  10 iGanagi 16 
                                       iG+n +i
  gi|386001790|ref|YP_005920089.1| 338 IGKNVVI 344
                                       4444433 PP

>> DUF3516  Domain of unknown function (DUF3516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00021      0.48     287     347 ..     201     266 ..     192     273 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00021
                           DUF3516 287 peearteeledliewLgelvrqvDsSLldeWealadpaaeeeeeaa.....eeeaaeavtaneraf 347
                                       p+  ++ e++d i+wL    r+v++S++d W + + +a++  e++       ++++e v + +r f
  gi|386001790|ref|YP_005920089.1| 201 PSWRNELEITDAIQWLLDSGRRVEASIVDGWWKDTGKAEDILEANRlildeMRPKNEGVLRSSRIF 266
                                       555566799*********************988776655554444445533333334455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 2230.75
//
Query:       gi|386001791|ref|YP_005920090.1|  [L=332]
Description: dTDP-glucose 4,6-dehydratase [Methanosaeta harundinacea 6Ac]
Scores for 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-82  275.3   0.0    9.6e-82  275.0   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.2e-61  205.5   0.0      1e-60  205.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.9e-17   63.3   0.0    2.2e-17   63.1   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      1e-15   57.5   0.0    1.3e-15   57.1   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.5e-13   48.7   0.0    2.5e-12   46.5   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    7.3e-13   48.3   0.0    3.7e-11   42.7   0.0    2.6  1  NAD_binding_4    Male sterility protein
    2.2e-06   27.7   0.0    3.5e-06   27.0   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    2.3e-05   23.9   0.8      0.002   17.6   0.4    2.8  2  adh_short        short chain dehydrogenase
     0.0043   17.3   0.0     0.0075   16.5   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.021   14.4   0.0    1.2  1  NmrA             NmrA-like family
       0.11   12.4   0.0        0.2   11.5   0.0    1.4  1  KR               KR domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.0   0.0   5.9e-85   9.6e-82       1     332 []       4     303 ..       4     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 275.0 bits;  conditional E-value: 5.9e-85
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+ GfiGs+++++ le+++e   iv+ +++ + ++ e+l+  +    ee++++++gD++D+  + +l++++  d
  gi|386001791|ref|YP_005920090.1|   4 LVTGGMGFIGSNFIRHYLERHQEA-RIVNVDALKAGSNPESLRGID----EERYTFVEGDISDRLLMADLVEKA--D 73 
                                       9*******************8887.68999999999999*999754....579*******************99..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v+n+AA+ hVd+s++ Pe ++  nv Gt+ +Lea r+ +  + +r++++St+EvYG+v +  ++Et  ++P sPY+
  gi|386001791|ref|YP_005920090.1|  74 AVVNFAAETHVDRSISGPEPFLASNVAGTFSILEALRTRN--PGARLVHISTDEVYGDVLSGSFRETDALRPSSPYS 148
                                       *************************************975..79********************************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+K+++d +v +y ++ygl a+++++ n+++pr+   f++++i++a+ r++  + +v+++G ++++Rdw +v D+++
  gi|386001791|ref|YP_005920090.1| 149 ASKAASDVFVSAYARTYGLSAMITRCTNNYGPRQ---FPEKLIPKAIIRANTSL-KVPIYGTGENVRDWIFVLDHCR 221
                                       *********************************6...************99987.8999****************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a+ ++l++++        ge+++v +  e+++l++++ +                gk +  ++++ +rpg++ ++  
  gi|386001791|ref|YP_005920090.1| 222 AVEMVLEAGE-------AGEVYNVSSGEERTNLAVVRALLEI------------LGKGEEAIEFVEDRPGHDLRYSL 279
                                       *********9.......6*****************9976543............24455678999************ PP

                                       -THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvrem 332
                                       d sk+++eLgW+p ++f+e+++e+
  gi|386001791|ref|YP_005920090.1| 280 DSSKIRRELGWRPDWGFREGMEET 303
                                       *********************986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   0.0   6.1e-64     1e-60       2     240 ..       4     238 ..       3     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 6.1e-64
                                       EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihl 71 
                                       lVtG+ GfiGs+++++ le++   +++++d l+ +sn ++l+ +     ++ve+d+ dr  +++l++  ++dav+++
  gi|386001791|ref|YP_005920090.1|   4 LVTGGMGFIGSNFIRHYLERHqeARIVNVDALKAGSNPESLRGIdeeryTFVEGDISDRLLMADLVE--KADAVVNF 78 
                                       9**************9999995555***************9999***********************..9******* PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHH CS
                         Epimerase  72 Aavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpnspYaaaKl 147
                                       Aa+ +v++s++ p+ f+ +n++gt  +lea+r++++  rl+++s++evYG++ +    et     l+p+spY+a+K+
  gi|386001791|ref|YP_005920090.1|  79 AAETHVDRSISGPEPFLASNVAGTFSILEALRTRNPGaRLVHISTDEVYGDVLSGSFRETD---ALRPSSPYSASKA 152
                                       **********************************8888***************95455555...89*********** PP

                                       HHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHH CS
                         Epimerase 148 ageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaill 224
                                       a++  v aya++ygl+a+i+r++n+yGpr   ++++++ip++i ++++   +v ++g+g+++Rd+++v D+++a+ +
  gi|386001791|ref|YP_005920090.1| 153 ASDVFVSAYARTYGLSAMITRCTNNYGPR---QFPEKLIPKAIIRANTSL-KVPIYGTGENVRDWIFVLDHCRAVEM 225
                                       *****************************...9*****************.************************** PP

                                       HHHHHTT-STTEEEEE CS
                         Epimerase 225 vlehvdagdkgeiyni 240
                                       vle+   g++ge+yn+
  gi|386001791|ref|YP_005920090.1| 226 VLEA---GEAGEVYNV 238
                                       ****...99999***8 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 !   63.1   0.0   1.3e-20   2.2e-17       1     167 [.       1     191 [.       1     304 [. 0.85

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.3e-20
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHHH--SEE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellkeakpdvv 55 
                                       m++lvtG+ G +Gs+ ++   e++ e+  ++ +                      e d++d+  +a+l+++   d+v
  gi|386001791|ref|YP_005920090.1|   1 MRLLVTGGMGFIGSNFIRHYLERHQEARIVNVDalkagsnpeslrgideerytfvEGDISDRLLMADLVEK--ADAV 75 
                                       89***************999998877777766677899*******************************98..789* PP

                                       EE------HHHHHHSHHHHHHHHTHHHHHHHHH..HHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHH CS
                     RmlD_sub_bind  56 vnaAAytavDkaEseeeaayavnaeavealAea..aaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKl 130
                                       vn AA t vD+  s +e   a n+ ++  + ea  +++ ga L+h+StD V+    +  ++e+d+  P + Y ++K+
  gi|386001791|ref|YP_005920090.1|  76 VNFAAETHVDRSISGPEPFLASNVAGTFSILEAlrTRNPGARLVHISTDEVYGDVLSGSFRETDALRPSSPYSASKA 152
                                       **************************99997762267779************9999999****************** PP

                                       HHHHHHHH....H-SSEEEEEE-SEESSSSS-HHHHHHHHH CS
                     RmlD_sub_bind 131 aGEqavla....agkkalivRtswvygekgknfvktmlrla 167
                                       a    v a    +g  a+i R +  yg   ++f ++++ +a
  gi|386001791|ref|YP_005920090.1| 153 ASDVFVSAyartYGLSAMITRCTNNYGP--RQFPEKLIPKA 191
                                       ******9955556667899998888876..55665555555 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 !   57.1   0.0   8.3e-19   1.3e-15       1     218 [.       4     216 ..       4     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 8.3e-19
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlas 75 
                                       +vtGg+GF+G++ +++ +++++   +  +D  +  +  e+l+ ++ +   ++egD+ d   + + +e++d+v+  a+
  gi|386001791|ref|YP_005920090.1|   4 LVTGGMGFIGSNFIRHYLERHQEARIVNVDALKAGSNPESLRGIDEERytFVEGDISDRLLMADLVEKADAVVNFAA 80 
                                       69*****************99755555555444445557777766665779************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkag.vrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesK 150
                                        + v       + +   nv GT ++lea ++ +   +lv+ S+ ev g+      +l g  +++    ++++y+ sK
  gi|386001791|ref|YP_005920090.1|  81 ETHVDRsISGPEPFLASNVAGTFSILEALRTRNpGARLVHISTDEVYGD------VLSGSFRETDALRPSSPYSASK 151
                                       ****9835568889**************987652579***********9......66677777788899******** PP

                         3Beta_HSD 151 alaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYv 218
                                       a ++ +v +       +   l     R +  yG+++  ++l p +   a++ l++  +g  e++ d+++v
  gi|386001791|ref|YP_005920090.1| 152 AASDVFVSAYAR--TYG---LSAMITRCTNNYGPRQfpEKLIPKAIIRANTSLKVPIYGTGENVRDWIFV 216
                                       998877765444..333...55555599999***97546677777777788889**************98 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.6e-15   2.5e-12       1     270 [.       3     275 ..       3     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.6e-15
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG+ G iGs+++r+ l+++ ++ ++++ d lk  +  ++l + ++++++++    v gd+ d+  +++++e  k
  gi|386001791|ref|YP_005920090.1|   3 LLVTGGMGFIGSNFIRHYLERH-QEARIVNVDALKAGSNPESL-RGIDEERYTF----VEGDISDRLLMADLVE--K 71 
                                       59*****************985.45677788888888877777.4666666633....58**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT.-SEEEEEEEGG..............GSS--SHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieag.vkkvvliStDK..............AvnPtnvmG 139
                                        d+v++ AA  hV    + p   +  Nv gt +++ea  + +   ++v iStD               A +P + + 
  gi|386001791|ref|YP_005920090.1|  72 ADAVVNFAAETHVDRSISGPEPFLASNVAGTFSILEALRTRNpGARLVHISTDEvygdvlsgsfretdALRPSSPYS 148
                                       ************************************9876652689*******64444444445555589******* PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGTT...SSHHHHHHHHHTTSSEEE..S-TT-EEEEE-HHHHHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlgSrG...SviplFkkqikeggpvtv..TdpemtRyfmtieeavq 211
                                       a+K++++ ++ a+a++        +++R  N  g r     +ip+   + ++  +v++  T ++ +R ++ + + ++
  gi|386001791|ref|YP_005920090.1| 149 ASKAASDVFVSAYARTY---GLSAMITRCTNNYGPRQfpeKLIPKAIIRANTSLKVPIygTGEN-VRDWIFVLDHCR 221
                                       **************999...78999999999999996333799987777777777787545555.566777777777 PP

                                       HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT--S CS
                   Polysacc_synt_2 212 LvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpGEkl 270
                                        v + l+ ++ ge++ +  Ge  + + +++al+e+ g+     ++ +i+++  RpG  l
  gi|386001791|ref|YP_005920090.1| 222 AVEMVLEAGEAGEVYNVSSGEERTNLAVVRALLEILGK-----GEEAIEFVEDRPGHDL 275
                                       77777788899*************************94.....5667999999999766 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   2.2e-14   3.7e-11       1     205 [.       5     176 ..       5     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.2e-14
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G+ +++  L++++e +i+ +              ++l+  + ++ l+   +er ++veGD+s+  l   
  gi|386001791|ref|YP_005920090.1|   5 VTGGMGFIGSNFIRHYLERHQEARIVNV--------------DALKAGSNPESLRGIDEERYTFVEGDISDRLL--- 64 
                                       79***************99998554432..............22222233333322347899********9875... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                          + +l+e+ d++++ aA +++d++++    +l+ Nv Gt  +le  ++++    l+h+ST  v+g+  +      
  gi|386001791|ref|YP_005920090.1|  65 ---MADLVEKADAVVNFAAETHVDRSISGpepFLASNVAGTFSILEALRTRNPGARLVHISTDEVYGDVLSG----- 133
                                       ...899*******************99866669****************999999*******7777666643..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                                  +  +++    +  Y+ sKa+++  v +++r  gl ++i R+++
  gi|386001791|ref|YP_005920090.1| 134 -----------SFRETDALRPSSPYSASKAASDVFVSAYARTYGLSAMITRCTN 176
                                       ...........3455666677889***************************986 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.2e-09   3.5e-06       1     131 [.       7     158 ..       7     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.2e-09
                                       TTTSHHHHHHHHHHHHC-....T-EEEEE..ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---T CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg....ghevtal..vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggg 71 
                                       G+ G +G+  +++ l+r+     ++v al    npe+l  + +ee+ + vegd++d   +a+ ++ adaVv  ++ +
  gi|386001791|ref|YP_005920090.1|   7 GGMGFIGSNFIRHYLERHqearIVNVDALkaGSNPESLRGI-DEERYTFVEGDISDRLLMADLVEKADAVVNFAAET 82 
                                       899**************755544555555323568888876.68*************************99988777 PP

                                       CCHHHH.............HHHHHHHHHHCT.--EEEEEEETTTTSGC.GCHHHHHHH.HCCHHHHHHHHHHHHHH CS
                    NAD_binding_10  72 gkdeeg.............aknivdaakeag.vkRfvlvsaigvgdev.pgefgewnk.ellkaylaakraaeell 131
                                       + d+ +             + +i++a+++ +   R+v +s+  v+ +v  g+f e++  +  ++y a k+a++  +
  gi|386001791|ref|YP_005920090.1|  83 HVDRSIsgpepflasnvagTFSILEALRTRNpGARLVHISTDEVYGDVlSGSFRETDAlRPSSPYSASKAASDVFV 158
                                       7765556777777777788999*****9987579********9986651556665544233455556666666555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   1.2e-06     0.002       4     167 ..       4     165 ..       2     174 .. 0.80
   2 ?   -0.7   0.0       0.5   8.2e+02     116     142 ..     220     246 ..     216     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                       EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkld 79 
                                       lvtG+++ IG ++ ++++++  +  +v+  + k+    ++l+   +++++++++D++dr  + +lveka       d
  gi|386001791|ref|YP_005920090.1|   4 LVTGGMGFIGSNFIRHYLERHQEARIVNVDALKAGSNPESLRGIdEERYTFVEGDISDRLLMADLVEKA-------D 73 
                                       8*******************9999999999999999*******9999**********************.......9 PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEE...........EGGGTSB-TT CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvs...........Svagkvpvag 145
                                       ++vn A+ t      + s +  e  ++ N+ g+f++ +a+ +    + ++r v +s           S     ++  
  gi|386001791|ref|YP_005920090.1|  74 AVVNFAAET----HVDRSISGPEPFLASNVAGTFSILEALRTR---NPGARLVHIStdevygdvlsgSFRETDALRP 143
                                       999999983....344455667888999999999998885544...6666666665222222222114555566777 PP

                                       BHHHHHHHHHHHHHHHHHHHHH CS
                         adh_short 146 vaaYsAsKaavagltrslakel 167
                                        ++YsAsKaa + ++++ a+ +
  gi|386001791|ref|YP_005920090.1| 144 SSPYSASKAASDVFVSAYARTY 165
                                       8999999999999999998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHCTTEEEEEEEEGGGTSB CS
                         adh_short 116 travlpamlkqssGrIvnvsSvagkvp 142
                                       +rav   + ++++G++ nvsS   +  
  gi|386001791|ref|YP_005920090.1| 220 CRAVEMVLEAGEAGEVYNVSSGEERTN 246
                                       55665666689**********876655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.6e-06    0.0075       3      80 ..       5      82 ..       3      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                                      EE--.SHHHHHHHH.HHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavae.llarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkegdlvvnl 76
                                      + G+ G++G+ +++ +l+rh++   +i+ +d  k++     +++    ++r ++++ d++++   +a l++++d+vvn 
  gi|386001791|ref|YP_005920090.1|  5 VTGGmGFIGSNFIRhYLERHQEA--RIVNVDALKAG--SNPESLrgiDEERYTFVEGDISDRLL-MADLVEKADAVVNF 78
                                      55666****98886155566555..99999999998..6666665579999999999****998.*************9 PP

                                      SSGG CS
                   Sacchrp_dh_NADP 77 sppi 80
                                      +  +
  gi|386001791|ref|YP_005920090.1| 79 AAET 82
                                      8665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05     0.021       2      72 ..       4      79 ..       3      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE-- CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvt 72
                                      lv+G+ G +G+ ++r+ l++  + r++  d      + e ++ + e+  ++v+gd+ d+ +++ +++++d+v    
  gi|386001791|ref|YP_005920090.1|  4 LVTGGMGFIGSNFIRHYLERHQEARIVNVDAlkagsNPESLRGIDEERYTFVEGDISDRLLMADLVEKADAVVNFA 79
                                      8******************888888888887787779999999***************************997554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012       0.2       4      76 ..       4      73 ..       2      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                      EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                                KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                      l+tGG+G +G  ++r+ +e++ ++++v +     +  ++ + ++ + +   + ++v+ D+sd+  ++ l+e+++
  gi|386001791|ref|YP_005920090.1|  4 LVTGGMGFIGSNFIRHYLERHqEARIVNVDAL--KAGSNPESLRGIDE--ERYTFVEGDISDRLLMADLVEKAD 73
                                      9***************9998856666666555..23333335555555..466788999999999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2046.00
//
Query:       gi|386001792|ref|YP_005920091.1|  [L=312]
Description: dTDP-4-dehydrorhamnose reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-68  229.3   0.0    6.2e-68  229.0   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    6.5e-23   81.4   0.0    1.2e-22   80.5   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.8e-18   67.1   0.1    1.1e-16   61.1   0.1    3.0  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.8e-12   47.0   1.1    2.6e-11   43.2   0.0    2.4  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.3e-09   35.6   0.1    1.7e-07   30.7   0.0    2.6  2  NAD_binding_4    Male sterility protein
      1e-08   34.5   0.0    1.8e-08   33.7   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
      0.049   13.5   0.0        1.7    8.5   0.0    2.3  2  KR               KR domain
        0.1   12.4   0.0        1.2    8.9   0.0    2.4  3  DFP              DNA / pantothenate metabolism flavoprotein
       0.15   11.6   0.1       0.25   10.8   0.1    1.3  1  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.0   0.0   3.1e-71   6.2e-68       1     282 [.       3     285 ..       3     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.0 bits;  conditional E-value: 3.1e-71
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE.-TT........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlal.tre........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       m++l+tG++G+lGs La+ + +eg++v +   r+        +ldl + ++v++ ++e+ p+v+ ++AA t+vD++E
  gi|386001792|ref|YP_005920091.1|   3 MRLLITGGSGLLGSSLAEVAVAEGHQVFSGyCRHspefgvavKLDLLEGAEVERSISEVAPQVIFHTAALTDVDRCE 79 
                                       89************************9987445589***************************************** PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEE CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkali 145
                                       +++++a + n+ ++e++A+aaa+vga+L++vStDyVFdGe  + Y+e+d+t+P+n Y+rtKl  E          l+
  gi|386001792|ref|YP_005920091.1|  80 DDPDLAWRTNVLGTERVARAAAEVGAHLVYVSTDYVFDGEGGM-YREEDRTDPVNCYARTKLSAEGFCD------LV 149
                                       ****************************************665.*******************998877......9* PP

                                       EEE-SEESS....SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-E CS
                     RmlD_sub_bind 146 vRtswvyge....kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlaneget 218
                                        Rts++yg+     + nf+  ++++++  ee+++v Dq+ +PT   +lA++ll++ e++++     gvyH+a++  +
  gi|386001792|ref|YP_005920091.1| 150 ARTSVIYGArpasGKVNFALWLIERLAAGEEVRIVTDQFITPTLNTNLARMLLEAGERRLS-----GVYHMAGATRV 221
                                       *******997886778*******************************************96.....*********** PP

                                       EHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHH CS
                     RmlD_sub_bind 219 swlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevl 282
                                       s+++fA +i++++g d+  + p   +++  +AkRP++S+Ldt+k+++     + + re+l+++ 
  gi|386001792|ref|YP_005920091.1| 222 SRYDFAVEIARAFGLDEGLIAPSRISDMRWRAKRPRDSSLDTSKAARLLAEGPSPLRESLRALR 285
                                       ************************************************9999999999998765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   6.2e-26   1.2e-22       2     159 ..       6     152 ..       5     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 6.2e-26
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       l+tG++G++Gs l++   ++g++v     + ++ +++       v+ldl++++++er ++e++p++++h Aa  +v+
  gi|386001792|ref|YP_005920091.1|   6 LITGGSGLLGSSLAEVAVAEGHQVFSGYCR-HSPEFG-----VAVKLDLLEGAEVERSISEVAPQVIFHTAALTDVD 76 
                                       9**********************6666555.233344.....457******************************** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                       +  +dp   +++n+ gt +++ aa + g+  l+++s++ v+     +   e+     + p + Ya++Kl +e  +  
  gi|386001792|ref|YP_005920091.1|  77 RCEDDPDLAWRTNVLGTERVARAAAEVGA-HLVYVSTDYVFDGEGGM-YREED---RTDPVNCYARTKLSAEGFCDL 148
                                       *****************************.***********988886.44444...47999***********99986 PP

                                       HHHH CS
                         Epimerase 156 yaaq 159
                                       +a++
  gi|386001792|ref|YP_005920091.1| 149 VART 152
                                       5554 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.1   5.7e-20   1.1e-16       1     165 [.       6     147 ..       6     158 .. 0.87
   2 ?    0.0   0.0      0.22   4.5e+02     311     331 ..     282     302 ..     257     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 5.7e-20
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG++G  Gs lae  +++g++v+    r+s              ++        +k Dl + +++er ++ev p+
  gi|386001792|ref|YP_005920091.1|   6 LITGGSGLLGSSLAEVAVAEGHQVFSGYCRHSP-------------EFG-----VAVKLDLLEGAEVERSISEVAPQ 64 
                                       9***********************764333332.............222.....24899****************** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        +++ AA   Vd+  ++P+  +++nvlGt r+  a+ ++g    ++++ +St+ v+   +   ++E+ +++P ++Ya
  gi|386001792|ref|YP_005920091.1|  65 VIFHTAALTDVDRCEDDPDLAWRTNVLGTERVARAAAEVG----AHLVYVSTDYVFDG-EGGMYREEDRTDPVNCYA 136
                                       ************************************9998....589*********44.44789************* PP

                                       HHHHHHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivv 165
                                        +Kl+a+ ++ 
  gi|386001792|ref|YP_005920091.1| 137 RTKLSAEGFCD 147
                                       *****998765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.22
                                       HHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 311 skakeeLgWkpkvsfeelvre 331
                                       + ++ee+gW+++ s  el++e
  gi|386001792|ref|YP_005920091.1| 282 RALREEIGWRARSSHPELCHE 302
                                       6689**********9999976 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5     0.051     1e+02       1      19 [.       5      23 ..       5      30 .. 0.83
   2 !   43.2   0.0   1.3e-14   2.6e-11      62     131 ..      47     115 ..      33     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.051
                                      EEEETTTSHHHHHHHHHHH CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqil 19
                                      +l+tG++G +Gs+l +  +
  gi|386001792|ref|YP_005920091.1|  5 LLITGGSGLLGSSLAEVAV 23
                                      59***********988665 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 1.3e-14
                                       -TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG CS
                   Polysacc_synt_2  62 dvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA 131
                                       d+ + +++e+ ++e+ ++v+fh+AAl  V  +e  p  a++tNvlgte v++aa e g  ++v++StD  
  gi|386001792|ref|YP_005920091.1|  47 DLLEGAEVERSISEVAPQVIFHTAALTDVDRCEDDPDLAWRTNVLGTERVARAAAEVGA-HLVYVSTDYV 115
                                       67778899************************************************996.69******65 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.041        81       1      15 [.       7      21 ..       7      35 .. 0.81
   2 !   30.7   0.0   8.7e-11   1.7e-07      89     186 ..      64     145 ..      49     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.041
                                      EE-TTSHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlek 15
                                      +TG++G LG+ L e 
  gi|386001792|ref|YP_005920091.1|  7 ITGGSGLLGSSLAEV 21
                                      8*********99775 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 8.7e-11
                                       -EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH CS
                     NAD_binding_4  89 dviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekld 162
                                       +vi+h aA +++d+  ++   ++r+Nv+Gt++v + a+++ +   l++vST yv + + g                 
  gi|386001792|ref|YP_005920091.1|  64 QVIFHTAALTDVDRCEDDpdlAWRTNVLGTERVARAAAEVGAH--LVYVSTDYVFDGEGGMY--------------- 123
                                       69*********99966666669****************99666..******99988888643............... PP

                                       --EEEETTTCCCHHHHHHHHHHHH CS
                     NAD_binding_4 163 ederaklkglpntYeqsKalaEkl 186
                                          +++ ++  n Y ++K  aE  
  gi|386001792|ref|YP_005920091.1| 124 --REEDRTDPVNCYARTKLSAEGF 145
                                       ..2334445566677777666655 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   9.1e-12   1.8e-08       1     155 [.       6     144 ..       6     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 9.1e-12
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlas 75 
                                       ++tGg+G lG++l +  v +++  +v +   r+spe        +v+  ++ D+++ +++e+ + +v  +v++h+a+
  gi|386001792|ref|YP_005920091.1|   6 LITGGSGLLGSSLAEVAVAEGH--QVFSGYCRHSPEF-------GVA--VKLDLLEGAEVERSISEVapQVIFHTAA 71 
                                       69************99999995..8888888888887.......777..88***************9567******* PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                       l+dv   ++  d   + nv GT+ v  a+ + g   lvY+S+ + v++   +  +     ++e  + ++++y+++K 
  gi|386001792|ref|YP_005920091.1|  72 LTDVDRcEDDPDLAWRTNVLGTERVARAAAEVGA-HLVYVST-DYVFD--GEGGMY----REEDRTDPVNCYARTKL 140
                                       ****9989999********************996.69***98.77888..233343....23334558899****99 PP

                         3Beta_HSD 152 laEk 155
                                        aE 
  gi|386001792|ref|YP_005920091.1| 141 SAEG 144
                                       9995 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00088       1.7       4      34 ..       6      36 ..       4      79 .. 0.78
   2 ?    2.8   0.0      0.05     1e+02      75      93 ..     202     220 ..     147     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00088
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRs 34
                                      litGG G LG +la+  +++g +      R+
  gi|386001792|ref|YP_005920091.1|  6 LITGGSGLLGSSLAEVAVAEGHQVFSGYCRH 36
                                      9******************999877777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.05
                                       HHHHSS---EEEE------ CS
                                KR  75 ikaeeppikGvihaAgvlr 93 
                                       ++a e++++Gv+h+Ag++r
  gi|386001792|ref|YP_005920091.1| 202 LEAGERRLSGVYHMAGATR 220
                                       2333488********9987 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0006       1.2      21      96 ..       4      76 ..       2      83 .. 0.75
   2 ?   -0.3   0.0       0.4   8.1e+02      35      52 ..      96     113 ..      93     124 .. 0.87
   3 ?   -2.0   0.0       1.4   2.8e+03      26      54 ..     160     189 ..     154     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0006
                                      EEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-.EEEE--SHHHHHHHHHHHHTT-SEEEE---S--EE CS
                               DFP 21 RfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegv.evvkvesaeemleaveealkeadivimaAAvaDyr 96
                                      R++    SG  G +lAe a+a+G++V   sg ++ + + gv   ++  + +e ++++ e ++  ++++++AA  D  
  gi|386001792|ref|YP_005920091.1|  4 RLLITGGSGLLGSSLAEVAVAEGHQVF--SGYCRHSPEFGVaVKLDLLEGAEVERSISEVAP--QVIFHTAALTDVD 76
                                      7777788******************97..555444433465235678888888888888866..8999999999975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.4
                                       HHHHHHHTT-EEEEEE-S CS
                               DFP  35 lAeaaaarGaeVtlvsgp 52 
                                       +A+aaa+ Ga+  +vs  
  gi|386001792|ref|YP_005920091.1|  96 VARAAAEVGAHLVYVSTD 113
                                       89***********99976 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.4
                                       ----HHHHHHHH.HHHHTT-EEEEEE-S-S CS
                               DFP  26 rSSGkmGyalAe.aaaarGaeVtlvsgpvs 54 
                                       ++SGk  +al   + +a+G eV++v+ +  
  gi|386001792|ref|YP_005920091.1| 160 PASGKVNFALWLiERLAAGEEVRIVTDQFI 189
                                       578888888865255678999999988753 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00013      0.25       2      26 ..       6      30 ..       5      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                      EESSTTSHHHHHHHHHHHHHT-EEE CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvr 26
                                      l++G++G +G+s++++++++gh+v+
  gi|386001792|ref|YP_005920091.1|  6 LITGGSGLLGSSLAEVAVAEGHQVF 30
                                      89**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1963.56
//
Query:       gi|386001793|ref|YP_005920092.1|  [L=365]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-32  111.0   0.0    6.9e-32  110.3   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-19   71.1   0.0    2.8e-19   69.9   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    9.4e-10   38.8   0.2    1.5e-09   38.0   0.2    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0056   17.1   0.1      0.013   15.9   0.1    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0077   15.1   0.0      0.016   14.1   0.0    1.4  2  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
       0.07   13.5   0.1        0.3   11.5   0.0    1.9  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   2.3e-35   6.9e-32      17     169 ..     192     342 ..     180     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2.3e-35
                                       EEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  17 iilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsredleell 90 
                                       + lsv+r+ +eK+++l  +af+ l+++     +lv++G   +  +++   ++  + ++ dnv++lgevs+e+l +l+
  gi|386001793|ref|YP_005920092.1| 192 FWLSVNRIYPEKRIELQFQAFRALPEE-----RLVVVGgysK-GDFAARYYKKLAENIPDNVTMLGEVSDEELFALY 262
                                       789*******************99665.....9999999*55.5555555555999********************* PP

                                       HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH..HHHHHH CS
                   Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede..elrerl 165
                                       ++++ ++++++ E fG++++EAma+g+pvia++ gg++e v dg+tG lv+p+ ae++aea+r++ e +    r+++
  gi|386001793|ref|YP_005920092.1| 263 SRCKGLICTAMDEDFGLTPVEAMASGKPVIAVKEGGFLESVIDGVTGRLVEPE-AESIAEAVREASERGclSYRVAC 338
                                       *****************************************************.***********999988777777 PP

                                       HHHH CS
                   Glycos_transf_1 166 gena 169
                                       +e+a
  gi|386001793|ref|YP_005920092.1| 339 RERA 342
                                       7765 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 ?   -3.1   0.0       3.3   9.8e+03      98     122 ..     156     182 ..     141     185 .. 0.53
   2 !   69.9   0.0   9.2e-23   2.8e-19       6     130 ..     195     325 ..     192     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.3
                                       EE-TGG.GTTT--T.TSSEE--TT-HH CS
                   Glyco_trans_1_4  98 Vatdvg.giaevvg.engllvppgdpe 122
                                       ++++v+  i+e+ g +++++ pp d+e
  gi|386001793|ref|YP_005920092.1| 156 ISSNVQrRIEEAYGrRSAVVYPPVDVE 182
                                       445554334444431333444555544 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 9.2e-23
                                       EES---GG.GTHHHHHHHHHHHH.HHEEEEEES---......HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEE CS
                   Glyco_trans_1_4   6 fvGrleenvkgvdllleavpllrkkdvrlvivGdgprp....eeleelaagleerveftGfv..edlaellaaadvf 76 
                                        v r++++ k+++l  +a+ +l ++  rlv+vG+ ++     + +++la+++ ++v+++G+v  e+l +l+++++ +
  gi|386001793|ref|YP_005920092.1| 195 SVNRIYPE-KRIELQFQAFRALPEE--RLVVVGGYSKGdfaaRYYKKLAENIPDNVTMLGEVsdEELFALYSRCKGL 268
                                       56788655.**************99..******54322344366666666999*********8777*********** PP

                                       EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailr 130
                                       +++   e fgl+ +Eama+g+pv+a + gg+ e v  g++g lv+p ++e++aea+ +
  gi|386001793|ref|YP_005920092.1| 269 ICTAmdEDFGLTPVEAMASGKPVIAVKEGGFLESVidGVTGRLVEP-EAESIAEAVRE 325
                                       9999999***********************977777********98.59******987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.2   5.2e-13   1.5e-09       1     170 []      13     183 ..      13     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.2e-13
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrrlrrllkrekpDv 75 
                                       vGG er++l Lar+L  +     ++t ++d+++ ++   ++v+ +      ++ ++l+ ++++  +rr     ++D 
  gi|386001793|ref|YP_005920092.1|  13 VGGGERVALALARGLGGD-----LITTDVDPDSVKRLgfDDVTIISLGK-TIPVPPLKQISASAIFRRCDLSDDYDF 83 
                                       7****************9.....99999999999996542222222222.222223333333333444444449999 PP

                    Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglye..............krllkarlkplsrllralerrllrradrvi 138
                                           +     +++ a++  +++p  +++ ++                + +lk+   ++ +l r++ +r +r++ r++
  gi|386001793|ref|YP_005920092.1|  84 FIFTG----NWCHYAAK--RHKPNLWYCYSPVRafydlrasvvsrqpNPILKSLAALWINLHRRFDQRSVRSVERIV 154
                                       95444....34444556..59**********************98887777777788888899999999******** PP

                    Glyco_transf_4 139 avSeatadelrerygvppekitVipnGvDler 170
                                       a+S  ++++++e yg   ++ +V++++vD+er
  gi|386001793|ref|YP_005920092.1| 155 AISSNVQRRIEEAYG---RRSAVVYPPVDVER 183
                                       ***************...789*********97 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   4.4e-06     0.013       1     155 [.      14     175 ..      14     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapg.apeleedgvrvhrlp.vprrpspladlaalralrrllrqrrerpd 75 
                                       gG++r++ +lar+L  +     ++t++ +p+   +l  d v++++l  + + p pl+  +a++ +rr     +  +d
  gi|386001793|ref|YP_005920092.1|  14 GGGERVALALARGLGGD-----LITTDVDPDsVKRLGFDDVTIISLGkTIPVP-PLKQISASAIFRRCD--LSDDYD 82 
                                       78888888888888888.....5554444442555778999999773344444.667899999999985..799999 PP

                   Glyco_trans_4_4  76 vvhahs.ptaglaarlarrrrgiplvvtlh..........glllrrgsgavrrly.......ralerrllrradavl 134
                                         +  + +       +a+ r+++ l++ +           +   r++++ +++l+       r++++r++r++ +++
  gi|386001793|ref|YP_005920092.1|  83 FFIFTGnW----CHYAAK-RHKPNLWYCYSpvrafydlraSVVSRQPNPILKSLAalwinlhRRFDQRSVRSVERIV 154
                                       99988844....566666.888777777755555554443344566655555554333566677788********** PP

                   Glyco_trans_4_4 135 vvseaeaeelralgvpadrvv 155
                                       ++s  + +++++ +++++ vv
  gi|386001793|ref|YP_005920092.1| 155 AISSNVQRRIEEAYGRRSAVV 175
                                       ************777777665 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         1     3e+03     216     252 ..     150     183 ..     134     184 .. 0.58
   2 !   14.1   0.0   5.4e-06     0.016     199     319 ..     204     329 ..     198     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1
                                       -EEEEE--..HHHHHHHHHHHHH-TTEEEE----HHH CS
                       Epimerase_2 216 vevvvpvhnnprtrkrlleeleelenvtlieplgyld 252
                                       ve +v +    ++++r++e++ + + + +++p+++++
  gi|386001793|ref|YP_005920092.1| 150 VERIVAIS--SNVQRRIEEAYGR-RSAVVYPPVDVER 183
                                       44445555..6666666665554.4666777777665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.4e-06
                                       HHHHHHHHHHHHHHHH--EEEEE--..HHHHHHHHHHHHH-.TTEEEE----HHHHHHHHHC-SEEEE.....S-H. CS
                       Epimerase_2 199 rlkeilealkalakekdvevvvpvhnnprtrkrlleeleel.envtlieplgyldflsllknaklvlt.....dSg. 268
                                       r++  ++a++al +e ++ vv  + + +   +  ++  e++ +nvt++  +  +++++l +++k ++      d g 
  gi|386001793|ref|YP_005920092.1| 204 RIELQFQAFRALPEE-RLVVVGGYSKGDFAARYYKKLAENIpDNVTMLGEVSDEELFALYSRCKGLICtamdeDFGl 279
                                       555667889999997.777888888888888888888888877********************98875466334454 PP

                                       HHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT- CS
                       Epimerase_2 269 GiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklled 319
                                       +   Ea++ g+pv+ + e +     ++  t +lv++++e+I +a++++ e 
  gi|386001793|ref|YP_005920092.1| 280 TPV-EAMASGKPVIAVKEGGFLESVIDGVTGRLVEPEAESIAEAVREASER 329
                                       445.************77777777777778899*************99854 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 ?   -1.1   0.0      0.86   2.6e+03       9      28 ..     158     177 ..     136     194 .. 0.65
   2 ?   11.5   0.0    0.0001       0.3       8      59 ..     265     326 ..     258     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.86
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltd 28 
                                         ++ r+ Ea++  + +++ 
  gi|386001793|ref|YP_005920092.1| 158 SNVQRRIEEAYGRRSAVVYP 177
                                       44556777777777777777 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0001
                   Glyco_trans_1_2   8 s.........espnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryl 59 
                                       +         e++ l  +Ea+a+G ++++ +  g+ e + +g ++ l+e + e++ae++r++
  gi|386001793|ref|YP_005920092.1| 265 CkglictamdEDFGLTPVEAMASGKPVIAVKEGGFLESVIDGVTGRLVEpEAESIAEAVREA 326
                                       44444455557899999*************99***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2233.06
//
Query:       gi|386001794|ref|YP_005920093.1|  [L=304]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-40  138.4   0.0      8e-40  137.2   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.2e-40  136.6   0.0    1.1e-39  136.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.1e-07   29.7   0.0    1.3e-06   27.6   0.0    1.8  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.5e-07   29.0   0.1    3.8e-06   26.2   0.1    2.0  1  RmlD_sub_bind    RmlD substrate binding domain
    3.1e-05   23.3   0.4      0.011   14.9   0.4    2.7  1  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.019   14.4   0.0    1.4  1  adh_short        short chain dehydrogenase
      0.017   15.0   0.0       0.12   12.3   0.0    2.2  1  NAD_binding_10   NAD(P)H-binding
      0.051   12.7   0.1      0.095   11.8   0.1    1.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0   3.6e-43     8e-40       1     331 [.       4     294 ..       4     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 3.6e-43
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l+e Ll+ g++v+++++    f+tg+ e+l+      l++nl++++g   + ++l     +  p+
  gi|386001794|ref|YP_005920093.1|   4 LVTGGAGFIGSNLVEDLLASGMDVVVLDN----FTTGSRENLEG-----LSGNLRIIEGSCLELQNL-----DLSPQ 66 
                                       9***********************99864....66677777764.....5689**********9988.....579** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       ++y+L+  s  +    kP  + e+ + G++ +Le+++++g    +r++ aSts +Y   q  p +E+  +  +  Y 
  gi|386001794|ref|YP_005920093.1|  67 AIYHLGIPSSSPMYKRKPLLVGEA-ISGMIAVLELAKKTG----ARVVYASTSSLYS-GQTPPHREEMEVFVTDYYT 137
                                       **********************99.************988....69**********4.456899************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                        a+ + + +++ y + +g+ a+  ++f  ++p+  ++    + +t+++ ++ +g+ +v+ +G+++++Rd+ +v+D+v
  gi|386001794|ref|YP_005920093.1| 138 EARFAMERMAELYGKLFGVRALGMRFFSVYGPHEAAKkEYANIVTQFLWEMMAGRVPVI-YGDGSQTRDFVYVRDVV 213
                                       *********************************987525667889999******98776.8**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +a++l++ ++ +   +++tg+++s + +ve+ + e+g +i +e               v  ++ ++y+r+     +l
  gi|386001794|ref|YP_005920093.1| 214 SALRLAMASNCTGALNVGTGRSYSFNAVVEILAGEMGLDIRAEH--------------VDNPI-KNYVRD-----TL 270
                                       **************************************987642..............22233.356665.....69 PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                       +d++ka+e Lg++++ ++ee++re
  gi|386001794|ref|YP_005920093.1| 271 ADTTKAEEVLGFRARHTLEEGIRE 294
                                       9*********************98 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   5.1e-43   1.1e-39       1     241 []       3     231 ..       3     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 5.1e-43
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAav 74 
                                       +lVtG++GfiGs+lv+ ll+ g +v++ld+ +++s+++++      +++e+  ++ ++l+       p+a++hl+  
  gi|386001794|ref|YP_005920093.1|   3 VLVTGGAGFIGSNLVEDLLASGMDVVVLDNFTTGSRENLEGLSgnlRIIEGSCLELQNLD-----LSPQAIYHLGIP 74 
                                       79*****************************88888776654477777777777666554.....4899*****997 PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHH CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagek 151
                                       ++ + +  +p  +  + + g+  +le a+k+g+ r++++s+s++Y  +++ p  e++   ++  +  Y  a  a+e+
  gi|386001794|ref|YP_005920093.1|  75 SSSPMYKRKPLLV-GEAISGMIAVLELAKKTGA-RVVYASTSSLYSGQTP-PHREEM---EVFVTDYYTEARFAMER 145
                                       7777777777775.569****************.************9999.977777...677899*********** PP

                                       HHHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                         Epimerase 152 lveayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                       ++e y + +g++a+ +r f++yGp+   ++e ++++++++  + +g+   +++gdg++ Rdf+yv+Dv+ a+ l+++
  gi|386001794|ref|YP_005920093.1| 146 MAELYGKLFGVRALGMRFFSVYGPHeAAKKEYANIVTQFLWEMMAGR-VPVIYGDGSQTRDFVYVRDVVSALRLAMA 221
                                       *************************888888****************.****************************9 PP

                                       HHTT-STTEEEEES CS
                         Epimerase 228 hvdagdkgeiyniG 241
                                            +  +++n+G
  gi|386001794|ref|YP_005920093.1| 222 S----NCTGALNVG 231
                                       8....334466665 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 !   27.6   0.0   5.9e-10   1.3e-06       1     229 [.       4     220 ..       4     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.9e-10
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++lv+ L+  +   +v vlD  +  +  +    +++  +ieg  ++ ++l+   +    + hl ++ 
  gi|386001794|ref|YP_005920093.1|   4 LVTGGAGFIGSNLVEDLLASG--MDVVVLDNFTTGSRENLEGLSGNLRIIEGSCLELQNLDLSPQA---IYHL-GIP 74 
                                       69******************9..6******7666665444445556669*******9999976654...4555.666 PP

                         3Beta_HSD  78 dvagklted.eimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        +  +++++  +    + G   vle ++k+g r +vY S+ +   +   + + +    ++e+e   +d y+e +   
  gi|386001794|ref|YP_005920093.1|  75 SSSPMYKRKpLLVGEAISGMIAVLELAKKTGAR-VVYASTSSLYSG---QTPPH----REEMEVFVTDYYTEARFAM 143
                                       6555555551456678***************76.79****999888...44444....3455666778888888777 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak......lglalfkigdeevlsdrvYvgNvawa 224
                                       E++     g +l +   +    +R   +yG+ +   ++ ++ +++       g   + +gd +++ d+vYv  v+ a
  gi|386001794|ref|YP_005920093.1| 144 ERMAEL-YG-KLFG---VRALGMRFFSVYGPHEAAKKEYANIVTQflwemmAGRVPVIYGDGSQTRDFVYVRDVVSA 215
                                       777544.44.2333...467789********9877766665555511111134556789****************99 PP

                         3Beta_HSD 225 hilAa 229
                                         lA+
  gi|386001794|ref|YP_005920093.1| 216 LRLAM 220
                                       88875 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 !   26.2   0.1   1.7e-09   3.8e-06       1     155 [.       1     170 [.       1     185 [. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.7e-09
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       m++lvtG+ G +Gs+L++ l ++g++v+ l++              +l + + + ++    + +p+++++++     
  gi|386001794|ref|YP_005920093.1|   1 MRVLVTGGAGFIGSNLVEDLLASGMDVVVLDNFttgsrenleglsgNLRIIEGSCLELQNLDLSPQAIYHLGIPSSS 77 
                                       89****************************7667788778888877777777777777779***********98887 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S CS
                     RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk 141
                                            ++ +  ++   +  a+ e+a+++ga +++ St   + G+ + p +e+ e+    +Y +++ a+E++ + +gk
  gi|386001794|ref|YP_005920093.1|  78 PMYKRKPLLVGEA-ISGMIAVLELAKKTGARVVYASTSSLYSGQ-TPPHREEMEVFVTDYYTEARFAMERMAELYGK 152
                                       7766666555443.566777779********************9.6679*********************9887554 PP

                                       ....SEEEEEE-SEESSS CS
                     RmlD_sub_bind 142 ....kalivRtswvygek 155
                                           +al +R+  vyg +
  gi|386001794|ref|YP_005920093.1| 153 lfgvRALGMRFFSVYGPH 170
                                       223366667888888765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.4   4.9e-06     0.011       1      27 [.       5      29 ..       5     215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.9e-06
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyl 27
                                      +TG+ GF+G+ L+e+LL +  +  +++
  gi|386001794|ref|YP_005920093.1|  5 VTGGAGFIGSNLVEDLLASGMD--VVV 29
                                      7****************99875..443 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.7e-06     0.019       3      34 ..       3      34 ..       1      59 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.7e-06
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrse 34
                                      vlvtG+++ IG ++++ l+++G++vvv+d+  
  gi|386001794|ref|YP_005920093.1|  3 VLVTGGAGFIGSNLVEDLLASGMDVVVLDNFT 34
                                      9**************************99755 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.3e-05      0.12       1     129 [.       7     145 ..       7     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.....HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.....peklaeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G +G+ lv+ lla+g ++v++l  n      e l+ l  + +l+++eg+ ++ + l       +a++  + +++
  gi|386001794|ref|YP_005920093.1|   7 GGAGFIGSNLVEDLLASG-MDVVVL-DNfttgsRENLEGL--SGNLRIIEGSCLELQNLDL---SPQAIYHLGIPSS 76 
                                       999**************5.999776.33232224555544..3799999998885555443...3334444443333 PP

                                       C....HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHH.HHHHHHHH CS
                    NAD_binding_10  73 k....deeg..........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkayl.aakraaee 129
                                       +    +             ++++++ ak++g  R+v+ s+   +  +  ++ e  + ++ +y+ +a  a+e+
  gi|386001794|ref|YP_005920093.1|  77 SpmykR--KpllvgeaisgMIAVLELAKKTGA-RVVYASTSSLYSGQTPPHREEMEVFVTDYYtEARFAMER 145
                                       333322..123555666779999999999998.777777777765333333333333445555155556665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.3e-05     0.095       1      28 [.       3      30 ..       3     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                                      EEEETTTSHHHHHHHHHHHHHB-SEEEE CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiil 28
                                      vlvtG++G iGs+lv+ +l++ +  ++l
  gi|386001794|ref|YP_005920093.1|  3 VLVTGGAGFIGSNLVEDLLASGMDVVVL 30
                                      8******************998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1850.04
//
Query:       gi|386001795|ref|YP_005920094.1|  [L=260]
Description: Polysaccharide ABC transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-22   80.1  25.3    1.5e-22   80.1  25.3    1.8  2  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1  25.3   8.4e-27   1.5e-22       3     207 ..      17     218 ..      15     221 .. 0.91
   2 ?    0.1   0.4     0.024   4.3e+02      99     123 ..     225     249 ..     219     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 8.4e-27
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferer 79 
                                       i+ l + +f++r++++ lg++w+l++pll++lv+ +vf++l + + +   + ll +++l++++   ts++++ ++++
  gi|386001795|ref|YP_005920094.1|  17 ILRLAWSDFKLRYKNSILGFFWSLLEPLLMLLVLYVVFSHLMKIQVEHYQLFLLLGIILWNFLDRGTSMGIFGIVGK 93 
                                       7889***********************************97543333334*************************** PP

                     ABC2_membrane  80 gvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslgllisala 155
                                       + l+++ ++p     + +++  ++ l++++l+ ++f++++ ++ g+ ++ ++++f++++ l+++++ +l+l++sal+
  gi|386001795|ref|YP_005920094.1|  94 PGLVQKVYFPR---DVLIISACATALMMTALEFVVFVAFMAVF-GVAPTaAVLYFPPIFALLFVLVFGLSLALSALN 166
                                       ***********...67777777777999999999999999998.****9888************************* PP

                     ABC2_membrane 156 psfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                       ++f+d+++++ ++l+  ++ +++++pi+  p  lq +  +nP++ ++   r 
  gi|386001795|ref|YP_005920094.1| 167 VYFRDVQFIWRVILQAGFFATPILYPITIFPADLQRLVMANPMARIITTSRD 218
                                       ******************************9999**********99987776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.024
                     ABC2_membrane  99 akvlvelpvsllqalifllivyflv 123
                                       a ++++l++ +l+a+++ll  y+++
  gi|386001795|ref|YP_005920094.1| 225 APAAGDLAYVALAAVVILLAGYLVF 249
                                       5667899999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1675.68
//
Query:       gi|386001796|ref|YP_005920095.1|  [L=430]
Description: Polysaccharide ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-29  101.4   0.0    2.3e-28   99.1   0.1    2.1  2  Wzt_C        Wzt C-terminal domain
    5.3e-23   82.0   0.0    1.8e-22   80.3   0.0    1.8  1  ABC_tran     ABC transporter
    8.6e-09   35.6   0.6    0.00031   20.7   0.5    2.5  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-05   24.6   0.0    2.9e-05   23.7   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00075   19.9   0.0     0.0011   19.4   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.001   19.0   0.2       0.48   10.3   0.1    2.3  2  NTPase_1     NTPase
     0.0011   19.5   0.0     0.0027   18.3   0.0    1.5  1  AAA_23       AAA domain
     0.0043   16.8   0.1      0.018   14.7   0.1    1.9  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.021   14.3   0.1      0.052   13.0   0.0    1.6  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.022   14.5   0.0      0.031   14.0   0.0    1.3  1  AAA_15       AAA ATPase domain
      0.024   13.6   0.1      0.037   13.0   0.1    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.039   14.4   0.0       0.34   11.3   0.0    2.1  1  AAA          ATPase family associated with various cellular a
      0.043   13.7   0.0      0.074   13.0   0.0    1.3  1  NACHT        NACHT domain
      0.055   13.4   0.0       0.14   12.0   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
       0.11   12.8   0.0       0.25   11.6   0.0    1.6  1  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.3   1.6e+03      98     128 ..     112     137 ..     100     158 .. 0.82
   2 !   99.1   0.1   1.9e-31   2.3e-28       3     142 ..     291     423 ..     290     424 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                             Wzt_C  98 pGeYlltvaledrdgeeneiydwlddalsfe 128
                                       +G Y   ++l  ++g    i d+++d++sf 
  gi|386001796|ref|YP_005920095.1| 112 VGMYATIMGL--SNGM---IRDRIEDVISFA 137
                                       6777777777..5555...9999**999995 PP

  == domain 2  score: 99.1 bits;  conditional E-value: 1.9e-31
                             Wzt_C   3 eryGsgeaeIedvelldaegeetstfesgeevtlrikvkahedvedpvfgfaikdrngqevfgtntelekksfelee 79 
                                       +r+G++++ I+dv ++++ g  +s f+s +++++ri+++++e+v+dpvfg+ +++ +g++++gtnt l++ +  +++
  gi|386001796|ref|YP_005920095.1| 291 RRWGNHKIAIKDVAFFNKFGSVSSRFNSFDPMKVRIYYEVNEAVSDPVFGIGLYTAEGLHLYGTNTALKDLK--FDR 365
                                       69****************************************************************999976..776 PP

                             Wzt_C  80 lkagervevefef.klpLapGeYlltvaledrdgeeneiydwlddalsfeVvssskntfvGlvd 142
                                       ++    +++++e+ k+p+ +G++ll+ a+++rd++   +ydw+d  +sfeV+s+   +++Gl++
  gi|386001796|ref|YP_005920095.1| 366 IER--DGYIDLEIdKIPMLAGKFLLSPAIQNRDYSI--TYDWIDKYYSFEVIST--GRDDGLFE 423
                                       655..45788888878*************9999987..*************833..34788875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   1.5e-25   1.8e-22       1     135 [.      45     176 ..      45     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.5e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++v++++ ege+v+i+G+nG+GKStLlk++a+ l+pt+G++ ++g+ +             +l+    ++p+ltvr
  gi|386001796|ref|YP_005920095.1|  45 LEDVTFSVTEGECVGIIGDNGSGKSTLLKVIANILRPTKGRVAVRGRMTP------------FLELGVGFQPDLTVR 109
                                       689***************************************55543333............333335556666666 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       en               +++ie+++s  gl  ++d ++    ++LS G+++r+a   a+ ++p++ll+DE 
  gi|386001796|ref|YP_005920095.1| 110 ENvgmyatimglsngMIRDRIEDVISFAGLGRFEDAKL----KNLSSGMQVRLAFSTAIQTDPDVLLVDEV 176
                                       66666666776666668999******************....****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.5   2.6e-07   0.00031       3      24 ..      59      80 ..      57     125 .. 0.82
   2 !   12.6   0.0   7.6e-05     0.091     236     299 ..     149     209 ..     120     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.6e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      ++iG+NgsGKS+LL+ +  + r
  gi|386001796|ref|YP_005920095.1| 59 GIIGDNGSGKSTLLKVIANILR 80
                                      79***************77654 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.6e-05
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       +lS+G++  la+ ta+  ++   ++ll+DE+ +  + +++ + +e++k+ +r+g+ +++++H+ 
  gi|386001796|ref|YP_005920095.1| 149 NLSSGMQVRLAFSTAIQTDP---DVLLVDEVLAVGDMEFQQKCFEVFKRYRREGVTILFVSHDL 209
                                       68****************99...9*******999999*************************85 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.4e-08   2.9e-05      15      50 ..      48      83 ..      37      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       t+++++ + + ++G++GsGKSTll  i+ +L p+k
  gi|386001796|ref|YP_005920095.1| 48 VTFSVTEGECVGIIGDNGSGKSTLLKVIANILRPTK 83
                                      455555444899********************9998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   9.3e-07    0.0011      24      63 ..      53      95 ..      34     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.3e-07
                            AAA_16 24 p..elvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      +  e+v ++G+ G+GKs+l++ +++ l+ ++g + +rg+ + +
  gi|386001796|ref|YP_005920095.1| 53 TegECVGIIGDNGSGKSTLLKVIANILRPTKGRVaVRGRMTPF 95
                                      2249********************9999998666699987776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1    0.0004      0.48       2      36 ..      58      94 ..      57     101 .. 0.81
   2 !    6.4   0.0    0.0064       7.7      92     115 ..     163     190 ..     147     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyte 36
                                      v i G  G+GK+Tl+k +++ l+     v v+G +t+
  gi|386001796|ref|YP_005920095.1| 58 VGIIGDNGSGKSTLLKVIANILRPTkgRVAVRGRMTP 94
                                      6788******************865335778888887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0064
                                       HH.HHH-EEEE--...-STTGGG-HHHH CS
                          NTPase_1  92 al.seadviviDE...iGkmElkskkfk 115
                                       a+ +++dv+++DE   +G mE++ k f+
  gi|386001796|ref|YP_005920095.1| 163 AIqTDPDVLLVDEvlaVGDMEFQQKCFE 190
                                       333789*******5555*****998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.2e-06    0.0027      11      42 ..      46      78 ..      39      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAikla 42
                                      +d+++   +   + I+G+NG+GK+T+l  i  +
  gi|386001796|ref|YP_005920095.1| 46 EDVTFSVtEGECVGIIGDNGSGKSTLLKVIANI 78
                                      55555555556889*************998755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.5e-05     0.018      16     121 ..      54     204 ..      47     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi.eastiakllkrlk.......... 81 
                                       +g  ++ + G  G+GK+t+lk+++++++  +grv   A  g++   L+ ++g+ +  t+ + +  ++          
  gi|386001796|ref|YP_005920095.1|  54 EG-ECVGIIGDNGSGKSTLLKVIANILRPTKGRV---AVRGRMTPFLELGVGFqPDLTVRENVGMYAtimglsngmi 126
                                       44.488899*******************997665...4455555555544444222233333333333344444445 PP

                            AAA_30  82 ..................................grarlepg.tllivDEagmv....dtkqlaallkaaekagakv 119
                                                                         + ++++++ ++l+vDE+  v     +++  +++k+ +++g+++
  gi|386001796|ref|YP_005920095.1| 127 rdriedvisfaglgrfedaklknlssgmqvrlafS-TAIQTDpDVLLVDEVLAVgdmeFQQKCFEVFKRYRREGVTI 202
                                       55555555555566666666666666666666643.34555556777777666522112333445556666656666 PP

                            AAA_30 120 il 121
                                       ++
  gi|386001796|ref|YP_005920095.1| 203 LF 204
                                       55 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.4e-05     0.052      25      48 ..      56      79 ..      35      92 .. 0.81
   2 ?   -2.4   0.0       2.2   2.6e+03     149     197 ..     158     207 ..     146     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-05
                                      SEEEEEESTTSSHHHHHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAilFvL 48
                                      +   i+G NGSGKs ll  i  +L
  gi|386001796|ref|YP_005920095.1| 56 ECVGIIGDNGSGKSTLLKVIANIL 79
                                      5678************99987666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivisl 197
                                       L f++       + l+De+ a  D +  +k  e++k+ + + + ++ +s+
  gi|386001796|ref|YP_005920095.1| 158 LAFSTAIQTDPDVLLVDEVLAVGDMEFQQKCFEVFKRYRREgVTILFVSH 207
                                       33333333333356789999998988888888888866554355555665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.031      28      47 ..      60      79 ..      42     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                            AAA_15 28 liGkNnsGKSsilealdlFl 47
                                      +iG N+sGKS++l+++  +l
  gi|386001796|ref|YP_005920095.1| 60 IIGDNGSGKSTLLKVIANIL 79
                                      9**************97665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.1e-05     0.037      17      62 ..      43      88 ..      29      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                      HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                              MeaB 17 ellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvav 62
                                      ++le ++ +  + + vG+ G  G+Gkstl++ ++  lr    rvav
  gi|386001796|ref|YP_005920095.1| 43 NVLEDVTFSVTEGECVGIIGDNGSGKSTLLKVIANILRPTKGRVAV 88
                                      678888888888999***********************99999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.34       3      71 ..      60     180 ..      58     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                                       EESSTTSSHHHHHHHHHHHHTHE..................................................EEEE CS
                               AAA   3 lyGppGtGKTllakavakelgve..................................................flei 29 
                                       ++G  G GK++l k +a+ l  +                                                  +   
  gi|386001796|ref|YP_005920095.1|  60 IIGDNGSGKSTLLKVIANILRPTkgrvavrgrmtpflelgvgfqpdltvrenvgmyatimglsngmirdriedV--- 133
                                       6899***************8422233344455556555666666666666666666664444444444444442... PP

                                       ETTTCSSS.............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA  30 sgsellsk.............yvgesekkirelfkeakekakpsilfiDEidala 71 
                                                                s +++r  f++a +   p +l++DE+ a++
  gi|386001796|ref|YP_005920095.1| 134 -------IsfaglgrfedaklKNLSSGMQVRLAFSTAIQTD-PDVLLVDEVLAVG 180
                                       .......0455555544455555568888999999888887.9999999987765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.2e-05     0.074       3      25 ..      58      80 ..      56      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                      v + G++GsGK+tLl+ +a  ++
  gi|386001796|ref|YP_005920095.1| 58 VGIIGDNGSGKSTLLKVIANILR 80
                                      5689*************998765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.14      69     122 ..      31      78 ..      13      93 .. 0.74
   2 ?   -2.6   0.0       3.7   4.4e+03      62      85 ..     186     208 ..     176     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       HHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  69 keelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       + +l++ +yev+ v       le+++  +++ +++ ++G  G GKStL++++++ 
  gi|386001796|ref|YP_005920095.1|  31 AGALRKNEYEVFNV-------LEDVTFSVTEgECVGIIGDNGSGKSTLLKVIANI 78 
                                       55555566666655.......667777666669999*************998764 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  62 eeeleelkeelealgyevllvsak 85 
                                       ++ + e+ +++++ g+++l+vs +
  gi|386001796|ref|YP_005920095.1| 186 QK-CFEVFKRYRREGVTILFVSHD 208
                                       44.777889999999999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.25       7     101 ..      57     177 ..      52     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..........................erpevvfvtlpsst..sskd 55 
                                       ++ ++G  G+GK+tll+ +++ l   +   +                          e+++ +  t+ +++    +d
  gi|386001796|ref|YP_005920095.1|  57 CVGIIGDNGSGKSTLLKVIANILR--PT--KgrvavrgrmtpflelgvgfqpdltvrENVGMY-ATIMGLSngMIRD 128
                                       6779*************9999983..22..234667777777777777775555443333333.3333322334666 PP

                            AAA_22  56 llrellralglelkaerlsseellealeqalrarav....ielliiDEaq 101
                                         +++ ++ gl++ +  ++++ l + ++  l    +    + +l++DE+ 
  gi|386001796|ref|YP_005920095.1| 129 RIEDVISFAGLGRFE-DAKLKNLSSGMQVRLAFSTAiqtdPDVLLVDEVL 177
                                       677777777776666.4444444444444333333333466677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3024.59
//
Query:       gi|386001797|ref|YP_005920096.1|  [L=468]
Description: hypothetical protein Mhar_1105 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-10   40.8   0.1    1.2e-09   38.7   0.0    2.2  1  Methyltransf_25  Methyltransferase domain
    1.9e-08   34.9   0.0    6.1e-08   33.2   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
      3e-08   33.7   0.1    1.1e-07   31.8   0.0    1.9  2  Methyltransf_23  Methyltransferase domain
    8.3e-07   28.9   0.2    7.8e-06   25.8   0.0    2.5  3  Methyltransf_31  Methyltransferase domain
    1.3e-05   25.9   1.3    0.00045   20.9   0.0    3.0  2  Methyltransf_12  Methyltransferase domain
    6.5e-05   22.9  10.6     0.0062   16.4   1.3    2.8  3  Apolipoprotein   Apolipoprotein A1/A4/E domain
    0.00061   19.9  14.9       0.45   10.5   9.7    3.4  2  DUF1640          Protein of unknown function (DUF1640)
     0.0013   19.0   0.5         19    5.6   0.0    4.3  4  DUF5403          Family of unknown function (DUF5403)
     0.0021   18.1   5.4        1.2    9.1   0.5    3.2  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
  ------ inclusion threshold ------
      0.014   14.7   0.1      0.028   13.7   0.1    1.5  1  KAP_NTPase       KAP family P-loop domain
      0.048   13.7  10.4        1.4    9.0   1.5    2.6  2  ATP-synt_B       ATP synthase B/B' CF(0)
      0.051   13.6   2.7      0.055   13.5   0.0    2.3  2  Methyltransf_32  Methyltransferase domain
      0.063   12.1  12.8      0.065   12.1  11.4    1.7  1  Mitofilin        Mitochondrial inner membrane protein
      0.063   13.2   0.0       0.13   12.1   0.0    1.5  1  UPF0146          Uncharacterised protein family (UPF0146)
       0.12   12.4   3.9        1.3    9.0   0.5    2.7  2  Phasin           Poly(hydroxyalcanoate) granule associated pr
       0.15   12.0   5.0        1.2    9.0   0.2    2.9  3  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
       0.16   12.2   0.2       0.96    9.6   0.1    1.8  2  T2SSN            Type II secretion system (T2SS), protein N
        0.2   11.6   6.1         50    3.9   0.1    4.7  6  DUF3658          Protein of unknown function
       0.72    9.5  10.1        1.4    8.6   0.7    3.9  4  Nbl1_Borealin_N  Nbl1 / Borealin N terminal
        1.1    8.4   8.4         12    5.0   1.2    2.5  2  DUF1682          Protein of unknown function (DUF1682)
        1.3    8.3   9.4        9.9    5.4   9.4    2.2  1  DUF4407          Domain of unknown function (DUF4407)
        2.3    6.0   8.6       0.28    9.1   0.5    2.4  3  Prominin         Prominin
        2.6    8.5   6.3        7.8    7.0   0.7    2.9  2  V-ATPase_G_2     Vacuolar (H+)-ATPase G subunit
        2.9    8.2  15.9        4.7    7.6   0.4    4.5  4  Halo_GVPC        Halobacterial gas vesicle protein C (GVPC) r
        3.6    8.3   9.1         18    6.0   0.3    3.5  4  DUF883           Bacterial protein of unknown function (DUF88


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.7e-12   1.2e-09       2      88 ..     321     406 ..     320     412 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.7e-12
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvssgalhhl 77 
                                       L++G Gt ++++++++     +v+g+D +++ +++a + +++ g  ++f+ +da dl+ f+ + fD+ +s+g+++h+
  gi|386001797|ref|YP_005920096.1| 321 LEVGVGTATMSIYFSRYS--FEVVGLDNDPNVVRNAIKVNKDLGGYAKFILMDAFDLNmFKGDYFDVAFSQGTMEHF 395
                                       89*************994..********************99999************879999*******988**** PP

                                       SHHHHHHHHHH CS
                   Methyltransf_25  78 sdedlekalke 88 
                                       +d+++ +++++
  gi|386001797|ref|YP_005920096.1| 396 NDAEIIEMISK 406
                                       *9999888775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   8.5e-11   6.1e-08       1      78 [.     321     399 ..     321     411 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8.5e-11
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhved 76 
                                       L+vG+Gt  ++ ++ ++  +vvg+D ++++++ a + +++ g   +f+ +da +l  f+ ++fD+ +s+ +++h++d
  gi|386001797|ref|YP_005920096.1| 321 LEVGVGTATMSIYFSRYSFEVVGLDNDPNVVRNAIKVNKDLGGYAKFILMDAFDLnMFKGDYFDVAFSQGTMEHFND 397
                                       89*************999*************998666655555678*********66******************86 PP

                                       HH CS
                   Methyltransf_11  77 pe 78 
                                        e
  gi|386001797|ref|YP_005920096.1| 398 AE 399
                                       54 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.5   2.5e+03      50      62 ..     155     185 ..     151     241 .. 0.63
   2 !   31.8   0.0   1.6e-10   1.1e-07       6     140 ..     298     446 ..     293     461 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                   Methyltransf_23  50 vDlspeaveiae..................k 62 
                                        D+s++++ei++                   
  gi|386001797|ref|YP_005920096.1| 155 QDISRQQHEIRAeldgqlgqvrsefrdeisR 185
                                       5777777777766666555555533332220 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.6e-10
                   Methyltransf_23   6 eeelsdklerllpklragg..rvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae.. 78 
                                       +e++  +++++++k   g+  ++L++G Gt +++ +++++ f+v+g D +p+ v  a      +k++ d    a+  
  gi|386001797|ref|YP_005920096.1| 298 HERFISLIKEIAQKAANGMvpKLLEVGVGTATMSIYFSRYSFEVVGLDNDPNVVRNA------IKVNKDLGGYAKfi 368
                                       577788888888764444466******************************977754......33333222222223 PP

                   Methyltransf_23  79 ..........pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl.......kedrllldwlylvp 138
                                                 + ++fd++ +  ++eh+ d +e + +i + l+    +++s+p  +        +++++ +dw+++ +
  gi|386001797|ref|YP_005920096.1| 369 lmdafdlnmfKGDYFDVAFSQGTMEHFND-AEIIEMISKQLEAAKFVIFSVPSIYYphkefgnERKMSKEDWEMILK 444
                                       3333344444777****************.999******************97666888888777888999999887 PP

                   Methyltransf_23 139 ag 140
                                       +g
  gi|386001797|ref|YP_005920096.1| 445 KG 446
                                       74 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.7   2.7e+03      62      86 ..      53      76 ..      33     151 .. 0.65
   2 ?   -0.7   0.0       1.6   1.1e+03      31      50 ..     292     311 ..     279     314 .. 0.83
   3 !   25.8   0.0   1.1e-08   7.8e-06       7     110 ..     320     417 ..     318     459 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                   Methyltransf_31 62 dieeleklledekfDlilsnevlna 86
                                      ++++le  +  +  D+i+sn+ ++ 
  gi|386001797|ref|YP_005920096.1| 53 EAQSLEDEIR-SDLDYINSNQNIHN 76
                                      4444443322.55777777766633 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                   Methyltransf_31  31 vvGiDiseeaielArenaqk 50 
                                         +iD+ e+ i+l +e+aqk
  gi|386001797|ref|YP_005920096.1| 292 TLNIDYHERFISLIKEIAQK 311
                                       578**************998 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 1.1e-08
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                       +l++G Gt + ++ + +      evvG+D+++++++ A +  ++lg   ++F   d+++l++ ++ + fD+ +s+++
  gi|386001797|ref|YP_005920096.1| 320 LLEVGVGTATMSIYFSRY---SFEVVGLDNDPNVVRNAIKVNKDLGGY-AKFILMDAFDLNM-FKGDYFDVAFSQGT 391
                                       688888887777766643...568****************77777764.8***********9.899*********** PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggillie 110
                                       + +++d  +i+e i++ l+    ++ +
  gi|386001797|ref|YP_005920096.1| 392 MEHFNDA-EIIEMISKQLEAAKFVIFS 417
                                       *999885.5667777777655555554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.37   2.7e+02      27      83 ..      19      81 ..      13      95 .. 0.80
   2 !   20.9   0.0   6.3e-07   0.00045       1      83 [.     321     401 ..     321     412 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.37
                   Methyltransf_12 27 Dispsaiedakeklakrennnnnnvelealdlldldgg.......ssfDlvvasnvlhhlkdir 83
                                      D+ + + ++ + + +kr++ + + v + ++++++++ +       s  D++ +++ +h+ + i 
  gi|386001797|ref|YP_005920096.1| 19 DVAELM-HKIRDRVRKRRGIDSSAVGIAQINSSSSEAQsledeirSDLDYINSNQNIHNENYII 81
                                      444444.499999999999999999999999988887799999999*****9999998765555 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 6.3e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+G Gt++++ ++ ++    e++g+D +p+++ + + k +k  +  ++++  +a d l+ ++g++fD+ ++ ++++
  gi|386001797|ref|YP_005920096.1| 321 LEVGVGTATMSIYFSRY--SFEVVGLDNDPNVV-RNAIKVNKDLGGYAKFILMDAFD-LNMFKGDYFDVAFSQGTME 393
                                       8****************..**************.55555555555566666666666.4566678************ PP

                   Methyltransf_12  78 hl..kdir 83 
                                       h+  ++i 
  gi|386001797|ref|YP_005920096.1| 394 HFndAEII 401
                                       *9444343 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.1   3.7e+03      32      47 ..      51      66 ..      46      70 .. 0.81
   2 !   12.0   2.2    0.0002      0.14      12     183 ..     164     218 ..     113     221 .. 0.54
   3 !   16.4   1.3   8.7e-06    0.0062      12      65 ..     216     269 ..     210     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                                      HHHHHHHHHHHHHHHH CS
                    Apolipoprotein 32 skeleelrarlraele 47
                                      s e+++l +++r++l+
  gi|386001797|ref|YP_005920096.1| 51 SSEAQSLEDEIRSDLD 66
                                      7889999999999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                                       HHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHH CS
                    Apolipoprotein  12 yaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaa 88 
                                        ++el  ql+++                                                                 
  gi|386001797|ref|YP_005920096.1| 164 IRAELDGQLGQV----------------------------------------------------------------- 175
                                       233444444444................................................................. PP

                                       CHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-T CS
                    Apolipoprotein  89 daeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelreklee 165
                                                                                                 e+++++s++  e+r++l+ 
  gi|386001797|ref|YP_005920096.1| 176 --------------------------------------------------------RSEFRDEISRQQHEIRAELDG 196
                                       ........................................................445555566666666666665 PP

                                       TSHHHH....HS--XXXXXXXX CS
                    Apolipoprotein 166 qaeelr....erleanleelka 183
                                       q+ ++r    +++ ++++e++a
  gi|386001797|ref|YP_005920096.1| 197 QLGQVRfefrDEISRQQHEIRA 218
                                       5554431111444444444444 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 8.7e-06
                                       HHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCC CS
                    Apolipoprotein  12 yaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlg 65 
                                        ++el  ql+++  e+rd +s  ++e+ra+l+ +l +vr+   + ++ + ++l 
  gi|386001797|ref|YP_005920096.1| 216 IRAELDGQLGQVRSEFRDEISRQQQEIRAELDGQLGQVRSEFREELNRILNMLD 269
                                       5899********99*************************999988888777776 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.11        82      45     108 ..      10      74 ..       6      78 .. 0.83
   2 !   10.5   9.7   0.00063      0.45      54     141 ..     141     252 ..     109     294 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                           DUF1640  45 kselekseylqkaalselrkevqisersefaalr.seteklqreleklkqkLreeidklkadirl 108
                                        +e++++   +   + ++r+ v++++  + +a+  ++ ++  +e + l+ ++r+++d +++++++
  gi|386001797|ref|YP_005920096.1|  10 YPEIKNEDIDVAELMHKIRDRVRKRRGIDSSAVGiAQINSSSSEAQSLEDEIRSDLDYINSNQNI 74 
                                       56778888888889999********9999888853677888999999999999999999998765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00063
                           DUF1640  54 lqkaalselrkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnle....Kgrireelaklea 126
                                       ++k +ls +r+++      + +++r    +l  +l ++++++r+ei++ +++ir +l+ +    + + r+e ++++ 
  gi|386001797|ref|YP_005920096.1| 141 EIKNNLSRIREDIGQDISRQQHEIR---AELDGQLGQVRSEFRDEISRQQHEIRAELDGQlgqvRFEFRDEISRQQH 214
                                       5555666666655443333333322...2344455555555555555555555544444311112223333333333 PP

                           DUF1640 127 ki.......................qelnnkidrevsa 141
                                       +i                       qe+ + +d ++ +
  gi|386001797|ref|YP_005920096.1| 215 EIraeldgqlgqvrsefrdeisrqqQEIRAELDGQLGQ 252
                                       33333333333333222222222224444444444444 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.1   7.7e+02      13      39 ..     144     170 ..     122     173 .. 0.85
   2 ?    5.5   0.1     0.029        21      13      39 ..     170     196 ..     159     198 .. 0.87
   3 ?    2.5   0.0      0.25   1.8e+02      15      39 ..     198     222 ..     196     225 .. 0.90
   4 ?    5.6   0.0     0.027        19      15      39 ..     224     248 ..     221     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.1
                           DUF5403  13 ahlpgvkaavaeelerraarvrAvvag 39 
                                        +l  +++++ + ++r++  +rA+++g
  gi|386001797|ref|YP_005920096.1| 144 NNLSRIREDIGQDISRQQHEIRAELDG 170
                                       5688899999***********999876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                           DUF5403  13 ahlpgvkaavaeelerraarvrAvvag 39 
                                        +l +v++++++e++r++  +rA+++g
  gi|386001797|ref|YP_005920096.1| 170 GQLGQVRSEFRDEISRQQHEIRAELDG 196
                                       56889******************9986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.25
                           DUF5403  15 lpgvkaavaeelerraarvrAvvag 39 
                                       l +v+ ++++e++r++  +rA+++g
  gi|386001797|ref|YP_005920096.1| 198 LGQVRFEFRDEISRQQHEIRAELDG 222
                                       7799*****************9986 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.027
                           DUF5403  15 lpgvkaavaeelerraarvrAvvag 39 
                                       l +v++++++e++r+++ +rA+++g
  gi|386001797|ref|YP_005920096.1| 224 LGQVRSEFRDEISRQQQEIRAELDG 248
                                       779******************9987 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.79   5.6e+02      75      93 ..      53      71 ..      19      76 .. 0.83
   2 !    9.1   0.5    0.0017       1.2      27      89 ..     137     196 ..     113     202 .. 0.79
   3 !    8.8   0.1    0.0021       1.5      36      97 ..     213     271 ..     204     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.79
                      Baculo_PEP_C 75 alnalqdtlrneLtnlnsi 93
                                        ++l+d++r++L+ +ns+
  gi|386001797|ref|YP_005920096.1| 53 EAQSLEDEIRSDLDYINSN 71
                                      45678899*****999997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                      Baculo_PEP_C  27 lqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89 
                                       l n++i ++l+++ ++i + ++  ++++++   eld +l ++ ++  d + + q ++r eL++
  gi|386001797|ref|YP_005920096.1| 137 LSNIEIKNNLSRIREDIGQDISRQQHEIRA---ELDGQLGQVRSEFRDEISRQQHEIRAELDG 196
                                       356788888888888888888888887777...888999999999999999999999999986 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0021
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                         ++ +++++qL+++ +++++   e++++ ++  ++L+ +l ++  ++r+eL+ + + l + 
  gi|386001797|ref|YP_005920096.1| 213 QHEIRAELDGQLGQVRSEFRD---EISRQQQEIRAELDGQLGQVRSEFREELNRILNMLDSK 271
                                       456677788888888888888...66666677777888888888888888877776665554 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.9e-05     0.028     188     303 ..      59     269 ..      56     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                        KAP_NTPase 188 eevlqlleavkllfslkpvvfilavDphviakaieansesllgeiaghdYlekiiqlpvyLppsglrevkkvlmea. 263
                                       +e+++ l++++   ++ + ++i+++   +i k + +  + +  +  +h+Y + +i++ ++L++s+ r +++++++  
  gi|386001797|ref|YP_005920096.1|  59 DEIRSDLDYINSNQNIHNENYIISSHRRIIGKFLVEGRRLV--NGEVHRYVDSVISKQIELNSSSARILNRLVARId 133
                                       56677788888888889999999999999999999997755..567**************************99887 PP

                        KAP_NTPase 264 ...veaseettesesrdetlgnsas.................................................... 285
                                          ++++e + + ++  e++g+  s                                                    
  gi|386001797|ref|YP_005920096.1| 134 kntLSNIEIKNNLSRIREDIGQDISrqqheiraeldgqlgqvrsefrdeisrqqheiraeldgqlgqvrfefrdeis 210
                                       78889999999999999999999996666666666666666666666666666666666666666666666666666 PP

                        KAP_NTPase 286 .........................................ksnlqlaldlskillted 303
                                                                                ++ ++ +  l++il+ +d
  gi|386001797|ref|YP_005920096.1| 211 rqqheiraeldgqlgqvrsefrdeisrqqqeiraeldgqlgQVRSEFREELNRILNMLD 269
                                       55555555555555555555555555555555555555555455555555555555555 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.5     0.002       1.4      68     122 ..     147     201 ..     141     204 .. 0.88
   2 ?    8.7   2.0    0.0024       1.7      75     122 ..     206     253 ..     201     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                        ATP-synt_B  68 aeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvval 122
                                       ++i+++  +++++++ ei+ae   ++ +++++ ++eI++++ +++aeL +q +++
  gi|386001797|ref|YP_005920096.1| 147 SRIREDIGQDISRQQHEIRAELDGQLGQVRSEFRDEISRQQHEIRAELDGQLGQV 201
                                       5788888999999999999999999999999999999999999999999988775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                        ATP-synt_B  75 kkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvval 122
                                       ++e+++++ ei+ae   ++ +++++ ++eI++++++++aeL +q +++
  gi|386001797|ref|YP_005920096.1| 206 RDEISRQQHEIRAELDGQLGQVRSEFRDEISRQQQEIRAELDGQLGQV 253
                                       578999***********************************9999887 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4       2.5   1.8e+03      62      62 ..     182     182 ..     115     251 .. 0.58
   2 ?   13.5   0.0   7.6e-05     0.055       7      76 ..     299     363 ..     297     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.5
                   Methyltransf_32  62 e 62 
                                       e
  gi|386001797|ref|YP_005920096.1| 182 E 182
                                       1 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.6e-05
                   Methyltransf_32   7 erlaelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgk 76 
                                       er+++l+++++++ a++    ++++vG G + +s   +     y+++vvg+d   ++v++a k+++ lg 
  gi|386001797|ref|YP_005920096.1| 299 ERFISLIKEIAQK-AANGMVPKLLEVGVGTATMSIYFSR----YSFEVVGLDNDPNVVRNAIKVNKDLGG 363
                                       689999***9999.6888899*********977765555....9***********************994 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  11.4   9.1e-05     0.065     264     388 ..     143     263 ..      94     288 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                         Mitofilin 264 qqelesiipeiitnlkednkklskddlnsliahAkteidqlskelaelkkeeekkieralekqkeelekqeealsar 340
                                       ++ l +i  +i + ++ ++ ++  ++l++ + +   e    ++e+++++ e +++++ +l +++ e+++  +++  +
  gi|386001797|ref|YP_005920096.1| 143 KNNLSRIREDIGQDISRQQHEI-RAELDGQLGQVRSE---FRDEISRQQHEIRAELDGQLGQVRFEFRDEISRQQHE 215
                                       4444444444444444444422.33344444433332...3455555555555555555555555555555555555 PP

                         Mitofilin 341 leeerakeerqlrlelereleeireeyeekLrteLerqaeaheehLkd 388
                                       + +e++ +  q+r e+  e+ ++++e + +L+ +L + +++  e L+ 
  gi|386001797|ref|YP_005920096.1| 216 IRAELDGQLGQVRSEFRDEISRQQQEIRAELDGQLGQVRSEFREELNR 263
                                       555555555556666666666666666666666655555555555543 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.13       5      58 ..     305     360 ..     301     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                       HHHHHHHS-SS...EEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE-- CS
                           UPF0146   5 akkiaeenarg...kvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrD 58 
                                       +k ia+++a+g   k+ EvG+G+ + ++ +++++++++v  D +++ +++ +++ +D
  gi|386001797|ref|YP_005920096.1| 305 IKEIAQKAANGmvpKLLEVGVGTAT-MSIYFSRYSFEVVGLDNDPNVVRNAIKVNKD 360
                                       5556655555544699******875.799*************999988888888776 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.075        54      55     107 ..     157     209 ..     117     218 .. 0.59
   2 ?    9.0   0.5    0.0018       1.3      50     100 ..     215     269 ..     206     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.075
                            Phasin  55 aeekleevresvkskveevkekaeeqwdklekafdervakaLsrlgvpsredv 107
                                       +  + +e+r +++ ++++v+++  ++ ++ ++ +   +   L ++    r+++
  gi|386001797|ref|YP_005920096.1| 157 ISRQQHEIRAELDGQLGQVRSEFRDEISRQQHEIRAELDGQLGQVRFEFRDEI 209
                                       34444445555555555555555555555555555555555554444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                            Phasin  50 ktkkvaeekleevr....esvkskveevkekaeeqwdklekafdervakaLsrlg 100
                                       + +++ + +l +vr    ++++ + +e+++++++q+ ++ + f e ++++L+ l+
  gi|386001797|ref|YP_005920096.1| 215 EIRAELDGQLGQVRsefrDEISRQQQEIRAELDGQLGQVRSEFREELNRILNMLD 269
                                       5556666666666655558888888888888889999999999999999988876 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8     0.096        69      14      48 ..     157     191 ..     154     226 .. 0.70
   2 ?    5.9   0.4     0.015        11      13      49 ..     208     244 ..     202     263 .. 0.81
   3 ?    9.0   0.2    0.0017       1.2      13      65 ..     234     286 ..     229     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.096
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH CS
                      Phage_Mu_Gam  14 lkreleeieaeaneeiaaikekleaeleplkkeie 48 
                                       ++r++ ei ae++ +  +++ ++ +e+++ + ei 
  gi|386001797|ref|YP_005920096.1| 157 ISRQQHEIRAELDGQLGQVRSEFRDEISRQQHEIR 191
                                       66777777777777777777777777777766664 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                      Phage_Mu_Gam  13 elkreleeieaeaneeiaaikekleaeleplkkeiey 49 
                                       e++r++ ei ae++ +  +++ ++ +e+++ ++ei +
  gi|386001797|ref|YP_005920096.1| 208 EISRQQHEIRAELDGQLGQVRSEFRDEISRQQQEIRA 244
                                       8899999999999999999999999999999999864 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHHH CS
                      Phage_Mu_Gam  13 elkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeankdeL 65 
                                       e++r+++ei ae++ +  +++ ++ +el+++ +  +   s l ++ +   +e+
  gi|386001797|ref|YP_005920096.1| 234 EISRQQQEIRAELDGQLGQVRSEFREELNRILNMLDSKDSSLSAWSKFYNNEI 286
                                       899**********************************9999999987666555 PP

>> T2SSN  Type II secretion system (T2SS), protein N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.48   3.4e+02     138     181 ..     151     193 ..     134     202 .. 0.72
   2 ?    9.6   0.1    0.0013      0.96     128     204 ..     190     273 ..     182     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                             T2SSN 138 gdlraelsceggqltltlsdqsgpLslegqgslnaagtyrvagt 181
                                        d+  ++s ++ +++++l++q g++++e++ ++++++ ++++++
  gi|386001797|ref|YP_005920096.1| 151 EDIGQDISRQQHEIRAELDGQLGQVRSEFRDEISRQQ-HEIRAE 193
                                       5667788999999999999888999999999988887.566554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                             T2SSN 128 v.sslsgslplgd..lraelsceggqltltlsdqsgpLslegqgslnaagt.yrvag..t.lkptaeappaLaqaLs 197
                                       + ++l g+l      +r e+s ++ +++++l++q g++++e++ +++++++  r++   +  + ++e++++L + L+
  gi|386001797|ref|YP_005920096.1| 190 IrAELDGQLGQVRfeFRDEISRQQHEIRAELDGQLGQVRSEFRDEISRQQQeIRAELdgQlGQVRSEFREELNRILN 266
                                       54555554443334456666666*********999************9998655444435678999*********** PP

                             T2SSN 198 llGrpda 204
                                       +l  +d+
  gi|386001797|ref|YP_005920096.1| 267 MLDSKDS 273
                                       9987776 PP

>> DUF3658  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.92   6.6e+02      43      74 ..     104     135 ..      92     155 .. 0.62
   2 ?    3.9   0.1     0.069        50      20      49 ..     154     183 ..     139     189 .. 0.86
   3 ?    3.7   0.1     0.076        55      22      49 ..     182     209 ..     170     214 .. 0.86
   4 ?    3.2   0.2      0.11        81      22      49 ..     208     235 ..     204     250 .. 0.89
   5 ?   -0.4   0.0       1.5     1e+03      22      44 ..     234     256 ..     223     261 .. 0.82
   6 ?    1.4   0.0       0.4   2.8e+02      42      68 ..     392     418 ..     388     423 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.92
                           DUF3658  43 edyfDdlileaakkewqkaarligevlghld.q 74 
                                       + y+D++i ++++ +  ++ar+ +++++++d +
  gi|386001797|ref|YP_005920096.1| 104 HRYVDSVISKQIELN-SSSARILNRLVARIDkN 135
                                       468999999999877.45555555555555533 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.069
                           DUF3658  20 WqelkrenaeLRiwkdgklvsveedyfDdl 49 
                                        q+++r+++e+R+  dg+l +v+ ++ D++
  gi|386001797|ref|YP_005920096.1| 154 GQDISRQQHEIRAELDGQLGQVRSEFRDEI 183
                                       57899********************99986 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.076
                           DUF3658  22 elkrenaeLRiwkdgklvsveedyfDdl 49 
                                       e++r+++e+R+  dg+l +v+ ++ D++
  gi|386001797|ref|YP_005920096.1| 182 EISRQQHEIRAELDGQLGQVRFEFRDEI 209
                                       689********************99986 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.11
                           DUF3658  22 elkrenaeLRiwkdgklvsveedyfDdl 49 
                                       e++r+++e+R+  dg+l +v+ ++ D++
  gi|386001797|ref|YP_005920096.1| 208 EISRQQHEIRAELDGQLGQVRSEFRDEI 235
                                       6899******************999986 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.5
                           DUF3658  22 elkrenaeLRiwkdgklvsveed 44 
                                       e++r+++e+R+  dg+l +v+ +
  gi|386001797|ref|YP_005920096.1| 234 EISRQQQEIRAELDGQLGQVRSE 256
                                       68999***********9998765 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.4
                           DUF3658  42 eedyfDdlileaakkewqkaarligev 68 
                                        e++ D+ i+e+++k+ + a+ +i +v
  gi|386001797|ref|YP_005920096.1| 392 MEHFNDAEIIEMISKQLEAAKFVIFSV 418
                                       68899***********99999999887 PP

>> Nbl1_Borealin_N  Nbl1 / Borealin N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.17   1.2e+02      11      41 ..     155     185 ..     146     191 .. 0.85
   2 ?    1.9   1.0      0.25   1.8e+02       8      41 ..     178     211 ..     171     217 .. 0.88
   3 ?    4.9   0.3     0.029        20       9      41 ..     205     237 ..     203     237 .. 0.91
   4 ?    8.6   0.7     0.002       1.4       8      42 ..     230     264 ..     229     264 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                   Nbl1_Borealin_N  11 lEveeRirrlraelelllktlrnrfelellr 41 
                                       + +  + +++rael+ +l ++r++f+ e+ r
  gi|386001797|ref|YP_005920096.1| 155 QDISRQQHEIRAELDGQLGQVRSEFRDEISR 185
                                       55677889*****************988876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.25
                   Nbl1_Borealin_N   8 nfdlEveeRirrlraelelllktlrnrfelellr 41 
                                       +f  E+  + +++rael+ +l ++r +f+ e+ r
  gi|386001797|ref|YP_005920096.1| 178 EFRDEISRQQHEIRAELDGQLGQVRFEFRDEISR 211
                                       68899**************999999888877765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.029
                   Nbl1_Borealin_N   9 fdlEveeRirrlraelelllktlrnrfelellr 41 
                                       f  E+  + +++rael+ +l ++r++f+ e+ r
  gi|386001797|ref|YP_005920096.1| 205 FRDEISRQQHEIRAELDGQLGQVRSEFRDEISR 237
                                       788999*********************988876 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.002
                   Nbl1_Borealin_N   8 nfdlEveeRirrlraelelllktlrnrfelellri 42 
                                       +f  E+  + +++rael+ +l ++r++f+ el+ri
  gi|386001797|ref|YP_005920096.1| 230 EFRDEISRQQQEIRAELDGQLGQVRSEFREELNRI 264
                                       58899*****************************8 PP

>> DUF1682  Protein of unknown function (DUF1682)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.2     0.016        12     245     285 ..     132     169 ..     105     195 .. 0.64
   2 ?    4.8   3.2     0.019        13     237     304 ..     198     268 ..     182     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                           DUF1682 245 iDklakraklrpevlkklkktReevekklkkeaeeekaEea 285
                                       iDk +     + e++++l + Re++ +++ ++++e +aE  
  gi|386001797|ref|YP_005920096.1| 132 IDKNT---LSNIEIKNNLSRIREDIGQDISRQQHEIRAELD 169
                                       33333...334589999999999999999999999999833 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                           DUF1682 237 llklvlrliDkla.kraklrpevlkklkktReevekklkkeaeeekaEeaq..ekkeeekkkereeklakl 304
                                       l ++ +++ D ++ ++ ++r+e   +l + R+e+ +++ ++++e +aE      + + e ++e +++l+ l
  gi|386001797|ref|YP_005920096.1| 198 LGQVRFEFRDEISrQQHEIRAELDGQLGQVRSEFRDEISRQQQEIRAELDGqlGQVRSEFREELNRILNML 268
                                       567778999999998899*****************************954411235555556656656555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   9.4     0.014       9.9     104     174 ..     179     253 ..      41     294 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                           DUF4407 104 FekeIdaelaeeqqeeakelkeqlaaaltaelaeleaqia.....alqaeidaaearldalraeaqkeldgtkgtg 174
                                       F++eI ++ +e+++e   +l  q++ ++++e+++ + +i+     +l +  ++ +++++++++e ++eldg+ g+ 
  gi|386001797|ref|YP_005920096.1| 179 FRDEISRQQHEIRAELDGQL-GQVRFEFRDEISRQQHEIRaeldgQLGQVRSEFRDEISRQQQEIRAELDGQLGQV 253
                                       33344444444444333333.3333334444444444444433333333334444444444444444444433322 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.43   3.1e+02     684     741 ..      51     113 ..      14     120 .. 0.68
   2 ?    0.7   0.5      0.14        99     349     398 ..     140     187 ..     104     201 .. 0.49
   3 ?    9.1   0.5   0.00039      0.28     657     743 ..     223     310 ..     198     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.43
                          Prominin 684 deensdlqesikkllaaver.....aenflkkngseiinneskklldrileqfeeYidwviee 741
                                       ++e+++l+++i+  l+ +++      en++  +  +ii +   +  + +++ +++Y+d vi++
  gi|386001797|ref|YP_005920096.1|  51 SSEAQSLEDEIRSDLDYINSnqnihNENYIISSHRRIIGKFLVEGRRLVNGEVHRYVDSVISK 113
                                       235555555555555555441111156778888888888888888888999999999888865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                          Prominin 349 ipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlente 398
                                       i   +kn+++++ +d+ +++++++++i+ +      ++ +++ +++++ +
  gi|386001797|ref|YP_005920096.1| 140 I--EIKNNLSRIREDIGQDISRQQHEIRAELDGQLGQVRSEFRDEISRQQ 187
                                       2..24444444444444444444444443332222333333333333333 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00039
                          Prominin 657 dlraiqqelvlplessvkklkksvk.kldeensdlqesikkllaaveraenflkkngseiinneskklldrileqfe 732
                                       +l ++ +e+ ++++++ ++++ ++  +l +  s+++e+++++l+ +++ +  l ++ + + n+ ++ ll+    + e
  gi|386001797|ref|YP_005920096.1| 223 QLGQVRSEFRDEISRQQQEIRAELDgQLGQVRSEFREELNRILNMLDSKDSSLSAWSKFYNNEITEDLLTLNIDYHE 299
                                       455666777777777777887777536888999******************************************** PP

                          Prominin 733 eYidwvieevt 743
                                       ++i+ ++e ++
  gi|386001797|ref|YP_005920096.1| 300 RFISLIKEIAQ 310
                                       ****9987655 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7     0.011       7.8      14      74 ..     165     222 ..     152     225 .. 0.85
   2 ?    6.3   2.1     0.017        12      15      75 ..     192     249 ..     189     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  14 EaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeara 74 
                                        aeLd +l + r e + e+++ + e   i +e + ++ ++  e+++e++++ ++ir+e + 
  gi|386001797|ref|YP_005920096.1| 165 RAELDGQLGQVRSEFRDEISRQQHE---IRAELDGQLGQVRFEFRDEISRQQHEIRAELDG 222
                                       5799999999999999999998876...888999999999999999999999999999765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  15 aeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireearar 75 
                                       aeLd +l + r e + e+++ + e   i +e + ++ ++ +e+++e++++ ++ir+e + +
  gi|386001797|ref|YP_005920096.1| 192 AELDGQLGQVRFEFRDEISRQQHE---IRAELDGQLGQVRSEFRDEISRQQQEIRAELDGQ 249
                                       688899999999999999987766...8889999999999999999999999999998765 PP

>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.4   9.7e+02       7      17 ..     156     166 ..     152     166 .. 0.92
   2 ?    4.6   0.4     0.056        40       4      17 ..     179     192 ..     177     193 .. 0.90
   3 ?    3.8   0.6     0.098        70       4      17 ..     205     218 ..     204     219 .. 0.92
   4 ?    7.6   0.4    0.0066       4.7       4      17 ..     231     244 ..     229     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                         Halo_GVPC   7 aIaafreefda 17 
                                       +I++++ e++a
  gi|386001797|ref|YP_005920096.1| 156 DISRQQHEIRA 166
                                       9********97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                         Halo_GVPC   4 LlaaIaafreefda 17 
                                       ++++I++++ e++a
  gi|386001797|ref|YP_005920096.1| 179 FRDEISRQQHEIRA 192
                                       79**********97 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.098
                         Halo_GVPC   4 LlaaIaafreefda 17 
                                       ++++I++++ e++a
  gi|386001797|ref|YP_005920096.1| 205 FRDEISRQQHEIRA 218
                                       69**********97 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0066
                         Halo_GVPC   4 LlaaIaafreefda 17 
                                       ++++I+++++e++a
  gi|386001797|ref|YP_005920096.1| 231 FRDEISRQQQEIRA 244
                                       79**********97 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.025        18      12      56 ..     144     188 ..     138     195 .. 0.79
   2 ?    2.1   0.3      0.42     3e+02      22      55 ..     180     213 ..     174     222 .. 0.66
   3 ?    4.4   1.1     0.079        57      23      59 ..     207     243 ..     186     254 .. 0.74
   4 ?    4.7   0.3     0.063        45      13      49 ..     223     259 ..     213     269 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                            DUF883  12 adleellkeaadeageeaeelRerleerlerarerlrdaeeavae 56 
                                       ++l  + ++ +++  ++ +e+R++l+ +l ++r+++rd   + ++
  gi|386001797|ref|YP_005920096.1| 144 NNLSRIREDIGQDISRQQHEIRAELDGQLGQVRSEFRDEISRQQH 188
                                       6677777888888999999***************99986655544 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.42
                            DUF883  22 adeageeaeelRerleerlerarerlrdaeeava 55 
                                        de  ++ +e+R++l+ +l ++r ++rd   + +
  gi|386001797|ref|YP_005920096.1| 180 RDEISRQQHEIRAELDGQLGQVRFEFRDEISRQQ 213
                                       4555667788888888888888877776544444 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.079
                            DUF883  23 deageeaeelRerleerlerarerlrdaeeavaerak 59 
                                       de  ++ +e+R++l+ +l ++r+++rd   + +++++
  gi|386001797|ref|YP_005920096.1| 207 DEISRQQHEIRAELDGQLGQVRSEFRDEISRQQQEIR 243
                                       5556777889999999999999888876665555554 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.063
                            DUF883  13 dleellkeaadeageeaeelRerleerlerarerlrd 49 
                                       +l ++ +e  de  ++ +e+R++l+ +l ++r+++r+
  gi|386001797|ref|YP_005920096.1| 223 QLGQVRSEFRDEISRQQQEIRAELDGQLGQVRSEFRE 259
                                       4445555666666777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 3162.20
//
Query:       gi|386001798|ref|YP_005920097.1|  [L=804]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-40  137.5   0.2    8.3e-27   93.8   0.0    2.3  2  Glycos_transf_1  Glycosyl transferases group 1
    7.2e-33  113.9   0.0    5.5e-19   68.9   0.0    2.5  2  Glyco_trans_1_4  Glycosyl transferases group 1
    6.5e-08   32.9   0.0    0.00015   22.1   0.0    2.5  2  Glyco_trans_1_2  Glycosyl transferases group 1
    1.1e-06   28.7   0.0    7.6e-06   26.0   0.0    2.1  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0021   16.8   0.2      0.029   13.0   0.0    2.3  2  Glyco_transf_20  Glycosyltransferase family 20
     0.0022   16.9   0.0     0.0038   16.1   0.0    1.3  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase


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 !   93.8   0.0   2.8e-30   8.3e-27      14     166 ..     203     352 ..     193     358 .. 0.93
   2 !   41.7   0.1   2.9e-14   8.6e-11      10     171 ..     606     773 ..     597     774 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.8e-30
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTT.CGGGEEECCHSSSHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelels.dnviflgevsredle 87 
                                       k++++ s   l+ +K+++ + kaf ++    + ++ lv++     eee +l++   +lel  +++i++ +v+++dl+
  gi|386001798|ref|YP_005920097.1| 203 KDRFVMSTVGLDFRKNISGIFKAFTKI----HYDLSLVVVCklMPEEERSLRDIWSNLELPpNKLILTNYVPVDDLI 275
                                       78999999999**************97....99*******99999999**********9963789************ PP

                                       HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
                   Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                       +l+ +a +f++ps +EgfG+++lEAm+ g+pvi+sn++ ++ev +++   + v+p++++++a+ai+ +l++++l  +
  gi|386001798|ref|YP_005920097.1| 276 TLYDAAEVFLFPSLYEGFGLPVLEAMSRGCPVITSNISSIPEVCENAA--IYVDPYKPDEIAKAIELILNKNKLKTK 350
                                       ************************************************..**********************99887 PP

                                       HH CS
                   Glycos_transf_1 165 lg 166
                                       l+
  gi|386001798|ref|YP_005920097.1| 351 LI 352
                                       75 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 2.9e-14
                                       TTTTT-EEEEE.ESS-TTTTTHHHHHHHHHCCCCC.HCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1  10 gknekkkiils.vgrlekeKgvdllikafallkkq.lnpnvklviaG..ngeeekelkklaeelelsdnviflgevs 82 
                                       ++n  +k+i+s  gr+  +K++++l+ a+ +l k+ +   ++l ++G    + + +++  +   +l+d v+++g+v+
  gi|386001798|ref|YP_005920097.1| 606 KFNLIDKVIISaFGRIIFTKRIHVLLYAISRLIKDkKIYGIHLYLVGelYDNVKSQIETIINDENLGDFVTITGYVD 682
                                       5555555555427****************987544499*********99889999********************** PP

                                       SSSHHHHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHH CS
                   Glycos_transf_1  83 redleellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklle 157
                                       +e+  ++lk+ di v   +        +l+  + +g+pvi++n+  ++e+  +   ++    +++e l+e++ +l++
  gi|386001798|ref|YP_005920097.1| 683 EEEFNKYLKITDICVNLRYPssGETSATLIKTLRYGIPVITTNYAQYKEYPDNCCWKVDLGDYEVELLSEYLLELVT 759
                                       ************9997755488778899**********************9999966666666************** PP

                                       SHHHHHHHHHHHHH CS
                   Glycos_transf_1 158 deelrerlgenark 171
                                       +ee r+ +++na++
  gi|386001798|ref|YP_005920097.1| 760 NEEARKIMSKNAYE 773
                                       ************86 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 !   68.9   0.0   1.8e-22   5.5e-19      14     133 ..     216     343 ..     205     344 .. 0.84
   2 !   42.5   0.0   2.6e-14   7.9e-11       4     132 ..     615     758 ..     612     760 .. 0.75

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.8e-22
                                       .GTHHHHHHHHHHHH.HHEEEEEES---....HHHHHHHTT-T...T.EEEE---..THHHHHHHH-SEEEE--..- CS
                   Glyco_trans_1_4  14 vkgvdllleavpllrkkdvrlvivGdgp..rpeeleelaagle..er.veftGfv..edlaellaaadvfvaPs..e 81 
                                       +k++  + +a+ +++  d+ lv+v +    ++++l++  ++le  ++  ++t +v  +dl  l++aa vf++Ps  e
  gi|386001798|ref|YP_005920097.1| 216 RKNISGIFKAFTKIH-YDLSLVVVCKLMpeEERSLRDIWSNLElpPNkLILTNYVpvDDLITLYDAAEVFLFPSlyE 291
                                       488899999999999.5599*****64224346777655444444555*******9999****************** PP

                                       --SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  82 gfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLle 133
                                       gfgl +lEam+ g+pv++++++ i+ev++++++ v+p +p+++a+ai+ +l+
  gi|386001798|ref|YP_005920097.1| 292 GFGLPVLEAMSRGCPVITSNISSIPEVCENAAIYVDPYKPDEIAKAIELILN 343
                                       **************************999999***************98876 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 2.6e-14
                                       EEEES---GG.GTHHHHHHHH.HHHH.HH...EEEEEES---....HHHHHHHT..T-T.TEEEE---..THHHHHH CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleav.pllrkkd...vrlvivGdgp..rpeeleelaa..gleerveftGfv..edlaell 70 
                                       i  +Gr+    k++++ll a+  l+++k+   ++l++vG+     ++++e  ++  +l + v++tG+v  e+ +++l
  gi|386001798|ref|YP_005920097.1| 615 ISAFGRIIFT-KRIHVLLYAIsRLIKDKKiygIHLYLVGELYdnVKSQIETIINdeNLGDFVTITGYVdeEEFNKYL 690
                                       6678898545.**********66666555679*******5322223577776667889899*******8667***** PP

                                       HH-SEEEE...--.---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-..HHHHHHHHHHHH CS
                   Glyco_trans_1_4  71 aaadvfva...Ps.egfglkllEamaaglpvVatdvggiaevvgengllvppgd..pealaeailrLl 132
                                       +  d++v+   Ps   ++ +l+  + +g+pv++t+ +  +e+  +  + v+ gd  +e l e +l+L+
  gi|386001798|ref|YP_005920097.1| 691 KITDICVNlryPSsGETSATLIKTLRYGIPVITTNYAQYKEYPDNCCWKVDLGDyeVELLSEYLLELV 758
                                       ********777775469******************977777554445666666655666666666665 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 !   22.1   0.0   5.1e-08   0.00015       1      67 [.     283     349 ..     283     373 .. 0.85
   2 !    8.3   0.0     0.001         3      48      91 ..     746     789 ..     706     790 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.1e-08
                   Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerr 67 
                                       ++L+ps +e++ l ++Ea+  G++++t+ +++++e  ++   +i+++   ++e+a++i+  l+  ++  
  gi|386001798|ref|YP_005920097.1| 283 VFLFPSLYEGFGLPVLEAMSRGCPVITSNISSIPEVCEN--AAIYVDpyKPDEIAKAIELILNKNKLKT 349
                                       589*********************************965..59999999*********99998777655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.001
                   Glyco_trans_1_2  48 dleelaekiryllanpeerraiaeaarervlaehtydhraeqll 91 
                                       ++e l e + +l++n+e r+ ++++a+e ++++ ++d+ + q+l
  gi|386001798|ref|YP_005920097.1| 746 EVELLSEYLLELVTNEEARKIMSKNAYEYARENNSMDRVVGQYL 789
                                       45666777788889*************************99988 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.6e-09   7.6e-06     118     168 ..     129     181 ..     110     183 .. 0.86
   2 ?   -0.5   0.0      0.36   1.1e+03      88     107 ..     711     729 ..     697     751 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.6e-09
                    Glyco_transf_4 118 plsrllralerrl..lrradrviavSeatadelrerygvppekitVipnGvDl 168
                                        l+ ++ ++ rrl  ++  d + a+Se+t+++l++++ +p+eki+Vi+ G D 
  gi|386001798|ref|YP_005920097.1| 129 VLEEFRIEYIRRLsfIKEFDMIYAISETTKRDLMDLLEIPEEKIRVIYAGLDK 181
                                       5566677777777789**********************************995 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.36
                    Glyco_transf_4  88 llalrrrlgiplVltvHgly 107
                                       l++ + r+gip+++t    y
  gi|386001798|ref|YP_005920097.1| 711 LIKTL-RYGIPVITTNYAQY 729
                                       33444.5********87777 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.042   1.3e+02     257     300 ..     185     228 ..     151     232 .. 0.86
   2 !   13.0   0.0   9.9e-06     0.029     357     444 ..     265     348 ..     251     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.042
                                       CSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHH CS
                   Glyco_transf_20 257 kkesvsekvkelkerfenkkklilgvDrlDyikGvkqkllafer 300
                                        ++s  ekv  +k++++ k + ++++  lD  k+++  ++af +
  gi|386001798|ref|YP_005920097.1| 185 ISQSSTEKVLDIKHKYRIKDRFVMSTVGLDFRKNISGIFKAFTK 228
                                       3456689999*******999*********************986 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.9e-06
                                       EES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT-TTTSEEE-TT-HHHHHHH CS
                   Glyco_transf_20 357 lersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsLkdaailvNPwdieevaea 433
                                       l++ ++ ++li l+ aa+v+l  sl +G  l  +e +     +  ++i S+ +   ++ ++aai v P+  +e+a+a
  gi|386001798|ref|YP_005920097.1| 265 LTNYVPVDDLITLYDAAEVFLFPSLYEGFGLPVLEAM----SRGCPVITSNISSIPEVCENAAIYVDPYKPDEIAKA 337
                                       4667999************************999965....46799******************************* PP

                                       HHHHHC--HHH CS
                   Glyco_transf_20 434 ikeaLkmseee 444
                                       i+  L+ ++ +
  gi|386001798|ref|YP_005920097.1| 338 IELILNKNKLK 348
                                       *9888876655 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0038     179     323 ..     202     347 ..     134     361 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                                       -SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHHHHHHHH-T....TEEEE----HH CS
                       Epimerase_2 179 kekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrlleeleele....nvtlieplgyl 251
                                        ++++v+ t+      d  +++  i++a+++++ +  + +vv++ + p+ ++ l++++++le    +++l++ + + 
  gi|386001798|ref|YP_005920097.1| 202 IKDRFVMSTVG----LDFRKNISGIFKAFTKIHYD--LSLVVVCKLMPEEERSLRDIWSNLElppnKLILTNYVPVD 272
                                       55555555542....22244577788888888776..8888888888******9888888866788*********** PP

                                       HHHHHHHC-SEEEES-...H.H..HHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT-..- CS
                       Epimerase_2 252 dflsllknaklvltdS...g.G..iqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklledkke 322
                                       d++ l  +a++ l  S   g G  +  Ea+s g pv++  +  + pe  e+++ ++ +++++eI +a+e +l++ ++
  gi|386001798|ref|YP_005920097.1| 273 DLITLYDAAEVFLFPSlyeGfGlpVL-EAMSRGCPVITS-NISSIPEVCENAAIYVDPYKPDEIAKAIELILNK-NK 346
                                       **************998885552266.**********99.8899****************************87.44 PP

                                       - CS
                       Epimerase_2 323 l 323
                                       l
  gi|386001798|ref|YP_005920097.1| 347 L 347
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (804 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 5058.70
//
Query:       gi|386001799|ref|YP_005920098.1|  [L=45]
Description: hypothetical protein Mhar_1107 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-07   30.3   3.5    4.3e-07   30.2   3.5    1.0  1  EamA            EamA-like transporter family
     0.0068   15.5   0.8     0.0068   15.5   0.8    1.0  1  Mg_trans_NIPA   Magnesium transporter NIPA
     0.0069   16.4   0.4     0.0077   16.3   0.4    1.0  1  TMEM234         Putative transmembrane family 234
  ------ inclusion threshold ------
      0.016   14.4   1.3      0.016   14.4   1.3    1.0  1  Nuc_sug_transp  Nucleotide-sugar transporter
       0.18   12.3   2.1       0.22   12.0   2.1    1.1  1  DUF202          Domain of unknown function (DUF202)


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 !   30.2   3.5   1.2e-10   4.3e-07      97     136 ..       4      43 ..       2      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.2e-10
                              EamA  97 itslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++sl+ ++t++l++++lge+++ + + gi+l++lG++li+
  gi|386001799|ref|YP_005920098.1|   4 MLSLAYILTALLAFYFLGEQISTLRWSGIILVVLGCILIM 43 
                                       678999********************************96 PP

>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.8   1.9e-06    0.0068      80     120 ..       3      43 ..       1      45 [] 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-06
                     Mg_trans_NIPA  80 PLGalsvivsavlasllLkekLkllgllGcllailGstvlv 120
                                       P+ +l+ i++a+la ++L e++ +l   G++l +lG ++++
  gi|386001799|ref|YP_005920098.1|   3 PMLSLAYILTALLAFYFLGEQISTLRWSGIILVVLGCILIM 43 
                                       7778999*****************************99886 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   2.2e-06    0.0077      79     115 ..       6      42 ..       3      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                           TMEM234  79 slafvfTvlte.lllgekvlkkktvlgmllvvvgialc 115
                                       sla+++T+l + ++lge ++++ ++ g++lvv+g +l+
  gi|386001799|ref|YP_005920098.1|   6 SLAYILTALLAfYFLGE-QISTLRWSGIILVVLGCILI 42 
                                       89********9555555.567789***********998 PP

>> Nuc_sug_transp  Nucleotide-sugar transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   4.6e-06     0.016     121     153 ..      10      42 ..       4      45 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                    Nuc_sug_transp 121 lttalfsvllLkrklskkqWlslllLvaGvalv 153
                                       + tal++  +L+ ++s+ +W  ++l+v+G +l+
  gi|386001799|ref|YP_005920098.1|  10 ILTALLAFYFLGEQISTLRWSGIILVVLGCILI 42 
                                       679**************************9887 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   6.2e-05      0.22      17      55 ..       6      42 ..       4      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.2e-05
                            DUF202 17 slalialglallrffltgepsalgkilglilivlgiltl 55
                                      sla i ++l+ + f   ge+ ++ ++ g+il+vlg++++
  gi|386001799|ref|YP_005920098.1|  6 SLAYILTALLAFYF--LGEQISTLRWSGIILVVLGCILI 42
                                      78888888888888..77777777***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 348.02
//
Query:       gi|386001800|ref|YP_005920099.1|  [L=246]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-22   79.0   0.0    5.4e-22   78.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    6.4e-18   65.3   0.0    1.3e-17   64.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    7.2e-16   58.5   0.0    1.2e-15   57.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    9.1e-15   54.8   0.0    1.3e-14   54.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    4.9e-12   46.4   0.0    9.5e-12   45.5   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    8.4e-10   38.4   0.0    1.2e-09   37.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-07   32.0   0.0    2.4e-07   30.8   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
    0.00031   19.4   0.0    0.00058   18.5   0.0    1.5  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
     0.0021   17.2   0.0     0.0028   16.8   0.0    1.2  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.023   14.0   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
      0.015   14.9   0.0      0.021   14.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.044   13.4   0.0      0.058   13.0   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.049   13.2   0.0      0.084   12.4   0.0    1.5  1  MTS              Methyltransferase small domain
       0.07   12.3   0.0       0.11   11.7   0.0    1.3  1  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
      0.085   12.8   0.0       0.12   12.3   0.0    1.3  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   4.5e-25   5.4e-22       1      96 []      45     134 ..      45     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 4.5e-25
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvGcGtG++++ +++ g +v g+D+s+e+lk +k +++++      ++++a +lp++d+++D+v++  vl+h+ed 
  gi|386001800|ref|YP_005920099.1|  45 LDVGCGTGLNSKSFERFG-HVSGLDMSEEALKFCKLRGRTDL-----IRGSADSLPVKDGTIDIVCALDVLEHIEDD 115
                                       8**************777.*******************9986.....9***************************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                        +a++e+ RvLkpgG+lv+
  gi|386001800|ref|YP_005920099.1| 116 FSAMQELNRVLKPGGFLVL 134
                                       ****************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   1.1e-20   1.3e-17       1      97 []      44     130 ..      44     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.1e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld+GcGtG +++ + + +  ++v g+D+see+l+ ++ r      + ++++g+a++lp +dg++D+v++  +l+h+
  gi|386001800|ref|YP_005920099.1|  44 ILDVGCGTGLNSKSFER-F--GHVSGLDMSEEALKFCKLRG-----RTDLIRGSADSLPVKDGTIDIVCALDVLEHI 112
                                       8**************85.5..7*****************99.....89**********************888***9 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +d d   a++e+ rvLkpgG
  gi|386001800|ref|YP_005920099.1| 113 ED-D-FSAMQELNRVLKPGG 130
                                       84.4.479***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   9.7e-19   1.2e-15       6     125 ..      23     151 ..      18     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 9.7e-19
                   Methyltransf_23   6 eeelsdklerllpk.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaep 79 
                                       +e + d + r+ p   +a  r+Ld+GcGtG ++++++++g +v g D+s+ea +  +  ++   +  ++  ++ +++
  gi|386001800|ref|YP_005920099.1|  23 RELITDMIRRVHPAsSKAALRILDVGCGTGLNSKSFERFG-HVSGLDMSEEALKFCKlrGRTDLIRGSA--DSLPVK 96 
                                       45556666666655368888****************6665.799*****98777655664444444444..578889 PP

                   Methyltransf_23  80 qgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl.........k 125
                                       +g++d++++ +vleh++d  ++++ +++ lkpgG l+l++p+            +
  gi|386001800|ref|YP_005920099.1|  97 DGTIDIVCALDVLEHIEDDFSAMQELNRVLKPGGFLVLTVPAFMFlwsshdevlH 151
                                       9***************************************953323332233331 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.1e-17   1.3e-14       2     126 ..      39     154 ..      38     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.1e-17
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       + +lr+lD+GCGtG  ++ +  +    ++v G+D+seea+++++ +       +  + +g++ +l+  ++d ++D++
  gi|386001800|ref|YP_005920099.1|  39 KAALRILDVGCGTGLNSKSFE-RF---GHVSGLDMSEEALKFCKLR------GRTDLIRGSADSLP--VKDGTIDIV 103
                                       6789*********97777776.65...68****************8......4567889*******..9******** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr...llaelpakveees 126
                                       ++ +vl ++ d  ++++e+ rvlkpgg l+++ p    l++  ++ +++++
  gi|386001800|ref|YP_005920099.1| 104 CALDVLEHIEDDFSAMQELNRVLKPGGFLVLTVPAfmfLWSSHDEVLHHKR 154
                                       *******************************99997774444444333333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   7.9e-15   9.5e-12       1      99 []      45     132 ..      45     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 7.9e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcGtG +++ +++     ++ g+D s++a+     k+ k ++ +++ ++  a++l  +dg  + D+v a++vl+
  gi|386001800|ref|YP_005920099.1|  45 LDVGCGTGLNSKSFERF---GHVSGLDMSEEAL-----KFCKLRG-RTDLIRGSADSLPVKDG--TIDIVCALDVLE 110
                                       8*************665...*************.....9999996.66899999999888887..9*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                       h++d  ++++++ ++LkpgG l
  gi|386001800|ref|YP_005920099.1| 111 HIEDDFSAMQELNRVLKPGGFL 132
                                       ********************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   9.7e-13   1.2e-09      44     150 ..      37     133 ..       3     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 9.7e-13
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                       ++k + ++lDv +Gtg      s+s ++ g+v +lD++e+ Lk  + + +       +++ ++a  Lp +d++ D+v
  gi|386001800|ref|YP_005920099.1|  37 SSKAALRILDVGCGTGLN----SKSFERFGHVSGLDMSEEALKFCKLRGR------TDLIRGSADSLPVKDGTIDIV 103
                                       4566679********954....67888999**************988754......589****************** PP

                                       EEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 121 tvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                            l  + D   a++e+ rvlkpGG lv
  gi|386001800|ref|YP_005920099.1| 104 CALDVLEHIEDDFSAMQELNRVLKPGGFLV 133
                                       ***************************886 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0     2e-10   2.4e-07      41     156 ..       3     134 ..       1     145 [. 0.76

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2e-10
                                       HHHHHHHHHHHHCTSSS-HHHHHHHHHC......TS-TTS-EEEES-TT-HHHHH--S-..EEEEESS-SS...... CS
                    Methyltransf_8  41 fdlyhkgfrsqvkkWPenPldviirklk......kkkdnlvvadlGcGeakiaeavrekekvrsfdlvavn...... 105
                                       +dly + f +   +W  +  +++i ++       + k+ l + d+GcG    +++ +++ +v  +d+          
  gi|386001800|ref|YP_005920099.1|   3 LDLYERMFSYEEGNWWYKGRRELITDMIrrvhpaSSKAALRILDVGCGTGLNSKSFERFGHVSGLDMSEEAlkfckl 79 
                                       689*********9*999998888877653666777788999*********999*************97543111111 PP

                                       ...TTEEES-TTS-S--TT-EEEEEEES---S..S-HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 106 ...ervvacdlakvPledesvdvavfclslmg..tnladflkeanrvlkvGGllkv 156
                                           +++      +P++d+++d+ v+ l ++   ++  + ++e nrvlk+GG+l +
  gi|386001800|ref|YP_005920099.1|  80 rgrTDLIRGSADSLPVKDGTIDI-VCALDVLEhiEDDFSAMQELNRVLKPGGFLVL 134
                                       11123344444579********9.57777765124555679***********9865 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.9e-07   0.00058      97     223 ..      21     140 ..       6     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.9e-07
                   Methyltransf_29  97 gadkYidklaelipliaaggkvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtk 173
                                       g ++ i ++ + ++  a+++    +lDvGCg     +  ++r      ++  D  e+ ++f   Rg   ++   ++ 
  gi|386001800|ref|YP_005920099.1|  21 GRRELITDMIRRVHP-ASSKAALRILDVGCGTGL-NSKSFERF---GHVSGLDMSEEALKFCKLRGRTDLIRG-SAD 91 
                                       555555444444443.356666678999999753.33334432...235567999999999999998877765.567 PP

                   Methyltransf_29 174 rlpyPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvlsappvy 223
                                        lp    + d++ C+   +++ e+d   + e++Rvl+pgG++vl+ p   
  gi|386001800|ref|YP_005920099.1|  92 SLPVKDGTIDIV-CALDVLEHIEDDFSAMQELNRVLKPGGFLVLTVPAFM 140
                                       899999999986.9999***************************988765 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.3e-06    0.0028      84     187 ..      30     135 ..      22     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                              DREV  84 iekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrd..rlkkkkynvlsale.lqetdvkldlilc 157
                                       i + +pas +   ++ld+G G G  +k   + f +v   ++se+  +  +l+ +   + +  + l   d  +d++ +
  gi|386001800|ref|YP_005920099.1|  30 IRRVHPASSKAALRILDVGCGTGLNSKSF-ERFGHVSGLDMSEEALKfcKLRGRTDLIRGSADsLPVKDGTIDIVCA 105
                                       6678899*9**************887776.57899***99999887622555555556667777888999******* PP

                              DREV 158 lnlldrcfdplklledirsalepngrviva 187
                                       l++l+   d +  ++++  +l+p g  +++
  gi|386001800|ref|YP_005920099.1| 106 LDVLEHIEDDFSAMQELNRVLKPGGFLVLT 135
                                       ***********************9987765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     2e-05     0.023      64     165 ..      42     135 ..      30     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGT CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehv 140
                                        ++Ld+GcG G l  ++ er++ +v gl +S+e  k +k r     ++ +++         d+ +d v +++++eh+
  gi|386001800|ref|YP_005920099.1|  42 LRILDVGCGTG-LNSKSFERFG-HVSGLDMSEEALKFCKLRGRTDLIRGSAD----SLPVKDGTIDIVCALDVLEHI 112
                                       589******98.5678899987.9************9987754333222222....222224699999999999999 PP

                                       SGGGHHHHHHHHHHHS-TT-EEEEE CS
                              CMAS 141 gkenydtffkklkkllkedGllllh 165
                                         + + + +++l+++lk++G l+l 
  gi|386001800|ref|YP_005920099.1| 113 EDD-FSA-MQELNRVLKPGGFLVLT 135
                                       755.443.68899999999988765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05     0.021      14     122 ..      41     150 ..      26     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakG.lsviqgdldkdlenfedksfdyvvlsqtlqatr 89 
                                         r+ld+GcG G   + +  e+  +  Gl+++ee+++ c  +G   +i+g +d+ l   +d + d+v     l  + 
  gi|386001800|ref|YP_005920099.1|  41 ALRILDVGCGTGLNSKSF--ERFGHVSGLDMSEEALKFCKLRGrTDLIRGSADS-L-PVKDGTIDIVCALDVLEHIE 113
                                       4589********877777..45666789***************44688998886.3.56899******99****999 PP

                              MetW  90 npkevldellri...grraivsfPnfGh.Wrvrlsll 122
                                       +  + ++el r+   g   +++ P f + W    ++l
  gi|386001800|ref|YP_005920099.1| 114 DDFSAMQELNRVlkpGGFLVLTVPAFMFlWSSHDEVL 150
                                       9988888887773335567888888876566655555 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05     0.058      24     103 ..      28     104 ..       2     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--....... CS
                              TPMT  24 pllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkeysageie 100
                                        ++++  + +++ka lr+l  +CG +l+ + +   g +v G+++se A++ f + ++ ++ ++  ++   ++ g+i+
  gi|386001800|ref|YP_005920099.1|  28 DMIRRVHP-ASSKAALRILDVGCGTGLNSKSFERFG-HVSGLDMSEEALK-FCKLRGRTDLIRGSADSLPVKDGTID 101
                                       44444444.4889999***************96555.6**********97.45666666666666666666667777 PP

                                       ... CS
                              TPMT 101 llc 103
                                       ++c
  gi|386001800|ref|YP_005920099.1| 102 IVC 104
                                       766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.1e-05     0.084      31      73 ..      40      79 ..      23     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.1e-05
                                      TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHH CS
                               MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesake 73
                                      ++ ++lD+GcG+G+ + ++ ++    +v  +d + +Al+++k 
  gi|386001800|ref|YP_005920099.1| 40 AALRILDVGCGTGLNSKSFERFG---HVSGLDMSEEALKFCKL 79
                                      4557*********8877776644...37888888899988876 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.9e-05      0.11     163     237 ..     100     175 ..      82     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
                                       EEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEE.ECS-SEEEETTEEEE---B-HHHHHHHHHHTTEEEEEE CS
                    NNMT_PNMT_TEMT 163 vtifcleaacedleeylralrnlasllkpGGhlvlgg.vleeseynvGekkfsllalekeevlealkkaglkveel 237
                                       + i c   + e++e  + a+++l ++lkpGG+lvl++ ++   + +  e   +  + +++++l+ lk +g+++++ 
  gi|386001800|ref|YP_005920099.1| 100 IDIVCALDVLEHIEDDFSAMQELNRVLKPGGFLVLTVpAFMFLWSSHDEVLHHKRRYTRKNLLQNLKISGFTINKS 175
                                       445555555677888899***************9876478888888888888888999999999999999998875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.12      11      68 ..      24      78 ..      22     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                   Methyltransf_32 11 elvakllkel..akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekae 68
                                      el+ ++++++  a++++al+++DvG+G g  s   +        +v g+d++ee  + ++
  gi|386001800|ref|YP_005920099.1| 24 ELITDMIRRVhpASSKAALRILDVGCGTGLNSKSFER-----FGHVSGLDMSEEALKFCK 78
                                      57778888887778999***********966666555.....689******999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1750.81
//
Query:       gi|386001801|ref|YP_005920100.1|  [L=643]
Description: hypothetical protein Mhar_1109 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4124.31
//
Query:       gi|386001802|ref|YP_005920101.1|  [L=224]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-23   82.4   0.1    3.8e-23   82.1   0.1    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    6.3e-08   32.8   0.0    7.9e-08   32.5   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.4e-05   24.0   0.1    3.8e-05   23.3   0.1    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.1   6.4e-27   3.8e-23       1     165 [.       3     161 ..       3     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.4e-27
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s++ip+yNee+ + ++l  l +    p  eiivv Dg  D+t++i+e+l+ ++p++ ++  +e+ Gk+ga+ +g+ra
  gi|386001802|ref|YP_005920101.1|   3 SIIIPAYNEESRITAVLLHLSEE--FPGQEIIVVCDGV-DGTKDIVENLSIKNPNIQILNFKEKLGKGGAIIEGFRA 76 
                                       8*****************99998..*************.************************************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       a+g+ i f+DaD  ++ d ++ + ++  +   d+v+++r+ + ++   +++ kr +  +++++   +   +    + 
  gi|386001802|ref|YP_005920101.1|  77 ANGEKIGFIDADESVNADEFKLMFDFDAE--IDGVIASRRLKTSKILVKQPIKR-RIASKCFNIFVRILFGLPFKDT 150
                                       ********************999887666..77799999999999888888887.5666666666666666666666 PP

                                       STCCCEEEEHH CS
                   Glycos_transf_2 155 igsaallrrea 165
                                        ++a +++rea
  gi|386001802|ref|YP_005920101.1| 151 QCGAKVFKREA 161
                                       66666666666 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 !   32.5   0.0   1.3e-11   7.9e-08       5     121 ..       3     110 ..       1     140 [. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.3e-11
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       ++++p++nee+++++vl +l+  e p  e++vv+d+ d +t + +e l  + p++  +++  +++lg++    a+ e
  gi|386001802|ref|YP_005920101.1|   3 SIIIPAYNEESRITAVLLHLSE-EFPGQEIIVVCDGVD-GTKDIVENLSIKNPNI--QILNFKEKLGKG---GAIIE 72 
                                       79****************9998.79*********9987.5688899988888886..888887777755...5567* PP

                   Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavg 121
                                       ++ra++++ + ++D+D  v  d +k +  f  +++++ v 
  gi|386001802|ref|YP_005920101.1|  73 GFRAANGEKIGFIDADESVNADEFKLMFDF--DAEIDGVI 110
                                       *******************99999986655..56666555 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 !   23.3   0.1   6.4e-09   3.8e-05       1     103 [.       3     100 ..       3     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.4e-09
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddg..Ssekfleevssiidlnllv.ylkdeddkayslaaarN 74 
                                       s++ip +++e r  i   +l+    + +  e+ivv dg   +++++e++ si++ n ++  +k+      +++ a  
  gi|386001802|ref|YP_005920101.1|   3 SIIIPAYNEESR--ITAVLLHLSEEF-PGQEIIVVCDGvdGTKDIVENL-SIKNPNIQIlNFKE----KLGKGGAII 71 
                                       79**********..999997766665.6677777776622466655555.57888888844444....49******* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekil 103
                                        G+  a+++ + F+DaD  +  D+f+ + 
  gi|386001802|ref|YP_005920101.1|  72 EGFRAANGEKIGFIDADESVNADEFKLMF 100
                                       *************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1480.13
//
Query:       gi|386001803|ref|YP_005920102.1|  [L=873]
Description: Peptidase C1A, papain, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-45  154.4   5.5    6.7e-45  153.8   5.5    1.2  1  Peptidase_C1    Papain family cysteine protease
    0.00042   20.7   1.1         12    6.4   0.1    4.3  4  DUF1964         Domain of unknown function (DUF1964)
  ------ inclusion threshold ------
       0.03   13.8   0.0      0.046   13.2   0.0    1.2  1  ABC_transp_aux  ABC-type uncharacterized transport system


Domain annotation for each model (and alignments):
>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8   5.5   1.1e-48   6.7e-45       2     213 ..     140     359 ..     139     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 1.1e-48
                                       TSCEETTTTTTG..SG---B-TSSBTHHHHHHHHHHHHHHHHHHS..SS---B-HHHHHHHSTTTSTGGGBB-HHHH CS
                      Peptidase_C1   2 pesvDwrekgga..vtpvkdqgsCGsCWafsavgaledrlaiktk..kklvslSeqelvdCskeenegCnGGlmena 74 
                                       p+s+Dwr+ gg    tp+++q+ CGsCWaf+  gale+r++i+ +  + + +lSeqe+++Cs     +C+G + +++
  gi|386001803|ref|YP_005920102.1| 140 PNSFDWRNAGGFdwTTPIRNQNPCGSCWAFAVCGALESRMKIAAGnpNLQPDLSEQEILSCSP---GDCSGWYLSST 213
                                       99******7766689****************************987788899*********98...89********* PP

                                       HHHHHHTEBEBTTTS--SSSCS....SS-CGCGGGSE......EBEESEEEEEESSBHHHHHHHHHHHSSEEEEEEC CS
                      Peptidase_C1  75 feyikkggivtekdypYkakeg....gkCkkkkkkek......vakikgygkvkenseealkkalakngPvsvaida 141
                                        +++  +g v+e++ypY a+++    g+C  ++++++      ++ +   g++++   +alk++++  gPv+  +++
  gi|386001803|ref|YP_005920102.1| 214 SDWMLCEGTVDESCYPYLASDTapcrGSCPDRESRRYyitdwcWVGDGPGGTINDAPLDALKEEITCCGPVATYMEV 290
                                       ******************99997777777777666555555433333444445555899****************** PP

                                       CSHHHHTEESSEESSTSCETSS-EEEEEEEEEEEET.TEEEEEEE-SBTTTSTBTTEEEEESSSSTGGGTTSS CS
                      Peptidase_C1 142 seedfqlYksGvyketecsktelnhavlivGygven.gkkyWivkNsWgtdwgekGYiriargknnecgiese 213
                                       ++ df  Y++G+yk+t+  + e  h v+ivG+g +  +  y i+kNsWgt wge+G++ri+ ++     ie+e
  gi|386001803|ref|YP_005920102.1| 291 YS-DFWGYSGGIYKKTTGATFEGGHFVVIVGWGYDAtNGWYLICKNSWGTGWGESGWFRIKWNE---VRIEDE 359
                                       **.6***********97777899***********995667899*****************9774...455555 PP

>> DUF1964  Domain of unknown function (DUF1964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0039        23       6      34 ..     670     698 ..     666     709 .. 0.86
   2 ?    2.9   0.0     0.024   1.5e+02       6      34 ..     716     744 ..     713     747 .. 0.87
   3 !    6.4   0.1    0.0021        12       3      34 ..     759     790 ..     758     795 .. 0.90
   4 ?   -0.2   0.0      0.23   1.4e+03       7      34 ..     809     836 ..     805     847 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0039
                                       EEEEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   6 fsysvdgDtsitfaWkgetssatLtfePk 34 
                                        sy  +gD+ ++ +W+g + +    f P+
  gi|386001803|ref|YP_005920102.1| 670 ISYGLNGDKPLAGDWNGDGKDTIGVFRPS 698
                                       79****************99999999996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.024
                                       EEEEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   6 fsysvdgDtsitfaWkgetssatLtfePk 34 
                                        +y   gD++++ +W+g + +    f P+
  gi|386001803|ref|YP_005920102.1| 716 ITYGLTGDQAVAGDWNGDGKDTIGVFRPS 744
                                       589999************99998889887 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0021
                                       GSEEEEEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   3 DGefsysvdgDtsitfaWkgetssatLtfePk 34 
                                       D + +y  +gD++++ +W+g + +    f P+
  gi|386001803|ref|YP_005920102.1| 759 DATITYGLNGDQAVAGDWNGDGKDTIGVFRPS 790
                                       77899****************99998889887 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.23
                                       EEEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   7 sysvdgDtsitfaWkgetssatLtfePk 34 
                                       +y   gD  +  +W+g++ +    f P+
  gi|386001803|ref|YP_005920102.1| 809 TYGISGDLPVVGDWNGNGKDTIGVFRPS 836
                                       788999999999*****99999999996 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.6e-06     0.046     176     222 ..     400     447 ..     364     450 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-06
                    ABC_transp_aux 176 nYnveevdldsedi..lpedidvlviakptkdlseeelykldqflmnGg 222
                                       +Y v++++ + +++  l + +dv++i +pt+++s +el ++++f+ +G 
  gi|386001803|ref|YP_005920102.1| 400 GYFVQSTTETPVTSnmL-NCYDVVIISNPTNSFSTSELAAIKEFVGRGR 447
                                       67777766665555434.77*************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (873 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 6251.30
//
Query:       gi|386001804|ref|YP_005920103.1|  [L=882]
Description: Integrins alpha chain [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-43  149.4   1.7    2.3e-43  148.8   1.7    1.2  1  Peptidase_C1    Papain family cysteine protease
     0.0054   16.2   0.0     0.0086   15.6   0.0    1.2  1  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
       0.01   16.2   0.3         80    3.8   0.0    4.1  4  DUF1964         Domain of unknown function (DUF1964)
        0.1   12.8   0.0        0.2   11.8   0.0    1.4  1  ThuA            Trehalose utilisation


Domain annotation for each model (and alignments):
>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   1.7   5.2e-47   2.3e-43       1     208 [.     122     333 ..     122     342 .. 0.88

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 5.2e-47
                                       STSCEETTT.TTTG.SG---B-TSSBTHHHHHHHHHHHHHHHHHHS..SS---B-HHHHHHHSTTTSTGGGBB-HHH CS
                      Peptidase_C1   1 lpesvDwre.kgga.vtpvkdqgsCGsCWafsavgaledrlaiktk..kklvslSeqelvdCskeenegCnGGlmen 73 
                                       +p ++Dwr+ +g + +tp+kdqg+CGs Waf+a ga+e+r++++ +  +   +lSeq l++C      +C+ G  + 
  gi|386001804|ref|YP_005920103.1| 122 VPGEWDWRNvSGDSwMTPIKDQGNCGSGWAFAALGAVEARMKLAANnpNLRPDLSEQYLLSCGP---GNCSSGSSNL 195
                                       6899*****755457****************************9997777789*********86...79******** PP

                                       HHHHHHHTEBEBTTTS--SSSCSSS-CGCGGGSE..EBEESEEEEEESS....BHHHHHHHHHHHSSEEEEEECCSH CS
                      Peptidase_C1  74 afeyikkggivtekdypYkakeggkCkkkkkkek..vakikgygkvken....seealkkalakngPvsvaidasee 144
                                       + +++  +g v++++  Y++ ++  C+++  +++   +ki+g   v+ +    +  ++++++   gPvs  + ++e 
  gi|386001804|ref|YP_005920103.1| 196 TADWLLCQGTVDDACFRYRGLDTVPCTESCFDRDarKYKIEGWCWVSGEpdviDVPRIQQEVLFGGPVSSKMAVYE- 271
                                       ********************99977777743333346788998888888888999*********************. PP

                                       HHHTEESSEESSTSCETSS-EEEEEEEEEEEETTEEEEEEE-SBTTTSTBTTEEEEESSSSTGG CS
                      Peptidase_C1 145 dfqlYksGvyketecsktelnhavlivGygvengkkyWivkNsWgtdwgekGYiriargknnec 208
                                       df lY   +y++  +        v i+G+g++n+++yWi+kNsWg+ wg++G++ri+ g +   
  gi|386001804|ref|YP_005920103.1| 272 DFYLYDDDIYEHA-AGALVGSQWVDILGWGTNNSTDYWICKNSWGAAWGDSGWFRIKMGDS-LI 333
                                       6***********5.555567899**********************************9966.44 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.9e-06    0.0086     149     222 ..     347     422 ..     328     443 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                    ABC_transp_aux 149 kvgfltghgelsls.spseadfleelee.nYnveevdldsedi.lpedidvlviakptkdlseeelykldqflmnGg 222
                                       kv f +ghg      +++ ++  ++l   +Y v + d ++ +  l e +dv+via+p  +++ +el ++++f+ +G 
  gi|386001804|ref|YP_005920103.1| 347 KVLFYEGHGPVYALlGNY-SEWGNRLAGnGYLVHSSDEANLTAeLLECYDVVVIANPGAAFTADELAAIKEFVGRGR 422
                                       567777777433332222.23445555558888888877655454489*************************9986 PP

>> DUF1964  Domain of unknown function (DUF1964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.018        81       8      34 ..     683     709 ..     678     720 .. 0.86
   2 ?    3.8   0.0     0.018        80       8      34 ..     729     755 ..     724     767 .. 0.86
   3 ?    3.0   0.0     0.031   1.4e+02       7      34 ..     774     801 ..     769     814 .. 0.84
   4 ?   -1.2   0.0      0.65   2.9e+03       8      34 ..     821     847 ..     816     858 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                                       EEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   8 ysvdgDtsitfaWkgetssatLtfePk 34 
                                       y  +gD++i+ +W g + +    f P+
  gi|386001804|ref|YP_005920103.1| 683 YGLNGDQAIAGDWDGDGKDTIGVFRPS 709
                                       8899************99999999996 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.018
                                       EEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   8 ysvdgDtsitfaWkgetssatLtfePk 34 
                                       y  +gD++++ +W+g + +    f P+
  gi|386001804|ref|YP_005920103.1| 729 YGLNGDQAVAGDWNGDGKDTIGVFRPS 755
                                       8899************99999999996 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.031
                                       EEEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   7 sysvdgDtsitfaWkgetssatLtfePk 34 
                                        y  +gD +++ +W+g + +    f P+
  gi|386001804|ref|YP_005920103.1| 774 VYGLNGDLAVAGDWNGDGKDTIGVFRPS 801
                                       6889*************99999999996 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.65
                                       EEEETTTEEEEEEE-SS-EEEEEE-GG CS
                           DUF1964   8 ysvdgDtsitfaWkgetssatLtfePk 34 
                                       y   gD  +  +W+g + +    f P+
  gi|386001804|ref|YP_005920103.1| 821 YGLTGDVPVVGDWNGDGKDTIGVFRPS 847
                                       67789999999*****99999999996 PP

>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.5e-05       0.2      30      79 ..     374     421 ..     351     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                                       HT-EEEEETTS.G--HHHHHT-SEEEEE-G..GS-HHHHHH.HHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  30 ngfevdatedaavfteenLaqydvvvflstegevldaaqeaalqryveaG 79 
                                       ng+ v++ +d+a +t+e L+ ydvvv  +  g+ ++a++ aa++++v  G
  gi|386001804|ref|YP_005920103.1| 374 NGYLVHS-SDEANLTAELLECYDVVVIANP-GAAFTADELAAIKEFVGRG 421
                                       5566644.56668***************99.8***************888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.25s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 5895.68
//
Query:       gi|386001805|ref|YP_005920104.1|  [L=713]
Description: Peptidase family C25 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-50  172.4   0.1    2.2e-50  172.0   0.1    1.1  1  Peptidase_C25   Peptidase family C25
    1.9e-20   72.9   0.0    3.2e-20   72.1   0.0    1.2  1  Propeptide_C25  Propeptide_C25
     0.0034   17.2   2.2      0.006   16.4   0.9    2.1  2  PKD             PKD domain
  ------ inclusion threshold ------
        8.7    7.0   8.6         70    4.1   5.0    3.7  3  RHS_repeat      RHS Repeat


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0   0.1   4.9e-54   2.2e-50      41     377 ..     290     597 ..     261     598 .. 0.79

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 4.9e-54
                                       ....SHHHHHHHHHHHHHHHHTT--SEEEEES-T..............TTS--EE-.....TTT-SEESHHHHS-T. CS
                     Peptidase_C25  41 aGekdaaairnflkyayknwsasklkYllLvGdtsivvkv.kspitksdliptyqiakslgnestiptDdyyasldg 116
                                       + +++a+a + +++ +y+    + l+YllLvGd         +++ ++   p  ++ +      tip+D++ya++ g
  gi|386001805|ref|YP_005920104.1| 290 SSTPSAEAVKEVVASVYAAH--PELEYLLLVGDI-----GrLPWRPNW--DPSSSFSSYF-PGMTIPSDYWYACVAG 356
                                       66789*************99..359********9.....334555555..4544444423.4556************ PP

                                       ....TSSS-SSEEEEE--SSHHHHHHHHHHHHHHHCT--S-G....GGGEEEEEE--.........HHTHHHHHHHH CS
                     Peptidase_C25 117 nedsddltpdlavGRipvtsaaeaaavvnKiiaYerntengsaagqwrnkvlliagdvvgeweaadgneiagttaet 193
                                           +dl+p++avGRi +++ ae+ + v+Ki+aYe+ ++    +g+w +kvllia +++   +++  +e  +t+ + 
  gi|386001805|ref|YP_005920104.1| 357 ----VDLYPEVAVGRITAKNDAEVGQQVAKILAYETGAR----TGDWASKVLLIAHAQEAPGKYQGCKESIRTAPY- 424
                                       ....*******************************9944....488***********3222222222222222222. PP

                                       HHHTSSGGGT-SEEEEE-SS--...............TTTTHHHHH--SEEEEES-EETTEE......TTTTEEHHH CS
                     Peptidase_C25 194 tpseynvnklyadlaayeaetetevpaanqp.l.lttqnllkalnqGvlfvnytGHGsetaw......adeslstnd 262
                                                 +a+  ay + ++       q  +  t+ ++l+a + Gv++vny+GHGs+t+w      a e++ t++
  gi|386001805|ref|YP_005920104.1| 425 -----ASPFSFAT--AYGSPPS-------QGgDgATNADVLAAAS-GVGIVNYRGHGSYTSWgpgwnyAGEEFGTSE 486
                                       .....22222333..3333333.......3345556677999999.****************99988888889**** PP

                                       HHT---TT--EEEEEESSSTT-TTSSS-.-HHHHHHHSTTSSEEEEEEESS---SS--SHHHHHHHHHHHHHHH... CS
                     Peptidase_C25 263 isaltntnklpiaitaaCltgafdeetkrsfgeklvlnangGavayigatrlgysgvndrlsraffealfadaartl 339
                                       + a+     +p ++++aC+++a+d+  + +++e++v   +g a a++ga+r +++  n+++ r +f+a+ +   ++l
  gi|386001805|ref|YP_005920104.1| 487 AHAMAGVA-FPAVLSIACYNAALDQAGD-CLAEAFV-KDDGSAAAFLGASRPSWTEPNHDFDRYLFNAMGNGGISDL 560
                                       *****976.**************88887.*******.9************************************9** PP

                                       T-S-SS-HHHHHHH...............EEEEE-TT-- CS
                     Peptidase_C25 340 Gealllaknelletglaqsiskgm.nkrtfnllGDPalr 377
                                       G +++ ak +++++++a+s   ++ n ++f llGDPal 
  gi|386001805|ref|YP_005920104.1| 561 GWVVNDAKVKVMAKYGATS--YAAdNVKMFLLLGDPALG 597
                                       *************988666..66768889********95 PP

>> Propeptide_C25  Propeptide_C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   7.2e-24   3.2e-20      14     193 ..      36     214 ..      26     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 7.2e-24
                                       E.EEETTEEEEEEE--S-EEEEEEETTEEEEEEE-TT-B----TTSB---BEEEEEE--SSEEEEEEEEEEEEEEE- CS
                    Propeptide_C25  14 LeSqeqsvtkiefrvanlkftsvekdkgvfqrisitegeslsekGepelPilsksiavpetreakvevvssktetle 90 
                                       + S++ s t +ef +  ++ ++       f + si+e +  +e G+pelP+ + ++avp   +++ +v+++   t+ 
  gi|386001805|ref|YP_005920104.1|  36 VSSSDASGTVVEFLLRGVRAEERAAGSEAFSVLSIPERGTTTEVGRPELPVVRAMVAVPAGAAVRATVLEASSSTYP 112
                                       3456777777999988888888888888************************************************* PP

                                       S--B-B---S-BTTS-GGGS-B-.--GG.GG--S-BS--SEEE---EEETTEEEEEEEE--EEEETTTTEEEEEEEE CS
                    Propeptide_C25  91 nvdiaPsksvvveredpekitYv.lndslYsqnkslPseiatlsdpaylRdvrvqevnlaPlqYnPvtkelllykki 166
                                          + P +   v+  ++++ + + +++++Ys+++++P+e + + +p++ Rd+ v e++  P+ +nP+t el++y++i
  gi|386001805|ref|YP_005920104.1| 113 GFRVRPFQPPEVD--GLSGYRGLlIDEEFYSRDGFYPEELVEVGPPGIWRDLVVVELQANPVAFNPATGELRVYDRI 187
                                       ******9988777..899988765999************************************************** PP

                                       EEEEE.....EEEEE-SS--------- CS
                    Propeptide_C25 167 kvaitfdrkaetaekrkeilnkvaksa 193
                                        v + ++    + e  +  + ++ ++ 
  gi|386001805|ref|YP_005920104.1| 188 LVRLDYEGGVLAKETAEPKFARIYREV 214
                                       **9988765555555555555555555 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   6.5e+03       8      29 ..      28      49 ..      26      50 .. 0.81
   2 !   16.4   0.9   1.3e-06     0.006      19      64 ..     630     682 ..     613     687 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                                      -BSSEEEEEEEES.-SS-SEEE CS
                               PKD  8 lvpgatvaftaavpdganvtys 29
                                      +++ga+v  +++ ++g+ v ++
  gi|386001805|ref|YP_005920104.1| 28 PEVGAEVLVSSSDASGTVVEFL 49
                                      6788899999999999999886 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.3e-06
                                       ES...-SS-SEEEEE--SS...--EEEEETTEEE..EEE-SSEEEEEEEEEE- CS
                               PKD  19 av..pdganvtysWdfgdg...svvqvlseptvt..htYlspGeYeVtvtasn 64 
                                       ++  pdg++v y+ d gdg    + +  s+ tv+  h ++++G+  V+v+a++
  gi|386001805|ref|YP_005920104.1| 630 SSsdPDGDRVKYTYDWGDGtfsETEFFDSGATVSlaHRWEAAGTRAVRVKAED 682
                                       3347*****************9888888888886559**************98 PP

>> RHS_repeat  RHS Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.76   3.4e+03       7      18 ..      35      46 ..      35      48 .. 0.81
   2 ?    0.3   0.0      0.24   1.1e+03       3      19 ..     364     381 ..     364     392 .. 0.76
   3 ?    4.1   5.0     0.016        70       8      23 ..     629     644 ..     617     645 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.76
                        RHS_repeat  7 LtevtdpsGrvt 18
                                      L++ +d+sG+v+
  gi|386001805|ref|YP_005920104.1| 35 LVSSSDASGTVV 46
                                      788899*99997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                        RHS_repeat   3 aaGrLtevtdp.sGrvtt 19 
                                       a+Gr+t++ d+  G++++
  gi|386001805|ref|YP_005920104.1| 364 AVGRITAKNDAeVGQQVA 381
                                       689****98887887764 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.016
                        RHS_repeat   8 tevtdpsGrvttYtYD 23 
                                       t+ +dp+G+++ YtYD
  gi|386001805|ref|YP_005920104.1| 629 TSSSDPDGDRVKYTYD 644
                                       7889***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 4727.92
//
Query:       gi|386001806|ref|YP_005920105.1|  [L=422]
Description: Cysteate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-33  115.9   2.4    2.9e-33  115.6   2.4    1.1  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.12   12.6   0.5       0.29   11.3   0.2    1.8  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   2.4   3.2e-37   2.9e-33      24     294 .]      91     374 ..      66     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 3.2e-37
                                       EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHT CS
                              PALP  24 lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrll 100
                                        +  +E    t+SfKd+ a   ++rl e ++++ +v+as+GN++ra A aa+++Gl++++vvp +   +++  +   
  gi|386001806|ref|YP_005920105.1|  91 YWPEREARMATCSFKDLEAPPTVERLMERKEGQALVVASAGNTARAFAQAASAAGLPLVLVVPTSGE-SRLWTTVPP 166
                                       78899********************88888***********************************98.999999988 PP

                                       T-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSS.HHHHHH CS
                              PALP 101 Gaevvev..ggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgG.gliaGi 174
                                          + +v  +gdy+ea ++aa+la e  g++      n+++ +g+g ++l  +  +g  pd+ + +vG+G g ia++
  gi|386001806|ref|YP_005920105.1| 167 SESICVVsvKGDYTEAIDLAARLAGE-AGFVGEGGARNVARRDGMGVVVLDAALAMGALPDHYFQAVGSGtGGIAAW 242
                                       887777777***************99.6666666666*********************************9****** PP

                                       HHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.........CGTTCCHHHHSEE CS
                              PALP 175 aaglke....rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg.........spselafelldrl 236
                                        a l+     r+++  +r+  ++++ +++l++++ +g   +  ++ ++  g+  +         ++   + ++l+++
  gi|386001806|ref|YP_005920105.1| 243 EASLRLigdgRFGSslPRLHLAQNSPCAPLYAAW-TG---SAAPQGSCPGGMYDDvlynrkppyAVPGGVRDALEGT 315
                                       ******9877555588******************.44...44566677777777766666766777777888889** PP

                                       EEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 237 vdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                        +++ ++s+ ea  a +l+ + egi + p++a+a+aal +++  g++k++d +++ +tg
  gi|386001806|ref|YP_005920105.1| 316 AGTVCAISNGEASLARQLFEEGEGIDILPAAAVAVAALqRAAASGSVKKDDLILLNITG 374
                                       ******************************************************99998 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1   9.8e+03      34      49 ..     119     134 ..     112     138 .. 0.56
   2 ?   11.3   0.2   3.2e-05      0.29      50      82 ..     346     378 ..     344     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                                       -GGGB--THHHH-B-G CS
                     ACP_syn_III_C  34 peekvvvnldeyGnts 49 
                                       ++e  +  ++  Gnt+
  gi|386001806|ref|YP_005920105.1| 119 RKEGQALVVASAGNTA 134
                                       4444445556666665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.2e-05
                                       GGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTE CS
                     ACP_syn_III_C  50 aasiplaLdeaveegklkpgdlvllvgfGaGlt 82 
                                       aa  + aL++a ++g +k+ dl+ll  +G+G++
  gi|386001806|ref|YP_005920105.1| 346 AAVAVAALQRAAASGSVKKDDLILLNITGGGVS 378
                                       788899*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2861.06
//
Query:       gi|386001807|ref|YP_005920106.1|  [L=256]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-13   49.7   0.0    8.5e-13   49.0   0.0    1.3  1  ABC_tran     ABC transporter
    2.7e-07   30.7   0.1      0.011   15.5   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.9e-05   24.1   0.0    6.9e-05   23.3   0.0    1.3  1  AAA_16       AAA ATPase domain
    0.00039   19.9   0.1       0.16   11.3   0.0    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00059   20.1   0.1     0.0038   17.5   0.1    2.0  1  AAA_22       AAA domain
     0.0033   16.9   0.1      0.044   13.2   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0038   16.9   0.2      0.011   15.4   0.1    1.9  1  AAA_29       P-loop containing region of AAA domain
     0.0076   16.8   0.0      0.011   16.2   0.0    1.2  1  AAA_23       AAA domain
     0.0078   16.1   0.0        0.4   10.6   0.0    2.1  2  ATPase_2     ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.026   14.3   0.2      0.088   12.5   0.2    2.0  1  AAA_30       AAA domain
      0.062   12.1   0.0      0.096   11.5   0.0    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.075   12.9   0.0       0.15   12.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.12   12.4   0.1       0.41   10.7   0.0    1.8  2  MMR_HSR1     50S ribosome-binding GTPase
        0.2   10.8   0.0       0.49    9.6   0.0    1.4  1  KAP_NTPase   KAP family P-loop domain
       0.25   10.2   0.0       0.36    9.6   0.0    1.2  1  AAA_35       AAA-like domain
       0.36   10.5   2.5        9.6    5.9   0.0    2.7  3  DUF1918      Domain of unknown function (DUF1918)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   7.6e-16   8.5e-13       6     135 ..      27     170 ..      24     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 7.6e-16
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                       l++++ge+++ivG++G+GKS+L++ + +  k       +il+dg + k   +    rk i+ l+q+ ++  ++tv++
  gi|386001807|ref|YP_005920106.1|  27 LEMRRGEIIGIVGPTGSGKSSLIADIEQFAKGdtpSGRRILIDGCEPKAeMRSDPRRKLIAQLSQNMHFLADMTVGD 103
                                       7899******************99887776653327778****999999345555677799**************** PP

                                       H............HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH.HHHHTSSEEEEEST CS
                                       x............xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          ABC_tran  79 n............esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalar.allkkpkllllDEp 135
                                                    +   + ie a +  g +  +d+++    + LSgGq + ++ a  a++++++++l+DE 
  gi|386001807|ref|YP_005920106.1| 104 FlrmhaksrgrppQVAGRvIELANTLTGEPVHPDQHL----TILSGGQSRALMAADiAVISDSPIVLIDEI 170
                                       **99875555444222222333333334444555555....9*******999888637899********95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.011       2      56 ..      35      75 ..      34     117 .. 0.74
   2 !   13.5   0.0   4.2e-05     0.047     237     272 ..     143     177 ..      91     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56
                                       +++Gp gsGKS+L+  ++ +a               g ++++ + l+d+++p+ 
  gi|386001807|ref|YP_005920106.1| 35 IGIVGPTGSGKSSLIADIEQFAK--------------GDTPSGRRILIDGCEPKA 75
                                      68****************88753..............334444444444444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.2e-05
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEng.LHP 272
                                       lS G+ r+  +++ ++   ++ +++liDE+En  +  
  gi|386001807|ref|YP_005920106.1| 143 LSGGQSRA-LMAADIAVISDS-PIVLIDEIENAgIKK 177
                                       49******.********9*99.*********964555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.2e-08   6.9e-05      16     162 ..      24     188 ..      21     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.2e-08
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                       +er+ + r+e++ ++G+ G+GKssl+  + + +++d    + i++ g   + e         +   r++l++ql ++
  gi|386001807|ref|YP_005920106.1|  24 VERLEMRRGEIIGIVGPTGSGKSSLIADIEQFAKGDtpsgRRILIDGCEPKAE-------MRSD-PRRKLIAQLSQN 92 
                                       688899999*********************99999999854666776666662.......2233.355666666666 PP

                            AAA_16  89 ................aesaeleawrekleeala...................avpelagaea......srllellk 124
                                                       a                +                    + +++++++       + ++l++
  gi|386001807|ref|YP_005920106.1|  93 mhfladmtvgdflrmhA----------------KsrgrppqvagrvielantlTGEPVHPDQHltilsgGQSRALMA 153
                                       44433333333333321................33333335555555566667666777777777777777777777 PP

                            AAA_16 125 rllallsrderplvlvlDdlqwadeaslqllaaLlrll 162
                                       + +a +s  +   ++++D+++ a    +++l++L  ++
  gi|386001807|ref|YP_005920106.1| 154 ADIAVISD-S--PIVLIDEIENAGIKKREALELLSGEG 188
                                       77766665.3..58899999999999999999987764 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00015      0.16      26      44 ..      34      52 ..      25      66 .. 0.84
   2 !    6.0   0.0    0.0064       7.2     136     170 ..     142     173 ..     124     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      +  ivGp GSGKs+l+  i
  gi|386001807|ref|YP_005920106.1| 34 IIGIVGPTGSGKSSLIADI 52
                                      668************9877 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0064
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                        LSgG+   ++ a    i  ++ +p++l+Dei+ a
  gi|386001807|ref|YP_005920106.1| 142 ILSGGQSRALMAAD---IAVISDSPIVLIDEIENA 173
                                       69999977554443...577899*********986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.4e-06    0.0038       4     112 ..      31     184 ..      28     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsstsskdllrel 60 
                                       +  i+ ++G++G+GK+ l++ + + ++     ++                    +                  +r+l
  gi|386001807|ref|YP_005920106.1|  31 RGEIIGIVGPTGSGKSSLIADIEQFAKG----DTpsgrrilidgcepkaemrsdP------------------RRKL 85 
                                       567899******************9843....22432233333333333333331..................5555 PP

                            AAA_22  61 lralglelka................................................erlsseellealeqalrar 89 
                                         +l ++ +                                                 ++++s++l++a        
  gi|386001807|ref|YP_005920106.1|  86 IAQLSQNMHFladmtvgdflrmhaksrgrppqvagrvielantltgepvhpdqhltilSGGQSRALMAA-------- 154
                                       555554444455556666666666666666666888999888877777765555555555555555422........ PP

                            AAA_22  90 av......ielliiDEaqhlr..seealeeL 112
                                        +       ++++iDE+++    + eale L
  gi|386001807|ref|YP_005920106.1| 155 -DiavisdSPIVLIDEIENAGikKREALELL 184
                                       .134444446789999999855458998888 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   3.9e-05     0.044       3      42 ..      35      77 ..      33     108 .. 0.79
   2 ?    1.6   0.1      0.14   1.6e+02      23      72 ..     183     237 ..     174     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaal...aemgkkvlivGCDPkaDs 42
                                      i i G  G+Gks  ++++ +     +  g+++li GC+Pka+ 
  gi|386001807|ref|YP_005920106.1| 35 IGIVGPTGSGKSSLIADIEQFAkgdTPSGRRILIDGCEPKAEM 77
                                      789999******99998866541115689***********974 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                         Fer4_NifH  23 alaemgkkvlivGCDPk...aDstrlllggkaqetvldtlrekgav.edv.kved 72 
                                        l+  gk v++v  DP      s r++++   +  v++t + +++v ed+ kv+d
  gi|386001807|ref|YP_005920106.1| 183 LLSGEGKIVVVVTHDPMlalMTSRRVVMKNGGMVRVIETTAGEQKVcEDLaKVDD 237
                                       5777899999999999733346889999988888899887766666699834555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     1e-05     0.011      16      39 ..      26      49 ..      21      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      ++e+++ +++ ++Gp+GsGKS+l+
  gi|386001807|ref|YP_005920106.1| 26 RLEMRRGEIIGIVGPTGSGKSSLI 49
                                      66777666999************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-05     0.011      21      51 ..      34      64 ..      25      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLygetprls 51
                                      +  I+Gp+G+GK++++  i     g+tp  +
  gi|386001807|ref|YP_005920106.1| 34 IIGIVGPTGSGKSSLIADIEQFAKGDTPSGR 64
                                      678*************988887777766544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00036       0.4      14      40 ..      26      52 ..      16      62 .. 0.88
   2 ?    3.7   0.0     0.043        48     113     142 ..     156     184 ..     125     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                          ATPase_2 14 ilerepneiyfiYGpegsGKtaLlkei 40
                                       le+ + ei+ i Gp gsGK++L+  i
  gi|386001807|ref|YP_005920106.1| 26 RLEMRRGEIIGIVGPTGSGKSSLIADI 52
                                      5788899****************9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.043
                          ATPase_2 113 ikkkgkkiiiiiDelqklidlglngaellv 142
                                       i      +i++iDe+ +++ ++ ++a +l+
  gi|386001807|ref|YP_005920106.1| 156 IAVISDSPIVLIDEIENAG-IKKREALELL 184
                                       55555679*********99.7766665555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   7.9e-05     0.088      15     108 ..      29     181 ..      21     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaag.............grviglAptgkaAkvLaeelgi.eastiakll 77 
                                       + +  +  ++Gp G+GK+ +++ +++ ++ +              +  +   p  k  ++L++++ + + +t+  +l
  gi|386001807|ref|YP_005920106.1|  29 MRRGEIIGIVGPTGSGKSSLIADIEQFAKGDTpsgrrilidgcepKAEMRSDPRRKLIAQLSQNMHFlADMTVGDFL 105
                                       555668889***************99988764466554444444322223334444444555555543556777777 PP

                            AAA_30  78 krlk.............................................grarlepgtllivDEagmvdtkqlaal 108
                                       + ++                                             + a ++++ ++++DE+  +++k+ +al
  gi|386001807|ref|YP_005920106.1| 106 RMHAksrgrppqvagrvielantltgepvhpdqhltilsggqsralmaaDIAVISDSPIVLIDEIENAGIKKREAL 181
                                       7777888888888888888888888888888888888888888888887656667778888888888887776665 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.5e-05     0.096      79     105 ..      25      50 ..      19      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                        Adeno_IVa2  79 sslnyglqPviGviyGPtGsGksqllr 105
                                         l++ +  +iG++ GPtGsGks l+ 
  gi|386001807|ref|YP_005920106.1|  25 ERLEMRRGEIIGIV-GPTGSGKSSLIA 50 
                                       568899999***75.**********96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.15      97     121 ..      30      54 ..      15      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                       CTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                        +++++ +vG++G GKS+Li  + +
  gi|386001807|ref|YP_005920106.1|  30 RRGEIIGIVGPTGSGKSSLIADIEQ 54 
                                       4678999*************98865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00037      0.41       2      18 ..      35      51 ..      34      62 .. 0.89
   2 ?   -1.4   0.0       2.2   2.4e+03      77     101 ..     161     184 ..     138     228 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                                      EEEEESTTSSHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLina 18
                                      ++ivG + +GKS+Li  
  gi|386001807|ref|YP_005920106.1| 35 IGIVGPTGSGKSSLIAD 51
                                      89************976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                       SEEEEEEETTTTCSHHHHHHHHHHH CS
                          MMR_HSR1  77 dlillvvdaseeklkpldeeleell 101
                                       d  ++++d + e+   +++e  ell
  gi|386001807|ref|YP_005920106.1| 161 DSPIVLID-EIENAGIKKREALELL 184
                                       33344444.2111112223333333 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00044      0.49      17      47 ..      29      59 ..      22      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00044
                        KAP_NTPase 17 latpivvgLygkWGsGKssllnkledelkef 47
                                      ++++ ++g+ g+ GsGKssl++ +e+  k  
  gi|386001807|ref|YP_005920106.1| 29 MRRGEIIGIVGPTGSGKSSLIADIEQFAKGD 59
                                      677889****************999866655 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00032      0.36      28      57 ..      29      58 ..      18      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                            AAA_35 28 ekpGalirikapkkmGKtSLlarilakakq 57
                                       ++G++i i +p   GK+SL+a i ++ak 
  gi|386001807|ref|YP_005920106.1| 29 MRRGEIIGIVGPTGSGKSSLIADIEQFAKG 58
                                      578*********************998875 PP

>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.043        48      19      34 ..      28      43 ..      21      44 .. 0.84
   2 ?    5.9   0.0    0.0085       9.6       4      31 ..     100     128 ..      98     135 .. 0.80
   3 ?   -3.6   0.1       7.8   8.7e+03      20      27 ..     246     253 ..     242     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.043
                                      -EEEEEEEE-S-SSS- CS
                           DUF1918 19 pereGeiveVrgedGa 34
                                      + r+Gei+++ g+ G+
  gi|386001807|ref|YP_005920106.1| 28 EMRRGEIIGIVGPTGS 43
                                      679**********996 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0085
                                       -TTEEEEES-TTTS--EEE.EEEEE-S-S CS
                           DUF1918   4 kvGDrlvvegrtvgepere.GeiveVrge 31 
                                       +vGD l ++ ++ g+p +  G ++e+ ++
  gi|386001807|ref|YP_005920106.1| 100 TVGDFLRMHAKSRGRPPQVaGRVIELANT 128
                                       69************998753899998765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.8
                                       EEEEEEEE CS
                           DUF1918  20 ereGeive 27 
                                        r+Ge+v+
  gi|386001807|ref|YP_005920106.1| 246 IRRGEVVG 253
                                       68999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1497.51
//
Query:       gi|386001808|ref|YP_005920107.1|  [L=232]
Description: Cobalamin synthesis protein, P47K [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-12   46.2   0.0    5.8e-12   45.6   0.0    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00046   19.9   0.0    0.00077   19.1   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
    0.00067   20.2   0.0     0.0013   19.2   0.0    1.6  1  AAA_18           AAA domain
    0.00074   19.9   0.0     0.0014   19.0   0.0    1.4  1  AAA_19           AAA domain
    0.00086   19.4   0.0      0.001   19.1   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00097   18.2   0.2      0.056   12.4   0.1    2.2  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0025   17.1   0.1     0.0049   16.2   0.1    1.6  1  Zeta_toxin       Zeta toxin
     0.0034   17.8   0.4      0.013   15.9   0.4    2.2  1  AAA_16           AAA ATPase domain
     0.0093   15.2   0.0      0.012   14.9   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.037   13.8   0.0      0.047   13.4   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.045   13.5   0.1      0.098   12.4   0.1    1.5  1  AAA_30           AAA domain
      0.052   13.5   0.0      0.093   12.6   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.054   12.6   0.4      0.089   11.9   0.2    1.4  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.063   13.0   0.0       0.23   11.2   0.0    1.8  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.067   12.4   0.0       0.11   11.8   0.0    1.2  1  KAP_NTPase       KAP family P-loop domain
      0.076   12.3   0.0       0.11   11.8   0.0    1.2  1  MipZ             ATPase MipZ
       0.11   12.4   0.1       0.76    9.7   0.0    2.0  2  NACHT            NACHT domain
       0.13   12.1   0.0       0.22   11.4   0.0    1.3  1  NTPase_1         NTPase
       0.14   12.3   0.1       0.22   11.7   0.1    1.7  1  AAA_33           AAA domain
       0.14   11.4   0.0        0.2   11.0   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
       0.19   11.2   0.0       0.26   10.7   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
       0.23   11.1   0.0       0.35   10.6   0.0    1.2  1  PRK              Phosphoribulokinase / Uridine kinase family


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   7.1e-15   5.8e-12       2     176 ..       3     164 ..       2     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 7.1e-15
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT..EEEETTTTECCHCTT-HHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve.ivelenGciCctlredllkelea 75 
                                       ++v++G +GsGKT++l h     ++ g + av+  +     +D ++ r+ gv+ +v l++  ++   +   + e+ +
  gi|386001808|ref|YP_005920107.1|   3 MVVVAGTPGSGKTSVLIHAArsLQQMGVRPAVVKIDCL-WTEDDARFRRLGVPvAVGLAKDMCPDHYSIYNVDEMLD 78 
                                       589*****************8878899***********.7888888888888879*****99999988888999999 PP

                                       HHHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  76 leereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                        +++e   dv+l Et G  +  ap                 v+v+D+    +++ + + k++  l++ad++v +K D
  gi|386001808|ref|YP_005920107.1|  79 WAKEE-GADVLLNETAGlCLRCAPY----------PDSALAVCVLDV----TSGPNAPLKVGPLLTTADVVVATKGD 140
                                       99999.7**********87888888..........567789******....99************************ PP

                                       HHCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 152 lldeeallekleerlrqlnpeakvl 176
                                       ++++++  e+++er+ + np+ +++
  gi|386001808|ref|YP_005920107.1| 141 MVSQAER-EVFRERVLEANPACRIV 164
                                       *****88.9********99988876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.4e-07   0.00077       2      93 ..       2      94 ..       1      98 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.4e-07
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHH CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.kkeeadpaavakeaveka 79
                                      ++++++G+ G+GKT+ l   a+ l+++g ++++v  D+         + l+  + v + k +  ++ ++  + e ++ a
  gi|386001808|ref|YP_005920107.1|  2 KMVVVAGTPGSGKTSVLIHAARSLQQMGVRPAVVKIDCLWTEDDARFRRLGVPVAVGLAKdMCPDHYSIYNVDEMLDWA 80
                                      57899**************************************************99998666677788889999**** PP

                                      HHTTSSEEEEEE-- CS
                             SRP54 80 keekidvvlvDTaG 93
                                      kee++dv+l  TaG
  gi|386001808|ref|YP_005920107.1| 81 KEEGADVLLNETAG 94
                                      *************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.7e-06    0.0013       1      41 [.       4      50 ..       4     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.....gvnlrdvakenglllev 41
                                      ++++GtpG+GKt++  + +++l ++     +v++ ++++e++ ++ +
  gi|386001808|ref|YP_005920107.1|  4 VVVAGTPGSGKTSVLIHAARSLqQMgvrpaVVKIDCLWTEDDARFRR 50
                                      78****************99997889999977777777776655544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.7e-06    0.0014      11      41 ..       2      32 ..       1      45 [. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvk 41
                                      k+++v + pG+GKT vl h+ + l+++g ++
  gi|386001808|ref|YP_005920107.1|  2 KMVVVAGTPGSGKTSVLIHAARSLQQMGVRP 32
                                      689999********************99654 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.2e-06     0.001       2      36 ..       4      38 ..       3     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaD 36
                                      ++++++ G+GKT+++++ ar+l++ g r ++v+ D
  gi|386001808|ref|YP_005920107.1|  4 VVVAGTPGSGKTSVLIHAARSLQQMGVRPAVVKID 38
                                      6899999**************************99 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   6.8e-05     0.056      31      66 ..       3      38 ..       1      42 [. 0.92
   2 ?    3.8   0.0     0.029        24     161     227 ..     122     183 ..      72     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      +v + G+PG+Gk  ++ + + +l++ G r av+ +D
  gi|386001808|ref|YP_005920107.1|  3 MVVVAGTPGSGKTSVLIHAARSLQQMGVRPAVVKID 38
                                      57799********999999***************99 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                                       --CC.CHHH-SEEEEE---.HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHH CS
                              MeaB 161 ikkG.ileiaDiivvnkaD.kkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaiee 227
                                       +k G +l  aD++v  k D  ++ae+   e+      e+  e++   +++++ ++ g+G +el++ i+e
  gi|386001808|ref|YP_005920107.1| 122 LKVGpLLTTADVVVATKGDmVSQAER---EVFR----ERVLEANPACRIVEANGLSGKGAAELAELIRE 183
                                       45554778899999999994334433...2221....22234556678889999999999999888877 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     6e-06    0.0049      17      49 ..       2      37 ..       2      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                        Zeta_toxin 17 klillgGqpGAGKselaellkdele...rqgnvvrl 49
                                      k+++++G pG+GK++++  ++++l+    +  vv++
  gi|386001808|ref|YP_005920107.1|  2 KMVVVAGTPGSGKTSVLIHAARSLQqmgVRPAVVKI 37
                                      689**************9999999853233344444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   1.6e-05     0.013      26      52 ..       3      29 ..       1     184 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekdg 52
                                      +v++ G +G+GK+s++ +++r+l++ g
  gi|386001808|ref|YP_005920107.1|  3 MVVVAGTPGSGKTSVLIHAARSLQQMG 29
                                      799***************999999884 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.012       2      25 ..       2      25 ..       1      44 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                           DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                      ++v+V G +G+GKt vl++++  l
  gi|386001808|ref|YP_005920107.1|  2 KMVVVAGTPGSGKTSVLIHAARSL 25
                                      689****************99988 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 ?   13.4   0.0   5.7e-05     0.047       2      29 ..       5      31 ..       4      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnr 29
                                      vv+G pG+GK++++ +++r+ l+   +r
  gi|386001808|ref|YP_005920107.1|  5 VVAGTPGSGKTSVLIHAARS-LQQMGVR 31
                                      9*****************99.4433444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012     0.098      20      47 ..       3      30 ..       1      40 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_30 20 vavltGpAGtGKttalkalreaweaagg 47
                                      ++v+ G +G+GKt +l ++++ +++ g 
  gi|386001808|ref|YP_005920107.1|  3 MVVVAGTPGSGKTSVLIHAARSLQQMGV 30
                                      789****************999998874 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.093       2      35 ..       4      37 ..       3      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKh 35
                                      + ++g+ gsGKT+ l +  + l++ g+r +++K 
  gi|386001808|ref|YP_005920107.1|  4 VVVAGTPGSGKTSVLIHAARSLQQMGVRPAVVKI 37
                                      6789****************************96 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00011     0.089      47      71 ..      11      35 ..       3      36 .. 0.92
   2 ?   -3.9   0.0       6.7   5.5e+03     177     198 ..     129     150 ..     127     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      -HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                      G+GKT++ i+ ++ lq+ g++++v+
  gi|386001808|ref|YP_005920107.1| 11 GSGKTSVLIHAARSLQQMGVRPAVV 35
                                      99*********************98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.7
                                       GG-SEEEE..........-TTT CS
                              LpxK 177 kradlvilngakaeeeeaekae 198
                                        +ad+v+ +++++ +++++++ 
  gi|386001808|ref|YP_005920107.1| 129 TTADVVVATKGDMVSQAEREVF 150
                                       5677777766666555554443 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.23       1      33 [.       6      38 ..       6      41 .. 0.96
   2 ?   -1.2   0.0       1.7   1.4e+03     159     208 ..     132     181 ..     122     200 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                      v+G++GsGKt+     +  l++ g ++avv +D
  gi|386001808|ref|YP_005920107.1|  6 VAGTPGSGKTSVLIHAARSLQQMGVRPAVVKID 38
                                      89****************************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                        ATP_bind_1 159 hvvvlnkfDllkek.lekeleffedvealslllekeeekykklaeaiaell 208
                                        vvv +k D++++  +e   e++ + +   ++ e + +   k a+++ael+
  gi|386001808|ref|YP_005920107.1| 132 DVVVATKGDMVSQAeREVFRERVLEANPACRIVEAN-GLSGKGAAELAELI 181
                                       588888888888554333334444443333333322.44444455555555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.11      23      67 ..       4      45 ..       2      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                        KAP_NTPase 23 vgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggd 67
                                      v++ g  GsGK+s+l    ++l+++   vr ++++++ +++++ d
  gi|386001808|ref|YP_005920107.1|  4 VVVAGTPGSGKTSVLIHAARSLQQM--GVRPAVVKIDCLWTED-D 45
                                      6778888******************..9**********99976.3 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.11       3      39 ..       4      39 ..       2      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39
                                      +v+     GsGk+ + +h a +L ++G+r a++ +d+
  gi|386001808|ref|YP_005920107.1|  4 VVV-AGTPGSGKTSVLIHAARSLQQMGVRPAVVKIDC 39
                                      344.44679**************************97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00093      0.76       2      26 ..       3      27 ..       2      35 .. 0.86
   2 ?    0.2   0.0      0.77   6.2e+02     117     159 ..     127     178 ..     119     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00093
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      +v++ G +GsGKT  l + a+ +++
  gi|386001808|ref|YP_005920107.1|  3 MVVVAGTPGSGKTSVLIHAARSLQQ 27
                                      699***********99998888876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.77
                                       TTT--EEEEEEECCCHHHHCTTSSCE...........EEEE--TCCHHHHHH CS
                             NACHT 117 llpeasllltvrpralrdleeqleea.........ivlevegfsesrrkqlv 159
                                       ll++a ++++++ + ++++e+ + ++         +++e +g+s + +++l+
  gi|386001808|ref|YP_005920107.1| 127 LLTTADVVVATKGDMVSQAEREVFRErvleanpacRIVEANGLSGKGAAELA 178
                                       7888889999999999887666666656666788888888888888888776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.22       2      29 ..       4      31 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                      EEEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvk 29
                                      v++ G pG+GKt ++  +++ l++ gv+
  gi|386001808|ref|YP_005920107.1|  4 VVVAGTPGSGKTSVLIHAARSLQQMGVR 31
                                      799********************99986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00027      0.22       1      32 [.       3      45 ..       3     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg...........avllssdt 32
                                      +v++ G pGsGK+ ++ + ++ l+            +l ++d+
  gi|386001808|ref|YP_005920107.1|  3 MVVVAGTPGSGKTSVLIHAARSLQqmgvrpavvkiDCLWTEDD 45
                                      6999***********9998888876656655444444445555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025       0.2      20      45 ..       2      27 ..       1      45 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                      XEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 20 dliiiAarpsmGktalalniaenaav 45
                                      +++++A+ p+ Gkt++ ++ a++  +
  gi|386001808|ref|YP_005920107.1|  2 KMVVVAGTPGSGKTSVLIHAARSLQQ 27
                                      589*****************998765 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.26       1      38 [.       1      38 [.       1      49 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                      E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvvidde 38
                                      M +vv+ G P sGK+++  + a+ l++ + +  v++ +
  gi|386001808|ref|YP_005920107.1|  1 MKMVVVAGTPGSGKTSVLIHAARSLQQMGVRPAVVKID 38
                                      889*************9999999999877766666655 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00043      0.35       2      40 ..       4      42 ..       3      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflr 40
                                      + vag  G+Gkt+v  +   ++++ +v++a+++ d + +
  gi|386001808|ref|YP_005920107.1|  4 VVVAGTPGSGKTSVLIHAARSLQQMGVRPAVVKIDCLWT 42
                                      569***************************998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1313.65
//
Query:       gi|386001809|ref|YP_005920108.1|  [L=226]
Description: Fe-S cluster domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   45.9   3.0    4.2e-12   45.5   0.5    2.3  2  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.5   2.4e-16   4.2e-12       1      32 [.       8      44 ..       8      45 .. 0.95
   2 ?   -0.1   0.1     0.041   7.4e+02      10      15 ..     100     105 ..     100     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.4e-16
                               FeS  1 LPgtNCgaCGypgCmafAealveg.....eaqledCp 32
                                      LPg+NCg+CG+++C++fA al++g     e ++e+Cp
  gi|386001809|ref|YP_005920108.1|  8 LPGYNCGECGFKSCREFARALLKGtdrgrEIEIELCP 44
                                      9***********************9999888999999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.041
                               FeS  10 GypgCm 15 
                                       G+p+C+
  gi|386001809|ref|YP_005920108.1| 100 GEPSCR 105
                                       9****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1403.04
//
Query:       gi|386001810|ref|YP_005920109.1|  [L=280]
Description: hypothetical protein Mhar_1118 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.65
# Mc/sec: 1298.93
//
Query:       gi|386001811|ref|YP_005920110.1|  [L=169]
Description: Sulfopyruvate decarboxylase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-11   44.1   0.2    3.7e-11   42.9   0.2    1.5  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.2   2.1e-15   3.7e-11       4     159 ..       7     162 ..       4     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.1e-15
                                       HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                      TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                       +ea+ r +k +g++ v  vp+ ++  ll  ++  ++ir+v +  E+  +++A g ++  + p+ ++  s  G+ n +
  gi|386001811|ref|YP_005920110.1|   7 SEAVYRGMKGAGIDFVASVPCVHLQGLLALVDTDPEIRHVPVTREEEGVGIAAGAYMGGKTPALLMQNS--GLGNSI 81 
                                       68999***********************9999999******9999999999998877766677766666..788999 PP

                                       HHHHHHH.HHT--EEEEEEE--CCCHH......S..TC--T.-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH.H CS
                      TPP_enzyme_N  81 talaeAk.vdriPllvlsgdrptslrg......qgvlqqel.dqlalfrpvtkyaervtspeelpealrrAirta.l 148
                                       +ala+ + + +iPll+++ +r+   +        g l + l d++a+        +++ + +e++e ++ A+++a +
  gi|386001811|ref|YP_005920110.1|  82 NALASLNgLYGIPLLLIVSHRGGVGETisgqvpMGRLTPKLlDAMAI-------PRFIPTLTEAEEKVALAWEIAlA 151
                                       9999887357********99887666655444434444333455555.......78899999999999999999966 PP

                                       SSS--EEEEEE CS
                      TPP_enzyme_N 149 sgrpgPvylel 159
                                        ++p +v+le+
  gi|386001811|ref|YP_005920110.1| 152 RRTPSAVLLEI 162
                                       66677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       167  (0.00931452); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); 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: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 939.25
//
Query:       gi|386001812|ref|YP_005920111.1|  [L=114]
Description: Acylphosphatase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   13.7   0.2      0.072   12.9   0.2    1.4  1  CdvA      CdvA-like coiled-coil domain
      0.095   13.4   0.0       0.18   12.5   0.0    1.7  1  PMC2NT    PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.1e-06     0.072      18      63 ..      63     108 ..      49     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-06
                              CdvA  18 styeeikekleealkklkekakelkeklkkrlkeledqikslekal 63 
                                       ++++ + ek +++l +++ ++ + k  +++r + +e  +++l+ a+
  gi|386001812|ref|YP_005920111.1|  63 EKMDTMLEKQDSTLGEIQGHRFDMKGYINQRFERIETDLAELKAAM 108
                                       78999**************************************997 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.18      65      92 .]      54      81 ..       2      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                            PMC2NT 65 veekfksvvdvvDsllEkadtcLDeltg 92
                                      v+e f ++++ +D++lEk d+ L e++g
  gi|386001812|ref|YP_005920111.1| 54 VKEGFGDLGEKMDTMLEKQDSTLGEIQG 81
                                      677999*****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 739.83
//
Query:       gi|386001813|ref|YP_005920112.1|  [L=162]
Description: Sulfopyruvate decarboxylase subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-19   70.7   0.0    1.9e-19   69.9   0.0    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   1.1e-23   1.9e-19      18     139 ..      18     124 ..       3     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.1e-23
                                       SSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHH CS
                      TPP_enzyme_C  18 prsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnl.pitvvvlnNegygmtggqqe 93 
                                       p+++   ++lg+mG + ++++G++la pdr+vvai GDG+ lm+l  l+t++ +   + ++v+l+N++yg tg q++
  gi|386001813|ref|YP_005920112.1|  18 PSNF---YMLGSMGLASSIGLGLALALPDRRVVAIDGDGSVLMNLGSLVTIADQEPeNYLLVILDNGCYGSTGSQPT 91 
                                       4444...469******************************************99988*****************987 PP

                                       HHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHH CS
                      TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleeal 139
                                        +             ++ d+a++ae++G++ +r+  + +eel++ l
  gi|386001813|ref|YP_005920112.1|  92 CTA------------RKADLARIAEGAGVTEVRLAAS-PEELRAGL 124
                                       654............467************5554333.57777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1059.53
//
Query:       gi|386001814|ref|YP_005920113.1|  [L=1806]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-144  479.2 198.4    3.1e-28   98.7  18.9    9.6  8  NosD             Periplasmic copper-binding protein (NosD)
   2.1e-123  407.9 216.8    1.2e-19   70.7  20.1   10.3 11  Beta_helix       Right handed beta helix region
  ------ inclusion threshold ------
        6.7    6.5  93.2       0.12   12.2   0.9   10.4 11  Pectate_lyase_3  Pectate lyase superfamily protein


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 !   58.2  35.3   1.2e-19   7.3e-16      15     168 ..     112     270 ..     103     270 .. 0.85
   2 !   27.9   6.6   2.2e-10   1.3e-06      83     151 ..     253     320 ..     250     347 .. 0.48
   3 !   62.5  22.3   5.7e-21   3.4e-17      33     168 ..     351     486 ..     343     490 .. 0.92
   4 !   49.9  20.8   4.1e-17   2.4e-13      15     154 ..     490     631 ..     486     644 .. 0.92
   5 !   98.7  18.9   5.2e-32   3.1e-28       4     199 ..     676     868 ..     673     873 .. 0.94
   6 !   62.8  11.2   4.8e-21   2.9e-17      32     182 ..     879    1008 ..     873    1016 .. 0.54
   7 !   83.6  18.3   2.1e-27   1.3e-23      20     200 ..    1042    1221 ..    1012    1228 .. 0.90
   8 !   75.6  15.4   5.8e-25   3.4e-21      19     167 ..    1243    1392 ..    1226    1393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.2e-19
                              NosD  15 rgngiqlensegseisnneisnsrdgi..lldnssnntitgntienlryGihlensesntiedntlssne.sGialm 88 
                                        ++gi++ + ++ +++n+   n+ +gi   +++++n  i +n+  n+++Gi+l++s++++i++n++s+n+  Gi lm
  gi|386001814|ref|YP_005920113.1| 112 LEAGIKIISDNNVVMNNEVRLNNGTGIfvSISSKNNSIINNNVSYNNKSGIFLWSSNESVISENIVSGNRwIGIRLM 188
                                       45788887777777777777788888874455555555555577777****************************** PP

                              NosD  89 sss.nntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegnt 163
                                       +ss +n+++nN++ +ne +Gi+++ s nn+i +N +  n+ +Gi +++s sn ++gN  ++n + G+ + +ss++ t
  gi|386001814|ref|YP_005920113.1| 189 DSSsGNIIDNNVVHHNEMHGISIESSVNNSIIENDAGyNELDGILIDGSPSNSLEGNDASYNAENGFRIQNSSHSLT 265
                                       *99555******************************99******************************888888888 PP

                              NosD 164 iynNy 168
                                       + +Ny
  gi|386001814|ref|YP_005920113.1| 266 LQDNY 270
                                       88887 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.2e-10
                              NosD  83 sGialmsssnn.tlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqki 151
                                       +G+ +++ss++ tl++N +++n++ Gi++++s++  +++N++  n++Gi+l++s ++ + +N   +n  +
  gi|386001814|ref|YP_005920113.1| 253 NGFRIQNSSHSlTLQDNYAKENRY-GISVQGSNDIYLKDNKAIGNGYGIYLSGSVRSIMDSNLMVEN-RY 320
                                       344444444444444444444433.444444444444444444444444444444444444444333.33 PP

  == domain 3  score: 62.5 bits;  conditional E-value: 5.7e-21
                              NosD  33 eisnsrdgi..lldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyG 107
                                        i++s+ +   ++ n++n+ti+g  ++n+  G++l+n+ ++ +edn +s +++Gi++++ss n l+ N +++nen G
  gi|386001814|ref|YP_005920113.1| 351 VIDDSSGAGavYCINCDNVTIKGLNLTNGFFGVYLSNTINSAVEDNRISLSWNGIYVENSSSNRLTANSVIENEN-G 426
                                       44444443367****************************************************************.* PP

                              NosD 108 illsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNy 168
                                       i+l+ ss+n + +N +++n++Gi le+s +n++ +N+ + n  +Gi l +ss+ n + +N 
  gi|386001814|ref|YP_005920113.1| 427 IFLNSSSENAVDGNIVVSNSYGIVLESSYENRVDSNNASLN-FVGIDLYKSSDYNIVQENV 486
                                       *****************************************.*****99999999999996 PP

  == domain 4  score: 49.9 bits;  conditional E-value: 4.1e-17
                              NosD  15 rgngiqlensegseisnneisnsrdgi..lldnssnntitgntienlryGihlenses.ntiedntlssnesGialm 88 
                                       +g gi+l++s +++i +n++sns++    l+dns +n+i++n  +n   Gi+l++++  n+i  n ++++  Gi++ 
  gi|386001814|ref|YP_005920113.1| 490 NGVGIHLNSSGKNSILGNDVSNSEYICiyLVDNSISNNIKKNNASNAWFGIYLTENSIeNIILYNDANDDLIGIFIR 566
                                       789********************999889999*********************877655****************** PP

                              NosD  89 sssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                       +s +n le+N+++ ne  Gi +++s+++++s+N++s+ + Gi++++s   ++++N  e+n  + ++
  gi|386001814|ref|YP_005920113.1| 567 DSPRNLLEGNRAKTNEFEGIRIQNSAGCSLSGNNASQGQWGIYINSSGMCVLRDNLMENN-LYNFH 631
                                       ***********************************************************9.77666 PP

  == domain 5  score: 98.7 bits;  conditional E-value: 5.2e-32
                              NosD   4 aisgdevlvsargngiqlensegseisnneisnsrdgilldnssnntitgntienl.ryGihlensesntiedntls 79 
                                       +i+ ++ ++ ++++gi+l n++gs+++ n+i +++ gill+++ +n+i gn +  + ++Gi+l  se+n +++n++ 
  gi|386001814|ref|YP_005920113.1| 676 NITVKDLILANNTYGIYLLNTTGSRVEMNRIFDNEFGILLNHCGENEIIGNEVDRSgASGIRLHRSERNLVSENEAC 752
                                       677888888889***************************************998888******************** PP

                              NosD  80 snesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilll 156
                                       +n++Gi l +s nnt++ N + +n + Gi+l++ss+n i  N +++n+ G+fle+s++n++t+N + +n + G+  l
  gi|386001814|ref|YP_005920113.1| 753 QNGRGIDLFESVNNTISRNLVYDNGK-GIYLDGSSQNLILSNDAVQNDFGLFLEGSDHNKLTSNDLREN-EGGLS-L 826
                                       ************************99.******************************************.99999.* PP

                              NosD 157 sssegntiynNyFinnsenvkydgsnnneWnttktsgtniigg 199
                                       + s +n + nN  i+n  n+  dg n  +++++    tn+i+g
  gi|386001814|ref|YP_005920113.1| 827 NRSGKNVLGNNLIIDNGYNFLVDGLNRSHFDNQV-DVTNLING 868
                                       ************************9999999888.55555554 PP

  == domain 6  score: 62.8 bits;  conditional E-value: 4.8e-21
                              NosD   32 neisnsrdgi...lldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnn 103 
                                        n+i +s++g     + n++n+t+++  ++ +r+Gi + ++ ++ti++n+ls+n +Gi+l++s++n +e N ++nn
  gi|386001814|ref|YP_005920113.1|  879 NTIVDSSSGAssvVCINCTNVTVKDLDLRGNREGIKFFETRDSTIKNNILSDNLYGISLERSTKNSVEANYLRNN 953 
                                        344444444334455556666666666666666666666666666666666666666666666556666666665 PP

                              NosD  104 enyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvk 177 
                                        ++ Gi+l+ds +n +++N++   n +Gi+l    +n +++N  ++n  + ++                       
  gi|386001814|ref|YP_005920113.1|  954 TY-GIFLNDSFDNLLEGNRAGeMNTYGIYLAFCRHNILRDNLMAGN-RYNFY----------------------- 1003
                                        55.6666666666666666655555666666666666666666555.55555....................... PP

                              NosD  178 ydgsn 182 
                                          g+n
  gi|386001814|ref|YP_005920113.1| 1004 ARGDN 1008
                                        44443 PP

  == domain 7  score: 83.6 bits;  conditional E-value: 2.1e-27
                              NosD   20 qlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnn 93  
                                        +    e+   ++  ++ + +gi+++n +  +  +n i ++  Gi+l+ns++n+i +n +s+n+ sG+++ +ss+n
  gi|386001814|ref|YP_005920113.1| 1042 YCLDCEDVMAEGLILQGNVYGICFENTTRSRADNNSIIKNIDGIFLDNSDGNVIIGNHISENNgSGLLILRSSAN 1116
                                        44555777778888999999*****************************************999*********** PP

                              NosD   94 tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynN 167 
                                        t+++Nt+++n + Gi ls+ssnn is+N++s n+++Gi le+s  n++  N+ ++n ++Gi  l+ s gn++ +N
  gi|386001814|ref|YP_005920113.1| 1117 TITKNTAKDNFGDGIRLSASSNNIISENVASaNDKTGIILERSPLNVVAANSAQEN-ECGIS-LNFSGGNLLKEN 1189
                                        ********************************************************.*****.************ PP

                              NosD  168 yFinnsenvkydgsnnneWnttktsgtniiggp 200 
                                        +F +n  +++ +gs+    +++    +ni+gg+
  gi|386001814|ref|YP_005920113.1| 1190 QFAENVRDFSAEGSQVKDLDNDV-DLSNIVGGE 1221
                                        *************9977776666.778888886 PP

  == domain 8  score: 75.6 bits;  conditional E-value: 5.8e-25
                              NosD   19 iqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnn 93  
                                        ++     + ++++ +i+n+++gi+l +  +  i+++ti+++  Gi l++s++n i  n +++n+ G+++++s+ n
  gi|386001814|ref|YP_005920113.1| 1243 VYCIDCFNITLEGLKIENNSNGIYLFHTAESAIRNCTISKNLVGIKLVTSSRNEIVANSVKENGLGVLVSNSEYN 1317
                                        455566777889999999999999999999999999999999999999999999999999999999999999999 PP

                              NosD   94 tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynN 167 
                                         ++ N++ +n+  Gi+l ds+ n i +N +s n ++Gi l+ s++n + gNr+++n+ + i + ++s++n++ +N
  gi|386001814|ref|YP_005920113.1| 1318 KISRNEFLKNRADGIMLIDSDRNRIFDNDASlNGESGILLDPSNKNDVIGNRLAENGAYRIKFDAGSNDNHLRGN 1392
                                        999999999999999999999999999999999999999999999999999999999999998899999988777 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 !   48.5  31.7   1.3e-16     8e-13      24     156 ..      89     222 ..      83     223 .. 0.85
   2 !   59.9  20.8   4.2e-20   2.5e-16      31     153 ..     191     310 ..     189     319 .. 0.92
   3 !   59.4  24.3     6e-20   3.6e-16      21     157 ..     356     486 ..     343     487 .. 0.95
   4 !   24.1  17.2   4.3e-09   2.6e-05      45     134 ..     467     556 ..     464     559 .. 0.82
   5 !   36.7  11.6   5.9e-13   3.5e-09      25     157 ..     562     705 ..     557     711 .. 0.69
   6 !   69.2  14.3   5.9e-23   3.5e-19       3     151 ..     669     810 ..     666     813 .. 0.94
   7 !   64.7  16.4   1.4e-21   8.3e-18       2     153 ..     712     856 ..     711     864 .. 0.92
   8 !   16.1   3.0   1.3e-06    0.0079      69     124 ..     799     852 ..     795     883 .. 0.74
   9 !   54.6  10.7   1.9e-18   1.1e-14       3     124 ..     891    1008 ..     889    1043 .. 0.84
  10 !   70.7  20.1     2e-23   1.2e-19       3     158 .]    1041    1191 ..    1038    1195 .. 0.94
  11 !   61.4  16.0   1.5e-20   8.8e-17       4     156 ..    1244    1392 ..    1241    1393 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.3e-16
                                       -SEEE-SSS-.EEES-EEES...-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEES-EEES-SS-SEE CS
                        Beta_helix  24 yGiylrgssnvvienneian...nsgsGiyilgssnntisnntisdnngggialf.gasnnlienneitdnggsGiy 96 
                                       + i l+ ++  ++++ + +n   n + Gi i + +nn++ nn+++ nng+gi ++  ++nn i nn+++ n++sGi+
  gi|386001814|ref|YP_005920113.1|  89 DSIILYADGI-ILQGFVATNsghNLEAGIKIIS-DNNVVMNNEVRLNNGTGIFVSiSSKNNSIINNNVSYNNKSGIF 163
                                       5566666665.7777666665666888899986.99999999**99999******9999999999999999999*** PP

                                       -TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix  97 lnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                       l +s+  +i++Ni+++n+  Gi ++dsss++ + nN++++n  +Gi + +s + + + +N
  gi|386001814|ref|YP_005920113.1| 164 LWSSNESVISENIVSGNRWIGIRLMDSSSGNIIDNNVVHHNEMHGISIESSVN-NSIIEN 222
                                       **9999**********************8888**************9999999.666655 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 4.2e-20
                                       SS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEE CS
                        Beta_helix  31 ssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiyln.yssnntie 106
                                       ss+++i+nn++++n ++Gi+i++s nn i +n    n  +gi ++g+  n +e+n+ + n+++G++++ +s+++t++
  gi|386001814|ref|YP_005920113.1| 191 SSGNIIDNNVVHHNEMHGISIESSVNNSIIENDAGYNELDGILIDGSPSNSLEGNDASYNAENGFRIQnSSHSLTLQ 267
                                       5556******************************99999*****************************55888**** PP

                                       S-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix 107 nNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                       +N++++n+ +Gi+++ s+ +++ ++N++ +n+ +Gi++ gs +   +
  gi|386001814|ref|YP_005920113.1| 268 DNYAKENR-YGISVQGSN-DIYLKDNKAIGNG-YGIYLSGSVR-SIM 310
                                       ********.*********.************8.*****99998.444 PP

  == domain 3  score: 59.4 bits;  conditional E-value: 6e-20
                                       -SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE- CS
                        Beta_helix  21 sggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiyl 97 
                                       sg+ ++y  +++nv+i++ +++n +++G+y++++ n+ +++n+is ++  gi+++++s n +  n +++n++ Gi+l
  gi|386001814|ref|YP_005920113.1| 356 SGAGAVYCINCDNVTIKGLNLTN-GFFGVYLSNTINSAVEDNRISLSW-NGIYVENSSSNRLTANSVIENEN-GIFL 429
                                       478899*****************.************************.*********************99.**** PP

                                       TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                        Beta_helix  98 nyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                       n+ss n + +Ni+ +n+ +Giv+++s  +++v  N+++ n  +Gi+++ ss+ + v +N+
  gi|386001814|ref|YP_005920113.1| 430 NSSSENAVDGNIVVSNS-YGIVLESSY-ENRVDSNNASLNF-VGIDLYKSSDYNIVQENV 486
                                       *****************.*********.************9.**************9997 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 4.3e-09
                                       SS-SEEE-TT.-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT...-- CS
                        Beta_helix  45 sgsGiyilgs.snntisnntisdnngggialfgasnnlienneitdnggsGiyln.yssnntienNiidnna...gs 116
                                       ++ Gi++++s ++n++++n+ + n+ +gi+l+ +++n i +n++++ +   iyl  +s +n i++N+    a     
  gi|386001814|ref|YP_005920113.1| 467 NFVGIDLYKSsDYNIVQENVATKNG-VGIHLNSSGKNSILGNDVSNSEYICIYLVdNSISNNIKKNN----AsnaWF 538
                                       567999*99999*************.****************************9444456666666....44447* PP

                                       SEE---TT---EEES-EE CS
                        Beta_helix 117 GividdsssnvtvtnNti 134
                                       Gi+++++s ++ +  N +
  gi|386001814|ref|YP_005920113.1| 539 GIYLTENSIENIILYNDA 556
                                       ********5555766655 PP

  == domain 5  score: 36.7 bits;  conditional E-value: 5.9e-13
                                       SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-........... CS
                        Beta_helix  25 GiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdn........... 90 
                                       Gi++r+s ++++e+n+   n ++Gi+i++s+++ +s+n+ s++  +gi+++ ++  ++++n +++n           
  gi|386001814|ref|YP_005920113.1| 562 GIFIRDSPRNLLEGNRAKTNEFEGIRIQNSAGCSLSGNNASQGQ-WGIYINSSGMCVLRDNLMENNlynfhaegeid 637
                                       9****************************************999.*********************77766544433 PP

                                       ........SS-SEE-TT-S-.....-EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEE CS
                        Beta_helix  91 ........ggsGiylnyssn.....ntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvr 154
                                               g                ++ e+ +id+  g+G+v+   ++n+tv++ ++ nn  +Gi++ ++ +   v+
  gi|386001814|ref|YP_005920113.1| 638 vdrsnsvdG----------KpiiylMRAEDLVIDSSDGAGVVYCIDCTNITVKDLILANNT-YGIYLLNTTG-SRVE 702
                                       333333331..........022222333444444444555555555556666666666554.6665555555.4444 PP

                                       S-E CS
                        Beta_helix 155 nNt 157
                                        N 
  gi|386001814|ref|YP_005920113.1| 703 MNR 705
                                       443 PP

  == domain 6  score: 69.2 bits;  conditional E-value: 5.9e-23
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S- CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasn 79 
                                       +++ +++n+t+k+ ++ n ++yGiyl ++++ ++e n+i + +++Gi ++ + +n i +n++ +++++gi l  + +
  gi|386001814|ref|YP_005920113.1| 669 VYCIDCTNITVKDLILAN-NTYGIYLLNTTGSRVEMNRIFD-NEFGILLNHCGENEIIGNEVDRSGASGIRLHRSER 743
                                       57778999**********.6*********************.*********************************** PP

                                       -EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS-- CS
                        Beta_helix  80 nlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnv 151
                                       nl++ ne   ng+ Gi l+ s nnti++N +++n+  Gi++d ss ++ +  N +++n+  G+++ gs++ +
  gi|386001814|ref|YP_005920113.1| 744 NLVSENEACQNGR-GIDLFESVNNTISRNLVYDNG-KGIYLDGSS-QNLILSNDAVQND-FGLFLEGSDH-N 810
                                       ***********99.*********************.*********.888*********8.9998888777.5 PP

  == domain 7  score: 64.7 bits;  conditional E-value: 1.4e-21
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78 
                                       gi++n +++ +i +n++++sg++Gi l  s+++++++ne  + +g Gi++ +s nntis+n ++dn+  gi+l+g+s
  gi|386001814|ref|YP_005920113.1| 712 GILLNHCGENEIIGNEVDRSGASGIRLHRSERNLVSENEACQ-NGRGIDLFESVNNTISRNLVYDNG-KGIYLDGSS 786
                                       99****************************************.************************.********* PP

                                       --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix  79 nnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153
                                       +nli  n+   n+  G++l++s++n+++ N +++n+  G++++ s+ +++  nN i +n+ + + v g ++  ++
  gi|386001814|ref|YP_005920113.1| 787 QNLILSNDAVQNDF-GLFLEGSDHNKLTSNDLRENE-GGLSLNRSG-KNVLGNNLIIDNG-YNFLVDGLNR-SHF 856
                                       ************76.*********************.*********.8889********8.5444555544.444 PP

  == domain 8  score: 16.1 bits;  conditional E-value: 1.3e-06
                                       SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT CS
                        Beta_helix  69 gggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdss 124
                                       ++g+ l+g+++n +  n+ ++n+g G++ln s  n++ nN i +n+ + + +d  +
  gi|386001814|ref|YP_005920113.1| 799 DFGLFLEGSDHNKLTSNDLRENEG-GLSLNRSGKNVLGNNLIIDNG-YNFLVDGLN 852
                                       488888888888888888888888.888888888888888888888.777777666 PP

  == domain 9  score: 54.6 bits;  conditional E-value: 1.9e-18
                                        EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix    3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77  
                                        +++ +++nvt+k+ ++++ ++ Gi++ ++++ +i+nn +++ + +Gi++++s++n ++ n+ ++n+ +gi l+++
  gi|386001814|ref|YP_005920113.1|  891 VVCINCTNVTVKDLDLRG-NREGIKFFETRDSTIKNNILSD-NLYGISLERSTKNSVEANYLRNNT-YGIFLNDS 962 
                                        667799999*********.6***************999999.************************.******** PP

                                        S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT CS
                        Beta_helix   78 snnlienneitdnggsGiylnyssnntienNiidnnagsGividdss 124 
                                          nl+e+n+  + +++Giyl  + +n++++N + +n+ + ++ +  +
  gi|386001814|ref|YP_005920113.1|  963 FDNLLEGNRAGEMNTYGIYLAFCRHNILRDNLMAGNR-YNFYARGDN 1008
                                        ************************************9.544444433 PP

  == domain 10  score: 70.7 bits;  conditional E-value: 2e-23
                                        EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix    3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfga 77  
                                        +++ ++++v  ++ ++++ + yGi+++++++ + +nn i + + +Gi + +s++n+i +n+is+nng+g+ +  +
  gi|386001814|ref|YP_005920113.1| 1041 VYCLDCEDVMAEGLILQG-NVYGICFENTTRSRADNNSIIK-NIDGIFLDNSDGNVIIGNHISENNGSGLLILRS 1113
                                        57788999999999****.6*********************.********************************* PP

                                        S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--E CS
                        Beta_helix   78 snnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvt 152 
                                        s n+i +n+  dn g+Gi+l+ ssnn+i++N++++n + Gi ++ s   ++v  N++  n  +Gi +++s++ + 
  gi|386001814|ref|YP_005920113.1| 1114 SANTITKNTAKDNFGDGIRLSASSNNIISENVASANDKTGIILERSP-LNVVAANSAQENE-CGISLNFSGG-NL 1185
                                        ***********************************************.7778********8.**********.99 PP

                                        EES-E. CS
                        Beta_helix  153 vrnNti 158 
                                        +++N++
  gi|386001814|ref|YP_005920113.1| 1186 LKENQF 1191
                                        999987 PP

  == domain 11  score: 61.4 bits;  conditional E-value: 1.5e-20
                                        EE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix    4 singssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78  
                                        ++ ++ n+t+++ +i+n +++Giyl ++    i+n++i++ +  Gi +  ss+n i  n++ +n+  g+ ++++ 
  gi|386001814|ref|YP_005920113.1| 1244 YCIDCFNITLEGLKIEN-NSNGIYLFHTAESAIRNCTISK-NLVGIKLVTSSRNEIVANSVKENG-LGVLVSNSE 1315
                                        66678899*********.6*********************.************************.********* PP

                                        --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EE CS
                        Beta_helix   79 nnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtv 153 
                                        +n i++ne+ +n+ +Gi+l +s++n+i +N ++ n++sGi +d+s+ ++ v +N++  n+ + i++  +s+++++
  gi|386001814|ref|YP_005920113.1| 1316 YNKISRNEFLKNRADGIMLIDSDRNRIFDNDASLNGESGILLDPSN-KNDVIGNRLAENGAYRIKFDAGSNDNHL 1389
                                        **********************************************.8888************************ PP

                                        ES- CS
                        Beta_helix  154 rnN 156 
                                        r+N
  gi|386001814|ref|YP_005920113.1| 1390 RGN 1392
                                        999 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  11.9   0.00098       5.9     131     211 ..     121     205 ..      20     210 .. 0.68
   2 ?    1.8   2.0     0.032   1.9e+02     144     181 ..     181     222 ..     168     236 .. 0.66
   3 ?   10.5   1.1   6.9e-05      0.41     135     206 ..     242     315 ..     235     321 .. 0.80
   4 ?    0.5   8.9     0.078   4.7e+02     146     214 ..     403     471 ..     311     513 .. 0.67
   5 ?   -0.6   2.0      0.17     1e+03     125     206 ..     542     622 ..     522     644 .. 0.64
   6 ?    1.1   0.1     0.049   2.9e+02     159     207 ..     656     706 ..     645     720 .. 0.69
   7 ?    3.7   0.3    0.0079        47     143     204 ..     731     793 ..     717     802 .. 0.65
   8 ?    2.2   0.5     0.023   1.4e+02     142     209 ..     770     842 ..     736     851 .. 0.56
   9 ?   12.2   0.9   2.1e-05      0.12     136     214 ..     883     957 ..     873     958 .. 0.85
  10 ?    7.1   5.8   0.00073       4.4     143     214 ..    1080    1154 ..    1057    1179 .. 0.53
  11 ?    5.7   3.0     0.002        12     148     211 ..    1243    1306 ..    1162    1311 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00098
                                       ES-SSEEE-SSS---TT---SS--E..EEEES-EEES-SS-SEEES..-EEEEEES-EEE-S--SEEE-T.T-EEEE CS
                   Pectate_lyase_3 131 envefemseasgtkhqgifiengsg..gflndlvfsglgdigiavg..nqqftvrnitfnnattgievlw.gwgwtl 202
                                       +n+++ ++e   ++++gif++ +s+  +++n+ v ++  + gi ++  n+ ++ +ni+  n   gi++ + ++g ++
  gi|386001814|ref|YP_005920113.1| 121 DNNVVMNNEVRLNNGTGIFVSISSKnnSIINNNVSYN-NKSGIFLWssNESVISENIVSGNRWIGIRLMDsSSGNII 196
                                       3333333333347777888555555326666666666.677777744466666678888888888888884555777 PP

                                       EEEEEESSS CS
                   Pectate_lyase_3 203 knvkinnce 211
                                        n+ +++ e
  gi|386001814|ref|YP_005920113.1| 197 DNNVVHHNE 205
                                       766665544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.032
                                       --TT--.-SS--EEEEES-EEES-SS-SEEE.S..-EEEEEE CS
                   Pectate_lyase_3 144 khqgif.iengsggflndlvfsglgdigiav.g..nqqftvr 181
                                          gi+ ++++sg+++++ v+ +++ +gi + +  n+ ++ +
  gi|386001814|ref|YP_005920113.1| 181 RWIGIRlMDSSSGNIIDNNVVHHNEMHGISIeSsvNNSIIEN 222
                                       445666577888888888788777999999943544443333 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 6.9e-05
                                       SEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E.EEEEEEE CS
                   Pectate_lyase_3 135 femseasgtkhqgifiengsggfl.ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg.wtlknvk 206
                                       +e ++as + ++g++i+n+s +   +d  ++   ++gi v g++++++++++  +++ gi+++ + + +  +n+ 
  gi|386001814|ref|YP_005920113.1| 242 LEGNDASYNAENGFRIQNSSHSLTlQDNYAKE-NRYGISVqGSNDIYLKDNKAIGNGYGIYLSGSVRsIMDSNLM 315
                                       566777768888*******997767*******.*******99*******************99755523333444 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.078
                                       TT---SS--EEEE.ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEE CS
                   Pectate_lyase_3 146 qgifiengsggfl.ndlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlknvkinncegGi 214
                                       +gi++en+s++ l  ++v+++  +i ++ ++++++  ni+++n + gi ++++ +  + +++ +   +Gi
  gi|386001814|ref|YP_005920113.1| 403 NGIYVENSSSNRLtANSVIENENGIFLNSSSENAVDGNIVVSN-SYGIVLESSYENRVDSNNASLNFVGI 471
                                       3677777777666667777774444444457777777777777.66666666555555555444444443 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.17
                                       EEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E. CS
                   Pectate_lyase_3 125 aqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg. 199
                                        +  s+en++++++ ++     gifi+++ ++ l+  +++ ++  gi++  +    ++ +  ++ + gi++++ +g 
  gi|386001814|ref|YP_005920113.1| 542 LTENSIENIILYNDAND--DLIGIFIRDSPRNLLEGNRAKTNEFEGIRIqNSAGCSLSGNNASQGQWGIYINS-SGm 615
                                       56677888877777666..567888888888888544444446677777335555555555555577777764.333 PP

                                       EEEEEEE CS
                   Pectate_lyase_3 200 wtlknvk 206
                                        +l+++ 
  gi|386001814|ref|YP_005920113.1| 616 CVLRDNL 622
                                       5555543 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.049
                                       ES-EEES-SS-SEEES..-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEE CS
                   Pectate_lyase_3 159 ndlvfsglgdigiavg..nqqftvrnitfnnattgievlwgwgwtlknvki 207
                                       +dlv++  ++ g+ +     ++tv+++   n+t gi++l ++g  ++ ++i
  gi|386001814|ref|YP_005920113.1| 656 EDLVIDSSDGAGVVYCidCTNITVKDLILANNTYGIYLLNTTGSRVEMNRI 706
                                       788888866666666346899*****************9866644443333 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.0079
                                       ---TT---SS--EEEEES-EEES-SS-SEEE..S-EEEEEES-EEE-S--SEEE-TT-E.EEEEE CS
                   Pectate_lyase_3 143 tkhqgifiengsggflndlvfsglgdigiav..gnqqftvrnitfnnattgievlwgwg.wtlkn 204
                                          +gi++++++++ +++ ++++  + gi +  + ++ + rn+++ n + gi+++ +++  +l+n
  gi|386001814|ref|YP_005920113.1| 731 SGASGIRLHRSERNLVSENEACQ-NGRGIDLfeSVNNTISRNLVYDN-GKGIYLDGSSQnLILSN 793
                                       34569999999999995555555.44555554237777778888888.99999988555355543 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.023
                                       S....---TT---SS--EEEE..ES-EEES-SS-SEEE.S..-EEEEEES-EEE-S--SEEE-T.T-EEEEEEEEEE CS
                   Pectate_lyase_3 142 g....tkhqgifiengsggfl..ndlvfsglgdigiav.g..nqqftvrnitfnnattgievlw.gwgwtlknvkin 208
                                            ++++gi+++ +s++ +  nd+v +    +g+ + g   ++ t +++    ++ g ++++ g+++  +n+ i+
  gi|386001814|ref|YP_005920113.1| 770 RnlvyDNGKGIYLDGSSQNLIlsNDAVQND---FGLFLeGsdHNKLTSNDLRE--NEGGLSLNRsGKNVLGNNLIID 841
                                       112334556777777777776766666655...56666442244444444443..4467776665666666666666 PP

                                       S CS
                   Pectate_lyase_3 209 n 209
                                       n
  gi|386001814|ref|YP_005920113.1| 842 N 842
                                       5 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 2.1e-05
                                       EEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSS CS
                   Pectate_lyase_3 136 emseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinnce 211
                                       ++s+++    + +++ n  + +++dl  +g  + gi++  + ++t++n+  +++  gi+++++++ +++++ + n +
  gi|386001814|ref|YP_005920113.1| 883 DSSSGA----SSVVCINCTNVTVKDLDLRG-NREGIKFfETRDSTIKNNILSDNLYGISLERSTKNSVEANYLRNNT 954
                                       444444....4777888888999*******.*******99*****************************99998888 PP

                                       EEE CS
                   Pectate_lyase_3 212 gGi 214
                                        Gi
  gi|386001814|ref|YP_005920113.1| 955 YGI 957
                                       777 PP

  == domain 10  score: 7.1 bits;  conditional E-value: 0.00073
                                        ---TT---SS--EEEE..ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E.EEEEEEEEESSSEE CS
                   Pectate_lyase_3  143 tkhqgifiengsggfl..ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg.wtlknvkinncegG 213 
                                        ++ +gif++n+ g+++  n++  ++ g   + + ++ + +++n +  n + gi+++ +++ ++ +nv   n ++G
  gi|386001814|ref|YP_005920113.1| 1080 KNIDGIFLDNSDGNVIigNHISENN-GSGLLILrSSANTITKNTAKDNFGDGIRLSASSNnIISENVASANDKTG 1153
                                        4455666666666655544444444.2222222234444444555555566666666444355555555555555 PP

                                        E CS
                   Pectate_lyase_3  214 i 214 
                                        i
  gi|386001814|ref|YP_005920113.1| 1154 I 1154
                                        4 PP

  == domain 11  score: 5.7 bits;  conditional E-value: 0.002
                                        ---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSS CS
                   Pectate_lyase_3  148 ifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinnce 211 
                                        +++ +  + +l+ l +++    gi + ++ ++++rn+t++++  gi++ ++++  ++++++++ +
  gi|386001814|ref|YP_005920113.1| 1243 VYCIDCFNITLEGLKIEN-NSNGIYLfHTAESAIRNCTISKNLVGIKLVTSSRNEIVANSVKENG 1306
                                        222222333344555555.5556665599999999999999999999999777777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1806 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.08u 0.38s 00:00:01.46 Elapsed: 00:00:00.52
# Mc/sec: 10364.33
//
Query:       gi|386001815|ref|YP_005920114.1|  [L=436]
Description: Dipeptidyl-peptidase 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.035   14.7   0.1      0.063   13.8   0.1    1.5  1  Peptidase_C39_2  Peptidase_C39 like family


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.5e-06     0.063      82     144 .]     118     169 ..      24     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
                   Peptidase_C39_2  82 sdtrgssieevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYdekgkrvyvnDPa 144
                                       +d  +  ie +kk+i  + P+++  +          ++  ++H+ +i+GY++ g + ++ D++
  gi|386001815|ref|YP_005920114.1| 118 KDDIQGIIEAAKKYIMTNGPIIAVYN----------DAVIGSHCLAIVGYTDAG-NWICKDSW 169
                                       344444569999*************6..........56679***********98.89999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3363.89
//
Query:       gi|386001816|ref|YP_005920115.1|  [L=423]
Description: Peptidase C1A, papain, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0024   18.4   0.1     0.0041   17.7   0.1    1.4  1  Peptidase_C39_2  Peptidase_C39 like family
  ------ inclusion threshold ------
      0.021   14.9   1.0        5.9    6.9   0.9    2.3  2  Peptidase_C1     Papain family cysteine protease


Domain annotation for each model (and alignments):
>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.5e-07    0.0041      69     144 .]      95     160 ..      26     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-07
                   Peptidase_C39_2  69 pivklaekygl.kvsdtrgssieevkkeidagkPvvvsvttfkplndgeikftssgHlvvitGYdekgkrvyvnDPa 144
                                       +++ ++++y + + ++++++ i+++k +++ + P+++  +          +   ++H+ +i+GY++ g + ++ D++
  gi|386001816|ref|YP_005920115.1|  95 AYKIAGSSYINsEGMNSVETIIAKAKVYLETNGPIIAKYN----------DDVIGSHCLAIVGYTDAG-NWICKDSW 160
                                       334445556656888999*********************6..........44469***********98.89999987 PP

>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0013        12      24      60 ..      31      70 ..       4      97 .. 0.81
   2 ?    6.9   0.9   0.00066       5.9     162     194 ..     137     166 ..      93     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0013
                                      BTHHHHHHHHHHHHHHHHHHS...SS---B-HHHHHHHST CS
                      Peptidase_C1 24 GsCWafsavgaledrlaiktk...kklvslSeqelvdCsk 60
                                        C a+++ +ale++l+i+      k+++lSe++l+   +
  gi|386001816|ref|YP_005920115.1| 31 DECVAYGTLAALESMLKIHYYndaAKEFDLSEDDLLAAMG 70
                                      56999*********9999976567899********98665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00066
                                       SS-EEEEEEEEEEEETTEEEEEEE-SBTTTSTB CS
                      Peptidase_C1 162 telnhavlivGygvengkkyWivkNsWgtdwge 194
                                           h ++ivGy        Wi+k sW  + g 
  gi|386001816|ref|YP_005920115.1| 137 VIGSHCLAIVGYTDA---GNWICKDSWPLNNGV 166
                                       3458********988...67*******877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2736.48
//
Query:       gi|386001817|ref|YP_005920116.1|  [L=1393]
Description: hypothetical protein Mhar_1125 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-59  201.4  19.4    5.5e-32  110.9  10.9    2.5  2  NosD        Periplasmic copper-binding protein (NosD)
    1.3e-31  108.7   8.2    5.5e-08   33.0   0.1    5.2  6  DUF11       Domain of unknown function DUF11
    1.4e-16   60.8  24.7    6.6e-09   35.8   5.3    2.7  2  Beta_helix  Right handed beta helix region
    3.2e-06   26.7  12.3     0.0014   18.0   1.4    3.1  2  DUF1565     Protein of unknown function (DUF1565)
     0.0023   18.2   0.0        1.9    8.8   0.0    2.9  2  Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6


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 !   95.2   1.3     1e-30   3.6e-27      94     239 ..     105     248 ..      83     250 .. 0.85
   2 !  110.9  10.9   1.5e-35   5.5e-32     107     240 ..     513     647 ..     481     648 .. 0.85

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1e-30
                              NosD  94 tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyF 169
                                       +++n+ ++ + ++G+ ++    n i+nN+++ n + Gi +e+ss+n +t+N++++n  +G   l +s++n ++ N F
  gi|386001817|ref|YP_005920116.1| 105 VVTNSGSKTDVDAGVRVTSE-RNVIRNNVAKeNAGCGILFESSSRNIVTHNEFSDN-PCGAG-LLNSSENVLFLNVF 178
                                       44455555555577776655.578*******9************************.*****.99999********* PP

                              NosD 170 innsenvkydgsnnneWnttktsgtniiggpylg..GNyWsdydgeDadgDGigDtpYeindgviDylplvn 239
                                        +n ++++ ++s   +Wn++++  + + + ++++  GN+Ws+y+g D+dgDGigD p+   ++  D+ pl+ 
  gi|386001817|ref|YP_005920116.1| 179 KDNGIDASSSNS-TSRWNSSDPISYRYRDETFTAilGNHWSEYSGPDTDGDGIGDLPHVFGAER-DEAPLIM 248
                                       ****99999776.9*******************999**********************888888.****986 PP

  == domain 2  score: 110.9 bits;  conditional E-value: 1.5e-35
                              NosD 107 GillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsn 182
                                       Gi +  s+nn i++N ++ n + G  l++ss+n+itgN+ e+n++  i  l+ss+gn iy N+Fin s  v  ++s 
  gi|386001817|ref|YP_005920116.1| 513 GIKV-LSNNNVIKDNIAKnNRGVGYLLRSSSGNVITGNTAEENRQGAIR-LESSNGNIIYLNNFINGSSPVGWSDS- 586
                                       4433.356677888888888899999*****************888888.***********************986. PP

                              NosD 183 nneWnttktsgtniiggpylg..GNyWsdydgeDadgDGigDtpYeindgv.iDylplvnp 240
                                       nn+Wn++  +++ ++g+++++  GNyWsdy+g DadgDGigDtpY+i++g+  D +pl++p
  gi|386001817|ref|YP_005920116.1| 587 NNTWNSPAAMTYRYNGTTFTSrlGNYWSDYSGVDADGDGIGDTPYDIPGGSdRDFYPLMSP 647
                                       ********99**********99**************************9988999***987 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.4   8.5e+03      22      79 ..     106     122 ..      89     133 .. 0.59
   2 !   32.7   0.0   1.9e-11   6.8e-08       2      89 ..     258     346 ..     257     348 .. 0.85
   3 !   29.6   0.0   1.8e-10   6.3e-07       1      79 [.     660     737 ..     660     765 .. 0.80
   4 ?   -2.4   0.1       1.7     6e+03      48      86 ..     837     874 ..     830     880 .. 0.65
   5 !   33.0   0.1   1.5e-11   5.5e-08      16      80 ..    1133    1200 ..    1111    1210 .. 0.88
   6 !   14.2   0.0   1.1e-05      0.04      15      82 ..    1257    1326 ..    1243    1332 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                             DUF11  22 vtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvt 79 
                                       vtN+g ++                                          + + vrvt
  gi|386001817|ref|YP_005920116.1| 106 VTNSGSKTD-----------------------------------------VDAGVRVT 122
                                       455554443.........................................33444443 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.9e-11
                             DUF11   2 tKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatlsftv 76 
                                       +K+ + +   pG  v++t+ v N g     +vvv D+lP gl+y         +  ++++  g+L+ ges ++++ +
  gi|386001817|ref|YP_005920116.1| 258 DKAGNVTSGEPGSVVKFTIDVANLGEMEFDRVVVADILPDGLEYLGDDRNgtVAGRKVTWELGRLPVGESMRVELLA 334
                                       67777778899**********************************99888444555677777*************99 PP

                             DUF11  77 rvtrtaasgaltn 89 
                                       r + t+  + +tn
  gi|386001817|ref|YP_005920116.1| 335 RISGTTLGN-ITN 346
                                       999998766.666 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 1.8e-10
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvr 77 
                                       l K  d++++rpG+++tyt+tv N+  +   ++vv+D+    +++vsvs + + ++ l+++ ++  ge + + + v+
  gi|386001817|ref|YP_005920116.1| 660 LSKVADRKTARPGEEITYTITVCNRNSTVPVDAVVEDIFDGPVELVSVSPA-PDGDGLWRFYEIGLGECREIVLVVK 735
                                       67999*******************9988888********999999999887.5555555555555555555555555 PP

                             DUF11  78 vt 79 
                                       ++
  gi|386001817|ref|YP_005920116.1| 736 AP 737
                                       54 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.7
                             DUF11  48 vsasqgtasaltsvgsLeagesatlsftvrvtrtaasga 86 
                                       + ++ ++  +l++ ++L++++++t +++++ ++t+as a
  gi|386001817|ref|YP_005920116.1| 837 ADHG-PSTLTLYRNRTLAYSSRWTEEAEAKNRATGASMA 874
                                       4444.2233344448899999999999999888888765 PP

  == domain 5  score: 33.0 bits;  conditional E-value: 1.5e-11
                             DUF11   16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtr 80  
                                         +yt+t+ N g++s++ v+v+D+ P+g ay s+s +     ++sa++  + L+ g++a + ++++vt 
  gi|386001817|ref|YP_005920116.1| 1133 AEYTITLENDGNRSLAPVRVKDLFPPGAAYRSSSLRpyrLTAGSAEWVLTHLAVGGRAEILLRLEVTD 1200
                                        79**********************************88866777788889**********99999986 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 1.1e-05
                             DUF11   15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrta 82  
                                         v+y+lt +N   +++  v  t  lP+g+++  +s     + ++ ++++  +L + +s+t+ f+v+++  +
  gi|386001817|ref|YP_005920116.1| 1257 RVVYNLTIRNEADDPR-VVAATCQLPEGMRLLDSSVPfssYDSGVVTWNLIDLLPFGSKTILFEVEASMNG 1326
                                        689*************.8888999************97666666677777999********9999998766 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 !   35.8   5.3   1.8e-12   6.6e-09       6     134 ..      95     178 ..      50     215 .. 0.54
   2 !   29.9  11.5   1.2e-10   4.4e-07      34     117 ..     497     580 ..     480     607 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.8e-12
                                       -SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---.....SEEE-TT-- CS
                        Beta_helix   6 ngssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn.....gggialfga 77 
                                       +g                                               s++++++ ++++++     + g+ +  +
  gi|386001817|ref|YP_005920116.1|  95 SG-----------------------------------------------SGAVLEGFVVTNSGsktdvDAGVRV-TS 123
                                       22...............................................3333333333333333321222222.23 PP

                                       S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EE CS
                        Beta_helix  78 snnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNti 134
                                        +n+i+nn   +n+g+Gi +++ss+n++++N +++n  +G  + +ss +++ + N++
  gi|386001817|ref|YP_005920116.1| 124 ERNVIRNNVAKENAGCGILFESSSRNIVTHNEFSDNP-CGAGLLNSS-ENVLFLNVF 178
                                       3344444444444444444444444444444444444.444444444.333333333 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.2e-10
                                       .EEES-EEES..-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES- CS
                        Beta_helix  34 vvienneian..nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienN 108
                                       + ie+ +  n   s+ Gi +l+ +nn+i++n   +n g+g  l+ +s+n+i +n+ ++n++  i+l++s+ n+i  N
  gi|386001817|ref|YP_005920116.1| 497 CFIEGLVAINsdLSEAGIKVLS-NNNVIKDNIAKNNRGVGYLLRSSSGNVITGNTAEENRQGAIRLESSNGNIIYLN 572
                                       4666544444466677777775.777777777777777777777777777777777777777777777777777777 PP

                                       EEESTT--S CS
                        Beta_helix 109 iidnnagsG 117
                                       ++ n + s 
  gi|386001817|ref|YP_005920116.1| 573 NFINGS-SP 580
                                       777666.44 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.4   3.9e-07    0.0014      14     141 ..      35     166 ..      33     196 .. 0.64
   2 !   10.7   3.6   6.5e-05      0.23      83     186 ..     483     575 ..     460     588 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-07
                           DUF1565  14 PfktiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagk.kvgplisgggddlsgv 89 
                                       P  +i  A+ +a +g++++++ GtY e+     Pl++       G  +g G   ++ ag     +++sg g  l+ +
  gi|386001817|ref|YP_005920116.1|  35 PSESIQAAIEGADPGDIVEVSSGTYRENVNVDRPLIL------FGVDTGGGR-PVVDAGGrGSAITLSGSGAVLE-G 103
                                       6678999****************************99......888888888.4444443144556777777666.3 PP

                           DUF1565  90 qnvtivlaneatiaGvtitNp.........nilkgtgvliesasak.ianNtitg.niadGie 141
                                         vt  + ++   aGv++t           +   g g+l es+s + +  N +++   + G+ 
  gi|386001817|ref|YP_005920116.1| 104 FVVTNSGSKTDVDAGVRVTSErnvirnnvaKENAGCGILFESSSRNiVTHNEFSDnPCGAGLL 166
                                       335555555555566666666556665444334566666666644414566666533444433 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.5e-05
                           DUF1565  83 gddlsgvqnvtivlaneatiaGvtitNpnilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGn 159
                                       g ++     +  v +++  i G+   N   l++ g+ + s + +i++N  ++n   G+ +       ++ gn+i+Gn
  gi|386001817|ref|YP_005920116.1| 483 GRFVT---TAITVSGERCFIEGLVAINS-DLSEAGIKVLSNNNVIKDNIAKNN--RGVGYL----LRSSSGNVITGN 549
                                       33332...33446789999****99999.66999**************99997..677544....446889****** PP

                           DUF1565 160 silfeknGiaisgasaavenki.enNii 186
                                       +  ++ +G +  ++s++  n i  nN i
  gi|386001817|ref|YP_005920116.1| 550 TAEENRQGAIRLESSNG--NIIyLNNFI 575
                                       ********998888887..444445554 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00054       1.9      28      86 ..     274     331 ..     260     335 .. 0.88
   2 !    6.0   0.0    0.0041        15      32      90 ..     681     735 ..     667     736 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00054
                        Chlam_OMP6  28 ypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskit 86 
                                       + i++   g  +   vv+++ lp   e++  d   t  a  k+ w++ rl  ge  ++ 
  gi|386001817|ref|YP_005920116.1| 274 FTIDVANLGEMEFDRVVVADILPDGLEYLGDDRNGT-VAGRKVTWELGRLPVGESMRVE 331
                                       78999999*********************9998877.57789************98875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0041
                        Chlam_OMP6  32 itavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskitvwvk 90 
                                       +        vd v+ + +   ve+v+      p++dg  +w+   +g ge   i + vk
  gi|386001817|ref|YP_005920116.1| 681 VCNRNSTVPVDAVVEDIFDGPVELVSVS----PAPDGDGLWRFYEIGLGECREIVLVVK 735
                                       4444455556777777777778887765....6699999***********999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 8660.24
//
Query:       gi|386001818|ref|YP_005920117.1|  [L=304]
Description: 4Fe-4S binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-69  233.0   0.0    4.9e-69  232.8   0.0    1.0  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    0.00012   22.0  11.4    0.00072   19.5   3.1    2.5  2  Fer4_6    4Fe-4S binding domain
    0.00042   20.2  13.3      0.044   13.9   2.4    2.5  2  Fer4_2    4Fe-4S binding domain
    0.00048   19.8  11.2      0.038   13.8   0.4    3.3  2  Fer4      4Fe-4S binding domain
     0.0025   18.2   3.5      0.097   13.1   0.1    2.3  2  Fer4_8    4Fe-4S dicluster domain
     0.0053   16.9   9.2      0.024   14.8   9.7    1.8  2  Fer4_9    4Fe-4S dicluster domain
     0.0057   17.2  11.3       0.15   12.7  13.1    2.2  2  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.025   14.7   5.1       0.11   12.7   0.2    2.3  2  Fer4_21   4Fe-4S dicluster domain
      0.039   14.1   0.9      0.063   13.5   0.9    1.2  1  Fer4_18   4Fe-4S dicluster domain
       0.13   12.4  13.6       0.72   10.0   2.3    2.2  2  Fer4_10   4Fe-4S dicluster domain
       0.76   10.6   6.3        0.6   10.9   0.2    2.9  3  Fer4_15   4Fe-4S single cluster domain
        1.1   10.3  12.4        5.9    7.9   5.5    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
        6.3    7.6  15.0       0.29   11.8   1.8    3.0  2  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.8   0.0   3.5e-72   4.9e-69     101     347 .]       2     295 ..       1     295 [. 0.99

  Alignments for each domain:
  == domain 1  score: 232.8 bits;  conditional E-value: 3.5e-72
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                            HcyBio 101 agkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNssee...tiytymgelkpnlgnatys 174
                                       +g+ v++e+e++++     + +e +++l+d+++a+l+++R+ ++nY+a+vN++ee   ti++ ++++ p  ++a++s
  gi|386001818|ref|YP_005920117.1|   2 EGEVVRVEVETDTG-----SGFEVDLKLADMPTARLFGTRHSFKNYSAFVNPGEErvaTIFH-ATTFDPCWNGASVS 72 
                                       7899*********9.....9**********************************99******.************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 175 gaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLavigdlkeMspeylrgaflt 251
                                       g+G+++Pl+nDp l+tig+Gtr+l++GaeG+v+g+GT+sspe++           +L+ ++d++ M+pey+ g+f t
  gi|386001818|ref|YP_005920117.1|  73 GCGRMNPLENDPLLETIGVGTRVLINGAEGFVLGRGTRSSPERP-----------NLSGYADMHGMDPEYM-GGFGT 137
                                       ********************************************...........****************.***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                            HcyBio 252 syGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael.................... 308
                                       s+Gpe+i ++++piPvl e +le++a  +  i+lpvvDv++r    ++lg+++Ya++                    
  gi|386001818|ref|YP_005920117.1| 138 SAGPECISSWAVPIPVLREGILERMASPEGSIPLPVVDVASR----QELGRATYADVwegvdlevsfdpgackrcta 210
                                       ******************************************....89***************************** PP

                                       .............................................xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 309 .............................................Gkieiegkev.ktarlsslkrareiaeeLkew 339
                                                                                    G++++ g+ev +++r+s++ ra+++aeeLk +
  gi|386001818|ref|YP_005920117.1| 211 crpeaicptgaiafrnflptldrrrcfncglcatscsgdvfrarlGSLRFAGREVpIVVRQSDRLRAERLAEELKGR 287
                                       *******************************************************99******************** PP

                                       xxxxxxxx RF
                            HcyBio 340 iekgeflL 347
                                       i++g+f++
  gi|386001818|ref|YP_005920117.1| 288 ILDGSFRM 295
                                       ******86 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.1   5.2e-07   0.00072       2      24 .]     198     222 ..     197     222 .. 0.96
   2 !    7.0   1.3    0.0048       6.6       5      20 ..     232     247 ..     229     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.2e-07
                            Fer4_6   2 veidpdkCigCgdC..vrvCPegai 24 
                                       v +dp +C  C +C  +++CP+gai
  gi|386001818|ref|YP_005920117.1| 198 VSFDPGACKRCTACrpEAICPTGAI 222
                                       78**********************8 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0048
                            Fer4_6   5 dpdkCigCgdCvrvCP 20 
                                       d+ +C  Cg C++ C 
  gi|386001818|ref|YP_005920117.1| 232 DRRRCFNCGLCATSCS 247
                                       888999*********6 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   3.4   0.00021      0.29       3      22 .]     198     219 ..     196     219 .. 0.86
   2 !   13.9   2.4   3.2e-05     0.044       3      20 ..     229     246 ..     228     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                            Fer4_2   3 vvvdtdrCigCgaCv.sa.CPa 22 
                                       v +d+ +C +C aC+  a CP+
  gi|386001818|ref|YP_005920117.1| 198 VSFDPGACKRCTACRpEAiCPT 219
                                       569***********98667**7 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.2e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       +  d++rC +Cg C ++C
  gi|386001818|ref|YP_005920117.1| 229 PTLDRRRCFNCGLCATSC 246
                                       5689************** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   4.7     0.003       4.2       2      23 ..     199     222 ..     198     223 .. 0.86
   2 !   13.8   0.4   2.7e-05     0.038       2      18 ..     230     246 ..     229     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.003
                                       EEETTTSSS-THH..HHHSTTTEE CS
                              Fer4   2 videekCigCGaC..vevCPvgAI 23 
                                        +d+  C +C aC  + +CP+gAI
  gi|386001818|ref|YP_005920117.1| 199 SFDPGACKRCTACrpEAICPTGAI 222
                                       689**********66679*****9 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.7e-05
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                       + d  +C +CG+C+  C
  gi|386001818|ref|YP_005920117.1| 230 TLDRRRCFNCGLCATSC 246
                                       67899************ PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7     0.018        25       4      17 ..     204     219 ..     201     231 .. 0.77
   2 !   13.1   0.1     7e-05     0.097       3      22 ..     234     255 ..     232     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                            Fer4_8   4 kCieCgaCq..saCpv 17 
                                       +C +C aC+  + Cp+
  gi|386001818|ref|YP_005920117.1| 204 ACKRCTACRpeAICPT 219
                                       7999999996666985 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7e-05
                            Fer4_8   3 ekCieCgaCqsaCp..vlrrtk 22 
                                       ++C +Cg+C ++C   v+r++ 
  gi|386001818|ref|YP_005920117.1| 234 RRCFNCGLCATSCSgdVFRARL 255
                                       69***********444444443 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   2.9    0.0037         5      34      51 .]     203     222 ..     178     222 .. 0.74
   2 !   14.8   9.7   1.8e-05     0.024       1      49 [.     204     249 ..     204     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                            Fer4_9  34 eaCigCgaCv..eaCpkgai 51 
                                        aC  C aC   ++Cp+gai
  gi|386001818|ref|YP_005920117.1| 203 GACKRCTACRpeAICPTGAI 222
                                       57999999976689999987 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.8e-05
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +C +C+aC  ++ Cp+g++  +++  +   r     +C+ Cg C+  C  +
  gi|386001818|ref|YP_005920117.1| 204 ACKRCTACrpEAICPTGAIAFRNFLPTLDRR-----RCFNCGLCATSCSGD 249
                                       599*****87788***********9999976.....4***********865 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   2.9    0.0017       2.4      30      52 .]     197     221 ..     172     221 .. 0.79
   2 !   12.7  13.1   0.00011      0.15       1      49 [.     204     247 ..     204     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                            Fer4_7  30 kveidpekClgCgaC..vavCPtga 52 
                                       +v +dp  C  C+aC  +a CPtga
  gi|386001818|ref|YP_005920117.1| 197 EVSFDPGACKRCTACrpEAICPTGA 221
                                       568999*********44569***98 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                            Fer4_7   1 rCigCgaCv..aaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       +C  C aC   a Cp++ai ++++        +++d ++C +Cg C++ C 
  gi|386001818|ref|YP_005920117.1| 204 ACKRCTACRpeAICPTGAIAFRNF-------LPTLDRRRCFNCGLCATSCS 247
                                       599*****65589********887.......489****************5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.9      0.05        68      40      57 ..     204     222 ..     193     224 .. 0.71
   2 ?   12.7   0.2   7.8e-05      0.11       3      19 ..     231     247 ..     229     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.05
                           Fer4_21  40 eCvGCnlCs..svCPvedci 57 
                                        C  C+ C   ++CP+ ++i
  gi|386001818|ref|YP_005920117.1| 204 ACKRCTACRpeAICPT-GAI 222
                                       6777888853379996.777 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.8e-05
                           Fer4_21   3 idedkCigCgkCliaCe 19 
                                       +d+ +C +Cg+C+++C+
  gi|386001818|ref|YP_005920117.1| 231 LDRRRCFNCGLCATSCS 247
                                       6899************8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9   4.6e-05     0.063      44      96 ..     188     247 ..     175     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                           Fer4_18  44 kkalkekeerkekgagdcidcescv..kvcPtg.idirkGl....qleciscllcidacd 96 
                                       +++ + ++++ + + g c  c +c   ++cPtg i  r+ l    +  c +c+lc  +c+
  gi|386001818|ref|YP_005920117.1| 188 ADVWEGVDLEVSFDPGACKRCTACRpeAICPTGaIAFRNFLptldRRRCFNCGLCATSCS 247
                                       55566667777778899*******6448****86899*9884333458**********96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  14.6    0.0037       5.1       2      55 ..     198     246 ..     197     247 .. 0.78
   2 ?   10.0   2.3   0.00052      0.72       3      19 ..     230     246 ..     228     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0037
                           Fer4_10   2 vvidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       v +d+  C rC++C+    CP+        ++a ++     +  +C +cg C+ +C
  gi|386001818|ref|YP_005920117.1| 198 VSFDPGACKRCTACRPeaICPT-------GAIAFRNFLPTLDRRRCFNCGLCATSC 246
                                       568999********97436***.......44555555555577************* PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00052
                           Fer4_10   3 vidddtCirCgkCvkaC 19 
                                        +d+ +C +Cg C ++C
  gi|386001818|ref|YP_005920117.1| 230 TLDRRRCFNCGLCATSC 246
                                       57999************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.0      0.49   6.8e+02       1      17 [.     198     214 ..     198     220 .. 0.86
   2 ?   -0.7   0.1       1.8   2.5e+03      58      65 ..     216     223 ..     214     224 .. 0.83
   3 ?   10.9   0.2   0.00043       0.6       2      22 ..     230     251 ..     230     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.49
                           Fer4_15   1 VvvDrdaCigcglCvae 17 
                                       V +D  aC  c +C  e
  gi|386001818|ref|YP_005920117.1| 198 VSFDPGACKRCTACRPE 214
                                       789999********765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                           Fer4_15  58 aCPvdAIr 65 
                                        CP++AI 
  gi|386001818|ref|YP_005920117.1| 216 ICPTGAIA 223
                                       5*****95 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00043
                           Fer4_15   2 vvDrdaCigcglCvaea.pevf 22 
                                       ++Dr +C  cglC++ +  +vf
  gi|386001818|ref|YP_005920117.1| 230 TLDRRRCFNCGLCATSCsGDVF 251
                                       68*************9944555 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.5    0.0043       5.9       2      30 ..     205     236 ..     204     238 .. 0.71
   2 ?    6.6   1.4     0.011        15       1      18 [.     235     252 ..     235     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
                           Fer4_16   2 CgtCgkCa..evCPtnaikek.kekeiearec 30 
                                       C++C++C    +CPt+ai  +   ++++ r+c
  gi|386001818|ref|YP_005920117.1| 205 CKRCTACRpeAICPTGAIAFRnFLPTLDRRRC 236
                                       *******73369******97722345566665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       rC +Cg Ca +C  ++++
  gi|386001818|ref|YP_005920117.1| 235 RCFNCGLCATSCSGDVFR 252
                                       6999********877765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   5.7       1.5   2.1e+03       4      16 ..     205     219 ..     202     220 .. 0.55
   2 ?   11.8   1.8   0.00021      0.29       3      15 ..     235     247 ..     232     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                            Fer4_4   4 CigCgsCvaa..CPq 16 
                                       C +C +C+    CP+
  gi|386001818|ref|YP_005920117.1| 205 CKRCTACRPEaiCPT 219
                                       555555543255776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       rC++Cg C  +C+
  gi|386001818|ref|YP_005920117.1| 235 RCFNCGLCATSCS 247
                                       8***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1714.85
//
Query:       gi|386001819|ref|YP_005920118.1|  [L=95]
Description: Putative methanogenesis marker 16 metalloprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-12   45.8   0.0    4.2e-12   45.6   0.0    1.1  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
  ------ inclusion threshold ------
      0.023   13.9   0.0      0.027   13.7   0.0    1.0  1  DUF4106   Protein of unknown function (DUF4106)
       0.13   12.0   0.7       0.19   11.5   0.7    1.3  1  DUF348    G5-linked-Ubiquitin-like domain
       0.14   10.5   0.0       0.14   10.5   0.0    1.0  1  DUF515    Protein of unknown function (DUF515)


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   9.4e-16   4.2e-12       1      50 [.      17      65 ..      17      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 9.4e-16
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaep 50
                                      avVlta+e+ ++ ++ g + ++eevDVVt++T++vms+++a+l+++ a p
  gi|386001819|ref|YP_005920118.1| 17 AVVLTAREVGEVLAD-GGRVSLEEVDVVTCATRAVMSGTYAVLSFPAAPP 65
                                      8************99.999***************************9877 PP

>> DUF4106  Protein of unknown function (DUF4106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.9e-06     0.027     126     204 ..      10      88 ..       2      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-06
                           DUF4106 126 tkkdlvnaflktksqvghyaadgtyvpaggtyipaggtyilavgiyippnppreapapglpktftsshghrhrhapk 202
                                       +k d  +a + t  +vg   adg  v      + +  t  + +g+y     p   pap   ++ + s   r    p 
  gi|386001819|ref|YP_005920118.1|  10 AKVDRGEAVVLTAREVGEVLADGGRVSLEEVDVVTCATRAVMSGTYAVLSFPAAPPAPSGGRSGSRSTASRESSGPA 86 
                                       57788899999*****************************************************99*****999999 PP

                           DUF4106 203 pt 204
                                       pt
  gi|386001819|ref|YP_005920118.1|  87 PT 88 
                                       98 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   4.2e-05      0.19      12      37 ..      18      44 ..      11      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                                      E----SSHHHHHHHT.T----TT-EEE CS
                            DUF348 12 vrTaadTVgdlLeea.gitlgeqDkVs 37
                                      v  +a+ Vg++L++   ++l+e+D+V+
  gi|386001819|ref|YP_005920118.1| 18 VVLTAREVGEVLADGgRVSLEEVDVVT 44
                                      34579********996788*******8 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.2e-05      0.14     259     323 ..      17      83 ..      10      95 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.2e-05
                            DUF515 259 lvlvrekqvGkliapGDevkvYaKde.atiayeivdssYvillllsv.eagsisvSEsqsqsssvse 323
                                       +v+  ++ vG+++a G +v++   d  +  +++++  +Y +l + ++  a+s + S s+s++s  s+
  gi|386001819|ref|YP_005920118.1|  17 AVVLTAREVGEVLADGGRVSLEEVDVvTCATRAVMSGTYAVLSFPAApPAPSGGRSGSRSTASRESS 83 
                                       6889999****************998555678899999*9997777788999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 613.71
//
Query:       gi|386001820|ref|YP_005920119.1|  [L=254]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-18   66.1   0.1      3e-17   63.0   0.1    2.1  1  Methyltransf_11  Methyltransferase domain
      1e-16   61.4   0.1    1.3e-08   35.4   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
    1.6e-13   50.8   0.0      2e-13   50.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.2e-10   41.2   0.0      1e-09   39.0   0.0    1.9  1  Methyltransf_12  Methyltransferase domain
    3.2e-09   36.8   0.0     0.0019   18.0   0.0    2.1  2  Methyltransf_31  Methyltransferase domain
    8.9e-09   35.0   0.0    7.2e-06   25.5   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.2e-05   25.1   0.0    8.1e-05   22.4   0.0    1.9  1  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
      0.034   13.1   0.0       0.58    9.0   0.0    2.0  2  Methyltransf_9   Protein of unknown function (DUF1698)
      0.056   13.3   0.0       0.58   10.0   0.0    2.0  2  Methyltransf_8   Hypothetical methyltransferase
      0.072   12.7   0.0       0.37   10.3   0.0    1.9  2  MetW             Methionine biosynthesis protein MetW
       0.09   12.3   0.0        1.3    8.6   0.0    2.1  2  MTS              Methyltransferase small domain
       0.23   10.9   0.0       0.72    9.3   0.0    1.7  2  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.1     2e-20     3e-17       1      96 []      50     177 ..      50     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2e-20
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHH....HHHHHHCCHHT-..........................EEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskeml....klakekaseegl..........................kvef 47 
                                       L++GcG+G+ ++ +  r  rv +vD+s+++l     la+e ++++gl                          ++e+
  gi|386001820|ref|YP_005920119.1|  50 LELGCGNGKTLQGMLGRPWRVAAVDVSPQALrlgrGLAEETGRRRGLlrpepstssgvrpppappadrvplanRLEL 126
                                       89*************888*************4444444555555555888788888777777888887777777777 PP

                                       TTEECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  48 vvadaeklpfednsfDlvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                       v ada +lpf+d+sfD+v++++vl h+   d+ ka +e+aRvLk  G+l++
  gi|386001820|ref|YP_005920119.1| 127 VSADAVHLPFRDSSFDAVFAFHVLGHLreGDRIKAAREAARVLKAKGRLFF 177
                                       ***************************8779*****************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.6e-08   5.3e-05       1      45 [.      49      91 ..      49      99 .. 0.91
   2 !   35.4   0.0   8.8e-12   1.3e-08      47      97 .]     123     173 ..     115     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.6e-08
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTT CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeg 45
                                      vL+lGcG+G++++ ++ r +  +v +vD+s+++l+  r  aee g
  gi|386001820|ref|YP_005920119.1| 49 VLELGCGNGKTLQGMLGR-P-WRVAAVDVSPQALRLGRGLAEETG 91
                                      9***************99.4.***************999887754 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 8.8e-12
                                       TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  47 nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       ++e+v +da +lpf d+sfD+v+++++l hl + d+ ka +e+arvLk +G
  gi|386001820|ref|YP_005920119.1| 123 RLELVSADAVHLPFRDSSFDAVFAFHVLGHLREGDRIKAAREAARVLKAKG 173
                                       8999********************877*********************988 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.3e-16     2e-13      10     134 ..      34     197 ..      23     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.3e-16
                   Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......................... 61 
                                       + +  rl+p l++g+rvL++GcG G +l+ +  +++ v++vD sp+a  + +                         
  gi|386001820|ref|YP_005920119.1|  34 RGAPRRLPP-LPEGARVLELGCGNGKTLQGMLGRPWRVAAVDVSPQALRLGRglaeetgrrrgllrpepstssgvrp 109
                                       455556665.9***********************************9999999999999999888888887777777 PP

                   Methyltransf_23  62 .................kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvp..dppellrqiatllkpgGylllse 119
                                                                ++d+   ++ + +fd + +++vl+h++  d  ++ r +a+ lk  G+l++ e
  gi|386001820|ref|YP_005920119.1| 110 ppappadrvplanrlelV-------SADAVHLPFRDSSFDAVFAFHVLGHLRegDRIKAAREAARVLKAKGRLFFIE 179
                                       777766666644332222.......222234444667***************999********************** PP

                   Methyltransf_23 120 plasl...kedrllldwl 134
                                       +++++    e   +++++
  gi|386001820|ref|YP_005920119.1| 180 FGVEDmraGEGVEVEEMT 197
                                       *99876553444444444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0     7e-13     1e-09       1      99 []      50     175 ..      50     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 7e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg............. 64 
                                       Le+GcG+G +l+ +l +  ++++ +vD+sp+a+ +  + la++ +++   ++ e   ++   ++             
  gi|386001820|ref|YP_005920119.1|  50 LELGCGNGKTLQGMLGR--PWRVAAVDVSPQAL-RLGRGLAEETGRRRGLLRPEPSTSSGVRPPpappadrvplanr 123
                                       8****************..**************.777777777777777777777666555555899********** PP

                   Methyltransf_12  65 ...............ssfDlvvasnvlhhl..kdirevldnirklLkpgGrl 99 
                                                      ssfD+v+a++vl hl   d+ ++ ++++++Lk  Grl
  gi|386001820|ref|YP_005920119.1| 124 lelvsadavhlpfrdSSFDAVFAFHVLGHLreGDRIKAAREAARVLKAKGRL 175
                                       *******************************99999*************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.3e-06    0.0049       4      52 ..      46      91 ..      44      94 .. 0.89
   2 !   18.0   0.0   1.2e-06    0.0019      55     114 ..     123     182 ..     119     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                   Methyltransf_31  4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklg 52
                                      g rvl+lGCG+G+ +  +    g   +v  +D s++a++l r  a++ g
  gi|386001820|ref|YP_005920119.1| 46 GARVLELGCGNGKTLQGML---GRPWRVAAVDVSPQALRLGRGLAEETG 91
                                      679**********999999...66789*************999998765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.2e-06
                   Methyltransf_31  55 nveFeqgdieeleklledekfDlilsnevl..naladpdkileeiervlkpggilliedprl 114
                                       ++e+  +d+ +l+  + d++fD ++++ vl      d  k+ +e+ rvlk +g+l   ++ +
  gi|386001820|ref|YP_005920119.1| 123 RLELVSADAVHLP--FRDSSFDAVFAFHVLghLREGDRIKAAREAARVLKAKGRLFFIEFGV 182
                                       67888899999**..***************8777788889999************9988873 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0016       2.4      33      97 ..      31      92 ..      27      97 .. 0.89
   2 !   25.5   0.0   4.8e-09   7.2e-06      99     155 ..     123     181 ..     117     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTS CS
                   Ubie_methyltran 33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegk 97
                                      r+W+    +l    +ga+vl++ +G g    +l+ ++g+  +v  +D++++ L+ g+  ++e+g 
  gi|386001820|ref|YP_005920119.1| 31 RIWRGAPRRLPPLPEGARVLELGCGNGK---TLQGMLGRPWRVAAVDVSPQALRLGRGLAEETGR 92
                                      789999999999999***********97...577889999*****************99998885 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 4.8e-09
                                       TEEEEE--TTT-TTS-T-EEEEEEES..-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE- CS
                   Ubie_methyltran  99 nieflqanaeeLpfeddsfDvvtvsf..GlrnvtDklkaLkeayrvlkpGGrlvvlefs 155
                                       ++e++ a+a +Lpf d sfD v   +  G     D+ ka +ea rvlk+ Grl+ +ef 
  gi|386001820|ref|YP_005920119.1| 123 RLELVSADAVHLPFRDSSFDAVFAFHvlGHLREGDRIKAAREAARVLKAKGRLFFIEFG 181
                                       7899****************997654124444589**********************96 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.4e-08   8.1e-05      36     155 ..      44     179 ..      38     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.4e-08
                                       S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHH...HHHHHHTT.....SGGGGGEEEE--........... CS
                              TPMT  36 kaglrvlvPlCGkaldlvwlAeqgrevvGvelselAve...kffeeanl.....epkvkelsgvke.........ys 95 
                                       ++g+rvl  +CG++  l+ +  + ++v++v++s++A++     +ee++      +p+ ++ sgv+            
  gi|386001820|ref|YP_005920119.1|  44 PEGARVLELGCGNGKTLQGMLGRPWRVAAVDVSPQALRlgrGLAEETGRrrgllRPEPSTSSGVRPppappadrvPL 120
                                       678999*9****************************97332355666557778967666666655332222111245 PP

                                       .........-TTT---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..EEE CS
                              TPMT  96 ageiellcgdvFtlraeelgkfdliydraalvAlppelreryakslaelLkpdgeglLvt 155
                                       a+++el+ +d+  l+ ++  +fd+++   +l  l + +r + a++ a++Lk++g+ +++ 
  gi|386001820|ref|YP_005920119.1| 121 ANRLELVSADAVHLPFRDS-SFDAVFAFHVLGHLREGDRIKAAREAARVLKAKGRLFFIE 179
                                       789**************99.9**********************************99986 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00039      0.58     104     149 ..      33      80 ..      23      87 .. 0.76
   2 ?    1.8   0.0     0.059        89     177     215 ..     134     175 ..     121     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00039
                                       HHHHGGGS.--.TT-EEEEET-TTSHHHHHHHHCT-SE.EEEE---HH CS
                    Methyltransf_9 104 Wdrvlphlsdl.kgrtildvGcgnGyhlwrmvgegakl.vvGidPsel 149
                                       W    + l++l +g ++l++GcgnG  l  m+g+  ++ +v + P+ l
  gi|386001820|ref|YP_005920119.1|  33 WRGAPRRLPPLpEGARVLELGCGNGKTLQGMLGRPWRVaAVDVSPQAL 80 
                                       6666677888845789*****************976642577777766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.059
                                       S-T.---EEEEEEES-GGG-S-H..HHHHHHHHCTEEEEEEE CS
                    Methyltransf_9 177 lpe.leafdtvfsmGvlyhrrsP..ldhllqlkdqlvkgGel 215
                                       lp   ++fd+vf+  vl h r    +   ++    l+++G l
  gi|386001820|ref|YP_005920119.1| 134 LPFrDSSFDAVFAFHVLGHLREGdrIKAAREAARVLKAKGRL 175
                                       5553578**********9977531144444444455666655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.2     3e+02      74     103 ..      47      77 ..      38      82 .. 0.77
   2 ?   10.0   0.0   0.00039      0.58     107     158 ..     125     179 ..     115     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.2
                                       S-EEEES-TT-HHH.HH--S-..EEEEESS- CS
                    Methyltransf_8  74 lvvadlGcGeakia.eavrekekvrsfdlva 103
                                         v +lGcG+ k      +++ +v ++d+ +
  gi|386001820|ref|YP_005920119.1|  47 ARVLELGCGNGKTLqGMLGRPWRVAAVDVSP 77 
                                       56899*****997635678888888888765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00039
                                       TEEES-TTS-S--TT-EEEEEEES---SS....-HHHHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_8 107 rvvacdlakvPledesvdvavfclslmgt....nladflkeanrvlkvGGllkvae 158
                                       ++v+ d  ++P  d+s d avf + ++g     +  +  +ea rvlk  G l+  e
  gi|386001820|ref|YP_005920119.1| 125 ELVSADAVHLPFRDSSFD-AVFAFHVLGHlregDRIKAAREAARVLKAKGRLFFIE 179
                                       4678999***********.56666666542223677889*********99998766 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00025      0.37      12      29 ..      44      61 ..      40      78 .. 0.87
   2 ?   -0.3   0.0      0.47     7e+02      71     101 ..     136     168 ..     125     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                              MetW 12 kpgsrvldlGcGdGelle 29
                                      ++g+rvl+lGcG+G+ l+
  gi|386001820|ref|YP_005920119.1| 44 PEGARVLELGCGNGKTLQ 61
                                      7899**********9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                              MetW  71 fedksfdyvvlsqtlqatrnpkevl..dellri 101
                                       f+d+sfd v     l  +r+ +++   +e  r+
  gi|386001820|ref|YP_005920119.1| 136 FRDSSFDAVFAFHVLGHLREGDRIKaaREAARV 168
                                       899999999999999988888877422455555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00086       1.3      32      75 ..      46      87 ..      37      97 .. 0.74
   2 ?    1.5   0.0      0.13   1.9e+02     122     138 ..     162     178 ..     127     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00086
                                      CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHH CS
                               MTS 32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenl 75
                                        +vl lGcG+G     ++ +    +v +vdv+ +Al++ +  +
  gi|386001820|ref|YP_005920119.1| 46 GARVLELGCGNGKTLQGMLGRP--WRVAAVDVSPQALRLGRGLA 87
                                      568*********7555444433..359999******99877655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                       HHHHHHHEEEEEEEEEE CS
                               MTS 122 iaeAkeaLkegGeLliV 138
                                        +eA+++Lk +G+L+++
  gi|386001820|ref|YP_005920119.1| 162 AREAARVLKAKGRLFFI 178
                                       579***********987 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   1.7e+03      36      44 ..      50      58 ..      45      86 .. 0.55
   2 ?    9.3   0.0   0.00048      0.72     133     172 ..     137     176 ..     120     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                      EEES-TTTH CS
                              CheR 36 wsagcssGe 44
                                      ++ gc++G+
  gi|386001820|ref|YP_005920119.1| 50 LELGCGNGK 58
                                      555555554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00048
                                       GG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEE CS
                              CheR 133 vlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLl 172
                                         +++D +f+  vl  ++e ++ k  ++ a+ lk++g+L+
  gi|386001820|ref|YP_005920119.1| 137 RDSSFDAVFAFHVLGHLREGDRIKAAREAARVLKAKGRLF 176
                                       5689**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1662.71
//
Query:       gi|386001821|ref|YP_005920120.1|  [L=313]
Description: hypothetical protein Mhar_1129 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.75    9.7   5.3        1.5    8.8   5.3    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.3   8.2e-05       1.5       8      26 .]     195     213 ..     193     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 8.2e-05
                        TAT_signal   8 LKgsAAaaAAaalggcaaa 26 
                                       + gsAAaaA +a++g+a+a
  gi|386001821|ref|YP_005920120.1| 195 IAGSAAAAASTATPGPAPA 213
                                       679*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2079.02
//
Query:       gi|386001822|ref|YP_005920121.1|  [L=375]
Description: hypothetical protein Mhar_1130 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2446.64
//
Query:       gi|386001823|ref|YP_005920122.1|  [L=448]
Description: Deoxyribodipyrimidine photo-lyase (DNA photolyase)(Photoreactivating enzyme) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-31  109.7   0.2    3.4e-31  108.5   0.2    1.7  1  DNA_photolyase  DNA photolyase
  ------ inclusion threshold ------
      0.053   14.0   0.1       0.18   12.3   0.1    1.9  1  Usp             Universal stress protein family


Domain annotation for each model (and alignments):
>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.2   3.8e-35   3.4e-31       1     162 [.      19     178 ..      19     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 3.8e-35
                                       EEEEESS---STT-HHHHHH....HCTTSEEEEEEEE-HHHHTCGS-CHHHHH..HHHHHHHHHHHHHHHTT--EEE CS
                    DNA_photolyase   1 vlvWfrrDlRlhDNpALaaA....aasgepvipvfvldpekahklrvgaarvd..fllesLadLdeeLrelgirLvv 71 
                                       v++W+ rD+R + N+ALa A    +++++p+++vf l++e     ++gaa ++  f+l++L++ +++Lr++ i++v+
  gi|386001823|ref|YP_005920122.1|  19 VIYWMTRDQRAEENWALAFAqelaLERRAPLAVVFALKEE-----FLGAAMRQygFMLRGLEEVERTLRDKEIPFVL 90 
                                       79****************6655559999************.....5566555556********************** PP

                                       EESSHHHHHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHH CS
                    DNA_photolyase  72 rrgdpadvlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpf 148
                                       ++gdp + +p++++e+ asa+v+++++   +r++ e+ +e l+   ++++++d+h++v+++ +  k+++++++F+p+
  gi|386001823|ref|YP_005920122.1|  91 LQGDPGETVPDFVREHSASALVTDFSPLATKRAWMEKAEEGLD---LPLREVDAHNVVPCWVASPKQEYAARTFRPK 164
                                       *****************************************97...9****************99999********* PP

                                       HHCHHHHHCS-TTS CS
                    DNA_photolyase 149 rkrwlkelkeplpa 162
                                        +r l  + e+ pa
  gi|386001823|ref|YP_005920122.1| 165 VRRLLPIFCEDPPA 178
                                       ***99877755554 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     2e-05      0.18      18     109 ..      34     113 ..      26     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHH CS
                               Usp  18 AlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaee 94 
                                       Al +A ela +r a+l ++ +++++  ga+      + +  +e e++ +            +++  +v+++gdp+e+
  gi|386001823|ref|YP_005920122.1|  34 ALAFAQELALERRAPLAVVFALKEEFLGAAMRQYGFMLRGLEEVERTLR------------DKEIPFVLLQGDPGET 98 
                                       89999999999999*9999999999999999999988888888888866............689************* PP

                                       HHHHHHHTTSSEEEE CS
                               Usp  95 ilevaeeedadliVv 109
                                         ++++e++a+ +V+
  gi|386001823|ref|YP_005920122.1|  99 VPDFVREHSASALVT 113
                                       ************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2986.22
//
Query:       gi|386001824|ref|YP_005920123.1|  [L=367]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-22   79.5   0.9      3e-22   78.3   0.9    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    6.3e-15   55.5   1.2    1.2e-14   54.5   1.2    1.5  1  OrfB_IS605      Probable transposase
     0.0008   19.7   1.7     0.0019   18.5   1.7    1.6  1  C1_2            C1 domain
     0.0049   16.9   0.1     0.0095   15.9   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0059   16.5   1.4      0.016   15.1   1.4    1.7  1  C1_1            Phorbol esters/diacylglycerol binding domain 
  ------ inclusion threshold ------
      0.099   12.3   4.2       0.36   10.5   4.2    2.0  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.12   12.5   3.6       0.82    9.8   0.3    2.8  2  UPF0547         Uncharacterised protein family UPF0547
       0.32   10.7   3.8        2.8    7.7   0.2    2.6  2  Rubredoxin_2    Rubredoxin metal binding domain
        1.4    8.7   6.0         40    4.1   6.2    2.4  2  zinc_ribbon_2   zinc-ribbon domain
        4.4    7.1   9.6        1.4    8.8   0.1    2.8  3  zf-C2H2_11      zinc-finger C2H2-type


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 !   78.3   0.9   1.7e-25     3e-22       1      68 [.     281     348 ..     281     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.7e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f++l+++++yka+   +++ +v+ +yTS++CseCg++ k +++g  f+C++Cgfe+++D+nA++Ni++
  gi|386001824|ref|YP_005920123.1| 281 FYQLEQFIRYKAEAIEKHTLLVDARYTSQKCSECGHIYKGNRNGSSFRCRKCGFELHADLNASRNIAQ 348
                                       899***************************************************************96 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   1.2   6.9e-18   1.2e-14       6     111 ..     161     259 ..     156     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 6.9e-18
                        OrfB_IS605   6 veve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                       +e++ +++ ++ k++giD Gi n+a++++++    +y+++++k++  ++a  ++elqsk  ks     a+rkl+rl 
  gi|386001824|ref|YP_005920123.1| 161 LEHDdPQPITEFKVLGIDRGIVNIAVCSDNT----FYNSKKVKNTRAKYAHLQKELQSKGTKS-----AKRKLKRLA 228
                                       44441444556699*****************....************************6666.....8******** PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkev.gvetL 111
                                        k +r+++++ h +++++++  ++v ++e+L
  gi|386001824|ref|YP_005920123.1| 229 GKERRFVTDVNHCISKQIVNSDYTVfALEDL 259
                                       ********************99988777777 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.7     1e-06    0.0019       4      44 ..     297     338 ..     295     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1e-06
                              C1_2   4 pHpLtlskgedssesfnCsaCgrkidgff....YsCseCdfslhv 44 
                                       +H+L  +    ++ s +Cs Cg+  +g++    ++C +C f lh 
  gi|386001824|ref|YP_005920123.1| 297 KHTLLVD---ARYTSQKCSECGHIYKGNRngssFRCRKCGFELHA 338
                                       4888888...999***********666666678***********7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.3e-06    0.0095      53      95 ..     291     335 ..     226     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.3e-06
                                       CC.TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS CS
                              HypA  53 egtvlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgsa 95 
                                       + +++e+ +L ++    + +C+eCg+ ++ +++  ++rC kCg +
  gi|386001824|ref|YP_005920123.1| 291 KAEAIEKHTLLVDARYTSQKCSECGHIYKGNRNgsSFRCRKCGFE 335
                                       56678999999******************66644699*****965 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.4   8.8e-06     0.016       9      40 ..     306     338 ..     298     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.8e-06
                                       SS--B-TTT-SB--S.SSS-EEEETTT--EE-C CS
                              C1_1   9 kqptfCkhCgeflwg.kekqglkCswCkllvHk 40 
                                       + +++C++Cg + +g  +   ++C+ C++  H 
  gi|386001824|ref|YP_005920123.1| 306 YTSQKCSECGHIYKGnRNGSSFRCRKCGFELHA 338
                                       5789****************************7 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.2    0.0002      0.36       2      25 ..     310     334 ..     309     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                       B-SSS--B--.--SSS----SSS-- CS
                    DNA_RNApol_7kD   2 iCgeCgaevs.lkkgdpiRCkeCGh 25 
                                       +C eCg+  +  ++g + RC++CG+
  gi|386001824|ref|YP_005920123.1| 310 KCSECGHIYKgNRNGSSFRCRKCGF 334
                                       6*********999***********8 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00046      0.82      15      24 ..     309     318 ..     307     319 .. 0.87
   2 ?    2.5   0.3     0.088   1.6e+02      16      23 ..     328     335 ..     325     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                           UPF0547  15 qfCphCGyvF 24 
                                       q+C++CG+++
  gi|386001824|ref|YP_005920123.1| 309 QKCSECGHIY 318
                                       99******87 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.088
                           UPF0547  16 fCphCGyv 23 
                                       +C+ CG++
  gi|386001824|ref|YP_005920123.1| 328 RCRKCGFE 335
                                       6*****97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.032        57       3       9 ..     311     317 ..     310     320 .. 0.80
   2 ?    7.7   0.2    0.0016       2.8       1      10 [.     327     336 ..     327     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.032
                      Rubredoxin_2   3 CsqCGfe 9  
                                       Cs+CG+ 
  gi|386001824|ref|YP_005920123.1| 311 CSECGHI 317
                                       9999986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       ++C++CGfe 
  gi|386001824|ref|YP_005920123.1| 327 FRCRKCGFEL 336
                                       8*******85 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6      0.03        53      15      21 ..     310     316 ..     307     318 .. 0.63
   2 ?    4.1   6.2     0.022        40       1      23 []     310     336 ..     310     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.03
                     zinc_ribbon_2  15 FCpyCGt 21 
                                        C++CG+
  gi|386001824|ref|YP_005920123.1| 310 KCSECGH 316
                                       4566655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.022
                     zinc_ribbon_2   1 fCpnCG...aelqdnakF.CpyCGtpl 23 
                                       +C++CG   + + +++ F C +CG++l
  gi|386001824|ref|YP_005920123.1| 310 KCSECGhiyKGNRNGSSFrCRKCGFEL 336
                                       688888333356778888******987 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.5       5.1   9.1e+03       4       8 ..      83      87 ..      82      88 .. 0.79
   2 ?    4.3   0.4     0.019        34       3      12 ..     307     316 ..     306     319 .. 0.84
   3 ?    8.8   0.1   0.00076       1.4       1      11 [.     323     333 ..     323     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.1
                        zf-C2H2_11  4 tcqCl 8 
                                      +c+C+
  gi|386001824|ref|YP_005920123.1| 83 ACKCR 87
                                      79997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                        zf-C2H2_11   3 stcqCleCGl 12 
                                       ++++C eCG 
  gi|386001824|ref|YP_005920123.1| 307 TSQKCSECGH 316
                                       699******6 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00076
                        zf-C2H2_11   1 destcqCleCG 11 
                                       + s+++C++CG
  gi|386001824|ref|YP_005920123.1| 323 NGSSFRCRKCG 333
                                       689*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2398.78
//
Query:       gi|386001825|ref|YP_005920124.1|  [L=51]
Description: hypothetical protein Mhar_1133 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-05   23.8   0.9    3.7e-05   23.6   0.9    1.1  1  DZR             Double zinc ribbon
    4.8e-05   23.4   2.0    7.9e-05   22.7   2.0    1.3  1  Zn-ribbon_8     Zinc ribbon domain
    0.00022   21.2   0.6    0.00023   21.1   0.6    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.003   17.4   3.0       0.44   10.5   0.2    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.004   17.0   1.7       0.01   15.8   1.7    1.7  1  DUF4428         Domain of unknown function (DUF4428)
     0.0095   15.9   0.3      0.012   15.6   0.3    1.2  1  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.011   15.5   0.3      0.011   15.5   0.3    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.018   14.9   0.7      0.025   14.5   0.7    1.2  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.019   15.5   2.9      0.021   15.3   2.9    1.1  1  DUF702          Domain of unknown function (DUF702)
       0.02   14.8   1.3      0.025   14.4   1.3    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.022   14.5   7.1       0.17   11.6   0.4    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.022   14.6   4.3       0.56   10.1   0.2    2.1  2  zf-trcl         Probable zinc-ribbon domain
      0.031   13.8   4.5       0.53    9.8   0.5    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.036   14.0   1.3       0.05   13.6   1.3    1.2  1  zf-RING_5       zinc-RING finger domain
      0.037   13.9   1.9        6.4    6.8   0.0    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.041   13.6   4.0      0.066   12.9   4.0    1.4  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.041   13.8   1.7      0.041   13.8   1.7    2.1  2  zinc_ribbon_4   zinc-ribbon domain
      0.059   13.4   1.1      0.079   13.0   1.1    1.2  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.08   12.2   0.1       0.08   12.2   0.1    1.1  1  CcmH            Cytochrome C biogenesis protein
        0.1   11.4   0.9       0.12   11.2   0.9    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.12   12.1   0.2       0.12   12.1   0.2    2.3  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.12   13.1   0.6       0.13   12.9   0.6    1.1  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
       0.12   12.4   2.5       0.84    9.7   2.7    1.9  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
       0.17   11.8   3.4        0.3   11.0   3.4    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.22   11.3   6.0         10    6.0   5.9    2.1  1  zinc_ribbon_5   zinc-ribbon domain
       0.25   10.8   5.0        1.2    8.6   0.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.29   11.6   4.3        1.8    9.0   0.2    2.6  3  zf-IS66         zinc-finger binding domain of transposase IS6
       0.34   10.6   2.9       0.71    9.5   0.2    2.0  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.49   10.4   5.8       0.87    9.6   1.1    2.1  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.9     6e-08   3.7e-05       8      39 ..      16      48 ..      12      51 .] 0.85

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6e-08
                               DZR  8 lppdarfCseCgtklkavaaedrCpsCgek.vd 39
                                      + ++  +C++Cg+k k + +  rCpsC++  v+
  gi|386001825|ref|YP_005920124.1| 16 IASKGYVCQDCGNKFKGMGRRVRCPSCQSRnVK 48
                                      5677789*********************98554 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   2.0   1.3e-07   7.9e-05       6      36 ..      21      47 ..      20      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-07
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.ev 36
                                      Y C++Cg++f  + +      + CP+C+s +v
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKFKGMGR-----RVRCPSCQSrNV 47
                                      9**********8874.....566******777 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.6   3.8e-07   0.00023      71      98 ..      21      48 ..      10      51 .] 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-07
                                      EEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsadve 98
                                      + C++Cg++f+   +++rCp+C+s++v+
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKFKGMGRRVRCPSCQSRNVK 48
                                      68*********666679*******9987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2    0.0007      0.44      29      39 .]      21      31 ..      17      31 .. 0.89
   2 !    7.6   0.2    0.0054       3.3       2      11 ..      38      47 ..      37      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0007
                           TFIIS_C 29 ykCtkCghrWr 39
                                      y+C +Cg++++
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKFK 31
                                      9********97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0054
                           TFIIS_C  2 kCpkCgsrea 11
                                      +Cp+C+sr++
  gi|386001825|ref|YP_005920124.1| 38 RCPSCQSRNV 47
                                      7******986 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.7   1.6e-05      0.01      20      35 ..      20      35 ..       9      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                           DUF4428 20 gyvCkdClkKlsefls 35
                                      gyvC+dC +K++++  
  gi|386001825|ref|YP_005920124.1| 20 GYVCQDCGNKFKGMGR 35
                                      9*********977654 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.9e-05     0.012       2      24 ..      22      44 ..      11      50 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-05
                                      --SSS-S--EE-SSEEE-TTT-- CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqe 24
                                       C++C ++ +  g++++C +Cq+
  gi|386001825|ref|YP_005920124.1| 22 VCQDCGNKFKGMGRRVRCPSCQS 44
                                      36666666666666666666665 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.3   1.7e-05     0.011     145     172 ..      19      46 ..       9      51 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                           TackOD1 145 evykCnsCkslfsepevkarClsCekes 172
                                       + y+C++C++ f+    ++rC sC++++
  gi|386001825|ref|YP_005920124.1|  19 KGYVCQDCGNKFKGMGRRVRCPSCQSRN 46 
                                       4578888888888888888888888765 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   4.1e-05     0.025       3      27 ..      19      43 ..      17      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                       Prok-RING_1  3 tgkkCpvCgkelkeedDiVvCpeCg 27
                                      +g  C+ Cg+++k     V Cp C 
  gi|386001825|ref|YP_005920124.1| 19 KGYVCQDCGNKFKGMGRRVRCPSCQ 43
                                      6789********************7 PP

>> DUF702  Domain of unknown function (DUF702)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.9   3.4e-05     0.021       2      30 ..      20      47 ..      19      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-05
                            DUF702  2 gisCqdCgnqakkdCahlrCRtCCksrgf 30
                                      g  CqdCgn+ k      rC +C +sr+ 
  gi|386001825|ref|YP_005920124.1| 20 GYVCQDCGNKFKGMGRRVRCPSC-QSRNV 47
                                      568*****************997.88876 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   4.1e-05     0.025      24      45 ..      21      44 ..      17      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.1e-05
                                      EE-HHHHHHHHH..TT-B-TTT-- CS
                        zf-C3HC4_3 24 vlCeeCaekllk..rkkkCpiCrr 45
                                      ++C++C +k++   r+ +Cp C++
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKFKGmgRRVRCPSCQS 44
                                      58********8799********97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00028      0.17       1      10 [.      21      30 ..      21      35 .. 0.89
   2 ?    6.4   1.5     0.012       7.5      16      22 ..      38      44 ..      38      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      YvC++CG+++
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKF 30
                                      9******976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                      Rubredoxin_2 16 rCpsCgs 22
                                      rCpsC+s
  gi|386001825|ref|YP_005920124.1| 38 RCPSCQS 44
                                      8****97 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00091      0.56       3      14 ..      19      30 ..      17      31 .. 0.88
   2 ?    6.4   0.6     0.014       8.3      33      42 ..      36      45 ..      32      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00091
                           zf-trcl  3 ktltCkdCgaef 14
                                      k ++C+dCg++f
  gi|386001825|ref|YP_005920124.1| 19 KGYVCQDCGNKF 30
                                      6689******98 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                           zf-trcl 33 pkRCkaCRka 42
                                      ++RC++C ++
  gi|386001825|ref|YP_005920124.1| 36 RVRCPSCQSR 45
                                      68*****875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00085      0.53      12      28 ..      13      29 ..       1      31 [. 0.69
   2 ?    6.2   0.3     0.011       7.1       2      10 ..      38      46 ..      37      51 .] 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00085
                                      HEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon 12 veDpergelvCtdCGlV 28
                                      ve  ++  +vC dCG+ 
  gi|386001825|ref|YP_005920124.1| 13 VESIASKGYVCQDCGNK 29
                                      666777889******85 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      +CP C s+n
  gi|386001825|ref|YP_005920124.1| 38 RCPSCQSRN 46
                                      7******98 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.3   8.1e-05      0.05      24      43 ..      22      43 ..      20      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.1e-05
                         zf-RING_5 24 fCekClkkll..ekeavCpiCr 43
                                      +C++C +k +  +++++Cp C+
  gi|386001825|ref|YP_005920124.1| 22 VCQDCGNKFKgmGRRVRCPSCQ 43
                                      8********************8 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0      0.01       6.4       5      14 ..      21      30 ..      12      33 .. 0.68
   2 ?    6.7   0.7     0.011       6.7       6      13 ..      38      45 ..      35      49 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.01
                    Zn_ribbon_SprT  5 YrCtgCgrey 14
                                      Y+C +Cg+++
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKF 30
                                      6666666554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                    Zn_ribbon_SprT  6 rCtgCgre 13
                                      rC++C+++
  gi|386001825|ref|YP_005920124.1| 38 RCPSCQSR 45
                                      68888843 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.0   0.00011     0.066       1      26 [.      21      45 ..      21      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      -B-SSS--B--.--SSS----SSS--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhR 26
                                      Y C +Cg++++ + ++  +RC  C +R
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNKFKgMGRR--VRCPSCQSR 45
                                      9**********78777..******888 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3      0.06        37      28      35 ..      23      30 ..      21      31 .. 0.69
   2 ?   13.8   1.7   6.6e-05     0.041      18      32 ..      29      43 ..      28      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.06
                     zinc_ribbon_4 28 CskCghvF 35
                                      C  Cg++F
  gi|386001825|ref|YP_005920124.1| 23 CQDCGNKF 30
                                      77777777 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.6e-05
                     zinc_ribbon_4 18 klpakgvkvrCskCg 32
                                      k+++ g++vrC+ C+
  gi|386001825|ref|YP_005920124.1| 29 KFKGMGRRVRCPSCQ 43
                                      88999*********9 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1   0.00013     0.079      37      68 ..      18      47 ..      12      50 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                       Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrhCpsCqkkat 68
                                       + y C++Cg+  ++    ++  CpsCq+++ 
  gi|386001825|ref|YP_005920124.1| 18 SKGYVCQDCGN--KFKGMGRRVRCPSCQSRNV 47
                                      56799*****7..4444455556*****9875 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.08      27      47 ..      28      48 ..      10      51 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHEE-TTSSS-BTT CS
                              CcmH 27 araralseeLRClvCqnqsia 47
                                      ++++ + + +RC+ Cq+ +++
  gi|386001825|ref|YP_005920124.1| 28 NKFKGMGRRVRCPSCQSRNVK 48
                                      6789999**********9986 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   0.00019      0.12     505     529 ..      18      46 ..      14      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                       --EEEETT.--..EESS..SB-TTT--BE CS
                              NRDD 505 pkidvCnecgy..kgei..ekCpkCgsee 529
                                        k  vC++cg   kg     +Cp+C+s++
  gi|386001825|ref|YP_005920124.1|  18 SKGYVCQDCGNkfKGMGrrVRCPSCQSRN 46 
                                       56679******7744446689*****877 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.1   3.2e+03       5      10 ..       1       6 [.       1      10 [. 0.68
   2 ?   12.1   0.2   0.00019      0.12      21      29 ..      20      28 ..      15      31 .. 0.84
   3 ?    0.7   0.1      0.74   4.6e+02      24      29 ..      39      44 ..      38      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.1
                     A2L_zn_ribbon  5 vCsvCg 10
                                      +C+v g
  gi|386001825|ref|YP_005920124.1|  1 MCTVGG 6 
                                      799755 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
                     A2L_zn_ribbon 21 ylvCieCga 29
                                      ++vC++Cg+
  gi|386001825|ref|YP_005920124.1| 20 GYVCQDCGN 28
                                      79******8 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.74
                     A2L_zn_ribbon 24 CieCga 29
                                      C+ C++
  gi|386001825|ref|YP_005920124.1| 39 CPSCQS 44
                                      999986 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   0.00021      0.13      11      35 ..      22      45 ..      18      51 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                        FYDLN_acid 11 iCpscgakFYDLnkdPivcpkcgee 35
                                      +C++cg+kF  ++++ + cp+c++ 
  gi|386001825|ref|YP_005920124.1| 22 VCQDCGNKFKGMGRR-VRCPSCQSR 45
                                      7*************9.9*****974 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.52   3.2e+02      24      32 ..      21      29 ..      15      32 .. 0.69
   2 ?    9.7   2.7    0.0014      0.84      17      36 ..      30      49 ..      21      51 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.52
                    zf-Sec23_Sec24 24 wiCnfCnhk 32
                                      ++C+ C++k
  gi|386001825|ref|YP_005920124.1| 21 YVCQDCGNK 29
                                      567777665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                    zf-Sec23_Sec24 17 idfggkrwiCnfCnhknevp 36
                                      +   g+r +C+ C+++n  p
  gi|386001825|ref|YP_005920124.1| 30 FKGMGRRVRCPSCQSRNVKP 49
                                      55569************766 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.4   0.00049       0.3      30      54 ..      22      44 ..      12      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgf 54
                                       C  Cg k k    gr+++Cp+C+ 
  gi|386001825|ref|YP_005920124.1| 22 VCQDCGNKFKG--MGRRVRCPSCQS 44
                                      6**********..**********86 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.9     0.017        10       5      32 ..      23      43 ..      21      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                     zinc_ribbon_5  5 CpdCdtkFklvdsklKksgkkVrCakCa 32
                                      C dC+ kFk         g +VrC  C 
  gi|386001825|ref|YP_005920124.1| 23 CQDCGNKFK-------GMGRRVRCPSCQ 43
                                      888888876.......678889999997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5     0.048        30      18      25 ..      22      29 ..      20      30 .. 0.85
   2 ?    8.6   0.4     0.002       1.2       3      14 ..      37      49 ..      36      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.048
                       zf-ribbon_3 18 vCpyCGtk 25
                                      vC  CG k
  gi|386001825|ref|YP_005920124.1| 22 VCQDCGNK 29
                                      7999*988 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                       zf-ribbon_3  3 vrCPnCGa.plss 14
                                      vrCP+C + ++++
  gi|386001825|ref|YP_005920124.1| 37 VRCPSCQSrNVKP 49
                                      79***98888775 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.9   1.8e+03       4      17 ..       2      13 ..       1      16 [. 0.75
   2 ?    9.0   0.2     0.003       1.8       3      20 ..      22      38 ..      21      38 .. 0.91
   3 ?    4.1   0.1       0.1        64       4      13 ..      39      49 ..      38      51 .] 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.9
                           zf-IS66  4 CpcCGgllkpiged 17
                                      C  +Gg+  +ig++
  gi|386001825|ref|YP_005920124.1|  2 CTVGGGP--EIGDV 13
                                      8899996..67776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.003
                           zf-IS66  3 tCpcCGgllkpigedrvr 20
                                      +C +CG + k +g + vr
  gi|386001825|ref|YP_005920124.1| 22 VCQDCGNKFKGMGRR-VR 38
                                      6******99****99.76 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.1
                           zf-IS66  4 CpcCGg.llkp 13
                                      Cp C++  +kp
  gi|386001825|ref|YP_005920124.1| 39 CPSCQSrNVKP 49
                                      99999855655 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0011      0.71       2      12 ..      20      30 ..      19      32 .. 0.86
   2 ?    1.7   0.2      0.32     2e+02       3      10 ..      37      44 ..      35      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                            zf_UBZ  2 tylCerCgkei 12
                                       y+C++Cg ++
  gi|386001825|ref|YP_005920124.1| 20 GYVCQDCGNKF 30
                                      69******987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.32
                            zf_UBZ  3 ylCerCgk 10
                                      + C+ C++
  gi|386001825|ref|YP_005920124.1| 37 VRCPSCQS 44
                                      57****86 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3      0.12        74      37      44 ..      20      27 ..      11      29 .. 0.60
   2 ?    3.4   0.3      0.12        75      18      27 ..      20      29 ..      17      33 .. 0.72
   3 ?    9.6   1.1    0.0014      0.87      17      27 ..      35      45 ..      30      51 .] 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                     Zn_Tnp_IS1595 37 lfqCkeCr 44
                                       + C++C+
  gi|386001825|ref|YP_005920124.1| 20 GYVCQDCG 27
                                      45555554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                     Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                      g vC  Cg++
  gi|386001825|ref|YP_005920124.1| 20 GYVCQDCGNK 29
                                      5678888875 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0014
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr 27
                                       +++CP C+sr
  gi|386001825|ref|YP_005920124.1| 35 RRVRCPSCQSR 45
                                      4578*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 336.40
//
Query:       gi|386001826|ref|YP_005920125.1|  [L=151]
Description: hypothetical protein Mhar_1134 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.34s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 820.41
//
Query:       gi|386001827|ref|YP_005920126.1|  [L=94]
Description: hypothetical protein Mhar_1135 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-26   90.1   0.4    9.8e-26   89.9   0.4    1.0  1  DUF2098   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.4   5.5e-30   9.8e-26       1      94 []       4      94 .]       4      94 .] 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 5.5e-30
                           DUF2098  1 eievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevidekekkkekeekekedleelekkekeleee 79
                                      ei+ Gs+VrY++TgTvG V+ +k+eedge+w++Ldst+LyY+ +tL++id   k  e++    ++++e+e+++k++ee+
  gi|386001827|ref|YP_005920126.1|  4 EISEGSIVRYAGTGTVGIVKVLKTEEDGERWALLDSTGLYYHLSTLQPID---KMPERRGIGGRTMAEMEERMKAEEER 79
                                      699***********************************************...89************************ PP

                           DUF2098 80 vdeeketdesceGGG 94
                                      + + k++des+e+GG
  gi|386001827|ref|YP_005920126.1| 80 MRSVKMEDESVESGG 94
                                      *************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 662.26
//
Query:       gi|386001828|ref|YP_005920127.1|  [L=364]
Description: hypothetical protein Mhar_1136 [Methanosaeta harundinacea 6Ac]
Scores for 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-61  206.6   0.0    4.7e-61  206.0   0.0    1.3  1  DUF2117   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.0   0.0   2.6e-65   4.7e-61       1     212 []      80     278 ..      80     278 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.0 bits;  conditional E-value: 2.6e-65
                           DUF2117   1 DivfLlnygksketGhvFgkiVverskekkpliqierpgekdgeiilwnekaeklakklseelglkivkpeevekei 77 
                                       D+v+Llny+k++etG +Fg++V+er+k +kpli +e +g   + ++   + a  +a++++  lg+++v++++   ++
  gi|386001828|ref|YP_005920127.1|  80 DVVVLLNYAKTAETGLAFGAMVAERAKPHKPLILAEYSGPFASVLA---GGAGGIAERIAGALGFPMVAAPQPPGMT 153
                                       9***************************************998877...88999**************999999988 PP

                           DUF2117  78 veskgkrvvrkiagvspgenilvnGiviGkaeseevtivaedgkivdikggeiKehGvekLgkvdlekaivktgllR 154
                                       + s+g++v+r+i g  pgen+ vnGiviG+ae+e+vti+a+dg+iv++ g+e+KehG+ek+ +vdle ai++tg +R
  gi|386001828|ref|YP_005920127.1| 154 A-SSGRTVTRTIFGAVPGENVSVNGIVIGRAEEERVTISATDGRIVQVLGAEVKEHGLEKIPSVDLEAAILRTGDVR 229
                                       7.89************************************************************************* PP

                           DUF2117 155 rskvkekllkkkklkkkkekkvgkvvlidHaaedvlelakkadlvvtvGDDTTavagd 212
                                       r++           +++ ++ + ++vlidHaae ++e+a++a ++vtvGDDTTa+ag+
  gi|386001828|ref|YP_005920127.1| 230 RTE---------ASARRVREPGRDAVLIDHAAEGTFEAARGAGVAVTVGDDTTAIAGE 278
                                       *22.........223345678999********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2321.29
//
Query:       gi|386001829|ref|YP_005920128.1|  [L=376]
Description: Transposase, IS605 OrfB family [Methanosaeta harundinacea 6Ac]
Scores for complete 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-23   81.7   0.0    6.4e-23   80.5   0.0    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    4.2e-21   75.4   0.0    9.2e-21   74.3   0.0    1.5  1  OrfB_IS605      Probable transposase
    2.1e-17   62.4   0.8    4.1e-17   61.4   0.8    1.5  1  HTH_OrfB_IS605  Helix-turn-helix domain
    0.00055   19.5   0.3    0.00092   18.8   0.3    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0034   17.4   0.3     0.0061   16.5   0.3    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.018   14.5   0.3       0.96    9.0   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.046   13.3   4.0        0.4   10.3   0.1    3.3  3  RecR            RecR protein
      0.055   13.2   0.3        5.9    6.7   0.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.093   12.4   0.3       0.69    9.6   0.0    2.3  2  GATA            GATA zinc finger


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 !   80.5   0.0   3.2e-26   6.4e-23       1      68 [.     291     358 ..     291     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 3.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       +r l ++++yka+ +G  v++v+p++TS+ Cs+Cg k++++ls+r+++Cp+Cg+ +drD nAaiNil+
  gi|386001829|ref|YP_005920128.1| 291 WRMLVTIISYKAESAGSIVVLVDPRNTSQLCSRCGLKVTKSLSDRVHECPQCGLIMDRDENAAINILR 358
                                       89999*************************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   4.6e-24   9.2e-21       3     117 ..     165     277 ..     163     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.6e-24
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve++++ +p+ k ++++giD+G++ +at+++++   ++ ++r+++s++k+lak++++l+++ k++  + ka + ++
  gi|386001829|ref|YP_005920128.1| 165 SVEIDDPpKPPWKDGSMVGIDVGLESFATLSNGE---KIDNPRFFRSEEKALAKAQRRLSKCEKGTPDRMKALKVVQ 238
                                       678777756777999*******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r+h++++++r  ++h+++++l+++   ++ e+L + +m 
  gi|386001829|ref|YP_005920128.1| 239 RIHERIANKRYYFAHQVSHNLVERFGLIAFEDLSITKML 277
                                       ***********************************9997 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 !   61.4   0.8   2.1e-20   4.1e-17       1      46 [.       1      45 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.1e-20
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeeg 46
                                      M +k++ky +yPT+ Q+  ++rt++ +R+VYN+ La+rk+a+e+eg
  gi|386001829|ref|YP_005920128.1|  1 M-RKSFKYPIYPTKSQQSRMERTLDLCRWVYNQTLAYRKDAWEKEG 45
                                      8.9*****************************************98 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   4.6e-07   0.00092       2      30 ..     317     345 ..     316     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                     zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                       t++ C+rCG ++ ++  ++   Cp+Cgl+
  gi|386001829|ref|YP_005920128.1| 317 TSQLCSRCGLKVTKSLSDRVHECPQCGLI 345
                                       789************************86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   3.1e-06    0.0061      10      44 ..     316     352 ..     312     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + ++ Cs+Cg k+ +  +   + Cp+Cg  +d +++ 
  gi|386001829|ref|YP_005920128.1| 316 NTSQLCSRCGLKVTKSLSdrVHECPQCGLIMDRDENA 352
                                       6789*********9777799********999998875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00048      0.96      12      30 ..     311     329 ..     306     335 .. 0.87
   2 ?    3.2   0.1     0.031        62      22      31 ..     339     348 ..     337     352 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00048
                                       HEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  12 veDpergelvCtdCGlVle 30 
                                       ++Dp ++  +C++CGl + 
  gi|386001829|ref|YP_005920128.1| 311 LVDPRNTSQLCSRCGLKVT 329
                                       79**************985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.031
                                       ESSSSBEEEE CS
                      TF_Zn_Ribbon  22 CtdCGlVled 31 
                                       C+ CGl+++ 
  gi|386001829|ref|YP_005920128.1| 339 CPQCGLIMDR 348
                                       9999999875 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2      0.34   6.7e+02       7      20 ..     211     224 ..     210     225 .. 0.90
   2 ?    1.8   0.1     0.089   1.8e+02      13      23 ..     315     325 ..     310     326 .. 0.75
   3 ?   10.3   0.1    0.0002       0.4      12      29 ..     332     349 ..     330     350 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.34
                                       HHHHHHHHH-EE-T CS
                              RecR   7 eaLqeakekvrhCs 20 
                                       +aL +a ++++ C+
  gi|386001829|ref|YP_005920128.1| 211 KALAKAQRRLSKCE 224
                                       699**********8 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.089
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +++ + CsrCg
  gi|386001829|ref|YP_005920128.1| 315 RNTSQLCSRCG 325
                                       666789****8 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0002
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + ++v+ C++Cg + ++d
  gi|386001829|ref|YP_005920128.1| 332 LSDRVHECPQCGLIMDRD 349
                                       679***********9987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.022        44      11      20 ..     316     325 ..     315     328 .. 0.77
   2 ?    6.7   0.1     0.003       5.9       8      20 ..     331     343 ..     330     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                     zinc_ribbon_2  11 dnakFCpyCG 20 
                                       ++++ C++CG
  gi|386001829|ref|YP_005920128.1| 316 NTSQLCSRCG 325
                                       5678899998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                     zinc_ribbon_2   8 elqdnakFCpyCG 20 
                                        l+d++  Cp+CG
  gi|386001829|ref|YP_005920128.1| 331 SLSDRVHECPQCG 343
                                       68999999****9 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00035      0.69      16      32 ..     314     330 ..     312     333 .. 0.87
   2 ?   -0.3   0.0      0.41   8.2e+02      21      28 ..     337     344 ..     335     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00035
                              GATA  16 pdgnksLCnaCGlyykk 32 
                                       p+++ +LC  CGl+  k
  gi|386001829|ref|YP_005920128.1| 314 PRNTSQLCSRCGLKVTK 330
                                       89999********9776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.41
                              GATA  21 sLCnaCGl 28 
                                       + C +CGl
  gi|386001829|ref|YP_005920128.1| 337 HECPQCGL 344
                                       57999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2324.50
//
Query:       gi|386001830|ref|YP_005920129.1|  [L=665]
Description: Stage II sporulation SpoIIE family protein [Methanosaeta harundinacea 6Ac]
Scores for 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-38  130.3   0.2    1.8e-37  129.2   0.2    1.6  1  SpoIIE    Stage II sporulation protein E (SpoIIE)
    1.1e-17   64.7   0.0    1.7e-17   64.0   0.0    1.3  1  dCache_1  Cache domain
  ------ inclusion threshold ------
      0.012   16.0   4.1      0.026   14.9   1.4    2.9  3  HAMP      HAMP domain


Domain annotation for each model (and alignments):
>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.2   2.9e-41   1.8e-37       2     191 ..     474     662 ..     473     664 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 2.9e-41
                                       TTEEEEEEEECSSSSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT.TTCEEEEEEEETTTTEEEE CS
                            SpoIIE   2 dgrlalvvgDvvGhGleAalimgllrsalrelataglepaevlkrlnralardleeeerfaTavlavydpstgkley 78 
                                       +g+ ++v++ v+G+Gl+Aa+ ++ +rs +r++a++  +pa++l+++n+ l  ++++  ++++++++++d+s++ l+y
  gi|386001830|ref|YP_005920129.1| 474 GGKAMVVLAEVSGKGLSAAMAAAVTRSHIRAAARRLGDPAKALRETNQNLVGNVRNG-MVVSCFCGILDLSSHALSY 549
                                       67889****************************************************.******************* PP

                                       EEESSSSEEEEETTSTEEEEE--SS--TTTSSST-EEEEEEE--TTEEEEEESCCCCSSSHHHHHHCCCHHCHHHHC CS
                            SpoIIE  79 anaGhpppllvrpdggtklllastglplGilpeadyetaelelepgdtlllyTDGvtEardsdgelfgkerllalla 155
                                       anaGh pp++v++ +g +  l+++ +++G+l++ d e +   ++pgd+l++y DG++E +d dge fg e l+ l++
  gi|386001830|ref|YP_005920129.1| 550 ANAGHVPPFIVSS-DGFVDTLVGGAIAMGALDHIDLEMEGWMIDPGDVLVIYNDGLIEVEDGDGERFGTESLITLVK 625
                                       *************.88999999999**************************************************** PP

                                       T.....HCCHHHHHHHHHHH.HTTSSSSS-EEEEEEE CS
                            SpoIIE 156 saegesleelldalveelle.lgsgeleDDitllvlr 191
                                       ++++++++++++ l +++++ +g+ + + D+  ++++
  gi|386001830|ref|YP_005920129.1| 626 ENREKPAQQIAKDLERRIEDhMGGVRGRPDAVAVIVK 662
                                       ***9**************9975555555555555554 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   2.9e-21   1.7e-17      68     248 ..      97     280 ..      71     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 2.9e-21
                          dCache_1  68 lksnpdi.sgvylvdadGqviassdpssppnleg..tddpadrdwykealaggggkpvisdpyvdqtggkpvitiav 141
                                       ++  +d+ +  y+ ++dG ++   +p+  + l+    +d+++r+wy ea+ +g  ++++++py++qt+g+  it+a+
  gi|386001830|ref|YP_005920129.1|  97 VQEEEDLiEQGYIGTSDGVLVL--WPDVTETLQLiaPFDFRERPWYLEAARAG--DTIWTKPYQSQTTGDISITCAT 169
                                       4334444367788889998876..343333444489*****************..9*******99999********* PP

                          dCache_1 142 piyddsgkfiGvlaadldldnlqdllsniklgetgyvfivdsdGniiahpdkdl.........lgknlrdelkaqea 209
                                       pi    g+  Gv+++d++l + +  l n++   +gy f++d++G +++ p ++           g+ l+++++++  
  gi|386001830|ref|YP_005920129.1| 170 PISA-EGNLSGVVGMDVSLAEMDLDLANFS---SGYPFLLDGQGAVVMKPPTPEgflwdeilePGSLLDSKNPELAE 242
                                       **96.6************999888888775...69*************99854558989999855556666666677 PP

                          dCache_1 210 lekalakiesgvssvklngeeylvayapiptglgWylvv 248
                                       l  a+   e+g+ +v+l++ +  + yap+p+  gW+l v
  gi|386001830|ref|YP_005920129.1| 243 LAEAMVRGEEGTAFVRLDKGSARIVYAPLPS-VGWSLGV 280
                                       88888889999999****9999899*****8.****987 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.81   4.9e+03      34      44 ..     237     247 ..     232     249 .. 0.77
   2 ?   14.9   1.4   4.3e-06     0.026      10      52 ..     367     409 ..     360     410 .. 0.93
   3 ?   -1.1   0.0      0.44   2.6e+03      17      32 ..     632     646 ..     630     649 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.81
                                       SSHHHHHHHHH CS
                              HAMP  34 rDEiGeLaraf 44 
                                       + E++eLa+a+
  gi|386001830|ref|YP_005920129.1| 237 NPELAELAEAM 247
                                       56999999986 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP  10 LrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       L+ +ar  +++++Gdl++r+  +g    ++La+af++M+  L+
  gi|386001830|ref|YP_005920129.1| 367 LEAVARGLEEVGRGDLEARIAGDGSRGARRLAEAFDEMALGLK 409
                                       5778999*******************************97775 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.44
                                       HHHHTTTBTSSTCCTT CS
                              HAMP  17 arriaaGdldtrlpvs 32 
                                       a++ia+ dl+ r++++
  gi|386001830|ref|YP_005920129.1| 632 AQQIAK-DLERRIEDH 646
                                       799999.*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3833.30
//
Query:       gi|386001831|ref|YP_005920130.1|  [L=287]
Description: hypothetical protein Mhar_1139 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.091   12.3   0.0        0.2   11.2   0.0    1.6  1  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.1e-05       0.2       2      22 ..     265     285 ..     264     287 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.1e-05
                                       HHHS-HHHHHHHHHHHTTT-- CS
                        Sigma70_r4   2 LasLpererevlelrfgeglT 22 
                                       ++sLp+++re+++ +f+   T
  gi|386001831|ref|YP_005920130.1| 265 IESLPPQHREIIKRYFENLAT 285
                                       689************987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1868.12
//
Query:       gi|386001832|ref|YP_005920131.1|  [L=332]
Description: ATPase associated with various cellular activities [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-63  211.0   0.2    9.2e-63  209.9   0.1    1.6  2  AAA_3            ATPase family associated with various cellul
    3.2e-16   58.9   0.0    6.9e-16   57.9   0.0    1.6  1  AAA_lid_2        AAA lid domain
    6.6e-12   45.6   0.0    1.1e-11   44.9   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)
    1.3e-07   32.1   0.0    2.4e-07   31.3   0.0    1.5  1  AAA              ATPase family associated with various cellul
    1.2e-06   27.7   0.0    3.6e-06   26.2   0.0    1.8  1  MCM              MCM P-loop domain
    0.00021   21.1   0.2     0.0019   17.9   0.2    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0007   19.3   0.1     0.0061   16.3   0.1    2.1  1  Sigma54_activat  Sigma-54 interaction domain
     0.0041   16.5   1.5      0.048   13.0   0.3    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.024   14.8   0.0      0.039   14.1   0.0    1.3  1  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.9   0.1   4.6e-66   9.2e-63       1     131 []      62     194 ..      62     194 .. 0.98
   2 ?   -3.3   0.0       3.8   7.5e+03      53      85 ..     295     328 ..     291     330 .. 0.58

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 4.6e-66
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrap 75 
                                       h+lle+ PGl+ktllvk++a++ +l+f+riq+tpdl+P+di+Gt+++ee e  k+f+f++Gp+fan++ladeinra+
  gi|386001832|ref|YP_005920131.1|  62 HILLESNPGLGKTLLVKTIASTTGLHFSRIQCTPDLMPADITGTTLIEEVEgsKHFRFEEGPIFANIVLADEINRAS 138
                                       9**********************************************99876699********************** PP

                             AAA_3  76 pktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       p+tqsa+leam+e+qvtv+++t++l+epf+vlatqnPie+eGt+plpeaqldrfll
  gi|386001832|ref|YP_005920131.1| 139 PRTQSAMLEAMQEKQVTVGKNTYRLEEPFFVLATQNPIEMEGTFPLPEAQLDRFLL 194
                                       ******************************************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                             AAA_3  53 efefkkGpvfan.llladeinrappktqsallea 85 
                                       ++e+ + p+f + ++l+ + +r    t+  + e+
  gi|386001832|ref|YP_005920131.1| 295 DLEVMARPIFRHrIILTFDSERRGVTTDQVISEI 328
                                       5667777787542666666666555555555555 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   3.5e-19   6.9e-16       4      73 .]     258     328 ..     255     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 3.5e-19
                         AAA_lid_2   4 rahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiveei 73 
                                       r+ + +e+g+s+r a++ l+ a++A+A+l grdyV   D++ +a+++++HR++   + e+ g+tt+++++ei
  gi|386001832|ref|YP_005920131.1| 258 RSWEGVEYGASPR-ASIGLILASKARALLSGRDYVDRADLEVMARPIFRHRIIltFDSERRGVTTDQVISEI 328
                                       677889*******.***************************************998999999******9986 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 !   44.9   0.0   5.3e-15   1.1e-11       1     138 []      62     192 ..      62     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 5.3e-15
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEES CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDE 73 
                                       ++lL  +pG gK+ l++ +a+ ++  +  +q+t d+ ++d++g + i+    +++ +++++p+      + i++ DE
  gi|386001832|ref|YP_005920131.1|  62 HILLESNPGLGKTLLVKTIASTTGLHFSRIQCTPDLMPADITGTTLIEevegSKHFRFEEGPIF-----ANIVLADE 133
                                       5788889****************************************9999999999*******.....9******* PP

                                       GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ++ra++ +++++l  + e+++ + +++ +   ++      f v+at np +  +  +l +a ++Rf
  gi|386001832|ref|YP_005920131.1| 134 INRASPRTQSAMLEAMQEKQVTVGKNTYRLE-EP------FFVLATQNPIEmEGTFPLPEAQLDRF 192
                                       **********************777776664.34......99*********999999999999998 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 !   31.3   0.0   1.2e-10   2.4e-07       1     129 [.      63     197 ..      63     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakekakpsilfiDEidal 70 
                                       +ll  +pG GKTll+k +a+++g +f +i+++  l         +++e e + +  f+e    a   i++ DEi + 
  gi|386001832|ref|YP_005920131.1|  63 ILLESNPGLGKTLLVKTIASTTGLHFSRIQCTPDLMPaditgttLIEEVEGSKHFRFEEGPIFA--NIVLADEINRA 137
                                       688999***********************99655522478888888999999999998877776..9********** PP

                                       HHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEE CS
                               AAA  71 aksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkie 129
                                        ++            ++++l+++++ +          e++++v+++ n         l++a l +Rf  k++
  gi|386001832|ref|YP_005920131.1| 138 SPRT-----------QSAMLEAMQEKQVTvgkntyrlEEPFFVLATQNPiemegTFPLPEAQL-DRFLLKVF 197
                                       9998...........999999999999999999999877677777766633322223555555.66666665 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.8e-09   3.6e-06      54     175 ..      57     177 ..      18     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.8e-09
                                       BCSS-EEEEEESSTSTHHHHHHHHHHHS..SSEEEEESSSSSSSHSSSEEEEESS..SSSEEEEETHHHHTTTSEEE CS
                               MCM  54 lrgdinvllvgdpgtaKsqlLkyvekla..pravytsgkgssaagLtaavvrdee..tgefvleaGalvladkGvcc 126
                                       + +  ++ll ++pg++K+ l+k++++++  + +   +      a++t +   +e   +++f +e G +      +++
  gi|386001832|ref|YP_005920131.1|  57 ILAGGHILLESNPGLGKTLLVKTIASTTglHFSRIQCTPDLMPADITGTTLIEEVegSKHFRFEEGPIFAN---IVL 130
                                       445569******************876422556666677777888876655555400566******98764...9** PP

                                       EESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 127 iDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                        De+++ + +++sa++Eam ++++++ K    + L+    vla  np++
  gi|386001832|ref|YP_005920131.1| 131 ADEINRASPRTQSAMLEAMQEKQVTVGKNT--YRLEEPFFVLATQNPIE 177
                                       ****************************98..99************985 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   9.7e-07    0.0019      11     113 ..      45     154 ..      35     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.7e-07
                            RuvB_N  11 gqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..lltnlee 84 
                                       gq++v e++ + i a         h+ll   PGlGkt l k ia+  g ++ +i ++P l  ++d+++  l+ ++e 
  gi|386001832|ref|YP_005920131.1|  45 GQKAVVEQILVGILA-------GGHILLESNPGLGKTLLVKTIASTTGLHFsRIQCTPDLM-PADITGttLIEEVEG 113
                                       555555555555554.......36***********************99974667778775.455543214555542 PP

                            RuvB_N  85 k............dvlfideihrlsraveevlysamedfrl 113
                                       +            ++++ dei r s+ ++  +  am++ ++
  gi|386001832|ref|YP_005920131.1| 114 SkhfrfeegpifaNIVLADEINRASPRTQSAMLEAMQEKQV 154
                                       21111111222225677788888888888888888877665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.1e-06    0.0061      13     146 ..      51     177 ..      43     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-06
                                       HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT..TS-TTCHHHHHHEBSSSSSTTTSS-BEH CS
                   Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavnca..aipeelleseLFGhekGaFtGAekekkG 87 
                                       eqi   +    ++l++ + G GK+ll ++i +++     +f +++c+   +p+++  ++L   ++G+     + ++G
  gi|386001832|ref|YP_005920131.1|  51 EQILVGILAGGHILLESNPGLGKTLLVKTIASTT---GLHFSRIQCTpdLMPADITGTTLIEEVEGSKH--FRFEEG 122
                                       5555555666677888888888888887776543...45677777764334666666666666665532..222233 PP

                                       HHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                   Sigma54_activat  88 lfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                        +      +++ Dei++ ++++Q+ +l+++qe++v+ vG+++ +  +  ++ at++ +e
  gi|386001832|ref|YP_005920131.1| 123 PIF---ANIVLADEINRASPRTQSAMLEAMQEKQVT-VGKNTYRLEEPFFVLATQNPIE 177
                                       332...357889*********************996.9**9999999999999988776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3   2.4e-05     0.048       5      44 ..      43      82 ..      40      91 .. 0.88
   2 ?    2.0   0.0     0.059   1.2e+02     109     158 ..     128     175 ..     124     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                      v+Gq++  + + + +  g ++ll  +pG GKt+l k ++s
  gi|386001832|ref|YP_005920131.1| 43 VVGQKAVVEQILVGILAGGHILLESNPGLGKTLLVKTIAS 82
                                      899**999999999877777999************99865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.059
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       +++ DE+   + ++  ++ e +++++vt+ ++++++e p  f ++a+ Np
  gi|386001832|ref|YP_005920131.1| 128 IVLADEINRASPRTQSAMLEAMQEKQVTVGKNTYRLEEP--FFVLATQNP 175
                                       56779*************************999988766..666777777 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     2e-05     0.039       5     101 ..      62     147 ..      59     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....EEEEETG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG....ivllDEi 77 
                                        ill  + g Gkt+l k++a++  +    ++ r+ ++  l   ++  +   ++++     ++eeg     ivl DEi
  gi|386001832|ref|YP_005920131.1|  62 HILLESNPGLGKTLLVKTIASTTGL----HFSRIQCTPDLMPADITGTTLIEEVEGSKHFRFEEGPifanIVLADEI 134
                                       68899999***************98....9******99888677765555555555555667777799********* PP

                                       GG-------------HHHHHHHHH CS
                             AAA_2  78 dKihpkessgadvSregVqrdLLq 101
                                        +++p+            q ++L 
  gi|386001832|ref|YP_005920131.1| 135 NRASPR-----------TQSAMLE 147
                                       *****5...........4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2193.23
//
Query:       gi|386001833|ref|YP_005920132.1|  [L=285]
Description: hypothetical protein Mhar_1141 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.3   0.1    2.7e-18   66.0   0.0    1.7  2  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   1.5e-22   2.7e-18       1      84 [.      36     115 ..      36     117 .. 0.93
   2 ?   -3.4   0.0      0.69   1.2e+04      60      71 ..     233     244 ..     218     252 .. 0.63

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.5e-22
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       g+++ g ReY+ gD+++ +dWk++ARt +lyvre e+er+  v ++ld+s++m +g    ek+  a ++a+  a+ +
  gi|386001833|ref|YP_005920132.1|  36 GISPVGYREYRKGDDFKFVDWKVYARTEKLYVREHEEERSLAVHILLDASSSMAFG----EKFAFASKLAVGFAYLA 108
                                       57899**************************************************8....68999999999999999 PP

                             DUF58  78 ldegdrv 84 
                                       ++e+ ++
  gi|386001833|ref|YP_005920132.1| 109 IKENEKF 115
                                       9998776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.69
                             DUF58  60 dekletavsaaa 71 
                                       +   e+a+++aa
  gi|386001833|ref|YP_005920132.1| 233 KVREEYAARMAA 244
                                       555666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1925.36
//
Query:       gi|386001834|ref|YP_005920133.1|  [L=405]
Description: hypothetical protein Mhar_1142 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-52  176.4   0.0    1.5e-51  174.5   0.0    1.8  2  Lar_N     Lactate racemase N-terminal domain
  ------ inclusion threshold ------
      0.086   13.1   0.0       0.15   12.3   0.0    1.4  1  DUF362    Domain of unknown function (DUF362)


Domain annotation for each model (and alignments):
>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.5   0.0   1.7e-55   1.5e-51       1     203 [.       5     197 ..       5     198 .. 0.96
   2 ?   -1.1   0.0     0.096   8.6e+02      70      98 ..     242     270 ..     231     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 1.7e-55
                             Lar_N   1 ygkkkleleipeenllgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilpll 77 
                                       yg++ ++l+++  +  +v+ p+e +  +de  +ie+aL+ pig   le+l+  +++ +i  sDiTRp p+++ilp l
  gi|386001834|ref|YP_005920133.1|   5 YGSGRIRLPVDGAEGFEVVLPEERPGAPDETGEIERALNVPIGP-GLEDLAG-SRRAAIMASDITRPAPTSKILPPL 79 
                                       9999**************************************96.9***998.699********************* PP

                             Lar_N  78 leelkeagvkdeditilvAtGlHrkqteeelkkilGeevvkrikvvnhdaedksslvklGttskGtpveinklvaea 154
                                       +++l++ g+  ++i +++++G+Hr++t ee+ ++lG +  +++  ++h   dk+++ +lG+ts+Gtpvei ++va +
  gi|386001834|ref|YP_005920133.1|  80 VRRLEALGI--SEIVVVFGLGTHRRMTVEEMDRLLGSS--ASLPSIQH---DKDRCIHLGETSRGTPVEILEEVAAS 149
                                       *********..77***********************65..68888888...79************************ PP

                             Lar_N 155 dlviltGfiepHyfaGfsGGrKsilpGvasretimanHkavlaepraal 203
                                       d +i tG+ie+Hy+aG+sGG+K++lpGv+s+++i++nH+++  +pra++
  gi|386001834|ref|YP_005920133.1| 150 DIKIGTGNIEYHYYAGYSGGAKALLPGVSSERSINKNHAMMA-DPRAKS 197
                                       ****************************************88.998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.096
                             Lar_N  70 skiilpllleelkeagvkdeditilvAtG 98 
                                        ++   ++++e+ + +v+ ++i + +A G
  gi|386001834|ref|YP_005920133.1| 242 AHRAGAKVVDEMYQRAVRPAEIVVACAGG 270
                                       566667899999999*******9999988 PP

>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05      0.15      75     175 ..     121     286 ..      66     303 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....... RF
                            DUF362  75 glegedevvvpvkgkhlkke.lkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs....... 142
                                        ++++d   + + g+++  + ++i ++v+  D+ I       H +ag++g+ K  l G+ s+++ ++ H+       
  gi|386001834|ref|YP_005920133.1| 121 IQHDKDRCIH-L-GETSRGTpVEILEEVAASDIKIGTGNIEYHYYAGYSGGAKAlLPGVSSERSINKNHAmmadpra 195
                                       3344433333.2.3322222499*******************************99999999998888877788888 PP

                                       ........................................................xxxxxxxxxxxxxxxxx.x.. RF
                            DUF362 143 ........................................................krdsekfaekiadlaka.l.. 160
                                                                                               +     + ++ +  a++ +  
  gi|386001834|ref|YP_005920133.1| 196 ksgrldnpvrldmeeaakiggldlilnvvlnskkeivravggdfvkahragakvvdE-----MYQRAVRPAEIvVac 267
                                       888888888888888888888888888888888888888888888887765554431.....333333333332244 PP

                                       ....xxxxxxxxxxxxxxx RF
                            DUF362 161 ....kpdlnvvdgikameg 175
                                           ++d+n+  + kame 
  gi|386001834|ref|YP_005920133.1| 268 aggrPKDINLFQAQKAMEN 286
                                       4441355888888887774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2383.76
//
Query:       gi|386001835|ref|YP_005920134.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386001835|ref|YP_005920134.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386001835|ref|YP_005920134.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386001835|ref|YP_005920134.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386001835|ref|YP_005920134.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386001835|ref|YP_005920134.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1848.47
//
Query:       gi|386001836|ref|YP_005920135.1|  [L=135]
Description: hypothetical protein Mhar_1144 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-57  192.9   0.0    1.6e-57  192.8   0.0    1.0  1  DUF1699         Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
       0.19   12.1   0.0       0.32   11.3   0.0    1.4  1  Tir_receptor_M  Translocated intimin receptor (Tir) intimin-b


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.8   0.0   1.8e-61   1.6e-57       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 1.8e-61
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirvvs+++ei++l++ne++vH+afrpsn d+l+l+k+cp+l+aiqvp+Sy+ktlsk++++fl++qgi+llegdvw
  gi|386001836|ref|YP_005920135.1|   1 MKIRVVSQRSEIADLSPNERMVHIAFRPSNVDLLDLIKACPRLRAIQVPPSYNKTLSKAIRLFLQMQGIDLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdi+eyy+v+e  ieri +l+s+g+s ++ +++++ +t+lspd+ik+++k
  gi|386001836|ref|YP_005920135.1|  78 GHRKDIDEYYMVDEGAIERIGDLISSGESIDDAVAQVTMTTRLSPDMIKYIAK 130
                                       **************************************************975 PP

>> Tir_receptor_M  Translocated intimin receptor (Tir) intimin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.6e-05      0.32      31      52 ..      94     115 ..      90     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                    Tir_receptor_M  31 iDenGnaiPsGeLkDDvvaqia 52 
                                       i+  G+ i sGe +DD vaq+ 
  gi|386001836|ref|YP_005920135.1|  94 IERIGDLISSGESIDDAVAQVT 115
                                       7889****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.74
# Mc/sec: 553.13
//
Query:       gi|386001837|ref|YP_005920136.1|  [L=489]
Description: hypothetical protein Mhar_1145 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   49.4   0.5    2.5e-12   46.2   0.2    2.1  2  Phospholip_B  Phospholipase B


Domain annotation for each model (and alignments):
>> Phospholip_B  Phospholipase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.2   1.4e-16   2.5e-12      55     344 ..      39     303 ..      22     327 .. 0.76
   2 !    1.2   0.0    0.0061   1.1e+02     456     495 ..     405     447 ..     321     471 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.4e-16
                      Phospholip_B  55 alatfkdsvnetGWgqLevetqsaysdtvqayaaGllEGaltaeniykhlsNtieavckkseelcksklrefleenl 131
                                       ++ +    + e+GW  L++e + + +        G+  G+l a++i +  + +   ++ +     ++  + f+e+  
  gi|386001837|ref|YP_005920136.1|  39 VTYNNGSRYEENGWIYLHIEGEPYDR--------GFQHGYLMAQEIGEIKRSLEYLTYWNTG--KEW--QFFVEAAE 103
                                       44444456788888888888876554........8888888888887665554433333332..334..67777777 PP

                      Phospholip_B 132 kyvkkqvkekkktdpywrqvalllaqldGlvaGynkkvaksekkkeldlsdllllnlagdledlkkal.ltkvk... 204
                                       +      +++++ d y    + +l+ ++G+ +G +    ++  + +++ +++l  n   +l d          +   
  gi|386001837|ref|YP_005920136.1| 104 RLFVLDQDMEEN-DTY----QEFLDEMKGIADGAQ----AA--DVNISWQEILAWNGYEELVDYWWPNeK---Sgky 166
                                       766666666665.555....789***********4....33..45599************9998543330...1345 PP

                      Phospholip_B 205 ......eeakcsaLvKllp..gvedlllghttwssyssmlRiyKkYklreedravvpgtnvsfSsyPgllaSlDDfy 273
                                             ++ +csa++   +     +++++h +w++++     + +  l     + ++g+++ + s Pg++ S  Df+
  gi|386001837|ref|YP_005920136.1| 167 adgekdDKDHCSAFIATGNatIDGRIVMAHNSWNEFEFGQ--FSNLILD---IEPSEGHRMFMQSAPGYIDSFADFF 238
                                       56777799*******9877433468***********9654..4444444...3355699****************** PP

                      Phospholip_B 274 itssrLvviettnevfnktLykkikpersvllwvRvmianrlaesgreWveiFsrensgTynnqwlvldyk 344
                                       +t+++L+ +ett++ f     +  +p  +v+ + R + a + +e  ++ v+i +++n g y n wl+ d++
  gi|386001837|ref|YP_005920136.1| 239 VTDAGLMGTETTIGGF-----SLYDPD-EVSEFFRIRRAMQYSEGLDQFVDIMKKNNNGGYANTWLLGDIN 303
                                       ************9976.....455788.999***********************************98876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.0061
                      Phospholip_B 456 aiaaRgDLnasggta...afGaiDlKvtsielveklqaravsG 495
                                        + aR+ ++ +g +      G +D Kv++++++++l++ a  G
  gi|386001837|ref|YP_005920136.1| 405 ELDAREYISQPGRPLpfqPRGTVDGKVMDSSMAKDLSFWARWG 447
                                       44444444433333356678****************9999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.37s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 2572.55
//
Query:       gi|386001838|ref|YP_005920137.1|  [L=299]
Description: hypothetical protein Mhar_1146 [Methanosaeta harundinacea 6Ac]
Scores for 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-17   61.6   0.0    4.7e-08   33.5   0.1    2.3  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   6.5e-10   1.2e-05       1      99 [.      73     178 ..      73     184 .. 0.83
   2 !   33.5   0.1   2.6e-12   4.7e-08      11      97 ..     214     296 ..     205     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.5e-10
                         Rhodanese   1 sakelkellekgkva...llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvv 70 
                                       +a+el+e+le++       + ++pp+    + I+ ++n+s+d++ + + s ++ l+ + +++      gi++++ vv
  gi|386001838|ref|YP_005920137.1|  73 TAEELVEMLESETKTlvaYVSISPPQG--SSYIEDSINLSSDRFFQKDDSGNEILKSVSRMAGAlgdaGITEEDGVV 147
                                       689999999776644677888888875..588*******8888888888888888888888887************* PP

                         Rhodanese  71 vycdgggraaaa..aallkklGyknvsvldG 99 
                                       +y+d  ++  ++   +++k+lG++nv++l G
  gi|386001838|ref|YP_005920137.1| 148 IYGDCFSCGDSTfvLWMMKYLGHQNVRILQG 178
                                       ***9999966666699******888****98 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2.6e-12
                         Rhodanese  11 kgkvallDvRppeeYekghIpgAvnv..skdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaal 85 
                                       +g+ +++D+R+++++e  hI gAvn+  +  + ++  k+++ l+e++ +l       ++++vvy d+   a+ a+++
  gi|386001838|ref|YP_005920137.1| 214 AGEFVVVDARTSDQFEIDHIDGAVNIdfNTLIEGDWIKDDSALAEIFVDL-----EGDSPIVVYSDNFREASIAWYA 285
                                       455569********************543333333334444444444444.....568*******999999999*** PP

                         Rhodanese  86 lkklGyknvsvl 97 
                                       l+ lG ++ +++
  gi|386001838|ref|YP_005920137.1| 286 LQHLG-YDARIY 296
                                       *****.577766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1663.26
//
Query:       gi|386001839|ref|YP_005920138.1|  [L=290]
Description: Aldo/keto reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-18   64.5   0.0    2.2e-15   56.6   0.0    2.1  2  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   1.2e-19   2.2e-15       2     194 ..      24     212 ..      23     217 .. 0.88
   2 !    6.0   0.0   0.00033         6     246     275 ..     226     254 ..     224     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.2e-19
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       +glG+  +    + +++ a+++++ a   Gi +fDtA++Y    se ++G +  + ++ r e++ ++K         
  gi|386001839|ref|YP_005920138.1|  24 VGLGGEGILRT-YGEEAGAAAVIEEAAIQGIAYFDTAPAY--SGSEGYYGTFWRSHPNLRGEIFQTSKS-------- 89 
                                       67777766664.8889999*********************..***************************........ PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-......HHHHHHHHHHHHHTTSEEEEEEES--.HHHHHHH CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslp.....sieevldaleelvkeGkiraiGvSnfs.veqleka 149
                                       ++ ++   r+ l+++lk+Lg+d +Dl+++H++    +         +l+a++e ++ G    iGv+++     +  a
  gi|386001839|ref|YP_005920138.1|  90 ASRTAMGARADLDRTLKTLGLDAIDLWQIHDVRTRQDlreieGPGGALEAFAEAKEVGRTELIGVTGHHdPSVVTYA 166
                                       999999*******************************66555555567******************99879999988 PP

                                       HHTTT--EEEEE-B-BTT...-HHHHTTHHHHHHHTT-EEEEBSTTGG CS
                      Aldo_ket_red 150 kkkkkvkivavqveynll...releeegllelckkkgvpliaysplgg 194
                                          +  ++ av +  n+l      +  g++ ++k+ g+++i + +lgg
  gi|386001839|ref|YP_005920138.1| 167 --VENWPVDAVLIPVNPLegvLGGFLDGTIGAAKERGIAVIGMKVLGG 212
                                       ..7788888888899999665566778888899999999999999997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00033
                                       HHHHHHTTSTT-SEEEE--SSHHHHHHHHG CS
                      Aldo_ket_red 246 lalryalsqpavgivipgasnieqlednld 275
                                       l lryal  + v+ +i+g+s++e+++  ++
  gi|386001839|ref|YP_005920138.1| 226 LLLRYAL-TQEVSLIIVGCSTPEEVRLLAR 254
                                       789****.799*************986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1770.13
//
Query:       gi|386001840|ref|YP_005920139.1|  [L=99]
Description: hypothetical protein Mhar_1147 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.0   0.0       0.11   12.6   0.0    1.3  1  ABM       Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-06      0.11       1      40 [.       1      40 [.       1      66 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-06
                                      CEEEEEEEEESTTGHHHHHHHHHHH.HHHHHHTSTTEEEEE CS
                               ABM  1 mviviaeirvkpgqaeafldafaea.vesllaeepGclgye 40
                                      m+  i ++++++++  ++ ++++++ ++ + +e pG++ y+
  gi|386001840|ref|YP_005920139.1|  1 MYLSIRRYKTDEEKVGEVMRLVEDRfLPRV-REIPGFIKYY 40
                                      788899***************998625566.7*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 605.79
//
Query:       gi|386001841|ref|YP_005920140.1|  [L=204]
Description: N-acetyltransferase GCN5 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-12   47.5   0.0    3.5e-12   47.2   0.0    1.2  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
    8.8e-06   25.9   0.0    1.2e-05   25.5   0.0    1.3  1  Acetyltransf_1  Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.18   12.3   0.0    1.5  1  Acetyltransf_7  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   5.8e-16   3.5e-12      47     137 ..      80     172 ..      43     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.8e-16
                    Acetyltransf_3  47 eeseeegyg..waivl.kdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvav 120
                                       ++ +++ +g  +ai +    +v+G++ +  ++ e++++e+ y   p+f gkGy+t ++  l+e a +  ++ r+ a+
  gi|386001841|ref|YP_005920140.1|  80 ADPRDRPWGgyLAI-DpLTAKVVGTCAFKARPAEEGSVEIAYFTFPPFEGKGYGTAMALRLIEMAESSRKVGRILAH 155
                                       44556667774555.6333347******************************************************* PP

                    Acetyltransf_3 121 idkeNeaSirvleklGf 137
                                       + +e ++S r+lek+G+
  gi|386001841|ref|YP_005920140.1| 156 TLPERSGSTRILEKAGM 172
                                       ****************9 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     2e-09   1.2e-05      38     116 ..      94     171 ..      52     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2e-09
                                       EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHH CS
                    Acetyltransf_1  38 aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveedndaairlYe 113
                                            +++G++ ++ +p   ++  + + ++  p + gkG+G+a+   l+e a++   + +i +++ +   ++ r +e
  gi|386001841|ref|YP_005920140.1|  94 DPLTAKVVGTCAFKARPA--EEGSVEIAYFTFPPFEGKGYGTAMALRLIEMAESSrKVGRILAHTLPERSGSTRILE 168
                                       444589**********99..7888888****************************666998778877799****999 PP

                                       HTT CS
                    Acetyltransf_1 114 klG 116
                                       k G
  gi|386001841|ref|YP_005920140.1| 169 KAG 171
                                       998 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05      0.18      12      47 ..      98     138 ..      68     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                       TEEEEEEEEEEES...TCTEE....EEE-GGGTTSSHHHHH.HH CS
                    Acetyltransf_7  12 gkivGfialslld...aeitr....laVdpeyrgkGiGraL.le 47 
                                        k+vG++a++ +    +         ++ p + gkG+G+a+ l+
  gi|386001841|ref|YP_005920140.1|  98 AKVVGTCAFKARPaeeG---SveiaYFTFPPFEGKGYGTAMaLR 138
                                       5889***9999995431...3454578*************9534 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1282.20
//
Query:       gi|386001842|ref|YP_005920141.1|  [L=289]
Description: O-methyltransferase involved in polyketide biosynthesis [Methanosaeta harundinacea 6Ac]
Scores for complete 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-14   53.8   0.0    3.3e-14   53.2   0.0    1.1  1  LCM       Leucine carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.9e-18   3.3e-14      64     184 ..      66     189 ..      59     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.9e-18
                                       HHHHHHHHHHHHHHHHH.HCTTESEEEEET-TT--HHHHHHHTT...TEEEEEEE-HHHHHHHHHHHHHSHHHHHEE CS
                               LCM  64 giavRtrffddllkaal.saagirqvViLGAGlDtrayRlpwla...glkvfEvDqpevlefKretlkelgaepkae 136
                                       +i+ R++f+    k  +  ++g  q+ViL++G  ++a+ l  ++    + vfEvD    +e K+++  +l  +    
  gi|386001842|ref|YP_005920141.1|  66 VILNRKHFIKRTAKGLIaGREGPVQIVILASGKSPLALELLVEEgsrISGVFEVDLAG-MEEKARLYSRLLPPGAGM 141
                                       6788999***99999998889988*******************97755569****987.588*****999999889* PP

                                       CSEEE--TTSHHHHHHHHHHTT-TTSEEEEEEESSGGGS-HHHHHHHH CS
                               LCM 137 lryvpvDlrdddwpeaLaaagfdpekptawvaeGvlvYLtpeasdall 184
                                       lr   +D   +d++e+La+ gf+p++p+++v+eG+ +YL++e  + ++
  gi|386001842|ref|YP_005920141.1| 142 LRCLEADVAGSDLAERLAEGGFNPDAPAIFVMEGISYYLSEEDLAGIV 189
                                       *****************************************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1765.31
//
Query:       gi|386001843|ref|YP_005920142.1|  [L=343]
Description: hypothetical protein Mhar_1151 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-12   47.6   0.8    3.2e-05   24.1   0.1    3.5  3  Nitroreductase  Nitroreductase family
    3.6e-07   30.0   0.0    0.00023   20.8   0.0    2.6  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   9.4e-06     0.084      17      44 ..      23      50 ..      22      63 .. 0.85
   2 !    7.2   0.0   0.00053       4.8     112     144 ..      71     103 ..      51     117 .. 0.85
   3 !   24.1   0.1   3.6e-09   3.2e-05       1     170 []     133     324 ..     133     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.4e-06
                                      HHHHHHHHHHHHTS--GGG---EEEEEE CS
                    Nitroreductase 17 keelekileaarraPsagnlqpwrfvvv 44
                                      +e+le +l+ a  aPs+ n qpwr+ v 
  gi|386001843|ref|YP_005920142.1| 23 DEKLEFLLRYAVLAPSGPNNQPWRLAVD 50
                                      6899********************9885 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00053
                                       HHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG CS
                    Nitroreductase 112 yryalldagaaaqnllLaAtalGlgscpiggfd 144
                                       +r++++++g+ ++nllLaA+ ++lg ++  ++d
  gi|386001843|ref|YP_005920142.1|  71 NRTTYMSLGCLLTNLLLAAEHFDLGYQVERFPD 103
                                       578899*******************88766555 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 3.6e-09
                                       HHH--B--.-B-S----HHHHHHHHHHH..............HTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHH CS
                    Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaa..............rraPsagnlqpwrfvvvqdkelryklaeaalelll 62 
                                       i +R++ R ++dd+p++++++e + ea                ra  a  l + + + + +k+ r++la +++ +  
  gi|386001843|ref|YP_005920142.1| 133 ITERHTNRgAYDDRPIEADKIEAMKEAVgdggfrldvltdpaERAAMAEVLGESHRIQLGNKAFRKDLARWIRRNDE 209
                                       789******************************9999999999999999999999999999****888888886655 PP

                                       HHHTT-SS-GGGGGG.................HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHH CS
                    Nitroreductase  63 kaeaqaelaqryrke.................elklkaqkalagapvlivivatldkserkaaerayryalldagaa 122
                                        a   +        +                 ++  k+ ++++ +p++ ++          + + ++r ++++ag+ 
  gi|386001843|ref|YP_005920142.1| 210 DAWDGLPGYAFGYSDfesyfgkfifgtfdtstSRARKEMALMRASPAVGIL----------STDAEERGTWVEAGMR 276
                                       5555554444444445666*************99*****************..........**************** PP

                                       HHHHHHHHHHTT-EEEEE-GGGGGHH...HHHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 123 aqnllLaAtalGlgscpiggfdeaae...evrkllglpdeeeivvliavGy 170
                                        ++l L+At lG+ +   +++ + ae   +++ +lg++    ++ li++Gy
  gi|386001843|ref|YP_005920142.1| 277 FERLFLTATKLGVRFDLFSQPVAIAElreRMAGILGVD---YPQILIRMGY 324
                                       **************999999997766555677777777...6777888887 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.6e-08   0.00023     155     206 ..      21      80 ..      17      89 .. 0.71
   2 !    6.3   0.0   0.00072       6.5       2      32 ..     129     160 ..     128     173 .. 0.90
   3 ?   -2.1   0.0      0.26   2.3e+03      78     100 ..     267     289 ..     238     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-08
                                       GS-HHHHHHHHHHHTS--GGG----EEE.E-SSEE..............EEE-S-HHHHHH CS
                    TM1586_NiRdase 155 elpewfkeileaarlAPsAlNqqpwrfelkdddeiki.........kasvlgklskiDlGI 206
                                       +++e+++ +l+ a lAPs  N+qpwr+ +++ +e+++          ++ +++ + + lG 
  gi|386001843|ref|YP_005920142.1|  21 KIDEKLEFLLRYAVLAPSGPNNQPWRLAVDG-NEVTVmadlgrtlpDVEPTNRTTYMSLGC 80 
                                       578999999*******************555.79999666666555233334555555555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00072
                                       HHHHHHH--B--.-B--S---HHHHHHHHH-- CS
                    TM1586_NiRdase   2 lyeaiekRhsvR.kYkdealeeelleelkeai 32 
                                       l+  i++Rh+ R +Y+d+++e +++e++kea+
  gi|386001843|ref|YP_005920142.1| 129 LFPEITERHTNRgAYDDRPIEADKIEAMKEAV 160
                                       66789*******77**************9987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHHHHHTT- CS
                    TM1586_NiRdase  78 edleekaGYygeqlvLkltalGl 100
                                       ++  ++aG   e+l L +t+lG+
  gi|386001843|ref|YP_005920142.1| 267 RGTWVEAGMRFERLFLTATKLGV 289
                                       45556777778888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2421.22
//
Query:       gi|386001844|ref|YP_005920143.1|  [L=380]
Description: hypothetical protein Mhar_1152 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-07   31.4   0.3       0.02   14.6   0.0    2.6  2  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   1.7e-06      0.03       2     129 ..      87     234 ..      86     236 .. 0.76
   2 !   14.6   0.0   1.1e-06      0.02     199     242 .]     294     338 ..     280     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-06
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE........................ CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel........................ 54 
                                       r++A+DGSn vv   + + + l+++ ++   ++  e+ ++    d  +  d+                         
  gi|386001844|ref|YP_005920143.1|  87 RIFAIDGSNVVV--FDLGAVSLNRIRAGYVVYRGTEWEKTAITCDDLFVADREnysqhfnryrkgifdieepfelqs 161
                                       89**********..4445555555555555555555555555555555555556899999***************** PP

                                       ....HHHHHHHHHHHHHH.HHHHHCGGCCSCEEEEECSHHCCCHHHHHHHHHHHHHHHHHHH.HHHTT-TTCEEEEE CS
                              NurA  55 ....errirllmetlElk.lgallleekgedllllDGsligslvefdelheeleyeeylysl.srlleaglnlvgva 125
                                           +r    ++ + E+  l +  le++  d++l+DG ++ +          + ++e+++++ +r+ e+g++l++++
  gi|386001844|ref|YP_005920143.1| 162 keelDRMATFYRDLQEHVaLFEAVLEAEAGDVVLYDGGFSLWRE--------PYHREVFDRIfERAGERGVDLLAIS 230
                                       **9999999999999999777778899999**********9999........7777777665344444499999999 PP

                                       SS-S CS
                              NurA 126 Ksfr 129
                                       Ks++
  gi|386001844|ref|YP_005920143.1| 231 KSSQ 234
                                       9985 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.1e-06
                                       EEEEHHHHHH.CCHHHHHHHHHH....TTB-SSSBCCHHHHHHHHCC CS
                              NurA 199 lrleipaevs.takdedvlslla..sqrlsisGYprpLalAhelaki 242
                                       +r++  a+++ + +++++l ++a  s+  +++GYp++L +Ah+++ki
  gi|386001844|ref|YP_005920143.1| 294 FRVD--APGRtAGSIDEILGRIAfySRSSESPGYPHALFRAHQEMKI 338
                                       6777..5667699********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2503.81
//
Query:       gi|386001845|ref|YP_005920144.1|  [L=554]
Description: hypothetical protein Mhar_1153 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-18   66.0   0.0    8.3e-18   65.3   0.0    1.3  1  DUF87          Helicase HerA, central domain
  ------ inclusion threshold ------
      0.012   15.0   0.0        1.1    8.5   0.0    2.2  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.098   11.2   0.0       0.16   10.5   0.0    1.3  1  DUF853         Bacterial protein of unknown function (DUF853)
       0.15   10.9   0.0       0.62    8.9   0.0    1.8  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   1.8e-21   8.3e-18       1     227 []     169     399 ..     169     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.8e-21
                             DUF87   1 ieiGrllsgse....vpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.....kkgatililDpHGEYgkal 68 
                                       +e+G l +gse    +pv l    +  +H++++++TG+GKSn+++v  ++ ++     + +  +li+DpHGEY   +
  gi|386001845|ref|YP_005920144.1| 169 VEVGLLRNGSEivegIPVALASFAM-DHHMGVFATTGMGKSNFMKVFAASCMKkasskESKFGLLIVDPHGEYILGN 244
                                       57888877777888899**999777.**************************9999877788************999 PP

                             DUF87  69 ........ekllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakee 133
                                                 ++++ ++ ++++p +       el+++ +++ p++++ l+   + +++++++++ + +++    + +
  gi|386001845|ref|YP_005920144.1| 245 egtkgllhLARYRDGIVCYSTDPRHkkdpAVSELTVKKSEILPQDIEVLYAW-TSAQREALEAISRVFFE----EGW 316
                                       99*****9999***********999999999*********************.44444445555555555....345 PP

                             DUF87 134 keklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsg 210
                                       +e++ + e  +k+  e    +e+      ++i+++ldk +++ + ++s+      +i++l       gk++ +d+  
  gi|386001845|ref|YP_005920144.1| 317 IEEFLTPEGAAKMIAEGF--HEKTVGRIGRTIKTILDKNRYISDFTSSI----PGIINSL-----LAGKVVLVDIPN 382
                                       555555555555555554..35555555555555555555555555555....5555555.....789999999999 PP

                             DUF87 211 vdelaqqlvvsvilrri 227
                                       + e+    + s ++r i
  gi|386001845|ref|YP_005920144.1| 383 LGERSELFLLSILSRAI 399
                                       88888888888888865 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00025       1.1      23      74 ..     177     229 ..     162     239 .. 0.83
   2 ?    4.1   0.0    0.0056        25     165     218 ..     436     488 ..     405     496 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00025
                                       EEET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEE CS
                      FtsK_SpoIIIE  23 gkei.sgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVql 74 
                                       g ei  g+p+ l    m  h+ v  +tg GKS++++++ +S + +++ +e ++
  gi|386001845|ref|YP_005920144.1| 177 GSEIvEGIPVALASFAMDHHMGVFATTGMGKSNFMKVFAASCMKKASSKESKF 229
                                       5677788899988889999*********************9999888887766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0056
                                       ...........-----------B-----EEEEEEC-HHHHHHHHHHH....HHH CS
                      FtsK_SpoIIIE 165 ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlved 218
                                       r  s++ +g ++gv + + +++   + ++l++++  ++ L la+++d   + e+
  gi|386001845|ref|YP_005920144.1| 436 RFESIAREGRKFGVGLCAITQQPKLIDKQLLSQFNTFVILGLADRNDR-TRLEE 488
                                       66789999******9988888888899********************4.44443 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.5e-05      0.16     278     365 ..     434     515 ..     360     522 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.5e-05
                            DUF853 278 lekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteL 354
                                       l + e + r  r  GvG+  +tq+P  + ++ L+q+ + v  +l     +d+  +  +a+    ++  ++   i+ L
  gi|386001845|ref|YP_005920144.1| 434 LARFESIAREGRKFGVGLCAITQQPKLIDKQLLSQFNTFVILGLAD--RNDRTRLEESAK----QDLSSLDVEIQTL 504
                                       57899999*****************************999888853..445555555544....44445555699** PP

                            DUF853 355 gvGealvsvLd 365
                                       + Gea++s+L+
  gi|386001845|ref|YP_005920144.1| 505 EKGEAIISTLK 515
                                       ********996 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00014      0.62      10      56 ..     189     241 ..     179     245 .. 0.71
   2 ?   -1.1   0.0      0.15   6.8e+02     258     285 ..     434     461 ..     432     499 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00014
                     TrwB_AAD_bind  10 pkeretqhilivGttGsGKtqalekllrairarg......draivlDltGafv 56 
                                          + ++h+ ++ ttG+GK++ ++ + ++  +++         +++D++G+++
  gi|386001845|ref|YP_005920144.1| 189 ASFAMDHHMGVFATTGMGKSNFMKVFAASCMKKAsskeskFGLLIVDPHGEYI 241
                                       4455678***************9987555544443443445689999999986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.15
                     TrwB_AAD_bind 258 leelksllaegRkfGgavvlglqsiaql 285
                                       l  ++s++ egRkfG+ + +  q+ + +
  gi|386001845|ref|YP_005920144.1| 434 LARFESIAREGRKFGVGLCAITQQPKLI 461
                                       6678899999999998766666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3454.44
//
Query:       gi|386001846|ref|YP_005920145.1|  [L=388]
Description: Ser/Thr protein phosphatase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-13   52.2   0.5    3.6e-13   50.5   0.5    1.8  1  Metallophos    Calcineurin-like phosphoesterase
    9.9e-11   42.1   0.2    1.4e-10   41.6   0.2    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.046   13.1   0.0         11    5.3   0.0    2.4  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.5   6.1e-17   3.6e-13       1     202 [.       1     203 [.       1     205 [. 0.64

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 6.1e-17
                                       EEEEEEESBTB..............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHH CS
                       Metallophos   1 lrilvigDlHl..............algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellella 58 
                                       ++i++++D Hl               +++  ++ + k++d++++   pd+v++aGD++++      +l   ++++l+
  gi|386001846|ref|YP_005920145.1|   1 MKIVHMADSHLgfsaygrvdrwgrnQREEMVYQGFSKTVDKIIDL-SPDAVVHAGDVFHHVrprirPLYV-FQQNLE 75 
                                       89*****************999999999999999999999*9999.**************9999988888.99999* PP

                                       HHHHHTSEEEEEC-TTS.......CHHHHHHHHHHHHHHH.....HHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                       Metallophos  59 alvkypipvylllGNHe.......gfeeellnkygylgif.....sepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                       +lv+ +i+v+++ GNH+              +++  ++ +     ++ +r+  e+f    + +      ++++++  
  gi|386001846|ref|YP_005920145.1|  76 RLVEAGIQVVIISGNHDapksyasL------SPFSLFEGMegvqiAHRYRH--ECF---EVGD---H--HFHCIPFC 136
                                       *****************43322220......22222222233322222222..222...1111...1..22222222 PP

                                       .CEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS...CSSSCSCCHHHHHHHHHHTTESEE CS
                       Metallophos 124 .spellvsldklgslnleleapepgdewlkdlekrekadwvivlgHsply...rgsgylfgdealedllkkygvdlv 196
                                        spe+                +e     +++l+++  +  ++++ H  ++   ++   + g++++++ + k+++ ++
  gi|386001846|ref|YP_005920145.1| 137 lSPED--------------YMEE--FRKMQELRAEMSGGRDVLVMHGLVEalwDRRLRTVGEHEIAESFLKGDLTYI 197
                                       11111..............1111..3333333334444444444444444456777778888888888888888888 PP

                                       EEESSS CS
                       Metallophos 197 isGHtH 202
                                         GH H
  gi|386001846|ref|YP_005920145.1| 198 ALGHYH 203
                                       888877 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.2   2.4e-14   1.4e-10       1     161 [.       1     236 [.       1     240 [. 0.68

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.4e-14
                     Metallophos_2   1 MklaiiSDlH...snldaleav................lealkevgvdaiihaGDl.eeeep.........evleel 48 
                                       Mk+++++D+H   s++ +++++                ++++ + ++da++haGD+   + p         + le+l
  gi|386001846|ref|YP_005920145.1|   1 MKIVHMADSHlgfSAYGRVDRWgrnqreemvyqgfsktVDKIIDLSPDAVVHAGDVfHHVRPrirplyvfqQNLERL 77 
                                       **********7775555555557777777889999999*****************8877777666666655577777 PP

                     Metallophos_2  49 lela.pvlaVrGNnD....................eevveedvlreaaelgtdl.....................pe 83 
                                        e   +v+++ GN+D                    +  ++++  +e  e+g+++                     + 
  gi|386001846|ref|YP_005920145.1|  78 VEAGiQVVIISGNHDapksyaslspfslfegmegvQ--IAHRYRHECFEVGDHHfhcipfclspedymeefrkmqEL 152
                                       7766*************************9986541..444444444444444446666666666666555543223 PP

                     Metallophos_2  84 eaelel.agekvlliHgdpl.........gvkdalaellkeaeegsdvvvcGHtHvp.evekeggvlvvnPGsvgep 149
                                       +ae  + +g++vl++Hg             +++++ae + +   + +++++GH H + +v k       + Gsv+  
  gi|386001846|ref|YP_005920145.1| 153 RAE--MsGGRDVLVMHGLVEalwdrrlrtVGEHEIAESFLK--GDLTYIALGHYHGQaRVAKN----AWYSGSVEYF 221
                                       333..248999******966977776555555555555555..4444********87333333....4456777666 PP

                     Metallophos_2 150 rdgdpe...tyaild 161
                                       r+++ +   +++++d
  gi|386001846|ref|YP_005920145.1| 222 RFSEAKdekGILLVD 236
                                       666555444555555 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.002        12      21      43 ..      35      57 ..      26      65 .. 0.88
   2 ?    5.3   0.0    0.0018        11      77     103 ..      69      95 ..      63     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.002
                                      HHHHHHHHHHH--SEEEEES--- CS
                     Metallophos_3 21 lerlveviedkdpDllvlvGdlv 43
                                      + ++v++i d +pD++v  Gd+ 
  gi|386001846|ref|YP_005920145.1| 35 FSKTVDKIIDLSPDAVVHAGDVF 57
                                      5799*****************96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHTT-SEEEEE--TTS--H CS
                     Metallophos_3  77 lldklfrelgeldvpafvvPGkrDaPl 103
                                       ++++ ++ l e++++++++ G++DaP 
  gi|386001846|ref|YP_005920145.1|  69 VFQQNLERLVEAGIQVVIISGNHDAPK 95 
                                       5667789999****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2694.60
//
Query:       gi|386001847|ref|YP_005920146.1|  [L=1062]
Description: hypothetical protein Mhar_1155 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-20   71.6   0.0    1.1e-19   70.8   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
    3.3e-17   63.7  26.1    1.2e-16   61.9  16.9    4.3  2  AAA_23           AAA domain
      9e-11   42.1   0.0    5.7e-10   39.4   0.0    2.0  2  AAA_15           AAA ATPase domain
    1.7e-07   30.9   0.0      3e-07   30.1   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    3.6e-06   26.7   0.1    3.6e-06   26.7   0.1    4.2  5  AAA_27           AAA domain
      4e-06   27.0   0.0    1.2e-05   25.5   0.0    1.9  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
    0.00017   22.1   0.2     0.0014   19.2   0.0    2.7  2  ABC_tran         ABC transporter
    0.00025   21.0   0.1      0.001   19.0   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
  ------ inclusion threshold ------
       0.11   12.8   6.2       0.79   10.1   0.8    3.7  2  Siah-Interact_N  Siah interacting protein, N terminal
       0.14   12.2   2.0       0.33   10.9   0.0    2.8  3  AAA_5            AAA domain (dynein-related subfamily)
        3.6    7.9   6.1         21    5.4   0.3    4.5  5  HALZ             Homeobox associated leucine zipper


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   6.6e-23   1.1e-19       2     217 ..       3    1053 ..       2    1056 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 6.6e-23
                                        EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkk 76  
                                        l++l ++nFk y+  +v ++f++++t i+G NGSGKs +++Ai + L  + a++      +d i++ ++ ++ + 
  gi|386001847|ref|YP_005920146.1|    3 LNSLSMKNFKKYR-GAVRVEFQDGLTGILGGNGSGKSTIVEAIAWALYGSRAST----VRRDFIKN-SRASERDD 71  
                                        78999*******8.99*******************************8777745....55789999.88899999 PP

                                        EEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H..HHHHHHHHCT.T-STT............. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxx............. RF
                             SMC_N   77 aeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtk..kevsellesa.giske............. 135 
                                         ev++ +++++k+     + +  +r +    e + +i+g+ v +  +ev   l++  +is               
  gi|386001847|ref|YP_005920146.1|   72 LEVTLSLQHDGKE----MTVLRAMRGKGMAPEARLRIDGELVASgtREVDARLSEIlQISFAdfmktfyarqkdl 142 
                                        9****99988888....44455555566666699******99876789999998752455559************ PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  143 dnlirdrgsekreylltllgldevrdgaleeiradlreaegevgrvegalgeigdvdllleegeravasareell 217 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  218 eakgreeeiatalegrrqklegeaerrrardalvgevarlradlaskeeaiasddrrlseieegrwrlfelepkl 292 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  293 trlrelrlrlegmeakrprhqallgrraqvgadlegrgrllsdsearlarlrdesreheairpqeeeyrrllsel 367 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  368 egmeakrdrfqelaslagrerarkeaaeenlarveeeirglsaaklriaeitpsleifrtlqemvrrqeregekd 442 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  443 rllsglrmrdqavrsrierlraeveriegevtrlgdleereadlvkkgevigrllagaeeelvglkfglevarre 517 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  518 lreaeaqrsriealgeeslcptcerplaeqrpflqekyraaasgakeristleglkgdllarveegrrsmertrr 592 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  593 elsriaelkaerggllaerrsllaqgqelsreaeeieaeigsigpvdydpdrlslleaevssllplvqeeqqlsv 667 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  668 riealpkkrseeevarealatsiarvaslaeemevlgyseeerlrarerigslrevhrrfsalaerireipavea 742 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  743 aadglrsevrrlrdelkgvdgemealgfdpaeyegligearslagaetaaneirlalaaegevsrhrgeaaaaas 817 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|386001847|ref|YP_005920146.1|  818 rlrgevaraeegivalafseeayrearssleeasrwleaarkeasagmvrlglaegnlerlrgeaarrreleara 892 
                                        *************************************************************************** PP

                                        ......................................................................CS-HH CS
                                        ......................................................................xxxxx RF
                             SMC_N  136 ......................................................................lLSgG 140 
                                                                                                                SgG
  gi|386001847|ref|YP_005920146.1|  893 aalrrrvqvvettrvlvnrfldailvrmrreiaesagrilqevtgkygrisideefnilvedegefypisRYSGG 967 
                                        *************************************************************************** PP

                                        HHHHHHHHHHHH........HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-S CS
                                        xxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                             SMC_N  141 ektLvalaLlfA........iqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekad 206 
                                        e  ++a+++++A          +    ++ +lDe+    D ++++ + ++l++  ++  Q++ is+  e+  + d
  gi|386001847|ref|YP_005920146.1|  968 EIDMIAVSVRIAiserlmrfSSNGPGYSFLILDEVFGSQDVEHRESMINMLRSLDDRfPQIFAISHIGEVQGQFD 1042
                                        ************7777544333334468*************************999967*******999999998 PP

                                        CEEEEEEEETT CS
                                        xxxxxxxxxxx RF
                             SMC_N  207 klvgvtkveng 217 
                                        + + v   e+g
  gi|386001847|ref|YP_005920146.1| 1043 NSILVVEDEDG 1053
                                        88888776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9  16.9   7.1e-20   1.2e-16       1     199 [.       5     237 ..       5     573 .. 0.82
   2 ?   -1.5   3.3       1.8     3e+03     135     190 ..     577     630 ..     552     735 .. 0.71

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 7.1e-20
                            AAA_23   1 kLkienfrsfrdqe.idFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.. 74 
                                       +L+++nf+++r+   ++F +glt I G NG+GK+Ti++Ai +aLyg   r s+      +++d+  +s+++ +    
  gi|386001847|ref|YP_005920146.1|   5 SLSMKNFKKYRGAVrVEFQDGLTGILGGNGSGKSTIVEAIAWALYGS--RAST------VRRDFIKNSRASERDDle 73 
                                       69********88555*******************************5..3333......555555555545555512 PP

                            AAA_23  75 veltfenkdgrytrsiererelskkkgkttkkaklellei..deleqfisellgskkiilnlilflgqerfeefel. 148
                                       v+l++++++++  +++ r    +    + +   ++el+    +e + ++se+l+++++ +   ++  q++ +++ + 
  gi|386001847|ref|YP_005920146.1|  74 VTLSLQHDGKE--MTVLRAMRGKGMAPEARLRIDGELVASgtREVDARLSEILQISFADFMKTFYARQKDLDNLIRd 148
                                       56666666664..6776666666666666666677777667899999*********999999999999996666664 PP

                            AAA_23 149 ..kdkke........................................................rleelekeleeled 167
                                         ++k e                                                        +             
  gi|386001847|ref|YP_005920146.1| 149 rgSEKREylltllgldevrdgaleeiradlreaegevgrvegalgeigdvdllleegeravasAR------------ 213
                                       44333336777777777777755555555555666444444444444444444444444333322............ PP

                            AAA_23 168 ekkllekleqekekekeleeleeeleeilkel 199
                                               e+++e + + ee+  +le   ++l
  gi|386001847|ref|YP_005920146.1| 214 --------EELLEAKGREEEIATALEGRRQKL 237
                                       ........333333333333333333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                            AAA_23 135 ilflgqerfeefelkdkkerleelekeleeledekkllekleqekekekeleelee 190
                                       ++   ++r  ++++ ++++r++el+ e   l +e++ l ++ qe++   e ee+e 
  gi|386001847|ref|YP_005920146.1| 577 LARVEEGRRSMERTRRELSRIAELKAERGGLLAERRSLLAQGQELS--REAEEIEA 630
                                       4445566666666666666777777776666666666555532222..22233332 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   3.5e-13   5.7e-10       1      67 [.       1      68 [.       1     149 [. 0.86
   2 ?   -0.0   0.0      0.34   5.6e+02     252     364 ..     920    1033 ..     907    1033 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.5e-13
                            AAA_15  1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedlei 67
                                      M++++++ kNF++++  v +++++ lt + G N+sGKS+i+ea+ + l  ++   +  ++i+++  ++
  gi|386001847|ref|YP_005920146.1|  1 MRLNSLSMKNFKKYRGaVRVEFQDGLTGILGGNGSGKSTIVEAIAWALYGSRASTVRRDFIKNSRASE 68
                                      9***************9***************************998888744444444555544444 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.34
                            AAA_15  252 idkklaeelkkilkkkidkikkfnykgkkneeieik.ddeelplnknGsGvqrllllillileaekk...dekee 322 
                                        +  ++ae++ +il++   k  ++ + + ++++i ++ ++e  p+++ + G   ++ +++ i+  e+    +++  
  gi|386001847|ref|YP_005920146.1|  920 MRREIAESAGRILQEVTGK--YGRISIDEEFNILVEdEGEFYPISRYSGGEIDMIAVSVRIAISERLmrfSSNGP 992 
                                        5555555555555555555..3444555555555558888899***********************999999999 PP

                            AAA_15  323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364 
                                         + +l+++E   ++  ++ +++i+ l++l +    Q++  +H
  gi|386001847|ref|YP_005920146.1|  993 GYSFLILDEVFGSQDVEHRESMINMLRSLDDRFP-QIFAISH 1033
                                        9********9999999999999999999988887.9988777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.8e-10     3e-07       1      50 [.       3      52 ..       3      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.8e-10
                            AAA_29  1 LkrlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      L++l++ N   ++g  ++e++ +g t + G +GsGKST++ Ai+  L++++
  gi|386001847|ref|YP_005920146.1|  3 LNSLSMKNFKKYRGaVRVEFQ-DGLTGILGGNGSGKSTIVEAIAWALYGSR 52
                                      6789999*******9999**8.779***********************987 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   2.2e-09   3.6e-06       1      91 [.       1      94 [.       1     125 [. 0.82
   2 ?   -2.5   1.6       1.9   3.1e+03      76     159 ..     334     419 ..     321     468 .. 0.53
   3 ?   -1.7   0.1       1.1   1.8e+03      82     127 ..     464     513 ..     437     527 .. 0.63
   4 ?   -1.8   0.4       1.2   1.9e+03     143     199 ..     680     736 ..     675     742 .. 0.84
   5 ?   -2.7   1.3       2.3   3.7e+03     138     197 ..     799     861 ..     796     868 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.2e-09
                            AAA_27  1 MrlerLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdllfGipert.kdnflh.....dakkLriga 72
                                      Mrl++L+++ + k+ +  +++f+   ++l+ i+G N +GKst+++Ai   l+G  ++t +++f+      ++++L++  
  gi|386001847|ref|YP_005920146.1|  1 MRLNSLSMKNFKKYRGAvRVEFQ---DGLTGILGGNGSGKSTIVEAIAWALYGSRASTvRRDFIKnsrasERDDLEVTL 76
                                      9**************98579997...8***************************99874678876222225679****9 PP

                            AAA_27 73 vleeadgeelefaRrkgrk 91
                                      +l ++dg+e+++ R  + k
  gi|386001847|ref|YP_005920146.1| 77 SL-QHDGKEMTVLRAMRGK 94
                                      99.8999999999876655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                            AAA_27  76 eadgeelefaRrkgrkktlldaddqalpeevlaallgg..ldretFealFgLdh.erL.reGGealleaegelgqlL 148
                                       ++++++l+  R  +r+++ +++++++     l + l+g  ++r++F++l +L   er  +e +e+ l+  +e  + L
  gi|386001847|ref|YP_005920146.1| 334 SDSEARLARLRDESREHEAIRPQEEEYR--RLLSELEGmeAKRDRFQELASLAGrERArKEAAEENLARVEEEIRGL 408
                                       5555555555666666666666655333..23333333114566666666664312220233333333333334455 PP

                            AAA_27 149 feasaGlaslr 159
                                        +a+  +a+++
  gi|386001847|ref|YP_005920146.1| 409 SAAKLRIAEIT 419
                                       55555555555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.1
                            AAA_27  82 lefaRrkgrkktlldaddqalp....eevlaallggldretFealFgLdh 127
                                        e++R  g+ + l d ++++ +     ev+ +ll+g+++e     FgL+ 
  gi|386001847|ref|YP_005920146.1| 464 AEVERIEGEVTRLGDLEEREADlvkkGEVIGRLLAGAEEELVGLKFGLEV 513
                                       55566666665555555553322223566677777777777777777764 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.2
                            AAA_27 143 elg.qlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       e++ ++L ++ a +asl+e +e L  + +e  + r++   +++e +++++++ +++re
  gi|386001847|ref|YP_005920146.1| 680 EVArEALATSIARVASLAEEMEVLGYSEEERLRARERIG-SLREVHRRFSALAERIRE 736
                                       444268999999999999******999999999999999.999999999999999987 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 2.3
                            AAA_27 138 leaegelgqlLfeasaGlaslrevleaLeaeadel.fkprkskk..rainealeeleeakkel 197
                                       l+aege+++   ea+a+ ++lr  +++ e+   +l f++++ ++   ++ ea + le+a+ke 
  gi|386001847|ref|YP_005920146.1| 799 LAAEGEVSRHRGEAAAAASRLRGEVARAEEGIVALaFSEEAYREarSSLEEASRWLEAARKEA 861
                                       678888888888888888888888777777665552444333332234555555555555554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   7.2e-09   1.2e-05      30      89 ..     961    1019 ..     946    1020 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.2e-09
                           SbcCD_C   30 sgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89  
                                        +++ SGGe   ++++ +  a++  + + +++ p +++++LDE F++ D e +++++++l+
  gi|386001847|ref|YP_005920146.1|  961 ISRYSGGEI-DMIAVSVRIAISERLMRFSSNGPGYSFLILDEVFGSQDVEHRESMINMLR 1019
                                        6788*****.999999999******999879**************************997 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.4e-07    0.0014      13      65 ..      26      76 ..      18     169 .. 0.71
   2 ?   -2.3   0.1       3.6   5.8e+03      58      58 ..     432     432 ..     339     483 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.4e-07
                                      EEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGGB-HHHCCHCEEEE- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp.teGeilldgkdlkeqeleslrkeigvlp 65
                                      +++i+G nG+GKSt+++++a  l    + ++    +d+ ++++ s r  ++v  
  gi|386001847|ref|YP_005920146.1| 26 LTGILGGNGSGKSTIVEAIAWALYGsRASTV---RRDFIKNSRASERDDLEVTL 76
                                      789****************965443255555...33333334444444444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                                       C CS
                                       x RF
                          ABC_tran  58 r 58 
                                        
  gi|386001847|ref|YP_005920146.1| 432 V 432
                                       0 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.2e-07     0.001       1      36 [.      26      58 ..      26     162 .. 0.79
   2 ?   -3.0   0.1         3   4.9e+03     130     185 ..     264     316 ..     221     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.2e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdel 36
                                      l+++ G NgsGKS++ +a+ ++      ++ +t  +
  gi|386001847|ref|YP_005920146.1| 26 LTGILGGNGSGKSTIVEAIAWAL---YGSRASTVRR 58
                                      699****************9993...3333333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3
                            AAA_21 130 lsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrll 185
                                       ++ ++++d+ + + + + ++r+++l++ l  l   r ++l++ +++++ ++++ ll
  gi|386001847|ref|YP_005920146.1| 264 KEEAIASDDRRLSEIEEGRWRLFELEPKLTRL---RELRLRLEGMEAKRPRHQALL 316
                                       33333333333333333333333333333333...555555555555555555444 PP

>> Siah-Interact_N  Siah interacting protein, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00049      0.79      15      47 ..     236     267 ..     233     281 .. 0.80
   2 ?    2.7   0.5     0.096   1.6e+02      18      51 ..     452     484 ..     449     492 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                   Siah-Interact_N  15 kLlekAtRkrVkdlLsaeirKleteilklkekq 47 
                                       kL  +A+R r +d+L  e+++l+ ++ ++ke++
  gi|386001847|ref|YP_005920146.1| 236 KLEGEAERRRARDALVGEVARLRADL-ASKEEA 267
                                       7999**********************.444443 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.096
                   Siah-Interact_N  18 ekAtRkrVkdlLsaeirKleteilklkekqkaka 51 
                                       ++A R+r+ + L ae+ ++e e+ +l + ++ +a
  gi|386001847|ref|YP_005920146.1| 452 DQAVRSRI-ERLRAEVERIEGEVTRLGDLEEREA 484
                                       68999999.579***********99988877665 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 ?   10.9   0.0    0.0002      0.33       5     109 ..      30     144 ..      28     180 .. 0.69
   2 ?   -2.5   0.1       2.9   4.7e+03      44      80 ..     447     485 ..     436     489 .. 0.61
   3 ?   -2.9   0.0       3.7   6.1e+03     101     134 ..     598     632 ..     586     635 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                       E--SSSSHHHHHHHGGGGB......S--EEEEE--TT--HHHHH--B--.........--------......G-SEE CS
                             AAA_5   5 vGppGtgKselaerlaaal......nreveyvqltrdtteedlkgrreikngttslvdsplvraar......egeil 69 
                                       +G  G+gKs+++e +a al      + +   + ++r  +++dl   ++++ ++++++     ra+r      e+++ 
  gi|386001847|ref|YP_005920146.1|  30 LGGNGSGKSTIVEAIAWALygsrasTVRRDFIKNSRASERDDLEVTLSLQHDGKEMTV---LRAMRgkgmapEARLR 103
                                       7999****************9877777777899***************9855555543...4455555678888888 PP

                                       EEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---.. CS
                             AAA_5  70 vlDEverae.sevlnsLlslleerrllleeggelvkakndd 109
                                       +++E+     +ev ++L  +l     ++++ +   +++ d+
  gi|386001847|ref|YP_005920146.1| 104 IDGELVASGtREVDARLSEILQISFADFMKTFYARQKDLDN 144
                                       88887766668888888877776666666665555555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                       -B--.........--------.........G-SEEEEESGGG--HH CS
                             AAA_5  44 rreikngttslvdsplvraar.........egeilvlDEveraese 80 
                                       +++++++  + +        +         ege+++l+++e+ e +
  gi|386001847|ref|YP_005920146.1| 447 GLRMRDQAVRSRI-------ErlraeveriEGEVTRLGDLEEREAD 485
                                       4444433333333.......33444444889999999999987766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.7
                                       SEEE---.......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5 101 elvkakndd.llerfrviatanpldrslnelspal 134
                                        + ka++ + l+er +++a + +l+r+ +e+ +++
  gi|386001847|ref|YP_005920146.1| 598 AELKAERGGlLAERRSLLAQGQELSREAEEIEAEI 632
                                       45566666666666777777777777777776665 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.5   5.6e+03      29      42 ..     248     261 ..     245     262 .. 0.81
   2 ?   -1.1   0.2       1.4   2.3e+03      26      41 ..     358     373 ..     357     375 .. 0.83
   3 ?   -0.1   0.0      0.68   1.1e+03      17      40 ..     455     478 ..     448     481 .. 0.75
   4 ?    5.4   0.3     0.013        21      17      39 ..     600     622 ..     598     626 .. 0.90
   5 ?    0.6   0.0      0.43     7e+02      30      42 ..     746     758 ..     739     764 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.5
                              HALZ  29 ekLkaelqeLkekl 42 
                                       ++L  e+++L++ l
  gi|386001847|ref|YP_005920146.1| 248 DALVGEVARLRADL 261
                                       78999999999866 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                              HALZ  26 kenekLkaelqeLkek 41 
                                       +e ++L++el+ + +k
  gi|386001847|ref|YP_005920146.1| 358 EEYRRLLSELEGMEAK 373
                                       57799*****999888 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.68
                              HALZ  17 LksdydsLkkenekLkaelqeLke 40 
                                        +s+ + L++e e+ + e+ +L +
  gi|386001847|ref|YP_005920146.1| 455 VRSRIERLRAEVERIEGEVTRLGD 478
                                       567788888888888888888765 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.013
                              HALZ  17 LksdydsLkkenekLkaelqeLk 39 
                                       Lk++   L++e+++L+a+ qeL+
  gi|386001847|ref|YP_005920146.1| 600 LKAERGGLLAERRSLLAQGQELS 622
                                       9999999**************97 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.43
                              HALZ  30 kLkaelqeLkekl 42 
                                        L++e+++L++ l
  gi|386001847|ref|YP_005920146.1| 746 GLRSEVRRLRDEL 758
                                       5777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1062 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 1.05u 0.33s 00:00:01.38 Elapsed: 00:00:00.49
# Mc/sec: 6476.91
//
Query:       gi|386001848|ref|YP_005920147.1|  [L=399]
Description: geranylgeranyl reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-11   42.7   4.0    1.3e-09   37.8   0.7    2.9  2  FAD_binding_3   FAD binding domain
    7.4e-09   35.6   8.0    0.00038   20.2   0.3    3.0  3  DAO             FAD dependent oxidoreductase
      1e-08   34.4   0.5    3.6e-08   32.5   0.6    1.7  2  HI0933_like     HI0933-like protein
    1.9e-08   33.9   0.2    3.1e-08   33.2   0.2    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.4e-07   28.8   0.9     0.0022   16.9   0.0    2.8  2  Trp_halogenase  Tryptophan halogenase
    8.2e-07   28.4   7.5     0.0074   15.4   0.0    2.9  2  Lycopene_cycl   Lycopene cyclase protein
    9.1e-07   28.6   5.4    1.4e-06   27.9   5.4    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
      1e-05   25.7   0.5      1e-05   25.7   0.5    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.6e-05   24.2   1.2      2e-05   23.9   1.2    1.3  1  GIDA            Glucose inhibited division protein A
    4.5e-05   22.7   8.0    7.4e-05   22.0   2.8    2.3  2  FAD_binding_2   FAD binding domain
    0.00099   18.4   0.2     0.0032   16.8   0.1    1.8  2  Thi4            Thi4 family
     0.0011   18.3   0.7     0.0019   17.6   0.7    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.015   15.9   0.4      0.041   14.5   0.1    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.03   14.2   0.3      0.051   13.4   0.3    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.059   12.6   0.3      0.089   12.0   0.3    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.095   12.3   0.2       0.19   11.4   0.2    1.4  1  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
       0.16   12.0   0.5       0.84    9.6   0.1    2.3  3  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.7   1.2e-12   1.3e-09       2     196 ..       4     184 ..       3     217 .. 0.77
   2 ?    3.3   0.1     0.038        40     287     337 ..     264     315 ..     258     324 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.2e-12
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       +dV+++GaGpaG m+a+  +eaG rvv+ e +s++      a+ l  r me  + l + +r+++        g  + 
  gi|386001848|ref|YP_005920147.1|   4 YDVAVIGAGPAGSMAAKKAAEAGARVVIFEEHSRAGWPVqCAGLLGVRAMEEAE-LAVGHRAIRPV-----RGSKVV 74 
                                       79******************************9998777257777888888654.33333333322.....233333 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                        +        ++l+ ++  ++  v+    ++r+L+++a++ g++v  +  v++l++ +    ++++  ++  +++v+
  gi|386001848|ref|YP_005920147.1|  75 SP------GGVQLTFRAPETKAWVVDRRIFDRALLAEAARSGADVMIASPVTGLLRGGGR--SVLKVGRSSDQRKVE 143
                                       33......3567776677778888888899*************************98776..888888888888*** PP

                                       EEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-S CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgiefegeetvyeagvldvlfda.dl 196
                                       a+ +v a+G+  ++++++gi    +++v  +  ++v f++ d 
  gi|386001848|ref|YP_005920147.1| 144 ARVVVSAEGVGARIARRAGIGP--PREVLSSAQVEVPFQVeDP 184
                                       *******************873..3444456677777766443 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.038
                                       EE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHH.TTSS-GGGGHHHHHH CS
                     FAD_binding_3 287 flaGDAaHihpPtgGqGlNtaiqDavnLawkLaavl.kGeAkeelLdtYeee 337
                                         +GDAa  + Pt G G+  ++  a   +   aa+  +G+ + ++L  Ye++
  gi|386001848|ref|YP_005920147.1| 264 IAVGDAAGQVKPTSGGGIYPGLVSAKIAGEVAAAAArEGDSSAARLCEYERR 315
                                       558**************99888888777765554441567777777777765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6   1.6e-06    0.0017       1      34 [.       5      40 ..       5      59 .. 0.94
   2 !   20.2   0.3   3.6e-07   0.00038     137     211 ..      85     162 ..      49     223 .. 0.63
   3 ?    0.9   0.1      0.26   2.7e+02      41     106 ..     291     352 ..     264     390 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags 34
                                      dv++iG+G +G+ +A  +a++g  V+++e +++ag+
  gi|386001848|ref|YP_005920147.1|  5 DVAVIGAGPAGSMAAKKAAEAGarVVIFEEHSRAGW 40
                                      8******************************99885 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.6e-07
                                       ETTE.EEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE...EECT.EEEEEEEEEEE--GGGHHHH CS
                               DAO 137 ypdt.gqv.dpakltaalaraaealGveilegtevtgleeedgkvwgve...rttp.gendaadavVnaaGawsdll 207
                                        p+t ++v d + + +al+++a++ G+++   ++vtgl + +  +  v    r ++  ++++a+ vV a G++++++
  gi|386001848|ref|YP_005920147.1|  85 APETkAWVvDRRIFDRALLAEAARSGADVMIASPVTGLLRGG--GRSVLkvgR-SSdQRKVEARVVVSAEGVGARIA 158
                                       555545555****************************95533..334434542.33233346788********9977 PP

                                       HTTC CS
                               DAO 208 gllk 211
                                       ++++
  gi|386001848|ref|YP_005920147.1| 159 RRAG 162
                                       3332 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.26
                                       EEEEESSSSTHHSTH.......HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEE.S...SHHHHHHHHHHHHHH CS
                               DAO  41 sgllhsglrylpeas.......elarlslealeelreleeelgididyrrtGllsla.a...deeelealdkllall 106
                                       +g +++                  arl+++ ++++++l +el+        G+++   +   ++eel++l +lla++
  gi|386001848|ref|YP_005920147.1| 291 AGEVAA--------AaaregdsSAARLCEYERRWRAALGRELR-------LGMIVHKmRaemTDEELDDLLRLLADR 352
                                       222333........02223333667999999888888888864.......222222211112333455554555543 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.6   3.4e-11   3.6e-08       1      43 [.       4      46 ..       4      49 .. 0.93
   2 ?   -1.2   0.0      0.59   6.2e+02     113     163 ..     100     152 ..      97     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.4e-11
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +dv+viG+G+AG maA +aa++g+rV+++e+ +++g  ++ +G
  gi|386001848|ref|YP_005920147.1|  4 YDVAVIGAGPAGSMAAKKAAEAGARVVIFEEHSRAGWPVQCAG 46
                                      59*******************************9998887777 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE--- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvkt...kseeeleadklvlAtG 163
                                       +all+e+ ++g +++  + v+++ +  ++   +k+   ++++++ea+ +v A G
  gi|386001848|ref|YP_005920147.1| 100 RALLAEAARSGADVMIASPVTGLLRGGGR-SVLKVgrsSDQRKVEARVVVSAEG 152
                                       57888999999999999999998665444.444443234666777776666655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2     3e-11   3.1e-08       1     114 [.       4     158 ..       4     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3e-11
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.................... 57 
                                       +dv+viG+GpAG  aa+++a+aga+v+++ +e    ++ ++    llgv++ +e ++                    
  gi|386001848|ref|YP_005920147.1|   4 YDVAVIGAGPAGSMAAKKAAEAGARVVIF-EEHSRAGW-PVQCAGLLGVRAMEEAELavghrairpvrgskvvspgg 78 
                                       69***************************.66666666.666677777777777666779999999*********** PP

                                       .........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .........................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs 109
                                                                   +  ++g +++ +++v+++ +g ++ +l+  +++d++k+++  +v A G 
  gi|386001848|ref|YP_005920147.1|  79 vqltfrapetkawvvdrrifdrallA--EAARSGADVMIASPVTGLLRGGGRSVLKVGRSSDQRKVEARVVVSAEGV 153
                                       **********************8551..45677899999999********99888888889*************998 PP

                                       EE-BC CS
                                       xxxxx RF
                       Pyr_redox_2 110 sprdl 114
                                        +r+ 
  gi|386001848|ref|YP_005920147.1| 154 GARIA 158
                                       87765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.4    0.0009      0.95       1      30 [.       5      31 ..       5      39 .. 0.82
   2 !   16.9   0.0   2.1e-06    0.0022     147     373 ..      89     322 ..      71     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0009
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtl 30
                                      ++ ++G+G+aG++aA   a+a+   ++v +
  gi|386001848|ref|YP_005920147.1|  5 DVAVIGAGPAGSMAAKKAAEAG---ARVVI 31
                                      589************9999888...55555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.1e-06
                                       -EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-T.TS-EEEE.EETTS-EEE-SEEEE-SGGG-IIIIIIT--- CS
                    Trp_halogenase 147 yAyhldaalyakfLrrvaearGvtrvegkvvevqlde.dgrvesl.rledgreveadlfiDcsGfrgllieqaLktg 221
                                        A+ +d++ +++ L + a + G +++ +  v+  l+    +v ++ r +d r+vea+ ++ + G  +++  +a   g
  gi|386001848|ref|YP_005920147.1|  89 KAWVVDRRIFDRALLAEAARSGADVMIASPVTGLLRGgGRSVLKVgRSSDQRKVEARVVVSAEGVGARIARRA---G 162
                                       59**********************************9655688874677899*****************9998...8 PP

                                       EEE-TTT---.-EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--T CS
                    Trp_halogenase 222 fedwsdvLlt.drAlavqveseelvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkl 296
                                       +    +vL      + +qve  e ve + +         W iP  + l   G+  +++ +     l++ll+  + ++
  gi|386001848|ref|YP_005920147.1| 163 IGPPREVLSSaQVEVPFQVEDPEMVEVFLGRDVAPGFFAWAIPAPEGLARvGLSCRNNAC---PYLKRLLKSPPIRS 236
                                       888888883213345555555568888877666666788*****9999997877777766...77999999999999 PP

                                       TTS-EEEE---EE.....ES-SEETTEEE-CCCTEE--CCCS-HHH..HHHHHHH.HHHHT--BTT--.HHHHHHHH CS
                    Trp_halogenase 297 eaeprkirfttGr.....rkqawvknvvalGlasgfvePlestsih..liqaalr.rLlallpdksde.paaiaefn 364
                                       +     +++ +G       +++   +++a+G+a+g v P  + +i+  l+ a +  +++a  ++++d+  a + e++
  gi|386001848|ref|YP_005920147.1| 237 RIRGGPLHLVVGGlplgpPASTVADGFIAVGDAAGQVKPTSGGGIYpgLVSAKIAgEVAAAAAREGDSsAARLCEYE 313
                                       999999999999889988999999*********************95556665542556666666666455788999 PP

                                       HHHHHHHHH CS
                    Trp_halogenase 365 revareler 373
                                       r+ +++l+r
  gi|386001848|ref|YP_005920147.1| 314 RRWRAALGR 322
                                       999888776 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   4.6   6.4e-05     0.067       1     144 [.       5     156 ..       5     184 .. 0.69
   2 !   15.4   0.0     7e-06    0.0074     243     333 ..     250     336 ..     247     352 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.4e-05
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecvehs....Wsgtivylddgk 73 
                                       Dv+viGaGpAg   A++   a++g +vv+ e      +p +       +++++ e +v+h+     +g  v  ++g 
  gi|386001848|ref|YP_005920147.1|   5 DVAVIGAGPAGSMAAKKA--AEAGARVVIFEEHSRAGWPVQCAGLLGVRAMEEAELAVGHRairpVRGSKVVSPGGV 79 
                                       9**********8877777..99********99999889888777777777777666666652222356677777777 PP

                     Lycopene_cycl  74 killg...raYgrvsskrlkeellerlvengvk.lleakvesveeeea..geslvvleggrkirarlvvdarglasl 144
                                       + +      +   v ++ + + ll + + +g+  +  + v+           ++   ++ rk++ar+vv a g++++
  gi|386001848|ref|YP_005920147.1|  80 QLTFRapeTKAWVVDRRIFDRALLAEAARSGADvMIASPVTGLLRGGGrsVLKVGRSSDQRKVEARVVVSAEGVGAR 156
                                       76666554445567888888888888775555414455666665555411122223456668888888888886654 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7e-06
                     Lycopene_cycl 243 iPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlwprerkrqreff 319
                                       +P+  g++++ ++   +a+G aag v+P+ G  +   l  a+ +a  +aaa++++   ++ +a+l   er+ ++++ 
  gi|386001848|ref|YP_005920147.1| 250 LPL--GPPASTVADGFIAVGDAAGQVKPTSGGGIYPGLVSAK-IAGEVAAAAARE--GDSSAARLCEYERRWRAALG 321
                                       788..9999999999************************999.666777776643..34444556666666666666 PP

                     Lycopene_cycl 320 rllgl.alllkldie 333
                                       r l l +++ k++ e
  gi|386001848|ref|YP_005920147.1| 322 RELRLgMIVHKMRAE 336
                                       655541455556655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   5.4   1.4e-09   1.4e-06       1     153 [.       5     162 ..       5     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.4e-09
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.qvvtgiareflerlrq.rggarl 75 
                                       Dv V+G+gpaG +AA  Aa+aGa+v++ ee+ + G  +  +++  +  ++ +e +v ++ +r ++       gg +l
  gi|386001848|ref|YP_005920147.1|   5 DVAVIGAGPAGSMAAKKAAEAGARVVIFEEHSRAGWPVQCAGLLGVRAMEEAElAVGHRAIRPVRGSKVVsPGGVQL 81 
                                       9**********************************988777777777767566355555555555433334555543 PP

                      FAD_oxidored  76 k....krskwntfepevakavleemlaeagvtvllntrlvevekegkr.iesvtveskegrktirAkvfiDATgdGd 147
                                       +    ++++w +++ +++ ++l +  a++g +v+  + +++  + g+r + +v    ++ +++++A+v++ A g G 
  gi|386001848|ref|YP_005920147.1|  82 TfrapETKAW-VVDRRIFDRALLAEAARSGADVMIASPVTGLLRGGGRsVLKVGR--SSDQRKVEARVVVSAEGVGA 155
                                       3333355555.69999999999988899999999999999999987543444433..44699999999999988763 PP

                      FAD_oxidored 148 .laalaG 153
                                        +a  aG
  gi|386001848|ref|YP_005920147.1| 156 rIARRAG 162
                                       2555555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.5   9.5e-09     1e-05       1      32 [.       8      39 ..       8      52 .. 0.95
   2 ?   -2.8   0.1       7.2   7.6e+03       6      29 ..     290     316 ..     289     320 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.5e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      ++GaG +G+ aA  +a+ag++v+++e ++r G
  gi|386001848|ref|YP_005920147.1|  8 VIGAGPAGSMAAKKAAEAGARVVIFEEHSRAG 39
                                      8*****************************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.2
                                       HHHHHHHHHHHC...CTEEEEEE-SSS CS
                     NAD_binding_8   6 lsGlvaAylLak...agfdvlllekrd 29 
                                       ++G vaA+++++     ++   +e+r+
  gi|386001848|ref|YP_005920147.1| 290 IAGEVAAAAAREgdsSAARLCEYERRW 316
                                       567777877776321234555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.2   1.9e-08     2e-05       1      42 [.       5      46 ..       5     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.9e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSS CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnp 42
                                      dv ViG+G AG+ AA +aa++Ga+v+++ ++      + C  
  gi|386001848|ref|YP_005920147.1|  5 DVAVIGAGPAGSMAAKKAAEAGARVVIFEEHSRAGWPVQCAG 46
                                      79**************************88877666666665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.8     7e-08   7.4e-05       1      35 [.       5      39 ..       5      59 .. 0.89
   2 ?    3.5   0.2     0.029        30     146     220 ..     101     170 ..      61     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      Dv ViG+G AG +AA +aaeaG++v++ e  ++ g
  gi|386001848|ref|YP_005920147.1|  5 DVAVIGAGPAGSMAAKKAAEAGARVVIFEEHSRAG 39
                                      9***************************9987754 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.029
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBS CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaett 220
                                       +l+++a + g d++   +++ L++ +gr +   v  ++++r+v  +  +vv+ ++G+g a + +++g ++ +e++
  gi|386001848|ref|YP_005920147.1| 101 ALLAEAARSGADVMIASPVTGLLRGGGR-SVLKVGRSSDQRKV--E-ARVVVSAEGVG-ARIARRAGIGPPREVL 170
                                       4677888889************995553.33445523444444..3.57888888888.5677777666666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     3e-06    0.0032      18      54 ..       4      39 ..       1      54 [. 0.87
   2 ?   -1.9   0.0       1.5   1.6e+03     153     172 ..     138     157 ..     134     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                       Dv+++GaG++G  aa+  a++ + +v+i+e++   G
  gi|386001848|ref|YP_005920147.1|  4 YDVAVIGAGPAGSMAAKKAAEA-GARVVIFEEHSRAG 39
                                      69******************99.********987666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                       B-EEEEEEEEEE--GSSSTT CS
                              Thi4 153 DPlvirakvvvdatGhdgei 172
                                       D   ++a+vvv+a G  + i
  gi|386001848|ref|YP_005920147.1| 138 DQRKVEARVVVSAEGVGARI 157
                                       667799*******9987766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   1.8e-06    0.0019      30      62 ..       5      37 ..       1      74 [. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                       v viG+G aG  A++ a++ ga+V++++  ++
  gi|386001848|ref|YP_005920147.1|  5 DVAVIGAGPAGSMAAKKAAEAGARVVIFEEHSR 37
                                      799************************997665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.8e-05     0.041       2      34 ..       6      38 ..       5      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      v+v+G+G  g ++A+ +ae g++V ++e +++ 
  gi|386001848|ref|YP_005920147.1|  6 VAVIGAGPAGSMAAKKAAEAGARVVIFEEHSRA 38
                                      89**************************98875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   4.9e-05     0.051       2      32 ..       6      36 ..       5      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdise 32
                                      vaviGaG  G+  a+ +a+ag +Vv+++ ++
  gi|386001848|ref|YP_005920147.1|  6 VAVIGAGPAGSMAAKKAAEAGARVVIFEEHS 36
                                      9************************998765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   8.4e-05     0.089       2      30 ..       8      35 ..       7      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.4e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      +iGaGPaG  aa ++ +ag  +++i E +
  gi|386001848|ref|YP_005920147.1|  8 VIGAGPAGSMAAKKAAEAGA-RVVIFEEH 35
                                      8******************9.799*9987 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00018      0.19      24      37 ..     214     227 ..     212     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                           zf-tcix  24 glsCkNkaCdqvfk 37 
                                       glsC+N+aC++ ++
  gi|386001848|ref|YP_005920147.1| 214 GLSCRNNACPYLKR 227
                                       89*********987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0008      0.84       1      37 [.       7      38 ..       7      45 .. 0.84
   2 ?   -0.9   0.1       1.4   1.4e+03     119     154 ..     114     152 ..      96     154 .. 0.63
   3 ?   -2.9   0.0       5.6   5.9e+03      42      79 ..     316     356 ..     312     372 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0008
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      a++GaGp+G +++++ ++        ++ +f++++  
  gi|386001848|ref|YP_005920147.1|  7 AVIGAGPAGSMAAKKAAEA-----GARVVIFEEHSRA 38
                                      89************98888.....6999999997764 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                     NAD_binding_9 119 vhraevvdleeradgqavll...adgaslaadaVvLAlG 154
                                       ++ + v+ l + +++  +     +d+++++a+ Vv A G
  gi|386001848|ref|YP_005920147.1| 114 MIASPVTGLLRGGGRSVLKVgrsSDQRKVEARVVVSAEG 152
                                       456777777776666432223347889999999999987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.6
                     NAD_binding_9  42 wrtdqseelllNvpasemslftddp..ptfaeWlrerga.l 79 
                                       wr++  +el+l + +++m +   d+  +++ + l++rg+ +
  gi|386001848|ref|YP_005920147.1| 316 WRAALGRELRLGMIVHKMRAEMTDEelDDLLRLLADRGDlI 356
                                       66666666777777777766555555677777777777642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2735.54
//
Query:       gi|386001849|ref|YP_005920148.1|  [L=326]
Description: L-alanine dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-107  359.5   0.9   1.4e-107  359.3   0.9    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    5.2e-05   23.3   0.0      8e-05   22.7   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.3   0.9  1.6e-111  1.4e-107       6     317 ..       6     317 ..       1     318 [. 0.97

  Alignments for each domain:
  == domain 1  score: 359.3 bits;  conditional E-value: 1.6e-111
                                       E-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTS CS
                   OCD_Mu_crystall   6 ltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksgl 82 
                                       l++++v++ l +++++ aveeafr+  +g +++pp+ +l+ ++++g+l+ mpayl+g +++gvK+vn+hpen+++g+
  gi|386001849|ref|YP_005920148.1|   6 LSEEDVKSSLTMAEAISAVEEAFREHGLGSAQMPPKSYLHYTKYQGDLRTMPAYLEGMDATGVKVVNVHPENPARGI 82 
                                       6789************************************************************************* PP

                                       SSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEE CS
                   OCD_Mu_crystall  83 ptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevri 159
                                       ptv+alvvL +p+tG+p+a+m +t+lt++RT+A++avaa+yLar+ +++++++GaG+qa+tql+ l + ++i++v +
  gi|386001849|ref|YP_005920148.1|  83 PTVMALVVLHSPKTGAPIAVMGGTHLTEMRTGAAGAVAARYLAREGSRRVGLLGAGAQARTQLLGLAETFEIETVLV 159
                                       ***************************************************************************** PP

                                       E-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HH CS
                   OCD_Mu_crystall 160 ydrdeeaaekfaenlqef.efevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLddd 235
                                        d++ e    +a ++++f   e + +++ ++ v +adi+vt+T++++p++ +ew++ G+hina+gada gk+eLd++
  gi|386001849|ref|YP_005920148.1| 160 ADISIERSRSLAGWAERFlAAEYVISSDIRD-VCDADILVTTTPSRRPLVREEWISRGTHINAIGADAAGKEELDPA 235
                                       *****************74788777777776.789****************************************** PP

                                       HHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHH CS
                   OCD_Mu_crystall 236 ilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvye 312
                                       ilkr++++vd+  qa ++Ge++v++ +g+la+ ++ a++gev+aGk+pGR ++ee+t+fds+Gla++Dva+a  vy 
  gi|386001849|ref|YP_005920148.1| 236 ILKRSKVVVDDIVQASHSGEVNVPLAEGLLAPGEIYATIGEVVAGKVPGRVREEEVTVFDSTGLAIQDVATAMGVYS 312
                                       ***************************************************************************** PP

                                       HHCCC CS
                   OCD_Mu_crystall 313 raeek 317
                                       ra+++
  gi|386001849|ref|YP_005920148.1| 313 RALAR 317
                                       *9875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   8.9e-09     8e-05       7     100 ..     124     218 ..     118     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.9e-09
                                       HS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.E.T-EEEEGCGHHHHHHT-SEEEE CS
                      Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkge.eiealkleelkellaeadvvis 81 
                                       l +  +++v l+GaG  a+  +  L++  +++ v+va  ++er ++la   +    +e++  ++++  + +ad++++
  gi|386001849|ref|YP_005920148.1| 124 LAREGSRRVGLLGAGAQARTQLLGLAETfEIETVLVADISIERSRSLAGWAERFlAAEYVISSDIR-DVCDADILVT 199
                                       55566899******************998******************9777554134677777777.56789***** PP

                                       -SSSSS-SB-HHHHHCCHH CS
                      Shikimate_DH  82 ataseepilekeeveealk 100
                                        t s+ p++++e++++  +
  gi|386001849|ref|YP_005920148.1| 200 TTPSRRPLVREEWISRGTH 218
                                       *************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2149.22
//
Query:       gi|386001850|ref|YP_005920149.1|  [L=194]
Description: hypothetical protein Mhar_1158 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-29  102.7   0.0    4.7e-29  101.5   0.0    1.5  2  DUF1638   Protein of unknown function (DUF1638)


Domain annotation for each model (and alignments):
>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.16     3e+03     133     148 ..      11      26 ..       8      28 .. 0.82
   2 !  101.5   0.0   2.6e-33   4.7e-29       2     160 ..      30     180 ..      29     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.16
                           DUF1638 133 eeraeefaarlglele 148
                                       ++++ee+a+ lg++ +
  gi|386001850|ref|YP_005920149.1|  11 KDEIEEIADDLGFPAR 26 
                                       6899*******99865 PP

  == domain 2  score: 101.5 bits;  conditional E-value: 2.6e-33
                           DUF1638   2 leaglHnrpeeLrealqeeidrakadydqIllgYGlCggalaglrsdecpveilkgddCislllgseeayaeelkde 78 
                                       leaglH +++ L eal++e++ ++ ++d+I++++G C++++a++    ++ ++l++++Ci++l+++++   ee +++
  gi|386001850|ref|YP_005920149.1|  30 LEAGLHVDFDGLAEALKRELEDCR-GFDGIVVAFGECHPRIAEI-LAPYNAVLLRCQNCIDALITRKKV--EEIAKR 102
                                       99*********************8.*******************.********************9999..776675 PP

                           DUF1638  79 kgtffltpgwvkewdrlvleky.g.eelarmifgkllkgYkrlvyidtgltddpeleeraeefaarlglelevipgg 153
                                          f+l+pgwvk w++++ e++ + +e+ar+ +      +k ++++dt l + +++ee + ef +++ +++e +p++
  gi|386001850|ref|YP_005920149.1| 103 GLYFYLSPGWVKGWRDMF-ERMsWsREEARFQLAP----FKGAIFLDT-LGNAQDYEEGLIEFLDFTLCPYEKMPVD 173
                                       66***************6.666677**********....*******99.9*************************** PP

                           DUF1638 154 lgllekl 160
                                       l +++ l
  gi|386001850|ref|YP_005920149.1| 174 LAHFRAL 180
                                       ***9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1251.18
//
Query:       gi|386001851|ref|YP_005920150.1|  [L=133]
Description: Thioredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-26   91.7   0.0    3.1e-26   91.3   0.0    1.2  1  Thioredoxin    Thioredoxin
      5e-07   30.1   0.4    1.3e-05   25.6   0.4    2.2  1  Thioredoxin_2  Thioredoxin-like domain
    1.4e-05   25.3   0.1      0.019   15.3   0.0    2.5  3  Thioredoxin_8  Thioredoxin-like
    0.00066   19.4   0.0    0.00084   19.1   0.0    1.4  1  Thioredoxin_9  Thioredoxin
    0.00088   18.7   0.0     0.0011   18.5   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0036   17.3   0.1     0.0084   16.1   0.1    1.7  2  Thioredoxin_3  Thioredoxin domain
     0.0096   14.9   0.0      0.013   14.5   0.0    1.3  1  Phosducin      Phosducin
  ------ inclusion threshold ------
      0.011   15.7   0.1        1.3    9.0   0.0    2.4  2  AhpC-TSA       AhpC/TSA family
      0.014   15.0   0.1        0.1   12.2   0.1    2.0  1  DUF953         Eukaryotic protein of unknown function (DUF953
      0.067   13.4   0.0       0.11   12.6   0.0    1.4  1  Thioredoxin_7  Thioredoxin-like
      0.075   13.0   0.0       0.13   12.2   0.0    1.4  1  HyaE           Hydrogenase-1 expression protein HyaE
       0.12   12.0   0.2        1.7    8.3   0.2    2.1  2  Redoxin        Redoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   2.1e-29   3.1e-26       6     103 .]      35     131 ..      30     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2.1e-29
                                       SHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                       Thioredoxin   6 tkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82 
                                       t+ + +e +     lv+v+++A+wCg+C+++ P++++la+e+++kv++ k++vden ++ +ky++ +iPtl++fk+g
  gi|386001851|ref|YP_005920150.1|  35 TDGTVDEVIGR-YPLVIVDCWAEWCGPCRMVGPVIDDLAKEMAGKVVFGKLNVDENMKTSTKYGIMAIPTLLVFKDG 110
                                       55555666666.889************************************************************** PP

                                       EEEEEEESS-HHHHHHHHHHH CS
                       Thioredoxin  83 kevkkyegarekeklaaflkk 103
                                       k +++++ga +k++l ++++k
  gi|386001851|ref|YP_005920150.1| 111 KLIDQMVGAYPKNTLSNKIQK 131
                                       ****************99975 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.4   8.9e-09   1.3e-05      29     107 ..      70     127 ..      44     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 8.9e-09
                     Thioredoxin_2  29 elddvtvrvllfplkpsfepkavaiwcakekkkafkd........ieenvelarkygvrgtPt.ivfldgkeivarl 96 
                                       +l                             +k++ +        ++en++ + kyg+ + Pt +vf dgk  ++++
  gi|386001851|ref|YP_005920150.1|  70 DL-----------------------------AKEMAGkvvfgklnVDENMKTSTKYGIMAIPTlLVFKDGK-LIDQM 116
                                       44.............................2233334444444468999*************888*****.99*** PP

                     Thioredoxin_2  97 pGyvpaeelea 107
                                       +G++p++ l+ 
  gi|386001851|ref|YP_005920150.1| 117 VGAYPKNTLSN 127
                                       ******99875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         7   1.1e+04      46      54 ..      12      20 ..       9      30 .. 0.52
   2 !   15.3   0.0   1.3e-05     0.019       3      44 ..      48      87 ..      46      93 .. 0.83
   3 !    8.4   0.0    0.0018       2.7      70      90 ..      88     108 ..      81     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7
                                      -HHHHHHHG CS
                     Thioredoxin_8 46 keeefekyl 54
                                      k+ee++k  
  gi|386001851|ref|YP_005920150.1| 12 KLEEMKKMA 20
                                      344444433 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsld 44
                                      +v++ ++a+wc pc+ + p +++l +++    kv++  +++d
  gi|386001851|ref|YP_005920150.1| 48 LVIVDCWAEWCGPCRMVGPVIDDLAKEMA--GKVVFGKLNVD 87
                                      699**********************9998..66666555555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                                       -HHHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8  70 krnklkkkynvkaiPtlvvld 90 
                                       ++ k   ky+++aiPtl+v +
  gi|386001851|ref|YP_005920150.1|  88 ENMKTSTKYGIMAIPTLLVFK 108
                                       56677899*********9976 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.7e-07   0.00084      50     107 ..      55     110 ..       1     130 [. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.7e-07
                                       -TT-HHHHHHHHHHHHHHHH.-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                     Thioredoxin_9  50 edwCgDaavnvPvlakiael.npnievkillrdenlelmdqyltngaraiPtliildee 107
                                       ++wCg ++++ Pv++ +a++ + ++ +  l  den ++  +y   g  aiPtl++++++
  gi|386001851|ref|YP_005920150.1|  55 AEWCGPCRMVGPVIDDLAKEmAGKVVFGKLNVDENMKTSTKY---GIMAIPTLLVFKDG 110
                                       78**************99651556666666666666666666...99******999765 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     7e-07    0.0011      46     104 ..      58     109 ..      54     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7e-07
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                       C +Cr + p ++ +ak +  +       ++F+k+++de++++  k+g+  +P ll+f+ 
  gi|386001851|ref|YP_005920150.1|  58 CGPCRMVGPVIDDLAKEMAGK-------VVFGKLNVDENMKTSTKYGIMAIPTLLVFKD 109
                                       999999999999999988877.......9****************************87 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.3     2e+03      20      31 ..      16      27 ..      10      60 .. 0.57
   2 !   16.1   0.1   5.6e-06    0.0084      10      59 ..      58     112 ..      49     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                                      HHHHCHCCTCEC CS
                     Thioredoxin_3 20 vkeaaaekgika 31
                                      +k++a+e+++++
  gi|386001851|ref|YP_005920150.1| 16 MKKMANEPKVDY 27
                                      556666666665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.6e-06
                                       STTCHHHHHHHHHHCHCCTCEC...EEECCTTHHHHHHCT-SSSSEEEC..TTCE CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgika...evekvtdfeeiekygVmsvPalvi..dgkv 59 
                                       C  C+ +  ++  +a+e+  k+   ++   +++++  kyg+m++P+l++  dgk+
  gi|386001851|ref|YP_005920150.1|  58 CGPCRMVGPVIDDLAKEMAGKVvfgKLNVDENMKTSTKYGIMAIPTLLVfkDGKL 112
                                       99999999999999***9766644344444666666**********954236776 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.7e-06     0.013     103     215 ..       5     117 ..       1     126 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.7e-06
                                       HHHHHHHHHHHHHHHH-------SE.EE--SHHHHHHHHHSS-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-T.T CS
                         Phosducin 103 lrkyrkqrmdemrqklskgprfkfv.lelesgeqfldtidkeqkitlivvhiyedgvkgtealnssliclaaeyp.t 177
                                       l++ r+++++em+ k+   p+ ++    l+  ++ +d +    +  l++v  + +    +  +   +  la e    
  gi|386001851|ref|YP_005920150.1|   5 LERIRRKKLEEMK-KMANEPKVDYPnSPLKVTDGTVDEV--IGRYPLVIVDCWAEWCGPCRMVGPVIDDLAKEMAgK 78 
                                       6777888888886.5666777766413466666665543..346678888888888888887777777899987537 PP

                                       SEEEEEEH.HHH--TTSS-TTT-SEEEEEETTEEEEEET CS
                         Phosducin 178 vkfckvka.svigasdrfsrdvlpallvykagellsnfv 215
                                       v f k++   ++ +s ++   ++p+llv+k g+l+ ++v
  gi|386001851|ref|YP_005920150.1|  79 VVFGKLNVdENMKTSTKYGIMAIPTLLVFKDGKLIDQMV 117
                                       99999986258999*********************9887 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00085       1.3      27      56 ..      48      76 ..      36      82 .. 0.86
   2 ?    4.3   0.0     0.024        37      88     120 ..      86     112 ..      80     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00085
                                      EEEEEEESTST-CCHHHHHHHHHHCHHHCC CS
                          AhpC-TSA 27 pvvlffypkdwcpvCttelpalaklyeefk 56
                                       v++ ++++ wc +C+   p + +l++e++
  gi|386001851|ref|YP_005920150.1| 48 LVIVDCWAE-WCGPCRMVGPVIDDLAKEMA 76
                                      589999999.********999999999987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.024
                                       E-TTSHHHHHTT-EETTTTECSCEEEEE-TTSB CS
                          AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvidkegk 120
                                        De+ k++++yg++      a+++  v+++ + 
  gi|386001851|ref|YP_005920150.1|  86 VDENMKTSTKYGIM------AIPTLLVFKDGKL 112
                                       79************......9999999876444 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     7e-05       0.1      36      99 ..      56     110 ..      53     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-05
                                       BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH..TS---SSSEEEEETSS CS
                            DUF953  36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRkdpklkltgvPtLlrwkgk 99 
                                        WC  C    pvi +  ke++  v++ + +v           + ++ +k+ ++++PtLl +k  
  gi|386001851|ref|YP_005920150.1|  56 EWCGPCRMVGPVIDDLAKEMAGKVVFGKLNVD---------ENMKTSTKYGIMAIPTLLVFKDG 110
                                       5**********************999888774.........44567779999999999988764 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.6e-05      0.11      20      81 ..      49     107 ..      46     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                                       EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---...SSEEEEE CS
                     Thioredoxin_7  20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg...vPvvafl 81 
                                       v+v+  a+wc++C+ +  +  +    k+ +a+k+v+ +++v+e+ +     +++g   +P+++++
  gi|386001851|ref|YP_005920150.1|  49 VIVDCWAEWCGPCRMVGPVIDDL--AKE-MAGKVVFGKLNVDENMKTS---TKYGimaIPTLLVF 107
                                       688999*******9998877655..888.************9988855...23336779999988 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     9e-05      0.13      63      99 ..      78     116 ..      60     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                                       EEEEETHH..HHHHHHHCCT-TSSSEEEEEETTEEEEEE CS
                              HyaE  63 aavvadre..qeealaerfgvlktPsllflrdgeylgvl 99 
                                        +v+++ +  ++ +   ++g++  P+ll+++dg+++  +
  gi|386001851|ref|YP_005920150.1|  78 KVVFGKLNvdENMKTSTKYGIMAIPTLLVFKDGKLIDQM 116
                                       455554440044455689***************998765 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0012       1.7      31      65 ..      49      81 ..      19      95 .. 0.82
   2 ?    3.5   0.0     0.036        54      90     137 ..      85     122 ..      69     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                      EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTE CS
                           Redoxin 31 vvvnfvpgafcPtCsaehpyleklaellkekgvdv 65
                                      v+v  ++  +c++C+   p +++la++ +++ v +
  gi|386001851|ref|YP_005920150.1| 49 VIVDCWAE-WCGPCRMVGPVIDDLAKE-MAGKVVF 81
                                      45678999.*******999*****999.6666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                                       EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCH CS
                           Redoxin  90 lsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepe 137
                                        +D++ + + ++G  ++       ++p++ ++ +dgk++   v++ p+
  gi|386001851|ref|YP_005920150.1|  85 NVDENMKTSTKYG--IM-------AIPTL-LVFKDGKLIDQMVGAYPK 122
                                       5677888888888..33.......77765.667999999999988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 961.89
//
Query:       gi|386001852|ref|YP_005920151.1|  [L=174]
Description: hypothetical protein Mhar_1160 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   14.0   0.0         52    4.3   0.0    3.0  3  DUF4277   Domain of unknown function (DUF4277)


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0029        52       6      74 ..       5      73 ..       2      78 .. 0.73
   2 ?    3.8   0.0     0.004        72      49      74 ..      91     116 ..      86     121 .. 0.88
   3 ?    2.2   0.0     0.012   2.2e+02      51      73 ..     136     158 ..     134     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0029
                           DUF4277  6 ldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLl 74
                                      + h+ l+a+++  + la    +  + ++q+++  + +  al    L    +pLy ++ +f+ k+l ++ 
  gi|386001852|ref|YP_005920151.1|  5 ISHIALMAAMLLIFALALPAAAEAGRSPQASTFGAVAYRALDPIDLSREAKPLYQVDAYFRIKDLREIA 73
                                      667777777777777777777777777777777777777776667777889**********99987765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.004
                           DUF4277  49 ngLgfvsrpLylfpeffedkplerLl 74 
                                       n+L    +pLy + ++f+ k+++++ 
  gi|386001852|ref|YP_005920151.1|  91 NVLTREAKPLYDVASYFRIKEVQEIA 116
                                       8898899************9999875 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.012
                           DUF4277  51 LgfvsrpLylfpeffedkplerL 73 
                                       Lg   +pLy ++ +f+ k+l ++
  gi|386001852|ref|YP_005920151.1| 136 LGRDPKPLYQVDAYFRLKDLREI 158
                                       666779**********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1309.75
//
Query:       gi|386001853|ref|YP_005920152.1|  [L=207]
Description: Phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-19   68.8   0.5    5.1e-19   68.3   0.5    1.2  1  Pribosyltran    Phosphoribosyl transferase domain
     0.0024   17.4   0.1     0.0045   16.4   0.0    1.3  1  UPRTase         Uracil phosphoribosyltransferase
     0.0034   16.9   0.3      0.039   13.5   0.3    2.0  1  PRTase_2        Phosphoribosyl transferase
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.031   13.8   0.0    1.6  1  GerE            Bacterial regulatory proteins, luxR family
      0.015   15.3   0.0      0.043   13.9   0.0    1.7  1  HTH_7           Helix-turn-helix domain of resolvase
      0.032   14.0   0.0       0.16   11.8   0.0    2.2  2  HTH_23          Homeodomain-like domain
      0.049   13.6   0.1       0.19   11.7   0.1    2.1  2  HTH_11          HTH domain
      0.057   13.6   0.0        3.7    7.8   0.0    2.6  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.061   12.9   0.2       0.27   10.8   0.0    2.2  2  Sigma70_r4      Sigma-70, region 4
      0.063   13.8   0.5        1.7    9.2   0.1    2.3  2  YflT            Heat induced stress protein YflT


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.5   2.9e-22   5.1e-19      19     128 ..      79     188 ..      64     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.9e-22
                                       TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-S CS
                      Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDD 95 
                                       + + le  +   dvvvgia  Gvp+a+ +a eL+v+la+   +k r ++ ++ ++ s   s++ +d+ +  ++iVDD
  gi|386001853|ref|YP_005920152.1|  79 ILDSLECSDSDVDVVVGIALSGVPLASMVAEELGVELAVYTPTKQRWSQETGETELSGTFSSNFADVVDAECVIVDD 155
                                       555555566789************************99999888888888888887777779*************** PP

                                       EESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HH CS
                      Pribosyltran  96 ildtGgTllaalelLkekgpeevriavlvdkpa 128
                                       ++++G+Tl++a+e L ++g+    i vl+dk+ 
  gi|386001853|ref|YP_005920152.1| 156 VITSGRTLEEAVEELNDHGASTNAIGVLLDKKG 188
                                       *********************999999999875 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.5e-06    0.0045     121     161 ..     147     184 ..     126     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.5e-06
                           UPRTase 121 ertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvla 161
                                       + + +++D vi +G+++ +a++ L ++g+ ++ I v   l 
  gi|386001853|ref|YP_005920152.1| 147 DAECVIVDDVITSGRTLEEAVEELNDHGASTNAIGV---LL 184
                                       56789***********************98876654...44 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.3   2.2e-05     0.039     121     150 ..     147     176 ..      60     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklpr 150
                                       ++e v+vDD i++G+t+ + +++l+++  +
  gi|386001853|ref|YP_005920152.1| 147 DAECVIVDDVITSGRTLEEAVEELNDHGAS 176
                                       4678********************998665 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.7e-05     0.031      13      35 ..      14      36 ..      11      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                      HHCTTS-HHHHHHHHTS-HHHHH CS
                              GerE 13 llaeGksnkeIAeelniSekTVk 35
                                      l aeG+   +IAeeln+S +TV+
  gi|386001853|ref|YP_005920152.1| 14 LKAEGLVEGQIAEELNVSRETVT 36
                                      56899999**************7 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05     0.043      19      38 ..      16      35 ..       5      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                      TTT--STTTSSSS---SSSS CS
                             HTH_7 19 eeGisiskIAkevnisRsTv 38
                                      +eG    +IA+e+n+sR+Tv
  gi|386001853|ref|YP_005920152.1| 16 AEGLVEGQIAEELNVSRETV 35
                                      5666668************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.9e-05      0.16      22      35 ..      23      36 ..      12      50 .. 0.87
   2 ?   -2.5   0.0       2.8   5.1e+03      23      29 ..     107     113 ..     105     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                            HTH_23 22 eIAreLgvsrrTvy 35
                                      +IA+eL+vsr Tv 
  gi|386001853|ref|YP_005920152.1| 23 QIAEELNVSRETVT 36
                                      8***********95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                            HTH_23  23 IAreLgv 29 
                                       +A+eLgv
  gi|386001853|ref|YP_005920152.1| 107 VAEELGV 113
                                       89***98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0001      0.19      20      32 ..      23      35 ..       9      36 .. 0.90
   2 ?   -3.2   0.0       4.6   8.3e+03      28      43 ..     159     174 ..     158     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                            HTH_11 20 eLAeeLnvSrrtv 32
                                      ++AeeLnvSr tv
  gi|386001853|ref|YP_005920152.1| 23 QIAEELNVSRETV 35
                                      7***********9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.6
                            HTH_11  28 SrrtvrrdIkaLeelg 43 
                                       S rt    +++L++ g
  gi|386001853|ref|YP_005920152.1| 159 SGRTLEEAVEELNDHG 174
                                       5677777777777665 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0021       3.7      26      40 ..      22      36 ..      12      41 .. 0.88
   2 ?    2.7   0.0      0.08   1.4e+02      21      35 ..     100     114 ..      98     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                                      HHHHHHHTS-HHHHH CS
                    Fe_dep_repress 26 kdlaerLnvspssVs 40
                                       ++ae+Lnvs  +V+
  gi|386001853|ref|YP_005920152.1| 22 GQIAEELNVSRETVT 36
                                      69************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.08
                                       SSB-HHHHHHHHTS- CS
                    Fe_dep_repress  21 kvvktkdlaerLnvs 35 
                                       +v+  +++ae+L+v+
  gi|386001853|ref|YP_005920152.1| 100 GVPLASMVAEELGVE 114
                                       688999*******97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.27      25      37 ..      23      35 ..      17      42 .. 0.90
   2 ?   -2.3   0.0       1.8   3.2e+03      20      30 ..     160     170 ..     156     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                      HHHHHHTS-HHHH CS
                        Sigma70_r4 25 EIgerlgiSrerV 37
                                      +I+e+l++Sre+V
  gi|386001853|ref|YP_005920152.1| 23 QIAEELNVSRETV 35
                                      8***********9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                                       T--HHHHHHHH CS
                        Sigma70_r4  20 glTleEIgerl 30 
                                       g+TleE  e+l
  gi|386001853|ref|YP_005920152.1| 160 GRTLEEAVEEL 170
                                       78999987776 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1       0.1   1.9e+02       5      27 ..       2      24 ..       1      25 [. 0.90
   2 ?    9.2   0.1   0.00096       1.7       3      34 ..     156     187 ..     155     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                              YflT  5 eneeellsaieelkaeGyneddi 27
                                      +n+++l+++  elkaeG  e +i
  gi|386001853|ref|YP_005920152.1|  2 KNIDSLIEKTAELKAEGLVEGQI 24
                                      68999*************99888 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00096
                              YflT   3 vyeneeellsaieelkaeGyneddiyvvakdk 34 
                                       v ++  +l +a+eel+++G +++ i v+  +k
  gi|386001853|ref|YP_005920152.1| 156 VITSGRTLEEAVEELNDHGASTNAIGVLLDKK 187
                                       6678899********************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1306.22
//
Query:       gi|386001854|ref|YP_005920153.1|  [L=160]
Description: hypothetical protein Mhar_1162 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-15   55.6   0.1    9.2e-15   54.9   0.1    1.3  1  PIN_6           PIN domain of ribonuclease
      0.003   17.0   0.3     0.0054   16.2   0.2    1.5  2  PIN_5           PINc domain ribonuclease
     0.0062   16.5   0.0     0.0094   16.0   0.0    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.018   15.1   7.6      0.086   12.9   0.8    2.4  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.023   14.7   3.1      0.037   14.0   3.1    1.3  1  DZR             Double zinc ribbon
      0.046   14.1   0.1       0.06   13.8   0.1    1.1  1  GcrA            GcrA cell cycle regulator
       0.19   11.7   5.4       0.28   11.1   5.4    1.2  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.39   10.9   0.3       0.39   10.9   0.3    2.2  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.93    9.8   2.7        4.1    7.7   2.8    1.9  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
          1    9.0   5.0       0.23   11.1   1.2    1.9  2  RecR            RecR protein
        1.2    9.0  10.4       0.71    9.8   1.9    2.5  2  Rad50_zn_hook   Rad50 zinc hook motif
        1.3    9.0   5.8        1.3    9.1   0.4    2.3  2  Ogr_Delta       Ogr/Delta-like zinc finger
        1.9    8.7   9.2        7.8    6.7   1.4    2.3  2  Zn-ribbon_8     Zinc ribbon domain
        2.6    7.8  10.3        2.4    7.9   2.4    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        3.8    7.0   9.3        1.3    8.5   0.6    2.3  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.1   7.7e-18   9.2e-15       1      89 []      12      93 ..      12      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 7.7e-18
                             PIN_6  1 lVlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktD 79
                                      +V+D++ +i       ++l  +++t+p V  E++d ++r rl++   + +++ P++e+++k++++a +tGD +vLS++D
  gi|386001854|ref|YP_005920153.1| 12 IVADSSVFIYG-----KDLDGEVITVPGVEGELKDLRSRMRLKI--SGARIEPPTAEALEKARAAADMTGDSAVLSEVD 83
                                      799******98.....67789**********************9..588999*************************** PP

                             PIN_6 80 ievlALtyeL 89
                                      +e+lA ++eL
  gi|386001854|ref|YP_005920153.1| 84 LEILAKALEL 93
                                      *******998 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.6   3.1e+03     162     175 ..      18      31 ..      14      51 .. 0.61
   2 !   16.2   0.2   4.5e-06    0.0054     156     191 ..      80     115 ..      62     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                             PIN_5 162 vllLAkELdaavvs 175
                                       v +  k+Ld++v++
  gi|386001854|ref|YP_005920153.1|  18 VFIYGKDLDGEVIT 31 
                                       55556666666655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.5e-06
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrl 191
                                       s+ Dl++l  A EL a + ++D  +++ a +lGl++
  gi|386001854|ref|YP_005920153.1|  80 SEVDLEILAKALELSARLATDDYALQNAALHLGLQV 115
                                       889******************************985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.9e-06    0.0094      34     101 ..      77     157 ..      58     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.9e-06
                                       ETTCT--HHHHHHHHHHHH....CC.TTTT-EEE.............EEEE--EEEETTTS-EEECHHHHHS-TTTS CS
                              HypA  34 GelsgvepeaLefafella....egtvlegaeLe.............ieevpvkvrCreCgkefeleekalrCpkCg 93 
                                         ls+v+ e+L+ a+el a    ++ +l++a L+              +  + ++rC  Cg+  e e    +Cp Cg
  gi|386001854|ref|YP_005920153.1|  77 AVLSEVDLEILAKALELSArlatDDYALQNAALHlglqvepiampriRRIAKRTCRCPGCGRPLEGE----ECPVCG 149
                                       5678888888888888765444367779999999999999*999995556678899*****999965....7***** PP

                                       SS-EEEEE CS
                              HypA  94 sadveivs 101
                                       +   +  +
  gi|386001854|ref|YP_005920153.1| 150 TPAKKRRG 157
                                       98766555 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 ?    6.1   1.0    0.0092        11       1      12 [.     132     143 ..     132     144 .. 0.84
   2 ?   12.9   0.8   7.2e-05     0.086       1      12 [.     144     155 ..     144     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0092
                    DNA_ligase_ZBD   1 hCPvCGsavvRe 12 
                                       +CP CG +++ e
  gi|386001854|ref|YP_005920153.1| 132 RCPGCGRPLEGE 143
                                       5********965 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.2e-05
                    DNA_ligase_ZBD   1 hCPvCGsavvRe 12 
                                       +CPvCG+++ + 
  gi|386001854|ref|YP_005920153.1| 144 ECPVCGTPAKKR 155
                                       5*******9865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.1   3.1e-05     0.037       8      40 ..     126     154 ..     123     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                               DZR   8 lppdarfCseCgtklkavaaedrCpsCgekvdp 40 
                                       + ++   C+ Cg +l+     + Cp Cg+++++
  gi|386001854|ref|YP_005920153.1| 126 IAKRTCRCPGCGRPLE----GEECPVCGTPAKK 154
                                       6677788********9....8********9875 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     5e-05      0.06      42     140 ..      47     155 ..      35     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                              GcrA  42 RLglsgrakaleptaaaarpkkaakaaaaaks...........sagrtalqlelaaevaaetaakvaervvedlsrl 107
                                       RL++sg   +  p +a a  +ka+ aa ++              a + +l  +la++ +a ++a+ +  + ++   +
  gi|386001854|ref|YP_005920153.1|  47 RLKISGARIE--PPTAEAL-EKARAAADMTGDsavlsevdleiLAKALELSARLATDDYALQNAALHLGLQVEPIAM 120
                                       6666664333..4333333.222222222222456777888878899999999****99999999999999999999 PP

                              GcrA 108 lqlleLsertCkwP.igdp.esedfaFCGnksseg 140
                                        ++  +++rtC+ P  g p e+e+   CG +++++
  gi|386001854|ref|YP_005920153.1| 121 PRIRRIAKRTCRCPgCGRPlEGEECPVCGTPAKKR 155
                                       99************446883468999***998765 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.4   0.00023      0.28       4      30 ..     130     152 ..     127     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpy 30 
                                         +Cp Cg++l+ e     Cp+Cgtp 
  gi|386001854|ref|YP_005920153.1| 130 TCRCPGCGRPLEGE----ECPVCGTPA 152
                                       578***********....7******96 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.1      0.75     9e+02      25      40 .]     122     137 ..     119     137 .. 0.67
   2 ?    0.1   1.7      0.81   9.6e+02      18      25 ..     133     140 ..     130     141 .. 0.76
   3 ?   10.9   0.3   0.00032      0.39      15      30 ..     142     157 ..     137     160 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.75
                     Auto_anti-p27  25 Lmrdr.kggkvyCvaCd 40 
                                         r r  + ++ C+ C+
  gi|386001854|ref|YP_005920153.1| 122 RIR-RiAKRTCRCPGCG 137
                                       555.3445789999996 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.81
                     Auto_anti-p27  18 CpvCgvPL 25 
                                       Cp Cg PL
  gi|386001854|ref|YP_005920153.1| 133 CPGCGRPL 140
                                       88888776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00032
                     Auto_anti-p27  15 aetCpvCgvPLmrdrk 30 
                                       +e CpvCg+P  + r+
  gi|386001854|ref|YP_005920153.1| 142 GEECPVCGTPAKKRRG 157
                                       799*******887664 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.8    0.0034       4.1      35      62 ..     130     155 ..     111     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                                       EEEEEESSB-SSCCCSB-TTT-SB-SEE CS
                         ProRS-C_1  35 kslcipfdqepseegtkCivcgkpakkw 62 
                                       + +c         eg++C vcg pakk+
  gi|386001854|ref|YP_005920153.1| 130 TCRCPGCG--RPLEGEECPVCGTPAKKR 155
                                       55555443..346899**********86 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       6.8   8.1e+03       6      13 ..      60      67 ..      60      68 .. 0.79
   2 ?   11.1   1.2   0.00019      0.23       9      37 ..     123     151 ..     121     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.8
                                      HHHHHHHH CS
                              RecR  6 aeaLqeak 13
                                      aeaL++a+
  gi|386001854|ref|YP_005920153.1| 60 AEALEKAR 67
                                      78999987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                       HHHHHHH-EE-TTT--EESSSS-CCCCST CS
                              RecR   9 LqeakekvrhCsrCgnlteedlCaICsdp 37 
                                       +++  ++  +C+ Cg   e + C++C  p
  gi|386001854|ref|YP_005920153.1| 123 IRRIAKRTCRCPGCGRPLEGEECPVCGTP 151
                                       677889999*****************776 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.9    0.0006      0.71      13      32 ..     124     143 ..     122     144 .. 0.80
   2 ?    5.1   2.0     0.017        20      19      28 ..     142     151 ..     141     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                                       HHHTT-SEE-TTT--EE-HH CS
                     Rad50_zn_hook  13 eelkeakgcCPlCgReldee 32 
                                         +++++ +CP CgR+l+ e
  gi|386001854|ref|YP_005920153.1| 124 RRIAKRTCRCPGCGRPLEGE 143
                                       567777779********998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                                       SEE-TTT--E CS
                     Rad50_zn_hook  19 kgcCPlCgRe 28 
                                       ++ CP+Cg +
  gi|386001854|ref|YP_005920153.1| 142 GEECPVCGTP 151
                                       348****976 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.7      0.14   1.7e+02       1       8 [.     132     139 ..     132     142 .. 0.85
   2 ?    9.1   0.4    0.0011       1.3       1      13 [.     144     156 ..     144     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                         Ogr_Delta   1 rCPhCgap 8  
                                       rCP Cg p
  gi|386001854|ref|YP_005920153.1| 132 RCPGCGRP 139
                                       7*****87 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                         Ogr_Delta   1 rCPhCgapaaart 13 
                                       +CP Cg+pa  r+
  gi|386001854|ref|YP_005920153.1| 144 ECPVCGTPAKKRR 156
                                       6********9986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.4    0.0065       7.8      24      36 ..     127     140 ..     114     143 .. 0.77
   2 ?    6.7   1.3    0.0066       7.9      27      38 ..     143     154 ..     139     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0065
                       Zn-ribbon_8  24 aplta.CPeCgsev 36 
                                       a+ t+ CP Cg ++
  gi|386001854|ref|YP_005920153.1| 127 AKRTCrCPGCGRPL 140
                                       457888*****876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0066
                       Zn-ribbon_8  27 taCPeCgsevrr 38 
                                       ++CP Cg ++++
  gi|386001854|ref|YP_005920153.1| 143 EECPVCGTPAKK 154
                                       46******9887 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.1     0.027        32      22      29 ..     131     138 ..     123     141 .. 0.67
   2 ?    7.9   2.4     0.002       2.4       6      19 ..     145     158 ..     145     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.027
                     zf-NADH-PPase  22 rvCpaCgl 29 
                                       ++Cp Cg+
  gi|386001854|ref|YP_005920153.1| 131 CRCPGCGR 138
                                       56666664 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.002
                     zf-NADH-PPase   6 CgrCGaptepaegg 19 
                                       C+ CG+p ++ +gg
  gi|386001854|ref|YP_005920153.1| 145 CPVCGTPAKKRRGG 158
                                       *********99998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.2     0.051        61       4      13 ..     132     141 ..     129     144 .. 0.79
   2 ?    8.5   0.6    0.0011       1.3       3      14 ..     143     154 ..     141     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.051
                       zf-ribbon_3   4 rCPnCGapls 13 
                                       rCP CG pl+
  gi|386001854|ref|YP_005920153.1| 132 RCPGCGRPLE 141
                                       8999998776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                       zf-ribbon_3   3 vrCPnCGaplss 14 
                                        +CP CG+p+++
  gi|386001854|ref|YP_005920153.1| 143 EECPVCGTPAKK 154
                                       58******9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1219.56
//
Query:       gi|386001855|ref|YP_005920154.1|  [L=135]
Description: hypothetical protein Mhar_1163 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.67
# Mc/sec: 609.29
//
Query:       gi|386001856|ref|YP_005920155.1|  [L=587]
Description: Metal ABC transporter, ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-35  122.3   0.0    4.7e-19   69.3   0.0    2.5  2  ABC_tran      ABC transporter
      3e-11   43.0   2.7    6.9e-11   41.8   2.7    1.7  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    5.4e-10   39.1   3.1    0.00041   19.8   0.3    3.8  3  SMC_N         RecF/RecN/SMC N terminal domain
      2e-09   37.7   7.7      0.012   15.4   0.0    4.0  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.4e-08   31.9   3.9    7.4e-08   31.9   3.9    2.5  2  Fer4          4Fe-4S binding domain
    1.6e-07   31.1  13.3    2.4e-06   27.4   2.8    2.4  2  Fer4_6        4Fe-4S binding domain
    0.00012   22.6   0.1       0.26   11.8   0.0    2.3  2  AAA_23        AAA domain
    0.00018   21.5   0.1        0.5   10.3   0.0    2.4  2  Rad17         Rad17 P-loop domain
     0.0005   19.8   0.5       0.27   11.0   0.2    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00064   19.8   6.1     0.0011   19.0   6.1    1.4  1  Fer4_21       4Fe-4S dicluster domain
     0.0017   18.5   7.4     0.0032   17.6   7.4    1.5  1  Fer4_9        4Fe-4S dicluster domain
     0.0032   17.4   0.6        1.6    8.6   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
     0.0034   17.9   1.3     0.0034   17.9   1.3    2.0  3  Fer4_7        4Fe-4S dicluster domain
     0.0037   17.3   2.3     0.0037   17.3   2.3    2.5  2  Fer4_2        4Fe-4S binding domain
      0.004   17.6   1.6       0.44   10.9   0.1    2.6  2  AAA_16        AAA ATPase domain
      0.006   16.7   1.4      0.006   16.7   1.4    2.2  2  Fer4_10       4Fe-4S dicluster domain
     0.0061   16.3   1.2        1.3    8.7   0.1    2.5  2  AAA_24        AAA domain
     0.0066   16.2   0.2        4.7    6.8   0.0    3.0  3  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.9   0.1        7.5    6.9   0.0    3.1  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.012   16.1   0.8        1.6    9.2   0.0    2.9  2  AAA           ATPase family associated with various cellular 
      0.035   14.5   0.2         10    6.5   0.0    2.4  2  RNA_helicase  RNA helicase
      0.037   14.1   0.3          4    7.5   0.0    3.1  3  AAA_14        AAA domain
      0.044   14.3   2.4         17    6.0   1.0    3.5  2  AAA_18        AAA domain
      0.056   13.4   1.1         13    5.7   0.1    3.2  3  AAA_5         AAA domain (dynein-related subfamily)
      0.058   14.3   1.3      0.058   14.3   1.3    1.9  1  Fer4_16       4Fe-4S double cluster binding domain
      0.099   12.3   1.7        7.5    6.1   0.1    2.4  2  SRP54         SRP54-type protein, GTPase domain
       0.15   11.9   1.5        7.4    6.5   0.1    2.5  2  NACHT         NACHT domain
        0.2   11.3   1.9         20    4.8   0.0    2.9  3  AAA_30        AAA domain
       0.25   11.9  12.4      0.069   13.7   3.0    2.4  2  Fer4_4        4Fe-4S binding domain
       0.33   10.7   0.7        2.7    7.8   0.1    2.2  2  MukB          MukB N-terminal
        1.1    9.2   3.5         40    4.1   0.5    3.4  3  NTPase_1      NTPase
        1.3    9.3   5.5        5.1    7.3   0.4    3.1  3  AAA_28        AAA domain
        9.1    6.9  11.1         78    3.9  11.1    2.2  1  Fer4_17       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   5.5e-16     3e-13      11     134 ..      95     231 ..      93     233 .. 0.71
   2 !   69.3   0.0   8.6e-22   4.7e-19       7     137 .]     354     475 ..     348     475 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 5.5e-16
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.......EET.TCEGGG..B-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxx.xxxxxx..xxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei.......lld.gkdlke..qeleslrkeigvlpqe.pqlfpeltv 76 
                                       g++++++G+nG GKSt +++l+gll p+ G+        +l  g  l +  ++  +   + ++ pq  +++ +    
  gi|386001856|ref|YP_005920155.1|  95 GKVTGLLGPNGIGKSTAVAILSGLLAPNLGRGasweevlHLTsGSALGDylRRVVEKGVKTAYKPQYvDRIPKS--- 168
                                       899************************88886333333333324444444433333334444555553222222... PP

                                       HHH...........HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxx...........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...........esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                                     ++  +  +++++++++l  l d+ +    s LSgG+ qrva++++ +++++++++DE
  gi|386001856|ref|YP_005920155.1| 169 --FtgtvrallertDE--RgaLSDLAERMNLLSLMDREI----SGLSGGELQRVAIVACAARDADVYFFDE 231
                                       ..12334567864333..35699**********999999....***************************9 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 8.6e-22
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenesde 83 
                                       ++++ge+v+i+G+nG GK+t +k+lag + pt G + l+ k + +   + l++e     +   + +++  +e +s++
  gi|386001856|ref|YP_005920155.1| 354 EIRRGEVVGILGPNGIGKTTYIKILAGAEVPTTGALDLKLKVSYK--PQYLKAEADLAVEG--FLRRI-SKEFDSSR 425
                                       6899********************************665332222..23333333333333..33333.35559999 PP

                                       CHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  84 eiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                         +++++ lg+++l ++++     +LSgG+ qrva++ +l ++++l+llDEp+a
  gi|386001856|ref|YP_005920155.1| 426 YQSEFVKPLGIEKLLEQPM----DELSGGELQRVAIVGCLSREADLYLLDEPSA 475
                                       9*****************9....*****************************75 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   2.7   1.3e-13   6.9e-11       1      35 []       1      32 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.3e-13
                                      --EEEES---------TTHHHHHTTSEEEESS--S CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                      mr+A++++d+C+P+KC   +c+ fcp   vrtg++
  gi|386001856|ref|YP_005920155.1|  1 MRIAVINRDRCQPRKCIR-ECEYFCPP--VRTGDE 32
                                      9*****************.********..****85 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   7.6e-07   0.00041      24     211 ..      95     276 ..      84     283 .. 0.68
   2 ?    3.8   0.0     0.063        34      25      41 ..     359     375 ..     340     379 .. 0.69
   3 !   12.7   0.0   0.00012     0.065     135     200 ..     445     508 ..     403     527 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.6e-07
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                        ++t ++GpNG GKs  +  ++ +L  +     r ++ ++++h   ++ s+   ++  ++++  k+    k++++ +
  gi|386001856|ref|YP_005920155.1|  95 GKVTGLLGPNGIGKSTAVAILSGLLAPNLG---RGASWEEVLHL--TSGSALGDYLRRVVEKGVKT--AYKPQYVDR 164
                                       578999*********999888888886555...99999999998..33333333444444444444..333333333 PP

                                       EEEETTSEEEEEE..TTEEE-HHHH...HHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxx..xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseyki..ngkevtkkev...sellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                         ++ +g+ +  +   +++   +++   ++ll+ ++ +++ LSgGe + va  ++ A  +++ a +y++Dei   LD
  gi|386001856|ref|YP_005920155.1| 165 IPKSFTGTVRALLerTDERGALSDLaerMNLLSLMDREISGLSGGELQRVA--IV-AC-AARDADVYFFDEISPYLD 237
                                       34444444444441123334445550005566666667889****976555..44.43.5678899*********** PP

                                       HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                         ++ + a+ +    ++  ++v+ ++ ++l    ++v +
  gi|386001856|ref|YP_005920155.1| 238 IYQRINAARAIGDLAETKAVMVVEHDLGLLDLLAENVHI 276
                                       ***********************9998888776666555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.063
                                       SEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnll 41 
                                       ++  i+GpNG GK+  +
  gi|386001856|ref|YP_005920155.1| 359 EVVGILGPNGIGKTTYI 375
                                       4678*********9765 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00012
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                       ++LSgGe + va+   +     + a lyllDe  a+LD +++   a+++++  ++    ++v+ ++  
  gi|386001856|ref|YP_005920155.1| 445 DELSGGELQRVAIVGCL----SREADLYLLDEPSAHLDVEQRMMAAKVMRRFAESaeRSVLVVDHDIY 508
                                       47999997655544433....47889**********************99655541155666666555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   7.4e-05      0.04       1      23 [.      97     119 ..      97     145 .. 0.86
   2 ?    0.6   0.0      0.72   3.9e+02     234     267 ..     203     233 ..     161     257 .. 0.73
   3 !    9.4   0.5    0.0015      0.84       2      22 ..     361     381 ..     360     398 .. 0.87
   4 !   15.4   0.0   2.3e-05     0.012     227     299 ..     437     507 ..     392     511 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-05
                            AAA_21   1 lnvliGpNgsGKSnLLdaldlla 23 
                                       +++l GpNg GKS+   +l++l 
  gi|386001856|ref|YP_005920155.1|  97 VTGLLGPNGIGKSTAVAILSGLL 119
                                       699*****************996 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.72
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpE 267
                                       ++ lS G ++  a+++  +r++   +++++DE+ 
  gi|386001856|ref|YP_005920155.1| 203 ISGLSGGELQRVAIVACAARDA---DVYFFDEIS 233
                                       7778999888877777777777...9******96 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0015
                            AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                        ++ GpNg GK++ +++l ++
  gi|386001856|ref|YP_005920155.1| 361 VGILGPNGIGKTTYIKILAGA 381
                                       689**************9765 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.3e-05
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkll...rrllellkelsrngaQviltTHSp 299
                                       ++  e p++elS G ++  a++  l r +   +l+l+DEp ++L+ +     +++++ + e ++    v+++ H+ 
  gi|386001856|ref|YP_005920155.1| 437 EKLLEQPMDELSGGELQRVAIVGCLSREA---DLYLLDEPSAHLDVEQRmmaAKVMRRFAESAE--RSVLVVDHDI 507
                                       4556899***********9********99...9*************444345666666644444..4555555555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.4   2.4e+03       2       8 ..       5      11 ..       4      12 .. 0.88
   2 !   31.9   3.9   1.4e-10   7.4e-08       1      24 []      41      64 ..      41      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.4
                                      EEETTTS CS
                              Fer4  2 videekC 8 
                                      vi+ ++C
  gi|386001856|ref|YP_005920155.1|  5 VINRDRC 11
                                      89***** PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.4e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +vi e++C+gCG+Cv  CP+gAI+
  gi|386001856|ref|YP_005920155.1| 41 PVITENLCVGCGICVRKCPFGAIS 64
                                      6899******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   2.9    0.0026       1.4       1      20 [.       3      25 ..       3      30 .. 0.91
   2 !   27.4   2.8   4.5e-09   2.4e-06       1      24 []      40      63 ..      40      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                            Fer4_6  1 vveidpdkCi..gC.gdCvrvCP 20
                                      +++i++d+C    C ++C+  CP
  gi|386001856|ref|YP_005920155.1|  3 IAVINRDRCQprKCiRECEYFCP 25
                                      689******9888*********9 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.5e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++i +++C+gCg Cvr CP+gai
  gi|386001856|ref|YP_005920155.1| 40 KPVITENLCVGCGICVRKCPFGAI 63
                                      6899*******************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0042       2.3      20      39 ..      96     115 ..      94     164 .. 0.91
   2 !   11.8   0.0   0.00048      0.26      17      39 ..     348     378 ..     333     430 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0042
                            AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                       ++t + GpNG GK+T +  +
  gi|386001856|ref|YP_005920155.1|  96 KVTGLLGPNGIGKSTAVAIL 115
                                       58999**********88665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00048
                            AAA_23  17 F........skgltlItGpNGaGKTTildAi 39 
                                       +           ++ I GpNG GKTT +  +
  gi|386001856|ref|YP_005920155.1| 348 LeaergeirRGEVVGILGPNGIGKTTYIKIL 378
                                       244444443345899***********98766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.003       1.6      50      73 ..     100     123 ..      93     138 .. 0.88
   2 !   10.3   0.0   0.00091       0.5      37      70 ..     350     383 ..     342     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                             Rad17  50 isGPsGCgkstvvkvLskelgikl 73 
                                       + GP G gkst+v +Ls  l+++l
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILSGLLAPNL 123
                                       67***************9888765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00091
                             Rad17  37 advLesrkkriLLisGPsGCgkstvvkvLskelg 70 
                                       a+  e r+ +++ i GP G gk+t +k+L+   +
  gi|386001856|ref|YP_005920155.1| 350 AERGEIRRGEVVGILGPNGIGKTTYIKILAGAEV 383
                                       55555566668899***************97655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.2    0.0005      0.27      23      48 ..      95     121 ..      87     125 .. 0.75
   2 ?    6.4   0.0     0.014       7.4      18      39 ..     354     375 ..     347     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                            AAA_29  23 g.atlltGpsGsGKSTllDAiqalLvp 48 
                                       g +t l Gp+G GKST +  ++ lL p
  gi|386001856|ref|YP_005920155.1|  95 GkVTGLLGPNGIGKSTAVAILSGLLAP 121
                                       557889***********9545555555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                            AAA_29  18 eidlkgatlltGpsGsGKSTll 39 
                                       ei++ +++ + Gp+G GK+T +
  gi|386001856|ref|YP_005920155.1| 354 EIRRGEVVGILGPNGIGKTTYI 375
                                       566555888***********76 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   6.1     2e-06    0.0011       1      58 [.       4      64 ..       4      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-06
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvl.....kvv.edeCvGCnlCssvCPvedcie 58
                                      A+i++d+C +  kC+  Ce  +    ++d +tv+     +v+ e+ CvGC +C+  CP  ++i+
  gi|386001856|ref|YP_005920155.1|  4 AVINRDRC-QPRKCIRECEYFCPPVRTGD-ETVTfpdgkPVItENLCVGCGICVRKCPF-GAIS 64
                                      78999999.66888888885444333333.3333355555653889************7.8886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   7.4   5.9e-06    0.0032       5      51 .]      16      63 ..       9      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.9e-06
                            Fer4_9  5 C.gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      C ++C++ Cp   + ++ ++  +      e+ C+gCg Cv +Cp gai
  gi|386001856|ref|YP_005920155.1| 16 CiRECEYFCPPVRTGDETVTFPDGKPVITENLCVGCGICVRKCPFGAI 63
                                      53468888888888877777777766666789************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.015         8      99     121 ..      95     117 ..      89     126 .. 0.86
   2 !    8.6   0.0    0.0029       1.6      99     130 ..     358     389 ..     346     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.015
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       +k++ l+G+ G+GKSt +  l +
  gi|386001856|ref|YP_005920155.1|  95 GKVTGLLGPNGIGKSTAVAILSG 117
                                       58899***********9887765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                                       TSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++ ++G+ G+GK+t i+ l++ +   tg++
  gi|386001856|ref|YP_005920155.1| 358 GEVVGILGPNGIGKTTYIKILAGAEVPTTGAL 389
                                       578899****************9988887766 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   2.3         4   2.2e+03      33      49 ..       6      25 ..       2      30 .. 0.67
   2 !   11.6  11.1   0.00059      0.32       5      52 .]      16      62 ..       9      62 .. 0.66
   3 !   17.9   1.3   6.3e-06    0.0034       2      21 ..      48      67 ..      47      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4
                            Fer4_7 33 idpekCl..gCga.CvavCP 49
                                      i+ ++C+   C + C+  CP
  gi|386001856|ref|YP_005920155.1|  6 INRDRCQprKCIReCEYFCP 25
                                      66677764455444888888 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00059
                            Fer4_7  5 C.gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C + C+  Cp  +++ de ++  +  k++i ++ C+gCg Cv+ CP+ga
  gi|386001856|ref|YP_005920155.1| 16 CiRECEYFCP-PVRTGDE-TVTFPDGKPVITENLCVGCGICVRKCPFGA 62
                                      3345555555.2223322.233344789999****************98 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 6.3e-06
                            Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                      C+gCg Cv+ Cp +ai++ +
  gi|386001856|ref|YP_005920155.1| 48 CVGCGICVRKCPFGAISIIN 67
                                      ***************99764 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.0      0.35   1.9e+02       3      21 ..       4      25 ..       2      26 .. 0.81
   2 !   17.3   2.3   6.8e-06    0.0037       2      21 ..      40      59 ..      39      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.35
                            Fer4_2  3 vvvdtdrC.ig.C.gaCvsaCP 21
                                      +v+++drC  + C + C   CP
  gi|386001856|ref|YP_005920155.1|  4 AVINRDRCqPRkCiRECEYFCP 25
                                      7899999965679999999999 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.8e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++v+ ++ C+gCg+Cv  CP
  gi|386001856|ref|YP_005920155.1| 40 KPVITENLCVGCGICVRKCP 59
                                      5788899************* PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.06        33      29      45 ..     100     116 ..      92     196 .. 0.81
   2 !   10.9   0.1   0.00081      0.44      21     142 ..     355     504 ..     347     518 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.06
                            AAA_16  29 lsGesGvGKsslvrell 45 
                                       l G+ G+GKs+ v  l 
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILS 116
                                       89*********996554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00081
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd.........................ggif..lrgkcdqlesaipys 70 
                                         r+e+v + G+ G+GK++ ++ l+ a   +                         +g++  ++ ++          
  gi|386001856|ref|YP_005920155.1| 355 IRRGEVVGILGPNGIGKTTYIKILAGAEVPTtgaldlklkvsykpqylkaeadlavEGFLrrISKEF---------- 421
                                       44568999*************8888533333233333333333333333333222211111222222.......... PP

                            AAA_16  71 alaqalareellrqlldeaesaeleawrekleeala.....................................avpe 110
                                                             + ++++ ++ + l+                                     ++++
  gi|386001856|ref|YP_005920155.1| 422 ----------------------DSSRYQSEFVKPLGieklleqpmdelsggelqrvaivgclsreadlylldePSAH 476
                                       ......................3344444444444444444454444444444455555555577777777777777 PP

                            AAA_16 111 lagaeasrllellkrllallsrderplvlvlD 142
                                       l+ +++   + +++r+++ ++r     vlv+D
  gi|386001856|ref|YP_005920155.1| 477 LDVEQRMMAAKVMRRFAESAER----SVLVVD 504
                                       7777777777777777755555....677776 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1  12.9    0.0025       1.4       2      56 .]       4      59 ..       3      59 .. 0.88
   2 !   16.7   1.4   1.1e-05     0.006       2      23 ..      41      62 ..      40      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +vi++d+C   +C  +C  +CP    + g +  + ++++  +    C gcg Cv++CP
  gi|386001856|ref|YP_005920155.1|  4 AVINRDRCqpRKCIrECEYFCPP--VRTGDETVTFPDGKPVITENLCVGCGICVRKCP 59
                                      68999***66699779*******..888888888999999999999***********9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.1e-05
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      +vi ++ C++Cg Cv+ CP+ +
  gi|386001856|ref|YP_005920155.1| 41 PVITENLCVGCGICVRKCPFGA 62
                                      68999**************955 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.015       7.9       5      22 ..      98     115 ..      95     240 .. 0.78
   2 !    8.7   0.1    0.0025       1.3       4      22 ..     360     378 ..     357     392 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                         + Gp+giGK+t ++ l
  gi|386001856|ref|YP_005920155.1|  98 TGLLGPNGIGKSTAVAIL 115
                                       5789*********99877 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0025
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        + i Gp+giGKTt +k l
  gi|386001856|ref|YP_005920155.1| 360 VVGILGPNGIGKTTYIKIL 378
                                       6789**********99876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0087       4.7      23      47 ..      96     119 ..      93     132 .. 0.87
   2 ?    3.9   0.0     0.065        35      25      43 ..     360     378 ..     341     379 .. 0.84
   3 ?    1.7   0.0      0.31   1.7e+02     324     362 ..     465     503 ..     414     510 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0087
                            AAA_15  23 eeltvliGkNnsGKSsilealdlFl 47 
                                       + +t l G+N++GKS+++ +l  +l
  gi|386001856|ref|YP_005920155.1|  96 K-VTGLLGPNGIGKSTAVAILSGLL 119
                                       4.78899***********9997666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.065
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +  + G+N++GK++ +++l
  gi|386001856|ref|YP_005920155.1| 360 VVGILGPNGIGKTTYIKIL 378
                                       55688**********9998 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.31
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviit 362
                                        +++l++EP ahL  ++ ++ +k +++ a++ +  v++ 
  gi|386001856|ref|YP_005920155.1| 465 ADLYLLDEPSAHLDVEQRMMAAKVMRRFAESAERSVLVV 503
                                       589**********************99999877666555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.014       7.5      26      48 ..     199     221 ..     185     231 .. 0.87
   2 ?    4.5   0.0     0.076        41      21      44 ..     435     458 ..     422     491 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaa 48 
                                       ++r++++lSGGe q +a +a aa
  gi|386001856|ref|YP_005920155.1| 199 MDREISGLSGGELQRVAIVACAA 221
                                       68999**********99999987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.076
                           SbcCD_C  21 gkekelsrssgtlSGGekqflayl 44 
                                       g ek l++ + +lSGGe q +a +
  gi|386001856|ref|YP_005920155.1| 435 GIEKLLEQPMDELSGGELQRVAIV 458
                                       556668888888999998766544 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 ?    4.5   0.2      0.08        43       3      22 ..     100     119 ..      98     236 .. 0.84
   2 ?    9.2   0.0     0.003       1.6       3      21 ..     363     381 ..     361     423 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.08
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       l Gp G+GK++++  +   l
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILSGLL 119
                                       78*********998876654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.003
                                       EESSTTSSHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavake 21 
                                       + Gp G+GKT+ +k +a  
  gi|386001856|ref|YP_005920155.1| 363 ILGPNGIGKTTYIKILAGA 381
                                       67**************976 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.043        23       3      20 ..     100     117 ..      99     137 .. 0.82
   2 ?    6.5   0.0     0.019        10       3      19 ..     363     379 ..     361     392 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.043
                      RNA_helicase   3 lyGpsgeGKStlakeLak 20 
                                       l Gp+g+GKSt++  L+ 
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILSG 117
                                       57**********998765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                      RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                       + Gp+g+GK+t++k La
  gi|386001856|ref|YP_005920155.1| 363 ILGPNGIGKTTYIKILA 379
                                       78***********9987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.51   2.8e+02       3      20 ..      96     113 ..      94     123 .. 0.85
   2 ?    0.8   0.0      0.84   4.5e+02      64      86 ..     223     245 ..     187     259 .. 0.75
   3 ?    7.5   0.0    0.0073         4       3      27 ..     359     383 ..     357     426 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.51
                            AAA_14   3 kilvitGaRrvGKTtllk 20 
                                       k+  + G+  +GK+t + 
  gi|386001856|ref|YP_005920155.1|  96 KVTGLLGPNGIGKSTAVA 113
                                       78899**********975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.84
                            AAA_14  64 kktylflDEiqevpewekalksl 86 
                                       +  + f+DEi+ + ++++ ++  
  gi|386001856|ref|YP_005920155.1| 223 DADVYFFDEISPYLDIYQRINAA 245
                                       56789*****9998888877765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0073
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                       +++ i G+  +GKTt++k l+  + 
  gi|386001856|ref|YP_005920155.1| 359 EVVGILGPNGIGKTTYIKILAGAEV 383
                                       7899*************99987666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.23   1.3e+02       3      25 ..     100     138 ..      99     199 .. 0.76
   2 ?    6.0   1.0     0.032        17       2      73 ..     362     504 ..     361     580 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.23
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf...............g 25 
                                       l G+ G GK+t    Ls +l  +               g
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILSGLLaPNlgrgasweevlhltsG 138
                                       78***********99988875445666666666666663 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf...................................................... 24 
                                       ++ G+ G GKtt  k L+  + +                                                      
  gi|386001856|ref|YP_005920155.1| 362 GILGPNGIGKTTYIKILAGAE-Vpttgaldlklkvsykpqylkaeadlavegflrriskefdssryqsefvkplgie 437
                                       677777777777777775442.2223333333344444444444444444444444444444444444444444445 PP

                            AAA_18  25 .................gvnlrdvakenglllevdpealdeskrldedkldklldaleenss...alee 73 
                                                        + +++++ +e +l+l ++p      +++++++ +k+++ + e+++      +
  gi|386001856|ref|YP_005920155.1| 438 klleqpmdelsggelqrVAIVGCLSREADLYLLDEPS--AHLDVEQRMMAAKVMRRFAESAErsvLVVD 504
                                       5555555555555555566667777777777777777..666666666666677777776555553333 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 ?    5.7   0.1     0.025        13       4      24 ..     100     122 ..      99     138 .. 0.81
   2 ?    1.3   0.0      0.58   3.1e+02      49      75 ..     208     233 ..     185     241 .. 0.77
   3 ?    2.8   0.1       0.2   1.1e+02       4      21 ..     363     380 ..     361     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.025
                                       EE--SSSSHHHHHHHGGGGB..S CS
                             AAA_5   4 LvGppGtgKselaerlaaal..n 24 
                                       L+Gp G+gKs+ +  l+ +l  n
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILSGLLapN 122
                                       89*************99998651 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.58
                                       ........--------G-SEEEEESGG CS
                             AAA_5  49 ngttslvdsplvraaregeilvlDEve 75 
                                       +g+ ++v  ++  aar ++++++DE+ 
  gi|386001856|ref|YP_005920155.1| 208 GGELQRVAIVAC-AARDADVYFFDEIS 233
                                       445555555555.999*********96 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                                       EE--SSSSHHHHHHHGGG CS
                             AAA_5   4 LvGppGtgKselaerlaa 21 
                                       ++Gp G+gK++ ++ la 
  gi|386001856|ref|YP_005920155.1| 363 ILGPNGIGKTTYIKILAG 380
                                       68*********9998875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.3   0.00011     0.058       2      18 ..      48      64 ..      47      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++Cg C+  CP +ai+
  gi|386001856|ref|YP_005920155.1| 48 CVGCGICVRKCPFGAIS 64
                                      ***************97 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.034        19       3      24 ..      97     118 ..      95     125 .. 0.83
   2 ?    6.1   0.1     0.014       7.5       3      22 ..     360     379 ..     359     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.034
                                       EEEEEESTTSSHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaal 24 
                                       v+ l+G++G+GK t++a L+ l
  gi|386001856|ref|YP_005920155.1|  97 VTGLLGPNGIGKSTAVAILSGL 118
                                       55689***********998765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                                       EEEEEESTTSSHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLa 22 
                                       v+ ++G++G+GKTt +  La
  gi|386001856|ref|YP_005920155.1| 360 VVGILGPNGIGKTTYIKILA 379
                                       56689*********998887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.072        39       5      24 ..     100     119 ..      96     136 .. 0.84
   2 ?    6.5   0.1     0.014       7.4       2      21 ..     360     379 ..     359     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.072
                                       EEC-TTTCHHHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklalaw 24 
                                       l G++G+GK+t ++ l  ++
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILSGLL 119
                                       78*********998776655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       +v + G++G+GKTt ++ la
  gi|386001856|ref|YP_005920155.1| 360 VVGILGPNGIGKTTYIKILA 379
                                       67799*********988665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.037        20      19      63 ..      96     146 ..      93     235 .. 0.78
   2 ?    4.6   0.1     0.045        24      19      40 ..     359     380 ..     352     397 .. 0.87
   3 ?   -1.0   0.0       2.3   1.2e+03      96     114 ..     480     498 ..     435     506 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.037
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g.....grviglAptgkaAkvLa 63 
                                       +v+ l Gp G GK+ta++ l  +++ + g     ++v+ l++ ++  + L+
  gi|386001856|ref|YP_005920155.1|  96 KVTGLLGPNGIGKSTAVAILSGLLAPNlGrgaswEEVLHLTSGSALGDYLR 146
                                       478899************999988877667777777777766666666666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
                            AAA_30  19 rvavltGpAGtGKttalkalre 40 
                                        v+ + Gp G GKtt +k l+ 
  gi|386001856|ref|YP_005920155.1| 359 EVVGILGPNGIGKTTYIKILAG 380
                                       488999***********98865 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.3
                            AAA_30  96 Eagmvdtkqlaallkaaek 114
                                       E  m+++k +++++++ae+
  gi|386001856|ref|YP_005920155.1| 480 EQRMMAAKVMRRFAESAER 498
                                       4456677777777777766 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.0      0.32   1.7e+02       9      15 ..      19      25 ..       9      35 .. 0.75
   2 ?   13.7   3.0   0.00013     0.069       2      17 .]      46      61 ..      45      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.32
                            Fer4_4  9 sCvaaCP 15
                                       C+++CP
  gi|386001856|ref|YP_005920155.1| 19 ECEYFCP 25
                                      5*****9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      + C+gCg Cv+ CP+g
  gi|386001856|ref|YP_005920155.1| 46 NLCVGCGICVRKCPFG 61
                                      57************86 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0049       2.7      27      55 ..      96     124 ..      93     130 .. 0.90
   2 ?    0.5   0.0      0.82   4.5e+02      28      57 ..     360     389 ..     354     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                                       HHHHHHS--SHHHHHHHHHHHHHHS--TT CS
                              MukB  27 lvttlsGgnGaGksttmaafvtaliPdls 55 
                                        vt l G nG Gkst++a +   l P+l 
  gi|386001856|ref|YP_005920155.1|  96 KVTGLLGPNGIGKSTAVAILSGLLAPNLG 124
                                       59***************999999999875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                                       HHHHHS--SHHHHHHHHHHHHHHS--TTT- CS
                              MukB  28 vttlsGgnGaGksttmaafvtaliPdlsll 57 
                                       v  + G nG Gk+t +  +  a +P    l
  gi|386001856|ref|YP_005920155.1| 360 VVGILGPNGIGKTTYIKILAGAEVPTTGAL 389
                                       556779********9999988888877666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.18        97       5      23 ..     101     119 ..      97     132 .. 0.84
   2 ?    0.4   0.0         1   5.4e+02      86     107 ..     214     235 ..     206     277 .. 0.70
   3 ?    4.1   0.5     0.074        40       2      19 ..     361     378 ..     360     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                                       E--TTSSHHHHHHHHHHHH CS
                          NTPase_1   5 TGppGvGKtTlvkkvlell 23 
                                        Gp G+GK+T v  ++ ll
  gi|386001856|ref|YP_005920155.1| 101 LGPNGIGKSTAVAILSGLL 119
                                       59*********98777666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                                       HHHHHHHHHHH-EEEE---STT CS
                          NTPase_1  86 lealrkalseadviviDEiGkm 107
                                       ++++ +a ++adv+  DEi + 
  gi|386001856|ref|YP_005920155.1| 214 VAIVACAARDADVYFFDEISPY 235
                                       456777889**********774 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.074
                                       EEEE--TTSSHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkv 19 
                                       v i Gp G+GKtT +k +
  gi|386001856|ref|YP_005920155.1| 361 VGILGPNGIGKTTYIKIL 378
                                       5688*********99855 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.21   1.1e+02       4      20 ..     100     116 ..      99     167 .. 0.84
   2 ?    7.3   0.4    0.0093       5.1       4      25 ..     363     384 ..     360     388 .. 0.85
   3 ?   -1.5   0.0       4.7   2.6e+03      53      82 ..     477     507 ..     467     514 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       ++G+ + GK+t ++ L+
  gi|386001856|ref|YP_005920155.1| 100 LLGPNGIGKSTAVAILS 116
                                       68***********9998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0093
                            AAA_28   4 itGgestGKTtlleaLaargyp 25 
                                       i+G+ + GKTt ++ La  ++p
  gi|386001856|ref|YP_005920155.1| 363 ILGPNGIGKTTYIKILAGAEVP 384
                                       99**************977665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.7
                            AAA_28  53 lafaervleeql.eeeaaaaankvlfcDrgl 82 
                                       l++++r++++++ ++ a+ a++ vl++D ++
  gi|386001856|ref|YP_005920155.1| 477 LDVEQRMMAAKVmRRFAESAERSVLVVDHDI 507
                                       4555555555543788888999999999876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  11.1      0.14        78      44      58 ..      46      60 ..       9      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      +lC++Cg C+rkCP 
  gi|386001856|ref|YP_005920155.1| 46 NLCVGCGICVRKCPF 60
                                      79***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 3486.24
//
Query:       gi|386001857|ref|YP_005920156.1|  [L=182]
Description: peptidyl-prolyl cis-trans isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-27   96.0   0.0    2.2e-27   95.2   0.0    1.4  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.0   1.2e-31   2.2e-27       4      93 ..       3     138 ..       1     139 [. 0.79

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.2e-31
                                       BB-TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTT....... CS
                            FKBP_C   4 eakegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYge....... 73 
                                       +ak gd V+vhy+g+ledg+vfdss   ++plef++G+g vi+Gfe a++gm+ Ge++++ ippe+aYg        
  gi|386001857|ref|YP_005920156.1|   3 RAKAGDAVRVHYAGRLEDGTVFDSS-AGKEPLEFTIGDGMVIPGFEAAVVGMSPGERKRVKIPPEEAYGPrrqemvm 78 
                                       49***********************.9*******************************************5555554 PP

                                       .....TTBCTTTB.TT.........................................SEEEEEEEE CS
                            FKBP_C  74 .....kglaggvippn.........................................atLvFeveL 93 
                                                   ip++                                         + L+Feve+
  gi|386001857|ref|YP_005920156.1|  79 everrC------IPQEfepevgqilqiggsrermlqvavsevtessvfldanhplagKPLLFEVEM 138
                                       444440......444455556666666666666666666666666666666677777999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2009  (0.112053); expected 358.6 (0.02)
Passed bias filter:                      851  (0.047465); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1184.47
//
Query:       gi|386001858|ref|YP_005920157.1|  [L=141]
Description: peptidyl-prolyl cis-trans isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-26   90.7   0.0    8.3e-26   90.2   0.0    1.3  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
     0.0052   16.7   0.0      0.036   14.1   0.0    2.2  2  DUF2187   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   9.2e-30   8.3e-26       4      93 ..       3     137 ..       1     138 [. 0.74

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 9.2e-30
                                       BB-TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTT....... CS
                            FKBP_C   4 eakegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYge....... 73 
                                       +akegd V++hykg +edg+vfdss +    l+f+vG+g vi+Gfeea++gmk+Ge +t+ti pe +Yg        
  gi|386001858|ref|YP_005920157.1|   3 QAKEGDSVSLHYKGSFEDGTVFDSS-ETHGALKFTVGRGTVIPGFEEAVVGMKLGEAKTVTIAPEKGYGPrkeellv 78 
                                       69***********************.999*****************************************5555555 PP

                                       ................................TTBCTTTB.TT................SEEEEEEEE CS
                            FKBP_C  74 ................................kglaggvippn................atLvFeveL 93 
                                                                                 +                +tLvF+  L
  gi|386001858|ref|YP_005920157.1|  79 riarqelppdldpavgqriefskgdqrfeltvS---------EvteeavtfdanhplagKTLVFDLLL 137
                                       555555555555555544444444444444441.........04444444444455555888888655 PP

>> DUF2187  Uncharacterized protein conserved in bacteria (DUF2187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.15   1.3e+03       2      14 ..       3      15 ..       2      29 .. 0.66
   2 !   14.1   0.0     4e-06     0.036       5      33 ..      93     121 ..      91     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                           DUF2187  2 kAkvGdiieFkkg 14
                                       Ak+Gd ++ + +
  gi|386001858|ref|YP_005920157.1|  3 QAKEGDSVSLHYK 15
                                      5899998876554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4e-06
                           DUF2187   5 vGdiieFkkgdlkltGiVekvnenSViVd 33 
                                       vG+ ieF kgd++++ +V +v e+ V  d
  gi|386001858|ref|YP_005920157.1|  93 VGQRIEFSKGDQRFELTVSEVTEEAVTFD 121
                                       8***********************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 885.04
//
Query:       gi|386001859|ref|YP_005920158.1|  [L=90]
Description: hypothetical protein Mhar_1167 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-32  111.9   2.1    1.3e-32  111.5   2.1    1.2  1  DUF2196   Uncharacterized conserved protein (DUF2196)


Domain annotation for each model (and alignments):
>> DUF2196  Uncharacterized conserved protein (DUF2196)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   2.1   7.4e-37   1.3e-32       1      61 []      28      88 ..      28      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 7.4e-37
                           DUF2196  1 dgktrkdikpGleVeivlkkdqrtGklteGiVkdilTnssthphGIKVrLedGeVGRVqei 61
                                      dgk+rkdikpG++Vei+lk dq+tGklteG+Vk+ilTnss+hphGIKVrL dG+VGRV++i
  gi|386001859|ref|YP_005920158.1| 28 DGKNRKDIKPGMKVEIILKRDQKTGKLTEGVVKEILTNSSFHPHGIKVRLADGQVGRVARI 88
                                      689*******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 596.61
//
Query:       gi|386001860|ref|YP_005920159.1|  [L=597]
Description: hypothetical protein Mhar_1168 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-28   99.6   0.2      2e-27   96.8   0.0    2.2  2  DUF262     Protein of unknown function DUF262
  ------ inclusion threshold ------
       0.17   10.6   0.0       0.26   10.0   0.0    1.2  1  LacY_symp  LacY proton/sugar symporter


Domain annotation for each model (and alignments):
>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   2.2e-31     2e-27       1     220 [.      13     218 ..      13     219 .. 0.82
   2 ?    0.1   0.2     0.087   7.8e+02     131     209 ..     302     378 ..     227     387 .. 0.52

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 2.2e-31
                            DUF262   1 ledllskskrg.lriPdfQRpyvWeeeqveeLiedllalkgyplGsivlw.......skaadsageleviDGQQRlt 69 
                                       +e ll++ k+g + iP++QRp+vW++ +v+ L+++l  ++gyp+G +++w       ++++ s+g++++iDGQQR+ 
  gi|386001860|ref|YP_005920159.1|  13 IETLLTRVKSGeMAIPEIQRPFVWSAVKVRNLLDSL--YQGYPVGYLITWrnpnvklKDGSTSSGKHILIDGQQRVI 87 
                                       6788899999999***********************..****************998777788************** PP

                            DUF262  70 Tltlllaatkeesekriknleaeiekekeeededrlkrreresdkellqkllrseklsleekeelaelnsltkkdl. 145
                                       +l+ ++ +              ++ +++++ +++r+ +++ +++ e l+  ++++     +    ++ +   ++ + 
  gi|386001860|ref|YP_005920159.1|  88 ALMAAVLG-------------LDVVDKNYKRIKIRIAFHPMKEQFEVLNASIEKDFSWIPDISVVFDPKTSIFDLVt 151
                                       ********.............77777888999999999999999999999999999887774444444444444446 PP

                            DUF262 146 ..akeekrneeknlikayevieeilksallsalktklslieieleseddedqayeiFerlNsrGvpLtasellkall 220
                                          +++   +++ +++ +e  +            t  ++  iel+s+ d++ + eiF+r+Ns GvpL++++  ++++
  gi|386001860|ref|YP_005920159.1| 152 ayCDKNPGATRDEIFRSIERMKG----------VTSNQIGLIELDSDFDIETVTEIFIRVNSEGVPLSQADFAMSKI 218
                                       66443334444444444444444..........5778999*****99************************988765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.087
                            DUF262 131 keelaelnsltkkdlakeekrneeknlikayevieeilksallsalktklslieielese...........ddedqa 196
                                       +      ++++ +++++   +++ ++l+k +  + +          +t+++++ i++ s            ++ + a
  gi|386001860|ref|YP_005920159.1| 302 L---LSGRNFETRQYEEVIVEDSFNRLKKGILRFMN----------ETNFKNLIIIIRSAgfvdssmirsqNSLNFA 365
                                       2...22223333333444556666666666666666..........3444544444442222223333334566666 PP

                            DUF262 197 yeiFerlNsrGvp 209
                                       y+++ +l ++G p
  gi|386001860|ref|YP_005920159.1| 366 YILYLTLRDQGIP 378
                                       6666666666655 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   2.9e-05      0.26     243     283 ..     527     567 ..     506     574 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.9e-05
                         LacY_symp 243 favffkslfespeaGtrvfGyvttagellnalimfiapliv 283
                                         ++f+ l+e   +G +++G +t ++el +  +m ++p  v
  gi|386001860|ref|YP_005920159.1| 527 PRIYFNQLLEQCCEGPKLYGNITDMDELKENFCMNCIPEGV 567
                                       5689**********************************766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4157.58
//
Query:       gi|386001861|ref|YP_005920160.1|  [L=166]
Description: hypothetical protein Mhar_1169 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   12.6   0.0      0.058   12.5   0.0    1.1  1  McrBC     McrBC 5-methylcytosine restriction system component


Domain annotation for each model (and alignments):
>> McrBC  McrBC 5-methylcytosine restriction system component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.2e-06     0.058     253     315 ..      38      96 ..       1     104 [. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-06
                             McrBC 253 ka.egeaefklkpDllikkkkeesivlDtKwKklekekakkkgisqsDlYQllaYaqayqaeqg 315
                                       k+ +++     +pD  i +  e   +lD+K++ l++     + + ++ lYQl  Ya +  +++g
  gi|386001861|ref|YP_005920160.1|  38 KNpRNRRAPDPRPDYAILRGPEVVSILDAKYRDLWE-----NPLPREMLYQLAIYALIGGRGAG 96 
                                       333344447889***776777899**********95.....5799999****999976665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1022.67
//
Query:       gi|386001862|ref|YP_005920161.1|  [L=164]
Description: hypothetical protein Mhar_1170 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-12   45.2   0.0    1.6e-11   44.4   0.0    1.5  1  Acylphosphatase  Acylphosphatase
      0.001   19.1   1.8     0.0014   18.6   1.0    1.6  2  DUF1664          Protein of unknown function (DUF1664)
     0.0093   15.9   0.7      0.011   15.7   0.7    1.2  1  CheZ             Chemotaxis phosphatase, CheZ


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   2.8e-15   1.6e-11       2      74 ..       4      79 ..       3     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.8e-15
                   Acylphosphatase  2 rllvtG.rVQgvgFRkfvrrlAkelglkGy.vrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveel 74
                                      ++l+tG  VQgvg+R f++++A   g++ + + N sd+ V ++ae ee+k++ ++e+l +  p+ a+v+ev +e+ 
  gi|386001862|ref|YP_005920161.1|  4 KALITGpMVQGVGYRIFLMHQAIIEGIERFsALNVSDNAVVVLAEAEEDKISNLKEFLLTHRPEhAQVSEVRIEDF 79
                                      6899**99********************999*****************************66666******99875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.53   3.2e+03     107     107 ..      80      80 ..      38     105 .. 0.60
   2 !   18.6   1.0   2.4e-07    0.0014      64     117 ..     108     162 ..      93     164 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.53
                           DUF1664 107 k 107
                                       k
  gi|386001862|ref|YP_005920161.1|  80 K 80 
                                       1 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-07
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseige.dvesvkeavegleskl 117
                                       +++r+ r+d+k+d + e + e+ ++v  +redl +i+   +e +++ + ++++k+
  gi|386001862|ref|YP_005920161.1| 108 MNERMGRMDEKMDRMLEKQDETVDQVRGLREDLGTIHAgRMERMERDIAEIKAKI 162
                                       6799********************************8537999999999998887 PP

>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7   1.8e-06     0.011      44     106 ..      82     145 ..      45     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                              CheZ  44 yvielTeqAAertldavekalpladklkeeakeleeewerllere.lekeefrelvkeveaflk 106
                                        v++l e  A  t++ ++ka p+  +++e++ +++e+++r+le++  +++++r l +++ ++ +
  gi|386001862|ref|YP_005920161.1|  82 LVMTLQEATALSTVEQMDKAIPILISMNERMGRMDEKMDRMLEKQdETVDQVRGLREDLGTIHA 145
                                       588999999********************************99995669999999888876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1081.70
//
Query:       gi|386001863|ref|YP_005920162.1|  [L=403]
Description: transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete 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  126.5   0.0    1.6e-36  126.2   0.0    1.0  1  Aminotran_1_2   Aminotransferase class I and II
    1.7e-05   23.8   0.0    1.9e-05   23.7   0.0    1.2  1  Aminotran_MocR  Alanine-glyoxylate amino-transferase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   1.8e-40   1.6e-36      11     359 ..      51     391 ..      47     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 1.8e-40
                                       TTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHH CS
                     Aminotran_1_2  11 ylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealif 86 
                                       +++     ++ eva+a+++   ++g+ + +y++++g+  l+e + + +  +++lk+++e +++ ++G+++++++l  
  gi|386001863|ref|YP_005920162.1|  51 PRFF----PVREVAEAAQKvLRESGEAALQYSTTEGYLPLRELIVERYA-RKGLKVDAE-EILITTGSQQGLDLLGK 121
                                       5666....99*********99999999**********************.99*******.***************** PP

                                       HHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                     Aminotran_1_2  87 llklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                       ++ l++gd+++v +pty   ++++ +   +++++pl+   + ++d  al  al+e p     + + +v + +NPtG+
  gi|386001863|ref|YP_005920162.1| 122 AF-LDKGDRVIVEEPTYLAAIQAFGIFEPKFRSVPLK---EDGIDPRALAVALSEGP----AKLFYAVPNFQNPTGV 190
                                       **.********************************88...559************65....3457899********* PP

                                       B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EEEEEEEHH CS
                     Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn..llivgslsKafGlaGeRvGyilgnaa 238
                                        +++e  ++++  ++ +  + + D+ Y+++ f  ++     + + ++     +++gs+sK   ++G+R+G++++ ++
  gi|386001863|ref|YP_005920162.1| 191 SYSEERRREVAGAMRGHATVFVEDDPYGELRFIGEE----APSMRRYLGgrAVLLGSFSKVI-SPGLRLGWACARSD 262
                                       ******************************998765....6778888888889*******87.6************9 PP

                                       HHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEE CS
                     Aminotran_1_2 239 vvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmfllt 310
                                       + + + +++++     s l q+++ + l d + + +++e+ r+ + ++r+ +++ ++e    g++++ +++gmfl++
  gi|386001863|ref|YP_005920162.1| 263 IMERMVIAKQASDLhtSILSQRIAYQYLVDND-VSQQMETVRSGYRRQRDLMVKMIEESfpaGVECTRPEGGMFLWV 338
                                       999998777766556599999*******9988.788********************999****************** PP

                                       EETHH.CHHHHHHHHHHTCTEEEEEGGGGTS....TTEEEEECTTS-HHHHHHH CS
                     Aminotran_1_2 311 dlsae.takelskkLleevgvyvtpgtsftv....pgrlRitvAglteeeleel 359
                                        l++  +  el+++ +++  v+ +pg+ f++     + lR+++++ +ee + e 
  gi|386001863|ref|YP_005920162.1| 339 TLPENmSSLELFDSAIKN-DVAFVPGQAFYAngggYNTLRLNFSNSDEERIVEG 391
                                       ***99999**********.**************99889*****99999887665 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.1e-09   1.9e-05     128     219 ..     131     220 ..     106     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-09
                                       EEEES--HHHHHHHHHHT-...EEEEEEEETTEE-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT. CS
                    Aminotran_MocR 128 lvtvpGydrhfllleelGi...elltvdlqddGpdvdaveklvaedasvkGilavpkysnptGetiseevarrlaa. 200
                                       +v  p y      ++ +Gi   ++ +v+l++dG d  a+    +e +  k  +avp++ nptG  +see+ r++a+ 
  gi|386001863|ref|YP_005920162.1| 131 IVEEPTYLAA---IQAFGIfepKFRSVPLKEDGIDPRALAVALSEGP-AKLFYAVPNFQNPTGVSYSEERRREVAGa 203
                                       5555555433...3444433337889**********99987777666.599***********************962 PP

                                       ---SSTT-EEEEE-TTSS- CS
                    Aminotran_MocR 201 lkaaapdfrifaddayavh 219
                                       ++  a  f    dd y   
  gi|386001863|ref|YP_005920162.1| 204 MRGHATVF--VEDDPYGEL 220
                                       55555433..246666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2542.75
//
Query:       gi|386001864|ref|YP_005920163.1|  [L=151]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-12   45.2   0.0    9.4e-12   44.8   0.0    1.1  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like
    1.1e-11   44.8   0.0      2e-11   43.9   0.0    1.4  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
    7.2e-07   29.3   0.0      1e-06   28.8   0.0    1.2  1  Pyridox_ox_2     Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.028   14.1   0.0       0.05   13.3   0.0    1.3  1  FMN_bind_2       Putative FMN-binding domain
      0.034   14.8   0.0      0.063   13.9   0.0    1.5  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   2.6e-15   9.4e-12       4     127 ..      15     137 ..      13     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.6e-15
                     Pyrid_ox_like   4 kklkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsG 80 
                                       k++++ ++d  ++ ++t e +++ ++r   +  ++e+g ++f t ++ +  +++rk++ v+++fs+++++k + v+G
  gi|386001864|ref|YP_005920163.1|  15 KEFTKFANDNPVGYVATAE-GNQPHVRAFLMWFADETG-FYFHTGEQKKVCQQLRKNPLVEVCFSSQNHDKIMRVAG 89 
                                       6677778888888888875.777888887777666666.9************************************* PP

                     Pyrid_ox_like  81 taevvedrakieelWs..pvvkawfpegkddpnltlikvtpeeaeyWds 127
                                       ++e+ +d      l +  p++ka   +g +dpnl + +++  ea++W  
  gi|386001864|ref|YP_005920163.1|  90 EMEFLDDAGLRARLIEerPFLKAIV-QGPEDPNLAIFRMHHGEARFWTM 137
                                       *******988888876337899999.9********************75 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   5.7e-15     2e-11       4      87 ..      16      97 ..      14      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.7e-15
                                      HHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEE CS
                    Putative_PNPOx  4 elreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtae 82
                                      e+ +f ++ +++ +AT+ e ++P+v++ l  + d++ g++f+t ++ +  ++l++np v ++f + + ++ +r+ G+ e
  gi|386001864|ref|YP_005920163.1| 16 EFTKFANDNPVGYVATA-EGNQPHVRAFLMWFADET-GFYFHTGEQKKVCQQLRKNPLVEVCFSSQNHDKIMRVAGEME 92
                                      78899999*********.8888******99977888.****************************************** PP

                                      EESCH CS
                    Putative_PNPOx 83 lvsdg 87
                                      +++d+
  gi|386001864|ref|YP_005920163.1| 93 FLDDA 97
                                      *9985 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.8e-10     1e-06       6      69 ..      18      85 ..      14      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.8e-10
                                      HHHHHC-SEEEEEEEETTEEEEEEEEEEEETTE.EEEEEETTSHCCHCCCT--...ECEEEEEEEEEE CS
                      Pyridox_ox_2  6 lalLdegevgrlafvddgepvilPvnyvvdgds.lyfhgakgsrlaaalrgap...vcvvvtevdglv 69
                                       ++ ++++vg +a++++++p+++ +  ++ +++ +yfh+ +  + +++lr++p   vc++ ++ d ++
  gi|386001864|ref|YP_005920163.1| 18 TKFANDNPVGYVATAEGNQPHVRAFLMWFADETgFYFHTGEQKKVCQQLRKNPlveVCFSSQNHDKIM 85
                                      5677899***********************9999****************666667999999888876 PP

>> FMN_bind_2  Putative FMN-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05      0.05      12      83 ..      14      81 ..      11      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                      HCHHHHHHHHS-EEEEEEEETTEEEEEEEE-EE...-TTSSEEEEEEETTSGGGGGT.TTS-EEEEEEEEEE CS
                        FMN_bind_2 12 leelrqlirenplgtLvtaiesglqashiPflldeeekgkgkLrgHlaraNpqakaleeeeevlvvfqgpda 83
                                      l+e  ++ ++np+g + ta+ +++++    + +  ++++    ++H  ++ + +++l+++  v v f+++++
  gi|386001864|ref|YP_005920163.1| 14 LKEFTKFANDNPVGYVATAEGNQPHVRAFLMWF--ADETG--FYFHTGEQKKVCQQLRKNPLVEVCFSSQNH 81
                                      678899****************99999888777..34455..8******************9*****99876 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.063      31      98 ..      33      93 ..      13      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                      .TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEEE CS
                   Pyridox_oxase_2 31 eegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkafv 98
                                      e ++P+vR   +  ++++   e+  + f+t  + + ++ql+ +n+ ve++f  +++ + +R++G++ +
  gi|386001864|ref|YP_005920163.1| 33 EGNQPHVRAFLM--WFAD---ETG-FYFHTGEQKKVCQQLR-KNPLVEVCFSSQNHDKIMRVAGEMEF 93
                                      356677776554..4443...344.8999999998899999.9*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1002.74
//
Query:       gi|386001865|ref|YP_005920164.1|  [L=125]
Description: hypothetical protein Mhar_1173 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00052   20.0   0.0    0.00083   19.4   0.0    1.3  1  HTH_20         Helix-turn-helix domain
    0.00078   19.6   3.1     0.0014   18.8   3.1    1.4  1  LIM            LIM domain
     0.0089   15.9   0.0      0.011   15.6   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.031   14.0   0.0      0.057   13.1   0.0    1.4  1  Sigma70_r4_2   Sigma-70, region 4
      0.049   13.5   0.0       0.08   12.8   0.0    1.4  1  MarR_2         MarR family
      0.059   13.1   0.0       0.14   12.0   0.0    1.6  1  LexA_DNA_bind  LexA DNA binding domain
      0.059   13.2   0.0        0.1   12.5   0.0    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.07   12.7   0.0       0.11   12.1   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.12   12.5   0.0       0.21   11.7   0.0    1.4  1  DUF2802        Protein of unknown function (DUF2802)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.1e-07   0.00083      10      58 ..      67     115 ..      65     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.1e-07
                                       HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                       +v+++i+ ++++++g++++e+ ++++ls++++ + +++L+   Lv++ r
  gi|386001865|ref|YP_005920164.1|  67 EVQAKIYELIRSRDGASPEEIGREFGLSPAEVQNEFAILRHCQLVKGKR 115
                                       699************************************9888887765 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.1   6.9e-07    0.0014      28      57 ..       6      35 ..       6      36 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.9e-07
                                      B-TTT-SB-CTT.CEEETTEEEEHHHHHHH CS
                               LIM 28 tCsdCqkeLkegsfyekdgklyCkkdylkk 57
                                      +C+ C++ L e+++++++g+ +C+++y+++
  gi|386001865|ref|YP_005920164.1|  6 RCQGCGQDLGEEELILHEGERLCEECYFDR 35
                                      6**************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.5e-06     0.011       5      62 ..      64     122 ..      59     125 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                                       HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEE CS
                              TrmB   5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklY 62 
                                       GL+e  ak+Y  + +++ a+ +ei +e g++ + v++    L  + lV+ ++ + ++l+
  gi|386001865|ref|YP_005920164.1|  64 GLTEVQAKIYELIRSRDGASPEEIGREFGLSPAEVQNEFAILRHCQLVKGKRAEgKMLF 122
                                       9********************************************99998775535555 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05     0.057      10      45 ..      64     100 ..      60     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                       TS-HHHHHHHHHHH.TS---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2  10 eLperqreifllry.leglsykEIAellgisegtVks 45 
                                        L+e q +i++l++  +g s +EI +++g+s++ V++
  gi|386001865|ref|YP_005920164.1|  64 GLTEVQAKIYELIRsRDGASPEEIGREFGLSPAEVQN 100
                                       69999*******8758*****************9987 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     4e-05      0.08       2      40 ..      64     100 ..      63     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                                       T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsr 40 
                                       glt  qa +   ++ r+g   ++ e+ r++gls++ v++
  gi|386001865|ref|YP_005920164.1|  64 GLTEVQAKIYELIRSRDG--ASPEEIGREFGLSPAEVQN 100
                                       666677777778999999..9**************9985 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05      0.14       2      51 ..      63     106 ..      62     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                                       X---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHH CS
                     LexA_DNA_bind   2 kkLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLe 51 
                                       ++LTe Q+++ +li++   + g  P   ei+r++gl+ p+ v++  + L+
  gi|386001865|ref|YP_005920164.1|  63 EGLTEVQAKIYELIRS---RDGASP--EEIGREFGLS-PAEVQNEFAILR 106
                                       68*************7...688888..7********7.999999887776 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.1e-05       0.1      11      35 ..      75      99 ..      65     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                     HTH_AsnC-type 11 aLqedaRisyaeLAervGlSestvl 35
                                      +++    +s +e++++ GlS+++v+
  gi|386001865|ref|YP_005920164.1| 75 LIRSRDGASPEEIGREFGLSPAEVQ 99
                                      55555558999*************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.6e-05      0.11       4      33 ..      68      97 ..      65     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpst 33
                                       + kI+el++   + s  e+ ++ glSp+ 
  gi|386001865|ref|YP_005920164.1| 68 VQAKIYELIRSRDGASPEEIGREFGLSPAE 97
                                      5669***********************975 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.21      41      61 ..      79      99 ..      65      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           DUF2802 41 rqGasveelaeecgLsraEAe 61
                                      r Gas ee+ +e+gLs aE++
  gi|386001865|ref|YP_005920164.1| 79 RDGASPEEIGREFGLSPAEVQ 99
                                      67*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 864.55
//
Query:       gi|386001866|ref|YP_005920165.1|  [L=112]
Description: Alkylhydroperoxidase like protein, AhpD family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-14   53.7   0.7    1.9e-14   53.5   0.7    1.1  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.7   1.1e-18   1.9e-14       1      79 [.      17      94 ..      17     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.1e-18
                                      HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHH CS
                               CMD  1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraA 79
                                      pe+l a++al   +l+ +g++  ke+ Liala ++a +c yCv a  r A +aG+++eei e++a++a    +  +++A
  gi|386001866|ref|YP_005920165.1| 17 PEALGAFEALSAEVLK-DGAIKGKEKALIALASAVAVNCRYCVGAQKRHASMAGASPEEILEAAAVGALVRLGSGFTYA 94
                                      8999***********9.*************************************************9998877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 810.08
//
Query:       gi|386001867|ref|YP_005920166.1|  [L=163]
Description: hypothetical protein Mhar_1175 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0053   16.8   0.5      0.011   15.8   0.5    1.5  1  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.029   14.6   0.0    1.4  1  DUF2293        Uncharacterized conserved protein (DUF2293)
      0.034   14.2   2.4      0.085   13.0   2.4    1.6  1  Zn-ribbon_8    Zinc ribbon domain
      0.058   13.3   4.2        1.4    8.9   0.3    2.6  2  zinc_ribbon_4  zinc-ribbon domain
        0.2   11.5   4.3       0.97    9.2   0.3    2.4  2  zinc_ribbon_5  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5     3e-06     0.011      68      97 ..       7      38 ..       3      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
                                      --EEEETTTS-EEECHHH...HHS-TTTSSS-E CS
                              HypA 68 pvkvrCreCgkefeleek...alrCpkCgsadv 97
                                       +++rC +Cg+++e + +    + Cp+C s+ v
  gi|386001867|ref|YP_005920166.1|  7 TMQLRCGRCGARWEYRGRaevYACCPQCRSK-V 38
                                      6799**********7764335458****995.3 PP

>> DUF2293  Uncharacterized conserved protein (DUF2293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     8e-06     0.029      44      69 ..      86     110 ..      84     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8e-06
                           DUF2293  44 AvlAhiRHthTdYDeLlkegvereeA 69 
                                       A+   iRH h++YDeL+ +  e+++A
  gi|386001867|ref|YP_005920166.1|  86 AISTAIRHDHSNYDELVIR-LEKKAA 110
                                       88899***********998.665555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.4   2.4e-05     0.085       6      37 ..      10      39 ..       7      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCgsevr 37
                                       rC +Cg + e + ++   +  a CP+C s+v+
  gi|386001867|ref|YP_005920166.1| 10 LRCGRCGARWEYRGRA---EVYAcCPQCRSKVK 39
                                      59*********77753...36666****99885 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00038       1.4      23      35 ..       7      19 ..       5      20 .. 0.81
   2 ?    5.2   0.4    0.0055        20       5      20 ..      31      46 ..      29      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00038
                     zinc_ribbon_4 23 gvkvrCskCghvF 35
                                      ++ +rC +Cg+ +
  gi|386001867|ref|YP_005920166.1|  7 TMQLRCGRCGARW 19
                                      5678999999998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0055
                     zinc_ribbon_4  5 CpsCkakyeiddeklp 20
                                      Cp+C +k +id e +p
  gi|386001867|ref|YP_005920166.1| 31 CPQCRSKVKIDLEGIP 46
                                      *******999977665 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4     0.021        74      26      32 ..      10      16 ..       5      18 .. 0.82
   2 ?    9.2   0.3   0.00027      0.97       5      15 ..      31      41 ..      29      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.021
                     zinc_ribbon_5 26 VrCakCa 32
                                       rC++C+
  gi|386001867|ref|YP_005920166.1| 10 LRCGRCG 16
                                      6999997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00027
                     zinc_ribbon_5  5 CpdCdtkFklv 15
                                      Cp+C++k k++
  gi|386001867|ref|YP_005920166.1| 31 CPQCRSKVKID 41
                                      *******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1135.06
//
Query:       gi|386001868|ref|YP_005920167.1|  [L=116]
Description: ribonuclease P protein component 4 [Methanosaeta harundinacea 6Ac]
Scores for 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-11   42.0   1.0    1.4e-10   41.3   1.0    1.4  1  Rpr2      RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   1.0   7.9e-15   1.4e-10       1      90 []      30     105 ..      30     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 7.9e-15
                                       HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E..... CS
                              Rpr2   1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkk 77 
                                       r++ L+ +a+  ++e++p+ s ++++ +r++ +++++r+p+ +kr++Ck C+++l pg t +vr++    +      
  gi|386001868|ref|YP_005920167.1|  30 RIERLFVLAEE-EHERHPERSDRYVEIARRMGMRMRVRIPRRLKRRICKGCRCYLSPGRT-RVRLRD---G------ 95 
                                       78899999**8.9*********************************************87.677853...2...... PP

                                       ....EEEEETTTT CS
                              Rpr2  78 kadvlvvtClaCg 90 
                                          +++vtCl+Cg
  gi|386001868|ref|YP_005920167.1|  96 ---MVTVTCLECG 105
                                       ...3569999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 685.39
//
Query:       gi|386001869|ref|YP_005920168.1|  [L=93]
Description: hypothetical protein Mhar_1177 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 625.54
//
Query:       gi|386001870|ref|YP_005920169.1|  [L=177]
Description: nucleoside-triphosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-48  165.6   0.0    1.2e-48  165.5   0.0    1.0  1  Ham1p_like   Ham1 family
  ------ inclusion threshold ------
      0.088   12.6   0.1       0.14   12.0   0.1    1.3  1  Shugoshin_C  Shugoshin C terminus
       0.17   11.6   0.0       0.24   11.2   0.0    1.3  1  DUF1678      Protein of unknown function (DUF1678)


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   0.0   2.1e-52   1.2e-48       1     187 []       2     173 ..       2     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 2.1e-52
                                       EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.H.TS-EEEEEEEEEEGGGT CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.a.glpvladDsgLevdaLn 74 
                                       i+f+TgN+gK++e++e+l++  +e +++       ++E+q +t+ee+a    r++++   g+ v+++D gL++d L 
  gi|386001870|ref|YP_005920169.1|   2 IYFVTGNRGKYEEAQELLGD--VEQRKI------GYPEIQaDTLEEVAVYGIRDVVDrLpGP-VMIEDAGLFIDSLM 69 
                                       89****************75..222222......4459**9***************744455.************** PP

                                       TTBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTG CS
                        Ham1p_like  75 glPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyD 151
                                       g+PGvysa++      d+ +++ +l+ +e+++ +r+A f++v+a+a+p+ e+ +lf+Ge+eGei+ eprg+ggfGyD
  gi|386001870|ref|YP_005920169.1|  70 GFPGVYSAYVF-----DTIGNEGILRLMEGRP-HRRAVFRSVVAYAEPGMEP-ILFSGELEGEIALEPRGSGGFGYD 139
                                       **********6.....56789*******9766.9**************6666.************************ PP

                                       GGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 152 piFvpeegektfaelskeeknaiShRgkAlekllef 187
                                       piF +  gekt+ae++ +ekn+iShRg ++++l+e+
  gi|386001870|ref|YP_005920169.1| 140 PIFRV--GEKTIAEMDLAEKNRISHRGGSIRALKEW 173
                                       *****..599***********************997 PP

>> Shugoshin_C  Shugoshin C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.3e-05      0.14       1      16 [.      94     111 ..      94     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                       Shugoshin_C   1 gRpsRra..rkvvsYKEP 16 
                                       gRp Rra  r+vv Y+EP
  gi|386001870|ref|YP_005920169.1|  94 GRPHRRAvfRSVVAYAEP 111
                                       8***************** PP

>> DUF1678  Protein of unknown function (DUF1678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     4e-05      0.24     133     172 ..      40      83 ..      15     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4e-05
                           DUF1678 133 lgspgirdvleelpdrl..ed..ilvrvlagwpahyssrleklv 172
                                       ++  girdv++ lp+ +  ed  ++++ l g+p  ys+++   +
  gi|386001870|ref|YP_005920169.1|  40 VAVYGIRDVVDRLPGPVmiEDagLFIDSLMGFPGVYSAYVFDTI 83 
                                       34456*********97633444489*************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1168.20
//
Query:       gi|386001871|ref|YP_005920170.1|  [L=325]
Description: hypothetical protein Mhar_1179 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-10   41.0   4.0    2.5e-06   27.7   3.0    3.1  2  DUF11        Domain of unknown function DUF11
    5.3e-06   26.6   0.2    0.00029   21.1   0.0    3.0  3  CARDB        CARDB
  ------ inclusion threshold ------
       0.11   13.3   0.0        1.5    9.6   0.0    2.4  1  N_BRCA1_IG   Ig-like domain from next to BRCA1 gene
       0.12   12.6   6.0       0.65   10.3   0.6    4.0  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   3.0   5.7e-10   2.5e-06       8      83 ..      83     165 ..      76     210 .. 0.89
   2 !   10.3   0.0   0.00015      0.68      18      83 ..     221     292 ..     216     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.7e-10
                             DUF11   8 s....evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvr 77 
                                       s    +v +G+  +yt  v+N+gpa++  ++ +   P+g+++ s++ s+g ++ + +v   g+L ag+  +l++ + 
  gi|386001871|ref|YP_005920170.1|  83 SakgeAVVAGESFSYTFEVRNSGPAASVIITTNLSIPEGVTLESFTVSRGEYDRRGGVwtvGDLSAGGVERLTVDLV 159
                                       33344999*******************555555555*****************99999999**************** PP

                             DUF11  78 vtrtaa 83 
                                       v+++  
  gi|386001871|ref|YP_005920170.1| 160 VAPSVP 165
                                       999875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                             DUF11  18 ytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsv....gsLeagesatlsftvrvtrtaa 83 
                                       y++ v N gp+ a +v   D+ P  + +  ++ +   +g            g+L++ge++++++    ++t+a
  gi|386001871|ref|YP_005920170.1| 221 YVVNVANHGPSYARNVWFMDLIPVVMWLNGARYRneaTGDEGDWI-GfldlGDLAPGETKRVRVYGDLSPTTA 292
                                       99*********************5444444444431212222233.258999*******99998777666665 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   6.4e-08   0.00029       3      71 ..      77     160 ..      75     182 .. 0.80
   2 ?    1.0   0.0      0.11   4.9e+02      15      38 ..     212     236 ..     201     239 .. 0.74
   3 ?   -0.3   0.0      0.29   1.3e+03      51      70 ..     267     286 ..     255     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.4e-08
                                       -EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEE..............SEE-CTEEEE CS
                             CARDB   3 DLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtv..............psLaagestt 64 
                                       DL vt++++ +++++ge+++ t++v+N+G aas  ++++l + + ++ +++tv                L+ag+ + 
  gi|386001871|ref|YP_005920170.1|  77 DLSVTSSAKGEAVVAGESFSYTFEVRNSGPAASVIITTNLSIPEGVTlESFTVsrgeydrrggvwtvGDLSAGGVER 153
                                       9***************************************9965555577777666666666666668888888887 PP

                                       EEEEEE- CS
                             CARDB  65 vsftwtt 71 
                                        ++  ++
  gi|386001871|ref|YP_005920170.1| 154 LTVDLVV 160
                                       7776665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                       EETTSEEEEEE.EEEE-SSS-EEEE CS
                             CARDB  15 afvgeentitv.tvkNqGtaasgat 38 
                                        + ge++ ++v +v+N+G  +++++
  gi|386001871|ref|YP_005920170.1| 212 EEGGEDMPLYVvNVANHGPSYARNV 236
                                       5556666666549******999875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.29
                                       EEEESEE-CTEEEEEEEEEE CS
                             CARDB  51 tvtvpsLaagesttvsftwt 70 
                                         ++  La+ge++ v++   
  gi|386001871|ref|YP_005920170.1| 267 FLDLGDLAPGETKRVRVYGD 286
                                       56778999999999998654 PP

>> N_BRCA1_IG  Ig-like domain from next to BRCA1 gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00034       1.5       4      43 ..      85     125 ..      82     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                        N_BRCA1_IG   4 dgtvvppgteftktWrlrNtGseaW.pagtklvfvgGdkmg 43 
                                       +g++v +g+ f  t+++rN+G++a     t+l + +G ++ 
  gi|386001871|ref|YP_005920170.1|  85 KGEAVVAGESFSYTFEVRNSGPAASvIITTNLSIPEGVTLE 125
                                       7999*****************98753455566666666654 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 ?   -3.2   0.0       2.4   1.1e+04      48      64 ..      69      85 ..      64      88 .. 0.62
   2 ?   10.3   0.6   0.00014      0.65       2      45 ..      90     133 ..      89     178 .. 0.73
   3 ?   -0.4   0.0       0.3   1.4e+03      52      68 ..     199     215 ..     185     236 .. 0.69
   4 ?    1.1   0.0      0.11   4.7e+02      46      78 ..     272     304 ..     268     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                       NPCBM_assoc 48 apGetveatvkVtppag 64
                                      + G+ +  ++ Vt++a+
  gi|386001871|ref|YP_005920170.1| 69 PGGALAALDLSVTSSAK 85
                                      55666666666666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa 45 
                                        +Ge+ ++t++v n+g aa   +  +ls PeG t +++++ +++
  gi|386001871|ref|YP_005920170.1|  90 VAGESFSYTFEVRNSGPAASVIITTNLSIPEGVTLESFTVSRGE 133
                                       589*****************************997777776655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.3
                       NPCBM_assoc  52 tveatvkVtppagaaaG 68 
                                       ++e+ v Vt p+  + G
  gi|386001871|ref|YP_005920170.1| 199 EAEVRVVVTCPSPEEGG 215
                                       45566666666655555 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.11
                       NPCBM_assoc  46 slapGetveatvkVtppagaaaGdyevtakarl 78 
                                       +lapGet ++ v    ++++a +   vt+++r+
  gi|386001871|ref|YP_005920170.1| 272 DLAPGETKRVRVYGDLSPTTARSNPGVTITVRW 304
                                       899*****9999888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2207.74
//
Query:       gi|386001872|ref|YP_005920171.1|  [L=414]
Description: Glutamyl-tRNA(Gln) amidotransferase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete 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-61  206.2   1.0    1.1e-60  204.5   0.8    1.8  2  Asparaginase    Asparaginase, N-terminal
      4e-30  104.4   0.3    1.9e-29  102.2   0.0    2.1  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    4.1e-13   48.4   0.0    8.6e-13   47.4   0.0    1.6  1  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
      0.017   14.7   0.0        1.6    8.2   0.0    2.2  2  Peripla_BP_4    Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.5   0.8   2.5e-64   1.1e-60       1     178 [.      73     255 ..      73     267 .. 0.97
   2 ?   -1.0   0.0      0.24   1.1e+03     133     162 ..     332     357 ..     324     366 .. 0.72

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 2.5e-64
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.y 76 
                                       kv +l+tGGTias++d+++ga++ ++saee+++++pel +ia++e +++ ni S+nm+ + w+ la+a+ +++e+ +
  gi|386001872|ref|YP_005920171.1|  73 KVSILSTGGTIASKVDYRTGAVTSQFSAEEIISSIPELLEIANYEGKVIYNILSENMKAEYWQVLARAVGSEIEKgA 149
                                       799**********************************************************************777* PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                       +g++++hGTDT+ ytA+aLs+m+k+ ++p+vl+Gsqr++++++sD+++N ++A++va+++  ia+v+vv++g+    
  gi|386001872|ref|YP_005920171.1| 150 AGVIITHGTDTMTYTAAALSFMVKT-PVPIVLVGSQRSSDRPSSDAAMNAISAARVATTD--IAEVTVVMHGStsdd 223
                                       *************************.********************************87..*************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEE CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaev 178
                                          ++r++rv+K+hts++daF+s+n  p+a+v
  gi|386001872|ref|YP_005920171.1| 224 fclVHRGTRVRKMHTSRRDAFRSINQHPIARV 255
                                       ******************************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                                       HHCGGTTSECEEEETTEEEETTTEEE-BSS CS
                      Asparaginase 133 aasseriagvlvvfngkllranrvtKvhts 162
                                       a      agv vv+  ++lr++ + +v  +
  gi|386001872|ref|YP_005920171.1| 332 A----TDAGVPVVITSQCLRGRVCDRVYDT 357
                                       3....3469999999999999988777655 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.29   1.3e+03      21      48 ..     146     171 ..     113     217 .. 0.57
   2 !  102.2   0.0   4.3e-33   1.9e-29       3     114 .]     287     398 ..     285     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                                       HTT--EEEEEEBTTTB--HHHHHHHHHH CS
                    Asparaginase_C  21 kkgakGvvlegtGvGnlpsallealkea 48 
                                       +kga Gv++  +  +     +  al+ +
  gi|386001872|ref|YP_005920171.1| 146 EKGAAGVIITHGTDTMTY--TAAALSFM 171
                                       555555555544333322..22333333 PP

  == domain 2  score: 102.2 bits;  conditional E-value: 4.3e-33
                                       EEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHH CS
                    Asparaginase_C   3 vvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkeler 79 
                                       +++k +pg +++++++++++g++G+vlegtG G++ s+++  +k a+++g++vv+tsqc++g+v + +y++g+++ +
  gi|386001872|ref|YP_005920171.1| 287 ALVKYFPGGSPDLFEECIAAGYRGIVLEGTGLGHVASDWVGSIKAATDAGVPVVITSQCLRGRVCDRVYDTGRDILA 363
                                       799************************************************************************** PP

                                       HTEEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                    Asparaginase_C  80 lgvisaddmtpeaarikLmlllgkgldpaevrklf 114
                                       +g+i+++d+ pe a +kLm++l+++ + +e ++++
  gi|386001872|ref|YP_005920171.1| 364 AGGIEGGDILPEVALVKLMWALANTGSVDEAEAVM 398
                                       *****************************999887 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   1.9e-16   8.6e-13       2      55 .]       3      51 ..       2      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.9e-16
                                      -TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  2 evGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      e GD+i v+k+g++ eG+lmP+     +  +v+K+++GYN+G++ e++  +ell
  gi|386001872|ref|YP_005920171.1|  3 ELGDRIAVTKDGVRREGVLMPSV----SGRVVIKMESGYNAGFDPERS-VVELL 51
                                      89*********************....*******************99.88876 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0056        25      48     159 ..     141     266 ..     112     283 .. 0.71
   2 ?    8.2   0.0   0.00036       1.6      48      85 ..     300     341 ..     298     366 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0056
                                       HHHHHHTT-SEEE.E--SSHHHHH.HHHHHHHHTT-EEEEESTT...GCTTT-CEEEEEC-HHHHHHHHHHHHHHHC CS
                      Peripla_BP_4  48 iedaiakgvdgii.vapvdstala.palkkakaaGIpVvafdsd...dapsgerlayvgfdneaaGelqaeylaekl 119
                                       + + i+kg+ g+i  + +d+ + + +al    +  +p+v + s+   d ps++ + +       a + +ae+ +   
  gi|386001872|ref|YP_005920171.1| 141 VGSEIEKGAAGVIiTHGTDTMTYTaAALSFMVKTPVPIVLVGSQrssDRPSSDAAMNAISAARVATTDIAEVTVVMH 217
                                       55789999885551566666555558999999999********9555555555555555555555555555544444 PP

                                       TTH.EEEEEE.TSCCCHHHHHHHHHHHHHHHHH......-T..TCEECC CS
                      Peripla_BP_4 120 ggkkgkvvil.aGspgdpnaeeriegfrkvlke......yp..gikiva 159
                                       g+ + +++++ +G+   + ++ r ++fr++ +       yp  +++i++
  gi|386001872|ref|YP_005920171.1| 218 GSTSDDFCLVhRGTRVRKMHTSRRDAFRSINQHpiarvlYPsrDLEILG 266
                                       44468999889999999999*******9998877777774434666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00036
                                       HHHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEE CS
                      Peripla_BP_4  48 iedaiakgvdgiivapvds....talapalkkakaaGIpVva 85 
                                       +e  ia+g+ gi++  +      +     +k+a++aG+pVv 
  gi|386001872|ref|YP_005920171.1| 300 FEECIAAGYRGIVLEGTGLghvaSDWVGSIKAATDAGVPVVI 341
                                       68889999999997766553334555569***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2615.95
//
Query:       gi|386001873|ref|YP_005920172.1|  [L=150]
Description: 50S ribosomal protein L10e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-32  110.0   0.1    9.4e-32  109.8   0.1    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.19   12.0   0.0    1.2  1  SpmSyn_N       S-adenosylmethionine decarboxylase N -terminal


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.1     1e-35   9.4e-32      15     132 .]       2     141 ..       1     141 [. 0.95

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1e-35
                                       TSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXEEEEE-... CS
                     Ribosomal_L16  15 rgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphhpvtkk... 76 
                                        gv+ +k  ++++g+        + Lva+e++q++++aleaar+++nryl +  g+   ++++rv+ph++++++   
  gi|386001873|ref|YP_005920172.1|   2 GGVPgSKVVHYDMGNlntefpvtLTLVAKEPCQIRHTALEAARVTANRYLMTYVGRlnfHMKLRVYPHQVLRENkqa 78 
                                       699999***************9999**************************99999999****************** PP

                                       ..SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                     Ribosomal_L16  77 ..agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktkiv 132
                                         ag+dR+++G+    Gk  g++arv ++q if++  a ++  +ak alrra +Klp+++ iv
  gi|386001873|ref|YP_005920172.1|  79 tgAGADRVSSGMrhafGKAVGTAARVDAEQKIFSVsTAPTSVPQAKMALRRAGHKLPTPIYIV 141
                                       ***********************************544368889**************99886 PP

>> SpmSyn_N  S-adenosylmethionine decarboxylase N -terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.1e-05      0.19      25      52 ..      48      75 ..      36      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                          SpmSyn_N 25 hGylatyigkngsfaslriyphGlvlld 52
                                      + yl ty+g+     +lr+yph ++  +
  gi|386001873|ref|YP_005920172.1| 48 NRYLMTYVGRLNFHMKLRVYPHQVLREN 75
                                      569*******************877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 978.21
//
Query:       gi|386001874|ref|YP_005920173.1|  [L=208]
Description: translation initiation factor 2 subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete 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-39  134.1   0.0    2.7e-39  133.6   0.0    1.2  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
    5.1e-12   45.6   0.4    1.3e-11   44.3   0.3    1.7  2  TRAM            TRAM domain
    0.00082   19.3   0.0     0.0015   18.5   0.0    1.4  1  DUF4265         Domain of unknown function (DUF4265)
  ------ inclusion threshold ------
      0.096   13.2   0.1       0.14   12.6   0.1    1.2  1  Cytochrom_c3_2  Cytochrome c3
       0.41   11.0   3.1        1.2    9.5   3.2    1.8  1  ZF-HD_dimer     ZF-HD protein dimerisation region
       0.43    9.9   0.1       0.43    9.9   0.1    1.6  2  zf-RanBP        Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.0   9.1e-43   2.7e-39       7     117 .]      21     129 ..      16     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 9.1e-43
                                       SSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHH CS
                      eIF-5_eIF-2B   7 kkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldky 83 
                                       +++r+ +p++++ +egk +tv++Nf+ ia+aLnrdp+h++k++l+e+gt+g+i e+++++++g+f++++le+++d+y
  gi|386001874|ref|YP_005920173.1|  21 TEDRFVIPPPKIFYEGK-TTVLENFAGIADALNRDPDHLMKFILQEMGTAGKI-EGQHAVFQGRFTEQNLERHIDSY 95 
                                       678**************.***********************************.9999******************* PP

                                       HHHHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                      eIF-5_eIF-2B  84 ieeyVlCkeCkspetelekeerllvlkCkaCgak 117
                                       ++eyV+C+eC++p+t+l++++r+l+lkC+aCga+
  gi|386001874|ref|YP_005920173.1|  96 VQEYVICSECHRPDTQLIRSDRVLMLKCEACGAH 129
                                       ********************************85 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.9   5.8e+03      24      37 ..      70      82 ..      68      96 .. 0.71
   2 !   44.3   0.3   4.3e-15   1.3e-11       3      62 .]     147     202 ..     146     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                                      EEET.TEEEEETT- CS
                              TRAM 24 Grtdngkvvfvpgd 37
                                      G+++ g+  +++g 
  gi|386001874|ref|YP_005920173.1| 70 GKIE-GQHAVFQGR 82
                                      7888.777777764 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 4.3e-15
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       ++G+t+e  +  ++ ++g+gi+r+d ++++fvpg+ +  Gd+V +kI+k     +++e++
  gi|386001874|ref|YP_005920173.1| 147 EEGETYELRIDSVG-RKGDGIARVD-KFMIFVPGTAK--GDIVRAKIKKISGTLAFSEVV 202
                                       58************.**********.***********..*****************9997 PP

>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.1e-07    0.0015       7      50 ..     161     206 ..     157     208 .] 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.1e-07
                           DUF4265   7 rlgegtyrldniPffakgvAlgDvvev..dedeerlafervvkesG 50 
                                       r g+g +r+d+  +f++g A+gD+v++  ++  ++laf++vv++ G
  gi|386001874|ref|YP_005920173.1| 161 RKGDGIARVDKFMIFVPGTAKGDIVRAkiKKISGTLAFSEVVERKG 206
                                       7899***********************9999999********9877 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.8e-05      0.14       4      44 ..      97     138 ..      94     155 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                                       CCT.TGGGTSSSST.-SSTTHHHHHHHHHHH--HHHCHTTSS CS
                    Cytochrom_c3_2   4 kegvkCadCHtkek.pkkdkaveeekClsCHgkleelakktk 44 
                                       +e v C++CH+ ++   ++++v + kC++C  +    ++ktk
  gi|386001874|ref|YP_005920173.1|  97 QEYVICSECHRPDTqLIRSDRVLMLKCEACGAHRPVRKRKTK 138
                                       56788******6552667779*********665555444444 PP

>> ZF-HD_dimer  ZF-HD protein dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.2   0.00041       1.2      36      53 ..     119     136 ..     102     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00041
                       ZF-HD_dimer  36 eaLkCaaCgChrnFHrre 53 
                                        +LkC aCg hr   +r+
  gi|386001874|ref|YP_005920173.1| 119 LMLKCEACGAHRPVRKRK 136
                                       579*********887776 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   1.0       1.7   5.2e+03       6      10 ..     101     105 ..     101     106 .. 0.81
   2 ?    9.9   0.1   0.00014      0.43      19      29 ..     121     131 ..     120     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                                       E-SSS CS
                          zf-RanBP   6 dCskC 10 
                                       +Cs C
  gi|386001874|ref|YP_005920173.1| 101 ICSEC 105
                                       59999 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                                       SB-TTT--BTS CS
                          zf-RanBP  19 tkCvaCqapkp 29 
                                       +kC+aC+a++p
  gi|386001874|ref|YP_005920173.1| 121 LKCEACGAHRP 131
                                       59********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1361.14
//
Query:       gi|386001875|ref|YP_005920174.1|  [L=77]
Description: hypothetical protein Mhar_1183 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 426.82
//
Query:       gi|386001876|ref|YP_005920175.1|  [L=247]
Description: F420-0:gamma-glutamyl ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-59  201.5   0.0    1.6e-59  201.2   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.047   13.8   0.1    1.6  1  Sigma70_r3   Sigma-70 region 3
       0.19   12.0   1.5          1    9.6   1.5    2.2  1  GGDEF_2      GGDEF-like domain


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.2   0.0   2.7e-63   1.6e-59       4     244 .]      12     217 ..      11     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 201.2 bits;  conditional E-value: 2.7e-63
                                       -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H........ CS
                       F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfs 80 
                                       +p ikegddla+++ e++      ++dgD+v+++++vv+kaeg+  +led +ps++Aeeia +l ++dp        
  gi|386001876|ref|YP_005920175.1|  12 LPAIKEGDDLAAMIRERFA-----VQDGDVVCIASTVVSKAEGRARRLEDYSPSPRAEEIAGRL-EKDP-------- 74 
                                       799*************999.....99**************************************.****........ PP

                                       ..........HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHH CS
                       F420_ligase  81 liLkalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeik 155
                                                 r+v++vl+e+++++ +  +l++ +       ++G++g+nagid+snv eg ++llP dp +saeei+
  gi|386001876|ref|YP_005920175.1|  75 ----------RFVQAVLEEAEEVLLDhpFLLVAT-------RFGHIGVNAGIDRSNVGEGRILLLPVDPGASAEEIR 134
                                       ..........***************999999999.......***********************************9 PP

                                       HHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-S CS
                       F420_ligase 156 kklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGs 232
                                       ++l    g+d++V++  +D++gr+++ + ++vaig++g+ alrd+rg++dl g+el++t +a++de++ +a+L++G+
  gi|386001876|ref|YP_005920175.1| 135 RRL----GRDCAVIV--TDTCGRPFRCGVAGVAIGWAGIAALRDWRGERDLEGRELEITLEAIADEVAGMANLLMGE 205
                                       998....89******..************************************************************ PP

                                       SSS---EEEEES CS
                       F420_ligase 233 adegtPvvlvrg 244
                                       a +gtP++++rg
  gi|386001876|ref|YP_005920175.1| 206 AGDGTPAAVLRG 217
                                       **********98 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.9e-06     0.047      20      48 ..      60      88 ..      45      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-06
                                      XXXHHHHHHHHTXXHHHHHHHHHHHXXXE CS
                        Sigma70_r3 20 ePtpeEiAeeLglseekVrevleaarepv 48
                                      +P +eEiA +L+ ++  V+ vle a+e++
  gi|386001876|ref|YP_005920175.1| 60 SPRAEEIAGRLEKDPRFVQAVLEEAEEVL 88
                                      799*********************99875 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.5   0.00017         1      54     104 ..      95     168 ..       8     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                           GGDEF_2  54 v................avrgdrlvlllpaedeedaeallerlarrlgg.......lsvriGiGspveglaglr 104
                                       +                 + g+  +lllp+++ ++ae++ +rl r ++        +++r+G+ +++ g+ag++
  gi|386001876|ref|YP_005920175.1|  95 LvatrfghigvnagidrSNVGEGRILLLPVDPGASAEEIRRRLGRDCAVivtdtcgRPFRCGVAGVAIGWAGIA 168
                                       2345555555555555566777889************99999999999999999999*******9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1556.72
//
Query:       gi|386001877|ref|YP_005920176.1|  [L=239]
Description: 2-phospho-L-lactate guanylyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-49  166.2   0.0    7.9e-49  165.8   0.0    1.1  1  CofC          Guanylyl transferase CofC like
    0.00053   20.4   0.0    0.00073   19.9   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8   0.0   8.8e-53   7.9e-49       2     209 ..       5     220 ..       4     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 8.8e-53
                              CofC   2 kviiPvsainsaktrlseilseeerkellkamlldvidalkrld.vlvv........sedeevleyaldelgvevvk 69 
                                       +v+iP++    ak+rls +ls  er+ l++aml dv+da+++l  v ++        +  e+ +  a +  g+ev+ 
  gi|386001877|ref|YP_005920176.1|   5 RVVIPFKLDC-AKSRLSTVLSTVERERLALAMLEDVVDAVSGLGtVTILlksplpggGVLEDKISGAGKRSGIEVLD 80 
                                       89****9877.******************************9775544422222222234555666777999**998 PP

                              CofC  70 ekekdlntavekafeeieek....eviiipsdiPlikkedvkdllelekradvviaPargGGtnllllrksalevky 142
                                          k+l++a++ ++e+ e k    +++i ++d+Pl++  d+ dl+ + +  dvviaP+rgGGtn++l+r   ++v y
  gi|386001877|ref|YP_005920176.1|  81 SP-KELDEALNLVIEAEERKgwpgDLLIAMADLPLMSPSDIADLVRTPG--DVVIAPGRGGGTNIILIRDPRFRVCY 154
                                       88.**********8877776444469***********************..************************** PP

                              CofC 143 edfsflkhleearkrglkvkiydsfylsvdinteedlgeillhGegtkakeylrklgfsvepeessa 209
                                        + sflkhl+ a + gl+v +++sf  s+di++++dl e l+hG g+ + e lr +gf+++ ++s +
  gi|386001877|ref|YP_005920176.1| 155 YGLSFLKHLRRAEELGLSVGVFESFRCSIDIDEPSDLVEALIHGRGR-TPELLRDMGFELSGKRSKS 220
                                       *********************************************96.789*********9999865 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 !   19.9   0.0   8.1e-08   0.00073      25     133 ..      34     145 ..      23     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.1e-08
                                       CHHHHHHHHHCTT.-CEEEEECSHC.........HHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEE CS
                      NTP_transf_3  25 pllervldalraagvdevvvvggde.........evlaalarlgvrvvededpgkgplaslaaalraaadadavlvl 92 
                                        +le v+da++ +  + v++  +++         ++  a +r+g++v+  +++    l  +  a ++ ++   +l++
  gi|386001877|ref|YP_005920176.1|  34 AMLEDVVDAVSGL--GTVTILLKSPlpgggvledKISGAGKRSGIEVLDSPKELDEALNLVIEAEERKGWPGDLLIA 108
                                       5999999999988..6888888886556666655666688999********999999999999999999******** PP

                                       ETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEE CS
                      NTP_transf_3  93 acDmPlltpelverllaaaaasgadvvvptyegerghpllf 133
                                       ++D+Pl++p+ ++ l++     ++dvv++  +g+  + +l+
  gi|386001877|ref|YP_005920176.1| 109 MADLPLMSPSDIADLVRT----PGDVVIAPGRGGGTNIILI 145
                                       ****************97....6667666666665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1760.72
//
Query:       gi|386001878|ref|YP_005920177.1|  [L=167]
Description: hypothetical protein Mhar_1186 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.2   0.0     0.0079   15.9   0.0    1.7  1  ACT       ACT domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.047   13.7   0.0    2.0  2  HTH_29    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.8e-07    0.0079      10      34 ..     105     129 ..     101     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.8e-07
                                       STTHHHHHHHHHHHTTSEEEEEEEE CS
                               ACT  10 rPGlLarvfgaladrgiNidsieqr 34 
                                       + GlL++v++a+a++g++i+ + + 
  gi|386001878|ref|YP_005920177.1| 105 QTGLLGEVASAVARYGLSIRQAVSD 129
                                       57*****************998875 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.2e-06     0.047      15      40 ..      44      69 ..      37      80 .. 0.88
   2 ?   -2.2   0.0      0.48   4.3e+03      15      26 ..     112     123 ..     104     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegG 40
                                      ++qiAk l+++rr v+++  + +e+G
  gi|386001878|ref|YP_005920177.1| 44 HAQIAKELDVDRRVVDTTAAAIVEDG 69
                                      79***********************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.48
                            HTH_29  15 vsqiAkllglsr 26 
                                       v+ +++++gls 
  gi|386001878|ref|YP_005920177.1| 112 VASAVARYGLSI 123
                                       677777788774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1298.17
//
Query:       gi|386001879|ref|YP_005920178.1|  [L=366]
Description: AAA ATPase family protein associated with various cellular activities [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-37  126.5   0.0    1.5e-36  125.7   0.0    1.4  1  AAA              ATPase family associated with various cellul
    1.6e-09   38.1   0.0      3e-09   37.2   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.1e-07   31.4   0.1    2.5e-07   30.2   0.0    1.5  2  TIP49            TIP49 P-loop domain
    2.1e-05   24.4   0.0    0.00013   21.8   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.5e-05   22.5   0.2    0.00016   21.4   0.2    1.6  1  AAA_lid_3        AAA+ lid domain
    7.5e-05   22.2   0.0    0.00033   20.1   0.0    2.1  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00026   20.2   0.0     0.0009   18.5   0.0    1.9  3  DUF815           Protein of unknown function (DUF815)
    0.00027   21.4   0.3     0.0071   16.7   0.2    2.6  1  AAA_16           AAA ATPase domain
    0.00034   20.4   0.0    0.00056   19.7   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
    0.00078   19.3   0.2     0.0037   17.1   0.1    2.2  2  Bac_DnaA         Bacterial dnaA  protein
    0.00092   19.2   0.1     0.0043   17.1   0.1    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00093   19.5   0.4      0.028   14.7   0.0    2.4  2  AAA_22           AAA domain
     0.0017   17.9   0.0       0.02   14.4   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
     0.0036   17.5   0.0     0.0071   16.5   0.0    1.5  1  AAA_33           AAA domain
     0.0045   16.7   0.0      0.049   13.3   0.1    2.2  1  Sigma54_activat  Sigma-54 interaction domain
     0.0049   17.1   0.0      0.021   15.0   0.0    2.2  2  AAA_28           AAA domain
     0.0071   16.1   0.0      0.012   15.3   0.0    1.5  1  AAA_24           AAA domain
     0.0098   16.4   0.0      0.022   15.3   0.0    1.7  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.034   14.5   0.0    1.5  1  RNA_helicase     RNA helicase
       0.04   13.3   0.0      0.074   12.4   0.0    1.3  1  IPT              Isopentenyl transferase
      0.052   13.5   0.0      0.094   12.7   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.06   13.0   0.2        1.8    8.2   0.0    2.8  3  Guanylate_kin    Guanylate kinase
      0.075   12.4   0.1       0.36   10.2   0.0    2.0  2  TniB             Bacterial TniB protein
      0.092   11.8   0.0       0.15   11.1   0.0    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.14   12.6   0.0       0.38   11.3   0.0    1.7  1  ABC_tran         ABC transporter
       0.16   11.9   0.0       0.29   11.0   0.0    1.4  1  Rad17            Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.0   2.2e-39   1.5e-36       1     131 [.     152     280 ..     152     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 2.2e-39
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +l+yGp GtGKT++aka+ +e++v+++ i++++l+ ++vge++++i++l ++a+++a p+i+fiDE+da+a +r  +
  gi|386001879|ref|YP_005920178.1| 152 ILFYGPSGTGKTMMAKALSRETKVPMIPIKATTLIGEFVGEGSRQIHGLYQRAEQMA-PCIIFIDELDAIALDRrYQ 227
                                       69******************************************************9.****************999 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       + +++ ++vvn+Llte+dg  ++++ v+ i+atn+++ ld+ ++ +Rf+++i+++
  gi|386001879|ref|YP_005920178.1| 228 DLRGDVSEVVNALLTEMDGIHSRKG-VCTIAATNKIEFLDESIR-SRFEEEIKFR 280
                                       999*******************877.******************.*******997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   4.3e-12     3e-09       5     105 ..     151     246 ..     149     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 4.3e-12
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                       +il+ gp+g+Gkt++akal++  +v    ++i + a++l+     e + +   + +  y++ae+    i+++DE+d 
  gi|386001879|ref|YP_005920178.1| 151 NILFYGPSGTGKTMMAKALSRETKV----PMIPIKATTLIG----EFVGEGSRQIHGLYQRAEQMApcIIFIDELDA 219
                                       89*********************98....************....888888888889999999999*********** PP

                                       ----...---------HHHHHHHHHHHH- CS
                             AAA_2  80 ihpk...essgadvSregVqrdLLqileg 105
                                       i+     +  + dvS  +V+++LL  ++g
  gi|386001879|ref|YP_005920178.1| 220 IALDrryQDLRGDVS--EVVNALLTEMDG 246
                                       **9878888899999..8*****998887 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   3.6e-10   2.5e-07      18      87 ..     113     184 ..      91     191 .. 0.83
   2 ?   -3.2   0.0       5.4   3.7e+03     276     288 ..     206     218 ..     201     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.6e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  18 eaekeeeglvGqkkareaagvivelikekklaG....ravLlaGpsgtGktalaiaiskelgedvpfvalsgse 87 
                                       ++e + + +vGq++ar+ + ++ +++ + ++ G    r +L+ GpsgtGkt +a a+s+e   +vp + ++++ 
  gi|386001879|ref|YP_005920178.1| 113 KSEVTFDDVVGQEEARRKMKIVERFLADPEIFGkwapRNILFYGPSGTGKTMMAKALSRET--KVPMIPIKATT 184
                                       445555699******************988776333368********************95..58888888775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.4
                                       XXXXXXXXXXXXX CS
                             TIP49 276 eivpGvlfiDevh 288
                                       ++ p ++fiDe  
  gi|386001879|ref|YP_005920178.1| 206 QMAPCIIFIDELD 218
                                       6789999999976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.9e-07   0.00013       5      96 ..     117     220 ..     114     279 .. 0.71
   2 ?   -3.0   0.0       7.8   5.4e+03       8      27 ..     316     335 ..     312     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-07
                            RuvB_N   5 sleeyigqekvkeklkif...ieaakk.reealdhvllyGpPGlGkttlakiiakelgvkl...kits..gPvl.ek 71 
                                       ++++ +gqe+ + k+ki+   ++  +   + a   +l+yGp G Gkt +ak +++e +v +   k+t+  g  + e 
  gi|386001879|ref|YP_005920178.1| 117 TFDDVVGQEEARRKMKIVerfLADPEIfGKWAPRNILFYGPSGTGKTMMAKALSRETKVPMipiKATTliGEFVgEG 193
                                       68999***********9722233333314568899**********************99651114443223323356 PP

                            RuvB_N  72 agdlaalltnleekd..vlfideihrl 96 
                                       ++++ +l ++ e+    ++fide+  +
  gi|386001879|ref|YP_005920178.1| 194 SRQIHGLYQRAEQMApcIIFIDELDAI 220
                                       777888887777654448888887654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.8
                            RuvB_N   8 eyigqekvkeklkifieaak 27 
                                        + g++ v++ lk++++ a 
  gi|386001879|ref|YP_005920178.1| 316 GFSGRDLVEKVLKVALHGAI 335
                                       57888888888888887764 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   2.4e-07   0.00016       2      44 ..     305     347 ..     304     348 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-07
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaa.lcreAallAlrrgikeitmedfe 44 
                                       +dl+++ ++TeG+SG Dl++ + + A + A+ +   +i+++++e
  gi|386001879|ref|YP_005920178.1| 305 LDLAAISRLTEGFSGRDLVEkVLKVALHGAIIDEV-TIEQRHLE 347
                                       69****************87466666666664444.44677766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.8e-07   0.00033       2      43 ..     118     170 ..     117     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.8e-07
                      Mg_chelatase   2 lkdvkGqeeakraleia........aaGg...HnlllvGppGsGKtmlakrlp 43 
                                       + dv+Gqeea+r ++i         + G+    n+l++Gp+G+GKtm+ak+l+
  gi|386001879|ref|YP_005920178.1| 118 FDDVVGQEEARRKMKIVerfladpeIFGKwapRNILFYGPSGTGKTMMAKALS 170
                                       6899999999999999633332333456533369****************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 !   18.5   0.0   1.3e-06    0.0009      14     129 ..     105     230 ..      97     293 .. 0.70
   2 ?   -1.5   0.0       1.6   1.1e+03     181     216 ..     268     303 ..     244     321 .. 0.74
   3 ?   -2.8   0.0       4.1   2.8e+03     118     137 ..     317     336 ..     311     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                            DUF815  14 galepveevdevklddLvgidkqkealventeqfle.....gl.pannvLLwGarGtGKSslvkallneyaeeg..L 82 
                                       ++ e+ +  +ev++dd+vg ++ +++++  +e+fl+     g+ + +n+L++G  GtGK  + kal +e++     +
  gi|386001879|ref|YP_005920178.1| 105 KKAEAAKIKSEVTFDDVVGQEEARRKMK-IVERFLAdpeifGKwAPRNILFYGPSGTGKTMMAKALSRETKVPMipI 180
                                       4567777788999********9999875.466666523333331458*******************99887665443 PP

                            DUF815  83 rlievekedlkelpklvellr...erperfilfvDDLsFeeeeeeyksLk 129
                                       +   +  e + e ++ ++ l    e+   +i+f+D L   + +++y+ L+
  gi|386001879|ref|YP_005920178.1| 181 KATTLIGEFVGEGSRQIHGLYqraEQMAPCIIFIDELDAIALDRRYQDLR 230
                                       33333333333333333333222244456899999999989999998887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                            DUF815 181 sLsdRFGlwlgFykldqeeYleiveklakklglele 216
                                       s+  RF   + F  ++ ee l+i+ + +++l +e+ 
  gi|386001879|ref|YP_005920178.1| 268 SIRSRFEEEIKFRLPNAEERLSILARNVETLPVEVG 303
                                       566788888888888888888888888877666655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.1
                            DUF815 118 FeeeeeeyksLksvLeGsle 137
                                       F  ++   k Lk++L G++ 
  gi|386001879|ref|YP_005920178.1| 317 FSGRDLVEKVLKVALHGAII 336
                                       77778888999999999985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2     1e-05    0.0071      24      49 ..     149     174 ..     134     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellrale 49 
                                       p+++l++G+sG+GK+ ++++l r+ +
  gi|386001879|ref|YP_005920178.1| 149 PRNILFYGPSGTGKTMMAKALSRETK 174
                                       799***************99998544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.1e-07   0.00056       7      70 ..     106     172 ..     102     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.1e-07
                         IstB_IS21   7 rlrlaklpaqktledidfraarsldkrkvkeL.atlsfiek..kenivllGpsGvGKshlaialgve 70 
                                       + ++ak++ + t++d+  +++   + ++v++  a  +   k    ni++ GpsG+GK+ +a al++e
  gi|386001879|ref|YP_005920178.1| 106 KAEAAKIKSEVTFDDVVGQEEARRKMKIVERFlADPEIFGKwaPRNILFYGPSGTGKTMMAKALSRE 172
                                       567899999999999999999888888888551555555541157*******************986 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.9   1.3e+03     166     185 ..      94     113 ..      74     136 .. 0.81
   2 !   17.1   0.1   5.4e-06    0.0037      33     187 ..     146     303 ..     112     333 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                                       --HHHHHHHHHHHHHHTT-- CS
                          Bac_DnaA 166 pdletrlailkkkieaekle 185
                                          etr+ + +kk+ea+k++
  gi|386001879|ref|YP_005920178.1|  94 VGSETRIVVERKKAEAAKIK 113
                                       56799999999999988876 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.4e-06
                                       .S--..EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GG CS
                          Bac_DnaA  33 kynP..lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiq 107
                                       k+ P  +++yg++G Gkt + ka++ e++      + + l +e F+ e  + ++       + +  +  ++ iD++ 
  gi|386001879|ref|YP_005920178.1| 146 KWAPrnILFYGPSGTGKTMMAKALSRETKVPMIPIKATTLIGE-FVGEGSRQIHG---LYQRAEQMAPCIIFIDELD 218
                                       455544899*********9999988877666655555555543.44444444333...2222233344466667666 PP

                                       GGTT-HHHHH...HHHHHHHHHHTTT-EEE....EEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHH CS
                          Bac_DnaA 108 flagkektqe...elfhtfnalleegkqvv....lssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkk 177
                                        +a   + q+   ++  ++nall e   +     +++  + +++e l++ +rsrfe  +  +   p+ e rl+il +
  gi|386001879|ref|YP_005920178.1| 219 AIALDRRYQDlrgDVSEVVNALLTEMDGIHsrkgVCTIAATNKIEFLDESIRSRFEEEI--KFRLPNAEERLSILAR 293
                                       666555544322256666666665544432222277778899**************976..556699999******* PP

                                       HHHHTT---- CS
                          Bac_DnaA 178 kieaeklevp 187
                                       ++e+  +ev 
  gi|386001879|ref|YP_005920178.1| 294 NVETLPVEVG 303
                                       **98777765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   6.2e-06    0.0043       1      76 [.     151     219 ..     151     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       ++l  Gp+GtgK+++a+ l++ ++ ++  +  t       l+g+     g+ s++   l++ a+   ++i+++DE++
  gi|386001879|ref|YP_005920178.1| 151 NILFYGPSGTGKTMMAKALSRETKVPMIPIKATT------LIGEFV---GEGSRQIHGLYQRAEqmAPCIIFIDELD 218
                                       57999***************98876655544443......333333...2223344555555555788888888887 PP

                                       G CS
                             AAA_5  76 r 76 
                                        
  gi|386001879|ref|YP_005920178.1| 219 A 219
                                       5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.1e-05     0.028       7      29 ..     151     173 ..     148     185 .. 0.83
   2 ?    2.4   0.1      0.25   1.7e+02      84     111 ..     202     239 ..     190     263 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                        ++ +G+sGtGKT+ ++ l ++ 
  gi|386001879|ref|YP_005920178.1| 151 NILFYGPSGTGKTMMAKALSRET 173
                                       6899**************99876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.25
                            AAA_22  84 qalraravielliiDEaqhlr...s........eealee 111
                                       q +++ a + ++ iDE + +    +         e+++ 
  gi|386001879|ref|YP_005920178.1| 202 QRAEQMA-PCIIFIDELDAIAldrRyqdlrgdvSEVVNA 239
                                       4444444.59********985544133444445444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.9e-05      0.02      34      58 ..     150     174 ..     148     186 .. 0.86
   2 ?    0.8   0.0      0.42   2.9e+02     100     115 ..     208     223 ..     194     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       +++l++Gp+GtGKt+++k l ++ +
  gi|386001879|ref|YP_005920178.1| 150 RNILFYGPSGTGKTMMAKALSRETK 174
                                       689**************99888765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.42
                             AAA_7 100 kklvvFvDDlnmpake 115
                                         +++F+D+l+  a +
  gi|386001879|ref|YP_005920178.1| 208 APCIIFIDELDAIALD 223
                                       569*******988877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-05    0.0071       2      47 ..     152     225 ..     152     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..........................d 47 
                                       +l+ G++G+GK+  a+ l ++++  ++ +   tl+   +g++ +++                           +
  gi|386001879|ref|YP_005920178.1| 152 ILFYGPSGTGKTMMAKALSRETKvpMIPIKATTLIGEFVGEGSRQIHglyqraeqmapciifideldaialdrR 225
                                       6899***************9999999999999999999997777665545555555555555555555555554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   7.1e-05     0.049      23      47 ..     150     174 ..     142     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                        ++l  G sGtGK+++a+a+ +++k
  gi|386001879|ref|YP_005920178.1| 150 RNILFYGPSGTGKTMMAKALSRETK 174
                                       689***************9977654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.5   4.5e+03      53      81 ..      50      75 ..      27      85 .. 0.60
   2 !   15.0   0.0   3.1e-05     0.021       1      36 [.     151     187 ..     151     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.5
                            AAA_28 53 lafaervleeqleeeaaa.aankvlfcDrg 81
                                        f++     ++e+       ++++++Dr 
  gi|386001879|ref|YP_005920178.1| 50 RLFERY----AREQWYGElVRPGCYLFDRR 75
                                      333332....22222222244677777775 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.1e-05
                            AAA_28   1 kivitGgestGKTtlleaLaar.gypvvpEaareile 36 
                                       +i + G+++tGKT +++aL+++ ++p++p  a++++ 
  gi|386001879|ref|YP_005920178.1| 151 NILFYGPSGTGKTMMAKALSREtKVPMIPIKATTLIG 187
                                       5899****************76589988766666654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.012       3      23 ..     150     172 ..     148     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel..g 23 
                                       ++il yGpsg+GKT++ak l  +
  gi|386001879|ref|YP_005920178.1| 150 RNILFYGPSGTGKTMMAKALsrE 172
                                       689***************99553 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.2e-05     0.022       1      24 [.     152     175 ..     152     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf 24 
                                       Il  G++G+GKt +ak+Ls+++++
  gi|386001879|ref|YP_005920178.1| 152 ILFYGPSGTGKTMMAKALSRETKV 175
                                       8999****************9765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.9e-05     0.034       1      22 [.     152     173 ..     152     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.9e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakal 22 
                                       i++yGpsg+GK+++ak L+++ 
  gi|386001879|ref|YP_005920178.1| 152 ILFYGPSGTGKTMMAKALSRET 173
                                       789**************99876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.074       5      31 ..     153     179 ..     150     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l +G+ +tGKt +a +l++et +p+i 
  gi|386001879|ref|YP_005920178.1| 153 LFYGPSGTGKTMMAKALSRETKVPMIP 179
                                       78**********************985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014     0.094      19      50 ..     149     182 ..     124     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..---- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkS 50 
                                        + il++G+ G+GKT+++++l ++ +v   ++k 
  gi|386001879|ref|YP_005920178.1| 149 PRNILFYGPSGTGKTMMAKALSRETKVPmiPIKA 182
                                       3459*******************99987455554 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.5   1.1e+03     141     179 ..      98     138 ..      84     140 .. 0.68
   2 ?    8.2   0.0    0.0026       1.8       3      27 ..     150     174 ..     148     185 .. 0.74
   3 ?    0.9   0.0      0.46   3.2e+02     109     145 ..     203     239 ..     197     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHGGGC..SSEEEEESSHHHHHHHHHHHH CS
                     Guanylate_kin 141 eklakrlaaaekelqeye..fdvvivnddleealkklkell 179
                                         + ++ ++ae++  ++e  fd v+ +++    +k ++++l
  gi|386001879|ref|YP_005920178.1|  98 TRIVVERKKAEAAKIKSEvtFDDVVGQEEARRKMKIVERFL 138
                                       44444444554444444445**9999999999999999887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                                       SEEEEESTTTSSHHHHHHHHHHHST CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselp 27 
                                       r +   gpsg+Gk ++ kaL +e +
  gi|386001879|ref|YP_005920178.1| 150 RNILFYGPSGTGKTMMAKALSRETK 174
                                       778899*************966554 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.46
                                       HHTTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHH CS
                     Guanylate_kin 109 rkaelspiivFikppslkelqrrlksrgkeqeeklak 145
                                       r+ +++p i+Fi      +l+rr +    + +e+++ 
  gi|386001879|ref|YP_005920178.1| 203 RAEQMAPCIIFIDELDAIALDRRYQDLRGDVSEVVNA 239
                                       567899******9999999999988777777776665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00052      0.36      12      58 ..     123     172 ..     114     183 .. 0.74
   2 ?   -0.9   0.1       1.3     9e+02     117     180 ..     206     274 ..     194     281 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00052
                              TniB  12 gyprakeilerLeeLleypk...rkrmpnlllvGdsnnGKtmivekFarl 58 
                                       g ++a++ ++  e+ l+ p+   +  ++n+l++G+s +GKtm+++  +r+
  gi|386001879|ref|YP_005920178.1| 123 GQEEARRKMKIVERFLADPEifgKWAPRNILFYGPSGTGKTMMAKALSRE 172
                                       5555666666666666666544356679***************9987766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                              TniB 117 elkvrvLiiDEihnllagsark..qreflnalksLgnelk..ipivlvGteealralr.tDpqlasRFe 180
                                       ++ + ++ iDE++ +   ++ +  +  + +++  L  e++   +  +v t +a++ ++  D+ + sRFe
  gi|386001879|ref|YP_005920178.1| 206 QMAPCIIFIDELDAIALDRRYQdlRGDVSEVVNALLTEMDgiHSRKGVCTIAATNKIEfLDESIRSRFE 274
                                       566667777777766433222111223333333333333321233344455555555423666666666 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00022      0.15     111     136 ..     147     171 ..     142     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                         Parvo_NS1 111 lgkrntvwfyGpantGktnlaeaIak 136
                                       + +rn ++fyGp  tGkt++a+a+ +
  gi|386001879|ref|YP_005920178.1| 147 WAPRN-ILFYGPSGTGKTMMAKALSR 171
                                       56677.89***************965 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00055      0.38      14      36 ..     152     174 ..     147     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00055
                                       EEEEESTTSSHHHHHHHHTTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllk 36 
                                       + + G++G+GK+ ++k+l++++k
  gi|386001879|ref|YP_005920178.1| 152 ILFYGPSGTGKTMMAKALSRETK 174
                                       6789***************9987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00042      0.29      26      74 ..     129     178 ..     125     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                             Rad17  26 kkieevkewlk.advLesrkkriLLisGPsGCgkstvvkvLskelgiklr 74 
                                       +k++ v+++l   ++  +   r +L  GPsG gk+ + k Ls+e  + ++
  gi|386001879|ref|YP_005920178.1| 129 RKMKIVERFLAdPEIFGKWAPRNILFYGPSGTGKTMMAKALSRETKVPMI 178
                                       677777777641455555556667899****************9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.69u 0.37s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 1987.74
//
Query:       gi|386001880|ref|YP_005920179.1|  [L=204]
Description: hypothetical protein Mhar_1189 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1280.79
//
Query:       gi|386001881|ref|YP_005920180.1|  [L=128]
Description: hypothetical protein Mhar_1190 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   13.4   0.0       0.12   13.0   0.0    1.2  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-06      0.12      10      89 ..      10      88 ..       8     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-06
                                      HHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHHHHCCHH CS
                              ASCH 10 livsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleewrevheefye 87
                                      +i++G+Kt + r+ + +++kv++d+ +    + ++  +  + +t+ +  ++ ++t e+ ++eg  s ee +e+ ++  +
  gi|386001881|ref|YP_005920180.1| 10 KILDGTKTMTRRSVKGRHYKVDQDYAVQ--PHRNKPSMFRIAITGKKLERLGDITPEDVKLEGYgSKEEFIEAWRSVNG 86
                                      69**********9999999999***999..9988999999999999999***************988888888777755 PP

                                      HH CS
                              ASCH 88 ee 89
                                      ++
  gi|386001881|ref|YP_005920180.1| 87 GY 88
                                      54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 857.22
//
Query:       gi|386001882|ref|YP_005920181.1|  [L=585]
Description: hypothetical protein Mhar_1191 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3712.95
//
Query:       gi|386001883|ref|YP_005920182.1|  [L=144]
Description: hypothetical protein Mhar_1192 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-15   55.3   0.0    9.1e-15   55.0   0.0    1.1  1  DUF4352   Domain of unknown function (DUF4352)
      0.007   16.3   0.1     0.0089   15.9   0.1    1.1  1  DUF5067   Domain of unknown function (DUF5067)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0     1e-18   9.1e-15      29     114 ..      48     132 ..      22     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1e-18
                                       -CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-B.EEESCCCCTTB--EEEE-TT-EEEEEEEEEES CS
                           DUF4352  29 eylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeyd.adlsasskaddlflgtlnpGkkvtGklvFdvp 104
                                       ++ q+++g+ +++vd+ ++N+g+++++v++++f+ + +d   y+ a  + + + d+l  +t++ G  v+Gk+v++vp
  gi|386001883|ref|YP_005920182.1|  48 PW-QAKPGYVYMVVDIELENHGYSKFDVSPYNFDAYVND-VLYTcAHATFDPSIDTLPIKTIQDGDVVSGKVVYEVP 122
                                       33.359******************************888.5555344444444444********************* PP

                                       TT-CGEEEEE CS
                           DUF4352 105 kgkkkleLey 114
                                       kg+ ++ +ey
  gi|386001883|ref|YP_005920182.1| 123 KGTREYYIEY 132
                                       *****99999 PP

>> DUF5067  Domain of unknown function (DUF5067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     1e-06    0.0089      41     117 ..      54     126 ..      33     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                                       CTCEEEEEEEEEE-SS-TTBCHHHHHHHEEEEEEEEE--B---S--TTHHHCCC.CSEE-TTSEEEEEEEEE-TTTT CS
                           DUF5067  41 gkpvlvvyyeftNnsdeeispssavsvylkAyQngveLetailaddekdkldnl.dkeikpgktvevviaYeLqdtd 116
                                       g   +vv+ e++N++ ++ +  s +++  +Ay n+v    a  ++d+   +d+l  k+i+ g+ v+++++Ye+++ +
  gi|386001883|ref|YP_005920182.1|  54 GYVYMVVDIELENHGYSKFD-VSPYNF--DAYVNDVLYTCAHATFDPS--IDTLpIKTIQDGDVVSGKVVYEVPKGT 125
                                       666789**************.889999..******9999999999999..655438*****************9987 PP

                                       S CS
                           DUF5067 117 s 117
                                        
  gi|386001883|ref|YP_005920182.1| 126 R 126
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 929.20
//
Query:       gi|386001884|ref|YP_005920183.1|  [L=131]
Description: hypothetical protein Mhar_1193 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.34   10.7   0.0    1.6  2  DUF2606   Protein of unknown function (DUF2606)


Domain annotation for each model (and alignments):
>> DUF2606  Protein of unknown function (DUF2606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0     0.063   1.1e+03      19      31 ..      10      22 ..       4      81 .. 0.59
   2 ?   10.7   0.0   1.9e-05      0.34      48      81 ..      69     102 ..      36     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.063
                           DUF2606 19 illsvlvlivmss 31
                                      ill  l+ ++m +
  gi|386001884|ref|YP_005920183.1| 10 ILLGCLLTCGMVA 22
                                      5555555555543 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 1.9e-05
                           DUF2606  48 vkdkkklPvkdvevilvkdessdeePskeiGiil 81 
                                         +k ++ + d  v lvk  s+d+ P keiG+ +
  gi|386001884|ref|YP_005920183.1|  69 TSEKYGKELGDNFVRLVKTFSPDDPPGKEIGEGI 102
                                       456777778888899****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 960.94
//
Query:       gi|386001885|ref|YP_005920184.1|  [L=217]
Description: hypothetical protein Mhar_1194 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1381.10
//
Query:       gi|386001886|ref|YP_005920185.1|  [L=291]
Description: Site-specific integrase/recombinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-25   89.5   0.0    3.2e-25   88.9   0.0    1.3  1  Phage_integrase  Phage integrase family
     0.0046   17.4   1.5     0.0068   16.9   0.1    2.0  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   3.6e-29   3.2e-25       3     171 ..     113     278 ..     111     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 3.6e-29
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                       ++e++v ++++ + +   i++ ++l++l+   lR +El +L+ +dldl++++i++  re+Kg+++ +  l++e +e 
  gi|386001886|ref|YP_005920185.1| 113 FDENDVLNIFSVCSN---IKHLAMLKTLFYGCLRSGELSKLEDNDLDLDKRTIRL--RETKGGRDDIALLNDECVET 184
                                       688999999999999...*************************************..******************** PP

                                       HHHHHHHH.CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHH.HHHHHHHHHHHCTSHHHHHHH CS
                   Phage_integrase  80 lkellska.leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtl.RhsfataLleagvdlrvvqkl 154
                                       l+ +l+ + + e e++  lf   + +   r ++ ++f  ++++agi+kp   H + Rhs at ++ +g d+r +++l
  gi|386001886|ref|YP_005920185.1| 185 LRIYLNIRpKIEVEGKYPLFFTDNFNLWDRGDIHRMFMGYKKKAGIKKPGAVHVFsRHSPATIMVAKGCDIRIIKEL 261
                                       ********7666677777899888999999************************99********************* PP

                                       HT-SSCCHHHHHHCCCH CS
                   Phage_integrase 155 lGHssisttqiYthvak 171
                                       l H++i+tt +Y+hva 
  gi|386001886|ref|YP_005920185.1| 262 LRHKDIRTTLRYAHVAN 278
                                       **************975 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   7.6e-07    0.0068       2      76 ..      22      92 ..      21      98 .. 0.93
   2 ?   -1.6   0.2      0.44     4e+03       4      20 ..     266     282 ..     264     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.6e-07
                   Phage_int_SAM_4  2 lerfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffyk 76
                                       e++ ++l+ +g++++Ti  Y   +  f+++ +   p+e  ++ + +Y   L+ ++ +s+s ++n   al+ +++
  gi|386001886|ref|YP_005920185.1| 22 VENYKRFLTNQGYRYQTISLYSGRVGKFIEYSR---PNEPCTKKADDYRDLLL-DQGASKSHVNNTVFALKKYFE 92
                                      5788999************************99...99999999******999.************999999886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.44
                   Phage_int_SAM_4   4 rfrealrlaglserTik 20 
                                       + r +lr+a+ +++T +
  gi|386001886|ref|YP_005920185.1| 266 DIRTTLRYAHVANETKR 282
                                       56789999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2071.86
//
Query:       gi|386001887|ref|YP_005920186.1|  [L=64]
Description: hypothetical protein Mhar_1196 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   62.4   0.3    2.7e-17   62.2   0.3    1.1  1  UPF0175   Uncharacterised protein family (UPF0175)


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.3   1.5e-21   2.7e-17      22      74 ..       1      53 [.       1      54 [. 0.96

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.5e-21
                           UPF0175 22 ialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeeleeDle 74
                                      +a+A kl+e+grlS+g Aa+lag++r  fl +La++gi+ ++++eeel ++ +
  gi|386001887|ref|YP_005920186.1|  1 MAAAAKLFEMGRLSSGAAARLAGIPRTLFLLKLADYGIDAFDLTEEELSKEAQ 53
                                      589**********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 417.11
//
Query:       gi|386001888|ref|YP_005920187.1|  [L=68]
Description: hypothetical protein Mhar_1197 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-09   36.9   0.0      4e-09   36.7   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   2.2e-13     4e-09      16      63 ..      15      62 ..       7      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.2e-13
                   HicB_lk_antitox 16 vvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssiee 63
                                        PdlpG+  ag+t ee  +  + aielhlegl ed+  ipep++ ++
  gi|386001888|ref|YP_005920187.1| 15 YCPDLPGVVAAGKTGEETAELMRKAIELHLEGLKEDNLPIPEPTTTAR 62
                                      57*****************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 551.28
//
Query:       gi|386001889|ref|YP_005920188.1|  [L=975]
Description: Alpha glucan phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-30  105.7   0.2    1.6e-29  102.6   0.0    2.5  2  DUF3417        Protein of unknown function (DUF3417)
      3e-24   85.3   0.0      4e-18   65.1   0.0    3.8  3  Phosphorylase  Carbohydrate phosphorylase
      8e-18   65.3   0.1    1.3e-17   64.6   0.1    1.3  1  Peptidase_C14  Caspase domain
    0.00071   18.9   0.0     0.0015   17.8   0.0    1.4  1  Peptidase_C25  Peptidase family C25
      0.004   16.7   0.4      0.013   15.1   0.4    1.8  1  Peptidase_C13  Peptidase C13 family
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.39   10.7   0.0    1.8  1  Raptor_N       Raptor N-terminal CASPase like domain
       0.16   11.8   0.0       0.26   11.2   0.0    1.2  1  Myc_N          Myc amino-terminal region


Domain annotation for each model (and alignments):
>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   6.1e-33   1.6e-29       1     109 []     270     380 ..     270     380 .. 0.97
   2 ?   -0.4   0.2      0.62   1.6e+03      23      53 ..     700     731 ..     691     739 .. 0.75

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 6.1e-33
                           DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksl.dpelweevghnPvklLeevsqerleelaedeeflarleavveefee 76 
                                       +p+++++L +La+nlwwsw++e reLF  l  +++w++ ghnPvk+++e++   ++ ++ d++fl+ ++av+++fe+
  gi|386001889|ref|YP_005920188.1| 270 IPDRIRNLGNLAYNLWWSWHPEGRELFIMLgGRAAWSRNGHNPVKMMHELDDGVFKLASMDPRFLRYYDAVMAKFER 346
                                       79****************************44789****************************************** PP

                           DUF3417  77 yleek.twfqkkaeeekkeaiAYFsaEfGlhesL 109
                                        ++    wf+++ +++k+ +iAYFsaE+Glh++L
  gi|386001889|ref|YP_005920188.1| 347 GMDPAsGWFKTNVADPKDCKIAYFSAEYGLHHAL 380
                                       ***9989************************997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.62
                           DUF3417  23 areLFksl.dpelweevghnPvklLeevsqer 53 
                                       + eL +++ d+ lw++ ++  +klL+e++++ 
  gi|386001889|ref|YP_005920188.1| 700 IWELMDEIpDAVLWKHHRRMKLKLLNEITERA 731
                                       45556666567899999999999999998765 PP

>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   1.3e-05     0.033      24      73 ..     386     436 ..     383     448 .. 0.88
   2 !   65.1   0.0   1.6e-21     4e-18     218     578 ..     529     881 ..     521     887 .. 0.81
   3 ?    1.5   0.0     0.027        68     680     710 ..     936     967 ..     927     968 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEEBTTC CS
                     Phosphorylase  24 GLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepdeWlk 73 
                                       GLG LA  +l  ++ l++p vG+g  Y  G   Q+i +dg+q  + ++  +
  gi|386001889|ref|YP_005920188.1| 386 GLGFLAGDYLKECSDLGVPIVGVGFMYPEGYLLQRItSDGWQAGACERLER 436
                                       9***********************************889***987776555 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 1.6e-21
                                       EEEEEESSTTTTHHHHHHHHHHHCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHSHHHHHHHHHHHHH CS
                     Phosphorylase 218 vaiqlnDtHPalaipelmriLvdeeglewdeaweitkktfaytnhtvlpealekwpvellekllprhleiieeiner 294
                                        +i+ln+  Pa+ai e +r  ++ +g + +ea e++kkt+ +t ht++p   +k++ +l++k +   ++++    e+
  gi|386001889|ref|YP_005920188.1| 529 SIIHLNEGQPAFAILERLRERIE-TGSRREEAEEVVKKTTLFTTHTLVPANQDKFSFQLMDKYFRTYIRLLGISCED 604
                                       579****************9965.58899**********************************99888877543344 PP

                                       HHHHHHHHSTT-HHHHHHHSSEETSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGG...EEE---- CS
                     Phosphorylase 295 fleevekklpedeeklerlsiieeekkvrmanlaivgshsvngvaalhsellkkevlkdfyelypek...fnnktnG 368
                                       f +   +   +d       s         m  +a+ +s   n v++ h e++ + + ++f + yp+    + n+tnG
  gi|386001889|ref|YP_005920188.1| 605 FFKLGIDP--RD-----PAS------GFDMTAFALRMSAYRNCVSKRHQEIVID-MWRNFWSDYPNDelpIDNVTNG 667
                                       43332222..22.....333......455999*******************976.66777777776434489***** PP

                                       B-CHHHCCCTSHHH.HHHHHHHCSSGGCCSGG..GGGGGGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                     Phosphorylase 369 itprrwlllanpel.aelitekigeewvkdle..eLkkLekladdkefleelaeikqenKerlaelikeke...... 436
                                       i    w+    ++l +++ ++ +g++w+++ +  ++ +L +   d+ + ++ +++k +  ++++e  +++       
  gi|386001889|ref|YP_005920188.1| 668 IHVPTWID---RDLgNKIFNKYLGRGWLEEHDdpRIWELMDEIPDAVLWKHHRRMKLKLLNEITERARKNWyscnep 741
                                       ******96...45515677899*****99876336999**********99999999987777777666643222223 PP

                                       ........SS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHH CS
                     Phosphorylase 437 ........gvevdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiikl 505
                                               gv +dp+ l    v  +  Y R +L +++ +++ ++i ++p   + p  +if+gka p  ++ k +++ 
  gi|386001889|ref|YP_005920188.1| 742 npktitpfGVMLDPNVLTIGFVHQFASYNRATL-IFRDLERLRKILTDP---YRPVQIIFAGKAHPDDQYGKILLQQ 814
                                       3333334455588888888889*********99.788888889999888...99*********************** PP

                                       HHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTC CS
                     Phosphorylase 506 insvaevvnndpevkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGa 578
                                       i +va+    +++ +++  ++f+e+y+  +a+ ++ + dl  +  + ++eA GT+ m   lnG   i+ + G 
  gi|386001889|ref|YP_005920188.1| 815 ILNVAS----NKDFGGR--IAFVEDYDQYIAQYMLRGVDLWLNNPIPSMEACGTSGMMASLNGVPQISIFGGW 881
                                       **9986....5666775..89******************************************9888776665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHCGG.GGBHHHHHHHHHHHTTT CS
                     Phosphorylase 680 ewakksilniaksg.kFssDrtikeYaeeiWk 710
                                       +w + +  ++ ++g +Fss r +keYae+ +k
  gi|386001889|ref|YP_005920188.1| 936 SWVNVMKEATMNTGsHFSSKRMVKEYAEKFYK 967
                                       5666666555555537***********99875 PP

>> Peptidase_C14  Caspase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.1     5e-21   1.3e-17       1     236 [.       5     226 ..       5     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 5e-21
                                       EEEEEEECSTTSSTCC.-STTHHHHHHHHHHHH.HHHTT.EEEEEEEGGEES-CHHHHHHHHHHHHCHSGGTTESEE CS
                     Peptidase_C14   1 kkAliIginnYpgtka.eLrGcanDaermaklL.vkrlg.FevenililtddptgknirkalkwlvksadhspgDsl 74 
                                       ++A++I  +++++ +  +L+ ++nD++++ ++L  k +g F+++      ++++  +i k+++++ k+a   ++D +
  gi|386001889|ref|YP_005920188.1|   5 RYAVLIASSQFQDSNLhNLKCPVNDVKDFNEVLiSKDYGnFSETL---PLENCDNFEIMKEMEKVFKKAS--KYDLV 76 
                                       68**********55548****************444566466666...999***************9999..9**** PP

                                       EEEEESEEET.........EEECTTC....SSEEEHHHHHHTTSTTTHGGGTTS-EEEEEESESSSBCBEEEEEEES CS
                     Peptidase_C14  75 vvhysGHGtrvpae.....civpvdv....nsliqdddirdlfggdklpslagkpktiiidaCrgglldkgiekdts 142
                                       +++ysGHG + ++          +d     ++ i++++i  +++ + + +      +ii+d+C      +g++ d+ 
  gi|386001889|ref|YP_005920188.1|  77 LIYYSGHGKQ-DRAgklhlATANTDIsllkSTSIPIENIKGFIDDSYVNN-----VIIILDCCY-----SGLAGDEL 142
                                       *********7.333677663334443666677888888877775444444.....479******.....66667777 PP

                                       -SSSHCCCHCHHHHHHCSHHCEEECTTTSEEEEESSSTTBSCEEETTTEE.HHHHHHHHHH.....HHHTTTSBHHH CS
                     Peptidase_C14 143 ptnkfeedssskekkpekqslsklpseadvlllsgcqddqtSadgsengs.aftqalqkvl.....eekggkislke 213
                                       ++++             +q +s ++ +++ ++l++++  q S+++ ++++ +ft+ l++ +     ++++g+i++  
  gi|386001889|ref|YP_005920188.1| 143 SRGS-----------VDEQLTSLFKETSGTYILTSSTSIQQSWESESENNgIFTKHLVEGIrswgaANNNGDITMDG 208
                                       7777...........6677799999999****************9999988**********7777777777777778 PP

                                       HHHHHHHHHCCTTTCTTSBEEEE CS
                     Peptidase_C14 214 llnkvrkrlkslkkkngykqrPg 236
                                       + + +++ + +l     +kq+P 
  gi|386001889|ref|YP_005920188.1| 209 IYSYIQEQM-KL----DRKQIPM 226
                                       888888888.44....4888885 PP

>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.7e-07    0.0015     238     356 ..      74     221 ..      46     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.7e-07
                                       --SEEEEES-EETTEETTTTE..EHHHHHT---TT...............--EEEEEESSSTT-TTSSS-..-HHHH CS
                     Peptidase_C25 238 GvlfvnytGHGsetawadesl..stndisaltntn...............klpiaitaaCltgafdeetkr.sfgek 296
                                          ++ y+GHG +++ +  +l   ++dis l+ t+               +  i+i ++C++g   +e +r s+ e+
  gi|386001889|ref|YP_005920188.1|  74 DLVLIYYSGHGKQDRAGKLHLatANTDISLLKSTSipienikgfiddsyvNNVIIILDCCYSGLAGDELSRgSVDEQ 150
                                       567899**********8888888888999999999999999999999899999************999988****** PP

                                       HH..HSTTSSEEEEEEESS---SS--SHHHHHHHHHHHHHHH.........T-S-SS-HHHHHHH...... CS
                     Peptidase_C25 297 lv..lnangGavayigatrlgysgvndrlsraffealfadaar......tlGealllaknelletgl...a 356
                                       l+    +  G + ++++t +  s  ++  ++++f + + +  r      + G++++ + ++++++     +
  gi|386001889|ref|YP_005920188.1| 151 LTslFKETSGTYILTSSTSIQQSWESESENNGIFTKHLVEGIRswgaanNNGDITMDGIYSYIQEQMkldR 221
                                       *9878889999999999999888888887777777777777766888888899999999999976334443 PP

>> Peptidase_C13  Peptidase C13 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4     5e-06     0.013      99     231 ..      65     216 ..      53     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                                       ----.--TTSEEEEEEES-EETT.....EEE-S.......SSSEEEHHHHHHHHHHHHHCT--SEEEEEEESTTGG. CS
                     Peptidase_C13  99 kvlk.sgkeDnvfiyltdhGapg.....vlevp.......eeddleakdLaeaLkkmhakkkykklviyleaceSg. 161
                                       kv k   k D v+iy++ hG ++      l+ +       +++++      e +k   ++   ++++i+l+ c+Sg 
  gi|386001889|ref|YP_005920188.1|  65 KVFKkASKYDLVLIYYSGHGKQDragklHLATAntdisllKSTSIPI----ENIKGFIDDSYVNNVIIILDCCYSGl 137
                                       555414678*************9999663433333122223333333....445555555555677*********75 PP

                                       ........GGTTT....S-TTSSEEEEESS-TTS--BEECE.CTTTTCEEEEHHHHHHHHHHHHS-TTT-BHHHHHH CS
                     Peptidase_C13 162 ........smfee....llkdinvyaltAanadessfgtycedeedgtylgdlfsvawledsddedlsketlekqfe 226
                                               s+ e+    +++   +y+lt++ + ++s+     ++e++  +++ ++    +  ++++    t++  ++
  gi|386001889|ref|YP_005920188.1| 138 agdelsrgSVDEQltslFKETSGTYILTSSTSIQQSWES---ESENNGIFTKHLVEGIRSWGAANNNGDITMDGIYS 211
                                       544444435544422223456679999999999999988...55555556555443333333334444566666666 PP

                                       HHHHH CS
                     Peptidase_C13 227 lvkkk 231
                                       +++++
  gi|386001889|ref|YP_005920188.1| 212 YIQEQ 216
                                       66665 PP

>> Raptor_N  Raptor N-terminal CASPase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.39      68     142 ..      57     137 ..      51     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                          Raptor_N  68 vedvkklcqslrrnakdervlfHYnGhgvprptengeiwvfdksytqyipls..laelqewlg....spsiyifDCs 138
                                       +e +k++ + +++ +k + vl++Y Ghg +    + ++   + + + ++++s  ++++   ++      +i i+DC+
  gi|386001889|ref|YP_005920188.1|  57 FEIMKEMEKVFKKASKYDLVLIYYSGHGKQDRAGKLHLATANTDISLLKSTSipIENIKGFIDdsyvNNVIIILDCC 133
                                       56677777778889999*************8999999999999988776655115677666652111568999***9 PP

                          Raptor_N 139 nAgl 142
                                        +gl
  gi|386001889|ref|YP_005920188.1| 134 YSGL 137
                                       9986 PP

>> Myc_N  Myc amino-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.26      99     154 ..     119     174 ..     105     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                             Myc_N  99 edaflks.iiiqDCmWSGfSaaeKlekvvsekLaslqaarkegaaakassasrersg 154
                                       +d+++++ iii DC +SG+   e     v e+L+sl ++ + + + + ss+s ++s 
  gi|386001889|ref|YP_005920188.1| 119 DDSYVNNvIIILDCCYSGLAGDELSRGSVDEQLTSLFKETSGTYILT-SSTSIQQSW 174
                                       566655517889*********999999********999888877733.333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (975 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 6064.37
//
Query:       gi|386001890|ref|YP_005920189.1|  [L=317]
Description: tyrosyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-56  191.0   0.0    3.3e-56  190.8   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
    0.00015   20.8   0.0      0.015   14.3   0.0    2.3  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.0   3.6e-60   3.3e-56       3     292 ..      27     309 ..      24     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 3.6e-60
                                       HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakg 79 
                                       +++ r y+G +P+gk+H G+++  +kl++lq ag +v++l+aDlhA+++++   +++++r+ +++        +a g
  gi|386001890|ref|YP_005920189.1|  27 KERPRGYVGYEPSGKVHMGHMLTANKLIDLQAAGFQVVVLLADLHAYLNEKG--TLEEVRATADYNRDC---FIALG 98 
                                       678899********************************************99..9*****999999999...***** PP

                                       CHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH.CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEE CS
                      tRNA-synt_1b  80 ldpekaevvlqsewlehlelaellrdlgklgslnrmlqfks.vkkrleegegislgeftYplLqaaDilllkadlvp 155
                                       ldpek+e+v++++++ + e+ + + ++++ ++lnr  +  + v +++ + +   +++++Ypl+qa Di++l++dl +
  gi|386001890|ref|YP_005920189.1|  99 LDPEKTEFVYGTDYQLEPEYVKNVLKMARNTTLNRARRSMDeVGRNMDN-P--HVSQMIYPLMQAVDIAALRVDLAV 172
                                       **********************99999999******8755538888888.4..8*********************** PP

                                       EEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC. CS
                      tRNA-synt_1b 156 gGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde. 231
                                       gG DQ+++  l+r+ +++++ +    +p++l +p+++gl+G+ KmS+S+gn +I  dd+ e+ +kki +a++  ++ 
  gi|386001890|ref|YP_005920189.1| 173 GGIDQRKIHMLAREEMPKLGLQ----PPVCLHTPIISGLNGG-KMSSSKGN-YISVDDSAEDLEKKIISAYCPAKDi 243
                                       *******************999....****************.********.*********************9999 PP

                                       .SHHHHHHHHHTHHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 232 .evekllklktelsn....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                        ++   +  k+ + +     +i r e+++g  ++ ++e l+a++  +++h+ dlkk + e ln++l
  gi|386001890|ref|YP_005920189.1| 244 eGNPVTELFKYHILPrlgaVTIRRPEKFGGDVTYDKYEALEADYLAGKMHPLDLKKSAVEHLNAIL 309
                                       88888888888888888889*******************************************998 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0     0.002        18      28      42 ..      33      47 ..       8      55 .. 0.76
   2 !   14.3   0.0   1.6e-06     0.015     261     307 ..     191     237 ..     163     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.002
                      tRNA-synt_1f 28 esGispSGliHiGnl 42
                                        G+ pSG++H+G +
  gi|386001890|ref|YP_005920189.1| 33 YVGYEPSGKVHMGHM 47
                                      569**********86 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.6e-06
                      tRNA-synt_1f 261 lggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrfl 307
                                       lg ++P+ +   +i+  +g+kmssSkGn+++++d  e +e+++++ +
  gi|386001890|ref|YP_005920189.1| 191 LGLQPPVCLHTPIISGLNGGKMSSSKGNYISVDDSAEDLEKKIISAY 237
                                       78899999999999988999***************999999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1930.78
//
Query:       gi|386001891|ref|YP_005920190.1|  [L=84]
Description: hypothetical protein Mhar_1200 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 535.69
//
Query:       gi|386001892|ref|YP_005920191.1|  [L=56]
Description: hypothetical protein Mhar_1201 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.004   16.5   3.9     0.0041   16.5   3.9    1.0  1  UbiA             UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.16   11.5   3.5       0.19   11.3   3.5    1.0  1  DUF1189          Protein of unknown function (DUF1189)
       0.35   11.3   7.6       0.38   11.2   7.6    1.1  1  PhoR             Phosphate regulon sensor protein PhoR
       0.37    9.5   2.8       0.36    9.6   2.8    1.0  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.9     9e-07    0.0041      61     107 ..       5      50 ..       2      56 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9e-07
                              UbiA  61 sGrispkealifaivllilgllllalllnpltallgllalllyvvYt 107
                                       sGri  +e +i+ +vl+++ ++ll + +  +++ l+l+a ++y+vY 
  gi|386001892|ref|YP_005920191.1|   5 SGRIRSREQKIILLVLAVVIVALL-WNFLGVILRLILFAAVVYLVYR 50 
                                       8***********************.6666667777777777999997 PP

>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.5   4.2e-05      0.19     154     192 ..      15      53 ..       7      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
                           DUF1189 154 lkiilvlilivlflvsllltlidalilaliglilarilk 192
                                       +++++++++iv++l+++l++++ ++++a++++++ r+l+
  gi|386001892|ref|YP_005920191.1|  15 IILLVLAVVIVALLWNFLGVILRLILFAAVVYLVYRLLQ 53 
                                       556788899999********************9988875 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.6   8.5e-05      0.38       6      46 ..      15      55 ..      10      56 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.5e-05
                              PhoR  6 llrlallllaallvgllvgalaallllalllllawhlyqll 46
                                      +++l+l++++++l++ ++g +  l+l+a++++l+++l q +
  gi|386001892|ref|YP_005920191.1| 15 IILLVLAVVIVALLWNFLGVILRLILFAAVVYLVYRLLQSW 55
                                      4556666666669********************99998865 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8   7.9e-05      0.36     389     438 ..      16      56 .]       3      56 .] 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.9e-05
                           DUF2207 389 gliilglilillallllvlllvfllilllillliaiivlllfsrllgrrt 438
                                       +l++l+++++  all     ++fl+++l ++l++a+++l++  rll+ +t
  gi|386001892|ref|YP_005920191.1|  16 ILLVLAVVIV--ALL-----WNFLGVILRLILFAAVVYLVY--RLLQSWT 56 
                                       2223332222..222.....888888888888888888887..5888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 379.46
//
Query:       gi|386001893|ref|YP_005920192.1|  [L=222]
Description: Molybdopterin-guanine dinucleotide biosynthesis protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-28   98.8   4.2      6e-28   98.2   4.2    1.2  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0072   16.1   0.0      0.011   15.5   0.0    1.2  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   4.2   6.7e-32     6e-28       3     156 ..       2     155 ..       1     161 [. 0.89

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 6.7e-32
                                       EEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTC..TS-EEE-TTSS-SHHHHHH CS
                      NTP_transf_3   3 iLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevlaalarl..gvrvvededpgkgplasla 77 
                                       iLAGG+++R g++Ka+l+  g++++e +++ ++++ ++++vvv++d + l++l++l  g+r+++d+ +g gp+a+la
  gi|386001893|ref|YP_005920192.1|   2 ILAGGAGRRIGSEKAFLEPFGRTMIEATVEVVEEV-AADLVVVARDFDQLSRLRGLvpGARLASDPVQGFGPVAGLA 77 
                                       9**********************************.78999999995556678777669****************** PP

                                       HHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHH..CTHTTHHH CS
                      NTP_transf_3  78 aalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaal..lgdqgarr 152
                                       a+++aa   d++l + cD+P+l+p ++e l++ a+  g+d++vp+ + ++ +pl +++r+ + ++a+  + ++g+rr
  gi|386001893|ref|YP_005920192.1|  78 AGMEAA-AGDYALAVGCDLPFLNPRVLELLFDLAE--GHDAAVPEGKSGFLEPLHAVYRAGPMARACreALAAGERR 151
                                       ****99.8************************986..8999*************99888887777774344689999 PP

                                       CHHH CS
                      NTP_transf_3 153 llrr 156
                                       + + 
  gi|386001893|ref|YP_005920192.1| 152 IRAP 155
                                       8775 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 !   15.5   0.0   1.2e-06     0.011       5      62 ..       2      56 ..       1      68 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-06
                                      EECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHH CS
                              IspD  5 ipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeql 62
                                      i A G G+R+++  +K+fle  g+t++e tv+++ +  a d +vv+ + d+ ++ + l
  gi|386001893|ref|YP_005920192.1|  2 ILAGGAGRRIGS--EKAFLEPFGRTMIEATVEVVEE-VAADLVVVARDFDQLSRLRGL 56
                                      7899*****976..69*****************998.677888888777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1405.66
//
Query:       gi|386001894|ref|YP_005920193.1|  [L=197]
Description: hypothetical protein Mhar_1203 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-63  213.2   0.0    2.9e-63  213.0   0.0    1.0  1  DUF2121   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.075   12.8   0.1       0.13   12.0   0.1    1.4  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> DUF2121  Uncharacterized protein conserved in archaea (DUF2121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0   0.0   3.3e-67   2.9e-63       1     196 []       1     187 [.       1     187 [. 0.99

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 3.3e-67
                           DUF2121   1 MslviayigkkgaviagDkReiafrgdeeerekLEeeLYsGeiktdeeLkkkaeelgvkikitddreKvrkvgdvlv 77 
                                       Mslv++++gkk+a++agDkR+iaf+g++ee   LEeeLY+Gei+++e+L++++eelg k++i+d+reKv+++g+vl+
  gi|386001894|ref|YP_005920193.1|   1 MSLVVGFAGKKRAIVAGDKRSIAFFGRAEE---LEEELYGGEIRSREDLQRRCEELGSKVAIADGREKVWDRGGVLA 74 
                                       9***************************99...******************************************** PP

                           DUF2121  78 GEVkeisaketkrrRiYatkgayaivelegsevtkkkkgesslivfGnkvtkeiankllkkevkkklslkeiekllk 154
                                       GEV+eisa++++rrRiY+++g+y +ve++g++++++k+g+s+li++Gn++t+++a k l +           e+ ++
  gi|386001894|ref|YP_005920193.1|  75 GEVTEISAERERRRRIYLVPGGYLLVEVDGKRAEISKRGASTLIILGNRFTRDFAFKRLGSGRP------PDEASIR 145
                                       ***********************************************************99998......88999** PP

                           DUF2121 155 eileevaektasvskeydllkkkkkldkkeaalekaikkDie 196
                                       +++ee+ ++tasvs +y++l++++ ++++eaal +a+++D+e
  gi|386001894|ref|YP_005920193.1| 146 ALFEEAGRATASVSPDYTVLTSSSIHRDPEAALLRALREDCE 187
                                       ****************************************96 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.5e-05      0.13      31      64 .]      82     112 ..      72     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                       E-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  31 ipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64 
                                        ++ +R++i+  +G+y lVe+   d ++++I  r
  gi|386001894|ref|YP_005920193.1|  82 AERERRRRIYLVPGGYLLVEV---DGKRAEISKR 112
                                       45667899*************...6689999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1378.87
//
Query:       gi|386001895|ref|YP_005920194.1|  [L=294]
Description: Bifunctional protein FolD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-62  208.4   3.3    4.6e-62  208.1   3.3    1.1  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    9.4e-34  116.2   0.0    1.4e-33  115.6   0.0    1.3  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   3.3   5.1e-66   4.6e-62       1     159 [.     131     288 ..     131     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 5.1e-66
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeit 77 
                                       hp+n+g l++g e l+pctpkg++  l++ g++legk++v+vG+sn+vgkpla+++l++natV+vch  tkdla++t
  gi|386001895|ref|YP_005920194.1| 131 HPMNMGSLLAGAEGLVPCTPKGIIWALERLGVDLEGKEAVIVGHSNVVGKPLAAMMLNRNATVSVCHVFTKDLASHT 207
                                       89*************************************************************************** PP

                                       CCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHH CS
                     THF_DHG_CYH_C  78 readivvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntle 154
                                       r+a+++vva+G+p+li+++mv++ga v DvGinrv +g++vGDv+f+ev  va+a+tPvpgGVGp+Tv +l+++t +
  gi|386001895|ref|YP_005920194.1| 208 RKAEVLVVAAGVPGLIRGDMVRPGAYVFDVGINRV-GGRTVGDVQFDEVIGVAAAVTPVPGGVGPLTVSILMSQTAK 283
                                       ***********************************.***************************************** PP

                                       HHHCH CS
                     THF_DHG_CYH_C 155 aakrq 159
                                       aa+++
  gi|386001895|ref|YP_005920194.1| 284 AAEMK 288
                                       *9875 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.0   1.6e-37   1.4e-33       1     116 []      13     128 ..      13     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.6e-37
                                       E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkl 77 
                                       ++dGkala+e+++e+k +v++l + g +p+La+i vgd+pas++Yvr k+ ac++vGi+se ++lpe +  +e+l++
  gi|386001895|ref|YP_005920194.1|  13 IIDGKALASEVEAETKVRVDELAALGGRPGLATIIVGDNPASAMYVRIKHSACDRVGIRSENVNLPEGAGIDEILET 89 
                                       79*********************9989************************************************** PP

                                       HHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  78 ieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       i+ lne+++v+Gil+qlPlp+++d  +++ ai+p+KDVD
  gi|386001895|ref|YP_005920194.1|  90 IRGLNEREDVSGILLQLPLPRELDPARAMAAIDPAKDVD 128
                                       **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1890.05
//
Query:       gi|386001896|ref|YP_005920195.1|  [L=414]
Description: Serine hydroxymethyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-171  570.8   0.1   1.4e-171  570.5   0.1    1.1  1  SHMT             Serine hydroxymethyltransferase
    0.00022   20.6   0.1     0.0017   17.7   0.1    2.0  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00068   18.9   0.0     0.0011   18.2   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.5   0.1  2.3e-175  1.4e-171       1     399 []       4     380 ..       4     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 570.5 bits;  conditional E-value: 2.3e-175
                                       HHHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHH CS
                              SHMT   1 leesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrake 77 
                                       l+++dpe+a++i++e erq++++elia+enfts+av+ea   v+tnkyaeGyPGkryyGGc fvd++e+la+dr++ 
  gi|386001896|ref|YP_005920195.1|   4 LDDVDPEIASAIRDELERQRNGLELIAAENFTSPAVMEAYNNVMTNKYAEGYPGKRYYGGCTFVDVAENLARDRCRA 80 
                                       5789************************************************************************* PP

                                       HCT-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTS CS
                              SHMT  78 lfkldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketg 154
                                       lf+++    +vnvqp+sGsqan+avy all+pgd+++g+ l +GGhl+hG++v++     s+k++++v+y+v++et+
  gi|386001896|ref|YP_005920195.1|  81 LFGAE----HVNVQPHSGSQANMAVYLALLKPGDTVMGMALDHGGHLSHGSPVNF-----SGKIYNVVHYGVNRETE 148
                                       *****....**********************************************.....***************** PP

                                       SB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESS CS
                              SHMT 155 lidydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttth 231
                                       ++dy e+   ake  Pk+iv+G+say+r+id+a lre+adevgayl++d+ahiaGlvaagv+psP+++advvtttth
  gi|386001896|ref|YP_005920195.1| 149 MLDYGEMLDIAKECSPKMIVTGASAYPRTIDFAALREVADEVGAYLMADIAHIAGLVAAGVHPSPIPHADVVTTTTH 225
                                       ***************************************************************************** PP

                                       STT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHH CS
                              SHMT 232 ktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlkn 308
                                       ktlrGprgg++++r              +e++  i+ avfPg+qGGPl+hviaakava+keal pefkvyq+q+++n
  gi|386001896|ref|YP_005920195.1| 226 KTLRGPRGGVVMCR--------------QEIAPAIDRAVFPGVQGGPLMHVIAAKAVAFKEALAPEFKVYQEQIVRN 288
                                       **************..............7899********************************************* PP

                                       HHHHHHHHHHTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHH CS
                              SHMT 309 akalaealkekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpalts 384
                                       a ++a +l e+ ++lvsgGtdnhl+lv+l +   +Gk+ae++le+  it nknt+P+d  s+++tsG+r+Gtpa+t+
  gi|386001896|ref|YP_005920195.1| 289 AAVIARTLLERDFELVSGGTDNHLMLVKLLKMPYSGKDAEAALERGGITLNKNTIPFDpTSPFITSGIRIGTPAVTT 365
                                       ***************************************************************************** PP

                                       TT--HHHHHHHHHHH CS
                              SHMT 385 rgfkeedlekvakfi 399
                                       rg+ke ++ ++a++i
  gi|386001896|ref|YP_005920195.1| 366 RGMKEPEMVQIAEMI 380
                                       ************987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.8e-07    0.0017      37     234 ..      74     279 ..      42     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-07
                                       HHHHHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HH CS
                   Beta_elim_lyase  37 Ledavaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdle 112
                                         d++++lfg+e++ +  ++G +An   + +ll++g+ v+     h+     g ++ ++g   + +    + + ++ 
  gi|386001896|ref|YP_005920195.1|  74 ARDRCRALFGAEHVnVQPHSGSQANMAVYLALLKPGDTVMGMALDHGGHLSHGSPVNFSGKIYNVVHYGVNRETEML 150
                                       4577888*****8725788***************************************9986666654443444444 PP

                                       HHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTS CS
                   Beta_elim_lyase 113 kleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyv 189
                                       +  ++++  ++    +k+i++          +      ++++++a++ g  l+ D A +a   ++ g++++ +  ++
  gi|386001896|ref|YP_005920195.1| 151 DYGEMLDIAKE--CSPKMIVTGASAY-----PR-TIDFAALREVADEVGAYLMADIAHIAGL-VAAGVHPSPI-PHA 217
                                       44455555334..6778876655444.....33.34567888899*************9975.5889999887.689 PP

                                       SEEEEESSSTT--SS-EEEEE-HH.....................HHHHHHHHHHHHT---S CS
                   Beta_elim_lyase 190 DsvtmslkKdllanvGgvlafrddel.................edylaerveqrkylggglr 234
                                       D+vt    K l  + Ggv++ r++ +                 +   a++v+++++l+ +++
  gi|386001896|ref|YP_005920195.1| 218 DVVTTTTHKTLRGPRGGVVMCRQEIApaidravfpgvqggplmHVIAAKAVAFKEALAPEFK 279
                                       ***********************955777777777777777743333466666666666555 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.9e-07    0.0011      55     355 ..      80     367 ..      31     370 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-07
                                       HHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES...S-THHHHHHHHTTSEEEEEEBEET.TT CS
                     Aminotran_1_2  55 kflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp...tyasyknilrlsggevvryplyse.ed 127
                                        ++g       ++  +v+  sG++a+ ++  +llk  pgd +   ++    + s+   ++ sg     +++    e+
  gi|386001896|ref|YP_005920195.1|  80 ALFG------AEHV-NVQPHSGSQANMAVYLALLK--PGDTVMGMALdhgGHLSHGSPVNFSGKIYNVVHYGVNrET 147
                                       4455......4445.9******************9..****986555111566666677777655444444422244 PP

                                       TEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHH CS
                     Aminotran_1_2 128 fhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatr 204
                                         ld  ++++    a+e ++  k+i++     P    ++ + l+++   a++ +++l+ D a+ ++   +     ++
  gi|386001896|ref|YP_005920195.1| 148 EMLDYGEMLD---IAKECSP--KMIVTGASAYPR--TIDFAALREV---ADEVGAYLMADIAHIAGLVAA----GVH 210
                                       4555555555...4445556..888887666664..5566778888...*****************9982....335 PP

                                       GGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 205 anveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqr 280
                                       +   ++ + +++++  K +   G R G + + ++++ ++ +++ p+     l+  ++a+a+  ++  + e++  +++
  gi|386001896|ref|YP_005920195.1| 211 PSPIPHAD-VVTTTTHKTL--RGPRGGVVMCRQEIAPAIDRAVFPGVQgGPLMHVIAAKAVAFKEALAPEFKVYQEQ 284
                                       55555555.6666666654..45555*******************999555556666777777777788******** PP

                                       HHHHHHHHHHHHHHSTEEEEC..CSCSSEEEEEETHH....CHHHHHHHHHHTCTEEEEEGGGGTS......TTEEE CS
                     Aminotran_1_2 281 lqkrrkelrdeLaelglkvla..sqsgmflltdlsae....takelskkLleevgvyvtpgtsftv......pgrlR 345
                                       + +++ ++   L e +++ ++   ++++ l+ +l+      +    +++ le+ g+ + ++t++        ++ +R
  gi|386001896|ref|YP_005920195.1| 285 IVRNAAVIARTLLERDFELVSggTDNHLMLVKLLKMPysgkD----AEAALERGGITLNKNTIPFDptspfiTSGIR 357
                                       ********9999999666655114566666666666644421....2223333344444433333233333366688 PP

                                       EECTTS-HHH CS
                     Aminotran_1_2 346 itvAglteee 355
                                       i  +++t+  
  gi|386001896|ref|YP_005920195.1| 358 IGTPAVTTRG 367
                                       8887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2409.76
//
Query:       gi|386001897|ref|YP_005920196.1|  [L=151]
Description: hypothetical protein Mhar_1206 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-26   92.7   0.1    4.3e-26   90.8   0.1    1.8  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.2e-15   57.2   0.8    2.2e-15   56.3   0.8    1.4  1  PUA       PUA domain
     0.0058   16.4   0.0      0.012   15.4   0.0    1.6  1  PUA_3     PUA-like domain
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.036   14.3   0.0    1.4  1  UPF0113   UPF0113 PUA domain
      0.078   12.9   0.0       0.16   11.9   0.0    1.4  2  DUF2944   Protein of unknown function (DUF2946)
        0.1   13.1   0.0       0.15   12.5   0.0    1.3  1  Tex_YqgF  Tex protein YqgF-like domain
       0.18   12.0   0.0       0.31   11.3   0.0    1.4  1  NUMOD4    NUMOD4 motif


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.1   1.7e-29   4.3e-26       2      71 .]       4      73 ..       3      73 .. 0.98
   2 ?   -0.8   0.0      0.67   1.7e+03      42      55 ..     109     121 ..      96     126 .. 0.62

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.7e-29
                            TGT_C2  2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                      r r+iad qFG+g+g+aLf+ed t+ +s+tgr+r+++ dger+at+ra+dg+ltLs  Ga++l + lppP
  gi|386001897|ref|YP_005920196.1|  4 RARMIADLQFGRGCGRALFGEDTTFMLSNTGRLRHLHRDGERIATVRARDGLLTLSALGAKLLYDFLPPP 73
                                      78******************************************************************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.67
                            TGT_C2  42 erlatlraqdgrlt 55 
                                       e ++ +  +dgrl+
  gi|386001897|ref|YP_005920196.1| 109 EEVLVV-DEDGRLI 121
                                       444443.6677665 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.8   8.8e-19   2.2e-15       2      71 ..      76     145 ..      75     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 8.8e-19
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                       rvv+ + ++  +++g   +a+ vv+v+ ++++g++V +vdedg+l+a G+a +  ee++ i +g++v ++
  gi|386001897|ref|YP_005920196.1|  76 RVVIRRDVAPYVAKGGTAFAKHVVSVDPEVRAGEEVLVVDEDGRLIATGRAVLAPEEMMAIRRGPAVLVR 145
                                       8*****************************************************************9876 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.8e-06     0.012      19      49 ..      94     124 ..      92     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.8e-06
                             PUA_3  19 fsneiasvegeledGdvVdvfsekgkflGtG 49 
                                       f++ + sv+ e+++G+ V v++e+g+ ++tG
  gi|386001897|ref|YP_005920196.1|  94 FAKHVVSVDPEVRAGEEVLVVDEDGRLIATG 124
                                       788999**********************998 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.4e-05     0.036      15      52 ..      90     127 ..      77     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                           UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGkir 52 
                                       G   + +++++++++v+ ++ v+V++e+g++++ G++ 
  gi|386001897|ref|YP_005920196.1|  90 GGTAFAKHVVSVDPEVRAGEEVLVVDEDGRLIATGRAV 127
                                       556789*****************************984 PP

>> DUF2944  Protein of unknown function (DUF2946)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   3.8e+03     111     136 ..      26      53 ..       7      64 .. 0.65
   2 ?   11.9   0.0   6.1e-05      0.16      75     127 ..      75     126 ..      68     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                           DUF2944 111 saalldeeGrlyl..eaeaelallddrd 136
                                       ++++l+++Grl    +  +++a ++ rd
  gi|386001897|ref|YP_005920196.1|  26 TTFMLSNTGRLRHlhRDGERIATVRARD 53 
                                       5566667777644335556666666666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.1e-05
                           DUF2944  75 qrvyveLeaaPyvvrleeeaaelkltthtgaelaevsaalldeeGrlyleaea 127
                                       qrv ++ ++aPyv++  ++ a++ ++ + +  +   + +++de+Grl+++ +a
  gi|386001897|ref|YP_005920196.1|  75 QRVVIRRDVAPYVAKGGTAFAKHVVSVDPEVRA-GEEVLVVDEDGRLIATGRA 126
                                       9****************9999988877777666.6778899*****9985443 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.9e-05      0.15       1      30 [.      96     125 ..      96     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                       .-EEEEE--STT-EEEEEE-TTS-EEEEEE CS
                          Tex_YqgF   1 kvvlglDPgyrtGcKlavvdetgkvletav 30 
                                       k v+++DP +r G  + vvde+g++++t  
  gi|386001897|ref|YP_005920196.1|  96 KHVVSVDPEVRAGEEVLVVDEDGRLIATGR 125
                                       5799********************998754 PP

>> NUMOD4  NUMOD4 motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.31      10      34 ..      25      47 ..      19      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                            NUMOD4 10 egkYevSnyGRvrslkrkvtkgriL 34
                                      +  ++ Sn+GR+r+l+r+   +ri 
  gi|386001897|ref|YP_005920196.1| 25 DTTFMLSNTGRLRHLHRD--GERIA 47
                                      557899**********99..66775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 950.67
//
Query:       gi|386001898|ref|YP_005920197.1|  [L=433]
Description: Cysteine desulfurase NifS [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-83  281.3   0.0    1.2e-83  281.1   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    2.3e-09   37.0   0.0      3e-09   36.6   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0036   16.7   0.2     0.0058   16.0   0.2    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.1   0.0   2.1e-87   1.2e-83       1     371 []      49     413 ..      49     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 2.1e-87
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       iy+d aAtt+  +eV++a++  + +  +n+ +s+h+ g  a +a+eeare+va+li+ae   e++ftsG+te+ nl+
  gi|386001898|ref|YP_005920197.1|  49 IYMDHAATTPMAPEVIEAMNAAFVEIFGNA-SSLHQPGLAARAALEEARERVARLIGAEA-GEVYFTSGGTESDNLA 123
                                       8*****************************.****************************6.**************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHH.HHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelak.rtgakvkvipldeegeldldelekllnektklvaithvsnvt 152
                                       ++++a +  ++g++i++t++eh a l p+++l++ ++g++v+++p+++eg++++++le++++e+t l++i+h++n++
  gi|386001898|ref|YP_005920197.1| 124 IRGAALAnRDRGRHIITTSIEHPAVLEPCRKLEEeEEGFEVTHLPVNREGLVEVEALEAAIREDTILISIMHANNEI 200
                                       ****9999************************86268**************************************** PP

                                       TEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STT CS
                       Aminotran_5 153 GtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllgge 229
                                       Gtiqp++e ++la ++g+++++Da+q+vg+ip +v++lgvD+l++s+hKl+gP+G+G+ly+rk  +  +ep+ +gg+
  gi|386001898|ref|YP_005920197.1| 201 GTIQPIAEAAELASDRGIVFHTDAVQTVGKIPAKVDDLGVDLLSISSHKLHGPKGVGALYIRK--KTPIEPIVFGGG 275
                                       ***************************************************************..99********** PP

                                       SEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHH.HCH..HHHHHHHHHHHHHHHHHHHHCTSTTEEEES.- CS
                       Aminotran_5 230 mveevsleettfaeapskfeaGTpnvagiiglgaaleyl.eei..gleaiekhekelaeyllerlkslpgvrlygpd 303
                                              +e++       +++GT+nv+gi+gl+aa e+  +++  ++ +i    ++la+y+le    ++++ ++g +
  gi|386001898|ref|YP_005920197.1| 276 -------HERG-------MRSGTENVPGIVGLAAASELAgRNLegEMVRISGMRDRLADYVLE---RVEETWVNG-S 334
                                       .......9999.......899*****************9765511455555556666666555...566667777.6 PP

                                       B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.............-EEEEE--TTS CS
                       Aminotran_5 304 kaerrasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.............gtvRaSlyiyn 363
                                       +++r ++ +++ f +++ e +   Ld +gIav++G++c+           a +             g++R+ l++ n
  gi|386001898|ref|YP_005920197.1| 335 RTKRLPNNLNLGFSYIEGEALLLRLDAKGIAVSTGSACSskktV------ASHvltaiglrpqeahGSLRITLGREN 405
                                       88*************************************55441......3334444556688888*********** PP

                                       -HHHHHHH CS
                       Aminotran_5 364 teeevdrl 371
                                       t eevdr+
  gi|386001898|ref|YP_005920197.1| 406 TDEEVDRV 413
                                       ******96 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   5.1e-13     3e-09      33     198 ..      91     249 ..      56     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.1e-13
                                       HHHHHHHHHHHHTT-SEEE..EES-HHHHHHHHH..HHH-..-TTEEEEEETT-HHHHSST.THHHHC.C--EEEEE CS
                   Beta_elim_lyase  33 tvnrLedavaelfgkeaal..fvpqGtaAnsill..kill..qrgeevivtepahihfdet.gaiael.agvklrdl 101
                                         ++  ++va+l+g+ea+   f+  Gt ++++++  ++l+   rg  +i t+  h    e  + ++e  +g +++ l
  gi|386001898|ref|YP_005920197.1|  91 ALEEARERVARLIGAEAGEvyFTSGGTESDNLAIrgAALAnrDRGRHIITTSIEHPAVLEPcRKLEEEeEGFEVTHL 167
                                       566788999*******753348888*********98677755788999999999987777559998888******** PP

                                       -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHH CS
                   Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaaksl 178
                                       + +++G +++e+leaai+e+      + lis+  +nn     + +++ ++e+a++a ++gi +h D+      ++++
  gi|386001898|ref|YP_005920197.1| 168 PVNREGLVEVEALEAAIRED------TILISIMHANNE----IGTIQPIAEAAELASDRGIVFHTDA------VQTV 228
                                       *9999**************4......56*********5....66888899***************96......5566 PP

                                       TS-CHHHHTT.SSEEEEESSS CS
                   Beta_elim_lyase 179 geivkemfsy.vDsvtmslkK 198
                                       g i++++ +  vD +++s  K
  gi|386001898|ref|YP_005920197.1| 229 GKIPAKVDDLgVDLLSISSHK 249
                                       666666663336777776666 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   9.6e-07    0.0058      40     150 ..     109     229 ..      90     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.6e-07
                                       EEEEESSHHHHHHHHHHHTTTT...TT-EEEEESSS-THHHHHHHHT.....T-EEEEE-B-TTTSSB-GGGCGGG- CS
                   DegT_DnrJ_EryC1  40 haiavssGtaAlhlaLralgvg...pgdeVIvpsltFvatanavlel.....gakpvfvDvdpdtynidpaaieaai 108
                                        +  +s Gt++  la+r   +    +g+ +I++s+   a  ++ ++l     g ++  + v+     ++++a+eaai
  gi|386001898|ref|YP_005920197.1| 109 EVYFTSGGTESDNLAIRGAALAnrdRGRHIITTSIEHPAVLEPCRKLeeeeeGFEVTHLPVN-REGLVEVEALEAAI 184
                                       45567889999999999844444459******************998333334455555555.6789********** PP

                                       -TTEEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 109 tertkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                        e t  I + h+    G +  +++  ++a++ g+++  Da + +G
  gi|386001898|ref|YP_005920197.1| 185 REDTILISIMHAnneIGTIQPIAEAAELASDRGIVFHTDAVQTVG 229
                                       ****99999888333577778888899***************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2853.01
//
Query:       gi|386001899|ref|YP_005920198.1|  [L=1003]
Description: hypothetical protein Mhar_1209 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-08   31.7   4.8    6.4e-07   29.0   4.8    2.3  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0013   18.6  20.7     0.0013   18.6  20.7    3.7  3  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.027   14.9   0.0       0.18   12.2   0.0    2.3  2  AAA_16        AAA ATPase domain
      0.083   12.2   0.2       0.15   11.4   0.2    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
       0.14   11.6   7.5        1.4    8.3   0.1    3.3  3  HNOBA         Heme NO binding associated
       0.18   12.1   0.7         24    5.3   0.1    2.7  2  DUF2811       Protein of unknown function (DUF2811)
       0.42   10.4  22.1       0.56   10.0  13.5    4.0  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
       0.49   10.5  15.4        1.3    9.1   2.5    4.1  4  ApoLp-III     Apolipophorin-III precursor (apoLp-III)
        1.6    9.3   9.1         23    5.5   7.8    3.5  2  ABC_tran      ABC transporter
        1.8    8.5  13.4         15    5.5  11.6    3.0  2  Wtap          WTAP/Mum2p family
        1.9    7.7   8.7         14    4.9   7.9    2.2  2  DUF4407       Domain of unknown function (DUF4407)
        2.3    8.5  23.3        5.4    7.3   0.7    4.7  3  DUF5082       Domain of unknown function (DUF5082)
        5.3    7.1   6.8        2.4    8.2   1.5    3.1  3  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   4.8   4.6e-10   6.4e-07      18     206 ..     344     951 ..     340     965 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.6e-10
                                       EEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE....S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                             SMC_N  18 vilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk....l 90 
                                        +l f+ ++ ai+G+ G GKs l+d +  +LG++s+k +   + ++     k+++s+   e +i+++  +++    l
  gi|386001899|ref|YP_005920198.1| 344 CQLSFNFELVAIIGNKGMGKSALTDML-ALLGNTSSKDFSFLNKQKFRDP-KNNKSL-DFEAQIIWESGEESlarcL 417
                                       5677888899***************99.89********999999998776.444444.4466777666555567787 PP

                                       SSSSSCEEEEEEEETTSE.EEEEETTEEE-H.HHHHHHHHCTT-STT.............................. CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxx.............................. RF
                             SMC_N  91 kiekeevsisrrvkrkge.seykingkevtk.kevsellesagiske.............................. 135
                                        ++ +e +++  ++  ++  e+  n++ +++ ++  + l+++ +s                                
  gi|386001899|ref|YP_005920198.1| 418 AEDVPEHEVELVKYIPQKfFEMITNENAIEEgSKFDKELKKVIFSHVdepnklgcasldelieyrteeikdvinsmr 494
                                       77888888888777766647888888888888999*****999999899**************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001899|ref|YP_005920198.1| 495 selkdinekiikleyltsedhkqdlgkqletkkqelsvhdssrpteidkpivspsieeafkdlrseietltsnitea 571
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001899|ref|YP_005920198.1| 572 ksqlnrsvkilasiskikgkienlrrmydnfviesseefdkigvkmesiarldinesliqqyereysnkqsqseeli 648
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001899|ref|YP_005920198.1| 649 drlennkkvseeklyslqstldeanrsyqhyldeitnwdqlreviigspdqhesieyyknalnessttlvddlskak 725
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001899|ref|YP_005920198.1| 726 lernskveaifleikklvniyidlykpvqdfidnhelidryqlnfnvsiiqqgfidaflshinqsakgtfhgtqdgr 802
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|386001899|ref|YP_005920198.1| 803 dklkeiidkydfnsisnvmqfiaeiqesieidkrdsinrvkiesqlrksfkkqdlyeflyslkylepryilqlggke 879
                                       ***************************************************************************** PP

                                       ..CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH.HHHHHHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ..lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv.kkvaellkeksknaQfivislreemlekad 206
                                         +LS Ge+ ++   L+f +   k  +  ++D  + +LD++ v + +a  + e++ + Q+++i+++ ++   +d
  gi|386001899|ref|YP_005920198.1| 880 llQLSPGERGVLL--LIFYLLVDKDDCPLIIDQPEDNLDNQSVyELIAPCISEARLRRQVFIITHNPNLAVVCD 951
                                       *********9865..67778888899999***********998467899*****************99876654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.3       1.5     2e+03     176     183 ..     238     245 ..      97     338 .. 0.62
   2 !   18.6  20.7   9.2e-07    0.0013      14     269 ..     341     593 ..     340     613 .. 0.56
   3 ?   -1.5  25.7       1.2   1.6e+03      83     368 ..     633     946 ..     584     947 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                            AAA_15 176 leeslkke 183
                                        +e + k 
  gi|386001899|ref|YP_005920198.1| 238 TIEAFDKA 245
                                       22222222 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 9.2e-07
                            AAA_15  14 lkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvefaekekak 90 
                                       +++++++++ el  +iG  + GKS ++++l l+ n+++k   ++ +++k+++++  ++++s d++ ++    ++ ++
  gi|386001899|ref|YP_005920198.1| 341 FENCQLSFNFELVAIIGNKGMGKSALTDMLALLGNTSSK---DFSFLNKQKFRDP-KNNKSLDFEAQIIW--ESGEE 411
                                       78999****99************************9944...4556666666666.33333333333333..23455 PP

                            AAA_15  91 eyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeekle....kekeelk 163
                                       +  ++l+++  + +         +l+k+i +k ++  +ne+  e  s ++k+ kk +++  +e+++    + +e ++
  gi|386001899|ref|YP_005920198.1| 412 SLARCLAEDVPEHEV--------ELVKYIPQKFFEMITNENAIEEGSKFDKELKKVIFSHVDEPNKlgcaSLDELIE 480
                                       555666666555555........555555555555555555555555555544444444444444400115566777 PP

                            AAA_15 164 idkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd...edsekkssllgklkekileealqekl... 234
                                       +  e++k++i+ +++ l       + ++++iikl++  ++ + +d   ++++kk++l     ++             
  gi|386001899|ref|YP_005920198.1| 481 YRTEEIKDVINSMRSEL-------KDINEKIIKLEYLTSEDHKQDlgkQLETKKQELSVHDSSRPT-------Eidk 543
                                       77999999999666666.......667788888888766544444332444444444433333333.......1233 PP

                            AAA_15 235 ...eeelteklkeiqeklkeidkklaeelk............kilkkkid 269
                                          + +++e++k++ ++++++ ++++e ++            +++k ki+
  gi|386001899|ref|YP_005920198.1| 544 pivSPSIEEAFKDLRSEIETLTSNITEAKSqlnrsvkilasiSKIKGKIE 593
                                       33566666666666666666666663333344433223332322222222 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.2
                            AAA_15  83 faekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekek 159
                                       +     + ey   + ++e+  + l+ +kk s+ k ++ + +l+  +  ++    ++ +  + +e  + + + +e+ +
  gi|386001899|ref|YP_005920198.1| 633 Y-----EREYSNKQSQSEELIDRLENNKKVSEEKLYSLQSTLDEANRSYQHYLDEITNWDQLREVIIGSPDQHESIE 704
                                       1.....22333333333333333333344444444444444444433333333333333333344444444444444 PP

                            AAA_15 160 eelkidkedlkklikkleeslkkee............elknvlksaiiklllisakRnvsdedsekkssllgklkek 224
                                       +     +e+ + l ++l++     +            e+k++ +  i++++  ++  ++ +  +  + ++  +++++
  gi|386001899|ref|YP_005920198.1| 705 YYKNALNESSTTLVDDLSKA----KlernskveaiflEIKKLVNIYIDLYKPVQDFIDNHELIDRYQLNFNVSIIQQ 777
                                       44444444444444444433....24444777777776666666666666666655555555555555555666666 PP

                            AAA_15 225 ileealqekleeelteklkeiq...eklkeidkklaeelkkilkkkidkik.kfnykgkkneeieik.......... 287
                                        + +a  ++ +++ +  +  +q   +klkei++k++ +  +++ ++i +i+ ++++ + ++ ++             
  gi|386001899|ref|YP_005920198.1| 778 GFIDAFLSHINQSAKGTFHGTQdgrDKLKEIIDKYDFNSISNVMQFIAEIQeSIEIDKRDSINRVKIesqlrksfkk 854
                                       55555444444444444444440004444444444333335555555555544555444444433336777788888 PP

                            AAA_15 288 ...................ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvli 345
                                                               +l + + G +  llli+ +l  +++         l+i++PE +L  q  ++li
  gi|386001899|ref|YP_005920198.1| 855 qdlyeflyslkylepryilQLGGKELLQLSPGERGVLLLIFYLLVDKDD-------CPLIIDQPEDNLDNQSVYELI 924
                                       899999999*********96666677899*************9999999.......99******************* PP

                            AAA_15 346 kllkelandnktQviitTHSphi 368
                                         +++ a+  + Qv+i TH+p +
  gi|386001899|ref|YP_005920198.1| 925 APCISEARLRR-QVFIITHNPNL 946
                                       **********9.*********86 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.18      25      88 ..     351     420 ..     342     499 .. 0.72
   2 ?   -0.8   0.2       1.2   1.7e+03     160     160 ..     667     667 ..     545     770 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_16  25 elvllsGesGvGKsslvrellralekd...ggif.lrgkcdqlesaipy....salaqalareellrqllde 88 
                                       elv ++G++G+GKs+l ++l+  l  +   ++ f  ++k+++ + + ++    +++++   +e+l r l+++
  gi|386001899|ref|YP_005920198.1| 351 ELVAIIGNKGMGKSALTDMLA-LLGNTsskDFSFlNKQKFRDPKNNKSLdfeaQIIWESG-EESLARCLAED 420
                                       799**************9988.33333454555545666666554544444523355555.33555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                            AAA_16 160 r 160
                                       +
  gi|386001899|ref|YP_005920198.1| 667 S 667
                                       1 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00011      0.15      48     159 ..     489     603 ..     477     640 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTS.SEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEE CS
                      Phos_pyr_kin  48 veaqleavledvkvdavKiGmlasaeiievvaeklkkykv.pvVlDPVmvaksgselleeeavealkeeLlplatvi 123
                                       v + +++ l+d++ + +K+  l+s++  + + ++l+ +k    V D    ++ ++++++++  ea+k+ L  + + +
  gi|386001899|ref|YP_005920198.1| 489 VINSMRSELKDINEKIIKLEYLTSEDHKQDLGKQLETKKQeLSVHDSSRPTEIDKPIVSPSIEEAFKD-LRSEIETL 564
                                       5566788899*************************77777699***********************98.******** PP

                                       E-BHHHHHHHHT---S...SHHHHHHHHHHHHHTT-SEE CS
                      Phos_pyr_kin 124 tPNlpEaeaLlgekik...teedmkeaakkllklgakaV 159
                                       t N+ Ea+  l++++k   + +++k   ++l+++  + V
  gi|386001899|ref|YP_005920198.1| 565 TSNITEAKSQLNRSVKilaSISKIKGKIENLRRMYDNFV 603
                                       ********8888777733355666666666666655554 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1       0.1   1.4e+02     156     212 ..     529     585 ..     522     586 .. 0.94
   2 ?    3.5   1.0     0.029        40     140     202 ..     603     661 ..     601     669 .. 0.83
   3 ?    8.3   0.1     0.001       1.4     153     203 ..     679     729 ..     667     736 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
                             HNOBA 156 DlplhdssrelvlagiqqsaelelaldqleeksaeLeesmkeleeekkrtdeLLysm 212
                                       +l++hdssr   + +   s ++e a++ l  + + L  +  e +++ +r+ ++L s+
  gi|386001899|ref|YP_005920198.1| 529 ELSVHDSSRPTEIDKPIVSPSIEEAFKDLRSEIETLTSNITEAKSQLNRSVKILASI 585
                                       899************************************************999886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.029
                             HNOBA 140 vvenleelrkvGlylsDlplhdssrelvlagiqqsaelelaldqleeksaeLeesmkeleeek 202
                                       v+e+ ee +k+G+ ++ +++ d    l+   +q + e+++++ q ee  ++Le++ k + eek
  gi|386001899|ref|YP_005920198.1| 603 VIESSEEFDKIGVKMESIARLDINESLI---QQYEREYSNKQSQSEELIDRLENNKK-VSEEK 661
                                       789999999************9999998...67788888899999999999998755.44444 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.001
                             HNOBA 153 ylsDlplhdssrelvlagiqqsaelelaldqleeksaeLeesmkeleeekk 203
                                       yl ++   d+ re+++ +  q++++e+ ++ l+e s+ L + +++ + e++
  gi|386001899|ref|YP_005920198.1| 679 YLDEITNWDQLREVIIGSPDQHESIEYYKNALNESSTTLVDDLSKAKLERN 729
                                       89999**********************************999999887775 PP

>> DUF2811  Protein of unknown function (DUF2811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.018        24      11      28 ..     673     690 ..     664     693 .. 0.82
   2 ?    4.4   0.1     0.033        46       6      29 ..     745     768 ..     742     772 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                           DUF2811  11 heslkkflethpnWDqdr 28 
                                       ++s +++l++  nWDq r
  gi|386001899|ref|YP_005920198.1| 673 NRSYQHYLDEITNWDQLR 690
                                       568899**********76 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.033
                           DUF2811   6 ipeeLheslkkflethpnWDqdrl 29 
                                       i  +L++ +++f+++h   D+++l
  gi|386001899|ref|YP_005920198.1| 745 IYIDLYKPVQDFIDNHELIDRYQL 768
                                       66789****************997 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.6   6.3e+03     107     150 ..      75     118 ..      55     123 .. 0.69
   2 ?    1.9   0.1      0.12   1.6e+02       2      29 ..     353     381 ..     352     411 .. 0.70
   3 ?   10.0  13.5    0.0004      0.56      61     301 ..     607     946 ..     552     948 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.6
                            AAA_21 107 eedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsr 150
                                       +  + +  + + r ++++  + +ls++++++ ++++++ di+++
  gi|386001899|ref|YP_005920198.1|  75 KNIDLILPVIELRLDKFGGTDSNLSKINFHIIFSNEVNPDIIHE 118
                                       45555555666777788888888888888888888888888775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl...drdv 29 
                                        ++iG  g GKS L d l ll  +   d  +
  gi|386001899|ref|YP_005920198.1| 353 VAIIGNKGMGKSALTDMLALLGNTsskD--F 381
                                       6899999**************7766431..1 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0004
                            AAA_21  61 eieeflsqgvryryglrlersqv....eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvs 133
                                       + e f++ gv+ + ++rl+ +      +e+ +s+++ ++  l+++ ++ ++  +       +  ++ ++s ++ + +
  gi|386001899|ref|YP_005920198.1| 607 SEE-FDKIGVKMESIARLDINESliqqYEREYSNKQSQSEELIDRLENNKKVSEEKLYSLQSTLDEANRSYQHYLDE 682
                                       444.5555555555555555555557777778887777777777777777777777777777788888888888888 PP

                            AAA_21 134 epndlqfgkaltditsrawsllllldglrke.........rigllnifadyfgfakekrllqrlvrslklveielsd 201
                                       + n++q  ++++ ++ +++s++  +++l +          +  l ++++ ++ f ++k+l+  +++ +k+v + +++
  gi|386001899|ref|YP_005920198.1| 683 ITNWDQLREVIIGSPDQHESIEYYKNALNESsttlvddlsKAKLERNSKVEAIFLEIKKLVNIYIDLYKPVQDFIDN 759
                                       88888888888888888888888888888888888888888888888888888888888888888888888644433 PP

                            AAA_21 202 lgegeeliasvderlrer........................................................... 219
                                               +++d+ ++                                                             
  gi|386001899|ref|YP_005920198.1| 760 H-------ELIDRYQLNFnvsiiqqgfidaflshinqsakgtfhgtqdgrdklkeiidkydfnsisnvmqfiaeiqe 829
                                       3.......233322222256677778899999999999999999999999999999999999999999999999999 PP

                            AAA_21 220 .................................gvvflengdgqelparel........SdGtkrllalltallral 255
                                                                               ++  ++ + +l        S G + +l l+ +ll + 
  gi|386001899|ref|YP_005920198.1| 830 sieidkrdsinrvkiesqlrksfkkqdlyeflyS-----LKYLEPRYILQLggkellqlSPGERGVLLLIFYLLVDK 901
                                       9999999999999999999999999999555542.....44444444444444444555***************999 PP

                            AAA_21 256 kkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSpll 301
                                       +    l+iD pE +L+ + + +l+   ++e++  + Qv++ TH+p l
  gi|386001899|ref|YP_005920198.1| 902 DD-CPLIIDQPEDNLDNQSVYELIaPCISEARL-RRQVFIITHNPNL 946
                                       99.999***********8887777788877766.9**********98 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.18   2.5e+02      39      68 ..     476     505 ..     445     531 .. 0.75
   2 ?    6.3   0.1    0.0069       9.6      53      88 ..     547     582 ..     535     619 .. 0.82
   3 ?    9.1   2.5   0.00092       1.3      28     123 ..     641     741 ..     624     757 .. 0.84
   4 ?   -1.0   0.1       1.2   1.7e+03      25      50 ..     807     832 ..     784     849 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.18
                         ApoLp-III  39 kqvikslqeelkkksdeleealkevkkkie 68 
                                        ++i+  +ee+k+ ++ + + lk++++ki 
  gi|386001899|ref|YP_005920198.1| 476 DELIEYRTEEIKDVINSMRSELKDINEKII 505
                                       455555566666666666666666666664 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0069
                         ApoLp-III  53 sdeleealkevkkkieetadklseenPevkkkaqel 88 
                                       s+ +eea+k+++++ie  + +++e++++++++++ l
  gi|386001899|ref|YP_005920198.1| 547 SPSIEEAFKDLRSEIETLTSNITEAKSQLNRSVKIL 582
                                       678899999999999999999999999888887755 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00092
                         ApoLp-III  28 Kensenlvdqlkqvikslqeelkkksdeleealkevkkkieeta..dklse...enPevkkkaqelqekvQsgvqsl 99 
                                       + +se+l+d+l++  k  +e+l   +++l+ea +  +  + e++  d+l+e    +P+  ++++ +++ + ++ ++l
  gi|386001899|ref|YP_005920198.1| 641 QSQSEELIDRLENNKKVSEEKLYSLQSTLDEANRSYQHYLDEITnwDQLREviiGSPDQHESIEYYKNALNESSTTL 717
                                       789*********************999**************9974579**9**9*********************** PP

                         ApoLp-III 100 vkesqklaeslkensqeakeklak 123
                                       v +  k+  + +++++++  +++k
  gi|386001899|ref|YP_005920198.1| 718 VDDLSKAKLERNSKVEAIFLEIKK 741
                                       **9999865555555555444444 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.2
                         ApoLp-III  25 etiKensenlvdqlkqvikslqeelk 50 
                                       e i ++  n ++++ q+i+++qe++ 
  gi|386001899|ref|YP_005920198.1| 807 EIIDKYDFNSISNVMQFIAEIQESIE 832
                                       34445555778888888888888775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.8     0.016        23      11      51 ..     350     391 ..     342     693 .. 0.81
   2 ?   -1.0   0.0       1.7   2.4e+03      61     120 ..     817     894 ..     742     911 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke 51 
                                        e+vai+G+ G GKS L  +la l +  + +  +  ++++++
  gi|386001899|ref|YP_005920198.1| 350 FELVAIIGNKGMGKSALTDMLALLGNTSSKDFSFLnKQKFRD 391
                                       589*****************9988777666654332334433 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                                       EEEE-SS.--S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTS...GGS-HHHHHHHH CS
                                       xxxxxxx.xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                          ABC_tran  61 igvlpqe.pqlfpeltvren...............esdeeiekalsklglkelkdtvvkssp...ssLSgGqkqrva 118
                                       i+ + q  +++++ +++ ++                ++++++++l +l+  e +  +++ ++    +LS G++  + 
  gi|386001899|ref|YP_005920198.1| 817 ISNVMQFiAEIQESIEIDKRdsinrvkiesqlrksFKKQDLYEFLYSLKYLE-PRYILQLGGkelLQLSPGERGVLL 892
                                       4444444333333333333344444433333332222333444444444333.222222222334667777776555 PP

                                       HH CS
                                       xx RF
                          ABC_tran 119 la 120
                                       l 
  gi|386001899|ref|YP_005920198.1| 893 LI 894
                                       54 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  11.6     0.011        15      12     155 ..     508     661 ..     480     662 .. 0.80
   2 ?   -0.9   0.1      0.99   1.4e+03       4      35 ..     660     691 ..     657     734 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                              Wtap  12 rlsakeqelqelksslqelkqslqpps...ssqlrqvllDPAvnlvfsrlrkeleeaenkleeaqeeLqa.lkftpd 84 
                                        + ++e   q+l ++l+  kq+l+  +    ++ ++ ++ P+++  f+ lr+e+e  +++++ea+++L++ +k  + 
  gi|386001899|ref|YP_005920198.1| 508 EYLTSEDHKQDLGKQLETKKQELSVHDssrPTEIDKPIVSPSIEEAFKDLRSEIETLTSNITEAKSQLNRsVKILAS 584
                                       455566666777788888888877744233449999********************************853788777 PP

                              Wtap  85 sqtGkrLmakcrvLe.....qENeELgkv.leegrvakLeselalqkkfveelkkaleeleelleeleeevevlqst 155
                                        ++ k  ++ +r+++     +  eE  k+ ++ +++a+L  + +l +++ +e+ ++++++eel++ le+  +v++++
  gi|386001899|ref|YP_005920198.1| 585 ISKIKGKIENLRRMYdnfviESSEEFDKIgVKMESIARLDINESLIQQYEREYSNKQSQSEELIDRLENNKKVSEEK 661
                                       77777778888887722222457999998689999********************************9998888776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.99
                              Wtap   4 rrealllarlsakeqelqelksslqelkqslq 35 
                                       ++ + l ++l +  ++ q++ +++++++q ++
  gi|386001899|ref|YP_005920198.1| 660 EKLYSLQSTLDEANRSYQHYLDEITNWDQLRE 691
                                       45566777788888888888888888877644 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   7.9      0.01        14     143     253 ..     524     689 ..     450     692 .. 0.57
   2 ?    2.9   2.6     0.043        59     108     168 ..     625     681 ..     619     758 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.01
                           DUF4407 143 a...............................alqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake. 187
                                       +                               +l++ei+++ + +++++ ++++ ++    + +++++Gk ++ ++ 
  gi|386001899|ref|YP_005920198.1| 524 EtkkqelsvhdssrpteidkpivspsieeafkDLRSEIETLTSNITEAKSQLNRSVKI--LASISKIKGKIENLRRm 598
                                       1222222233334444444444444444444455555555555555555555555444..44455556666666666 PP

                           DUF4407 188 ...........................kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaa 237
                                                                  +++ ++++++e  + +++  +++ +++l+++++  e+++ + +++ ++a+
  gi|386001899|ref|YP_005920198.1| 599 ydnfviesseefdkigvkmesiarldiNESLIQQYEREYSNKQSQ--SEELIDRLENNKKVSEEKLYSLQSTLDEAN 673
                                       666666677777777777777777777777777777777777777..888888888888888888888888888888 PP

                           DUF4407 238 aaddGllarlealdrl 253
                                       ++ +++l++++  d+l
  gi|386001899|ref|YP_005920198.1| 674 RSYQHYLDEITNWDQL 689
                                       8888888887766665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.043
                           DUF4407 108 Idaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeld 168
                                       I++ l++++++e +  ++q    +++ +++le++ +  ++++ +++++ld++++ +q  ld
  gi|386001899|ref|YP_005920198.1| 625 INESLIQQYEREYSNKQSQ----SEELIDRLENNKKVSEEKLYSLQSTLDEANRSYQHYLD 681
                                       5555555555555555444....55666666666666666666666666665555554443 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.6     0.079   1.1e+02       9      51 ..     487     531 ..     480     543 .. 0.72
   2 ?    7.3   0.7    0.0039       5.4      85     121 ..     549     585 ..     545     587 .. 0.88
   3 ?    4.3   8.4     0.035        48      70     117 ..     627     675 ..     580     680 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.079
                           DUF5082   9 qaqiaelrseiaaleekIerLk..eaktklsdekeslkqkkkkle 51 
                                       +  i ++rse+++++ekI +L+  +  ++ +d  ++l++kk++l+
  gi|386001899|ref|YP_005920198.1| 487 KDVINSMRSELKDINEKIIKLEylTSEDHKQDLGKQLETKKQELS 531
                                       566899***************966445555555566666666554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0039
                           DUF5082  85 kldelidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                        ++e+ + + +EIe+L + i+ea++ l+++ + l s+
  gi|386001899|ref|YP_005920198.1| 549 SIEEAFKDLRSEIETLTSNITEAKSQLNRSVKILASI 585
                                       5899999********************9998877776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.035
                           DUF5082  70 girs.nlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsq 117
                                       + +  ++e +y++ +++ +elid++e+  +  e++++++q+ ld  +++
  gi|386001899|ref|YP_005920198.1| 627 ESLIqQYEREYSNKQSQSEELIDRLENNKKVSEEKLYSLQSTLDEANRS 675
                                       3333489999999999**********99999999999999999988776 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.64   8.8e+02      65      94 ..     475     504 ..     452     513 .. 0.63
   2 ?    8.2   1.5    0.0017       2.4      80     125 ..     542     594 ..     472     604 .. 0.56
   3 ?   -1.9   0.1       2.2     3e+03      28      68 ..     643     683 ..     625     695 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.64
                      Baculo_PEP_C  65 ldtlltnLtdalnalqdtlrneLtnlnsil 94 
                                       ld+l++  t+ ++ + +++r+eL+ +n ++
  gi|386001899|ref|YP_005920198.1| 475 LDELIEYRTEEIKDVINSMRSELKDINEKI 504
                                       444444445555555555556666555554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                      Baculo_PEP_C  80 q.....dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl..dlgalsq 125
                                              +++++ + l s++ +L+s++t  +s Ln  ++ l+++  ++g++++
  gi|386001899|ref|YP_005920198.1| 542 DkpivsPSIEEAFKDLRSEIETLTSNITEAKSQLNRSVKILASIskIKGKIEN 594
                                       04444455666666666666666666666666666655555555333444433 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtl 68 
                                       q+ +++  l++ ++  e++L +l++ l ++  + ++ ld+ 
  gi|386001899|ref|YP_005920198.1| 643 QSEELIDRLENNKKVSEEKLYSLQSTLDEANRSYQHYLDEI 683
                                       44444444444444444455555554444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1003 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1693  (0.094428); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.08u 0.38s 00:00:01.46 Elapsed: 00:00:00.55
# Mc/sec: 5447.44
//
Query:       gi|386001900|ref|YP_005920199.1|  [L=82]
Description: hypothetical protein Mhar_1210 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.21   11.5   4.1       0.25   11.3   4.1    1.1  1  YqhR         Conserved membrane protein YqhR
       0.32   11.2   6.3       0.27   11.4   5.3    1.4  1  DUF2178      Predicted membrane protein (DUF2178)
        9.7    5.8  12.5       0.27   10.9   0.7    2.2  2  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.1   4.1e-05      0.25      72     117 ..       7      55 ..       2      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                              YqhR  72 ivligvvsigvallyyvllkkikslwag...ilyGvvlwllvfyvlnPl 117
                                       +++ g+v i+v +ly ++  +   + ag   ++ Gv l+++v   lnP+
  gi|386001900|ref|YP_005920199.1|   7 LIMAGIVLITVGILYTLVSARAGVVLAGlgtVAAGVFLFTIVPNPLNPI 55 
                                       799******************9999887333678********9999998 PP

>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.3   4.5e-05      0.27       3      45 ..       7      54 ..       6      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.5e-05
                           DUF2178  3 iivavialvglgi.wa....aignvllaviavaaGvllaillkkkvee 45
                                      +i+a i+l+ +gi +     ++g vl+++ +vaaGv+l+ ++ + ++ 
  gi|386001900|ref|YP_005920199.1|  7 LIMAGIVLITVGIlYTlvsaRAGVVLAGLGTVAAGVFLFTIVPNPLNP 54
                                      699999999999974467789999999*************99877765 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   5.1      0.13   7.6e+02      13      71 ..       8      25 ..       2      48 .. 0.47
   2 ?   10.9   0.7   4.5e-05      0.27       4      23 ..      55      74 ..      52      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.13
                                      XXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 13 wligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGciga 71
                                      +++givl+ vG+ ++                                         + +
  gi|386001900|ref|YP_005920199.1|  8 IMAGIVLITVGILYT-----------------------------------------LVS 25
                                      455666666663332.........................................222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.5e-05
                                      XXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  4 llfffnllfwligivllavG 23
                                      + fffn l++l+g+ ++avG
  gi|386001900|ref|YP_005920199.1| 55 IAFFFNGLLVLCGLWMVAVG 74
                                      67*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 524.46
//
Query:       gi|386001901|ref|YP_005920200.1|  [L=429]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-36  125.0   0.0      6e-36  124.2   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
        0.2   11.4   2.4       0.39   10.5   2.4    1.5  1  SHOCT         Short C-terminal domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2   0.0   6.7e-40     6e-36       1     234 [.     101     360 ..     101     363 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 6.7e-40
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....................TS-BSBESSSB-HHHHHHH- CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..................aivevgadgeidvEklaalk 59 
                                       i++ +p++ +i++alG+ +kvv+ + +++ +l     e                   + +e++++ +i +E +a l 
  gi|386001901|ref|YP_005920200.1| 101 IITREPDTCRIVIALGEGEKVVASEQAVKSCLCPTTFETfeegclecyssilggrlaDLPETSTRYDIYYELIASLN 177
                                       67889999*******************99999888776688889999999988888888****************** PP

                                       -SEEEE-GGG...GGGHHHHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS CS
                      Peripla_BP_2  60 PDlvilskglgltdedeellksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksai 132
                                       PD++i s         + + k g+p+v+   + +     ++l+ +i+++g +l++edeae+l+ +++sk+++++s  
  gi|386001901|ref|YP_005920200.1| 178 PDVIITSGAT---NVPDFESKIGCPVVVAGGDGWNytrdDGLYGMIEVIGDVLEREDEAEELIGFVESKIEMVRSVS 251
                                       *****99988...777778899******************************************************* PP

                                       -TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHT.S--EES.TTT--......STT-EEE-HHHHHHH--SEEEEEE CS
                      Peripla_BP_2 133 dsekpkpvlvfggadeggyvvagsnsyigdllda.lgieni.aaesk......kseyeeisaEqilasdpdvifvsg 201
                                       d + +++ +++++a++g+++ +++  +++d++++   ++++ +a +       +++ +++  Eqi a++pd+ifv++
  gi|386001901|ref|YP_005920200.1| 252 DGIPEDEKPLVYFAPRGAKLGFYDPKEGRDFTRTfTSYDPLdIAGGRnvaegaEGYEINVAVEQIIAWNPDYIFVAC 328
                                       ***9999*************************999999999766666899999************************ PP

                                       HHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 202 raeadnktgleflkenpllaelpAvkngrVyal 234
                                       + + +  ++ + +k++p l+++ Av+ng+Vy +
  gi|386001901|ref|YP_005920200.1| 329 S-TPEDAEVIDWIKSSPDLQSIAAVQNGNVYNC 360
                                       *.*****************************87 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.4   4.4e-05      0.39       2      19 ..      52      69 ..      52      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.4e-05
                             SHOCT  2 aLekLkeLyarGeIteEE 19
                                      +Le  ++ +a+GeIt+EE
  gi|386001901|ref|YP_005920200.1| 52 ELEAAQAALAAGEITDEE 69
                                      68999999********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2788.92
//
Query:       gi|386001902|ref|YP_005920201.1|  [L=254]
Description: Methyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-13   50.1   0.1    5.6e-13   49.4   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    9.4e-11   41.7   0.0    1.1e-10   41.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.9e-10   39.1   0.0    1.4e-09   38.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    3.9e-08   33.9   0.0    9.1e-08   32.8   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    1.8e-07   30.5   0.0    2.4e-07   30.1   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.7e-06   27.7   0.0    2.7e-06   27.0   0.0    1.2  1  MTS              Methyltransferase small domain
    3.4e-06   26.5   0.0    4.9e-06   26.0   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
    4.4e-06   26.6   0.0    6.1e-06   26.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      6e-06   26.1   0.0    8.6e-06   25.6   0.0    1.2  1  Met_10           Met-10+ like-protein
    5.7e-05   23.0   0.0    8.5e-05   22.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    9.4e-05   21.9   0.0    0.00013   21.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00013   21.4   0.0    0.00018   21.0   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00022   20.7   0.0    0.00042   19.8   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00092   18.6   0.0     0.0013   18.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0013   18.7   0.1     0.0025   17.8   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
     0.0039   16.3   0.0     0.0057   15.8   0.0    1.2  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.016   14.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.01   15.6   0.0      0.017   14.8   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
      0.025   14.0   0.0      0.043   13.3   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.096   12.3   0.0       0.15   11.7   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.19   11.7   0.0        0.3   11.0   0.0    1.5  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.1   6.5e-16   5.6e-13       1      91 [.      35     123 ..      35     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 6.5e-16
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS..SSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp..fedgsfDlvvssgal 74 
                                       vLd+G+GtGrl+  +ak +  +kvt+vD s +ml++ +e+++eegl n +++q+  ed+   ++ +  D+v++s++l
  gi|386001902|ref|YP_005920201.1|  35 VLDVGAGTGRLSVPIAKMV--KKVTAVDQSRGMLNYLEENMAEEGLsNYRCIQKRWEDVRlgEDIEAHDVVIASHSL 109
                                       9*****************9..9************************************762256779******8777 PP

                                       GGSSHHHHHHHHHHHHH CS
                   Methyltransf_25  75 hhlsdedlekalkeiar 91 
                                        +++   l++al+++  
  gi|386001902|ref|YP_005920201.1| 110 GMFD---LQEALAKMDA 123
                                       7775...7777777765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   1.3e-13   1.1e-10       2     113 ..      30     137 ..      29     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.3e-13
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled..ekfD 76 
                                       d +++vlD+G+GtG+l+  +a ++   ++v+ +D s  ++++ +en ++ gl+n++  q  +e+    l +  e  D
  gi|386001902|ref|YP_005920201.1|  30 DPDCTVLDVGAGTGRLSVPIA-KMV--KKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQKRWEDVR--LGEdiEAHD 101
                                       6799*****************.554..58***********************************77..3333689** PP

                   Methyltransf_31  77 lilsnevlnaladpdkileeiervlkpggilliedpr 113
                                       ++++   l  + d++++l ++  + k   ++ ++  +
  gi|386001902|ref|YP_005920201.1| 102 VVIASHSL-GMFDLQEALAKMDAAAKRRVYIFTAAGK 137
                                       ****9999.99*******9999999888887766655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.6e-12   1.4e-09       1      87 [.      36     124 ..      36     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.6e-12
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T..T-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfed..nsfDlvvssevlhhv 74 
                                       LdvG+GtGrl+ ++ak +++v++vD s  ml++ +e+  eegl + ++++ + e++ + +  +  D+v++s++l  +
  gi|386001902|ref|YP_005920201.1|  36 LDVGAGTGRLSVPIAKMVKKVTAVDQSRGMLNYLEENMAEEGLsNYRCIQKRWEDVRLGEdiEAHDVVIASHSLGMF 112
                                       8*******************************************9**********99888567************** PP

                                       CCHHHHHHHHHHH CS
                   Methyltransf_11  75 edpekalkeiaRv 87 
                                        d+++al+++   
  gi|386001902|ref|YP_005920201.1| 113 -DLQEALAKMDAA 124
                                       .688888877655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.1e-10   9.1e-08       1      94 [.      36     126 ..      36     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-10
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+GtG+l+ ++++    +++t+vD s+ +++  +e +a+++  n  +++ + +d+   ++ ++ D+v+as+ l 
  gi|386001902|ref|YP_005920201.1|  36 LDVGAGTGRLSVPIAKM--VKKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQKRWEDVRLGEDIEAHDVVIASHSLG 110
                                       8****************..**************7777777777777777777777776666555************* PP

                   Methyltransf_12  78 hlkdirevldnirklLk 94 
                                        + d++e+l+++ ++ k
  gi|386001902|ref|YP_005920201.1| 111 MF-DLQEALAKMDAAAK 126
                                       96.99999999987766 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.9e-10   2.4e-07      23      73 ..      24      74 ..      18     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.9e-10
                                      HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
                            RrnaAD 23 ldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73
                                      +  l+l ++ tvl++g+G+G l++++ak++k+v+++ + + +++ l++++ 
  gi|386001902|ref|YP_005920201.1| 24 VASLQLDPDCTVLDVGAGTGRLSVPIAKMVKKVTAVDQSRGMLNYLEENMA 74
                                      6789999***************************************99776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   3.2e-09   2.7e-06      27     102 ..      27     104 ..      20     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.2e-09
                                       CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTSTTS-EE CS
                               MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeveekkfd 99 
                                       l+ + + +vlD+G+G+G l++ +ak+ ++  vt+vd++   l+  +en+++++l+    ++ +++dv    + +  d
  gi|386001902|ref|YP_005920201.1|  27 LQLDPDCTVLDVGAGTGRLSVPIAKMVKK--VTAVDQSRGMLNYLEENMAEEGLSnyrcIQKRWEDVRLGEDIEAHD 101
                                       55666778******************999..9*********************999888888999988776666777 PP

                                       EEE CS
                               MTS 100 liv 102
                                       +++
  gi|386001902|ref|YP_005920201.1| 102 VVI 104
                                       776 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.8e-09   4.9e-06      49     151 ..      33     138 ..      17     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.8e-09
                                       C-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC...TTTTT-EEEEEE. CS
                              GidB  49 rdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee...kqeeekydvvts. 121
                                         +v+DvG+G G  ++p+a  +  +k+t ++++    ++Lee ++e +l+n++ +++r e+    +  e  dvv++ 
  gi|386001902|ref|YP_005920201.1|  33 C-TVLDVGAGTGRLSVPIA--KMVKKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQKRWEDvrlGEDIEAHDVVIAs 106
                                       3.69********9999976..6667899*********************************7765556666666531 PP

                                       C-SS..SHHHHHHHHCCCEEEEEEEEEEESS- CS
                              GidB 122 RAla..slnelteillkllkegglilalKGks 151
                                         l+   l+e  + +    k + +i+   Gk+
  gi|386001902|ref|YP_005920201.1| 107 HSLGmfDLQEALAKMDAAAKRRVYIFTAAGKW 138
                                       33331134444455555555555555555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   7.2e-09   6.1e-06      13     100 ..      20     117 ..       1     160 [. 0.72

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.2e-09
                   Methyltransf_23  13 lerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaae 78 
                                       +er ++   l+++  vLd+G+GtG+l+  +++ +++vt+vD+s+ + + +e         + ++ qk  +       
  gi|386001902|ref|YP_005920201.1|  20 TERQVASlqLDPDCTVLDVGAGTGRLSVPIAKMVKKVTAVDQSRGMLNYLEenmaeeglsNYRCIQKRWE------- 89 
                                       333333222555559*****************************99998866666666655555555555....... PP

                   Methyltransf_23  79 pqg........kfdlIvlrevlehvpdppe 100
                                         +          d+++++++l+ ++  ++
  gi|386001902|ref|YP_005920201.1|  90 --DvrlgedieAHDVVIASHSLGMFDLQEA 117
                                       ..0223344558899999999998865444 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     1e-08   8.6e-06      88     152 ..      19      81 ..      11     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1e-08
                                       HHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
                            Met_10  88 eaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv 152
                                        +Er+    + +++ +V+dv AG G +++piak    k+v a+d      +yl+en++   ++++
  gi|386001902|ref|YP_005920201.1|  19 RTERQVASLQLDPDCTVLDVGAGTGRLSVPIAK--MVKKVTAVDQSRGMLNYLEENMAEEGLSNY 81 
                                       4677666667999********************..77889*****************98888876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   9.9e-08   8.5e-05      66     126 ..      24      81 ..      10     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.9e-08
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSE CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenv 126
                                       +  l+l++   vL+vG+G+G l++ +a++v++++   ++++++ + +  ++n+ +++l+n 
  gi|386001902|ref|YP_005920201.1|  24 VASLQLDPDCTVLDVGAGTGRLSVPIAKMVKKVT---AVDQSRGMLNYLEENMAEEGLSNY 81 
                                       56799**************************988...99*******999999999998864 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.6e-07   0.00013      48     139 ..      32     121 ..      11     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                                       TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-..T-EEEEEE CS
                   Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed..dsfDvvtv 122
                                         +vlDv +Gtg l++ ++++v+   kv+ +D +  mL+  e+ + eeg +n + +q   e++   +  ++ Dvv  
  gi|386001902|ref|YP_005920201.1|  32 DCTVLDVGAGTGRLSVPIAKMVK---KVTAVDQSRGMLNYLEENMAEEGLSNYRCIQKRWEDVRLGEdiEAHDVVIA 105
                                       3489****************997...69999**************************98887655332499***999 PP

                                       ES-GGG-S-HHHHHHHH CS
                   Ubie_methyltran 123 sfGlrnvtDklkaLkea 139
                                       s+ l    D ++aL ++
  gi|386001902|ref|YP_005920201.1| 106 SHSLGM-FDLQEALAKM 121
                                       998854.4677777665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.2e-07   0.00018      30     109 ..      31     114 ..       5     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-07
                                       -S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----...S-EEEEE.EE CS
                              TehB  30 kpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakld...erydfil.st 102
                                         + vld+g g gr s+ ++ +  +vta+d+    +++lee +  e l+n ++     ++++l    e +d ++ s 
  gi|386001902|ref|YP_005920201.1|  31 PDCTVLDVGAGTGRLSVPIAKMVKKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQKRWEDVRLGediEAHDVVIaSH 107
                                       3499****************************************999988555444444444430014556554133 PP

                                       SSGGGS- CS
                              TehB 103 vvlmfle 109
                                        + mf  
  gi|386001902|ref|YP_005920201.1| 108 SLGMFDL 114
                                       4445554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.9e-07   0.00042     160     232 ..      30     105 ..      20     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.9e-07
                              PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk....eekadviv 231
                                        ++ +vlDvG+G+G L++  ak+  kkv+avD     ++  +eN++  ++++ ++ ++   e ++     e +dv++
  gi|386001902|ref|YP_005920201.1|  30 DPDCTVLDVGAGTGRLSVPIAKM-VKKVTAVDQSRGMLNYLEENMAEEGLSNyRC-IQKRWEDVRlgedIEAHDVVI 104
                                       57789*****************9.689********************99999544.655444443333456789999 PP

                              PrmA 232 a 232
                                       a
  gi|386001902|ref|YP_005920201.1| 105 A 105
                                       8 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-06    0.0013      49     126 ..      18      93 ..       4     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-- CS
                              CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedld 125
                                       +++++ +  l+l+p  t+Ld+G+G G l +  ++    kv ++  S+   ++ +++++e++l++ + ++ + +ed++
  gi|386001902|ref|YP_005920201.1|  18 HRTERQVASLQLDPDCTVLDVGAGTGRLSVPIAKM-VKKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQ-KRWEDVR 92 
                                       566778899*******************9988877.6789*********************99988887.5799986 PP

                                       - CS
                              CMAS 126 e 126
                                        
  gi|386001902|ref|YP_005920201.1|  93 L 93 
                                       4 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.9e-06    0.0025      13      66 ..      30      81 ..      20     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                   Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledk 66
                                      +++ +v+D+G+  g l++ ++  +++kkv+a+D ++g l+  +en++++gl++ 
  gi|386001902|ref|YP_005920201.1| 30 DPDCTVLDVGAGTGRLSVPIA--KMVKKVTAVDQSRGMLNYLEENMAEEGLSNY 81
                                      45669**************99..699************************9873 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.7e-06    0.0057      95     134 ..      32      71 ..      18      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkk 134
                                       d ++ld+GaG G ++  +a+++++v a + s  m + l+ 
  gi|386001902|ref|YP_005920201.1|  32 DCTVLDVGAGTGRLSVPIAKMVKKVTAVDQSRGMLNYLEE 71 
                                       679*******************************999875 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.9e-05     0.016      42      92 ..      32      82 ..      18     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.T CS
                     Cons_hypoth95 42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.e 92
                                      +++vLD+ aG+G l++  +   +kk+++v++++ +++ l+en++e +l++ +
  gi|386001902|ref|YP_005920201.1| 32 DCTVLDVGAGTGRLSV-PIAKMVKKVTAVDQSRGMLNYLEENMAEEGLSNyR 82
                                      578************9.699************************99988742 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     2e-05     0.017      47     130 ..      32     109 ..      13     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                   Methyltransf_16  47 klsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWge.eleedllekeev 121
                                       +++vl++G+GtG   + +a++    kv+  D++  +l+ l++n++ ++  l+ + +  +  W++ +l ed+ e+   
  gi|386001902|ref|YP_005920201.1|  32 DCTVLDVGAGTGRLSVPIAKM--VKKVTAVDQSRgMLNYLEENMAEEG--LS-NYRCIQKRWEDvRLGEDI-EA--H 100
                                       689******************..8899999*9988*********9955..44.445555578551343333.44..4 PP

                   Methyltransf_16 122 DlilaaDcv 130
                                       D+++a+  +
  gi|386001902|ref|YP_005920201.1| 101 DVVIASHSL 109
                                       888888655 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-05     0.043       4      58 ..      34      86 ..      31      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrg 58
                                      +vl++G G G++ v +Ak+   k++ +++ ++ +++++ +++++++l+N r++++
  gi|386001902|ref|YP_005920201.1| 34 TVLDVGAGTGRLSVPIAKMV--KKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQK 86
                                      689***************97..66789*************************975 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.15       3      66 ..      26      86 ..      24     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                      HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES CS
                   Methyltr_RsmB-F  3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivlea 66
                                       L++ ++ t+lD+ a+ G     ia++    ++v+Avd+++  l+ ++en+   g+ n  +++ 
  gi|386001902|ref|YP_005920201.1| 26 SLQLDPDCTVLDVGAGTGRLSVPIAKM---VKKVTAVDQSRGMLNYLEENMAEEGLSNYRCIQK 86
                                      578888999****************99...678********************99999998875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036       0.3      23      65 ..      29      67 ..      12     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                   Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelve 65
                                       ++++tv+DvGaG g Ls  +a     +  kv+++d ++ + +
  gi|386001902|ref|YP_005920201.1| 29 LDPDCTVLDVGAGTGRLSVPIAK----MVKKVTAVDQSRGMLN 67
                                      46789***************999....5678999998776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1790.31
//
Query:       gi|386001903|ref|YP_005920202.1|  [L=261]
Description: hypothetical protein Mhar_1214 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  129.0   2.8    2.4e-37  128.6   2.8    1.1  1  Band_7    SPFH domain / Band 7 family
     0.0033   17.2   0.2      0.011   15.4   0.1    1.8  2  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   2.8   2.7e-41   2.4e-37       2     177 ..      24     193 ..      23     194 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 2.7e-41
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i+++ e++vv+rfGkl + ++pGl +i+P+++++++v++rv++ldv++ +tv+++D+++v +d++++y+v +   k+
  gi|386001903|ref|YP_005920202.1|  24 ITRQYERAVVFRFGKLLGEKGPGLFLIIPIVDRIVKVDLRVRELDVPR-QTVISSDNVSVEVDAVIYYKV-TSSTKA 98 
                                       6899********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       + +v    +++++    +++ +lr v+++++l+++lsnr+el++e+k+ l e  + +G+ v+ ++++d+ +p++  +
  gi|386001903|ref|YP_005920202.1|  99 IVEV----EDYEAATALLAQTTLRDVLGQNELDTILSNRDELNKEVKTILDEMTDPWGIKVVTATLRDVALPENMLR 171
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeae 177
                                       a+a+ ++ae+e++a+i  ae+e
  gi|386001903|ref|YP_005920202.1| 172 AIARQAEAEREKRARIILAEGE 193
                                       *******************997 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.3   2.7e+03     128     153 ..      19      44 ..      16      56 .. 0.81
   2 !   15.4   0.1   1.3e-06     0.011     140     209 ..     112     179 ..      84     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.3
                          Band_7_1 128 fdteeiseqlkslivtrlsdvlaesk 153
                                       f++ +i+ q+ + +v r++++l+e++
  gi|386001903|ref|YP_005920202.1|  19 FSSMKITRQYERAVVFRFGKLLGEKG 44 
                                       66778889999999999999988875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-06
                          Band_7_1 140 livtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       l +t+l dvl+++++  +   ++ +el +++k  l+e  +  G+++   ++++++lpe++ +a+ ++a++
  gi|386001903|ref|YP_005920202.1| 112 LAQTTLRDVLGQNELDTI--LSNRDELNKEVKTILDEMTDPWGIKVVTATLRDVALPENMLRAIARQAEA 179
                                       456678888888888765..5899*****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1612.69
//
Query:       gi|386001904|ref|YP_005920203.1|  [L=365]
Description: ABC transporter, iron chelate uptake transporter family, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-90  302.5  33.6    3.6e-90  302.2  33.6    1.1  1  FecCD       FecCD transport family
    0.00012   21.7  22.0    0.00012   21.7  22.0    1.5  2  ABC-3       ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.2  33.6     4e-94   3.6e-90       3     312 .]      41     357 ..      32     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 302.2 bits;  conditional E-value: 4e-94
                             FecCD   3 llllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLa 72 
                                       +ll+ + ++lg+ +i++++ ++al++k        d+l + +v+++r+pr++ ++l+G++L+v+G+++Q+v++NpLa
  gi|386001904|ref|YP_005920203.1|  41 VLLTGVIITLGPLDITVADAYRALISKFypdyfnvDPLTSRVVWNIRFPRIVGGILAGFGLGVCGCVMQAVLKNPLA 117
                                       4556666899****************999*9*99999999************************************* PP

                             FecCD  73 dPsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalt 148
                                       +P +lGissga +g+ +a++l+ +   + + l+  afl+all +++++ la   kga++++liLaGiav++++sa++
  gi|386001904|ref|YP_005920203.1| 118 SPFTLGISSGAQFGISIAAVLGvSVVGGPYLLIGNAFLFALLCSGFIIGLA-AVKGATSETLILAGIAVNYFFSAMS 193
                                       **********************8889999**********************.************************* PP

                             FecCD 149 sllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllll 225
                                       +l+++++n+e+l+ ++ w +G+l+  swsk+ +ll +++++++ll+l a +l++++ gdetAks+Gvn ervr+ ++
  gi|386001904|ref|YP_005920203.1| 194 QLFKYFANDEQLRLMTSWGMGDLAAFSWSKISILLGVFAICIPLLMLKAWDLNIMTSGDETAKSIGVNAERVRVYIM 270
                                       ***************************************************************************** PP

                             FecCD 226 llvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliG 302
                                       l+++l++a++v+++G+igF+GL++Ph+arl++g dhr l+p+s++lGa +l++ad +a +l++pt +p+gi+t++iG
  gi|386001904|ref|YP_005920203.1| 271 LISSLVVATVVCFTGTIGFIGLVAPHMARLILGGDHRFLIPASGILGASVLIAADGVAMNLIAPTVIPTGIMTSVIG 347
                                       ***************************************************************************** PP

                             FecCD 303 apffiylllr 312
                                       +pff+yl+l+
  gi|386001904|ref|YP_005920203.1| 348 VPFFMYLMLK 357
                                       *******986 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       0.5   4.5e+03     131     137 ..      35      41 ..      26      54 .. 0.44
   2 !   21.7  22.0   1.3e-08   0.00012       9     253 ..      91     353 ..      85     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.5
                             ABC-3 131 aiieavv 137
                                       aii+ +v
  gi|386001904|ref|YP_005920203.1|  35 AIIASIV 41 
                                       1111111 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.3e-08
                             ABC-3   9 llasilvslacallgsfv..vlrr..qsllgdalsHaalpGvalayllgvn.......lllgailvgliaavalell 74 
                                       ++++il +   ++ g+ +  vl+   +s +  ++s  a  G+ +a +lgv+       l+  a+l++l+++ ++  l
  gi|386001904|ref|YP_005920203.1|  91 IVGGILAGFGLGVCGCVMqaVLKNplASPFTLGISSGAQFGISIAAVLGVSvvggpylLIGNAFLFALLCSGFIIGL 167
                                       5566666666666666532266654478899999999**************999999666679************** PP

                             ABC-3  75 krktklkedtai..givlsvflalglvlvslikk.skvdl.dsyLfGniltisqedliliaiieavvllllllfwke 147
                                       ++ +   ++t+i  gi +  f++    l+++  +  +  l +s+ +G++++ s   + +++ + a+++ ll+l+  +
  gi|386001904|ref|YP_005920203.1| 168 AAVKGATSETLIlaGIAVNYFFSAMSQLFKYFANdEQLRLmTSWGMGDLAAFSWSKISILLGVFAICIPLLMLKAWD 244
                                       99999999987666********98888888887765555516899******************************** PP

                             ABC-3 148 lllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvs 224
                                       l ++t   e+Ak++g++ ++++++++++ +l v++++ + G i  i l ++P ++ + l+ + + l+  + +lg+  
  gi|386001904|ref|YP_005920203.1| 245 LNIMTSGDETAKSIGVNAERVRVYIMLISSLVVATVVCFTGTIGFIGL-VAPHMARLILGGDHRFLIPASGILGASV 320
                                       *************************99999999999999999988885.7898888888888888888888877655 PP

                             ABC-3 225 vva..GlllSyyld..latGavivlvatllfll 253
                                       ++a  G+++  ++   ++tG +  ++ + +f+ 
  gi|386001904|ref|YP_005920203.1| 321 LIAadGVAMNLIAPtvIPTGIMTSVIGVPFFMY 353
                                       543337777777665556666655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2063.76
//
Query:       gi|386001905|ref|YP_005920204.1|  [L=293]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-33  116.8   0.0    1.5e-33  116.2   0.0    1.2  1  ABC_tran      ABC transporter
    1.9e-09   37.8   0.0    1.3e-06   28.5   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.9e-07   29.4   0.1    2.8e-05   23.7   0.1    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.3e-05   25.8   0.0      2e-05   25.2   0.0    1.3  1  AAA_23        AAA domain
    1.4e-05   24.7   0.1    4.6e-05   23.1   0.0    1.9  2  AAA_29        P-loop containing region of AAA domain
    3.1e-05   23.9   0.0    4.4e-05   23.4   0.0    1.2  1  AAA_15        AAA ATPase domain
    0.00038   20.9   0.0     0.0006   20.2   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0013   17.6   0.1       0.81    8.4   0.0    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0014   17.9   2.1      0.017   14.3   2.1    2.0  1  NB-ARC        NB-ARC domain
     0.0024   17.6   0.0     0.0042   16.8   0.0    1.5  1  AAA_30        AAA domain
      0.003   16.4   0.1     0.0079   15.0   0.0    1.6  2  RNA12         RNA12 protein
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.021   14.2   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.022   14.4   0.0      0.038   13.6   0.0    1.3  1  AAA_27        AAA domain
      0.027   14.7   0.2       0.17   12.1   0.0    2.0  2  AAA_22        AAA domain
      0.033   14.4   0.0       0.13   12.4   0.0    1.9  2  AAA_33        AAA domain
      0.034   14.1   0.1       0.19   11.6   0.0    2.0  2  NACHT         NACHT domain
      0.043   13.1   0.0      0.068   12.4   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.044   13.7   0.1      0.091   12.7   0.0    1.5  2  Rad17         Rad17 P-loop domain
      0.069   13.0   0.0       0.13   12.2   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.088   12.5   0.0       0.12   12.0   0.0    1.2  1  AAA_24        AAA domain
        0.1   11.5   0.0       0.24   10.3   0.0    1.5  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.11   12.8   0.0       0.22   11.9   0.0    1.5  1  AAA_19        AAA domain
       0.15   12.0   0.0       0.26   11.2   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   1.9e-36   1.5e-33       1     137 []      20     167 ..      20     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 1.9e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       lk+vs+++ ++++v ivG+nG+GKStL+k++ +   p++G+il+d k++++ ++ +  k+++++pq  ++ f+   v
  gi|386001905|ref|YP_005920204.1|  20 LKDVSFEIGPSRLVTIVGPNGSGKSTLIKCIDRIIAPEKGSILIDRKEVTKMDRMEIAKNLSYVPQSsARTFSSN-V 95 
                                       79*****************************************************************54444444.7 PP

                                       HHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++               +++e++ ++l+ lg++el+ +      ++LSgGq+q+v +aral+++ k++llDEpt+
  gi|386001905|ref|YP_005920204.1|  96 FDTvlmgrrphigwlsssDDEERVWEVLRLLGIEELAMSGF----AELSGGQQQKVLIARALVQETKVMLLDEPTS 167
                                       777899999******98888888999******999888887....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.6e-09   1.3e-06       2      95 ..      33     118 ..      32     133 .. 0.77
   2 !    7.4   0.0    0.0042       3.3     235     273 ..     137     172 ..     135     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.6e-09
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                         ++GpNgsGKS+L++++d +               + +g + i+++  ++ ++++++  ++  + q++  +++ ++
  gi|386001905|ref|YP_005920204.1|  33 VTIVGPNGSGKSTLIKCIDRI-------------IAPEKGSILIDRKEVTKMDRMEIAKNLS-YVPQSSARTFSSNV 95 
                                       579***************998.............5688899999999999999999999999.88888888888888 PP

                            AAA_21  79 ersqv......eeklssvetlle 95 
                                        +  +        +lss+++ ++
  gi|386001905|ref|YP_005920204.1|  96 FDTVLmgrrphIGWLSSSDDEER 118
                                       88777555555555555554444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0042
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                       +elS G+++   l++  l +    ++ l+DEp ++L+ +
  gi|386001905|ref|YP_005920204.1| 137 AELSGGQQQK-VLIARALVQET--KVMLLDEPTSNLDIW 172
                                       6899999999.66666666665..8***********974 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   3.6e-08   2.8e-05      25     193 ..      31     191 ..      20     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.6e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       ++  ivGpNGSGKs l+  i         + +  ek s li + ke  ++++ e++  ++   ++ + ++ + ++  
  gi|386001905|ref|YP_005920204.1|  31 RLVTIVGPNGSGKSTLIKCID--------RIIAPEKGSILIDR-KEVTKMDRMEIAKNLSYVPQS-SARTFSSNVFD 97 
                                       5678****************3........45667888999998.999999999999888665555.33344445555 PP

                                       EEETTSEEEEEETTEEE-H...HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtk...kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       +v  + + ++    ++  +    ev +ll  +++ ++   +LSgG+++     +l+A   v+ + ++llDe  ++LD
  gi|386001905|ref|YP_005920204.1|  98 TVLMGRRPHIGWLSSSDDEervWEVLRLLGIEELAMSgfaELSGGQQQK----VLIARALVQETKVMLLDEPTSNLD 170
                                       5555555444443444444001555555555555444666899**8763....33344455888999********** PP

                                       HHHHHHHHHHHHHHCTTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkeksknaQfi 193
                                         +   v +++    k+  + 
  gi|386001905|ref|YP_005920204.1| 171 IWHQLDVMNIVSDLVKKRRMT 191
                                       999999999888777665544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.5e-08     2e-05      11      40 ..      21      51 ..      13      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-08
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAik 40
                                      +d++++ ++  l+ I+GpNG+GK+T++ +i 
  gi|386001905|ref|YP_005920204.1| 21 KDVSFEIGPsRLVTIVGPNGSGKSTLIKCID 51
                                      566677755589*****************95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     6e-08   4.6e-05      15      50 ..      23      58 ..      19      61 .. 0.86
   2 ?   -3.0   0.0         8   6.3e+03      44      55 ..     225     237 ..     224     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6e-08
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       ++ei ++  + ++Gp+GsGKSTl+  i  ++ p+k
  gi|386001905|ref|YP_005920204.1| 23 VSFEIGPSRLVTIVGPNGSGKSTLIKCIDRIIAPEK 58
                                      567888888899*************99999999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8
                            AAA_29  44 alLvpak.kvrfN 55 
                                        +L+p++ ++ +N
  gi|386001905|ref|YP_005920204.1| 225 SVLTPENiEAIYN 237
                                       699**99888888 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.6e-08   4.4e-05      14      69 ..      20      72 ..      19      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.6e-08
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                      lkdv+ ++ ++ l +++G+N+sGKS++++ +d ++  +    k  i i+ +++ +++
  gi|386001905|ref|YP_005920204.1| 20 LKDVSFEIGPSrLVTIVGPNGSGKSTLIKCIDRIIAPE----KGSILIDRKEVTKMD 72
                                      577777777777**********************9988....444444444444443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.7e-07    0.0006      24      62 ..      30      69 ..      21     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.7e-07
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdg.giflrgkcdq 62
                                      ++lv ++G+ G+GKs+l++++ r +  ++  i++  k + 
  gi|386001905|ref|YP_005920204.1| 30 SRLVTIVGPNGSGKSTLIKCIDRIIAPEKgSILIDRKEVT 69
                                      389********************99988525545444444 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0     0.001      0.81     244     266 ..      30      52 ..      24      57 .. 0.88
   2 !    7.1   0.1    0.0026         2     323     362 ..     139     178 ..     132     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                                       SSEEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAlek 266
                                         +++IvG++  GKsTL++ +++
  gi|386001905|ref|YP_005920204.1|  30 SRLVTIVGPNGSGKSTLIKCIDR 52 
                                       56889**************9987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHH CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDerm 362
                                        SG   q + i++al  ++k++L+DE ts   + ++ + m
  gi|386001905|ref|YP_005920204.1| 139 LSGGQQQKVLIARALVQETKVMLLDEPTSNLDIWHQLDVM 178
                                       599999**********************988777765555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.1   2.1e-05     0.017      21     148 ..      31     206 ..      23     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE........................................ CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnksdevegrFdsvawv........................................ 57 
                                        +v++vG  G+GK+tl+k i +  +  +g     + +                                        
  gi|386001905|ref|YP_005920204.1|  31 RLVTIVGPNGSGKSTLIKCIDRIIAPEKGS----ILIdrkevtkmdrmeiaknlsyvpqssartfssnvfdtvlmgr 103
                                       479***************998764444332....22222333677999999999*********************** PP

                                       .....EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE......EE-SHHHH.. CS
                            NB-ARC  58 .....vvsktdkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlD......DVweeedwdk 120
                                             +s +d++e+++e +l+ L+ +e  ++ ++e       k  + r+L +   +++lD      D+w++ d  +
  gi|386001905|ref|YP_005920204.1| 104 rphigWLSSSDDEERVWE-VLRLLGIEELAMSGFAELSGgqqQKVLIARALVQETKVMLLDeptsnlDIWHQLDVMN 179
                                       *****************9.9*****99999999998776766888899*************9999999999988777 PP

                                       ...HHHHCHTTSEEEEEESBCCCCCCS- CS
                            NB-ARC 121 igvvlparenrlrvllTTRdeevanavs 148
                                       i   l  +++r+ vl+   d ++a++ s
  gi|386001905|ref|YP_005920204.1| 180 IVSDLV-KKRRMTVLMALHDLNLASRYS 206
                                       777777.889999999888888877665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.4e-06    0.0042      18     101 ..      30     135 ..      26     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.4e-06
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaag......grviglAptgkaAkvLaeelgieastiakllkrlk....... 81 
                                        r+++++Gp G+GK+t++k + ++++ ++      ++ +      + Ak+L+   +  a+t  + +  +        
  gi|386001905|ref|YP_005920204.1|  30 SRLVTIVGPNGSGKSTLIKCIDRIIAPEKgsilidRKEVTKMDRMEIAKNLSYVPQSSARTFSSNVFDTVlmgrrph 106
                                       57999******************999996133333222222223333444443333344444444443335555566 PP

                            AAA_30  82 ........grarlepg.tllivDEagmvd 101
                                               +++r+++  +ll + E +m +
  gi|386001905|ref|YP_005920204.1| 107 igwlsssdDEERVWEVlRLLGIEELAMSG 135
                                       66666666334444444666666666654 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05    0.0079      18      72 ..      31      82 ..      25     126 .. 0.81
   2 ?   -1.5   0.1         1   7.8e+02     309     355 ..     148     194 ..     142     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                             RNA12 18 tFivvkGPrGSGkkeLv..ldrvlkdrkkvlvidCdelvkarndaelisaaAsqlGY 72
                                        +++ GP GSGk+ L+  +dr+++ +k  + id +e++k   d + i   A++l Y
  gi|386001905|ref|YP_005920204.1| 31 RLVTIVGPNGSGKSTLIkcIDRIIAPEKGSILIDRKEVTK--MDRMEI---AKNLSY 82
                                      5799************8778****************9986..344433...445555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                             RNA12 309 iieqsaeeilkmflldseeakkakwtkeqaWklikklskkgsieyne 355
                                       +i ++ ++ +k++lld+  ++ + w++ ++ ++++ l kk  ++  +
  gi|386001905|ref|YP_005920204.1| 148 LIARALVQETKVMLLDEPTSNLDIWHQLDVMNIVSDLVKKRRMTVLM 194
                                       68888888899999989999999999999999999998887766555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.021      25      69 ..      33      77 ..      27     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkee 69
                                      + +vGp GsGK+ l+k++  +++p + +  ++ ++++ + +++ +
  gi|386001905|ref|YP_005920204.1| 33 VTIVGPNGSGKSTLIKCIDRIIAPEKGSILIDRKEVTKMDRMEIA 77
                                      5689********************998888888777766664443 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.9e-05     0.038      19      48 ..      23      52 ..      19      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      ++f+ + ++l  i+GpN +GKst+++ i +
  gi|386001905|ref|YP_005920204.1| 23 VSFEIGPSRLVTIVGPNGSGKSTLIKCIDR 52
                                      67788899****************998865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.17       6      25 ..      31      50 ..      28      96 .. 0.87
   2 ?    0.4   0.1      0.95   7.4e+02      86     125 ..     148     192 ..     110     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                            AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                      ++++++G+ G+GK+tl++ +
  gi|386001905|ref|YP_005920204.1| 31 RLVTIVGPNGSGKSTLIKCI 50
                                      5789************9976 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.95
                            AAA_22  86 lrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvql 125
                                       l ara    ++++++DE    l+   + ++++ +++l++  +  +++
  gi|386001905|ref|YP_005920204.1| 148 LIARALvqeTKVMLLDEPTSnLDiwhQLDVMNIVSDLVK--KRRMTV 192
                                       333333455569999998777877755888888777777..555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.13       1      17 [.      32      48 ..      32      97 .. 0.85
   2 ?   -0.5   0.0       1.6   1.2e+03      16      33 ..     150     180 ..     143     252 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            AAA_33  1 lvllvGlpGsGKstlae 17
                                      lv +vG++GsGKstl++
  gi|386001905|ref|YP_005920204.1| 32 LVTIVGPNGSGKSTLIK 48
                                      7899**********987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                            AAA_33  16 aerllkklgavllssdt.............l 33 
                                       a+ l++++++ ll+++t             +
  gi|386001905|ref|YP_005920204.1| 150 ARALVQETKVMLLDEPTsnldiwhqldvmnI 180
                                       5556666666666666544444333333330 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024      0.19       1      22 [.      31      52 ..      31      60 .. 0.84
   2 ?    0.1   0.0      0.86   6.7e+02      89     158 ..     135     192 ..      85     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                      SCEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklal 22
                                      rlv + G++GsGK+tL++ + +
  gi|386001905|ref|YP_005920204.1| 31 RLVTIVGPNGSGKSTLIKCIDR 52
                                      7899************998755 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.86
                                       -STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHHH CS
                             NACHT  89 glDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfsesrrkql 158
                                       g+ el+   +q          + li ++l++e++++l   p++  d+ +ql       v +++++rr ++
  gi|386001905|ref|YP_005920204.1| 135 GFAELSGGQQQ----------KVLIARALVQETKVMLLDEPTSNLDIWHQLDVM--NIVSDLVKKRRMTV 192
                                       55555554444..........457888889999998888888888887777655..55566666665555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.7e-05     0.068      18      91 ..      32      99 ..      26     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqea 91
                                      l+ ++G  G+GKs+l++ +++ ++++++ + +d+ ++ ++ ++  ei     k+ s + q+ a++++ ++++ +
  gi|386001905|ref|YP_005920204.1| 32 LVTIVGPNGSGKSTLIKCIDRIIAPEKGSILIDRKEVTKMDRM--EIA----KNLSYVPQSSARTFSSNVFDTV 99
                                      68899****************************9988877755..433....3666666666666666666655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.091      36      71 ..      21      56 ..      17      81 .. 0.86
   2 ?   -2.8   0.0       6.5     5e+03     128     170 ..     152     194 ..     132     203 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                             Rad17 36 kadvLesrkkriLLisGPsGCgkstvvkvLskelgi 71
                                      k  + e  + r++ i GP G gkst +k + ++ ++
  gi|386001905|ref|YP_005920204.1| 21 KDVSFEIGPSRLVTIVGPNGSGKSTLIKCIDRIIAP 56
                                      55667778899*****************99887665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.5
                             Rad17 128 dlrtdkklilvedlPnkfyrds.dalrevirkylrssealplil 170
                                        l  + k++l+++  ++  +     + +++   ++ ++  ++++
  gi|386001905|ref|YP_005920204.1| 152 ALVQETKVMLLDEPTSNLDIWHqLDVMNIVSDLVKKRRM-TVLM 194
                                       445556666666655554443323445555555555554.5555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.13      92     120 ..      22      51 ..       4      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinall 120
                                       +++ ++   +++++vG+ G GKStLi+ ++
  gi|386001905|ref|YP_005920204.1|  22 DVSFEIGPsRLVTIVGPNGSGKSTLIKCID 51 
                                       5566666558999*************9886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.12       5      73 ..      33      98 ..      30     116 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDt 73
                                      + i+Gp+g+GK+tl+k + ++  +i  ekG+  +d +++ ++  +e  ++     +   +++++ v+Dt
  gi|386001905|ref|YP_005920204.1| 33 VTIVGPNGSGKSTLIKCI-DR--IIAPEKGSILIDRKEVTKMDRMEIAKNLSYVPQSSARTFSSNVFDT 98
                                      689**************9.55..5666777766666665555444333333333355556666666665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031      0.24      14      49 ..      15      50 ..       7      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlveal 49
                                      ++  +l+ ++ + G ++ v + G  G+Gkstl++ +
  gi|386001905|ref|YP_005920204.1| 15 NSSPILKDVSFEIGPSRLVTIVGPNGSGKSTLIKCI 50
                                      57889***************************9865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.22       9     122 ..      29     178 ..      23     198 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.atTiHrlal....... 77 
                                       +++++ ++++ G+GK++++k+i +++  ++g     i    +t+   +e++++l+ + ++ a+T+ +  +       
  gi|386001905|ref|YP_005920204.1|  29 PSRLVTIVGPNGSGKSTLIKCIDRIIAPEKGS--ILIDRKEVTKMDRMEIAKNLSYVPQSsARTFSSNVFdtvlmgr 103
                                       578899****************9999999976..3444455666666777787755544458888765447777777 PP

                            AAA_19  78 ......................ldfddlltealelle......eaeeekklqeeellivDE.fqdvd.elqyrLl 122
                                                             l++++l +  ++ l           +  +qe+++++ DE ++++d + q  ++
  gi|386001905|ref|YP_005920204.1| 104 rphigwlsssddeervwevlrlLGIEELAMSGFAELSggqqqkVLIARALVQETKVMLLDEpTSNLDiWHQLDVM 178
                                       777777666666665555555533333332222222254443211223444444477777755667766665554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.26      16      39 ..      26      49 ..      22      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlke 39
                                      e +p++ + i Gp gsGK++L+k 
  gi|386001905|ref|YP_005920204.1| 26 EIGPSRLVTIVGPNGSGKSTLIKC 49
                                      567899999*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 1872.31
//
Query:       gi|386001906|ref|YP_005920205.1|  [L=307]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-28   97.5   0.0    1.2e-27   97.1   0.0    1.2  1  ABC_tran      ABC transporter
    3.6e-11   43.4   0.7    2.7e-05   24.1   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-05   24.9   0.0    3.4e-05   24.5   0.0    1.3  1  AAA_23        AAA domain
    4.3e-05   22.4   0.0      0.035   12.8   0.0    2.0  2  AAA_13        AAA domain
    0.00061   19.5   0.0      0.001   18.8   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
     0.0095   15.7   0.0        4.3    6.9   0.0    2.1  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.3   0.0       0.02   14.8   0.0    1.2  1  Rad17         Rad17 P-loop domain
      0.027   14.9   0.1       0.17   12.3   0.1    2.2  1  AAA           ATPase family associated with various cellular 
      0.084   12.6   0.0       0.13   11.9   0.0    1.3  1  AAA_30        AAA domain
       0.17   11.6   0.0       0.35   10.6   0.0    1.5  2  AAA_24        AAA domain
       0.21   11.2   0.2       0.34   10.5   0.2    1.3  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.23   11.9   0.0       0.46   10.9   0.0    1.7  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   8.2e-31   1.2e-27       2     136 ..      47     190 ..      46     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 8.2e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       + v+l +++ge+ +i+G+nGaGK+tL+k+l+ l  pt+G+ +++g d+++ e  ++r++ig ++ +  ++  +lt r
  gi|386001906|ref|YP_005920205.1|  47 DGVDLLIRKGEVFGILGPNGAGKTTLIKILCTLILPTAGRAKVNGYDVER-ESGRVRESIGLVTTDeRSFYWRLTGR 122
                                       789999********************************************.999***********95555568889* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e+++ ++++l  ++lk+ +d++      ++S G+kqr+a+ar ll++p +l++DEpt
  gi|386001906|ref|YP_005920205.1| 123 ENleffaslhnfysdEARDVVDDLLGVVDLKYAADERF----LTYSAGMKQRMAIARGLLNDPAVLFMDEPT 190
                                       ***********955444444666666666666666666....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.8   2.3e-06    0.0035       2      19 ..      59      76 ..      58      98 .. 0.88
   2 !   24.1   0.0   1.8e-08   2.7e-05     237     299 ..     163     224 ..     105     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       ++ GpNg+GK++L+++l
  gi|386001906|ref|YP_005920205.1| 59 FGILGPNGAGKTTLIKIL 76
                                      689**************9 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.8e-08
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell..kelsrngaQviltTHSp 299
                                        S G+k+  a++  ll ++   ++l+ DEp  +L+P +   l +++  ++ +++g  ++++TH+ 
  gi|386001906|ref|YP_005920205.1| 163 YSAGMKQRMAIARGLLNDP---AVLFMDEPTRSLDPGAAQGLRDFIkgEIVRERGKTIFISTHNL 224
                                       4666766666666666666...*************************999999**********96 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.3e-08   3.4e-05      20      59 ..      57      95 ..      46     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.3e-08
                            AAA_23 20 gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfe 59
                                       ++ I GpNGaGKTT++  ++      ++r + +   + e
  gi|386001906|ref|YP_005920205.1| 57 EVFGILGPNGAGKTTLIKILCTLILPTAGRAKVNG-YDVE 95
                                      5899*****************98888777777654.2333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0009       1.3      21      39 ..      61      79 ..      57      97 .. 0.87
   2 !   12.8   0.0   2.3e-05     0.035     526     572 ..     180     225 ..     173     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0009
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NGaGKTtL ++l  l
  gi|386001906|ref|YP_005920205.1| 61 ILGPNGAGKTTLIKILCTL 79
                                      679*********9988665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.3e-05
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                          + ++D P  SLD ++      +ik ++  ++  k +fi+THnle
  gi|386001906|ref|YP_005920205.1| 180 DPAVLFMDEPTRSLDPGAAQGLRDFIKGEI-VRERGKTIFISTHNLE 225
                                       567999***********************9.68999*********98 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   6.8e-07     0.001      18      55 ..      52      90 ..      45      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.8e-07
                            AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                       i+ kg ++ + Gp+G+GK+Tl+  + +l++p+  +++ N
  gi|386001906|ref|YP_005920205.1| 52 LIR-KGeVFGILGPNGAGKTTLIKILCTLILPTAgRAKVN 90
                                      555.444899**********************98777777 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0029       4.3      28      44 ..      61      77 ..      53     100 .. 0.88
   2 !    6.7   0.0    0.0033       4.9     322     365 ..     179     223 ..     160     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
                            AAA_15 28 liGkNnsGKSsileald 44
                                      + G+N++GK++++++l 
  gi|386001906|ref|YP_005920205.1| 61 ILGPNGAGKTTLIKILC 77
                                      67************995 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0033
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllk.elandnktQviitTHS 365
                                       +++++l+++EP  +L p a + l + +k e++++  + ++i+TH+
  gi|386001906|ref|YP_005920205.1| 179 NDPAVLFMDEPTRSLDPGAAQGLRDFIKgEIVRERGKTIFISTHN 223
                                       6899***********************9678888888*******8 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05      0.02      44     101 ..      55     113 ..      46     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                             Rad17  44 kkriLLisGPsGCgkstvvkvLsk.elgiklrewlnpvslkepdnqksdfkgltekesr 101
                                       k ++  i GP G gk+t +k+L   +l +  r  +n+  +   + ++ +  gl+ +++r
  gi|386001906|ref|YP_005920205.1|  55 KGEVFGILGPNGAGKTTLIKILCTlILPTAGRAKVNGYDVERESGRVRESIGLVTTDER 113
                                       45677899**************872566677999****999999999999999887664 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012      0.17       4      22 ..      62      80 ..      60     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                      ESSTTSSHHHHHHHHHHHH CS
                               AAA  4 yGppGtGKTllakavakel 22
                                       Gp G GKT+l+k +++ +
  gi|386001906|ref|YP_005920205.1| 62 LGPNGAGKTTLIKILCTLI 80
                                      7***************985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.8e-05      0.13      14      49 ..      53      89 ..      47     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.8e-05
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkal.reaweaag.grv 49
                                      + +g  v  + Gp G+GKtt++k l + ++ +ag  +v
  gi|386001906|ref|YP_005920205.1| 53 IRKG-EVFGILGPNGAGKTTLIKILcTLILPTAGrAKV 89
                                      4445.48999*************994444555552344 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.35       5      32 ..      59      84 ..      55     113 .. 0.82
   2 ?   -2.8   0.0       2.9   4.4e+03      67      82 ..     215     232 ..     179     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfidte 32
                                      + i Gp+g+GKTtl+k l   +l++ t 
  gi|386001906|ref|YP_005920205.1| 59 FGILGPNGAGKTTLIKIL--CTLILPTA 84
                                      679************998..67776665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                            AAA_24  67 ktlviDt..ideleelcl 82 
                                       kt++i t  ++e+eelc+
  gi|386001906|ref|YP_005920205.1| 215 KTIFISThnLEEAEELCD 232
                                       344443222444555554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00023      0.34       2      21 ..      58      77 ..      57      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      v+++ G+ G+GKTtL++ l+
  gi|386001906|ref|YP_005920205.1| 58 VFGILGPNGAGKTTLIKILC 77
                                      67899**********99877 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031      0.46       3      26 ..      61      84 ..      59     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                      + Gp+g GK+tl+k L++ +l + 
  gi|386001906|ref|YP_005920205.1| 61 ILGPNGAGKTTLIKILCTLILPTA 84
                                      68***************9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1913.69
//
Query:       gi|386001907|ref|YP_005920206.1|  [L=270]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-18   64.3  27.1    1.6e-17   63.6  27.1    1.3  1  ABC2_membrane    ABC-2 type transporter
    1.5e-09   37.5  26.8    1.5e-09   37.5  26.8    1.8  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6  27.1   1.8e-21   1.6e-17       7     209 ..      12     223 ..       7     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.8e-21
                     ABC2_membrane   7 lkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.............pgllffsvlflafsalts 70 
                                       +kr+++++   ++ + ++rl+++++ +l + +v   +g+   g+++             +g+ f   l++++ ++++
  gi|386001907|ref|YP_005920206.1|  12 VKRSYILQMSYKFEF-FLRLFFMFFNILTYYFVAKLIGT--AGMKYlepyggdyfsfvlIGIAFSGYLMVSLRGFSE 85 
                                       678888777777777.77888888888888888886652..233334557888888887777777777777666666 PP

                     ABC2_membrane  71 vapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaas 145
                                       + +  e+ +g+le +lv+p+  +sa+++ ++l++++++ + +l++l+i ++l g+ l   +++ +l++l lt++++s
  gi|386001907|ref|YP_005920206.1|  86 S-VRDEQMMGTLEAMLVTPT-DASAIITLSTLWSFIFASFRVLLYLVIGVLL-GVSLAgaNVLAALIILGLTIVCFS 159
                                       6.999999************.******************************9.999987666*************** PP

                     ABC2_membrane 146 slgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       s+g+l +++ + f+ +  + +l+++   l++G+f+pi+ +p+wlq +++l+P+ty ++++r++l
  gi|386001907|ref|YP_005920206.1| 160 SIGILSASFIMIFKRGDPINMLFMSTSELFGGVFFPISVLPSWLQTVSHLLPMTYSLNGMRHAL 223
                                       *************************************************************987 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   3.7      0.41   3.7e+03     230     252 ..      23      44 ..       8      52 .. 0.64
   2 !   37.5  26.8   1.7e-13   1.5e-09     163     343 ..      62     250 ..      47     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.41
                   ABC2_membrane_3 230 glgipfg.nlglllllfllfglay 252
                                       +  ++f+  l+++++++l +++++
  gi|386001907|ref|YP_005920206.1|  23 K--FEFFlRLFFMFFNILTYYFVA 44 
                                       3..555556667777777777765 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.7e-13
                   ABC2_membrane_3 163 lvgliliilifitasfiav.....siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglg 232
                                       +++++li ++f ++++++      s+  E   +++e +lv++ +++++++ + l++f+ + + +ll+l++  ++g++
  gi|386001907|ref|YP_005920206.1|  62 YFSFVLIGIAFSGYLMVSLrgfseSVRDEQMMGTLEAMLVTPTDASAIITLSTLWSFIFASFRVLLYLVIgvLLGVS 138
                                       33333333333333333333333356677777999**********************************88799966 PP

                   ABC2_membrane_3 233 ipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffggl.fpledlpsalkwifsiiPffa 308
                                       +   n++++l+ + l + +++++g l  s++   + +  + +++++ +s +fgg+ fp++ lps+l++++ ++P+++
  gi|386001907|ref|YP_005920206.1| 139 LAGANVLAALIILGLTIVCFSSIGILSASFIMIFKRGDPINMLFMS-TSELFGGVfFPISVLPSWLQTVSHLLPMTY 214
                                       6666******999999**********99998877777777777777.5555555526699999************** PP

                   ABC2_membrane_3 309 pglgllrli.tgdplweillsliilalfavvyllla 343
                                         +g+   + +g++l e+++ +++l+lf+++++ ++
  gi|386001907|ref|YP_005920206.1| 215 SLNGMRHALlQGYTLRELAPEIGALVLFSAILVPAS 250
                                       ********65999*****************998666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1517.12
//
Query:       gi|386001908|ref|YP_005920207.1|  [L=565]
Description: Phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-22   78.9  10.1    5.9e-11   42.6   0.7    3.4  4  HEAT_2         HEAT repeats
    7.8e-10   38.2   1.7       0.47   10.9   0.0    4.9  4  HEAT           HEAT repeat
    0.00022   21.3   1.8          1    9.4   0.0    4.7  6  Cnd1           non-SMC mitotic condensation complex subunit 1
  ------ inclusion threshold ------
      0.013   15.6   0.6      0.045   13.9   0.6    1.9  1  ArnB_C         Archaellum regulatory network B, C-terminal do
      0.041   14.2   7.0       0.39   11.0   0.3    3.5  2  DUF2935        Domain of unknown function (DUF2935)
      0.064   13.7   0.3         36    5.0   0.0    3.6  2  Rnk_N          Rnk N-terminus
      0.084   13.3   0.2       0.74   10.3   0.0    2.6  2  FtsA           Cell division protein FtsA
       0.29   11.7   4.0        7.8    7.1   0.5    3.9  4  HEAT_EZ        HEAT-like repeat
        1.1    9.3   0.0        1.1    9.3   0.0    4.0  5  SapB_1         Saposin-like type B, region 1
        1.8    8.9   5.7        4.7    7.6   0.2    3.4  4  TetR_C_11      Tetracyclin repressor-like, C-terminal domain
        4.4    6.8   9.6        7.6    6.0   0.5    3.1  3  Lipoprotein_2  Borrelia lipoprotein


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.3   1.1e-10   1.8e-07      15      88 .]      17      99 ..      11      99 .. 0.78
   2 !   42.6   0.7   3.6e-14   5.9e-11       6      88 .]      81     171 ..      77     171 .. 0.82
   3 !   26.3   0.2   4.5e-09   7.3e-06       6      57 ..     116     172 ..     113     204 .. 0.64
   4 ?   -2.1   0.0       3.3   5.4e+03      60      73 ..     503     516 ..     460     523 .. 0.65

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.1e-10
                            HEAT_2 15 evrraairaLg.....rignpealpaLvellededpavRraaaeaLgai....gd.pealpaLkellddddddvvReaA 83
                                      e r +a++ L        + ++a + L++l  ded+ vR  aa+aLga      d ++a++ L + l+ d+d++vR +A
  gi|386001908|ref|YP_005920207.1| 17 EDREEAVDRLStnfaiLPNKESAWQDLIRLTGDEDSFVRSGAADALGAAfsavPDkDSAWQDLIR-LTGDEDSYVRSEA 94
                                      5677777777775533335679999*********************9543443343779*****8.668899999**** PP

                            HEAT_2 84 aeaLa 88
                                      a aL+
  gi|386001908|ref|YP_005920207.1| 95 ANALG 99
                                      *9996 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 3.6e-14
                            HEAT_2   6 qalendpdpevrraairaLg....rignp.ealpaLvellededpavRraaaeaLg....aigd.pealpaLkelld 72 
                                         l+ d+d +vr +a+ aLg     i ++ +a + L++l  ded++vR +aa+aLg    ai d ++a++ L +l  
  gi|386001908|ref|YP_005920207.1|  81 R-LTGDEDSYVRSEAANALGaafsAISDKgSAWQDLHRLTGDEDSYVRSEAADALGaafsAIPDkEAAWQDLHRLS- 155
                                       4.559***************988655554599***********************9544445554889*****955. PP

                            HEAT_2  73 dddddvvReaAaeaLa 88 
                                        d+d++vR +A ++L+
  gi|386001908|ref|YP_005920207.1| 156 GDEDSYVRVSANHSLG 171
                                       7788899999998885 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 4.5e-09
                            HEAT_2   6 qalendpdpevrraairaLg....rignp.ealpaLvellededpavRraaaeaLga 57 
                                        +l+ d+d +vr +a++aLg     i ++  a + L++l  ded++vR  a ++Lg+
  gi|386001908|ref|YP_005920207.1| 116 HRLTGDEDSYVRSEAADALGaafsAIPDKeAAWQDLHRLSGDEDSYVRVSANHSLGR 172
                                       456678888888888888887765554441557777777788888888888888874 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.3
                            HEAT_2  60 dpealpaLkelldd 73 
                                       +p+++++L + +dd
  gi|386001908|ref|YP_005920207.1| 503 TPDDVEHLSKVVDD 516
                                       47778888877754 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00035      0.57       5      26 ..      43      64 ..      42      68 .. 0.90
   2 !   10.9   0.0   0.00029      0.47       5      26 ..      79     100 ..      78     104 .. 0.90
   3 !    9.3   0.0   0.00088       1.4       9      26 ..     118     136 ..     115     140 .. 0.87
   4 ?    2.3   0.0      0.16   2.6e+02       8      25 ..     154     171 ..     151     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                                      HHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAakaLga 26
                                      l++l  D++++VR+ Aa aLga
  gi|386001908|ref|YP_005920207.1| 43 LIRLTGDEDSFVRSGAADALGA 64
                                      577789**************97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00029
                                       HHHHHT-SSHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLga 26 
                                       l++l  D+++ VR+ Aa+aLga
  gi|386001908|ref|YP_005920207.1|  79 LIRLTGDEDSYVRSEAANALGA 100
                                       577789**************97 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00088
                                       H.T-SSHHHHHHHHHHHHH CS
                              HEAT   9 l.sDpspeVReaAakaLga 26 
                                       l  D+++ VR+ Aa aLga
  gi|386001908|ref|YP_005920207.1| 118 LtGDEDSYVRSEAADALGA 136
                                       448**************97 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.16
                                       HHT-SSHHHHHHHHHHHH CS
                              HEAT   8 llsDpspeVReaAakaLg 25 
                                       l  D+++ VR +A  +Lg
  gi|386001908|ref|YP_005920207.1| 154 LSGDEDSYVRVSANHSLG 171
                                       349*********988887 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00063         1      22      82 ..      75     134 ..      53     138 .. 0.81
   2 !    6.5   0.0    0.0048       7.9      23      82 ..     112     170 ..      90     180 .. 0.73
   3 ?    2.0   0.0      0.12   1.9e+02      22      43 ..     147     168 ..     144     197 .. 0.76
   4 ?   -2.1   0.0       2.1   3.4e+03      11      20 ..     290     299 ..     254     310 .. 0.55
   5 ?   -2.2   0.0       2.3   3.8e+03     119     138 ..     378     398 ..     363     429 .. 0.57
   6 ?    4.1   0.2     0.027        45     115     149 ..     463     497 ..     430     505 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00063
                              Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilndmvkekg.flselaklleDenprVvanalaal 82 
                                         ++L +   Ded+yVR  aa ++   ++   + +kg   ++l +l  De++ V++ a  al
  gi|386001908|ref|YP_005920207.1|  75 AWQDLIRLTGDEDSYVRSEAANALGAAFS--AISDKGsAWQDLHRLTGDEDSYVRSEAADAL 134
                                       5678888899***********99987665..6889998999999999***999999987776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0048
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaal 82 
                                        ++L++   Ded+yVR  aa ++   +++   ke    ++l +l  De++ V+ +a ++l
  gi|386001908|ref|YP_005920207.1| 112 WQDLHRLTGDEDSYVRSEAADALGAAFSAIPDKEA-AWQDLHRLSGDEDSYVRVSANHSL 170
                                       57899999999999999999888776654333333.577777777777777777776666 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                              Cnd1  22 lvepLrkrLkDedpyVRktaai 43 
                                         ++L++   Ded+yVR  a  
  gi|386001908|ref|YP_005920207.1| 147 AWQDLHRLSGDEDSYVRVSANH 168
                                       5689999999*******98865 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.1
                              Cnd1  11 gcirvpnlve 20 
                                        c+r+ +l+e
  gi|386001908|ref|YP_005920207.1| 290 YCVRFAELLE 299
                                       2444444444 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 2.3
                              Cnd1 119 ilefLlsyipkdkq.eaeslv 138
                                       ile + ++ p++k+ +a +l+
  gi|386001908|ref|YP_005920207.1| 378 ILEDMCDFLPPKKReHACELA 398
                                       444455555444441222222 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.027
                              Cnd1 115 gqitilefLlsy.ipkdkqeaeslveklcprlqhan 149
                                       + + i+ ++l++  +k+ +e+ +lv+++ +++qh++
  gi|386001908|ref|YP_005920207.1| 463 E-KAIIATILDHsEKKEMEEILDLVKQILAKIQHQK 497
                                       3.34555555550566667999***********986 PP

>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.7e-05     0.045      19      77 ..     229     285 ..     220     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                       HHHTT-HHHHHHHHHHHHHHHHHHT.-HHHHHHHTT--S-HHH.......HHHHHHHHHT CS
                            ArnB_C  19 aleagnlkeATrilqeleeiAeqTr.rieliEaTrrLsrdlesteklskedlSEvtrklr 77 
                                       ++++g   e  + l+e++++ e  r +++l+Ea ++Ls++l+++++l  + l E+ r lr
  gi|386001908|ref|YP_005920207.1| 229 EISEG---EVEKYLKEAKDASEGSRsKEDLLEAVENLSNALKEAQRLREKNLYEIQRDLR 285
                                       56666...5668999*******9997899****************************998 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.6     0.036        58      34      90 ..     240     299 ..     161     407 .. 0.84
   2 ?   11.0   0.3   0.00024      0.39      32     110 ..     430     510 ..     421     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.036
                           DUF2935  34 keakef...kkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkell 90 
                                       keak+     ++ e+ll+ +++ls+ l  a+   e++++++ ++   +++  ++F++ l+
  gi|386001908|ref|YP_005920207.1| 240 KEAKDAsegSRSKEDLLEAVENLSNALKEAQRLREKNLYEIQRDLRVYSQYCVRFAELLE 299
                                       333333333666677777777777777666677777777777777777777777766554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                           DUF2935  32 likeakefkkeFekllaeavelseglv.rasseleeavakLneealk.ltreliqFkkellekvlscklfsiiypll 106
                                       + k+ + +k e++++  e  el++ ++ r++ +++  +a++ +++ k +++e+ ++ k++l k++ +kl++ ++p  
  gi|386001908|ref|YP_005920207.1| 430 YGKQFEYIKSELDEIKLEMKELQQKILdRLDVNEKAIIATILDHSEKkEMEEILDLVKQILAKIQHQKLRGPVTPDD 506
                                       556777788888888888888888887899999*********9998779*************************999 PP

                           DUF2935 107 idHi 110
                                       ++H 
  gi|386001908|ref|YP_005920207.1| 507 VEHL 510
                                       9886 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.022        36      10      35 ..     376     401 ..     376     403 .. 0.93
   2 ?    4.5   0.1      0.03        49       5      26 ..     502     523 ..     502     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.022
                                       HHHHHHHHHCTTTTSSTTHHHHHHHH CS
                             Rnk_N  10 leRLeaLldsladrdppaaeaLeaEL 35 
                                       +e+Le++ d l+ +++++a +L++E+
  gi|386001908|ref|YP_005920207.1| 376 AEILEDMCDFLPPKKREHACELAEEI 401
                                       599**********************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.03
                                       EEHHHHHHHHHHHHCTTTTSST CS
                             Rnk_N   5 itelDleRLeaLldsladrdpp 26 
                                       +t  D e L++ +d ++ r+++
  gi|386001908|ref|YP_005920207.1| 502 VTPDDVEHLSKVVDDARLRAAD 523
                                       7999**********88765444 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.6   2.6e+03      36      51 ..     254     272 ..     164     281 .. 0.60
   2 ?   10.3   0.0   0.00045      0.74      17      88 ..     303     492 ..     301     518 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                                       H...HHHHHT--HHHHHHH CS
                                       x...xxxxxxxxxxxxxxx RF
                              FtsA  36 d...iakalrtaveeAeri 51 
                                       d   +++ l++a++eA+r+
  gi|386001908|ref|YP_005920207.1| 254 DlleAVENLSNALKEAQRL 272
                                       2333444455555555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00045
                                       TTEEEEEEEES--HHHHHHHHHHHHT--HHHHHHH.HHHH--S--.........EEEEEHHHHH............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.........xxxxxxxxxx............. RF
                              FtsA  17 dgalvhlrvigvggngitkdiakalrtaveeAeri.kikyGsala.........ekeigrkels............. 70 
                                       ++a++ ++ + +gg+ + k i++ + +  e A+++ k++ G+ ++                  +             
  gi|386001908|ref|YP_005920207.1| 303 EKAPRTVKLLRIGGKRVEKQIKEKIDEIQEIAKELcKMTVGTEVEplgrevnqqA--------Keispesylrseks 371
                                       6678899999**********************66615677777778855433331........13447777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              FtsA  71 ............................................................................. 70 
                                                                                                                    
  gi|386001908|ref|YP_005920207.1| 372 ilriaeiledmcdflppkkrehacelaeeiykcctledriikleaainyiqpkidierygkqfeyikseldeiklem 448
                                       77777777777777877777777777788888888888888888888888888888888888888888888888888 PP

                                       ..........................GGGGSTTHHHHHHHHHT- CS
                                       ..........................xxxxxxxxxxxxxxxxxx RF
                              FtsA  71 ..........................ggsalpnleelaeralsp 88 
                                                                 ++ +++ + +l++++l+ 
  gi|386001908|ref|YP_005920207.1| 449 kelqqkildrldvnekaiiatildhsEKKEMEEILDLVKQILAK 492
                                       88888888888888888888888888888888888888888743 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.07   1.1e+02      33      54 ..      43      64 ..      43      65 .. 0.79
   2 ?    7.1   0.5    0.0048       7.8       2      54 ..      53     100 ..      52     101 .. 0.79
   3 ?    1.2   0.1      0.35   5.6e+02      39      54 ..     121     136 ..     115     137 .. 0.70
   4 ?    1.3   0.1      0.32   5.2e+02       3      53 ..     126     171 ..     124     172 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.07
                           HEAT_EZ 33 LlalLnddsdeVRaaAagaLgn 54
                                      L++l  d+++ VR  Aa aLg+
  gi|386001908|ref|YP_005920207.1| 43 LIRLTGDEDSFVRSGAADALGA 64
                                      5667778888999999999985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0048
                           HEAT_EZ   2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLgn 54 
                                       +vR +Aa aLG+ a+ + ++   + ++++++ +     d+d  VR  Aa aLg+
  gi|386001908|ref|YP_005920207.1|  53 FVRSGAADALGA-AFSAVPDKDSAWQDLIRLTG-----DEDsYVRSEAANALGA 100
                                       689999999985.44445566668889999999.....999788********96 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.35
                           HEAT_EZ  39 ddsdeVRaaAagaLgn 54 
                                       d+++ VR  Aa aLg+
  gi|386001908|ref|YP_005920207.1| 121 DEDSYVRSEAADALGA 136
                                       4555888888888885 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.32
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaLg 53 
                                       vR  Aa aLG+ a+ + ++ + + +++ ++ +     d+d  VR  A + Lg
  gi|386001908|ref|YP_005920207.1| 126 VRSEAADALGA-AFSAIPDKEAAWQDLHRLSG-----DEDsYVRVSANHSLG 171
                                       78888888874.33344444444444444444.....444455666665555 PP

>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.96   1.6e+03      21      32 ..     230     241 ..     227     242 .. 0.67
   2 ?   -1.3   0.1       1.4   2.3e+03       9      33 ..     238     262 ..     236     262 .. 0.76
   3 ?    0.8   2.1      0.32   5.3e+02      13      35 ..     319     339 ..     317     341 .. 0.85
   4 ?    9.3   0.0    0.0007       1.1      14      38 .]     363     387 ..     363     387 .. 0.97
   5 ?   -3.7   0.3       7.9   1.3e+04      24      32 ..     480     488 ..     476     489 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.96
                                       --HHHHHHHHHH CS
                            SapB_1  21 kTeeeIieaLek 32 
                                        +e e++++L++
  gi|386001908|ref|YP_005920207.1| 230 ISEGEVEKYLKE 241
                                       567778888876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHH-SS--HHHHHHHHHHH CS
                            SapB_1   9 vVkeveklLkdNkTeeeIieaLekv 33 
                                         ke+++  +  +++e+++ea+e++
  gi|386001908|ref|YP_005920207.1| 238 YLKEAKDASEGSRSKEDLLEAVENL 262
                                       5677777777778999999999985 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.32
                                       HHHHH-SS--HHHHHHHHHHHHH CS
                            SapB_1  13 veklLkdNkTeeeIieaLekvCs 35 
                                       vek++k++   +eI e  +++C+
  gi|386001908|ref|YP_005920207.1| 319 VEKQIKEK--IDEIQEIAKELCK 339
                                       88999999..9999999999998 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0007
                                       HHHH-SS--HHHHHHHHHHHHHHS- CS
                            SapB_1  14 eklLkdNkTeeeIieaLekvCskLP 38 
                                       e++L++ k+   I e Le  C+ LP
  gi|386001908|ref|YP_005920207.1| 363 ESYLRSEKSILRIAEILEDMCDFLP 387
                                       79**********************9 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 7.9
                                       HHHHHHHHH CS
                            SapB_1  24 eeIieaLek 32 
                                       eeI++++++
  gi|386001908|ref|YP_005920207.1| 480 EEILDLVKQ 488
                                       678887776 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.25   4.1e+02       2      50 ..      34      81 ..      33      97 .. 0.68
   2 ?    5.3   0.1     0.015        24       1      50 [.      69     117 ..      69     121 .. 0.86
   3 ?    7.6   0.2    0.0029       4.7       2      53 ..     106     155 ..     105     173 .. 0.87
   4 ?   -1.8   0.0       2.4   3.9e+03       9      41 ..     253     283 ..     250     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                         TetR_C_11  2 pDtGslrgDLrallralaealaspragallrallaeaqrdpelaealre 50
                                      p   s  +DL++l  +   +++s  a+++l a ++++ +++ + + l +
  gi|386001908|ref|YP_005920207.1| 34 PNKESAWQDLIRLTGDEDSFVRS-GAADALGAAFSAVPDKDSAWQDLIR 81
                                      66677888888888888888888.5666666666666666555555444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                         TetR_C_11   1 vpDtGslrgDLrallralaealaspragallrallaeaqrdpelaealre 50 
                                       vpD +s  +DL++l  +    ++s +a+ +l a +++++++  + + l++
  gi|386001908|ref|YP_005920207.1|  69 VPDKDSAWQDLIRLTGDEDSYVRS-EAANALGAAFSAISDKGSAWQDLHR 117
                                       79****************999999.6888888889999888888888877 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0029
                         TetR_C_11   2 pDtGslrgDLrallralaealaspragallrallaeaqrdpelaealrerll 53 
                                        D Gs  +DL++l  +    ++s +a+++l a ++++ +++++ + l++ l 
  gi|386001908|ref|YP_005920207.1| 106 SDKGSAWQDLHRLTGDEDSYVRS-EAADALGAAFSAIPDKEAAWQDLHR-LS 155
                                       699**************999999.7999999999***999999999998.54 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.4
                         TetR_C_11   9 gDLrallralaealaspragallrallaeaqrd 41 
                                       +DL++ +++l +al +  a++l    l e+qrd
  gi|386001908|ref|YP_005920207.1| 253 EDLLEAVENLSNALKE--AQRLREKNLYEIQRD 283
                                       7999999999999988..466555555555555 PP

>> Lipoprotein_2  Borrelia lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2       0.2   3.3e+02      70     113 ..     230     271 ..     223     282 .. 0.61
   2 ?    4.5   0.2     0.013        21      65     107 ..     317     359 ..     295     384 .. 0.75
   3 ?    6.0   0.5    0.0047       7.6      35      94 ..     431     487 ..     423     516 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                     Lipoprotein_2  70 lvegkldkivegakkaseaalgeigdlignvaaadadaaagade 113
                                         eg+++k  ++ak ase++ ++  +++ +++ +  +a + a+ 
  gi|386001908|ref|YP_005920207.1| 230 ISEGEVEKYLKEAKDASEGSRSK--EDLLEAVENLSNALKEAQR 271
                                       45778888888888888888877..4444444444344444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                     Lipoprotein_2  65 ksveklvegkldkivegakkaseaalgeigdlignvaaadada 107
                                       k vek +++k+d+i e ak+  + + g+  + +g +++++a++
  gi|386001908|ref|YP_005920207.1| 317 KRVEKQIKEKIDEIQEIAKELCKMTVGTEVEPLGREVNQQAKE 359
                                       4599**************9999999888678888888777554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0047
                     Lipoprotein_2  35 getvesvktkLnkivaelkeekkknaegteksveklvegkldkive.gakkaseaalgeig 94 
                                       g+++e +k++L++i  e+ke ++k  +  + + +  +      i + + kk  e++l+ ++
  gi|386001908|ref|YP_005920207.1| 431 GKQFEYIKSELDEIKLEMKELQQKILDRLDVNEKAII----ATILDhSEKKEMEEILDLVK 487
                                       789999****************999997665555444....44444344444555554432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1521  (0.0848346); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.88u 0.37s 00:00:01.25 Elapsed: 00:00:00.54
# Mc/sec: 3138.07
//
Query:       gi|386001909|ref|YP_005920208.1|  [L=106]
Description: putative nucleotidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-09   35.9   0.3      8e-09   35.7   0.3    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
    4.1e-07   30.0   0.1    4.8e-07   29.8   0.1    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00059   20.0   0.0    0.00065   19.9   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.047   13.5   0.0    1.1  1  DUF294          Putative nucleotidyltransferase DUF294
       0.13   12.1   0.0       0.13   12.1   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.3   2.2e-12     8e-09       2      74 ..      11      77 ..       8     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.2e-12
                                      HHHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE CS
                      NTP_transf_2  2 kklleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv 74
                                      ++l+ e+ke  +   + + lfGSy rG++   SD+Dl+++ +   sr        ++  i + + e + l+ d+v
  gi|386001909|ref|YP_005920208.1| 11 EELKAEMKESLGdkLVGLLLFGSYSRGDYSASSDVDLVILAEGVLSRA-------ERDLIDDLIAE-RSLRHDVV 77
                                      5666677776667789999************************97752.......22222222222.33344444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   1.4e-10   4.8e-07      11      68 ..      23      78 ..       9     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.4e-10
                                      HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEE CS
                           Polbeta 11 keielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvd 68
                                      +++  ++lFGS+ +g++  +SD+Dl +l +  l+  e+  + + +++++   + D+v+
  gi|386001909|ref|YP_005920208.1| 23 DKLVGLLLFGSYSRGDYSASSDVDLVILAEGVLSRAERDLIDDLIAERS--LRHDVVI 78
                                      5788899*************************88888888888888884..4555555 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.8e-07   0.00065       9      71 ..       8      71 ..       1      94 [. 0.67

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHHHH.HH-TT.-EEEE-HHHHTT-.SEESSEEEEEEBTTBSTTSS--HHHHHHHHHHHH CS
                    DNA_pol_B_palm  9 alealvkkaak.eldpe.vevivcGSYRRga.essGDvDvlitkkdakseskklkklleklvkklk 71
                                      +l + +k+++k +l ++ v ++  GSY Rg  + s DvD++i  +++ s+   +++l+++l+++ +
  gi|386001909|ref|YP_005920208.1|  8 KLLEELKAEMKeSLGDKlVGLLLFGSYSRGDySASSDVDLVILAEGVLSR--AERDLIDDLIAERS 71
                                      44445554444044444488999******9725689**********9995..46888888886533 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.3e-05     0.047      29      89 ..       3      65 ..       1      73 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                            DUF294 29 dallrrlielaeeelgkp..pvpfallvmGSeGReEqtlktDqDnalvledeeeeaareyfae 89
                                      ++++ +l+e +++e+++   +  + ll +GS  R++   ++D D  ++ e   ++a+r+ +++
  gi|386001909|ref|YP_005920208.1|  3 RKAVLKLLEELKAEMKESlgDKLVGLLLFGSYSRGDYSASSDVDLVILAEGVLSRAERDLIDD 65
                                      5678899999999999955589999*********************99998777777776665 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05      0.13      88     131 ..      21      64 ..       2      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                     Adenyl_cycl_N  88 keaaieglylmGStgsiaqsekSDlDiWvchrselsaeelelLe 131
                                          ++ gl l GS +   +s++SD+D+ +  +  ls+ e++l++
  gi|386001909|ref|YP_005920208.1|  21 LGDKLVGLLLFGSYSRGDYSASSDVDLVILAEGVLSRAERDLID 64 
                                       346899************************99999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 669.59
//
Query:       gi|386001910|ref|YP_005920209.1|  [L=290]
Description: methyltransferase domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-13   48.7   0.0    1.8e-12   47.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.5e-10   41.2   0.0    2.2e-10   40.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.5e-09   37.3   0.0    2.1e-09   36.8   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    6.2e-08   32.6   0.0    8.9e-08   32.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-07   32.5   0.0    1.7e-07   31.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.4e-07   31.3   0.0      4e-07   30.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.7e-07   29.7   0.0    5.3e-07   29.2   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
    1.5e-05   24.6   0.0    2.3e-05   24.0   0.0    1.2  1  MTS              Methyltransferase small domain
    7.3e-05   22.2   0.0    0.00011   21.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00013   21.8   0.1    0.00018   21.3   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00092   18.3   0.0     0.0013   17.8   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0027   17.1   0.0     0.0038   16.7   0.0    1.1  1  TehB             Tellurite resistance protein TehB
      0.003   16.7   0.0      0.004   16.3   0.0    1.2  1  DREV             DREV methyltransferase
      0.004   16.6   0.1      0.004   16.6   0.1    1.6  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.016   14.7   0.0       0.03   13.8   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
      0.019   14.7   0.1      0.043   13.6   0.1    1.5  1  Met_10           Met-10+ like-protein
      0.024   14.0   0.0      0.034   13.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.041   13.8   0.0      0.063   13.2   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.044   13.4   0.0      0.086   12.5   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.098   12.2   0.0       0.14   11.7   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
       0.14   11.9   0.0        0.2   11.4   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   2.1e-15   1.8e-12       1      97 []      68     163 ..      68     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.1e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT...TEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg...sfDlvvssga 73 
                                       vLd+G+G+G+l++ +a+r+  ++vt+v+++++m+   +e+++ee++ n+e+vq+  ed++ +d+    +D+v++s++
  gi|386001910|ref|YP_005920209.1|  68 VLDIGAGPGTLAIPFAQRV--KHVTAVEPAKGMVLVLQEKMAEEQVsNIEIVQKRWEDVNVADDlktPYDVVIASFS 142
                                       9*****************9..9**********************99************987665556*******988 PP

                                       GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                       l +   +d++ a++++     +gG
  gi|386001910|ref|YP_005920209.1| 143 LGM---ADIRGAIEKMIASAAKGG 163
                                       665...679999999998888887 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   2.6e-13   2.2e-10      10     133 ..      50     183 ..      33     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.6e-13
                   Methyltransf_23  10 sdklerll.pk.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqe 75 
                                       s+ +e++  ++   +++rvLdiG+G G+l+  +++++++vt+v++   +v  ++         ++   qk  +d + 
  gi|386001910|ref|YP_005920209.1|  50 SHRVEETIaGTeITPDSRVLDIGAGPGTLAIPFAQRVKHVTAVEPAKGMVLVLQekmaeeqvsNIEIVQKRWEDVNV 126
                                       55555544233368899****************************99999988899999999999999999999999 PP

                   Methyltransf_23  76 aaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldw 133
                                       a++ +  +d+++++++l+ + d   ++ ++ +  + gG ++l  ++ + ++dr+ +d 
  gi|386001910|ref|YP_005920209.1| 127 ADDLKTPYDVVIASFSLG-MADIRGAIEKMIASAAKGGTIYLYHFAGETHWDRDCRDL 183
                                       *****************9.57889*********************9999999997764 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.5e-12   2.1e-09      18      85 ..      52     121 ..      47     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                            RrnaAD  18 vineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                        ++e +  ++++++  vl+ig+G+G l  ++a+r+k+v+++E  + ++ +lq+k+   + +++++v++  
  gi|386001910|ref|YP_005920209.1|  52 RVEETIAGTEITPDSRVLDIGAGPGTLAIPFAQRVKHVTAVEPAKGMVLVLQEKMAeeQVSNIEIVQKRW 121
                                       567778889**********************************************977889999999855 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0     1e-10   8.9e-08       3     114 ..      64     172 ..      62     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-10
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...ekfD 76 
                                        + rvlD+G+G G+l++ +a+++   ++v+ ++  + ++ + +e+ ++ +++n+e  q  +e+ +  ++d    ++D
  gi|386001910|ref|YP_005920209.1|  64 PDSRVLDIGAGPGTLAIPFAQRV---KHVTAVEPAKGMVLVLQEKMAEEQVSNIEIVQKRWEDVN--VADdlkTPYD 135
                                       6789****************987...78***********************************98..7777889*** PP

                   Methyltransf_31  77 lilsnevlnaladpdkileeiervlkpggilliedprl 114
                                       ++++  +   +ad   ++e+++    +gg + + ++ +
  gi|386001910|ref|YP_005920209.1| 136 VVIAS-FSLGMADIRGAIEKMIASAAKGGTIYLYHFAG 172
                                       ***96.556**********************9988874 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     2e-10   1.7e-07       1      98 [.      69     164 ..      69     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2e-10
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnn..nnvelealdlldldggssfDlvvasnv 75 
                                       L+iG+G G+l+ +++++   +++t+v++ + ++   +ek+a+++  n    + ++e+ +++d+ +   +D+v+as+ 
  gi|386001910|ref|YP_005920209.1|  69 LDIGAGPGTLAIPFAQR--VKHVTAVEPAKGMVLVLQEKMAEEQVSNIeiVQKRWEDVNVADDLK-TPYDVVIASFS 142
                                       8****************..**************66666666555554400455566666554444.6********** PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGr 98 
                                       l   +dir +++++ +  ++gG 
  gi|386001910|ref|YP_005920209.1| 143 LGM-ADIRGAIEKMIASAAKGGT 164
                                       **9.7*********999999997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   4.7e-10     4e-07       1      94 [.      69     165 ..      69     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.7e-10
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT...-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn...sfDlvvssevlhh 73 
                                       Ld+G+G G la ++a+r+++v++v+++k m+ + +ek  ee++ ++e+v+ + e+++++d+    +D+v++s++l  
  gi|386001910|ref|YP_005920209.1|  69 LDIGAGPGTLAIPFAQRVKHVTAVEPAKGMVLVLQEKMAEEQVsNIEIVQKRWEDVNVADDlktPYDVVIASFSLGM 145
                                       8************************************9999999*************99976669*******99987 PP

                                       -CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGll 94 
                                         d + a++++     +gG++
  gi|386001910|ref|YP_005920209.1| 146 A-DIRGAIEKMIASAAKGGTI 165
                                       7.6777777777777777766 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.2e-10   5.3e-07      33     147 ..      51     168 ..      38     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.2e-10
                                       HCHHHHHHHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC CS
                              GidB  33 rhlldslsvlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee 109
                                       + + + +++ e+  ++r  v+D+G+G+G  +ip a  +  +++t +e+ +  +  L+e ++e +++n+eiv++r e+
  gi|386001910|ref|YP_005920209.1|  51 HRVEETIAGTEITPDSR--VLDIGAGPGTLAIPFA--QRVKHVTAVEPAKGMVLVLQEKMAEEQVSNIEIVQKRWED 123
                                       55667777777777777..*********9999976..6677899********************************* PP

                                       ....TTTTT-EEEEEEC...-SSSHHHHHHHHCCCEEEEEEEEEE CS
                              GidB 110 ....kqeeekydvvtsR...Alaslnelteillkllkegglilal 147
                                            + + +ydvv++    ++a ++  +e +     +gg+i+++
  gi|386001910|ref|YP_005920209.1| 124 vnvaDDLKTPYDVVIASfslGMADIRGAIEKMIASAAKGGTIYLY 168
                                       9988788999***98632227777777777777777888888777 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.7e-08   2.3e-05      32     127 ..      65     161 ..      55     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-ST..TTTSTTS-EEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdv..leeveekkfdliv 102
                                       + +vlD+G+G G l++ +a++ ++  vt+v+  +  + + +e +++++++    v+ +++dv   ++++   +d+++
  gi|386001910|ref|YP_005920209.1|  65 DSRVLDIGAGPGTLAIPFAQRVKH--VTAVEPAKGMVLVLQEKMAEEQVSnieiVQKRWEDVnvADDLK-TPYDVVI 138
                                       568******************999..9*******99*****9999999999666666676651156666.99***** PP

                                       E---STTTCHCHHHHHHHHHHHHHH CS
                               MTS 103 sNPPfhagkatelavaeeliaeAke 127
                                           f  g a    ++e++ia+A++
  gi|386001910|ref|YP_005920209.1| 139 AS--FSLGMADIRGAIEKMIASAAK 161
                                       85..999999999999999999875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07   0.00011      47     154 ..      64     170 ..      40     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T...-EEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedd...sfDvv 120
                                       + ++vlD+ +G g la+ +++ v++   v+ ++  + m+ v ++k+ ee ++nie +q   e+++  dd    +Dvv
  gi|386001910|ref|YP_005920209.1|  64 PDSRVLDIGAGPGTLAIPFAQRVKH---VTAVEPAKGMVLVLQEKMAEEQVSNIEIVQKRWEDVNVADDlktPYDVV 137
                                       4569****************99986...777788999****************************99962225799* PP

                                       EEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 121 tvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                         sf l  ++D+  a++++      GG+++   f
  gi|386001910|ref|YP_005920209.1| 138 IASFSL-GMADIRGAIEKMIASAAKGGTIYLYHF 170
                                       ****99.589**********99999999998766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   2.1e-07   0.00018      70     148 ..      61     139 ..      46     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.1e-07
                                       T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEE...S-GGGTTGGG-SE CS
                              PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvv...gDGrkGyeekaPY 143
                                       e+++ +rvL++G+G G l+  +a+ v++++   ++e  k +v   ++++ +++++n+ +v     D +   + k+PY
  gi|386001910|ref|YP_005920209.1|  61 EITPDSRVLDIGAGPGTLAIPFAQRVKHVT---AVEPAKGMVLVLQEKMAEEQVSNIEIVQkrwEDVNVADDLKTPY 134
                                       6899***********************999...9***************9999998877642226888888889999 PP

                                       EEEEE CS
                              PCMT 144 daihv 148
                                       d+++ 
  gi|386001910|ref|YP_005920209.1| 135 DVVIA 139
                                       98875 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.5e-06    0.0013     203     262 ..      66     125 ..      32     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                   tRNA_U5-meth_tr 203 gdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeelt 262
                                       + +l++  G G +++++a+++++v a e ak  v + q  +a++++ n++i++   e++ 
  gi|386001910|ref|YP_005920209.1|  66 SRVLDIGAGPGTLAIPFAQRVKHVTAVEPAKGMVLVLQEKMAEEQVSNIEIVQKRWEDVN 125
                                       46799999********************************************88777765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.4e-06    0.0038      20     126 ..      54     161 ..      35     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-06
                                       HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTE...EEEE--GGG-.-- CS
                              TehB  20 sevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlkni...stalydinea.kl 92 
                                        e +   +i   ++vld+g g g  ++ ++    +vta++  +  +  l+e +  e+++ni   + +  d+n a +l
  gi|386001910|ref|YP_005920209.1|  54 EETIAGTEITPDSRVLDIGAGPGTLAIPFAQRVKHVTAVEPAKGMVLVLQEKMAEEQVSNIeivQKRWEDVNVAdDL 130
                                       4666777888889*************************************999888877761115677899977358 PP

                                       -S-EEEEEEESSGGGS-GGGHHHHHHHHHHTEEE CS
                              TehB  93 derydfilstvvlmfleaeripsiienmqectkv 126
                                       +  yd ++++  l       i   ie m   +  
  gi|386001910|ref|YP_005920209.1| 131 KTPYDVVIASFSLG---MADIRGAIEKMIASAAK 161
                                       99999999876653...34445555555544444 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.7e-06     0.004      95     144 ..      65     115 ..      42     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkky.nvlsale 144
                                       d ++ld+GaG G ++   a+ +++v a e ++ m   l+ k   + +s++e
  gi|386001910|ref|YP_005920209.1|  65 DSRVLDIGAGPGTLAIPFAQRVKHVTAVEPAKGMVLVLQEKMAeEQVSNIE 115
                                       789*******************************99998774312334433 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       2.6   2.2e+03      91     104 ..       3      16 ..       1      23 [. 0.84
   2 !   16.6   0.1   4.6e-06     0.004     159     233 ..      62     140 ..      52     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.6
                              PrmA  91 eveeedWaeewkky 104
                                        + e dW e w ++
  gi|386001910|ref|YP_005920209.1|   3 PITEIDWNEVWNDQ 16 
                                       5889*******987 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.6e-06
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.....eekadvi 230
                                       + ++++vlD+G+G G Lai  a+   k+v+av   +  v v +e ++  +v++   v+   e ++     ++++dv+
  gi|386001910|ref|YP_005920209.1|  62 ITPDSRVLDIGAGPGTLAIPFAQ-RVKHVTAVEPAKGMVLVLQEKMAEEQVSNIEIVQKRWEDVNvaddlKTPYDVV 137
                                       567889*************9876.689**************************55576544443224456699**** PP

                              PrmA 231 vaN 233
                                       +a 
  gi|386001910|ref|YP_005920209.1| 138 IAS 140
                                       *96 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05      0.03       4      57 ..      67     118 ..      64     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEE CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilr 57 
                                        vl+iG G G++ +  A++   k + ++E  + +v  + +k+++++++N++i++
  gi|386001910|ref|YP_005920209.1|  67 RVLDIGAGPGTLAIPFAQRV--KHVTAVEPAKGMVLVLQEKMAEEQVSNIEIVQ 118
                                       589**************997..55679************************997 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     5e-05     0.043      92     152 ..      55     114 ..      35     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                                       HHHHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
                            Met_10  92 erlakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv 152
                                       e++a + + ++ +V+d+ AG G +aip a+  + k v a++     v  l+e ++  +v+++
  gi|386001910|ref|YP_005920209.1|  55 ETIAGTeITPDSRVLDIGAGPGTLAIPFAQ--RVKHVTAVEPAKGMVLVLQEKMAEEQVSNI 114
                                       46666668999******************9..9999****9988888889998888888764 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-05     0.034      48     132 ..      50     138 ..      12     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                                       HHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HH.....HHHHHHHHHHTS-SSS-EEEEES CS
                              CMAS  48 laKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSke.....qaklakkrvdeldlerkvevkll 119
                                       +++++ ++   e+ p +++LdiG+G G+l++  ++r   +v ++   k      q+k+a+++v ++++ +k+  ++ 
  gi|386001910|ref|YP_005920209.1|  50 SHRVEETIAGTEITPDSRVLDIGAGPGTLAIPFAQR-VKHVTAVEPAKGmvlvlQEKMAEEQVSNIEIVQKRWEDVN 125
                                       55677778888999******************9999.4456666655551111155555555555555444444444 PP

                                       -GGG-----SEEE CS
                              CMAS 120 dyedldekvdrvv 132
                                          dl+ ++d v+
  gi|386001910|ref|YP_005920209.1| 126 VADDLKTPYDVVI 138
                                       4445555777765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.4e-05     0.063      11      69 ..      61     116 ..      50     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-05
                   Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkiev 69 
                                        ++++srv+DiG+  g l+i  +  +++k+v+a++ ++g +   +e+++++++++ ie+
  gi|386001910|ref|YP_005920209.1|  61 EITPDSRVLDIGAGPGTLAIPFA--QRVKHVTAVEPAKGMVLVLQEKMAEEQVSN-IEI 116
                                       477899****************9..58999********************99964.554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001     0.086      40     117 ..      63     137 ..      49     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                         ++rvLD+ aG G+l++  + R  k++++ve  k +v +l+e+++e ++++   e+++++ e+++     k ++d+
  gi|386001910|ref|YP_005920209.1|  63 TPDSRVLDIGAGPGTLAIPFAQRV-KHVTAVEPAKGMVLVLQEKMAEEQVSN--IEIVQKRWEDVNVADDLKTPYDV 136
                                       56789*************999886.**********************99987..44445544444444444556666 PP

                                       E CS
                     Cons_hypoth95 117 v 117
                                       v
  gi|386001910|ref|YP_005920209.1| 137 V 137
                                       6 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.14      10      39 ..      61      91 ..      52     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                              MetW 10 likpgsrvldlGcGdGell.ellkeekqvdg 39
                                       i p srvld+G+G G+l   + +  k+v++
  gi|386001910|ref|YP_005920209.1| 61 EITPDSRVLDIGAGPGTLAiPFAQRVKHVTA 91
                                      589**************95144455566554 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024       0.2      23     107 ..      63     138 ..      41     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                            DUF938  23 akttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappa 99 
                                           +rvL+i++G G  A+ fA+++++++  + ++++ +   ++  ++e  +sn++      v++ +++v+  a   
  gi|386001910|ref|YP_005920209.1|  63 T-PDSRVLDIGAGPGTLAIPFAQRVKHVT--AVEPAKGMVLVLQEKMAEEQVSNIEI-----VQKRWEDVN-VADDL 130
                                       3.3448******************99876..44555555545666666666666653.....333334444.44455 PP

                            DUF938 100 pasidail 107
                                       ++++d+++
  gi|386001910|ref|YP_005920209.1| 131 KTPYDVVI 138
                                       66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2048.40
//
Query:       gi|386001911|ref|YP_005920210.1|  [L=512]
Description: Extracellular solute-binding protein, family 5 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-71  241.5   0.0    1.8e-71  241.1   0.0    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.1   0.0     1e-75   1.8e-71       3     370 ..      77     425 ..      75     430 .. 0.90

  Alignments for each domain:
  == domain 1  score: 241.1 bits;  conditional E-value: 1e-75
                                       EESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEE CS
                         SBP_bac_5   3 vpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvr 79 
                                        paLAe  we  +    y f L +gv+++DG+p+tAeDvvf+ e++ d+++++  +s +      +++ea  dytv+
  gi|386001911|ref|YP_005920210.1|  77 LPALAEG-WEYLEAENAYSFELQEGVTWHDGEPFTAEDVVFTVEYIQDHPYQWVDSSII------ESAEAAGDYTVK 146
                                       59*****.699999999************************************998886......8*********** PP

                                       EEESSETTTTTTHCHHHHHHHGC.CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSSE CS
                         SBP_bac_5  80 ftlkkpnalfltllaavpasiak.kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkldr 154
                                       ++l++p+a+f+ l+a + + ++   +   +d +++  +e++vgtGP++l+++++ + +  +e+ + Y+  g+pk+ r
  gi|386001911|ref|YP_005920210.1| 147 LYLTEPYAPFMDLVACTLPILPRhIWEGVSDPEGARDDEALVGTGPFRLADYNKAHgTYLYEAYDGYY-MGAPKVGR 222
                                       ****************9999999445556666677888999*************884666999999*9.9******* PP

                                       EEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS CS
                         SBP_bac_5 155 iefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAi 231
                                       i+f  i +++++ aal++G +  +a++pp+ + +l+ a  l+v +e++  +   l++N++k+pf+d+++R+Al+yAi
  gi|386001911|ref|YP_005920210.1| 223 IVFVKI-SDQTAPAALRQGSA-AAASVPPEAVSSLEGAG-LEV-IEGAFDWNAKLMINHQKEPFSDPEFRRALAYAI 295
                                       ******.9*************.************86665.555.6******************************** PP

                                       -HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTS CS
                         SBP_bac_5 232 Dreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgs 307
                                       Dre++v++vl+g + ++    +pp s+++++  + +  +ydp+ A+ ++++ Gy ++  +       +l+ +    +
  gi|386001911|ref|YP_005920210.1| 296 DREALVEIVLRGEGLAGSPGmVPPDSDWYNPAVEAY--EYDPDLARGMIEDLGYSGTEVE-------VLVAERGIVG 363
                                       *************98888777********9998886..89*****************732.......2344444445 PP

                                       HHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHH CS
                         SBP_bac_5 308 paekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpfl 370
                                        + +++aeli +ql+++G++v+++++d  at ++ v ++dfd++llg g+  +dpd+   + l
  gi|386001911|ref|YP_005920210.1| 364 WPGSRAAELIEEQLEDAGLEVTLRSLDG-ATLDTLVMAWDFDLALLGHGGLGADPDYLRRMTL 425
                                       55669***********************.**************************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2898.70
//
Query:       gi|386001912|ref|YP_005920211.1|  [L=267]
Description: hypothetical protein Mhar_1223 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-14   53.8   0.1    3.7e-14   53.2   0.1    1.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1     2e-18   3.7e-14       1      72 [.     146     231 ..     146     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2e-18
                          CxxCxxCC   1 eCkeCgaCCk.elkvklteedlerlkaaevaeeeeeskkiak.............adgrCvfldeetklCkiYeeRp 63 
                                       eC++Cg CC+ ++ ++l+++d+erl+a+  +   e+ + +a+             ++ +C flde ++lCki+  Rp
  gi|386001912|ref|YP_005920211.1| 146 ECRMCGLCCTlSTPITLEPQDVERLSAHLGIGIRETVEVYAHrvevggyeawamkTTLPCGFLDEAEGLCKIHGARP 222
                                       6*********9999*************9999888888888889***********999******************** PP

                          CxxCxxCC  64 kicrlfpas 72 
                                        icr+fp+ 
  gi|386001912|ref|YP_005920211.1| 223 MICRTFPHL 231
                                       *******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1652.41
//
Query:       gi|386001913|ref|YP_005920212.1|  [L=351]
Description: dipeptide/oligopeptide/nickel ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-37  128.6   9.9    2.2e-37  128.6   9.9    1.9  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.14   2.6e+03     158     174 ..      38      54 ..      22      57 .. 0.66
   2 ?   -2.9   0.1      0.26   4.7e+03      44      57 ..     120     133 ..      85     142 .. 0.56
   3 !  128.6   9.9   1.3e-41   2.2e-37       1     184 [.     143     348 ..     143     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                      BPD_transp_1 158 vlalviavlllnlvadi 174
                                       ++++ +++l ln+v+  
  gi|386001913|ref|YP_005920212.1|  38 YAVAFLLILTLNFVLPR 54 
                                       56667777777777655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.26
                      BPD_transp_1  44 vilsilghlilpvi 57 
                                       vil+ l ++ l   
  gi|386001913|ref|YP_005920212.1| 120 VILDFLPWTLLLTG 133
                                       33333333333333 PP

  == domain 3  score: 128.6 bits;  conditional E-value: 1.3e-41
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlil 54 
                                       g++lGi ++++r+++ldk+l++   +l ++P f ++i+l+l+f                         l+il+hl+ 
  gi|386001913|ref|YP_005920212.1| 143 GLVLGIESGFRRGRRLDKALLGGLMFLNGFPDFFMGIVLLLLFgvlmgvvplsgaltpysglaglpLALDILHHLMA 219
                                       799***************************************************************9999******* PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       p+++l+l+  + + +l+r+ ++ +l +++v +ara+G+s+ +i ++++ +n+l p++t+ ++ ++++++ga+++e++
  gi|386001913|ref|YP_005920212.1| 220 PLAALVLVRVTSPYLLTRNTMITTLRESFVMTARAKGCSEGRIKYRHAGRNSLLPVVTSTGMMIPHMITGALFVEIV 296
                                       ***************************************************************************** PP

                      BPD_transp_1 132 gswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +s+pG+g ll +++l +dy++i+ g++l++++avl+ nl++d+l+  ldprv+
  gi|386001913|ref|YP_005920212.1| 297 FSYPGVGWLLYNSLLTRDYPLIQ-GILLMVTVAVLAANLLVDLLYSRLDPRVS 348
                                       ***********************.***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1828.27
//
Query:       gi|386001914|ref|YP_005920213.1|  [L=287]
Description: binding-protein-dependent transport system inner membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-18   64.7  12.2    8.6e-18   64.7  12.2    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne
    8.9e-07   28.8   0.0    8.9e-07   28.8   0.0    3.4  4  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.21   1.9e+03     161     171 ..      21      31 ..      10      43 .. 0.53
   2 !   64.7  12.2   9.6e-22   8.6e-18       2     184 ..      94     277 ..      93     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.21
                      BPD_transp_1 161 lviavlllnlv 171
                                       l++++lll ++
  gi|386001914|ref|YP_005920213.1|  21 LIALMLLLAIF 31 
                                       22222222222 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 9.6e-22
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalr 77 
                                       +l+G  aa  +++  d++ +++++++ ++P ++++il+        +l   +l  +++l++ls+++ +r+ir++ l 
  gi|386001914|ref|YP_005920213.1|  94 VLIGGTAA-IFGGLYDRFWMRVVDATIAIPDVIVIILVA------AYLRPNVLFmILLLSALSWPGGARVIRAQTLT 163
                                       78999999.************************999999......999*999998********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                         ++++v aar+ Ga+  ++++++++P ++p++++ +i  + +++   + l+flg    ++++    ++g++++++ 
  gi|386001914|ref|YP_005920213.1| 164 LKERMHVSAARTFGAGWPHLLFRHIVPDLAPVLVAIMIQDARRAVFMEAGLSFLG----ISDP-SVMSWGKMIQYAR 235
                                       *******************************************************....3333.3344555555444 PP

                      BPD_transp_1 155 ............nggvlalviavlllnlvadilqrlldprvr 184
                                                     + +al + ++ l++  ++l  +ldpr+r
  gi|386001914|ref|YP_005920213.1| 236 vftflevwkwwlLPTGIALSATLIGLSFTGYALESALDPRLR 277
                                       555556999***99**************************98 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   9.9e-11   8.9e-07       5      42 ..       4      43 ..       3      57 .. 0.87
   2 ?   -3.5   0.1       1.2   1.1e+04       4      11 ..      65      72 ..      64      73 .. 0.83
   3 ?   -1.2   0.6      0.22     2e+03      15      34 ..      85     105 ..      85     112 .. 0.73
   4 ?   -2.6   3.0      0.62   5.5e+03      23      34 ..     125     136 ..     124     151 .. 0.60

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 9.9e-11
                            OppC_N  5 dawrrFkrNklAvvglvilllllliaifaPliaPydp..q 42
                                      d+wr  +   +   gl +++l+ll+aifaPl++Py+p  +
  gi|386001914|ref|YP_005920213.1|  4 DVWREVLGSNVGRMGLLLIALMLLLAIFAPLLTPYSPreN 43
                                      7999999999*************************99752 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                            OppC_N  4 qdawrrFk 11
                                      qd+w +++
  gi|386001914|ref|YP_005920213.1| 65 QDIWTQLL 72
                                      899*9987 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.22
                            OppC_N  15 lAvvglvillllll.iaifaP 34 
                                       +A+++ +i +l+   +aif+ 
  gi|386001914|ref|YP_005920213.1|  85 VALLSGFISVLIGGtAAIFGG 105
                                       588999999988884457765 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 0.62
                            OppC_N  23 lllllliaifaP 34 
                                       ++++l++a + P
  gi|386001914|ref|YP_005920213.1| 125 IVIILVAAYLRP 136
                                       444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1679.22
//
Query:       gi|386001915|ref|YP_005920214.1|  [L=574]
Description: Oligopeptide/dipeptide ABC transporter, ATPase subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-60  202.8   0.0    3.1e-30  105.5   0.0    2.2  2  ABC_tran         ABC transporter
      2e-24   85.8   0.0    1.7e-15   57.3   0.0    2.4  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
      1e-16   61.6   1.4    3.3e-05   23.9   0.1    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      8e-11   42.4   3.7    2.9e-05   24.3   0.1    3.9  2  AAA_22           AAA domain
      4e-10   39.5   0.3    4.9e-06   26.1   0.1    2.9  2  SMC_N            RecF/RecN/SMC N terminal domain
    6.6e-06   26.0   0.2      0.018   14.8   0.0    2.5  2  AAA_24           AAA domain
    9.2e-06   25.7   1.9      0.056   13.4   0.0    2.9  3  RsgA_GTPase      RsgA GTPase
    2.2e-05   24.1   4.5      0.059   13.1   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
    4.9e-05   23.8   4.8      0.029   14.8   0.3    2.8  2  AAA_16           AAA ATPase domain
    7.6e-05   23.2   0.4        0.2   12.1   0.0    3.3  2  AAA              ATPase family associated with various cellul
    0.00017   21.6   3.2      0.021   14.7   0.1    2.5  2  NACHT            NACHT domain
    0.00029   21.0   0.0       0.11   12.6   0.0    2.7  2  AAA_33           AAA domain
    0.00035   20.3   5.7        2.3    7.9   0.0    4.0  4  IstB_IS21        IstB-like ATP binding protein
     0.0004   20.0   3.9       0.28   10.7   0.1    3.5  4  AAA_25           AAA domain
     0.0005   20.0   0.6       0.57   10.1   0.0    2.4  2  APS_kinase       Adenylylsulphate kinase
    0.00054   20.5   0.2       0.87   10.0   0.0    2.3  2  AAA_23           AAA domain
    0.00072   19.5   2.4       0.19   11.6   0.2    2.7  2  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00085   19.1   0.0       0.32   10.7   0.0    2.7  3  PRK              Phosphoribulokinase / Uridine kinase family
     0.0012   18.2   1.4        0.4   10.0   0.1    2.4  2  ATPase           KaiC
     0.0015   19.1   0.1        2.3    8.8   0.0    2.5  2  AAA_18           AAA domain
     0.0027   17.7   2.6        1.2    9.2   0.1    3.6  3  AAA_5            AAA domain (dynein-related subfamily)
     0.0041   16.9   1.5       0.86    9.3   0.1    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0047   16.9   4.1       0.15   12.0   0.3    2.3  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0071   15.8   0.9        4.3    6.7   0.0    3.1  3  PhoH             PhoH-like protein
     0.0072   16.0   0.0       0.72    9.5   0.0    2.5  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0073   15.5   2.7      0.074   12.2   0.4    2.7  2  NB-ARC           NB-ARC domain
     0.0075   16.3   1.3        3.8    7.6   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0078   15.6   0.7        0.8    9.0   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0087   16.3   2.6        1.3    9.2   0.2    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
     0.0091   15.3   0.5       0.13   11.5   0.0    2.4  2  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.011   15.4   4.0        1.5    8.5   0.9    3.6  3  AAA_30           AAA domain
      0.018   14.5   2.3          3    7.2   0.1    2.5  2  Pox_A32          Poxvirus A32 protein
      0.023   14.9   0.6        5.7    7.2   0.2    3.8  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.035   12.3   0.2        1.5    6.9   0.0    2.1  2  Myosin_head      Myosin head (motor domain)
      0.036   14.2   3.3          2    8.4   0.3    2.5  2  DUF87            Helicase HerA, central domain
      0.036   14.4   0.1        3.3    8.1   0.0    2.5  2  RNA_helicase     RNA helicase
      0.038   14.1   0.1       0.11   12.6   0.1    1.8  1  DUF2620          Protein of unknown function DUF2620
      0.041   13.4   0.5       0.91    9.0   0.1    2.2  2  AAA_7            P-loop containing dynein motor region
      0.049   12.9   0.4        1.2    8.3   0.0    2.2  2  Septin           Septin
       0.12   12.3   3.9        2.3    8.1   0.2    2.8  3  NTPase_1         NTPase
       0.13   12.5   0.6         21    5.3   0.4    2.5  2  AAA_28           AAA domain
       0.17   11.6   1.1         15    5.3   0.3    2.7  2  DEAD             DEAD/DEAH box helicase
       0.19   11.8   4.1        3.9    7.5   0.3    2.6  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.22   11.8   2.3        9.2    6.6   0.0    3.4  3  AAA_19           AAA domain
       0.31    9.8   1.0         11    4.7   0.1    2.1  2  DLIC             Dynein light intermediate chain (DLIC)
       0.36   10.0   1.6        8.9    5.4   0.1    2.3  2  TIP49            TIP49 P-loop domain
       0.37   10.2   3.4         69    2.8   0.1    3.9  4  TniB             Bacterial TniB protein
        0.4   10.4   2.7        3.7    7.2   0.1    2.7  2  Sigma54_activat  Sigma-54 interaction domain
        1.1    9.3   3.4         13    5.9   0.0    3.5  3  Cuticle_1        Crustacean cuticle protein repeat


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   1.1e-29     4e-27       2     137 .]      18     172 ..      17     172 .. 0.94
   2 !  105.5   0.0   8.6e-33   3.1e-30       2     137 .]     323     472 ..     322     472 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.1e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.teGeilldgkdlke....qeleslrkeigvlpqe..pqlf 71 
                                         v+l+l +g  +ai+Ge+GaGK+tL  +l+gll+   +G+illdgkdl       ++++  ke+++++q+  + l+
  gi|386001915|ref|YP_005920214.1|  18 AGVDLDLLRGDSLAIIGESGAGKTTLGLALMGLLEGkVSGRILLDGKDLVPldevARRRIRGKEMAMVFQNveDALN 94 
                                       67999***************************999868***********9999999999************999*** PP

                                       TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       p +tv ++               e + +++++ + +gl e k +     p++LSgG+kqr  +a+al+++p++l+lD
  gi|386001915|ref|YP_005920214.1|  95 PIMTVSDQvgeaiyvhreradpgEVEGRVSRLFRAVGLGEAKGRSY---PHQLSGGEKQRALIAMALANDPQVLILD 168
                                       ***************9999998888888************888886...9*************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Epta
  gi|386001915|ref|YP_005920214.1| 169 EPTA 172
                                       **97 PP

  == domain 2  score: 105.5 bits;  conditional E-value: 8.6e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltv 76 
                                       + v+l+l+ege++a+vGe+G+GK+tL+k+++gl + +eG ++l+g++l + + + + ++++++ q+  +++  ++tv
  gi|386001915|ref|YP_005920214.1| 323 DGVDLTLYEGETIALVGESGSGKTTLAKTVIGLFDLAEGVVRLEGEPLLR-RGRDFYQKVQMIYQNpkESISHRMTV 398
                                       789***********************************************.66777789*******8888999999* PP

                                       HHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        e               e+ + ++k+l++++l+  +d  +k+ p+++SgG+ qrva+aral+ +pkll++DEpt+
  gi|386001915|ref|YP_005920214.1| 399 LEAvtepllvqkvggaaERMKIAKKVLEEVELPS-NDAFLKKYPHQISGGEGQRVAIARALVLNPKLLIADEPTS 472
                                       999******99999875555559***********.99999*********************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   4.7e-18   1.7e-15       1      65 []     221     281 ..     221     281 .. 0.91
   2 !   26.3   0.0   2.2e-08     8e-06       1      31 [.     523     553 ..     523     571 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 4.7e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE g++++l+ +p+HPYT++L+rs p ++  kd l++i+g+   ++    GCpF++RC+++ e+C
  gi|386001915|ref|YP_005920214.1| 221 VELGDTQDLLGSPRHPYTRGLIRSSPNMTTTKD-LQGIPGRM--VHGV-PGCPFSDRCTQRIEIC 281
                                       8********************************.77777775..5555.5**************9 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.2e-08
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldre 31 
                                       vE+gp+ ++ + p HPYT++Ll+++p+ld++
  gi|386001915|ref|YP_005920214.1| 523 VEEGPAGEVTTAPVHPYTRKLLEAAPDLDER 553
                                       8**************************9865 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3      0.02       7.5       3      22 ..      31      50 ..      29      70 .. 0.84
   2 !   17.8   0.0   6.1e-06    0.0022     234     298 ..     141     201 ..     111     205 .. 0.83
   3 !    9.4   0.0    0.0022      0.81       3      26 ..     336     362 ..     335     390 .. 0.75
   4 !   23.9   0.1   8.9e-08   3.3e-05     250     301 ..     457     506 ..     427     508 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      ++iG  g+GK++L  al +l
  gi|386001915|ref|YP_005920214.1| 31 AIIGESGAGKTTLGLALMGL 50
                                      79***********9999666 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.1e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHS 298
                                       +++lS G k+  al+++ l+ ++   +l++DEp ++L+    +++ +llke  +   ++ ++ TH+
  gi|386001915|ref|YP_005920214.1| 141 PHQLSGGEKQR-ALIAMALANDP--QVLILDEPTASLDAVTKAEITRLLKERME--DKIaVVITHD 201
                                       6899*******.78877777776..9*************888999999965555..2444667776 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0022
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl...d 26 
                                       +l+G  gsGK++L ++  +l++l    
  gi|386001915|ref|YP_005920214.1| 336 ALVGESGSGKTTLAKTVIGLFDLaegV 362
                                       79***************9998875441 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 8.9e-08
                            AAA_21 250 allralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                       al   +   +ll+ DEp + L+P++++++l+ll ++ +++g  +++ TH+  l
  gi|386001915|ref|YP_005920214.1| 457 ALVLNP---KLLIADEPTSALDPSVQAKILKLLlNIQEERGLAILFITHDIAL 506
                                       333333...89999****************9997777779*********9766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.6   0.00018     0.067       6      38 ..      28      98 ..      25     205 .. 0.57
   2 !   24.3   0.1     8e-08   2.9e-05       8     128 ..     335     500 ..     330     508 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00018
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee........................................e 38
                                       +l+++GesG+GKTtl   l+  l+   +                                            
  gi|386001915|ref|YP_005920214.1| 28 DSLAIIGESGAGKTTLGLALMGLLEGKVS--GrilldgkdlvpldevarrrirgkemamvfqnvedalnpimT 98
                                      5799************9988877742222..134555555555555555555555555555555555555551 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 8e-08
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............. 70 
                                       ++++GesG+GKTtl++++   +d          +vv+ +   +    +d+++++  ++++++++             
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVIGLFDL-------AEGVVRLEGEPLLrRGRDFYQKVQMIYQNPKESishrmtvleavte 404
                                       89********************86.......4455544444443455555555555555555555555555555555 PP

                            AAA_22  71 .................................erlsseellealeqalrarav...ielliiDEaqh.lr...see 107
                                                                        +    +      ++ + ara    ++lli DE    l+   +++
  gi|386001915|ref|YP_005920214.1| 405 pllvqkvggaaermkiakkvleevelpsndaflKKYPHQISGGEGQRVAIARALvlnPKLLIADEPTSaLDpsvQAK 481
                                       55555555666656665666655533333366533333333344444444444478899999999999898644477 PP

                            AAA_22 108 aleeLrsllnlsrkgvqliLv 128
                                       +l+ L ++++  + g++++++
  gi|386001915|ref|YP_005920214.1| 482 ILKLLLNIQE--ERGLAILFI 500
                                       7777766666..888888666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.3e-08   4.9e-06      28     205 ..      31     208 ..      21     220 .. 0.68
   2 !   10.0   0.0    0.0011      0.42      25     205 ..     333     510 ..     325     522 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-08
                                       EEEESTTSSHHHHHHHHHHHCTT..TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGer.sakklrseklsdlihk.skekasvkkaeveitfdnedkk.lkiekeevsisr 101
                                       ai+G+ G+GK+ l  A++ +L  + s + l   + +dl+   + +++++   e++++f+n +++  +i + + ++  
  gi|386001915|ref|YP_005920214.1|  31 AIIGESGAGKTTLGLALMGLLEGKvSGRIL--LDGKDLVPLdEVARRRIRGKEMAMVFQNVEDAlNPIMTVSDQVGE 105
                                       899999999999999997666433133333..345677776567888888999999999988873222222222222 PP

                                       EEETTSEEEEEETTEEE-H....HHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                       xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtk....kevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                                +++ ++++        vs+l++ +g+ +        +LSgGek+ + +a+ +A    +p+ + +lDe 
  gi|386001915|ref|YP_005920214.1| 106 --------AIYVHRERADPgeveGRVSRLFRAVGLGEAkgrsyphQLSGGEKQRALIAMALA---NDPQ-VLILDEP 170
                                       ........2333333332200114456666666666556666666******99877777765...4555.5699*** PP

                                       TTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 168 daaLDeknvkkvaellkeksknaQfivislreemleka 205
                                        a LD+   +++ +llke+ ++   +vi+++  + ++ 
  gi|386001915|ref|YP_005920214.1| 171 TASLDAVTKAEITRLLKERMEDKIAVVITHDISTAARL 208
                                       ******************************97776655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.....SSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.....lkiekee 96 
                                       +  a+vG+ GSGK+ l   +  ++  ++   + + + + l+ +   +++    +v+++++n++++     ++ e+  
  gi|386001915|ref|YP_005920214.1| 333 ETIALVGESGSGKTTLAKTVIGLFDLAE--GVVRLEGEPLLRR--GRDFY--QKVQMIYQNPKESishrmTVLEAVT 403
                                       56789**************966666444..4666778899987..44544..4699999999998433221111111 PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                         + ++++ +   ++ki +k  ++ e+ +  +  + +++++SgGe + va+a  + +   +p  l + De  +aLD 
  gi|386001915|ref|YP_005920214.1| 404 EPLLVQKVGGAAERMKIAKKVLEEVELPSNDAFLKKYPHQISGGEGQRVAIARALVL---NP-KLLIADEPTSALDP 476
                                       222333333333567777777777776666666666677*****9999998876544...34.47899********* PP

                                       HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkekskn..aQfivislreemleka 205
                                       +  +k+ +ll + +++    ++ i+++  + +k+
  gi|386001915|ref|YP_005920214.1| 477 SVQAKILKLLLNIQEErgLAILFITHDIALARKV 510
                                       9999999998765555336677777776666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0033       1.2       4      21 ..      29      46 ..      26      56 .. 0.85
   2 !   14.8   0.0   4.9e-05     0.018       4      41 ..     334     368 ..     331     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0033
                            AAA_24  4 kiliyGpsgiGKTtlake 21
                                      +++i+G+sg+GKTtl + 
  gi|386001915|ref|YP_005920214.1| 29 SLAIIGESGAGKTTLGLA 46
                                      689***********9765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.9e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldad 41 
                                        i+++G+sg+GKTtlak+    + ++d+ +G+ +l++ 
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAKTV---IGLFDLAEGVVRLEGE 368
                                       699**************99...6666776666666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2    0.0014      0.53      96     122 ..      24      50 ..      20      61 .. 0.83
   2 ?   -1.3   0.1       4.9   1.8e+03       5      51 ..     150     198 ..     147     210 .. 0.70
   3 !   13.4   0.0   0.00015     0.056      97     131 ..     330     364 ..     320     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
                                       HCTTSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpe 122
                                       ll+++  +++G+SG+GK+tL  al++ 
  gi|386001915|ref|YP_005920214.1|  24 LLRGDSLAIIGESGAGKTTLGLALMGL 50 
                                       6788999*************8777765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.9
                                       S-EETTTTEES--EEEEE..EESTTTT--HHHHHHHHHHHHHTT-EEEE CS
                       RsgA_GTPase   5 knelvrpkvaNvdqlliv..vslkepelslnlldrfLvlaeekgiepvi 51 
                                       + +l+  + aN  q+li+   +++ + +++  ++r+L +  e +i +vi
  gi|386001915|ref|YP_005920214.1| 150 QRALIAMALANDPQVLILdePTASLDAVTKAEITRLLKERMEDKIAVVI 198
                                       5666677777777777763312333477778888888888888888887 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00015
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelktgevs 131
                                        +++t++lvG+SG GK+tL +++++  +l+ g v+
  gi|386001915|ref|YP_005920214.1| 330 YEGETIALVGESGSGKTTLAKTVIGLFDLAEGVVR 364
                                       46799****************99987777766665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.9   0.00039      0.14      22      46 ..      26      51 ..      17      57 .. 0.77
   2 !   13.1   0.1   0.00016     0.059      14      38 ..     324     348 ..     320     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                            AAA_29 22 kg.atlltGpsGsGKSTllDAiqalL 46
                                      +g +  ++G+sG+GK+Tl  A++ lL
  gi|386001915|ref|YP_005920214.1| 26 RGdSLAIIGESGAGKTTLGLALMGLL 51
                                      344899***********977777666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                            AAA_29  14 ghtieidlkgatlltGpsGsGKSTl 38 
                                       g ++++ + +++ l+G+sGsGK+Tl
  gi|386001915|ref|YP_005920214.1| 324 GVDLTLYEGETIALVGESGSGKTTL 348
                                       5566666455999***********9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.6    0.0021      0.78      25      63 ..      28      62 ..      22     198 .. 0.68
   2 !   14.8   0.3   7.9e-05     0.029      24      57 ..     332     366 ..     325     500 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0021
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       ++ ++GesG GK++l  +l+  le++    ++g+    
  gi|386001915|ref|YP_005920214.1| 28 DSLAIIGESGAGKTTLGLALMGLLEGK----VSGRILLD 62
                                      5799************99999888888....44444444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.9e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lr 57 
                                       +e + l+GesG+GK++l++++   +  ++g++ l+
  gi|386001915|ref|YP_005920214.1| 332 GETIALVGESGSGKTTLAKTVIGLFDLAEGVVrLE 366
                                       57899*************99976555554444333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.025       9.3       3      35 ..      32      67 ..      30     200 .. 0.57
   2 !   12.1   0.0   0.00056       0.2       2      49 ..     336     384 ..     335     401 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.025
                                      EESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelg...vefleisgsell 35
                                      ++G  G GKT+l  a++  l+   +  + ++g++l+
  gi|386001915|ref|YP_005920214.1| 32 IIGESGAGKTTLGLALMGLLEgkvSGRILLDGKDLV 67
                                      7899************99985222222444444444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00056
                                       EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirel 49 
                                        l+G  G GKT+lak v+  ++    +++++g  ll     +  +k++++
  gi|386001915|ref|YP_005920214.1| 336 ALVGESGSGKTTLAKTVIGLFDlaEGVVRLEGEPLL-RRGRDFYQKVQMI 384
                                       699**************9986532447777777776.3344445555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.5     0.016       5.7       3      21 ..      30      48 ..      28      58 .. 0.81
   2 !   14.7   0.1   5.8e-05     0.021       2      21 ..     334     353 ..     333     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      +++ Ge+G GKTtL   l+
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALM 48
                                      689**********966665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.8e-05
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       +++l Ge+GsGKTtL++ ++
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAKTVI 353
                                       899*************9987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.054        20       4      21 ..      32      49 ..      30     117 .. 0.83
   2 !   12.6   0.0   0.00031      0.11       3      36 ..     336     373 ..     335     410 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.054
                            AAA_33  4 lvGlpGsGKstlaerllk 21
                                      ++G +G+GK+tl   l+ 
  gi|386001915|ref|YP_005920214.1| 32 IIGESGAGKTTLGLALMG 49
                                      689********9877765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00031
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdtlrrr 36 
                                        lvG +GsGK+tla+ ++   +    +v+l+   l+rr
  gi|386001915|ref|YP_005920214.1| 336 ALVGESGSGKTTLAKTVIGLFDlaegVVRLEGEPLLRR 373
                                       689************99532223344777766665555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0093       3.4      46      67 ..      26      47 ..      17      56 .. 0.89
   2 ?   -1.8   0.0       6.1   2.2e+03     110     137 ..      65      92 ..      57     100 .. 0.85
   3 ?    5.0   0.1     0.049        18     105     151 ..     158     204 ..     143     213 .. 0.79
   4 !    7.9   0.0    0.0063       2.3      46      66 ..     331     351 ..     323     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0093
                         IstB_IS21 46 kkenivllGpsGvGKshlaial 67
                                      + ++++++G sG+GK+ l  al
  gi|386001915|ref|YP_005920214.1| 26 RGDSLAIIGESGAGKTTLGLAL 47
                                      56789*************9997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.1
                         IstB_IS21 110 dllilDdlgllpldqaeaellfeviekr 137
                                       dl+ lD+++   +  +e +++f+ +e++
  gi|386001915|ref|YP_005920214.1|  65 DLVPLDEVARRRIRGKEMAMVFQNVEDA 92 
                                       78889********999999999999876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.049
                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekrye.rrsiiitsnlpf 151
                                           +++lilD+  +  ld   ++++ +++++r e + +++it +++ 
  gi|386001915|ref|YP_005920214.1| 158 LANDPQVLILDEP-TASLDAVTKAEITRLLKERMEdKIAVVITHDIST 204
                                       445679******7.5789999************983558999988765 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0063
                         IstB_IS21  46 kkenivllGpsGvGKshlaia 66 
                                       + e i+l+G sG GK+ la +
  gi|386001915|ref|YP_005920214.1| 331 EGETIALVGESGSGKTTLAKT 351
                                       5689**************965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.2    0.0082         3      31      54 ..      25      48 ..      20      58 .. 0.88
   2 ?   -0.0   0.1       1.5   5.5e+02      72     150 ..     104     169 ..      82     199 .. 0.61
   3 !   10.7   0.1   0.00077      0.28      30      50 ..     329     349 ..     323     372 .. 0.90
   4 ?   -1.3   0.0       3.7   1.4e+03     165     188 ..     478     502 ..     454     503 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                            AAA_25 31 pagelallaGapgtGKttlaldla 54
                                       +g+  +++G +g+GKttl l l+
  gi|386001915|ref|YP_005920214.1| 25 LRGDSLAIIGESGAGKTTLGLALM 48
                                      47899999***********99886 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.5
                            AAA_25  72 gkVlyvsaEds.edelrrRlravgeal...rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegv 143
                                       g  +yv+ E +   e++ R++++++a+   ++++r + ++l g  +++                  l+a + + +++
  gi|386001915|ref|YP_005920214.1| 104 GEAIYVHRERAdPGEVEGRVSRLFRAVglgEAKGRSYPHQLSGGeKQRA-----------------LIAMALA-NDP 162
                                       6666777776545588888888888887775555555555544433333.................3333333.344 PP

                            AAA_25 144 rlvviDp 150
                                       +++++D 
  gi|386001915|ref|YP_005920214.1| 163 QVLILDE 169
                                       4444443 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00077
                            AAA_25  30 lpagelallaGapgtGKttla 50 
                                       l +ge+++l+G +g+GKttla
  gi|386001915|ref|YP_005920214.1| 329 LYEGETIALVGESGSGKTTLA 349
                                       6689****************8 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.7
                            AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                       v +++++ l +i+++ g a+l++ H
  gi|386001915|ref|YP_005920214.1| 478 VqAKILKLLLNIQEERGLAILFITH 502
                                       5578999999************999 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0072       2.6       5      40 ..      30      65 ..      26      69 .. 0.88
   2 !   10.1   0.0    0.0016      0.57       2      40 ..     332     369 ..     331     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0072
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      + + G sg+GK+t+  al   L+ k    +lLdG  
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMGLLEGKVSGRILLDGKD 65
                                      56789***************99999999999**975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0016
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40 
                                       g ++ l G sgsGK+t+a+++   L++    v++L+G+ 
  gi|386001915|ref|YP_005920214.1| 332 GETIALVGESGSGKTTLAKTVI-GLFDLAEGVVRLEGEP 369
                                       67999**************997.7888888888888875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0024      0.87      22      47 ..      30      55 ..      16      78 .. 0.83
   2 !    8.2   0.1     0.009       3.3      20      36 ..     333     349 ..     315     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0024
                            AAA_23 22 tlItGpNGaGKTTildAiklaLyget 47
                                       +I+G+ GaGKTT+  A+   L g++
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMGLLEGKV 55
                                      58***********9888777776665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.009
                            AAA_23  20 gltlItGpNGaGKTTil 36 
                                          +++G+ G+GKTT+ 
  gi|386001915|ref|YP_005920214.1| 333 ETIALVGESGSGKTTLA 349
                                       56789**********95 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.014       5.1       2      24 ..      30      52 ..      29      56 .. 0.85
   2 !   11.6   0.2   0.00053      0.19       2      23 ..     335     356 ..     334     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                              MobB  2 lgivgksgsGKTtLleklipelk 24
                                      l+i+g sg+GKTtL   l+  l+
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMGLLE 52
                                      789***********888887765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00053
                              MobB   2 lgivgksgsGKTtLleklipel 23 
                                       +++vg sgsGKTtL + +i  +
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVIGLF 356
                                       789**************99876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.038        14       3      24 ..      31      52 ..      30      91 .. 0.85
   2 ?   -2.2   0.0       7.9   2.9e+03     126     149 ..     186     209 ..     148     213 .. 0.79
   3 !   10.7   0.0   0.00088      0.32       2      27 ..     335     360 ..     334     411 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.038
                               PRK  3 gvagsSGaGkttvarklekifg 24
                                      ++ g+SGaGktt+  +l  +++
  gi|386001915|ref|YP_005920214.1| 31 AIIGESGAGKTTLGLALMGLLE 52
                                      799*********9888877766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.9
                               PRK 126 vaelldlkiyvdisidlelarklq 149
                                       ++e ++ ki v+i +d+  a +l+
  gi|386001915|ref|YP_005920214.1| 186 LKERMEDKIAVVITHDISTAARLT 209
                                       677788899999999999988885 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00088
                               PRK   2 IgvagsSGaGkttvarklekifgrek 27 
                                       I++ g+SG+Gktt+a+++  +f  ++
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVIGLFDLAE 360
                                       99***************999998433 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.012       4.2      17      37 ..      25      45 ..      19      57 .. 0.89
   2 !   10.0   0.1    0.0011       0.4      16      38 ..     329     351 ..     321     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                            ATPase 17 pegrvvlitGepGtGKtifal 37
                                       +g +  i Ge+G+GKt+++l
  gi|386001915|ref|YP_005920214.1| 25 LRGDSLAIIGESGAGKTTLGL 45
                                      6789999***********997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                            ATPase  16 ipegrvvlitGepGtGKtifalq 38 
                                       ++eg+++ ++Ge+G+GKt++a++
  gi|386001915|ref|YP_005920214.1| 329 LYEGETIALVGESGSGKTTLAKT 351
                                       6899****************975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.012       4.5       3      44 ..      32      72 ..      30     122 .. 0.66
   2 !    8.8   0.0    0.0062       2.3       1      17 [.     335     351 ..     335     385 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.012
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpe 44
                                      + G +G+GKttl+ +L  +  + g +++ ++ ++  l + d+ 
  gi|386001915|ref|YP_005920214.1| 32 IIGESGAGKTTLGLALMGL--LeGKVSGRILLDGKDLVPLDEV 72
                                      8899************555..1455555555555555555554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0062
                            AAA_18   1 IlltGtpGvGKttlake 17 
                                       I+l G +G+GKttlak 
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKT 351
                                       899************96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.06        22       3      25 ..      31      53 ..      29      93 .. 0.84
   2 ?    1.2   0.0      0.93   3.4e+02      11      47 ..     178     214 ..     176     224 .. 0.90
   3 !    9.2   0.1    0.0032       1.2       3      20 ..     336     353 ..     334     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.06
                                      EEE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnr 25
                                       ++G++G gK++l   l  +l+ 
  gi|386001915|ref|YP_005920214.1| 31 AIIGESGAGKTTLGLALMGLLEG 53
                                      689**********9999888844 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.93
                                       SHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B-- CS
                             AAA_5  11 gKselaerlaaalnreveyvqltrdtteedlkgrrei 47 
                                        K e+++ l++++++++ +v  ++  t++ l+ ++ +
  gi|386001915|ref|YP_005920214.1| 178 TKAEITRLLKERMEDKIAVVITHDISTAARLTDKMAV 214
                                       6999**************************9998876 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0032
                                       EEE--SSSSHHHHHHHGG CS
                             AAA_5   3 lLvGppGtgKselaerla 20 
                                        LvG++G+gK++la+ + 
  gi|386001915|ref|YP_005920214.1| 336 ALVGESGSGKTTLAKTVI 353
                                       59************9875 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.023       8.4       5      23 ..      31      49 ..      28      52 .. 0.85
   2 !    9.3   0.1    0.0024      0.86       3      21 ..     334     352 ..     332     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                         PduV-EutP  5 lliGkvgsGKttLtqalkg 23
                                       +iG++g+GKttL  al g
  gi|386001915|ref|YP_005920214.1| 31 AIIGESGAGKTTLGLALMG 49
                                      589**********988865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0024
                         PduV-EutP   3 killiGkvgsGKttLtqal 21 
                                        i l+G++gsGKttL++++
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAKTV 352
                                       588************9976 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4     0.036        13      19      39 ..      27      47 ..      13      56 .. 0.77
   2 !   12.0   0.3   0.00042      0.15      19      42 ..     332     355 ..     316     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                                      TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                      gd +++ G+ GaGKTtl  +l
  gi|386001915|ref|YP_005920214.1| 27 GDSLAIIGESGAGKTTLGLAL 47
                                      778999**********97665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00042
                                       TEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglaka 42 
                                       g++i+L G+ G+GKTtl++ ++  
  gi|386001915|ref|YP_005920214.1| 332 GETIALVGESGSGKTTLAKTVIGL 355
                                       788****************98765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.012       4.3      21      91 ..      29      97 ..      22     122 .. 0.65
   2 ?    0.3   0.0       1.1     4e+02     131     157 ..     177     204 ..     160     219 .. 0.68
   3 ?    5.1   0.1     0.037        14      20      38 ..     333     351 ..     325     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                                      EEEEE--TTSSTTHHHHHHHHHHHHTTS-S.EEEEE.E-S--TT----SS---------TTTHHHHHHHTTTS CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvk.riilt.rpaveageelGflpgdleekvdpylrplydaLkdll 91
                                       + +iG++G+GKt l +al    l ++kv+ ri+l  +  v   +e+        + +++ ++ + daL+ ++
  gi|386001915|ref|YP_005920214.1| 29 SLAIIGESGAGKTTLGLAL--MGLLEGKVSgRILLDgKDLVP-LDEVARRRI-RGKEMAMVFQNVEDALNPIM 97
                                      5679*********998764..445555554266554233333.344554555.35566667777777777666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                                       --HHHHHHHH.TTB-TT-EEEEEE---- CS
                              PhoH 131 ttkeqmkmfl.tRlGenskvvvtGdvtq 157
                                       +tk+++  +l  R+  +  vv+t+d++ 
  gi|386001915|ref|YP_005920214.1| 177 VTKAEITRLLkERMEDKIAVVITHDIST 204
                                       455555554426999999*******986 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.037
                                       SEEEEE--TTSSTTHHHHH CS
                              PhoH  20 divfaiGpaGtGKtylava 38 
                                       + +  +G++G+GKt la +
  gi|386001915|ref|YP_005920214.1| 333 ETIALVGESGSGKTTLAKT 351
                                       567889**********964 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.091        33      12      32 ..      25      45 ..      22     108 .. 0.88
   2 !    9.5   0.0     0.002      0.72       4      37 ..     321     355 ..     318     427 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.091
                                      BTT-EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 12 vqGqrtlipgafgvGktvisq 32
                                       +G  ++i+g++g Gkt++  
  gi|386001915|ref|YP_005920214.1| 25 LRGDSLAIIGESGAGKTTLGL 45
                                      799**************9864 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                                       HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   4 vlDal.fpivqGqrtlipgafgvGktvisqslskq 37 
                                       ++D + +++ +G++++++g++g Gkt+++++++  
  gi|386001915|ref|YP_005920214.1| 321 AVDGVdLTLYEGETIALVGESGSGKTTLAKTVIGL 355
                                       5665547999*******************998765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.16        58      22      36 ..      29      43 ..      22      48 .. 0.88
   2 !   12.2   0.4    0.0002     0.074      22      45 ..     334     357 ..     322     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                                      EEEEEESTTSSHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttl 36
                                       +a+ G  G GKttl
  gi|386001915|ref|YP_005920214.1| 29 SLAIIGESGAGKTTL 43
                                      579***********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0002
                                       EEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksd 45 
                                        +alvG  G+GKttlak ++  +d
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAKTVIGLFD 357
                                       689**************9976555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.018       6.7       2      22 ..      30      50 ..      29      60 .. 0.81
   2 ?    7.6   0.0      0.01       3.8       2      21 ..     335     354 ..     334     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                       ai+G + +GK+tL  al+g 
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMGL 50
                                      69************9999875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.01
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       +a+vG + +GK+tL ++ +g
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVIG 354
                                       89************999876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.076        28      24      46 ..      29      51 ..      24      62 .. 0.89
   2 !    9.0   0.0    0.0022       0.8      22      46 ..     332     356 ..     317     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.076
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsll 46
                                      +l ++G +G+GKt l  +l++ll
  gi|386001915|ref|YP_005920214.1| 29 SLAIIGESGAGKTTLGLALMGLL 51
                                      6889***************9998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0022
                      Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsll 46 
                                       g  + lvG +GsGKt lak + +l+
  gi|386001915|ref|YP_005920214.1| 332 GETIALVGESGSGKTTLAKTVIGLF 356
                                       557899**************99886 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.023       8.4       2      20 ..      30      48 ..      29      54 .. 0.87
   2 !    9.2   0.2    0.0037       1.3       2      19 ..     335     352 ..     334     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                                      EEEESSTTSSHHHHHHCHC CS
                               Roc  2 vvlvGdsgvGKtsllkrfv 20
                                      + ++G+sg+GKt+l   ++
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALM 48
                                      579**********977766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0037
                                       EEEESSTTSSHHHHHHCH CS
                               Roc   2 vvlvGdsgvGKtsllkrf 19 
                                       + lvG+sg+GKt+l+k +
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTV 352
                                       789***********9876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       0.6   2.2e+02      21      35 ..      32      46 ..      26      66 .. 0.78
   2 !   11.5   0.0   0.00035      0.13      19      53 ..     335     369 ..     332     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.6
                        Zeta_toxin 21 lgGqpGAGKselael 35
                                      + G +GAGK++l  +
  gi|386001915|ref|YP_005920214.1| 32 IIGESGAGKTTLGLA 46
                                      5599******98655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00035
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                       i l+G +G+GK++la+ +   ++ +++vvrl++  
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVIGLFDLAEGVVRLEGEP 369
                                       7799**************************98765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.08        29      21      43 ..      30      52 ..      23     103 .. 0.86
   2 ?   -1.0   0.0       3.4   1.3e+03      86     114 ..     158     188 ..     121     214 .. 0.67
   3 ?    8.5   0.9     0.004       1.5      20      96 ..     334     469 ..     325     500 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.08
                            AAA_30 21 avltGpAGtGKttalkalreawe 43
                                       ++ G  G+GKtt+  al  ++e
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMGLLE 52
                                      5789*********9777766666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                            AAA_30  86 lepg.tllivDE.agmvdtkqlaallkaaek 114
                                       l+++ ++li DE ++ +d+ + a++++ +++
  gi|386001915|ref|YP_005920214.1| 158 LANDpQVLILDEpTASLDAVTKAEITRLLKE 188
                                       3344488888884333455554444444444 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.004
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.g...............................................gr 48 
                                       + +l+G  G+GKtt+ k++  +++ a g                                               ++
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAKTVIGLFDLAeGvvrlegepllrrgrdfyqkvqmiyqnpkesishrmtvleavtepllvQK 410
                                       6789*************999888877467777777777777777777777777777777777777777777777777 PP

                            AAA_30  49 viglAptgkaAkvLaeelgieast..iakllkrlk.........grarlepgtllivDE 96 
                                       v g+A   k Ak++ ee++++++   ++k+ ++           +ra + + +lli DE
  gi|386001915|ref|YP_005920214.1| 411 VGGAAERMKIAKKVLEEVELPSNDafLKKYPHQISggegqrvaiARALVLNPKLLIADE 469
                                       77777777777777777777655311333333333666666665434444446666666 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.015       5.6      16      35 ..      30      49 ..      23      60 .. 0.85
   2 ?    7.2   0.1    0.0082         3      16      32 ..     335     351 ..     329     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.015
                           Pox_A32 16 lalvGgsGsGktvyLlsLlr 35
                                      la++G+sG+Gkt+  l+L+ 
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMG 49
                                      89***********9888875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0082
                           Pox_A32  16 lalvGgsGsGktvyLls 32 
                                       +alvG+sGsGkt+  + 
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKT 351
                                       89**********97665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.016       5.7      32      89 ..     143     187 ..     133     188 .. 0.71
   2 ?    2.2   0.0      0.58   2.1e+02      63      88 ..     461     486 ..     431     488 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +lSGGekq ++ +a+a  l           +++++++LDE  ++lD+ + a++ +ll+
  gi|386001915|ref|YP_005920214.1| 143 QLSGGEKQRAL-IAMA--L----------ANDPQVLILDEPTASLDAVTKAEITRLLK 187
                                       67888884332.2222..1..........23588999999999999999988888876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.58
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllell 88 
                                       +++l++ DE  s lD+  +a++l+ll
  gi|386001915|ref|YP_005920214.1| 461 NPKLLIADEPTSALDPSVQAKILKLL 486
                                       46788888888888888888888876 PP

>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.053        20      86     101 ..      28      43 ..      24      56 .. 0.82
   2 ?    6.9   0.0    0.0042       1.5      86     109 ..     333     356 ..     328     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.053
                                       EEEEEESSTTSSHHHH CS
                       Myosin_head  86 qsilisGEsGAGKtea 101
                                        s+ i GEsGAGKt  
  gi|386001915|ref|YP_005920214.1|  28 DSLAIIGESGAGKTTL 43 
                                       578899********75 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0042
                                       EEEEEESSTTSSHHHHHHHHHHHH CS
                       Myosin_head  86 qsilisGEsGAGKteatKkvlqyl 109
                                        +i + GEsG GKt  +K v+  +
  gi|386001915|ref|YP_005920214.1| 333 ETIALVGESGSGKTTLAKTVIGLF 356
                                       578899**************9876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0056         2      14      44 ..      18      48 ..       9      63 .. 0.70
   2 ?    5.7   0.2     0.039        14      26      42 ..     335     351 ..     323     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0056
                             DUF87 14 vyldlnklvtrHlAilgsTGsGKSntvavLl 44
                                      + +dl+ l   +lAi+g++G+GK+++   L+
  gi|386001915|ref|YP_005920214.1| 18 AGVDLDLLRGDSLAIIGESGAGKTTLGLALM 48
                                      567777788899***********98754444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.039
                             DUF87  26 lAilgsTGsGKSntvav 42 
                                       +A +g++GsGK+++++ 
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKT 351
                                       799***********997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.21        79       3      23 ..      32      52 ..      30      69 .. 0.81
   2 ?    8.1   0.0    0.0091       3.3       1      19 [.     335     353 ..     335     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.21
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      + G+sg GK+tl   L+  l+
  gi|386001915|ref|YP_005920214.1| 32 IIGESGAGKTTLGLALMGLLE 52
                                      89*********9887776555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0091
                      RNA_helicase   1 iwlyGpsgeGKStlakeLa 19 
                                       i l+G+sg GK+tlak+++
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVI 353
                                       5689***********9965 PP

>> DUF2620  Protein of unknown function DUF2620
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00031      0.11       9      50 ..     177     218 ..     174     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00031
                           DUF2620   9 lekeeikelieklaedkvevtvksDldAamkvksgeaDyylG 50 
                                       + k+ei++l+++ +edk+ v++++D+  a ++ +  a +y G
  gi|386001915|ref|YP_005920214.1| 177 VTKAEITRLLKERMEDKIAVVITHDISTAARLTDKMAVLYAG 218
                                       789*****************************9999999987 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 ?    2.2   0.0      0.31   1.1e+02      34      53 ..      28      47 ..      20      56 .. 0.78
   2 ?    9.0   0.1    0.0025      0.91      27      54 ..     326     353 ..     324     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.31
                             AAA_7 34 kpvllvGptGtGKtviikdl 53
                                       ++ ++G++G GKt++   l
  gi|386001915|ref|YP_005920214.1| 28 DSLAIIGESGAGKTTLGLAL 47
                                      66789*********986555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0025
                             AAA_7  27 elllknkkpvllvGptGtGKtviikdll 54 
                                       +l l ++  + lvG++G+GKt+++k+++
  gi|386001915|ref|YP_005920214.1| 326 DLTLYEGETIALVGESGSGKTTLAKTVI 353
                                       5667788999*************99876 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.22        81       7      21 ..      30      44 ..      27      54 .. 0.85
   2 ?    8.3   0.0    0.0033       1.2       6      26 ..     334     354 ..     331     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.22
                                      EEEEEBTTSSCCCCC CS
                            Septin  7 lmvvGesglGkttli 21
                                      l ++Gesg Gkttl 
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLG 44
                                      6799*********95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                                       EEEEEEBTTSSCCCCCCTTSS CS
                            Septin   6 tlmvvGesglGkttlintlfe 26 
                                       t+ +vGesg Gkttl +t++ 
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAKTVIG 354
                                       7889*************9875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.091        33       2      25 ..      30      53 ..      29      60 .. 0.81
   2 ?   -2.1   0.0       8.5   3.1e+03      94     123 ..     160     187 ..     136     226 .. 0.53
   3 ?    8.1   0.2    0.0062       2.3       2      22 ..     335     355 ..     334     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.091
                                      EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                                      ++i G++G GKtTl   ++ ll+ 
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLGLALMGLLEG 53
                                      5789**********9988888854 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.5
                                       HHH-EEEE--.-STTGGG-HHHHHHHHHHHT CS
                          NTPase_1  94 seadviviDE.iGkmElkskkfkeaveevLk 123
                                       ++++v+++DE   ++    ++ k +++++Lk
  gi|386001915|ref|YP_005920214.1| 160 NDPQVLILDEpTASLD---AVTKAEITRLLK 187
                                       5666777777112222...222333333333 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0062
                                       EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                       +++ G++G+GKtTl k v+ l
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAKTVIGL 355
                                       7899************99876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.077        28       3      20 ..      31      48 ..      29     117 .. 0.75
   2 ?    5.3   0.4     0.059        21       2      17 ..     335     350 ..     334     359 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.077
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                      +i+G +++GKTtl  aL 
  gi|386001915|ref|YP_005920214.1| 31 AIIGESGAGKTTLGLALM 48
                                      79***********88775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.059
                            AAA_28   2 ivitGgestGKTtlle 17 
                                       i+++G +++GKTtl++
  gi|386001915|ref|YP_005920214.1| 335 IALVGESGSGKTTLAK 350
                                       89************97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.097        36      11      73 ..      24     188 ..      20     223 .. 0.63
   2 ?    5.3   0.3      0.04        15      11      31 ..     329     349 ..     324     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.097
                                       HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................................ 47 
                                       +l+g+++ + +e G+GKT+  l  +   ++e   k                                          
  gi|386001915|ref|YP_005920214.1|  24 LLRGDSLAIIGESGAGKTTLGLALMG--LLEG--KVSgrilldgkdlvpldevarrrirgkemamvfqnvedalnpi 96 
                                       56788899999999999987443333..3342..2222355555555666666666666666666666666667777 PP

                                       .................................................................-EEEEE.ESSHH CS
                                       .................................................................xxxxxx.xxxxx RF
                              DEAD  48 .................................................................pkaliv.ePtre 58 
                                                                                                        p++li+ ePt +
  gi|386001915|ref|YP_005920214.1|  97 mtvsdqvgeaiyvhreradpgevegrvsrlfravglgeakgrsyphqlsggekqraliamalandPQVLILdEPTAS 173
                                       77777776666666666667777777777777777777777777777777777666666666666666666567777 PP

                                       HHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD  59 Laeqtlnnlkkfkky 73 
                                       L   t  ++++++k+
  gi|386001915|ref|YP_005920214.1| 174 LDAVTKAEITRLLKE 188
                                       766666666666664 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.04
                                       HHTTCEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlaf 31 
                                       +++g+ + + +e GsGKT+ +
  gi|386001915|ref|YP_005920214.1| 329 LYEGETIALVGESGSGKTTLA 349
                                       45899999**********985 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.011       3.9       5      25 ..      33      53 ..      30      67 .. 0.86
   2 ?    4.7   0.3     0.083        30       6      21 ..     339     354 ..     335     362 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
                                      ESSTTSSHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  5 stkGGvGKTtlaanLaralar 25
                                       + +G+GKTtl ++L+ +l  
  gi|386001915|ref|YP_005920214.1| 33 IGESGAGKTTLGLALMGLLEG 53
                                      578*************99975 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.083
                                       SSTTSSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                              CbiA   6 tkGGvGKTtlaanLar 21 
                                       + +G+GKTtla + + 
  gi|386001915|ref|YP_005920214.1| 339 GESGSGKTTLAKTVIG 354
                                       78********977665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.5   1.8e+02      10      27 ..      27      44 ..      22      99 .. 0.88
   2 ?    6.6   0.0     0.025       9.2      10      35 ..     332     357 ..     326     372 .. 0.85
   3 ?   -0.3   0.0       3.3   1.2e+03      99     127 ..     458     488 ..     389     502 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.5
                            AAA_19 10 ekvllvtaGpGtGKTrvl 27
                                       + l++++  G GKT++ 
  gi|386001915|ref|YP_005920214.1| 27 GDSLAIIGESGAGKTTLG 44
                                      56789**********975 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallv 35 
                                        +++++++  G+GKT++ k+++ l+ 
  gi|386001915|ref|YP_005920214.1| 332 GETIALVGESGSGKTTLAKTVIGLFD 357
                                       67899*************99998765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.3
                            AAA_19  99 klqeeellivDE.fqdvd.elqyrLlkallg 127
                                        + + +lli DE ++ +d  +q ++lk ll+
  gi|386001915|ref|YP_005920214.1| 458 LVLNPKLLIADEpTSALDpSVQAKILKLLLN 488
                                       3447778999996688998889999988774 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.064        23      25      51 ..      27      53 ..      21      62 .. 0.79
   2 ?    4.7   0.1      0.03        11      24      50 ..     331     357 ..     326     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.064
                              DLIC 25 gksvlvlGedgsGkttliaklqGveee 51
                                      g s+ ++Ge+g+Gkttl   l G+ e 
  gi|386001915|ref|YP_005920214.1| 27 GDSLAIIGESGAGKTTLGLALMGLLEG 53
                                      77899************8888886554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.03
                              DLIC  24 sgksvlvlGedgsGkttliaklqGvee 50 
                                        g ++ ++Ge+gsGkttl   + G+ +
  gi|386001915|ref|YP_005920214.1| 331 EGETIALVGESGSGKTTLAKTVIGLFD 357
                                       578899************988888765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2       0.1        38      48      73 ..      25      50 ..      14      63 .. 0.80
   2 ?    5.4   0.1     0.024       8.9      50     117 ..     332     402 ..     322     430 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 48 laGravLlaGpsgtGktalaiaiske 73
                                      l G ++ + G+sg+Gkt l +a+   
  gi|386001915|ref|YP_005920214.1| 25 LRGDSLAIIGESGAGKTTLGLALMGL 50
                                      5677888*************998655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXX-S-E CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle...vkktevltqalrksigvrikeekev 117
                                       G ++ l+G+sg+Gkt la ++   +      v l g  + +      +k  ++ q+ + si  r+   + v
  gi|386001915|ref|YP_005920214.1| 332 GETIALVGESGSGKTTLAKTVIGLFDLAEGVVRLEGEPLLRRGrdfYQKVQMIYQNPKESISHRMTVLEAV 402
                                       88999*************87765555445555555555554431123555666666666665555555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.24        86      34      51 ..      26      43 ..      22      45 .. 0.88
   2 ?    0.1   0.0       1.3   4.6e+02     106     142 ..     148     182 ..     134     208 .. 0.73
   3 ?    2.8   0.1      0.19        69      37      53 ..     334     350 ..     330     354 .. 0.88
   4 ?    1.7   0.1       0.4   1.5e+02      72     157 ..     406     497 ..     384     508 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.24
                              TniB 34 rmpnlllvGdsnnGKtmi 51
                                      r  +l ++G+s  GKt++
  gi|386001915|ref|YP_005920214.1| 26 RGDSLAIIGESGAGKTTL 43
                                      56789***********96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqref 142
                                       +++++ +++  + +++vLi+DE    l   a ++ e+
  gi|386001915|ref|YP_005920214.1| 148 EKQRALIAMALANDPQVLILDEPTASL--DAVTKAEI 182
                                       667777777788899*******87776..34444444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.19
                              TniB  37 nlllvGdsnnGKtmive 53 
                                        + lvG+s  GKt++++
  gi|386001915|ref|YP_005920214.1| 334 TIALVGESGSGKTTLAK 350
                                       5789**********987 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.4
                              TniB  72 vlvvqappkpdekrlyaaiLealgaplkara......rvskleqqvlrllre..lkvrvLiiDEihnllagsarkqr 140
                                       +lv ++   ++  ++ +++Le+++ p +         ++s  e q +++ r+  l++++Li DE  ++l    + q 
  gi|386001915|ref|YP_005920214.1| 406 LLVQKVGGAAERMKIAKKVLEEVELPSNDAFlkkyphQISGGEGQRVAIARAlvLNPKLLIADEPTSAL--DPSVQA 480
                                       5555555556666666666666666643321222233333333333333333117899******99999..556677 PP

                              TniB 141 eflnalksLgnelkipi 157
                                       ++l +l ++++e  ++i
  gi|386001915|ref|YP_005920214.1| 481 KILKLLLNIQEERGLAI 497
                                       78887777777766555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.33   1.2e+02      25      39 ..      30      44 ..      23      56 .. 0.84
   2 ?    7.2   0.1      0.01       3.7      23      42 ..     333     352 ..     320     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.33
                                      EEEECSTTSSHHHHH CS
                   Sigma54_activat 25 vlitGesGtGKella 39
                                      + i GesG+GK++l 
  gi|386001915|ref|YP_005920214.1| 30 LAIIGESGAGKTTLG 44
                                      5699*******9876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.01
                                       S-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat  23 lsvlitGesGtGKellarai 42 
                                        ++ ++GesG+GK++la+++
  gi|386001915|ref|YP_005920214.1| 333 ETIALVGESGSGKTTLAKTV 352
                                       57889************986 PP

>> Cuticle_1  Crustacean cuticle protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       5.4     2e+03      21      30 ..      29      38 ..      19      38 .. 0.80
   2 ?    5.9   0.0     0.035        13       9      29 ..     323     342 ..     318     343 .. 0.89
   3 ?    1.5   0.1      0.84   3.1e+02      21      32 ..     521     532 ..     518     533 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.4
                         Cuticle_1 21 nivliGpSGa 30
                                      + ++iG+SGa
  gi|386001915|ref|YP_005920214.1| 29 SLAIIGESGA 38
                                      67899***97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.035
                         Cuticle_1   9 DGtnvqfthgvanivliGpSG 29 
                                       DG    + +g+ +i+l+G+SG
  gi|386001915|ref|YP_005920214.1| 323 DGVDLTLYEGE-TIALVGESG 342
                                       888888999**.********9 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.84
                         Cuticle_1  21 nivliGpSGaVl 32 
                                       +iv +Gp+G V+
  gi|386001915|ref|YP_005920214.1| 521 KIVEEGPAGEVT 532
                                       79*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 3717.35
//
Query:       gi|386001916|ref|YP_005920215.1|  [L=221]
Description: hypothetical protein Mhar_1227 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1407.78
//
Query:       gi|386001917|ref|YP_005920216.1|  [L=588]
Description: hypothetical protein Mhar_1228 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-11   42.5   0.0    0.00021   21.4   0.0    2.6  2  Nitroreductase  Nitroreductase family


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-08   0.00021      25     157 ..     124     250 ..     117     255 .. 0.80
   2 !   18.1   0.0   1.2e-07    0.0021     116     160 ..     517     560 ..     510     570 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-08
                                       HHHHTS--GGG---EEEEEE..-CCCH......HHHHHHHHHHHHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEE CS
                    Nitroreductase  25 eaarraPsagnlqpwrfvvv.qdkelr......yklaeaalelllkaeaqaelaqryrkeelklkaqkalagapvli 94 
                                       +a r  Ps+gnl+p++ +++  +   +      + + +  ++l  + + +           +++ +  +l + +vl+
  gi|386001917|ref|YP_005920216.1| 124 WALRVNPSSGNLHPTEGYLIsGPVPGLfdfptvAHYTPREHGLEVRSRFS-----------EEAWRETRLPEGTVLV 189
                                       566889**************444444433333333333333333333333...........4577778899999999 PP

                                       EE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S CS
                    Nitroreductase  95 vivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp 157
                                        ++  + +  +k++era ry +l++g+a+  l +a +alG+ +  + g+  ++  ++ llg++
  gi|386001917|ref|YP_005920216.1| 190 GLNSIPWREAWKYGERAFRYLHLNVGHALAALSIASAALGWRATLLDGVGTDD--LALLLGVA 250
                                       99999999*********************************************..*9999997 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S...S CS
                    Nitroreductase 116 lldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp.dee 160
                                       l ++g++ q+l+L+A+a+Gl  c ig + ++   +   lgl+  e 
  gi|386001917|ref|YP_005920216.1| 517 LWECGIVGQTLYLEAEAAGLRGCGIGCYFDDP--LSSALGLSgTEL 560
                                       789*****************************..*******94334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3894.85
//
Query:       gi|386001918|ref|YP_005920217.1|  [L=170]
Description: Rhodanese-like domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-11   43.2   0.0    7.3e-11   42.5   0.0    1.3  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   4.1e-15   7.3e-11      10     105 ..      78     158 ..      67     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 4.1e-15
                         Rhodanese  10 ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaall 86 
                                       ++++++++DvRp++ Y+ ghIp ++nv             p+ el+  +      ++kt+ v+c     +a+a a++
  gi|386001918|ref|YP_005920217.1|  78 GDESIVIVDVRPAAGYDSGHIPASINV-------------PFPELIPNMDMV--PEDKTIAVVCTFDTNSAFAVAAM 139
                                       344445*********************.............999999999998..***************99999999 PP

                         Rhodanese  87 kklGykn.vsvldGGfkawk 105
                                       +  G  +  +v+ GG+ aw 
  gi|386001918|ref|YP_005920217.1| 140 RIFG-DRdAWVVVGGIPAWL 158
                                       999*.666***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1103.10
//
Query:       gi|386001919|ref|YP_005920218.1|  [L=723]
Description: Alpha glucan phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-31  107.2   0.0    2.1e-30  105.4   0.0    2.0  2  DUF3417        Protein of unknown function (DUF3417)
    6.4e-28   97.5   0.0    4.3e-13   48.5   0.0    3.1  3  Phosphorylase  Carbohydrate phosphorylase


Domain annotation for each model (and alignments):
>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   2.3e-34   2.1e-30       1     109 []      12     122 ..      12     122 .. 0.97
   2 ?   -3.1   0.0       1.2   1.1e+04      54      80 ..     556     581 ..     549     585 .. 0.73

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 2.3e-34
                           DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksl.dpelweevghnPvklLeevsqerleelaedeeflarleavveefee 76 
                                       lp++++kL +La+nlww+w++e reLF  l  +++w++ ghnPvk+++e++   l+ ++ d++fl+ ++av+++fe 
  gi|386001919|ref|YP_005920218.1|  12 LPARIAKLGDLAYNLWWTWHPEGRELFMMLgGRAAWSRNGHNPVKMMHELDDGVLRLASLDPRFLRYYDAVMARFEG 88 
                                       8*****************************44789****************************************** PP

                           DUF3417  77 yleek.twfqkkaeeekkeaiAYFsaEfGlhesL 109
                                        ++ +  wf ++  ++k+++iAYFsaE+Glh++L
  gi|386001919|ref|YP_005920218.1|  89 DMDPTsGWFCNNIGDPKDKTIAYFSAEYGLHHAL 122
                                       ***9989************************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                           DUF3417  54 leelaedeeflarleavveefeeylee 80 
                                       + ++a+d++f  r+   ve++++yl++
  gi|386001919|ref|YP_005920218.1| 556 VFNAAADKGFEGRIA-FVEDYDQYLAQ 581
                                       456788888888874.67888888875 PP

>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.7e-08   0.00087      23      77 ..     127     182 ..     122     194 .. 0.87
   2 !   27.3   0.0   1.2e-10   1.1e-06     218     281 ..     271     333 ..     263     338 .. 0.93
   3 !   48.5   0.0   4.8e-17   4.3e-13     323     581 ..     362     625 ..     356     629 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.7e-08
                                       SHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEEBTTCCG-T CS
                     Phosphorylase  23 GGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepdeWlkkgnp 77 
                                       GGLG LA  +l  ++ l++pavG+g  Y  G   Q+i  dg+q  + ++  +++ p
  gi|386001919|ref|YP_005920218.1| 127 GGLGFLAGDYLKECSDLGVPAVGVGFMYPEGYLLQRItPDGWQAGACEKLDRENAP 182
                                       9************************************679***9888876666665 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.2e-10
                                       EEEEEESSTTTTHHHHHHHHHHHCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHS CS
                     Phosphorylase 218 vaiqlnDtHPalaipelmriLvdeeglewdeaweitkktfaytnhtvlpealekwpvellekll 281
                                       ++++ln+ HPa+ai e +r  v e+g+++dea e++++ + +t ht +p   +k+p++l+ek +
  gi|386001919|ref|YP_005920218.1| 271 AVLHLNEGHPAFAILERIREGV-ERGMSLDEAAEVVRRSTVFTTHTPVPAGHDKFPLSLMEKYF 333
                                       789****************986.67***********************************9975 PP

  == domain 3  score: 48.5 bits;  conditional E-value: 4.8e-17
                                       EHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGG..EEE----B-CHHHCCCTSHHHHHH.HHHHCSSGGCC CS
                     Phosphorylase 323 rmanlaivgshsvngvaalhsellkkevlkdfyelypek..fnnktnGitprrwlllanpelael.itekigeewvk 396
                                       +m  +a+ ++h+ n v++ h e+ k+   + + +  +e   +  +tnGi    w+     +l ++  ++ +g++w++
  gi|386001919|ref|YP_005920218.1| 362 NMTAFALRMCHHRNCVSRRHLEVTKDMWHHLWPDHSTEDvpIDHVTNGIHVPSWIDR---RLGNItFNRYLGRDWLE 435
                                       79999*******************99888888777665422789**********965...555541678999***98 PP

                                       SGGG..GGGGGGGCCSHHHHHH........HHHHHHHHHHHHHHHHHHHHSS-.....--TTSEEEEEES-SCCCCT CS
                     Phosphorylase 397 dlee..LkkLekladdkeflee........laeikqenKerlaelikekegve.....vdpeslfdvqvkRlheYkR 458
                                       + ++  + +L +   d+ + ++        +++ik + + +  +  +e++++      +dp++l     +R+  YkR
  gi|386001919|ref|YP_005920218.1| 436 KHDNplIWELLDEIPDDVLWADhlrmkrslINKIKDRARDKWRDPESESRTIMafgtlLDPTTLTLGFARRFASYKR 512
                                       77654356666666555555440000111134555555555555444433322444448899998889********* PP

                                       HHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHH CS
                     Phosphorylase 459 qlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiiklinsvaevvnndpevkdklkvvflenynvsl 535
                                        +L +L+  ++ ++i ++p     p  +if+gka p  ++ k +++ + + a    +d+  ++  +++f+e+y+  l
  gi|386001919|ref|YP_005920218.1| 513 ATL-LLRNPERLRRILTDP---QRPVQIIFAGKAHPDDQQSKLLLQQVFNAA----ADKGFEG--RIAFVEDYDQYL 579
                                       *99.688899999999998...7899****************9988777655....4777777..589********* PP

                                       HHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                     Phosphorylase 536 aekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                       a+ ++ + d+  +     +eASGT+ mk +lnG   ++ +DG  vE
  gi|386001919|ref|YP_005920218.1| 580 AQYLVHGVDVWVNNPRPPMEASGTSGMKAALNGVPQLSVFDGWWVE 625
                                       ******************************************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (723 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 4289.90
//
Query:       gi|386001920|ref|YP_005920219.1|  [L=546]
Description: Thermosome subunit delta [Methanosaeta harundinacea 6Ac]
Scores for complete 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-183  610.3  20.6   2.7e-183  610.1  20.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
     0.0042   16.6   0.3     0.0085   15.6   0.0    1.6  2  TrwC        TrwC relaxase


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.1  20.6    3e-187  2.7e-183       1     490 [.      35     522 ..      35     523 .. 0.99

  Alignments for each domain:
  == domain 1  score: 610.1 bits;  conditional E-value: 3e-187
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a +v+ttlGPkGmdKmlv+  g+vv+TnDG+tilke++iehPaak++ve+a++qd+evGDGTtt+v+LageLl++a
  gi|386001920|ref|YP_005920219.1|  35 VATAVRTTLGPKGMDKMLVDTLGDVVITNDGVTILKEMDIEHPAAKMMVEIAKTQDDEVGDGTTTAVVLAGELLKKA 111
                                       5889************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l+++++hpt+i  gy+ a+e+a+++Lke+  +i+++ +d+e L+k+a t++++k +   ++el++l v+Avk+i 
  gi|386001920|ref|YP_005920219.1| 112 EELLDQEIHPTVIAAGYRAAAERAMDILKEM--AIKVSPNDDELLKKIAITAMTGKGSGVARNELAELSVKAVKAIV 186
                                       *******************************..7777788*********************************9999 PP

                                       CCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHH CS
                        Cpn60_TCP1 155 enekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeele 231
                                       ++++++d+++i v+k+ gg ++ds+lv G+v+dk+ l+p+mpkk+++ak++ll++ +eiekte++++++++++++l+
  gi|386001920|ref|YP_005920219.1| 187 DEDGTVDVDNITVEKKVGGGITDSQLVYGMVIDKERLHPNMPKKVKDAKIALLNTAIEIEKTEVDAKIEITSPDQLQ 263
                                       999************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC CS
                        Cpn60_TCP1 232 klekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpee 308
                                       +++++ee++l++++ ki+++g+nvv+cqkgiddla+hflak+g+ ++rr+kk+d+e+la+atG+++v+s+ dl ++e
  gi|386001920|ref|YP_005920219.1| 264 AFLDQEETMLKDMVNKIVSTGANVVFCQKGIDDLAQHFLAKAGVYTIRRIKKSDMEKLARATGGRIVTSIHDLAESE 340
                                       ***************************************************************************** PP

                                       -EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHH CS
                        Cpn60_TCP1 309 lGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelak 385
                                       lG a+ vee+ki  +++t++ e++++k+++i+lrg t++v+de+ ra edAl+vv  a+ed+ + pGGGa e+ela 
  gi|386001920|ref|YP_005920219.1| 341 LGRAGLVEEKKIAGDDMTFVVECENPKSVSIILRGGTEHVVDELDRAMEDALRVVGVALEDSLLMPGGGAPEIELAL 417
                                       ***************************************************************************** PP

                                       HHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEE CS
                        Cpn60_TCP1 386 klkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDp 462
                                       +l+eya +v g+eqlaieafa+ALe+ipktLaeNaG+d+i++l  lr++h+kg k++g+d+e+g+++d+ e+gvv+p
  gi|386001920|ref|YP_005920219.1| 418 RLREYAATVGGREQLAIEAFAEALEIIPKTLAENAGFDQIDTLVALRSSHEKGVKTAGLDMETGKPSDMQEKGVVEP 494
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 463 lkvkrqalksAteaastiLrideiikak 490
                                       ++vk+qa++sA+e+a +iLrid++i  k
  gi|386001920|ref|YP_005920219.1| 495 MRVKTQAINSAAESAVMILRIDDVIASK 522
                                       *************************976 PP

>> TrwC  TrwC relaxase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.72   6.4e+03     105     125 ..     123     143 ..     112     154 .. 0.72
   2 !   15.6   0.0   9.5e-07    0.0085      52     116 ..     329     394 ..     240     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.72
                              TrwC 105 aieaahdaAvkaalalleeea 125
                                        i+a  +aA+++a+++l e a
  gi|386001920|ref|YP_005920219.1| 123 VIAAGYRAAAERAMDILKEMA 143
                                       366667888888888888744 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 9.5e-07
                              TrwC  52 llegrhpdtgerlgrakesaererkavagfDltfsa....PKSvSllalvgdderraaieaahdaAvka 116
                                       ++  +h  ++++lgra      e+k++ag D+tf +    PKSvS++   g++++  ++ +a+++A + 
  gi|386001920|ref|YP_005920219.1| 329 IVTSIHDLAESELGRAGLV---EEKKIAGDDMTFVVecenPKSVSIILRGGTEHVVDELDRAMEDALRV 394
                                       3333344478888886665...359********9644444******97766666656666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3484.68
//
Query:       gi|386001921|ref|YP_005920220.1|  [L=135]
Description: 50S ribosomal protein L24 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-16   60.0   0.1    2.5e-16   59.3   0.1    1.4  1  Spt5-NGN         Early transcription elongation factor of RNA
    1.3e-07   31.3   1.0    2.3e-05   24.2   0.2    2.4  2  KOW              KOW motif
  ------ inclusion threshold ------
      0.013   15.4   0.4      0.021   14.8   0.4    1.3  1  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.1   4.2e-20   2.5e-16      21      84 .]       3      66 ..       1      66 [. 0.94

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 4.2e-20
                          Spt5-NGN 21 kkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEvedll 84
                                      + i++la+ke+++I++ ++pd lkGy++vEA+ ++ ve+a++g+p++r+v +g +++ Eve++l
  gi|386001921|ref|YP_005920220.1|  3 NLIAQLARKEKYDITALLVPDVLKGYVLVEAKAPEIVEEAIQGVPHARSVIKGASSFGEVEHFL 66
                                      45677899999***************************************************98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   3.8e-09   2.3e-05       2      32 .]      78     108 ..      77     108 .. 0.94
   2 !    5.6   0.0    0.0027        16       1       9 [.     121     129 ..     121     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.8e-09
                                       TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       G +V+ +sGp+kG+ ++V++vd  k+ ++v+
  gi|386001921|ref|YP_005920220.1|  78 GAIVELISGPFKGEMARVKRVDIGKEEITVE 108
                                       999********************99999987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0027
                                       TTSEEEESS CS
                               KOW   1 pGdhVkVvs 9  
                                       +GdhV+V+s
  gi|386001921|ref|YP_005920220.1| 121 RGDHVRVLS 129
                                       6******97 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   3.5e-06     0.021      22      51 .]      97     127 ..      94     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
                                       EEEEESSEEEEEEES.SSTEEEEETTEEEEE CS
                   Glyco_hydro_65C  22 rVrvtpeevtvtles.gepltievyGeevtL 51 
                                       rV++++ee+tv+l +   p++i+v+G  v++
  gi|386001921|ref|YP_005920220.1|  97 RVDIGKEEITVELFEaMVPIPITVRGDHVRV 127
                                       79************8455*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 876.30
//
Query:       gi|386001922|ref|YP_005920221.1|  [L=159]
Description: 50S ribosomal protein L11 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-24   84.9   0.3    4.7e-24   84.0   0.3    1.4  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    2.6e-20   72.7   1.3    2.6e-20   72.7   1.3    1.6  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.3   5.2e-28   4.7e-24       2      62 ..       2      61 ..       1      64 [. 0.94

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 5.2e-28
                   Ribosomal_L11_N  2 kkvvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqd 62
                                      k+ +++v++ vp+GkA+++PplGpaLGplG+n+++++k++n+aT+d +g+++pVk+tv   
  gi|386001922|ref|YP_005920221.1|  2 KFLASFVEVLVPGGKASAGPPLGPALGPLGVNVADVVKKINEATADLNGMQVPVKVTV-RS 61
                                      78899*****************************************************.44 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.5   4.4e+03      35      57 ..      38      60 ..      32      61 .. 0.54
   2 !   72.7   1.3   2.9e-24   2.6e-20       2      70 .]      71     137 ..      70     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.5
                                      HHHHHHHHGGGHT.XS.SHHHHHH CS
                     Ribosomal_L11 35 vyeIAkiKksdln.aalsleaavk 57
                                      v++I ++   dln ++++++ +v+
  gi|386001922|ref|YP_005920221.1| 38 VKKINEATA-DLNgMQVPVKVTVR 60
                                      444444444.66666666666655 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 2.9e-24
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       tPpts+l++k++g+ekgsg+   ++vG+++++qv+++A iK+++l +  s+++a+k+++gt+ smGi+V
  gi|386001922|ref|YP_005920221.1|  71 TPPTSALVLKEVGLEKGSGNA-LQIVGNLTMEQVVKVAGIKRKNLLSV-SMKSAAKEVIGTCGSMGITV 137
                                       9*******************6.688*****************888866.******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1085.43
//
Query:       gi|386001923|ref|YP_005920222.1|  [L=212]
Description: 50S ribosomal protein L1P [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-43  147.8   0.0      4e-43  147.5   0.0    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.0   2.2e-47     4e-43       6     204 .]      18     207 ..       9     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 2.2e-47
                                       -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT CS
                      Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyk 82 
                                       +++f esv++a+nl ++++ ++ +r+ ++i Lph+ g+++k+++++ +++a     a+ ag  + vi+ ++l +   
  gi|386001923|ref|YP_005920222.1|  18 ERRFSESVDLAINLHNIDMSQPANRVDEEIILPHGRGRSAKVAVFASGETAL---MAQRAG-ADLVISPDELGELGD 90 
                                       679*************************************************...999999.899************ PP

                                       -HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEE CS
                      Ribosomal_L1  83 sfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsv 159
                                       ++++ rk+++e+  f+a+ ++mp+++k LG+++gkr+kmP p       + d++  +++  +  v vr+++  ++++
  gi|386001923|ref|YP_005920222.1|  91 DKKRARKIADEYTYFIAETSLMPTIGKKLGPILGKRGKMPLPL--PP--NVDITPIIKRQRN-LVRVRSRDRLTFHM 162
                                       *******************************************..42..459*******999.************** PP

                                       EEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 160 kvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                       +vG+ +++ +++aeN+eav ++l+++++ +++n+ks+y+kttm+p
  gi|386001923|ref|YP_005920222.1| 163 AVGSREMEVQKIAENVEAVTTKLEQALKDGKQNLKSVYVKTTMGP 207
                                       ********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      833  (0.046461); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1655.47
//
Query:       gi|386001924|ref|YP_005920223.1|  [L=326]
Description: 50S ribosomal protein L10 [Methanosaeta harundinacea 6Ac]
Scores for complete 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   76.4   0.1    2.5e-21   75.7   0.1    1.4  1  Ribosomal_L10  Ribosomal protein L10
    2.3e-19   69.2   0.3    4.8e-19   68.1   0.3    1.5  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
  ------ inclusion threshold ------
      0.042   14.0   0.1        0.1   12.8   0.1    1.6  1  MazG           MazG nucleotide pyrophosphohydrolase domain
       0.86   10.2  20.7       0.24   12.0  16.8    2.2  2  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.1   5.6e-25   2.5e-21       3      98 ..      12     107 ..      10     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 5.6e-25
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS..SSCGCCSSS CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeee.klkellkgp 78 
                                       +++K+e v+el e+++++++v +v +++++++qlq+lR +lr+  a++k+v+n+++rrA+e+ +e+   l++ +  +
  gi|386001924|ref|YP_005920223.1|  12 PKWKIEEVEELVERINSTQVVGLVGLAEIPAKQLQDLRSELRDV-ATIKMVRNNIARRAIEKCSEKVfPLADGIDRQ 87 
                                       79*****************************************9.*****************9997555******** PP

                                       EEEEEESS-TCHHHHCCCCC CS
                     Ribosomal_L10  79 valvftnedpvalakvleef 98 
                                       +a++ft+ +p+ l k+lee 
  gi|386001924|ref|YP_005920223.1|  88 TAFIFTDVNPFRLCKMLEEK 107
                                       *****************986 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.3   1.1e-22   4.8e-19       2      71 .]     114     183 ..     114     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1.1e-22
                      RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       +aG +A++d++i++g+++  Pg+++ +L+++g+p+ +k Gk+v++e ++v+++Get++++ a++L+l++i
  gi|386001924|ref|YP_005920223.1| 114 KAGGKAPKDIVIEKGETSFSPGPMVGKLQAAGIPAAIKSGKVVINETKVVVEEGETVSAQLAEVLSLMEI 183
                                       89*****************************************************************998 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.2e-05       0.1       8      47 ..      13      66 ..       7      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHHHHHHT..............T-HHHHHHHHHHHHHHHHHHHHHH CS
                              MazG  8 aylleEvgEvaeaIkk..............edrdeleeELGDvLlqvlflania 47
                                      ++ +eEv+E++e I++              ++ ++l++EL Dv    +   nia
  gi|386001924|ref|YP_005920223.1| 13 KWKIEEVEELVERINStqvvglvglaeipaKQLQDLRSELRDVATIKMVRNNIA 66
                                      5669************999999999999999999********966666555555 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.6   7.2e+03       7      13 ..     146     152 ..     122     178 .. 0.56
   2 ?   12.0  16.8   5.3e-05      0.24      36      87 ..     267     321 ..     236     325 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                       XXXXXXX CS
                     Ribosomal_60s   7 ikkvlka 13 
                                       i++ +k+
  gi|386001924|ref|YP_005920223.1| 146 IPAAIKS 152
                                       2233333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.3e-05
                                       XXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--SS--STT CS
                     Ribosomal_60s  36 eellangaakla....aaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedddmGfgL 87 
                                       e lla +aa ++     + + +a a aa+a a+++eek++e+e+eE e+  +G gL
  gi|386001924|ref|YP_005920223.1| 267 EALLARAAADASvltnLVEGGPAEAPAAGAPAEKEEEKAEEAEKEENEEAGLG-GL 321
                                       56677777776678864445555555555555555555555555333344555.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2228.45
//
Query:       gi|386001925|ref|YP_005920224.1|  [L=101]
Description: 50S ribosomal protein L12 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-18   65.1  15.4    7.7e-18   64.9  15.4    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
       0.13   11.7   0.3       0.14   11.6   0.3    1.1  1  CAP_N          Adenylate cyclase associated (CAP) N terminal


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9  15.4   8.5e-22   7.7e-18       2      88 .]      17     100 ..      16     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 8.5e-22
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                     Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEe 78 
                                       +++e ik++l aagv ++++r+k+lv+aleg+die++l+++ +   a+aaa+aaaa+aaa aaa+e+++ +ee+  e
  gi|386001925|ref|YP_005920224.1|  17 VSEEGIKTILGAAGVAADEVRIKALVSALEGVDIEDVLSKAPSV--AVAAAPAAAAPAAAPAAAEEAEEDKEEA--E 89 
                                       799**************************************877..6666666666555555555555555554..5 PP

                                       --SS--.STTT CS
                     Ribosomal_60s  79 edddmG.fgLF 88 
                                       e   +G ++LF
  gi|386001925|ref|YP_005920224.1|  90 ESGIEGlGALF 100
                                       66688888998 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   1.6e-05      0.14     224     280 ..      46     100 ..      33     101 .] 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                                       TSBE.......SSC--XXXXXXX....XXXXXXXX......XXXXXXXXXXXXXXXXX CS
                             CAP_N 224 kGkdaeealkaaaaaasaaaaggpppPpPpPppasvf.eeesaaasasaaaggmsavF 280
                                       +G+d+e++l++   a+s+a a++p++++P  +pa++  +ee++++++++  +g++a+F
  gi|386001925|ref|YP_005920224.1|  46 EGVDIEDVLSK---APSVAVAAAPAAAAPAAAPAAAEeAEEDKEEAEESGIEGLGALF 100
                                       58888888753...33444444433444444344333134444666667777888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 714.12
//
Query:       gi|386001926|ref|YP_005920225.1|  [L=267]
Description: hypothetical protein Mhar_1237 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-07   29.4   0.0    8.5e-07   29.0   0.0    1.1  1  dCache_1        Cache domain
     0.0036   17.4   0.0     0.0066   16.6   0.0    1.4  1  sCache_3_2      Single cache domain 3
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.023   15.0   0.0    1.4  1  Hydrolase       haloacid dehalogenase-like hydrolase
       0.14   12.0   0.0       0.33   10.8   0.0    1.6  1  IclR            Bacterial transcriptional regulator
       0.23   11.2   0.1       0.61    9.9   0.0    1.6  2  SNCAIP_SNCA_bd  Synphilin-1 alpha-Synuclein-binding domain


Domain annotation for each model (and alignments):
>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.4e-10   8.5e-07      80     208 ..      90     220 ..      71     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.4e-10
                          dCache_1  80 vdadGqviassdpssppnlegtddpadrdwykealaggg..gkpvisdpy.vdqtggkpvitiavpiyddsgkfiGv 153
                                       +d +G+++ + ++++   +++++ + d++ ++e la+++  g      +y ++ ++g p + +a+p++d++g+  G+
  gi|386001926|ref|YP_005920225.1|  90 IDLNGTILEVAPEEY--RYVVGERIDDQEHIQELLATRRpaGL-----AYiIS-VEGIPAMDFASPVFDEDGRLMGA 158
                                       478899988766655..55558999999********9955422.....33232.459************99****** PP

                          dCache_1 154 laadldldnlqd.llsniklgetgyvfivdsdGniiahpdkdllgknlrdelkaq......e 208
                                       +++ +++++l    l   ++ ++ +++ + +dG+i+++ d +++g n +    +       e
  gi|386001926|ref|YP_005920225.1| 159 VTVLVNATELFGeALAPHQPEGHAKIWAMLPDGTIVYDVDGEQIGRNTFTDPLFAeftellE 220
                                       *********9984666666666779*******************876665544424444330 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0066      56     124 ..      87     161 ..      55     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                        sCache_3_2  56 vvitDeegrvlahpdpa...evgrklsgpataaalkagrayvgtv...tgtlgpslrvklPvfdadgrviGivsv 124
                                       ++ +D+ g++l  +  +   +vg+++ +  +++ l a r  +g +    + + p+++ + Pvfd+dgr++G+v v
  gi|386001926|ref|YP_005920225.1|  87 CITIDLNGTILEVAPEEyryVVGERIDDQEHIQELLATRRPAGLAyiiSVEGIPAMDFASPVFDEDGRLMGAVTV 161
                                       556789999988844445789*****888888888888888887755577888********************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   6.5e-06     0.023       1     132 [.      85     224 ..      85     253 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.5e-06
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH..HHCHHHHHHHHHHHHHHHHHHHHHH..ETTTE...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx...... RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg..sehpigkalvaaakarsgaltgfat..figrg...... 67 
                                       ++++ +D+ GT+++  p+  + +v   ++ ++ ++    +++p g a++   +++  +  +fa   f + g      
  gi|386001926|ref|YP_005920225.1|  85 VDCITIDLNGTILEVAPEEYRYVVGERIDDQEHIQELlaTRRPAGLAYIISVEGI--PAMDFASpvFDEDGrlmgav 159
                                       5899*********999666665555545555555555677788888888777777..33444442233444445666 PP

                                       HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ayaigkpewltal..dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLka 132
                                       +++++  e++ +   +  p+ +a+i +   +g +v+ ++++  +  t+ dp  ++ e  e+++  ++
  gi|386001926|ref|YP_005920225.1| 160 TVLVNATELFGEAlaPHQPEGHAKIWAMLPDGTIVYDVDGEQIGRNTFTDP--LFAEFTELLEVARK 224
                                       77777777777777777777777777777777777777*************..*******9998664 PP

>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.2e-05      0.33      50     108 ..     112     170 ..      99     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.2e-05
                                       --SHHHHHHHHHHHHHHTSEEEES.SSSTTEEEEEEEEE-TTSSEEEEEEEEEETTTSHH CS
                              IclR  50 itdpeeLleeLakvReqGyavdre.EeeegvrciAapifdasgevvaAvsvsgptarlte 108
                                       i d+e+++e La+ R  G a+  + E    +   A p+fd+ g+ ++Av+v ++++ l  
  gi|386001926|ref|YP_005920225.1| 112 IDDQEHIQELLATRRPAGLAYIISvEGIPAMD-FASPVFDEDGRLMGAVTVLVNATELFG 170
                                       77889999999999999999876513333333.7*****************998877655 PP

>> SNCAIP_SNCA_bd  Synphilin-1 alpha-Synuclein-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00017      0.61      24      43 ..     110     129 ..     108     131 .. 0.92
   2 ?   -3.6   0.0       2.6   9.4e+03      36      44 ..     173     181 ..     172     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                    SNCAIP_SNCA_bd  24 eRInlQkhlQrLleaqkaeG 43 
                                       eRI  Q+h+Q Ll ++++ G
  gi|386001926|ref|YP_005920225.1| 110 ERIDDQEHIQELLATRRPAG 129
                                       9***************9998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.6
                    SNCAIP_SNCA_bd  36 leaqkaeGr 44 
                                       l ++++eG 
  gi|386001926|ref|YP_005920225.1| 173 LAPHQPEGH 181
                                       5799***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1934.94
//
Query:       gi|386001927|ref|YP_005920226.1|  [L=90]
Description: Chromosomal protein MC1c [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-38  130.3   0.4    3.1e-38  130.0   0.4    1.1  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.4   1.7e-42   3.1e-38       1      96 []       3      88 ..       3      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.7e-42
                               MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWle 79
                                      +krnfalrd+dG+ei+vf+GkqPrqaaLkaa+r+ t+          irLre+Gtkkvh+++g+++ + +P+++pdW++
  gi|386001927|ref|YP_005920226.1|  3 NKRNFALRDADGTEIGVFTGKQPRQAALKAANRGYTD----------IRLRERGTKKVHLFKGERKLVVKPSNAPDWMP 71
                                      59**********************************9..........******************************** PP

                               MC1 80 dkitkanvskqgiekle 96
                                      ++i+k+nv+k giekl+
  gi|386001927|ref|YP_005920226.1| 72 KEIWKPNVKKVGIEKLD 88
                                      ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 693.13
//
Query:       gi|386001928|ref|YP_005920227.1|  [L=252]
Description: Adenylylsulfate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-28   97.8   0.0    7.9e-28   97.3   0.0    1.2  1  APS_kinase       Adenylylsulphate kinase
    1.1e-13   51.6   0.0    1.4e-13   51.2   0.0    1.1  1  AAA_33           AAA domain
    9.6e-08   32.6   0.0    1.4e-07   32.1   0.0    1.2  1  AAA_18           AAA domain
    1.6e-07   31.1   0.0    1.9e-07   30.8   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
    0.00011   21.6   0.0    0.00018   20.8   0.0    1.4  1  Zeta_toxin       Zeta toxin
    0.00018   20.6   0.1    0.00029   19.9   0.1    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0002   21.8   0.0    0.00028   21.3   0.0    1.2  1  AAA_16           AAA ATPase domain
    0.00026   21.4   0.6     0.0037   17.7   0.3    2.0  2  AAA              ATPase family associated with various cellul
     0.0016   18.3   0.0      0.013   15.3   0.0    2.1  1  CPT              Chloramphenicol phosphotransferase-like prot
     0.0022   17.3   0.1      0.014   14.7   0.1    1.9  1  6PF2K            6-phosphofructo-2-kinase
     0.0036   17.2   0.1     0.0057   16.6   0.1    1.3  1  NTPase_1         NTPase
     0.0046   17.2   0.4      0.012   15.9   0.4    1.7  1  AAA_28           AAA domain
     0.0097   15.6   0.1      0.033   13.9   0.1    1.7  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.035   14.0   0.2      0.068   13.1   0.2    1.4  1  NACHT            NACHT domain
       0.04   14.2   0.1      0.073   13.3   0.1    1.5  1  AAA_22           AAA domain
      0.058   13.8   0.0       0.11   13.0   0.0    1.5  1  RNA_helicase     RNA helicase
      0.065   13.1   0.0       0.11   12.4   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.069   12.9   0.0      0.088   12.6   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.09   13.2   0.3       0.22   12.0   0.3    1.7  1  AAA_17           AAA domain
      0.099   12.4   0.0       0.15   11.8   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.14   11.9   0.1       0.25   11.0   0.1    1.4  1  Thymidylate_kin  Thymidylate kinase
       0.14   11.3   0.1       0.22   10.7   0.1    1.2  1  NB-ARC           NB-ARC domain
       0.17   11.9   0.2       0.28   11.2   0.2    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
       0.22   10.6   0.8        6.9    5.8   0.8    2.1  1  DUF815           Protein of unknown function (DUF815)


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   1.1e-30   7.9e-28       2     154 ..      74     230 ..      73     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 1.1e-30
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEE CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivl 78 
                                       + v+w+tGl g GK+t+a+ ++ +L+ +gi+v++L+ d++R+ ++ + ++++ +R+     +a +akll++ag+ v+
  gi|386001928|ref|YP_005920227.1|  74 SWVIWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELDEIRRVITPEPTYTDLEREVVYASLAYMAKLLSEAGTNVI 150
                                       679************************************************************************** PP

                                       EE----SHHHHHHHHHHHHCHTEEEEEEEE--HHHHHHHT........TTSHHHHHHTTSSSSHTTTSS-----SS- CS
                        APS_kinase  79 vafisPyreeReaarelleealkfievfvdtplevceerD........pkglYkkareGeikeftGidspYeaPenp 147
                                       v + +  r+ R+ ar l+    +f ev+v+++l  c er+        p+g+Y+ka +     ++G++ +Ye+P++p
  gi|386001928|ref|YP_005920227.1| 151 VDATANRRRYRDLARMLVP---TFAEVYVKASLPACIERErgrkavysPRGIYAKAVD-DGATVPGVNVAYEEPKSP 223
                                       *******************...4*************99865555555589******98.56789************* PP

                                       SEEEETT CS
                        APS_kinase 148 elvvdtd 154
                                       e+vvd++
  gi|386001928|ref|YP_005920227.1| 224 EVVVDAE 230
                                       ****976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   1.9e-16   1.4e-13       1     120 [.      76     192 ..      76     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.9e-16
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrn 72 
                                       ++++ GlpG+GK+tla+++ ++l      + +l+ d++rr ++++  ++ td    ++ +y+ l+ +a+   +ag n
  gi|386001928|ref|YP_005920227.1|  76 VIWFTGLPGCGKTTLARGVKARLEgrgirVKVLELDEIRRVITPE--PTYTD--LEREVVYASLAYMAKLLSEAGTN 148
                                       799****************88888797877888888888888854..33333..345779999999998888999** PP

                            AAA_33  73 vildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                       vi+dat  +rr r+  + l++     ++ v+v+++   + eR + R+a
  gi|386001928|ref|YP_005920227.1| 149 VIVDATANRRRYRDLARMLVP----TFAEVYVKASLPACIERERGRKA 192
                                       **********99999999999....6678*****************87 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.9e-10   1.4e-07       1     114 [.      77     191 ..      77     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.9e-10
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe..aldeskrldedkldklldaleenssaleegk 75 
                                       I+ tG pG+GKttla+ ++ rl+   +  +v+  ++++   +pe   +d +++++   l++  ++l e+      g 
  gi|386001928|ref|YP_005920227.1|  77 IWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELDEIRRVITPEptYTDLEREVVYASLAYMAKLLSEA------GT 147
                                       899***************999944555567888999999999998888888888888888888888886......89 PP

                            AAA_18  76 nlvidghlaeleseaakdikk.....vvLtaspeelleRlekRg 114
                                       n+++d   +  ++ ++ ++       v+++as   ++eR + R+
  gi|386001928|ref|YP_005920227.1| 148 NVIVDATANRRRYRDLARMLVptfaeVYVKASLPACIERERGRK 191
                                       *******999998888887779*****************99986 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.6e-10   1.9e-07       4     125 ..      77     194 ..      73     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.6e-10
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH...TTSS.S--GGGHHHHHHHHHHHHHHHHTT.SEEEE- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg..iekds.ykdsakekalRsslrsavkrdLskekvVIvD 77 
                                       + +tGlP  GK+t+a+ ++  le ++++v v++ + ++  i+ ++ y+d ++e  + +sl   +k   +  + VIvD
  gi|386001928|ref|YP_005920227.1|  77 IWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELDEIRrvITPEPtYTDLEREV-VYASLAYMAKLLSEAGTNVIVD 152
                                       569******************************998887844444488776664.445555555544456799**** PP

                                       S---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S CS
                             KTI12  78 slnyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeey 125
                                       +++  + +R     +a++   t++ vyv+a+l  +++++  r+    y
  gi|386001928|ref|YP_005920227.1| 153 ATANRRRYR----DLARMLVPTFAEVYVKASLPACIERERGRKAV--Y 194
                                       **9888887....58*********************999888765..4 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.4e-07   0.00018      19      95 ..      77     157 ..      69     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.4e-07
                        Zeta_toxin  19 illgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh...Peyeeilkadpkkaseltqkdaselvekllqea 91 
                                       i   G pG+GK++la+ +k++le r+ +v +l+ D++R+ +   P y +++++ ++   +++ k  se +++++  a
  gi|386001928|ref|YP_005920227.1|  77 IWFTGLPGCGKTTLARGVKARLEgRGIRVKVLELDEIRRVItpePTYTDLEREVVYASLAYMAKLLSEAGTNVIVDA 153
                                       556799****************97777888899******98666778777777777777777777777666666666 PP

                        Zeta_toxin  92 ieng 95 
                                       + n+
  gi|386001928|ref|YP_005920227.1| 154 TANR 157
                                       6555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.9e-07   0.00029      29      66 ..      74     111 ..      59     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.9e-07
                                       SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                       + v+ +tG+PG Gk tl   + ++l  rG rv vl +D
  gi|386001928|ref|YP_005920227.1|  74 SWVIWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELD 111
                                       66899******************************988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.7e-07   0.00028      26     106 ..      76     147 ..      62     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.7e-07
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                       ++ ++G +G+GK++l+r ++ +le++g   +r k  +l      + + ++++ e  +++l++e   a+l++ ++ l 
  gi|386001928|ref|YP_005920227.1|  76 VIWFTGLPGCGKTTLARGVKARLEGRG---IRVKVLEL------DEIRRVITPEPTYTDLEREVVYASLAYMAKLLS 143
                                       6889**********************8...66666666......556777777788888887777766666666555 PP

                            AAA_16 103 eala 106
                                       ea +
  gi|386001928|ref|YP_005920227.1| 144 EAGT 147
                                       5444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   4.9e-06    0.0037       2      34 ..      78     110 ..      77     112 .. 0.82
   2 ?    4.0   0.0     0.083        62      60     112 ..     106     160 ..      99     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.9e-06
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTC CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsel 34 
                                        ++G pG+GKT+la+ v   l+ + +++++ el
  gi|386001928|ref|YP_005920227.1|  78 WFTGLPGCGKTTLARGVKARLEGRGIRVKVLEL 110
                                       589**************9999877777766655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.083
                                       EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..G CS
                               AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr..p 112
                                       ++l +DEi ++++ + + ++ e+e v + L  + + +++   +viv +++nr  +
  gi|386001928|ref|YP_005920227.1| 106 KVLELDEIRRVITPEPTYTDLEREVVYASLAYMAKLLSEAGTNVIVDATANRrrY 160
                                       68999*****999993344444444444454444445555678999999999444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-05     0.013      62     130 ..     125     190 ..      74     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                       -HHHHHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHH CS
                               CPT  62 gpeldlllaalyeavaamaraGnnvivDdvilekewlvdllrrllsgldvllVGvrcplevlerReler 130
                                       + e++ ++a+l+   +  ++aG+nvivD +  +++   dl+r l+    +  V v+++l+   +Re++r
  gi|386001928|ref|YP_005920227.1| 125 DLEREVVYASLAYMAKLLSEAGTNVIVD-ATANRRRYRDLARMLV--PTFAEVYVKASLPACIERERGR 190
                                       5567888999999999999*********.666666689**96666..4566677888888888888877 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.8e-05     0.014      12      88 ..      73     138 ..      64     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS---GGGGSTT-HHHHHHHHHHHHHHHHHH CS
                             6PF2K  12 sklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaskalsdaeffrpdneealklreklalaalkdl 88 
                                          vi + GLp  gKt++++ +   l+  g+r kv ++ ++rr ++ +++ ++           l +++  a l  +
  gi|386001928|ref|YP_005920227.1|  73 MSWVIWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELDEIRRVITPEPTYTD-----------LEREVVYASLAYM 138
                                       55688899***********************************9987744433...........3334444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.7e-06    0.0057       2      39 ..      77     114 ..      76     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.7e-06
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                                       +  TG pG GKtTl + v   l+ +g++v+ +   e+r
  gi|386001928|ref|YP_005920227.1|  77 IWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELDEIR 114
                                       668*************************9877766666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   1.6e-05     0.012       2      42 ..      77     125 ..      76     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gyp..vv..pEaareileeklakg 42 
                                       i +tG +++GKTtl++  +ar    g++  v+   E+ r i+ e + ++
  gi|386001928|ref|YP_005920227.1|  77 IWFTGLPGCGKTTLARGVKARlegrGIRvkVLelDEIRRVITPEPTYTD 125
                                       789************9999888877665325565676666666665444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.4e-05     0.033      16      52 ..      72     108 ..      68     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaaggrvigl 52 
                                       s  +v   tG +G GKtt+ +++++ +e +g rv +l
  gi|386001928|ref|YP_005920227.1|  72 SMSWVIWFTGLPGCGKTTLARGVKARLEGRGIRVKVL 108
                                       56678889**********************9999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   9.1e-05     0.068       2      24 ..      76      98 ..      75     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-05
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      +++ +G +G+GKTtL++++   +
  gi|386001928|ref|YP_005920227.1| 76 VIWFTGLPGCGKTTLARGVKARL 98
                                      699**************987766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.8e-05     0.073      10      32 ..      79     101 ..      75     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.8e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldee 32 
                                        tG +G+GKTtl+r ++ +l+ +
  gi|386001928|ref|YP_005920227.1|  79 FTGLPGCGKTTLARGVKARLEGR 101
                                       69***************999643 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014      0.11       1      24 [.      77     100 ..      77     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallk 24 
                                       iw++G +g+GK+tla+ + ++l++
  gi|386001928|ref|YP_005920227.1|  77 IWFTGLPGCGKTTLARGVKARLEG 100
                                       8**************998777774 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.11       1      33 [.      76     108 ..      76     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                       v+ ++g  g+GKTtL   + + l+ rg+rv ++
  gi|386001928|ref|YP_005920227.1|  76 VIWFTGLPGCGKTTLARGVKARLEGRGIRVKVL 108
                                       57899*************************987 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.088       2      34 ..      80     112 ..      79     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34 
                                       +G +G GKtt+ + +   le rg +v+v+ LD 
  gi|386001928|ref|YP_005920227.1|  80 TGLPGCGKTTLARGVKARLEGRGIRVKVLELDE 112
                                       799****************************95 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00029      0.22       1      19 [.      80      98 ..      80     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                                      EE-TTSSHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklveky 19
                                      +G+PG+GK+t+++ ++ ++
  gi|386001928|ref|YP_005920227.1| 80 TGLPGCGKTTLARGVKARL 98
                                      7***********9998766 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.15       1      53 [.      76     128 ..      76     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleer 53 
                                       vI  +g  G+Gktt+ar ++ ++++ +++ ++ e+d++ r+   e  ++  er
  gi|386001928|ref|YP_005920227.1|  76 VIWFTGLPGCGKTTLARGVKARLEGRGIRVKVLELDEIRRVITPEPTYTDLER 128
                                       67789999*********************9999*9999998888877776665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00034      0.25       3      27 ..      81     105 ..      79     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                       ESTTSSHHHHHHHHHHHHHHTTE.E CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikv 27 
                                       Gl G GKtt a+ +k+rl+ +gi+v
  gi|386001928|ref|YP_005920227.1|  81 GLPGCGKTTLARGVKARLEGRGIRV 105
                                       999*******************994 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00029      0.22      20      41 ..      74      95 ..      69     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      SEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqil 41
                                      s v+ + G +G+GKttla+ + 
  gi|386001928|ref|YP_005920227.1| 74 SWVIWFTGLPGCGKTTLARGVK 95
                                      468999************9875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00038      0.28       5      32 ..      80     108 ..      77     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                       E--SSSSHHHHHHHGGGGB.S--EEEEE- CS
                             AAA_5   5 vGppGtgKselaerlaaal.nreveyvql 32 
                                        G pG+gK++la+ ++a+l +r + ++ l
  gi|386001928|ref|YP_005920227.1|  80 TGLPGCGKTTLARGVKARLeGRGIRVKVL 108
                                       799***************98666666555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.8    0.0092       6.9      59      97 ..      80     112 ..      69     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0092
                            DUF815  59 wGarGtGKSslvkallneyaeegLrlievekedlkelpk 97 
                                       +G  G+GK +l + + ++++ +g+r+  +      el++
  gi|386001928|ref|YP_005920227.1|  80 TGLPGCGKTTLARGVKARLEGRGIRVKVL------ELDE 112
                                       67778888888888888887777654222......2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1811.73
//
Query:       gi|386001929|ref|YP_005920228.1|  [L=366]
Description: glyceraldehyde-3-phosphate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2301.29
//
Query:       gi|386001930|ref|YP_005920229.1|  [L=352]
Description: tRNA-splicing endonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-50  169.1   4.4    5.4e-25   87.3   1.5    2.4  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    3.7e-40  135.4   0.2    5.9e-21   73.9   0.0    2.6  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0031   17.7   0.2        2.7    8.2   0.0    2.8  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.1   3.3e-27     2e-23       1      85 []      80     163 ..      80     163 .. 0.98
   2 !   87.3   1.5   9.1e-29   5.4e-25       1      85 []     258     344 ..     258     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 3.3e-27
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklila 75 
                                       f+ +y+vy+dLre+Gy+v++G    +dFrvY  +++p+++ +e+ V+vvse+e++++++l++ +++a++++K+l+la
  gi|386001930|ref|YP_005920229.1|  80 FEFRYVVYKDLRERGYYVQPG---VTDFRVYprGGKPGKTPAEFYVHVVSEREPVPLKELVEPAKIARQMRKRLMLA 153
                                       899******************...78******999****************************************** PP

                                       EETTTSCEEE CS
                     tRNA_int_endo  76 ivdaegdvty 85 
                                       +vd+e d+t+
  gi|386001930|ref|YP_005920229.1| 154 VVDEESDITF 163
                                       ********96 PP

  == domain 2  score: 87.3 bits;  conditional E-value: 9.1e-29
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklil 74 
                                       f++k  vyrdLr++ +vv++G+kFG++FrvY   +++++  hseylV+ v+e++ +++p +s+avrlahsv+K++++
  gi|386001930|ref|YP_005920229.1| 258 FDMKRLVYRDLRDRRLVVKTGFKFGSHFRVYkrvEGSKKVPHSEYLVHSVPEGHIFHLPVVSRAVRLAHSVRKQMVF 334
                                       78999**************************999999**************************************** PP

                                       EEETTTSCEEE CS
                     tRNA_int_endo  75 aivdaegdvty 85 
                                       a   + ++v+y
  gi|386001930|ref|YP_005920229.1| 335 ARQ-EGDEVKY 344
                                       *95.7777876 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.1   4.1e-20   2.4e-16       3      67 .]       8      70 ..       6      70 .. 0.96
   2 !   73.9   0.0   9.8e-25   5.9e-21       3      66 ..     184     247 ..     182     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.1e-20
                                      EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
                   tRNA_int_endo_N  3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                      geLsgd+vl+    a  +lye+g +G+      L+LslvEA+YLl++G+++v+ gge l+f+ ++
  gi|386001930|ref|YP_005920229.1|  8 GELSGDKVLLGG-AATGELYEQGSFGR-PVPGGLHLSLVEAAYLLDRGRISVRVGGEDLDFQSFF 70
                                      9**********8.99************.8********************************9885 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 9.8e-25
                                       EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHH CS
                   tRNA_int_endo_N   3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfeel 66 
                                       ++L++drv+++d ea++ l+e gfYGk   + +LqLslvE++YLlekG+l++v ++g pl++ee+
  gi|386001930|ref|YP_005920229.1| 184 ATLLEDRVMLWDPEASEALHEGGFYGK-PVGGRLQLSLVESAYLLEKGVLRIVdRSGAPLTPEEF 247
                                       89*************************.8**********************************98 PP

>> tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00045       2.7      48      71 ..      35      58 ..      21      59 .. 0.84
   2 !    6.8   0.1    0.0013       7.8      47      70 ..     210     234 ..     146     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00045
                   tRNA_int_end_N2 48 rrgrlwLlpeEaLYLvErGsldir 71
                                        g l L   Ea YL++rG++ +r
  gi|386001930|ref|YP_005920229.1| 35 VPGGLHLSLVEAAYLLDRGRISVR 58
                                      567889999***********9887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0013
                   tRNA_int_end_N2  47 a.rrgrlwLlpeEaLYLvErGsldi 70 
                                       +   grl L   E  YL+E G l i
  gi|386001930|ref|YP_005920229.1| 210 KpVGGRLQLSLVESAYLLEKGVLRI 234
                                       44689****************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1919.47
//
Query:       gi|386001931|ref|YP_005920230.1|  [L=160]
Description: hypothetical protein Mhar_1242 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-17   60.1   3.4    5.7e-06   26.1   0.1    3.3  3  TPR_2     Tetratricopeptide repeat
    1.5e-15   56.3   0.1    4.6e-05   23.1   0.0    3.3  3  TPR_1     Tetratricopeptide repeat
    5.9e-13   48.3   0.3     0.0046   16.6   0.0    3.1  3  TPR_11    TPR repeat
    1.9e-10   41.2  15.0    0.00021   21.8   5.3    3.2  3  TPR_16    Tetratricopeptide repeat
    3.1e-09   36.9  16.0     0.0022   18.7   2.1    3.7  4  TPR_14    Tetratricopeptide repeat
    1.6e-08   34.6  11.0    2.4e-08   34.0   5.9    2.2  2  TPR_9     Tetratricopeptide repeat
    2.3e-08   33.6   0.0       0.16   12.3   0.0    3.6  4  TPR_8     Tetratricopeptide repeat
    2.7e-08   34.2   9.5    2.6e-05   24.6   2.2    2.2  2  TPR_19    Tetratricopeptide repeat
    1.3e-07   31.5   0.1        1.5    9.4   0.0    4.3  3  TPR_17    Tetratricopeptide repeat
    5.9e-07   29.1   2.6      0.051   13.6   0.3    3.5  3  TPR_7     Tetratricopeptide repeat
      9e-06   25.8   0.2      0.016   15.4   0.0    2.1  2  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
    1.1e-05   25.6   5.7      0.054   13.8   2.0    3.2  3  TPR_12    Tetratricopeptide repeat
    0.00059   19.1   2.8    0.00077   18.8   2.8    1.1  1  TPR_15    Tetratricopeptide repeat
     0.0014   19.1   4.6        3.8    8.4   0.0    4.1  4  TPR_6     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.021   13.8   0.1      0.054   12.4   0.0    1.5  2  NARP1     NMDA receptor-regulated protein 1


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.8e-07   0.00021       4      34 .]      34      64 ..      32      64 .. 0.93
   2 !   12.5   0.1   0.00011      0.13       6      34 .]      69      97 ..      65      97 .. 0.91
   3 !   26.1   0.1   4.7e-09   5.7e-06       4      34 .]     101     131 ..      98     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.8e-07
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                                      l   G+++++ g+++ Al+a+ +A e dP+n
  gi|386001931|ref|YP_005920230.1| 34 LILEGDSHLREGNLDLALRAYLRATEKDPGN 64
                                      6788*************************87 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                             TPR_2  6 nlGlayyklgdyeeAleafekAleldPnn 34
                                      + +++y  +g+y eA++  ++A ++dP +
  gi|386001931|ref|YP_005920230.1| 69 RAARVYGMMGRYMEAIASIDRAAAIDPAD 97
                                      7799***********************75 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 4.7e-09
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++ +G ++++l +  +Ale+fe+A +ldP++
  gi|386001931|ref|YP_005920230.1| 101 WMGRGFLLLRLERRRDALECFERAAALDPED 131
                                       999**************************86 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.9e-05     0.023       8      34 .]      38      64 ..      34      64 .. 0.92
   2 !   15.3   0.0   1.1e-05     0.013       9      32 ..      72      95 ..      67      97 .. 0.91
   3 !   23.1   0.0   3.8e-08   4.6e-05       4      34 .]     101     131 ..      98     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                                      G  +++ g++d Al +y +A e +P n
  gi|386001931|ref|YP_005920230.1| 38 GDSHLREGNLDLALRAYLRATEKDPGN 64
                                      778999*******************87 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      HHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  9 nayfklgkydeAleyyekALelnP 32
                                       +y  +g+y eA++  ++A  ++P
  gi|386001931|ref|YP_005920230.1| 72 RVYGMMGRYMEAIASIDRAAAIDP 95
                                      6899*******************9 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 3.8e-08
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + ++G ++++l++  +Ale++e+A  l+P++
  gi|386001931|ref|YP_005920230.1| 101 WMGRGFLLLRLERRRDALECFERAAALDPED 131
                                       999**************************86 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.4e-06    0.0077       1      30 [.      38      67 ..      38      68 .. 0.93
   2 !   16.6   0.0   3.9e-06    0.0046       7      40 ..      77     110 ..      71     112 .. 0.92
   3 !   12.6   0.1   6.9e-05     0.083      12      36 ..     116     140 ..     115     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.4e-06
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30
                                      Gd     G+++ A+ aY +A + dP na a
  gi|386001931|ref|YP_005920230.1| 38 GDSHLREGNLDLALRAYLRATEKDPGNAAA 67
                                      8888999******************99976 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.9e-06
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                        G+y eAi++  +A ++dP +a  + ++G+++++
  gi|386001931|ref|YP_005920230.1|  77 MGRYMEAIASIDRAAAIDPADAGPWMGRGFLLLR 110
                                       69***************************99987 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 6.9e-05
                            TPR_11  12 eAieaYkkAlkldPdnaeayynLGl 36 
                                       +A+e++++A +ldP++  a y +++
  gi|386001931|ref|YP_005920230.1| 116 DALECFERAAALDPEDRYARYLIAE 140
                                       69*******************9886 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   5.3   1.8e-07   0.00021       3      68 .]      37      98 ..      35      98 .. 0.89
   2 !   15.7   0.5   1.4e-05     0.017       3      49 ..      70     113 ..      69     114 .. 0.92
   3 !   18.2   3.7   2.4e-06    0.0029       7      45 ..     108     143 ..     107     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-07
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68
                                      +++++lr g+ d A++a+ +a+++d   P   +A+   ++++   gr+ eA+a +++a++ +p ++
  gi|386001931|ref|YP_005920230.1| 37 EGDSHLREGNLDLALRAYLRATEKD---P-GNAAAKRAARVYGMMGRYMEAIASIDRAAAIDPADA 98
                                      799**********************...8.6777777888888889****************9985 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49 
                                       +ar +   g+y +A+a  ++a + d   P++a  ++++g ++lr+ r
  gi|386001931|ref|YP_005920230.1|  70 AARVYGMMGRYMEAIASIDRAAAID---PADAGPWMGRGFLLLRLER 113
                                       57788889*****************...***************9876 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2.4e-06
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                       +lr+ + +dA++ +e+a ++d   P+++ A++l ++ a 
  gi|386001931|ref|YP_005920230.1| 108 LLRLERRRDALECFERAAALD---PEDRYARYLIAETAE 143
                                       8999*****************...***********9886 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.8     3e-06    0.0036       9      39 ..      39      69 ..      32      71 .. 0.90
   2 !   12.7   0.7   0.00015      0.18       3      42 ..      66     105 ..      65     107 .. 0.89
   3 !   18.7   2.1   1.8e-06    0.0022       4      43 ..     101     140 ..      99     141 .. 0.92
   4 ?   -0.5   0.0       2.6   3.1e+03      23      39 ..     141     157 ..     138     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                            TPR_14  9 eallalGdpdeAiallrralalaPddaeawl 39
                                      + +l+ G++d A++++ ra +++P++a+a +
  gi|386001931|ref|YP_005920230.1| 39 DSHLREGNLDLALRAYLRATEKDPGNAAAKR 69
                                      6799***********************9986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a +++a+++   G++ eAia  +ra a +P+da  w+  +
  gi|386001931|ref|YP_005920230.1|  66 AAKRAARVYGMMGRYMEAIASIDRAAAIDPADAGPWMGRG 105
                                       6678999**************************9998766 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.8e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++ ++ +ll+l++ ++A+++++ra al+P+d+ a++l a+
  gi|386001931|ref|YP_005920230.1| 101 WMGRGFLLLRLERRRDALECFERAAALDPEDRYARYLIAE 140
                                       7778899***************************999886 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.6
                            TPR_14  23 llrralalaPddaeawl 39 
                                        ++++ +++P+d  a++
  gi|386001931|ref|YP_005920230.1| 141 TAEEMRRANPADGLAHR 157
                                       56777788998888876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.038        46       5      39 ..      41      74 ..      38      84 .. 0.65
   2 !   34.0   5.9     2e-11   2.4e-08      11      68 ..      80     138 ..      72     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.038
                             TPR_9  5 aireedweralavverllllaPddpeerrdRGlll 39
                                      ++re + + al+++ r    +P  +   r  ++++
  gi|386001931|ref|YP_005920230.1| 41 HLREGNLDLALRAYLRATEKDPGNAAAKRA-ARVY 74
                                      677777777888877777777777666653.5555 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2e-11
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap.dapdaeai 68 
                                       + +a+a ++r  +++P d++ ++ RG+ll +l++ + Al+++e+++al+p d+ ++++i
  gi|386001931|ref|YP_005920230.1|  80 YMEAIASIDRAAAIDPADAGPWMGRGFLLLRLERRRDALECFERAAALDPeDRYARYLI 138
                                       6689**********************************************544444444 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0064       7.7       8      32 ..      38      62 ..      34      64 .. 0.87
   2 !   10.1   0.0   0.00064      0.77       8      34 .]      71      97 ..      69      97 .. 0.91
   3 !   12.3   0.0   0.00013      0.16       4      34 .]     101     131 ..      98     131 .. 0.92
   4 ?   -2.3   0.0       6.2   7.5e+03       4      16 ..     135     147 ..     134     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0064
                                      HHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  8 gsiylklgdyeeAkeyyekaleldp 32
                                      g+ +l  g+++ A  +y +a+e dp
  gi|386001931|ref|YP_005920230.1| 38 GDSHLREGNLDLALRAYLRATEKDP 62
                                      89999***************99666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00064
                                      HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  8 gsiylklgdyeeAkeyyekaleldpdn 34
                                      +++y  +g+y eA++++ +a  +dp++
  gi|386001931|ref|YP_005920230.1| 71 ARVYGMMGRYMEAIASIDRAAAIDPAD 97
                                      789999*******************85 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++  g ++l l++   A e++e+a  ldp++
  gi|386001931|ref|YP_005920230.1| 101 WMGRGFLLLRLERRRDALECFERAAALDPED 131
                                       7788999**********************86 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHTT- CS
                             TPR_8   4 yynlgsiylklgd 16 
                                        y+++ + +++ +
  gi|386001931|ref|YP_005920230.1| 135 RYLIAETAEEMRR 147
                                       5888888887766 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.2   2.2e-08   2.6e-05       2      59 ..      42      98 ..      41     104 .. 0.95
   2 !   14.1   0.9   4.3e-05     0.051       6      42 ..     113     149 ..     108     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                            TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59
                                      l eg+++ Al+++ +a ++dp+na+a+   A+++  +g++ eA+a +d++ + dp da
  gi|386001931|ref|YP_005920230.1| 42 LREGNLDLALRAYLRATEKDPGNAAAKR-AARVYGMMGRYMEAIASIDRAAAIDPADA 98
                                      789*************************.***********************999875 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.3e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqld 42 
                                       +  +Al+ +e+a + dp++ +ar+l Ae   ++ + +
  gi|386001931|ref|YP_005920230.1| 113 RRRDALECFERAAALDPEDRYARYLIAETAEEMRRAN 149
                                       6689************************998887766 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0022       2.6       1      15 [.      53      67 ..      53      85 .. 0.65
   2 !    9.4   0.0    0.0012       1.5       3      33 ..      88     118 ..      87     119 .. 0.88
   3 !    6.9   0.0    0.0078       9.3       1      24 [.     120     143 ..     120     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0022
                            TPR_17  1 lylkaleldPnnada 15
                                      +yl+a e+dP na a
  gi|386001931|ref|YP_005920230.1| 53 AYLRATEKDPGNAAA 67
                                      59**********754 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        +a+++dP +a ++  ++ lll++ + ++A+
  gi|386001931|ref|YP_005920230.1|  88 DRAAAIDPADAGPWMGRGFLLLRLERRRDAL 118
                                       589*******************998777765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0078
                            TPR_17   1 lylkaleldPnnadaynnLAelll 24 
                                       ++++a++ldP + +a ++ Ae+ +
  gi|386001931|ref|YP_005920230.1| 120 CFERAAALDPEDRYARYLIAETAE 143
                                       89**********999999999865 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00023      0.27       6      35 ..      38      65 ..      38      66 .. 0.93
   2 ?    2.1   0.0       0.2   2.4e+02       6      32 ..      71      97 ..      68     100 .. 0.75
   3 !   13.6   0.3   4.3e-05     0.051      10      35 ..     109     132 ..     107     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdpeda 35
                                      ++ + r+G+ + A++ y +  a++kdp++a
  gi|386001931|ref|YP_005920230.1| 38 GDSHLREGNLDLALRAYLR--ATEKDPGNA 65
                                      6789***************..******987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.2
                             TPR_7  6 arlysrlGdyeeAielyeqsLaltkdp 32
                                      ar+y  +G+y eAi    ++ a++ ++
  gi|386001931|ref|YP_005920230.1| 71 ARVYGMMGRYMEAIASIDRAAAIDPAD 97
                                      66677789999***9999966666554 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 4.3e-05
                             TPR_7  10 srlGdyeeAielyeqsLaltkdpeda 35 
                                        rl ++++A+e++e+  a + dped+
  gi|386001931|ref|YP_005920230.1| 109 LRLERRRDALECFER--AAALDPEDR 132
                                       6899***********..888888875 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.016      22      81 ..      30      89 ..      15      90 .. 0.92
   2 !    8.7   0.1    0.0016       1.9       6      32 ..     115     141 ..     111     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                                      -HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3 22 spedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                      ++ed+ l + ++++ g+ + A++ + +a +++   +++  +A+++  +++y eAia +++
  gi|386001931|ref|YP_005920230.1| 30 NLEDLILEGDSHLREGNLDLALRAYLRATEKDPGNAAAKRAARVYGMMGRYMEAIASIDR 89
                                      789999**********************88888889*******************99876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHH.HHH--HHHHHHHHHH CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlc 32 
                                       ++A+ ++er+ a ++e+ +++yl A++
  gi|386001931|ref|YP_005920230.1| 115 RDALECFERAAALDPEDRYARYLIAET 141
                                       799********************9986 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0029       3.5      45      73 ..      31      59 ..      16      62 .. 0.76
   2 !   13.8   2.0   4.5e-05     0.054       8      76 ..      69     129 ..      64     130 .. 0.84
   3 !   10.3   0.3   0.00056      0.66       8      33 ..     103     128 ..      97     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                            TPR_12 45 attlrnLgrlyralgryeeAlelleeala 73
                                      ++ l+  g+ +++ g+++ Al+++ +a++
  gi|386001931|ref|YP_005920230.1| 31 LEDLILEGDSHLREGNLDLALRAYLRATE 59
                                      55677888889999999999999988876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.5e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       + a v+  +gry eA++  ++a +i    + +          + g l+++l+r ++Ale +e+a a+++
  gi|386001931|ref|YP_005920230.1|  69 RAARVYGMMGRYMEAIASIDRAAAID---PADAG-----PWMGRGFLLLRLERRRDALECFERAAALDP 129
                                       6799999***************9999...43444.....45699********************99875 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00056
                            TPR_12   8 nlaavlrrlgrydeAlellekaleia 33 
                                        ++ +l+rl+r  +Ale++e+a ++ 
  gi|386001931|ref|YP_005920230.1| 103 GRGFLLLRLERRRDALECFERAAALD 128
                                       56777778888888888888877665 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.8   6.5e-07   0.00077     151     267 ..      36     151 ..      28     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.5e-07
                            TPR_15 151 araelyrqegqtdaAlrdyreAlalapdssel.raallWlliDlgrraeLrellkawkaraesdasLwgplaaAlll 226
                                       + + ++++eg+ d Alr+y +A +++p+++++ raa ++ +   gr+ e+ + + +  a   +da  w   ++ ll+
  gi|386001931|ref|YP_005920230.1|  36 LEGDSHLREGNLDLALRAYLRATEKDPGNAAAkRAARVYGMM--GRYMEAIASIDRAAAIDPADAGPWMGRGFLLLR 110
                                       5567899*********************99883466778777..999985555555555559999999999****** PP

                            TPR_15 227 LgrpkkALeylrkqakenrkdplwllaYADaleqagradeA 267
                                       L+r + ALe +++ a+  ++d   +   A++ e   ra+ A
  gi|386001931|ref|YP_005920230.1| 111 LERRRDALECFERAAALDPEDRYARYLIAETAEEMRRANPA 151
                                       **********************9999999999988777665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0032       3.8       7      32 ..      38      63 ..      34      64 .. 0.91
   2 ?    2.9   0.1      0.17     2e+02       5      27 ..      69      91 ..      69      96 .. 0.82
   3 ?    4.7   0.0     0.047        56       6      31 ..     104     129 ..     101     131 .. 0.79
   4 ?    2.5   0.1      0.24   2.9e+02       1      19 [.     133     151 ..     133     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                                      HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                      + s+++ g+ d Al+a+ r  ++ P+
  gi|386001931|ref|YP_005920230.1| 38 GDSHLREGNLDLALRAYLRATEKDPG 63
                                      78999999**************9996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  5 klalsyrklgdtdkAlealerli 27
                                      ++a+ y ++g++ +A++  +r  
  gi|386001931|ref|YP_005920230.1| 69 RAARVYGMMGRYMEAIASIDRAA 91
                                      6799****99*****99877765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       ++ ++++l + ++Ale +er     P
  gi|386001931|ref|YP_005920230.1| 104 RGFLLLRLERRRDALECFERAAALDP 129
                                       566777766999********988777 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkA 19 
                                       +A y++a+  +++ ++  A
  gi|386001931|ref|YP_005920230.1| 133 YARYLIAETAEEMRRANPA 151
                                       79*******9998666555 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.86     1e+03     309     327 ..      37      55 ..      34      61 .. 0.83
   2 ?   12.4   0.0   4.5e-05     0.054     199     274 ..      71     149 ..      57     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.86
                                       HHHHHHHTT-HHHHHHHHH CS
                             NARP1 309 dgeaylrqkklglALKrfh 327
                                        g+++lr+++l lAL+ + 
  gi|386001931|ref|YP_005920230.1|  37 EGDSHLREGNLDLALRAYL 55 
                                       58999********999875 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HH...HHHHHHHHHHH CS
                             NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRy...iNskcakymLr 272
                                       A  y  +g++ +A+  id+a + +p     ++ ++ +l +    ++A e+ e+a +lD +DRy   + ++ a+ m r
  gi|386001931|ref|YP_005920230.1|  71 ARVYGMMGRYMEAIASIDRAAAIDPADAGPWMGRGFLLLRLERRRDALECFERAAALDPEDRYaryLIAETAEEMRR 147
                                       778999*******************************************************8622255666666766 PP

                                       TT CS
                             NARP1 273 ad 274
                                       a+
  gi|386001931|ref|YP_005920230.1| 148 AN 149
                                       66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 943.90
//
Query:       gi|386001932|ref|YP_005920231.1|  [L=88]
Description: Elongation factor 1-beta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-18   64.9   0.0    6.2e-18   64.8   0.0    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
       0.16   11.5   0.1       0.22   11.0   0.1    1.1  1  DUF5555   Family of unknown function (DUF5555)


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   6.9e-22   6.2e-18       3      88 ..       7      86 ..       5      88 .] 0.93

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 6.9e-22
                                      EEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SE CS
                           EF1_GNE  3 vlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVq 80
                                       l+v+Pe ++ d+e++++ +k+ +l++ + ++  + ++piafGlk+L + ++  +   +t+ le +++ ++g     Vq
  gi|386001932|ref|YP_005920231.1|  7 KLKVMPEGADADMEKMKAGIKA-ALPEgARLHG-FAEVPIAFGLKALMVAVILAEGVTGTEGLEAAVAGVDG-----VQ 78
                                      69********************.55555****5.**************************************.....** PP

                                      EEEEEEEE CS
                           EF1_GNE 81 sveivsfn 88
                                      sve++++ 
  gi|386001932|ref|YP_005920231.1| 79 SVEVEEVG 86
                                      ****9985 PP

>> DUF5555  Family of unknown function (DUF5555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   2.5e-05      0.22     244     274 ..       9      38 ..       3      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.5e-05
                           DUF5555 244 dlrpkGaraddrrplragrklhlpeaarlsG 274
                                        + p+Ga a d   ++ag k  lpe arl G
  gi|386001932|ref|YP_005920231.1|   9 KVMPEGADA-DMEKMKAGIKAALPEGARLHG 38 
                                       4579*****.8889***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.52
# Mc/sec: 510.24
//
Query:       gi|386001933|ref|YP_005920232.1|  [L=227]
Description: Aspartate/glutamate/uridylate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-12   46.0   0.6    3.5e-06   26.8   0.0    2.1  2  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0     2e-10   3.5e-06       2      85 ..       3      66 ..       2      91 .. 0.76
   2 !   17.9   0.2     1e-07    0.0018     154     187 ..     111     144 ..      92     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2e-10
                                      EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHH CS
                         AA_kinase  2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevat 78
                                       +V+K+GGs+++       r++++ + al+ +g++  +V Ggg+++d    l  +++ls++ ++               
  gi|386001933|ref|YP_005920232.1|  3 FCVIKIGGSLIS---V--SRDIVRGLGALSGDGEPFLIVPGGGAMADLVRGLydEYHLSEETAH--------------- 61
                                      79**********...3..4679*********************999888888666888888876............... PP

                                      HHHHHHH CS
                         AA_kinase 79 rdalasl 85
                                        ++a+l
  gi|386001933|ref|YP_005920232.1| 62 --WMAIL 66
                                      ..33333 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1e-07
                                       E.EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCES CS
                         AA_kinase 154 e.lgrgssDtiaallAealgAdkliiltdVdGVyd 187
                                         ++  +sD +aal+A  l++  l+ +tdVdG++ 
  gi|386001933|ref|YP_005920232.1| 111 RkSWDYTSDAVAALVASRLKV-DLVKATDVDGIFL 144
                                       2588999**************.899********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 00:00:00.49
# Mc/sec: 1381.76
//
Query:       gi|386001934|ref|YP_005920233.1|  [L=91]
Description: MutT-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-12   47.1   0.0    2.6e-12   46.9   0.0    1.0  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   1.5e-16   2.6e-12      37     123 ..       1      79 [.       1      87 [. 0.85

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.5e-16
                                       CBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHH CS
                             NUDIX  37 vepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfleevegelepndenevsevrwvple 113
                                       +epgEt+eeA+rRE++EEtGl+  l++l+g    ++++++++++ h +++ +l+   gel+ + ++   +++ +ple
  gi|386001934|ref|YP_005920233.1|   1 MEPGETVEEAVRREAREETGLDILLIKLVG----VYSSPDRDPRGHVVSVSYLAWGRGELAAGSDAT--SAEVFPLE 71 
                                       59*******************999999999....8999999999******************95555..5566**** PP

                                       HHHHHHTHCT CS
                             NUDIX 114 ellkeklaae 123
                                       +l  ++la +
  gi|386001934|ref|YP_005920233.1|  72 AL--PPLAFD 79 
                                       99..444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.34s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 494.49
//
Query:       gi|386001935|ref|YP_005920234.1|  [L=565]
Description: glutamyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-60  205.3   0.0    1.2e-60  205.0   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    3.3e-20   72.7   0.0    5.1e-20   72.1   0.0    1.3  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.0   0.0   1.4e-64   1.2e-60       2     312 ..     101     406 ..     100     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 1.4e-64
                                       -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--H..HHHHHHHHHHHHTT---SSEEEEGGG CS
                      tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpereke..eaeesiledlkwlgikwdekptyqsd 76 
                                       V+ RfaP+P+G + iG+a+ +++n  + ++++G+f+lR++DTdp  + +  ea    led  wlg  + ++++ +sd
  gi|386001935|ref|YP_005920234.1| 101 VVMRFAPNPNGPPTIGSARGIIINSEYVRRYGGRFLLRFDDTDPVNKRPmlEAYGWYLEDCRWLGAVP-DEVVVASD 176
                                       899****************************************97665522777789***********.669***** PP

                                       GHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTT CS
                      tRNA-synt_1c  77 rfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkidee 153
                                       r+  ++++aeeLi++G AYvc c++   ++++ +  ++++++r+++ +en +l+ +em +g    ++av+R+k + +
  gi|386001935|ref|YP_005920234.1| 177 RLPLYYEVAEELIRNGGAYVCRCEQAAFKALKDA--AAACPHRSQSPQENISLW-REMIEGPLGPGEAVLRVKTEIA 250
                                       ********************************99..99999*************.89******************99 PP

                                       SS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-E CS
                      tRNA-synt_1c 154 ss.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevpp 229
                                       ++  ++rD  + ri  +    h++ ++k+++ P  df  ++ D+l ++th+lr+++ +d+++++  l++ +g++ p+
  gi|386001935|ref|YP_005920234.1| 251 HKdPALRDWAAFRIVTAD---HPRAGHKYRVWPLLDFESAVEDHLLGVTHILRGKDLMDSERRQKYLYDHMGWKYPT 324
                                       999***************...******************************************************** PP

                                       EEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHH CS
                      tRNA-synt_1c 230 fiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnreskslea 306
                                        ih   +   +    S   l    +  ++ +wdd r++++++lrr+G+ +e+ r+++ + ++ + + ++++++s+ a
  gi|386001935|ref|YP_005920234.1| 325 TIHWGRIKIHQFGSFSTSALRRALEAGEYSGWDDARMPTVRALRRRGIRAEALRKFMIELGVGETD-ISISMDSVYA 400
                                       ****999999999**************************************************999.9999999999 PP

                                       HHHHHH CS
                      tRNA-synt_1c 307 fdrkkL 312
                                        +rk +
  gi|386001935|ref|YP_005920234.1| 401 ENRKII 406
                                       888866 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   5.7e-24   5.1e-20       1     174 []     410     551 ..     410     551 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 5.7e-24
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveev 77 
                                       A+R+++V+dpv ++i++   + +e++++p+hp   +lg r++p + +++++++D+ +lk g ++rLk+l+n+++   
  gi|386001935|ref|YP_005920234.1| 410 ARRRFFVKDPVPLEIDG---EVPEVATAPFHPT-LDLGLREIPAGAKLLVSADDLPDLKVGGKLRLKDLCNLEFIAT 482
                                       89**************4...4679*********.8***************************************544 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepa 153
                                         d       l++++ g++ ++a++ k  iihW +  + v++                 +++pd     + g++e  
  gi|386001935|ref|YP_005920234.1| 483 --D------PLRARVIGTDPHQAKEMKLrIIHWAP-PDGVPV----------------RVMRPDDV---DAGIGEVG 531
                                       ..2......36789999999999999999*****9.69****................9******8...68****** PP

                    tRNA-synt_1c_C 154 lanlkkgdivQfeRiGyfrvd 174
                                       +++   g++vQfeR+G++r+d
  gi|386001935|ref|YP_005920234.1| 532 IRE-DDGKVVQFERYGFVRID 551
                                       **9.99*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3670.30
//
Query:       gi|386001936|ref|YP_005920235.1|  [L=204]
Description: hypothetical protein Mhar_1248 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1253.33
//
Query:       gi|386001937|ref|YP_005920236.1|  [L=275]
Description: Digeranylgeranylglyceryl phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-43  149.0  18.9    1.6e-43  148.9  18.5    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        6.3    6.9   6.8        1.2    9.2   0.3    2.5  3  MpPF26    M penetrans paralogue family 26


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9  18.5   1.7e-47   1.6e-43       3     244 ..      21     251 ..      19     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 1.7e-47
                              UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllil 79 
                                       i+al+gl++a  g+++  +++l++++++++++a+na+NdyfDreiDa   ++p RP++s risp+ a++++i+l++l
  gi|386001937|ref|YP_005920236.1|  21 IAALIGLMVADSGPLPV-TAALVFIAVFAVTGAGNAVNDYFDREIDAV--NRPGRPIPSKRISPERAFAWSILLFLL 94 
                                       6799******9999988.99999*************************..*************************** PP

                              UbiA  80 gllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfllt 156
                                       g +++ ll+np+++++++++ +l+++Y    lK ++++g++ +g   g  +l+g aa +g++ ++++l++la  l t
  gi|386001937|ref|YP_005920236.1|  95 GSAVA-LLINPVAFAIAVANSILLYLYA-RNLKVTPFFGNLAVGYLTGSTFLFGGAA-GGDVGITLFLFLLA-TLAT 167
                                       *****.**********************.6*************************99.78877776666666.999* PP

                              UbiA 157 waialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarl 233
                                       +a  + +d++d+ gDr+ g +tlp+v+G+++a  l  ++ +vl+++  ll +++ l+ ++l+a+ +a l++l a+  
  gi|386001937|ref|YP_005920236.1| 168 LAREVEKDIEDVPGDRASGARTLPIVIGERRASHL--AASFVLIAI--LLSYLAPLGRAYLAAVTVADLLFLAALAS 240
                                       *********************************84..334444333..44555555555555555555555555555 PP

                              UbiA 234 vrrrdakkaak 244
                                       + r +a +a+k
  gi|386001937|ref|YP_005920236.1| 241 ILRGEAPRAQK 251
                                       55555544444 PP

>> MpPF26  M penetrans paralogue family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00014       1.2       9      63 ..      83     138 ..      76     144 .. 0.84
   2 ?   -3.1   0.1      0.87   7.8e+03      16      24 ..     157     165 ..     151     170 .. 0.47
   3 ?    0.9   0.1     0.053   4.7e+02      24      65 ..     219     264 ..     200     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00014
                            MpPF26   9 kklsltiiilyllatvlllvsllayivllskskllskey.eeesslleaelligvl 63 
                                       ++ +++i++++l  +v+ll+  +a++++ ++s ll+ ++ +++ +++ ++l++g l
  gi|386001937|ref|YP_005920236.1|  83 RAFAWSILLFLLGSAVALLINPVAFAIAVANSILLYLYArNLKVTPFFGNLAVGYL 138
                                       789*************************9999998866525678888888888876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.87
                            MpPF26  16 iilyllatv 24 
                                       ++l+llat+
  gi|386001937|ref|YP_005920236.1| 157 LFLFLLATL 165
                                       333444433 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.053
                            MpPF26  24 v....lllvsllayivllskskllskeyeeesslleaelligvlli 65 
                                       +    l  v+++++++l++ +++l  e+  ++++l+a ++ +++  
  gi|386001937|ref|YP_005920236.1| 219 LgrayLAAVTVADLLFLAALASILRGEAPRAQKMLKAGMAAALVAF 264
                                       1455577789999999999999999999999998888555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1781.43
//
Query:       gi|386001938|ref|YP_005920237.1|  [L=182]
Description: hypothetical protein Mhar_1250 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1289.55
//
Query:       gi|386001939|ref|YP_005920238.1|  [L=370]
Description: anthranilate phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-56  189.4   0.0    1.2e-55  188.8   0.0    1.3  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    5.2e-12   45.4   0.0    1.3e-11   44.1   0.0    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   0.0   1.4e-59   1.2e-55       4     253 .]      83     340 ..      80     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 1.4e-59
                                       BEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEE CS
                   Glycos_transf_3   4 lvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflf 80 
                                       l +++gTG dg  tfNiStaa+iv+AaaGv++akhg r+++s +G++D+Lealgv++e  p  v++++e++g+g+  
  gi|386001939|ref|YP_005920238.1|  83 LFENCGTGMDGVDTFNISTAASIVAAAAGVPMAKHGARAITSRCGTIDILEALGVEVEAGPLLVKRSIERAGIGIFN 159
                                       6789**********************************************************************996 PP

                                       HHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.T.....S CS
                   Glycos_transf_3  81 apeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.d.....G 151
                                         + +        +  ++ + Tv n+ G L npa ++  l gvyskel+ ++ae+++ +g +ra+vv+g +     G
  gi|386001939|ref|YP_005920238.1| 160 GMSPLVHPLGLGRILSKIRFGTVLNIAGSLANPAMPRLGLRGVYSKELVVPTAEAMRMIGYSRAMVVCGlSadgrrG 236
                                       6655555567889999***************************************************9764455558 PP

                                       HHHHHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSH.HHHHHHHTTHHTSCHHHHHHHHHHHHHHHH CS
                   Glycos_transf_3 152 ldevsllakttvaelk.dgeiteytlepedfglkraelealeggep.kenaeilkavlegkksaakrdlvllnagaa 226
                                       +devs+ + t+vael  dg+i ++ l p dfg    +  +l   e+ +e a +l +vl+g+++  +  ++ +n + +
  gi|386001939|ref|YP_005920238.1| 237 MDEVSPSGRTLVAELRgDGRIATFDLLPRDFGADPVDERDLLPREDiTEEATVLLRVLAGREGGPREAAICINSAPI 313
                                       ***********************************9999988776669****************999********** PP

                                       HHHTTSSSSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 227 lvlagkadslkegvakaeevidsGkAl 253
                                       l+l+gkadsl eg    +e+++sG Al
  gi|386001939|ref|YP_005920238.1| 314 LLLSGKADSLPEGYSISKEILRSGDAL 340
                                       ************************995 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.5e-15   1.3e-11       4      59 ..      12      67 ..      11      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.5e-15
                                      HHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHH CS
                   Glycos_trans_3N  4 ikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAm 59
                                      +++l+ ge+Lt+ e++ +++ +l++e tda  +AfL+A+ +kG ++eEia+  eA+
  gi|386001939|ref|YP_005920238.1| 12 LNRLIAGESLTRKEAKGMFSSVLSDEQTDAHQGAFLAAITAKGPSPEEIAGGWEAI 67
                                      5799***********************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2608.65
//
Query:       gi|386001940|ref|YP_005920239.1|  [L=345]
Description: Alcohol dehydrogenase, zinc-containing [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-25   89.7   0.8    1.9e-25   88.9   0.8    1.4  1  ADH_N          Alcohol dehydrogenase GroES-like domain
    1.5e-08   34.7   0.0    2.1e-08   34.2   0.0    1.2  1  ADH_zinc_N     Zinc-binding dehydrogenase
     0.0013   17.9   0.3     0.0021   17.2   0.3    1.3  1  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.032   12.9   0.2      0.045   12.5   0.2    1.1  1  HI0933_like    HI0933-like protein
      0.035   14.7   0.6      0.077   13.6   0.6    1.5  1  DUF2285        Uncharacterized conserved protein (DUF2285)
       0.11   11.7   0.4       0.15   11.2   0.4    1.1  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.13   11.5   0.0       0.16   11.2   0.0    1.2  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.8   7.4e-29   1.9e-25       4     106 ..      27     126 ..      24     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 7.4e-29
                                       EEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG CS
                             ADH_N   4 vlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenl 80 
                                       ++++v+a++iC +D++++++  +     p ilGHE++G+v+e +    + +vG+rV ++p +sc++C++C++g+enl
  gi|386001940|ref|YP_005920239.1|  27 LVLEVEACSICSTDVKMVRQ-GQRDLVCPRILGHEVSGVVAERD--GAGPRVGERVQIYPGVSCAKCPSCRRGAENL 100
                                       6789***************9.699*****************955..45789************************** PP

                                       -TTBEETTTSS-SSSBSEEEECGGGE CS
                             ADH_N  81 CeeakllgvsldGgfaeyvvvpekkl 106
                                       C + ++lg+sldGgfae++ vp++++
  gi|386001940|ref|YP_005920239.1| 101 CGKVRILGFSLDGGFAERLAVPAESV 126
                                       **********************8865 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   8.3e-12   2.1e-08       3     129 ..     176     304 ..     174     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 8.3e-12
                                       HHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHC CS
                        ADH_zinc_N   3 GlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkl 78 
                                       G++   lA   Ga  v  + + ee++++ak   ad+v+ + ++dl++   e+t+g+g+dv++ ++ +  +  + l+l
  gi|386001940|ref|YP_005920239.1| 176 GVLHAILAQERGAsMVAIAEPLEERARIAKGW-ADQVLRPGREDLQDGAMEATDGRGFDVAILASRDRPVDGSLLAL 251
                                       6777789999***555559999***9999977.9******666***********************8888889999* PP

                                       EEEEEEEEECSC...TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  79 lkpgGrlvvvGg...gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                       l+p+Gr+ ++ g   +++   +dl+ l+++e  i G  +++ r e  eal+l++
  gi|386001940|ref|YP_005920239.1| 252 LAPRGRISLFSGlppSFERPRLDLNLLHYREHLIAGAYGCT-RAENGEALELIT 304
                                       **********99875445555********************.999999999976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   8.4e-07    0.0021       2      54 ..     167     217 ..     166     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.4e-07
                                       EEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG--S-EE-TT..SSG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavvekeqefggatawsqGgidavlspeqk 54 
                                       vi+ G+G AG   A+ a+e+G+  va+ e  +e    + ++ G++d vl+p  +
  gi|386001940|ref|YP_005920239.1| 167 VIIFGAGPAGVLHAILAQERGAsMVAIAEPLEE---RARIAKGWADQVLRPGRE 217
                                       9*********************99*********...************965542 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.7e-05     0.045       2      27 ..     166     191 ..     165     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                       SEEEE--SHHHHHHHHHHHHTT--EE CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVl 27 
                                       +vi+ G+G+AG++ Ai a++rg++ +
  gi|386001940|ref|YP_005920239.1| 166 SVIIFGAGPAGVLHAILAQERGASMV 191
                                       69******************998754 PP

>> DUF2285  Uncharacterized conserved protein (DUF2285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6     3e-05     0.077      47      96 ..     177     225 ..     175     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                           DUF2285  47 lLqalDarlagaslreiAevlfgaervaaedWkdsalrsrvrrlvrrgra 96 
                                       +L+a+ a+++gas   iAe l ++ r+a+  W+d+ lr   ++l   + +
  gi|386001940|ref|YP_005920239.1| 177 VLHAILAQERGASMVAIAEPLEERARIAK-GWADQVLRPGREDLQDGAME 225
                                       6889999********************88.*****999877776666655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4     6e-05      0.15       1      28 [.     168     195 ..     168     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilE 28 
                                       iI GaGPaG+  ai +++ g + + i E
  gi|386001940|ref|YP_005920239.1| 168 IIFGAGPAGVLHAILAQERGASMVAIAE 195
                                       899*****************98777755 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.2e-05      0.16       3      30 ..     166     193 ..     165     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlv 30 
                                       +V+I GaGpaG++ a l +e+G ++v +
  gi|386001940|ref|YP_005920239.1| 166 SVIIFGAGPAGVLHAILAQERGASMVAI 193
                                       599********************95544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2269.22
//
Query:       gi|386001941|ref|YP_005920240.1|  [L=277]
Description: D-tyrosyl-tRNA(Tyr) deacylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-64  214.9   0.0    9.4e-64  214.7   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.7   0.0   5.3e-68   9.4e-64       4     203 ..      66     259 ..      63     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 5.3e-68
                                       --SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS-- CS
                    tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPt 80 
                                       ++ li+f+SrH++++g p L+ H++Gn+gea lGG+ +ela+aaP +lk+++++l ++   +e+fevtlEatHHGPt
  gi|386001941|ref|YP_005920240.1|  66 SPALIVFASRHQAKDGAPRLCGHFSGNPGEAVLGGRARELAVAAPGALKSFISNLVAHP--VEGFEVTLEATHHGPT 140
                                       6789*******************************************************..**************** PP

                                       ---S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGG CS
                    tRNA_deacylase  81 elkvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyal 157
                                       +l+vPs+F+EiGS e+eW+d++a+eava+++l+l e +    ++++g+GGgHY++r+++l+let++a+Gh++sky++
  gi|386001941|ref|YP_005920240.1| 141 NLTVPSFFAEIGSCEREWSDPAAGEAVARSILDLEELH---PPAFLGFGGGHYVTRQNRLLLETKIAFGHLFSKYQA 214
                                       **********************************7777...9*********************************** PP

                                       GG--HHHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-E CS
                    tRNA_deacylase 158 eelkeevikqaleksegadvalidkkslkseqkeaieelleelgie 203
                                       ++l+ e++++a +ks +a  a++d+ksl+s ++e+i  +lee g++
  gi|386001941|ref|YP_005920240.1| 215 RDLDLEIVEEARMKS-EAVGAYLDRKSLRSAEREKISGALEEIGLQ 259
                                       ***************.**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1684.97
//
Query:       gi|386001942|ref|YP_005920241.1|  [L=353]
Description: AsnC family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-05   25.1   0.0       0.14   12.1   0.0    2.4  2  MarR           MarR family
    1.5e-05   24.8   0.0       0.38   10.7   0.0    3.2  3  MarR_2         MarR family
    0.00018   21.3   0.1        1.2    9.0   0.0    3.3  3  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00096   18.7   0.0       0.12   12.0   0.0    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0061   16.6   0.0          4    7.6   0.0    2.4  2  HTH_3          Helix-turn-helix
  ------ inclusion threshold ------
      0.039   13.7   0.0        7.7    6.4   0.0    2.4  2  HTH_23         Homeodomain-like domain
      0.053   13.4   0.0        1.3    8.9   0.0    2.6  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.079   12.9   0.0        3.9    7.5   0.0    2.7  3  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.18   11.9   0.0         17    5.5   0.0    2.4  2  HTH_29         Winged helix-turn helix


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.1e-05      0.14       1      36 [.       5      40 ..       5      51 .. 0.91
   2 !   10.6   0.0   0.00021      0.42      22      54 ..     209     241 ..     200     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHH CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtr 36
                                      lt  + ++L+ l++ ++ls ++La k+gv++st+ +
  gi|386001942|ref|YP_005920241.1|  5 LTSKEKLVLYGLARYPGLSDIDLAGKIGVDRSTIFK 40
                                      67888899*************************976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
                              MarR  22 eLakklgvskstvtrvldrLekkGlieRskspe 54 
                                       eL ++ g+s++t++    +  + Gl+ R+ + +
  gi|386001942|ref|YP_005920241.1| 209 ELSRRTGISRPTISGKRNKFFQSGLLARQANVN 241
                                       99***************************9976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0012       2.4       3      51 ..       5      51 ..       3      60 .. 0.89
   2 !   10.7   0.0   0.00019      0.38      26      60 ..     209     243 ..     188     245 .. 0.83
   3 ?    1.9   0.0       0.1   2.1e+02      42      56 ..     309     323 ..     309     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      lt  +  vL+ L+r pg  l+  +la + g+++s++ +  +++ +  +v
  gi|386001942|ref|YP_005920241.1|  5 LTSKEKLVLYGLARYPG--LSDIDLAGKIGVDRSTIFKSKRKFREWEMV 51
                                      6778889**********..*****************9998888888777 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                                       HHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  26 elarrlglsksavsrilkrLvaaGLverrpgpeDk 60 
                                       el rr+g+s++++s   +++ + GL+ r+++ + k
  gi|386001942|ref|YP_005920241.1| 209 ELSRRTGISRPTISGKRNKFFQSGLLARQANVNWK 243
                                       99**************************9987765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.1
                                       HHHHHHTTSEEEEES CS
                            MarR_2  42 lkrLvaaGLverrpg 56 
                                       +k L++ GLve+rp+
  gi|386001942|ref|YP_005920241.1| 309 VKALSEVGLVEERPS 323
                                       7899*********96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0021       4.1       6      53 ..       5      52 ..       2      76 .. 0.90
   2 !    9.0   0.0   0.00063       1.2       6      48 ..     188     230 ..     184     244 .. 0.84
   3 ?    0.2   0.0      0.34   6.8e+02      43      57 ..     309     323 ..     305     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      L++ E  v   L ++  ++  ++a ++gv+rs++ ++ r+  +  +V+
  gi|386001942|ref|YP_005920241.1|  5 LTSKEKLVLYGLARYPGLSDIDLAGKIGVDRSTIFKSKRKFREWEMVQ 52
                                      88899999999999999*******************999999988887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00063
                                       HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                              TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLed 48 
                                       L+e +  + la +k+  ++  e+++++g++r+++    ++  +
  gi|386001942|ref|YP_005920241.1| 188 LTEKDRLALLAFVKYPALSDLELSRRTGISRPTISGKRNKFFQ 230
                                       8999999**************************9765555555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.34
                                       HHHHHHCTSEEEESS CS
                              TrmB  43 LrsLedkGlVerekg 57 
                                       ++ L++ GlVe +++
  gi|386001942|ref|YP_005920241.1| 309 VKALSEVGLVEERPS 323
                                       6789*******9875 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 ?    4.2   0.0     0.016        31      13      34 ..      17      38 ..       8      41 .. 0.89
   2 !   12.0   0.0   5.8e-05      0.12       2      35 ..     189     222 ..     188     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
                            HTH_24 13 qknprisqreLAerlglSpstv 34
                                       + p++s  +LA ++g+ +st+
  gi|386001942|ref|YP_005920241.1| 17 ARYPGLSDIDLAGKIGVDRSTI 38
                                      56799***************97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.8e-05
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvn 35 
                                        e+dr  L +  k p +s  eL++r+g+S++t++
  gi|386001942|ref|YP_005920241.1| 189 TEKDRLALLAFVKYPALSDLELSRRTGISRPTIS 222
                                       6788888999999999****************86 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0038       7.5       9      26 ..      21      38 ..      20      40 .. 0.91
   2 !    7.6   0.0     0.002         4      12      27 ..     207     222 ..     204     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0038
                                      THHHHHHHHHHTSSHHHH CS
                             HTH_3  9 glsqeeLAeklGvsrsti 26
                                      gls  +LA k+Gv rsti
  gi|386001942|ref|YP_005920241.1| 21 GLSDIDLAGKIGVDRSTI 38
                                      89999************9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       HHHHHHHHTSSHHHHH CS
                             HTH_3  12 qeeLAeklGvsrstis 27 
                                         eL++++G+sr tis
  gi|386001942|ref|YP_005920241.1| 207 DLELSRRTGISRPTIS 222
                                       569************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0039       7.7      14      43 ..      16      47 ..       9      49 .. 0.85
   2 ?    4.8   0.0     0.012        25      16      35 ..     201     222 ..     187     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0039
                            HTH_23 14 lae..GlsvreIAreLgvsrrTvyrwlkryre 43
                                      la+  Gls  + A + gv r+T+ + ++++re
  gi|386001942|ref|YP_005920241.1| 16 LARypGLSDIDLAGKIGVDRSTIFKSKRKFRE 47
                                      455669999999***************99986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                            HTH_23  16 e..GlsvreIAreLgvsrrTvy 35 
                                       +   ls  e +r+ g+sr T++
  gi|386001942|ref|YP_005920241.1| 201 KypALSDLELSRRTGISRPTIS 222
                                       3355788899**********96 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.14   2.7e+02      21      34 ..      25      38 ..      16      44 .. 0.86
   2 ?    8.9   0.0   0.00067       1.3       3      34 ..     190     221 ..     188     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                     HTH_AsnC-type 21 aeLAervGlSestv 34
                                       +LA ++G+++st+
  gi|386001942|ref|YP_005920241.1| 25 IDLAGKIGVDRSTI 38
                                      58**********97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00067
                     HTH_AsnC-type   3 eiDrkILeaLqedaRisyaeLAervGlSestv 34 
                                       e Dr  L a  + + +s  eL++r+G+S++t+
  gi|386001942|ref|YP_005920241.1| 190 EKDRLALLAFVKYPALSDLELSRRTGISRPTI 221
                                       677777777778889999************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.1     2e+02      22      49 ..      22      49 ..      12      57 .. 0.83
   2 ?    7.5   0.0     0.002       3.9      22      54 ..     205     237 ..     186     244 .. 0.86
   3 ?   -2.9   0.0       3.6   7.1e+03      43      59 ..     310     326 ..     308     333 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTT CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreg 49
                                      l+  +lA  +G+ r+t+ +  +++++  
  gi|386001942|ref|YP_005920241.1| 22 LSDIDLAGKIGVDRSTIFKSKRKFREWE 49
                                      56679************99999888755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglisrg 54 
                                       l+  el+++ G++r t+s   +++ + gl+ r+
  gi|386001942|ref|YP_005920241.1| 205 LSDLELSRRTGISRPTISGKRNKFFQSGLLARQ 237
                                       7889********************999999864 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.6
                                       HHHHHTTSEEET.EEEEE CS
                         HTH_Crp_2  43 seLkreglisrg.rriri 59 
                                       ++L++ gl++ +    +i
  gi|386001942|ref|YP_005920241.1| 310 KALSEVGLVEERpS-YVI 326
                                       78999999996523.444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0085        17      21      46 ..      30      55 ..      21      63 .. 0.85
   2 ?    3.7   0.0     0.031        61      18      41 ..     210     233 ..     209     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0085
                            HTH_29 21 llglsrrtvyrwlkrfeegGlaalld 46
                                        g++r+t+++ ++ f+e++   ll+
  gi|386001942|ref|YP_005920241.1| 30 KIGVDRSTIFKSKRKFREWEMVQLLN 55
                                      579****************9988887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                            HTH_29  18 iAkllglsrrtvyrwlkrfeegGl 41 
                                       + +++g+sr+t+   ++ f + Gl
  gi|386001942|ref|YP_005920241.1| 210 LSRRTGISRPTISGKRNKFFQSGL 233
                                       789*********988888877774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 2011.65
//
Query:       gi|386001943|ref|YP_005920242.1|  [L=216]
Description: Metallo-beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-17   62.4   0.2    8.6e-12   45.5   0.0    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0057   16.6   0.0     0.0085   16.0   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0083   15.6   0.0      0.013   15.0   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   1.4e-15   8.6e-12       6      69 ..      51     114 ..      48     128 .. 0.93
   2 !   15.2   0.0   2.8e-06     0.017     125     197 .]     133     200 ..     118     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.4e-15
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatd 69 
                                       ++++li  + + i++DtG+++e + +  +l+ lgl p+ vd v++TH H+DH G+++ + +a+ 
  gi|386001943|ref|YP_005920242.1|  51 SSATLILAGSRKIVVDTGCEGEGEPITNRLKELGLAPEYVDIVVNTHDHPDHSGNNRLFSRARI 114
                                       789********************************************************99876 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.8e-06
                                       HECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 125 vtggpghghghgvvey.gggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++ +pgh++++++v +   ++++++GDal+   + +   ++r + +r  ++ + ++      +   aev+vpgH
  gi|386001943|ref|YP_005920242.1| 133 IMETPGHTADSISVVCeSPRRIVVAGDALPLMGNYLKWVPPRLHVDRGMALRSMAR------IVEVAEVVVPGH 200
                                       6789***********955689******************66666666555555555......456899999999 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0085       8      76 ..      52     126 ..      49     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                     Lactamase_B_3   8 nsflletagarilvDPf.........kanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslevgg 75 
                                       ++ l+  +  +i+vD +         ++ ++++  +e +D+v+ +++++dH   ++l +   ++++l++++ le g+
  gi|386001943|ref|YP_005920242.1|  52 SATLILAGSRKIVVDTGcegegepitNRLKELGLAPEYVDIVVNTHDHPDHSGNNRLFS---RARILSGKGGLEEGD 125
                                       444555556899999887666666652245666667*****************999888...999999977665554 PP

                     Lactamase_B_3  76 l 76 
                                       l
  gi|386001943|ref|YP_005920242.1| 126 L 126
                                       4 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-06     0.013       1      45 [.      61     104 ..      61     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-06
                                       SEEEES--TTHHHH.HTCGGS--S.SS--..SEEEEE-SS--HHHHG CS
                     Lactamase_B_2   1 rriLiDagpdlrqq.alralqPve.lrdelppidaVllthaHyDHla 45 
                                       r i++D+g +  +   +    + + l   ++ +d V+ th+H DH  
  gi|386001943|ref|YP_005920242.1|  61 RKIVVDTGCEGEGEpITN---RLKeLGLAPEYVDIVVNTHDHPDHSG 104
                                       679999999943333333...33446777889*************83 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.38s 00:00:00.93 Elapsed: 00:00:00.58
# Mc/sec: 1123.79
//
Query:       gi|386001944|ref|YP_005920243.1|  [L=446]
Description: Adenylosuccinate lyase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-50  170.4   0.1    1.2e-49  169.4   0.0    1.5  2  Lyase_1      Lyase
    8.9e-22   77.4   1.0    3.3e-21   75.6   1.0    2.0  1  ADSL_C       Adenylosuccinate lyase C-terminus
    0.00096   19.2   0.9     0.0024   17.9   0.2    2.0  2  ASL_C        Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.015   15.7   0.4      0.079   13.4   0.1    2.5  2  FumaraseC_C  Fumarase C C-terminus
       0.39   11.5   2.9        1.2   10.0   0.3    2.9  3  ASL_C2       Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   0.0   3.5e-53   1.2e-49       8     310 ..      13     293 ..       7     295 .. 0.88
   2 ?   -2.5   0.0      0.74   2.7e+03     234     260 ..     387     413 ..     349     439 .. 0.63

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 3.5e-53
                                       CHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHH CS
                           Lyase_1   8 dklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavn 84 
                                       +++ + ++e+ r++         ++aal++a +++++++  +a++i +a++    e         k i+ ++g+++ 
  gi|386001944|ref|YP_005920243.1|  13 PEMKDLWSEEYRFRCLFR-----VEAALARAEEELGLIPPGAADDIGRAAEGASPERA-------KEIEDEIGHDMM 77 
                                       566666666666666666.....99**********************99998888333.......446777777776 PP

                                       HHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTE CS
                           Lyase_1  85 mnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlq 161
                                       + +   ++e  +   e+ ++vh g++snD+ +Ta  l++k++l ++L++++++  ++l ++a+e+k  v +GrTh+q
  gi|386001944|ref|YP_005920243.1|  78 A-VVHALAEACE---EAGEWVHLGATSNDILDTATGLQIKASL-AVLEEKVKRVLRVLLARAEEHKGLVCAGRTHGQ 149
                                       6.6666665555...9***************************.99******************************* PP

                                       EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHH CS
                           Lyase_1 162 dAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsfe 237
                                         +P+t g  ++ +a ++ r++erl ++++r  v++++g++++ ++++ad  + + +v++ l  +     ++ +  +
  gi|386001944|ref|YP_005920243.1| 150 IGVPTTYGLRFAVWASEMARHLERLAQMKPRAAVGKMSGAVGTQAAFGADGmKIQARVMELLD-L-----TEVDVSN 220
                                       **************************************************9444444444444.4.....5688888 PP

                                       HHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                           Lyase_1 238 avsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                       +v +rD+++e++ ++ l+a  L k++ ++r l+ +e+ +v + + +++ GSS+MP+K+NP+++E + g a+ v
  gi|386001944|ref|YP_005920243.1| 221 QVVQRDRHAEMICWMGLVASTLDKICVEIRTLQRSEIAEVSEVFGKRQVGSSTMPHKRNPIKSEQVCGLARIV 293
                                       99**************************************************************999888655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.74
                                       SHHHHHHC-HHHHHHHHHHHHHHHHHH CS
                           Lyase_1 234 nsfeavsdrDavvellgalkllatsLs 260
                                        s++av++   ++ +l+  +++a++Ls
  gi|386001944|ref|YP_005920243.1| 387 SSMRAVEEDRTLASVLAEEETVAAHLS 413
                                       445555555555555555555555554 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   1.0   9.1e-25   3.3e-21       1      72 [.     359     436 ..     359     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 9.1e-25
                                       TGGGHHHHHHHHHH.TH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHH CS
                            ADSL_C   1 GlifservllaLvk.glgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivd 71 
                                       Gl ++e+v+++L+k g+gR++A+e+ +  +m+a ee   l+ +La++++v+ + s ee+d+l+dp++y+g a e+vd
  gi|386001944|ref|YP_005920243.1| 359 GLNMAESVMVELAKrGVGRQKAHEIMRSSSMRAVEEdrtLASVLAEEETVAaHlSSEEIDRLLDPHRYIGTAVEQVD 435
                                       899**********66************************************76*999******************** PP

                                       H CS
                            ADSL_C  72 r 72 
                                       r
  gi|386001944|ref|YP_005920243.1| 436 R 436
                                       9 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.1   3.8e+03      48      65 ..     112     129 ..     102     138 .. 0.78
   2 !   17.9   0.2   6.7e-07    0.0024       5     115 .]     310     427 ..     308     427 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                                       HHT-GGGGHHHHHHHHHH CS
                             ASL_C  48 LdenwevlaEaiqtvlrr 65 
                                       ++++ +vl E ++ vlr 
  gi|386001944|ref|YP_005920243.1| 112 IKASLAVLEEKVKRVLRV 129
                                       667788999999999985 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 6.7e-07
                                       --TCHHHHHTTC.HHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGG.GHHHHHHHHHHT..T-TTHHHHHHH CS
                             ASL_C   5 RDLtdStvlRnl.gvalahslialksllkglsklevneealaedLdenwev.laEaiqtvlrre..giekpYeklke 77 
                                       RDLt+S+  R l   a+ ++   l+ +++ l+ l++nee+++++L+    + +aE++ + l +   g +k++e +++
  gi|386001944|ref|YP_005920243.1| 310 RDLTNSSCERILfPEAFIFTDHILALTARILEGLSINEEQVERNLQLLRGLnMAESVMVELAKRgvGRQKAHEIMRS 386
                                       9*********98434454444445557899****************9876559****9999766226799******9 PP

                                       HHTTS---HHHHHHHHHCS-.S-HHHH.HHHHC.--CCC-- CS
                             ASL_C  78 ltrgkkitkeslkefiesle.vseeak.eeLka.ltpatYi 115
                                           +  + ++l++++++ e v ++ + ee+ + l p++Yi
  gi|386001944|ref|YP_005920243.1| 387 SSMRAVEEDRTLASVLAEEEtVAAHLSsEEIDRlLDPHRYI 427
                                       98888888888888887764354443314443314577775 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         5   1.8e+04      25      36 ..     342     353 ..     340     358 .. 0.56
   2 ?   13.4   0.1   2.2e-05     0.079      20      51 ..     390     425 ..     376     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 5
                                       T--HHHHHHHTT CS
                       FumaraseC_C  25 gktlreavlelg 36 
                                       g ++ e  +e++
  gi|386001944|ref|YP_005920243.1| 342 GLSINEEQVERN 353
                                       555555555554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.2e-05
                                       HHHHHT--HHHHHHHTT-.....-HHHHHHHT-HHH CS
                       FumaraseC_C  20 eAlkegktlreavlelgl....lteeeldelldpek 51 
                                       +A++e++tl  +  e++     l++ee+d+lldp +
  gi|386001944|ref|YP_005920243.1| 390 RAVEEDRTLASVLAEEETvaahLSSEEIDRLLDPHR 425
                                       699*********9996555666************86 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.5   8.9e+03      36      57 ..      54      75 ..      25      90 .. 0.64
   2 ?    0.0   0.1      0.41   1.5e+03      25      63 ..      90     128 ..      73     130 .. 0.57
   3 ?   10.0   0.3   0.00032       1.2      11      67 ..     370     426 ..     363     428 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                                      T--GGG--HHHHHHH-TT--GG CS
                            ASL_C2 36 gkeleeltleelkeisplleed 57
                                      g+++e+++ e  kei++ +  d
  gi|386001944|ref|YP_005920243.1| 54 GRAAEGASPERAKEIEDEIGHD 75
                                      5556666666666666554433 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHTT--GGG--HHHHHHH-TT..--GGGGGGSS CS
                            ASL_C2  25 vgravrlaeekgkeleeltleelkeispl..leedveeaLd 63 
                                       +g+ v+l   ++  l+++t  ++k  ++l  lee+v+++L 
  gi|386001944|ref|YP_005920243.1|  90 AGEWVHLGATSNDILDTATGLQIK--ASLavLEEKVKRVLR 128
                                       344444433334445566666666..333448888988886 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00032
                                       HHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHHH CS
                            ASL_C2  11 LvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpeas 67 
                                       L+++G+   +AHei  +   +a e++++l+ +  ee   ++ +l+ e++ + Ldp++ 
  gi|386001944|ref|YP_005920243.1| 370 LAKRGVGRQKAHEIMRSSSMRAVEEDRTLASVLAEEET-VAAHLSsEEIDRLLDPHRY 426
                                       889999999********999999999999988777766.6777888*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2756.10
//
Query:       gi|386001945|ref|YP_005920244.1|  [L=608]
Description: 5'-Nucleotidase-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-40  136.9   0.0    9.5e-40  136.4   0.0    1.2  1  5_nucleotid_C  5'-nucleotidase, C-terminal domain
    4.8e-09   37.0   0.0    7.7e-09   36.3   0.0    1.4  1  Metallophos    Calcineurin-like phosphoesterase
     0.0012   19.1   0.0     0.0061   16.8   0.0    2.1  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.0   1.6e-43   9.5e-40       1     157 [.     381     557 ..     381     558 .. 0.93

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 1.6e-43
                                       EEEEESSB....---HHTS--HHHHHHHHHH.............TGSTT--EEEEEGGG----B.........TTTE CS
                     5_nucleotid_C   1 vigtttveldgrdlalrtgetnlgnliadal.............raaagadialangggiradl.........paGd 55 
                                       v+g++t+++++  ++ ++ge++lgnliada+              + +ga +a++n+ggiradl         ++G+
  gi|386001945|ref|YP_005920244.1| 381 VVGSVTADITRD-AS-ESGESALGNLIADAQlfatsaggegggkADGMGAVVAFMNPGGIRADLlfdqaggeeAPGE 455
                                       688899976664.44.49*************99999998888888888889***********9999999999999** PP

                                       EEHHHHHHHS-S--EEEEEEEEHHHHHHHHHH.HTTTTTS--TT-EEEE.SEEEEE-TTS-TT--EEEESSS-BEEE CS
                     5_nucleotid_C  56 itvkdlltvlpfgntlvvveltGaqlkeaLenesvsaskaasgrflqvs.Glrytydlskpagervtslsvtvngkp 131
                                       +t++++++v+pf+n+l+v++ltG+++k++Le e+  +++ +++r+l++s Gl y +  s+p+g++v   s+++ g p
  gi|386001945|ref|YP_005920244.1| 456 VTRQEAFNVQPFDNKLIVLNLTGEEIKAVLE-EQFDNPEPGRNRILHISeGLIYAWRRSAPPGDKVDISSIKIGGVP 531
                                       *******************************.5999*******************************99******** PP

                                       --TTSEEEEEEEHHHHTTGGG-HHHH CS
                     5_nucleotid_C 132 ldddktYkvatnsylasggdgfsmlk 157
                                       +d++ tY+va n +la+ggdgf +++
  gi|386001945|ref|YP_005920244.1| 532 IDPQGTYRVAANHFLAEGGDGFATFA 557
                                       **********************9886 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   1.3e-12   7.7e-09       3     203 ..      60     308 ..      58     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.3e-12
                                       EEEEESBTB....................TTCCTHHHHHHHHHHHHHHHTTESEEEEE.STSSSSS.......HHHH CS
                       Metallophos   3 ilvigDlHl....................algggqlddllkllddllreekpdlvlla.GDlvdrg.......dlek 51 
                                       il i+DlH+                      ++g+ ++l ++++ l +  +pd +l+  GD++  +         e 
  gi|386001945|ref|YP_005920244.1|  60 ILAINDLHGqleppqgratvgydskceplMVEVGGAEYLSTAIKGLVAT-NPDTILVSaGDNIGASpllsalfHDEP 135
                                       99***************************8889****************.******999**9999998888876666 PP

                                       HHHHHHHHHHHHTSEEEEEC-TTS....................CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEE CS
                       Metallophos  52 ellellaalvkypipvylllGNHe....................gfee.ellnkygylgifsepwrsdaevfnnlpl 107
                                        ++e l+ ++      y + GNHe                    g+++ + +   g+ ++ +++   +++   ++p 
  gi|386001945|ref|YP_005920244.1| 136 -TIEALSLMGFD----YSAVGNHEfdegagelfrmqhgcchpeeGCQDgDRFVGAGFRYLAANVLDEETGETIFPPF 207
                                       .77777888883....********55555555555554443333222212222222222223333333444445555 PP

                                       EEEETTEEEEEEEESE.....CEEETHHHHHHHHHHHSCHHHHCC..HHHHHHHHHHTTCSEEEEEESSESS....C CS
                       Metallophos 108 aslgsgslkvlllhGg.....spellvsldklgslnleleapepg..dewlkdlekrekadwvivlgHsply....r 173
                                       a+   g   v +++ g     +p  +v ++ + +l++++ea+  +   e lk+    e++++ +vl H +       
  gi|386001945|ref|YP_005920244.1| 208 AVREAG--GVPVAFIGaslksTPA-IVVPSGVAGLQFIDEADAINgcVEALKE----EGVEIFVVLLHDGGFsaglP 277
                                       555555..5666666655554444.59*************9999888888888....89999999999999966643 PP

                                       SSSCSCCHHHHH....HH.HHHTTESEEEEESSSS CS
                       Metallophos 174 gsgylfgdeale....dl.lkkygvdlvisGHtHv 203
                                       + g        e     +   +++vdl i GH+H+
  gi|386001945|ref|YP_005920244.1| 278 NEGMEPC----EeledIIrRTDGDVDLFITGHSHQ 308
                                       3333333....1333355577777**********7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.27   1.6e+03       4      42 ..      61     125 ..      59     177 .. 0.55
   2 !   16.8   0.0     1e-06    0.0061      94     148 ..     264     327 ..     241     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                     Metallophos_2   4 aiiSDlH.........................snldaleavlealkevgvdaiiha.GDleeeep 42 
                                       ++i DlH                         +  ++l ++++ l ++++d+i+++ GD  +++p
  gi|386001945|ref|YP_005920244.1|  61 LAINDLHgqleppqgratvgydskceplmvevGGAEYLSTAIKGLVATNPDTILVSaGDNIGASP 125
                                       55666664444444444444444444444444445566666777777888888776688323333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1e-06
                     Metallophos_2  94 vlliHgdpl.........gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvge 148
                                       v l+H+            +  ++l++ +++++ ++d+++ GH+H+++++  +g+lv  +Gs g 
  gi|386001945|ref|YP_005920244.1| 264 VVLLHDGGFsaglpnegmEPCEELEDIIRRTDGDVDLFITGHSHQAYISMVDGRLVTQAGSHGK 327
                                       455555544666666666777889999999777778************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3909.89
//
Query:       gi|386001946|ref|YP_005920245.1|  [L=473]
Description: Transporter, YbiR family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-35  121.2  32.3      6e-35  120.9  22.8    2.2  2  CitMHS        Citrate transporter


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9  22.8   3.4e-39     6e-35       4     282 ..      87     405 ..      83     409 .. 0.79
   2 !    7.6   0.8   0.00011       1.9     112     168 ..     406     471 ..     402     473 .] 0.84

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 3.4e-39
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                            CitMHS   4 lileklrldvvallvlvllvltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllv 79 
                                       +i++ +   +va+lv+    +++  al +i  +++l+l+g++++g alee+G   +l+ +llr++++  d l++++ 
  gi|386001946|ref|YP_005920245.1|  87 MIWQIMLAGAVAVLVAGS--ISPAAALGAINMDVMLFLFGMFVVGVALEESGYLASLSYRLLRRTRN-VDqLVIAVL 160
                                       556666666666655555..9*********************************************8.6779999** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            CitMHS  80 lltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll... 153
                                       ++++llsa++ nd+ ++i +p+++ la++ + +p+lll+ la++  ig++++piG+p            +nll+   
  gi|386001946|ref|YP_005920245.1| 161 FGAGLLSALLMNDTLAIIGTPLLIHLANKYGISPRLLLLSLAFGVTIGSVASPIGNP------------QNLLIalg 225
                                       *****************************9999999*********************............****9888 PP

                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxx RF
                            CitMHS 154 ...............lalllvgllplvllfmfgvalalpvnap..................kvkkqkaiieaiarsl 197
                                                      l           +++      +l+ +++                  +++     ++++++  
  gi|386001946|ref|YP_005920245.1| 226 gsvpnpfvtffrhlaL----------PTAV------NLLLAYGvlrllcrrefgretlnhiQDAVVDPDLARLSKLS 286
                                       8865533333333331..........3333......33444445555555555555544445555555555666655 PP

                                       xxxxxxxxxx....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 198 lpvatillla....................................ykkveWsvlllfaGvfllvgaleqtGileal 238
                                       l v+t+l+++                                     +kv+W +l++fa +f+l++ + ++G l+a 
  gi|386001946|ref|YP_005920245.1| 287 LGVVTALIAFkivsvslglpsplglteiallsalpillasprrlelARKVDWRTLVFFASMFVLMESVWNSGRLQAA 363
                                       555666655588888888888888888888888999999*********************************77777 PP

                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 239 adllgag.gplvalalvlgliallsafisnvavaalmapialgma 282
                                       ++    g    +++ ++l+ +al s+++snv+++al +p++ +++
  gi|386001946|ref|YP_005920245.1| 364 MNGS--GfEA-TSVPAILATSALASQLVSNVPFVALYLPLLSTLD 405
                                       7666..3222.444556777888****************998766 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00011
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxx RF
                            CitMHS 112 lppllliplalaaniggaltpiGtpttraaarpglslpnlll.....................lalllvgllplvll 167
                                       +++ ++++la ++ i g lt+iG               n+++                     +  +l++l++ ++l
  gi|386001946|ref|YP_005920245.1| 406 SSVEAMMALAAGSTIAGNLTIIGAA------------SNVIIvqngerrgaaltftdfmkvgaPLTALNLLVYWIFL 470
                                       566699*******************............**99999999999998888888888777778877887776 PP

                                       x RF
                            CitMHS 168 f 168
                                        
  gi|386001946|ref|YP_005920245.1| 471 S 471
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2974.44
//
Query:       gi|386001947|ref|YP_005920246.1|  [L=406]
Description: Putative methanogenesis marker protein 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-94  317.3   0.7      2e-94  316.5   0.7    1.4  2  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.16   2.8e+03     281     320 ..      19      58 ..       8      61 .. 0.64
   2 !  316.5   0.7   1.1e-98     2e-94       1     323 []      69     377 ..      69     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.16
                              YcaO 281 dleedletllerlkaagld.vlvvdltrp.dlglpvvkvivP 320
                                       ++ee le++  +++ ag+  v  +d+t+   +g+pv   i P
  gi|386001947|ref|YP_005920246.1|  19 SPEETLERIAPKMELAGITrV--ADITNLdRIGIPVFSSIRP 58 
                                       667777777777777777733..5666545788888776666 PP

  == domain 2  score: 316.5 bits;  conditional E-value: 1.1e-98
                              YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvrasyrel.egegaldpeelglyseeekdaadfvlepfdpdrp 76 
                                       nGkGat+++Ar+sa++E++Erysae    +d++ +++s + l +g +a+dp++l l+            +  dp++p
  gi|386001947|ref|YP_005920246.1|  69 NGKGATPAEARVSAMMEGIERYSAE---VHDRQLLVESHSRLsAGVEAVDPRDLALP------------DGADPGMP 130
                                       8*********************999...34555555*********************............789***** PP

                              YcaO  77 idwvpgwsltdgeevlvPanlvylyeppegea.rlfletsnGlAaGntleeAilhGllEliERdafalawyerlplp 152
                                       ++wv g++l+ +eev++Pa++v++  p ++e  +lf++++nGlA+Gn leeA++hGl+E+iERda +la   + + p
  gi|386001947|ref|YP_005920246.1| 131 MPWVLGYDLIGEEEVMLPASAVFH--PLPREYpQLFRTNTNGLASGNVLEEAVFHGLSEVIERDAWSLAEAVKRTGP 205
                                       ************************..77777779*******************************999988888888 PP

                              YcaO 153 ridlasdpeirellerlreagievrlldatldlgipvvaavlvd....pklllvagaGahldpevAlerAltElaqs 225
                                        +   +d  +r+ll+r+++a +evr++d+t+d+g+p++aa ++d    +++ll++g+G+h ++ vA++rAltE+aqs
  gi|386001947|ref|YP_005920246.1| 206 LVTEVEDGLARSLLDRFAQAEVEVRIKDITSDIGVPTIAAASDDlklkDPALLTIGMGTHTNAGVAVLRALTEVAQS 282
                                       6663369*************************************8774449999*********************** PP

                              YcaO 226 rltlisgaredpdfdeeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerlkaagld.vl 301
                                       rlt+i+gared++  ++++++ ++er++r +++w++++ ++ +++ +   +++s+d+ +d++ +l+rl +agld ++
  gi|386001947|ref|YP_005920246.1| 283 RLTQIHGAREDTTT-ADFRRQIGYERTKRLNRHWFESTGTEPFREIR---SQDSDDFLDDINLMLKRLGDAGLDrAI 355
                                       **************.89*****************9777775777754...44569********************** PP

                              YcaO 302 vvdltrpdlglpvvkvivPgle 323
                                       vvdltrp++g+pvv+v+vPgle
  gi|386001947|ref|YP_005920246.1| 356 VVDLTRPEIGVPVVRVVVPGLE 377
                                       ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2484.10
//
Query:       gi|386001948|ref|YP_005920247.1|  [L=217]
Description: TfuA-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-45  152.6   0.1    6.1e-45  151.8   0.1    1.4  1  TfuA      TfuA-like protein


Domain annotation for each model (and alignments):
>> TfuA  TfuA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   0.1   3.4e-49   6.1e-45       1     120 []      51     168 ..      51     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 3.4e-49
                              TfuA   1 DGvfeqepavahkEilaalkegvavvGaasmGALRAaElaafGmigvGeiyeayrsgeledDdeVavlhapaelgye 77 
                                       DGvf+qe+avahkE+l+al+ gvavvGa+smGALRAaEla+fGm+gvGei++ yr+g+l +DdeVa++++p   +++
  gi|386001948|ref|YP_005920247.1|  51 DGVFFQESAVAHKEVLRALEMGVAVVGASSMGALRAAELASFGMEGVGEIFRLYRDGVLISDDEVALIFDPI--SFA 125
                                       9**********************************************************************9..8** PP

                              TfuA  78 alsealvnlratlkaaveegiiseeeaaallelakelyykert 120
                                       +lse+lvn+r++++aa e+g i++ +a+++l++a++ly+++r+
  gi|386001948|ref|YP_005920247.1| 126 PLSEPLVNVRENVRAARERGSIDAVSAEKILAAASSLYFPKRS 168
                                       *****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1340.12
//
Query:       gi|386001949|ref|YP_005920248.1|  [L=92]
Description: Molybdopterin synthase subunit MoaD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-18   64.6   0.0    1.1e-17   64.4   0.0    1.0  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   6.1e-22   1.1e-17       2      77 .]       6      92 .]       5      92 .] 0.97

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 6.1e-22
                                      EETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEE CS
                              ThiS  2 llfaelrelag.eeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDeva 69
                                      + fa++r l g e+e+ laeg+ v++lle+L+ r +el           ++ ++v+vNg++  +  +++t+l++gDeva
  gi|386001949|ref|YP_005920248.1|  6 KAFARYRALLGsESEVKLAEGAAVSDLLESLASRSGELRgqlfddsgrVREDLNVMVNGRHFLSlAGEETPLAEGDEVA 84
                                      669*********************************************99**************77************* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      ++p+V GG
  gi|386001949|ref|YP_005920248.1| 85 LFPAVVGG 92
                                      *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 590.26
//
Query:       gi|386001950|ref|YP_005920249.1|  [L=242]
Description: MoeB/thiF molybdopterin or thiamine synthase protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-61  206.2   0.0    5.7e-61  206.0   0.0    1.0  1  ThiF             ThiF family
     0.0042   17.4   0.3      0.012   15.9   0.3    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.031   14.3   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.022   14.3   0.1       0.03   13.9   0.1    1.2  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.0   0.0   1.3e-64   5.7e-61       1     216 [.       7     208 ..       7     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.0 bits;  conditional E-value: 1.3e-64
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       y+rq+ l+ge+gq++L++s+ l+vGaGglGs + ++La +Gvg++ +vD D++e+sNlnRq+l+ +ed G+pKa +a
  gi|386001950|ref|YP_005920249.1|   7 YDRQIPLFGEEGQRRLARSTALVVGAGGLGSAVSVYLAVAGVGRIVVVDGDVVEVSNLNRQILHWPEDLGRPKAASA 83 
                                       89*************************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                       a+ l+ +np+veve v+   + ++ l  l+ ++D+VvdalDn+++r+l+n a+   ++pl +++ +g++gq+++iip
  gi|386001950|ref|YP_005920249.1|  84 ADTLRGLNPEVEVEEVPLFADGRN-LPGLVAKADAVVDALDNFSSRHLLNGAALDADVPLFHGAISGLDGQATTIIP 159
                                       ********************9999.569************************************************* PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklen 216
                                       g t+c++C +p   + p+e+kvp++          ++t++v+++++a+e++k+l g   + +
  gi|386001950|ref|YP_005920249.1| 160 GATPCLRCIFP---RPPPEEKVPAL----------GATCGVIGSIQATEVVKHLTGLGASLA 208
                                       **********9...99999998877..........9******************76555444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   2.6e-06     0.012       2      87 ..      28     132 ..      27     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-06
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....................TTTCEEEEE--TT CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.....................lgvrfeaialdae 57 
                                       l++GaG+ G+av  +la  +    +i+v+d +  ++ +l  ++                     l++++e +++   
  gi|386001950|ref|YP_005920249.1|  28 LVVGAGGLGSAVSVYLAVAGVG--RIVVVDGDVVEVSNLNRQIlhwpedlgrpkaasaadtlrgLNPEVEVEEVPLF 102
                                       89***************99866..***************9999*********************999*******999 PP

                                       THHHHHHHHHTTSSEEEE-SSGGGHHHHHH CS
                   Sacchrp_dh_NADP  58 nyeavLaallkegdlvvnlsppissldvlk 87 
                                        +   L  l++++d+vv+++ ++ss+ +l 
  gi|386001950|ref|YP_005920249.1| 103 ADGRNLPGLVAKADAVVDALDNFSSRHLLN 132
                                       99999******************9998775 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     7e-06     0.031       9      55 ..      21      67 ..      15      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-06
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHH CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaee 55
                                      +l+++++l++GaG +++ v  +L+ +gv ++vv+  ++  +++l ++
  gi|386001950|ref|YP_005920249.1| 21 RLARSTALVVGAGGLGSAVSVYLAVAGVGRIVVVDGDVVEVSNLNRQ 67
                                      68899*****************************9888888887766 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.8e-06      0.03       5      46 ..      29      71 ..      25      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                                      EE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS CS
                    UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipi 46
                                      v+G+G +G   ++ la +g   +++vD d   v++ln++ ++ 
  gi|386001950|ref|YP_005920249.1| 29 VVGAGGLGSAVSVYLAVAGvGRIVVVDGDVVEVSNLNRQILHW 71
                                      9******************779***************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1518.94
//
Query:       gi|386001951|ref|YP_005920250.1|  [L=155]
Description: hypothetical protein Mhar_1263 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-53  179.4   0.0    4.9e-53  179.2   0.0    1.0  1  DUF1890          Domain of unknown function (DUF1890)
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.24   11.6   0.0    1.3  1  Flavodoxin_NdrI  NrdI Flavodoxin like


Domain annotation for each model (and alignments):
>> DUF1890  Domain of unknown function (DUF1890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.2   0.0   5.5e-57   4.9e-53       1     139 []      15     154 ..      15     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 5.5e-57
                                       EEE---S-STTHHHHHHHHHHHHHCTTEEEEEEE-HHHHHHHHHHSTT-SS-SEEEEHHHHHHH--TT..S-SEEEE CS
                           DUF1890   1 lillGCPevPvqtplalylanklkkkgievvvagnpaalkLlkvaDpekhYvkelvdldkaleeieek..dvdlllg 75 
                                       lillGCPevPvqt++alyla++l+++g evvvag+ aalkL k+aDp +hY++e++++d+++++i+e+  d+d +++
  gi|386001951|ref|YP_005920250.1|  15 LILLGCPEVPVQTSIALYLAYRLRERGDEVVVAGTGAALKLTKLADPLGHYLGETTNIDRCIASISEGkaDFDQCFA 91 
                                       89*****************************************************************99******** PP

                                       EESSHHHHHHHHHHHHHH-.SEEEEEEE-S-HHHHHHHHHH--EEEEE--SS--HHHHHHHHHH CS
                           DUF1890  76 fvhnDagvsyavtlkavlnkakliaivfgkdaeelaeliefdaeviaaravHnpkplkkkldev 139
                                       f+h+Dag++ya t++++   a l++++fg++aeelae++efd+++ +a+avH+p plk+ ldev
  gi|386001951|ref|YP_005920250.1|  92 FAHSDAGITYAGTISYISR-ALLFVLIFGRSAEELAETVEFDCRKLVAKAVHDPLPLKRLLDEV 154
                                       ****************666.*****************************************997 PP

>> Flavodoxin_NdrI  NrdI Flavodoxin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.7e-05      0.24      52      91 ..      55      94 ..      38     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.7e-05
                                      STSS-HHHHHHHTSHHHHHCEEEEEEEE-GGGGGGTTHHH CS
                   Flavodoxin_NdrI 52 kkavpkqvieflnkeknrkllrGviasGnrnfgeqyalaa 91
                                       +++ ++++++l +++n + +++ i+ G   f + +a+a 
  gi|386001951|ref|YP_005920250.1| 55 LTKLADPLGHYLGETTNIDRCIASISEGKADFDQCFAFAH 94
                                      345899******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1027.42
//
Query:       gi|386001952|ref|YP_005920251.1|  [L=90]
Description: hypothetical protein Mhar_1264 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-38  129.9   0.1    3.6e-38  129.8   0.1    1.0  1  DUF1894   Domain of unknown function (DUF1894)


Domain annotation for each model (and alignments):
>> DUF1894  Domain of unknown function (DUF1894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.1     2e-42   3.6e-38       1      88 []       1      87 [.       1      87 [. 0.98

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 2e-42
                                      B---HHH--S-SS-EEESSHHHHHHHHTTSEEEEES--EEESSS---SS----EEEE--S-EEEE---SS-EEEEE-SS CS
                           DUF1894  1 maCleklkyeillkeasfkeceeyikkkakevyevepgykilgvrliGvppipvgideekilfpytkPCyGtfvlkvke 79
                                      m+Cle++kye+ll+++sfke++eyikk++k+++ev+pgy+il+v+liGvpp+ +gid+++++fpytkPCyGtfvl+v e
  gi|386001952|ref|YP_005920251.1|  1 MGCLEEMKYEVLLSQCSFKEAREYIKKNFKDTVEVPPGYRILNVHLIGVPPLLIGIDGDRVIFPYTKPCYGTFVLRV-E 78
                                      89***************************************************************************.9 PP

                                      -GGGHHHHH CS
                           DUF1894 80 seeeieklr 88
                                      +++ei +lr
  gi|386001952|ref|YP_005920251.1| 79 AADEIGRLR 87
                                      999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 565.79
//
Query:       gi|386001953|ref|YP_005920252.1|  [L=92]
Description: Molybdopterin synthase subunit MoaD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-15   57.5   0.1    1.8e-15   57.3   0.1    1.1  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.083   12.7   0.1       0.16   11.8   0.1    1.5  2  TrkA_C    TrkA-C domain


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 !   57.3   0.1   2.1e-19   1.8e-15       2      77 .]       6      92 .]       5      92 .] 0.97

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.1e-19
                                      EETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEE CS
                              ThiS  2 llfaelrelag.eeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDeva 69
                                      + fa+ re++g e  ++l+egst+a+lle+++  +p+l+            +v v++N + +++ +   t+l +gDeva
  gi|386001953|ref|YP_005920252.1|  6 RSFARFREVVGeEAAFDLPEGSTLADLLEEVASAHPGLErvlselegaGGIGVTVLLNRRGADPsDLRRTVLEEGDEVA 84
                                      569*******************************************99779*************99************* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      ilpp++GG
  gi|386001953|ref|YP_005920252.1| 85 ILPPFSGG 92
                                      *******9 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.84   7.5e+03       6      14 ..      23      31 ..      20      32 .. 0.60
   2 ?   11.8   0.1   1.8e-05      0.16      18      55 ..      48      85 ..      35      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.84
                                      EE--GGGTT CS
                            TrkA_C  6 vpagsplvG 14
                                      +p+gs l++
  gi|386001953|ref|YP_005920252.1| 23 LPEGSTLAD 31
                                      566666654 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.8e-05
                                      HHHTHHHH...S-EEEEEE-T-EEES--TT-B--TT-EEEE CS
                            TrkA_C 18 kelnlrar...gvlvvairRggeliipsgdtvLeeGDvllv 55
                                      +e  l+     gv+v+  rRg   ++    tvLeeGD++ +
  gi|386001953|ref|YP_005920252.1| 48 SE--LEGAggiGVTVLLNRRG-ADPSDLRRTVLEEGDEVAI 85
                                      55..44445578999999999.9***************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 590.43
//
Query:       gi|386001954|ref|YP_005920253.1|  [L=129]
Description: Molybdopterin synthase subunit MoaE [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.6e-32  109.8   0.2    9.8e-32  109.6   0.2    1.0  1  MoaE        MoaE protein
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.12   12.2   0.0    1.2  1  Baculo_E25  Occlusion-derived virus envelope protein E25


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.2   1.1e-35   9.8e-32       2     113 .]       5     112 ..       4     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.1e-35
                                       ESS---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-E CS
                              MoaE   2 teepldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlG 78 
                                       t+ +l++++++a  ++p+aGAvv F+GtvRd+     ++ +e eay+++ae++l++i +ea+ +++l++v vvHr+G
  gi|386001954|ref|YP_005920253.1|   5 TDGELSLEDLVAGAKRPDAGAVVAFLGTVRDD----GISGVEVEAYREVAEEELARIRDEAMGTFDLKSVDVVHRVG 77 
                                       777899999999899***************55....59*************************************** PP

                                       EEETTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                              MoaE  79 elevgeasvvvavssahRkeafeaceylidelKkr 113
                                       +l vge +v+++++++hR++af+ ce++++e+K+r
  gi|386001954|ref|YP_005920253.1|  78 RLGVGEDIVLIVATAPHRQAAFRGCEFVLEEIKRR 112
                                       *********************************86 PP

>> Baculo_E25  Occlusion-derived virus envelope protein E25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.12      38      78 ..       2      43 ..       1      77 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                        Baculo_E25 38 vsvaekplsiddivkeGsdk..vGansvflGvvydeglksvna 78
                                      + +++  ls++d+v    ++   Ga   flG+v d+g+++v+ 
  gi|386001954|ref|YP_005920253.1|  2 IEITDGELSLEDLVAGA-KRpdAGAVVAFLGTVRDDGISGVEV 43
                                      56899999****99755.5423788889***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 906.44
//
Query:       gi|386001955|ref|YP_005920254.1|  [L=456]
Description: GvpD gas vesicle, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-38  130.8   0.0    2.6e-37  128.6   0.0    1.8  2  GvpD           GvpD gas vesicle protein
    9.3e-13   48.0   0.1    1.4e-11   44.2   0.0    2.2  2  ATPase         KaiC
    5.2e-05   23.7   0.0    0.00012   22.6   0.0    1.6  1  AAA_16         AAA ATPase domain
    0.00073   19.8   0.0     0.0023   18.2   0.0    1.8  1  AAA_22         AAA domain
     0.0011   18.6   0.0     0.0041   16.7   0.0    2.0  2  AAA_25         AAA domain
     0.0013   18.1   0.0       0.37   10.1   0.0    2.3  2  DnaB_C         DnaB-like helicase C terminal domain
     0.0015   18.3   0.0      0.022   14.5   0.0    2.3  2  AAA_24         AAA domain
     0.0039   17.6   0.0       0.01   16.2   0.0    1.7  1  AAA            ATPase family associated with various cellular
      0.005   16.0   0.0     0.0087   15.3   0.0    1.4  1  NB-ARC         NB-ARC domain
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.031   13.5   0.0    1.3  1  DUF2075        Uncharacterized conserved protein (DUF2075)
      0.025   14.4   0.0       0.04   13.7   0.0    1.2  1  AAA_11         AAA domain
      0.031   14.8   0.1      0.055   14.0   0.1    1.6  1  AAA_18         AAA domain
      0.031   14.0   0.0       0.15   11.8   0.0    2.0  2  IstB_IS21      IstB-like ATP binding protein
      0.047   12.9   0.0      0.077   12.2   0.0    1.2  1  TIP49          TIP49 P-loop domain
      0.052   13.5   0.0      0.097   12.6   0.0    1.4  1  NACHT          NACHT domain
      0.056   14.0   0.0      0.097   13.2   0.0    1.4  1  ABC_tran       ABC transporter
      0.059   13.0   0.0      0.084   12.5   0.0    1.5  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.064   13.0   0.0        0.1   12.3   0.0    1.3  1  AAA_30         AAA domain
      0.065   12.1   0.0       0.11   11.4   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.12   11.8   0.0        4.2    6.6   0.0    2.2  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.12   12.4   0.0       0.22   11.5   0.0    1.6  1  AAA_14         AAA domain
       0.14   12.5   0.0       0.27   11.6   0.0    1.4  1  AAA_19         AAA domain
       0.22   11.4   0.4       0.43   10.5   0.1    1.7  1  NTPase_1       NTPase


Domain annotation for each model (and alignments):
>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   0.0   3.4e-40   2.6e-37       2     296 ..       8     313 ..       7     318 .. 0.82
   2 ?   -0.2   0.0      0.38     3e+02     377     461 ..     347     436 ..     335     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 3.4e-40
                              GvpD   2 eqffdgeaGktllikGaPGtGktlftlrgldvlrresdvlyvstrvddetvseayfsgeaeldktalldllkdplel 78 
                                       + ff  e G+tllikG PGtGkt+++l+ + ++ + ++ +y+strv    v+ ++      +  +++++  +  + l
  gi|386001955|ref|YP_005920254.1|   8 HDFFRVEEGQTLLIKGMPGTGKTTLALEIMSSVCERENGMYISTRVSPGRVHAMFPWIGDIIPSANVVNATQK-MLL 83 
                                       68****************************************************9555556667777777765.567 PP

                              GvpD  79 dldvdvPiekldlesllefvdei...aaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvl 152
                                       +  ++v  e    e++l+f +     a   + ++i +dsw+ +++y a+     +  + ++ ++  +ar+ g++l+ 
  gi|386001955|ref|YP_005920254.1|  84 ESLRNVGREGSSYETVLDFFKTFldqAGDMDDPMIVIDSWDAIINYTAAILGGAQ--HSLEQNICEFARDMGIHLIF 158
                                       778889999999888888877641113445789***************9987665..5788899999********** PP

                              GvpD 153 vletaansrleyivdGvvtl.nvk......eddr..grlr...rdlrleklrGvrignrlqPftladGkfksitrv. 216
                                       v+e+a+  +l+yivdGvvtl nv+       d+r  g++    r++rl+klrGv i+++++  tl dG+f    ++ 
  gi|386001955|ref|YP_005920254.1| 159 VSESAELLPLDYIVDGVVTLkNVRmaaplsGDNRpeGMTTrysREIRLDKLRGVEIKQKIYTCTLHDGRFCYFEPAl 235
                                       ********************9664333333466555776522379***************************99973 PP

                              GvpD 217 elvtidtvtdeakyePla.ndkakfsvglrdldkllseGtdrGsvvildlgkdlsrdawsvlvlaairdflsqemgv 292
                                       e + ++     +  e +a   +   s+g+ d d+++ +G d Gs  +l++ +  ++  + vl+  a  + + +   v
  gi|386001955|ref|YP_005920254.1| 236 ENLSPQI-GIVCDLERIAdPREDSISTGIDDFDRIT-GGLDFGSCNVLEIDHGVGKRYYQVLTALA-SNSVKNGRAV 309
                                       5566666.56678898884456789*********97.89***********9999999999998655.4566667777 PP

                              GvpD 293 avvp 296
                                        +vp
  gi|386001955|ref|YP_005920254.1| 310 HIVP 313
                                       7777 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                              GvpD 377 iaivervreesegPllyvismdtayeafetrlgdfanyva.......lrndavilivkdgtelrtradrvadmhirl 446
                                        +  +  re++  P+l ++  d +  af+     ++n            +d  +++vk g +       +ad+++ +
  gi|386001955|ref|YP_005920254.1| 347 FKHWDSLRERTGRPILNILGLDSMEFAFGY--ERMLNSTSrmfqkwkETSDVNVVVVKSGQKSIRMTSHIADTYFVI 421
                                       556677899999999999999999999986..444554444446755567888999999998888888999999999 PP

                              GvpD 447 elsgdaivlygenkl 461
                                       +    ++ lyg  + 
  gi|386001955|ref|YP_005920254.1| 422 KELNGGLCLYGLIPR 436
                                       888888888886665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.8e-14   1.4e-11      17     221 ..      14     225 ..       6     233 .. 0.78
   2 ?    1.2   0.1      0.25     2e+02       1      26 [.     259     283 ..     259     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.8e-14
                            ATPase  17 pegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdl...ekleeegklaiidase 90 
                                        eg++ li G pGtGKt++al+ + + +e+  e+g+++++  ++  ++  +  +G  +   + +++++k+ +  + +
  gi|386001955|ref|YP_005920254.1|  14 EEGQTLLIKGMPGTGKTTLALEIMSSVCER--ENGMYISTRVSPGRVHAMFPWIGDIIpsaNVVNATQKMLLESLRN 88 
                                       6899******************99999999..***************999998884331112334444444444444 PP

                            ATPase  91 saeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeav..aReilrqlvrvl.kklgvTailvse 163
                                        ++e    ++ e +  + +++ +   ++    +viDs +++ +y++   +  a + l q + ++ +++g+  i+vse
  gi|386001955|ref|YP_005920254.1|  89 VGRE---GSSYETVLDFFKTFLDQAGDMDDPMIVIDSWDAIiNYTAA-ILggAQHSLEQNICEFaRDMGIHLIFVSE 161
                                       4433...24455566666666666778888***********544443.33247788877666666************ PP

                            ATPase 164 kssseeaaggygveefivdgvivLdlkeiee.............elvRtleivkmRgtkhskkehpfeIte 221
                                          s   a+   +  +ivdgv+ L++ +++              +  R ++ +k+Rg ++++k+++ +  +
  gi|386001955|ref|YP_005920254.1| 162 ---S---AELLPL-DYIVDGVVTLKNVRMAAplsgdnrpegmttRYSREIRLDKLRGVEIKQKIYTCTLHD 225
                                       ...3...334444.57***********9999************99*******************9987665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.25
                            ATPase   1 vktgIeglDeilkgGipegrvvlitG 26 
                                       ++tgI  +D+i+ gG+  g+   +  
  gi|386001955|ref|YP_005920254.1| 259 ISTGIDDFDRIT-GGLDFGSCNVLEI 283
                                       58*********7.9998777665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.5e-07   0.00012      18     142 ..      12     121 ..       5     159 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-07
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                       rv +g  + +l+ G++G+GK++l+ e++ ++++++ g +++++            +  ++     + ++     ++ 
  gi|386001955|ref|YP_005920254.1|  12 RVEEG--QTLLIKGMPGTGKTTLALEIMSSVCEREnGMYISTRVSPG-------RVHAMF---PWIGDIIPS--ANV 74 
                                       37777..57*************************6677777777666.......122222...334444433..334 PP

                            AAA_16  94 leawrekleealaavpelagaea..srllellkrllallsrderplvlvlD 142
                                       ++a ++ l+e+l+   ++ ++++  + +l+ +k +l+++   ++   +v+D
  gi|386001955|ref|YP_005920254.1|  75 VNATQKMLLESLR---NVGREGSsyETVLDFFKTFLDQAGDMDD-PMIVID 121
                                       4444444444444...3333333336777777777777777666.555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     3e-06    0.0023       5     128 ..      16     159 ..      12     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...........erpevv.......fvtlpsst...sskdllrel 60 
                                        + l++ G +GtGKTtl+ +++++ +e+++  +           +    +           ps +     +++l e 
  gi|386001955|ref|YP_005920254.1|  16 GQTLLIKGMPGTGKTTLALEIMSSVCERENGMYistrvspgrvhA----MfpwigdiI---PSANvvnATQKMLLES 85 
                                       67799*********************9987777999988765553....234434321...2222244446667777 PP

                            AAA_22  61 lralglelkaerlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliL 127
                                       lr++g+e+++   +  ++++++ +++ + ++ ++++iD  + ++  +        + + +++ +++   + g++li+
  gi|386001955|ref|YP_005920254.1|  86 LRNVGREGSS-YETVLDFFKTFLDQAGDMDD-PMIVIDSWDAIInyTaailggaqHSLEQNICEFAR--DMGIHLIF 158
                                       8888888888.99999999999999999999.******99996657323333332333333444444..77777777 PP

                            AAA_22 128 v 128
                                       v
  gi|386001955|ref|YP_005920254.1| 159 V 159
                                       6 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.3e-06    0.0041      31      74 ..      14      58 ..       7      62 .. 0.79
   2 ?   -3.3   0.0       7.4   5.8e+03     166     181 ..     344     359 ..     336     364 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.3e-06
                            AAA_25 31 pagelallaGapgtGKttlaldlalavatGkpwlg...pvapeqgkV 74
                                       +g + l+ G pgtGKttlal+++ +v++ +   g   + ++ +g+V
  gi|386001955|ref|YP_005920254.1| 14 EEGQTLLIKGMPGTGKTTLALEIMSSVCERE--NGmyiSTRVSPGRV 58
                                      68999999********************654..24445555566665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.4
                            AAA_25 166 galvealeriarrtga 181
                                       + l+++++++++rtg 
  gi|386001955|ref|YP_005920254.1| 344 ETLFKHWDSLRERTGR 359
                                       6788999***999995 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00047      0.37      17      48 ..      14      45 ..      10      55 .. 0.84
   2 ?    5.7   0.0     0.011       8.2       2      41 ..     259     298 ..     258     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00047
                                      XTTXEEEEEEXTTSSHHHHHHHHHHHHHHCST CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 17 qkgdliiiAarpsmGktalalniaenaavkek 48
                                      ++g+ ++i + p++Gkt+lal+i+++++++e+
  gi|386001955|ref|YP_005920254.1| 14 EEGQTLLIKGMPGTGKTTLALEIMSSVCEREN 45
                                      5788899*****************99987554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                                       BXSSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDkltsGlqkgdliiiAarpsmGktalalniae 41 
                                       +stg +d+D++t+Gl  g   ++    ++Gk    +  a 
  gi|386001955|ref|YP_005920254.1| 259 ISTGIDDFDRITGGLDFGSCNVLEIDHGVGKRYYQVLTAL 298
                                       79*****************************875544442 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.9e-05     0.022       3      85 ..      17     134 ..      15     149 .. 0.68
   2 ?    1.1   0.0      0.36   2.8e+02      98     129 ..     370     402 ..     354     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie................................ 47 
                                       + +li G +g+GKTtla+e+     ++  e+G+         +++                                
  gi|386001955|ref|YP_005920254.1|  17 QTLLIKGMPGTGKTTLALEI--MSSVCERENGMYISTRVSPGRVHamfpwigdiipsanvvnatqkmlleslrnvgr 91 
                                       678999**************..5556777777643222222223344466666666777777777777778888888 PP

                            AAA_24  48 ...swedfldevvel..aaeladyktlviDtideleelclaev 85 
                                          s+e++ld+++++  +a + d   +viD+ d + +++ a +
  gi|386001955|ref|YP_005920254.1|  92 egsSYETVLDFFKTFldQAGDMDDPMIVIDSWDAIINYTAAIL 134
                                       8888888888888886544444455888888888877666655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.36
                            AAA_24  98 kgdgkGygelaeefrrllkklqelrk.nvifia 129
                                         +++Gy ++ +  +r+ +k +e+ + nv+++ 
  gi|386001955|ref|YP_005920254.1| 370 MEFAFGYERMLNSTSRMFQKWKETSDvNVVVVK 402
                                       67899********************99999885 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05      0.01       1      71 [.      19     127 ..      19     147 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                                       EEEESSTTSSHHHHHHHHHHHH.........THE......................EEEEETTTCSSS.....STTH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gve......................fleisgsellsk.....yvge 41 
                                       +l+ G pGtGKT+la  +++++         + +                      +++   + ll++       g 
  gi|386001955|ref|YP_005920254.1|  19 LLIKGMPGTGKTTLALEIMSSVcerengmyiS-TrvspgrvhamfpwigdiipsanVVNATQKMLLESlrnvgREGS 94 
                                       5889***************9964443322220.02222222333333333322222333333333333555555555 PP

                                       HHHHHHHHHHHHHHTS...TSEEEEEETGGGHH CS
                               AAA  42 sekkirelfkeakeka...kpsilfiDEidala 71 
                                       s + + ++fk+   +a   +   ++iD  da++
  gi|386001955|ref|YP_005920254.1|  95 SYETVLDFFKTFLDQAgdmDDPMIVIDSWDAII 127
                                       666666666654444445444666666666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05    0.0087      17      45 ..      15      41 ..       6      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqilnksd 45
                                      e q   + + Gm+G GKttla +i+++  
  gi|386001955|ref|YP_005920254.1| 15 EGQ--TLLIKGMPGTGKTTLALEIMSSVC 41
                                      445..7899***************99854 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.031       3      25 ..      18      40 ..      16      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                       +l++G +GtGKt ++l+++  +
  gi|386001955|ref|YP_005920254.1| 18 TLLIKGMPGTGKTTLALEIMSSV 40
                                      689****************9988 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.1e-05      0.04      15      44 ..      14      43 ..       7      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                            AAA_11 15 seseitliqGPPGtgKTktivellsqllsr 44
                                      +e +  li+G PGtgKT+  +e++s++ +r
  gi|386001955|ref|YP_005920254.1| 14 EEGQTLLIKGMPGTGKTTLALEIMSSVCER 43
                                      566678******************998644 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     7e-05     0.055       2      21 ..      20      39 ..      19     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7e-05
                            AAA_18  2 lltGtpGvGKttlakeLskr 21
                                      l+ G+pG+GKttla e+ ++
  gi|386001955|ref|YP_005920254.1| 20 LIKGMPGTGKTTLALEIMSS 39
                                      688************99655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.15      44      76 ..      13      45 ..       4      54 .. 0.85
   2 ?   -1.2   0.0       1.9   1.5e+03      56      79 ..     285     310 ..     276     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavragl 76
                                      +e+ + +++ G +G+GK+ la  +  + ++++ 
  gi|386001955|ref|YP_005920254.1| 13 VEEGQTLLIKGMPGTGKTTLALEIMSSVCEREN 45
                                      678899******************999998764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                         IstB_IS21  56 sGvGKshla..ialgveavraglsvl 79 
                                        GvGK +    +al+ + v++g +v 
  gi|386001955|ref|YP_005920254.1| 285 HGVGKRYYQvlTALASNSVKNGRAVH 310
                                       6999998642279999***9999986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.9e-05     0.077      50      76 ..      16      42 ..       9      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 50 GravLlaGpsgtGktalaiaiskelge 76
                                      G+++L++G +gtGkt la+ i  ++ e
  gi|386001955|ref|YP_005920254.1| 16 GQTLLIKGMPGTGKTTLALEIMSSVCE 42
                                      899*****************9988765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.097       2      24 ..      18      40 ..      17      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      +++++G +G GKTtL+ ++++  
  gi|386001955|ref|YP_005920254.1| 18 TLLIKGMPGTGKTTLALEIMSSV 40
                                      799****************9876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.097       6      35 ..      11      40 ..       9     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                      EEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStLlkllagll 35
                                      + ++eg+++ i G  G+GK+tL+  ++  +
  gi|386001955|ref|YP_005920254.1| 11 FRVEEGQTLLIKGMPGTGKTTLALEIMSSV 40
                                      789*******************75554443 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.084       8      65 ..      10     105 ..       5     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                       ATP-synt_ab   8 lfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg.................................... 48 
                                       +f + +Gq++li g  g+Gkt+++ +++    +++   y+                                     
  gi|386001955|ref|YP_005920254.1|  10 FFRVEEGQTLLIKGMPGTGKTTLALEIMSSVCERENGMYIStrvspgrvhamfpwigdiipsanvvnatqkmllesl 86 
                                       678899******************66665544443444444346677777777777777777777777777777777 PP

                                       ..ESEEHHHHHHHHHHCHH CS
                                       ..xxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ..iGergnevaevleefpe 65 
                                         +G  g++ + vl+ f++
  gi|386001955|ref|YP_005920254.1|  87 rnVGREGSSYETVLDFFKT 105
                                       7766555555555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1      17      47 ..      15      56 ..       9     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_30 17 gdrvavltGpAGtGKttalkal.reaweaa.g.........g 47
                                      + ++ +++G +GtGKtt+  ++   + e++ g         g
  gi|386001955|ref|YP_005920254.1| 15 EGQTLLIKGMPGTGKTTLALEImSSVCEREnGmyistrvspG 56
                                      446889**********97555548888888555555555551 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.11      13      46 ..      14      47 ..       9      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                     TrwB_AAD_bind 13 retqhilivGttGsGKtqalekllrairargdra 46
                                      +e q +li G  G+GKt+ + +++ ++ +r++ +
  gi|386001955|ref|YP_005920254.1| 14 EEGQTLLIKGMPGTGKTTLALEIMSSVCERENGM 47
                                      57788899********************999876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.078        61      40      62 ..      17      39 ..       4      45 .. 0.77
   2 ?    6.6   0.0    0.0054       4.2     147     228 ..     114     205 ..      88     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.078
                                      .SEEEE--TTSSHHHHHHHHHHH CS
                      FtsK_SpoIIIE 40 shllvaGatgsGKStalntLilS 62
                                      + ll+ G +g+GK+t    ++ S
  gi|386001955|ref|YP_005920254.1| 17 QTLLIKGMPGTGKTTLALEIMSS 39
                                      4699**********987666666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0054
                                       --B-TT-...............................----.-------B-----EEEEEEC-HHHHHHHHHHH.. CS
                      FtsK_SpoIIIE 147 gdvflvlDnyddlaaene.........ritsLsnqgpsygvh.vlvtagrelekrpslvvivderieLrlaapkdss 213
                                        d ++v+D +d++ +  +             + +    +g+h + v++ +el ++ ++v++v  +   r+aap +  
  gi|386001955|ref|YP_005920254.1| 114 DDPMIVIDSWDAIINYTAailggaqhsLEQNICEFARDMGIHlIFVSESAELLPLDYIVDGVVTLKNVRMAAPLSGD 190
                                       46777777777777666667777666533334444444555515688899999********************9999 PP

                                       ..HHHHHHHHHHHCG CS
                      FtsK_SpoIIIE 214 vlvedaivRlarkgr 228
                                        + e++ +R  r  r
  gi|386001955|ref|YP_005920254.1| 191 NRPEGMTTRYSREIR 205
                                       999999999888866 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.22       3      38 ..      17      51 ..      15     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinl 38
                                      + l+i+G+  +GKTtl+ +++++   ++e+ +yi+ 
  gi|386001955|ref|YP_005920254.1| 17 QTLLIKGMPGTGKTTLALEIMSSVC-ERENGMYIST 51
                                      6799*****************8888.9999999986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00035      0.27      10      38 ..      16      44 ..      10      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                       ++ll+ + pGtGKT++  +i++ + e++
  gi|386001955|ref|YP_005920254.1| 16 GQTLLIKGMPGTGKTTLALEIMSSVCERE 44
                                      6789999**********999998877655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00055      0.43       2      25 ..      19      42 ..      18      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00055
                                      EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                                      ++i G+pG+GKtTl   +++ + +
  gi|386001955|ref|YP_005920254.1| 19 LLIKGMPGTGKTTLALEIMSSVCE 42
                                      6799************99987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 2397.40
//
Query:       gi|386001956|ref|YP_005920255.1|  [L=158]
Description: hypothetical protein Mhar_1268 [Methanosaeta harundinacea 6Ac]
Scores for complete 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   22.5   0.0    0.00025   21.4   0.0    1.6  1  FaeA             FaeA-like protein
     0.0012   18.3   0.0     0.0028   17.2   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0021   18.2   0.0      0.004   17.3   0.0    1.4  1  Phage_r1t_holin  Putative lactococcus lactis phage r1t holin
     0.0034   17.1   0.1      0.013   15.3   0.0    1.9  2  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.6   2.2      0.046   13.5   1.2    2.3  2  LacI             Bacterial regulatory proteins, lacI family
      0.015   15.2   0.4       0.03   14.2   0.1    1.6  2  TrmB             Sugar-specific transcriptional regulator Trm
       0.02   14.7   0.1        0.1   12.4   0.0    2.1  2  HTH_23           Homeodomain-like domain
      0.039   14.1   0.5       0.11   12.7   0.1    1.8  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.041   12.7   0.0      0.054   12.3   0.0    1.1  1  HTH_micro        HTH-like
      0.077   13.5   0.0       0.25   11.9   0.0    1.9  2  LZ_Tnp_IS481     leucine-zipper of insertion element IS481
      0.089   12.8   0.1       0.32   11.0   0.0    1.9  2  HTH_11           HTH domain
      0.095   12.7   0.0       0.16   11.9   0.0    1.3  1  TBPIP            TBPIP/Hop2 winged helix domain
       0.16   12.1   0.2        1.4    9.0   0.0    2.2  2  z-alpha          Adenosine deaminase z-alpha domain


Domain annotation for each model (and alignments):
>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.8e-07   0.00025       3      58 ..      27      80 ..      25      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EE CS
                              FaeA  3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlW 58
                                      e Il+ + + + + +T ++A+ +g+s   a  YL  L+ egk + + v  G s lW
  gi|386001956|ref|YP_005920255.1| 27 ERILQAIEDSEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEGKCEFVEV--GPSKLW 80
                                      7899999998999*****************************998887..456666 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0028       5      45 ..      26      67 ..      22      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                            HTH_24  5 drkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      + +IL+++++ + +++  ++A+  g+S++t  ++l  L++eG
  gi|386001956|ref|YP_005920255.1| 26 EERILQAIEDsEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEG 67
                                      679*******9999*************************999 PP

>> Phage_r1t_holin  Putative lactococcus lactis phage r1t holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.9e-06     0.004      20      54 ..      29      65 ..      20      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                   Phage_r1t_holin 20 llgllgagatglldvdwaaaasvaalaAv..vSvltS 54
                                      +l ++    +gl+ vd+a++a+v+ ++A+  +Svl+S
  gi|386001956|ref|YP_005920255.1| 29 ILQAIEDSEVGLTTVDVAKVAGVSKTTAIkyLSVLKS 65
                                      677888889*******************8889***99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.2e-06     0.013       7      46 ..      28      67 ..      28      70 .. 0.96
   2 ?   -1.1   0.1       1.2   1.7e+03      21      21 ..     115     115 ..      89     133 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.2e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelG 46
                                      +iL+a++    +lt  ++A+ +g++k+t+  +L+ L  +G
  gi|386001956|ref|YP_005920255.1| 28 RILQAIEDSEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEG 67
                                      69**********************************9887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       H CS
                          HTH_IclR  21 l 21 
                                       l
  gi|386001956|ref|YP_005920255.1| 115 L 115
                                       2 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.66   9.1e+02      31      40 ..      26      35 ..      23      37 .. 0.82
   2 ?   13.5   1.2   3.3e-05     0.046       4      17 ..      44      57 ..      41      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.66
                                      HHHHHHHHHH CS
                              LacI 31 rerVeaamee 40
                                       er+++a+e 
  gi|386001956|ref|YP_005920255.1| 26 EERILQAIED 35
                                      69******96 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.3e-05
                                      HHHHHCTS-HHHHH CS
                              LacI  4 DVArlAGVSkaTVS 17
                                      DVA+ AGVSk+T+ 
  gi|386001956|ref|YP_005920255.1| 44 DVAKVAGVSKTTAI 57
                                      9***********85 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.2e-05      0.03       8      58 ..      24      75 ..      20      83 .. 0.83
   2 ?   -2.8   0.0       4.4     6e+03      25      35 ..     121     131 ..     119     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                      HHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  8 eyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +yE ++ +a+  ++  +t+ ++a+ +gv+++++ ++L+ L++ G  e ++  
  gi|386001956|ref|YP_005920255.1| 24 SYEERILQAIEdSEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEGKCEFVEVG 75
                                      67777777777778899************************99977766655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                                       HCHHCCCTTSS CS
                              TrmB  25 adeiaeelgvp 35 
                                        +ei+e+l v+
  gi|386001956|ref|YP_005920255.1| 121 LEEISEDLTVS 131
                                       68999999876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.5e-05       0.1       6      39 ..      27      61 ..      22      68 .. 0.78
   2 ?   -0.8   0.1       1.1   1.5e+03      18      31 ..     119     132 ..     101     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-05
                            HTH_23  6 eRlr.illllaeGlsvreIAreLgvsrrTvyrwlk 39
                                      eR++ ++    +Gl++ ++A+  gvs+ T  ++l+
  gi|386001956|ref|YP_005920255.1| 27 ERILqAIEDSEVGLTTVDVAKVAGVSKTTAIKYLS 61
                                      444447777778*****************987765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                            HTH_23  18 lsvreIAreLgvsr 31 
                                       ++ +eI++ L vs 
  gi|386001956|ref|YP_005920255.1| 119 ARLEEISEDLTVSL 132
                                       56788888888875 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.1e-05      0.11       7      50 ..      23      67 ..      19      77 .. 0.88
   2 ?   -1.0   0.0       1.5   2.1e+03      23      35 ..     119     131 ..     116     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                                      HHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                    Fe_dep_repress  7 EdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdG 50
                                        Y e I+++ e +++  +t d+a++ +vs+ ++ + l+ L+++G
  gi|386001956|ref|YP_005920255.1| 23 ASYEERILQAIEdSEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEG 67
                                      5677999*****888889999********************9998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                       B-HHHHHHHHTS- CS
                    Fe_dep_repress  23 vktkdlaerLnvs 35 
                                       ++  +++e L vs
  gi|386001956|ref|YP_005920255.1| 119 ARLEEISEDLTVS 131
                                       5678999999998 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.9e-05     0.054     196     238 ..      28      70 ..      19      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                         HTH_micro 196 qikkkienteeGitskdlkdkfGislkqglklLnklieeeeds 238
                                       +i + ie +e G+t+ d+ +  G+s   + k+L  l  e + +
  gi|386001956|ref|YP_005920255.1|  28 RILQAIEDSEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEGKCE 70 
                                       68899****************************9998876655 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 ?   11.9   0.0   0.00018      0.25      27      53 ..      41      67 ..      27      76 .. 0.88
   2 ?   -2.9   0.0       7.7   1.1e+04      71      80 ..     136     145 ..     123     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                      LZ_Tnp_IS481 27 tvaqvarelGvslrtaykwlarfraeG 53
                                      t  +va+ +Gvs+ ta k+l+ +++eG
  gi|386001956|ref|YP_005920255.1| 41 TTVDVAKVAGVSKTTAIKYLSVLKSEG 67
                                      56789*********************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.7
                      LZ_Tnp_IS481  71 taPerveavl 80 
                                       + Pe+vea++
  gi|386001956|ref|YP_005920255.1| 136 VRPEKVEALI 145
                                       4577777665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.32       3      43 ..      27      67 ..      26      77 .. 0.83
   2 ?   -1.4   0.1       1.7   2.4e+03      19      28 ..     122     131 ..     118     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      + il+ + +++  ++  + A+  +vS++t  +++  L++ g
  gi|386001956|ref|YP_005920255.1| 27 ERILQAIEDSEVGLTTVDVAKVAGVSKTTAIKYLSVLKSEG 67
                                      57888885555559999999999****************99 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                            HTH_11  19 eeLAeeLnvS 28 
                                       ee++e L vS
  gi|386001956|ref|YP_005920255.1| 122 EEISEDLTVS 131
                                       7899999998 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.16      29      58 ..      50      79 ..      39      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                             TBPIP 29 klgKtavqkaLdeLvdegkiieKeyGKqki 58
                                      +++Kt++ k L  L++egk+ + e G +k+
  gi|386001956|ref|YP_005920255.1| 50 GVSKTTAIKYLSVLKSEGKCEFVEVGPSKL 79
                                      79*******************999987776 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.001       1.4       1      33 [.      21      53 ..      21      70 .. 0.86
   2 ?    0.6   0.0      0.44   6.1e+02       9      26 ..     117     131 ..     112     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                                      HHHHHHHHHHHHHHHC-TTCECCHHHHHHHHCC CS
                           z-alpha  1 iaqeqaekilelLeelgekkaatalalergLst 33
                                      ++++ +e+il+++e+++ +  +  +a+  g+s+
  gi|386001956|ref|YP_005920255.1| 21 DMASYEERILQAIEDSEVGLTTVDVAKVAGVSK 53
                                      68999**********************999984 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.44
                                       HHHHHHHC-TTCECCHHH CS
                           z-alpha   9 ilelLeelgekkaatala 26 
                                       i+ +Lee++e+  +    
  gi|386001956|ref|YP_005920255.1| 117 IIARLEEISEDLTV---S 131
                                       77889999987654...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 854.44
//
Query:       gi|386001957|ref|YP_005920256.1|  [L=225]
Description: Tetrahydromethanopterin S-methyltransferase, subunit A, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-54  183.9   0.0    2.4e-54  183.6   0.0    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6   0.0   1.3e-58   2.4e-54       4     149 ..      30     170 ..      27     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 1.3e-58
                                       --TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE---T CS
                              MtrA   4 paegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGaevk 80 
                                        a  WP ++G+y+ Gd+ s +avvtl+s l+     + Gaai Gp+ktenlG+ekvv n+isn++irfl+v+G e k
  gi|386001957|ref|YP_005920256.1|  30 EAGRWPPLRGEYSLGDPGSRIAVVTLASSLR-----APGAAIWGPCKTENLGVEKVVGNLISNSEIRFLLVCGEESK 101
                                       5778************************986.....469************************************** PP

                                       TT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHHH CS
                              MtrA  81 GhitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikelv 149
                                       Gh+ G+++ alh+nG+dk+++ivg++GaiPfienl+ ea++rfq+qve++d i+  d ++i+  ++e  
  gi|386001957|ref|YP_005920256.1| 102 GHLPGDSIVALHRNGIDKDGRIVGSRGAIPFIENLSPEAIDRFQRQVEVIDRIGLVDEDEIERIVREHR 170
                                       *************************************************************99998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1608.77
//
Query:       gi|386001958|ref|YP_005920257.1|  [L=261]
Description: hypothetical protein Mhar_1270 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-28   95.0   0.2    9.5e-06   25.4   0.0    6.8  7  TPR_2            Tetratricopeptide repeat
    1.3e-22   78.0   0.0    0.00097   19.2   0.0    5.9  6  TPR_8            Tetratricopeptide repeat
    2.6e-22   77.7   0.0      7e-06   25.6   0.0    6.5  7  TPR_1            Tetratricopeptide repeat
    1.6e-19   70.2   0.1    3.6e-08   33.8   0.0    4.1  4  TPR_19           Tetratricopeptide repeat
    3.8e-19   67.7  12.6    3.3e-05   24.3   0.5    6.8  7  TPR_14           Tetratricopeptide repeat
    1.4e-16   60.8   5.0    5.4e-07   30.2   1.9    4.3  4  TPR_16           Tetratricopeptide repeat
    5.9e-15   55.2   7.9    0.00015   21.8   0.1    4.2  4  TPR_9            Tetratricopeptide repeat
    1.7e-11   43.6   1.0     0.0052   16.4   0.0    5.4  6  TPR_11           TPR repeat
    4.8e-09   36.4   8.0    0.00082   19.6   0.1    5.7  7  TPR_12           Tetratricopeptide repeat
    8.8e-08   32.3   1.1        2.9    8.7   0.1    6.0  6  TPR_6            Tetratricopeptide repeat
    2.8e-07   30.4   0.0     0.0019   18.4   0.0    4.7  5  TPR_17           Tetratricopeptide repeat
    6.8e-07   28.9   3.5        2.4    8.4   0.0    5.6  5  TPR_7            Tetratricopeptide repeat
    2.9e-05   23.8  12.7        9.4    6.3   0.5    6.6  7  TPR_10           Tetratricopeptide repeat
    0.00011   22.2   0.3        4.8    7.2   0.0    3.5  3  DUF3856          Domain of Unknown Function (DUF3856)
    0.00013   22.3   5.3      0.065   13.9   0.6    4.8  4  TPR_4            Tetratricopeptide repeat
    0.00022   21.4   0.0       0.25   11.6   0.0    3.7  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00044   20.3   0.0        5.3    7.2   0.0    4.3  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
      0.008   16.6   0.0        4.4    7.7   0.0    3.3  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0096   16.0   0.9        2.3    8.3   0.1    3.8  4  MIT              MIT (microtubule interacting and transport) 
  ------ inclusion threshold ------
      0.023   14.3   0.2          4    7.1   0.0    3.0  3  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
      0.034   14.2   0.0        1.2    9.2   0.0    2.6  3  SRP_TPR_like     Putative TPR-like repeat
      0.099   11.6   0.0       0.83    8.6   0.0    2.1  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
        0.1   12.9   0.0       0.85   10.0   0.0    2.5  3  TPR_20           Tetratricopeptide repeat
       0.22   11.0   0.8         50    3.5   0.0    3.2  3  SHNi-TPR         SHNi-TPR
        5.3    7.5   6.2        5.9    7.4   0.1    4.1  4  PPR              PPR repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.4e-06     0.006       5      34 .]       6      35 ..       3      35 .. 0.92
   2 !   20.5   0.1   4.6e-07   0.00033       2      34 .]      37      69 ..      36      69 .. 0.96
   3 !   13.1   0.0   0.00011      0.08       2      34 .]      71     103 ..      70     103 .. 0.89
   4 !    7.6   0.0    0.0066       4.8      10      26 ..     113     129 ..     112     131 .. 0.88
   5 ?   -0.4   0.0       2.4   1.7e+03       1      18 [.     140     157 ..     140     171 .. 0.87
   6 ?    2.1   0.1      0.38   2.7e+02      13      33 ..     186     206 ..     184     207 .. 0.90
   7 !   25.4   0.0   1.3e-08   9.5e-06       3      33 ..     210     240 ..     208     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.4e-06
                             TPR_2  5 ynlGlayyklgdyeeAleafekAleldPnn 34
                                      ++ G  +++ +++eeA+e+f++ +e dP +
  gi|386001958|ref|YP_005920257.1|  6 FAEGIFLMHTDRFEEAVEFFREIVEADPSD 35
                                      678999**********************75 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.6e-07
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                      e++y l+ ay+ +g+++e ++  e+A  l P++
  gi|386001958|ref|YP_005920257.1| 37 EGWYKLAVAYLGAGRLDEGRASAERAFDLRPED 69
                                      89*****************************86 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00011
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       e+l  lG +   ++d e Ale+f++A++  P++
  gi|386001958|ref|YP_005920257.1|  71 EILDLLGGISSLKNDDEGALEYFDRAIAAKPDH 103
                                       77888899999999***************9986 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0066
                             TPR_2  10 ayyklgdyeeAleafek 26 
                                        +++l++ eeA+ea+++
  gi|386001958|ref|YP_005920257.1| 113 TLRNLDRVEEAKEAYRQ 129
                                       5889***********98 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 2.4
                             TPR_2   1 aealynlGlayyklgdye 18 
                                       +e ++ l+ a + +gd++
  gi|386001958|ref|YP_005920257.1| 140 PEEWNDLAGAIFDRGDWQ 157
                                       578999999999999997 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.38
                             TPR_2  13 klgdyeeAleafekAleldPn 33 
                                       kl++y+  +e+ e+ +e  P+
  gi|386001958|ref|YP_005920257.1| 186 KLKRYDAVAELAEELVEAMPD 206
                                       899**************9997 PP

  == domain 7  score: 25.4 bits;  conditional E-value: 1.3e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++ +G a++ l +y+eA+e f++A+ ldP+
  gi|386001958|ref|YP_005920257.1| 210 GWMVRGIALIGLERYDEAVESFDRAILLDPT 240
                                       6999**************************7 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00014     0.097      11      34 .]      12      35 ..       6      35 .. 0.88
   2 !   18.2   0.0   2.8e-06     0.002       2      34 .]      37      69 ..      36      69 .. 0.95
   3 !   10.0   0.0    0.0012      0.83       3      34 .]      72     103 ..      70     103 .. 0.89
   4 !    9.8   0.0    0.0013      0.96      10      29 ..     113     132 ..     107     135 .. 0.89
   5 ?   -1.6   0.0         6   4.3e+03      12      29 ..     185     202 ..     184     206 .. 0.73
   6 !   19.2   0.0   1.3e-06   0.00097       3      32 ..     210     239 ..     208     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                      HHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 11 ylklgdyeeAkeyyekaleldpdn 34
                                      ++ + ++eeA+e++++ +e+dp++
  gi|386001958|ref|YP_005920257.1| 12 LMHTDRFEEAVEFFREIVEADPSD 35
                                      67789*****************85 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.8e-06
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      e +y+l+ +yl  g+++e  ++ e+a +l+p++
  gi|386001958|ref|YP_005920257.1| 37 EGWYKLAVAYLGAGRLDEGRASAERAFDLRPED 69
                                      78*****************************85 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++ +lg i + ++d e A ey+ +a+ ++pd+
  gi|386001958|ref|YP_005920257.1|  72 ILDLLGGISSLKNDDEGALEYFDRAIAAKPDH 103
                                       66688999999*******************97 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0013
                                       HHHHTT-HHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekale 29 
                                       ++++l + eeAke+y++ + 
  gi|386001958|ref|YP_005920257.1| 113 TLRNLDRVEEAKEAYRQGVG 132
                                       7899************9875 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 6
                                       HHTT-HHHHHHHHHHHHH CS
                             TPR_8  12 lklgdyeeAkeyyekale 29 
                                       +kl++y++  e  e+ +e
  gi|386001958|ref|YP_005920257.1| 185 SKLKRYDAVAELAEELVE 202
                                       689999987777776666 PP

  == domain 6  score: 19.2 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                        ++  g +++ l++y+eA+e++ +a+ ldp
  gi|386001958|ref|YP_005920257.1| 210 GWMVRGIALIGLERYDEAVESFDRAILLDP 239
                                       6899999**********************9 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00039      0.28      11      34 .]      12      35 ..       7      35 .. 0.87
   2 !   14.8   0.0   2.7e-05     0.019       2      34 .]      37      69 ..      36      69 .. 0.95
   3 !    9.8   0.0     0.001      0.73      15      34 .]      84     103 ..      76     103 .. 0.85
   4 !    6.9   0.0    0.0082       5.8       3      26 ..     106     129 ..     105     133 .. 0.87
   5 ?    0.0   0.0       1.2   8.7e+02       2      32 ..     141     171 ..     140     173 .. 0.80
   6 ?   -2.0   0.0       5.4   3.9e+03      12      19 ..     185     192 ..     184     204 .. 0.80
   7 !   25.6   0.0   9.8e-09     7e-06       3      33 ..     210     240 ..     208     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                                      HHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 11 yfklgkydeAleyyekALelnPnn 34
                                      +++  +++eA+e++++ +e +P++
  gi|386001958|ref|YP_005920257.1| 12 LMHTDRFEEAVEFFREIVEADPSD 35
                                      677889****************86 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + +y l++ay+  g++de  +  e+A  l+P++
  gi|386001958|ref|YP_005920257.1| 37 EGWYKLAVAYLGAGRLDEGRASAERAFDLRPED 69
                                      78****************************986 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.001
                                       T-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  15 gkydeAleyyekALelnPnn 34 
                                       ++ + Aley+++A+   P++
  gi|386001958|ref|YP_005920257.1|  84 NDDEGALEYFDRAIAAKPDH 103
                                       66688**********99986 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0082
                                       HHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyek 26 
                                        +  + +++++l + +eA e+y++
  gi|386001958|ref|YP_005920257.1| 106 GWISKIMTLRNLDRVEEAKEAYRQ 129
                                       577788999*************98 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       + ++ l+ a f  g+++  +e+ +  L l+P
  gi|386001958|ref|YP_005920257.1| 141 EEWNDLAGAIFDRGDWQATIEFLDFLLDLEP 171
                                       56888888889999**999999988888877 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 5.4
                                       HHTT-HHH CS
                             TPR_1  12 fklgkyde 19 
                                        kl++yd 
  gi|386001958|ref|YP_005920257.1| 185 SKLKRYDA 192
                                       68999996 PP

  == domain 7  score: 25.6 bits;  conditional E-value: 9.8e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                        +  +G a+  l++ydeA+e +++A+ l+P+
  gi|386001958|ref|YP_005920257.1| 210 GWMVRGIALIGLERYDEAVESFDRAILLDPT 240
                                       6999**************************6 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0     5e-11   3.6e-08       5      66 ..      16      77 ..       7      79 .. 0.94
   2 !   11.1   0.0   0.00062      0.45       9      48 ..      88     127 ..      84     131 .. 0.94
   3 ?    2.1   0.0       0.4   2.9e+02       3      58 ..     152     173 ..     138     178 .. 0.62
   4 !   18.0   0.0   4.3e-06    0.0031       5      57 ..     188     240 ..     185     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5e-11
                            TPR_19  5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66
                                       +++eA+++++++ ++dp + e ++ LA a+l +g+lde +a  +++ +  p d+++ +Ll+
  gi|386001958|ref|YP_005920257.1| 16 DRFEEAVEFFREIVEADPSDVEGWYKLAVAYLGAGRLDEGRASAERAFDLRPEDPEILDLLG 77
                                      589****************************************************9999885 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00062
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                        Al+++ +a++++p++++ ++  +  l +l +++eA+++ 
  gi|386001958|ref|YP_005920257.1|  88 GALEYFDRAIAAKPDHLRGWISKIMTLRNLDRVEEAKEAY 127
                                       79***********************************975 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.4
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       ++gd ++ +++l  +l+ +p+                                  +
  gi|386001958|ref|YP_005920257.1| 152 DRGDWQATIEFLDFLLDLEPE----------------------------------E 173
                                       556666666666666666665..................................3 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 4.3e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++y++ ++l e++ ++ p+    ++   +al+ l ++deA +  d++ + dp 
  gi|386001958|ref|YP_005920257.1| 188 KRYDAVAELAEELVEAMPDFVPGWMVRGIALIGLERYDEAVESFDRAILLDPT 240
                                       589999*****************************************999997 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.2e-07   0.00016       8      43 ..       9      44 ..       3      45 .. 0.91
   2 !   24.3   0.5   4.6e-08   3.3e-05       2      42 ..      37      77 ..      36      79 .. 0.94
   3 !   10.9   0.1   0.00098       0.7      16      39 ..      85     108 ..      81     112 .. 0.89
   4 ?    2.2   0.1       0.6   4.3e+02      11      27 ..     114     130 ..     110     139 .. 0.87
   5 ?    3.8   0.0      0.18   1.3e+02       1      37 [.     140     176 ..     140     180 .. 0.90
   6 ?    2.2   0.0      0.58   4.1e+02      13      40 ..     186     213 ..     184     217 .. 0.83
   7 !   14.0   0.0   9.6e-05     0.069       4      38 ..     211     245 ..     208     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-07
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawlllaq 43
                                      + +l++ ++++eA++ +r++++++P+d e w+ la 
  gi|386001958|ref|YP_005920257.1|  9 GIFLMHTDRFEEAVEFFREIVEADPSDVEGWYKLAV 44
                                      789******************************995 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 4.6e-08
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42
                                      e +++la a+l +G++de +a ++ra +l P+d+e++ ll+
  gi|386001958|ref|YP_005920257.1| 37 EGWYKLAVAYLGAGRLDEGRASAERAFDLRPEDPEILDLLG 77
                                      78*********************************998775 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00098
                            TPR_14  16 dpdeAiallrralalaPddaeawl 39 
                                       d ++A+++++ra+a+ Pd+++ w+
  gi|386001958|ref|YP_005920257.1|  85 DDEGALEYFDRAIAAKPDHLRGWI 108
                                       5678****************9996 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.6
                            TPR_14  11 llalGdpdeAiallrra 27 
                                       l++l++ +eA +++r+ 
  gi|386001958|ref|YP_005920257.1| 114 LRNLDRVEEAKEAYRQG 130
                                       78999*********997 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.18
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaea 37 
                                       pe + +la a + +Gd+++ i+ l+ +l+l P+++ +
  gi|386001958|ref|YP_005920257.1| 140 PEEWNDLAGAIFDRGDWQATIEFLDFLLDLEPEEPSY 176
                                       68899************************99998865 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.58
                            TPR_14  13 alGdpdeAiallrralalaPddaeawll 40 
                                        l ++d+ ++l+++++++ Pd+   w+ 
  gi|386001958|ref|YP_005920257.1| 186 KLKRYDAVAELAEELVEAMPDFVPGWMV 213
                                       578999999********99999888876 PP

  == domain 7  score: 14.0 bits;  conditional E-value: 9.6e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       ++ ++ al  l+++deA++ ++ra+ l+P+  ea+
  gi|386001958|ref|YP_005920257.1| 211 WMVRGIALIGLERYDEAVESFDRAILLDPTGNEAR 245
                                       8899************************9755555 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0031       2.2      38      67 ..       6      35 ..       5      36 .. 0.88
   2 !   30.2   1.9   7.5e-10   5.4e-07       1      66 [.      40     102 ..      40     103 .. 0.97
   3 ?    5.1   0.0     0.049        35       7      57 ..     114     163 ..     109     174 .. 0.82
   4 !   14.3   0.1   6.7e-05     0.048      10      61 ..     187     235 ..     184     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                            TPR_16 38 lllgdaalrqgrlaeAaalyraalraapda 67
                                      ++ g  + +  r++eA++++r+ ++a+p++
  gi|386001958|ref|YP_005920257.1|  6 FAEGIFLMHTDRFEEAVEFFREIVEADPSD 35
                                      56677888999*****************87 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 7.5e-10
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++la a+l ag+ d+ +a +e+a +++   P+++e l llg +   +++ ++A++++++a++a pd
  gi|386001958|ref|YP_005920257.1|  40 YKLAVAYLGAGRLDEGRASAERAFDLR---PEDPEILDLLGGISSLKNDDEGALEYFDRAIAAKPD 102
                                       799************************...99999*****************************98 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.049
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaaly 57 
                                       ++++ + ++A +a+++ +  +  + +++e ++ l+ a + +g++++ ++++
  gi|386001958|ref|YP_005920257.1| 114 LRNLDRVEEAKEAYRQGVGVA-LTLRDPEEWNDLAGAIFDRGDWQATIEFL 163
                                       66777999********99999.77889999************999866665 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 6.7e-05
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +++yd+ a+++e+++++    Pd +  ++ +g a+  + r++eA++ +++a+
  gi|386001958|ref|YP_005920257.1| 187 LKRYDAVAELAEELVEAM---PDFVPGWMVRGIALIGLERYDEAVESFDRAI 235
                                       678888888999999999...9999999999999999999999998888876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   4.3e-06    0.0031       6      65 ..      13      72 ..       7      79 .. 0.93
   2 !    7.3   0.1    0.0073       5.3       9      50 ..      84     125 ..      76     129 .. 0.81
   3 !   10.8   0.1   0.00056       0.4      27      63 ..     138     174 ..     133     177 .. 0.91
   4 !   21.8   0.1   2.1e-07   0.00015       9      71 ..     188     250 ..     184     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.3e-06
                             TPR_9  6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      +  +++e+a +    ++  +P d+e ++  ++++   G+l +++a  e++ +l p++p++
  gi|386001958|ref|YP_005920257.1| 13 MHTDRFEEAVEFFREIVEADPSDVEGWYKLAVAYLGAGRLDEGRASAERAFDLRPEDPEI 72
                                      67899999***********************************************99986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                       +d e al++ +r ++ +Pd+ + +    + l  l+++++A +
  gi|386001958|ref|YP_005920257.1|  84 NDDEGALEYFDRAIAAKPDHLRGWISKIMTLRNLDRVEEAKE 125
                                       78899*****************99877777777777777765 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00056
                             TPR_9  27 ddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +dpee+ d + + + +G+++a ++ L+  l+l+p+ p
  gi|386001958|ref|YP_005920257.1| 138 RDPEEWNDLAGAIFDRGDWQATIEFLDFLLDLEPEEP 174
                                       79********************************977 PP

  == domain 4  score: 21.8 bits;  conditional E-value: 2.1e-07
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                       +++++  + +e l+   Pd +  ++ RG++l  l+++ +A++ +++++ l+p   +a+ ++++
  gi|386001958|ref|YP_005920257.1| 188 KRYDAVAELAEELVEAMPDFVPGWMVRGIALIGLERYDEAVESFDRAILLDPTGNEAREMKKR 250
                                       57888888999999999***************************************9999876 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.2e-06    0.0052       9      40 ..      17      48 ..      15      50 .. 0.93
   2 ?    4.0   0.0     0.056        40      18      35 ..      60      77 ..      49      79 .. 0.80
   3 ?    3.6   0.0     0.074        53       7      26 ..      83     102 ..      82     105 .. 0.92
   4 ?   -0.4   0.0       1.4   9.8e+02       9      19 ..     119     129 ..     114     132 .. 0.83
   5 ?   -1.8   0.0       3.7   2.7e+03       5      28 ..     151     174 ..     149     179 .. 0.73
   6 !   12.6   0.0   0.00011      0.08       7      26 ..     221     240 ..     215     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.2e-06
                            TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                      ++eeA+e +++ ++ dP+++e +y+L++ay+ 
  gi|386001958|ref|YP_005920257.1| 17 RFEEAVEFFREIVEADPSDVEGWYKLAVAYLG 48
                                      68****************************86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.056
                            TPR_11 18 kkAlkldPdnaeayynLG 35
                                      ++A +l+P+++e++  LG
  gi|386001958|ref|YP_005920257.1| 60 ERAFDLRPEDPEILDLLG 77
                                      7999*********87776 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.074
                            TPR_11   7 qGkyeeAieaYkkAlkldPd 26 
                                       +++ e+A+e + +A++ +Pd
  gi|386001958|ref|YP_005920257.1|  83 KNDDEGALEYFDRAIAAKPD 102
                                       6889************9998 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.4
                            TPR_11   9 kyeeAieaYkk 19 
                                       + eeA eaY++
  gi|386001958|ref|YP_005920257.1| 119 RVEEAKEAYRQ 129
                                       689******99 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 3.7
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdna 28 
                                       +++G++ + ie +   l+l P+ +
  gi|386001958|ref|YP_005920257.1| 151 FDRGDWQATIEFLDFLLDLEPEEP 174
                                       789999888877776777777766 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 0.00011
                            TPR_11   7 qGkyeeAieaYkkAlkldPd 26 
                                       + +y+eA+e++ +A+ ldP+
  gi|386001958|ref|YP_005920257.1| 221 LERYDEAVESFDRAILLDPT 240
                                       579****************7 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.019        14      11      32 ..      10      31 ..       8      38 .. 0.75
   2 !   19.6   0.1   1.1e-06   0.00082       6      75 ..      39     100 ..      35     102 .. 0.89
   3 ?    0.0   0.0       1.5   1.1e+03      12      28 ..     113     129 ..     107     142 .. 0.71
   4 ?    2.2   0.0      0.31   2.2e+02       6      32 ..     143     169 ..     141     173 .. 0.88
   5 ?   -2.1   0.0         7     5e+03      57      73 ..     186     202 ..     184     205 .. 0.60
   6 !    7.4   0.0    0.0075       5.4      10      30 ..     215     235 ..     211     243 .. 0.75
   7 ?   -2.4   0.0       8.4     6e+03      63      75 ..     243     255 ..     241     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                            TPR_12 11 avlrrlgrydeAlellekalei 32
                                       +l++  r++eA e++++ +e+
  gi|386001958|ref|YP_005920257.1| 10 IFLMHTDRFEEAVEFFREIVEA 31
                                      5677888888888888877765 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.1e-06
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++la++++ +gr+de ++  e+a +++     p+ p+ +  l +++ l    ++ e Ale++ +a+a++
  gi|386001958|ref|YP_005920257.1|  39 WYKLAVAYLGAGRLDEGRASAERAFDLR-----PEDPEILDLLGGISSLK---NDDEGALEYFDRAIAAK 100
                                       569*************************.....99999877777777775...9************9986 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.5
                            TPR_12  12 vlrrlgrydeAlellek 28 
                                       +lr l r +eA e +++
  gi|386001958|ref|YP_005920257.1| 113 TLRNLDRVEEAKEAYRQ 129
                                       56666677777666655 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.31
                            TPR_12   6 lnnlaavlrrlgrydeAlellekalei 32 
                                       +n la + + +g+++  +e+l+  l++
  gi|386001958|ref|YP_005920257.1| 143 WNDLAGAIFDRGDWQATIEFLDFLLDL 169
                                       5579***************99988775 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 7
                            TPR_12  57 algryeeAlelleeala 73 
                                       +l+ry++  el ee ++
  gi|386001958|ref|YP_005920257.1| 186 KLKRYDAVAELAEELVE 202
                                       55666666666666555 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0075
                            TPR_12  10 aavlrrlgrydeAlellekal 30 
                                       + +l  l+rydeA e +++a+
  gi|386001958|ref|YP_005920257.1| 215 GIALIGLERYDEAVESFDRAI 235
                                       556666788888888888876 PP

  == domain 7  score: -2.4 bits;  conditional E-value: 8.4
                            TPR_12  63 eAlelleealaia 75 
                                       eA+e+ +++l+ +
  gi|386001958|ref|YP_005920257.1| 243 EAREMKKRTLEYL 255
                                       7777777777765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.095        68      14      31 ..      16      33 ..       5      35 .. 0.83
   2 !    8.7   0.1     0.004       2.9       2      31 ..      38      67 ..      37      69 .. 0.87
   3 ?    3.9   0.0      0.14     1e+02      11      32 ..      82     102 ..      74     103 .. 0.77
   4 ?    2.8   0.1       0.3   2.2e+02      10      25 ..     114     129 ..     111     129 .. 0.84
   5 ?   -0.6   0.0       3.9   2.8e+03      11      31 ..     152     171 ..     146     172 .. 0.75
   6 ?    4.6   0.0     0.086        62       8      29 ..     216     237 ..     213     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.095
                                      HHHHHHHHHHHHHHHH-T CS
                             TPR_6 14 gdtdkAlealerlikeYP 31
                                      ++ ++A+e ++++++  P
  gi|386001958|ref|YP_005920257.1| 16 DRFEEAVEFFREIVEADP 33
                                      6899**********9888 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYP 31
                                        ykla +y+ +g+ d+ ++  er  +  P
  gi|386001958|ref|YP_005920257.1| 38 GWYKLAVAYLGAGRLDEGRASAERAFDLRP 67
                                      57*********99*******9999877766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6  11 rklgdtdkAlealerlikeYPd 32 
                                       +k  d + Ale+++r i   Pd
  gi|386001958|ref|YP_005920257.1|  82 LKN-DDEGALEYFDRAIAAKPD 102
                                       445.999********9976555 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealer 25 
                                       +r+l++ ++A+ea+++
  gi|386001958|ref|YP_005920257.1| 114 LRNLDRVEEAKEAYRQ 129
                                       6778899*******97 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 3.9
                                       HHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  11 rklgdtdkAlealerlikeYP 31 
                                        + gd+++ +e l+ l++  P
  gi|386001958|ref|YP_005920257.1| 152 DR-GDWQATIEFLDFLLDLEP 171
                                       44.5******99998888766 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.086
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerlike 29 
                                        +++ l ++d+A+e ++r i  
  gi|386001958|ref|YP_005920257.1| 216 IALIGLERYDEAVESFDRAILL 237
                                       56666569**********9865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-06    0.0019       2      31 ..      25      54 ..      24      57 .. 0.89
   2 ?    0.5   0.0       1.4   9.9e+02       3      33 ..      60      90 ..      59      91 .. 0.84
   3 ?    3.1   0.0      0.21   1.5e+02       2      34 .]      93     125 ..      92     125 .. 0.91
   4 ?    1.0   0.0      0.98     7e+02       3      34 .]     198     229 ..     196     229 .. 0.84
   5 ?   -1.5   0.0         6   4.3e+03       2      11 ..     231     240 ..     231     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-06
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmt 31
                                      +++ +e dP++++ ++ LA+++l +G+l++
  gi|386001958|ref|YP_005920257.1| 25 FREIVEADPSDVEGWYKLAVAYLGAGRLDE 54
                                      77889*********************9987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                            TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtAr 33
                                      ++a +l P +++ + +L+ + + ++d + A+
  gi|386001958|ref|YP_005920257.1| 60 ERAFDLRPEDPEILDLLGGISSLKNDDEGAL 90
                                      6788899*******99999999888888776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a++  P++   +  +  +l+++ + ++A++
  gi|386001958|ref|YP_005920257.1|  93 FDRAIAAKPDHLRGWISKIMTLRNLDRVEEAKE 125
                                       89*********9999999999999999999975 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.98
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++ +e  P+ ++ +  ++ +l  + ++++A++
  gi|386001958|ref|YP_005920257.1| 198 EELVEAMPDFVPGWMVRGIALIGLERYDEAVE 229
                                       666677799999**********999**99975 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 6
                            TPR_17   2 ylkaleldPn 11 
                                       + +a+ ldP+
  gi|386001958|ref|YP_005920257.1| 231 FDRAILLDPT 240
                                       6799*99997 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.028        20      13      35 ..      16      36 ..       9      37 .. 0.82
   2 ?   -1.0   0.0       3.4   2.4e+03       5      17 ..      42      54 ..      39      71 .. 0.61
   3 !    8.4   0.0    0.0033       2.4       2      33 ..      73     102 ..      72     105 .. 0.84
   4 ?    2.0   0.3      0.36   2.6e+02       9      29 ..     114     138 ..     112     174 .. 0.77
   5 !    8.3   0.0    0.0035       2.5      12      34 ..     221     241 ..     215     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                             TPR_7 13 GdyeeAielyeqsLaltkdpeda 35
                                       ++eeA+e++++   ++ dp+d+
  gi|386001958|ref|YP_005920257.1| 16 DRFEEAVEFFRE--IVEADPSDV 36
                                      58*********9..888888776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                             TPR_7  5 LarlysrlGdyee 17
                                      La++y   G+ +e
  gi|386001958|ref|YP_005920257.1| 42 LAVAYLGAGRLDE 54
                                      7777776666655 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0033
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       L+ L+ + s  +d e A+e++ +  a++  p+
  gi|386001958|ref|YP_005920257.1|  73 LDLLGGISSLKNDDEGALEYFDR--AIAAKPD 102
                                       67899999999************..7776665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.36
                             TPR_7   9 ysrlGdyeeAielyeq....sLalt 29 
                                        ++l + eeA e y+q    +L l+
  gi|386001958|ref|YP_005920257.1| 114 LRNLDRVEEAKEAYRQgvgvALTLR 138
                                       5777888888888888555544444 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0035
                             TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                       l +y+eA+e + +  a+  dp++
  gi|386001958|ref|YP_005920257.1| 221 LERYDEAVESFDR--AILLDPTG 241
                                       679**********..99999987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.015        11       9      30 ..       9      30 ..       9      31 .. 0.89
   2 ?    6.3   0.5     0.013       9.4       8      31 ..      42      65 ..      40      66 .. 0.92
   3 ?    4.6   0.0     0.043        31       8      31 ..      76      99 ..      71     100 .. 0.83
   4 ?    3.0   0.1      0.14     1e+02      10      27 ..     112     129 ..     112     134 .. 0.88
   5 ?    1.1   0.0      0.56     4e+02       6      20 ..     144     158 ..     144     164 .. 0.87
   6 ?   -2.2   0.1       5.8   4.2e+03      13      30 ..     185     202 ..     184     204 .. 0.64
   7 ?    5.3   0.1     0.026        19       9      29 ..     215     235 ..     214     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                            TPR_10  9 analrqrgrydeAealleeala 30
                                      ++ l ++ r++eA+++++e ++
  gi|386001958|ref|YP_005920257.1|  9 GIFLMHTDRFEEAVEFFREIVE 30
                                      67889999***********987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                            TPR_10  8 LanalrqrgrydeAealleealai 31
                                      La+a+   gr+de +a +e+a ++
  gi|386001958|ref|YP_005920257.1| 42 LAVAYLGAGRLDEGRASAERAFDL 65
                                      9*******************9876 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.043
                            TPR_10  8 LanalrqrgrydeAealleealai 31
                                      L+ + +  ++ ++A++++++a+a+
  gi|386001958|ref|YP_005920257.1| 76 LGGISSLKNDDEGALEYFDRAIAA 99
                                      77777778999***********85 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                            TPR_10  10 nalrqrgrydeAeallee 27 
                                       ++lr++ r +eA + +++
  gi|386001958|ref|YP_005920257.1| 112 MTLRNLDRVEEAKEAYRQ 129
                                       689**********99998 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.56
                            TPR_10   6 nNLanalrqrgryde 20 
                                       n+La a ++rg++++
  gi|386001958|ref|YP_005920257.1| 144 NDLAGAIFDRGDWQA 158
                                       89***********97 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 5.8
                            TPR_10  13 rqrgrydeAealleeala 30 
                                       ++++ryd+  +l+ee ++
  gi|386001958|ref|YP_005920257.1| 185 SKLKRYDAVAELAEELVE 202
                                       566777776677777655 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.026
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       ++al  + rydeA++ +++a+
  gi|386001958|ref|YP_005920257.1| 215 GIALIGLERYDEAVESFDRAI 235
                                       78899999********99998 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.021        15      16      82 ..       2      63 ..       1      67 [. 0.81
   2 !    7.2   0.0    0.0067       4.8      79     125 ..      87     129 ..      74     148 .. 0.84
   3 ?    5.6   0.0     0.021        15      64      82 ..     217     235 ..     210     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
                                      HHHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 16 aekqleegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkal 82
                                      +e ++ eg +   ++ +++a+e+ r i + +  d eG+       l+ a+++ gr de+  sa++a+
  gi|386001958|ref|YP_005920257.1|  2 GEDRFAEGIFLMHTDRFEEAVEFFREIVEADPSDVEGWY-----KLAVAYLGAGRLDEGRASAERAF 63
                                      567777888888888899999999999999999999975.....56778888999999999999885 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0067
                                       HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrm 125
                                       + al+yf+r    + d  + Wi+ ++    +l +l r +ea +a+r+
  gi|386001958|ref|YP_005920257.1|  87 EGALEYFDRAIAAKPDHLRGWISKIM----TLRNLDRVEEAKEAYRQ 129
                                       569******************98765....78999999999999886 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.021
                                       HHHHTT-HHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkal 82 
                                       al++l rydea+es d+a+
  gi|386001958|ref|YP_005920257.1| 217 ALIGLERYDEAVESFDRAI 235
                                       7889999999999998886 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.18   1.3e+02       6      26 .]       7      27 ..       5      27 .. 0.83
   2 !   13.9   0.6     9e-05     0.065       5      26 .]      40      61 ..      36      61 .. 0.90
   3 ?    0.1   0.0       2.6   1.9e+03      11      26 .]     114     129 ..     107     129 .. 0.84
   4 ?    2.0   0.0      0.62   4.4e+02       6      25 ..     213     232 ..     210     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                             TPR_4  6 aLArallalGdldeAraller 26
                                      a +  l ++ +++eA + +++
  gi|386001958|ref|YP_005920257.1|  7 AEGIFLMHTDRFEEAVEFFRE 27
                                      567788999*******99986 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9e-05
                             TPR_4  5 laLArallalGdldeAraller 26
                                      + LA a+l +G+lde ra +er
  gi|386001958|ref|YP_005920257.1| 40 YKLAVAYLGAGRLDEGRASAER 61
                                      569***************9997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.6
                             TPR_4  11 llalGdldeAraller 26 
                                       l  l + +eA ++ ++
  gi|386001958|ref|YP_005920257.1| 114 LRNLDRVEEAKEAYRQ 129
                                       677899****999887 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.62
                             TPR_4   6 aLArallalGdldeAralle 25 
                                       +++ al  l ++deA + ++
  gi|386001958|ref|YP_005920257.1| 213 VRGIALIGLERYDEAVESFD 232
                                       6899999999*****98665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00035      0.25      24      80 ..       3      60 ..       1      62 [. 0.90
   2 ?    0.1   0.0       1.3   9.5e+02      13      77 ..      60     125 ..      57     129 .. 0.69
   3 ?    1.6   0.0      0.47   3.3e+02      29      73 ..     146     191 ..     135     200 .. 0.77
   4 ?    3.3   0.0      0.13        94      60      81 ..     212     233 ..     184     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                                      HHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3 24 edayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                      ed+++ +  l ++ ++++A e++r+  + ++++ + +y +A ++l  ++++e++a  e
  gi|386001958|ref|YP_005920257.1|  3 EDRFAEGIFLMHTDRFEEAVEFFREIvEADPSDVEGWYKLAVAYLGAGRLDEGRASAE 60
                                      56677777889999***************************************98766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                                       HHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  13 erllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       er++   +e+pe + ll+    l ++ + A+e++++a   ++ +l+ ++ +  +l  L+++eeA  
  gi|386001958|ref|YP_005920257.1|  60 ERAFDLRPEDPEILDLLGGISSLKNDDEGALEYFDRAiAAKPDHLRGWISKIMTLRNLDRVEEAKE 125
                                       666666667777666666666667777778888888878888888777777777777777777755 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.47
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HH CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkye 73 
                                       lA + + +g+++  +e+l+ + +l+++ + + + +   l kLk+y+
  gi|386001958|ref|YP_005920257.1| 146 LAGAIFDRGDWQATIEFLDFLlDLEPEEPSYKFNKLGPLSKLKRYD 191
                                       7889999*********999888888777777666666666666666 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  60 ylfAqcllkLkkyeeAiaaLek 81 
                                       ++ + +l+ L++y+eA+  +++
  gi|386001958|ref|YP_005920257.1| 212 MVRGIALIGLERYDEAVESFDR 233
                                       566668899*******998875 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.1   3.7e+03      16      33 ..      17      34 ..      15      35 .. 0.87
   2 !    7.2   0.0    0.0073       5.3       4      41 ..      39      76 ..      36      81 .. 0.89
   3 ?    0.0   0.0       1.3   9.1e+02      22      33 ..     161     172 ..     149     176 .. 0.85
   4 ?   -1.6   0.0         4   2.9e+03      13      33 ..     186     206 ..     184     207 .. 0.80
   5 ?    6.2   0.0     0.015        11       9      42 ..     216     249 ..     214     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.1
                                      -HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 16 eYseArryvdalLeiEPe 33
                                      +++eA ++ + + e +P+
  gi|386001958|ref|YP_005920257.1| 17 RFEEAVEFFREIVEADPS 34
                                      6899****9999999996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0073
                                      HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C  4 lYylAlGhyklgeYseArryvdalLeiEPenrQaqsLk 41
                                       Y lA++++  g+ +e r  +++   + Pe    ++L 
  gi|386001958|ref|YP_005920257.1| 39 WYKLAVAYLGAGRLDEGRASAERAFDLRPEDPEILDLL 76
                                      699**************************999888885 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHTTS CS
                        Fis1_TPR_C  22 ryvdalLeiEPe 33 
                                       +++d lL +EPe
  gi|386001958|ref|YP_005920257.1| 161 EFLDFLLDLEPE 172
                                       7999*******8 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 4
                                       HHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                                       kl++Y+   ++++ l e  P+
  gi|386001958|ref|YP_005920257.1| 186 KLKRYDAVAELAEELVEAMPD 206
                                       899999988888888887776 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.015
                                       HHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQaqsLke 42 
                                       ++ + l +Y+eA +  d+ + ++P  + a++ k+
  gi|386001958|ref|YP_005920257.1| 216 IALIGLERYDEAVESFDRAILLDPTGNEAREMKK 249
                                       788899*******************999999886 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.1   8.1e+02      81     118 ..      14      51 ..       7      60 .. 0.82
   2 !    7.7   0.0    0.0062       4.4      65     111 ..     130     182 ..     102     260 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                         + ++ a+e+   +v+adp++ e    +a a+   g+
  gi|386001958|ref|YP_005920257.1|  14 HTDRFEEAVEFFREIVEADPSDVEGWYKLAVAYLGAGR 51 
                                       567788999************99988888888876666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0062
                                       HTT......SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHH CS
                   Alkyl_sulf_dimr  65 lmG......gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkad 111
                                        +G      + e+  + a + +++gd ++ +e+l++l+  +pe+ + k  k  
  gi|386001958|ref|YP_005920257.1| 130 GVGvaltlrDPEEWNDLAGAIFDRGDWQATIEFLDFLLDLEPEEPSYKFNKLG 182
                                       45555556666666667777777777777777777777776665433333222 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.7   1.2e+03      28      49 ..      19      39 ..      16      54 .. 0.60
   2 ?    0.7   0.0      0.78   5.6e+02      30      53 ..      89     111 ..      87     125 .. 0.51
   3 ?    2.3   0.0      0.25   1.8e+02      20      33 ..     120     133 ..     112     145 .. 0.81
   4 !    8.3   0.1    0.0032       2.3      24      61 ..     221     259 ..     220     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                               MIT 28 kealelLlqalkekneerrell 49
                                      +ea+e + +++   ++++ e +
  gi|386001958|ref|YP_005920257.1| 19 EEAVEFFREIVE-ADPSDVEGW 39
                                      567777776664.444554444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.78
                               MIT  30 alelLlqalkekneerrellreki 53 
                                       ale++  a++ k   +   + +ki
  gi|386001958|ref|YP_005920257.1|  89 ALEYFDRAIAAKP-DHLRGWISKI 111
                                       8899999998433.3333333333 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.25
                               MIT  20 yeeAlelYkealel 33 
                                        eeA e+Y++++++
  gi|386001958|ref|YP_005920257.1| 120 VEEAKEAYRQGVGV 133
                                       699*******9987 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0032
                               MIT  24 lelYkealelLlqalk.ekneerrellrekieeYleRae 61 
                                       le Y ea+e +  a+    + +    +++++ eYl+ a+
  gi|386001958|ref|YP_005920257.1| 221 LERYDEAVESFDRAILlDPTGNEAREMKKRTLEYLKEAK 259
                                       689************955555888889********9885 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0056         4      48      77 ..       5      34 ..       1      85 [. 0.85
   2 ?    0.4   0.0      0.64   4.6e+02      67     120 ..     113     166 ..     103     171 .. 0.71
   3 ?    3.1   0.0     0.094        67      41      93 ..     204     256 ..     184     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0056
                        HrpB1_HrpK 48 dllegvlliergrweeAlrlLreveaeasg 77
                                      ++ eg+ l++  r+eeA+  +re+ ++ ++
  gi|386001958|ref|YP_005920257.1|  5 RFAEGIFLMHTDRFEEAVEFFREIVEADPS 34
                                      6789*******************9977665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.64
                        HrpB1_HrpK  67 lLreveaeasgtpyakaLlAlcLaalrDeeWrayAeevlesdadpdalaLvkaL 120
                                       +Lr+++  ++  ++    + ++L  ++ eeW  +A  +  + + +++++ ++ L
  gi|386001958|ref|YP_005920257.1| 113 TLRNLDRVEEAKEAYRQGVGVALTLRDPEEWNDLAGAIFDRGDWQATIEFLDFL 166
                                       666666555555555555678888888899999999999887777777776665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.094
                        HrpB1_HrpK  41 rPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalr 93 
                                        P ++   ++ g+ li  +r++eA+  +       + ++ a ++    L++l+
  gi|386001958|ref|YP_005920257.1| 204 MPDFVPGWMVRGIALIGLERYDEAVESFDRAILLDPTGNEAREMKKRTLEYLK 256
                                       577777789999*************9999888888888888888777777665 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.27   1.9e+02      22      39 ..      10      27 ..       4      48 .. 0.80
   2 ?   -2.7   0.0       8.1   5.8e+03      20      36 ..     110     126 ..      92     133 .. 0.71
   3 ?    9.2   0.0    0.0016       1.2       3      38 ..     188     232 ..     186     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                      SRP_TPR_like 22 valiklekyeeaLkllkk 39
                                      + l++ +++eea+++ ++
  gi|386001958|ref|YP_005920257.1| 10 IFLMHTDRFEEAVEFFRE 27
                                      67999*******999876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.1
                      SRP_TPR_like  20 kvvaliklekyeeaLkl 36 
                                       k+++l +l++ eea ++
  gi|386001958|ref|YP_005920257.1| 110 KIMTLRNLDRVEEAKEA 126
                                       67777777777777554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                      SRP_TPR_like   3 eeyekilrlegkelkkf.........kvvaliklekyeeaLkllk 38 
                                       ++y+ +++l+++ ++           + +ali le+y+ea++  +
  gi|386001958|ref|YP_005920257.1| 188 KRYDAVAELAEELVEAMpdfvpgwmvRGIALIGLERYDEAVESFD 232
                                       678888888888888878889999999*************98765 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0012      0.83     243     282 ..      11      50 ..       6      57 .. 0.89
   2 ?    0.3   0.0      0.37   2.7e+02     233     285 ..      69     121 ..      60     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                                       HHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT CS
                             ChAPs 243 fllskkkeelAlevakravksaPsefktWalLvkvYikle 282
                                       fl++ ++ e A+e  ++ v++ Ps+ + W++L+  Y+  +
  gi|386001958|ref|YP_005920257.1|  11 FLMHTDRFEEAVEFFREIVEADPSDVEGWYKLAVAYLGAG 50 
                                       99999999***************************98766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HH CS
                             ChAPs 233 daelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledie 285
                                       d e+L+l       k+++e Ale  +ra+ + P   + W+    +  +l+ +e
  gi|386001958|ref|YP_005920257.1|  69 DPEILDLLGGISSLKNDDEGALEYFDRAIAAKPDHLRGWISKIMTLRNLDRVE 121
                                       55666666666667889999*******************97666666666555 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012      0.85       9      40 ..      23      54 ..      15      65 .. 0.88
   2 ?   -1.0   0.0       3.3   2.3e+03      19      45 ..      67      93 ..      50     108 .. 0.58
   3 ?   -1.6   0.0       5.1   3.6e+03      34      67 ..     220     254 ..     192     258 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                            TPR_20  9 aeleaalaanpddldarldlAlallaagryee 40
                                      + +++ ++a+p+d++  ++lA a+l agr +e
  gi|386001958|ref|YP_005920257.1| 23 EFFREIVEADPSDVEGWYKLAVAYLGAGRLDE 54
                                      5578889*********************9876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
                            TPR_20 19 pddldarldlAlallaagryeeAleqL 45
                                      p+d ++   l      +++ e Ale +
  gi|386001958|ref|YP_005920257.1| 67 PEDPEILDLLGGISSLKNDDEGALEYF 93
                                      555555555555555555555555533 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.1
                            TPR_20  34 aagryeeAleqLleilkrdrkw.eddaarkqllki 67 
                                         +ry+eA+e + + +  d +  e  +++k+ l++
  gi|386001958|ref|YP_005920257.1| 220 GLERYDEAVESFDRAILLDPTGnEAREMKKRTLEY 254
                                       55677777777655444443331344556665555 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.53   3.8e+02      14      22 ..      15      23 ..      13      27 .. 0.79
   2 ?    3.0   0.0     0.096        69       2      11 ..      71      80 ..      70      84 .. 0.89
   3 ?    3.5   0.0     0.069        50      15      28 ..     222     235 ..     221     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.53
                          SHNi-TPR 14 nenFpqAve 22
                                      +++F++Ave
  gi|386001958|ref|YP_005920257.1| 15 TDRFEEAVE 23
                                      689****98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.096
                          SHNi-TPR  2 dvydlLGEis 11
                                      +++dlLG is
  gi|386001958|ref|YP_005920257.1| 71 EILDLLGGIS 80
                                      89*******9 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.069
                          SHNi-TPR  15 enFpqAveDlrkaL 28 
                                       e++++Ave +++a+
  gi|386001958|ref|YP_005920257.1| 222 ERYDEAVESFDRAI 235
                                       9*******999996 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0082       5.9      13      28 ..      15      30 ..      12      32 .. 0.85
   2 ?   -1.9   0.0       7.4   5.3e+03      17      25 ..      87      95 ..      83      97 .. 0.82
   3 ?   -1.3   0.0       4.8   3.4e+03      14      24 ..     118     128 ..     114     129 .. 0.80
   4 ?   -1.1   0.0       4.2     3e+03      15      25 ..     223     233 ..     219     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                               PPR 13 nGkleeAlelfkeMke 28
                                        ++eeA+e+f+e++e
  gi|386001958|ref|YP_005920257.1| 15 TDRFEEAVEFFREIVE 30
                                      5799*********987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.4
                               PPR 17 eeAlelfke 25
                                      e Ale+f++
  gi|386001958|ref|YP_005920257.1| 87 EGALEYFDR 95
                                      789****97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.8
                               PPR  14 GkleeAlelfk 24 
                                        ++eeA+e ++
  gi|386001958|ref|YP_005920257.1| 118 DRVEEAKEAYR 128
                                       6899**99876 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.2
                               PPR  15 kleeAlelfke 25 
                                       +++eA+e f++
  gi|386001958|ref|YP_005920257.1| 223 RYDEAVESFDR 233
                                       79****98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1519.71
//
Query:       gi|386001959|ref|YP_005920258.1|  [L=663]
Description: UvrABC system protein B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-28   98.6   0.9    5.8e-28   96.9   0.2    2.2  2  UvrB_inter  UvrB interaction domain
    6.5e-20   70.7   0.2      2e-19   69.1   0.2    1.9  1  UvrB        Ultra-violet resistance protein B
    3.6e-16   59.5   0.1    8.6e-16   58.3   0.1    1.6  1  Helicase_C  Helicase conserved C-terminal domain
    4.3e-12   46.4   0.0    4.5e-11   43.0   0.0    2.3  2  ResIII      Type III restriction enzyme, res subunit
    2.2e-09   36.8   2.4    7.5e-09   35.1   2.4    2.0  1  UVR         UvrB/uvrC motif
    0.00015   21.6   0.0     0.0018   18.0   0.0    2.5  2  AAA_30      AAA domain
    0.00016   21.5   0.0     0.0093   15.8   0.0    3.0  3  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.036   14.4   1.5          5    7.5   0.2    2.7  2  AAA_19      AAA domain
      0.067   13.2   0.0       0.21   11.6   0.0    1.9  1  UB2H        Bifunctional transglycosylase second domain
      0.071   13.2   0.2       0.22   11.6   0.2    1.8  1  DUF87       Helicase HerA, central domain
      0.079   13.3   0.0       0.39   11.1   0.0    2.2  2  AAA_16      AAA ATPase domain
       0.21   11.2   1.2       0.33   10.5   0.3    1.8  2  SRP54       SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.2   3.9e-31   5.8e-28       1      91 []     170     259 ..     170     259 .. 0.99
   2 ?   -1.4   0.0       1.8   2.7e+03      52      75 ..     474     497 ..     467     505 .. 0.70

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 3.9e-31
                        UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgksl 77 
                                       +elkvg++++r+e+l++Lv  qYern++el +G Fr++G+t++++p +  ++++rie+fgde+e+i+eid +tg   
  gi|386001959|ref|YP_005920258.1| 170 FELKVGDRVSRREILERLVASQYERNEMELAPGRFRAKGETIDLVPGY-FNNILRIELFGDEVERISEIDRQTGVRR 245
                                       58**********************************************.6*************************** PP

                        UvrB_inter  78 ekleeitifPakhf 91 
                                       e++  ++++Pa+h+
  gi|386001959|ref|YP_005920258.1| 246 EDMRYFYVYPARHY 259
                                       *************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                        UvrB_inter  52 vairieffgdeiesireidpltgk 75 
                                       + ir      ei++i++ + + + 
  gi|386001959|ref|YP_005920258.1| 474 NGIRARYLHSEIQTIERTEIIREL 497
                                       567777788888888877766655 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.2   1.3e-22     2e-19       1      43 []     557     599 ..     557     599 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.3e-22
                                       EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXXX CS
                              UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKkir 43 
                                       lYAD++TdS++ A+++Te+RR++Q++YN+ehgI+P+ti+K+ir
  gi|386001959|ref|YP_005920258.1| 557 LYADRMTDSVRGAVAKTEERRALQMRYNQEHGIVPQTIIKPIR 599
                                       8****************************************96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   5.8e-19   8.6e-16      14     109 ..     449     549 ..     439     551 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 5.8e-19
                                       TTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi 89 
                                       + g+++l+ + t++ +e+ +++l  k+gi++ +lh+e+++ er ei+++ + g++dvL+  + + +G+dip+v ++ 
  gi|386001959|ref|YP_005920258.1| 449 AAGDRALVTTLTKKLAEElTDYL-AKNGIRARYLHSEIQTIERTEIIRELRLGKFDVLVGINLLREGLDIPEVGFIG 524
                                       6789999*******888767777.7889************************************************* PP

                                       ESSSS.....SSHHHHHHHHTTSSS CS
                        Helicase_C  90 nfdlp.....rnvtsyiqriGRtgR 109
                                       ++d++     r+ +s+iq iGR+ R
  gi|386001959|ref|YP_005920258.1| 525 ILDADkegflRDERSLIQTIGRASR 549
                                       *****77777778**********99 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0     3e-14   4.5e-11       2     125 ..      22     137 ..      21     150 .. 0.74
   2 ?    0.4   0.0      0.37   5.5e+02     134     145 ..     336     350 ..     288     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 3e-14
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       +e++  Q eai++l++ l+  +++   +   TG+GKT++ ak+i++++k      +l+++++k+l  q+++ef++f+
  gi|386001959|ref|YP_005920258.1|  22 FEPKGSQPEAIDKLVSGLE-SGQRLQTLLGVTGSGKTYTVAKVIDAVKK-----PTLVIAHNKTLAAQLYNEFREFF 92 
                                       567778************9.88888889999*****************9.....8********************** PP

                                       GG........GEEEESSS-B--.......-SEEEEEHHHHHHTH....... CS
                            ResIII  79 seayke....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeees 125
                                       +e++ e        ++ +++++       k+ ++++ +s++ ++e+ + + 
  gi|386001959|ref|YP_005920258.1|  93 PENRVEyfvsYYDYYQPESYIP------AKDQYIEKDSSINPKIEQMRLAA 137
                                       **98554444333344444444......66666666666666664444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.37
                                       S...EEEEETGGGTT CS
                            ResIII 134 d...viiiDEaHrlg 145
                                       +   +++iDE+H + 
  gi|386001959|ref|YP_005920258.1| 336 PedfLLVIDESHQTI 350
                                       24458999**99876 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   2.4     5e-12   7.5e-09       2      36 .]     618     652 ..     617     652 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5e-12
                               UVR   2 klikeLeeemeeAaenedFEkAAklRDqinalkkq 36 
                                       +++ eLe+em  Aa+++dFE+A +lR  i++l+k+
  gi|386001959|ref|YP_005920258.1| 618 NVVIELEAEMRAAADALDFERAIQLRETIKKLEKE 652
                                       6899*****************************85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0018       6      65 ..      28      87 ..      24     149 .. 0.83
   2 ?    0.1   0.0      0.37   5.5e+02      44      82 ..     449     495 ..     440     557 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                            AAA_30  6 Qaaaveal...ltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaee 65
                                      Q +a+++l   l+sg+r+++l G+ G+GKt++++++ +a++   ++ +++A++++ A++L +e
  gi|386001959|ref|YP_005920258.1| 28 QPEAIDKLvsgLESGQRLQTLLGVTGSGKTYTVAKVIDAVK---KPTLVIAHNKTLAAQLYNE 87
                                      666666662225699******************99999998...5679999999999999766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.37
                            AAA_30  44 aaggrviglAptgkaAkvLae...elgieastiakllkrlk.....g 82 
                                       aag r ++ + t+k A++L++   + gi+a+ +++ +++ +     +
  gi|386001959|ref|YP_005920258.1| 449 AAGDRALVTTLTKKLAEELTDylaKNGIRARYLHSEIQTIErteiiR 495
                                       46778889999999999999633366799999999887776555552 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.2e-06    0.0093      15      73 ..      44      94 ..      26     119 .. 0.75
   2 ?    0.2   0.0      0.37   5.5e+02     124     169 ..     340     402 ..     337     410 .. 0.51
   3 ?    0.6   0.0      0.28   4.2e+02      47     103 ..     451     507 ..     432     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-06
                                      CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73
                                      +   + + TGsGKT   +  v+++v       ++ +l+++  + La q +n++++f+ +
  gi|386001959|ref|YP_005920258.1| 44 RLQTLLGVTGSGKTYT-VAKVIDAV-------KKPTLVIAHNKTLAAQLYNEFREFFPE 94
                                      44457789******98.67888788.......3457********************975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.37
                                       EEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT..........................SEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldqgfsdfinrilnqlpqitcdgklq..........................rqvivlSATl 169
                                       +lV+DE ++   q  +  ++   ++ +        +                          r vi++SAT+
  gi|386001959|ref|YP_005920258.1| 340 LLVIDESHQTIPQ-LRAMYKGDRSRKK--------SlvdygfrlpsafdnrplrfeeferfmRSVIFVSATP 402
                                       5788888877766.2222222111111........1222333344455555555666666655577777776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.28
                                       S-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                              DEAD  47 gpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvg 103
                                       g +al+ + t++Lae+  + l k +     r+l + i+  ++++ +++l+ g  d++vg
  gi|386001959|ref|YP_005920258.1| 451 GDRALVTTLTKKLAEELTDYLAKNGIR--ARYLhSEIQTIERTEIIRELRLGkFDVLVG 507
                                       668999999999999999999887775..445447788899999999998555999887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0033         5      10      37 ..      43      70 ..      34      85 .. 0.81
   2 ?    5.4   0.0     0.014        21      33      78 ..     446     508 ..     428     655 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvel 37
                                      +++  +++  G+GKT+++ +++  +++ 
  gi|386001959|ref|YP_005920258.1| 43 QRLQTLLGVTGSGKTYTVAKVIDAVKKP 70
                                      6677899**************9988765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                            AAA_19  33 llvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.....................l 78 
                                        +v++g    ++ l+ ++t++ a+el++ la+ g +a+ +H+                        +
  gi|386001959|ref|YP_005920258.1| 446 RVVAAG----DRALVTTLTKKLAEELTDYLAKNGIRARYLHSEIQtierteiirelrlgkfdvlvgI 508
                                       333333....7899**************998777776666633112333333555555555555550 PP

>> UB2H  Bifunctional transglycosylase second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.21       1      47 [.     172     218 ..     172     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                              UB2H   1 LypGaalsaaqleqeLellgYrkvsnvtrpGeyavsgnriellrRgF 47 
                                       L+ G+++s+ ++ + L + +Y +++   +pG ++ +g++i+l    F
  gi|386001959|ref|YP_005920258.1| 172 LKVGDRVSRREILERLVASQYERNEMELAPGRFRAKGETIDLVPGYF 218
                                       789*************************************9976555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00015      0.22      28      48 ..      48      68 ..      46      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                             DUF87 28 ilgsTGsGKSntvavLleell 48
                                       lg TGsGK++tva  ++ + 
  gi|386001959|ref|YP_005920258.1| 48 LLGVTGSGKTYTVAKVIDAVK 68
                                      59************9887665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.39      10      57 ..      30      75 ..      25     145 .. 0.74
   2 ?   -1.6   0.0       2.1   3.1e+03      41      87 ..     456     499 ..     446     577 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                            AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflr 57
                                      e++  +++ + sg+ +l  l G  G+GK+  v ++ +a++k   ++++
  gi|386001959|ref|YP_005920258.1| 30 EAIDKLVSGLESGQ-RLQTLLGVTGSGKTYTVAKVIDAVKKP-TLVIA 75
                                      56677777777887.9999*****************999988.33322 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.1
                            AAA_16  41 vrellralekdggiflrgkcdqlesaipysa.laqalareellrqlld 87 
                                       v++l + l ++    l+    +++  ++y++  +q+++r e++r+l  
  gi|386001959|ref|YP_005920258.1| 456 VTTLTKKLAEE----LTDYLAKNGIRARYLHsEIQTIERTEIIRELRL 499
                                       55555555555....555555554445554446666666666666544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00022      0.33       5      27 ..      47      69 ..      43      83 .. 0.84
   2 ?   -2.5   0.0       2.3   3.4e+03     107     157 ..     607     656 ..     601     657 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                      EEEESTTSSHHHHHHHHHHHHHH CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkk 27
                                       l+G++G+GKT t+aK+ + +kk
  gi|386001959|ref|YP_005920258.1| 47 TLLGVTGSGKTYTVAKVIDAVKK 69
                                      589*************9988776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                       HHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTT CS
                             SRP54 107 kikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgG 157
                                       +++++ k+d   +v++  ++  a++ a +F++a+++   i  kl++++k G
  gi|386001959|ref|YP_005920258.1| 607 ETRHIPKSDIPNVVIELEAEMRAAADALDFERAIQLRETI-KKLEKESKVG 656
                                       5555556666667888888899999999999999999876.6888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 5140.65
//
Query:       gi|386001960|ref|YP_005920259.1|  [L=104]
Description: Carboxymuconolactone decarboxylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-13   49.2   0.0    4.6e-13   49.0   0.0    1.0  1  CMD       Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.069   11.7   0.0      0.075   11.6   0.0    1.0  1  LRIF1     Ligand-dependent nuclear receptor-interacting facto


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   5.1e-17   4.6e-13       1      83 [.      19     101 ..      19     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 5.1e-17
                                       HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHH.HTT--HHHHHHHHHHHHHHHSHHHH CS
                               CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAl.eaGvteeeiaevlaqaaayagwpaa 76 
                                       p+l++a++ l+ea++  +  Ld k++ Lial+++aa   e   +  ++ A+ e Gvt++ei +vl++   ++g+p +
  gi|386001960|ref|YP_005920259.1|  19 PDLYEAIVGLNEATYT-GKVLDYKTQKLIALGIAAASSDERATKKQMMSAKkEFGVTKDEIVDVLRVVLLTSGMPPF 94 
                                       99*************9.999*********************88999999999************************* PP

                                       HHHHHHH CS
                               CMD  77 raAlaaa 83 
                                       ++A++++
  gi|386001960|ref|YP_005920259.1|  95 TKAMKIL 101
                                       ****987 PP

>> LRIF1  Ligand-dependent nuclear receptor-interacting factor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.3e-06     0.075     521     561 ..      51      91 ..      32     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-06
                             LRIF1 521 aqirsqekslqkqdaelrkkFGltkdlrVyLtripltssse 561
                                       a + s+e+ ++kq +  +k+FG+tkd+ V   r+ l +s  
  gi|386001960|ref|YP_005920259.1|  51 AAASSDERATKKQMMSAKKEFGVTKDEIVDVLRVVLLTSGM 91 
                                       55678999999**********************99887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 686.43
//
Query:       gi|386001961|ref|YP_005920260.1|  [L=712]
Description: Sodium/hydrogen exchanger [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-61  205.9  53.9    1.1e-60  205.5  53.9    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    9.9e-24   83.8   0.6      2e-23   82.9   0.6    1.6  1  TrkA_N          TrkA-N domain
    6.2e-16   58.0   0.2    6.2e-16   58.0   0.2    2.2  2  TrkA_C          TrkA-C domain
  ------ inclusion threshold ------
      0.058   13.8   0.3       0.15   12.5   0.3    1.6  1  NAD_binding_7   Putative NAD(P)-binding
       0.27    9.1   0.5       0.47    8.3   0.5    1.3  1  Prominin        Prominin


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.5  53.9   3.1e-64   1.1e-60       1     379 [.       9     374 ..       9     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.5 bits;  conditional E-value: 3.1e-64
                                       XHHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHH CS
                    Na_H_Exchanger   1 ivllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlk 77 
                                       i++++l++++++++  rl++p++vg++++G++ Gp+gl l+++  e++e++se+g++lllF++G+e+++++l++ ++
  gi|386001961|ref|YP_005920260.1|   9 IIIIFLISIIAIFVGARLRVPVVVGFLVTGIVAGPHGLRLVHEV-EQIEFFSEVGVVLLLFAIGIEFSFERLLRIRR 84 
                                       4666666666666899****************************.******************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHH CS
                    Na_H_Exchanger  78 silllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDav 154
                                       ++l+++ l+v+it+++ ++l+++   lg+p+ e++++g+++++++++vvl+il+++ +v++  g  +lg+++++D++
  gi|386001961|ref|YP_005920260.1|  85 AALVGGPLQVAITLLA-TTLIGI--ELGLPVNESIFAGFLIALSSTAVVLKILQDRDEVDTPHGGNTLGILIFQDIA 158
                                       ****************.777886..5799************************************************ PP

                                       CCCCCHHHHHHTX..XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 155 avvllavllalak..eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaall 229
                                       +v++  +++ la   +    ++ l++l++ + +v+++++ ++l+++ ll  + r   +++el++l v+l++l++a++
  gi|386001961|ref|YP_005920260.1| 159 VVPMMLFVPLLAAeeSTGLSVALLMMLAKGAGIVVLVIVSAKLLVPALLYQVVRL--RSSELFLLTVILICLAVAWV 233
                                       ************963333333445599999************************9..9******************* PP

                                       HHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTH CS
                    Na_H_Exchanger 230 aellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillg 306
                                       + + g+s +lgaflaGl++se+++s ++  ++ +f  ++f  +fFv++G+ ld+ ++   ++ + lv+++ + ++l 
  gi|386001961|ref|YP_005920260.1| 234 SYSAGLSLALGAFLAGLIISESDYSYHALGNVIPFK-DVFTSFFFVSIGMLLDVGFF---FESFELVAGAALGVVLL 306
                                       ************************************.9*******************...9**************** PP

                                       HHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                    Na_H_Exchanger 307 rilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                                       +++++  ++ llg+++r+ +++g++++q+g+++++l   g ++g++ r  y l+++v ++t+       +p++
  gi|386001961|ref|YP_005920260.1| 307 KAAVAGGVSVLLGYPIRTGVLAGLALAQIGEFSFILSKTGLDSGIMGRGEYQLFLAVSILTMA-----ATPFV 374
                                       **************************************************************9.....44443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.6   5.6e-27     2e-23       2     114 ..     412     524 ..     411     526 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 5.6e-27
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                       +i+G+G vGr+la+  + g+  ++v + ++e+v+  r++g+++ +gdat+e vL++a++++a++v++a++d  a+  
  gi|386001961|ref|YP_005920260.1| 412 VIVGYGFVGRTLAKAARVGELTYMVLEMNPEKVRGERANGVPIHYGDATQEIVLRHADVDTARVVVVAVSDEMATRR 488
                                       8*****************7756******************************************************* PP

                                       HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                            TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                       +v+la+ +npk +i+ar+++ ++a  l++lgad+v+
  gi|386001961|ref|YP_005920260.1| 489 IVELARRINPKVYIMARVRHLAEAAPLYDLGADEVV 524
                                       **********************************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2         1   3.6e+03       4      31 ..     476     504 ..     473     511 .. 0.68
   2 !   58.0   0.2   1.7e-19   6.2e-16       1      66 [.     586     653 ..     586     657 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                                       EEEE--GGGTTSBHHHHTHHHH...S-EEEE CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrar...gvlvva 31 
                                       v+v+ +  ++ +++ e  l +r   +v ++a
  gi|386001961|ref|YP_005920260.1| 476 VVVAVSDEMATRRIVE--LARRinpKVYIMA 504
                                       5666677788888888..7666667777776 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 1.7e-19
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       +v v+v + +p  Gk l el lr++ gv+v++i R+ g +++p  +t++e+GDvll++g+++++a+ r
  gi|386001961|ref|YP_005920260.1| 586 VVTVKVEEKAPASGKALEELELRKKlGVNVIGILRDsGNILNPVRETEIEAGDVLLLLGTSEQIAKTR 653
                                       67899***********************************************************9976 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.2e-05      0.15       7      84 ..     408     495 ..     405     508 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtv..vapevkeele....elvk.....laeeel..ekdlegadlviaatd 70 
                                       + + ++vG G v+ + ++     + +  v  + pe    +     + v      +++e +  ++d++ a +v++a++
  gi|386001961|ref|YP_005920260.1| 408 ENHLVIVGYGFVGRTLAKAARVGELTYMVleMNPEK---VRgeraNGVPihygdATQEIVlrHADVDTARVVVVAVS 481
                                       678999999999976444444443333331255552...22323322332222133333366899************ PP

                     NAD_binding_7  71 drelneriaeaaka 84 
                                       d+   +ri+e+a++
  gi|386001961|ref|YP_005920260.1| 482 DEMATRRIVELARR 495
                                       ************95 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5   0.00013      0.47     423     475 ..      25      77 ..      16      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00013
                          Prominin 423 csllllivvililgLlcGilGlsrtatptdrgcskntGasfLlvgvglsFlff 475
                                        + + ++v +l++g++ G  Gl+  ++  + ++ +++G ++Ll+++g+ F f 
  gi|386001961|ref|YP_005920260.1|  25 RLRVPVVVGFLVTGIVAGPHGLRLVHEVEQIEFFSEVGVVLLLFAIGIEFSFE 77 
                                       5567799******************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4607.86
//
Query:       gi|386001962|ref|YP_005920261.1|  [L=389]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-28   99.2   0.1      6e-28   98.3   0.1    1.5  1  Radical_SAM  Radical SAM superfamily
    3.8e-10   40.1   0.4      9e-10   38.9   0.4    1.7  1  SPASM        Iron-sulfur cluster-binding domain
    9.1e-09   35.7   0.0    1.5e-08   35.0   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    4.9e-05   23.5   0.0    8.9e-05   22.6   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.1   1.3e-31     6e-28       2     166 ..      46     201 ..      45     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.3e-31
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       ++tr Cnl+C +C++     +e  +++l +ee +++++el+    +  +il+ggepll ++f+ +++++++    g+
  gi|386001962|ref|YP_005920261.1|  46 NITRHCNLNCDHCYIDA---TEAAAEELKLEEGIRLIDELA-ALKIPMLILTGGEPLLSRNFYAYAFHAREV---GL 115
                                       689*************8...7*******************5.555**************************7...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpG 154
                                       r++++tngtl+++e++++l+e++v +v ++l++  +e  +++++  ++ +++ +e+l ++reag+k +  r+++ + 
  gi|386001962|ref|YP_005920261.1| 116 RTVISTNGTLITPEVARLLREAEVRYVGVSLDSCRPE-AHDRFRgVKGAYDRAIEGLANAREAGLK-TGLRVTLTK- 189
                                       *************************************.7888877*********************.888888888. PP

                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 155 endeeleellel 166
                                        n++e+ +ll+l
  gi|386001962|ref|YP_005920261.1| 190 DNWHEVPALLDL 201
                                       999999999887 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.4     2e-13     9e-10       1      68 []     291     355 ..     291     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2e-13
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIw...nseeyqefrkskkfplielCrnCp 68 
                                       C+a+ + + In+ GdV pC     ++  e+++Gn+re s++eIw    s+e+ ++r   + +l   C +C+
  gi|386001962|ref|YP_005920261.1| 291 CTAGVKVANINHRGDVLPC-----HFMPEVVVGNVRERSFKEIWmddPSPELLALR-DIRSKLTGACGDCE 355
                                       88899999***********.....57778***************655555666677.34455555688885 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   3.5e-12   1.5e-08       3     131 ..      37     158 ..      35     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.5e-12
                           Fer4_12   3 GeGvrlslf..vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvk 77 
                                       Ge++ ++++  +  Cnl+C+ C+  +t    ++   + e   ++i++l+  +i+ l+l+GGEPll    + ++  + 
  gi|386001962|ref|YP_005920261.1|  37 GEKKPVVMWniTRHCNLNCDHCYIDATEAAAEEL--KLEEGIRLIDELAALKIPMLILTGGEPLL---SRNFYAYAF 108
                                       77777888888999*********88888776655..5566779**********************...677777788 PP

                           Fer4_12  78 evkeekpekdiwlytgytleelskkekeellkeidv.lvdGkfeesledeslrfr 131
                                       + +e ++  ++++++g+ +         +ll+e +v  v + ++  + + + rfr
  gi|386001962|ref|YP_005920261.1| 109 HAREVGL-RTVISTNGTLITPEV----ARLLREAEVrYVGVSLDSCRPEAHDRFR 158
                                       8888888.589999998765443....4566666665666666666666666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     2e-08   8.9e-05       5      71 ..      48     107 ..      44     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklv 71 
                                       +  Cnl+C  C+  +  +  +++ + ee + + +++l + +i    l ltGGePL+    ++++   
  gi|386001962|ref|YP_005920261.1|  48 TRHCNLNCDHCYIDA-TEAAAEELKLEEGI-RLIDELAALKI--PMLILTGGEPLLS---RNFYAYA 107
                                       678*********777.46667777777777.88878888887..66*********76...4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2354.17
//
Query:       gi|386001963|ref|YP_005920262.1|  [L=490]
Description: Uroporphyrinogen III synthase/methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-49  166.9   3.0    1.6e-48  165.5   0.9    2.4  3  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    8.4e-45  152.9   0.2    1.5e-44  152.1   0.2    1.4  1  HEM4          Uroporphyrinogen-III synthase HemD
  ------ inclusion threshold ------
       0.13   12.6   0.0        2.1    8.7   0.0    2.5  2  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   0.9   2.7e-52   1.6e-48       1     212 [.       8     219 ..       8     220 .. 0.90
   2 ?    0.4   0.0     0.085   5.1e+02     131     187 ..     337     392 ..     325     400 .. 0.68
   3 ?   -3.1   0.0         1   6.2e+03      20      40 ..     444     466 ..     442     480 .. 0.63

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 2.7e-52
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k++lVG+GpGdpellT++A+r+l++adv+l d+ + ++ +l ++ e      + gk   ++   +eei++ l+e+ r
  gi|386001963|ref|YP_005920262.1|   8 KVWLVGAGPGDPELLTLKARRLLEEADVILFDR-LLSSEILGWAGEG-AEMIDVGKLPGRHKLSQEEINALLVEKGR 82 
                                       799***************************9*9.7666666777765.3333444445577777************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpglak 148
                                       +gk Vv+l++GDP+v+g+g+e+  al+a  a +++ev+PGv+s+ +++a +gip+t++g++++++      +p  +k
  gi|386001963|ref|YP_005920262.1|  83 EGKVVVRLKGGDPFVFGRGGEEGLALAA--ARVPFEVVPGVTSAISVPAGAGIPVTHRGVATAFTvvtgheEP--GK 155
                                       ***********************99999..99*************************************6444..56 PP

                      TP_methylase 149 eeereleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       eee ++eal+  g+t+v+l+++++lae + +L++  ++++t p+a++er+  ++ervv+gtl+++
  gi|386001963|ref|YP_005920262.1| 156 EEELDWEALARVGGTIVVLMGVSRLAENVSALLRGgRDPKT-PAALIERGWSPEERVVVGTLGDV 219
                                       7**********************************888766.********************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.085
                      TP_methylase 131 plteggevlsvllpglakeeereleallangdtlvllkaprklaelaelLkea.lydd 187
                                        l+e+g + s++ p  + +++ +  al+ ++  ++ll + +  +el+e+L ea +  d
  gi|386001963|ref|YP_005920262.1| 337 ALAERGLSASIV-PE-SFSSRGLALALAPRFKKVLLLRSAKGSPELVEILEEAgVEVD 392
                                       577778888888.44.223444444555557778888888889999999999955444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1
                      TP_methylase  20 lralktadvv.lgddsr.aleil 40 
                                       ++ l +a+vv +g+ +r ale l
  gi|386001963|ref|YP_005920262.1| 444 RERLSEAKVVaIGPPTRsALEEL 466
                                       67888888885555544555544 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.1   0.2   2.6e-48   1.5e-44       9     232 .]     269     484 ..     262     484 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 2.6e-48
                                       HTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHH CS
                              HEM4   9 arGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavGpaTar 85 
                                       ++G+ p+++P i +   + +++l + ++     + d+++ftSa++ e+   al+  e + + l++  +a++Gp+T +
  gi|386001963|ref|YP_005920262.1| 269 SLGFRPILAPSIAFLELPLPKDLPERIE-----AADCVVFTSATGAEI---ALR-DEGLAALLRRSVLATIGPRTEE 336
                                       58**************999999999998.....99*************...776.7888899999999********* PP

                                       HHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHH CS
                              HEM4  86 aLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeeepeelk 162
                                       aL e+gl +++vp+ +++++gLa +la++ ++  vlllr+ +++++l+e Lee+g+evdev++Y+   a +  ++l 
  gi|386001963|ref|YP_005920262.1| 337 ALAERGLSASIVPE-SFSSRGLALALAPRFKK--VLLLRSAKGSPELVEILEEAGVEVDEVHLYDI--APSGDSRLD 408
                                       *************9.*******9999865555..********************************..667899999 PP

                                       HHHHTT--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHHHH CS
                              HEM4 163 ealkagevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeeptaeglva 232
                                        ++ +g  d+ +ftS st+rnll+++k+        + l e+kv+aiGp T+ al++lg++vdv+++++t +++++
  gi|386001963|ref|YP_005920262.1| 409 WLILRGTPDVFAFTSGSTARNLLARAKELDaegrlrERLSEAKVVAIGPPTRSALEELGVRVDVMPDRYTFGAMLE 484
                                       ***************************999*******************************************985 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00035       2.1      24      75 ..      63     137 ..      49     211 .. 0.71
   2 ?    0.8   0.0     0.095   5.7e+02      48     107 ..     302     396 ..     288     402 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........................C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................x RF
                       Radical_SAM  24 grgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla........................v 75 
                                       +  + ls+eei +++ e   + g+ +v l gg+p++  +  e+ ++la+ +                        +
  gi|386001963|ref|YP_005920262.1|  63 PGRHKLSQEEINALLVEK-GREGKVVVRLKGGDPFVFGRGGEEGLALAAARvpfevvpgvtsaisvpagagipvtH 137
                                       5678899******99888.4889********************999999999999955555555555555544443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.095
                                       EEEEEESSTGGGSTTHHHHHHHHHHTC................CCTEEEEEEECSSCHG.................H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxx.................x RF
                       Radical_SAM  48 kevilgggepllypdfvellerlakla................vpgiritvetngtlpd.................e 91 
                                        +   +g e  l+++   +l+r++ la                 + +  ++++ g+ +                  +
  gi|386001963|ref|YP_005920262.1| 302 VFTSATGAEIALRDEGLAALLRRSVLAtigprteealaerglsASIVPESFSSRGLALAlaprfkkvlllrsakgsP 378
                                       45555677777777777777777777777777777777666663333333333333333444444455555555558 PP

                                       HHHHHHHHTT..-SEEEE CS
                                       xxxxxxxxxx..xxxxxx RF
                       Radical_SAM  92 eklerllelg..vdrvsl 107
                                       e +e l e+g  vd v+l
  gi|386001963|ref|YP_005920262.1| 379 ELVEILEEAGveVDEVHL 396
                                       888888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3696.92
//
Query:       gi|386001964|ref|YP_005920263.1|  [L=273]
Description: Hydroxymethylbilane synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-60  202.0   0.0    1.1e-59  201.4   0.0    1.2  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    2.2e-10   40.8   0.3    4.5e-10   39.8   0.3    1.5  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.4   0.0   1.2e-63   1.1e-59      31     197 ..       2     169 ..       1     174 [. 0.95

  Alignments for each domain:
  == domain 1  score: 201.4 bits;  conditional E-value: 1.2e-63
                    Porphobil_deam  31 vtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlptelpeglelaavlkredprDvlvvks..s 105
                                       + +ktkGD++ld pL++++g+glF+ke+++ +l+geid+aVhS+KDlp++ pegl+++avl+r++p Dvlv ++  s
  gi|386001964|ref|YP_005920263.1|   2 KVVKTKGDHVLDLPLHRVSGRGLFVKEIDDLMLAGEIDVAVHSMKDLPSKRPEGLVIGAVLPRDSPLDVLVSDDgvS 78 
                                       679********************************************************************644889 PP

                    Porphobil_deam 106 leelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAaAGLkRlgleerisevlspeel 182
                                       ++ l+egavvgT+S+RR+aql+++rpdl +++lRGn++tRlrkl+eg+y ai+LA AG++R+g++ +    l+pe +
  gi|386001964|ref|YP_005920263.1|  79 IDGLEEGAVVGTCSMRRAAQLRRARPDLVIESLRGNLETRLRKLEEGRYRAIVLALAGIERMGYSPNYAV-LDPERF 154
                                       ***************************************************************7776654.****** PP

                    Porphobil_deam 183 lpavgQGalavevrk 197
                                       +p++ QGa+av + +
  gi|386001964|ref|YP_005920263.1| 155 VPSANQGAIAVVATE 169
                                       ***********9876 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.3   5.1e-14   4.5e-10       3      68 ..     187     253 ..     186     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.1e-14
                                       HHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE....-GGGHHHHHHH CS
                   Porphobil_deamC   3 evlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakg....eleeaeelGkk 68 
                                       e+ +ER +l+e +G+C vP +++a+++++e ++  + vlsldg +    +ae+++     le a+el  +
  gi|386001964|ref|YP_005920263.1| 187 EAECERVFLEEIGGSCVVPMAAFARLSGDE-ISVLAEVLSLDGAR--SVRAEGRIsaadHLEGARELSRR 253
                                       6789***********************989.************77..77777777556677777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2064.68
//
Query:       gi|386001965|ref|YP_005920264.1|  [L=422]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-63  214.6   0.0    2.3e-63  214.2   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.2   0.0   1.3e-67   2.3e-63       9     373 ..      31     389 ..      25     415 .. 0.88

  Alignments for each domain:
  == domain 1  score: 214.2 bits;  conditional E-value: 1.3e-67
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                        ++ +++aeG  l+ ++g+r++D   ++ +++lGh+hP v++ v +q+++ ++     + +e  + la+ ++ + p 
  gi|386001965|ref|YP_005920264.1|  31 YPFYVSRAEGPHLWTKEGQRLIDYCLAYGPMILGHRHPLVMERVVKQLEQGWLYG---TPSELEVSLAKRIVGHYPS 104
                                       45889**********************************************9887...8899999***********9 PP

                                       ..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  86 gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                        +d++ ++ +G+eA+++Al++ar       +t + +i++++g+fHG   + l  +gs  +  tl  p + +v++  +
  gi|386001965|ref|YP_005920264.1| 105 -IDMLRFVSTGTEATMAALRIARG------YTGRDRIVKVEGGFHGAHDAVLVKAGS--GATTLGVPDSLGVPKDTA 172
                                       .***********************......9**************************..777777777888888888 PP

                                       TBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT. CS
                       Aminotran_3 163 pdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf. 238
                                       + ++++++n+      l ++ea     + evaAvi+Ep+ g+ G v ++p++l+++r l+++h+vlli+DEv tGf 
  gi|386001965|ref|YP_005920264.1| 173 KNTIQVPYND------LGAMEAALTGFDGEVAAVIMEPVLGNIGPVLPEPGYLEGARRLTEEHGVLLIFDEVITGFr 243
                                       889*******......566677668899************************************************8 PP

                                       .TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHT CS
                       Aminotran_3 239 .GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieee 311
                                        +  G   A + +gv pD++tl+K ++gG+p+ +v +++e+m+++ap++   +++Tf G p+  a+ +a+l+++e e
  gi|386001965|ref|YP_005920264.1| 244 lSLGG---AQARYGVVPDMTTLGKIIGGGFPIGVVGGRRELMEMVAPSGgiyQAGTFNGSPVSLAAGMATLDVLEGE 317
                                       77788...99999**********************************999*************************** PP

                                       THHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE CS
                       Aminotran_3 312 kllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvl 373
                                         le+ + +g+ l+++L ++ ++     +v g   ++ i ++ +a ++             +++ +++++Gv 
  gi|386001965|ref|YP_005920264.1| 318 RTLERLDSVGEDLRKALAQIVEDLGLSYSVVGTASIFKI-FFGAAPKNYaealrcdkagyLAFFRRMLKAGVF 389
                                       ******************998876555555555555555.444444333455666666665566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2939.09
//
Query:       gi|386001966|ref|YP_005920265.1|  [L=413]
Description: hypothetical protein Mhar_1278 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-126  421.0   0.2   4.8e-126  420.8   0.2    1.0  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.8   0.2  2.7e-130  4.8e-126       1     372 [.       4     389 ..       4     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 420.8 bits;  conditional E-value: 2.7e-130
                            DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdveeeehehehrslaeieei 77 
                                       l++d+ssG+sGDm++++Lldlgad++++++a+e++g+   +lei++++k++isa +v++  ++  +  r+lae +++
  gi|386001966|ref|YP_005920265.1|   4 LLFDPSSGASGDMIMASLLDLGADPDAVRKAVESVGC---TLEISRAEKHHISAARVRI--HAGGKRYRTLAEARSV 75 
                                       689********************************96...9******************..579999********** PP

                            DUF111  78 ieaaslsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtv 154
                                       ++aa+l++++++++++i+e+laeAe++vhgv+ eev fhE+Ga+Da++di g a+a ++Lg ++vv+ p+++GsGtv
  gi|386001966|ref|YP_005920265.1|  76 LAAAALAPQARDRSMKIMEILAEAEGRVHGVSGEEVRFHEIGALDALADIAGSAAAWESLGADRVVVLPISVGSGTV 152
                                       ***************************************************************************** PP

                            DUF111 155 rcahGilPvPaPAvlellkelklkl..gevegElvTPTGaAilaalaeefg.slpamkvekiGyGaGkrdleeipnv 228
                                        +ahG+lPvPaPA+le+lk++ l    g+vegEl+TPTGaAilaa+a+e   ++p ++  ++GyGaG++dl ++pn+
  gi|386001966|ref|YP_005920265.1| 153 VAAHGRLPVPAPATLEILKGSALLWrgGPVEGELLTPTGAAILAAFADEAAaEYPLIRAGASGYGAGSKDL-AVPNL 228
                                       *******************999877999**********************99*******************.8**** PP

                            DUF111 229 lRvll.........eeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlck 296
                                       lR+++         +e++ + ++++vv+letn+DD+++evlg +le L+eaGAlDv+++p+lmKKgRpa l++vl+k
  gi|386001966|ref|YP_005920265.1| 229 LRTVIgepaapkgpGESHPHPHHDRVVQLETNVDDVTGEVLGGLLEILMEAGALDVTIVPALMKKGRPASLIQVLAK 305
                                       ***********9997788899******************************************************** PP

                            DUF111 297 eedaeeleellfretttlGvRese.verlvlereietvetelg....evrvKva...eevvkvkpEyedvkkiAeet 365
                                       +e+ae+l++++++et++lGvR ++  +r+v+ere ++v +e++    +vr+Kv+   +e++++k+E++d+++iA+e+
  gi|386001966|ref|YP_005920265.1| 306 KEEAERLARIVMKETGSLGVRVFPsLHRFVAEREEREVGFEIEgrpfRVRLKVSlidGEILRIKAEHDDCRRIARES 382
                                       ************************9****************9999**********9777****************** PP

                            DUF111 366 glplkev 372
                                       glpl+ev
  gi|386001966|ref|YP_005920265.1| 383 GLPLREV 389
                                       ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2741.23
//
Query:       gi|386001967|ref|YP_005920266.1|  [L=918]
Description: Formate dehydrogenase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-84  282.4   0.0    7.7e-84  282.1   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    4.4e-30  104.0   0.0    9.1e-30  102.9   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    4.1e-20   71.5   2.5    5.7e-20   71.1   0.5    2.4  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    7.6e-19   67.5   0.1    2.4e-18   66.0   0.1    1.9  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
      8e-09   34.9   7.5    0.00064   19.2   3.6    3.0  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    5.7e-07   30.0  19.5      5e-06   27.0   7.7    4.5  3  Fer4_7           4Fe-4S dicluster domain
    6.8e-07   28.9   1.4    6.8e-07   28.9   1.4    4.1  5  Fer4             4Fe-4S binding domain
    7.5e-06   26.0   7.5    7.5e-06   26.0   7.5    4.2  5  Fer4_9           4Fe-4S dicluster domain
    2.3e-05   24.4   4.4    2.3e-05   24.4   4.4    3.0  1  Fer4_21          4Fe-4S dicluster domain
    0.00011   22.1  10.0    0.00035   20.5   0.7    4.3  4  Fer4_6           4Fe-4S binding domain
     0.0027   18.6   3.8     0.0027   18.6   3.8    3.7  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0072   16.4   5.1     0.0072   16.4   5.1    4.1  3  Fer4_10          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.018   16.0   6.0      0.018   16.0   6.0    5.0  4  Fer4_3           4Fe-4S binding domain
       0.71   10.7   6.9         14    6.5   0.5    3.1  2  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.1   0.0     6e-87   7.7e-84       1     418 [.     299     709 ..     299     722 .. 0.94

  Alignments for each domain:
  == domain 1  score: 282.1 bits;  conditional E-value: 6e-87
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R+++P++R   r +G+F++++ +eAl+l+a+++ +++++ygpd+    ss++ + +e+ ++ +kl+++++g  ++++
  gi|386001967|ref|YP_005920266.1| 299 RITTPLIR---R-NGRFEEATLEEALDLVARRFSEIRDEYGPDSLGALSSSRCT-NEENYLVQKLARAVFG--TNNV 368
                                       9*******...9.********************************966665555.****************..9*** PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a++++a  +      +gs+ +     +n++ ++e++d+ +++GsN  e +pi+  +++kaa k+ +k+iv +pr
  gi|386001967|ref|YP_005920266.1| 369 DNCARVCHAPSVtglaACFGSGAA-----TNSFDQIEDADVLFVIGSNTTEAHPIVGLKVIKAANKG-TKIIVADPR 439
                                       *********999887666666533.....446669***************************99995.********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                       + el  +a  wl ++pgt  al+++m++vil+e+++d ef++++t g+ee+++ ++++++e+++++++v+a+ + e 
  gi|386001967|ref|YP_005920266.1| 440 KIELVDRAKVWLNLRPGTNIALLNGMMNVILREGLEDGEFIASRTEGFEEFRKVVDGYTPERAAEITGVPAADIVEA 516
                                       ***************************************************************************** PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       ar +a++++ +mii+  g++++  g+a++  + nLa+l+gnvg+  +g+  l+Gq++++g a+++galp     ++ 
  gi|386001967|ref|YP_005920266.1| 517 ARLYASAEK-AMIIYSLGMTEHVTGTANVISLGNLAMLTGNVGRRSTGVMPLRGQNNVQG-ACDMGALPNNHVGYQP 591
                                       ******999.**************************************************.*******999999999 PP

                                       TT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHT.TSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSS CS
                     Molybdopterin 305 ke...ekikfaaeqpgnlgnfprnlfversnllks.sgkkvlyllgnnpevdhadenevekalekldlvvvldgrlt 377
                                       ++    + kf   +   l+  p+ +++e+ + l +  g++ ly+lg++p ++++d+n+v   le l+++vv +++ t
  gi|386001967|ref|YP_005920266.1| 592 VTdarVRSKFEEAWGVRLPADPGLTSTEMLERLAEgRGIRGLYILGEDPAQTDPDTNRVRSSLEALEFLVVQEIFPT 668
                                       9999988999999999*************987765269*************************************** PP

                                       HHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT CS
                     Molybdopterin 378 stalyaDiiLPaatwyEkedlytndegrfqhlkqavsppge 418
                                       +t +yaD+iLPaa++ E ++++tn+e+r+q+ ++a++p g 
  gi|386001967|ref|YP_005920266.1| 669 ETTKYADVILPAASFAECDGTFTNGERRIQRVNRAIPPLGG 709
                                       *************************************9885 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0   7.1e-33   9.1e-30       1     111 []     804     910 ..     804     910 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 7.1e-33
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l+L+tgr++++++ + +tr++     + p e++ei+p+dA+ lGi+dG++V v+srrG+v+v+a+vte   +Gv+f+
  gi|386001967|ref|YP_005920266.1| 804 LILTTGRRREHYNCGSMTRRSKGIMWVWPeETIEISPADAEDLGIEDGETVLVRSRRGEVRVKARVTEKSSRGVAFL 880
                                       79*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksva 111
                                        f++ +     + +N lt++a+dp+++tpe+k++a
  gi|386001967|ref|YP_005920266.1| 881 SFHYAN-----VLTNLLTNAALDPVAKTPEYKACA 910
                                       ****99.....*********************996 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         5   6.4e+03       6      12 ..     213     219 ..     211     220 .. 0.83
   2 !   71.1   0.5   4.4e-23   5.7e-20       1      52 [.     241     292 ..     241     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5
                                       EE-SSBT CS
                    Molybdop_Fe4S4   6 taCpyCg 12 
                                       + C++Cg
  gi|386001967|ref|YP_005920266.1| 213 SDCKFCG 219
                                       77****9 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 4.4e-23
                                       SEEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4   1 ekvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52 
                                       ek++ t+CpyCgvgC +++ v+d++iv++ +d+++pvn+g+lCvKGr++l+ 
  gi|386001967|ref|YP_005920266.1| 241 EKTISTVCPYCGVGCRMKLGVEDERIVSIAPDREGPVNRGQLCVKGRFGLDE 292
                                       6999********************************************9986 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.1   1.9e-21   2.4e-18       3      81 ..       3      78 ..       1      79 [. 0.96

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.9e-21
                            Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnv.racstpvedGlkvetq 80
                                      ++tlt+DG+evtv  G t+++A+ ++g ++p++c++      l+++g+C+ C+V veg      +c t +e+G++v+t 
  gi|386001967|ref|YP_005920266.1|  3 EITLTIDGREVTVLSGATILDAARKAGSYLPALCHH----PDLKPIGSCKLCIVAVEGLDHYpTSCNTLAEEGMVVKTR 77
                                      79**********************************....89****************99988**************98 PP

                            Fer2_4 81 t 81
                                      t
  gi|386001967|ref|YP_005920266.1| 78 T 78
                                      7 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   3.6     5e-07   0.00064       1      26 [.      85     112 ..      85     126 .. 0.82
   2 !   16.4   0.1   3.6e-06    0.0047      16      40 .]     127     151 ..     124     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5e-07
                   NADH-G_4Fe-4S_3   1 RktilellLa..nHpldCltCdknGnCe 26 
                                       R+ +le+lLa  nHp  Cl Cd+  +C+
  gi|386001967|ref|YP_005920266.1|  85 RRHTLEMLLAltNHPTSCLFCDRKNECT 112
                                       899999997555***************3 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.6e-06
                   NADH-G_4Fe-4S_3  16 CltCdknGnCeLQdlayelgveesr 40 
                                       C  C++ G+CeLQ+ ++ +g e++r
  gi|386001967|ref|YP_005920266.1| 127 CKFCPQDGSCELQEAVEFVGLEKVR 151
                                       899*****************99986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.5     0.041        53       4      48 ..     126     184 ..     123     187 .. 0.59
   2 !   27.0   7.7   3.9e-09     5e-06       2      52 .]     174     229 ..     173     229 .. 0.75
   3 !   17.9   3.9   2.8e-06    0.0036       2      41 ..     215     255 ..     214     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.041
                            Fer4_7   4 gCgaCva..aCp.vkaieldeeenek...........gtekveidpekClgCgaCvavC 48 
                                       gC++C +   C  ++a+e+   e+ +           + +  + +++ C+ C +Cv+vC
  gi|386001967|ref|YP_005920266.1| 126 GCKFCPQdgSCElQEAVEFVGLEKVRyqlhfrnmpvlREPFFDRNYNLCIMCSRCVRVC 184
                                       77777642257677777777655555334333332222233466777899999999999 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.9e-09
                            Fer4_7   2 CigCgaCvaaCp....vkaieldeeenekgtekv....eidpekClgCgaCvavCPtga 52 
                                       Ci C +Cv++C+     ++++ +++ +    +++     +  ++C +CgaCv+vCPtga
  gi|386001967|ref|YP_005920266.1| 174 CIMCSRCVRVCSeirgEGVLKSNPDFHR---MHWigppSLLDSDCKFCGACVDVCPTGA 229
                                       ***********95555666666665433...333334488889**************98 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.8e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekC.lgC 41 
                                       C  CgaCv++Cp++a++++ ++ +++ +++  +  +C +gC
  gi|386001967|ref|YP_005920266.1| 215 CKFCGACVDVCPTGALSVRSDKWARPEKTISTVCPYCgVGC 255
                                       899*************9998877776555555544444444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       6.1   7.8e+03      11      16 ..      47      52 ..      46      53 .. 0.77
   2 ?   -3.5   0.3       8.7   1.1e+04       9      14 ..     125     130 ..     125     131 .. 0.81
   3 !   13.6   1.8   3.4e-05     0.044       4      18 ..     170     184 ..     167     185 .. 0.93
   4 !   28.9   1.4   5.3e-10   6.8e-07       6      23 ..     213     230 ..     210     231 .. 0.92
   5 ?   -3.4   1.0       8.4   1.1e+04      13      18 ..     370     375 ..     370     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.1
                                      -THHHH CS
                              Fer4 11 CGaCve 16
                                      C++C+ 
  gi|386001967|ref|YP_005920266.1| 47 CKLCIV 52
                                      999986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.7
                                       SS-THH CS
                              Fer4   9 igCGaC 14 
                                       +gC+ C
  gi|386001967|ref|YP_005920266.1| 125 VGCKFC 130
                                       689888 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3.4e-05
                                       ETTTSSS-THHHHHS CS
                              Fer4   4 deekCigCGaCvevC 18 
                                       ++++Ci C +Cv vC
  gi|386001967|ref|YP_005920266.1| 170 NYNLCIMCSRCVRVC 184
                                       899************ PP

  == domain 4  score: 28.9 bits;  conditional E-value: 5.3e-10
                                       TTSSS-THHHHHSTTTEE CS
                              Fer4   6 ekCigCGaCvevCPvgAI 23 
                                       ++C +CGaCv+vCP+gA+
  gi|386001967|ref|YP_005920266.1| 213 SDCKFCGACVDVCPTGAL 230
                                       68***************8 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 8.4
                                       HHHHHS CS
                              Fer4  13 aCvevC 18 
                                       +C+ vC
  gi|386001967|ref|YP_005920266.1| 370 NCARVC 375
                                       5***** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.4       1.5   1.9e+03      33      44 ..      84     113 ..      46     121 .. 0.63
   2 !    9.2   4.7     0.001       1.3       4      47 ..     126     185 ..     125     189 .. 0.65
   3 !   26.0   7.5   5.9e-09   7.5e-06       2      50 ..     174     229 ..     173     230 .. 0.72
   4 ?   -0.7   0.3       1.3   1.7e+03       5      21 ..     248     264 ..     246     285 .. 0.73
   5 ?   -3.3   0.1       8.5   1.1e+04       7      14 ..     370     377 ..     369     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                            Fer4_9  33 e...............eaCigCga...Cve 44 
                                       +               ++C++C +   C+e
  gi|386001967|ref|YP_005920266.1|  84 MrrhtlemllaltnhpTSCLFCDRkneCTE 113
                                       022334567777777888999988778874 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.001
                            Fer4_9   4 gCgaC..veaCpagvvvedaaerkarlraase..............eaCigCgaCveaCp 47 
                                       gC+ C    +C+ + +ve  + +k+r++                  + Ci+C +Cv +C 
  gi|386001967|ref|YP_005920266.1| 126 GCKFCpqDGSCELQEAVEFVGLEKVRYQLHFRnmpvlrepffdrnyNLCIMCSRCVRVCS 185
                                       566663223365555555555555555443336677777888888899***********7 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 5.9e-09
                            Fer4_9   2 CtgCgaCveaCpagvv..vedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                       C+ C +Cv++C       v ++++ + r+++ +      ++C +CgaCv++Cp+ga
  gi|386001967|ref|YP_005920266.1| 174 CIMCSRCVRVCSEIRGegVLKSNPDFHRMHWIGPpslldSDCKFCGACVDVCPTGA 229
                                       ***********544331144444555555444447779999*************97 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.3
                            Fer4_9   5 CgaCveaCpagvvveda 21 
                                       C +C   C +++ ved+
  gi|386001967|ref|YP_005920266.1| 248 CPYCGVGCRMKLGVEDE 264
                                       99999999988877665 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 8.5
                            Fer4_9   7 aCveaCpa 14 
                                       +C ++C a
  gi|386001967|ref|YP_005920266.1| 370 NCARVCHA 377
                                       57777755 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   4.4   1.8e-08   2.3e-05       6      57 ..     172     230 ..     169     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvl........kvvedeCvGCnlCssvCPvedci 57 
                                       + Ci C +C+ +C++   + + +++   +         +++++C  C  C++vCP+ +++
  gi|386001967|ref|YP_005920266.1| 172 NLCIMCSRCVRVCSEIRGEGVLKSNPDFHrmhwigppSLLDSDCKFCGACVDVCPT-GAL 230
                                       78************98888874443332224478886778***************6.665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       5.8   7.4e+03      11      17 ..      46      52 ..      33      53 .. 0.61
   2 !   20.5   0.7   2.7e-07   0.00035       5      21 ..     170     186 ..     166     193 .. 0.87
   3 !   15.0   2.8   1.5e-05     0.019       9      24 .]     215     230 ..     212     230 .. 0.86
   4 ?   -0.3   0.4         1   1.3e+03      14      20 ..     370     376 ..     369     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.8
                            Fer4_6 11 gCgdCvr 17
                                      +C  C++
  gi|386001967|ref|YP_005920266.1| 46 SCKLCIV 52
                                      5999976 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.7e-07
                            Fer4_6   5 dpdkCigCgdCvrvCPe 21 
                                       ++++Ci C +CvrvC e
  gi|386001967|ref|YP_005920266.1| 170 NYNLCIMCSRCVRVCSE 186
                                       78*************97 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.5e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C  Cg+Cv+vCP+ga+
  gi|386001967|ref|YP_005920266.1| 215 CKFCGACVDVCPTGAL 230
                                       555***********97 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1
                            Fer4_6  14 dCvrvCP 20 
                                       +C+rvC 
  gi|386001967|ref|YP_005920266.1| 370 NCARVCH 376
                                       7*****6 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.5    0.0095        12       2      12 ..     174     184 ..     159     189 .. 0.76
   2 !   18.6   3.8   2.1e-06    0.0027       2      31 ..     215     244 ..     214     266 .. 0.81
   3 ?   -1.4   0.1       3.7   4.8e+03      57      64 ..     368     375 ..     344     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0095
                           Fer4_16   2 CgtCgkCaevC 12 
                                       C+ C +C+ vC
  gi|386001967|ref|YP_005920266.1| 174 CIMCSRCVRVC 184
                                       66666666666 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.1e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieareci 31 
                                       C+ Cg+C++vCPt+a++ +++k ++++++i
  gi|386001967|ref|YP_005920266.1| 215 CKFCGACVDVCPTGALSVRSDKWARPEKTI 244
                                       99***************9955444455444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.7
                           Fer4_16  57 CdiCqdvC 64 
                                        d+C++vC
  gi|386001967|ref|YP_005920266.1| 368 VDNCARVC 375
                                       57888888 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.5   0.00041      0.53       5      19 ..     170     184 ..     167     199 .. 0.78
   2 !   16.4   5.1   5.6e-06    0.0072       6      45 ..     212     251 ..     208     257 .. 0.85
   3 ?   -3.2   0.2       7.7   9.8e+03      14      19 ..     370     375 ..     358     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                           Fer4_10   5 dddtCirCgkCvkaC 19 
                                       + + Ci C +Cv++C
  gi|386001967|ref|YP_005920266.1| 170 NYNLCIMCSRCVRVC 184
                                       567899999999999 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 5.6e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekC 45 
                                       d+ C  Cg+Cv++CP+ + sv+  + a +e+++++++  C
  gi|386001967|ref|YP_005920266.1| 212 DSDCKFCGACVDVCPTGALSVRSDKWARPEKTISTVCPYC 251
                                       678*************999999999999999999987777 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.7
                           Fer4_10  14 kCvkaC 19 
                                       +C ++C
  gi|386001967|ref|YP_005920266.1| 370 NCARVC 375
                                       344444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.5   0.00072      0.93       1      11 [.     174     184 ..     174     186 .. 0.95
   2 ?   16.0   6.0   1.4e-05     0.018       1      15 []     215     229 ..     215     229 .. 0.97
   3 ?   -2.0   0.4       7.9     1e+04       9      13 ..     246     250 ..     245     254 .. 0.78
   4 ?   -2.0   0.3       7.6   9.7e+03       7      11 ..     371     375 ..     367     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00072
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C++C++Cv+vC
  gi|386001967|ref|YP_005920266.1| 174 CIMCSRCVRVC 184
                                       *********** PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.4e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  CgaCv+vCP+gA
  gi|386001967|ref|YP_005920266.1| 215 CKFCGACVDVCPTGA 229
                                       99************9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.9
                            Fer4_3   9 evCPv 13 
                                        vCP+
  gi|386001967|ref|YP_005920266.1| 246 TVCPY 250
                                       59**7 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.6
                            Fer4_3   7 CvevC 11 
                                       C +vC
  gi|386001967|ref|YP_005920266.1| 371 CARVC 375
                                       99999 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5     0.011        14       6      21 ..     172     187 ..     166     194 .. 0.85
   2 ?    5.9   1.1     0.017        22       7      20 ..     214     227 ..     211     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                           Fer4_15   6 daCigcglCvaeapev 21 
                                       ++Ci+c +Cv++++e+
  gi|386001967|ref|YP_005920266.1| 172 NLCIMCSRCVRVCSEI 187
                                       68***********875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.017
                           Fer4_15   7 aCigcglCvaeape 20 
                                        C  cg+Cv+++p+
  gi|386001967|ref|YP_005920266.1| 214 DCKFCGACVDVCPT 227
                                       7***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (918 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 5451.91
//
Query:       gi|386001968|ref|YP_005920267.1|  [L=260]
Description: hypothetical protein Mhar_1280 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-09   35.0   0.0    2.1e-08   33.9   0.0    1.5  2  DUF364    Putative heavy-metal chelation
  ------ inclusion threshold ------
       0.06   13.6   0.1       0.13   12.5   0.1    1.6  1  DUF4213   Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.74   6.6e+03      64      85 ..      80     101 ..      73     104 .. 0.75
   2 !   33.9   0.0   2.3e-12   2.1e-08      14      99 ..     155     244 ..     143     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.74
                            DUF364  64 dvviitGstLvngtlerllela 85 
                                         ++ ++  +  gtle +lel+
  gi|386001968|ref|YP_005920267.1|  80 GQAFTSARGVFAGTLEGVLELS 101
                                       5566677777889999999986 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.3e-12
                            DUF364  14 VvvVGyfap.vlkklke..kgaeltvlelnpnlleeeegdl.pdeaaeellpeadvviitGstLvngtlerllela. 85 
                                       V++VG ++p +l  l e    +++ v +l +  + ++   +   +  e l +++ +v+itG+tLvngt+++llela 
  gi|386001968|ref|YP_005920267.1| 155 VGLVG-LQPaILSSLVEvfGPERVMVSDLASAGETRSGVKIlDGALPEPLFERCPLVLITGTTLVNGTIDALLELAf 230
                                       77888.556566666652234667777777754444444445777778899***********************984 PP

                            DUF364  86 kkaaevvlvGPsap 99 
                                       + +++vv +G ++ 
  gi|386001968|ref|YP_005920267.1| 231 RLENRVVFYGTTVA 244
                                       57899999999875 PP

>> DUF4213  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.5e-05      0.13      31      73 ..      77     118 ..      64     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                           DUF4213  31 ggaGlAyteagklvgkparelaelllswnplersvGlAaiNAl 73 
                                       g++G A+t+a  +   +++ ++el l  n++er+v +++iNA+
  gi|386001968|ref|YP_005920267.1|  77 GSCGQAFTSARGVFAGTLEGVLELSL-DNTFERAVLVSTINAV 118
                                       89******444444478888888888.9**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1692.53
//
Query:       gi|386001969|ref|YP_005920268.1|  [L=256]
Description: Formate dehydrogenase family accessory protein FdhD [Methanosaeta harundinacea 6Ac]
Scores for complete 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-53  181.8   0.2      5e-44  150.8   0.1    2.0  2  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.3e-11   4.1e-07       2      54 ..      50     102 ..      49     117 .. 0.90
   2 !  150.8   0.1   2.8e-48     5e-44      96     236 ..     115     255 ..     104     256 .] 0.95

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.3e-11
                                       --EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTT CS
                         FdhD-NarQ   2 eEepltivvngrelatlmatpadleelalGfllsegliesaediesievdede 54 
                                        Ee+++++++g  +a l+++p++leela+G+ll+eg ++ +ed+ s +v  +e
  gi|386001969|ref|YP_005920268.1|  50 IEERVALILDGMMVAELFCLPSQLEELAVGHLLCEGHLRGIEDLVSARVAGKE 102
                                       79********************************************9998775 PP

  == domain 2  score: 150.8 bits;  conditional E-value: 2.8e-48
                                       ----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHHHHHHHHHHHT.TSS-SS CS
                         FdhD-NarQ  96 tlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnAlDkviGaallegldlsd 172
                                       + ++++sdl++++e +++++d +++++ ++++tgg+H+a ++ ++g l  ++eDv+R  A+Dk++G al++g d s+
  gi|386001969|ref|YP_005920268.1| 115 EARPTASDLRIRPEVVFKALDMINDAALVWRRTGGTHSALVLGEEGALSSFCEDVSRSSAVDKAVGSALMAGADPSR 191
                                       34445679********************************************************************* PP

                                       SEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE-GGGE CS
                         FdhD-NarQ 173 kilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtgaeRi 236
                                       ++l+++gRlss +v Ka +agipvlvs+++p + ++elAe++g+tl++f+r  ++ vY+g+eRi
  gi|386001969|ref|YP_005920268.1| 192 SVLITTGRLSSAIVSKAGMAGIPVLVSRAGPLNAGIELAERLGMTLAAFARRPNLYVYAGKERI 255
                                       ***************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1593.85
//
Query:       gi|386001970|ref|YP_005920269.1|  [L=651]
Description: Formate dehydrogenase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-88  295.5   0.0    7.9e-88  295.3   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    1.4e-31  108.8   0.0    3.2e-31  107.6   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.047   13.7   0.0      0.095   12.7   0.0    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.3   0.0   1.3e-91   7.9e-88       1     432 []      32     455 ..      32     455 .. 0.93

  Alignments for each domain:
  == domain 1  score: 295.3 bits;  conditional E-value: 1.3e-91
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl+yP++R      ++Fvr+sW+eAl+l a+ l    +++gp++   f +++ +++e+ ++++kl++llg++   ++
  gi|386001970|ref|YP_005920269.1|  32 RLEYPLKR---D-GDEFVRISWEEALDLAARGLAGSAQDHGPESLG-FLASSRCNNEENYLMQKLARLLGSP---NV 100
                                       9*******...6.899**************************9999.66667777****************7...77 PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+l+++ ++     ++g     + +++n+l+dl ns+ i+++G+N +e +p++ +r   +a++++akviv +pr
  gi|386001970|ref|YP_005920269.1| 101 DNCARLCHSPTVvglgAVLG-----TGAMTNNLGDLKNSSCIFAIGTNFAEAHPVV-SRWVEKAKESGAKVIVADPR 171
                                       88899988776645533333.....4578999************************.99999999999********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                        ++++  ad++l i+pg+d +l+ +m++vi++e + d+ f++ +t g+e ++  l +++  ++++ ++v+a+ + + 
  gi|386001970|ref|YP_005920269.1| 172 ITSTSWMADLHLRINPGSDIDLLRGMMKVIVDEELADERFIEERTEGFEILAASLRGYSLAKASEMTGVPAEEIAQA 248
                                       ***8889*****************************************************************99999 PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       ar +a     s  ++ +g++++  g++++++ ++Lal  g++g+pg+g+  ++Gq++++g ++++g ++  ++ ++ 
  gi|386001970|ref|YP_005920269.1| 249 ARIYARSPA-SSLLYSMGITQHICGTDNVKTCATLALVAGQMGRPGAGVWPMRGQNNVQG-NCDMGGMAEFYPGYRR 323
                                       998888888.66666*********************************************.9999999888888888 PP

                                       TT....HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSS CS
                     Molybdopterin 305 ke....ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlt 377
                                        +      +++aa++ ++l++ p+ +++e+ +++ ++++k++y++g++p++ +a++n+++ al +ld++vv ++++t
  gi|386001970|ref|YP_005920269.1| 324 ASdpksIDFFKAAWEAEDLPLGPGLTATEMTEAALEGKIKAMYIIGEDPVTCDANINKTKAALDNLDFLVVQEIFMT 400
                                       888976778889***************************************************************** PP

                                       HHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHHH CS
                     Molybdopterin 378 stalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLakk 432
                                        ta++aD++LPaa+w Ek++ yt++e+r+q ++qav+p geak+  ++++++ k+
  gi|386001970|ref|YP_005920269.1| 401 ATARMADLVLPAAAWAEKDGSYTSMERRVQWIDQAVPPVGEAKEGLWVINEIGKR 455
                                       ****************************************************986 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   5.3e-35   3.2e-31       2     109 ..     541     642 ..     540     644 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 5.3e-35
                                       EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEE CS
                   Molydop_binding   2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmp 77 
                                        L tgr + +++s+ +tr++++l +++p  +veinpedAa+l i +Gd+V+ve+ rG++e+ra+vt+rv+pG+vfmp
  gi|386001970|ref|YP_005920269.1| 541 LLSTGRIVVHYNSGSMTRRSPSLLDRDPeLYVEINPEDAARLLICEGDMVKVETVRGEAEARARVTKRVKPGMVFMP 617
                                       699************************************************************************** PP

                                       SSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding  78 fgwweagekggnaNaltddatdplsgtpefks 109
                                       f+w +       +N +t+da+dp++++pe+k 
  gi|386001970|ref|YP_005920269.1| 618 FHWQA-------TNIITSDALDPIAKIPEYKM 642
                                       ***88.......******************96 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.095      32      55 .]       6      29 ..       1      29 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                      -TTSTTTTT---HHHHTCHHCCCB CS
                    Molybdop_Fe4S4 32 dpdhpvnegrlCvKGrtllervyn 55
                                       + hp+ eg lC+KG+++le+++n
  gi|386001970|ref|YP_005920269.1|  6 MKGHPACEGALCPKGNAVLEILNN 29
                                      577*****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4253.76
//
Query:       gi|386001971|ref|YP_005920270.1|  [L=439]
Description: Molybdenum formylmethanofuran dehydrogenase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-07   29.7   0.0    4.4e-07   29.2   0.0    1.3  1  Molybdopterin  Molybdopterin oxidoreductase
  ------ inclusion threshold ------
      0.033   13.9   0.0       0.15   11.8   0.0    2.1  2  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.9e-11   4.4e-07       1     176 [.      48     212 ..      48     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.9e-11
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       R++ Pm+      +G+ + v W eA e  a+ l +    + p    +   g+ +s+e++ ++  l + lg      +
  gi|386001971|ref|YP_005920270.1|  48 RIREPMMT---V-DGEQRAVPWAEAIERAAEILIE---SKRP----LIFMGSETSCEAMEVGLHLGEFLGA----AV 109
                                       999*****...6.9999********9999999988...8888....7777888999999999888888888....67 PP

                                       ECCGGGTTHHHH...CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHH........HHHHHHHHHTTC-E CS
                     Molybdopterin  78 dwyadlppasaq...qtigsdsrsnyessnpledlensdliilwGsNvreerpil........narirkaalkkkak 143
                                       d++  ++++ ++   q  +++ + + + ++++      dl + wGsN+ e +p           ++  ++ +++   
  gi|386001971|ref|YP_005920270.1| 110 DSNSTVCHGPTAmgiQ--EAGRVGATAGNSKIR----GDLAVYWGSNPLESMPRHmsryaiypRGHWTRRGRFD-RT 179
                                       7777777777655323..333355566666666....9*************99997777666666666666664.78 PP

                                       EEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHH CS
                     Molybdopterin 144 vivigpryaellkfadewlaikpgtdaalalam 176
                                       vi ++pr + +++  d+++ +kp++d +l+ a+
  gi|386001971|ref|YP_005920270.1| 180 VITVDPRRSPTAENSDLHVQLKPNSDYELLSAL 212
                                       *****************************6554 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.7e-05      0.15       1      29 [.      69      96 ..      69     118 .. 0.80
   2 ?   -1.9   0.0      0.28   2.5e+03       2      34 ..     237     269 ..     236     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHH-SSEEEEE-CHHCHTTGHH CS
                      TPP_enzyme_M  1 iekaaellkaakrpvilvGggvarsgase 29
                                      ie+aae+l ++krp+i++G++++  +a e
  gi|386001971|ref|YP_005920270.1| 69 IERAAEILIESKRPLIFMGSETS-CEAME 96
                                      79******************998.44444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.28
                                       HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHH CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrel 34 
                                       e++++++k      i+vG g+a+s  ++  +el
  gi|386001971|ref|YP_005920270.1| 237 EEMVDMMKGCNFGTIYVGLGIASSYGKHRNAEL 269
                                       67788888888899******9988666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3035.69
//
Query:       gi|386001972|ref|YP_005920271.1|  [L=130]
Description: Molybdenum formylmethanofuran dehydrogenase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete 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-08   33.1   0.0    4.8e-08   33.0   0.0    1.2  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.7e-12   4.8e-08       3     108 ..       7     103 ..       5     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.7e-12
                                       EEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTE..EEEEEEEEESSB-TTEEEEE CS
                   Molydop_binding   3 LitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrG..svevrakvtervrpGvvfmp 77 
                                       L++g++ ++       ++  +++k e++v+ inp+d + lG     +V+v+   G  sv v a+ + +++pG+vfmp
  gi|386001972|ref|YP_005920271.1|   7 LNSGSTINEGRLAKGGDKFTEAYKMECAVCSINPADFEVLG--RPNRVRVAEVDGsrSVAVHAREDGSIPPGQVFMP 81 
                                       677777777777777888889999999**************..999*********99999999************** PP

                                       SSHCC.....S-GHCTS--SCSTTT--CSTT CS
                   Molydop_binding  78 fgwweagekggnaNaltddatdplsgtpefk 108
                                        + w+        N+++d + +  +g+p +k
  gi|386001972|ref|YP_005920271.1|  82 RAIWA--------NVVVD-PETFSTGSPLYK 103
                                       *****........99994.444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 750.82
//
Query:       gi|386001973|ref|YP_005920272.1|  [L=274]
Description: Molybdenum formylmethanofuran dehydrogenase subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-07   30.8  20.5    4.5e-07   29.6  20.3    1.5  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  20.3   2.5e-11   4.5e-07      31     169 ..      93     226 ..      80     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.5e-11
                                       EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--SEEEEES CS
                             GXGXG  31 tikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaeeniivGnvvlygatgGklfir 107
                                       + +i+++GsaG  lg  +  G ++++ G+a   +G +++gG + + ++     +++ ++  G     g+tgGk+ i 
  gi|386001973|ref|YP_005920272.1|  93 SGRIEIRGSAGMHLGSEM-AGGEIRVRGNAGPWAGMNMTGGLLEVGGDVG---DHAGSAYRG--SWRGMTGGKILIC 163
                                       45799*************.899*************************994...344444445..578********** PP

                                       SB--SSTTTT-SS-EEEESEB-SSTTTT-.EEEEEEE-S-B-SSBTTT--EEEEEEE-SSSTH CS
                             GXGXG 108 gkageRfavrnsgatavvegvgdhgceYm.tGGvvvvLgktgrnfaaGmsgGiayvldedekf 169
                                       g+a +  +  + g ++vv+g  ++ c     GG +vv  +  r ++a m gG++ vl + ++f
  gi|386001973|ref|YP_005920272.1| 164 GNARSQLGGGMAGGEIVVGGSVENFCGIRqNGGLIVVGKDAVRGVGAEMVGGSIVVLGRIQQF 226
                                       *********************66655555055555555556899***********99766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1776.90
//
Query:       gi|386001974|ref|YP_005920273.1|  [L=589]
Description: Molybdenum formylmethanofuran dehydrogenase subunit A [Methanosaeta harundinacea 6Ac]
Scores for 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-95  320.4   4.7    3.6e-95  320.2   4.7    1.1  1  Amidohydro_3  Amidohydrolase family
    2.7e-05   23.7   2.0      0.035   13.4   0.0    2.9  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.29   10.8   0.0    1.6  1  GSIII_N       Glutamine synthetase type III N terminal


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.2   4.7     6e-99   3.6e-95       1     473 []      45     521 ..      45     521 .. 0.97

  Alignments for each domain:
  == domain 1  score: 320.2 bits;  conditional E-value: 6e-99
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerf 76 
                                       e+iDa+G++v+PG+vDsH+H+ag++vn+ rl+r++d        ++  vr + +       ++g+G+++++++++++
  gi|386001974|ref|YP_005920273.1|  45 ETIDARGKTVMPGGVDSHAHVAGAKVNAgRLMRPED--------HIGSVRHRTEI-----AHSGSGYTVPSVYKQGY 108
                                       79**********************************........78889999998.....57*************** PP

                      Amidohydro_3  77 pyalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlapl 153
                                        y+ +++++v+e+a+++l+a++tH+++r++++ld+            g++l+ +n+++++++l+ g           
  gi|386001974|ref|YP_005920273.1| 109 EYSAMGYTTVFEAAMPPLEARHTHEEMRSTPMLDM------------GAYLVLGNNWFLMRYLHQG----------- 162
                                       **********************************8............*****************99........... PP

                      Amidohydro_3 154 areaeaaavaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls 223
                                       ++e+ aa+va++++ +++yGi++v       +++g+nv+sld+++++fe+ta+e      +i++l++++erlg p s
  gi|386001974|ref|YP_005920273.1| 163 EIEKAAAYVAWMMKTHKAYGIKCVnpagvenWGWGKNVHSLDEPNIHFEVTARE------VIHGLAEVNERLGMPIS 233
                                       ******************************************************......889************** PP

                      Amidohydro_3 224 ..........pgseeltigavklfadgvl................gsrtalltepyf.....tgwpdfedea..lae 267
                                                 pg++e+t++++++  d ++                + ++++l++ +f     t+w+dfe++a  la+
  gi|386001974|ref|YP_005920273.1| 234 lhlhannlghPGNAEITKDSLAIPSDFAPvqkmgvewaetkmdphRAQSVYLAHAQFnafggTSWRDFESGAegLAR 310
                                       **************************5555555556899999999******************************** PP

                      Amidohydro_3 268 lvaaadergldvaihaigdaavd..dvldafeaa......aekngnqdrrrlehaegv...tesqiervaalqvaag 333
                                       +v++ad++ +d + + +g a+ +  d++   + +      ++k++n+d+ +le ++gv   t+ + +++ a+q+a+g
  gi|386001974|ref|YP_005920273.1| 311 YVNKADHVVIDNGAVPFGPATCMtgDGPSIHDLYvlagigGQKWSNTDV-ELECGSGVlpfTYLKGNPISAIQWAIG 386
                                       *************************999999999999***********9.*************************** PP

                      Amidohydro_3 334 vqpvfnfedelldsrlgperargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.......... 399
                                       ++                        + ++ ++++k+++++D +++g+f+++p ++a++m++ +r++          
  gi|386001974|ref|YP_005920273.1| 387 LE------------------------MLLMVDDPWKTIMTTDhPNGGVFTKYPQVIAWLMSRRARDAtaaechkwgy 439
                                       **........................99************************************************* PP

                      Amidohydro_3 400 ...evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.....vrltvvd 468
                                           + + ++e++l e++ l+++++A+++g+  rkG+L++Gad+D++v+d+dp  + p++  e+      + lt++d
  gi|386001974|ref|YP_005920273.1| 440 drsSLGGVEREMTLFEIAILTRANAARTIGMAYRKGHLGAGADGDVAVYDIDPENFNPADSDEVIrafsrADLTIKD 516
                                       *********************************************************996655559*********** PP

                      Amidohydro_3 469 Grvvy 473
                                       G+vv+
  gi|386001974|ref|YP_005920273.1| 517 GKVVV 521
                                       ***97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.6   0.00027       1.6       1      20 [.      53      71 ..      53     248 .. 0.73
   2 !   13.4   0.0   5.9e-06     0.035     261     344 .]     435     520 ..     389     521 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00027
                                      EEEE-EEEEEEECETTECSS CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqsllrg 20
                                      +v+PG++D+H H+ +   ++
  gi|386001974|ref|YP_005920273.1| 53 TVMPGGVDSHAHVAGAK-VN 71
                                      69**********98554.33 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT........CGGGTTTC CS
                      Amidohydro_1 261 lrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi........laafvglk 329
                                        ++++   r++l ++ e  ++l e+  ++  n+A+ +g++ ++G + +G d D +v d d+         + +   +
  gi|386001974|ref|YP_005920273.1| 435 HKWGY--DRSSLGGV-EREMTLFEIAILTRANAARTIGMAYRKGHLGAGADGDVAVYDIDPenfnpadsDEVIRAFS 508
                                       44444..44444445.555999998888889**************************87554555454444444444 PP

                                       TSEEEEEEEETTEEE CS
                      Amidohydro_1 330 kdgnvkkvivkGklv 344
                                       +    + +i++Gk+v
  gi|386001974|ref|YP_005920273.1| 509 R---ADLTIKDGKVV 520
                                       4...55666677765 PP

>> GSIII_N  Glutamine synthetase type III N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.9e-05      0.29      62     102 ..       9      46 ..       4      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                           GSIII_N  62 tHwFqPltgltaekhdsflelekdgkvieefsgkelikgEp 102
                                        H+F Pl+g+ +e +d f++   dgkv++++sg +l+  E+
  gi|386001974|ref|YP_005920273.1|   9 GHVFDPLNGIDGEVMDVFIK---DGKVVNDLSGADLAWAET 46 
                                       6******************6...99***********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 3440.27
//
Query:       gi|386001975|ref|YP_005920274.1|  [L=342]
Description: Molybdenum formylmethanofuran dehydrogenase, subunit F [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-52  171.8  80.4    1.6e-08   34.0   3.4    8.2  8  Fer4      4Fe-4S binding domain
    3.4e-40  136.4  92.3    1.3e-12   48.1   8.9    5.5  6  Fer4_7    4Fe-4S dicluster domain
    1.3e-34  118.9  50.6    8.5e-11   42.6   6.1    7.3  7  Fer4_16   4Fe-4S double cluster binding domain
    4.5e-33  112.0  85.7    4.4e-07   29.7   2.7    8.2  8  Fer4_6    4Fe-4S binding domain
    1.8e-32  111.2  56.6    4.1e-09   36.4   5.4    6.1  7  Fer4_9    4Fe-4S dicluster domain
    1.2e-31  108.6  62.8    3.8e-07   30.1   8.7    7.2  8  Fer4_10   4Fe-4S dicluster domain
    6.7e-30  103.0  63.5    1.1e-06   28.7   7.6    6.6  6  Fer4_21   4Fe-4S dicluster domain
    3.4e-26   89.7  77.8    2.9e-05   23.9   2.0    8.2  8  Fer4_2    4Fe-4S binding domain
    6.3e-22   77.8  52.0      9e-09   35.7   4.8    5.8  5  Fer4_8    4Fe-4S dicluster domain
    8.2e-18   63.4  73.9     0.0003   21.0   2.0    8.2  8  Fer4_4    4Fe-4S binding domain
    8.8e-18   64.6  55.2    3.4e-05   24.3   5.6    6.9  7  Fer4_17   4Fe-4S dicluster domain
      4e-13   49.3 108.5     0.0053   17.6   5.6    8.3  8  Fer4_3    4Fe-4S binding domain
    6.1e-10   39.7  59.9      0.062   14.0   0.2    8.7  8  Fer4_15   4Fe-4S single cluster domain
    7.4e-10   39.2  73.7      0.046   14.3   2.6    8.3  8  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.3e-08   35.0  59.4      0.031   14.5   0.3    7.8  7  Fer4_18   4Fe-4S dicluster domain
    7.7e-07   29.9  65.4      0.078   13.8   1.0    8.1  9  Fer4_22   4Fe-4S dicluster domain
     0.0014   18.7   0.5     0.0014   18.7   0.5    6.3  7  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   4.8   2.9e-09     3e-06       4      21 ..      17      34 ..      15      34 .. 0.89
   2 !   22.8   2.1   5.2e-08   5.5e-05       7      24 .]      61      78 ..      56      78 .. 0.89
   3 !   28.2   6.0     1e-09   1.1e-06       4      24 .]     101     121 ..      98     121 .. 0.90
   4 !   34.0   3.4   1.5e-11   1.6e-08       1      24 []     139     162 ..     139     162 .. 0.95
   5 !   19.1   1.3   7.6e-07    0.0008       6      23 ..     176     193 ..     172     194 .. 0.88
   6 !   30.7   3.5   1.7e-10   1.8e-07       5      24 .]     211     230 ..     207     230 .. 0.90
   7 !   32.2   2.2   5.6e-11   5.9e-08       3      23 ..     265     285 ..     263     286 .. 0.92
   8 !   21.1   3.1   1.7e-07   0.00018       1      23 [.     312     334 ..     312     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.9e-09
                                      ETTTSSS-THHHHHSTTT CS
                              Fer4  4 deekCigCGaCvevCPvg 21
                                       +ekCigCG+Cv++CP g
  gi|386001975|ref|YP_005920274.1| 17 LPEKCIGCGTCVQICPKG 34
                                      59**************76 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 5.2e-08
                                      TSSS-THHHHHSTTTEEE CS
                              Fer4  7 kCigCGaCvevCPvgAIt 24
                                       C++C +C+ vCP+gA++
  gi|386001975|ref|YP_005920274.1| 61 GCVFCALCARVCPTGALE 78
                                      5***************85 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 1e-09
                                       ETTTSSS-THHHHHSTTTEEE CS
                              Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                         e+C++CG+C+evCP g+I+
  gi|386001975|ref|YP_005920274.1| 101 VNERCVHCGLCAEVCPQGCIE 121
                                       679****************96 PP

  == domain 4  score: 34.0 bits;  conditional E-value: 1.5e-11
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++id ++C++CG C+ vCP +AIt
  gi|386001975|ref|YP_005920274.1| 139 IQIDLDRCVHCGWCAAVCPKDAIT 162
                                       68*********************7 PP

  == domain 5  score: 19.1 bits;  conditional E-value: 7.6e-07
                                       TTSSS-THHHHHSTTTEE CS
                              Fer4   6 ekCigCGaCvevCPvgAI 23 
                                         C +C +Cv+ CP +A+
  gi|386001975|ref|YP_005920274.1| 176 QICQACRTCVDTCPANAL 193
                                       57***************8 PP

  == domain 6  score: 30.7 bits;  conditional E-value: 1.7e-10
                                       TTTSSS-THHHHHSTTTEEE CS
                              Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                        + Ci+CGaC+++CPv AI+
  gi|386001975|ref|YP_005920274.1| 211 RDACIYCGACAQACPVAAIS 230
                                       799***************96 PP

  == domain 7  score: 32.2 bits;  conditional E-value: 5.6e-11
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                        d + C gCG+Cv vCPv+A+
  gi|386001975|ref|YP_005920274.1| 265 TDRDACLGCGNCVIVCPVNAL 285
                                       699*****************8 PP

  == domain 8  score: 21.1 bits;  conditional E-value: 1.7e-07
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       vv+d++ C  C +C  +CP++AI
  gi|386001975|ref|YP_005920274.1| 312 VVVDQDVCGSCATCSLICPTEAI 334
                                       69********************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   2.3   7.2e-07   0.00076      27      51 ..      10      34 ..       3      35 .. 0.77
   2 !   29.5  10.9   7.8e-10   8.2e-07       1      52 []      20      76 ..      20      76 .. 0.75
   3 !   48.1   8.9   1.3e-15   1.3e-12       1      52 []     104     160 ..     104     160 .. 0.86
   4 !   34.4  11.5   2.3e-11   2.5e-08       2      52 .]     178     228 ..     177     228 .. 0.92
   5 !   37.8  12.5     2e-12   2.1e-09       1      52 []     213     284 ..     213     284 .. 0.68
   6 !   34.0   6.5     3e-11   3.2e-08       1      52 []     269     333 ..     269     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.2e-07
                            Fer4_7 27 gtekveidpekClgCgaCvavCPtg 51
                                      g +  ++ pekC+gCg Cv+ CP+g
  gi|386001975|ref|YP_005920274.1| 10 GEKAQVYLPEKCIGCGTCVQICPKG 34
                                      434445679**************87 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.8e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.gt..ekv...eidpekClgCgaCvavCPtga 52
                                      +CigCg Cv+ Cp + + +  +   + g   +     + ++  C++C  C++vCPtga
  gi|386001975|ref|YP_005920274.1| 20 KCIGCGTCVQICPKGELVIGSVGAVArGLidK-EfleKRNSGGCVFCALCARVCPTGA 76
                                      7****************999884433133431.1232456778*************98 PP

  == domain 3  score: 48.1 bits;  conditional E-value: 1.3e-15
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.gt....ekveidpekClgCgaCvavCPtga 52 
                                       rC++Cg C+++Cp+++iel+++  ++ g      k++id ++C++Cg C+avCP++a
  gi|386001975|ref|YP_005920274.1| 104 RCVHCGLCAEVCPQGCIELEDRRLAEdGSlrleGKIQIDLDRCVHCGWCAAVCPKDA 160
                                       8******************9875444322555589*******************997 PP

  == domain 4  score: 34.4 bits;  conditional E-value: 2.3e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C  C+ Cv++Cp++a+  +   + + +ekv+++ + C++CgaC+++CP+ a
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPANALFNRSWRQGEIVEKVTHRRDACIYCGACAQACPVAA 228
                                       99**************998877777779********************986 PP

  == domain 5  score: 37.8 bits;  conditional E-value: 2e-12
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt...ekv..................eidpekClgCgaCvavCPtga 52 
                                       +Ci CgaC++aCpv ai++++ +  +++   + +                  + d + ClgCg+Cv vCP++a
  gi|386001975|ref|YP_005920274.1| 213 ACIYCGACAQACPVAAISVRKTAIVPEMkgkK-AfekklseaaprptltsilKTDRDACLGCGNCVIVCPVNA 284
                                       5*****************99743333222220.1222223333444445555999****************97 PP

  == domain 6  score: 34.0 bits;  conditional E-value: 3e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaie........ldeeenek.....gtekveidpekClgCgaCvavCPtga 52 
                                       +C gCg+Cv +Cpv+a++        l+e e+++       + v++d++ C +C  C   CPt+a
  gi|386001975|ref|YP_005920274.1| 269 ACLGCGNCVIVCPVNALSdpylaaghLNELEKKPlleveNGAIVVVDQDVCGSCATCSLICPTEA 333
                                       5*****************5544444433333332444433388899*****************87 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.6   2.8e-05      0.03      53      66 ..      20      33 ..       7      43 .. 0.67
   2 !   18.3   0.2   3.3e-06    0.0034       2      28 ..      62      88 ..      61      98 .. 0.82
   3 !   20.8   1.2   5.4e-07   0.00057       1      22 [.     104     125 ..     104     137 .. 0.85
   4 !   19.5   0.8   1.4e-06    0.0014       1      21 [.     145     165 ..     145     173 .. 0.89
   5 !   17.2   0.9   7.1e-06    0.0075       2      26 ..     178     199 ..     177     212 .. 0.77
   6 !   42.6   6.1     8e-14   8.5e-11       2      67 .]     214     283 ..     213     288 .. 0.66
   7 !   14.8   1.4   3.9e-05     0.041       2      22 ..     319     339 ..     318     342 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-05
                           Fer4_16 53 aitgCdiCqdvCPa 66
                                      +++gC++C+++CP 
  gi|386001975|ref|YP_005920274.1| 20 KCIGCGTCVQICPK 33
                                      55555555555553 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.3e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiear 28
                                      C+ C  Ca vCPt+a++ + + ++e++
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPTGALEVRVSGKAEKD 88
                                      999**************9966665544 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 5.4e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                       rC+ Cg CaevCP+++i+ + +
  gi|386001975|ref|YP_005920274.1| 104 RCVHCGLCAEVCPQGCIELEDR 125
                                       6*****************9843 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 1.4e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                       rC+ Cg Ca vCP +ai+ +k
  gi|386001975|ref|YP_005920274.1| 145 RCVHCGWCAAVCPKDAITFQK 165
                                       6****************9884 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 7.1e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeie 26 
                                       C+ C+ C+++CP+na+ ++   +++
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPANALFNR---SWR 199
                                       ***************9877...444 PP

  == domain 6  score: 42.6 bits;  conditional E-value: 8e-14
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.....ntaekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                       C+ Cg+Ca++CP++ai+ +k + i ++++ ++       +   + + ++  ++ + a+ gC++C+ vCP+n
  gi|386001975|ref|YP_005920274.1| 214 CIYCGACAQACPVAAISVRK-TAIVPEMKGKKafekkLSEAAPRPTLTSILKTDRDACLGCGNCVIVCPVN 283
                                       *****************994.444433333332333322222223333333444699************98 PP

  == domain 7  score: 14.8 bits;  conditional E-value: 3.9e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       Cg+C  C  +CPt+ai  +k+
  gi|386001975|ref|YP_005920274.1| 319 CGSCATCSLICPTEAIWLEKR 339
                                       ****************88755 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.8   6.1e-08   6.4e-05       6      22 ..      18      34 ..      15      38 .. 0.88
   2 !   10.2   4.3    0.0006      0.64       9      24 .]      62      77 ..      62      77 .. 0.89
   3 !   14.5   7.1   2.7e-05     0.029       7      23 ..     103     119 ..     101     120 .. 0.88
   4 !   22.6   3.6   7.2e-08   7.6e-05       1      24 []     138     161 ..     138     161 .. 0.95
   5 !   19.4   2.7   7.5e-07   0.00079       5      24 .]     174     193 ..     171     193 .. 0.92
   6 !   18.7   4.6   1.3e-06    0.0014       1      24 []     206     229 ..     206     229 .. 0.95
   7 !   29.7   2.7   4.2e-10   4.4e-07       5      24 .]     266     285 ..     262     285 .. 0.94
   8 !   17.6   4.2   2.8e-06     0.003       1      24 []     311     334 ..     311     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.1e-08
                            Fer4_6  6 pdkCigCgdCvrvCPeg 22
                                      p+kCigCg Cv +CP g
  gi|386001975|ref|YP_005920274.1| 18 PEKCIGCGTCVQICPKG 34
                                      89*************75 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0006
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      C+ C  C+rvCP+ga+
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPTGAL 77
                                      666***********97 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.7e-05
                            Fer4_6   7 dkCigCgdCvrvCPega 23 
                                       ++C++Cg C+ vCP g 
  gi|386001975|ref|YP_005920274.1| 103 ERCVHCGLCAEVCPQGC 119
                                       79************775 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 7.2e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +++id d+C++Cg C++vCP +ai
  gi|386001975|ref|YP_005920274.1| 138 KIQIDLDRCVHCGWCAAVCPKDAI 161
                                       689*****************9998 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 7.5e-07
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       d++ C  C+ Cv+ CP++a+
  gi|386001975|ref|YP_005920274.1| 174 DDQICQACRTCVDTCPANAL 193
                                       999***************97 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 1.3e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +v++ +d+Ci Cg+C+ +CP +ai
  gi|386001975|ref|YP_005920274.1| 206 KVTHRRDACIYCGACAQACPVAAI 229
                                       68999****************998 PP

  == domain 7  score: 29.7 bits;  conditional E-value: 4.2e-10
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       d+d+C+gCg+Cv+vCP +a+
  gi|386001975|ref|YP_005920274.1| 266 DRDACLGCGNCVIVCPVNAL 285
                                       9****************997 PP

  == domain 8  score: 17.6 bits;  conditional E-value: 2.8e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +v++d+d C +C  C  +CP+ ai
  gi|386001975|ref|YP_005920274.1| 311 IVVVDQDVCGSCATCSLICPTEAI 334
                                       69*******************998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.8   2.8e-07    0.0003      33      49 ..      15      34 ..       6      36 .. 0.73
   2 !   36.4   5.4   3.9e-12   4.1e-09       1      50 [.      20      76 ..      20      77 .. 0.96
   3 !   26.1  11.3   6.7e-09   7.1e-06       2      51 .]      62     120 ..      61     120 .. 0.88
   4 !   19.7   0.3   6.6e-07    0.0007      33      51 .]     140     161 ..     121     161 .. 0.75
   5 !   31.5  11.6   1.4e-10   1.5e-07       2      51 .]     178     229 ..     177     229 .. 0.83
   6 !   19.5   0.6   7.5e-07   0.00079      33      50 ..     257     284 ..     234     285 .. 0.69
   7 !   22.7   9.0     8e-08   8.4e-05       1      51 []     269     334 ..     269     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-07
                            Fer4_9 33 e...eaCigCgaCveaCpkg 49
                                          e+CigCg+Cv++Cpkg
  gi|386001975|ref|YP_005920274.1| 15 VylpEKCIGCGTCVQICPKG 34
                                      134468************97 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 3.9e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkga 50
                                      kC+gCg+Cv+ Cp+g  v  +++  ar  +++e         C++C  C+ +Cp+ga
  gi|386001975|ref|YP_005920274.1| 20 KCIGCGTCVQICPKGELVIGSVGAVARGLIDKEflekrnsGGCVFCALCARVCPTGA 76
                                      7***************************99999*******99*************97 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 6.7e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCgaCveaCpkgai 51 
                                       C+ C  C ++Cp+g+ + + +++  + + + +         e+C++Cg C+e+Cp+g+i
  gi|386001975|ref|YP_005920274.1|  62 CVFCALCARVCPTGALEVRVSGKAEKDDSYLNfalsptlvnERCVHCGLCAEVCPQGCI 120
                                       ****************8888887777655544899*********************987 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 6.6e-07
                            Fer4_9  33 e...eaCigCgaCveaCpkgai 51 
                                       +   ++C++Cg C+++Cpk+ai
  gi|386001975|ref|YP_005920274.1| 140 QidlDRCVHCGWCAAVCPKDAI 161
                                       044468*************997 PP

  == domain 5  score: 31.5 bits;  conditional E-value: 1.4e-10
                            Fer4_9   2 CtgCgaCveaCpagvv.vedaaerkarlraase.eaCigCgaCveaCpkgai 51 
                                       C  C++Cv+ Cpa++  ++++ ++++  + +   +aCi CgaC++aCp  ai
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPANALfNRSWRQGEIVEKVTHRrDACIYCGACAQACPVAAI 229
                                       **************9867777777766665555789************9887 PP

  == domain 6  score: 19.5 bits;  conditional E-value: 7.5e-07
                            Fer4_9  33 e..........eaCigCgaCveaCpkga 50 
                                                  +aC+gCg Cv +Cp +a
  gi|386001975|ref|YP_005920274.1| 257 PtltsilktdrDACLGCGNCVIVCPVNA 284
                                       1444445555579************986 PP

  == domain 7  score: 22.7 bits;  conditional E-value: 8e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpkgai 51 
                                       +C gCg+Cv +Cp ++ ++   +    ++ +++               + C +C +C  +Cp++ai
  gi|386001975|ref|YP_005920274.1| 269 ACLGCGNCVIVCPVNALSDPYLAAGHLNELEKKpllevengaivvvdqDVCGSCATCSLICPTEAI 334
                                       6****************999999998888877799*************99*************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   8.7   3.6e-10   3.8e-07       4      56 .]      16      73 ..      13      73 .. 0.93
   2 !   13.6   1.2   5.1e-05     0.054       5      32 ..      58      85 ..      54      91 .. 0.69
   3 !   24.1  13.9   2.8e-08   2.9e-05       6      56 .]     102     157 ..      97     157 .. 0.93
   4 !   19.2   2.2   9.3e-07   0.00098       1      22 [.     138     159 ..     138     167 .. 0.86
   5 !   28.4  13.1   1.2e-09   1.3e-06       4      56 .]     173     225 ..     170     225 .. 0.83
   6 !   19.0   2.8   1.1e-06    0.0011       2      28 ..     207     233 ..     206     252 .. 0.68
   7 !   23.5   0.1   4.1e-08   4.4e-05       3      23 ..     264     284 ..     262     308 .. 0.77
   8 !   16.3   0.8   7.3e-06    0.0077       2      21 ..     312     331 ..     311     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.6e-10
                           Fer4_10  4 idddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + +++Ci+Cg+Cv+ CP         + +a+g +++e  ++ +++ C +c  C+++CP
  gi|386001975|ref|YP_005920274.1| 16 YLPEKCIGCGTCVQICPKGElvigsVGAVARGLIDKEFLEKRNSGGCVFCALCARVCP 73
                                      6689**************88***9999999999999999999***************9 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.1e-05
                           Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgea 32
                                      ++  C+ C+ C ++CP+ + +v+++g+a
  gi|386001975|ref|YP_005920274.1| 58 NSGGCVFCALCARVCPTGALEVRVSGKA 85
                                      5667************977444444444 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.8e-08
                           Fer4_10   6 ddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        ++C++Cg C ++CP+       ++    g    e+++++++++C +cg C+++CP
  gi|386001975|ref|YP_005920274.1| 102 NERCVHCGLCAEVCPQGCieledRRLAEDGSLRLEGKIQIDLDRCVHCGWCAAVCP 157
                                       689*************8899999888999999999********************9 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 9.3e-07
                           Fer4_10   1 kvvidddtCirCgkCvkaCPad 22 
                                       k++id d+C++Cg C ++CP d
  gi|386001975|ref|YP_005920274.1| 138 KIQIDLDRCVHCGWCAAVCPKD 159
                                       589*****************84 PP

  == domain 5  score: 28.4 bits;  conditional E-value: 1.2e-09
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +dd+ C  C++Cv+ CPa++  ++   + ++ e+v +  ++C+ cgaC++aCP
  gi|386001975|ref|YP_005920274.1| 173 RDDQICQACRTCVDTCPANALFNRSWRQGEIVEKVTHRRDACIYCGACAQACP 225
                                       6999**************8855555566666666667779************9 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 1.1e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvga 28 
                                       v + +d Ci Cg+C +aCP+ + sv++
  gi|386001975|ref|YP_005920274.1| 207 VTHRRDACIYCGACAQACPVAAISVRK 233
                                       567789**************6533333 PP

  == domain 7  score: 23.5 bits;  conditional E-value: 4.1e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadl 23 
                                       + d+d C++Cg+Cv +CP+++
  gi|386001975|ref|YP_005920274.1| 264 KTDRDACLGCGNCVIVCPVNA 284
                                       5799***************65 PP

  == domain 8  score: 16.3 bits;  conditional E-value: 7.3e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                       vv+d+d C  C++C   CP+
  gi|386001975|ref|YP_005920274.1| 312 VVVDQDVCGSCATCSLICPT 331
                                       799****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.3   6.8e-06    0.0072      33      53 ..      13      33 ..       5      39 .. 0.76
   2 !   26.9  10.1   3.7e-09   3.9e-06       5      57 ..      18      77 ..      15      79 .. 0.73
   3 !   23.4   1.6   4.5e-08   4.8e-05      35      58 ..      99     121 ..      84     122 .. 0.87
   4 !   28.7   7.6     1e-09   1.1e-06       2      53 ..     140     190 ..     139     194 .. 0.82
   5 !   27.0  12.6   3.4e-09   3.6e-06       5      55 ..     211     283 ..     207     286 .. 0.71
   6 !   16.2   1.2   8.3e-06    0.0088      28      57 ..     306     334 ..     300     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.8e-06
                           Fer4_21 33 vlkvvedeCvGCnlCssvCPv 53
                                         ++ ++C+GC  C+++CP 
  gi|386001975|ref|YP_005920274.1| 13 AQVYLPEKCIGCGTCVQICPK 33
                                      444568999999999999994 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.7e-09
                           Fer4_21  5 edkCigCgkCliaCedtshqai.........eidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      ++kCigCg C++ C++ +   i          id++   k  +  Cv C+lC+ vCP+ +++
  gi|386001975|ref|YP_005920274.1| 18 PEKCIGCGTCVQICPK-GELVIgsvgavargLIDKEFLEKRNSGGCVFCALCARVCPT-GAL 77
                                      589************7.4444444444465435544455666889************6.766 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 4.5e-08
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedcie 58 
                                       ++v+++Cv C lC++vCP ++cie
  gi|386001975|ref|YP_005920274.1|  99 TLVNERCVHCGLCAEVCP-QGCIE 121
                                       5689**************.7***8 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 1e-09
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvv..edeCvGCnlCssvCPv 53 
                                       +id d+C++Cg C+ +C+    +ai++++    +    ++ C +C  C++ CP 
  gi|386001975|ref|YP_005920274.1| 140 QIDLDRCVHCGWCAAVCP---KDAITFQKPFAGEFFrdDQICQACRTCVDTCPA 190
                                       5999**************...5***9987765555422668************6 PP

  == domain 5  score: 27.0 bits;  conditional E-value: 3.4e-09
                           Fer4_21   5 edkCigCgkCliaCedtshqai......eidaktvl.................kvvedeCvGCnlCssvCPved 55 
                                       +d Ci Cg C++aC+ +++         e+++k+ +                 k+  d C GC  C++vCPv +
  gi|386001975|ref|YP_005920274.1| 211 RDACIYCGACAQACPVAAISVRktaivpEMKGKKAFekklseaaprptltsilKTDRDACLGCGNCVIVCPV-N 283
                                       689************765432233336634444333555666677777777768899**************9.4 PP

  == domain 6  score: 16.2 bits;  conditional E-value: 8.3e-06
                           Fer4_21  28 idaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +++ +++ v +d C  C+ Cs +CP+ ++i
  gi|386001975|ref|YP_005920274.1| 306 VENGAIVVVDQDVCGSCATCSLICPT-EAI 334
                                       55566777889**************7.766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   2.0   2.7e-08   2.9e-05       4      21 ..      15      32 ..      12      33 .. 0.91
   2 ?    3.4   3.8     0.092        97      10      22 .]      62      74 ..      56      74 .. 0.85
   3 !   18.3   3.4   1.6e-06    0.0017       7      22 .]     102     117 ..      97     117 .. 0.85
   4 !   18.8   2.0   1.1e-06    0.0012       2      21 ..     138     157 ..     137     158 .. 0.94
   5 !   16.0   2.8   9.1e-06    0.0096       4      22 .]     172     190 ..     169     190 .. 0.89
   6 !   16.5   3.5     6e-06    0.0063       7      21 ..     211     225 ..     205     226 .. 0.87
   7 !   21.1   2.7   2.1e-07   0.00022       5      21 ..     265     281 ..     262     282 .. 0.91
   8 !   14.6   3.4   2.5e-05     0.026       2      22 .]     311     331 ..     310     331 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.7e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+ +++CigCg+Cv+ CP
  gi|386001975|ref|YP_005920274.1| 15 VYLPEKCIGCGTCVQICP 32
                                      6889*************9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.092
                            Fer4_2 10 CigCgaCvsaCPa 22
                                      C+ C  C  +CP+
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPT 74
                                      66699*******7 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.6e-06
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                        +rC++Cg C  +CP+
  gi|386001975|ref|YP_005920274.1| 102 NERCVHCGLCAEVCPQ 117
                                       589************6 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 1.1e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++++d drC++Cg C  +CP
  gi|386001975|ref|YP_005920274.1| 138 KIQIDLDRCVHCGWCAAVCP 157
                                       689****************9 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 9.1e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       + d ++C +C++Cv+ CPa
  gi|386001975|ref|YP_005920274.1| 172 FRDDQICQACRTCVDTCPA 190
                                       67889*************8 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 6e-06
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +d+Ci CgaC +aCP
  gi|386001975|ref|YP_005920274.1| 211 RDACIYCGACAQACP 225
                                       79************* PP

  == domain 7  score: 21.1 bits;  conditional E-value: 2.1e-07
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                        d+d+C+gCg Cv +CP
  gi|386001975|ref|YP_005920274.1| 265 TDRDACLGCGNCVIVCP 281
                                       699************** PP

  == domain 8  score: 14.6 bits;  conditional E-value: 2.5e-05
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                        vvvd d C +C +C   CP+
  gi|386001975|ref|YP_005920274.1| 311 IVVVDQDVCGSCATCSLICPT 331
                                       689*****************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   6.9   5.1e-07   0.00054       3      64 ..      19      75 ..      17      76 .. 0.73
   2 !   27.9   9.0   2.3e-09   2.4e-06       3      64 ..     103     159 ..     101     160 .. 0.80
   3 !    9.0   1.2    0.0018       1.9      51      64 ..     178     191 ..     174     202 .. 0.74
   4 !   35.7   4.8   8.6e-12     9e-09       3      64 ..     212     283 ..     210     284 .. 0.74
   5 ?    6.5   0.6     0.011        12       4      17 ..     318     331 ..     311     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.1e-07
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ekCi+Cg C + Cp  +         arg   + +  e++     + + C+ c  C++vCp+g
  gi|386001975|ref|YP_005920274.1| 19 EKCIGCGTCVQICPKGELVIgSVGAVARGLIDK-EFLEKR-----NSGGCVFCALCARVCPTG 75
                                      69************7776663444455555444.333333.....5799************87 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.3e-09
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       e+C++Cg+C + Cp    + +++  a+++    + + q       l++C++cg C+ vCp++
  gi|386001975|ref|YP_005920274.1| 103 ERCVHCGLCAEVCPQGCIELEDRRLAEDGSLRLEGKIQI-----DLDRCVHCGWCAAVCPKD 159
                                       69************8888887777777776663444444.....69**************86 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0018
                            Fer4_8  51 CttcgaCtevCpvg 64 
                                       C++c+ C++ Cp +
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPAN 191
                                       66777777777654 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 8.6e-12
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee..........eealwsCttcgaCtevCpvg 64 
                                       ++Ci CgaC +aCpv+  +  k    ++ + ++ + e++  e+          ++  ++C++cg+C+ vCpv+
  gi|386001975|ref|YP_005920274.1| 212 DACIYCGACAQACPVAAISVrKTAIVPEMKGKK-AFEKKLSEAaprptltsilKTDRDACLGCGNCVIVCPVN 283
                                       58************8887773444444444444.44444433367788999999999**************97 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.011
                            Fer4_8   4 kCieCgaCqsaCpv 17 
                                        C+ C  C   Cp+
  gi|386001975|ref|YP_005920274.1| 318 VCGSCATCSLICPT 331
                                       57777777777774 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.0   2.9e-07    0.0003       1      16 [.      18      33 ..      18      39 .. 0.93
   2 ?    5.7   2.6     0.024        25       4      17 .]      62      75 ..      55      75 .. 0.88
   3 !   16.5   3.5     8e-06    0.0084       2      17 .]     103     118 ..     102     118 .. 0.94
   4 !   16.7   1.4   7.1e-06    0.0075       2      16 ..     144     158 ..     143     167 .. 0.90
   5 !   14.5   2.4   3.7e-05     0.039       4      16 ..     178     190 ..     175     195 .. 0.91
   6 !   10.3   2.4   0.00081      0.85       2      16 ..     212     226 ..     211     233 .. 0.92
   7 !   17.1   2.5   5.3e-06    0.0056       2      17 .]     268     283 ..     267     284 .. 0.92
   8 ?    3.1   3.5      0.16   1.7e+02       1      16 [.     316     331 ..     316     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+CigCg Cv +CP 
  gi|386001975|ref|YP_005920274.1| 18 PEKCIGCGTCVQICPK 33
                                      69*************6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      C+ C  C ++CP+g
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPTG 75
                                      888*********86 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 8e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       erC++Cg C  +CPqg
  gi|386001975|ref|YP_005920274.1| 103 ERCVHCGLCAEVCPQG 118
                                       8*************96 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 7.1e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       +rC++Cg C a+CP 
  gi|386001975|ref|YP_005920274.1| 144 DRCVHCGWCAAVCPK 158
                                       9*************4 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 3.7e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+ C+ Cv++CP 
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPA 190
                                       ************6 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00081
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + Ci Cg+C  aCP+
  gi|386001975|ref|YP_005920274.1| 212 DACIYCGACAQACPV 226
                                       78************6 PP

  == domain 7  score: 17.1 bits;  conditional E-value: 5.3e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + C+gCg Cv++CP++
  gi|386001975|ref|YP_005920274.1| 268 DACLGCGNCVIVCPVN 283
                                       78************75 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.16
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       q+ C  C  C  +CP+
  gi|386001975|ref|YP_005920274.1| 316 QDVCGSCATCSLICPT 331
                                       577888999******7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.9   7.6e-05      0.08      42      59 ..      17      34 ..       1      36 [. 0.70
   2 !   19.4   8.1   1.1e-06    0.0012       1      59 [.      20      75 ..      20      76 .. 0.79
   3 !   13.7   4.8   6.8e-05     0.071      42      59 ..     101     118 ..      82     120 .. 0.85
   4 !   20.8  12.6     4e-07   0.00042       1      59 [.     104     159 ..     104     160 .. 0.82
   5 !   13.5  11.2   7.6e-05     0.081       2      57 ..     178     225 ..     177     226 .. 0.81
   6 !   24.3   5.6   3.2e-08   3.4e-05       1      58 [.     213     282 ..     213     285 .. 0.62
   7 ?    5.5   0.1     0.024        26      46      58 ..     319     331 ..     290     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-05
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                        ++Ci+Cg C++ CP+g
  gi|386001975|ref|YP_005920274.1| 17 LPEKCIGCGTCVQICPKG 34
                                      557888888888888875 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.1e-06
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleea.ekeekaslCieCgeCerkCPqg 59
                                      +Ci+Cg C++ Cp +e        ++r     l++++  ++++ + C+ C +C+r+CP g
  gi|386001975|ref|YP_005920274.1| 20 KCIGCGTCVQICPKGELVIGSVGAVARG----LIDKEfLEKRNSGGCVFCALCARVCPTG 75
                                      6**************9966655555554....44444256789***************76 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 6.8e-05
                           Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                       + ++C++Cg+C+++CPqg
  gi|386001975|ref|YP_005920274.1| 101 VNERCVHCGLCAEVCPQG 118
                                       5689************97 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 4e-07
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       rC +Cg C+++Cp++ +   e ++l+++ +l l ++   +   ++C++Cg C+++CP++
  gi|386001975|ref|YP_005920274.1| 104 RCVHCGLCAEVCPQGCIEL-EDRRLAEDGSLRLEGK--IQIDLDRCVHCGWCAAVCPKD 159
                                       7*************87755.5677999977754444..4679***************86 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 7.6e-05
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       C+ C+ C++ Cp ++  +    ++++    +++e++   ++ + Ci Cg C+++CP
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPANALFNR---SWRQG---EIVEKV--THRRDACIYCGACAQACP 225
                                       *************999876...44444...445554..578899***********9 PP

  == domain 6  score: 24.3 bits;  conditional E-value: 3.2e-08
                           Fer4_17   1 rCiqCgyClpeCpsyea.............ydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +Ci Cg+C+++Cp  ++              +  +kkl +aa    l+  + ++  + C++Cg+C+ +CP 
  gi|386001975|ref|YP_005920274.1| 213 ACIYCGACAQACPVAAIsvrktaivpemkgKKAFEKKLSEAAPRPTLTS-ILKTDRDACLGCGNCVIVCPV 282
                                       6************977744433333322111112444444443333333.3457899*************6 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.024
                           Fer4_17  46 CieCgeCerkCPq 58 
                                       C +C  C+  CP 
  gi|386001975|ref|YP_005920274.1| 319 CGSCATCSLICPT 331
                                       5555666655554 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   5.6     5e-06    0.0053       1      14 [.      21      34 ..      21      34 .. 0.97
   2 !   13.2   6.1   0.00013      0.13       1      15 []      62      76 ..      62      76 .. 0.98
   3 !   11.2  11.3   0.00054      0.57       1      14 [.     105     118 ..     105     119 .. 0.95
   4 !   13.9   6.6   7.9e-05     0.083       1      15 []     146     160 ..     146     160 .. 0.98
   5 ?    6.6   6.0     0.016        17       1      15 []     178     192 ..     178     192 .. 0.93
   6 !   12.2   6.7   0.00027      0.28       1      14 [.     214     227 ..     214     228 .. 0.92
   7 !   14.9   6.6   3.7e-05     0.039       1      15 []     270     284 ..     270     284 .. 0.98
   8 ?    4.5   4.0     0.078        82       3      15 .]     321     333 ..     319     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5e-06
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gCg+Cv+ CP+g
  gi|386001975|ref|YP_005920274.1| 21 CIGCGTCVQICPKG 34
                                      ************98 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C +C +vCP+gA
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPTGA 76
                                      **************9 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00054
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C++Cg+C evCP g
  gi|386001975|ref|YP_005920274.1| 105 CVHCGLCAEVCPQG 118
                                       ************98 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 7.9e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++Cg C  vCP++A
  gi|386001975|ref|YP_005920274.1| 146 CVHCGWCAAVCPKDA 160
                                       *************98 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.016
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++Cv+ CP +A
  gi|386001975|ref|YP_005920274.1| 178 CQACRTCVDTCPANA 192
                                       999*********987 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00027
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ CgaC ++CPv 
  gi|386001975|ref|YP_005920274.1| 214 CIYCGACAQACPVA 227
                                       9***********85 PP

  == domain 7  score: 14.9 bits;  conditional E-value: 3.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg Cv vCPv+A
  gi|386001975|ref|YP_005920274.1| 270 CLGCGNCVIVCPVNA 284
                                       *************99 PP

  == domain 8  score: 4.5 bits;  conditional E-value: 0.078
                            Fer4_3   3 gCgaCvevCPvgA 15 
                                        C +C   CP+ A
  gi|386001975|ref|YP_005920274.1| 321 SCATCSLICPTEA 333
                                       4889******876 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.7   0.00038       0.4       6      20 ..      19      33 ..      18      46 .. 0.92
   2 ?    5.4   0.6      0.03        31       8      20 ..      62      74 ..      58      90 .. 0.72
   3 !    8.8   1.3    0.0026       2.8       6      30 ..     103     128 ..     100     136 .. 0.81
   4 !   11.0   1.9   0.00052      0.55       1      20 [.     139     158 ..     139     165 .. 0.89
   5 ?    4.8   1.8     0.047        49       4      20 ..     174     190 ..     172     197 .. 0.87
   6 !    9.8   3.8    0.0012       1.3       5      22 ..     211     227 ..     207     254 .. 0.76
   7 !   14.0   0.2   5.9e-05     0.062       3      19 ..     265     281 ..     263     302 .. 0.87
   8 !    9.4   1.9    0.0016       1.7       1      20 [.     312     331 ..     312     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                           Fer4_15  6 daCigcglCvaeape 20
                                      ++Cigcg Cv+ +p+
  gi|386001975|ref|YP_005920274.1| 19 EKCIGCGTCVQICPK 33
                                      68***********97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.03
                           Fer4_15  8 CigcglCvaeape 20
                                      C  c+lC++++p+
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPT 74
                                      8889999998875 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0026
                           Fer4_15   6 daCigcglCvaeap.evfeldedgla 30 
                                       ++C  cglC++++p   +el+++ la
  gi|386001975|ref|YP_005920274.1| 103 ERCVHCGLCAEVCPqGCIELEDRRLA 128
                                       79***********6156777777666 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00052
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       + +D d+C  cg C+a++p+
  gi|386001975|ref|YP_005920274.1| 139 IQIDLDRCVHCGWCAAVCPK 158
                                       689***************85 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.047
                           Fer4_15   4 DrdaCigcglCvaeape 20 
                                       D + C+ c  Cv+ +p 
  gi|386001975|ref|YP_005920274.1| 174 DDQICQACRTCVDTCPA 190
                                       7889***********85 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.0012
                           Fer4_15   5 rdaCigcglCvaeapevf 22 
                                       rdaCi cg+C++++p v 
  gi|386001975|ref|YP_005920274.1| 211 RDACIYCGACAQACP-VA 227
                                       9*************8.44 PP

  == domain 7  score: 14.0 bits;  conditional E-value: 5.9e-05
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                        DrdaC gcg+Cv ++p
  gi|386001975|ref|YP_005920274.1| 265 TDRDACLGCGNCVIVCP 281
                                       5************9998 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.0016
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       VvvD+d C +c+ C   +p+
  gi|386001975|ref|YP_005920274.1| 312 VVVDQDVCGSCATCSLICPT 331
                                       89**************9984 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.6   4.3e-05     0.046       4      18 ..      19      33 ..      18      34 .. 0.93
   2 ?    4.5   1.6     0.049        52       5      17 ..      61      73 ..      58      75 .. 0.88
   3 !   11.8   1.9   0.00026      0.28       1      18 [.     101     117 ..     101     118 .. 0.93
   4 !    9.5   3.8    0.0013       1.4       1      18 [.     141     158 ..     141     159 .. 0.95
   5 !   11.9   1.1   0.00024      0.25       3      18 ..     175     190 ..     174     206 .. 0.87
   6 !   10.3   2.8   0.00073      0.77       3      17 ..     211     225 ..     207     231 .. 0.94
   7 !   10.2   2.7   0.00082      0.86       2      17 ..     266     281 ..     265     283 .. 0.95
   8 !    8.2   4.0    0.0033       3.5       1      17 [.     314     330 ..     314     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      ++Ci+cg+Cv+++P+
  gi|386001975|ref|YP_005920274.1| 19 EKCIGCGTCVQICPK 33
                                      79************6 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.049
                           Fer4_13  5 tCiacgaCvelaP 17
                                       C+ c++C+ ++P
  gi|386001975|ref|YP_005920274.1| 61 GCVFCALCARVCP 73
                                      7************ PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00026
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       V+ ++C+ cg+C+e++P+
  gi|386001975|ref|YP_005920274.1| 101 VN-ERCVHCGLCAEVCPQ 117
                                       67.9*************6 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0013
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D d+C+ cg C++++P+
  gi|386001975|ref|YP_005920274.1| 141 IDLDRCVHCGWCAAVCPK 158
                                       899**************6 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00024
                           Fer4_13   3 rdtCiacgaCvelaPd 18 
                                        + C ac +Cv+++P 
  gi|386001975|ref|YP_005920274.1| 175 DQICQACRTCVDTCPA 190
                                       477************6 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00073
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       rd Ci cgaC++++P
  gi|386001975|ref|YP_005920274.1| 211 RDACIYCGACAQACP 225
                                       689***********9 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.00082
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       Drd C +cg+Cv ++P
  gi|386001975|ref|YP_005920274.1| 266 DRDACLGCGNCVIVCP 281
                                       99*************9 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0033
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD+d C +c++C  ++P
  gi|386001975|ref|YP_005920274.1| 314 VDQDVCGSCATCSLICP 330
                                       9**************** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.8   0.00025      0.26      55      74 ..      15      34 ..       2      40 .. 0.77
   2 !   14.5   0.3   2.9e-05     0.031      50      74 ..      51      75 ..      40      85 .. 0.83
   3 !    7.4   3.5    0.0045       4.7      58      74 ..     102     118 ..      80     127 .. 0.84
   4 !    7.1   9.6    0.0056       5.9      54      96 ..     139     189 ..     121     203 .. 0.75
   5 !    9.6   1.7   0.00093      0.98      55      79 ..     208     233 ..     195     239 .. 0.77
   6 !   10.7   1.0   0.00042      0.44      49      74 ..     258     283 ..     233     285 .. 0.67
   7 ?    4.3   0.3     0.042        44      57      74 ..     315     332 ..     293     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                           +ci c++cv++cP g
  gi|386001975|ref|YP_005920274.1| 15 VYLPEKCIGCGTCVQICPKG 34
                                      445578************86 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.9e-05
                           Fer4_18 50 keerkekgagdcidcescvkvcPtg 74
                                      ke  +++++g c+ c  c +vcPtg
  gi|386001975|ref|YP_005920274.1| 51 KEFLEKRNSGGCVFCALCARVCPTG 75
                                      566678899***************8 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0045
                           Fer4_18  58 agdcidcescvkvcPtg 74 
                                       +  c++c+ c +vcP g
  gi|386001975|ref|YP_005920274.1| 102 NERCVHCGLCAEVCPQG 118
                                       567************87 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0056
                           Fer4_18  54 kekgagdcidcescvkvcPtg.idirkGlqle.......ciscllcidacd 96 
                                        + +   c++c+ c +vcP + i  +k +  e       c +c  c+d+c 
  gi|386001975|ref|YP_005920274.1| 139 IQIDLDRCVHCGWCAAVCPKDaITFQKPFAGEffrddqiCQACRTCVDTCP 189
                                       5556678************8548888876433223344499********95 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.00093
                           Fer4_18  55 ekgagdcidcescvkvcPt.gidirk 79 
                                       ++    ci c++c + cP+  i +rk
  gi|386001975|ref|YP_005920274.1| 208 THRRDACIYCGACAQACPVaAISVRK 233
                                       456678************83588887 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00042
                           Fer4_18  49 ekeerkekgagdcidcescvkvcPtg 74 
                                       +  +  +++   c+ c+ cv vcP++
  gi|386001975|ref|YP_005920274.1| 258 TLTSILKTDRDACLGCGNCVIVCPVN 283
                                       445556677889************85 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.042
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                       ++  c +c +c  +cPt+
  gi|386001975|ref|YP_005920274.1| 315 DQDVCGSCATCSLICPTE 332
                                       4566999*********96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.7   9.8e-05       0.1      77      94 ..      16      33 ..       1      35 [. 0.75
   2 !    7.7   0.5     0.006       6.3       2      14 ..      62      74 ..      50      87 .. 0.69
   3 !   10.1   2.4    0.0011       1.1       1      24 [.     104     126 ..     104     142 .. 0.80
   4 !    7.7   2.7    0.0062       6.6      81      94 ..     145     158 ..     135     160 .. 0.63
   5 ?    2.6   2.7      0.23   2.4e+02      78      95 ..     174     191 ..     160     192 .. 0.78
   6 !    7.8   2.5    0.0056       5.9      78      94 ..     210     226 ..     192     229 .. 0.74
   7 ?    6.9   2.8     0.011        12       2      16 ..     214     228 ..     213     251 .. 0.73
   8 !   13.8   1.0   7.4e-05     0.078      73      95 ..     261     283 ..     232     284 .. 0.75
   9 ?    5.8   2.2     0.024        25       2      14 ..     319     331 ..     318     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      +  ++C+GCg C++ cp+
  gi|386001975|ref|YP_005920274.1| 16 YLPEKCIGCGTCVQICPK 33
                                      55678***********97 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.006
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C+ C+ C+ vCpt
  gi|386001975|ref|YP_005920274.1| 62 CVFCALCARVCPT 74
                                      5555555555555 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0011
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedet 24 
                                       rC++Cg C+ vCp   C+++ed+ 
  gi|386001975|ref|YP_005920274.1| 104 RCVHCGLCAEVCPQ-GCIELEDRR 126
                                       7************8.588888876 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0062
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                        Cv Cg C ++cp+
  gi|386001975|ref|YP_005920274.1| 145 RCVHCGWCAAVCPK 158
                                       55555555555554 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.23
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       + + C  C  C+++cp++
  gi|386001975|ref|YP_005920274.1| 174 DDQICQACRTCVDTCPAN 191
                                       677899999999999875 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0056
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                        + +C+ Cg C +acpv
  gi|386001975|ref|YP_005920274.1| 210 RRDACIYCGACAQACPV 226
                                       56677777777777775 PP

  == domain 7  score: 6.9 bits;  conditional E-value: 0.011
                           Fer4_22   2 ClsCgaCtlvCptCs 16 
                                       C+ CgaC+ +Cp   
  gi|386001975|ref|YP_005920274.1| 214 CIYCGACAQACPVAA 228
                                       999999999999765 PP

  == domain 8  score: 13.8 bits;  conditional E-value: 7.4e-05
                           Fer4_22  73 fkekfgesgCvGCgRCieacpvk 95 
                                          k+++ +C GCg C+ +cpv+
  gi|386001975|ref|YP_005920274.1| 261 SILKTDRDACLGCGNCVIVCPVN 283
                                       45567899999999999999975 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.024
                           Fer4_22   2 ClsCgaCtlvCpt 14 
                                       C sC++C+l+Cpt
  gi|386001975|ref|YP_005920274.1| 319 CGSCATCSLICPT 331
                                       99**********9 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.44   4.6e+02      71      86 ..      17      32 ..       3      39 .. 0.70
   2 !    9.3   1.9    0.0012       1.2      41      90 ..      63     120 ..      50     128 .. 0.67
   3 !   18.7   0.5   1.3e-06    0.0014      46      98 ..     111     169 ..     109     173 .. 0.80
   4 ?   -0.5   0.3       1.3   1.4e+03      71      82 ..     174     185 ..     168     202 .. 0.77
   5 ?   -0.3   4.2       1.1   1.2e+03      49      90 ..     187     229 ..     181     240 .. 0.74
   6 ?   -0.3   0.5       1.1   1.1e+03      68      88 ..     263     283 ..     252     294 .. 0.83
   7 ?    3.8   0.6     0.059        63      65      91 ..     309     335 ..     289     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                                      -CCC--S--HHHHH-T CS
                            ETF_QO 71 naqnCvhCktCdikdp 86
                                        + C+ C tC    p
  gi|386001975|ref|YP_005920274.1| 17 LPEKCIGCGTCVQICP 32
                                      4679*******66555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                                       HHS-THHHH-TTS-EEEEETT..TTSSE..EEEE-....CCC--S--HHHHH-TT--E CS
                            ETF_QO  41 kyagpeqryCPagvyeivede..eakek..klqin....aqnCvhCktCdikdpsqni 90 
                                       ++ + ++r+CP g  e+  +   e++++  ++ ++     + CvhC  C    p+  i
  gi|386001975|ref|YP_005920274.1|  63 VFCALCARVCPTGALEVRVSGkaEKDDSylNFALSptlvNERCVHCGLCAEVCPQGCI 120
                                       5778899*********97644113333311333322222578*******877777666 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.3e-06
                                       HHHH-TTS-EEEEETT..T....TSSEEEEE-CCC--S--HHHHH-TT--EEE---STT CS
                            ETF_QO  46 eqryCPagvyeivede..e....akekklqinaqnCvhCktCdikdpsqniewvvPeGg 98 
                                       ++ +CP g  e+ ++   e      e k+qi+   CvhC  C    p++ i+++ P  g
  gi|386001975|ref|YP_005920274.1| 111 CAEVCPQGCIELEDRRlaEdgslRLEGKIQIDLDRCVHCGWCAAVCPKDAITFQKPFAG 169
                                       677999999999885532223334567899************************99766 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.3
                                       -CCC--S--HHH CS
                            ETF_QO  71 naqnCvhCktCd 82 
                                       + q C  C+tC 
  gi|386001975|ref|YP_005920274.1| 174 DDQICQACRTCV 185
                                       678999999995 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.1
                                       H-TTS-.EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO  49 yCPagv.yeivedeeakekklqinaqnCvhCktCdikdpsqni 90 
                                        CPa+  ++   ++ +  +k++     C++C +C    p   i
  gi|386001975|ref|YP_005920274.1| 187 TCPANAlFNRSWRQGEIVEKVTHRRDACIYCGACAQACPVAAI 229
                                       688864155555566677888889999*******887777666 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1.1
                                       EEE-CCC--S--HHHHH-TT- CS
                            ETF_QO  68 lqinaqnCvhCktCdikdpsq 88 
                                       l+ +   C+ C  C i  p +
  gi|386001975|ref|YP_005920274.1| 263 LKTDRDACLGCGNCVIVCPVN 283
                                       6778889*******9988865 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.059
                                       SEEEEE-CCC--S--HHHHH-TT--EE CS
                            ETF_QO  65 ekklqinaqnCvhCktCdikdpsqnie 91 
                                       +  ++++   C  C tC++  p++ i 
  gi|386001975|ref|YP_005920274.1| 309 GAIVVVDQDVCGSCATCSLICPTEAIW 335
                                       4556788899************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2125.49
//
Query:       gi|386001976|ref|YP_005920275.1|  [L=203]
Description: Molybdenum formylmethanofuran dehydrogenase, subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-25   87.1   0.0    1.2e-24   86.8   0.0    1.1  1  FmdE         FmdE, Molybdenum formylmethanofuran dehydrogenas
  ------ inclusion threshold ------
      0.035   13.5   1.6      0.064   12.7   1.6    1.3  1  zf-ribbon_3  zinc-ribbon domain
      0.041   13.9   0.2      0.071   13.1   0.2    1.4  1  HypA         Hydrogenase/urease nickel incorporation, metallo


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.0   2.1e-28   1.2e-24       1     123 [.      23     148 ..      23     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.1e-28
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEET. CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkr. 76 
                                       fHG+l+ g+ +G+++ ++a++ lg  e   +++l++++et+sCl+DA+qvl gct+G++ l+++++gk+a+t+ +r 
  gi|386001976|ref|YP_005920275.1|  23 FHGYLSTGVFVGIQIYDIARRTLGFSE---GDRLFVTCETSSCLPDAFQVLGGCTIGNKGLRIENLGKMAATISRRa 96 
                                       9***********************853...59********************************************7 PP

                                       ....TT-EEEEEEE-....CCTHHHHHHHCCT--.GGGS-HHHHHHHHHHHHHHHH CS
                              FmdE  77 ....ktgkavrlklk....eelpelreklakgka.keekeeeeleeeleeaikkil 123
                                           ++ ++ r +l+     ++p+l+++ +k ++ +    +ee  + l +a ++++
  gi|386001976|ref|YP_005920275.1|  97 prgaERVNGKRTVLDpaktASYPRLHSWQMKIDKvP----HEEAISDLIRAEEAVY 148
                                       76664444444444487*99***********75544....4444444444444444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6   1.1e-05     0.064       5      22 ..     168     187 ..     166     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                       zf-ribbon_3   5 CPnCGa.p.lssddnvCpyC 22 
                                       C++CG+   l+ d + C++C
  gi|386001976|ref|YP_005920275.1| 168 CNSCGEsFvLQGDERSCKSC 187
                                       ******989*********** PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.2e-05     0.071      67      96 ..     162     191 ..     136     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       E--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  67 vpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       ++  + C++Cg++f l+ ++ +C++C +++
  gi|386001976|ref|YP_005920275.1| 162 EKRIAVCNSCGESFVLQGDERSCKSCAQRS 191
                                       445689*********9988889****9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1220.37
//
Query:       gi|386001977|ref|YP_005920276.1|  [L=189]
Description: Glutamine amidotransferase class-I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-18   67.8   0.0    1.3e-18   67.4   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    4.3e-08   33.2   0.2    2.1e-06   27.6   0.2    2.1  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.052   13.1   0.0      0.077   12.6   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      0.075   12.1   0.0        2.1    7.3   0.0    2.4  3  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      0.076   12.8   0.0       0.27   11.1   0.0    1.8  2  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   3.7e-22   1.3e-18      13     175 ..      23     173 ..      16     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.7e-22
                                       HHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHT CS
                            GATase  13 lvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGmQllaief 88 
                                       +++ + ++g + evv +++  e +      +d i++ g   +   +   i++ +++ + ++P+LGIC GmQ++a  f
  gi|386001977|ref|YP_005920276.1|  23 IARIVSRAGSEFEVVHFTEVTEDE---ILRADRIVLCGTALKDDlYLRRIDLFSWIGDLDKPVLGICAGMQVIAALF 96 
                                       677788889999999998633333...479********999999999****************************** PP

                                       TTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEE CS
                            GATase  89 grkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfv 165
                                       g++vv++ +       + + +  +  l g++++++ +h H++ v+    +p+g++ +a    + e+++i + ++p++
  gi|386001977|ref|YP_005920276.1|  97 GGEVVPQPKI--GLEAIDIVE--ETPLLGTPRRIEGYHLHNFGVT----LPQGFDLVAGR-PG-EVEAIKHADRPVY 163
                                       ********43..344444444..45899*****************....7******9999.66.8************ PP

                                       EESSBTTSTT CS
                            GATase 166 gvQFHPEsts 175
                                       g+ FHPE++ 
  gi|386001977|ref|YP_005920276.1| 164 GIIFHPEVRN 173
                                       *******976 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2     6e-10   2.1e-06     103     216 .]      77     170 ..      66     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6e-10
                     Peptidase_C26 103 ergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaik 179
                                       + ++P+lgiC G+q+++  +GG+++ + +                  a+++++++ l       +ie   lH+++++
  gi|386001977|ref|YP_005920276.1|  77 DLDKPVLGICAGMQVIAALFGGEVVPQPK--------------IGLEAIDIVEETPLLGTPR--RIEGYHLHNFGVT 137
                                       6789*******************988766..............2356899*****9999887..899999999*996 PP

                     Peptidase_C26 180 elaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        l +++  +A  + g +Eai++ +   +v+g+ +HPE
  gi|386001977|ref|YP_005920276.1| 138 -LPQGFDLVAGRP-GEVEAIKHAD--RPVYGIIFHPE 170
                                       .899*****9876.899****999..46********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05     0.077      26      88 ..      36      92 ..      30     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                          GATase_3 26 rvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88
                                       v+f +++++++ + ad ++l+G+   ++d  +lr+ +l  +i ++   ++pvlgiC+G+q+ 
  gi|386001977|ref|YP_005920276.1| 36 VVHFTEVTEDEILR-ADRIVLCGT--ALKDDLYLRRIDLFSWIGDL---DKPVLGICAGMQVI 92
                                      67888888888866.999999998..47888899998999999995...78**********86 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.026        92      19      54 ..      24      57 ..      21      65 .. 0.78
   2 ?    7.3   0.0    0.0006       2.1      88     106 ..      77      95 ..      67     120 .. 0.77
   3 ?   -2.2   0.0      0.47   1.7e+03     206     230 ..     149     173 ..     146     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.026
                          GATase_5 19 aaafekaGfeavdvhmsdllegrvslddfqilalpG 54
                                      a+ +++aG e + vh+++++e++  + ++  ++l+G
  gi|386001977|ref|YP_005920276.1| 24 ARIVSRAGSEFEVVHFTEVTEDE--ILRADRIVLCG 57
                                      67889**************7776..55666666676 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0006
                          GATase_5  88 redtlaLGiCnGfqlLvkl 106
                                       + d+ +LGiC G+q+++ l
  gi|386001977|ref|YP_005920276.1|  77 DLDKPVLGICAGMQVIAAL 95 
                                       558899********99887 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.47
                          GATase_5 206 pegiagitspdGRvlalmpHpervv 230
                                       p ++++i  +d  v++++ Hpe  +
  gi|386001977|ref|YP_005920276.1| 149 PGEVEAIKHADRPVYGIIFHPEVRN 173
                                       6789999999999999*****9765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.5e-05      0.27      59      91 ..      70     102 ..      26     117 .. 0.84
   2 ?   -0.7   0.0      0.31   1.1e+03     152     173 ..     150     173 ..     138     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHTT.--EEEETHHHHHHCCEETTBSS- CS
                               SNO  59 dllefvknsekvvlGtCaGlillskelenelvk 91 
                                       dl+  + + +k+vlG CaG+ ++++  ++e v+
  gi|386001977|ref|YP_005920276.1|  70 DLFSWIGDLDKPVLGICAGMQVIAALFGGEVVP 102
                                       588889999***************999888554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                                       TEEEEEE..ETTEEEESS-GGGST CS
                               SNO 152 geivvak..qkkilatsfhPelae 173
                                       ge+ ++k   + + ++ fhPe+ +
  gi|386001977|ref|YP_005920276.1| 150 GEVEAIKhaDRPVYGIIFHPEVRN 173
                                       655555531447788999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1136.92
//
Query:       gi|386001978|ref|YP_005920277.1|  [L=226]
Description: Putative ATP binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-65  220.3   0.0    2.3e-65  220.1   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   0.0   1.3e-69   2.3e-65       5     218 ..       5     222 ..       1     223 [. 0.96

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 1.3e-69
                   Diphthami_syn_2   5 vlysGGkDsilaLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgtl 81 
                                       vl+sGGkDs++a  +a++   v  L++++s n++symfh++n+    l ae+vG+p  +  taGeee e  dL + +
  gi|386001978|ref|YP_005920277.1|   5 VLFSGGKDSVYACRRAMETDSVACLITMVSANPDSYMFHTPNIAWAGLIAEAVGVPQLNWPTAGEEEAELSDLSDAI 81 
                                       8*********************************************************************9998776 PP

                   Diphthami_syn_2  82 kk.ld...veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGr 154
                                          +d   ve++v+Gaies yq  r++r+Crel l    PLW+ d +e+l   v+e+fevi+++v a+ ldes++G 
  gi|386001978|ref|YP_005920277.1|  82 AAaVDeygVEGIVTGAIESVYQAARVQRICRELDLWCYNPLWQIDQLEYLRLLVSEGFEVIITGVFAYPLDESFVGA 158
                                       43133444********************************************************************* PP

                   Diphthami_syn_2 155 ridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                       rid   i++l++l ++y+i+++gegGe+et+vlD+P+fk+r+ev ++ k++d+ rg l i+ a+
  gi|386001978|ref|YP_005920277.1| 159 RIDGPRIEKLEDLRDRYAINPSGEGGEIETIVLDGPVFKRRVEVLKAVKEYDNYRGRLIIKEAR 222
                                       ************************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1588.29
//
Query:       gi|386001979|ref|YP_005920278.1|  [L=560]
Description: AMP-forming acetyl-CoA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-72  243.5   0.0    3.7e-72  243.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      5e-24   85.1   1.4    1.2e-23   83.8   1.4    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.2   0.0   4.1e-76   3.7e-72       5     422 ..      43     458 ..      39     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 243.2 bits;  conditional E-value: 4.1e-76
                                       HHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   5 aaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       a+  pdk alv+   +g+   lT++el++r++++A+ +++ G++kgd V++ l+ ++++ + ++++ k+Gav++p  
  gi|386001979|ref|YP_005920278.1|  43 AEMAPDKKALVWcndRGDELILTFGELKRRSDQAANLFKKCGIRKGDSVMLTLKGRYDFWICMVGLHKVGAVAIPAT 119
                                       67889*******999888999******************99************************************ PP

                                       TTS-HHHHHHHHHHHTESEEE......ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS. CS
                       AMP-binding  79 ptltaeelayiledseakvli......atvdselleklleaaakleavklvivldadellkeeelkeeeeseekae. 148
                                         l+a+++ay +++++ k+++              ++++ a  +le  k v  l  d++++  +l+++ e +++++ 
  gi|386001979|ref|YP_005920278.1| 120 HMLRAKDIAYRISKADLKMIVsiaedgV------PDEVDGACRDLEGAKPVRALVGDGVDRPGWLDFRRELAAASPe 190
                                       *********************6654331......3344444444444444444555555555556555555544423 PP

                                       ..-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSCHHHHHHHH CS
                       AMP-binding 149 ..kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahifglilell 222
                                         +p+  e++++ d+++  +TSGTTG PK V + + + +  + ++k ++   ++ ed   +++++  ++  +   ++
  gi|386001979|ref|YP_005920278.1| 191 feRPPGREATENGDVLLAYFTSGTTGYPKMVKHDQTYPLGHILTAKfWQ---NVVEDGLHYTVADTGWAKCVWGQIY 264
                                       333556678999***********************99999989976333...34345566999******99989999 PP

                                       HHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHH CS
                       AMP-binding 223 lallsGatvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspe 298
                                       +  ++G+ v  ++ d ++d+++++e+ +k++vt+++++P++++ +++ + +      ++d+ssl++++++gepl+p+
  gi|386001979|ref|YP_005920278.1| 265 GQWIAGSGVFAYDYD-RFDAGRMMEMATKHGVTTFCAPPTIYRFMIKgDMS------RYDFSSLKYAVTAGEPLNPT 334
                                       999999988888855.67999**********************99994433......45****************** PP

                                       HHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET... CS
                       AMP-binding 299 llrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp... 372
                                       + + f + +g +++egYG+TEt ++++++p +++  k+gs Gkp pg ++ +vD +  + +  geeGe+++r     
  gi|386001979|ref|YP_005920278.1| 335 VYDLFFEATGLRLMEGYGQTETVVAIANFPMMNP--KPGSMGKPSPGYDIVLVDKD-DRICDVGEEGEIVIRTDegk 408
                                       ***999999999**************97776666..89*****************9.9**************87666 PP

                                       ..TS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 373 ..gvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                         g++  Y+ +p++ + ++   +++++TGD +++dedGyl+++gR++d+ik+
  gi|386001979|ref|YP_005920278.1| 409 ppGLFIDYHLDPDRMRNTWH--DDYYHTGDTAWMDEDGYLWFIGRTDDMIKS 458
                                       678***************97..57**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   1.4   1.4e-27   1.2e-23       1      76 []     467     545 ..     467     545 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.4e-27
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evE+al+shpaV e+aV Gv d+++G++++a Vvl +g  + e+le eL+ hv+k  +py+ p+ ++fv++lpkt s
  gi|386001979|ref|YP_005920278.1| 467 EVENALMSHPAVMECAVTGVADPLRGQVVKATVVLTKGhtPsEELEVELQNHVKKVTAPYKYPRIIEFVEALPKTIS 543
                                       8**********************************778532344********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|386001979|ref|YP_005920278.1| 544 GK 545
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3947.35
//
Query:       gi|386001980|ref|YP_005920279.1|  [L=326]
Description: hypothetical protein Mhar_1292 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-06   27.7   0.0    1.1e-05   25.0   0.0    2.1  1  Hpr_kinase_C  HPr Serine kinase C-terminal domain
    0.00064   18.5   0.0    0.00078   18.2   0.0    1.1  1  PEPCK_ATP     Phosphoenolpyruvate carboxykinase
     0.0085   16.3   0.0      0.028   14.6   0.0    1.9  2  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.055   13.7   0.0      0.098   12.9   0.0    1.4  1  AAA_28        AAA domain
       0.14   12.1   0.0        0.3   11.1   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.16   11.6   0.0        4.7    6.7   0.0    2.3  2  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.7e-09   1.1e-05       8      58 ..     120     171 ..     117     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.7e-09
                                       EEESEEEEETTEEEEEEESTCHHHHHHHHHHHTTT-.EEEEESSEEEEEETT CS
                      Hpr_kinase_C   8 svhGvlvdvygvGvLitGesgvGKselaleLikrgh.rLvaDDaveikride 58 
                                       svhG ++d+ g G+ + G sg GK+  +  L++r   r+v+DD    +  ++
  gi|386001980|ref|YP_005920279.1| 120 SVHGACLDLRGRGICLLGGSGAGKTTHTYGLLRRPEtRVVSDDWFFARIYGD 171
                                       79********************************76599***9865555544 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.6e-07   0.00078     156     258 ..      77     186 ..      16     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-07
                                       S-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHH.HTT-EEEEEEEEE-T.TS-EEEEEE-TTSSHHHHH.... CS
                         PEPCK_ATP 156 etvvalnlekklvlilgteYaGEikKsifsvmnyllp.kkgvlsmhcsanvgekkgdvalfFGLSGtGKTtLs.... 227
                                       e  v+ + ++k++ +++ +Y G ik   +s++  +l  ++g+ s+h ++    + g    ++G SG+GKTt +    
  gi|386001980|ref|YP_005920279.1|  77 EDRVFYDPQSKTAFLVNVTYYGWIKSLALSAAGDVLEdQHGIYSVHGACLDL-R-GRGICLLGGSGAGKTTHTygll 151
                                       6779999*************************99998799******988655.3.455667899*******887777 PP

                                       -BTTB-EEESS...EEEE-SS-.EEES-SEEEEE- CS
                         PEPCK_ATP 228 adperkligdD...ehgwsdeg.vfniegGcYaKt 258
                                         pe +++ dD     ++ d+   f+ e  +Y+++
  gi|386001980|ref|YP_005920279.1| 152 RRPETRVVSDDwffARIYGDDVlAFGSEKNFYIRA 186
                                       8999******9333234455533677787777775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   3.4e+03      25      35 ..      67      77 ..      41     115 .. 0.51
   2 !   14.6   0.0   9.4e-06     0.028       4      65 ..     135     201 ..     133     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                            AAA_33 25 avllssdtlrr 35
                                       +++s +++ +
  gi|386001980|ref|YP_005920279.1| 67 LYVVSDPEMGE 77
                                      23333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.4e-06
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqq....sktdytrvl.drlyqilnelark 65 
                                       l G +G+GK+t   +ll++  + ++s d ++ r++g+d+      k+ y+r++ +++++   +l++k
  gi|386001980|ref|YP_005920279.1| 135 LLGGSGAGKTTHTYGLLRRPETRVVSDDWFFARIYGDDVLafgsEKNFYIRAElSEIWREFGGLIEK 201
                                       6799*************998899999999999***96654333345566664324555555566655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.3e-05     0.098       2      28 ..     133     160 ..     132     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvp 28 
                                       i+++Gg+++GKTt +  L +r +++vv 
  gi|386001980|ref|YP_005920279.1| 133 ICLLGGSGAGKTTHTYGLLRRpETRVVS 160
                                       89**************999998999983 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001       0.3      19      59 ..     130     169 ..     102     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                       TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59 
                                       g+ i+L G  GaGKTt + gl++  +  +v S  +  ++ Y
  gi|386001980|ref|YP_005920279.1| 130 GRGICLLGGSGAGKTTHTYGLLRRPET-RVVSDDWFFARIY 169
                                       4559******************99754.6666665555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0016       4.7      78     122 ..      42      87 ..      37     103 .. 0.83
   2 ?    2.2   0.0     0.037   1.1e+02      36      54 ..     133     151 ..     122     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                            AAA_25  78 saEdsedelrrRlravgealrddarllvldlagv.eslpLfakdrg 122
                                         E+ +d++++ ++ + +++r  arl+v++ +++ e++  ++++++
  gi|386001980|ref|YP_005920279.1|  42 GSEEVRDRWEENFYNISQNIRSHARLYVVSDPEMgEDRVFYDPQSK 87 
                                       679999************************9999887766665554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.037
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       + l G +g+GKtt ++ l 
  gi|386001980|ref|YP_005920279.1| 133 ICLLGGSGAGKTTHTYGLL 151
                                       5678889******998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2165.30
//
Query:       gi|386001981|ref|YP_005920280.1|  [L=113]
Description: hypothetical protein Mhar_1293 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-12   46.4   0.0    5.2e-12   46.2   0.0    1.0  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   2.9e-16   5.2e-12      16     117 .]      13     113 .]       5     113 .] 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.9e-16
                                       HHHHHHHHHHHHHTTT......-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT- CS
                              DrsE  16 aarealelalaaaalg......hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaakargl 86 
                                       + r++l l++++++l        e ++    +Gv +llk   a p     l e++++l++ gv++ vC  ++ a+g+
  gi|386001981|ref|YP_005920280.1|  13 KDRASLALNNVNNLLAdlgddlVEAEILANSEGVAALLK---ASP-----LGERVEELAARGVRFAVCSRTLRAMGI 81 
                                       56666777777766667779999999*************...666.....*************************** PP

                                       -GGGE-.T--EEEE-HHHHHHHHHH-SEEEE- CS
                              DrsE  87 dededl.gvgvevsglgelaelqnegdrvitf 117
                                        e+e +  ++v++ g gel++ q+eg++++++
  gi|386001981|ref|YP_005920280.1|  82 GEEEVMaVAEVVPTGTGELVKRQSEGWAYVRP 113
                                       *88755445********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 765.77
//
Query:       gi|386001982|ref|YP_005920281.1|  [L=265]
Description: haloacid dehalogenase domain-containing protein hydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-12   47.0   0.0      1e-11   45.6   0.0    1.7  2  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.049   14.0   0.0      0.077   13.4   0.0    1.4  1  HAD          haloacid dehalogenase-like hydrolase
      0.055   13.2   0.0       0.32   10.7   0.0    1.9  2  Hydrolase_3  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.32   1.9e+03       5      25 ..       2      22 ..       1      41 [. 0.80
   2 !   45.6   0.0   1.7e-15     1e-11     113     210 .]     133     222 ..      72     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.32
                                      EEESBTTTBCHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  5 vfDkdGTLttgepsvedvivs 25
                                      +fD+ GT ++  ++ +++ ++
  gi|386001982|ref|YP_005920281.1|  2 IFDVAGTMLEMYRVAKEISQE 22
                                      7******99888777776655 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 1.7e-15
                                       HHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES...STTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                         Hydrolase 113 iadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet...vakpspegkvaaireL 186
                                       ++   +++p ++ea+a+L  +g ++++++gd+ +    + +  G           i+        +p+ k+++++ L
  gi|386001982|ref|YP_005920281.1| 133 VSTGGRPFPALEEALAELEGMGADIYVASGDSMRSLSVLTRCRG-----------IKReriYPASKPRRKEEIVEGL 198
                                       4466679*****************************98888899...........6666788999************ PP

                                       TSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 187 qgkpeevamVGDgvnDaaalaaAg 210
                                       + + + v+mVGDg+nD  al+aA+
  gi|386001982|ref|YP_005920281.1| 199 KDDYKLVVMVGDGLNDRYALKAAD 222
                                       ***********************8 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.077     103     188 .]     130     219 ..      85     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                               HAD 103 rvvvvSgg.lrplvepllaelg...adevlat.elevdd.....rltgelglegkpvrgegkvaalrewlaaegegi 169
                                       ++ v +gg + p +e+ lael    ad  +a+ +          +lt+  g+    ++ + k+++ +e    eg ++
  gi|386001982|ref|YP_005920281.1| 130 THSVSTGGrPFPALEEALAELEgmgADIYVASgD----SmrslsVLTRCRGIKRERIYPASKPRRKEE--IVEGLKD 200
                                       5666677678899999998777788777777732....1334589***********************..******* PP

                               HAD 170 dleevvayGDspsDlpllr 188
                                       d++ vv +GD+ +D  +l+
  gi|386001982|ref|YP_005920281.1| 201 DYKLVVMVGDGLNDRYALK 219
                                       **************98875 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.12   7.1e+02      20      46 ..     143     169 ..     134     180 .. 0.82
   2 ?   10.7   0.0   5.3e-05      0.32     192     244 ..     191     247 ..     184     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHTTSEEEEE-SS-HHHHH CS
                       Hydrolase_3  20 tkeaikklkekgikvviATGRslravl 46 
                                         ea+++l+  g  + +A+G s+r+++
  gi|386001982|ref|YP_005920281.1| 143 LEEALAELEGMGADIYVASGDSMRSLS 169
                                       678999999999999999999888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-....HHHHHHSSEEE- CS
                       Hydrolase_3 192 lkklakelnisleeviafGDgeNDieMLeaaglgvAmgnas....eevkkaAdyvtk 244
                                        +++++ l+ + + v+ +GDg ND   L+aa+lgv   + +    +e+ +aAd v++
  gi|386001982|ref|YP_005920281.1| 191 KEEIVEGLKDDYKLVVMVGDGLNDRYALKAADLGVLTVQQEsrppKELMEAADEVID 247
                                       566777777788889*******************97544321222567777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1785.44
//
Query:       gi|386001983|ref|YP_005920282.1|  [L=189]
Description: hypothetical protein Mhar_1295 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0066   16.2   0.0      0.014   15.2   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.024   14.2   0.0    1.4  1  HTH_24     Winged helix-turn-helix DNA-binding
      0.027   14.3   0.0      0.071   13.0   0.0    1.7  1  HTH_5      Bacterial regulatory protein, arsR family
      0.045   13.7   0.0       0.13   12.2   0.0    1.8  1  DASH_Dad4  DASH complex subunit Dad4
       0.06   13.2   0.0       0.12   12.2   0.0    1.5  1  MarR_2     MarR family
      0.067   13.3   0.4       0.31   11.2   0.4    1.9  1  MbeD_MobD  MbeD/MobD like


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.8e-06     0.014       8      35 ..     102     129 ..     101     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.8e-06
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHH CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStv 35 
                                       ++d+l+e+p++ t sel + +gl+k+tv
  gi|386001983|ref|YP_005920282.1| 102 LIDLLRERPGRYTTSELVEMLGLNKTTV 129
                                       79*************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.1e-06     0.024       8      44 ..     102     139 ..      95     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.1e-06
                            HTH_24   8 ILelLqknpr.isqreLAerlglSpstvnrrlkrLeee 44 
                                       ++ lL++ p+  + +eL e+lgl ++tv + +kr +++
  gi|386001983|ref|YP_005920282.1| 102 LIDLLRERPGrYTTSELVEMLGLNKTTVITVMKRAVDM 139
                                       56788888888***********************8876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.071       8      32 ..     103     129 ..     101     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       HHHHTT..SSEEHHHHHHHHTS-HHHH CS
                             HTH_5   8 LklLae..gelcvcelaeelglsqstv 32 
                                       + lL+e  g ++ +el+e+lgl++ tv
  gi|386001983|ref|YP_005920282.1| 103 IDLLRErpGRYTTSELVEMLGLNKTTV 129
                                       7899**7777***************99 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05      0.13       7      37 ..      47      77 ..      44      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                         DASH_Dad4  7 eqqsalLsRIiknvekLnesvvelnkeleei 37
                                      +q  +lL R+i  v+ L++ v++l++++++ 
  gi|386001983|ref|YP_005920282.1| 47 QQDVDLLGRLIDQVDHLSKEVADLKSQMKTR 77
                                      67789********************999865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.1e-05      0.12      11      47 ..     103     138 ..      95     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                                       HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLva 47 
                                       +  L+ rpgr  t +el++ lgl k +v  + kr+v+
  gi|386001983|ref|YP_005920282.1| 103 IDLLRERPGR-YTTSELVEMLGLNKTTVITVMKRAVD 138
                                       5678999996.7****************999999886 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4    0.0001      0.31      31      66 ..      37      75 ..       3      79 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                         MbeD_MobD 31 aelqrmfeltqrena...aLseqvtgLsqQVesLseqvr 66
                                      +++ +m   +q++      L  qv++Ls+ V +L  q++
  gi|386001983|ref|YP_005920282.1| 37 ENISNMLTAKQQDVDllgRLIDQVDHLSKEVADLKSQMK 75
                                      344445555555543777899999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1192.82
//
Query:       gi|386001984|ref|YP_005920283.1|  [L=270]
Description: HAD-superfamily hydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-21   76.7   0.0    2.2e-21   75.9   0.0    1.4  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    7.6e-21   74.0   0.6    1.5e-19   69.8   0.0    2.4  2  Hydrolase_like  HAD-hyrolase-like
      4e-13   50.2   2.0    2.1e-09   38.0   1.9    2.4  1  Hydrolase       haloacid dehalogenase-like hydrolase
    2.6e-11   43.9   0.1    9.9e-08   32.3   0.0    2.5  3  HAD_2           Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   4.8e-25   2.2e-21       1     100 [.      22     119 ..      22     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 4.8e-25
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       fl+D+dGvL+ ++++ipga+eal +l+++g++  +++N +sks++++a  l +lg++i++e+++t+a+aaa  l++ 
  gi|386001984|ref|YP_005920283.1|  22 FLIDLDGVLYVDKTPIPGAKEALAQLEERGYRRRFVSNTTSKSRRGLAGFLGALGFEISAEEIFTPAVAAAGRLRS- 97 
                                       79*************************************************************************9. PP

                                       SXXXEEEEESXHHHHHHHHHTTX CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeagf 100
                                        ++++++++ ++ lre ++eag+
  gi|386001984|ref|YP_005920283.1|  98 -RNERCFLVAGPSLREDFDEAGV 119
                                       .8899999999******999996 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.044     2e+02      22      34 ..     126     137 ..      89     139 .. 0.75
   2 !   69.8   0.0   3.5e-23   1.5e-19       2      74 ..     193     265 ..     192     266 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.044
                                       GGEEEEES-TTTH CS
                    Hydrolase_like  22 eevlmiGDrlatD 34 
                                        +++++GD  ++D
  gi|386001984|ref|YP_005920283.1| 126 VDCVVVGDA-EAD 137
                                       469*****9.888 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 3.5e-23
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       +gKP+p ++  al++lg+ pee  miGD++++D+ gA+n+G+k++LV+tG++r+e+++   ++p+ ++ ++ae
  gi|386001984|ref|YP_005920283.1| 193 VGKPSPDFFALALRDLGASPEEAAMIGDDINSDVGGAKNVGMKGILVRTGKYREEAVAPSGISPDLILGSIAE 265
                                       49******************************************************996669*****999887 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   1.9   4.7e-13   2.1e-09       3     210 .]      21     233 ..      19     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 4.7e-13
                                       EEEEESBTTTBCHH...HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHH CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttge...psvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpew 76 
                                       ++++D+dG+L+  +   p  +++++++                     ++   r+  +++ +      +  +g   +
  gi|386001984|ref|YP_005920283.1|  21 AFLIDLDGVLYVDKtpiPGAKEALAQL---------------------EERGYRRRFVSNTTS-----KSRRGLAGF 71 
                                       899********6665778888888888.....................666666666677777.....555555555 PP

                                       HHHH.......HCHHHHHHHHHHHHHHCHHHHHH..................TTHHHHHHHHHHTHHBHTTHHHHHH CS
                                       xxxx.......xxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  77 ltal.......dippdlgaaigsaqsqgrtvall..................qaralavftiadplkvkpeaaeava 128
                                       l al       +i +   aa g + s+ +  +l+                  ++  + v+  a+ ++ ++ +  a++
  gi|386001984|ref|YP_005920283.1|  72 LGALgfeisaeEIFTPAVAAAGRLRSRNERCFLVagpslredfdeagvgvaeEGVDCVVVGDAEADFTYDRLNRAFR 148
                                       55553333334444444444444455555555447777777777777777777777778888888888888888888 PP

                                       HHHHTTEEEEEEESSEHHHHHHHHHH.TT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                         Hydrolase 129 sLkaagievvlltgdnpetaeraanq.lG.ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvn. 201
                                            g +++ l  d   +    +   +G + +  +   ++  e v+kpsp+ +  a+r L+++pee am+GD +n 
  gi|386001984|ref|YP_005920283.1| 149 MVM-EGSRIIALEKDRYWMGAGGLTLaAGpFVAAlEYASGRKAELVGKPSPDFFALALRDLGASPEEAAMIGDDINs 224
                                       877.57888888888888877555555885333324555555555******************************** PP

                                       HHHHHHHTT CS
                                       xxxxxxxxx RF
                         Hydrolase 202 DaaalaaAg 210
                                       D+ +++++g
  gi|386001984|ref|YP_005920283.1| 225 DVGGAKNVG 233
                                       ****99987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00029       1.3      79     108 ..      35      64 ..      23      87 .. 0.81
   2 ?   -3.7   0.1       2.5   1.1e+04     155     165 ..     128     138 ..     127     139 .. 0.84
   3 !   32.3   0.0   2.2e-11   9.9e-08     134     178 .]     194     239 ..     182     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00029
                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsksrea 108
                                       +p++g+ke+L +L+e+gy+   v++ ++++
  gi|386001984|ref|YP_005920283.1|  35 TPIPGAKEALAQLEERGYRRRFVSNTTSKS 64 
                                       79*****************99888776554 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
                             HAD_2 155 viyvGDsptDi 165
                                       +++vGD   D+
  gi|386001984|ref|YP_005920283.1| 128 CVVVGDAEADF 138
                                       789***99996 PP

  == domain 3  score: 32.3 bits;  conditional E-value: 2.2e-11
                             HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                        KP+p+ ++ al+ l++++ee+ ++GD + +D+ +ak++g+k i v
  gi|386001984|ref|YP_005920283.1| 194 GKPSPDFFALALRDLGASPEEAAMIGDDInSDVGGAKNVGMKGILV 239
                                       59***************************9***********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1874.41
//
Query:       gi|386001985|ref|YP_005920284.1|  [L=187]
Description: Putative metalloendopeptidase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-09   36.1   0.0    7.6e-09   35.7   0.0    1.3  1  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   4.2e-13   7.6e-09       2      74 ..      38     118 ..      37     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.2e-13
                                       EESSEEEEETTT-EEEESSSEEEEEEEEET........TTEEEEEEEECTCEEEEEEEESEESS-TTEEE-TTCEEE CS
                     Peptidase_M23   2 fhkGidiaapkgtpVlAaadGtVvfagkke........gyGnvviidhgdgystlyahlskisvkegqkVkaGqvIG 70 
                                        h G+d+ ap+g++V ++ + tV+++g+ +        +   ++++++++g +   a l + +v++g++++ Gq++G
  gi|386001985|ref|YP_005920284.1|  38 RHCGVDLYAPAGSKVASIGEATVLEVGPFTnprsvpywNETLYLLVEDEGGRFFKLAELASAEVRVGDRIESGQILG 114
                                       69**************************55578897544456677788999************************** PP

                                       EEBS CS
                     Peptidase_M23  71 tvgs 74 
                                       +vgs
  gi|386001985|ref|YP_005920284.1| 115 RVGS 118
                                       ***7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1057.75
//
Query:       gi|386001986|ref|YP_005920285.1|  [L=199]
Description: hypothetical protein Mhar_1298 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-51  172.7   0.0    5.7e-51  172.5   0.0    1.0  1  DUF2284   Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.0   3.2e-55   5.7e-51       2     164 .]      24     198 ..      23     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 3.2e-55
                           DUF2284   2 lidaedivveervrlkCekgCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeedd...keemkevke 75 
                                        i+a d+vv+++vrlkC++gC+ Yg++l CPP+ pt+ee++++l+eY+ +++ +++a +++ +     +++++  ++
  gi|386001986|ref|YP_005920285.1|  24 EISAGDVVVANWVRLKCRYGCQAYGRHLGCPPYSPTPEETQRVLEEYRVGVIARFEAVADPAFPPqrlHHHLWGSIN 100
                                       699**********************************************************99999999******** PP

                           DUF2284  76 elekillelekeafeagypkalalsagsCtlCetCayeegep.........CrhpekarpsmealGidvfktaekag 143
                                       ++++++++le++af agy+ka++++a +Ct+CetC  ee+e          Crh++k+rpsmea Gidvf+t+e+ag
  gi|386001986|ref|YP_005920285.1| 101 AVHETIFQLERSAFLAGYYKAFGFNALPCTFCETCIPEEREGaidltevrsCRHKNKVRPSMEASGIDVFATLERAG 177
                                       ***************************************8779********************************** PP

                           DUF2284 144 lelevgkeeketvslvglvLl 164
                                       ++l v++++++ v+l+glvLl
  gi|386001986|ref|YP_005920285.1| 178 CDLAVLDSYSKGVALFGLVLL 198
                                       *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1149.87
//
Query:       gi|386001987|ref|YP_005920286.1|  [L=132]
Description: hypothetical protein Mhar_1299 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 869.06
//
Query:       gi|386001988|ref|YP_005920287.1|  [L=171]
Description: XRE family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-09   37.5   0.4    4.4e-09   36.3   0.1    1.7  2  HTH_3           Helix-turn-helix
     0.0087   16.4   0.8      0.046   14.1   0.0    2.2  2  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   14.5   0.5       0.03   13.9   0.5    1.3  1  PrpR_N          Propionate catabolism activator
      0.035   13.4   0.1      0.048   13.0   0.1    1.2  1  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
      0.068   13.6   0.0       0.16   12.4   0.0    1.7  1  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.11   13.2   1.5       0.72   10.5   0.1    2.5  3  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
       0.12   12.2   0.2       0.33   10.8   0.0    1.9  2  DUF3368         Domain of unknown function (DUF3368)
       0.13   12.3   0.0       0.19   11.8   0.0    1.3  1  Imm8            Immunity protein 8
        0.3   10.9   3.2       0.82    9.5   0.0    2.9  3  HTH_psq         helix-turn-helix, Psq domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   2.2e-12   4.4e-09       2      47 ..      23      68 ..      19      72 .. 0.95
   2 ?   -3.3   0.0       5.1     1e+04      35      44 ..     139     148 ..     138     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.2e-12
                                      HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                             HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                      ke + +lgls +e+++++ +++st+++i++G+r+P+++tl  + k+
  gi|386001988|ref|YP_005920287.1| 23 KEVLAELGLSAREFSAVSSIPQSTLYKIMSGHREPNITTLRQIVKT 68
                                      88999**************************************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.1
                                       CSBHHHHHHH CS
                             HTH_3  35 nPsletlkkl 44 
                                       +P++e+l+ +
  gi|386001988|ref|YP_005920287.1| 139 SPTVEKLLSI 148
                                       5888888765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.3e-05     0.046       9      53 ..      18      68 ..      15      78 .. 0.82
   2 ?    0.4   0.3      0.42   8.3e+02       2      24 ..      99     133 ..      98     167 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                            HTH_31  9 lRera.......GLsqeevAerlgvsestlsrlEqGrrgrpspavlealara 53
                                      lRe+        GLs +e  + + + +stl ++++G r +p   +l++++  
  gi|386001988|ref|YP_005920287.1| 18 LREAMkevlaelGLSAREFSAVSSIPQSTLYKIMSGHR-EPNITTLRQIVKT 68
                                      455555557777**************************.8*******99865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.42
                            HTH_31   2 LGalLralRera............GLsqeevAerl 24 
                                       +G++L  lRe +            +  ++ +A+++
  gi|386001988|ref|YP_005920287.1|  99 IGDRLLVLREYSatnieeaivaavRAERDGAAALV 133
                                       67788888876655555555555555555555555 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   1.5e-05      0.03      60     159 ..      65     168 ..      59     171 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                            PrpR_N  60 ilralkqakklg.ekialvgfeniikglktlselldldiei...ytinseeeaeaavkelkaegvevvvGdgvvadl 132
                                       i++ ++ ++      ia+++ + +++++k+ +  ++ ++ +   y+ ++ eea  a  ++ ++g  ++v+  +v+ +
  gi|386001988|ref|YP_005920287.1|  65 IVKTIRDLEGAEtGFIAVIAARPVLDEIKEKRTRIGDRLLVlreYSATNIEEAIVAAVRAERDGAAALVCAPIVSPT 141
                                       5666666666664579999999999999999998876655533366666777777777778899******9999999 PP

                            PrpR_N 133 Aek.aGlksvlltsgkesvrqAieeAle 159
                                       +ek + +++  +   +es+ +Aie A +
  gi|386001988|ref|YP_005920287.1| 142 VEKlLSIPVATIIP-RESLVRAIEVAAR 168
                                       99944555555555.9999999999975 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.4e-05     0.048      85     175 ..       5      95 ..       2     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                    ALIX_LYPXL_bnd  85 reileeAsesDkivrqklqenkedlelLsgpeeeleaalpssssaaa.sesveeqirklrsllekldelkaereqll 160
                                       ++++ +A +sD+++r++++e+ ++l l  + e +  +++p+s+  ++ s   e++i +lr++++ + +l+ + + ++
  gi|386001988|ref|YP_005920287.1|   5 EKLMRAAFASDEKLREAMKEVLAELGLS-AREFSAVSSIPQSTLYKImSGHREPNITTLRQIVKTIRDLEGAETGFI 80 
                                       566788999********99998888865.4566777779*887665579********************99888877 PP

                    ALIX_LYPXL_bnd 161 kdlkekaendDitpk 175
                                         +      d i++k
  gi|386001988|ref|YP_005920287.1|  81 AVIAARPVLDEIKEK 95 
                                       766555555555555 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-05      0.16       3      47 ..      23      66 ..      21      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                            HTH_26  3 relmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiC 47
                                      +e++a+ g+++ e++  + i ++tl+++ +g  + ++++tL  i 
  gi|386001988|ref|YP_005920287.1| 23 KEVLAELGLSAREFSAVSSIPQSTLYKIMSGH-REPNITTLRQIV 66
                                      89*****************************7.799999998875 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00036      0.72      31      65 ..       5      39 ..       2      45 .. 0.87
   2 ?    0.8   0.0      0.41   8.1e+02      66      80 ..      63      77 ..      57      87 .. 0.83
   3 ?   -2.2   0.0       3.4   6.8e+03       5      16 ..     112     123 ..      90     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                    Mg_chelatase_C 31 geelrevceldeeaeelleeaierlglsaRaydri 65
                                      ++ +r++++ de+ +e ++e++++lglsaR ++ +
  gi|386001988|ref|YP_005920287.1|  5 EKLMRAAFASDEKLREAMKEVLAELGLSAREFSAV 39
                                      567889999*********************99876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.41
                    Mg_chelatase_C 66 lkvArTiADLegsee 80
                                       ++ +Ti DLeg+e+
  gi|386001988|ref|YP_005920287.1| 63 RQIVKTIRDLEGAET 77
                                      56789******9985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.4
                    Mg_chelatase_C   5 aevrerVaaAre 16 
                                       ++++e ++aA +
  gi|386001988|ref|YP_005920287.1| 112 TNIEEAIVAAVR 123
                                       344445555444 PP

>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         3     6e+03      19      27 ..      21      29 ..      17      32 .. 0.72
   2 ?   10.8   0.0   0.00017      0.33      11      39 ..      74     104 ..      72     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3
                           DUF3368 19 svkplldaL 27
                                      ++k++l +L
  gi|386001988|ref|YP_005920287.1| 21 AMKEVLAEL 29
                                      478888776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                           DUF3368  11 AKqrGlIps..vkplldaLiqaGfrispkly 39 
                                         + G+I    ++p+ld+++++  ri ++l+
  gi|386001988|ref|YP_005920287.1|  74 GAETGFIAViaARPVLDEIKEKRTRIGDRLL 104
                                       56789999999*****************997 PP

>> Imm8  Immunity protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.5e-05      0.19      36      89 ..      70     123 ..      51     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-05
                              Imm8  36 egekGadlFqvlvctpewleknvekespllgrhlLiveeydleeikaaiekive 89 
                                       ++ +Ga+   + v+  + + +++++++  +g  lL+++ey+  +i++ai   v 
  gi|386001988|ref|YP_005920287.1|  70 RDLEGAETGFIAVIAARPVLDEIKEKRTRIGDRLLVLREYSATNIEEAIVAAVR 123
                                       677888888899999999999999999********************9987765 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00041      0.82       2      40 ..      15      54 ..      14      56 .. 0.87
   2 ?    0.3   0.4       0.3     6e+02       2      11 ..     115     124 ..     114     129 .. 0.80
   3 ?   -1.5   0.0       1.1   2.2e+03       2      10 ..     156     164 ..     154     166 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00041
                           HTH_psq  2 pealaaAleavv..nGkmSirkAArkYgiPrsTLwrrkrgk 40
                                      +e+l +A + v+   G +S r+ + +  iP sTL++  +g+
  gi|386001988|ref|YP_005920287.1| 15 DEKLREAMKEVLaeLG-LSAREFSAVSSIPQSTLYKIMSGH 54
                                      7999999999*96444.******************998887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                           HTH_psq   2 pealaaAlea 11 
                                       +ea+ aA++a
  gi|386001988|ref|YP_005920287.1| 115 EEAIVAAVRA 124
                                       89******98 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                           HTH_psq   2 pealaaAle 10 
                                       +e+l +A+e
  gi|386001988|ref|YP_005920287.1| 156 RESLVRAIE 164
                                       345555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1066.29
//
Query:       gi|386001989|ref|YP_005920288.1|  [L=330]
Description: ABC transporter, substrate-binding protein, aliphatic sulfonates family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-31  108.1   0.1    8.7e-31  107.5   0.1    1.2  1  NMT1_2          NMT1-like family
      2e-13   50.8   0.0    2.6e-13   50.4   0.0    1.2  1  NMT1            NMT1/THI5 like
    0.00017   21.2   0.0    0.00024   20.8   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
    0.00028   20.4   0.0      0.073   12.5   0.0    2.7  3  NMT1_3          NMT1-like family


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.1   1.9e-34   8.7e-31       2     248 ..      29     262 ..      28     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.9e-34
                            NMT1_2   2 apekeqlklGfialtdaaplvvakekglfake....Glt.velekqaswaelrdkllagelDaahv.ltpapllidl 72 
                                       +++ ++l++G+++ t+ +  +va e+g+        G++ v+  ++ s++  ++++l+g+lD+a+v  +p +++i +
  gi|386001989|ref|YP_005920288.1|  29 KAKITTLRIGYQPSTHQVAEMVAMEEGWWLADlkpfGIEeVKDFEFPSGPPEMQAMLGGSLDIAYVgAAPPISAIAQ 105
                                       678899*********998887777777654444999***************************************** PP

                            NMT1_2  73 GiggakadmkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGld 149
                                       G+     d k++a++++nG +++++ +         ++ k+lv++       ++a+  pgs +d+ +r wL  +G+d
  gi|386001989|ref|YP_005920288.1| 106 GL-----DAKIVAAVQKNGSDLVVRPE------VAYDGPKSLVGR-------TVATFPPGSIQDTVFRKWLLDNGVD 164
                                       **.....*****************987......778899999765.......5668899****************** PP

                            NMT1_2 150 peadvklvvvpppqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntara 226
                                       p +  ++  + p ++v + +a+++d+ + + P ++  +  g G  ++ s+e w+dh ++ l+v+ +++ + p+++++
  gi|386001989|ref|YP_005920288.1| 165 P-DGLDIKSMDPGAAVTAISAKRVDAVFLPHPAPSIIELAGNGKAVVASGEMWPDHACCCLVVSGKLMREEPELVEQ 240
                                       *.778888899****************************************************************** PP

                            NMT1_2 227 lvkalleAtkwldakkenraea 248
                                       ++k++++At+++++++e +a++
  gi|386001989|ref|YP_005920288.1| 241 IIKTHIRATEFINENPERAAAI 262
                                       *************877777665 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   5.8e-17   2.6e-13      38     216 .]      84     259 ..      47     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.8e-17
                                       HHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHH CS
                              NMT1  38 vasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkalla 113
                                       +  g  d++       + a a+gl+ + vaa+ q++ s l+v+ +   + pk+L G+++++++ ++++++++++ l 
  gi|386001989|ref|YP_005920288.1|  84 MLGGSLDIAYVGAAPPISAIAQGLDAKIVAAV-QKNGSDLVVRPEVAYDGPKSLVGRTVATFPpGSIQDTVFRKWLL 159
                                       55566666666666677888999999999886.6999***********************8887999********** PP

                                       HTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH CS
                              NMT1 114 kdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvpdyyslvlitnekllke 190
                                        +g+dp+ + + +++   +++a+ +++vDa++    +   +el+  gk   ++ ++   +pd     l+++ kl++e
  gi|386001989|ref|YP_005920288.1| 160 DNGVDPDGLDIKSMDPGAAVTAISAKRVDAVFLPHPAPSIIELAGNGK---AVVASGEMWPDHACCCLVVSGKLMRE 233
                                       **************9999999***********8888877777665554...34444445567788899********* PP

                                       -HHHHHHHHHHHHHHHHHHHHSHHHH CS
                              NMT1 191 npelvkkFlrAlkkGyeyalahPeea 216
                                       +pelv+++++   +++e++ ++Pe+a
  gi|386001989|ref|YP_005920288.1| 234 EPELVEQIIKTHIRATEFINENPERA 259
                                       ************************97 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   5.3e-08   0.00024      43     164 ..      81     193 ..      79     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.3e-08
                                       HHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTT CS
                    Phosphonate-bd  43 vealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsG 118
                                       ++a+  g++Dia++g+ + + a +q  +++ +a+ ++        s ++vr++ +++  + L g+t+a   p S   
  gi|386001989|ref|YP_005920288.1|  81 MQAMLGGSLDIAYVGAAPPISAIAQGlDAKIVAAVQK------NGSDLVVRPEVAYDGPKSLVGRTVATFPPGSIQD 151
                                       69*******************9988558877777775......67889****************************8 PP

                                       THHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEE CS
                    Phosphonate-bd 119 ylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavs 164
                                       +++ + lL  ++g+dp+ + +   s +  aav a+ ++++da +++
  gi|386001989|ref|YP_005920288.1| 152 TVFRKWLL--DNGVDPDGL-DI-KSMDPGAAVTAISAKRVDAVFLP 193
                                       88877766..9****9854.33.45668899999999999999865 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0032        14     147     177 ..      75     105 ..      53     116 .. 0.76
   2 !   12.5   0.0   1.6e-05     0.073      84     182 ..     111     206 ..     107     212 .. 0.90
   3 ?   -0.9   0.0       0.2   8.9e+02     236     278 ..     234     276 ..     222     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0032
                            NMT1_3 147 lgygesadalkdgqldgaalvaGvPvsavtq 177
                                        +  + ++a+  g ld a + a++P+sa++q
  gi|386001989|ref|YP_005920288.1|  75 PSGPPEMQAMLGGSLDIAYVGAAPPISAIAQ 105
                                       44567899*********************98 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.6e-05
                            NMT1_3  84 aitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgq 160
                                       ++++++++   lvv+ +   +  + l g++v+  p+gs +++ +r+ l   g++ + l++ +++++g +++a+  ++
  gi|386001989|ref|YP_005920288.1| 111 IVAAVQKNGSDLVVRPEVAYDGPKSLVGRTVATFPPGSIQDTVFRKWLLDNGVDPDGLDI-KSMDPGAAVTAISAKR 186
                                       567788888999999999999999******************************999996.999************* PP

                            NMT1_3 161 ldgaalvaGvPvsavtqlaase 182
                                       +d+++l+  +P+ ++ +la + 
  gi|386001989|ref|YP_005920288.1| 187 VDAVFLP--HPAPSIIELAGNG 206
                                       *******..8999999988665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.2
                            NMT1_3 236 deelvYeitkaifenldelnsihkaakeislekalaglpvplH 278
                                       ++elv +i+k+    ++++n+  + a +i  +k+ ++l v  H
  gi|386001989|ref|YP_005920288.1| 234 EPELVEQIIKTHIRATEFINENPERAAAIYTAKTNQNLTVIEH 276
                                       4789999999999999999999999999988888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2033.35
//
Query:       gi|386001990|ref|YP_005920289.1|  [L=269]
Description: ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-20   73.6  16.7    2.7e-20   72.9  16.7    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9  16.7   1.5e-24   2.7e-20       2     169 ..      87     248 ..      78     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.5e-24
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       +++G+ ++   +++ d++++p++++++ +P+++++++ +       ++g +  ++ ++++++a+++++++ + ++rs
  gi|386001990|ref|YP_005920289.1|  87 LPIGMAMG--WSRVADRVFDPIVELIRPIPPLAWIPFAI------IWFGLTPQAAGFIVFVGAVFPILINSYVGFRS 155
                                       56777777..*****************************......9******************************* PP

                      BPD_transp_1  79 lpkdlveaaralGasrwq.ifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyse 152
                                       +p+ +ve a +lGa+r + ++r+v++P+alp+i++g+++a+g+++   v++e++g+++   lg++l++ ++  ++++
  gi|386001990|ref|YP_005920289.1| 156 VPRIYVESAMVLGATRNRdLIRYVAIPSALPSIAAGIRIAMGIAWMCIVAAEMFGASTRsgLGYRLWDYYSLHMMDL 232
                                       ***************9875999*********************************986444********99999996 PP

                      BPD_transp_1 153 isnggvlalviavllln 169
                                           ++++l+++ ll+ 
  gi|386001990|ref|YP_005920289.1| 233 VF-LYMIVLGLLGLLID 248
                                       66.66666666555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1907.49
//
Query:       gi|386001991|ref|YP_005920290.1|  [L=105]
Description: hypothetical protein Mhar_1303 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-40  135.7   0.4    8.9e-40  135.5   0.4    1.0  1  YbjQ_1    Putative heavy-metal-binding


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.4     5e-44   8.9e-40       2     104 .]       1     104 [.       1     104 [. 0.98

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 5e-44
                            YbjQ_1   2 ivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAvv 78 
                                       +++tt+s++gk++v+++giv+ge++ ++n++kd++ag+r++vGG+++aye+el++a+e Al++++eeA++lGAnAv+
  gi|386001991|ref|YP_005920290.1|   1 MISTTPSVDGKRVVKYFGIVSGEAILGANIFKDLFAGIRDIVGGRSGAYEKELRRAKEIALSEMEEEAARLGANAVL 77 
                                       589************************************************************************** PP

                            YbjQ_1  79 gvrldtseige.kgmlevlayGTAVkv 104
                                       +v+ld++++g+ +gml+v+a+GTAV v
  gi|386001991|ref|YP_005920290.1|  78 SVDLDYETLGQnGGMLMVSASGTAVLV 104
                                       *********999*************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 629.88
//
Query:       gi|386001992|ref|YP_005920291.1|  [L=379]
Description: Elongation factor Tu, domain 2 protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-11   44.0   0.1    8.8e-11   42.0   0.1    2.1  2  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0014   18.4   0.0     0.0029   17.5   0.0    1.5  1  GTP_EFTU_D4  Elongation factor Tu domain 4


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   9.8e-15   8.8e-11       1      74 []     219     286 ..     219     286 .. 0.96
   2 ?   -1.7   0.0      0.45     4e+03      14      29 ..     355     369 ..     353     376 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 9.8e-15
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       Gtv+lg+  +G+++k +++r+l+ ++t       +++s++++  d d+a+ag++aG+ ++ ++ ++ + +Gd+l+
  gi|386001992|ref|YP_005920291.1| 219 GTVVLGTMAEGVIRKHETLRVLPgDRT------AQVRSIQKHDDDFDWARAGDRAGIALKNIEADE-LDRGDVLA 286
                                       9********************997766......9********************************.9*****95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.45
                                       ETTEEEEEEC.TCTTSE CS
                       GTP_EFTU_D2  14 kkGdevrilg.ndtskk 29 
                                       ++Gd+ +i++  ++  k
  gi|386001992|ref|YP_005920291.1| 355 RPGDRAVICPlEGS--K 369
                                       79999999996654..3 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.3e-07    0.0029      18      85 ..     220     285 ..     207     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-07
                                       CEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-EE CS
                       GTP_EFTU_D4  18 paivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdil 85 
                                        ++ G ++ +Gvi+   +l    G +  ++++iq++++  + a+aG++ +i++++     +++ gd+l
  gi|386001992|ref|YP_005920291.1| 220 TVVLG-TMAEGVIRKHETLRVLPGDRTAQVRSIQKHDDDFDWARAGDRAGIALKNI-EADELDRGDVL 285
                                       57888.999*******************************************9964.47778888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 2685.71
//
Query:       gi|386001993|ref|YP_005920292.1|  [L=640]
Description: Threonyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-49  165.4   0.0    1.5e-48  164.4   0.0    1.6  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    8.2e-17   61.1   4.3    1.1e-16   60.8   0.3    2.7  3  HGTP_anticodon  Anticodon binding domain
    2.1e-14   53.9   0.3      4e-14   53.0   0.3    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4   0.0   2.5e-52   1.5e-48       1     137 []       1     137 [.       1     137 [. 0.98

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 2.5e-52
                                       -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvv 75 
                                       m+lLlih+d++e+eak+++ ++ae  ee ek+grleeal++FiavEk De +  +++++ +kei++va++vka++++
  gi|386001993|ref|YP_005920292.1|   1 MQLLLIHSDYIEFEAKRPT-PVAEkvEEREKSGRLEEALCAFIAVEKMDEIDIPAAIAAGAKEIASVAEQVKAERIM 76 
                                       9******************.99998999************************************************* PP

                                       EEE-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                       tRNA-Thr_ED  76 lypyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                       lypyaHLss+l++p++a+e+l+ lee+l+++  ev+raPFGwyk+f++sckGhpL+elsr+i
  gi|386001993|ref|YP_005920292.1|  77 LYPYAHLSSQLSAPKAAVEVLRGLEEALRQD-REVARAPFGWYKAFRLSCKGHPLSELSRSI 137
                                       *****************************97.9***************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.1     6e+02      46      66 ..      45      65 ..      43      76 .. 0.78
   2 ?   -2.2   0.1      0.77   4.6e+03      12      47 ..     375     410 ..     370     414 .. 0.72
   3 !   60.8   0.3   1.8e-20   1.1e-16       1      92 [.     526     616 ..     526     618 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.1
                                      HHHHHTT-SEEEEE-HHHHHH CS
                    HGTP_anticodon 46 readllgipfavvvGekelek 66
                                      +++d++ ip a+  G+ke+ +
  gi|386001993|ref|YP_005920292.1| 45 EKMDEIDIPAAIAAGAKEIAS 65
                                      6799**************975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.77
                                       HHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHH CS
                    HGTP_anticodon  12 eeleeyakklaeeLraagirvelddsnesigkkire 47 
                                       +e+e+ ++   + L++ag++ + ++ + ++ k + e
  gi|386001993|ref|YP_005920292.1| 375 REFENQYRTSISVLKEAGLDLDDYEVAIRFTKEFYE 410
                                       457777777778899999877777777777777766 PP

  == domain 3  score: 60.8 bits;  conditional E-value: 1.8e-20
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv vip++e   ++++ a+++a ++   g+r+++dd++e++gkkir+a + ++p++vv+G++ele+g ++v  r++ 
  gi|386001993|ref|YP_005920292.1| 526 QVRVIPVAE---RHQPRAEEVAGAI---GFRTDVDDRDETVGKKIRDAGREWVPYVVVIGDDELESGRLAVTVRAES 596
                                       89*******...9*********987...7*********************************************665 PP

                                       EE.....EEEETTHHHHHHH CS
                    HGTP_anticodon  78 eq.....ervsldelveklk 92 
                                       e      +++++d+l + + 
  gi|386001993|ref|YP_005920292.1| 597 EPkkpfkVEMTIDDLRARIA 616
                                       44346668999999988775 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.3   6.6e-18     4e-14       3     178 ..     298     505 ..     296     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 6.6e-18
                                       EEETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxx RF
                      tRNA-synt_2b   3 ledrndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.eas 75 
                                       +e + +r++ L+  ++ +   +  d    s+r LPlk++++++  +R+E++ ++ GL R+r F++ d +  +a  a+
  gi|386001993|ref|YP_005920292.1| 298 IEAE-KRSFFLRFAACFGQFLMSHDM-TLSYRsLPLKMIEMTRYsFRREQRgELVGLRRLRAFTMPDMHTLCAdMAE 372
                                       5555.699****************99.556555*******99854******8999******************8799 PP

                                       HHHHHHHHHHHHHHHHHHTT.SC....EEEEEEGTTSC..............................BTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx..............................xxxxxxxxx RF
                      tRNA-synt_2b  76 lddslrdlikaisriferlglef....raiielmsaks..............................adykdkkef 118
                                       +  ++++  ++   ++++ gl             ++++                              +    k ef
  gi|386001993|ref|YP_005920292.1| 373 ATREFENQYRTSISVLKEAGLDLddyeV----AIRFTKefyeenrefveglvgivnkpvliemweerfFYFVLKFEF 445
                                       *********************8755431....222222223455677777777777888888888874334567788 PP

                                       EEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                      tRNA-synt_2b 119 eavsesltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                       + v+  l+k+  ++t+q +  + ++r ++++ d ++  +++i+++ +  g +eRl+ a+le+
  gi|386001993|ref|YP_005920292.1| 446 NFVDA-LDKASALSTVQID-VENADRYEIDYTDPEGALRRPIILHCSpSGaIERLMYALLEK 505
                                       88888.*************.999************************9999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3989.69
//
Query:       gi|386001994|ref|YP_005920293.1|  [L=359]
Description: Cell surface glycoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-37  128.3  15.8    4.6e-37  127.6  15.8    1.3  1  NosD        Periplasmic copper-binding protein (NosD)
    2.8e-22   79.2  34.1    3.6e-13   49.6  14.7    2.2  2  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 !  127.6  15.8   5.1e-41   4.6e-37      24     238 ..     112     334 ..      84     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 5.1e-41
                              NosD  24 segseisnneisnsrdgilldnssnntitgntienl...ryGihlensesntiedntlssne..sGialmsssnntl 95 
                                       s+g+ i++n i+ns  gi+l+ s++n+i++n++e +    ++++++ +e+n+++dn l++ +  +Gi l +s nn++
  gi|386001994|ref|YP_005920293.1| 112 SDGNIIRENVIRNSGFGICLTRSKENNISQNHVECSgfmGTAVFFNICENNILKDNCLRGGWggNGIHLLESDNNVI 188
                                       489999*************************999889999************************************* PP

                              NosD  96 enNtisnnen..yGillsdssnntisnNtis..nnnkGiflensssntitgNriesnqkiGilllsssegntiynNy 168
                                        +N++++ +    Gi+l+ s+ n +++Nt++   ++  i l +s++n+i +N++++n + G+  + +s+gn+iy N+
  gi|386001994|ref|YP_005920293.1| 189 VGNVAQDRSWlgRGIYLDSSNCNFVKGNTATggPEGCSIALFRSNKNKIVQNNLTDNADSGLK-IYHSSGNLIYLNN 264
                                       ******9998889*****************966778889999*********************.************* PP

                              NosD 169 FinnsenvkydgsnnneWnttktsgtniiggpylg..GNyWsdydgeDadgDGigDtpYeindgviDylplv 238
                                       F +n+ n   + ++   W+++++  + + g+++++  GN+Ws y+g Da gDGigD+p++ ++g  D++pl+
  gi|386001994|ref|YP_005920293.1| 265 FDENK-NDPFSRNSTSFWHSPEPIVYRYGGNNFTAylGNFWSVYSGHDAEGDGIGDSPHRFEGGE-DRFPLI 334
                                       *5555.55555556***************************************************.****96 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 !   49.6  14.7     4e-17   3.6e-13      11     141 ..      96     224 ..      87     227 .. 0.89
   2 !   43.2  11.4   3.9e-15   3.5e-11      21     115 ..     173     270 ..     172     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 4e-17
                                       .EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---..SEEE-TT--S--EEES- CS
                        Beta_helix  11 vtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnn..gggialfgasnnlienn 85 
                                       +t++++ +++    Gi + +++n +i++n+i n sg+Gi +++s++n+is n+++ ++  g+++ ++   nn++++n
  gi|386001994|ref|YP_005920293.1|  96 ITFEGFRLTD---LGIDVISDGN-IIRENVIRN-SGFGICLTRSKENNISQNHVECSGfmGTAVFFNICENNILKDN 167
                                       4666666666...5*********.*********.*********************999999999999********** PP

                                       EEES-.SS-SEE-TT-S--EEES-EEESTT..--SEE---TT---EEES-EEES-SSEE CS
                        Beta_helix  86 eitdn.ggsGiylnyssnntienNiidnna..gsGividdsssnvtvtnNtitnnkgaG 141
                                       + +   gg+Gi+l  s+nn+i +N++ + +  g Gi++d+s+ n+ v++Nt+t+   +G
  gi|386001994|ref|YP_005920293.1| 168 CLRGGwGGNGIHLLESDNNVIVGNVAQDRSwlGRGIYLDSSNCNF-VKGNTATGGP-EG 224
                                       ****98778*********************************444.8*****9876.55 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 3.9e-15
                                       -SS-SEEE-SSS-.EEES-EEES..-SS-SEEE-TT-S-EEES-EEE---.SEEE-TT--S--EEES-EEES-SS-S CS
                        Beta_helix  21 sggyGiylrgssnvvienneian..nsgsGiyilgssnntisnntisdnn.gggialfgasnnlienneitdnggsG 94 
                                       +gg+Gi+l +s+n+vi +n+ ++  + g Giy+ +s+ n +++nt +++  g  ialf +++n i  n+ tdn++sG
  gi|386001994|ref|YP_005920293.1| 173 WGGNGIHLLESDNNVIVGNVAQDrsWLGRGIYLDSSNCNFVKGNTATGGPeGCSIALFRSNKNKIVQNNLTDNADSG 249
                                       58999********9999999999999999*****9999********9999999999999999***********999* PP

                                       EE-TT-S--EEES-EEESTT- CS
                        Beta_helix  95 iylnyssnntienNiidnnag 115
                                       + ++ ss n i  N++d+n++
  gi|386001994|ref|YP_005920293.1| 250 LKIYHSSGNLIYLNNFDENKN 270
                                       *99999999999999999993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2026.22
//
Query:       gi|386001995|ref|YP_005920294.1|  [L=281]
Description: hypothetical protein Mhar_1307 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1635.99
//
Query:       gi|386001996|ref|YP_005920295.1|  [L=215]
Description: hypothetical protein Mhar_1308 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1329.19
//
Query:       gi|386001997|ref|YP_005920296.1|  [L=156]
Description: Ribosomal-protein-alanine acetyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-17   61.6   0.1    9.1e-17   61.4   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-12   47.1   0.0    2.9e-12   46.6   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      5e-12   46.1   0.1    7.4e-12   45.5   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.4e-06   28.2   0.1    1.9e-06   27.8   0.1    1.2  1  FR47             FR47-like protein
    2.7e-06   27.5   0.0    4.4e-05   23.6   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    8.7e-06   26.5   0.0    9.9e-06   26.3   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0028   17.8   0.0     0.0048   17.0   0.0    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.022   14.4   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.029   14.1   0.1      0.036   13.8   0.1    1.3  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   4.6e-20   9.1e-17      19     117 .]      39     133 ..      17     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 4.6e-20
                                       HHHHH..HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTT CS
                    Acetyltransf_1  19 aseee..feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareeg 93 
                                       +++    f+e     + ++lvaee+g+++G++ ++ + +    ++ +  +aV++ yrg+G+G++Ll +l+e++r+ g
  gi|386001997|ref|YP_005920296.1|  39 DPYLLtyFYEN---YPTSFLVAEEGGRIVGMVLGFRQSP---LEGRVFWIAVRSGYRGRGVGRRLLMELLEIFRRLG 109
                                       44444222222...3447888***********9999999...67888889*************************** PP

                                       E.SEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  94 i.kkivlaveedndaairlYeklGF 117
                                       + +   l+v+++n++a++lY  lGF
  gi|386001997|ref|YP_005920296.1| 110 VvDV-ILEVRATNKRAQGLYVDLGF 133
                                       *555.89*************88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   1.5e-15   2.9e-12      31     109 ..      52     136 ..      42     156 .] 0.85

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.5e-15
                   Acetyltransf_10  31 alllvaeeggkivGvi.elrdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfY 101
                                       + +lvaeegg+ivG++ + r++    ++  ++V++ yrg+G+g++Ll++++e +++ g     l+v+a++  a+++Y
  gi|386001997|ref|YP_005920296.1|  52 TSFLVAEEGGRIVGMVlGFRQSPlegRVFWIAVRSGYRGRGVGRRLLMELLEIFRRLGVVDvILEVRATNkRAQGLY 128
                                       6799************5448777888****************************99999999*************** PP

                   Acetyltransf_10 102 eklGFkav 109
                                         lGF+  
  gi|386001997|ref|YP_005920296.1| 129 VDLGFEIF 136
                                       *****976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   3.7e-15   7.4e-12       4      75 ..      53     134 ..      48     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.7e-15
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEE...EEEEEETHHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea..ae...kgii...leqlelnaekaikfY 69 
                                       +++Vae++g+ivG++   +++   +   ++aV+  yrg+G+Gr+Ll    ++    g+    le ++ ++++a+++Y
  gi|386001997|ref|YP_005920296.1|  53 SFLVAEEGGRIVGMVLGFRQSpleGRVFWIAVRSGYRGRGVGRRLLMEllEIfrrLGVVdviLE-VRATNKRAQGLY 128
                                       699**********9998888887667777****************9632422444553222123.3334459***** PP

                                       HHTTEE CS
                    Acetyltransf_7  70 eklGFe 75 
                                         lGFe
  gi|386001997|ref|YP_005920296.1| 129 VDLGFE 134
                                       *****8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   9.4e-10   1.9e-06      18      80 ..      72     136 ..      58     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 9.4e-10
                                       E-TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  18 rkdg.gelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       +++  g ++ + v+   r+rG g+rl  +l +  ++ g  +v+l v+a+N++++ ly  lGfe  
  gi|386001997|ref|YP_005920296.1|  72 QSPLeGRVFWIAVRSGYRGRGVGRRLLMELLEIFRRLGvVDVILEVRATNKRAQGLYVDLGFEIF 136
                                       5555599999**************************7736999*******************976 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.2e-08   4.4e-05       2     114 ..      16     117 ..      15     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.2e-08
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtg 78 
                                       ir+ ++ d+ e+++l ++a + ++++l  ++++++++     +l+ae++g++vg++  ++++  +       + v +
  gi|386001997|ref|YP_005920296.1|  16 IRRFEPPDYSEAVALDAEAGGGHDPYL--LTYFYENYPT--SFLVAEEGGRIVGMVLGFRQSP-LE------GRVFW 81 
                                       8999999******************97..6666666655..5*************99998652.33......5689* PP

                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE-- CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfP 114
                                       +av   +rgrgv ++Ll ++le  r  g+  ++l  
  gi|386001997|ref|YP_005920296.1|  82 IAVRSGYRGRGVGRRLLMELLEIFRRLGVVDVILEV 117
                                       **********************99988887777665 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     5e-09   9.9e-06      52     138 .]      50     134 ..      15     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5e-09
                    Acetyltransf_3  52 egygwaivlkdtgviGsv.glrdleeedeeaelgymlaps.fwgkGyateavralleyafeelglerlvavidkeNe 126
                                           +++ +++++++G+v g+r+ + e   + + ++  +s ++g+G+++  +  lle++ ++lg+  ++ ++ ++N+
  gi|386001997|ref|YP_005920296.1|  50 YPTSFLVAEEGGRIVGMVlGFRQSPLE---GRVFWIAVRSgYRGRGVGRRLLMELLEIF-RRLGVVDVILEVRATNK 122
                                       34559996666657****888877777...88888877888*****************9.9999************* PP

                    Acetyltransf_3 127 aSirvleklGfe 138
                                       + + ++  lGfe
  gi|386001997|ref|YP_005920296.1| 123 RAQGLYVDLGFE 134
                                       ***********7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.4e-06    0.0048      52     145 ..      54     144 ..      42     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                    Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvyla.erdnnkeglgrelidaleqvlkeqnienllaeiaspnensi 126
                                       flvae  +rivG+  +    +   ++     +++a +   + +g+gr l+  l +++++ ++     e+ ++n+ ++
  gi|386001997|ref|YP_005920296.1|  54 FLVAEeGGRIVGMVLGFRQSP--LEG---RVFWIAvRSGYRGRGVGRRLLMELLEIFRRLGVVDVILEVRATNKRAQ 125
                                       666666777777655443333..222...3467776777899*********************************** PP

                    Acetyltransf_4 127 qfhkalGFelvgifkkcik 145
                                        ++  lGFe+    k+++ 
  gi|386001997|ref|YP_005920296.1| 126 GLYVDLGFEIFTTAKNYYP 144
                                       **********999999875 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.022      88     139 ..      85     135 ..      77     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                                          +rg+g++++ll +l++ +f++ ++  v++E +++N+ra  l+  +Gfe 
  gi|386001997|ref|YP_005920296.1|  85 RSGYRGRGVGRRLLMELLE-IFRRLGVVDVILEVRATNKRAQGLYVDLGFEI 135
                                       45689***********997.79999*************************85 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.8e-05     0.036      61      89 ..      76     104 ..      48     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                              PanZ  61 eaelsdlcVRevTRrRGVgsyLleearrq 89 
                                       e+++  + VR   R RGVg++Ll e ++ 
  gi|386001997|ref|YP_005920296.1|  76 EGRVFWIAVRSGYRGRGVGRRLLMELLEI 104
                                       77888899***************887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 935.54
//
Query:       gi|386001998|ref|YP_005920297.1|  [L=257]
Description: hypothetical protein Mhar_1310 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.2   0.0         19    5.1   0.0    2.4  2  ChiC      Chitinase C


Domain annotation for each model (and alignments):
>> ChiC  Chitinase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.001        19      52      76 ..      94     118 ..      85     123 .. 0.91
   2 ?    4.5   0.0    0.0017        30     126     154 ..     127     155 ..     122     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.001
                              ChiC  52 yPinpklkitNnstktlPgGteleF 76 
                                        Pi  ++++ N s+ ++P+ t+++F
  gi|386001998|ref|YP_005920297.1|  94 LPIRADIRLFNSSGGEVPAETRVDF 118
                                       59********************999 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0017
                              ChiC 126 lapGasvevdlkyylPvsgpsnftvkvgg 154
                                       + +G++v+ +l+y lP++    ++++ +g
  gi|386001998|ref|YP_005920297.1| 127 VVAGEEVDGHLNYTLPIADQRFVVLAEEG 155
                                       668**************987766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1808.72
//
Query:       gi|386001999|ref|YP_005920298.1|  [L=257]
Description: Beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-21   75.4   1.1    1.7e-20   73.9   1.1    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
      2e-05   24.2   0.0    3.1e-05   23.6   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   1.1   1.9e-24   1.7e-20       6     197 .]      54     234 ..      50     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.9e-24
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +++yl++ + ++++iD+G ++ a+ ++++ ++lg++p ++ ++i TH H+DHiGg + ++++t++ v++ +++ +  
  gi|386001999|ref|YP_005920298.1|  54 CSVYLVDAGSELVMIDAGAGPGAEAILRNVRSLGFDPSRIGYLIATHCHIDHIGGIARIRDETGCLVICSEADREGI 130
                                       89**************************************************************9888777766666 PP

                                       HCHHHHHHHHHCCHH.TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  83 fmeeaddaasrkgll.lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       +  e+   a    ++ + +v++d p   eee+   +    +  +++g+++g++ +vv+++g ++lf  D+  + + +
  gi|386001999|ref|YP_005920298.1| 131 ELGEPRLTAADLYGIeYWPVRVDLPLDGEEEDLRLGEREFRIIAIPGHTPGSIAVVVDLEGLRFLFGQDVHGPFSDA 207
                                       66666555555444465566666666666666666666777777788888888888999999999977777755555 PP

                                       CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +++             ++ +++s+++l +l+a++l+ gH
  gi|386001999|ref|YP_005920298.1| 208 WGSD------------VSRWRRSMERLLDLEADLLCEGH 234
                                       5555............77777777777777777776555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.5e-09   3.1e-05       3     142 ..      66     199 ..      57     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.5e-09
                                       EEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                       + iDag +  +  +  l++v+ l  ++++i  ++ th+H+DH+ g+  +r  +     +++++  ++ +e + ++l 
  gi|386001999|ref|YP_005920298.1|  66 VMIDAGAGPGA--EAILRNVRsLGFDPSRIGYLIATHCHIDHIGGIARIRDET--GCLVICSEADREGIELGEPRLT 138
                                       45666666333..33335667789999***********************933..3557788776666666655544 PP

                                       CHTT.....TTEEEEEE-.......TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS CS
                     Lactamase_B_2  79 leee.....pavnvheld.......wgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigD 142
                                                      ++         +e ++lg  + e++++++++ ++          ++++++ +g r++++ D
  gi|386001999|ref|YP_005920298.1| 139 AADLygieyW-----PVRvdlpldgEEEDLRLG--EREFRIIAIPGHTPG--------SIAVVVDLEGLRFLFGQD 199
                                       4444333321.....222222222234444444..335666666666666........666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1428.89
//
Query:       gi|386002000|ref|YP_005920299.1|  [L=331]
Description: RNA 3'-terminal phosphate cyclase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-75  251.8   0.0    4.8e-75  251.6   0.0    1.1  1  RTC         RNA 3'-terminal phosphate cyclase
    1.1e-13   51.6   0.7    2.1e-13   50.6   0.7    1.5  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.6   0.0   5.3e-79   4.8e-75       2     221 ..       9     318 ..       8     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 251.6 bits;  conditional E-value: 5.3e-79
                                       TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikagey 78 
                                       gegGgqi+Rta+aLsa+tg+pvrI++IR+ R++PGL++qh ta+ +laki++a++eg + gs+e+ F+Pg++++g y
  gi|386002000|ref|YP_005920299.1|   9 GEGGGQIVRTAVALSAVTGEPVRITRIREMRPNPGLSPQHSTAISALAKISDARTEGVRPGSREVLFSPGRVRGGVY 85 
                                       89*************************************************************************** PP

                                       EEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  79 evdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGg 155
                                       +++igtAGs++ll+ +llp+l+ a++p +lt++GgT+v+++p++d+l +v lp++++fg ++++l++++rG++p+Gg
  gi|386002000|ref|YP_005920299.1|  86 DFEIGTAGSVSLLIHCLLPALARADGPATLTVRGGTDVRWSPTIDHLSRVALPAFASFG-VRARLTVERRGYFPRGG 161
                                       ***********************************************************.7**************** PP

                                       EEEEEEEE-.-S---EB............................................................ CS
                                       xxxxxxxxxxxxxxxxx............................................................ RF
                               RTC 156 Gevelevepskklkpie............................................................ 172
                                       G v+le+ p  +l   +                                                            
  gi|386002000|ref|YP_005920299.1| 162 GLVTLETVPG-ELVRADlsapvagavegvshssnlpehvvrrqaeaaigvlrragfdaeiaaearalpstgsgitlw 237
                                       *******984.67777788999******************************************************* PP

                                       ..................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHHH CS
                                       ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ..................................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieqf 215
                                                                         a+vD+hl+dql++++aLa g  ++++ e+t+h+ t+i+++++f
  gi|386002000|ref|YP_005920299.1| 238 sgwkggsalgerglpaervgslaaeelvaqlaskAAVDRHLADQLVPYLALAGG--SYTAPEVTSHASTNIWTASRF 312
                                       ****************************************************98..6******************** PP

                                       SS-EEE CS
                                       xxxxxx RF
                               RTC 216 lgvkfk 221
                                       l+  ++
  gi|386002000|ref|YP_005920299.1| 313 LDRVIS 318
                                       *98765 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.7   2.4e-17   2.1e-13       9     102 ..     186     268 ..     183     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.4e-17
                                       EEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-TT- CS
                        RTC_insert   9 irGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgekgv 85 
                                       ++Gv+++++++ +v +r++eaa gvL++++ d +i+++     +++  s G+gi+L+   +      g++alge+g 
  gi|386002000|ref|YP_005920299.1| 186 VEGVSHSSNLPEHVVRRQAEAAIGVLRRAGFDAEIAAE-----ARALPSTGSGITLWSGWK------GGSALGERGL 251
                                       89********************************9999.....5677899*******9995......58******** PP

                                       -HHHHHHHHHHHHHHHH CS
                        RTC_insert  86 ppedvGeeaaeeLleei 102
                                       p+e+vG  aaeeL++++
  gi|386002000|ref|YP_005920299.1| 252 PAERVGSLAAEELVAQL 268
                                       *************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 2147.49
//
Query:       gi|386002001|ref|YP_005920300.1|  [L=91]
Description: DNA-directed RNA polymerase subunit L [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-15   56.1   0.0    2.9e-15   55.8   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.015   14.7   0.0    1.3  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   3.2e-19   2.9e-15       2      75 .]      13      85 ..      12      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 3.2e-19
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdeleee 75
                                      l++e+ gE hTL+nlLr++ll++++V +a+Y+ ++P+  +  +r  t+ + +p+  L++ ++++  +++e+eee
  gi|386002001|ref|YP_005920300.1| 13 LHLEFFGESHTLLNLLRTELLEDDRVLIATYDAKFPMMTNPIFRLRTR-DVDPVLLLNEVASRIAGMVEEFEEE 85
                                      7899**********************************9999999997.69********************985 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-06     0.015       5      36 ..      18      58 ..       5      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-06
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxx RF
                         RNA_pol_L  5 rgvdhtlgNaLRrillsevpgvaiea..........pvvkvn 36
                                       g++htl N LR  ll e   v i++          p+++++
  gi|386002001|ref|YP_005920300.1| 18 FGESHTLLNLLRTELL-EDDRVLIATydakfpmmtnPIFRLR 58
                                      699*************.9999888887888877777444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 703.41
//
Query:       gi|386002002|ref|YP_005920301.1|  [L=191]
Description: hypothetical protein Mhar_1314 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-12   45.4   0.3    8.6e-12   44.7   0.3    1.4  1  ECR1_N         Exosome complex exonuclease RRP4 N-terminal re
     0.0034   18.0   0.2     0.0069   17.0   0.1    1.6  2  EXOSC1         Exosome component EXOSC1/CSL4
  ------ inclusion threshold ------
      0.017   15.1   0.4      0.028   14.4   0.4    1.3  1  DZR            Double zinc ribbon
      0.029   14.1   1.0      0.053   13.3   1.0    1.4  1  DUF3039        Protein of unknown function (DUF3039)
      0.062   13.2   2.3        0.3   11.0   2.3    2.0  1  Nudix_N_2      Nudix N-terminal
       0.11   12.9   0.4        4.9    7.6   0.0    2.4  3  S1             S1 RNA binding domain
       0.23   11.5   1.2       0.58   10.2   0.9    1.7  2  HypA           Hydrogenase/urease nickel incorporation, metal
       0.45   10.2   4.7        2.5    7.8   4.7    2.0  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.3   3.8e-15   8.6e-12       1      37 [.       9      45 ..       9      46 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.8e-15
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      iV+PG+v++ +eef +G+GTY rgg++ +s +G++ev
  gi|386002002|ref|YP_005920301.1|  9 IVIPGDVVGASEEFSPGEGTYLRGGHLLSSSTGVLEV 45
                                      9*********************************998 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         8   1.8e+04      94     103 ..       8      17 ..       3      19 .. 0.69
   2 !   17.0   0.1   3.1e-06    0.0069       3      58 ..      65     126 ..      63     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8
                                       CTEECTTEEE CS
                            EXOSC1  94 emfrpGDIvr 103
                                       +++ pGD+v 
  gi|386002002|ref|YP_005920301.1|   8 NIVIPGDVVG 17 
                                       5677899885 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.1e-06
                                       -TT-EEEEEEEEEESSEEEEEEEEECTB.....SBCCCEEECCCTTSS--STS.TTSSCCHC CS
                            EXOSC1   3 kegdvVLarvtrlrkkqalveilsvege.....nnvlsdsgvgangegavkei.eaggglds 58 
                                       k gdvV +++t+l+ + a++ +  ++g       n+ + ++++ +++++vkei ++ g  d+
  gi|386002002|ref|YP_005920301.1|  65 KNGDVVVGQITDLKDSLAILRLAFKRGCearpiFNTEALLHISRVKSSYVKEIrQVLGLRDI 126
                                       579*********************9998777776777899*************555554444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.3e-05     0.028      13      37 ..     152     176 ..     146     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                               DZR  13 rfCseCgtklkavaaedrCpsCgek 37 
                                        +C++C ++lk   +  +Cp+C++ 
  gi|386002002|ref|YP_005920301.1| 152 AYCGRCASPLKLDGKRLVCPECEQV 176
                                       69*********9999*******986 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   2.4e-05     0.053      25      52 ..     149     176 ..     147     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                           DUF3039  25 pVvALCGkvwvptrdpkkfPvCpeCkei 52 
                                        V+A CG++  p +   k  vCpeC+++
  gi|386002002|ref|YP_005920301.1| 149 VVKAYCGRCASPLKLDGKRLVCPECEQV 176
                                       599**********************986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.3   0.00013       0.3       2      31 ..     153     176 ..     152     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                       B-TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2   2 FCsqCGtpvelripdgDnreRlvCpaCgti 31 
                                       +C  C++p++l         RlvCp C+ +
  gi|386002002|ref|YP_005920301.1| 153 YCGRCASPLKLDG------KRLVCPECEQV 176
                                       9*******99987......6*******987 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.8   1.5e+04      60      69 ..      42      51 ..      42      54 .. 0.74
   2 ?    3.0   0.0     0.057   1.3e+02       1      24 [.      63      86 ..      63      93 .. 0.83
   3 ?    7.6   0.0    0.0022       4.9      27      62 ..      99     133 ..      96     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.8
                                      EEEEETTTTE CS
                                S1 60 vlkvdkdrrr 69
                                      vl+vd  rr+
  gi|386002002|ref|YP_005920301.1| 42 VLEVDAGRRS 51
                                      7888888886 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.057
                                      HSTTTCEEEEEEEEEETTEEEEEE CS
                                S1  1 kpekgevveGeVtsvtkgGafVel 24
                                      k++ g+vv G +t++ +  a+ +l
  gi|386002002|ref|YP_005920301.1| 63 KLKNGDVVVGQITDLKDSLAILRL 86
                                      5789**********9998777776 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0022
                                       TEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEE CS
                                S1  27 gvegfvpaselsrdarvedpdevlkvGdevkvkvlk 62 
                                       + e+++++s +++   v+++ +vl   d vk+k+++
  gi|386002002|ref|YP_005920301.1|  99 NTEALLHISRVKSS-YVKEIRQVLGLRDIVKAKIID 133
                                       5799**********.9******************97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   2.5e+03      31      68 ..      69     110 ..      57     115 .. 0.63
   2 ?   10.2   0.9   0.00026      0.58      69      96 ..     150     177 ..     132     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                       EEEETTCT--HHH..HHHHHHHHHCC.T.TT.T-EEEEEEE- CS
                              HypA  31 vevGelsgvepea..Lefafellaegtv.le.gaeLeieevp 68 
                                       v vG+++ ++ +   L+ af+  +e  + ++ +a L+i++v+
  gi|386002002|ref|YP_005920301.1|  69 VVVGQITDLKDSLaiLRLAFKRGCEARPiFNtEALLHISRVK 110
                                       677777777664333777777776666643324556666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                                       -EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsad 96 
                                       vk++C +C +  +l+ k+l Cp+C++ +
  gi|386002002|ref|YP_005920301.1| 150 VKAYCGRCASPLKLDGKRLVCPECEQVE 177
                                       6899*********9988899****9865 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.7    0.0011       2.5       5      28 ..     153     174 ..     152     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                     zf-NADH-PPase   5 FCgrCGaptepaeggwarvCpaCg 28 
                                       +CgrC++p ++  +g  +vCp C 
  gi|386002002|ref|YP_005920301.1| 153 YCGRCASPLKL--DGKRLVCPECE 174
                                       9*******987..55588888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1329.97
//
Query:       gi|386002003|ref|YP_005920302.1|  [L=197]
Description: Ribosomal L11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-13   49.5   0.0    4.8e-13   49.0   0.0    1.1  1  MTS              Methyltransferase small domain
      4e-09   36.3   0.1      5e-09   36.0   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.3e-08   35.4   0.1    1.9e-08   34.9   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    2.2e-08   34.0   0.0    2.6e-08   33.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.8e-07   29.4   0.4    5.6e-06   26.2   0.4    2.0  1  UPF0020          Putative RNA methylase family UPF0020
    3.2e-06   27.7   0.1    7.4e-06   26.5   0.1    1.6  2  Methyltransf_11  Methyltransferase domain
     0.0033   17.3   0.0     0.0036   17.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.013   15.1   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.014   15.1   0.0      0.021   14.6   0.0    1.3  1  Met_10           Met-10+ like-protein
      0.014   15.4   0.0      0.017   15.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.024   15.4   0.0      0.035   14.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      0.025   14.2   0.0      0.033   13.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.098   12.4   0.0       0.24   11.1   0.0    1.6  2  N6_N4_Mtase      DNA methylase
       0.19   11.4   0.0       0.25   11.1   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   3.7e-16   4.8e-13      19     112 ..      33     124 ..      30     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.7e-16
                                       HHHHHHHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST CS
                               MTS  19 GsklLletlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve 94 
                                       +s+lL ++l    l+g+v DlGcG+Gvl++ +a    +   + v+ d   l++a+en+ + +++v++v  dv   + 
  gi|386002003|ref|YP_005920302.1|  33 ASELLYSALLRGdLEGTVCDLGCGTGVLAIGAALLGGR--AVGVELDPSPLRIARENALRLGADVQFVRGDVATVAL 107
                                       79999999877669*******************99999..799*****************************98888 PP

                                       TS-EEEEEE---STTTCH CS
                               MTS  95 ekkfdlivsNPPfhagka 112
                                        k + ++v+NPPf a++ 
  gi|386002003|ref|YP_005920302.1| 108 -KGVSTVVMNPPFGAQRG 124
                                       .9***********99876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   3.9e-12     5e-09     163     212 ..      48      96 ..      28     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.9e-12
                              PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveak 212
                                        +v D+G+G+G+Lai+aa+Lg  ++v+v +D+  +++a+eNa + + + +
  gi|386002003|ref|YP_005920302.1|  48 GTVCDLGCGTGVLAIGAALLGG-RAVGVELDPSPLRIARENALRLGADVQ 96 
                                       49*******************7.578***************987655555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.5e-11   1.9e-08       1      61 [.      50     108 ..      50     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.5e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfe 61 
                                       v dlGcGtG l++ +a   g ++ +gv+++++ l++are+a + g++v+fv+gd+ ++ ++
  gi|386002003|ref|YP_005920302.1|  50 VCDLGCGTGVLAIGAALL-G-GRAVGVELDPSPLRIARENALRLGADVQFVRGDVATVALK 108
                                       79**************88.5.9*********************************988765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.1e-11   2.6e-08       6      65 ..      49     104 ..      45     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.1e-11
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee 65 
                                       +v+DlGCGtG l++ +a +lg  ++ vG++ ++  ++ Arena +lg d v+F +gd+ +
  gi|386002003|ref|YP_005920302.1|  49 TVCDLGCGTGVLAIGAA-LLG--GRAVGVELDPSPLRIARENALRLGAD-VQFVRGDVAT 104
                                       79***************.775..7899*********************8.*******987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.4   4.4e-09   5.6e-06      31     139 ..      49     127 ..      26     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.4e-09
                                       -EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEE CS
                           UPF0020  31 pllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdlief 107
                                       +  D  CG+G ++I aallg +++                          g++ld++ ++ areNa +   g  ++f
  gi|386002003|ref|YP_005920302.1|  49 TVCDLGCGTGVLAIGAALLGGRAV--------------------------GVELDPSPLRIARENALRL--GADVQF 97 
                                       566667***************999..........................***************9765..66799* PP

                                       EE--GGG--STTS---EEEE----------HH CS
                           UPF0020 108 sqadaakLrlkegevdvivtnpPYGerlgskk 139
                                       +  d+a +   +g v ++v npP+G   gs +
  gi|386002003|ref|YP_005920302.1|  98 VRGDVATVA-LKG-VSTVVMNPPFGAQRGSLG 127
                                       *******99.775.99*********9877755 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   5.8e-09   7.4e-06       2      58 ..      52     108 ..      51     115 .. 0.94
   2 ?   -3.0   0.0       9.1   1.2e+04      45      58 ..     159     172 ..     138     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.8e-09
                                       EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfe 58 
                                       d+GcGtG la   a  g+r vgv+l++  l++a+e+a + g  v+fv++d+ ++ ++
  gi|386002003|ref|YP_005920302.1|  52 DLGCGTGVLAIGAALLGGRAVGVELDPSPLRIARENALRLGADVQFVRGDVATVALK 108
                                       9**************************************************998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.1
                                       EEETTEECCCTSS- CS
                   Methyltransf_11  45 vefvvadaeklpfe 58 
                                         + v++++k+pf+
  gi|386002003|ref|YP_005920302.1| 159 EPCKVEEVQKIPFP 172
                                       34677888888886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0036      19      62 ..      43     100 ..      24     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                   Methyltransf_23  19 klraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..............k 62 
                                       + +  g v+d+GcGtG l+  ++  g   +gv+l+p    ia+              +
  gi|386002003|ref|YP_005920302.1|  43 RGDLEGTVCDLGCGTGVLAIGAALLGGRAVGVELDPSPLRIARenalrlgadvqfvrG 100
                                       4677899***************************999998888766666555555550 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     1e-05     0.013      41     127 ..      47     123 ..      32     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       eg +v Dl +G+G+l++ A+  g  +av ve d++ ++i +en  +l+++  ++ ++ d +  +lk       +  v
  gi|386002003|ref|YP_005920302.1|  47 EG-TVCDLGCGTGVLAIGAALLG-GRAVGVELDPSPLRIARENALRLGAD--VQFVRGDVATVALKG------VSTV 113
                                       44.489**************999.89**********************66..788888888777766......5679 PP

                                       EE--SSSTTC CS
                     Cons_hypoth95 118 flDPPyakel 127
                                        ++PP+ ++ 
  gi|386002003|ref|YP_005920302.1| 114 VMNPPFGAQR 123
                                       99****9875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.021     103     180 ..      49     121 ..      42     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                       EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TTT CS
                            Met_10 103 vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpks 179
                                       +V+d+  G G +ai +a    + r ++++l+P+  +  +en    ++   v+ + +D+++v+  + +  vvmn p  
  gi|386002003|ref|YP_005920302.1|  49 TVCDLGCGTGVLAIGAAL--LGGRAVGVELDPSPLRIARENAL--RLGADVQFVRGDVATVAL-KGVSTVVMNPPFG 120
                                       7****************9..556679**************986..578889999*******95.5567899998865 PP

                                       G CS
                            Met_10 180 a 180
                                       a
  gi|386002003|ref|YP_005920302.1| 121 A 121
                                       5 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.3e-05     0.017      26      91 ..      47     104 ..      27     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                   Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                                       + tv+D+G+G g L+   al    ++ + vg+++  +  + a++ a +lg    ++++f  +++++
  gi|386002003|ref|YP_005920302.1|  47 EGTVCDLGCGTGVLAIGAAL----LGGRAVGVELDPSPLRIARENALRLG----ADVQFVRGDVAT 104
                                       679***************99....7************************9....456666666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.7e-05     0.035       2      56 ..      52     103 ..      51     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnveleal 56 
                                       ++GcGtG l+   +    + + +gv+++ps +  a+e   + +  ++++v+ ++ 
  gi|386002003|ref|YP_005920302.1|  52 DLGCGTGVLAIGAALL--GGRAVGVELDPSPLRIARENALRLG-ADVQFVRGDVA 103
                                       89*****999999888..**************77776666655.46666666555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.033       3      82 ..      49     120 ..      47     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                       ++ Dl +G+G  +i  al + + +++e +++ l +a +Na        +++v gdv ++  k     +  + v++ p
  gi|386002003|ref|YP_005920302.1|  49 TVCDLGCGTGVLAIGAALLGGRAVGVELDPSPLRIARENALRL--GADVQFVRGDVATVALK----GV--STVVMNP 117
                                       578*************************************988..67899*****9875433....23..4577777 PP

                   Methyltransf_15  80 PwG 82 
                                       P G
  gi|386002003|ref|YP_005920302.1| 118 PFG 120
                                       777 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.24     176     230 ..      28      85 ..      13      86 .. 0.79
   2 ?   -1.6   0.0       1.4   1.7e+03       1      15 [.     110     124 ..     110     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                       --HHHHHHHHHHHS-T...T-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       N6_N4_Mtase 176 kPvallerlIklstkk...gdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                        P   + +l+ + +     +++v D  +G+G  a+ a+ lg +++G+e +++ +++a 
  gi|386002003|ref|YP_005920302.1|  28 TPSTVASELLYSALLRgdlEGTVCDLGCGTGVLAIGAALLGGRAVGVELDPSPLRIAR 85 
                                       5555666666555555344678****************************99888775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       EEEEEE--SSSSSCS CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkd 15 
                                       v ++v  pP+++++ 
  gi|386002003|ref|YP_005920302.1| 110 VSTVVMNPPFGAQRG 124
                                       678999****99987 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.25      68     132 ..      41     101 ..      17     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       ll+ +    v ++G+G+G l+ + a l+g  gr+v++e  ++  + a++n  +l+++ v++v gD
  gi|386002003|ref|YP_005920302.1|  41 LLRGDLEGTVCDLGCGTGVLA-IGAALLG--GRAVGVELDPSPLRIARENALRLGAD-VQFVRGD 101
                                       33334456899*******996.6677776..5669***************9999986.6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 1099.29
//
Query:       gi|386002004|ref|YP_005920303.1|  [L=785]
Description: hypothetical protein Mhar_1316 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-42  143.7  14.8    1.9e-12   47.3   0.4    5.0  6  TPR_12    Tetratricopeptide repeat
    2.8e-20   70.7  13.2     0.0013   18.7   1.1    7.5  6  TPR_2     Tetratricopeptide repeat
    1.6e-18   65.7   9.8    5.1e-05   22.9   0.0    6.6  6  TPR_1     Tetratricopeptide repeat
    3.2e-18   64.4  12.4     0.0022   17.9   0.2    7.3  7  TPR_7     Tetratricopeptide repeat
    5.2e-14   51.6  11.6      0.013   15.4   0.8    6.0  5  TPR_10    Tetratricopeptide repeat
    3.3e-13   48.7  14.6      0.013   15.7   0.0    7.1  7  TPR_8     Tetratricopeptide repeat
    4.9e-11   42.6   5.3    1.5e-08   34.4   0.5    2.7  2  TPR_MalT  MalT-like TPR region
      1e-09   38.3   0.1    9.2e-06   25.3   0.2    2.8  3  SNAP      Soluble NSF attachment protein, SNAP
    1.6e-07   30.9   1.6        0.6    9.8   0.1    5.3  4  TPR_11    TPR repeat
    0.00054   20.6  21.7        9.6    7.3   0.1    8.0  6  TPR_14    Tetratricopeptide repeat
      0.001   19.3   1.7        5.1    7.7   0.0    4.1  3  TPR_17    Tetratricopeptide repeat
     0.0016   18.5   2.1      0.013   15.6   0.9    2.9  3  DUF3856   Domain of Unknown Function (DUF3856)
     0.0032   17.9   0.9     0.0032   17.9   0.9    5.5  4  TPR_4     Tetratricopeptide repeat
     0.0098   15.6   0.2       0.45   10.2   0.1    2.7  3  RPN7      26S proteasome subunit RPN7
  ------ inclusion threshold ------
      0.028   14.7   0.1      0.069   13.4   0.1    1.7  1  Coat_F    Coat F domain
       0.03   14.4   0.2        2.7    8.1   0.0    3.5  4  Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
      0.084   12.9   0.2        1.2    9.2   0.2    2.8  3  DUF627    Protein of unknown function (DUF627)
       0.13   11.9   0.1        3.1    7.6   0.1    2.5  2  Dpy-30    Dpy-30 motif
       0.77   10.5   4.7         58    4.6   0.1    5.5  4  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.035        33      50      73 ..      68      91 ..      66      95 .. 0.92
   2 !   42.9   0.7   4.6e-14   4.4e-11       4      77 .]     101     172 ..      98     172 .. 0.94
   3 !   47.3   0.4     2e-15   1.9e-12       2      76 ..     139     211 ..     138     212 .. 0.93
   4 !   44.5   0.1   1.5e-14   1.4e-11       2      77 .]     179     252 ..     178     252 .. 0.95
   5 !   42.7   0.1   5.4e-14   5.1e-11       1      76 [.     218     291 ..     218     292 .. 0.96
   6 ?   -2.9   0.1       9.1   8.6e+03      29      52 ..     333     355 ..     329     357 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                            TPR_12 50 nLgrlyralgryeeAlelleeala 73
                                       Lg+++r++g++  A + +++al 
  gi|386002004|ref|YP_005920303.1| 68 RLGDICRLAGHLGIAARCYNKALS 91
                                      59********************95 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 4.6e-14
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                        ++nnl++v++r+g +  Al ++eka e +++   +d+  +a++l n+g +yr ++ y+eAl+  +++l+i+++
  gi|386002004|ref|YP_005920303.1| 101 VLYNNLGQVHARQGYLGRALHYYEKAAEGFSSQ--GDSGSLAQVLGNMGSAYRSSESYDEALDSCRKSLEIFRE 172
                                       57889*************************999..88999*******************************985 PP

  == domain 3  score: 47.3 bits;  conditional E-value: 2e-15
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a++l n+++++r  + ydeAl+ ++k+lei+r+l  +d  ++a+    +gr++ ++g+y+ Al+ +e++la +e
  gi|386002004|ref|YP_005920303.1| 139 LAQVLGNMGSAYRSSESYDEALDSCRKSLEIFREL--EDESGVAQMTGSIGRIHAEMGEYDLALQEYEKSLADFE 211
                                       689999***************************99..66668*****************************9665 PP

  == domain 4  score: 44.5 bits;  conditional E-value: 1.5e-14
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       va++   ++ +++++g+yd Al+ +ek+l+ +++l  +d  ++a++l+ +gr+  + ++ + A+ +++++++i+e+
  gi|386002004|ref|YP_005920303.1| 179 VAQMTGSIGRIHAEMGEYDLALQEYEKSLADFEQL--GDQRQVAWILNRMGRVNAEIEKRDVAIGYYNRSMEIFEE 252
                                       67888889*************************99..7888********************************986 PP

  == domain 5  score: 42.7 bits;  conditional E-value: 5.4e-14
                            TPR_12   1 dvatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +va++ln+++ v ++ ++ d A+ ++++++ei++++  ++++++  +l nLgrl++ +g+++ A ++le +l++ +
  gi|386002004|ref|YP_005920303.1| 218 QVAWILNRMGRVNAEIEKRDVAIGYYNRSMEIFEEI--GQRHNAGVVLANLGRLHLDRGDLDLAADHLETSLDLIR 291
                                       6899**99****************************..8888******************************9977 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 9.1
                            TPR_12  29 aleiarrllGpdhpltattlrnLg 52 
                                       a e++ ++   +++++a++l  L+
  gi|386002004|ref|YP_005920303.1| 333 AAELFIEA-SSYYAGAAECLDELA 355
                                       44445333.245556666665555 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00064       0.6       6      29 ..      68      91 ..      66      95 .. 0.93
   2 !   18.7   1.1   1.4e-06    0.0013       3      29 ..     102     128 ..     100     128 .. 0.94
   3 !   14.0   0.0   4.3e-05      0.04       1      31 [.     140     170 ..     140     173 .. 0.91
   4 !   12.4   0.1   0.00014      0.13       7      29 ..     186     208 ..     185     212 .. 0.92
   5 ?    4.2   0.0      0.06        57       3      32 ..     222     251 ..     220     253 .. 0.90
   6 !   12.8   0.0    0.0001     0.097       4      32 ..     263     291 ..     261     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00064
                             TPR_2  6 nlGlayyklgdyeeAleafekAle 29
                                      +lG++++ +g++  A+++++kAl+
  gi|386002004|ref|YP_005920303.1| 68 RLGDICRLAGHLGIAARCYNKALS 91
                                      89********************97 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.4e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                       +++nlG++++++g + +Al+++ekA e
  gi|386002004|ref|YP_005920303.1| 102 LYNNLGQVHARQGYLGRALHYYEKAAE 128
                                       69***********************76 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4.3e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a++l n+G ay+ +  y+eAl+ ++k+le+ 
  gi|386002004|ref|YP_005920303.1| 140 AQVLGNMGSAYRSSESYDEALDSCRKSLEIF 170
                                       568899***********************97 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00014
                             TPR_2   7 lGlayyklgdyeeAleafekAle 29 
                                       +G++++++g+y+ Al+ +ek+l+
  gi|386002004|ref|YP_005920303.1| 186 IGRIHAEMGEYDLALQEYEKSLA 208
                                       699*****************996 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       +l+++G++ ++  + + A+ +++++ e+ +
  gi|386002004|ref|YP_005920303.1| 222 ILNRMGRVNAEIEKRDVAIGYYNRSMEIFE 251
                                       799*********************999875 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 0.0001
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                       l nlG++++ +gd++ A++++e +l l  
  gi|386002004|ref|YP_005920303.1| 263 LANLGRLHLDRGDLDLAADHLETSLDLIR 291
                                       789**********************9865 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0098       9.2       6      29 ..      68      91 ..      66      92 .. 0.93
   2 !   12.8   0.8   8.3e-05     0.078       3      28 ..     102     127 ..     100     128 .. 0.93
   3 !   22.9   0.0   5.4e-08   5.1e-05       1      31 [.     140     170 ..     140     173 .. 0.93
   4 !   11.4   0.1   0.00023      0.22       7      28 ..     186     207 ..     184     208 .. 0.92
   5 ?   -0.6   0.0       1.4   1.4e+03       2      30 ..     221     249 ..     220     252 .. 0.76
   6 !   11.8   0.0   0.00018      0.17       3      33 ..     262     292 ..     261     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0098
                                      HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1  6 nlGnayfklgkydeAleyyekALe 29
                                      +lG +++  g +  A  +y+kAL+
  gi|386002004|ref|YP_005920303.1| 68 RLGDICRLAGHLGIAARCYNKALS 91
                                      89********************96 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekAL 28 
                                        ++nlG+++ ++g +  Al yyekA 
  gi|386002004|ref|YP_005920303.1| 102 LYNNLGQVHARQGYLGRALHYYEKAA 127
                                       69**********************96 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 5.4e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a++l n+G ay++ + ydeAl+ ++k Le+ 
  gi|386002004|ref|YP_005920303.1| 140 AQVLGNMGSAYRSSESYDEALDSCRKSLEIF 170
                                       7899*************************96 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00023
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyyekAL 28 
                                       +G ++ ++g+yd Al+ yek L
  gi|386002004|ref|YP_005920303.1| 186 IGRIHAEMGEYDLALQEYEKSL 207
                                       799*****************98 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        +l+++G +  + +k d A+ yy++  e+
  gi|386002004|ref|YP_005920303.1| 221 WILNRMGRVNAEIEKRDVAIGYYNRSMEI 249
                                       66778887777777777799999998887 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       +l nlG +++  g++d A ++ e  L l  +
  gi|386002004|ref|YP_005920303.1| 262 VLANLGRLHLDRGDLDLAADHLETSLDLIRK 292
                                       588***********************99665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.37   3.5e+02       4      32 ..      68      96 ..      66     100 .. 0.81
   2 !   17.9   0.2   2.3e-06    0.0022       2      33 ..     103     134 ..     102     137 .. 0.87
   3 !   15.4   0.0   1.4e-05     0.013       2      35 ..     143     176 ..     142     177 .. 0.92
   4 !   13.6   0.1   5.3e-05      0.05       4      27 ..     185     208 ..     184     217 .. 0.90
   5 ?    1.5   0.0      0.41   3.9e+02       2      29 ..     223     250 ..     222     256 .. 0.78
   6 !   15.5   0.0   1.4e-05     0.013       2      28 ..     263     290 ..     262     297 .. 0.88
   7 ?   -2.2   0.0       6.2   5.9e+03      12      24 ..     341     353 ..     333     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.37
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdp 32
                                      +L+++++  G+   A+++y ++L  t d+
  gi|386002004|ref|YP_005920303.1| 68 RLGDICRLAGHLGIAARCYNKALSQTTDQ 96
                                      79999999999999*******88555555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.3e-06
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++nL++++ r+G+  +A+ +ye++ +  ++++
  gi|386002004|ref|YP_005920303.1| 103 YNNLGQVHARQGYLGRALHYYEKAAEGFSSQG 134
                                       8**********************887666665 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.4e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       L n++++y++   y+eA++ +++sL++ ++ ed+
  gi|386002004|ref|YP_005920303.1| 143 LGNMGSAYRSSESYDEALDSCRKSLEIFRELEDE 176
                                       89************************99988876 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 5.3e-05
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLa 27 
                                        ++r++ ++G+y+ A++ ye+sLa
  gi|386002004|ref|YP_005920303.1| 185 SIGRIHAEMGEYDLALQEYEKSLA 208
                                       58*******************994 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.41
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLalt 29 
                                       L++++r+  +  +++ Ai++y +s+++ 
  gi|386002004|ref|YP_005920303.1| 223 LNRMGRVNAEIEKRDVAIGYYNRSMEIF 250
                                       6677777777889999*****9988775 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 1.4e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.al 28 
                                       L nL+rl+ ++Gd + A++++e sL  +
  gi|386002004|ref|YP_005920303.1| 263 LANLGRLHLDRGDLDLAADHLETSLdLI 290
                                       89*********************99444 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 6.2
                             TPR_7  12 lGdyeeAielyeq 24 
                                         +y+ A+e++ +
  gi|386002004|ref|YP_005920303.1| 341 SSYYAGAAECLDE 353
                                       6789999999877 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   1.4e-05     0.013       5      30 ..     103     128 ..     101     129 .. 0.94
   2 !   14.2   0.0   3.3e-05     0.031       2      35 ..     140     173 ..     139     176 .. 0.93
   3 !   10.6   0.0   0.00043       0.4       8      34 ..     186     212 ..     179     215 .. 0.88
   4 ?    1.0   0.0      0.46   4.4e+02       1      35 [.     219     253 ..     219     257 .. 0.89
   5 !   12.6   0.0    0.0001     0.097       5      34 ..     263     292 ..     261     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                            TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                                       +nNL+ ++ ++g + +A+ ++e+a +
  gi|386002004|ref|YP_005920303.1| 103 YNNLGQVHARQGYLGRALHYYEKAAE 128
                                       9**********************975 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.3e-05
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                       A  l N++ a+r+   ydeA++ ++++l+i r+l
  gi|386002004|ref|YP_005920303.1| 140 AQVLGNMGSAYRSSESYDEALDSCRKSLEIFREL 173
                                       78899*************************9886 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00043
                            TPR_10   8 LanalrqrgrydeAealleealairrr 34 
                                       +++++ ++g+yd A++ +e++la  ++
  gi|386002004|ref|YP_005920303.1| 186 IGRIHAEMGEYDLALQEYEKSLADFEQ 212
                                       89********************97665 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.46
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrl 35 
                                       +A +ln ++++  +  ++d A  ++ ++++i +++
  gi|386002004|ref|YP_005920303.1| 219 VAWILNRMGRVNAEIEKRDVAIGYYNRSMEIFEEI 253
                                       6899*****************99999999998775 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.0001
                            TPR_10   5 lnNLanalrqrgrydeAealleealairrr 34 
                                       l NL++++ +rg++d A ++le +l++ r+
  gi|386002004|ref|YP_005920303.1| 263 LANLGRLHLDRGDLDLAADHLETSLDLIRK 292
                                       78***********************99776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.26   2.5e+02       6      29 ..      68      91 ..      68      94 .. 0.92
   2 !   13.6   0.3   6.1e-05     0.058       3      28 ..     102     127 ..     100     128 .. 0.94
   3 !   15.7   0.0   1.4e-05     0.013       1      30 [.     140     169 ..     140     172 .. 0.93
   4 !   10.9   0.1   0.00047      0.44       6      28 ..     185     207 ..     180     208 .. 0.92
   5 ?   -0.3   0.0       1.8   1.7e+03       5      30 ..     224     249 ..     222     253 .. 0.62
   6 !    9.7   0.0    0.0011         1       4      33 ..     263     292 ..     261     293 .. 0.91
   7 ?   -2.5   0.1       9.1   8.6e+03      12      26 ..     500     514 ..     496     515 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.26
                                      HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8  6 nlgsiylklgdyeeAkeyyekale 29
                                      +lg+i++  g +  A  +y+kal+
  gi|386002004|ref|YP_005920303.1| 68 RLGDICRLAGHLGIAARCYNKALS 91
                                      589999999*************97 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekal 28 
                                       +y+nlg+++  +g +  A  yyeka 
  gi|386002004|ref|YP_005920303.1| 102 LYNNLGQVHARQGYLGRALHYYEKAA 127
                                       69**********************96 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.4e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+++ n+gs+y++ + y+eA  +++k le+
  gi|386002004|ref|YP_005920303.1| 140 AQVLGNMGSAYRSSESYDEALDSCRKSLEI 169
                                       68999***********************98 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00047
                                       HHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekal 28 
                                        +g+i+ ++g+y+ A + yek l
  gi|386002004|ref|YP_005920303.1| 185 SIGRIHAEMGEYDLALQEYEKSL 207
                                       59*******************87 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.8
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekalel 30 
                                       +++g++  + ++ + A+ yy++  e+
  gi|386002004|ref|YP_005920303.1| 224 NRMGRVNAEIEKRDVAIGYYNRSMEI 249
                                       56666666666677777777776665 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       + nlg+++l+ gd++ A   +e  l+l ++
  gi|386002004|ref|YP_005920303.1| 263 LANLGRLHLDRGDLDLAADHLETSLDLIRK 292
                                       78***********************99876 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 9.1
                                       HHTT-HHHHHHHHHH CS
                             TPR_8  12 lklgdyeeAkeyyek 26 
                                       +++  ++ A++++e 
  gi|386002004|ref|YP_005920303.1| 500 ETMAYLKRAESAFEL 514
                                       566677788888876 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.4   0.00083      0.78      83     150 ..      66     128 ..      59     146 .. 0.82
   2 !   34.4   0.5   1.6e-11   1.5e-08      14     176 ..     153     314 ..     147     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00083
                          TPR_MalT  83 llqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGie 150
                                       + ++++i +  G+L  A++ y++al + t+q+ +      +l+  l++++  ++ L +A ++ +++ e
  gi|386002004|ref|YP_005920303.1|  66 IKRLGDICRLAGHLGIAARCYNKALSQTTDQHVR-----SVLYNNLGQVHARQGYLGRALHYYEKAAE 128
                                       5578888888999999999999999988888888.....48888889999999999999999888765 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.6e-11
                          TPR_MalT  14 sgdaeralelArqALallpeddllar.iaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaei 89 
                                       s+  ++al+ +r+ L++++e +  +  +++t ++G+++   G+ + Alq +++  +   q +  +++++ l + + +
  gi|386002004|ref|YP_005920303.1| 153 SESYDEALDSCRKSLEIFRELEDESGvAQMTGSIGRIHAEMGEYDLALQEYEKSLADFEQLGDQRQVAWILNRMGRV 229
                                       66778999999999999999777777578899********************************************* PP

                          TPR_MalT  90 lvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvl 166
                                         +  + + A+  y+++++  +e g+++   +g++l+ l++l+++++dL+ A++hl+ +++l+++  + +++ a   
  gi|386002004|ref|YP_005920303.1| 230 NAEIEKRDVAIGYYNRSMEIFEEIGQRH--NAGVVLANLGRLHLDRGDLDLAADHLETSLDLIRKNMQPVRANAVSW 304
                                       ***************************8..7889999****************************866666777777 PP

                          TPR_MalT 167 larialaqGd 176
                                       l  +++ +G+
  gi|386002004|ref|YP_005920303.1| 305 LSAVRAIRGR 314
                                       8888888776 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   9.8e-09   9.2e-06      47     180 ..      75     205 ..      68     213 .. 0.87
   2 !    9.7   0.0   0.00053       0.5      90     158 ..     236     303 ..     206     323 .. 0.86
   3 ?   -1.8   0.0       1.7   1.6e+03      30      45 ..     329     344 ..     307     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.8e-09
                                       HTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              SNAP  47 lakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkkeiae 122
                                       la ++  A++++ ka +    + +++  +  y + +++  ++    +A + +ekA+e + ++g     A+   +++ 
  gi|386002004|ref|YP_005920303.1|  75 LAGHLGIAARCYNKALSQ---TTDQHVRSVLYNNLGQVHARQgYLGRALHYYEKAAEGFSSQGDSGSLAQVLGNMGS 148
                                       566666777777776543...45777778888888888777658889****************************** PP

                                       HHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              SNAP 123 lyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyek 180
                                        y +  + +++A+++ +k  e++++ e ++   ++   +  ++ae+++y+ A++ yek
  gi|386002004|ref|YP_005920303.1| 149 AYRSS-ESYDEALDSCRKSLEIFRELEDESGVAQMTGSIGRIHAEMGEYDLALQEYEK 205
                                       ***99.**************************************************98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00053
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              SNAP  90 peeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcl 158
                                        + A+  +++++ei+ e g+ ++a+    +++ l  +  gdl+ A ++ e+  +l +++ +  +an + 
  gi|386002004|ref|YP_005920303.1| 236 RDVAIGYYNRSMEIFEEIGQRHNAGVVLANLGRLHLDR-GDLDLAADHLETSLDLIRKNMQPVRANAVS 303
                                       5579999*****************************99.***************999999888888765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHH CS
                              SNAP  30 kaeeAadlyeqAAnay 45 
                                       +  eAa+l+++A   y
  gi|386002004|ref|YP_005920303.1| 329 DGPEAAELFIEASSYY 344
                                       4456666766666555 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.4    0.0013       1.2       1      42 []      70     114 ..      70     114 .. 0.84
   2 ?    4.1   0.0     0.039        37       1      20 [.     147     166 ..     147     170 .. 0.82
   3 !    9.8   0.1   0.00064       0.6       1      21 [.     187     207 ..     187     209 .. 0.92
   4 ?    1.0   0.0      0.37   3.5e+02       1      23 [.     267     289 ..     267     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna...eayynLGlayykqG 42 
                                       Gd+++  G +  A  +Y+kAl  + d+     +y+nLG+++++qG
  gi|386002004|ref|YP_005920303.1|  70 GDICRLAGHLGIAARCYNKALSQTTDQHvrsVLYNNLGQVHARQG 114
                                       888888899999999999999999998533259**********99 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       G ay++   y+eA+ + +k 
  gi|386002004|ref|YP_005920303.1| 147 GSAYRSSESYDEALDSCRKS 166
                                       89***********9875555 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00064
                            TPR_11   1 GdayyeqGkyeeAieaYkkAl 21 
                                       G++  e G+y+ A+++Y+k l
  gi|386002004|ref|YP_005920303.1| 187 GRIHAEMGEYDLALQEYEKSL 207
                                       89999*************987 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.37
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G++  ++G+++ A  ++++ l+l
  gi|386002004|ref|YP_005920303.1| 267 GRLHLDRGDLDLAADHLETSLDL 289
                                       78889***********9998887 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.053        50       6      34 ..      68      96 ..      66     104 .. 0.89
   2 ?    4.8   0.2     0.068        64       7      29 ..     106     128 ..      99     135 .. 0.90
   3 ?    5.7   0.0     0.033        31       7      31 ..     146     170 ..     140     183 .. 0.87
   4 ?    7.3   0.1      0.01       9.6       8      32 ..     187     211 ..     180     229 .. 0.78
   5 ?    6.2   0.1     0.023        22       6      29 ..     265     288 ..     262     301 .. 0.84
   6 ?    0.2   0.2         2   1.9e+03      18      35 ..     395     412 ..     392     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.053
                            TPR_14  6 alaeallalGdpdeAiallrralalaPdd 34
                                      +l+++++ +G +  A++++++al++  d+
  gi|386002004|ref|YP_005920303.1| 68 RLGDICRLAGHLGIAARCYNKALSQTTDQ 96
                                      799999******************98876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.068
                            TPR_14   7 laeallalGdpdeAiallrrala 29 
                                       l+++++++G + +A+ ++++a +
  gi|386002004|ref|YP_005920303.1| 106 LGQVHARQGYLGRALHYYEKAAE 128
                                       89*****************9965 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.033
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       +++a++ ++ +deA++ +r+ l+ +
  gi|386002004|ref|YP_005920303.1| 146 MGSAYRSSESYDEALDSCRKSLEIF 170
                                       689******************9976 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.01
                            TPR_14   8 aeallalGdpdeAiallrralalaP 32 
                                       ++++++ G++d A++ +++ la++ 
  gi|386002004|ref|YP_005920303.1| 187 GRIHAEMGEYDLALQEYEKSLADFE 211
                                       8999******************775 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.023
                            TPR_14   6 alaeallalGdpdeAiallrrala 29 
                                        l++++l +Gd+d A+++l+  l+
  gi|386002004|ref|YP_005920303.1| 265 NLGRLHLDRGDLDLAADHLETSLD 288
                                       599*****************9887 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 2
                            TPR_14  18 deAiallrralalaPdda 35 
                                       +e +a+l+ al++a d+ 
  gi|386002004|ref|YP_005920303.1| 395 EEGVAALNSALSRAEDSS 412
                                       788999999999999875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0054       5.1       1      31 [.      85     118 ..      85     121 .. 0.84
   2 ?    1.9   0.0       0.4   3.7e+02       2      33 ..     123     160 ..     122     161 .. 0.76
   3 ?    6.1   0.0     0.018        17      11      32 ..     258     279 ..     242     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
                            TPR_17   1 lylkaleldPnn...adaynnLAelllknGdlmt 31 
                                       +y kal +  +    +++ynnL+++++++G l++
  gi|386002004|ref|YP_005920303.1|  85 CYNKALSQTTDQhvrSVLYNNLGQVHARQGYLGR 118
                                       799999998887799************9995555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.4
                            TPR_17   2 ylkaleldPnn......adaynnLAelllknGdlmtAr 33 
                                       y+ka+e   +       a ++ n++ ++++   +++A+
  gi|386002004|ref|YP_005920303.1| 123 YEKAAEGFSSQgdsgslAQVLGNMGSAYRSSESYDEAL 160
                                       788888864444456679999999*9999999999986 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.018
                            TPR_17  11 nnadaynnLAelllknGdlmtA 32 
                                       n  +++ nL++l+l +Gdl+ A
  gi|386002004|ref|YP_005920303.1| 258 NAGVVLANLGRLHLDRGDLDLA 279
                                       557899************9977 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1      0.01       9.4      79     133 ..     117     173 ..      97     182 .. 0.60
   2 !   15.6   0.9   1.4e-05     0.013      22     132 ..     153     252 ..     142     256 .. 0.83
   3 ?    4.1   0.0     0.047        44      65     104 ..     223     262 ..     218     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                                       HHHHHHHHHH--TTSTHHHH..HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                           DUF3856  79 dkalryfnrrGeleqdeGkl..WiaavfsravaleelGrkdealkafrmagemiaer 133
                                        +al+y+++  e  + +G      +++ + + a+ +  ++deal++ r++ e+  e 
  gi|386002004|ref|YP_005920303.1| 117 GRALHYYEKAAEGFSSQGDSgsLAQVLGNMGSAYRSSESYDEALDSCRKSLEIFREL 173
                                       566666666665433333321023455566777777777777777777777766654 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.4e-05
                                       HT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHH CS
                           DUF3856  22 egayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGkl 98 
                                        ++y+ea +s+rk+le+ r +  e      G  a +  ++    a++g+yd al+  +k+l  f++ G+ +q     
  gi|386002004|ref|YP_005920303.1| 153 SESYDEALDSCRKSLEIFRELEDE-----SGV-AQMTGSIGRIHAEMGEYDLALQEYEKSLADFEQLGDQRQV---A 220
                                       679**************9988655.....565.555678999999********************99997774...6 PP

                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmagemiae 132
                                       Wi   + r    +e+ ++d a+ +++ + e+ +e
  gi|386002004|ref|YP_005920303.1| 221 WILNRMGRVN--AEIEKRDVAIGYYNRSMEIFEE 252
                                       8876665555..5899999999999999999887 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.047
                                       HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHH CS
                           DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWiaavf 104
                                       l ++gr ++ +e  d a+ y+nr  e+ ++ G+   a v+
  gi|386002004|ref|YP_005920303.1| 223 LNRMGRVNAEIEKRDVAIGYYNRSMEIFEEIGQRHNAGVV 262
                                       6789999********************9999998777665 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.045        43       6      21 ..     105     120 ..     101     120 .. 0.88
   2 ?    0.8   0.0       1.1   1.1e+03       8      25 ..     187     204 ..     187     205 .. 0.87
   3 !   17.9   0.9   3.4e-06    0.0032       2      25 ..     261     284 ..     260     285 .. 0.93
   4 ?   -1.2   0.1         5   4.7e+03       6      16 ..     732     742 ..     719     744 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.045
                             TPR_4   6 aLArallalGdldeAr 21 
                                       +L+++++++G l +A+
  gi|386002004|ref|YP_005920303.1| 105 NLGQVHARQGYLGRAL 120
                                       8*********999996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                             TPR_4   8 ArallalGdldeAralle 25 
                                       +r +++ G++d A++  e
  gi|386002004|ref|YP_005920303.1| 187 GRIHAEMGEYDLALQEYE 204
                                       6899*********99776 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 3.4e-06
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       ++l++L+r++l++Gdld A+++le
  gi|386002004|ref|YP_005920303.1| 261 VVLANLGRLHLDRGDLDLAADHLE 284
                                       5799*******************9 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 5
                             TPR_4   6 aLArallalGd 16 
                                       +L+ +++++G+
  gi|386002004|ref|YP_005920303.1| 732 DLGDLAFRRGE 742
                                       68888888886 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00048      0.45      23     144 ..      86     211 ..      83     222 .. 0.85
   2 ?    3.9   0.1     0.042        40      19      70 ..     163     214 ..     151     283 .. 0.72
   3 ?    4.6   0.1     0.026        24      13     124 ..     197     311 ..     189     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                                       HHHHHHTT-HHHHHH.HHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              RPN7  23 lkdakenlgkeeirr.akldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskylek 98 
                                       +++a ++ ++  +r  ++++l++ +++ g l  Al +y+++ e  +s + + ++   l  ++ ++   +++++ l+ 
  gi|386002004|ref|YP_005920303.1|  86 YNKALSQTTDQHVRSvLYNNLGQVHARQGYLGRALHYYEKAAEGFSSQGDSGSLAQVLGNMGSAYRSSESYDEALDS 162
                                       56667777888888635789********************************************************* PP

                                       HHCSSS-...--.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GGGT CS
                              RPN7  99 akellek...ggdwerknrlkvyeGlallairkfkeAaellldilstft 144
                                       ++++le     +d++  +++  + G ++++++++  A ++  ++l++f+
  gi|386002004|ref|YP_005920303.1| 163 CRKSLEIfreLEDESGVAQMTGSIGRIHAEMGEYDLALQEYEKSLADFE 211
                                       **99987333667888888888889999999999999999998888884 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHH CS
                              RPN7  19 LdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslk 70 
                                        ++ l+  +e + ++ +++    +++ ++++g+++ Al+ y++ + +  +l+
  gi|386002004|ref|YP_005920303.1| 163 CRKSLEIFRELEDESGVAQMTGSIGRIHAEMGEYDLALQEYEKSLADFEQLG 214
                                       5555555556666778999999999999999999999999999877666655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHH...HHHHHHHHHHHT CS
                              RPN7  13 ekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkid...mllnlirvaiff 86 
                                       +  l+e ++ l d ++ + + +++   ++ ++  ++i +++ A+ +y+r +e     ++  +   +l nl r+ + +
  gi|386002004|ref|YP_005920303.1| 197 DLALQEYEKSLADFEQLGDQRQVAWILNRMGRVNAEIEKRDVAIGYYNRSMEIFEEIGQRHNagvVLANLGRLHLDR 273
                                       56678888888888888888888889999999999999*********997766655555554222566888999*** PP

                                       T-HHHHHHHHHHHHCSSS---.HHHHHHHHHHHHHHHH CS
                              RPN7  87 ndwdlvskylekakellekggdwerknrlkvyeGlall 124
                                       +d dl+  +le+  +l+ k  +  r n ++  +++ ++
  gi|386002004|ref|YP_005920303.1| 274 GDLDLAADHLETSLDLIRKNMQPVRANAVSWLSAVRAI 311
                                       *********99999999987665555555555555544 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.3e-05     0.069      16      47 ..      82     113 ..      81     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                            Coat_F  16 aarnyataitEasnpelRqtlkqilneeiemq 47 
                                       aar+y+ a+ +++++++R++l + l + ++ q
  gi|386002004|ref|YP_005920303.1|  82 AARCYNKALSQTTDQHVRSVLYNNLGQVHARQ 113
                                       689************************99877 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.47   4.5e+02      25      60 ..      82     117 ..      79     126 .. 0.83
   2 ?    8.1   0.0    0.0029       2.7      25      78 ..     119     175 ..     113     177 .. 0.81
   3 ?    1.2   0.0      0.42     4e+02      40      64 ..     177     201 ..     175     215 .. 0.81
   4 ?   -3.1   0.0       9.4   8.9e+03      37      60 ..     463     486 ..     456     492 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.47
                          Rapsyn_N  25 alrvWrkvLkktsdregkfrvLGcLitahsemGkyk 60 
                                       a r + k+L +t+d++ +  +   L + h+  G   
  gi|386002004|ref|YP_005920303.1|  82 AARCYNKALSQTTDQHVRSVLYNNLGQVHARQGYLG 117
                                       678999*********999999999999998887655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0029
                          Rapsyn_N  25 alrvWrkvLkkts...dregkfrvLGcLitahsemGkykealefalaqldiareled 78 
                                       al+ + k+ ++ s   d++   +vLG +  a+     y eal+   + l+i reled
  gi|386002004|ref|YP_005920303.1| 119 ALHYYEKAAEGFSsqgDSGSLAQVLGNMGSAYRSSESYDEALDSCRKSLEIFRELED 175
                                       66666666666551114555689*********************************8 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.42
                          Rapsyn_N  40 egkfrvLGcLitahsemGkykeale 64 
                                       +g  ++ G + + h+emG y  al+
  gi|386002004|ref|YP_005920303.1| 177 SGVAQMTGSIGRIHAEMGEYDLALQ 201
                                       566788999999********88776 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9.4
                          Rapsyn_N  37 sdregkfrvLGcLitahsemGkyk 60 
                                       s   g+    G L+ a   +G++ 
  gi|386002004|ref|YP_005920303.1| 463 SAGRGCKEACGQLLPAFKTLGRFI 486
                                       556677788899999999999985 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0012       1.2      54     106 ..     111     169 ..      81     171 .. 0.82
   2 ?   -2.3   0.0       4.6   4.3e+03      48      68 ..     232     252 ..     228     272 .. 0.68
   3 ?   -0.3   0.0       1.1   1.1e+03      51      88 ..     275     312 ..     238     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                            DUF627  54 vkfayllasvecfseave.ls.....rfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                       +++ yl  ++  +++a e +s        A+ L +++s ++s   Y +a+ +++++L +
  gi|386002004|ref|YP_005920303.1| 111 ARQGYLGRALHYYEKAAEgFSsqgdsGSLAQVLGNMGSAYRSSESYDEALDSCRKSLEI 169
                                       56677777777777665415577777889***************************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.6
                            DUF627  48 ktedpdvkfayllasvecfse 68 
                                       ++e++dv + y   s e f+e
  gi|386002004|ref|YP_005920303.1| 232 EIEKRDVAIGYYNRSMEIFEE 252
                                       667777777777777777655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                            DUF627  51 dpdvkfayllasvecfseavelsrfyArsLfelasqlg 88 
                                       d d+ + +l  s++ ++++++  r  A s + + + ++
  gi|386002004|ref|YP_005920303.1| 275 DLDLAADHLETSLDLIRKNMQPVRANAVSWLSAVRAIR 312
                                       56888899999999999999988888877776666555 PP

>> Dpy-30  Dpy-30 motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0033       3.1      17      29 ..     657     669 ..     656     671 .. 0.92
   2 ?    1.3   0.0       0.3   2.8e+02      27      36 ..     716     725 ..     716     727 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0033
                                       HHHHHHHH--SSH CS
                            Dpy-30  17 GLtelAkeRPeDP 29 
                                       GLte+A+ RP+ P
  gi|386002004|ref|YP_005920303.1| 657 GLTEVARNRPPSP 669
                                       9*********988 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                                       SSHHHHHHHH CS
                            Dpy-30  27 eDPieyLAeY 36 
                                       +DP+++LA +
  gi|386002004|ref|YP_005920303.1| 716 RDPLRFLARF 725
                                       6*******87 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.5   2.3e+03       4      23 ..     150     170 ..     145     176 .. 0.50
   2 ?    4.6   0.1     0.062        58       6      25 ..     186     205 ..     185     212 .. 0.88
   3 ?    1.5   0.0       0.6   5.6e+02       3      24 ..     263     284 ..     261     288 .. 0.87
   4 ?   -0.3   0.1       2.3   2.2e+03       2      14 ..     503     520 ..     502     539 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.5
                                       HHHHHHHHH.HHHHHHHHHHH CS
                             TPR_6   4 yklalsyrk.lgdtdkAleal 23 
                                       y+  +sy + l+  +k+le++
  gi|386002004|ref|YP_005920303.1| 150 YRSSESYDEaLDSCRKSLEIF 170
                                       444445554444444555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealer 25 
                                       +++ + ++g++d Al+ +e+
  gi|386002004|ref|YP_005920303.1| 186 IGRIHAEMGEYDLALQEYEK 205
                                       799***************98 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAleale 24 
                                       l +l+++++  gd d A + le
  gi|386002004|ref|YP_005920303.1| 263 LANLGRLHLDRGDLDLAADHLE 284
                                       679*******89*****99887 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHH.....H CS
                             TPR_6   2 Alyklalsyrkl.....g 14 
                                       A++k+a+s ++l     g
  gi|386002004|ref|YP_005920303.1| 503 AYLKRAESAFELaapdlG 520
                                       899*****9996455550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.79u 0.31s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 4521.04
//
Query:       gi|386002005|ref|YP_005920304.1|  [L=408]
Description: L-threonine ammonia-lyase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-82  275.9   6.4    5.6e-82  275.5   6.4    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme
    5.1e-06   26.2   0.1    1.5e-05   24.7   0.1    1.8  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.5   6.4   6.2e-86   5.6e-82       3     294 .]      22     309 ..      20     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 275.5 bits;  conditional E-value: 6.2e-86
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       + + +TPlvr++ +s+  g+++ lKlEsl+ +gSfK+Rga+y l++ +e+ g  +vv+as+GNh++++A+aa+++ +
  gi|386002005|ref|YP_005920304.1|  22 GRVIRTPLVRSDTFSRMAGAEVHLKLESLQAGGSFKVRGAAYKLLKRREEIGPLGVVAASAGNHAQGVALAARAAAI 98 
                                       56789*****************************************99988************************** PP

                                       EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTT CS
                              PALP  80 kvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlgg 156
                                       ++tiv+p +as +k+++++++Gaev++ g++  e+ ++a+e+a+e  g+ +++++d+p++i+g+gtiglEile+l +
  gi|386002005|ref|YP_005920304.1|  99 PATIVMPVWASMGKQEATKSYGAEVILAGDSLAESISIAREMAEE--GRPFIHPYDDPDIIAGQGTIGLEILEDL-P 172
                                       *********************************************..999*************************.6 PP

                                       TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHH CS
                              PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafell 233
                                       +pd +vvpvGgGgli+Gia ++k+ rp+++++gv+++ +++  ++lr g+rvtv+ +++iadg++v++++e +f+l+
  gi|386002005|ref|YP_005920304.1| 173 DPDLIVVPVGGGGLIGGIASAIKAVRPETEIVGVQAAACPSALEALRSGERVTVEAKRSIADGISVRQVGEANFPLI 249
                                       ***************************************************************************** PP

                                       SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 234 drlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       ++l+  +v v + e+++a+  l +r ++++e ++aa laal l+++ +++ g +vv++++g
  gi|386002005|ref|YP_005920304.1| 250 RELLSGVVLVEEGEIASAVLALLERKKVLAEGAGAAPLAAL-LASKLAFPMGCKVVLVISG 309
                                       *****************************************.****************998 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   1.7e-09   1.5e-05       8      63 ..     339     394 ..     334     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-09
                                       ESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHH CS
                               ACT   8 pDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealk 63 
                                       +D+PG Lar+++++a+ g N+ +i++++ ++++ ++ + v+++ e +   ++e++k
  gi|386002005|ref|YP_005920304.1| 339 EDVPGSLARLLSLVAEKGGNVLHIHHARGGEEISSFKTRVDLEVETRGRGMIEEIK 394
                                       7****************************998777777777777777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2666.89
//
Query:       gi|386002006|ref|YP_005920305.1|  [L=799]
Description: ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-27   95.9   9.6    1.5e-16   60.6   1.2    4.7  6  FtsX      FtsX-like permease family
    5.2e-27   95.5  13.0    3.4e-14   53.7   0.4    2.7  3  MacB_PCD  MacB-like periplasmic core domain
  ------ inclusion threshold ------
      0.039   14.2   0.3      0.039   14.2   0.3    3.5  5  DUF2304   Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.1   6.5e+03      19      33 ..      26      40 ..      20      53 .. 0.48
   2 ?    0.2   2.1      0.17     1e+03      22      47 ..     256     281 ..     248     286 .. 0.74
   3 !   48.8   1.8   1.3e-16   7.6e-13       2      96 .]     286     384 ..     285     384 .. 0.92
   4 ?   -3.1   0.2       1.9   1.1e+04      34      44 ..     441     451 ..     433     468 .. 0.53
   5 ?   -1.5   0.5      0.61   3.7e+03      19      35 ..     671     685 ..     658     695 .. 0.51
   6 !   60.6   1.2   2.6e-20   1.5e-16       2      96 .]     698     792 ..     697     792 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                              FtsX 19 llllteillitlval 33
                                      l ++  +l++++  l
  gi|386002006|ref|YP_005920305.1| 26 LSVTAVALAVSISLL 40
                                      222222222222222 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                              FtsX  22 lteillitlvalviGlglgllaaqll 47 
                                       ++ +l i++v +++++g+++++  l+
  gi|386002006|ref|YP_005920305.1| 256 FWRSLSIFFVMIIAAFGIAAIMNMLV 281
                                       77888999999999988888776554 PP

  == domain 3  score: 48.8 bits;  conditional E-value: 1.3e-16
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs....selkisidlitvliiiv 74 
                                       re+g+l+alG+ ++++l+++++e+ +++l++ +iG glgll + +l ++  ++  +    s++++ id+ ++ + ++
  gi|386002006|ref|YP_005920305.1| 286 REMGMLLALGADRGRILRIFIYESGILGLLGGIIGSGLGLLGILALGSFRFEVTAGgrelSSIPLVIDPKDFPTYVL 362
                                       8*************************************9999999777766666557889***************** PP

                              FtsX  75 lllllallagllsiskilkkep 96 
                                       ++l l llag++++++++  +p
  gi|386002006|ref|YP_005920305.1| 363 FALGLSLLAGAYPALRAASLDP 384
                                       ****************998776 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.9
                              FtsX  34 viGlglgllaa 44 
                                        +G+++g+++ 
  gi|386002006|ref|YP_005920305.1| 441 SVGVAVGVIIM 451
                                       22222222222 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 0.61
                              FtsX  19 llllteillitlvalvi 35 
                                       l++++ il+i+  a+vi
  gi|386002006|ref|YP_005920305.1| 671 LIFYSMILAIS--AFVI 685
                                       33333333333..2222 PP

  == domain 6  score: 60.6 bits;  conditional E-value: 2.6e-20
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       re+gil a+G+ ++++l+++l+e+ll++l++ v+G ++glla  l+ +++ s +++  l++ + +  vl  i+++l 
  gi|386002006|ref|YP_005920305.1| 698 REVGILMAMGADRASILKIFLLENLLLALPGGVLGALFGLLAGDLIATFGPSGFGGVPLSFDLGPDLVLYSILFALA 774
                                       8**************************************************************************** PP

                              FtsX  79 lallagllsiskilkkep 96 
                                       l  lagl+++++++  +p
  gi|386002006|ref|YP_005920305.1| 775 LNFLAGLYPAIRASGLDP 792
                                       ************987765 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.6   3.7e-17   2.2e-13       1     193 [.      24     231 ..      24     233 .. 0.74
   2 ?   -2.9   0.8       1.2   7.5e+03       3      21 ..     264     282 ..     263     310 .. 0.78
   3 !   53.7   0.4   5.7e-18   3.4e-14       1     194 [.     435     643 ..     435     644 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3.7e-17
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdve.alrr..evp.veavapvv 73 
                                       ++l+v ++a++v    +++slg+g+q+ ++  ++  + l +v++++++ge     +++ +l+r  +++ v+++++ +
  gi|386002006|ref|YP_005920305.1|  24 TILSVTAVALAVSISLLFTSLGNGSQELLTGIVE--EKLPHVRISPAEGEK-YIHLYRgLLARasAIEgVSSASAAL 97 
                                       79*****************************998..556678887644444.2233334444422445566666655 PP

                          MacB_PCD  74 ....tvrgggsgeeevtvvgvdpdyfk.vfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl... 139
                                           tv++ ++  +++ ++g dp++ + ++++  ++++G f   +++ +g++ vv+g +la++l  +vGd++ +   
  gi|386002006|ref|YP_005920305.1|  98 stqaTVSFKEK-RRNALLRGIDPAEEDaIYKIssSIVAGEF---SEILDGKK-VVMGFKLADELGlKVGDRMVVsfp 169
                                       55543333332.45599***887444437777633588965...67776777.9*********99************ PP

                          MacB_PCD 140 ....kpftVvGvledppgsgsalgddavylplttlqrrs........itvrlkdgadleaaaaele 193
                                            +++ vG++++  g  + l++  +y++l+t+++          + +rl+d   +e++aa+++
  gi|386002006|ref|YP_005920305.1| 170 rartTDLELVGIFDT--G--TPLDERIAYVSLRTAREFLgegdvvtsVELRLDDIREAEEVAAAID 231
                                       **9999*******43..4..4588999****9998333356666666****************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                          MacB_PCD   3 ltvLGiaiGvaaviaivsl 21 
                                       + ++  a+G+aa++ +++l
  gi|386002006|ref|YP_005920305.1| 264 FVMIIAAFGIAAIMNMLVL 282
                                       67889999****9988876 PP

  == domain 3  score: 53.7 bits;  conditional E-value: 5.7e-18
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsq.isdlgnlvtvtpgkgsgeslsdpdvealrr...evp.veavapv 72 
                                       +++t+L++ ++v+++i+ ++l+eg++ ++  + i+++ + ++v+pg+g  ++l+  ++++l++   e p v+av+++
  gi|386002006|ref|YP_005920305.1| 435 TAFTLLSVGVAVGVIIMSIGLTEGVRTQIVANtIEKNPH-LYVQPGRG-EDHLR--LYRTLSErvwEHPgVVAVSAR 507
                                       899*****************************5555555.66999863.33334..34445323566799****998 PP

                          MacB_PCD  73 v....tvrgggsgeeevtvvgvdpdyfk.vfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl.. 139
                                       +    ++r +++  e+v  vgvdp+  + + g+  + ++G   ++++l+ +++++ +g +lae+l  + G++  l  
  gi|386002006|ref|YP_005920305.1| 508 LvgqgAARHRDN-VEGVEFVGVDPGPEDlLMGVqaSALSG---NFSELNFKRRSAFLGVKLAEKLEiRPGESFDLvl 580
                                       756542233332.244889999985555444553234678...448888899************88*99****999* PP

                          MacB_PCD 140 ....kpftVvGvledppgsgsalgddavylplttl........qrrsitvrlkdgadleaaaaelek 194
                                           ++++V+G +e+  g+    +++ vyl l+t+         +++i vrl++ + + aaaa+le+
  gi|386002006|ref|YP_005920305.1| 581 qdrtVRLKVAGLVEK--GTV--KDESLVYLHLKTAqdlvgegdVVSEIGVRLSEFEEAPAAAAALER 643
                                       999999*******55..544..34778****8887343554433555*****************986 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.4       2.5   1.5e+04      28      40 ..      26      38 ..      10      44 .. 0.43
   2 ?    0.5   0.4      0.11   6.9e+02      59      88 ..     255     284 ..     245     293 .. 0.70
   3 ?   -1.0   0.3      0.33     2e+03      50      81 ..     421     452 ..     409     456 .. 0.53
   4 ?   14.2   0.3   6.6e-06     0.039      47      85 ..     652     690 ..     649     707 .. 0.72
   5 ?   -4.1   0.2         3   1.8e+04      63      76 ..     761     774 ..     758     779 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
                           DUF2304 28 leysllwlllali 40
                                      l+ + + l++++ 
  gi|386002006|ref|YP_005920305.1| 26 LSVTAVALAVSIS 38
                                      2222222333333 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                           DUF2304  59 Gvgrgtnllfllgivfllvilfslslklsk 88 
                                       G+ r ++++f+++i+++ + ++ + l l+k
  gi|386002006|ref|YP_005920305.1| 255 GFWRSLSIFFVMIIAAFGIAAIMNMLVLEK 284
                                       777777777777777777776666666655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.33
                           DUF2304  50 iltvlanllGvgrgtnllfllgivfllvilfs 81 
                                       ++ ++ ++l   rgt + +l + v++ vi++s
  gi|386002006|ref|YP_005920305.1| 421 AAVAVRHILSNRRGTAFTLLSVGVAVGVIIMS 452
                                       44445555555555555555554444444443 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 6.6e-06
                           DUF2304  47 fpqiltvlanllGvgrgtnllfllgivfllvilfslslk 85 
                                       + +    +a+++G+++ +nl+f+ +i+++  +++ +++ 
  gi|386002006|ref|YP_005920305.1| 652 WQEYSREIARFVGTQSRINLIFYSMILAISAFVIANTTI 690
                                       5667789***************99998876555544432 PP

  == domain 5  score: -4.1 bits;  conditional E-value: 3
                           DUF2304  63 gtnllfllgivfll 76 
                                       g++l+++ ++++l 
  gi|386002006|ref|YP_005920305.1| 761 GPDLVLYSILFALA 774
                                       67777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 4827.85
//
Query:       gi|386002007|ref|YP_005920306.1|  [L=99]
Description: hypothetical protein Mhar_1319 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-23   81.1   0.1      7e-23   80.7   0.1    1.1  1  DUF1805   Domain of unknown function (DUF1805)


Domain annotation for each model (and alignments):
>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.1   3.9e-27     7e-23       1      63 []      36      99 .]      36      99 .] 0.98

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.9e-27
                                      E-TT--HHHHHHTT--EEE-.....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                           DUF1805  1 mCGaLdvealeklgdlaarvivag.sGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63
                                      +CGa+dv+ale+++++aa+v++++ +++++ledlla++v++++ aA++lG+ +Gm+gkeaL++l
  gi|386002007|ref|YP_005920306.1| 36 GCGAFDVAALERFRYPAAKVKPTRgPSIADLEDLLAGEVKDANAAAASLGVAVGMSGKEALDLL 99
                                      7************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 695.26
//
Query:       gi|386002008|ref|YP_005920307.1|  [L=68]
Description: hypothetical protein Mhar_1320, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-06   27.2   0.1    4.1e-06   27.0   0.1    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    1.4e-05   25.1   0.0    1.8e-05   24.7   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   4.6e-10   4.1e-06       7      39 ..      36      67 ..      27      68 .] 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.6e-10
                                      HHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEE CS
                      NTP_transf_2  7 elkelepvakvvlfGSyarGtalkgSDiDllvv 39
                                      +  + ++   v +fGS+arG+  + SDiDllv 
  gi|386002008|ref|YP_005920307.1| 36 IAAK-DGARNVRVFGSVARGEDDEMSDIDLLVE 67
                                      4443.337889********************95 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0     2e-09   1.8e-05       1      37 [.      31      66 ..      31      68 .] 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2e-09
                                      -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEE CS
                           Polbeta  1 ekikeilekekeielaylFGSrakgkareeSDiDlav 37
                                      e+i  i+ k+ + + + +FGS+a+g+  e SDiDl v
  gi|386002008|ref|YP_005920307.1| 31 EEILRIAAKD-GARNVRVFGSVARGEDDEMSDIDLLV 66
                                      6788899999.9999********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 466.42
//
Query:       gi|386002009|ref|YP_005920308.1|  [L=292]
Description: hypothetical protein Mhar_1321 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-13   49.2  14.9    1.4e-06   28.3   2.9    3.9  3  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.6   4.8e-06     0.086      25      47 ..       2      25 ..       2      26 .. 0.94
   2 !   28.3   2.9   7.8e-11   1.4e-06       1      47 [.      22      69 ..      22      70 .. 0.96
   3 !   17.7   0.1   1.6e-07    0.0029       1      30 [.      77     106 ..      77     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-06
                    Pentapeptide_3 25 nadF.gsadFsgarFtgdvdFsga 47
                                      n++F ++++F +++F g+++F+g+
  gi|386002009|ref|YP_005920308.1|  2 NSVFcRDSNFLESHFIGNANFGGT 25
                                      799*******************98 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 7.8e-11
                    Pentapeptide_3  1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47
                                      F g++F++  +F+ ++F++ asF+ a F ++ +F ga F++d++F+ a
  gi|386002009|ref|YP_005920308.1| 22 FGGTVFYRGPSFEAVNFEKNASFDLAEFkSEPSFNGAYFKRDATFNYA 69
                                      89**************************99***************987 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 1.6e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgs 30 
                                       F+g+nF g+a+ +++tF+++++ ++a F++
  gi|386002009|ref|YP_005920308.1|  77 FVGVNFGGDANYTKTTFNKPVYLKEAIFSR 106
                                       99**************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1921.73
//
Query:       gi|386002010|ref|YP_005920309.1|  [L=405]
Description: phosphoglycerate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-116  388.1   0.3   4.3e-116  388.0   0.3    1.0  1  PGK       Phosphoglycerate kinase
  ------ inclusion threshold ------
      0.017   15.3   0.2      0.048   13.9   0.2    1.7  1  SRP54_N   SRP54-type protein, helical bundle domain
      0.036   13.8   0.0      0.094   12.4   0.0    1.7  1  TadZ_N    Pilus assembly protein TadZ N-terminal


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.0   0.3  7.2e-120  4.3e-116       2     377 ..       8     387 ..       7     388 .. 0.94

  Alignments for each domain:
  == domain 1  score: 388.0 bits;  conditional E-value: 7.2e-120
                                       GGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHH CS
                               PGK   2 kdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsel 78 
                                       +d+ +k++r+lvRvD+N+p++ +gki dd+r+r+++pT++ l  ++a+vvl++H++r  g+k+ ++l+++a+rLs+l
  gi|386002010|ref|YP_005920309.1|   8 DDFPIKNQRILVRVDLNAPMDPNGKILDDKRFRSHIPTLRDL--EEARVVLMAHQSRA-GKKDFTTLEAHAKRLSQL 81 
                                       8999**************************************..8899*********8.89**************** PP

                                       HTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTT...TT-H......HHHHHHHHT-SEEEE--GGGTTS CS
                               PGK  79 lgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEe...knde......elakklasladvyVnDAFgtahr 146
                                       l +eV +v+d++g++++eai+++++g+vllLeN+rfy+eE+   +  +      ++++kl+ l+d++VnDAF+++hr
  gi|386002010|ref|YP_005920309.1|  82 LRREVGYVDDIFGSHAREAIKAMRAGDVLLLENTRFYSEENisrS--PeehsksHMVRKLSPLFDLFVNDAFAVSHR 156
                                       ****************************************63331..13333347********************** PP

                                       --TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHH CS
                               PGK 147 ahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFl 221
                                       +h S+vg++++l++aaG+lmekE++ l+k ++ +e+p +++lGG+k +d ikvi+n++++   d++++ G++a +F 
  gi|386002010|ref|YP_005920309.1| 157 SHLSVVGFTEFLPSAAGRLMEKEIDSLDKGVRGNEHPSIFVLGGTKADDSIKVIQNVFQRGgvDQVLVSGVVATVFQ 233
                                       ************99*********************************************9666************** PP

                                       HHTT-B-TTSS--G.......GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-H CS
                               PGK 222 kaqgleigkslvee.......dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigp 291
                                        a+g+++g++  e        d++ +ak+llek      ki++p+Dv+++++    e+  v+++++ped  + Dig 
  gi|386002010|ref|YP_005920309.1| 234 MAAGVNVGNKNREFvagldyaDQVAIAKDLLEKNP---GKIVVPTDVALERDG---ERLDVAMDKVPEDLLIADIGL 304
                                       ********999977777777789*********987...89**********832...23456899************* PP

                                       HHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSS CS
                               PGK 292 ktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGG 368
                                       +ti  f++ i+eak+vv+nG++G+fe+ekfa GT++i+ka++e+   a+si+GGg++ aa+e+lgl++k+shvStGG
  gi|386002010|ref|YP_005920309.1| 305 ETIVDFSKRIREAKIVVLNGTAGIFENEKFALGTTEILKAATES---AFSIAGGGHTSAAIEELGLESKFSHVSTGG 378
                                       *****************************************995...7***************************** PP

                                       HHHHHHHCT CS
                               PGK 369 gAsLelLeg 377
                                       gAs+++L+g
  gi|386002010|ref|YP_005920309.1| 379 GASISYLSG 387
                                       *******98 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     8e-06     0.048      21      56 ..     284     319 ..     277     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8e-06
                                       HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
                           SRP54_N  21 edleealkeleeaLleaDVgvkvvkklienvkkkav 56 
                                       e l+ a++++ e Ll aD+g+++  ++ ++++++++
  gi|386002010|ref|YP_005920309.1| 284 ERLDVAMDKVPEDLLIADIGLETIVDFSKRIREAKI 319
                                       668889999***********************9775 PP

>> TadZ_N  Pilus assembly protein TadZ N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05     0.094      89     132 ..      53      98 ..      40      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       HHHHHH..HHHT-SEEEETT-BHHHHHHHHHHHHTTS-SS--XXXX CS
                            TadZ_N  89 qlvlaa..mragardfitygaraseltglirrlggrlpsvpvsaar 132
                                       ++vl a   rag +df t  a a  l+ l+rr  g +  +  s ar
  gi|386002010|ref|YP_005920309.1|  53 RVVLMAhqSRAGKKDFTTLEAHAKRLSQLLRREVGYVDDIFGSHAR 98 
                                       5566552269**********************99999888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2532.71
//
Query:       gi|386002011|ref|YP_005920310.1|  [L=311]
Description: Phosphoesterase, RecJ domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   41.5   0.0    2.2e-10   40.7   0.0    1.4  1  DHH       DHH family
    9.3e-07   29.3   4.0    1.9e-06   28.3   4.0    1.6  1  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   2.5e-14   2.2e-10       2     101 .]       3     135 ..       2     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.5e-14
                                       EEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan.......................................llvDhneksqavegea 39 
                                       +l ++hkn D D++g+a+al++                                       ++vD+    q      
  gi|386002011|ref|YP_005920310.1|   3 VLYLCHKNADPDALGAAFALQEafggdlgavegvsrtgaslleaigaeilidppveeydlvVVVDTAVGLQVGGI-- 77 
                                       56679*****************99999988888888888888888888888888888887779999888877754.. PP

                                       CCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  40 keeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                         + +d  +iDHHr g+ +e     + l+ p+ staeiv+e+l ++++ +s+e a +ll+gi
  gi|386002011|ref|YP_005920310.1|  78 --RLKDYAVIDHHREGDLLEGA--AFHLQRPADSTAEIVWEILARSGIVPSREAALALLVGI 135
                                       ..88999*********544444..68889*******************************98 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   4.0   2.1e-10   1.9e-06      70     132 ..     222     288 ..     201     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-10
                                       TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHH CS
                             DHHA1  70 pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipaekleeale 132
                                       + +++v +  gd +++s+r++++    g+d+++++ ++ ++ gggGGGH+ Aa++  p +k +e+l+
  gi|386002011|ref|YP_005920310.1| 222 ADVALVGGVHGDLCRISGRARRSavlaGLDLSAILGDLGEASGGGGGGHRGAAALEAPGGKPKEILA 288
                                       7899999999997777777776677*****************************8888777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2110.85
//
Query:       gi|386002012|ref|YP_005920311.1|  [L=442]
Description: Trk system potassium uptake protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-54  181.9   1.8    1.9e-27   95.8   0.8    2.3  2  TrkA_N           TrkA-N domain
    6.9e-23   80.3   0.7    2.4e-11   43.3   0.1    3.4  3  TrkA_C           TrkA-C domain
    1.1e-09   38.6   0.6    2.6e-05   24.6   0.3    2.4  2  NAD_binding_7    Putative NAD(P)-binding
    1.6e-07   31.7   0.6    0.00026   21.3   0.2    2.6  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    5.6e-07   29.1   1.1      0.015   14.6   0.0    2.3  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    3.5e-06   27.3   0.3     0.0024   18.0   0.1    2.6  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    3.9e-06   26.9   0.6    0.00034   20.6   0.4    2.3  2  NAD_binding_10   NAD(P)H-binding
    4.9e-06   26.6   0.5       0.08   13.0   0.0    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    3.9e-05   23.8   0.0        0.3   11.4   0.0    2.8  3  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    4.2e-05   24.0   1.1        1.5    9.4   0.0    4.3  4  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    6.1e-05   22.4   0.2      0.065   12.5   0.0    2.3  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00012   21.6   0.4     0.0059   16.1   0.2    2.2  2  Epimerase        NAD dependent epimerase/dehydratase family
    0.00014   21.5   0.0        2.8    7.5   0.0    3.3  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00015   22.3   0.1       0.28   11.7   0.0    2.3  2  XdhC_C           XdhC Rossmann domain
    0.00021   21.0   0.0       0.11   12.2   0.0    2.4  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00031   21.2   0.2        1.2    9.8   0.0    2.7  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00048   19.8   0.4      0.015   14.9   0.3    2.2  2  NmrA             NmrA-like family
    0.00078   18.8   0.0       0.91    8.7   0.1    2.3  2  FAD_binding_3    FAD binding domain
      0.001   18.9   0.0        1.2    9.0   0.0    3.0  2  Rossmann-like    Rossmann-like domain
     0.0015   18.4   0.1       0.69    9.8   0.0    2.8  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0028   17.2   0.7          1    8.8   0.1    2.3  2  DUF1188          Protein of unknown function (DUF1188)
  ------ inclusion threshold ------
      0.015   14.6   0.1        3.1    7.1   0.0    2.9  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.019   14.6   0.0        2.3    7.7   0.0    2.3  2  DAO              FAD dependent oxidoreductase
      0.022   14.7   0.4       0.18   11.8   0.0    2.5  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.086   12.2   0.5        4.9    6.4   0.0    2.9  3  ThiF             ThiF family


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.8   2.6e-30   1.9e-27       1     103 [.       3     103 ..       3     120 .. 0.93
   2 !   84.9   0.0   6.5e-27   4.7e-24       1     116 []     225     341 ..     225     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 2.6e-30
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i i G+G+vG++la+eLs+++ dv+vid++ +++e+l+e  ++v++g+a++ ++L eagie+ad+v+a+tg+de+n+
  gi|386002012|ref|YP_005920311.1|   3 IFITGAGDVGYHLARELSQDY-DVTVIDQKSRACERLEEIDVRVLQGNAANAQLLVEAGIEDADIVVAVTGNDEVNM 78 
                                       6799*****************.6****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehae 103
                                       +++ +a +l    ++iar++++++++
  gi|386002012|ref|YP_005920311.1|  79 ITCISASHLGV-ERTIARVSNSDYID 103
                                       ******98777.69*********975 PP

  == domain 2  score: 84.9 bits;  conditional E-value: 6.5e-27
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgdde 74 
                                       ++i+G G vG  la+ L++ +  d  +++ d +r++el+ee   + +++gd+td +++++ ++ ++dav  +tg de
  gi|386002012|ref|YP_005920311.1| 225 VMIVGGGVVGFYLAKWLEKmDF-DLKLVEIDNDRCQELAEELpdTLILNGDGTDISLIKAENVGSMDAVFSVTGFDE 300
                                       69*****************666.7******************6666999**************************** PP

                                       HHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  75 anilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       +n+l++llak+l  + ki+ar++++++++l++ +g+d++isp
  gi|386002012|ref|YP_005920311.1| 301 KNLLCSLLAKQLGAD-KIVARVDRSDYIDLFEMVGVDHAISP 341
                                       **********98886.8***********************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.5   3.2e+03       7      19 ..      96     108 ..      92     118 .. 0.78
   2 !   43.3   0.1   3.3e-14   2.4e-11       1      69 [.     150     216 ..     150     217 .. 0.96
   3 !   33.6   0.0   3.7e-11   2.6e-08       3      69 ..     371     435 ..     369     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.5
                                       E--GGGTTSBHHH CS
                            TrkA_C   7 pagsplvGktlke 19 
                                        ++s ++++++k+
  gi|386002012|ref|YP_005920311.1|  96 VSNSDYIDQPMKD 108
                                       47999****9999 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 3.3e-14
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       l+e++v+++ pl+G +++ ++l++ +++++ai+Rg+e++i++ +  +++GD+l++ ++ +++ +lr+++
  gi|386002012|ref|YP_005920311.1| 150 LIELAVGEEVPLAG-PISKIDLPE-NCRIAAIKRGEEILIARKEESIRAGDRLILTCEAKSVPKLRKII 216
                                       57999999999999.9********.*****************************************987 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 3.7e-11
                                       EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       e++  +++++ Gk  +e ++++ g+++  i Rg ++iip+ dt+ +eGD+++v++ p++  ++++l+
  gi|386002012|ref|YP_005920311.1| 371 ELRAEKEAKILGKNAAE-KMPK-GAILGTIMRGSQPIIPTLDTEVKEGDRIFVLALPKASPKVKALF 435
                                       889999***********.****.***************************************99998 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   3.6e-08   2.6e-05      10      76 ..       3      78 ..       1      99 [. 0.73
   2 !   11.9   0.0   0.00032      0.23       6      99 ..     221     328 ..     216     330 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.6e-08
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.........laeeel..ekdlegadlviaatddrelne 76
                                      + + G+G+v+++ +r l +   +vtv++++ ++++e+l +         +a+ +l  e+ +e+ad+v+a+t ++e+n 
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQD-YDVTVIDQK-SRACERLEEidvrvlqgnAANAQLlvEAGIEDADIVVAVTGNDEVNM 78
                                      7899************9998.9********.56666444411222112122222234777****************96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00032
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee............l.ekdlegadlviaat 69 
                                          kv++vGgG v+   ++ l + + ++++v  + ++ ++el +  +++            +  +++  +d v+ +t
  gi|386002012|ref|YP_005920311.1| 221 ASHKVMIVGGGVVGFYLAKWLEKMDFDLKLVEID-NDRCQELAEELPDTlilngdgtdislIkAENVGSMDAVFSVT 296
                                       5689***********9999999999999998888.556666555444332222222332222335588899999999 PP

                     NAD_binding_7  70 ddrelneriaeaaka..rrilvnvadkpelcd 99 
                                         +e n     +ak+  + + v ++d+++  d
  gi|386002012|ref|YP_005920311.1| 297 GFDEKNLLCSLLAKQlgADKIVARVDRSDYID 328
                                       99988888888888744556888888777655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   3.6e-07   0.00026       1      80 [.       3      74 ..       3     111 .. 0.83
   2 !    8.3   0.0    0.0036       2.6       1      64 [.     225     290 ..     225     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.6e-07
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSG CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlspp 79
                                      + i GaG vG  +a++l++      ++tv+d++ + +e+l     ++++   + +a+n + +++a ++++d+vv ++++
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQDY----DVTVIDQKSRACERL----EEIDVRVLQGNAANAQLLVEAGIEDADIVVAVTGN 73
                                      6789***************65....56*************....579*************977777********99887 PP

                                      G CS
                   Sacchrp_dh_NADP 80 i 80
                                       
  gi|386002012|ref|YP_005920311.1| 74 D 74
                                      4 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0036
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH......TTTCEEEEE--TTTHHHHHH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka......lgvrfeaialdaenyeavLa 64 
                                       v+i+G+G vG  +a+ l++  d+  ++ +++ +++++++la+++      +g   ++  + aen+ + ++
  gi|386002012|ref|YP_005920311.1| 225 VMIVGGGVVGFYLAKWLEKM-DF--DLKLVEIDNDRCQELAEELpdtlilNGDGTDISLIKAENVGS-MD 290
                                       789***************97.67..799*************99888888777777777777777766.55 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.6   8.4e-05      0.06      30      97 ..       2      69 ..       1      81 [. 0.84
   2 !   14.6   0.0   2.1e-05     0.015      27      69 ..     221     263 ..     216     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.4e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHH.HHHHHH-SEEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeell.aeavkeadvvig 97
                                      ++++ G+G +G + ++  +  + +Vtv+D ++++ e+le++  ++++  +++++ll +  +++ad+v+ 
  gi|386002012|ref|YP_005920311.1|  2 QIFITGAGDVGYHLARELS-QDYDVTVIDQKSRACERLEEIDVRVLQGNAANAQLLvEAGIEDADIVVA 69
                                      5899*******99777654.4889********************9999988888651667*******85 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.1e-05
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                       +  kv+++GgGv+G   ++   +++ + ++++++ +r ++l +
  gi|386002012|ref|YP_005920311.1| 221 ASHKVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNDRCQELAE 263
                                       5679*********************************999876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.4e-06    0.0024       2      96 ..       3     103 ..       2     111 .. 0.83
   2 !    6.8   0.0      0.01       7.1       2      42 ..     225     265 ..     224     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.4e-06
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC.......SEEEE-SSSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl.......dvvitmvkagkavde 71 
                                       i + G G  G ++a++l +++y+v+v++ ++ ++e+l +  +++++  ++ ++ l         +++ v+ +++v+ 
  gi|386002012|ref|YP_005920311.1|   3 IFITGAGDVGYHLAREL-SQDYDVTVIDQKSRACERLEEIDVRVLQGNAANAQLLveagiedADIVVAVTGNDEVNM 78 
                                       6788***********98.579*****************999666655554444445557887567788999999*99 PP

                                       HHHSHCCC--TT-EEEE-S---HHH CS
                     NAD_binding_2  72 viegllealkkgdilidgstssped 96 
                                       ++   +++l  ++++  +s+s++ d
  gi|386002012|ref|YP_005920311.1|  79 ITCISASHLGVERTIARVSNSDYID 103
                                       999999***************9977 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42 
                                       + ++G Gv G  +a+ l+k ++++ +++ ++++++el++e 
  gi|386002012|ref|YP_005920311.1| 225 VMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNDRCQELAEEL 265
                                       6689*********************************9885 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 !   20.6   0.4   4.8e-07   0.00034       3      93 ..       8      92 ..       7     111 .. 0.78
   2 ?    4.3   0.0     0.045        32       5      87 ..     232     323 ..     229     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.8e-07
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCCHHHHHHH CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggkdeegakn 80
                                       G vG +l++el ++  ++vt++  ++   ++le e  ++v++g++ +++ l ea +++ad+Vv+ +g+++     +++
  gi|386002012|ref|YP_005920311.1|  8 AGDVGYHLARELSQD--YDVTVIDQKSRACERLE-EIDVRVLQGNAANAQLLVEAgIEDADIVVAVTGNDEV---NMIT 80
                                      699*********988..89998766666667786.79***********987655549**********96554...5666 PP

                                      HHHHHHHCT--EE CS
                    NAD_binding_10 81 ivdaakeagvkRf 93
                                      ++ a    gv+R 
  gi|386002012|ref|YP_005920311.1| 81 CISASH-LGVERT 92
                                      666653.455554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHHH.HHHTT-SEEEES---TCC...... CS
                    NAD_binding_10   5 kvGrllvkellargghevtalvRnpeklaeleae.eglevvegdvtdvedla.ealkgadaVvsalggggk...... 73 
                                        vG +l+k l +  +++++++  + ++ +el++e + + ++ gd td + ++ e +   daV+s +g ++k      
  gi|386002012|ref|YP_005920311.1| 232 VVGFYLAKWLEKM-DFDLKLVEIDNDRCQELAEElPDTLILNGDGTDISLIKaENVGSMDAVFSVTGFDEKnllcsl 307
                                       5666666555554.7999999889999999986668888999****9988751567778*******99888777666 PP

                                       ..HHHHHHHHHHHHHH CS
                    NAD_binding_10  74 ..deegaknivdaake 87 
                                         ++ ga++iv+ +++
  gi|386002012|ref|YP_005920311.1| 308 laKQLGADKIVARVDR 323
                                       5433447777766555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2    0.0003      0.21      14      87 ..       2      75 ..       1      93 [. 0.80
   2 !   13.0   0.0   0.00011      0.08       4      85 ..     214     298 ..     211     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                      EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisatasee 87
                                      ++ + GaG ++  +a+ L++   v+ +    R  er +e+  ++ +g+ ++a+ l e    +++ad+v++ t+  e
  gi|386002012|ref|YP_005920311.1|  2 QIFITGAGDVGYHLARELSQDyDVTVIDQKSRACERLEEIDVRVlQGNAANAQLLVEA--GIEDADIVVAVTGNDE 75
                                      68999*************9664455555557999******877758887777777665..5*********999776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                                       HHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHH....HHHHT- CS
                      Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelk....ellaea 76 
                                       k + e+ +++kv+++G G ++  +ak L +  ++ +  +  + +r +elaeel ++ i   + ++++    e + ++
  gi|386002012|ref|YP_005920311.1| 214 KIIHEDTASHKVMIVGGGVVGFYLAKWLEKMDFD-LKLVEIDNDRCQELAEELPDTLILNGDGTDISlikaENVGSM 289
                                       66778999********************999888.99999999********99888665544444431112456677 PP

                                       SEEEE-SSS CS
                      Shikimate_DH  77 dvvisatas 85 
                                       d v+s t+ 
  gi|386002012|ref|YP_005920311.1| 290 DAVFSVTGF 298
                                       777777765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0018       1.3       2      37 ..       6      40 ..       5      60 .. 0.82
   2 ?   -2.5   0.0       8.9   6.4e+03       9      36 ..     122     149 ..     122     161 .. 0.75
   3 !   11.4   0.0   0.00042       0.3       1      29 [.     227     255 ..     227     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                       GaG  G  +A++L+++ +dv+++++ +r + r+  
  gi|386002012|ref|YP_005920311.1|  6 TGAGDVGYHLARELSQD-YDVTVIDQKSRACERLEE 40
                                      59999999999999996.*********998766655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.9
                                       HHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8   9 lvaAylLakagfdvlllekrdrlGGraa 36 
                                       lv+A ++ k+ +    +e+r+  GG+a 
  gi|386002012|ref|YP_005920311.1| 122 LVMAERIVKELYFPSMVERRRLAGGKAE 149
                                       5677777777777788899999999986 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00042
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                       IvG+G+ G ++A  L k +fd  l+e  +
  gi|386002012|ref|YP_005920311.1| 227 IVGGGVVGFYLAKWLEKMDFDLKLVEIDN 255
                                       9***********************99876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0021       1.5       4      57 ..       4      52 ..       2      74 .. 0.63
   2 ?    3.9   0.0      0.11        82      50      92 ..     185     227 ..     171     227 .. 0.79
   3 !    7.9   0.0    0.0065       4.7       1      90 [.     224     317 ..     224     321 .. 0.61
   4 ?   -1.6   0.1       5.9   4.2e+03      18      57 ..     352     387 ..     344     395 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                                      EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHH CS
                     F420_oxidored  4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdnee 57
                                      +i GaG++g  la+ l++     ++++v+ + ++++a e  ee+ v+v +++++ 
  gi|386002012|ref|YP_005920311.1|  4 FItGAGDVGYHLARELSQD----YDVTVI-D-QKSRACERLEEIDVRVLQGNAAN 52
                                      666***********99998....788877.3.33334444455555555544333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                                       EECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored  50 vtavdneeaaeeadvvvlavkpedveevlselakdalkgklvi 92 
                                       +    +ee ++  d ++l++  + v+++ + + +d+ ++k+ i
  gi|386002012|ref|YP_005920311.1| 185 ILIARKEESIRAGDRLILTCEAKSVPKLRKIIHEDTASHKVMI 227
                                       344469999999***************9999988888888876 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0065
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvla 68 
                                       k+ i+G+G +g+ la+ l + +    ++ ++ + ++++ +elaeel           +++   ++e + + d v+  
  gi|386002012|ref|YP_005920311.1| 224 KVMIVGGGVVGFYLAKWLEKMD---FDLKLV-EIDNDRCQELAEELPdtlilngdgTDISL-IKAENVGSMDAVFSV 295
                                       67899***********999999...555544.55666666666666555557776633333.223444446666655 PP

                                       S-HHHHHHHHHHCGHHHHTTSE CS
                     F420_oxidored  69 vkpedveevlselakdalkgkl 90 
                                         +     ++s lak++ ++k+
  gi|386002012|ref|YP_005920311.1| 296 TGFDEKNLLCSLLAKQLGADKI 317
                                       5555555555555555555555 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 5.9
                                       HHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHH CS
                     F420_oxidored  18 llaagaqpheivvansrnpekaeelaeelgvkvtavdnee 57 
                                       l++ g    e +  + +++ ++ el++e ++k+ +++++e
  gi|386002012|ref|YP_005920311.1| 352 LIRGG---DEAI-SSGKEEAEILELRAEKEAKILGKNAAE 387
                                       66666...5555.456777778888888888888755554 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0022       1.6     145     181 ..       3      38 ..       1      93 [. 0.74
   2 !   12.5   0.0     9e-05     0.065     143     176 ..     223     256 ..     197     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllral 181
                                       i + G+G +G  lA +l++  ++vt++++ +r ++ l
  gi|386002012|ref|YP_005920311.1|   3 IFITGAGDVGYHLARELSQD-YDVTVIDQKSRACERL 38 
                                       66777777777777776554.7777777777777333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9e-05
                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardr 176
                                        ++++vGgG++G  lA  l k+  +  lve  + 
  gi|386002012|ref|YP_005920311.1| 223 HKVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDND 256
                                       5555555555555555555555555444444333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   8.2e-06    0.0059       1      71 [.       3      70 ..       3      94 .. 0.85
   2 ?    3.6   0.0     0.054        39       2      69 ..     226     293 ..     225     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.2e-06
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl 71
                                      i++tGa G +G +l+++l + +y+v+++d++s+a ++ ++ d+++ +++  +++ l ++  e ++d+v+ +
  gi|386002012|ref|YP_005920311.1|  3 IFITGA-GDVGYHLARELSQ-DYDVTVIDQKSRACERLEEIDVRVLQGNAANAQLLVEAGIE-DADIVVAV 70
                                      789998.***********96.7*********9999998888889999999999998888775.88888876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.054
                                       EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEE CS
                         Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavi 69 
                                       +++G+ G +G +l+k l++ +   +++ +d+++ ++  ++l+d+ + ++d td s +++  +   +dav+
  gi|386002012|ref|YP_005920311.1| 226 MIVGG-GVVGFYLAKWLEKMDfdLKLVEIDNDRCQELAEELPDTLILNGDGTDISLIKA-ENVGSMDAVF 293
                                       67888.***************7677999****999999999998999999999884443.3323566665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015        11       1      46 [.       1      45 [.       1      64 [. 0.87
   2 ?    4.5   0.0     0.032        23     131     171 ..     101     138 ..      76     149 .. 0.78
   3 !    7.5   0.0    0.0038       2.8       2      41 ..     224     263 ..     223     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi 46
                                      m+i + G+G vG   a  l++   +v+++D  +++ + l++ ++ +
  gi|386002012|ref|YP_005920311.1|  1 MQIFITGAGDVGYHLARELSQ-DYDVTVIDQKSRACERLEEIDVRV 45
                                      7999**************987.58********99999998776665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.032
                                       CHHHHHHHHCSS-TTCEEEEE------TTSHHHHHHS-S-E CS
                    UDPG_MGDP_dh_N 131 lvkkileeaskkkgvdfdvvsnPEflregsavkdllnpdrv 171
                                        +++ ++   ++k++ ++++ +PE +    +vk+l  p +v
  gi|386002012|ref|YP_005920311.1| 101 YIDQPMK---DRKNIGIGLMICPELVMAERIVKELYFPSMV 138
                                       4444443...444689*******************998876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0038
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklns 41 
                                       k+ ++G G vG   a  l ++ +++ +v id+ + ++l +
  gi|386002012|ref|YP_005920311.1| 224 KVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNDRCQELAE 263
                                       899******************************9999876 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00038      0.28       2      75 ..       4      82 ..       3     121 .. 0.60
   2 !    8.5   0.0    0.0038       2.7       1      33 [.     225     257 ..     225     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE........-EEEE--S-HHHHHHHHHHHSS.S--SE CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade........tavvvlthdhklDaealeaalr.kkaay 71
                                      +i Gag+v+ +lar +++ +++vtv+d+++++   er++e d         + + +l +    Da+++ a+   +++++
  gi|386002012|ref|YP_005920311.1|  4 FITGAGDVGYHLARELSQ-DYDVTVIDQKSRA--CERLEEIDVrvlqgnaaN-AQLLVEAGIEDADIVVAVTGnDEVNM 78
                                      799***********9986.9*********963..455554444566777752.33333333445555555543222445 PP

                                      EEES CS
                            XdhC_C 72 igll 75
                                      i ++
  gi|386002012|ref|YP_005920311.1| 79 ITCI 82
                                      4444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0038
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGG CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreef 33 
                                       ++i+G+g v+  la+ +++++f++ +v+ +++ 
  gi|386002012|ref|YP_005920311.1| 225 VMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNDR 257
                                       68*********************9998776642 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00015      0.11       1      54 [.       3      57 ..       3      81 .. 0.83
   2 !    6.5   0.0    0.0084         6       1      38 [.     225     263 ..     225     285 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrp 54
                                      i+i GaG +G  la +L++  +dvt+i+++   +e+l++ ++r+ + +  + +l++
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQ-DYDVTVIDQKSrACERLEEIDVRVLQGNaANAQLLV 57
                                      89***************66.9**********99999*9999998877765555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0084
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38 
                                       + i+G G +G +la  L k   d  l+  ++ r+++l +
  gi|386002012|ref|YP_005920311.1| 225 VMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNdRCQELAE 263
                                       58******************9999999999989998776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0031       2.2       2      41 ..       3      42 ..       2      62 .. 0.85
   2 !    9.8   0.0    0.0016       1.2       1      32 [.     224     255 ..     224     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0031
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDee 41
                                      + + G+G++g  lA +l++   +Vtv++ +++ + rl++ +
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQ-DYDVTVIDQKSRACeRLEEID 42
                                      7899*************98.448********9996666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0016
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversd 32 
                                       kv++vGgG++g  lA+ l ++  + ++ve  +
  gi|386002012|ref|YP_005920311.1| 224 KVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDN 255
                                       799***************99998888888655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   2.1e-05     0.015       4      80 ..       5      77 ..       3      93 .. 0.85
   2 ?    2.8   0.0       0.1        72       8      78 ..     231     302 ..     225     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                      SSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---GGS-HHH CS
                              NmrA  4 iGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgfyskeie 80
                                      i ++G  G +++r l +++++v ++  d+ks + + l+e  v +++g++ + ++lvea ++++d v +vtg  ++e++
  gi|386002012|ref|YP_005920311.1|  5 ITGAGDVGYHLAREL-SQDYDVTVI--DQKSRACERLEEIDVRVLQGNAANAQLLVEAgIEDADIVVAVTG--NDEVN 77
                                      667899999999986.567888765..99**************************99989***********..66665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                                       SHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHH.STTEEE.ES-TT-HHHHH.HHHTT-SEEEE---GGS-H CS
                              NmrA   8 GrqGksvvrallkaghkvralvRdtkselakslke.aGvelv.kgdlddkeslv.ealkgvdvvfsvtgfyske 78 
                                       G  G ++++ l k +++ + +  + ++++ ++l+e  + +l+ +gd  d ++++ e +   d+vfsvtgf +k+
  gi|386002012|ref|YP_005920311.1| 231 GVVGFYLAKWLEKMDFDLKLV--EIDNDRCQELAEeLPDTLIlNGDGTDISLIKaENVGSMDAVFSVTGFDEKN 302
                                       566666666666666666644..55677788886526999999***999999973678899********98765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0013      0.91       3      37 ..       2      35 ..       1      96 [. 0.86
   2 !    8.0   0.0    0.0021       1.5       3      31 ..     224     252 ..     222     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37
                                      ++ I GaG +G  la++Ls+   +v+++++ s++ 
  gi|386002012|ref|YP_005920311.1|  2 QIFITGAGDVGYHLARELSQD-YDVTVIDQKSRAC 35
                                      6789*****************.*******998765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlve 31 
                                       +V+IVG+G +G+ la+ L +   +  lve
  gi|386002012|ref|YP_005920311.1| 224 KVMIVGGGVVGFYLAKWLEKMDFDLKLVE 252
                                       79****************98766666666 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1      0.01       7.2      13      86 ..       3      71 ..       1      86 [. 0.78
   2 !    9.0   0.0    0.0017       1.2       8      61 ..     220     272 ..     210     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                     Rossmann-like 13 vGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraelllla.vPdaelpglvk 86
                                      + i +aG vG  l+  l + ++ v+ i   s     ra +rl +++v  ++  aa+a+ll+ a + da++   v+
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQ-DYDVTVIDQKS-----RACERLEEIDVRVLQGNAANAQLLVEAgIEDADIVVAVT 71
                                      5688999999999999976.77777776554.....677889999999999999999999976467777665555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                     Rossmann-like   8 sarlsvGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvle 61 
                                       +a  +v i++ G vG  l++ le+ +  +  +    +  +e+ae  lPd+ +l+
  gi|386002012|ref|YP_005920311.1| 220 TASHKVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNDRCQELAE-ELPDTLILN 272
                                       5667899***************************99*9999998.59**99987 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 ?    5.4   0.1     0.022        16       2      40 ..       3      40 ..       2      75 .. 0.74
   2 !    9.8   0.0   0.00096      0.69       1      44 [.     224     267 ..     224     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                      + + GaG +G  +a  + s++++V+++d +++a e+ +e
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLAREL-SQDYDVTVIDQKSRACERLEE 40
                                      66789999999999876.568999999998888887655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00096
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                       kv ++G G++G  +a+ + + +++ +lv+i++++ ++ +e++ +
  gi|386002012|ref|YP_005920311.1| 224 KVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDNDRCQELAEELPD 267
                                       699*******************************9999988766 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0014         1      45     108 ..       2      74 ..       1     112 [. 0.75
   2 !    6.7   0.0    0.0063       4.5      34      78 ..     214     258 ..     199     302 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                       EEEEES-CCCHHHHHHHHCCCEEEEEEESSGGGGGGSSST.........HHHHHHHHTTS---SEEEE---TT CS
                           DUF1188  45 nvlviGaYltGaaiakkLskkeevtlvDiephlkellekd.........vefklsleevernadlviDltGlG 108
                                       ++ + Ga  +G  +a++Ls++ +vt++D +++  e le+           + +l +e   ++ad+v+ +tG  
  gi|386002012|ref|YP_005920311.1|   2 QIFITGAGDVGYHLARELSQDYDVTVIDQKSRACERLEEIdvrvlqgnaANAQLLVEAGIEDADIVVAVTGND 74 
                                       6889999999******************998766655554466777755555555566688999999999855 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0063
                                       HHHTT--E..EEEEEES-CCCHHHHHHHHCCC.EEEEEEESSGGGG CS
                           DUF1188  34 eyleeeeleeknvlviGaYltGaaiakkLskk.eevtlvDiephlk 78 
                                       + ++ e+  +++v+++G  ++G ++ak L+k   ++ lv+i++   
  gi|386002012|ref|YP_005920311.1| 214 KIIH-EDTASHKVMIVGGGVVGFYLAKWLEKMdFDLKLVEIDNDRC 258
                                       4444.556689*******************9988999999876433 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.055        39      39      80 ..       3      43 ..       1      71 [. 0.77
   2 ?    7.1   0.0    0.0043       3.1      27      70 ..     213     256 ..     189     269 .. 0.78
   3 ?   -0.5   0.0      0.93   6.6e+02     104     129 ..     376     401 ..     370     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.055
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80
                                      + i G+G++G ++a+ l++ + +v+++d++ ++ e+ ee  v
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQ-DYDVTVIDQKSRACERLEEIDV 43
                                      6799***********9985.7778888888776665555554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0043
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                       +++  ++ +  +v i+G G +G  +ak l+++++++  ++  ++
  gi|386002012|ref|YP_005920311.1| 213 RKIIHEDTASHKVMIVGGGVVGFYLAKWLEKMDFDLKLVEIDND 256
                                       56777889999*******************99988776666554 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.93
                                       TTTTSBSHHHHHCSTTTEEEEESS-G CS
                      2-Hacid_dh_C 104 etrhlinaeelakmkkgailiNtaRG 129
                                       +  +++++++ +km+kgail  + RG
  gi|386002012|ref|YP_005920311.1| 376 KEAKILGKNAAEKMPKGAILGTIMRG 401
                                       5568999999*********9777777 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0033       2.3       2      33 ..       3      35 ..       2      38 .. 0.86
   2 ?    4.6   0.0     0.028        20       2      19 ..     225     242 ..     224     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0033
                                      EEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg.Vtllekgdiag 33
                                      + i G+G +G   A+eL++   Vt+++++++a+
  gi|386002012|ref|YP_005920311.1|  3 IFITGAGDVGYHLARELSQDYdVTVIDQKSRAC 35
                                      6788*************99747******97765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.028
                                       EEEECTSHHHHHHHHHHH CS
                               DAO   2 vviiGGGiiGlstAyeLa 19 
                                       v i+GGG++G   A +L 
  gi|386002012|ref|YP_005920311.1| 225 VMIVGGGVVGFYLAKWLE 242
                                       89********99998884 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.5   1.1e+03      19      72 ..      27      76 ..      11     104 .. 0.62
   2 ?   11.8   0.0   0.00024      0.18       9      55 ..     308     354 ..     303     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                                      EEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHH CS
                        ADH_zinc_N 19 avdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatl 72
                                      ++d +++ +e ++++ + ++  +     ++++    g e++d+v+ ++G ++ +
  gi|386002012|ref|YP_005920311.1| 27 VIDQKSRACERLEEIDVRVLQGN---AANAQLLVEAGIEDADIVVAVTG-NDEV 76
                                      55555554444444443333333...34444444445567777777777.4444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00024
                                       HHHHTT-.EEEE.EESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTT CS
                        ADH_zinc_N   9 lAkalGa.evia.vdsseeklelakklGadevinykeadlverikeltg 55 
                                       lAk lGa +++a vd+s+  ++l +  G+d++i + +   v+++ +l +
  gi|386002012|ref|YP_005920311.1| 308 LAKQLGAdKIVArVDRSDY-IDLFEMVGVDHAISPGR-VTVDAVLKLIR 354
                                       89**********8888886.9**************77.55555555553 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.44   3.1e+02      20      37 ..       2      19 ..       1      21 [. 0.90
   2 ?    1.4   0.1      0.24   1.7e+02      78     119 ..      31      73 ..      25      94 .. 0.82
   3 ?    6.4   0.0    0.0069       4.9      17      52 ..     221     257 ..     198     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.44
                                      EEEEE--SHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknL 37
                                      ++++ GaG +G  l+++L
  gi|386002012|ref|YP_005920311.1|  2 QIFITGAGDVGYHLAREL 19
                                      799***********9998 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.24
                                       HHHHHHT-TTSEEEEEES-CCG.CCS-HHHHTT-SEEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritd.etvleellesvDlVvdalDn 119
                                       + +++e+  +++v+ ++++  + + ++e  +e++D+Vv  + n
  gi|386002012|ref|YP_005920311.1|  31 KSRACERLEEIDVRVLQGNAANaQLLVEAGIEDADIVVAVTGN 73 
                                       567888889999999999999966678899******9988766 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0069
                                       HTSEEEEE--SHHHHHHHHHHHHHTTT.EEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                              ThiF  17 rdskvllvGaGglGsellknLalsGvg.kltlvDnDk 52 
                                       ++ kv++vG G +G +l+k L ++ +  kl  +DnD+
  gi|386002012|ref|YP_005920311.1| 221 ASHKVMIVGGGVVGFYLAKWLEKMDFDlKLVEIDNDR 257
                                       349**********************977999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2845.00
//
Query:       gi|386002013|ref|YP_005920312.1|  [L=204]
Description: Phage SPO1 DNA polymerase-related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-44  149.9   0.0    6.8e-44  149.6   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   0.0   3.8e-48   6.8e-44       1     154 [.      51     192 ..      51     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 3.8e-48
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaei 77 
                                       pgegp+ a++++vGe Pg+eed+tg+pF+grag  l+++l+eag++r      +v+itnvvkcrpp+nr  p+++e+
  gi|386002013|ref|YP_005920312.1|  51 PGEGPARAEILLVGEGPGREEDRTGRPFVGRAGSVLDRCLEEAGIER-----SRVFITNVVKCRPPENR-RPKRKEV 121
                                       79*********************************************.....*****************.******* PP

                                       TCCHHHHHHHHHHHHSSEEEEESHHHHHH...HHHHSCESCCCSCT.SEEEEES-SSTTTTTTTTSHHHHHHHHHHH CS
                               UDG  78 kacaplleeeiellkprlivllGktaakall.geklgklrgklleakirvlplphPsplnrnffksnpelkaeawed 153
                                       +ac+ +l+++iell+pr ++l+G+ aa+a+l  e +g+lrg++++   r+l+++hP++++rn       l++++++d
  gi|386002013|ref|YP_005920312.1| 122 EACRIYLDAQIELLQPRTVILMGNAAARAVLdVEGIGELRGRVIRG--RFLVTFHPAAVLRN-----GNLREAFIAD 191
                                       ******************************96669***********..9*************.....4444444466 PP

                                       H CS
                               UDG 154 L 154
                                       L
  gi|386002013|ref|YP_005920312.1| 192 L 192
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1324.97
//
Query:       gi|386002014|ref|YP_005920313.1|  [L=77]
Description: hypothetical protein Mhar_1326 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.41
# Mc/sec: 560.42
//
Query:       gi|386002015|ref|YP_005920314.1|  [L=421]
Description: nucleotidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-34  120.2   0.0    1.6e-34  119.6   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    5.5e-10   38.6   5.2    2.1e-05   24.1   1.5    3.6  3  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
      0.035   14.5   0.0       0.07   13.5   0.0    1.6  1  NTP_transf_3     MobA-like NTP transferase domain
      0.098   12.4   2.5        1.6    8.6   0.1    3.3  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


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 !  119.6   0.0   3.6e-38   1.6e-34       6     244 ..       9     249 ..       4     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 3.6e-38
                                       --S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEE.ETTTHHHHHHHHTTSGGGT........S CS
                   NTP_transferase   6 aGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvl.tqehsflveeqlkegskfg........v 73 
                                       +GG GtRL+PLt +++k+lv   ++  +i + +  la +g+++ ++ +   e+   +++++k+g+ f          
  gi|386002015|ref|YP_005920314.1|   9 VGGGGTRLYPLTLDQPKPLVDLCDT-AIIATLFRVLAIQGCRRFVLGSkGAENTLPLNNYFKAGEGFFkrlgisdiE 84 
                                       69***********************.*****************4333313567778999999998776899998855 PP

                                       EEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTT.SEEEEEEE.SS-CTTS CS
                   NTP_transferase  74 evlialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakg.tvtfgivp.veeatey 148
                                       e ++  +   kg+Ad+++  a++++ +++   +lv++gD +i+ ++++++++++ek+a + tv++   +  ee ++y
  gi|386002015|ref|YP_005920314.1|  85 EFAYQPQYADKGSADSLRYCANYFDIDED---MLVVSGDNVIDINLKDFIDFHREKGA-IlTVALKELDgGEEVSQY 157
                                       66777788888**************9996...**************************.447777765526788*** PP

                                       EEEEECTTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECST CS
                   NTP_transferase 149 GvieadeegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfk 224
                                       Gv+++d++ r++ fvEKP+  k  s ++++  Y+f +e+ + la+     ++ +d ++d++p+++e+g++   +  k
  gi|386002015|ref|YP_005920314.1| 158 GVARIDDDLRIRGFVEKPAPGKEpSRMINTAFYIFSPEIRKVLAD---MGDSARDIGGDLIPYLTEHGYPVFGYPVK 231
                                       ******************96554499*****************65...788899*********************** PP

                                       TEE-EEEXSSHHHHHHHHHH CS
                   NTP_transferase 225 daeyWsDvGtldslleanek 244
                                       +  yW D+Gt++ ll a+++
  gi|386002015|ref|YP_005920314.1| 232 G--YWIDIGTPERLLSAAMD 249
                                       *..9***********99986 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   1.5   4.7e-09   2.1e-05       2      36 .]     293     326 ..     292     326 .. 0.96
   2 !    8.4   0.0   0.00041       1.8      10      34 ..     335     358 ..     327     360 .. 0.82
   3 !    5.8   0.1    0.0027        12       3      22 ..     372     391 ..     366     393 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.7e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       ++IG n+ I +++vi ++ +IG  + I++g+vi+g
  gi|386002015|ref|YP_005920314.1| 293 VFIGRNCSIEKGVVI-EDSHIGHTSLIERGSVIKG 326
                                       89*************.*****************86 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00041
                                       E-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvi 34 
                                       I  ++++ + +++G++++Ig  +v+
  gi|386002015|ref|YP_005920314.1| 335 IKRGSYL-NRAIVGRHSTIGTKCVL 358
                                       5557777.999*********99987 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0027
                                       EEETTEEE-TTEEEETTEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkI 22 
                                       v+G+nv++   +v+g+++ +
  gi|386002015|ref|YP_005920314.1| 372 VVGENVILPQESVVGPGTRV 391
                                       55666666666666655544 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05      0.07       6      96 ..      10     121 ..       8     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       ESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHH..........HHTTCTS-....E CS
                      NTP_transf_3   6 GGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd.eevla..........alarlgvr....v 62 
                                       GG ++R+      ++K+l++l+++ +++ +++ l+ +g+++ v+  +  e+ l+           ++rlg++    +
  gi|386002015|ref|YP_005920314.1|  10 GGGGTRLypltlDQPKPLVDLCDTAIIATLFRVLAIQGCRRFVLGSKGaENTLPlnnyfkagegFFKRLGISdieeF 86 
                                       99*****7777678*************************99999876624444344555555553455554422234 PP

                                       EE-TTS.S-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                      NTP_transf_3  63 vededp.gkgplaslaaalraaadadavlvlacDm 96 
                                       ++++++ +kg + sl+  ++    ++ +lv+++D 
  gi|386002015|ref|YP_005920314.1|  87 AYQPQYaDKGSADSLRYCANYFDIDEDMLVVSGDN 121
                                       55555537899999999988887888888888886 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 ?    8.6   0.1   0.00035       1.6      18      32 ..     293     307 ..     283     309 .. 0.69
   2 ?    1.2   0.0      0.07   3.1e+02      19      27 ..     351     359 ..     343     360 .. 0.57
   3 ?   -0.6   0.1      0.27   1.2e+03       5      29 ..     374     388 ..     372     391 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00035
                                       EEE-TT-EE-TT-EE CS
                         Hexapep_2  18 vslGdncvvgaGvvi 32 
                                       v +G+nc ++ Gvvi
  gi|386002015|ref|YP_005920314.1| 293 VFIGRNCSIEKGVVI 307
                                       446777777777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.07
                                       EE-TT-EE- CS
                         Hexapep_2  19 slGdncvvg 27 
                                       ++G +cv++
  gi|386002015|ref|YP_005920314.1| 351 TIGTKCVLD 359
                                       466666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.27
                                       -TT-EE-TT-EESEEE-TT-EE-TT CS
                         Hexapep_2   5 GdnCliGanagiGvslGdncvvgaG 29 
                                       G+n          v+l  ++vvg+G
  gi|386002015|ref|YP_005920314.1| 374 GEN----------VILPQESVVGPG 388
                                       333..........444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 3174.98
//
Query:       gi|386002016|ref|YP_005920315.1|  [L=399]
Description: Threo-isocitrate dehydrogenase [NAD] [Methanosaeta harundinacea 6Ac]
Scores for 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-67  225.7   0.0    1.4e-66  225.0   0.0    1.2  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0   0.0   7.9e-71   1.4e-66       2     318 ..      46     354 ..      45     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 7.9e-71
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS...SSS-HHHHHHHHHSSEEEEEE---CS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg...eplpeetleaikeadvvllgavgtpk 75 
                                       i ++ gdgiGp ++++a++vl+++ +++    ++e +dv+g +i+e     +++p+  l+ +k+ +++l+g+++tpk
  gi|386002016|ref|YP_005920315.1|  46 IGVVGGDGIGPYICAEAKRVLEHMLQAEVSAGKVEIRDVSGLTIEERAramKAIPAGVLDELKRCHAILKGPLTTPK 122
                                       78999************************999*********999998767799************************ PP

                                       ....SSSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GG CS
                            Iso_dh  76 ....ekevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifte 148
                                             ++++ n  +a+r+eldlfan+rpvkv           +   +++d + +Re+t+g Y+   k  +    t+
  gi|386002016|ref|YP_005920315.1| 123 kgdpWPNLESAN--VAMRRELDLFANVRPVKVP----------S---QGIDWIFFRENTEGAYILGSKGLNV---TD 181
                                       776556777777..*****************98..........2...4799************988887776...58 PP

                                       GEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHH CS
                            Iso_dh 149 evavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamq 224
                                       e a+d  + ++++ eri+++af+ A+k+g ++vt+v+Kanv+k+s+  + +++ +va+ +yp+i l++ ++D +a++
  gi|386002016|ref|YP_005920315.1| 182 EIAFDFTVTTTQGAERIVHLAFDHAKKNGVNRVTAVTKANVIKTSDgKFLEVARKVAK-DYPEIDLDEWFIDIMAAK 257
                                       9*********************************************999999999999.****************** PP

                                       HH..HSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-...S-THHHHHH CS
                            Iso_dh 225 lv..kspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdk...aNpiavilS 296
                                       lv  k+ +qf V+v +Nl+GDi+ Deaa   G++G + Sa++g k+  +fEa+HGsap++   +    a p++++ +
  gi|386002016|ref|YP_005920315.1| 258 LVdpKRRTQFRVVVLPNLYGDIITDEAAEFQGGVGTAGSANIG-KRYSMFEAIHGSAPRMVEEGRaqyADPSSMMRA 333
                                       **4445599**********************************.79*************9866655569******** PP

                                       HHHHHHHTTT-HHHHHHHHHHH CS
                            Iso_dh 297 aalmLryslgleeaAdkiekAv 318
                                       aa++L + +g  e+A+++e A+
  gi|386002016|ref|YP_005920315.1| 334 AAMLLGH-IGFVEKARRLEMAL 354
                                       *******.***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2838.78
//
Query:       gi|386002017|ref|YP_005920316.1|  [L=333]
Description: Serine/threonine protein kinase RIO2 (RIO kinase 2) [Methanosaeta harundinacea 6Ac]
Scores for complete 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-39  134.0   0.0    6.4e-39  133.5   0.0    1.2  1  RIO1            RIO1 family
    8.2e-17   61.2   0.0    1.7e-16   60.2   0.0    1.5  1  Rio2_N          Rio2, N-terminal
    7.7e-06   25.4   0.1    0.00017   21.0   0.1    2.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    2.6e-05   24.3   4.1    0.00023   21.2   0.0    2.5  2  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.018   14.4   0.0    1.3  1  Pkinase         Protein kinase domain
       0.07   13.0   0.2       0.22   11.4   0.2    1.9  1  MarR_2          MarR family
      0.087   12.1   0.0       0.15   11.3   0.0    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
       0.15   11.6   0.0       0.24   11.0   0.0    1.2  1  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.0   2.8e-42   6.4e-39      12     181 ..     134     292 ..     116     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 2.8e-42
                                       EEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE-- CS
                              RIO1  12 evaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefi 88 
                                        +a+K+++ ++t+Fk++++ ++  ++    + +  + + ++l a +E r Lk+l+ + v+vP+p++l +h+lvme  
  gi|386002017|ref|YP_005920316.1| 134 PLAVKFHRQGRTSFKHVRRAREHLAD----HPRCAWIHAARLGAAREWRTLKALHPE-VRVPRPVALSHHALVMEHA 205
                                       79******************999999....4579**********************9.******************* PP

                                       EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEETTSTTHHHHH CS
                              RIO1  89 gedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQaveldhpnalefL 164
                                       g  g++++++   e     e  +e +lee++ +  + g vHaDLS yNvlv e+ +vviID++Qav+ ++p+a+e+L
  gi|386002017|ref|YP_005920316.1| 206 G--GTELYRVVLEE----PEPFLELILEEVASAW-RRGFVHADLSAYNVLVGEEgEVVIIDWPQAVSRRDPRARELL 275
                                       *..*****997655....88999**********9.9****************999********************** PP

                                       HHHHHHHHHHHHTTC-- CS
                              RIO1 165 erDveniikfFrrkgve 181
                                       erDv+n+ + F rk+  
  gi|386002017|ref|YP_005920316.1| 276 ERDVKNLLDHFARKYRL 292
                                       *************9865 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   7.4e-20   1.7e-16       3      82 .]      10      89 ..       8      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 7.4e-20
                            Rio2_N  3 yLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvk 81
                                       L++++  +L+avE gmr +e+ ++e +  ++rl+ +   + l rl+ +kl+sr+t +y+GY++ + +yD  AL+ lv 
  gi|386002017|ref|YP_005920316.1| 10 RLDRKEIALLKAVERGMRTSEWASMEDVVARARLSPKAAASGLARLVGKKLVSRTTEPYEGYQIGFVAYDLVALSDLVA 88
                                      58899999*******************************************************************9987 PP

                            Rio2_N 82 r 82
                                      r
  gi|386002017|ref|YP_005920316.1| 89 R 89
                                      6 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   7.7e-08   0.00017      50     190 ..     164     286 ..     135     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.7e-08
                               Kdo  50 rfk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallk 125
                                        +  + r++a+rE+r lk+L+   v+vp+pva            +l++e+  g++   ++l++    +e   + +l+
  gi|386002017|ref|YP_005920316.1| 164 AWIhAARLGAAREWRTLKALHP-EVRVPRPVALSH--------HALVMEHAGGTELYRVVLEE----PEPFLELILE 227
                                       34448899************97.6*******9864........469****9998877777776....4555555555 PP

                               Kdo 126 avgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsf 190
                                       +v+       r+g  Hadl a n+l+ +e+    e+++iD  +a  r    a+   e+d ++L+  f
  gi|386002017|ref|YP_005920316.1| 228 EVA----SAWRRGFVHADLSAYNVLVGEEG----EVVIIDWPQAVSRRDprARELLERDVKNLLDHF 286
                                       555....55678*****************9....*******99987764245555678888777665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.6     0.021        46      35      97 ..     171     228 ..     127     232 .. 0.64
   2 !   21.2   0.0     1e-07   0.00023     152     195 ..     225     262 ..     214     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHH CS
                               APH  35 eeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpellea 97 
                                         ++re + l++L+   v+vP+++a       + ++++++e  +g+ l+r   ++ ++ l+ +le+
  gi|386002017|ref|YP_005920316.1| 171 LGAAREWRTLKALHPE-VRVPRPVA-------LSHHALVMEHAGGTELYRvvlEEPEPFLELILEE 228
                                       2233444455555555.59999999.......4556679999999999997665555556655555 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1e-07
                                       HHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT CS
                               APH 152 vlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfed 195
                                       +l+++a  ++    ++++H Dl+  N+lv +++  v  +iD+  
  gi|386002017|ref|YP_005920316.1| 225 ILEEVASAWR----RGFVHADLSAYNVLVGEEGEVV--IIDWPQ 262
                                       5556666666....9***************887777..****55 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.2e-06     0.018      72     143 ..     197     261 ..     176     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                                       EEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGT CS
                           Pkinase  72 elylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFG 143
                                       +  lv+e++ g+el +++        ee + +++ ile ++  +++g++H Dl   N+L+ e+ge+ i+D+ 
  gi|386002017|ref|YP_005920316.1| 197 HHALVMEHAGGTELYRVVL-------EEPEPFLELILEEVASAWRRGFVHADLSAYNVLVGEEGEVVIIDWP 261
                                       6678999999999888885.......455678888888888889**************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   9.8e-05      0.22       9      57 ..      17      67 ..       9      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.8e-05
                                      HHHHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2  9 rvLaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                       +L a+ r+ +     ++ ++++r +ls+ a+   l+rLv + Lv r++ p
  gi|386002017|ref|YP_005920316.1| 17 ALLKAVERGMRTseWASMEDVVARARLSPKAAASGLARLVGKKLVSRTTEP 67
                                      555555555543666799***************************999865 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.9e-05      0.15     122     147 ..     235     260 ..     196     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
                                       TTEEEST-SGGGEEEEETTEEEE-ST CS
                       Pkinase_Tyr 122 kklvHrdlaarNvLlsenkvvkisDf 147
                                       + +vH dl+a NvL+ e+  v i D 
  gi|386002017|ref|YP_005920316.1| 235 RGFVHADLSAYNVLVGEEGEVVIIDW 260
                                       789***************99999885 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.24     139     171 ..     227     260 ..     209     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                       HCHGG-..EEEE-S--SGGGEEE.-CTTEEEE--G CS
                    Choline_kinase 139 eelesp..vvfcHnDlqegNillnkeekklvlIDF 171
                                       ee  s     f H Dl   N+l+  ee+++v+ID+
  gi|386002017|ref|YP_005920316.1| 227 EEVASAwrRGFVHADLSAYNVLV-GEEGEVVIIDW 260
                                       4444444478*************.9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1940.13
//
Query:       gi|386002018|ref|YP_005920317.1|  [L=669]
Description: hypothetical protein Mhar_1330 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-46  157.7   0.0      4e-46  156.2   0.0    1.7  1  DUF460        Protein of unknown function (DUF460)
    0.00027   21.4  13.1     0.0022   18.5   0.5    2.6  3  Fez1          Fez1
    0.00073   19.8   1.7    0.00073   19.8   1.7    3.3  3  acVLRF1       Actinobacteria/chloroflexi VLRF1 release factor
  ------ inclusion threshold ------
       0.14   12.5  11.1        1.4    9.3   2.1    2.6  2  Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
        3.3    7.5  14.0       0.54   10.1   2.5    2.3  2  Spc29         Spindle Pole Component 29
        7.3    6.4  19.8       0.56   10.0   5.1    3.0  2  DivIC         Septum formation initiator


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.2   0.0   1.3e-49     4e-46       5     141 .]     225     354 ..     222     354 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 1.3e-49
                            DUF460   5 kdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvivA 81 
                                        d +++ve ve+ +++fepl +kr+ ++i GiDPG+tt+ia+ldl+ge+++l+ssr++ + evie++s  Gk+++vA
  gi|386002018|ref|YP_005920317.1| 225 GDAQIRVEGVERPRLKFEPL-RKRRGYIIAGIDPGTTTAIAALDLEGELVDLTSSRTMATPEVIEWLSIRGKTLVVA 300
                                       699*****************.9******************************************************* PP

                            DUF460  82 tDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       tDvsp+p +v+k++r+++avl++P  d+s+eeK++la++      + y++dHeRDalaAA
  gi|386002018|ref|YP_005920317.1| 301 TDVSPTPGAVEKVKRAFSAVLFSPGGDISAEEKIALARE------YGYRNDHERDALAAA 354
                                       ***************************************......999***********9 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.2   1.2e+04      36      49 ..     174     187 ..     149     194 .. 0.53
   2 !    8.8   3.7   0.00069       2.1     114     156 ..     406     464 ..     338     473 .. 0.64
   3 !   18.5   0.5   7.5e-07    0.0022      44     154 ..     480     662 ..     470     667 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.2
                              Fez1  36 lkaqlrelraklee 49 
                                       +ka  re++++l+e
  gi|386002018|ref|YP_005920317.1| 174 VKALSREVEERLRE 187
                                       23333333333333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00069
                              Fez1 114 a.................lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqas 156
                                       +                 l+++ a+++rq +e++++lk+ ve+l++eL+eer ++ + ++
  gi|386002018|ref|YP_005920317.1| 406 RpappqapqeapssedadLSMQVAENRRQ-QEQIRRLKEFVEELKGELAEERAARRRLEA 464
                                       24455555555555555444444445555.589*******************99887755 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 7.5e-07
                              Fez1  44 rakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa...... 114
                                        ++++ +e+ei++l+  l++  + + +++++l+r+k  +el +e v++  +e++++ +e+   ++e+ + +      
  gi|386002018|ref|YP_005920317.1| 480 DQEIRIREKEIERLRGLLRQERKTNRRLKARLRREKRAEELEEEAVGRPTKEVASFSREAILEAAERLH-Igkgdvi 555
                                       478999*************************************************96644443333222.25799** PP

                              Fez1 115 ................................................................lesdeakaqrqea 127
                                                                                                       ++ ++a+aq +e+
  gi|386002018|ref|YP_005920317.1| 556 llldasgggpntadllielgveavvvetemepsveghlmdggvpvlssrevpvrrvsgialvgpEDLERARAQWSER 632
                                       **************************************************************997778888888888 PP

                              Fez1 128 eeleelkreverlra...eLkeerqkkeeq 154
                                       +++++ +r++e l++   e + er+k e+q
  gi|386002018|ref|YP_005920317.1| 633 KAVRDARRKTEWLEGmiqEYRAERRKDERQ 662
                                       888888888777766222666677777776 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   4.5e+03      78      96 ..      95     102 ..      64     132 .. 0.55
   2 !   19.8   1.7   2.4e-07   0.00073      38      69 ..     157     188 ..     129     221 .. 0.81
   3 ?   -5.8   6.1         6   1.8e+04      83     103 ..     505     525 ..     431     548 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                           acVLRF1  78 vlgGdrslvaevledarla 96 
                                       v+gG           +r +
  gi|386002018|ref|YP_005920317.1|  95 VTGG-----------ERAE 102
                                       2233...........3333 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.4e-07
                           acVLRF1  38 aaGGwSqqRfaRrrenqadalleavaeaaarl 69 
                                        +GGwSq+R+ R++ ++++al ++v+e++++ 
  gi|386002018|ref|YP_005920317.1| 157 GRGGWSQKRYTRKIHGSVKALSREVEERLREE 188
                                       47*************************99875 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 6
                           acVLRF1  83 rslvaevledarlaplatlar 103
                                       r+l a+++ ++r ++l++ a+
  gi|386002018|ref|YP_005920317.1| 505 RRLKARLRREKRAEELEEEAV 525
                                       333444444444344433333 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.0    0.0019       5.7       6      35 ..     438     467 ..     433     483 .. 0.80
   2 ?    9.3   2.1   0.00046       1.4      10      52 ..     487     528 ..     478     534 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0019
                      Lzipper-MIP1   6 rssLeqeveqLqerLqeeeklrraLekals 35 
                                          L++ ve+L+ +L ee++ rr Le  ++
  gi|386002018|ref|YP_005920317.1| 438 IRRLKEFVEELKGELAEERAARRRLEAKIE 467
                                       457999********************9883 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00046
                      Lzipper-MIP1  10 eqeveqLqerLqeeeklrraLekalssssdgsllslstllpkk 52 
                                       e+e+e+L+  L++e+k++r L+  l +++++++l  ++ + ++
  gi|386002018|ref|YP_005920317.1| 487 EKEIERLRGLLRQERKTNRRLKARLRREKRAEELEEEA-VGRP 528
                                       79*********************995555555555544.5555 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.5   0.00018      0.54      96     161 ..     410     473 ..     392     479 .. 0.75
   2 ?    1.5   5.9     0.075   2.2e+02     121     156 ..     478     513 ..     470     537 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                             Spc29  96 isspglapsdesrldsiyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeev 161
                                        ++p  aps e     +  +v +  + + ++   k+ ++eLk el ++r+  + L  k+++l ++ 
  gi|386002018|ref|YP_005920317.1| 410 PQAPQEAPSSED--ADLSMQVAENRRQQEQIRRLKEFVEELKGELAEERAARRRLEAKIERLMDRS 473
                                       334444444444..334456666678899********************************98875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.075
                             Spc29 121 elekklddqkleIkeLkreleqqrtvnseLqekvae 156
                                       + ++ +  ++ eI+ L+  l q+r  n+ L+ ++ +
  gi|386002018|ref|YP_005920317.1| 478 KRDQEIRIREKEIERLRGLLRQERKTNRRLKARLRR 513
                                       3366899999*********************99977 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.1   0.00019      0.56      24      66 ..     422     463 ..     415     474 .. 0.81
   2 ?    0.9   6.7      0.13     4e+02      22      61 ..     486     524 ..     481     525 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXX CS
                             DivIC  24 qeiaalqaelaklkaeneeLeaevkdLksdedyieerARselg 66 
                                       +++  + ae+ ++++++++L++ v++L ++e + e+ AR++l 
  gi|386002018|ref|YP_005920317.1| 422 ADLSMQVAENRRQQEQIRRLKEFVEEL-KGELAEERAARRRLE 463
                                       667778888999999999999999999.688888888888874 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                             DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLksdedyieerA 61 
                                        ++ei++l   l + +++n++L+a++++  +  + +ee A
  gi|386002018|ref|YP_005920317.1| 486 REKEIERLRGLLRQERKTNRRLKARLRRE-KRAEELEEEA 524
                                       689**************************.6999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1622  (0.090468); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.90u 0.33s 00:00:01.23 Elapsed: 00:00:00.51
# Mc/sec: 3953.86
//
Query:       gi|386002019|ref|YP_005920318.1|  [L=297]
Description: quinolinate synthase A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.6e-120  400.7   0.0     4e-120  400.5   0.0    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.5   0.0  2.2e-124    4e-120       2     298 ..       5     295 ..       4     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 400.5 bits;  conditional E-value: 2.2e-124
                                       HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT-- CS
                              NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleag 78 
                                       +i +lk+e+navilaHnYq  e+qe+ad+ GDSleL+r+aa++eaevi+fcGV+FMaeta+iLspek+v++p + a+
  gi|386002019|ref|YP_005920318.1|   5 DILRLKRERNAVILAHNYQPGEVQEVADLRGDSLELSRAAAREEAEVIIFCGVDFMAETAAILSPEKRVVMPAAGAS 81 
                                       6999************************************************************************* PP

                                       -HHHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.S CS
                              NadA  79 CsladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklge 155
                                       C++a+mita++++ +kee p+aavv+YvNssaevKa+sdi+cTS+n v+vv +l e+++lf+PD+nLgryva+ + e
  gi|386002019|ref|YP_005920318.1|  82 CPMASMITARDLRGFKEENPGAAVVCYVNSSAEVKAESDICCTSANGVEVVASLAEETVLFVPDRNLGRYVARFT-E 157
                                       *************************************************************************99.5 PP

                                       EEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHH CS
                              NadA 156 kkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglv 232
                                       kkii+w+g+C+vH+++++e+v+++ + hp+a+vlvHPEc++ev+++ad v STs++ + +kes+++efiigTe+g+ 
  gi|386002019|ref|YP_005920318.1| 158 KKIITWNGYCYVHDRYTPEDVSRACALHPEAEVLVHPECRPEVIDLADGVYSTSGMARRAKESPSREFIIGTEVGMN 234
                                       68*************************************************************************** PP

                                       HHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHH CS
                              NadA 233 erlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalerml 298
                                       +rlk+e+p+kef+ ls    e+avC +Mkk+tle++ +aLe+le+ +++v+eeva +A++a+erml
  gi|386002019|ref|YP_005920318.1| 235 YRLKEENPGKEFYPLS----EKAVCLDMKKTTLERVRSALETLEP-RVTVPEEVAGRARVAIERML 295
                                       *************553....3689*********************.*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1832.03
//
Query:       gi|386002020|ref|YP_005920319.1|  [L=59]
Description: hypothetical protein Mhar_1332 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 410.27
//
Query:       gi|386002021|ref|YP_005920320.1|  [L=196]
Description: hypothetical protein Mhar_1333 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1169.43
//
Query:       gi|386002022|ref|YP_005920321.1|  [L=425]
Description: hypothetical protein Mhar_1334 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.8e-114  382.6   0.0   2.1e-114  382.4   0.0    1.0  1  HI0933_like    HI0933-like protein
    2.2e-10   40.3   0.0    0.00044   19.6   0.1    2.6  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.8e-08   33.3   0.5    1.2e-06   27.9   0.4    2.3  2  FAD_binding_2  FAD binding domain
    1.5e-07   31.4   0.9     0.0063   16.1   0.1    2.4  2  DAO            FAD dependent oxidoreductase
    6.9e-07   29.4   0.1    2.4e-06   27.7   0.1    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.7e-06   27.5   0.0    2.9e-06   26.7   0.0    1.3  1  Thi4           Thi4 family
    6.6e-06   25.6   0.1    2.7e-05   23.6   0.0    1.9  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.3e-05   24.5   0.7       0.12   11.5   0.0    2.3  2  GIDA           Glucose inhibited division protein A
     0.0026   16.9   0.9       0.01   14.9   0.2    2.0  2  Lycopene_cycl  Lycopene cyclase protein
     0.0039   17.7   0.2        3.9    8.1   0.0    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0046   16.4   0.1     0.0076   15.6   0.1    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
  ------ inclusion threshold ------
       0.15   12.0   0.0        0.7    9.9   0.0    2.1  1  NAD_binding_9  FAD-NAD(P)-binding
       0.21   10.8   0.3       0.46    9.7   0.3    1.6  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.4   0.0  1.5e-117  2.1e-114       2     408 ..      16     412 ..      15     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 382.4 bits;  conditional E-value: 1.5e-117
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGGT-EEEETT-SGGGEEES...STTTTHHHHHHS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgGrcNvTnlseepeellsrypenpkflksalsrft 78 
                                       d+iv+G+G+AGl++A+sa+  + +Vl+lek++++grK+lisG GrcN+T+ + e++++l++y + ++fl+ al  ft
  gi|386002022|ref|YP_005920321.1|  16 DLIVVGAGPAGLFCAASASGGNLKVLVLEKKSSPGRKLLISGSGRCNLTH-DGEARAFLDHYGDAGRFLRPALLGFT 91 
                                       78************************************************.************************** PP

                                       HHHHHHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEE CS
                       HI0933_like  79 nedlialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeelea 155
                                       n+dl+a++ee+g+ +++ + g++Fp++++++d++++ll+e+++++v++   ++v+s+ek+e+g f v++ +++  ++
  gi|386002022|ref|YP_005920321.1|  92 NRDLVAFFEERGLSMTTLEGGKVFPETQRSRDVLTVLLAECEARKVEISGGKTVTSIEKSEEG-FLVAC-GNDIHRS 166
                                       ***********************************************************9999.*****.99***** PP

                                       SEEEE----SS-GGGT--SHHHHHHHHTT--EEEEEEES--EE--HHHHHCGGGTT-EEEEEEE....ECTTEEEEE CS
                       HI0933_like 156 dklvlAtGGlSiPklGstgkgyklaeqfghtivplrpalvpltlkesklklkelsGvslkavvlsl.kkkkkatekg 231
                                       + lv+AtGG S+P +Gs g+gy++a ++gh+i+++ pal p  +++  +  ++l+G+sl+   +s+ +++k+++  g
  gi|386002022|ref|YP_005920321.1| 167 RFLVIATGGRSYPATGSAGDGYSFAGALGHSIAEVGPALAPVRIRDYPF--ADLAGISLPGARVSIfRGRKAKEGVG 241
                                       ********************************************98876..9*************9999999999** PP

                                       EEEE-SSEEESHHHHHHTTT-......-TT--EEEECSTTS-...HHHHHHHHHHHTTTSBHHHHHTTT.S-HHHHH CS
                       HI0933_like 232 ellfThrGlsGpailqlSsyvakalekkeeetleidllPdldaeelkaalekekekeskkslknalael.lpkrlve 307
                                       ++lfTh GlsGp il lS+ +      ++++ l++ l+   ++ee++++l +  e+e  ++l+++lael +p rlv 
  gi|386002022|ref|YP_005920321.1| 242 DVLFTHDGLSGPGILDLSRDI------RAGDLLRVSLAGLRKKEEMERWLLARSEEEGGRNLRSVLAELaVPARLVS 312
                                       *********************......9*************************************9986489***** PP

                                       HHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE--SEE--TTT-SEEEEEE-GGGB-TTT-BBTTSTTEEE-GGG CS
                       HI0933_like 308 vlleealieeedkklaqlskkelkklaealkaltvkvngteglrkaevTaGGVdlkevssktmeskkvpgLffaGEv 384
                                       ++le  +i  +d k+a+++++ + +la+ l  +++ v +  g++ a+ T GGV+l+ev+sktmesk v+gL+f+GEv
  gi|386002022|ref|YP_005920321.1| 313 RVLELLEI-PQDLKCASMTRRMRIDLADRLSGFPLIVDEVGGYDSAMATRGGVALSEVDSKTMESKLVSGLYFVGEV 388
                                       *****999.999***************************************************************** PP

                                       BSEEE-TTTHHHHHHHHHHHHHHH CS
                       HI0933_like 385 lDvegvtGGynlqaAwasgyaAGk 408
                                       lDv+g+tGGynlqaA+++g++A+k
  gi|386002022|ref|YP_005920321.1| 389 LDVDGDTGGYNLQAAFSTGLLAAK 412
                                       **********************97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.2e-07   0.00044       1      30 [.      18      46 ..      18      53 .. 0.92
   2 !   17.6   0.0   1.3e-06    0.0018      83     139 ..     124     180 ..      66     187 .. 0.74
   3 ?   -2.1   0.0       1.3   1.8e+03     289     305 .]     369     386 ..     364     386 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      i++GaGPaGl +a  +   +l ++l+lEk+
  gi|386002022|ref|YP_005920321.1| 18 IVVGAGPAGLFCAASASGGNL-KVLVLEKK 46
                                      89*******************.7******8 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                       Pyr_redox_3  83 aleYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPn 139
                                       +l  l + ++  +++i   ++V+s++k++egf v + ++  ++++++iAtG  ++P 
  gi|386002022|ref|YP_005920321.1| 124 VLTVLLAECEARKVEISGGKTVTSIEKSEEGFLVACGNDIHRSRFLVIATGGRSYPA 180
                                       44444455678899*************************************988886 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.3
                       Pyr_redox_3 289 lteeteet.nvpglflaG 305
                                       ++++t+e+  v+gl+++G
  gi|386002022|ref|YP_005920321.1| 369 VDSKTMESkLVSGLYFVG 386
                                       56677766269*****99 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.4   8.6e-10   1.2e-06       1      47 [.      16      62 ..      16     114 .. 0.84
   2 ?    3.3   0.0     0.026        36     370     410 ..     358     399 ..     231     405 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.6e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgida 47
                                      D+iV+G+G AGL +A++a+  +lkv+v+ek+++ g  + +s+ g + 
  gi|386002022|ref|YP_005920321.1| 16 DLIVVGAGPAGLFCAASASGGNLKVLVLEKKSSPGRKLLISGSGRCN 62
                                      89******************************999899999766544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                                       EEES-EEEBETTSBESTTEEESSBTEEE-STCE..ESSSSTTS CS
                     FAD_binding_2 370 hytmgGvetdengrvldadgqpipGLYAaGeva..aggvhgan 410
                                         t gGv+  e       + + ++GLY +Gev+   g+ +g+n
  gi|386002022|ref|YP_005920321.1| 358 MATRGGVALSEVDSK-TMESKLVSGLYFVGEVLdvDGDTGGYN 399
                                       667777766553332.478999**********98777777777 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.5e-06    0.0063       1      33 [.      16      50 ..      16      60 .. 0.90
   2 !   13.5   0.1   2.9e-05      0.04     130     205 ..     108     178 ..      58     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.5e-06
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiag 33
                                      d++++G+G +Gl++A  ++  g   V++lek++ +g
  gi|386002022|ref|YP_005920321.1| 16 DLIVVGAGPAGLFCAASASG-GnlkVLVLEKKSSPG 50
                                      789***************66.4599*******9998 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.9e-05
                                       TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHH CS
                               DAO 130 gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsd 205
                                        l g+ ++p+t     + ++  l++++ea+ vei  g +vt++e+ +  +  v   + g+  ++ + +V+a+G  s 
  gi|386002022|ref|YP_005920321.1| 108 TLEGGKVFPETQ--RSRDVLTVLLAECEARKVEISGGKTVTSIEKSE-EGFLV---ACGNDiHRSRFLVIATGGRSY 178
                                       456777888844..58999999*********************7754.33444...22655444477******8875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.7e-09   2.4e-06       1      65 [.      19      83 ..      19      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.7e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETT..CEECTS---EEETTHHHHCHHHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpg..vrvdygahifhgsgyypnvrrll 65
                                      +vGaG +Gl +A+ ++  +++vl+lek +++G ++     +    ++d  a++f + + y  + r+l
  gi|386002022|ref|YP_005920321.1| 19 VVGAGPAGLFCAASASGGNLKVLVLEKKSSPGRKLLISGSGRcnLTHDGEARAFLD-H-YGDAGRFL 83
                                      8*******************************888877776555999999999999.4.66666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.1e-09   2.9e-06      18      80 ..      15      76 ..       1      79 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.1e-09
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdel 80
                                       D+++vGaG++GL +a   +   +lkv++le++ spG      G    ++    +a+++Ld  
  gi|386002022|ref|YP_005920321.1| 15 WDLIVVGAGPAGLFCAASASGG-NLKVLVLEKKSSPGRKLLISGSGRCNLTHDGEARAFLDHY 76
                                      69**************998887.**************99999999999999999999999875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   2.7e-05       2     114 ..      16     180 ..      15     201 .. 0.75
   2 ?   -0.7   0.0      0.49   6.8e+02     256     291 ..     362     404 ..     351     407 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       d++v+G+GpAGl +a  ++  ++kv+++ +++  ++++ l+s   +    +  +a+                     
  gi|386002022|ref|YP_005920321.1|  16 DLIVVGAGPAGLFCAASASGGNLKVLVL-EKKSSPGRKLLISGSGRCNLTHDGEARafldhygdagrflrpallgft 91 
                                       789*************************.88889999999976444444444334448889999999999******* PP

                                       ........................HHHHCHHHHCCCCHC...CTCEEEEESCEEEEETEEEC.......TCEEEEEE CS
                                       ........................xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx.......xxxxxxxx RF
                       Pyr_redox_2  58 ........................evvkklnqgielllg...eevvkidpgkkkvklekkke.......gdeekiay 100
                                                                ++++ +  +++ll+   + +v+i  g k+v+  +k+e       g+  +i  
  gi|386002022|ref|YP_005920321.1|  92 nrdlvaffeerglsmttleggkvfPETQRSRDVLTVLLAeceARKVEI-SGGKTVTSIEKSEegflvacGN--DIHR 165
                                       ********************9999555566666666666554446666.5555777776664455553333..3333 PP

                                       .SEEEE---EEE-BC CS
                                       .xxxxxxxxxxxxxx RF
                       Pyr_redox_2 101 .dklvlAtGssprdl 114
                                          lv+AtG+++   
  gi|386002022|ref|YP_005920321.1| 166 sRFLVIATGGRSYPA 180
                                       4889*****988654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.49
                                       TEE...E--TTS.BES.STTEEE-GGGC..TECCSS--HHHHH CS
                                       xxx...xxxxxx.xxx.xxxxxxxxxxx..xxxxxxxxxxxxx RF
                       Pyr_redox_2 256 ggi...vvdefl.rtn.vpgiyaiGDva..ggkggpelaqaAv 291
                                       gg+   +vd++  +++ v g+y +G v   +g++g  + qaA 
  gi|386002022|ref|YP_005920321.1| 362 GGValsEVDSKTmESKlVSGLYFVGEVLdvDGDTGGYNLQAAF 404
                                       44445567765538888*********99885555555556665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   9.3e-05      0.13       1      31 [.      16      46 ..      16      73 .. 0.86
   2 !   11.5   0.0   8.5e-05      0.12     345     390 ..     368     420 ..     348     422 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      d+iV+G+G AG+ +A+ a+  ++kvl + +k
  gi|386002022|ref|YP_005920321.1| 16 DLIVVGAGPAGLFCAASASGGNLKVLVLEKK 46
                                      689**********************998555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.5e-05
                                       GB-T.TSBBSSSBTEEE-CGG...GTB-S.HHHHHH..HHHHHHHHHHHHHCT CS
                              GIDA 345 qlln.tLetkkvkgLflAGqi...nGteG.YeEaaa..qGllAGinaarkakg 390
                                       ++ + t+e+k v+gL++ G++    G +G Y   aa  +GllA+  + r++++
  gi|386002022|ref|YP_005920321.1| 368 EVDSkTMESKLVSGLYFVGEVldvDGDTGgYNLQAAfsTGLLAAKSIRRRLAE 420
                                       45555**************8622267654687666666******999998876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   7.4e-06      0.01       1      35 [.      16      48 ..      16      54 .. 0.89
   2 ?    0.1   0.0      0.24   3.4e+02     229     282 ..     142     196 ..     117     208 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.4e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      D++v+GaGpAgl  Aa    +  +lkv+++e   s
  gi|386002022|ref|YP_005920321.1| 16 DLIVVGAGPAGLFCAASA--SGGNLKVLVLEKKSS 48
                                      9***************99..999******986554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                     Lycopene_cycl 229 glkvkevveeEqgviPvtlggslprleqkvlaiGaaaglvhPaT.....GYsvarslae 282
                                       g  v ++++ E+g + v+ g ++ r    v+a G+++    PaT     GYs+a +l +
  gi|386002022|ref|YP_005920321.1| 142 GKTVTSIEKSEEGFL-VACGNDIHRSRFLVIATGGRSY---PATgsagdGYSFAGALGH 196
                                       455677788888877.4477777777777777776664...555222234666666654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0028       3.9       2      36 ..      17      51 ..      16      54 .. 0.91
   2 !    6.9   0.0    0.0068       9.3       8      72 ..      89     154 ..      89     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0028
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                      ++vvG+G  gl +A+ ++  + kV v+e ++ + r
  gi|386002022|ref|YP_005920321.1| 17 LIVVGAGPAGLFCAASASGGNLKVLVLEKKSSPGR 51
                                      68**************************9998874 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0068
                                       SHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox   8 GyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedg 72 
                                       G+++ +l +++ e g + t +e ++ +   +  +++ ++l  + e++++e+  +++v++ie+se+g
  gi|386002022|ref|YP_005920321.1|  89 GFTNRDLVAFFEERGLSMTTLEGGKVFPeTQRSRDVLTVLLAECEARKVEISGGKTVTSIEKSEEG 154
                                       67777778888888888888888888777888889999999**********************998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.5e-06    0.0076       1      35 [.      16      50 ..      16      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      D++VvG+gpaG+ +A +A     kvl++e++   G
  gi|386002022|ref|YP_005920321.1| 16 DLIVVGAGPAGLFCAASASGGNLKVLVLEKKSSPG 50
                                      99***************************998776 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00051       0.7       2     154 ..      19     174 ..      18     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpasemslftddp........... 66 
                                       +vGaGp+Gl +++       ++ +l++ + ++ s+pg++   + +   +l       e  +f d+            
  gi|386002022|ref|YP_005920321.1|  19 VVGAGPAGLFCAASA-----SGGNLKVLVLEKkSSPGRKLLISGSGRCNLTHDG---EARAFLDHYgdagrflrpal 87 
                                       8********998653.....3678********7777*88888888765554444...44444444444589999888 PP

                     NAD_binding_9  67 .....ptfaeWlrergaleeaeeldpddfvpRalyGrYlrdlfeellarlpegvtvevh.raevvdleeradgqavl 137
                                            ++++ + +erg   ++++l+++++ p    +   rd+++ lla+++++ +ve+   ++v+++e++++g+ v 
  gi|386002022|ref|YP_005920321.1|  88 lgftnRDLVAFFEERGL--SMTTLEGGKVFPETQRS---RDVLTVLLAECEAR-KVEISgGKTVTSIEKSEEGFLV- 157
                                       88888888888888884..35788888877776654...68888888888654.7777734588899999998744. PP

                     NAD_binding_9 138 ladgaslaadaVvLAlG 154
                                         +++ ++ + +v+A+G
  gi|386002022|ref|YP_005920321.1| 158 ACGNDIHRSRFLVIATG 174
                                       44555668888888888 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00033      0.46       4      38 ..      17      51 ..      15     182 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38
                                       ++VGaGpaGl  a   s    +v+++ek s+  +
  gi|386002022|ref|YP_005920321.1| 17 LIVVGAGPAGLFCAASASGGNLKVLVLEKKSSPGR 51
                                      689**********9998888899999999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2607.12
//
Query:       gi|386002023|ref|YP_005920322.1|  [L=268]
Description: hypothetical protein Mhar_1335 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-10   40.2   0.0    5.5e-09   36.1   0.0    2.5  2  Abhydrolase_1  alpha/beta hydrolase fold
      4e-07   30.9   2.6    5.7e-07   30.4   2.6    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0019   17.5   0.0      0.016   14.5   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.055   13.0   0.0       0.77    9.3   0.0    2.1  2  DLH            Dienelactone hydrolase family
       0.18   11.4   0.0       0.27   10.8   0.0    1.2  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.25   9.1e+02       3      22 ..      19      36 ..      17      52 .. 0.70
   2 !   36.1   0.0   1.5e-12   5.5e-09      64     223 ..      60     220 ..      40     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                                      EEEE-STTTCGGGGTTGHHH CS
                     Abhydrolase_1  3 lvilhGlpgssdvwaergla 22
                                      + +lhG+pg  +  a   +a
  gi|386002023|ref|YP_005920322.1| 19 VALLHGGPGARGEMAP--VA 36
                                      6799*****7776554..44 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 1.5e-12
                                       HHH...HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE...CSSCCHHHHHHHHHHHHHHCHHCHHHHH CS
                     Abhydrolase_1  64 dri...ldalgddkltlvGhSmGGmialayaaeyperVkalvllga...idpaaslieaqrqqaksfpdffdgyaad 134
                                       + +   l+a gd + +l+G+S+GG +++ +aae+p+ V +l+l+g     +  as  ++ r+++ ++ +  +   + 
  gi|386002023|ref|YP_005920322.1|  60 EELrrdLEAAGDPPMALIGFSWGGWLGFILAAEHPDLVGKLILVGCapfEERRASAVHLTRMSRLGVEERREASSIL 136
                                       43333499*************************************96665555555555555666665555555555 PP

                                       HHHHHHHHHHHCCSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHH CS
                     Abhydrolase_1 135 carnpagplladelaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvl 211
                                              + +a e+ a + r+ + +++  +d+++ +  ++ d    + ++++ ++e ++ + s+ ll   r+   + 
  gi|386002023|ref|YP_005920322.1| 137 RLLEGPEVAGAEEMDAALRRLGAIFSK--ADSYDPILPESVDVDLQPEAFQAVWREAAELRKSGRLLELGRR---IE 208
                                       555555566778888888888888888..9999999999999999999999999999999999887777666...99 PP

                                       SEEEEEEETTCS CS
                     Abhydrolase_1 212 aptlvisgtsDp 223
                                       +p++ i+g++Dp
  gi|386002023|ref|YP_005920322.1| 209 CPVVAIQGEHDP 220
                                       999999999998 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   2.6   1.6e-10   5.7e-07      32     212 ..       7     252 ..       5     260 .. 0.46

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.6e-10
                                       E--TTST...........................S-GGCS--HHHCHHHHHHHCCTT......TTSE.EEEEETCHH CS
                     Abhydrolase_6  32 pDlpGhG...........................rsdpppldledladlaalldelaa....gggpv.vlvGHSlGG 76 
                                       +Dl+ hG                           +s +    l+++  ++ +++el+      g+p+  l+G S+GG
  gi|386002023|ref|YP_005920322.1|   7 IDLRRHGrppytvallhggpgargemapvarvlsSSRGVLEPLQRATSVRGQVEELRRdleaAGDPPmALIGFSWGG 83 
                                       57777773333333333333333333333333222222223333332222233333223333567777********* PP

                                       HHHHH.HHHCC..EE..EEES-................----TTT........S----TTHHHHHH...TT-CCCCH CS
                     Abhydrolase_6  77 alala.aaplalvvg..vlldppp..............talpagl........laaalelllalla...llrllawl 125
                                       +l+   aa ++++vg  +l+   p                             ++ +l+ll+++      ++++a++
  gi|386002023|ref|YP_005920322.1|  84 WLGFIlAAEHPDLVGklILVGCAPfeerrasavhltrmS-----RlgveerreASSILRLLEGPEVagaEEMDAALR 155
                                       *88885555778899976666633344443333332220.....012232222111111111111111111111222 PP

                                       CCH.......S-HSCCCCHHHC...CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCC CS
                     Abhydrolase_6 126 sre.......plprlfladeda...daawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerll 191
                                       +++       ++++ + + +d     +a++a ++++a l+++  ll     +++ +p++ + g+ Dp+ ++ ++  l
  gi|386002023|ref|YP_005920322.1| 156 RLGaifskadSYDPILPESVDVdlqPEAFQAVWREAAELRKSGRLLE--LGRRIECPVVAIqGEHDPHPAEGVRLPL 230
                                       11122222233332222222213345777777777777777666444..5555555553335899999998877666 PP

                                       H..STTEEETCE...SSS-HHHH CS
                     Abhydrolase_6 192 a..qagarlpvvlpgaGHlphle 212
                                          + ++r+  +l  +GH p++e
  gi|386002023|ref|YP_005920322.1| 231 SsvLKSFRF-FLLQESGHKPWIE 252
                                       677788888.9999999966664 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.5e-06     0.016      72     110 ..      68     106 ..       7     133 .. 0.84
   2 ?    0.6   0.0     0.078   2.8e+02     182     203 ..     199     220 ..     182     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                       Hydrolase_4  72 ehpelplfllGhSmGGliallyllrypdkvaglilsaPa 110
                                         ++ p+ l+G S+GG + + +++++pd v +lil++ a
  gi|386002023|ref|YP_005920322.1|  68 AAGDPPMALIGFSWGGWLGFILAAEHPDLVGKLILVGCA 106
                                       34456***********************999***99876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.078
                       Hydrolase_4 182 rleeraakitlPllllhGeaDk 203
                                       rl+e   +i+ P+  ++Ge+D+
  gi|386002023|ref|YP_005920322.1| 199 RLLELGRRIECPVVAIQGEHDP 220
                                       5677778999***********7 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00022      0.77      99     130 ..      73     104 ..      43     128 .. 0.78
   2 ?    1.6   0.0     0.046   1.7e+02     139     159 ..     203     223 ..     196     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00022
                               DLH  99 kvgvvGfCmGGalalllaaevpevdaavafYG 130
                                        ++++Gf +GG+l + laae p + + ++  G
  gi|386002023|ref|YP_005920322.1|  73 PMALIGFSWGGWLGFILAAEHPDLVGKLILVG 104
                                       5789****************987776665555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.046
                               DLH 139 eaakikapilalfgeeDefip 159
                                         ++i++p++a+ ge+D++ +
  gi|386002023|ref|YP_005920322.1| 203 LGRRIECPVVAIQGEHDPHPA 223
                                       56789************9865 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.6e-05      0.27     115     142 ..      71      99 ..      60     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.6e-05
                                       CC.EEEEEETHHHHHHHHHHHCSTTTCCE CS
                          Esterase 115 dg.ravaGqSmGGlgALilalkhpdrFgs 142
                                       d  +a++G+S GG    ila++hpd+ g 
  gi|386002023|ref|YP_005920322.1|  71 DPpMALIGFSWGGWLGFILAAEHPDLVGK 99 
                                       4469*********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1817.98
//
Query:       gi|386002024|ref|YP_005920323.1|  [L=119]
Description: glyoxalase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-08   34.7   0.0    3.4e-08   34.2   0.0    1.2  1  Glyoxalase_6  Glyoxalase-like domain
    2.7e-08   34.1   0.0    1.2e-06   28.8   0.0    2.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0052   17.1   0.0      0.082   13.2   0.0    2.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   5.7e-12   3.4e-08       6     106 ..      11     111 ..       5     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.7e-12
                      Glyoxalase_6   6 aadpaalaaFwaaalgweveree.......aaledpegvgpaaedaatllfqrvpepaknrvHldlavedldaevar 75 
                                       ++dp++++ F+++++gw++er e       +      g gp    +   ++++++ p++      ++v+dl+ ++a+
  gi|386002024|ref|YP_005920323.1|  11 VDDPERAVNFYSEVFGWRLERWEpfdywlaY-----TGEGP----GIDGALKPRESPGE-GTMNTIEVPDLEVAMAK 77 
                                       78*******************9955433211.....22222....33444555555545.578899*********** PP

                      Glyoxalase_6  76 lvalGArvlreprdgthgr...vlaDPeGneFcv 106
                                       +   G++v++e     + +    ++DPeGn+F +
  gi|386002024|ref|YP_005920323.1|  78 VAIEGGEVISEIMTVPGVGrfaRCRDPEGNVFGI 111
                                       **********9988776667************76 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.9e-10   1.2e-06       3     124 ..       5     107 ..       3     111 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.9e-10
                                       EEEEEEESHHHHHHHHHHHHHTSEEEEEEEE......EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCT CS
                        Glyoxalase   3 dhvallvgdleksldFYtkvLGfklvkktdn......teeteglriaffhaggghielvlneapsgaakhvkkieet 73 
                                        h+ ++v+d+e++++FY +v+G++l + +++      t            +g g  + +  +  +g+ +        
  gi|386002024|ref|YP_005920323.1|   5 IHFEIPVDDPERAVNFYSEVFGWRLERWEPFdywlayT-----------GEGPGIDGALKPRESPGEGTM------- 63 
                                       599***********************999944333332...........222222222222222222222....... PP

                                       SEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSE CS
                        Glyoxalase  74 vhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGi 124
                                              + +v d++ a  +++ +g++v  e+ + +  +++ + +rDp G+
  gi|386002024|ref|YP_005920323.1|  64 ------NTIEVPDLEVAMAKVAIEGGEVISEIMTVPGVGRFAR-CRDPEGN 107
                                       ......3556666666666666666666666666666666655.6666666 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.4e-05     0.082       2      41 ..       6      40 ..       5     100 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                      EEEEE-S-HHHHHHHHHH.TT-E..ESS--E.EETTTTEEEE CS
                      Glyoxalase_4  2 QigivVeDleaavarfsallGvg..pwqryrdepqevdlafa 41
                                      + +i V+D e+av+++s+++G++   w+++ +        +a
  gi|386002024|ref|YP_005920323.1|  6 HFEIPVDDPERAVNFYSEVFGWRleRWEPFDY-------WLA 40
                                      78899****************64223444333.......223 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       187  (0.01043); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 896.22
//
Query:       gi|386002025|ref|YP_005920324.1|  [L=78]
Description: hypothetical protein Mhar_1337 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   13.6   0.1      0.086   13.3   0.1    1.3  1  DUF4790   Domain of unknown function (DUF4790)


Domain annotation for each model (and alignments):
>> DUF4790  Domain of unknown function (DUF4790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.8e-06     0.086      45      78 ..      41      74 ..      13      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                           DUF4790 45 aldavrlvRvlayttlwpplhtkkelkkfekkff 78
                                       ++++ + R +a+ ++w p  t +e+k+f kk f
  gi|386002025|ref|YP_005920324.1| 41 LYNMIDIERDIAMVVVWKPETTVREIKEFDKKWF 74
                                      6788999**********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 687.24
//
Query:       gi|386002026|ref|YP_005920325.1|  [L=121]
Description: hypothetical protein Mhar_1338 [Methanosaeta harundinacea 6Ac]
Scores for 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-14   51.0   0.1    1.3e-13   50.4   0.1    1.3  1  Cupin_2          Cupin domain
    8.1e-05   22.6   0.0    9.9e-05   22.3   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    9.8e-05   22.3   0.1    0.00012   22.0   0.1    1.2  1  AraC_binding     AraC-like ligand binding domain
     0.0007   19.2   0.0    0.00092   18.8   0.0    1.1  1  Cupin_1          Cupin
     0.0013   18.4   0.0     0.0024   17.5   0.0    1.5  1  Cupin_3          Protein of unknown function (DUF861)
     0.0016   18.6   0.0     0.0018   18.4   0.0    1.1  1  Ectoine_synth    Ectoine synthase
     0.0039   16.9   0.0     0.0051   16.5   0.0    1.2  1  AraC_binding_2   AraC-binding-like domain
  ------ inclusion threshold ------
      0.087   12.6   0.0      0.096   12.4   0.0    1.1  1  EutQ             Ethanolamine utilisation protein EutQ
      0.095   12.9   0.0       0.13   12.5   0.0    1.1  1  CENP-C_C         Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   6.5e-17   1.3e-13       3      70 ..      41     108 ..      39     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 6.5e-17
                                       EEEETTEEEEEEC.SSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGesapshr.HpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                        +l pGe + +h   + + e++++leG+g++++dge  +++++++vy+p+g   +++N g + + +l++
  gi|386002026|ref|YP_005920325.1|  41 ARLGPGEASTPHQlKSSS-EVYFILEGRGRIHIDGESRDVGPDQAVYIPPGSIQHIENVGGGRLIFLCM 108
                                       6789***77777747776.***********************************************996 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     5e-08   9.9e-05      63     133 ..      36     106 ..      29     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5e-08
                   MannoseP_isomer  63 yqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkipleli 133
                                       y + +  + Pge  + ++    +e + +++G  ++++d e+  +  ++ +yip g+i  +en G   l ++
  gi|386002026|ref|YP_005920325.1|  36 YSLAHARLGPGEASTPHQLKSSSEVYFILEGRGRIHIDGESRDVGPDQAVYIPPGSIQHIENVGGGRLIFL 106
                                       55666667788888888888999****************************************98777655 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   5.9e-08   0.00012      16      67 ..      49     101 ..      35     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.9e-08
                                       EEEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTS CS
                      AraC_binding  16 fpphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsed 67 
                                         ph+     ++  ++eG+gr++++g+  d+gp++ + +ppg +  +e  ++ 
  gi|386002026|ref|YP_005920325.1|  49 STPHQLKsSSEVYFILEGRGRIHIDGESRDVGPDQAVYIPPGSIQHIENVGGG 101
                                       455555558899*******************************9999888765 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.6e-07   0.00092      32     115 ..      35     110 ..      21     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                                       TEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEE CS
                           Cupin_1  32 gisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepav 108
                                       g s+a  +l pg  + Ph   +++e+ ++l+G+gr  + + g+     ++++ + +++++P+g ++ + n g    +
  gi|386002026|ref|YP_005920325.1|  35 GYSLAHARLGPGEASTPHQLKSSSEVYFILEGRGR--IHIDGE-----SRDVGPDQAVYIPPGSIQHIENVG-GGRL 103
                                       66888999999999*********************..555553.....688********************9.7788 PP

                                       EEEEEES CS
                           Cupin_1 109 aivvfdt 115
                                       ++ ++ +
  gi|386002026|ref|YP_005920325.1| 104 IFLCMVS 110
                                       8877765 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.2e-06    0.0024      25      60 ..      57      91 ..      43      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                                      SEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 25 edEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                       +E  +ileG+ ++   +ge + +++  +v++p+g+
  gi|386002026|ref|YP_005920325.1| 57 SSEVYFILEGRGRIHI-DGESRDVGPDQAVYIPPGS 91
                                      4899************.******************8 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.2e-07    0.0018      32     115 ..      33     117 ..       2     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.2e-07
                                       SSSSEEEEEEE-TT--.EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TT.EEEEETTT-EEEEEESS.-EEEEE CS
                     Ectoine_synth  32 gmGfslhettikagte.telkYknHleavycieGegeveeledgevyeikpg.tlYlldkhdkHllrakk.elrlvc 105
                                        mG+sl +  +  g+  t  + k   e  +++eG+g+++   dge  ++ p   +Y+     +H+ +     l  +c
  gi|386002026|ref|YP_005920325.1|  33 SMGYSLAHARLGPGEAsTPHQLKSSSEVYFILEGRGRIHI--DGESRDVGPDqAVYIPPGSIQHIENVGGgRLIFLC 107
                                       6***********998615567899999999********87..6999999886269**********9988779***** PP

                                       EEES--XSSS CS
                     Ectoine_synth 106 vFnPpltGke 115
                                       + +Pp   +e
  gi|386002026|ref|YP_005920325.1| 108 MVSPPWRKEE 117
                                       ****987665 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.6e-06    0.0051      48     102 ..      50     104 ..      32     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                    AraC_binding_2  48 rpselddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlrwsadceql 102
                                       +p +l +   v ++l+Gr++++ +g+  ++gp++av + pg  + ++  ++ + +
  gi|386002026|ref|YP_005920325.1|  50 TPHQLKSSSEVYFILEGRGRIHIDGESRDVGPDQAVYIPPGSIQHIENVGGGRLI 104
                                       444455566799****************************987777766666655 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05     0.096      95     143 ..      57     105 ..      25     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                              EutQ  95 ydeidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtdeakfly 143
                                         e+ +++eGr  + idG     ++ + ++iP gs  +    +  ++++
  gi|386002026|ref|YP_005920325.1|  57 SSEVYFILEGRGRIHIDGESRDVGPDQAVYIPPGSIQHIENVGGGRLIF 105
                                       46999*****************************965555555555444 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.6e-05      0.13      18      74 ..      42      98 ..      36     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                                      EE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE- CS
                          CENP-C_C 18 kLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNk 74
                                      +L pg+  ++++ k+ + v+++++Gr ++ + ++s  +g+ +  ++P g+   ieN 
  gi|386002026|ref|YP_005920325.1| 42 RLGPGEASTPHQLKSSSEVYFILEGRGRIHIDGESRDVGPDQAVYIPPGSIQHIENV 98
                                      58899999999*******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 833.12
//
Query:       gi|386002027|ref|YP_005920326.1|  [L=167]
Description: cytosine deaminase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-20   73.0   0.0    1.8e-20   72.7   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.5e-19   69.4   0.0    3.2e-19   69.1   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
    0.00069   19.7   0.1     0.0084   16.2   0.1    2.1  1  Bd3614-deam      Bd3614-like deaminase
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.029   14.5   0.0    1.3  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
      0.088   12.7   0.0        0.5   10.2   0.0    1.8  2  APOBEC_N         APOBEC-like N-terminal domain
      0.099   12.7   0.1        2.9    8.0   0.0    2.3  2  ComZ             ComZ
       0.16   11.7   0.0       0.19   11.5   0.0    1.2  1  DUF2284          Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.0   7.2e-24   1.8e-20       1     100 [.      16     113 ..      16     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 7.2e-24
                                       HHHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE CS
                   dCMP_cyt_deam_1   1 mekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv 77 
                                       m+ d +++  a+++a+    +  +++Gav+v++g+ii++g n++ ++ ++ iHAE+ ++++a ++gg    g+tly 
  gi|386002027|ref|YP_005920326.1|  16 MKRDLEFMGAAMEEARAGLVEGGVPIGAVLVEEGRIIGRGRNRRVQEEDQLIHAEIDCLRNARRTGG--YAGTTLYS 90 
                                       678899**********9889******************************************99854..569***** PP

                                       EE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  78 tlePCsmCakaiiqsgikkvvvg 100
                                       t+ PC  Ca a +q+gik+vv g
  gi|386002027|ref|YP_005920326.1|  91 TMMPCYLCAGAAVQFGIKRVVAG 113
                                       *********************87 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   1.2e-22   3.2e-19       4     135 ..      20     149 ..      17     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.2e-22
                       MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtle 80 
                                        +++  a++e+++++  ++++igav v+++++i+rg n++ ++++ + HaEi+ l+ A   ++     ++tly t  
  gi|386002027|ref|YP_005920326.1|  20 LEFMGAAMEEARAGLVEGGVPIGAVLVEEGRIIGRGRNRRVQEEDQLIHAEIDCLRNARRTGGY---AGTTLYSTMM 93 
                                       678999****************************************************665555...5********* PP

                       MafB19-deam  81 pCdmCagaivqaglkklvygagnpkslnkLkvkekngrvelv...eddckeilkgffk 135
                                       pC  Caga vq g+k++v g ++     + ++  + + +++v     + keil +f++
  gi|386002027|ref|YP_005920326.1|  94 PCYLCAGAAVQFGIKRVVAGEAESAPEARAFM--EAHGIDVVdlnLAEAKEILAEFIR 149
                                       *******************9993333333333..333333343446677888888887 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   3.3e-06    0.0084      68     101 ..      76     109 ..      39     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                       Bd3614-deam  68 eeerrpleegarllvtlqcCkmCAalvvaaadap 101
                                       ++ r    +g++l++t+ +C +CA+ +v+++ ++
  gi|386002027|ref|YP_005920326.1|  76 NARRTGGYAGTTLYSTMMPCYLCAGAAVQFGIKR 109
                                       444555568*****************99988755 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.1e-05     0.029      15      63 ..      59     105 ..      48     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                             SNAD4  15 gvlknkke..haEllflekikseldpsqeyrvtwylswsPCaeCaekiaef 63 
                                       +v +++++  haE+  l++     ++      t+y ++ PC+ Ca + ++f
  gi|386002027|ref|YP_005920326.1|  59 RV-QEEDQliHAEIDCLRNA---RRTGGYAGTTLYSTMMPCYLCAGAAVQF 105
                                       33.3434458*********9...446677889*************999888 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002       0.5      48      95 ..      67     105 ..      53     113 .. 0.75
   2 ?    0.1   0.0      0.24   6.3e+02     121     166 ..     115     157 ..     103     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                       BCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHHH CS
                          APOBEC_N  48 kHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaaf 95 
                                        HaE   l+     ++r+++     tlY+++ PC      Ca + ++f
  gi|386002027|ref|YP_005920326.1|  67 IHAEIDCLR-----NARRTGGYAGTTLYSTMMPCYL----CAGAAVQF 105
                                       455544444.....56668899999***********....99877766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                                       HHHHH..HHHHHHTTEEEEE--HHHHHHHHHHHB--TT------TT CS
                          APOBEC_N 121 keaekeglrllkqagveleimkekdfkycwqnfveeeeekfkaWdg 166
                                        e++ e++  +++ g+ +  ++  + k +++ f+ +++    +Wd+
  gi|386002027|ref|YP_005920326.1| 115 AESAPEARAFMEAHGIDVVDLNLAEAKEILAEFI-RRRP--GLWDR 157
                                       45667788889999****9999999999999999.3333..33665 PP

>> ComZ  ComZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.07   1.8e+02       2      22 ..      18      35 ..      17      42 .. 0.73
   2 ?    8.0   0.0    0.0011       2.9      15      28 ..     119     132 ..     116     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.07
                              ComZ  2 ksleFlqIAmkylPeakkeLe 22
                                      + leF+  Am    ea++ L 
  gi|386002027|ref|YP_005920326.1| 18 RDLEFMGAAME---EARAGLV 35
                                      789******97...6666555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
                              ComZ  15 PeakkeLekkGIel 28 
                                       Pea++++e +GI++
  gi|386002027|ref|YP_005920326.1| 119 PEARAFMEAHGIDV 132
                                       ************86 PP

>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.4e-05      0.19      69     138 ..      59     135 ..      23     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.4e-05
                           DUF2284  69 emkevkeelekillelekeafeagypka.lalsagsCtlCetCayeegep......CrhpekarpsmealGidvfkt 138
                                       +++e  + ++  +  l+++    gy+ + l  ++ +C lC+  a++ g +       +   +ar  mea+Gidv+++
  gi|386002027|ref|YP_005920326.1|  59 RVQEEDQLIHAEIDCLRNARRTGGYAGTtLYSTMMPCYLCAGAAVQFGIKrvvageAESAPEARAFMEAHGIDVVDL 135
                                       556666667777777777777777776515556789****98666665445666667888899***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1050.73
//
Query:       gi|386002028|ref|YP_005920327.1|  [L=324]
Description: saccharopine dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0049   17.1   0.0      0.011   16.0   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-07     0.011      55     101 ..       5      51 ..       3      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-07
                                       -TTTHHHHHHHHHTTSSEEEE-SSGG.GHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  55 daenyeavLaallkegdlvvnlsppi.ssldvlkaCietgvhyvdtsi 101
                                       ++ ++++ L ++ +++dlv+++++ + + ++ ++a++++g++ +d+ +
  gi|386002028|ref|YP_005920327.1|   5 TPPDPPS-LREAFQGADLVIDAATTVpFIETTARAALAAGADWIDIHY 51 
                                       6778899.9*****************9999***************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2285.20
//
Query:       gi|386002029|ref|YP_005920328.1|  [L=553]
Description: hypothetical protein Mhar_1341 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-36  123.0   6.2    1.7e-18   66.7   0.3    3.7  4  TPR_12       Tetratricopeptide repeat
    1.3e-26   91.7   5.7    3.9e-08   32.9   0.1    4.8  4  TPR_10       Tetratricopeptide repeat
    2.2e-16   58.6   0.5     0.0014   18.6   0.1    4.4  4  TPR_2        Tetratricopeptide repeat
    1.4e-15   56.3   0.1    9.2e-05   22.1   0.0    3.6  3  TPR_1        Tetratricopeptide repeat
    3.8e-11   42.3   0.0      0.044   14.0   0.0    3.6  3  TPR_8        Tetratricopeptide repeat
    5.5e-11   41.7   0.5     0.0089   16.0   0.0    4.3  4  TPR_7        Tetratricopeptide repeat
    6.7e-09   35.3   0.1      0.022   14.4   0.0    3.8  4  TPR_11       TPR repeat
      4e-08   33.0   0.0    6.5e-08   32.3   0.0    1.3  1  TPR_MalT     MalT-like TPR region
    2.8e-07   30.8  15.8       0.31   12.0   0.5    5.9  5  TPR_14       Tetratricopeptide repeat
    8.6e-06   25.8   7.7      0.015   15.5   0.2    4.1  3  TPR_9        Tetratricopeptide repeat
    3.1e-05   24.5  15.0     0.0021   18.7   3.5    4.5  3  TPR_16       Tetratricopeptide repeat
    8.6e-05   22.9   0.2        4.8    8.0   0.0    4.3  3  TPR_6        Tetratricopeptide repeat
    0.00045   20.4   0.2        9.5    6.9   0.0    3.8  3  TPR_17       Tetratricopeptide repeat
     0.0018   18.7   0.1     0.0061   16.9   0.0    2.1  1  AAA_16       AAA ATPase domain
     0.0041   16.8   0.2        1.7    8.3   0.0    3.2  3  TPR_21       Tetratricopeptide repeat-like domain
  ------ inclusion threshold ------
       0.02   15.5  17.0       0.22   12.3   0.1    5.5  4  TPR_4        Tetratricopeptide repeat
      0.021   15.1   0.0       0.19   12.0   0.0    2.3  2  AAA_22       AAA domain
      0.057   13.9   0.3      0.057   13.9   0.3    2.8  3  TPR_19       Tetratricopeptide repeat
       0.24   11.3   0.0       0.49   10.3   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.91    9.7   3.5         51    4.1   0.0    3.9  4  DUF2379      Protein of unknown function (DUF2379)


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       7.2   6.4e+03      30      65 ..     176     189 ..     169     194 .. 0.47
   2 !   41.7   0.1   1.2e-13   1.1e-10       4      74 ..     371     441 ..     367     444 .. 0.94
   3 !   66.7   0.3   1.9e-21   1.7e-18       6      75 ..     457     526 ..     452     528 .. 0.95
   4 !   32.8   0.1   7.1e-11   6.4e-08       6      51 ..     499     544 ..     497     550 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.2
                            TPR_12  30 leiarrllGpdhpltattlrnLgrlyralgryeeAl 65 
                                        ++ar+l  + hpl                     l
  gi|386002029|ref|YP_005920328.1| 176 AALAREL--DRHPLS--------------------L 189
                                       3333333..333332....................2 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.2e-13
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +l+++++ l+r+g++  +   le+ + i +rl+Gpdhp++at l+nLg ++ralg++  A++ +e+a+ai
  gi|386002029|ref|YP_005920328.1| 371 LLLSQVGLYLHRRGDLRGSKGVLETLIVIDERLHGPDHPELATDLNNLGSVLRALGDLLGARRSFERAIAI 441
                                       456689***************************************************************98 PP

  == domain 3  score: 66.7 bits;  conditional E-value: 1.9e-21
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        nnl++vlr+lg++  A + +e+al+i r+++Gp+h  ta+ l+nLg++++++g++e A++ +++a++++
  gi|386002029|ref|YP_005920328.1| 457 ENNLGTVLRALGDLPAAVAAFERALAIDREAYGPNHFKTAIRLNNLGEVLQEMGDLEGARDSYQRAYRVF 526
                                       479****************************************************************986 PP

  == domain 4  score: 32.8 bits;  conditional E-value: 7.1e-11
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnL 51 
                                       lnnl++vl+++g+++ A++ +++a+++++++lGp h++t ++  nL
  gi|386002029|ref|YP_005920328.1| 499 LNNLGEVLQEMGDLEGARDSYQRAYRVFSQILGPGHHYTRRAEENL 544
                                       579*************************************998887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     8e-05     0.071       6      42 .]     374     410 ..     372     410 .. 0.94
   2 !   17.0   0.1   4.4e-06     0.004       5      31 ..     415     441 ..     411     444 .. 0.94
   3 !   32.9   0.1   4.3e-11   3.9e-08       6      40 ..     458     492 ..     458     493 .. 0.99
   4 !   28.2   0.1   1.4e-09   1.2e-06       1      41 [.     495     535 ..     495     536 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealairrrllGpdHPd 42 
                                       +  + +l++rg++ ++   le  + i +rl+GpdHP+
  gi|386002029|ref|YP_005920328.1| 374 SQVGLYLHRRGDLRGSKGVLETLIVIDERLHGPDHPE 410
                                       667999******************************7 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.4e-06
                            TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                                       lnNL+ +lr++g++ +A++ +e+a+ai
  gi|386002029|ref|YP_005920328.1| 415 LNNLGSVLRALGDLLGARRSFERAIAI 441
                                       8*************************9 PP

  == domain 3  score: 32.9 bits;  conditional E-value: 4.3e-11
                            TPR_10   6 nNLanalrqrgrydeAealleealairrrllGpdH 40 
                                       nNL+ +lr++g++ +A+a +e+alai r+++Gp+H
  gi|386002029|ref|YP_005920328.1| 458 NNLGTVLRALGDLPAAVAAFERALAIDREAYGPNH 492
                                       9********************************** PP

  == domain 4  score: 28.2 bits;  conditional E-value: 1.4e-09
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrllGpdHP 41 
                                       tA  lnNL+ +l+++g++++A++ +++a+++  ++lGp H 
  gi|386002029|ref|YP_005920328.1| 495 TAIRLNNLGEVLQEMGDLEGARDSYQRAYRVFSQILGPGHH 535
                                       7888************************************6 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.2   2.9e+03       4      31 ..     373     400 ..     371     402 .. 0.78
   2 !   16.7   0.0   6.3e-06    0.0056       4      31 ..     415     442 ..     412     444 .. 0.92
   3 !   18.6   0.1   1.5e-06    0.0014       5      32 ..     458     485 ..     457     487 .. 0.94
   4 !   17.7   0.0   2.9e-06    0.0026       3      29 ..     498     524 ..     496     528 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                       l + Gl + ++gd+   +  +e  + +d
  gi|386002029|ref|YP_005920328.1| 373 LSQVGLYLHRRGDLRGSKGVLETLIVID 400
                                       6678999999999998888888777665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.3e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                       l+nlG ++++lgd+  A++ fe+A++++
  gi|386002029|ref|YP_005920328.1| 415 LNNLGSVLRALGDLLGARRSFERAIAIE 442
                                       89***********************986 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.5e-06
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                       +nlG ++++lgd+  A++afe+Al++d 
  gi|386002029|ref|YP_005920328.1| 458 NNLGTVLRALGDLPAAVAAFERALAIDR 485
                                       69************************97 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 2.9e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                        l+nlG+++ ++gd+e A++ +++A +
  gi|386002029|ref|YP_005920328.1| 498 RLNNLGEVLQEMGDLEGARDSYQRAYR 524
                                       589**********************87 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   7.6e-05     0.068       4      32 ..     415     443 ..     412     445 .. 0.93
   2 !   22.1   0.0     1e-07   9.2e-05       5      32 ..     458     485 ..     454     486 .. 0.94
   3 !   17.2   0.0   3.7e-06    0.0033       4      27 ..     499     522 ..     496     527 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnP 32 
                                       l+nlG +++ lg++  A   +e+A+ +++
  gi|386002029|ref|YP_005920328.1| 415 LNNLGSVLRALGDLLGARRSFERAIAIEE 443
                                       79***********************9986 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALelnP 32 
                                       +nlG +++ lg++  A++++e+AL ++ 
  gi|386002029|ref|YP_005920328.1| 458 NNLGTVLRALGDLPAAVAAFERALAIDR 485
                                       8*************************96 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekA 27 
                                       l+nlG +++++g+++ A + y++A
  gi|386002029|ref|YP_005920328.1| 499 LNNLGEVLQEMGDLEGARDSYQRA 522
                                       89*********************9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00026      0.23       4      32 ..     415     443 ..     415     445 .. 0.93
   2 !   14.0   0.0   4.9e-05     0.044       5      32 ..     458     485 ..     458     486 .. 0.95
   3 !   12.3   0.0   0.00018      0.16       4      29 ..     499     524 ..     496     527 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++nlgs+++ lgd+  A  ++e+a+ +++
  gi|386002029|ref|YP_005920328.1| 415 LNNLGSVLRALGDLLGARRSFERAIAIEE 443
                                       589**********************9986 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +nlg +++ lgd+ +A++++e+al +d+
  gi|386002029|ref|YP_005920328.1| 458 NNLGTVLRALGDLPAAVAAFERALAIDR 485
                                       69************************97 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekale 29 
                                       ++nlg +++++gd+e A  +y++a +
  gi|386002029|ref|YP_005920328.1| 499 LNNLGEVLQEMGDLEGARDSYQRAYR 524
                                       79*********************975 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.8   5.2e+03      14      32 ..     155     171 ..     155     174 .. 0.81
   2 !    9.6   0.0    0.0011      0.97       2      32 ..     415     445 ..     414     449 .. 0.91
   3 !   16.0   0.0   9.9e-06    0.0089       3      35 ..     458     490 ..     458     491 .. 0.94
   4 !   11.1   0.0   0.00037      0.33       2      25 ..     499     522 ..     499     532 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.8
                             TPR_7  14 dyeeAielyeqsLaltkdp 32 
                                       d +eA++++ q  ++++++
  gi|386002029|ref|YP_005920328.1| 155 DLQEAAGFLLQ--RTERED 171
                                       56899999999..888765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       L+nL+++ ++lGd   A + +e+++a+++++
  gi|386002029|ref|YP_005920328.1| 415 LNNLGSVLRALGDLLGARRSFERAIAIEESQ 445
                                       89*********************99998876 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 9.9e-06
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +nL+ + ++lGd   A+  +e++La++++ +++
  gi|386002029|ref|YP_005920328.1| 458 NNLGTVLRALGDLPAAVAAFERALAIDREAYGP 490
                                       79*************************998876 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00037
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqs 25 
                                       L+nL+++ +++Gd e A + y+++
  gi|386002029|ref|YP_005920328.1| 499 LNNLGEVLQEMGDLEGARDSYQRA 522
                                       89********************95 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0013       1.2       1      29 [.     419     447 ..     419     448 .. 0.94
   2 !   14.4   0.0   2.5e-05     0.022       1      25 [.     461     485 ..     461     487 .. 0.91
   3 ?   -2.6   0.0         5   4.5e+03      15      24 ..     491     500 ..     491     501 .. 0.83
   4 !    7.3   0.1     0.004       3.6       1      20 [.     503     522 ..     503     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnae 29 
                                       G +++++G++ +A  ++++A+++ +++++
  gi|386002029|ref|YP_005920328.1| 419 GSVLRALGDLLGARRSFERAIAIEESQPT 447
                                       889*********************99986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.5e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                       G +++++G++++A++a+++Al++d 
  gi|386002029|ref|YP_005920328.1| 461 GTVLRALGDLPAAVAAFERALAIDR 485
                                       6689*******************96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5
                            TPR_11  15 eaYkkAlkld 24 
                                       +++k+A++l+
  gi|386002029|ref|YP_005920328.1| 491 NHFKTAIRLN 500
                                       5789****98 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.004
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       G ++ e G++e+A  +Y++A
  gi|386002029|ref|YP_005920328.1| 503 GEVLQEMGDLEGARDSYQRA 522
                                       5667799************9 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   7.2e-11   6.5e-08      31     159 ..     403     534 ..     377     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 7.2e-11
                          TPR_MalT  31 lpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallall..qqaeilvaqGrLheAletyeq 105
                                       l+  d+++ ++ + +lG +    Gdl  A+++++ a+++  ++  +++   a++   ++ +l+a G+L +A+  +e+
  gi|386002029|ref|YP_005920328.1| 403 LHGPDHPELATDLNNLGSVLRALGDLLGARRSFERAIAIEESQPTPDRLKIAIRenNLGTVLRALGDLPAAVAAFER 479
                                       6667777777788899************************999999998888887799******************* PP

                          TPR_MalT 106 alqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epea 159
                                       al+  +e+ +++ +   + l  l+++l E++dLe+A++  q++ ++  q  +p +
  gi|386002029|ref|YP_005920328.1| 480 ALAIDREAYGPNHFKTAIRLNNLGEVLQEMGDLEGARDSYQRAYRVFSQIlGPGH 534
                                       *************9999999************************99988656644 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   3.2       2.8   2.5e+03      13      43 ..     168     197 ..     154     198 .. 0.61
   2 ?    3.3   0.0      0.21   1.9e+02       6      38 ..     375     412 ..     369     418 .. 0.78
   3 !   11.7   0.1   0.00041      0.37       7      35 ..     418     446 ..     415     454 .. 0.87
   4 !   12.0   0.5   0.00035      0.31       7      31 ..     460     484 ..     459     499 .. 0.89
   5 !    8.0   0.1    0.0065       5.9       7      29 ..     502     524 ..     496     539 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.8
                            TPR_14  13 alGdpdeAiallrralalaPddaeawlllaq 43 
                                       +++d  +A+al+r++ +++P ++e+  ++ +
  gi|386002029|ref|YP_005920328.1| 168 EREDASGAAALAREL-DRHPLSLELAAAYIR 197
                                       245555666666666.999999988877765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
                            TPR_14   6 alaeallalGdpdeAiallrrala.....laPddaeaw 38 
                                       + + +l ++Gd++++  +l+ ++      ++Pd++e+ 
  gi|386002029|ref|YP_005920328.1| 375 QVGLYLHRRGDLRGSKGVLETLIViderlHGPDHPELA 412
                                       55677899*************99966666668888775 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00041
                            TPR_14   7 laeallalGdpdeAiallrralalaPdda 35 
                                       l+++l+alGd+ +A++ ++ra+a   +++
  gi|386002029|ref|YP_005920328.1| 418 LGSVLRALGDLLGARRSFERAIAIEESQP 446
                                       799********************876654 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00035
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       l+ +l+alGd+ +A+a+++rala +
  gi|386002029|ref|YP_005920328.1| 460 LGTVLRALGDLPAAVAAFERALAID 484
                                       7889******************976 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0065
                            TPR_14   7 laeallalGdpdeAiallrrala 29 
                                       l+e+l + Gd+++A++ ++ra +
  gi|386002029|ref|YP_005920328.1| 502 LGEVLQEMGDLEGARDSYQRAYR 524
                                       899*****************977 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.6e-05     0.015      24      71 ..     405     454 ..     378     456 .. 0.82
   2 ?    6.4   0.3     0.011       9.6      36      61 ..     461     486 ..     459     500 .. 0.88
   3 ?    5.9   0.2     0.016        15      35      55 ..     502     522 ..     494     540 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                             TPR_9  24 l..aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                          +P+ + ++   G +l  lG+l +A++ +e+++a++++ p+ ++++ +
  gi|386002029|ref|YP_005920328.1| 405 GpdHPELATDLNNLGSVLRALGDLLGARRSFERAIAIEESQPTPDRLKIA 454
                                       35578888888999*************************99999998866 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                             TPR_9  36 GlllaqlGclsaAladLeaylalapd 61 
                                       G +l  lG+l aA+a++e++la++ +
  gi|386002029|ref|YP_005920328.1| 461 GTVLRALGDLPAAVAAFERALAIDRE 486
                                       677888***************99875 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.016
                             TPR_9  35 RGlllaqlGclsaAladLeay 55 
                                        G +l+++G+l++A++  +++
  gi|386002029|ref|YP_005920328.1| 502 LGEVLQEMGDLEGARDSYQRA 522
                                       699**************9997 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.4       1.7   1.5e+03      17      37 ..     175     195 ..     166     197 .. 0.73
   2 !    9.4   0.0    0.0019       1.7      27      61 ..     405     439 ..     402     447 .. 0.83
   3 !   18.7   3.5   2.3e-06    0.0021       2      63 ..     459     525 ..     458     528 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.7
                            TPR_16  17 aaaleaalkrdpssPdaaeAl 37 
                                       aaal + l+r+p s + a+A+
  gi|386002029|ref|YP_005920328.1| 175 AAALARELDRHPLSLELAAAY 195
                                       566668888887777777776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                            TPR_16  27 dpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +p++P+ a  l++lg ++ ++g+l +A+  +++a+
  gi|386002029|ref|YP_005920328.1| 405 GPDHPELATDLNNLGSVLRALGDLLGARRSFERAI 439
                                       6888999999999***************7777776 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.3e-06
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd.....aaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       +l++ ++++gd ++A+aa+e+al+ d++        +a  l++lg+++ + g+l++A++ y++a+r 
  gi|386002029|ref|YP_005920328.1| 459 NLGTVLRALGDLPAAVAAFERALAIDREAYGpnhfkTAIRLNNLGEVLQEMGDLEGARDSYQRAYRV 525
                                       68999*********************88888*****************999************9975 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.29   2.6e+02       6      27 ..     418     439 ..     417     441 .. 0.89
   2 ?    6.6   0.0     0.015        14       5      27 ..     459     481 ..     459     483 .. 0.91
   3 !    8.0   0.0    0.0053       4.8       5      26 ..     501     522 ..     501     527 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                       l+  +r+lgd   A++ +er i
  gi|386002029|ref|YP_005920328.1| 418 LGSVLRALGDLLGARRSFERAI 439
                                       788999999***********98 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       +l+  +r+lgd  +A++a+er +
  gi|386002029|ref|YP_005920328.1| 459 NLGTVLRALGDLPAAVAAFERAL 481
                                       589999**99**********987 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerl 26 
                                       +l++ ++++gd + A++ ++r 
  gi|386002029|ref|YP_005920328.1| 501 NLGEVLQEMGDLEGARDSYQRA 522
                                       5899****************96 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.022        20       9      33 ..     408     432 ..     407     433 .. 0.87
   2 ?    3.3   0.0      0.15   1.3e+02      17      33 ..     458     474 ..     458     475 .. 0.89
   3 ?    6.9   0.0     0.011       9.5      16      33 ..     499     516 ..     476     517 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                            TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                       +P  a  +nnL+ +l+ +Gdl  Ar
  gi|386002029|ref|YP_005920328.1| 408 HPELATDLNNLGSVLRALGDLLGAR 432
                                       57888889************98876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                            TPR_17  17 nnLAelllknGdlmtAr 33 
                                       nnL+++l+ +Gdl  A+
  gi|386002029|ref|YP_005920328.1| 458 NNLGTVLRALGDLPAAV 474
                                       8***********98875 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                            TPR_17  16 ynnLAelllknGdlmtAr 33 
                                       +nnL+e+l + Gdl+ Ar
  gi|386002029|ref|YP_005920328.1| 499 LNNLGEVLQEMGDLEGAR 516
                                       89*************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.9e-06    0.0061       3      46 ..      15      52 ..      13     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.9e-06
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellr 46
                                       GR   l+ L++ l+   +   + vll G+ G+GKs++++e  r
  gi|386002029|ref|YP_005920328.1| 15 SGRSSTLKDLQDRLK---D---GPVLLLGPDGIGKSAIAEEYGR 52
                                      588888888877776...3...46***************99876 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.17   1.5e+02     153     181 ..     419     450 ..     411     462 .. 0.77
   2 ?    4.5   0.0     0.028        25     149     192 ..     457     503 ..     447     504 .. 0.81
   3 !    8.3   0.0    0.0019       1.7     150     174 ..     500     524 ..     490     529 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
                            TPR_21 153 GDilvaqgkldeAraaYqaAlaaleeka...r 181
                                       G +l a g+l  Ar  +++A+a  e++    r
  gi|386002029|ref|YP_005920328.1| 419 GSVLRALGDLLGARRSFERAIAIEESQPtpdR 450
                                       99******************997777655444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.028
                            TPR_21 149 aelrGDilvaqgkldeAraaYqaAlaaleeka...rellqlKlddLa 192
                                       ++  G +l a g+l  A aa+++Ala   e     +  + ++l++L+
  gi|386002029|ref|YP_005920328.1| 457 ENNLGTVLRALGDLPAAVAAFERALAIDREAYgpnHFKTAIRLNNLG 503
                                       566699*******************9887776776666777777776 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0019
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                       +  G++l ++g+l+ Ar+ Yq+A++
  gi|386002029|ref|YP_005920328.1| 500 NNLGEVLQEMGDLEGARDSYQRAYR 524
                                       5569*******************86 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.5   2.2e+03      10      18 ..     379     387 ..     377     394 .. 0.82
   2 ?    3.5   0.1      0.16   1.5e+02       6      26 .]     417     437 ..     415     437 .. 0.88
   3 ?   12.3   0.1   0.00024      0.22       6      26 .]     459     479 ..     458     479 .. 0.95
   4 ?    8.2   0.1    0.0049       4.4       6      23 ..     501     518 ..     498     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.5
                             TPR_4  10 allalGdld 18 
                                        l+++Gdl 
  gi|386002029|ref|YP_005920328.1| 379 YLHRRGDLR 387
                                       79*****85 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                             TPR_4   6 aLArallalGdldeAraller 26 
                                       +L+ +l alGdl  Ar+ +er
  gi|386002029|ref|YP_005920328.1| 417 NLGSVLRALGDLLGARRSFER 437
                                       7999********999998886 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00024
                             TPR_4   6 aLArallalGdldeAraller 26 
                                       +L+ +l alGdl++A a++er
  gi|386002029|ref|YP_005920328.1| 459 NLGTVLRALGDLPAAVAAFER 479
                                       79****************997 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0049
                             TPR_4   6 aLArallalGdldeAral 23 
                                       +L+++l++ Gdl+ Ar+ 
  gi|386002029|ref|YP_005920328.1| 501 NLGEVLQEMGDLEGARDS 518
                                       8***************85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.19       5     100 ..      30     117 ..      26     119 .. 0.89
   2 ?   -0.5   0.0       1.6   1.4e+03      75      99 ..     369     401 ..     355     426 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellea 81 
                                       +g +++ G+ G+GK+  ++++ + +  e       ++ + v +  +  +++ +  l++ lg + ++  ++ ++l   
  gi|386002029|ref|YP_005920328.1|  30 DGPVLLLGPDGIGKSAIAEEYGRIHFSE------YDHRLWVRAWDGAVLASDYASLAEPLGIPSEE-DGDVSDLAGS 99 
                                       577899*****************98655......88899999999999999999999999999999.9999999999 PP

                            AAA_22  82 leqalraravielliiDEa 100
                                       ++ ++++r++  ll+ D a
  gi|386002029|ref|YP_005920328.1| 100 VRAHFEERGR-WLLVFDGA 117
                                       9999999999.99999865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                            AAA_22  75 seellealeqalrarav........ielliiDE 99 
                                        + ll+++  +l++r++          l++iDE
  gi|386002029|ref|YP_005920328.1| 369 ASLLLSQVGLYLHRRGDlrgskgvlETLIVIDE 401
                                       4445588888888888888888899999****9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.6       5.8   5.2e+03       4      27 ..     169     191 ..     155     197 .. 0.53
   2 ?   -1.3   0.0       3.7   3.4e+03       3      19 ..     424     440 ..     404     451 .. 0.58
   3 ?   13.9   0.3   6.3e-05     0.057       2      50 ..     465     521 ..     464     527 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                            TPR_19   4 egdyaeAlalleqalqedpknaea 27 
                                       ++d   A+al ++ l+  p ++e+
  gi|386002029|ref|YP_005920328.1| 169 REDASGAAALARE-LDRHPLSLEL 191
                                       3444445555555.4555544444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.7
                            TPR_19   3 aegdyaeAlalleqalq 19 
                                       a gd+  A + +e+a++
  gi|386002029|ref|YP_005920328.1| 424 ALGDLLGARRSFERAIA 440
                                       33444445555555444 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 6.3e-05
                            TPR_19   2 laegdyaeAlalleqalqedpk.......naearl.lLAeallalgqldeAealLda 50 
                                        a gd+ +A+a++e+al+ d +         ++rl +L e+l ++g+l+ A++  ++
  gi|386002029|ref|YP_005920328.1| 465 RALGDLPAAVAAFERALAIDREaygpnhfKTAIRLnNLGEVLQEMGDLEGARDSYQR 521
                                       678**************997777777799999999999**************98776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00055      0.49      87     116 ..      18      47 ..      13      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                                       HTTHHHHHHHCTTSEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLi 116
                                       +++l++l+++lkd  ++l+G+ G+GKS++ 
  gi|386002029|ref|YP_005920328.1|  18 SSTLKDLQDRLKDGPVLLLGPDGIGKSAIA 47 
                                       56799**********************986 PP

>> DUF2379  Protein of unknown function (DUF2379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.1   9.6e+02      21      48 ..     153     180 ..     149     202 .. 0.72
   2 ?    4.1   0.0     0.057        51      84     105 ..     422     443 ..     417     447 .. 0.90
   3 ?   -0.8   0.0       1.8   1.6e+03      84     104 ..     464     484 ..     447     492 .. 0.84
   4 ?    2.3   0.1       0.2   1.8e+02      84      99 ..     506     521 ..     493     547 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.1
                           DUF2379  21 pleLtdevralLrrtarevaiseadaee 48 
                                       pl L+++   lL+rt re a  +a  ++
  gi|386002029|ref|YP_005920328.1| 153 PLDLQEAAGFLLQRTEREDASGAAALAR 180
                                       7888888888999998887765554444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.057
                           DUF2379  84 lrdagDldgArqelrevLavEv 105
                                       lr  gDl gAr+ +++ +a+E 
  gi|386002029|ref|YP_005920328.1| 422 LRALGDLLGARRSFERAIAIEE 443
                                       6889****************95 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                           DUF2379  84 lrdagDldgArqelrevLavE 104
                                       lr  gDl +A + +++ La++
  gi|386002029|ref|YP_005920328.1| 464 LRALGDLPAAVAAFERALAID 484
                                       7889************99986 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.2
                           DUF2379  84 lrdagDldgArqelre 99 
                                       l++ gDl+gAr   ++
  gi|386002029|ref|YP_005920328.1| 506 LQEMGDLEGARDSYQR 521
                                       799********87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3224.60
//
Query:       gi|386002030|ref|YP_005920329.1|  [L=161]
Description: Nuclease (SNase domain protein) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-09   38.6   0.0    1.5e-09   38.3   0.0    1.1  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   8.5e-14   1.5e-09       1      83 [.      65     148 ..      65     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 8.5e-14
                                       EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S.SBSTTSEEEEEEEET......TEEHHHHHH CS
                             SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk.kkDkygrllayvyln......kknineeLv 70 
                                       +vrL+++daPe         p gk +k f+++ +++++v ++++d   +D+ygr +   y++       +n+n+ Lv
  gi|386002030|ref|YP_005920329.1|  65 RVRLADVDAPEMD------TPAGKASKFFAETILTGETVHLDVDDLrGRDRYGRWICLAYVEdpetgeLINFNAMLV 135
                                       79***********......88899999999999999999999999899******9999999999**999******** PP

                                       HTTSSEE---BTT CS
                             SNase  71 keGlArvyevyek 83 
                                         G A+v  + ++
  gi|386002030|ref|YP_005920329.1| 136 TSGHAVVKDFKDN 148
                                       ******8887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1081.38
//
Query:       gi|386002031|ref|YP_005920330.1|  [L=101]
Description: rubrerythrin [Methanosaeta harundinacea 6Ac]
Scores for complete 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-08   33.8   3.1    5.7e-08   33.2   3.1    1.2  1  Rubrerythrin  Rubrerythrin
    0.00033   21.0   0.7    0.00043   20.6   0.4    1.3  1  DUF2383       Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.013   14.5   0.3      0.015   14.3   0.3    1.1  1  Mn_catalase   Manganese containing catalase
       0.12   12.4   4.7       0.26   11.2   4.7    1.6  1  Ferritin      Ferritin-like domain
       0.97    9.7   5.6         13    6.0   2.4    2.0  2  UPF0149       Uncharacterised protein family (UPF0149)


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   3.1   1.6e-11   5.7e-08       5      73 ..      28      93 ..      25     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.6e-11
                                      HHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS---- CS
                      Rubrerythrin  5 kAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyae 73
                                      + ia+E++a +lY+ lae ++   +  ++++ ++A+eEr Ha+ + +ll++l p++e e  e+ re++e
  gi|386002031|ref|YP_005920330.1| 28 YMIAAEYEAVQLYMQLAESTD--DELAKAVLVDIADEERVHAGEFLRLLQELAPDEE-EKYEEGREEVE 93
                                      5699*****************..555588999*************************.55555555554 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   1.2e-07   0.00043       2      63 ..      22      83 ..      21      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----- CS
                           DUF2383  2 vieaLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggeped 63
                                       i+a+  +i++++ +++ y++ ae  +d+  k++l +ia+e + +a e+   +++l  + e+
  gi|386002031|ref|YP_005920330.1| 22 LIRAIRYMIAAEYEAVQLYMQLAESTDDELAKAVLVDIADEERVHAGEFLRLLQELAPDEEE 83
                                      57889999*****************************************9999998866665 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.2e-06     0.015     138     198 ..      21      81 ..      17      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-06
                       Mn_catalase 138 nliaDlranlaaEakarlqverlyeltddpgvrdmlsfLlaRelvHqlafekAleeleeee 198
                                       +li  +r  +aaE +a   +++l e tdd  ++  l  +   e+vH  +f + l+el + e
  gi|386002031|ref|YP_005920330.1|  21 ELIRAIRYMIAAEYEAVQLYMQLAESTDDELAKAVLVDIADEERVHAGEFLRLLQELAPDE 81 
                                       677788999***********************************************99887 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.7   7.4e-05      0.26       3      59 ..      25      78 ..      23     101 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          Ferritin  3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalG 59
                                      a++  +a+e++a ++y+++a   +++  +++   + + a+eer ha +++  +++l 
  gi|386002031|ref|YP_005920330.1| 25 AIRYMIAAEYEAVQLYMQLAESTDDELAKAV---LVDIADEERVHAGEFLRLLQELA 78
                                      77889****************9999999888...***************99999885 PP

>> UPF0149  Uncharacterised protein family (UPF0149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.005        18      30      79 ..      11      54 ..       8      67 .. 0.81
   2 ?    6.0   2.4    0.0036        13     125     161 ..      67      99 ..      58     101 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.005
                                      HHCT.HHHCCCHHHHCCCC.......STCHHHHHHHHHHHHHHHHHHCTT CS
                           UPF0149 30 lcgpellppeeWlpallgeapafsdeeegeallallkrlyneiaaqLade 79
                                      l+++++l pee + a+   +      + + ++++l ++l +++ ++La +
  gi|386002031|ref|YP_005920330.1| 11 LACDRKLTPEELIRAIRYMI------AAEYEAVQLYMQLAESTDDELAKA 54
                                      45677899999999999988......888999***************984 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHCT---TTTS-SSHHHHHHHHHHHHHH CS
                           UPF0149 125 laelLedlaalarleiaeeeeedeedeealeelieav 161
                                       ++e L+ l++la +e    ee+ ee  e+ ee+ie++
  gi|386002031|ref|YP_005920330.1|  67 AGEFLRLLQELAPDE----EEKYEEGREEVEEIIEEL 99 
                                       678888888888877....788888888999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 632.70
//
Query:       gi|386002032|ref|YP_005920331.1|  [L=230]
Description: hypothetical protein Mhar_1344 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-54  184.5   5.9    1.4e-54  184.5   5.9    1.4  2  Vut_1     Putative vitamin uptake transporter
     0.0035   17.3   0.1     0.0091   15.9   0.1    1.7  1  MRAP      Melanocortin-2 receptor accessory protein family


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.77   6.9e+03      51      51 ..      24      24 ..       6      50 .. 0.49
   2 !  184.5   5.9   1.6e-58   1.4e-54       1     149 [.      58     219 ..      58     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.77
                             Vut_1 51 p 51
                                       
  gi|386002032|ref|YP_005920331.1| 24 A 24
                                      1 PP

  == domain 2  score: 184.5 bits;  conditional E-value: 1.6e-58
                             Vut_1   1 taGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa.........ealesvfgltprivla 68 
                                       +a+vl++++tfl+tdi+se++Gk++ar +v++g++an+++l+ +l+al + a         +++++v+g++pr+v+a
  gi|386002032|ref|YP_005920331.1|  58 PAAVLVYASTFLLTDILSELFGKEKARLAVWAGLAANVVMLVSVLIALRWSAsplmdpglaSSFDAVYGFAPRVVAA 134
                                       689********************************************9999888999999999************** PP

                             Vut_1  69 sliaylvsqlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg....eqlleiilsqylikllial 141
                                       s++aylvsq +dv+++h++k++t+gk+lwlrn++St+ sq++dtlif+t+af+g    ++l++++++qy+ikllia+
  gi|386002032|ref|YP_005920331.1| 135 SMVAYLVSQHHDVWAYHFWKEKTGGKRLWLRNNASTAASQAIDTLIFITLAFYGilpnSVLIQMMVGQYAIKLLIAA 211
                                       ****************************************************99*********************** PP

                             Vut_1 142 ldtplvyl 149
                                       ldtp++yl
  gi|386002032|ref|YP_005920331.1| 212 LDTPFIYL 219
                                       *******8 PP

>> MRAP  Melanocortin-2 receptor accessory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     1e-06    0.0091      40      69 ..      85     114 ..      79     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                              MRAP  40 iafWvsLavfvvllflvLlylsksGspqqr 69 
                                       +a+W +La+ vv+l  vL+ l +s sp ++
  gi|386002032|ref|YP_005920331.1|  85 LAVWAGLAANVVMLVSVLIALRWSASPLMD 114
                                       689***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1530.57
//
Query:       gi|386002033|ref|YP_005920332.1|  [L=368]
Description: replication factor C small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-19   69.1   0.1    8.7e-19   67.7   0.1    1.8  1  Rep_fac_C        Replication factor C C-terminal domain
    3.7e-16   59.7   0.0    3.4e-15   56.6   0.0    2.1  2  AAA              ATPase family associated with various cellul
    5.7e-13   49.0   0.0    3.4e-08   33.4   0.0    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.5e-08   34.6   0.0    1.2e-07   31.6   0.0    2.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.6e-07   30.7   0.8    0.00012   22.5   0.0    3.0  3  AAA_16           AAA ATPase domain
    5.9e-05   23.3   0.1    0.00012   22.3   0.1    1.6  1  AAA_assoc_2      AAA C-terminal domain
     0.0001   21.8   0.0      0.065   12.6   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0004   20.3   0.0    0.00087   19.3   0.0    1.6  1  Rad17            Rad17 P-loop domain
    0.00047   20.2   0.0     0.0012   18.9   0.0    1.7  1  AAA_14           AAA domain
    0.00076   19.5   0.0       0.01   15.8   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
     0.0015   18.3   0.1      0.039   13.7   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
     0.0025   17.1   0.0      0.023   13.9   0.0    2.2  2  TIP49            TIP49 P-loop domain
      0.003   17.4   0.0     0.0062   16.4   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0044   17.3   0.1        3.1    8.1   0.0    2.6  2  AAA_22           AAA domain
     0.0066   16.2   0.0        1.3    8.7   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0089   15.6   0.0       0.02   14.4   0.0    1.6  2  AAA_7            P-loop containing dynein motor region
     0.0099   14.6   0.0      0.079   11.7   0.0    2.0  2  SNF2_N           SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.032   14.9   0.0        4.1    8.1   0.1    2.7  2  TPR_16           Tetratricopeptide repeat
      0.042   14.0   0.0       0.12   12.5   0.0    1.7  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.043   13.5   0.0        0.1   12.3   0.0    1.6  1  AAA_24           AAA domain
      0.046   13.3   0.0        0.1   12.2   0.0    1.7  1  AAA_25           AAA domain
       0.06   13.3   0.6       0.89    9.6   0.1    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
      0.061   13.8   0.8         16    6.1   0.0    2.9  2  TPR_19           Tetratricopeptide repeat
      0.074   13.9   0.4        2.8    9.0   0.1    2.8  2  TPR_14           Tetratricopeptide repeat
       0.11   12.3   0.0       0.18   11.6   0.0    1.6  1  AAA_11           AAA domain
       0.12   12.5   0.5       0.35   11.0   0.1    2.0  1  TPR_9            Tetratricopeptide repeat
       0.17   12.3   0.0       0.37   11.2   0.0    1.5  1  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.1   1.3e-21   8.7e-19       2      87 ..     271     359 ..     270     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.3e-21
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS.....S-HHHHHHHHHHHHHHHHHHHCT CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq...eelpeaqkleilellgeiekrlveG 75 
                                       +p++i+++++++l+g+f++a++ l++ll  +G+s+ed++ q+hr   +     el+  + +++++++gei++r++eG
  gi|386002033|ref|YP_005920332.1| 271 RPEQIRDLMKTALAGNFTQARSLLDDLLLVQGLSGEDVIIQIHRQTLSLldsHELSGPTLVRLMDRIGEIDFRMTEG 347
                                       79********************************************9997554588999****************** PP

                                       H-HHHHHHHHHH CS
                         Rep_fac_C  76 asehlqlsalla 87 
                                       a+e++ql+alla
  gi|386002033|ref|YP_005920332.1| 348 ANERIQLEALLA 359
                                       **********98 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 !   56.6   0.0   5.2e-18   3.4e-15       1     128 [.      85     201 ..      85     205 .. 0.88
   2 ?    0.6   0.0       1.1   7.2e+02      92     119 ..     253     279 ..     232     289 .. 0.66

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.2e-18
                                       EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidala 71 
                                       +l++GppG+GKT++a ++++el       +f+e+++s+ +   +    +k++++ + a   + + +++f+DE+dal+
  gi|386002033|ref|YP_005920332.1|  85 LLFSGPPGVGKTAAAISMVRELfgeewRGNFIELNASDER--GIDVVRHKVKDFARIAPLGNaEFKVIFLDEADALT 159
                                       69*******************865554699**********..88888888888888886666556***********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                       ++            +++L + ++++++    + +++ +n+ +k+ +++  +R+ +  
  gi|386002033|ref|YP_005920332.1| 160 NDA-----------QSALRRTMERYSS---ICRFVLSCNYSSKIIEPIQ-SRCAVYR 201
                                       888...........*************...599****************.9*98765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                       HHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  92 eldgvkkkeskvivigatnrpdkldpal 119
                                        +++  + e+++  i+at rp+++ + +
  gi|386002033|ref|YP_005920332.1| 253 LMEESVT-EETIYQITATARPEQIRDLM 279
                                       3333333.56699999999999998765 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   6.6e-05     0.044       1      49 [.      65     112 ..      65     123 .. 0.92
   2 !   33.4   0.0   5.2e-11   3.4e-08      84     162 ..     125     205 ..     114     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-05
                   DNA_pol3_delta2   1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallceekn 49 
                                       gqee++k l++ ++s ++ h +Lf+G+ g+gk ++a  ++++l+ ee +
  gi|386002033|ref|YP_005920332.1|  65 GQEEIVKRLKSYVRSRNVPH-LLFSGPPGVGKTAAAISMVRELFGEEWR 112
                                       6999***********99999.8*********************998765 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 5.2e-11
                   DNA_pol3_delta2  84 kldqir.elieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                        +d +r ++++++   p   ++ k+i +++a+ +t+ A+ al +t+E  s+   f+L  + ++k++++i+SRc +++
  gi|386002033|ref|YP_005920332.1| 125 GIDVVRhKVKDFARIAPLGnAEFKVIFLDEADALTNDAQSALRRTMERYSSICRFVLSCNYSSKIIEPIQSRCAVYR 201
                                       68889944555555566655789****************************************************** PP

                   DNA_pol3_delta2 159 fspl 162
                                       f++l
  gi|386002033|ref|YP_005920332.1| 202 FRSL 205
                                       *987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.9e-10   1.2e-07       2     111 ..      56     173 ..      55     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.9e-10
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel.....gvk.lkitsg.....P 67 
                                       rP sl++ +gqe++ ++lk ++     r++++ h+l++GpPG+Gkt+ a  + +el       + ++  ++      
  gi|386002033|ref|YP_005920332.1|  56 RPMSLDDVVGQEEIVKRLKSYV-----RSRNVPHLLFSGPPGVGKTAAAISMVRELfgeewRGNfIELNASdergiD 127
                                       9*****************9887.....667899*************9998887776322222221222221111112 PP

                            RuvB_N  68 vl.ekagdlaallt.nleekdvlfideihrlsraveevlysamedf 111
                                       v+ +k +d+a +      e +v+f+de   l++ ++  l  +me +
  gi|386002033|ref|YP_005920332.1| 128 VVrHKVKDFARIAPlGNAEFKVIFLDEADALTNDAQSALRRTMERY 173
                                       2314556776664312245578888888888888888888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.9e-07   0.00012       2      57 ..      63     112 ..      62     142 .. 0.74
   2 ?    4.9   0.1     0.047        31     134     161 ..     145     172 ..     119     182 .. 0.71
   3 ?    0.6   0.1      0.98   6.5e+02      80     116 ..     273     308 ..     210     359 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.9e-07
                            AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslv.rellralekdggiflr 57 
                                       +vG ee +++L+s+++   s   + +l+sG++GvGK++ +  ++++ + ++     r
  gi|386002033|ref|YP_005920332.1|  63 VVGQEEIVKRLKSYVR---SRNVPHLLFSGPPGVGKTAAAiSMVRELFGEE----WR 112
                                       69************98...33459**************9955555544444....33 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.047
                            AAA_16 134 erplvlvlDdlqwadeaslqllaaLlrl 161
                                       ++  v++lD+++ +  + +++l+ ++++
  gi|386002033|ref|YP_005920332.1| 145 AEFKVIFLDEADALTNDAQSALRRTMER 172
                                       3347******************999887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.98
                            AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaea 116
                                       e +r+l   a + ++ ++r  l++ l  v+ l+g++ 
  gi|386002033|ref|YP_005920332.1| 273 EQIRDLMKTALAGNFTQARSLLDDLLL-VQGLSGEDV 308
                                       333333333333344444444444333.444444444 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 !   22.3   0.1   1.8e-07   0.00012       4      51 ..     222     263 ..     219     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                       AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledl 51 
                                        +k++++ ++a++ +a GD+Rka+n+L++a  ++e+       t+e++
  gi|386002033|ref|YP_005920332.1| 222 GVKVTPEGMRAIVYVARGDMRKAINALQAASLMEESV------TEETI 263
                                       68999***********************999988753......33333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   9.8e-05     0.065       2      42 ..      60     102 ..      59     124 .. 0.77
   2 !    6.7   0.0    0.0062       4.1     107     147 ..     147     186 ..     139     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.8e-05
                      Mg_chelatase   2 lkdvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrl 42 
                                       l dv+Gqee  + l+  +      +ll+ GppG GKt  a  +
  gi|386002033|ref|YP_005920332.1|  60 LDDVVGQEEIVKRLKsyVRSRNVPHLLFSGPPGVGKTAAAISM 102
                                       7899999998888873355566779************988655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0062
                      Mg_chelatase 107 nGvLfLDElpefkrkvlevLRePledgevtisrakakvefp 147
                                         v+fLDE+  +++++  +LR+ +e+ + +i r   ++++ 
  gi|386002033|ref|YP_005920332.1| 147 FKVIFLDEADALTNDAQSALRRTMERYS-SICRFVLSCNYS 186
                                       569*********************9865.566666666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-06   0.00087       6      69 ..      48     106 ..      45     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                             Rad17   6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69 
                                        e W+eky+P  ++++    + ++ +k ++++  +++     LL sGP+G gk+ +   + +el
  gi|386002033|ref|YP_005920332.1|  48 EEIWIEKYRPMSLDDVVGQEEIVKRLKSYVRSRNVPH-----LLFSGPPGVGKTAAAISMVREL 106
                                       689*************988877788877777766664.....7**********98755444443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.8e-06    0.0012       5      98 ..      85     182 ..      81     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek..lkeekktylflDEiqev. 76 
                                       l+ +G+  vGKT  +  +++el+    + +++++n  der  +     k+   + +   l + + +++flDE+  + 
  gi|386002033|ref|YP_005920332.1|  85 LLFSGPPGVGKTAAAISMVRELFgeEWRGNFIELNASDERGIDVVRH-KVK-DFARIapLGNAEFKVIFLDEADALt 159
                                       5678999*************999887789999999999999765544.233.333332444568899******9873 PP

                            AAA_14  77 pewekalkslvdeg.knldvivt 98 
                                       +++++al++ ++++ + ++++++
  gi|386002033|ref|YP_005920332.1| 160 NDAQSALRRTMERYsSICRFVLS 182
                                       67**********99444666665 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 !   15.8   0.0   1.5e-05      0.01       7      58 ..      65     116 ..      63     141 .. 0.92
   2 ?    0.6   0.0      0.73   4.9e+02     129     155 ..     143     171 ..     134     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                            ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58 
                                        Qee++++l++ + s++  ++l+  + G+GKT  a++++++l+ ++++ +f+
  gi|386002033|ref|YP_005920332.1|  65 GQEEIVKRLKSYVRSRNVPHLLFSGPPGVGKTAAAISMVRELFGEEWRGNFI 116
                                       599**********989999*************************99988887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.73
                                       HTTT-SEEEEETGGGTTS...TTTHHHHH CS
                            ResIII 129 lrdrfdviiiDEaHrlgak..kswreile 155
                                       ++ +f+vi+ DEa  l+ +  ++ r+ +e
  gi|386002033|ref|YP_005920332.1| 143 GNAEFKVIFLDEADALTNDaqSALRRTME 171
                                       67789999999997777753324444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.8e-05     0.039      46     124 ..      81     162 ..      62     175 .. 0.68
   2 ?    2.0   0.1      0.22   1.5e+02       3      41 ..     243     281 ..     241     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLve.elkrarrdgklaralkrllkv..dllilDdlgl 119
                                       +   +++ Gp+GvGK+  ai++ +e   ++++  f+ +++  e  + + r++ k   +++ l ++  +++ lD+   
  gi|386002033|ref|YP_005920332.1|  81 NVPHLLFSGPPGVGKTAAAISMVRELFGEEWRGNFIELNASDErGIDVVRHKVKDFARIAPLGNAefKVIFLDEADA 157
                                       33468999***********************9999988765431355555555544444444433226777777666 PP

                         IstB_IS21 120 lpldq 124
                                       l+ d 
  gi|386002033|ref|YP_005920332.1| 158 LTNDA 162
                                       66555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                         IstB_IS21   3 rletrlrlaklpaqktledidfraarsldkrkvkeLatl 41 
                                       +  + l++a l  + + e+  ++ +  + ++++++L+++
  gi|386002033|ref|YP_005920332.1| 243 KAINALQAASLMEESVTEETIYQITATARPEQIRDLMKT 281
                                       56678999*************************999765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.4e-05     0.023      42      87 ..      76     122 ..      54     140 .. 0.77
   2 ?    0.5   0.0       0.4   2.7e+02     280     305 ..     148     173 ..     126     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX..XXXXXXXXX CS
                             TIP49  42 likekklaGravLlaGpsgtGktalaiaiskelg.edv..pfvalsgse 87 
                                        ++++++    +L++Gp+g Gkta ai++ +el  e+    f+ l++s+
  gi|386002033|ref|YP_005920332.1|  76 YVRSRNVP--HLLFSGPPGVGKTAAAISMVRELFgEEWrgNFIELNASD 122
                                       56666665..79********************95355422688888876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 280 GvlfiDevhmlDiecfsylnralese 305
                                        v+f+De+  l  ++ s l r++e  
  gi|386002033|ref|YP_005920332.1| 148 KVIFLDEADALTNDAQSALRRTMERY 173
                                       59*********************964 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.3e-06    0.0062       1      88 [.      84     172 ..      84     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.3e-06
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk..Gpvfanllladeinrap 75 
                                       h+l+ g PG++kt ++ ++ + l  e  r  f  +l  sd  G++v+++k k+f   +  G    ++++ de +  +
  gi|386002033|ref|YP_005920332.1|  84 HLLFSGPPGVGKTAAAISMVRELFGEEWRGNFI-ELNASDERGIDVVRHKVKDFARIAplGNAEFKVIFLDEADALT 159
                                       99*********************99999*9997.799****************9754323888999*********** PP

                             AAA_3  76 pktqsalleamee 88 
                                         +qsal  +me 
  gi|386002033|ref|YP_005920332.1| 160 NDAQSALRRTMER 172
                                       ********99985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0046       3.1       7      29 ..      84     106 ..      78     136 .. 0.80
   2 ?    6.5   0.0     0.014       9.5      81     118 ..     138     172 ..     124     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0046
                            AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                       +l+  G++G+GKT  +  ++++l
  gi|386002033|ref|YP_005920332.1|  84 HLLFSGPPGVGKTAAAISMVREL 106
                                       78899********9987776665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                            AAA_22  81 aleqalraravielliiDEaqhlrseealeeLrsllnl 118
                                       +++   +a ++  ++ +DEa+ l +++a + Lr+ ++ 
  gi|386002033|ref|YP_005920332.1| 138 RIAPLGNAEFK--VIFLDEADAL-TNDAQSALRRTMER 172
                                       45555555566..**********.88888888777663 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0019       1.3      10      59 ..      68     121 ..      63     126 .. 0.79
   2 ?    4.9   0.0      0.03        20      91     119 ..     144     172 ..     137     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETT CS
                   Sigma54_activat  10 elleqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavnca 59 
                                       e+++++k++++++   ++l  G  G+GK+  a ++ +    ++ +++f+++n +
  gi|386002033|ref|YP_005920332.1|  68 EIVKRLKSYVRSRnvPHLLFSGPPGVGKTAAAISMVRelFGEEWRGNFIELNAS 121
                                       55666777776665568999************9999856678889999999986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.03
                                       HTTTSEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  91 kadgGtlfLDeigelplelQekLlrvlqe 119
                                       +a+  ++fLDe   l+ ++Q+ L r +++
  gi|386002033|ref|YP_005920332.1| 144 NAEFKVIFLDEADALTNDAQSALRRTMER 172
                                       677789*****************999986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-05      0.02      34      72 ..      83     121 ..      70     156 .. 0.91
   2 ?   -3.5   0.0       9.2   6.1e+03     123     150 ..     251     279 ..     240     291 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72 
                                        ++l+ Gp G+GKt+ + +++++l  e++  ++i+++a+
  gi|386002033|ref|YP_005920332.1|  83 PHLLFSGPPGVGKTAAAISMVRELFGEEWRGNFIELNAS 121
                                       589*******************************99986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.2
                             AAA_7 123 iellRqlldyggwYdrkkl.efkeikdvq 150
                                         l+   + ++ +Y+ + +   ++i+d++
  gi|386002033|ref|YP_005920332.1| 251 ASLMEESVTEETIYQITATaRPEQIRDLM 279
                                       44555555555555553322445555544 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 ?    0.4   0.0      0.32   2.1e+02      59      77 ..      86     104 ..      73     118 .. 0.82
   2 !   11.7   0.0   0.00012     0.079     159     212 ..     128     182 ..     124     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.32
                                       EE---TTS--HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  59 iLaDemGLGKTvqvlalil 77 
                                       +++  +G+GKT  +++++ 
  gi|386002033|ref|YP_005920332.1|  86 LFSGPPGVGKTAAAISMVR 104
                                       666779**********997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                                       HHHHHT......TTS-S-S-SEEEES-GGGT--T.TSHHHHHHHH---S-EEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 159 vlsreaelqkkrsvlkqvewkrvvlDEghtlkns.tskaaeavskLstsnrwilt 212
                                       v++ +++ ++++ +l + e k + lDE+  l n  +s ++ +++++s+  r +l+
  gi|386002033|ref|YP_005920332.1| 128 VVRHKVKDFARIAPLGNAEFKVIFLDEADALTNDaQSALRRTMERYSSICRFVLS 182
                                       6676777779999*********************99***************9998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0061       4.1       2      23 ..     230     251 ..     230     256 .. 0.91
   2 ?    3.6   0.0      0.17   1.1e+02      10      34 ..     284     308 ..     284     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0061
                            TPR_16   2 alaraalragdyddAaaaleaa 23 
                                       ++a  ++++gd ++A++al+aa
  gi|386002033|ref|YP_005920332.1| 230 MRAIVYVARGDMRKAINALQAA 251
                                       57999***************98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaa 34 
                                       ag++++A+ +l+ +l  ++ s +++
  gi|386002033|ref|YP_005920332.1| 284 AGNFTQARSLLDDLLLVQGLSGEDV 308
                                       79*************9988776665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018      0.12       5      82 ..      84     160 ..      80     171 .. 0.82
   2 ?   -2.4   0.1       6.9   4.6e+03      30      48 ..     240     258 ..     208     274 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                       -EEEE--TTSSHHHHHHHHHHHTT-.....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   5 silllgptgvGktelakalaellfv.kkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                        +l+ gp gvGkt +a ++ + lf  + + ++i ++as+    + v+h v+ +   +p   g +e  +++lDE d  
  gi|386002033|ref|YP_005920332.1|  84 HLLFSGPPGVGKTAAAISMVRELFGeEWRGNFIELNASDERGIDVVRHKVKDFARIAPL--GNAEFKVIFLDEADAL 158
                                       679*************99999999534457899999999988999*****998777664..667888******9977 PP

                                       -- CS
                             AAA_2  81 hp 82 
                                       ++
  gi|386002033|ref|YP_005920332.1| 159 TN 160
                                       76 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                                       ....-EEEEEGGG------ CS
                             AAA_2  30 kkekkliradaselleeee 48 
                                       + +k++  + a +l+ee  
  gi|386002033|ref|YP_005920332.1| 240 DMRKAINALQAASLMEESV 258
                                       3344444455555555222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1       6      91 ..      86     172 ..      83     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                            AAA_24   6 liyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDt 73 
                                       l  Gp+g+GKT  a ++           +++ ++  +  + +d+ +        +++d++   +  +a++k++++D 
  gi|386002033|ref|YP_005920332.1|  86 LFSGPPGVGKTAAAISMvrelfgeewRGNFIELNASD-ERGIDVVRH-------KVKDFARIAPLGNAEFKVIFLDE 154
                                       557**************66666663333333333322.223444442.......3556666669999********** PP

                            AAA_24  74 ideleelclaevirqnek 91 
                                       +d l + +   ++r  e+
  gi|386002033|ref|YP_005920332.1| 155 ADALTNDAQSALRRTMER 172
                                       *****9999888776665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015       0.1      37      65 ..      86     113 ..      59     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_25  37 llaGapgtGKttlaldlalavatGkpwlg 65 
                                       l+ G+pg+GKt++a++++ ++  G++w g
  gi|386002033|ref|YP_005920332.1|  86 LFSGPPGVGKTAAAISMVRELF-GEEWRG 113
                                       678****************999.888988 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0013      0.89       1      87 [.      84     168 ..      84     175 .. 0.59
   2 ?   -2.5   0.0       7.3   4.8e+03      27      45 ..     261     279 ..     242     296 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                       EEEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........--------....G-SEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilv 70 
                                       ++l  GppG+gK+  a ++ + l   +++ + + l+++  e+ +   r+  + +   +             e ++++
  gi|386002033|ref|YP_005920332.1|  84 HLLFSGPPGVGKTAAAISMVRELfgeEWRGNFIELNAS-DERGIDVVRH--KVKDFARIA------PlgnaEFKVIF 151
                                       68999*********999888877766666666666552.2222222222..222222223......13344667777 PP

                                       EESGGG--HHHHHHHHH CS
                             AAA_5  71 lDEveraesevlnsLls 87 
                                       lDE + +  +++++L +
  gi|386002033|ref|YP_005920332.1| 152 LDEADALTNDAQSALRR 168
                                       77777777777777765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.3
                                       EEEEE--TT--HHHHH--B CS
                             AAA_5  27 veyvqltrdtteedlkgrr 45 
                                        +++q+t+  ++e+++  +
  gi|386002033|ref|YP_005920332.1| 261 ETIYQITATARPEQIRDLM 279
                                       3345555555555555444 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.025        16      32      54 ..     232     254 ..     226     260 .. 0.87
   2 ?    5.1   0.0     0.051        34      38      54 ..     284     300 ..     281     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                            TPR_19  32 AeallalgqldeAealLdalpee 54 
                                       A++++a g+  +A+++L+a+ ++
  gi|386002033|ref|YP_005920332.1| 232 AIVYVARGDMRKAINALQAASLM 254
                                       999***************99876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.051
                            TPR_19  38 lgqldeAealLdalpee 54 
                                       +g++++A+ lLd+l++ 
  gi|386002033|ref|YP_005920332.1| 284 AGNFTQARSLLDDLLLV 300
                                       69**********99875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0042       2.8       6      27 ..     230     251 ..     229     258 .. 0.93
   2 ?    1.6   0.0         1   6.7e+02      14      28 ..     284     298 ..     274     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0042
                            TPR_14   6 alaeallalGdpdeAiallrra 27 
                                       ++a ++ a+Gd ++Ai++l++a
  gi|386002033|ref|YP_005920332.1| 230 MRAIVYVARGDMRKAINALQAA 251
                                       689*****************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1
                            TPR_14  14 lGdpdeAiallrral 28 
                                       +G++ +A+ ll+++l
  gi|386002033|ref|YP_005920332.1| 284 AGNFTQARSLLDDLL 298
                                       79**********986 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   0.00027      0.18      18      42 ..      81     107 ..      66     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                            AAA_11  18 e..itliqGPPGtgKTktivellsqll 42 
                                       +    l++GPPG gKT + ++++++l 
  gi|386002033|ref|YP_005920332.1|  81 NvpHLLFSGPPGVGKTAAAISMVRELF 107
                                       3444799************99999995 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00053      0.35      35      68 ..     231     266 ..     229     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                             TPR_9  35 RGlllaqlGclsaAladLeaylalap..dapdaeai 68 
                                       R+++++ +G++++A+++L+a+  +++    +++++i
  gi|386002033|ref|YP_005920332.1| 231 RAIVYVARGDMRKAINALQAASLMEEsvTEETIYQI 266
                                       9*******************9977665555555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00056      0.37       2      40 ..      86     121 ..      85     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpe 40 
                                       +++Gp+g+GK+ +a +++++l    +++++++++  n++
  gi|386002033|ref|YP_005920332.1|  86 LFSGPPGVGKTAAAISMVRELF---GEEWRGNFIELNAS 121
                                       799**************99998...66677777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 2208.47
//
Query:       gi|386002034|ref|YP_005920333.1|  [L=268]
Description: hypothetical protein Mhar_1346 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.7  12.2    1.3e-05   25.3   0.9    4.3  3  DUF333    Domain of unknown function (DUF333)
  ------ inclusion threshold ------
        4.1    6.9   6.6        3.3    7.2   0.0    2.3  2  DUF4244   Protein of unknown function (DUF4244)


Domain annotation for each model (and alignments):
>> DUF333  Domain of unknown function (DUF333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.9   1.4e-09   1.3e-05       1      47 [.      27      64 ..      27      65 .. 0.90
   2 !   22.0   1.8   1.6e-08   0.00014       9      47 ..      72     113 ..      70     114 .. 0.93
   3 ?    0.6   0.0     0.076   6.8e+02       1      10 [.     182     191 ..     182     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-09
                            DUF333  1 gmaNPAsvyCvkqGGkleiakdadGgqvgyCqlpdGkrceEwaLyrg 47
                                      g+a+PA vyC+  G++ +     +    g C++pdG+++ +w++yrg
  gi|386002034|ref|YP_005920333.1| 27 GIADPACVYCEALGYNCS-----N----GNCTFPDGSSVPAWEFYRG 64
                                      689************863.....4....78****************8 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.6e-08
                            DUF333   9 yCvkqGGkleiakdadGg...qvgyCqlpdGkrceEwaLyrg 47 
                                       +C+ qG++ e ++++ Gg   ++++C++ d ++c E + + g
  gi|386002034|ref|YP_005920333.1|  72 FCELQGYRIESRTEDMGGwtsEYAVCVFDDCSECGEEEHFAG 113
                                       9****************9999***************998765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.076
                            DUF333   1 gmaNPAsvyC 10 
                                       gm++PA+v C
  gi|386002034|ref|YP_005920333.1| 182 GMTEPAEVDC 191
                                       79******99 PP

>> DUF4244  Protein of unknown function (DUF4244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   3.7     0.064   5.8e+02      20      30 ..      13      23 ..       6      24 .. 0.90
   2 ?    7.2   0.0   0.00036       3.3       5      22 ..      82      98 ..      78      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.064
                           DUF4244 20 vgtlAAvafAa 30
                                      v++lAA+a+Aa
  gi|386002034|ref|YP_005920333.1| 13 VALLAAAALAA 23
                                      789*******7 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00036
                           DUF4244  5 arlredaGmsTaEYAvgt 22
                                      + ++ed G  T+EYAv +
  gi|386002034|ref|YP_005920333.1| 82 S-RTEDMGGWTSEYAVCV 98
                                      3.456**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1674.08
//
Query:       gi|386002035|ref|YP_005920334.1|  [L=485]
Description: Succinate-semialdehyde dehydrogenase [NADP+] (Ssdh) [Methanosaeta harundinacea 6Ac]
Scores for complete 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-166  554.6   0.0   1.6e-166  554.4   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.042   13.3   0.0      0.088   12.2   0.0    1.4  1  DUF1487   Protein of unknown function (DUF1487)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.4   0.0  1.8e-170  1.6e-166       9     462 .]      24     477 ..      16     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 554.4 bits;  conditional E-value: 1.8e-170
                                       EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHH CS
                            Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplae 85 
                                          +nPatge +a+v+ +++++++ a++aA++af+awa+ +++ R+ +Lr+ a++++e+ ee+a l+t+e+Gkpla 
  gi|386002035|ref|YP_005920334.1|  24 ALITNPATGEAVAEVALGGRSEARLALEAAARAFPAWAEREPRVRGGLLRRGAEAVREEIEEIALLLTMEQGKPLAY 100
                                       5679************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE- CS
                            Aldedh  86 araeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPa 162
                                       ar+ev+ +++ l+yyae+ e+++gev+pss ++++lv r+PlGv ++I+PWN+P+ l+awk+apalaaG+tvv KP+
  gi|386002035|ref|YP_005920334.1| 101 ARREVAGSAEALEYYAEEGERITGEVVPSSGRSRSLVIRQPLGVAAVISPWNYPVDLLAWKVAPALAAGCTVVAKPS 177
                                       *****************************99********************************************** PP

                                       TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE--- CS
                            Aldedh 163 eetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGk 239
                                       +++pl a++++ +++ aglP+gv+n+v+gsg+evg alve+p  +kvsftG+t++g++i+++aak++kr++lElGG+
  gi|386002035|ref|YP_005920334.1| 178 SQAPLAATRFVMAVAGAGLPAGVINLVHGSGQEVGGALVESPIPRKVSFTGETDTGKEIMAKAAKTVKRLSLELGGH 254
                                       ***************************************************************************** PP

                                       EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHH CS
                            Aldedh 240 nplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaq 316
                                       +p+iv++daDld a++a+v+ af+n+GQ+Ci+++r++vqe +++ef  k+ve++++l++gd+ld+++d+GP+ seaq
  gi|386002035|ref|YP_005920334.1| 255 APAIVCDDADLDGAAAACVQRAFSNMGQICISVNRIYVQEAVAEEFAGKVVERTERLRIGDGLDPNVDLGPIFSEAQ 331
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHS CS
                            Aldedh 317 lekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNd 392
                                       ++k e+++++a e+ga++l Gg+  e ++ ++g+f+ Ptvl+ ++p+mr+++eE+FGPV+++++f+++eea+++aN+
  gi|386002035|ref|YP_005920334.1| 332 RKKTEDHIADALERGARVLWGGRrPEGEKFRRGFFFLPTVLDRMDPSMRMMREETFGPVAPMMSFSTDEEALRLANA 408
                                       ***********************9999************************************************** PP

                                       SSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 393 teyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       ++yGLaa+vft d++r + +aerleaG+v++N+++   + a pfgG+k+SglGre+++ +l ey+e k++
  gi|386002035|ref|YP_005920334.1| 409 SRYGLAAYVFTGDMKRGLFFAERLEAGSVGVNTTSPIVPGA-PFGGWKESGLGRERSRCALYEYMEEKHI 477
                                       **********************************9999999.************************9986 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.8e-06     0.088       9      60 ..     258     311 ..     255     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.8e-06
                           DUF1487   9 vifedgDlnsalealveslkePfa..egavatvlveesirdefvervrsklkpl 60 
                                       ++++d+Dl+ a+ a v+     ++  + +v  + v+e++++ef  +v ++ ++l
  gi|386002035|ref|YP_005920334.1| 258 IVCDDADLDGAAAACVQRAFSNMGqiCISVNRIYVQEAVAEEFAGKVVERTERL 311
                                       89**********99999888887722467889***************9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3148.10
//
Query:       gi|386002036|ref|YP_005920335.1|  [L=309]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta harundinacea 6Ac]
Scores for 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-46  156.6   0.0    8.6e-46  156.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.3e-44  152.2   0.0    4.9e-44  151.1   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.7e-19   69.9   0.0    2.3e-19   69.5   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    8.4e-17   61.2   0.0    9.7e-16   57.7   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.1e-13   50.6   0.0    1.5e-12   47.8   0.0    2.0  2  NAD_binding_10   NAD(P)H-binding
      2e-11   43.5   0.0    3.1e-11   42.9   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      2e-09   37.0   0.0    1.3e-07   31.0   0.0    2.8  1  NAD_binding_4    Male sterility protein
     0.0012   18.5   0.0     0.0018   17.9   0.0    1.3  1  NmrA             NmrA-like family
     0.0012   18.4   0.2      0.022   14.2   0.0    2.5  2  adh_short        short chain dehydrogenase
     0.0016   18.7   0.0      0.003   17.8   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.031   14.4   0.0    1.4  1  ABM              Antibiotic biosynthesis monooxygenase
      0.065   13.5   0.0       0.14   12.4   0.0    1.5  1  TrkA_N           TrkA-N domain
      0.094   12.3   0.0       0.19   11.3   0.0    1.4  1  E3_UFM1_ligase   E3 UFM1-protein ligase 1
       0.12   11.8   0.2         12    5.3   0.0    2.3  2  tify             tify 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 !  156.3   0.0   6.7e-49   8.6e-46       3     241 .]       1     233 [.       1     233 [. 0.96

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 6.7e-49
                                       EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                         Epimerase   3 VtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAav 74 
                                       +tG++GfiGs+lv++l + + +v++ld+ ss++++  +++l     +lve+dl+dr+a+e+++k  ++d v+hlAa 
  gi|386002036|ref|YP_005920335.1|   1 MTGGAGFIGSHLVDRLIDYN-RVTVLDNFSSGKAEHIEDHLknpnfTLVEGDLLDRKAVEAALK--GCDLVFHLAAN 74 
                                       69***************954.6*******999999999999***********************..*********** PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHH CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagek 151
                                        +v++ +ed +  +++n++ t+nlle +r +gv  + f s+s+vYG+   +p+ e    gpl p s Y+a+Kla e 
  gi|386002036|ref|YP_005920335.1|  75 PDVKVGAEDSKTHLHQNVIATYNLLESMRLRGVAEIAFTSTSTVYGEAGIVPTPEGY--GPLLPISLYGASKLACEA 149
                                       **********************************************99998855555..8***************** PP

                                       HHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 152 lveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       l+ a+  +++++  i+r  n++G r      ++vi  +i+k+ +   e+++lg+g+++  +l v+D++ea+++++++
  gi|386002036|ref|YP_005920335.1| 150 LISAFCGTFDMRSWIFRFANIVGDR----GTHGVIVDFINKLTASPAELLILGSGRQRKSYLLVDDCIEAMVYAVAR 222
                                       *************************....999************999*****************************9 PP

                                       HTT-STTEEEEES CS
                         Epimerase 229 vdagdkgeiyniG 241
                                         ag   +++n+G
  gi|386002036|ref|YP_005920335.1| 223 --AGGRVNVFNVG 233
                                       ..66777899998 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 !  151.1   0.0   3.8e-47   4.9e-44       3     330 ..       2     299 ..       1     301 [. 0.82

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 3.8e-47
                                       ETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEE CS
                     GDP_Man_Dehyd   3 TGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdev 79 
                                       TG+aGfiGs+l+++L++   +v+++++ s s ++++ie   k      ++n++l++gDl D++++e +l+ +  d v
  gi|386002036|ref|YP_005920335.1|   2 TGGAGFIGSHLVDRLIDY-NRVTVLDNFS-SGKAEHIEDHLK------NPNFTLVEGDLLDRKAVEAALKGC--DLV 68 
                                       9***************95.6676666554.445555554443......569*******************98..9** PP

                                       EE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHHHH CS
                     GDP_Man_Dehyd  80 ynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPYaa 155
                                       ++LAA   V+v  e++++ +  nv++t++LLe +r  g++    + ++Sts+vYG++  vp  E   p+ P s Y+a
  gi|386002036|ref|YP_005920335.1|  69 FHLAANPDVKVGAEDSKTHLHQNVIATYNLLESMRLRGVA---EIAFTSTSTVYGEAGIVPTPEGyGPLLPISLYGA 142
                                       ***********************************99985...7888**************988659********** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyvea 232
                                       +Kl+++ ++ ++  ++++   + ++ n  + r g +     i++++ + ++   e l+lG ++++++++ v+D +ea
  gi|386002036|ref|YP_005920335.1| 143 SKLACEALISAFCGTFDMRSWIFRFANIVGDR-GTH---GVIVDFINKLTASPAELLILGSGRQRKSYLLVDDCIEA 215
                                       ******************************99.455...56************************************ PP

                                       HHHHHHC..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 233 mwlmlqq..dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       m+ ++ +  ++ + +++++ +++ v e++++ +++++ +    g     v r     + +  ++ +  r g+v+++l
  gi|386002036|ref|YP_005920335.1| 216 MVYAVARagGRVNVFNVGSADSVDVTEIADVVVEKMKLS----G-----V-R----YRYTGGIEGRGWR-GDVRTML 277
                                       **9998722344444444444444455544444444332....2.....2.1....2333456666776.7999999 PP

                                       B-THHHHHHH----SS-HHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvr 330
                                         ++ ++ eLgW+pk+s +e ++
  gi|386002036|ref|YP_005920335.1| 278 LSIEALE-ELGWRPKYSSRESIE 299
                                       9998776.9********999887 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 !   69.5   0.0   1.8e-22   2.3e-19       3     229 ..       2     220 ..       1     223 [. 0.84

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.8e-22
                         3Beta_HSD   3 tGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlasl 76 
                                       tGgaGF+G++lv +L++ ++   v vlD     + +++ ++l++ n + ++egD++d + +e+al+g d+v+hla+ 
  gi|386002036|ref|YP_005920335.1|   2 TGGAGFIGSHLVDRLIDYNR---VTVLDnfsSGKAEHIEDHLKNPNFT-LVEGDLLDRKAVEAALKGCDLVFHLAAN 74 
                                       9******************7...7777733145555555555555555.**************************** PP

                         3Beta_HSD  77 vdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKal 152
                                        dv+     +++  + nv  T n+le+ +  gv  + +tS+  v g+      i+   E  + + l+ + y  sK  
  gi|386002036|ref|YP_005920335.1|  75 PDVKVgAEDSKTHLHQNVIATYNLLESMRLRGVAEIAFTSTSTVYGE----AGIVPTPE-GYGPLLPISLYGASKLA 146
                                       **97537777889999*****************************99....44554555.567899*********** PP

                         3Beta_HSD 153 aEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvawahil 227
                                        E+l+ +  g       ++     R a i G++ +  ++v ++++l+ +  +l+ +g+ ++ +++  v+    a + 
  gi|386002036|ref|YP_005920335.1| 147 CEALISAFCG-----TFDMRSWIFRFANIVGDRGThgVIVDFINKLTASPAELLILGSGRQRKSYLLVDDCIEAMVY 218
                                       *****98888.....55899999999999999865226889999999999999999999999999999999999888 PP

                         3Beta_HSD 228 Aa 229
                                       A+
  gi|386002036|ref|YP_005920335.1| 219 AV 220
                                       86 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   7.5e-19   9.7e-16       4     250 ..       2     254 ..       1     271 [. 0.77

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 7.5e-19
                                       ETTTSHHHHHHHHHHHHHB-SEEEEEES.-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                   Polysacc_synt_2   4 tGagGsiGselvrqilkkkpkkiiller.dElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                       tG++G iGs+lv+++++ +  ++ +l++ +  k  +ie++l    k+ ++    + v gd+ d++ +e al+  ++d
  gi|386002036|ref|YP_005920335.1|   2 TGGAGFIGSHLVDRLIDYN--RVTVLDNfSSGKAEHIEDHL----KNPNF----TLVEGDLLDRKAVEAALK--GCD 66 
                                       9**************9875..66666652455677777777....33333....3457**************..*** PP

                                       EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG.....SS..........--SHHHHH CS
                   Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA.....vn..........PtnvmGat 141
                                       +vfh AA   V +  e     +++Nv++t n++e     gv ++ + St        +           P++++Ga+
  gi|386002036|ref|YP_005920335.1|  67 LVFHLAANPDVKVGAEDSKTHLHQNVIATYNLLESMRLRGVAEIAFTSTSTVygeagIVptpegygpllPISLYGAS 143
                                       ************************************************98652222311233333333389****** PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETTGTTS..SHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlgSrGS..viplFkkqikeg.gpvtv.TdpemtRyfmtieeavqLvl 214
                                       K+++e l+ a+  +    +++  + Rf N++g rG   vi  F +++++   ++ +    +  + ++ +++ ++ ++
  gi|386002036|ref|YP_005920335.1| 144 KLACEALISAFCGTF---DMRSWIFRFANIVGDRGThgVIVDFINKLTASpAELLIlGSGRQRKSYLLVDDCIEAMV 217
                                       **********99887...899999********999555888888888777666665155566667899999999999 PP

                                       HHHHH--SS-EEEE--...-EEEHHHHHHHH....... CS
                   Polysacc_synt_2 215 qalalakggeifvldmG..epvkivdlakalielsgle 250
                                       +a+a+a gg + v ++G  ++v ++++a  ++e ++l+
  gi|386002036|ref|YP_005920335.1| 218 YAVARA-GGRVNVFNVGsaDSVDVTEIADVVVEKMKLS 254
                                       998876.5566666665227899999999998766543 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.2e-15   1.5e-12       1     105 [.       3     122 ..       3     181 .. 0.80
   2 ?    0.6   0.1      0.36   4.6e+02      65      91 ..     229     257 ..     209     274 .. 0.70

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.2e-15
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.....HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.....peklaeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G +G++lv++l++ +  +vt+l  n     +e++++  ++++ ++vegd++d +++++alkg+d V+  +++ +
  gi|386002036|ref|YP_005920335.1|   3 GGAGFIGSHLVDRLIDYN--RVTVL-DNfssgkAEHIEDHLKNPNFTLVEGDLLDRKAVEAALKGCDLVFHLAANPD 76 
                                       99***************7..56555.22232338888887799**************************99996655 PP

                                       C.....HHHH........HHHHHHHHHHCT--EEEEEEETTTTSGC CS
                    NAD_binding_10  73 k.....deeg........aknivdaakeagvkRfvlvsaigvgdev 105
                                             d+++        + n+++ ++  gv  + + s+  v+ e+
  gi|386002036|ref|YP_005920335.1|  77 VkvgaeDSKThlhqnviaTYNLLESMRLRGVAEIAFTSTSTVYGEA 122
                                       5555443333567778899999******************999653 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.36
                                       EES---TCC..HHHHHHHHHHHHHHCT-- CS
                    NAD_binding_10  65 vsalggggk..deegaknivdaakeagvk 91 
                                       v+++g+ ++   +e+a+ +v+ +k +gv+
  gi|386002036|ref|YP_005920335.1| 229 VFNVGSADSvdVTEIADVVVEKMKLSGVR 257
                                       33444444445566699999999999995 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 !   42.9   0.0   2.5e-14   3.1e-11       5     233 ..       1     253 [.       1     265 [. 0.78

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.5e-14
                                       EESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE---- CS
                     RmlD_sub_bind   5 vtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAy 61 
                                       +tG+ G +Gs+L+++l   +  v+ l++                     e dl d++av+++lk   +d+v ++AA 
  gi|386002036|ref|YP_005920335.1|   1 MTGGAGFIGSHLVDRLIDYN-RVTVLDNFssgkaehiedhlknpnftlvEGDLLDRKAVEAALKG--CDLVFHLAAN 74 
                                       59***********9998766.4555533345899*****************************99..9********* PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqav 136
                                        +v    ++++   + n+ a+ +l e  + +g+  + + St  V+  +   p  e   +  P+++YG++Kla E  +
  gi|386002036|ref|YP_005920335.1|  75 PDVKVGAEDSKTHLHQNVIATYNLLESMRLRGVAeIAFTSTSTVYGEAGIVPtPEGYGPLLPISLYGASKLACEALI 151
                                       ***9988889999999****************7538899******9998888344567899**************** PP

                                       HH....H-SSEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GG CS
                     RmlD_sub_bind 137 la....agkkalivRtswvygekgkn..fvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeeke 205
                                        a       + +i+R++ + g++g     v  + +l ++  el +     q  s   ++d  e++++++++a     
  gi|386002036|ref|YP_005920335.1| 152 SAfcgtFDMRSWIFRFANIVGDRGTHgvIVDFINKLTASPAELLILGSgrQRKSYLLVDDCIEAMVYAVARAG---G 225
                                       **555434589*********99776522566777888898998887641133333334444444444444443...3 PP

                                       G-EEEE---BS-EEHHHHHHHHHHHHCH CS
                     RmlD_sub_bind 206 lagvyHlanegetswlefArailkeaga 233
                                          v+ +++++++   e+A++++++++ 
  gi|386002036|ref|YP_005920335.1| 226 RVNVFNVGSADSVDVTEIADVVVEKMKL 253
                                       5778888888888888888888887765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.1e-10   1.3e-07       2     215 ..       2     180 ..       1     216 [. 0.80

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.1e-10
                                       E-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--H CS
                     NAD_binding_4   2 TGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLse 78 
                                       TG+ GF+G++L+ +L++ +   ++++l   +sg   +e +         +++l+     + + veGDl      L+ 
  gi|386002036|ref|YP_005920335.1|   2 TGGAGFIGSHLVDRLIDYN---RVTVLDNFSSG--KAEHI---------EDHLK---NPNFTLVEGDL------LDR 55 
                                       ****************998...58888777777..33444.........33333...556799*****......778 PP

                                       HHHHHHHHH--EEEE--SS-S.S...TTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS- CS
                     NAD_binding_4  79 edlqelaeevdviihsaAtvnfd...epykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvy 152
                                       ++++   + +d+++h aA+ +++   e+ k+ l  Nv +t ++le  + l+    + + ST++v+ge    +     
  gi|386002036|ref|YP_005920335.1|  56 KAVEAALKGCDLVFHLAANPDVKvgaEDSKTHLHQNVIATYNLLESMR-LRGVAEIAFTSTSTVYGEAG--I----- 124
                                       89999*************98876222588899*************888.555559************99..3..... PP

                                       H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSS.T-- CS
                     NAD_binding_4 153 eegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgeskt.Gwi 215
                                               + + e          Y  sK + E l+ +     +++  i+R  +i+g+  t G+i
  gi|386002036|ref|YP_005920335.1| 125 --------VPTPEGYGPLLPISLYGASKLACEALISAFCGTFDMRSWIFRFANIVGDRGThGVI 180
                                       ........667788888888889****************999999***********77664554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.4e-06    0.0018       4      73 ..       2      73 ..       1      86 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                                      SSTTSHHHHHHHHHHHHHT-EEEEEES-S....-SHHHH.HHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  4 iGaTGrqGksvvrallkaghkvralvRdt....kselak.slkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      +G++G +G+++v+ l++ + +v +l  d     k e ++ +lk+   +lv+gdl d++ +++alkg d+vf   +
  gi|386002036|ref|YP_005920335.1|  2 TGGAGFIGSHLVDRLIDYN-RVTVL--DNfssgKAEHIEdHLKNPNFTLVEGDLLDRKAVEAALKGCDLVFHLAA 73
                                      79*************9965.33333..33345666666515666666788*********************8766 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.7e-05     0.022       6      71 ..       2      65 ..       1     161 [. 0.77
   2 ?   -3.3   0.0       3.9     5e+03      71      89 ..     220     236 ..     211     251 .. 0.42

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                      ESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                         adh_short  6 tGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                      tG+++ IG  ++++l+  +  +v+ + s+ k+e++ ++lk+   +++ +++D+ dr++vea+++ +
  gi|386002036|ref|YP_005920335.1|  2 TGGAGFIGSHLVDRLIDYNRVTVLDNFSSGKAEHIEDHLKN--PNFTLVEGDLLDRKAVEAALKGC 65
                                      9*****************8877778889999999****998..68****************99877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
                                       HHHHHSSESEEEE---SS- CS
                         adh_short  71 avkklgkldvLvnNAGitg 89 
                                       ++   g+++v+  N+G + 
  gi|386002036|ref|YP_005920335.1| 220 VARAGGRVNVF--NVGSAD 236
                                       32333333322..333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06     0.003       5      79 ..       4      74 ..       2      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                      --SHHHHHHHHHHHCTCCT-GEEEEEE.SSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSG CS
                   Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvad.rskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlspp 79
                                      GaG++G+ +++ l + +    ++tv d +s  k+e++ +++++++f+ ++ d  +++a ++a+lk+ dlv +l+ +
  gi|386002036|ref|YP_005920335.1|  4 GAGFIGSHLVDRLIDYN----RVTVLDnFSSGKAEHIEDHLKNPNFTLVEGDLLDRKA-VEAALKGCDLVFHLAAN 74
                                      89*****9988888776....67888835777899999999*****************.************99876 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.5e-05     0.031      35      72 ..       6      45 ..       2      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                      TEEEEEEEEEETSTTEEEEEEEESS..HHHHHHHHTSHHH CS
                               ABM 35 GclgyellrstedpdevvvieeWes..eaaleahlksphf 72
                                      G++g +l+    d+++v+v+  + s  ++++e+hlk+p+f
  gi|386002036|ref|YP_005920335.1|  6 GFIGSHLVDRLIDYNRVTVLDNFSSgkAEHIEDHLKNPNF 45
                                      9*******99***************99999********99 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.14       5      76 ..       4      78 ..       3     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                      S-SHHHHHHHHHHHHTTEEEEEEESSH.HHHHHHHHTT....SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkde.erveelreeg....levvvgdatdeevLeeagiekadaviaatgddean 76
                                      G+G +G++l+++L +++ +v+v d+    ++e+++++     ++ v gd  d++++e+a ++ +d+v  ++ + +++
  gi|386002036|ref|YP_005920335.1|  4 GAGFIGSHLVDRLIDYN-RVTVLDNFSsGKAEHIEDHLknpnFTLVEGDLLDRKAVEAA-LKGCDLVFHLAANPDVK 78
                                      899************99.5*****866356777777776655779**********9765.77777777777666655 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.19      26      91 ..     180     247 ..     176     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                    E3_UFM1_ligase  26 vieivnkliek..klldlihtldGkeYlTpeqLekeikdelekagGRvnlvdLakilnvdlshiekka 91 
                                       +++ +nkl+++  +ll l   +  k+Yl  +   + +   + +agGRvn++++ ++ +vd++ i + +
  gi|386002036|ref|YP_005920335.1| 180 IVDFINKLTASpaELLILGSGRQRKSYLLVDDCIEAMVYAVARAGGRVNVFNVGSADSVDVTEIADVV 247
                                       79999999987213344445567799****999999**************************997765 PP

>> tify  tify domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0097        12      14      29 ..      21      36 ..      20      36 .. 0.92
   2 ?    3.9   0.3     0.026        33      12      21 ..     224     232 ..     224     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0097
                              tify 14 kVvVfDdvpaeKAkaI 29
                                      +V V D+++  KA+ I
  gi|386002036|ref|YP_005920335.1| 21 RVTVLDNFSSGKAEHI 36
                                      79***********976 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                              tify  12 gGkVvVfDdv 21 
                                       gG+V+Vf+ v
  gi|386002036|ref|YP_005920335.1| 224 GGRVNVFN-V 232
                                       8******9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1893.81
//
Query:       gi|386002037|ref|YP_005920336.1|  [L=232]
Description: Transcriptional regulator, CopG family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-11   43.1   0.3    5.3e-11   42.0   0.3    1.6  1  RHH_1           Ribbon-helix-helix protein, copG family
    0.00033   20.6   0.1     0.0007   19.5   0.1    1.5  1  RHH_3           Ribbon-helix-helix domain
     0.0073   16.8   0.3      0.021   15.3   0.0    1.8  2  BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin sys
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.038   14.3   0.0    1.4  1  DUF3181         Protein of unknown function (DUF3181)
      0.053   13.5   0.4       0.18   11.9   0.1    2.0  2  HTH_19          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.3   1.5e-14   5.3e-11       1      36 [.      58      93 ..      58      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.5e-14
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlrey 36
                                      rv+i ld+e++++++e+++++g S+Sel+ReAl++y
  gi|386002037|ref|YP_005920336.1| 58 RVTIALDDETAKLFREMREDLGISQSELMREALKFY 93
                                      8********************************998 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.9e-07    0.0007       3      39 ..      57      93 ..      56      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-07
                             RHH_3  3 trttvsidpelaekLkaLSekTrIprSklldeAiell 39
                                      +r+t+++d+e a+  ++  e ++I +S+l +eA++ +
  gi|386002037|ref|YP_005920336.1| 57 ERVTIALDDETAKLFREMREDLGISQSELMREALKFY 93
                                      79*******************************9865 PP

>> BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.8e-06     0.021      20      54 ..      30      74 ..      16      85 .. 0.77
   2 ?   -1.8   0.0       1.3   4.5e+03       5      14 ..     154     163 ..     139     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.8e-06
                    BrnA_antitoxin 20 vlpe..........argrpkrplestKkkvtlRLDadVleaFkat 54
                                      ++p+          +rg ++ +++++ ++vt+ LD ++++ F+++
  gi|386002037|ref|YP_005920336.1| 30 IAPSeepdrkkgkyMRGERRLDMAKAPERVTIALDDETAKLFREM 74
                                      3333444555777788899999899999***************87 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                    BrnA_antitoxin   5 ltdesdlara 14 
                                       +++e++ ++ 
  gi|386002037|ref|YP_005920336.1| 154 AHAEEFKKKN 163
                                       3333222222 PP

>> DUF3181  Protein of unknown function (DUF3181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.038       7      56 ..     116     174 ..     114     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                           DUF3181   7 eigeeiyidvakWhLyLkda..........klhtalAeelyplleeekeleeaavekvLk 56 
                                       ++ge+i +d+ +W L+L+ +          ++h++++e  + +++ +k+ + +av + L+
  gi|386002037|ref|YP_005920336.1| 116 SVGEHIILDIDHWILFLSFIethpererfwEMHQQVSEAHAEEFK-KKNHKAEAVLRRLE 174
                                       58****************999999******************999.55556667766665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     5e-05      0.18       2      22 ..      69      89 ..      68      95 .. 0.88
   2 ?   -1.6   0.0      0.78   2.8e+03      37      53 ..     161     177 ..     156     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                            HTH_19  2 erLkeaReelgltqeelaerl 22
                                      + ++e+Re lg++q el++++
  gi|386002037|ref|YP_005920336.1| 69 KLFREMREDLGISQSELMREA 89
                                      578***************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.78
                            HTH_19  37 kdvpsaelllkiaealg 53 
                                       k++++ae +l+++e+++
  gi|386002037|ref|YP_005920336.1| 161 KKNHKAEAVLRRLELCN 177
                                       45677777755555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1420.44
//
Query:       gi|386002038|ref|YP_005920337.1|  [L=152]
Description: hypothetical protein Mhar_1351 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-22   78.3   0.0    6.5e-22   78.0   0.0    1.1  1  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   3.6e-26   6.5e-22       1     131 [.      27     145 ..      27     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 3.6e-26
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-S.....TCHHHHHHHHCS--TTTTSEEE--SS-SEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetd.....sCldDAiqvltgctlGkgnlivmdygkkalt 72 
                                       fHGHl+p+lvlG+rm+  a++el+        e++a v+t      sCl D+iqv  gctlG+gn+ v++ g  ++ 
  gi|386002038|ref|YP_005920337.1|  27 FHGHLGPFLVLGVRMGLFARRELDSA----PGEMEAAVKTGavpslSCLLDGIQVSAGCTLGRGNISVEPPGIAEAE 99 
                                       9**********************843....679*******************************************9 PP

                                       EEETTT-EEEEEEE-CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                              FmdE  73 fkkrktgkavrlklkeelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                       f    +g+ v+++++   +e+  ++++ ++            leea++ki + ++eelf
  gi|386002038|ref|YP_005920337.1| 100 FS--ASGRRVTIRAR---AEVVGEIKSWRE--------RYASLEEAARKISKRSDEELF 145
                                       98..57888888888...444444444333........123467788888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 944.58
//
Query:       gi|386002039|ref|YP_005920338.1|  [L=119]
Description: hypothetical protein Mhar_1350 [Methanosaeta harundinacea 6Ac]
Scores for complete 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   0.0    5.4e-09   35.8   0.0    1.1  1  ydhR            Putative mono-oxygenase ydhR
  ------ inclusion threshold ------
      0.011   15.8   0.2      0.015   15.4   0.2    1.2  1  ABM             Antibiotic biosynthesis monooxygenase
      0.097   12.6   0.0       0.12   12.3   0.0    1.2  1  Chitin_synth_1  Chitin synthase


Domain annotation for each model (and alignments):
>> ydhR  Putative mono-oxygenase ydhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   9.1e-13   5.4e-09      13      66 ..      20      73 ..       8      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 9.1e-13
                                      HHHHHHHHHHHHHHHTTSTTEEEEEEEEETTTTEEEEEEEESSHHHHHHHHHHH CS
                              ydhR 13 geelaealkelaesiaeepGliwKiWteneetkeaGGiYlFedeasaeaYlemh 66
                                       e+++e++    e++ e pGl +K+W +++e++e G +Y+F++e+++++Yl   
  gi|386002039|ref|YP_005920338.1| 20 VEAMREKFLISYEAFREMPGLYSKVWWSDPERGEWGALYIFRTEEELQEYLRSD 73
                                      5667777777779999**********************************9844 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   2.5e-06     0.015      11      74 ..      16      77 ..       8      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                                      STTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHH CS
                               ABM 11 kpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfka 74
                                      +p++ ea +++f    e+  +e+pG  +  ++  + +++e+  +  +++e+ l+++l+s+ +++
  gi|386002039|ref|YP_005920338.1| 16 DPENVEAMREKFLISYEAF-REMPGLYSKVWWS-DPERGEWGALYIFRTEEELQEYLRSDRWRK 77
                                      79999************99.6***********7.999999**********************97 PP

>> Chitin_synth_1  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05      0.12     110     157 ..      57     105 ..      32     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                    Chitin_synth_1 110 qllfclkeknakkinShrWlfnafarl.lqPevcvlldvGtkpgkksly 157
                                         +f + e+ ++ + S rW  +   +   +Pev+++ldvG+ + k++++
  gi|386002039|ref|YP_005920338.1|  57 LYIFRTEEELQEYLRSDRWRKKIPEKYgYKPEVVAVLDVGAILCKEAVV 105
                                       67899999999999*****8776544338***************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 761.30
//
Query:       gi|386002040|ref|YP_005920339.1|  [L=278]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-11   42.5   9.2    5.3e-08   32.4   1.6    2.4  2  Fer4      4Fe-4S binding domain
    8.5e-09   35.4   4.5    2.6e-05   24.3   0.1    2.5  2  Fer4_10   4Fe-4S dicluster domain
    5.5e-08   33.3  11.7    4.4e-07   30.4  11.4    2.2  2  Fer4_7    4Fe-4S dicluster domain
      2e-07   30.8  12.6    3.6e-06   26.8   2.3    2.6  2  Fer4_6    4Fe-4S binding domain
    4.3e-07   29.6  13.1    4.2e-06   26.5   3.2    2.8  2  Fer4_2    4Fe-4S binding domain
    2.2e-06   27.8   9.1    5.6e-06   26.4   9.1    1.8  1  Fer4_9    4Fe-4S dicluster domain
    1.3e-05   25.8   4.7     0.0021   18.8   0.2    2.6  2  Fer4_15   4Fe-4S single cluster domain
    6.5e-05   23.8   5.9      0.011   16.6   0.6    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00013   22.0  13.3    0.00018   21.5  10.3    2.3  2  Fer4_21   4Fe-4S dicluster domain
     0.0006   20.2   8.8     0.0073   16.7   0.2    2.6  2  Fer4_8    4Fe-4S dicluster domain
    0.00098   19.6   8.1      0.044   14.3   0.2    2.5  2  Fer4_17   4Fe-4S dicluster domain
     0.0055   17.1   3.4     0.0055   17.1   3.4    2.7  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.019   15.8  10.5       0.84   10.5   1.1    2.5  2  Fer4_22   4Fe-4S dicluster domain
       0.04   14.8   4.8       0.04   14.8   4.8    3.4  3  Fer4_3    4Fe-4S binding domain
      0.048   14.2   1.3      0.048   14.2   1.3    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.16   12.1   0.0        7.9    6.7   0.0    3.2  4  CtsR_C    CtsR C-terminal dimerization domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.1   2.2e-05     0.025       5      22 ..     199     216 ..     195     216 .. 0.87
   2 !   32.4   1.6   4.7e-11   5.3e-08       1      23 [.     224     246 ..     224     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       TTTSSS-THHHHHSTTTE CS
                              Fer4   5 eekCigCGaCvevCPvgA 22 
                                       ++ C gC++Cve C +gA
  gi|386002040|ref|YP_005920339.1| 199 TDGCRGCNRCVERCSFGA 216
                                       788***********9887 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 4.7e-11
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       vv+d+++C gCG+Cv+ CP+ A 
  gi|386002040|ref|YP_005920339.1| 224 VVFDPDRCYGCGLCVSTCPTKAR 246
                                       689*****************995 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.1   0.00015      0.17       4      19 ..     197     212 ..     194     221 .. 0.83
   2 !   24.3   0.1   2.3e-08   2.6e-05       2      24 ..     224     250 ..     223     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                           Fer4_10   4 idddtCirCgkCvkaC 19 
                                       + +d C +C++Cv+ C
  gi|386002040|ref|YP_005920339.1| 197 LSTDGCRGCNRCVERC 212
                                       6778999*****9999 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.3e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl....t 24 
                                       vv+d+d+C +Cg Cv+ CP+++    +
  gi|386002040|ref|YP_005920339.1| 224 VVFDPDRCYGCGLCVSTCPTKArrlvE 250
                                       799*****************6543331 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.8    0.0001      0.12      29      52 .]     193     216 ..     165     216 .. 0.82
   2 !   30.4  11.4   3.9e-10   4.4e-07       2      52 .]     202     245 ..     201     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                            Fer4_7  29 ekveidpekClgCgaCvavCPtga 52 
                                       + + ++ + C gC++Cv++C +ga
  gi|386002040|ref|YP_005920339.1| 193 DIISLSTDGCRGCNRCVERCSFGA 216
                                       556778899***********9997 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.9e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C gC++Cv+ C+ +a +l +        +v++dp++C+gCg Cv++CPt+a
  gi|386002040|ref|YP_005920339.1| 202 CRGCNRCVERCSFGANRLVN-------GRVVFDPDRCYGCGLCVSTCPTKA 245
                                       *****************965.......489*******************87 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   2.8    0.0017       1.9       9      23 ..     202     216 ..     200     217 .. 0.94
   2 !   26.8   2.3   3.2e-09   3.6e-06       2      23 ..     224     245 ..     223     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                            Fer4_6   9 CigCgdCvrvCPega 23 
                                       C gC++Cv  C +ga
  gi|386002040|ref|YP_005920339.1| 202 CRGCNRCVERCSFGA 216
                                       99**********998 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.2e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       v++dpd+C gCg Cv+ CP++a
  gi|386002040|ref|YP_005920339.1| 224 VVFDPDRCYGCGLCVSTCPTKA 245
                                       89*****************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   2.4    0.0036       4.1       7      20 ..     199     212 ..     193     214 .. 0.84
   2 !   26.5   3.2   3.7e-09   4.2e-06       2      22 .]     223     243 ..     222     243 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                            Fer4_2   7 tdrCigCgaCvsaC 20 
                                       td C gC+ Cv  C
  gi|386002040|ref|YP_005920339.1| 199 TDGCRGCNRCVERC 212
                                       789*******9888 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 3.7e-09
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +vv+d+drC gCg Cvs CP+
  gi|386002040|ref|YP_005920339.1| 223 RVVFDPDRCYGCGLCVSTCPT 243
                                       799*****************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   9.1     5e-09   5.6e-06       2      50 ..     202     245 ..     201     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C gC++Cve C +g+++  +++     +     +C+gCg Cv  Cp++a
  gi|386002040|ref|YP_005920339.1| 202 CRGCNRCVERCSFGANRLVNGRVVFDPD-----RCYGCGLCVSTCPTKA 245
                                       ****************999988888764.....6************985 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.8     0.004       4.5       5      19 ..     199     213 ..     195     219 .. 0.84
   2 !   18.8   0.2   1.8e-06    0.0021       1      20 [.     224     243 ..     224     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.004
                           Fer4_15   5 rdaCigcglCvaeap 19 
                                        d C gc++Cv++++
  gi|386002040|ref|YP_005920339.1| 199 TDGCRGCNRCVERCS 213
                                       699**********95 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.8e-06
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       Vv+D d+C gcglCv  +p+
  gi|386002040|ref|YP_005920339.1| 224 VVFDPDRCYGCGLCVSTCPT 243
                                       89****************85 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.6    0.0019       2.1       2      16 ..     202     216 ..     198     227 .. 0.80
   2 !   16.6   0.6   9.9e-06     0.011       1      18 [.     230     247 ..     230     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0019
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C +C++C+e C  +a
  gi|386002040|ref|YP_005920339.1| 202 CRGCNRCVERCSFGA 216
                                       888888888887665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.9e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       rC +Cg C+++CPt+a +
  gi|386002040|ref|YP_005920339.1| 230 RCYGCGLCVSTCPTKARR 247
                                       69************9955 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   3.6   0.00094       1.1      32      51 ..     193     212 ..     163     219 .. 0.68
   2 !   21.5  10.3   1.6e-07   0.00018       5      53 ..     199     243 ..     196     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00094
                           Fer4_21  32 tvlkvvedeCvGCnlCssvC 51 
                                        ++ + +d C GCn C++ C
  gi|386002040|ref|YP_005920339.1| 193 DIISLSTDGCRGCNRCVERC 212
                                       566778999********999 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.6e-07
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                        d C gC++C+  C+ ++   +++    ++    d+C GC lC+s CP+
  gi|386002040|ref|YP_005920339.1| 199 TDGCRGCNRCVERCSFGANRLVNG----RVVFDPDRCYGCGLCVSTCPT 243
                                       688************877777765....456789**************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.5     0.015        16      49      62 ..     200     213 ..     167     217 .. 0.86
   2 !   16.7   0.2   6.5e-06    0.0073       3      22 ..     229     248 ..     227     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                            Fer4_8  49 wsCttcgaCtevCp 62 
                                       + C +c++C+e+C 
  gi|386002040|ref|YP_005920339.1| 200 DGCRGCNRCVERCS 213
                                       67999999999996 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.5e-06
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk 22 
                                       ++C +Cg+C s+Cp+  r+ 
  gi|386002040|ref|YP_005920339.1| 229 DRCYGCGLCVSTCPTKARRL 248
                                       68***********9544433 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   2.9    0.0039       4.4      45      57 ..     201     213 ..     168     225 .. 0.79
   2 !   14.3   0.2   3.9e-05     0.044       1      15 [.     230     244 ..     226     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0039
                           Fer4_17  45 lCieCgeCerkCP 57 
                                        C +C++C+++C 
  gi|386002040|ref|YP_005920339.1| 201 GCRGCNRCVERCS 213
                                       4555555555554 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.9e-05
                           Fer4_17   1 rCiqCgyClpeCpsy 15 
                                       rC +Cg C+  Cp+ 
  gi|386002040|ref|YP_005920339.1| 230 RCYGCGLCVSTCPTK 244
                                       455555555555554 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.4     0.067        75       2      16 ..     200     214 ..     199     215 .. 0.84
   2 !   17.1   3.4   4.9e-06    0.0055       1      16 [.     228     243 ..     228     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.067
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C gC +Cv  C++
  gi|386002040|ref|YP_005920339.1| 200 DGCRGCNRCVERCSF 214
                                       67********98876 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.9e-06
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       ++rC gCg Cv++CP+
  gi|386002040|ref|YP_005920339.1| 228 PDRCYGCGLCVSTCPT 243
                                       69*************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5    0.0016       1.8      78      93 ..     198     213 ..     193     216 .. 0.86
   2 ?   10.5   1.1   0.00075      0.84      77      95 ..     226     244 ..     217     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                           Fer4_22  78 gesgCvGCgRCieacp 93 
                                       ++ gC GC+RC+e+c 
  gi|386002040|ref|YP_005920339.1| 198 STDGCRGCNRCVERCS 213
                                       6789***********7 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00075
                           Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                       f+   C GCg C+++cp+k
  gi|386002040|ref|YP_005920339.1| 226 FDPDRCYGCGLCVSTCPTK 244
                                       5677899999999999875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         7   7.8e+03       5       9 ..     155     159 ..     149     160 .. 0.57
   2 ?   10.2   3.7    0.0011       1.2       1      15 []     202     216 ..     202     216 .. 0.95
   3 ?   14.8   4.8   3.6e-05      0.04       1      15 []     231     245 ..     231     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7
                            Fer4_3   5 gaCve 9  
                                       +aC++
  gi|386002040|ref|YP_005920339.1| 155 YACLQ 159
                                       48987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC++Cve C  gA
  gi|386002040|ref|YP_005920339.1| 202 CRGCNRCVERCSFGA 216
                                       99*********9998 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.6e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg+Cv  CP++A
  gi|386002040|ref|YP_005920339.1| 231 CYGCGLCVSTCPTKA 245
                                       99***********98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.0      0.43   4.9e+02       4      16 ..     200     212 ..     198     213 .. 0.90
   2 ?   14.2   1.3   4.2e-05     0.048       2      17 ..     227     242 ..     225     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.43
                           Fer4_13   4 dtCiacgaCvela 16 
                                       d C +c+ Cve +
  gi|386002040|ref|YP_005920339.1| 200 DGCRGCNRCVERC 212
                                       79********988 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.2e-05
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D d+C +cg+Cv+++P
  gi|386002040|ref|YP_005920339.1| 227 DPDRCYGCGLCVSTCP 242
                                       889************* PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.5   1.7e+03      18      38 ..      28      48 ..      27      56 .. 0.77
   2 ?   -1.3   0.0       2.2   2.4e+03      16      32 ..      68      84 ..      66      86 .. 0.81
   3 ?   -0.1   0.0      0.89     1e+03      32      47 ..      97     112 ..      87     123 .. 0.84
   4 ?    6.7   0.0     0.007       7.9      17      35 ..     133     151 ..     131     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                            CtsR_C 18 seqdaeaiiqrLleegliter 38
                                      se ++ +i++r++e++l   r
  gi|386002040|ref|YP_005920339.1| 28 SEPTILRILDRMMESDLFRGR 48
                                      566788999999999987655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                            CtsR_C 16 siseqdaeaiiqrLlee 32
                                       +s q+a+++++ L ++
  gi|386002040|ref|YP_005920339.1| 68 VVSTQRAKDFLDALSNS 84
                                      578999*****999876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.89
                            CtsR_C  32 egliterEakLmkaal 47 
                                       ++ + +rE+ L+k ++
  gi|386002040|ref|YP_005920339.1|  97 QEALGRREGTLIKELT 112
                                       678899******9765 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.007
                            CtsR_C  17 iseqdaeaiiqrLleegli 35 
                                       is+++a+ +++rL eeg i
  gi|386002040|ref|YP_005920339.1| 133 ISSAEAKGLLDRLREEGCI 151
                                       899*************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1569.09
//
Query:       gi|386002041|ref|YP_005920340.1|  [L=160]
Description: hypothetical protein Mhar_1353 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.18   11.7   0.1    1.3  1  Peptidase_S55  SpoIVB peptidase S55
       0.13   12.0   0.1       0.88    9.3   0.0    2.0  2  Peptidase_S29  Hepatitis C virus NS3 protease


Domain annotation for each model (and alignments):
>> Peptidase_S55  SpoIVB peptidase S55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     2e-05      0.18     174     204 ..     118     147 ..     116     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                     Peptidase_S55 174 GmSGsPiiqngklvGavthvlvndptkGYgi 204
                                       G SG+P+ q+gk+vG ++ + +n   kG +i
  gi|386002041|ref|YP_005920340.1| 118 GESGTPLFQDGKVVGILSSINLNA-GKGTAI 147
                                       88**************99988764.455555 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.062   5.6e+02      73     114 ..      32      75 ..      20     101 .. 0.72
   2 ?    9.3   0.0   9.8e-05      0.88     108     140 ..     118     149 ..     108     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.062
                     Peptidase_S29  73 sdlylvtrda...dliearrrgdkrvellsprelselkGssGsPi 114
                                        ++y + r a   dl  ++ r + +v+ ++p +l ++k s   P 
  gi|386002041|ref|YP_005920340.1|  32 VSVYHIMRLAgtkDLTIGTARAK-VVADCKPFDLIYFKASGCEPT 75 
                                       55666666542335666666666.667788888888888877775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 9.8e-05
                     Peptidase_S29 108 GssGsPilCdsGhvvGllvaavcsggvvkavrf 140
                                       G sG+P++ ++G vvG+l ++  + g+ +a+  
  gi|386002041|ref|YP_005920340.1| 118 GESGTPLF-QDGKVVGILSSINLNAGKGTAISA 149
                                       88****76.78**********999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 997.30
//
Query:       gi|386002042|ref|YP_005920341.1|  [L=127]
Description: hypothetical protein Mhar_1354 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-32  111.6   0.3      2e-32  111.3   0.3    1.1  1  DUF2149   Uncharacterized conserved protein (DUF2149)


Domain annotation for each model (and alignments):
>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.3   1.1e-36     2e-32       1      92 []      30     121 ..      30     121 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.1e-36
                           DUF2149   1 lsgvaNLfDvalVlavallvalvsslnlqellsseedvtvvkkpgkekmeiivkegeelkkakesaekasgkGerlG 77 
                                       lsgvaNLfD+a+V+a+all+alv s+n+ ell++e +vt+vk+pg+++m+ii+ke ++++  ++++++a+g+G+r+G
  gi|386002042|ref|YP_005920341.1|  30 LSGVANLFDAAMVFAIALLLALVISYNIPELLNPEASVTIVKNPGDPNMQIIIKEMDQIQILNMTDKIAGGQGTRMG 106
                                       79*************************************************************************** PP

                           DUF2149  78 tayrlkdGkliyVPe 92 
                                       tayrl++G ++yVPe
  gi|386002042|ref|YP_005920341.1| 107 TAYRLENGMIVYVPE 121
                                       **************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 807.98
//
Query:       gi|386002043|ref|YP_005920342.1|  [L=221]
Description: hypothetical protein Mhar_1355 [Methanosaeta harundinacea 6Ac]
Scores for complete 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   41.2   0.0    1.9e-10   40.6   0.0    1.3  1  MotA_ExbB  MotA/TolQ/ExbB proton channel family
  ------ inclusion threshold ------
      0.082   12.7   1.2       0.62    9.9   0.5    2.3  2  LapA_dom   Lipopolysaccharide assembly protein A domain
       0.54   10.5   5.2       0.28   11.4   0.7    2.5  3  DUF2530    Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   3.2e-14   1.9e-10      30     124 ..     105     196 ..      81     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.2e-14
                                       HHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSGGCTHHHHHHHHHHHHHHHHHHHH CS
                         MotA_ExbB  30 aleealsreeerlekglsilatigslaPllGLlGTVlGlieafqaladagsadlakvapgiaeALiaTalGlvvAip 106
                                        le+al+ +e  + k l+ +++ + + P+lGL+GT++ +  a+ +l+     +++++a ++  A+ +T++Gl+v  +
  gi|386002043|ref|YP_005920342.1| 105 RLEKALQDAELGMGKALEPVKIGVRVGPMLGLMGTLIPMGPALISLSR---GEIQQMADSLVIAFSTTVIGLAVGGI 178
                                       68999999999************************************9...567*********************99 PP

                                       HHHHHHHHHHHHHHHHHH CS
                         MotA_ExbB 107 avlaynklkrkverlvle 124
                                       ++ +y++ +r +++ +++
  gi|386002043|ref|YP_005920342.1| 179 CYGVYTVKNRWYRQDMSD 196
                                       999999888887776665 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5    0.0001      0.62       6      49 ..       8      51 ..       6      63 .. 0.61
   2 ?    0.7   0.0     0.077   4.6e+02      25      47 ..     167     189 ..     153     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0001
                          LapA_dom  6 Vtvnflfaqv.elpLsllllvafgiGa.llgwllslwsylrlrrel 49
                                      V++ f+f+++  +p++l ll+ fg  + llg l+s +     rr l
  gi|386002043|ref|YP_005920342.1|  8 VNLLFVFSTAlLYPVILALLLLFGWSLaLLGSLISEY--TSRRRDL 51
                                      5555558885577777777777776665555555433..3455554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.077
                          LapA_dom  25 vafgiGallgwllslwsylrlrr 47 
                                        + +iG+ +g++   +  +++r+
  gi|386002043|ref|YP_005920342.1| 167 STTVIGLAVGGICYGVYTVKNRW 189
                                       35689999999988888888877 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.27   1.6e+03      11      33 ..      19      41 ..      11      52 .. 0.63
   2 ?   -1.8   0.0      0.63   3.8e+03      47      58 ..     130     141 ..     118     145 .. 0.80
   3 ?   11.4   0.7   4.7e-05      0.28      36      63 ..     160     187 ..     150     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                           DUF2530 11 tdprpvivvgtllWlvalvvllv 33
                                      + p+  +++    W +al+  l+
  gi|386002043|ref|YP_005920342.1| 19 LYPVILALLLLFGWSLALLGSLI 41
                                      44444445555567777766554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.63
                           DUF2530  47 aGlvvGllGlai 58 
                                       +G ++Gl+G+ i
  gi|386002043|ref|YP_005920342.1| 130 VGPMLGLMGTLI 141
                                       677889999876 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 4.7e-05
                           DUF2530  36 daleswlpvclaGlvvGllGlaiflwQR 63 
                                       d+l  ++ ++++Gl+vG + ++++++  
  gi|386002043|ref|YP_005920342.1| 160 DSLVIAFSTTVIGLAVGGICYGVYTVKN 187
                                       45566899****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1446.92
//
Query:       gi|386002044|ref|YP_005920343.1|  [L=215]
Description: membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-52  178.0  16.6      2e-52  177.9  16.6    1.0  1  DUF2162          Predicted transporter (DUF2162)
  ------ inclusion threshold ------
        0.5   10.8   6.8        3.4    8.1   6.8    2.2  1  DUF805           Protein of unknown function (DUF805)
        6.2    6.8  17.4      0.077   13.0   6.4    2.2  2  MARVEL           Membrane-associating domain


Domain annotation for each model (and alignments):
>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.9  16.6   3.3e-56     2e-52       9     222 ..       2     209 ..       1     210 [. 0.96

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 3.3e-56
                           DUF2162   9 ailifgiKtGlglglsnlsrkklllilllYlllflllalllssldekllesllrygmvlhllmAlllialGlytlkk 85 
                                       +i++f++K+ lg+gl++lsrk++l i ++Yl+l+l+++l+++ + e++++s++++g+ +hl ++lll+a+G+ t ++
  gi|386002044|ref|YP_005920343.1|   2 GIIVFALKVSLGCGLASLSRKETLSIGASYLALSLVMGLAVGLVPEAAITSIMGMGVAMHLGISLLLVAVGVSTARE 78 
                                       799************************************************************************** PP

                           DUF2162  86 wkkskkdvssrtflalvlPCPvCltailfsiillasslglspvevglvlglvflilvlvtyllsrkivkltktnypi 162
                                       w++ ++d+s++tf++l++PCP+Cl+a+++s+ +la +l++++++vg+v+gl+f+i++ +++ ++ +     ++++p+
  gi|386002044|ref|YP_005920343.1|  79 WNRRGRDLSRKTFWVLSVPCPACLAATFLSCSALAGLLDVPGWKVGAVVGLIFFISIAILSATFGR-----AGRAPS 150
                                       ************************************************************999994.....566*** PP

                           DUF2162 163 iLGnlmlfiGlyfLlsaliipniaqakaiylspltessieslllvlvlllallllGfllr 222
                                       +LGn+m+f+Gl++Lls+l+ip++ +a +++  p+ ++  ++l+  ++++l+l++lGf+ r
  gi|386002044|ref|YP_005920343.1| 151 ALGNAMIFVGLFYLLSILLIPAYLKAASTPFVPIPIP-ASDLIPSYLFILGLVGLGFVGR 209
                                       ************************************4.77777779***********865 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.8   0.00058       3.4      21      80 ..      36     126 ..      18     211 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00058
                            DUF805  21 lllvivlallaavlaa....aavasalsvvlallllvpslavtv.......RRlHDtgrsgwllllllvp....... 79 
                                       l++ +++ l+     +    +++++ +   + l + ++ +av v       RR +D+ r+ +++l +  p       
  gi|386002044|ref|YP_005920343.1|  36 LVMGLAVGLVP----EaaitSIMGMGV--AMHLGISLLLVAVGVstarewnRRGRDLSRKTFWVLSVPCPaclaatf 106
                                       22222222222....133222222222..2223333333333333455666***********975444433333333 PP

                            DUF805  80 ...................l 80 
                                                          +
  gi|386002044|ref|YP_005920343.1| 107 lscsalaglldvpgwkvgaV 126
                                       33333333333333333331 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   3.3      0.18   1.1e+03      17     128 ..       2     105 ..       1     115 [. 0.46
   2 ?   13.0   6.4   1.3e-05     0.077      12      88 ..     127     199 ..     122     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.18
                            MARVEL  17 aiiilgliasliakldqllgspssalnfavfvavfsflyalfllvlylfknsaftsilwplidlivdalaallwlva 93 
                                       +ii+++l  sl+    ++l s s +  +++ ++ +++ + +++l++ l    a+t  ++  + +++++ ++ll ++ 
  gi|386002044|ref|YP_005920343.1|   2 GIIVFALKVSLG----CGLASLSRKETLSIGASYLALSL-VMGLAVGLVPEAAIT--SIMGMGVAMHLGISLLLVAV 71 
                                       567777777766....44444444444444333333332.222222222222333..33344556666677777777 PP

                            MARVEL  94 fialaaglrdiscafe....snqysasltvrcgqaqaav 128
                                       ++  a  ++      +    s  +   l+v c++  aa+
  gi|386002044|ref|YP_005920343.1|  72 GVSTAREWNR-----RgrdlSRKTFWVLSVPCPACLAAT 105
                                       7777777776.....222333333334444444444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.3e-05
                            MARVEL  12 lqlvfaiiilgliasliakldqllgspssalnfavfvavfsflyalfllvlylfk.nsaftsilwplidlivdalaa 87 
                                       + l+f i i +l+a+++     ++g+++sal+ a+ + ++ +l++++l+ +yl   ++ f +i +p  dli + l++
  gi|386002044|ref|YP_005920343.1| 127 VGLIFFISIAILSATFG-----RAGRAPSALGNAMIFVGLFYLLSILLIPAYLKAaSTPFVPIPIPASDLIPSYLFI 198
                                       55788888999999999.....8999999999999999999999*********99**************99887776 PP

                            MARVEL  88 l 88 
                                       l
  gi|386002044|ref|YP_005920343.1| 199 L 199
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1503.72
//
Query:       gi|386002045|ref|YP_005920344.1|  [L=1504]
Description: Cobaltochelatase CobN subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1098.1   0.0          0 1097.9   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1097.9   0.0         0         0       2    1088 ..     258    1361 ..     257    1362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1097.9 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewyk....kakkekaptv 72  
                                        +Y+++ggveN+k l +yla+ +lg  e  v++pv++p++ i hpd+++lf ++++yl+wy+    ++++e apt+
  gi|386002045|ref|YP_005920344.1|  258 EYWNYGGVENMKGLYSYLARAFLG-LEVPVRAPVPTPRAYISHPDSPDLFLQTSSYLQWYRshsgHRYDELAPTI 331 
                                        7**********************8.66689********************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   73 gilfyrahllagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpa 147 
                                        g++   ++ ++    + +a++rale+rg+nv+ + +++     + +++++f  +g++ vda++ t  f+l+ g  
  gi|386002045|ref|YP_005920344.1|  332 GVMNLASDPVTSS--MRTAIVRALEARGANVIDIGFEN-----TTTIQDFFILNGSTIVDAVLLTKPFRLNYGDP 399 
                                        *********9988..679****************5555.....78999****9*****************87765 PP

                                        xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  148 eeeeeeaeeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetev 221 
                                        ee       ealkelnvPvl+a  l++q+ eeW+++ +Gl p +l +++a+pE+d +iep++i+++      te 
  gi|386002045|ref|YP_005920344.1|  400 EEG-----IEALKELNVPVLNAmKLWYQTPEEWRNE-TGLFPAELYFKIAMPEMDAVIEPMMIAGR------TEK 462 
                                        444.....4578*********************998.****************************4......567 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  222 ekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdvee 296 
                                         ++ p++ +++++ad+a +wa+L r pn+ekk aii++n+  g+++lg a++++vp+Sl  +L+ l+  GY+ve 
  gi|386002045|ref|YP_005920344.1|  463 GTFDPVQSQIDWLADRAIAWAELGRRPNSEKKAAIIYYNHGGGKDNLG-ATYINVPRSLRVILQGLNGSGYRVEG 536 
                                        89**********************************************.77**********************76 PP

                                        xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      CobN-Mg_chel  297 lpesgdeLiellleggtndpew......eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppge.mveee 364 
                                        +  ++++L++l+ ++gtn  +w      ++++ g+a+l+pa++Y ewf+e+++++++ev+e Wg+ppge mv+ e
  gi|386002045|ref|YP_005920344.1|  537 TVPDEQDLVDLMAHQGTNVGTWapeeleKMVRAGNATLIPADDYLEWFSEIDPAKQREVTEIWGPPPGEiMVY-E 610 
                                        6559**************999999666444455************************************6666.5 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  365 ksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlP 439 
                                        +++++++vip+l++Gnv++++QP+rg+ ++++ lyh++d+pP+hqY+AfYlWlr+ f+ad +vH+GkHGt+Ew+P
  gi|386002045|ref|YP_005920344.1|  611 NESGSYFVIPKLSFGNVILAPQPTRGWLQNSTILYHNKDIPPHHQYIAFYLWLRRGFDADFIVHLGKHGTQEWTP 685 
                                        6777*********************************************************************** PP

                                        xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  440 GKqvgls.eecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeea 513 
                                        GK+ g+s ++c+P il++dlP++YpYiv+n++EG+qAKRR+ Avii HltPp++ ++lyg++++L e   +Y+++
  gi|386002045|ref|YP_005920344.1|  686 GKESGISrDQCWPGILIQDLPVIYPYIVDNIAEGSQAKRRGDAVIITHLTPPIVASGLYGNFTHLAETAFNYHQV 760 
                                        *******9******************************************************************9 PP

                                        xxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  514 esldperlkalre.qilelveelnldkdlg.leeakeeeeeefeellekldgyleelkeaqirdglhilGeapeg 586 
                                        e++    +kal++ +i++ +eel+ld+dl+ + ++ ++++e+f+ ++e+l++yl +lk++ +++glh++ ++peg
  gi|386002045|ref|YP_005920344.1|  761 ENA---SVKALYKeEIIARCEELHLDEDLDkNLSELSRDPEAFDGFVEELEHYLYDLKKEFMPYGLHTFATPPEG 832 
                                        776...66676666***************95223467799*********************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  587 eqlvdlvvailrleneegesltealaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeea 661 
                                         ++ ++v+++l      g+++++++a  + +d  ++         ++ d  ++l++++ +l++++++++++++ a
  gi|386002045|ref|YP_005920344.1|  833 GARLEMVQSML------GDDYKREVALMISYDDYPN--------PSRLDKERELDNASLALLAAVIDDKTSPDLA 893 
                                        ***********......9********9976554443........334444578999************9999999 PP

                                        xxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  662 eaeeleeeeeeeee.....................eteeEitallraLdGeyippgpsGdptrgraevLPTGrNf 715 
                                        + e+ +++  + ++                     ++ eE+ ++++a + ey+pp+p++dp+r+++ vLPTGrNf
  gi|386002045|ref|YP_005920344.1|  894 QGEVFSNRPGAGTAnrsenltallalalsrsegldASVEEVPRFINASESEYTPPSPADDPIRDPN-VLPTGRNF 967 
                                        99888888887777899*****************7666**************************77.******** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  716 ysvDpraiPteaAwevGkklaeellerylqeh.geyPekvglslwgtetmrteGediAqiLallGvrPvwdaagr 789 
                                        +s+ pr +Pt+aAwevG +lae+l+e y++e+ g+yP+k++++lw+ +t+ + G  +A+iL l+G++Pvwd+ g 
  gi|386002045|ref|YP_005920344.1|  968 HSISPRMVPTPAAWEVGSELAEDLIEVYRAEEnGTYPRKLAIVLWAWATTDH-GVVEAEILRLVGAEPVWDSYGG 1041
                                        *****************************9988**************99875.********************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                      CobN-Mg_chel  790 vvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaelee..... 859 
                                        v+d++l p++eLgRPRiDV+v  SG+ RD+fp+ ++l+d+a++l+a+   +++ N+vr++++e ++el +     
  gi|386002045|ref|YP_005920344.1| 1042 VSDVRLTPSSELGRPRIDVVVVPSGLHRDLFPEKLQLIDRAIRLAANDSATDYPNYVRENSEEIRSELLAtgnys 1116
                                        *********************************************************************977664 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xx RF
                      CobN-Mg_chel  860 keeaeeratyRvFgskpGaYgagvqelies.snWedeedLaeaYlnwssyaYgkgaegeeaee..........af 923 
                                        +e+ae  a+ R+F +++G+Yg ++++ +++ ++We++++L +++++++sy+Yg g+ g++ ++          ++
  gi|386002045|ref|YP_005920344.1| 1117 EEDAEFLAASRIFLEAAGTYGPNLDSPVSAsDTWENDSKLGDLFIDRMSYIYGDGVWGSRTPSgkdyaavqteVY 1191
                                        446779************************9**********************88444444444455555555** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  924 earLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnp.enpkvrtlkeeiarelrs 997 
                                        +++L++v++++++++s+ ++++d dd+yq+lGG+++avr+++g +p++y++d + + ++ k + lk +++relrs
  gi|386002045|ref|YP_005920344.1| 1192 RRNLAEVEAAAHHTNSNLYGFIDNDDVYQYLGGISMAVRTVTGVAPNLYVTDARARgAAGKAEPLKSFFTRELRS 1266
                                        *****************************************************876155699************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  998 rvlNPkWiegmmrhGykGafelaatvdnlfgwdata.dvvddwvyeevaetYvlDee...vrefleekNpwAlre 1068
                                        r+ NPkWiegm+ +Gy+G +e++++v++l+gwd+t  d+v++ +++e++++Yv+D++   +ref++ekNp+A++ 
  gi|386002045|ref|YP_005920344.1| 1267 RYYNPKWIEGMKGEGYSGGREMDKFVEHLWGWDVTVpDLVTETMWNEAYDVYVKDKYdmgLREFFDEKNPYAYQV 1341
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1069 iaerLlEaarrglWeaseet 1088
                                        +++r+lEa r+g+W+++ee+
  gi|386002045|ref|YP_005920344.1| 1342 VTARMLEASRKGYWHPTEEM 1361
                                        ***************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.95u 0.39s 00:00:01.34 Elapsed: 00:00:00.54
# Mc/sec: 8315.22
//
Query:       gi|386002046|ref|YP_005920345.1|  [L=508]
Description: Cobaltochelatase CobN subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-65  216.1  32.9      6e-10   39.3   0.1    9.3  9  PQQ_3     PQQ-like domain
    2.6e-48  164.7  10.4    2.2e-23   83.1   1.4    4.5  3  PQQ_2     PQQ-like domain
    1.9e-40  134.9  14.1    5.2e-08   32.5   0.0    9.3  9  PQQ       PQQ enzyme repeat
     0.0053   17.3   0.0       0.01   16.4   0.0    1.5  1  DUF4430   Domain of unknown function (DUF4430)
  ------ inclusion threshold ------
      0.055   13.4   0.0         16    5.5   0.0    3.2  3  DUF4905   Domain of unknown function (DUF4905)
       0.19   11.8   5.1        5.4    7.0   0.1    4.4  5  SUKH-4    SUKH-4 immunity protein


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   4.2e-05      0.13       4      40 .]      50      95 ..      49      95 .. 0.85
   2 !   37.7   1.0   6.3e-13   1.9e-09       1      40 []      96     136 ..      96     136 .. 0.93
   3 !   15.9   0.1   4.6e-06     0.014       1      39 [.     137     181 ..     137     181 .. 0.84
   4 !   30.4   0.1   1.3e-10   3.8e-07       1      39 [.     182     221 ..     182     222 .. 0.94
   5 !   26.6   0.1     2e-09     6e-06       2      40 .]     224     261 ..     224     261 .. 0.97
   6 !   32.7   0.1   2.4e-11     7e-08       1      39 [.     262     299 ..     262     300 .. 0.94
   7 !   33.7   0.2   1.2e-11   3.5e-08       1      38 [.     301     338 ..     301     340 .. 0.95
   8 !   39.3   0.1     2e-13     6e-10       1      37 [.     341     377 ..     341     380 .. 0.96
   9 !    5.5   0.0    0.0088        26      17      40 .]     389     412 ..     378     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                             PQQ_3  4 lWsvqlpg..pvnsspavdgglvyvgtg.......dGtlyAlDaet 40
                                      lW+ ++ +  +v++s+ ++g +vyv+++          l +lDa++
  gi|386002046|ref|YP_005920345.1| 50 LWREKVTAkgYVGGSASISGERVYVSSWpdmsyqgEQALGCLDARD 95
                                      7888776555999***************999999999999999886 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 6.3e-13
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G vlW+ +l+g  + s+pav+ glv++g++ G ly+lDaet
  gi|386002046|ref|YP_005920345.1|  96 GSVLWRNPLGGkGGASTPAVSRGLVFAGSWYGDLYCLDAET 136
                                       89*********6666999**********************9 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 4.6e-06
                             PQQ_3   1 GevlWsvql...pg..pvnsspavdgglvyvgtg.dGtlyAlDae 39 
                                       Ge++W++++   p    v ssp+v g lv+v+t  dGtl+ lD e
  gi|386002046|ref|YP_005920345.1| 137 GETVWNRTVerdPQwwGVASSPLVIGELVFVSTFsDGTLHVLDLE 181
                                       8999999663324477888999*********************75 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 1.3e-10
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       G++lW+ +++  + ++spa+ +g+vy+++gd  ly++D+ 
  gi|386002046|ref|YP_005920345.1| 182 GDELWNISTGKiDPYTSPAAEEGRVYFAGGDPALYCIDTS 221
                                       99********997779**********************85 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 2e-09
                             PQQ_3   2 evlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       e+lW+ ++ gp++++p ++gg+ y++t    l+AlDa t
  gi|386002046|ref|YP_005920345.1| 224 EILWRAPTNGPITTTPGIGGGRAYFATR-EDLRALDAST 261
                                       68*************************8.********87 PP

  == domain 6  score: 32.7 bits;  conditional E-value: 2.4e-11
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       Ge++W  +l g + sspa++ g+vy+gt+dG+l +l+a 
  gi|386002046|ref|YP_005920345.1| 262 GEEVWVAPLKGTT-SSPAISSGRVYIGTDDGRLACLNAS 299
                                       99********855.***********************96 PP

  == domain 7  score: 33.7 bits;  conditional E-value: 1.2e-11
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDa 38 
                                       G ++Ws ++++ v ssp+v+g++vy g++ G +yAl+ 
  gi|386002046|ref|YP_005920345.1| 301 GSLVWSAEVDSSVRSSPLVAGDRVYLGSHRGVVYALNR 338
                                       889*********************************97 PP

  == domain 8  score: 39.3 bits;  conditional E-value: 2e-13
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlD 37 
                                       G ++W++++++++ ssp +++g++y+g++dG lyA+ 
  gi|386002046|ref|YP_005920345.1| 341 GSEVWRYETGAYLMSSPSFSDGVLYIGSDDGCLYAFG 377
                                       889********************************95 PP

  == domain 9  score: 5.5 bits;  conditional E-value: 0.0088
                             PQQ_3  17 pavdgglvyvgtgdGtlyAlDaet 40 
                                       +++++g+  ++++dG+++A+D +t
  gi|386002046|ref|YP_005920345.1| 389 VLLGDGRFNAAAEDGSVRAVDERT 412
                                       4667777778888********887 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   1.1   4.7e-20   1.4e-16       4     104 ..      87     190 ..      84     200 .. 0.86
   2 !   40.2   0.0   9.6e-14   2.9e-10      13     101 ..     182     267 ..     181     269 .. 0.91
   3 !   83.1   1.4   7.4e-27   2.2e-23       3     142 ..     252     381 ..     250     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.7e-20
                             PQQ_2   4 vvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegp.....vvgaplva 75 
                                        + +lda++G++lWr  l  +  gg s++ +s+g +f+++ +g l++lda+tG+ +W++t+e       v ++plv 
  gi|386002046|ref|YP_005920345.1|  87 ALGCLDARDGSVLWRNPL--GGKGGASTPAVSRGLVFAGSWYGDLYCLDAETGETVWNRTVERDpqwwgVASSPLVI 161
                                       5679************99..66788888999******************************664222225555**** PP

                             PQQ_2  76 egrvvvva.sdgqlialdaedGkrlWstqq 104
                                       ++ v+v + sdg+l  ld   G++lW++  
  gi|386002046|ref|YP_005920345.1| 162 GELVFVSTfSDGTLHVLD-LEGDELWNIST 190
                                       ******************.9******9654 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 9.6e-14
                             PQQ_2  13 GaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqli 89 
                                       G elW  +   +++  +s a  ++g+++ a+g + l+++d+++ ++lW++  +gp+ ++p + +gr+++++  + l+
  gi|386002046|ref|YP_005920345.1| 182 GDELWNIST-GKIDPYTSPAA-EEGRVYFAGGDPALYCIDTSSFEILWRAPTNGPITTTPGIGGGRAYFAT-REDLR 255
                                       889999976.34677775566.************************************************7.889** PP

                             PQQ_2  90 aldaedGkrlWs 101
                                       alda +G+++W 
  gi|386002046|ref|YP_005920345.1| 256 ALDASTGEEVWV 267
                                       ***********6 PP

  == domain 3  score: 83.1 bits;  conditional E-value: 7.4e-27
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrv 79 
                                       ++++alda tG+e+W   l     g +s +  s g+++++t+ grl++l+a++G+++W++++++ v+++plva++rv
  gi|386002046|ref|YP_005920345.1| 252 EDLRALDASTGEEVWVAPL----KGTTSSPAISSGRVYIGTDDGRLACLNASDGSLVWSAEVDSSVRSSPLVAGDRV 324
                                       5789*************65....555556677********************************************* PP

                             PQQ_2  80 vvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdG 142
                                       ++ +  g+++al+  dG ++W+ ++++     +   +sp+++++++++g  +g l+a+  +  
  gi|386002046|ref|YP_005920345.1| 325 YLGSHRGVVYALNRSDGSEVWR-YETG-----AYLMSSPSFSDGVLYIGSDDGCLYAFGEEGS 381
                                       **********************.9999.....5566789999999999999999888764444 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00032      0.97      15      35 ..      91     111 ..      90     114 .. 0.84
   2 !   18.9   0.7   3.5e-07     0.001       1      36 [.     118     153 ..     118     155 .. 0.88
   3 ?    2.3   0.0     0.061   1.8e+02       4      24 ..     166     186 ..     164     193 .. 0.81
   4 !    8.0   0.0   0.00096       2.9       1      32 [.     204     235 ..     204     241 .. 0.90
   5 !   22.3   0.0   2.8e-08   8.3e-05      12      37 ..     254     279 ..     244     280 .. 0.87
   6 !   32.5   0.0   1.7e-11   5.2e-08       1      37 [.     282     318 ..     282     319 .. 0.96
   7 !   30.3   0.0   8.5e-11   2.5e-07       1      31 [.     322     352 ..     322     358 .. 0.91
   8 !    9.8   0.0   0.00026      0.79       1      16 [.     362     377 ..     362     383 .. 0.88
   9 ?    1.4   0.0      0.12   3.5e+02       9      19 ..     402     412 ..     398     424 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00032
                                       EETTTCCEEEEEESSSCGSSE CS
                               PQQ  15 lDadTGkvlWrfktggpvlsl 35 
                                       lDa++G vlWr ++gg+  ++
  gi|386002046|ref|YP_005920345.1|  91 LDARDGSVLWRNPLGGKGGAS 111
                                       9**********9999976665 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.5e-07
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       g v++gs  G ly lDa+TG+ +W   ++ +++++ 
  gi|386002046|ref|YP_005920345.1| 118 GLVFAGSWYGDLYCLDAETGETVWNRTVERDPQWWG 153
                                       6799********************988888888875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.061
                                       EEE.ETTSEEEEEETTTCCEEE CS
                               PQQ   4 ylg.sadGylyAlDadTGkvlW 24 
                                       ++    dG+l  lD   G++lW
  gi|386002046|ref|YP_005920345.1| 166 FVStFSDGTLHVLD-LEGDELW 186
                                       5555789*******.8899999 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.00096
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpv 32 
                                       g+vy +  d  ly +D ++ ++lWr +t+gp+
  gi|386002046|ref|YP_005920345.1| 204 GRVYFAGGDPALYCIDTSSFEILWRAPTNGPI 235
                                       6899999999********************98 PP

  == domain 5  score: 22.3 bits;  conditional E-value: 2.8e-08
                                       EEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  12 lyAlDadTGkvlWrfktggpvlslpi 37 
                                       l+AlDa+TG+++W+ +++g   s  i
  gi|386002046|ref|YP_005920345.1| 254 LRALDASTGEEVWVAPLKGTTSSPAI 279
                                       89*****************9998765 PP

  == domain 6  score: 32.5 bits;  conditional E-value: 1.7e-11
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                       g+vy+g++dG+l  l+a++G ++W+ ++++ v+s+p+
  gi|386002046|ref|YP_005920345.1| 282 GRVYIGTDDGRLACLNASDGSLVWSAEVDSSVRSSPL 318
                                       78*********************************97 PP

  == domain 7  score: 30.3 bits;  conditional E-value: 8.5e-11
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSC CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggp 31 
                                       ++vylgs  G++yAl++++G ++Wr++tg+ 
  gi|386002046|ref|YP_005920345.1| 322 DRVYLGSHRGVVYALNRSDGSEVWRYETGAY 352
                                       689*************************975 PP

  == domain 8  score: 9.8 bits;  conditional E-value: 0.00026
                                       TEEEEEETTSEEEEEE CS
                               PQQ   1 gvvylgsadGylyAlD 16 
                                       gv+y+gs+dG+lyA+ 
  gi|386002046|ref|YP_005920345.1| 362 GVLYIGSDDGCLYAFG 377
                                       789***********86 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.12
                                       TSEEEEEETTT CS
                               PQQ   9 dGylyAlDadT 19 
                                       dG ++A+D +T
  gi|386002046|ref|YP_005920345.1| 402 DGSVRAVDERT 412
                                       9*******998 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.5e-06      0.01       3      72 ..     412     487 ..     410     489 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                           DUF4430   3 tvfdvleaaakkkedkteaqsge.....hyitsIngleqdtakksyWmyevN...GepsdvGagsyklkdgdkivfr 71 
                                       t++ +l +a ++ + +  +++++     + + sI+g+e    ++++W y vN     ++++G +   l++gd++ f+
  gi|386002046|ref|YP_005920345.1| 412 TALGALMKASEVGGFEITFDGSYvddygLLVRSIDGIE--ARAGEFWIYWVNypeEPMPSEGPDRFPLEEGDRVLFY 486
                                       67777777788877777777777788889********5..55555555555544399*******************9 PP

                           DUF4430  72 y 72 
                                       +
  gi|386002046|ref|YP_005920345.1| 487 L 487
                                       6 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.017        51      32      83 .]      49     100 ..      45     100 .. 0.94
   2 ?    5.5   0.0    0.0054        16      23      48 ..     130     155 ..     128     175 .. 0.76
   3 ?   -2.4   0.0       1.5   4.5e+03      68      83 .]     251     266 ..     249     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                           DUF4905  32 llfedlvleekwwtgleaiykgvlllhkyekpdsPehkgliaiDiktgkllW 83 
                                       ll+ + v    +  g ++i+ + +++  +++ +   ++ l  +D++ g +lW
  gi|386002046|ref|YP_005920345.1|  49 LLWREKVTAKGYVGGSASISGERVYVSSWPDMSYQGEQALGCLDARDGSVLW 100
                                       678999999999999************************************* PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0054
                           DUF4905  23 saldletgkllfedlvleekwwtgle 48 
                                       ++ld etg++ ++++v  +  w g++
  gi|386002046|ref|YP_005920345.1| 130 YCLDAETGETVWNRTVERDPQWWGVA 155
                                       79************999886555554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
                           DUF4905  68 hkgliaiDiktgkllW 83 
                                       +++l a+D+ tg+ +W
  gi|386002046|ref|YP_005920345.1| 251 REDLRALDASTGEEVW 266
                                       57899*******9999 PP

>> SUKH-4  SUKH-4 immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0018       5.4      52     102 ..      95     146 ..      14     169 .. 0.66
   2 ?   -1.7   0.0       0.9   2.7e+03     143     167 ..     245     266 ..     218     271 .. 0.78
   3 ?    2.1   0.2      0.06   1.8e+02      65     103 ..     272     310 ..     252     322 .. 0.76
   4 ?   -0.5   0.0      0.38   1.1e+03      68      95 ..     315     342 ..     306     358 .. 0.78
   5 ?    0.5   0.0      0.18   5.5e+02      82     104 ..     379     413 ..     343     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                            SUKH-4  52 eaavadlelvaaerseelpaeaggllvLGalesaslvldpgtGa.Vlavdle 102
                                       + +v ++  +  ++++  pa  +gl+  G++ ++ ++ld++tG+ V+ ++ e
  gi|386002046|ref|YP_005920345.1|  95 DGSVLWRNPLGGKGGASTPAVSRGLVFAGSWYGDLYCLDAETGEtVWNRTVE 146
                                       4455555555667788899999*********************636655555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.9
                            SUKH-4 143 rlaarlrerLraiDPaAfadpesfW 167
                                       r++ + re+Lra+D  A ++ e +W
  gi|386002046|ref|YP_005920345.1| 245 RAYFATREDLRALD--A-STGEEVW 266
                                       66778899999999..4.5667777 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.06
                            SUKH-4  65 rseelpaeaggllvLGalesaslvldpgtGaVlavdlee 103
                                       + +  pa   g + +G+++++  +l++ +G+ ++ ++ +
  gi|386002046|ref|YP_005920345.1| 272 GTTSSPAISSGRVYIGTDDGRLACLNASDGSLVWSAEVD 310
                                       44556666777889****************998877655 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.38
                            SUKH-4  68 elpaeaggllvLGalesaslvldpgtGa 95 
                                         p  ag+ + LG++ + +++l++ +G+
  gi|386002046|ref|YP_005920345.1| 315 SSPLVAGDRVYLGSHRGVVYALNRSDGS 342
                                       56778999999****9999999999885 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.18
                            SUKH-4  82 l............esaslvldpgtGaVlavdleee 104
                                                    +++ + + +++G+V avd++++
  gi|386002046|ref|YP_005920345.1| 379 EgskvifegevllGDGRFNAAAEDGSVRAVDERTA 413
                                       2444444444466788899999*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2988.20
//
Query:       gi|386002047|ref|YP_005920346.1|  [L=408]
Description: Pyrrolo-quinoline quinone [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-44  149.0  24.6    1.7e-05   25.1   0.0    8.4  8  PQQ_3     PQQ-like domain
    3.2e-39  134.9   8.1    5.3e-21   75.3   0.3    3.2  3  PQQ_2     PQQ-like domain
    1.6e-23   81.4   7.6     0.0056   16.6   0.0    8.9  9  PQQ       PQQ enzyme repeat
     0.0009   19.1   0.3        2.6    8.1   0.0    4.2  4  Kelch_2   Kelch motif
  ------ inclusion threshold ------
       0.11   12.3   0.8         37    4.3   0.0    3.4  3  DUF4905   Domain of unknown function (DUF4905)
       0.22   11.1   7.3        6.6    6.4   0.0    4.3  4  Kelch_1   Kelch motif


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.6e-07     0.002       3      39 ..      64      99 ..      63     100 .. 0.90
   2 !    8.8   0.0   0.00079       2.4       1      29 [.     101     134 ..     101     142 .. 0.73
   3 !   18.3   0.1   8.1e-07    0.0024       1      32 [.     144     178 ..     144     183 .. 0.86
   4 !   24.2   0.2   1.1e-08   3.4e-05       3      38 ..     190     229 ..     189     230 .. 0.94
   5 !   25.1   0.0   5.7e-09   1.7e-05       1      37 [.     232     272 ..     232     275 .. 0.93
   6 !   20.1   0.0   2.1e-07   0.00064       1      40 []     276     319 ..     276     319 .. 0.95
   7 !   24.0   0.4   1.3e-08   3.9e-05       1      40 []     320     366 ..     320     366 .. 0.88
   8 !   21.4   1.0   8.4e-08   0.00025       1      36 [.     367     398 ..     367     401 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.6e-07
                             PQQ_3  3 vlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39
                                      +lW+++++++++ss+ v++glv+v +    ++AlD  
  gi|386002047|ref|YP_005920346.1| 64 TLWTREIGAQAGSSVSVAEGLVFVNCV-DEIVALDQG 99
                                      69**********************986.999999965 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00079
                             PQQ_3   1 GevlWsvql..pgpvnssp...avdgglvyvgtg 29 
                                       Ge++W+ ++   g+v +s    ++++g++y++++
  gi|386002047|ref|YP_005920346.1| 101 GETIWAAPFerNGDVCCSWftpVYSDGRLYFSGM 134
                                       7888888553356666544555*********986 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 8.1e-07
                             PQQ_3   1 GevlWsv...qlpgpvnsspavdgglvyvgtgdGt 32 
                                       Ge++Ws+   +  g+v +spav +g+v ++++dG+
  gi|386002047|ref|YP_005920346.1| 144 GEEIWSFappSGRGAVDGSPAVEDGKVIASDWDGH 178
                                       9******6643334999****************97 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 1.1e-08
                             PQQ_3   3 vlWsvqlpgpvnsspavdgglvyvgtg....dGtlyAlDa 38 
                                       ++W++++ g+++s+pa+++g+v++g++     G++y+ D 
  gi|386002047|ref|YP_005920346.1| 190 EIWNFTVEGAAQSTPAIADGRVVFGAWewglGGKIYCADL 229
                                       89**********************************9775 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 5.7e-09
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg....dGtlyAlD 37 
                                       G ++Ws q+     +s+av +g+vy++t+    +G l Al 
  gi|386002047|ref|YP_005920346.1| 232 GSEIWSIQTENSPCGSAAVHDGTVYMTTYnfngNGDLLALS 272
                                       889*******9889***********************9996 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 2.1e-07
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg.....dGtlyAlDaet 40 
                                       G +lW++++  p+ s+p++++g+vyv +g       + yA++a+t
  gi|386002047|ref|YP_005920346.1| 276 GSLLWRREIS-PTDSTPTLAEGKVYVCGGvegfsSSKTYAFEAAT 319
                                       889******9.899**************************99998 PP

  == domain 7  score: 24.0 bits;  conditional E-value: 1.3e-08
                             PQQ_3   1 GevlWsv....qlpgpvnsspavdgglvyvgtg....dGtlyAlDaet 40 
                                       Ge++W++    +++ +  +s+a+++glv+vg +     G+ +AlDa+t
  gi|386002047|ref|YP_005920346.1| 320 GELVWETdeaeKIG-DWRCSMAYADGLVFVGRPdfddFGGTVALDAAT 366
                                       99*****5554444.677****************************98 PP

  == domain 8  score: 21.4 bits;  conditional E-value: 8.4e-08
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       G+v+Ws++ +g   sspav+++ v++++  G++yA+
  gi|386002047|ref|YP_005920346.1| 367 GKVVWSHPGGG---SSPAVADRMVFTVGK-GRVYAF 398
                                       9*******554...79************8.*****9 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.3   7.1e-13   2.1e-09       9     127 ..      58     172 ..      52     174 .. 0.84
   2 !   75.3   0.3   1.8e-24   5.3e-21       6     183 ..     137     305 ..     132     312 .. 0.87
   3 !   40.7   0.6   6.8e-14     2e-10       6      91 ..     313     398 ..     308     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 7.1e-13
                             PQQ_2   9 daatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettl..egpvvga...plvaegrvv 80 
                                       +++t  +lW+ +++ + g+ v   v ++g +fv    +++vald  tG+ +W + +  +g v+ +   p  ++gr++
  gi|386002047|ref|YP_005920346.1|  58 APRTNHTLWTREIGAQAGSSV--SV-AEGLVFVN-CVDEIVALDQGTGETIWAAPFerNGDVCCSwftPVYSDGRLY 130
                                       578999*****9966666666..78.*******6.********************96666666669*9********9 PP

                             PQQ_2  81 vvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvv 127
                                       +   + +   l+a++G++ Ws++  s+     ++++spav++++v++
  gi|386002047|ref|YP_005920346.1| 131 FS--GMETKCLNATTGEEIWSFAPPSGR---GAVDGSPAVEDGKVIA 172
                                       99..568889***********7666644...4559999999988886 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.8e-24
                             PQQ_2   6 saldaatGaelWrvdlarp.....lgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                       ++l+a+tG+e+W++ +  p      +g +  av +g+++++  +g    +l+ a+ +++W++t+eg ++++p +a+g
  gi|386002047|ref|YP_005920346.1| 137 KCLNATTGEEIWSFAP--PsgrgaVDGSP--AVEDGKVIASDWDGHHYRCLEEASEREIWNFTVEGAAQSTPAIADG 209
                                       5799**********55..22234489999..9988888888889********************************* PP

                             PQQ_2  78 rvvvva....sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvges....sgklvaldpkdGkvlW 146
                                       rvv+ a     +g ++  d e G + Ws+q ++++       +s av+++tv++ +     +g+l al+++dG++lW
  gi|386002047|ref|YP_005920346.1| 210 RVVFGAwewgLGGKIYCADLEEGSEIWSIQTENSP------CGSAAVHDGTVYMTTYnfngNGDLLALSLSDGSLLW 280
                                       ******9998888***************9999944......44688888888888888888**************** PP

                             PQQ_2 147 erelaaprgtselsrvgdisgrpvvaegtVyassgqg 183
                                        re++ +             ++p++aeg+Vy+++g +
  gi|386002047|ref|YP_005920346.1| 281 RREISPTD------------STPTLAEGKVYVCGGVE 305
                                       **997766............9************9876 PP

  == domain 3  score: 40.7 bits;  conditional E-value: 6.8e-14
                             PQQ_2   6 saldaatGaelWrvdlarp.lgggvsravlsggtlfva....tgggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                       +a++aatG+++W++d a++  ++  s a+ ++g +fv+    +++g  valdaatGkv+W+    g   ++p va+ 
  gi|386002047|ref|YP_005920346.1| 313 YAFEAATGELVWETDEAEKiGDWRCSMAY-ADGLVFVGrpdfDDFGGTVALDAATGKVVWSHPGGG---SSPAVADR 385
                                       79************996644555555599.********99999******************99444...588***** PP

                             PQQ_2  78 rvvvvasdgqlial 91 
                                       +v+ v ++g+++a+
  gi|386002047|ref|YP_005920346.1| 386 MVFTV-GKGRVYAF 398
                                       **999.57777765 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.64   1.9e+03      18      35 ..      60      77 ..      60      79 .. 0.81
   2 !    7.9   0.0     0.001       3.1       1      26 [.      83     107 ..      83     108 .. 0.88
   3 !   15.4   0.0   4.3e-06     0.013      13      30 ..     137     154 ..     132     158 .. 0.86
   4 ?    1.3   0.0      0.12   3.7e+02      22      37 ..     190     205 ..     189     206 .. 0.90
   5 !    9.5   0.0   0.00033      0.98       9      30 ..     221     242 ..     217     249 .. 0.89
   6 !   12.2   0.0   4.3e-05      0.13       9      33 ..     265     289 ..     253     294 .. 0.86
   7 !   12.1   0.1   4.9e-05      0.15      11      28 ..     311     328 ..     304     335 .. 0.84
   8 !   16.6   0.0   1.9e-06    0.0056      11      27 ..     358     374 ..     355     381 .. 0.87
   9 ?   -0.8   0.0       0.6   1.8e+03       3      15 ..     386     398 ..     384     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.64
                                      TTCCEEEEEESSSCGSSE CS
                               PQQ 18 dTGkvlWrfktggpvlsl 35
                                      +T+  lW+ ++g+   s+
  gi|386002047|ref|YP_005920346.1| 60 RTNHTLWTREIGAQAGSS 77
                                      58999***9999877665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.001
                                       TEEEEEETTSEEEEEETTTCCEEEEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrf 26 
                                       g v++ + d  ++AlD  TG+ +W  
  gi|386002047|ref|YP_005920346.1|  83 GLVFVNCVD-EIVALDQGTGETIWAA 107
                                       568888999.9*************75 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 4.3e-06
                                       EEEETTTCCEEEEEESSS CS
                               PQQ  13 yAlDadTGkvlWrfktgg 30 
                                         l+a+TG+++W+f +++
  gi|386002047|ref|YP_005920346.1| 137 KCLNATTGEEIWSFAPPS 154
                                       579***********9987 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.12
                                       EEEEEESSSCGSSESE CS
                               PQQ  22 vlWrfktggpvlslpi 37 
                                       ++W f ++g+ +s+p+
  gi|386002047|ref|YP_005920346.1| 190 EIWNFTVEGAAQSTPA 205
                                       89***********996 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.00033
                                       TSEEEEEETTTCCEEEEEESSS CS
                               PQQ   9 dGylyAlDadTGkvlWrfktgg 30 
                                       +G++y  D++ G ++W+ +t++
  gi|386002047|ref|YP_005920346.1| 221 GGKIYCADLEEGSEIWSIQTEN 242
                                       79***************99986 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 4.3e-05
                                       TSEEEEEETTTCCEEEEEESSSCGS CS
                               PQQ   9 dGylyAlDadTGkvlWrfktggpvl 33 
                                       +G l+Al +++G +lWr ++++ + 
  gi|386002047|ref|YP_005920346.1| 265 NGDLLALSLSDGSLLWRREISPTDS 289
                                       899****************999876 PP

  == domain 7  score: 12.1 bits;  conditional E-value: 4.9e-05
                                       EEEEEETTTCCEEEEEES CS
                               PQQ  11 ylyAlDadTGkvlWrfkt 28 
                                       + yA+ a+TG+++W++++
  gi|386002047|ref|YP_005920346.1| 311 KTYAFEAATGELVWETDE 328
                                       67*************986 PP

  == domain 8  score: 16.6 bits;  conditional E-value: 1.9e-06
                                       EEEEEETTTCCEEEEEE CS
                               PQQ  11 ylyAlDadTGkvlWrfk 27 
                                         +AlDa+TGkv+W+++
  gi|386002047|ref|YP_005920346.1| 358 GTVALDAATGKVVWSHP 374
                                       578***********986 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 0.6
                                       EEEEETTSEEEEE CS
                               PQQ   3 vylgsadGylyAl 15 
                                       ++ +   G++yA+
  gi|386002047|ref|YP_005920346.1| 386 MVFTVGKGRVYAF 398
                                       5556678*****8 PP

>> Kelch_2  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.94   2.8e+03       8      18 ..     123     133 ..     116     134 .. 0.87
   2 ?   -2.2   0.0       1.6   4.7e+03       2      16 ..     243     257 ..     242     257 .. 0.86
   3 !    8.1   0.0   0.00088       2.6      11      31 ..     295     313 ..     288     330 .. 0.70
   4 !    5.5   0.0     0.006        18       5      20 ..     386     401 ..     384     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.94
                           Kelch_2   8 svpggkiyvvG 18 
                                       ++++g++y+ G
  gi|386002047|ref|YP_005920346.1| 123 VYSDGRLYFSG 133
                                       688*****988 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                           Kelch_2   2 rgghsssvpggkiyv 16 
                                       + + s++v +g +y+
  gi|386002047|ref|YP_005920346.1| 243 SPCGSAAVHDGTVYM 257
                                       67999******9996 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00088
                           Kelch_2  11 ggkiyvvGGahtdnpnlsssd 31 
                                       +gk+yv+GG+   ++++s   
  gi|386002047|ref|YP_005920346.1| 295 EGKVYVCGGV--EGFSSSKTY 313
                                       79********..555555444 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.006
                           Kelch_2   5 hsssvpggkiyvvGGa 20 
                                       ++++v+ g++y +GGa
  gi|386002047|ref|YP_005920346.1| 386 MVFTVGKGRVYAFGGA 401
                                       678999*********9 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.33   9.8e+02      70      83 .]      92     105 ..      90     105 .. 0.93
   2 ?    4.0   0.0     0.015        45      40      83 .]     240     280 ..     223     280 .. 0.73
   3 ?    4.3   0.0     0.012        37      62      83 .]     350     371 ..     310     371 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.33
                           DUF4905  70 gliaiDiktgkllW 83 
                                       +++a+D  tg+++W
  gi|386002047|ref|YP_005920346.1|  92 EIVALDQGTGETIW 105
                                       69************ PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.015
                           DUF4905  40 eekwwtgleaiykgvlllhkyekpdsPehkgliaiDiktgkllW 83 
                                        e+  +g +a+ +g++++  y+ +    + +l+a+ +  g llW
  gi|386002047|ref|YP_005920346.1| 240 TENSPCGSAAVHDGTVYMTTYNFNG---NGDLLALSLSDGSLLW 280
                                       455568999************9776...4689999999999998 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.012
                           DUF4905  62 kpdsPehkgliaiDiktgkllW 83 
                                       +pd  +  g +a+D+ tgk++W
  gi|386002047|ref|YP_005920346.1| 350 RPDFDDFGGTVALDAATGKVVW 371
                                       6777778899************ PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.43   1.3e+03      10      16 ..     220     226 ..     219     227 .. 0.86
   2 ?   -0.3   0.1      0.27   8.1e+02       5      15 ..     246     256 ..     244     256 .. 0.88
   3 ?    6.4   0.0    0.0022       6.6      12      22 ..     296     306 ..     291     315 .. 0.81
   4 ?    4.9   0.3    0.0067        20       6      19 ..     387     400 ..     385     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.43
                                       ETTEEEE CS
                           Kelch_1  10 vggkiYv 16 
                                       +ggkiY+
  gi|386002047|ref|YP_005920346.1| 220 LGGKIYC 226
                                       69****9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                                       EEEEEETTEEE CS
                           Kelch_1   5 agavvvggkiY 15 
                                        +a+v++g +Y
  gi|386002047|ref|YP_005920346.1| 246 GSAAVHDGTVY 256
                                       689*******9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0022
                                       TEEEEEEEBCS CS
                           Kelch_1  12 gkiYviGGsdg 22 
                                       gk+Yv+GG  g
  gi|386002047|ref|YP_005920346.1| 296 GKVYVCGGVEG 306
                                       9*******987 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0067
                                       EEEEETTEEEEEEE CS
                           Kelch_1   6 gavvvggkiYviGG 19 
                                       +++v  g++Y++GG
  gi|386002047|ref|YP_005920346.1| 387 VFTVGKGRVYAFGG 400
                                       678999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2648.90
//
Query:       gi|386002048|ref|YP_005920347.1|  [L=428]
Description: Pyrrolo-quinoline quinone [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-38  130.9  27.7    5.4e-06   26.7   0.4    8.3  8  PQQ_3     PQQ-like domain
    3.1e-38  131.7   4.2    8.1e-20   71.4   0.3    4.0  4  PQQ_2     PQQ-like domain
    5.6e-17   60.8  15.3    8.8e-05   22.3   0.1    7.8  9  PQQ       PQQ enzyme repeat
    0.00099   19.3   2.4       0.87   10.0   0.0    4.7  4  Kelch_6   Kelch motif
  ------ inclusion threshold ------
       0.15   12.1   1.3         24    4.9   0.1    3.3  3  SUKH-4    SUKH-4 immunity protein


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.1e-06    0.0039       3      40 .]      49      85 ..      48      85 .. 0.88
   2 !   26.7   0.4   1.5e-09   5.4e-06       1      40 []      86     127 ..      86     127 .. 0.92
   3 !    6.0   0.0    0.0049        18       1      31 [.     128     159 ..     128     171 .. 0.84
   4 !   26.1   0.5   2.4e-09   8.6e-06       1      40 []     174     215 ..     174     215 .. 0.96
   5 !    7.3   0.1     0.002         7       9      29 ..     236     256 ..     233     276 .. 0.81
   6 !   16.7   1.0   2.1e-06    0.0077       5      39 ..     281     318 ..     279     319 .. 0.87
   7 !   20.8   0.0   1.1e-07   0.00039       1      37 [.     320     362 ..     320     364 .. 0.84
   8 !   24.0   0.0   1.1e-08   3.9e-05       3      36 ..     370     405 ..     369     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                             PQQ_3  3 vlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                      +lWs +l  +v  +p v++g vyv +gdGtl +lD et
  gi|386002048|ref|YP_005920347.1| 49 ILWSCDLI-RVDIPPIVADGSVYVLAGDGTLSSLDGET 85
                                      67888887.777789********************887 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.5e-09
                             PQQ_3   1 GevlWsvqlpgpvn..sspavdgglvyvgtgdGtlyAlDaet 40 
                                       G+++W+ q+ g v   s+pa++gg++ ++t+ G l ++Da+t
  gi|386002048|ref|YP_005920347.1|  86 GDLRWEAQTEGWVFqtSTPALAGGRILAATDSGDLASFDAQT 127
                                       99*********55555999*********************98 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0049
                             PQQ_3   1 GevlWsvqlpgpvnssp.avdgglvyvgtgdG 31 
                                       Ge++W++ l ++    p +  +gl+y g g G
  gi|386002048|ref|YP_005920347.1| 128 GEEVWTRHLTDRRFEVPiTCFDGLIYLGEGSG 159
                                       99********95555554889******98866 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 2.4e-09
                             PQQ_3   1 GevlWsv..qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge++W+   ++ g+ ++++av+g++++ g+ dG l ++D +t
  gi|386002048|ref|YP_005920347.1| 174 GEEVWNLsrDTTGYMGCGAAVAGDYLVYGSNDGLLLCVDRKT 215
                                       99*****998899**************************988 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.002
                             PQQ_3   9 lpgpvnsspavdgglvyvgtg 29 
                                        pg++ +s+ + +g vy++++
  gi|386002048|ref|YP_005920347.1| 236 DPGRIRASVSYKDGSVYTTSE 256
                                       599***************998 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 2.1e-06
                             PQQ_3   5 Wsvqlpgpvnsspavdgglvyvgtg....dGtlyAlDae 39 
                                       Ws +++   +s+pav++g+vy g g     G l++lD  
  gi|386002048|ref|YP_005920347.1| 281 WSSSVGF-STSTPAVYDGRVYLGVGehgyPGALTCLDDS 318
                                       7777775.4599*************************65 PP

  == domain 7  score: 20.8 bits;  conditional E-value: 1.1e-07
                             PQQ_3   1 GevlWsvqlpgpvnsspavd.....gglvyvgtg.dGtlyAlD 37 
                                       G+++Ws+++ + v+ssp+++      ++v++++  +G++y+++
  gi|386002048|ref|YP_005920347.1| 320 GDLIWSYPVEAGVKSSPVISaagesPRIVFTAARvNGSIYCIE 362
                                       99***************66544443478999999*******96 PP

  == domain 8  score: 24.0 bits;  conditional E-value: 1.1e-08
                             PQQ_3   3 vlWsv..qlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       +lW++  q +g++ +++av++g+vy+gt+ G ly+l
  gi|386002048|ref|YP_005920347.1| 370 LLWRFdpQDDGYILAGAAVSEGRVYFGTEKGILYCL 405
                                       89***998899************************9 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.3   2.3e-23   8.1e-20      57     231 ..      48     216 ..      41     217 .. 0.82
   2 !   48.9   0.1   1.6e-16   5.9e-13      30     180 ..     102     255 ..     100     259 .. 0.81
   3 !   24.0   0.1   7.1e-09   2.5e-05      14      75 ..     278     339 ..     247     352 .. 0.78
   4 !    8.8   0.0   0.00031       1.1       3      52 ..     356     406 ..     354     410 .. 0.73

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 2.3e-23
                             PQQ_2  57 kvlWettl.egpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessg 132
                                       ++lW+ +l +  v  +p va+g v+v a+dg+l+ ld e+G++ W+ q ++     + ++++pa+ag+++++++ sg
  gi|386002048|ref|YP_005920347.1|  48 RILWSCDLiR--VDIPPIVADGSVYVLAGDGTLSSLDGETGDLRWEAQTEG----WVFQTSTPALAGGRILAATDSG 118
                                       6777777733..45789*****************************55555....599******************* PP

                             PQQ_2 133 klvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgqgr......llaldlatgrrlw..skei 201
                                       +l+ +d+++G+++W r l++ r           +   +  +g +y  +g+gr        +ld    + +w  s++ 
  gi|386002048|ref|YP_005920347.1| 119 DLASFDAQTGEEVWTRHLTDRR----------FEVPITCFDGLIYLGEGSGRgrgekrYFCLDEDGEE-VWnlSRDT 184
                                       ******************8855..........3445555589********965555557888666555.67557779 PP

                             PQQ_2 202 ssinglp.ildgdllyvvsa.gelialdratG 231
                                       ++++g+  +++gd+l+++s+ g l+++dr+tG
  gi|386002048|ref|YP_005920347.1| 185 TGYMGCGaAVAGDYLVYGSNdGLLLCVDRKTG 216
                                       99999962689********55**********9 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 1.6e-16
                             PQQ_2  30 sravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgap.lvaegrvvvva......sdgqlialdaedGkrl 99 
                                       s++ l+gg++++at++g l+++da tG+++W++ l+ +  + p +  +g +++        +++++  ld edG+++
  gi|386002048|ref|YP_005920347.1| 102 STPALAGGRILAATDSGDLASFDAQTGEEVWTRHLTDRRFEVPiTCFDGLIYLGEgsgrgrGEKRYFCLD-EDGEEV 177
                                       56888******************************666555555***********6665544448888**.****** PP

                             PQQ_2 100 WstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgtselsrvgdisgrpvvaegt 175
                                       W+  ++++  +        avagd++v g  +g l ++d k+G++ +  +l    r + + s  g+i +++  ++g+
  gi|386002048|ref|YP_005920347.1| 178 WNLSRDTTGYMG----CGAAVAGDYLVYGSNDGLLLCVDRKTGDLSDILNLsDGSRIGFAASDPGRIRASVSYKDGS 250
                                       **6666644444....6667789**********************99999966666666666777788887777778 PP

                             PQQ_2 176 Vyass 180
                                       Vy  s
  gi|386002048|ref|YP_005920347.1| 251 VYTTS 255
                                       88765 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 7.1e-09
                             PQQ_2  14 aelWrvdlarplgggvsravlsggtlfva....tgggrlvaldaatGkvlWettlegpvvgaplva 75 
                                       ++ W++++  ++++ +  + + +g+++ +    ++ g l++ld +tG ++W++ +e+ v+++p ++
  gi|386002048|ref|YP_005920347.1| 278 NLGWSSSV--GFSTST--PAVYDGRVYLGvgehGYPGALTCLDDSTGDLIWSYPVEAGVKSSPVIS 339
                                       34566655..455555..888999999999888899***********************9999765 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.00031
                             PQQ_2   3 gvvsaldaa..tGaelWrvdlarplgggvsravlsggtlfvatgggrlvald 52 
                                       g++++++      ++lWr+d+++  g ++++a +s+g+++ +t++g l++l+
  gi|386002048|ref|YP_005920347.1| 356 GSIYCIEDGgsEPRLLWRFDPQD-DGYILAGAAVSEGRVYFGTEKGILYCLS 406
                                       6666666532233689***9965.4566666666****************97 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   2.4e-08   8.8e-05       1      32 [.      67      98 ..      67     104 .. 0.94
   2 !   13.1   0.0     2e-05     0.071       1      26 [.     109     134 ..     108     140 .. 0.84
   3 ?    1.4   0.0     0.097   3.5e+02      14      24 ..     169     178 ..     168     179 .. 0.88
   4 !    5.9   0.1    0.0038        14       4      21 ..     200     217 ..     198     218 .. 0.90
   5 ?   -1.7   0.0      0.91   3.3e+03       4      14 ..     232     242 ..     230     242 .. 0.87
   6 ?   -3.8   0.1       4.2   1.5e+04       8      13 ..     295     300 ..     294     301 .. 0.84
   7 !   20.8   0.0   7.1e-08   0.00026       5      37 ..     305     337 ..     302     338 .. 0.91
   8 ?   -3.7   0.0       4.1   1.5e+04       5      14 ..     350     360 ..     347     361 .. 0.70
   9 ?    0.3   0.0      0.22   7.9e+02      22      30 ..     370     378 ..     369     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.4e-08
                                      TEEEEEETTSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ  1 gvvylgsadGylyAlDadTGkvlWrfktggpv 32
                                      g vy+   dG+l  lD +TG+++W+ +t+g+v
  gi|386002048|ref|YP_005920347.1| 67 GSVYVLAGDGTLSSLDGETGDLRWEAQTEGWV 98
                                      689**************************987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2e-05
                                       TEEEEEETTSEEEEEETTTCCEEEEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrf 26 
                                       g++ ++++ G l  +Da TG+++W+ 
  gi|386002048|ref|YP_005920347.1| 109 GRILAATDSGDLASFDAQTGEEVWTR 134
                                       455666******************86 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.097
                                       EEETTTCCEEE CS
                               PQQ  14 AlDadTGkvlW 24 
                                        lD ++G+++W
  gi|386002048|ref|YP_005920347.1| 169 CLD-EDGEEVW 178
                                       689.9****** PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0038
                                       EEEETTSEEEEEETTTCC CS
                               PQQ   4 ylgsadGylyAlDadTGk 21 
                                       ++gs+dG l+ +D++TG+
  gi|386002048|ref|YP_005920347.1| 200 VYGSNDGLLLCVDRKTGD 217
                                       678**************8 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 0.91
                                       EEEETTSEEEE CS
                               PQQ   4 ylgsadGylyA 14 
                                       +++s++G+++A
  gi|386002048|ref|YP_005920347.1| 232 FAASDPGRIRA 242
                                       6789*****98 PP

  == domain 6  score: -3.8 bits;  conditional E-value: 4.2
                                       TTSEEE CS
                               PQQ   8 adGyly 13 
                                       +dG++y
  gi|386002048|ref|YP_005920347.1| 295 YDGRVY 300
                                       799998 PP

  == domain 7  score: 20.8 bits;  conditional E-value: 7.1e-08
                                       EEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   5 lgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                        + ++G l  lD +TG+++W++++++ v s+p+
  gi|386002048|ref|YP_005920347.1| 305 EHGYPGALTCLDDSTGDLIWSYPVEAGVKSSPV 337
                                       57899**************************97 PP

  == domain 8  score: -3.7 bits;  conditional E-value: 4.1
                                       EE.ETTSEEEE CS
                               PQQ   5 lg.sadGylyA 14 
                                        +   +G +y 
  gi|386002048|ref|YP_005920347.1| 350 TAaRVNGSIYC 360
                                       55578999996 PP

  == domain 9  score: 0.3 bits;  conditional E-value: 0.22
                                       EEEEEESSS CS
                               PQQ  22 vlWrfktgg 30 
                                       +lWrf++++
  gi|386002048|ref|YP_005920347.1| 370 LLWRFDPQD 378
                                       578888776 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.078   2.8e+02       9      23 ..      64      78 ..      63     104 .. 0.69
   2 ?    1.2   0.0      0.14     5e+02       7      38 ..     145     175 ..     140     186 .. 0.79
   3 ?    1.1   0.2      0.15   5.3e+02       8      26 ..     293     308 ..     285     326 .. 0.71
   4 !   10.0   0.0   0.00024      0.87       9      38 ..     353     379 ..     345     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.078
                           Kelch_6  9 svggkiYifGGytds 23
                                      +++g++Y++ G +  
  gi|386002048|ref|YP_005920347.1| 64 VADGSVYVLAGDGTL 78
                                      7899*****998764 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                           Kelch_6   7 lvsvggkiYifGGytdsspylnkvwvydpetk 38 
                                       +++ +g iY+  G++  +   ++++++d +  
  gi|386002048|ref|YP_005920347.1| 145 ITCFDGLIYLGEGSGR-GRGEKRYFCLDEDGE 175
                                       67899******99999.788889999887665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.15
                           Kelch_6   8 vsvggkiYifGGytdsspy 26 
                                       ++++g++Y+  G  +   y
  gi|386002048|ref|YP_005920347.1| 293 AVYDGRVYLGVGEHG---Y 308
                                       67*******999877...3 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00024
                           Kelch_6   9 svggkiYif..GGytdsspylnkvwvydpetk 38 
                                        v+g+iY++  GG+       + +w++dp+++
  gi|386002048|ref|YP_005920347.1| 353 RVNGSIYCIedGGSEP-----RLLWRFDPQDD 379
                                       489*************.....********975 PP

>> SUKH-4  SUKH-4 immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.015        55      73     103 ..     148     184 ..     120     194 .. 0.82
   2 ?    4.9   0.1    0.0067        24      70      95 ..     192     217 ..     184     229 .. 0.91
   3 ?   -0.6   0.0      0.34   1.2e+03      77     100 ..     299     326 ..     282     358 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                            SUKH-4  73 aggllvLGal......esaslvldpgtGaVlavdlee 103
                                        +gl+ LG+       e+++++ld++  +V+ +++++
  gi|386002048|ref|YP_005920347.1| 148 FDGLIYLGEGsgrgrgEKRYFCLDEDGEEVWNLSRDT 184
                                       5678888888888899****************99986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0067
                            SUKH-4  70 paeaggllvLGalesaslvldpgtGa 95 
                                       +a ag++lv G+ ++  l++d++tG 
  gi|386002048|ref|YP_005920347.1| 192 AAVAGDYLVYGSNDGLLLCVDRKTGD 217
                                       6889********************95 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.34
                            SUKH-4  77 lvLGal....esaslvldpgtGaVlavd 100
                                       + LG      ++a  +ld+ tG  ++  
  gi|386002048|ref|YP_005920347.1| 299 VYLGVGehgyPGALTCLDDSTGDLIWSY 326
                                       444444448899999******9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2908.39
//
Query:       gi|386002049|ref|YP_005920348.1|  [L=1854]
Description: hypothetical protein Mhar_1361 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-29  101.9   0.0    6.6e-06   26.3   0.0    5.6  4  DUF11            Domain of unknown function DUF11
    1.1e-13   50.6   0.4    5.8e-06   25.9   0.0    4.3  4  Prenyltrans      Prenyltransferase and squalene oxidase repea
    1.6e-10   40.6   2.3    1.7e-05   24.1   2.7    2.9  3  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
    3.9e-08   32.7   0.0     0.0018   17.5   0.0    2.5  2  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
    6.1e-06   26.4   0.3        7.1    7.0   0.0    5.3  5  Chlam_OMP6       Chlamydia cysteine-rich outer membrane prote
      3e-05   24.2  22.1    0.00085   19.6   0.1    5.7  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.3e-05   24.4   0.0       0.67   10.6   0.0    3.2  2  DUF4430          Domain of unknown function (DUF4430)
     0.0038   17.1  13.3       0.42   10.5   1.3    4.1  3  PEGA             PEGA domain
  ------ inclusion threshold ------
       0.11   12.7   1.2       0.96    9.6   0.0    3.1  4  Top6b_C          Type 2 DNA topoisomerase 6 subunit B C-termi


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.3e-09   6.6e-06       1      89 [.     965    1057 ..     965    1059 .. 0.78
   2 !   17.9   0.0   1.5e-06    0.0029       1      51 [.    1089    1140 ..    1089    1289 .. 0.79
   3 !   24.6   0.0   1.1e-08   2.3e-05      17      79 ..    1588    1653 ..    1581    1663 .. 0.89
   4 !   24.9   0.1   9.2e-09   1.8e-05      15      82 ..    1711    1780 ..    1694    1786 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.3e-09
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlP..aglayvsvsas...qgtasaltsv.gsLeages 69  
                                        +tK  ++  ++pG+ ++yt+t  N  p ++++v++ D lP  ++++y             + +++   ++++g+ 
  gi|386002049|ref|YP_005920348.1|  965 VTKKAENNSANPGEILNYTITICNDCPYALTDVQIADDLPeeSSFEYA--DPWpnsADGDHLEWNLpDEIPPGGC 1037
                                        689999999*******************************55444443..3222223356677787999999999 PP

                             DUF11   70 atlsftvrvtrtaasgaltn 89  
                                          ++++v+v+ ++ s +l n
  gi|386002049|ref|YP_005920348.1| 1038 EVINLRVKVNDKPPSAILEN 1057
                                        99999999998877655555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.5e-06
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasa.ngvvvtDtlPaglayvsvsas 51  
                                        +tKt dk+ v  G +v+y + v N +++ + ++v+v+D     ++++++  +
  gi|386002049|ref|YP_005920348.1| 1089 VTKTADKESVERGKKVKYKIEVYNIYAVESlKEVTVKDAFSRDVEFITADPA 1140
                                        79*************************9888*********777776665544 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 1.1e-08
                             DUF11   17 tytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvt 79  
                                        +y++t++N g++++  + ++D+ P+g ++v +s +    ++ sa++++ +L  g+ +++++ + v+
  gi|386002049|ref|YP_005920348.1| 1588 RYNITLKNDGNRALGPLAIRDLFPPGARFVNASERttgLSNESAEWTFLNLGLGGVLRITLWLDVS 1653
                                        7*******************************9998777788899999999999999998887776 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 9.2e-09
                             DUF11   15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsvgsLeagesatlsftvrvtrta 82  
                                         vtyt+t +N g +s   + vtD+lP ++++  +s +       + ++++  +L + e  t+ + +++ r +
  gi|386002049|ref|YP_005920348.1| 1711 VVTYTVTIQNLGEDSK-VAAVTDILPDSMRFLDSSPKpssvD-GNAVTWTLIDLGPYEAETIVYGAEALRGG 1780
                                        79*************9.9****************99977633.34466777999999999999999887766 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.9e-09   5.8e-06       2      21 ..      57      76 ..      56      97 .. 0.88
   2 !    8.5   0.2   0.00084       1.7       8      21 ..     195     208 ..     191     227 .. 0.90
   3 !    9.8   0.0   0.00031      0.62       4      23 ..     239     258 ..     237     269 .. 0.84
   4 ?    0.4   0.0      0.29   5.8e+02      10      18 ..     297     305 ..     294     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                                      HHHHHHHHHHHHSHTTS-BB CS
                       Prenyltrans  2 dvekavefLlscQnedGGwg 21
                                       ++kav +LlscQnedGG+g
  gi|386002049|ref|YP_005920348.1| 57 AIRKAVSYLLSCQNEDGGFG 76
                                      689****************9 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00084
                                       HHHHHHSHTTS-BB CS
                       Prenyltrans   8 efLlscQnedGGwg 21 
                                        +++s+Q+ +GGwg
  gi|386002049|ref|YP_005920348.1| 195 SYIKSKQHSSGGWG 208
                                       7************8 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHSHTTS-BBSS CS
                       Prenyltrans   4 ekavefLlscQnedGGwggr 23 
                                       + a+ ++++ Qn+dGG+ ++
  gi|386002049|ref|YP_005920348.1| 239 QDALGYIRREQNDDGGFPSS 258
                                       67899************876 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.29
                                       HHHHSHTTS CS
                       Prenyltrans  10 LlscQnedG 18 
                                       LlscQ+++G
  gi|386002049|ref|YP_005920348.1| 297 LLSCQQKSG 305
                                       8*****999 PP

>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.8e-05     0.057     205     232 ..      54      81 ..      41     118 .. 0.85
   2 !    8.3   0.3   0.00056       1.1     162     227 ..     147     208 ..     142     213 .. 0.81
   3 !   24.1   2.7   8.3e-09   1.7e-05     160     294 ..     189     319 ..     173     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                       TSHHHHHHHHHHHTT--TTSSBB--GGG CS
                   SQHop_cyclase_C 205 eepvirkavdWlksvqnedGGWGesaes 232
                                       e+p+irkav++l s qnedGG+G++ ++
  gi|386002049|ref|YP_005920348.1|  54 EDPAIRKAVSYLLSCQNEDGGFGNEPDA 81 
                                       689********************97665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB CS
                   SQHop_cyclase_C 162 kraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavgedleepvirkavdWlksvqnedGGWG 227
                                         +++y+++ +++  + +Gr   + ++    +l +laa+ge  +++  +  ++++ks+q++ GGWG
  gi|386002049|ref|YP_005920348.1| 147 VAGIDYVERLKDKAKPPYGR---ENLFSESYILLGLAAAGEAGSAE-AQAFASYIKSKQHSSGGWG 208
                                       56788888888888888888...5689999999****999887655.4667899***********9 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 8.3e-09
                                       HHHHHHHHHHHHS-TTS----SSBSSHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--GGGGT-G CS
                   SQHop_cyclase_C 160 alkraveylkkeqepdGsWfGrWGvnyiyGtwsvlsalaavgedleepvirkavdWlksvqnedGGWGesaesykdp 236
                                        ++   +y+k++q+++G W    G+  +  t    sal a+ged + + i+ a+ ++++ qn+dGG+  s  s    
  gi|386002049|ref|YP_005920348.1| 189 EAQAFASYIKSKQHSSGGWGWGGGAPDLDTTGIGASALLAAGEDPAGQRIQDALGYIRREQNDDGGFPSSGMSP--- 262
                                       4455678************55568999****************************************9887774... PP

                                       GGTT-SSBBHHHHHHHHHHHHHTTGGGSH...HHHHHHHHHHHH--TTS-..----S--EEEE CS
                   SQHop_cyclase_C 237 klagkgestasqtaWallallaagevese...avkrGiaylletqkedGt..WeeeaytgtGf 294
                                              s a +  Wa++a  aag    e   + +  +++ll++q++ G   W+ ++  g+Gf
  gi|386002049|ref|YP_005920348.1| 263 ------DSNAISDYWAMMASNAAGVNPAEwgkERETPVSHLLSCQQKSGVfwWKPDSQGGAGF 319
                                       ......45667778********9987654211556689**********965466677778888 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.9e-05     0.058      46      89 ..      57     101 ..      50     107 .. 0.90
   2 !   17.5   0.0   8.9e-07    0.0018      31     106 ..     173     248 ..     167     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                   SQHop_cyclase_N  46 eeekiakylrsqqredGgWelypggp.gdlsttveaYlALkllGd 89 
                                        ++k++ yl+s q+edGg++  p+ + + l  t +a +AL l+Gd
  gi|386002049|ref|YP_005920348.1|  57 AIRKAVSYLLSCQNEDGGFGNEPDAArSSLMPTANAAMALALTGD 101
                                       57899******************99889****************8 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.9e-07
                   SQHop_cyclase_N  31 eyillrefl.geddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGdspdapalarArefilar 106
                                        yill     ge  ++e++++a y+ s+q++ GgW+   gg+ dl tt     AL  +G +p  ++++ A  +i+++
  gi|386002049|ref|YP_005920348.1| 173 SYILLGLAAaGEAGSAEAQAFASYIKSKQHSSGGWGW-GGGAPDLDTTGIGASALLAAGEDPAGQRIQDALGYIRRE 248
                                       57888777779999*********************96.68889*****9999*****************99999864 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   2.3e+03      12      50 ..     863     901 ..     852     929 .. 0.70
   2 ?    2.1   0.0      0.12   2.4e+02      28      74 ..     982    1028 ..     958    1046 .. 0.75
   3 !    7.0   0.0    0.0035       7.1      28      87 ..    1106    1171 ..    1091    1175 .. 0.75
   4 !    6.5   0.0    0.0051        10      26      89 ..    1587    1650 ..    1580    1652 .. 0.92
   5 ?    3.0   0.0     0.063   1.3e+02      27      82 ..    1713    1767 ..    1694    1773 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                        Chlam_OMP6  12 veisqavpeyatvgspypieitavgkkdcvdvvitqqlp 50 
                                       +++s   p+   vg p+ i++++       ++v   q  
  gi|386002049|ref|YP_005920348.1| 863 MDVSLHPPDEVVVGDPFKIKVVSEEYDASWNLVTVPQKG 901
                                       567777899999*******99987776666766655554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                        Chlam_OMP6   28 ypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwki 74  
                                        y i i         dv i+++lp e  f  +dp    +   +l w++
  gi|386002049|ref|YP_005920348.1|  982 YTITICNDCPYALTDVQIADDLPEESSFEYADPWPNSADGDHLEWNL 1028
                                        445555555555589******************88766656777875 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0035
                        Chlam_OMP6   28 ypieitavgkkdcv.dvvitqqlpcevefvrsdpastpta.dg....klvwkidrlgqgekskitv 87  
                                        y ie++ +   + + +v + + +  +vef+++dpa      +g     +vw+ d +  g+   it+
  gi|386002049|ref|YP_005920348.1| 1106 YKIEVYNIYAVESLkEVTVKDAFSRDVEFITADPAPIDGYeEGdrfsDIVWTFDEIKPGDFEDITL 1171
                                        7788877766554416888899999**********876531332233699****999999888886 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0051
                        Chlam_OMP6   26 spypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskitvwv 89  
                                        + y i +   g++    + i + +p  + fv++   +t  ++    w+   lg g   +it+w+
  gi|386002049|ref|YP_005920348.1| 1587 ARYNITLKNDGNRALGPLAIRDLFPPGARFVNASERTTGLSNESAEWTFLNLGLGGVLRITLWL 1650
                                        56888888999999999999999****************************************7 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.063
                        Chlam_OMP6   27 pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgek 82  
                                         y + i   g    v   +t+ lp  + f+ s p  +      + w++  lg  e 
  gi|386002049|ref|YP_005920348.1| 1713 TYTVTIQNLGEDSKVA-AVTDILPDSMRFLDSSPKPSSVDGNAVTWTLIDLGPYEA 1767
                                        5888888888766665.5799*************98887777788*9999987665 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.3e-07   0.00085      12      62 ..     486     535 ..     481     559 .. 0.85
   2 !    8.2   0.7    0.0014       2.9      16      64 ..     692     735 ..     671     758 .. 0.79
   3 !    6.6   1.2    0.0048       9.5      13      60 ..     898     940 ..     894     956 .. 0.83
   4 ?    1.4   0.2       0.2     4e+02      14      47 ..    1229    1260 ..    1219    1293 .. 0.78
   5 ?   -2.5   0.2       3.3   6.6e+03      13      35 ..    1710    1732 ..    1704    1732 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.3e-07
                   CarboxypepD_reg  12 apiagatVtvtnadtgtvastttdadGaf.rlrglppgtysvtvsapGyata 62 
                                       ap++gatVtv+  +++++a  ttd+dG+   +++ +pg+y+v++ ++Gy  +
  gi|386002049|ref|YP_005920348.1| 486 APVEGATVTVK--SDTSSADYTTDKDGKTpEITFKEPGEYRVEAKKDGYIDT 535
                                       7**********..78999999******86589999**************665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttdadGaf.rlrglppgtysvtvsapGyatatr 64 
                                       gatVt+       + + tt+adG+   + + ++g+y+v++ +pGy  + +
  gi|386002049|ref|YP_005920348.1| 692 GATVTIG------SETYTTGADGYTpEIMFTTAGEYRVRADKPGYVGTYY 735
                                       5666666......68889999997646778899************87765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0048
                   CarboxypepD_reg  13 piagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGya 60 
                                       p +gatVtv       +++ tt+adG+ +   l+  g+y+v++s+p y 
  gi|386002049|ref|YP_005920348.1| 898 PQKGATVTVG------SKTYTTGADGNTSNITLTWkGEYKVKASKPDYI 940
                                       6789999999......799999****9886656667********99985 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.2
                   CarboxypepD_reg   14 iagatVtvtnadtgtvastttdadGafrlrglpp 47  
                                         a a+V+vt  d gt+ st+   +G++  ++l  
  gi|386002049|ref|YP_005920348.1| 1229 SASANVEVT--DPGTELSTREHGSGSYESEDLVV 1260
                                        5789*****..89**************9888765 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 3.3
                   CarboxypepD_reg   13 piagatVtvtnadtgtvastttd 35  
                                         +   tVt++n +++++  ++td
  gi|386002049|ref|YP_005920348.1| 1710 RVVTYTVTIQNLGEDSKVAAVTD 1732
                                        45566777777666666666665 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00053       1.1      46      70 ..     623     647 ..     622     648 .. 0.93
   2 !   10.6   0.0   0.00034      0.67      45      68 ..     823     846 ..     818     849 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00053
                           DUF4430  46 yevNGepsdvGagsyklkdgdkivf 70 
                                       ++vNG ++ vG ++y l+dgd i+ 
  gi|386002049|ref|YP_005920348.1| 623 FYVNGGQAPVGLDQYLLSDGDWITI 647
                                       99*******************9985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                           DUF4430  45 myevNGepsdvGagsyklkdgdki 68 
                                       +y+v+G++++vG ++y l+dgd i
  gi|386002049|ref|YP_005920348.1| 823 VYYVDGVSPSVGLDQYFLTDGDWI 846
                                       599*******************87 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2   0.00058       1.2       3      47 ..     492     534 ..     481     543 .. 0.79
   2 !   10.5   1.3   0.00021      0.42       6      46 ..     686     731 ..     684     739 .. 0.82
   3 ?    2.9   0.8      0.05        99       9      45 ..     898     939 ..     894     946 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00058
                              PEGA   3 tltirSnpeGatVyidGkylGkTPvtlsleaGnyslrvekeGYed 47 
                                       t+t++S+ + a  + d+   GkTP  +  e+G+y+++ +k+GY d
  gi|386002049|ref|YP_005920348.1| 492 TVTVKSDTSSADYTTDK--DGKTPEITFKEPGEYRVEAKKDGYID 534
                                       56666666666666655..69***7777***************55 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00021
                              PEGA   6 irSnpeGatVyidGkyl..G...kTPvtlsleaGnyslrvekeGYe 46 
                                       ++  ++GatV+i+ +++  G    TP  +   aG+y++r  k+GY 
  gi|386002049|ref|YP_005920348.1| 686 VTVHQQGATVTIGSETYttGadgYTPEIMFTTAGEYRVRADKPGYV 731
                                       556799******998875525559**6666***************6 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.05
                              PEGA   9 npeGatVyidGkylG......kTPvtlsleaGnyslrvekeGY 45 
                                        ++GatV+++ k++        +++tl+  +G+y+++ +k+ Y
  gi|386002049|ref|YP_005920348.1| 898 PQKGATVTVGSKTYTtgadgnTSNITLTW-KGEYKVKASKPDY 939
                                       589******99887444766555667765.8*******99998 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.5   1.5e+04      71      88 ..     677     694 ..     671     697 .. 0.71
   2 ?   -1.3   0.0       1.2   2.3e+03      69      90 ..     884     905 ..     869     913 .. 0.79
   3 ?   -2.3   0.1       2.5     5e+03      28      92 ..    1101    1172 ..    1085    1187 .. 0.61
   4 ?    9.6   0.0   0.00048      0.96      24      92 ..    1704    1773 ..    1699    1781 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.5
                                       SSEEE-EEE---TT-EEE CS
                           Top6b_C  71 neydlkWelsvsageskv 88 
                                       +eyd  W+l    ++ ++
  gi|386002049|ref|YP_005920348.1| 677 EEYDASWNLVTVHQQGAT 694
                                       699999998766555554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                       -SSSEEE-EEE---TT-EEEE- CS
                           Top6b_C  69 mdneydlkWelsvsageskvle 90 
                                       + +eyd  W+l   +++ ++++
  gi|386002049|ref|YP_005920348.1| 884 VSEEYDASWNLVTVPQKGATVT 905
                                       5699******999888877765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                                        SS-EEEEEEE----..-----EEE--EES-----------EE...E-SSSE.EE-EEE.---TT-EEEE--- CS
                           Top6b_C   28 gdgvevslkvkNfs..dkkeefelheilpaeieeaspeakvv...emdney.dlkWel.svsageskvleYs 92  
                                        g+ v+ +++v N    ++ +e+++++ ++ ++e +++++  +   e ++ + d++W+  ++++g+ + ++ +
  gi|386002049|ref|YP_005920348.1| 1101 GKKVKYKIEVYNIYavESLKEVTVKDAFSRDVEFITADPAPIdgyEEGDRFsDIVWTFdEIKPGDFEDITLE 1172
                                        245666777777431256678889999988888888888776222233333366777634666666655555 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00048
                                        E--SSS-.EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EE.E---TT-EEEE--- CS
                           Top6b_C   24 veengdg.vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWe.lsvsageskvleYs 92  
                                        v+en+   v+ +++++N ++ ++   +++ilp +++  + ++k  ++d++  ++W+ + +++ e +++ Y 
  gi|386002049|ref|YP_005920348.1| 1704 VDENDPRvVTYTVTIQNLGEDSKVAAVTDILPDSMRFLDSSPKPSSVDGN-AVTWTlIDLGPYEAETIVYG 1773
                                        667766678999*************************9999*99999998.57787357999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1854 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.98u 0.30s 00:00:01.28 Elapsed: 00:00:00.49
# Mc/sec: 11400.97
//
Query:       gi|386002050|ref|YP_005920349.1|  [L=134]
Description: hypothetical protein Mhar_1362 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-26   89.6   0.0    1.6e-25   88.9   0.0    1.4  1  Fer4_19   Divergent 4Fe-4S mono-cluster
    1.9e-16   60.0   0.4    3.6e-16   59.1   0.4    1.5  1  zf-CDGSH  Iron-binding zinc finger CDGSH type
  ------ inclusion threshold ------
      0.082   13.5   0.1       0.36   11.4   0.1    1.9  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.16   12.1   1.8       0.51   10.5   0.0    2.6  3  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   3.6e-29   1.6e-25       1      63 [.       4      66 ..       4      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 3.6e-29
                           Fer4_19  1 yegeeitiednrelCihsgnCvkglpevFdpkrkpwikpdeasteeiievverCPSGALsyve 63
                                      y++ eit+ +++e Cih+++C +glp+vF+p++ pw++ ++a+ +ei+++++rCPSGALsy +
  gi|386002050|ref|YP_005920349.1|  4 YTNGEITVFWDPERCIHAAECLRGLPGVFNPQKSPWVDMEGATSDEIMAAIDRCPSGALSYRR 66
                                      89***********************************************************87 PP

>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.4     8e-20   3.6e-16       1      48 []      89     133 ..      89     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 8e-20
                          zf-CDGSH   1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsHk 48 
                                       +GPllV+G++ l  +dg+ +  + +   +aLCrCgrS++kP+CDgsH+
  gi|386002050|ref|YP_005920349.1|  89 DGPLLVKGRCSLFGEDGRLIAEEGQ---FALCRCGRSAKKPLCDGSHR 133
                                       7*****************9998877...*******************6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     8e-05      0.36       2      55 ..      14      61 ..      13      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-05
                           Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPves 55
                                      D ++Ci  + C    P vF  ++     v +e+ t     +++++A+d CP  +
  gi|386002050|ref|YP_005920349.1| 14 DPERCIHAAECLRGLPGVFNPQKS--PWVDMEGAT----SDEIMAAIDRCPSGA 61
                                      7899***************87764..444444444....4579********987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011      0.51       2      16 ..      11      25 ..      10      26 .. 0.86
   2 ?   -0.3   0.0       0.3   1.3e+03      19      24 .]      57      62 ..      52      62 .. 0.81
   3 ?   -3.1   0.1       2.2   9.9e+03       7      11 ..     126     130 ..     124     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                            Fer4_6  2 veidpdkCigCgdCv 16
                                      v +dp++Ci+  +C 
  gi|386002050|ref|YP_005920349.1| 11 VFWDPERCIHAAECL 25
                                      89*******988886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.3
                            Fer4_6 19 CPegai 24
                                      CP ga+
  gi|386002050|ref|YP_005920349.1| 57 CPSGAL 62
                                      999986 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.2
                            Fer4_6   7 dkCig 11 
                                        +C+g
  gi|386002050|ref|YP_005920349.1| 126 PLCDG 130
                                       68986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 932.14
//
Query:       gi|386002051|ref|YP_005920350.1|  [L=315]
Description: tungsten ABC transporter substrate-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-21   76.2   0.0    4.3e-21   75.8   0.0    1.1  1  PBP_like_2      PBP superfamily domain
    5.8e-09   36.0   0.0    1.1e-08   35.1   0.0    1.4  1  SBP_bac_11      Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.084   12.2   0.0       0.13   11.6   0.0    1.4  1  LysR_substrate  LysR substrate binding domain
       0.11   12.4   0.0         12    5.7   0.0    2.1  2  SBP_bac_1       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   9.7e-25   4.3e-21      12     282 .]      36     266 ..      21     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 9.7e-25
                        PBP_like_2  12 ifga.Gsttpapalrklada.fekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaangaggl 85 
                                       ++++ +++ ++++l++ +++ fe+  ++++v++ s+G+g +i++  +gd+d+++++++ +e++++ +g++  +    
  gi|386002051|ref|YP_005920350.1|  36 LRIStTTSLYDTLLLDEMEDiFEEM-YNVDVRTVSGGTGIAIERAVKGDADLILVHDVERERKFIeDGYGLSR---- 107
                                       5555055667889999**9999999.7*************************************999888888.... PP

                        PBP_like_2  86 iqvpvaigaialvvnkdnpln....lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqg 158
                                         + +a++ +++v+++d+p++     + +a+++I+         ++   + g +k+v+r+d+sg      t+  e+ 
  gi|386002051|ref|YP_005920350.1| 108 --TCFAYNYFIIVGPEDDPAGitglNASDAMRAIMLH-------GVE--NPGEVKFVSRGDDSG------THAREKL 167
                                       ..***************99998888788999999873.......344..5699***********......******* PP

                        PBP_like_2 159 pwtasgigasg..segvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplaw 233
                                       +w+ +g+ +    ++g+ ++++++g++ ++ +a++   +gy+l d     + ++++                + ++ 
  gi|386002051|ref|YP_005920350.1| 168 LWDRAGLDYAEiaTSGNWYVEAGQGMGPTLMMADEM--EGYTLCD-----TSTFAA----------------FRRDL 221
                                       ***999997777788888889************999..79****9.....333333................44455 PP

                        PBP_like_2 234 slqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsde 282
                                       +l+p+     + +  l + + ++ ++p +y+++n ++a++F+++l+s e
  gi|386002051|ref|YP_005920350.1| 222 DLVPLI----ESDEFLINVYAAVPVSPAVYPDTNCEMARNFINFLVSAE 266
                                       566666....4577788*************9***************975 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.5e-12   1.1e-08      12     228 ..      49     275 ..      36     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEESTT CS
                        SBP_bac_11  12 alrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviavpkg 88 
                                        l+e+ + Fe+ ++v+v+  +gg g ++++  +g ++D+++  + +  ++ +++g++   s++ +a++   i+ p++
  gi|386002051|ref|YP_005920350.1|  49 LLDEMEDIFEEMYNVDVRTVSGGTGIAIERAVKG-DADLILVHDVERERKFIEDGYGL--SRTCFAYNYFIIVGPED 122
                                       4789******************************.9**********************..***************** PP

                                       -TT---SHHH....HHHS..........S--.EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHT.EEEEESSHHH CS
                        SBP_bac_11  89 npkkikgwad....Llkp..........glk.lavadPttspsGlaalalleaagaqellkalekk.vvklgessrq 149
                                        p++i+g+++       +          ++k + + d   s++  + + l+++ag ++   a +++  v  g++ ++
  gi|386002051|ref|YP_005920350.1| 123 DPAGITGLNAsdamR--AimlhgvenpgEVKfVSRGD--DSGTHAREKLLWDRAGLDYAEIATSGNwYVEAGQGMGP 195
                                       ******998855440..34555445556666344555..4666667778999***9444444445437766776666 PP

                                       HHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE.-T....T--HHHHHHHHHTTSHHHH CS
                        SBP_bac_11 150 lltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlk.ka....akreaAraFlafLrspeaq 221
                                       +l   +a+e + ++   +++  a+ + +l++v+l e+  +  + ++aav+   a    ++ e Ar F++fL s+e+q
  gi|386002051|ref|YP_005920350.1| 196 TLM--MADEMEGYTLCDTSTF-AAFRRDLDLVPLIESDEF-LINVYAAVPVsPAvypdTNCEMARNFINFLVSAEGQ 268
                                       554..5555554444444433.45799*****99998887.55555555552446654677**************** PP

                                       HHHHHTT CS
                        SBP_bac_11 222 ailrkyG 228
                                       +++++yG
  gi|386002051|ref|YP_005920350.1| 269 DLIAEYG 275
                                       ******9 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05      0.13       5      66 ..      33     101 ..      30     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                                       CEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSS.......C CS
                    LysR_substrate   5 rgrLrigapptlaryllppllarfraryPevelelvegdseelldllaegelDlairagpp.......e 66 
                                       +  Lri+++++l  +ll + +++  ++  +v+++ v+g +   +++  +g++Dl ++++ +       +
  gi|386002051|ref|YP_005920350.1|  33 KELLRISTTTSLYDTLLLDEMEDIFEEMYNVDVRTVSGGTGIAIERAVKGDADLILVHDVErerkfieD 101
                                       5679*****************************************************999855555544 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0027        12      11      73 ..      46     106 ..      39     129 .. 0.74
   2 ?    4.6   0.0    0.0058        26     284     314 ..     234     268 ..     219     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0027
                                       HHHHHHH....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBEC CS
                         SBP_bac_1  11 qalvaka....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllp 73 
                                       + l+ ++    fe+  ++++V+ +s+g+g  ++    +  +Gd + D+i v d  + +++++ g+ l 
  gi|386002051|ref|YP_005920350.1|  46 DTLLLDEmediFEEM-YNVDVRTVSGGTGIAIE----RAVKGD-A-DLILVhDVERERKFIEDGYGLS 106
                                       555556666689996.69999999998888888....888888.5.*****99999999999887555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0058
                                       EEEEEEEEBTTCSTHHH....HHHHHHHHTSHHHH CS
                         SBP_bac_1 284 lgayglaipkgsknpea....AkkFldfllspeaq 314
                                       +++y  + ++ + +p+     A+ F++fl s+e+q
  gi|386002051|ref|YP_005920350.1| 234 INVYAAVPVSPAVYPDTncemARNFINFLVSAEGQ 268
                                       6889999999999999999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2002.35
//
Query:       gi|386002052|ref|YP_005920351.1|  [L=231]
Description: Tungsten transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-10   41.6  18.4    1.1e-10   41.6  18.4    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6  18.4   5.9e-15   1.1e-10       2     176 ..      45     226 ..      44     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5.9e-15
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirr 73 
                                       +++G l+  ++n+++++++ +li++l+slP++ ++++++l++     + + +l ++  ++++  ++ ++p+++ ++ 
  gi|386002052|ref|YP_005920351.1|  45 VPIGGLIH-FHNFFGKRAVINLIQTLYSLPTVTVGLVVFLLLsrsgpFGSLGLLFTPAGMVVGQTVLITPIMIGLTI 120
                                       78899999.9*****************************999***777776677777778***************** PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleai 145
                                       aal+ +    + +a+ lGasr q +   ++  a+  +++ ++l fg++l +  ++ ++g++       l+t +   +
  gi|386002052|ref|YP_005920351.1| 121 AALSGVGPAVRDTALSLGASRYQAIL-TIMGEAKAAMMAAVLLGFGRALSEVGVAMMIGGNIRghtrvLTTAIALET 196
                                       ***********************777.899*****************************777545444444444444 PP

                      BPD_transp_1 146 lgydyseisnggvlalviavlllnlvadilq 176
                                       +   + +  +++ ++lv + ll+nl+++  q
  gi|386002052|ref|YP_005920351.1| 197 SRGEIELS-MALGIILVSISLLVNLLVNRAQ 226
                                       44444444.4888888888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1528.97
//
Query:       gi|386002053|ref|YP_005920352.1|  [L=240]
Description: ABC transporter-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-32  110.7   0.0      1e-31  110.2   0.0    1.2  1  ABC_tran     ABC transporter
    2.2e-09   37.6   0.0    0.00011   22.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.2e-05   25.6   0.1    9.4e-05   22.7   0.1    2.0  1  AAA_22       AAA domain
    0.00072   20.0   0.9     0.0022   18.4   0.9    1.9  1  AAA_16       AAA ATPase domain
    0.00098   18.6   0.0      0.048   13.1   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0012   18.6   1.1     0.0097   15.6   0.9    2.2  1  AAA_30       AAA domain
     0.0016   18.7   0.6      0.022   15.0   0.6    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0059   16.4   0.0       0.66    9.7   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
     0.0076   16.0   0.0      0.014   15.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.024   14.5   0.9       0.58   10.0   0.2    2.5  3  NACHT        NACHT domain
       0.03   14.5   0.4      0.096   12.9   0.4    1.9  1  AAA_33       AAA domain
      0.037   14.5   0.0      0.056   13.9   0.0    1.2  1  AAA_23       AAA domain
      0.043   13.7   0.0       0.22   11.4   0.0    1.9  2  RsgA_GTPase  RsgA GTPase
      0.066   13.8   0.1       0.67   10.5   0.0    2.1  2  AAA_18       AAA domain
      0.087   11.9   0.1       0.21   10.6   0.0    1.6  2  T2SSE        Type II/IV secretion system protein
       0.11   12.0   1.5       0.36   10.4   1.3    2.2  1  AAA_25       AAA domain
       0.12   12.0   0.1       0.24   10.9   0.0    1.6  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.18   11.6   0.0       0.37   10.5   0.0    1.5  1  DEAD         DEAD/DEAH box helicase
       0.18   11.7   0.0       0.35   10.8   0.0    1.4  1  Rad17        Rad17 P-loop domain
       0.22   11.5   0.1       0.42   10.6   0.1    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.22   11.9   0.5        5.6    7.4   0.1    2.3  2  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   1.2e-34     1e-31       1     137 []      17     163 ..      17     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.2e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpelt 75 
                                       l+ vsl   +ge++a++G++GaGK+tLl++l  l  p+ G++l+dg d++e    ++ +r+++++++q+p++f+ + 
  gi|386002053|ref|YP_005920352.1|  17 LRGVSLRADRGEVLAVIGPTGAGKTTLLRILDLLDPPDGGRVLFDGVDVTEdeGARSAARRRMAMVFQKPTIFNLS- 92 
                                       6789***********************************************8888999***************999. PP

                                       HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v++n             ++++++  al+ +gl + +d++     ssLSgG+ qrvalaral+++p+llllDE+ta
  gi|386002053|ref|YP_005920352.1|  93 VEKNvayglsmrgitgaAARDRVRGALRDVGLAGYEDRRP----SSLSGGEGQRVALARALVTEPELLLLDEATA 163
                                       9***************999999*****************9....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-07   0.00011       3      53 ..      31      78 ..      29     105 .. 0.67
   2 !   13.8   0.0   4.3e-05     0.037     236     298 ..     134     193 ..     108     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlyd 53
                                      ++iGp g+GK++LL++ldll   d+   g+  +++  +++++ +++  ++ 
  gi|386002053|ref|YP_005920352.1| 31 AVIGPTGAGKTTLLRILDLL---DPPDGGRVLFDGVDVTEDEGARSAARRR 78
                                      79******************...6666666665555555555555555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.3e-05
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +lS G  +  al+ al   +    lll+DE  ++L+P+  +++ el++ +  +++ v+++TH+
  gi|386002053|ref|YP_005920352.1| 134 SLSGGEGQRVALARALVTEP---ELLLLDEATANLDPRTAEKIEELIEGAVLRKIAVVMATHD 193
                                       55666655556777777666...9***********************5555556********8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.1e-07   9.4e-05       4     114 ..      26     178 ..      23     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdl.lrellralglelka....... 70 
                                       +  +l+v+G++G+GKTtllr l   ++ +      + +v+   v+++++++ ++  +r+++  ++ ++         
  gi|386002053|ref|YP_005920352.1|  26 RGEVLAVIGPTGAGKTTLLRILDLLDPPD------GGRVLfdGVDVTEDEGARSAaRRRMAMVFQKPTIFnlsvekn 96 
                                       56789*****************9999755......666667788888888666665888888888777778888888 PP

                            AAA_22  71 ...............................erlsseell.ealeqalrarav...ielliiDEaqh.lr..seeal 109
                                                                      e  + + l     ++ + ara    +ell++DEa   l+  ++e +
  gi|386002053|ref|YP_005920352.1|  97 vayglsmrgitgaaardrvrgalrdvglagyEDRRPSSLSgGEGQRVALARALvtePELLLLDEATAnLDprTAEKI 173
                                       8888888888888888888888888888888666666666688888887777788999******9998987558888 PP

                            AAA_22 110 eeLrs 114
                                       eeL +
  gi|386002053|ref|YP_005920352.1| 174 EELIE 178
                                       88755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   2.6e-06    0.0022      19      63 ..      22      66 ..      14     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-06
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      +r++r+e++ ++G+ G GK++l+r l   l    gg +l    d  
  gi|386002053|ref|YP_005920352.1| 22 LRADRGEVLAVIGPTGAGKTTLLRILD-LLDPPdGGRVLFDGVDVT 66
                                      678889*****************8777.555554344433333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.041        35      26      41 ..      29      44 ..      20      49 .. 0.86
   2 !   13.1   0.0   5.6e-05     0.048     135     197 ..     133     192 ..      59     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.041
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                      + a++Gp G+GK+ ll
  gi|386002053|ref|YP_005920352.1| 29 VLAVIGPTGAGKTTLL 44
                                      679**********987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.6e-05
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC.TTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks.knaQfivisl 197
                                       ++LSgGe + vala  +    v    l llDe  a+LD +  +k+ el++ +   +  +++ ++
  gi|386002053|ref|YP_005920352.1| 133 SSLSGGEGQRVALARAL----VTEPELLLLDEATANLDPRTAEKIEELIEGAVlRKIAVVMATH 192
                                       489****9988887654....4455699*********************955403344444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.9   1.1e-05    0.0097      15     110 ..      24     178 ..      19     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaag..............................grviglAptgkaAkv 61 
                                       +++  v ++ Gp G+GKtt+l+ l  +   +g                               +++ l+ ++++A  
  gi|386002053|ref|YP_005920352.1|  24 ADRGEVLAVIGPTGAGKTTLLRILDLLDPPDGgrvlfdgvdvtedegarsaarrrmamvfqkPTIFNLSVEKNVAYG 100
                                       55667999****************99999997455555555555444444444444444444344444444444444 PP

                            AAA_30  62 Laeelgieastiakllkrlk......................................grarlepgtllivDEagmv 100
                                       L+   gi            +                                      +ra +++ +ll+ DEa   
  gi|386002053|ref|YP_005920352.1| 101 LSMR-GI------------TgaaardrvrgalrdvglagyedrrpsslsggegqrvalARALVTEPELLLLDEATAN 164
                                       3321.22............0111111122222244466666666666666777777765555666677777777655 PP

                            AAA_30 101 ....dtkqlaallk 110
                                            ++++++l++
  gi|386002053|ref|YP_005920352.1| 165 ldprTAEKIEELIE 178
                                       43334444444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6   2.6e-05     0.022      28      88 ..     130     177 ..     112     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       r+ ++lSGGe+q    +ala a   l+       + ++l++LDEA ++lD+++++++ el+
  gi|386002053|ref|YP_005920352.1| 130 RRPSSLSGGEGQR---VALARA---LV-------TEPELLLLDEATANLDPRTAEKIEELI 177
                                       5666777777743...344422...22.......3489***************99987776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00078      0.66      45      69 ..      25      49 ..      13      90 .. 0.81
   2 ?    4.7   0.0     0.026        22     104     149 ..     148     192 ..     135     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00078
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgv 69
                                      ++ e ++++Gp+G+GK+ l   l  
  gi|386002053|ref|YP_005920352.1| 25 DRGEVLAVIGPTGAGKTTLLRILDL 49
                                      678999***********99766655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                         IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                       + +++++ll+lD+  + +ld   ae++ e+ie ++ r+  ++ +  
  gi|386002053|ref|YP_005920352.1| 148 ALVTEPELLLLDEA-TANLDPRTAEKIEELIEGAVLRKIAVVMATH 192
                                       4456789*****95.689**************99998877776654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.014      15      43 ..      20      47 ..      15      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiq 43
                                       +++ d+ ++  ++Gp+G+GK+Tll  i 
  gi|386002053|ref|YP_005920352.1| 20 VSLRADRGEVLAVIGPTGAGKTTLL-RIL 47
                                      56777866699*************9.455 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00068      0.58       2      19 ..      29      46 ..      28      50 .. 0.88
   2 ?   -1.6   0.0       2.7   2.3e+03      85     110 ..      58      80 ..      45      91 .. 0.64
   3 ?    2.1   0.0      0.18   1.6e+02      90     129 ..     158     193 ..     133     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                                      CEEEEC-TTTCHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqk 19
                                      ++++ G+ G GKTtLl+ 
  gi|386002053|ref|YP_005920352.1| 29 VLAVIGPTGAGKTTLLRI 46
                                      789*************85 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                       EEEE-STT-SS-TCH.........HH CS
                             NACHT  85 lilDglDelvtdlgqkekqpvrtlLs 110
                                        ++Dg+D +++  g+  + ++r+ ++
  gi|386002053|ref|YP_005920352.1|  58 VLFDGVDVTED-EGA--RSAARRRMA 80 
                                       68999998886.444..345555554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.18
                                       STT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                             NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                       lDe+ + l++    ++ + ++eli++++l++  ++++++ 
  gi|386002053|ref|YP_005920352.1| 158 LDEATANLDP----RTAEKIEELIEGAVLRKIAVVMATHD 193
                                       5777777777....78899999999999999999888765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   0.00011     0.096       1      33 [.      29     111 ..      29     208 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_33   1 lvllvGlpGsGKstlaerl..lkklg.......avllssdt.................................... 32 
                                       ++ ++G+ G+GK+tl++ l  l + +       +v +++d+                                    
  gi|386002053|ref|YP_005920352.1|  29 VLAVIGPTGAGKTTLLRILdlLDPPDggrvlfdGVDVTEDEgarsaarrrmamvfqkptifnlsveknvayglsmrg 105
                                       6779************9765444443555555666666666777775555555555555555555555555555555 PP

                            AAA_33  33 .....l 33 
                                            +
  gi|386002053|ref|YP_005920352.1| 106 itgaaA 111
                                       555443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.5e-05     0.056      23      39 ..      31      47 ..      20      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                      +++Gp+GaGKTT+l+ +
  gi|386002053|ref|YP_005920352.1| 31 AVIGPTGAGKTTLLRIL 47
                                      679**********9866 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.22      99     119 ..      27      47 ..      13      69 .. 0.90
   2 ?   -0.3   0.0         1   8.6e+02      26     108 ..     192     211 ..     156     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                       TSEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinal 119
                                       +++ +++G++G+GK+tL+  l
  gi|386002053|ref|YP_005920352.1|  27 GEVLAVIGPTGAGKTTLLRIL 47 
                                       58899************9877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                                       TTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEE CS
                       RsgA_GTPase  26 kepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkts 102
                                       ++ +                                                                +++l+d+++
  gi|386002053|ref|YP_005920352.1| 192 HDLDQ---------------------------------------------------------------ARRLADRVA 205
                                       33333...............................................................345666666 PP

                                       EEECST CS
                       RsgA_GTPase 103 vlvGqS 108
                                       vl+G S
  gi|386002053|ref|YP_005920352.1| 206 VLMGGS 211
                                       666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00078      0.67       3      18 ..      32      47 ..      30      80 .. 0.88
   2 ?    1.1   0.1      0.62   5.3e+02      72     113 ..     151     203 ..     112     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00078
                            AAA_18  3 ltGtpGvGKttlakeL 18
                                      + G+ G+GKttl + L
  gi|386002053|ref|YP_005920352.1| 32 VIGPTGAGKTTLLRIL 47
                                      89***********999 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.62
                            AAA_18  72 eegknlvidghlaeleseaakdikk...........vvLtaspeelleRlekR 113
                                       +e++ l++d   a+l +  a +i             vv+ +++   ++Rl++R
  gi|386002053|ref|YP_005920352.1| 151 TEPELLLLDEATANLDPRTAEKIEEliegavlrkiaVVMATHDLDQARRLADR 203
                                       55667777777777777777777767777777888899999999999999999 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.21     131     148 ..      29      46 ..      11      59 .. 0.80
   2 ?   -2.2   0.0         2   1.7e+03     112     133 ..     167     188 ..     149     207 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                             T2SSE 131 lilvsGgTgsGKttllya 148
                                       ++ v G+Tg GKttll +
  gi|386002053|ref|YP_005920352.1|  29 VLAVIGPTGAGKTTLLRI 46 
                                       45599**********976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                             T2SSE 112 ealkekiaevlrkavrerglil 133
                                       ++++eki+e+++ av ++  ++
  gi|386002053|ref|YP_005920352.1| 167 PRTAEKIEELIEGAVLRKIAVV 188
                                       3444555555555554444443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00042      0.36      31      50 ..      25      44 ..      18     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       +ge+ +++G++g+GKttl+
  gi|386002053|ref|YP_005920352.1| 25 DRGEVLAVIGPTGAGKTTLL 44
                                      689***************97 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029      0.24       2      19 ..      29      46 ..      28      58 .. 0.87
   2 ?   -2.7   0.0       4.5   3.9e+03      26      32 ..     182     188 ..     153     207 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                      EEEEEESTTCCHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnh 19
                                      v+ + G+ G+GKTtLl+ 
  gi|386002053|ref|YP_005920352.1| 29 VLAVIGPTGAGKTTLLRI 46
                                      67899**********985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                                       SS-EEEE CS
                              cobW  26 glklavi 32 
                                        +k+av+
  gi|386002053|ref|YP_005920352.1| 182 LRKIAVV 188
                                       2233332 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00044      0.37      14     102 ..      27     208 ..      15     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................................... 47 
                                       g+ + v ++TG+GKT+   + +l+ + +    +g                                           
  gi|386002053|ref|YP_005920352.1|  27 GEVLAVIGPTGAGKTTL--LRILDLL-D--PPDGgrvlfdgvdvtedegarsaarrrmamvfqkptifnlsveknva 98 
                                       56677999*******98..5555555.2..22224667777777777888999999999999999999999999999 PP

                                       ...............................................-EEEEEESSHHHHHHHHHHHHHHTTT.ST. CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxx.xx. RF
                              DEAD  48 ...............................................pkalivePtreLaeqtlnnlkkfkky.id. 75 
                                                                                       +al+ eP   L  +   nl  ++ + i+ 
  gi|386002053|ref|YP_005920352.1|  99 yglsmrgitgaaardrvrgalrdvglagyedrrpsslsggegqrvalARALVTEPELLLLDEATANLDPRTAEkIEe 175
                                       99999999999999999999999999999999999999999999999888888888777777777776666643444 PP

                                       ......SEEEEEETTSSHHHHHHHHHTTCSEEE CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 ......lrvlliiggvaardqlskldngvdivv 102
                                             lr  +++  +   dq ++l  +v +++
  gi|386002053|ref|YP_005920352.1| 176 liegavLRKIAVVMATHDLDQARRLADRVAVLM 208
                                       444555666666666777777777766666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00041      0.35      34      65 ..      16      47 ..       8      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                       l+  +L   + ++L + GP+G gk+t +++L
  gi|386002053|ref|YP_005920352.1| 16 ILRGVSLRADRGEVLAVIGPTGAGKTTLLRIL 47
                                      5666778888888*****************98 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00049      0.42      18      38 ..      26      46 ..       9      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                                      HTEEEEEEESTTSSHHHHHHH CS
                              TsaE 18 lgdvilLeGdLGaGKTtlvrg 38
                                       g+v++  G+ GaGKTtl r 
  gi|386002053|ref|YP_005920352.1| 26 RGEVLAVIGPTGAGKTTLLRI 46
                                      37899*************986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0065       5.6       3      17 ..      32      46 ..      30      49 .. 0.88
   2 ?    2.5   0.0      0.22   1.9e+02      58     115 ..     152     197 ..     133     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                                      EESSTTSSHHHHHHH CS
                               AAA  3 lyGppGtGKTllaka 17
                                      ++Gp G GKT+l + 
  gi|386002053|ref|YP_005920352.1| 32 VIGPTGAGKTTLLRI 46
                                      79**********986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.22
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkl 115
                                       +p  l++DE+ a    r          +++++ + ++g     +k+ v++at++ d+ 
  gi|386002053|ref|YP_005920352.1| 152 EPELLLLDEATANLDPR----------TAEKIEELIEGAVL--RKIAVVMATHDLDQA 197
                                       57888888888887777..........67777777777777..478888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1515.47
//
Query:       gi|386002054|ref|YP_005920353.1|  [L=226]
Description: hypothetical protein Mhar_1366 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-68  226.2  32.9      9e-15   54.0   1.3    5.7  6  Pentapeptide    Pentapeptide repeats (8 copies)
    2.6e-29  101.2   0.0    1.6e-09   37.8   0.0    3.4  4  Pentapeptide_4  Pentapeptide repeats (9 copies)
    1.2e-24   86.2   0.0    4.8e-05   23.4   0.0    5.0  4  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.26   10.4   0.0        4.7    6.3   0.0    2.4  3  DUF5508         Family of unknown function (DUF5508)


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.9   3.8e-17   1.7e-13       1      38 [.      29      66 ..      29      68 .. 0.97
   2 !   44.2   0.9   2.2e-15     1e-11       2      38 ..      70     106 ..      69     108 .. 0.88
   3 !   54.0   1.3     2e-18     9e-15       1      39 [.      79     117 ..      79     117 .. 0.99
   4 !   43.0   0.9   5.5e-15   2.5e-11       1      38 [.     109     146 ..     109     146 .. 0.98
   5 !   43.9   0.1     3e-15   1.3e-11       1      40 []     144     183 ..     144     183 .. 0.97
   6 !   44.8   0.2   1.5e-15   6.9e-12       1      36 [.     184     219 ..     184     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3.8e-17
                                      -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide  1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38
                                      A+++gA++sg nLsga+l g+nL gA+l+gAdLsg++L
  gi|386002054|ref|YP_005920353.1| 29 ADFRGADFSGMNLSGADLQGSNLMGASLRGADLSGVDL 66
                                      8************************************9 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 2.2e-15
                                       B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                        L  A+L+ anLsga+lsgA+++gA+l gAdL++a+L
  gi|386002054|ref|YP_005920353.1|  70 KLVSADLRSANLSGADLSGAKFSGADLAGADLREARL 106
                                       5888999999999999999999999999999999987 PP

  == domain 3  score: 54.0 bits;  conditional E-value: 2e-18
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       AnLsgA+Lsga++sga+l gA+L++A l gA Lsga+L+
  gi|386002054|ref|YP_005920353.1|  79 ANLSGADLSGAKFSGADLAGADLREARLVGAELSGADLR 117
                                       9************************************97 PP

  == domain 4  score: 43.0 bits;  conditional E-value: 5.5e-15
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       A+LsgA+L+   + ga+l+gA+Lt+A+lsgAdL+ga+L
  gi|386002054|ref|YP_005920353.1| 109 AELSGADLRSLAMAGADLRGATLTRADLSGADLRGAKL 146
                                       89**********************************97 PP

  == domain 5  score: 43.9 bits;  conditional E-value: 3e-15
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       A L +A+L+ga+L+ga+l gA+L gA l +++Lsga L+g
  gi|386002054|ref|YP_005920353.1| 144 AKLIEADLRGAKLRGADLAGADLAGAKLVRSKLSGAVLRG 183
                                       7899**********************************98 PP

  == domain 6  score: 44.8 bits;  conditional E-value: 1.5e-15
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsga 36 
                                       ++L gA+L+ga+Lsga+ls+A++++A l+gA L+g+
  gi|386002054|ref|YP_005920353.1| 184 SSLVGADLCGADLSGADLSRADFRSAKLEGAILEGV 219
                                       589*******************************97 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   3.6e-13   1.6e-09       5      76 ..      28     100 ..      27     101 .. 0.95
   2 !   31.7   0.0   2.8e-11   1.3e-07       9      76 ..      82     150 ..      81     151 .. 0.94
   3 !   25.7   0.0   2.1e-09   9.3e-06       2      76 ..     115     190 ..     114     191 .. 0.91
   4 !   20.9   0.0   6.8e-08    0.0003       2      66 ..     150     214 ..     144     223 .. 0.42

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 3.6e-13
                    Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                       r+ f+++++s++n+s a+l+++n++++ l  + ++  +l  +++  +dl++a++sg +l++++fs+  l ++d
  gi|386002054|ref|YP_005920353.1|  28 RADFRGADFSGMNLSGADLQGSNLMGASLRGADLSGVDLGRSKLVSADLRSANLSGADLSGAKFSGaDLAGAD 100
                                       678*************************************************************987898877 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 2.8e-11
                    Pentapeptide_4   9 nncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                        +++ls++ Fs a+l +++++e+rl+ ++++ ++l+++  a++dl+ a++++ +l+++ +++ kl ++d
  gi|386002054|ref|YP_005920353.1|  82 SGADLSGAKFSGADLAGADLREARLVGAELSGADLRSLAMAGADLRGATLTRADLSGADLRGaKLIEAD 150
                                       5899********************************************************987997776 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 2.1e-09
                    Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                       ++++  + +++l +++++ a+l ++++++++l ++ ++ ++l+ +d+a++dl+ a + ++ l+++++++ +l+++d
  gi|386002054|ref|YP_005920353.1| 115 DLRSLAMAGADLRGATLTRADLSGADLRGAKLIEADLRGAKLRGADLAGADLAGAKLVRSKLSGAVLRGsSLVGAD 190
                                       56677788999********************************************************987899887 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 6.8e-08
                    Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknv 66 
                                       +++ +++++++l++++++ a+l ++ ++++ l   ++  ++l  +d++++dl ra F    l+++
  gi|386002054|ref|YP_005920353.1| 150 DLRGAKLRGADLAGADLAGAKLVRSKLSGAVLRGSSLVGADLCGADLSGADLSRADFRSAKLEGA 214
                                       33334444444444444444444444444444333333333333333333333333333333333 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.3e-08     6e-05       4      47 ..      29      69 ..      27      70 .. 0.65
   2 !   23.4   0.0   1.1e-08   4.8e-05       3      45 ..      78     117 ..      76     120 .. 0.85
   3 !   17.9   0.0   5.7e-07    0.0026       3      38 ..     128     161 ..     108     175 .. 0.50
   4 !   16.1   0.0   2.1e-06    0.0096       2      44 ..     177     216 ..     151     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.3e-08
                    Pentapeptide_3  4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47
                                      a F+ga dF+g + sga + +++++ +a+++ga  + +vd++++
  gi|386002054|ref|YP_005920353.1| 29 ADFRGA-DFSGMNLSGA-DLQGSNLMGASLRGADLS-GVDLGRS 69
                                      556666.6666666666.777777777777777776.7777665 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.1e-08
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                                        an+sga d++ga Fsga +  +ad+++a++ ga  + ++d++
  gi|386002054|ref|YP_005920353.1|  78 SANLSGA-DLSGAKFSGA-DLAGADLREARLVGAELS-GADLR 117
                                       6899999.9999999999.999999999999999998.88876 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 5.7e-07
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarF 38 
                                       ga++++a d++ga  +ga    +ad+++a ++ga  
  gi|386002054|ref|YP_005920353.1| 128 GATLTRA-DLSGADLRGA-KLIEADLRGAKLRGADL 161
                                       3333333.4444444444.23333333333333333 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 2.1e-06
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                                       sga+++g+ ++ ga   ga + s+ad+++adF+ a  + ++ +
  gi|386002054|ref|YP_005920353.1| 177 SGAVLRGS-SLVGADLCGA-DLSGADLSRADFRSAKLE-GAIL 216
                                       56666666.6665555555.555555555555555555.4444 PP

>> DUF5508  Family of unknown function (DUF5508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.001       4.7     148     177 ..      29      59 ..      24      67 .. 0.83
   2 ?    1.1   0.0     0.041   1.8e+02     144     166 ..      80     102 ..      70     129 .. 0.80
   3 ?   -2.7   0.0      0.59   2.6e+03     145     161 ..     186     202 ..     154     212 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.001
                           DUF5508 148 ldfkgcffsgqnfsnydiqyvn.wgtslfdv 177
                                        df+g+ fsg n+s  d+q  n  g+sl   
  gi|386002054|ref|YP_005920353.1|  29 ADFRGADFSGMNLSGADLQGSNlMGASLRGA 59 
                                       59*****************998447777655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.041
                           DUF5508 144 nlrgldfkgcffsgqnfsnydiq 166
                                       nl g d+ g+ fsg +++  d++
  gi|386002054|ref|YP_005920353.1|  80 NLSGADLSGAKFSGADLAGADLR 102
                                       89999999999999999888876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.59
                           DUF5508 145 lrgldfkgcffsgqnfs 161
                                       l g d+ g+ +sg ++s
  gi|386002054|ref|YP_005920353.1| 186 LVGADLCGADLSGADLS 202
                                       34445555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       120  (0.00669307); expected 358.6 (0.02)
Passed bias filter:                      102  (0.00568911); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1935.12
//
Query:       gi|386002055|ref|YP_005920354.1|  [L=403]
Description: hypothetical protein Mhar_1367 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-37  126.8  40.2    4.6e-36  124.6  40.2    1.8  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
       0.15   13.0   0.1       0.15   13.0   0.1    2.7  4  DUF4834          Domain of unknown function (DUF4834)
        1.5    8.7   3.9          1    9.3   0.5    2.3  2  DUF1514          Protein of unknown function (DUF1514)
        5.8    6.9   9.8       0.16   12.0   1.1    2.8  3  TMEM18           Transmembrane protein 18


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6  40.2     1e-39   4.6e-36       6     324 ..      11     357 ..       6     359 .. 0.81

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 1e-39
                   AI-2E_transport   6 vllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvplliaqltq 81 
                                       +l++ ++++ ++++ ++ ++l+++++ay+l+p   +L + ++ +rv+a l + +++l++lv+++ ++   l + + +
  gi|386002055|ref|YP_005920354.1|  11 ILIAAVAGVFYVTQNFITTILLSFFFAYVLHPFHLRLyALTRRRRVSALLSISIVFLIFLVFVLSVIN-ALTTEVLE 86 
                                       334444444444446**********************9999999999999999998888877666555.77777777 PP

                   AI-2E_transport  82 lvkslp.......ayidslqnilnelpslleele.n.....................liqalkqslskilsnilssi 129
                                       l k+         ++ d+    + ++++ l ++  +                     l+++  + + ++l + +s +
  gi|386002055|ref|YP_005920354.1|  87 LSKNQDyfdeaasKFADQTAGDFFDWTRGLAVERsPqavapylghaldqaeeqigavLAAPGTWLVPEVLPRARSIL 163
                                       77777788888886666666666666666655554477666666633333333444444444444444444444444 PP

                   AI-2E_transport 130 lnsllsllasllglilslvlvllllffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliig 206
                                       +  +  ++++l+ l+ ++ + +ll+++ll+dg    +++l llper  + v+++l el+ ++ ++++  ++ ++++g
  gi|386002055|ref|YP_005920354.1| 164 TGLADWIAKNLPILMAQFGVAILLTYYLLVDGAGSIEKFLGLLPER--AIVRRFLTELNAIYNSLFNVYLINSFLTG 238
                                       55555566777888999***************************99..9**************************** PP

                   AI-2E_transport 207 vlvfigllilgvpyalllailvglanliPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklm 282
                                       +++++++l++gvpy++l+++++ +++l P+iG   v++p+a++ l++++    + +++++ ++++++ +ni +P l 
  gi|386002055|ref|YP_005920354.1| 239 LIAAFVYLFIGVPYPFLWGMVTAVFALMPLIGTSAVYVPMALYYLIFQDyLRVAALLILGTVFLNVFPENIMRPALA 315
                                       *************************************************7888888888999*************** PP

                   AI-2E_transport 283 gkrlglhplvillsllaggklfGlvGlilavpltavikaile 324
                                       + ++ +hp+++ll++ a +   G++G+i+++ l++++ a+++
  gi|386002055|ref|YP_005920354.1| 316 KAGAAIHPAITLLAFAAPIFAIGVMGVIVGPALYGFVLAAYR 357
                                       *************************************99986 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.3         4   1.8e+04       3      15 ..      26      38 ..      24      48 .. 0.53
   2 ?   13.0   0.1   3.4e-05      0.15       4      51 ..      59     106 ..      56     121 .. 0.88
   3 ?   -1.7   0.1       1.4   6.1e+03      14      31 ..     289     306 ..     280     318 .. 0.74
   4 ?   -3.2   0.5       3.8   1.7e+04      10      26 ..     333     349 ..     325     363 .. 0.58

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4
                           DUF4834  3 fLlfilifiiail 15
                                      f+  il+ +++ +
  gi|386002055|ref|YP_005920354.1| 26 FITTILLSFFFAY 38
                                      5555533333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.4e-05
                           DUF4834   4 Llfilifiiailviglsilsvilrtvfglgsrkkssksaqkqfgnstn 51 
                                       Ll i i++++ lv++ls+++++  +v+ l++++   ++a+++f+ +t 
  gi|386002055|ref|YP_005920354.1|  59 LLSISIVFLIFLVFVLSVINALTTEVLELSKNQDYFDEAASKFADQTA 106
                                       78999***********************99999988888888887765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.4
                           DUF4834  14 ilviglsilsvilrtvfg 31 
                                       + v +l il++++ +vf 
  gi|386002055|ref|YP_005920354.1| 289 LRVAALLILGTVFLNVFP 306
                                       567788888999888875 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.8
                           DUF4834  10 fiiailviglsilsvil 26 
                                        i+ai v+g+++  +++
  gi|386002055|ref|YP_005920354.1| 333 PIFAIGVMGVIVGPALY 349
                                       35566666665554444 PP

>> DUF1514  Protein of unknown function (DUF1514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   0.00023         1       4      36 ..      61      93 ..      59     100 .. 0.80
   2 ?   -0.7   0.2       0.3   1.3e+03       1      18 [.     255     272 ..     255     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                           DUF1514  4 visivlailLLvllsiisdkakeieaLeYmndY 36
                                       isiv+ i+L+ +ls+i     e+  L    dY
  gi|386002055|ref|YP_005920354.1| 61 SISIVFLIFLVFVLSVINALTTEVLELSKNQDY 93
                                      69**************98877777666655555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.3
                           DUF1514   1 mWivisivlailLLvlls 18 
                                       +W +++ v+a++ L+  s
  gi|386002055|ref|YP_005920354.1| 255 LWGMVTAVFALMPLIGTS 272
                                       59999******9999776 PP

>> TMEM18  Transmembrane protein 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   3.5e-05      0.16      15      73 ..      39      96 ..      25      99 .. 0.72
   2 ?   -1.5   0.0      0.54   2.4e+03       5      25 ..     228     248 ..     224     252 .. 0.82
   3 ?   -1.8   0.4      0.66   2.9e+03      13      52 ..     268     307 ..     253     313 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                            TMEM18 15 gliafhllllviilltrrsqnlqlvlfllllllvllaeqiNelaaknweefskqnYFDs 73
                                      +l  fhl l  +    rr + l  + +++l++lv++ + iN l  +  e   +q+YFD+
  gi|386002055|ref|YP_005920354.1| 39 VLHPFHLRLYAL-TRRRRVSALLSISIVFLIFLVFVLSVINALTTEVLELSKNQDYFDE 96
                                      344455443332.2335567777888999999**************99999999****8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.54
                            TMEM18   5 avdwsepwlvgliafhllllv 25 
                                       +v + + +l+glia  + l++
  gi|386002055|ref|YP_005920354.1| 228 NVYLINSFLTGLIAAFVYLFI 248
                                       788889999999999998876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.66
                            TMEM18  13 lvgliafhllllviilltrrsqnlqlvlfllllllvllae 52 
                                       l+g  a+++ + +  l+++++ ++ ++l+l +++l ++ e
  gi|386002055|ref|YP_005920354.1| 268 LIGTSAVYVPMALYYLIFQDYLRVAALLILGTVFLNVFPE 307
                                       5556666666666666666666666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.35s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2287.91
//
Query:       gi|386002056|ref|YP_005920355.1|  [L=155]
Description: hypothetical protein Mhar_1368 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-27   95.1   0.0    2.8e-27   94.5   0.0    1.3  1  TFX_C         DNA_binding protein, TFX, C-term
    4.7e-07   29.2   2.4      1e-06   28.1   2.4    1.6  1  Sigma70_r4    Sigma-70, region 4
    2.6e-06   27.0   1.2    9.2e-06   25.3   1.2    1.8  1  Sigma70_r4_2  Sigma-70, region 4
    3.6e-05   23.6   0.2    8.3e-05   22.5   0.2    1.6  1  HTH_37        Helix-turn-helix domain
    0.00017   21.1   0.2    0.00027   20.4   0.2    1.3  1  GerE          Bacterial regulatory proteins, luxR family
    0.00035   20.9   2.2      0.001   19.3   2.2    2.0  1  HTH_31        Helix-turn-helix domain
    0.00036   20.2   2.1    0.00049   19.8   0.6    2.0  2  HTH_23        Homeodomain-like domain
     0.0011   19.0   0.2     0.0026   17.8   0.2    1.7  1  HTH_3         Helix-turn-helix
     0.0028   17.9   0.2     0.0057   16.9   0.2    1.5  1  KORA          TrfB plasmid transcriptional repressor
     0.0066   16.4   1.0      0.022   14.7   0.5    2.3  2  HTH_Crp_2     Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.5   0.1      0.047   13.5   0.1    1.5  1  HTH_38        Helix-turn-helix domain
      0.023   14.9   0.0      0.041   14.1   0.0    1.3  1  UPF0122       Putative helix-turn-helix protein, YlxM / p13 l
      0.025   14.7   0.9      0.064   13.4   0.1    2.1  2  HTH_28        Helix-turn-helix domain
      0.037   14.1   0.1      0.064   13.3   0.1    1.4  1  HTH_19        Helix-turn-helix domain
      0.044   13.9   0.1      0.098   12.8   0.1    1.6  1  HTH_7         Helix-turn-helix domain of resolvase
       0.05   13.5   0.8       0.15   12.0   0.2    2.2  2  MarR_2        MarR family


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   2.5e-30   2.8e-27       1      83 []      67     149 ..      67     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.5e-30
                                       SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESS CS
                             TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyite 77 
                                       Ar Tl+ +++++apv++t+++Gtdlfd+p ++++ead+agik++  ++e++ ++re+apea+k+rv+ +dlev ite
  gi|386002056|ref|YP_005920355.1|  67 ARATLRDWRMIQAPVSLTVPAGTDLFDLPGLVFREADRAGIKLDIGSVEIVVQVREKAPEALKKRVTVRDLEVAITE 143
                                       89*************************************************************************** PP

                                       SSSEEE CS
                             TFX_C  78 dGeirv 83 
                                       dG + v
  gi|386002056|ref|YP_005920355.1| 144 DGLVLV 149
                                       **8865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   2.4   9.1e-10     1e-06       5      47 ..      22      63 ..      20      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9.1e-10
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrk 47
                                      L+ r+  vl+lr+ +gl+++E++e+lg +r+ V+ +ekrA ++
  gi|386002056|ref|YP_005920355.1| 22 LTRRQVAVLKLRR-QGLSQQEVAEILGTTRSNVSILEKRAHQN 63
                                      899*********8.899***********************765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.2   8.2e-09   9.2e-06       6      44 ..      16      54 ..      15      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.2e-09
                                      HHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHH CS
                      Sigma70_r4_2  6 ealaeLperqreifllryleglsykEIAellgisegtVk 44
                                      ea++ L +r++ ++l  + +gls++E+Ae+lg++ ++V 
  gi|386002056|ref|YP_005920355.1| 16 EAMEGLLTRRQVAVLKLRRQGLSQQEVAEILGTTRSNVS 54
                                      7999999*****************************995 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   7.4e-08   8.3e-05      27      60 ..      32      65 ..      14      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.4e-08
                                      HHHCT--HHHHHHHHT--HHHHHHHHTT--TT-- CS
                            HTH_37 27 iekrelsqseaaqllgiaqPkvsrllrgklsrfs 60
                                      +++++lsq+e+a++lg+++++vs l++   +++s
  gi|386002056|ref|YP_005920355.1| 32 LRRQGLSQQEVAEILGTTRSNVSILEKRAHQNVS 65
                                      6789***********************9999987 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   2.4e-07   0.00027       3      36 ..      22      55 ..      20      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                      S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHH CS
                              GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkv 36
                                      L++R++ vL+l  +G+s +e+Ae+l+    +V++
  gi|386002056|ref|YP_005920355.1| 22 LTRRQVAVLKLRRQGLSQQEVAEILGTTRSNVSI 55
                                      9**************************9999987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.2   9.2e-07     0.001      11      46 ..      33      68 ..       4      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.2e-07
                            HTH_31 11 eraGLsqeevAerlgvsestlsrlEqGrrgrpspav 46
                                      +r+GLsq+evAe lg ++s +s lE  +++++s+a 
  gi|386002056|ref|YP_005920355.1| 33 RRQGLSQQEVAEILGTTRSNVSILEKRAHQNVSRAR 68
                                      368***********************9999998874 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.6   4.4e-07   0.00049       6      40 ..      24      59 ..      21      66 .. 0.79
   2 ?   -0.8   0.1       1.3   1.4e+03      23      38 ..      60      75 ..      55      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                            HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      +R+ ++l l++ Gls++e+A++Lg +r+ v+   kr
  gi|386002056|ref|YP_005920355.1| 24 RRQVAVLKLRRqGLSQQEVAEILGTTRSNVSILEKR 59
                                      666755555544***************988777776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                            HTH_23 23 IAreLgvsrrTvyrwl 38
                                      + +   + r T++ w+
  gi|386002056|ref|YP_005920355.1| 60 AHQNVSRARATLRDWR 75
                                      5566677899999996 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.3e-06    0.0026       6      31 ..      33      58 ..      29      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                      HHTTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  6 kqlglsqeeLAeklGvsrstisriEn 31
                                        +glsq+e+Ae lG +rs +s +E+
  gi|386002056|ref|YP_005920355.1| 33 RRQGLSQQEVAEILGTTRSNVSILEK 58
                                      357****************9997766 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   5.1e-06    0.0057      30      74 ..      35      80 ..      12      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.1e-06
                              KORA 30 egkkqadvatelgltkqavsqavkrvwaahaere.epaglerVsvl 74
                                      +g +q++va+ lg t+ +vs ++kr+ ++      + +++  +++ 
  gi|386002056|ref|YP_005920355.1| 35 QGLSQQEVAEILGTTRSNVSILEKRAHQNVSRARaTLRDWRMIQAP 80
                                      5679************************987655588999999875 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5     2e-05     0.022      21      39 ..      36      54 ..      20      85 .. 0.85
   2 ?   -3.2   0.0       7.6   8.6e+03      54      63 ..     130     138 ..     125     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                      EHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                       l+q+e A++lG+tr+ vs
  gi|386002056|ref|YP_005920355.1| 36 GLSQQEVAEILGTTRSNVS 54
                                      59***************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.6
                                       TEEEEES-HH CS
                         HTH_Crp_2  54 grririldle 63 
                                       +r ++++dle
  gi|386002056|ref|YP_005920355.1| 130 KR-VTVRDLE 138
                                       34.8888875 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.2e-05     0.047      14      35 ..      30      51 ..      24      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-05
                            HTH_38 14 erllaeGlslreIArrLgrsps 35
                                       +l+ +Gls+ e+A +Lg  +s
  gi|386002056|ref|YP_005920355.1| 30 LKLRRQGLSQQEVAEILGTTRS 51
                                      57899**************998 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.6e-05     0.041      15      61 ..      19      64 ..      13      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                           UPF0122 15 qsLLTekqanylelyyadDlSlsEiAeefnvsrqavydnikrtekll 61
                                      + LLT +q+ +l+l   + lS +E+Ae   ++r+ v+   kr+++ +
  gi|386002056|ref|YP_005920355.1| 19 EGLLTRRQVAVLKLR-RQGLSQQEVAEILGTTRSNVSILEKRAHQNV 64
                                      68***********96.789****************987777777655 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.7e-05     0.064       2      34 ..      25      58 ..      23      63 .. 0.76
   2 ?   -1.4   0.1       2.3   2.6e+03      26      33 ..      68      75 ..      60      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                            HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWik 34
                                      R  +++ l +++ s+ e+A++lg++r+ v+ + k
  gi|386002056|ref|YP_005920355.1| 25 RQVAVLKLRRQGlSQQEVAEILGTTRSNVSILEK 58
                                      5566777776666*************98875555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                            HTH_28 26 rrtvyrWi 33
                                      r t+++W+
  gi|386002056|ref|YP_005920355.1| 68 RATLRDWR 75
                                      78999996 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.7e-05     0.064      12      34 ..      36      58 ..      29      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                            HTH_19 12 gltqeelaerlgisrskisaiEn 34
                                      gl+q+e+ae lg++rs  s +E+
  gi|386002056|ref|YP_005920355.1| 36 GLSQQEVAEILGTTRSNVSILEK 58
                                      9****************998885 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.7e-05     0.098      13      36 ..      28      51 ..      20      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
                                      GGGSSTTTT--STTTSSSS---SS CS
                             HTH_7 13 rvvkLleeGisiskIAkevnisRs 36
                                       v+kL+++G s +++A++++++Rs
  gi|386002056|ref|YP_005920355.1| 28 AVLKLRRQGLSQQEVAEILGTTRS 51
                                      699********************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00013      0.15      14      41 ..      32      56 ..      19      63 .. 0.76
   2 ?   -2.8   0.0       5.4     6e+03      20      27 ..     127     137 ..     120     139 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2 14 Lgrrpgrdltvgelarrlglsksavsri 41
                                      L rr g  l+++e+a+ lg ++s+vs +
  gi|386002056|ref|YP_005920355.1| 32 L-RRQG--LSQQEVAEILGTTRSNVSIL 56
                                      4.4455..9****************966 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.4
                                       S...EEEHHHH CS
                            MarR_2  20 r...dltvgel 27 
                                           ++tv++l
  gi|386002056|ref|YP_005920355.1| 127 AlkkRVTVRDL 137
                                       24446788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1008.22
//
Query:       gi|386002057|ref|YP_005920356.1|  [L=115]
Description: hypothetical protein Mhar_1369 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 809.48
//
Query:       gi|386002058|ref|YP_005920357.1|  [L=111]
Description: CutA1 divalent ion tolerance protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-31  106.2   0.0      7e-31  106.0   0.0    1.0  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   3.9e-35     7e-31       2      98 ..       7     101 ..       5     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 3.9e-35
                                       EEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS- CS
                             CutA1   2 lvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevp 78 
                                       +vl+tap  +   +lar +v e laACvni + ++S+Y W+g+++e++E ll+ikt +ek+e l +r++e+hpy++p
  gi|386002058|ref|YP_005920357.1|   7 VVLTTAP-PNGSGRLARLIVGEGLAACVNISQ-VRSTYLWEGEVKEEAEDLLIIKTMKEKLEPLASRIREVHPYDLP 81 
                                       5556665.777899***************999.******************************************** PP

                                       EEEEEEESEEEHHHHHHHHH CS
                             CutA1  79 eiialpieagseaYlkWiee 98 
                                       eiialpi  g++ Yl+W+++
  gi|386002058|ref|YP_005920357.1|  82 EIIALPIRGGDDGYLDWVSR 101
                                       ******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 911.70
//
Query:       gi|386002059|ref|YP_005920358.1|  [L=147]
Description: hypothetical protein Mhar_1371 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-15   56.7   0.0      4e-15   56.3   0.0    1.2  1  HIT       HIT domain
    3.1e-11   43.8   0.0      4e-11   43.4   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0062   16.4   0.0     0.0082   16.0   0.0    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   6.7e-19     4e-15       4      96 ..      19     106 ..      16     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.7e-19
                                       C-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGG CS
                               HIT   4 ipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngah 80 
                                       ++++ ++eddl+la+ldi+p ++gh Lvipk+h++ +hdlteee+  l+++++ v +++ + +  +++ ++      
  gi|386002059|ref|YP_005920358.1|  19 AKARRIFEDDLSLAILDINPFSRGHSLVIPKRHVPWWHDLTEEEVESLFRVARTVSQKIMRAYDPDFVAIYA----- 90 
                                       57889*******************************************************977766666655..... PP

                                       GT-SSSS-EEEEEEC- CS
                               HIT  81 agqsvahlHiHviprr 96 
                                        g  ++h Hi ++p++
  gi|386002059|ref|YP_005920358.1|  91 RGRRIPHTHIFLVPTY 106
                                       9999*****9999876 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   6.7e-15     4e-11       2      86 ..       9      90 ..       8     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 6.7e-15
                                      -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEE CS
                            DcpS_C  2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdae 80
                                      ++f++++ g+ ++r ++ed+  +++ Di+p ++ h lvipkr+++  +dLt+e+++ l ++ +++ + i++ y   d++
  gi|386002059|ref|YP_005920358.1|  9 CIFCDIVAGRAKARRIFEDDLSLAILDINPFSRGHSLVIPKRHVPWWHDLTEEEVESLFRVARTVSQKIMRAY---DPD 84
                                      9****************************************************99888777777766666666...677 PP

                                      EE--SC CS
                            DcpS_C 81 elrvgv 86
                                      ++ ++ 
  gi|386002059|ref|YP_005920358.1| 85 FVAIYA 90
                                      777665 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0082      39     108 ..      33     104 ..       4     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                       ---.S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHH.HHHHHTT--EEEEEE-SSS-----EEEEE CS
                          CwfJ_C_1  39 lpk.gpLssgHvliipieHisallsldeevldeirkfrkalv.kmykkqdkdavvfEissersvHlaiqvip 108
                                       +   +p s gH l+ip  H++    l ee+ +++ +  +++  k+  + d d v      +r +H++i ++p
  gi|386002059|ref|YP_005920358.1|  33 ILDiNPFSRGHSLVIPKRHVPWWHDLTEEEVESLFRVARTVSqKIMRAYDPDFVAIYARGRRIPHTHIFLVP 104
                                       44448899********************9999999988888615699*****999888899******99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 964.31
//
Query:       gi|386002060|ref|YP_005920359.1|  [L=556]
Description: Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-45  154.6   0.0    4.9e-45  154.1   0.0    1.2  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    7.3e-27   94.6   0.1    1.4e-26   93.6   0.1    1.5  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    1.8e-07   30.9   1.0      1e-05   25.2   0.6    2.5  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
     0.0034   17.7   0.0     0.0079   16.5   0.0    1.6  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.0   1.1e-48   4.9e-45       3     222 ..     199     424 ..     197     432 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 1.1e-48
                                       HHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCH CS
                             POR_N   3 aiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienl 79 
                                        +++g+d ++aYP+TPss +++ la  + ++ +   +vv  e+Ei+ i ++ G a+aG ++a+ TSg G+ Lm e +
  gi|386002060|ref|YP_005920359.1| 199 LLRGGLDAYVAYPMTPSSGVLHFLAGVAGEFSI---KVVHPENEIAVILMAEGFAYAGKKTAVGTSGGGFCLMNEGM 272
                                       678999**********************99996...9**************************************** PP

                                       HHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEE CS
                             POR_N  80 glaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPviv 151
                                        la+++e+P+v+ v +Ra+pstg++++t+q Dl ++      +++ +v+++++++eaf   + A+ lA+++++Pv++
  gi|386002060|ref|YP_005920359.1| 273 SLAGMAEIPLVVLVSQRAGPSTGVPTYTAQADLPFVMsagqgEFPRLVIVPGDAEEAFFWSATALGLAWRYQIPVVL 349
                                       *************************************9*************************************** PP

                                       EEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX......SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXH CS
                             POR_N 152 lfDgfllshevekvelpdeedelklikekleeyerkey......aldpekpiargtaanpdtglehrekgneaedaa 222
                                       l+D++l  +++ + ++++  d+ +++   ++ + +++       +++p  ++ r +a ++++++ h  +g  +e+ a
  gi|386002060|ref|YP_005920359.1| 350 LSDKTLS-ESAYSFNIEEARDIPDIAPVLWDGEGDYQRyaspedGISPLAFPPRAGAVVKANSYAHLPSGITTEE-A 424
                                       *****98.9999999999888888777666655555543446667777777778888888888888888887777.4 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.1   3.1e-30   1.4e-26       1     176 [.      13     167 ..      11     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 3.1e-30
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       +G+G+  ag ++a+ +   Gy  +++ +y+s irGgh ++ vr++ + ++ + + +++d+l+al+++t+++hl +l+
  gi|386002060|ref|YP_005920359.1|  13 AGDGIAEAGMVIARLYNQLGYCLYQYLDYPSLIRGGHNFAIVRAAGK-KIGAHR-DGVDYLLALNQDTIDRHLWRLN 87 
                                       5*********************************************9.899999.9********************* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeai 154
                                       +g ++iy+s+e+k ++   a                g++++ +a+e+g  ++a+N+ ++Gal++++g+++e +e+++
  gi|386002060|ref|YP_005920359.1|  88 EGAVVIYDSDEVKAPPAGGA----------------GLPLKSFAREAGAPPIARNVGLIGALSGAAGIEEEIVEKVL 148
                                       *********87666655553................89***********9*************************** PP

                                       HCCS-CH.HHHHHHHHHHHHHH CS
                               POR 155 kkrfpkkkeviekNlkafragy 176
                                       +k+++k    i++Nl+++r+g+
  gi|386002060|ref|YP_005920359.1| 149 RKEIRK---YIDENLEVARRGR 167
                                       *****6...7**********98 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.6   2.3e-09     1e-05      23     107 ..     214     296 ..     190     317 .. 0.82
   2 ?    3.4   0.0     0.012        53      80     100 ..     334     354 ..     318     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.3e-09
                                       --CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE CS
                      TPP_enzyme_N  23 pGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgd 99 
                                       p s++l++l  ++ e +i+vv   +E +++ +A+g+a a +k +v   tsg G+  +  ++  A  + iPl+vl+ +
  gi|386002060|ref|YP_005920359.1| 214 PSSGVLHFLAGVAGEFSIKVVHPENEIAVILMAEGFAYAGKKTAV--GTSGGGFCLMNEGMSLAGMAEIPLVVLVSQ 288
                                       5666777777777777***********************987665..78999************************* PP

                                       --CCCHHS CS
                      TPP_enzyme_N 100 rptslrgq 107
                                       r+  ++g 
  gi|386002060|ref|YP_005920359.1| 289 RAGPSTGV 296
                                       99888773 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHT--EEEEEEE- CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdr 100
                                        tal  A++ +iP+++ls  +
  gi|386002060|ref|YP_005920359.1| 334 ATALGLAWRYQIPVVLLSDKT 354
                                       799**************9665 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0079      32      77 ..     485     526 ..     465     547 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                       EEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II  32 lrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       + + ++ PFP++++ke+l++v++ ++++ n +    Gql++ +++ 
  gi|386002060|ref|YP_005920359.1| 485 IAPVVVSPFPADRFKEALRGVERTISVETNST----GQLARLIRSY 526
                                       6678999************************5....9999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3616.24
//
Query:       gi|386002061|ref|YP_005920360.1|  [L=284]
Description: 2-oxoglutarate ferredoxin oxidoreductase beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  100.7   0.0    8.7e-29  100.3   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    8.3e-10   38.7   0.1    1.8e-09   37.6   0.0    1.5  2  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
  ------ inclusion threshold ------
      0.073   11.9   0.0       0.11   11.3   0.0    1.2  1  XFP_N         XFP N-terminal domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   1.5e-32   8.7e-29       2     153 .]      51     198 ..      50     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 1.5e-32
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+               yl+ +++++ +G+++p+A+G+kla+pd +v+++vGDG+ +   l +l+ a++rn+ it
  gi|386002061|ref|YP_005920360.1|  51 IGCHGK----------IADYLHlNSFYAIHGRAIPVATGIKLANPDLNVICFVGDGDAYAEgLDHLIFAAKRNVEIT 117
                                       788887..........3444444889*************************************************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       ++v++N++yg+t gq   ++p g + +s+p g +  p+++ +l+ a G +  ar  ++ ++ l+e+++ea+ ++g+a
  gi|386002061|ref|YP_005920360.1| 118 TIVHDNRVYGLTTGQytpTSPSGFSGRSTPGGLEVSPINPLELIFASGGTfIARGYSNRIDLLKETMREAILHRGFA 194
                                       ***************9998899999999999989****************8887778889***************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +++v
  gi|386002061|ref|YP_005920360.1| 195 FLDV 198
                                       **97 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.8   1.7e+04      14      28 ..     122     136 ..     117     137 .. 0.71
   2 !   37.6   0.0     3e-13   1.8e-09       1      62 [.     202     263 ..     202     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.8
                                       XX-EEEGGGST---E CS
                        PFO_beta_C  14 kervykleedgyDps 28 
                                       ++rvy l + +y p+
  gi|386002061|ref|YP_005920360.1| 122 DNRVYGLTTGQYTPT 136
                                       678888887667665 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 3e-13
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT----....-EEEEEEEETTS--HHHHHH CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgd....kiplGifYkeekptyeerle 62 
                                       C tF  +n +d Y+ r+y lee  +Dp+d   A e+++ew+     +iplGif ++  pt+ +++e
  gi|386002061|ref|YP_005920360.1| 202 CATF--FNMYDLYNRRTYALEE--HDPEDPVLAQERMREWDYnsegPIPLGIFHRRAAPTFGDNFE 263
                                       9999..9**************9..9**************97777778**************99986 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.8e-05      0.11     143     171 ..      71      99 ..      66     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                             XFP_N 143 GyalshayGavldnPdlivacvvGdGeae 171
                                       G a+ +a+G  l nPdl v+c vGdG+a 
  gi|386002061|ref|YP_005920360.1|  71 GRAIPVATGIKLANPDLNVICFVGDGDAY 99 
                                       668889********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2167.62
//
Query:       gi|386002062|ref|YP_005920361.1|  [L=53]
Description: rubredoxin-type Fe(Cys)4 protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-26   90.7   5.1    4.7e-26   90.6   5.1    1.0  1  Rubredoxin       Rubredoxin
    0.00017   21.6   0.1    0.00023   21.2   0.1    1.2  1  PHD_4            PHD-finger
    0.00026   20.4   0.8       0.32   10.6   0.1    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0023   17.8   0.7       0.87    9.6   0.0    2.1  2  ADK_lid          Adenylate kinase, active site lid
     0.0053   16.0   3.1      0.038   13.3   0.5    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
     0.0072   16.7   0.5        2.4    8.7   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
     0.0072   16.3   0.1       0.39   10.8   0.0    2.1  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
     0.0092   15.6   0.6        1.7    8.3   0.5    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
     0.0094   16.1   2.3      0.094   12.8   2.3    2.0  1  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.013   15.2   0.8          3    7.7   0.0    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.016   15.1   3.4       0.21   11.5   0.3    2.2  2  Nudix_N_2        Nudix N-terminal
      0.018   15.2   1.4        1.4    9.2   0.1    2.1  2  zf-nanos         Nanos RNA binding domain
      0.019   14.6   1.7       0.24   11.1   0.2    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.04   13.3   0.2       0.36   10.3   0.0    2.0  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
      0.045   13.6   1.9        1.5    8.8   0.3    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.045   13.6   3.0        3.2    7.7   0.4    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.049   13.6   4.7          3    7.8   0.1    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.062   13.1   1.5        2.2    8.2   0.3    2.1  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.064   13.3   0.1      0.073   13.1   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.085   13.2   1.1          6    7.3   0.2    2.1  2  C1_2             C1 domain
      0.086   12.8   1.7        9.6    6.2   0.2    2.0  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   13.2   1.5       0.66   10.7   0.0    2.0  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.16   12.4   1.6        5.6    7.5   0.1    2.4  2  Zn-C2H2_12       Autophagy receptor zinc finger-C2H2 domain
       0.28   11.7   3.3        6.4    7.4   0.5    2.2  2  zf-C2H2          Zinc finger, C2H2 type
       0.51   11.3   2.6         27    6.0   0.1    2.2  2  zf-C2H2_4        C2H2-type zinc finger
       0.68   10.0   2.3         22    5.2   0.7    2.2  2  zf-C2H2_6        C2H2-type zinc finger
        1.5    8.6   7.1        7.9    6.3   0.8    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   5.1     7e-29   4.7e-26       1      47 []       4      50 ..       4      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 7e-29
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      +y C+vCgy+Ydp+kGdpd+g++pgT+FedlPddW+CP+Cg++ke F
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYIYDPEKGDPDSGVTPGTAFEDLPDDWTCPVCGATKEVF 50
                                      79******************************************998 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   3.4e-07   0.00023      31      67 ..       5      43 ..       1      44 [. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.4e-07
                             PHD_4 31 meCsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67
                                       +C+vC  i  pe  +     ++g++ edlp +W Cp C
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYIYDPEKGDPDsgVTPGTAFEDLPDDWTCPVC 43
                                      68**********988776556789*************** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00048      0.32      20      37 ..       5      22 ..       1      24 [. 0.81
   2 !    8.9   0.1    0.0016       1.1       2      12 ..      39      49 ..      38      53 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                                      EEESSSSBEEEECCCCCC CS
                      TF_Zn_Ribbon 20 lvCtdCGlVlednsideg 37
                                      ++Ct CG++ + +  d+ 
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYIYDPEKGDPD 22
                                      899999999988888875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                      +CP+Cg t+ v
  gi|386002062|ref|YP_005920361.1| 39 TCPVCGATKEV 49
                                      6*****98733 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0013      0.87       1      12 [.       4      15 ..       4      37 .. 0.86
   2 !    7.0   0.4    0.0084       5.6       2      10 ..      38      46 ..      38      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                      EEE-TTT--EEE CS
                           ADK_lid  1 RrvCpkCGrsYh 12
                                      R +C  CG +Y 
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYIYD 15
                                      99*********7 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0084
                                      EE-TTT--E CS
                           ADK_lid  2 rvCpkCGrs 10
                                      ++Cp CG++
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCGAT 46
                                      9******96 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.06        40       6      12 ..       6      12 ..       2      13 .. 0.84
   2 !   13.3   0.5   5.7e-05     0.038       3      11 ..      36      44 ..      34      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.06
                                      E-SSS-- CS
                          zf-RanBP  6 dCskClv 12
                                      +C++C++
  gi|386002062|ref|YP_005920361.1|  6 TCTVCGY 12
                                      6999987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.7e-05
                                      SSEE-SSS- CS
                          zf-RanBP  3 gdWdCskCl 11
                                      +dW+C++C+
  gi|386002062|ref|YP_005920361.1| 36 DDWTCPVCG 44
                                      89******8 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0037       2.4      13      22 ..       3      12 ..       1      15 [. 0.87
   2 ?    6.8   0.0     0.015        10      15      21 ..      38      44 ..      24      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0037
                         zf-H2C2_2 13 kpyeCplCdk 22
                                      k+y+C +C++
  gi|386002062|ref|YP_005920361.1|  3 KRYTCTVCGY 12
                                      78******99 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                         zf-H2C2_2 15 yeCplCd 21
                                      ++Cp+C+
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCG 44
                                      79****8 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.073        48      22      31 ..       3      12 ..       1      15 [. 0.83
   2 !   10.8   0.0   0.00059      0.39      23      35 ..      37      49 ..      26      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.073
                    zf-Sec23_Sec24 22 krwiCnfCnh 31
                                      kr++C  C+ 
  gi|386002062|ref|YP_005920361.1|  3 KRYTCTVCGY 12
                                      899*****86 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00059
                    zf-Sec23_Sec24 23 rwiCnfCnhknev 35
                                       w+C+ C+   ev
  gi|386002062|ref|YP_005920361.1| 37 DWTCPVCGATKEV 49
                                      6*******98877 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.5    0.0026       1.7       6      15 ..       4      13 ..       1      15 [. 0.84
   2 ?    5.7   0.0     0.016        11       8      20 ..      39      51 ..      35      53 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                                      EEE-TTT--E CS
                   Desulfoferrod_N  6 vYkCevCGni 15
                                       Y C+vCG i
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYI 13
                                      59******87 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                                      E-TTT--EEEECC CS
                   Desulfoferrod_N  8 kCevCGniVeVle 20
                                       C vCG   eV e
  gi|386002062|ref|YP_005920361.1| 39 TCPVCGATKEVFE 51
                                      6*****9999987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.3   0.00014     0.094       6      34 ..       5      45 ..       4      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                       Zn-ribbon_8  6 YrCeeCghefe...........vlqsisdaplta.CPeCgs 34
                                      Y C+ Cg  ++           +  ++ d p+   CP Cg+
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYIYDpekgdpdsgvtPGTAFEDLPDDWtCPVCGA 45
                                      99*********888888887764443446667777****98 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.011       7.6       3      10 ..       4      11 ..       2      13 .. 0.85
   2 ?    7.7   0.0    0.0045         3       2      15 ..      36      49 ..      35      53 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                     A2L_zn_ribbon  3 lkvCsvCg 10
                                       ++C+vCg
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCG 11
                                      689****8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                     A2L_zn_ribbon  2 nlkvCsvCggngil 15
                                      ++++C vCg  +++
  gi|386002062|ref|YP_005920361.1| 36 DDWTCPVCGATKEV 49
                                      67889999877766 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00032      0.21      21      31 ..       3      13 ..       2      14 .. 0.91
   2 ?    4.6   0.2     0.047        31      25      30 ..      40      45 ..      38      49 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                      -EEEETTTTEE CS
                         Nudix_N_2 21 eRlvCpaCgti 31
                                       R++C+ Cg+i
  gi|386002062|ref|YP_005920361.1|  3 KRYTCTVCGYI 13
                                      5*********9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.047
                                      ETTTTE CS
                         Nudix_N_2 25 CpaCgt 30
                                      Cp Cg+
  gi|386002062|ref|YP_005920361.1| 40 CPVCGA 45
                                      555554 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.032        21      32      41 ..       3      12 ..       1      16 [. 0.85
   2 ?    9.2   0.1    0.0021       1.4      34      44 ..      38      48 ..      36      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.032
                          zf-nanos 32 rkyvCpiCga 41
                                      ++y+C++Cg 
  gi|386002062|ref|YP_005920361.1|  3 KRYTCTVCGY 12
                                      58******95 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                          zf-nanos 34 yvCpiCgatgd 44
                                       +Cp+Cgat++
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCGATKE 48
                                      59*******87 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1       0.1        67       6      11 ..       6      11 ..       1      14 [. 0.78
   2 ?   11.1   0.2   0.00036      0.24       5      17 ..      38      51 ..      35      53 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.1
                           zf-RRN7  6 pCgvCg 11
                                       C vCg
  gi|386002062|ref|YP_005920361.1|  6 TCTVCG 11
                                      588887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                           zf-RRN7  5 ppCgvCgc.rsftl 17
                                      + C+vCg+ +++++
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCGAtKEVFE 51
                                      78******656655 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.29   1.9e+02      11      40 ..       6      11 ..       1      17 [. 0.67
   2 ?   10.3   0.0   0.00054      0.36       7      20 ..      35      48 ..      29      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                       Vps36-NZF-N 11 vCpICsfsNevpsnfdpnastplPpClaCG 40
                                      +C++C                        G
  gi|386002062|ref|YP_005920361.1|  6 TCTVC------------------------G 11
                                      45555........................4 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00054
                       Vps36-NZF-N  7 tatWvCpICsfsNe 20
                                        +W+Cp+C  + e
  gi|386002062|ref|YP_005920361.1| 35 PDDWTCPVCGATKE 48
                                      568******98765 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3    0.0023       1.5      21      32 ..       4      15 ..       1      18 [. 0.81
   2 ?    4.7   0.1     0.042        28      16      32 ..      36      48 ..      34      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                                      EEEESSSS-EEE CS
                    RNA_POL_M_15KD 21 nfeCrqCgYeep 32
                                      ++ C  CgY++ 
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYIYD 15
                                      588******995 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.042
                                      CSCCCEEEESSSS-EEE CS
                    RNA_POL_M_15KD 16 dkegknfeCrqCgYeep 32
                                      d+++    C  Cg+ ++
  gi|386002062|ref|YP_005920361.1| 36 DDWT----CPVCGATKE 48
                                      6777....999*99988 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0048       3.2      25      37 ..       1      13 [.       1      15 [. 0.81
   2 ?    7.0   0.1     0.008       5.3       2      13 ..      39      50 ..      38      53 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                           TFIIS_C 25 mtvfykCtkCghr 37
                                      m   y+Ct Cg+ 
  gi|386002062|ref|YP_005920361.1|  1 MAKRYTCTVCGYI 13
                                      5678*******86 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.008
                           TFIIS_C  2 kCpkCgsreayf 13
                                      +Cp Cg ++ +f
  gi|386002062|ref|YP_005920361.1| 39 TCPVCGATKEVF 50
                                      7******99887 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.0     0.005       3.3       5      12 ..       5      12 ..       4      18 .. 0.79
   2 ?    7.8   0.1    0.0045         3       4      12 ..      37      45 ..      35      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.005
                    Zn_ribbon_SprT  5 YrCtgCgr 12
                                      Y+Ct Cg 
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGY 12
                                      9******4 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0045
                    Zn_ribbon_SprT  4 vYrCtgCgr 12
                                       ++C+ Cg 
  gi|386002062|ref|YP_005920361.1| 37 DWTCPVCGA 45
                                      59******5 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0032       2.2      14      25 ..       5      16 ..       1      21 [. 0.81
   2 ?    4.3   0.0     0.052        34      14      20 ..      38      44 ..      32      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0032
                         zf-C2H2_3 14 sqCkeCgMvYnp 25
                                       +C++Cg +Y p
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYIYDP 16
                                      57********87 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.052
                         zf-C2H2_3 14 sqCkeCg 20
                                       +C++Cg
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCG 44
                                      57****9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011     0.073      70      96 ..       4      47 ..       1      52 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      EEEETTTS-EEECHH.H.HH...............S-TTTSSS- CS
                              HypA 70 kvrCreCgkefelee.k.al...............rCpkCgsad 96
                                      +++C++Cg+ ++ e+ + +                +Cp Cg+++
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYIYDPEKgDpDSgvtpgtafedlpddwTCPVCGATK 47
                                      689*********886444337899*****************975 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2     0.009         6      32      43 ..       4      15 ..       1      17 [. 0.78
   2 ?    5.3   0.0     0.038        25      16      28 ..      35      47 ..      29      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                              C1_2 32 fYsCseCdfslh 43
                                      +Y+C+ C ++ +
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYIYD 15
                                      599999999877 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                              C1_2 16 sesfnCsaCgrki 28
                                       ++++C +Cg + 
  gi|386002062|ref|YP_005920361.1| 35 PDDWTCPVCGATK 47
                                      6789*****9874 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.023        16      46      57 ..       4      15 ..       2      18 .. 0.73
   2 ?    6.2   0.2     0.014       9.6      30      39 ..      39      48 ..      37      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.023
                    OrfB_Zn_ribbon 46 tfkCpnCgfead 57
                                      +++C+ Cg+ +d
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCGYIYD 15
                                      677888887765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                    OrfB_Zn_ribbon 30 tCseCgsknk 39
                                      tC++Cg++++
  gi|386002062|ref|YP_005920361.1| 39 TCPVCGATKE 48
                                      7899988876 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.59   3.9e+02      41      47 .]       4      10 ..       2      12 .. 0.72
   2 ?   10.7   0.0   0.00099      0.66       3      14 ..      38      49 ..      36      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.59
                           zf-ISL3 41 RyrCkeC 47
                                      Ry+C  C
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVC 10
                                      7788766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00099
                           zf-ISL3  3 hrCPnCgsktvv 14
                                      ++CP Cg+++ v
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCGATKEV 49
                                      8*******9865 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.098        65       2      12 ..       6      16 ..       6      18 .. 0.84
   2 ?    7.5   0.1    0.0085       5.6       2       8 ..      39      45 ..      39      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.098
                        Zn-C2H2_12  2 eCPlCseqFpk 12
                                      +C +C++++ +
  gi|386002062|ref|YP_005920361.1|  6 TCTVCGYIYDP 16
                                      588******87 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0085
                        Zn-C2H2_12  2 eCPlCse 8 
                                      +CP+C+ 
  gi|386002062|ref|YP_005920361.1| 39 TCPVCGA 45
                                      6****85 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5    0.0097       6.4       1      10 [.       5      14 ..       5      17 .. 0.88
   2 ?    5.1   0.1     0.055        37       2       7 ..      39      44 ..      38      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0097
                                      EEETTTTEEE CS
                           zf-C2H2  1 ykCpdCgksF 10
                                      y+C++Cg+ +
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYIY 14
                                      9******876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.055
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +Cp+Cg
  gi|386002062|ref|YP_005920361.1| 39 TCPVCG 44
                                      8****9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.046        30       1      10 [.       5      14 ..       5      18 .. 0.81
   2 ?    6.0   0.1     0.041        27       2       9 ..      39      46 ..      38      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.046
                         zf-C2H2_4  1 fkCpiCgksF 10
                                      ++C++Cg  +
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYIY 14
                                      89****8766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.041
                         zf-C2H2_4  2 kCpiCgks 9 
                                      +Cp+Cg++
  gi|386002062|ref|YP_005920361.1| 39 TCPVCGAT 46
                                      7****875 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.7     0.033        22       1       8 [.       4      11 ..       4      12 .. 0.89
   2 ?    4.5   0.0     0.053        35       4      10 ..      40      46 ..      38      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                         zf-C2H2_6  1 vheCsvCs 8 
                                      ++ C+vC+
  gi|386002062|ref|YP_005920361.1|  4 RYTCTVCG 11
                                      599****7 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.053
                         zf-C2H2_6  4 CsvCsks 10
                                      C+vC+++
  gi|386002062|ref|YP_005920361.1| 40 CPVCGAT 46
                                      *****86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.8     0.016        11       1       9 [.       5      13 ..       5      15 .. 0.88
   2 ?    6.3   0.8     0.012       7.9      15      22 ..      38      45 ..      38      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y C  CG+ 
  gi|386002062|ref|YP_005920361.1|  5 YTCTVCGYI 13
                                      99*****96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                      Rubredoxin_2 15 GrCpsCgs 22
                                      + Cp Cg+
  gi|386002062|ref|YP_005920361.1| 38 WTCPVCGA 45
                                      99****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 326.39
//
Query:       gi|386002063|ref|YP_005920362.1|  [L=176]
Description: Ferritin, Dps family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-43  146.7   1.5    4.7e-43  146.5   1.5    1.1  1  Ferritin  Ferritin-like domain
  ------ inclusion threshold ------
      0.079   11.7   0.0       0.17   10.6   0.0    1.5  2  DUF4432   Domain of unknown function (DUF4432)


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   1.5   5.3e-47   4.7e-43       3     141 ..      11     145 ..       9     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 5.3e-47
                                       HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.C CS
                          Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.f 78 
                                       aLneq+ +el+++y+ylam+++++  +l+g+a++++ qa+ee+ h++k++++++a+Gg     rael +ie+p   +
  gi|386002063|ref|YP_005920362.1|  11 ALNEQVRAELYSSYLYLAMSAHFSAANLPGFANWMRVQAQEELMHGMKIYDFVIARGG-----RAELLAIEKPSFeW 82 
                                       8*********************************************************.....***********9** PP

                                       SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  79 gsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                       +s++ev+e+++ hekkvt  ++ l+++a+ e+D at ++l++f+eeq+e+e++ ++++ek+++
  gi|386002063|ref|YP_005920362.1|  83 ASPLEVVEEVFRHEKKVTGLIHALADVAAGEKDQATSNMLQWFVEEQVEEEANAREIVEKVRL 145
                                       ***********************************************************9876 PP

>> DUF4432  Domain of unknown function (DUF4432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   1.9e-05      0.17     224     262 ..      13      51 ..       5      57 .. 0.89
   2 ?   -3.0   0.0      0.28   2.5e+03      34      51 ..      77      94 ..      61     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.9e-05
                                       TSEEEEEEE-SSSS-EEEEEEETTTS-EEEEEEEES-T- CS
                           DUF4432 224 kgetlaalvnkklglgvavkfdkdqLPvltlWkntgage 262
                                       +++++a+l+++ l l+++ +f++++LP +++W +++a+e
  gi|386002063|ref|YP_005920362.1|  13 NEQVRAELYSSYLYLAMSAHFSAANLPGFANWMRVQAQE 51 
                                       7899****************************9999864 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.28
                                      TEEE----S-----GGG- CS
                           DUF4432 34 gvrlgwdspvgvvapalv 51
                                        ++ w sp +vv+  + 
  gi|386002063|ref|YP_005920362.1| 77 KPSFEWASPLEVVEEVFR 94
                                      556778888776665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1291.88
//
Query:       gi|386002064|ref|YP_005920363.1|  [L=316]
Description: Putative 6-phosphogluconate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-36  126.0   0.0    2.5e-36  125.2   0.0    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.9e-12   47.2   0.0    2.3e-12   46.9   0.0    1.1  1  6PGD            6-phosphogluconate dehydrogenase, C-terminal 
    8.9e-06   25.2   0.0    1.4e-05   24.5   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0003   21.3   0.0    0.00072   20.1   0.0    1.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.045   14.0   0.0      0.079   13.2   0.0    1.4  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.0   7.1e-40   2.5e-36       1     153 [.       8     163 ..       8     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 7.1e-40
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.akaaesieelvasldvvitmvkagkavdeviegl 76 
                                       k+g++GlG+MG n+al  +++g+ v++  r+++   e    + + a++ i +++++ +v+ + ++ag+ vd+vie+l
  gi|386002064|ref|YP_005920363.1|   8 KLGILGLGKMGGNLALLAKEKGIAVVGKSRSAKPHLERKGVKvVGAYDPIVDFLDQPRVIYISIPAGPTVDKVIEEL 84 
                                       689************************999977665555555244445556999999******************** PP

                                       CCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEE.. CS
                     NAD_binding_2  77 lealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaiga.. 151
                                       ++ l++gd++idg++s + d+ +++++l+++g+ fld++ SGG+ gA+kG+  +mvGG+++ f+ ++p+l++++a  
  gi|386002064|ref|YP_005920363.1|  85 VPLLDSGDVVIDGGNSFYLDSVRREEDLADNGIFFLDCGTSGGVDGARKGP-CFMVGGNKDGFKVAEPILTSLAAeg 160
                                       ***************************************************.**********************966 PP

                                       .EE CS
                     NAD_binding_2 152 .kv 153
                                        ++
  gi|386002064|ref|YP_005920363.1| 161 aCI 163
                                       343 PP

>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   6.5e-16   2.3e-12       1     117 [.     171     279 ..     171     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 6.5e-16
                              6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkg.elesyLieitakilrkkdeedgkplvdki 76 
                                       Gh+ K+v  G+e +++q+i+E ++ll++     + +++++F+ W +g +++ +L+e  ak l+++     +++  ++
  gi|386002064|ref|YP_005920363.1| 171 GHFTKLVQDGVEAAMLQAIGEGVSLLRES--DFHLDMEKIFKGWARGaTVRGWLVELMAKSLAEQRF---SDVPTHV 242
                                       9**************************86..457789**********778************98884...2345555 PP

                              6PGD  77 lDkagqkGTgkwtvqealelgvpvptiaeavfaRllSslke 117
                                           +  G  +w v +ale +vp+p+ia+a +  + S +k+
  gi|386002064|ref|YP_005920363.1| 243 ----EDTGEVNWLVHDALEKEVPIPVIAQAAMELFRSRDKN 279
                                       ....5567789*******************98877777665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     4e-09   1.4e-05      35     110 ..       5      82 ..       1      99 [. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4e-09
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC..EECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv..elvsleellaesDivslhlpltpetrhli 109
                                       +++++Gi+GlG++G ++a ++k+ g+ v++ +rs k+  e + ++v   ++ + ++l +  ++ + +p+ p   ++i
  gi|386002064|ref|YP_005920363.1|   5 KDMKLGILGLGKMGGNLALLAKEKGIAVVGKSRSAKPHLERKGVKVvgAYDPIVDFLDQPRVIYISIPAGPTVDKVI 81 
                                       7899******************************998773333333346899*****************99988888 PP

                                       S CS
                      2-Hacid_dh_C 110 n 110
                                       +
  gi|386002064|ref|YP_005920363.1|  82 E 82 
                                       6 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     2e-07   0.00072       1      94 [.       8      97 ..       8     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE..CHHHHHHH-SEEEE-S-H.HHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtav..dneeaaeeadvvvlavkp.edvee 76
                                      k+gi+G G+mg  la+ + ++g     +v + sr+ +      e+ gvkv +   +  + +++  v+ ++++    v++
  gi|386002064|ref|YP_005920363.1|  8 KLGILGLGKMGGNLALLAKEKG---IAVV-GKSRSAK---PHLERKGVKVVGAydPIVDFLDQPRVIYISIPAgPTVDK 79
                                      79**************999999...7777.7666655...5556666666652116678888999******98468999 PP

                                      HHHHCGHHHHTTSEEEEE CS
                     F420_oxidored 77 vlselakdalkgklvisv 94
                                      v++el + +++g +vi+ 
  gi|386002064|ref|YP_005920363.1| 80 VIEELVPLLDSGDVVIDG 97
                                      *****999999****995 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05     0.079       1     104 [.     169     275 ..     169     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                    NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaek..aGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlml 75 
                                       G+G+ +Klv   + a+ l a++E++ l++   + ld+ek+++   +++    +l + + +++++++f     + +++
  gi|386002064|ref|YP_005920363.1| 169 GSGHFTKLVQDGVEAAMLQAIGEGVSLLREsdFHLDMEKIFKGWARGATVRGWLVELMAKSLAEQRFSD---VPTHV 242
                                       9***************************98335689999998887777666666667777888888765...78888 PP

                    NAD_binding_11  76 KDlglalel...areagaplpllala.eqlyaa 104
                                        D g ++ l   a e ++p+p++a+a ++l+++
  gi|386002064|ref|YP_005920363.1| 243 EDTGEVNWLvhdALEKEVPIPVIAQAaMELFRS 275
                                       887766655222556788888877651566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1974.33
//
Query:       gi|386002065|ref|YP_005920364.1|  [L=186]
Description: hypothetical protein Mhar_1377 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-49  165.6  13.5    6.3e-49  165.6  13.5    2.0  2  Mntp      Putative manganese efflux pump
  ------ inclusion threshold ------
        7.2    6.6   9.7       0.63   10.1   3.1    2.3  2  IncE      Inclusion membrane protein E


Domain annotation for each model (and alignments):
>> Mntp  Putative manganese efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   1.6    0.0014        12      76      95 ..       4      23 ..       1      31 [. 0.84
   2 !  165.6  13.5     7e-53   6.3e-49       4     152 .]      33     180 ..      29     180 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0014
                              Mntp 76 ksllllaiatSiDAlavGls 95
                                      +s ll+a++ S+DA+av ++
  gi|386002065|ref|YP_005920364.1|  4 ISSLLIALGLSMDAFAVSVT 23
                                      677899***********987 PP

  == domain 2  score: 165.6 bits;  conditional E-value: 7e-53
                              Mntp   4 lkealkialifGlfqalmpliGwllGkllselieavdhwiafllLlllGlkmivealkeeeeekkekeelslkslll 80 
                                       l+ al +a++fG fqa+mp+iGwl G  +s+l +++dhwiaf+lL+l+G+kmi+e+++ e +e+++ + l+l+ l+l
  gi|386002065|ref|YP_005920364.1|  33 LRGALAAAIFFGGFQAFMPVIGWLGGIGFSDLASSYDHWIAFALLALIGGKMIFESMTVEPSERSA-DLLDLRLLTL 108
                                       678999*******************************************************99998.79******** PP

                              Mntp  81 laiatSiDAlavGlsLallkvnillavlliGlvtlvlsllGlllGrklgsllgkkaeilGGliLiliGlkil 152
                                       laiatSiDAlavG+++a+l+v+il++v++iG+vt++ls+lG+++G+++  ll +++e++GGliLi+iGlkil
  gi|386002065|ref|YP_005920364.1| 109 LAIATSIDALAVGVTFAFLDVSILVPVAIIGTVTFALSFLGVFIGSRFVGLLDNRVEVAGGLILIGIGLKIL 180
                                       ***********************************************************************8 PP

>> IncE  Inclusion membrane protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4     0.066     6e+02      47      67 ..       6      26 ..       2      46 .. 0.77
   2 ?   10.1   3.1     7e-05      0.63      46      97 ..     107     158 ..      89     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.066
                                      XXXXXXXXXXXXXXXXXXXXX CS
                              IncE 47 iiclalgiaaaavgvscsgfa 67
                                       + +alg++  a  vs++g a
  gi|386002065|ref|YP_005920364.1|  6 SLLIALGLSMDAFAVSVTGGA 26
                                      456788888888888877755 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              IncE  46 siiclalgiaaaavgvscsgfaiglgviaillgivlfaisaldvledhglvg 97 
                                       +++++a  i a avgv+ + + + + v   ++g v fa+s l v+    +vg
  gi|386002065|ref|YP_005920364.1| 107 TLLAIATSIDALAVGVTFAFLDVSILVPVAIIGTVTFALSFLGVFIGSRFVG 158
                                       56789999*******************9999***********9987766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1313.05
//
Query:       gi|386002066|ref|YP_005920365.1|  [L=223]
Description: SAM-dependent methyltransferase, UbiE/COQ5 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-16   60.0   0.1    4.6e-16   59.2   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    5.1e-13   49.5   0.1      1e-12   48.5   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    5.4e-07   29.2   0.1    1.6e-06   27.7   0.0    1.7  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.3e-07   28.8   0.0    1.2e-06   28.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.6e-06   28.8   0.0    2.7e-06   28.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    0.00066   19.5   0.0    0.00094   19.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.096   12.3   0.0       0.15   11.7   0.0    1.3  1  PsaL             Photosystem I reaction centre subunit XI
       0.17   12.0   0.0       0.27   11.4   0.0    1.3  1  GSH-S_N          Prokaryotic glutathione synthetase, N-termin


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   2.1e-19   4.6e-16       1      96 []      47     132 ..      47     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.1e-19
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L+vG+GtGr++++l      ++g+D+s +m+++a++++      v++v++ ae+lpf+d+ fD v++  v + + d 
  gi|386002066|ref|YP_005920365.1|  47 LEVGVGTGRFSAPLG----VTFGLDPSVAMMEAARRRG------VTCVRGVAERLPFRDGAFDQVLMVTVDFLLSDK 113
                                       89*************....799*********9997776......678*********************999999*** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       ++a++e+aRvL pgG +v+
  gi|386002066|ref|YP_005920365.1| 114 MAAFREMARVLAPGGAVVV 132
                                       ***************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   4.7e-16     1e-12       2      97 .]      47     128 ..      47     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.7e-16
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG.S CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh.l 77 
                                       L++G GtGr+++ l          g+D+s +m+eaar+r       v++v+g ae+lpf dg fD v+++ +  + l
  gi|386002066|ref|YP_005920365.1|  47 LEVGVGTGRFSAPLGVT------FGLDPSVAMMEAARRRG------VTCVRGVAERLPFRDGAFDQVLMVTV-DFlL 110
                                       89************755......59**************9......9**********************866.4424 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       s  d  +a++e+arvL pgG
  gi|386002066|ref|YP_005920365.1| 111 S--DKMAAFREMARVLAPGG 128
                                       5..6679************9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     7e-10   1.6e-06      99     151 ..      80     132 ..      65     141 .. 0.83
   2 ?   -1.7   0.0      0.66   1.5e+03     201     218 ..     171     188 ..     166     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7e-10
                                       TEEEEE--TTT-TTS-T-EE...EEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  99 nieflqanaeeLpfeddsfD...vvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        +  + + ae+Lpf d++fD   +vtv f    ++Dk  a++e+ rvl pGG++vv
  gi|386002066|ref|YP_005920365.1|  80 GVTCVRGVAERLPFRDGAFDqvlMVTVDFL---LSDKMAAFREMARVLAPGGAVVV 132
                                       688999**************4444688886...59******************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.66
                                       HHHHHHHHHHTTEEEEEE CS
                   Ubie_methyltran 201 qetlkeliedaGfksvey 218
                                        e++++l++ aGf    +
  gi|386002066|ref|YP_005920365.1| 171 PEEMADLLKAAGFADLAF 188
                                       688999999999987655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   5.4e-10   1.2e-06      14     163 ..      31     186 ..      11     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.4e-10
                   Methyltransf_23  14 erllpk...lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdl 85 
                                        +l++    l++  r L++G GtG+++  l        g D+s ++ e a+  +  + + + +     ++ +g fd 
  gi|386002066|ref|YP_005920365.1|  31 SELAAVkssLPRFDRGLEVGVGTGRFSAPLG----VTFGLDPSVAMMEAARrrGVTCVRGVAE---RLPFRDGAFDQ 100
                                       33332233466777**************772....2359999999888887763333333333...666699***** PP

                   Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpag........rhisffsarslkel 154
                                       + +  v   + d  +++r +a+ l+pgG +++  ++++++  r+++  + +++ +        +  +f   +++++l
  gi|386002066|ref|YP_005920365.1| 101 VLMVTVDFLLSDKMAAFREMARVLAPGGAVVVGFIDRESPVGRRYQREKGDREGEsdgvdgfyGEARFLAPEEMADL 177
                                       ***************************************88888888666654445445434455599999****** PP

                   Methyltransf_23 155 leeaGlevv 163
                                       l++aG+ ++
  gi|386002066|ref|YP_005920365.1| 178 LKAAGFADL 186
                                       ******876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.2e-09   2.7e-06       1      98 [.      47     129 ..      47     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+G GtG+++++l          g+D+s +++        + +++ +++v+  a+ l  +dg  +fD v++  v  
  gi|386002066|ref|YP_005920365.1|  47 LEVGVGTGRFSAPLGVT------FGLDPSVAMM-------EAARRRGVTCVRGVAERLPFRDG--AFDQVLMVTVDF 108
                                       8*************888......8*********.......33444568899999999999998..9*********99 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                        l d+ +++++++++L+pgG 
  gi|386002066|ref|YP_005920365.1| 109 LLSDKMAAFREMARVLAPGGA 129
                                       99******************6 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.2e-07   0.00094       8     113 ..      47     136 ..      44     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.2e-07
                   Methyltransf_31   8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                       l++G GtG+++  l          +G+D s  + e Ar +        v+  +g +e l+  + d  fD +l   v 
  gi|386002066|ref|YP_005920365.1|  47 LEVGVGTGRFSAPLG-------VTFGLDPSVAMMEAARRR-------GVTCVRGVAERLP--FRDGAFDQVLMVTVD 107
                                       678888888888777.......2589************97.......78888888888**..********9998777 PP

                   Methyltransf_31  85 naladpdkileeiervlkpggilliedpr 113
                                        +l+d+ ++++e+ rvl pgg++++  ++
  gi|386002066|ref|YP_005920365.1| 108 FLLSDKMAAFREMARVLAPGGAVVVGFID 136
                                       99**********************98776 PP

>> PsaL  Photosystem I reaction centre subunit XI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.6e-05      0.15      25      54 ..      27      56 ..      23      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                                      HHHHHHSTTT-TT--HHHHHHHHHHHHHHH CS
                              PsaL 25 kaflnnLpaYRkglspllRGlEiGlAhGYf 54
                                      +a+l++L a +++l  + RGlE+G+  G f
  gi|386002066|ref|YP_005920365.1| 27 AAYLSELAAVKSSLPRFDRGLEVGVGTGRF 56
                                      589**********************99977 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.27      16      49 ..      65      98 ..      60     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                           GSH-S_N 16 kkDttfalmleaqarghevfvleaadLslregka 49
                                        D ++a+m++a +rg +++   a++L +r+g  
  gi|386002066|ref|YP_005920365.1| 65 GLDPSVAMMEAARRRGVTCVRGVAERLPFRDGAF 98
                                      5699****************99999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1356.38
//
Query:       gi|386002067|ref|YP_005920366.1|  [L=319]
Description: hypothetical protein Mhar_1379 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2204.44
//
Query:       gi|386002068|ref|YP_005920367.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002068|ref|YP_005920367.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002068|ref|YP_005920367.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002068|ref|YP_005920367.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002068|ref|YP_005920367.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002068|ref|YP_005920367.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2055.38
//
Query:       gi|386002069|ref|YP_005920368.1|  [L=378]
Description: Aspartate aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for 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-61  209.2   0.0    1.2e-61  209.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0018   16.9   0.0     0.0029   16.2   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.021   14.2   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.04   14.0   0.0       0.23   11.5   0.0    2.0  2  Rsbr_N           Rsbr N terminal
      0.063   12.2   0.0        0.1   11.6   0.0    1.2  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.0   0.0   3.2e-65   1.2e-61       2     363 .]      30     373 ..      29     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.0 bits;  conditional E-value: 3.2e-65
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi+Lg++e+++d    t++++  a+++  +  ++ + y+p+ g pel+ a+a+ l++++++++ ++  v v +Ga+
  gi|386002069|ref|YP_005920368.1|  30 DVIDLGVGEPDFD----TPKNICDAAIR--SLARGDTHYLPTSGIPELRAAIAEKLSQENGIEVSPD-LVSVVPGAK 99 
                                       79***********....**********9..88888999*****************************.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +i a++++l l+ gde ++  p++ sy+++++ +gg v+  ++    d +    +l + ++       ktk+ilv+
  gi|386002069|ref|YP_005920368.1| 100 MAIFAAMQAL-LDEGDEGVLIGPSWVSYEPCINFAGGRVRWAEV----DDRFEPVSLADSITP------KTKMILVN 165
                                       **********.****************************99994....468999********9......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                       sp+NPtG+v+ +  le++ dla  + l++++De+Y++  +g +d+ ++   ++   + +++v+++sK ++++G+R+G
  gi|386002069|ref|YP_005920368.1| 166 SPSNPTGAVFGRRILEEIRDLAVDHDLMVLSDEIYEKIIYG-QDHLSI-GSFSGMEErTVTVNGFSKCYAMTGWRLG 240
                                       *****************************************.677785.33333333479***************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       y++g ++v ++++++ ++  s  ++ +q+a ++al+ +++   +++ m++++ +rr+ l+++Lae+g+ +  + +++
  gi|386002069|ref|YP_005920368.1| 241 YLAGPQEVMKWVNRILSHSVShaTTFVQWAGVEALKGPQE---SINGMVAEFRARRDLLVAGLAEIGIRCPLPGGAF 314
                                       ***************************************7...9********************************* PP

                                       EEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       +++ d+s+    +++++ +l e  ++ tpg+ f+     ++Ri++ + ++e l+e++ ++
  gi|386002069|ref|YP_005920368.1| 315 YVFPDVSEFgGGDSFAERMLSEAMLAATPGSAFGPggVDHVRISY-AASRERLTEALARI 373
                                       *******989999**********************99889*****.99999999999987 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.1e-07    0.0029      77     171 ..      99     195 ..      84     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.1e-07
                                       HHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT-- CS
                   Cys_Met_Meta_PP  77 maAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkv 153
                                         Ai+aa++all +Gde v+    + + +  ++    ++   +++ d  ++ +l+  i+++tk++++ +p+np+  v
  gi|386002069|ref|YP_005920368.1|  99 KMAIFAAMQALLDEGDEGVLIGPSWVSYEPCINFAGGRVRW-AEVDDRFEPVSLADSITPKTKMILVNSPSNPTGAV 174
                                       5689999999999**99888777766666666555554432.3445566788999*******************988 PP

                                       --...HHHHHHHHHHTT-EEE CS
                   Cys_Met_Meta_PP 154 vD...iekiaklakkagvlvv 171
                                            +e+i +la +++++v+
  gi|386002069|ref|YP_005920368.1| 175 FGrriLEEIRDLAVDHDLMVL 195
                                       653335666666666666665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.8e-06     0.021      48     144 ..      99     197 ..      65     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
                                       HHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GG CS
                   DegT_DnrJ_EryC1  48 taAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhly 121
                                         A+  a++al +++gde +    ++v+   ++  +g ++  ++vd      +p +++  it++tk Il   p +  
  gi|386002069|ref|YP_005920368.1|  99 KMAIFAAMQAL-LDEGDEGVLIGPSWVSYEPCINFAGGRVRWAEVDD---RFEPVSLADSITPKTKMILvnsPSNPT 171
                                       45888888885.445799999999**********************4...4689**************944456788 PP

                                       GB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 122 Gqva...dmdalkaiaakhglkvieD 144
                                       G+v+    +++++++a +h+l+v++D
  gi|386002069|ref|YP_005920368.1| 172 GAVFgrrILEEIRDLAVDHDLMVLSD 197
                                       999855459***************99 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.32   1.1e+03      73      95 ..      61      83 ..      22      94 .. 0.80
   2 ?   11.5   0.0   6.5e-05      0.23      12      93 ..     179     258 ..     174     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                                      HHHHHHHHHHHHHHHHHHHHH.. CS
                            Rsbr_N 73 LkyltkgLqefrkvvlellseed 95
                                        + t+g+ e+r ++ e+ls+e+
  gi|386002069|ref|YP_005920368.1| 61 HYLPTSGIPELRAAIAEKLSQEN 83
                                      445699*************9987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHTTSSS-.--HHHHHHHHHHHHHHHHH-SS.-SSTTHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
                            Rsbr_N  12 wlkelkelrkeeslqtisdevyektskefvdlilssveegneeleekleefaerlvqlGwpLkyltkgLqefrkvvl 88 
                                        l+e+++l+ +++l+++sde+yek+     +l + s + g ee + +++ f++    +Gw L yl+ g qe+ k v 
  gi|386002069|ref|YP_005920368.1| 179 ILEEIRDLAVDHDLMVLSDEIYEKIIYGQDHLSIGSFS-GMEERTVTVNGFSKCYAMTGWRLGYLA-GPQEVMKWVN 253
                                       57899999********************99999****9.6677779*******************8.6677777777 PP

                                       HHHHH CS
                            Rsbr_N  89 ellse 93 
                                       ++ls+
  gi|386002069|ref|YP_005920368.1| 254 RILSH 258
                                       77765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05       0.1      67     175 ..      95     197 ..      73     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                                       ESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEE CS
                       Aminotran_5  67 tsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklv 143
                                       + G+  ai +++++l   l++gde v+      +   p+    ++ g +v+++++d+  + ++  l++ +++ktk++
  gi|386002069|ref|YP_005920368.1|  95 VPGAKMAIFAAMQAL---LDEGDEGVLIGPSWVSYE-PCI---NFAGGRVRWAEVDD--RFEPVSLADSITPKTKMI 162
                                       556666777777777...777777666655444444.444...45699*******66..577789************ PP

                                       EEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 144 aithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                        ++  sn tG ++    +eei +la +++ +vl D
  gi|386002069|ref|YP_005920368.1| 163 LVNSPSNPTGAVFGrriLEEIRDLAVDHDLMVLSD 197
                                       **********9763233788888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 3105.38
//
Query:       gi|386002070|ref|YP_005920369.1|  [L=136]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-34  116.5   0.4    8.6e-34  116.4   0.4    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.017   14.4   0.5      0.099   11.9   0.2    2.2  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.4   9.6e-38   8.6e-34       2     140 ..       2     133 ..       1     134 [. 0.95

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 9.6e-38
                                       EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCH CS
                     DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetph 78 
                                       +++++Vva+fn++it ++    +++++ +g+  e + + +VPG++++pla+kkla++ + +dav+++G+vi+Get h
  gi|386002070|ref|YP_005920369.1|   2 IKLGFVVAEFNRDITYQMEILGREHAEFLGA--EVVATLHVPGVYDMPLAVKKLAAK-EDVDAVVTIGCVIQGETGH 75 
                                       5899**************************7..59*********************5.447**************** PP

                                       HHHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHHH CS
                     DMRL_synthase  79 feyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanll 140
                                       +e+va+++s+++m+++l+ ++Pv+ g+  ++ ++ +a++r+     ++ ++a+eaa++m++ l
  gi|386002070|ref|YP_005920369.1|  76 DEIVAQQASRKIMDLALEFDKPVTLGISGPKmSRMDAHSRI-----DYSKRAVEAAVKMVKRL 133
                                       *******************************99********.....899999******99865 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.01        90      81     104 ..      26      49 ..      10      50 .. 0.74
   2 ?   11.9   0.2   1.1e-05     0.099       7      61 ..      33      86 ..      29      99 .. 0.85
   3 ?   -0.3   0.0     0.061   5.5e+02     151     172 ..     113     134 ..      98     136 .] 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.01
                                       HHHHHHTT-SEEEEE--TTS--HH CS
                     Metallophos_3  81 lfrelgeldvpafvvPGkrDaPle 104
                                         + lg   v ++ vPG  D Pl 
  gi|386002070|ref|YP_005920369.1|  26 HAEFLGAEVVATLHVPGVYDMPLA 49 
                                       44568888999**********985 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.1e-05
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT-- CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerre 61
                                       v+a  ++ g +++   ++++++  d+D++v +G ++++e+  de   aq++ r+
  gi|386002070|ref|YP_005920369.1| 33 EVVATLHVPGVYDMPLAVKKLAAKEDVDAVVTIGCVIQGETGHDEIV-AQQASRK 86
                                      5788888888888777788888888********************99.7777765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.061
                                       SSS-EEEHHHHHHHGGGGGGS- CS
                     Metallophos_3 151 efrLkYPaweveyrLkvlkelk 172
                                       + r+ Y ++ ve ++k++k lk
  gi|386002070|ref|YP_005920369.1| 113 HSRIDYSKRAVEAAVKMVKRLK 134
                                       6789999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 977.77
//
Query:       gi|386002071|ref|YP_005920370.1|  [L=288]
Description: Branched-chain amino acid aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-56  190.1   0.0    5.6e-56  189.9   0.0    1.0  1  Aminotran_4  Amino-transferase class IV
  ------ inclusion threshold ------
       0.14   12.3   0.1       0.34   11.1   0.0    1.6  2  AD           Anticodon-binding domain


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9   0.0   6.2e-60   5.6e-56       1     223 []      30     256 ..      30     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 6.2e-60
                       Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg.aatse 76 
                                       g+fE++r+yng++f+l+eH++RL  sa++++le+p++eee+ ++++e+l++n+ + +++r+lv+rg g+lg ++ ++
  gi|386002071|ref|YP_005920370.1|  30 GVFEGIRAYNGRVFRLEEHVKRLYDSAKAIMLEIPMTEEEMAAAIRETLRKNGLSDAYIRPLVTRGVGDLGlDPRKC 106
                                       8*****************************9*****************************************99999 PP

                       Aminotran_4  77 psvavyvsalppgpeseke....lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtE 149
                                       ++  v++++ ++++ + +     l+++t +++r ++    p++K+lnyl+n+la+ ea+ +g +e++++d++gn++E
  gi|386002071|ref|YP_005920370.1| 107 AKPTVMIISQKWDAMYGDLydvgLTAITVTVRRNSPAALPPNIKSLNYLNNILAKIEANVKGGNEAIFLDDAGNISE 183
                                       999999999999999999999**99999999********************************************** PP

                       Aminotran_4 150 gstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                       gs  N+f+vk+ge+ tP  ++  L+Gitr a++e a a+g  v+e+++ l dl  ade+f+t+t+++v pv++i
  gi|386002071|ref|YP_005920370.1| 184 GSGDNIFVVKDGEISTPYTAN-NLKGITRLAVIEVALARGYGVKEANLGLFDLYTADEIFVTGTAAEVAPVTKI 256
                                       *****************5555.8*************************************************97 PP

>> AD  Anticodon-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.96   8.6e+03      13      45 ..      46      78 ..      44      81 .. 0.50
   2 ?   11.1   0.0   3.8e-05      0.34      51      73 ..     185     207 ..     154     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.96
                                AD 13 reaiaeakekeksigkgvskeaqalFdalsktl 45
                                      +e +++  +++k+i  ++++   ++  a+++tl
  gi|386002071|ref|YP_005920370.1| 46 EEHVKRLYDSAKAIMLEIPMTEEEMAAAIRETL 78
                                      445555555555555555555555555555554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.8e-05
                                AD  51 kgkeIvVldeviIspPYkvenvk 73 
                                       +g++I+V+++ +Is PY+++n k
  gi|386002071|ref|YP_005920370.1| 185 SGDNIFVVKDGEISTPYTANNLK 207
                                       689******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1878.63
//
Query:       gi|386002072|ref|YP_005920371.1|  [L=130]
Description: hypothetical protein Mhar_1384 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-37  128.6   0.0    1.3e-37  128.4   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   7.5e-42   1.3e-37       1     114 [.      14     126 ..      14     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 7.5e-42
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssl 76 
                                       dit++v+eav esgv eG++lv++ htt++++inE+ ++++ +Dl + l  l+p+   Y h+   ++na+aHl+++l
  gi|386002072|ref|YP_005920371.1|  14 DITRQVNEAVGESGVAEGICLVYTLHTTTGIVINEA-ETGLVADLLRRLMSLAPPGdGYLHD-RIDENAHAHLQAVL 88 
                                       8**********************************9.******************99*****.5557********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                       lg+s tipve+g lalGtwq++++veldgpr+R+v+v+
  gi|386002072|ref|YP_005920371.1|  89 LGNSRTIPVEEGCLALGTWQRVLFVELDGPRRRNVIVR 126
                                       ***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 811.29
//
Query:       gi|386002073|ref|YP_005920372.1|  [L=211]
Description: hypothetical protein Mhar_1385 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1314.78
//
Query:       gi|386002074|ref|YP_005920373.1|  [L=357]
Description: Beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-07   29.0   0.0    7.3e-05   22.4   0.1    2.5  2  Lactamase_B_2  Beta-lactamase superfamily domain
    7.7e-06   26.1   4.8    8.9e-06   25.8   0.4    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   8.1e-09   7.3e-05       3      62 ..      49      98 ..      47     115 .. 0.79
   2 !    4.0   0.0    0.0034        31     135     188 ..     244     295 ..     186     308 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.1e-09
                                      EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEE CS
                     Lactamase_B_2  3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplya 62
                                      iLiDag  +++ +  a         + + d+++lth H+DH+ +l+ l+  r +   l++
  gi|386002074|ref|YP_005920373.1| 49 ILIDAGAPVVERMIEA--------GVTAPDLLFLTHPHFDHVSDLDRLANSRMRG--LMV 98
                                      8999999988774444........5889********************9954433..444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0034
                                       EEEEEESS-S---HHHH..HHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHC CS
                     Lactamase_B_2 135 krvyyigDtgyipeeig..erlggadllllditayeddemirhmgHltpeeaveaa 188
                                       ++v+ +gD ++++e +     l+++ +l+ld++  +      +++H+++ee  +++
  gi|386002074|ref|YP_005920373.1| 244 RSVVISGDFKTMEEGVLesPDLRDPACLVLDANTIKA-P---GDYHASLEEERALI 295
                                       46999********7655236899********997777.3...69999998765555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.4   9.9e-10   8.9e-06      14      66 ..      45      90 ..      31      93 .. 0.92
   2 ?    1.6   0.5     0.026   2.3e+02     128     191 ..     229     345 ..     187     350 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.9e-10
                                      TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTT CS
                       Lactamase_B 14 dggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglve 66
                                      +g +iLiD+G +  + ++       + +   +d ++lTH+H+DH+++l+ l++
  gi|386002074|ref|YP_005920373.1| 45 PGAHILIDAGAPVVERMI-------EAGVTAPDLLFLTHPHFDHVSDLDRLAN 90
                                      6889***********995.......89**********************9986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.026
                                       TTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.......................................... CS
                       Lactamase_B 128 gpghghghgvveygggkvlftGDallagetgridl.......................................... 162
                                       g+g+ +++g  + + ++v+++GD+   +e ++ ++                                          
  gi|386002074|ref|YP_005920373.1| 229 GFGPVGSPGGDGPRVRSVVISGDFKTMEEGVLESPdlrdpaclvldantikapgdyhasleeeralidrwtsgeeev 305
                                       56666666666777788899999888888888888666666776666666666666666665555555566666666 PP

                                       ............TTCEEE-SHCHHHHHHHHHHHHHHHCHS CS
                       Lactamase_B 163 ...........tlrgaevrdpsdaekyldsllklaglkae 191
                                                   +rg++  +  d e+++++++   ++k+ 
  gi|386002074|ref|YP_005920373.1| 306 lvlfnhlsgfgDYRGGFYDHVPDDEEWRAAARFPTKPKVT 345
                                       6666666666655666666666666666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2615.18
//
Query:       gi|386002075|ref|YP_005920374.1|  [L=362]
Description: hypothetical protein Mhar_1387 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2681.30
//
Query:       gi|386002076|ref|YP_005920375.1|  [L=671]
Description: hypothetical protein Mhar_1388 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-14   53.1   0.1    6.7e-14   52.3   0.1    1.4  1  Transglut_core  Transglutaminase-like superfamily
    1.4e-07   31.8   0.0    6.7e-07   29.7   0.0    2.1  2  LTD             Lamin Tail Domain
     0.0026   17.3   0.0       0.11   12.0   0.0    2.5  1  DUF553          Transglutaminase-like domain
     0.0059   16.8   0.0      0.064   13.5   0.0    2.5  2  Gmad2           Immunoglobulin-like domain of bacterial spore
  ------ inclusion threshold ------
       0.25   11.3   0.6         31    4.6   0.1    2.7  2  Y_Y_Y           Y_Y_Y domain
       0.27   11.0   0.0       0.45   10.3   0.0    1.2  1  Acetyltransf_2  N-acetyltransferase


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   2.2e-17   6.7e-14       2     111 ..     181     293 ..     180     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.2e-17
                    Transglut_core   2 alaeeltagakdplekakaiyewvrknveys...aprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvv 75 
                                       +la+ l a ak+++e+a+aiy+wv +++ey+   a   + ++r+++ vle ++G+c ++++lf  l+  +G++a v+
  gi|386002076|ref|YP_005920375.1| 181 DLARYLEAPAKNDEERARAIYRWVTDRIEYDveaAMMGGGRGRTPQVVLEDRRGVCSEYSALFERLCQLSGLEAEVI 257
                                       68999999***********************8755555556666********************************* PP

                    Transglut_core  76 tgylsgeeekeq.svasedaHawvevylegygWvplD 111
                                        gy +g   ++   + +  +Haw+ v + +++W  lD
  gi|386002076|ref|YP_005920375.1| 258 RGYGKGYGYAVGsGIPRISNHAWNAVRI-DGTWRLLD 293
                                       *****886555565666667********.99997766 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.2e-10   6.7e-07       3     107 ..      33     127 ..      31     132 .. 0.89
   2 ?   -3.6   0.0       4.7   1.4e+04      36      66 ..     283     308 ..     275     308 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.2e-10
                               LTD   3 aaagdvvIsevmedgagnnan.efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsas 77 
                                       +++++v I++v  +++g++++ e+ el+N +  + + +gw++   +ge  t+p gt ++++ + + v+ ++g     
  gi|386002076|ref|YP_005920375.1|  33 PSPPTVAIARVETNPPGSDGGrEWAELFNDGALDAEVGGWRILTRTGEgVTIPPGT-IVPSRARLRVAFDGG----- 103
                                       57889************9999*************************99********.**********99954..... PP

                               LTD  78 ngskasssavwnnggdavaLydasgevvds 107
                                               ++++++g++++L++ s + vd+
  gi|386002076|ref|YP_005920375.1| 104 ------EGPSLSDEGESISLLNESARAVDE 127
                                       ......346777789999999988888885 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.7
                               LTD  36 vdLs.gwkledasgeytfpngtgtlaageyvv 66 
                                       v +   w+l d++       g g+l++ge +v
  gi|386002076|ref|YP_005920375.1| 283 VRIDgTWRLLDST------WGAGHLEPGEGFV 308
                                       4444246777766......3336899998765 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.6e-05      0.11      12     127 ..     190     294 ..     178     305 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                            DUF553  12 kensketiinvlewvdenikYdyekaevvetllvlWatfftlskvdskilklietpkeilktkkgiCrDYaiLTaal 88 
                                        +n +e + ++ +wv + i+Yd+e a +                     + + +tp+ +l+ + g+C+ Y+ L   l
  gi|386002076|ref|YP_005920375.1| 190 AKNDEERARAIYRWVTDRIEYDVEAAMMG--------------------GGRGRTPQVVLEDRRGVCSEYSALFERL 246
                                       45666666677777777777777766666....................356679****************998885 PP

                            DUF553  89 Llnlniskvylvsv..tfenskvg........HaavavkidgtyfvlDq 127
                                         +l   ++ ++    + ++  vg        Ha  av+idgt+ +lD 
  gi|386002076|ref|YP_005920375.1| 247 C-QLSGLEAEVIRGygKGYGYAVGsgiprisnHAWNAVRIDGTWRLLDS 294
                                       4.44433334443300223333335566777799999999999988885 PP

>> Gmad2  Immunoglobulin-like domain of bacterial spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.38   1.1e+03      64      82 ..     418     434 ..     390     438 .. 0.70
   2 !   13.5   0.0   2.1e-05     0.064      30      79 ..     506     553 ..     503     558 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.38
                             Gmad2  64 efkapepgkgtlevyelsa 82 
                                       +  ap pg++tl++y+  +
  gi|386002076|ref|YP_005920375.1| 418 RAAAPGPGDYTLRIYS--R 434
                                       4445559999999975..4 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.1e-05
                             Gmad2  30 vnvrlrddagevlaegfvtAdegapkfgdFeatvefkapepgkgtlevye 79 
                                       +  rl d++g+ l e+ + ++  +++ g + +t +f++  +g++tl++y+
  gi|386002076|ref|YP_005920375.1| 506 LLARLLDGEGRELPEERTISQRVVGEEGGYGVTASFPK--AGNYTLRIYA 553
                                       5689*********************************6..8*******86 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 ?    4.1   0.1     0.015        46      38      53 ..     424     439 ..     422     448 .. 0.82
   2 ?    4.6   0.1      0.01        31      37      50 ..     543     556 ..     531     569 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                                       SEEEEEEEEEEETTS- CS
                             Y_Y_Y  38 pGdYtlkVkakdndgq 53 
                                       pGdYtl+++ +   g+
  gi|386002076|ref|YP_005920375.1| 424 PGDYTLRIYSRRGGGE 439
                                       9********9876665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.01
                                       -SEEEEEEEEEEET CS
                             Y_Y_Y  37 ppGdYtlkVkakdn 50 
                                       ++G+Ytl+++ak  
  gi|386002076|ref|YP_005920375.1| 543 KAGNYTLRIYAKRG 556
                                       68*********975 PP

>> Acetyltransf_2  N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.45      39     109 ..     226     299 ..     223     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                                       HHTTST--B-HHHHHHHHHHHHHHTT-EEEEEEEE..EETTGGSSS.SSSCEEEEEEEEETTEEEEE-SSSSCG CS
                    Acetyltransf_2  39 klVkkkRGGyCyelNgLlarvLkelGFevtllagr..vvvkaeeaa.stertHllllVtidgetylvDvGFGgs 109
                                       ++V + R G C e   L++r+ +  G e +++ g+   +  a ++   +  +H+ + V+idg+  l+D+ +G  
  gi|386002076|ref|YP_005920375.1| 226 QVVLEDRRGVCSEYSALFERLCQLSGLEAEVIRGYgkGYGYAVGSGiPRISNHAWNAVRIDGTWRLLDSTWGAG 299
                                       68999999**********************9987621444444443378899***********99******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4550.89
//
Query:       gi|386002077|ref|YP_005920376.1|  [L=436]
Description: Cation diffusion facilitator family transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-33  114.1  11.4    8.7e-33  113.7  11.4    1.1  1  Cation_efflux  Cation efflux family
    2.2e-14   53.5   0.0    4.5e-14   52.6   0.0    1.5  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
    2.7e-14   53.0   0.5    4.4e-14   52.4   0.5    1.3  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.04   13.7   0.0       0.33   10.7   0.0    2.1  2  CT_C_D         Carboxyltransferase domain, subdomain C and D


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7  11.4   1.9e-36   8.7e-33       2     199 .]      54     242 ..      53     242 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.9e-36
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalkls.rkppderfpfGygrlevlgalvsgll 77 
                                       +lsll+nl+l  ++l +  +++Slal ada+hs++d+++++ l+l++++s r++  + fp+G++++e+l+a+v +ll
  gi|386002077|ref|YP_005920376.1|  54 LLSLLVNLSLVGIKLLLSEISGSLALRADAVHSVVDVFGSTALILGVVISgRRS--KSFPYGLYKVENLVAVVISLL 128
                                       689***********************************************7777..99******************* PP

                     Cation_efflux  78 llglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvl 154
                                       l+++a+ +  ea   +     +  + g++l+ +++ + v l++  +  r+g+k++s++l a+  + + D+lt l+v 
  gi|386002077|ref|YP_005920376.1| 129 LFLTAYEIGREAMMGTA---AEAAPGGWVLLAVAALVPVPLLFGSYEVRVGKKHSSPSLVADGRQFRADVLTELVVF 202
                                       *****************...899999*************************************************** PP

                     Cation_efflux 155 vsalvillfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                        ++ ++l++ l+    +D va+ +i+++i+ +++++l++ +++Ll
  gi|386002077|ref|YP_005920376.1| 203 AALAGQLVG-LP----LDRVAAGIIAVLIIRAGWEILVSGMRVLL 242
                                       ****99998.55....9*************************997 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0     1e-17   4.5e-14       2      92 ..     338     432 ..     337     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1e-17
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEE..E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSS..CHHHHHHHCTT CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenr..veeaadaegggggklaqllaeegvdvvivgki..Gpralakleaa 74 
                                       g++v+ hFG++pyFa+++ + +++++  +   ++++ + e+g+g k+a+ll +++ dvv++g+   G+++  +l++a
  gi|386002077|ref|YP_005920376.1| 338 GGKVSRHFGESPYFALVDFDLKGRRVEGQTiiSNPYRELEKGKGLKVAALLLAKKPDVVVAGESlaGKGPGYALAEA 414
                                       789*****************999999888899999****************************999*********** PP

                                       TSEEEES-SSBHHHHHHH CS
                     Nitro_FeMo-Co  75 gievykgaggtveealke 92 
                                       g+e +++++ +++e+++e
  gi|386002077|ref|YP_005920376.1| 415 GVETVMTEAADLQEVVAE 432
                                       ***************987 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.5   9.7e-18   4.4e-14       2      78 ..     247     322 ..     246     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 9.7e-18
                                       ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       d++++++i+++i+++p+v+ v+++  r+sG+++fv+ ++ +  +  + +aH+ ++++e +i+e++p+v +vliH+eP
  gi|386002077|ref|YP_005920376.1| 247 DSATLRRIEATIEAHPEVSIVEEVLGRNSGRYLFVEAKVAFRVT-DLARAHQASQRIEGDIREAVPNVDRVLIHYEP 322
                                       667899***********************************877.******************************** PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.13   5.7e+02     169     185 ..     141     157 ..     136     162 .. 0.78
   2 ?   10.7   0.0   7.3e-05      0.33       9      73 ..     277     337 ..     271     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                       EEEEE-S-B---SEEEE CS
                            CT_C_D 169 qtgiyplesPGGWqliG 185
                                       ++g  + ++PGGW l+ 
  gi|386002077|ref|YP_005920376.1| 141 MMGTAAEAAPGGWVLLA 157
                                       567778899****9976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.3e-05
                                       TEEEEEE-SS--HHHHHHHHHHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHH CS
                            CT_C_D   9 eallvefgeeisealskrvlalaaalrakalpgvvelvpayrsllvefdpealdaaellaalkal 73 
                                       ++l+ve++ +++ ++++r+++++++++     ++ e+vp ++ +l++++p+  d+ + + al++l
  gi|386002077|ref|YP_005920376.1| 277 RYLFVEAKVAFRVTDLARAHQASQRIEG----DIREAVPNVDRVLIHYEPKPKDHIRYAVALADL 337
                                       6788888888888888888888888888....8****************9988877777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2881.41
//
Query:       gi|386002078|ref|YP_005920377.1|  [L=639]
Description: N-terminal domain intergin-like repeats and c-terminal-cell wall-associated hydrolase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-45  152.7  50.1    7.7e-05   22.7   0.3   11.1 11  FG-GAP           FG-GAP repeat
      2e-39  134.0  92.4    2.7e-07   31.1   4.3    8.2 11  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
    3.2e-17   62.5   2.0       0.48    9.8   0.0    9.8 10  TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal reg
    5.2e-10   39.1  20.2          4    7.4   0.1    9.8 10  DUF1416          Protein of unknown function (DUF1416)
    4.2e-08   33.1   3.7     0.0038   16.8   0.2    3.5  3  PQQ_2            PQQ-like domain
     0.0098   15.4   9.4         65    2.9   0.0    7.6 10  DUF899           Bacterial protein of unknown function (DUF89
  ------ inclusion threshold ------
      0.053   13.5   0.0    4.9e+02    0.8   0.0    6.0  9  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   7.1e-07    0.0018       7      30 ..      65      84 ..      63      89 .. 0.76
   2 !   17.7   0.7   1.1e-06    0.0029       7      19 ..     115     127 ..     113     139 .. 0.83
   3 !   21.5   0.3   7.3e-08   0.00019       3      33 ..     161     187 ..     159     190 .. 0.83
   4 !   15.6   0.1   5.3e-06     0.013       3      33 ..     211     237 ..     209     240 .. 0.84
   5 !   16.1   0.2   3.7e-06    0.0095       7      33 ..     265     287 ..     263     290 .. 0.82
   6 ?   -1.4   0.2       1.1   2.7e+03      14      32 ..     343     357 ..     343     360 .. 0.76
   7 !   22.7   0.3     3e-08   7.7e-05       3      33 ..     382     408 ..     380     411 .. 0.86
   8 !   21.5   0.4   7.5e-08   0.00019       3      33 ..     432     458 ..     430     461 .. 0.83
   9 !   18.2   0.1   8.1e-07    0.0021       3      33 ..     482     508 ..     480     511 .. 0.87
  10 !   17.0   0.1   1.9e-06    0.0048       3      33 ..     532     558 ..     530     561 .. 0.84
  11 !   15.6   0.1   5.3e-06     0.013       3      32 ..     582     607 ..     580     610 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.1e-07
                                      EESTSSSSS-EEEEEETT-ETCST CS
                            FG-GAP  7 vgDvNGDGyaDLavGApeskggay 30
                                       gD+NGDG++DL+      ++ a+
  gi|386002078|ref|YP_005920377.1| 65 PGDFNGDGFTDLLFY----DPAAG 84
                                      7***********965....55555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.1e-06
                                       EESTSSSSS-EEE CS
                            FG-GAP   7 vgDvNGDGyaDLa 19 
                                        gD+NGDG++DL+
  gi|386002078|ref|YP_005920377.1| 115 PGDFNGDGFTDLL 127
                                       7***********8 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 7.3e-08
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygGa 33 
                                       +++  gD+NGDG++DL+      ++ a++G 
  gi|386002078|ref|YP_005920377.1| 161 SIIVPGDFNGDGFTDLLFY----DPAAGQGE 187
                                       67899***********987....77777775 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 5.3e-06
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygGa 33 
                                       +s+  gD+NGD y+DL+      ++ a++G 
  gi|386002078|ref|YP_005920377.1| 211 SSIVPGDFNGDEYTDLLFY----DPAAGQGE 237
                                       899*************987....77777775 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 3.7e-06
                                       EESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   7 vgDvNGDGyaDLavGApeskggaygGa 33 
                                        gD+N DGy+DL+      ++ a++G 
  gi|386002078|ref|YP_005920377.1| 265 PGDFNSDGYTDLLFY----DPAAGQGE 287
                                       69**********987....77777775 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 1.1
                                       SS-EEEEEETT-ETCSTTB CS
                            FG-GAP  14 GyaDLavGApeskggaygG 32 
                                       GyaDL+      ++ a++G
  gi|386002078|ref|YP_005920377.1| 343 GYADLLFY----DPAAGQG 357
                                       9****977....7777776 PP

  == domain 7  score: 22.7 bits;  conditional E-value: 3e-08
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygGa 33 
                                       +++  gD+NGDG++DL+      +++a++G 
  gi|386002078|ref|YP_005920377.1| 382 SIIVPGDFNGDGFTDLLFY----DPSAGQGE 408
                                       67899************98....99999986 PP

  == domain 8  score: 21.5 bits;  conditional E-value: 7.5e-08
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygGa 33 
                                       +++  gD+NGDG++DL+      ++ a++G 
  gi|386002078|ref|YP_005920377.1| 432 SAIVPGDFNGDGFTDLLFY----DPAAGQGE 458
                                       67899***********987....77777775 PP

  == domain 9  score: 18.2 bits;  conditional E-value: 8.1e-07
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygGa 33 
                                       +s+  g +NGDG++DL+      +++a++G 
  gi|386002078|ref|YP_005920377.1| 482 SSIVPGEFNGDGFTDLLFY----DPSAGQGE 508
                                       8999*************98....99999986 PP

  == domain 10  score: 17.0 bits;  conditional E-value: 1.9e-06
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTBE CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygGa 33 
                                       +s+  g +NGDG++DL+      ++ a++G 
  gi|386002078|ref|YP_005920377.1| 532 SSIVPGEFNGDGFTDLLFY----DPAAGQGE 558
                                       8999************987....77777775 PP

  == domain 11  score: 15.6 bits;  conditional E-value: 5.3e-06
                                       SSEEEESTSSSSS-EEEEEETT-ETCSTTB CS
                            FG-GAP   3 yslavgDvNGDGyaDLavGApeskggaygG 32 
                                       +++  g +NGDG++DL+      ++ a++G
  gi|386002078|ref|YP_005920377.1| 582 STIVPGEFNGDGFTDLLFY----DPAAGQG 607
                                       6788999*********987....7777776 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.4   1.1e-05     0.029      26      60 ..      33      77 ..      14      78 .. 0.59
   2 !   29.1   3.2   4.4e-10   1.1e-06       1      60 [.      67     127 ..      67     128 .. 0.86
   3 !   30.4   4.2   1.8e-10   4.5e-07       1      60 [.     117     177 ..     117     178 .. 0.87
   4 !   28.7   3.7   5.7e-10   1.5e-06       1      60 [.     167     227 ..     167     228 .. 0.87
   5 !   26.6   1.5   2.5e-09   6.5e-06       1      60 [.     217     277 ..     217     278 .. 0.87
   6 !   11.4   0.2   0.00014      0.36       1      36 [.     267     304 ..     267     317 .. 0.81
   7 !   19.1   1.1   5.7e-07    0.0015       6      60 ..     343     398 ..     340     399 .. 0.78
   8 !   31.1   4.3     1e-10   2.7e-07       1      60 [.     388     448 ..     388     449 .. 0.86
   9 !   28.7   2.3   5.8e-10   1.5e-06       1      60 [.     438     498 ..     438     499 .. 0.89
  10 !   25.8   1.5   4.5e-09   1.2e-05       2      60 ..     489     548 ..     488     549 .. 0.89
  11 !   25.2   1.5   7.2e-09   1.8e-05       2      60 ..     539     598 ..     538     599 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                              VCBS 26 dGtftdvtktslgg......sgggtg....vavgDlDgDGdlDll 60
                                      +G++++ ++   g       + ++++    +++gD++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 33 TGQGEFYSTDGAGNadllknYRNWRAtwsmIVPGDFNGDGFTDLL 77
                                      44444444432222345544333333556699***********98 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 4.4e-10
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D++gDG+ Dl++ ++  g  ++y  +g G+ +  +++s+    ++  +++gD++gDG +Dll
  gi|386002078|ref|YP_005920377.1|  67 DFNGDGFTDLLFYDPaaGEGEFYSTDGRGDIRLLQSHSGWRR-TWSMIVPGDFNGDGFTDLL 127
                                       9************85468899****99999998888777776.45559************98 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 1.8e-10
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D++gDG+ Dl++ ++  g+ ++y  +g+G+ +  +++s+    ++  +++gD++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 117 DFNGDGFTDLLFYDSaaGQGEFYATDGTGNIRLLQSHSGWRR-TWSIIVPGDFNGDGFTDLL 177
                                       9************744599**********9999888777766.455699***********98 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 5.7e-10
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D++gDG+ Dl++ ++  g+ ++y  +g+G+ +   + ++    ++ ++++gD++gD ++Dll
  gi|386002078|ref|YP_005920377.1| 167 DFNGDGFTDLLFYDPaaGQGEFYATDGSGNIRLLKASDGWRR-TWSSIVPGDFNGDEYTDLL 227
                                       9************855699**********9988776555555.7889*************98 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 2.5e-09
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D++gD + Dl++ ++  g+ ++y  +g+G+ +   ++s+    ++  + +gD++ DG++Dll
  gi|386002078|ref|YP_005920377.1| 217 DFNGDEYTDLLFYDPaaGQGEFYATDGTGNIRLLKSHSGWRR-TWSMIMPGDFNSDGYTDLL 277
                                       9************855699**********9998887777766.455599***********98 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00014
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtkts 36 
                                       D++ DG+ Dl++ ++  g+ ++y  +g+G+ +  +++s
  gi|386002078|ref|YP_005920377.1| 267 DFNSDGYTDLLFYDPaaGQGEFYATDGSGNIRLLQSHS 304
                                       9************8556999999999999977666555 PP

  == domain 7  score: 19.1 bits;  conditional E-value: 5.7e-07
                              VCBS   6 GrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       G++Dl++ ++  g+ ++y  +g+G+ +   + s+    ++  +++gD++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 343 GYADLLFYDPaaGQGEFYSTDGSGNIQLLKSSSGWR-RTWSIIVPGDFNGDGFTDLL 398
                                       899999998546999999999999988775444433.3455599***********98 PP

  == domain 8  score: 31.1 bits;  conditional E-value: 1e-10
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D++gDG+ Dl++ ++  g+ ++y  +g+G+ +   + ++    ++ ++++gD++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 388 DFNGDGFTDLLFYDPsaGQGEFYATDGSGNIRLLKASDGWRR-TWSAIVPGDFNGDGFTDLL 448
                                       9************743699**********9988766555555.7889*************98 PP

  == domain 9  score: 28.7 bits;  conditional E-value: 5.8e-10
                              VCBS   1 DldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       D++gDG+ Dl++ ++  g+ ++y  +g+G+ +  +++s+    ++ ++++g ++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 438 DFNGDGFTDLLFYDPaaGQGEFYATDGTGNIRHLQSHSGWRR-TWSSIVPGEFNGDGFTDLL 498
                                       9************855699*********99999888777766.789**************98 PP

  == domain 10  score: 25.8 bits;  conditional E-value: 4.5e-09
                              VCBS   2 ldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       ++gDG+ Dl++ ++  g+ ++y  +g+G+ +   ++s+    ++ ++++g ++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 489 FNGDGFTDLLFYDPsaGQGEFYATDGSGNIRLLKSHSGWRR-TWSSIVPGEFNGDGFTDLL 548
                                       8***********743699***********999887777766.789**************98 PP

  == domain 11  score: 25.2 bits;  conditional E-value: 7.2e-09
                              VCBS   2 ldgDGrlDlvvand..gglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDll 60 
                                       ++gDG+ Dl++ ++  g+ ++y  +g+G+ +   ++s+    ++ ++++g ++gDG +Dll
  gi|386002078|ref|YP_005920377.1| 539 FNGDGFTDLLFYDPaaGQGEFYATDGTGNIRLLKSHSGWRR-TWSTIVPGEFNGDGFTDLL 598
                                       8***********855699**********9999887777766.7889*************98 PP

>> TcdB_toxin_midN  Insecticide toxin TcdB middle/N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0063        16      34      54 ..      66      86 ..      58     105 .. 0.82
   2 !    6.1   0.0    0.0024       6.2      34      69 ..     116     150 ..     106     154 .. 0.79
   3 !    8.7   0.0    0.0004         1      34      73 ..     166     204 ..     160     206 .. 0.86
   4 ?    2.1   0.0     0.041   1.1e+02      34      70 ..     216     251 ..     209     254 .. 0.84
   5 ?   -1.2   0.0      0.43   1.1e+03      34      56 ..     266     288 ..     261     302 .. 0.75
   6 !    9.8   0.0   0.00019      0.48      34      73 ..     387     425 ..     378     427 .. 0.86
   7 !    5.5   0.0    0.0038       9.7      34      55 ..     437     458 ..     429     474 .. 0.79
   8 ?    4.0   0.0     0.011        28      35      70 ..     488     522 ..     479     525 .. 0.78
   9 !    4.6   0.0    0.0074        19      35      70 ..     538     572 ..     530     576 .. 0.84
  10 ?    3.2   0.0     0.019        49      35      73 ..     588     625 ..     579     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0063
                   TcdB_toxin_midN 34 aDldGdGladlvltipsagtg 54
                                      +D++GdG+ dl+   p ag g
  gi|386002078|ref|YP_005920377.1| 66 GDFNGDGFTDLLFYDPAAGEG 86
                                      6***********999988844 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0024
                   TcdB_toxin_midN  34 aDldGdGladlvltipsagtgavqkatsllgkpgLL 69 
                                       +D++GdG+ dl+   + ag g+   at  +g+  LL
  gi|386002078|ref|YP_005920377.1| 116 GDFNGDGFTDLLFYDSAAGQGEF-YATDGTGNIRLL 150
                                       6************9999996666.444557777766 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0004
                   TcdB_toxin_midN  34 aDldGdGladlvltipsagtgavqkatsllgkpgLLkkid 73 
                                       +D++GdG+ dl+   p ag g+   at   g+  LLk++d
  gi|386002078|ref|YP_005920377.1| 166 GDFNGDGFTDLLFYDPAAGQGEF-YATDGSGNIRLLKASD 204
                                       6******************7777.4556689999999987 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.041
                   TcdB_toxin_midN  34 aDldGdGladlvltipsagtgavqkatsllgkpgLLk 70 
                                       +D++Gd   dl+   p ag g+   at  +g+  LLk
  gi|386002078|ref|YP_005920377.1| 216 GDFNGDEYTDLLFYDPAAGQGEF-YATDGTGNIRLLK 251
                                       6******************7777.5566689999998 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.43
                   TcdB_toxin_midN  34 aDldGdGladlvltipsagtgav 56 
                                       +D++ dG  dl+   p ag g+ 
  gi|386002078|ref|YP_005920377.1| 266 GDFNSDGYTDLLFYDPAAGQGEF 288
                                       69**********99999985444 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00019
                   TcdB_toxin_midN  34 aDldGdGladlvltipsagtgavqkatsllgkpgLLkkid 73 
                                       +D++GdG+ dl+   psag g+   at   g+  LLk++d
  gi|386002078|ref|YP_005920377.1| 387 GDFNGDGFTDLLFYDPSAGQGEF-YATDGSGNIRLLKASD 425
                                       6******************7777.4556689999999987 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.0038
                   TcdB_toxin_midN  34 aDldGdGladlvltipsagtga 55 
                                       +D++GdG+ dl+   p ag g+
  gi|386002078|ref|YP_005920377.1| 437 GDFNGDGFTDLLFYDPAAGQGE 458
                                       7************999998433 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.011
                   TcdB_toxin_midN  35 DldGdGladlvltipsagtgavqkatsllgkpgLLk 70 
                                        ++GdG+ dl+   psag g+   at   g+  LLk
  gi|386002078|ref|YP_005920377.1| 488 EFNGDGFTDLLFYDPSAGQGEF-YATDGSGNIRLLK 522
                                       69***************96666.3444466777776 PP

  == domain 9  score: 4.6 bits;  conditional E-value: 0.0074
                   TcdB_toxin_midN  35 DldGdGladlvltipsagtgavqkatsllgkpgLLk 70 
                                        ++GdG+ dl+   p ag g+   at  +g+  LLk
  gi|386002078|ref|YP_005920377.1| 538 EFNGDGFTDLLFYDPAAGQGEF-YATDGTGNIRLLK 572
                                       69****************7777.5566699999998 PP

  == domain 10  score: 3.2 bits;  conditional E-value: 0.019
                   TcdB_toxin_midN  35 DldGdGladlvltipsagtgavqkatsllgkpgLLkkid 73 
                                        ++GdG+ dl+   p ag g+ +      g+  LLk++d
  gi|386002078|ref|YP_005920377.1| 588 EFNGDGFTDLLFYDPAAGQGEFYSTDG-GGNLALLKASD 625
                                       69**************99777654444.67777777765 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.13   3.4e+02      55      77 ..      82     104 ..      70     112 .. 0.85
   2 !    7.4   0.1    0.0016         4      53      77 ..     130     154 ..     117     162 .. 0.85
   3 ?    4.1   0.1     0.017        42      55      76 ..     182     203 ..     169     213 .. 0.85
   4 !    5.4   0.0    0.0064        16      55      77 ..     232     254 ..     219     263 .. 0.85
   5 !    5.0   0.0    0.0086        22      55      77 ..     282     304 ..     274     317 .. 0.86
   6 ?   -1.4   0.0      0.84   2.2e+03      56      76 ..     354     374 ..     351     381 .. 0.83
   7 ?    4.1   0.0     0.017        44      56      76 ..     404     424 ..     390     437 .. 0.83
   8 !    5.7   0.0    0.0054        14      55      77 ..     453     475 ..     438     488 .. 0.85
   9 !    4.8   0.0    0.0097        25      56      77 ..     504     525 ..     490     538 .. 0.85
  10 !    5.6   0.0    0.0056        14      55      77 ..     553     575 ..     535     587 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                           DUF1416  55 aeGefrFfaapGeWtvRalarkg 77 
                                       a+Ge  F++++G+  +R l++++
  gi|386002078|ref|YP_005920377.1|  82 AAGEGEFYSTDGRGDIRLLQSHS 104
                                       568889************99875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                           DUF1416  53 tsaeGefrFfaapGeWtvRalarkg 77 
                                        sa+G+  F+a++G+ ++R l++++
  gi|386002078|ref|YP_005920377.1| 130 DSAAGQGEFYATDGTGNIRLLQSHS 154
                                       5899*****************9875 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.017
                           DUF1416  55 aeGefrFfaapGeWtvRalark 76 
                                       a+G+  F+a++G+ ++R l+++
  gi|386002078|ref|YP_005920377.1| 182 AAGQGEFYATDGSGNIRLLKAS 203
                                       679999***********99865 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0064
                           DUF1416  55 aeGefrFfaapGeWtvRalarkg 77 
                                       a+G+  F+a++G+ ++R l++++
  gi|386002078|ref|YP_005920377.1| 232 AAGQGEFYATDGTGNIRLLKSHS 254
                                       679999*************9875 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.0086
                           DUF1416  55 aeGefrFfaapGeWtvRalarkg 77 
                                       a+G+  F+a++G+ ++R l++++
  gi|386002078|ref|YP_005920377.1| 282 AAGQGEFYATDGSGNIRLLQSHS 304
                                       578999*************9876 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 0.84
                           DUF1416  56 eGefrFfaapGeWtvRalark 76 
                                       +G+  F++++G+ ++  l+++
  gi|386002078|ref|YP_005920377.1| 354 AGQGEFYSTDGSGNIQLLKSS 374
                                       68889*******999999876 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.017
                           DUF1416  56 eGefrFfaapGeWtvRalark 76 
                                       +G+  F+a++G+ ++R l+++
  gi|386002078|ref|YP_005920377.1| 404 AGQGEFYATDGSGNIRLLKAS 424
                                       68889***********99876 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.0054
                           DUF1416  55 aeGefrFfaapGeWtvRalarkg 77 
                                       a+G+  F+a++G+ ++R l++++
  gi|386002078|ref|YP_005920377.1| 453 AAGQGEFYATDGTGNIRHLQSHS 475
                                       679999*************9876 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.0097
                           DUF1416  56 eGefrFfaapGeWtvRalarkg 77 
                                       +G+  F+a++G+ ++R l++++
  gi|386002078|ref|YP_005920377.1| 504 AGQGEFYATDGSGNIRLLKSHS 525
                                       68889*************9876 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.0056
                           DUF1416  55 aeGefrFfaapGeWtvRalarkg 77 
                                       a+G+  F+a++G+ ++R l++++
  gi|386002078|ref|YP_005920377.1| 553 AAGQGEFYATDGTGNIRLLKSHS 575
                                       679999*************9876 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   4.2e-05      0.11      35     225 ..      84     290 ..      56     314 .. 0.67
   2 !   16.8   0.2   1.5e-06    0.0038      31     203 ..     401     588 ..     348     595 .. 0.55
   3 ?    2.5   0.1     0.036        91      31      56 ..     601     626 ..     575     634 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                             PQQ_2  35 sggtlfvatgggrlvaldaatG.kvlWettlegpvvga.........plvaegrvvvvasdgqlialdaedG.krlW 100
                                       ++g +++++g+g +  l   +G + +W+  ++g + g+             +g+ ++ ++ g+++ l +++G +r W
  gi|386002078|ref|YP_005920377.1|  84 GEGEFYSTDGRGDIRLLQSHSGwRRTWSMIVPGDFNGDgftdllfydSAAGQGEFYATDGTGNIRLLQSHSGwRRTW 160
                                       56666666666666666666664455666666666666555544443333344445555555555555555533356 PP

                             PQQ_2 101 stqqrs...eepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgtselsrvgdisgrpvvae 173
                                       s+   +   +   + +   +pa +++++++ + sg++  l ++dG ++   ++   + +++e+  ++ +++ p   +
  gi|386002078|ref|YP_005920377.1| 161 SIIVPGdfnGDGFTDLLFYDPAAGQGEFYATDGSGNIRLLKASDGWRRTWSSIvPGDFNGDEY--TDLLFYDPAAGQ 235
                                       654444221122223444456666999999999999999999999666444454999999987..688999999999 PP

                             PQQ_2 174 gtVyassgqgrllaldlatgrrl.wske.issinglpildgdllyvvsa...gelia 225
                                       g+ ya  g g++  l+ ++g r+ ws + ++ +n+      dll+++ a   ge++a
  gi|386002078|ref|YP_005920377.1| 236 GEFYATDGTGNIRLLKSHSGWRRtWSMImPGDFNS--DGYTDLLFYDPAagqGEFYA 290
                                       99999999998555599999988899887777777..44445555555335555555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.5e-06
                             PQQ_2  31 ravlsggtlfvatgggrlvaldaatG.kvlWettlegpvvga.........plvaegrvvvvasdgqlialdaedG. 96 
                                       +++ ++g +++++g+g++  l+a++G + +W++ ++g + g+         p   +g+ ++ ++ g+++ l +++G 
  gi|386002078|ref|YP_005920377.1| 401 DPSAGQGEFYATDGSGNIRLLKASDGwRRTWSAIVPGDFNGDgftdllfydPAAGQGEFYATDGTGNIRHLQSHSGw 477
                                       35556666666667777777777776455566666666666666666666666666666666666666666666663 PP

                             PQQ_2  97 krlWstqqrseepaelrssaspava.......gdtvvvgessgklvaldpkdGkvlWerel.aaprgtselsrvgdi 165
                                       +r Ws    +    e+ +++   +        ++++++ + sg++  l   +G ++   ++     +++   +++ +
  gi|386002078|ref|YP_005920377.1| 478 RRTWSSIVPG----EFNGDGFTDLLfydpsagQGEFYATDGSGNIRLLKSHSGWRRTWSSIvPGEFNGD--GFTDLL 548
                                       3456622222....1222222222222444446677777777777777777774443333324444222..256666 PP

                             PQQ_2 166 sgrpvvaegtVyassgqgrllaldlatgrrl.wske.iss 203
                                       ++ p   +g+ ya  g g++  l+ ++g r+ ws++ +++
  gi|386002078|ref|YP_005920377.1| 549 FYDPAAGQGEFYATDGTGNIRLLKSHSGWRRtWSTIvPGE 588
                                       6666666667777777776333366666666666665555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.036
                             PQQ_2  31 ravlsggtlfvatgggrlvaldaatG 56 
                                       ++  ++g +++++ggg+l+ l+a++G
  gi|386002078|ref|YP_005920377.1| 601 DPAAGQGEFYSTDGGGNLALLKASDG 626
                                       45557888888888888888888888 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   5.3e+03     123     144 ..      50      71 ..      45      73 .. 0.87
   2 ?   -1.0   0.0       0.4     1e+03     120     144 ..      97     121 ..      88     148 .. 0.84
   3 ?   -1.8   0.0      0.72   1.8e+03     119     144 ..     146     171 ..     140     174 .. 0.87
   4 ?    2.9   0.0     0.026        65     119     144 ..     196     221 ..     190     235 .. 0.89
   5 ?    0.7   0.0      0.13   3.3e+02     119     144 ..     246     271 ..     237     298 .. 0.89
   6 ?   -0.3   0.0      0.24   6.2e+02     119     144 ..     367     392 ..     361     398 .. 0.89
   7 ?    0.3   0.0      0.16   4.1e+02     119     144 ..     417     442 ..     410     448 .. 0.88
   8 ?    2.8   0.0     0.029        74     118     144 ..     466     492 ..     459     498 .. 0.89
   9 ?    2.2   0.0     0.044   1.1e+02     119     144 ..     517     542 ..     510     550 .. 0.89
  10 ?    1.3   0.0     0.079     2e+02     119     145 ..     567     593 ..     559     638 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                            DUF899 123 ykrrmGwtlpwvssaesdfnrd 144
                                       +k+ + w+  w   +  dfn d
  gi|386002078|ref|YP_005920377.1|  50 LKNYRNWRATWSMIVPGDFNGD 71 
                                       688899*******999999976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.4
                            DUF899 120 leaykrrmGwtlpwvssaesdfnrd 144
                                       +  ++ + Gw+  w   +  dfn d
  gi|386002078|ref|YP_005920377.1|  97 IRLLQSHSGWRRTWSMIVPGDFNGD 121
                                       5667889999999999999999987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.72
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrd 144
                                       ++  ++ + Gw+  w   +  dfn d
  gi|386002078|ref|YP_005920377.1| 146 NIRLLQSHSGWRRTWSIIVPGDFNGD 171
                                       567789999**************987 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.026
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrd 144
                                       ++  +k+  Gw+  w s +  dfn d
  gi|386002078|ref|YP_005920377.1| 196 NIRLLKASDGWRRTWSSIVPGDFNGD 221
                                       56778999****************87 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.13
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrd 144
                                       ++  +k + Gw+  w   +  dfn d
  gi|386002078|ref|YP_005920377.1| 246 NIRLLKSHSGWRRTWSMIMPGDFNSD 271
                                       6778999*****************98 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 0.24
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrd 144
                                       +++ +k   Gw+  w   +  dfn d
  gi|386002078|ref|YP_005920377.1| 367 NIQLLKSSSGWRRTWSIIVPGDFNGD 392
                                       788999*****************987 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.16
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrd 144
                                       ++  +k+  Gw+  w + +  dfn d
  gi|386002078|ref|YP_005920377.1| 417 NIRLLKASDGWRRTWSAIVPGDFNGD 442
                                       56778999***************987 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.029
                            DUF899 118 ekleaykrrmGwtlpwvssaesdfnrd 144
                                        ++ +++ + Gw+  w s +  +fn d
  gi|386002078|ref|YP_005920377.1| 466 GNIRHLQSHSGWRRTWSSIVPGEFNGD 492
                                       5788999*****************987 PP

  == domain 9  score: 2.2 bits;  conditional E-value: 0.044
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrd 144
                                       ++  +k + Gw+  w s +  +fn d
  gi|386002078|ref|YP_005920377.1| 517 NIRLLKSHSGWRRTWSSIVPGEFNGD 542
                                       5777899****************987 PP

  == domain 10  score: 1.3 bits;  conditional E-value: 0.079
                            DUF899 119 kleaykrrmGwtlpwvssaesdfnrdf 145
                                       ++  +k + Gw+  w + +  +fn d 
  gi|386002078|ref|YP_005920377.1| 567 NIRLLKSHSGWRRTWSTIVPGEFNGDG 593
                                       6778999****************9884 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.19   4.9e+02      24      50 ..     141     167 ..     132     168 .. 0.85
   2 ?   -0.6   0.0      0.54   1.4e+03      24      50 ..     191     217 ..     186     218 .. 0.86
   3 ?   -0.5   0.0      0.49   1.3e+03      24      50 ..     241     267 ..     236     268 .. 0.77
   4 ?   -2.4   0.0       1.9   4.9e+03      24      36 ..     291     303 ..     288     316 .. 0.75
   5 ?    0.7   0.0       0.2   5.1e+02      24      50 ..     362     388 ..     359     389 .. 0.87
   6 ?   -1.5   0.0         1   2.6e+03      24      50 ..     412     438 ..     407     439 .. 0.79
   7 ?   -3.7   0.0       4.8   1.2e+04      24      32 ..     462     470 ..     460     487 .. 0.73
   8 ?   -1.7   0.0       1.1   2.9e+03      24      49 ..     512     537 ..     507     539 .. 0.76
   9 ?   -0.6   0.0      0.53   1.4e+03      24      49 ..     562     587 ..     557     589 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                                       EETTEEEEEEEETHHHHHHHTTS-TTS CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeGd 50 
                                       +Dgtg+i++    ++ +++ + + +Gd
  gi|386002078|ref|YP_005920377.1| 141 TDGTGNIRLLQSHSGWRRTWSIIVPGD 167
                                       7********999988888888888887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.54
                                       EETTEEEEEEEETHHHHHHHTTS-TTS CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeGd 50 
                                       +Dg+g+i++   +++ +++ +++ +Gd
  gi|386002078|ref|YP_005920377.1| 191 TDGSGNIRLLKASDGWRRTWSSIVPGD 217
                                       7********999988888888888887 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.49
                                       EETTEEEEEEEETHHHHHHHTTS-TTS CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeGd 50 
                                       +Dgtg+i++    ++ +++ + + +Gd
  gi|386002078|ref|YP_005920377.1| 241 TDGTGNIRLLKSHSGWRRTWSMIMPGD 267
                                       7*******9988777777666666666 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.9
                                       EETTEEEEEEEET CS
                   tRNA_anti-codon  24 rDgtgriqvvlfr 36 
                                       +Dg+g+i++    
  gi|386002078|ref|YP_005920377.1| 291 TDGSGNIRLLQSH 303
                                       79*****998766 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.2
                                       EETTEEEEEEEETHHHHHHHTTS-TTS CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeGd 50 
                                       +Dg+g+iq+   +++ +++ + + +Gd
  gi|386002078|ref|YP_005920377.1| 362 TDGSGNIQLLKSSSGWRRTWSIIVPGD 388
                                       6********999998888888888887 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 1
                                       EETTEEEEEEEETHHHHHHHTTS-TTS CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeGd 50 
                                       +Dg+g+i++   +++ +++ + + +Gd
  gi|386002078|ref|YP_005920377.1| 412 TDGSGNIRLLKASDGWRRTWSAIVPGD 438
                                       7*******9988877777777777776 PP

  == domain 7  score: -3.7 bits;  conditional E-value: 4.8
                                       EETTEEEEE CS
                   tRNA_anti-codon  24 rDgtgriqv 32 
                                       +Dgtg+i+ 
  gi|386002078|ref|YP_005920377.1| 462 TDGTGNIRH 470
                                       699999985 PP

  == domain 8  score: -1.7 bits;  conditional E-value: 1.1
                                       EETTEEEEEEEETHHHHHHHTTS-TT CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeG 49 
                                       +Dg+g+i++    ++ +++ +++ +G
  gi|386002078|ref|YP_005920377.1| 512 TDGSGNIRLLKSHSGWRRTWSSIVPG 537
                                       7*******988877777666666665 PP

  == domain 9  score: -0.6 bits;  conditional E-value: 0.53
                                       EETTEEEEEEEETHHHHHHHTTS-TT CS
                   tRNA_anti-codon  24 rDgtgriqvvlfreeatklaenlkeG 49 
                                       +Dgtg+i++    ++ +++ +++ +G
  gi|386002078|ref|YP_005920377.1| 562 TDGTGNIRLLKSHSGWRRTWSTIVPG 587
                                       7*******988777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       108  (0.00602376); expected 358.6 (0.02)
Passed bias filter:                       94  (0.0052429); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3975.37
//
Query:       gi|386002079|ref|YP_005920378.1|  [L=344]
Description: hypothetical protein Mhar_1391 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 2285.58
//
Query:       gi|386002080|ref|YP_005920379.1|  [L=464]
Description: Drug resistance transporter, EmrB/QacA subfamily [Methanosaeta harundinacea 6Ac]
Scores for complete 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-55  186.9  48.7    4.9e-55  186.9  48.7    1.8  2  MFS_1       Major Facilitator Superfamily
    1.3e-09   37.0  17.1    3.1e-08   32.5   6.6    2.3  2  MFS_3       Transmembrane secretion effector
    6.8e-06   25.2  12.2      0.017   14.0   0.1    2.3  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.13   12.3   0.4        0.3   11.2   0.4    1.6  1  Adipogenin  Adipogenin


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.9  48.7   1.1e-58   4.9e-55       4     352 ..      18     403 ..      15     404 .. 0.90
   2 ?   -0.3   0.7      0.09     4e+02     148     168 ..     430     450 ..     400     463 .. 0.44

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 1.1e-58
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       + fl+ ++ s +++alp a++e++ +++ ++++++t   l+aa++ +p+Grl+d +Gr+rv+ +g++++  ++ll++
  gi|386002080|ref|YP_005920379.1|  18 SSFLTPFMGSSVNIALP-AIGEEFSLDAVTLSWVATSAVLAAAIFLVPFGRLADIHGRKRVFTWGVVTYTGSALLCA 93 
                                       689**************.******************************************************78888 PP

                             MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyil 157
                                       +a+s ++l+++r+ qG+g++++f +g a+++  fp +erg+a+g+  a++ lG  lgp lggll+  +gWravf+ +
  gi|386002080|ref|YP_005920379.1|  94 LATSAPMLIAFRFTQGMGGAMIFGTGTAILTSAFPARERGKALGVSVAAVYLGLTLGPSLGGLLTFTFGWRAVFLSN 170
                                       756666*********************************************************************** PP

                             MFS_1 158 aivsllafvlfllllpeepperkrkspkeee.........................................kgtgp 193
                                        +v+ll+++l +++ ++ +++++r ++ +++                                         +++  
  gi|386002080|ref|YP_005920379.1| 171 LPVGLLLLLL-IAWRLRGEVAEARGESFDLLgsalyclgllatiygfsrlpepvgggllllglagiaafalwESRTT 246
                                       *******885.566777777777777777778****************************************99999 PP

                             MFS_1 194 aplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdr 270
                                       +pl++  ++++ ++++ +  +a+l++ ++++g+ +ll l lq v g+s + +agl+l++  l+++++all+g+lsdr
  gi|386002080|ref|YP_005920379.1| 247 SPLLE-TSLFRDNRPFALSNLAALINYTATFGVGFLLSLHLQYVQGFS-AREAGLVLMAQPLLMIFVALLSGWLSDR 321
                                       9****.9*******99768888888889********************.8*************************** PP

                             MFS_1 271 lgrrrrlllallllllaalglallavt..ssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfnta 344
                                       +++    +la+l++ l++++l+ l     ++++++++ +l+++G+g+g+++++ ++++++++ p+  g as+  +t+
  gi|386002080|ref|YP_005920379.1| 322 MSP---GILAGLGMGLTTASLLTLLDLgrETSLWSVIgSLMILGLGVGLFSSPNTNAVMSSVQPRFYGVASSTLGTM 395
                                       887...555555555555555555555564555555549999*********************************** PP

                             MFS_1 345 gslggalg 352
                                       +  g +l+
  gi|386002080|ref|YP_005920379.1| 396 RLSGHMLS 403
                                       99998886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.09
                             MFS_1 148 lgWravfyilaivsllafvlf 168
                                       l+ +a+ +++a++s+l++   
  gi|386002080|ref|YP_005920379.1| 430 LSGQASLLAFAALSFLGIFAS 450
                                       233444444444444443322 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   6.6   6.9e-12   3.1e-08      45     194 ..      45     190 ..      31     205 .. 0.84
   2 !   10.0   2.8   4.6e-05      0.21      46     129 ..     296     378 ..     282     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.9e-12
                             MFS_3  45 lmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalnd 121
                                       ++   v  +a L   ++ ++ G laD++ r++v+ ++ +   ++s+ll  la    +s  +l+a+ +  g+G a+  
  gi|386002080|ref|YP_005920379.1|  45 VTLSWVATSAVLAAAIFLVPFGRLADIHGRKRVFTWGVV-TYTGSALLCALA----TSAPMLIAFRFTQGMGGAMIF 116
                                       45566889999*********************9999865.567787777776....46789**************** PP

                             MFS_3 122 PaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsy.lalivallrwkrevr 194
                                        +  A++    ++r+  +A  ++   + +  + GP lgG+l  ++G  ++f  n     l l+++ +r + ev 
  gi|386002080|ref|YP_005920379.1| 117 GTGTAILTSAFPARERGKALGVSVAAVYLGLTLGPSLGGLLTFTFGWRAVFLSNLPVGlLLLLLIAWRLRGEVA 190
                                       ***************************************************99975540445555555665554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 4.6e-05
                             MFS_3  46 mvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaaln.d 121
                                          lv  a  L ++++++l+G l+D ++    +la+  + ++++ llt+l +   +s w+++++ +++g+G  l  +
  gi|386002080|ref|YP_005920379.1| 296 EAGLVLMAQPLLMIFVALLSGWLSDRMSP--GILAGLGMGLTTASLLTLLDLGRETSLWSVIGSLMILGLGVGLFsS 370
                                       5568999999****************996..6899************************************987515 PP

                             MFS_3 122 PaWqAsvg 129
                                       P  +A+++
  gi|386002080|ref|YP_005920379.1| 371 PNTNAVMS 378
                                       66666554 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   8.4     1e-05     0.045     260     383 ..      45     167 ..      38     169 .. 0.90
   2 !   14.0   0.1   3.8e-06     0.017      22      62 ..     282     323 ..     272     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                        MFS_1_like 260 tllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaave 336
                                        +l+ + +  v+a  ++++   +l ++ G  ++ ++++++y+   ll a+ ++a +++ + + +g+  ++++++++ 
  gi|386002080|ref|YP_005920379.1|  45 VTLSWVATSAVLAAAIFLVPFGRLADIHGRKRVFTWGVVTYTGSALLCALATSAPMLIAFRFTQGMGGAMIFGTGTA 121
                                       56777778889999999999********************************************************* PP

                        MFS_1_like 337 yvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                           ++p + +++  g+ +++ + lG  lG  +GGll  +++ + +F
  gi|386002080|ref|YP_005920379.1| 122 ILTSAFPARERGKALGVSVAA-VYLGLTLGPSLGGLLTFTFGWRAVF 167
                                       ****************98776.5599999999999987777776666 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.8e-06
                        MFS_1_like  22 ltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfg 62 
                                       l+++l+  +g++a+e g+++++ pl+ i+ +++ g+l+Dr+ 
  gi|386002080|ref|YP_005920379.1| 282 LSLHLQyVQGFSAREAGLVLMAQPLLMIFVALLSGWLSDRMS 323
                                       6899*9779*******************************85 PP

>> Adipogenin  Adipogenin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   6.6e-05       0.3      12      35 ..     157     183 ..     151     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.6e-05
                        Adipogenin  12 ltlsf...lvfwlclpvalllfllivw 35 
                                       lt++f    vf   lpv+lll+lli w
  gi|386002080|ref|YP_005920379.1| 157 LTFTFgwrAVFLSNLPVGLLLLLLIAW 183
                                       55655334589999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3302.87
//
Query:       gi|386002081|ref|YP_005920380.1|  [L=141]
Description: Dinitrogenase iron-molybdenum cofactor biosynthesis [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-25   87.0   0.2    1.1e-24   86.6   0.2    1.2  1  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
       0.11   12.1   0.1       0.13   11.9   0.1    1.1  1  NIF3             NIF3 (NGG1p interacting factor 3)
       0.15   12.1   3.0       0.49   10.4   0.6    2.0  2  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.2   1.8e-28   1.1e-24       4      94 ..      15     102 ..      12     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.8e-28
                                       CB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEE CS
                     Nitro_FeMo-Co   4 rvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievyk 80 
                                         d++FGr+ yF+i++v++  ++ ++n    +a+a++g+g+++aq++a++g+ ++i+g+iGp+a++ l+aag++vy 
  gi|386002081|ref|YP_005920380.1|  15 PADPRFGRCAYFVIVDVDTMVAESISNS---SASAASGAGIQAAQTIANAGAAALITGNIGPNAAETLKAAGVKVYL 88 
                                       679***************9999999999...9********************************************* PP

                                       S-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  81 gaggtveealkevl 94 
                                       ++ggtv+ea+++++
  gi|386002081|ref|YP_005920380.1|  89 ASGGTVREAVERFK 102
                                       ***********997 PP

>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.1e-05      0.13     175     221 ..      43      89 ..      25     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                              NIF3 175 kvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidv 221
                                       +    +G+G +  ++++++ga +liTG +  ++a ++k++g++v+++
  gi|386002081|ref|YP_005920380.1|  43 SASAASGAGIQAAQTIANAGAAALITGNIGPNAAETLKAAGVKVYLA 89 
                                       556789***********************************999875 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   8.2e-05      0.49      11      37 ..      36      66 ..      28     100 .. 0.72
   2 ?    2.3   0.1     0.025   1.5e+02       6      27 ..     102     122 ..      97     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.2e-05
                                      EEEEEEEEEEEGGGCHHHHHHHHHHH....H CS
                   Semialdhyde_dhC 11 lervivatyqavSGaGkkgvreLlkq....v 37
                                       e+++ ++ +a+SGaG ++ +++++      
  gi|386002081|ref|YP_005920380.1| 36 AESISNSSASAASGAGIQAAQTIANAgaaaL 66
                                      688999***********97777766644430 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                                       HCTT.EEEEEEEEEEEGGGCHH CS
                   Semialdhyde_dhC   6 dalgelervivatyqavSGaGk 27 
                                       ++ gel++++ a++q  SG G+
  gi|386002081|ref|YP_005920380.1| 102 KK-GELTETSSASVQPHSGMGR 122
                                       44.89999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1016.83
//
Query:       gi|386002082|ref|YP_005920381.1|  [L=119]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-21   75.2   0.0      5e-21   74.9   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   2.8e-25     5e-21       2      94 ..      14     101 ..      13     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 2.8e-25
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       ++ +++hFGra++F+i+++++g+v++++n      +++ gg g +++l++++g++v+++g+ Gp+a++ +e  giev
  gi|386002082|ref|YP_005920381.1|  14 EELICAHFGRAETFTIVDIDSGDVEVLKNT-----SEHMGGTGLPPELISARGAHVMLAGGLGPKAVKMFEGFGIEV 85 
                                       688***************************.....889999************************************ PP

                                       EES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykgaggtveealkevl 94 
                                       + ga gtv++a+++++
  gi|386002082|ref|YP_005920381.1|  86 FIGATGTVRDAIADWK 101
                                       *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 848.45
//
Query:       gi|386002083|ref|YP_005920382.1|  [L=153]
Description: hypothetical protein Mhar_1395 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0064   16.9   0.0     0.0078   16.6   0.0    1.1  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.3e-07    0.0078       1     107 []      13     130 ..      13     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.3e-07
                                       HHHHHHHHHHHH.....HCT-HHHHHHCEEEEEEEE-TT..S-EEEHHHHHHHH....HCCHCEEEEEEEEEEEEEE CS
                           DUF4440   1 iaaleealeeaf.....vagdaealaallapdavlvgps..gtvldkeelleal....eagfaagrslelteeevrv 66 
                                       i +l+eal++ +     ++ d+ +l+ l+ ++ +l++ +    ++++ ++++a+     ag +   s +   e++++
  gi|386002083|ref|YP_005920382.1|  13 IDELTEALYSCIsfrkgERPDLHRLKGLFIDEGMLINNNddPLIFSIHQFVDAIdcqiSAGSLTSFSEREVAERTEI 89 
                                       56777787777777877899****************777313335*********44333333333333444588899 PP

                                       ETTEEEEEEEEEEEECC.TTEEEEEEEEEEEEEEEETTEEEE CS
                           DUF4440  67 lgdlAvvtgrytfegrg.dgepvegrgrftsvwrkegggWri 107
                                        g +A  + +y ++  + d +p++  g  +  ++k +g Wr+
  gi|386002083|ref|YP_005920382.1|  90 FGKIAHRFSTYEARFDPeDADPISI-GINSIQLVKVEGSWRV 130
                                       9****99999888885538899977.99************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1076.23
//
Query:       gi|386002084|ref|YP_005920383.1|  [L=785]
Description: hypothetical protein Mhar_1396 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-19   70.1   1.1      8e-05   22.9   0.0    4.0  4  DUF11           Domain of unknown function DUF11
    0.00045   20.4   0.0       0.98    9.6   0.0    2.9  2  bMG10           Bacterial Alpha-2-macroglobulin MG10 domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   8.9e-09     8e-05       3      68 ..      54     120 ..      52     132 .. 0.85
   2 ?   -3.2   0.0       1.2   1.1e+04      62      77 ..     169     184 ..     148     204 .. 0.46
   3 !   20.9   0.0   3.7e-08   0.00033      16      81 ..     530     599 ..     519     607 .. 0.83
   4 !   22.2   0.1   1.4e-08   0.00013       3      83 ..     638     719 ..     636     724 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.9e-09
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.qgtasaltsvgsLeage 68 
                                       K  +++ v pG+ + y +   N g ++++gv +t   P+g+++v++s   ++     + +g+L +ge
  gi|386002084|ref|YP_005920383.1|  54 KIASATSVSPGEPLYYAIFYENDGDTDLTGVDITESYPPGTEFVQASIDpKPGTVNVWEIGDLSPGE 120
                                       7778899****************************************99643444456668888887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                             DUF11  62 gsLeagesatlsftvr 77 
                                        ++   ++a ++++v+
  gi|386002084|ref|YP_005920383.1| 169 ATIDSDQTAPVNASVS 184
                                       2223333333333333 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 3.7e-08
                             DUF11  16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsvgsLeagesatlsftvrvtrt 81 
                                        tyt+   N g ++++ v v+D+ P+g  ++   +      +   a+++ + L  g  at+ f+++vt++
  gi|386002084|ref|YP_005920383.1| 530 ATYTISIENDGDRALAPVYVRDIFPPGSVFIHPASVrpteLNDKYANWTLTHLGIGDVATIIFSLEVTKA 599
                                       69*************************999854444465655556777779*************999986 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 1.4e-08
                             DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftv 76 
                                       Kt +   ++ G  v y + v N  ++++  ++vtD lP+g+++   +     + +++ +++ +++e+  + t++++v
  gi|386002084|ref|YP_005920383.1| 638 KTAQLD-PQNGSIVWYKIYVNNDANSDR-AATVTDQLPEGMKLLDPTFPassEDNGTITWNLEDIEPFDTETITYSV 712
                                       555554.899*****************9.***************9998855544555566669************** PP

                             DUF11  77 rvtrtaa 83 
                                       ++  +++
  gi|386002084|ref|YP_005920383.1| 713 EALHAGR 719
                                       *988877 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0   0.00054       4.9      29      99 ..     532     598 ..     519     605 .. 0.85
   2 !    9.6   0.0   0.00011      0.98      22     101 ..     643     719 ..     630     729 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00054
                             bMG10  29 vrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyreirddrvvffadylpk 99 
                                       +++ ++   +r+l  v+++d +P G   + p++ + +e +++y+    ++  ++  i d ++ +f  ++ k
  gi|386002084|ref|YP_005920383.1| 532 YTISIENDGDRALAPVYVRDIFPPGSVFIHPASVRPTELNDKYA----NWTLTHLGIGDVATIIFSLEVTK 598
                                       5666666778889************************9999995....88899999999888888766665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                             bMG10  22 klkvGdkvrvrltvttprdl.eyvaledplPAGlepvnpslgtesesaeeyewleeltefsyreirddr.vvffady 96 
                                         + G+ v  ++ v+ ++   +   + d+lP G+++++p++  +se++   +     ++ ++ e  d + +++ ++ 
  gi|386002084|ref|YP_005920383.1| 643 DPQNGSIVWYKIYVNNDANSdRAATVTDQLPEGMKLLDPTFPASSEDNGTIT-----WNLEDIEPFDTEtITYSVEA 714
                                       6789***********9997758889****************88877766664.....44555554444404455566 PP

                             bMG10  97 lpkgt 101
                                       l +g+
  gi|386002084|ref|YP_005920383.1| 715 LHAGR 719
                                       66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 5071.31
//
Query:       gi|386002085|ref|YP_005920384.1|  [L=183]
Description: hypothetical protein Mhar_1397 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1286.31
//
Query:       gi|386002086|ref|YP_005920385.1|  [L=230]
Description: hypothetical protein Mhar_1398 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1683.12
//
Query:       gi|386002087|ref|YP_005920386.1|  [L=231]
Description: hypothetical protein Mhar_1399 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1478.59
//
Query:       gi|386002088|ref|YP_005920387.1|  [L=147]
Description: Alkylhydroperoxidase like protein, AhpD family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-15   54.9   0.8    9.5e-15   54.4   0.8    1.3  1  CMD            Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.017   14.1   0.0      0.021   13.8   0.0    1.1  1  PA26           PA26 p53-induced protein (sestrin)
      0.043   13.7   0.1      0.096   12.5   0.1    1.7  1  Rad50_zn_hook  Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.8   1.6e-18   9.5e-15      10      69 ..      53     112 ..      44     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.6e-18
                                       HHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHH CS
                               CMD  10 lreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaa 69 
                                       +++a++ +  +Ld+ ++eLi++av+aa +c +C++ H+r+A+++G t++ei ++l +a  
  gi|386002088|ref|YP_005920387.1|  53 HNNAIIRSSKALDLETQELISIAVAAAIRCSHCLKLHLRIAKRMGITDDEIGAALLIAGN 112
                                       55667775677********************************************99865 PP

>> PA26  PA26 p53-induced protein (sestrin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-06     0.021      11      92 ..      10      90 ..       2     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-06
                              PA26 11 ilqessekeetkklleeaflssgrvdqvtqvlglHPqylesflrtqnfllrgdgpLpleyRhYiailaaaRhqcsyLvk 89
                                      il++ +e++ ++++le+   + g+v  +   +   P++l + +  +n+++r++  L le+ + i+i  aa  +cs  +k
  gi|386002088|ref|YP_005920387.1| 10 ILDKGTEQT-AEDMLESIEKAYGEVPYIFGFMKDKPELLVTKILHNNAIIRSSKALDLETQELISIAVAAAIRCSHCLK 87
                                      555554333.44455666667899****************************************************999 PP

                              PA26 90 lhe 92
                                      lh 
  gi|386002088|ref|YP_005920387.1| 88 LHL 90
                                      986 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.6e-05     0.096      13      26 ..     124     137 ..     114     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                       HHHTT-SEE-TTT- CS
                     Rad50_zn_hook  13 eelkeakgcCPlCg 26 
                                        el+e+k+ CP+C+
  gi|386002088|ref|YP_005920387.1| 124 RELNEEKDACPVCQ 137
                                       69***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1062.73
//
Query:       gi|386002089|ref|YP_005920388.1|  [L=302]
Description: hypothetical protein Mhar_1401 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-118  392.9   0.1   6.6e-118  392.7   0.1    1.0  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.7   0.1  3.7e-122  6.6e-118       5     270 ..       1     264 [.       1     265 [. 0.99

  Alignments for each domain:
  == domain 1  score: 392.7 bits;  conditional E-value: 3.7e-122
                             MCR_C   5 tyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsptLar 81 
                                       +++GGvykhd+++el+eDlGGy+lqknv+++ev+l +lvP+ed++++e+l+kel+gkl++aPlagteiavv+ptLa+
  gi|386002089|ref|YP_005920388.1|   1 MFTGGVYKHDLVTELVEDLGGYLLQKNVTQSEVILLMLVPHEDMPVLEALTKELKGKLERAPLAGTEIAVVTPTLAI 77 
                                       79*************************************************************************** PP

                             MCR_C  82 hhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedievPv 158
                                       hhlPh+aCDvaeylrr+Gak+nmiG++rGv+k+iaq++e+e++linehD++vf++Gnf+dCi k ke+l+++++vPv
  gi|386002089|ref|YP_005920388.1|  78 HHLPHPACDVAEYLRRHGAKSNMIGMSRGVAKKIAQMDEYETALINEHDAVVFTFGNFADCILK-KEHLYRTLTVPV 153
                                       ***************************************************************9.9*********** PP

                             MCR_C 159 vvtggPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkkeieeq 235
                                       +vtggP +++ e++p+a +yv ++Griahr rk++ei +ld++v +v++ ld+ r++++kDpl+++p rv+++++eq
  gi|386002089|ref|YP_005920388.1| 154 IVTGGP-DMRKEDLPYAFEYVPNVGRIAHRSRKATEIGSLDNIVAAVGRALDSVRTSISKDPLTTTPPRVMDAVREQ 229
                                       ******.9********************************************************************* PP

                             MCR_C 236 veeieevlsPapitlqldglrvklpydeyaekiee 270
                                       v+++  ++sP pi+l+l+glr+klpy+ey+e+++ 
  gi|386002089|ref|YP_005920388.1| 230 VPDVLISHSPLPIALNLNGLRIKLPYEEYHEAVAG 264
                                       *******************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1935.54
//
Query:       gi|386002090|ref|YP_005920389.1|  [L=191]
Description: hypothetical protein Mhar_1402 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-59  200.1   0.0    2.2e-59  200.0   0.0    1.0  1  DUF2113   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0   0.0   1.2e-63   2.2e-59       6     184 ..      15     188 ..       9     189 .. 0.97

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 1.2e-63
                           DUF2113   6 tdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedkeegkvkikiedE 82 
                                        +e+ga++Y+eii+dilqDl+l+rsi+rl+vy+d+ +p+F++ +++r +++p++++dv+++ +   eg ++i++edE
  gi|386002090|ref|YP_005920389.1|  15 GEEYGAKKYREIIMDILQDLGLIRSIGRLYVYVDILVPYFAVFGMIRGKLPPLRVRDVGDLVA--AEGGYQITVEDE 89 
                                       5899***********************************************************..************ PP

                           DUF2113  83 tylpelLkkLwekygrenveqpdRfeiiiesdedleeleelvVaDpkeelkkkvidaliriaPEGfrvrkealedns 159
                                       ++++ l++ Lwe+ygre+veqpdR+ +++ sd+++   eelvVaD ++e++++++dal+ri PEGfr+r++ + ++s
  gi|386002090|ref|YP_005920389.1|  90 EHMAGLIRALWEAYGREKVEQPDRNVLVVLSDQSP---EELVVADLETEFRRDLMDALVRISPEGFRNRRNEMGKES 163
                                       ********************************988...*************************************** PP

                           DUF2113 160 fvfvAseetlkeewieeakelkeel 184
                                       f+f+A+eet+++e++ eake++  +
  gi|386002090|ref|YP_005920389.1| 164 FFFLAAEETITPELVAEAKEKIGGM 188
                                       *******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1264.56
//
Query:       gi|386002091|ref|YP_005920390.1|  [L=408]
Description: Putative CoA-substrate-specific enzyme activase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-58  196.8   4.7    6.4e-58  196.3   4.7    1.2  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
    0.00025   21.4   0.1     0.0022   18.4   0.1    2.3  1  FtsA         Cell division protein FtsA
     0.0054   15.6   0.4      0.014   14.2   0.1    1.8  3  MreB_Mbl     MreB/Mbl protein
  ------ inclusion threshold ------
      0.071   11.7   3.1       0.49    8.9   0.2    2.3  2  MutL         MutL protein
       0.44   10.2   3.9       0.67    9.6   0.3    2.7  3  Hydant_A_N   Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.3   4.7   1.8e-61   6.4e-58       2     266 ..     149     401 ..     148     402 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.3 bits;  conditional E-value: 1.8e-61
                                       EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTC CS
                       BcrAD_BadFG   2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlp 78 
                                       GiD+GsTttk v+m++++ + + ++ +++ l+s++          a+++ale ag e+ +ie +  ++tgyGr+ ++
  gi|386002091|ref|YP_005920390.1| 149 GIDSGSTTTKSVVMRDNEVIGTGWVPTTEVLKSAE---------AAYNAALESAGVERGEIEGL--GTTGYGRQLVG 214
                                       9****************877777777777777665.........9*****************77..*********** PP

                                       TTBSEEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT-- CS
                       BcrAD_BadFG  79 ekfekeiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmg 152
                                       ++f+++ i++ei+v+++Gav+l++ ++   tv+digG+d+k+i +++g + +f+m++ ca+ +Gr+l+++a++l+++
  gi|386002091|ref|YP_005920390.1| 215 KEFGAKLIQEEITVNSKGAVFLADSQKgaaTVIDIGGMDNKAISVQDGVPGTFTMGGICAGASGRFLELTARRLGVE 291
                                       ***************************************************************************** PP

                                       TTTHHHHHTT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG CS
                       BcrAD_BadFG 153 lreldglaekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvak 228
                                       + el+ la k++ +k  +ns+c vf  + l++ ls g   ed+   +++++a++v +++ ++ +v++ v+++GG+a 
  gi|386002091|ref|YP_005920390.1| 292 ITELGKLALKGDhRKVPMNSYCIVFGTQSLVNSLSAGSRPEDVAMAACHSVAEQVFEQQLQEVEVKEPVIMVGGTAL 368
                                       ************66699************************************************************ PP

                                       -HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHH CS
                       BcrAD_BadFG 229 neaavkelrklvkenygevkininpdsiytgalGAalf 266
                                        e++ +++     e+ ++ k+ ++ +++y g +GA+l+
  gi|386002091|ref|YP_005920390.1| 369 IEGLPRAM-----EQLLGLKVIVPEYAQYIGCVGASLL 401
                                       ********.....999999*****************97 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   6.1e-07    0.0022       1     103 []     148     394 ..     148     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.1e-07
                                       EEEEE-SSSEEEEEEETTEEEEEEEES-...-HHHHHHHHHHHHT--HHHH..HHHHHH......H--S--EEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx..xxxxxx......xxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgalvhlrvigv...ggngitkdiakalrtaveeA..erikik......yGsalaekeigr 66 
                                       a++D G+++t+ +v++d+     +vig+   +   + k+++ a++ a+e+A  er +i+      yG +l  ke+g 
  gi|386002091|ref|YP_005920390.1| 148 AGIDSGSTTTKSVVMRDN-----EVIGTgwvPTTEVLKSAEAAYNAALESAgvERGEIEglgttgYGRQLVGKEFGA 219
                                       79***************6.....555555556788999999999999999966666653333333666666666665 PP

                                       HHHH......................................................................... CS
                                       xxxx......................................................................... RF
                              FtsA  67 kels......................................................................... 70 
                                       k ++                                                                         
  gi|386002091|ref|YP_005920390.1| 220 KLIQeeitvnskgavfladsqkgaatvidiggmdnkaisvqdgvpgtftmggicagasgrfleltarrlgveitelg 296
                                       5555666688888999999999999999999999999999999999999999999999999999999999******* PP

                                       ....................................................................GGGGSTTHH CS
                                       ....................................................................xxxxxxxxx RF
                              FtsA  71 ....................................................................ggsalpnle 79 
                                                                                                           g++ +++l 
  gi|386002091|ref|YP_005920390.1| 297 klalkgdhrkvpmnsycivfgtqslvnslsagsrpedvamaachsvaeqvfeqqlqevevkepvimvgGTALIEGLP 373
                                       ***************************************************************************** PP

                                       HHHHHHH..T-..HHHT-GGGHHHHH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxx RF
                              FtsA  80 elaeral..spkleevsdpeyasalg 103
                                       +++e+ l  +     v  peya  +g
  gi|386002091|ref|YP_005920390.1| 374 RAMEQLLglK-----VIVPEYAQYIG 394
                                       *****97331.....45678887665 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.3   4.7e+03     266     301 ..      71     107 ..      67     111 .. 0.77
   2 ?   -3.3   0.1      0.87   3.1e+03     144     154 ..     241     251 ..     215     259 .. 0.58
   3 !   14.2   0.1     4e-06     0.014     273     315 ..     356     398 ..     333     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.3
                                       HHHHHHHHHH-EEEESGGGGSB.THHHHHHHHHSS-E CS
                          MreB_Mbl 266 peLaadivdrgivltGGgallk.gldkllseetglpv 301
                                       p+La  ++  + + +  ga+++ +l+k+++e+ ++pv
  gi|386002091|ref|YP_005920390.1|  71 PDLADAVFVATCFRCAEGAIVRsELRKYIHENSRIPV 107
                                       7788878777777777777776369999999999988 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.87
                                       SS-EEEEEE-S CS
                          MreB_Mbl 144 psgnmvvdiGg 154
                                         +  v+diGg
  gi|386002091|ref|YP_005920390.1| 241 KGAATVIDIGG 251
                                       33456888887 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4e-06
                                       HHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHH CS
                          MreB_Mbl 273 vdrgivltGGgallkgldkllseetglpvkvaedpltcvakGt 315
                                       v++ ++++GG+al++gl + +++ +gl+v+v e +    + G+
  gi|386002091|ref|YP_005920390.1| 356 VKEPVIMVGGTALIEGLPRAMEQLLGLKVIVPEYAQYIGCVGA 398
                                       677899*************************998876666665 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00014      0.49       4      50 ..     150     192 ..     148     212 .. 0.80
   2 ?    2.8   0.3    0.0096        34     234     269 ..     232     264 ..     226     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00014
                              MutL   4 iDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealee 50 
                                       iD GSttTk +++++     +++g++  pTt   +    ++++ale+
  gi|386002091|ref|YP_005920390.1| 150 IDSGSTTTKSVVMRD----NEVIGTGWVPTTEVLKSAEAAYNAALES 192
                                       799********9999....57*********98556666666666654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0096
                              MutL 234 avellaeeeekglgdllvvDvGGaTTdvhsvaegsp 269
                                       ++ +la+ ++k  g + v+D+GG+    +sv +g p
  gi|386002091|ref|YP_005920390.1| 232 GAVFLAD-SQK--GAATVIDIGGMDNKAISVQDGVP 264
                                       5667788.444..89***************977755 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.16   5.6e+02      45      96 ..      93     143 ..      88     145 .. 0.70
   2 ?    9.6   0.3   0.00019      0.67       3      59 ..     149     202 ..     147     221 .. 0.77
   3 ?   -1.5   0.0      0.49   1.7e+03     153     173 ..     334     354 ..     314     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.16
                        Hydant_A_N  45 evleesiprtskidvvrmGTTvatNa..llerkgervaLittkgfrdlleigrq 96 
                                       + l++ i+++s+i v+ ++ T  t a  ll r +   aL+tt +f+ ll+ +rq
  gi|386002091|ref|YP_005920390.1|  93 SELRKYIHENSRIPVLSYSFTERTTAetLLTRME---ALVTTAKFKGLLSRERQ 143
                                       5566677778888888888887775522444443...89999999999999888 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00019
                        Hydant_A_N   3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidv 59 
                                       gID G+T T  v+++++ e++ +  +++t  +v +    a + +le+++ ++++i+ 
  gi|386002091|ref|YP_005920390.1| 149 GIDSGSTTTKSVVMRDN-EVIGTGWVPTT--EVLKSAEAAYNAALESAGVERGEIEG 202
                                       9**************87.99999999999..66666666666666666666666664 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.49
                        Hydant_A_N 153 iavvllhSylnpehElrvaei 173
                                       +a +  hS++    E++ +e+
  gi|386002091|ref|YP_005920390.1| 334 VAMAACHSVAEQVFEQQLQEV 354
                                       677788888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2568.90
//
Query:       gi|386002092|ref|YP_005920391.1|  [L=145]
Description: hypothetical protein Mhar_1404 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-62  207.9   0.0    6.7e-62  207.8   0.0    1.0  1  DUF2112   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.8   0.0   3.8e-66   6.7e-62       1     143 []       2     144 ..       2     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 207.8 bits;  conditional E-value: 3.8e-66
                           DUF2112   1 mkvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligpl 77 
                                       +kv+v+P++s+iladlver+ghe+l+++ke+++ v+t++ldsppln+t+edpkkGlkyaav+vPsGvrGR++ligp+
  gi|386002092|ref|YP_005920391.1|   2 VKVMVYPPTSMILADLVERTGHEALVVSKEVRKMVNTPGLDSPPLNMTPEDPKKGLKYAAVDVPSGVRGRMALIGPM 78 
                                       69*************************************************************************** PP

                           DUF2112  78 ieeaeaaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                       ieeaeaai+v ++++++gc+GCartnel+++l+r+k+iP+le+e+P +e  a+++v+ki+eFL++l
  gi|386002092|ref|YP_005920391.1|  79 IEEAEAAIVVMNDRCTLGCTGCARTNELTRFLLRTKRIPLLEMEFPGDELAARRFVSKIREFLEGL 144
                                       ***************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1055.91
//
Query:       gi|386002093|ref|YP_005920392.1|  [L=141]
Description: hypothetical protein Mhar_1405 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-43  144.4   0.0    1.1e-42  143.9   0.0    1.2  1  DUF2102   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
       0.31   10.7   1.5       0.84    9.3   0.1    2.1  2  P66_CC    Coiled-coil and interaction region of P66A and P66B


Domain annotation for each model (and alignments):
>> DUF2102  Uncharacterized protein conserved in archaea (DUF2102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0   1.2e-46   1.1e-42       1     103 []       6     109 ..       6     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 1.2e-46
                           DUF2102   1 lvvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRak 77 
                                       +vv ++e++v+ps+++ k+yel +d+++ketCfG++++geee+++  vee+rk+d+++if+k+Rgfppgd+rrCR++
  gi|386002093|ref|YP_005920392.1|   6 YVVTSQESDVLPSDIALKIYELGRDINVKETCFGVIIDGEEEDIRATVEELRKMDESNIFIKDRGFPPGDPRRCRGH 82 
                                       7999************************************************************************* PP

                           DUF2102  78 r.ggaRpGfhqlekEvelleliskaLe 103
                                       r ggaRpGf+++++E e+l+lis+aLe
  gi|386002093|ref|YP_005920392.1|  83 RgGGARPGFYMMQHESEILPLISRALE 109
                                       *99**********************97 PP

>> P66_CC  Coiled-coil and interaction region of P66A and P66B with MBD2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3     0.098   8.8e+02       9      19 ..      48      58 ..      45      61 .. 0.79
   2 ?    9.3   0.1   9.4e-05      0.84      11      22 ..     106     117 ..     104     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.098
                            P66_CC  9 mikkLreeLRn 19
                                       i++  eeLR+
  gi|386002093|ref|YP_005920392.1| 48 DIRATVEELRK 58
                                      58888899995 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 9.4e-05
                            P66_CC  11 kkLreeLRnEEa 22 
                                       ++L+++LR EEa
  gi|386002093|ref|YP_005920392.1| 106 RALEADLRGEEA 117
                                       89*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 949.83
//
Query:       gi|386002094|ref|YP_005920393.1|  [L=504]
Description: Putative methanogenesis marker protein 3 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   15.0   0.2         12    6.1   0.0    4.1  5  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.27   4.9e+03     114     127 ..      81      94 ..      47      98 .. 0.78
   2 ?   -0.7   0.0     0.087   1.6e+03     123     141 ..     146     164 ..     141     175 .. 0.84
   3 ?    0.3   0.0     0.042   7.5e+02      11      37 ..     200     225 ..     194     240 .. 0.82
   4 ?    2.0   0.0     0.013   2.3e+02     120     135 ..     282     297 ..     242     315 .. 0.82
   5 ?    6.1   0.0   0.00068        12      10      33 ..     373     396 ..     364     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.27
                     Pro_isomerase 114 aphldgkytvFGkV 127
                                       a + dg  ++FG V
  gi|386002094|ref|YP_005920393.1|  81 ARWSDGAAVAFGPV 94 
                                       66888888888877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.087
                     Pro_isomerase 123 vFGkVveGmdvvekiekve 141
                                       vF  Vv G d++ ++ek++
  gi|386002094|ref|YP_005920393.1| 146 VFAAVVGGKDLLGRLEKGD 164
                                       89*************9985 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.042
                     Pro_isomerase  11 rivieLfadkaPktvenFlklvkegfY 37 
                                       ri++eL ++  P+ +e Fl+ +++g++
  gi|386002094|ref|YP_005920393.1| 200 RIEVELLEEA-PQGAEFFLAATRDGVF 225
                                       7999998776.**********999965 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.013
                     Pro_isomerase 120 kytvFGkVveGmdvve 135
                                       +  v G+V++Gmd+v+
  gi|386002094|ref|YP_005920393.1| 282 SQSVVGTVTSGMDLVK 297
                                       46899********996 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.00068
                     Pro_isomerase  10 GrivieLfadkaPktvenFlklvk 33 
                                        +++ieL++d aPkt + F+++v 
  gi|386002094|ref|YP_005920393.1| 373 RMVAIELYDDLAPKTLDYFRHVVG 396
                                       6799***************99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2973.79
//
Query:       gi|386002095|ref|YP_005920394.1|  [L=525]
Description: Methyl coenzyme M reductase system, component A2 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-49  168.1   0.0    6.7e-27   94.7   0.0    2.5  2  ABC_tran      ABC transporter
      2e-05   24.2   0.2       0.12   12.2   0.0    2.4  2  AAA_29        P-loop containing region of AAA domain
    2.6e-05   24.2   0.4      0.093   12.6   0.0    2.6  2  RsgA_GTPase   RsgA GTPase
    3.7e-05   23.3   2.0      0.035   13.5   0.0    3.5  4  SMC_N         RecF/RecN/SMC N terminal domain
    0.00037   20.4   0.6        3.4    7.4   0.1    3.3  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00089   19.7   0.2       0.35   11.2   0.0    2.6  2  AAA_16        AAA ATPase domain
     0.0039   16.4   1.7        1.6    7.9   0.2    3.1  4  NB-ARC        NB-ARC domain
     0.0067   16.7   1.0        4.6    7.5   0.3    2.7  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.011   15.9   0.7       0.58   10.2   0.0    2.3  2  DUF87         Helicase HerA, central domain
      0.014   15.1   0.2        1.7    8.3   0.0    2.7  3  AAA_30        AAA domain
      0.016   15.4   0.7       0.56   10.4   0.3    2.6  2  AAA_33        AAA domain
      0.016   15.7   0.9       0.58   10.7   0.3    2.6  2  AAA_18        AAA domain
      0.023   14.9   0.1         15    5.9   0.0    3.3  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.029   13.7   0.3        2.9    7.2   0.1    2.4  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.037   13.9   0.7        2.1    8.2   0.2    2.4  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.048   13.4   0.0        2.5    7.8   0.0    2.3  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.048   13.4   0.7       0.81    9.4   0.1    2.6  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.055   13.5   2.2        9.3    6.4   0.1    3.2  3  MMR_HSR1      50S ribosome-binding GTPase
       0.12   12.0   0.4          2    8.1   0.2    2.4  2  AAA_24        AAA domain
       0.12   12.8   0.0        7.3    7.0   0.0    2.2  2  AAA_23        AAA domain
       0.13   12.0   0.1         49    3.6   0.0    3.3  3  IstB_IS21     IstB-like ATP binding protein
       0.15   11.8   0.7        3.6    7.4   0.1    2.4  2  zf-CSL        CSL zinc finger
       0.16   12.0   0.0        1.9    8.6   0.0    2.3  2  DUF5532       Family of unknown function (DUF5532)
       0.34    9.5   0.7        6.5    5.3   0.3    2.5  3  AAA_13        AAA domain
        1.2    9.3   2.9        3.9    7.7   0.7    2.7  3  AAA_28        AAA domain
        1.4    8.9   3.1         15    5.5   0.1    2.4  2  NACHT         NACHT domain
        1.4    8.5   5.5         19    4.8   0.4    3.9  4  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   2.2e-22   1.5e-19       1     136 [.      11     191 ..      11     192 .. 0.81
   2 !   94.7   0.0     1e-29   6.7e-27       2     136 ..     296     450 ..     295     451 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 2.2e-22
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx................................. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei................................. 42 
                                       l++v+l+++ege ++i+G++G+GKS Ll +l g +      G++                                 
  gi|386002095|ref|YP_005920394.1|  11 LRHVNLEIEEGESLGILGRSGSGKSVLLHVLRGVEPFeeITGSViyhvarcpqcshveppsragescrcggtfqpfe 87 
                                       678******************************98664467888999999999999999999999998888777776 PP

                                       .EETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTT CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  43 .lldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren............esdeeiekalsklglkelkdtvvkss 105
                                         + +  +++ +++ ++++i+++ q    l  + +v  n             s ++++++l+++++++   +v+   
  gi|386002095|ref|YP_005920394.1|  88 aDFVSLGINDPKRRDVSRRIAIMLQRtFALYGDERVIVNvmraveeasggsISVNRAADLLDEVNMSHRMMHVA--- 161
                                       63334444457777778888887777444444454666678887778888777778999999999999766666... PP

                                       SGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 106 pssLSgGqkqrvalarallkkpkllllDEpt 136
                                        ++LSgG+kqrv+lar l+k p +ll+DEp+
  gi|386002095|ref|YP_005920394.1| 162 -RELSGGEKQRVVLARQLAKSPMMLLADEPS 191
                                       .*****************************6 PP

  == domain 2  score: 94.7 bits;  conditional E-value: 1e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlf 71 
                                       ++vsl+++ege+ ++vG +GaGK+tL k+l g + pt+G i+++ g+d+ +      + + ++ k +g+l+qe +l 
  gi|386002095|ref|YP_005920394.1| 296 DEVSLEVYEGEIFGLVGTSGAGKTTLSKMLNGIVMPTSGGIWCRvGDDWVDmtilgaDHKGRATKYMGMLHQEYTLY 372
                                       79***************************************99988888888999989999**************** PP

                                       TTSBHHHH............HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxx............xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren............esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       p  +v +n             +++++ + l ++g +e  +++v++++p++LS+G++ rva+a++l+k+p++++lDEp
  gi|386002095|ref|YP_005920394.1| 373 PYRSVIDNltesiglslpfeLAERKAIHTLVTVGFSEeEAERVLTKNPNELSEGERHRVAMAQVLIKEPRIVVLDEP 449
                                       *******************87777788888888887725666777888***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|386002095|ref|YP_005920394.1| 450 T 450
                                       9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00017      0.12      16      39 ..      15      38 ..       7      42 .. 0.81
   2 !    9.4   0.1    0.0013      0.84      16      38 ..     299     321 ..     292     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       +ei++ ++  + G+sGsGKS ll
  gi|386002095|ref|YP_005920394.1| 15 NLEIEEGESLGILGRSGSGKSVLL 38
                                      56777555888**********998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                            AAA_29  16 tieidlkgatlltGpsGsGKSTl 38 
                                       ++e+ + +++ l+G+sG+GK+Tl
  gi|386002095|ref|YP_005920394.1| 299 SLEVYEGEIFGLVGTSGAGKTTL 321
                                       555654448889**********9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0015      0.98      88     122 ..       9      44 ..       1      60 [. 0.78
   2 !   12.6   0.0   0.00014     0.093      90     121 ..     295     327 ..     253     359 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       e+l++++ ++++ +   ++G SG GKS L+ +l++ 
  gi|386002095|ref|YP_005920394.1|   9 EALRHVNLEIEEgESLGILGRSGSGKSVLLHVLRGV 44 
                                       566677777777688889**************9974 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                                       HHHHH.HHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  90 leelk.ellkdktsvlvGqSGvGKStLinallp 121
                                       ++e++ e+ ++++  lvG SG+GK+tL ++l++
  gi|386002095|ref|YP_005920394.1| 295 VDEVSlEVYEGEIFGLVGTSGAGKTTLSKMLNG 327
                                       555551445669999************999976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.099        65      28      42 ..      25      39 ..      10      44 .. 0.77
   2 !   13.5   0.0   5.3e-05     0.035      97     204 ..     125     229 ..      97     241 .. 0.74
   3 ?   -1.5   0.0         2   1.4e+03      26      41 ..     307     322 ..     295     329 .. 0.81
   4 ?    3.5   0.0     0.061        40     134     205 ..     420     489 ..     392     501 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.099
                                      EEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlld 42
                                       i+G+ GSGKs ll 
  gi|386002095|ref|YP_005920394.1| 25 GILGRSGSGKSVLLH 39
                                      699********9876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.3e-05
                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                       v+++r v++    ++ +n+      ev+   +++++ + +LSgGek+ v l    A q +k   + l De    LD 
  gi|386002095|ref|YP_005920394.1| 125 VNVMRAVEEASGGSISVNRAADLLDEVNMSHRMMHVAR-ELSGGEKQRVVL----ARQLAKSPMMLLADEPSGTLDP 196
                                       56677777777777777777777777777777777766.5******97655....5555555556667********* PP

                                       HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkekskn..aQfivislreemlek 204
                                       k    v e ++++ ++  + +i++s+  +++ +
  gi|386002095|ref|YP_005920394.1| 197 KTADLVHESIRRAVDDfnMTMIITSHWPDVMVE 229
                                       ***********9887644788999997765543 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2
                                       EEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnll 41 
                                       +  +vG  G+GK+ l 
  gi|386002095|ref|YP_005920394.1| 307 IFGLVGTSGAGKTTLS 322
                                       5579********9875 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.061
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                       +++LS Ge+  va+a ++    +k   +++lDe    +D      v++ + +++++    f+++s++ ++++++
  gi|386002095|ref|YP_005920394.1| 420 PNELSEGERHRVAMAQVL----IKEPRIVVLDEPTGTMDLITKIDVSKSVLNARDElgETFLIVSHDMDFVQNV 489
                                       5689*****999999884....5666799**********999999999888888775678******99999886 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016        11       3      22 ..      25      44 ..      23      59 .. 0.85
   2 !    7.4   0.1    0.0051       3.4       1      79 [.     307     379 ..     307     388 .. 0.75
   3 ?    5.2   0.0     0.023        15     172     266 ..     345     449 ..     342     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      ++ G+ gsGKS LL  l+++
  gi|386002095|ref|YP_005920394.1| 25 GILGRSGSGKSVLLHVLRGV 44
                                      699***********999876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0051
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       + +l+G  g+GK++L + l      ++ v ++    + ++g ++++  + + d +++++     ++++ + y y+  
  gi|386002095|ref|YP_005920394.1| 307 IFGLVGTSGAGKTTLSKML------NGIVMPTSGGIWCRVGDDWVDMTILGADHKGRATKYMGMLHQEYTLYPYRSV 377
                                       578****************......5557888888888888888888888888777777666666666666666666 PP

                            AAA_21  78 le 79 
                                       ++
  gi|386002095|ref|YP_005920394.1| 378 ID 379
                                       55 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.023
                            AAA_21 172 fadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.............gvvflengdgqelpar 235
                                       +++++ +a++k++++++++ l++    +    + ++l +s+ + l+++             g+  +e ++    +++
  gi|386002095|ref|YP_005920394.1| 345 VDMTILGADHKGRATKYMGMLHQEYTLYPYRSVIDNLTESIGLSLPFElaerkaihtlvtvGFSEEEAERVLTKNPN 421
                                       566677788888888888888888888888888888888888888888888888888888888888999999999** PP

                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEp 266
                                       elS+G ++  a++  l+  +   +++++DEp
  gi|386002095|ref|YP_005920394.1| 422 ELSEGERHRVAMAQVLIKEP---RIVVLDEP 449
                                       *********9*******988...*******9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00053      0.35       9      63 ..       8      64 ..       6      92 .. 0.73
   2 ?    5.8   0.1     0.024        16      25      44 ..     306     325 ..     293     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                            AAA_16  9 leqLlsalervrsgrpelvllsGesGvGKsslvrellr.....alekdggiflrgkcdql 63
                                      +e+L+++   + +g  e++ + G sG+GKs l+  l+      +++++ +i+  ++c q+
  gi|386002095|ref|YP_005920394.1|  8 VEALRHVNLEIEEG--ESLGILGRSGSGKSVLLHVLRGvepfeEITGS-VIYHVARCPQC 64
                                      55555544445555..78999************777644433355554.77777777777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                            AAA_16  25 elvllsGesGvGKsslvrel 44 
                                       e+  l+G sG GK++l ++l
  gi|386002095|ref|YP_005920394.1| 306 EIFGLVGTSGAGKTTLSKML 325
                                       667799*********98776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.01       6.9      19      38 ..      22      39 ..       7      49 .. 0.81
   2 ?   -0.9   0.0       1.1   7.6e+02     190     229 ..     130     169 ..     119     186 .. 0.75
   3 !    7.9   0.2    0.0024       1.6      19      40 ..     306     325 ..     290     350 .. 0.80
   4 ?   -3.5   0.0       6.8   4.5e+03      81     110 ..     421     447 ..     411     459 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                                      CSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 19 qslvvalvGmgGvGKttlak 38
                                      +   +++ G+ G+GK++l++
  gi|386002095|ref|YP_005920394.1| 22 E--SLGILGRSGSGKSVLLH 39
                                      4..689***********975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                       HHHHCTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHHCTGC CS
                            NB-ARC 190 ivekckGlPlalkvlggllstkktveewkkvlekleskll 229
                                        ve+ +G  ++++  ++ll   ++ +++ +v+ +l+  + 
  gi|386002095|ref|YP_005920394.1| 130 AVEEASGGSISVNRAADLLDEVNMSHRMMHVARELSGGEK 169
                                       4677778889999999999988********9999985444 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0024
                                       CSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  19 qslvvalvGmgGvGKttlakqi 40 
                                       +  + +lvG  G GKttl+k  
  gi|386002095|ref|YP_005920394.1| 306 E--IFGLVGTSGAGKTTLSKML 325
                                       4..899************9864 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6.8
                                       TTSSSS-STTSHHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  81 ddleekeeveslkrklvrlLltkrfllvlD 110
                                       +   e +e+e     + ++L++   ++vlD
  gi|386002095|ref|YP_005920394.1| 421 N---ELSEGERHRVAMAQVLIKEPRIVVLD 447
                                       3...33444445678899999998888888 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.013       8.7       7      48 ..      23      70 ..      18      79 .. 0.64
   2 !    7.5   0.3     0.007       4.6      10      25 ..     310     325 ..     303     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlp 48
                                      +l + G sG+GK++ll  l+   + e+           ++p++ +v++p
  gi|386002095|ref|YP_005920394.1| 23 SLGILGRSGSGKSVLLHVLRGVEPFEEIT-GsviyhvaRCPQCSHVEPP 70
                                      56689**********98776554322222.2455555555555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.007
                            AAA_22  10 vtGesGtGKTtllrrl 25 
                                       ++G sG+GKTtl ++l
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSKML 325
                                       89**********9987 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00088      0.58      24      43 ..      22      41 ..       5      42 .. 0.88
   2 ?    3.5   0.3     0.097        65      26      43 ..     308     325 ..     299     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00088
                             DUF87 24 rHlAilgsTGsGKSntvavL 43
                                      ++l+ilg++GsGKS +  vL
  gi|386002095|ref|YP_005920394.1| 22 ESLGILGRSGSGKSVLLHVL 41
                                      679***********999887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.097
                             DUF87  26 lAilgsTGsGKSntvavL 43 
                                       ++ +g++G+GK+++ + L
  gi|386002095|ref|YP_005920394.1| 308 FGLVGTSGAGKTTLSKML 325
                                       7899********998866 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.057        38      22      40 ..      25      43 ..      10      59 .. 0.82
   2 ?   -3.0   0.1       7.6     5e+03      69      96 ..     156     189 ..     127     209 .. 0.50
   3 ?    8.3   0.0    0.0025       1.7      20      63 ..     307     363 ..     297     466 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.057
                            AAA_30 22 vltGpAGtGKttalkalre 40
                                       + G+ G+GK+ +l +lr 
  gi|386002095|ref|YP_005920394.1| 25 GILGRSGSGKSVLLHVLRG 43
                                      578***********99975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.6
                            AAA_30  69 eastiakllkrlk......grarlepg.tllivDE 96 
                                       + + +a+ l+  +      +  +l+++  +l+ DE
  gi|386002095|ref|YP_005920394.1| 156 RMMHVARELSGGEkqrvvlA-RQLAKSpMMLLADE 189
                                       33333333322224444432.23333335555555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0025
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.g............grviglAptgkaAkvLa 63 
                                       +  l+G  G+GKtt+ k l+ ++    g            ++++g+ ++g+a k ++
  gi|386002095|ref|YP_005920394.1| 307 IFGLVGTSGAGKTTLSKMLNGIVMPTsGgiwcrvgddwvdMTILGADHKGRATKYMG 363
                                       66799************9988776664568888888888777777777777777776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0       0.2   1.4e+02       6      20 ..      28      42 ..      25      92 .. 0.85
   2 ?   10.4   0.3   0.00084      0.56       4      32 ..     310     344 ..     307     450 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
                            AAA_33  6 GlpGsGKstlaerll 20
                                      G +GsGKs l++ l 
  gi|386002095|ref|YP_005920394.1| 28 GRSGSGKSVLLHVLR 42
                                      89*******998765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00084
                            AAA_33   4 lvGlpGsGKstlaerl....lkklg..avllssdt 32 
                                       lvG +G+GK+tl++ l    +   g  ++++  d 
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSKMLngivMPTSGgiWCRVGDDW 344
                                       79***********9886654333336666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.28   1.8e+02       3      19 ..      26      42 ..      24      66 .. 0.75
   2 ?   10.7   0.3   0.00087      0.58       3      18 ..     310     325 ..     309     351 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.28
                            AAA_18  3 ltGtpGvGKttlakeLs 19
                                      + G +G+GK+ l + L+
  gi|386002095|ref|YP_005920394.1| 26 ILGRSGSGKSVLLHVLR 42
                                      8899********99995 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00087
                            AAA_18   3 ltGtpGvGKttlakeL 18 
                                       l Gt+G+GKttl+k L
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSKML 325
                                       89***********988 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.022        15      21      42 ..     152     173 ..     138     208 .. 0.75
   2 ?    5.0   0.0     0.043        28      62      77 ..     439     454 ..     396     457 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                           SbcCD_C  21 gkekelsrssgtlSGGekqfla 42 
                                       + + ++ + +++lSGGekq ++
  gi|386002095|ref|YP_005920394.1| 152 NMSHRMMHVARELSGGEKQRVV 173
                                       55667888999*******8765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.043
                           SbcCD_C  62 palrlvfLDEAFsklD 77 
                                       + +r+v+LDE  +++D
  gi|386002095|ref|YP_005920394.1| 439 KEPRIVVLDEPTGTMD 454
                                       359***********99 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.041        27       8      47 ..       7      46 ..       2      61 .. 0.81
   2 ?    7.2   0.1    0.0044       2.9      27      49 ..     310     332 ..     298     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.041
                      Mg_chelatase  8 qeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllp 47
                                      + ea r +++ +  g +l ++G +GsGK++l + l ++ p
  gi|386002095|ref|YP_005920394.1|  7 EVEALRHVNLEIEEGESLGILGRSGSGKSVLLHVLRGVEP 46
                                      55666667777777788999***********999988765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0044
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsllppl 49 
                                       lvG++G+GKt l k l++++ p 
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSKMLNGIVMPT 332
                                       89****************98775 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.092        61       2      19 ..      24      41 ..      23      59 .. 0.85
   2 ?    8.2   0.2    0.0032       2.1       1      19 [.     307     325 ..     307     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.092
                              MobB  2 lgivgksgsGKTtLlekl 19
                                      lgi g+sgsGK  Ll+ l
  gi|386002095|ref|YP_005920394.1| 24 LGILGRSGSGKSVLLHVL 41
                                      799***********9866 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0032
                              MobB   1 vlgivgksgsGKTtLlekl 19 
                                       ++g+vg+sg+GKTtL + l
  gi|386002095|ref|YP_005920394.1| 307 IFGLVGTSGAGKTTLSKML 325
                                       689***********97765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0       0.1        67       3      51 ..      25      68 ..      24      79 .. 0.66
   2 ?    7.8   0.0    0.0037       2.5       1      23 [.     307     329 ..     307     371 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdlele 51
                                      g+ g SG+Gk+ + + l+ +         ei+g ++  + r+ +  ++e
  gi|386002095|ref|YP_005920394.1| 25 GILGRSGSGKSVLLHVLRGVEP-----FEEITGSVIYHVARCPQCSHVE 68
                                      899********99887765433.....2245566666666666655555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0037
                               PRK   1 vIgvagsSGaGkttvarklekif 23 
                                       + g+ g SGaGktt+++ l+ i+
  gi|386002095|ref|YP_005920394.1| 307 IFGLVGTSGAGKTTLSKMLNGIV 329
                                       56999**********99998776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.47   3.1e+02       6      24 ..      26      44 ..      23      56 .. 0.87
   2 ?    9.4   0.1    0.0012      0.81       6      23 ..     310     327 ..     306     333 .. 0.89
   3 ?   -2.6   0.0       6.5   4.3e+03      95     108 ..     455     465 ..     452     491 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.47
                         PduV-EutP  6 liGkvgsGKttLtqalkge 24
                                      ++G++gsGK  L + l+g 
  gi|386002095|ref|YP_005920394.1| 26 ILGRSGSGKSVLLHVLRGV 44
                                      68***********999984 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                         PduV-EutP   6 liGkvgsGKttLtqalkg 23 
                                       l+G++g+GKttL++ l+g
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSKMLNG 327
                                       89**************98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.5
                         PduV-EutP  95 iitkidlaedeeni 108
                                       +itkid+++   ++
  gi|386002095|ref|YP_005920394.1| 455 LITKIDVSK---SV 465
                                       688888873...33 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.014       9.3       2      21 ..      24      43 ..      23     154 .. 0.87
   2 ?   -2.4   0.0       7.4   4.9e+03      25      43 ..     185     203 ..     173     277 .. 0.66
   3 ?    5.3   0.4     0.029        19       3      19 ..     309     325 ..     307     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                       +i+Gr+ +GKS L+  l g
  gi|386002095|ref|YP_005920394.1| 24 LGILGRSGSGKSVLLHVLRG 43
                                      589************99876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.4
                                       EESSSTTSSSSEEEEEEEE CS
                          MMR_HSR1  25 ivsdkpgtTrdinegrvkl 43 
                                         +d+p  T+d++++ + +
  gi|386002095|ref|YP_005920394.1| 185 LLADEPSGTLDPKTADLVH 203
                                       5567777777777766652 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.029
                                       EEEESTTSSHHHHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinal 19 
                                       ++vG + +GK+tL + l
  gi|386002095|ref|YP_005920394.1| 309 GLVGTSGAGKTTLSKML 325
                                       89***********8877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.35   2.3e+02       4      20 ..      23      39 ..      20      47 .. 0.83
   2 ?    8.1   0.2    0.0031         2       6      28 ..     309     329 ..     305     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.35
                            AAA_24  4 kiliyGpsgiGKTtlak 20
                                      ++ i G sg+GK+ l+ 
  gi|386002095|ref|YP_005920394.1| 23 SLGILGRSGSGKSVLLH 39
                                      5789*********9875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                            AAA_24   6 liyGpsgiGKTtlakelgpkplf 28 
                                        ++G sg+GKTtl k+l  + ++
  gi|386002095|ref|YP_005920394.1| 309 GLVGTSGAGKTTLSKML--NGIV 329
                                       689************99..4444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.15     1e+02      23      39 ..      25      41 ..       7      44 .. 0.80
   2 ?    7.0   0.0     0.011       7.3      18      35 ..     304     321 ..     292     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                       I G  G+GK+ +l  +
  gi|386002095|ref|YP_005920394.1| 25 GILGRSGSGKSVLLHVL 41
                                      69*********999765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                            AAA_23  18 skgltlItGpNGaGKTTi 35 
                                       +  ++ ++G  GaGKTT+
  gi|386002095|ref|YP_005920394.1| 304 EGEIFGLVGTSGAGKTTL 321
                                       557999***********8 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.074        49      44      64 ..      18      38 ..       4      57 .. 0.83
   2 ?    1.1   0.0      0.42   2.8e+02      74     114 ..     135     175 ..     127     226 .. 0.73
   3 ?    2.8   0.0      0.13        87      47      65 ..     305     323 ..     285     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.074
                         IstB_IS21 44 iekkenivllGpsGvGKshla 64
                                      ie+ e++ +lG sG GKs l 
  gi|386002095|ref|YP_005920394.1| 18 IEEGESLGILGRSGSGKSVLL 38
                                      889999************885 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.42
                         IstB_IS21  74 aglsvlfvrvedLveelkrarrdgklaralkrllkvdllil 114
                                       +g s++  r++dL+ e+++ +r  ++ar+l+   k ++++ 
  gi|386002095|ref|YP_005920394.1| 135 SGGSISVNRAADLLDEVNMSHRMMHVARELSGGEKQRVVLA 175
                                       56677888888888888888888888888877777666654 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.13
                         IstB_IS21  47 kenivllGpsGvGKshlai 65 
                                        e + l+G sG+GK+ l+ 
  gi|386002095|ref|YP_005920394.1| 305 GEIFGLVGTSGAGKTTLSK 323
                                       566789*********9976 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.24   1.6e+02      43      51 ..      57      65 ..      45      67 .. 0.83
   2 ?    7.4   0.1    0.0054       3.6      20      34 ..      76      90 ..      74     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
                                      -EEEETTSS CS
                            zf-CSL 43 vvvqCssCS 51
                                       v++C++CS
  gi|386002095|ref|YP_005920394.1| 57 HVARCPQCS 65
                                      599*****9 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0054
                                      EETTSSEEEEEHHHH CS
                            zf-CSL 20 pCRCgdeFelteedl 34
                                      +CRCg++F+  e+d+
  gi|386002095|ref|YP_005920394.1| 76 SCRCGGTFQPFEADF 90
                                      7*******9888876 PP

>> DUF5532  Family of unknown function (DUF5532)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.2   7.9e+02      61      88 ..     255     282 ..     241     284 .. 0.76
   2 ?    8.6   0.0    0.0029       1.9      36      70 ..     395     429 ..     392     441 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                           DUF5532  61 Lnalsltsetdvreedsqpvltckvvrk 88 
                                         a++ + e+  + +   p+++ck + k
  gi|386002095|ref|YP_005920394.1| 255 FVAMAGKIEDRKKTDVGSPIIRCKDLSK 282
                                       3688999999999999********9866 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                           DUF5532  36 eskKsnllkthgislkEAqkmLsqnLnalsltset 70 
                                       e k  + l t g s +EA ++L++n n ls  ++ 
  gi|386002095|ref|YP_005920394.1| 395 ERKAIHTLVTVGFSEEEAERVLTKNPNELSEGERH 429
                                       567778899****************9988755444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5     1e+03      21      40 ..      26      45 ..      26      56 .. 0.85
   2 ?    5.3   0.3    0.0098       6.5      23      38 ..     312     327 ..     307     333 .. 0.88
   3 ?    1.2   0.0      0.17   1.1e+02     498     577 ..     421     489 ..     409     502 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                            AAA_13 21 iYGwNGaGKTtLSrllrsle 40
                                      i G+ G+GK+ L  +lr +e
  gi|386002095|ref|YP_005920394.1| 26 ILGRSGSGKSVLLHVLRGVE 45
                                      66999**********99986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0098
                            AAA_13  23 GwNGaGKTtLSrllrs 38 
                                       G+ GaGKTtLS++l+ 
  gi|386002095|ref|YP_005920394.1| 312 GTSGAGKTTLSKMLNG 327
                                       889*********9976 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.17
                            AAA_13 498 etLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                       ++LSeGE+  +a+          +  i++ +ivv+D P   +D      v+  + +    ++  + ++i  H ++f 
  gi|386002095|ref|YP_005920394.1| 421 NELSEGERHRVAMA---------QVLIKEPRIVVLDEPTGTMDLITKIDVSKSVLNAR--DELGETFLIVSHDMDFV 486
                                       67999999888874.........23356899999999999999888888877666664..66777777778888887 PP

                            AAA_13 575 kev 577
                                       ++v
  gi|386002095|ref|YP_005920394.1| 487 QNV 489
                                       766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.1   2.1e+03       4      20 ..      26      42 ..      25      60 .. 0.82
   2 ?   -1.3   0.0       3.3   2.2e+03     123     154 ..     188     219 ..     141     223 .. 0.69
   3 ?    7.7   0.7    0.0058       3.9       4      20 ..     310     326 ..     308     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.1
                            AAA_28  4 itGgestGKTtlleaLa 20
                                      i+G +++GK+ ll  L 
  gi|386002095|ref|YP_005920394.1| 26 ILGRSGSGKSVLLHVLR 42
                                      78999*******98775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                            AAA_28 123 ddgeRredleereaiderlrealrelgipvii 154
                                       d    + d++ +  ++e +r a++++++ +ii
  gi|386002095|ref|YP_005920394.1| 188 DEPSGTLDPKTADLVHESIRRAVDDFNMTMII 219
                                       44444568888999999999999999988887 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0058
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       ++G++++GKTtl++ L+
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSKMLN 326
                                       79***********9986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.023        15       5      19 ..      26      40 ..      23      42 .. 0.88
   2 ?    2.9   0.6      0.14        94       5      18 ..     310     323 ..     307     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.023
                                      EEC-TTTCHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqk 19
                                      + G++GsGK++Ll+ 
  gi|386002095|ref|YP_005920394.1| 26 ILGRSGSGKSVLLHV 40
                                      78**********985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                                       EEC-TTTCHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlq 18 
                                       l G +G GKTtL +
  gi|386002095|ref|YP_005920394.1| 310 LVGTSGAGKTTLSK 323
                                       78*********965 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.57   3.8e+02       4      18 ..      25      39 ..      23      48 .. 0.84
   2 ?    1.0   0.0      0.42   2.8e+02      27     110 ..     105     210 ..      95     242 .. 0.70
   3 ?    4.8   0.4     0.029        19       3      17 ..     308     322 ..     306     331 .. 0.85
   4 ?    0.7   0.0      0.53   3.5e+02      39      68 ..     479     508 ..     471     522 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.57
                                      EEEESTTCCHHHHHH CS
                              cobW  4 vltGflGsGKTtLln 18
                                      ++ G  GsGK+ Ll 
  gi|386002095|ref|YP_005920394.1| 25 GILGRSGSGKSVLLH 39
                                      578999******996 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                                       S-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH......................T CS
                              cobW  27 lklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere......................e 81 
                                       +++a+++     +  D++++ +    + e + G i  + + dll e++   ++                       +
  gi|386002095|ref|YP_005920394.1| 105 RRIAIMLQRTFALYGDERVIVNVMRAVEEASGGSISVNRAADLLDEVNMSHRMMhvarelsggekqrvvlarqlakS 181
                                       66777766666677778888777777888888888888888888888887777777777888877777777777733 PP

                                       T-SEEEEEECTTTTHHHHHTTSHHHHHCC CS
                              cobW  82 rldviliEttGlaePapvafteeelksdl 110
                                        + ++  E +G ++P++  + +e++++++
  gi|386002095|ref|YP_005920394.1| 182 PMMLLADEPSGTLDPKTADLVHESIRRAV 210
                                       33344448888888888744455555444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.029
                                       EEEEESTTCCHHHHH CS
                              cobW   3 tvltGflGsGKTtLl 17 
                                       ++l+G  G+GKTtL 
  gi|386002095|ref|YP_005920394.1| 308 FGLVGTSGAGKTTLS 322
                                       6799*********94 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.53
                                       CHCCCCCCHCCCT.EEEETTTTECCHCTT- CS
                              cobW  39 vsiDaellretgveivelenGciCctlred 68 
                                       vs+D +++++ ++ +  + nG+i +    +
  gi|386002095|ref|YP_005920394.1| 479 VSHDMDFVQNVCDRAALMRNGKIVHVGTPE 508
                                       799********99**********9985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 3081.16
//
Query:       gi|386002096|ref|YP_005920395.1|  [L=219]
Description: Phenylacrylic acid decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-26   90.4   0.1    1.3e-25   90.0   0.1    1.2  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.1   7.4e-30   1.3e-25       3     125 ..      22     182 ..      20     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 7.4e-30
                                       EEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHHCT................ CS
                      Flavoprotein   3 illgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaaredpilhielrr................ 63 
                                       +++gi+G+++++++++lle L + g  +++v+t+aA+++i+ e       e++  ++e+                  
  gi|386002096|ref|YP_005920395.1|  22 VVVGISGASGVVYGIRLLEVLADLGSTTHLVMTEAARRIIEIE------TEESPIDVEMMAdrvysprdftaciasg 92 
                                       89***************************************88......2333444555223567777899999999 PP

                                       ..TESEEEEEEEEHHHHHHHHTT--SSHH............................HHHHHTHCCTTEEEEE.--H CS
                      Flavoprotein  64 ..wadllviaPasantlakianGiadnll............................tlilratakkpiliaPamnp 110
                                         ++d++v+aP+s+ tla ia G++d+l+                             +++ a+++++++i+P ++p
  gi|386002096|ref|YP_005920395.1|  93 scKFDAMVVAPCSMRTLAGIASGVSDTLItraadvclkerrrlilvpresplnlvhlKNMV-AATEAGAIILP-PSP 167
                                       99**************************************************999963334.5789*******.*** PP

                                       HCCTCSTCHHHHHHH CS
                      Flavoprotein 111 amyenpqtlknlekl 125
                                        +y++p+t+  +++ 
  gi|386002096|ref|YP_005920395.1| 168 GFYSKPETIGGMVDA 182
                                       ********9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1455.19
//
Query:       gi|386002097|ref|YP_005920396.1|  [L=304]
Description: deoxyhypusine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.5e-100  334.6   0.0   5.1e-100  334.4   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.4   0.0  2.9e-104  5.1e-100       1     287 [.      17     295 ..      17     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 334.4 bits;  conditional E-value: 2.9e-104
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       el++ +e +gf a++l+ea++i+++m ++ + t f++l+++++++G+r+i++ l++++ +dv+vtT++++ +D+i+ 
  gi|386002097|ref|YP_005920396.1|  17 ELVRMMEGCGFGARRLAEAVNIYEEM-QSGEYTRFFTLAGAMVPAGMRNILSSLIRDGRIDVLVTTGANLVHDIIEG 92 
                                       699***********************.78899********************************************* PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSily 154
                                       +++ ++lgd e++d+eLre+g+ Ri++++v ++++ +fe+ ++eil + ++    ++ +el++ lG+ i+de+Sil+
  gi|386002097|ref|YP_005920396.1|  93 FSH-HVLGDPEASDSELRESGVSRIYDVYVGDDDFVRFEELLQEILPQGKD----MTGTELLRVLGSGIEDERSILR 164
                                       *99.********************************************998....8********************* PP

                                DS 155 wAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnan.lm 230
                                       +A+++++pvfcpal+D+++G+q++lf+   +++ l++d++ D+ el di++ a+++g++i+GGGvpK+++l+a+ ++
  gi|386002097|ref|YP_005920396.1| 165 AAADARVPVFCPALSDSMIGLQAWLFR---QTHPLEVDLFGDVGELVDICYGAERSGIVIIGGGVPKNFALQAMlVT 238
                                       ***************************...7899****************************************555 PP

                                DS 231 rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                        n +d a+++tt++++ G+lsga+l+EavSwgki+++a++v+vy+DaTi +PL+va+
  gi|386002097|ref|YP_005920396.1| 239 PNSFDLAIQLTTDRPEAGGLSGASLSEAVSWGKISPGARKVTVYGDATINFPLMVAS 295
                                       79*****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 2248.79
//
Query:       gi|386002098|ref|YP_005920397.1|  [L=131]
Description: F420H2 dehydrogenase, subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-28   98.4   2.0    2.1e-28   98.4   2.0    1.9  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
        0.1   12.6   0.4        0.1   12.6   0.4    2.6  2  MatC_N       Dicarboxylate carrier protein MatC N-terminus


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.028   2.5e+02      38      52 ..       6      20 ..       2      24 .. 0.85
   2 !   98.4   2.0   2.3e-32   2.1e-28       4      99 .]      28     130 ..      25     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.028
                                      HHCHHHHHHHHHHHH CS
                       Oxidored_q4 38 fsvkfylvallFliF 52
                                      + v +y+  ++Fli 
  gi|386002098|ref|YP_005920397.1|  6 VAVDYYIPLIMFLII 20
                                      6799********985 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 2.3e-32
                                       HHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST.........HHHH CS
                       Oxidored_q4   4 llllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel.......glfg 73 
                                       +l++ ++++p+k++ +k+++YE G++p++ea ++++v++yl+a++F+iFDvev+fl+pw+ ++ ++         ++
  gi|386002098|ref|YP_005920397.1|  28 ALAAVKIISPQKSTFQKRATYEGGLRPIREAIIQYNVQYYLFAIVFVIFDVEVLFLYPWIYVYASEaipafggVSIA 104
                                       577889999****************************************************9998855544433555 PP

                                       HHHHHHHHHHHHHHHHHHHHH-S-XX CS
                       Oxidored_q4  74 liemllFllillvglvYewkkgaLeW 99 
                                       ++ ml+F+++ll+gl+Y +kk+aL+W
  gi|386002098|ref|YP_005920397.1| 105 ITGMLIFIVVLLIGLLYDIKKEALRW 130
                                       89************************ PP

>> MatC_N  Dicarboxylate carrier protein MatC N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   1.1e-05       0.1      93     130 ..      11      46 ..       5      52 .. 0.88
   2 ?   -1.4   3.8      0.24   2.2e+03     111     114 ..     101     104 ..      46     128 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                            MatC_N  93 aipwvlfllaalltalGalspaavaivaPvalsfakky 130
                                        ip+++fl+ ++l  +Gal  aav i++P   +f k+ 
  gi|386002098|ref|YP_005920397.1|  11 YIPLIMFLIIGALVPIGAL--AAVKIISPQKSTFQKRA 46 
                                       59***************97..89******999998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.24
                            MatC_N 111 lspa 114
                                       +s a
  gi|386002098|ref|YP_005920397.1| 101 VSIA 104
                                       3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 922.34
//
Query:       gi|386002099|ref|YP_005920398.1|  [L=190]
Description: F420H2 dehydrogenase, subunit B [Methanosaeta harundinacea 6Ac]
Scores for 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-19   70.6   0.0    1.7e-19   69.9   0.0    1.4  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   9.7e-24   1.7e-19      33     128 ..      93     174 ..      67     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 9.7e-24
                                       --HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S- CS
                       Oxidored_q6  33 dskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvp 109
                                       ++         +++dv++++G +trk  +a+++l+e  +++k+v+a+G+CA++GG +  +++++    +++ ++  p
  gi|386002099|ref|YP_005920398.1|  93 TP---------RQVDVMIISGYITRKYLPAIKNLWEEIPEPKWVMAIGECAISGGPF--YDSYNI---INDTSKFFP 155
                                       33.........49********************************************..664444...4589999** PP

                                       E.EEE-SSS--HHHHHHHH CS
                       Oxidored_q6 110 vdinipGCPphpeailetl 128
                                       +d++ipGCPp+pe+++e++
  gi|386002099|ref|YP_005920398.1| 156 IDVFIPGCPPRPEKFIEGF 174
                                       ***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1461.78
//
Query:       gi|386002100|ref|YP_005920399.1|  [L=571]
Description: F420H2 dehydrogenase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-79  264.4   0.2    8.5e-76  254.6   0.2    2.3  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    2.8e-29  102.2   0.0    5.2e-29  101.3   0.0    1.4  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    1.7e-07   30.6   0.1    3.3e-07   29.6   0.0    1.5  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.6   0.2   1.4e-79   8.5e-76       5     271 .]     329     571 .]     326     571 .] 0.97

  Alignments for each domain:
  == domain 1  score: 254.6 bits;  conditional E-value: 1.4e-79
                                       HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHS CS
                    Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtk 81 
                                        ++fly++ +Re +l ++e+vtGaR+++s++r+GGv++Dlp+g+ +++ ++lk +++k +e+++l+++++i++kR++
  gi|386002100|ref|YP_005920399.1| 329 YSPFLYMIIDREDVLTCIESVTGARINHSFVRFGGVRNDLPDGFKDMTLDTLKMIREKTAEYKDLFSSDSIYRKRME 405
                                       689************************************************************************** PP

                                       SSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    Complex1_49kDa  82 gvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqalek 158
                                       g+g+ls ++a +lg++Gp lRas  +yD+R+++pY  Y ++df+v++++egD+ +R+ vr++E+ +S+ Iieq+l++
  gi|386002100|ref|YP_005920399.1| 406 GIGTLSPQDARRLGVSGPPLRASDTPYDMRREDPYLLYRDMDFEVITRKEGDSKARVEVRLDEILESCYIIEQCLDQ 482
                                       ***************************************************************************** PP

                                       --.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-H CS
                    Complex1_49kDa 159 lpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirap 235
                                       +p+gp++ae             k              ++k  +ge+y +vE  +Ge+g+++vsdgs+kp ++k r p
  gi|386002100|ref|YP_005920399.1| 483 IPNGPIMAEGV----------PK--------------KIKPEPGEAYYRVEDHRGEMGFFVVSDGSDKPVKVKARGP 535
                                       *****999542..........22..............346789********************************** PP

                                       HHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 236 sfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                        ++++qal+ ll+g ++aDvvai gs+d +++evDR
  gi|386002100|ref|YP_005920399.1| 536 VYAYFQALPPLLEGVYIADVVAIAGSMDACTSEVDR 571
                                       ***********************************9 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   8.7e-33   5.2e-29       2     116 ..      33     148 ..      32     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 8.7e-33
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--.S-.-EEEEEE....-S-BEE--TTT-ST CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsl.eknerirvkvevdeeepevpSvtdlfpg 76 
                                       +++p+++++v+k+l+d+   gfd+ s  ++vD+  e+ fev  +l+s  ++++   +kv++++e+p+v+S+t l+ +
  gi|386002100|ref|YP_005920399.1|  33 TIKPDRIVDVCKYLRDN--HGFDHYSGAVGVDRInEGLFEVTEMLASHgSHQVVALLKVKTKRESPSVKSLTGLYWN 107
                                       689*************5..89***********66789**********9666666669999999************** PP

                                       HHHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-.TTSTTS CS
                    Complex1_30kDa  77 adwyEREayDmfGivfeghpdlrrillpedfegh.PLRkdf 116
                                       a+wyERE+++m+Gi+feghp+l  +ll ++ +g  P+Rkdf
  gi|386002100|ref|YP_005920399.1| 108 ANWYEREIWEMLGINFEGHPELYPLLLADELVGVwPWRKDF 148
                                       ***************************99975544*****9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   5.5e-11   3.3e-07       1      68 [.     248     315 ..     248     325 .. 0.97
   2 ?   -3.8   0.0      0.75   4.5e+03     210     224 ..     546     560 ..     536     564 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.5e-11
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                       +G+E+i+++r+ ++   +++R C   + +   a   ave+ lgi+ p+ a++ir +++    +++h++
  gi|386002100|ref|YP_005920399.1| 248 KGIEKIMENRTYQQGIPITDRLCYMAAITNNEAYCGAVERLLGIEAPERAQYIRMILQELSRIQSHLL 315
                                       59****************************************************************86 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.75
                                       HHHHTHHHHHHHHHH CS
                      NiFeSe_Hases 210 fveevylpDvlaiak 224
                                         e vy++Dv+aia 
  gi|386002100|ref|YP_005920399.1| 546 LLEGVYIADVVAIAG 560
                                       67889*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3483.95
//
Query:       gi|386002101|ref|YP_005920400.1|  [L=347]
Description: F420H2 dehydrogenase, subunit H [Methanosaeta harundinacea 6Ac]
Scores for complete 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-107  359.6  20.7   1.6e-107  359.3  20.7    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.3  20.7  8.7e-112  1.6e-107       4     297 ..      27     338 ..      24     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 359.3 bits;  conditional E-value: 8.7e-112
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SST.TTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHH CS
                            NADHdh   4 llllvvlllvvalltlleRkvlAriqdRlGPnrvG.plGllqplaDalKlllKediipkkadkllfllapvlalila 79 
                                       ++l  v+ +v++ll++leRkv++ +q R+GPnrvG  +G+lq+ aDa+Kl++Ked+ip++adk +f++ap++a++++
  gi|386002101|ref|YP_005920400.1|  27 AILASVINVVAMLLVWLERKVMGDFQARYGPNRVGgRWGVLQLGADAIKLFTKEDVIPRGADKPVFVWAPIVAVATT 103
                                       444545666666**********************8699*************************************** PP

                                       HCTTTTS-SSS..........SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  80 llafaviPfge..........vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalgls 146
                                       +l+  ++Pfg+          v+a+++++ ++i a +s++++  ++aGw+sn+kY++lGa+R +a mi+yEv++g++
  gi|386002101|ref|YP_005920400.1| 104 MLVAGALPFGAviidgreiplVVANMDISAFYIEAALSIMAISAFMAGWSSNNKYSMLGAFRGIARMIAYEVPMGVC 180
                                       **********55566788999******************************************************** PP

                                       HHHHHHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHH CS
                            NADHdh 147 llavvllagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalffla 223
                                       +++v+++a+sl++ eiv+aq++iwf+l+q+++f+if ial+  ++r+PFD +eae+E++aG++tEYsg++f+l++++
  gi|386002101|ref|YP_005920400.1| 181 VISVAIMAHSLNVVEIVHAQQGIWFALAQPIGFVIFGIALITDLGRMPFDQTEAEEEIIAGYNTEYSGIRFGLLYFQ 257
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHCT.SS-HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHH CS
                            NADHdh 224 eyanmvlvsalavllFlgGwllpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplala 293
                                       ey+ m+l s+l+v l+lgGw++p++       +++wf++K++++l+ +iwir +lpR+R+dq+++lgwk+llpl+++
  gi|386002101|ref|YP_005920400.1| 258 EYIVMLLGSILLVHLYLGGWNGPVIpvisfisPMIWFFMKLVIVLVALIWIRVSLPRFRIDQVTDLGWKILLPLSMV 334
                                       ***********************999*************************************************** PP

                                       HHHH CS
                            NADHdh 294 nlll 297
                                       nl +
  gi|386002101|ref|YP_005920400.1| 335 NLGW 338
                                       *976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2138.03
//
Query:       gi|386002102|ref|YP_005920401.1|  [L=185]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-11   42.5  22.5    9.6e-06   25.2   9.3    2.3  2  Fer4            4Fe-4S binding domain
    1.7e-10   41.3  13.7    4.1e-10   40.1  13.7    1.7  1  Fer4_7          4Fe-4S dicluster domain
    4.4e-09   36.3  20.9    5.3e-07   29.6  11.7    2.1  2  Fer4_10         4Fe-4S dicluster domain
    2.9e-08   33.8  26.1    2.2e-06   27.7  13.8    2.0  2  Fer4_9          4Fe-4S dicluster domain
    7.3e-07   28.9  11.4     0.0014   18.6   2.3    2.4  2  Fer4_2          4Fe-4S binding domain
      3e-06   27.3  29.2    0.00032   20.8  16.1    2.2  2  Fer4_21         4Fe-4S dicluster domain
    1.1e-05   25.8  11.8     0.0015   19.0  13.6    2.4  2  Fer4_8          4Fe-4S dicluster domain
    1.6e-05   25.7  17.1     0.0016   19.4   2.0    3.0  2  Fer4_16         4Fe-4S double cluster binding domain
    7.2e-05   23.3  12.6     0.0038   17.7   0.5    2.8  3  Fer4_17         4Fe-4S dicluster domain
     0.0007   19.6  21.8      0.016   15.2   9.1    2.4  2  Fer4_6          4Fe-4S binding domain
    0.00073   19.9  16.0     0.0044   17.4   4.5    2.4  2  Fer4_4          4Fe-4S binding domain
  ------ inclusion threshold ------
       0.44   11.4  16.3       0.26   12.1   3.2    2.7  3  Fer4_22         4Fe-4S dicluster domain
          1    9.2   6.9        1.6    8.6   6.9    1.3  1  Coilin_N        Coilin N-terminus
        1.4    8.8   8.8        1.6    8.6   7.7    1.6  2  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
        1.4    9.7  23.5        1.2   10.0   2.8    3.4  2  Fer4_15         4Fe-4S single cluster domain
        3.7    7.8  17.9        1.5    9.0   1.3    3.2  3  Fer4_18         4Fe-4S dicluster domain
          6    8.1  24.7       0.36   11.9   8.2    2.4  2  Fer4_3          4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   9.3   9.1e-09   9.6e-06       7      24 .]      44      61 ..      41      61 .. 0.95
   2 !   23.1   5.3   4.2e-08   4.4e-05       1      22 [.      79     100 ..      79     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 9.1e-09
                                      TSSS-THHHHHSTTTEEE CS
                              Fer4  7 kCigCGaCvevCPvgAIt 24
                                      kCigCGaC+ +CP+++I+
  gi|386002102|ref|YP_005920401.1| 44 KCIGCGACARICPNDCIK 61
                                      9***************96 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 4.2e-08
                                       EEEETTTSSS-THHHHHSTTTE CS
                              Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                       ++id+ +C++CG+Cv+ CP  +
  gi|386002102|ref|YP_005920401.1|  79 PQIDYGRCMFCGLCVDDCPASC 100
                                       68*****************876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1  13.7   3.9e-13   4.1e-10       1      50 [.      44      98 ..      44     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.9e-13
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt.....ekveidpekClgCgaCvavCPt 50
                                      +CigCgaC++ Cp+++i+l  +++ +++     ++++id+ +C++Cg Cv+ CP+
  gi|386002102|ref|YP_005920401.1| 44 KCIGCGACARICPNDCIKLVAYSRGNPVknkklQYPQIDYGRCMFCGLCVDDCPA 98
                                      7*****************985433332223333889******************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  11.7   5.1e-10   5.3e-07       5      56 .]      41      97 ..      37      97 .. 0.93
   2 !   18.8   1.7   1.2e-06    0.0013       3      24 ..      80     140 ..      78     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.1e-10
                           Fer4_10  5 dddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +  +Ci+Cg+C + CP d       s g+  ++++ +  ++++++C++cg Cv+ CP
  gi|386002102|ref|YP_005920401.1| 41 EIRKCIGCGACARICPNDCiklvaYSRGNPVKNKKLQYPQIDYGRCMFCGLCVDDCP 97
                                      5679*************99****9999999999999999*****************9 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.2e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.......................................t 24 
                                       +id  +C+ Cg Cv+ CPa+                                        +
  gi|386002102|ref|YP_005920401.1|  80 QIDYGRCMFCGLCVDDCPASClimskqfeisgwnrediiydpediavglysdqelaelaeE 140
                                       689999*************777777777777766666666666666666655555544441 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   4.4   1.4e-06    0.0015      20      51 .]      31      60 ..      20      60 .. 0.69
   2 !   27.7  13.8   2.1e-09   2.2e-06       1      49 [.      44      99 ..      44     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                            Fer4_9 20 daaerkarlraaseeaCigCgaCveaCpkgai 51
                                       +aer + + +    +CigCgaC+ +Cp+++i
  gi|386002102|ref|YP_005920401.1| 31 PDAERGVHVLEI--RKCIGCGACARICPNDCI 60
                                      444444444444..46*************987 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.1e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkg 49
                                      kC+gCgaC + Cp++ ++  a  r + +++++         +C++Cg Cv+ Cp  
  gi|386002102|ref|YP_005920401.1| 44 KCIGCGACARICPNDCIKLVAYSRGNPVKNKKLqypqidyGRCMFCGLCVDDCPAS 99
                                      7****************999999999999888899*****99************86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.3   1.3e-06    0.0014       8      22 .]      43      57 ..      36      57 .. 0.86
   2 !   15.2   1.9   1.6e-05     0.017       2      22 .]      78      98 ..      77      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                            Fer4_2  8 drCigCgaCvsaCPa 22
                                      ++CigCgaC   CP+
  gi|386002102|ref|YP_005920401.1| 43 RKCIGCGACARICPN 57
                                      69************5 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.6e-05
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++++d  rC+ Cg Cv+ CPa
  gi|386002102|ref|YP_005920401.1| 78 YPQIDYGRCMFCGLCVDDCPA 98
                                      589*****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   5.1   9.9e-07     0.001      32      58 ..      35      61 ..      26      62 .. 0.79
   2 !   20.8  16.1     3e-07   0.00032       6      59 .]      43     103 ..      39     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.9e-07
                           Fer4_21 32 tvlkvve.deCvGCnlCssvCPvedcie 58
                                      + ++v+e  +C+GC  C+ +CP +dci+
  gi|386002102|ref|YP_005920401.1| 35 RGVHVLEiRKCIGCGACARICP-NDCIK 61
                                      5555654379************.7***8 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3e-07
                           Fer4_21   6 dkCigCgkCliaCedtshqai........eidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                        kCigCg C+  C++ +++ +        + ++ ++ ++   +C+ C lC++ CP   c+ m
  gi|386002102|ref|YP_005920401.1|  43 RKCIGCGACARICPNDCIKLVaysrgnpvKNKKLQYPQIDYGRCMFCGLCVDDCPA-SCLIM 103
                                       69************9777777776555322222234466689*************6.88765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  13.6   1.4e-06    0.0015       2      64 ..      42      99 ..      41     100 .. 0.65
   2 !   15.0   1.3   2.4e-05     0.026       4      20 ..      85     131 ..      82     181 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                            Fer4_8  2 lekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ++kCi+CgaC   Cp   ++  +  + ++ ++ ++  q  q        ++C+ cg C++ Cp +
  gi|386002102|ref|YP_005920401.1| 42 IRKCIGCGACARICPndCIKLVAYSRGNPVKN-KK-LQYPQ-----IDYGRCMFCGLCVDDCPAS 99
                                      78************955333333222222222.22.23333.....3579*************85 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.4e-05
                            Fer4_8   4 kCieCgaCqsaCp..............................vlrr 20 
                                       +C+ Cg+C + Cp                              ++++
  gi|386002102|ref|YP_005920401.1|  85 RCMFCGLCVDDCPasclimskqfeisgwnrediiydpediavgLYSD 131
                                       8***********97777655555555555555544445544442222 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.0   1.5e-06    0.0016       1      24 [.      44      67 ..      44      84 .. 0.76
   2 !   10.0   7.6    0.0012       1.3       1      34 [.      85     137 ..      85     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                      +C++Cg+Ca +CP ++ik  ++ +
  gi|386002102|ref|YP_005920401.1| 44 KCIGCGACARICPNDCIKLVAYSR 67
                                      5****************9884444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie..arecisy.................n 34 
                                       rC  Cg C++ CP++++ + k++ei   +re+i y                  
  gi|386002102|ref|YP_005920401.1|  85 RCMFCGLCVDDCPASCLIMSKQFEISgwNREDIIYdpediavglysdqelaeL 137
                                       6999************9999666654113333333455555555533333331 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   3.6e-06    0.0038      42      59 ..      41      58 ..       8      60 .. 0.79
   2 !   11.3   2.7   0.00038       0.4      42      58 ..      82      98 ..      61     101 .. 0.75
   3 ?    6.4   6.9     0.012        13       1      14 [.      85      98 ..      85     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      ++ +Ci+Cg C+r CP++
  gi|386002102|ref|YP_005920401.1| 41 EIRKCIGCGACARICPND 58
                                      7899************97 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00038
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                        ++C+ Cg+C+ +CP+
  gi|386002102|ref|YP_005920401.1| 82 DYGRCMFCGLCVDDCPA 98
                                      6789999*******997 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                           Fer4_17  1 rCiqCgyClpeCps 14
                                      rC+ Cg C++ Cp 
  gi|386002102|ref|YP_005920401.1| 85 RCMFCGLCVDDCPA 98
                                      57777777777774 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   9.1   1.5e-05     0.016       8      22 ..      44      58 ..      42      60 .. 0.88
   2 !    9.9   4.8   0.00073      0.77       2      22 ..      79      99 ..      78     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                            Fer4_6  8 kCigCgdCvrvCPeg 22
                                      kCigCg+C+r+CP +
  gi|386002102|ref|YP_005920401.1| 44 KCIGCGACARICPND 58
                                      8************65 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00073
                            Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                                      ++id+ +C  Cg Cv+ CP+ 
  gi|386002102|ref|YP_005920401.1| 79 PQIDYGRCMFCGLCVDDCPAS 99
                                      7899***************96 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   4.5   4.1e-06    0.0044       3      15 ..      44      56 ..      42      67 .. 0.92
   2 !    7.8   3.7    0.0049       5.1       3      16 ..      85      98 ..      83     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-06
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +CigCg+C ++CP
  gi|386002102|ref|YP_005920401.1| 44 KCIGCGACARICP 56
                                      7************ PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0049
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      rC  Cg Cv+ CP 
  gi|386002102|ref|YP_005920401.1| 85 RCMFCGLCVDDCPA 98
                                      8999*********4 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.2   0.00025      0.26      78      94 ..      41      57 ..       7      60 .. 0.76
   2 ?    5.2   3.1     0.036        38      75      94 ..      79      98 ..      65     100 .. 0.75
   3 ?    3.0   5.9      0.18   1.9e+02       1      24 [.      85     107 ..      85     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      +  +C+GCg C + cp+
  gi|386002102|ref|YP_005920401.1| 41 EIRKCIGCGACARICPN 57
                                      77889999999999997 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.036
                           Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                       +++   C+ Cg C++ cp+
  gi|386002102|ref|YP_005920401.1| 79 PQIDYGRCMFCGLCVDDCPA 98
                                      56677789999999999987 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.18
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedet 24 
                                       rC+ Cg C   Cp+ sC  ++++ 
  gi|386002102|ref|YP_005920401.1|  85 RCMFCGLCVDDCPA-SCLIMSKQF 107
                                       79999999999996.344444443 PP

>> Coilin_N  Coilin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.9    0.0015       1.6      66     133 ..     117     183 ..     113     185 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                          Coilin_N  66 vlrdndcirVklegsetkleaqesededsresasksasttkqkkkkKrekkqeeqdeqkasqaakdkk 133
                                       ++ d + i V    s ++l + ++e ++++e ++++a+++ + kk+K  k  +e d+ + ++aak+kk
  gi|386002102|ref|YP_005920401.1| 117 IIYDPEDIAV-GLYSDQELAELAEEARKAEEEKKRKAAEAAKAKKEKAAKAADEGDKGSGEKAAKKKK 183
                                       7888899999.444446666666666666666666666666666666666666666555555555554 PP

>> DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.5   6.9e+03      47      64 ..      72      89 ..      69      93 .. 0.81
   2 ?    8.6   7.7    0.0015       1.6      77     115 ..     130     168 ..     123     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.5
                    DNA_pol3_a_NII 47 kkkkldklleeyikfgFg 64
                                      k+kkl + + +y +++F+
  gi|386002102|ref|YP_005920401.1| 72 KNKKLQYPQIDYGRCMFC 89
                                      888999988899999887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                    DNA_pol3_a_NII  77 sseeeieefeeqkeeeeekaikeaieakekkeaekkkke 115
                                       s++e+ e  ee++++eeek+ k a +ak kke+ +k ++
  gi|386002102|ref|YP_005920401.1| 130 SDQELAELAEEARKAEEEKKRKAAEAAKAKKEKAAKAAD 168
                                       578999*****************9999999999888766 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.8    0.0011       1.2       5      20 ..      42      57 ..      39      62 .. 0.86
   2 ?    3.0  12.9      0.17   1.8e+02       3      43 ..      81     140 ..      80     170 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                           Fer4_15  5 rdaCigcglCvaeape 20
                                        +Cigcg+C++ +p+
  gi|386002102|ref|YP_005920401.1| 42 IRKCIGCGACARICPN 57
                                      568***********95 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                           Fer4_15   3 vDrdaCigcglCvaea.......pevfeldedglasvl.................lddgeiaeg..e 43 
                                       +D  +C+ cglCv+ +       ++ fe+ +    +++                            e
  gi|386002102|ref|YP_005920401.1|  81 IDYGRCMFCGLCVDDCpasclimSKQFEISGWNREDIIydpediavglysdqelaE-------LaeE 140
                                       8999************8888888777777777777777444444444433333220.......1222 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   9.9      0.44   4.7e+02      58      74 ..      42      58 ..      25      96 .. 0.59
   2 ?    9.0   1.3    0.0014       1.5      54      75 ..      79     100 ..      60     117 .. 0.75
   3 ?    2.2   0.5      0.19     2e+02      19      56 ..     128     165 ..     109     176 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                        +ci c++c ++cP +
  gi|386002102|ref|YP_005920401.1| 42 IRKCIGCGACARICPND 58
                                      5689**********975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                           Fer4_18  54 kekgagdcidcescvkvcPtgi 75 
                                        + + g c+ c+ cv+ cP   
  gi|386002102|ref|YP_005920401.1|  79 PQIDYGRCMFCGLCVDDCPASC 100
                                       4556788999999999999765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.19
                           Fer4_18  19 lydeetllvvydakrGekiagrkkekkalkekeerkek 56 
                                       ly ++ l+   + +r  +  +++k+++a k k+e+++k
  gi|386002102|ref|YP_005920401.1| 128 LYSDQELAELAEEARKAEEEKKRKAAEAAKAKKEKAAK 165
                                       45555555444444444444444444444443333333 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.2   0.00034      0.36       1      14 [.      45      58 ..      45      59 .. 0.94
   2 ?    2.0   8.5       0.5   5.3e+02       1      12 [.      86      97 ..      86     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gCgaC + CP++
  gi|386002102|ref|YP_005920401.1| 45 CIGCGACARICPND 58
                                      ************86 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.5
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+ Cg+Cv+ CP
  gi|386002102|ref|YP_005920401.1| 86 CMFCGLCVDDCP 97
                                      99******9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2135  (0.119081); expected 358.6 (0.02)
Passed bias filter:                      904  (0.0504211); expected 358.6 (0.02)
Passed Vit filter:                       163  (0.00909142); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 1168.05
//
Query:       gi|386002103|ref|YP_005920402.1|  [L=99]
Description: NADH:ubiquinone oxidoreductase J [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-21   74.3   9.8      8e-21   74.3   9.8    1.8  2  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        0.3   11.1   2.5       0.24   11.4   1.7    1.3  1  DUF3043      Protein of unknown function (DUF3043)
       0.72   10.0  13.3        0.4   10.9  11.3    1.5  2  DUF4040      Domain of unknown function (DUF4040)
        6.3    6.3  11.7        7.6    6.0  11.7    1.0  1  DUF1700      Protein of unknown function (DUF1700)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.6      0.11   4.7e+02     121     142 ..       8      29 ..       2      31 .. 0.73
   2 !   74.3   9.8   1.8e-24     8e-21       2      67 ..      30      95 ..      29      99 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                       TTTHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q3 121 tkyllpfelasllLLvaligai 142
                                       ++  +++el ++ LL+++i  +
  gi|386002103|ref|YP_005920402.1|   8 YDIRFLIELGAFSLLAVIILGL 29 
                                       5566788888888888888765 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 1.8e-24
                                      HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS--- CS
                       Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeee 67
                                      ++l+++s+n+v+s+l+L+ sf +va+l+i+l+a+F++++q+lvY+GA+ vl+lF+iml+++  +ee
  gi|386002103|ref|YP_005920402.1| 30 SILTVYSRNIVHSGLYLLGSFAAVAALYIFLNATFVGVAQVLVYIGAVGVLILFAIMLTKKTLMEE 95
                                      799*******************************************************85544444 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.7   5.4e-05      0.24      66     125 ..      34      93 ..      30      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                           DUF3043  66 ryvRDlVDsrrnlgelflplalvvlvlllvslvkvpevq.avvsllllvllllvvidgill 125
                                       +y R++V s  +l + f  +a ++++l  + +v v++v   + ++++l+l+++++   +l+
  gi|386002103|ref|YP_005920402.1|  34 VYSRNIVHSGLYLLGSFAAVAALYIFLNAT-FVGVAQVLvYIGAVGVLILFAIMLTKKTLM 93 
                                       699***************999999999333.444444440444556667777777666655 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.21   9.4e+02      20      33 ..      13      26 ..      10      29 .. 0.70
   2 ?   10.9  11.3   8.9e-05       0.4       1      66 [.      24      89 ..      24      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                           DUF4040 20 villgvvGllvall 33
                                      +i lg+++ll++++
  gi|386002103|ref|YP_005920402.1| 13 LIELGAFSLLAVII 26
                                      56678888887765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.9e-05
                           DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlp 66
                                      ++++ +++++v +r+ +++ ++l     +va+l+++l+A  v  +q++v  g ++vl+l+a+  ++
  gi|386002103|ref|YP_005920402.1| 24 VIILGLSILTVYSRNIVHSGLYLLGSFAAVAALYIFLNATFVGVAQVLVYIGAVGVLILFAIMLTK 89
                                      578999*************999999999********************************998765 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.7    0.0017       7.6      84     158 ..      12      88 ..       7      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0017
                           DUF1700  84 avigLsllnlilvlipliviislvlsllvvalallvsplvll..vksllkgfeelslnvfvsigllglGllllivay 158
                                         i L+ ++l+ v+i  ++i++++   +v + + l++ ++ +  ++++l++ +   ++v v ig++g+ +l++i+  
  gi|386002103|ref|YP_005920402.1|  12 FLIELGAFSLLAVIILGLSILTVYSRNIVHSGLYLLGSFAAVaaLYIFLNATFVGVAQVLVYIGAVGVLILFAIMLT 88 
                                       5689999**************************99998865412678999999999999999999988888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 650.53
//
Query:       gi|386002104|ref|YP_005920403.1|  [L=88]
Description: F420H2 dehydrogenase, subunit J [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-09   36.8   1.1    3.7e-09   36.4   1.1    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.052   14.0   2.5       0.11   13.0   2.5    1.5  1  FtsX         FtsX-like permease family


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   1.1   4.1e-13   3.7e-09      81     143 ..       8      80 ..       2      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.1e-13
                                       HHHHHHHHHHTT--................--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q3  81 ligllllallllllles..........sssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaiv 143
                                       +++l++la l++ll  +          s +  + + a +s i  ig  +ft y+++fe+++l+LL+a+igai+
  gi|386002104|ref|YP_005920403.1|   8 ILMLIFLATLIVLLAATpwggeemgsySFEPREGNRAPESGIGDIGVEIFTLYIVAFEVLGLVLLAAMIGAIY 80 
                                       2233333333333232345579999773333367778889*******************************97 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.5   1.2e-05      0.11      25      95 ..       8      85 ..       3      86 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                              FtsX 25 illitlvalviGlglgllaaqllsdvllssvf.......s...selkisidlitvliiivlllllallagllsiskilk 93
                                      il+++++a++i    +l+a+      ++s+ f       +   +  +i + ++t++i+++ +l l+lla+++ ++ +++
  gi|386002104|ref|YP_005920403.1|  8 ILMLIFLATLIV---LLAATPWGGEEMGSYSFepregnrApesGIGDIGVEIFTLYIVAFEVLGLVLLAAMIGAIYVAR 83
                                      566666666666...4444444444444444445555550555999***********************9999999999 PP

                              FtsX 94 ke 95
                                      ke
  gi|386002104|ref|YP_005920403.1| 84 KE 85
                                      87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 596.86
//
Query:       gi|386002105|ref|YP_005920404.1|  [L=100]
Description: F420H2 dehydrogenase, subunit K [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-22   78.7   6.6    2.3e-22   78.6   6.6    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   6.6   1.3e-26   2.3e-22       2     103 ..       7      95 ..       6     100 .] 0.96

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.3e-26
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       + ll+ ++f+iGlyg+l++rn +k ++++e+++n++n++lv+++++               ++ +q+++L+ i+++a
  gi|386002105|ref|YP_005920404.1|   7 YVLLASAMFTIGLYGLLTQRNGIKLMMCVEILLNSANINLVAFSAYL-------------PNVNGQVFALFSIALAA 70 
                                       678999****************************************9.............9**************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvqel 103
                                       ae+ vg a+l++lyr ygt++++++
  gi|386002105|ref|YP_005920404.1|  71 AEAGVGFAILITLYRLYGTIELDNI 95 
                                       **********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 779.41
//
Query:       gi|386002106|ref|YP_005920405.1|  [L=652]
Description: F420H2 dehydrogenase, subunit L [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-77  258.1  24.3    9.6e-77  258.1  24.3    2.3  2  Proton_antipo_M  Proton-conducting membrane transporter
    5.2e-17   61.7   0.7    5.2e-17   61.7   0.7    3.5  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
    0.00024   20.8   0.2    0.00095   18.9   0.2    2.0  1  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
  ------ inclusion threshold ------
      0.062   12.9   0.0      0.062   12.9   0.0    4.3  4  NADH5_C          NADH dehydrogenase subunit 5 C-terminus


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3      0.34   1.5e+03     244     276 ..      87     122 ..      56     126 .. 0.68
   2 !  258.1  24.3   2.1e-80   9.6e-77       1     282 [.     128     420 ..     128     436 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.34
                   Proton_antipo_M 244 ilalvllvlllsla...GlPptagFlskfliLeaav 276
                                       +++++ l+ + +l+   G P++a +++++ +++aa+
  gi|386002106|ref|YP_005920405.1|  87 VTFVCTLIHTYALGymeGDPGMARYFAEAGLFTAAM 122
                                       344444444444444478888888888888887776 PP

  == domain 2  score: 258.1 bits;  conditional E-value: 2.1e-80
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..... 72 
                                       +++Ll+l++++Elv+l++ylLig+w++kp++++A+ k+fl+t++g++++L gi+lly+++ +l++     a      
  gi|386002106|ref|YP_005920405.1| 128 SDNLLQLFIFWELVGLCSYLLIGFWYRKPSAASAAKKAFLVTRVGDVMFLAGIVLLYTNMVKLNLVLPEGAYllqfq 204
                                       79*********************************************************996666432222234554 PP

                   Proton_antipo_M  73 .....elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavss 143
                                             + +   +l++++++l+ g++ Ks+q+plh+Wlpda +e+Pt vsa++ Aat+v+agv+l++r+++l+  ++
  gi|386002106|ref|YP_005920405.1| 205 tiydsLTLIPPDQLTWIAIFLFGGAVGKSGQFPLHVWLPDA-MEGPTTVSAMIhAATMVTAGVYLVARMFPLFY-AA 279
                                       555545666667889**************************.********************************.9* PP

                   Proton_antipo_M 144 neisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFl 217
                                       ++   +++ +++ ++l++++++l+ +diKr+lAyS++s+lGym+ al+     ++ +v  +i+hl+ h++fkallFl
  gi|386002106|ref|YP_005920405.1| 280 PNGLTVVAYVGAFTALFAATMGLVMFDIKRVLAYSTVSQLGYMMAALGFgaaVGATAVGVSIFHLIGHSFFKALLFL 356
                                       **********************************************998434466667778**************** PP

                   Proton_antipo_M 218 lagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslil 282
                                       +agsvi++   t+d+r++gg  k+m  + l++l + l+laG P t+gF+sk++i+  a++ +++ 
  gi|386002106|ref|YP_005920405.1| 357 CAGSVIHAV-GTNDMREMGGVLKHMKWTGLTMLAGSLTLAGFPYTTGFFSKDEIIILAFENGAFG 420
                                       *****9987.9********************************************9999987654 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.7   1.2e-20   5.2e-17      11      55 ..      69     113 ..      63     115 .. 0.94
   2 ?   -1.9   0.0      0.82   3.7e+03      30      37 ..     250     257 ..     249     258 .. 0.91
   3 ?   -3.5   0.4       2.5   1.1e+04      27      40 ..     284     297 ..     283     303 .. 0.79
   4 ?   -3.0   0.1       1.8   8.2e+03       7      36 ..     508     537 ..     506     545 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.2e-20
                   Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                       s++ g+l+D+l ++mll+vtfv +l+h Y++gYM++d+g++R+fa
  gi|386002106|ref|YP_005920405.1|  69 SFNAGILIDPLAIVMLLMVTFVCTLIHTYALGYMEGDPGMARYFA 113
                                       6899****************************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.82
                   Proton_antipo_N  30 tfvsllvh 37 
                                       t+vs+++h
  gi|386002106|ref|YP_005920405.1| 250 TTVSAMIH 257
                                       89*****9 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.5
                   Proton_antipo_N  27 lvvtfvsllvhlYS 40 
                                       +vv  v+++  l++
  gi|386002106|ref|YP_005920405.1| 284 TVVAYVGAFTALFA 297
                                       68888998888887 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.8
                   Proton_antipo_N   7 vgglsieigfllDklsalmllvvtfvsllv 36 
                                       +gg +++++    +l    l ++ +v+ ++
  gi|386002106|ref|YP_005920405.1| 508 IGGHHVSHAHVHEPLIFKLLPIIIGVGGII 537
                                       566777777777888888888899988776 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   2.1e-07   0.00095      92     211 ..     457     575 ..     440     582 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-07
                   Proton_antipo_C  92 yPhEsdntmlfpllvLvlftlfvGliGip..fnqegidldilskwLtpsinllhknsnesvdwyefltnaifSvsia 166
                                         hEs++ ml pl++L++f lf+G+   +  ++  g ++d +   +     +  ++ ++ + + e l+   + + i 
  gi|386002106|ref|YP_005920405.1| 457 HKHESPWIMLGPLVILAIFALFMGMPSQEgfYHYVGNNFDHFGVDFEELAVIGGHHVSH-AHVHEPLIFKLLPIIIG 532
                                       459*********************97766655666677777766665555544333333.56777777788999999 PP

                   Proton_antipo_C 167 lfGifiAsllYkpvysslqnldlinsfvkkgpkrilldkiinviy 211
                                       + Gi++A l+Y + ++++++  ++++ +    k +l   ++n iy
  gi|386002106|ref|YP_005920405.1| 533 VGGIIVAALFYSR-WKRFDPGMVTSERDPL-RKILLKRYYQNEIY 575
                                       9999999999999.8888887777766552.23333344455555 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.57   2.6e+03      38      54 ..      36      52 ..      32      72 .. 0.62
   2 ?   -0.9   2.5      0.23     1e+03      41     111 ..     262     325 ..     241     354 .. 0.59
   3 ?   12.9   0.0   1.4e-05     0.062       1      45 [.     439     481 ..     439     484 .. 0.92
   4 ?    4.6   0.8    0.0049        22      62     181 .]     522     643 ..     514     643 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.57
                           NADH5_C 38 lgsiiaGsllswlifpk 54
                                      +++ +aG++ls  if +
  gi|386002106|ref|YP_005920405.1| 36 VLATFAGFILSFGIFRE 52
                                      45566666666666653 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                           NADH5_C  41 iiaGsllswlifpktpvitlplllKllallvtilGlllglelsklslkllkkslklnlssfssslwFlpsl 111
                                       ++aG++l   +fp   +   p  l     +v  +G++++l  +++ l ++  +     +s +s+l+++   
  gi|386002106|ref|YP_005920405.1| 262 VTAGVYLVARMFP--LFYAAPNGL----TVVAYVGAFTALFAATMGLVMFDIKRV-LAYSTVSQLGYMMAA 325
                                       5677777777777..222222222....234455666666666666555555433.556666666666554 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 1.4e-05
                           NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGs 45 
                                       Y++Rl ++++ g+ r    ++ +e+ +++l p+++La++++++G+
  gi|386002106|ref|YP_005920405.1| 439 YTFRLWFLTFDGEARS--DYHKHESPWIMLGPLVILAIFALFMGM 481
                                       9*********997765..67889*********************7 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0049
                           NADH5_C  62 lllKllallvtilGlllglelsklslkllkkslkl...nlssfssslwFlpslshrllsklsLklgqklakqlDqgW 135
                                       l+ Kll++++ + G++++  + +    +    +++    l   +    + +++ +  +  +  +   ++++ +D+  
  gi|386002106|ref|YP_005920405.1| 522 LIFKLLPIIIGVGGIIVAALFYSRWKRFDPGMVTSerdPLRKILLKRYYQNEIYTLWFAEKVVYGIAIVSNMIDLKI 598
                                       56666666666666666666555555554444444444555555555555555555555554444444444466666 PP

                           NADH5_C 136 lEklgpkglaklllklskliqnlqkglikiyLlsflltllllllll 181
                                       ++    ++++ +++ +  ++ +lq+g i+ yL+ ++l + +ll+l+
  gi|386002106|ref|YP_005920405.1| 599 IDGA-VNKISAISVGIGGTVRKLQTGVIQNYLTAIVLGVAVLLILI 643
                                       6544.35577788888889999***************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 3728.99
//
Query:       gi|386002107|ref|YP_005920406.1|  [L=499]
Description: F420H2 dehydrogenase, subunit M [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-75  253.6  27.6    4.6e-75  252.5  27.6    1.6  1  Proton_antipo_M  Proton-conducting membrane transporter
     0.0088   16.1   0.2     0.0088   16.1   0.2    3.2  3  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.04   14.0   0.4       0.04   14.0   0.4    4.6  4  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.5  27.6   7.7e-79   4.6e-75       1     288 [.     124     419 ..     124     424 .. 0.90

  Alignments for each domain:
  == domain 1  score: 252.5 bits;  conditional E-value: 7.7e-79
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg......tlefeelska 71 
                                       a d +l+y+++E+vl+p+++Lig+w+   ++ +A++k+f++t ++sli+Ll+i+ ly          t ++ +l++a
  gi|386002107|ref|YP_005920406.1| 124 ALDFFLFYIFWEVVLIPMFFLIGIWGGP-RKDYAAIKFFIYTHVASLIMLLSIFGLYFSYRtpegmrTFDMMTLLQA 199
                                       57899********************765.99***********************88865432444444455555555 PP

                   Proton_antipo_M  72 l..elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssne 145
                                       +  ++ ++ + l+l+++ ll+g+lvK+++vp+h+Wlpda+veaPt++s+llAa+l+k+g+++l+r+++++   +s  
  gi|386002107|ref|YP_005920406.1| 200 TgdSTIFSPMLLNLIFFGLLFGFLVKMPAVPFHTWLPDAHVEAPTAGSVLLAALLLKMGGYGLFRIVMPMLpNVSSH 276
                                       4977888888999*******************************************************99999999* PP

                   Proton_antipo_M 146 isqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsv 222
                                       +  l++++++is+++g+++alaq d+K+++AySs+sh+Gy+l+++++ ++ +v++a+++ ++h+l++  lF+ ag +
  gi|386002107|ref|YP_005920406.1| 277 YITLMAVIGVISIIYGGFLALAQKDLKKMVAYSSVSHMGYVLLGAGALSVLSVQGAMFQQFSHGLITCVLFMSAGTI 353
                                       **************************************************************************777 PP

                   Proton_antipo_M 223 iyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vv 288
                                        +++  tr i ++ggL+ +mP +a+++l ++++  GlP++ gF++++++L++a++  ++ ++++ + 
  gi|386002107|ref|YP_005920406.1| 354 -QHTAGTRIISDLGGLSDRMPKFAVLMLAGFMASLGLPGMCGFVAEVSVLAGAYQNLPVYVLIViFG 419
                                       .5566*************************************************9876544444144 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.5e-06    0.0088       2      57 ..      61     111 ..      60     112 .. 0.83
   2 ?   -1.3   0.5      0.39   2.3e+03      25      41 ..     159     175 ..     154     180 .. 0.69
   3 ?   -4.1   0.6         3   1.8e+04      23      34 ..     278     289 ..     273     290 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-06
                   Proton_antipo_N   2 ftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                       ++W++   l ++ ++ +D++ +  +l+ t+vs lv +YS+g   + ++ ++Ffa+l
  gi|386002107|ref|YP_005920406.1|  61 YDWVP--ALGVKYTVGVDGIGLPLILLSTIVSILVVVYSWG---EKTRSNQFFALL 111
                                       67777..345888899************************9...556777888776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                   Proton_antipo_N  25 mllvvtfvsllvhlYSi 41 
                                         ++ t v++l++l Si
  gi|386002107|ref|YP_005920406.1| 159 KFFIYTHVASLIMLLSI 175
                                       55667777777777665 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3
                   Proton_antipo_N  23 almllvvtfvsl 34 
                                       ++ ++v+ ++s 
  gi|386002107|ref|YP_005920406.1| 278 ITLMAVIGVISI 289
                                       567777777774 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   6.7e-06      0.04      45      93 ..      61     105 ..       5     122 .. 0.81
   2 ?    1.1   1.1      0.07   4.2e+02       5      49 ..     138     181 ..     129     197 .. 0.54
   3 ?   -1.2   0.9      0.36   2.2e+03      25      66 ..     275     318 ..     255     350 .. 0.58
   4 ?   -0.7   0.1      0.25   1.5e+03      59      76 ..     448     465 ..     407     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.7e-06
                     Oxidored_q5_N  45 sssfslsnlsyllglDslSapLilLSlWllpLmilASqkhlkkepknrq 93 
                                       ++      ++y++g+D + +pLilLS+ ++ L+++ S+   +      +
  gi|386002107|ref|YP_005920406.1|  61 YDWVPALGVKYTVGVDGIGLPLILLSTIVSILVVVYSWGEKTR----SN 105
                                       4455556789************************999877666....23 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.07
                     Oxidored_q5_N   5 llptlmliplvllskkkllwststlvslllallsll.llnlsssfs 49 
                                       l+p+++li ++   +k +  + +++++ + +l++ll +  +   fs
  gi|386002107|ref|YP_005920406.1| 138 LIPMFFLIGIWGGPRKDYAAIKFFIYTHVASLIMLLsI--FGLYFS 181
                                       56666666665555555555555555555555544422..222233 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.36
                     Oxidored_q5_N  25 ststlvslllallsll..llnlsssfslsnlsyllglDslSapL 66 
                                       s+++++++++ ++s++   +    +  l+++  + ++ ++ + L
  gi|386002107|ref|YP_005920406.1| 275 SHYITLMAVIGVISIIygGFLALAQKDLKKMVAYSSVSHMGYVL 318
                                       33334444444444442223333344444444455555555544 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.25
                     Oxidored_q5_N  59 lDslSapLilLSlWllpL 76 
                                        D  S+ ++ +S+ +l +
  gi|386002107|ref|YP_005920406.1| 448 KDPHSYEILSMSILILLI 465
                                       477777777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3221.82
//
Query:       gi|386002108|ref|YP_005920407.1|  [L=492]
Description: F420H2 dehydrogenase, subunit N [Methanosaeta harundinacea 6Ac]
Scores for 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-62  209.0  27.9    8.4e-62  209.0  27.9    2.6  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   6.3      0.29   5.2e+03      20     129 ..      26      86 ..       8     121 .. 0.47
   2 !  209.0  27.9   4.7e-66   8.4e-62       2     292 ..     123     430 ..     122     431 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.29
                   Proton_antipo_M  20 lLiglwkkkpksleAslklflltllgsliLLlgilllyn..ltgtlefeelskalelglnslelllllllllvgllv 94 
                                       +Ligl+    ks +   +l l +l++sl+L++g  +  +  + gtle+++ls+++                      
  gi|386002108|ref|YP_005920407.1|  26 VLIGLF---MKSKNLMGYLSLAGLVASLFLVMGADMTKGplIFGTLEVDALSQFF---------------------- 77 
                                       223333...2333333455566666666666665444322245555555555553...................... PP

                   Proton_antipo_M  95 KsaqvplhlWlpdayveaPtpvsallAatlvkagv 129
                                                                   + v++++
  gi|386002108|ref|YP_005920407.1|  78 --------------------------KLVFVAVAL 86 
                                       ..........................222233333 PP

  == domain 2  score: 209.0 bits;  conditional E-value: 4.7e-66
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglns 78 
                                        d+++l++g+El +l++y ++++ k++ ++leA++k+f+ ++++s ++L+g++lly+l+gt+ + e++ a +     
  gi|386002108|ref|YP_005920407.1| 123 IDIVTLFVGFELASLATYAMAAFDKER-QNLEAAMKYFIFGSVSSAMMLFGFSLLYGLSGTTRLAEIAAA-SVETMG 197
                                       5899*******************9777.9****************************************9.888899 PP

                   Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllila 154
                                       +++l++ll++++g+ +K+a+vp+h+W pd y++aPt v+a+lAa   k+g  + ++++++       e++  ++il 
  gi|386002108|ref|YP_005920407.1| 198 PATLVALLFVVAGFGFKMALVPFHMWAPDTYEGAPTIVTAFLAAGSKKMGFVAAFKVIFIALiALRFEWYLAFAILV 274
                                       999***************************************999**********9999988788999********* PP

                   Proton_antipo_M 155 iismllgslvalaqtdiKrllAySsishlGymlialav...at.........qygveaaiihllthalfkallFlla 219
                                       +i+m lg++va+ q ++Kr+lAySs++  Gy+ ia++v   a          q g+++ ++++l ha++k + F++a
  gi|386002108|ref|YP_005920407.1| 275 AITMTLGNVVAIWQKSVKRMLAYSSVAYAGYIAIAFVVvgaAEhggldlavaQNGLASGLMLILGHAFMKTGAFIAA 351
                                       *********************************9998854422112222222556777788999**********999 PP

                   Proton_antipo_M 220 gsviyere......ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vva 289
                                         v y         + +d+++y+gL  + Pi+a ++l++l+sl+G+PptagF++kf++  +a++ +l++l+++  + 
  gi|386002108|ref|YP_005920407.1| 352 AVVGYM-AlsegrkNPDDLEQYAGLGRRAPITAFCMLIFLFSLSGIPPTAGFVGKFMLWGSAIDSGLVWLAVLfALN 427
                                       665543.224445599******************************************************9996666 PP

                   Proton_antipo_M 290 svl 292
                                       s+l
  gi|386002108|ref|YP_005920407.1| 428 SAL 430
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3318.51
//
Query:       gi|386002109|ref|YP_005920408.1|  [L=188]
Description: YeeE/YedE family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-15   57.8   9.0    1.6e-15   57.5   9.0    1.1  1  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   9.0   9.1e-20   1.6e-15       7     150 ..      38     182 ..      32     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 9.1e-20
                       Sulf_transp   7 agairdivvekdgrllralllaiavaavgfqllaaaglidlpksafpvvglivGGllFGvGMalaGgCasgtlyrvG 83 
                                       +  i  +++  d++ ++++++a++v +vg++ll ++gl+ l ++a ++ + ++GGl+FGvG  l G C++++   vG
  gi|386002109|ref|YP_005920408.1|  38 YDVIVGQLLLADFTVFKVMASAVIVGMVGIHLLRSLGLASLHPKAGSWGSSALGGLIFGVGFGLLGYCPGTAAGAVG 114
                                       56677889999****************************************************************** PP

                       Sulf_transp  84 eGslralitllffilgavalltgilsswleqlles.tvskeslyetlglsplllialllliallllvk 150
                                       +Gs+ al+  ++ il ++ + +   +s+ e +l   +  +++++e lg++p++++++ +li l +l++
  gi|386002109|ref|YP_005920408.1| 115 QGSIDALLGGVGGILLGAGIFAWRYPSLEERVLRRgEFGDKTIPEILGVNPWMVVIPTALILLGVLFW 182
                                       *********999999888777777778877766551568899*************9987775544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1165.51
//
Query:       gi|386002110|ref|YP_005920409.1|  [L=172]
Description: YeeE/YedE family lipoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-32  112.9  11.8    2.5e-32  112.7  11.8    1.0  1  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7  11.8   1.4e-36   2.5e-32     173     309 ..       5     161 ..       1     162 [. 0.80

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1.4e-36
                       Sulf_transp 173 frkpwslvlgavllgllavlawllsak.tgrsfglg.........ftvpgakilqylvlgtskflnwgvvlvlGiil 239
                                           ws+++ +  +g+l++la+lls   +g+s++++         f ++  ++   +  + + +++w+vvlv+Gi++
  gi|386002110|ref|YP_005920409.1|   5 EMDLWSPYVVGAGIGALNTLAFLLSDRpIGTSSAYArgsgmieraFRGSKVEAKA-YYRKFEPVVDWEVVLVFGIVV 80 
                                       5667********************9875788877642222222223333333333.33466788************* PP

                       Sulf_transp 240 Gaflaallsgefkleapkar...........ellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvfll 305
                                       Gafl+a+lsg+f++ea +a            +++aa++GG+lMG Gar+AgGC++G+g+sg+a+l+ s+wla+++++
  gi|386002110|ref|YP_005920409.1|  81 GAFLSAVLSGSFRVEAVPALwaarfgpdpilRIAAAFAGGVLMGLGARWAGGCTSGHGISGTAQLAASSWLAVACFF 157
                                       ***************8765334567777788********************************************** PP

                       Sulf_transp 306 lGav 309
                                       +G+v
  gi|386002110|ref|YP_005920409.1| 158 IGGV 161
                                       **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1083.37
//
Query:       gi|386002111|ref|YP_005920410.1|  [L=355]
Description: hypothetical protein Mhar_1423 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-66  223.9   0.0    2.4e-66  223.6   0.0    1.1  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr
  ------ inclusion threshold ------
      0.071   13.6   0.0       0.21   12.2   0.0    1.8  1  Chitin_bind_4    Insect cuticle protein
       0.16   11.7   0.0       0.28   10.9   0.0    1.3  1  Acetyltransf_2   N-acetyltransferase


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.6   0.0     4e-70   2.4e-66       1     234 [.      93     350 ..      93     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 223.6 bits;  conditional E-value: 4e-70
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       ++LlTD+G+++  vga++g i+s++p+ari  itH++++f+v+e+++lLa+a++y+p+gtv++a V+pgvgt++r++
  gi|386002111|ref|YP_005920410.1|  93 VVLLTDYGTSGFRVGALEGSIYSENPQARISTITHQVSAFNVAEGSYLLAKAARYYPPGTVFVAEVNPGVGTDERSI 169
                                       79*************************************************************************** PP

                                       EEEETTS.EEEEESSSTTHHHH...SEEEEEEGSSCC......--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGG CS
                   SAM_adeno_trans  78 vveakgg.yfvgPDNGlltlal...lleeaveieeee......ssatFhgrDvFapvaarlaagvsleelgeeldpe 144
                                       vve+++g +fvgPDNGl+t ++   ++++++e++  +         tF+g +v+ pv+a laag +++ +g+e+++ 
  gi|386002111|ref|YP_005920410.1| 170 VVETEDGkLFVGPDNGLFTDVMedlGVARVWEVRGLNltrsggDPVTFNGVEVYGPVGAILAAGADPAGVGPEVSD- 245
                                       *****998***********999888779999999544566788559**************************9986. PP

                                       GS-SSS......ECSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTC..EE........EEEEESSGGGSTTTSEEE CS
                   SAM_adeno_trans 145 elvrle......ederlegevlyvDrFGNvitniskelleelekerk..va........klkkvetyaevaegella 205
                                         vrle      e +++ g v y+D +GN++tni++ell  ++ + +  v+         + + +tya+v+ ge ++
  gi|386002111|ref|YP_005920410.1| 246 -PVRLErqragvEGDEVVGAVAYIDPWGNLVTNIPEELLGGTDIGPGdrVEisvngsriDALFGTTYADVPVGEWVV 321
                                       .56666544543367788*****************99998776665566115667887644555************* PP

                                       EE-TTSEEEEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 206 lvnssglleiavnkgsaaellglkvgdev 234
                                       lv+  g leiavn+gsaa +lg++ g+ v
  gi|386002111|ref|YP_005920410.1| 322 LVGILGRLEIAVNMGSAAGALGVAEGSAV 350
                                       *************************9988 PP

>> Chitin_bind_4  Insect cuticle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.5e-05      0.21       6      43 ..     242     276 ..     242     276 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                     Chitin_bind_4   6 etsdgikreeegrtgtedeglvvqGsYsyvdpdGktrt 43 
                                       e+sd+  r e +r   + eg++v G   y+dp G ++t
  gi|386002111|ref|YP_005920410.1| 242 EVSDP-VRLERQR--AGVEGDEVVGAVAYIDPWGNLVT 276
                                       67888.5534444..577****************9886 PP

>> Acetyltransf_2  N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.7e-05      0.28      63     101 ..     102     140 ..      93     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                                       TT-EEEEEEEEEETTGGSSSSSSCEEEEEEEEETTEEEE CS
                    Acetyltransf_2  63 lGFevtllagrvvvkaeeaastertHllllVtidgetyl 101
                                        GF+v  l g+++ ++++a  ++ tH++   ++++ +yl
  gi|386002111|ref|YP_005920410.1| 102 SGFRVGALEGSIYSENPQARISTITHQVSAFNVAEGSYL 140
                                       6*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2354.81
//
Query:       gi|386002112|ref|YP_005920411.1|  [L=600]
Description: citrate transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-54  185.3  16.7    2.4e-54  184.6  16.7    1.3  1  CitMHS    Citrate transporter
    9.8e-12   44.5   0.1    7.3e-06   25.7   0.0    2.5  2  TrkA_C    TrkA-C domain


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.6  16.7   2.7e-58   2.4e-54       1     300 []      20     547 ..      20     547 .. 0.89

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 2.7e-58
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                       ++l+++e++r d+va++v+++l    ++++++alsg+as++++ +++ mi+g+++e++G+++r+++ +lr+ag+ ++
  gi|386002112|ref|YP_005920411.1|  20 ILLFVTEAVRVDLVAIIVVLILaltgLVSPPQALSGLASNAVVSMAAIMILGKGMERAGVVNRISRAVLRVAGSDER 96 
                                       589**************99999******************************************************* PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 .llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglsl 148
                                        ll +++ +++++saf++n g +++++p++l++ k+ +++p++ ll+p+++aa +gg+l+++G +            
  gi|386002112|ref|YP_005920411.1|  97 rLLGVTSSVVGMISAFMQNLGSAALFLPAILRISKS-TGTPASrLLMPMGFAAILGGTLSMVGSS------------ 160
                                       ***********************************7.****************************............ PP

                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx... RF
                            CitMHS 149 pnlll.....................lalllvgllplvllfmfgvalalpvnap.kvkkqkaiieaiarsllpv... 200
                                       p ++l                     ++ll  g+ ++++++     + l+++ + + ++ +   ++i+++ lp    
  gi|386002112|ref|YP_005920411.1| 161 PLIILndllrqggeepfgifsvtpigIVLLGSGIGYFMIFG-----DRLLPKRGlSEDDFRSQEDLIETWRLPSivs 232
                                       88888999999999999999997755555555556666666.....4444444435666666666777777777999 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|386002112|ref|YP_005920411.1| 233 yyfvswksdlvdkaredlrlrrnygitllaivegkmvtyspwrrtrfaagqelallgepedverfaaehdlwkitde 309
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|386002112|ref|YP_005920411.1| 310 srfcdllsqaeagfaeivvrprapivgktpreisirrnygvepiillsgtreerkefddrplspgdtfvihglwdri 386
                                       9999999999999**************************************************************** PP

                                       ....................................................xxxxxxx.............xxxxx RF
                            CitMHS 201 ....................................................atillla.............ykkve 212
                                                                                           a     +             y +++
  gi|386002112|ref|YP_005920411.1| 387 rkigsdqnfvlltpveagvldpskaipatlcflgavalslagvqlsialltgA-----LamvllkvisideaYGAID 458
                                       ********999999999999999999999999998888887777776666552.....04445579*********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 213 WsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlgliallsafisnvavaalmapialgmapal 285
                                       W +++l+aG+++l+ a+e+tG + ++a+++ +   g + +++l++v++l +lls+ isnva+++l++p+a+ ma ++
  gi|386002112|ref|YP_005920411.1| 459 WRTIVLLAGLIPLGIAMEETGAAGLIAQSMMDqlrGaPTILVLLAVAALATLLSLTISNVAATVLLVPLAMIMARDM 535
                                       ****************************995559854665666777888888************************9 PP

                                       xxxxxxxxxxxxxxx RF
                            CitMHS 286 gllspsplalalavg 300
                                       +   ++p alal+vg
  gi|386002112|ref|YP_005920411.1| 536 A---IDPRALALLVG 547
                                       9...999*****998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.1e-10   7.3e-06       9      67 ..     239     299 ..     231     301 .. 0.94
   2 !   16.2   0.2   7.6e-07    0.0068       2      64 ..     324     388 ..     323     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.1e-10
                                       -GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   9 gsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                        s lv+k   +l+lr++ g++++ai+ g ++ ++p   t++ +G +l ++g+p+d++++++
  gi|386002112|ref|YP_005920411.1| 239 KSDLVDKAREDLRLRRNyGITLLAIVEGkMVTYSPWRRTRFAAGQELALLGEPEDVERFAA 299
                                       588999999*******************9*****************************987 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.6e-07
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlae 64 
                                       +e++v++ +p+vGkt +e+ +r++ gv  + +  g  e     +d  L +GD+ ++ g  + +++
  gi|386002112|ref|YP_005920411.1| 324 AEIVVRPRAPIVGKTPREISIRRNyGVEPIILLSGtREERKEFDDRPLSPGDTFVIHGLWDRIRK 388
                                       79**************************9999877788999999999999999999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3761.97
//
Query:       gi|386002113|ref|YP_005920412.1|  [L=158]
Description: Putative small multi-drug export protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-38  130.5   1.6    6.6e-38  130.1   1.6    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein
  ------ inclusion threshold ------
       0.19   11.0   0.0       0.25   10.6   0.0    1.2  1  Glyco_hydro_62   Glycosyl hydrolase family 62


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   1.6   7.4e-42   6.6e-38       1     121 []      24     146 ..      24     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 7.4e-42
                   Sm_multidrug_ex   1 Elrgaiplgi.llgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaek.ksekiekygfl 75 
                                       Elrg+iplgi ++gl+pl+a+++sv+gnl pv+ +ll+l++++++l +++  + +f++l +++ k ++e+ ++yg++
  gi|386002113|ref|YP_005920412.1|  24 ELRGSIPLGIaVYGLSPLEAYAISVAGNLAPVVPLLLYLEPVSRWLMRYRPGHAFFSWLFTRTYKrHAERHRRYGLF 100
                                       9*********556**************************************************995666667***** PP

                   Sm_multidrug_ex  76 GLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +L+lFva+PLp+TGawtGs+ia+++gl++++a+ ai++Gv++ag I
  gi|386002113|ref|YP_005920412.1| 101 ALALFVAVPLPVTGAWTGSAIAFIFGLRFREAFSAIAAGVIVAGGI 146
                                       *******************************************966 PP

>> Glyco_hydro_62  Glycosyl hydrolase family 62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.8e-05      0.25      65     103 ..      43      81 ..      31     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.8e-05
                    Glyco_hydro_62  65 asasqtatsfkavaptlfyfapkkiwvlayqwgpttfsy 103
                                       a a  +a + + v p l+y++p + w++ y+ g + fs+
  gi|386002113|ref|YP_005920412.1|  43 AYAISVAGNLAPVVPLLLYLEPVSRWLMRYRPGHAFFSW 81 
                                       556778899999**********************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1162.96
//
Query:       gi|386002114|ref|YP_005920413.1|  [L=127]
Description: hypothetical protein Mhar_1426 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 935.98
//
Query:       gi|386002115|ref|YP_005920414.1|  [L=157]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   45.8   0.1    8.5e-12   45.4   0.1    1.3  1  LTD       Lamin Tail Domain
  ------ inclusion threshold ------
       0.14   12.1   0.1       0.94    9.4   0.0    2.0  2  CBM_20    Starch binding domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.1   9.4e-16   8.5e-12       5     106 ..      16     110 ..      12     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 9.4e-16
                               LTD   5 agdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.........ytfpngtgtlaageyvvvwsgsg 72 
                                       +g+vv++ev  ++ag++   +velyN+++++vdL+ w+++ + +          + +p+gt ++++g+y+v   +  
  gi|386002115|ref|YP_005920414.1|  16 SGSVVVNEVELNPAGEGI-LWVELYNSGEEPVDLGQWSVAIEVTLvapgiwtgvIPIPKGT-SIPPGGYYVAEGDRR 90 
                                       799**********88776.************************889999999999999999.********9988842 PP

                               LTD  73 ttsasngskasssavwnn.ggdavaLydasgevvd 106
                                                      w   ++ +v+L+++s  +vd
  gi|386002115|ref|YP_005920414.1|  91 ---------------WIHgNNATVVLRTDSWAEVD 110
                                       ...............22213334445544444444 PP

>> CBM_20  Starch binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0001      0.94      26      85 ..      47      99 ..      36     109 .. 0.75
   2 ?    0.5   0.0     0.065   5.8e+02      35      71 ..     112     147 ..     105     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0001
                            CBM_20 26 eLGnWnpkkavklsaseqtssyplWsttvslpagtkieYkyikkdsdgsvtWesgenrsl 85
                                       LG+W+++  v l a        +W++ + +p+gt+i    + +++  + +W +g+n ++
  gi|386002115|ref|YP_005920414.1| 47 DLGQWSVAIEVTLVA------PGIWTGVIPIPKGTSIPPGGYYVAEG-DRRWIHGNNATV 99
                                      7******88888883......579***********998765555553.677887777766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.065
                            CBM_20  35 avklsaseqtssyplWst.tvslpagtkieYkyikkds 71 
                                         +l+ +e  +++  Ws     +  gt+  + +ik + 
  gi|386002115|ref|YP_005920414.1| 112 THPLNDEE--GNDFSWSRyPNGVDTGTRSDWAFIKATP 147
                                       44555443..4788888855688899999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1066.90
//
Query:       gi|386002116|ref|YP_005920415.1|  [L=152]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-12   47.1   0.0      4e-12   46.5   0.0    1.2  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   2.2e-16     4e-12       6     107 ..      19     111 ..      16     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.2e-16
                               LTD   6 gdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge......ytfpngtgtlaageyvvvwsgsgttsa 76 
                                       g vvI+ev  +++++++ e+velyN++ ++vd s w++    +       +++p+ t ++a+g+ +v   +      
  gi|386002116|ref|YP_005920415.1|  19 GGVVINEVELGPPEGGN-EWVELYNNGIEEVDVSRWSVWIVDQSpswtgvMKIPQDT-VMAPGSFFVAEGDR----- 88 
                                       78**********87776.******************9887776678**********9.*****999988883..... PP

                               LTD  77 sngskasssavwnnggdavaLydasgevvds 107
                                               + + n+g  +v+L++++g vvd+
  gi|386002116|ref|YP_005920415.1|  89 --------QWIHNTGTGTVILKTDEGAVVDE 111
                                       ........346666888999**99**99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1015.61
//
Query:       gi|386002117|ref|YP_005920416.1|  [L=155]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   57.2   0.1    2.7e-15   56.7   0.1    1.3  1  LTD       Lamin Tail Domain
  ------ inclusion threshold ------
      0.032   14.4   0.1      0.054   13.7   0.1    1.4  1  DUF2749   Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.1     3e-19   2.7e-15       2     107 ..      19     112 ..      18     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 3e-19
                               LTD   2 aaaagdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge....ytfpngtgtlaageyvvvwsgsgtt 74 
                                       a+ ag+vvI+ev  +++gn++  +velyN +++av++sgw ++ ++ +    +++p+gt ++ +++y++   +    
  gi|386002117|ref|YP_005920416.1|  19 ATGAGSVVINEVEINPPGNAT-RWVELYNGGDEAVEISGWVVTIYNLPwagpIVIPQGT-VISPKGYYIAEGD---- 89 
                                       57899***********99887.************************99***********.*******998887.... PP

                               LTD  75 sasngskasssavwnn.ggdavaLydasgevvds 107
                                                  ++w + ++ +vaL+da g  vd+
  gi|386002117|ref|YP_005920416.1|  90 -----------PQWRGeDEGSVALVDAIGMKVDE 112
                                       ...........46777455578899998888885 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.1e-06     0.054       4      54 ..       6      54 ..       3      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-06
                           DUF2749  4 rilIvlviavaagagtilwlvvqpragtsgsgeaqRehrerFfgadkdrdv 54
                                       ilI l iava++a+++  +v++    ++  ++++    e + g+d + ++
  gi|386002117|ref|YP_005920416.1|  6 GILISLYIAVALSATGAGSVVINEVEINPPGNATRW-V-ELYNGGDEAVEI 54
                                      59********************99888877665543.3.466666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1055.12
//
Query:       gi|386002118|ref|YP_005920417.1|  [L=150]
Description: hypothetical protein Mhar_1430 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-16   58.6   0.1    7.9e-16   58.4   0.1    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   4.4e-20   7.9e-16       1     105 [.      10     126 ..      10     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4.4e-20
                                       TEEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEECTTT............EE-S-EEEEEEEEEEE CS
                            DUF296   1 rphvlrlepGediveaieefarkrgiraacvlsaiGavsnvtrladgee............kllgrfeilslsGtil 65 
                                       r++v+r+e+Ge+++ ++++f  ++g+++++v +++Ga+++ + l+ g++             l+g +ei++l Gt+ 
  gi|386002118|ref|YP_005920417.1|  10 RVFVIRMEEGEEMIGSLARFLAEKGVESGIV-HFLGALREGR-LIMGPRearvppgppfveDLEGGWEIFGL-GTVY 83 
                                       789****************************.**********.666666577888888777667********.**** PP

                                       ETT.....EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE- CS
                            DUF296  66 pdg.....lHlhvslagedgqvvgGhlaegplvaattvevvvaef 105
                                       p++     +H+h+s++++ g+ ++G+l+e  + a+ +ve vv e+
  gi|386002118|ref|YP_005920417.1|  84 PGEggapsIHIHASVGRA-GRGLTGCLRER-AQAYLVVEAVVFEV 126
                                       *5557999*********7.*********66.***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.52
# Mc/sec: 868.44
//
Query:       gi|386002119|ref|YP_005920418.1|  [L=608]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-122  406.9   0.0   5.9e-122  406.6   0.0    1.1  1  Radical_SAM_N  Radical SAM N-terminal
    1.5e-24   87.0   0.0    2.2e-24   86.5   0.0    1.2  1  DUF3362        Domain of unknown function (DUF3362)
    3.1e-19   70.0   0.2    1.6e-18   67.6   0.1    2.1  2  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
       0.09   12.8   0.0         17    5.5   0.0    2.6  2  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.6   0.0  1.3e-125  5.9e-122       2     298 .]       9     305 ..       8     305 .. 0.97

  Alignments for each domain:
  == domain 1  score: 406.6 bits;  conditional E-value: 1.3e-125
                     Radical_SAM_N   2 lpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsaG 78 
                                       lp+s +e ++ g+d++Dv+lvsgD YvDhpsfg+ ligr+L+++G+ vg+++qPd+++++df++lG Prlffgv++G
  gi|386002119|ref|YP_005920418.1|   9 LPISMEEARRDGIDRFDVVLVSGDGYVDHPSFGVGLIGRVLQDAGYSVGVVPQPDFRREDDFRALGAPRLFFGVASG 85 
                                       8**************************************************************************** PP

                     Radical_SAM_N  79 nlDsmvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrsi 155
                                       n+Dsmvn+y+ + ++r++D y+pgg+   RPdra+ivY+n+++ +++dvpv+lGgiEaSLRr+ahYD+wsd+vr si
  gi|386002119|ref|YP_005920418.1|  86 NVDSMVNNYSPALRRRRRDVYSPGGRP-LRPDRAAIVYANRVHALFPDVPVILGGIEASLRRFAHYDFWSDSVRGSI 161
                                       *************************98.9************************************************ PP

                     Radical_SAM_N 156 lldskadllvyGmgeraiveiakrlakgeeveelkdirgtavllkkea..kakekevielpsyeevkedkklyaeaf 230
                                       l+d+ adl+vyGmger+i+e+a+rla geev +++d++gta++++ ++   ++++  +e+ps+ ev++dk +yaeaf
  gi|386002119|ref|YP_005920418.1| 162 LADAPADLVVYGMGERPILEVARRLAGGEEVGAIRDVPGTAFKMEVREwrVSERQGLVEIPSFGEVAADKMRYAEAF 238
                                       ******************************************99974443444489********************* PP

                     Radical_SAM_N 231 rlleeetnplnakalvqkhgdravvlnppalplsteelDevyelpyarkahpsykkkkipalemikfS 298
                                       rl + e++p++++++vq h +++vv npp+lpl+teelDe+yelp++r+ahpsy +++ipale ++fS
  gi|386002119|ref|YP_005920418.1| 239 RLHYGEQDPFRGRTIVQPHPKTVVVANPPSLPLTTEELDEIYELPFTRAAHPSY-REEIPALEPVRFS 305
                                       ******************************************************.599********98 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   4.9e-28   2.2e-24       1      85 [.     529     607 ..     529     608 .] 0.97

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 4.9e-28
                           DUF3362   1 dqVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgekerrlhkAllrYhdpknwpllreALkkmGredLiGn 77 
                                       +qVq+F P+Pm+++t++Yhtg++p t       +v+v+rg +e+ +++All+Y d  n  l+re L+ +GredLiG 
  gi|386002119|ref|YP_005920418.1| 529 EQVQDFTPTPMTVSTCIYHTGLDPFT-----GSPVHVPRG-REKEIQRALLQYWDKRNEGLVREGLRLAGREDLIGD 599
                                       7*************************.....99****995.89********************************** PP

                           DUF3362  78 gkkhLipt 85 
                                       g ++L+p+
  gi|386002119|ref|YP_005920418.1| 600 GPECLVPK 607
                                       ******95 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   1.3e+03      54     105 ..     224     287 ..     183     290 .. 0.76
   2 !   67.6   0.1   3.7e-22   1.6e-18       2     167 .]     307     521 ..     306     521 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                                       SSTGGGSTTHHHHHHHHHHTC..........CCTEEEEEEECSSCHG..HHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                       Radical_SAM  54 ggepllypdfvellerlakla..........vpgiritvetngtlpd..eeklerllelgvdrv 105
                                        ge+ +++  + +++rl+  +           p  +++v++n++ +    e l+++ el+++r 
  gi|386002119|ref|YP_005920418.1| 224 FGEVAADKMRYAEAFRLHYGEqdpfrgrtivQPHPKTVVVANPPSLPltTEELDEIYELPFTRA 287
                                       4667777777788888888778899999999899999999999998788888888888877765 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 3.7e-22
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx................. RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly................. 60 
                                       ++ rgC + CsfC+ +++  +++ ++s+s+e++++e++ l   +g ++++  +gg p+++                 
  gi|386002119|ref|YP_005920418.1| 307 TTHRGCFGSCSFCSLTHH--QGRIVQSRSIESVVREAEGLTSLPGfKGVIQDVGG-PTANmygmacsrwragagaag 380
                                       6789*************8..********************977788999999999.********************* PP

                                       .....................TTHHHHHHHHHHTCCCTEEEEEEECSSCHG..........HHHHHHHHHTT.-SEE CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxx.xxxx RF
                       Radical_SAM  61 .....................pdfvellerlaklavpgiritvetngtlpd..........eeklerllelg.vdrv 105
                                                            ++ vell+rl+++  pg++ +++t+g+++d          ee+l  l   +   ++
  gi|386002119|ref|YP_005920418.1| 381 gvgacadrlcspdcptlkadhRRQVELLRRLREI--PGVKRVFVTSGIRHDliladrtgagEEYLYDLSCHHvSGHL 455
                                       ********************99999999999999..9************************9999999999999*** PP

                                       EEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 106 slgleaaddekvlklmn..rghtfeevlealeklreagikr...vvdrivglpGendeeleellell 167
                                        +  e+++d+ vl +m+  ++  +ee+ + ++++ ++ +k+   v ++i g+pG   ++++el+e+l
  gi|386002119|ref|YP_005920418.1| 456 KVAPEHVSDR-VLARMHkpPRAALEEFRDEFKRASRKVGKEqylVPYFISGHPGCELRDMVELAEYL 521
                                       **********.7777766999999**********99977779********************99875 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0037        17       9      34 ..      34      59 ..      26      74 .. 0.84
   2 ?    4.3   0.0    0.0088        40      72      94 ..     123     145 ..     115     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0037
                       B12-binding  9 ggdlhplGlavlaaalrdagfeVqll 34
                                      + d++++G+ ++ ++l+dag++V ++
  gi|386002119|ref|YP_005920418.1| 34 YVDHPSFGVGLIGRVLQDAGYSVGVV 59
                                      579*******************9665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0088
                       B12-binding  72 vellkrirprvkvvvGGahpsld 94 
                                       ++++++  p+v+v++GG+ +sl 
  gi|386002119|ref|YP_005920418.1| 123 ANRVHALFPDVPVILGGIEASLR 145
                                       56688899**********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 3597.11
//
Query:       gi|386002120|ref|YP_005920419.1|  [L=345]
Description: Methyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-56  189.1   0.1    9.1e-56  188.8   0.1    1.1  1  Met_10           Met-10+ like-protein
    5.8e-12   45.3   0.1    1.4e-11   44.1   0.1    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    7.6e-09   35.3   0.1    1.2e-07   31.4   0.0    2.5  3  MTS              Methyltransferase small domain
    3.7e-07   30.8   0.2    9.8e-07   29.4   0.1    1.8  1  Methyltransf_25  Methyltransferase domain
    3.9e-06   26.6   0.0    7.4e-06   25.7   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    6.8e-06   25.7   0.2    1.1e-05   25.0   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      2e-05   24.4   0.0    4.1e-05   23.4   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    3.2e-05   23.9   0.5    0.00015   21.7   0.1    2.1  2  ADH_zinc_N       Zinc-binding dehydrogenase
      4e-05   24.2   0.1    9.5e-05   23.0   0.1    1.7  1  Methyltransf_11  Methyltransferase domain
    0.00014   21.2   0.3    0.00023   20.4   0.3    1.3  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00054   19.7   0.2     0.0016   18.1   0.2    1.7  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0012   19.8   1.2      0.012   16.6   0.2    2.4  2  Methyltransf_24  Methyltransferase domain
     0.0043   16.6   0.0     0.0065   16.0   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0064   16.2   0.0      0.011   15.4   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.019   14.1   0.0      0.029   13.5   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
      0.033   14.0   0.0       0.05   13.4   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
      0.085   12.3   0.0       0.12   11.8   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.096   12.8   0.0       0.18   11.9   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.16   11.3   0.0       0.23   10.8   0.0    1.2  1  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.21   10.6   0.1        0.3   10.0   0.1    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   0.1     1e-58   9.1e-56       2     199 .]      86     277 ..      85     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 1e-58
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +fe++Gd++il+  ++          +i+ ++ +v++v++  + vege+Rt+++e++aG+++t+t+h+E+g r+++D
  gi|386002120|ref|YP_005920419.1|  86 SFEVVGDIAILEGADQEAA------AAIIAVHrNVRAVISPLTAVEGEYRTRRFEHVAGEARTTTVHREHGLRYRID 156
                                       79*********98776554......44555555******************************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       + + yf ++l +Er r+a+lv+ ge  vd+fAG+Gpfa+ iak  ++ rv+a+d+nP++v++l+en +lN++ ++v 
  gi|386002120|ref|YP_005920419.1| 157 LERAYFTPRLGTERLRVASLVRRGEAAVDMFAGVGPFALLIAK--RGARVVAVDKNPDAVRLLRENANLNRITDMV- 230
                                       *******************************************..99*****************************. PP

                                       EEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                        +++D++++++   + adrv+mnlp+sa +Fl+++++++kdggv+hy
  gi|386002120|ref|YP_005920419.1| 231 ILEADAADLAEefANRADRVIMNLPHSARDFLGAAMKVAKDGGVVHY 277
                                       89*******9988899******************************9 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   1.6e-14   1.4e-11       1      42 [.       6      47 ..       6      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.6e-14
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S- CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkee 42
                                      ++kV ++egE  R++L e+g++d+++KI+s+++ ly P+ e 
  gi|386002120|ref|YP_005920419.1|  6 GLKVRRREGEVFRRRLVEMGAFDPGRKIRSEGEDLYMPILEL 47
                                      79*************************************985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.39   3.5e+02     114     146 ..      40      72 ..      33      96 .. 0.78
   2 !   31.4   0.0   1.4e-10   1.2e-07      31     107 ..     179     256 ..     166     272 .. 0.85
   3 ?   -2.2   0.0       2.8   2.5e+03      71     102 ..     294     325 ..     290     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHH CS
                               MTS 114 elavaeeliaeAkeaLkegGeLliVanrklgye 146
                                        +  + el +eAke L++ Ge+ +V  ++ + e
  gi|386002120|ref|YP_005920419.1|  40 LYMPILELSREAKEELSSLGEFDLVEAEFREEE 72 
                                       5566778999*************9998877655 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.4e-10
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeveekkfdlivs 103
                                       + + ++D+ +G+G+ ++ +ak+  +  v++vd++  A+++ +en++ n++     +e+ a d+ ee++ ++ d +++
  gi|386002120|ref|YP_005920419.1| 179 RGEAAVDMFAGVGPFALLIAKRGAR--VVAVDKNPDAVRLLRENANLNRITdmviLEADAADLAEEFA-NRADRVIM 252
                                       56679****************9888..9**********************997767777788888888.9******* PP

                                       ---S CS
                               MTS 104 NPPf 107
                                       N P 
  gi|386002120|ref|YP_005920419.1| 253 NLPH 256
                                       *885 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.8
                                       HHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
                               MTS  71 akenleanklevevvasdvleeveekkfdliv 102
                                        +e ++a+++++e++ + v+   +++++++++
  gi|386002120|ref|YP_005920419.1| 294 VEEAASASGVKAEILRRGVVRSYAPHQYNIVI 325
                                       67788999999999999999999999999998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.1e-09   9.8e-07       2      97 .]     184     273 ..     183     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.1e-09
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS.SSTTTEEEEEEESTGGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp.fedgsfDlvvssgalhh 76 
                                       +d+ +G G ++l +akr+  a+v++vD ++++++  re+a+ +++ ++ ++++da dl  + +++ D v+++  l h
  gi|386002120|ref|YP_005920419.1| 184 VDMFAGVGPFALLIAKRG--ARVVAVDKNPDAVRLLRENANLNRItDMVILEADAADLAeEFANRADRVIMN--LPH 256
                                       68899************5..********************9998899**********9734578*******5..566 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                            ++++l  + +v k+gG
  gi|386002120|ref|YP_005920419.1| 257 ----SARDFLGAAMKVAKDGG 273
                                       ....45789999999999998 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.2e-09   7.4e-06      42     139 ..     180     272 ..     170     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.2e-09
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       g+  +D+faG G  +l  + Rg +++v+v+k++ av++l+en +  ++++ + +l  da++ +++ a   ++ d v 
  gi|386002120|ref|YP_005920419.1| 180 GEAAVDMFAGVGPFALLIAKRG-ARVVAVDKNPDAVRLLRENANLNRITD-MVILEADAADLAEEFA---NRADRVI 251
                                       55679*****************.6899******************99997.9999999999888884...4569999 PP

                                       E--SSSTTCH.HHHHHHHHHT CS
                     Cons_hypoth95 119 lDPPyakellieevlelleek 139
                                       ++ P  + +++ ++++  ++ 
  gi|386002120|ref|YP_005920419.1| 252 MNLPHSARDFLGAAMKVAKDG 272
                                       999999888877777666655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.2   1.2e-08   1.1e-05     157     255 ..     175     274 ..     167     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.2e-08
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleval.seellk..eekadvi 230
                                       +lv++ge  +D+ +G G  a+  ak ga +vvavD ++ Av+  +eNa+lN++++ + + + +++l +  +++ad +
  gi|386002120|ref|YP_005920419.1| 175 SLVRRGEAAVDMFAGVGPFALLIAKRGA-RVVAVDKNPDAVRLLRENANLNRITDMVILEAdAADLAEefANRADRV 250
                                       57999*********************98.699***********************7755321344443566789999 PP

                              PrmA 231 vaNILaevlielaedikklvkeggl 255
                                       + N L +   +++  ++k+ k+gg+
  gi|386002120|ref|YP_005920419.1| 251 IMN-LPHSARDFLGAAMKVAKDGGV 274
                                       999.566667777777777777776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.6e-08   4.1e-05       6     104 ..     182     272 ..     178     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.6e-08
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                         +D  +G G +++ +a++   +a+vv +D +++a++l rena  + ++ +   ++d+ +l + ++ ++ D ++ n 
  gi|386002120|ref|YP_005920419.1| 182 AAVDMFAGVGPFALLIAKR---GARVVAVDKNPDAVRLLRENANLNRITDMVILEADAADLAEEFA-NRADRVIMNL 254
                                       67899************65...799***********************************776688.8999999973 PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpg 104
                                       +     +  ++l+ + +v k+g
  gi|386002120|ref|YP_005920419.1| 255 PH----SARDFLGAAMKVAKDG 272
                                       33....3344455555555555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.91   8.1e+02      24      72 ..      49      96 ..      45     106 .. 0.72
   2 !   21.7   0.1   1.7e-07   0.00015       1      95 [.     189     286 ..     189     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.91
                                      HHHHHHHHHTT.ESEEEET..TTCHHHHHHHHHTTTSSEEEEEESSCSHHHH CS
                        ADH_zinc_N 24 eeklelakklG.adeviny..keadlverikeltggegvdvvfecvGsgatl 72
                                      +e  e + +lG  d v  +  +e ++ e ++ l    g +++fe+vG+ a l
  gi|386002120|ref|YP_005920419.1| 49 REAKEELSSLGeFDLVEAEfrEE-EPRETVEGLL---GRKASFEVVGDIAIL 96
                                      55568888999555555555433.8999999999...889999999966655 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT.ESEEEET....TTC.HHHHHHHHHTTTSSEEEEEESSCSHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklG.adeviny....kea.dlverikeltggegvdvvfecvGsgat 71 
                                       gvG +a+ +Ak  Ga+v+avd +++ ++l++++   +++ +      +a dl e+ +     + v   + +++  + 
  gi|386002120|ref|YP_005920419.1| 189 GVGPFALLIAK-RGARVVAVDKNPDAVRLLRENAnLNRITDMvileADAaDLAEEFANRA--DRVIMNLPHSA-RDF 261
                                       89999999999.6*******************7535555555665455556666666666..46777777888.99* PP

                                       HHHHHHCEEEEEEEEECSC.TSSEE CS
                        ADH_zinc_N  72 leaalkllkpgGrlvvvGg.gkgee 95 
                                       l aa+k++k gG + ++++ ++++ 
  gi|386002120|ref|YP_005920419.1| 262 LGAAMKVAKDGGVVHYYAIaPEDDL 286
                                       ******************9655543 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   1.1e-07   9.5e-05       5      94 ..     188     275 ..     184     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-07
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CCHHH CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaekl.pfednsfDlvvssevlhhvedpek 79 
                                       +G G +a  +akrgarvv+vD ++ +++l +e+a+ +++  + +++ada +l     n  D v+++      +  ++
  gi|386002120|ref|YP_005920419.1| 188 AGVGPFALLIAKRGARVVAVDKNPDAVRLLRENANLNRItDMVILEADAADLaEEFANRADRVIMNL--P--HSARD 260
                                       799***********************************998899*******9533346889888773..4..44689 PP

                                       HHHHHHHHEEEEEEE CS
                   Methyltransf_11  80 alkeiaRvLkpgGll 94 
                                       +l  +++v k gG++
  gi|386002120|ref|YP_005920419.1| 261 FLGAAMKVAKDGGVV 275
                                       999999999999975 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   2.6e-07   0.00023      75     149 ..     202     275 ..     183     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                                       EEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEE CS
                               TRM  75 kevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglL 149
                                        +v+a D ++ Av l++eN++ln + ++v  +  dA+ l +e  +r d + +    s+ +fl +a++ +k++g++
  gi|386002120|ref|YP_005920419.1| 202 ARVVAVDKNPDAVRLLRENANLNRITDMVILEA-DAADLAEEFANRADRVIMNLPHSARDFLGAAMKVAKDGGVV 275
                                       57999**********************666655.******9999999999999888**************99986 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   1.8e-06    0.0016      12      93 ..     183     260 ..     176     271 .. 0.80
   2 ?    5.6   0.0     0.012        11     104     137 ..     245     278 ..     244     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                                       EEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE- CS
                   Methyltr_RsmB-F  12 ilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaP 88 
                                        +D+ a+ G    +i    k  ++vvAvd+n   ++ + en +   +t++ +leaDa    +  ++   Dr+++  P
  gi|386002120|ref|YP_005920419.1| 183 AVDMFAGVGPFALLI---AKRGARVVAVDKNPDAVRLLRENANLNRITDMVILEADAADLAEEFAN-RADRVIMNLP 255
                                       556666655544443...46789********9999999999888888999***********99996.99******** PP

                                       -CCGG CS
                   Methyltr_RsmB-F  89 Csgtg 93 
                                        s+  
  gi|386002120|ref|YP_005920419.1| 256 HSARD 260
                                       99975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                                       H--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE CS
                   Methyltr_RsmB-F 104 rrkekdiaqlaklqkellsaaidllkkgGvlvYs 137
                                       +r ++ i++l +  ++ l aa+++ k gGv+ Y 
  gi|386002120|ref|YP_005920419.1| 245 NRADRVIMNLPHSARDFLGAAMKVAKDGGVVHYY 278
                                       688999*************************985 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.49   4.4e+02      23      61 ..     115     165 ..      94     188 .. 0.67
   2 !   16.6   0.2   1.3e-05     0.012      18     102 ..     197     276 ..     166     277 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.49
                   Methyltransf_24  23 a...grlvavdhdpg.........aeeaaalareaglddrvrlikadseea 61 
                                       +   + l+av+ + +         +++++ + re+gl+ r++l +a +   
  gi|386002120|ref|YP_005920419.1| 115 RaviSPLTAVEGEYRtrrfehvagEARTTTVHREHGLRYRIDLERAYFTPR 165
                                       345555666666555555554544667777777899999999988887544 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.3e-05
                   Methyltransf_24  18 lrrngagrlvavdhdpgaeeaaalare.aglddr..vrlikadseealaslaagsiDllfiDgghaaeavledleal 91 
                                       + ++g  r+vavd++p   +a +l+re a+l+++  + +++ad+ ++++++a  + D +++  +h+a++   +l a+
  gi|386002120|ref|YP_005920419.1| 197 IAKRG-ARVVAVDKNP---DAVRLLREnANLNRItdMVILEADAADLAEEFA-NRADRVIMNLPHSARD---FLGAA 265
                                       33334.49********...777777775666666446677************.88*********97765...55599 PP

                   Methyltransf_24  92 lprlapggvvl 102
                                        ++ ++ggvv+
  gi|386002120|ref|YP_005920419.1| 266 MKVAKDGGVVH 276
                                       99999999986 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.3e-06    0.0065       3      64 ..     182     242 ..     180     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.3e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellak 64 
                                         +D+f+G G  +  +a+ + +v+a+++n++ + +  +Na++  + d + l  +d  +l ++
  gi|386002120|ref|YP_005920419.1| 182 AAVDMFAGVGPFALLIAKRGARVVAVDKNPDAVRLLRENANLNRITDMVIL-EADAADLAEE 242
                                       579**************************************9999887754.5555555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.011      76     134 ..     201     259 ..     168     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                                       H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE------- CS
                           UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPYGer 134
                                        ++++++D+++ +v+  reNa+  +++d + +++ daa+L  +  +  d ++ n+P   r
  gi|386002120|ref|YP_005920419.1| 201 GARVVAVDKNPDAVRLLRENANLNRITDMVILEA-DAADLAeEFANRADRVIMNLPHSAR 259
                                       56699************************98887.******555559*********8665 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05     0.029      75     170 ..     133     225 ..     121     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                   Methyltrans_SAM  75 sevlvgeldespvvvesglkyqldigrnqnfglfldmrlgrdwvqena...kdknvlnlfaytcgfsvaaiaggask 148
                                        e ++ge   + v  e+gl+y++d+ r   +      rlg + ++  +   ++   +++fa    f++  ia    +
  gi|386002120|ref|YP_005920419.1| 133 FEHVAGEARTTTVHREHGLRYRIDLERAYFTP-----RLGTERLRVASlvrRGEAAVDMFAGVGPFALL-IAKRGAR 203
                                       58899**********************86555.....4444433333211145668999**99999876.5655567 PP

                   Methyltrans_SAM 149 vvnvdmargslnkgrdnhrlng 170
                                       vv vd    ++   r+n +ln 
  gi|386002120|ref|YP_005920419.1| 204 VVAVDKNPDAVRLLRENANLNR 225
                                       999***9999999999999996 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-05      0.05       9      62 ..     166     228 ..     119     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                   Methyltransf_23   9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........k 62 
                                       l  +++r++   r+g   +d+ +G+G ++ +++++g+ v++vD +p av +++          
  gi|386002120|ref|YP_005920419.1| 166 LGTERLRVASLVRRGEAAVDMFAGVGPFALLIAKRGARVVAVDKNPDAVRLLRenanlnritD 228
                                       5566777776568888999999****************************9986555544430 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.12      23      96 ..     171     243 ..     157     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                       HHHCCCS-S-E.EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-E CS
                              TehB  23 veavkivkpgk.vldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakldery 96 
                                       +  + +v+ g  ++d+  g g  +l ++  g  v a+dkn +++  l+e ++ + +++    +++ ++a+l e++
  gi|386002120|ref|YP_005920419.1| 171 LRVASLVRRGEaAVDMFAGVGPFALLIAKRGARVVAVDKNPDAVRLLRENANLNRITD--MVILEADAADLAEEF 243
                                       55556666654268******************************99988777666663..344566666666655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.18      13      67 ..     192     258 ..     189     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                       HHHHHHHHTT-EEEEE-SSHHHHHHHHHTT............EEE-SSHHHHHHHCSEEEE-SSSHH CS
                     NAD_binding_2  13 nmalnllkagykvavynrtkekveelvaeg............akaaesieelvasldvvitmvkagk 67 
                                       ++al ++k+g +v++++ ++++v+ l ++             a+aa+ +ee+++++d vi+ +++++
  gi|386002120|ref|YP_005920419.1| 192 PFALLIAKRGARVVAVDKNPDAVRLLRENAnlnritdmvileADAADLAEEFANRADRVIMNLPHSA 258
                                       6788899*****************999998999*******99999*****************99865 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.23       4      56 ..     184     235 ..     182     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                       EEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS- CS
                     DNA_methylase   4 idLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk 56 
                                       +d+faG+G f+l  ++ g   v+a++++++a+ +++ n +   i D+  ++ +
  gi|386002120|ref|YP_005920419.1| 184 VDMFAGVGPFALLIAKRG-ARVVAVDKNPDAVRLLRENANLNRITDMVILEAD 235
                                       8***********888887.88999***************96666666555544 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00033       0.3     205     266 ..     183     244 ..     172     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                   tRNA_U5-meth_tr 205 llelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeeltealk 266
                                        ++++ G G f+l +a++  +v+a +    +v   + n + n+i+++ i+   a +l+e ++
  gi|386002120|ref|YP_005920419.1| 183 AVDMFAGVGPFALLIAKRGARVVAVDKNPDAVRLLRENANLNRITDMVILEADAADLAEEFA 244
                                       57899********************************************9998877776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2224.69
//
Query:       gi|386002121|ref|YP_005920420.1|  [L=395]
Description: magnesium chelatase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   47.1   0.0    5.6e-12   46.3   0.0    1.4  1  VWA_2         von Willebrand factor type A domain
    3.6e-12   46.9   0.0      5e-12   46.4   0.0    1.2  1  VWA           von Willebrand factor type A domain
    1.7e-05   24.3   0.5    3.2e-05   23.4   0.5    1.4  1  VWA_CoxE      VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
        0.1   13.6   0.1        5.8    8.0   0.1    2.5  2  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   1.3e-15   5.6e-12       1     106 [.     206     310 ..     206     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.3e-15
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       + +vlDtS Sm++        ea ++ v +ll +   ++drv+lv+ s+ ++ v++p+t   a+ ++ l+++e+ gg
  gi|386002121|ref|YP_005920420.1| 206 VAIVLDTSFSMEEA------SEATRRVVLELLRDAyqRRDRVALVSCSGrEAAVVLPFTPAAATAKRHLDGIEY-GG 275
                                       679**********8......8999******99944446***********88**********************8.6* PP

                             VWA_2  75 gtnlaaaLqlarkalkkrr...kgekrvivlitDg 106
                                        t la++L + +++l ++r    ++  ++vlitDg
  gi|386002121|ref|YP_005920420.1| 276 TTPLASGLAKGSALLARERdkePSAIPILVLITDG 310
                                       ***************999988999999*******9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.1e-15     5e-12       2     151 ..     206     356 ..     205     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.1e-15
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysggg 77 
                                       +++vlD+S sm ee  e +++ + +l+++ +  ++++rv+lv+ s+  + ++ +++     ++++++l+ +  ++gg
  gi|386002121|ref|YP_005920420.1| 206 VAIVLDTSFSM-EEASEATRRVVLELLRDAY--QRRDRVALVSCSGReAAVVLPFTPAA--ATAKRHLDGI--EYGG 275
                                       89*********.8888999999999999999..************988*********77..9********8..999* PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.........HTHHHHHHHHGCTEEEEEEEESSSHHH CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksndg.........dpkeaaneakeqgikvfavGvgnadek 145
                                       tt ++++l+++   l +++ +  + a  +++l+tdG  n           + +eaa+e+k+ g  + +v vg    +
  gi|386002121|ref|YP_005920420.1| 276 TTPLASGLAKGSALLARERDK-EPSAIPILVLITDGSANVPlevagdpgqEAEEAARELKRTGFHLLVVDVGAGGSE 351
                                       ***********9966666666.889**********99999668999999999***************9999776655 PP

                                       HHHHHH CS
                               VWA 146 elLnki 151
                                           +i
  gi|386002121|ref|YP_005920420.1| 352 L-AGRI 356
                                       5.5555 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.5   7.1e-09   3.2e-05      14     186 ..     142     343 ..     131     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.1e-09
                          VWA_CoxE  14 rrr..rrrkrrrrgrriDlrrtlranlrhgge................lvelvrrkp..rerkprelvllvDvSgSm 70 
                                       r r  r r  r++ +++ l  t+ra+l+  g                      +r++  r++ ++ + +++D S Sm
  gi|386002121|ref|YP_005920420.1| 142 RGRyvRARMPRSKTKDVALAPTIRAALARSGGsvgaggeagvegfsvrE--EDLREKvrRRKVSTHVAIVLDTSFSM 216
                                       33334477788889999999******9877777999*********9642..33333221344455677899****** PP

                          VWA_CoxE  71 aays....aiflallhAllqqlprtevfaFdtrlvdlTral..rerDpaeaLarvsaavedlgGgTrigaalaefle 141
                                       ++ s    +++l ll+ + q+++r+ ++  + r + +   +  +++ +++ L+ ++      gG+T ++++la+   
  gi|386002121|ref|YP_005920420.1| 217 EEASeatrRVVLELLRDAYQRRDRVALVSCSGREAAVVLPFtpAAATAKRHLDGIE-----YGGTTPLASGLAKGSA 288
                                       *9883333466777777777777999999988866665555323336777777777.....*************999 PP

                          VWA_CoxE 142 lvtrpaLsrra...vvvlvsD.......glergdreellaelarlvrrarrlvwl 186
                                       l +r+  ++ +   ++vl++D          +++ +e++++ ++l+r +++l+++
  gi|386002121|ref|YP_005920420.1| 289 LLARERDKEPSaipILVLITDgsanvplEVAGDPGQEAEEAARELKRTGFHLLVV 343
                                       99887645555122579****88888775679999****************9987 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0013       5.8      85     122 ..     189     226 ..     125     227 .. 0.66
   2 ?    3.0   0.0     0.044     2e+02      15      57 ..     330     375 ..     317     393 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                                       .-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHH CS
                      ADH_zinc_N_2  85 aqadileelaalieeGklrpvvdrvfpleeaaeAhryl 122
                                       + +d+ e++ +   + ++ +v+d +f++eea eA r++
  gi|386002121|ref|YP_005920420.1| 189 REEDLREKVRRRKVSTHVAIVLDTSFSMEEASEATRRV 226
                                       445544566666667899****************9986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.044
                                       HHHH-TT-EEEEEES-H..HHHH.HHHHHHEEEEEEEEE----....S CS
                      ADH_zinc_N_2  15 eaatggegvDvvldtvg..gealleaslkvlpggGrlvsiggpp...l 57 
                                       ++++++ g+ + +  vg  g +l+ ++ ++ +g Gr+v +g+p+   +
  gi|386002121|ref|YP_005920420.1| 330 ARELKRTGFHLLVVDVGagGSELAGRI-SAAAG-GRYVRMGRPSqeeI 375
                                       466667778776666777667674555.55566.******98755553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2457.85
//
Query:       gi|386002122|ref|YP_005920421.1|  [L=423]
Description: Protoporphyrin IX magnesium-chelatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-22   76.9   1.9      2e-21   75.6   1.9    1.8  1  AAA_lid_2        AAA lid domain
    1.2e-12   47.7   2.0    2.5e-08   33.6   0.0    3.2  4  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.8e-09   36.7   0.1    1.9e-05   24.7   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    3.1e-06   26.5   0.1    0.00011   21.4   0.0    2.4  2  MCM              MCM P-loop domain
    9.8e-05   22.1   0.7      0.027   14.2   0.0    3.0  3  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.043   14.2   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.032   14.1   0.0          1    9.2   0.0    2.2  2  AAA_3            ATPase family associated with various cellul
       0.13   11.9   0.3        7.1    6.3   0.0    2.2  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   1.9   9.1e-25     2e-21       3      71 ..     351     419 ..     349     421 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 9.1e-25
                         AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeive 71 
                                        +a++aie+gv+g+Rad+++ r+ArA+Aa+egr++V   D+ +aa++VL+HR+r+ p++eg  + e+++
  gi|386002122|ref|YP_005920421.1| 351 NIARIAIEFGVDGHRADIMIERTARANAAFEGRERVEAADIVAAAEMVLPHRMRKTPFDEGDYSPERLR 419
                                       68999*******************************************************977777766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   8.7e-05       0.2       2      50 ..      93     143 ..      92     145 .. 0.88
   2 !   33.6   0.0   1.1e-11   2.5e-08      88     158 ..     202     272 ..     198     280 .. 0.96
   3 ?    0.6   0.0      0.13     3e+02     187     203 ..     279     295 ..     274     299 .. 0.80
   4 ?   -3.6   0.0       2.7     6e+03      47      79 ..     378     409 ..     360     415 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.7e-05
                      Mg_chelatase   2 lkdvkGqeeakraleiaaaG..gHnlllvGppGsGKtmlakrlpsllppls 50 
                                       ++ ++Gqe+ kral + a+      +l+ G  G+ K+   + l+++lp+++
  gi|386002122|ref|YP_005920421.1|  93 FAAIVGQEKMKRALILNAINpsIGGVLIRGEKGTAKSTAVRGLAEVLPEIE 143
                                       6789***********99985114579**********************975 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 1.1e-11
                      Mg_chelatase  88 aalvGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                        al Gg +  +pG ++ a++G+L++DE+  ++  v+++L +    g  +++r   ++++pa+f +v +mNp
  gi|386002122|ref|YP_005920421.1| 202 RALRGGERAFEPGVLAEANRGILYVDEINLLDDYVVDALLDAAAMGMNVVEREGVSASHPASFIIVGSMNP 272
                                       6899******************************************************************9 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.13
                      Mg_chelatase 187 gplldRidlqvevkkle 203
                                         lldRi lqvev+ ++
  gi|386002122|ref|YP_005920421.1| 279 PQLLDRIALQVEVEGIS 295
                                       579*********98765 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.7
                      Mg_chelatase  47 pplseeealevakiasvagkkeeekllkrrpfr 79 
                                       ++ + +e +e+a i + a+     + +++ pf 
  gi|386002122|ref|YP_005920421.1| 378 AAFEGRERVEAADIVAAAE-MVLPHRMRKTPFD 409
                                       5556667777777776666.5556666666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00038      0.84       2      24 ..     118     140 ..     117     149 .. 0.86
   2 !   24.7   0.0   8.7e-09   1.9e-05      19     137 ..     168     284 ..     163     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                                       EEEE--SSSSHHHHHHHGGGGBS CS
                             AAA_5   2 vlLvGppGtgKselaerlaaaln 24 
                                       vl+ G++Gt+Ks+ ++ la++l 
  gi|386002122|ref|YP_005920421.1| 118 VLIRGEKGTAKSTAVRGLAEVLP 140
                                       899****************9983 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 8.7e-09
                                       GGGGB....S--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHH CS
                             AAA_5  19 laaal....nreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLls 87 
                                       la+ +     r++ +v l+ + te+ ++g+++++    +g++++++++l +a     il++DE++ +++ v+++L  
  gi|386002122|ref|YP_005920421.1| 168 LAEGVlpteLRPMRVVDLPVGATEDRVVGSLDMEralrGGERAFEPGVLAEAN--RGILYVDEINLLDDYVVDAL-- 240
                                       555444555678889999999*****************************554..46*****************9.. PP

                                       HHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  88 lleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                        l+   +  ++  e++++++   ++ f +++++np +    el p+l++R
  gi|386002122|ref|YP_005920421.1| 241 -LDAAAMG-MNVVEREGVSASHPAS-FIIVGSMNPEE---GELRPQLLDR 284
                                       .7777777.6666666666543333.*********99...5666777777 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.031        69      26      83 ..      96     141 ..      87     149 .. 0.65
   2 !   21.4   0.0     5e-08   0.00011     106     180 ..     205     279 ..     192     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.031
                                       SSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                               MCM  26 iyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapr 83 
                                       i+g+e++k+a++l  + ++               vl+ g+ gtaKs+ ++ +++++p+
  gi|386002122|ref|YP_005920421.1|  96 IVGQEKMKRALILNAINPSI------------GGVLIRGEKGTAKSTAVRGLAEVLPE 141
                                       55555555555555444332............13788888888888888877777765 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 5e-08
                                       SSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCT CS
                               MCM 106 etgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydk 180
                                       + ge ++e G l  a++G++++De++  ++   +al++a    +  + + G+ a+ +a   ++ ++np++g+  +
  gi|386002122|ref|YP_005920421.1| 205 RGGERAFEPGVLAEANRGILYVDEINLLDDYVVDALLDAAAMGMNVVEREGVSASHPASFIIVGSMNPEEGELRP 279
                                       5678899********************************9999999***********************998655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.016        35      19      41 ..     112     134 ..      96     146 .. 0.75
   2 !   14.2   0.0   1.2e-05     0.027      85     143 ..     212     272 ..     200     289 .. 0.80
   3 ?    0.1   0.0      0.26   5.8e+02     128     156 ..     323     351 ..     316     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                                       CTSSS-EEEECSTTSSHHHHHHH CS
                   Sigma54_activat  19 aktdlsvlitGesGtGKellara 41 
                                        ++   vli+Ge+Gt K++  r 
  gi|386002122|ref|YP_005920421.1| 112 NPSIGGVLIRGEKGTAKSTAVRG 134
                                       4445679**********988765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHH..HHHSEEESBTSSSEEE--EEEEEEESS CS
                   Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrv..lqegevervGsskeikvdvriiaatne 143
                                       + G + +a+ G+l++Dei+ l+  +   Ll +  +  + ver G s+++++++ i+ + n 
  gi|386002122|ref|YP_005920421.1| 212 EPGVLAEANRGILYVDEINLLDDYVVDALLDAaaMGMNVVEREGVSASHPASFIIVGSMNP 272
                                       45****************************75227788999***99999999999988774 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.26
                                       SSEEE--EEEEEEESS-HHHHHHTTSS-H CS
                   Sigma54_activat 128 skeikvdvriiaatnedleeaveegkfre 156
                                        +++k++ ri+aa +  ++ av +g++r+
  gi|386002122|ref|YP_005920421.1| 323 AENRKLTSRIVAAKKALPRVAVGRGELRN 351
                                       5789999*********9999999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.043      19      88 ..     110     179 ..      96     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde 88 
                                       +  ++ + vl++Ge+G+ Ks+ vr l++ l + ++++  r  cd  + +      a+ l +e++l  +l++
  gi|386002122|ref|YP_005920421.1| 110 AINPSIGGVLIRGEKGTAKSTAVRGLAEVLPEIEVVVgCRFGCDPRDGEKLCWECAERL-AEGVLPTELRP 179
                                       34455589*******************87777788878888888774443334455555.33555555555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.057   1.3e+02       2      23 ..     118     139 ..     117     145 .. 0.91
   2 ?    9.2   0.0   0.00045         1      64     115 ..     222     275 ..     200     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.057
                             AAA_3   2 vllegvPGlaktllvkalakal 23 
                                       vl++g  G+ak ++v+ la++l
  gi|386002122|ref|YP_005920421.1| 118 VLIRGEKGTAKSTAVRGLAEVL 139
                                       899****************987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00045
                             AAA_3  64 nllladeinrappktqsallea..meerqvtvegethklpepflvlatqnPieq 115
                                        +l +dein     +  all+a  m  + v  eg + + p  f+++   nP e 
  gi|386002122|ref|YP_005920421.1| 222 GILYVDEINLLDDYVVDALLDAaaMGMNVVEREGVSASHPASFIIVGSMNPEEG 275
                                       48899***************85338889999999*****************875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0032       7.1      21      43 ..     118     140 ..     102     150 .. 0.84
   2 ?    3.6   0.1     0.021        48      88     120 ..     220     251 ..     165     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       +++ G  Gt K+ta+++l+e++ 
  gi|386002122|ref|YP_005920421.1| 118 VLIRGEKGTAKSTAVRGLAEVLP 140
                                       6899***************9976 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                            AAA_30  88 pgtllivDEagmvdtkqlaallkaaekagakvi 120
                                       ++ +l vDE+ ++d   ++all+aa+  g+ v+
  gi|386002122|ref|YP_005920421.1| 220 NRGILYVDEINLLDDYVVDALLDAAAM-GMNVV 251
                                       447899******************988.88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3178.55
//
Query:       gi|386002123|ref|YP_005920422.1|  [L=134]
Description: hypothetical protein Mhar_1435 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.57   10.7   4.9          1    9.9   0.2    2.3  2  TraL         TraL protein
        4.6    5.9   7.3        5.6    5.6   7.4    1.3  1  DUF2207      Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> TraL  TraL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00011         1      16      68 ..       5      59 ..       4      64 .. 0.75
   2 ?    2.7   0.6      0.02   1.8e+02      20      58 ..      69     105 ..      61     121 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                              TraL 16 welDealv..illllvvgillgqfviglv.lglllvlllrklkkgrgdgfllhllY 68
                                      we+D+ +     + +++gi++ ++vig + +g++++++ +  ++ +g+ f l+llY
  gi|386002123|ref|YP_005920422.1|  5 WEIDVSVSdiGSVFTLLGIAVTSAVIGAAeIGYTMLWITS-AYERNGKDFFLDLLY 59
                                      77777775325567789***********977777766655.566667778888888 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.02
                              TraL  20 ealvillllvvgillgqfviglvlglllvlllrklkkgr 58 
                                        ++v  ++ v+ +    f++ + ++l+ +  l++ +k +
  gi|386002123|ref|YP_005920422.1|  69 YVIV--AGSVILVSAIIFMTTMSISLVYLNNLSTKRKRT 105
                                       4444..333333333344444445555554444444444 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.4   0.00062       5.6     372     430 ..      59     131 ..      14     134 .] 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00062
                           DUF2207 372 fdkkgkkklkklsalglgliilglilillallllvll..............lvfllilllillliaiivlllf 430
                                       + +k  + + +++++g ++++ ++i+++   ++lv+l              l++l++l+l+ll++ ++ ++++
  gi|386002123|ref|YP_005920422.1|  59 YASKYTWTAEYVIVAGSVILVSAIIFMTTMSISLVYLnnlstkrkrtnlspLFGLYFLGLLLLIVTLLSAIML 131
                                       5555566666777777777777777777777777777999*******66664444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 875.75
//
Query:       gi|386002124|ref|YP_005920423.1|  [L=736]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-97  322.4   0.0    1.9e-47  161.0   0.0    2.4  2  AAA              ATPase family associated with various cellul
    2.5e-32  110.4   1.6    7.2e-15   54.5   0.1    2.8  2  AAA_lid_3        AAA+ lid domain
    3.5e-30  104.0   0.1      3e-29  101.0   0.1    2.5  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    2.4e-15   56.1   0.1    2.6e-14   52.7   0.1    2.6  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    3.8e-14   53.4   0.5    9.8e-06   26.1   0.0    3.6  2  AAA_16           AAA ATPase domain
    8.6e-14   51.7   0.2    2.1e-05   24.5   0.0    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
      2e-13   50.4   0.0    2.3e-05   24.2   0.0    3.3  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.4e-11   44.8   0.0      7e-05   23.0   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
    8.7e-11   41.6   0.0     0.0004   19.7   0.0    3.4  4  TIP49            TIP49 P-loop domain
    3.5e-10   40.3   0.4     0.0098   16.2   0.0    3.8  3  AAA_22           AAA domain
    1.7e-09   38.0   0.0    0.00096   19.3   0.0    2.6  2  AAA_33           AAA domain
      5e-08   33.0   0.0      0.005   16.9   0.0    2.4  2  AAA_14           AAA domain
    6.5e-08   33.2   0.1      0.019   15.5   0.0    3.2  2  AAA_18           AAA domain
      1e-06   29.1   0.0     0.0071   16.6   0.0    2.6  2  AAA_28           AAA domain
    1.9e-06   27.7   0.1      0.056   13.2   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    2.8e-06   26.9   0.0       0.08   12.3   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.9e-06   26.9   0.0      0.083   12.4   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    4.8e-06   26.5   0.0      0.069   13.0   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    5.6e-06   26.2   0.0       0.16   11.6   0.0    2.9  2  Sigma54_activat  Sigma-54 interaction domain
    6.1e-06   26.6   0.0       0.17   12.3   0.0    2.5  2  RNA_helicase     RNA helicase
    6.2e-06   25.6   0.1      0.047   13.0   0.0    2.5  2  Zeta_toxin       Zeta toxin
    7.2e-06   25.5   0.0      0.017   14.4   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    7.8e-06   26.4   0.0      0.058   13.9   0.0    2.5  2  ABC_tran         ABC transporter
    1.3e-05   24.6   0.1        0.5    9.7   0.0    3.3  3  ATPase           KaiC
    2.9e-05   24.1   0.0       0.27   11.2   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0001   21.6   0.0       0.11   11.6   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    0.00013   21.8   0.0        0.3   10.8   0.0    2.5  2  AAA_24           AAA domain
    0.00017   21.2   3.8       0.23   11.0   0.1    3.8  2  AAA_25           AAA domain
    0.00019   21.3   0.0       0.25   11.1   0.0    2.4  2  AAA_11           AAA domain
    0.00026   21.3   0.3        1.1    9.6   0.0    2.7  2  AAA_19           AAA domain
    0.00029   20.0   0.0        0.5    9.4   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00031   20.9   0.3        0.4   10.8   0.0    2.8  2  Cytidylate_kin2  Cytidylate kinase-like family
    0.00038   20.6   0.0       0.67   10.1   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00048   19.9   0.6       0.97    9.1   0.0    2.6  2  AAA_30           AAA domain
    0.00061   19.3   0.1       0.87    9.0   0.0    2.4  2  PhoH             PhoH-like protein
    0.00074   19.5   0.1        2.9    7.8   0.0    3.2  3  NACHT            NACHT domain
    0.00076   19.4   0.1       0.17   11.9   0.1    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00089   19.6   0.1       0.25   11.6   0.0    2.7  2  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0013   18.6   0.0       0.37   10.6   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
     0.0015   17.8   0.0        1.2    8.3   0.0    2.5  2  NB-ARC           NB-ARC domain
      0.002   18.0   0.0         12    5.7   0.0    3.5  3  Bac_DnaA         Bacterial dnaA  protein
     0.0037   16.7   0.0        4.7    6.6   0.0    3.6  4  TniB             Bacterial TniB protein
     0.0039   17.6   0.0        2.1    8.8   0.0    2.9  2  AAA_17           AAA domain
     0.0048   17.0   0.0        3.6    7.7   0.0    2.6  2  SKI              Shikimate kinase
     0.0072   16.3   0.0        5.6    6.9   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
     0.0072   16.3   0.1         24    4.8   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0089   15.4   0.3       0.46    9.8   0.0    2.7  2  IPT              Isopentenyl transferase
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.97    9.6   0.0    2.4  2  Torsin           Torsin
      0.013   15.4   0.3        3.3    7.6   0.0    3.0  3  NTPase_1         NTPase
      0.028   14.1   0.1        3.1    7.5   0.0    2.3  2  Cytidylate_kin   Cytidylate kinase
      0.029   14.1   0.0        5.1    6.8   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.032   13.9   0.0        7.7    6.1   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.063   13.2   0.0        3.3    7.6   0.0    2.6  2  Rad17            Rad17 P-loop domain
      0.081   13.4   0.2        6.6    7.3   0.1    2.8  2  DUF234           Archaea bacterial proteins of unknown functi
      0.098   11.9   0.0        7.4    5.7   0.0    3.2  4  KAP_NTPase       KAP family P-loop domain
       0.13   11.7   0.0        5.6    6.3   0.0    2.4  2  KTI12            Chromatin associated protein KTI12
       0.17   11.6   1.8         72    3.0   0.0    4.1  4  Guanylate_kin    Guanylate kinase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.0   6.1e-50   1.9e-47       1     131 [.     226     355 ..     226     356 .. 0.97
   2 !  159.1   0.0   2.3e-49   7.3e-47       1     130 [.     498     627 ..     498     629 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 6.1e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+G pGtGKTl+aka+a+e++++f++i g+e++sky gese+++re+f+ea ++  psi+fiDE+d++a++r + 
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFFSIAGPEVMSKYYGESEQRLREIFEEANRST-PSIIFIDELDSIAPKRGEV 301
                                       79***************************************************9997.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLl+++dg+k++ ++v+vigatnr+d +dpal+r gRfdr+iei+
  gi|386002124|ref|YP_005920423.1| 302 TGEVERRVVAQLLAMMDGLKER-GQVVVIGATNRIDAIDPALRRpGRFDREIEIG 355
                                       *********************7.66***************************996 PP

  == domain 2  score: 159.1 bits;  conditional E-value: 2.3e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vllyGppGtGKTl+a+ava+e++++f++++g++llsk+vgesek +re+fk+a++ + p i+f+DE+da+a+ r  +
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISVKGPQLLSKWVGESEKAVREVFKKARQVS-PAIIFFDELDAIAPMRgME 573
                                       79******************************************************9.****************888 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       +  + +ervvnqLl+eldg+++ ++ v+vigatnrpd +dpallr gRfdr +++
  gi|386002124|ref|YP_005920423.1| 574 EGPRTSERVVNQLLAELDGLETLKD-VVVIGATNRPDIIDPALLRsGRFDRLLFV 627
                                       8999******************755.*************************9887 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1   2.6e-17   8.2e-15       1      42 [.     378     419 ..     378     438 .. 0.89
   2 !   54.5   0.1   2.3e-17   7.2e-15       1      43 [.     651     695 ..     651     697 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.6e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                       +v+l++LA rT+G++GAD++alc+eAa+  lrr ++ei+ +d
  gi|386002124|ref|YP_005920423.1| 378 SVSLEDLADRTNGFVGADISALCKEAAMKVLRRHLPEISFDD 419
                                       69*******************************988887665 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 2.3e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedf 43 
                                       dv+l+eLAe+Te ++G Dl++lcreA++lAlr++ +  e++m++ 
  gi|386002124|ref|YP_005920423.1| 651 DVSLEELAELTESFVGSDLESLCREAVMLALREDPEasEVEMRHY 695
                                       9*********************************88645**9996 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.1   9.7e-32     3e-29       1      84 [.       5      88 ..       5      90 .. 0.98
   2 ?   -0.9   0.0       6.1   1.9e+03      20      41 ..     211     232 ..     210     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 9.7e-32
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L+Va+a+++d+ rgi+r+dp+++  l+l+pgd++eieg+r+++a+vw+a+++d+++++Ir+dg++R+n+gvsiGd+V+
  gi|386002124|ref|YP_005920423.1|  5 QLKVAKAYPNDSARGIARLDPNALLTLRLSPGDIIEIEGRRTSAAKVWRADRQDWSQDYIRIDGFIRHNVGVSIGDRVK 83
                                      69******99********************************************************************* PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      +r+a+
  gi|386002124|ref|YP_005920423.1| 84 IRRAK 88
                                      **986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.1
                                       -HHHHHHHTS-TTSEEEEECCC CS
                           CDC48_N  20 dpedmeelglepgdvveiegkr 41 
                                       +pe++++lg+ep + v ++g+ 
  gi|386002124|ref|YP_005920423.1| 211 HPEVFNRLGIEPPKGVLLHGSP 232
                                       6899*********999999854 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       2.4   7.5e+02      33      46 ..       3      30 ..       1      51 [. 0.48
   2 !   52.7   0.1   8.3e-17   2.6e-14       2      64 .]     106     177 ..     105     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.4
                                      CEEEEEEEECCCC..............S CS
                           CDC48_2 33 eiklvVvstePkg..............p 46
                                      ei+l+V++  P++              +
  gi|386002124|ref|YP_005920423.1|  3 EIQLKVAKAYPNDsargiarldpnallT 30
                                      5666666666665444433333333322 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 8.3e-17
                                       .SCCCCH.HHHCCCTTEEE-TTEEEEECCT........CCCEEEEEEEECCCCSCEEECTSCCEEESTTCCE CS
                           CDC48_2   2 idgdema.ylkrqFlgrpvtkGdlvvfefk........gqeiklvVvstePkgpvgitetTeielgtkpvev 64 
                                       ++g+++a ++krq l+rp++ Gd+++++ +        + +++lv+++t+P g+v+ite Te+ l ++pv++
  gi|386002124|ref|YP_005920423.1| 106 YYGEDAAeQIKRQTLKRPIVRGDVLPIMSSsghpfigrMEAVPLVIADTDPEGVVVITERTEVSLLDRPVKG 177
                                       67777888*****************9988777788888*******************************985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.5e-07   7.8e-05      23     140 ..     222     329 ..     193     337 .. 0.68
   2 !   26.1   0.0   3.1e-08   9.8e-06      24     139 ..     495     601 ..     470     602 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.5e-07
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawr 98 
                                        p  vll+G +G+GK+ ++++l+++ +++   f++    +  ++  y+    q l r e++++ ++    +    + 
  gi|386002124|ref|YP_005920423.1| 222 PPKGVLLHGSPGTGKTLIAKALANETNAN---FFSIAGPEV-MS-KYYGeSEQRL-R-EIFEEANRS---TPSIIFI 288
                                       3499*******************988877...544444444.11.3322233333.3.444444433...5556666 PP

                            AAA_16  99 ekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       ++l++ +   +e++g+ ++r+ ++l ++++ l+++++ +v++
  gi|386002124|ref|YP_005920423.1| 289 DELDSIAPKRGEVTGEVERRVVAQLLAMMDGLKERGQ-VVVI 329
                                       666777779999999999***********99999777.5543 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.1e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p+ vll+G++G+GK+ ++r+++r+ +++   f++ k  ql     +s ++    + + +r++  +a++ +++     
  gi|386002124|ref|YP_005920423.1| 495 PRGVLLYGPPGTGKTLIARAVARETKAN---FISVKGPQL-----LSKWVGES-E-KAVREVFKKARQVSPAIIFFD 561
                                       499*******************988877...999999999.....44455555.3.555555555444333333333 PP

                            AAA_16 101 leealaavpelagaea.....srllellkrllallsrderplvl 139
                                        ++   a+++++g e+     +r+ ++l + l+ l++ ++ +v+
  gi|386002124|ref|YP_005920423.1| 562 ELD---AIAPMRGMEEgprtsERVVNQLLAELDGLETLKD-VVV 601
                                       333...3445666665666668888888888888888666.554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   2.4e-07   7.6e-05       1     135 [.     225     343 ..     225     345 .. 0.64
   2 !   24.5   0.0   6.8e-08   2.1e-05       1     134 [.     497     615 ..     497     618 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.4e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL G pGtgK+ +a+ la  +n++++ +++++ +++     + ++          ++ ++a+  +++i+++DE++
  gi|386002124|ref|YP_005920423.1| 225 GVLLHGSPGTGKTLIAKALANETNANFFSIAGPEVMSKYYGESEQRL---------REIFEEANrsTPSIIFIDELD 292
                                       59********************************9986543333333.........455555555889999999999 PP

                                       G--HH...HHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  76 raese...vlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                        + ++   v++++ +    + l +++g ++ +         + vi+++n+ d     ++palr
  gi|386002124|ref|YP_005920423.1| 293 SIAPKrgeVTGEVERRVVAQLLAMMDGLKERGQ--------VVVIGATNRID----AIDPALR 343
                                       887641113333333333333333333333322........77777777777....6666666 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.8e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ +a+ +a+ +++++  v +++      l+ ++   ++ ++ v  ++++a + +++i+++DE++ 
  gi|386002124|ref|YP_005920423.1| 497 GVLLYGPPGTGKTLIARAVARETKANFISVKGPQ------LLSKWV--GESEKAVREVFKKARQvSPAIIFFDELDA 565
                                       59*****************************998......888898..56667777777766669***********6 PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkakndd..llerfrviatanpldrslnelspal 134
                                       + +         +ee  +  e   ++  a+ d+   l+++ vi+++n++d     ++pal
  gi|386002124|ref|YP_005920423.1| 566 IAPMRG------MEEGPRTSERVVNQLLAELDGleTLKDVVVIGATNRPD----IIDPAL 615
                                       665444......44444444444444444444322334488888888888....556655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.3e-08   2.3e-05      34     103 ..     224     301 ..     214     349 .. 0.80
   2 !   21.5   0.0     5e-07   0.00016      36      69 ..     498     531 ..     490     570 .. 0.85
   3 ?   -0.5   0.0       2.9   9.2e+02      23      42 ..     611     630 ..     589     642 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.3e-08
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                         vll+G+PG Gkt +ak +a+e ++++ + +gP +      e ++ l  ++ + +++   ++fide+  ++++  e
  gi|386002124|ref|YP_005920423.1| 224 KGVLLHGSPGTGKTLIAKALANETNANFFSIAGPEVmskyygESEQRLREIFEEANRStpSIIFIDELDSIAPKRGE 300
                                       579*******************************8733333334566888887665432279*****9999887776 PP

                            RuvB_N 103 v 103
                                       v
  gi|386002124|ref|YP_005920423.1| 301 V 301
                                       6 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       vllyGpPG Gkt +a+ +a+e ++++ +  gP l
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISVKGPQL 531
                                       9*******************************87 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.9
                            RuvB_N  23 ieaakkreealdhvllyGpP 42 
                                       i+ a  r+   d +l++GpP
  gi|386002124|ref|YP_005920423.1| 611 IDPALLRSGRFDRLLFVGPP 630
                                       66677888888999999998 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.2e-07     7e-05       6     105 ..     226     319 ..     222     323 .. 0.85
   2 !   18.8   0.0   4.4e-06    0.0014       6     105 ..     498     592 ..     493     597 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.2e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll g+ g+Gkt++akala+  ++    ++  +   e++     + + ++++  ++   +a+ +   i+++DE+d i
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNA----NFFSIAGPEVMS----KYYGESEQRLREIFEEANRSTpsIIFIDELDSI 294
                                       578899****************96....999999999999....77777777777877777777799********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++ + +v r  V+  LL +++g
  gi|386002124|ref|YP_005920423.1| 295 APKrGEVTGEVERR-VVAQLLAMMDG 319
                                       **988888888886.66668888886 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.4e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++a+a+a+  ++    ++i +   +ll     + + ++++  ++  ++a +    i+++DE+d i
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKA----NFISVKGPQLLS----KWVGESEKAVREVFKKARQVSpaIIFFDELDAI 566
                                       6899****************9995....9**********9....66666666666777777776688********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +p  + ++    +e V++ LL  l+g
  gi|386002124|ref|YP_005920423.1| 567 APMrGMEEGPRTSERVVNQLLAELDG 592
                                       **975555556678888888876665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.2   1.3e+03     166     197 ..      28      59 ..      22      75 .. 0.81
   2 ?   -1.2   0.0       2.9     9e+02     159     185 ..     112     138 ..      78     146 .. 0.84
   3 !   17.1   0.0   7.7e-06    0.0024      51      97 ..     224     268 ..     220     302 .. 0.86
   4 !   19.7   0.0   1.3e-06    0.0004      51     106 ..     496     550 ..     489     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.2
                                       HHHHT--TT-EEEEETTT--EEE-SSS-SS-- CS
                             TIP49 166 llkekvkegDviviekesGkvkklGrsearak 197
                                       ll+ +++ gD+i ie ++ +  k+ r++ +  
  gi|386002124|ref|YP_005920423.1|  28 LLTLRLSPGDIIEIEGRRTSAAKVWRADRQDW 59 
                                       66778999*******99999999999887654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                                       -HHHHHHHHHHT--TT-EEEEETTT-- CS
                             TIP49 159 gskiaeellkekvkegDviviekesGk 185
                                       +++i  + lk+ + +gDv+ i ++sG+
  gi|386002124|ref|YP_005920423.1| 112 AEQIKRQTLKRPIVRGDVLPIMSSSGH 138
                                       678999999999**********99997 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 7.7e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl G +gtGkt +a a+++e +    f +++g ev s     +e
  gi|386002124|ref|YP_005920423.1| 224 KGVLLHGSPGTGKTLIAKALANETN--ANFFSIAGPEVMSKYYGESE 268
                                       89********************987..78*********997665555 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 1.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r+vLl Gp+gtGkt +a a+++e   +  f++++g ++ s  v  +e ++ + ++k+
  gi|386002124|ref|YP_005920423.1| 496 RGVLLYGPPGTGKTLIARAVARET--KANFISVKGPQLLSKWVGESEkAVREVFKKA 550
                                       89********************96..589************9999884567778877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00021     0.067       8      30 ..     226     248 ..     221     264 .. 0.80
   2 ?    6.5   0.0     0.029       9.3      71     131 ..     264     332 ..     246     338 .. 0.74
   3 !   16.2   0.0   3.1e-05    0.0098       8      51 ..     498     532 ..     493     603 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00021
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G +GtGKT+ ++ l+++ +
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETN 248
                                       689****************9974 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.029
                            AAA_22  71 erlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtp 131
                                       ++ s+++l+e +e+a r++    ++ iDE + +   +         +++ +L  +++  +   q++++G +
  gi|386002124|ref|YP_005920423.1| 264 YGESEQRLREIFEEANRSTPS--IIFIDELDSIApkRgevtgeveRRVVAQLLAMMDGLKERGQVVVIGAT 332
                                       467889999999999999988..**********87624455666677777777777766666777777766 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 3.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                       ++++G++GtGKT+ +r ++++          ++ +++v+ p++ 
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARET---------KANFISVKGPQLL 532
                                       689*****************99.........7777777766654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.1e-06   0.00096       2      47 ..     226     295 ..     226     360 .. 0.71
   2 !   16.0   0.0   3.2e-05      0.01       2      40 ..     498     538 ..     498     607 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.1e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt......................d 47 
                                       vll+G pG+GK+  a+ l++++   ++ ++ ++++++++g+ +q+++                       
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNanFFSIAGPEVMSKYYGESEQRLReifeeanrstpsiifideldsiA 295
                                       799****************999999999************888888755555555555555555555550 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgt 40 
                                       vll G+pG+GK+  a+ ++++++  ++ +  ++l+++ +g+
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKanFISVKGPQLLSKWVGE 538
                                       7899******************9767777777777666664 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.6e-05     0.005       5     103 ..     226     334 ..     223     354 .. 0.76
   2 !   13.6   0.0   0.00017     0.052       5      85 ..     498     585 ..     495     607 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G   +GKT ++k l++e      +++ i+  +   k + ++e+ l++i+e+++++  +++f+DE   +     
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETN---ANFFSIAGPEVMSKYYGESEQRLREIFEEANRSTPSIIFIDELDSIapkrg 299
                                       78999999***********8888...999999998888877777665566666665556899*******99988888 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSnsk 103
                                              +++   l  ++d  +++++v+v G  + 
  gi|386002124|ref|YP_005920423.1| 300 evtgeveRRVVAQLLAMMDgLKERGQVVVIGATNR 334
                                       88887776666666666664335678888887665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00017
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT +++ +++e      +++ ++  +   k   ++ek  +++++k+++    ++f+DE   +     
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETK---ANFISVKGPQLLSKWVGESEKAVREVFKKARQVSPAIIFFDELDAIapmrg 571
                                       7899***************9988...8888888888777777777767777777655557899*****988866666 PP

                            AAA_14  77 .....pewekalks 85 
                                            ++ e+++++
  gi|386002124|ref|YP_005920423.1| 572 meegpRTSERVVNQ 585
                                       65555455555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00019     0.059       1      25 [.     226     268 ..     226     330 .. 0.72
   2 !   15.5   0.0     6e-05     0.019       1      25 [.     498     540 ..     498     603 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00019
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G pG+GKt +ak+L++++ ++                  
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETnANffsiagpevmskyygesE 268
                                       7899**************9998322565555544444444443 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G+pG+GKt +a+++++++ ++                  
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETkANfisvkgpqllskwvgesE 540
                                       799***************9998444565555554544444443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.2e-05    0.0071       2      47 ..     226     276 ..     225     306 .. 0.79
   2 !    9.8   0.0    0.0028      0.89       2      23 ..     498     520 ..     497     578 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalp 47 
                                       + + G ++tGKT +++aLa++     +++  pE++ +++ e  ++ +++ +
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANEtnanFFSIAgPEVMSKYYGESEQRLREIFE 276
                                       6799***************65555345566899999888777666665554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0028
                            AAA_28   2 ivitGgestGKTtlleaLaar.g 23 
                                       + + G+++tGKT +++a a++ +
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVAREtK 520
                                       6799***************6542 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00049      0.15      48      72 ..     224     248 ..     218     261 .. 0.85
   2 !   13.2   0.0   0.00018     0.056      48      74 ..     496     522 ..     491     540 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00049
                         IstB_IS21  48 enivllGpsGvGKshlaialgveav 72 
                                       ++++l G +G+GK+ +a al+ e+ 
  gi|386002124|ref|YP_005920423.1| 224 KGVLLHGSPGTGKTLIAKALANETN 248
                                       6899*****************9875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00018
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavra 74 
                                        +++l Gp+G+GK+ +a a+++e+ ++
  gi|386002124|ref|YP_005920423.1| 496 RGVLLYGPPGTGKTLIARAVARETKAN 522
                                       5799****************9987655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00035      0.11      25      43 ..     226     244 ..     223     302 .. 0.88
   2 !   12.3   0.0   0.00025      0.08      25      42 ..     498     515 ..     492     522 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll G+pG+GKt++ak+l+
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALA 244
                                       79**************986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00025
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+GppG+GKt++a+++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAV 515
                                       89*************987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00027     0.083      31      62 ..     221     252 ..     212     295 .. 0.84
   2 !   11.8   0.0    0.0004      0.12      34      62 ..     496     523 ..     483     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkeky 62 
                                       +  k vll G+ GtGKt+i+k l ++ + + +
  gi|386002124|ref|YP_005920423.1| 221 EPPKGVLLHGSPGTGKTLIAKALANETNANFF 252
                                       55688*****************9999985544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0004
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkeky 62 
                                       + vll+Gp GtGKt+i++ + ++ +  ++
  gi|386002124|ref|YP_005920423.1| 496 RGVLLYGPPGTGKTLIARAVARETK-ANF 523
                                       679***************9999887.444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00022     0.069       2      30 ..     226     254 ..     225     269 .. 0.91
   2 !   10.7   0.0    0.0011      0.35       2      31 ..     498     527 ..     497     567 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00022
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktl++kala+  +++f  i
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFFSI 254
                                       89********************9999765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll g PG++ktl+++a+a+  +++f  ++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISVK 527
                                       7999******************99997765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00086      0.27      23      47 ..     224     248 ..     215     301 .. 0.90
   2 !   11.6   0.0   0.00052      0.16      23      54 ..     496     524 ..     481     536 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00086
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         vl++G  GtGK+l+a+a+ ++++
  gi|386002124|ref|YP_005920423.1| 224 KGVLLHGSPGTGKTLIAKALANETN 248
                                       569****************987665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00052
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfv 54 
                                         vl+ G  GtGK+l+ara+ +++k   ++f+
  gi|386002124|ref|YP_005920423.1| 496 RGVLLYGPPGTGKTLIARAVARETK---ANFI 524
                                       579****************987665...4455 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00055      0.17       1      26 [.     226     251 ..     226     292 .. 0.79
   2 !   11.8   0.0   0.00075      0.24       1      26 [.     498     523 ..     498     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00055
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++l+G++g+GK+++ak La++   ++
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANF 251
                                       689**************999988666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00075
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+++a+ +a++   ++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANF 523
                                       689**************999877555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00015     0.047      14      46 ..     221     251 ..     214     263 .. 0.87
   2 !    9.8   0.0    0.0014      0.44      16      50 ..     495     527 ..     485     533 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnv 46 
                                       e Pk +ll G+pG GK+ +a++l++e+  + n+
  gi|386002124|ref|YP_005920423.1| 221 EPPKGVLLHGSPGTGKTLIAKALANET--NANF 251
                                       56999********************98..5555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       P  +ll G pG GK+ +a+++++e+  + n++ ++
  gi|386002124|ref|YP_005920423.1| 495 PRGVLLYGPPGTGKTLIARAVARET--KANFISVK 527
                                       77899*******************9..88888876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.3e-05     0.017       4      58 ..     226     273 ..     223     306 .. 0.67
   2 !    9.0   0.0    0.0024      0.74       4      39 ..     498     526 ..     495     567 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekk 58 
                                       vl +G +GtGKt+++ +l++e        +a+++s  +p+v+ +++ + +++  ++
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANET-------NANFFSIAGPEVMsKYYGESEQRL-RE 273
                                       6889****************98.......555555555554425555555544.33 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsv 39 
                                       vl  G +GtGKt+++ +++ e        +a+++sv
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARET-------KANFISV 526
                                       6789***********9999887.......4444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0032         1       6      38 ..     218     250 ..     216     327 .. 0.80
   2 !   13.9   0.0   0.00018     0.058       8     102 ..     492     600 ..     489     606 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0032
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpt 38 
                                       l +++ + v + G+ G+GK+ ++k+la++++ +
  gi|386002124|ref|YP_005920423.1| 218 LGIEPPKGVLLHGSPGTGKTLIAKALANETNAN 250
                                       5677888899*****************998764 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00018
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.... RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.... 79 
                                       +++ + v + G+ G+GK+ +++++a+++k  +  i ++g +l ++   +++k ++ ++++  q+ p +   ++    
  gi|386002124|ref|YP_005920423.1| 492 IRPPRGVLLYGPPGTGKTLIARAVARETK--ANFISVKGPQLLSKWVGESEKAVREVFKKaRQVSPAIIFFDEldai 566
                                       556667899******************97..688999*999999999999999999999988999999877778999 PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGE CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvv 102
                                                  +s++ ++++l++l+  e+ ++vv
  gi|386002124|ref|YP_005920423.1| 567 apmrgmeegprTSERVVNQLLAELDGLETLKDVV 600
                                       9999999888877777999998888777766665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0021      0.67      15      38 ..     219     242 ..     212     251 .. 0.83
   2 ?    1.1   0.0      0.64     2e+02     110     154 ..     270     320 ..     254     335 .. 0.66
   3 !    9.7   0.0    0.0016       0.5      14      37 ..     490     513 ..     484     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   + vl+ G+pGtGKt++a+ 
  gi|386002124|ref|YP_005920423.1| 219 GIEPPKGVLLHGSPGTGKTLIAKA 242
                                       66777889************9975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                            ATPase 110 elaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                       +l+e+ +e +    + + iD ++++     e + +v R+ + ql+ ++ +l
  gi|386002124|ref|YP_005920423.1| 270 RLREIFEEANRstpSIIFIDELDSIapkRGEVTGEVERRVVAQLLAMMDGL 320
                                       555555555543335666665555532166777788999999999999544 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0016
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   r vl++G pGtGKt++a 
  gi|386002124|ref|YP_005920423.1| 490 MGIRPPRGVLLYGPPGTGKTLIAR 513
                                       58888999*************986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0017      0.54      20      51 ..     224     257 ..     196     271 .. 0.76
   2 !   11.2   0.0   0.00086      0.27      21      51 ..     497     529 ..     471     534 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0017
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G  G+GKT ++++la++ + +  ++  P
  gi|386002124|ref|YP_005920423.1| 224 KGVLLHGSPGTGKTLIAKALANETNANffSIAGP 257
                                       449******************9998766666555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00086
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        +lL+G+ G+GKT ++r++a++ + +  +vk P
  gi|386002124|ref|YP_005920423.1| 497 GVLLYGPPGTGKTLIARAVARETKANfiSVKGP 529
                                       499*******************99887777776 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00035      0.11      52     116 ..     222     291 ..     215     335 .. 0.74
   2 !    7.4   0.0    0.0071       2.2      53      82 ..     495     524 ..     482     566 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       p + vLL G+ GtGK  + kal ne++++   +   ev  +   e ++ ++++    +r++  i+f+D L
  gi|386002124|ref|YP_005920423.1| 222 PPKGVLLHGSPGTGKTLIAKALANETNANFFSIAgpEVMSKYYGESEQRLREIFeeaNRSTPSIIFIDEL 291
                                       55789**********************9996654337766655544443333331114455578888887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0071
                            DUF815  53 annvLLwGarGtGKSslvkallneyaeegL 82 
                                        + vLL+G  GtGK  + +a+ +e++++ +
  gi|386002124|ref|YP_005920423.1| 495 PRGVLLYGPPGTGKTLIARAVARETKANFI 524
                                       5679******************99988764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0052       1.6       5      26 ..     226     249 ..     223     301 .. 0.66
   2 !   10.8   0.0   0.00096       0.3       5      22 ..     498     515 ..     495     552 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0052
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkp 26 
                                       +l+ G++g+GKT +ak l  + ++
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALanETNA 249
                                       799*************99554443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00096
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g+GKT +a+  
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAV 515
                                       79***********99877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7     0.012       3.8      36     153 ..     226     334 ..     221     340 .. 0.54
   2 !   11.0   0.1   0.00074      0.23      36     147 ..     498     601 ..     470     607 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagve 112
                                       +ll G pgtGKt +a  la ++    +++       g+ ++    +     ++Rlr+++e++  +++  ++ +   +
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETN--ANFFS----IAGPEVMSKYYGES---EQRLREIFEEA-NRSTPSIIFI---D 289
                                       6899********99988887654..35655....34444444443333...45666666554.3445555544...2 PP

                            AAA_25 113 slpLfakdrggtl..l.tadvdaleaaieeveg.vrlvviDplsr 153
                                       +l+ +a++rg+ +  +  ++v++l a ++  ++  ++vvi   +r
  gi|386002124|ref|YP_005920423.1| 290 ELDSIAPKRGEVTgeVeRRVVAQLLAMMDGLKErGQVVVIGATNR 334
                                       234445555555543213344444444444433456666655555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00074
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv 111
                                       +ll+G+pgtGKt +a  +a ++    ++   +  p+    ++   E +  e+ +++r+v  a+ + ++l+++     
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETK--ANFISvK-GPQLLSKWVGESEKAVREVFKKARQVSPAIIFFDELDAI----- 566
                                       69***********9877776654..2333321.235555566666666555555555555555333333333..... PP

                            AAA_25 112 eslpLfakdrggtlltadvdaleaaieeveg.vrlvv 147
                                          p++ ++ g  + +++v++l a+++  e   ++vv
  gi|386002124|ref|YP_005920423.1| 567 --APMRGMEEGPRTSERVVNQLLAELDGLETlKDVVV 601
                                       ..34445555666667777777777776666444555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0093       2.9      19      42 ..     225     248 ..     211     286 .. 0.73
   2 !   11.1   0.0   0.00079      0.25      20      73 ..     498     549 ..     475     561 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0093
                            AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                        +l++G PGtgKT    +l ++ +
  gi|386002124|ref|YP_005920423.1| 225 GVLLHGSPGTGKTLIAKALANETN 248
                                       479**********98888888876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00079
                            AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAvDeller 73 
                                       +l+ GPPGtgKT    ++ ++     k +    ++p++L    ++S++Av e+ ++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARET----KANFISVKGPQLLskWVGESEKAVREVFKK 549
                                       799*********9999999988....333455555665522467777777777666 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0073       2.3      11      35 ..     224     248 ..     220     281 .. 0.79
   2 !    9.6   0.0    0.0035       1.1      12      36 ..     497     521 ..     491     568 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0073
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                       k +l+ + pGtGKT + k+  ++ +
  gi|386002124|ref|YP_005920423.1| 224 KGVLLHGSPGTGKTLIAKALANETN 248
                                       56899*********99988776655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0035
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallve 36 
                                        +l+ ++pGtGKT + +++ ++ ++
  gi|386002124|ref|YP_005920423.1| 497 GVLLYGPPGTGKTLIARAVARETKA 521
                                       5899*********999888777655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0035       1.1     117     137 ..     226     246 ..     220     250 .. 0.90
   2 !    9.4   0.0    0.0016       0.5     117     136 ..     498     517 ..     493     523 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v+++G++ tGkt +a+a+a+ 
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANE 246
                                       899***************985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt +a+a a+
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVAR 517
                                       89***************986 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0013       0.4       6      54 ..     230     281 ..     226     331 .. 0.77
   2 ?    7.1   0.0     0.017       5.3       8      55 ..     504     552 ..     500     593 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0013
                   Cytidylate_kin2   6 reyGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde..rs 54 
                                       ++ G+g++ i++aLA++ + +f++ + +e ++k  g se+ + e ++e  rs
  gi|386002124|ref|YP_005920423.1| 230 GSPGTGKTLIAKALANETNANFFSIAGPEVMSKYYGESEQRLrEIFEEanRS 281
                                       678***************************************7777774322 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde.rsr 55 
                                        G+g++ i++a+A + + +f++ + ++ ++k  g se+ v+ev + ++ 
  gi|386002124|ref|YP_005920423.1| 504 PGTGKTLIARAVARETKANFISVKGPQLLSKWVGESEKAVREVFKkARQ 552
                                       59*************************************9655442433 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0021      0.67      24      51 ..     226     251 ..     221     299 .. 0.59
   2 ?    7.7   0.0     0.011       3.6      24      47 ..     498     521 ..     493     571 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0021
                                       EEEEEETT--HHHHHHCC--TTS-EE-- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwlei 51 
                                       v+l G +G+gk+l+A++L+++   +   
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNAN--F 251
                                       99****************9987653..3 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l+Ar+ + +   
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKA 521
                                       9***************99876554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0052       1.6      21      45 ..     226     250 ..     216     340 .. 0.86
   2 !    9.1   0.0    0.0031      0.97      21      43 ..     498     520 ..     488     529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0052
                            AAA_30  21 avltGpAGtGKttalkalreaweaa 45 
                                       ++l+G +GtGKt + kal++  +a+
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNAN 250
                                       6899*************98766655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0031
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       ++l Gp+GtGKt + +a+++  +
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETK 520
                                       6789************9977655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0075       2.4      22      42 ..     226     246 ..     219     253 .. 0.85
   2 !    9.0   0.0    0.0028      0.87      22      41 ..     498     517 ..     492     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0075
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   G+ GtGKt++a ala e
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANE 246
                                       6778***********999865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVAR 517
                                       6679***********99985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0      0.01       3.3       3      23 ..     226     246 ..     224     252 .. 0.89
   2 !    7.8   0.0    0.0092       2.9       3      25 ..     498     520 ..     496     527 .. 0.88
   3 ?   -1.5   0.0       6.5   2.1e+03      57     113 ..     531     587 ..     529     596 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G +G GKT  ++ la +
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANE 246
                                       79**************99976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0092
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       v+l G++G GKT  ++ +a++ +
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETK 520
                                       899**************999876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 6.5
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..........HHHHH CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.kekqpvrtlLseli 113
                                       ll +   e++++v+ev++   ++   + + +D lD ++   g  ++++ ++++ ++l+
  gi|386002124|ref|YP_005920423.1| 531 LLSKWVGESEKAVREVFKKARQV-SPAIIFFDELDAIAPMRGMeEGPRTSERVVNQLL 587
                                       55666677888888866654444.4444669999999987776644555555555544 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00053      0.17      18      44 ..     420     446 ..     414     450 .. 0.89
   2 ?    4.3   0.0      0.13        41      28      45 ..     689     706 ..     682     713 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00053
                            Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                       dip++ l e +vt +Df++alk+  p+
  gi|386002124|ref|YP_005920423.1| 420 DIPEEVLEEMSVTADDFDDALKEIEPS 446
                                       7999999999*************9998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                            Vps4_C  28 pvtlkDflkalkkarptV 45 
                                       +v++++  +alk++rp+ 
  gi|386002124|ref|YP_005920423.1| 689 EVEMRHYREALKRVRPSF 706
                                       89**************96 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00079      0.25       2      31 ..     226     255 ..     225     317 .. 0.85
   2 ?    4.9   0.0     0.088        28       2      30 ..     498     526 ..     497     529 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00079
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                       +++hG+P +GKt +a +La + +a +++i 
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFFSIA 255
                                       689**********************99996 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.088
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt +a ++a++ +a ++++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISV 526
                                       5789*****************99999887 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0012      0.37       4      34 ..     226     256 ..     224     328 .. 0.90
   2 ?    5.3   0.0     0.051        16       4      37 ..     498     531 ..     496     560 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                       +lL+G++ +GK+ +a+al + +++ ++ ++ 
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFFSIAG 256
                                       89***********************999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.051
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDaf 37 
                                       +lL G + +GK+ +ara+   +++ ++ ++  ++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISVKGPQL 531
                                       89******************99999998876555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0038       1.2      23      48 ..     226     248 ..     211     282 .. 0.76
   2 ?    6.7   0.0     0.011       3.5      23      44 ..     498     519 ..     492     527 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
                                       EEEEESTTSSHHHHHHHHCCSHCCCC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdeve 48 
                                       v l+G +G GKt +ak   n+   ++
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANE---TN 248
                                       789************999888...33 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt +a+ + ++ 
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARET 519
                                       679**************99884 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.038        12      37      63 ..     226     252 ..     221     382 .. 0.69
   2 ?    3.3   0.0       0.2        62     154     211 ..     387     449 ..     380     456 .. 0.77
   3 ?    4.6   0.0     0.078        25      37      65 ..     498     526 ..     491     574 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                       ++++g+ G Gkt + ka++ne+ +n+ 
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFF 252
                                       79****************999877754 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                                       HHHSSEEEE-----HHHHHHHHHHHHHHTT--..--TTHHH...HHHHH--S-HHHHHHHHHH CS
                          Bac_DnaA 154 rfeaGlvvdieppdletrlailkkkieaekle..vpeevle...fiaervtdnvRelegalnr 211
                                       r +  + +di+   +e ++++l++++ + +++  +peevle     a+ ++d ++e+e +  r
  gi|386002124|ref|YP_005920423.1| 387 RTNGFVGADISALCKEAAMKVLRRHLPEISFDddIPEEVLEemsVTADDFDDALKEIEPSAMR 449
                                       5555566789999999***********9999889*****862225689999999999976554 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.078
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                                       +++yg+ G Gkt + +a++ e+++n+ + 
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISV 526
                                       79*****************9999887665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.055        17      34      60 ..     222     248 ..     198     260 .. 0.82
   2 ?   -0.4   0.0       2.1   6.6e+02     116     170 ..     279     339 ..     257     352 .. 0.60
   3 ?    6.6   0.0     0.015       4.7      35      61 ..     495     521 ..     469     531 .. 0.81
   4 ?   -1.4   0.0       4.2   1.3e+03     106     132 ..     541     567 ..     533     591 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.055
                              TniB  34 rmpnlllvGdsnnGKtmivekFarlhp 60 
                                        ++ +ll+G + +GKt i++  a++ +
  gi|386002124|ref|YP_005920423.1| 222 PPKGVLLHGSPGTGKTLIAKALANETN 248
                                       46789**************99887765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                              TniB 116 relkvrvLiiDEihnll..agsa..rkqreflnalksLgnelk..ipivlvGteealralr 170
                                       ++  + ++ iDE++++   +g++  +  r+++++l  +++ lk    +v++G ++ ++a++
  gi|386002124|ref|YP_005920423.1| 279 NRSTPSIIFIDELDSIApkRGEVtgEVERRVVAQLLAMMDGLKerGQVVVIGATNRIDAID 339
                                       4456789999**9999733333311445666666666666654114577777777777665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.015
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhpp 61 
                                       ++ +ll+G++ +GKt i++  ar+ ++
  gi|386002124|ref|YP_005920423.1| 495 PRGVLLYGPPGTGKTLIARAVARETKA 521
                                       3689**************999988765 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.2
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnll 132
                                       k+ ++v +  r++++ ++ +DE++ + 
  gi|386002124|ref|YP_005920423.1| 541 KAVREVFKKARQVSPAIIFFDELDAIA 567
                                       555667777789999*******99875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.057        18       2      26 ..     230     254 ..     229     298 .. 0.85
   2 !    8.8   0.0    0.0066       2.1       1      26 [.     501     526 ..     501     567 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.057
                                       E-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsa 26 
                                       G PG GK+ +++ l+ + +  ++s 
  gi|386002124|ref|YP_005920423.1| 230 GSPGTGKTLIAKALANETNANFFSI 254
                                       89***************99988874 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0066
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ ++++ +  ++s 
  gi|386002124|ref|YP_005920423.1| 501 YGPPGTGKTLIARAVARETKANFISV 526
                                       7***************9997777764 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.012       3.6       1      22 [.     232     253 ..     232     281 .. 0.81
   2 ?    6.6   0.0     0.025       7.8       1      22 [.     504     525 ..     504     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k+lA++ + +f+ 
  gi|386002124|ref|YP_005920423.1| 232 PGTGKTLIAKALANETNANFFS 253
                                       69****************9985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ +++++A++ + +fi 
  gi|386002124|ref|YP_005920423.1| 504 PGTGKTLIARAVARETKANFIS 525
                                       69*****************996 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.018       5.6      22      50 ..     221     249 ..     194     291 .. 0.80
   2 ?    6.9   0.0     0.019       5.9      23      73 ..     494     538 ..     464     575 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllk 50 
                                       +  k +l++   GtGKTl+a +l+ +   
  gi|386002124|ref|YP_005920423.1| 221 EPPKGVLLHGSPGTGKTLIAKALANETNA 249
                                       7778999*************988877665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.019
                                       TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHH CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtlee 73 
                                         + +l+  + GtGKTl+a +++++ + +      ++ v + +ll+++  e
  gi|386002124|ref|YP_005920423.1| 494 PPRGVLLYGPPGTGKTLIARAVARETKAN------FISVKGPQLLSKWVGE 538
                                       5567789999*********9999988875......3335666666666654 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.075        24      83     162 ..     248     329 ..     235     334 .. 0.66
   2 ?    4.6   0.0     0.084        27      23      44 ..     498     519 ..     488     528 .. 0.79
   3 ?    1.4   0.0      0.82   2.6e+02     107     133 ..     540     569 ..     519     605 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.075
                          ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqkli....dlglngaellvkeLlnliesltke 155
                                       + ++ + ++ e++++   + ++ + +++e+ +++ +  ii+iDel  +     +++ + ++ +v++Ll +++  +ke
  gi|386002124|ref|YP_005920423.1| 248 NANFFSIAGPEVMSKYYGESEQRLREIFEEANRS-TPSIIFIDELDSIApkrgEVTGEVERRVVAQLLAMMDG-LKE 322
                                       4455555556666666667788899999999888.44899****99886211145555788899999999988.455 PP

                          ATPase_2 156 khlcvvi 162
                                       +  +vvi
  gi|386002124|ref|YP_005920423.1| 323 RGQVVVI 329
                                       5555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.084
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       +++YGp g GKt + + ++ + 
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARET 519
                                       689*********8877776655 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.82
                          ATPase_2 107 elllekikkkgkk...iiiiiDelqklidl 133
                                       e++ +++ kk+++    ii++Del  +  +
  gi|386002124|ref|YP_005920423.1| 540 EKAVREVFKKARQvspAIIFFDELDAIAPM 569
                                       455556666666677678899***998744 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.23        74       5      28 ..     227     250 ..     224     255 .. 0.88
   2 !    9.8   0.0    0.0015      0.46       5      57 ..     499     551 ..     496     603 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.23
                               IPT   5 lifGatttGKtaeaiklaketgap 28 
                                       l++G+ +tGKt  a +la+et a 
  gi|386002124|ref|YP_005920423.1| 227 LLHGSPGTGKTLIAKALANETNAN 250
                                       789*****************9875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                               IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqcyselavgsGrpleeelegtr 57 
                                       l++G+ +tGKt  a ++a+et a  i++   q  s+    s +++ e +++ r
  gi|386002124|ref|YP_005920423.1| 499 LLYGPPGTGKTLIARAVARETKANFISVKGPQLLSKWVGESEKAVREVFKKAR 551
                                       89***********************9998877777776667666666666655 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0031      0.97      57      77 ..     227     247 ..     219     254 .. 0.87
   2 ?    3.3   0.0      0.26        82      56      77 ..     498     519 ..     463     527 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0031
                                       EEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenl 77 
                                        +hG +GtGk  +a+ +a+++
  gi|386002124|ref|YP_005920423.1| 227 LLHGSPGTGKTLIAKALANET 247
                                       58****************986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.26
                                       EEEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaenl 77 
                                       + ++G +GtGk  +a+ +a ++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARET 519
                                       5689************999765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.094        30       2      32 ..     226     256 ..     225     271 .. 0.83
   2 ?   -1.6   0.0       7.1   2.2e+03      81     104 ..     267     291 ..     257     314 .. 0.79
   3 ?    7.6   0.0     0.011       3.3       2      32 ..     498     528 ..     497     544 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.094
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ G+pG+GKt + k ++++ + + ++++G
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFFSIAG 256
                                       6789********9999999988777777776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.1
                                       HHHHHHHHHHHHH.HHH-EEEE--- CS
                          NTPase_1  81 feelalealrkal.seadviviDEi 104
                                        e+   e++++a+ s++ +i iDE 
  gi|386002124|ref|YP_005920423.1| 267 SEQRLREIFEEANrSTPSIIFIDEL 291
                                       566777778888767788*****96 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.011
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + + v+++ k + ++v+G
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKANFISVKG 528
                                       6788******************999999998 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.094        30       3      28 ..     228     253 ..     226     256 .. 0.89
   2 ?    7.5   0.0    0.0099       3.1       4      28 ..     501     525 ..     498     527 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.094
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + G  g+GK  +a+ala++ ++++++
  gi|386002124|ref|YP_005920423.1| 228 LHGSPGTGKTLIAKALANETNANFFS 253
                                       56888*****************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0099
                                       E-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                        GP g+GK  +ara+a++ ++++++
  gi|386002124|ref|YP_005920423.1| 501 YGPPGTGKTLIARAVARETKANFIS 525
                                       6******************999986 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.016       5.1       2      70 ..     227     290 ..     226     296 .. 0.64
   2 ?    5.1   0.0      0.05        16       5      70 ..     502     562 ..     498     567 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       + hG pG GK+ + + l+++     +n + + ++ + +  ++ + ++ r  + f++a+    +  i+++DE
  gi|386002124|ref|YP_005920423.1| 227 LLHGSPGTGKTLIAKALANE-----TNANFFSIAGPEVmsKYYGESEQRLREIFEEANRS--TPSIIFIDE 290
                                       68**********99999999.....44444555555446444455555544444444443..367788887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.05
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       G pG GK+ + r ++r+   ++ +++    ll++++ ++++   + ++++ +  +      i+++DE
  gi|386002124|ref|YP_005920423.1| 502 GPPGTGKTLIARAVARETkANFISVKG-PQLLSKWVGESEKAVREVFKKARQ-VS----PAIIFFDE 562
                                       78***************9977666666.89*****96666664444443333.33....35889998 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.024       7.7      18      66 ..     227     281 ..     224     324 .. 0.77
   2 ?    5.2   0.0     0.046        14      18      65 ..     499     552 ..     496     601 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.024
                                       EEEESTTSSHHHHHHHHHHHSSTS......SEEEEEEESEEHHHHHHHHHHCHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd......daiiyvgiGergnevaevleefpeg 66 
                                       l+ g  g+Gkt i+++l++++n++        +     Ge ++ ++e++ee +++
  gi|386002124|ref|YP_005920423.1| 227 LLHGSPGTGKTLIAKALANETNANffsiagPEVMSKYYGESEQRLREIFEEANRS 281
                                       678999**************99886655532455556888888888888887764 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.046
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE........ESEEHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg........iGergnevaevleefpe 65 
                                       l+ g  g+Gkt i+++++++++++   i v         +Ge ++ v+ev+++ ++
  gi|386002124|ref|YP_005920423.1| 499 LLYGPPGTGKTLIARAVARETKAN--FISVKgpqllskwVGESEKAVREVFKKARQ 552
                                       678999**************8666..333334555555599999999999988766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.46   1.4e+02      48      76 ..     226     254 ..     216     292 .. 0.74
   2 ?    7.6   0.0     0.011       3.3      46     112 ..     496     563 ..     485     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.46
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrew 76 
                                       +L+ G +G gk+ + k L+ e   ++   
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNANFFSI 254
                                       68899999999999999999987766555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkel 112
                                       r +L+ GP+G gk+ + + +++e   +++    p +l +     ++ ++ +++k  +  + i  f el
  gi|386002124|ref|YP_005920423.1| 496 RGVLLYGPPGTGKTLIARAVARETKANFISVKGPQLLSKWVGeSEKAVREVFKKARQVSPAIIFFDEL 563
                                       557999**********************9999999886544337778888888888888888888887 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.44   1.4e+02      20      45 ..     653     678 ..     641     686 .. 0.79
   2 ?    7.3   0.1     0.021       6.6       7      41 ..     685     719 ..     683     722 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.44
                            DUF234  20 vlekikeelneyvgkvFEelvrelll 45 
                                        le+++e  +++vg+  E+l+re+++
  gi|386002124|ref|YP_005920423.1| 653 SLEELAELTESFVGSDLESLCREAVM 678
                                       448888889**************987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.021
                            DUF234   7 pnrseielgeseevlekikeelneyvgkvFEelvr 41 
                                       p+ se+e++++ e+l++++++++e +g  +E++ +
  gi|386002124|ref|YP_005920423.1| 685 PEASEVEMRHYREALKRVRPSFEENMGRYYERINE 719
                                       67899**************************9976 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.5   7.9e+02      20      47 ..     223     250 ..     210     262 .. 0.86
   2 ?    5.7   0.0     0.023       7.4     168     196 ..     279     305 ..     257     312 .. 0.71
   3 ?   -0.7   0.0       2.1   6.8e+02     257     305 ..     397     446 ..     394     451 .. 0.86
   4 ?    0.2   0.0       1.1   3.6e+02      19      47 ..     494     522 ..     487     573 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.5
                        KAP_NTPase  20 pivvgLygkWGsGKssllnkledelkef 47 
                                       p  v L g  G+GK+ + + l +e + +
  gi|386002124|ref|YP_005920423.1| 223 PKGVLLHGSPGTGKTLIAKALANETNAN 250
                                       5568899999*******99999998865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.023
                        KAP_NTPase 168 LdalqkrlVvviDdLDrceteevlqllea 196
                                           +++ +++iD+LD++ +++   + e+
  gi|386002124|ref|YP_005920423.1| 279 N--RSTPSIIFIDELDSIAPKRGEVTGEV 305
                                       2..46999**********99987777666 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.1
                        KAP_NTPase 257 kkvlmea.veaseettesesrdetlgnsasksnlqlaldlskilltedfs 305
                                        ++++ea ++ ++++ ++ s d+++ ++++++ +++a+d+ + l+ +++s
  gi|386002124|ref|YP_005920423.1| 397 SALCKEAaMKVLRRHLPEISFDDDIPEEVLEEMSVTADDFDDALKEIEPS 446
                                       56788888***************************999999988877755 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.1
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledelkef 47 
                                       +p  v Lyg+ G+GK+ +   + +e k +
  gi|386002124|ref|YP_005920423.1| 494 PPRGVLLYGPPGTGKTLIARAVARETKAN 522
                                       55668899999999998888888887766 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.018       5.6       4      28 ..     226     258 ..     225     323 .. 0.66
   2 ?    2.8   0.0      0.21        67       4      28 ..     498     522 ..     497     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.018
                                       EEEE--TTSSHHHHHHHHHHHHHH........T CS
                             KTI12   4 vvltGlPssGKstrakeLakalee........e 28 
                                       v+l G P +GK+ +ak La++ ++        e
  gi|386002124|ref|YP_005920423.1| 226 VLLHGSPGTGKTLIAKALANETNAnffsiagpE 258
                                       799****************98877555555550 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                                       EEEE--TTSSHHHHHHHHHHHHHHT CS
                             KTI12   4 vvltGlPssGKstrakeLakaleee 28 
                                       v+l G P +GK+ +a+ +a++ +++
  gi|386002124|ref|YP_005920423.1| 498 VLLYGPPGTGKTLIARAVARETKAN 522
                                       899*************999987775 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.55   1.7e+02       4      31 ..     225     252 ..     223     259 .. 0.85
   2 ?    1.9   0.0       0.5   1.6e+02      74      94 ..     259     279 ..     245     292 .. 0.81
   3 ?    3.0   0.0      0.23        72       3      30 ..     496     523 ..     494     531 .. 0.88
   4 ?    0.1   0.0       1.7   5.5e+02      77      96 ..     534     553 ..     529     570 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.55
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                        v l g  g+Gk  + kaL +e + +f 
  gi|386002124|ref|YP_005920423.1| 225 GVLLHGSPGTGKTLIAKALANETNANFF 252
                                       68899**************999988883 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.5
                                       ETTEEEEEEHHHHHHHHHTTS CS
                     Guanylate_kin  74 fsgnlygtsveaieevlekgk 94 
                                       + +++yg+s +  +e++e++ 
  gi|386002124|ref|YP_005920423.1| 259 VMSKYYGESEQRLREIFEEAN 279
                                       7789*************9875 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.23
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r v l gp g+Gk  +  a+ +e + +f
  gi|386002124|ref|YP_005920423.1| 496 RGVLLYGPPGTGKTLIARAVARETKANF 523
                                       6789****************99999988 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.7
                                       EEEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                       +  g+s +a++ev++k+++v
  gi|386002124|ref|YP_005920423.1| 534 KWVGESEKAVREVFKKARQV 553
                                       56799************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.54
# Mc/sec: 4102.89
//
Query:       gi|386002125|ref|YP_005920424.1|  [L=83]
Description: PRC-barrel domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-13   50.8   0.0    1.4e-13   50.7   0.0    1.0  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   7.6e-18   1.4e-13       2      76 ..       2      80 ..       1      83 [] 0.94

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 7.6e-18
                                      EECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT..........-EEEEEGG.CEECCCTEEEETTS CS
                               PRC  2 defrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi.....gekevliPfdlavkigkdriivdap 75
                                        ++a++l Gke++t  G+ lG+++++++d+++gr+  l+v+     ++     ++k +l+Pf   v + kd+i+vd+ 
  gi|386002125|ref|YP_005920424.1|  2 PKIYARSLAGKEIVTMGGTVLGELENIILDPETGRLIDLLVKPDPEIDParyrrEGKLILVPFS-SVCALKDYIVVDEK 79
                                      579****************************************988777***************.************87 PP

                                      - CS
                               PRC 76 k 76
                                      +
  gi|386002125|ref|YP_005920424.1| 80 R 80
                                      6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 514.41
//
Query:       gi|386002126|ref|YP_005920425.1|  [L=219]
Description: peptidyl-prolyl cis-trans isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-48  164.9   0.1    2.1e-48  164.6   0.1    1.1  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   0.1   1.2e-52   2.1e-48       2     157 ..      72     216 ..      71     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 1.2e-52
                     Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipd 78 
                                       v +et+ +G+i+i+L +d  P+t++nF kl+ +gfYdg++FhRvi+gfm+qgGdp+g+++       gg   ++i+d
  gi|386002126|ref|YP_005920425.1|  72 VLLETN-MGEIKIRLRDDM-PVTAGNFEKLAADGFYDGVIFHRVIDGFMIQGGDPSGTGR-------GG-PGYTIKD 138
                                       6789*7.********9998.**********************************999865.......33.2469*** PP

                     Pro_isomerase  79 EitsklkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde.erpkknvkiv 154
                                       E++ + +++rG+++ma++g  pn++gsqFfI+l +++ ld+ + vFG+Vv Gmdvv+ i +v+t   +rp+k+v+iv
  gi|386002126|ref|YP_005920425.1| 139 EFAARNRNDRGTISMANAG--PNTGGSQFFINLVDNNRLDRMHPVFGEVVGGMDVVDMIGRVKTGPgDRPTKDVVIV 213
                                       **988899*********98..8*******************************************9**********9 PP

                     Pro_isomerase 155 sae 157
                                       +a+
  gi|386002126|ref|YP_005920425.1| 214 RAR 216
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1637.71
//
Query:       gi|386002127|ref|YP_005920426.1|  [L=704]
Description: Oligosaccharyl transferase, STT3 subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-23   81.7  13.7    1.1e-22   80.6  13.7    1.4  1  STT3      Oligosaccharyl transferase STT3 subunit
      3e-11   43.5   0.0    5.6e-11   42.6   0.0    1.4  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
    2.2e-10   41.0  12.3    2.2e-10   41.0  12.3    3.1  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6  13.7   1.9e-26   1.1e-22      29     486 ..      32     506 ..      25     508 .. 0.75

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.9e-26
                                       S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC.HHHHHHHH CS
                              STT3  29 ylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld.vsirevcl 104
                                        ++ +D++Y  R + +++++       ++ + wfd+s  yP G  + ++pl     ++ +a++  + +  s+  v+ 
  gi|386002127|ref|YP_005920426.1|  32 LFYGSDSFYHMRRILYTVDH-------FPSTLWFDPSINYPEGLELLWPPLFDQA-VAGAALLLGAGSpRSVEMVAA 100
                                       57889********9999999.......8***********************9887.666666666666688889999 PP

                                       CCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTC CS
                              STT3 105 wlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnki 181
                                       + p++lgsL+ I +y+l+rel++++a+ll+All ai P  +s ++    D++++e ++l++ +f+++ a+k++++  
  gi|386002127|ref|YP_005920426.1| 101 VAPPILGSLTIISVYLLARELFGPRAALLSALLFAINPQHVSISIFARPDHHVLETFILVSFVFLLVLALKRGDGWP 177
                                       99************************************************************************888 PP

                                       HHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHH.HHCTTT..........S-CCHHHHH................. CS
                              STT3 182 slaviaaliiflivlaWggyailiyallllfila.lLiigr..........felklkiav................. 230
                                        + ++a+++ + + ++W g a  + a+l++ i+a +L   r          f                         
  gi|386002127|ref|YP_005920426.1| 178 WPGAAAGVSAAALAYTWIGAAAYFGAFLAFVIIAaTLDLRRgvssrpclqvF-------Llvfgvalvlalpfwwvg 247
                                       8899***************976666666555444044444476666644431.......033444445555666655 PP

                                       ....HHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHHTT..HHHHT CS
                              STT3 231 ....tfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfislfqpgi.lsevl 302
                                            f+ ++a+lv  + +l++ g  + +    i++     ll  +++ s  +l  +l+++    l++ gi ++  +
  gi|386002127|ref|YP_005920426.1| 248 wmapSFFALAAVLVTTAALLPLTGAFSRRGVPWIALPPLLLLLGYLLLSSAFALEGWLGVQR---LLDEGIdYFFGG 321
                                       65554444444444444444444333333333333333333333333333333323333333...555553134444 PP

                                       T--GGGHHHHHHHHHHHHCCCCCCTS---.....--TTHHHHHH.HHHS---S--CCHHHCCSSST.TTTCCCHHHC CS
                              STT3 303 gligevvtalavlglialwlgilyslldl.....eyaklkikii.ilvsvwlpvgllaltkglrfl.iftvPlgiif 372
                                       +l+ +v  a+ + g++ +++++ ++l        ++  ++i  +  l  vw +  ll++++  rfl +f++ +++  
  gi|386002127|ref|YP_005920426.1| 322 ALSWQVAEAVPLYGVVRPFTVVGFNLTAAvlgfaHLWRSDIDRLqLLFLVWTVSLLLLAVFQNRFLyVFSASMAVLM 398
                                       55588888888888888887666666666666665556666544145678999889999****************** PP

                                       HHCCHHCTCHHHHHHHHHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCT.TT CS
                              STT3 373 vgllleflavfvkiysvsqilfsgvvvillmltllpvlallaavkiskifstykdekeakikvaakavaptksnglk 449
                                       + ++l+ + +++++     +l   ++++ l  +ll+ l l +av +s++fs   + +e+ +          +++ + 
  gi|386002127|ref|YP_005920426.1| 399 ALFFLRAATLLSDGGW---RLGDRRISRYLNPLLLILLLLPSAVSVSEVFSIRPAVVESGWDRPL---QWLEERSAD 469
                                       *************988...66777777777789999999*******************9999722...345666667 PP

                                       TTHHHTTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              STT3 450 eslewkantnrdsvvitwwdyghilaveadrpVtfdg 486
                                        s  w   t   + v twwd g  + + +  pV+++g
  gi|386002127|ref|YP_005920426.1| 470 SSAPWEGDTAAGAGVLTWWDRGNWVLYLSGWPVVANG 506
                                       77777*****************************998 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   9.4e-15   5.6e-11       1      59 [.     619     674 ..     619     700 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 9.4e-15
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-S CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetn 59 
                                       GA+i+G ++ +  vt+s++l+tnqgr  +Y+++    +dG++e++vPYst +  dg  +
  gi|386002127|ref|YP_005920426.1| 619 GARIRGACPGDGPVTLSLNLTTNQGRPLNYTRSG-LPRDGRYEMVVPYSTGR--DGGLA 674
                                       9********************************9.6**************95..44333 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0  12.3   3.7e-14   2.2e-10      20     158 ..      95     245 ..      73     246 .. 0.73
   2 ?   -1.6   1.6      0.45   2.7e+03      52      91 ..     257     296 ..     251     305 .. 0.74
   3 !    5.1   4.3    0.0041        24      54     114 ..     343     401 ..     325     438 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.7e-14
                             PMT_2  20 selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpd..aplvllwalalylllrale 94 
                                        e+++ +++ ++g+lti+ +yllar+lfg+raall+all a+ p+ v +s   +pd  ++ ++ ++ +++ll+ al+
  gi|386002127|ref|YP_005920426.1|  95 VEMVAAVAPPILGSLTIISVYLLARELFGPRAALLSALLFAINPQHVSISIFARPDhhVLETFILVSFVFLLVLALK 171
                                       467777888899***************************************99997336667888888899999999 PP

                             PMT_2  95 knk.lkyw..llagvlfGlgflsKytaallliaallyllis....arr.ilke...kkpylalllalllfspvli 158
                                       ++  +  w  ++agv++++  ++   aa +  a+l++++i      rr +      ++++l+  +al+l++p+++
  gi|386002127|ref|YP_005920426.1| 172 RGDgW-PWpgAAAGVSAAALAYTWIGAAAYFGAFLAFVIIAatldLRRgVSSRpclQVFLLVFGVALVLALPFWW 245
                                       99944.554667777777777777777777777888777776776555233333434444455566666666554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                             PMT_2  52 allaalllavvplfvalsalftpdaplvllwalalylllr 91 
                                       a++ +  +a++pl +a s+ + p ++l +l++l+ ylll 
  gi|386002127|ref|YP_005920426.1| 257 AAVLVTTAALLPLTGAFSRRGVPWIALPPLLLLLGYLLLS 296
                                       3444445666888888888999888888888888888875 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0041
                             PMT_2  54 laalllavvplfvalsalftpdaplvllwalalylllraleknklkywllagvlfGlgfls 114
                                       ++  l+a+v+ f+ l     +d +++l++++++ lll a+ +n++  +++++ +++l+ l+
  gi|386002127|ref|YP_005920426.1| 343 VGFNLTAAVLGFAHLW-RSDIDRLQLLFLVWTVSLLLLAVFQNRF-LYVFSASMAVLMALF 401
                                       5555566666444444.4789***********************7.777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4642.11
//
Query:       gi|386002128|ref|YP_005920427.1|  [L=361]
Description: hypothetical protein Mhar_1440 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   15.1   0.0        1.6    8.8   0.0    2.5  2  BsuPI     Intracellular proteinase inhibitor


Domain annotation for each model (and alignments):
>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0038        68      63      96 ..      68     102 ..      65     106 .. 0.85
   2 ?    8.8   0.0   8.8e-05       1.6      69      98 ..     273     302 ..     267     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0038
                                       -EEEEE-TT-EEEEEEEE..S---SEEEEEEEEE- CS
                             BsuPI  63 lssetlepgesatyeetwd.edlepGeYtleaelv 96 
                                       ++++tl+ +   t+ +twd +  e G+Yt+ a l+
  gi|386002128|ref|YP_005920427.1|  68 IQTKTLDLDGPGTWVATWDvGGAEDGSYTACAKLI 102
                                       5778888888899******9999******998876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 8.8e-05
                                       -TT-EEEEEEEE.S---SEEEEEEEEE--E CS
                             BsuPI  69 epgesatyeetwdedlepGeYtleaelvae 98 
                                        +g+  t+e +w+++lepG Y+l+++l ++
  gi|386002128|ref|YP_005920427.1| 273 LAGDDETVEISWNGTLEPGIYRLTIQLLGN 302
                                       58999*******************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2529.66
//
Query:       gi|386002129|ref|YP_005920428.1|  [L=248]
Description: 5-carboxymethyl-2-hydroxymuconate delta-isomerase [Methanosaeta harundinacea 6Ac]
Scores for 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-67  225.0   0.0      1e-66  224.7   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.7   0.0   5.7e-71     1e-66       1     218 []      43     237 ..      43     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 224.7 bits;  conditional E-value: 5.7e-71
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       k+vc+glny  h++e++   ++ p      ep++flk++++++gpg++i++P +s ++dyE+E+avvig+++r+v  
  gi|386002129|ref|YP_005920428.1|  43 KVVCVGLNYLLHAKELK---MDLPT-----EPIIFLKPPTAVIGPGADIVMPPSSSQVDYEGEVAVVIGRRCRDV-R 110
                                       689************97...66777.....888******************************************.8 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntk 154
                                       + eAe++i+Gy  +nDv+aRdlq+++    +w+++ksfdtf+p+Gp +v +    dp++l++++rvng ++q+snt+
  gi|386002129|ref|YP_005920428.1| 111 AFEAEEYILGYSNFNDVTARDLQRRDG---QWTRAKSFDTFAPLGPYVVEA----DPSSLAIETRVNGRVRQSSNTS 180
                                       99*************************...******************984....5679****************** PP

                                       GTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 155 dmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       d+ifs++el++ +s ++tL pGd+i+tGTp+gvg        l +gD veve+eglG+lrn+V+
  gi|386002129|ref|YP_005920428.1| 181 DLIFSIPELVEFISGIMTLLPGDVIATGTPPGVG-------SLSAGDLVEVEVEGLGTLRNPVV 237
                                       ********************************99.......4*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1762.34
//
Query:       gi|386002130|ref|YP_005920429.1|  [L=256]
Description: Oxidoreductase FAD/NAD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-11   41.8   6.5    7.3e-11   41.7   1.7    2.5  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    4.5e-05   24.1   0.1     0.0019   18.8   0.1    2.2  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.092   13.1   0.7       0.19   12.1   0.7    1.5  1  Prokineticin     Prokineticin
       0.18   11.8   1.1       0.41   10.7   1.1    1.5  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.04   1.8e+02       1      13 [.     179     191 ..     179     196 .. 0.92
   2 !   41.7   1.7   1.6e-14   7.3e-11       2      41 ..     202     235 ..     201     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.04
                                       ----SSSSSSS-T CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClg 13 
                                       e +Ma+ +G C g
  gi|386002130|ref|YP_005920429.1| 179 EPMMADVIGRCAG 191
                                       789********86 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.6e-14
                                       ---SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   2 erMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       ++ +CG+G+C++C ++ +g       rvC++GPvF+ad++
  gi|386002130|ref|YP_005920429.1| 202 RYFKCGMGICGSCSLDPSG------IRVCVEGPVFRADRL 235
                                       789**************75......8***********987 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   4.2e-07    0.0019       1     107 [.      95     185 ..      95     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.2e-07
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSH CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrv 77 
                                       +++gG+G aP+  + +a++e+     +v+ + + r  +dll+ +++e++     g+  v+++    ++g+ g  gr 
  gi|386002130|ref|YP_005920429.1|  95 LVGGGVGAAPLALLGEAAAEA---GIEVTTLLASRCCDDLLFLKRFERI-----GE-VVITT----DDGSLGICGRA 158
                                       79********99888888886...79***********************.....53.34444....45555567777 PP

                                       HHHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  78 qdalleellslkkeethvyvCGppgMikav 107
                                       ++ l   +l+  +e +++y+CGp++M+++v
  gi|386002130|ref|YP_005920429.1| 159 SAGL--SALQ-LQEFDQIYLCGPEPMMADV 185
                                       7777..3334.37999***********987 PP

>> Prokineticin  Prokineticin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   4.2e-05      0.19      20      51 ..     194     225 ..     180     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                      Prokineticin  20 avitGacdkdvqcGaglccavslwvrslrlct 51 
                                       + i  + d+  +cG+g+c + sl   ++r+c+
  gi|386002130|ref|YP_005920429.1| 194 TKIQASIDRYFKCGMGICGSCSLDPSGIRVCV 225
                                       5578889************************7 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   9.1e-05      0.41      40      63 ..     194     217 ..     174     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                            Fer2_3  40 eevdptlafrasCregiCGscava 63 
                                       ++++ ++  + +C+ giCGsc++ 
  gi|386002130|ref|YP_005920429.1| 194 TKIQASIDRYFKCGMGICGSCSLD 217
                                       66778888889**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1728.66
//
Query:       gi|386002131|ref|YP_005920430.1|  [L=329]
Description: Dihydroorotate oxidase B, catalytic subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-55  186.6   0.2    6.8e-55  186.3   0.2    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    1.7e-07   31.0   4.4    2.8e-07   30.3   4.4    1.4  1  NMO           Nitronate monooxygenase
    2.6e-07   30.0   2.2     0.0027   16.9   0.2    2.1  2  Dus           Dihydrouridine synthase (Dus)
     0.0013   18.3   0.3     0.0039   16.7   0.1    1.8  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.014   14.5   1.0      0.028   13.4   1.0    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.022   14.1   0.3      0.041   13.2   0.3    1.5  1  TMP-TENI      Thiamine monophosphate synthase
       0.25   10.5   2.3       0.33   10.1   0.5    2.0  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
       0.26   10.4   1.8        0.2   10.8   0.2    1.5  2  DUF561        Protein of unknown function (DUF561)
       0.62    9.3   5.7       0.64    9.3   3.0    2.1  2  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3   0.2   3.4e-58   6.8e-55       2     294 ..      32     310 ..      31     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 3.4e-58
                                       G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-H CS
                            DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGl 77 
                                       l+ +v g++ + p++lAaG+ + + + l+  +l  +ga+ ++sv+  p+eG+  P+v++++ +  +lN++Gl+n+  
  gi|386002131|ref|YP_005920430.1|  32 LSGEVGGIRMESPVMLAAGILGTTGASLRRAALAgAGAVVTKSVGVAPREGHRGPTVVQVEGG--LLNAMGLPNPSY 106
                                       66788999********************9999988****************************..************ PP

                                       HHHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCC.TSCCCGCHHHHHHHH CS
                            DHO_dh  78 davlekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntp.glrdlqekeelkail 153
                                        +  e++   r        +++++s+ ++    ++++vev+  ++  ad +elN+S+P++   +++++ +    +++
  gi|386002131|ref|YP_005920430.1| 107 RNFQEEIDIGRGG-----GAPVVASIFGAG---AEEFVEVATGLD--ADGFELNLSCPHAErLGAEIGCEACNVEAI 173
                                       ******9999866.....579********9...********9886..9*************8677888777777778 PP

                                       HHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHH CS
                            DHO_dh 154 lkvvkevskvpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdi 229
                                       +++vke  +vpv+vKl+P+++d +    a++   ++++ +i+    t++ +aid++s  ++  n++GGlsG+a+k++
  gi|386002131|ref|YP_005920430.1| 174 TRAVKEEVNVPVWVKLTPNVADVVGLGLAAERGgADGVVAIN----TLRAMAIDVESGMPILGNRFGGLSGPAIKPV 246
                                       888888888*******************99998788888888....899999************************* PP

                                       HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH.HHGTCHHHHHHHHHHHH CS
                            DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv.fegpkiakkikkeleel 294
                                       a++ +++l++ l+  ip+IgvGGi s eDa e+++aGA  vqv+tal   eg+ +++ i  +l + 
  gi|386002131|ref|YP_005920430.1| 247 AVRCVYDLASALE--IPVIGVGGIASWEDAAEMMMAGARGVQVGTALGmVEGYGVFRSIAAGLSAY 310
                                       *************..*******************************96268999999999999876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   4.4   1.4e-10   2.8e-07     141     225 ..     212     291 ..     137     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.4e-10
                               NMO 141 ptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAs 217
                                       + i +  ++ +  ++G+ +    G   GG  G p+++    ++ v   ++a++iPvi  GGi   ++ a ++ +GA 
  gi|386002131|ref|YP_005920430.1| 212 VAINTLRAMAIDVESGMPI---LGNRFGGLSG-PAIK-PVAVRCVYDLASALEIPVIGVGGIASWEDAAEMMMAGAR 283
                                       4445555555555555544...59999*****.6664.568999999****************************** PP

                               NMO 218 gvqigtrf 225
                                       gvq+gt++
  gi|386002131|ref|YP_005920430.1| 284 GVQVGTAL 291
                                       ******97 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1     2e-05      0.04      70     129 ..     134     189 ..     121     212 .. 0.85
   2 !   16.9   0.2   1.4e-06    0.0027     173     214 ..     249     289 ..     242     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                       HHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEE CS
                               Dus  70 eaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvki 129
                                       e+++++  l+ad+ +lN+ CP  +  + ++G+    ++  v+ i +av++ v++Pv vk 
  gi|386002131|ref|YP_005920430.1| 134 EFVEVATGLDADGFELNLSCPHAERLGAEIGC----EACNVEAITRAVKEEVNVPVWVKL 189
                                       67777888999***********9999888888....677899***************997 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESC CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigr 214
                                       + ++++  a++ipvi+ G+I ++eda +++   Ga gv +g 
  gi|386002131|ref|YP_005920430.1| 249 RCVYDLASALEIPVIGVGGIASWEDAAEMMMA-GARGVQVGT 289
                                       568999************************99.*****9996 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.82   1.6e+03      61     194 ..     169     185 ..     159     188 .. 0.52
   2 !   16.7   0.1   1.9e-06    0.0039      63     223 ..     249     291 ..     235     302 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.82
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEE CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykva 137
                                       n +++                                                                        
  gi|386002131|ref|YP_005920430.1| 169 NVEAI------------------------------------------------------------------------ 173
                                       44444........................................................................ PP

                                       ETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEE CS
                      His_biosynth 138 ikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipv 194
                                                                                    t++++e+v++pv
  gi|386002131|ref|YP_005920430.1| 174 ---------------------------------------------TRAVKEEVNVPV 185
                                       .............................................444444444444 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEET CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaik 139
                                        +v                                                                          
  gi|386002131|ref|YP_005920430.1| 249 RCVYD------------------------------------------------------------------------ 253
                                       34444........................................................................ PP

                                       TTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSE CS
                      His_biosynth 140 gwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvda 216
                                                                                     la+a++ipvi  GG++s ed +e+  +g+++
  gi|386002131|ref|YP_005920430.1| 254 ----------------------------------------------LASALEIPVIGVGGIASWEDAAEMMMAGARG 284
                                       ..............................................5555566666666666666666666666666 PP

                                       EEESHHH CS
                      His_biosynth 217 vivgsal 223
                                       v vg+al
  gi|386002131|ref|YP_005920430.1| 285 VQVGTAL 291
                                       6666555 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.0   1.4e-05     0.028     195     241 ..     247     293 ..     233     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllag 241
                                       Av  v++ a+  ++pvi  GGi + +d +  + aGa  v +G  l  
  gi|386002131|ref|YP_005920430.1| 247 AVRCVYDLASALEIPVIGVGGIASWEDAAEMMMAGARGVQVGTALGM 293
                                       788899999*********************************99965 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   2.1e-05     0.041     135     180 ..     244     290 ..     230     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGit.lenvaevleagadgvavvsa 180
                                       +p+ +  + +la+aleiPv+ +GGi   e++ae++ aga+gv v +a
  gi|386002131|ref|YP_005920430.1| 244 KPVAVRCVYDLASALEIPVIGVGGIAsWEDAAEMMMAGARGVQVGTA 290
                                       77888888999**************6379*************98766 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   2.5e+03      14      35 ..     163     185 ..     155     188 .. 0.64
   2 ?   -0.3   0.0      0.25     5e+02       4      37 ..     199     232 ..     196     234 .. 0.72
   3 ?   10.1   0.5   0.00016      0.33     111     177 ..     226     292 ..     212     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                       SEEEEESHHHH.HHHHTT--S-E CS
                              NanE  14 vgiriegvedi.kaikavvdlPi 35 
                                       +g  +  ve i +a+k++v++P+
  gi|386002131|ref|YP_005920430.1| 163 IGCEACNVEAItRAVKEEVNVPV 185
                                       55555566666247888888886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.25
                                       HHHHHHHHT-SEEEE.ESHHHHHHHHTT--S-EEE CS
                              NanE   4 makaaeqaGavgiri.egvedikaikavvdlPiiG 37 
                                       + +aae +Ga g+ + ++++   ai  +  +Pi+G
  gi|386002131|ref|YP_005920430.1| 199 LGLAAERGGADGVVAiNTLR-AMAIDVESGMPILG 232
                                       5689******9986514444.45677888889887 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00016
                                       TT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 111 lGvdivGttlsGytkeeekaepDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsait 177
                                        G+ i+G  + G  + + k    ++ v +l +a ++ vi  G i + e a++++  G+  v vG+a+ 
  gi|386002131|ref|YP_005920430.1| 226 SGMPILGNRFGGLSGPAIKPV-AVRCVYDLASAlEIPVIGVGGIASWEDAAEMMMAGARGVQVGTALG 292
                                       567777777777766666543.356677776654799*****************************96 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       3.3   6.5e+03      52      66 ..     173     187 ..     168     188 .. 0.68
   2 ?   10.8   0.2   9.9e-05       0.2     174     217 ..     247     291 ..     241     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.3
                            DUF561  52 lvkkvksvsniPiCv 66 
                                       + + vk+ +n+P+ v
  gi|386002131|ref|YP_005920430.1| 173 ITRAVKEEVNVPVWV 187
                                       556677777777755 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.9e-05
                            DUF561 174 tlastyeiskkvslPvicasGlsdvtvpl.alslgasGiGigsav 217
                                       ++ ++y +++++++Pvi   G+++       + +ga G+ +g a+
  gi|386002131|ref|YP_005920430.1| 247 AVRCVYDLASALEIPVIGVGGIASWEDAAeMMMAGARGVQVGTAL 291
                                       5779******************997644414678*******9886 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.21   4.2e+02     151     182 ..     159     189 ..     150     228 .. 0.57
   2 ?    9.3   3.0   0.00032      0.64     169     209 ..     253     293 ..     208     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                                       BSSSTTS----S-HHHHHHHHHH-SS-BEEES CS
                              ThiG 151 laapiGsglGllnkealkiiieeakvPvivDA 182
                                       l+a iG     + ++  + + ee++vPv v  
  gi|386002131|ref|YP_005920430.1| 159 LGAEIGCEAC-NVEAITRAVKEEVNVPVWVKL 189
                                       4444554432.223344677888899987754 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00032
                                       HHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                              ThiG 169 iiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                                        + + +++Pvi   Gi s +daa+ m  Ga +v + ta+ +
  gi|386002131|ref|YP_005920430.1| 253 DLASALEIPVIGVGGIASWEDAAEMMMAGARGVQVGTALGM 293
                                       3455679*******************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2055.05
//
Query:       gi|386002132|ref|YP_005920431.1|  [L=475]
Description: hypothetical protein Mhar_1444 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.3   3.4    0.00023   21.0   0.4    2.3  2  DUF4573   Domain of unknown function (DUF4573)
  ------ inclusion threshold ------
       0.17   12.3   0.0        1.1    9.8   0.0    2.0  2  Rimk_N    RimK PreATP-grasp domain


Domain annotation for each model (and alignments):
>> DUF4573  Domain of unknown function (DUF4573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.39   3.5e+03     138     167 ..     156     187 ..     147     191 .. 0.59
   2 !   21.0   0.4   2.6e-08   0.00023       1     117 [.     325     439 ..     325     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.39
                           DUF4573 138 ePlegsqevep..aeevqlieplgeveqiqpl 167
                                       eP +gs++ +   aee   +ep+ e  +  +l
  gi|386002132|ref|YP_005920431.1| 156 EPMKGSRSGHLigAEEEPQMEPSAEMTNGSLL 187
                                       45666665554224555556666665555555 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.6e-08
                           DUF4573   1 aidpsrpteeiqPlkgvkeieppqpggkdd..plgaeekkkdlravteveplkgvaeieplkavseiqPlravserd 75 
                                       +i+p +p  +++P k+v ++ p +p+ + +  p++  +++   +av+  ++l g+ e+ p       +Pl  v +  
  gi|386002132|ref|YP_005920431.1| 325 NINPAKPKVNVNPTKPVVNVSPGKPAIEVEaaPPNETGNET-DGAVSYYDSLEGREETGPFSSSGGSEPLVLVNQTA 400
                                       58999********************9887622455555544.59*****************************9988 PP

                           DUF4573  76 plgaveeieppraasemkPlktaeniepleaarelePeeavg 117
                                       p      i+p  +   ++  +++  i+p+ +++ ++++ea g
  gi|386002132|ref|YP_005920431.1| 401 PV---TLINPTGTITIVNSTGEVTLIDPSLPVKVINSSEAEG 439
                                       75...559999999999999*************999999976 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00012       1.1      23      59 ..      26      62 ..      23      67 .. 0.89
   2 ?   -0.6   0.0       0.2   1.8e+03      32      51 ..     317     336 ..     309     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                            Rimk_N 23 ekrghevevldplrcylkieaekpevyykgekleefd 59
                                      e+rg  + v+d + +++ +e+++p+++y+ e+++  d
  gi|386002132|ref|YP_005920431.1| 26 EARGTVIAVIDGKTFEIMMERSDPRIIYNVERVTLAD 62
                                      89***************************99887766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
                            Rimk_N  32 ldplrcylkieaekpevyyk 51 
                                       ++++r++++i+ +kp+v ++
  gi|386002132|ref|YP_005920431.1| 317 VNISRLSVNINPAKPKVNVN 336
                                       68899999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3417.47
//
Query:       gi|386002133|ref|YP_005920432.1|  [L=418]
Description: ATP-dependent RNA helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-49  167.5   0.0      1e-48  165.4   0.0    1.8  2  DEAD        DEAD/DEAH box helicase
    1.1e-32  112.6   0.0    3.6e-32  111.0   0.1    1.8  2  Helicase_C  Helicase conserved C-terminal domain
    3.1e-06   27.3   0.0    5.3e-06   26.5   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
    2.2e-05   24.3   0.8    0.00078   19.2   0.0    2.8  3  AAA_30      AAA domain
    0.00034   21.0   0.0      0.065   13.6   0.0    2.2  2  AAA_19      AAA domain
  ------ inclusion threshold ------
      0.073   13.3   0.1       0.23   11.7   0.1    1.9  1  AAA_22      AAA domain
       0.12   12.3   0.0       0.35   10.8   0.0    1.8  1  Flavi_DEAD  Flavivirus DEAD domain
       0.13   11.0   0.0        0.6    8.8   0.0    2.0  3  UTP25       Utp25, U3 small nucleolar RNA-associated SSU proc


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.0   4.5e-52     1e-48       1     174 [.      25     194 ..      25     196 .. 0.96
   2 ?   -0.6   0.0      0.44   9.8e+02      65     104 ..     258     301 ..     238     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 4.5e-52
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyi 74 
                                       t+iQaeaip++l+g+d+l+ a+TG+GKT+af++pvlq+++e+   +   +p+al+++PtreLa q+ + + ++++++
  gi|386002133|ref|YP_005920432.1|  25 TPIQAEAIPHLLRGEDLLGIAQTGTGKTAAFVLPVLQRISEErrrTVPGAPRALVLAPTRELAAQIDESFGTYGQFL 101
                                       89*************************************99988778889*************************** PP

                                       TSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  75 dlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                       + +  +++ggv+++ q+++l++gv+ +v+tpgrl+dl+++g+++l+ ++f+VlDEadr+ld+gf ++++ri+++l  
  gi|386002133|ref|YP_005920432.1| 102 QFSHAAVFGGVSQEPQVKALSRGVEALVATPGRLLDLMEQGHIDLKGIEFFVLDEADRMLDMGFAKDVHRIVSAL-- 176
                                       *99*****************999****************************************************.. PP

                                       HCTTSTTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 152 itcdgklqrqvivlSATlpkdvk 174
                                            +++r+ +++ AT+++++ 
  gi|386002133|ref|YP_005920432.1| 177 -----PKKRHSLFFAATMSREIG 194
                                       .....56778********98775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.44
                                       HHHHHHTTTSTSEEEEEETTSSHHHHHHHHH...TT.CSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx.xxxxxxx RF
                              DEAD  65 nnlkkfkkyidlrvlliiggvaardqlskld...ng.vdivvgt 104
                                       +++ k++   ++r+ +i g+ ++++ l++l+   +g ++++v+t
  gi|386002133|ref|YP_005920432.1| 258 DRVAKVLTRSGIRADAIHGDRTQNQRLAALRgfkAGrLQVLVAT 301
                                       44555555566788899999999999999943323368888887 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.4   5.5e+03      18      61 ..      76     123 ..      71     131 .. 0.65
   2 !  111.0   0.1   1.6e-35   3.6e-32       5     111 .]     234     339 ..     230     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                                       EEEEEESSHH...HHHHHHHH..HHHT...TSTEEEESTTSTHHHHHHHHHH CS
                        Helicase_C  18 kilifvntid...rlekvkll..lekk...gikvavlhgelpqnereeileq 61 
                                       ++l+ ++t++   +++  + +         +++ a++ g  +q+ + ++l++
  gi|386002133|ref|YP_005920432.1|  76 RALVLAPTRElaaQID--ESFgtY--GqflQFSHAAVFGGVSQEPQVKALSR 123
                                       6778888888433333..333221..13367888888888888888887765 PP

  == domain 2  score: 111.0 bits;  conditional E-value: 1.6e-35
                                       HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                        Helicase_C   5 allellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                        l+ ll +++  +++l+f++t++r+++v  +l+++gi++ ++hg+ +qn+r+++l+ f++g+ +vL+atd+a+rGid
  gi|386002133|ref|YP_005920432.1| 234 LLIGLL-QQKFLKRVLVFTRTKRRADRVAKVLTRSGIRADAIHGDRTQNQRLAALRGFKAGRLQVLVATDIAARGID 309
                                       566677.788899************9966666899****************************************** PP

                                       STTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       ++++++Vin+dlp +++sy++riGRtgRag
  gi|386002133|ref|YP_005920432.1| 310 VEDISHVINYDLPNEPESYVHRIGRTGRAG 339
                                       ****************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.4e-09   5.3e-06      26     170 ..      40     190 ..      22     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.4e-09
                                       EEEEEESTTSTHHHHH.HHHHHHH-S..........-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS CS
                            ResIII  26 rglikmaTGtGKTlva.aklierllkkgkee.....kflflvprkslleqtleefkkflseayke....igkkvsgd 92 
                                        +l  + TGtGKT    + + +r+++++++      ++l+l+p+++l  q  e f  + +  + +     g++ ++ 
  gi|386002133|ref|YP_005920432.1|  40 DLLGIAQTGTGKTAAFvLPVLQRISEERRRTvpgapRALVLAPTRELAAQIDESFGTYGQFLQFShaavFGGVSQEP 116
                                       5566789*******99677778888877777*********************8885555554444222344444444 PP

                                       -B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT-.--SEEEEE CS
                            ResIII  93 kkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekf.keavllgl 165
                                       + ka    s   + lv+t  +l   +     e+ + + + +++++ DEa r+ ++   k + +i+ ++ k+   l +
  gi|386002133|ref|YP_005920432.1| 117 QVKA---LSRGVEALVATPGRLLDLM-----EQGHIDLKGIEFFVLDEADRMLDMgfaKDVHRIVSALpKKRHSLFF 185
                                       4444...88899***********999.....99999999999***********996666777777666455788888 PP

                                       ESS-S CS
                            ResIII 166 TATpe 170
                                        AT+ 
  gi|386002133|ref|YP_005920432.1| 186 AATMS 190
                                       88875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.5e-07   0.00078       6     102 ..      28     163 ..      24     186 .. 0.68
   2 ?    2.4   0.0     0.049   1.1e+02      46      81 ..     244     282 ..     233     311 .. 0.73
   3 ?   -2.7   0.1       1.8   4.1e+03     149     176 ..     354     381 ..     340     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.5e-07
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKt..talkalreaweaag......grviglAptgkaAkvLaeelgieastia 74 
                                       Qa+a+ +ll ++d   +  +  GtGKt  ++l +l+++ e++        r ++lApt + A+++ e++g+ ++ ++
  gi|386002133|ref|YP_005920432.1|  28 QAEAIPHLLRGED--LLGIAQTGTGKTaaFVLPVLQRISEERRrtvpgaPRALVLAPTRELAAQIDESFGTYGQFLQ 102
                                       9***********9..7777889****944468899999999976888888889**************9996444333 PP

                            AAA_30  75 kllkrlk.................................grarlepgtllivDEag.mvdt 102
                                        + ++                                   g+ +l+  + ++ DEa  m+d+
  gi|386002133|ref|YP_005920432.1| 103 -FSHAAVfggvsqepqvkalsrgvealvatpgrlldlmeqGHIDLKGIEFFVLDEADrMLDM 163
                                       .2222224444455566666666667777777777777664455555577777777524444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.049
                            AAA_30  46 ggrviglAptgkaAkvLae...elgieastiakllkrlk 81 
                                        +rv++++ t++ A+++a+    +gi+a+ i+   ++++
  gi|386002133|ref|YP_005920432.1| 244 LKRVLVFTRTKRRADRVAKvltRSGIRADAIHGDRTQNQ 282
                                       478999999999999988544488999999997666665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.8
                            AAA_30 149 aeLtevvRqkeseeraaalalregdaee 176
                                         L+++ R +++++r++ ++  + +a++
  gi|386002133|ref|YP_005920432.1| 354 SFLRDIERLTRTKIREVEHRYHSEEAKN 381
                                       5688888888888888888887777664 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.9e-05     0.065       1     133 [.      28     184 ..      28     187 .. 0.61
   2 !    5.5   0.0     0.009        20      42      75 ..     244     277 ..     219     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkp....eeillvaftgrAakelrerlaalgaeatTi 72 
                                       q ea+   l+ + ll +a  GtGKT   +  v   ++++++       + l++a+t+  a ++ e+  ++g+  +  
  gi|386002133|ref|YP_005920432.1|  28 QAEAIPhLLRGEDLLGIAQTGTGKTAAFVLPVLQRISEERRRTvpgaPRALVLAPTRELAAQIDESFGTYGQFLQFS 104
                                       66777557788888889********9766555444444433333566899****************98888777666 PP

                            AAA_19  73 Hrlal.............ldfddlltealelle.eaeeekklqeeellivDEfq.dvd....elqyrLlkallgekk 130
                                       H+  +              +++ l+ ++  ll+  ++ + +l+  e ++ DE+  ++d    +   r+++al+++++
  gi|386002133|ref|YP_005920432.1| 105 HAAVFggvsqepqvkalsRGVEALVATPGRLLDlMEQGHIDLKGIEFFVLDEADrMLDmgfaKDVHRIVSALPKKRH 181
                                       65533666666666666633333343344444453355666644448888887535552111223566666666666 PP

                            AAA_19 131 kll 133
                                       +l+
  gi|386002133|ref|YP_005920432.1| 182 SLF 184
                                       555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.009
                            AAA_19  42 peeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                       ++++l+ + t+r a+++++ l+  g +a+ iH+ 
  gi|386002133|ref|YP_005920432.1| 244 LKRVLVFTRTKRRADRVAKVLTRSGIRADAIHGD 277
                                       489******************99999******64 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0001      0.23      11     118 ..      44     175 ..      41     193 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                            AAA_22  11 tGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka.............er 72 
                                       ++++GtGKT      + q      + eer+++v     + ++   ++l+ ++ + +g  +               ++
  gi|386002133|ref|YP_005920432.1|  44 IAQTGTGKTAAFVLPVLQR-----ISEERRRTVpgAPRALVLAPTRELAAQIDESFGTYGQFlqfshaavfggvsQE 115
                                       5788999998887777776.....23346666644222333335566777777777755555777777788888844 PP

                            AAA_22  73 lsseellealeqalrarav..............ielliiDEaqh.lrseealeeLrsllnl 118
                                        + ++l + +e  + + ++              ie++++DEa++ l  +   +++++++  
  gi|386002133|ref|YP_005920432.1| 116 PQVKALSRGVEALVATPGRlldlmeqghidlkgIEFFVLDEADRmL-DMGFAKDVHRIVSA 175
                                       4444444444444444444444444455555559**********66.67777776666555 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.35      13      54 ..      47      95 ..      42     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                      TTS-TTTTHHHHHHHHHHHTT--EE.......EEESSHHHHHHHHHHTT CS
                        Flavi_DEAD 13 PGaGktrkvlpelvkeaierrlrtl.......vLaPtrvvlaemeealk 54
                                       G+Gkt  ++  ++++  e+r rt+       vLaPtr  +a + e++ 
  gi|386002133|ref|YP_005920432.1| 47 TGTGKTAAFVLPVLQRISEERRRTVpgapralVLAPTRELAAQIDESFG 95
                                      699***9988888888888877764333333399999999999988775 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.34   7.5e+02      75      92 ..      74      91 ..      58     107 .. 0.84
   2 ?   -3.4   0.0       1.4   3.1e+03     189     218 ..     146     176 ..     143     182 .. 0.69
   3 ?    8.8   0.0   0.00027       0.6     328     417 ..     242     329 ..     208     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.34
                             UTP25 75 rpkvLillptreaalevv 92
                                       p+ L+l+ptre a ++ 
  gi|386002133|ref|YP_005920432.1| 74 APRALVLAPTRELAAQID 91
                                      5899**********9875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                             UTP25 189 LsSiEvlivdqadvl.emQnwehvetvlkhl 218
                                       L  iE +++d+ad +  m   + v+ +++ l
  gi|386002133|ref|YP_005920432.1| 146 LKGIEFFVLDEADRMlDMGFAKDVHRIVSAL 176
                                       5679999999999751466666666666555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00027
                             UTP25 328 skssgiliyipsyfdfvrvrnylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikgvkkv 404
                                       +  +++l++  +     rv + l ++ +   ai+   ++++   a + F+ g+ +vl+ t+ +   r  +++++++v
  gi|386002133|ref|YP_005920432.1| 242 KFLKRVLVFTRTKRRADRVAKVLTRSGIRADAIHGDRTQNQRLAALRGFKAGRLQVLVATDIAA--RGIDVEDISHV 316
                                       556677888888888889999999999999999999999998899999*************885..99********* PP

                             UTP25 405 ilYklPenpefys 417
                                       i Y+lP++pe y 
  gi|386002133|ref|YP_005920432.1| 317 INYDLPNEPESYV 329
                                       *********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2711.49
//
Query:       gi|386002134|ref|YP_005920433.1|  [L=102]
Description: hypothetical protein Mhar_1446 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.2   11.8   0.0        8.3    6.6   0.0    2.1  2  Phenol_monoox  Phenol hydroxylase conserved region


Domain annotation for each model (and alignments):
>> Phenol_monoox  Phenol hydroxylase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00047       8.3      29      58 ..      33      62 ..      30      65 .. 0.90
   2 ?    3.4   0.0    0.0049        87      18      44 ..      71      97 ..      69     102 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00047
                     Phenol_monoox 29 lplppdmpFgalvekvlkpligahPdfari 58
                                      ++l + + Fg l+ +++ + ig++Pd +++
  gi|386002134|ref|YP_005920433.1| 33 IRLRQGLFFGLLILAAVCGCIGEEPDSSEV 62
                                      67889999******************9987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0049
                     Phenol_monoox 18 ddhllFcapvalplppdmpFgalvekv 44
                                      dd l F  p + +l+ d +F++l+++ 
  gi|386002134|ref|YP_005920433.1| 71 DDGLGFPPPSCGCLEGDEKFEELLSAG 97
                                      56677999**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 667.43
//
Query:       gi|386002135|ref|YP_005920434.1|  [L=117]
Description: hypothetical protein Mhar_1447 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.1   4.3     0.0071   16.1   4.3    2.0  2  Mntp      Putative manganese efflux pump
  ------ inclusion threshold ------
       0.11   12.8   6.6      0.047   14.0   3.8    1.7  1  YwiC      YwiC-like protein


Domain annotation for each model (and alignments):
>> Mntp  Putative manganese efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5     0.059   5.3e+02      85     121 ..      14      50 ..       5      59 .. 0.55
   2 !   16.1   4.3   7.9e-07    0.0071     102     152 .]      52     110 ..      37     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.059
                              Mntp  85 tSiDAlavGlsLallkvnillavlliGlvtlvlsllG 121
                                       +Si    v l++ +  v+ l + ++ +++t +l+l G
  gi|386002135|ref|YP_005920434.1|  14 VSIFFSIVALAILVNAVEFLCSSAIPAVFTHILALSG 50 
                                       4443333333334445555555555555555555555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7.9e-07
                              Mntp 102 nillavlliGlvtl........vlsllGlllGrklgsllgkkaeilGGliLiliGlkil 152
                                       +++   lli+l t+        ++sl+++ +G+ lg+++ ++ +++GG iL ++Gl +l
  gi|386002135|ref|YP_005920434.1|  52 STIENYLLIALYTFffmlddmvIFSLAAFAAGSSLGERYARWCKVVGGTILAILGLLLL 110
                                       5555555555555511111111568899***************************9775 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.8   5.2e-06     0.047      13      84 ..      38     117 .]      33     117 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-06
                              YwiC  13 vPlllGlllag...pvwahllllvawlvgYlaffplllllka.....rrrarylkplliYgavallllllalllqpa 81 
                                       +P+++  +la     ++   ll ++  + +++   +   l a     +  +ry+++  + g+  l++l l+ll++p+
  gi|386002135|ref|YP_005920434.1|  38 IPAVFTHILALsgtSTIENYLLIALYTFFFMLDDMVIFSLAAfaagsSLGERYARWCKVVGGTILAILGLLLLFAPH 114
                                       56666666554444566666666777777777777777777687776699*************************** PP

                              YwiC  82 llw 84 
                                       llw
  gi|386002135|ref|YP_005920434.1| 115 LLW 117
                                       *99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 868.33
//
Query:       gi|386002136|ref|YP_005920435.1|  [L=312]
Description: hypothetical protein Mhar_1448 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00052   20.2   0.0    0.00097   19.3   0.0    1.4  1  Glutaredoxin  Glutaredoxin
  ------ inclusion threshold ------
        5.5    7.4   6.4         12    6.2   0.4    2.6  3  Wzz           Chain length determinant protein


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-07   0.00097       4      58 ..      60     126 ..      57     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-07
                                       EESTSSHHHHHHHHHHHHTT...GG...EEEEEGCCSH..HHHHHHHHHH....TSSSSSEEEETTE CS
                      Glutaredoxin   4 ftkptCpyCkkakrlLkelg...vk...feeidvdkde..eireelkels....gvrtvPqvfidgk 58 
                                       f  ptCp C   k +++ l+   v+   f  +dv+k e  ++  e+ +      +  tvP++f++g+
  gi|386002136|ref|YP_005920435.1|  60 FYLPTCPTCGEQKPIFEALKregVPgarFYSVDVSKPEgfALFREMAKDGgiavESLTVPTIFVGGR 126
                                       6679*****9999998777655544555********88887777777777899999*********97 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1    0.0067        60      10      35 ..       9      34 ..       4      38 .. 0.89
   2 ?    6.2   0.4    0.0014        12       5      36 ..     222     253 ..     220     257 .. 0.91
   3 ?   -2.7   0.1      0.84   7.5e+03      24      32 ..     269     277 ..     257     285 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0067
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               Wzz 10 svLwkrkklIilvtllfallaviyaf 35
                                      + ++k+++ I l++ll +l+a+ ya+
  gi|386002136|ref|YP_005920435.1|  9 GHIFKSRFNIGLLALLLILGALSYAL 34
                                      56899*******************96 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               Wzz   5 LieLlsvLwkrkklIilvtllfallaviyafl 36 
                                       Li Ll  +++r++ +++v  ++++ +++y ++
  gi|386002136|ref|YP_005920435.1| 222 LIGLLAGVRDRRRAWLIVGSFVLASGALYFLI 253
                                       899**************************865 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.84
                                       XXXXXXXXX CS
                               Wzz  24 llfallavi 32 
                                       +l++l++++
  gi|386002136|ref|YP_005920435.1| 269 ILTILIGLV 277
                                       333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1812.86
//
Query:       gi|386002137|ref|YP_005920436.1|  [L=139]
Description: hypothetical protein Mhar_1449 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0044   16.6   0.0      0.012   15.2   0.0    1.8  1  HTH_24       Winged helix-turn-helix DNA-binding
      0.008   16.8   0.1       0.12   13.1   0.0    2.2  2  RPA_C        Replication protein A C terminal
  ------ inclusion threshold ------
      0.043   14.1   0.0       0.12   12.7   0.0    1.6  2  DUF4883      DOmain of unknown function (DUF4883)
       0.09   12.6   0.3       0.25   11.2   0.2    1.9  2  TFIIE_alpha  TFIIE alpha subunit
      0.095   12.8   0.0       0.16   12.0   0.0    1.3  1  UPF0147      Uncharacterised protein family (UPF0147)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-06     0.012       1      48 []       1      49 [.       1      49 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                            HTH_24  1 ldetdrkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + e+d kIL e++q + +is + +Ae+l l +  v  +   L+++G+++
  gi|386002137|ref|YP_005920436.1|  1 MQEIDMKILsEVVQSEHGISDSYIAEKLRLDLERVGDHFVMLKKDGFVE 49
                                      569******777777888****************************996 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   3.3e-05      0.12      55      97 ..       6      48 ..       1      49 [. 0.89
   2 ?    1.6   0.0      0.12   4.5e+02      53      68 ..      84      99 ..      75     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                                      HHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 55 lnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      + ++ + ++se+G++ ++ia+klrl+ + v      L ++G +
  gi|386002137|ref|YP_005920436.1|  6 MKILSEVVQSEHGISDSYIAEKLRLDLERVGDHFVMLKKDGFV 48
                                      67888899**********************9999999999975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                                      HHHHHHHH.SXSTTTE CS
                             RPA_C 53 qvlnlikqspeseeGv 68
                                      ++++++k+++e++eG+
  gi|386002137|ref|YP_005920436.1| 84 MMIQVLKEAVEKDEGI 99
                                      7899999999999998 PP

>> DUF4883  DOmain of unknown function (DUF4883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.84     3e+03      48      57 ..      39      48 ..       5      60 .. 0.61
   2 ?   12.7   0.0   3.3e-05      0.12      21      58 ..      84     121 ..      79     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.84
                           DUF4883 48 lksLkkenfi 57
                                      +  Lkk+ f+
  gi|386002137|ref|YP_005920436.1| 39 FVMLKKDGFV 48
                                      3334444443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.3e-05
                           DUF4883  21 lklsvldtnlykeievdkeeieiiknflksLkkenfie 58 
                                       + ++vl+  ++k++ ++k e++ i+++l+ Lk++++++
  gi|386002137|ref|YP_005920436.1|  84 MMIQVLKEAVEKDEGIPKPEKKSITDMLDDLKDNQYVS 121
                                       56899*******************************94 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   6.9e-05      0.25      20      64 ..      11      55 ..       1      98 [. 0.85
   2 ?   -0.3   0.0      0.26   9.3e+02      40      53 ..     103     116 ..      69     122 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                                      HHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE CS
                       TFIIE_alpha 20 dvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd 64
                                      +v+ ++  +++  +a++l++dl+ ++     L+++++v+  r  d
  gi|386002137|ref|YP_005920436.1| 11 EVVQSEHGISDSYIAEKLRLDLERVGDHFVMLKKDGFVELIRTFD 55
                                      5666777899****************************9988877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.26
                                       -HHHHHHHHHHHHH CS
                       TFIIE_alpha  40 dlnelrklLnrLye 53 
                                       +++ +  +L +L++
  gi|386002137|ref|YP_005920436.1| 103 EKKSITDMLDDLKD 116
                                       34445555555555 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05      0.16       8      49 ..      85     127 ..      81     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                                       HHHHH.HHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHH CS
                           UPF0147   8 vielL.eeiiedtsvPrniRraakeakekLkdekeslavraat 49 
                                       +i++L e + +d+ +P+  ++++++++++Lkd++   ++ +a 
  gi|386002137|ref|YP_005920436.1|  85 MIQVLkEAVEKDEGIPKPEKKSITDMLDDLKDNQYVSGLSTAA 127
                                       67888456889**********************9988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 780.51
//
Query:       gi|386002138|ref|YP_005920437.1|  [L=93]
Description: hypothetical protein Mhar_1450 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 682.62
//
Query:       gi|386002139|ref|YP_005920438.1|  [L=331]
Description: hypothetical protein Mhar_1451 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0046   16.8   0.0       0.01   15.7   0.0    1.6  1  EF-hand_8  EF-hand domain pair


Domain annotation for each model (and alignments):
>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.6e-07      0.01      30      53 ..      48      71 ..      43      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.6e-07
                         EF-hand_8 30 ilfrefDtdgdGkisfeEFcvlle 53
                                      +l+++fD d+ Gk+s++ F+ ll 
  gi|386002139|ref|YP_005920438.1| 48 ALISAFDPDNTGKVSQTKFYKLLY 71
                                      79******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2441.11
//
Query:       gi|386002140|ref|YP_005920439.1|  [L=416]
Description: 5-methylthioadenosine/S-adenosylhomocysteine deaminase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-66  223.9   0.0    3.9e-66  223.7   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    2.2e-12   47.2   0.3      1e-09   38.4   0.1    2.1  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.052   12.9   0.0      0.075   12.4   0.0    1.3  1  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.7   0.0   6.6e-70   3.9e-66       4     343 ..      53     389 ..      50     390 .. 0.94

  Alignments for each domain:
  == domain 1  score: 223.7 bits;  conditional E-value: 6.6e-70
                                       E-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHH CS
                      Amidohydro_1   4 PGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgieal 66 
                                        Gl++aH+Hl ++l+rg      l+ wl          ++ e+++++++ g+ ++++sG+t  +dm++     ++  
  gi|386002140|ref|YP_005920439.1|  53 SGLVNAHTHLAMTLFRGYaddmELMPWLsekiwpleakLTAEDIRWGVKLGCLEMIRSGITCYNDMYY----FMDEA 125
                                       69******************99999999****************************************....9**** PP

                                       HHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHH CS
                      Amidohydro_1  67 leaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakk 143
                                       ++a++e+  glr+++++v +d++     ++ +e +++++      k+d+++ +a++ph+ +++s+e+l+ al++a+k
  gi|386002140|ref|YP_005920439.1| 126 ARATKEM--GLRAVLSGVLFDMRP--DLIEDAEPFIRRW------KNDDLIVPAVGPHAVYTCSEETLSRALDLAEK 192
                                       ******8..***********9655..3588999999998......6999**************************** PP

                                       HTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHH CS
                      Amidohydro_1 144 rdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpf 220
                                       +d++++iH++et+ eve   +  g     ++++e+++slg+l + ++++ah+v+l+p ++ +++ r  +++vahc  
  gi|386002140|ref|YP_005920439.1| 193 HDVMIHIHLSETRSEVESFAKNRG-----KSPVEYLDSLGFLSD-RVVAAHCVWLSPQDVSIIADR--GVNVAHCSI 261
                                       ****************77777777.....56*************.*********************..********* PP

                                       HHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHT CS
                      Amidohydro_1 221 snsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkal 297
                                       sn++l+sg+++l ++ ++G+++ lgtDga+s+nslnl++e++  +  q+ +++++++  + + e+ rmaT n+  a+
  gi|386002140|ref|YP_005920439.1| 262 SNHKLASGIAPLDRLARAGARICLGTDGASSNNSLNLFQEMKTTAIAQK-CAHSRPDL-FAAGEVWRMATENAYTAF 336
                                       *********************************************6666.77766566.****************** PP

                                       T-TTTSSSS-TTSB--EEEECC.CT..........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 298 glddkvGsievGkdADlvvvdl.di..........laafvglkkdgnvkkvivkGkl 343
                                       +l  + G + +G  ADl ++dl ++           +++v++++ g v ++iv+G++
  gi|386002140|ref|YP_005920439.1| 337 RL--DMG-LRAGAIADLSLIDLkKPwfcpladdniVSHLVYSAQ-GGVETTIVGGRV 389
                                       **..8**.**************7557788888888*******99.55********87 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00049         3       1      25 [.      42      66 ..      42      80 .. 0.84
   2 !   38.4   0.1   1.7e-13     1e-09     257     472 ..     175     390 ..     121     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00049
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg 25
                                      evi  +G+l + G+v +HtHla + 
  gi|386002140|ref|YP_005920439.1| 42 EVIEGRGKLAISGLVNAHTHLAMTL 66
                                      678889**************88664 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 1.7e-13
                      Amidohydro_3 257 wpdfedealaelvaaadergldvaihaigdaavddvldafeaa.....aekngnqdrr.rlehaegvtesqiervaa 327
                                       + ++++e+l + +++a ++++ ++ih  ++ +  + ++  +        + +g+   r  ++h+ ++++++++ +a+
  gi|386002140|ref|YP_005920439.1| 175 VYTCSEETLSRALDLAEKHDVMIHIHLSETRSEVESFAKNRGKspveyLDSLGFLSDRvVAAHCVWLSPQDVSIIAD 251
                                       44588999*******************99999994444444445766645555444445****************** PP

                      Amidohydro_3 328 lqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevl 402
                                        +v  + + ++n+           + a+g++p+ +l +ag +++lg+D  +  ++++ + ++ ++   ++ + +   
  gi|386002140|ref|YP_005920439.1| 252 RGVNVAHCSISNH-----------KLASGIAPLDRLARAGARICLGTDgaSSNNSLNLFQEMKTTAIAQKCAHS--- 314
                                       ********88888...........89**********************999999*************9999775... PP

                      Amidohydro_3 403 rpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld........adpldvdppelaear.......... 461
                                        +   +   e+ ++ T+++ +a++l+    +L++Ga ADl ++d               ++++   +          
  gi|386002140|ref|YP_005920439.1| 315 -RPDLFAAGEVWRMATENAYTAFRLDM---GLRAGAIADLSLIDlkkpwfcpL-----ADDNI---Vshlvysaqgg 379
                                       .5559********************99...5*************955333321.....23333...23447777899 PP

                      Amidohydro_3 462 vrltvvdGrvv 472
                                       v+ t+v+Grv+
  gi|386002140|ref|YP_005920439.1| 380 VETTIVGGRVL 390
                                       *********96 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05     0.075     109     187 ..     179     269 ..     166     337 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS............EEEETT--S-HHHHHHHHHTTEE CS
                        TatD_DNase 109 qeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeaka............kvvlHsfsgsaeeakkflklgyy 173
                                        ee + + l+lA++++ ++ iHl ++  ++ +++k+ +++++             v  H+   s + ++ ++++g+ 
  gi|386002140|ref|YP_005920439.1| 179 SEETLSRALDLAEKHDVMIHIHLSETRSEVESFAKNRGKSPVeyldslgflsdrVVAAHCVWLSPQDVSIIADRGVN 255
                                       689999**********************9999998877666666777777777566789988888888888888888 PP

                                       EEE-GGGGTTTTHH CS
                        TatD_DNase 174 islsglltfknake 187
                                       ++   +++ k a+ 
  gi|386002140|ref|YP_005920439.1| 256 VAHCSISNHKLASG 269
                                       77777766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2389.35
//
Query:       gi|386002141|ref|YP_005920440.1|  [L=416]
Description: hypothetical protein Mhar_1453 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-05   23.3   0.0     0.0042   17.3   0.0    2.9  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.0     0.008   1.4e+02      41      78 ..     191     230 ..     187     231 .. 0.81
   2 !   17.3   0.0   2.4e-07    0.0042       2      78 ..     280     355 ..     279     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.008
                       NPCBM_assoc  41 pasaaslapGetve..atvkVtppagaaaGdyevtakarl 78 
                                       p+ a sl  Ge++e   ++ V++ ++a aG y+  +++++
  gi|386002141|ref|YP_005920440.1| 191 PQLAGSLSGGEALErpMEFSVRAESSASAGVYPMLLEVSY 230
                                       55566788888887446899*************9999986 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.4e-07
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslsl.PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       +pG++ +l+l+++n+g+ +a++v+ +l + P   + ++ +  ++ +++pG+++ ++  + +   a++G++ ++ ++r
  gi|386002141|ref|YP_005920440.1| 280 SPGRSSALELVMANGGDVPAREVRARLLVqP-PFN-STGEEVELGDIEPGKRAASEYPLEVDRLADPGERALVWQVR 354
                                       89*********************99988843.345.346666667***************************99999 PP

                       NPCBM_assoc  78 l 78 
                                       +
  gi|386002141|ref|YP_005920440.1| 355 Y 355
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 3012.83
//
Query:       gi|386002142|ref|YP_005920441.1|  [L=263]
Description: Fructose bisphosphate aldolase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-58  198.2   0.1    1.8e-58  198.0   0.1    1.1  1  DeoC          DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.043   13.4   0.0    1.6  1  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
      0.062   12.7   0.1          1    8.8   0.0    2.1  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   0.1     3e-62   1.8e-58       1     235 []      19     235 ..      19     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 3e-62
                                       EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTT CS
                              DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskq 77 
                                       +vi+++D++v  +++ ++      +++++ ++ ++++ga+a ++++g +  ++++y++d +l+++l+++t l ++++
  gi|386002142|ref|YP_005920441.1|  19 TVIIPMDHGVTVGPIRGI------KNVREAADLVAAGGADAAVVHKGAATFGHRGYGRDLGLILHLSASTNLGPDPN 89 
                                       69****************......8**************************************************** PP

                                       EEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  78 rdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                        +v+ va+veea++ GAd v++ v++   g+e+e+++l  +++ + +c+e+g+pl++++y+r+++i+de+ ++d +a
  gi|386002142|ref|YP_005920441.1|  90 NKVL-VATVEEALKIGADGVSIQVNV---GAEDEARMLSTLGETARRCQEWGMPLLAMMYPRGKKIDDEH-RADYIA 161
                                       ****.*********************...*****************************************.****** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvls 228
                                       +Aarv+aelGaD++K+++         +d ++f++v++++pvp +v++GG+   +e++fle+v  A+  aga Gv++
  gi|386002142|ref|YP_005920441.1| 162 HAARVGAELGADVVKTSYS--------GDPDSFREVVDGCPVP-LVIAGGPrteTEAEFLEMVAGAI-GAGARGVAI 228
                                       *******************........****************.*********99************.********* PP

                                       SHHHHTT CS
                              DeoC 229 GRaifqk 235
                                       GR++fq+
  gi|386002142|ref|YP_005920441.1| 229 GRNVFQH 235
                                       *****97 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.2e-06     0.043      90     220 ..     112     240 ..      20     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-06
                                       EEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTHHHHH CS
                         OMPdecase  90 vtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetlnatee 166
                                       v+v a  +  +++ l e+a+++++ g+ +la+m   g+  + e   ++ +++aar  + e    G+ + +t    + 
  gi|386002142|ref|YP_005920441.1| 112 VNVGAEDEARMLSTLGETARRCQEWGMPLLAMMYPRGKKIDDE-HRADYIAHAARVGA-E---LGADVVKTSY--SG 181
                                       66666666789999999999999999************99999.45555555555544.5...5777777744..44 PP

                                       HTTCSCEEEHHHTT......EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHH CS
                         OMPdecase 167 daddfihltpgigl......eqggdgkgqqyntpekligiagadiiivGRgIlkagdpve 220
                                       d d f  ++ g+ +        + ++++   +++ ++ig aga  + +GR +++ +dp  
  gi|386002142|ref|YP_005920441.1| 182 DPDSFREVVDGCPVplviagGPRTETEAEFLEMVAGAIG-AGARGVAIGRNVFQHRDPTL 240
                                       578***********9997776666777777778888888.89***************975 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.019   1.1e+02      68      97 ..      35      64 ..      17      92 .. 0.84
   2 ?    8.8   0.0   0.00017         1       2      92 ..      98     180 ..      97     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHHHHHTBSEEEEEBCCGBCT CS
                      AP_endonuc_2 68 svdalkraielaaaLGapllvlhpGtagag 97
                                       ++++++a++l aa Ga+  v+h G a++g
  gi|386002142|ref|YP_005920441.1| 35 GIKNVREAADLVAAGGADAAVVHKGAATFG 64
                                      48899******************8865444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00017
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiel 78 
                                       ++a ++G+dgv +    +    ++  ++l e +++++e g+ + ++ ++ +   +de+    r     d++ +a++ 
  gi|386002142|ref|YP_005920441.1|  98 EEALKIGADGVSIQVNVGAEDEARMLSTLGETARRCQEWGMPLLAMMYPRGKKIDDEH----R----ADYIAHAARV 166
                                       5677888888777666666665556688899999999999999999999999998874....7....8999999999 PP

                                       HHHHTBSEEEEEBC CS
                      AP_endonuc_2  79 aaaLGapllvlhpG 92 
                                        a+LGa+++ +  +
  gi|386002142|ref|YP_005920441.1| 167 GAELGADVVKTSYS 180
                                       99999999988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1969.92
//
Query:       gi|386002143|ref|YP_005920442.1|  [L=352]
Description: Rhodanese domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-20   73.2   0.0    1.5e-13   51.2   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   8.4e-18   1.5e-13      15     104 ..     126     212 ..     116     214 .. 0.75
   2 !   19.6   0.0   5.5e-08   0.00099       5     101 ..     244     340 ..     241     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 8.4e-18
                         Rhodanese  15 allDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel...gidnkktvvvycdgggraaaaaallkk 88 
                                       +llD+R+pe+Ye+gh+pgA+n+ +++l+ ++  + + ++   e   l   g+++ + +vvy++g ++ a + ++l +
  gi|386002143|ref|YP_005920442.1| 126 VLLDARSPEDYERGHLPGARNLYWRSLRAGDVLDLEVAA--GE---LrrlGVNETDSIVVYGRGDDS-AYLFWALDY 196
                                       39********************55444444333333322..23...233688**********99999.777777778 PP

                         Rhodanese  89 lGyknvsvldGGfkaw 104
                                       lG++++s+ldG ++a+
  gi|386002143|ref|YP_005920442.1| 197 LGHQDLSLLDGDVEAF 212
                                       **777*******9998 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 5.5e-08
                         Rhodanese   5 lkellekgkvallDvR.ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellel....gidnkktvvvycdg 75 
                                       lke +++ +v+++D+R +  + ++++I ++  + +       + +ea+ l+ peel +l    g+ +    +vy+  
  gi|386002143|ref|YP_005920442.1| 244 LKEAQGSVRVQIVDTRsSYSDRAASRISNSMYFkPE---EIYSDPEARTLKSPEELDQLflrrGLEDRMVQIVYGTP 317
                                       78889999999*****54444788*********544...44555666666666666666665888888888888855 PP

                         Rhodanese  76 ggraaaaaallkklGyknvsvldGGf 101
                                           + ++ +lk++G ++  vldG +
  gi|386002143|ref|YP_005920442.1| 318 EA--CGLYVALKAMG-YRATVLDGTW 340
                                       55..5999999*9**.7999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 2215.15
//
Query:       gi|386002144|ref|YP_005920443.1|  [L=131]
Description: hypothetical protein Mhar_1456 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-12   47.3   0.5      5e-12   46.3   0.5    1.5  1  HTH_32        Homeodomain-like domain
    3.1e-12   46.3   0.1    5.6e-12   45.5   0.1    1.4  1  HTH_29        Winged helix-turn helix
    2.2e-09   37.3   2.0    5.6e-09   36.0   2.0    1.7  1  HTH_28        Helix-turn-helix domain
    1.9e-07   30.7   0.4    3.9e-07   29.7   0.4    1.5  1  HTH_23        Homeodomain-like domain
    0.00023   20.7   1.3    0.00066   19.3   0.1    2.3  2  HTH_33        Winged helix-turn helix
    0.00067   20.1   0.8     0.0011   19.4   0.8    1.4  1  LZ_Tnp_IS481  leucine-zipper of insertion element IS481


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 !   46.3   0.5   1.7e-15     5e-12       3      73 .]      50     120 ..      48     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.7e-15
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallree.prWsprqlaarlaeregvkvShstvyriL 73 
                                       + w +R+n++G+egLk+r+ +grp+kls+++r+ +  llr++ p   + ++++ l+ ++gv++   +++ iL
  gi|386002144|ref|YP_005920443.1|  50 YTWQRRWNDGGYEGLKPRHGGGRPPKLSAAERETLAMLLRQRgP-SRTGEVRDLLRGEFGVEYTSKQIRIIL 120
                                       89****************999******************76524.456689999955559999999999876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   1.9e-15   5.6e-12       1      62 [.      22      81 ..      22      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.9e-15
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62
                                      R++ ++  ++G+s v   A+l+g++r+  y+w++r++ gG ++l++r+++grp + ls++++
  gi|386002144|ref|YP_005920443.1| 22 RLHFIRYRYQGLS-VEASAHLVGVTRSVGYTWQRRWNDGGYEGLKPRHGGGRPPK-LSAAER 81
                                      777888889***8.****************************************6.***998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   2.0   1.9e-12   5.6e-09       1      52 []      21      72 ..      21      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.9e-12
                            HTH_28  1 qRleiikllaaGhsvreaArelgisrrtvyrWikryeegGiagLvprrrrpr 52
                                      +Rl+ i++  +G sv + A+++g++r+  y W +r++ gG +gL+pr++++r
  gi|386002144|ref|YP_005920443.1| 21 RRLHFIRYRYQGLSVEASAHLVGVTRSVGYTWQRRWNDGGYEGLKPRHGGGR 72
                                      6999999999***************************************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.4   1.3e-10   3.9e-07       5      50 .]      20      65 ..      18      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.3e-10
                            HTH_23  5 reRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegll 50
                                      ++Rl+ ++   +Glsv++ A + gv+r+  y w +r++ +G egl+
  gi|386002144|ref|YP_005920443.1| 20 LRRLHFIRYRYQGLSVEASAHLVGVTRSVGYTWQRRWNDGGYEGLK 65
                                      79***********************************99*****96 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.69   2.1e+03      34      40 ..      48      54 ..      44      56 .. 0.80
   2 !   19.3   0.1   2.2e-07   0.00066       7      36 ..      96     125 ..      94     131 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.69
                            HTH_33 34 lGfsyqk 40
                                       G+++q+
  gi|386002144|ref|YP_005920443.1| 48 VGYTWQR 54
                                      5899996 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.2e-07
                            HTH_33   7 larlaqlieerfgvsysvsgvyrlLkrlGf 36 
                                       + ++++l++ +fgv+y++++++ +Lk lG 
  gi|386002144|ref|YP_005920443.1|  96 TGEVRDLLRGEFGVEYTSKQIRIILKGLGV 125
                                       6789************************95 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 !   19.4   0.8   3.7e-07    0.0011      20      78 ..      27      84 ..       3      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.7e-07
                      LZ_Tnp_IS481 20 rvvedrrtvaqvarelGvslrtaykwlarfraeGldGlldrssrPrrvPkataPervea 78
                                      r   +  +v   a+ +Gv++ ++y w  r+   G +Gl  r     r Pk +a er+  
  gi|386002144|ref|YP_005920443.1| 27 RYRYQGLSVEASAHLVGVTRSVGYTWQRRWNDGGYEGLKPRHGGG-RPPKLSAAERETL 84
                                      333456678899999**************************8754.5699999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 983.87
//
Query:       gi|386002145|ref|YP_005920444.1|  [L=111]
Description: L-2,4-diaminobutyric acid acetyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.026   14.7   0.0    1.1  1  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-06     0.026      28      55 ..      60      87 ..      34     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-06
                                      HHSTTCEEEEEEETTEEEEEEEEEEEET CS
                    Acetyltransf_1 28 fsleaegllvaeedgeliGfisllkipd 55
                                       +  a+++ vaeedge++Gf++++  pd
  gi|386002145|ref|YP_005920444.1| 60 CRHFADTCSVAEEDGEIVGFLTGYLPPD 87
                                      3334447777**************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 684.17
//
Query:       gi|386002146|ref|YP_005920445.1|  [L=91]
Description: L-2,4-diaminobutyric acid acetyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-06   26.7   0.0      8e-06   26.1   0.0    1.3  1  Acetyltransf_1  Acetyltransferase (GNAT) family
     0.0024   18.2   0.0     0.0032   17.9   0.0    1.2  1  Acetyltransf_7  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.028   14.4   0.0    1.3  1  FR47            FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.3e-09     8e-06      66     112 ..       1      47 [.       1      51 [. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
                                       EEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHH CS
                    Acetyltransf_1  66 laVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlY 112
                                       +aV+p +rg GlG++L+++++ r    g++ ++ +++++n+a++rl+
  gi|386002146|ref|YP_005920445.1|   1 MAVDPRRRGCGLGKLLIREVLSRPALTGCRFLETTITPSNEASRRLF 47 
                                       69********************99999**999999*9********98 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.4e-07    0.0032      30      60 ..       1      36 [.       1      53 [. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.4e-07
                                      EEE-GGGTTSSHHHHHHHH..TT...SEEE.EEEEEE CS
                    Acetyltransf_7 30 laVdpeyrgkGiGraLlea..ae...kgii.leqlel 60
                                      +aVdp  rg G+G+ L++    +   +g++ le ++ 
  gi|386002146|ref|YP_005920445.1|  1 MAVDPRRRGCGLGKLLIREvlSRpalTGCRfLE-TTI 36
                                      89***************9644115557876322.222 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.7e-06     0.028      27      76 ..       1      51 [.       1      60 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-06
                                      EEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT CS
                              FR47 27 lqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklG 76
                                      + v+p  r+ Glg++l++++  + a  g   l   + +sN++s+rl+ +l 
  gi|386002146|ref|YP_005920445.1|  1 MAVDPRRRGCGLGKLLIREVLSRPALTGCRFLeTTITPSNEASRRLFLSLA 51
                                      57999***************99999999876637899**********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 625.77
//
Query:       gi|386002147|ref|YP_005920446.1|  [L=439]
Description: Diaminobutyrate--2-oxoglutarate aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-80  270.4   0.0    2.6e-80  270.1   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.026   13.7   0.0      0.052   12.7   0.0    1.5  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.1   0.0   2.9e-84   2.6e-80       8     404 ..      20     412 ..      14     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 270.1 bits;  conditional E-value: 2.9e-84
                                       -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHH..HHTT-S---TTTCEEHHHH.HHHHHHHH CS
                       Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavke..qaaklshvsfgaltnepal.klaekllk 81 
                                       ++++v tka+G+ l+d+ g+ y+D++++  ++n Gh++P++ + + +   a++++h    a++ ++a  ++ e  l 
  gi|386002147|ref|YP_005920446.1|  20 HFPVVFTKARGATLEDEGGNVYIDFLAGAGALNYGHNDPALKAKLLDyiEADQIVHGLDMATGAKQAFmEAFES-LI 95 
                                       6679*************************************988876235677888876666666554133344.44 PP

                                       HCT-..S..EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TS CS
                       Aminotran_3  82 lapkgld..kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpe 156
                                       l p  +   + f+  +G++Ave+A+K+ar+       t ++ i++f+++fHG tlg++++tg+ +  ++++g  + +
  gi|386002147|ref|YP_005920446.1|  96 LSPRRMRykMQFTGPTGTNAVEAAMKIARN------FTDRQTIVSFTNGFHGVTLGSVAATGN-SHFRDGCGMQPQG 165
                                       5555554449999*****************......***************************.************* PP

                                       EEEE-TTBGGGTB-HHHHHHHHHHHHHHHH...CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEE CS
                       Aminotran_3 157 vvrlkypdeevlkeneeeeaalleeleale...kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvlli 230
                                       + +++y+  +            +e+l ++        d+ aAvivE++qgegG++va +e+l+ l ++c+kh++lli
  gi|386002147|ref|YP_005920446.1| 166 TAFMPYDGYMGDGIDT------TEYLDKMLadgSSGLDHPAAVIVETVQGEGGINVARNEWLRSLEAVCRKHGILLI 236
                                       *******744443333......444555444447888999************************************* PP

                                       EE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGT.TSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHH CS
                       Aminotran_3 231 vDEvqtGfGrTGklfAlehagvspDlmtlaKaltg.GlplsavlataevmqalapgshgsTfgGnplacavalavle 306
                                       vDE+q G GrTG++f  e+ag+spD++tl+K+l+g Glpls vl + e+ ++++pg+h +Tf Gn la + a+a+le
  gi|386002147|ref|YP_005920446.1| 237 VDEIQAGCGRTGTFFSFEEAGISPDIITLSKSLSGyGLPLSLVLMKPEL-DQWKPGEHNGTFRGNNLAFVTARAALE 312
                                       *********************************9967**********97.6788**********************9 PP

                                       HHHH.TTHHHHHHHHHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETT.. CS
                       Aminotran_3 307 iiee.ekllenaqelgaalkegLeelqkky.evikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGd.. 379
                                          +   + ++++++g +++e+Le+l + +   + + Rg+G+m a++++  + ++  +i + a ekG+++ ++G+  
  gi|386002147|ref|YP_005920446.1| 313 EYWRdGSFEREVRRKGGIVRERLERLVDLDeRGVLSARGRGMMQALDCTIGELAT--RISALAFEKGLIMETSGSdd 387
                                       876538999*******************99899***************9988866..9****************988 PP

                                       TEEEE---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 380 nvirllppliitdeeidelleilkk 404
                                       +v++ l pl+i+dee++ +l+il++
  gi|386002147|ref|YP_005920446.1| 388 QVLKCLMPLTISDEELERGLSILEE 412
                                       *********************9986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.8e-06     0.052     149     235 ..     199     281 ..     164     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-06
                                       EEEEEEESS-TTT--B--HHHH.HHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTT CS
                     Aminotran_1_2 149 tkvilvesphNPtGtvatleel.eklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKaf 223
                                       +  ++ve+++   G    ++e+ + l ++++k+++ll+vDe+ ag   + + +    ++ e+++  ++i  +lsK++
  gi|386002147|ref|YP_005920446.1| 199 PAAVIVETVQGEGGINVARNEWlRSLEAVCRKHGILLIVDEIQAGCGRTGT-F---FSFEEAGISpDII--TLSKSL 269
                                       56777777777778777777663678889*************999998843.3...4455555554444..789999 PP

                                       SSGGG-EEEEEE CS
                     Aminotran_1_2 224 GlaGeRvGyilg 235
                                       + +G+ +  +l 
  gi|386002147|ref|YP_005920446.1| 270 SGYGLPLSLVLM 281
                                       988876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3184.62
//
Query:       gi|386002148|ref|YP_005920447.1|  [L=163]
Description: Ectoine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-55  185.3   0.0    8.9e-30  103.5   0.0    2.0  2  Ectoine_synth  Ectoine synthase
     0.0032   17.2   0.4       0.97    9.2   0.3    2.3  2  Cupin_2        Cupin domain


Domain annotation for each model (and alignments):
>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.0   9.9e-34   8.9e-30       1      76 [.       1      76 [.       1      83 [. 0.97
   2 !   80.0   0.0   1.9e-26   1.7e-22      73     126 ..      96     149 ..      89     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 9.9e-34
                                      -EEEEHHHHTTSTTEEEETTEEEEEEE-GGGSSSSEEEEEEE-TT--EEEE-TT-EEEEEEEE--EEEEETTT--E CS
                     Ectoine_synth  1 mivrtleeiekterevksenweskRlllkddgmGfslhettikagtetelkYknHleavycieGegeveeledgev 76
                                      mivr+l+e+e+t r+v + nwes+Rlllk dgmGfs+h+tti+ gtet + YknHle+vyc+eGegeve le ge 
  gi|386002148|ref|YP_005920447.1|  1 MIVRRLSEAERTGRRVVAANWESTRLLLKGDGMGFSFHITTIYPGTETLICYKNHLESVYCLEGEGEVEVLEGGEA 76
                                      9**********************************************************************99975 PP

  == domain 2  score: 80.0 bits;  conditional E-value: 1.9e-26
                                       T--EEEE-TTEEEEETTT-EEEEEESS-EEEEEEEES--XSSSTTTTBXXXXXX CS
                     Ectoine_synth  73 dgevyeikpgtlYlldkhdkHllrakkelrlvcvFnPpltGkevHdedgvyple 126
                                        g+v++i pgt+Y+ld+hd+Hllrak+ lrl+cvFnPpl G+evHde+g+yple
  gi|386002148|ref|YP_005920447.1|  96 GGRVFKIAPGTIYALDRHDRHLLRAKTPLRLACVFNPPLRGREVHDEEGAYPLE 149
                                       699************************************************986 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3   0.00011      0.97       5      37 ..      42      74 ..      38      79 .. 0.70
   2 !    5.9   0.0    0.0012        11      35      71 .]      96     130 ..      93     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                                      EETTEEEEEECSSSEEEEEEEEESEEEEE.ECTE CS
                           Cupin_2  5 lppGesapshrHpgedeffyVleGegelt.vdge 37
                                      + pG+++   +  +  e +y+leGege++ ++g 
  gi|386002148|ref|YP_005920447.1| 42 IYPGTETLICYKNHL-ESVYCLEGEGEVEvLEGG 74
                                      556665555554555.88**********976654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0012
                                       CTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
                           Cupin_2  35 dgeeveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                                       +g+++++ +G ++  +++ +H +r  +  p+rl +v+
  gi|386002148|ref|YP_005920447.1|  96 GGRVFKIAPGTIYALDRHDRHLLRAKT--PLRLACVF 130
                                       78999******************9999..99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1212.13
//
Query:       gi|386002149|ref|YP_005920448.1|  [L=107]
Description: cupin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-12   46.2   0.1    3.4e-12   45.9   0.1    1.1  1  Cupin_2       Cupin domain
     0.0016   18.3   0.1     0.0021   18.0   0.1    1.1  1  AraC_binding  AraC-like ligand binding domain
      0.006   16.3   0.0     0.0071   16.0   0.0    1.2  1  Cupin_3       Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.018   15.2   0.0    1.2  1  CENP-C_C      Mif2/CENP-C like
      0.035   13.7   0.0      0.045   13.4   0.0    1.1  1  DMSP_lyase    Dimethlysulfonioproprionate lyase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.1   9.6e-16   3.4e-12       4      62 ..      34      91 ..      31      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 9.6e-16
                                      EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SS CS
                           Cupin_2  4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgd 62
                                      +l  G   p+h+Hp+e +++y ++G++ l +++ee+e e+Gds+ +p g++H+    +d
  gi|386002149|ref|YP_005920448.1| 34 RLSRGSHLPQHSHPQE-QTGYMVSGRMLLSIGSEEFEAERGDSWCIPGGVEHGALILED 91
                                      566788899*******.***********************************9755444 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.9e-07    0.0021      13      59 ..      38      84 ..      28      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.9e-07
                                      T-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-E CS
                      AraC_binding 13 dhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepH 59
                                      + + p+h h++ + +y+++G+  l+++ ++++++ Gd   +p g+ H
  gi|386002149|ref|YP_005920448.1| 38 GSHLPQHSHPQEQTGYMVSGRMLLSIGSEEFEAERGDSWCIPGGVEH 84
                                      45569*********************************999999999 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-06    0.0071      25      61 ..      48      83 ..      37     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
                                      SEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3 25 edEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                      ++++ y+++G++ +   g+e++e + GD++ +p g +
  gi|386002149|ref|YP_005920448.1| 48 QEQTGYMVSGRMLLSI-GSEEFEAERGDSWCIPGGVE 83
                                      45666***********.****************9983 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.1e-06     0.018      26      68 ..      41      83 ..      32      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                                      EEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-E CS
                          CENP-C_C 26 kkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagne 68
                                       +++s+ +  + y + Gr+  ++  ++f + +g+++ +P g e
  gi|386002149|ref|YP_005920448.1| 41 LPQHSHPQEQTGYMVSGRMLLSIGSEEFEAERGDSWCIPGGVE 83
                                      579999999999***************************8865 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.045     107     152 ..      40      84 ..      35      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                        DMSP_lyase 107 rYPdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikh 152
                                       + P+H+h++e + +++sg ++++ g +e ++ + G+++  + g++h
  gi|386002149|ref|YP_005920448.1|  40 HLPQHSHPQEQTGYMVSGRMLLSIGSEE-FEAERGDSWCIPGGVEH 84 
                                       67********************999999.78899999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      136  (0.00758548); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 724.10
//
Query:       gi|386002150|ref|YP_005920449.1|  [L=220]
Description: hypothetical protein Mhar_1462 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.13   11.5   0.2        0.2   10.9   0.2    1.2  1  LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic
        1.5    7.5   2.1        8.3    5.0   0.0    2.0  2  DUF2207    Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic anhydrases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   2.2e-05       0.2      56      78 ..      72      97 ..      67     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.2e-05
                                      BGGG--TTHHHHHHHHHTTS-T...T CS
                         LCIB_C_CA 56 GLaGfpfaGktGlgAalsHvPd...d 78
                                      ++aG+ f+G  G++A + H P    +
  gi|386002150|ref|YP_005920449.1| 72 SMAGVAFLGPVGMAALCRHCPHysrG 97
                                      79*******************97643 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0   0.00093       8.3     379     444 ..      36     101 ..      22     102 .. 0.83
   2 ?    1.7   0.9    0.0097        87     391     430 ..     128     171 ..     116     181 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.00093
                           DUF2207 379 klkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGael 444
                                       ++  + +  l +++l++ ++ ++ ++ ++++ +l++ + ++++++ + ++ + r  +++++ G++l
  gi|386002150|ref|YP_005920449.1|  36 ERRLFVLSQLPFFFLSFSGMGAVGAATGVWWPLLAYSMAGVAFLGPVGMAALCRHCPHYSRGGTRL 101
                                       555666777778888888888888888999******************************999875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.0097
                           DUF2207 391 iilglilillallllvll....lvfllilllillliaiivlllf 430
                                       +il++++ill+ +++++     l++ +   l+++l++++ +l +
  gi|386002150|ref|YP_005920449.1| 128 VILFIAFILLFPIVVQGYgawqLSGRGPAPLGIALAGLGTALAA 171
                                       22222222222222222233565555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1360.81
//
Query:       gi|386002151|ref|YP_005920450.1|  [L=149]
Description: hypothetical protein Mhar_1463 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 919.22
//
Query:       gi|386002152|ref|YP_005920451.1|  [L=252]
Description: hypothetical protein Mhar_1464 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.4   0.0    2.7e-06   27.2   0.0    2.0  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
      1e-09   38.2   0.0    5.1e-09   36.0   0.0    2.2  3  Sulfatase      Sulfatase
    2.5e-05   23.8   0.0    0.00012   21.5   0.0    1.9  2  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
       0.14   11.4   0.0       0.25   10.6   0.0    1.3  1  Arena_ncap_C   Arenavirus nucleocapsid C-terminal domain


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0     6e-10   2.7e-06       5      65 ..      45     103 ..      41     113 .. 0.83
   2 !   22.5   0.0   1.7e-08   7.5e-05     157     233 ..     157     227 ..     108     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6e-10
                                       EETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--S CS
                      Phosphodiest   5 slDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivg 65 
                                       ++D+l   l   l   lpn++++a+eg+  +     + t T p+ as++TGl P +HGi +
  gi|386002152|ref|YP_005920451.1|  45 IVDSLGYGLYTSLEPYLPNMRKMAREGLLLE--AEAVATSTTPAIASILTGLLPQNHGISN 103
                                       5777777777766449***************..5566677889***************965 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.7e-08
                                       HHCHTHSHHHHHCT.....SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEE CS
                      Phosphodiest 157 ldaafakvvlekel.....ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniil 228
                                       +d++     + +++     ++p++l+ ++ ++D++ H+ G   +e+++a + +D  ig++ +a+ er       +++
  gi|386002152|ref|YP_005920451.1| 157 FDRQ-----ILARSiealeGDPRVLVAHFVGIDRAAHRGG-GIEEIREAASAIDGLIGEMAAAISER-----AILMV 222
                                       2223.....3333334445******************998.9999**********************.....889** PP

                                       EES-- CS
                      Phosphodiest 229 vSDHG 233
                                        +DH 
  gi|386002152|ref|YP_005920451.1| 223 CGDHP 227
                                       ***95 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.23     1e+03     294     309 .]       5      20 ..       2      20 .. 0.86
   2 !   36.0   0.0   1.1e-12   5.1e-09       7      99 ..      45     129 ..      40     183 .. 0.86
   3 ?   -2.3   0.0       0.5   2.3e+03     222     259 ..     204     236 ..     195     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.23
                                       EEGGGHHHHHHHHTTE CS
                         Sulfatase 294 vshiDlfptildlagi 309
                                       + ++D++pt+++++g+
  gi|386002152|ref|YP_005920451.1|   5 IKLVDVAPTMARVLGV 20 
                                       6789********9996 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 1.1e-12
                                       EESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHCTTTS- CS
                         Sulfatase   7 laddlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggglpqtea 83 
                                       ++d+l   + gly    ++ pn+ ++a+egl++    +a+ +++p+ a++ltg+ p+n+g+ +++    +    +  
  gi|386002152|ref|YP_005920451.1|  45 IVDSL---GYGLYTSLEPYLPNMRKMAREGLLLEAEAVAT-STTPAIASILTGLLPQNHGISNTS----QASESEIR 113
                                       67888...5577777788899***************9995.*******************98888....7889999* PP

                                       HHHHHHHHTT-EEEEE CS
                         Sulfatase  84 tLpellkeaGYntaai 99 
                                       +L+e+  + G+++a++
  gi|386002152|ref|YP_005920451.1| 114 SLLEWAGSEGVRSAVV 129
                                       **********999765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTT CS
                         Sulfatase 222 DdligrvlaaLeenglldntlvvftSDhgasleesngp 259
                                       D lig+  aa+     ++ +++++ +Dh  + ++ +g+
  gi|386002152|ref|YP_005920451.1| 204 DGLIGEMAAAI-----SERAILMVCGDHPIHAGKLQGV 236
                                       55555555555.....8899999999999988765555 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.12   5.5e+02       2      35 ..      40      92 ..      39     113 .. 0.62
   2 !   21.5   0.0   2.7e-08   0.00012     118     186 ..     160     227 ..     122     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                                      EEEEEEETTBB----...................GGGTTHHHS--HHHHHHHH CS
                                      xxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  2 kvvlvvlDGlGeapa...................delnaihvAktPtldkLkk 35
                                      +v+l ++D+lG++                      e++a+  + tP + ++ +
  gi|386002152|ref|YP_005920451.1| 40 RVALAIVDSLGYGLYtslepylpnmrkmaregllLEAEAVATSTTPAIASILT 92
                                      68899999999887655555666655555555554455566666666666544 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT.-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 118 evaekaldailsgkfdlvvvniknaDmvGHtg.dleatiaaieaaDeavkeildaieqvdgilvvtADHg 186
                                       ++  + ++a+ +g+  ++v +++  D ++H+g  +e+  +a  a+D  ++e+  ai++   il+v++DH+
  gi|386002152|ref|YP_005920451.1| 160 QILARSIEAL-EGDPRVLVAHFVGIDRAAHRGgGIEEIREAASAIDGLIGEMAAAISERA-ILMVCGDHP 227
                                       5667788999.776889*************9736999999******************99.********7 PP

>> Arena_ncap_C  Arenavirus nucleocapsid C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.6e-05      0.25      78     133 ..      82     139 ..      65     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
                                       TB-TTHHHHHHHHS-TT-EE..EESSHH.HHHHHHHHTT-TTSEEEE-B--HHHHTTTH CS
                      Arena_ncap_C  78 daqpgllsavigalprnmvi..tcqgsd.dirklldsqgrkdiklidvkltkedsrkye 133
                                       ++ p + s + g+lp+n  i  t+q s+ +ir ll+  g   ++   v + +e +r ++
  gi|386002152|ref|YP_005920451.1|  82 STTPAIASILTGLLPQNHGIsnTSQASEsEIRSLLEWAGSEGVRS-AVVMEEEGARTFQ 139
                                       689*************98883357888648*******99999986.4668888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1603.01
//
Query:       gi|386002153|ref|YP_005920452.1|  [L=366]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-42  143.9   0.0    9.8e-42  143.5   0.0    1.1  1  DUF362    Domain of unknown function (DUF362)
    1.8e-07   30.8  13.7    3.1e-05   23.8   3.6    2.4  2  Fer4_2    4Fe-4S binding domain
    4.6e-06   26.2  16.2     0.0066   16.2   2.6    2.9  2  Fer4      4Fe-4S binding domain
    9.1e-06   26.5   3.7      0.032   15.2   0.6    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    5.3e-05   23.3  10.0     0.0011   19.1  11.1    2.1  3  Fer4_9    4Fe-4S dicluster domain
    0.00016   22.2  10.7    0.00061   20.3  11.0    1.8  1  Fer4_7    4Fe-4S dicluster domain
    0.00034   20.7   8.7     0.0014   18.7   8.8    1.9  2  Fer4_21   4Fe-4S dicluster domain
    0.00055   19.9  13.2      0.072   13.2   4.1    2.6  2  Fer4_6    4Fe-4S binding domain
    0.00062   20.3   5.2       0.28   11.8   0.2    2.3  2  Fer4_17   4Fe-4S dicluster domain
      0.002   18.5   2.8       0.74   10.3   0.3    2.3  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   16.4   8.8      0.029   15.2   1.2    2.4  2  Fer4_22   4Fe-4S dicluster domain
      0.017   15.6  13.1       0.57   10.8   2.0    2.3  2  Fer4_4    4Fe-4S binding domain
      0.027   14.6  13.5       0.14   12.3   2.3    2.2  2  Fer4_10   4Fe-4S dicluster domain
       0.19   10.9   0.5       0.31   10.2   0.5    1.2  1  Lar_N     Lactate racemase N-terminal domain
       0.93   10.3  12.2        4.7    8.0   2.5    2.5  2  Fer4_15   4Fe-4S single cluster domain
        2.8    9.1  19.1        9.9    7.4   3.8    2.6  2  Fer4_3    4Fe-4S binding domain
        5.2    7.7  11.7        7.3    7.2   1.9    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5   0.0   9.3e-45   9.8e-42       2     203 .]      42     311 ..      41     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 9.3e-45
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxx..xxx RF
                            DUF362   2 aiKpNlgeagnpegatthpevvravvellkeagagkiivgdspglyv.srgka..hrevaeeagydelaega..dia 73 
                                       aiK+++ge+gn ++  ++p++vr+vv+ +ke g g+++++d+ +ly  sr++a  h+ +a ++g+d  + ga  +ia
  gi|386002153|ref|YP_005920452.1|  42 AIKLHFGEQGNETY--VRPAFVRPVVDKVKEVG-GRPFLTDTATLYGgSRKDAvgHLLTALAHGFDLSSAGAplIIA 115
                                       8**********998..***************99.9**********8558888899***********97778889*** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....... RF
                            DUF362  74 dglegedevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs....... 142
                                       dgl g++ v+v++ g+hl+  +kia +++ a ++I+l+++KgH++ag++ga+Kn ++Gc++ sgka++H        
  gi|386002153|ref|YP_005920452.1| 116 DGLSGKNFVEVEIGGRHLQG-VKIAGDLAAAASMIVLSHFKGHSMAGFGGAIKNlGMGCAPPSGKADQHWaskpava 191
                                       *******9999996667666.******************************************************** PP

                                       ..................................................xxxxxxxxxxxxxxxxx.x..xxx... RF
                            DUF362 143 ..................................................krdsekfaekiadlaka.l..kpd... 163
                                                                                         ++    f ++++++a + +  k     
  gi|386002153|ref|YP_005920452.1| 192 eegctgcgrcaslcsrsaivlevgkawvdpevctgcgaclacpegamdldWERMPIFIQRLVEYALGaVsgK-Vgrl 267
                                       ************************************************97555889***********88752.3455 PP

                                       ..xxxxxxx.....xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                            DUF362 164 ..lnvvdgi.....kamegegpsggskelglv.laStDpvalDaaaad 203
                                         +n+v+++     +a + + p      +++  laS+Dpva+Daa++d
  gi|386002153|ref|YP_005920452.1| 268 gfINFVMDVtpecdCAPWSDPPIV----PDVGiLASKDPVAVDAASLD 311
                                       678999999565554444455522....223259***********976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.5   0.00013      0.13       3      20 ..     188     205 ..     186     207 .. 0.83
   2 !   23.8   3.6     3e-08   3.1e-05       2      22 .]     216     235 ..     215     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       ++v ++ C+gCg C s C
  gi|386002153|ref|YP_005920452.1| 188 PAVAEEGCTGCGRCASLC 205
                                       5566788*********99 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3e-08
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +++vd++ C+gCgaC  aCP+
  gi|386002153|ref|YP_005920452.1| 216 KAWVDPEVCTGCGAC-LACPE 235
                                       68*************.****5 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.6   6.2e-06    0.0066       5      23 ..     192     210 ..     188     211 .. 0.85
   2 !   14.3   5.9   2.6e-05     0.027       2      22 ..     218     237 ..     217     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.2e-06
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       ee C+gCG+C++ C   AI
  gi|386002153|ref|YP_005920452.1| 192 EEGCTGCGRCASLCSRSAI 210
                                       789***********88877 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.6e-05
                                       EEETTTSSS-THHHHHSTTTE CS
                              Fer4   2 videekCigCGaCvevCPvgA 22 
                                        +d+e C+gCGaC  +CP gA
  gi|386002153|ref|YP_005920452.1| 218 WVDPEVCTGCGACL-ACPEGA 237
                                       69***********5.677776 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   3.1e-05     0.032       2      24 ..     195     217 ..     194     222 .. 0.84
   2 !   12.2   0.1   0.00025      0.27       2      20 ..     224     241 ..     223     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                       C++Cg+Ca+ C  +ai  +  k 
  gi|386002153|ref|YP_005920452.1| 195 CTGCGRCASLCSRSAIVLEVGKA 217
                                       ****************9885555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++Cg+C+ +CP++a++ +
  gi|386002153|ref|YP_005920452.1| 224 CTGCGACL-ACPEGAMDLD 241
                                       *******8.8******988 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.4   6.2e-05     0.065      33      51 .]     187     210 ..     171     211 .. 0.70
   2 !   19.1  11.1     1e-06    0.0011       2      50 ..     195     237 ..     194     238 .. 0.91
   3 !   13.2   1.5   7.2e-05     0.076       2      24 ..     224     245 ..     223     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                            Fer4_9  33 e.....eaCigCgaCveaCpkgai 51 
                                       +     e C+gCg+C+  C + ai
  gi|386002153|ref|YP_005920452.1| 187 KpavaeEGCTGCGRCASLCSRSAI 210
                                       13333468***********99887 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       CtgCg+C + C   ++v + ++  +  +      C+gCgaC+ aCp+ga
  gi|386002153|ref|YP_005920452.1| 195 CTGCGRCASLCSRSAIVLEVGKAWVDPEV-----CTGCGACL-ACPEGA 237
                                       *********************99999854.....*******8.799987 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 7.2e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaer 24 
                                       CtgCgaC + Cp g++  d+ + 
  gi|386002153|ref|YP_005920452.1| 224 CTGCGACLA-CPEGAMDLDWERM 245
                                       *******99.*****99887765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  11.0   5.8e-07   0.00061       2      52 .]     195     237 ..     194     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.8e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C+gCg+C++ C+ +ai l+       + k+ +dpe C+gCgaC  +CP ga
  gi|386002153|ref|YP_005920452.1| 195 CTGCGRCASLCSRSAIVLE-------VGKAWVDPEVCTGCGACL-ACPEGA 237
                                       ******************3.......458899***********7.699887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.5   8.4e-05     0.089      35      52 ..     189     206 ..     177     212 .. 0.74
   2 !   18.7   8.8   1.3e-06    0.0014       3      57 ..     190     238 ..     188     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-05
                           Fer4_21  35 kvvedeCvGCnlCssvCP 52 
                                       +v e+ C+GC  C+s C 
  gi|386002153|ref|YP_005920452.1| 189 AVAEEGCTGCGRCASLCS 206
                                       567889999999999995 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.3e-06
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       + e+ C gCg+C+  C+     ai ++   ++ v  + C+GC  C+  CP e+++
  gi|386002153|ref|YP_005920452.1| 190 VAEEGCTGCGRCASLCS---RSAIVLEVG-KAWVDPEVCTGCGACL-ACP-EGAM 238
                                       67999***********9...588887644.457999*********8.599.5665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.7   0.00023      0.25       6      24 .]     192     210 ..     187     210 .. 0.79
   2 !   13.2   4.1   6.9e-05     0.072       2      23 ..     217     237 ..     216     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                       ++ C+gCg+C++ C   ai
  gi|386002153|ref|YP_005920452.1| 192 EEGCTGCGRCASLCSRSAI 210
                                       555**********997776 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.9e-05
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       + +dp+ C+gCg+C  +CPega
  gi|386002153|ref|YP_005920452.1| 217 AWVDPEVCTGCGACL-ACPEGA 237
                                       789***********6.799987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.0   0.00078      0.82      45      57 ..     194     206 ..     170     217 .. 0.73
   2 !   11.8   0.2   0.00027      0.28       2      17 ..     224     238 ..     223     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00078
                           Fer4_17  45 lCieCgeCerkCP 57 
                                        C++Cg+C++ C 
  gi|386002153|ref|YP_005920452.1| 194 GCTGCGRCASLCS 206
                                       5666666666664 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00027
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C++Cg+Cl+ Cp ++ 
  gi|386002153|ref|YP_005920452.1| 224 CTGCGACLA-CPEGAM 238
                                       *********.**8765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3    0.0007      0.74      49      62 ..     193     206 ..     151     214 .. 0.77
   2 !    8.4   0.1    0.0028         3       4      16 ..     223     234 ..     220     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0007
                            Fer4_8  49 wsCttcgaCtevCp 62 
                                       + Ct+cg+C++ C 
  gi|386002153|ref|YP_005920452.1| 193 EGCTGCGRCASLCS 206
                                       56777777777775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0028
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                        C++CgaC + Cp
  gi|386002153|ref|YP_005920452.1| 223 VCTGCGACLA-CP 234
                                       5999999988.87 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.2   2.7e-05     0.029      76      94 ..     189     207 ..     179     209 .. 0.81
   2 ?    5.1   1.2     0.039        41      78      93 ..     220     234 ..     212     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                        + e+gC+GCgRC + c  
  gi|386002153|ref|YP_005920452.1| 189 AVAEEGCTGCGRCASLCSR 207
                                       56789************85 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.039
                           Fer4_22  78 gesgCvGCgRCieacp 93 
                                       + ++C+GCg C + cp
  gi|386002153|ref|YP_005920452.1| 220 DPEVCTGCGACLA-CP 234
                                       5679*******74.65 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.6    0.0013       1.3       2      15 ..     193     206 ..     192     209 .. 0.89
   2 ?   10.8   2.0   0.00054      0.57       1      15 [.     221     234 ..     221     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e C+gCg+C + C+
  gi|386002153|ref|YP_005920452.1| 193 EGCTGCGRCASLCS 206
                                       56*********996 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00054
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +e C+gCg+C a CP
  gi|386002153|ref|YP_005920452.1| 221 PEVCTGCGACLA-CP 234
                                       588*******99.88 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  14.7   0.00094         1       6      55 ..     192     233 ..     187     234 .. 0.78
   2 ?   12.3   2.3   0.00013      0.14       2      22 ..     217     236 ..     216     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       ++ C++Cg+C + C +       +++  e ++  +++e CtgcgaC + C
  gi|386002153|ref|YP_005920452.1| 192 EEGCTGCGRCASLC-S------RSAIVLEVGKAWVDPEVCTGCGACLA-C 233
                                       688***********.4......5666666666666999********85.5 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                           Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                       + +d++ C++Cg+C + CP  
  gi|386002153|ref|YP_005920452.1| 217 AWVDPEVCTGCGACLA-CPEG 236
                                       5789**********97.*993 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00029      0.31     145     188 ..     136     179 ..     129     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                             Lar_N 145 veinklvaeadlviltGfiepHyfaGfsGGrKsilpGvasreti 188
                                       v+i    a a  +i++   + H +aGf+G  K +  G+a  +  
  gi|386002153|ref|YP_005920452.1| 136 VKIAGDLAAAASMIVLSHFKGHSMAGFGGAIKNLGMGCAPPSGK 179
                                       667777888999999999********************976555 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.3    0.0086       9.1       5      19 ..     192     206 ..     189     217 .. 0.81
   2 ?    8.0   2.5    0.0044       4.7       2      19 ..     218     234 ..     217     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0086
                           Fer4_15   5 rdaCigcglCvaeap 19 
                                       ++ C+gcg+C+ +++
  gi|386002153|ref|YP_005920452.1| 192 EEGCTGCGRCASLCS 206
                                       578**********96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0044
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       +vD + C+gcg+C+a  p
  gi|386002153|ref|YP_005920452.1| 218 WVDPEVCTGCGACLAC-P 234
                                       69***********984.4 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.8    0.0094       9.9       1      12 [.     195     206 ..     195     209 .. 0.87
   2 ?    7.2   7.4     0.011        11       1      15 []     224     237 ..     224     237 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0094
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       CtgCg+C   C 
  gi|386002153|ref|YP_005920452.1| 195 CTGCGRCASLCS 206
                                       ********9996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       CtgCgaC+ +CP+gA
  gi|386002153|ref|YP_005920452.1| 224 CTGCGACL-ACPEGA 237
                                       ********.****98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.9    0.0069       7.3       3      17 ..     192     206 ..     190     208 .. 0.87
   2 ?    5.6   2.5     0.022        23       1      16 [.     219     233 ..     219     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0069
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       ++ C++cg C++l+ 
  gi|386002153|ref|YP_005920452.1| 192 EEGCTGCGRCASLCS 206
                                       589**********95 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       VD + C++cgaC + +
  gi|386002153|ref|YP_005920452.1| 219 VDPEVCTGCGACLA-C 233
                                       899*********74.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2788.56
//
Query:       gi|386002154|ref|YP_005920453.1|  [L=693]
Description: CoA-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-74  249.8   0.1    3.6e-74  249.0   0.1    1.4  1  ATP-grasp_5    ATP-grasp domain
      3e-45  153.4   0.7    6.2e-45  152.4   0.7    1.6  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.3e-21   77.3   0.0    3.8e-21   75.7   0.0    1.9  1  CoA_binding_2  CoA binding domain
    1.6e-10   41.5   0.1    6.1e-10   39.6   0.0    2.1  2  CoA_binding    CoA binding domain
     0.0059   16.2   0.4       0.01   15.4   0.4    1.3  1  ATP-grasp_2    ATP-grasp domain
  ------ inclusion threshold ------
      0.077   12.5   0.0       0.16   11.4   0.0    1.5  1  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.0   0.1   1.2e-77   3.6e-74       2     222 .]      17     231 ..      16     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 249.0 bits;  conditional E-value: 1.2e-77
                       ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevr 78 
                                       a ae+r++L e+e+k++le +gi+++ + +a+s+eeav +ae+igypvvlKi+sp+++hK+d+gGv+l+lk +eev 
  gi|386002154|ref|YP_005920453.1|  17 AEAEDRRYLMEHEVKAVLEGLGISTTGSGVARSEEEAVGMAEAIGYPVVLKIASPEVVHKSDAGGVKLDLKGPEEVG 93 
                                       77899************************************************************************ PP

                       ATP-grasp_5  79 aaaeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlar 155
                                       +a++e++e+++     ++i gv+Vq+ma+  g+E ivgv++Dp+FGp+++fGlGG+ ve+l+dv+++  p+++++a+
  gi|386002154|ref|YP_005920453.1|  94 RAYAEMVEAFRG----KEIFGVSVQRMAP-PGTEAIVGVARDPTFGPILMFGLGGIFVEILRDVSLRSIPITEADAE 165
                                       *********966....89***********.9********************************************** PP

                       ATP-grasp_5 156 eliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                       ++i+ +k  +ll+g+rg+  ad+ al+ ll+++s+Lvv +peI e+d+nP++ ++eg  ++Dari +
  gi|386002154|ref|YP_005920453.1| 166 DMIRGIKGRPLLEGYRGR-SADIPALKALLLEISDLVVRHPEIGEMDLNPVILYPEGYAVVDARIII 231
                                       ******************.*********************************************986 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.7   2.1e-48   6.2e-45       1     137 [.     398     533 ..     398     534 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 2.1e-48
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G+i+lisq G  a a + w  ++ ++f  v+++Gn++d++++d+le++++d++++v+++ylEs++ gr+f++aarr
  gi|386002154|ref|YP_005920453.1| 398 KGNIGLISQAGVCA-AGMLWGLRHIMDFGIVATIGNKLDINETDMLEAVSADENVEVVCMYLESVKGGRRFIDAARR 473
                                       69*******99655.5566888888**************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                       ++r+kp+++lksGr+eag+ra+asht+++ag+d v++a+f qaGv+r+++ e +f++a++
  gi|386002154|ref|YP_005920453.1| 474 ITREKPIIALKSGRTEAGKRAVASHTASIAGDDLVYSAVFSQAGVIRARDYEHMFNLARA 533
                                       *********************************************************987 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   1.3e-24   3.8e-21       1     115 [.     255     381 ..     255     382 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.3e-24
                                       --EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivke 74 
                                       r+iaV+Gas ++gk g  v+ +l +   +g + +p+np++e+i g k+y+++++ ++p+d+++++++++ tpe+vke
  gi|386002154|ref|YP_005920453.1| 255 RSIAVIGASGTRGKLGWNVFCNLINhdfQG-ELYPINPRAESIMGIKAYPRISAVKKPIDVAVILVQASMTPEVVKE 330
                                       79***********************78778.9*********************857********************* PP

                                       HHHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  75 alalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilveg 115
                                       +++ g+k v++ ++            +ee+ ++ +++g+r++g++C ++++
  gi|386002154|ref|YP_005920453.1| 331 CCDSGVKYVIVESAgfaemgeagrRIEEEMKAITDAYGVRLLGPNCSGIIN 381
                                       **********************999999*******************9975 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   2.1e-13   6.1e-10       3      92 ..     254     341 ..     252     345 .. 0.95
   2 ?   -2.8   0.0       3.7   1.1e+04      43      53 ..     664     674 ..     648     683 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.1e-13
                                       TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqe 77 
                                       + +++viGa+g+ ++++  +f + ++  ++ +++++npr  ++ + g+++y+ ++ +++   +dvavi+v a    e
  gi|386002154|ref|YP_005920453.1| 254 PRSIAVIGASGTRGKLGwNVFCNLINHDFQgELYPINPR--AESIMGIKAYPRISAVKKP--IDVAVILVQASMTPE 326
                                       5789***********************************..*******************..*************** PP

                                       HHHHHHHTT-SEEEE CS
                       CoA_binding  78 avdelveagikgivi 92 
                                       +v+e+ + g+k +++
  gi|386002154|ref|YP_005920453.1| 327 VVKECCDSGVKYVIV 341
                                       ***********9987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                       CEETTEEEESC CS
                       CoA_binding  43 tevlglpvyks 53 
                                        e  g+pvy++
  gi|386002154|ref|YP_005920453.1| 664 MENAGIPVYQT 674
                                       45568888866 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   3.3e-06      0.01       2      76 ..      25     100 ..      24     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-06
                                       E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEE.E--SSSTCCCTTCEEE.ESSHHHHHHHHHCCT CS
                       ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvK.aQvlaGGRGKagGvkl.vkskeeakeaakell 76 
                                       l E++ k +l+  g++++ + va+s+eea  +a+ +g  + v+K a   +  +  agGvkl  k +ee+ +a  e++
  gi|386002154|ref|YP_005920453.1|  25 LMEHEVKAVLEGLGISTTGSGVARSEEEAVGMAEAIGYPV-VLKiASPEVVHKSDAGGVKLdLKGPEEVGRAYAEMV 100
                                       78************************************99.77747888999999****985678888888777775 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.5e-05      0.16      12      46 ..      37      69 ..      27      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                                      TT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEET CS
                       CPSase_L_D2 12 invpvvpssaapvetleealaiakeigyPviikaa 46
                                      +++ +  s  a  +++eea+ +a+ igyPv++k a
  gi|386002154|ref|YP_005920453.1| 37 LGISTTGSGVA--RSEEEAVGMAEAIGYPVVLKIA 69
                                      55555555444..9******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4735.43
//
Query:       gi|386002155|ref|YP_005920454.1|  [L=161]
Description: hypothetical protein Mhar_1467 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1188.66
//
Query:       gi|386002156|ref|YP_005920455.1|  [L=155]
Description: hypothetical protein Mhar_1468 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0093   16.3   0.0      0.017   15.5   0.0    1.5  1  MREG      Melanoregulin


Domain annotation for each model (and alignments):
>> MREG  Melanoregulin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.2e-07     0.017      32      81 ..      95     144 ..      60     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.2e-07
                              MREG  32 qkrsklekgseeyrkLsldiealrqvrrevrdrWkkiLekLGfkkeadsl 81 
                                       ++r  +++g + + +L   + a ++++  + ++W+k++ +LG++ e++ +
  gi|386002156|ref|YP_005920455.1|  95 RERCAIKEGINAFARLGAGLVAKQHCKTCIESHWRKVFADLGMNLEVEEM 144
                                       567788999***********************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1096.38
//
Query:       gi|386002157|ref|YP_005920456.1|  [L=4560]
Description: hypothetical protein Mhar_1469 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.9e-188  610.8 175.3    3.5e-14   52.9   1.6   30.0 30  DUF11       Domain of unknown function DUF11
    1.4e-13   51.2   0.1    1.4e-12   48.0   0.1    3.0  1  LTD         Lamin Tail Domain
    1.8e-13   50.8  16.8        2.9    8.1   0.0   15.8 20  bMG10       Bacterial Alpha-2-macroglobulin MG10 domain
    2.7e-08   34.0  10.9        0.2   12.0   0.1   11.0 14  Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.4    0.0012       5.5       8      51 ..      79     122 ..      74     161 .. 0.82
   2 ?    1.6   0.0     0.076   3.4e+02      40      85 ..     267     308 ..     229     315 .. 0.69
   3 !   32.4   0.3   1.9e-11   8.5e-08       2      80 ..     339     415 ..     338     423 .. 0.88
   4 ?   -2.2   0.1       1.2   5.2e+03      14      36 ..     465     487 ..     455     528 .. 0.67
   5 !    4.5   0.0    0.0099        45       1      83 [.     580     667 ..     580     674 .. 0.77
   6 !   21.9   0.4   3.7e-08   0.00017      19      75 ..    1015    1081 ..    1007    1094 .. 0.68
   7 !   31.0   0.0   5.1e-11   2.3e-07      12      80 ..    1135    1216 ..    1127    1220 .. 0.90
   8 !   42.2   0.8   1.7e-14   7.5e-11       1      83 [.    1258    1341 ..    1258    1348 .. 0.91
   9 !    7.5   0.0    0.0011       5.1      17      51 ..    1388    1421 ..    1386    1473 .. 0.82
  10 !   20.0   0.6   1.4e-07   0.00063      11      76 ..    1523    1596 ..    1514    1608 .. 0.72
  11 !    6.3   0.1    0.0027        12      11      51 ..    1643    1684 ..    1634    1721 .. 0.79
  12 !   21.9   2.0   3.7e-08   0.00016       2      89 ..    1769    1870 ..    1768    1872 .. 0.76
  13 !    6.4   0.5    0.0024        11      12      52 ..    1925    1985 ..    1919    2024 .. 0.69
  14 !   32.7   0.6   1.5e-11   6.6e-08       1      89 [.    2060    2156 ..    2060    2158 .. 0.80
  15 !    8.2   0.3   0.00069       3.1      12      79 ..    2211    2298 ..    2205    2311 .. 0.78
  16 !   34.9   0.1   3.1e-12   1.4e-08       1      90 [.    2346    2447 ..    2346    2448 .. 0.88
  17 !   33.7   3.9   7.3e-12   3.3e-08       6      89 ..    2489    2577 ..    2486    2579 .. 0.76
  18 !   30.2   3.9   9.1e-11   4.1e-07       9      90 ..    2613    2698 ..    2601    2699 .. 0.78
  19 !   28.0   2.2   4.6e-10     2e-06      12      89 ..    2739    2817 ..    2722    2819 .. 0.79
  20 !   31.3   2.4   4.1e-11   1.8e-07      10      91 .]    2854    2939 ..    2840    2939 .. 0.83
  21 !   33.9   2.9   6.3e-12   2.8e-08       9      91 .]    2973    3059 ..    2961    3059 .. 0.85
  22 !   32.1   2.5   2.4e-11   1.1e-07      11      91 .]    3095    3179 ..    3081    3179 .. 0.84
  23 !   31.7   2.9     3e-11   1.4e-07       9      91 .]    3213    3299 ..    3207    3299 .. 0.85
  24 !   33.8   0.1   6.9e-12   3.1e-08       6      89 ..    3333    3417 ..    3327    3419 .. 0.80
  25 !   26.0   0.2   1.9e-09   8.4e-06       2      89 ..    3449    3537 ..    3448    3539 .. 0.77
  26 !   34.2   1.6   5.2e-12   2.4e-08       9      90 ..    3573    3658 ..    3561    3659 .. 0.79
  27 !   52.9   1.6   7.7e-18   3.5e-14       1      87 [.    3688    3775 ..    3688    3779 .. 0.88
  28 !   24.8   0.0   4.3e-09   1.9e-05       1      80 [.    3807    3885 ..    3807    3890 .. 0.89
  29 !   17.6   0.0   7.6e-07    0.0034      16      79 ..    4288    4354 ..    4278    4365 .. 0.75
  30 !   18.8   0.0   3.2e-07    0.0014      13      90 ..    4410    4486 ..    4399    4487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                             DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                       + v+  + + +++   Ntg+++ n++ ++ t P+g++y  +++ 
  gi|386002157|ref|YP_005920456.1|  79 ASVNICESTGFVVYINNTGTTPENDILLNVTIPSGFSYDDGTTV 122
                                       5689999******************************9888876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.076
                             DUF11  40 PaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasg 85 
                                       P g +  s ++s    s   + g+L+age+ +l f +++ +++ sg
  gi|386002157|ref|YP_005920456.1| 267 PDGSECWSWRSS----SLGATNGDLAAGERIRLDFNLTAGCATPSG 308
                                       666666666666....3444449***************99887665 PP

  == domain 3  score: 32.4 bits;  conditional E-value: 1.9e-11
                             DUF11   2 tKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                        Kt + +e+ +Gd v+ t+tv Ntg  +a +v+ +Dtl +gl++ s  +  g    ++s   +++g+   ++++v+v
  gi|386002157|ref|YP_005920456.1| 339 AKTPTVVEAGAGDVVNWTITVENTGLGPAFNVRMNDTLSSGLNLLSIDSPGGGL--NWSYDVIPPGGVEVVNISVNV 413
                                       688888899*****************************************5555..5555569**********9999 PP

                             DUF11  79 tr 80 
                                       t+
  gi|386002157|ref|YP_005920456.1| 414 TA 415
                                       86 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.2
                             DUF11  14 dtvtytltvtNtgpasangvvvt 36 
                                       + v + + vtN g+   ++++++
  gi|386002157|ref|YP_005920456.1| 465 GRVPVYVNVTNEGAGGITELQLR 487
                                       56788999999999988888876 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.0099
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasa..ngvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatl 72 
                                       + Kt ++s +  G++v++ l vt t ++    ++ ++ D  P+++  + +  +   +g+ + ++  + Le g ++  
  gi|386002157|ref|YP_005920456.1| 580 VSKTANRSVIYLGEEVEFDLEVTYTAGSCGenTTRTIVDSYPSNFLVIDSAGGvndSGNRTITWADQLLEDGVTWNK 656
                                       68*****************9999988776533566899999999985555555755555555555488899999999 PP

                             DUF11  73 sftvrvtrtaa 83 
                                       ++++++ r aa
  gi|386002157|ref|YP_005920456.1| 657 TIRLSADRDAA 667
                                       99999888776 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 3.7e-08
                             DUF11   19 tltvtNtgpasangvvvtDtlPaglayvsvsas..........qgtasaltsvgsLeagesatlsft 75  
                                         + vtNtg  +a++v+v+Dtl + l+yvs++              ++++l+s g++++ +++ +++ 
  gi|386002157|ref|YP_005920456.1| 1015 KIYVTNTGSGTAYNVTVNDTLDSDLSYVSSRIDgsadpanttvVDANHVLWSLGDMPPKKQRVIEMD 1081
                                        689******************8888888888873333333322222223444477777777766555 PP

  == domain 7  score: 31.0 bits;  conditional E-value: 5.1e-11
                             DUF11   12 pGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsL..........eagesatls 73  
                                         Gd+ ++ ++v+N  + ++++v v+  lPag +yv++s++ + +s++++    g+L          ++g+s t++
  gi|386002157|ref|YP_005920456.1| 1135 CGDNSSFLIVVRNGAGPTLYNVSVKEALPAGIEYVPGSSQVAGGSTTSTNfsgGDLewrfdqpegwPPGKSVTIT 1209
                                        69**************************************6666655555678999******************* PP

                             DUF11   74 ftvrvtr 80  
                                        f v+vt 
  gi|386002157|ref|YP_005920456.1| 1210 FDVNVTS 1216
                                        ****986 PP

  == domain 8  score: 42.2 bits;  conditional E-value: 1.7e-14
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.qgtasaltsvgsLeagesatlsf 74  
                                        +tKt + +++ +G  vt t+ +  +g+++a++v++ D+lP+++ yvs++   + t   ++ +g+L+ ges+t+++
  gi|386002157|ref|YP_005920456.1| 1258 ITKTPELTRAGFGRIVTWTIYLYSNGGDPATNVTLFDLLPENTVYVSATPEpNDTDPLRWDFGTLNFGESRTVTL 1332
                                        79999999******************************************977788888888************* PP

                             DUF11   75 tvrvtrtaa 83  
                                         ++vt + a
  gi|386002157|ref|YP_005920456.1| 1333 NANVTYQIA 1341
                                        ***997766 PP

  == domain 9  score: 7.5 bits;  conditional E-value: 0.0011
                             DUF11   17 tytltvtNtgpasangvvvtDtlPaglayvsvsas 51  
                                        ++t+t  N+g a+  + +v+ +lP g+ y  +sa 
  gi|386002157|ref|YP_005920456.1| 1388 NFTITINNNGSAAY-TPRVEEVLPVGFVYKAGSAI 1421
                                        69********9998.99***********9999887 PP

  == domain 10  score: 20.0 bits;  conditional E-value: 1.4e-07
                             DUF11   11 rpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas........qgtasaltsvgsLeagesatlsftv 76  
                                        + G+  + t+ vtN+g+++a++v+v D+l  g+ +v    +        +g  + +++  +++ g+++   +t+
  gi|386002157|ref|YP_005920456.1| 1523 TIGGSAQWTIKVTNSGNSAAYNVTVIDILGDGFVGVAEGDGnktaddptSGYTTIRWTNLTIPVGGTWERGLTA 1596
                                        78999***************************999999888555555544444445554666666666655555 PP

  == domain 11  score: 6.3 bits;  conditional E-value: 0.0027
                             DUF11   11 rpGdtvtytltvtNtgpasa.ngvvvtDtlPaglayvsvsas 51  
                                        + G+  ++t+ v   g     n++++ DtlPagl+y s +  
  gi|386002157|ref|YP_005920456.1| 1643 TIGGFANFTIRVEYWGEGENyNNTRIVDTLPAGLKYDSYQCV 1684
                                        567777888888888877766***************988766 PP

  == domain 12  score: 21.9 bits;  conditional E-value: 3.7e-08
                             DUF11    2 tKtvdks.evrpGdtvtytltvtNt..gpasangvvvtDtlPaglayvsvsas........qgtasaltsv..gs 63  
                                         Kt d+s  v +G++v+yt+ vt t  ++++a ++v++D  P+gla+v++s +        q   +  ++    +
  gi|386002157|ref|YP_005920456.1| 1769 EKTPDPSgIVVAGGEVRYTIRVTHTaaSASDAFDLVINDSIPSGLAFVPGSNTsslttsfsQTGQNLSWTLsrLN 1843
                                        677777777899*******98887722555669******************998888888766666677777778 PP

                             DUF11   64 Leagesatlsftvrvtrtaasga.ltn 89  
                                        L   +s  l++ v+v      ++ l n
  gi|386002157|ref|YP_005920456.1| 1844 LTGANSVLLTYNVTVDLDVLGNTtLLN 1870
                                        888888888888887655544444555 PP

  == domain 13  score: 6.4 bits;  conditional E-value: 0.0024
                             DUF11   12 pGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.....................q 52  
                                         G+ v+yt+ v  + +a+  ++ v+DtlP+gl y + s                       +
  gi|386002157|ref|YP_005920456.1| 1925 IGESVNYTIEVDLP-NATVGDLWVNDTLPSGLIYNTTSLVvldkfgsvltptetlsdpndgT 1985
                                        7999*****99844.55667*************99888776655555555555555555444 PP

  == domain 14  score: 32.7 bits;  conditional E-value: 1.5e-11
                             DUF11    1 ltKtvdks.evrpGdtvtytltvtNtgpasa..ngvvvtDtlPaglayvsvsas....qgtasaltsvgsLeage 68  
                                        +tKt++++ ++  Gdt+ y + vtN+ p+ +   ++v+tD  P gl+yv +s s     ++ ++++++ sL+  +
  gi|386002157|ref|YP_005920456.1| 2060 ITKTFSPAgPFSVGDTIHYEINVTNSAPSRRtaFDLVITDEIPVGLSYVNSSDSgvysGSNRTVTWTFASLALDS 2134
                                        79*****99****************9876553389*******************998444455666779999999 PP

                             DUF11   69 satlsftvrvtrtaasga.ltn 89  
                                         +++++ v+v      ++ l n
  gi|386002157|ref|YP_005920456.1| 2135 WLKVTYNVTVDLDVLGNTtLLN 2156
                                        9999888888665554444666 PP

  == domain 15  score: 8.2 bits;  conditional E-value: 0.00069
                             DUF11   12 pGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.....................qgtasaltsvgsLe 65  
                                         G+ v+yt+ v  + +a+  ++ v+DtlP+gl y + s                       ++t   ++s+g+ +
  gi|386002157|ref|YP_005920456.1| 2211 IGESVNYTIEVDLP-NATVGDLWVNDTLPSGLIYNTTSLVvldkfgavltpaetlsdpndgTSTVYINWSFGTFN 2284
                                        7999*****99844.55667**************99998899999999999999988887766777777778888 PP

                             DUF11   66 agesatlsftvrvt 79  
                                        ++e + + +t  + 
  gi|386002157|ref|YP_005920456.1| 2285 NSEDRDIVITFDAI 2298
                                        88887766554443 PP

  == domain 16  score: 34.9 bits;  conditional E-value: 3.1e-12
                             DUF11    1 ltKtvdks.evrpGdtvtytltvtNtg..pasangvvvtDtlPaglayvsvsas.........qgtasaltsvgs 63  
                                        +tK+v++   v+ Gd+v++tl+v  tg  +++a+++v++D+lP gl+yvs++++          g+ + ++s  +
  gi|386002157|ref|YP_005920456.1| 2346 ITKSVEPFsVVKLGDEVRFTLVVNHTGlsTSDAYDLVIEDVLPLGLTYVSNTSTpeanssayhPGNRTIRWSYDR 2420
                                        79999997699************8887226667*********************9999999887888888888** PP

                             DUF11   64 Leagesatlsftvrvtrtaasgaltnv 90  
                                        Le  ++  l++ ++v ++++ ++++n 
  gi|386002157|ref|YP_005920456.1| 2421 LEDPGEVVLTYNATVDARPEGLIFRNS 2447
                                        ***************999997767775 PP

  == domain 17  score: 33.7 bits;  conditional E-value: 7.3e-12
                             DUF11    6 dks.evrpGd...tvtytltvtNtgpasangvvvtDtlPagla.yvsvsasqgtasaltsv...gsLeagesatl 72  
                                        dk+ +v +G     v++t+tv Ntg+a++n vvvtDtlP gl   v++  +++ +++   v   g++ +g+s+ l
  gi|386002157|ref|YP_005920456.1| 2489 DKVaNVSSGStstRVNFTITVNNTGNATLNPVVVTDTLPVGLDdPVPSGDGSAFGNV--VVwnlGQMDPGASRAL 2561
                                        5544566666555799**************************823444444444444..44458*********** PP

                             DUF11   73 sftvrvtrtaasgaltn 89  
                                         +t+  + +a  + ltn
  gi|386002157|ref|YP_005920456.1| 2562 WLTAHINGSAFGN-LTN 2577
                                        ******9999988.777 PP

  == domain 18  score: 30.2 bits;  conditional E-value: 9.1e-11
                             DUF11    9 evrpGd...tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvr 77  
                                        +v++G     v++tl+v Ntg+a++  vvvtDtlP gl    +s + gta+ ++ v   g +  g+s+tl +t+ 
  gi|386002157|ref|YP_005920456.1| 2613 NVTSGStstRVNFTLVVNNTGNATLDPVVVTDTLPFGLDDPLASGG-GTATGNVVVwslGPMDSGASRTLWVTAH 2686
                                        455555445799***********************99995555555.444333333447**************** PP

                             DUF11   78 vtrtaasgaltnv 90  
                                         + +a  + ltn 
  gi|386002157|ref|YP_005920456.1| 2687 INGSAYGN-LTNL 2698
                                        **999988.8886 PP

  == domain 19  score: 28.0 bits;  conditional E-value: 4.6e-10
                             DUF11   12 pGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvtrtaa 83  
                                        +   v++tl+v Ntg+a++  vvvtDtlP gl    +s + g+ s ++ v   g +   +s+tl +t+  + +  
  gi|386002157|ref|YP_005920456.1| 2739 ASTRVNFTLVVNNTGNATLDPVVVTDTLPFGLDDPVASDG-GSTSGNVVVwnlGPMDSRASRTLWVTAHINGSRF 2812
                                        33489***************************98888888.555555555456999999********99998888 PP

                             DUF11   84 sgaltn 89  
                                         + ltn
  gi|386002157|ref|YP_005920456.1| 2813 GN-LTN 2817
                                        77.777 PP

  == domain 20  score: 31.3 bits;  conditional E-value: 4.1e-11
                             DUF11   10 vrpGd...tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrv 78  
                                        v +G     v++tl+v Ntg+a++  vvvtDtlP gl    +s + g+a  ++ v   g++  g s+tl +t+  
  gi|386002157|ref|YP_005920456.1| 2854 VSSGStstRVNFTLVVNNTGNATLDPVVVTDTLPFGLDDPIASDG-GSAFGNVVVwnlGRMDRGDSRTLWVTAHI 2927
                                        44555444799***************************8888888.5555555555689**************** PP

                             DUF11   79 trtaasgaltnva 91  
                                        + +a  + ltnva
  gi|386002157|ref|YP_005920456.1| 2928 NGSAYGN-LTNVA 2939
                                        *****98.99997 PP

  == domain 21  score: 33.9 bits;  conditional E-value: 6.3e-12
                             DUF11    9 evrpGd...tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvr 77  
                                        +v++G     v++tl+v Ntg+a++  vvvtDtlP gl    +s + g+as ++ v   g++  g s+tl +t+ 
  gi|386002157|ref|YP_005920456.1| 2973 NVTSGStstRVNFTLIVNNTGNATLDPVVVTDTLPFGLDDPVASDG-GSASGNVVVwnlGQMDSGDSRTLWLTAH 3046
                                        455555445799***************************8888888.666666666668**************** PP

                             DUF11   78 vtrtaasgaltnva 91  
                                         + +a  + ltnva
  gi|386002157|ref|YP_005920456.1| 3047 INGSAYGN-LTNVA 3059
                                        ******98.99997 PP

  == domain 22  score: 32.1 bits;  conditional E-value: 2.4e-11
                             DUF11   11 rpGd...tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvt 79  
                                         +G     v++tl+v Ntg+a++  +vvtDtlP gl    +s + g+as ++ v   g++  g s+tl +t+  +
  gi|386002157|ref|YP_005920456.1| 3095 SSGStstRVNFTLVVNNTGNATLDPAVVTDTLPFGLDDPVASDG-GSASGNVVVwnlGRMDRGDSRTLWLTAHIN 3168
                                        4454444799***************************8888888.666666666668****************** PP

                             DUF11   80 rtaasgaltnva 91  
                                         +a  + ltnva
  gi|386002157|ref|YP_005920456.1| 3169 GSAYGN-LTNVA 3179
                                        ****98.99997 PP

  == domain 23  score: 31.7 bits;  conditional E-value: 3e-11
                             DUF11    9 evrpGd...tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvr 77  
                                        +v +G     v++tl+v Ntg+a++  vvvtDtlP gl    +s + gtas ++ v   g++  g s+t  +t+ 
  gi|386002157|ref|YP_005920456.1| 3213 NVSSGSastRVNFTLVVNNTGNATLDPVVVTDTLPFGLDDPVASDG-GTASGNVVVwnlGRMDRGDSRTPWLTAH 3286
                                        34444444489****************************9888888.78877777777899************** PP

                             DUF11   78 vtrtaasgaltnva 91  
                                         + +a  + ltnva
  gi|386002157|ref|YP_005920456.1| 3287 INGSAYGN-LTNVA 3299
                                        *****998.99997 PP

  == domain 24  score: 33.8 bits;  conditional E-value: 6.9e-12
                             DUF11    6 dksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvr 77  
                                        d +      +vt+t+ v Ntg++ +  vvv DtlP gl+yvs+    g+ s +t +   gs+ +ge + +++ + 
  gi|386002157|ref|YP_005920456.1| 3333 DIPVGEVCTNVTFTIFVNNTGNVRLDPVVVADTLPLGLEYVSSAPP-GARSGNTIIwnlGSMDPGEMRIVNLVAH 3406
                                        5454555569*********************************999.444444444566***********99999 PP

                             DUF11   78 vtrtaasgaltn 89  
                                         + +a  + l+n
  gi|386002157|ref|YP_005920456.1| 3407 INGSAFGE-LQN 3417
                                        99988866.666 PP

  == domain 25  score: 26.0 bits;  conditional E-value: 1.9e-09
                             DUF11    2 tKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatlsf 74  
                                        +K+vd +       v++t+ v Ntg++++  v v+DtlP gl     s++   + + ++++ g+L+ ge +tl +
  gi|386002157|ref|YP_005920456.1| 3449 DKSVDIPVGSRSTRVNFTILVNNTGNVALDPVLVEDTLPFGLDDPVPSSGgiISGNVVTWNLGRLNVGENRTLWL 3523
                                        67777777777779****************************85544444342222245555***********99 PP

                             DUF11   75 tvrvtrtaasgaltn 89  
                                        ++  + +a  + ltn
  gi|386002157|ref|YP_005920456.1| 3524 SAHINGSAYGD-LTN 3537
                                        99999888766.666 PP

  == domain 26  score: 34.2 bits;  conditional E-value: 5.2e-12
                             DUF11    9 evrpGd...tvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvr 77  
                                        +v++G     v++tl+v Ntg+a++  vvvtDtlP gl   + s++   +  + a+++ g++ +g s+tl +t+ 
  gi|386002157|ref|YP_005920456.1| 3573 NVTSGStstRVNFTLVVNNTGNATLDPVVVTDTLPFGLDEPETSSGgsiT-GGVATWGLGRMDPGDSRTLWLTAH 3646
                                        455555445799***********************999966666664321.23356666**************** PP

                             DUF11   78 vtrtaasgaltnv 90  
                                         + +a  + ltn+
  gi|386002157|ref|YP_005920456.1| 3647 INGSAFGT-LTNF 3658
                                        **999977.8886 PP

  == domain 27  score: 52.9 bits;  conditional E-value: 7.7e-18
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatls 73  
                                        + Ktvd++ ++ G   t+t++vtNtg+a++  v vtDtlP  ++yvs++     + + ++++ g+L+ + s+t+ 
  gi|386002157|ref|YP_005920456.1| 3688 VEKTVDSPVAKNGSVATFTIIVTNTGNATLDPVIVTDTLPFCFEYVSSTENgtAAGGVVTWNLGRLNSSDSRTIL 3762
                                        68************************************************9544444456666************ PP

                             DUF11   74 ftvrvtrtaasgal 87  
                                        +++rv+++ a   l
  gi|386002157|ref|YP_005920456.1| 3763 LEARVNCSEAGV-L 3775
                                        *******99854.5 PP

  == domain 28  score: 24.8 bits;  conditional E-value: 4.3e-09
                             DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsft 75  
                                        +tK  dk ev+  d+vtyt+tv N g+ + ++v+v D+    +++ s + + +  + ++ +g+L++ge   ++++
  gi|386002157|ref|YP_005920456.1| 3807 ITKVADKCEVQECDEVTYTITVCNHGGLPEENVTVWDVFYGDVEILSITPA-PDPDRKWHFGTLQPGECVVIKIK 3880
                                        79*************************************999999999998.77778888899999998888888 PP

                             DUF11   76 vrvtr 80  
                                        ++v+ 
  gi|386002157|ref|YP_005920456.1| 3881 IKVPE 3885
                                        77765 PP

  == domain 29  score: 17.6 bits;  conditional E-value: 7.6e-07
                             DUF11   16 vtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvt 79  
                                         tyt+   N g+a++  + v+D+ P+g  +v++s + + ++  +     + ++ g+   + +++ vt
  gi|386002157|ref|YP_005920456.1| 4288 ATYTIRIENDGNAALGPIYVKDLFPPGAVFVESSLRPSDITDSYANwtpTHIAIGGVVEIVVKLDVT 4354
                                        69********************************993322222222444666666666666666665 PP

  == domain 30  score: 18.8 bits;  conditional E-value: 3.2e-07
                             DUF11   13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvtrtaas 84  
                                        G  v y +   N+  +++  ++vtD lP+g+++  +s+  ++++    v    ++ + e++t+++++r+++ ++ 
  gi|386002157|ref|YP_005920456.1| 4410 GMVVLYRIDIENRADVTR-VARVTDHLPEGMTFLDSSTPVASYDGVEVVwnlIDIGPFETRTIELSARASAPGR- 4482
                                        557889999********9.9*******************5555544444444999**************99999. PP

                             DUF11   85 galtnv 90  
                                          +tnv
  gi|386002157|ref|YP_005920456.1| 4483 --YTNV 4486
                                        ..7887 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.1   3.1e-16   1.4e-12       4     111 ..     153     253 ..     151     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 3.1e-16
                               LTD   4 aagdvvIsevmedgagnnan.efvelyNtsskavdLsgwkledasge.ytfpngt....gtlaageyvvvwsgsgtt 74 
                                       ++  vv++e+ +++ g ++  e +elyN++ + v+ s w+++da+++  ++  ++      l++g+ + v   +   
  gi|386002157|ref|YP_005920456.1| 153 TETGVVLNEIFPNPIGVETSnESFELYNAGASLVNVSQWYIKDAADHtVQIGPNVisgsLNLPPGGFLWVRIPG--- 226
                                       5679************9999*************************999555555567778************94... PP

                               LTD  75 sasngskasssavwnnggdavaLydasgevvdsvgyg 111
                                                 + ++n+ggd+v+L+d s+ +vdsv+y 
  gi|386002157|ref|YP_005920456.1| 227 ----------QSILNTGGDTVRLFDGSNVLVDSVTYP 253
                                       ..........579999*********99999*****95 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.22   9.9e+02       8      58 ..     335     384 ..     329     397 .. 0.77
   2 ?    3.7   0.0     0.015        68      39      72 ..    1151    1184 ..    1135    1205 .. 0.77
   3 ?   -2.2   0.0         1   4.5e+03      41      66 ..    1663    1688 ..    1651    1699 .. 0.80
   4 ?    4.0   0.0     0.012        53      28      71 ..    1787    1829 ..    1766    1850 .. 0.64
   5 ?    3.6   0.0     0.016        73      24      61 ..    1924    1962 ..    1902    1981 .. 0.84
   6 !    6.2   0.0    0.0026        12      21      68 ..    2066    2119 ..    2041    2145 .. 0.75
   7 ?    3.5   0.0     0.017        74      24      61 ..    2210    2248 ..    2188    2272 .. 0.85
   8 !    8.1   0.0   0.00065       2.9      22      85 ..    2355    2421 ..    2339    2436 .. 0.75
   9 ?   -0.9   0.0      0.38   1.7e+03      29      54 ..    2503    2530 ..    2486    2537 .. 0.67
  10 ?   -3.8   0.0         3   1.3e+04      32      54 ..    2626    2650 ..    2611    2651 .. 0.68
  11 ?   -3.2   0.0         2   9.1e+03      32      54 ..    2746    2770 ..    2732    2784 .. 0.72
  12 ?   -3.5   0.0       2.6   1.1e+04      31      54 ..    2865    2890 ..    2849    2894 .. 0.70
  13 ?   -2.6   0.0       1.3   5.8e+03      28      55 ..    2982    3011 ..    2966    3047 .. 0.75
  14 ?   -2.5   0.0       1.2   5.5e+03      29      55 ..    3223    3251 ..    3207    3267 .. 0.68
  15 ?   -1.6   0.0      0.64   2.9e+03      37      58 ..    3353    3374 ..    3334    3378 .. 0.76
  16 ?   -0.8   0.0      0.36   1.6e+03      29      68 ..    3583    3624 ..    3556    3647 .. 0.70
  17 !    5.9   0.0    0.0031        14      22      63 ..    3696    3739 ..    3679    3762 .. 0.76
  18 ?   -2.9   0.0       1.7   7.5e+03      21      42 ..    3865    3888 ..    3857    3890 .. 0.78
  19 ?    3.5   0.0     0.018        79      95     129 ..    4279    4313 ..    4271    4339 .. 0.85
  20 ?   -0.0   0.1      0.21   9.3e+02      29      65 ..    4413    4450 ..    4404    4489 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                             bMG10   8 yeklegkevsksdaklkvGdkvrvrltvttpr..dleyvaledplPAGlepvn 58 
                                       + k++++++     ++ +Gd+v +++tv+     +  +v ++d l +Gl+++ 
  gi|386002157|ref|YP_005920456.1| 335 FLKVAKTPTVV---EAGAGDVVNWTITVENTGlgPAFNVRMNDTLSSGLNLLS 384
                                       55555555554...5999***********655478899999999999998765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.015
                             bMG10   39 rdleyvaledplPAGlepvnpslgtesesaeeye 72  
                                         +l++v +++ lPAG+e v  s++ +  s + ++
  gi|386002157|ref|YP_005920456.1| 1151 PTLYNVSVKEALPAGIEYVPGSSQVAGGSTTSTN 1184
                                        5789*************99888877777666654 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1
                             bMG10   41 leyvaledplPAGlepvnpslgtese 66  
                                        +++  ++d lPAGl+    +  ++++
  gi|386002157|ref|YP_005920456.1| 1663 YNNTRIVDTLPAGLKYDSYQCVNDTK 1688
                                        567789********987776666655 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.012
                             bMG10   28 kvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeey 71  
                                        ++rv+ t  + +d  + +++d++P+Gl  v   ++t+s + +++
  gi|386002157|ref|YP_005920456.1| 1787 TIRVTHTAASASDAFDLVINDSIPSGLAFVP-GSNTSSLTTSFS 1829
                                        33444444455688899**********9874.333333333333 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.016
                             bMG10   24 kvGdkvrvrltvttpr.dleyvaledplPAGlepvnpsl 61  
                                        + G+ v  +++v  p+ ++ +  ++d lP+Gl    +sl
  gi|386002157|ref|YP_005920456.1| 1924 TIGESVNYTIEVDLPNaTVGDLWVNDTLPSGLIYNTTSL 1962
                                        579**********888577************97766665 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.0026
                             bMG10   21 a..klkvGdkvrvrltvt..tprdl..eyvaledplPAGlepvnpslgtesesa 68  
                                        +   ++vGd++  +++vt  +p+++   + ++ d++P Gl  vn+s++  +++ 
  gi|386002157|ref|YP_005920456.1| 2066 PagPFSVGDTIHYEINVTnsAPSRRtaFDLVITDEIPVGLSYVNSSDSGVYSGS 2119
                                        155799***********954454442246899************9876555544 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.017
                             bMG10   24 kvGdkvrvrltvttpr.dleyvaledplPAGlepvnpsl 61  
                                        + G+ v  +++v  p+ ++ +  ++d lP+Gl    +sl
  gi|386002157|ref|YP_005920456.1| 2210 TIGESVNYTIEVDLPNaTVGDLWVNDTLPSGLIYNTTSL 2248
                                        579**********888577************97766665 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.00065
                             bMG10   22 klkvGdkvrvrltvt....tprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyrei 85  
                                         +k Gd+vr +l v+    + +d ++ ++ed lP Gl+ v +++  e +s  ++  +++ +++sy  +
  gi|386002157|ref|YP_005920456.1| 2355 VVKLGDEVRFTLVVNhtglSTSDAYDLVIEDVLPLGLTYVSNTSTPEANSSAYH-PGNRTIRWSYDRL 2421
                                        5899*****999998534356799*****************8886666665555.4666666666555 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 0.38
                             bMG10   29 vrvrltvt..tprdleyvaledplPAGl 54  
                                        v  ++tv+   +++l+ v++ d lP Gl
  gi|386002157|ref|YP_005920456.1| 2503 VNFTITVNntGNATLNPVVVTDTLPVGL 2530
                                        4444444431555889999999999887 PP

  == domain 10  score: -3.8 bits;  conditional E-value: 3
                             bMG10   32 rltvt..tprdleyvaledplPAGl 54  
                                        +l v+   +++l+ v++ d lP Gl
  gi|386002157|ref|YP_005920456.1| 2626 TLVVNntGNATLDPVVVTDTLPFGL 2650
                                        4444431455889999999999776 PP

  == domain 11  score: -3.2 bits;  conditional E-value: 2
                             bMG10   32 rltvt..tprdleyvaledplPAGl 54  
                                        +l v+   +++l+ v++ d lP Gl
  gi|386002157|ref|YP_005920456.1| 2746 TLVVNntGNATLDPVVVTDTLPFGL 2770
                                        4444431456889999999999887 PP

  == domain 12  score: -3.5 bits;  conditional E-value: 2.6
                             bMG10   31 vrltvt..tprdleyvaledplPAGl 54  
                                         +l v+   +++l+ v++ d lP Gl
  gi|386002157|ref|YP_005920456.1| 2865 FTLVVNntGNATLDPVVVTDTLPFGL 2890
                                        44444431455889999999999776 PP

  == domain 13  score: -2.6 bits;  conditional E-value: 1.3
                             bMG10   28 kvrvrltvt..tprdleyvaledplPAGle 55  
                                        +v  +l v+   +++l+ v++ d lP Gl 
  gi|386002157|ref|YP_005920456.1| 2982 RVNFTLIVNntGNATLDPVVVTDTLPFGLD 3011
                                        455666666413458899******998885 PP

  == domain 14  score: -2.5 bits;  conditional E-value: 1.2
                             bMG10   29 vrvrltvt..tprdleyvaledplPAGle 55  
                                        v  +l v+   +++l+ v++ d lP Gl 
  gi|386002157|ref|YP_005920456.1| 3223 VNFTLVVNntGNATLDPVVVTDTLPFGLD 3251
                                        44444444314568899*******98884 PP

  == domain 15  score: -1.6 bits;  conditional E-value: 0.64
                             bMG10   37 tprdleyvaledplPAGlepvn 58  
                                         + +l+ v++ d lP Gle v 
  gi|386002157|ref|YP_005920456.1| 3353 GNVRLDPVVVADTLPLGLEYVS 3374
                                        3447899************886 PP

  == domain 16  score: -0.8 bits;  conditional E-value: 0.36
                             bMG10   29 vrvrltvt..tprdleyvaledplPAGlepvnpslgtesesa 68  
                                        v  +l v+   +++l+ v++ d lP Gl   ++s+g + +++
  gi|386002157|ref|YP_005920456.1| 3583 VNFTLVVNntGNATLDPVVVTDTLPFGLDEPETSSGGSITGG 3624
                                        444455544145589**********99987776766665555 PP

  == domain 17  score: 5.9 bits;  conditional E-value: 0.0031
                             bMG10   22 klkvGdkvrvrltvt.tpr.dleyvaledplPAGlepvnpslgt 63  
                                         +k G++ + ++ vt t + +l+ v++ d lP ++e v ++ + 
  gi|386002157|ref|YP_005920456.1| 3696 VAKNGSVATFTIIVTnTGNaTLDPVIVTDTLPFCFEYVSSTENG 3739
                                        5899999999999997554488**************99876554 PP

  == domain 18  score: -2.9 bits;  conditional E-value: 1.7
                             bMG10   21 a..klkvGdkvrvrltvttprdle 42  
                                           +l+ G+ v +++++++p++ +
  gi|386002157|ref|YP_005920456.1| 3865 HfgTLQPGECVVIKIKIKVPERQD 3888
                                        245899*************99876 PP

  == domain 19  score: 3.5 bits;  conditional E-value: 0.018
                             bMG10   95 dylpkgtytfeylvravtpGtfsvppakaeemYaP 129 
                                        d+++k +y  +y++r+ + G+ +++p  +++ + P
  gi|386002157|ref|YP_005920456.1| 4279 DNCSKTKYIATYTIRIENDGNAALGPIYVKDLFPP 4313
                                        67788899999999999999999999888876654 PP

  == domain 20  score: -0.0 bits;  conditional E-value: 0.21
                             bMG10   29 vrvrltvttprdleyva.ledplPAGlepvnpslgtes 65  
                                        v+ r++++  +d++ va + d lP G++ +++s   +s
  gi|386002157|ref|YP_005920456.1| 4413 VLYRIDIENRADVTRVArVTDHLPEGMTFLDSSTPVAS 4450
                                        55556666666554443355666666555554443333 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.2   9.2e+02      27      73 ..    1013    1066 ..     996    1075 .. 0.79
   2 ?   -2.8   0.0       1.7   7.8e+03      28      86 ..    1275    1331 ..    1253    1333 .. 0.76
   3 ?    2.5   0.0     0.039   1.8e+02      28      78 ..    1786    1843 ..    1762    1854 .. 0.72
   4 !    4.8   0.0    0.0077        35      28      86 ..    2078    2139 ..    2057    2144 .. 0.75
   5 ?   -2.4   0.0       1.3   5.9e+03      33      66 ..    2371    2402 ..    2344    2428 .. 0.66
   6 ?   -4.1   0.0         4   1.8e+04      27      52 ..    2504    2529 ..    2492    2551 .. 0.80
   7 ?   -2.8   0.0       1.8   8.2e+03      28      74 ..    2745    2790 ..    2721    2803 .. 0.71
   8 ?    0.3   0.0       0.2   8.8e+02      28      89 ..    2865    2923 ..    2833    2925 .. 0.71
   9 ?   -2.5   0.0       1.5   6.5e+03      29      81 ..    2986    3037 ..    2960    3043 .. 0.69
  10 ?   -2.0   0.0         1   4.6e+03      32      82 ..    3109    3158 ..    3080    3164 .. 0.69
  11 ?    0.6   0.0      0.16   7.1e+02      28      81 ..    3225    3277 ..    3197    3284 .. 0.73
  12 !    4.7   0.0     0.008        36      28      82 ..    3345    3398 ..    3326    3405 .. 0.81
  13 !   12.0   0.1   4.5e-05       0.2       9      82 ..    3685    3758 ..    3678    3765 .. 0.75
  14 ?   -3.9   0.0         4   1.8e+04      45      78 ..    4431    4464 ..    4413    4471 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.2
                        Chlam_OMP6   27 pypieitavgkkdcvdvvitqqlpcevefvrs......dpastptadgk.lvwk 73  
                                         + i +t +g   + +v + + l  +  +v+s      dpa+t   d + ++w 
  gi|386002157|ref|YP_005920456.1| 1013 SWKIYVTNTGSGTAYNVTVNDTLDSDLSYVSSridgsaDPANTTVVDANhVLWS 1066
                                        57789999999999***************9865555558998888886515565 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                        Chlam_OMP6   28 ypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskit 86  
                                        + i +++ g   + +v + + lp ++ +v++ p         l w    l  ge   +t
  gi|386002157|ref|YP_005920456.1| 1275 WTIYLYSNGGDPATNVTLFDLLPENTVYVSATPEP--NDTDPLRWDFGTLNFGESRTVT 1331
                                        55667777888889999999999999999998864..4445688888888888877666 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.039
                        Chlam_OMP6   28 ypiei..tavgkkdcvdvvitqqlpcevefvrsdpastpt.....adgklvwkidrlg 78  
                                        y i +  ta+   d+ d+vi + +p    fv    +s+ t     +  +l w++ rl 
  gi|386002157|ref|YP_005920456.1| 1786 YTIRVthTAASASDAFDLVINDSIPSGLAFVPGSNTSSLTtsfsqTGQNLSWTLSRLN 1843
                                        5565511577889******************755444333111112346889999986 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0077
                        Chlam_OMP6   28 ypieit..avgkkdcvdvvitqqlpcevefvrs.dpastptadgklvwkidrlgqgekskit 86  
                                        y i++t  a  ++ + d+vit+++p+   +v+s d      ++  + w+   l      k+t
  gi|386002157|ref|YP_005920456.1| 2078 YEINVTnsAPSRRTAFDLVITDEIPVGLSYVNSsDSGVYSGSNRTVTWTFASLALDSWLKVT 2139
                                        66666522567999****************97616666677777888999888877777766 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 1.3
                        Chlam_OMP6   33 tavgkkdcvdvvitqqlpcevefvrsdpastpta 66  
                                        t     d+ d+vi + lp    +v+    stp a
  gi|386002157|ref|YP_005920456.1| 2371 TGLSTSDAYDLVIEDVLPLGLTYVSNT--STPEA 2402
                                        445578999**********99999753..33333 PP

  == domain 6  score: -4.1 bits;  conditional E-value: 4
                        Chlam_OMP6   27 pypieitavgkkdcvdvvitqqlpce 52  
                                         + i +  +g+     vv+t+ lp+ 
  gi|386002157|ref|YP_005920456.1| 2504 NFTITVNNTGNATLNPVVVTDTLPVG 2529
                                        46788888999999999999999975 PP

  == domain 7  score: -2.8 bits;  conditional E-value: 1.8
                        Chlam_OMP6   28 ypieitavgkkdcvdvvitqqlpceve.fvrsdpastptadgklvwki 74  
                                        + + +  +g+     vv+t+ lp   +  v sd  st      +vw++
  gi|386002157|ref|YP_005920456.1| 2745 FTLVVNNTGNATLDPVVVTDTLPFGLDdPVASDGGSTS--GNVVVWNL 2790
                                        556667788888888999****9887526888888764..34566665 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 0.2
                        Chlam_OMP6   28 ypieitavgkkdcvdvvitqqlpceve.fvrsdpastptadgklvwkidrlgqgekskitvwv 89  
                                        + + +  +g+     vv+t+ lp   +  + sd  s+      +vw++ r+ +g+    t+wv
  gi|386002157|ref|YP_005920456.1| 2865 FTLVVNNTGNATLDPVVVTDTLPFGLDdPIASDGGSAF--GNVVVWNLGRMDRGDSR--TLWV 2923
                                        55566778888888899******887526888887654..34689******999864..5555 PP

  == domain 9  score: -2.5 bits;  conditional E-value: 1.5
                        Chlam_OMP6   29 pieitavgkkdcvdvvitqqlpceve.fvrsdpastptadgklvwkidrlgqge 81  
                                         + +  +g+     vv+t+ lp   +  v sd  s+      +vw++ ++  g+
  gi|386002157|ref|YP_005920456.1| 2986 TLIVNNTGNATLDPVVVTDTLPFGLDdPVASDGGSAS--GNVVVWNLGQMDSGD 3037
                                        4556677777777899999999876426788876643..345788888877776 PP

  == domain 10  score: -2.0 bits;  conditional E-value: 1
                        Chlam_OMP6   32 itavgkkdcvdvvitqqlpceve.fvrsdpastptadgklvwkidrlgqgek 82  
                                        +  +g+      v+t+ lp   +  v sd  s+      +vw++ r+ +g+ 
  gi|386002157|ref|YP_005920456.1| 3109 VNNTGNATLDPAVVTDTLPFGLDdPVASDGGSAS--GNVVVWNLGRMDRGDS 3158
                                        5556666666678888888776425777766543..44679*****999975 PP

  == domain 11  score: 0.6 bits;  conditional E-value: 0.16
                        Chlam_OMP6   28 ypieitavgkkdcvdvvitqqlpceve.fvrsdpastptadgk.lvwkidrlgqge 81  
                                        + + +  +g+     vv+t+ lp   +  v sd     ta g+ +vw++ r+ +g+
  gi|386002157|ref|YP_005920456.1| 3225 FTLVVNNTGNATLDPVVVTDTLPFGLDdPVASDGG---TASGNvVVWNLGRMDRGD 3277
                                        55666778888888899*****9886525777765...45554178*****99997 PP

  == domain 12  score: 4.7 bits;  conditional E-value: 0.008
                        Chlam_OMP6   28 ypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgek 82  
                                        + i +  +g+     vv+++ lp   e+v+s p  + +    ++w++  +  ge 
  gi|386002157|ref|YP_005920456.1| 3345 FTIFVNNTGNVRLDPVVVADTLPLGLEYVSSAPPGARSG-NTIIWNLGSMDPGEM 3398
                                        667777888888889******************887654.579999998888875 PP

  == domain 13  score: 12.0 bits;  conditional E-value: 4.5e-05
                        Chlam_OMP6    9 drnveisqavpeyatvgs..pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqge 81  
                                        d +ve +   p  a  gs   + i +t +g+     v++t+ lp   e+v+s    t +a g + w++ rl   +
  gi|386002157|ref|YP_005920456.1| 3685 DIEVEKTVDSP-VAKNGSvaTFTIIVTNTGNATLDPVIVTDTLPFCFEYVSSTENGT-AAGGVVTWNLGRLNSSD 3757
                                        55555554444.34444422688999999**99999****************98877.5789999*****98766 PP

                        Chlam_OMP6   82 k 82  
                                         
  gi|386002157|ref|YP_005920456.1| 3758 S 3758
                                        5 PP

  == domain 14  score: -3.9 bits;  conditional E-value: 4
                        Chlam_OMP6   45 itqqlpcevefvrsdpastptadgklvwkidrlg 78  
                                        +t+ lp  + f+ s    +      +vw++  +g
  gi|386002157|ref|YP_005920456.1| 4431 VTDHLPEGMTFLDSSTPVASYDGVEVVWNLIDIG 4464
                                        7899999999998865555555557889876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (4560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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):               4  [number of targets reported over threshold]
# CPU time: 1.39u 0.35s 00:00:01.73 Elapsed: 00:00:00.55
# Mc/sec: 24823.31
//
Query:       gi|386002158|ref|YP_005920457.1|  [L=274]
Description: F420-dependent methylenetetrahydromethanopterin dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.8e-118  394.2   0.1   3.2e-118  394.0   0.1    1.0  1  MTD       methylene-5,6,7,8-tetrahydromethanopterin dehydroge


Domain annotation for each model (and alignments):
>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.0   0.1  1.8e-122  3.2e-118       1     274 []       2     272 ..       2     272 .. 0.99

  Alignments for each domain:
  == domain 1  score: 394.0 bits;  conditional E-value: 1.8e-122
                                       EEEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHH CS
                               MTD   1 vkigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkar 77 
                                       +kig+iklGn+++slv dl+lDe+a+R+d+evr ++ gak++ +e+e + ++lk + p+lv++++Pnaa+pgpt+ar
  gi|386002158|ref|YP_005920457.1|   2 FKIGFIKLGNVASSLVADLALDEIAERTDVEVRSLSFGAKMTVKEAE-MSAELKGWGPQLVVIVGPNAATPGPTAAR 77 
                                       59********************************************9.999************************** PP

                                       HHHHHSSS-EEEEEEGGGGGGH.HHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                               MTD  78 ellsekdvpaivisDapgkkek.deleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqee 153
                                        l+  +dvp+ivisD+p+kke+ ++le+eg+GYii+++DpliGa+refLDp+emalfn+d+lkvL+++G vRlvqee
  gi|386002158|ref|YP_005920457.1|  78 ALY--RDVPTIVISDGPSKKEArEALEAEGFGYIILPFDPLIGAKREFLDPAEMALFNSDALKVLSICGSVRLVQEE 152
                                       ***..9**************999****************************************************** PP

                                       HHHHHHHHTTT-GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHHHH CS
                               MTD 154 ldkviekvkagkeielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivasahe 230
                                       ld +++++ +g  ++lP+i+ ++e +++++ f+nPYa+aka++a+++a++va id++aCf+ kel++++l++a++he
  gi|386002158|ref|YP_005920457.1| 153 LDGAMASIISGA-PRLPTILSSPEGCTDRMAFRNPYARAKAIGALHMAQTVAGIDAAACFRLKELDRIALTAAAGHE 228
                                       ***********9.9*************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTT---B--B-TTSSB--BSSTTS--- CS
                               MTD 231 llraaakLadeaReieksndtvlRkphakdGkvlsktkllekPe 274
                                       ++raaa+LadeaRe+eks+d+v+R+pha++G++l+kt ll+kPe
  gi|386002158|ref|YP_005920457.1| 229 VMRAAARLADEARELEKSTDSVSRRPHARSGAILAKTGLLDKPE 272
                                       *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1906.65
//
Query:       gi|386002159|ref|YP_005920458.1|  [L=134]
Description: hypothetical protein Mhar_1471 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-34  116.2   1.5    4.8e-34  116.0   0.5    1.6  2  DUF126         Aconitase X swivel domain
  ------ inclusion threshold ------
      0.038   13.7   0.3      0.073   12.8   0.3    1.5  1  PEP-utilizers  PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.5   5.4e-38   4.8e-34       1      80 []      24     103 ..      24     103 .. 0.99
   2 ?   -2.0   0.0      0.35   3.1e+03       5      16 ..     119     130 ..     117     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 5.4e-38
                                       --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT- CS
                            DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadi 77 
                                       +Sflg vdpetG+v+d+gh+l g+ i gk+L++p+gkGStvgsyv+++l+k+g+aPaA+i+ + +pi+a+Gai+++i
  gi|386002159|ref|YP_005920458.1|  24 ISFLGTVDPETGEVVDPGHQLFGKAIGGKVLIFPGGKGSTVGSYVIYQLKKRGVAPAAMINLRSEPIVAVGAIISGI 100
                                       8**************************************************************************** PP

                                       -EE CS
                            DUF126  78 Plv 80 
                                       Plv
  gi|386002159|ref|YP_005920458.1| 101 PLV 103
                                       *97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.35
                                       S-B-TTT-BB-S CS
                            DUF126   5 ggvdpetGkvid 16 
                                       + vd+++G+vi 
  gi|386002159|ref|YP_005920458.1| 119 VTVDADRGRVIV 130
                                       679999999985 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   8.1e-06     0.073      39      73 .]      92     126 ..      90     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-06
                                       HHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers  39 AivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       A+ A   giP V g+++   +l+eg+l+tvD+++G
  gi|386002159|ref|YP_005920458.1|  92 AVGAIISGIPLVDGLPADILRLEEGTLVTVDADRG 126
                                       6666778***********99*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 871.24
//
Query:       gi|386002160|ref|YP_005920459.1|  [L=387]
Description: putative aconitase subunit 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-150  501.1   0.0     2e-150  501.0   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.0   0.0  1.1e-154    2e-150       1     401 []       1     381 [.       1     381 [. 0.98

  Alignments for each domain:
  == domain 1  score: 501.0 bits;  conditional E-value: 1.1e-154
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+L++eee+  +Ge G+ l+kameilvalG+i+gA+rL+pv s++v+gvs ktig+agle++++l+   +kv+vp++
  gi|386002160|ref|YP_005920459.1|   1 MHLSREEERAHQGELGDSLRKAMEILVALGDIYGADRLIPVRSVQVAGVSFKTIGEAGLEWISDLQ---GKVAVPAV 74 
                                       9*****************************************************************...******** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyll.gnapkkGehlawsESsavvyaNSvlGarT 153
                                       lnp+g+dl+rw+e+g+de+fa+kq +++eay++lGv++ +tCtpy++  +  ++G+hlawsESsav++aNSv+GarT
  gi|386002160|ref|YP_005920459.1|  75 LNPAGMDLHRWREMGIDESFAKKQLEVVEAYRRLGVSPDCTCTPYQIrPDFARRGDHLAWSESSAVSFANSVIGART 151
                                       **********************************************8688999************************ PP

                            DUF521 154 nreggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKa 230
                                       nreggpsalaaA++G+tp+yG+hl+enR+pt+ + v+a+  + +dyg+lG++vG++vge++P +   ++p+ delKa
  gi|386002160|ref|YP_005920459.1| 152 NREGGPSALAAALVGKTPRYGYHLEENRVPTINIAVDAD-LKPSDYGILGFIVGREVGEGVPQFIFRRRPDIDELKA 227
                                       ************************************999.9************************************ PP

                            DUF521 231 lgAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElr 307
                                       lgAa+aasg+val+++e+  Pea          + ae+i++t++dl++v+ee   a++e+vd+va+GcPh+s +El+
  gi|386002160|ref|YP_005920459.1| 228 LGAAMAASGSVALYYFEEGGPEA---------PKGAEEIEVTAADLRAVREEN--APDEEVDIVAIGCPHTSERELE 293
                                       **********************2.........345899*************66..99******************** PP

                            DUF521 308 elaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlp 384
                                       ela+ll  ++kkv++elw++t+r ++e++ rl  vek+e +G++vl+dtCmvvsp++++  ++k+++nSgKa+ Y+p
  gi|386002160|ref|YP_005920459.1| 294 ELARLL--EGKKVERELWICTARGIAERCPRL--VEKIEGSGARVLCDTCMVVSPASDR--YNKMMVNSGKALAYVP 364
                                       ******..88888*******************..***********************95..9*************** PP

                            DUF521 385 gltgvkvalgsleecve 401
                                        l+++k+a+gs +ecve
  gi|386002160|ref|YP_005920459.1| 365 TLCKMKAAYGSAAECVE 381
                                       ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2466.48
//
Query:       gi|386002161|ref|YP_005920460.1|  [L=307]
Description: Methyltetrahydromethanopterin S-methyltransferase, subunit H, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-98  328.2   0.0    4.7e-98  328.0   0.0    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.0   0.0  2.6e-102   4.7e-98       1     296 [.       6     295 ..       6     298 .. 0.98

  Alignments for each domain:
  == domain 1  score: 328.0 bits;  conditional E-value: 2.6e-102
                              MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGetee 77 
                                       ++q+v+++aGvkiGGqpGe+Pt+l gtify + ++ved  +G fd+ aae li++q+ ls++tGnPa++++  +t e
  gi|386002161|ref|YP_005920460.1|   6 RDQEVVNVAGVKIGGQPGENPTALCGTIFYQGQRLVEDPVRGRFDEGAAEGLIERQTALSEETGNPAVLHIYARTRE 82 
                                       68*************************************************************************** PP

                              MtrH  78 aivkyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmd 154
                                       a+ +y+dfv  ++ +Pl++ds++a  ++a a+ ++e+Gladr+iynsi +++  +e eal++ +v++ai+l++ p d
  gi|386002161|ref|YP_005920460.1|  83 AFGRYLDFVDGLWSGPLILDSAEAGTRIAMAEAVSEIGLADRCIYNSIGIATTPQEEEALAHGEVDSAILLGYSPAD 159
                                       ***************************************************************************** PP

                              MtrH 155 ptvegklkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdw 231
                                        tveg + +l eg+ + + gl++la +  i++ lid  v+plg+gag +++a++  kak+GlP Gsgihn++s+W w
  gi|386002161|ref|YP_005920460.1| 160 STVEGTIRVLAEGGPGRKEGLVDLARRLEINNILIDPGVVPLGDGAGRSLRATVLAKAKFGLPAGSGIHNAVSSWRW 236
                                       ***************************************************************************** PP

                              MtrH 232 lrefkkkekekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgv 296
                                       lr      ke+++   v+d ++   ++++g+dfvlyGPie a +vfP+ am+dili+eaak+l v
  gi|386002161|ref|YP_005920460.1| 237 LRS-----KERGT-RLVCDAASAGFEILAGGDFVLYGPIERAGEVFPVAAMADILISEAAKDLEV 295
                                       *96.....45555.569********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2081.77
//
Query:       gi|386002162|ref|YP_005920461.1|  [L=533]
Description: UvrABC system protein C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.8e-47  158.7   0.0    2.4e-46  157.4   0.0    1.7  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    4.5e-09   36.4   0.0    9.9e-09   35.4   0.0    1.6  1  GIY-YIG     GIY-YIG catalytic domain
    1.5e-08   34.1   5.0      3e-08   33.2   5.0    1.5  1  UVR         UvrB/uvrC motif
  ------ inclusion threshold ------
      0.071   13.4   0.0       0.14   12.4   0.0    1.5  1  PPP5        PPP5 TPR repeat region


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.4   6.1e+03     128     143 ..     229     244 ..     204     270 .. 0.52
   2 !  157.4   0.0   5.4e-50   2.4e-46       2     154 .]     372     520 ..     371     520 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.4
                                       EEEE--TT-HHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N 128 evlelkkssealkllq 143
                                       + +el+ + +al+ lq
  gi|386002162|ref|YP_005920461.1| 229 QAMELRDEIRALESLQ 244
                                       2233333333333333 PP

  == domain 2  score: 157.4 bits;  conditional E-value: 5.4e-50
                                       HHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.....-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N   2 ellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllkefskl 78 
                                       e+l+l+ +p+ +e++D+Sh+ g++tvgsmv f+ g+p+k+ yR+f++++v++ dD+a++ e++rRr+ rl++e  ++
  gi|386002162|ref|YP_005920461.1| 372 EALSLPGPPNVVEVFDVSHLAGSFTVGSMVQFRGGRPDKRGYRRFRVRTVDGIDDFASIGEIVRRRYLRLKEEGGEM 448
                                       89*************************************************************************** PP

                                       -SEEEESSSHHHHHHHHHHHHHTT----EEEEES............SSSEE........EE--TT-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  79 PdLiliDGGkgqlnaakevleelglkipvvglaKdkkrktrakaeereeev........lelkkssealkllqrird 147
                                       PdLi+iDGGkgql aa++ l+ lgl+ipv+++aK +++            +        l ++++++a  ++q++rd
  gi|386002162|ref|YP_005920461.1| 449 PDLIVIDGGKGQLWAATQELRGLGLTIPVISIAKREEE------------IyvpgrlrpLPIRRDDKAALFVQEMRD 513
                                       **********************************3333............222333344****************** PP

                                       HHHHHHH CS
                                       xxxxxxx RF
                        UvrC_HhH_N 148 eaHrfAI 154
                                       eaHrfAI
  gi|386002162|ref|YP_005920461.1| 514 EAHRFAI 520
                                       ******8 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   2.2e-12   9.9e-09       3      78 .]      29     103 ..      27     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.2e-12
                                       EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHH..HHHHHHHHHHHTTSSS CS
                           GIY-YIG   3 gvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksea..lelEkklikkyksnky 77 
                                       g+Y++++ e+ +iYvG++++l+kR  +++++++   ++   + + + + l ++ tkse+  l lE++likk+ + ky
  gi|386002162|ref|YP_005920461.1|  29 GCYLFKDDEGAVIYVGKARDLKKRVASYFQKRELDPKTS--ALVSAASGLDFIVTKSEVeaLLLENALIKKHWP-KY 102
                                       9************************************99..6777777777777777777699*********99.99 PP

                                       S CS
                           GIY-YIG  78 n 78 
                                       n
  gi|386002162|ref|YP_005920461.1| 103 N 103
                                       8 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   5.0   6.6e-12     3e-08       2      35 ..     209     242 ..     208     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 6.6e-12
                               UVR   2 klikeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                       +li +L+eem  ++e+++FE+A++lRD+i+al+ 
  gi|386002162|ref|YP_005920461.1| 209 ELIGSLKEEMAALSERQEFEQAMELRDEIRALES 242
                                       7899****************************96 PP

>> PPP5  PPP5 TPR repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05      0.14       3      45 ..     217     260 ..     215     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                              PPP5   3 eceklirreaFekAIeveekesasetl.dlesieveksYdGprL 45 
                                       e+  l  r++Fe+A e +++ +a+e+l d ++ie +k Yd   L
  gi|386002162|ref|YP_005920461.1| 217 EMAALSERQEFEQAMELRDEIRALESLqDRQQIERDKRYDEDVL 260
                                       5667789********************88**********97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3537.15
//
Query:       gi|386002163|ref|YP_005920462.1|  [L=86]
Description: hypothetical protein Mhar_1475 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.15   12.0   0.1    1.0  1  Ferlin_C  Ferlin C-terminus
       0.14   12.1   0.5       0.17   11.7   0.5    1.1  1  DUF412    Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> Ferlin_C  Ferlin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.7e-05      0.15      94     151 ..      16      74 ..       6      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                          Ferlin_C  94 lekpnrpktsfswlvnrlKtfif.fiWkkykkyiiallilallalflvlllytlPgqis 151
                                       +++ nr+     +l +  Kt+i+  ++    +y+i+  + ++ a+++ +++ t+P +++
  gi|386002163|ref|YP_005920462.1|  16 IDRGNRKAKVAGVLKSLSKTIIIaTVFDMIAQYLIFDQVRVIPAIIVGVFVLTVPYSLA 74 
                                       57889***9***********87526899999************************9886 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   1.9e-05      0.17      29      76 ..      24      71 ..      20      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                            DUF412 29 rvikatrfaikvmpalavltlvlqlylagsealpqailtalfllsLPl 76
                                      +v  +++   k++ +  v+ ++ q+ + ++  +  ai++++f+l++P 
  gi|386002163|ref|YP_005920462.1| 24 KVAGVLKSLSKTIIIATVFDMIAQYLIFDQVRVIPAIIVGVFVLTVPY 71
                                      66777888889999999****************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 583.91
//
Query:       gi|386002164|ref|YP_005920463.1|  [L=87]
Description: hypothetical protein Mhar_1476 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-09   35.9   0.1    7.9e-09   35.7   0.1    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0056   16.8   0.0      0.006   16.7   0.0    1.1  1  DUF5012          Domain of unknown function (DUF5012)
  ------ inclusion threshold ------
      0.074   13.4   0.1      0.093   13.0   0.1    1.2  1  DUF1024          Protein of unknown function (DUF1024)
       0.12   12.4   0.0       0.15   12.0   0.0    1.1  1  PHD_like         Antitoxin of toxin-antitoxin, RelE / RelB, T


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   1.8e-12   7.9e-09       1      53 [.      35      86 ..      35      87 .] 0.91

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.8e-12
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedge 53
                                      + ++iekd++  y  +  +l+Gc++ g+  eea++n ++ai+lh+++++edge
  gi|386002164|ref|YP_005920463.1| 35 FSVVIEKDKS-GYFALCSELQGCYTQGEAYEEALENVEDAISLHVKDILEDGE 86
                                      6789999876.6777899*********************************98 PP

>> DUF5012  Domain of unknown function (DUF5012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-06     0.006      13      63 ..      16      66 ..       3      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                                      EE-SSEEEEE.SS-EEE---EEEEEEEETTEEEES-TTTTTTTTSST--TT CS
                           DUF5012 13 tvaeGskrlsggavveyagyevtiekiaPGlfyisdflGGyydqraGyGaa 63
                                      +v +   r  +g  ++  +++v+iek + G f +   l G y q+  y +a
  gi|386002164|ref|YP_005920463.1| 16 KVSDQDLRCKNGGCMKNYRFSVVIEKDKSGYFALCSELQGCYTQGEAYEEA 66
                                      5667777888877777779***************************99765 PP

>> DUF1024  Protein of unknown function (DUF1024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.1e-05     0.093      25      63 ..      49      87 .]      36      87 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                           DUF1024 25 llkeiedvykkaqafdeilegmtnaiqhsvkegieldea 63
                                      l  e++  y + +a++e le + +ai   vk+ +e  ea
  gi|386002164|ref|YP_005920463.1| 49 LCSELQGCYTQGEAYEEALENVEDAISLHVKDILEDGEA 87
                                      6789999************************99987665 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05      0.15      52     107 ..      30      84 ..      22      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                                       ...TT--EEEEEEEETTEEEEEECCGTEEEEESSHHHHHHHHHHHHHHHHHHHHHT CS
                          PHD_like  52 drgyklepeieeekdgevytltldelevyvegstkeeaaedLvedlldYaqdYlnr 107
                                        ++y++ ++ie++k g    l  +    y++g++ eea+e+  + +    +d l++
  gi|386002164|ref|YP_005920463.1|  30 MKNYRFSVVIEKDKSGYF-ALCSELQGCYTQGEAYEEALENVEDAISLHVKDILED 84 
                                       589999999988887766.555555679**************99999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 555.98
//
Query:       gi|386002165|ref|YP_005920464.1|  [L=86]
Description: AbrB family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-08   33.8   0.3    3.6e-08   33.1   0.3    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0038   17.2   0.2     0.0082   16.1   0.0    1.6  2  MraZ            MraZ protein, putative antitoxin-like


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 !   33.1   0.3   4.1e-12   3.6e-08       2      41 ..       5      45 ..       4      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4.1e-12
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrpl 41
                                      +v+n+g+v++P e+r++l+i+ Gde  +ev    + il+++
  gi|386002165|ref|YP_005920464.1|  5 RVDNKGRVVLPNELRRKLDINSGDEFAVEVLAPdSVILKKV 45
                                      89*****************************9988887776 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.1e-07    0.0082       9      29 ..       5      25 ..       3      35 .. 0.88
   2 ?   -1.8   0.1      0.35   3.1e+03      50      59 ..      64      73 ..      52      81 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.1e-07
                                      EB-TTSEEE--CHHHHHTTSC CS
                              MraZ  9 elDakGRlllPaklreeakle 29
                                       +D kGR+ lP++lr+++  +
  gi|386002165|ref|YP_005920464.1|  5 RVDNKGRVVLPNELRRKLDIN 25
                                      58**************99765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.35
                                      HHHHHCHHTS CS
                              MraZ 50 ekyeeelaee 59
                                      ek+e+e+ ee
  gi|386002165|ref|YP_005920464.1| 64 EKLEAEIEEE 73
                                      4555554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 555.12
//
Query:       gi|386002166|ref|YP_005920465.1|  [L=136]
Description: Nucleotide binding protein, putative, containing PIN domain [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-10   40.1   1.0      7e-10   39.5   1.0    1.4  1  PIN       PIN domain
    3.1e-07   31.1   0.1    6.6e-07   30.1   0.1    1.5  1  PIN_3     PIN domain
  ------ inclusion threshold ------
      0.062   13.8   0.1       0.46   10.9   0.0    2.0  2  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   1.0   1.2e-13     7e-10       2     120 ..       1     111 [.       1     113 [. 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
                                       EE-HHHHHHHH..TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   2 vlDTsvliall..rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       ++DT+ +ia++  r+   +e +++ll+++ elv  ++ ++E ++ ++r        ++   l++ll+ + +++ + e
  gi|386002166|ref|YP_005920465.1|   1 MIDTNLFIAAVkgRRTRSTELLLALLDGPIELVADDILISEYARYARR-------FEADPFLEILLKKVVVIEQSIE 70 
                                       59*********988888899999999999*******************.......9999999999************ PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       ++++ + ++        D ++aAt+++ +++li t+D++f+r+ 
  gi|386002166|ref|YP_005920465.1|  71 DVLKCKPFFPPD--EGGDIVHAATCLHAKAILI-TNDTHFNRIR 111
                                       **********97..99*****************.********86 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   1.1e-10   6.6e-07       3     116 .]       1     106 [.       1     106 [. 0.77

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-10
                             PIN_3   3 vlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvalerkava 79 
                                       ++Dtn +++a+  + + ++ +l al +g+i+lv++  l+ E++r +      ++f+++ +    ll k      +v 
  gi|386002166|ref|YP_005920465.1|   1 MIDTNLFIAAVKGRRTRSTELLLALLDGPIELVADDILISEYARYA------RRFEADPFLE-ILLKK------VVV 64 
                                       79*****************************************666......4444444544.33333......344 PP

                             PIN_3  80 pdaelrpllkcr......DpdDqkvlelAlaaradvlVTkdra 116
                                        +++ + +lkc+         D  +++++l a +++l+T d++
  gi|386002166|ref|YP_005920465.1|  65 IEQSIEDVLKCKpffppdEGGDIVHAATCLHA-KAILITNDTH 106
                                       555555555666666673557***********.9******985 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.8e-05      0.46       2      47 ..       1      44 [.       1      49 [. 0.80
   2 ?    1.0   0.0     0.088   5.3e+02     111     143 ..      56      85 ..      43     107 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.8e-05
                            PIN_12  2 fiDTnifldeffrlseeealkklleliesgkiklivpdivldEflk 47
                                      +iDTn+f+    + +   + + ll+l+ +g i+l+  di + E+ +
  gi|386002166|ref|YP_005920465.1|  1 MIDTNLFIA-AVKGRRTRSTELLLALL-DGPIELVADDILISEYAR 44
                                      59******7.88888885556665555.568************987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.088
                            PIN_12 111 kvipetndevkkilerafkkkpPfskkkkkgfg 143
                                       +++ ++ + +++ +e+++k+kp f     ++ g
  gi|386002166|ref|YP_005920465.1|  56 EILLKKVVVIEQSIEDVLKCKPFF---PPDEGG 85 
                                       555555666777788888888888...223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 863.04
//
Query:       gi|386002167|ref|YP_005920466.1|  [L=136]
Description: hypothetical protein Mhar_1479 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-17   62.1   0.1    7.7e-17   61.9   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   4.3e-21   7.7e-17       1     121 [.       5     128 ..       5     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 4.3e-21
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpid 74 
                                       i++D++++ +++ r+ ++++ + ++le++  + ++++ +v+ E+++ l r   + + + + + + ll   ++i+++d
  gi|386002167|ref|YP_005920466.1|   5 IFVDSNIWCYYFdRSAVEHDLVSERLEDAleSGVAINTVVAMEVAHYLIR---NLGPSGKTKMDVLLSYPMEIVDFD 78 
                                       79************************************************...9*********************** PP

                                       HHHHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  75 aeiaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrvak 121
                                         ia++  e+ ++++   ++  Da i+A ++e gi++++t D  f+r+++
  gi|386002167|ref|YP_005920466.1|  79 QYIARRSIEYLARLShtgIGGRDATILASMEELGIEKLMTHDQAFKRIDF 128
                                       ************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 766.67
//
Query:       gi|386002168|ref|YP_005920467.1|  [L=199]
Description: NAD(P)H dehydrogenase (Quinone) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-36  124.6   0.0    4.6e-36  124.4   0.0    1.0  1  Flavodoxin_2  Flavodoxin-like fold
    5.3e-16   58.7   0.0    7.2e-16   58.3   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase


Domain annotation for each model (and alignments):
>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   0.0   5.1e-40   4.6e-36       1     178 [.       1     172 [.       1     191 [. 0.82

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 5.1e-40
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTTC.HHHHHHH.HHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeekp.adveseq.iek 74 
                                       m++ +i +hp+p +sf+ a+a+a+veal+++g h v  +dLya+ f+p l    +       +++  d + +  +++
  gi|386002168|ref|YP_005920467.1|   1 MRVSVILGHPEP-GSFNFAIAEAAVEALTQNG-HGVSFHDLYAErFDPILPGPEIP------KGAaLDPAIKShCDE 69 
                                       8999********.6******************.******************98777......3333555566666** PP

                                       HHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.E..ETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS- CS
                      Flavodoxin_2  75 llaadaivlqfPlwwfgvPailKgwiDrvltagfaf.y..teeggegrgggLkgkkalvivttGgpeesyqergleg 148
                                       ++aad iv+++P ww   PailKgw+Drv ++g a+ +  ++ g++   g+L+ + alv +t++ pee  +     g
  gi|386002168|ref|YP_005920467.1|  70 IAAADGIVIVHPNWWGQPPAILKGWVDRVIRPGVAYeFveGDGGEGVPVGLLRARCALVFNTSNTPEERER--EAFG 144
                                       ************************************9975444433445555599***********88755..5678 PP

                                       S-HHHHHHHHHHHHHHTT-EEEEEEEEESC CS
                      Flavodoxin_2 149 aamdellpplrgilgfiGikdvepvlvegv 178
                                        +++ l+   r i+g++G++dv+  ++  v
  gi|386002168|ref|YP_005920467.1| 145 DPLETLW--KRCIFGLCGVNDVRRRTFSVV 172
                                       8******..*************87766443 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0     8e-20   7.2e-16       1     100 [.       1     100 [.       1     135 [. 0.90

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 8e-20
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHTCGGSHHHHHHHHHHHH-SCE CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlesegqtsddvaellekiaaadal 76 
                                       m++ vi G + +gs+++++ae+a eal ++g  v++ dl      p  l+  + ++    ++++++  + iaaad++
  gi|386002168|ref|YP_005920467.1|   1 MRVSVILGHPEPGSFNFAIAEAAVEALTQNGHGVSFHDLYAErFDP-ILPGPEIPKGAALDPAIKSHCDEIAAADGI 76 
                                       9**************************************9997777.888888888899****************** PP

                                       EEEEEECTTCE-HHHHHHHHCHT- CS
                           FMN_red  77 iivtPeYngsysgllKnalDrlsr 100
                                       +iv P ++g+++++lK   Dr+ r
  gi|386002168|ref|YP_005920467.1|  77 VIVHPNWWGQPPAILKGWVDRVIR 100
                                       *********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1170.28
//
Query:       gi|386002169|ref|YP_005920468.1|  [L=184]
Description: PBS lyase HEAT domain-containing protein repeat-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-18   66.4   4.7    2.3e-12   47.1   0.3    2.2  2  HEAT_2          HEAT repeats
    4.8e-08   32.9   3.5     0.0088   16.6   0.1    4.0  4  HEAT_PBS        PBS lyase HEAT-like repeat
    2.4e-05   24.2   0.4         22    5.7   0.0    4.3  4  HEAT            HEAT repeat
    0.00044   20.7   5.6       0.57   10.8   0.1    3.6  4  HEAT_EZ         HEAT-like repeat
    0.00093   19.3   0.1      0.013   15.5   0.1    2.5  2  Cnd1            non-SMC mitotic condensation complex subunit 
  ------ inclusion threshold ------
      0.016   13.7   0.0      0.019   13.4   0.0    1.1  1  Vitellogenin_N  Lipoprotein amino terminal region
      0.021   14.8   0.1         18    5.5   0.0    3.1  3  Arm             Armadillo/beta-catenin-like repeat
       0.12   10.9   0.1        4.9    5.6   0.0    2.1  2  Adaptin_N       Adaptin N terminal region


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.5     1e-09   2.3e-06      19      83 ..      29     100 ..      24     100 .. 0.75
   2 !   47.1   0.3     1e-15   2.3e-12       1      83 [.      82     165 ..      82     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1e-09
                            HEAT_2  19 aairaLg......rignpea...lpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvReaA 83 
                                       +ai+aL+      ++  p+a   ++ L e++ +  ++ vR++a++aL++ g  e+++ L  +l+ d++dvv++ A
  gi|386002169|ref|YP_005920468.1|  29 EAIDALAgpqvpeNL--PDAswpVEKLAEVVsKEGNMLVRANAVNALAKKGGAEVVEPLVSALK-DPEDVVKANA 100
                                       577777755332222..34455799999999667899999999999999999999999999996.5788888765 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 1e-15
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvell..ededpavRraaaeaLgaigdpealpaLkelldddd 75 
                                       +++L++al +dp++ v+++a   L+ +g + +++ + ell  + +++++R  aa+ Lg++ d+++l++Lk++  +d+
  gi|386002169|ref|YP_005920468.1|  82 VEPLVSAL-KDPEDVVKANAMVGLAGLGRELVQDRMAELLadREANEEIRGGAAWVLGEMMDEKSLKHLKKASEEDE 157
                                       589*****.9******************************544489******************************* PP

                            HEAT_2  76 ddvvReaA 83 
                                       +++vR  A
  gi|386002169|ref|YP_005920468.1| 158 SPFVRVHA 165
                                       ****9765 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 ?    0.7   0.1      0.54   1.2e+03      12      21 ..      25      34 ..      24      35 .. 0.85
   2 !   16.6   0.1   3.9e-06    0.0088       1      27 []      65      91 ..      65      91 .. 0.98
   3 ?    1.1   0.2      0.41   9.1e+02       1      25 [.      96     120 ..      96     122 .. 0.73
   4 !   12.3   0.0    0.0001      0.23       2      26 ..     130     154 ..     129     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.54
                                      CTSGGGHHHH CS
                          HEAT_PBS 12 lgdeeaipaL 21
                                      lg +eai+aL
  gi|386002169|ref|YP_005920468.1| 25 LGETEAIDAL 34
                                      68899***99 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.9e-06
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR++A+ aL++ g  e++++L+ aL+d
  gi|386002169|ref|YP_005920468.1| 65 VRANAVNALAKKGGAEVVEPLVSALKD 91
                                      9************************98 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       v ++A+ +L+ lg e + ++  e+L
  gi|386002169|ref|YP_005920468.1|  96 VKANAMVGLAGLGRELVQDRMAELL 120
                                       678999*****99866666666655 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLq 26 
                                       R  Aa+ Lg++ de ++ +L++a +
  gi|386002169|ref|YP_005920468.1| 130 RGGAAWVLGEMMDEKSLKHLKKASE 154
                                       899******************9976 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.017        39      13      25 ..      62      74 ..      54      75 .. 0.89
   2 !    5.7   0.0    0.0098        22       2      25 ..      82     105 ..      81     110 .. 0.82
   3 ?    5.4   0.0     0.012        26       6      28 ..     117     141 ..     112     143 .. 0.84
   4 ?    3.3   0.0     0.056   1.2e+02       4      18 ..     148     163 ..     146     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                                      SHHHHHHHHHHHH CS
                              HEAT 13 speVReaAakaLg 25
                                      ++ VR++A++aL+
  gi|386002169|ref|YP_005920468.1| 62 NMLVRANAVNALA 74
                                      789********97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0098
                                       HHHHHHHHT-SSHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLg 25 
                                       + +l+++l+Dp+  V ++A   L+
  gi|386002169|ref|YP_005920468.1|  82 VEPLVSALKDPEDVVKANAMVGLA 105
                                       6789999**********9976665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.012
                                       HHHHT-..SSHHHHHHHHHHHHHHH CS
                              HEAT   6 lkllsD..pspeVReaAakaLgala 28 
                                        +ll D   + e+R  Aa+ Lg+++
  gi|386002169|ref|YP_005920468.1| 117 AELLADreANEEIRGGAAWVLGEMM 141
                                       677888878999**********997 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.056
                                       HHHHHH.T-SSHHHHH CS
                              HEAT   4 lllkll.sDpspeVRe 18 
                                       +l k+  +D+sp+VR 
  gi|386002169|ref|YP_005920468.1| 148 HLKKASeEDESPFVRV 163
                                       56677779*******5 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.5   7.9e+03      21      28 ..      34      41 ..      18      44 .. 0.59
   2 ?    3.0   0.2     0.067   1.5e+02      43      53 ..      64      74 ..      58      75 .. 0.68
   3 !   10.0   1.5   0.00044      0.99       3      49 ..      65     101 ..      63     105 .. 0.84
   4 !   10.8   0.1   0.00025      0.57      19      55 .]     105     140 ..      98     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.5
                           HEAT_EZ 21 llqplvpe 28
                                      l  p+vpe
  gi|386002169|ref|YP_005920468.1| 34 LAGPQVPE 41
                                      33445555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.067
                           HEAT_EZ 43 eVRaaAagaLg 53
                                      +VRa+A+ aL+
  gi|386002169|ref|YP_005920468.1| 64 LVRANAVNALA 74
                                      56666666665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00044
                           HEAT_EZ   3 vRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAa 49 
                                       vR++A++aL+      +   +    e++ +L+++L+d++d V+a+A 
  gi|386002169|ref|YP_005920468.1|  65 VRANAVNALA------KKGGA----EVVEPLVSALKDPEDVVKANAM 101
                                       8999999995......67777....99999*****999999999996 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00025
                           HEAT_EZ  19 pellqplvpeilpaLlalLnddsd..eVRaaAagaLgnl 55 
                                       + l + lv++ +++Ll    d ++  e+R+ Aa+ Lg +
  gi|386002169|ref|YP_005920468.1| 105 AGLGRELVQDRMAELL---ADREAneEIRGGAAWVLGEM 140
                                       4555566667777777...888888788*********86 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.9e-06     0.013       2      67 ..      65     120 ..      64     154 .. 0.65
   2 ?    1.6   0.0      0.11   2.5e+02      56      82 ..     143     169 ..     123     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                              Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselakll 67 
                                       +Ra+a+ +l+         ++vepL ++LkD++  V+ +a++++a L  +++v+     +++a+ll
  gi|386002169|ref|YP_005920468.1|  65 VRANAVNALAKKGG----AEVVEPLVSALKDPEDVVKANAMVGLAGLG-RELVQ-----DRMAELL 120
                                       77777777764444....45667777899****************993.33333.....3455555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                              Cnd1  56 ekgflselakll.eDenprVvanalaal 82 
                                       ek  l++l+k+  eDe+p V+  a+a++
  gi|386002169|ref|YP_005920468.1| 143 EK-SLKHLKKASeEDESPFVRVHAKASI 169
                                       33.3666666665667777766666655 PP

>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.5e-06     0.019     517     616 ..      72     164 ..      47     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                                       HHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHT-- CS
                    Vitellogenin_N 517 aLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAvlalmetkP 593
                                       aL+  G      v+ep+++  +  +++v+++a+  L        ++v++ + +++ ++  + e+R  A+++l e   
  gi|386002169|ref|YP_005920468.1|  72 ALAKKG---GAEVVEPLVSALKDPEDVVKANAMVGLA---GLGRELVQDRMAELLADREANEEIRGGAAWVLGEM-M 141
                                       444444...44566777777799***********999...67789******************************.6 PP

                                       -HHHHHHHHHHHTT-S-HHHHHH CS
                    Vitellogenin_N 594 saallqriaestnkdpskqVaaf 616
                                         + l+++ +  ++d+s  V+  
  gi|386002169|ref|YP_005920468.1| 142 DEKSLKHLKKASEEDESPFVRVH 164
                                       6667*************999865 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.42   9.5e+02       7      17 ..      63      73 ..      62      75 .. 0.81
   2 ?    5.5   0.0    0.0081        18      12      32 ..      80     100 ..      78     107 .. 0.86
   3 ?    5.0   0.0     0.012        26      20      39 ..     119     140 ..     115     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.42
                                      HHHHTTHHHHH CS
                               Arm  7 avieaGavppL 17
                                      ++++a+av +L
  gi|386002169|ref|YP_005920468.1| 63 MLVRANAVNAL 73
                                      68999999998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0081
                                       THHHHHHHHTTTSSHHHHHHH CS
                               Arm  12 GavppLvrLLssedeevqeeA 32 
                                        +v+pLv+ L+++ + v+ +A
  gi|386002169|ref|YP_005920468.1|  80 EVVEPLVSALKDPEDVVKANA 100
                                       68*********9999999888 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.012
                                       HTT..TSSHHHHHHHHHHHHHH CS
                               Arm  20 LLs..sedeevqeeAawALsNL 39 
                                       LL     +ee++  Aaw L+ +
  gi|386002169|ref|YP_005920468.1| 119 LLAdrEANEEIRGGAAWVLGEM 140
                                       56667899***********976 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.012        27      90     134 ..      60     100 ..      56     110 .. 0.76
   2 ?    5.6   0.0    0.0022       4.9     417     447 ..     114     145 ..     107     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.012
                                       SSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHH CS
                         Adaptin_N  90 dpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkA 134
                                         n+l+r++A+++L++ + +e++e l+ a+    kd++ +v+ +A
  gi|386002169|ref|YP_005920468.1|  60 EGNMLVRANAVNALAKKGGAEVVEPLVSAL----KDPEDVVKANA 100
                                       679999999999999999999999887665....55565665555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0022
                                       HHHCCTCCG.XXSHHHHHHHHHHHHHTTTTXT CS
                         Adaptin_N 417 ekLaellek.ieseearaaaiWllGeygelvs 447
                                        ++aell +  ++ee+r +a+W+lGe  ++ s
  gi|386002169|ref|YP_005920468.1| 114 DRMAELLADrEANEEIRGGAAWVLGEMMDEKS 145
                                       589999999778889***********988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1148.32
//
Query:       gi|386002170|ref|YP_005920469.1|  [L=195]
Description: Indolepyruvate ferredoxin oxidoreductase, beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-40  137.8   0.3    4.7e-40  137.5   0.3    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.5   0.3   2.6e-44   4.7e-40       1     175 [.      14     190 ..      14     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 2.6e-44
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv+++++i+++aa r+G+ v + +++g+++rGg+++ h+r++ +  +++i+ g+ad+l+a++++++ +++++l 
  gi|386002170|ref|YP_005920469.1|  14 GGQGVILISEIIGRAALREGLSVRGVETHGMAQRGGSVINHIRVGCR-YSAMISPGGADVLLAMEPAEALRYAHYLS 89 
                                       9*********************************************9.99****************9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl......gvrvygvdatkiakeiggneraaNtvmlGalaallglple 148
                                       p+g++++n+  + p +++     +++++e l        rv ++dat++a e+g  + a+N+vmlGala+ l +++ 
  gi|386002170|ref|YP_005920469.1|  90 PEGVALVNTRPVLPVTVTTGEASYPAVEEILaplrrvASRVRAIDATALAAEAGS-PQATNVVMLGALARHLPMEEA 165
                                       ****************************999*********************888.***************99999* PP

                                       HHHHHHHCCS-CH.HHHHHHHHHHHHH CS
                               POR 149 aleeaikkrfpkkkeviekNlkafrag 175
                                       +l+ea+ +++p k   ie N kaf++g
  gi|386002170|ref|YP_005920469.1| 166 TLLEALTETVPAK--YIEINRKAFELG 190
                                       ***********95..9*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1205.07
//
Query:       gi|386002171|ref|YP_005920470.1|  [L=597]
Description: Indolepyruvate ferredoxin oxidoreductase, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-23   83.3   0.1    3.7e-23   82.0   0.1    1.7  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      2e-15   57.2   0.6    4.4e-08   33.2   0.3    2.4  2  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    1.4e-05   24.7  18.6    0.00024   20.8   6.2    3.2  3  Fer4          4Fe-4S binding domain
    3.4e-05   23.7  18.0     0.0035   17.3   2.5    3.4  3  Fer4_2        4Fe-4S binding domain
    4.4e-05   24.0   8.5      0.011   16.2   2.4    2.7  2  Fer4_7        4Fe-4S dicluster domain
     0.0001   22.3  12.0    0.00075   19.6  12.2    2.3  2  Fer4_10       4Fe-4S dicluster domain
    0.00017   21.5  18.8    0.00052   20.0   4.2    3.5  3  Fer4_6        4Fe-4S binding domain
    0.00019   21.7  12.9     0.0063   16.9   3.0    2.7  2  Fer4_4        4Fe-4S binding domain
    0.00029   20.9  11.7     0.0069   16.5  12.4    2.4  2  Fer4_21       4Fe-4S dicluster domain
     0.0012   19.0  11.8     0.0021   18.2  10.9    2.0  2  Fer4_9        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   14.2   0.3       0.11   12.1   0.2    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
       0.13   13.2  10.0        0.2   12.6   3.2    2.4  2  Fer4_16       4Fe-4S double cluster binding domain
       0.37   11.5   9.8          6    7.7   0.9    2.7  2  Fer4_15       4Fe-4S single cluster domain
        2.1    9.0  12.3        5.1    7.7   3.7    2.6  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
        8.6    6.9  13.1        1.8    9.1   2.5    2.6  2  Fer4_8        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.1   3.1e-26   3.7e-23       1     152 [.     385     525 ..     385     526 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 3.1e-26
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+t+      +v     +++  ++ +mG ++ ++ G+ +  ++r++ a+ GD++fl+  l+ l +a+++++ +t
  gi|386002171|ref|YP_005920470.1| 385 DIGCYTM------GV--GMGTVD--TCLCMGASITVGAGIRFGGEERPICAVLGDSTFLHAgLPGLLNAAYNGARMT 451
                                       8999999......22..445555..9****************88899****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       v +l+N++++mtg+q++p  g + +g+    ++p+++++++++lGa  + + +++d+e +  ++++a+++ g ++++
  gi|386002171|ref|YP_005920470.1| 452 VAILDNSITAMTGHQPHPGSGATAAGDP---SPPLSLEEICRSLGAGfVETADPYDLEATISTFERARDHPGLSVVV 525
                                       *********************9998876...9***************888************************996 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.3   3.7e-11   4.4e-08       2      66 ..      14      75 ..      13      92 .. 0.92
   2 !   21.9   0.0     1e-07   0.00012     122     183 ..     130     190 ..     111     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.7e-11
                                      HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEE CS
                             POR_N  2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTa 66
                                      + ++ag  v+++YP TPssei++ la l+++ ++   +v    +E  a++++iGA+++Gar+a++
  gi|386002171|ref|YP_005920470.1| 14 GILEAGAGVVSGYPGTPSSEIVDYLAPLAKELGI---HVEWSVNEKVAMEVAIGASWTGARSAVT 75
                                      67789999*********************99997...999999******************9975 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1e-07
                                       EEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HEEEEEEC-SGG.GS-----SBXX CS
                             POR_N 122 vlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshevekvelpdeedelklikeklee 183
                                        l +++ qea d++l+Af l+e++ vPv++    +++sh++ +ve+ +  + ++  + ++++
  gi|386002171|ref|YP_005920470.1| 130 CLDPADPQEARDMTLRAFDLSEEFGVPVMLR-PTTRVSHARADVEVGPPGERRAELSFDKDP 190
                                       57799***********************975.678899*******99888443333333333 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.3   1.5e+03       6      12 ..     358     364 ..     356     364 .. 0.85
   2 !   11.2   0.9   0.00021      0.26       3      16 ..     546     559 ..     544     560 .. 0.90
   3 !   20.8   6.2     2e-07   0.00024       6      23 ..     576     593 ..     572     594 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                                       TTSSS-T CS
                              Fer4   6 ekCigCG 12 
                                        +C gCG
  gi|386002171|ref|YP_005920470.1| 358 ALCPGCG 364
                                       68****9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                                       EETTTSSS-THHHH CS
                              Fer4   3 ideekCigCGaCve 16 
                                       +d ekC gC  Cv 
  gi|386002171|ref|YP_005920470.1| 546 VDSEKCGGCQVCVR 559
                                       8***********96 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2e-07
                                       TTSSS-THHHHHSTTTEE CS
                              Fer4   6 ekCigCGaCvevCPvgAI 23 
                                        +C+gCG C+ +CP gA 
  gi|386002171|ref|YP_005920470.1| 576 ALCTGCGVCAAICPAGAV 593
                                       58***************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.6   1.9e+03       7      14 ..     357     364 ..     354     365 .. 0.84
   2 !   17.3   2.5   2.9e-06    0.0035       2      22 .]     543     564 ..     542     564 .. 0.90
   3 !   13.3   3.9   5.5e-05     0.066       9      22 .]     577     590 ..     570     590 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.6
                            Fer4_2   7 tdrCigCg 14 
                                       ++ C gCg
  gi|386002171|ref|YP_005920470.1| 357 PALCPGCG 364
                                       678****8 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.9e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsa.CPa 22 
                                       + +vd+++C gC  Cv   CPa
  gi|386002171|ref|YP_005920470.1| 543 RLAVDSEKCGGCQVCVRFgCPA 564
                                       6799************888**8 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 5.5e-05
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                        C+gCg C   CPa
  gi|386002171|ref|YP_005920470.1| 577 LCTGCGVCAAICPA 590
                                       5*******999**8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.4   0.00057      0.68      27      49 ..     540     563 ..     506     565 .. 0.77
   2 !   16.2   2.4   9.6e-06     0.011       2      18 ..     578     594 ..     569     597 .] 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00057
                            Fer4_7  27 gtekveidpekClgCgaCva.vCP 49 
                                       +++++++d+ekC gC++Cv+  CP
  gi|386002171|ref|YP_005920470.1| 540 RRPRLAVDSEKCGGCQVCVRfGCP 563
                                       4578899***********986677 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 9.6e-06
                            Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                       C+gCg C+a Cp++a+e
  gi|386002171|ref|YP_005920470.1| 578 CTGCGVCAAICPAGAVE 594
                                       77777777777777765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6  12.2   6.3e-07   0.00075       4      56 .]     546     589 ..     543     589 .. 0.81
   2 !   12.3   3.2   0.00012      0.14       6      21 ..     575     590 ..     570     595 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.3e-07
                           Fer4_10   4 idddtCirCgkCvka.CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+++C +C+ Cv++ CPa         ++  +++v      Ctgcg C+++CP
  gi|386002171|ref|YP_005920470.1| 546 VDSEKCGGCQVCVRFgCPA---------IEF-DGKVARINALCTGCGVCAAICP 589
                                       799***********99***.........444.4444444568***********9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                           Fer4_10   6 ddtCirCgkCvkaCPa 21 
                                          C++Cg C + CPa
  gi|386002171|ref|YP_005920470.1| 575 NALCTGCGVCAAICPA 590
                                       467************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.31   3.7e+02       6      13 ..     357     364 ..     357     365 .. 0.85
   2 !    8.5   1.6    0.0019       2.3       3      21 ..     545     564 ..     544     567 .. 0.92
   3 !   20.0   4.2   4.3e-07   0.00052       2      23 ..     571     592 ..     570     593 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.31
                            Fer4_6   6 pdkCigCg 13 
                                       p +C gCg
  gi|386002171|ref|YP_005920470.1| 357 PALCPGCG 364
                                       679****9 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                            Fer4_6   3 eidpdkCigCgdCvrv.CPe 21 
                                       ++d +kC gC  Cvr  CP+
  gi|386002171|ref|YP_005920470.1| 545 AVDSEKCGGCQVCVRFgCPA 564
                                       69*************99997 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 4.3e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       v+    +C+gCg C+++CP+ga
  gi|386002171|ref|YP_005920470.1| 571 VARINALCTGCGVCAAICPAGA 592
                                       5666789*************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   2.5    0.0015       1.8       1      15 [.     548     563 ..     548     569 .. 0.91
   2 !   16.9   3.0   5.3e-06    0.0063       4      17 .]     578     591 ..     575     591 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                            Fer4_4   1 qerCigCgsCvaa.CP 15 
                                       +e+C gC +Cv++ CP
  gi|386002171|ref|YP_005920470.1| 548 SEKCGGCQVCVRFgCP 563
                                       589**********999 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.3e-06
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C+gCg+C a+CP g
  gi|386002171|ref|YP_005920470.1| 578 CTGCGVCAAICPAG 591
                                       ************75 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.4   0.00041      0.48      30      53 ..     540     564 ..     528     567 .. 0.73
   2 !   16.5  12.4   5.8e-06    0.0069       3      58 ..     546     594 ..     545     595 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
                           Fer4_21  30 aktvlkvvedeCvGCnlCssv.CPv 53 
                                        + +l+v +++C GC++C+   CP 
  gi|386002171|ref|YP_005920470.1| 540 RRPRLAVDSEKCGGCQVCVRFgCPA 564
                                       44577899**********9855985 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.8e-06
                           Fer4_21   3 idedkCigCgkClia.CedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d++kC gC+ C+   C+     aie+d+k   + ++  C+GC +C+++CP  +++e
  gi|386002171|ref|YP_005920470.1| 546 VDSEKCGGCQVCVRFgCP-----AIEFDGKV--ARINALCTGCGVCAAICPA-GAVE 594
                                       799999999999965377.....9***9764..57899*************5.7776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.4   8.8e+03      35      40 ..     359     364 ..     337     365 .. 0.72
   2 !   18.2  10.9   1.8e-06    0.0021       1      50 [.     550     592 ..     550     593 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.4
                            Fer4_9  35 aCigCg 40 
                                        C gCg
  gi|386002171|ref|YP_005920470.1| 359 LCPGCG 364
                                       577776 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.8e-06
                            Fer4_9   1 kCtgCgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kC gC+ Cv+  Cpa  + ++ a+  a         C+gCg C+++Cp ga
  gi|386002171|ref|YP_005920470.1| 550 KCGGCQVCVRFgCPAIEFDGKVARINAL--------CTGCGVCAAICPAGA 592
                                       7*******9988***9998876655544........************997 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2     9e-05      0.11       6      76 ..      10      83 ..       7     159 .. 0.90
   2 ?   -2.0   0.0         2   2.3e+03      79     105 ..     436     462 ..     422     520 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9e-05
                                      HHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N  6 alvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76
                                      a+++ + ++g+ +v g+pG+ + +++d+l+      gi+v  +++E +a+  A g +    + +v + ++g ++
  gi|386002171|ref|YP_005920470.1| 10 AIAKGILEAGAGVVSGYPGTPSSEIVDYLAPLAkelGIHVEWSVNEKVAMEVAIGASWTGARSAVTMKHVGLNV 83
                                      577777889****************99998777778********************999999999999999765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                       CHHHHHHHHHHT--EEEEEEE--CCCH CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslr 105
                                       +l++l +A++++  + v   d++ +  
  gi|386002171|ref|YP_005920470.1| 436 GLPGLLNAAYNGARMTVAILDNSITAM 462
                                       577888888888777666555554444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.6     0.062        75       1      14 [.     550     564 ..     541     576 .. 0.72
   2 ?   12.6   3.2   0.00017       0.2       2      18 ..     578     594 ..     577     597 .] 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.062
                           Fer4_16   1 rCgtCgkCaev.CPt 14 
                                       +Cg+C+ C+   CP+
  gi|386002171|ref|YP_005920470.1| 550 KCGGCQVCVRFgCPA 564
                                       477777776533665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C++Cg Ca +CP++a++
  gi|386002171|ref|YP_005920470.1| 578 CTGCGVCAAICPAGAVE 594
                                       9***********99986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9     0.005         6       3      25 ..     546     568 ..     544     574 .. 0.78
   2 ?    7.5   2.3    0.0056       6.7       7      20 ..     577     590 ..     575     595 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.005
                           Fer4_15   3 vDrdaCigcglCvaeapevfeld 25 
                                       vD ++C gc +Cv+     +e+d
  gi|386002171|ref|YP_005920470.1| 546 VDSEKCGGCQVCVRFGCPAIEFD 568
                                       9************8644455555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                           Fer4_15   7 aCigcglCvaeape 20 
                                       +C+gcg+C+a +p 
  gi|386002171|ref|YP_005920470.1| 577 LCTGCGVCAAICPA 590
                                       7***********96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.4     0.017        20       1      15 [.     546     560 ..     546     568 .. 0.87
   2 ?    7.7   3.7    0.0042       5.1       4      18 ..     576     590 ..     574     591 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                           Fer4_13   1 VDrdtCiacgaCvel 15 
                                       VD ++C +c++Cv +
  gi|386002171|ref|YP_005920470.1| 546 VDSEKCGGCQVCVRF 560
                                       9***********986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0042
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                         C++cg+C++++P 
  gi|386002171|ref|YP_005920470.1| 576 ALCTGCGVCAAICPA 590
                                       67************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.4       0.1   1.2e+02       2      18 ..     548     565 ..     547     575 .. 0.80
   2 ?    9.1   2.5    0.0015       1.8      50      63 ..     577     590 ..     566     592 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                            Fer4_8   2 lekCieCgaCq.saCpvl 18 
                                        ekC++C+ C    Cp++
  gi|386002171|ref|YP_005920470.1| 548 SEKCGGCQVCVrFGCPAI 565
                                       589*******96669876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                            Fer4_8  50 sCttcgaCtevCpv 63 
                                        Ct+cg C+  Cp 
  gi|386002171|ref|YP_005920470.1| 577 LCTGCGVCAAICPA 590
                                       56666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):              15  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3509.23
//
Query:       gi|386002172|ref|YP_005920471.1|  [L=270]
Description: Alpha-acetolactate decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-82  275.1   0.0    3.8e-82  274.9   0.0    1.0  1  AAL_decarboxy  Alpha-acetolactate decarboxylase


Domain annotation for each model (and alignments):
>> AAL_decarboxy  Alpha-acetolactate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.9   0.0   2.1e-86   3.8e-82       1     218 [.      41     258 ..      41     259 .. 0.99

  Alignments for each domain:
  == domain 1  score: 274.9 bits;  conditional E-value: 2.1e-86
                     AAL_decarboxy   1 lyqvstlsaLmegvyegtltvsellkhGdfGlGTfeeldGEliildgkvYqlksdgsvrevddeektPFavvtkfep 77 
                                       l+qvst++aL+  vy+g l+v+ l+++GdfG+GTf++l+GE+i+ldg +Yq+k+dg +++v+d+ +tPFa+vt+f++
  gi|386002172|ref|YP_005920471.1|  41 LFQVSTIDALLLAVYDGVLSVGVLKEKGDFGIGTFDKLEGEMILLDGICYQVKEDGFAYVVSDDLTTPFASVTFFDH 117
                                       79*************************************************************************** PP

                     AAL_decarboxy  78 ektvklkealskeeleealeellpskNlfyairidGtfksvkvRsvpkqekpyeplaevakkqsefefenveGtlvG 154
                                       ++tv ++ea++ +el   le+ lpskN+fyairidGtf +v++Rsvp+qe+py+ l++v+++q++fefen +Gt+vG
  gi|386002172|ref|YP_005920471.1| 118 DETVLIEEAANLTELVGILEASLPSKNVFYAIRIDGTFPYVRTRSVPAQERPYPLLVDVTANQTVFEFENASGTIVG 194
                                       ***************************************************************************** PP

                     AAL_decarboxy 155 frtPeylqginvaGlHlHFisddrkfGGHvldfeleeveveiakisklelelpedeeFeeadlk 218
                                       f+tP++++ginv+G HlHFi+ddrk+GGH+ld++++ vev++++++++ ++lp + +F + dl+
  gi|386002172|ref|YP_005920471.1| 195 FWTPQFAAGINVPGSHLHFITDDRKAGGHILDLRVDGVEVALDVTASILMALPAEGDFFDLDLT 258
                                       **********************************************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1693.79
//
Query:       gi|386002173|ref|YP_005920472.1|  [L=646]
Description: hypothetical protein Mhar_1485 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   18.1   0.1     0.0043   17.3   0.1    1.4  1  HHH_3     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.4e-07    0.0043      13      63 ..      39      89 ..      36      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-07
                             HHH_3 13 aeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpktfeqlagf 63
                                      a e++    +g k+A+ +++ R   G+f+s+++    + +g++ f q+ + 
  gi|386002173|ref|YP_005920472.1| 39 AIEIEGERDIGIKIAESLLDRRARLGGFQSLDQVAATPQVGEARFSQIVKT 89
                                      5556666679*************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4089.85
//
Query:       gi|386002174|ref|YP_005920473.1|  [L=435]
Description: histidinol dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.8e-170  566.0   5.7   5.8e-170  565.7   5.7    1.0  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.7   5.7  3.2e-174  5.8e-170       6     409 .]      25     427 ..      21     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 565.7 bits;  conditional E-value: 3.2e-174
                                       ---HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC CS
                     Histidinol_dh   6 edseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaq 82 
                                        d+++v+ +v ei+++v+e+Gd+al ++te+FD+v+   ++rv ++eie+a ++++e+lk+ale a eni +fh+++
  gi|386002174|ref|YP_005920473.1|  25 VDVQSVMPAVVEIVNEVQERGDRALADLTERFDGVR-IGKVRVGKDEIEKAGDQVPEKLKKALEIALENIAAFHHQE 100
                                       578899***************************874.678************************************* PP

                                       ----EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHH CS
                     Histidinol_dh  83 keseeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaak 158
                                       ++++ +++et+pgv++gq+v+p+++vG YvPgG+aaypS++lm++vpAkvAgv++++v+tPp  +gkvnp +l+aa+
  gi|386002174|ref|YP_005920473.1| 101 LDRDLWMTETSPGVMAGQMVVPLDSVGAYVPGGRAAYPSSALMTVVPAKVAGVERVIVCTPPGkEGKVNPITLVAAE 177
                                       **99***********************************************************9************* PP

                                       HCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHH CS
                     Histidinol_dh 159 lagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAa 235
                                       +ag+deiy+vGG+qA+aa+A+Gtesi++v+kivGPGniyV+aAK l++++v+iDm+aGPsEvl+iaD ta+pe++A+
  gi|386002174|ref|YP_005920473.1| 178 MAGADEIYRVGGVQAVAAMAFGTESIRPVQKIVGPGNIYVTAAKLLLRSTVEIDMPAGPSEVLIIADYTAEPEVLAS 254
                                       ***************************************************************************** PP

                                       HHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEE CS
                     Histidinol_dh 236 DLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlel 312
                                       D+++qaEHd+++ +vlvt++e+la a+++evekq++e+ r ei+++slek +ai+++ ++eeai+++n++ApEHle+
  gi|386002174|ref|YP_005920473.1| 255 DMIAQAEHDPQSISVLVTDDEDLAIATRAEVEKQAKETARWEIVKESLEK-AAILVAGSMEEAISFSNSFAPEHLEI 330
                                       **************************************************.99************************ PP

                                       ESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHH CS
                     Histidinol_dh 313 qvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeav 389
                                        v+dp+++l +i+naG++flG+y+p+++gDYa+GtnhvLPTsg+Ar++sgl+v+ F+kki+vq++ske+l+ l++a+
  gi|386002174|ref|YP_005920473.1| 331 IVRDPMTVLGEIRNAGSVFLGPYTPVAAGDYASGTNHVLPTSGYARAFSGLNVDAFVKKITVQKISKEGLSLLKDAI 407
                                       ***************************************************************************** PP

                                       HHHHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 390 etlAeaEgLeaHaeavkvRl 409
                                       + lAeaEgL+aHae+v+ Rl
  gi|386002174|ref|YP_005920473.1| 408 TILAEAEGLDAHAESVRKRL 427
                                       *****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2903.83
//
Query:       gi|386002175|ref|YP_005920474.1|  [L=560]
Description: DNA ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-57  193.8   0.0    5.3e-57  192.8   0.0    1.5  2  DNA_ligase_A_M  ATP dependent DNA ligase domain
    1.1e-34  120.2   0.0    1.1e-31  110.5   0.0    2.4  2  DNA_ligase_A_N  DNA ligase N terminus
    3.8e-16   59.5   0.0    1.1e-15   58.0   0.0    1.9  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    1.8e-05   25.1   0.0    3.4e-05   24.2   0.0    1.5  1  RNA_ligase      RNA ligase


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.5   6.9e+03      28      48 ..     111     131 ..      92     146 .. 0.59
   2 !  192.8   0.0   1.2e-60   5.3e-57       2     204 .]     227     420 ..     226     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.5
                                       ESSEEEEEEEETTEEEEEETT CS
                    DNA_ligase_A_M  28 yDGeRaqvhkegdkvklfSRr 48 
                                       ++GeR+ + +  +++ l+ R+
  gi|386002175|ref|YP_005920474.1| 111 LEGERLTILEVHSRFLLIARA 131
                                       455555544444555555554 PP

  == domain 2  score: 192.8 bits;  conditional E-value: 1.2e-60
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDG 78 
                                       mLA+  + i   + ++ ++a+ vE+KyDG R+q+hk g++v++fSRrl+ +t+++pe+v ++ke + ++   +ilDG
  gi|386002175|ref|YP_005920474.1| 227 MLAQLGSGIAGSVAEM-GTAA-VEVKYDGSRVQIHKRGEEVEIFSRRLERVTRSLPEIVSFVKEGVRAE--AAILDG 299
                                       9**************9.6666.9*******************************************986..7***** PP

                                       EEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE CS
                    DNA_ligase_A_M  79 ElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvel 155
                                       E+va   e+g++lpfq++ +r+++k++ve ++k+++l l++FD++yl+g  l+depl+eRr+lLe++     d+  l
  gi|386002175|ref|YP_005920474.1| 300 EAVA-RGEDGRPLPFQEILKRFRRKYRVEGAAKRIPLELMLFDLIYLNGRVLIDEPLRERRRLLESVA----DEKIL 371
                                       ****.6888**********************************************************9....55569 PP

                                       --EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 156 aeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                       a +++++d ee++ ++eeai+eg+EG+++K+p+s+Y pgkr+knwlK+K
  gi|386002175|ref|YP_005920474.1| 372 AGQKVTDDPEEVAGIYEEAIAEGHEGVMLKSPESPYAPGKRGKNWLKIK 420
                                       9***********************************************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   2.5e-35   1.1e-31       1     173 []       3     181 ..       3     181 .. 0.93
   2 !   11.5   0.0   6.4e-05      0.29      64     111 ..     176     218 ..     175     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.5e-35
                                       BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH..SS-CCCS------HHHHHHHHHHHHT-- CS
                    DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL..llPdydgreygigesllakalaealgls 75 
                                       +F+ +ael+++iee     +ek ++la+f+r++e+ ++ +++p + +   +P+  +  +g+g+s+l+ al++a+g  
  gi|386002175|ref|YP_005920474.1|   3 SFESFAELCARIEE-IGGSIEKADLLASFLRDLEE-EELSVVPSFVMgsPFPASSDLLLGVGPSTLYDALSKAFGAA 77 
                                       6999**********.66679************986.55478888888****************************99 PP

                                       HHHHHHHHHHHS-HHHHHHHHHCCHHHH.....------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HH CS
                    DNA_ligase_A_N  76 kkkikdalakvgDlgevaeevlskrstl.....akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspe 146
                                       + ++++ l+++gD+g va+e+ +k ++       + ++lti ev++ +  +a+a g++s+++k+k l+ l+++a+++
  gi|386002175|ref|YP_005920474.1|  78 PSEVQELLRRTGDVGAVAAELAKKGRSStlstfLEGERLTILEVHSRFLLIARAsGRRSQTAKMKHLRYLFSEAGAT 154
                                       999*****************99887777799999999***************9999********************* PP

                                       HHHHHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 147 Eakyliriilkdlriglsektvldala 173
                                       Ea+y++r+ l+d+rig++e+ v+da a
  gi|386002175|ref|YP_005920474.1| 155 EARYMARLALEDMRIGVGEGIVRDAVA 181
                                       ************************986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHHHH------BH CS
                    DNA_ligase_A_N  64 lakalaealglskkkikdalakvgDlgevaeevlskrstlakksplti 111
                                       ++ a+a+a+g+s+++++  ++ + Dlg va ++++ r +     +lti
  gi|386002175|ref|YP_005920474.1| 176 VRDAVAKAFGISPEEVERGYNFTSDLGLVARQAKEGRLQ-----ELTI 218
                                       5789******************************99987.....7777 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   2.6e-19   1.1e-15       2      99 .]     441     533 ..     440     533 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.6e-19
                                       GGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEEC.TTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   2 gglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerk.kppfaekvpeeekrdvWvePelvveVkfa 75 
                                       ++ +gs+ l+  d  +g+le vg v+tG++d++l+el++ +++l     + +    + e      v+Pe+v+eV+f+
  gi|386002175|ref|YP_005920474.1| 441 ATFFGSYRLASPDpeTGRLEDVGWVATGITDEMLAELTELFRDLVLVaGEGM----EVE------VKPEVVFEVAFE 507
                                       6789*********99**************************85554403333....223......89********** PP

                                       EEECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka..slRfPrfkrlReDk 99 
                                       ei++s++y++  +lRfPr++r+R+Dk
  gi|386002175|ref|YP_005920474.1| 508 EIQKSKSYSSgyALRFPRLVRIRDDK 533
                                       *************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.6e-09   3.4e-05       4     161 .]     246     420 ..     243     420 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.6e-09
                                       EEEEE-SSEEEEEEEE.TTEEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES......... CS
                        RNA_ligase   4 vvtEKlDGtnfriylv.kevgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig......... 69 
                                        v++K DG++++i++  +ev ++sR+ +  +          r   +  + +ke  + e  il GE +          
  gi|386002175|ref|YP_005920474.1| 246 AVEVKYDGSRVQIHKRgEEVEIFSRRLERvT----------RSLPEIVSFVKEGVRAEAAILDGEAVArgedgrplp 312
                                       599***********98533999999999931..........2222333344444446679********777665554 PP

                                       ..SS........TTSS............EEEEEEEEEEE.CTT..BECE--HHHH.HHHHHCCTB..EEEEE.SS.H CS
                        RNA_ligase  70 .hsi......kygglpk...........efyvFdifdir.dke..eqrylspdev.ealakglgtvpvlyegkfl.a 123
                                        + i      k                 e+++Fd++ ++      ++   +++++ e +a++    ++l + k++ +
  gi|386002175|ref|YP_005920474.1| 313 fQEIlkrfrrK-----YrvegaakriplELMLFDLIYLNgR-VliDEPLRERRRLlESVADE----KILAGQKVTdD 379
                                       43334443333.....044566789999********98842.22222222223333444443....46666666667 PP

                                       HHHHCCC...HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 124 aeellel..llskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                        ee++ +  +    +  EG+ +k++++ y   k+ ++++K+k
  gi|386002175|ref|YP_005920474.1| 380 PEEVAGIyeE-AIAEGHEGVMLKSPESPYApGKRgKNWLKIK 420
                                       7777777541.33569***************9999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3548.72
//
Query:       gi|386002176|ref|YP_005920475.1|  [L=317]
Description: Homoserine dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  109.7   0.0    2.2e-31  109.1   0.0    1.3  1  Homoserine_dh    Homoserine dehydrogenase
      3e-11   44.0   0.0      5e-11   43.3   0.0    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.023   15.4   0.1       0.16   12.7   0.0    2.1  2  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.0   3.7e-35   2.2e-31       1      93 [.     149     241 ..     149     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 3.7e-35
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P+i+ +++ l g++i +i+Gi+ngt+nyilt+m ee+ ++s +l eaqelG+aeaDp  Dv+G+D+a K++ila+ +
  gi|386002176|ref|YP_005920475.1| 149 PLISLIEKNLVGNEILSIRGIFNGTCNYILTRMMEEKYTYSYALTEAQELGIAEADPAYDVDGIDTAGKVVILANSI 225
                                       99*********************************9999************************************** PP

                                       CTTT--GGGSEE--ST CS
                     Homoserine_dh  78 fgleveledvevegis 93 
                                       fg+  ++edv+v+gi+
  gi|386002176|ref|YP_005920475.1| 226 FGMGAKYEDVSVTGIE 241
                                       ***************8 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   8.3e-15     5e-11       1     116 [.       7     140 ..       7     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 8.3e-15
                                       --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT.....HHHHHT--CB---HHHHHHHH....S-EE CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd.....rkallasealtldlddliahl....dpdv 62 
                                       G+G +G +vle ++r+++      ++l++v v+d + +l + d     r+  +++ +  ++l  + +++    d d+
  gi|386002176|ref|YP_005920475.1|   7 GFGIVGHGVLEVVRRKRELlrsmgLDLRVVSVTDIKgTLFDGDgidpsRLHGAKTLEGIANLGIIGKEAiqeiDSDL 83 
                                       99***************99***9999999999999988888889976655555555555666555554477779*** PP

                                       EEE-S--HHHHT.....THHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  63 vVEcasseavae.....lvlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                       vVE+++ + v++     ++++aLk gk+vvt nkg l+  + ++ Lr++a++ng  + +
  gi|386002176|ref|YP_005920475.1|  84 VVEVTPTNIVHGqpglgHIEEALKLGKHVVTSNKGPLV--VGFNHLRDLARENGLMLKY 140
                                       ***********6444448********************..*************987766 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   1.8e+03       8      30 ..       9      31 ..       5      40 .. 0.84
   2 ?   12.7   0.0   2.7e-05      0.16      76     128 ..      70     123 ..      53     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                                      SHHHHHHHHHHHHCTTTEEEEEE CS
                   DXP_reductoisom  8 GSIGtqtLdvieenpdkfevval 30
                                      G +G+  L+v++++++  + ++l
  gi|386002176|ref|YP_005920475.1|  9 GIVGHGVLEVVRRKRELLRSMGL 31
                                      77999********9998777666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.7e-05
                                       EESHHHHHHHHCHTT-SEEEE--S.SGGGHHHHHHHHHTTSEEEE--SHHHHHH CS
                   DXP_reductoisom  76 lvGeealkelaeeeeadvvvaaiv.GaaGLkptlaaikagkriaLANKEsLVva 128
                                       ++G+ea++e+ +   ++v  + iv G  GL    +a+k gk+++ +NK  LVv+
  gi|386002176|ref|YP_005920475.1|  70 IIGKEAIQEIDSDLVVEVTPTNIVhGQPGLGHIEEALKLGKHVVTSNKGPLVVG 123
                                       68999999999999999887766549*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2081.90
//
Query:       gi|386002177|ref|YP_005920476.1|  [L=152]
Description: Amino acid-binding ACT domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.071   13.2   0.2       0.15   12.2   0.2    1.5  1  Sigma70_r1_1  Sigma-70 factor, region 1.1


Domain annotation for each model (and alignments):
>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   8.1e-06      0.15      33      59 ..      37      63 ..      34      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.1e-06
                                      S--HHHHHHHHHHHHCCT-EEE-SS-. CS
                      Sigma70_r1_1 33 eldseqiediiemLedmgIdvveeaed 59
                                      e+d+ +i++i   L+d+gI vv+  ed
  gi|386002177|ref|YP_005920476.1| 37 EIDPSNIDNIKRHLQDNGIVVVRAGED 63
                                      799*******************97774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1166.13
//
Query:       gi|386002178|ref|YP_005920477.1|  [L=252]
Description: NH(3)-dependent NAD(+) synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-77  258.6   0.0      5e-77  258.3   0.0    1.0  1  NAD_synthase   NAD synthase
    8.9e-05   21.4   0.0     0.0096   14.8   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
    0.00083   19.1   0.1     0.0012   18.6   0.1    1.2  1  Asn_synthase   Asparagine synthase
      0.009   15.5   0.0      0.018   14.6   0.0    1.5  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.088   12.8   0.0        1.2    9.2   0.0    2.8  4  DUF3606        Protein of unknown function (DUF3606)
       0.12   12.1   1.3        3.1    7.6   0.1    3.1  4  HTH_38         Helix-turn-helix domain
       0.18   11.5   0.0         10    5.8   0.0    2.3  2  CENP-B_N       CENP-B N-terminal DNA-binding domain


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.3   0.0   1.9e-80     5e-77       4     242 .]       9     247 ..       7     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 258.3 bits;  conditional E-value: 1.9e-80
                                       HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                      NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievkti 79 
                                       +l +f++++v+ agakg+vlG+SGG+DS++va lav+algk++vl+lllP   v+++edv da+++a  lgie ++i
  gi|386002178|ref|YP_005920477.1|   9 HLAKFIRDQVEAAGAKGAVLGISGGLDSATVAFLAVRALGKDRVLGLLLPeAGVTPKEDVLDARKVASILGIEAEEI 85 
                                       5789**********************************************999************************ PP

                                       --HHHHHHHHH.HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  80 dikpivrafeq.elkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       di++++r++ +    +a+  +++gNlkaR+Rm+ily +an l++lvlgTgn++E+++Gy Tk+GD aad++pia+l+
  gi|386002178|ref|YP_005920477.1|  86 DISQVLRSYFAvLPAKAAPAVVNGNLKARVRMTILYWHANLLGRLVLGTGNRTEILLGYSTKFGDSAADVLPIAGLY 162
                                       **********9444455589********************************************************* PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklv 232
                                       K ev++La++l+vP+r+l+k+P+A+L+pgqtDe eLgi+Y+    iL+ +e ++s++++++  e+ +e+   +e ++
  gi|386002178|ref|YP_005920477.1| 163 KDEVRDLARRLGVPDRILDKAPTAGLWPGQTDEGELGITYQDANAILRGLEAGRSRNDLAA--EFGREELALVEGRI 237
                                       **********************************************************887..999*********** PP

                                       HHTGGGGSSS CS
                      NAD_synthase 233 kksehKrklp 242
                                          +hKr+lp
  gi|386002178|ref|YP_005920477.1| 238 AAGRHKRELP 247
                                       ********98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.7e-06    0.0096       4      72 ..      27      89 ..      24      95 .. 0.79
   2 !    4.6   0.0    0.0047        12     165     186 ..     155     176 ..     150     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.7e-06
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      v ++SgG DS+ +a+l  ++  + + + l l e       + + +ed+ da++va+ lgi+ e +d+++
  gi|386002178|ref|YP_005920477.1| 27 VLGISGGLDSATVAFLAVRALGKDRVLGLLLPEA------GVTPKEDVLDARKVASILGIEAEEIDISQ 89
                                      6799*******99999888875544444444433......467789******************99876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0047
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla 186
                                       ++P++ l K+evr++A++ g++
  gi|386002178|ref|YP_005920477.1| 155 VLPIAGLYKDEVRDLARRLGVP 176
                                       79***************99876 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   4.6e-07    0.0012       5      81 ..       9      89 ..       5      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.6e-07
                      Asn_synthase  5 lLedaVkrrlradvpvGalL..SGGlDSSliaalaarqsksplktFsigfee...kgsdeakyakevaehlgtehtelv 78
                                      +L++ ++++++a    Ga+L  SGGlDS+++a+la r +  + +   + + e      +++  a++va  lg+e  e+ 
  gi|386002178|ref|YP_005920477.1|  9 HLAKFIRDQVEAAGAKGAVLgiSGGLDSATVAFLAVRALG-KDRVLGLLLPEagvTPKEDVLDARKVASILGIEAEEID 86
                                      6666677777777777777666***************997.56666666633456999****************99998 PP

                      Asn_synthase 79 lte 81
                                      +++
  gi|386002178|ref|YP_005920477.1| 87 ISQ 89
                                      875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     7e-06     0.018       2      62 ..      26      88 ..      25     111 .. 0.76
   2 ?   -3.3   0.0       2.1   5.3e+03     157     176 ..     157     176 ..     155     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7e-06
                                      EEEE--SSHHHHHHHHHHHHH-..SEEEEEEE.ESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  2 avvllSGGlDSttvlalakkeg..kevealtf.dYgqrhkkeleaakkiakelgveehkildld 62
                                      av+ +SGGlDS+tv++la ++   ++v  l + + g   k+++  a+k+a+ lg+ e + +d++
  gi|386002178|ref|YP_005920477.1| 26 AVLGISGGLDSATVAFLAVRALgkDRVLGLLLpEAGVTPKEDVLDARKVASILGI-EAEEIDIS 88
                                      7899**************9987333444333324566677788888888888888.77778876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                       TTTT--HHHHHHHHHHTTHH CS
                              QueC 157 PlidlsKaeivklgkelgvp 176
                                       P+  l K e+  l+ +lgvp
  gi|386002178|ref|YP_005920477.1| 157 PIAGLYKDEVRDLARRLGVP 176
                                       89999999999999999986 PP

>> DUF3606  Protein of unknown function (DUF3606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.7   9.5e+03      38      45 ..      43      50 ..      42      51 .. 0.83
   2 ?   -2.1   0.0       1.5   3.8e+03      41      49 ..     147     155 ..     146     155 .. 0.89
   3 ?    9.2   0.0   0.00045       1.2      18      38 ..     163     183 ..     158     183 .. 0.92
   4 ?   -1.3   0.0      0.86   2.2e+03      41      53 ..     213     225 ..     197     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.7
                           DUF3606 38 AVraVGns 45
                                      AVra G +
  gi|386002178|ref|YP_005920477.1| 43 AVRALGKD 50
                                      99999987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                           DUF3606  41 aVGnsakkV 49 
                                       + G+sa++V
  gi|386002178|ref|YP_005920477.1| 147 KFGDSAADV 155
                                       78*****98 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00045
                           DUF3606  18 eyevayWakklgvteeqLraA 38 
                                       ++ev+ +a++lgv+++ L +A
  gi|386002178|ref|YP_005920477.1| 163 KDEVRDLARRLGVPDRILDKA 183
                                       68**************99887 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.86
                           DUF3606  41 aVGnsakkVrayL 53 
                                       ++G+s+ +++a+ 
  gi|386002178|ref|YP_005920477.1| 213 EAGRSRNDLAAEF 225
                                       5899999999886 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.8   1.2e+04      24      31 ..      72      79 ..      71      79 .. 0.85
   2 ?   -2.8   0.0       2.3   5.8e+03       9      19 ..     136     146 ..     135     149 .. 0.77
   3 ?    1.5   0.0     0.097   2.5e+02      23      32 ..     166     175 ..     158     176 .. 0.86
   4 ?    7.6   0.1    0.0012       3.1       5      32 ..     200     227 ..     199     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.8
                            HTH_38 24 reIArrLg 31
                                      r++A +Lg
  gi|386002178|ref|YP_005920477.1| 72 RKVASILG 79
                                      89999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                            HTH_38   9 eReeIerllae 19 
                                       +R eI  +++ 
  gi|386002178|ref|YP_005920477.1| 136 NRTEILLGYST 146
                                       58999998876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.097
                            HTH_38  23 lreIArrLgr 32 
                                       +r+ ArrLg+
  gi|386002178|ref|YP_005920477.1| 166 VRDLARRLGV 175
                                       79******96 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0012
                            HTH_38   5 LsleeReeIerllaeGlslreIArrLgr 32 
                                       ++ ++ + I r+l++G s  + A + gr
  gi|386002178|ref|YP_005920477.1| 200 ITYQDANAILRGLEAGRSRNDLAAEFGR 227
                                       5889999********************9 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.026        66      25      36 ..     166     177 ..     163     182 .. 0.86
   2 ?    5.8   0.0     0.004        10      14      33 ..     207     226 ..     200     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.026
                                       HHHHHHHHT--C CS
                          CENP-B_N  25 kaelarrfnvpe 36 
                                       +++larr++vp 
  gi|386002178|ref|YP_005920477.1| 166 VRDLARRLGVPD 177
                                       689*******96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.004
                                       HHHHHHHCTT-HHHHHHHHT CS
                          CENP-B_N  14 evIqrleegeSkaelarrfn 33 
                                       ++ + le g S+++la +f+
  gi|386002178|ref|YP_005920477.1| 207 AILRGLEAGRSRNDLAAEFG 226
                                       788999**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1608.49
//
Query:       gi|386002179|ref|YP_005920478.1|  [L=385]
Description: hypothetical protein Mhar_1491 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-26   90.7   0.4    2.4e-25   89.4   0.0    1.8  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    5.9e-18   65.5   0.0    9.5e-18   64.8   0.0    1.3  1  eRF1_2          eRF1 domain 2
    1.2e-14   54.7   0.3    3.5e-14   53.2   0.1    1.9  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    8.1e-07   29.5   0.0      2e-06   28.3   0.0    1.6  1  eRF1_3          eRF1 domain 3
    5.2e-05   23.3   0.1    5.2e-05   23.3   0.1    2.3  3  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
    0.00045   20.8   0.0     0.0017   18.9   0.0    2.0  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
       0.41   10.8   4.5          1    9.5   4.4    1.7  1  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.6   6.6e+03     102     111 ..      61      70 ..      26      83 .. 0.61
   2 !   89.4   0.0   9.3e-29   2.4e-25       1     133 [.     127     258 ..     127     264 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                    baeRF_family10 102 aalldrlpka 111
                                        a++++lp++
  gi|386002179|ref|YP_005920478.1|  61 RAMEEALPAD 70 
                                       2334444444 PP

  == domain 2  score: 89.4 bits;  conditional E-value: 9.3e-29
                    baeRF_family10   1 PylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevA 77 
                                       P+l pL+++ d+y  yg++l+d ++aRlf v+ +  eev +++++  g++k+ggw sq+rf r ++  ++ +l evA
  gi|386002179|ref|YP_005920478.1| 127 PFLLPLAKLRDDYLDYGLLLLDSREARLFCVRSDVPEEVGRLSADLMGKHKKGGW-SQMRFNRLRKGAVRSFLSEVA 202
                                       9******************************************************.********************* PP

                    baeRF_family10  78 ellaklleergverlvlgGdeeetaalldrlpkalrarvvgtlplpvdasaaaVle 133
                                       e +++ + +++++ lv++G+ ++++++l++lp +l ++v + ++lp+da++++++e
  gi|386002179|ref|YP_005920478.1| 203 EDVRESCLRHKTRGLVVAGPGDAKKEFLELLPHDLGRKVLAVVDLPIDAPQRKLVE 258
                                       ***************************************************99876 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   3.7e-21   9.5e-18       1     111 [.     141     246 ..     141     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 3.7e-21
                                       EEEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTE CS
                            eRF1_2   1 kvglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdkl 77 
                                       ++gl++ld +eA ++ +++ + e + +++ ++ +Khk+Gg s+ rf+Rlr+ ++++fl +vae + +  l   ++k 
  gi|386002179|ref|YP_005920478.1| 141 DYGLLLLDSREARLFCVRSDVPEEVGRLSADLMGKHKKGGWSQMRFNRLRKGAVRSFLSEVAEDVRESCL---RHKT 214
                                       69******************************************************************55...79** PP

                                       SEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE CS
                            eRF1_2  78 kgiilagpgfvkeefldkdlldaelkkkviklvd 111
                                       +g+++agpg++k+efl+  ll ++l  kv+ +vd
  gi|386002179|ref|YP_005920478.1| 215 RGLVVAGPGDAKKEFLE--LLPHDLGRKVLAVVD 246
                                       ***************97..566666667766666 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1   1.4e-17   3.5e-14       6     115 ..     146     255 ..     141     271 .. 0.77
   2 ?   -2.3   0.0       1.9     5e+03      80     104 ..     341     365 ..     328     382 .. 0.73

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.4e-17
                           acVLRF1   6 llvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.vvlgG 81 
                                       ll+ r +  +  v+++  +++ + + d +g++++GGwSq Rf R r + +++ l++vae++++ + +++ + +v++G
  gi|386002179|ref|YP_005920478.1| 146 LLDSREA-RLFCVRSDVPEEVGRLSADLMGKHKKGGWSQMRFNRLRKGAVRSFLSEVAEDVRESCLRHKTRgLVVAG 221
                                       4555555.666667777778888899***************************************9999999***** PP

                           acVLRF1  82 drslvaevledar..laplatlareelldvpdprra 115
                                       +  + +e+le     l++   ++++  l +  p+r+
  gi|386002179|ref|YP_005920478.1| 222 PGDAKKEFLELLPhdLGRKVLAVVD--LPIDAPQRK 255
                                       **********944123332222222..345555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                           acVLRF1  80 gGdrslvaevledarlaplatlare 104
                                       gG+ s+v+ v e  +la+ +++ +e
  gi|386002179|ref|YP_005920478.1| 341 GGPTSAVDVVNELYELAERTGAEVE 365
                                       7888888888877666665555444 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   7.7e-10     2e-06      13     111 ..     281     385 .]     272     385 .] 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 7.7e-10
                                       HHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS...........-HHH-HHHHHHHHHHHHHH CS
                            eRF1_3  13 eelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv...........ketgeelelvelieelven 77 
                                        ++ ++ g+av Gve ++ ale g v+ L+++ +     ++ +++++           +++g  +++v++++el+e 
  gi|386002179|ref|YP_005920478.1| 281 AQILRG-GLAVRGVEATKVALEAGRVSVLVLLKDASAPGWIcERCQAlearrrpppacPNCGGPTSAVDVVNELYEL 356
                                       556655.999***************************9999888888****************************** PP

                                       HHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS CS
                            eRF1_3  78 veesgakveiisseseeGeqlvkafgGiaaiLRy 111
                                       +e +ga+ve++ +     + l ++  G++a+LRy
  gi|386002179|ref|YP_005920478.1| 357 AERTGAEVEFVEE----DACL-ASGEGVGALLRY 385
                                       **********955....4566.777899999999 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.6     4e+03     109     131 ..      44      66 ..      37      81 .. 0.56
   2 !   23.3   0.1     2e-08   5.2e-05      33     103 ..     171     241 ..     142     279 .. 0.84
   3 ?   -1.6   0.1      0.97   2.5e+03      62      78 ..     348     364 ..     345     372 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                     baeRF_family2 109 ggraagadrealaeevaealaer 131
                                        +r+++a+++++ ++  +a++e 
  gi|386002179|ref|YP_005920478.1|  44 ASREEEAENRSFVARRSRAMEEA 66 
                                       55555555555555555555444 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2e-08
                     baeRF_family2  33 dpvhkvraggwshrryqrraeeswerNaeavAeevdrlvresgaelVvlaGDvrarsllrdeLpervrelv 103
                                       d + k ++ggws+ r+ r  + +++    +vAe v + + +++ + +v+aG   a +   + Lp+ + + v
  gi|386002179|ref|YP_005920478.1| 171 DLMGKHKKGGWSQMRFNRLRKGAVRSFLSEVAEDVRESCLRHKTRGLVVAGPGDAKKEFLELLPHDLGRKV 241
                                       45678889*******************************************************99986655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.97
                     baeRF_family2  62 avAeevdrlvresgael 78 
                                       +v  e+ +l++++gae+
  gi|386002179|ref|YP_005920478.1| 348 DVVNELYELAERTGAEV 364
                                       56677777777777776 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.6e-07    0.0017      43     122 ..     168     245 ..     142     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
                    baeRF_family12  43 gssdrpGrsssggagrsameetdfkeqeeerFakeladeLkkrakegkferlvlvappetlgelrkhlhkevkkrlv 119
                                       +s+d  G+++ gg +  +m     ++ +   F+ e+a+++++ ++++k   lv+ +p ++ +e+ + l+ ++ +++ 
  gi|386002179|ref|YP_005920478.1| 168 LSADLMGKHKKGGWS--QMRFNRLRKGAVRSFLSEVAEDVRESCLRHKTRGLVVAGPGDAKKEFLELLPHDLGRKVL 242
                                       556666777777777..33333334447788*****************************************99986 PP

                    baeRF_family12 120 gei 122
                                       + +
  gi|386002179|ref|YP_005920478.1| 243 AVV 245
                                       654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.4    0.0004         1       8      36 ..     321     344 ..     318     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0004
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                       Ce+C+   e+++    +p++aCP+Cg+++
  gi|386002179|ref|YP_005920478.1| 321 CERCQ-ALEARR----RPPPACPNCGGPT 344
                                       99999.888776....46788*****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2322.20
//
Query:       gi|386002180|ref|YP_005920479.1|  [L=249]
Description: Hydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-09   35.2   0.0    1.7e-08   33.5   0.0    1.8  1  AXE1           Acetyl xylan esterase (AXE1)
    5.2e-07   29.2   0.3    0.00013   21.4   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    6.8e-07   29.0   0.0    3.2e-06   26.8   0.0    1.8  1  Peptidase_S9   Prolyl oligopeptidase family
    0.00013   22.6   0.0    0.00018   22.2   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
    0.00042   19.9   0.0     0.0011   18.6   0.0    1.7  1  DLH            Dienelactone hydrolase family
     0.0011   18.7   0.0     0.0052   16.4   0.0    1.8  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0023   17.8   0.0     0.0031   17.4   0.0    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.065   13.2   0.0       0.16   11.9   0.0    1.6  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
        0.1   11.3   0.0       0.14   10.8   0.0    1.1  1  PhoPQ_related  PhoPQ-activated pathogenicity-related protein


Domain annotation for each model (and alignments):
>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   8.5e-12   1.7e-08      65     204 ..      20     150 ..       8     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 8.5e-12
                                       GGEEEEEEEEEES.SS.SSEEEEEEEE-TT--GGGHHHHHHH.HHTT-EEEEEE-TTTS..SSB-SSCCSS-SSSST CS
                              AXE1  65 rgarikaklvlPkeke.eklPavvefhGYegsrgeihdllny.aaaGyavvvmdvRGqggesedkvgskgnkakGfi 139
                                       rga++ a l  P++k+ e  P vv   G + ++ + + l +  +  Gya++++d R  gg   d+ g  +       
  gi|386002180|ref|YP_005920479.1|  20 RGAEVAALLREPSAKRpEGFPGVVLLPGATVTKEQEQGLAELlSGLGYATIALDQRNRGG--VDVGGDLE-----MF 89 
                                       556666666666543324456666666665555444444433134566666666666662..33333332.....22 PP

                                       TTTTTSTTT-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEE CS
                              AXE1 140 irGlldkeklyyrrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvad 204
                                       i G    e   + ++  Da  ++e+++  pe+D++R++ lG+s GG  a+ ++al++r + vva 
  gi|386002180|ref|YP_005920479.1|  90 INGQEPTE---H-KMVHDALAAAEVLRMQPEIDPDRIVYLGESNGGRFAIIASALDRRSRGVVAI 150
                                       33433333...3.3446*********************************************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   6.3e-08   0.00013       7     108 ..      42     151 ..      40     167 .. 0.85
   2 !    6.2   0.0    0.0027       5.5     194     237 ..     193     235 ..     169     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.3e-08
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.......gkrghvpsfddyvdDlaafvekvkeehpel 76 
                                       vvl++G + + ++ + lae L   G+a++alD+r  G  +          g+ p  +++v D+ a+ e ++ + +  
  gi|386002180|ref|YP_005920479.1|  42 VVLLPGATVTKEQEQGLAELLSGLGYATIALDQRNRGGVDvggdlemFINGQEPTEHKMVHDALAAAEVLRMQPEID 118
                                       89999999999999***************************999988888999**************9999444444 PP

                       Hydrolase_4  77 ..plfllGhSmGGliallyllrypdkvaglilsa 108
                                         +++ lG+S GG  a+ + +  ++  +g++ ++
  gi|386002180|ref|YP_005920479.1| 119 pdRIVYLGESNGGRFAIIASALDRR-SRGVVAIS 151
                                       478999*******888877744443.35777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0027
                       Hydrolase_4 194 llllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                       l ++h+++D+v++ + + ++y+++    k +++ + + H   +E
  gi|386002180|ref|YP_005920479.1| 193 LVMIHSKNDTVIPVDSASRTYQKALE-PKAMHIVDCATHGRCGE 235
                                       789******************99996.99999999999976666 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.6e-09   3.2e-06       8     167 ..      60     214 ..      56     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.6e-09
                                       HHHHCCT-EEEEE-..-TTSSTTHCHHHHTTSGG..GGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHH CS
                      Peptidase_S9   8 qlladrGyvvvvan..irGsggyGeafhdagkrk..lgqnefdDfiaaaealakegyvdserlaitGgSyGGyltga 80 
                                       +ll+ +Gy+ ++ +  +rG+ + G + +  ++++  +  + ++D +aaae l  +  +d++r++  G S+GG  +  
  gi|386002180|ref|YP_005920479.1|  60 ELLSGLGYATIALDqrNRGGVDVGGDLEMFINGQepTEHKMVHDALAAAEVLRMQPEIDPDRIVYLGESNGGRFAII 136
                                       57788899888887446899999*99998776662256789*******************************88877 PP

                                       HHH.H-GGG-SEEEEESE---CCCHHCSTTSTHHHCCCC--TTTCHHHHHHHHHH-CGGG--..---EEEEEEETT- CS
                      Peptidase_S9  81 aln.qrpdlFkaavaevpvvdvlrydsdtdllteeymewgnpeeneegykelspyspldnvk..aypplLlihGlaD 154
                                       a + +r ++  +a++ ++ +dv     d   l +  m  +++         l +++p + ++     +l +ih+ +D
  gi|386002180|ref|YP_005920479.1| 137 ASAlDRRSRGVVAISTCG-YDVEGEEID---LLR--MSGPDA---VRF---LRSIDPDTYLEriPPRRLVMIHSKND 201
                                       777344444444444443.566666666...322..332333...333...33333333333334555666788888 PP

                                       SSS-THHHHHHHH CS
                      Peptidase_S9 155 drvppaealklva 167
                                       + +p+ +a + ++
  gi|386002180|ref|YP_005920479.1| 202 TVIPVDSASRTYQ 214
                                       8888877776665 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     9e-08   0.00018       1     133 [.      42     195 ..      42     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9e-08
                                       EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTST.............S-GGCS--HHHCHHHHHHHCCTT.. CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhG.............rsdpppldledladlaalldelaa. 62 
                                       v+ll+Ga  ++++     La+ll++  ++++a+D ++ G             +    p+++  ++d +a+++ l++ 
  gi|386002180|ref|YP_005920479.1|  42 VVLLPGATVTKEQ--EQGLAELLSGLgYATIALDQRNRGgvdvggdlemfinG--QEPTEHKMVHDALAAAEVLRMq 114
                                       7999**8865444..447877777777999********767777666666542..3334444455554444444444 PP

                                       ....TTSEEEEEETCHHHHHHHHHHCC..EE..EEES-.....----TTT....S----TTHHHHHHTT-CCCCHCC CS
                     Abhydrolase_6  63 ...gggpvvlvGHSlGGalalaaaplalvvg..vlldppp...talpagl....laaalelllallallrllawlsr 127
                                          +++++v +G S GG  a  a +l ++++  v++++++    +    +    l++  + + ++l++  ++++l r
  gi|386002180|ref|YP_005920479.1| 115 peiDPDRIVYLGESNGGRFAIIASALDRRSRgvVAISTCGydvEG----EeidlLRMSGPDAVRFLRSIDPDTYLER 187
                                       55679999**********999988899555558888884432211....1333344444444444444444666655 PP

                                       HS-HS..C CS
                     Abhydrolase_6 128 eplpr..l 133
                                        p++r   
  gi|386002180|ref|YP_005920479.1| 188 IPPRRlvM 195
                                       44443422 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.3e-07    0.0011       8     127 ..      31     149 ..      24     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-07
                               DLH   8 pkna...kkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvldd 81 
                                       p ++    +p+vv ++ +   +++ +  +e l   GY+ +a d   r++    d   + +++ +  +++ e+k+++d
  gi|386002180|ref|YP_005920479.1|  31 PSAKrpeGFPGVVLLPGATVTKEQEQGLAELLSGLGYATIALDQRNRGG---VDVGGDLEMFINGQEPT-EHKMVHD 103
                                       54444345799999999999999999999**************999999...45556666666667777.6677777 PP

                               DLH  82 lkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaava 127
                                       + aa + l+ +pe ++++++  G   GG++a+  +a + +  ++va
  gi|386002180|ref|YP_005920479.1| 104 ALAAAEVLRMQPEIDPDRIVYLGESNGGRFAIIASALDRRSRGVVA 149
                                       77******************************99999877777765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.6e-06    0.0052       3     118 ..      42     164 ..      38     185 .. 0.78
   2 ?   -0.0   0.0      0.28   5.6e+02     213     250 ..     192     230 ..     168     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                                       EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB...........CHHSHHHHHHHHHHHHHH CS
                     Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin..........ddygtasvaddldrilda 69 
                                       +v+l+G + + + + +  la+ L+  g+ +i+lD+r+ g  + + +  +          +  ++a  a+ + r +  
  gi|386002180|ref|YP_005920479.1|  42 VVLLPGATVTKEQEQG--LAELLSGLGYATIALDQRNRGGVDVGGDLEMfingqeptehKMVHDALAAAEVLRMQPE 116
                                       6788888877777666..****************************9777777775553223666666777788999 PP

                                       CTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHH CS
                     Abhydrolase_1  70 lgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqr 118
                                        + d+++++G S GG++a  + a+ + r +++v+++++ +  + +e ++
  gi|386002180|ref|YP_005920479.1| 117 IDPDRIVYLGESNGGRFAIIASAL-DRRSRGVVAISTCGYDVEGEEIDL 164
                                       *******************99998.888999999999555555444443 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                                       EEEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSS CS
                     Abhydrolase_1 213 ptlvisgtsDplvpp.kaledlaqllpkkrlvvisdagH 250
                                         ++i++ +D ++p  +a++ ++++l  k  ++++ a H
  gi|386002180|ref|YP_005920479.1| 192 RLVMIHSKNDTVIPVdSASRTYQKALEPKAMHIVDCATH 230
                                       5688999********999999999987777877777766 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0031      48      95 ..     100     144 ..      95     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHT CS
                     Abhydrolase_3  48 avedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrarde 95 
                                        v+dalaa++ l+ q    ++dp+riv +G+S GG +a  ++   r++
  gi|386002180|ref|YP_005920479.1| 100 MVHDALAAAEVLRMQP---EIDPDRIVYLGESNGGRFAIIASALDRRS 144
                                       5889******999995...8*****************99887444433 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     8e-05      0.16       9      63 ..     107     161 ..     106     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8e-05
                                       HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEE CS
                            BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegkl 63 
                                       a++ l+ +p++  d+i  lG S Gg  a++ ++     + vv+i+ + + veg++
  gi|386002180|ref|YP_005920479.1| 107 AAEVLRMQPEIDPDRIVYLGESNGGRFAIIASALDRRSRGVVAISTCGYDVEGEE 161
                                       67889***********************9888887799******99998777665 PP

>> PhoPQ_related  PhoPQ-activated pathogenicity-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.9e-05      0.14     239     303 ..     167     232 ..     155     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.9e-05
                     PhoPQ_related 239 lktpefkkLlkivDplsYlerl.tipkyiinasgDdffvpdstkfyfekLkgekalrivPnssHgl 303
                                       + +p   + l+ +Dp +Yler+      +i + +D    +ds++  ++k  ++ka++iv  + Hg 
  gi|386002180|ref|YP_005920479.1| 167 MSGPDAVRFLRSIDPDTYLERIpPRRLVMIHSKNDTVIPVDSASRTYQKALEPKAMHIVDCATHGR 232
                                       567778889999**********44455679999**************************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1575.31
//
Query:       gi|386002181|ref|YP_005920480.1|  [L=93]
Description: nucleotidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-16   58.7   0.3    6.1e-16   58.5   0.3    1.0  1  NTP_transf_2    Nucleotidyltransferase domain
    3.3e-11   43.1   0.0    3.9e-11   42.9   0.0    1.1  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.033   14.4   0.0      0.038   14.2   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.3     1e-19   6.1e-16       5      94 ..      11      91 ..       7      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1e-19
                                      HHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                      NTP_transf_2  5 leelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83
                                       +e+k++++v k+ +fGSyarG+ ++ SD+D+lv ++e++         ++ +   +fleel+ +evdlvt + l  p+
  gi|386002181|ref|YP_005920480.1| 11 EKEVKRKFGVRKIGIFGSYARGEEKERSDVDVLVEFEEPTF--------RNFMGLVFFLEELFDREVDLVTVKGLS-PY 80
                                      699************************************76........79********************99999.88 PP

                                      EEEEEECEEEH CS
                      NTP_transf_2 84 lvksileerpl 94
                                      ++ +++ e ++
  gi|386002181|ref|YP_005920480.1| 81 IRPYVEREVVW 91
                                      88888877665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   6.5e-15   3.9e-11       7      80 ..      14      85 ..       7      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 6.5e-15
                                      HHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHH CS
                           Polbeta  7 lekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyei 80
                                      ++++ +++ + +FGS+a+g+ +e+SD+D+ v ++e  ++ + + l   le++   ++vDlv+++  +p+++  +
  gi|386002181|ref|YP_005920480.1| 14 VKRKFGVRKIGIFGSYARGEEKERSDVDVLVEFEEP-TFRNFMGLVFFLEEL-FDREVDLVTVKGLSPYIRPYV 85
                                      4556699****************************9.***************.88*******997778877555 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.4e-06     0.038      20      54 ..      13      51 ..       2      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                                      HH-TT...-EEEE-HHHHTT-S.EESSEEEEEEBTTBST CS
                    DNA_pol_B_palm 20 eldpe...vevivcGSYRRgae.ssGDvDvlitkkdaks 54
                                      e++++    ++ + GSY Rg+e +  DvDvl+  ++ + 
  gi|386002181|ref|YP_005920480.1| 13 EVKRKfgvRKIGIFGSYARGEEkERSDVDVLVEFEEPTF 51
                                      44444222567899*****9862579******9777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 588.14
//
Query:       gi|386002182|ref|YP_005920481.1|  [L=106]
Description: hypothetical protein Mhar_1494 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-22   77.9   0.1    6.2e-22   77.7   0.1    1.0  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.1   3.5e-26   6.2e-22       3     118 ..       6      99 ..       4     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 3.5e-26
                                       HHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHH CS
                             DUF86   3 ealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepw 79 
                                       ++++ l + +e+ d e+++sd++  +a  r l++igEa+++++++                      +++ +pe++w
  gi|386002182|ref|YP_005920481.1|   6 DEIDFLLSECEGVDAEDLMSDKVLSRACVRSLEIIGEAVKNVSQE----------------------IKDGHPEIDW 60 
                                       5566666666799********************************......................********** PP

                                       HHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                             DUF86  80 rkmiglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                       r ++g+R++L+H+Y+gid++ v ++++e+++ l++ +e+
  gi|386002182|ref|YP_005920481.1|  61 RLIAGMRDKLIHQYFGIDWDVVTNVLNEEIRPLKAEIET 99 
                                       **********************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 670.36
//
Query:       gi|386002183|ref|YP_005920482.1|  [L=319]
Description: Prenyltransferase, UbiA family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-40  136.9  25.1      9e-40  136.5  25.1    1.1  1  UbiA             UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.67   10.0   4.7       0.54   10.3   0.9    2.7  2  Phage_holin_2_1  Bacteriophage P21 holin S
        6.9    6.5   6.4        1.7    8.5   1.2    2.1  2  Fig1             Ca2+ regulator and membrane fusion protein F


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5  25.1   1.5e-43     9e-40       5     246 ..      41     287 ..      36     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 1.5e-43
                              UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                       al+++ ++ag  p +l +++++lg+++a+++++++Nd  D++ Da     p+RPl+s ++++ +al+++++l+ +++
  gi|386002183|ref|YP_005920482.1|  41 ALLAAYATAGALPAALPFAIATLGAYAAITSSYVYNDCCDVDVDAV--GMPDRPLPSSQVTRSAALAYSALLFGIAA 115
                                       4555555667777779******************************..***************************** PP

                              UbiA  82 lllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl........sllalllal 150
                                       +++ ++lnp +++ ++ a ++  vY+    Kr+t++   ++g++fg++p++ w a++           ++ alll++
  gi|386002183|ref|YP_005920482.1| 116 AVA-FYLNPESLVALIGATMIMAVYS-KAAKRTTPFSWALVGLSFGIVPVGVWLAMAPAGilkdgpglHAGALLLGA 190
                                       ***.**********************.5***************************8887789*************** PP

                              UbiA 151 avflltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaala 226
                                       ++ +  w++  + + rd+egDr+ gi+t+pv++G   ++ l +a++++++ll+++l ++ +l+++y+++al++++++
  gi|386002183|ref|YP_005920482.1| 191 MICITDWGFTNCDASRDVEGDRREGIPTFPVTYGIPLTAKLvAAAWVVGVLLSIALGVATGLGPIYFAAALVAGGWM 267
                                       ****************************************9766666666666999********************* PP

                              UbiA 227 llraarlvrrrdakkaakff 246
                                       ++  + +v++ +a++++++f
  gi|386002183|ref|YP_005920482.1| 268 IAQTVGFVKTPTAARGERTF 287
                                       ****************9998 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       0.2   1.2e+03      25      42 ..     144     161 ..     130     166 .. 0.73
   2 ?   10.3   0.9     9e-05      0.54      26      54 ..     230     257 ..     221     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                   Phage_holin_2_1  25 dklspeeWsaigvlgglv 42 
                                       +  +p  W+ +g+  g+v
  gi|386002183|ref|YP_005920482.1| 144 KRTTPFSWALVGLSFGIV 161
                                       566788999999877775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9e-05
                   Phage_holin_2_1  26 klspeeWsaigvlgglvigllTyltnlYF 54 
                                       kl  + W ++gvl ++++g++T l   YF
  gi|386002183|ref|YP_005920482.1| 230 KLVAAAW-VVGVLLSIALGVATGLGPIYF 257
                                       5666677.79*****************99 PP

>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.2   0.00028       1.7     105     185 ..      88     168 ..      50     170 .. 0.80
   2 ?    0.5   0.3      0.08   4.8e+02     105     151 ..     225     271 ..     215     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00028
                              Fig1 105 ipllPfkskavskvalvlsflllllwlvgalwqhvassaastlveeasmgivkskvGkkaealgWfafaf.lllvcl 180
                                       +p  P++s +v++ a ++ + +ll+ + +a+  + + ++ ++l++++   +v sk  k+ + ++W+ +++ + +v +
  gi|386002183|ref|YP_005920482.1|  88 MPDRPLPSSQVTRSAALAYS-ALLFGIAAAVAFYLNPESLVALIGATMIMAVYSKAAKRTTPFSWALVGLsFGIVPV 163
                                       788899**999888765555.456666777778889999**************************999997889999 PP

                              Fig1 181 glwvl 185
                                       g+w+ 
  gi|386002183|ref|YP_005920482.1| 164 GVWLA 168
                                       99975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.08
                              Fig1 105 ipllPfkskavskvalvlsflllllwlvgalwqhvassaastlveea 151
                                       ipl++    a+  v ++ls++l +++++g ++   a +a   +++++
  gi|386002183|ref|YP_005920482.1| 225 IPLTAKLVAAAWVVGVLLSIALGVATGLGPIYFAAALVAGGWMIAQT 271
                                       55555555556667788899999999999999999999988888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2024.75
//
Query:       gi|386002184|ref|YP_005920483.1|  [L=238]
Description: glucose-6-phosphate isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-41  142.2   0.0    1.2e-41  142.0   0.0    1.1  1  GPI       Glucose-6-phosphate isomerase (GPI)
    0.00036   20.2   0.1    0.00073   19.2   0.1    1.5  1  Cupin_2   Cupin domain
  ------ inclusion threshold ------
      0.041   13.5   0.0      0.061   12.9   0.0    1.2  1  Cupin_1   Cupin


Domain annotation for each model (and alignments):
>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   0.0     2e-45   1.2e-41       5     179 ..      19     188 ..      15     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 2e-45
                               GPI   5 rdlaavladeealkaltetldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevd.rr 80 
                                       rd+  vl d         + d++ +Y+ +d + + ++g+ + +++++yd+t+i+P  +G E++kt GHyH+ v    
  gi|386002184|ref|YP_005920483.1|  19 RDMDDVLYDRRW---ARGAEDQELYYMYRDLFLSRRDGDLFVEQGIRYDITIIPPRMLGREYVKTAGHYHPTVPgEA 92 
                                       555555555522...234678999************************************************98899 PP

                               GPI  81 strPEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdviak 157
                                        t+PEvYevl+Gea +lL++ +     dv vv   +++ v+vPP ygH++in +++ L man+v + ++++Y++i  
  gi|386002184|ref|YP_005920483.1|  93 VTYPEVYEVLEGEATYLLQREDL---SDVLVVRAMEGDKVVVPPGYGHITINESNKRLKMANFVARGFSSIYEPIRE 166
                                       ********************988...9************************************************** PP

                               GPI 158 arGmaayiieegevlrkrkndd 179
                                       ++G a+ + e+g v+ +r ++ 
  gi|386002184|ref|YP_005920483.1| 167 RGGGAYFLTEDGFVENPRCEEA 188
                                       ************9998887765 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.2e-07   0.00073      21      67 ..      97     149 ..      80     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
                                       EEEEEEESEEEEEECTE......EEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                           Cupin_2  21 effyVleGegeltvdge......eveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                       e++ VleGe+++ +  e      +v+  +Gd v++p+g  H  +N++++ +++
  gi|386002184|ref|YP_005920483.1|  97 EVYEVLEGEATYLLQREdlsdvlVVRAMEGDKVVVPPGYGHITINESNKRLKM 149
                                       7778*********8866688899999***********************9997 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.061      55     105 ..      96     145 ..      83     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                                       -EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSS CS
                           Cupin_1  55 teiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgde 105
                                       +e+  vl+Ge++  ++  ++ + +   +  eGd +vvP+g+ h ++n  ++
  gi|386002184|ref|YP_005920483.1|  96 PEVYEVLEGEAT-YLLQREDLSDVLVVRAMEGDKVVVPPGYGHITINESNK 145
                                       677778888888.44444444555555699*****************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1434.16
//
Query:       gi|386002185|ref|YP_005920484.1|  [L=162]
Description: hypothetical protein Mhar_1496 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 933.63
//
Query:       gi|386002186|ref|YP_005920485.1|  [L=284]
Description: Iron sulfur cluster/nucleotide binding domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-16   61.0   0.0    1.4e-16   60.7   0.0    1.1  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    2.3e-09   36.7  18.8    2.9e-05   23.7   5.7    2.6  2  Fer4          4Fe-4S binding domain
    3.5e-09   36.5   0.1    1.8e-05   24.4   0.1    2.7  2  ParA          NUBPL iron-transfer P-loop NTPase
    5.7e-09   36.4   8.1    0.00065   20.2   2.2    2.4  2  Fer4_7        4Fe-4S dicluster domain
    4.2e-08   32.9  19.0     0.0005   20.0   6.4    2.5  2  Fer4_6        4Fe-4S binding domain
    4.6e-08   32.7  14.7     0.0011   19.0   4.8    2.6  2  Fer4_2        4Fe-4S binding domain
    4.8e-08   33.0   8.2     0.0013   18.8   0.1    2.5  2  Fer4_10       4Fe-4S dicluster domain
    1.2e-07   31.8   0.2       0.01   15.7   0.4    2.1  2  AAA_31        AAA domain
    2.1e-05   24.5   0.0      0.013   15.4   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
    0.00022   21.0   0.1      0.028   14.2   0.0    2.4  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
    0.00024   21.2  16.4    0.00024   21.2  16.4    2.1  1  Fer4_21       4Fe-4S dicluster domain
    0.00032   20.3   1.6       0.12   12.0   1.2    2.3  2  AAA_25        AAA domain
    0.00048   20.6   7.7       0.22   12.1   0.2    2.3  2  Fer4_17       4Fe-4S dicluster domain
    0.00065   20.6  12.0      0.019   15.9   0.5    2.4  2  Fer4_16       4Fe-4S double cluster binding domain
    0.00092   19.3  17.4      0.024   14.8  18.4    2.3  3  Fer4_9        4Fe-4S dicluster domain
      0.001   18.6   0.0        0.2   11.0   0.0    2.3  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
     0.0018   17.5   1.9     0.0051   16.0   1.8    1.7  2  ArsA_ATPase   Anion-transporting ATPase
     0.0058   17.0   0.1      0.025   14.9   0.0    1.9  2  AAA_16        AAA ATPase domain
     0.0067   16.7   0.2       0.04   14.2   0.3    2.1  2  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.016   14.9   0.2       0.22   11.1   0.5    2.1  2  SRP54         SRP54-type protein, GTPase domain
      0.037   14.2   0.0       0.11   12.6   0.0    1.9  1  AAA_33        AAA domain
      0.044   13.7   0.5       0.34   10.8   0.3    2.1  2  NACHT         NACHT domain
      0.051   13.1   0.4        3.4    7.2   0.0    2.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.052   13.3   0.0      0.083   12.6   0.0    1.3  1  AAA_24        AAA domain
      0.054   11.7   0.2       0.11   10.7   0.0    1.5  2  FTHFS         Formate--tetrahydrofolate ligase
      0.063   12.5   0.4       0.16   11.2   0.3    1.7  2  MipZ          ATPase MipZ
      0.065   14.0   8.4       0.23   12.2   0.2    2.7  2  Fer4_15       4Fe-4S single cluster domain
      0.069   12.3   2.0        1.3    8.1   0.9    2.2  2  NB-ARC        NB-ARC domain
      0.091   12.5   2.7      0.096   12.4   0.5    2.0  2  AAA_30        AAA domain
       0.12   12.7   0.0        1.2    9.4   0.0    2.4  3  AAA_22        AAA domain
       0.13   12.9  22.7       0.12   12.9   2.7    2.7  2  Fer4_4        4Fe-4S binding domain
       0.22   10.9   1.7       0.34   10.3   0.9    1.7  2  PhoH          PhoH-like protein
       0.22   11.9   0.0       0.51   10.8   0.0    1.8  1  RNA_helicase  RNA helicase
        1.4    9.4  19.6        4.2    7.9   7.0    2.4  2  Fer4_8        4Fe-4S dicluster domain
          2    9.6  21.4        6.4    8.0   5.9    2.6  2  Fer4_3        4Fe-4S binding domain
        2.6    8.7  13.8          2    9.0   2.3    2.5  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   2.9e-19   1.4e-16       1     123 [.       4     257 ..       4     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 2.9e-19
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ++++s+kGG+GKTt++a+La++ +    + ++ D+D++a+ l++   l++++++                       
  gi|386002186|ref|YP_005920485.1|   4 LVVISGKGGTGKTTMTASLAALAKG---EMVVADCDVDAPDLHL--LLKPQVREtfdfyglevasidpekctkcgkc 75 
                                       589*****************97666...8999***********4..444444444699999999999********** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386002186|ref|YP_005920485.1|  76 eeacrfcaisdfavdpaacegcrvctvvcpseavamtdrisghafvsdtrfgtmvhaelfpgeeasgklvtmvrela 152
                                       ***************************************************************************** PP

                                       ..............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEES CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..............................................dlkrllellealgkkkalllkiagvvlnrvd 85 
                                                                                     dl+r+l ++e++g +       a v +n++d
  gi|386002186|ref|YP_005920485.1| 153 aqvaeregrdlviidgspgigcpviasitgtdlalvmtepsisgahDLERILAVVEHFGVE-------ALVAVNKHD 222
                                       ***********************************************************99.......9******** PP

                                       S...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  86 geneetllkealeelkqrygvpvlgviprdeavaeapa 123
                                        +     + e + el++++g  + g++p+d +v+ a  
  gi|386002186|ref|YP_005920485.1| 223 LN---PDMTERIGELCRDLGFDLAGKLPFDPGVVGAMV 257
                                       98...8899999*******************9987665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   5.7   5.8e-08   2.9e-05       2      19 ..      63      80 ..      62      85 .. 0.89
   2 !   18.5   5.2   2.5e-06    0.0012       3      22 ..      89     108 ..      87     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.8e-08
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                       id+ekC++CG+C+e+C 
  gi|386002186|ref|YP_005920485.1| 63 SIDPEKCTKCGKCEEACR 80
                                      69***************6 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.5e-06
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                       +d+  C gC  C  vCP +A
  gi|386002186|ref|YP_005920485.1|  89 VDPAACEGCRVCTVVCPSEA 108
                                       8****************999 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   3.5e-08   1.8e-05       5      52 ..       3      47 ..       1      64 [. 0.79
   2 !    9.0   0.0    0.0018      0.88      97     226 ..     145     263 ..     140     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.5e-08
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllg 52
                                       ++v+SgKGG GK+t++++lA aLak ++ v   D D+  p++  ll+
  gi|386002186|ref|YP_005920485.1|  3 QLVVISGKGGTGKTTMTASLA-ALAKGEMVV--ADCDVDAPDLHLLLK 47
                                      689*****************9.577766655..577777777766665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                              ParA  97 skaikqllkdvew.gelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvve 172
                                        +++++l ++v+  +  D++iiD  PG g   ++ +     + a+++t p    ++d ++ ++++++  v+ l  v+
  gi|386002186|ref|YP_005920485.1| 145 VTMVRELAAQVAErEGRDLVIIDGSPGIGCPVIASITGT--DLALVMTEPSISGAHDLERILAVVEHFGVEALVAVN 219
                                       56788888888762458999*******998876655554..679999999999999999999999999988776554 PP

                              ParA 173 Nmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplv 226
                                              p+         ++   +l+++lg++l g++p+dp ++ a+ + k+lv
  gi|386002186|ref|YP_005920485.1| 220 KH--DLNPD--------MTERIGELCRDLGFDLAGKLPFDPGVVGAMVQRKTLV 263
                                       32..22232........3445567777777777777777777777776666555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   2.2   1.3e-06   0.00065      27      49 ..      58      80 ..      32      83 .. 0.66
   2 !   19.3   0.4   2.5e-06    0.0013       1      22 [.      93     114 ..      87     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-06
                            Fer4_7 27 gtekveidpekClgCgaCvavCP 49
                                      g e + idpekC+ Cg+C+++C 
  gi|386002186|ref|YP_005920485.1| 58 GLEVASIDPEKCTKCGKCEEACR 80
                                      557889****************6 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.5e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                       +C gC+ C+++Cp++a+ ++++
  gi|386002186|ref|YP_005920485.1|  93 ACEGCRVCTVVCPSEAVAMTDR 114
                                       5999999999999999988775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   6.4     1e-06    0.0005       1      19 [.      61      79 ..      61      84 .. 0.91
   2 !   18.3   4.8   3.6e-06    0.0018       3      23 ..      88     108 ..      87     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                            Fer4_6  1 vveidpdkCigCgdCvrvC 19
                                      v+ idp+kC+ Cg+C+ +C
  gi|386002186|ref|YP_005920485.1| 61 VASIDPEKCTKCGKCEEAC 79
                                      688**************** PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.6e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                       ++dp +C gC+ C++vCP  a
  gi|386002186|ref|YP_005920485.1|  88 AVDPAACEGCRVCTVVCPSEA 108
                                       69****************876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.3   2.3e-06    0.0012       3      20 ..      62      79 ..      60      81 .. 0.91
   2 !   19.0   4.8   2.1e-06    0.0011       3      21 ..      87     105 ..      85     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      + +d+++C+ Cg+C  aC
  gi|386002186|ref|YP_005920485.1| 62 ASIDPEKCTKCGKCEEAC 79
                                      679*************** PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.1e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++vd+++C gC+ C+ +CP
  gi|386002186|ref|YP_005920485.1|  87 FAVDPAACEGCRVCTVVCP 105
                                       689**************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   3.8   2.4e-05     0.012       3      19 ..      63      79 ..      55      82 .. 0.68
   2 !   18.8   0.1   2.6e-06    0.0013       4      34 ..      89     117 ..      87     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-05
                           Fer4_10  3 vidddtCirCgkCvkaC 19
                                       id+++C++CgkC +aC
  gi|386002186|ref|YP_005920485.1| 63 SIDPEKCTKCGKCEEAC 79
                                      45666666666666666 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.6e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgease 34 
                                       +d+  C +C+ C+ +CP+  ++v  ++ +s+
  gi|386002186|ref|YP_005920485.1|  89 VDPAACEGCRVCTVVCPS--EAVAMTDRISG 117
                                       6899**************..55555555444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   2.1e-05      0.01       1      39 [.       1      38 [.       1      45 [. 0.85
   2 !   14.0   0.0   7.1e-05     0.035     118     167 ..     161     210 ..     106     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                            AAA_31  1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlD 39
                                      +k ++++  KGG GKTT +  laa lak ++ v  +D+D
  gi|386002186|ref|YP_005920485.1|  1 MKQLVVISGKGGTGKTTMTASLAA-LAKGEMVVADCDVD 38
                                      67789999**************96.78888777777777 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.1e-05
                            AAA_31 118 YDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieev 167
                                        D++iiD +P +g+ ++ +++  d  ++ ++++    + le++l  +e++
  gi|386002186|ref|YP_005920485.1| 161 RDLVIIDGSPGIGCPVIASITGTDLALVMTEPSISGAHDLERILAVVEHF 210
                                       6*******************************999999999999998876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.011       5.5     100     121 ..       3      24 ..       1      35 [. 0.85
   2 !   15.4   0.0   2.7e-05     0.013      21      77 ..     185     240 ..     156     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                                       SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                       +++v+ G+ G GK+t+  +l+ 
  gi|386002186|ref|YP_005920485.1|   3 QLVVISGKGGTGKTTMTASLAA 24 
                                       789*************999875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.7e-05
                                       EEEESTTTT--.HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS CS
                       RsgA_GTPase  21 ivvslkepels.lnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgy 77 
                                       + + ++ep++s  + l+r+L+++e+ g+e ++++nK Dl  +++  e++ e  ++lg+
  gi|386002186|ref|YP_005920485.1| 185 LALVMTEPSISgAHDLERILAVVEHFGVEALVAVNKHDLNPDMT--ERIGELCRDLGF 240
                                       455555677663568************************99988..777777777665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.059        29      36      57 ..       5      26 ..       2      46 .. 0.81
   2 !   14.2   0.0   5.6e-05     0.028      24     104 ..     152     231 ..     132     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.059
                            RuvB_N 36 vllyGpPGlGkttlakiiakel 57
                                      v+++G  G Gktt+++ +a+  
  gi|386002186|ref|YP_005920485.1|  5 VVISGKGGTGKTTMTASLAALA 26
                                      8899**********98887644 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.6e-05
                            RuvB_N  24 eaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdv..lfideihrlsr 98 
                                       +a  + +e  d v++ G+PG+G   +a+i  ++l   +   + P ++ a dl  +l+ +e+  v  l   + h l++
  gi|386002186|ref|YP_005920485.1| 152 AAQVAEREGRDLVIIDGSPGIGCPVIASITGTDLALVM---TEPSISGAHDLERILAVVEHFGVeaLVAVNKHDLNP 225
                                       3444566789********************99998654...57999******9999999876542255555677777 PP

                            RuvB_N  99 aveevl 104
                                        + e +
  gi|386002186|ref|YP_005920485.1| 226 DMTERI 231
                                       766655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2  16.4   4.8e-07   0.00024       1      59 []      62     111 ..      62     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.8e-07
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       A id++kC +CgkC  aC+     ai+      ++v    C GC +C+ vCP +++++m
  gi|386002186|ref|YP_005920485.1|  62 ASIDPEKCTKCGKCEEACR---FCAIS-----DFAVDPAACEGCRVCTVVCP-SEAVAM 111
                                       79*****************...45554.....4789999*************.588877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.2   0.00023      0.12      34      55 ..       3      24 ..       1      33 [. 0.88
   2 ?    6.5   0.0     0.011       5.7     120     149 ..     139     167 ..      93     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                            AAA_25 34 elallaGapgtGKttlaldlal 55
                                       l+++ G +gtGKtt++ +la+
  gi|386002186|ref|YP_005920485.1|  3 QLVVISGKGGTGKTTMTASLAA 24
                                      6899****************96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                            AAA_25 120 drggtlltadvdaleaaieevegvrlvviD 149
                                       ++ g+l+t  v++l+a++ e+eg +lv+iD
  gi|386002186|ref|YP_005920485.1| 139 EASGKLVT-MVRELAAQVAEREGRDLVIID 167
                                       44555555.5799***************** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.8    0.0011      0.54      45      56 ..      68      79 ..      57      88 .. 0.75
   2 !   12.1   0.2   0.00043      0.22       1      17 [.      93     109 ..      93     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                           Fer4_17 45 lCieCgeCerkC 56
                                      +C++Cg+Ce++C
  gi|386002186|ref|YP_005920485.1| 68 KCTKCGKCEEAC 79
                                      677777777776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00043
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       +C +C+ C+ +Cps + 
  gi|386002186|ref|YP_005920485.1|  93 ACEGCRVCTVVCPSEAV 109
                                       59999999999998765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   5.4    0.0079       3.9       1      18 [.      68      85 ..      68      91 .. 0.87
   2 !   15.9   0.5   3.7e-05     0.019       2      20 ..      94     112 ..      93     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0079
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++CgkC e+C   ai+
  gi|386002186|ref|YP_005920485.1| 68 KCTKCGKCEEACRFCAIS 85
                                      5***********988887 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.7e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C +C+ C+ vCP++a+ ++
  gi|386002186|ref|YP_005920485.1|  94 CEGCRVCTVVCPSEAVAMT 112
                                       **************98876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   7.5    0.0014      0.71      34      47 ..      67      80 ..      46      84 .. 0.68
   2 !   14.8  18.4   4.8e-05     0.024       1      50 [.      68     108 ..      68     109 .. 0.93
   3 !   11.7   3.3   0.00045      0.22       1      19 [.      93     111 ..      93     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                            Fer4_9 34 eaCigCgaCveaCp 47
                                      e+C++Cg+C+eaC 
  gi|386002186|ref|YP_005920485.1| 67 EKCTKCGKCEEACR 80
                                      56777777777775 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.8e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kCt+Cg+C+eaC ++++++ a+            aC gC+ C+ +Cp++a
  gi|386002186|ref|YP_005920485.1|  68 KCTKCGKCEEACRFCAISDFAVDPA---------ACEGCRVCTVVCPSEA 108
                                       7*****************9999987.........5************986 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00045
                            Fer4_9   1 kCtgCgaCveaCpagvvve 19 
                                       +C gC+ C+ +Cp+++v +
  gi|386002186|ref|YP_005920485.1|  93 ACEGCRVCTVVCPSEAVAM 111
                                       5999999999999888754 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00041       0.2       3      54 ..       5      53 ..       3      65 .. 0.78
   2 ?    5.0   0.0     0.029        15     188     244 ..     226     280 ..     200     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqet 54
                                      + i GkGG Gk+t ++ l aala+ g  +++  CD  a   +lll+ ++ et
  gi|386002186|ref|YP_005920485.1|  5 VVISGKGGTGKTTMTASL-AALAK-G-EMVVADCDVDAPDLHLLLKPQVRET 53
                                      7899*******9887765.45664.3.4567889999988889888777766 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                         Fer4_NifH 188 dereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarki 244
                                       d +e i ++ ++lg ++  ++P d  v  a +++kt++e +      +  r+l +ki
  gi|386002186|ref|YP_005920485.1| 226 DMTERIGELCRDLGFDLAGKLPFDPGVVGAMVQRKTLVEVEGPVG--DAIRDLWDKI 280
                                       5678999*******************************9977655..6666666655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.8     1e-05    0.0051       2      23 ..       3      24 ..       2      33 .. 0.86
   2 ?   -2.7   0.0       5.2   2.6e+03     103     134 ..     134     170 ..     116     172 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                                      EEEEEEESTTSSHHHHHHHHHH CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatav 23
                                      ++++++GKGG GKtt+ a++a+
  gi|386002186|ref|YP_005920485.1|  3 QLVVISGKGGTGKTTMTASLAA 24
                                      5799***************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.2
                                       SSTTHHHHHHHHHHHHHHH.....CSSSSEEEEESBS CS
                       ArsA_ATPase 103 slPGideilsfeellkyvk.....eeeydvvvlDtaP 134
                                        +PG +    + ++++++       e  d v++D +P
  gi|386002186|ref|YP_005920485.1| 134 LFPGEEASGKLVTMVRELAaqvaeREGRDLVIIDGSP 170
                                       4577777777777777666555545567888888777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.1e-05     0.025      25      63 ..       3      38 ..       1      70 [. 0.78
   2 ?   -0.4   0.0       2.7   1.3e+03      12      36 ..     148     173 ..     127     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.1e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +lv++sG  G+GK+++  +l+  ++++ +  + ++cd  
  gi|386002186|ref|YP_005920485.1|  3 QLVVISGKGGTGKTTMTASLAALAKGE-M--VVADCDVD 38
                                      589******************766666.4..44444444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.7
                            AAA_16  12 Llsalervrsgrp.elvllsGesGvG 36 
                                       ++++  +v++ ++  lv++ G +G+G
  gi|386002186|ref|YP_005920485.1| 148 VRELAAQVAEREGrDLVIIDGSPGIG 173
                                       44455555555555677777777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   8.1e-05      0.04       2      28 ..       5      33 ..       4      36 .. 0.84
   2 ?   -0.8   0.0       3.2   1.6e+03      60      81 ..     148     169 ..     125     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar..gypvvp 28
                                      +vi+G  +tGKTt+++ Laa   g  vv+
  gi|386002186|ref|YP_005920485.1|  5 VVISGKGGTGKTTMTASLAALakGEMVVA 33
                                      8******************7545777765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.2
                            AAA_28  60 leeqleeeaaaaankvlfcDrg 81 
                                       ++e +++ a++++++++++D +
  gi|386002186|ref|YP_005920485.1| 148 VRELAAQVAEREGRDLVIIDGS 169
                                       4444566777788999999987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00045      0.22       3      27 ..       4      28 ..       2      38 .. 0.85
   2 ?    1.1   0.0       0.5   2.5e+02      66      91 ..     143     168 ..     124     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                                      EEEEEESTTSSHHHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkk 27
                                      ++++ G  G+GKTt +a Laal k 
  gi|386002186|ref|YP_005920485.1|  4 LVVISGKGGTGKTTMTASLAALAKG 28
                                      68899***************98775 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.5
                                       SCHHHHHHHHHHHHHHTTSSEEEEEE CS
                             SRP54  66 adpaavakeavekakeekidvvlvDT 91 
                                       +    v + a + a++e+ d+v++D 
  gi|386002186|ref|YP_005920485.1| 143 KLVTMVRELAAQVAEREGRDLVIIDG 168
                                       333444455778888999******96 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00023      0.11       1      99 [.       4     214 ..       4     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdt............................................. 32 
                                       lv++ G  G+GK+t   +l++  +++ +  d                                              
  gi|386002186|ref|YP_005920485.1|   4 LVVISGKGGTGKTTMTASLAALAKGEMVVADCdvdapdlhlllkpqvretfdfyglevasidpekctkcgkceeacr 80 
                                       79999**************9666655555554447788888888888888888888888888888888888888888 PP

                            AAA_33  33 ........................................lrrrlfgtdqqsktdytr.vldrlyqilnelarkal. 67 
                                                                               ++++ fgt ++ +  + + ++ +l  +++ela++++ 
  gi|386002186|ref|YP_005920485.1|  81 fcaisdfavdpaacegcrvctvvcpseavamtdrisghafVSDTRFGTMVHAELFPGEeASGKLVTMVRELAAQVAe 157
                                       88888888888888888877777777777766666666664444444444433333322666666677777666653 PP

                            AAA_33  68 sagrn.vildat........................nlsrrerarflklarrlgvpv 99 
                                       ++gr+ vi+d                             +++ +r+l++++++gv+ 
  gi|386002186|ref|YP_005920485.1| 158 REGRDlVIIDGSpgigcpviasitgtdlalvmtepsISGAHDLERILAVVEHFGVEA 214
                                       566666666766777777777777777776655555555677777777777777664 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00069      0.34       2      25 ..       4      27 ..       3      36 .. 0.88
   2 ?    0.5   0.0      0.98   4.9e+02      69      89 ..     148     168 ..     139     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00069
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      lv++ G+ G GKTt+ ++la +++
  gi|386002186|ref|YP_005920485.1|  4 LVVISGKGGTGKTTMTASLAALAK 27
                                      79*****************98776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.98
                                       S-CCHHHHCCSCCCEEEEEE- CS
                             NACHT  69 vsevwavllelperlLlilDg 89 
                                       v+e  a ++e++ r L i+Dg
  gi|386002186|ref|YP_005920485.1| 148 VRELAAQVAEREGRDLVIIDG 168
                                       566777788888888888888 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.062        31       6      27 ..       5      26 ..       3      35 .. 0.84
   2 ?    7.2   0.0    0.0068       3.4      87     136 ..     176     228 ..     141     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.062
                                      EEEEESTTSSHHHHHHHHHHHT CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlykt 27
                                      ++i g   +GKtT+t +L + +
  gi|386002186|ref|YP_005920485.1|  5 VVISGKGGTGKTTMTASLAALA 26
                                      678888899********98765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0068
                                       HHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...H CS
                          GTP_EFTU  87 virglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...k 136
                                       vi+++  +D+a+++ + +    +  e++l ++   gv+  v++NK D      
  gi|386002186|ref|YP_005920485.1| 176 VIASITGTDLALVMTEPSISGAHDLERILAVVEHFGVEALVAVNKHDLNpdmT 228
                                       7889999999999999999999999**********************874433 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017     0.083       2      32 ..       2      36 ..       1      56 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                            AAA_24  2 klkiliyGpsgiGKTtlakel....gpkplfidte 32
                                      k+ ++i G+ g+GKTt+ ++l    + + ++ d++
  gi|386002186|ref|YP_005920485.1|  2 KQLVVISGKGGTGKTTMTASLaalaKGEMVVADCD 36
                                      66799***************999999999999987 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.5       3.1   1.5e+03      67      79 ..      11      23 ..       6      31 .. 0.81
   2 ?   10.7   0.0   0.00022      0.11     355     422 ..     195     261 ..     179     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                                      T--SHHHHHHHHH CS
                             FTHFS 67 lGeGKttttigLa 79
                                       G GKtt+t +La
  gi|386002186|ref|YP_005920485.1| 11 GGTGKTTMTASLA 23
                                      699*****99987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHCTTT--EEEEEE--TT--HHHHHHHHHHHHCTTSEEEEE-HHHHGGGGGHHHHHH CS
                             FTHFS 355 kGlanlekhienvkkfgvpvvvainkfktDteaelelvkelaeakavevalsevwakGgeGalelaea 422
                                       +G+++le+ ++ v++fgv+++va+nk++    + +e + el+++ ++++a    +  G  Ga+   ++
  gi|386002186|ref|YP_005920485.1| 195 SGAHDLERILAVVEHFGVEALVAVNKHDLNP-DMTERIGELCRDLGFDLAGKLPFDPGVVGAMVQRKT 261
                                       6999*********************987654.456889999999999999999999999998765555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00033      0.16       3      39 ..       4      39 ..       2      44 .. 0.87
   2 ?   -2.8   0.0       6.1     3e+03      89     109 ..     151     171 ..     138     185 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39
                                      +v+   kGG+Gk+t++  +a aL+k  + va  d+d+
  gi|386002186|ref|YP_005920485.1|  4 LVVISGKGGTGKTTMTASLA-ALAKGEMVVADCDVDA 39
                                      678889******99998876.89999999******97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHH-SEEEEE.--S CS
                              MipZ  89 leelvadleaeldfivid.tPG 109
                                       l++ va+  +  d+++id +PG
  gi|386002186|ref|YP_005920485.1| 151 LAAQVAE-REGRDLVIIDgSPG 171
                                       3333333.23468888884466 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.3      0.17        86       3      18 ..      64      79 ..      63      86 .. 0.88
   2 ?   12.2   0.2   0.00046      0.23       3      20 ..      89     106 ..      87     159 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.17
                           Fer4_15  3 vDrdaCigcglCvaea 18
                                      +D ++C+ cg C +++
  gi|386002186|ref|YP_005920485.1| 64 IDPEKCTKCGKCEEAC 79
                                      9***********9998 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00046
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       vD  aC+gc +C  ++p 
  gi|386002186|ref|YP_005920485.1|  89 VDPAACEGCRVCTVVCPS 106
                                       99**************63 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9    0.0027       1.3      22      39 ..       4      21 ..       1      30 [. 0.86
   2 ?    3.1   0.0     0.091        45       3      38 ..     146     179 ..     144     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                                      EEEEEESTTSSHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakq 39
                                      +v ++G+gG GKtt+ ++
  gi|386002186|ref|YP_005920485.1|  4 LVVISGKGGTGKTTMTAS 21
                                      789***********9876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC   3 ksvekviekLlekdelqslvvalvGmgGvGKttlak 38 
                                       ++v++++ +  e ++ +  +v + G +G+G  ++a+
  gi|386002186|ref|YP_005920485.1| 146 TMVRELAAQVAEREGRD--LVIIDGSPGIGCPVIAS 179
                                       68999999999999999..99*********999987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00019     0.096      19      43 ..       3      27 ..       1      37 [. 0.87
   2 ?   -0.7   0.1         2     1e+03      30      30 ..     173     173 ..     138     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                            AAA_30 19 rvavltGpAGtGKttalkalreawe 43
                                      +++v+ G  GtGKtt+ ++l+++++
  gi|386002186|ref|YP_005920485.1|  3 QLVVISGKGGTGKTTMTASLAALAK 27
                                      689***************9998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                            AAA_30  30 G 30 
                                       G
  gi|386002186|ref|YP_005920485.1| 173 G 173
                                       2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0024       1.2       5      29 ..       2      26 ..       1      54 [. 0.81
   2 ?   -0.3   0.0       2.4   1.2e+03      76      98 ..     145     167 ..     122     173 .. 0.63
   3 ?   -1.7   0.0       6.4   3.2e+03      38      61 ..     258     281 ..     218     284 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                      ++++v+ G  GtGKTt  + l+  +
  gi|386002186|ref|YP_005920485.1|  2 KQLVVISGKGGTGKTTMTASLAALA 26
                                      5789**************9999887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.4
                            AAA_22  76 eell.ealeqalraravielliiD 98 
                                         ++ e+ +q +++ ++  l+iiD
  gi|386002186|ref|YP_005920485.1| 145 VTMVrELAAQVAEREGR-DLVIID 167
                                       44552334444444444.777777 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.4
                            AAA_22  38 erpevvfvtlpsstsskdllrell 61 
                                       +r+++v+v+ p++   +dl+ ++ 
  gi|386002186|ref|YP_005920485.1| 258 QRKTLVEVEGPVGDAIRDLWDKIR 281
                                       567778888888888888888875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   9.1      0.01         5       1      15 [.      66      80 ..      66      82 .. 0.91
   2 ?   12.9   2.7   0.00024      0.12       3      16 ..      93     106 ..      91     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+C+ Cg+C+ aC 
  gi|386002186|ref|YP_005920485.1| 66 PEKCTKCGKCEEACR 80
                                      69************6 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00024
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C gC++C+ +CP+
  gi|386002186|ref|YP_005920485.1|  93 ACEGCRVCTVVCPS 106
                                       699**********6 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00068      0.34      19      42 ..       2      25 ..       1      34 [. 0.85
   2 ?   -2.3   0.0       4.9   2.4e+03      18      42 ..     160     184 ..     149     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00068
                                      -SEEEEE--TTSSTTHHHHHHHHH CS
                              PhoH 19 ndivfaiGpaGtGKtylavalave 42
                                      +++v++ G+ GtGKt ++ +la+ 
  gi|386002186|ref|YP_005920485.1|  2 KQLVVISGKGGTGKTTMTASLAAL 25
                                      689**************9998864 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                                       H-SEEEEE--TTSSTTHHHHHHHHH CS
                              PhoH  18 kndivfaiGpaGtGKtylavalave 42 
                                         d+v++ G+ G G   +a  ++ +
  gi|386002186|ref|YP_005920485.1| 160 GRDLVIIDGSPGIGCPVIASITGTD 184
                                       5689999999999999999888766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     0.001      0.51       1      27 [.       5      36 ..       5     112 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.....k 27
                                      ++++G+ g+GK+t++ +La+   +++     +
  gi|386002186|ref|YP_005920485.1|  5 VVISGKGGTGKTTMTASLAALAKGEMvvadcD 36
                                      689**************998777666555542 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.0    0.0083       4.2       3      19 ..      67      83 ..      65      93 .. 0.76
   2 ?    7.1   4.5     0.015       7.3      50      63 ..      93     106 ..      88     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0083
                            Fer4_8  3 ekCieCgaCqsaCpvlr 19
                                      ekC++Cg C++aC ++ 
  gi|386002186|ref|YP_005920485.1| 67 EKCTKCGKCEEACRFCA 83
                                      68888888888887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                            Fer4_8  50 sCttcgaCtevCpv 63 
                                       +C +c+ Ct+vCp 
  gi|386002186|ref|YP_005920485.1|  93 ACEGCRVCTVVCPS 106
                                       79999999999997 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.5     0.027        13       1      12 [.      69      80 ..      69      83 .. 0.90
   2 ?    8.0   5.9     0.013       6.4       1      15 []      94     108 ..      94     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.027
                            Fer4_3  1 CtgCgaCvevCP 12
                                      Ct Cg C+e+C+
  gi|386002186|ref|YP_005920485.1| 69 CTKCGKCEEACR 80
                                      ***********8 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.013
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC+ C +vCP+ A
  gi|386002186|ref|YP_005920485.1|  94 CEGCRVCTVVCPSEA 108
                                       99**********876 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.3    0.0039         2       1      16 [.      64      79 ..      64      81 .. 0.94
   2 ?    4.5   4.0       0.1        51       1      18 [.      89     106 ..      89     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D ++C+ cg+C e++
  gi|386002186|ref|YP_005920485.1| 64 IDPEKCTKCGKCEEAC 79
                                      899***********99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.1
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD   C +c +C  ++P 
  gi|386002186|ref|YP_005920485.1|  89 VDPAACEGCRVCTVVCPS 106
                                       8999*************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1829.43
//
Query:       gi|386002187|ref|YP_005920486.1|  [L=276]
Description: Iron sulfur cluster/nucleotide binding domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-15   55.9   0.0    5.1e-15   55.7   0.0    1.1  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    3.4e-14   52.9   0.0    1.3e-05   24.8   0.0    2.9  2  ParA      NUBPL iron-transfer P-loop NTPase
    2.4e-09   36.6  15.6    1.4e-05   24.7   1.4    2.8  3  Fer4      4Fe-4S binding domain
    6.1e-08   32.7   4.4    6.1e-08   32.7   4.4    1.9  2  Fer4_21   4Fe-4S dicluster domain
    9.3e-07   28.7  16.0    7.1e-05   22.7   2.1    2.8  3  Fer4_6    4Fe-4S binding domain
    1.6e-06   28.1  12.3     0.0014   18.7   2.8    2.7  3  Fer4_10   4Fe-4S dicluster domain
    5.5e-06   26.9  10.2    1.8e-05   25.2   9.7    2.1  2  Fer4_7    4Fe-4S dicluster domain
    6.6e-06   26.2   0.0      0.018   15.0   0.0    2.2  2  AAA_31    AAA domain
    1.8e-05   25.6   4.9      0.035   15.0   0.2    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    5.9e-05   23.2   9.6    0.00015   21.8   8.9    2.0  2  Fer4_9    4Fe-4S dicluster domain
    0.00014   21.8   3.2    0.00014   21.8   3.2    2.9  3  Fer4_2    4Fe-4S binding domain
     0.0002   21.8   6.3        0.2   12.1   0.6    2.6  2  Fer4_8    4Fe-4S dicluster domain
     0.0017   18.8   9.8       0.13   12.8   1.0    2.4  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.093   12.3   0.0       0.16   11.5   0.0    1.3  1  AAA_25    AAA domain
       0.16   11.2   0.0       0.19   10.9   0.0    1.1  1  DUF2075   Uncharacterized conserved protein (DUF2075)
       0.18   12.6   5.8       0.83   10.4   1.0    2.5  2  Fer4_15   4Fe-4S single cluster domain
       0.19   10.6   0.1       0.26   10.2   0.1    1.1  1  GGGtGRT   GGGtGRT protein
        0.2   12.1   0.0       0.43   11.0   0.0    1.5  1  AAA       ATPase family associated with various cellular acti
       0.37   11.8  21.1       0.73   10.9   6.3    3.1  3  Fer4_3    4Fe-4S binding domain
        1.7    9.2  10.6        1.1    9.8   2.3    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        4.3    8.2  14.8        8.8    7.2   4.0    2.3  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   5.9e-18   5.1e-15       1     126 [.       2     251 ..       2     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 5.9e-18
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++as+kGG+GKT +a+nLa+++      V l+D+D++ +n+ +++ + +++e                        
  gi|386002187|ref|YP_005920486.1|   2 ISVASGKGGTGKTLVATNLAASIGS----VELLDCDVEEPNSYLFFPDLEERESsdcnvpipvidedrctrcgrcse 74 
                                       789*********************9....**************9888888888899********************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386002187|ref|YP_005920486.1|  75 fcayhalavfpkevllfpelchgcggcdlvcpegavsmgtraigkihrarsggvrllwgelfigepmatpliravka 151
                                       ***************************************************************************** PP

                                       .........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...- CS
                                       .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .........................................dlkrllellealgkkkalllkiagvvlnrvdgenee 90 
                                                                                dl+  +++++++ ++        gvv+nr +    +
  gi|386002187|ref|YP_005920486.1| 152 eargdlllvdsppgtacpvieavrgsdfcllvteptpfglyDLSIAVQVVRRMEIP-------CGVVVNRSGIG--D 219
                                       **************************************999999999999999998.......9*********9..8 PP

                                       TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  91 tllkealeelkqrygvpvlgviprdeavaeaparge 126
                                       +  ++ +e++    g+p+l +ip + ++ae+ +rg 
  gi|386002187|ref|YP_005920486.1| 220 RGVYDYCERE----GIPILLEIPMKREIAELTSRGA 251
                                       9999999998....*****************99986 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.5e-08   1.3e-05       6      47 ..       2      39 ..       1      64 [. 0.80
   2 !   23.3   0.0   4.3e-08   3.6e-05     112     238 ..     155     264 ..     138     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsi 47
                                      i v+SgKGG GK+ va+nlA+++     +v llD D+  p+ 
  gi|386002187|ref|YP_005920486.1|  2 ISVASGKGGTGKTLVATNLAASIG----SVELLDCDVEEPNS 39
                                      89******************9995....68899999988775 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.3e-08
                              ParA 112 lDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgektei 188
                                        D+L++D PPGt+   +  +     + +++Vt p    l d + a+++++++++++ Gvv N sg+           
  gi|386002187|ref|YP_005920486.1| 155 GDLLLVDSPPGTACPVIEAVRGS--DFCLLVTEPTPFGLYDLSIAVQVVRRMEIPC-GVVVNRSGI----------- 217
                                       499*********98888777766..579**************************96.999998886........... PP

                              ParA 189 fgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakal 238
                                        g+ g+ +++e+ g+p+l eip++ ei+e + +g  +  ++   e ++++
  gi|386002187|ref|YP_005920486.1| 218 -GDRGVYDYCEREGIPILLEIPMKREIAELTSRGALF--SKVMVEWQEKF 264
                                       .456888999999999999999999999999998843..33344455555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.4   1.7e-08   1.4e-05       1      18 [.      59      76 ..      59      81 .. 0.92
   2 !   21.5   1.6   1.7e-07   0.00014       5      23 ..      92     110 ..      88     111 .. 0.91
   3 ?   -2.3   0.3       5.4   4.6e+03      17      20 ..     167     170 ..     166     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                                      EEEETTTSSS-THHHHHS CS
                              Fer4  1 vvideekCigCGaCvevC 18
                                      +vide++C++CG+C e C
  gi|386002187|ref|YP_005920486.1| 59 PVIDEDRCTRCGRCSEFC 76
                                      69**************** PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.7e-07
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       +e+C gCG C  vCP gA 
  gi|386002187|ref|YP_005920486.1|  92 PELCHGCGGCDLVCPEGAV 110
                                       8****************97 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.4
                                       HSTT CS
                              Fer4  17 vCPv 20 
                                       +CPv
  gi|386002187|ref|YP_005920486.1| 167 ACPV 170
                                       8**7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   4.4   7.1e-11   6.1e-08       2      59 .]      60     112 ..      59     112 .. 0.92
   2 ?   -1.6   0.1       3.7   3.2e+03      50      57 ..     167     174 ..     166     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.1e-11
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       +ided+C  Cg+C   C    + a+ + +k+v  +  + C GC  C  vCP e++++m
  gi|386002187|ref|YP_005920486.1|  60 VIDEDRCTRCGRCSEFCA---YHALAVFPKEV-LLFPELCHGCGGCDLVCP-EGAVSM 112
                                       79***************9...89999999998.56799*************.899988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                           Fer4_21  50 vCPvedci 57 
                                        CPv +++
  gi|386002187|ref|YP_005920486.1| 167 ACPVIEAV 174
                                       6***9987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   2.1   8.4e-08   7.1e-05       1      24 []      58      81 ..      58      81 .. 0.94
   2 !   14.7   2.1   2.8e-05     0.024       6      23 ..      92     109 ..      91     110 .. 0.94
   3 ?   -2.6   0.1       8.1   6.9e+03      17      21 ..     166     170 ..     166     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.4e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++id+d+C+ Cg+C   C + a+
  gi|386002187|ref|YP_005920486.1| 58 IPVIDEDRCTRCGRCSEFCAYHAL 81
                                      69*****************99886 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.8e-05
                            Fer4_6   6 pdkCigCgdCvrvCPega 23 
                                       p++C gCg C  vCPega
  gi|386002187|ref|YP_005920486.1|  92 PELCHGCGGCDLVCPEGA 109
                                       89**************99 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.1
                            Fer4_6  17 rvCPe 21 
                                       ++CP 
  gi|386002187|ref|YP_005920486.1| 166 TACPV 170
                                       68995 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.8   1.7e-06    0.0014       2      21 ..      59      77 ..      58      89 .. 0.87
   2 !   15.5   0.5   1.6e-05     0.014       6      38 ..      92     124 ..      87     129 .. 0.76
   3 ?   -2.4   0.0       6.3   5.4e+03      18      21 ..     167     170 ..     166     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      +vid+d+C+rCg+C ++C a
  gi|386002187|ref|YP_005920486.1| 59 PVIDEDRCTRCGRCSEFC-A 77
                                      68****************.4 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeav 38 
                                       ++ C +Cg C  +CP  + s+g++++ +++ a 
  gi|386002187|ref|YP_005920486.1|  92 PELCHGCGGCDLVCPEGAVSMGTRAIGKIHRAR 124
                                       689*************88777776666666555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.3
                           Fer4_10  18 aCPa 21 
                                       aCP+
  gi|386002187|ref|YP_005920486.1| 167 ACPV 170
                                       8998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   9.7   2.1e-08   1.8e-05       1      52 []      65     109 ..      65     109 .. 0.95
   2 !   12.3   1.9   0.00023      0.19       2      20 ..      95     113 ..      94     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.1e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       rC+ Cg+C + C ++a+ + ++       +v + pe C gCg C  vCP ga
  gi|386002187|ref|YP_005920486.1|  65 RCTRCGRCSEFCAYHALAVFPK-------EVLLFPELCHGCGGCDLVCPEGA 109
                                       8******************997.......58999***************997 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                            Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                       C gCg C  +Cp +a+++ 
  gi|386002187|ref|YP_005920486.1|  95 CHGCGGCDLVCPEGAVSMG 113
                                       9999999999999999876 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.018       3      28 ..       1      26 [.       1      50 [. 0.90
   2 !    9.1   0.0    0.0013       1.1     116     166 ..     153     203 ..     139     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                            AAA_31  3 vIaianqKGGvGKTTtsvnlaaalak 28
                                      +I++a  KGG GKT  ++nlaa++ +
  gi|386002187|ref|YP_005920486.1|  1 MISVASGKGGTGKTLVATNLAASIGS 26
                                      59********************9875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                            AAA_31 116 deYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktiee 166
                                        + D+ ++D pP   + ++ a+  sd ++ +++++++ l+ l+  ++ +++
  gi|386002187|ref|YP_005920486.1| 153 ARGDLLLVDSPPGTACPVIEAVRGSDFCLLVTEPTPFGLYDLSIAVQVVRR 203
                                       4569***********************************999888777765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.8   0.00037      0.32       1      19 [.      65      83 ..      65      90 .. 0.85
   2 !   15.0   0.2   4.1e-05     0.035       2      23 ..      95     116 ..      94     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      rC++Cg+C e C  +a+  
  gi|386002187|ref|YP_005920486.1| 65 RCTRCGRCSEFCAYHALAV 83
                                      6************999865 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.1e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                       C++Cg C  vCP++a+++ +++
  gi|386002187|ref|YP_005920486.1|  95 CHGCGGCDLVCPEGAVSMGTRA 116
                                       ***************9988554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   3.3   0.00035       0.3      34      50 ..      64      80 ..      44      81 .. 0.73
   2 !   21.8   8.9   1.8e-07   0.00015       1      50 [.      65     109 ..      65     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                            Fer4_9 34 eaCigCgaCveaCpkga 50
                                      ++C+ Cg+C e C  +a
  gi|386002187|ref|YP_005920486.1| 64 DRCTRCGRCSEFCAYHA 80
                                      57999999999998775 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.8e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +Ct+Cg+C e C +++     +e     +      C+gCg C  +Cp+ga
  gi|386002187|ref|YP_005920486.1|  65 RCTRCGRCSEFCAYHALAVFPKEVLLFPE-----LCHGCGGCDLVCPEGA 109
                                       6*************999999888887763.....6************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.2   1.6e-07   0.00014       2      20 ..      58      76 ..      57      78 .. 0.91
   2 !    9.1   1.0    0.0017       1.5       7      22 .]      92     107 ..      86     107 .. 0.87
   3 ?   -2.3   0.4       7.5   6.4e+03      18      21 ..     166     169 ..     166     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                       +v+d+drC++Cg C   C
  gi|386002187|ref|YP_005920486.1| 58 IPVIDEDRCTRCGRCSEFC 76
                                      699**************99 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       ++ C gCg C  +CP+
  gi|386002187|ref|YP_005920486.1|  92 PELCHGCGGCDLVCPE 107
                                       788************5 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7.5
                            Fer4_2  18 saCP 21 
                                       +aCP
  gi|386002187|ref|YP_005920486.1| 166 TACP 169
                                       79*9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.6   0.00023       0.2       4      62 ..      65      77 ..      60      89 .. 0.65
   2 !   11.8   0.7   0.00029      0.25      50      64 ..      94     108 ..      90     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                            Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                      +C++Cg+C                                              +e C 
  gi|386002187|ref|YP_005920486.1| 65 RCTRCGRC----------------------------------------------SEFCA 77
                                      45555555..............................................55554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00029
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                        C++cg C+ vCp+g
  gi|386002187|ref|YP_005920486.1|  94 LCHGCGGCDLVCPEG 108
                                       7************86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.1     0.001      0.89      44      59 ..      64      79 ..      45      81 .. 0.84
   2 !   12.8   1.0   0.00015      0.13      44      59 ..      93     108 ..      86     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C+ Cg+C++ C ++
  gi|386002187|ref|YP_005920486.1| 64 DRCTRCGRCSEFCAYH 79
                                      5799999999988876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       +lC++Cg+C+ +CP+g
  gi|386002187|ref|YP_005920486.1|  93 ELCHGCGGCDLVCPEG 108
                                       68************86 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.16      37      58 ..       4      25 ..       2      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                            AAA_25 37 llaGapgtGKttlaldlalava 58
                                      +  G +gtGKt +a++la+++ 
  gi|386002187|ref|YP_005920486.1|  4 VASGKGGTGKTLVATNLAASIG 25
                                      6689***************985 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.19       5      25 ..       4      24 ..       1      50 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                           DUF2075  5 lVtGvaGtGKtvvllnllael 25
                                      + +G+ GtGKt+v+ nl+a +
  gi|386002187|ref|YP_005920486.1|  4 VASGKGGTGKTLVATNLAASI 24
                                      678***************998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0   0.00098      0.83       2      18 ..      60      76 ..      60      87 .. 0.88
   2 ?    4.0   0.3     0.097        82       6      20 ..      93     107 ..      88     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00098
                           Fer4_15  2 vvDrdaCigcglCvaea 18
                                      v+D+d+C+ cg+C + +
  gi|386002187|ref|YP_005920486.1| 60 VIDEDRCTRCGRCSEFC 76
                                      69***********9877 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.097
                           Fer4_15   6 daCigcglCvaeape 20 
                                       ++C gcg C  ++pe
  gi|386002187|ref|YP_005920486.1|  93 ELCHGCGGCDLVCPE 107
                                       68*******999997 PP

>> GGGtGRT  GGGtGRT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00031      0.26     251     279 ..       2      31 ..       1      34 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                           GGGtGRT 251 fsvasG.GGtGrtlhpdnlaaGpasyGltd 279
                                        svasG GGtG+tl   nlaa   s  l d
  gi|386002187|ref|YP_005920486.1|   2 ISVASGkGGTGKTLVATNLAASIGSVELLD 31 
                                       69***9899************988877766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00051      0.43       4      29 ..       6      32 ..       4      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                                      ESSTTSSHHHHHHHHHHHHT.HEEEEE CS
                               AAA  4 yGppGtGKTllakavakelg.veflei 29
                                      +G  GtGKTl+a  +a ++g ve+l  
  gi|386002187|ref|YP_005920486.1|  6 SGKGGTGKTLVATNLAASIGsVELLDC 32
                                      6999*************9964666655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.5    0.0045       3.8       1      15 []      66      80 ..      66      80 .. 0.95
   2 ?   10.9   6.3   0.00086      0.73       1      15 []      95     109 ..      95     109 .. 0.98
   3 ?   -1.5   0.1       8.2     7e+03      10      13 ..     167     170 ..     166     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0045
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg+C e C ++A
  gi|386002187|ref|YP_005920486.1| 66 CTRCGRCSEFCAYHA 80
                                      ***********9987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00086
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg C  vCP+gA
  gi|386002187|ref|YP_005920486.1|  95 CHGCGGCDLVCPEGA 109
                                       **************9 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 8.2
                            Fer4_3  10 vCPv 13 
                                       +CPv
  gi|386002187|ref|YP_005920486.1| 167 ACPV 170
                                       8*96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.3    0.0013       1.1       1      16 [.      61      76 ..      61      79 .. 0.94
   2 ?    3.9   1.4     0.095        81       4      18 ..      93     107 ..      92     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D+d+C+ cg C e++
  gi|386002187|ref|YP_005920486.1| 61 IDEDRCTRCGRCSEFC 76
                                      89************99 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.095
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       + C +cg C  ++P+
  gi|386002187|ref|YP_005920486.1|  93 ELCHGCGGCDLVCPE 107
                                       56************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.0      0.01       8.8      77      93 ..      61      77 ..      49      81 .. 0.86
   2 ?    6.8   2.7     0.014        12      81      94 ..      94     107 ..      78     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                           Fer4_22 77 fgesgCvGCgRCieacp 93
                                      ++e  C+ CgRC+e c 
  gi|386002187|ref|YP_005920486.1| 61 IDEDRCTRCGRCSEFCA 77
                                      57889***********7 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                        C GCg C+ +cp+
  gi|386002187|ref|YP_005920486.1|  94 LCHGCGGCDLVCPE 107
                                       68888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1685.09
//
Query:       gi|386002188|ref|YP_005920487.1|  [L=150]
Description: hypothetical protein Mhar_1500 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   13.2   0.0       0.18   12.1   0.0    1.6  1  MORN_2    MORN repeat variant


Domain annotation for each model (and alignments):
>> MORN_2  MORN repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     1e-05      0.18       3      16 ..      74      87 ..      73      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1e-05
                            MORN_2  3 GeekeYyenGklke 16
                                       e+++Y +nG+l+ 
  gi|386002188|ref|YP_005920487.1| 74 MEWRWYAPNGQLYA 87
                                      69**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 947.42
//
Query:       gi|386002189|ref|YP_005920488.1|  [L=219]
Description: hypothetical protein Mhar_1502 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-44  150.1   0.0    5.8e-44  149.8   0.0    1.1  1  DUF5616   Domain of unknown function (DUF5616)
    1.3e-17   63.2   0.1      2e-17   62.6   0.1    1.3  1  DUF434    Protein of unknown function (DUF434)
  ------ inclusion threshold ------
      0.059   13.0   0.0       0.12   12.0   0.0    1.5  1  UPF0181   Uncharacterised protein family (UPF0181)


Domain annotation for each model (and alignments):
>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   9.7e-48   5.8e-44       2     139 ..      69     206 ..      68     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 9.7e-48
                           DUF5616   2 eelkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDk 78 
                                       e+l+g++++iDG+Nvlit+es+lsg+ ++lcdDg++RD++g++++y+ +e t  a+  il++l+ ++v++++++lD+
  gi|386002189|ref|YP_005920488.1|  69 ERLAGRTVAIDGYNVLITVESLLSGAAVYLCDDGFLRDVRGIFRSYRSSEVTAPAIGEILSVLEGAGVAQAEVILDQ 145
                                       6899************************************************************************* PP

                           DUF5616  79 pvSnSgelaklireileeaglegevelvknvDkeLkeseeivatsDsvildkvksvldlaa 139
                                       ++S+Sgela++ir  l++ g++ge+++++++D++Lk + + vat D+ i+d++ + +dl+a
  gi|386002189|ref|YP_005920488.1| 146 QISRSGELAATIRGALADFGVQGEATTARDADRRLKVAPHPVATGDGGIIDAALEAVDLPA 206
                                       ***********************************************************97 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   3.4e-21     2e-17       2      56 .]      10      64 ..       9      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 3.4e-21
                            DUF434  2 LkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                      L+ Aae++ryLL+RGYp+  a+++V++h +L +++R +L+R++++++ ++ar++K
  gi|386002189|ref|YP_005920488.1| 10 LNLAAEEIRYLLDRGYPSGPAVRFVSDHRRLPREDRFVLSRVAVPSALAAARRKK 64
                                      899**************************************************98 PP

>> UPF0181  Uncharacterised protein family (UPF0181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.12      16      40 ..      13      37 ..      10      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                           UPF0181 16 AVEkIqeLmaqGmssgeAIalVAqe 40
                                      A+E+I+ L+ +G  sg A+++V+++
  gi|386002189|ref|YP_005920488.1| 13 AAEEIRYLLDRGYPSGPAVRFVSDH 37
                                      9*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 1479.14
//
Query:       gi|386002190|ref|YP_005920489.1|  [L=179]
Description: Fumarase, beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-28   98.5   0.0    3.8e-28   98.2   0.0    1.0  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.0   2.1e-32   3.8e-28      32     205 ..       5     168 ..       2     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 2.1e-32
                        Fumerase_C  32 LnqketeeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPvktpedeavgsaGPT 108
                                       L++++  ee++++++g+ + +sG++++aRD +H+ l+    +ge+lp  ++l + viY++GP    +d +v saGPT
  gi|386002190|ref|YP_005920489.1|   5 LKTPISGEEVAALRAGDLVWISGTVYTARDRVHALLA----SGEKLP--IDLAGAVIYHCGPL--IRDGTVLSAGPT 73 
                                       66778889*************************9887....8*****..9************8..5677889***** PP

                        Fumerase_C 109 TatRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvefeelGm.EAiyei 184
                                       T++R  +++++++   g++ +++Kg+ s+++ ea++  +++YL   GG   la++++ +v+ ++ +elGm E ++e+
  gi|386002190|ref|YP_005920489.1|  74 TSGRVGRFTREVVG-LGVRLIVGKGGISEEA-EALR-GRAAYLAYPGGCGALAARQL-SVKQLHLPELGMaEGLWEL 146
                                       ************98.799**********986.6665.6899*******777777776.7999*************** PP

                        Fumerase_C 185 evedf.pafvvvddkGndlfke 205
                                         e   p +v++d++G dl++e
  gi|386002190|ref|YP_005920489.1| 147 VAEGWgPMIVAIDASGGDLYRE 168
                                       ***9878999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.33s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1219.83
//
Query:       gi|386002191|ref|YP_005920490.1|  [L=266]
Description: Fumarase, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-83  278.6   0.0    5.7e-83  278.4   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.4   0.0   3.2e-87   5.7e-83       7     269 ..       3     256 ..       1     257 [. 0.96

  Alignments for each domain:
  == domain 1  score: 278.4 bits;  conditional E-value: 3.2e-87
                          Fumerase   7 alkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetgdleea 83 
                                       +l +a+t lp +v ea+++a++kE+s +a+++l+++leN+eiAa + +plCqDTG++v+ ++ig +++ +   leea
  gi|386002191|ref|YP_005920490.1|   3 VLARAETVLPLWVEEAIREAAAKERSAIARSQLSAILENVEIAAAGGVPLCQDTGLPVFRLEIGLNLS-IPPFLEEA 78 
                                       57899**************************************************************7.7889**** PP

                          Fumerase  84 ineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnpsdgle 156
                                       i+eGvr+a++e plR+++v dpl+rkn+gd    ++P  + ++lvpgd l+it+++kG+Gsen s+l+mlnp+d   
  gi|386002191|ref|YP_005920490.1|  79 IAEGVRRATEEVPLRPNAV-DPLTRKNSGDntgpGIP-DLIVDLVPGDFLRITAFPKGAGSENGSFLAMLNPAD--- 150
                                       *******************.**********7777778.8899******************************76... PP

                          Fumerase 157 gvkkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiGpqGlG 233
                                       + ++fv  +v++  ++aC P+++gvgiGgt++ a +lak+al+r  g+++       l+++ll++in+lg Gp+GlG
  gi|386002191|ref|YP_005920490.1| 151 DPIEFVAREVAKRAGRACAPVFVGVGIGGTFDLAPRLAKRALFRMPGTSE-------LDRKLLTDINRLGTGPMGLG 220
                                       9*****************************************88776655.......999***************** PP

                          Fumerase 234 GkttvldvkierlprhiAslpvavnvsCsadRrakv 269
                                       G++t+l+v+ie++ +h+Aslpvavn++C+a+R+a++
  gi|386002191|ref|YP_005920490.1| 221 GDSTALAVRIETALCHTASLPVAVNLQCWANRSASA 256
                                       ********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1976.47
//
Query:       gi|386002192|ref|YP_005920491.1|  [L=241]
Description: hypothetical protein Mhar_1504 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-63  214.5   0.0    1.5e-63  214.3   0.0    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   0.0   8.3e-68   1.5e-63       2     219 ..       5     219 ..       4     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 8.3e-68
                            DUF166   2 vltsgeyGervvenilnepdferslivavvevpeeldefiedpeelLpe......lkeaDiviaytlhpDlllelae 72 
                                       v+ +g+yGer++e+i++++dfe    v+ ve+p+ l+efiedpee+L         +++ ++i+y+lhpD++ e+a 
  gi|386002192|ref|YP_005920491.1|   5 VVIRGKYGERLIETIRERTDFE----VVSVEIPQALPEFIEDPEEFLDGldldpeFFSSELIITYSLHPDVTPEIAV 77 
                                       8999******************....*********************8777777799******************** PP

                            DUF166  73 kakekkvkalivpaeapkaglrkelkekleelgievavpkpfCsleeegkpkideFleefGkPelevevkdgkikkV 149
                                       +a +++++a+ivp   ++ag   el++ ++++gi ++v++++C+l++ g + +d+F+e++G+P+levev+dg+i++ 
  gi|386002192|ref|YP_005920491.1|  78 RAGKGGAQAVIVPGGIGRAGSVPELQKIADRYGIYIEVDEICCTLDPCGVEAVDAFAEKLGRPRLEVEVEDGRIARA 154
                                       ***************************************************************************** PP

                            DUF166 150 eVlrsapCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                       eVlr++pCGstw+va++++G+ ve+a+ +ag+ +q YpC+A+++     +e+++h++g++hk a+e+Al+
  gi|386002192|ref|YP_005920491.1| 155 EVLRGSPCGSTWHVARDIVGVTVEDAPPRAGLLCQMYPCRAVRG-----GEGGIHTSGDLHKAAMEEALG 219
                                       ********************************************.....*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1603.42
//
Query:       gi|386002193|ref|YP_005920492.1|  [L=459]
Description: Cobyrinic acid a,c-diamide synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-40  139.1   0.0    1.8e-40  138.6   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    6.9e-19   68.2   0.0    1.2e-18   67.4   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      3e-16   59.8   0.5    1.6e-09   37.9   0.0    2.3  2  AAA_26         AAA domain
     0.0039   16.9   0.0     0.0064   16.2   0.0    1.3  1  Peptidase_S51  Peptidase family S51
     0.0099   15.2   0.0       0.02   14.2   0.0    1.5  1  DUF1611        Domain of unknown function (DUF1611_C) P-loop 
  ------ inclusion threshold ------
      0.073   12.5   0.0       0.22   11.0   0.0    1.7  2  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
       0.16   11.8   0.0        0.3   11.0   0.0    1.4  1  MobB           Molybdopterin guanine dinucleotide synthesis p


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.0     7e-44   1.8e-40       1     193 [.     254     443 ..     254     446 .. 0.91

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 7e-44
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       +iav +++a+ +y+  ++++L++ +++  +f+p  ++ l+e ad ++l+Gg++++ + +l+++  ++ +ik+aa +g
  gi|386002193|ref|YP_005920492.1| 254 RIAVGYDEAFCFYYaeNFEILRKLGAEIEFFSP-IRDPLPE-ADGLYLGGGYPELYSRELEES-PTRHEIKKAAGDG 327
                                       69*******************************.8888966.*****************9988.999********** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel........aaegeevkGyEi 144
                                       +p++g+CGGl++L+e+++ ++g     +e ++ g+L+++t+++  +l+    g+ve         +a+g+ ++G+E+
  gi|386002193|ref|YP_005920492.1| 328 MPIYGECGGLMYLCESVVSKDGD----SEKKMAGVLPATTAMTG-RLQ--ALGYVEGdvvaenpvVARGSVIRGHEF 397
                                       ********************998....899**************.555..4444444445699998999******** PP

                          GATase_3 145 HsGrtilkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdn 193
                                       H+++   +++a+ ++++++g+++  ++dG+v++    ++lG+YlH +f  
  gi|386002193|ref|YP_005920492.1| 398 HYSKMDCARDARFAYRFRRGKGIVgDRDGLVEH----ETLGSYLHTHFST 443
                                       *****************88666556******88....**********975 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   4.5e-22   1.2e-18       1     125 [.       5     188 ..       5     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4.5e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep................... 54 
                                       +++a+t++GvGKTt+++++++al rrgl V++++++p+    ++        ++   +                   
  gi|386002193|ref|YP_005920492.1|   5 VLVAGTSSGVGKTTVVLGMMAALRRRGLVVAPFKVGPDFIDPSHhaaiC--GRPS--Rnldtfmmgrdgvrrsfarg 77 
                                       689***********************************88777755331..2222..1447788888888889999* PP

                                       ..........................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS CS
                                       ..........................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                              CbiA  55 ..........................................dlkrllellealgkkkall...lkiagvvlnrvdg 86 
                                                                                 ++   +++++a+  +++     +ki g+vlnrv++
  gi|386002193|ref|YP_005920492.1|  78 vegadvaviegvmglydgldatdvassasvakalgapvllvmNVHGTSRSAAAMALGYRSYdpgVKISGLVLNRVGS 154
                                       ******************************************9999999****9999999999************** PP

                                       ...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  87 eneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                       +++  ll+eal+ l    g+p+l+++pr+ ++  +p+r+
  gi|386002193|ref|YP_005920492.1| 155 DRHRGLLEEALAPL----GIPILASLPRRGEI-ALPSRH 188
                                       *************9....***********998.677776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   2.9e-07   0.00074       3      36 ..       5      38 ..       4      40 .. 0.90
   2 !   37.9   0.0   6.1e-13   1.6e-09      99     191 ..      81     179 ..      68     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-07
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                      ++v+gt+ gvGKT+v lg ++al+r+g  v+ fK
  gi|386002193|ref|YP_005920492.1|  5 VLVAGTSSGVGKTTVVLGMMAALRRRGLVVAPFK 38
                                      79*********************99998777665 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 6.1e-13
                            AAA_26  99 adivvVEGagglgvpitee..llnadiaknlgapvilVarggl..gtinqllltiealrqknvrvlGvilNkvrnpe 171
                                       ad+ v+EG+ gl +++ ++  ++ a +ak+lgapv+lV++++   ++ ++++l + ++   +v++ G++lN+v +++
  gi|386002193|ref|YP_005920492.1|  81 ADVAVIEGVMGLYDGLDATdvASSASVAKALGAPVLLVMNVHGtsRSAAAMALGYRSYDP-GVKISGLVLNRVGSDR 156
                                       7999**********97665348889***************96622567777777777777.9***********9997 PP

                            AAA_26 172 ...nvetlekksgipvlGvvPyl 191
                                           +e++ +  gip+l+++P  
  gi|386002193|ref|YP_005920492.1| 157 hrgLLEEALAPLGIPILASLPRR 179
                                       3335555555577********86 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.5e-06    0.0064      74     144 ..     285     354 ..     261     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTTTS-GGG CS
                     Peptidase_S51  74 eeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsysdspik 144
                                       + i++ l ead++y+gGG      ++l+e  + + +++a  +g+++ G   G +  +es+ +++  ds +k
  gi|386002193|ref|YP_005920492.1| 285 SPIRDPLPEADGLYLGGGYPELYSRELEESPTRHEIKKAAGDGMPIYGECGGLMYLCESVVSKD-GDSEKK 354
                                       346677778***********999************************************99998.666654 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.7e-06      0.02      13      47 ..       3      37 ..       1      45 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                           DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaafv 47
                                      + vlv GT++ vGK t  l + +al++rGl +a +
  gi|386002193|ref|YP_005920492.1|  3 PCVLVAGTSSGVGKTTVVLGMMAALRRRGLVVAPF 37
                                      679**************************987755 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.74   1.9e+03       9      30 ..      12      33 ..       7      48 .. 0.84
   2 ?   11.0   0.0   8.4e-05      0.22     170     215 ..     138     183 ..     117     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.74
                         Fer4_NifH  9 GGiGksttsqnlsaalaemgkk 30
                                       G+Gk+t +  ++aal ++g  
  gi|386002193|ref|YP_005920492.1| 12 SGVGKTTVVLGMMAALRRRGLV 33
                                      599************9998855 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.4e-05
                         Fer4_NifH 170 ksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivr 215
                                          gv+++Gl+ n    d++r+l+e+  + lg+++l+ +Pr  ++ 
  gi|386002193|ref|YP_005920492.1| 138 YDPGVKISGLVLNRVGSDRHRGLLEEALAPLGIPILASLPRRGEIA 183
                                       3457*********88999***********************98875 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012       0.3       4      34 ..       7      38 ..       4      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                              MobB  4 ivgk.sgsGKTtLleklipelkarglrvgtiK 34
                                      ++g+ sg GKTt +  ++++l++rgl v+  K
  gi|386002193|ref|YP_005920492.1|  7 VAGTsSGVGKTTVVLGMMAALRRRGLVVAPFK 38
                                      4444389********************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3138.66
//
Query:       gi|386002194|ref|YP_005920493.1|  [L=926]
Description: Putative helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-21   75.6   0.0    1.1e-20   74.3   0.0    1.8  1  ResIII          Type III restriction enzyme, res subunit
    2.7e-11   43.4   2.4      7e-11   42.1   2.4    1.8  1  HNH             HNH endonuclease
    8.1e-11   42.2   0.0      2e-10   41.0   0.0    1.7  1  Helicase_C      Helicase conserved C-terminal domain
    9.1e-11   41.8   0.0    1.7e-10   40.9   0.0    1.4  1  DEAD            DEAD/DEAH box helicase
    8.6e-10   38.3   4.3    1.3e-09   37.7   2.6    2.2  2  HNH_5           HNH endonuclease
    3.5e-07   30.1   0.0    5.8e-07   29.4   0.0    1.3  1  SWI2_SNF2       SWI2/SNF2 ATPase
     0.0003   19.8   0.0    0.00059   18.8   0.0    1.4  1  AAA_34          P-loop containing NTP hydrolase pore-1
     0.0018   18.2   0.0     0.0049   16.9   0.0    1.8  1  Ada_Zn_binding  Metal binding domain of Ada
     0.0057   16.5   0.0      0.019   14.9   0.0    1.9  1  HNH_4           HNH endonuclease
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.032   13.6   0.0    1.4  1  ATPase          KaiC
      0.053   13.2   0.0       0.15   11.7   0.0    1.8  2  Terminase_6     Terminase-like family
      0.077   12.9   0.7       0.24   11.4   0.7    1.8  1  Endonuclease_7  Recombination endonuclease VII
       0.11   12.2   0.0       0.24   11.1   0.0    1.4  1  IstB_IS21       IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   8.3e-24   1.1e-20       5     170 ..      26     202 ..      22     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 8.3e-24
                                       -HHHHHHHHHHT........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   5 reyQeeaienlleklks..krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                        ++Q  ai++l   ++   + +  ++++++TG GKT++a+++  + + + ++ k+l l+++ +lleq+ + +++ + 
  gi|386002194|ref|YP_005920493.1|  26 ASHQSAAIDKLYRWYEGnpEPQAGAILVLPTGGGKTFTAVRFLCKTALSDGY-KVLWLAHTHHLLEQAFKSLEEDIG 101
                                       67999999999977766657777999*************7666555555444.****************88877777 PP

                                       G........GEEEESSS-B--........-SEEEEEHHHHHHTH........H..HHTTT-SEEEEETGGGTTS.TT CS
                            ResIII  80 eayke....igkkvsgdkkka.kekdstnkkilvttiqsldadseeeeeesee..llrdrfdviiiDEaHrlgakks 149
                                       + ++     +  +vsg k++    + + + +++++t q++ ++ +e+ ++ e   ++ ++++++++DEaH++ a  s
  gi|386002194|ref|YP_005920493.1| 102 QIAEPrgslKVRVVSGTKDHYpVYEIKPDDDVVIATLQTIAKAHKEHHRALEAflKSAGKKLFVVFDEAHHAPA-PS 177
                                       6655566667777888888776556677999*************777544444004455666************.99 PP

                                       THHH....HHT---SEEEEEESS-S CS
                            ResIII 150 wrei....lekfkeavllglTATpe 170
                                       +r++     +k+++ ++lglTATp 
  gi|386002194|ref|YP_005920493.1| 178 YRKLiqslRDKIPRMYVLGLTATPS 202
                                       99963665677788*********95 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   2.4   5.1e-14     7e-11       1      45 [.     679     721 ..     679     723 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 5.1e-14
                               HNH   1 CeyCgrkfhksealevdHiipisqggaddieNlqllCksCHnkkh 45 
                                       C  Cg +   +++l+vdHi+p+  gg+++ eNlq+lC +C+nkk 
  gi|386002194|ref|YP_005920493.1| 679 CLCCGTTK--RSFLQVDHIDPRYLGGSNNPENLQTLCGECNNKKR 721
                                       999**995..457******************************95 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.5e-13     2e-10      11     110 ..     290     397 ..     279     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.5e-13
                                       HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT........STHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C  11 kleeeggkilifvntidrlek.vklllekkgikvavlhge........lpqnereeileqfnkgesdvLiatdvaer 78 
                                        ++++ gk++if+ ++ ++e  +++l ek+g+++  +++            ++++++le+f++g+ dv++  +++ +
  gi|386002194|ref|YP_005920493.1| 290 GNRKKYGKTIIFADRWYQCEAiAEYL-EKRGVNAGSVYSHvtrgvnkkSADENNRRVLEAFKAGKLDVILNVRMLTE 365
                                       568999*************9977777.7777888777777555555545556666********************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       G d+p+++  ++    ++   + q++GR+ R+
  gi|386002194|ref|YP_005920493.1| 366 GTDLPDAESAFITRQTTSRNLLTQMVGRALRG 397
                                       *****************************996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   1.3e-13   1.7e-10      15     170 ..      48     202 ..      27     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.3e-13
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.....SEEEEEETTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.....lrvlliiggva 86 
                                          ++  +TG GKT  ++  ++++      ++g k+l ++ t+ L eq ++ l++ + +i      l+v  +++g++
  gi|386002194|ref|YP_005920493.1|  48 AGAILVLPTGGGKTFTAVRFLCKTA----LSDGYKVLWLAHTHHLLEQAFKSLEEDIGQIAeprgsLKVR-VVSGTK 119
                                       4578899***************888....57**********************99999877788877776.667888 PP

                                       HHHHHHHHHTTCSEEEEEHHHHHH.HH.HCTSSH.....CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  87 ardqlskldngvdivvgtpgrldd.ll.stgkln.....lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                        +  + +++ + d+v++t + +++ +  + + l+       +  f+V+DEa+     ++++ i+++  ++p+     
  gi|386002194|ref|YP_005920493.1| 120 DHYPVYEIKPDDDVVIATLQTIAKaHKeHHRALEaflksAGKKLFVVFDEAHHAPAPSYRKLIQSLRDKIPR----- 191
                                       88999999888************9555523334455333444579********************9999942..... PP

                                       TTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxx RF
                              DEAD 157 klqrqvivlSATlp 170
                                            v+ l+AT++
  gi|386002194|ref|YP_005920493.1| 192 ---MYVLGLTATPS 202
                                       ...23999999997 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.8   2.4e+03      23      37 ..      56      70 ..      51      71 .. 0.85
   2 !   37.7   2.6   9.7e-13   1.3e-09       1      46 [.     679     723 ..     679     730 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                             HNH_5 23 lGGkltisnlvtlCk 37
                                       GG +t++ ++ lCk
  gi|386002194|ref|YP_005920493.1| 56 TGGGKTFTAVRFLCK 70
                                      6899999*******8 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 9.7e-13
                             HNH_5   1 CiyCgkeiaekelseeHIiPeslGGkltisnlvtlCkkCNqkkgqk 46 
                                       C  Cg ++ +  l+ +HI P+ lGG++ ++nl+tlC +CN+kk ++
  gi|386002194|ref|YP_005920493.1| 679 CLCCGTTKRS-FLQVDHIDPRYLGGSNNPENLQTLCGECNNKKRTD 723
                                       9999999555.88******************************876 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.2e-10   5.8e-07       2     160 ..      29     204 ..      28     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.2e-10
                         SWI2_SNF2   2 Qyravekavervke..gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka.... 72 
                                       Q  a+ k+ +  +   + + g ++   +G GK++t v +  k +    + +kv+ +   + L +Q +k +++     
  gi|386002194|ref|YP_005920493.1|  29 QSAAIDKLYRWYEGnpEPQAGAILVLPTGGGKTFTAVRFLCKTAL--SDGYKVLWLAHTHHLLEQAFKSLEEDigqi 103
                                       5566666555555444445566666779*******9977666666..6899******************99854433 PP

                         SWI2_SNF2  73 ....geekpkqaesrkeLkelle.kesekiifttiqKfeeeek...ekl..evlsereniivlvDEaHRs...qyge 136
                                           g+ k++ ++ +k+     e k +++++++t+q +++++k   ++l     s+ ++++v++DEaH      y +
  gi|386002194|ref|YP_005920493.1| 104 aeprGSLKVRVVSGTKDHYPVYEiKPDDDVVIATLQTIAKAHKehhRALeaFLKSAGKKLFVVFDEAHHApapSYRK 180
                                       33321222223333333333333155999999999998744331222232134566789*********994445779 PP

                         SWI2_SNF2 137 lakklrkalpnaafigFTGTPilk 160
                                       l ++lr+ +p++ ++g+T TP  +
  gi|386002194|ref|YP_005920493.1| 181 LIQSLRDKIPRMYVLGLTATPSYT 204
                                       999******************765 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.3e-07   0.00059      61     185 ..      48     174 ..      14     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.3e-07
                            AAA_34  61 aGfllGDgaGvGkgrqiagiilenllqgrkkavwvsvsedLkeDaerDlk.digas.....eievvalnklkegkki 131
                                       aG +l   +G Gk+ +   ++++  l++  k++w+  +++L+e a + l+ dig+      +++v++++ +k +  +
  gi|386002194|ref|YP_005920493.1|  48 AGAILVLPTGGGKTFTAVRFLCKTALSDGYKVLWLAHTHHLLEQAFKSLEeDIGQIaeprgSLKVRVVSGTKDHYPV 124
                                       66667777999************************************995489876445555666666666666555 PP

                            AAA_34 132 keseelkeGvlFvtYstliseskkkkksrleqlveWlgedfdGvivfDEchkak 185
                                         + + ++ v+ +t +t  +++k+++ + le +++  g++   ++vfDE+h+a 
  gi|386002194|ref|YP_005920493.1| 125 -YEIKPDDDVVIATLQTIAKAHKEHH-RALEAFLKSAGKK--LFVVFDEAHHAP 174
                                       .788999***********99988866.8899999999987..47*******985 PP

>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.5e-06    0.0049      13      64 ..     867     919 ..     858     920 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.5e-06
                                       CCTTBEEEETTTTEEE-TT-SSS-S-.SCCEEEESSHHHHHHTT-EEETTTTT CS
                    Ada_Zn_binding  13 adgsFvyavkttgiyCrpsCparlPk.renveFfdtaaeAeaagfrpCkrcrP 64 
                                       a++  +++    + y  psC   +    e+   f++a++A++ g+ pC+ c+P
  gi|386002194|ref|YP_005920493.1| 867 AEDMNFVGSIDSNKYHLPSCGWAKKIpLEDLISFPNAEAAKSLGYIPCRVCEP 919
                                       5556678888888999999986544346888889******************9 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.019      17      53 ..     688     724 ..     684     725 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                       ..SEEEESSTTTT---BSGGGEEEES-GGGGTSSSSS CS
                             HNH_4  17 keydiDHilPrsrskdDsvsNkVLvlrdaNqeKsnrt 53 
                                       + +++DHi Pr ++  +   N+   + ++N++K+ +t
  gi|386002194|ref|YP_005920493.1| 688 SFLQVDHIDPRYLGGSNNPENLQTLCGECNNKKRTDT 724
                                       5689*****************************9876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.032      28     120 ..      56     147 ..      34     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                            ATPase  28 pGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee.egklaiidasesaeesaeekdked 103
                                       +G GKt+ a +Fl k a + g++++  +   + + l + +ksl  d+ ++ e +g+l +  +s ++++++  + k d
  gi|386002194|ref|YP_005920493.1|  56 TGGGKTFTAVRFLCKTALSDGYKVLWLAH--THHLLEQAFKSLEEDIGQIAEpRGSLKVRVVSGTKDHYPVYEIKPD 130
                                       799**********************9875..566799999*******998653788988888888888887788888 PP

                            ATPase 104 leelieelaeaikeika 120
                                        + +i++l+++ k+ k+
  gi|386002194|ref|YP_005920493.1| 131 DDVVIATLQTIAKAHKE 147
                                       88888888888777665 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.15       2     121 ..      52     186 ..      51     207 .. 0.67
   2 ?   -3.8   0.0       6.1   8.4e+03     177     206 ..     268     298 ..     262     306 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       EEE-SSS-HHHHHHHHHHHHHHSSSS.-EEEEE.ESSHHHHHHHHHHHHHHHHTS-T..TTS--EEEE-SSEEEE.. CS
                       Terminase_6   2 ilggrqsGKTfagarellrhalgrgprnqvfls.asktqareeggqfekgigelake..ildiefeesaknlvvl.. 73 
                                       ++ + + GKTf+  r+l++ al  g+   v +   + + +++ +   e++ig++a+    l+++     ++++++  
  gi|386002194|ref|YP_005920493.1|  52 LVLPTGGGKTFTAVRFLCKTALSDGY--KVLWLaHTHHLLEQAFKSLEEDIGQIAEPrgSLKVRVV---SGTKDHyp 123
                                       567899*******************9..55555166666666655566666666665333555555...66666677 PP

                                       ......TTS-EEEEES.....SHHHHHT........S--SEEEEESGGGSTTHHHHHHHHHHH CS
                       Terminase_6  74 ......snGaslhflslese.taggiqG........aqidliyfDElteipksqelekvtrlr 121
                                             ++  ++  l + ++ +++ +++         +  ++ fDE+ + p+  + +++++lr
  gi|386002194|ref|YP_005920493.1| 124 vyeikpDDDVVIATLQTIAKaHKEHHRAleaflksaGKKLFVVFDEAHHAPAPSYRKLIQSLR 186
                                       777887333333333333333555555555555554566688888888888888888887775 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.1
                                       HHHHHHHHHTS-HHH.HHHHHS---TTCTCE CS
                       Terminase_6 177 edlieeleaeysvee.rarllrGewidtsgs 206
                                       ed ie+l ++  ++e + + + G+ +  + +
  gi|386002194|ref|YP_005920493.1| 268 EDIIEQLAENRARNEyIGATYVGNRKKYGKT 298
                                       6677788777777776677777777763333 PP

>> Endonuclease_7  Recombination endonuclease VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   0.00017      0.24      10      65 ..     663     720 ..     654     736 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                       SHHHHHHTT---TTSE-TTT--EEETTS--EEEEE-T...TT--.....EEEEEHHHHH.HHH CS
                    Endonuclease_7  10 itkeerkalleaqggkCaiCqerekektkalavDHdH...ktgk....vRgllCgsCNtalGk 65 
                                       +t+ee+ ++ e+++ +C  C +   +k+  l+vDH       g         lCg CN+   k
  gi|386002194|ref|YP_005920493.1| 663 LTEEEKIKIKERDEYTCLCCGT---TKRSFLQVDHIDpryLGGSnnpeNLQTLCGECNNK--K 720
                                       4899999**************7...555566777765554333366668899******87..4 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.24      48      89 ..      48      91 ..      39     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                         IstB_IS21 48 enivllGpsGvGKshlaia.lgveavraglsvlfvr.vedLvee 89
                                      ++ +l+ p+G GK++ a+  l + a  +g++vl++  ++ L+e+
  gi|386002194|ref|YP_005920493.1| 48 AGAILVLPTGGGKTFTAVRfLCKTALSDGYKVLWLAhTHHLLEQ 91
                                      5678999**********9736888999*******8624556554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (926 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 5691.61
//
Query:       gi|386002195|ref|YP_005920494.1|  [L=191]
Description: Iron-sulfur flavoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-32  112.7   0.0    1.6e-32  112.4   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.2e-10   40.6   0.0    2.8e-10   40.2   0.0    1.1  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.03   14.1   0.1       0.04   13.7   0.1    1.2  1  DUF2284       Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.0   2.8e-36   1.6e-32       1     152 [.       1     158 [.       1     161 [. 0.88

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 2.8e-36
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.......---HCHGHTCGGSHHHHHHHHHHH CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc.....alcdkdlesegqtsddvaellekia 71 
                                       mk+++++GS+r+++nt  l+++++e+l+++++e+el++la+  i +c     ++ ++d  +   ++d v+e+++k+ 
  gi|386002195|ref|YP_005920494.1|   1 MKVVAFNGSARRDGNTAILVRRVLEELEKEDIETELVQLAGErIRGCtacrgCVANQDRRC-TIDDDVVNECIRKMV 76 
                                       9**********************************************88866555655543.5666667******** PP

                                       H-SCEEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECS CS
                           FMN_red  72 aadaliivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpra 146
                                       +ad++i+++P+Y++ +s+ +K+++Dr+++  ++++  +r K++a+v+++  r+g+ ++  +  + + + +++v++++
  gi|386002195|ref|YP_005920494.1|  77 EADGIILASPTYFADVSAEMKALIDRAGFvaRANGGLFRRKVGAAVVAV-RRAGAIHTFDSINHFFFISEMVVPGSS 152
                                       **********************************************666.556666666666666669********9 PP

                                       EEEETS CS
                           FMN_red 147 avavgk 152
                                       ++++g+
  gi|386002195|ref|YP_005920494.1| 153 YWNLGF 158
                                       999876 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   4.7e-14   2.8e-10       1     133 [.       1     126 [.       1     144 [. 0.75

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.7e-14
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHC.C..HHHHTT.C.HHHHHHH. CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaa.k..layeek.p.adveseq. 71 
                                       mk++  n++ r  + ++  l ++++e+lek++  e + + L+ + +  +t+    + +   ++++  +  d   ++ 
  gi|386002195|ref|YP_005920494.1|   1 MKVVAFNGSARR-DGNTAILVRRVLEELEKED-IETELVQLAGERIRGCTA----CrGcvANQDRRcTiDDDVVNEc 71 
                                       8999********.5999***************.9*********85555554....2313335555565566666667 PP

                                       HHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTS..EEEEEEE CS
                      Flavodoxin_2  72 iekllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgk..kalvivt 133
                                       i k+ +ad i+l++P ++  v+a +K+ iDr   agf     +    +gg+++ k   a+v+v 
  gi|386002195|ref|YP_005920494.1|  72 IRKMVEADGIILASPTYFADVSAEMKALIDR---AGFVA---R---ANGGLFRRKvgAAVVAVR 126
                                       *******************************...69977...2...223555555433444444 PP

>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.7e-06      0.04      77     124 ..      20      67 ..       6      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                           DUF2284  77 lekillelekeafeagypkalalsagsCtlCetCayeegepCrhpeka 124
                                       ++++l eleke +e++  +  +     Ct C+ C++++++ C   + +
  gi|386002195|ref|YP_005920494.1|  20 VRRVLEELEKEDIETELVQLAGERIRGCTACRGCVANQDRRCTIDDDV 67 
                                       6788999***********************************876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1095.84
//
Query:       gi|386002196|ref|YP_005920495.1|  [L=931]
Description: DNA polymerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.2e-103  345.0   0.0   7.9e-103  344.6   0.0    1.1  1  DNA_pol_B       DNA polymerase family B
    2.9e-42  145.0   0.0    1.7e-41  142.5   0.0    1.9  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
     0.0024   17.6   0.0     0.0041   16.8   0.0    1.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
       0.06   13.3   0.0       0.14   12.2   0.0    1.6  1  RNase_H_2       RNase_H superfamily
       0.18   11.6   0.0       0.93    9.3   0.1    2.2  2  WIYLD           Ubiquitin-binding WIYLD domain


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.6   0.0  2.2e-106  7.9e-103       5     457 ..     418     879 ..     415     881 .. 0.90

  Alignments for each domain:
  == domain 1  score: 344.6 bits;  conditional E-value: 2.2e-106
                                       HHHHS-HHHHHHHHHHHHHHHTTBE-B-.....----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHH CS
                         DNA_pol_B   5 rvledgqqirveslLlrlakeegfilpd.....rtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqa 76 
                                        v+ +gq   ve +L+r+++e+g+++p       +++++ ++++ +G+ VlePkkgl +  vl+lD+ SLYPsi++a
  gi|386002196|ref|YP_005920495.1| 418 DVIDGGQTGMVENFLFRKFQERGRVIPPkpdadLSSARAAQSSELKGGEVLEPKKGLVE-DVLILDYRSLYPSIMMA 493
                                       6899**********************986777644444455546*************76.59*************** PP

                                       TT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHH CS
                         DNA_pol_B  77 hNlcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalld 153
                                       hNlcy+t+v++e+  +          v   p++ efv + ++ g++p +L dlla+R+ ik+++k++++e e+ +ld
  gi|386002196|ref|YP_005920495.1| 494 HNLCYSTVVTDERPPS----G----GVVKPPSGGEFVLPGEAPGIVPGVLSDLLAQRTDIKRRMKSASEE-ERSILD 561
                                       **********998855....2....366779999*********************************999.****** PP

                                       HHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT....SSG.GGT-SS............ CS
                         DNA_pol_B 154 kqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekk.aellsk.llalpeeae......... 219
                                       +qQ+alK++ Ns+YG+ G+a  rl++l+lA+ vT+ GR+++++tk++ve+    ++++ ++ lpee++         
  gi|386002196|ref|YP_005920495.1| 562 AQQYALKILLNSFYGYSGYARARLYSLPLANAVTSFGRTNILNTKRMVEEIgSVYVRDgKALLPEEMAsasgdsfpa 638
                                       *************************************************9953334445566666653356788989 PP

                                       .......T-EEEEEBSSEEEEE-......S-.SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEE CS
                         DNA_pol_B 220 ....ee.klkviYGDTDSvfiel......kv.kdveellkigkelaeevseklfkkplklefekvykkllLisKKkY 284
                                           ++ +l+v+YGDTDSvfi+l      +v  ++ee+  +g ++ae v++ ++++p++l fe+   + l++ KK+Y
  gi|386002196|ref|YP_005920495.1| 639 vgefKRfDLSVVYGDTDSVFIRLkpfggsGVkPTLEEAELVGGKIAETVTS-RLPPPMELVFEAFARRGLFLVKKRY 714
                                       9877668****************99988744478999999***********.99*********************** PP

                                       EEEEEEESSTTS..EEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHH.HHHHTT-S CS
                         DNA_pol_B 285 aglkvektskan..klliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvl.eeleenkv 358
                                       a  ++ek   +   k+ ++G+++vRrd+c+l++++ ++ lel+l +     ++ee+++  ks++++++  +l++   
  gi|386002196|ref|YP_005920495.1| 715 ALWVFEKVGGEWrdKIKVRGMETVRRDWCELTSKTLNRSLELVLME----GRVEEAVDLAKSVIDRLQrLDLRKDPE 787
                                       ***999665544668*******************************....**************8887668888888 PP

                                       -GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHC CS
                         DNA_pol_B 359 plekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvlek 435
                                        le++vl+++++k++++yk+k+ ph+++a+++++r + +p+vgdr+++viv           l  +raedp+y+le+
  gi|386002196|ref|YP_005920495.1| 788 ILEDLVLTRRYTKSTASYKNKQ-PHVQLAEKMRARGGPVPSVGDRVPFVIVRGR-------GLFVDRAEDPSYALEN 856
                                       9********************9.*****************************95.......59************** PP

                                       CSEB-HHHHHH.TTHHHHHHHHT CS
                         DNA_pol_B 436 nlpidieyYls.qllkevarlle 457
                                       +l id++yY++ q+l+++ rll+
  gi|386002196|ref|YP_005920495.1| 857 GLLIDTDYYINkQILPPLLRLLA 879
                                       ********************997 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.0   4.7e-45   1.7e-41       5     336 ..      29     349 ..      25     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 4.7e-45
                                       TSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCH CS
                    DNA_pol_B_exo1   5 gksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpne 81 
                                       g+ v v++ gf+pyfY+++  ++    + + +    +++++ +    + e v + + +gy+++p+++lkv+ ++p+ 
  gi|386002196|ref|YP_005920495.1|  29 GRPVTVQASGFRPYFYARID-ER---RIDSAI----DGIREMGL---SAEAVDRFRPVGYQRRPSKMLKVVAKDPKS 94 
                                       66788999***********9.22...233333....34433333...567888999********99*********** PP

                                       HHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE......................TEEEEGCC--C- CS
                    DNA_pol_B_exo1  82 lkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk......................kylvraegkisn 136
                                       ++ +r+ + +   + +vye+dv +  rflid ++ g++w +v+                      +++ r+ g +  
  gi|386002196|ref|YP_005920495.1|  95 VRDFRESVLSVPGVLEVYETDVLFKNRFLIDLDLGGMRWAEVEagnggsdletapagsatigpvpYTSLRPAGAGPA 171
                                       *******************************************9999886666666555555555555555555554 PP

                                       .SEEEEEETTTSCEETTT.........CC....S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS. CS
                    DNA_pol_B_exo1 137 cdveidcdvddliakpke.........se....pplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekep 200
                                            + +         +         ++    +plr l+FDIec  + g +p +e    p+i++s+++d     + 
  gi|386002196|ref|YP_005920495.1| 172 VAGGAERE---------KvpgaearggAKaipnAPLRTLAFDIECLPLHGAMPSPET--SPVIMVSLAFDPPY--KG 235
                                       44444444.........0454444444556899************************..**********7644..35 PP

                                       SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHC CS
                    DNA_pol_B_exo1 201 earklftlrecaseeeedfeltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakel 277
                                        + ++++ r  +               p+ +vl++  E+++L +f+e++k+ydPdv+ gYN  +FD+pY+++Ra+ l
  gi|386002196|ref|YP_005920495.1| 236 REDLVLVGRDLD--------------CPRGDVLCCGGERAMLARFVEILKDYDPDVLAGYNSAEFDFPYLEERARRL 298
                                       555778888888..............57889********************************************99 PP

                                       CTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHHHHHHHSSSSG-SHHH CS
                    DNA_pol_B_exo1 278 ykvklsklgrlnkggrskvseigfskqarekvkisgrihlDlyrvvkrklklpsYkLna 336
                                       ++    ++gr  +gg   v++i ++    + v+i gri++Dl+++v+ +++l+ Y+L +
  gi|386002196|ref|YP_005920495.1| 299 NVEV--RVGR--DGGPWRVRKIVNQ----TRVEITGRIVVDLLPLVRSSFSLKRYTLRN 349
                                       9733..4555..89***********....***************************975 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.1e-06    0.0041      36      87 ..     258     310 ..     252     418 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-06
                    DNA_pol_B_exo2  36 sekelikkffegvekkkpq.lVsfngrgfDlpvleyralkhgvsapkyfdegd 87 
                                        e++++++f e+++ + p  l ++n+ +fD+p le ra + +v+++   d g 
  gi|386002196|ref|YP_005920495.1| 258 GERAMLARFVEILKDYDPDvLAGYNSAEFDFPYLEERARRLNVEVRVGRDGGP 310
                                       5899*************983679***************999998876555555 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.8e-05      0.14      44     133 ..     259     372 ..     257     400 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                         RNase_H_2  44 ekailelflellekk..kalvtfngksFDvpflkrlfkkyklde......................eefrhiDLlke 96 
                                       e+a+l  f+e+l+++  + l  +n ++FD+p+l++++++ +++                         +  +DLl  
  gi|386002196|ref|YP_005920495.1| 259 ERAMLARFVEILKDYdpDVLAGYNSAEFDFPYLEERARRLNVEVrvgrdggpwrvrkivnqtrveiTGRIVVDLLPL 335
                                       5677777889999995556999***************9988887778888888888777766655555577888888 PP

                         RNase_H_2  97 lrkkkl.esysLksvekelgierreedlsGsqavklyq 133
                                       +r++   ++y L +   el    + +d++ +++ +l++
  gi|386002196|ref|YP_005920495.1| 336 VRSSFSlKRYTLRNASLELLGVEK-HDVDPKEMEALWT 372
                                       877655577888888877544444.4777777777764 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00026      0.93       3      26 ..      47      70 ..      45      72 .. 0.89
   2 ?    1.7   0.0     0.065   2.3e+02      10      23 ..      67      80 ..      64      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                             WIYLD  3 sgkeRidaAidamkelGfskeqvr 26
                                      + ++Rid Aid ++e+G s+e v 
  gi|386002196|ref|YP_005920495.1| 47 IDERRIDSAIDGIREMGLSAEAVD 70
                                      679****************99886 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.065
                             WIYLD 10 aAidamkelGfske 23
                                       A+d++++ G++++
  gi|386002196|ref|YP_005920495.1| 67 EAVDRFRPVGYQRR 80
                                      69*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (931 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.82u 0.37s 00:00:01.19 Elapsed: 00:00:00.57
# Mc/sec: 4922.93
//
Query:       gi|386002197|ref|YP_005920496.1|  [L=138]
Description: hypothetical protein Mhar_1509 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 926.38
//
Query:       gi|386002198|ref|YP_005920497.1|  [L=133]
Description: hypothetical protein Mhar_1510 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 956.58
//
Query:       gi|386002199|ref|YP_005920498.1|  [L=593]
Description: hypothetical protein Mhar_1511 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-57  190.0 141.6    2.9e-09   36.9   7.6    9.9 11  Pentapeptide_3   Pentapeptide repeats (9 copies)
    0.00045   19.8  42.1     0.0017   18.0   0.5   12.7 12  Pentapeptide     Pentapeptide repeats (8 copies)
  ------ inclusion threshold ------
        0.3   11.1   2.0       0.78    9.8   2.0    1.7  1  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.4     4e-11   2.4e-07       4      47 ..      45      89 ..      43      90 .. 0.90
   2 !   36.9   7.6   4.9e-13   2.9e-09       1      47 [.      64     111 ..      64     112 .. 0.96
   3 !   33.6   5.8   5.4e-12   3.2e-08       1      47 [.     108     154 ..     108     155 .. 0.97
   4 !   27.5   8.0   4.2e-10   2.5e-06       1      47 [.     130     176 ..     130     177 .. 0.97
   5 !   24.6   6.5   3.4e-09     2e-05       1      48 []     140     188 ..     140     188 .. 0.97
   6 !   30.9   2.1   3.8e-11   2.3e-07       8      47 ..     181     220 ..     178     221 .. 0.93
   7 !   32.2   8.2   1.4e-11   8.6e-08       1      47 [.     228     274 ..     228     275 .. 0.96
   8 !   29.6   6.7   9.6e-11   5.8e-07       1      47 [.     271     320 ..     271     321 .. 0.96
   9 !   25.4   9.6   1.9e-09   1.1e-05       1      44 [.     306     350 ..     306     351 .. 0.97
  10 !   31.5   4.6   2.4e-11   1.4e-07       5      47 ..     354     397 ..     352     398 .. 0.94
  11 !   27.6   4.8   3.9e-10   2.3e-06       1      44 [.     372     416 ..     372     420 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4e-11
                    Pentapeptide_3  4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47
                                      + ++++    ++t +g ++F+++ F g +dFs++ F +d+dF+ +
  gi|386002199|ref|YP_005920498.1| 45 SDVKKNIEIKNCTITGKVDFKETIFhGLVDFSDTKFMQDTDFKST 89
                                      5567777889********************************976 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 4.9e-13
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F++++F+g +dF+++ F ++++F++++F +++ F+++ F g++dF+ +
  gi|386002199|ref|YP_005920498.1|  64 FKETIFHGLVDFSDTKFMQDTDFKSTNFrDEVIFENTYFFGNADFEKV 111
                                       99**************************88***************976 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 5.4e-12
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       F+ +nF++ ++F  + F++ a F++a+F++a F++++Ft++++F+ +
  gi|386002199|ref|YP_005920498.1| 108 FEKVNFTRKVNFLQTKFEKNAIFEGANFTEAYFQRTNFTQNANFKSS 154
                                       899*****************************************976 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 4.2e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F+ganF+ a +F +++F++ a+F+++ F + ad+ ++ F  +vdF+++
  gi|386002199|ref|YP_005920498.1| 130 FEGANFTEA-YFQRTNFTQNANFKSSEFkEFADLKEVKFGNNVDFTNT 176
                                       9********.******************99*********999***987 PP

  == domain 5  score: 24.6 bits;  conditional E-value: 3.4e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsgat 48 
                                       F+++nF+++a+F  + F+  a+ ++  F +++dF ++ F+++ dF++a+
  gi|386002199|ref|YP_005920498.1| 140 FQRTNFTQNANFKSSEFKEFADLKEVKFgNNVDFTNTGFKKGGDFKHAH 188
                                       99**************************77*****************96 PP

  == domain 6  score: 30.9 bits;  conditional E-value: 3.8e-11
                    Pentapeptide_3   8 gaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       g  dF +a+F+g a F+n dF g + +++a F gdvdFs+ 
  gi|386002199|ref|YP_005920498.1| 181 GG-DFKHAHFNGNAIFRNVDFgGAIELENAKFLGDVDFSHI 220
                                       66.9*****************88****************96 PP

  == domain 7  score: 32.2 bits;  conditional E-value: 1.4e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                       F ++nFs+ ++F+++ Fsga +F++a+F g+a F+ a+F gd+ F+ a
  gi|386002199|ref|YP_005920498.1| 228 FYRTNFSKKTNFTNSGFSGA-YFESATFgGDAKFESATFGGDAKFDYA 274
                                       899*****************.9******88***************976 PP

  == domain 8  score: 29.6 bits;  conditional E-value: 9.6e-11
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF...gsadFsgarFtgdvdFsga 47 
                                       F+ a F + adF+ a F++ + Fs+a F   + a+F ga F+g++ F+++
  gi|386002199|ref|YP_005920498.1| 271 FDYAKFNNIADFSAAKFNNQTQFSSAEFsnnDIAWFKGAKFYGESKFKNT 320
                                       999***************************55****************98 PP

  == domain 9  score: 25.4 bits;  conditional E-value: 1.9e-09
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFg.sadFsgarFtgdvdF 44 
                                       F+ga F+g   F ++ F++ +sF ++ F+ + +F +++F g++ F
  gi|386002199|ref|YP_005920498.1| 306 FKGAKFYGESKFKNTQFNNETSFISSEFSiDTTFMNSTFFGNAIF 350
                                       99**************************88***********9988 PP

  == domain 10  score: 31.5 bits;  conditional E-value: 2.4e-11
                    Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                        F+g+a+F ++ F g + F+ +dF g+adF+++ F g++dF+ +
  gi|386002199|ref|YP_005920498.1| 354 DFKGNAYFNHTKFLGKTEFQKSDFnGNADFEDTEFLGETDFNQS 397
                                       69**********************88***************976 PP

  == domain 11  score: 27.6 bits;  conditional E-value: 3.9e-10
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdF 44 
                                       F+ + F g+adF+++ F g ++F+++ F g+ dF ++ F+g +++
  gi|386002199|ref|YP_005920498.1| 372 FQKSDFNGNADFEDTEFLGETDFNQSEFrGDLDFTKVYFEGLLNM 416
                                       88999***********************99*********976766 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.013        79      22      40 .]      74      93 ..      60      93 .. 0.71
   2 !    4.0   0.1    0.0068        40      15      24 ..     105     114 ..      96     125 .. 0.62
   3 !   18.0   0.5   2.8e-07    0.0017       1      19 [.     128     146 ..     126     169 .. 0.56
   4 ?    0.2   0.1       0.1   6.2e+02      15      31 ..     170     187 ..     158     191 .. 0.52
   5 !    3.9   0.3    0.0069        41      15      31 ..     192     209 ..     169     213 .. 0.68
   6 ?    0.2   0.0       0.1   6.1e+02      17      29 ..     227     234 ..     212     235 .. 0.62
   7 !    6.8   0.2   0.00089       5.3      21      40 .]     237     256 ..     235     256 .. 0.75
   8 ?    1.2   0.5     0.049   2.9e+02      21      39 ..     269     288 ..     264     289 .. 0.58
   9 ?    0.8   0.4     0.065   3.9e+02       7      15 ..     281     289 ..     280     313 .. 0.56
  10 ?   -1.2   0.0      0.29   1.7e+03      18      25 ..     306     313 ..     304     324 .. 0.45
  11 ?   -1.8   0.2      0.44   2.6e+03      26      40 .]     343     357 ..     339     357 .. 0.67
  12 ?    1.4   0.3     0.044   2.7e+02      21      26 ..     381     386 ..     358     401 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.013
                                      EECT-.B-TT-EECCEEECT CS
                      Pentapeptide 22 nLtgA.nlsgAdLsganLsg 40
                                      +++++  ++++d++ +n+++
  gi|386002199|ref|YP_005920498.1| 74 DFSDTkFMQDTDFKSTNFRD 93
                                      45555556777777777775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0068
                                       ECCCESEEEC CS
                      Pentapeptide  15 ganlsgAnLt 24 
                                       +a+++  n+t
  gi|386002199|ref|YP_005920498.1| 105 NADFEKVNFT 114
                                       3333333333 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.8e-07
                                       -B-TT-B-CCSCCEECCCE CS
                      Pentapeptide   1 AnLsgAnLsganLsganls 19 
                                       A+++gAn+++a+++++n++
  gi|386002199|ref|YP_005920498.1| 128 AIFEGANFTEAYFQRTNFT 146
                                       3444444444444444443 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.1
                                       ECCCESEEECT-.B-TT- CS
                      Pentapeptide  15 ganlsgAnLtgA.nlsgA 31 
                                       +++++++ + +  ++ +A
  gi|386002199|ref|YP_005920498.1| 170 NVDFTNTGFKKGgDFKHA 187
                                       344444444444444444 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.0069
                                       ECCCESEEECT-.B-TT- CS
                      Pentapeptide  15 ganlsgAnLtgA.nlsgA 31 
                                       +a +++ ++ gA +l++A
  gi|386002199|ref|YP_005920498.1| 192 NAIFRNVDFGGAiELENA 209
                                       456666666666555555 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.1
                                       CCESEEECT-B-T CS
                      Pentapeptide  17 nlsgAnLtgAnls 29 
                                       n++++     n+s
  gi|386002199|ref|YP_005920498.1| 227 NFYRT-----NFS 234
                                       44444.....443 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.00089
                                       EEECT-B-TT-EECCEEECT CS
                      Pentapeptide  21 AnLtgAnlsgAdLsganLsg 40 
                                       +n+t++ +sgA ++ a + g
  gi|386002199|ref|YP_005920498.1| 237 TNFTNSGFSGAYFESATFGG 256
                                       78888888888888888765 PP

  == domain 8  score: 1.2 bits;  conditional E-value: 0.049
                                       EEECT-B-TT.-EECCEEEC CS
                      Pentapeptide  21 AnLtgAnlsg.AdLsganLs 39 
                                       A++++A +++ Ad+s a+++
  gi|386002199|ref|YP_005920498.1| 269 AKFDYAKFNNiADFSAAKFN 288
                                       56666666654555555554 PP

  == domain 9  score: 0.8 bits;  conditional E-value: 0.065
                                       B-CCSCCEE CS
                      Pentapeptide   7 nLsganLsg 15 
                                       ++s a++++
  gi|386002199|ref|YP_005920498.1| 281 DFSAAKFNN 289
                                       444444432 PP

  == domain 10  score: -1.2 bits;  conditional E-value: 0.29
                                       CESEEECT CS
                      Pentapeptide  18 lsgAnLtg 25 
                                       ++gA+++g
  gi|386002199|ref|YP_005920498.1| 306 FKGAKFYG 313
                                       55555554 PP

  == domain 11  score: -1.8 bits;  conditional E-value: 0.44
                                       -B-TT-EECCEEECT CS
                      Pentapeptide  26 AnlsgAdLsganLsg 40 
                                       + + +A ++ ++++g
  gi|386002199|ref|YP_005920498.1| 343 TFFGNAIFMLSDFKG 357
                                       556777777777776 PP

  == domain 12  score: 1.4 bits;  conditional E-value: 0.044
                                       EEECT- CS
                      Pentapeptide  21 AnLtgA 26 
                                       A++ ++
  gi|386002199|ref|YP_005920498.1| 381 ADFEDT 386
                                       333333 PP

>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.0   0.00013      0.78      11      48 ..     503     540 ..     502     541 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                   TMEMspv1-c74-12  11 vvivLgiFlyiGLsiyqKikqirgkkk.DKKeierkedk 48 
                                       v+i  +iF+ +  +i+ Ki  ir kk+  K +ie+k  k
  gi|386002199|ref|YP_005920498.1| 503 VIIPASIFV-LSFAIFYKIINIRSKKRrSKEKIEEKSFK 540
                                       555566776.6899*********998626778**99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3551.93
//
Query:       gi|386002200|ref|YP_005920499.1|  [L=336]
Description: O-sialoglycoprotein endopeptidase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-89  298.3   0.3    7.7e-89  298.0   0.3    1.0  1  Peptidase_M22   Glycoprotease family
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.062   12.9   0.0    1.3  1  Carbam_trans_N  Carbamoyltransferase N-terminus
      0.041   14.0   0.2        7.2    6.7   0.0    2.2  2  PPE             PPE family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.0   0.3   1.3e-92   7.7e-89       8     271 .]      38     303 ..      34     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 298.0 bits;  conditional E-value: 1.3e-92
                                       EEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--E CS
                     Peptidase_M22   8 asqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPl 84 
                                       ++++++++++GG++P++a+++H+ ++ p++ e+l++a  +   +da+a+++gPGl+++Lr ++++A++lal +++Pl
  gi|386002200|ref|YP_005920499.1|  38 EESATYVPAKGGIHPREAAQHHAGHMAPVVGEVLDAARRDGIAIDAVAFSQGPGLGPCLRTVATAARALALRFGVPL 114
                                       344556799******************************************************************** PP

                                       EEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHH CS
                     Peptidase_M22  85 vgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkiekl 161
                                       vgVnh++ah++ ++ +++  +Pvvl+vsGg++qv++ + gry+i+getld+ +g+aldk+ar +glp+pggpk+e l
  gi|386002200|ref|YP_005920499.1| 115 VGVNHCIAHIEVGKWKTGAADPVVLYVSGGNSQVLALRRGRYRIFGETLDISVGNALDKFARQVGLPHPGGPKLEAL 191
                                       **************9998899****************99************************************** PP

                                       HCTC.S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGX CS
                     Peptidase_M22 162 akeg.kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaan 236
                                       ak++ ++i +p+++kg+d+sfsGl ta++++++k + +d++ sfqe+++++lve+teral++ ++ke++++GGv+an
  gi|386002200|ref|YP_005920499.1| 192 AKSAkEYIPLPYVVKGMDLSFSGLSTAAAQAAKKyDLADVCSSFQETAFAMLVEVTERALAHAEKKEVLLVGGVGAN 268
                                       **99788*************************8877***************************************** PP

                                       HHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 237 krLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       +rLre+l+ ++ee+g+++++P+++++ dn+ mia+
  gi|386002200|ref|YP_005920499.1| 269 SRLREMLNIMCEERGAQFFVPEMRFMGDNGSMIAY 303
                                       *********************************97 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.062     261     332 ..     222     299 ..     206     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                    Carbam_trans_N 261 arekde...dlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklN..sallesglFedvwvq..PaanDs 330
                                       a++k     d+  s+q+    ++vev++ + ++ + +   l GGv++N  l   ++++ +    + +v+   +++D+
  gi|386002200|ref|YP_005920499.1| 222 AAKK-YdlaDVCSSFQETAFAMLVEVTERALAHAEKKEVLLVGGVGANSRLRemLNIMCEERGAQFFVPemRFMGDN 297
                                       2222.1345***************************************87651134555555566666522467777 PP

                    Carbam_trans_N 331 Gs 332
                                       Gs
  gi|386002200|ref|YP_005920499.1| 298 GS 299
                                       76 PP

>> PPE  PPE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0012       7.2      10      61 ..      85     137 ..      81     142 .. 0.88
   2 ?    4.8   0.3    0.0045        27      72     125 ..     215     268 ..     211     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                                       HHHHS--SHHHHHH.HHHHHHHHHHHHHHHHHHHHHHTTTT.TTS-SHHHHHH CS
                               PPE  10 llyaGpgsgpllaA.aaaWdgLaaelasaaaelesvlaelaaeaWqGpssaam 61 
                                         ++Gpg gp l   a+a ++La  +      +++ +a ++ ++W+  +++ +
  gi|386002200|ref|YP_005920499.1|  85 AFSQGPGLGPCLRTvATAARALALRFGVPLVGVNHCIAHIEVGKWKTGAADPV 137
                                       5689******8864399*****************************9999866 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHT-TTSTT CS
                               PPE  72 LsaaaaqaeeaAaqaeaaaaaYeaAlaamvppaeiaanraelaalvatnffGqn 125
                                       Ls+aaaqa+++   a++  +  e+A+a+ v+ +e a  +ae++ ++    +G+n
  gi|386002200|ref|YP_005920499.1| 215 LSTAAAQAAKKYDLADVCSSFQETAFAMLVEVTERALAHAEKKEVLLVGGVGAN 268
                                       78999999999999999999999**********999999998887766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2438.12
//
Query:       gi|386002201|ref|YP_005920500.1|  [L=494]
Description: Phosphoribosylamine--glycine ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-60  202.3   0.0    5.9e-59  199.1   0.0    2.1  2  GARS_A    Phosphoribosylglycinamide synthetase, ATP-grasp (A)
      9e-24   84.1   0.0    2.2e-23   82.9   0.0    1.7  1  GARS_N    Phosphoribosylglycinamide synthetase, N domain
    2.1e-22   79.2   1.4    2.8e-22   78.8   0.2    1.9  2  GARS_C    Phosphoribosylglycinamide synthetase, C domain


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.1   0.0   9.8e-63   5.9e-59       1     194 []     128     349 ..     128     349 .. 0.95
   2 ?    0.6   0.0     0.069   4.1e+02     146     183 ..     390     430 ..     386     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 199.1 bits;  conditional E-value: 9.8e-63
                                       HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE....EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS CS
                            GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeataka....lVvKadglaagKgvivakseeealkavkeilek 73 
                                       +sK +akdll+++g+p++++++f dpeea  y++++ a++    lVvKadglaagKg iv+ seeea +av+ i+++
  gi|386002201|ref|YP_005920500.1| 128 GSKGYAKDLLRDIGVPIPRHRSFGDPEEALGYVSSFYADNpgmnLVVKADGLAAGKGSIVCGSEEEAASAVQRIMVE 204
                                       69********************************99877667889*****************************987 PP

                                       .-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCE..................EEEECECEE CS
                            GARS_A  74 .kkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDk..................gpnTGGmGa 131
                                        + fGeag++vv+Ee+leG E+ ++a++dg+tv pl++a d+kr++   +                  +pnTGGmG 
  gi|386002201|ref|YP_005920500.1| 205 pRLFGEAGRRVVLEERLEGRELMFFAVTDGRTVLPLESAMDYKRAFAPGEevairlynrlsgdpnldhNPNTGGMGG 281
                                       478******************************************987777************************** PP

                                       EES-TTS-HHHHHHHHHHTHHHHHHHHHCT.T---EEEEEEEEEEE.TTE...EEEEEEESS--TTCH CS
                            GARS_A 132 yspapvvteellekikeeileptveglkke.gipfkGvLyaglmlv.edg...pkvlefnvRfgDpet 194
                                       ysp+p++  +l e+i+eei  pt+ g++++ g +++G++y glm++ e+g   pkvle+nvR gDpe+
  gi|386002201|ref|YP_005920500.1| 282 YSPHPWLDGDLAERIMEEIAVPTIRGFRERsGFEYRGMIYFGLMVSeEEGervPKVLEINVRLGDPEA 349
                                       ***************************9863689************6666****************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.069
                                       HHHHTHHHHHHHHHCTT---EEEEEEEEEEE.TTE..EEEE CS
                            GARS_A 146 ikeeileptveglkkegipfkGvLyaglmlv.edg..pkvl 183
                                       i  ++++p++ g+++e+  + G  y+++ +   d+  p vl
  gi|386002201|ref|YP_005920500.1| 390 ISGRVVKPAASGVQEERPGYPGSHYTNMPIRgLDKvdPDVL 430
                                       56789*********************998864333456666 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   3.6e-27   2.2e-23       2      90 .]      24     127 ..      23     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 3.6e-27
                                       EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG................TTHHHHHHHHHHCTESEEEE-SHHH CS
                            GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt................edlealvefakeekidlvvvGpeap 62 
                                       kvLvv  GGR +a+a+++a+sp ve+vyvapgNag                 +++++l++fa++e++dl++vGpe  
  gi|386002201|ref|YP_005920500.1|  24 KVLVVDAGGRGNAIAHAFARSPLVERVYVAPGNAGSsmiekceialskgrplKEIADLATFARREAVDLTFVGPEGY 100
                                       8***********************************999999999988888877889******************** PP

                                       HHTTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  63 LvaGvadaleeekgikvfGpskeaAqlE 90 
                                       L +G+++ ++ee g++++Gp++ea+ lE
  gi|386002201|ref|YP_005920500.1| 101 LSDGIVNLFSEE-GLEAVGPRREASVLE 127
                                       *********877.************998 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.9   1.1e+04      38      50 ..      21      33 ..      16      44 .. 0.55
   2 !   78.8   0.2   4.7e-26   2.8e-22       9      79 ..     407     492 ..     399     493 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                                      -SSEEEEEEEEES CS
                            GARS_C 38 sGGRvlavvavge 50
                                      sG +vl v a g 
  gi|386002201|ref|YP_005920500.1| 21 SGAKVLVVDAGGR 33
                                      5555555554433 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 4.7e-26
                                       TTTTSS--ST-EEBS.....TTEEEEESSEE..........EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TT CS
                            GARS_C   9 kGYPgsyekgkeitg.....egvkvfhagtk..........lvtsGGRvlavvavgetleeArakayeavkkikfeg 70 
                                        GYPgs  ++++i+g      +v v+h+gt+          l t+GGRvl+vv+ g+tl +Ar++aye++++i+f+g
  gi|386002201|ref|YP_005920500.1| 407 PGYPGSHYTNMPIRGldkvdPDVLVYHNGTAfgrdargaerLFTTGGRVLTVVGRGATLPAARERAYENIRRIRFNG 483
                                       59***********99*****8899*******99******************************************** PP

                                       EE--STTTH CS
                            GARS_C  71 lfyRkDIGa 79 
                                       + yR+DIG 
  gi|386002201|ref|YP_005920500.1| 484 IRYRRDIGL 492
                                       *******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3648.84
//
Query:       gi|386002202|ref|YP_005920501.1|  [L=441]
Description: glutamine synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-134  446.3   0.0   7.4e-134  446.1   0.0    1.0  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    7.4e-31  105.7   0.0    1.3e-30  105.0   0.0    1.4  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
     0.0057   16.5   0.0      0.016   15.0   0.0    1.8  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.1   0.0  1.2e-137  7.4e-134       2     345 .]     105     437 ..     104     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 446.1 bits;  conditional E-value: 1.2e-137
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR+vlkra+++++e+G++++vgpElEFflf+ e+ ++            ++rp++ +gyf++ pvd ae++rrei
  gi|386002202|ref|YP_005920501.1| 105 GDPRYVLKRAMKKAEEMGYSMNVGPELEFFLFNMENGRA------------TTRPHDFAGYFDFGPVDLAEEIRREI 169
                                       79*******************************887744............78999********************* PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       v al+++g+++eashhEva gQ+Ei++ + +al++aDnvvtfK+v++++A k+gl+atFmpKp++g++GsgmHv++S
  gi|386002202|ref|YP_005920501.1| 170 VLALTDMGFKIEASHHEVARGQHEIDFTYGEALRTADNVVTFKYVTRTIAMKNGLAATFMPKPIYGAAGSGMHVNIS 246
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-T CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipas 232
                                       l+   ++n+f+d+d++++ls+larhf gGll+ha+a+ta+t+p +nSYkRlv+g+eaPv++ w+  NRs l+R+p +
  gi|386002202|ref|YP_005920501.1| 247 LF-RGEENAFFDPDAKMQLSDLARHFAGGLLEHAPAITAVTNPLINSYKRLVSGFEAPVYIGWSGPNRSSLIRVPSG 322
                                       **.788*********************************************************************** PP

                                       SGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCS CS
                        Gln-synt_C 233 kekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeed 307
                                       ++ ++r+E+R+pd+s+ PYL +Aa+laAgldG+++k++pg+pv+ ++yels+eer  +gi+ lP++l+eAl++leed
  gi|386002202|ref|YP_005920501.1| 323 RGLSTRLEFRSPDPSCSPYLGFAAILAAGLDGVKRKIDPGDPVDMNIYELSDEERdrLGIKLLPSNLREALDRLEED 399
                                       *******************************************************99******************** PP

                                       HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 308 ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                        +++++lge+v++++++l + E++ ++  v++we+ery
  gi|386002202|ref|YP_005920501.1| 400 RIVRDALGEHVFANFMRLGSLEWKMYNNFVHPWEVERY 437
                                       ************************************98 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   2.1e-34   1.3e-30       1      83 []      15      98 ..      15      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 2.1e-34
                                      T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEEEE CS
                        Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktarvi 77
                                      +v+ ++lqFtDi+g +k+v+ipa++l  +al+ g +FDGSsiegfa+i+eSDmlL+Pd+s+++i+P+r+++  ++ar+i
  gi|386002202|ref|YP_005920501.1| 15 NVESLRLQFTDIQGLVKSVSIPATRL-GKALDSGTGFDGSSIEGFARIQESDMLLRPDISSFAILPWRAREnrNVARLI 92
                                      6899**********************.******************************************8889****** PP

                                      EEEE-T CS
                        Gln-synt_N 78 cdvydp 83
                                      cdvy+p
  gi|386002202|ref|YP_005920501.1| 93 CDVYKP 98
                                      ****97 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-06     0.016       6      65 ..       7      64 ..       3     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                                      .....------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT CS
                      Gln-synt_N_2  6 vveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidev 65
                                      ++e ++ ++ve +++ ++d +G+++  ++p ++L + L sG G+    ++++    i+e+
  gi|386002202|ref|YP_005920501.1|  7 LLETIRDRNVESLRLQFTDIQGLVKSVSIPATRLGKALDSGTGFDG--SSIEGFARIQES 64
                                      68999**************************************964..344445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 2446.85
//
Query:       gi|386002203|ref|YP_005920502.1|  [L=106]
Description: hypothetical protein Mhar_1517 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.6   0.4        0.4   10.8   0.0    2.1  2  Mrr_N     Mrr N-terminal domain
       0.12   12.7   1.6       0.34   11.3   0.3    1.9  2  TBCA      Tubulin binding cofactor A
       0.15   11.4   0.5       0.64    9.4   0.2    1.8  2  Sec15     Exocyst complex subunit Sec15-like


Domain annotation for each model (and alignments):
>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.037   2.2e+02      19      43 ..      11      35 ..       9      39 .. 0.83
   2 ?   10.8   0.0   6.7e-05       0.4      18      65 ..      53     104 ..      39     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.037
                             Mrr_N 19 rlkeirervaerfglseeeraellp 43
                                      ++ke+ + +++r +++++  + l++
  gi|386002203|ref|YP_005920502.1| 11 SIKEVNRNLQDRESMTDYSIEYLKK 35
                                      6799999999999999998887765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.7e-05
                             Mrr_N  18 hrlkeirervaerfglseeeraellpsgkq....trfknrvgWartyLkkag 65 
                                       +   e+++r  + ++++  e+ae+l++ k+    ++++n  +War++L  ag
  gi|386002203|ref|YP_005920502.1|  53 KEEIEVVNRSGKAAKFKMAEVAEMLTDTKKilefNLIDNVDRWARSKLEGAG 104
                                       233356666677789**********999999999**************9987 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   5.7e-05      0.34      41      86 ..      10      55 ..       8      58 .. 0.88
   2 ?    1.5   0.2     0.063   3.7e+02      30      56 ..      57      83 ..      49      90 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                              TBCA 41 ydlkkqeevleetkamipdlkkrlekavekLeelleeeeeleetee 86
                                      +++k+ ++ l++ ++m   + + l+ka+ +L+e+l++ +  + +ee
  gi|386002203|ref|YP_005920502.1| 10 WSIKEVNRNLQDRESMTDYSIEYLKKACRDLSEILAAGKAADLKEE 55
                                      6899999*****************************9976554554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.063
                              TBCA 30 eklkadgdedeydlkkqeevleetkam 56
                                      e ++  g++ ++++ +  e+l +tk++
  gi|386002203|ref|YP_005920502.1| 57 EVVNRSGKAAKFKMAEVAEMLTDTKKI 83
                                      444444433344444445555555554 PP

>> Sec15  Exocyst complex subunit Sec15-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.053   3.1e+02       1      15 [.       2      16 ..       2      29 .. 0.73
   2 ?    9.4   0.2   0.00011      0.64     103     161 ..      30      93 ..      26     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.053
                                      HHHHHHHT------- CS
                             Sec15  1 Yekvlkvcwlkesel 15
                                      Y+kv+++cw  ++ +
  gi|386002203|ref|YP_005920502.1|  2 YDKVITICWSIKEVN 16
                                      9********877643 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00011
                                       HHTTTHHHHHHTTS---S.........TTT--TT--...--THHHHHHHHHHHHHHHHHHHHHH CS
                             Sec15 103 leyfetackelekllaqerssqrg..gnieqnsaee...iklkaskkfkearkaAekkifelvd 161
                                       +ey+++ac+ l+++la+ ++ +     ++ ++s ++      +  +++++++k  e ++++ vd
  gi|386002203|ref|YP_005920502.1|  30 IEYLKKACRDLSEILAAGKAADLKeeIEVVNRSGKAakfKMAEVAEMLTDTKKILEFNLIDNVD 93 
                                       79***************98887775533445555552322234456999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 694.44
//
Query:       gi|386002204|ref|YP_005920503.1|  [L=282]
Description: putative endonuclease 4 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-33  115.7   0.0    2.2e-33  115.5   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.22   11.7   0.0    1.2  1  NAGPA         Phosphodiester glycosidase


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   2.5e-37   2.2e-33       1     210 []      18     237 ..      18     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 2.5e-37
                                       HHHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHH CS
                      AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear...reesvdal 72 
                                       +++a++aG d++++f r+++ ++ +   +e + e+r+ l+ +g+      +  ++   + ++  ++    ++sv+al
  gi|386002204|ref|YP_005920503.1|  18 VDRAEKAGCDTFQIFSRNPRGWRFKeiPEEVAMEFRRKLALTGIS-----PVVDHMPYLPNLATPKedvYARSVEAL 89 
                                       5899*******************8877777777777777777777.....33333333333233334588999**** PP

                                       HHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHH CS
                      AP_endonuc_2  73 kraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarl 147
                                        +++e++a LG+p+lv+h G   ++ ++++e  +er ae++ +++    ++ v l+lEt+  s ++ g+  e+la++
  gi|386002204|ref|YP_005920503.1|  90 AEELERCAILGIPYLVTHLG---SHLDSGKEGGFERTAEGISRALSSV-ENEVILLLETTSDSKNSVGGsfEDLAEI 162
                                       ********************...************************7.699****************9******** PP

                                       HHHHTTTT.EEEEEEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 148 ldavdspn.vgvclDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                       +++v+++  vg c+Dt+H++ a       e  +++++ +++      +k vH++D+kg+lg++ drh+ ig Gei
  gi|386002204|ref|YP_005920503.1| 163 MRRVGREDrVGACFDTCHAFVAgyelrtAEGAAETMESFDEAvgisrLKVVHLNDSKGPLGSKLDRHEHIGLGEI 237
                                       *************************9998888888888888888889**************************97 PP

>> NAGPA  Phosphodiester glycosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.22      62     129 ..      93     167 ..      71     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                             NAGPA  62 vkea.vgagplLv.kngkivktsadggsgrapRtaiGvt.....adgtllllv...vdgrqsaGatlkelaellkkl 128
                                       ++   + + p+Lv   g   +++++gg     Rta G++      +++++ll     d ++s G ++ +lae++++ 
  gi|386002204|ref|YP_005920503.1|  93 LERCaILGIPYLVtHLGSHLDSGKEGG---FERTAEGISralssVENEVILLLettSDSKNSVGGSFEDLAEIMRRV 166
                                       444436555999977777777888887...5********99988555555554333555888************998 PP

                             NAGPA 129 G 129
                                       G
  gi|386002204|ref|YP_005920503.1| 167 G 167
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1854.19
//
Query:       gi|386002205|ref|YP_005920504.1|  [L=199]
Description: hypothetical protein Mhar_1519 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-06   26.4   9.6     0.0056   16.9   0.7    2.2  2  DUF2878          Protein of unknown function (DUF2878)


Domain annotation for each model (and alignments):
>> DUF2878  Protein of unknown function (DUF2878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   3.1   3.2e-06     0.058      43     119 ..       4      89 ..       1     101 [. 0.71
   2 !   16.9   0.7   3.1e-07    0.0056      32     100 ..     108     177 ..      91     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-06
                           DUF2878  43 psrkaelklllavlllGlllDslllalgvlsfaa......lsasllPlWll...lLWllfaltlnhslawlrkrpll 110
                                        ++++ ++l l+ ++lG l++++ +a g+  +a+      ++++ +P W     ++Wl+++ +l       +++  l
  gi|386002205|ref|YP_005920504.1|   4 GHPRRAAALALTGAVLGPLTEAACVAGGLWIYAEtgglpyVPPWNFPAWASfppAIWLIVGAVLGPGWMRGSSSRAL 80 
                                       578899999999**********************9766666667777776433357777776666554444445555 PP

                           DUF2878 111 aallgavgg 119
                                       a+ l++vg+
  gi|386002205|ref|YP_005920504.1|  81 ALALAGVGA 89 
                                       555555655 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.1e-07
                           DUF2878  32 llllllhlalspsrkaelklllavlllGlllDslllalgvlsfaa.lsasllPlWlllLWllfaltlnhs 100
                                         +l++ ++l+ +++++l+++ a +llG l++sl + +g  s++a ++   +P +++l  ++f+  l h+
  gi|386002205|ref|YP_005920504.1| 108 GSVLAAAVVLAFRERSTLAMMGAGALLGPLVESLPISAGAWSYSApADLFGMPGYMILAYAIFGALLGHA 177
                                       333333455678999999999************************7777889************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1322.23
//
Query:       gi|386002206|ref|YP_005920505.1|  [L=147]
Description: Response regulator receiver protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   73.7   0.0    1.5e-20   73.4   0.0    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.18   11.8   0.0    1.3  1  Rad10         Binding domain of DNA repair protein Ercc1 (rad
       0.14   12.1   0.0       0.27   11.2   0.0    1.4  2  TORC_M        Transducer of regulated CREB activity middle do


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 !   73.4   0.0   2.5e-24   1.5e-20       1     109 [.      24     141 ..      24     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.5e-24
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHH....HHHH....ESEEEEESSCSSSEHHHHHHHHHHC CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealell....keek....vdlillDinmpgmdGlellkeiree 68 
                                       +l+v+D+p+ +el+ +ll++  + +++  a+d++eal++l    +  +    +dlillDi++p+++G+ell+++++ 
  gi|386002206|ref|YP_005920505.1|  24 ILLVEDNPDDVELTCRLLRRICLeRDIFLATDAEEALKILesilE--EggalPDLILLDIKLPRLSGMELLERLKAS 98 
                                       89************9999954442478899999999999955442..14589************************* PP

                                       T..TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHH CS
                      Response_reg  69 d..pelpviiltahseeedavealkagaddflsKpfdpeeLlk 109
                                       +  + +pv++lt+   +e++++ +++ga+ +l Kp++++eLl 
  gi|386002206|ref|YP_005920505.1|  99 PelRGIPVVMLTGSIVSEHIQKSYDLGAVSYLLKPISEDELLL 141
                                       99999***********************************986 PP

>> Rad10  Binding domain of DNA repair protein Ercc1 (rad10/Swi10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     3e-05      0.18      65     112 ..      20      65 ..       5      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                             Rad10  65 yklrvlLvlvDvedseevlkeLnkicilndltlllawsaeeaarylet 112
                                       +kl++lLv  + +d e +++ L +ic+  d  ++la  aeea ++le+
  gi|386002206|ref|YP_005920505.1|  20 NKLKILLVEDNPDDVELTCRLLRRICLERD--IFLATDAEEALKILES 65 
                                       6899*****999***************965..799*********9996 PP

>> TORC_M  Transducer of regulated CREB activity middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.7     1e+04      77      88 ..       7      18 ..       4      21 .. 0.74
   2 ?   11.2   0.0   4.5e-05      0.27      87     122 ..      49      84 ..      45      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.7
                            TORC_M 77 rpkscevpgini 88
                                       pks ev g   
  gi|386002206|ref|YP_005920505.1|  7 DPKSSEVRGERP 18
                                      589999988665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.5e-05
                            TORC_M  87 nifpspdqeatlsllpaalnTGGsLPDLtnlhfpsP 122
                                       +if  +d e +l  l + l+ GG LPDL  l ++ P
  gi|386002206|ref|YP_005920505.1|  49 DIFLATDAEEALKILESILEEGGALPDLILLDIKLP 84 
                                       79**************************99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1018.46
//
Query:       gi|386002207|ref|YP_005920506.1|  [L=305]
Description: hypothetical protein Mhar_1521 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-21   75.4   0.1    5.2e-20   72.5   0.1    2.0  1  Radical_SAM   Radical SAM superfamily
    1.3e-17   63.8   0.0    2.6e-17   62.9   0.0    1.5  1  Wyosine_form  Wyosine base formation


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.1   5.8e-24   5.2e-20       2     166 ..      51     228 ..      50     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 5.8e-24
                                       EEESEESS--TTTSCCTT..........................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet..........................vrregrgrslsveeileevkelkaekgvkevil 52 
                                       ++t  Cn+rC +C+rp +                           + +g + + +    lee+k+      +++ i+
  gi|386002207|ref|YP_005920506.1|  51 TPTLLCNHRCLHCWRPIDeipatsgewiepeelldgilseqrrlISGYGGAPETTDPGRLEEAKSP-----AHVAIS 122
                                       78889************9666655555555555555555544442222222222222233333333.....566677 PP

                                       ESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM  53 gggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfe 128
                                       ++gep+lyp + el+e+ +++   g++ +++tngt p     e+  e ++++++++l+a+d+e++++  n r +t+ 
  gi|386002207|ref|YP_005920506.1| 123 LMGEPTLYPMIGELVEEVKRR---GMTAFLVTNGTSP-----EAVGEVRPTQLYISLNAPDEETYRQVSNpRDDTWG 191
                                       7*******************8...************9.....99999999*************************** PP

                                       HHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 129 evlealeklreagikrvvdrivglpGendeeleellel 166
                                       ++le+l+++r++  +  v+r+++ ++ n ++ + +++l
  gi|386002207|ref|YP_005920506.1| 192 RFLESLDMMRDSPSR-RVVRLTLARNLNLKDPRGYARL 228
                                       ************888.7999999999999988877776 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   2.9e-21   2.6e-17       2      63 .]     232     292 ..     231     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 2.9e-21
                                       HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       aepdFvEvKay+++G sr+rL ++++P+h+ev  fa++l++ ++ Y l    + Srv+ll+r
  gi|386002207|ref|YP_005920506.1| 232 AEPDFVEVKAYMHLGLSRKRLGRDAMPTHDEVMGFARELSDILG-YPLKNHVPLSRVALLSR 292
                                       89******************************************.**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1876.50
//
Query:       gi|386002208|ref|YP_005920507.1|  [L=246]
Description: Periplasmic copper-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-17   63.8  15.4    1.9e-17   63.4  15.4    1.2  1  NosD             Periplasmic copper-binding protein (NosD)
    1.5e-09   37.9  23.1    2.8e-09   37.0  23.0    1.5  1  Beta_helix       Right handed beta helix region
      0.001   18.4  13.6       0.06   12.7  13.6    2.1  1  DUF1565          Protein of unknown function (DUF1565)
  ------ inclusion threshold ------
       0.14   12.1   0.1       0.29   11.1   0.1    1.6  1  KOW              KOW motif
        1.6    8.5  12.0        4.8    7.0  12.0    2.0  1  Pectate_lyase_3  Pectate lyase superfamily protein


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 !   63.4  15.4   5.3e-21   1.9e-17      83     238 ..      95     245 ..      89     246 .] 0.81

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 5.3e-21
                              NosD  83 sGialmsssnn.tlenNtisnnen....yGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGi 153
                                       +G +++ + +  ++++ +++n+ n    +Gi ++ s+n+ti+ N +s n ++Gi l ++ + t++gN++++n ++Gi
  gi|386002208|ref|YP_005920507.1|  95 NGSCITVNADGaVVDKMRVTNSGNlsgdAGIQVQ-SNNCTITSNIASgNGGSGIILVGARNCTLRGNTVSNN-TVGI 169
                                       4555555555556777777777777777788886.67799********************************.**** PP

                              NosD 154 lllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDt....pYe 226
                                       l l++s +n+++nN + nn+ +++  +++ n Wn                GN++s ++++D ++D i+D+     + 
  gi|386002208|ref|YP_005920507.1| 170 L-LTNSADNLVFNNRLYNNT-DMDAFDDGVNLWNDGA------------IGNHYSSFNCTDLNNDTICDVivnaVFA 232
                                       *.**************6665.554444459***9999............9*******************74444677 PP

                              NosD 227 indgv.iDylplv 238
                                       i++g  iD lplv
  gi|386002208|ref|YP_005920507.1| 233 IPGGGsIDDLPLV 245
                                       775555*****97 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 !   37.0  23.0   7.7e-13   2.8e-09       3      99 ..      99     201 ..      67     230 .. 0.58

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 7.7e-13
                                       EEE-SS-E.EEESEEEES-....SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT CS
                        Beta_helix   3 isingssnvtiknntisns....ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf 75 
                                       i +n ++   ++++ ++ns    g++Gi++++++ ++i++n  ++n+gsGi + g+ n+t+++nt+s+n+ +gi l+
  gi|386002208|ref|YP_005920507.1|  99 ITVNADGA-VVDKMRVTNSgnlsGDAGIQVQSNN-CTITSNIASGNGGSGIILVGARNCTLRGNTVSNNT-VGILLT 172
                                       34444444.5555555555555555555555544.35555555556666666666666666666666555.666666 PP

                                       --S--EEES-EEES-.....SS-SEE-TT CS
                        Beta_helix  76 gasnnlienneitdn.....ggsGiylny 99 
                                       ++  nl+ nn+ ++n      ++G++l +
  gi|386002208|ref|YP_005920507.1| 173 NSADNLVFNNRLYNNtdmdaFDDGVNLWN 201
                                       66666666666666643333222444433 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7  13.6   1.7e-05      0.06      17     196 ..      44     200 ..      40     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                           DUF1565  17 tiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagkkvgplisgggddlsgvqnvt 93 
                                       +i  A+ +a +g+v+ +  Gt+s +   t P+v+       G+    G            pli+ +g+  s      
  gi|386002208|ref|YP_005920507.1|  44 SIQEAIDIASPGDVVLVRSGTFSGNVNVTKPIVL------RGEMWHGGD----------LPLINAQGNG-S----CI 99 
                                       5778888888888888888888888888888888......455555555..........4566666655.2....22 PP

                           DUF1565  94 ivlaneatiaGvtitNpni.lkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGnsilfeknGia 169
                                        v a+ a +  +++tN      + g+ ++s + +i +N  +gn++ Gi            + +  Gn++ +++ Gi 
  gi|386002208|ref|YP_005920507.1| 100 TVNADGAVVDKMRVTNSGNlSGDAGIQVQSNNCTITSNIASGNGGSGIILVGA------RNCTLRGNTVSNNTVGIL 170
                                       356677889999*****66266789**********************976555......578899999999999998 PP

                           DUF1565 170 isgasaa..venkienNiivkNli.Gvvan 196
                                        ++++     +n++ nN+ +     Gv+  
  gi|386002208|ref|YP_005920507.1| 171 LTNSADNlvFNNRLYNNTDMDAFDdGVNLW 200
                                       776665533567777776444333455544 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   8.2e-05      0.29       1      14 [.      54      67 ..      54      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                                      TTSEEEESSSTTTT CS
                               KOW  1 pGdhVkVvsGphkG 14
                                      pGd+V V sG++ G
  gi|386002208|ref|YP_005920507.1| 54 PGDVVLVRSGTFSG 67
                                      8***********98 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  12.0    0.0013       4.8      64     161 ..      86     183 ..      41     228 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0013
                                       TTEEEEE-TT-......SS--SEEES-TTT-..-EEEEEEEEEEEGGGG-SS---S.SEEEES-EEEEEEEEEEES- CS
                   Pectate_lyase_3  64 grpvlkaaaaf......vgaglidgdpyvsggsealiatnnfyrqirnlkiditav.apgatgihwqtaqatslenv 133
                                       + p + a+++       +  +++d+ +++++   +l  ++ + +q  n +i+++ +  +g++gi  + a++ +    
  gi|386002208|ref|YP_005920507.1|  86 DLPLINAQGNGscitvnADGAVVDKMRVTNS--GNLSGDAGIQVQSNNCTITSNIAsGNGGSGIILVGARNCT---- 156
                                       5555555444433332111112222222212..3444455555555555554443322222333333333333.... PP

                                       SSEEE-SSS---TT---SS--EEEE.ES- CS
                   Pectate_lyase_3 134 efemseasgtkhqgifiengsggfl.ndl 161
                                        ++ ++ s ++ +gi++ n++ + + n+ 
  gi|386002208|ref|YP_005920507.1| 157 -LRGNTVS-NNTVGILLTNSADNLVfNNR 183
                                       .3333333.33344555555554444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1579.49
//
Query:       gi|386002209|ref|YP_005920508.1|  [L=60]
Description: Cold shock DNA binding domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-16   58.7   0.4    4.1e-16   58.6   0.4    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.3   1.0      0.022   14.5   1.0    1.5  1  OB_RNB    Ribonuclease B OB domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.4   4.6e-20   4.1e-16       6      65 ..       2      58 ..       1      59 [. 0.97

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4.6e-20
                                      EEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  6 kwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      k fn+ k fGFI+ +dg  d FvH s ++     s++eg++V+Fevv g++gp+A++V k
  gi|386002209|ref|YP_005920508.1|  2 KFFNRTKHFGFIAGDDGT-DYFVHSSGLKPGV--SIDEGDKVSFEVVAGDRGPKAEKVEK 58
                                      89****************.*************..************************87 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.0   2.4e-06     0.022       8      52 ..       8      54 ..       3      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
                                      SS-EEEEECT.TEEEEE-HHHHT...TS-TT-EEEEEEEESSSEEEEE CS
                            OB_RNB  8 kGFGFlipdegkeDifippeqmk...kamhGDrVlvritkgdrrgrre 52
                                      k FGF+  d+ ++D+f++++ +k   ++  GD+V  ++  gdr+ + e
  gi|386002209|ref|YP_005920508.1|  8 KHFGFIAGDD-GTDYFVHSSGLKpgvSIDEGDKVSFEVVAGDRGPKAE 54
                                      569******8.***********94434557999999999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 397.44
//
Query:       gi|386002210|ref|YP_005920509.1|  [L=157]
Description: PHP domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-16   58.9   0.7    4.3e-16   58.4   0.1    1.6  2  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.43   7.7e+03      22      27 ..       9      14 ..       6      15 .. 0.80
   2 !   58.4   0.1   2.4e-20   4.3e-16       2      56 .]      75     127 ..      74     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.43
                             PHP_C 22 SDAHrl 27
                                      SD H l
  gi|386002210|ref|YP_005920509.1|  9 SDGHLL 14
                                      9***87 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 2.4e-20
                             PHP_C   2 eaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                        aN  Arr A +lglp+++GSDAH+++ VG ++T +   ++   ++leairegr+
  gi|386002210|ref|YP_005920509.1|  75 LANFWARRGATRLGLPMVAGSDAHSARSVGLGVTIVTVGED--GDVLEAIREGRV 127
                                       58999**********************************99..**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 993.44
//
Query:       gi|386002211|ref|YP_005920510.1|  [L=412]
Description: 3-isopropylmalate dehydratase large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-98  331.0   0.5    1.8e-96  324.0   0.5    2.2  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.024   13.3   0.0      0.037   12.8   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.0   0.5    2e-100   1.8e-96      10     461 .]      17     404 ..       6     404 .. 0.90

  Alignments for each domain:
  == domain 1  score: 324.0 bits;  conditional E-value: 2e-100
                         Aconitase  10 eeeg..iayv.pdrvllqdvtgvqalvdlaaareav.rrlggtlatidhlvpvdlvidhsvgaeealeknledefer 82 
                                       +e g  ++   +d  +++d t+v a++ + +++++  +++++ +   dh vp++     s       +      ++r
  gi|386002211|ref|YP_005920510.1|  17 AEAGeiVE-AeVDYAMSHDGTSVLAIKAFTEMGSERvWDPERIVVPFDHIVPAN----NS------TA----ADLQR 78 
                                       22333333.24799***************99987655*****************....22......22....33334 PP

                         Aconitase  83 nkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqpl 159
                                          +++  ++a  +  +++++ g+GI+Hqv +E+g+alpg+++vg DSH++++g++G++++GvG ++++++     l
  gi|386002211|ref|YP_005920510.1|  79 ---MVR--SWARDQGIVHFFEGGRGICHQVFPEEGFALPGTLLVGADSHSCTYGAFGAFGTGVGATDMAEIYSRGRL 150
                                       ...222..3777776789*********************************************************** PP

                         Aconitase 160 elkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpv 236
                                       ++k+p+++ v+++G+l+e+v akDl l ++g ++++g++ +++E+ Ge+vesLs+ +r+T++NM++E+GA+++++p 
  gi|386002211|ref|YP_005920510.1| 151 WFKVPETIAVRISGRLGEMVLAKDLTLMLVGAIGADGATYRALEYLGETVESLSISGRMTLCNMGVEMGAKAAIVPA 227
                                       ***************************************************************************** PP

                         Aconitase 237 dektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefke 313
                                       d +t eYL+  gr+  +     y+       +++d++ +yd ++e+d+s+l+p+va p+r++++ p+ +l+      
  gi|386002211|ref|YP_005920510.1| 228 DGTTEEYLR--GRARGP-----YQ------PVRSDPG-SYDAEMEFDVSDLSPQVAVPFRVDQVRPVGDLA------ 284
                                       *********..997777.....33......3668988.9****************************3333...... PP

                         Aconitase 314 elekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkay 390
                                                              ++vd+++ig CTN+++ed+++aa++l+     g++vk+  +t+v P+S++v  +
  gi|386002211|ref|YP_005920510.1| 285 ----------------------GTEVDQVFIGTCTNGRLEDLEIAARILK-----GREVKA--RTLVIPASREVLLQ 332
                                       ......................34699***********************.....******..************** PP

                         Aconitase 391 leaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                                       +  +G+le L +aG+ + ++gC++C+g   + ++e+e+++s+ NRNF gR+g+++  yLaSP+ ++a+A++G
  gi|386002211|ref|YP_005920510.1| 333 ALSSGVLEALVRAGAMIGTPGCGPCLGaHMGVIAEEEVCLSTANRNFPGRMGKGGLVYLASPATAAASAISG 404
                                       ***************************999****************************************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-06     0.037     288     357 ..     285     354 ..     252     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-06
                            DUF521 288 eekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtC 357
                                        ++vd v++G c    le+l+  a++lkg+++ + ++l++ +srev  +a ++g++e l +aG+ + +  C
  gi|386002211|ref|YP_005920510.1| 285 GTEVDQVFIGtCTNGRLEDLEIAARILKGREV-KARTLVIPASREVLLQALSSGVLEALVRAGAMIGTPGC 354
                                       56899999996778899999999****87777.57789999***********************9988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2650.72
//
Query:       gi|386002212|ref|YP_005920511.1|  [L=614]
Description: ATP-citrate lyase subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-21   76.7   0.0    1.3e-20   73.8   0.0    2.3  1  Citrate_synt  Citrate synthase, C-terminal domain
    2.1e-13   50.4   0.1    4.8e-13   49.2   0.1    1.6  1  Ligase_CoA    CoA-ligase
    1.9e-10   41.3   0.0    6.9e-10   39.5   0.0    2.0  2  CoA_binding   CoA binding domain
    5.7e-05   22.9   0.1     0.0013   18.5   0.0    2.3  2  Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   2.9e-24   1.3e-20     158     359 ..     391     600 ..     334     602 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 2.9e-24
                                       HHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHT.TT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSS CS
                      Citrate_synt 158 mlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaS.tladlysaiaagigalkGplhgganeavlkmleeigs 233
                                       ++++k+  + +a++++l+l ++aDH+ ++S++   +vaS ++ dl++++a+g+ +  Gp+ gga + + + ++++++
  gi|386002212|ref|YP_005920511.1| 391 LWFKKEIPPWAAEFIELVLQIVADHGPAVSAAHNAIVAScAGKDLITSLASGLLTI-GPRFGGAIDDAAREFKRARD 466
                                       67777899999****************999888777777589*************9.******************77 PP

                                       GG.GHHHHHHHHHHTTTS--TTBC-SSS..SS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHGC CS
                      Citrate_synt 234 aeveveeylekvlakekerlpGfGHrvy..kksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekeek 308
                                       + +  ee+++ ++ak+   +pG+GHr+   k+ D+R+++l  +a+e ++   + +ll+ a  ++e++ +    k+  
  gi|386002212|ref|YP_005920511.1| 467 SGLSPEEFVRGMKAKG-VNIPGIGHRIKsvKNPDKRVELLIGYARENFA---RTDLLDYALSVQEITTA----KK-G 534
                                       766***********96.*********9755899***********99776...778**************....34.7 PP

                                       T-EB-THHHHHHHHHHT.T.......--GGG.........HHHHHHHHHHHHHHHHHHHHH.HT----- CS
                      Citrate_synt 309 nlypNvDfysgvlyral.g.......ipeel.........ftvlfaisRvaGwlAhileql.adnkiiR 359
                                       nl  NvD   g+l+  l g                        lfa++R++G++ hil+q+  d++++R
  gi|386002212|ref|YP_005920511.1| 535 NLILNVDGCIGILFIDLmGscevfdeR---EidevirygyLNGLFALGRSIGIIGHILDQKrLDSRLYR 600
                                       9**********9985542433332220...1333346565899*****************889999998 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   1.1e-16   4.8e-13       1     152 [.     175     299 ..     175     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.1e-16
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++G++ +ea ++i  +               s+  e i++G+d+++         +++ ++++ ++ a+pev++i
  gi|386002212|ref|YP_005920511.1| 175 VSKSGGMLNEAFNIIARN--------------SSGVVEGIAIGGDRYP---------GSNLMDHILRFEANPEVAII 228
                                       5799**************..............***************9.........******************** PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH........HHHHHHHTTTSSEEE-SSHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGtead..pqels.eqakaleeagveiasskaqalraak 151
                                        + +++G g+ e+ + e lka +        +p+v +v+Gt+    p+ ++ ++a+a ++  +e+a++k+ al+ a+
  gi|386002212|ref|YP_005920511.1| 229 ACLGEVG-GTDEYRIVEALKADQIK------KPLVIWVTGTCSKilPGSVQfGHAGAKAQTDLETADAKNRALKEAG 298
                                       *******.*****998888775444......6************9999*999*********************9998 PP

                                       H CS
                        Ligase_CoA 152 a 152
                                       a
  gi|386002212|ref|YP_005920511.1| 299 A 299
                                       7 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.5e-13   6.9e-10       2      96 .]      11     115 ..      10     115 .. 0.93
   2 ?   -2.8   0.0       2.3     1e+04      42      93 ..     309     359 ..     277     360 .. 0.59

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.5e-13
                                       TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEE.C-TTTTT.CEET......TEEEESCHHHHHHHCT.TTEEEEE CS
                       CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfg.vnprkvg.tevl......glpvyksvdeleekte.vdvavit 69 
                                       ++t+ +v+G + ++i+ +++f+  +++++++v+  +np+ +g ++v        lp+yk++ e+ + ++ ++v+v +
  gi|386002212|ref|YP_005920511.1|  11 RNTRAFVYGLQTNAIQRMLDFDYLCRREVPSVAAiINPNRGGvQKVFwgteeiLLPMYKTIPEAAAAHPfAEVMVNF 87 
                                       789***************************66662799999977887*********************88******* PP

                                       S-HHHHHHHHHHHHH.TT-SEEEEESST CS
                       CoA_binding  70 vPaesaqeavdelve.agikgiviiteg 96 
                                       ++ +sa ++++e+++   ik+++ii+eg
  gi|386002212|ref|YP_005920511.1|  88 ASFRSAFDTTMEALAsPTIKTVAIIAEG 115
                                       **************999*********97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                                       TCEETTEEEESCHHHHHHHC.T.TTEEEEES-HHHHHHHHHHHHHTT-SEEEEE CS
                       CoA_binding  42 gtevlglpvyksvdeleekt.e.vdvavitvPaesaqeavdelveagikgivii 93 
                                       g+e++g+  y +   +e k+ e ++ ++  +P++ a+++ +  v+++ ++i+ i
  gi|386002212|ref|YP_005920511.1| 309 GDEIRGV--Y-ERLLAEGKVrEpEEPEIPKIPMDYAKAVSEGIVRKSTNLICTI 359
                                       5555553..3.2233444443335556666777777777777777777777655 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.039   1.8e+02      51      84 ..     102     135 ..      87     154 .. 0.71
   2 !   18.5   0.0   2.9e-07    0.0013       1     124 [.     169     301 ..     169     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.039
                      Succ_CoA_lig  51 edpetkvillylEsirdgrkflsaarraark..kpv 84 
                                       + p +k++++  E++ ++  +++++ ++ark  k +
  gi|386002212|ref|YP_005920511.1| 102 ASPTIKTVAIIAEGVPER--MARVMAATARKmkKTI 135
                                       57999*********9874..3333333333331444 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.9e-07
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGnea..dvdvadlleylaedpetkvillylE.sirdgrkflsa 74 
                                       pG+++++s+SG+++ + ++  a+++ g+ + + +G       ++ d +  +++ pe+ +i++  E +  d  + ++a
  gi|386002212|ref|YP_005920511.1| 169 PGSVGFVSKSGGMLNEAFNIIARNSSGVVEGIAIGGDRypGSNLMDHILRFEANPEVAIIACLGEvGGTDEYRIVEA 245
                                       79********************************9854125677888889999************44556899**** PP

                      Succ_CoA_lig  75 arraarkkpvvvlksGr........seagaraaashtgalagsd....avvdaafrqaGvlr 124
                                       +++ + kkp+v++  G+                  h ga a+ d    ++ + a+++aG+++
  gi|386002212|ref|YP_005920511.1| 246 LKADQIKKPLVIWVTGTcskilpgsV------QFGHAGAKAQTDletaDAKNRALKEAGAIV 301
                                       **99999*******999543333321......233333333322111134445566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 3605.92
//
Query:       gi|386002213|ref|YP_005920512.1|  [L=425]
Description: ATP-citrate lyase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-89  296.2   0.0    8.5e-89  295.7   0.0    1.2  1  Citrate_bind  ATP citrate lyase citrate-binding
      1e-08   35.0   0.0      2e-08   34.1   0.0    1.5  1  ATP-grasp_2   ATP-grasp domain


Domain annotation for each model (and alignments):
>> Citrate_bind  ATP citrate lyase citrate-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.7   0.0   9.5e-93   8.5e-89       1     177 [.     244     422 ..     244     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 9.5e-93
                      Citrate_bind   1 relskeeayiaeldaktgaslKltvlnpkgriwtlvaGGGasvvyaDtiadlglaselanYgeysGapseeqtyeya 77 
                                       r+l++eea i+e+d++tgaslKlt+lnp+gr+wt+vaGGGasv+yaDti+dlg+a elanYgeysG+ps+e+tyey+
  gi|386002213|ref|YP_005920512.1| 244 RALTEEEAWIKEIDSRTGASLKLTILNPRGRVWTMVAGGGASVIYADTICDLGFAGELANYGEYSGDPSTEDTYEYT 320
                                       6789************************************************************************* PP

                      Citrate_bind  78 ktildlmtrekrpdg..kvliiGggianftnvaatfkgiiraleelksklkehkvkiyvrrggpnyqeglkamkelg 152
                                       ktildlmtre++p+g  k+l+iGggianft+va+tfkg++ ale++k++l+e+ v+iyvrrggpny+egl++m++lg
  gi|386002213|ref|YP_005920512.1| 321 KTILDLMTREEDPEGrpKYLLIGGGIANFTDVAKTFKGVVMALEDYKERLREAGVEIYVRRGGPNYEEGLRIMRKLG 397
                                       ***************999*********************************************************** PP

                      Citrate_bind 153 eelglpikvfgpethitaivklalg 177
                                       e+lg+pi+v+gpeth+t iv++alg
  gi|386002213|ref|YP_005920512.1| 398 ERLGVPIHVYGPETHMTRIVSMALG 422
                                       ***********************97 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.2e-12     2e-08      36     201 ..      50     206 ..       6     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.2e-12
                                       HHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEEEE---E..CEEEEEE CS
                       ATP-grasp_2  36 klgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGkkvekvlveealdi..kkElYls 110
                                        +++k+lvvK   l G RG  g + l +s +eak +++e +g e+     g+   + ++ l+e  ++   ++ElY++
  gi|386002213|ref|YP_005920512.1|  50 WVKKKRLVVKPDQLFGKRGAHGLILLDASWDEAKGYIQENMGREVL---VGSVVGTLDTFLIEPFIPHgpEEELYVA 123
                                       478999**************************************99...66667788999***98875338999999 PP

                                       EEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHH CS
                       ATP-grasp_2 111 ivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqareiakklglekelvkkaakiikklyklf 187
                                       i  +r+++  v+ +S +GGvdiE+    + e ++ +++d+    +e    +    +gl ++ +  +a +ik ly+l+
  gi|386002213|ref|YP_005920512.1| 124 IKSERDKD--VIYFSPRGGVDIEA----NWESVTEIPVDILARPEELDLGS-KLPAGLADR-LAPTAAFIKGLYRLY 192
                                       98888765..7889********95....8899********98877765544.446788876.5567789******** PP

                                       HHTTEEEEEEEEEE CS
                       ATP-grasp_2 188 veldatlvEiNPLv 201
                                       ++l    +EiNP+v
  gi|386002213|ref|YP_005920512.1| 193 RDLGFAYLEINPFV 206
                                       ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3012.54
//
Query:       gi|386002214|ref|YP_005920513.1|  [L=336]
Description: hypothetical protein Mhar_1528 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   18.3   0.0     0.0018   17.7   0.0    1.1  1  PrmA      Ribosomal protein L11 methyltransferase (PrmA)
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.043   13.4   0.0    1.3  1  MTS       Methyltransferase small domain


Domain annotation for each model (and alignments):
>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     2e-07    0.0018     153     210 ..     198     257 ..     195     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-07
                              PrmA 153 ealeklvkege..evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkve 210
                                       ++le+l  +g+  +v Dv +G G L ++a++ ga++vv  D    Av+ a  N+e N+  
  gi|386002214|ref|YP_005920513.1| 198 KILEELYFRGKltTVADVLCGPGTLGLVAVLAGAERVVLNDAWLPAVEDAILNLEANRSL 257
                                       67888766665559*******************************************754 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-06     0.043      32      80 ..     209     256 ..     197     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-06
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTG CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankl 80 
                                         +v+D+ cG G lg+++  +  e +v+l d+   A+e a  nlean+ 
  gi|386002214|ref|YP_005920513.1| 209 LTTVADVLCGPGTLGLVAVLAGAE-RVVLNDAWLPAVEDAILNLEANRS 256
                                       4579************99887777.8********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2272.33
//
Query:       gi|386002215|ref|YP_005920514.1|  [L=397]
Description: Pentapeptide repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-24   85.5  24.2    6.2e-10   38.5   5.6    4.4  4  Pentapeptide    Pentapeptide repeats (8 copies)
    7.4e-16   58.1   0.9    9.9e-11   41.7   0.8    2.5  3  Pentapeptide_4  Pentapeptide repeats (9 copies)
      6e-11   42.3   4.7      6e-05   23.1   3.6    3.3  3  Pentapeptide_3  Pentapeptide repeats (9 copies)
    8.1e-09   34.8   7.5    1.1e-08   34.4   7.5    1.1  1  DUF2254         Predicted membrane protein (DUF2254)
  ------ inclusion threshold ------
       0.87    9.5   0.0       0.87    9.5   0.0    2.3  3  DUF5412         Family of unknown function (DUF5412)


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.021        75       2      20 ..     185     203 ..     185     203 .. 0.86
   2 !   26.6   3.2   9.7e-10   3.5e-06       8      40 .]     206     238 ..     206     238 .. 0.96
   3 !   38.5   5.6   1.7e-13   6.2e-10       1      39 [.     234     272 ..     234     272 .. 0.98
   4 !   38.1   3.2   2.4e-13   8.5e-10       1      37 [.     269     305 ..     269     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.021
                                       B-TT-B-CCSCCEECCCES CS
                      Pentapeptide   2 nLsgAnLsganLsganlsg 20 
                                       nL+g++Ls   L g  lsg
  gi|386002215|ref|YP_005920514.1| 185 NLEGVDLSDQLLPGIELSG 203
                                       8999999999999998886 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 9.7e-10
                                       -CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   8 LsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       L+ ++++++ l gAn+++An++ AdLs a+L+g
  gi|386002215|ref|YP_005920514.1| 206 LQKSKFNNSTLFGANFNNANFYMADLSHARLRG 238
                                       7899***************************98 PP

  == domain 3  score: 38.5 bits;  conditional E-value: 1.7e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       A+L+gAn+s a L +a+ls+A+L++A l++A L+ganLs
  gi|386002215|ref|YP_005920514.1| 234 ARLRGANFSDAMLGRADLSRADLSSAHLNDASLNGANLS 272
                                       89************************************7 PP

  == domain 4  score: 38.1 bits;  conditional E-value: 2.4e-13
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsgan 37 
                                       AnLs+A L  anL++a l gAnL+gA + +AdL+ga 
  gi|386002215|ref|YP_005920514.1| 269 ANLSEAKLNMANLTKAYLGGANLIGAKFDNADLNGAF 305
                                       8999999999999999999999999999999999995 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.4   8.7e+03      62      71 ..     185     194 ..     167     201 .. 0.56
   2 !   41.7   0.8   2.8e-14   9.9e-11       1      75 [.     209     284 ..     206     286 .. 0.93
   3 !   22.3   0.0   3.1e-08   0.00011      11      69 ..     249     307 ..     246     324 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.4
                    Pentapeptide_4  62 nlknvnfsdk 71 
                                       nl++v +sd+
  gi|386002215|ref|YP_005920514.1| 185 NLEGVDLSDQ 194
                                       4555555554 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 2.8e-14
                    Pentapeptide_4   1 aeftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                                       ++f ++++ +++++n+nF+ a+l  ++++++++s++++ +++ls +d++ ++l++as+ g nl+++++++  l+++
  gi|386002215|ref|YP_005920514.1| 209 SKFNNSTLFGANFNNANFYMADLSHARLRGANFSDAMLGRADLSRADLSSAHLNDASLNGANLSEAKLNMaNLTKA 284
                                       589999999***********************************************************86589876 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 3.1e-08
                    Pentapeptide_4  11 cklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfs 69 
                                       ++ls++++s a+l+d+++++++ls+++++ +nl ++ + +++l  a F + +l+++ ++
  gi|386002215|ref|YP_005920514.1| 249 ADLSRADLSSAHLNDASLNGANLSEAKLNMANLTKAYLGGANLIGAKFDNADLNGAFLD 307
                                       55666666666666666666666666666666666666666666666666666555553 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   3.6   1.7e-08     6e-05       3      47 ..     208     249 ..     198     250 .. 0.77
   2 !    7.2   0.0    0.0016       5.8      21      47 ..     249     274 ..     245     277 .. 0.61
   3 !   10.3   0.0   0.00017       0.6       4      33 ..     279     306 ..     276     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.7e-08
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                        + F ++ ++ ga+F++a +F  ad++ a+++ga+F+ d+ +++a
  gi|386002215|ref|YP_005920514.1| 208 KSKFNNS-TLFGANFNNA-NFYMADLSHARLRGANFS-DAMLGRA 249
                                       5677777.7778888888.788888888888888888.8877765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                    Pentapeptide_3  21 asFsnadFgsadFsgarFtgdvdFsga 47 
                                       a+ s+ad++sa++ +a  + ++++s+a
  gi|386002215|ref|YP_005920514.1| 249 ADLSRADLSSAHLNDASLN-GANLSEA 274
                                       4556666666666666666.6666655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00017
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadF 33 
                                       an+++a ++ ga+ +ga  F+nad+++a +
  gi|386002215|ref|YP_005920514.1| 279 ANLTKA-YLGGANLIGA-KFDNADLNGAFL 306
                                       688888.9999999999.799999988765 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   7.5   2.9e-12   1.1e-08       4     160 ..      23     179 ..      20     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.9e-12
                           DUF2254   4 lwfipllivllavllal.llllldealslsldleelkegaeaaralLstiagsmltvagfvfSitvvalqlassqfs 79 
                                       +wf +++++l++ ++a+ +  +ld+ +s++  l  + +++e+ar +Ls+++ +  ++ g+ f++  +++q+  +++s
  gi|386002215|ref|YP_005920514.1|  23 FWFWAVILLLVSPIVAFaIYQTLDQLVSANYHLGAIWASSEDARYILSALSQAQAAIFGIFFTLNFIVFQTQIGNVS 99 
                                       9***8888888866665156677999999998888877*************************************** PP

                           DUF2254  80 PRllrnfmrdrvtqvvLGtfigtfvYsllvlrairteeevpqlsvlvalllaivsvllLiyFihhlarsiqvsnvia 156
                                       P +++  +++    +++ +f+ ++   l+ lr i  +++  ++ ++  + l i+++l+Li + + +  s+  + +i+
  gi|386002215|ref|YP_005920514.1| 100 PATIKRSLQSYKLLFIFIVFLISISVDLIFLRYIPPNND-LEINIFWPISLSIFAILILIPYMRFTLMSLVKDAIIE 175
                                       ***********************************7754.57**********************9999999999999 PP

                           DUF2254 157 rvee 160
                                       +v +
  gi|386002215|ref|YP_005920514.1| 176 EVRS 179
                                       9975 PP

>> DUF5412  Family of unknown function (DUF5412)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.58   2.1e+03       5      26 ..      24      45 ..      20      88 .. 0.65
   2 ?   -3.7   0.7       2.9     1e+04      10      22 ..     113     125 ..     106     133 .. 0.55
   3 ?    9.5   0.0   0.00024      0.87      11      51 ..     147     187 ..     137     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.58
                           DUF5412  5 ivllililllviliaiviywkf 26
                                      +  ++++ll+  ++a+ iy ++
  gi|386002215|ref|YP_005920514.1| 24 WFWAVILLLVSPIVAFAIYQTL 45
                                      4445555556667777777655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                           DUF5412  10 lilllviliaivi 22 
                                       l++++v+li+i +
  gi|386002215|ref|YP_005920514.1| 113 LFIFIVFLISISV 125
                                       3444555555544 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00024
                           DUF5412  11 illlviliaiviywkffdlerlpkgellkeskSPdgtYtln 51 
                                       i l++++i+i+i +  f+l  l k+ +++e+ S    Y+l+
  gi|386002215|ref|YP_005920514.1| 147 ISLSIFAILILIPYMRFTLMSLVKDAIIEEVRSGKARYNLE 187
                                       4567778888889999999999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2404.91
//
Query:       gi|386002216|ref|YP_005920515.1|  [L=285]
Description: hypothetical protein Mhar_1530 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-23   82.8   2.1    4.9e-23   81.6   2.1    1.6  1  DUF3307   Protein of unknown function (DUF3307)
  ------ inclusion threshold ------
        0.5   10.5   1.2        1.2    9.3   0.1    2.0  2  SLATT_3   SMODS and SLOG-associating 2TM effector domain 3
          6    4.9   8.5        0.2    9.8   0.4    2.0  2  Dpy19     Q-cell neuroblast polarisation


Domain annotation for each model (and alignments):
>> DUF3307  Protein of unknown function (DUF3307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   2.1   8.2e-27   4.9e-23       2     111 ..      25     130 ..      23     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 8.2e-27
                           DUF3307   2 llllLlaHllgDFvlQsdklvkkKeskklkskllllHalihvlllvllllllkikleqllillvvivlsHllIDvlK 78 
                                       l+ll+  H+l+DFvlQ++++v+ K +   +s++l+lH+++++ll+  +++     +  + ++++  +lsHl+ID++K
  gi|386002216|ref|YP_005920515.1|  25 LILLVFSHMLADFVLQPNRWVDGKYEDGWRSRYLYLHVCVVALLAGSVAWAFLGLF-PAALVFASFFLSHLVIDIVK 100
                                       7888899***********************************87766666665555.889999999*********** PP

                           DUF3307  79 sklkkkkkalaaFliDQllHlivlilvllills 111
                                       s    +++++ +F+ DQ++H+i++ilv ++l+ 
  gi|386002216|ref|YP_005920515.1| 101 SR---REDTVRSFVGDQAAHMIIIILVWMTLFH 130
                                       *9...799*******************555544 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0002       1.2      24      70 ..      58     104 ..      50     116 .. 0.90
   2 ?   -1.0   0.1      0.29   1.7e+03      28      65 ..     220     257 ..     209     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                           SLATT_3  24 lrlvllvvAAlaaalslkvgsvdlaallaalafllalvievvlarrr 70 
                                       l l + vvA la+++++ +  + +aal+ a  fl  lvi +v +rr+
  gi|386002216|ref|YP_005920515.1|  58 LYLHVCVVALLAGSVAWAFLGLFPAALVFASFFLSHLVIDIVKSRRE 104
                                       678999*************9999******************999886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.29
                           SLATT_3  28 llvvAAlaaalslkv..gsvdlaallaalafllalvievv 65 
                                       ll++A   +++ +++   +++++ + ++l f +a++++++
  gi|386002216|ref|YP_005920515.1| 220 LLIAA--KSIFRYNTnrITGEYILFGTLLSFSIAIFVGFF 257
                                       34444..344444442367778888888888888888765 PP

>> Dpy19  Q-cell neuroblast polarisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   3.4e-05       0.2     423     496 ..      56     141 ..      18     145 .. 0.86
   2 ?   -1.5   2.6     0.088   5.3e+02     218     272 ..     209     268 ..     201     282 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.4e-05
                             Dpy19 423 vYhllqllvftllallimrLklLwtphlcviaslvlskklfkfllk............kifisavlavlllsmsvkg 487
                                        Y  l+++v  lla ++   +l ++p   v+as++ls+ +  ++++            +  ++++++++ + ++ + 
  gi|386002216|ref|YP_005920515.1|  56 RYLYLHVCVVALLAGSVAWAFLGLFPAALVFASFFLSHLVIDIVKSrredtvrsfvgdQAAHMIIIILVWMTLFHPD 132
                                       6999********************************99997777777777777777778888899999999999988 PP

                             Dpy19 488 vpnleeels 496
                                       ++ l+ +ls
  gi|386002216|ref|YP_005920515.1| 133 FSSLQGRLS 141
                                       888887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.088
                             Dpy19 218 Fvlltqilslfaldllgli.pte....klalillihllslllafvlqfgnsmlllsllls 272
                                       F+++ q  ++ +l  ++ i  ++    + + il+  lls+ +a+++ f+ + +l+ +l+ 
  gi|386002216|ref|YP_005920515.1| 209 FIIFQQYTAIGLLIAAKSIfRYNtnriTGEYILFGTLLSFSIAIFVGFFANLFLSLFLPE 268
                                       444444444333333322211222233445578888888888888888877777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1978.19
//
Query:       gi|386002217|ref|YP_005920516.1|  [L=238]
Description: hypothetical protein Mhar_1531 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0006   19.3   0.1     0.0018   17.8   0.1    1.8  1  Sigma70_r4    Sigma-70, region 4
     0.0028   17.3   0.0     0.0052   16.4   0.0    1.5  1  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1     2e-07    0.0018      15      41 ..     172     198 ..     171     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-07
                                       HHHTTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4  15 lrfgeglTleEIgerlgiSrerVrqie 41 
                                       ++++eg+Tl+EIge+l+i  ++V+ ++
  gi|386002217|ref|YP_005920516.1| 172 MYRLEGRTLKEIGEMLNIDGSAVHYRL 198
                                       7889**************888887665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.8e-07    0.0052      20      49 ..     171     200 ..     153     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.8e-07
                                       HHHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2  20 llryleglsykEIAellgisegtVksrlsR 49 
                                       ++++leg + kEI e+l+i  ++V +rl++
  gi|386002217|ref|YP_005920516.1| 171 VMYRLEGRTLKEIGEMLNIDGSAVHYRLAQ 200
                                       4789***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1671.84
//
Query:       gi|386002218|ref|YP_005920517.1|  [L=378]
Description: hypothetical protein Mhar_1533 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-38  133.3  42.1    1.5e-38  133.0  42.1    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0  42.1   8.5e-43   1.5e-38       5     301 .]      38     349 ..      35     349 .. 0.92

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 8.5e-43
                   LPG_synthase_TM   5 lalsalllall.lrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfv 80 
                                       l+l+++ ++++ lr+++l+++a++l+ l+   l +al+l+ll v ++al Wr + ++l+   s+++l+++yl ++f+
  gi|386002218|ref|YP_005920517.1|  38 LVLLGVGIYIAyLRHLGLGEVAESLEGLSLAALSAALALSLLMVGFNALSWRRMAEELDLSASFGDLFMIYLSSIFA 114
                                       4555555555557******************************99******************************** PP

                   LPG_synthase_TM  81 nnvtPgalg.Gevvrayllkr.kegvslskalasvvverlldllalvllgllallllggllaegaavllllalalll 155
                                       nn++P ++  Ge +r y+l+r   g ++ +alasv + r++  + ++l ++l+++++++l+a  + ++l++ +++++
  gi|386002218|ref|YP_005920517.1| 115 NNLIPTGSFsGETARTYFLARiGGGGRYDAALASVAASRIITAVPFILGMVLGIGYITRLHAVPG-WALTACFGMMV 190
                                       *********************9999**********************************998766.99999999999 PP

                   LPG_synthase_TM 156 lavlalllllllrrrlarlarvlkrlarllarfarklasakr..............klvlasprrlllafllslliw 218
                                       + v a +++  + + +++++r   + ++ l+r+ r+     r               l++++++++l a+++ ++ w
  gi|386002218|ref|YP_005920517.1| 191 FSVSAGFAFVGICFEERWMQRTAAAAVGPLERIFRRELD--RevcsgavsgfmqsmILLRERRGAILEALAWAIAGW 265
                                       999999999999999999999999999988877755544..2469***********9999999************** PP

                   LPG_synthase_TM 219 llealtlylllralgvdvslallllillaltlvgalpp.lPgGlGvrEaalalllallGvsaaealaaallyrlitl 294
                                       ++ ++++ +++++lgv+vs++++l+++ +++++++lp+ lPgG+G++E+++++l++++Gv+  +a+a+++l+rl++l
  gi|386002218|ref|YP_005920517.1| 266 ISLVMVALAAFASLGVEVSPLAILAVYSVVIVFQTLPLgLPGGIGLVEILMTALFSAIGVPIHDAAAVTILIRLVQL 342
                                       ************************8888888888888659************************************* PP

                   LPG_synthase_TM 295 ylllllG 301
                                       ++l+llG
  gi|386002218|ref|YP_005920517.1| 343 WFLALLG 349
                                       *****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2732.52
//
Query:       gi|386002219|ref|YP_005920518.1|  [L=58]
Description: hypothetical protein Mhar_1534 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-27   96.1   5.0    1.3e-27   96.0   5.0    1.0  1  DUF5350   Family of unknown function (DUF5350)


Domain annotation for each model (and alignments):
>> DUF5350  Family of unknown function (DUF5350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   5.0   7.2e-32   1.3e-27       1      56 [.       1      56 [.       1      57 [. 0.98

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 7.2e-32
                           DUF5350  1 MGKTGsveWvkvKgrkgqirlVpkkegekkkpGPnQrfkssgkkrrikrrsakaiv 56
                                      MGKTGsv+W+k+Kgrkgqir+Vp++e+++k+pGP Q+++ssg++rr+++rsakai 
  gi|386002219|ref|YP_005920518.1|  1 MGKTGSVQWTKIKGRKGQIRQVPNSESTHKNPGPLQKYTSSGARRRKIARSAKAIA 56
                                      *****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 358.62
//
Query:       gi|386002220|ref|YP_005920519.1|  [L=378]
Description: Thiamine biosynthesis/tRNA modification protein ThiI [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-51  173.2   0.0    5.9e-51  172.9   0.0    1.1  1  ThiI           Thiamine biosynthesis protein (ThiI)
    8.5e-18   64.8   0.0    1.2e-17   64.4   0.0    1.2  1  THUMP          THUMP domain
    9.4e-05   22.0   0.0       0.25   10.8   0.0    2.3  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
       0.24   10.2   0.0       0.51    9.1   0.0    1.5  2  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.9   0.0   1.3e-54   5.9e-51       1     195 [.     170     360 ..     170     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 1.3e-54
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       g+q + laL+SgGiDSpVaa+++++RGc + l++++ +p+   +a  + e+ ae l ++ ++ +++++ v+    l 
  gi|386002220|ref|YP_005920519.1| 170 GSQPRMLALISGGIDSPVAAWMMMRRGCPISLLYFDPRPY--VHALPQAERSAEALRRWTSGRRINFIGVPIGAGLA 244
                                       68899******************************86666..5788899999************************9 PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiik 154
                                        i   ++++ t++l++r m+riA +v eee+a  +vtG sLgqVaSqt  N+ + ++ ++l+i  PLi++dK ei +
  gi|386002220|ref|YP_005920519.1| 245 RIA-GAEPRATCLLCRRLMYRIAGMVMEEEEAFGVVTGYSLGQVASQTPANIMAEQSGIDLPIYHPLIAMDKSEITD 320
                                       986.678899******************************************************************* PP

                              ThiI 155 lAkeigtyeisiekedkCsvlakhPttkakleevekaeekl 195
                                       lA++igty   +    +C++ +k+P t+a+ ee++ +ee+l
  gi|386002220|ref|YP_005920519.1| 321 LARKIGTYRA-TADAGTCTAAPKRPMTRARAEEIRGMEEEL 360
                                       ********85.56779*******************999987 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   2.7e-21   1.2e-17       6     143 ..      36     159 ..      31     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.7e-21
                                       HHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                             THUMP   6 llkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeee 82 
                                        lke +++  r   ++gri+ve++++       ++ e+l+ ++g+++ +pv + c  dl  i + a+ +  ++    
  gi|386002220|ref|YP_005920519.1|  36 DLKEAGID-HRASLERGRIFVETSNP-------RAPEILSNVFGVVSTSPV-RSCKPDLGAIAAVASDLAAERRPS- 102
                                       56666666.45667789999999866.......89999*************.*******************99987. PP

                                       T-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP  83 ketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                         +Fa+r++r g    ++s ei+  vG+a++e+tg+ Vdl++P++ ++ve ++dk+++++d
  gi|386002220|ref|YP_005920519.1| 103 --SFAIRARRGGG--GISSTEIAVFVGDAVRERTGAAVDLTDPEVEIFVEAREDKVLVFTD 159
                                       ..********888..8******************************************986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   5.5e-05      0.25       2      32 ..     175     205 ..     174     225 .. 0.90
   2 !    9.0   0.0    0.0002      0.91     150     178 ..     302     330 ..     286     346 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEE CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfd 32 
                                        + l+SGG+DS +++++++++g  + +l fd
  gi|386002220|ref|YP_005920519.1| 175 MLALISGGIDSPVAAWMMMRRGCPISLLYFD 205
                                       6789******************999999887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
                                       S--EEE-TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 150 kkieieaPlidlsKaeivklgkelgvple 178
                                        ++ i  Pli+++K+ei  l+ ++g  + 
  gi|386002220|ref|YP_005920519.1| 302 IDLPIYHPLIAMDKSEITDLARKIGTYRA 330
                                       467899******************95332 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00011      0.51       3      28 ..     175     200 ..     173     232 .. 0.86
   2 ?   -2.8   0.0      0.47   2.1e+03     165     185 ..     307     327 ..     305     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00011
                     tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevi 28 
                                       +++++SgG+DS vaa ++ ++g  + 
  gi|386002220|ref|YP_005920519.1| 175 MLALISGGIDSPVAAWMMMRRGCPIS 200
                                       67899**************9997665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.47
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagl 185
                                       + Pl  + K+e+ ++A+++g 
  gi|386002220|ref|YP_005920519.1| 307 YHPLIAMDKSEITDLARKIGT 327
                                       679999**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2395.98
//
Query:       gi|386002221|ref|YP_005920520.1|  [L=76]
Description: hypothetical protein Mhar_1536 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 462.56
//
Query:       gi|386002222|ref|YP_005920521.1|  [L=54]
Description: hypothetical protein Mhar_1537 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 361.35
//
Query:       gi|386002223|ref|YP_005920522.1|  [L=110]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-15   56.1   0.5      2e-14   53.2   0.0    2.4  3  HTH_5            Bacterial regulatory protein, arsR family
    3.2e-10   39.9   0.1    6.6e-10   38.9   0.0    1.6  2  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.029   14.3   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.044   13.5   0.0       0.79    9.5   0.0    2.1  2  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.045   13.4   0.0      0.064   12.9   0.0    1.2  1  RP-C             Replication protein C N-terminal domain
      0.068   13.4   0.0       0.18   12.0   0.0    1.7  2  HTH_34           Winged helix DNA-binding domain
      0.086   12.4   0.0       0.14   11.8   0.0    1.3  1  HTH_CodY         CodY helix-turn-helix domain
        0.1   12.5   0.0       0.23   11.4   0.0    1.7  2  MarR             MarR family
       0.13   12.6   0.0        0.2   12.0   0.0    1.4  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16   3.2e+02       4      13 ..       9      18 ..       8      19 .. 0.91
   2 !   53.2   0.0     1e-17     2e-14       1      46 [.      18      63 ..      18      64 .. 0.98
   3 ?   -2.1   0.0       1.9   3.8e+03      11      23 ..      84      97 ..      81     103 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                                      HHHHHHHHTT CS
                             HTH_5  4 RlkILklLae 13
                                      R+kIL +L++
  gi|386002223|ref|YP_005920522.1|  9 RVKILAALSD 18
                                      9*******86 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 1e-17
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      dp Rl+I+ +L  +e+cvce++ ++g  qst+S HL++L eaG++e
  gi|386002223|ref|YP_005920522.1| 18 DPIRLEIIEFLGGEERCVCEIVPAFGRAQSTISKHLSILNEAGILE 63
                                      8******************************************986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.9
                                      HTT.SSEEHHHHHH CS
                             HTH_5 11 Lae.gelcvcelae 23
                                      L+e  +l   e++e
  gi|386002223|ref|YP_005920522.1| 84 LREvDSLALEEISE 97
                                      55655666666665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   3.3e-13   6.6e-10       2      57 ..      11      65 ..      10      69 .. 0.96
   2 ?   -2.3   0.1       2.4   4.8e+03      17      31 ..      82      96 ..      79      99 .. 0.53

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.3e-13
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +i+ AL++P R++i   L ++e++++ e+  +++ +++t+s+HL +L eag++e++
  gi|386002223|ref|YP_005920522.1| 11 KILAALSDPIRLEIIEFL-GGEERCVCEIVPAFGRAQSTISKHLSILNEAGILERR 65
                                      5899**************.***********************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                      HHHSTCTTB-HHHHH CS
                            HTH_20 17 raLaraegltasela 31
                                      ++L++ + l ++e+ 
  gi|386002223|ref|YP_005920522.1| 82 DLLREVDSLALEEIS 96
                                      444333556666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.4e-05     0.029      25      67 ..      35      78 ..      28      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                      HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                              TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67
                                      + ei  + g+ +s++ + L+ L ++G+ er+  g+++lYr+ +p
  gi|386002223|ref|YP_005920522.1| 35 VCEIVPAFGRAQSTISKHLSILNEAGILERRIdGKRTLYRVKNP 78
                                      56888899********************987647899***9998 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0004      0.79      17      47 ..      35      65 ..      23      73 .. 0.87
   2 ?    1.8   0.0       0.1   2.1e+02       5      23 ..      80      98 ..      78     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0004
                          HTH_DeoR 17 veelvellgvSeaTiRRDLneLeeqglltRt 47
                                      v e+v  +g ++ Ti + L++L e+g+l+R 
  gi|386002223|ref|YP_005920522.1| 35 VCEIVPAFGRAQSTISKHLSILNEAGILERR 65
                                      5689999*********************996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.1
                          HTH_DeoR  5 ilellkqqgklsveelvel 23
                                      + +ll++ ++l +ee++el
  gi|386002223|ref|YP_005920522.1| 80 LFDLLREVDSLALEEISEL 98
                                      6789************996 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.064      79     117 ..      40      76 ..      36      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                              RP-C  79 ralglsestlrrhlaaLveaGliirrDspngkRyarrdr 117
                                        a+g+++st+++hl+ L eaG++ rr   +gkR  +r +
  gi|386002223|ref|YP_005920522.1|  40 PAFGRAQSTISKHLSILNEAGILERR--IDGKRTLYRVK 76 
                                       589*********************99..45777666655 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     9e-05      0.18       1      49 [.      20      67 ..      20      76 .. 0.84
   2 ?   -2.2   0.0       2.4   4.9e+03       8      23 ..      83      98 ..      79     104 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9e-05
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                      +Rl+++ +L  +++ +  e+  a +  ++ +s+hl++L++ag +e++++
  gi|386002223|ref|YP_005920522.1| 20 IRLEIIEFLGGEER-CVCEIVPAFGRAQSTISKHLSILNEAGILERRID 67
                                      79999999987655.567889999999***************9999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                            HTH_34  8 yLasvdeadfvelkea 23
                                      +L +vd+   +e++e 
  gi|386002223|ref|YP_005920522.1| 83 LLREVDSLALEEISEL 98
                                      5666777777776654 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05      0.14      13      59 ..      41      86 ..      32      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                          HTH_CodY 13 riGitrsvivnaLrkLesaGiiesrsLGmkGtYlkvlnekflkeLkk 59
                                        G ++s i   L  L+ aGi+e r  G k t  +v n ++++ L++
  gi|386002223|ref|YP_005920522.1| 41 AFGRAQSTISKHLSILNEAGILERRIDG-KRTLYRVKNPRLFDLLRE 86
                                      56888999***************99877.667779****99999886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.23      22      51 ..      37      66 ..       9      69 .. 0.89
   2 ?   -2.1   0.0       1.9   3.8e+03       6      23 ..      81      98 ..      76     104 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 22 eLakklgvskstvtrvldrLekkGlieRsk 51
                                      e+  ++g  +st+++ l  L ++G +eR+ 
  gi|386002223|ref|YP_005920522.1| 37 EIVPAFGRAQSTISKHLSILNEAGILERRI 66
                                      788999**********************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                      HHHHHHHHHSTTEEHHHH CS
                              MarR  6 fviLrilyeqgplsvseL 23
                                      f++Lr +++     +seL
  gi|386002223|ref|YP_005920522.1| 81 FDLLREVDSLALEEISEL 98
                                      566665554444444455 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001       0.2      33      65 ..      44      76 ..      32     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                      --HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
                   Penicillinase_R 33 laysTVktllrrLvkKgllsrekegrafiYspl 65
                                       a+sT+   l+ L + g+l+r+ +g++++Y+  
  gi|386002223|ref|YP_005920522.1| 44 RAQSTISKHLSILNEAGILERRIDGKRTLYRVK 76
                                      479***************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 815.03
//
Query:       gi|386002224|ref|YP_005920523.1|  [L=341]
Description: Permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-68  229.5  21.0    5.9e-68  229.2  21.0    1.1  1  ArsP_1    Predicted permease


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.2  21.0   3.3e-72   5.9e-68      10     293 ..       2     337 ..       1     338 [. 0.91

  Alignments for each domain:
  == domain 1  score: 229.2 bits;  conditional E-value: 3.3e-72
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1  10 asilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkGaplga 85 
                                       +++  ++l++L+++f+i+gai++ +++e++ +++g ++++ + + va+ +G +l+vCsc+++P+++++ ++Ga++g+
  gi|386002224|ref|YP_005920523.1|   2 EYLSAHVLTCLIPAFFIAGAIAALLQREAVLKYFGkDAPKWLCYSVASTSGTILAVCSCTILPMFAGIHRRGAGIGP 78 
                                       79999************************************************************************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                            ArsP_1  86 avaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek........ 154
                                       a+aFl+a+Pain +a++lt+ +lg++l++ari +a++v+++igl++  +f++  + + a   +   +++        
  gi|386002224|ref|YP_005920523.1|  79 ATAFLFAGPAINLLAVVLTARVLGLELGAARIAAAVSVSVLIGLIMAAIFDRGSEDQEAAPCPA-PSPSaeaglerp 154
                                       ***************************************************9988888865544.33335678888* PP

                                       .......................................xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 155 .......................................ltlkpkle..alkafaknevkewlelgkyLiiGvaiag 190
                                                                               +l+++++  ++ +f  +++   ++++++L++G++i g
  gi|386002224|ref|YP_005920523.1| 155 gyippifvgllvavllaatsglalgakaaivsilvlasgWLLSARFTdlEKASFFGETWWLTRRIFPLLLVGTFITG 231
                                       ******************************999888877344444442223447777777678888*********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 191 viqaflpesvllsllggnsvsssllamligvvlyvcslgevpfiaalf...esglalGsalAfLlagpllslpelli 264
                                       vi  +lp + + +++g+ ++ + ++a+l+g++ly+ +l evp++ + f   +  +a G+al++Llagp++slp++++
  gi|386002224|ref|YP_005920523.1| 232 VIGYYLPVDLIRTVFGESDFAACFVASLMGALLYMPTLLEVPIVGTMFgysSGAMAPGPALSLLLAGPSMSLPSMIV 308
                                       **********************************************99443467*********************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 265 llkvlkkklvavllglvvvsvvlaglvin 293
                                       +  + ++k+++v++ lv+++++++g++++
  gi|386002224|ref|YP_005920523.1| 309 IWRIIGSKRASVYISLVILLSTVMGMIYG 337
                                       ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2550.50
//
Query:       gi|386002225|ref|YP_005920524.1|  [L=191]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1294.26
//
Query:       gi|386002226|ref|YP_005920525.1|  [L=381]
Description: cytochrome c biogenesis protein transmembrane region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-14   53.2  14.2    4.8e-14   52.8  14.2    1.2  1  DsbD      Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8  14.2   2.7e-18   4.8e-14       2     182 ..     165     344 ..     164     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.7e-18
                              DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevi 78 
                                       + aGl++ + PC+l+++ ++l+ ++ +s + ++ +   + v     +F lG+ +++ ++gl+   l ++   ++   
  gi|386002226|ref|YP_005920525.1| 165 LAAGLIAGFNPCLLAVL-VFLASMT-LSRSGRRRD---LAV--MVGFFCLGIFVMYYLFGLGLFRLFSIP-SFEASF 233
                                       789***********998.6666666.444444443...333..3469****************9999988.99**** PP

                              DsbD  79 rrvaglivillGlhflgvfk......ievleklklllkikkk.aelsvlgalllGltFalgwsPCigPvlasvlala 148
                                       r + +l+ ++lG ++++  +      i++++ +  l   kk+ +  s+l  +l+G +F+l+ +PC+g v  +++ + 
  gi|386002226|ref|YP_005920525.1| 234 RLILTLLLLVLGATQIEDARrlhrggISLFKAEWALGYFKKSlERYSILSYFLIGALFSLVKAPCVGAVYIAIIGII 310
                                       ****************96667888887777777666555444166789***************************** PP

                              DsbD 149 askeslakgallllvyvlGlaipfllvglllell 182
                                        s++ ++ g+++ll+y lG ++p++++g+++ l 
  gi|386002226|ref|YP_005920525.1| 311 QSQGYASAGTVYLLLYNLGVVLPVMILGMVIALG 344
                                       ****************************998753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2541.94
//
Query:       gi|386002227|ref|YP_005920526.1|  [L=488]
Description: hypothetical protein Mhar_1542 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-17   62.9   0.0    3.1e-07   30.9   0.0    2.4  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.7e-11   3.1e-07      15     107 .]     148     244 ..     140     244 .. 0.70
   2 !   29.4   0.0     5e-11     9e-07      10      94 ..     276     357 ..     271     366 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.7e-11
                         Rhodanese  15 a.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvy.....cdgggr.aa 80 
                                       + +lD++p+++     ++gA++v     +++  + +    +  e++e     gi++++ vv+y     c gg   a+
  gi|386002227|ref|YP_005920526.1| 148 DlILDISPEAD---EYLEGALSV----NYEEFVTRDGRIRTTSEIAEIlgnaGISRDDAVVIYgeclpCGGGPVpAT 217
                                       249****7776...4599*****....3333333333333334444444668***********66666667777677 PP

                         Rhodanese  81 aaaallkklGyknvsvldGGfkawkea 107
                                       ++++llk+lG++nv++ldG +++wk+a
  gi|386002227|ref|YP_005920526.1| 218 FTYWLLKYLGHENVRILDGNIDDWKAA 244
                                       7799999***888***********985 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 5e-11
                         Rhodanese  10 ekgkvallDvRppeeYek.ghIpgAvnv.skdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaa 84 
                                       ++gk++++D R++e+ ++  +Ipg+vn+ + ++l ++k   a++le + ++    ++++++vvvy ++g   a  + 
  gi|386002227|ref|YP_005920526.1| 276 KSGKAQIVDGRAAEA-ADpASIPGSVNIpAETILEGEKIKGAEDLEAIFKD----LRKDRPVVVYTNTGVNGAVFWF 347
                                       566778******999.666*********54445455555555555544444....556*************777799 PP

                         Rhodanese  85 llkklGyknv 94 
                                        l+ +Gy  v
  gi|386002227|ref|YP_005920526.1| 348 VLEMMGYDAV 357
                                       9988996445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3181.88
//
Query:       gi|386002228|ref|YP_005920527.1|  [L=88]
Description: Redox-active disulfide protein 2 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-27   94.3   1.3    3.8e-27   94.1   1.3    1.0  1  Thioredoxin_3  Thioredoxin domain
    0.00061   20.0   0.2      0.017   15.3   0.0    1.9  2  Thioredoxin_4  Thioredoxin
     0.0025   18.0   0.2     0.0038   17.4   0.2    1.4  1  Glutaredoxin   Glutaredoxin
     0.0071   16.3   0.0     0.0075   16.2   0.0    1.1  1  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.095   13.6   0.1       0.11   13.4   0.1    1.1  1  Ribosomal_L17  Ribosomal protein L17


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   1.3   1.1e-30   3.8e-27       1      75 [.      12      86 ..      12      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 1.1e-30
                                      EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      m+i+vlg+gCakC+ l+k+v++a+ae g++aev+kv+ ++ei+++gVm++Pal+idg+ v++G++ps++ei+ +l
  gi|386002228|ref|YP_005920527.1| 12 MKIEVLGTGCAKCKSLAKNVEKAVAEAGVEAEVVKVESLQEIMNRGVMMTPALFIDGEAVAVGRAPSVAEIKGML 86
                                      89**********************************************************************987 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.2    0.0029        10      24      49 ..      20      46 ..      13      49 .. 0.82
   2 !   15.3   0.0   4.7e-06     0.017     113     165 ..      31      87 ..      29      88 .] 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0029
                                      T-HHHHHHHHHHH.HHHHHHHHTTSEE CS
                     Thioredoxin_4 24 rCphCakfeeeve.klleeyidtGkvk 49
                                       C  C+ ++++ve ++ e  ++++ vk
  gi|386002228|ref|YP_005920527.1| 20 GCAKCKSLAKNVEkAVAEAGVEAEVVK 46
                                      7************66888889988777 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.7e-06
                                       HTS-------HHHHHHH..HHHHHHHT--SS-EEEETTEE..E-TT--HHHHHHHHT CS
                     Thioredoxin_4 113 feacleeekldalveae..skeakkagiestPtfiingek..veepqtyeelkalid 165
                                       +e++++e  ++a+v++   ++e  ++g+ +tP ++i+ge   v ++++++e+k +++
  gi|386002228|ref|YP_005920527.1|  31 VEKAVAEAGVEAEVVKVesLQEIMNRGVMMTPALFIDGEAvaVGRAPSVAEIKGMLK 87 
                                       67778888888888654115666889*************955578999999988876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.1e-06    0.0038      12      59 ..      21      70 ..       8      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH..TSSSSSEEEETTEE CS
                      Glutaredoxin 12 CkkakrlLkelgvkfeeidvdkdeeireelkels..gvrtvPqvfidgkh 59
                                      C+k k l+k+   +++e  v+++    e l+e++  gv+  P +fidg+ 
  gi|386002228|ref|YP_005920527.1| 21 CAKCKSLAKNVEKAVAEAGVEAEVVKVESLQEIMnrGVMMTPALFIDGEA 70
                                      555555555555555555555554444444444444************96 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.1e-06    0.0075      23      78 ..      14      66 ..       4      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                                      EEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin 23 veFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78
                                      +e   + C++Ck+la  +ek+  e   +  ++kv+  ++     + +v + P+l +
  gi|386002228|ref|YP_005920527.1| 14 IEVLGTGCAKCKSLAKNVEKAVAEAGVEAEVVKVESLQE---IMNRGVMMTPALFI 66
                                      6777788*****************998888888876544...44558888888843 PP

>> Ribosomal_L17  Ribosomal protein L17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     3e-05      0.11       4      49 ..       6      52 ..       5      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                      HHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHH.H-SHHHHHHHHH CS
                     Ribosomal_L17  4 nlvtsLleherIetTlakAkelrklaeklitlak.kgelaarrkala 49
                                       +v ++++ e + t  ak+k+l+k +ek ++ a  ++e+ + +++++
  gi|386002228|ref|YP_005920527.1|  6 RMVEAMMKIEVLGTGCAKCKSLAKNVEKAVAEAGvEAEVVKVESLQE 52
                                      5899999***********************99962333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 617.59
//
Query:       gi|386002229|ref|YP_005920528.1|  [L=131]
Description: hypothetical protein Mhar_1544 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-32  110.5   0.7    4.8e-32  110.2   0.7    1.1  1  DGC       DGC domain


Domain annotation for each model (and alignments):
>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.7   2.7e-36   4.8e-32       3     105 ..      23     124 ..      21     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 2.7e-36
                               DGC   3 vsCsGasnvGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCpleCakkilekagvkpdehl 79 
                                       ++C+G+snvGq++n+aav+lakeg +k++clag+ga++++++ +ak+  k++aidGCp++Cakkil++ag+ ++  +
  gi|386002229|ref|YP_005920528.1|  23 LACAGGSNVGQISNQAAVELAKEGRGKFFCLAGIGAHIDAMILSAKER-KLVAIDGCPVQCAKKILDHAGLPAALAV 98 
                                       79*********************************************7.**************************** PP

                               DGC  80 vvtdlgikkeekldlseeeiekvvea 105
                                       vvtdlgi+k+ +l+++++++e+v+e+
  gi|386002229|ref|YP_005920528.1|  99 VVTDLGIEKSPRLEVEAADCERVAER 124
                                       **********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 911.69
//
Query:       gi|386002230|ref|YP_005920529.1|  [L=291]
Description: Methyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-39  135.1   0.0    2.5e-39  134.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.1e-24   84.2   0.0    1.5e-23   83.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    5.5e-23   81.4   0.0    1.1e-22   80.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.1e-19   70.7   0.0    1.8e-19   70.1   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.4e-13   49.5   0.0    8.4e-13   48.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    9.4e-11   41.8   0.0    1.3e-10   41.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.9e-10   40.2   0.0    5.1e-10   39.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.8e-09   37.4   0.1    2.4e-09   37.0   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    8.5e-08   31.9   0.0    1.3e-07   31.3   0.0    1.4  1  MTS              Methyltransferase small domain
    1.5e-06   28.3   0.0    3.1e-06   27.2   0.0    1.5  1  Methyltransf_8   Hypothetical methyltransferase
    5.6e-06   26.4   0.0    8.4e-06   25.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    1.5e-05   24.5   0.0      2e-05   24.0   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    3.4e-05   23.6   0.0    5.1e-05   23.1   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0016   17.9   0.0     0.0042   16.6   0.0    1.6  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.011   14.9   0.0      0.018   14.2   0.0    1.2  1  Methyltransf_3   O-methyltransferase
      0.039   13.9   0.1        0.1   12.6   0.1    1.7  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.041   13.8   0.0      0.061   13.2   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.042   14.0   0.0      0.092   12.8   0.0    1.6  1  FtsJ             FtsJ-like methyltransferase
      0.064   12.4   0.0       0.39    9.8   0.0    1.9  2  Fibrillarin      Fibrillarin
       0.14   11.4   0.0        0.2   11.0   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
       0.15   11.8   0.1       0.24   11.1   0.1    1.3  1  Methyltransf_16  Lysine methyltransferase
       0.18   11.3   0.0       0.24   10.9   0.0    1.2  1  DOT1             Histone methylation protein DOT1
       0.21   11.2   0.0       0.35   10.5   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.0   3.2e-42   2.5e-39       2     144 ..      83     221 ..      82     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 3.2e-42
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++g +vlDlG+G+G+++f +a+++gp+++v+GiD++ee++e+Ar+na+  g++nveF+ g+ie+++   ed ++Dl+
  gi|386002230|ref|YP_005920529.1|  83 REGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMTEEMVERARANAEAGGFKNVEFRLGEIESIP--AEDGSVDLV 157
                                       57899*************************************************************..89******* PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.evvegakigtqkdel 144
                                       +sn+v+n++ d++++++e+ rvl+pgg+l+++d+ llaelp+ v+++ +ay ++v ga     kd++
  gi|386002230|ref|YP_005920529.1| 158 ISNCVINLVLDKEAAFKEAYRVLRPGGRLAVSDIVLLAELPDLVRDSVEAYvGCVAGAA---RKDDY 221
                                       **************************************************999998887...55554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   1.9e-26   1.5e-23       1      97 []      88     184 ..      88     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.9e-26
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       vLdlG G G +++ +a ++g ++kv+g+D++eem+e+ar++ae+ g+ nvef+ g++e++p edgs+Dlv+s+ + +
  gi|386002230|ref|YP_005920529.1|  88 VLDLGSGAGFDSFLAASKVGpRGKVIGIDMTEEMVERARANAEAGGFkNVEFRLGEIESIPAEDGSVDLVISN-CvI 163
                                       9******************669********************99999*************************5.658 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       +++   d e+a+ke++rvL+pgG
  gi|386002230|ref|YP_005920529.1| 164 NLVL--DKEAAFKEAYRVLRPGG 184
                                       8876..5679************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   1.4e-25   1.1e-22       1      96 []      89     188 ..      89     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 1.4e-25
                                       EEET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       Ld+G+G+G  +   a k g  ++v+g+D+++em+++a+++a+  g+ +vef+ +++e++p ed+s+Dlv+s+ v++ 
  gi|386002230|ref|YP_005920529.1|  89 LDLGSGAGFDSFLAAsKVGprGKVIGIDMTEEMVERARANAEAGGFkNVEFRLGEIESIPAEDGSVDLVISNCVINL 165
                                       8**********9999555599******************************************************** PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       v d e+a+ke++RvL+pgG+l++
  gi|386002230|ref|YP_005920529.1| 166 VLDKEAAFKEAYRVLRPGGRLAV 188
                                       ********************975 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   2.2e-22   1.8e-19      43     152 ..      80     189 ..      76     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.2e-22
                                       --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEE CS
                   Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDv 119
                                       v+ ++g++vlD+ +G+g  +f  +++vg +gkv+++D+ e+m++ +++ ++  g++n+ef  ++ e +p ed+s D+
  gi|386002230|ref|YP_005920529.1|  80 VSIREGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMTEEMVERARANAEAGGFKNVEFRLGEIESIPAEDGSVDL 156
                                       67799***********************************************************************9 PP

                                       EEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 120 vtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                       v     +  v Dk+ a+keayrvl+pGGrl v 
  gi|386002230|ref|YP_005920529.1| 157 VISNCVINLVLDKEAAFKEAYRVLRPGGRLAVS 189
                                       98777788899******************9885 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.1e-15   8.4e-13       1      99 []      89     186 ..      89     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.1e-15
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++G+G G  ++  + k  p+ +++g+D  ++++e+a++   + + +n+++   e +++  +dg  s+Dlv++++v+
  gi|386002230|ref|YP_005920529.1|  89 LDLGSGAGFDSFLAASKVgPRGKVIGIDMTEEMVERARANAEAGGFKNVEFRLGEIESIPAEDG--SVDLVISNCVI 163
                                       8************99999****************888888887777666665555566555555..*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                       + + d+++++++++++L+pgGrl
  gi|386002230|ref|YP_005920529.1| 164 NLVLDKEAAFKEAYRVLRPGGRL 186
                                       *********************97 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   1.6e-13   1.3e-10      20     120 ..      82     191 ..      70     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.6e-13
                   Methyltransf_23  20 lraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                        r+g  vLd+G G G      +++ g   +v+g+D+ +e+ve+a+      ++k+ ++     ++++ ++g+ dl++
  gi|386002230|ref|YP_005920529.1|  82 IREGETVLDLGSGAGfDSFLAASKVGPrgKVIGIDMTEEMVERARanaeagGFKNVEFRLGEIESIPAEDGSVDLVI 158
                                       578899*********76666679999999***************9*9999988888888888899999********* PP

                   Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllsep 120
                                       ++ v++ v d +++++ +++ l+pgG+l +s++
  gi|386002230|ref|YP_005920529.1| 159 SNCVINLVLDKEAAFKEAYRVLRPGGRLAVSDI 191
                                       ******************************995 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   6.5e-13   5.1e-10      67     131 ..      78     142 ..      72     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6.5e-13
                                       HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                        l+++++g+ vL++GsG+G+ + + a  vg++g+v++i+ ++e+ve+a++n ++ + +nv ++ g
  gi|386002230|ref|YP_005920529.1|  78 ALVSIREGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMTEEMVERARANAEAGGFKNVEFRLG 142
                                       57899********************************************************9987 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   3.1e-12   2.4e-09     159     262 ..      82     192 ..      77     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.1e-12
                              PrmA 159 vkegeevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadviv 231
                                       ++ege+vlD+G G+G  + +aa+k+g + kv+++D+ e  v+ a++Nae  + ++ ++++   e++++ ++++d+++
  gi|386002230|ref|YP_005920529.1|  82 IREGETVLDLGSGAGFDSfLAASKVGPRgKVIGIDMTEEMVERARANAEAGGFKNvEFRLGEIESIPAeDGSVDLVI 158
                                       6899************99679*****7549************************999988777777754899***** PP

                              PrmA 232 aNILaevlie...laedikklvkeggllilSGil 262
                                       +N + + +++     +++++++++gg+l++S i+
  gi|386002230|ref|YP_005920529.1| 159 SNCVINLVLDkeaAFKEAYRVLRPGGRLAVSDIV 192
                                       **9999886422267899*************985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.7e-10   1.3e-07      31     137 ..      84     188 ..      63     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.7e-10
                                       TCSEEEEET-TTSHHHHHHH.HHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTT.STTS-EEEEEE- CS
                               MTS  31 lsgkvlDlGcGaGvlgaala.kespeaevtlvdvdarAlesakenleankle.vevvasdvlee.veekkfdlivsN 104
                                       + ++vlDlG+GaG+ +  +a k  p+ +v  +d   + +e a++n+ea +++ ve++  ++ +  +e++++dl++sN
  gi|386002230|ref|YP_005920529.1|  84 EGETVLDLGSGAGFDSFLAAsKVGPRGKVIGIDMTEEMVERARANAEAGGFKnVEFRLGEIESIpAEDGSVDLVISN 160
                                       4678**********99776616679999************************9*****99998515699******** PP

                                       --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                         +    +      e+ ++eA ++L++gG+L +
  gi|386002230|ref|YP_005920529.1| 161 CVINLVLD-----KEAAFKEAYRVLRPGGRLAV 188
                                       *9999998.....78889************975 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0     4e-09   3.1e-06     112     159 ..     143     191 ..     135     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4e-09
                                       -TTS-S--TT-EEEEEE.ES---SS-HHHHHHHHHHHEEEEEEEEEEEE CS
                    Methyltransf_8 112 dlakvPledesvdvavf.clslmgtnladflkeanrvlkvGGllkvaev 159
                                       ++  +P+ed+svd+++  c+  ++ + +   kea+rvl++GG l v+++
  gi|386002230|ref|YP_005920529.1| 143 EIESIPAEDGSVDLVISnCVINLVLDKEAAFKEAYRVLRPGGRLAVSDI 191
                                       6889*********999549999999********************9987 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.1e-08   8.4e-06      25      93 ..      84     148 ..      77     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-08
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeat 93 
                                       + +tv+D+G+G g+ sf  a+ ++  + kv+gid+ ee+ve+a++ ae+ g  f k+++f  ++ie++ 
  gi|386002230|ref|YP_005920529.1|  84 EGETVLDLGSGAGFDSFLAAS-KVGPRGKVIGIDMTEEMVERARANAEAGG--F-KNVEFRLGEIESIP 148
                                       5689*************9999.7778************************9..9.99999999988765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.6e-08     2e-05      59     170 ..      81     194 ..      76     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.6e-08
                                       T--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SE CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdr 130
                                       ++++G+t+Ld+G G G     a+++ +   kv+g+ + +e  ++a+++ ++ ++ ++ve +l + e ++     vd 
  gi|386002230|ref|YP_005920529.1|  81 SIREGETVLDLGSGAGFDSFLAASKVGprGKVIGIDMTEEMVERARANAEAGGF-KNVEFRLGEIESIPAedgSVDL 156
                                       6899********************9983358****************9988885.689*********9876789*** PP

                                       EEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                              CMAS 131 vvsvgafehvgkenydtffkklkkllkedGllllhtitsl 170
                                       v+s  +++ v  ++  + fk+++++l+++G+l++  i+ l
  gi|386002230|ref|YP_005920529.1| 157 VISNCVINLVLDKE--AAFKEAYRVLRPGGRLAVSDIVLL 194
                                       ********998775..669*************99988765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.5e-08   5.1e-05      75     129 ..     108     161 ..      98     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.5e-08
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnp 129
                                       ++ k++g+D+ +++v++ar Nae+ g  + +ef+  ++ ++++++g+vd++++n 
  gi|386002230|ref|YP_005920529.1| 108 PRGKVIGIDMTEEMVERARANAEAGGF-KNVEFRLGEIESIPAEDGSVDLVISNC 161
                                       56689*****************97776.579***********9999*******95 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.3e-06    0.0042       4      58 ..      87     142 ..      84     150 .. 0.91
   2 ?   -2.3   0.0       3.3   2.6e+03      99     115 ..     172     188 ..     168     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                                       EEEEET-TTS.HHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES CS
                    Methyltransf_4   4 vvleiGcGkG.eflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrg 58 
                                       +vl++G+G G ++ +a +k  P  +++Gi++ +++v+++ +++ea ++kN++   g
  gi|386002230|ref|YP_005920529.1|  87 TVLDLGSGAGfDSFLAASKVGPRGKVIGIDMTEEMVERARANAEAGGFKNVEFRLG 142
                                       799*******88999***********************************987665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.3
                                       HHHHHHHHEEEEEEEEE CS
                    Methyltransf_4  99 llkelarvLkkgGvlel 115
                                         ke+ rvL++gG l +
  gi|386002230|ref|YP_005920529.1| 172 AFKEAYRVLRPGGRLAV 188
                                       56888999*****9864 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.018      42     108 ..      79     144 ..      75     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                    Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegda 108
                                       Lv++ +   vl++G   G+  +  a ++ + Gk++ id+ +e +e a+   + ag  + +e++ g+ 
  gi|386002230|ref|YP_005920529.1|  79 LVSIREGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMTEEMVERARANAE-AGGFKNVEFRLGEI 144
                                       899999***************************************9998776.55557789988875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00013       0.1      15      87 ..     108     188 ..      94     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                       -..EEEEEESSHHHHHHHHHTT.ESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSC......SHHHHHHHHHCEEE CS
                        ADH_zinc_N  15 a..eviavdsseeklelakklG.adevinykeadlverikeltg.gegvdvvfecvG......sgatleaalkllkp 81 
                                          +vi++d +ee +e a+ +  a  + n  e     +i+++   ++ vd+v+           +a++++a+++l+p
  gi|386002230|ref|YP_005920529.1| 108 PrgKVIGIDMTEEMVERARANAeAGGFKNV-E-FRLGEIESIPAeDGSVDLVISNCVinlvldKEAAFKEAYRVLRP 182
                                       355899999999999999996548888888.3.366777777755778999764333255557899*********** PP

                                       EEEEEE CS
                        ADH_zinc_N  82 gGrlvv 87 
                                       gGrl+v
  gi|386002230|ref|YP_005920529.1| 183 GGRLAV 188
                                       ***987 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.9e-05     0.061      12      74 ..      82     144 ..      77     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                       +++g++v+D G+  g+ ++ ++ k g   kvi +D+ e+ +e+a++n+e  g+ +++e+rl++ 
  gi|386002230|ref|YP_005920529.1|  82 IREGETVLDLGSGAGFDSFLAAsKVGPRGKVIGIDMTEEMVERARANAEAGGF-KNVEFRLGEI 144
                                       78999*********998876652567889********************9999.579***9974 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.092      19      96 ..      82     162 ..      76     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS........HHH...TTEEEECS-CCCSSHHHHHCHCH CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm........apl...pgvttiqgditdpetiekikeal 83 
                                       +++g+tv+Dlg++ G  s  ++ ++g++gkv+++D+  +m        +     ++v++  g i +  +++      
  gi|386002230|ref|YP_005920529.1|  82 IREGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMtEEMveraranaE-AggfKNVEFRLGEIESIPAED------ 151
                                       46899***********9*******************7777665543320.122345555555554444333...... PP

                                       HHSSEEEEEE--S CS
                              FtsJ  84 serkvdlvvsDga 96 
                                           vdlv+s  +
  gi|386002230|ref|YP_005920529.1| 152 --GSVDLVISNCV 162
                                       ..34555555554 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0005      0.39      50     108 ..      64     122 ..      52     131 .. 0.89
   2 ?   -0.0   0.0       0.5   3.9e+02     167     208 ..     150     192 ..     144     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0005
                                       TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                       Fibrillarin  50 pfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                       p+ s l+ +  + ++ + i++g+ vL lG+++G      +  vg++g+v ++++++ ++
  gi|386002230|ref|YP_005920529.1|  64 PRGSNLGLGCGNPIALVSIREGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMTEEMV 122
                                       56678888888899999*****************9999999************998776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.5
                                       EEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHH.TTEEEEEEE CS
                       Fibrillarin 167 eggyllisikarsidvtkepeevfkeeveklke.eglkvleqv 208
                                       e+g + ++i    i+ + + e+ fke  + l+   +l v + v
  gi|386002230|ref|YP_005920529.1| 150 EDGSVDLVISNCVINLVLDKEAAFKEAYRVLRPgGRLAVSDIV 192
                                       6899999999999*************99999862346666655 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025       0.2      46     127 ..      83     165 ..      75     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                       -CCC-.EEEETSTTTTTHHHHH.HH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEE CS
                              GidB  46 kekrdkviDvGsGaGlPGipLa.iarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvt 120
                                        e + +v+D+GsGaG+ +   a  + p  k++ ++ +e  ++  +   e+ + +nve+   ++e+   e  ++d+v+
  gi|386002230|ref|YP_005920529.1|  83 REGE-TVLDLGSGAGFDSFLAAsKVGPRGKVIGIDMTEEMVERARANAEAGGFKNVEFRLGEIESiPAEDGSVDLVI 158
                                       3333.5**********9966541577888888888888888888888888888888888888888777778888888 PP

                                       EC-SSSH CS
                              GidB 121 sRAlasl 127
                                       s  + +l
  gi|386002230|ref|YP_005920529.1| 159 SNCVINL 165
                                       8777665 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00031      0.24      46      91 ..      84     131 ..      78     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                   Methyltransf_16  46 sklsvlELGsGtGlvGlavaell.peakviltDlee.llellkkniel 91 
                                       ++ +vl+LGsG+G     +a+++ p+ kvi  D+ e ++e  + n e+
  gi|386002230|ref|YP_005920529.1|  84 EGETVLDLGSGAGFDSFLAASKVgPRGKVIGIDMTEeMVERARANAEA 131
                                       6789************9999998899***9888755499999999988 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031      0.24      38      86 ..      80     129 ..      75     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                       TT--TT-EEEEES-TTSHHHHHHHHHH--S.EEEEEE--HHHHHHHHHHH CS
                              DOT1  38 vnlkkedvFvDLGSGvGnvvlqaalevgck.lsvGvEimdnaselaekqk 86 
                                       v +++ ++ +DLGSG G   ++aa +vg + + +G++++++  e a++++
  gi|386002230|ref|YP_005920529.1|  80 VSIREGETVLDLGSGAGFDSFLAASKVGPRgKVIGIDMTEEMVERARANA 129
                                       67889999******************99763678****999988887765 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00044      0.35      36      87 ..      80     131 ..      76     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                             GCD14  36 LelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefre 87 
                                       + +++G  v++ G G+g  s   a  v+P+G++  ++  e+ +e+ar + + 
  gi|386002230|ref|YP_005920529.1|  80 VSIREGETVLDLGSGAGFDSFLAASKVGPRGKVIGIDMTEEMVERARANAEA 131
                                       5799******************************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1778.54
//
Query:       gi|386002231|ref|YP_005920530.1|  [L=163]
Description: Arsenate reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   60.0   0.1    4.4e-16   59.6   0.1    1.2  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   2.4e-20   4.4e-16       1     134 [.      23     154 ..      23     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 2.4e-20
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       vlf C+ N++RS+mAe l+r++     ++e+ e++SaG++   +  ++prav+v++e  i++sg++++  s+ e   
  gi|386002231|ref|YP_005920530.1|  23 VLFLCTHNSARSQMAEGLLRDL-----YGERYEANSAGVE---ATAVHPRAVSVMEEIEIDISGQRSKAASDLEDIV 91 
                                       89********************.....7779*********...99***************************99999 PP

                                       SSEEEESSHHHHHHHHHHCCT..TGGGGEEEGGGGSSTSS---HT......TSSHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkreleslape..kekakvkllgeyteqldieDPy......ygeieafeevldei 134
                                       +D+ +++++++  e++++  +     ++    +e   ++  eDP+       ++  af++++dei
  gi|386002231|ref|YP_005920530.1|  92 FDVAVTVCDRAR-EACPVCTTdlDLPSRAPKARE-VIHKSFEDPAavsgteEEQLCAFRQARDEI 154
                                       ********9987.777765553322222222233.345566666644432233355666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1212.68
//
Query:       gi|386002232|ref|YP_005920531.1|  [L=81]
Description: Ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-14   53.1   2.3    4.6e-14   52.7   2.3    1.2  1  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
    1.9e-13   50.9   2.9    2.3e-13   50.7   2.9    1.1  1  Fer4_15        4Fe-4S single cluster domain
    2.9e-05   24.1   3.0    8.1e-05   22.7   3.0    1.7  1  Fer4_10        4Fe-4S dicluster domain
    2.9e-05   23.7   5.7    0.00024   20.8   1.3    2.3  2  Fer4           4Fe-4S binding domain
    0.00046   21.1   2.0     0.0032   18.4   0.2    2.1  2  Fer4_16        4Fe-4S double cluster binding domain
     0.0011   19.1   5.1      0.043   14.0   2.0    2.2  3  Fer4_9         4Fe-4S dicluster domain
     0.0016   19.0   0.7     0.0025   18.3   0.7    1.4  1  Fer4_17        4Fe-4S dicluster domain
     0.0024   18.4   2.6     0.0078   16.8   2.7    1.8  1  Fer4_7         4Fe-4S dicluster domain
     0.0072   16.4   3.8      0.016   15.4   3.8    1.8  1  Fer4_21        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.1   1.6      0.018   15.5   1.6    1.4  1  Fer4_8         4Fe-4S dicluster domain
      0.032   14.7   1.1      0.032   14.7   1.1    2.1  2  Fer4_4         4Fe-4S binding domain
      0.048   13.8   1.1      0.048   13.8   1.1    2.2  2  Fer4_2         4Fe-4S binding domain
       0.15   12.4   0.0       0.18   12.1   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
       0.23   11.6   5.5       0.43   10.7   0.8    2.3  2  Fer4_6         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   2.3   3.6e-17   4.6e-14       1      58 []       6      73 ..       6      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 3.6e-17
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqpts..........eeekadaeeAadaCPvesIgv 58
                                      ++rd Ci+cg+C+  +P++F ed+++g+s v e+++           ++ + +++eA +aCP e I+v
  gi|386002232|ref|YP_005920531.1|  6 IERDGCISCGQCWGSCPEFFIEDPDDGRSSVSEERRIagkldegsapDQFEGCLREAEEACPAEVIQV 73
                                      79******************************9544444444445547779***************87 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   2.9   1.8e-16   2.3e-13       2      66 .]       5      73 ..       4      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.8e-16
                           Fer4_15  2 vvDrdaCigcglCvaeapevfelde.dglasvl....lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      +++rd Ci+cg+C+  +pe+f +d  dg +sv     ++ g+++eg  pd+ e + +eA +aCP+++I+v
  gi|386002232|ref|YP_005920531.1|  5 KIERDGCISCGQCWGSCPEFFIEDPdDGRSSVSeerrIA-GKLDEGSAPDQFEGCLREAEEACPAEVIQV 73
                                      69**********************944666666777643.567788**********************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   3.0   6.3e-08   8.1e-05       3      56 .]       5      67 ..       3      78 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.3e-08
                           Fer4_10  3 vidddtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcg.aCveaCP 56
                                      +i++d Ci Cg+C  +CP  +        +sv+ +  + ++  +  ++++ +gc  +  eaCP
  gi|386002232|ref|YP_005920531.1|  5 KIERDGCISCGQCWGSCPEFFiedpddgrSSVSEERRIAGKLDEGSAPDQFEGCLrEAEEACP 67
                                      7999***************88998888863333333333333333344444555336666666 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.3   1.8e-07   0.00024       2      23 ..       5      26 ..       4      27 .. 0.85
   2 ?    5.2   0.2     0.016        20      15      24 .]      63      72 ..      63      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      +i  + Ci CG+C   CP   I
  gi|386002232|ref|YP_005920531.1|  5 KIERDGCISCGQCWGSCPEFFI 26
                                      578899************7655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                      HHHSTTTEEE CS
                              Fer4 15 vevCPvgAIt 24
                                      +e+CP ++I+
  gi|386002232|ref|YP_005920531.1| 63 EEACPAEVIQ 72
                                      59*****995 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   2.5e-06    0.0032       2      28 ..      11      37 ..      10      62 .. 0.72
   2 ?    2.9   0.2      0.17   2.1e+02      10      20 ..      64      74 ..      56      81 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiear 28
                                      C++Cg+C  +CP+  i+ + + +    
  gi|386002232|ref|YP_005920531.1| 11 CISCGQCWGSCPEFFIEDPDDGRSSVS 37
                                      *****************9954443333 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                           Fer4_16 10 evCPtnaikek 20
                                      e+CP+++i+  
  gi|386002232|ref|YP_005920531.1| 64 EACPAEVIQVS 74
                                      79****99865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.0   3.3e-05     0.043      35      48 ..      10      23 ..       2      26 .. 0.77
   2 !   12.6   5.6     9e-05      0.11       2      47 ..      11      67 ..      10      71 .. 0.70
   3 ?    5.4   0.1     0.017        21       9      21 ..      63      75 ..      56      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                            Fer4_9 35 aCigCgaCveaCpk 48
                                       Ci+Cg+C   Cp+
  gi|386002232|ref|YP_005920531.1| 10 GCISCGQCWGSCPE 23
                                      69999999999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9e-05
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCp 47
                                      C++Cg+C  +Cp   +++ + +r    ++++              e C+  ++ +eaCp
  gi|386002232|ref|YP_005920531.1| 11 CISCGQCWGSCPEFFIEDPDDGRSSVSEERRIagkldegsapdqfEGCL--REAEEACP 67
                                      9999999999999998888888877776665567777777776665565..45555555 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.017
                            Fer4_9  9 veaCpagvvveda 21
                                      +eaCpa+v++ + 
  gi|386002232|ref|YP_005920531.1| 63 EEACPAEVIQVSP 75
                                      799*****99876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7     2e-06    0.0025       2      59 ..      11      69 ..      10      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                           Fer4_17  2 CiqCgyClpeCpsyea..ydnepkkllraakl.glleeaekeekaslCieCgeCerkCPqg 59
                                      Ci+Cg C  +Cp + +   d+ + ++ ++ ++ g+l+e ++ ++++ C+   e e++CP++
  gi|386002232|ref|YP_005920531.1| 11 CISCGQCWGSCPEFFIedPDDGRSSVSEERRIaGKLDEGSAPDQFEGCLR--EAEEACPAE 69
                                      ************87663233346677777777568888888889999974..456777766 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.7   6.1e-06    0.0078       2      51 ..      11      69 ..      10      78 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.1e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenek........gtekveidpekClgCga.CvavCPtg 51
                                      Ci Cg+C   Cp   ie +++ + +        g+ +    p++  gC +  +++CP++
  gi|386002232|ref|YP_005920531.1| 11 CISCGQCWGSCPEFFIEDPDDGRSSvseerriaGKLDEGSAPDQFEGCLReAEEACPAE 69
                                      ************99999665322222211111133333556788899977799999986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.8   1.2e-05     0.016       2      20 ..       5      23 ..       4      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                           Fer4_21  2 ridedkCigCgkCliaCed 20
                                      +i++d Ci+Cg+C  +C++
  gi|386002232|ref|YP_005920531.1|  5 KIERDGCISCGQCWGSCPE 23
                                      5999*************97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.6   1.4e-05     0.018       4      51 ..      10      58 ..       7      70 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                            Fer4_8  4 kCieCgaCqsaCpvlrrtk..khlldargeaaedvqeeqvleeeealwsC 51
                                       Ci Cg C  +Cp +  ++  + + +  +e+   + + ++ ++ + ++ C
  gi|386002232|ref|YP_005920531.1| 10 GCISCGQCWGSCPEFFIEDpdDGRSSVSEERRI-AGKLDEGSAPDQFEGC 58
                                      6***********955554421222222222222.3333333334445555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.1   2.5e-05     0.032       2      15 ..       9      22 ..       7      40 .. 0.88
   2 ?   -0.5   0.1       1.9   2.5e+03      13      16 ..      65      68 ..      63      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + Ci Cg+C  +CP
  gi|386002232|ref|YP_005920531.1|  9 DGCISCGQCWGSCP 22
                                      56***********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                            Fer4_4 13 aCPq 16
                                      aCP 
  gi|386002232|ref|YP_005920531.1| 65 ACPA 68
                                      7996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   3.8e-05     0.048       4      22 .]       5      23 ..       3      23 .. 0.82
   2 ?    1.0   0.2      0.44   5.6e+02      18      22 .]      64      68 ..      57      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                            Fer4_2  4 vvdtdrCigCgaCvsa.CPa 22
                                      ++++d Ci+Cg C +  CP+
  gi|386002232|ref|YP_005920531.1|  5 KIERDGCISCGQC-WGsCPE 23
                                      68999********.555995 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                            Fer4_2 18 saCPa 22
                                       aCPa
  gi|386002232|ref|YP_005920531.1| 64 EACPA 68
                                      68997 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.18       9      52 ..      18      61 ..      14      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                      CCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHH CS
                     Nitro_FeMo-Co  9 FGrapyFaiyeveegevkivenrveeaadaegggggklaqllae 52
                                       G++p+F+i + ++g+ ++ e+r  + + +eg+++++++  l e
  gi|386002232|ref|YP_005920531.1| 18 WGSCPEFFIEDPDDGRSSVSEERRIAGKLDEGSAPDQFEGCLRE 61
                                      59********************9444555555677777666655 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00034      0.43       4      21 ..       6      23 ..       3      26 .. 0.85
   2 ?    3.2   0.3     0.083   1.1e+02      16      24 .]      63      71 ..      57      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                            Fer4_6  4 idpdkCigCgdCvrvCPe 21
                                      i +d Ci+Cg C   CPe
  gi|386002232|ref|YP_005920531.1|  6 IERDGCISCGQCWGSCPE 23
                                      67788*******999996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.083
                            Fer4_6 16 vrvCPegai 24
                                      + +CP+ +i
  gi|386002232|ref|YP_005920531.1| 63 EEACPAEVI 71
                                      579**9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 624.80
//
Query:       gi|386002233|ref|YP_005920532.1|  [L=100]
Description: hypothetical protein Mhar_1548 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-07   30.2   0.0    4.8e-07   29.8   0.0    1.2  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.7e-11   4.8e-07       7      83 ..      18      92 ..      13      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.7e-11
                                      .-HHHHHHT--TT-..EEEE-GGGGGGGBTTBTTHHHHHTSSSEEEEEHHHHHHTT-TTSB-TTSEEE-..HHHHHHHH CS
                              DsrH  7 nalksclrllqegD..avlLieDgVyaalkgsrllkalkeasvklyaLkeDleARGlteqlsegvkvid..ydgfVelt 81
                                      ++ k c++ll  ++  +++L +DgVy +l++++++      s++++a  eD+ ARG+     ++vkv++  y+ +Ve++
  gi|386002233|ref|YP_005920532.1| 18 DRSKLCMKLLARSEraRLYLAGDGVYHLLEDKAVFP----PSCEIFACLEDVAARGVV--ARKEVKVLEefYNILVEDV 90
                                      37889999995554449*************875555....45778*************..789*****999*****999 PP

                                      HH CS
                              DsrH 82 vk 83
                                      ++
  gi|386002233|ref|YP_005920532.1| 91 ME 92
                                      98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 613.83
//
Query:       gi|386002234|ref|YP_005920533.1|  [L=114]
Description: hypothetical protein Mhar_1549 [Methanosaeta harundinacea 6Ac]
Scores for 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-13   48.7   0.0      1e-12   48.4   0.0    1.0  1  DrsE      DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.083   13.0   0.0        0.2   11.8   0.0    1.7  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   1.1e-16     1e-12       2     115 ..       3     112 ..       2     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.1e-16
                                       EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEH CS
                              DrsE   2 kvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCg 78 
                                       +vf+l  ++pygse   ++l  a aa++ + ev v +ygdGv+l+l+gq++++ + +nlae l a+ e+  ++++ +
  gi|386002234|ref|YP_005920533.1|   3 SVFYLLDSAPYGSE-KALGLLNAAAASLGKMEVTVGLYGDGVYLALRGQDSKGLGVPNLAEILYAYGEM--RVVAHE 76 
                                       699999********.999999999999999*******************************99999999..7***** PP

                                       HHHHHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEE CS
                              DrsE  79 qaakargldededlgvgvevsglgelaelqnegdrvi 115
                                        ++++rgl ++ ++  +ve+++  ++ ++++e+d +i
  gi|386002234|ref|YP_005920533.1|  77 PSLAKRGLFCEGLI-ETVELADEEAFLKAVKESDCLI 112
                                       *********98888.8****************99665 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05       0.2      22      81 ..      36     105 ..      19     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                                       EEE-GGGGGGGBTTBTTHH....HHHTS.....SSEEEEEHHHHHHTT-T.TSB-TTSEEE-HHHHHHHH CS
                              DsrH  22 vlLieDgVyaalkgsrllk....alkea.....svklyaLkeDleARGlt.eqlsegvkvidydgfVelt 81 
                                       v L +DgVy+al+g++ +     +l+e+     +++++a ++ l  RGl  e l+e v++ d + f + +
  gi|386002234|ref|YP_005920533.1|  36 VGLYGDGVYLALRGQDSKGlgvpNLAEIlyaygEMRVVAHEPSLAKRGLFcEGLIETVELADEEAFLKAV 105
                                       56899*******9987643222245555777899****************999*****999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 785.38
//
Query:       gi|386002235|ref|YP_005920534.1|  [L=122]
Description: hypothetical protein Mhar_1550 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-16   59.9   0.0    3.2e-16   59.7   0.0    1.0  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.8e-20   3.2e-16       1     116 [.       2     119 ..       2     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.8e-20
                                       -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEE CS
                              DrsE   1 kkvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvC 77 
                                       k ++i+   gpy se+a +a ++a aa++   +v++f+y d+v+++++gq   pa + +   l++ l+e g+++ +C
  gi|386002235|ref|YP_005920534.1|   2 KTLTIILADGPYISEYAEIAKNIADAALKRY-HVNIFLYLDAVHIPRRGQ--RPAFFADEGGLFADLAERGATIRAC 75 
                                       67899*********************99887.9***************77..67779999***************** PP

                                       HHHHHHTT--GGGE-...T-..-EEEE-HHHHHHHHHH-SEEEE CS
                              DrsE  78 gqaakargldededl...gv..gvevsglgelaelqnegdrvit 116
                                         +a+arg+ ++ed    +   g+++s+l +l ++++e+d vit
  gi|386002235|ref|YP_005920534.1|  76 SRCAAARGYLAEEDGtrrEYheGIKISSLYDLPDMISESDGVIT 119
                                       **********988777652266*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 816.45
//
Query:       gi|386002236|ref|YP_005920535.1|  [L=276]
Description: hypothetical protein Mhar_1551 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-12   44.4   0.5      2e-11   43.3   0.5    1.6  1  FeS          Putative Fe-S cluster
    5.1e-07   29.7   0.0      2e-06   27.8   0.0    2.0  2  HTH_20       Helix-turn-helix domain
      3e-06   27.0   0.0    6.3e-06   26.0   0.0    1.5  1  HTH_5        Bacterial regulatory protein, arsR family
     0.0071   16.3   0.2      0.014   15.4   0.2    1.5  1  YhfH         YhfH-like protein
     0.0073   16.8   0.1      0.075   13.6   0.0    2.2  2  AAA_assoc_C  C-terminal AAA-associated domain
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.084   12.8   0.0    1.7  1  HTH_12       Ribonuclease R winged-helix domain
       0.15   12.1   0.0        0.3   11.1   0.0    1.5  1  TBP          Transcription factor TFIID (or TATA-binding prot


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.5     8e-15     2e-11       1      33 []     224     256 ..     224     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 8e-15
                               FeS   1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33 
                                       LP+t+Cg+CG+++C  f   l++ge++l++C+p
  gi|386002236|ref|YP_005920535.1| 224 LPQTDCGECGEQSCYSFSIRLMAGEVSLDLCKP 256
                                       9******************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   7.7e-10     2e-06       3      55 ..      22      71 ..      20      73 .. 0.92
   2 ?   -3.4   0.0       4.2   1.1e+04       2      15 ..     114     127 ..     102     133 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 7.7e-10
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +  A+a+  Rr++++ L  ++++t +e+ e++   k+ l+yHL++Le+agL+e
  gi|386002236|ref|YP_005920535.1| 22 VSNAMANVPRRKMMAFL-AGGERTSEEIGEAV--GKSMLDYHLKILEQAGLIE 71
                                      66899**99********.*************6..7777**************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                                       HHHHHHS-HHHHHH CS
                            HTH_20   2 qiaeALahPvRrri 15 
                                       q++  +a+ +  ri
  gi|386002236|ref|YP_005920535.1| 114 QLLPCIADSTKFRI 127
                                       44445566666666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.5e-09   6.3e-06       4      46 ..      31      71 ..      28      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.5e-09
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      R+k++ +La ge+++ e+ e++g+  s +++HLk+L++aGL+e
  gi|386002236|ref|YP_005920535.1| 31 RRKMMAFLAGGERTSEEIGEAVGK--SMLDYHLKILEQAGLIE 71
                                      99*******************996..69*************96 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   5.5e-06     0.014       4      22 ..     217     235 ..     215     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                              YhfH   4 iveFfrnLPkKkCteCGke 22 
                                       ++e++r LP+  C eCG++
  gi|386002236|ref|YP_005920535.1| 217 PMEIYRYLPQTDCGECGEQ 235
                                       79***************96 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.9e-05     0.075      19      55 ..      62      98 ..      55     117 .. 0.87
   2 ?    0.2   0.0      0.41   1.1e+03      14      44 ..     145     175 ..     141     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                       AAA_assoc_C 19 eaaelLglveveegdielTelGrkfveadikerKeif 55
                                      +++e  gl+e+  g+++l e G++f+e+++++ K+ +
  gi|386002236|ref|YP_005920535.1| 62 KILEQAGLIEIGAGKVRLSEFGKNFMETKVEKPKDAV 98
                                      5677889************************999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                       AAA_assoc_C  14 LlpiveaaelLglveveegdielTelGrkfv 44 
                                       L+p  +  e +g + +++gd+ +T  G+  v
  gi|386002236|ref|YP_005920535.1| 145 LFPRGRYSERIGALIIQRGDVLITIYGTGSV 175
                                       77777788888888999*******9997655 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05     0.084      24      62 ..      46      83 ..      42      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                            HTH_12 24 kkrgydigeravRyrLrkleergltrrvgyagreltEkG 62
                                      +++g+++g+  + y+L++le+ gl++  g ++ +l E G
  gi|386002236|ref|YP_005920535.1| 46 EEIGEAVGKSMLDYHLKILEQAGLIE-IGAGKVRLSEFG 83
                                      4679********************98.455555666655 PP

>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012       0.3      42      83 ..     159     198 ..     147     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
                               TBP  42 vyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                                       +++  +  v ++i+ +G+v++t  k e e+r +++++ ++++
  gi|386002236|ref|YP_005920535.1| 159 IIQ--RGDVLITIYGTGSVTMTMIKGEAEARGVLAELREKIN 198
                                       444..346999********************99999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1901.66
//
Query:       gi|386002237|ref|YP_005920536.1|  [L=467]
Description: cytochrome c biogenesis protein transmembrane region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   77.6  10.7    1.9e-21   77.0  10.7    1.4  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
    2.5e-09   37.4  20.4      2e-06   27.9   3.4    2.9  2  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
    7.6e-07   29.1   0.0    2.3e-06   27.6   0.0    1.8  1  AhpC-TSA  AhpC/TSA family
      6e-06   26.0   0.0    1.1e-05   25.1   0.0    1.4  1  Redoxin   Redoxin
  ------ inclusion threshold ------
      0.067   13.0   2.5        1.4    8.7   0.5    2.5  2  DUF443    Protein of unknown function (DUF443)
        0.1   12.7   0.3        0.1   12.7   0.3    2.5  3  MpPF26    M penetrans paralogue family 26


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0  10.7   6.3e-25   1.9e-21       2     211 ..     220     457 ..     219     459 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 6.3e-25
                              DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkv.....kvllkallFvlGlslvfvslglsaaflgqllkd 73 
                                       f+ G+++++sPC l+l+ a++syi +     v ++++       + l   + F lG+++vf  lgl ++ lg  ++d
  gi|386002237|ref|YP_005920536.1| 220 FGLGIITSFSPCSLALLIAMFSYIMTSRRRKVLSDEEDYgssarEGLWIGIAFTLGMAIVFFVLGLFISNLGVFVRD 296
                                       778*********************9988777766655444334577888999********************99987 PP

                              DsbD  74 vkevirrvaglivillGlhflgvfkievleklkll........................lkikkkaelsvlgalllG 126
                                       + +    +ag++ + lG+++   +  e+le  k                               k+++ ++ga+ lG
  gi|386002237|ref|YP_005920536.1| 297 S-RFFDLAAGILLVALGINVFKPIG-EILEPIKARlparrgeeeefrerkglmeravnlSIGLFKHSV-FIGAFTLG 370
                                       5.6889999********99765333.344433333345556666666666666777664222334444.78****** PP

                              DsbD 127 ltFalgwsPC.igPvlasvlalaaskeslakgallllvyvlGlaipfllvglllellkkkl.kslkkyskaveiagg 201
                                       + Falgw+PC i+ v+ +++ l +++ s+++g l+l+v+ +G ++p++ ++ ++ ++  kl +      +a+ +a g
  gi|386002237|ref|YP_005920536.1| 371 VFFALGWAPCaISLVFPALIWLISQDISALTGGLMLFVFGVGHGVPIIPIATFSRSFGGKLgEEYLAVGSAIVKAFG 447
                                       **********55889999*************************************9986652455666677888889 PP

                              DsbD 202 vllvllGvll 211
                                       +++++ G+++
  gi|386002237|ref|YP_005920536.1| 448 IMIIITGLVY 457
                                       9999999876 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 !   13.3   9.1     2e-05      0.06     116     198 ..     214     313 ..     166     314 .. 0.80
   2 !   27.9   3.4   6.8e-10     2e-06     117     197 ..     362     454 ..     333     456 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                            DsbD_2 116 kslasalllGllnGllpCgl..vysalllalas.............gsaleGalvmlaFgLGTlpalllfglllgll 177
                                        +l ++++lG+++++ pC l  + +++ ++++s             +sa eG ++ +aF LG  ++++++gl+++ l
  gi|386002237|ref|YP_005920536.1| 214 VTLIGMFGLGIITSFSPCSLalLIAMFSYIMTSrrrkvlsdeedygSSAREGLWIGIAFTLGMAIVFFVLGLFISNL 290
                                       577899************77536667777777666667667777767999*************************** PP

                            DsbD_2 178 skklr.kkllr.lagvllillgl 198
                                       +  +r  +++  +ag+ll++lg+
  gi|386002237|ref|YP_005920536.1| 291 GVFVRdSRFFDlAAGILLVALGI 313
                                       **999668888677899999886 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 6.8e-10
                            DsbD_2 117 slasalllGlln..GllpCgl..vysalllalas.gsaleGalvmlaFgLGTlpalllfglllgllskklr...... 182
                                        + +a++lG+++  G++pC++  v++al++ +++  sal+G+l++++Fg+G  ++++ ++++++ ++ kl       
  gi|386002237|ref|YP_005920536.1| 362 VFIGAFTLGVFFalGWAPCAIslVFPALIWLISQdISALTGGLMLFVFGVGHGVPIIPIATFSRSFGGKLGeeylav 438
                                       4668999997643399***76559999**9997747*************************9999988777344444 PP

                            DsbD_2 183 .kkllrlagvllillg 197
                                         +++++ g+++i+ g
  gi|386002237|ref|YP_005920536.1| 439 gSAIVKAFGIMIIITG 454
                                       4666666666666666 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   7.6e-10   2.3e-06       4      57 ..      38      90 ..      37     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 7.6e-10
                                      B----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCC CS
                          AhpC-TSA  4 kapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefke 57
                                      +apdf+++++dg+++slsd++g++vvl +++  ++p C +  +ala ++ e++ 
  gi|386002237|ref|YP_005920536.1| 38 RAPDFSGTTQDGQNFSLSDFEGEVVVLHITNI-ESPLCIECEKALASQIGELQR 90
                                      59********************9999998888.***********9999999885 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.8e-09   1.1e-05       5     129 ..      38     169 ..      34     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.8e-09
                                       BB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HH...HHHTHH.HHHTHHHHHHCS.TTTEEEEEESSSHH. CS
                           Redoxin   5 kaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPt...Csaehp.yleklaellkek.gvdvvavvadndaf. 75 
                                       +aPdf+   +++dg+++sls+f+g +vv+ +     +P    C + +  ++ +l++l ++k +v+ v +++ ++++ 
  gi|386002237|ref|YP_005920536.1|  38 RAPDFSG--TTQDGQNFSLSDFEGEVVVLHITNI-ESPLcieCEKALAsQIGELQRLVENKpDVNLVTLNVRKNPYs 111
                                       58****6..56***************88888877.99994445555559*****999877758999999**999998 PP

                                       ......HHHHHHHTT-TSEEEE-.TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEE CS
                           Redoxin  76 ......vkefwgkeglkfpvlsD.gsaaftkalGlrleedaseg.lrtpryavidedgkvvy 129
                                               ++wg ++++++ + D +   +++ +  +++  + eg +  p+  +id++g vv 
  gi|386002237|ref|YP_005920536.1| 112 kdgstlSESWWG-TEVSWIWAEDfEPYRIAARYV-DFT--NFEGgFSNPTILLIDREGMVVG 169
                                       888884444444.445777777775555555554.232..2233467788888888877765 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.5   0.00047       1.4      99     179 ..     231     306 ..     213     317 .. 0.78
   2 ?    3.3   0.1      0.02        61      24      42 ..     382     400 ..     377     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00047
                            DUF443  99 llivlllvlvlriyiskklkkklynevelekkskekiilipkslknfllllfaylfflglvilalvalietqniiil 175
                                       + ++ll++++ +i+ s++ +k l +e ++  +++e +++       f l + + +f+lgl+i  l +++    ++ l
  gi|386002237|ref|YP_005920536.1| 231 CSLALLIAMFSYIMTSRR-RKVLSDEEDYGSSAREGLWIGI----AFTLGMAIVFFVLGLFISNLGVFVRDSRFFDL 302
                                       677777777777777777.89999999************99....77778888889999999999999876666655 PP

                            DUF443 176 ivll 179
                                        + +
  gi|386002237|ref|YP_005920536.1| 303 AAGI 306
                                       5544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                            DUF443  24 ikilfPflnwliPkkvyki 42 
                                       i+++fP l+wli++ +  +
  gi|386002237|ref|YP_005920536.1| 382 ISLVFPALIWLISQDISAL 400
                                       799**********988766 PP

>> MpPF26  M penetrans paralogue family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.5   7.6e+03     106     123 ..       9      25 ..       5      32 .. 0.40
   2 ?   12.7   0.3   3.5e-05       0.1      13      80 ..     222     290 ..     210     299 .. 0.77
   3 ?   -3.3   1.7         3   8.9e+03      56      73 ..     434     451 ..     382     458 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                            MpPF26 106 liigifilpifsiidcfi 123
                                       li+g +     ++++ f 
  gi|386002237|ref|YP_005920536.1|   9 LIVGAIT-LTAVLVALFS 25 
                                       3333332.2233333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.5e-05
                            MpPF26  13 ltiiilyllatvlllvsllayivllskskllskeyeeesslleaelligvllillidi..fyivnfilei 80 
                                       l ii  +++  ++ll+++ +yi+++  +k+ls e    ss  e+ l ig+ + l ++i  f++  fi  +
  gi|386002237|ref|YP_005920536.1| 222 LGIITSFSPCSLALLIAMFSYIMTSRRRKVLSDEEDYGSSAREG-LWIGIAFTLGMAIvfFVLGLFISNL 290
                                       55788899999*********************996666666666.7788888888888667777777665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3
                            MpPF26  56 aelligvllillidifyi 73 
                                         l++g  ++ + +i++i
  gi|386002237|ref|YP_005920536.1| 434 EYLAVGSAIVKAFGIMII 451
                                       344555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3081.75
//
Query:       gi|386002238|ref|YP_005920537.1|  [L=184]
Description: hypothetical protein Mhar_1553 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.6   0.2      0.068   12.9   0.2    1.3  1  DUF4538   Domain of unknown function (DUF4538)


Domain annotation for each model (and alignments):
>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.8e-06     0.068       7      27 ..      19      39 ..      15      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-06
                           DUF4538  7 vllvggvvgliglalYPiiia 27
                                      v+lv+g+v+++ +a YP+  +
  gi|386002238|ref|YP_005920537.1| 19 VILVAGLVAVVSAAEYPVGSE 39
                                      799**************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1255.87
//
Query:       gi|386002239|ref|YP_005920538.1|  [L=86]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-05   24.6   0.6    4.3e-05   23.3   0.6    1.8  1  HTH_5     Bacterial regulatory protein, arsR family
    5.2e-05   23.2   0.3     0.0004   20.4   0.0    2.0  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.6   4.8e-09   4.3e-05       1      21 [.      10      30 ..      10      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.8e-09
                                      SHHHHHHHHHHTTSSEEHHHH CS
                             HTH_5  1 dptRlkILklLaegelcvcel 21
                                      dp Rl ILklL+++elcvce+
  gi|386002239|ref|YP_005920538.1| 10 DPFRLAILKLLRDNELCVCEI 30
                                      789*****************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.4e-08    0.0004       1      29 [.       2      29 ..       2      31 .. 0.85
   2 ?    1.1   0.0     0.046   4.1e+02      44      61 .]      31      48 ..      28      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.4e-08
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHH CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltase 29
                                      +++++A+a+P R++il++L r+ +l++ e
  gi|386002239|ref|YP_005920538.1|  2 AEVFKAMADPFRLAILKLL-RDNELCVCE 29
                                      689****************.877777655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.046
                                      HHHHHHHCTTEEEECTEE CS
                            HTH_20 44 HLrvLeeagLvevvregr 61
                                      +L +L +  Lv+ ++eg+
  gi|386002239|ref|YP_005920538.1| 31 NLSILKRQALVKDRKEGK 48
                                      5789999********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 628.16
//
Query:       gi|386002240|ref|YP_005920539.1|  [L=358]
Description: Arsenical-resistance protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-63  213.5  15.4    2.2e-63  213.5  15.4    2.2  2  SBF       Sodium Bile acid symporter family
  ------ inclusion threshold ------
        0.4   11.0   0.1        0.4   11.0   0.1    3.0  4  KASH      Nuclear envelope localisation domain


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5  15.4   2.4e-67   2.2e-63       1     194 [.      58     255 ..      58     256 .. 0.99
   2 ?   -2.8   3.8      0.46   4.2e+03      38      84 ..     267     330 ..     260     346 .. 0.61

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 2.4e-67
                               SBF   1 ailLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggam 77 
                                       a++Lilmm+p+++kv++e+l+e++++ k l l+l+l+wv++P+lmf+la+++lrd+   p l+vGlil+g+a+++am
  gi|386002240|ref|YP_005920539.1|  58 AVGLILMMYPPLAKVKYEDLGEVFRDTKVLGLSLFLNWVVGPVLMFGLAILFLRDH---PHLMVGLILIGIARCIAM 131
                                       589*****************************************************...****************** PP

                               SBF  78 snvwtylakGdlelsvvlvalstllailltPlllyllaksl.......eqttlkvpieeivksvlivviiPliaGil 147
                                       + vw++la+G +e++++lv ++++++++++++++yl+++ l       e+  ++++++ei+ksv+++++iP++aGi+
  gi|386002240|ref|YP_005920539.1| 132 VVVWNELACGCTEYCAGLVGFNSIFQVFFYSVYAYLFITVLppilgiaEGLVVAITMAEIAKSVFVYLGIPFLAGII 208
                                       ***************************************************************************** PP

                               SBF 148 lryillkhkGrewfeskllpavspisligllltivvifalkgelive 194
                                       +r +l++++G +w+e+ ++p++sp++li+ll+tivv+f+lkge+ive
  gi|386002240|ref|YP_005920539.1| 209 TRFVLIRRRGMSWYEEWFIPKISPLTLIALLFTIVVMFSLKGEYIVE 255
                                       *********************************************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.46
                               SBF  38 wvikPllmfilakillrdl.................klepelavGlilvglapggamsnvwtyl 84 
                                       ++i  llmfila  +   +                 + e  +av++ + g+ +g a + v++ l
  gi|386002240|ref|YP_005920539.1| 267 LIIYFLLMFILAFYISYKMgvgyentaalsftaasnNFELAIAVAVAVFGINSGEAFAAVIGPL 330
                                       4555566777776443333666666666666666665566666666666666666666665555 PP

>> KASH  Nuclear envelope localisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.1   9.5e+03      10      29 ..      22      41 ..      18      44 .. 0.66
   2 ?   -3.2   0.4       1.2   1.1e+04      17      17 ..     100     100 ..      87     111 .. 0.54
   3 ?   -1.4   0.3      0.34     3e+03      11      23 ..     232     244 ..     230     251 .. 0.45
   4 ?   11.0   0.1   4.5e-05       0.4       5      28 ..     260     283 ..     259     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                              KASH 10 lpLqllLllllllalLvpls 29
                                      +++ ++++l +++ +L+p +
  gi|386002240|ref|YP_005920539.1| 22 VWIFAAMVLGIGMGYLFPGV 41
                                      56667777777777777765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                              KASH  17 l 17 
                                       +
  gi|386002240|ref|YP_005920539.1| 100 V 100
                                       2 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.34
                              KASH  11 pLqllLlllllla 23 
                                       pL+l+ ll+ +++
  gi|386002240|ref|YP_005920539.1| 232 PLTLIALLFTIVV 244
                                       5553333333322 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 4.5e-05
                              KASH   5 vlraalpLqllLllllllalLvpl 28 
                                       vlr+a+pL + +ll+++la+ ++ 
  gi|386002240|ref|YP_005920539.1| 260 VLRVAIPLIIYFLLMFILAFYISY 283
                                       89*****************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2112.34
//
Query:       gi|386002241|ref|YP_005920540.1|  [L=310]
Description: Rhodanese domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-14   53.7   0.0    6.3e-09   36.3   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-06     0.021      28      99 ..     110     183 ..      82     187 .. 0.86
   2 !   36.3   0.0   3.5e-13   6.3e-09      12      97 ..     220     301 ..     210     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                         Rhodanese  28 ghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggraaaa..aallkklGyknvsvld 98 
                                       + I g++++     s++  + + +l+ ++el+      gi+ +++vv+y+d  ++   +  ++++k+lG+++v +l+
  gi|386002241|ref|YP_005920540.1| 110 SYIGGSISL----PSKGFIQADGSLKSVDELAGVlgwaGITAEDEVVLYGDCFSCGDLTfvYWIMKYLGHQKVEILR 182
                                       679999999....8888888888899999999999999*************999966666899******777****9 PP

                         Rhodanese  99 G 99 
                                       G
  gi|386002241|ref|YP_005920540.1| 183 G 183
                                       8 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 3.5e-13
                         Rhodanese  12 gkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.....gidnkktvvvycdgggraaaaa 83 
                                       g+ +++D+R+p+++ +ghI gA+n+      +++++ +++  +++++++l     +id++++v vy ++gg a+  +
  gi|386002241|ref|YP_005920540.1| 220 GQFVVVDARTPDQFGEGHIDGALNI------EFNRVIDDS--WIKDDSALaeifaDIDPDRPVAVYSKNGGTASIIW 288
                                       44559********************......333333333..333333333356779***************8888* PP

                         Rhodanese  84 allkklGyknvsvl 97 
                                       ++l+  G  +v+++
  gi|386002241|ref|YP_005920540.1| 289 YALTLQG-RDVKLY 301
                                       ***9999.889887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1859.14
//
Query:       gi|386002242|ref|YP_005920541.1|  [L=186]
Description: hypothetical protein Mhar_1557 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1375.99
//
Query:       gi|386002243|ref|YP_005920542.1|  [L=134]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-18   66.4   0.4      5e-16   58.5   0.2    2.2  2  HTH_20         Helix-turn-helix domain
    3.3e-18   65.3   0.3    5.9e-18   64.5   0.3    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
    2.8e-05   23.9   0.0      6e-05   22.9   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00045   20.0   0.1      0.072   12.8   0.0    2.2  2  DUF4423        Domain of unknown function (DUF4423)
     0.0016   18.2   0.1      0.002   18.0   0.1    1.1  1  DUF742         Protein of unknown function (DUF742)
     0.0018   18.8   0.2     0.0045   17.5   0.0    1.8  2  HTH_27         Winged helix DNA-binding domain
     0.0066   16.2   0.9      0.023   14.5   0.2    2.2  3  HTH_IclR       IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   14.9   0.2       0.04   13.5   0.0    1.9  2  HTH_24         Winged helix-turn-helix DNA-binding
      0.027   14.4   0.2       0.07   13.0   0.1    1.8  2  MarR_2         MarR family
      0.028   14.6   0.4      0.085   13.1   0.2    1.9  2  PaaX           PaaX-like protein
      0.043   13.8   0.0      0.082   12.9   0.0    1.4  1  HTH_45         Winged helix-turn-helix
       0.05   13.9   0.1       0.11   12.9   0.1    1.6  1  Rrf2           Transcriptional regulator
      0.082   12.7   0.2        1.7    8.4   0.0    2.2  2  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0072       9.9      26      50 ..      13      39 ..       3      42 .. 0.88
   2 !   58.5   0.2   3.6e-19     5e-16       2      61 .]      51     109 ..      50     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0072
                                      -HHHHHHHH..TS-HHHHHHHHHHHHH CS
                            HTH_20 26 taselaerl..dlskntlsyHLrvLee 50
                                      +++ la+++  +++ +++s++L++L e
  gi|386002243|ref|YP_005920542.1| 13 SVERLARLMgdRCKAKNASKRLQTLTE 39
                                      788999999766*************87 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 3.6e-19
                                       HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20   2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       ++++A+a+P R++il++L r+++l++ e++ +l  ++++ s+HL +L +agLv+ ++eg+
  gi|386002243|ref|YP_005920542.1|  51 EVFRAMADPFRLAILQLL-REGELCVCEIMTALNRPQSSTSHHLSILKRAGLVKERKEGK 109
                                       79****************.***************************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.3   4.3e-21   5.9e-18       1      46 [.      58     103 ..      58     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 4.3e-21
                                       SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       dp Rl IL+lL+egelcvce++ +l+ +qs +ShHL++L+ aGLV+
  gi|386002243|ref|YP_005920542.1|  58 DPFRLAILQLLREGELCVCEIMTALNRPQSSTSHHLSILKRAGLVK 103
                                       788******************************************7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.3e-08     6e-05      15      63 ..      65     114 ..      63     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-08
                                       HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
                              TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63 
                                       l Ll++g++ + ei  +l++p+s+    L+ L+++GlV+ +k+    +Yr
  gi|386002243|ref|YP_005920542.1|  65 LQLLREGELCVCEIMTALNRPQSSTSHHLSILKRAGLVKERKEGkWSRYR 114
                                       579***********************************999966244666 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.012        16      34      64 ..       9      39 ..       5      41 .. 0.91
   2 !   12.8   0.0   5.2e-05     0.072      19      78 ..      57     112 ..      43     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                           DUF4423 34 dfkadpeelakrlrpkisaeevekalefLlk 64
                                      + ++++e la+ ++ +++a+ ++k l++L++
  gi|386002243|ref|YP_005920542.1|  9 PQDPSVERLARLMGDRCKAKNASKRLQTLTE 39
                                      667899***********************86 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.2e-05
                           DUF4423  19 ssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78 
                                        ++  ++i++ll+  +++  + e+  +l+   +++ +++ l++L+++gl+k+ ++gk+ +
  gi|386002243|ref|YP_005920542.1|  57 ADPFRLAILQLLR--EGELCVCEIMTALN--RPQSSTSHHLSILKRAGLVKERKEGKWSR 112
                                       5555556666544..44558889999999..99************************975 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.4e-06     0.002       3      91 ..      11     108 ..       9     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                            DUF742   3 kgalvRpyaltgGrtrpee.dldletlvvaeagapea.......arlqpehrailrLcre.plsVaelaAelklPvg 70 
                                       ++ ++R+  l g+r ++++ + +l+tl +   +a  a       a + p + ail+L re  l V e+  +l+ P +
  gi|386002243|ref|YP_005920542.1|  11 DPSVERLARLMGDRCKAKNaSKRLQTLTEKIDEARIAaevevfrAMADPFRLAILQLLREgELCVCEIMTALNRPQS 87 
                                       5677888888888888888777787777666543311344555578889999********9**************** PP

                            DUF742  71 vvrvLlsdLldaglltvrapv 91 
                                        +   ls L  agl++ r+  
  gi|386002243|ref|YP_005920542.1|  88 STSHHLSILKRAGLVKERKEG 108
                                       **************9988765 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 ?   -2.1   0.0       4.2   5.8e+03      33      44 ..      28      39 ..      16      40 .. 0.65
   2 !   17.5   0.0   3.3e-06    0.0045      21      66 ..      75     117 ..      61     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.2
                            HTH_27 33 shisyslkkLte 44
                                       ++s+ l  Lte
  gi|386002243|ref|YP_005920542.1| 28 KNASKRLQTLTE 39
                                      445566666666 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.3e-06
                            HTH_27  21 ladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66 
                                         +++ +ln+ +s++s  l+ L ++GLv +++  ++++ +r+rl++
  gi|386002243|ref|YP_005920542.1|  75 VCEIMTALNRPQSSTSHHLSILKRAGLV-KER--KEGKWSRYRLSE 117
                                       568999**********************.333..55888****998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.8   3.9e+03       1       8 [.      13      20 ..       9      22 .. 0.54
   2 ?   -1.9   0.0       2.2     3e+03      36      44 ..      31      39 ..      29      40 .. 0.75
   3 !   14.5   0.2   1.6e-05     0.023       6      50 ..      62     104 ..      62     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                                      HHHHHHHH CS
                          HTH_IclR  1 sldRalai 8 
                                      s++R +++
  gi|386002243|ref|YP_005920542.1| 13 SVERLARL 20
                                      45555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                                      HHHHHHHHH CS
                          HTH_IclR 36 hRlLqtLve 44
                                      +  LqtL+e
  gi|386002243|ref|YP_005920542.1| 31 SKRLQTLTE 39
                                      566999987 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.6e-05
                                       HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       laiL++l+e+     + e+  ++  p S+++++L+ L + G+v+ 
  gi|386002243|ref|YP_005920542.1|  62 LAILQLLREGELC--VCEIMTALNRPQSSTSHHLSILKRAGLVKE 104
                                       6899999998887..9***************************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.4   4.7e+03      35      44 ..      31      40 ..      28      40 .. 0.76
   2 ?   13.5   0.0   2.9e-05      0.04       2      48 .]      58     103 ..      58     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                            HTH_24 35 nrrlkrLeee 44
                                      ++rl+ L+e+
  gi|386002243|ref|YP_005920542.1| 31 SKRLQTLTEK 40
                                      7899999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.9e-05
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       d  +++IL+lL++ + ++  e+  +l+ ++s ++ +l  L+++Gl+k
  gi|386002243|ref|YP_005920542.1|  58 DPFRLAILQLLRE-GELCVCEIMTALNRPQSSTSHHLSILKRAGLVK 103
                                       5678999999999.*******************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.7   6.5e+03      21      31 ..      11      21 ..       8      22 .. 0.66
   2 ?   13.0   0.1   5.1e-05      0.07      12      56 ..      65     107 ..      61     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.7
                                      EEEHHHHHHHH CS
                            MarR_2 21 dltvgelarrl 31
                                      d +v  lar +
  gi|386002243|ref|YP_005920542.1| 11 DPSVERLARLM 21
                                      55788888866 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.1e-05
                                       HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       + L r+++  l v e+  +l+ ++s++s +l  L +aGLv +r+ 
  gi|386002243|ref|YP_005920542.1|  65 LQLLREGE--LCVCEIMTALNRPQSSTSHHLSILKRAGLVKERKE 107
                                       56677777..88999*************************99965 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.4   1.9e+03      40      40 ..      48      48 ..      17      83 .. 0.59
   2 ?   13.1   0.2   6.1e-05     0.085      44      68 ..      93     117 ..      75     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                              PaaX 40 v 40
                                       
  gi|386002243|ref|YP_005920542.1| 48 A 48
                                      1 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.1e-05
                              PaaX  44 lsRlakaGwlvrekegrrsfYrLsd 68 
                                       ls l++aG++++ keg+ s YrLs+
  gi|386002243|ref|YP_005920542.1|  93 LSILKRAGLVKERKEGKWSRYRLSE 117
                                       6779********************8 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-05     0.082      10      54 ..      63     107 ..      60     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkske 54 
                                       +IL+ ++ege    +im + n   + ++  L++L   gl+k++ke
  gi|386002243|ref|YP_005920542.1|  63 AILQLLREGELCVCEIMTALNRPQSSTSHHLSILKRAGLVKERKE 107
                                       7***************************************87543 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     8e-05      0.11      15      69 ..      63     117 ..      61     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-05
                                       HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE.TTT-TCEEESS CS
                              Rrf2  15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv.rGkgGGyrLak 69 
                                       ++L++ +e+e + + ei +  n ++s  ++ l+ L++aglvk + +Gk   yrL++
  gi|386002243|ref|YP_005920542.1|  63 AILQLLREGE-LCVCEIMTALNRPQSSTSHHLSILKRAGLVKERkEGKWSRYRLSE 117
                                       5666777766.88999*************************976269999999876 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.13   1.8e+02      26      53 ..      12      40 ..       8      41 .. 0.82
   2 ?    8.4   0.0    0.0013       1.7      28      60 ..      75     107 ..      74     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.13
                                      --HHHHHHHHTS-..HHHHHHHHHHHHHT CS
                     LexA_DNA_bind 26 PsireiaralglkS.psaveehLkaLerK 53
                                      Ps+  +ar +g +  ++ + ++L++L  K
  gi|386002243|ref|YP_005920542.1| 12 PSVERLARLMGDRCkAKNASKRLQTLTEK 40
                                      89999999998775267899999999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                                       HHHHHHHHTS-.HHHHHHHHHHHHHTTSE.E-GG CS
                     LexA_DNA_bind  28 ireiaralglkSpsaveehLkaLerKGyi.erdp 60 
                                       + ei+ al+    s+  +hL  L+r G++ er++
  gi|386002243|ref|YP_005920542.1|  75 VCEIMTALNRP-QSSTSHHLSILKRAGLVkERKE 107
                                       56999999965.89999***********934555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 924.43
//
Query:       gi|386002244|ref|YP_005920543.1|  [L=312]
Description: Rhodanese domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-15   55.6   0.0      4e-08   33.7   0.0    2.3  2  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
      0.061   13.3   0.1        0.1   12.6   0.1    1.3  1  DUF2335    Predicted membrane protein (DUF2335)


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.6e-08   0.00086       1      99 [.      83     184 ..      83     186 .. 0.73
   2 !   33.7   0.0   4.4e-12     4e-08      11      97 ..     220     302 ..     209     310 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.6e-08
                         Rhodanese   1 sakelkell.ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvy 72 
                                       +a+el+e+l +++++++  v++++  + + I+g+++++++ + +a+ s +p  el +         g+++++ +v+y
  gi|386002244|ref|YP_005920543.1|  83 TAEELRERLgAERRPIIAYVSNSPPSSGSYIEGSISLPSKGFIQADGSLKPVEELAA----VlgraGVTEEDDLVLY 155
                                       578888888555555566666555547899*******55555555555555544444....44556*********** PP

                         Rhodanese  73 cdgggraaaa..aallkklGyknvsvldG 99 
                                       +d  ++  ++  ++++k+lG+++v +l+G
  gi|386002244|ref|YP_005920543.1| 156 GDCFSCGDFTfvYWIMKYLGHQKVEILRG 184
                                       ***99988888899******777****98 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 4.4e-12
                         Rhodanese  11 kgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallk 87 
                                       +g+ +++D+R+p+++  ghI gAvn+ +++  ++    +++++l e +++l  d+++++ vy ++gg a+ ++ +l 
  gi|386002244|ref|YP_005920543.1| 220 SGGLVVVDARTPDQFGGGHIDGAVNIDFNRVIDG-SWIKDDAALAEVFAPL--DPDRPIAVYSKNGGTASIVWFALA 293
                                       455569********************22222222.2334555666667776..***************888899888 PP

                         Rhodanese  88 klGyknvsvl 97 
                                         G  + s++
  gi|386002244|ref|YP_005920543.1| 294 LQG-RDASLY 302
                                       778.667766 PP

>> DUF2335  Predicted membrane protein (DUF2335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.2e-05       0.1       1      16 [.     207     222 ..     207     222 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                           DUF2335   1 PsPevLeqYesilPGa 16 
                                       P+Pe L++Yes+ +G+
  gi|386002244|ref|YP_005920543.1| 207 PHPELLAEYESVASGG 222
                                       9************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1966.64
//
Query:       gi|386002245|ref|YP_005920544.1|  [L=375]
Description: hypothetical protein Mhar_1560 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2469.21
//
Query:       gi|386002246|ref|YP_005920545.1|  [L=297]
Description: hypothetical protein Mhar_1561 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          6    6.9   7.1        1.3    9.1   0.5    2.6  3  DUF997    Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.5   7.3e-05       1.3      31      67 ..      99     135 ..      94     136 .. 0.86
   2 ?    3.9   0.5     0.003        54      11      44 ..     124     157 ..     119     171 .. 0.82
   3 ?   -3.3   0.1      0.52   9.3e+03      48      53 ..     199     204 ..     187     210 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 7.3e-05
                            DUF997  31 eveeyyilglPlWfflscillpilfivlvillvkfvF 67 
                                       ++e+y++l +P W  +s ++    ++ l + ++  vF
  gi|386002246|ref|YP_005920545.1|  99 NQEKYGLLSFPKWTYISFFMAKYGLFSLSYGMIAAVF 135
                                       5789***************999988888888888777 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.003
                            DUF997  11 lltllyflwwllfaYglgskeveeyyilglPlWf 44 
                                       + +   +++ ++f+Y+l  ++ ++y +  +PlW 
  gi|386002246|ref|YP_005920545.1| 124 FSLSYGMIAAVFFGYILLYSNMNKYILETVPLWA 157
                                       5555567888999****9999999999999***6 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.52
                            DUF997  48 cillpi 53 
                                        i+++i
  gi|386002246|ref|YP_005920545.1| 199 AIFGFI 204
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2081.22
//
Query:       gi|386002247|ref|YP_005920546.1|  [L=358]
Description: hypothetical protein Mhar_1562 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        1.8    8.1   9.0       0.12   11.9   2.0    2.3  3  Ni_hydr_CYTB  Prokaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0     7e-06      0.12      35     113 ..      79     153 ..      64     158 .. 0.67
   2 ?   -0.6   0.1     0.048   8.7e+02      50      86 ..     179     216 ..     155     256 .. 0.57
   3 ?   -3.7   0.0      0.44   7.9e+03      13      29 ..     327     343 ..     327     352 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-06
                                       -S-GGG-.....HHHHHHHHHHHHHHHHHHHHHHH------------STTTSSSSS----------------TT.TH CS
                      Ni_hydr_CYTB  35 ywgdsgk.....aralHklaGlvllalllfrllwlkkakkpspriifrqikrdltlllrgrkpeagknnplqkl.vh 105
                                       +w  +++     ++ +H+laG++l++l+l+r l+l          if +++++++ +  +   ++++n   ++  ++
  gi|386002247|ref|YP_005920546.1|  79 NWPNLFAfklgrILFYHRLAGVALFGLTLYRPLLL----------IFANVFEYFFIFYEATRLRRDPNRLTEWElIG 145
                                       3333332334334555*******************..........89999988888877777777777777666344 PP

                                       HHHHHHHH CS
                      Ni_hydr_CYTB 106 lllyvllv 113
                                       ++ ++l+v
  gi|386002247|ref|YP_005920546.1| 146 AAAFILIV 153
                                       44444443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHHH.------------STTTSSSSS- CS
                      Ni_hydr_CYTB  50 Glvllalllfrllwl.kkakkpspriifrqikrdltll 86 
                                       +l++l+ + + ++++ ++  +  pr++ r  + d  ++
  gi|386002247|ref|YP_005920546.1| 179 ALLVLVGWGAGIVMGlWWLLRGVPRAVERPSILDDPKT 216
                                       44555555444444433344444444444444444444 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHS CS
                      Ni_hydr_CYTB  13 nallvvllllsgllian 29 
                                       nal++vlll   + +  
  gi|386002247|ref|YP_005920546.1| 327 NALFMVLLLTLNITLYD 343
                                       56777777766555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2250.89
//
Query:       gi|386002248|ref|YP_005920547.1|  [L=256]
Description: endonuclease/exonuclease/phosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.6   0.0      2e-15   57.0   0.0    1.3  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
     0.0073   16.1   0.0       0.43   10.4   0.0    2.1  2  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   2.2e-19     2e-15       1     233 []      23     245 ..      23     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.2e-19
                                       EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggav 77 
                                       +t+Nv+++        +r drla+ l+++ a v+gLQE+d ++   ++  l   + +++          +g +g+++
  gi|386002248|ref|YP_005920547.1|  23 MTYNVGNG-------LARPDRLASALRSSGAGVIGLQELDQSQSRALEGSL--SEEYPYQI-----LLPAGFEGMGL 85 
                                       8******8.......2379*******************9999988877777..44444444.....4679999**** PP

                                       EECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEECCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  78 lsrfpltslfrrtfiefndlvaalrreplaakleqlniashrdhdlvrdlqllalllqvealnadrgapvivaGDfN 154
                                       lsr+p ts ++ +++ + dl  +l  e  + +  +  ++++ +   +    +     ++ +  a +  p +++GD+N
  gi|386002248|ref|YP_005920547.1|  86 LSRYPATSAEVISLPPTADLICTLDLEGRKVTIIVAHPPPPISFSGMGFGGRTEARIRRVIEAATSAPPSVILGDLN 162
                                       ********************************9999999999999999999999999999999999999999***** PP

                                       SSTSGGGBSCGHHHHHHCTTTHHSSCESCETTTTTTTTTTTEB-B...................EEEEEECHHHCCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxx RF
                     Exo_endo_phos 155 arpsdddsrvlrtrglalapapvglyllgggptptyvtraggsrl...................Drilaspalalfr 212
                                       a+++      lr +gl++a      +  g+g+  t + r g++r                    D+i+ +++    +
  gi|386002248|ref|YP_005920547.1| 163 AASWQKTCCQLRGAGLLDAF-----AAAGRGRGSTLPVRLGRWRRleavnrilmglpllplvrvDYIWHTSDIQALG 234
                                       ******************96.....4555555555555555555469999999*****************9999999 PP

                                       EEEEEECCHHEECTSSCSSSB CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 213 sgvlppplalvrrealtlSDH 233
                                       ++ +++ +          SDH
  gi|386002248|ref|YP_005920547.1| 235 AWLGEDAG----------SDH 245
                                       99998888..........**9 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   4.8e-05      0.43      17      65 ..     138     183 ..     135     205 .. 0.84
   2 !    3.6   0.0    0.0062        55      90     118 ..     221     248 ..     219     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.8e-05
                   Exo_endo_phos_2  17 lestlekllselksp.kiiilGDfNakhplWgsedtdssargeeLiefle 65 
                                       +e+ +++++++++s  + +ilGD+Na   +W+++ ++   rg  L++++ 
  gi|386002248|ref|YP_005920547.1| 138 TEARIRRVIEAATSApPSVILGDLNAA--SWQKTCCQ--LRGAGLLDAFA 183
                                       5678999999999889*********96..68876677..88888888776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0062
                   Exo_endo_phos_2  90 iDltltsdnlalskleleeedlgSDHrpi 118
                                       +D ++ +++++        ed gSDH+p+
  gi|386002248|ref|YP_005920547.1| 221 VDYIWHTSDIQAL-GAWLGEDAGSDHLPV 248
                                       6888888888888.3334569******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1504.33
//
Query:       gi|386002249|ref|YP_005920548.1|  [L=263]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-31  108.4   0.0    5.7e-31  107.9   0.0    1.2  1  ABC_tran      ABC transporter
    6.7e-10   39.3   1.0    2.5e-05   24.2   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.7e-05   25.1   0.3    8.5e-05   22.8   0.3    1.9  1  AAA_22        AAA domain
    1.8e-05   25.2   0.0    3.1e-05   24.4   0.0    1.5  1  AAA_16        AAA ATPase domain
    4.1e-05   23.1   0.4     0.0017   17.8   0.4    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    8.4e-05   23.2   0.1    0.00012   22.7   0.1    1.3  1  AAA_23        AAA domain
    0.00021   21.2   0.1    0.00044   20.1   0.1    1.6  2  AAA_15        AAA ATPase domain
    0.00048   19.8   0.1    0.00096   18.8   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0044   17.4   0.2      0.046   14.1   0.2    2.2  1  AAA           ATPase family associated with various cellular 
     0.0062   16.3   0.0     0.0096   15.7   0.0    1.5  1  AAA_30        AAA domain
     0.0075   15.1   0.6        1.9    7.2   0.1    3.0  2  ABC_ATPase    Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.027   13.8   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.017   14.3   0.3      0.035   13.3   0.0    1.6  2  NB-ARC        NB-ARC domain
      0.021   14.2   0.6        1.2    8.5   0.1    2.2  2  TniB          Bacterial TniB protein
       0.03   14.3   0.1       0.57   10.2   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
      0.033   14.4   0.3        0.1   12.8   0.1    1.9  2  AAA_33        AAA domain
      0.037   13.9   0.4       0.16   11.9   0.1    1.9  2  NTPase_1      NTPase
      0.046   14.0   0.1       0.71   10.1   0.1    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.055   13.4   0.2       0.11   12.4   0.1    1.6  1  RsgA_GTPase   RsgA GTPase
      0.057   12.4   0.0      0.098   11.6   0.0    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.062   12.9   0.1       0.14   11.8   0.0    1.6  2  SRP54         SRP54-type protein, GTPase domain
      0.077   12.9   0.0       0.13   12.1   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.087   12.5   0.0       0.14   11.9   0.0    1.3  1  AAA_24        AAA domain
       0.11   12.4   0.5       0.26   11.2   0.5    1.9  1  NACHT         NACHT domain
       0.11   12.8   0.5       0.22   11.8   0.5    1.9  1  AAA_19        AAA domain
       0.13   12.2   0.1       0.25   11.2   0.1    1.5  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.13   11.9   0.1       0.26   10.8   0.1    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.13   11.4   0.0       0.17   11.0   0.0    1.3  1  G-alpha       G-protein alpha subunit
       0.15   12.1   0.0       0.29   11.1   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.27    9.8   0.2        2.4    6.7   0.1    1.9  2  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   9.5e-34   5.7e-31       1     137 []      19     166 ..      19     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 9.5e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                       l++++l +  +e++ +vG+nG+GK+tL+k++ + lkp +G+i ld g++l++ +++++ + ig++pq ++   ++tv
  gi|386002249|ref|YP_005920548.1|  19 LDDLNLVVGDSEVLSLVGPNGSGKTTLIKCIDRILKP-KGTIILDgGRNLQSLSRQEVARFIGYVPQSTTSSLTTTV 94 
                                       7899********************************8.99999**9**********************99999999* PP

                                       HHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++             ++e+i+++++ ++l ++++  + ++ s+LSgGqkqrv +aral+++p++lllDEpt+
  gi|386002249|ref|YP_005920548.1|  95 FDTilmgrrprmgwrVAEEDIDRVVEVMRLLHVEEFAL-KDFSELSGGQKQRVLIARALAQEPEVLLLDEPTS 166
                                       **********9999888888999999999999777777.778*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   4.2e-08   2.5e-05       4      24 ..      34      54 ..      31      89 .. 0.81
   2 !   13.7   0.1   6.8e-05      0.04     211     273 ..     109     171 ..      87     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.2e-08
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      l+GpNgsGK++L++++d +  
  gi|386002249|ref|YP_005920548.1| 34 LVGPNGSGKTTLIKCIDRILK 54
                                      9***************99854 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.8e-05
                            AAA_21 211 svderlrer...gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                       +v+e +++r    +++l+ +     +++elS G+k+   ++ al++ +    +ll+DEp ++L+ k
  gi|386002249|ref|YP_005920548.1| 109 RVAEEDIDRvveVMRLLHVEEFALKDFSELSGGQKQRVLIARALAQEP---EVLLLDEPTSNLDVK 171
                                       4444444445557888888888888999*********55555555544...9***********974 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3   1.4e-07   8.5e-05       7     131 ..      31     197 ..      27     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.4e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.........erpevv..fvtlpsstsskdllrellralglelka.. 70 
                                       +l ++G+ G+GKTtl++ + + l+    +            r ev+    ++p+st+s+   + +  +l  ++ +  
  gi|386002249|ref|YP_005920548.1|  31 VLSLVGPNGSGKTTLIKCIDRILKPKGTIILdggrnlqslSRQEVArfIGYVPQSTTSSLTTTVFDTILMGRRPRmg 107
                                       6889******************9644444448888888885555554334445555444445555555555555599 PP

                            AAA_22  71 .......................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsll 116
                                                              + ++ +el   + ++ l ara    +e+l++DE    l+   + ea+ ++rs++
  gi|386002249|ref|YP_005920548.1| 108 wrvaeedidrvvevmrllhveefALKDFSELSgGQKQRVLIARALaqePEVLLLDEPTSnLDvkhQLEAMDTVRSIV 184
                                       ***********************999999999999999999999999*********9999*99766*********** PP

                            AAA_22 117 nlsrkgvqliLvGtp 131
                                       +  ++g++ +++++ 
  gi|386002249|ref|YP_005920548.1| 185 K--KTGISAVMAIHD 197
                                       *..****99998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.2e-08   3.1e-05      21      64 ..      26      73 ..      13     174 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.2e-08
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql....e 64
                                       g++e++ l+G+ G+GK++l++++ r l+ +g i l g         +
  gi|386002249|ref|YP_005920548.1| 26 VGDSEVLSLVGPNGSGKTTLIKCIDRILKPKGTIILDGGRNLQslsrQ 73
                                      356699*******************99999985554444333324321 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4   2.8e-06    0.0017      24     184 ..      29     181 ..       4     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk.lkiekeevs 98 
                                       +++ ++vGpNGSGK+ l+  i  +L  + +          +i    ++ +s+++ ev+ ++    ++ ++  ++ v 
  gi|386002249|ref|YP_005920548.1|  29 SEVLSLVGPNGSGKTTLIKCIDRILKPKGT----------IILDgGRNLQSLSRQEVARFIGYVPQStTSSLTTTVF 95 
                                       567899***************666653333..........2222244444555555555443322220122223333 PP

                                       EEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                        +  + r  +  +++ ++++ +  ev++ll+ +++  +   +LSgG+k+ v +a  +A    +   + llDe  ++L
  gi|386002249|ref|YP_005920548.1|  96 DTILMGRRPRMGWRVAEEDIDRvVEVMRLLHVEEFALKdfsELSGGQKQRVLIARALA----QEPEVLLLDEPTSNL 168
                                       3344445555667777777776688888888888765433378999998666665544....333456889988888 PP

                                       -HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                             SMC_N 172 Deknvkkvaellk 184
                                       D k+  +  + ++
  gi|386002249|ref|YP_005920548.1| 169 DVKHQLEAMDTVR 181
                                       8888766555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.9e-07   0.00012      16      43 ..      23      53 ..       3      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.9e-07
                            AAA_23 16 dF...skgltlItGpNGaGKTTildAiklaL 43
                                      ++   ++ +  ++GpNG+GKTT++ +i  +L
  gi|386002249|ref|YP_005920548.1| 23 NLvvgDSEVLSLVGPNGSGKTTLIKCIDRIL 53
                                      336677788899***************7665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   7.4e-07   0.00044      24      50 ..      29      56 ..       1      97 [. 0.82
   2 ?   -1.9   0.0       3.6   2.1e+03     322     355 ..     154     187 ..     141     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.4e-07
                            AAA_15 24 e.ltvliGkNnsGKSsilealdlFlnnk 50
                                      + +  l+G+N+sGK+++++ +d +l+ k
  gi|386002249|ref|YP_005920548.1| 29 SeVLSLVGPNGSGKTTLIKCIDRILKPK 56
                                      34899*******************9987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                       +++ +ll++EP  +L  ++q + +++ +++++++
  gi|386002249|ref|YP_005920548.1| 154 QEPEVLLLDEPTSNLDVKHQLEAMDTVRSIVKKT 187
                                       5678999999999999999999999999999875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.6e-06   0.00096      23      50 ..      30      57 ..      19      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                            AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++  l+Gp+GsGK+Tl+  i  +L p+ 
  gi|386002249|ref|YP_005920548.1| 30 EVLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      46789***************99999976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   7.8e-05     0.046       3      37 ..      34      69 ..      32     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-05
                                      EESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCSSS CS
                               AAA  3 lyGppGtGKTllakavakelgve.fleisgsellsk 37
                                      l+Gp G GKT+l+k + + l+ +  + ++g + l++
  gi|386002249|ref|YP_005920548.1| 34 LVGPNGSGKTTLIKCIDRILKPKgTIILDGGRNLQS 69
                                      89*************999986332344444444433 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   1.6e-05    0.0096      16      47 ..      28      58 ..      22     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaagg 47
                                      ++  v  l+Gp G+GKtt++k + ++++ +g 
  gi|386002249|ref|YP_005920548.1| 28 DS-EVLSLVGPNGSGKTTLIKCIDRILKPKGT 58
                                      34.58999*****************9998882 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.026        16     246     266 ..      31      51 ..      27      67 .. 0.86
   2 !    7.2   0.1    0.0031       1.9     324     415 ..     139     215 ..     127     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                                       EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 246 vtlIvGggfhGKsTLLeAlek 266
                                       v  +vG++  GK+TL++ +++
  gi|386002249|ref|YP_005920548.1|  31 VLSLVGPNGSGKTTLIKCIDR 51 
                                       6778*************9986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0031
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q + i++al  + ++lL+DE ts     ++ e m+                vr+++kk+g+s ++ +  ++ 
  gi|386002249|ref|YP_005920548.1| 139 SGGQKQRVLIARALAQEPEVLLLDEPTSNLDVKHQLEAMDT---------------VRSIVKKTGISAVMAIHDLNL 200
                                       88889999999999999999999999986555554444444...............444444445555554444444 PP

                                       CTTT-SEEEEEETTE CS
                        ABC_ATPase 401 yldvAdtvilmeeyk 415
                                         + +d  ++++e +
  gi|386002249|ref|YP_005920548.1| 201 AARYSDSLVMLKEGR 215
                                       444444444444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.5e-05     0.027      24      49 ..      31      56 ..      13      81 .. 0.83
   2 ?   -2.7   0.0       5.1   3.1e+03       2      31 ..     135     164 ..     134     188 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppl 49
                                       l lvGp GsGKt l+k++  +l p 
  gi|386002249|ref|YP_005920548.1| 31 VLSLVGPNGSGKTTLIKCIDRILKPK 56
                                      4669******************9875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                      Mg_chelatase   2 lkdvkGqeeakraleiaaaGgHnlllvGpp 31 
                                       ++++ G ++++  +  a a + ++ll+  p
  gi|386002249|ref|YP_005920548.1| 135 FSELSGGQKQRVLIARALAQEPEVLLLDEP 164
                                       566666666666666666666665555544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05     0.035      15      40 ..      26      49 ..      14      57 .. 0.81
   2 ?   -2.3   0.1       3.4     2e+03      72     110 ..     121     162 ..     110     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                                      TTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqi 40
                                       ++++  v++lvG  G+GKttl+k i
  gi|386002249|ref|YP_005920548.1| 26 VGDSE--VLSLVGPNGSGKTTLIKCI 49
                                      45666..***************9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                                       XHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  72 ilkeLslseddleekeeves...lkrklvrlLltkrfllvlD 110
                                       +++ L+ +e  l+ ++e          + r+L +   +l+lD
  gi|386002249|ref|YP_005920548.1| 121 VMRLLHVEEFALKDFSELSGgqkQRVLIARALAQEPEVLLLD 162
                                       455555555555555554444335556788888888888888 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.047        28      38      54 ..      32      48 ..      23     128 .. 0.90
   2 ?    8.5   0.1     0.002       1.2     116     159 ..     152     193 ..     136     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.047
                              TniB 38 lllvGdsnnGKtmivek 54
                                      l lvG+   GKt++++ 
  gi|386002249|ref|YP_005920548.1| 32 LSLVGPNGSGKTTLIKC 48
                                      789***********985 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.002
                              TniB 116 relkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                        + +++vL++DE  + l   +++q e++ +++s+  +  i+ v+
  gi|386002249|ref|YP_005920548.1| 152 LAQEPEVLLLDEPTSNL--DVKHQLEAMDTVRSIVKKTGISAVM 193
                                       456899******99999..899*******************997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00095      0.57       4      25 ..      34      55 ..      31      70 .. 0.82
   2 ?    2.0   0.0      0.32   1.9e+02      19      56 ..     148     185 ..     114     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                                      EE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnr 25
                                      LvGp G+gK++l++ + + l+ 
  gi|386002249|ref|YP_005920548.1| 34 LVGPNGSGKTTLIKCIDRILKP 55
                                      9************999998844 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                                       GGGGBS--EEEEE--TT--HHHHH--B--......... CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvd 56 
                                       +a+al +e e+ +l + t+  d+k ++e ++  +s v+
  gi|386002249|ref|YP_005920548.1| 148 IARALAQEPEVLLLDEPTSNLDVKHQLEAMDTVRSIVK 185
                                       67788888888888888888888888886655555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00017       0.1       2      28 ..      32      61 ..      31      98 .. 0.80
   2 ?   -2.2   0.0       6.9   4.1e+03      16      32 ..     149     165 ..     142     198 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                            AAA_33  2 vllvGlpGsGKstlaerl...lkklgavll 28
                                      + lvG++GsGK+tl++ +   lk+ g+++l
  gi|386002249|ref|YP_005920548.1| 32 LSLVGPNGSGKTTLIKCIdriLKPKGTIIL 61
                                      679***********8743222666666655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.9
                            AAA_33  16 aerllkklgavllssdt 32 
                                       a+ l+++  + ll+++t
  gi|386002249|ref|YP_005920548.1| 149 ARALAQEPEVLLLDEPT 165
                                       34444444455555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00026      0.16       4      29 ..      34      59 ..      31      74 .. 0.89
   2 ?   -0.3   0.0       1.4   8.5e+02      94     155 ..     154     219 ..     141     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                                      EE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvk 29
                                      + Gp G+GKtTl+k + + lk +g  
  gi|386002249|ref|YP_005920548.1| 34 LVGPNGSGKTTLIKCIDRILKPKGTI 59
                                      78******************999875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                       HHH-EEEE--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
                          NTPase_1  94 seadviviDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfev 155
                                       +e++v+++DE   ++ +k + +  ++v+ ++k ++   ++ ih  +   +  +++   k+++++ v
  gi|386002249|ref|YP_005920548.1| 154 QEPEVLLLDEpTSNLDVKHQlEAMDTVRSIVKkTGISAVMAIHDLNlAARYSDSLVMLKEGRIYAV 219
                                       566666666633445555542455678888887788888888887776777777777777777775 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0012      0.71      28      89 ..     133     181 ..     118     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +++++lSGG+kq +    +a ala    +       +++++LDE  s+lD + + +++++++
  gi|386002249|ref|YP_005920548.1| 133 KDFSELSGGQKQRV---LIARALA----Q------EPEVLLLDEPTSNLDVKHQLEAMDTVR 181
                                       67788888888433...3332222....2......4889************99999999875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00018      0.11      77     120 ..       6      50 ..       1      65 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       ++ l  s  +++ l++l+ ++ d ++  lvG+ G GK+tLi+ ++
  gi|386002249|ref|YP_005920548.1|   6 IKNLSFSYGSRRILDDLNLVVGDsEVLSLVGPNGSGKTTLIKCID 50 
                                       55666777778889999999998899***************9876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016     0.098      14      57 ..      14      57 ..       3      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrG 57
                                       ++++l+ l    G ++v+ l G  G+Gk tl++ +   l+ +G
  gi|386002249|ref|YP_005920548.1| 14 GSRRILDDLNLVVGDSEVLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      5899*****************************99988888777 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.14       3      29 ..      31      57 ..      29      61 .. 0.82
   2 ?   -2.6   0.0       6.1   3.6e+03      97     112 ..     169     184 ..     145     196 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                      EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkeg 29
                                      v+ lvG++G+GKTt +  + ++lk +g
  gi|386002249|ref|YP_005920548.1| 31 VLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      7889**********9988887777665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.1
                                       THHHHHHHHHHHHHHH CS
                             SRP54  97 ndkelmeelkkikkvv 112
                                         k+ +e +++++++v
  gi|386002249|ref|YP_005920548.1| 169 DVKHQLEAMDTVRSIV 184
                                       3333344444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.13      45      77 ..      29      61 ..      16     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                             Rad17 45 kriLLisGPsGCgkstvvkvLskelgiklrewl 77
                                       ++L + GP G gk+t +k + ++l +k    l
  gi|386002249|ref|YP_005920548.1| 29 SEVLSLVGPNGSGKTTLIKCIDRILKPKGTIIL 61
                                      56899******************9998865554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.14       6      30 ..      33      62 ..      29     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            AAA_24  6 liyGpsgiGKTtlakel.....gpkplfid 30
                                       ++Gp+g+GKTtl+k +     ++ ++++d
  gi|386002249|ref|YP_005920548.1| 33 SLVGPNGSGKTTLIKCIdrilkPKGTIILD 62
                                      589************997777666666666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00044      0.26       2      22 ..      31      51 ..      30     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      ++ l G++GsGKTtL++ + +
  gi|386002249|ref|YP_005920548.1| 31 VLSLVGPNGSGKTTLIKCIDR 51
                                      57799**********998755 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   0.00037      0.22      10      38 ..      29      57 ..      24     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                      ++vl ++++ G+GKT+++k+i ++l+  g
  gi|386002249|ref|YP_005920548.1| 29 SEVLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      678999**************988887655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00042      0.25       1      28 [.      31      58 ..      31      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                              MobB  1 vlgivgksgsGKTtLleklipelkargl 28
                                      vl++vg +gsGKTtL++ + ++lk +g 
  gi|386002249|ref|YP_005920548.1| 31 VLSLVGPNGSGKTTLIKCIDRILKPKGT 58
                                      689*************999888888775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00044      0.26       2      19 ..      31      48 ..      30      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                      EEEEEESTTCCHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnh 19
                                      v+ l+G+ GsGKTtL++ 
  gi|386002249|ref|YP_005920548.1| 31 VLSLVGPNGSGKTTLIKC 48
                                      6789***********975 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.17      26      71 ..      32      90 ..      24     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                      EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHH CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsi 71
                                      l l+G ++SGK+T++k + ++ k++              s++e+a +  ++ + + +s+
  gi|386002249|ref|YP_005920548.1| 32 LSLVGPNGSGKTTLIKCIDRILKPKgtiildggrnlqsLSRQEVARFIGYVPQSTTSSL 90
                                      6699***************9888876777666666555555555555554444444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00048      0.29      18      43 ..      26      53 ..      14      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                                      H..TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakal 43
                                      +  ++v+ L G+ G+GKTtl++ + + l
  gi|386002249|ref|YP_005920548.1| 26 VgdSEVLSLVGPNGSGKTTLIKCIDRIL 53
                                      2445789***************987766 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.004       2.4      23      39 ..      36      52 ..      33      67 .. 0.88
   2 ?    0.8   0.0      0.24   1.4e+02     526     562 ..     155     190 ..     148     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.004
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NG+GKTtL + ++ +
  gi|386002249|ref|YP_005920548.1| 36 GPNGSGKTTLIKCIDRI 52
                                      99********9999875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkak 562
                                       + ++  +D P S LD +++  ++  ++s + kk+ ++
  gi|386002249|ref|YP_005920548.1| 155 EPEVLLLDEPTSNLDVKHQLEAMDTVRSIV-KKTGIS 190
                                       678999***************999999997.677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 1600.47
//
Query:       gi|386002250|ref|YP_005920549.1|  [L=357]
Description: iron chelate uptake ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-95  319.3  39.7    2.8e-95  318.9  39.7    1.0  1  FecCD     FecCD transport family
     0.0011   18.6  23.0     0.0011   18.6  23.0    1.7  1  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.9  39.7   3.1e-99   2.8e-95       3     312 .]      35     351 ..      31     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.9 bits;  conditional E-value: 3.1e-99
                             FecCD   3 llllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLa 72 
                                       ++l  ++ +lg++ki+p ev+ a+l++        +s+ ++iv++lrl rvl+a+++G++LavaGa +Q++++NpLa
  gi|386002250|ref|YP_005920549.1|  35 VVLAGVAATLGSAKITPVEVYTAILARFfpdtfqtTSFIETIVWQLRLHRVLMAIFAGMGLAVAGAAMQGILKNPLA 111
                                       5666777899**************99989999999999999************************************ PP

                             FecCD  73 dPsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalt 148
                                       +P +lGi s+a++ga la++l+  ++++++ ++  af++ +la++ v+ la + kg++p+++iLaGia+ +l+sa+t
  gi|386002250|ref|YP_005920549.1| 112 SPFTLGIASAASFGASLAIILGaGFASGQWLIVGNAFIFTMLASMTVYGLA-RYKGITPETMILAGIAIMYLFSAMT 187
                                       **********************98899999999******************.************************* PP

                             FecCD 149 sllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllll 225
                                       s+l+++ ++e++++++fw++Gsl++ sw+kv+++++++++++++l+++a +++++  gdetAkslGvnve vr+l++
  gi|386002250|ref|YP_005920549.1| 188 SFLQYIGKSEQVHEVVFWMMGSLGRSSWDKVAIIAMVTVVCTVALVYFAWDINAMGAGDETAKSLGVNVEFVRVLCM 264
                                       ***************************************************************************** PP

                             FecCD 226 llvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliG 302
                                       +l++l+ta++++++G+igF+GL++Phi r++vg dhr llp+sal+Gal+ll+ad++ar++l+p+ lpvgi+t+++G
  gi|386002250|ref|YP_005920549.1| 265 MLASLITASVICFTGTIGFIGLVAPHITRMVVGGDHRFLLPASALVGALILLAADTVARTVLAPVILPVGIMTSFLG 341
                                       ***************************************************************************** PP

                             FecCD 303 apffiylllr 312
                                       +pffiyl+lr
  gi|386002250|ref|YP_005920549.1| 342 VPFFIYLFLR 351
                                       *******987 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  23.0   1.2e-07    0.0011      31     226 ..     111     316 ..      82     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-07
                             ABC-3  31 qsllgdalsHaalpGvalayllgvn.......lllgailvgliaavalellkrktklkedtai..givlsvflalgl 98 
                                       +s +  +++ aa  G  la++lg         ++  a++++++a++++  l+r + +  +t+i  gi +   ++   
  gi|386002250|ref|YP_005920549.1| 111 ASPFTLGIASAASFGASLAIILGAGfasgqwlIVGNAFIFTMLASMTVYGLARYKGITPETMIlaGIAIMYLFSAMT 187
                                       566777888888888889988888766777756667999****************9999997666999999998888 PP

                             ABC-3  99 vlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllll 173
                                        ++++i k     ++  +++G++   s + + +ia++++v+ ++l++f  ++ ++    e+Ak+ g++v+++++l +
  gi|386002250|ref|YP_005920549.1| 188 SFLQYIGKseQVHEVVFWMMGSLGRSSWDKVAIIAMVTVVCTVALVYFAWDINAMGAGDETAKSLGVNVEFVRVLCM 264
                                       88888876445567888899********************************************************* PP

                             ABC-3 174 alialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvv 226
                                       +l +l  + ++ + G i  i l ++P +t + ++ + + ll  ++l+g++ ++
  gi|386002250|ref|YP_005920549.1| 265 MLASLITASVICFTGTIGFIGL-VAPHITRMVVGGDHRFLLPASALVGALILL 316
                                       ***************9999885.799999999888888888888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2331.21
//
Query:       gi|386002251|ref|YP_005920550.1|  [L=166]
Description: hypothetical protein Mhar_1566 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1230.88
//
Query:       gi|386002252|ref|YP_005920551.1|  [L=118]
Description: hypothetical protein Mhar_1567 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 853.12
//
Query:       gi|386002253|ref|YP_005920552.1|  [L=216]
Description: Ser/Thr protein phosphatase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-13   50.4   0.0    6.8e-13   49.1   0.0    1.6  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    6.1e-12   45.4   0.0    6.3e-11   42.1   0.0    2.1  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    9.5e-12   45.8   0.0    2.4e-11   44.5   0.0    1.6  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.1e-16   6.8e-13       7     157 ..       2     200 ..       1     208 [. 0.71

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.1e-16
                     Metallophos_2   7 SDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela........pvlaVrGNnD............. 62 
                                       +DlH++ ++    l+al++v++d+i ++GDl   +++  +e++++a        pvl+V+GN+D             
  gi|386002253|ref|YP_005920552.1|   2 ADLHGRSEE----LSALRGVEADLIAFCGDL--HNLDRGDEARRVAealaglgpPVLIVPGNMDpketapsvwkaag 72 
                                       677744443....556677778********9..55544444444444447788*************99999999999 PP

                     Metallophos_2  63 ...................eevveedvlreaaelgtdlpeeaele.l.........agekvlliHgdpl........ 102
                                                          + +v++d +r + + + ++++++    l          ++k+ l+H+ p         
  gi|386002253|ref|YP_005920552.1|  73 lrivhrrshrhgdcgfigfGGMVIRDPMRLQSPARYYHTDDDIYRsLtrlygdisdCRRKIVLTHQPPRgsrdliys 149
                                       999999999999888888833344444444444444444333333124455555545567******98788988888 PP

                     Metallophos_2 103 ...gvkdalaellkeaeegsdvvvcGHtHvp.evekeggvlvvnPGsvgeprdgdpety 157
                                           ++ +l++ ++e     d+++cGH+H+  +  ++g ++vvn G+++++       +
  gi|386002253|ref|YP_005920552.1| 150 gerTGSFGLRRFVEE--RHPDLLICGHIHEDrGYGEIGPTRVVNVGEMRRG------YA 200
                                       876666666666666..7778*********98999************9998......44 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.025   1.5e+02      13      55 ..       3      40 ..       1      44 [. 0.73
   2 !   42.1   0.0     1e-14   6.3e-11      84     249 ..      43     207 ..      35     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.025
                                      --TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHH CS
                     Metallophos_3 13 dlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesa 55
                                      dl+g+ e l  l +v    ++Dl+ + Gdl ++  ++de ++ 
  gi|386002253|ref|YP_005920552.1|  3 DLHGRSEELSALRGV----EADLIAFCGDL-HNLDRGDEARRV 40
                                      677777777666554....799*******9.888888887765 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 1e-14
                                       HHHTT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BSSSS-EEEHHH CS
                     Metallophos_3  84 elgeldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevliaGmGGeivdgekeeefrLkYPawe 160
                                       +l  l+ p+++vPG++D P e+    +++     + l++vh      +G+  ++G+GG ++      +   +Y + +
  gi|386002253|ref|YP_005920552.1|  43 ALAGLGPPVLIVPGNMD-PKETA-PSVWK----AAGLRIVHRR-SHRHGDCGFIGFGGMVIRDPMRLQSPARYYHTD 112
                                       66777889999***999.44433.33444....4679999987.578899*********997666555555555544 PP

                                       HH.HH.GGGG.GGS--.-EEEEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEE CS
                     Metallophos_3 161 ve.yr.Lkvl.kelkd.rrkvlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlv 231
                                        + yr L +l  ++ d rrk++l ++pP g  ++    +  gs  +  +v + +P++ ++gh + ++   e+g t v
  gi|386002253|ref|YP_005920552.1| 113 DDiYRsLTRLyGDISDcRRKIVLTHQPPRGSRDLIYSGERTGSFGLRRFVEERHPDLLICGHIHEDRgyGEIGPTRV 189
                                       44233333331445554899*************6666699***********************99998899****** PP

                                       EE--BGGGTEEEEEETTT CS
                     Metallophos_3 232 vnPGaleeGdfavvdlee 249
                                       vn G+++ G  av++l+e
  gi|386002253|ref|YP_005920552.1| 190 VNVGEMRRGYAAVIELDE 207
                                       **************9976 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   4.1e-15   2.4e-11       7     204 .]       2     178 ..       1     178 [. 0.69

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 4.1e-15
                                       ESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEEST..SSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHHH CS
                       Metallophos   7 gDlHlalgggqlddllkllddllreekpdlvllaGD..lvdrgdlekellellaalvkypipvylllGNHegfeeel 81 
                                       +DlH     g+ ++l +l   +    ++dl+ ++GD  + drgd   +++e la l++   pv +++GN +  +e  
  gi|386002253|ref|YP_005920552.1|   2 ADLH-----GRSEELSALR-GV----EADLIAFCGDlhNLDRGDEARRVAEALAGLGP---PVLIVPGNMD-PKETA 64 
                                       8999.....9999999877.55....88******************************...**********.44433 PP

                                       HHHHHHHHHH.....HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH CS
                       Metallophos  82 lnkygylgif.....sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd 153
                                       ++ ++  g+      s+ + ++    +++   +       v+ ++               l+ + ++ + +d++++ 
  gi|386002253|ref|YP_005920552.1|  65 PSVWKAAGLRivhrrSHRHGDC----GFIGFGG------MVIRDPMR-------------LQSPARYYHTDDDIYRS 118
                                       3333322222323223333333....3444444......33333333.............22222222222444444 PP

                                       ....HHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 154 ....lekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHvy 204
                                           + + ++ + +ivl+H p+       +sg   g+  l+++ ++  +dl i+GH+H++
  gi|386002253|ref|YP_005920552.1| 119 ltrlYGDISDCRRKIVLTHQPPRgsrdlIYSGERTGSFGLRRFVEERHPDLLICGHIHED 178
                                       44455557779999*********999999999999999999*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1472.77
//
Query:       gi|386002254|ref|YP_005920553.1|  [L=149]
Description: hypothetical protein Mhar_1569 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.072   13.5   0.0        0.1   12.9   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
       0.17   12.0   0.0       0.28   11.3   0.0    1.3  1  HTH_56           Cch helix turn helix domain


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05       0.1      32      68 ..      90     126 ..      74     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                                       ---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----X CS
                   Penicillinase_R  32 elaysTVktllrrLvkKgllsrekegrafiYsplvse 68 
                                       + + sTV t l+r+++ g+l+r+ + ++ +Y+  ++e
  gi|386002254|ref|YP_005920553.1|  90 DIKLSTVSTYLSRMYQDGVLERRGNRNQRQYRLITEE 126
                                       4788*********************999999865554 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.1e-05      0.28      50      94 ..      80     124 ..      80     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
                            HTH_56  50 lknvfdkileeagFedtkvvlkelkekGllesekdrntkkrtvkk 94 
                                       lk+  + i+++ + + +++ l+++ + G+le+  +rn++++++ +
  gi|386002254|ref|YP_005920553.1|  80 LKDRYEIIVDDIKLSTVSTYLSRMYQDGVLERRGNRNQRQYRLIT 124
                                       5788899*********************************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 815.97
//
Query:       gi|386002255|ref|YP_005920554.1|  [L=641]
Description: hypothetical protein Mhar_1570 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-82  278.2   1.1    1.8e-82  277.7   1.1    1.2  1  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
       0.79   10.1   8.7       0.15   12.4   4.3    2.1  2  2TM       2TM domain


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 !  277.7   1.1     2e-86   1.8e-82       3     492 .]      53     577 ..      51     577 .. 0.93

  Alignments for each domain:
  == domain 1  score: 277.7 bits;  conditional E-value: 2e-86
                           DUF2207   3 esydvdatvqedGsldvtEtitydf..dgsrhgiyrdrdlplrtydvdgsgnsvriki....rddvtepyykessdd 73 
                                       e+y++d++   +G+l   E++ y++  +g+++++yr +++p     ++++ n++r+++    ++ +t+ y k+ +++
  gi|386002255|ref|YP_005920554.1|  53 EEYRADLY--LNGTL--MEKYLYQIrrSGQYRMLYRPWKVP----LTQEQINRSRVELlaidPPPGTIAYIKDFKGH 121
                                       56667777..89***..******************999995....688999999*******999999********** PP

                           DUF2207  74 g............................tlstgthtyeisYtvknavtkykdvaelywnvigngwdvpienvtitv 122
                                       +                            ++s+g++++ + +++++++++++++a+l+ ++  +  ++p++ vti +
  gi|386002255|ref|YP_005920554.1| 122 VeilngnydaaseiqslafqneagcyrpeRFSAGSYEISYLFKIRPPLEYDEEYAHLNLKLADE--HIPYKAVTIAI 196
                                       ***********************************************************76644..5********** PP

                           DUF2207 123 tlPseaksggdlrawlHgldgsttvkkddgsvtftarnlppgeglevrvlfptnnarktsgnkldeilkeeqk.... 195
                                       + P    +g   r++ H+     ++++++g+v++ +++ +++e lev++lf           +++ ++ +e+     
  gi|386002255|ref|YP_005920554.1| 197 HDP----DGLVRRIFPHT----PMETRQEGEVWLLTGSSKEDELLEVEILF-----------SPEVLNMMEGFprfv 254
                                       999....88999******....888999***********************...........678899999999999 PP

                           DUF2207 196 ...ntreraarlslallillilllilllllllllliklllwkkygrepkvkev.dpeYerdvPedlsPavvgylvkg 268
                                          +++  +a+ + + +++++l  +l++++++l++i +l+++++gre  v +  +  Y   +P++ +P+vv+++++g
  gi|386002255|ref|YP_005920554.1| 255 adiEDKTVSANVKSSGNFFMMLDRLLAIFIIILPAILYLVYRRWGREEFVVVPeTLSY---LPQKRKPWVVNLVFNG 328
                                       999999*******************************************977545555...7*************** PP

                           DUF2207 269 ..dkvdengltAtlldLavkgyitieeekkkkkkgkdtltilkkndeeldpyEkalldlLfdkseeg.ks....... 335
                                          + d+ng++AtlldL+ + +i+ie+++ ++++g  +++i+k+++ee+d+yEk++ld+L+++s++g  +       
  gi|386002255|ref|YP_005920554.1| 329 dvFEADTNGFYATLLDLYLRNVIEIERTQGTEEEGL-KIRISKDHKEECDKYEKQVLDFLKRHSRDGiFNtilfeih 404
                                       **7799**************************9998.57****************************888***9999 PP

                           DUF2207 336 lkeikkyakkskk.kakkfkkalkkwksavkkkergyfdkkg...............kkklkklsalglgliilgli 396
                                       ++++ ++a+  ++ + +++++++k++++ v++++++ f +k+               ++ + +  + ++ +ii+++i
  gi|386002255|ref|YP_005920554.1| 405 IDRLVREAEMGRTkELTRVHEEMKRLMNLVDEETSNEFLNKSplthrrlinspkkwiRSLKISDLINATPFIIFFVI 481
                                       8888888888888899****************666666666668888889988899999999999999********* PP

                           DUF2207 397 lillallllvlllvfllilllillliaiivlllfsrllgrrteeGaellakwkgFkkyLeDfsefkerppedlelwe 473
                                       +il++ +l+++l++++l+ +li+++++i v++ +s+l+gr++  +++++ +w++Fk +L+Df+ ++++ pedle+w+
  gi|386002255|ref|YP_005920554.1| 482 FILFIRFLFGVLWSPILFKGLIIFMQMIPVFIAPSALFGRWKGGYYREKLEWDSFKSHLSDFATIQKYAPEDLEIWK 558
                                       ***************************************************************************** PP

                           DUF2207 474 ryLvYAtalGvadkvakql 492
                                       ++LvY+talG++dkva+++
  gi|386002255|ref|YP_005920554.1| 559 EWLVYGTALGIGDKVAEAM 577
                                       ****************998 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.1   9.4e+03      17      30 ..     280     294 ..     276     327 .. 0.61
   2 ?   12.4   4.3   1.7e-05      0.15      15      67 ..     477     523 ..     453     532 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                               2TM  17 lvvYlivni.flili 30 
                                       l++++i+   +l l+
  gi|386002255|ref|YP_005920554.1| 280 LAIFIIILPaILYLV 294
                                       567777777344333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                               2TM  15 rhlvvYlivniflilinlgsswflw.pilfWgiglllhalkvFg.tekffgkeWe 67 
                                       + +v++++++ fl+++       lw pilf g++++++ + vF   +++fg+ W+
  gi|386002255|ref|YP_005920554.1| 477 IFFVIFILFIRFLFGV-------LWsPILFKGLIIFMQMIPVFIaPSALFGR-WK 523
                                       2334444444444444.......566*****************955888886.64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 4057.48
//
Query:       gi|386002256|ref|YP_005920555.1|  [L=203]
Description: LemA family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-34  116.7   0.1      1e-33  116.3   0.1    1.1  1  LemA             LemA family
  ------ inclusion threshold ------
      0.011   16.0   0.0        2.8    8.2   0.0    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
      0.069   13.2   1.2       0.14   12.2   0.1    2.0  2  Col_cuticle_N    Nematode cuticle collagen N-terminal domain
        0.1   12.0   0.2       0.16   11.4   0.2    1.2  1  DUF3552          Domain of unknown function (DUF3552)
        0.2   11.3   2.5         15    5.3   0.0    3.0  3  Nbl1_Borealin_N  Nbl1 / Borealin N terminal


Domain annotation for each model (and alignments):
>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.1   2.8e-37     1e-33       2     141 ..      43     181 ..      42     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 2.8e-37
                              LemA   2 wsqidvqlkrRaDlipnLvetvkgyakhEketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLk 78 
                                       +sq+ v++k+R D+i +Lv++vk ya++E+e+le++  +R+++a+ +++ e ++ e + ++ +++l+avaE YP+L+
  gi|386002256|ref|YP_005920555.1|  43 LSQMRVAMKKRLDMIEQLVDSVKSYARFEREVLERISGMRSRVAS-ADPIELTRIEGESKGVFGNLVAVAEGYPQLR 118
                                       6899***************************************55.56678999*********************** PP

                              LemA  79 anenfleLqeelegtEnriavaRrrYneavreyntkiesfpsnivaklfgfkekelfeaeeae 141
                                       ++e+++  ++ ++g+E++i+ +R  Yn+ v+++nt ++sfps+ v  l++f +++++++ee+e
  gi|386002256|ref|YP_005920555.1| 119 TSETVMMTMDAIKGVEDEISRHRYTYNNIVQNFNTILDSFPSKYVTYLVKFGRMDYLNFEEDE 181
                                       **********************************************************98876 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00079       2.8       9      60 ..      14      68 ..       9      91 .. 0.76
   2 ?    5.8   0.0    0.0047        17      19      64 ..     114     159 ..     106     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00079
                            DUF948  9 AFvvL...viflivvllklkktldeaaatieelekqvdpilkevedllakvnell 60
                                      AF++L   +++ i + ++l+++   a+at+ +++  +++ l+ +e+l++ v+  +
  gi|386002256|ref|YP_005920555.1| 14 AFLLLlssAVYFISIYNRLQRLRHGAEATLSQMRVAMKKRLDMIEQLVDSVKSYA 68
                                      5555522258888899999*****************************9999844 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0047
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvn 64 
                                       ++ l+ ++t+  + ++i+++e+++       ++++++ n++l+   
  gi|386002256|ref|YP_005920555.1| 114 YPQLRTSETVMMTMDAIKGVEDEISRHRYTYNNIVQNFNTILDSFP 159
                                       56678899999999**************************998765 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     4e-05      0.14       2      33 ..       9      40 ..       8      49 .. 0.85
   2 ?   -1.4   0.1      0.72   2.6e+03      30      46 ..     121     137 ..     119     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                     Col_cuticle_N  2 vavalStvailsslitlpsiyndiqsfqsevl 33
                                      +a+  +++ +lss +++ siyn +q ++   +
  gi|386002256|ref|YP_005920555.1|  9 AAILTAFLLLLSSAVYFISIYNRLQRLRHGAE 40
                                      68888999*****************9997665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.72
                     Col_cuticle_N  30 sevldemdefktradda 46 
                                       ++v+  md  k++ d++
  gi|386002256|ref|YP_005920555.1| 121 ETVMMTMDAIKGVEDEI 137
                                       57999999999988865 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   4.4e-05      0.16     104     151 ..      39      86 ..      29     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                           DUF3552 104 keesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtkeeA 151
                                        e++l++ +  +k++ + +e+  +++++  + +r+ Lerisg+ +  A
  gi|386002256|ref|YP_005920555.1|  39 AEATLSQMRVAMKKRLDMIEQLVDSVKSYARFEREVLERISGMRSRVA 86 
                                       6999***************************************98655 PP

>> Nbl1_Borealin_N  Nbl1 / Borealin N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6     0.017        61      15      39 ..      30      54 ..      28      59 .. 0.87
   2 ?    5.3   0.0    0.0042        15       8      25 ..      69      86 ..      68      88 .. 0.88
   3 ?    0.1   0.0      0.18   6.5e+02      13      33 ..     133     153 ..     131     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                   Nbl1_Borealin_N 15 eRirrlraelelllktlrnrfelel 39
                                      +R +rlr  +e +l ++r +++ +l
  gi|386002256|ref|YP_005920555.1| 30 NRLQRLRHGAEATLSQMRVAMKKRL 54
                                      699**************99988665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0042
                   Nbl1_Borealin_N  8 nfdlEveeRirrlraele 25
                                      +f+ Ev eRi+ +r+ ++
  gi|386002256|ref|YP_005920555.1| 69 RFEREVLERISGMRSRVA 86
                                      7*************9876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.18
                   Nbl1_Borealin_N  13 veeRirrlraelelllktlrn 33 
                                       ve+ i+r r  ++++++++++
  gi|386002256|ref|YP_005920555.1| 133 VEDEISRHRYTYNNIVQNFNT 153
                                       77888999999******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      846  (0.0471861); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1125.37
//
Query:       gi|386002257|ref|YP_005920556.1|  [L=127]
Description: hypothetical protein Mhar_1573 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 805.77
//
Query:       gi|386002258|ref|YP_005920557.1|  [L=773]
Description: Phosphoribosylformylglycinamidine synthase II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-39  135.1   0.0    1.5e-19   70.7   0.1    2.4  2  AIRS_C          AIR synthase related protein, C-terminal doma
    4.1e-35  120.3   2.5    1.5e-16   60.8   0.9    2.6  2  AIRS            AIR synthase related protein, N-terminal doma
    8.3e-12   45.5   0.0    1.6e-11   44.5   0.0    1.5  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   1.1e-20   6.7e-17       4     150 ..     217     376 ..     216     382 .. 0.84
   2 !   70.7   0.1   2.5e-23   1.5e-19       1     153 [.     600     745 ..     600     748 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1.1e-20
                                       EEEEEEET...SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHH...HTTECEEEE--TTHHH CS
                            AIRS_C   4 dvliltgs...lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaal...kglvkaahDvTgGGLl 73 
                                       dv+++ ++   +G+gg++ ++++++ ee+++  + a q+ d++l++ l ++++al  l   +g   +++D++gGG++
  gi|386002258|ref|YP_005920557.1| 217 DVIVVGKPtdsSGFGGVT-FASEELREEDEEANRgAIQIPDPFLKNVLFKANEALFKLtreEGITIGFKDLGGGGFT 292
                                       89999999999*******.6666666666665557999**********************999999*********** PP

                                       HHHHHHHHTTTEEEEEECG.THHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHH........HTTCCCEEE CS
                            AIRS_C  74 galaemapasgvgaeidld.kvpifdelesplemllsensGrllvavppeeadavlaile........eeglpeaav 141
                                       +a +em + +g g+ +dld   ++ d l  p+ ++++e+++r ++++ppe  +++l+i +         eg   a+v
  gi|386002258|ref|YP_005920557.1| 293 CASSEMGASAGYGMDLDLDlLHKVSDDL-PPEVVACAETQERFMLICPPELTERALKIYNenwdlpnvYEGA-RASV 367
                                       *******************544444444.99***************************99544444433455.7999 PP

                                       EEEEEESSS CS
                            AIRS_C 142 IGevtakee 150
                                       +G+vt  ++
  gi|386002258|ref|YP_005920557.1| 368 VGKVTTNGR 376
                                       999998766 PP

  == domain 2  score: 70.7 bits;  conditional E-value: 2.5e-23
                                       STTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHH CS
                            AIRS_C   1 kpGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlga 75 
                                       ++Gd ++l+g+  + lgg+ ++  +++ +   ++     ++   le+ +iy++   +a+ + v aahD+++GGL+ +
  gi|386002258|ref|YP_005920557.1| 600 RAGDSIYLLGPrfDELGGSEYYRTVWGAAGRNVP-----VVRFDLERSMIYAVIDSIAE-KTVVAAHDISNGGLAAT 670
                                       68*********************99999998887.....*******************8.***************** PP

                                       HHHHHHT..TTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C  76 laemapa..sgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                       +aema    +++g+ +dld   + + l  +  + +se+sG  l+ +++ +++ + +il+ +gl e  ++G+vt+++e
  gi|386002258|ref|YP_005920557.1| 671 AAEMALVgrGDLGIDLDLD--AAGSDL-PADRLVFSESSG-FLLECKAGSEEDLERILKGCGL-EIIRLGKVTDSPE 742
                                       *****87336788888888..444444.557777777777.55677777777***********.8*********998 PP

                                       EEE CS
                            AIRS_C 151 lsv 153
                                       l +
  gi|386002258|ref|YP_005920557.1| 743 LVM 745
                                       765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.9   2.5e-20   1.5e-16       2      94 .]      81     197 ..      80     197 .. 0.92
   2 !   58.4   0.0   1.4e-19   8.3e-16       2      94 .]     461     587 ..     460     587 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.5e-20
                                       SSE.........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC............HHHH CS
                              AIRS   2 Daa.........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp............wlee 57 
                                       Da+         vv++ +shn+p+ + p ++ +a++++++++D+ +mGA+ +a  + l ++             +e+
  gi|386002258|ref|YP_005920557.1|  81 DAGivaiddewcVVIAHESHNHPSQILPNEG-AATGIGGIVRDVNCMGAKVVATADPLRFGdpfgedknhvrwVAEG 156
                                       666544444444699****************.****************************************88899 PP

                                       HHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  58 vvrglaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                       vv+g+ +++++lgvp++ Gd+ f+++    ++++v+a+G+v
  gi|386002258|ref|YP_005920557.1| 157 VVDGIWQYGNALGVPIMAGDVVFDDSfdtnCLVNVVAIGVV 197
                                       ***********************9999999*********97 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 1.4e-19
                                       SSE...........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHH CS
                              AIRS   2 Daa...........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleev 58 
                                       Da+           +++++d ++ +  ++p+   Ga+ava++++++aa GA+P  l+++l+++         +++e+
  gi|386002258|ref|YP_005920557.1| 461 DAGliapvrgkkfgIALSVDANPFYGRISPYWA-GATAVAEAMRNVAAIGATPATLTDCLNFGnpekpeafwEFREC 536
                                       66644343333333599***9999999****99.******************************************* PP

                                       HHHHHHHHHHTT-........EEEEEEEEEESS.......EEEEEEEEEEE CS
                              AIRS  59 vrglaeaaeelgv........plvgGdtsfsne.......ptisvtavGlv 94 
                                       vrgla+aa++l          p+v+G++sf+ne       p++ +++vGl+
  gi|386002258|ref|YP_005920557.1| 537 VRGLADAAKALWLkgyedtpvPIVSGNVSFYNEspegtvdPSPIIACVGLI 587
                                       *******77764444444444**********999***************85 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   2.8e-15   1.6e-11       5      50 .]      15      57 ..      11      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.8e-15
                    FGAR-AT_linker  5 nkelglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                       ++ gl+Ls  E + ++ea   lgr+Pt  El+ +  +wSEHC++K
  gi|386002258|ref|YP_005920557.1| 15 LRSAGLGLSVPEARSVAEA---LGRDPTIPELFNYDTMWSEHCSYK 57
                                      5789***************...9**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 4637.47
//
Query:       gi|386002259|ref|YP_005920558.1|  [L=266]
Description: Phosphoribosylformylglycinamidine synthase I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-52  178.4   0.0    1.6e-52  178.2   0.0    1.0  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    2.3e-09   37.3   0.0    3.8e-09   36.6   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    1.4e-08   34.6   0.0    3.4e-08   33.3   0.0    1.6  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    4.4e-08   33.1   0.0    7.2e-08   32.4   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
    5.8e-05   23.0   0.0    9.8e-05   22.3   0.0    1.3  1  SNO            SNO glutamine amidotransferase family
     0.0029   17.4   0.0     0.0045   16.8   0.0    1.3  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   0.0   5.2e-56   1.6e-52       3     260 .]       2     262 ..       1     262 [. 0.89

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 5.2e-56
                          GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklr 79 
                                       k+a++ ++G+n+e e+  a + aG + + +  +   + +++l+ f + ++pGGfsy D l +g++++     +e + 
  gi|386002259|ref|YP_005920558.1|   2 KIAVVQFPGTNCEHETLVAAKSAGLSGEIFRWN---RPAEELSGFDGYIIPGGFSYQDRLRAGAIAS-----KEPVM 70 
                                       89*************************887555...45789**********************9887.....47789 PP

                          GATase_5  80 ealekflnredtlaLGiCnGfqlLvklglvpggeieea..eksptltrNksgr..fesrlvsv.vvsek...spsvf 148
                                       +al++  +r ++ ++GiCnGfq+Lv+ gl+pg    +a  ++++   + ++ r  f + ++++ +       s s++
  gi|386002259|ref|YP_005920558.1|  71 DALREEAER-GKPIIGICNGFQILVEAGLLPGLGGIDAalASNVMVSKGEIVRrgFYCAWTTLrHEAPPkrcSGSFL 146
                                       999999999.**********************77666335888888888887667********63322234588999 PP

                          GATase_5 149 lkgmeglslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpH 225
                                       l+ +e +++p ah+eG++v+ +++ +++l++ +qv++rY++e+g++  eyp+N NgS e++agi++p+G vl++mpH
  gi|386002259|ref|YP_005920558.1| 147 LEVGELVRMPLAHAEGNLVTVDPDLMARLNEDHQVVFRYCNEAGEVDPEYPVNINGSLENVAGICNPEGNVLGMMPH 223
                                       9**************************************************************************** PP

                          GATase_5 226 pervveavqksiipeeeeee....vspwlrlFenavkyv 260
                                       per++ a+q +  ++ ++ +     +p+ r+Fe++ +y+
  gi|386002259|ref|YP_005920558.1| 224 PERSSFAWQLPPADPAKSVGdmeaPGPGRRIFESMKRYI 262
                                       ***********88875553234568**********9995 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.3e-12   3.8e-09      16      91 ..      20     119 ..      11     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.3e-12
                                       HHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHH CS
                            GATase  16 alvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQl 83 
                                       a+ ++g++ e+++++ +aee     +++dg +++gG+ +            e  ++a++e +e+++Pi+GIC G+Q+
  gi|386002259|ref|YP_005920558.1|  20 AAKSAGLSGEIFRWNRPAEEL----SGFDGYIIPGGFSYQDrlragaiasKEPVMDALREEAERGKPIIGICNGFQI 92 
                                       567789999******999999....69************999999997766777888888888************** PP

                                       HHHHTTT...................E CS
                            GATase  84 laiefgr...................k 91 
                                       l+++                      +
  gi|386002259|ref|YP_005920558.1|  93 LVEAGLLpglggidaalasnvmvskgE 119
                                       *99854455555666666655555550 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.1e-11   3.4e-08      27      90 ..      31      95 ..      24     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.1e-11
                          GATase_3 27 vrfvplkdeslgedadlvilpGgkdtiqdl...allresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                                      +r+ + + e+l    d +i+pGg+++ ++l   a++ ++ + +a++e ae+g+p++giC G+q+L e
  gi|386002259|ref|YP_005920558.1| 31 FRWNR-PAEELSG-FDGYIIPGGFSYQDRLragAIASKEPVMDALREEAERGKPIIGICNGFQILVE 95
                                      56666.8999955.*********8877666222677889999**********************976 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.4e-11   7.2e-08      59     115 ..      40     101 ..       8     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.4e-11
                                       CCG-SEEEE--BHHHHHHHHT.....SHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                         DJ-1_PfpI  59 aaeyDalvlpGGragperlre.....nekvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                        + +D  ++pGG +  +rlr+     +e v++ ++e ae+gk++  IC g q+L++ag+l+g
  gi|386002259|ref|YP_005920558.1|  40 LSGFDGYIIPGGFSYQDRLRAgaiasKEPVMDALREEAERGKPIIGICNGFQILVEAGLLPG 101
                                       5679**********999998633322679******************************987 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.3e-08   9.8e-05      22      82 ..      28      94 ..       5     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.3e-08
                                      E...EEE-SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHC CS
                               SNO 22 n...ktvkrkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGlills 82
                                      +   +  +  e+l + d+ iiPGG s       + ++ +  ++++l+e ++++ k+++G C G+ +l 
  gi|386002259|ref|YP_005920558.1| 28 GeifRWNRPAEELSGFDGYIIPGGFSYQdrlrAGAIASKEPVMDALREEAERG-KPIIGICNGFQILV 94
                                      34433445679*************997522225679***************99.*********97764 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-06    0.0045      98     120 ..      73      94 ..      37     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnv 120
                                       +r++ erg+Pi+giC G+q+l v
  gi|386002259|ref|YP_005920558.1|  73 LREEAERGKPIIGICNGFQIL-V 94 
                                       68899***************9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1691.81
//
Query:       gi|386002260|ref|YP_005920559.1|  [L=157]
Description: hypothetical protein Mhar_1576 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-07   31.5   0.0      0.016   15.4   0.0    2.1  2  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     9e-07     0.016       6      75 ..       7      74 ..       1      76 [. 0.80
   2 !   14.6   0.0   1.6e-06     0.029      13      75 ..      95     155 ..      85     157 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9e-07
                                      EEE-TTS--HHHHHHHHHHHHT.THTT.EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEE CS
                              PurS  6 VtlKkgvlDpqGkavkkalksl.gyee.vedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyei 75
                                      V lK  + D+++ +vk++l++  gye+  +d+r  ++ ++e+++   ++  + +++++++ L+N + e+y+ 
  gi|386002260|ref|YP_005920559.1|  7 VWLK--IPDAEAATVKNTLRRRmGYEGvLTDLRRERLWSIEVDDG-VDDPMDLARRLARD-LVNENKESYRA 74
                                      4444..99***********9766****568*************76.44567888999888.89999999986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.6e-06
                                       --HHHH.HHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEE CS
                              PurS  13 lDpqGk.avkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyei 75 
                                        D ++  a+k+   +lg+e v+ v    + +l l++ +    ++++ee++e lL+Np    yei
  gi|386002260|ref|YP_005920559.1|  95 EDGEAVsALKRLRDRLGFEMVRGVERSVVWKLALSSPNP---RRTAEEIAEGLLINPHKDFYEI 155
                                       5555541444444577*******************8765...679************8777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1055.99
//
Query:       gi|386002261|ref|YP_005920560.1|  [L=788]
Description: Putative ATP-dependent RNA helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   86.9   0.0    4.1e-21   75.4   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    4.5e-23   82.2   0.0    8.3e-23   81.3   0.0    1.5  1  ERCC4          ERCC4 domain
    7.5e-18   64.9   0.0      2e-17   63.6   0.0    1.7  2  DEAD           DEAD/DEAH box helicase
    2.1e-17   63.7   0.0    3.8e-17   62.8   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
    8.9e-12   44.9   0.0    3.1e-11   43.2   0.0    1.9  1  HHH_2          Helix-hairpin-helix motif
    4.1e-11   43.3   0.0    6.4e-10   39.5   0.0    2.8  2  HHH_5          Helix-hairpin-helix domain
    3.8e-08   32.8   0.2      3e-06   26.8   0.1    3.0  2  HHH            Helix-hairpin-helix motif
     0.0024   18.1   0.0      0.012   15.9   0.0    2.1  1  HHH_3          Helix-hairpin-helix motif
     0.0038   17.8   0.2      0.023   15.3   0.0    2.4  2  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
     0.0094   15.2   0.0       0.02   14.2   0.0    1.4  1  DUF2075        Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.028   14.8   0.1        4.1    7.8   0.0    3.1  2  HHH_8          Helix-hairpin-helix domain
      0.038   13.2   0.1      0.067   12.4   0.1    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00096       1.4       7     100 ..      49     145 ..      43     158 .. 0.79
   2 !   75.4   0.0   2.8e-24   4.1e-21       7     110 ..     357     474 ..     351     475 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00096
                                       HHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGGTSS CS
                        Helicase_C   7 lellkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfn.kgesdvLiatdvaerG 79 
                                       + l   + ++gk+l  ++t+  +e+   +le+    +  va ++ge+  + r+e+ e+ +   ++  +i  d ++r 
  gi|386002261|ref|YP_005920560.1|  49 MVL-IARLNRGKVLFLAPTKPLVEQHASFLENVladSTIVASFTGEILPERRKEMWEEAKiVVSTPQVIENDLLSRR 124
                                       334.48899************9999555545556778999*******************95455569********** PP

                                       STSTTESEEEESSSSSSHHHH CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsy 100
                                       i + +v+++i+ ++ r v +y
  gi|386002261|ref|YP_005920560.1| 125 ISLRDVSCIIFDEAHRAVGNY 145
                                       **********99999887544 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 2.8e-24
                                       HHHH...HHTTTTSEEEEEESSHHHHHH.HHHHHHHT..........TSTEEEESTTSTHHHHHHHHHHHHTTSSSE CS
                        Helicase_C   7 lell...kleeeggkilifvntidrlek.vklllekk..........gikvavlhgelpqnereeileqfnkgesdv 69 
                                       lel+    + + +++i++f+n++d++++ +++l+e            g ++ + +  l+q+ + eil++f++g ++v
  gi|386002261|ref|YP_005920560.1| 357 LELVkeqLTAKADSRIMVFTNYRDTASSvLDYLREAGdeiirpvrfvGQSSRASDEGLSQRRQAEILQKFREGAYNV 433
                                       44444333678999**********887778888655577666666677777777778******************** PP

                                       EEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  70 LiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       Liat+v+e+Gidip  +lV ++++  +  + iqr+GRtgRa
  gi|386002261|ref|YP_005920560.1| 434 LIATSVGEEGIDIPATDLVLFYEPVPSEIRSIQRKGRTGRA 474
                                       ****************************************8 PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   5.6e-26   8.3e-23       1     155 [.     582     700 ..     582     701 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 5.6e-26
                                       EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCC..SH CS
                             ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikd..gr 75 
                                       +D+re  +++ +  le++gv v+ + l++gdy ++   +++               v +erk+add+v+s+    + 
  gi|386002261|ref|YP_005920560.1| 582 VDPRE--RSLARM-LESMGVGVTLRVLEVGDY-VV---SDR---------------VGIERKTADDFVDSLVGaeRN 636
                                       79***..779999.******************.**...9**...............***************666699 PP

                                       HHHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHH CS
                             ERCC4  76 leeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaew 152
                                       ++ q+++l+r +y++pil++eg d y r+               +++++i +aL+++++dfgv i+ t ++ et+ +
  gi|386002261|ref|YP_005920560.1| 637 IFAQLKDLAR-SYERPILILEGRDLYARQ---------------VHPNAIRGALASIAVDFGVAIIPTADEDETVSV 697
                                       **********.*****************9...............*******************************99 PP

                                       HHH CS
                             ERCC4 153 lan 155
                                       +a+
  gi|386002261|ref|YP_005920560.1| 698 IAA 700
                                       976 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   1.3e-20     2e-17       4     136 ..      21     144 ..      18     176 .. 0.83
   2 ?   -3.0   0.0       3.5   5.2e+03      37      87 ..     358     408 ..     353     437 .. 0.60

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.3e-20
                                       HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                       Q e    +l + + lv  +TG GKT ++l+ +++++      ++ k+l+++Pt+ L+eq+++ l++++     ++++
  gi|386002261|ref|YP_005920560.1|  21 QLELAASAL-QASTLVVLPTGLGKTVVALMVLIARL------NRGKVLFLAPTKPLVEQHASFLENVLADS--TIVA 88 
                                       556666666.45899******************877......6679***********************64..4555 PP

                                       EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq 136
                                        ++g+   + ++++ ++++ivv+tp+ + + l +++++l++v+++++DEa+r   +
  gi|386002261|ref|YP_005920560.1|  89 SFTGEILPERRKEMWEEAKIVVSTPQVIENDLLSRRISLRDVSCIIFDEAHRAVGN 144
                                       67777777888888799************96666999**************98776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.5
                                       HHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  37 qivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaa 87 
                                       + v e+ + k   ++++ +  r  a  +l+ l++ +++i +r + ++g++++
  gi|386002261|ref|YP_005920560.1| 358 ELVKEQlTAKADSRIMVFTNYRDTASSVLDYLREAGDEI-IRPVRFVGQSSR 408
                                       444444556777778888888888888888888888875.345545554333 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 !   62.8   0.0   2.6e-20   3.8e-17      22     169 ..      28     170 ..      10     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.6e-20
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkk 94 
                                         +   l++++TG GKT+va + li+rl +     k+lfl+p+k l+eq  + ++++l + +     +g+++ +++k
  gi|386002261|ref|YP_005920560.1|  28 ALQASTLVVLPTGLGKTVVAlMVLIARLNRG----KVLFLAPTKPLVEQHASFLENVLADSTIVasfTGEILPERRK 100
                                       5677899*************99999999996....9**************999999988876334544555555554 PP

                                       --.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---....SEEEEEES CS
                            ResIII  95 kakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke....avllglTA 167
                                       +      +++ki+v+t q + +d+      s + +     +ii+DEaHr+ ++ ++  i+e + +     ++lg+TA
  gi|386002261|ref|YP_005920560.1| 101 EM----WEEAKIVVSTPQVIENDL-----LSRRISLRDVSCIIFDEAHRAVGNYAYVYIAERYGRegtdRLVLGITA 168
                                       44....99****************.....99999999999************8899999777633355599999999 PP

                                       S- CS
                            ResIII 168 Tp 169
                                        p
  gi|386002261|ref|YP_005920560.1| 169 SP 170
                                       88 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   2.1e-14   3.1e-11       7      53 ..     734     780 ..     730     783 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.1e-14
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                       +I+ VG+++Ak+L ++F+s+++  +as+eeL ev+ +G+++A+ i+e
  gi|386002261|ref|YP_005920560.1| 734 SIPGVGNAVAKNLLRHFGSVERVFAASAEELKEVELVGPKTAERIRE 780
                                       7********************************************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.3     2e+03      11      35 ..     323     349 ..     323     356 .. 0.64
   2 !   39.5   0.0   4.3e-13   6.4e-10       4      52 ..     732     779 ..     729     780 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                                       -HHHHHHHHTT.T--.SHHHHHHS-HH CS
                             HHH_5  11 GpktAlallsa.Gie.svedlaaadve 35 
                                       G k A+++ +   +e  v dla++dv+
  gi|386002261|ref|YP_005920560.1| 323 GSKAAKRIMEDpRVEeAVGDLARMDVD 349
                                       677777777771133235588888876 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 4.3e-13
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52 
                                       + s++G+G ++A++ll++ ++sve + aa++eeL ++  +G+ktAeri 
  gi|386002261|ref|YP_005920560.1| 732 VSSIPGVGNAVAKNLLRH-FGSVERVFAASAEELKEVELVGPKTAERIR 779
                                       569***************.*****************************7 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.085   1.3e+02      15      28 ..     734     747 ..     731     749 .. 0.80
   2 !   26.8   0.1     2e-09     3e-06       1      29 [.     752     780 ..     752     781 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.085
                                       TSTT-SHHHHHHHH CS
                               HHH  15 alPGVGpktAeaIl 28 
                                       ++PGVG ++A   l
  gi|386002261|ref|YP_005920560.1| 734 SIPGVGNAVAKNLL 747
                                       69****99998666 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 2e-09
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                       s+e++++as eeL++++ VGpktAe+I++
  gi|386002261|ref|YP_005920560.1| 752 SVERVFAASAEELKEVELVGPKTAERIRE 780
                                       6799***********************86 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.9e-06     0.012      17      62 ..     733     780 ..     729     782 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.9e-06
                             HHH_3  17 qklpGlgpklAknIvayReknGpf..ksreeLlkvkglgpktfeqlag 62 
                                       + +pG+g ++Akn++++  +  ++  +s eeL++v+ +gpkt e++++
  gi|386002261|ref|YP_005920560.1| 733 SSIPGVGNAVAKNLLRHFGSVERVfaASAEELKEVELVGPKTAERIRE 780
                                       679************99877753334799****************986 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         3   4.5e+03      69      87 ..     323     341 ..     281     371 .. 0.48
   2 !   15.3   0.0   1.5e-05     0.023      21      53 ..     733     766 ..     725     782 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                        5_3_exonuc  69 lskkLatiktdvplelele 87 
                                        sk   +i +d  +e ++ 
  gi|386002261|ref|YP_005920560.1| 323 GSKAAKRIMEDPRVEEAVG 341
                                       3333333333333322222 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.5e-05
                        5_3_exonuc  21 pGvpgiGektAakLlkeygsleeilenld.elke 53 
                                         +pg+G+  A++Ll+++gs+e ++++ + elke
  gi|386002261|ref|YP_005920560.1| 733 SSIPGVGNAVAKNLLRHFGSVERVFAASAeELKE 766
                                       679**********************977545555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.3e-05      0.02      11     101 ..      40     142 ..      35     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                           DUF2075  11 GtGKtvvllnllael..........eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef 77 
                                       G GKtvv+l +l +            ++ + ++++ ++ N     ++   ++++  ++++ke  e+ + ++ + +  
  gi|386002261|ref|YP_005920560.1|  40 GLGKTVVALMVLIARlnrgkvlflaPTKPLVEQHASFLENVLADSTIVASFTGEILPERRKEMWEEAKIVVSTPQVI 116
                                       88******999988756666666665666666666666777777777777777779**************9999966 PP

                           DUF2075  78 ..kkaeekkeepkedvvivDEAhrll 101
                                         +   ++ + +++ ++i+DEAhr+ 
  gi|386002261|ref|YP_005920560.1| 117 enDLLSRRISLRDVSCIIFDEAHRAV 142
                                       86777888899*************96 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.072   1.1e+02      43      62 ..     725     745 ..     716     749 .. 0.72
   2 ?    7.8   0.0    0.0027       4.1      44      67 ..     760     782 ..     752     783 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.072
                                       HHHTT..HCTTSTT--HHHHHH CS
                             HHH_8  43 tslee..eltklpgiGkkiaak 62 
                                       ++ ++   ++++pg+G+++a+ 
  gi|386002261|ref|YP_005920560.1| 725 KE-QQeyLVSSIPGVGNAVAKN 745
                                       44.23445689*******9985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0027
                                       HHTTHCTTSTT--HHHHHHHHHHH CS
                             HHH_8  44 sleeeltklpgiGkkiaakieeil 67 
                                       s+ee l+++  +G+k+a++i+e++
  gi|386002261|ref|YP_005920560.1| 760 SAEE-LKEVELVGPKTAERIRELV 782
                                       4466.*****************86 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.5e-05     0.067      90     154 ..     415     477 ..     410     499 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                     ERCC3_RAD25_C  90 seaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkk 154
                                       s++ + +ilqkf++  ++n+++   vg++ iD+P    ++     + s  +  qr Gr  ra+++
  gi|386002261|ref|YP_005920560.1| 415 SQRRQAEILQKFREG-AYNVLIATSVGEEGIDIPATDLVL-FYEPVPSEIRSIQRKGRTGRARAG 477
                                       6777899*****987.89999999**********777665.556677888889999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 4687.27
//
Query:       gi|386002262|ref|YP_005920561.1|  [L=38]
Description: hypothetical protein Mhar_1578 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.50
# Mc/sec: 229.02
//
Query:       gi|386002263|ref|YP_005920562.1|  [L=171]
Description: hypothetical protein Mhar_1579 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   12.8   0.0        2.9    7.8   0.0    2.2  2  Csm1_B    Csm1 subunit domain B


Domain annotation for each model (and alignments):
>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00016       2.9      22      52 ..      24      54 ..      18      87 .. 0.82
   2 ?    3.0   0.0     0.005        90      42      72 ..     113     141 ..     108     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHTT--CCCEEEEETTEEEEEEE CS
                            Csm1_B 22 eeivdelleklelsranllYagGGhfylLlp 52
                                      e+++ +l  +++l+r+++lY++G    +L +
  gi|386002263|ref|YP_005920562.1| 24 EVLIASLNGQASLQRVQVLYVSGNSSRILDK 54
                                      56777888899************99998865 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.005
                                       EETTEEEEEEE--HHHHHHHHHHHHHHHHHC CS
                            Csm1_B  42 agGGhfylLlpntekvkekleeiekelnewl 72 
                                       a+GG ++lL + ++  ++ l+ei+k  ++++
  gi|386002263|ref|YP_005920562.1| 113 ASGGSAVLLYSPST--DRHLDEISKFADRIF 141
                                       67888888876554..566777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1075.59
//
Query:       gi|386002264|ref|YP_005920563.1|  [L=104]
Description: hypothetical protein Mhar_1580 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 681.21
//
Query:       gi|386002265|ref|YP_005920564.1|  [L=682]
Description: DNA polymerase B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-14   53.6   0.0    2.6e-10   39.6   0.0    3.0  2  DNA_pol_B  DNA polymerase family B


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.4e-14   2.6e-10      43     202 ..     316     452 ..     285     465 .. 0.85
   2 !    7.2   0.0   9.7e-05       1.7     283     408 ..     513     626 ..     510     646 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.4e-14
                                       -S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS-- CS
                         DNA_pol_B  43 gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleveveprlvefvkksvre 119
                                       + +G+++++P+ g+++   + lDF S YPsii+ + l+++t+  s+                 +p +  +++ + r+
  gi|386002265|ref|YP_005920564.1| 316 ADKGGMIFQPRPGVHERA-CELDFTSFYPSIIVNYHLSPETVGGSRPV---------------GP-GPGGFRGPARR 375
                                       369************976.78********************9987654...............23.234567899** PP

                                       -HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHH CS
                         DNA_pol_B 120 gllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLek 196
                                       g l ++++ ll+ R + k+ lk+++       +     alK +  + +G+tG++n ++  +++ + +T i R+ L++
  gi|386002265|ref|YP_005920564.1| 376 GFLCEVIEPLLELRLKTKR-LKKAEPR-----YGGLDSALKWMLVTCFGYTGYKNAKFGRIEVHEAITRISRDLLLQ 446
                                       ****************985.7888777.....788889*************************************** PP

                                       HHHHHH CS
                         DNA_pol_B 197 tkelve 202
                                       +ke+ e
  gi|386002265|ref|YP_005920564.1| 447 AKEIAE 452
                                       *99987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 9.7e-05
                                       EEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHH.HHHHTT-S CS
                         DNA_pol_B 283 kYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvl.eeleenkv 358
                                       +Y gl  +     ++l  +Gv   Rrd  ++v+++  +v+e++ ++    r+++e + +  + lk ++  +    ++
  gi|386002265|ref|YP_005920564.1| 513 RYFGLLSS-----GRLKLRGVAARRRDTPEYVRRMQMEVIEKMGEA----RNIDELRLIKPEALKIARrYRQWLPNA 580
                                       78888888.....999***************************999....777777666666665444333344667 PP

                                       -GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEE CS
                         DNA_pol_B 359 plekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvi 408
                                       + +++v+ +++sk      +k+ +++++++ +++r + ++++g  ++Yv+
  gi|386002265|ref|YP_005920564.1| 581 DPSELVVRRRISKL---GRQKRCAQASAIEAYRRR-GVKVSPGMAVEYVV 626
                                       88999999999994...456666666666666555.57788888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 4444.70
//
Query:       gi|386002266|ref|YP_005920565.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002266|ref|YP_005920565.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002266|ref|YP_005920565.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002266|ref|YP_005920565.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002266|ref|YP_005920565.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002266|ref|YP_005920565.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1873.20
//
Query:       gi|386002267|ref|YP_005920566.1|  [L=108]
Description: hypothetical protein Mhar_1583 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.13   12.4   0.3       0.18   12.0   0.3    1.3  1  CEP209_CC5  Coiled-coil region of centrosome protein CE290


Domain annotation for each model (and alignments):
>> CEP209_CC5  Coiled-coil region of centrosome protein CE290
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3     1e-05      0.18      79     109 ..      48      78 ..      42     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                        CEP209_CC5  79 kqkeeikylknlieeqertisklEeeivqln 109
                                       ++k++iky + + +e e  i+ lE++ vql 
  gi|386002267|ref|YP_005920566.1|  48 NHKDKIKYKNIIRSEIELCIAALEQDRVQLL 78 
                                       689*****999999**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 767.92
//
Query:       gi|386002268|ref|YP_005920567.1|  [L=214]
Description: Translin family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-05   24.6   0.0    0.00023   21.2   0.0    2.0  1  Translin  Translin family
     0.0021   18.5   4.2     0.0092   16.4   0.4    2.3  2  BMFP      Membrane fusogenic activity
  ------ inclusion threshold ------
      0.043   13.6   0.0       0.14   12.0   0.0    1.9  2  UBA_4     UBA-like domain


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.8e-08   0.00023      43     191 ..      58     183 ..      21     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.8e-08
                                       HHHHHHHHHHTTSS..........GHHHHGGGTH.HHHHHHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS- CS
                          Translin  43 keakeklkeiakllasvaeelqgsnayrYqrqisgglqeliealsfahYletqtLitleevqkilealkeneedafh 119
                                         a e+l++i +ll       ++++  rY+  + g+ qe+ ea   ++ ++++t+ +  ev+  ++           
  gi|386002268|ref|YP_005920567.1|  58 GRAGEDLASILNLL-------KEHPDVRYSGLVDGAEQEYAEARIVYSLITEGTIPHPREVGVEMT----------- 116
                                       55555555555555.......777888999999999999999999999888888888888887776........... PP

                                       --HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHHHHHHHTS----HH...HHHHHTTHHHHH CS
                          Translin 120 ltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrelragfellnlkndsakdlrkKldvlkqsv 191
                                            Yl Gl d +gEL R     + lg  e +    l+ ++e++  + +++ +   +k +r+K dv ++ +
  gi|386002268|ref|YP_005920567.1| 117 ----SYLAGLGDAVGELRRHILDLIRLGRPE-EGEVHLAAMEEIYHLLMSFDYPDAVTKGMRRKGDVARSLL 183
                                       ....5*****************999999977.899999********99999999555899******998766 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   1.5e-06    0.0092       4      67 ..       3      66 ..       1      73 [. 0.94
   2 ?    3.4   0.3     0.017     1e+02      52      77 .]     177     208 ..     173     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                              BMFP  4 prilddlakkvgdalpaaagvreeieknvravlqealsklDLVtREEFdvqrevlartreklea 67
                                      p ++d+la+ ++ +l++  ++ree+ +  rav+++  + +  V R E+d   +++ r+ e l++
  gi|386002268|ref|YP_005920567.1|  3 PSTADELAEEISHHLEEKDRAREEALALTRAVVRSSGAAIRSVHRGELDRALDLAGRAGEDLAS 66
                                      7889******************************************************999986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                              BMFP  52 dvqrevlartrekle......aLearvaaLEa 77 
                                       dv r +l rtr  l+      +Le ++ +LE+
  gi|386002268|ref|YP_005920567.1| 177 DVARSLLDRTRGDLTnaigqrRLEVQLRELEE 208
                                       89999********999999999*******995 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.55   3.3e+03      24      35 ..      45      56 ..      44      56 .. 0.83
   2 ?   12.0   0.0   2.4e-05      0.14      16      33 ..     177     194 ..     167     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.55
                             UBA_4 24 annWdLerAisl 35
                                      ++ + L+rA++l
  gi|386002268|ref|YP_005920567.1| 45 VHRGELDRALDL 56
                                      68899****985 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.4e-05
                             UBA_4  16 ekArqlLeannWdLerAi 33 
                                       ++Ar+lL+++ +dL +Ai
  gi|386002268|ref|YP_005920567.1| 177 DVARSLLDRTRGDLTNAI 194
                                       99***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1358.85
//
Query:       gi|386002269|ref|YP_005920568.1|  [L=257]
Description: AP endonuclease, family 2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-28   98.1   0.0    5.6e-28   97.8   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   3.1e-32   5.6e-28       3     209 ..      19     215 ..      17     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 3.1e-32
                                       HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHH CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraiel 78 
                                       +++++G+ g E+   + +  +    e++   r++++ ++l i+ + ++++ +    +  +   +ee ++++k++i +
  gi|386002269|ref|YP_005920568.1|  19 QLEDLGYSGWEIVNEGRQRLT---AETIPLAREIVETTDLVITIHLPYSDLNLASMN--Q-PiWEETLRQMKECISF 89 
                                       6789****************9...59***************9999999999998874..3.359999********** PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTT CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavds 153
                                       a+++ + l v+hpG  + ++k+ ++ awe+ + +l+e++d+a++ g+++a+E++ + ++ lg+  ee++ +l+ v++
  gi|386002269|ref|YP_005920568.1|  90 ASEF-CGLAVVHPGYLSPLGKQMPDRAWEQNILGLQEICDHAAEFGMRIAVENMLKIESMLGRtpEEIQGILENVRR 165
                                       ****.**********99*****************************************99999************** PP

                                       TTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 154 pnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGe 209
                                       +n+g+++D+gH++ + ++vd++l al++++ hvH++D+kg     rd+h+p+  G+
  gi|386002269|ref|YP_005920568.1| 166 ENLGFVFDVGHANTN-GNVDSFL-ALKEKMIHVHVHDNKG----ARDEHLPVKSGN 215
                                       *************99.8998888.6999************....********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1843.70
//
Query:       gi|386002270|ref|YP_005920569.1|  [L=138]
Description: hypothetical protein Mhar_1586 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-13   51.3   0.0    9.7e-13   48.4   0.0    1.9  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   5.4e-17   9.7e-13       1     118 [.       3     108 ..       3     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 5.4e-17
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.... CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.... 73 
                                       ++++ra v++TE  ekV+ al+ l+p +e      +aeG +          ++++   ++l  +++llre++i    
  gi|386002270|ref|YP_005920569.1|   3 EVSLRAAVRPTESPEKVAGALEALFPGIE-----VDAEGGF----------ISGRGGAASLAAFHRLLREQRIldta 64 
                                       589***********************995.....5666655..........46655679**************7655 PP

                                       .HHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEEEEE CS
                       RNA_binding  74 .keLlkeleervdekgklylrldKQaaylgklslvegdd...vIkvkik 118
                                        +++l+++       + + +rl+KQaa +g+++++ +++   +I+v+i+
  gi|386002270|ref|YP_005920569.1|  65 rSVMLQGVVA-----DAVQFRLNKQAATVGRINFPPEEEplgSIHVEIR 108
                                       5555555555.....89*********************99******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 947.32
//
Query:       gi|386002271|ref|YP_005920570.1|  [L=413]
Description: Peptide chain release factor subunit 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-43  146.5   0.0    9.7e-43  145.7   0.0    1.4  1  eRF1_2          eRF1 domain 2
    1.9e-31  108.9   0.0    5.7e-31  107.3   0.0    1.8  2  eRF1_3          eRF1 domain 3
    4.5e-13   49.6   0.1    7.5e-13   48.9   0.1    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    5.6e-12   46.1   0.0    1.2e-11   45.0   0.0    1.5  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    8.6e-12   45.2   0.0    2.1e-11   43.9   0.0    1.7  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
      0.058   14.0   0.0       0.12   13.0   0.0    1.6  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   0.0   3.3e-46   9.7e-43       2     131 ..     140     269 ..     139     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 3.3e-46
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +glivld++eAtig+l+g+++e +k++++svP+K+++Ggqs++rf+ lr  +++ef+k+++++a++afl++d+++l+
  gi|386002271|ref|YP_005920570.1| 140 FGLIVLDRREATIGTLRGKQVEAIKHLTSSVPGKQRKGGQSSHRFQQLRLIAIHEFYKRIGDSATEAFLSIDRKDLE 216
                                       89*************************************************************************** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHH CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevl 131
                                       gi+++gp+++keef+d+ +l++el+++++  +dv y++esgl e++e+a+e+l
  gi|386002271|ref|YP_005920570.1| 217 GILIGGPSPTKEEFVDGAFLHHELQQRILEALDVTYTDESGLYELVEAAQERL 269
                                       ************************************************99988 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.3   6.8e+03      59      95 ..      48      86 ..      27      92 .. 0.59
   2 !  107.3   0.0   1.9e-34   5.7e-31       2     112 ..     275     409 ..     274     410 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                                      -HHH-HHHHHH..HHHHHHHHHHHTT-EEEEE-TTSHHH CS
                            eRF1_3 59 ketgeelelve..lieelvenveesgakveiisseseeG 95
                                      +e+g+  ++ +  +  ++ +  e++ a++ +i++  ++G
  gi|386002271|ref|YP_005920570.1| 48 DEHGQASNIKSklTRTNVQSALESVMARLRLIPKAPPNG 86
                                      344544444335333444455577777777777766655 PP

  == domain 2  score: 107.3 bits;  conditional E-value: 1.9e-34
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS................... CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv................... 58 
                                        qek ++ +f++el  d+g+a YG++ev++ l mgAv+tLL+se+l+++r   ++ ++                   
  gi|386002271|ref|YP_005920570.1| 275 TQEKLVMRRFMKELVSDKGLASYGEKEVRENLTMGAVDTLLLSEDLRKTRARiVCTNAscdfsedatrssnspppgt 351
                                       699**********************************************98855555599***************** PP

                                       .-HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 .ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                         ++g++l l +   +i +l +++eesg +v+iis+++eeG+ql++afgGiaaiLR++
  gi|386002271|ref|YP_005920570.1| 352 cLRCGSQLALADevdIISDLSRMAEESGSSVKIISTDFEEGAQLLRAFGGIAAILRFR 409
                                       *88998887777777******************************************8 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   2.5e-16   7.5e-13       3     126 ..     127     254 ..     126     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.5e-16
                    baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAel 79 
                                       l+pL + l + + +g++++dr++a + + ++ ++e  +++++ vpg++++gg+ s +rfq+ +   +++++k++++ 
  gi|386002271|ref|YP_005920570.1| 127 LTPLEDMLADKKTFGLIVLDRREATIGTLRGKQVEAIKHLTSSVPGKQRKGGQ-SSHRFQQLRLIAIHEFYKRIGDS 202
                                       79***************************************************.*********************** PP

                    baeRF_family10  80 lakll...eergverlvlgGdeeetaalld..rlpkalrarvvgtlplpvda 126
                                       +++++   +++++e +++gG+   +++++d   l+ +l++r+ + l++  ++
  gi|386002271|ref|YP_005920570.1| 203 ATEAFlsiDRKDLEGILIGGPSPTKEEFVDgaFLHHELQQRILEALDVTYTD 254
                                       **9983334666*********99999999744799********999888744 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   4.2e-15   1.2e-11       4     126 ..     142     267 ..     139     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4.2e-15
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarll....aeesae 76 
                                       +++l+rr + ++g+++g++++a k+ t+ v g+ ++GG+S  Rf++ r   + + ++++ + a + +    +    +
  gi|386002271|ref|YP_005920570.1| 142 LIVLDRREA-TIGTLRGKQVEAIKHLTSSVPGKQRKGGQSSHRFQQLRLIAIHEFYKRIGDSATEAFlsidR----K 213
                                       5899*****.******************************************************99954322....2 PP

                           acVLRF1  77 ....vvlgGdrslvaevledarlaplatlare..elldvpdprravLedavrrara 126
                                           +++gG+  + +e+ + a l++  +l+++  e+ldv   +++ L + v+ a++
  gi|386002271|ref|YP_005920570.1| 214 dlegILIGGPSPTKEEFVDGAFLHH--ELQQRilEALDVTYTDESGLYELVEAAQE 267
                                       3567****************77554..33333346888888888888888887765 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   7.2e-15   2.1e-11       2     128 ..      13     133 ..      12     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 7.2e-15
                                       EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdk 76 
                                       +ll+   + +++g+++++L++++d+++++++  +++++++++++++k +r         ++v+++L++ + ++++ +
  gi|386002271|ref|YP_005920570.1|  13 RLLEDlrSKSGRGTELISLYIPPDKQISDVTAQLRDEHGQASNIKSKLTR---------TNVQSALESVMARLRLIP 80 
                                       66666657789*************************************99.........9***************** PP

                                       T...SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  77 d...agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                       +   +gv  + G v  + +   ++ + +  le+++p+ +++++ ++sf l +L+++
  gi|386002271|ref|YP_005920570.1|  81 KappNGVAIFVGAVDIGGN---KTDMYSRVLEPPEPIVTYRYHcDSSFLLTPLEDM 133
                                       *9999***********999...8******************999*********997 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     4e-05      0.12      42     130 ..     165     256 ..     142     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-05
                    baeRF_family12  42 egssdrpGrsssggagrsameetdfke..q.eeerFakeladeLkk...rakegkferlvlvappetlgelrkh..l 110
                                        ++s  pG+++ gg++     ++ f++  + + ++F+k++ d   +    + +++ e + + +p +t +e+ +   l
  gi|386002271|ref|YP_005920570.1| 165 HLTSSVPGKQRKGGQS-----SHRFQQlrLiAIHEFYKRIGDSATEaflSIDRKDLEGILIGGPSPTKEEFVDGafL 236
                                       5677778887777777.....44444433568999*****998888333567899****************98555* PP

                    baeRF_family12 111 hkevkkrlvgeiaknltkhp 130
                                       h e+++r+ + ++ ++t+++
  gi|386002271|ref|YP_005920570.1| 237 HHELQQRILEALDVTYTDES 256
                                       *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2755.17
//
Query:       gi|386002272|ref|YP_005920571.1|  [L=244]
Description: Purine nucleoside phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-40  139.4   0.8    1.1e-40  139.3   0.8    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.3   0.8   6.4e-45   1.1e-40      13     233 ..      10     224 ..       1     225 [. 0.92

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 6.4e-45
                                       HHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--...SSHHHHHHHHHHHHHHHC--SEEEEEEEEEESSTTT CS
                         PNP_UDP_1  13 ellaespleetpfgregrgfkfvtGtlkgkpvvivstG...iGkpnaavvaeirllkefgvkaiiriGtaGglnpdl 86 
                                           +    +tp+gr       +t   ++++ +i ++G   + ++ ++++a +++  + g+ ++++++t+G++ +  
  gi|386002272|ref|YP_005920571.1|  10 GGEPSL--IDTPYGRL---MAAATELCGREVLFIPRHGeahLPPHRVNYRALLWAARASGAVRVVSTNTVGSM-AWH 80 
                                       555555..66677666...6677777799999********99999999*************************.778 PP

                                       -TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHHHH CS
                         PNP_UDP_1  87 kvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteaelr 163
                                       +vG +vip+d+++f+  +p+++++ee + ++d +++ ++pe r++l + aea g+ v  G++++++g++ e++a++r
  gi|386002272|ref|YP_005920571.1|  81 PVGSLVIPTDFVDFTKSRPSTFFEEE-AVHVDLTAP-YCPEVRRALAAGAEAAGALVSDGIYVCTEGPHLESPAQIR 155
                                       9***********************99.*********.**************************************** PP

                                       HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHH CS
                         PNP_UDP_1 164 llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalllall 233
                                       +lr++g d+v+M+++++++lArel++++a+i++v+++aag   ++ + +e+   ++++a+ + ++++a++
  gi|386002272|ref|YP_005920571.1| 156 MLRQFG-DVVGMTGYPEVVLARELELCYASICIVTNPAAGMRKDSMSAAEIRTEMAISARLLREVIEAAI 224
                                       ******.***********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1562.14
//
Query:       gi|386002273|ref|YP_005920572.1|  [L=257]
Description: hypothetical protein Mhar_1589 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-22   78.4   0.0    7.2e-22   77.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    7.7e-20   71.4   0.0    1.1e-19   70.9   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    2.8e-17   62.9   0.0    3.5e-17   62.6   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.1e-12   48.5   0.0    1.7e-12   47.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.2e-11   44.8   0.0    1.6e-11   44.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.4e-08   33.7   0.0    3.3e-08   33.3   0.0    1.1  1  MTS              Methyltransferase small domain
    2.3e-07   30.4   0.0      3e-07   30.0   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      1e-05   25.2   0.0    1.4e-05   24.8   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    3.7e-05   23.4   0.0    5.1e-05   23.0   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    6.7e-05   22.9   0.0    9.9e-05   22.4   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00045   19.7   0.0     0.0006   19.3   0.0    1.2  1  TehB             Tellurite resistance protein TehB
     0.0011   18.3   0.0     0.0016   17.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0037   16.3   0.0     0.0046   15.9   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0081   15.3   0.0      0.011   14.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.023   13.8   0.0      0.031   13.4   0.0    1.2  1  DREV             DREV methyltransferase
      0.048   13.5   0.0      0.077   12.8   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
      0.074   12.7   0.0       0.12   12.0   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.16   11.3   0.0       0.21   11.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.27   10.4   0.0        3.3    6.8   0.0    2.0  2  N2227            N2227-like protein


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   7.6e-25   7.2e-22       1      94 [.      51     145 ..      51     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 7.6e-25
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS.S-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklp.fednsfDlvvssevlhhved 76 
                                       Ld+GcG G+l+++la+ ga v++v+ s +ml+ a ++ + e+l+++++++d+ +lp ++d sfD+vv ++v++  +d
  gi|386002273|ref|YP_005920572.1|  51 LDAGCGDGYLSRKLAELGAAVTAVEASSQMLAFALAEEEAEPLSIRYHEGDIAHLPfLADRSFDAVVTNNVIQDAAD 127
                                       8******************************9999999999999***********96799***************** PP

                                       HHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  77 pekalkeiaRvLkpgGll 94 
                                        e  ++e+ R+L+pgG+ 
  gi|386002273|ref|YP_005920572.1| 128 FEGSFRELSRLLRPGGIY 145
                                       ****************86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.2e-22   1.1e-19       1      97 []      50     143 ..      50     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.2e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS.STTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpf.edgsfDlvvssgalhh 76 
                                       +Ld+GcG G l+++la+ +  a vt+v+ s++ml+ a ++ e+e l++++++gd+ +lpf +d+sfD+vv +++++ 
  gi|386002273|ref|YP_005920572.1|  50 ILDAGCGDGYLSRKLAELG--AAVTAVEASSQMLAFALAEEEAEPLSIRYHEGDIAHLPFlADRSFDAVVTNNVIQ- 123
                                       8***************995..*****************99999999*************87999*******87766. PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                        + +d e  ++e++r+L+pgG
  gi|386002273|ref|YP_005920572.1| 124 -DAADFEGSFRELSRLLRPGG 143
                                       .56799**************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   3.7e-20   3.5e-17       4     108 ..      47     146 ..      44     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 3.7e-20
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g+r+lD+GCG G+l+ +la elg  a v+ ++ s +++ +A ++ +   l+ ++ ++gdi +l+  l+d++fD +++
  gi|386002273|ref|YP_005920572.1|  47 GKRILDAGCGDGYLSRKLA-ELG--AAVTAVEASSQMLAFALAEEEAEPLS-IRYHEGDIAHLPF-LADRSFDAVVT 118
                                       789****************.665..89****************98888886.************7.799******** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggill 108
                                       n+v+++ ad +  ++e++r+l+pggi+l
  gi|386002273|ref|YP_005920572.1| 119 NNVIQDAADFEGSFRELSRLLRPGGIYL 146
                                       *************************986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.8e-15   1.7e-12       1      98 [.      51     144 ..      51     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.8e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+ GcG+G l+r l+e   ++ +t+v+ s+++++ a ++  ++  ++    e +  +l  l+++ sfD+vv +nv++
  gi|386002273|ref|YP_005920572.1|  51 LDAGCGDGYLSRKLAEL--GAAVTAVEASSQMLAFALAEEEAEP-LSIRYHEGDIAHLPFLADR-SFDAVVTNNVIQ 123
                                       89***************..**************66666655555.5666666666666666665.************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                         +d + +++++ +lL+pgG+
  gi|386002273|ref|YP_005920572.1| 124 DAADFEGSFRELSRLLRPGGI 144
                                       ********************7 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   1.7e-14   1.6e-11      10     119 ..      35     148 ..      11     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.7e-14
                   Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae........ 78 
                                       +  ++++l+ +  g+r+Ld GcG+G+l++ l+e g+ vt+v++s+++ + a          + e+ea++        
  gi|386002273|ref|YP_005920572.1|  35 DPIILEALG-DVGGKRILDAGCGDGYLSRKLAELGAAVTAVEASSQMLAFA---------LA-EEEAEPlsiryheg 100
                                       333444443.55567*****************************9988854.........33.33333445555555 PP

                   Methyltransf_23  79 ........pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllse 119
                                                +++fd +v ++v+    d++  +r + +ll+pgG  l+  
  gi|386002273|ref|YP_005920572.1| 101 diahlpflADRSFDAVVTNNVIQDAADFEGSFRELSRLLRPGGIYLH-I 148
                                       55555556667*******************************96544.3 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   3.5e-11   3.3e-08      22     140 ..      37     150 ..      29     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.5e-11
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTT..STTS CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvlee..veek 96 
                                       ++le+l +   +++lD GcG G+l+ +la+      vt+v+++ + l++a +  ea+ l++++++ d+ +   ++++
  gi|386002273|ref|YP_005920572.1|  37 IILEALGDVGGKRILDAGCGDGYLSRKLAELGAA--VTAVEASSQMLAFALAEEEAEPLSIRYHEGDIAHLpfLADR 111
                                       6788888888899*****************9877..9******************************987522569* PP

                                       -EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEE CS
                               MTS  97 kfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVan 140
                                       +fd++v+N  +++  +      e  ++e  + L++gG  l ++n
  gi|386002273|ref|YP_005920572.1| 112 SFDAVVTNNVIQDAAD-----FEGSFRELSRLLRPGGIYLHIVN 150
                                       ********98888777.....66667777777777777666665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   3.2e-10     3e-07      41     150 ..      40     146 ..      31     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.2e-10
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TT.S-T- CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpf.edds 116
                                       +  ++  g+++lD  +G g l+ kl++       v+ ++ +++mL  + +  + e   +i++  ++  +Lpf  d s
  gi|386002273|ref|YP_005920572.1|  40 EALGDVGGKRILDAGCGDGYLSRKLAELG---AAVTAVEASSQMLAFALAEEEAE-PLSIRYHEGDIAHLPFlADRS 112
                                       566778899***********999998764...46899999*****9987654333.459************94469* PP

                                       EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 117 fDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                       fD v     +++ +D + +++e+ r l+pGG+ +
  gi|386002273|ref|YP_005920572.1| 113 FDAVVTNNVIQDAADFEGSFRELSRLLRPGGIYL 146
                                       *******************************864 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.5e-08   1.4e-05      14     101 ..      47     138 ..      36     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak......Glsviqgdldkdlenfedksfdyvvlsqt 84 
                                       g r+ld GcGdG l + l+e  +     +e +++ +a ++a        +  ++gd+   l + +d+sfd vv +  
  gi|386002273|ref|YP_005920572.1|  47 GKRILDAGCGDGYLSRKLAE-LGAAVTAVEASSQMLAFALAEeeaeplSIRYHEGDIA-HLPFLADRSFDAVVTNNV 121
                                       679***************77.9999999****99988777652222223555777774.799*************** PP

                              MetW  85 lqatrnpkevldellri 101
                                       +q   + +  ++el r+
  gi|386002273|ref|YP_005920572.1| 122 IQDAADFEGSFRELSRL 138
                                       **988877666666554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.4e-08   5.1e-05      39     141 ..      42     144 ..       6     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.4e-08
                              NodS  39 laqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervk.esshiswivsdvqq..fstdekfdlivv 112
                                       l++     +l+ Gc  G l+ +la +   +t v+  ++ +a a    + e   i +++ d+ +  f +d+ fd +v 
  gi|386002273|ref|YP_005920572.1|  42 LGDVGGKRILDAGCGDGYLSRKLAELGAAVTAVEASSQMLAFALAEEEaEPLSIRYHEGDIAHlpFLADRSFDAVVT 118
                                       4454556789**************************99887765444304468********983356899******* PP

                              NodS 113 aevlyyiedvaelraavrnlvsllapdgq 141
                                        +v   i+d a++ ++ r+l +ll+p+g 
  gi|386002273|ref|YP_005920572.1| 119 NNV---IQDAADFEGSFRELSRLLRPGGI 144
                                       999...79******************986 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-07   9.9e-05      17      66 ..      38      83 ..      31     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                   Methyltransf_32 17 lkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvek 66
                                      + e+  + g ++++D+G+G gYLs+ la     ++  v++++a++++ + 
  gi|386002273|ref|YP_005920572.1| 38 ILEALGDVGGKRILDAGCGDGYLSRKLAE----LGAAVTAVEASSQMLAF 83
                                      555556678899****************9....69********9998765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.3e-07    0.0006      23     105 ..      39     122 ..      33     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.3e-07
                                       HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---..-S-EE CS
                              TehB  23 veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakl..deryd 97 
                                       +ea   v   ++ld gcg+g  s  l+ lg  vta++  ++ +af    +e e l+ i+    di ++ +  d+ +d
  gi|386002273|ref|YP_005920572.1|  39 LEALGDVGGKRILDAGCGDGYLSRKLAELGAAVTAVEASSQMLAFALAEEEAEPLS-IRYHEGDIAHLPFlaDRSFD 114
                                       566666777899**********************************999******9.99999999998764478888 PP

                                       EEEEESSG CS
                              TehB  98 filstvvl 105
                                        +++  v+
  gi|386002273|ref|YP_005920572.1| 115 AVVTNNVI 122
                                       88877665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0016      54     163 ..      38     146 ..      33     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SS.S-EEEEES-GGG---.-- CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldle.rkvevklldyedlde.kv 128
                                       ile l+   G+++Ld GcG G+l r+ +e  ++ v ++  S++  + a ++ +++ l+ r +e ++++   l++  +
  gi|386002273|ref|YP_005920572.1|  38 ILEALGDVGGKRILDAGCGDGYLSRKLAEL-GAAVTAVEASSQMLAFALAEEEAEPLSiRYHEGDIAHLPFLADrSF 113
                                       566777778****************99988.***********9998876666665554266778888888888879* PP

                                       SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEE CS
                              CMAS 129 drvvsvgafehvgkenydtffkklkkllkedGlll 163
                                       d+vv+ ++++    + ++  f++l++ll+++G+ l
  gi|386002273|ref|YP_005920572.1| 114 DAVVTNNVIQD--AADFEGSFRELSRLLRPGGIYL 146
                                       *****999986..6789999**********99865 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.9e-06    0.0046     108     191 ..      39     121 ..      30     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                                       GGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T-..-- CS
                    Methyltransf_9 108 lphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpel..ea 182
                                       l+ l d+ g++ild Gcg+Gy   r ++e  + v  ++ s++ l    a ++      r h+    i +lp l   +
  gi|386002273|ref|YP_005920572.1|  39 LEALGDVGGKRILDAGCGDGYL-SRKLAELGAAVTAVEASSQMLAFALAEEEAEPLSIRYHEG--DIAHLPFLadRS 112
                                       66789999************96.5777787788899999999887655555555555555554..566666541146 PP

                                       EEEEEEES- CS
                    Methyltransf_9 183 fdtvfsmGv 191
                                       fd+v +  v
  gi|386002273|ref|YP_005920572.1| 113 FDAVVTNNV 121
                                       777766655 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.011      32      80 ..      48      95 ..      22     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      SEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEE CS
                            RrnaAD 32 ltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkv 80
                                      + +l+ g G G l+++La+    v+++E  ++++++  ++ +++e+l +
  gi|386002273|ref|YP_005920572.1| 48 KRILDAGCGDGYLSRKLAELGAAVTAVEASSQMLAFALAE-EEAEPLSI 95
                                      579****************************999886662.34666665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05     0.031      94     129 ..      46      81 ..      37     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmr 129
                                         k++ld G GdG +++++a+    v a e+s++m 
  gi|386002273|ref|YP_005920572.1|  46 GGKRILDAGCGDGYLSRKLAELGAAVTAVEASSQML 81 
                                       5689******************************96 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.2e-05     0.077      74     154 ..      48     145 ..      29     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-05
                                       S-EEEES-TT-....HHH......HH--S-..EEEEESS-SST.....TEEES-TTS-S.--TT-EEEEEEES---. CS
                    Methyltransf_8  74 lvvadlGcGea....kia......eavrekekvrsfdlvavne.....rvvacdlakvP.ledesvdvavfclslm. 133
                                       + + d GcG+     k+a      +av+ + ++ +f l+  +      r    d+a++P l+d s d +v    +  
  gi|386002273|ref|YP_005920572.1|  48 KRILDAGCGDGylsrKLAelgaavTAVEASSQMLAFALAEEEAeplsiRYHEGDIAHLPfLADRSFDAVVTNNVIQd 124
                                       56889999996222245566555556778889999999865541121156778******679*****9998766542 PP

                                       SS-HHHHHHHHHHHEEEEEEE CS
                    Methyltransf_8 134 gtnladflkeanrvlkvGGll 154
                                       + +++   +e  r+l++GG++
  gi|386002273|ref|YP_005920572.1| 125 AADFEGSFRELSRLLRPGGIY 145
                                       6799999************86 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.12      30      84 ..      39      93 ..       4     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      HHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGG CS
                              TPMT 30 ldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepk 84
                                      l+al    g+r+l  +CG ++    lAe g  v +ve s + ++ + +e++ ep 
  gi|386002273|ref|YP_005920572.1| 39 LEALGDVGGKRILDAGCGDGYLSRKLAELGAAVTAVEASSQMLAFALAEEEAEPL 93
                                      445666778999*****************************99999999988885 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.21     161     233 ..      46     119 ..      37     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDev..AvkvakeNaelNkvea.klevalseellkeekadvivaN 233
                                       +g+++lD G+G G L+   a Lga+ v+av   ++  A   a+e ae  +++  + ++ ++   l+++++d +v N
  gi|386002273|ref|YP_005920572.1|  46 GGKRILDAGCGDGYLSRKLAELGAA-VTAVEASSQmlAFALAEEEAEPLSIRYhEGDI-AHLPFLADRSFDAVVTN 119
                                       6789*******************96.66776665511555556655555554422222.33333346788888877 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0035       3.3      59      92 ..      48      81 ..      21      91 .. 0.88
   2 ?    1.5   0.0      0.14   1.4e+02     163     200 ..     109     146 ..      85     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0035
                                      -EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                             N2227 59 vkilvPGaGlGrlavelatkgyqvegnEfsyfml 92
                                       +il  G+G G l+ +la++g +v ++E s  ml
  gi|386002273|ref|YP_005920572.1| 48 KRILDAGCGDGYLSRKLAELGAAVTAVEASSQML 81
                                      579999************************9998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                       HTT-EEEEEEES-TTSSS-HHHHHHHHHHHEEEEEEEE CS
                             N2227 163 aaesydvvvtcfFiDtaeNvleYletiekvlkpgglwi 200
                                       a+ s+d+vvt+  i  a      ++ ++++l+pgg++ 
  gi|386002273|ref|YP_005920572.1| 109 ADRSFDAVVTNNVIQDAADFEGSFRELSRLLRPGGIYL 146
                                       4789**********999999999999*******99654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1720.16
//
Query:       gi|386002274|ref|YP_005920573.1|  [L=122]
Description: hypothetical protein Mhar_1590 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00036   20.3   0.5     0.0031   17.3   0.1    2.2  2  PKD       PKD domain
    0.00076   20.2   0.3     0.0048   17.6   0.3    2.2  1  Big_7     Bacterial Ig domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.028   14.5   0.0    1.3  1  BiPBP_C   Penicillin-Binding Protein C-terminus Family
      0.055   13.8   0.0      0.081   13.3   0.0    1.3  1  HYR       HYR domain
      0.077   13.2   3.4       0.16   12.2   1.4    2.5  2  He_PIG    Putative Ig domain
       0.14   12.4   0.0       0.18   12.0   0.0    1.2  1  DUF4625   Domain of unknown function (DUF4625)
       0.16   12.5   0.0       0.26   11.7   0.0    1.3  1  Cadherin  Cadherin domain
        1.1    9.0   0.1        1.1    9.0   0.1    2.6  3  SprB      SprB repeat


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.061   1.4e+02      33      55 ..      25      48 ..      23      50 .. 0.88
   2 !   17.3   0.1   1.4e-06    0.0031       4      67 ..      46     110 ..      44     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.061
                                      -SS.--EEEEETTEEEEEE-SSEE CS
                               PKD 33 gdg.svvqvlseptvthtYlspGe 55
                                      gdg s+ ++ s+ tv +t +++G+
  gi|386002274|ref|YP_005920573.1| 25 GDGaSPEGSASGLTVAITSPATGS 48
                                      89999999********99999997 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.4e-06
                                       --S--BSSEEEEEEEES..-SS-SEEEEE--SS--EEEEETTEEEEEE-S..SEEEEEEEEEE-SS- CS
                               PKD   4 sptvlvpgatvaftaav.pdganvtysWdfgdgsvvqvlseptvthtYls..pGeYeVtvtasnavg 67 
                                       +++ l+  ++++f++      ++++y+W       ++ ++ +++   +++  +G Y+Vt+ta++ +g
  gi|386002274|ref|YP_005920573.1|  46 TGSLLSGDEPIRFEGEAtGGRKPYAYRWSSSL--DGTLSTKSSFEAPPSEmsRGRYVVTLTATDGAG 110
                                       56778888999999999778899*****9998..466677788888888778************998 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.1e-06    0.0048       2      70 .]      38     119 ..      38     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.1e-06
                                       EEEEEE--TT--EB.TSEEEEEEEEE-SS-E..EEEEEEETTEE.........EEEE-SSSEEEEEE--.....SEE CS
                             Big_7   2 tvtitsPangatvs.ggtvtisasAsddggv..skVefyvdgtl.g.......lgtdtsapysltwttta..ltagt 65 
                                       tv+itsPa g+ +s  +++ ++++A+        +   ++dgtl +        ++++ + y +t+t+t+  ++ g+
  gi|386002274|ref|YP_005920573.1|  38 TVAITSPATGSLLSgDEPIRFEGEATGGRKPyaYRWSSSLDGTLsTkssfeapPSEMSRGRYVVTLTATDgaGARGE 114
                                       8*************999**********96662244455799999668888877667777999999999998899999 PP

                                       EEEEE CS
                             Big_7  66 htltV 70 
                                        ++tV
  gi|386002274|ref|YP_005920573.1| 115 ASITV 119
                                       99998 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.028       5      85 ..      32     111 ..      28     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                           BiPBP_C   5 assaasplrIafPadGailaldpdipkrqrlqlkarggea..plrWll..dgeplaetkrgrelawqpepGrhrLtv 77 
                                       +s+++ ++ I++Pa G+ l  d+ i    r+  +a gg++   +rW    dg++  + +++++   + ++Gr+ +t+
  gi|386002274|ref|YP_005920573.1|  32 GSASGLTVAITSPATGSLLSGDEPI----RFEGEATGGRKpyAYRWSSslDGTLS-TKSSFEAPPSEMSRGRYVVTL 103
                                       66778899*************9855....99999999955487778534499998.445555555555*****9999 PP

                           BiPBP_C  78 vDaaGrvd 85 
                                       +  +G+ +
  gi|386002274|ref|YP_005920573.1| 104 TATDGAGA 111
                                       77766654 PP

>> HYR  HYR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.081      40      81 .]      80     121 ..      68     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                               HYR  40 qaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81 
                                       + +  s++ +p ++++ G  +Vt +a+D +g +++ + tVtv
  gi|386002274|ref|YP_005920573.1|  80 TLSTKSSFEAPPSEMSRGRYVVTLTATDGAGARGEASITVTV 121
                                       556678899999****************************98 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   7.3e-05      0.16      22      49 .]      78     110 ..      35     110 .. 0.76
   2 ?   -1.9   0.0       1.7   3.9e+03      36      44 ..     113     121 ..     111     121 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                            He_PIG  22 tGtitGt.....pdqtvapGsytftVtatdgsg 49 
                                       +Gt++       p +    G+y +t+tatdg+g
  gi|386002274|ref|YP_005920573.1|  78 DGTLSTKssfeaPPSEMSRGRYVVTLTATDGAG 110
                                       5666666666664444455***********986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                            He_PIG  36 GsytftVta 44 
                                       G+ ++tVt+
  gi|386002274|ref|YP_005920573.1| 113 GEASITVTV 121
                                       566677775 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     8e-05      0.18      73     131 ..      65     121 ..      51     122 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8e-05
                           DUF4625  73 gekewsfeksydlsgskkeyelheeieiPadaeaGdYhlvirvtDasGneteesreiki 131
                                       g k++++  s +l g+ ++++  e  ++P+++ +G Y +++++tD +G   e s+++++
  gi|386002274|ref|YP_005920573.1|  65 GRKPYAYRWSSSLDGTLSTKSSFE--APPSEMSRGRYVVTLTATDGAGARGEASITVTV 121
                                       567777777776666654443333..589*******************99998887765 PP

>> Cadherin  Cadherin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.26      51      93 .]      79     122 .]      75     122 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       TEEEESSTC-TTTS....SEEEEEEEEEECTGCCEEEEEEEEEEEEE CS
                          Cadherin  51 gdlsttkpLdrEsq....geYeLtveatDesgspplsstttvtvtVl 93 
                                       g+lst+++ + + +    g+Y++t+ atD +   + ++++++tvtVl
  gi|386002274|ref|YP_005920573.1|  79 GTLSTKSSFEAPPSemsrGRYVVTLTATDGA---GARGEASITVTVL 122
                                       777777777777767777************6...8889999999885 PP

>> SprB  SprB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00051       1.1      21      34 ..      62      75 ..      61      77 .. 0.91
   2 ?   -2.5   0.2       2.1   4.7e+03      17      24 ..     101     108 ..     101     111 .. 0.71
   3 ?    0.7   0.2      0.21   4.7e+02      15      21 ..     115     121 ..     113     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                              SprB 21 vsGGtapYtYswng 34
                                      ++GG  pY Y w++
  gi|386002274|ref|YP_005920573.1| 62 ATGGRKPYAYRWSS 75
                                      8***********97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                              SprB  17 ItvtvsGG 24 
                                       +t+t++ G
  gi|386002274|ref|YP_005920573.1| 101 VTLTATDG 108
                                       68888755 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.21
                              SprB  15 GsItvtv 21 
                                        sItvtv
  gi|386002274|ref|YP_005920573.1| 115 ASITVTV 121
                                       5899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 759.56
//
Query:       gi|386002275|ref|YP_005920574.1|  [L=254]
Description: CO dehydrogenase maturation factor [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-14   52.6   0.0    6.9e-14   52.0   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.3e-09   37.9   0.1      8e-06   25.5   0.0    2.3  2  ParA         NUBPL iron-transfer P-loop NTPase
    2.7e-07   30.7   0.0    4.3e-07   30.0   0.0    1.4  1  AAA_31       AAA domain
    1.8e-06   27.6   0.1    1.7e-05   24.4   0.1    2.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    8.3e-05   22.8   0.1    0.00049   20.3   0.1    2.0  2  DUF87        Helicase HerA, central domain
    8.5e-05   22.1   0.1      0.053   13.0   0.1    2.1  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    0.00014   22.1   0.0    0.00031   20.9   0.0    1.6  1  AAA_33       AAA domain
     0.0012   19.2   0.0      0.002   18.5   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0016   18.2   0.6     0.0087   15.8   0.6    2.0  1  AAA_30       AAA domain
     0.0017   18.9   0.0      0.002   18.6   0.0    1.5  1  ABC_tran     ABC transporter
     0.0029   16.8   0.0      0.036   13.2   0.0    2.2  2  ArsA_ATPase  Anion-transporting ATPase
     0.0044   16.8   0.0      0.069   12.9   0.0    2.1  2  AAA_24       AAA domain
      0.008   16.0   0.0      0.014   15.2   0.0    1.5  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
  ------ inclusion threshold ------
      0.014   15.7   0.0       0.15   12.4   0.0    2.1  2  AAA_22       AAA domain
      0.033   13.4   0.2      0.068   12.3   0.2    1.5  1  NB-ARC       NB-ARC domain
      0.044   14.2   0.0        0.1   13.0   0.0    1.6  1  AAA          ATPase family associated with various cellular a
      0.061   13.2   0.2       0.15   12.0   0.1    1.8  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.066   11.9   0.4      0.098   11.3   0.4    1.1  1  PEPCK_ATP    Phosphoenolpyruvate carboxykinase
      0.069   12.1   0.1       0.11   11.5   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.11   12.3   0.3        0.4   10.5   0.0    2.0  2  AAA_26       AAA domain
       0.16   11.6   1.0        4.9    6.7   0.3    2.7  2  SRP54        SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   8.1e-17   6.9e-14       6     127 ..       8     230 ..       6     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 8.1e-17
                                       SSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCH.........HTTEB-HHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx.................. RF
                              CbiA   6 tkGGvGKTtlaanLaralar.rglrVllvDaDpqannlai.........leglendiep.................. 54 
                                       +kGG+GKTtl+a ++r l r r+  Vl+vDaD    ++++          +                          
  gi|386002275|ref|YP_005920574.1|   8 GKGGTGKTTLTALILRELVRrREGTVLAVDADANECLASVlgadgtptlSD-------Mlqkykrqreespeltgid 77 
                                       7*****************997799**********99999766555555533.......15555555899******** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386002275|ref|YP_005920574.1|  78 ifqnlfdsllmegeqdgyemlimgrgegsgcfcavndllqavfektveggtysyllmdceagvehiarktsgkinda 154
                                       ***************************************************************************** PP

                                       ............CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ............dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeava 119
                                                   +lkr+  +++++g +    ++   vv+n+ ++e + ++ kea e l    g + lg ip+d +++
  gi|386002275|ref|YP_005920574.1| 155 iivtdaskvsldTLKRIRDVASEVGAT----IERYYVVANKTRPE-MLEKVKEAAESL----GFKYLGAIPEDPNFT 222
                                       ***************************....99*********998.677788888887....*************** PP

                                       CCCHHTS- CS
                                       xxxxxxxx RF
                              CbiA 120 eapargep 127
                                       e + +g++
  gi|386002275|ref|YP_005920574.1| 223 EVAYQGKT 230
                                       99988876 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00047       0.4      11      42 ..       8      40 ..       2      78 .. 0.81
   2 !   25.5   0.0   9.4e-09     8e-06     103     245 ..     120     251 ..     108     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00047
                              ParA 11 gKGGVGKStvavnlAlaLa.kkglkvgllDaDi 42
                                      gKGG GK+t+++ +  +L  +++ +v  +DaD 
  gi|386002275|ref|YP_005920574.1|  8 GKGGTGKTTLTALILRELVrRREGTVLAVDADA 40
                                      9**********9999988636677788889995 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 9.4e-09
                              ParA 103 llkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvc 179
                                       + k+ve g+  yL++D+  G   e+++   + ++++a+iVt   +v+l+  k+  +++++v ++    +e   ++v+
  gi|386002275|ref|YP_005920574.1| 120 FEKTVEGGTYSYLLMDCEAGV--EHIARKTSGKINDAIIVTDASKVSLDTLKRIRDVASEVGAT----IER--YYVV 188
                                       345567788999****97666..777777778889***************99988888777765....454..4444 PP

                              ParA 180 pkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                        + +++ e++  ++++++ae+lg+++lg+ip dp+++e + +gk+++   ++s+a +a ++i++++
  gi|386002275|ref|YP_005920574.1| 189 AN-KTRPEML--EKVKEAAESLGFKYLGAIPEDPNFTEVAYQGKTVFDLPDDSPAVEAARKITDQI 251
                                       33.4455555..6789*****************************9999999**********9998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   5.1e-10   4.3e-07      10     169 ..       9     180 ..       1     188 [. 0.79

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.1e-10
                            AAA_31  10 KGGvGKTTtsvnlaaala.klgkkvLlvDlDpQanattglgiekne.iektlyevlieeknikeaiiktkvenl.dl 83 
                                       KGG GKTT +  +   l  +++  vL vD+D+ + +++ lg + +  ++ +l +   ++++  e+   + ++nl d 
  gi|386002275|ref|YP_005920574.1|   9 KGGTGKTTLTALILRELVrRREGTVLAVDADANECLASVLGADGTPtLSDMLQKYKRQREESPELTGIDIFQNLfDS 85 
                                       9*******776666655549999******************874441555555555566666666666679999988 PP

                            AAA_31  84 ipssidLaeaeielvelekk.......eeilkellekvkde..YDyiiiDcpPsLglltenaLvasdsviipvqaea 151
                                       +  + +  ++e+ +++  +        ++ l+ ++ek  +   Y y ++Dc   ++ ++++     +  ii+++a++
  gi|386002275|ref|YP_005920574.1|  86 LLMEGEQDGYEMLIMGRGEGsgcfcavNDLLQAVFEKTVEGgtYSYLLMDCEAGVEHIARKTSGKINDAIIVTDASK 162
                                       8888899999999999988877777766668888877655345********************************** PP

                            AAA_31 152 yaleGleqllktieevkk 169
                                        +l++l+++ +  +ev  
  gi|386002275|ref|YP_005920574.1| 163 VSLDTLKRIRDVASEVGA 180
                                       *****9999887777655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1     2e-08   1.7e-05       3     245 ..       4     252 ..       2     254 .] 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2e-08
                         Fer4_NifH   3 iaiyGkGGiGksttsqnlsaalaemg.kkvlivGCDPkaDstrlllggkaqetvldtlrekgav..e..dvkvedvv 74 
                                       + ++GkGG Gk+t ++ ++  l+++    vl v  D  +  +  +lg+  ++t+ d+l++ + +  e  +++  d+ 
  gi|386002275|ref|YP_005920574.1|   4 LGFFGKGGTGKTTLTALILRELVRRReGTVLAVDADANECLA-SVLGADGTPTLSDMLQKYKRQreEspELTGIDIF 79 
                                       679**********99999999987663789999999876555.899************9876654232246667888 PP

                         Fer4_NifH  75 kkGyggvkc.vesGGPep...GvGCaGrgvitaielleelgayddlDfvlyD.vLGDvvCGGfalP.iredkaqevy 145
                                       ++ +  +    e  G e    G+G  G g   a++ l +  + + ++   y  +L D   G   +    ++k ++ +
  gi|386002275|ref|YP_005920574.1|  80 QNLFDSLLMeGEQDGYEMlimGRG-EGSGCFCAVNDLLQAVFEKTVEGGTYSyLLMDCEAGVEHIArKTSGKINDAI 155
                                       887777543157778775322555.466777777766554444456666665245666665443330345788999* PP

                         Fer4_NifH 146 ivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkk 222
                                       ivt++   +l +  +i     +     +++   ++ n +   +  e +++ ae+lg k l ++P d + ++   + k
  gi|386002275|ref|YP_005920574.1| 156 IVTDASKVSLDTLKRIRDVASEVGA--TIERYYVVAN-KTRPEMLEKVKEAAESLGFKYLGAIPEDPNFTEVAYQGK 229
                                       *******999888887666555543..3666778999.66788899******************************* PP

                         Fer4_NifH 223 tvieyapeseqakeyrelarkil 245
                                       tv++  ++s+  +  r++ ++il
  gi|386002275|ref|YP_005920574.1| 230 TVFDLPDDSPAVEAARKITDQIL 252
                                       **********9999999999886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   5.7e-07   0.00049      28      61 ..       6      39 ..       3      42 .. 0.92
   2 ?    0.0   0.0      0.88   7.5e+02     118     118 ..     113     113 ..      39     200 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.7e-07
                             DUF87 28 ilgsTGsGKSntvavLleellekkgatililDpH 61
                                       +g+ G+GK++++a++l+el++++ +t+l +D++
  gi|386002275|ref|YP_005920574.1|  6 FFGKGGTGKTTLTALILRELVRRREGTVLAVDAD 39
                                      69***************************99985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.88
                             DUF87 118 r 118
                                        
  gi|386002275|ref|YP_005920574.1| 113 N 113
                                       0 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   6.2e-05     0.053       1      45 [.       1      45 [.       1      62 [. 0.83
   2 !    7.1   0.0    0.0038       3.3     106     149 ..     117     162 ..      99     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhe.lgesvlviDlspdnlLr 45
                                      mk+l + G +GG+G+t+l+a + + l +  +  vl++D+ +++ L+
  gi|386002275|ref|YP_005920574.1|  1 MKILGFFG-KGGTGKTTLTALILRELVRrREGTVLAVDADANECLA 45
                                      77778877.8**********9888776515669*******999987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0038
                          CBP_BcsQ 106 laalkelk..eqyrwillDlpagasaltrellaladlvllvvepda 149
                                       +a +++    ++y+++l+D+ ag ++++r++  + +  + v+ +  
  gi|386002275|ref|YP_005920574.1| 117 QAVFEKTVegGTYSYLLMDCEAGVEHIARKTSGKINDAIIVTDASK 162
                                       444444334789*********************9999999998765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.6e-07   0.00031       4     107 ..       6     190 ..       3     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.6e-07
                            AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdt............................................ 32 
                                       + G  G+GK+tl   +l++l     +++l+ d+                                            
  gi|386002275|ref|YP_005920574.1|   6 FFGKGGTGKTTLTALILRELVrrreGTVLAVDAdaneclasvlgadgtptlsdmlqkykrqreespeltgidifqnl 82 
                                       78999*******98887777777779999999999***************999999999999999999999999999 PP

                            AAA_33  33 ................................lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil.. 75 
                                                                       l++++f++ ++  t+ + +l ++ + ++ +ark+  + +++i+  
  gi|386002275|ref|YP_005920574.1|  83 fdsllmegeqdgyemlimgrgegsgcfcavndLLQAVFEKTVEGGTY-SYLLMDCEAGVEHIARKTSGKINDAIIvt 158
                                       99999999999999999999999999999999999999888888875.777889*****999998886666666668 PP

                            AAA_33  76 datnlsrrerarflklarrlgvpvrivvvetd 107
                                       da  +s ++ +r++ +a++ g+ ++  +v + 
  gi|386002275|ref|YP_005920574.1| 159 DASKVSLDTLKRIRDVASEVGATIERYYVVAN 190
                                       **********************9988887664 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06     0.002      30     106 ..       7      72 ..       2     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                            AAA_16  30 sGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                        G  G+GK++l   +lr+l +++ g +l+ ++d +          ++l + ++l + ++++ s+ l+ ++++ ee+ 
  gi|386002275|ref|YP_005920574.1|   7 FGKGGTGKTTLTALILRELVRRReGTVLAVDADAN----------ECL-A-SVLGADGTPTLSDMLQKYKRQREESP 71 
                                       6999******************7799988888888..........666.5.66677777766666666666666654 PP

                            AAA_16 106 a 106
                                       +
  gi|386002275|ref|YP_005920574.1|  72 E 72 
                                       4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6     1e-05    0.0087      25     118 ..       8     181 ..       2     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                            AAA_30  25 GpAGtGKttalkal.reaweaaggrviglAptgkaAkvLaeelgi.eastiakllkrlk.................. 81 
                                       G  GtGKtt+ + + re++++++g   +lA  + a + La  lg+  + t+  +l+++k                  
  gi|386002275|ref|YP_005920574.1|   8 GKGGTGKTTLTALIlRELVRRREG--TVLAVDADANECLASVLGAdGTPTLSDMLQKYKrqreespeltgidifqnl 82 
                                       889*********999****99955..568999999999999999856789999998888888888888888888777 PP

                            AAA_30  82 ..............................................................grarlepgtllivDE 96 
                                                                                                     ++++ + ++ +iv  
  gi|386002275|ref|YP_005920574.1|  83 fdsllmegeqdgyemlimgrgegsgcfcavndllqavfektveggtysyllmdceagvehiaRKTSGKINDAIIVTD 159
                                       77777777777777777777777777777777777777777777777777777777777664222233337777777 PP

                            AAA_30  97 agmvdtkqlaallkaaekagak 118
                                       a+ v+ ++l+++ + a++ ga+
  gi|386002275|ref|YP_005920574.1| 160 ASKVSLDTLKRIRDVASEVGAT 181
                                       7777777777777777776665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-06     0.002      12      51 ..       2      42 ..       1     211 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                                      SEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkp.teGeilldgkdlke 51
                                      ++++++G+ G+GK+tL +l++++l    eG++l  ++d +e
  gi|386002275|ref|YP_005920574.1|  2 KILGFFGKGGTGKTTLTALILRELVRrREGTVLAVDADANE 42
                                      5789**************99987644499**9665666555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   4.2e-05     0.036       1      44 [.       1      45 [.       1      85 [. 0.82
   2 ?    1.6   0.0      0.15   1.2e+02     211     272 ..     156     216 ..     117     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-E.EEEE-STTTHHH CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkv.llistDPAhsls 44
                                      +k++ + GKGG GKtt+ a +  +l + ++ + l +  D    l+
  gi|386002275|ref|YP_005920574.1|  1 MKILGFFGKGGTGKTTLTALILRELVRRREGTvLAVDADANECLA 45
                                      7899999***********999999888877550446666555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                                       EEEESSHHHHHHHHHHHHHHHHTT..-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 211 lVvipEklslkEteRaikeLkkyg..ikvdavivNkllpeeeqenCeflearkkiqkkylkeie 272
                                       +V+ + k+sl+  +R     +++g  i+   v+ Nk  pe  +   ++ ea +++  kyl  i 
  gi|386002275|ref|YP_005920574.1| 156 IVTDASKVSLDTLKRIRDVASEVGatIERYYVVANKTRPEMLE---KVKEAAESLGFKYLGAIP 216
                                       5666666666666666665555551133345666666666655...345555555555555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0     8e-05     0.069       7      60 ..       6      75 ..       2     101 .. 0.74
   2 ?    1.8   0.0      0.19   1.6e+02      24      54 ..     129     173 ..     119     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-05
                            AAA_24  7 iyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........swedfldevvel........a 60
                                       +G+ g+GKTtl + +  + l+   e+ + ++dad  +++          ++ d+l++++           
  gi|386002275|ref|YP_005920574.1|  6 FFGKGGTGKTTLTALI-LRELVRRREGTVLAVDADANECLAsvlgadgtpTLSDMLQKYKRQreespeltG 75
                                      58**************.899999999988899888888777888888888999999999888444444440 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                            AAA_24  24 pkplfidtekGlksldadkfpdie..............swedfld 54 
                                       ++ l++d+e+G+ ++  +   +i+              +++ ++d
  gi|386002275|ref|YP_005920574.1| 129 YSYLLMDCEAGVEHIARKTSGKINdaiivtdaskvsldTLKRIRD 173
                                       567999********9999999888766666655554444444444 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.6e-05     0.014       1      38 [.       8      46 ..       8      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpv.yvDlDvGqseis 38
                                      G+  +GK+Tl++l+l +++r+ + +v  vD+D + +  s
  gi|386002275|ref|YP_005920574.1|  8 GKGGTGKTTLTALILRELVRRREGTVlAVDADANECLAS 46
                                      66789**************99985555*****9887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.15      10      63 ..       6      66 ..       2     101 .. 0.76
   2 ?    1.2   0.0      0.49   4.2e+02      55     117 ..     114     176 ..     103     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee......erpevvfvtlpsst.sskdllrellra 63
                                       +G  GtGKTtl + +l++l+++ + +       ++  +++v  + +t +++d+l++  r+
  gi|386002275|ref|YP_005920574.1|  6 FFGKGGTGKTTLTALILRELVRRREGTVlavdadANECLASVLGADGTpTLSDMLQKYKRQ 66
                                      68999***************98865555777775555555666666667777777766665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.49
                            AAA_22  55 dllrellralglelkaerlsseellealeqalrarav..ielliiDEaqhlrseealeeLrslln 117
                                       dll+++++++ +++ +    + ++ + +e+ +r+++     ++i+ +a ++ s + l+ +r+ + 
  gi|386002275|ref|YP_005920574.1| 114 DLLQAVFEKTVEGGTY-SYLLMDCEAGVEHIARKTSGkiNDAIIVTDASKV-SLDTLKRIRDVAS 176
                                       5666666666655555.3333333334444444444456689999999999.8888888887654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2     8e-05     0.068      22      43 ..       3      24 ..       1      35 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                                      EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                      ++++ G+gG GKttl + il++
  gi|386002275|ref|YP_005920574.1|  3 ILGFFGKGGTGKTTLTALILRE 24
                                      899**************99988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012       0.1       3      57 ..       6      67 ..       4      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                      EESSTTSSHHHHHHHHHHHH......THEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS CS
                               AAA  3 lyGppGtGKTllakavakel......gvefleisgsell.skyvgesekkirelfkeakeka 57
                                      ++G  GtGKT+l   + +el       v  +  ++ e+l s +  ++   +++++++ k+++
  gi|386002275|ref|YP_005920574.1|  6 FFGKGGTGKTTLTALILRELvrrregTVLAVDADANECLaSVLGADGTPTLSDMLQKYKRQR 67
                                      799****************9655543355788888888844444556777888888876665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00018      0.15       1      26 [.       3      28 ..       3      53 .. 0.85
   2 ?   -2.8   0.0       6.6   5.6e+03      76      98 ..      68      90 ..      34      92 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                              MobB  1 vlgivgksgsGKTtLleklipelkar 26
                                      +lg+ gk g+GKTtL   +++el +r
  gi|386002275|ref|YP_005920574.1|  3 ILGFFGKGGTGKTTLTALILRELVRR 28
                                      799******************99876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.6
                              MobB 76 eaelsleellarlse.vDlvlvEG 98
                                      e++++l  + + +++  D +l+EG
  gi|386002275|ref|YP_005920574.1| 68 EESPELTGI-DIFQNlFDSLLMEG 90
                                      223333322.22222277777776 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00012     0.098     215     237 ..       6      28 ..       3      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                       EEE-TTSSHHHHH-BTTB-EEES CS
                         PEPCK_ATP 215 fFGLSGtGKTtLsadperkligd 237
                                       fFG  GtGKTtL+a   r+l++ 
  gi|386002275|ref|YP_005920574.1|   6 FFGKGGTGKTTLTALILRELVRR 28 
                                       9*************999999975 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.11      31      78 ..       3      49 ..       1      59 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilG 78
                                       +G+ G  G+Gk tl+  +  el+rr    +vlavD  ++    s+lG
  gi|386002275|ref|YP_005920574.1|  3 ILGFFGKGGTGKTTLTALILRELVRRR-EGTVLAVDADANECLASVLG 49
                                      68***************9999*99985.568*****999998888888 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3   1.1e+03      11      28 ..      11      28 ..       9      33 .. 0.82
   2 ?   10.5   0.0   0.00047       0.4     156     196 ..     181     223 ..     140     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                            AAA_26 11 gvGKTvvslgLvralkrk 28
                                      g GKT+++++++r l r+
  gi|386002275|ref|YP_005920574.1| 11 GTGKTTLTALILRELVRR 28
                                      67******9999988654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00047
                            AAA_26 156 nvrvlGvilNkvrnp..envetlekksgipvlGvvPylpdlea 196
                                        ++   v++Nk+r++  e+v+++ ++ g + lG++P +p+ ++
  gi|386002275|ref|YP_005920574.1| 181 TIERYYVVANKTRPEmlEKVKEAAESLGFKYLGAIPEDPNFTE 223
                                       4556679****8888888********************98765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0057       4.9       4      35 ..       4      36 ..       1      45 [. 0.74
   2 ?    2.7   0.0     0.098        83     101     141 ..     164     208 ..      41     213 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0057
                                      EEEEESTTSSHHHHHHHHHHHHHHT.TS-EEEE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkke.gkkvllv 35
                                      + ++G  G+GKTt +a + + l ++ + +vl v
  gi|386002275|ref|YP_005920574.1|  4 LGFFGKGGTGKTTLTALILRELVRRrEGTVLAV 36
                                      55899**********998888777724444444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.098
                                       HHHHHHHHHHHH....SSSEEEEEEETTBHTHHHHHHHHHHHHSS CS
                             SRP54 101 lmeelkkikkvv....kpdevllvldattgqeavkqakaFkeavg 141
                                        ++ lk+i++v+    +++e ++v+   t  e+++++k+ +e++g
  gi|386002275|ref|YP_005920574.1| 164 SLDTLKRIRDVAsevgATIERYYVVANKTRPEMLEKVKEAAESLG 208
                                       233333333333444566777777777777777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1554.24
//
Query:       gi|386002276|ref|YP_005920575.1|  [L=198]
Description: 30S ribosomal protein S3Ae [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-69  232.6   0.5    3.7e-69  232.4   0.5    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.043   13.7   0.0      0.075   12.9   0.0    1.4  1  DoxA            TQO small subunit DoxA
      0.055   13.4   0.1        2.2    8.2   0.0    2.4  2  RNaseH_like     Ribonuclease H-like


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.4   0.5   6.2e-73   3.7e-69       5     202 .]       9     195 ..       4     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 6.2e-73
                                       --S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEEES CS
                    Ribosomal_S3Ae   5 kvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieevqg 80 
                                       +   k+k+K+Wy+v  P++fgk+++G+tl+       +++++l+grv+e++l++Ltn++ k+  ++klk+++++v+g
  gi|386002276|ref|YP_005920575.1|   9 SDSRKVKTKQWYKVVGPEMFGKSPVGETLA-------SDPSNLMGRVIETTLGELTNNFsKQ--NTKLKFRVDQVAG 76 
                                       4455899***********************.......**********************555..************* PP

                                       SEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  81 knaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteea 157
                                       ++a+t+F g+elt+D++rslv++++s+I+ i+dv+t+Dgy +rv++ +fT kr   a+++q+k+Ir+++ +i++e+a
  gi|386002276|ref|YP_005920575.1|  77 DSAYTSFVGHELTSDYVRSLVKRRTSRIDSIIDVTTSDGYRVRVKPSCFTVKR---ARTTQVKTIRNIASNIIQEKA 150
                                       *****************************************************...********************* PP

                                       HHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 158 seldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                        +ldl++++++++   l+ +i+k ak+Iyplr+veirK+++l  P
  gi|386002276|ref|YP_005920575.1| 151 GTLDLNQFIQEVVLGRLSLDIYKDAKDIYPLRRVEIRKTEILAGP 195
                                       **************77*************************9765 PP

>> DoxA  TQO small subunit DoxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.075      19      87 ..      55     122 ..      50     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                              DoxA  19 eitgaklaengtLvleitrveGpdvYgafvikiellnstgkvvlelnqeeLaslpssnIknkyvakvkq 87 
                                       e+t+  +++n++L++++ +v+G  +Y +fv + el  +    +++   + + s+ +   ++ y  +vk+
  gi|386002276|ref|YP_005920575.1|  55 ELTNNFSKQNTKLKFRVDQVAGDSAYTSFVGH-ELTSDYVRSLVKRRTSRIDSIIDVTTSDGYRVRVKP 122
                                       567777789********************965.666666666666677777776666666666555554 PP

>> RNaseH_like  Ribonuclease H-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00037       2.2     112     135 ..     103     126 ..      49     130 .. 0.92
   2 ?    3.1   0.0     0.013        80      53      87 ..     131     165 ..     126     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00037
                       RNaseH_like 112 likevvgmvegsgfeakiKPesfa 135
                                        i++++++ ++ g+++++KP  f+
  gi|386002276|ref|YP_005920575.1| 103 RIDSIIDVTTSDGYRVRVKPSCFT 126
                                       5899****************9886 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                       RNaseH_like  53 rkkkerkikslrekiflEtslslevaskleellle 87 
                                       r+++++ i+++ + i++E + +l++ + ++e++l 
  gi|386002276|ref|YP_005920575.1| 131 RTTQVKTIRNIASNIIQEKAGTLDLNQFIQEVVLG 165
                                       4567799*********************9997754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1200.28
//
Query:       gi|386002277|ref|YP_005920576.1|  [L=445]
Description: hypothetical protein Mhar_1593 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3002.52
//
Query:       gi|386002278|ref|YP_005920577.1|  [L=384]
Description: Putative type A flavoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-07   32.0   0.0    2.1e-07   31.2   0.0    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0026   17.3   0.1     0.0074   15.8   0.0    1.7  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   2.3e-11   2.1e-07       4     153 ..      24     159 ..      21     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.3e-11
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       ++ n+y++ g++++ LiD+  ++ a+ +++   ++ l+++++d+ +  H+  DH G+ + + e+++ + +++    +
  gi|386002278|ref|YP_005920577.1|  24 TSYNAYVVGGGEKTALIDAADPPFAEALLD--NLEALGLDRIDYMVANHAEQDHSGAIPAILERYPMALVVCTPRCK 98 
                                       567*************************98..88999999************************************* PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTT.STSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggp.ghghghgvveygggkvlftGDall 153
                                       +l+ ++++  a+++              + e++ +  +g+++l++ ++p +h +  +v +++++ +lf  D++ 
  gi|386002278|ref|YP_005920577.1|  99 ELLVDHLQIPAEKF-------------LTVEDRSTLSLGGKTLEFLYTPwVHWPETMVTYLKEDEILFPCDFFG 159
                                       *******9988887.............66666666666666666666665888999999999999999999875 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.2e-07    0.0074      27     116 ..      59     141 ..      38     152 .. 0.79
   2 ?   -2.5   0.0      0.33     3e+03      41      62 ..     253     274 ..     252     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.2e-07
                                       -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTE CS
                     Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggl 103
                                        l++id  +  ha+ DH   ++ + e++p  + +++++++ + l ++++        a+++ +++   +++lg+  l
  gi|386002278|ref|YP_005920577.1|  59 GLDRIDYMVANHAEQDHSGAIPAILERYPM-ALVVCTPRCKELLVDHLQIP------AEKFLTVEDRSTLSLGGKTL 128
                                       4679**********************8884.3356************7543......55777999999999999999 PP

                                       EEEEEEE-EE--C CS
                     Lactamase_B_2 104 eitatparhksgr 116
                                       e+  tp  h+ ++
  gi|386002278|ref|YP_005920577.1| 129 EFLYTPWVHWPET 141
                                       9999999998765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.33
                                       HHHHGGGGCCCCC--EEEEEEE CS
                     Lactamase_B_2  41 yDHlaglltlrelrpkklplya 62 
                                       +DHl+g+l  r +  +++++ +
  gi|386002278|ref|YP_005920577.1| 253 VDHLTGALIARGIGVRRFDIAV 274
                                       6999999888875455566644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2536.81
//
Query:       gi|386002279|ref|YP_005920578.1|  [L=338]
Description: 2-dehydropantoate 2-reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-38  129.3   0.1    1.2e-37  128.9   0.1    1.2  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal
    8.7e-19   67.7   0.0    2.2e-17   63.1   0.0    2.6  2  ApbA      Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.1   1.4e-41   1.2e-37       1     125 []     211     334 ..     211     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1.4e-41
                            ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       d+r+ +w Kl  na+inp+tal++ kng +l sp+l+ +v+ +++E++avae+eg +++e  + e v++v+e+taan
  gi|386002279|ref|YP_005920578.1| 211 DFRRQQWMKLFANAVINPITALTREKNGIVL-SPHLAPVVELIVQECVAVAEKEGESFDEPAVLEFVRTVAENTAAN 286
                                       6899**************************9.***********************99******************** PP

                            ApbA_C  78 rsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellkale 125
                                       +sSMlqDv++gr+tEid+inG+v+ +A+++ +e+P+ne+l+ ++ a+e
  gi|386002279|ref|YP_005920578.1| 287 TSSMLQDVLRGRETEIDAINGFVLDRARRHAMEAPANEMLWGMVGAIE 334
                                       *******************************************98875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   2.5e-21   2.2e-17       1     149 [.       4     185 ..       4     188 .. 0.91
   2 ?   -2.0   0.0      0.28   2.5e+03      99     126 ..     251     278 ..     236     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2.5e-21
                                       EEEES-SHHHHHHHHHHHHHTHC..........................EEEE-SCHHHHHHHHHCEEEEETTCEEE CS
                              ApbA   1 iailGaGaiGsllaakLakagad..........................vtlilrsrrlealkknGlrltseggeei 51 
                                       ++i GaGaiGs++++ L+++  +                          v l++r  ++e+++++Gl +t  +++  
  gi|386002279|ref|YP_005920578.1|   4 VLIYGAGAIGSFFGYLLSEQELEdgagsageegtgaedtkrgalpaveeVALLGRPGHIERIRERGLLVTLAEKDSP 80 
                                       68***************997777799999********************************************7777 PP

                                       EEECEEECCH....SCCCCS-ESEEEE-SSGGGHHHHHHHHGG..GECTC...EEEEEESSSSCHHHHHTTTSTTSE CS
                              ApbA  52 lrppealsae....ekselepidlvivtvKayqteealeeikp..lldpn...tvvlllqNGlgheeelrealpkpr 119
                                       l+ +   +++      +++   ++vivtvK+y++ +++eeik   ll+ +   +  +ll NG+g+ e+++     +r
  gi|386002279|ref|YP_005920578.1|  81 LSIRFRHAFAglgeFAQSDFAPEVVIVTVKTYSLPAVAEEIKGsgLLTGKlsdSRFVLLMNGMGNRERFDLSG--AR 155
                                       7777777777889988899999******************985336777665679**************9887..9* PP

                                       EEEEEEE-EEEEEETTEEEECS--EEEEEE CS
                              ApbA 120 vlggvtthgatregpgevhhagkgeikige 149
                                       ++ ++t++g++ +g+g++ ++g+g+++++e
  gi|386002279|ref|YP_005920578.1| 156 IYEAITSFGVVLSGDGRIGLKGQGKTVFEE 185
                                       **************************9986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.28
                                       EEESSSSCHHHHHTTTSTTSEEEEEEEE CS
                              ApbA  99 lllqNGlgheeelrealpkprvlggvtt 126
                                       l++q+ + ++e+  e +++p vl  v t
  gi|386002279|ref|YP_005920578.1| 251 LIVQECVAVAEKEGESFDEPAVLEFVRT 278
                                       5666666666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2213.96
//
Query:       gi|386002280|ref|YP_005920579.1|  [L=234]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-16   59.3   0.1    5.5e-16   58.7   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
    1.4e-15   57.4   0.1    2.1e-15   56.9   0.1    1.2  1  NodS             Nodulation protein S (NodS)
      2e-12   47.6   0.0    3.1e-12   47.0   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    8.8e-12   45.6   0.0    1.5e-11   44.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      6e-11   42.8   0.0    8.7e-11   42.3   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    8.4e-10   38.7   0.0    1.1e-09   38.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.3e-08   33.8   0.0      3e-08   33.4   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00014   21.2   0.0    0.00019   20.7   0.0    1.2  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
    0.00021   20.8   1.7     0.0005   19.5   1.7    1.6  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0004   20.1   0.0     0.0012   18.6   0.0    1.6  2  TPMT             Thiopurine S-methyltransferase (TPMT)
    0.00063   19.7   0.0     0.0011   18.9   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
     0.0015   18.1   0.1     0.0038   16.7   0.1    1.7  2  Methyltransf_4   Putative methyltransferase
     0.0025   17.1   0.0     0.0029   16.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0077   17.2   0.0      0.011   16.7   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.032   13.9   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.033   13.2   0.9      0.044   12.7   0.9    1.1  1  Hyphal_reg_CWP   Hyphally regulated cell wall protein N-termi
      0.036   13.3   0.0      0.049   12.9   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
       0.08   12.7   0.0        0.2   11.4   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.13   12.1   0.2       0.35   10.7   0.0    1.7  2  POTRA_2          POTRA domain, ShlB-type
       0.14   11.5   0.0       0.28   10.6   0.0    1.5  1  Spermine_synth   Spermine/spermidine synthase domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.1   6.2e-19   5.5e-16       5     114 ..      54     165 ..      52     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 6.2e-19
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                       +r+l++GC++ + t  +  +++p+aevv +Dis +ai++A+en   l+++nv+F  +di e + + + d+ fD+i+ 
  gi|386002280|ref|YP_005920579.1|  54 NRILEIGCAEAAQTRMII-QAFPEAEVVAVDISSNAIRRAKEN---LKSNNVTFLDADILEcIAN-IDDKYFDIIIW 125
                                       689*******99999999.99*********************7...7799***********8887.899******** PP

                   Methyltransf_31  81 nevl......naladpdkileeiervlkpggilliedprl 114
                                        e l        + d  + +e+i++ l++ gil+++++  
  gi|386002280|ref|YP_005920579.1| 126 SESLyyvgdrLSTRDIFELFEKITNKLNNAGILCMANIIN 165
                                       ****55554444444445555**************99873 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.1   2.3e-18   2.1e-15      13     127 ..      21     140 ..      11     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.3e-18
                              NodS  13 laaedPwrldanefeqerlaqilrlslaqgsi.adalevGcaaGalterlapyc..krltvvdvveeaiararervk 86 
                                       ++ edPw   ++++eq+++ + l l +  +     +le+Gca  a t ++        +  vd+ ++ai ra+e +k
  gi|386002280|ref|YP_005920579.1|  21 FKKEDPWMYFSSDYEQKKYIRQLSLLVDRKPTpNRILEIGCAEAAQTRMIIQAFpeAEVVAVDISSNAIRRAKENLK 97 
                                       5679***************99998877666551669***********9986554114566789*************9 PP

                              NodS  87 esshiswivsdvqqf..st.dekfdlivvaevlyyiedvaelra 127
                                         ++++++ +d+ +   +  d+ fd+i+ +e lyy++d    r 
  gi|386002280|ref|YP_005920579.1|  98 S-NNVTFLDADILECiaNIdDKYFDIIIWSESLYYVGDRLSTRD 140
                                       8.99*******9775223324668*************9877665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   3.4e-15   3.1e-12       1      80 [.      56     135 ..      56     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3.4e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvssgalh 75 
                                       +L++Gc +   t+++ +++++a+v++vDis++++++a+e+++++  nv+f+ +d+ +   + +d+ fD+++ s +l 
  gi|386002280|ref|YP_005920579.1|  56 ILEIGCAEAAQTRMIIQAFPEAEVVAVDISSNAIRRAKENLKSN--NVTFLDADILEciANIDDKYFDIIIWSESLY 130
                                       8******************99********************765..8********8832357999*******98898 PP

                                       GSSHH CS
                   Methyltransf_25  76 hlsde 80 
                                       ++ d+
  gi|386002280|ref|YP_005920579.1| 131 YVGDR 135
                                       87543 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   1.6e-14   1.5e-11       1      99 []      57     158 ..      57     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.6e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       LeiGc  ++ +r++ +++p++e+++vDis++ai +ake l++++  + +   le +  +   + ++fD+++ s+ l 
  gi|386002280|ref|YP_005920579.1|  57 LEIGCAEAAQTRMIIQAFPEAEVVAVDISSNAIRRAKENLKSNNVTFLDADILECIANI---DDKYFDIIIWSESLY 130
                                       8********************************99999988877544444444444433...346************ PP

                   Methyltransf_12  78 hl......kdirevldnirklLkpgGrl 99 
                                       ++      +di e++++i + L++ G+l
  gi|386002280|ref|YP_005920579.1| 131 YVgdrlstRDIFELFEKITNKLNNAGIL 158
                                       ***9999999999999999999888865 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   9.8e-14   8.7e-11       1      95 [.      57     159 ..      57     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 9.8e-14
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.T.SS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaek.l.pfednsfDlvvssevlhh 73 
                                       L++Gc   + ++ + +++  a+vv+vD+s +++++ake+ + ++  v+f+ ad+ + + ++ d++fD+++ se+l +
  gi|386002280|ref|YP_005920579.1|  57 LEIGCAEAAQTRMIIQAFpeAEVVAVDISSNAIRRAKENLKSNN--VTFLDADILEcIaNIDDKYFDIIIWSESLYY 131
                                       89*************9999***********************98..9********96459***************** PP

                                       -......CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  74 v......edpekalkeiaRvLkpgGllv 95 
                                       v       d  +++++i   L + G+l+
  gi|386002280|ref|YP_005920579.1| 132 VgdrlstRDIFELFEKITNKLNNAGILC 159
                                       *876666588899999999999988886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.2e-12   1.1e-09       5      99 ..      35     136 ..      31     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.2e-12
                   Methyltransf_23   5 reeelsdklerllpklraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiaekakkaqkdqfdeqeaae. 78 
                                       +++++ + l  l++++++++r+L+iGc++   ++ + ++++  +v++vD+s++a+ +a++  k++++ f   ++ e 
  gi|386002280|ref|YP_005920579.1|  35 EQKKYIRQLSLLVDRKPTPNRILEIGCAEAAQTRMIiQAFPEaEVVAVDISSNAIRRAKENLKSNNVTFLDADILEc 111
                                       56788899999*******************8888773555447**************************77766668 PP

                   Methyltransf_23  79 ....pqgkfdlIvlrevlehvpdpp 99 
                                           ++++fd+I+ +e+l+ v d  
  gi|386002280|ref|YP_005920579.1| 112 ianiDDKYFDIIIWSESLYYVGDRL 136
                                       8889999*************99843 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   3.4e-11     3e-08      31     137 ..      52     160 ..      42     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.4e-11
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE--- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPP 106
                                       + +++l +Gc   + + ++ ++ peaev++vd++ +A++ akenl++n++  +++   ++++++++k fd+i+    
  gi|386002280|ref|YP_005920579.1|  52 TPNRILEIGCAEAAQTRMIIQAFPEAEVVAVDISSNAIRRAKENLKSNNVTfLDADILECIANIDDKYFDIIIWSES 128
                                       4567**********************************************9999999999************96544 PP

                                       .STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                               MTS 107 .fhagkatelavaeeliaeAkeaLkegGeLli 137
                                        +  g   +++ + el+++  + L++ G L +
  gi|386002280|ref|YP_005920579.1| 129 lYYVGDRLSTRDIFELFEKITNKLNNAGILCM 160
                                       15667777777888888888888888888776 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.1e-07   0.00019      62     112 ..      53      99 ..      35     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                   Methyltransf_33  62 aatlvelGsGsseKtrlLLealeaaekeltYvplDvseeaLeealealaae 112
                                        ++++e+G++++ +tr++++a+++a    + v++D+s +a+++a e+l+++
  gi|386002280|ref|YP_005920579.1|  53 PNRILEIGCAEAAQTRMIIQAFPEA----EVVAVDISSNAIRRAKENLKSN 99 
                                       4589******************866....79*****************874 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.7   5.6e-07    0.0005     182     265 ..      74     167 ..      42     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.6e-07
                              PrmA 182 LgakkvvavDiDevAvkvakeNaelNkvea.kleva.lseellkeekadviv........aNIL.aevlielaedik 247
                                       +  ++vvavDi + A++ akeN++ N+v+    ++    +++ +++ +d+i+           L  + + el e+i+
  gi|386002280|ref|YP_005920579.1|  74 FPEAEVVAVDISSNAIRRAKENLKSNNVTFlDADILeCIANI-DDKYFDIIIwseslyyvGDRLsTRDIFELFEKIT 149
                                       55689***********************98655553133444.4588999973221111133332456899999999 PP

                              PrmA 248 klvkeggllilSGilkek 265
                                       + +++ g+l +  i++++
  gi|386002280|ref|YP_005920579.1| 150 NKLNNAGILCMANIINQQ 167
                                       999999999999999988 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06    0.0012      10      86 ..      27     102 ..      22     125 .. 0.79
   2 ?   -1.4   0.0       1.7   1.6e+03     160     196 ..     164     201 ..     146     219 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                       HHTT--TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HH..HHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGG CS
                              TPMT  10 weeeqipfhqeevnpllkkfldalkakaglrvlvPlCGkald..lvwlAeqgrevvGvelselAvekffeeanlepk 84 
                                       w     +++q++  ++l+ ++d+ k    +r+l  +C +a    ++  A ++ evv+v++s +A++++ +e+  + +
  gi|386002280|ref|YP_005920579.1|  27 WMYFSSDYEQKKYIRQLSLLVDR-KP-TPNRILEIGCAEAAQtrMIIQAFPEAEVVAVDISSNAIRRA-KENLKSNN 100
                                       66666789999999999999999.55.555********997633677799*****************5.55444555 PP

                                       GG CS
                              TPMT  85 vk 86 
                                       v+
  gi|386002280|ref|YP_005920579.1| 101 VT 102
                                       54 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                                       -S----SS----HHHH.HHHHGGTEEEEEEEETT--TT CS
                              TPMT 160 qaeheGPPfsvpeael.eallsagfkvaeleeedalee 196
                                       + +++GP + ++++ + + ++s    + e  +++ ++e
  gi|386002280|ref|YP_005920579.1| 164 INQQNGPEYFITKEAImNSYFSLLASLMENIHKSRFVE 201
                                       55667888887775541445554433333333444444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06    0.0011       7      86 ..      45     123 ..      40     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeev 83 
                                        +++  ++ +r++ iG+  +  + ++++     +v+a+Di+++++++aken+++++++  +++ + + +++++++ +
  gi|386002280|ref|YP_005920579.1|  45 LLVDRKPTPNRILEIGCAEAAQTRMIIQAFPEAEVVAVDISSNAIRRAKENLKSNNVT-FLDADILECIANIDDKYF 120
                                       55556667789*******************************************9984.566666666666655545 PP

                   Methyltransf_18  84 dtv 86 
                                       d++
  gi|386002280|ref|YP_005920579.1| 121 DII 123
                                       555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.2e-06    0.0038       5      65 ..      56     113 ..      53     124 .. 0.84
   2 ?   -3.0   0.0         5   4.5e+03      99     115 ..     144     160 ..     138     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-06
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHH CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvll 65 
                                       +leiGc++   +  + +++P+ ++++++i+++ ++++ ++   l+ +N+  l  d l+ + 
  gi|386002280|ref|YP_005920579.1|  56 ILEIGCAEAAQTRMIIQAFPEAEVVAVDISSNAIRRAKEN---LKSNNVTFLDADILECIA 113
                                       79****************************9999988765...567788888888877765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5
                                       HHHHHHHHEEEEEEEEE CS
                    Methyltransf_4  99 llkelarvLkkgGvlel 115
                                       l +++ ++L++ G+l +
  gi|386002280|ref|YP_005920579.1| 144 LFEKITNKLNNAGILCM 160
                                       55677777777777765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.3e-06    0.0029      64     173 ..      54     169 ..      14     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                                       -EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEES-GG CS
                              CMAS  64 mtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsvgafe 138
                                       +++L+iGc   + +r  ++ + +++vv++ +S++  ++ak+++++ +++      l    ++d+  +d ++  + + 
  gi|386002280|ref|YP_005920579.1|  54 NRILEIGCAEAAQTRMIIQAFpEAEVVAVDISSNAIRRAKENLKSNNVTFLDADILECIANIDDkYFDIIIWSESLY 130
                                       689*********99999999978*********************999876555555667899886789999999988 PP

                                       GTSGG....GHHHHHHHHHHHS-TT-EEEEEEEEE--HH CS
                              CMAS 139 hvgke....nydtffkklkkllkedGllllhtitslhkk 173
                                        vg +       + f+k++++l++ G+l +  i+ +++ 
  gi|386002280|ref|YP_005920579.1| 131 YVGDRlstrDIFELFEKITNKLNNAGILCMANIINQQNG 169
                                       887542111555679999999999999999998877654 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-05     0.011       1     102 [.      57     159 ..      57     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiD...... 71 
                                       +EiG+ +   t ++ +a+ +++   +vavd      +a + a+e+  +++v+++ ad  e +a+ +++ +D      
  gi|386002280|ref|YP_005920579.1|  57 LEIGCAEAAQTRMIIQAFPEAE---VVAVDISS---NAIRRAKENLKSNNVTFLDADILECIANIDDKYFDiiiwse 127
                                       7******************998...7*****99...77777788777899*********************555555 PP

                   Methyltransf_24  72 .llfiDgghaaeavledleallprlapggvvl 102
                                        l+++    ++++  e +e + ++l++ g++ 
  gi|386002280|ref|YP_005920579.1| 128 sLYYVGDRLSTRDIFELFEKITNKLNNAGILC 159
                                       54444444455777777888888888888775 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05     0.032      10      83 ..      54     123 ..      46     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                                       -EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEE CS
                   Methyltr_RsmB-F  10 etilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDri 83 
                                       ++il++ +a  ++T  i +   ++++vvAvd++++ ++r +enlk  +vt    l aD+ +    + ++ fD i
  gi|386002280|ref|YP_005920579.1|  54 NRILEIGCAEAAQTRMIIQA-FPEAEVVAVDISSNAIRRAKENLKSNNVT---FLDADILECIANIDDKYFDII 123
                                       689****************9.7899****************999987777...888998888888888888866 PP

>> Hyphal_reg_CWP  Hyphally regulated cell wall protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   4.9e-05     0.044       8     111 ..      79     182 ..      74     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                    Hyphal_reg_CWP   8 alaleisentvdrgainlgigdltInsgaylsiinnalsafvgdlsvenngglyitstssllalsvtlasatgsieN 84 
                                       ++a++is+n + r + nl+ +++t  +  +l  i n++ ++ + + + +++  y+ +  s+  +   ++++t++++N
  gi|386002280|ref|YP_005920579.1|  79 VVAVDISSNAIRRAKENLKSNNVTFLDADILECIANIDDKYFD-IIIWSESLYYVGDRLSTRDIFELFEKITNKLNN 154
                                       789***********************************99998.7899********9999999888889******** PP

                    Hyphal_reg_CWP  85 nGiivf.nseesltassyklvgasFeNn 111
                                        Gi+ + n +++++ ++y ++ + ++N+
  gi|386002280|ref|YP_005920579.1| 155 AGILCMaNIINQQNGPEYFITKEAIMNS 182
                                       ****996778888899999998888885 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.5e-05     0.049      64     129 ..      54     116 ..       8     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                       SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEES-TTTS-----S CS
                    Methyltransf_2  64 kslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvgGdffkdslPeaD 129
                                       ++++++G    a  ++i +a+P+ +v+  D++ + +++Ake     ++++v+f + d+  + + + D
  gi|386002280|ref|YP_005920579.1|  54 NRILEIGCAEAAQTRMIIQAFPEAEVVAVDISsNAIRRAKEN---LKSNNVTFLDADIL-ECIANID 116
                                       578999999**********************73689999999...56688999999998.6666544 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023       0.2      75     123 ..      54     101 ..      14     116 .. 0.86
   2 ?   -2.5   0.0       3.9   3.5e+03      23      41 ..     189     207 ..     185     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                       -EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  75 arvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                       +r+Le+G+    +t ++ + + e   vv+++ + + +++ak+nlk +++
  gi|386002280|ref|YP_005920579.1|  54 NRILEIGCAEAAQTRMIIQAFPEAE-VVAVDISSNAIRRAKENLKSNNV 101
                                       79*******9999999999987765.******************98765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                                       HHHHHS-GGGGSSCGGGGG CS
                              PCMT  23 ealeevdReefvpesfkek 41 
                                         +e++ +++fv+++  + 
  gi|386002280|ref|YP_005920579.1| 189 SLMENIHKSRFVEQKKSSG 207
                                       5688888888888755444 PP

>> POTRA_2  POTRA domain, ShlB-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.6     5e+03      34      47 ..     106     119 ..      86     121 .. 0.76
   2 ?   10.7   0.0   0.00039      0.35      26      62 ..     131     167 ..     128     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHHH CS
                           POTRA_2  34 adlnqlakeltnay 47 
                                       ad+ + ++++ ++y
  gi|386002280|ref|YP_005920579.1| 106 ADILECIANIDDKY 119
                                       78888888888887 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
                                       CSSSEEEHHHHHHHHHHHHHHHHHTT-TT-EEEEEEC CS
                           POTRA_2  26 ylgkclgladlnqlakeltnayiekGYvtsrvllppq 62 
                                       y+g  l++ d+++l  ++tn++ ++G +     +++q
  gi|386002280|ref|YP_005920579.1| 131 YVGDRLSTRDIFELFEKITNKLNNAGILCMANIINQQ 167
                                       899***********************88766666666 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00031      0.28      16     153 ..      50     183 ..      36     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                                       SSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS. CS
                    Spermine_synth  16 hknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgdgfkflkayek. 91 
                                       ++ p ++L iG     ++r +++     +++ vdi +++i   k++l+s ++  f d        d  + ++++ + 
  gi|386002280|ref|YP_005920579.1|  50 KPTPNRILEIGCAEAAQTRMIIQAFPEAEVVAVDISSNAIRRAKENLKSNNVT-FLD-------ADILECIANIDDk 118
                                       45789999999999999999998775789999999999999999999999888.544.......4666777777776 PP

                                       -EEEEEEECCS.TTCSSCG.CSSHHHHHHHHHTEEEEEEEEEEE.EETTTCHHHHHHHHHHHHTT CS
                    Spermine_synth  92 kfdvvivdsld.pvgpaen.lFskeffdllkkvlkedGviilqa.ekpelekelvinvdksgkqv 153
                                        fd++i  ++   vg   +    +e f+ + ++l++ G++++ +  +     e++i+ ++ ++++
  gi|386002280|ref|YP_005920579.1| 119 YFDIIIWSESLyYVGDRLStRDIFELFEKITNKLNNAGILCMANiINQQNGPEYFITKEAIMNSY 183
                                       78999988877677766554444667888888899999888877644444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1476.87
//
Query:       gi|386002281|ref|YP_005920580.1|  [L=94]
Description: hypothetical protein Mhar_1597 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.25   11.3   2.9       0.89    9.5   0.2    2.3  2  Pox_A_type_inc  Viral A-type inclusion protein repeat
       0.29   11.0   2.9         12    5.9   0.1    3.0  3  PKcGMP_CC       Coiled-coil N-terminus of cGMP-dependent prot


Domain annotation for each model (and alignments):
>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0001      0.89       6      16 ..      23      33 ..      20      33 .. 0.91
   2 ?    1.8   0.2     0.027   2.5e+02      11      18 ..      69      76 ..      66      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                    Pox_A_type_inc  6 lRsRIsDLErq 16
                                      l++RI++LE++
  gi|386002281|ref|YP_005920580.1| 23 LKERIRSLEKK 33
                                      8********86 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.027
                    Pox_A_type_inc 11 sDLErqLs 18
                                       +LE++L+
  gi|386002281|ref|YP_005920580.1| 69 KELESRLE 76
                                      69****96 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0013        12       8      16 ..      25      33 ..      23      36 .. 0.88
   2 ?   -1.0   0.0      0.19   1.7e+03       7      11 ..      42      46 ..      39      47 .. 0.86
   3 ?    3.9   0.1    0.0053        48       8      19 ..      66      77 ..      63      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0013
                         PKcGMP_CC  8 ERIRELEkr 16
                                      ERIR LEk+
  gi|386002281|ref|YP_005920580.1| 25 ERIRSLEKK 33
                                      9******97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.19
                         PKcGMP_CC  7 DERIR 11
                                      +ERI+
  gi|386002281|ref|YP_005920580.1| 42 EERIK 46
                                      89998 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0053
                         PKcGMP_CC  8 ERIRELEkrlae 19
                                      E ++ELE rl+ 
  gi|386002281|ref|YP_005920580.1| 66 ESVKELESRLEM 77
                                      567999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 625.50
//
Query:       gi|386002282|ref|YP_005920581.1|  [L=456]
Description: hypothetical protein Mhar_1598 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-08   34.2  32.0    0.00078   19.7   1.5    7.2  7  TPR_12         Tetratricopeptide repeat
    0.00026   20.7  26.9        0.8    9.6   0.0    9.0 10  TPR_1          Tetratricopeptide repeat
    0.00065   19.5  13.2        3.5    7.9   0.1    7.4  7  TPR_7          Tetratricopeptide repeat
    0.00096   19.0   2.5    0.00096   19.0   2.5    6.7  8  TPR_10         Tetratricopeptide repeat
      0.001   18.5  21.4       0.79    9.1   7.9    4.6  5  SNAP           Soluble NSF attachment protein, SNAP
  ------ inclusion threshold ------
       0.72    9.4   3.8        6.4    6.4   0.9    3.2  2  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
        3.1    8.2  33.2        3.7    8.0   0.2    9.1  9  TPR_8          Tetratricopeptide repeat
        7.6    6.3  19.0        5.2    6.8   0.2    6.8  7  TPR_11         TPR repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.043        96      47      73 ..      37      63 ..      24      67 .. 0.77
   2 ?    4.3   0.1     0.022        49      16      58 ..      94     134 ..      86     138 .. 0.80
   3 !    7.7   5.0    0.0019       4.3      10      62 ..     150     200 ..     146     220 .. 0.80
   4 ?    1.4   1.1      0.18   4.1e+02      20      51 ..     209     241 ..     202     255 .. 0.55
   5 !    5.6   0.2    0.0086        19      20      56 ..     259     293 ..     244     302 .. 0.75
   6 !    6.5   0.1    0.0045        10      20      35 ..     314     329 ..     303     347 .. 0.72
   7 !   19.7   1.5   3.5e-07   0.00078      18      72 ..     362     414 ..     361     419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.043
                            TPR_12 47 tlrnLgrlyralgryeeAlelleeala 73
                                       l   ++ +  +g+ e+A++++ + l+
  gi|386002282|ref|YP_005920581.1| 37 LLAKCADDFAGMGQEEKARSIYDQILK 63
                                      566778888888999999998888776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                            TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyral 58 
                                        ++++ A e +++a+ ++++    +  + a+++++Lg+ + ++
  gi|386002282|ref|YP_005920581.1|  94 EENLALAVEAFQEAIGLFKAE--AHPIEHAQAQNGLGISLVRQ 134
                                       688999************655..43466699999999988766 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0019
                            TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgrye 62 
                                       + ++  +++++ A+  +e+a  i+ +   +   ++a+t +n+g++y++l +  
  gi|386002282|ref|YP_005920581.1| 150 GGAEEGAKNLHRAILAFEAAQKIYAAE--GRGQEEAQTENNIGDAYLLLSQIG 200
                                       556667899999************887..77789************9988764 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.18
                            TPR_12  20 deAlellekaleia.rrllGpdhpltattlrnL 51 
                                       d+  e +e+al+ +  +++ +d+++t ++l   
  gi|386002282|ref|YP_005920581.1| 209 DKGMEAYEAALRFRtAEAYPEDYAETKNSLGRA 241
                                       555566777777774344555554444444433 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.0086
                            TPR_12  20 deAlellekaleiarrllGpdhpltattlrnLgrlyr 56 
                                       + A++ +++alei+++   p+  + a+t+   gr++ 
  gi|386002282|ref|YP_005920581.1| 259 ERAISSFRAALEIRTKEGHPQ--ERAETQTLFGRALV 293
                                       67999*********9995455..56777776666654 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.0045
                            TPR_12  20 deAlellekaleiarr 35 
                                        +A+e +e+al++++r
  gi|386002282|ref|YP_005920581.1| 314 KKAIEAYEEALAVRTR 329
                                       4566666666666654 PP

  == domain 7  score: 19.7 bits;  conditional E-value: 3.5e-07
                            TPR_12  18 rydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++ +A+  +e+ale+++  l+ d +++a+t++nLg +yr+l r+e+ +e le+++
  gi|386002282|ref|YP_005920581.1| 362 NLKQAIGAFEEALEVRT--LDADPEGYAETQNNLGVAYRKLSRLEDREENLERSI 414
                                       6789************5..5677777*******************9988888886 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.015        33      13      29 ..      93     109 ..      92     112 .. 0.85
   2 ?   -2.6   0.0       2.5   5.7e+03       1      16 [.     121     136 ..     121     138 .. 0.80
   3 ?    0.1   0.2      0.36   8.1e+02      14      30 ..     156     172 ..     147     173 .. 0.81
   4 ?    2.5   0.1     0.066   1.5e+02       1      17 [.     183     199 ..     183     205 .. 0.80
   5 ?   -0.5   0.1      0.57   1.3e+03      18      29 ..     209     220 ..     204     222 .. 0.79
   6 ?    1.9   0.0       0.1   2.2e+02      17      30 ..     258     271 ..     257     272 .. 0.89
   7 !    7.8   0.7    0.0013       2.9      18      30 ..     314     326 ..     313     327 .. 0.88
   8 ?    5.0   0.0     0.011        24      16      30 ..     362     376 ..     362     377 .. 0.89
   9 !    9.6   0.0   0.00036       0.8       1      18 [.     387     404 ..     387     405 .. 0.90
  10 ?   -1.3   0.1      0.99   2.2e+03      15      28 ..     408     421 ..     406     422 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.015
                                       HTT-HHHHHHHHHHHHH CS
                             TPR_1  13 klgkydeAleyyekALe 29 
                                       k +++  A+e++++A+ 
  gi|386002282|ref|YP_005920581.1|  93 KEENLALAVEAFQEAIG 109
                                       6689999********96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHTT- CS
                             TPR_1   1 akalynlGnayfklgk 16 
                                       a+a ++lG  + ++ +
  gi|386002282|ref|YP_005920581.1| 121 AQAQNGLGISLVRQSE 136
                                       78999***99887766 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.36
                                       TT-HHHHHHHHHHHHHH CS
                             TPR_1  14 lgkydeAleyyekALel 30 
                                        +++  A+ ++e A ++
  gi|386002282|ref|YP_005920581.1| 156 AKNLHRAILAFEAAQKI 172
                                       689999*******9987 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.066
                                       HHHHHHHHHHHHHTT-H CS
                             TPR_1   1 akalynlGnayfklgky 17 
                                       a++ +n+G ay+ l + 
  gi|386002282|ref|YP_005920581.1| 183 AQTENNIGDAYLLLSQI 199
                                       56789*******99876 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHH CS
                             TPR_1  18 deAleyyekALe 29 
                                       d+  e+ye AL+
  gi|386002282|ref|YP_005920581.1| 209 DKGMEAYEAALR 220
                                       777899999996 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHH CS
                             TPR_1  17 ydeAleyyekALel 30 
                                       ++ A+  ++ ALe+
  gi|386002282|ref|YP_005920581.1| 258 LERAISSFRAALEI 271
                                       589**********8 PP

  == domain 7  score: 7.8 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHH CS
                             TPR_1  18 deAleyyekALel 30 
                                       ++A+e+ye+AL +
  gi|386002282|ref|YP_005920581.1| 314 KKAIEAYEEALAV 326
                                       79*********86 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.011
                                       -HHHHHHHHHHHHHH CS
                             TPR_1  16 kydeAleyyekALel 30 
                                       ++++A+ ++e+ALe+
  gi|386002282|ref|YP_005920581.1| 362 NLKQAIGAFEEALEV 376
                                       6799*********97 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHTT-HH CS
                             TPR_1   1 akalynlGnayfklgkyd 18 
                                       a++ +nlG+ay+kl +++
  gi|386002282|ref|YP_005920581.1| 387 AETQNNLGVAYRKLSRLE 404
                                       7889**********9988 PP

  == domain 10  score: -1.3 bits;  conditional E-value: 0.99
                                       T-HHHHHHHHHHHH CS
                             TPR_1  15 gkydeAleyyekAL 28 
                                       ++++  + +ye AL
  gi|386002282|ref|YP_005920581.1| 408 ENLERSILAYEAAL 421
                                       678999999*9999 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   3.8e+03      12      26 ..      48      62 ..      35      69 .. 0.70
   2 ?    1.2   0.0      0.22   4.8e+02      15      28 ..     104     115 ..      96     126 .. 0.83
   3 ?   -2.6   0.1       3.6     8e+03      22      29 ..     215     222 ..     212     229 .. 0.58
   4 ?    3.4   0.0     0.042        93      16      34 ..     259     277 ..     257     279 .. 0.86
   5 !    7.9   0.1    0.0016       3.5      16      35 ..     314     333 ..     307     334 .. 0.87
   6 ?    3.3   0.0     0.045     1e+02      15      29 ..     363     377 ..     360     385 .. 0.71
   7 ?    4.7   0.5     0.017        37       3      17 ..     391     405 ..     391     435 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                             TPR_7 12 lGdyeeAielyeqsL 26
                                      +G+ e+A ++y q L
  gi|386002282|ref|YP_005920581.1| 48 MGQEEKARSIYDQIL 62
                                      677799999999977 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                             TPR_7  15 yeeAielyeqsLal 28 
                                       ++eAi+l+++  + 
  gi|386002282|ref|YP_005920581.1| 104 FQEAIGLFKA--EA 115
                                       899****998..65 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.6
                             TPR_7  22 yeqsLalt 29 
                                       ye++L+++
  gi|386002282|ref|YP_005920581.1| 215 YEAALRFR 222
                                       55544443 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.042
                             TPR_7  16 eeAielyeqsLaltkdped 34 
                                       e+Ai+ ++++L+++  +++
  gi|386002282|ref|YP_005920581.1| 259 ERAISSFRAALEIRTKEGH 277
                                       89**********9988876 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0016
                             TPR_7  16 eeAielyeqsLaltkdpeda 35 
                                       ++Aie ye++La++ +++++
  gi|386002282|ref|YP_005920581.1| 314 KKAIEAYEEALAVRTREDHP 333
                                       79*******99999888876 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.045
                             TPR_7  15 yeeAielyeqsLalt 29 
                                        ++Ai+ +e++L+++
  gi|386002282|ref|YP_005920581.1| 363 LKQAIGAFEEALEVR 377
                                       589999999966555 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.017
                             TPR_7   3 lnLarlysrlGdyee 17 
                                       +nL+++y++l + e+
  gi|386002282|ref|YP_005920581.1| 391 NNLGVAYRKLSRLED 405
                                       79*******766655 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.2   7.1e+03      16      29 ..      49      62 ..      47      63 .. 0.67
   2 ?   -1.7   0.0       1.3   2.9e+03      22      41 ..      95     117 ..      84     118 .. 0.55
   3 ?   -1.9   0.0       1.5   3.4e+03       2      15 ..     121     134 ..     121     139 .. 0.81
   4 ?   -0.1   0.1      0.41   9.1e+02      15      36 ..     198     219 ..     187     220 .. 0.66
   5 ?    2.8   0.2      0.05   1.1e+02      10      41 ..     243     278 ..     232     279 .. 0.83
   6 !    5.8   0.2    0.0058        13      17      40 ..     312     332 ..     305     334 .. 0.52
   7 ?   -0.8   0.1      0.72   1.6e+03      18      32 ..     363     377 ..     361     378 .. 0.73
   8 !   19.0   2.5   4.3e-07   0.00096       2      36 ..     387     421 ..     387     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.2
                            TPR_10 16 grydeAealleeal 29
                                      g+ ++A+ ++++ l
  gi|386002282|ref|YP_005920581.1| 49 GQEEKARSIYDQIL 62
                                      66677777777755 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                            TPR_10  22 ealleealairrrllG....pdHP 41 
                                       e+l   a+++ +++ G    + HP
  gi|386002282|ref|YP_005920581.1|  95 ENL-ALAVEAFQEAIGlfkaEAHP 117
                                       444.55666666666555555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                            TPR_10   2 AsslnNLanalrqr 15 
                                       A ++n L++ l ++
  gi|386002282|ref|YP_005920581.1| 121 AQAQNGLGISLVRQ 134
                                       789******99776 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.41
                            TPR_10  15 rgrydeAealleealairrrll 36 
                                       +  +++A + l++ +++++++l
  gi|386002282|ref|YP_005920581.1| 198 QIGGAKAAEALDKGMEAYEAAL 219
                                       3334445555599999999887 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.05
                            TPR_10  10 nalrqrgrydeAealleealairrrllG....pdHP 41 
                                       +al q+ ++d  e +le+a++  r++l+    + HP
  gi|386002282|ref|YP_005920581.1| 243 MALAQLAEGDLREVHLERAISSFRAALEirtkEGHP 278
                                       567777888888999999999999999988888887 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.0058
                            TPR_10  17 rydeAealleealairrrllGpdH 40 
                                        +++A + +eeala+r r   +dH
  gi|386002282|ref|YP_005920581.1| 312 GLKKAIEAYEEALAVRTR---EDH 332
                                       445555555555555544...455 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 0.72
                            TPR_10  18 ydeAealleealair 32 
                                       +++A   +eeal++r
  gi|386002282|ref|YP_005920581.1| 363 LKQAIGAFEEALEVR 377
                                       566777789999886 PP

  == domain 8  score: 19.0 bits;  conditional E-value: 4.3e-07
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrll 36 
                                       A ++nNL++a+r++ r+++ e+ le+++ +++++l
  gi|386002282|ref|YP_005920581.1| 387 AETQNNLGVAYRKLSRLEDREENLERSILAYEAAL 421
                                       789*****************************997 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.48   1.1e+03     158     182 ..      38      62 ..      22      65 .. 0.81
   2 ?    4.1   0.1     0.011        26     127     153 ..      94     119 ..      77     128 .. 0.68
   3 !    8.5   7.0   0.00052       1.2      89     157 ..     158     227 ..     152     251 .. 0.62
   4 !    9.1   7.9   0.00035      0.79      33     150 ..     203     332 ..     202     375 .. 0.79
   5 !    8.0   0.7   0.00074       1.7      90     181 ..     313     420 ..     305     427 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHTT-HHHHHHHHHHHH CS
                              SNAP 158 llkvAelsaelekyekAieiyekva 182
                                       l k+A+  a +++ ekA  iy+++ 
  gi|386002282|ref|YP_005920581.1|  38 LAKCADDFAGMGQEEKARSIYDQIL 62 
                                       6799999999999999999999986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                                       TT--HHHHHHHHHHHHHHHHHTT-HHH CS
                              SNAP 127 elgdlekAieaYekAaelyeqeeakal 153
                                       e ++l  A+ea+++A  l++ e    +
  gi|386002282|ref|YP_005920581.1|  94 E-ENLALAVEAFQEAIGLFKAEAHPIE 119
                                       3.5788888888888888888875544 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00052
                                       -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT........--HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                              SNAP  89 speeAvealekAieiytekgrfrraAklkkeiaelyekel........gdlekAieaYekAaelyeqeeakalankc 157
                                       + ++A+ a+e+A +iy+ +gr ++ A+ +++i++ y            + l+k +eaYe A  +        +a+  
  gi|386002282|ref|YP_005920581.1| 158 NLHRAILAFEAAQKIYAAEGRGQEEAQTENNIGDAYLLLSqiggakaaEALDKGMEAYEAALRF-------RTAEAY 227
                                       6678999999999999999999999999999999887543223333334466666666666433.......222222 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT- CS
                              SNAP  33 eAadlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkvspeeAvealekAieiytekgr 109
                                       +Aa+ +++  +ay  a +++ A +  ++ Ae++++l+ ++ a  +++e    +++v+ e+A++++++A ei t++g 
  gi|386002282|ref|YP_005920581.1| 203 KAAEALDKGMEAYEAALRFRTAEAYPEDYAETKNSLGRAEMALAQLAEG--DLREVHLERAISSFRAALEIRTKEGH 277
                                       6899999999999999999999888899999999999999999999876..589*********************** PP

                                       HHHHHHHHHHHHH..HHHHTT--............HHHHHHHHHHHHHHHHHTT- CS
                              SNAP 110 frraAklkkeiae..lyekelgd............lekAieaYekAaelyeqeea 150
                                        ++ A+ +   +   ++e e +             l+kAieaYe+A  + + e+ 
  gi|386002282|ref|YP_005920581.1| 278 PQERAETQTLFGRalVLEAEPQAvegeirwsdregLKKAIEAYEEALAVRTREDH 332
                                       ******99988772245666533666677777778***********988777764 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.00074
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT.........--HHHHHHHHHHHHHHHHHTT....-HHH CS
                              SNAP  90 peeAvealekAieiytekgrfrraAklkkeiaelyekel.........gdlekAieaYekAaelyeqee....akal 153
                                        ++A+ea+e+A ++ t+++  r+ A+ k  ++e +   +         ++l++Ai a+e+A e+ + +        +
  gi|386002282|ref|YP_005920581.1| 313 LKKAIEAYEEALAVRTREDHPREFAETKSLLGEALVILAgaangpadgANLKQAIGAFEEALEVRTLDAdpegYAET 389
                                       579******************************88755544455555566***********9976544321222223 PP

                                       HHH...HHHHHHHHHHHTT-HHHHHHHHHHH CS
                              SNAP 154 ank...cllkvAelsaelekyekAieiyekv 181
                                       +n+   ++ k+  l+ ++e++e++i +ye  
  gi|386002282|ref|YP_005920581.1| 390 QNNlgvAYRKLSRLEDREENLERSILAYEAA 420
                                       3331224556666777777888888888865 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.9    0.0028       6.4      52      78 ..      99     125 ..      84     266 .. 0.85
   2 ?    1.7   0.1     0.078   1.8e+02      77     111 ..     380     414 ..     313     422 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                     PI3K_P85_iSH2  52 qaleaFneaikmFeeqiklqekfskea 78 
                                       +a+eaF+eai +F+ + + +e  + + 
  gi|386002282|ref|YP_005920581.1|  99 LAVEAFQEAIGLFKAEAHPIEHAQAQN 125
                                       689***************999988876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.078
                     PI3K_P85_iSH2  77 eaqehEieklqenleqlksrlkelhsskekLeedl 111
                                       +a+++   + q+nl  + ++l+ l++  e+Le ++
  gi|386002282|ref|YP_005920581.1| 380 DADPEGYAETQNNLGVAYRKLSRLEDREENLERSI 414
                                       34577778889999999999999999999999877 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.19   4.2e+02      14      29 ..      48      63 ..      45      63 .. 0.87
   2 ?    3.3   0.2     0.053   1.2e+02      14      30 ..      94     110 ..      91     114 .. 0.85
   3 ?    2.0   0.2      0.14   3.2e+02      14      32 ..     156     174 ..     148     176 .. 0.83
   4 ?    0.7   0.6      0.35   7.9e+02      17      28 ..     208     219 ..     187     224 .. 0.59
   5 ?   -2.1   0.1       2.8   6.3e+03      10      22 ..     234     246 ..     231     250 .. 0.69
   6 ?    5.0   0.0     0.015        34      17      31 ..     258     272 ..     257     275 .. 0.88
   7 ?    4.1   0.3     0.028        64      18      29 ..     314     325 ..     313     328 .. 0.87
   8 ?    0.2   0.1      0.51   1.1e+03      16      30 ..     362     376 ..     361     377 .. 0.84
   9 ?    8.0   0.2    0.0017       3.7       1      28 [.     387     414 ..     387     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                                      TT-HHHHHHHHHHHHH CS
                             TPR_8 14 lgdyeeAkeyyekale 29
                                      +g+ e+A + y + l+
  gi|386002282|ref|YP_005920581.1| 48 MGQEEKARSIYDQILK 63
                                      8**********99875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.053
                                       TT-HHHHHHHHHHHHHH CS
                             TPR_8  14 lgdyeeAkeyyekalel 30 
                                        +++  A+e++++a+ l
  gi|386002282|ref|YP_005920581.1|  94 EENLALAVEAFQEAIGL 110
                                       578999*********88 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.14
                                       TT-HHHHHHHHHHHHHHHH CS
                             TPR_8  14 lgdyeeAkeyyekaleldp 32 
                                        ++++ A+ ++e a ++  
  gi|386002282|ref|YP_005920581.1| 156 AKNLHRAILAFEAAQKIYA 174
                                       58999*********99975 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekal 28 
                                       +++ +e+ye al
  gi|386002282|ref|YP_005920581.1| 208 LDKGMEAYEAAL 219
                                       455566666666 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 2.8
                                       HHHHTT-HHHHHH CS
                             TPR_8  10 iylklgdyeeAke 22 
                                       +  +lg+ e+A +
  gi|386002282|ref|YP_005920581.1| 234 TKNSLGRAEMALA 246
                                       5567888888865 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHH CS
                             TPR_8  17 yeeAkeyyekaleld 31 
                                       +e A+++++ ale++
  gi|386002282|ref|YP_005920581.1| 258 LERAISSFRAALEIR 272
                                       699**********97 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekale 29 
                                       ++A+e+ye+al 
  gi|386002282|ref|YP_005920581.1| 314 KKAIEAYEEALA 325
                                       79********96 PP

  == domain 8  score: 0.2 bits;  conditional E-value: 0.51
                                       -HHHHHHHHHHHHHH CS
                             TPR_8  16 dyeeAkeyyekalel 30 
                                       ++++A+ ++e+ale 
  gi|386002282|ref|YP_005920581.1| 362 NLKQAIGAFEEALEV 376
                                       67899999****986 PP

  == domain 9  score: 8.0 bits;  conditional E-value: 0.0017
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekal 28 
                                       ae  +nlg +y+kl ++e  +e +e+ +
  gi|386002282|ref|YP_005920581.1| 387 AETQNNLGVAYRKLSRLEDREENLERSI 414
                                       67889******************99987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.44   9.8e+02       9      21 ..      96     108 ..      93     110 .. 0.82
   2 ?   -2.9   0.0       2.5   5.7e+03      32      39 ..     187     194 ..     187     197 .. 0.77
   3 ?    0.1   0.1      0.29   6.5e+02      12      29 ..     216     233 ..     207     244 .. 0.58
   4 ?    0.6   0.0      0.21   4.7e+02      10      24 ..     258     272 ..     257     274 .. 0.90
   5 ?    6.8   0.2    0.0023       5.2      10      23 ..     313     326 ..     309     328 .. 0.87
   6 ?    4.4   0.3     0.014        31      27      40 ..     386     399 ..     362     401 .. 0.71
   7 ?   -0.0   0.1      0.33   7.3e+02       9      22 ..     409     422 ..     407     426 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.44
                            TPR_11   9 kyeeAieaYkkAl 21 
                                       ++  A+ea+++A+
  gi|386002282|ref|YP_005920581.1|  96 NLALAVEAFQEAI 108
                                       56779*******9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                            TPR_11  32 ynLGlayy 39 
                                       +n+G+ay+
  gi|386002282|ref|YP_005920581.1| 187 NNIGDAYL 194
                                       58999997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.29
                            TPR_11  12 eAieaYkkAlkldPdnae 29 
                                       eA  ++++A ++ +d+ae
  gi|386002282|ref|YP_005920581.1| 216 EAALRFRTAEAYPEDYAE 233
                                       333344555555555555 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.21
                            TPR_11  10 yeeAieaYkkAlkld 24 
                                       +e Ai ++++Al+++
  gi|386002282|ref|YP_005920581.1| 258 LERAISSFRAALEIR 272
                                       799**********96 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0023
                            TPR_11  10 yeeAieaYkkAlkl 23 
                                       +++AieaY++Al+ 
  gi|386002282|ref|YP_005920581.1| 313 LKKAIEAYEEALAV 326
                                       689*********86 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.014
                            TPR_11  27 naeayynLGlayyk 40 
                                       +ae  +nLG+ay k
  gi|386002282|ref|YP_005920581.1| 386 YAETQNNLGVAYRK 399
                                       899999***99976 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 0.33
                            TPR_11   9 kyeeAieaYkkAlk 22 
                                       ++e +i aY++Al+
  gi|386002282|ref|YP_005920581.1| 409 NLERSILAYEAALR 422
                                       68999*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3032.67
//
Query:       gi|386002283|ref|YP_005920582.1|  [L=279]
Description: hypothetical protein Mhar_1599 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-46  157.4  43.2    5.1e-46  157.2  43.2    1.0  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2  43.2   2.9e-50   5.1e-46       1     236 []       9     268 ..       9     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 2.9e-50
                              TauE   1 lllagllaGfvagllGiGggliavPlLllll.........ppavavatsllavvatslsgalahrrrgnvdwrllll 68 
                                       l+lag++aGf +g+lG+Gg +i+vP+ l++l         + ++a +t+l+++++t++ +al h+rrg+v  r++ll
  gi|386002283|ref|YP_005920582.1|   9 LVLAGVAAGFASGMLGVGGCFIMVPVQLWVLtasgieptmATRIAFGTALAVALPTAINAALGHHRRGAVVPRAALL 85 
                                       579**************************534789999989999********************************* PP

                              TauE  69 lllgsliGallGallllllpsellkllfgvlllllallmllrkkr....srakgrerrptaillvliggl.vGllsG 140
                                       l+l++l+Ga+lG+ + +  p++ll+++fg++++++al+m++ +       +++g  +r++     l+ gl +G++sG
  gi|386002283|ref|YP_005920582.1|  86 LGLAGLVGAFLGGAVTAKAPGDLLRIAFGLVVIAAALRMATAPDLtaggGEGDGTIPRSDGC--YLLLGLpLGFISG 160
                                       ***************************************99776655443333333444444..4444666****** PP

                              TauE 141 llGiGgGfllvpllllllglplkkavatslllilvislagalgyal............agavdwpllllllpgallG 205
                                       l+GiGgG+++vp+l   +gl +++av+ts+++i+++s  g+l+y++            +g++++  ++ll+ +++ +
  gi|386002283|ref|YP_005920582.1| 161 LVGIGGGVMMVPVLSTAMGLGIHRAVGTSSAAIILTSSGGVLSYVYhglgvpglppfsLGYLNLLQVALLAGASIPT 237
                                       ********************************************6667778888888899999999999******** PP

                              TauE 206 allGarlarrlsertlrrlfallllvlgvkl 236
                                       a +G+r+a+r+ + +lr++f ll++++g+ +
  gi|386002283|ref|YP_005920582.1| 238 ARIGVRAAHRIRADRLRKVFTLLMVYIGLEM 268
                                       ****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1730.33
//
Query:       gi|386002284|ref|YP_005920583.1|  [L=843]
Description: Peptidase U32 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-113  376.9   0.0    7.3e-83  277.3   0.0    2.2  2  Peptidase_U32  Peptidase family U32
    2.4e-18   66.7   0.0    5.8e-18   65.5   0.0    1.6  1  DUF3656        Collagenase


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.3   0.0   8.2e-87   7.3e-83       1     230 [.      73     305 ..      73     308 .. 0.93
   2 !   97.5   0.0     7e-32   6.2e-28       7     229 ..     626     839 ..     622     843 .] 0.83

  Alignments for each domain:
  == domain 1  score: 277.3 bits;  conditional E-value: 8.2e-87
                     Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeika 77 
                                       le++++ l +l+e+g+dav vqD+gv+ lar+ +pelelh+Stq++it+ e++r+ +++G sr+vlaRElsl+e+++
  gi|386002284|ref|YP_005920583.1|  73 LEEVAAHLLSLYEAGADAVLVQDLGVVSLARDLVPELELHASTQMTITSIEGARWAADMGLSRAVLARELSLAEVEE 149
                                       578999999******************************************************************** PP

                     Peptidase_U32  78 ikekvpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekge....eepieedekgtyl 150
                                       i+++   +elEvfvhGalc++ysG+cllss+++grs+nrg+caqpcr++yrl+++++++     ++ +e   +g+yl
  gi|386002284|ref|YP_005920583.1| 150 IARAS-PIELEVFVHGALCYSYSGQCLLSSVIGGRSGNRGSCAQPCRKPYRLLRSRRRDAfgrpLQLEEIPTEGRYL 225
                                       *****.8********************************************998887654111133344556677** PP

                     Peptidase_U32 151 lspkdlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfl 227
                                       ls++dl+++ ++++l+ a +++lKIeGRm+speyv tvv++Yr+a+d + +g ++ +ee +++l+ ++nr +t+g +
  gi|386002284|ref|YP_005920583.1| 226 LSTRDLSVYPHIEDLARASIAALKIEGRMRSPEYVRTVVSIYRRALDGISEGGWSPSEEDERDLALAFNRTFTPGCI 302
                                       **************************************************************************998 PP

                     Peptidase_U32 228 lgr 230
                                        g 
  gi|386002284|ref|YP_005920583.1| 303 GGA 305
                                       776 PP

  == domain 2  score: 97.5 bits;  conditional E-value: 7e-32
                     Peptidase_U32   7 yleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikekvp 83 
                                       +l  l+e++v  v+v  +g++  ++e  p++++ +S+  n++ns av++l+    sr+ l+ Els++e+++++ ++ 
  gi|386002284|ref|YP_005920583.1| 626 ALSLLKEVEVAEVMVEGVGLAGAVKEGRPDMRVSASVGLNVWNSLAVELLAPE-LSRLTLSPELSAREVEELCGRAR 701
                                       678899*********************************************99.*******************9998 PP

                     Peptidase_U32  84 ....dvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeep.ieedekgtyllspkd 155
                                             +lEv+v+G++  ++  +cllss+       + e a +    +    e+e+g   p ++  e  t++ ++ +
  gi|386002284|ref|YP_005920583.1| 702 stsePPDLEVLVQGNVEAMVAENCLLSSAP-----GCEEVAASGDPFWG--IEDETGRVFPvRADGEGRTHVQNAVE 771
                                       777789***********************3.....23333333333344..3344444444044455556******* PP

                     Peptidase_U32 156 lclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfllg 229
                                       l+l+++lp+l+  Gv+s+ I+ R +++ey+ ++v++Y++a++         +  l++e ++++ +g+t g +l+
  gi|386002284|ref|YP_005920583.1| 772 LSLLDQLPKLAGLGVSSIAIDARGRTAEYARRIVEIYDDALKGGD------LDRLRREAREISLGGTTGGAFLR 839
                                       **************************************9998843......45578888888777777776665 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   6.4e-22   5.8e-18      20     106 ..     404     506 ..     389     507 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 6.4e-22
                           DUF3656  20 seerkipvdlelaakegeplkltvtde................leeAkkrplteenirkqLsklGgtpFeleeieid 80 
                                       +++r+ip+dl+++ +   +  l+ ++                 +e A++rpl++e+i++qL+k+GgtpF ++ +e+d
  gi|386002284|ref|YP_005920583.1| 404 RSRREIPIDLSVRWEGR-RPVLEGKAHlpdgkvvathlesdfaMELARERPLSAEEIEAQLRKTGGTPFAIGTVEMD 479
                                       67899****99954444.3334444334455666666777899********************************** PP

                           DUF3656  81 ldgl.fiPvseLnelRRealekLeear 106
                                       + g  f P++e+n+lRRe+le  e+++
  gi|386002284|ref|YP_005920583.1| 480 YPGRlFAPLGEINRLRREFLELAEREV 506
                                       *8555****************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 6062.94
//
Query:       gi|386002285|ref|YP_005920584.1|  [L=96]
Description: hypothetical protein Mhar_1601 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.038   13.9   0.9      0.059   13.3   0.9    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-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 ?   13.3   0.9   3.3e-06     0.059      22      56 ..      13      48 ..       8      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-06
                    OrfB_Zn_ribbon 22 vnpayTSktCseCgsknke.alsgrtfkCpnCgfea 56
                                        p y S tC +Cg+ + +  ++g+ ++C++ g+ a
  gi|386002285|ref|YP_005920584.1| 13 LRPDYRSGTCCVCGHLLANhLKEGDGWRCTERGLDA 48
                                      678999************988999*****9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 608.36
//
Query:       gi|386002286|ref|YP_005920585.1|  [L=263]
Description: hypothetical protein Mhar_1602 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-61  206.6   3.1    4.2e-61  206.4   3.1    1.0  1  DNA_alkylation  DNA alkylation repair enzyme
  ------ inclusion threshold ------
      0.014   15.8   0.1         14    6.1   0.0    3.1  4  HEAT_2          HEAT repeats


Domain annotation for each model (and alignments):
>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   3.1   4.7e-65   4.2e-61       2     213 .]      37     252 ..      36     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 4.7e-65
                    DNA_alkylation   2 kaeLealadpekaeemqryfkegdeflGvkvpelrklakeffkelkle..eelqelaeeLwksperEerllAldllt 76 
                                       ++eL + ad++++e+ qr+fke+ +f+Gvk+ ++r++ak+ ++++k    +el++l+eeL+ks++ Ee  +A+++++
  gi|386002286|ref|YP_005920585.1|  37 RRELIERADEKTRESGQRFFKEEAKFHGVKAAAVREIAKRRYRDVKDLnkKELFSLCEELLKSDYGEEAAIAFEWAY 113
                                       789*************************************99999998999************************** PP

                    DNA_alkylation  77 qakkklaeadlelyeklve.tinnWdlvDslaskivgalladkperrdllkeWaksenlWerRaAivatlklikk.t 151
                                         +k++++ad++++e ++  ++nnW+ +D+l+++ +g +l+++pe  ++lk W+ sen+W+rRaA+v+++  ++k  
  gi|386002286|ref|YP_005920585.1| 114 SLRKRYEPADFAVFEGWLSqYVNNWAKCDTLCNHALGTFLEMYPEYVAKLKGWTGSENRWLRRAAAVTLILPARKgL 190
                                       ******************99*******************************************************99 PP

                    DNA_alkylation 152 dlellleiaeelladkedfiqkAiGwaLrelsktdpdlveeFlekhakrmprlslreAiekl 213
                                        le+++ei ++ll+d +d++qk++Gw+L+e+sk ++++v+e++ k+++ mpr++lr+Aiek+
  gi|386002286|ref|YP_005920585.1| 191 FLEDVFEISDLLLQDGDDLVQKGYGWLLKEASKSHQQEVFEYVLKKKAVMPRTALRYAIEKM 252
                                       9***********************************************************97 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.72   6.4e+03      62      80 ..      31      49 ..      20      51 .. 0.57
   2 ?    6.0   0.0    0.0017        16      11      67 ..      60     127 ..      56     138 .. 0.75
   3 ?    6.1   0.0    0.0016        14      23      55 ..     148     182 ..     143     212 .. 0.79
   4 ?   -1.4   0.0      0.34   3.1e+03      59      59 ..     237     237 ..     198     262 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.72
                            HEAT_2 62 ealpaLkellddddddvvR 80
                                      e+++ L++ l +  d+ +R
  gi|386002286|ref|YP_005920585.1| 31 EVISDLRRELIERADEKTR 49
                                      4455555555544444444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0017
                            HEAT_2  11 dpdpevrraairaLg........rignpealpaLvell.ed..edpavRraaaeaLgaigdpealpaL 67 
                                        +++ v++aa+r+++        +++ +e++ ++ ell +d  e++a+  + a +L +  +p++ ++ 
  gi|386002286|ref|YP_005920585.1|  60 AKFHGVKAAAVREIAkrryrdvkDLNKKELFSLCEELLkSDygEEAAIAFEWAYSLRKRYEPADFAVF 127
                                       56788**********77666665566669999999999555666777888877788777777666555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0016
                            HEAT_2  23 aLgrign..pealpaLvellededpavRraaaeaL 55 
                                       aLg++ +  pe+++ L  +  +e+++ Rraaa +L
  gi|386002286|ref|YP_005920585.1| 148 ALGTFLEmyPEYVAKLKGWTGSENRWLRRAAAVTL 182
                                       66666543378899999999999999999999887 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.34
                            HEAT_2  59 g 59 
                                       +
  gi|386002286|ref|YP_005920585.1| 237 K 237
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1444.28
//
Query:       gi|386002287|ref|YP_005920586.1|  [L=182]
Description: Peptide methionine sulfoxide reductase MsrA [Methanosaeta harundinacea 6Ac]
Scores for complete 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-68  227.9   0.2    6.5e-68  227.7   0.2    1.0  1  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7   0.2   3.6e-72   6.5e-68       1     152 [.      28     179 ..      28     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 3.6e-72
                                       EEEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-T CS
                              PMSR   1 eavlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDp 77 
                                       +a++a+GCFWgve++f++l+Gv+st+vGY+gG+t+nptYeevc+++tghaEavevvydp++vs+eell+lf++ihDp
  gi|386002287|ref|YP_005920586.1|  28 KATFAAGCFWGVEAAFRDLEGVISTAVGYTGGSTTNPTYEEVCTDRTGHAEAVEVVYDPKVVSFEELLDLFWSIHDP 104
                                       589************************************************************************** PP

                                       T-SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS-- CS
                              PMSR  78 tqlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpegyc 152
                                       t++nrqg DvG+qYrsai+++++eq+++a++ +e+lq++  ++++ivtei p++ fy+aeeyHqqY+ek+ ++ c
  gi|386002287|ref|YP_005920586.1| 105 TTMNRQGPDVGSQYRSAIFFHDPEQEAEARAKMERLQSSGLYRREIVTEIVPASGFYRAEEYHQQYFEKHGRRSC 179
                                       **********************************************************************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1125.28
//
Query:       gi|386002288|ref|YP_005920587.1|  [L=427]
Description: hypothetical protein Mhar_1604 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2439.16
//
Query:       gi|386002289|ref|YP_005920588.1|  [L=261]
Description: hypothetical protein Mhar_1605 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   13.0   1.3        0.2   11.6   1.3    1.8  1  PEGA      PEGA domain


Domain annotation for each model (and alignments):
>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.3   1.1e-05       0.2       5      40 ..     181     216 ..     178     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                              PEGA   5 tirSnpeGatVyidGkylGkTPvtlsleaGnyslrv 40 
                                       t++S+ +G tV++dG+++G   +   ++ G+y++ v
  gi|386002289|ref|YP_005920588.1| 181 TVSSQYKGYTVVVDGVQIGTEGTGSDVPDGRYTFNV 216
                                       89*****************66666669999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1451.22
//
Query:       gi|386002290|ref|YP_005920589.1|  [L=455]
Description: Beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   72.1   0.0    5.2e-10   39.8   0.0    2.9  3  Rhodanese    Rhodanese-like domain
    9.1e-08   32.3   4.2    2.9e-07   30.7   1.6    2.7  2  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.45     4e+03      66     106 ..     170     217 ..     159     218 .. 0.59
   2 !   29.0   0.0   1.4e-10   1.2e-06       1     106 [.     253     342 ..     253     343 .. 0.85
   3 !   39.8   0.0   5.8e-14   5.2e-10       7     106 ..     361     448 ..     355     449 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.45
                         Rhodanese  66 kktvvvycdgggraaaaaallkk....lGy..kn.vsvldGGfkawke 106
                                       ++ v+   ++g ++a aa ++ +    lG   k+  ++  GG++++ e
  gi|386002290|ref|YP_005920589.1| 170 GDGVIACPAHGAGSACAASIADRkwttLGIerKRnPKLQVGGVEEFVE 217
                                       566777777888855554433322444554334448888888888865 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.4e-10
                         Rhodanese   1 sakelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdggg 77 
                                       s++e++e  e+g   +lD+R++ ++ + h+pgA+n+            a        +l+    +++ + +++++++
  gi|386002290|ref|YP_005920589.1| 253 SPEEFEESAEDGL--VLDTRTELAFGAAHVPGALNI----------WLAGVPSFAGWFLP----YDRDILLVDETSD 313
                                       6899999999996..9********************..........55555555555555....5************ PP

                         Rhodanese  78 raaaaaallkklGykn.vsvldGGfkawke 106
                                         + a++ l++ Gy +   +l GG+ aw  
  gi|386002290|ref|YP_005920589.1| 314 L-SIATRRLRRIGYDRlAGHLAGGMVAWHM 342
                                       *.777888888*****************86 PP

  == domain 3  score: 39.8 bits;  conditional E-value: 5.8e-14
                         Rhodanese   7 ellekgkva..llDvRppeeYek.ghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraa 80 
                                       +l +++k    +lDvR ++e ++ g+I+gA  +                +lpe+++e    ++++v+++c +g r++
  gi|386002290|ref|YP_005920589.1| 361 RLDSEEKENawILDVRGDDEVKRsGRITGAHQI-------------HITKLPERIREV--PRNRPVYIFCGSGLRSM 422
                                       44433333358**********99**********.............***********9..***************** PP

                         Rhodanese  81 aaaallkklGyknvsvldGGfkawke 106
                                        aa +l++ G++++ v+ GG+ aw++
  gi|386002290|ref|YP_005920589.1| 423 VAASILRREGLEEMTVILGGLAAWSS 448
                                       **********999***********97 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.6   3.2e-11   2.9e-07       4     165 ..      11     149 ..       9     182 .. 0.80
   2 ?   -0.6   0.1      0.12   1.1e+03      75     140 ..     221     288 ..     209     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.2e-11
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       + ++sy++ +++++++iD+  + e  r +     +++++  + +++ TH   D i g  +l+ +t++ v++   ++ 
  gi|386002290|ref|YP_005920589.1|  11 LAHYSYIVGDGNEAVVIDPRRDCEVYRRM-----AEREGMGIATILETHRNEDYIIGSLELAARTGAEVFHADGHLD 82 
                                       5689***********************99.....8****************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCC..EEEECTTTSSH CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggk..vlftGDallag 155
                                       +  ++++                      +  +   +    +   t+g++ g++++ +++  g+  ++ftGDal+ag
  gi|386002290|ref|YP_005920589.1|  83 YRYGDAV---------------------EDGMRWKVGRLEIEAISTPGHTLGSMSYLLRDARGDpwIVFTGDALFAG 138
                                       **99999.....................566666677777777777777777777777775554669********** PP

                                       HCCCCCC..TT CS
                       Lactamase_B 156 etgridl.tlr 165
                                       + gr+d+  ++
  gi|386002290|ref|YP_005920589.1| 139 DLGRVDFmGMD 149
                                       *******5333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.12
                                       CEHHHHCCHCHHHHHHHHHCCHH..TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE CS
                       Lactamase_B  75 vaeeapalfmeeaddaasrkgll..lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey 140
                                       v++e p +f+e++       ++l  l+ +  ++p+++ee  ++++  + +++   g +h +g + +++
  gi|386002290|ref|YP_005920589.1| 221 VELEMPPYFREMERLNLAGAPHLatLPDPATISPEEFEESAEDGLVLDTRTELAFGAAHVPGALNIWL 288
                                       44444444444444444433333777777788888888888888888888888888888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2731.97
//
Query:       gi|386002291|ref|YP_005920590.1|  [L=135]
Description: hypothetical protein Mhar_1607 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 839.30
//
Query:       gi|386002292|ref|YP_005920591.1|  [L=217]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-22   79.6   0.7    1.4e-11   45.1   0.0    2.3  2  ABC_tran         ABC transporter
    1.8e-06   28.0   1.8    5.9e-05   23.0   0.3    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.4e-05   23.0   2.3       0.01   15.3   0.2    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
    5.8e-05   23.0   0.1    0.00076   19.3   0.0    1.9  2  AAA_15           AAA ATPase domain
    7.2e-05   23.4   0.1    9.2e-05   23.0   0.1    1.4  1  AAA_23           AAA domain
    0.00028   20.6   0.1    0.00049   19.8   0.1    1.3  1  AAA_29           P-loop containing region of AAA domain
    0.00039   20.8   0.0     0.0006   20.2   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0024   17.9   0.1        1.8    8.5   0.1    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0034   17.1   0.1     0.0045   16.7   0.1    1.4  1  AAA_30           AAA domain
     0.0047   17.1   0.0     0.0099   16.0   0.0    1.7  1  AAA_33           AAA domain
     0.0066   16.4   0.2      0.073   13.0   0.0    2.1  2  NACHT            NACHT domain
     0.0091   16.3   0.7      0.028   14.7   0.7    1.7  1  AAA_22           AAA domain
     0.0093   16.4   0.0      0.019   15.4   0.0    1.5  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   15.2   0.3       0.93    8.9   0.1    2.1  2  TniB             Bacterial TniB protein
      0.012   14.8   0.5      0.024   13.8   0.5    1.6  1  NB-ARC           NB-ARC domain
      0.021   13.6   0.1        2.9    6.6   0.0    2.2  2  ABC_ATPase       Predicted ATPase of the ABC class
      0.022   14.8   0.1      0.054   13.5   0.1    1.7  1  AAA_14           AAA domain
      0.023   14.6   0.0      0.031   14.2   0.0    1.2  1  Rad17            Rad17 P-loop domain
      0.046   13.6   0.1      0.067   13.1   0.1    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
      0.059   13.3   0.3       0.16   11.9   0.1    1.7  2  NTPase_1         NTPase
      0.065   13.1   0.1       0.13   12.2   0.1    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.069   12.7   0.0       0.12   12.0   0.0    1.3  1  AAA_27           AAA domain
      0.074   12.6   0.1       0.16   11.6   0.1    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.079   12.6   0.1        0.2   11.3   0.0    1.7  2  SRP54            SRP54-type protein, GTPase domain
       0.09   12.5   0.1       0.18   11.6   0.0    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
        0.1   12.3   0.0       0.14   11.8   0.0    1.2  1  AAA_24           AAA domain
       0.11   11.4   0.0       0.13   11.2   0.0    1.2  1  AAA_PrkA         PrkA AAA domain
       0.14   12.5   0.4       0.26   11.6   0.4    1.7  1  AAA_19           AAA domain
       0.15   11.5   0.0        0.3   10.4   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.16   10.5   0.1       0.25    9.9   0.0    1.3  2  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.17   11.9   0.0       0.32   11.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.2   3.6e-11   2.1e-08       4      53 ..      22      70 ..      20      74 .. 0.89
   2 !   45.1   0.0   2.4e-14   1.4e-11      81     137 .]      67     122 ..      66     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3.6e-11
                                      EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqe 53
                                      +s+ +  +e++ ivG+nG+GK+tL+k + + lkp eG illdg  +++++
  gi|386002292|ref|YP_005920591.1| 22 LSFVVGDSEVLSIVGPNGSGKTTLIKGIDRILKP-EGAILLDGGRVSDED 70
                                      7899999**************************8.9******88877755 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 2.4e-14
                                       HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       sde+i+k+++ ++l ++++  + ++ s+LSgG kqr+ +aral+++p++lllDEpt+
  gi|386002292|ref|YP_005920591.1|  67 SDEDIDKVVEMMKLLHVEEFAL-KDFSELSGGDKQRILIARALCQEPEILLLDEPTS 122
                                       5788999*********877777.788*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3     1e-07   5.9e-05       4      23 ..      34      53 ..      31      74 .. 0.80
   2 ?    4.6   0.1     0.042        24     234     269 ..      91     123 ..      66     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1e-07
                            AAA_21  4 liGpNgsGKSnLLdaldlla 23
                                      ++GpNgsGK++L++ +d + 
  gi|386002292|ref|YP_005920591.1| 34 IVGPNGSGKTTLIKGIDRIL 53
                                      9***************8874 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEng 269
                                       ++elS G k+   l++  l + +   +ll+DEp ++
  gi|386002292|ref|YP_005920591.1|  91 FSELSGGDKQR-ILIARALCQEP--EILLLDEPTSN 123
                                       66777787777.66666665555..9*******985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.8e-05      0.01      24      44 ..      29      49 ..      22      56 .. 0.85
   2 !    8.0   0.1    0.0029       1.7     111     190 ..      59     143 ..      49     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                      +++ +ivGpNGSGK+ l+  i
  gi|386002292|ref|YP_005920591.1| 29 SEVLSIVGPNGSGKTTLIKGI 49
                                      56789************9988 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0029
                                       EEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 111 ykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                       + ++g +v+ +++ +++e++++            +LSgG+k+     +l+A   ++   + llDe  ++ D k+  k
  gi|386002292|ref|YP_005920591.1|  59 ILLDGGRVSDEDIDKVVEMMKLLHVeefalkdfsELSGGDKQ----RILIARALCQEPEILLLDEPTSNQDVKHQLK 131
                                       6788999999999999988888776688888999******98....566677778888999**************** PP

                                       HHHHHHHHCTTS CS
                                       xxxxxxxxxxxx RF
                             SMC_N 179 vaellkekskna 190
                                       v e +++  k++
  gi|386002292|ref|YP_005920591.1| 132 VMETVRSLVKKT 143
                                       *99999887765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-06   0.00076      24      77 ..      30      78 ..      21     107 .. 0.74
   2 ?    1.8   0.0      0.27   1.6e+02     323     355 ..     111     143 ..     100     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                            AAA_15 24 eltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdi 77
                                      e+  ++G+N+sGK+++++ +d +l+ +      +i ++   +++++ ++   ++
  gi|386002292|ref|YP_005920591.1| 30 EVLSIVGPNGSGKTTLIKGIDRILKPE-----GAILLDGGRVSDEDIDKVVEMM 78
                                      4889*******************9966.....5555555555555555554444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.27
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandn 355
                                       ++ ill++EP  ++  ++q  ++++ ++l++++
  gi|386002292|ref|YP_005920591.1| 111 EPEILLLDEPTSNQDVKHQLKVMETVRSLVKKT 143
                                       578***************************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   1.6e-07   9.2e-05      14      42 ..      21      52 ..      12     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-07
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAikla 42
                                      e+ F   ++ +  I+GpNG+GKTT++  i  +
  gi|386002292|ref|YP_005920591.1| 21 ELSFvvgDSEVLSIVGPNGSGKTTLIKGIDRI 52
                                      5666777788899*************999765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   8.4e-07   0.00049      23      50 ..      30      57 ..      21      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.4e-07
                            AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++  ++Gp+GsGK+Tl+  i  +L p+ 
  gi|386002292|ref|YP_005920591.1| 30 EVLSIVGPNGSGKTTLIKGIDRILKPEG 57
                                      46789****************9999975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     1e-06    0.0006      22      63 ..      27      68 ..      22     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      g++e++ ++G+ G+GK++l++ + r l+ +g+i+l g  ++ 
  gi|386002292|ref|YP_005920591.1| 27 GDSEVLSIVGPNGSGKTTLIKGIDRILKPEGAILLDGGRVSD 68
                                      567899******************999999988887766655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0032       1.8       4      24 ..      34      54 ..      32      90 .. 0.85
   2 !    7.3   0.0    0.0074       4.3      19      58 ..     104     143 ..      95     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                                      EE--SSSSHHHHHHHGGGGBS CS
                             AAA_5  4 LvGppGtgKselaerlaaaln 24
                                      +vGp G+gK++l++ + + l+
  gi|386002292|ref|YP_005920591.1| 34 IVGPNGSGKTTLIKGIDRILK 54
                                      79***********99988875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0074
                                       GGGGBS--EEEEE--TT--HHHHH--B--.........-- CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvdsp 58 
                                       +a+al++e e+ +l + t+ +d+k ++++++  +slv++ 
  gi|386002292|ref|YP_005920591.1| 104 IARALCQEPEILLLDEPTSNQDVKHQLKVMETVRSLVKKT 143
                                       799**************************88888777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   7.8e-06    0.0045      18      46 ..      29      57 ..      22     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.8e-06
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaag 46
                                        v  ++Gp G+GKtt++k++ ++++ +g
  gi|386002292|ref|YP_005920591.1| 29 SEVLSIVGPNGSGKTTLIKGIDRILKPEG 57
                                      358899*****************999887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05    0.0099       2      29 ..      32      62 ..      31     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                            AAA_33  2 vllvGlpGsGKstlaerl...lkklgavlls 29
                                      + +vG++GsGK+tl++++   lk++ga+ll+
  gi|386002292|ref|YP_005920591.1| 32 LSIVGPNGSGKTTLIKGIdriLKPEGAILLD 62
                                      6689**********99876668888888887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00013     0.073       2      23 ..      31      52 ..      30      59 .. 0.84
   2 ?    1.4   0.0      0.46   2.6e+02     112     155 ..     103     144 ..      69     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                      ++ + G++GsGKTtL++++ + 
  gi|386002292|ref|YP_005920591.1| 31 VLSIVGPNGSGKTTLIKGIDRI 52
                                      67799***********999665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.46
                                       HHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHH CS
                             NACHT 112 lirkkllpeasllltvrpralrdleeqleeaivlevegfsesrr 155
                                       li ++l++e  +ll   p++ +d+++ql+      v++++++ r
  gi|386002292|ref|YP_005920591.1| 103 LIARALCQEPEILLLDEPTSNQDVKHQLKVM--ETVRSLVKKTR 144
                                       8999999999999999999999999999766..55666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7   4.9e-05     0.028       7     124 ..      31     146 ..      27     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseell.ea 81 
                                       +l ++G+ G+GKTtl++ + + l+        + + ++ +    + +  d   e+ + l++e  a  ++ +el    
  gi|386002292|ref|YP_005920591.1|  31 VLSIVGPNGSGKTTLIKGIDRILK--------PEGAILLDGGRVSdEDIDKVVEMMKLLHVEEFA-LKDFSELSgGD 98 
                                       689**************9999994........444445444444422222244444455555555.77888888788 PP

                            AAA_22  82 leqalrarav...ielliiDEaqhlr....seealeeLrsllnlsrkgvq 124
                                        ++ l ara    +e+l++DE         + +++e++rsl++  ++ ++
  gi|386002292|ref|YP_005920591.1|  99 KQRILIARALcqePEILLLDEPTSNQdvkhQLKVMETVRSLVK--KTRIS 146
                                       8888888877888888888886654324344777777777777..66665 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 !   15.4   0.0   3.3e-05     0.019       3      66 ..      34     119 ..      32     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
                                       EESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCSSS......................STTHHHHHHHHHHHHHHHT CS
                               AAA   3 lyGppGtGKTllakavakelgve.fleisgsellsk......................yvgesekkirelfkeakek 56 
                                       ++Gp G GKT+l+k + + l+ e  + ++g ++ ++                          + +k r l+++a  +
  gi|386002292|ref|YP_005920591.1|  34 IVGPNGSGKTTLIKGIDRILKPEgAILLDGGRVSDEdidkvvemmkllhveefalkdfSELSGGDKQRILIARALCQ 110
                                       79*****************9755434444444443334444444444444445555444455666777777776666 PP

                                       STSEEEEEET CS
                               AAA  57 akpsilfiDE 66 
                                       + p il++DE
  gi|386002292|ref|YP_005920591.1| 111 E-PEILLLDE 119
                                       5.89999998 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.037        21      38      54 ..      32      48 ..      27      58 .. 0.85
   2 ?    8.9   0.1    0.0016      0.93     119     159 ..     111     149 ..      92     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                              TniB 38 lllvGdsnnGKtmivek 54
                                      l +vG+   GKt++++ 
  gi|386002292|ref|YP_005920591.1| 32 LSIVGPNGSGKTTLIKG 48
                                      789***********985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                              TniB 119 kvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       ++++L++DE  +     +++q +++++++sL  + +i+ v+
  gi|386002292|ref|YP_005920591.1| 111 EPEILLLDEPTSNQ--DVKHQLKVMETVRSLVKKTRISAVM 149
                                       6789*****88766..999*******************985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   4.1e-05     0.024      17      41 ..      28      50 ..      23     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                      +++  v+++vG  G+GKttl+k i 
  gi|386002292|ref|YP_005920591.1| 28 DSE--VLSIVGPNGSGKTTLIKGID 50
                                      445..9**************99885 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.005       2.9     246     266 ..      31      51 ..      27      55 .. 0.90
   2 ?    5.2   0.0     0.013       7.5     322     372 ..      93     143 ..      61     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.005
                                       EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 246 vtlIvGggfhGKsTLLeAlek 266
                                       v  IvG++  GK+TL++ +++
  gi|386002292|ref|YP_005920591.1|  31 VLSIVGPNGSGKTTLIKGIDR 51 
                                       789**************9975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG-- CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekep 372
                                       + SG   q   i++al  + ++lL+DE ts +   ++ + m+ + s  k++
  gi|386002292|ref|YP_005920591.1|  93 ELSGGDKQRILIARALCQEPEILLLDEPTSNQDVKHQLKVMETVRSLVKKT 143
                                       45899999999*******************999888777777665555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.4e-05     0.054       3      84 ..      30     131 ..      28     145 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe......kllelileklke........... 62 
                                       ++l i+G+  +GKTtl+k +  + l k+e  + ++  + +d+++++        +++e+ l+ ++e           
  gi|386002292|ref|YP_005920591.1|  30 EVLSIVGPNGSGKTTLIKGID-RIL-KPEGAILLDGGRVSDEDIDKVVemmkllHVEEFALKDFSElsggdkqrili 104
                                       7899************98874.444.688888888777666444432211222222222222222244455556666 PP

                            AAA_14  63 .....ekktylflDEiqevpewekalk 84 
                                            ++ ++l+lDE    +++++ lk
  gi|386002292|ref|YP_005920591.1| 105 aralcQEPEILLLDEPTSNQDVKHQLK 131
                                       666666788888888777777766666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.4e-05     0.031      46     170 ..      30     149 ..      17     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkeleLkdakylk 121
                                       ++L i GP G gk+t +k + ++l ++    l++  + + d  ++ ++  l+++e+     ++ f+el   d +   
  gi|386002292|ref|YP_005920591.1|  30 EVLSIVGPNGSGKTTLIKGIDRILKPEGAILLDGGRVSDEDIdKVVEMMKLLHVEE---FALKDFSELSGGDKQRIL 103
                                       5899*********************9999999999988888778888888888888...457789998544444433 PP

                             Rad17 122 lqklGddlrtdkklilvedlP.nkfyrdsdalrevirkylrssealplil 170
                                       +      l  + +++l+++   n+  +   ++ e +r  ++ ++  + ++
  gi|386002292|ref|YP_005920591.1| 104 I---ARALCQEPEILLLDEPTsNQDVKHQLKVMETVRSLVKKTRI-SAVM 149
                                       3...46666777777777744344444445555666666666665.5555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.067      20      44 ..      29      53 ..      23     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl 44
                                      +e++ i Gp gsGKt+L+k i   l
  gi|386002292|ref|YP_005920591.1| 29 SEVLSIVGPNGSGKTTLIKGIDRIL 53
                                      67899*************9876555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00028      0.16       3      28 ..      33      58 ..      31      67 .. 0.88
   2 ?   -1.4   0.0       3.3   1.9e+03     113     155 ..     131     175 ..     103     188 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                      EEE--TTSSHHHHHHHHHHHH...GG CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgv 28
                                       i Gp G+GKtTl+k + + lk +g 
  gi|386002292|ref|YP_005920591.1| 33 SIVGPNGSGKTTLIKGIDRILKPEGA 58
                                      588***************99998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
                          NTPase_1 113 kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfev 155
                                       k+ e+v+ ++k +    ++ ih  +   +  +++   k++kv+ +
  gi|386002292|ref|YP_005920591.1| 131 KVMETVRSLVKkTRISAVMGIHDLNpGARYSDSLVMLKEGKVYAI 175
                                       445566666665555566666666554555566666666666654 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00022      0.13       1      27 [.      31      57 ..      31      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                              MobB  1 vlgivgksgsGKTtLleklipelkarg 27
                                      vl+ivg +gsGKTtL++ + ++lk +g
  gi|386002292|ref|YP_005920591.1| 31 VLSIVGPNGSGKTTLIKGIDRILKPEG 57
                                      799*************99888777666 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.12      17      49 ..      20      52 ..       5      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       +l+f  +++++  i+GpN +GK+t++++i ++
  gi|386002292|ref|YP_005920591.1| 20 VELSFVVGDSEVLSIVGPNGSGKTTLIKGIDRI 52
                                      57899999999999**************99876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00027      0.16       2      19 ..      31      48 ..      30      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                      EEEEEESTTCCHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnh 19
                                      v+ ++G+ GsGKTtL++ 
  gi|386002292|ref|YP_005920591.1| 31 VLSIVGPNGSGKTTLIKG 48
                                      6789***********985 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035       0.2       3      28 ..      31      56 ..      29      61 .. 0.81
   2 ?   -2.3   0.0       4.9   2.8e+03      85     114 ..     113     142 ..      99     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                      v+ +vG++G+GKTt +  + ++lk e
  gi|386002292|ref|YP_005920591.1| 31 VLSIVGPNGSGKTTLIKGIDRILKPE 56
                                      7789**********998887777665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                                       SEEEEEE--SSTTHHHHHHHHHHHHHHHSS CS
                             SRP54  85 dvvlvDTaGrlqndkelmeelkkikkvvkp 114
                                       +++l+D    +q  k+ ++ ++++++ vk+
  gi|386002292|ref|YP_005920591.1| 113 EILLLDEPTSNQDVKHQLKVMETVRSLVKK 142
                                       444555444455555555555555555554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.18       1      23 [.      34      56 ..      34      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                      +vGp GsGKtt+++ +  il+ +
  gi|386002292|ref|YP_005920591.1| 34 IVGPNGSGKTTLIKGIDRILKPE 56
                                      79************999988765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.14       6      23 ..      33      54 ..      29     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            AAA_24  6 liyGpsgiGKTtlakel....g 23
                                       i+Gp+g+GKTtl+k +    +
  gi|386002292|ref|YP_005920591.1| 33 SIVGPNGSGKTTLIKGIdrilK 54
                                      699************9944442 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.13      89     148 ..      30      89 ..      26     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                          AAA_PrkA  89 qilyllGPvggGksslverlkklleaapiyalegsPvfeePlhlipeelrkkleeeygir 148
                                       ++l ++GP g+Gk++l++ + ++l+ +    l+g  v +e +  + e ++    ee+ ++
  gi|386002292|ref|YP_005920591.1|  30 EVLSIVGPNGSGKTTLIKGIDRILKPEGAILLDGGRVSDEDIDKVVEMMKLLHVEEFALK 89 
                                       6999*********************99999999999999988888777777767777665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00044      0.26      10      38 ..      29      57 ..      24     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                      ++vl ++++ G+GKT+++k+i ++l+ +g
  gi|386002292|ref|YP_005920591.1| 29 SEVLSIVGPNGSGKTTLIKGIDRILKPEG 57
                                      67899**************9988887665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00052       0.3      25      48 ..      32      55 ..      21      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpp 48
                                      l +vGp GsGKt l+k +  +l p
  gi|386002292|ref|YP_005920591.1| 32 LSIVGPNGSGKTTLIKGIDRILKP 55
                                      4589***************99976 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00043      0.25     447     503 ..      43     104 ..      28     107 .. 0.72
   2 ?   -3.9   0.0       6.4   3.7e+03     465     486 ..     126     147 ..     119     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                   Methyltransf_29 447 edillemdRilRPeGavii...rdkvevlekvkkllkalkWevkltekeeeske..kekilv 503
                                       ++++  +dRil+PeGa+++   r + e ++kv +++k l+ e+ + ++ +e +   k++il+
  gi|386002292|ref|YP_005920591.1|  43 TTLIKGIDRILKPEGAILLdggRVSDEDIDKVVEMMKLLHVEEFALKDFSELSGgdKQRILI 104
                                       5667789**********995556678899999999999998876665533333212555665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.4
                   Methyltransf_29 465 irdkvevlekvkkllkalkWev 486
                                       ++ + +v+e+v++l+k+ + ++
  gi|386002292|ref|YP_005920591.1| 126 VKHQLKVMETVRSLVKKTRISA 147
                                       5566677777777777666554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00056      0.32      19      43 ..      29      53 ..      16      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00056
                                      TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakal 43
                                      ++v+ + G+ G+GKTtl++g+ + l
  gi|386002292|ref|YP_005920591.1| 29 SEVLSIVGPNGSGKTTLIKGIDRIL 53
                                      5678999*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1432.16
//
Query:       gi|386002293|ref|YP_005920592.1|  [L=201]
Description: type 12 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-13   48.8   0.0    1.2e-12   48.3   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    7.5e-11   42.6   0.0      1e-10   42.1   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    2.1e-07   31.6   0.0      3e-07   31.1   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    3.3e-07   30.3   0.0    4.5e-07   29.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00064   19.5   0.0    0.00076   19.3   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    0.00098   18.5   0.0     0.0012   18.2   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.043   13.4   0.0    1.3  1  Methyltransf_28  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   4.8e-16   1.2e-12       2      94 ..       2     100 ..       1     102 [. 0.94

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 4.8e-16
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC..T.SS-TT-EEEEEEES-C CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaek..l.pfednsfDlvvssevl 71 
                                       +vG G+G +ae  a+rg  +r++ vD+s++m +l+k++ ++++   ++ f++a++ +  l  ++d+++D +++ +++
  gi|386002293|ref|YP_005920592.1|   2 EVGPGKGEFAESGARRGslSRYYIVDMSERMQDLVKARLENADTstELVFIHAELDRdpLsEIPDGTIDKIIMINAF 78 
                                       89***************************************999998899999999767667*************** PP

                                       CC-CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgGll 94 
                                       + + +p++al e++R+LkpgGl+
  gi|386002293|ref|YP_005920592.1|  79 QDI-NPKHALWEFRRILKPGGLF 100
                                       ***.6****************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   4.1e-14     1e-10       3      97 .]       2      98 ..       1      98 [. 0.88

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.1e-14
                                      EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS...SSTTTEEEEEEESTGGG CS
                   Methyltransf_25  3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp...fedgsfDlvvssgalhh 76
                                      ++G G+G++++  a+r++ ++++ vD+se+m + +++r+e+++   ++ f+++++++ p    +dg++D +++++a++ 
  gi|386002293|ref|YP_005920592.1|  2 EVGPGKGEFAESGARRGSLSRYYIVDMSERMQDLVKARLENADTstELVFIHAELDRDPlseIPDGTIDKIIMINAFQD 80
                                      89**************769********************99777679999*****77552235**********988777 PP

                                      SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25 77 lsdedlekalkeiarvLkpgG 97
                                      ++    ++al e++r+LkpgG
  gi|386002293|ref|YP_005920592.1| 81 IN---PKHALWEFRRILKPGG 98
                                      66...5689***********9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.2e-10     3e-07       1      99 []       1     100 [.       1     100 [. 0.77

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.2e-10
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakren..nnnnnvelealdlldldgg...ssfDlvva 72 
                                       +e+G G G++++  +++ + ++y+ vD s+++ +  k++l   +   + +      ++d l+   +   ++ D +++
  gi|386002293|ref|YP_005920592.1|   1 MEVGPGKGEFAESGARRGSLSRYYIVDMSERMQDLVKARLENADTstELVFIHAELDRDPLS---EipdGTIDKIIM 74 
                                       69******************************955555555555400333333333333333...2567******** PP

                   Methyltransf_12  73 snvlhhlkdirevldnirklLkpgGrl 99 
                                       +n+++ + +++ +l ++r+ LkpgG +
  gi|386002293|ref|YP_005920592.1|  75 INAFQDI-NPKHALWEFRRILKPGGLF 100
                                       ******9.9999*************75 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.7e-10   4.5e-07      27     134 ..       1     119 [.       1     140 [. 0.80

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.7e-10
                   Methyltransf_23  27 LdiGcGtGillevlrengf..svtgvDlspeaveiae....kakkaqkdqfdeqeaae..........pqgkfdlIv 87 
                                       +++G+G+G+++e+ +++g    ++ vD+s++++++++    +a+++    f                 p+g++d I+
  gi|386002293|ref|YP_005920592.1|   1 MEVGPGKGEFAESGARRGSlsRYYIVDMSERMQDLVKarleNADTSTELVFIH----AeldrdplseiPDGTIDKII 73 
                                       79************99998889*************987777444444444422....13334667777999****** PP

                   Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwl 134
                                       +++ +  + +p ++l  ++++lkpgG++   + ++s  e+ +++d l
  gi|386002293|ref|YP_005920592.1|  74 MINAFQDI-NPKHALWEFRRILKPGGLFRANVTDRSVREETAADDDL 119
                                       *9999998.56999**************9999999987777776655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     3e-07   0.00076       9     128 ..       2     115 ..       1     152 [. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3e-07
                   Methyltransf_31   9 DlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieelekl.ledekfDlilsnev 83 
                                       ++G G+Ge++   a + g+ ++++ +D+se++  l ++++++   + ++ F +++    + + + d ++D i+  ++
  gi|386002293|ref|YP_005920592.1|   2 EVGPGKGEFAESGA-RRGSLSRYYIVDMSERMQDLVKARLENADTStELVFIHAELDRDPLSeIPDGTIDKIIMINA 77 
                                       7899********99.88999************999999999988777*********99888889**********999 PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggilliedprllaelpakveeeska 128
                                       ++++ +p+ +l e  r lkpgg + ++  +      ++v+ee  a
  gi|386002293|ref|YP_005920592.1|  78 FQDI-NPKHALWEFRRILKPGGLFRANVTD------RSVREETAA 115
                                       9776.68899999************99888......444444443 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.9e-07    0.0012      74     150 ..      22     101 ..       2     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.9e-07
                                       EEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-T...TS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEE CS
                   Ubie_methyltran  74 kvvvlDinenmLkvgekklkeegki.nieflqanaeeLp...feddsfDvvtvsfGlrnvtDklkaLkeayrvlkpG 146
                                       +  ++D++e m +  +++l++  ++ ++ f++a+  + p     d++ D + +   ++++   ++aL e +r+lkpG
  gi|386002293|ref|YP_005920592.1|  22 RYYIVDMSERMQDLVKARLENADTStELVFIHAELDRDPlseIPDGTIDKIIMINAFQDINP-KHALWEFRRILKPG 97 
                                       6689****************9887769******987755111467999*9988666665543.579*********** PP

                                       EEEE CS
                   Ubie_methyltran 147 Grlv 150
                                       G + 
  gi|386002293|ref|YP_005920592.1|  98 GLFR 101
                                       *875 PP

>> Methyltransf_28  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.043      23     121 ..       1      88 [.       1     172 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                   Methyltransf_28  23 iElGpGkGtLmadvLrtlrkflpefyealeyhlvEaSpqlrerQknrLkekakevkk.estvkslgvkveWleelke 98 
                                       +E+GpGkG+++++  r             +y++v++S+++++  k+rL++++ +++   ++++ + ++   l+e+++
  gi|386002293|ref|YP_005920592.1|   1 MEVGPGKGEFAESGARRGSLS--------RYYIVDMSERMQDLVKARLENADTSTELvFIHAELDRDP---LSEIPD 66 
                                       59*********9988888877........9*******************9875554443333333332...444444 PP

                   Methyltransf_28  99 ipeetgfilanEffDaLPihqfe 121
                                             +i+ n f D  P h+++
  gi|386002293|ref|YP_005920592.1|  67 G-TIDKIIMINAFQDINPKHALW 88 
                                       4.477788888888877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1390.59
//
Query:       gi|386002294|ref|YP_005920593.1|  [L=396]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-20   72.0   0.0    8.7e-20   71.3   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   4.9e-24   8.7e-20      10     234 ..      98     331 ..      91     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 4.9e-24
                                       HHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG........GGGHHH..H CS
                      Peripla_BP_2  10 eillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl.....gltdedeel..l 79 
                                       e+l  l ++  +v ++  ts+++ +  + ++i+++g+ +++d E+++++ PDl+i+ +g      g + e +++  +
  gi|386002294|ref|YP_005920593.1|  98 ETLRTLQVPLDLVVIADHTSGHYSYFSDFSDIPSLGHFHDPDAEAIVQANPDLLIVHPGSgggrfGAFYEPFMEkmE 174
                                       566666677777777777888888877777***************************99999666555554433114 PP

                                       HHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-T CS
                      Peripla_BP_2  80 ksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvags 156
                                         gi +     s   + + e+++ lg l+++e+ea k+  ++++ l  +++++ ++++++ + ++   +    + +s
  gi|386002294|ref|YP_005920593.1| 175 GTGITVACLACSRP-DIYSEEVEKLGVLFEREEEAAKFLDFYEGVLGTVEERTGNLTEEERPKVYCESD---RYKTS 247
                                       45555555555555.*****************************************8888886666666...58888 PP

                                       TSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..........HHHT-S--HHHHT-SHHHHTS CS
                      Peripla_BP_2 157 nsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr..........aeadnktgleflkenpllael 223
                                       +++i ++   +g++ i++    ++ +ei++E++++++pdvi+   +          ++a++ ++ ++++ + +la++
  gi|386002294|ref|YP_005920593.1| 248 DNNIDPIEM-AGGRFIFDL---GQTAEIDPEAVVSANPDVIIRLLSeedpdekmaeDTANAEAIIQEIMDRQELANV 320
                                       888877655.99****665...7****************************************************** PP

                                       HHHHTT-EEEE CS
                      Peripla_BP_2 224 pAvkngrVyal 234
                                       +Avkng Vy +
  gi|386002294|ref|YP_005920593.1| 321 NAVKNGEVYLV 331
                                       *********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2597.13
//
Query:       gi|386002295|ref|YP_005920594.1|  [L=1258]
Description: Cobaltochelatase CobN subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
          0 1093.7   0.0          0 1093.5   0.0    1.0  1  CobN-Mg_chel     CobN/Magnesium Chelatase
    5.5e-05   23.3   0.0    0.00012   22.2   0.0    1.5  1  DUF3479          Domain of unknown function (DUF3479)


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1093.5   0.0         0         0       2    1088 ..     157    1236 ..     156    1237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1093.5 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Y+++gg+eN++nll    ++ lg + +++++p+e+p+ giyhp +   f++l+e+le   +  +e++pt+g lf
  gi|386002295|ref|YP_005920594.1|  157 RYWRYGGKENYRNLLLHFLNEHLGCDLPKAKDPQEFPKYGIYHPVY-GSFDDLDEFLES--SGFSEDRPTIGYLF 228 
                                        8****************9999999899999*************986.689999999988..68************ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpaeeee 151 
                                        y + ++++  + ++al ++l +  +n +pv++++   ++ +a++++f k+g++ +dal+n+t f+l++gp ++++
  gi|386002295|ref|YP_005920594.1|  229 YGNMHFDQCQSTLKALAEKLGD--VNLVPVYSDG--IHNLRAMRKFFFKDGRSIIDALVNLTWFRLNGGPLGGNH 299 
                                        ********************98..6889999999..89999*****************************88777 PP

                                        xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                      CobN-Mg_chel  152 eeaeeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeee.eeteveky 224 
                                        +  +++ lk lnvPv+++ +++s+++e+W es++Glsp ++ m v++pEldG+iep++  + ++ +  e +++++
  gi|386002295|ref|YP_005920594.1|  300 Q-LTRDLLKDLNVPVFTPaPMYSREVEKWMESPTGLSPPEVIMAVIWPELDGCIEPIPACGVQSFKvGELDAQDV 373 
                                        6.566778***************************************************998854559999**** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  225 epipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpe 299 
                                         pi++r++r+a+++++w rLr++pn+ek+vai+++nyppge++lg a++Ldv++S+ +lL++++eeGY+v+  pe
  gi|386002295|ref|YP_005920594.1|  374 IPIDDRISRIAARIRNWNRLRKMPNDEKRVAIVVYNYPPGEANLGRASYLDVFKSVRRLLERMAEEGYRVDL-PE 447 
                                        **********************************************************************76.86 PP

                                        xxxxxx.xx..xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  300 sgdeLi.el..lleggtndpew..eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgek 369 
                                        +  +L+ +   ++++     +w  ++   +++ +++ae Y+++f++Lpee+ ++++e Wgeppg    + ++ ++
  gi|386002295|ref|YP_005920594.1|  448 KDLHLLfQDfsIVNS----GTWfsKDETLKSCPSMKAEGYRRFFASLPEEMGSDMIESWGEPPG----KVMTLGE 514 
                                        554444132114444....446553333479*********************************....677789* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  370 klvipglqlGnvfvgvQPargyeedps..klyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKq 442 
                                        +++ipg+++Gnvfvg+QPar   +d++  +  hd++ pP+hqY+AfY Wl+ +++ad vvHvG+HG  E++ GK+
  gi|386002295|ref|YP_005920594.1|  515 EILIPGIEFGNVFVGIQPARPPLGDQDlaSATHDKTKPPHHQYVAFYEWLEMVWKADLVVHVGTHGLAEFMKGKE 589 
                                        ********************98888776689******************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  443 vglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesld 517 
                                        vg+s++c+Pd+l+g++PhlY Y v n +E ++AKRR y++i+ ++ Pp+t ++ly+e+aeL++lide+ ea+ +d
  gi|386002295|ref|YP_005920594.1|  590 VGMSSSCFPDLLIGNMPHLYFYHVVNTSEVVIAKRRLYGTIVGYNSPPYTASDLYEEYAELQDLIDEHSEAQVQD 664 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  518 perlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdl 592 
                                        p+r +++re ile+++eln++++               e ++ l+++l e+k++ i+dglh+lG  ++ + ++++
  gi|386002295|ref|YP_005920594.1|  665 PQRCERVREMILEKARELNFEAE---------------E-VDLLHDQLYEMKRRIIPDGLHVLGDKYDPDVMKQF 723 
                                        ********************532...............2.889******************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  593 vvailrleneegesltealaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeele 667 
                                        vv ilr+++ee +sl++ lae+ g+d+d   +++       ++ le+++e +++lv+ +++ ++e+++ e+  + 
  gi|386002295|ref|YP_005920594.1|  724 VVFILRYDREELKSLNRILAESEGIDYDFALKNR----VGFAKDLEQIDEWCRRLVDVAIDLSTEAAADESGLSG 794 
                                        **************************98754444....445788999*************987766555444444 PP

                                        xxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  668 eeeeeeee...............eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPtea 727 
                                        e ++e                  +   E+++++r+L  e+++ g +Gd++r+++ vLPTGrN+ ++Dp +iPt+a
  gi|386002295|ref|YP_005920594.1|  795 EGKKE--LiktlsyglrlmesysQNGGELENFVRGLGSEFVEQGDGGDVIRSPE-VLPTGRNLTQFDPTKIPTPA 866 
                                        44444..14599**********7777*************************966.******************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  728 AwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaagrvvdlelipleeLg 802 
                                        A+e+G ++ae+++++y++++g+ Pe+ g++lwg et++t+Ge+++qiL +lGv+  +       +l l+pleeLg
  gi|386002295|ref|YP_005920594.1|  867 AFERGAEIAENTVSKYMEKNGTCPETTGVILWGFETTKTGGESVGQILSYLGVKVERAPGSFAPKLSLVPLEELG 941 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxx..xxx RF
                      CobN-Mg_chel  803 RPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaelee........keeae..era 867 
                                        RPRiD +v+i+GffRD+fpn++elld+a++lva ldEp ++N+vrkh+ e+ ++l++         +e++  ++a
  gi|386002295|ref|YP_005920594.1|  942 RPRIDCLVNICGFFRDMFPNVVELLDQAFNLVAGLDEPLDMNYVRKHSIENLERLKSgeddggsnLDEKTliRMA 1016
                                        *******************************************************99988776542244479*** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  868 tyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsreh 942 
                                        + R+Fg+++G+Yg+ +  l+e+s W++e++Lae+Y++++s+ Y k+ +++++e++++++L+rvd+v q +d++  
  gi|386002295|ref|YP_005920594.1| 1017 NGRIFGPRAGEYGTRMLPLVEDSIWKTEDELAEVYIQSMSHLYAKNLHAVKSEAVYRSNLARVDLVSQVRDTHDR 1091
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  943 dlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGaf 1017
                                        +++d+d+y++++GGl++avr+++g++pe++++d+ + e++++++++++++r +r+r+lNPkWi+gm +h+++Ga+
  gi|386002295|ref|YP_005920594.1| 1092 EIVDLDHYFEYFGGLSNAVRTARGERPEMLISDT-TGEAIQTEDVRDAVTRGVRTRLLNPKWIDGMLKHDFHGAQ 1165
                                        **********************************.789************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1018 elaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                        ++a++++n++g  at++ vd+w++ ++a++Y++D+evre+l e+N  A  eiaerL Ea++rg+W+asee+
  gi|386002295|ref|YP_005920594.1| 1166 QVAERLENVLGLAATTHSVDNWIWSSIADRYIFDDEVRERLLENNRFAAVEIAERLFEAEKRGYWDASEEE 1236
                                        ********************************************************************997 PP

>> DUF3479  Domain of unknown function (DUF3479)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.4e-08   0.00012      12     128 ..      11     131 ..       3     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                           DUF3479  12 asalkraaaelnrelp.elelsvfadeelrekpealeelaaavaeAdifiasllfdedqvealrealeaarekldav 87 
                                       a+ l+ aa+e+++e+  +l+l+++  + ++e++ +   l++++++ d++++ +       e + +al+ +++   +v
  gi|386002295|ref|YP_005920594.1|  11 AKSLALAAQEIQAEFRlDLDLKIYYPRTIDEEEVDEVLLREDLKRSDAVFVDIRGEGHASEVVYNALKDEKN---IV 84 
                                       5678889*************************8888889************976666666777888888555...55 PP

                           DUF3479  88 lvfeS.apelmrltkvGsFsmak.ge....gspsavkallkklksgk 128
                                       + + S  + +mr+t++GsFs ++  +    g+ + ++++ kk+++ +
  gi|386002295|ref|YP_005920594.1|  85 VNLSSpFSRMMRITRLGSFSGSRlADrinpGEVRDPEEVWKKIQRAE 131
                                       555552358**********9887733455677777777777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 7793.72
//
Query:       gi|386002296|ref|YP_005920595.1|  [L=398]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-23   81.1   0.0    1.3e-22   80.5   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   7.3e-27   1.3e-22       3     234 ..      94     332 ..      93     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 7.3e-27
                                       E-SHHHHHHHHHTT-GG.GEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG.......GG CS
                      Peripla_BP_2   3 slspsvteillalGatd.kvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl....gltde 74 
                                       +++p + e+l  + +++  +vgv    ++ +   + + + +++g+  e+d+E+++al PD+vi+ +g     g  + 
  gi|386002296|ref|YP_005920595.1|  94 CTTPQQLETLRSIKVPKeTIVGVPQDMERYSYLSEFA-DLPSIGHFYEFDLETILALEPDVVIVHPGPgpsgGFDEL 169
                                       5555556666555433202444444333333333333.99****************************999888888 PP

                                       GHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..E CS
                      Peripla_BP_2  75 deellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggy 151
                                        ++l++sg  ++ ++ +   e + e ++ lg l+++  ea+++  ++++ l ++++ ++++ +++ ++++  ++   
  gi|386002296|ref|YP_005920595.1| 170 LSKLDASGLTVFRFRCNVP-ETYSEDVEKLGILFERGTEAREFLDFYEGVLGSVEDEVSEIPEDERPMVYCEYD--- 242
                                       8999999999999999988.******************************************************... PP

                                       EEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..........HHHT-S--HHHHT-SH CS
                      Peripla_BP_2 152 vvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr..........aeadnktgleflkenp 218
                                       v+ +s s++ +++  +g+++i++    +   e+++E++ a++pdvi+   +          + ++ k+  e++++ +
  gi|386002296|ref|YP_005920595.1| 243 VYKTSPSDVYPITM-AGGRYIFEG--AGPVREVDPEAVIAANPDVIIRLVSyddfdakaagDYSRLKAAREEVMNKT 316
                                       ************99.*********..7*******************************9999999************ PP

                                       HHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 219 llaelpAvkngrVyal 234
                                       +l++++Av++ rVya+
  gi|386002296|ref|YP_005920595.1| 317 ELQGVKAVQEERVYAM 332
                                       **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2585.42
//
Query:       gi|386002297|ref|YP_005920596.1|  [L=270]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-31  109.0   0.0    6.1e-31  107.8   0.0    1.6  2  ABC_tran      ABC transporter
    7.2e-10   39.2   1.0    2.6e-05   24.2   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.9e-05   25.0   0.3    9.2e-05   22.7   0.3    1.9  1  AAA_22        AAA domain
    1.9e-05   25.1   0.0    3.6e-05   24.2   0.0    1.5  1  AAA_16        AAA ATPase domain
    4.3e-05   23.1   0.4     0.0019   17.7   0.4    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    8.6e-05   23.1   0.1    0.00012   22.6   0.1    1.3  1  AAA_23        AAA domain
    0.00022   21.1   0.1    0.00046   20.0   0.1    1.6  2  AAA_15        AAA ATPase domain
     0.0005   19.8   0.1      0.001   18.8   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0047   17.4   0.1      0.051   14.0   0.1    2.2  1  AAA           ATPase family associated with various cellular 
     0.0066   16.2   0.0       0.01   15.6   0.0    1.5  1  AAA_30        AAA domain
     0.0086   14.9   0.6        2.2    7.0   0.1    3.0  2  ABC_ATPase    Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.028   13.8   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.018   14.3   0.3      0.037   13.2   0.0    1.6  2  NB-ARC        NB-ARC domain
      0.023   14.1   0.6        1.3    8.4   0.1    2.2  2  TniB          Bacterial TniB protein
      0.033   14.2   0.1       0.59   10.1   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
      0.034   14.3   0.3       0.12   12.5   0.1    1.9  2  AAA_33        AAA domain
      0.038   13.9   0.4       0.16   11.8   0.1    2.0  2  NTPase_1      NTPase
      0.045   14.0   0.1       0.75   10.1   0.1    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.054   13.4   0.1       0.12   12.3   0.1    1.6  1  RsgA_GTPase   RsgA GTPase
      0.061   12.3   0.0        0.1   11.6   0.0    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.064   12.9   0.1       0.14   11.8   0.0    1.6  2  SRP54         SRP54-type protein, GTPase domain
      0.081   12.8   0.0       0.14   12.0   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.091   12.5   0.0       0.15   11.8   0.0    1.3  1  AAA_24        AAA domain
        0.1   12.9   0.3       0.21   11.9   0.3    1.9  1  AAA_19        AAA domain
       0.11   12.4   0.5       0.28   11.1   0.5    1.9  1  NACHT         NACHT domain
       0.13   12.1   0.1       0.26   11.2   0.1    1.5  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.13   11.8   0.1       0.27   10.8   0.1    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   11.3   0.0       0.21   10.7   0.0    1.2  1  G-alpha       G-protein alpha subunit
       0.16   12.0   0.0        0.3   11.1   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.29    9.7   0.2        2.5    6.7   0.1    1.9  2  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   0.0     1e-33   6.1e-31       1     137 []      19     166 ..      19     166 .. 0.95
   2 ?   -1.7   0.0       6.5   3.9e+03      99     120 ..     246     267 ..     206     270 .] 0.71

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 1e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                       l++++l +  +e++ +vG+nG+GK+tL+k++ + lkp +G+i ld g++l++ +++++ + ig++pq ++   ++tv
  gi|386002297|ref|YP_005920596.1|  19 LDDLNLVVGDSEVLSLVGPNGSGKTTLIKCIDRILKP-KGTIILDgGRNLQSLSRQEVARFIGYVPQSTTSSLTTTV 94 
                                       7899********************************8.99999**9**********************99999999* PP

                                       HHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++             ++e+i+++++ ++l ++++  + ++ s+LSgGqkqrv +aral+++p++lllDEpt+
  gi|386002297|ref|YP_005920596.1|  95 FDTilmgrrprmgwrVAEEDIDRVVEVMRLLHVEEFAL-KDFSELSGGQKQRVLIARALAQEPEVLLLDEPTS 166
                                       **********9999888888999999999999777777.778*****************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.5
                                       CBGESTTSGGS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  99 dtvvksspssLSgGqkqrvala 120
                                       d++     +sL gG+k+ ++  
  gi|386002297|ref|YP_005920596.1| 246 DRPYVVPIRSLNGGEKRDLSFN 267
                                       3343344588889998887765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   4.4e-08   2.6e-05       4      24 ..      34      54 ..      31      89 .. 0.81
   2 !   13.6   0.1   7.1e-05     0.042     211     273 ..     109     171 ..      87     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.4e-08
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      l+GpNgsGK++L++++d +  
  gi|386002297|ref|YP_005920596.1| 34 LVGPNGSGKTTLIKCIDRILK 54
                                      9***************99854 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.1e-05
                            AAA_21 211 svderlrer...gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                       +v+e +++r    +++l+ +     +++elS G+k+   ++ al++ +    +ll+DEp ++L+ k
  gi|386002297|ref|YP_005920596.1| 109 RVAEEDIDRvveVMRLLHVEEFALKDFSELSGGQKQRVLIARALAQEP---EVLLLDEPTSNLDVK 171
                                       4444444445557888888888888999*********55555555544...9***********974 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   1.5e-07   9.2e-05       7     131 ..      31     197 ..      27     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.........erpevv..fvtlpsstsskdllrellralglelka.. 70 
                                       +l ++G+ G+GKTtl++ + + l+    +            r ev+    ++p+st+s+   + +  +l  ++ +  
  gi|386002297|ref|YP_005920596.1|  31 VLSLVGPNGSGKTTLIKCIDRILKPKGTIILdggrnlqslSRQEVArfIGYVPQSTTSSLTTTVFDTILMGRRPRmg 107
                                       6889******************9644444448888888885555554334445555444445555555555555599 PP

                            AAA_22  71 .......................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsll 116
                                                              + ++ +el   + ++ l ara    +e+l++DE    l+   + ea+ ++rs++
  gi|386002297|ref|YP_005920596.1| 108 wrvaeedidrvvevmrllhveefALKDFSELSgGQKQRVLIARALaqePEVLLLDEPTSnLDvkhQLEAMDTVRSIV 184
                                       ***********************999999999999999999999999*********9999*99766*********** PP

                            AAA_22 117 nlsrkgvqliLvGtp 131
                                       +  ++g++ +++++ 
  gi|386002297|ref|YP_005920596.1| 185 K--KTGISAVMAIHD 197
                                       *..****99998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   6.1e-08   3.6e-05      21      64 ..      26      73 ..      13     163 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.1e-08
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql....e 64
                                       g++e++ l+G+ G+GK++l++++ r l+ +g i l g         +
  gi|386002297|ref|YP_005920596.1| 26 VGDSEVLSLVGPNGSGKTTLIKCIDRILKPKGTIILDGGRNLQslsrQ 73
                                      356699*******************99999985554443333323321 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   3.1e-06    0.0019      24     183 ..      29     180 ..       4     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk.lkiekeevs 98 
                                       +++ ++vGpNGSGK+ l+  i  +L  + +          +i    ++ +s+++ ev+ ++    ++ ++  ++ v 
  gi|386002297|ref|YP_005920596.1|  29 SEVLSLVGPNGSGKTTLIKCIDRILKPKGT----------IILDgGRNLQSLSRQEVARFIGYVPQStTSSLTTTVF 95 
                                       567899***************666653333..........2222244444555555555443322220122223333 PP

                                       EEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                        +  + r  +  +++ ++++ +  ev++ll+ +++  +   +LSgG+k+ v +a  +A    +   + llDe  ++L
  gi|386002297|ref|YP_005920596.1|  96 DTILMGRRPRMGWRVAEEDIDRvVEVMRLLHVEEFALKdfsELSGGQKQRVLIARALA----QEPEVLLLDEPTSNL 168
                                       3344445555667777777766688888888888765433378999988666655544....333456788888888 PP

                                       -HHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                             SMC_N 172 Deknvkkvaell 183
                                       D k+  +  + +
  gi|386002297|ref|YP_005920596.1| 169 DVKHQLEAMDTV 180
                                       888776655555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1     2e-07   0.00012      16      43 ..      23      53 ..       3      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2e-07
                            AAA_23 16 dF...skgltlItGpNGaGKTTildAiklaL 43
                                      ++   ++ +  ++GpNG+GKTT++ +i  +L
  gi|386002297|ref|YP_005920596.1| 23 NLvvgDSEVLSLVGPNGSGKTTLIKCIDRIL 53
                                      336677788899***************7665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   7.8e-07   0.00046      24      50 ..      29      56 ..       1      97 [. 0.82
   2 ?   -2.0   0.0       3.7   2.2e+03     322     355 ..     154     187 ..     141     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.8e-07
                            AAA_15 24 e.ltvliGkNnsGKSsilealdlFlnnk 50
                                      + +  l+G+N+sGK+++++ +d +l+ k
  gi|386002297|ref|YP_005920596.1| 29 SeVLSLVGPNGSGKTTLIKCIDRILKPK 56
                                      34899*******************9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                       +++ +ll++EP  +L  ++q + +++ +++++++
  gi|386002297|ref|YP_005920596.1| 154 QEPEVLLLDEPTSNLDVKHQLEAMDTVRSIVKKT 187
                                       5678999999999999999999999999999875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.7e-06     0.001      23      50 ..      30      57 ..      19      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                            AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++  l+Gp+GsGK+Tl+  i  +L p+ 
  gi|386002297|ref|YP_005920596.1| 30 EVLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      46789***************99999976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   8.5e-05     0.051       3      37 ..      34      69 ..      32     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.5e-05
                                      EESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCSSS CS
                               AAA  3 lyGppGtGKTllakavakelgve.fleisgsellsk 37
                                      l+Gp G GKT+l+k + + l+ +  + ++g + l++
  gi|386002297|ref|YP_005920596.1| 34 LVGPNGSGKTTLIKCIDRILKPKgTIILDGGRNLQS 69
                                      89*************999986332344444444433 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05      0.01      16      47 ..      28      58 ..      22     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaagg 47
                                      ++  v  l+Gp G+GKtt++k + ++++ +g 
  gi|386002297|ref|YP_005920596.1| 28 DS-EVLSLVGPNGSGKTTLIKCIDRILKPKGT 58
                                      34.58999*****************9998882 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.027        16     246     266 ..      31      51 ..      27      67 .. 0.86
   2 !    7.0   0.1    0.0037       2.2     324     415 ..     139     215 ..     133     233 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.027
                                       EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 246 vtlIvGggfhGKsTLLeAlek 266
                                       v  +vG++  GK+TL++ +++
  gi|386002297|ref|YP_005920596.1|  31 VLSLVGPNGSGKTTLIKCIDR 51 
                                       6778*************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0037
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q + i++al  + ++lL+DE ts     ++ e m+                vr+++kk+g+s ++ +  ++ 
  gi|386002297|ref|YP_005920596.1| 139 SGGQKQRVLIARALAQEPEVLLLDEPTSNLDVKHQLEAMDT---------------VRSIVKKTGISAVMAIHDLNL 200
                                       88888999999999999999999999986555554444444...............444444455555555555555 PP

                                       CTTT-SEEEEEETTE CS
                        ABC_ATPase 401 yldvAdtvilmeeyk 415
                                         + +d  ++++e +
  gi|386002297|ref|YP_005920596.1| 201 AARYSDSLVMLKEGR 215
                                       455555555444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.7e-05     0.028      24      49 ..      31      56 ..      13      81 .. 0.83
   2 ?   -2.7   0.0       5.4   3.2e+03       2      31 ..     135     164 ..     134     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppl 49
                                       l lvGp GsGKt l+k++  +l p 
  gi|386002297|ref|YP_005920596.1| 31 VLSLVGPNGSGKTTLIKCIDRILKPK 56
                                      4669******************9875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                      Mg_chelatase   2 lkdvkGqeeakraleiaaaGgHnlllvGpp 31 
                                       ++++ G ++++  +  a a + ++ll+  p
  gi|386002297|ref|YP_005920596.1| 135 FSELSGGQKQRVLIARALAQEPEVLLLDEP 164
                                       566666666666666666666666555544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.1e-05     0.037      15      40 ..      26      49 ..      14      57 .. 0.81
   2 ?   -2.4   0.1       3.6   2.1e+03      72     110 ..     121     162 ..     110     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      TTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqi 40
                                       ++++  v++lvG  G+GKttl+k i
  gi|386002297|ref|YP_005920596.1| 26 VGDSE--VLSLVGPNGSGKTTLIKCI 49
                                      45666..***************9876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                                       XHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  72 ilkeLslseddleekeeves...lkrklvrlLltkrfllvlD 110
                                       +++ L+ +e  l+ ++e          + r+L +   +l+lD
  gi|386002297|ref|YP_005920596.1| 121 VMRLLHVEEFALKDFSELSGgqkQRVLIARALAQEPEVLLLD 162
                                       455555555555555554444335556788888888888888 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.049        29      38      54 ..      32      48 ..      23     128 .. 0.90
   2 ?    8.4   0.1    0.0022       1.3     117     159 ..     153     193 ..     137     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.049
                              TniB 38 lllvGdsnnGKtmivek 54
                                      l lvG+   GKt++++ 
  gi|386002297|ref|YP_005920596.1| 32 LSLVGPNGSGKTTLIKC 48
                                      789***********985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                              TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                       + +++vL++DE  + l   +++q e++ +++s+  +  i+ v+
  gi|386002297|ref|YP_005920596.1| 153 AQEPEVLLLDEPTSNL--DVKHQLEAMDTVRSIVKKTGISAVM 193
                                       56899******99999..899*******************997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00099      0.59       4      25 ..      34      55 ..      31      70 .. 0.82
   2 ?    1.9   0.0      0.34     2e+02      19      56 ..     148     185 ..     115     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00099
                                      EE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnr 25
                                      LvGp G+gK++l++ + + l+ 
  gi|386002297|ref|YP_005920596.1| 34 LVGPNGSGKTTLIKCIDRILKP 55
                                      9************999998844 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.34
                                       GGGGBS--EEEEE--TT--HHHHH--B--......... CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvd 56 
                                       +a+al +e e+ +l + t+  d+k ++e ++  +s v+
  gi|386002297|ref|YP_005920596.1| 148 IARALAQEPEVLLLDEPTSNLDVKHQLEAMDTVRSIVK 185
                                       67788888888888888888888888886655555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00021      0.12       2      27 ..      32      60 ..      31      77 .. 0.76
   2 ?   -2.3   0.0       7.5   4.5e+03      16      32 ..     149     165 ..     143     198 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                            AAA_33  2 vllvGlpGsGKstlaerl...lkklgavl 27
                                      + lvG++GsGK+tl++ +   lk+ g+++
  gi|386002297|ref|YP_005920596.1| 32 LSLVGPNGSGKTTLIKCIdriLKPKGTII 60
                                      679***********874322266666555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.5
                            AAA_33  16 aerllkklgavllssdt 32 
                                       a+ l+++  + ll+++t
  gi|386002297|ref|YP_005920596.1| 149 ARALAQEPEVLLLDEPT 165
                                       44445444455555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00027      0.16       4      29 ..      34      59 ..      31      74 .. 0.89
   2 ?   -0.3   0.0       1.5   8.9e+02      94     155 ..     154     219 ..     141     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                      EE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvk 29
                                      + Gp G+GKtTl+k + + lk +g  
  gi|386002297|ref|YP_005920596.1| 34 LVGPNGSGKTTLIKCIDRILKPKGTI 59
                                      78******************999875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                                       HHH-EEEE--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
                          NTPase_1  94 seadviviDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfev 155
                                       +e++v+++DE   ++ +k + +  ++v+ ++k ++   ++ ih  +   +  +++   k+++++ v
  gi|386002297|ref|YP_005920596.1| 154 QEPEVLLLDEpTSNLDVKHQlEAMDTVRSIVKkTGISAVMAIHDLNlAARYSDSLVMLKEGRIYAV 219
                                       566666666633445555542455678888887788888888887776777777777777777775 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0012      0.75      28      89 ..     133     181 ..     118     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +++++lSGG+kq +    +a ala    +       +++++LDE  s+lD + + +++++++
  gi|386002297|ref|YP_005920596.1| 133 KDFSELSGGQKQRV---LIARALA----Q------EPEVLLLDEPTSNLDVKHQLEAMDTVR 181
                                       67788888888433...3332222....2......4889************99999999875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0002      0.12      77     120 ..       6      50 ..       1      64 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                       SEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       ++ l  s  +++ l++l+ ++ d ++  lvG+ G GK+tLi+ ++
  gi|386002297|ref|YP_005920596.1|   6 IKNLSFSYGSRRILDDLNLVVGDsEVLSLVGPNGSGKTTLIKCID 50 
                                       55666777778889999999998899***************9876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017       0.1      14      57 ..      14      57 ..       3      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrG 57
                                       ++++l+ l    G ++v+ l G  G+Gk tl++ +   l+ +G
  gi|386002297|ref|YP_005920596.1| 14 GSRRILDDLNLVVGDSEVLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      5899*****************************99988888777 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.14       3      29 ..      31      57 ..      29      61 .. 0.82
   2 ?   -2.7   0.0       6.5   3.9e+03      97     112 ..     169     184 ..     146     196 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                      EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkeg 29
                                      v+ lvG++G+GKTt +  + ++lk +g
  gi|386002297|ref|YP_005920596.1| 31 VLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      7889**********9988887777665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                                       THHHHHHHHHHHHHHH CS
                             SRP54  97 ndkelmeelkkikkvv 112
                                         k+ +e +++++++v
  gi|386002297|ref|YP_005920596.1| 169 DVKHQLEAMDTVRSIV 184
                                       3333344444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.14      45      77 ..      29      61 ..      16     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                             Rad17 45 kriLLisGPsGCgkstvvkvLskelgiklrewl 77
                                       ++L + GP G gk+t +k + ++l +k    l
  gi|386002297|ref|YP_005920596.1| 29 SEVLSLVGPNGSGKTTLIKCIDRILKPKGTIIL 61
                                      56899******************9998865554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.15       6      30 ..      33      62 ..      29     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                            AAA_24  6 liyGpsgiGKTtlakel.....gpkplfid 30
                                       ++Gp+g+GKTtl+k +     ++ ++++d
  gi|386002297|ref|YP_005920596.1| 33 SLVGPNGSGKTTLIKCIdrilkPKGTIILD 62
                                      589************997777666666666 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00035      0.21      10      38 ..      29      57 ..      24     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                      ++vl ++++ G+GKT+++k+i ++l+  g
  gi|386002297|ref|YP_005920596.1| 29 SEVLSLVGPNGSGKTTLIKCIDRILKPKG 57
                                      678999**************988887655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00046      0.28       2      22 ..      31      51 ..      30     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      ++ l G++GsGKTtL++ + +
  gi|386002297|ref|YP_005920596.1| 31 VLSLVGPNGSGKTTLIKCIDR 51
                                      57799**********998755 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00044      0.26       1      28 [.      31      58 ..      31      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                              MobB  1 vlgivgksgsGKTtLleklipelkargl 28
                                      vl++vg +gsGKTtL++ + ++lk +g 
  gi|386002297|ref|YP_005920596.1| 31 VLSLVGPNGSGKTTLIKCIDRILKPKGT 58
                                      689*************999888888775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00046      0.27       2      19 ..      31      48 ..      30      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                                      EEEEEESTTCCHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnh 19
                                      v+ l+G+ GsGKTtL++ 
  gi|386002297|ref|YP_005920596.1| 31 VLSLVGPNGSGKTTLIKC 48
                                      6789***********975 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034      0.21      26      71 ..      32      90 ..      24     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                                      EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHH CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsi 71
                                      l l+G ++SGK+T++k + ++ k++              s++e+a +  ++ + + +s+
  gi|386002297|ref|YP_005920596.1| 32 LSLVGPNGSGKTTLIKCIDRILKPKgtiildggrnlqsLSRQEVARFIGYVPQSTTSSL 90
                                      6699***************9888876777666666555555555555544444444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0005       0.3      18      43 ..      26      53 ..      14      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                                      H..TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakal 43
                                      +  ++v+ L G+ G+GKTtl++ + + l
  gi|386002297|ref|YP_005920596.1| 26 VgdSEVLSLVGPNGSGKTTLIKCIDRIL 53
                                      24457899**************987766 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0041       2.5      23      39 ..      36      52 ..      33      67 .. 0.88
   2 ?    0.7   0.0      0.26   1.5e+02     526     562 ..     155     190 ..     148     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0041
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NG+GKTtL + ++ +
  gi|386002297|ref|YP_005920596.1| 36 GPNGSGKTTLIKCIDRI 52
                                      99********9999875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkak 562
                                       + ++  +D P S LD +++  ++  ++s + kk+ ++
  gi|386002297|ref|YP_005920596.1| 155 EPEVLLLDEPTSNLDVKHQLEAMDTVRSIV-KKTGIS 190
                                       678999***************999999997.677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 1641.03
//
Query:       gi|386002298|ref|YP_005920597.1|  [L=357]
Description: iron chelate uptake ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-95  319.3  39.7    2.8e-95  318.9  39.7    1.0  1  FecCD     FecCD transport family
     0.0011   18.6  23.0     0.0011   18.6  23.0    1.7  1  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.9  39.7   3.1e-99   2.8e-95       3     312 .]      35     351 ..      31     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.9 bits;  conditional E-value: 3.1e-99
                             FecCD   3 llllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLa 72 
                                       ++l  ++ +lg++ki+p ev+ a+l++        +s+ ++iv++lrl rvl+a+++G++LavaGa +Q++++NpLa
  gi|386002298|ref|YP_005920597.1|  35 VVLAGVAATLGSAKITPVEVYTAILARFfpdtfqtTSFIETIVWQLRLHRVLMAIFAGMGLAVAGAAMQGILKNPLA 111
                                       5666777899**************99989999999999999************************************ PP

                             FecCD  73 dPsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalt 148
                                       +P +lGi s+a++ga la++l+  ++++++ ++  af++ +la++ v+ la + kg++p+++iLaGia+ +l+sa+t
  gi|386002298|ref|YP_005920597.1| 112 SPFTLGIASAASFGASLAIILGaGFASGQWLIVGNAFIFTMLASMTVYGLA-RYKGITPETMILAGIAIMYLFSAMT 187
                                       **********************98899999999******************.************************* PP

                             FecCD 149 sllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllll 225
                                       s+l+++ ++e++++++fw++Gsl++ sw+kv+++++++++++++l+++a +++++  gdetAkslGvnve vr+l++
  gi|386002298|ref|YP_005920597.1| 188 SFLQYIGKSEQVHEVVFWMMGSLGRSSWDKVAIIAMVTVVCTVALVYFAWDINAMGAGDETAKSLGVNVEFVRVLCM 264
                                       ***************************************************************************** PP

                             FecCD 226 llvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliG 302
                                       +l++l+ta++++++G+igF+GL++Phi r++vg dhr llp+sal+Gal+ll+ad++ar++l+p+ lpvgi+t+++G
  gi|386002298|ref|YP_005920597.1| 265 MLASLITASVICFTGTIGFIGLVAPHITRMVVGGDHRFLLPASALVGALILLAADTVARTVLAPVILPVGIMTSFLG 341
                                       ***************************************************************************** PP

                             FecCD 303 apffiylllr 312
                                       +pffiyl+lr
  gi|386002298|ref|YP_005920597.1| 342 VPFFIYLFLR 351
                                       *******987 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  23.0   1.2e-07    0.0011      31     226 ..     111     316 ..      82     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-07
                             ABC-3  31 qsllgdalsHaalpGvalayllgvn.......lllgailvgliaavalellkrktklkedtai..givlsvflalgl 98 
                                       +s +  +++ aa  G  la++lg         ++  a++++++a++++  l+r + +  +t+i  gi +   ++   
  gi|386002298|ref|YP_005920597.1| 111 ASPFTLGIASAASFGASLAIILGAGfasgqwlIVGNAFIFTMLASMTVYGLARYKGITPETMIlaGIAIMYLFSAMT 187
                                       566777888888888889988888766777756667999****************9999997666999999998888 PP

                             ABC-3  99 vlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllll 173
                                        ++++i k     ++  +++G++   s + + +ia++++v+ ++l++f  ++ ++    e+Ak+ g++v+++++l +
  gi|386002298|ref|YP_005920597.1| 188 SFLQYIGKseQVHEVVFWMMGSLGRSSWDKVAIIAMVTVVCTVALVYFAWDINAMGAGDETAKSLGVNVEFVRVLCM 264
                                       88888876445567888899********************************************************* PP

                             ABC-3 174 alialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvv 226
                                       +l +l  + ++ + G i  i l ++P +t + ++ + + ll  ++l+g++ ++
  gi|386002298|ref|YP_005920597.1| 265 MLASLITASVICFTGTIGFIGL-VAPHITRMVVGGDHRFLLPASALVGALILL 316
                                       ***************9999885.799999999888888888888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 1942.13
//
Query:       gi|386002299|ref|YP_005920598.1|  [L=681]
Description: Magnesium-chelatase subunit ChlD [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   73.0   0.3    3.9e-20   71.5   0.3    1.8  1  AAA_lid_2        AAA lid domain
    2.2e-15   57.2   0.0    5.9e-15   55.8   0.0    1.7  1  VWA_2            von Willebrand factor type A domain
    1.7e-10   40.7   0.3    2.4e-07   30.3   0.0    2.7  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.7e-09   38.2   0.0    2.7e-09   37.5   0.0    1.3  1  VWA              von Willebrand factor type A domain
    1.8e-09   37.7   0.0    1.3e-05   25.3   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    7.8e-06   25.1   0.4     0.0012   18.0   0.0    3.3  3  MCM              MCM P-loop domain
     0.0039   17.6   0.0      0.014   15.8   0.0    1.9  1  AAA_16           AAA ATPase domain
     0.0054   16.5   0.0        0.4   10.4   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.036   13.7   0.7       0.48   10.0   0.1    2.3  2  CobT_C           Cobalamin biosynthesis protein CobT VWA doma
       0.04   14.2   0.0       0.13   12.5   0.0    1.8  2  AAA_22           AAA domain
      0.045   14.2   0.0       0.35   11.3   0.0    2.5  1  AAA              ATPase family associated with various cellul
      0.099   12.5   0.0        6.2    6.7   0.0    2.8  3  AAA_3            ATPase family associated with various cellul
          1   10.0   4.9       0.15   12.7   0.5    2.0  1  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.3   2.8e-23   3.9e-20       3      72 ..     267     336 ..     265     337 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2.8e-23
                         AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                       + a+ +i lgv ++Ra+++++r+A+++Aa+egr+ V + Dv++a +l+L+HR+r +p++++  +ee+++e
  gi|386002299|ref|YP_005920598.1| 267 AMASACIDLGVKSHRAEIVITRTAKTIAAFEGRTWVEQRDVERAMKLALPHRMRSKPFEPPSLNEERLKE 336
                                       56899********************************************************999998876 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 !   55.8   0.0   4.3e-18   5.9e-15       1     106 [.     480     586 ..     480     587 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4.3e-18
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       ++fv+D SgSm++     +r+e ak a+ ++l  s++ +d+vg v+f++ ++evl+p++++ +  +++lr+l + gg
  gi|386002299|ref|YP_005920598.1| 480 VLFVVDASGSMGSV----RRMESAKGAILSMLMdSYQkRDKVGMVAFRKgEAEVLLPPSSSVDLAMKRLRELPT-GG 551
                                       79***********9....6********99877746655***********78**********************7.69 PP

                             VWA_2  75 gtnlaaaLqlarkalkkrr...kgekrvivlitDg 106
                                       +t l +++ +   al+++    + +k ++vli+Dg
  gi|386002299|ref|YP_005920598.1| 552 KTPLSSGIAKGLRALQAEIkkdSETKPIMVLISDG 586
                                       999988888888888776667779**********9 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0     0.002       2.7       2      49 ..      11      60 ..      10      67 .. 0.87
   2 !   30.3   0.0   1.8e-10   2.4e-07      93     158 ..     123     188 ..     115     196 .. 0.93
   3 ?   -1.4   0.0      0.91   1.3e+03     187     203 ..     195     211 ..     189     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaGgH..nlllvGppGsGKtmlakrlpsllppl 49
                                      +++++Gqee k al + a+      +l+ G  G+ K+   ++l++ll+++
  gi|386002299|ref|YP_005920598.1| 11 FTSIVGQEEMKFALILNAINPRigGVLIRGDKGTAKSTAVRALAELLADI 60
                                      5789************9987542279*********************986 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 1.8e-10
                      Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       g +   pG ++ a++G+L++DE+  ++ +v +vL +    g  +++r   +v +pa+f lv +mNp
  gi|386002299|ref|YP_005920598.1| 123 GIKALDPGILAAANRGILYIDEVNLLDDHVADVLLDSAAMGVNVVEREGISVAHPAKFILVGTMNP 188
                                       566889***********************************************************9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.91
                      Mg_chelatase 187 gplldRidlqvevkkle 203
                                         lldR+ lqv+v++++
  gi|386002299|ref|YP_005920598.1| 195 PQLLDRFGLQVNVESID 211
                                       579**********8775 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0     2e-12   2.7e-09       2     138 ..     480     618 ..     480     656 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2e-12
                                       EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGG CS
                               VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgg 76 
                                       + fv+D+Sgsm + +++e++k +i +++ + +  +++++vg+v f +  +++  + ++  s + +++ l++l   +g
  gi|386002299|ref|YP_005920598.1| 480 VLFVVDASGSMgSVRRMESAKGAILSMLMDSY--QKRDKVGMVAFRKGeAEVLLPPSS--SVDLAMKRLREL--PTG 550
                                       68*********6678899******99998888..9**********9554999999999..679********8..566 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.......HTHHHHHHHHGCTEEEEEEE CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndg.......dpkeaaneakeqgikvfavG 138
                                       g+t + ++++++l+ l+ + ++  +++k +++l++dG+ n +       ++   +++a+ +g+ +++v 
  gi|386002299|ref|YP_005920598.1| 551 GKTPLSSGIAKGLRALQAEIKK-DSETKPIMVLISDGRANVStggnikeELMAISEQARMSGVHTIVVD 618
                                       66669********966666555.5589************994489777777777778888888887775 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00052      0.72       2      23 ..      36      57 ..      35      70 .. 0.87
   2 !   25.3   0.0   9.1e-09   1.3e-05      27     138 .]      96     201 ..      87     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      vl+ G++Gt+Ks+ ++ la++l
  gi|386002299|ref|YP_005920598.1| 36 VLIRGDKGTAKSTAVRALAELL 57
                                      8999****************99 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 9.1e-09
                                       EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-S CS
                             AAA_5  27 veyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeg 99 
                                       + +v l+ + te+ ++g+++++    +g ++l +++l   a +  il++DEv+ ++++v+++Ll         +e  
  gi|386002299|ref|YP_005920598.1|  96 TPVVDLPLGSTEDRVVGSLDVEraikEGIKALDPGILA--AANRGILYIDEVNLLDDHVADVLLDSAAMGVNVVERE 170
                                       55677777899**********99999999999999998..55667******************76666666665555 PP

                                       SSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5 100 gelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       g  v ++++     f +++t+np +    el p+l++Rf
  gi|386002299|ref|YP_005920598.1| 171 GISVAHPAK-----FILVGTMNPEE---GELRPQLLDRF 201
                                       555555554.....*********99...77889999999 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.083   1.2e+02      60      80 ..      36      56 ..      10      64 .. 0.81
   2 !   18.0   0.0   8.9e-07    0.0012     103     180 ..     118     195 ..      89     225 .. 0.87
   3 ?    1.2   0.0      0.12   1.6e+02      25      69 ..     492     538 ..     472     596 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.083
                                      EEEEESSTSTHHHHHHHHHHH CS
                               MCM 60 vllvgdpgtaKsqlLkyvekl 80
                                      vl+ gd gtaKs+ ++++++l
  gi|386002299|ref|YP_005920598.1| 36 VLIRGDKGTAKSTAVRALAEL 56
                                      8999********988887665 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 8.9e-07
                                       EESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCC CS
                               MCM 103 rdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagryd 179
                                       r  ++g  +l+ G l  a++G+++iDe++  +++  ++l++        + + Gi +  +a+  ++  +np++g+  
  gi|386002299|ref|YP_005920598.1| 118 RAIKEGIKALDPGILAAANRGILYIDEVNLLDDHVADVLLDSAAMGVNVVEREGISVAHPAKFILVGTMNPEEGELR 194
                                       5555666789******************************99888888999*********************99765 PP

                                       T CS
                               MCM 180 k 180
                                       +
  gi|386002299|ref|YP_005920598.1| 195 P 195
                                       5 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                                       TSSS-HHHHHHHHHHHH---EBBBSSSSB..BCSS-EEEEEESSTST CS
                               MCM  25 siyghedvkkaillqlfggvkkkledktk..lrgdinvllvgdpgta 69 
                                       s+  +e+ k ail +l+ +++k+++ ++    +g+ +vll   ++++
  gi|386002299|ref|YP_005920598.1| 492 SVRRMESAKGAILSMLMDSYQKRDKVGMVafRKGEAEVLLPPSSSVD 538
                                       67778999**************9988776546789999886555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05     0.014      19     154 ..      28     155 ..      17     167 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy..salaqalareellrqlldeaesae 93 
                                       +  +r + vl++G++G+ Ks+ vr+l+ +l +d + +++g    +    py      +++ +++   +++++ +   
  gi|386002299|ref|YP_005920598.1|  28 AINPRIGGVLIRGDKGTAKSTAVRALA-ELLAD-IPVVEGCPFNC---NPYnpEEMCDLCQERGENLKVASRRTPVV 99 
                                       44566689*******************.67777.77888888888...66632112222222222222222222222 PP

                            AAA_16  94 leawrekleealaavpelagaea....srllellkrll.allsrderplvlvlDdlqwadeaslql 154
                                         +   + +++++         +    +++ e +k+l    l+   r  +l +D++  +d++ +++
  gi|386002299|ref|YP_005920598.1| 100 DLPLGSTEDRVVG---------SldveRAIKEGIKALDpGILAAANR-GILYIDEVNLLDDHVADV 155
                                       2222222222222.........1223234444444444444444233.677777777777776666 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.034        47      24      46 ..      35      57 ..      17      80 .. 0.70
   2 !   10.4   0.0   0.00029       0.4      84     141 ..     127     186 ..     117     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.034
                                      -EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat 24 svlitGesGtGKellaraiheas 46
                                       vli+G++Gt K++  ra+ e  
  gi|386002299|ref|YP_005920598.1| 35 GVLIRGDKGTAKSTAVRALAELL 57
                                      69************999998744 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00029
                                       -BEHHHHHTTTSEEEEETGGGS-HHHHHHHHH..HHHHSEEESBTSSSEEE--EEEEEEE CS
                   Sigma54_activat  84 ekkGlfekadgGtlfLDeigelplelQekLlr..vlqegevervGsskeikvdvriiaat 141
                                          G + +a+ G+l++De++ l+ ++   Ll   ++  + ver G s  +++++ ++ + 
  gi|386002299|ref|YP_005920598.1| 127 LDPGILAAANRGILYIDEVNLLDDHVADVLLDsaAMGVNVVEREGISVAHPAKFILVGTM 186
                                       5679*******************9999999962245666777777777777776666555 PP

>> CobT_C  Cobalamin biosynthesis protein CobT VWA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00035      0.48       2      30 ..     467     496 ..     466     525 .. 0.82
   2 ?    1.5   0.0      0.14   1.9e+02     132     170 ..     573     605 ..     560     620 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00035
                            CobT_C   2 frkkkearavdavvtllldlsGsmrG.rki 30 
                                       fr+k+  r v avv  ++d sGsm+  r++
  gi|386002299|ref|YP_005920598.1| 467 FREKERVRKVSAVVLFVVDASGSMGSvRRM 496
                                       89999*******************963444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                            CobT_C 132 rmedkkillvisdGaPvddstlsvaaGdylerhlrtvik 170
                                         e k i+++isdG         v++G  +++ l  + +
  gi|386002299|ref|YP_005920598.1| 573 DSETKPIMVLISDGRAN------VSTGGNIKEELMAISE 605
                                       579999********765......5667777777766654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.6e-05      0.13       9     130 ..      37     185 ..      34     190 .. 0.78
   2 ?   -3.2   0.0       6.7   9.3e+03      91     112 ..     575     600 ..     526     620 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsst..sskdllrellralglelka.......... 70 
                                       ++ G +Gt K+t +r l+e l         + +vv    ++++  +  +  dl++e  ++l++   +          
  gi|386002299|ref|YP_005920598.1|  37 LIRGDKGTAKSTAVRALAELLA--------DIPVVegcPFNCNPYNpeEMCDLCQERGENLKVASRRtpvvdlplgs 105
                                       788******************5........9999999955555555559999**********98888*******998 PP

                            AAA_22  71 ..........erlsseellealeqalraravielliiDEaqhlr.s..eealeeLrsllnl.......srkgvqliL 127
                                                  +   +e ++al   + a+a +++l iDE+  l+ +  + +l    + +n+         ++ ++iL
  gi|386002299|ref|YP_005920598.1| 106 tedrvvgsldVERAIKEGIKALDPGILAAANRGILYIDEVNLLDdHvaDVLLDSAAMGVNVveregisVAHPAKFIL 182
                                       88877766655555555556666666666669***********7635466666667777778888888889999999 PP

                            AAA_22 128 vGt 130
                                       vGt
  gi|386002299|ref|YP_005920598.1| 183 VGT 185
                                       998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.7
                            AAA_22  91 v...ielliiDEaqhlrs..eealeeL 112
                                           i +li D   ++ s   ++ eeL
  gi|386002299|ref|YP_005920598.1| 575 EtkpIMVLISDGRANV-StgGNIKEEL 600
                                       1333355555555555.3333333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.35       1     131 [.      36     208 ..      36     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                       EEEESSTTSSHHHHHHHHHHHH.......THE...............................EEEEETTTCSSS.. CS
                               AAA   1 vllyGppGtGKTllakavakel.......gve...............................fleisgsellsk.. 37 
                                       vl+ G +Gt K+++++a+a+ l       g                                 ++ + + +  +   
  gi|386002299|ref|YP_005920598.1|  36 VLIRGDKGTAKSTAVRALAELLadipvveG-CpfncnpynpeemcdlcqergenlkvasrrtpVVDLPLGSTEDRvv 111
                                       688999**************9754433331.0233333344444443333433333333333344444444444444 PP

                                       STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                               AAA  38 yvgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatn 110
                                          + e+ i+e +k++        +  il iDE+  l  +  +   +++   vn+  +e   v +  +k+i++g+ n
  gi|386002299|ref|YP_005920598.1| 112 GSLDVERAIKEGIKALDPGIlaaaNRGILYIDEVNLLDDHVADVLLDSAAMGVNVVEREGISVAH-PAKFILVGTMN 187
                                       333466666666666544336665569********997777666667777777777666666666.578******** PP

                                       S.GGGSTHHHHSTTSSEEEETT CS
                               AAA 111 r.pdkldpallrgRfdrkieie 131
                                         + +l p+ll +Rf  ++++e
  gi|386002299|ref|YP_005920598.1| 188 PeEGELRPQLL-DRFGLQVNVE 208
                                       9899*******.9**9988876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.099   1.4e+02       2      23 ..      36      57 ..      35      60 .. 0.91
   2 ?    6.7   0.0    0.0045       6.2      65     116 ..     139     192 ..     127     203 .. 0.86
   3 ?   -2.4   0.0       2.9     4e+03      50      77 ..     243     270 ..     235     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.099
                             AAA_3  2 vllegvPGlaktllvkalakal 23
                                      vl++g  G+ak ++v+ala+ l
  gi|386002299|ref|YP_005920598.1| 36 VLIRGDKGTAKSTAVRALAELL 57
                                      7999***************987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0045
                             AAA_3  65 llladeinrappktqsalle..ameerqvtvegethklpepflvlatqnPieqe 116
                                       +l  de+n    ++   ll+  am  + v  eg + + p +f+++ t nP e e
  gi|386002299|ref|YP_005920598.1| 139 ILYIDEVNLLDDHVADVLLDsaAMGVNVVEREGISVAHPAKFILVGTMNPEEGE 192
                                       7889***************855789999999999****************8754 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.9
                             AAA_3  50 kekefefkkGpvfanllladeinrappk 77 
                                       + +   + +  ++++ ll d++ ra++ 
  gi|386002299|ref|YP_005920598.1| 243 DLRLRIMDAKEILSDALLGDDLLRAMAS 270
                                       4444445566789999999999998875 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   0.00011      0.15      33      91 ..     253     312 ..     220     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                    Mg_chelatase_C  33 elrevceldeeaeelleeaierlgl.saRaydrilkvArTiADLegseeieeehlaeAlq 91 
                                       e+ + + l ++  + + +a+ +lg+ s Ra   i + A+TiA  eg++ +e++++++A++
  gi|386002299|ref|YP_005920598.1| 253 EILSDALLGDDLLRAMASACIDLGVkSHRAEIVITRTAKTIAAFEGRTWVEQRDVERAMK 312
                                       5555555555555555555555554399******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.89u 0.35s 00:00:01.24 Elapsed: 00:00:00.54
# Mc/sec: 3773.58
//
Query:       gi|386002300|ref|YP_005920599.1|  [L=287]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-32  112.9   0.0    2.5e-32  112.3   0.0    1.3  1  ABC_tran  ABC transporter
    5.3e-14   52.7   2.0    2.1e-10   40.9   0.6    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00028   20.7   0.0       0.49   10.0   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0019   18.7   2.1     0.0053   17.3   2.1    1.7  1  AAA_23    AAA domain
     0.0021   17.5   0.1     0.0087   15.5   0.1    1.9  1  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.01   16.2   0.3      0.052   14.0   0.3    2.1  1  AAA       ATPase family associated with various cellular acti
      0.013   15.2   0.5      0.028   14.1   0.5    1.7  1  AAA_30    AAA domain
      0.019   15.2   0.0      0.048   13.9   0.0    1.7  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.025   14.9   0.1      0.049   14.0   0.1    1.5  1  AAA_16    AAA ATPase domain
      0.045   13.4   0.2      0.081   12.6   0.2    1.4  1  SRP54     SRP54-type protein, GTPase domain
      0.067   12.3   0.0      0.081   12.1   0.0    1.1  1  G-alpha   G-protein alpha subunit
      0.072   12.7   0.4       0.29   10.7   0.0    1.9  2  AAA_27    AAA domain
      0.087   12.6   0.0       0.15   11.8   0.0    1.3  1  AAA_29    P-loop containing region of AAA domain
       0.13   11.8   0.2       0.46   10.0   0.0    1.9  2  cobW      CobW/HypB/UreG, nucleotide-binding domain
       0.17   11.3   0.0       0.27   10.6   0.0    1.2  1  TehB      Tellurite resistance protein TehB
       0.17   12.0   0.7       0.48   10.6   0.7    1.7  1  AAA_33    AAA domain
       0.18   12.0   1.1       0.66   10.3   1.1    2.1  1  AAA_22    AAA domain
        0.2   10.3   0.6       0.76    8.4   0.2    2.0  2  AAA_13    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.0   2.5e-35   2.5e-32       3     136 ..      22     163 ..      20     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 2.5e-35
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                       +++l +++ge+ +++G+nGaGK+t +++l+ l+kpt+G+++++g d+   + +  ++++g+++q+ +l++eltvren
  gi|386002300|ref|YP_005920599.1|  22 RLDLRVEKGELFGFLGPNGAGKTTTMRMLTTLTKPTSGKVEINGFDVAA-DGRNIKASFGIVQQHLSLNRELTVREN 97 
                                       6899*********************************************.9999*********************** PP

                                       .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    e++e+i+++l+ ++++e++d+ +      +S+G+k+r ++aral+ +pkl++lDEpt
  gi|386002300|ref|YP_005920599.1|  98 lelharlhhigrrERKERIDELLDYVEMTEKQDQLI----DRISEGMKRRTMIARALIHRPKLIFLDEPT 163
                                       ************99999******************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.7   5.7e-05     0.056       2      94 ..      33     111 ..      32     116 .. 0.74
   2 !   40.9   0.6   2.1e-13   2.1e-10     166     297 ..      76     193 ..      53     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNg+GK++ ++ l  l              ++  + ++ ++ +d  ++   ++ ++   ++q+   + +l++
  gi|386002300|ref|YP_005920599.1|  33 FGFLGPNGAGKTTTMRMLTTL--------------TKPTSGKVEINGFDVAADGRNIKASFG-IVQQHLSLNRELTV 94 
                                       5789**************766..............566777778888888888888888888.88888777777777 PP

                            AAA_21  79 ersqv.eeklssvetll 94 
                                        ++    ++l + ++++
  gi|386002300|ref|YP_005920599.1|  95 RENLElHARLHHIGRRE 111
                                       77777666666555555 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 2.1e-13
                            AAA_21 166 igllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtk 242
                                       ++ + i++ ++  ++e++ ++ l+ + +l +i  +  +e++++            + ++e++  q+  ++ +S+G+k
  gi|386002300|ref|YP_005920599.1|  76 KASFGIVQQHLSLNRELTVRENLELHARLHHIGRRERKERIDE-----------LLDYVEMTEKQDQLIDRISEGMK 141
                                       5566667777777777777777777777777666666555544...........7889******************* PP

                            AAA_21 243 rllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       r   +++  l  ++  +l+++DEp  gL+ +  rr+++l+++ ++ ga v+ltTH
  gi|386002300|ref|YP_005920599.1| 142 RR-TMIARALIHRP--KLIFLDEPTVGLDAQTRRRVWDLIRAMNSDGATVFLTTH 193
                                       **.****9999888..7***********************999999********* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00049      0.49      25      55 ..      32      70 ..      22     139 .. 0.66
   2 !    9.0   0.0     0.001         1     288     364 ..     127     193 ..     105     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekkn.........k 55
                                      l  + G+N++GK++ +++l  + + ++  +          
  gi|386002300|ref|YP_005920599.1| 32 LFGFLGPNGAGKTTTMRMLTTLTKPTSG-KveingfdvaA 70
                                      55689**************999997722.23554555552 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                            AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++++ +++ + G++r   ++  +++          +++++++EP + L  q  + +++l++ + +d+   v++tTH
  gi|386002300|ref|YP_005920599.1| 127 EKQDQLIDRISEGMKRRTMIARALIHR---------PKLIFLDEPTVGLDAQTRRRVWDLIRAMNSDGA-TVFLTTH 193
                                       677777777777777777666544443.........367***********************9999997.9****** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.1   5.4e-06    0.0053      20      49 ..      31      59 ..      19     161 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.4e-06
                            AAA_23 20 gltlItGpNGaGKTTildAiklaLygetpr 49
                                       l+ + GpNGaGKTT ++ ++  +   t++
  gi|386002300|ref|YP_005920599.1| 31 ELFGFLGPNGAGKTTTMRMLTTLTKP-TSG 59
                                      6999**************99875433.333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   8.7e-06    0.0087      29     215 ..      35     211 ..      11     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.7e-06
                                       EEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  29 ivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                        +GpNG+GK+  +  +  +L + ++ k+  + ++ +     ++ +++++ v+ +++ + + ++ e+ e+  + + + 
  gi|386002300|ref|YP_005920599.1|  35 FLGPNGAGKTTTMRML-TTLTKPTSGKVEINGFD-VAAD-GRNIKASFGIVQQHLSLNRELTVRENLELHARLHHIG 108
                                       5799999999999988.78887777666665554.4444.7888899999999988877776666666666665555 PP

                                       TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHH..HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 106 kgeseykingkevtkkevsellesagiskelLSgGektLval..aLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                         e + +i+    +  ++ e+ e+++  ++ +S G k  +++  aL+      ++  l +lDe    LD++ +++v 
  gi|386002300|ref|YP_005920599.1| 109 RRERKERID----ELLDYVEMTEKQDQLIDRISEGMKRRTMIarALI------HRPKLIFLDEPTVGLDAQTRRRVW 175
                                       555555555....46789999999999999*****886555500555......44458889**************** PP

                                       HHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkekskn.aQfivislreemlekadklvgvtkve 215
                                       +l+++ +++ a ++ +++  e  e   k vg+ ++ 
  gi|386002300|ref|YP_005920599.1| 176 DLIRAMNSDgATVFLTTHYIEEAEALCKRVGIIHQG 211
                                       ****76555499999999999998888888888854 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   5.3e-05     0.052       3      66 ..      35     161 ..      33     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT++++ + + ++  +  +ei+g ++  +                                        
  gi|386002300|ref|YP_005920599.1|  35 FLGPNGAGKTTTMRMLTTLTKptSGKVEINGFDVAADgrnikasfgivqqhlslnreltvrenlelharlhhigrre 111
                                       68****************99854557999999999666777787887777777777777777788888888777777 PP

                                       .......................STTHHHHHHHHHHHHHHHTS.........TSEEEEEET CS
                               AAA  38 .......................yvgesekkirelfkeakeka.........kpsilfiDE 66 
                                                               ++e+          +k+ +         +p+ +f+DE
  gi|386002300|ref|YP_005920599.1| 112 rkeridelldyvemtekqdqlidRISEG----------MKR-RtmiaralihRPKLIFLDE 161
                                       7777777776553222222222222222..........222.1244455555577777777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   2.8e-05     0.028      20      68 ..      32      81 ..      24     194 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgi 68
                                      +    Gp G+GKtt+++ l+ + +   g+v +     +a  + +++++gi
  gi|386002300|ref|YP_005920599.1| 32 LFGFLGPNGAGKTTTMRMLTTLTKPTSGKVEINGFDVAADGRnIKASFGI 81
                                      55678****************99999778877666555544336666665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.8e-05     0.048      62      89 ..     152     179 ..     140     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       ++++l+fLDE   +lD+++++++ +l++
  gi|386002300|ref|YP_005920599.1| 152 HRPKLIFLDEPTVGLDAQTRRRVWDLIR 179
                                       6899********************9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.9e-05     0.049      19     143 ..      27     161 ..      17     190 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql.......esaipysa.laqalareellrqlld 87 
                                       v +g  el  + G+ G GK++ +r+l   l+k     ++gk + +       +++i  s  ++q+    +l r+l  
  gi|386002300|ref|YP_005920599.1|  27 VEKG--ELFGFLGPNGAGKTTTMRMLT-TLTKP----TSGKVEINgfdvaadGRNIKASFgIVQQH-L-SLNRELTV 94 
                                       5555..567789***************.68888....56666666332233444433333344444.2.33333333 PP

                            AAA_16  88 e........aesaeleawrekleeala..............avpelagaea...srllellkrll..allsrderpl 137
                                       +        +            +   +              +  e          r+ e +kr    a++   +rp 
  gi|386002300|ref|YP_005920599.1|  95 RenlelharL------------HHIGRrerkeridelldyvEMTEKQ---DqliDRISEGMKRRTmiARALI-HRPK 155
                                       3111121211............1111122234444444343222222...2444777777776663244444.5567 PP

                            AAA_16 138 vlvlDd 143
                                       +++lD+
  gi|386002300|ref|YP_005920599.1| 156 LIFLDE 161
                                       888884 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   8.1e-05     0.081       6      38 ..      35      67 ..      31      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++G++GaGKTtt+  L  l k    kv +   D
  gi|386002300|ref|YP_005920599.1| 35 FLGPNGAGKTTTMRMLTTLTKPTSGKVEINGFD 67
                                      79***************9999998888887776 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05     0.081      28     108 ..      35     126 ..      24     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                                       EEESTTSSHHHHHHHHHHHCS----HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT..................HHHC CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkgfseeelatwraviqlnivrsiktilealesleselsesf...........elqe 93 
                                       +lG ++ GK+T+++ l +l k++  + e++ +        +++   i++++ sl+ el+ +              +e
  gi|386002300|ref|YP_005920599.1|  35 FLGPNGAGKTTTMRMLTTLTKPTSGKVEINGFDVAADGRNIKASFGIVQQHLSLNRELTVREnlelharlhhiGRRE 111
                                       79*********************888888777776666666666667777777655553332334444445556666 PP

                                       -SS-SCCCS-HCHHH CS
                           G-alpha  94 lkerldplkkveasl 108
                                       +ker+d+l+++ +  
  gi|386002300|ref|YP_005920599.1| 112 RKERIDELLDYVEMT 126
                                       666666665554432 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.29      18      49 ..      22      53 ..      15      57 .. 0.87
   2 ?   -0.7   0.2      0.87   8.6e+02      68     117 ..      92     143 ..      77     148 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +ld++ e+ +l   +GpN AGK+t++r ++ l
  gi|386002300|ref|YP_005920599.1| 22 RLDLRVEKGELFGFLGPNGAGKTTTMRMLTTL 53
                                      688888888888899***********998876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.87
                            AAA_27  68 LrigavleeadgeelefaR..rkgrkktlldaddqa.lpeevlaallggldre 117
                                       L ++  le ++   +++ R  rk+r ++lld  + +  ++++++++ +g++r+
  gi|386002300|ref|YP_005920599.1|  92 LTVRENLELHAR-LHHIGRreRKERIDELLDYVEMTeKQDQLIDRISEGMKRR 143
                                       444444443333.2223221145566677776554415577777788888776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.15      19      55 ..      27      64 ..      19      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      ++  g  + + Gp+G+GK+T +  +++l  p++ kv+ N
  gi|386002300|ref|YP_005920599.1| 27 VEK-GeLFGFLGPNGAGKTTTMRMLTTLTKPTSgKVEIN 64
                                      443.3377799***********99999888887777766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00046      0.46       5      49 ..      35      78 ..      31      92 .. 0.86
   2 ?   -1.5   0.0       1.6   1.6e+03      74      92 ..     263     281 ..     252     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                                      EEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC CS
                              cobW  5 ltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret 49
                                      + G+ G+GKTt ++ l++ ++  +  v +N f  v+ D++ ++++
  gi|386002300|ref|YP_005920599.1| 35 FLGPNGAGKTTTMRMLTTLTKPTSGKVEINGFD-VAADGRNIKAS 78
                                      56889************9999999999999999.99999988876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                       HHHHHHHTT-SEEEEEECT CS
                              cobW  74 ealeereerldviliEttG 92 
                                        +++ re++l+ ++iE tG
  gi|386002300|ref|YP_005920599.1| 263 GNIVIRESNLEDVFIELTG 281
                                       555666679999****999 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.27      49     126 ..      62     146 ..      56     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                                       HHTT-EEEEEES-.HHHHHHHHH.......HHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-GGGHHHHH CS
                              TehB  49 sllgydvtawdkn.ensiaflee.......ikekenlknistalydineaklderydfilstvvlmfleaeripsii 117
                                       +++g+dv a  +n + s + +++       ++ +enl+ ++++l +i   + +er d +l  v +   + + i +i 
  gi|386002300|ref|YP_005920599.1|  62 EINGFDVAADGRNiKASFGIVQQhlslnreLTVRENLE-LHARLHHIGRRERKERIDELLDYVEMTEKQDQLIDRIS 137
                                       68999999998884457777765211111145689999.************************************** PP

                                       HHHHHTEEE CS
                              TehB 118 enmqectkv 126
                                       e m++ t +
  gi|386002300|ref|YP_005920599.1| 138 EGMKRRTMI 146
                                       ****99975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   0.00048      0.48       4     106 ..      35     192 ..      32     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdt................................................ 32 
                                       + G++G+GK+t  + l       +l+++t                                                
  gi|386002300|ref|YP_005920599.1|  35 FLGPNGAGKTTTMRMLT------TLTKPTsgkveingfdvaadgrnikasfgivqqhlslnreltvrenlelharlh 105
                                       78**********99876......677777666667777778888888888888888888888888777777444444 PP

                            AAA_33  33 .......lrrrlfgtdqqskt.............dytrvldrlyqilne..larkal.sagrnvildat..nlsrre 84 
                                                           +             ++ ++ dr+ + +++  ++++al  + + + ld +   l++++
  gi|386002300|ref|YP_005920599.1| 106 higrrerK------------EridelldyvemteKQDQLIDRISEGMKRrtMIARALiHRPKLIFLDEPtvGLDAQT 170
                                       44433320............123344444444334444555554444431123333313344455588734445788 PP

                            AAA_33  85 rarflklarrlgvpvrivvvet 106
                                       r+r+  l r +++  + v+++t
  gi|386002300|ref|YP_005920599.1| 171 RRRVWDLIRAMNSDGATVFLTT 192
                                       8888888888887766666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   0.00066      0.66      12      29 ..      37      54 ..      28     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                            AAA_22 12 GesGtGKTtllrrlleql 29
                                      G+ G+GKTt++r+l+   
  gi|386002300|ref|YP_005920599.1| 37 GPNGAGKTTTMRMLTTLT 54
                                      9*************9876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00076      0.76      23      43 ..      37      56 ..      34      95 .. 0.81
   2 ?   -1.0   0.0      0.51   5.1e+02     525     570 ..     152     194 ..     145     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00076
                            AAA_13 23 GwNGaGKTtLSrllrslelge 43
                                      G NGaGKTt  r+l  l++  
  gi|386002300|ref|YP_005920599.1| 37 GPNGAGKTTTMRMLTTLTK-P 56
                                      99*************9964.2 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                          k +++D P   LD++    v  li++     ++ + +f+ TH 
  gi|386002300|ref|YP_005920599.1| 152 HRPKLIFLDEPTVGLDAQTRRRVWDLIRAMN---SDGATVFLTTHY 194
                                       567899**********************996...89999******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1684.17
//
Query:       gi|386002301|ref|YP_005920600.1|  [L=247]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-22   78.8  21.2    3.7e-22   78.8  21.2    1.9  2  ABC2_membrane    ABC-2 type transporter
    3.2e-08   33.1  30.6    3.2e-08   33.1  30.6    1.9  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8  21.2   4.1e-26   3.7e-22       3     207 ..       6     212 ..       4     215 .. 0.91
   2 ?   -0.7   1.9      0.09     8e+02     127     144 ..     221     238 ..     213     246 .. 0.51

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 4.1e-26
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn.lg.nsedglnr..pgllffsvlflafsaltsvapvf 75 
                                       ++++l+ +++ + r+ + +l++ l++p+l+++ fg   g+ +  + +++l++  pg+++ ++++ +f+++ +  +v 
  gi|386002301|ref|YP_005920600.1|   6 FYTILWADLMIMRRRMTRYLVTTLVSPILYLFAFGWGLGRdISiEGASYLDFviPGIIALTAMNSSFVGAGARLNVD 82 
                                       889************************************863343444443377*******************9999 PP

                     ABC2_membrane  76 erergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrfflflllllltalaasslglli 151
                                           +++++ l  p+ s+ + v++k+++ + ++l+ +++fl+++++l   + l  + lfl+ l+lt l +s+lg+l 
  gi|386002301|ref|YP_005920600.1|  83 RLFFRSFDEFLMVPI-STLSLVFGKAMIGVFRGLVSSIAFLAVALLLSpTFSL--GPLFLVSLVLTCLSFSFLGVLA 156
                                       99*************.***************************9998335555..6899****************** PP

                     ABC2_membrane 152 salapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                       + la+s+ed+++++sl+llp+++l+G f++++++ + l+   y++Plt+    lr+
  gi|386002301|ref|YP_005920600.1| 157 ALLAKSHEDMNTFSSLILLPMTFLAGTFFSLSQVSGALKLGLYVLPLTHSSLCLRA 212
                                       **********************************88*************8666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.09
                     ABC2_membrane 127 lsrfflflllllltalaa 144
                                       +++f+ ++l+++l++ a+
  gi|386002301|ref|YP_005920600.1| 221 WTSFVVICLFVFLFLAAS 238
                                       433444444444443333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3     0.048   4.3e+02       3      20 ..      24      41 ..      22      57 .. 0.82
   2 !   33.1  30.6   3.5e-12   3.2e-08     196     344 ..      93     239 ..      49     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.048
                   ABC2_membrane_3  3 fliitlllPiilvlllgl 20
                                      +l++tl++Pi++++ +g+
  gi|386002301|ref|YP_005920600.1| 24 YLVTTLVSPILYLFAFGW 41
                                      688999999999998876 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 3.5e-12
                   ABC2_membrane_3 196 lvsgvsplqywlskilgdflvyllqlllilllafglgipfgnlglll.llfllfglayialgyllsslfknsetaqi 271
                                       l+ ++s+l+++++k  + ++ +l++++ +l++a+    p ++lg l+ + ++l +l++++lg l   l k++e++++
  gi|386002301|ref|YP_005920600.1|  93 LMVPISTLSLVFGKAMIGVFRGLVSSIAFLAVALL-LSPTFSLGPLFlVSLVLTCLSFSFLGVLAALLAKSHEDMNT 168
                                       46689************************997444.1466699988879999************************* PP

                   ABC2_membrane_3 272 lifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavvylllal 344
                                       + ++++l++ ++ g +f+l+++++alk  ++++P+++ +l l   + ++p+   ++s+++ +lf++++l++++
  gi|386002301|ref|YP_005920600.1| 169 FSSLILLPMTFLAGTFFSLSQVSGALKLGLYVLPLTHSSLCLRAAALNQPF--PWTSFVVICLFVFLFLAASI 239
                                       *****9955555555566****************************99944..58999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:01.26
# Mc/sec: 594.40
//
Query:       gi|386002302|ref|YP_005920601.1|  [L=353]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-18   65.0   0.8      3e-15   56.5   0.1    2.1  2  Peripla_BP_2  Periplasmic binding protein
    0.00031   20.8   0.4    0.00068   19.7   0.4    1.6  1  CheY-binding  CheY binding


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1   0.00036       3.2       1      58 [.      49     106 ..      49     107 .. 0.84
   2 !   56.5   0.1   3.3e-19     3e-15      83     234 ..     140     298 ..     124     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00036
                                       EEE-SHHHHHHHHHTT-GGGEEE.B-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvg.vdtttsdpldadkleeaivevgadgeidvEklaal 58 
                                       i++l+++ +e +  lG+ +k+vg vd + + +++ +  + +  +vg+ +e+++Ek+a+l
  gi|386002302|ref|YP_005920601.1|  49 IVVLNSDAAEAVSILGEVEKIVGsVDISYKAHYFTEFSR-DWETVGTWKEFNYEKIADL 106
                                       8*********************83455556666665554.99***************98 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 3.3e-19
                                       S-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE...EEEE-TT CS
                      Peripla_BP_2  83 iptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggade.ggyvvagsn 157
                                       i+++  +  +  e+l+e++  lge+l++e+eae++  ++ +k a++ +a++ +  p+ ++  g+a + g+    g +
  gi|386002302|ref|YP_005920601.1| 140 IEVLGLDLYKP-ENLEEEMALLGEVLDRESEAEAYNLWVGEKKASVVEAVSGLgRPRVYVEGGSASDlGALWTYGQG 215
                                       66666666666.9****************************************445555555555559999999*** PP

                                       STTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH........HHHT-S--HHHHT-SHHHHTSHHH CS
                      Peripla_BP_2 158 syigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr........aeadnktgleflkenpllaelpAv 226
                                       s  ++++  +g+en++a+   +++ ++ +E++la  p+vi+  +          + +  +++ +++++p++ ++pA+
  gi|386002302|ref|YP_005920601.1| 216 SAPSEMIALAGGENVIAA--DEANPKVEWETVLALMPEVIIKVPAainqlgwtNTTEMEAFVGEIESRPGADSTPAA 290
                                       ******************..8********************99999***9999888999999999************ PP

                                       HTT-EEEE CS
                      Peripla_BP_2 227 kngrVyal 234
                                       + grVy +
  gi|386002302|ref|YP_005920601.1| 291 EDGRVYVI 298
                                       ******85 PP

>> CheY-binding  CheY binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.4   7.6e-08   0.00068       3      40 ..     141     178 ..     139     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.6e-08
                      CheY-binding   3 eLsgvkekDvelLleELgnLGevseqekagdslevtLe 40 
                                       e+ g++    e+L+eE+++LGev+++e +++ +++++ 
  gi|386002302|ref|YP_005920601.1| 141 EVLGLDLYKPENLEEEMALLGEVLDRESEAEAYNLWVG 178
                                       55666666679*************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2187.94
//
Query:       gi|386002303|ref|YP_005920602.1|  [L=98]
Description: hypothetical protein Mhar_1619 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-11   41.7   0.0    7.3e-11   41.7   0.0    1.6  2  PQ-loop   PQ loop repeat
    2.5e-10   40.2   1.1    2.9e-10   40.1   1.1    1.1  1  MtN3_slv  Sugar efflux transporter for intercellular exchange
  ------ inclusion threshold ------
       0.01   15.6   2.6        1.3    8.8   0.1    2.5  2  DUF5353   Family of unknown function (DUF5353)


Domain annotation for each model (and alignments):
>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   1.2e-14   7.3e-11       3      59 ..       8      64 ..       7      66 .. 0.93
   2 ?   -1.6   0.3      0.41   2.5e+03       3      17 ..      69      83 ..      67      84 .. 0.58

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.2e-14
                           PQ-loop  3 eilgyislvlwlvsyiPQiikNykrkSteGlSilflllwllGdilsllylilngfpp 59
                                      e++gy++++l+++ ++PQ++k  ++kS++ +S+l+++   lG +l+l+y +    +p
  gi|386002303|ref|YP_005920602.1|  8 EVVGYAAAALTMFGFLPQLLKMVRTKSVDDVSLLMMVQMGLGVSLWLAYGLHLENSP 64
                                      799**********************************************99877665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.41
                           PQ-loop  3 eilgyislvlwlvsy 17
                                      +++++ +l+l lv+y
  gi|386002303|ref|YP_005920602.1| 69 NFVSLSILALGLVVY 83
                                      556666666666665 PP

>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   1.1   4.8e-14   2.9e-10       4      85 ..      11      89 ..       8      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 4.8e-14
                          MtN3_slv  4 gllcvvftvavFlsPlsilrkiikkksveelsfllflagllsallWllYGllkkdaliiivNlvgvlleliylllflvy 82
                                      g ++  +t++ F   l++l k++++ksv+++s+l+++   l+ +lWl YGl +++  +i+ N+v + + ++ l+++  y
  gi|386002303|ref|YP_005920602.1| 11 GYAAAALTMFGF---LPQLLKMVRTKSVDDVSLLMMVQMGLGVSLWLAYGLHLENSPLIVANFVSLSILALGLVVYFRY 86
                                      555555555555...79999*********************************************************99 PP

                          MtN3_slv 83 akk 85
                                      + +
  gi|386002303|ref|YP_005920602.1| 87 TTN 89
                                      976 PP

>> DUF5353  Family of unknown function (DUF5353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00022       1.3      34      51 ..       5      22 ..       3      26 .. 0.91
   2 ?    6.3   0.2    0.0014       8.1       3      30 ..      62      87 ..      60      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00022
                           DUF5353 34 LtwkvvglwagavGafav 51
                                      ++w+vvg +a+a+ +f++
  gi|386002303|ref|YP_005920602.1|  5 MDWEVVGYAAAALTMFGF 22
                                      79**************97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0014
                           DUF5353  3 dnpvvvgNavlvavlsagLGfgAYrkya 30
                                      ++p++v+N v + +l+  LG   Y +y+
  gi|386002303|ref|YP_005920602.1| 62 NSPLIVANFVSLSILA--LGLVVYFRYT 87
                                      78************97..5555566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 612.16
//
Query:       gi|386002304|ref|YP_005920603.1|  [L=140]
Description: hypothetical protein Mhar_1620 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.4  10.2    2.5e-18   66.2  10.2    1.6  1  PsiE      Phosphate-starvation-inducible E
  ------ inclusion threshold ------
       0.12   12.3   3.6        0.5   10.3   0.2    2.1  2  DUF412    Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> PsiE  Phosphate-starvation-inducible E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2  10.2   2.8e-22   2.5e-18       1      67 [.      56     122 ..      56     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.8e-22
                              PsiE   1 lgdiLllLillEllrtivaylkehriavrlvieaaiiavaRklIildlkdggyltllglaaailaLg 67 
                                       +g +Ll+Li +Ell+t+++yl e++i v++v+++aiia+aRk+Iild+ +  ++tl+g+aa++++L+
  gi|386002304|ref|YP_005920603.1|  56 FGYFLLVLIGIELLETFRIYLAEKVINVQVVLLVAIIAIARKVIILDVTKLPSMTLIGIAAIVVSLS 122
                                       789*************************************************************997 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5    0.0091        82      32      59 ..      10      37 ..       4      61 .. 0.79
   2 ?   10.3   0.2   5.6e-05       0.5      37      88 ..      82     133 ..      67     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0091
                            DUF412 32 katrfaikvmpalavltlvlqlylagse 59
                                      +a+ +  ++m+al+v+ ++ +l++   +
  gi|386002304|ref|YP_005920603.1| 10 NAVLILLTWMMALVVFLATAELFYIVAK 37
                                      67778899********999998876544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.6e-05
                            DUF412  37 aikvmpalavltlvlqlylagsealpqailtalfllsLPlQGlywlGkrakt 88 
                                        ++v+  +a+++++ ++++ + ++lp+  l+++ ++ + l + y+l k++++
  gi|386002304|ref|YP_005920603.1|  82 NVQVVLLVAIIAIARKVIILDVTKLPSMTLIGIAAIVVSLSAGYYLVKKSQQ 133
                                       467888899999**************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 779.05
//
Query:       gi|386002305|ref|YP_005920604.1|  [L=212]
Description: hypothetical protein Mhar_1621 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1225.15
//
Query:       gi|386002306|ref|YP_005920605.1|  [L=98]
Description: hypothetical protein Mhar_1622 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 596.45
//
Query:       gi|386002307|ref|YP_005920606.1|  [L=305]
Description: prephenate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-48  163.6   0.0    4.9e-48  163.4   0.0    1.0  1  PDH             Prephenate dehydrogenase
    1.9e-06   27.4   0.0    3.3e-06   26.6   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.1e-05   25.7   0.0    1.8e-05   24.9   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    2.9e-05   24.6   0.0    6.5e-05   23.4   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.018   15.4   0.0    1.3  1  Phage_Gp19      Phage protein Gp19/Gp15/Gp42
      0.018   14.6   0.0       0.03   13.9   0.0    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
       0.12   12.4   1.1       0.29   11.1   0.1    1.9  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
        0.2   11.3   0.1       0.44   10.2   0.1    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.0   2.2e-51   4.9e-48       1     257 [.      27     273 ..      27     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.2e-51
                                       HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE CS
                               PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitD 77 
                                       +ar+ + +gf v+v g +   +k e a++lg+ ++ + + ++v   d+v+l+vP++ +++v++e+ap +k++ l++D
  gi|386002307|ref|YP_005920606.1|  27 FARFFKGQGFLVSVWGPS---GKVEVAERLGVSFASDLP-AEVAASDVVLLSVPIQETAKVIEEIAPRMKPGSLLMD 99 
                                       689999999999999976...556677899*******96.999********************************** PP

                                       --S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEE CS
                               PDH  78 vgsvKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvi 154
                                       v+s K  +++++ +  ++g+++ g+hPm+G+            + ++ viL P       +l  + e+++e garv+
  gi|386002307|ref|YP_005920606.1| 100 VTSLKRGPMEAMLRWAPQGVEVLGTHPMFGP--------TIPTLRGQTVILVPATGRCDFWLSPMEEIFREGGARVE 168
                                       *******************************........999*************9999****************** PP

                                       E--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHH CS
                               PDH 155 lmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavl 227
                                        +++eeHDr++avv+ l+h+++i++  tl     d   +r++ s+ ++ ++    Ri +++Pel+a+i+ eN e   
  gi|386002307|ref|YP_005920606.1| 169 ILEAEEHDRIMAVVQALTHFAYISIGSTLRSLDFDVARSRRFMSPVYEIMIdfvgRILAQSPELYASIQ-ENPE-AR 243
                                       ********************************************************************8.6777.79 PP

                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                               PDH 228 ealdkfikelkklkelienedaeeLvellk 257
                                        +++ +i+e+++l++l  ++d+  ++e ++
  gi|386002307|ref|YP_005920606.1| 244 RVREAYIHECERLSKLADEGDTSGFMEAMN 273
                                       9**************************996 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.5e-09   3.3e-06      36     125 ..      12      99 ..       2     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.5e-09
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSBSH CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpetrhlina 111
                                       +k + + G+G  G+ +a+ +k+ g+ v ++ +s k e  +e+lgv+++ +l + +a sD+v l +p++ et ++i+ 
  gi|386002307|ref|YP_005920606.1|  12 KKMLIVGGTGGTGSWFARFFKGQGFLVSVWGPSGKVEV-AERLGVSFAsDLPAEVAASDVVLLSVPIQ-ETAKVIE- 85 
                                       44445558***************************888.9999**99889****************75.6777775. PP

                                       HHHHCSTTTEEEEE CS
                      2-Hacid_dh_C 112 eelakmkkgailiN 125
                                       e   +mk+g++l+ 
  gi|386002307|ref|YP_005920606.1|  86 EIAPRMKPGSLLMD 99 
                                       45578898888875 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   8.2e-09   1.8e-05       6      95 ..      19     106 ..      15     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 8.2e-09
                                       --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--T CS
                     NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkk 82 
                                       G+G  Gs +a+ ++ +g+ v+v+  +  kve +   g++ a+++ + va+ dvv++ v+  +++ +vie++++++k+
  gi|386002307|ref|YP_005920606.1|  19 GTGGTGSWFARFFKGQGFLVSVWGPS-GKVEVAERLGVSFASDLPAEVAASDVVLLSVPI-QETAKVIEEIAPRMKP 93 
                                       89999*******************87.999999999*********9999**********8.77899*********** PP

                                       T-EEEE-S---HH CS
                     NAD_binding_2  83 gdilidgstsspe 95 
                                       g++l+d+++ +  
  gi|386002307|ref|YP_005920606.1|  94 GSLLMDVTSLKRG 106
                                       *******998754 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.9e-08   6.5e-05       4      95 ..      16     101 ..      13     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.9e-08
                                       EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored   4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79 
                                       i+ G+G  g+ +a+ +  +g     ++v     p+   e ae+lgv+  +   +e+a+ +dvv+l+v+ + +++v++
  gi|386002307|ref|YP_005920606.1|  16 IVgGTGGTGSWFARFFKGQG-----FLVS-VWGPSGKVEVAERLGVSFASDLPAEVAA-SDVVLLSVPIQETAKVIE 85 
                                       55678888888888777777.....4433.6788888999*******99977777776.****************** PP

                                       HCGHHHHTTSEEEEES CS
                     F420_oxidored  80 elakdalkgklvisvl 95 
                                       e+a++ + g+l+ +v+
  gi|386002307|ref|YP_005920606.1|  86 EIAPRMKPGSLLMDVT 101
                                       ************9997 PP

>> Phage_Gp19  Phage protein Gp19/Gp15/Gp42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   8.1e-06     0.018       5      74 ..     170     235 ..     167     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-06
                        Phage_Gp19   5 leaeEkdraeaLlevasdelereikkvgkdldkmiaasaefraavksvaadvVaravltatdrePmgqlS 74 
                                       leaeE+dr++a ++         i  + ++ld  +a s+ f   v +++ d V r++     ++P+ ++S
  gi|386002307|ref|YP_005920606.1| 170 LEAEEHDRIMAVVQALTHFAYISIGSTLRSLDFDVARSRRFMSPVYEIMIDFVGRIL----AQSPELYAS 235
                                       89************999999999**********************************....445777766 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05      0.03       5      92 ..      12      98 ..      10     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                      S-EEEE.S-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE.HHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                              IlvN  5 kkiavi.GyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt.vaeavkkadvvmiliPDelqkevyeeei 81
                                      kk+ ++ G G  G   a+ ++ +g+ v v   +g+  v+ A++ g++ ++ +   v+++dvv++ +P +  ++v+ eei
  gi|386002307|ref|YP_005920606.1| 12 KKMLIVgGTGGTGSWFARFFKGQGFLVSVWGPSGK--VEVAERLGVSFASdLPAEVAASDVVLLSVPIQETAKVI-EEI 87
                                      5555552799***************9999888888..7777777776554144456789****************.99* PP

                                      GGG--TT-EEE CS
                              IlvN 82 epnlkegkala 92
                                      +p +k g+ l+
  gi|386002307|ref|YP_005920606.1| 88 APRMKPGSLLM 98
                                      ******99875 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.58   1.3e+03       6      31 ..      19      44 ..      15      53 .. 0.76
   2 ?   11.1   0.1   0.00013      0.29      57     100 ..      55      98 ..      48     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.58
                                      --SHHHHHHHHHHHTTT--EEEE-S- CS
                    NAD_Gly3P_dh_N  6 GaGswGtalAkvlaenghevrlwvre 31
                                      G+G  G+ +A+ ++ +g  v++w+ +
  gi|386002307|ref|YP_005920606.1| 19 GTGGTGSWFARFFKGQGFLVSVWGPS 44
                                      77888888999999999999998754 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                                       EEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEE CS
                    NAD_Gly3P_dh_N  57 lvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailv 100
                                       + + +dl + ++ +d+++l vP q +++v++++++ +k+   l+
  gi|386002307|ref|YP_005920606.1|  55 VSFASDLPAEVAASDVVLLSVPIQETAKVIEEIAPRMKPGSLLM 98 
                                       678899999*************************9999887666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0002      0.44      41      97 ..      55      96 ..      15     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                      EEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEE CS
                              ApbA 41 lrltseggeeilrppealsaeekselepidlvivtvKayqteealeeikplldpntv 97
                                      +++ s+                 +e +  d+v+++v+ + t++++eei+p+++p + 
  gi|386002307|ref|YP_005920606.1| 55 VSFASDL---------------PAEVAASDVVLLSVPIQETAKVIEEIAPRMKPGSL 96
                                      4333333...............23456679**********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1781.58
//
Query:       gi|386002308|ref|YP_005920607.1|  [L=267]
Description: shikimate 5-dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-25   88.4   0.0    5.1e-25   87.5   0.0    1.5  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    1.1e-14   53.9   0.1    2.4e-14   52.8   0.1    1.7  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    6.9e-12   45.6   0.0      1e-11   45.0   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    4.5e-05   23.9   0.2    0.00013   22.5   0.2    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00046   19.6   0.1    0.00075   18.9   0.1    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0016   18.7   0.0     0.0035   17.6   0.0    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0023   17.5   0.1     0.0046   16.5   0.1    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0034   17.5   0.1      0.006   16.7   0.1    1.4  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
  ------ inclusion threshold ------
      0.012   14.9   1.2       0.17   11.2   0.9    2.1  2  ThiF             ThiF family
       0.02   15.3   0.1      0.034   14.6   0.1    1.4  1  NAD_binding_7    Putative NAD(P)-binding
      0.033   13.5   0.1       0.46    9.8   0.1    2.1  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.052   14.3   0.3       0.54   11.1   0.1    2.2  2  GARS_N           Phosphoribosylglycinamide synthetase, N doma


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   3.4e-28   5.1e-25       1      83 []       6      87 ..       6      87 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 3.4e-28
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT- CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigA 79
                                      v+G+p++hSlSPa++naaf algl ++y af+v++++l++a+ +++a g+ Gln TiP+Kea++++++  +e+A+a+gA
  gi|386002308|ref|YP_005920607.1|  6 VFGDPVEHSLSPAMQNAAFSALGLSARYLAFRVKKERLKDAILGAEAMGFGGLNLTIPLKEAALSIVE-PDENAAAMGA 83
                                      89*****************************************************************7.********** PP

                                      -SEE CS
                    Shikimate_dh_N 80 vNti 83
                                      vNt+
  gi|386002308|ref|YP_005920607.1| 84 VNTV 87
                                      ***8 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.1   1.6e-17   2.4e-14       1      31 []     231     261 ..     231     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.6e-17
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       G+ MLv+Qga++ e+WTGr++P++vM+eal+
  gi|386002308|ref|YP_005920607.1| 231 GVPMLVHQGALSIEIWTGRKAPADVMEEALR 261
                                       899**************************97 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0     7e-15     1e-11       9      84 ..     113     184 ..     105     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 7e-15
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84 
                                       ++++++vl+iGaG  a+ +a++L+ +g++ + +aNR++era +la +++g       l+el++l+  a+vv+ at+
  gi|386002308|ref|YP_005920607.1| 113 RVAGRRVLIIGAGGAAKAIARQLALSGAE-LSIANRDRERALDLAASVGGR---GYGLSELDRLIPWAEVVVNATS 184
                                       56789***********************9.******************999...999*****************98 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   8.6e-08   0.00013       2      49 ..     119     162 ..     118     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.6e-08
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-E CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvk 49 
                                       + iiGaG  ++a+a++l+ +g    e+ +a +r+ e+a  la+++g +
  gi|386002308|ref|YP_005920607.1| 119 VLIIGAGGAAKAIARQLALSG---AELSIA-NRDRERALDLAASVGGR 162
                                       679******************...****88.***********999844 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     5e-07   0.00075      30      99 ..     110     183 ..      98     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5e-07
                                       SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee....eeeelgvelvsleellaesDivslhl 99 
                                        g +++g++v iiG+G  ++a+a+ l+  g+++ + +r +++      ++   g+ l +l+ l+ ++++v++++
  gi|386002308|ref|YP_005920607.1| 110 AGVRVAGRRVLIIGAGGAAKAIARQLALSGAELSIANRDRERALdlaaSVGGRGYGLSELDRLIPWAEVVVNAT 183
                                       57799********************************998876655444445677888***********99876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.4e-06    0.0035       1      98 [.     119     230 ..     119     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..................TTTCEEEEE--TTTH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..................lgvrfeaialdaeny 59 
                                       vliiGaG+ ++a+a+ la ++    e+ +a r++e++  laa++                    v+++++ +   ++
  gi|386002308|ref|YP_005920607.1| 119 VLIIGAGGAAKAIARQLALSGA---ELSIANRDRERALDLAASVggrgyglseldrlipwaeVVVNATSVGMREGDP 192
                                       89******************97...6**************9999887777777777777766555555555555555 PP

                                       HHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  60 eavLaallkegdlvvnlsppissldvlkaCietgvhyvd 98 
                                       + v  +l ++g++v + + +    ++l+ ++++g++ +d
  gi|386002308|ref|YP_005920607.1| 193 RIVDGRLFRQGQIVFDIVYNR-ETELLQDAARAGARIID 230
                                       555557777777777765444.44555555666777666 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.1e-06    0.0046       3      66 ..     115     181 ..     113     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHH...TT-EEEEHHHHHHT-SEEEE CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAke...egfevltvaeavkkadvvmi 66 
                                        g+++ +iG G  ++a a++l  sg ++ +++r+ ++ ++ A +   +g+   +++ ++ +a+vv++
  gi|386002308|ref|YP_005920607.1| 115 AGRRVLIIGAGGAAKAIARQLALSGAELSIANRDRERALDLAASvggRGYGLSELDRLIPWAEVVVN 181
                                       6899*********************************999998722244556666677889998875 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     4e-06     0.006      17      87 ..     110     184 ..      93     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                                       H-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHC....TT-EE--HHHCTTT-SEEEE-SS CS
                     AdoHcyase_NAD  17 tdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaam....eGfevvtleevvkkadivvtttG 87 
                                       + v +aG+ ++++G G   k  a+ l   Ga + +++ d   al  a      G+ + +l+ ++  a++vv +t 
  gi|386002308|ref|YP_005920607.1| 110 AGVRVAGRRVLIIGAGGAAKAIARQLALSGAELSIANRDRERALDLAAsvggRGYGLSELDRLIPWAEVVVNATS 184
                                       56789***********************************99987443123358*****************9985 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   0.00011      0.17      15      42 ..     113     140 ..     101     150 .. 0.88
   2 ?    1.7   0.0     0.091   1.4e+02      83     129 ..     171     222 ..     167     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       HHHTSEEEEE--SHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  15 kLrdskvllvGaGglGsellknLalsGv 42 
                                       +++  +vl++GaGg    ++++LalsG 
  gi|386002308|ref|YP_005920607.1| 113 RVAGRRVLIIGAGGAAKAIARQLALSGA 140
                                       566789*********************6 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.091
                                       HT-TTSEEEEEES-CCGCC.....S-HHHHTT-SEEEEESSSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  83 einpdveveavteritdet.....vleellesvDlVvdalDniearrlvnra 129
                                       ++ p++ev+    +++ ++     v   l+++ ++V+d + n+e+ +l + a
  gi|386002308|ref|YP_005920607.1| 171 RLIPWAEVVVNATSVGMREgdpriVDGRLFRQGQIVFDIVYNRETELLQDAA 222
                                       6677777777777774433344556779***************999876554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.3e-05     0.034       4      69 ..     113     183 ..     111     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel.....ekdlegadlviaat 69 
                                       ++ g++vl++G+G  A   +r+l+ +ga++ +   + +++l+   ++  + +     ++ + +a++v+ at
  gi|386002308|ref|YP_005920607.1| 113 RVAGRRVLIIGAGGAAKAIARQLALSGAELSIANRDRERALDLAASVGGRGYglselDRLIPWAEVVVNAT 183
                                       7899**************************99888844444433333333332221155566677777776 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00031      0.46      22     112 ..     102     214 ..      98     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                                       HHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT.................T-EEEEE-TTSCCHHHHHCCSS CS
                     THF_DHG_CYH_C  22 gvvellketgielegkkvvvvGrsnivgkplallLlek.................natVtvchsktkdlaeitread 81 
                                       g ++ l+ +g+ ++g++v+++G++    k++a  L+ +                  a V       ++l++++  a+
  gi|386002308|ref|YP_005920607.1| 102 GALRALEGAGVRVAGRRVLIIGAGGAA-KAIARQLALSgaelsianrdreraldlAASVGGRGYGLSELDRLIPWAE 177
                                       566677778888888888888876653.3333333332122333344444455445555555566688888899999 PP

                                       EEEE-S......S-TT-B-GGGS-TT-EEEE---EEC CS
                     THF_DHG_CYH_C  82 ivvvav......GkpelikaemvkegavviDvGinrv 112
                                       +vv a+      G p+++++  +++g++v D+ +nr 
  gi|386002308|ref|YP_005920607.1| 178 VVVNATsvgmreGDPRIVDGRLFRQGQIVFDIVYNRE 214
                                       999886555566899*****************99997 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.45   6.7e+02      43      89 ..      34      81 ..       3      82 .. 0.72
   2 ?   11.1   0.1   0.00036      0.54       2      23 ..     118     139 ..     117     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.45
                                      HHHHHHHCTESEEEE-SHHHHHTTHHHHHHHHH.T-EEES--CCCCHH CS
                            GARS_N 43 lvefakeekidlvvvGpeapLvaGvadaleeek.gikvfGpskeaAql 89
                                      l+  +k+e+ + ++ G ea+ + G+  ++  ++  ++++ p+++aA +
  gi|386002308|ref|YP_005920607.1| 34 LAFRVKKERLKDAILGAEAMGFGGLNLTIPLKEaALSIVEPDENAAAM 81
                                      444578888999999999999999988876666699999999999976 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                                       EEEEEESSHHHHHHHHHHTTST CS
                            GARS_N   2 kvLvvGsGGRehalawklaqsp 23 
                                       +vL++G GG  +a+a++la s 
  gi|386002308|ref|YP_005920607.1| 118 RVLIIGAGGAAKAIARQLALSG 139
                                       79****************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1750.22
//
Query:       gi|386002309|ref|YP_005920608.1|  [L=514]
Description: Putative thymidine phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-14   53.8   0.1    5.9e-14   52.3   0.0    1.8  2  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.2e-09   37.7   0.0      3e-09   36.4   0.0    1.6  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    2.2e-07   30.6   0.1    5.3e-07   29.4   0.1    1.7  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
     0.0027   16.6   0.0     0.0041   16.0   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.38   1.7e+03     189     216 ..      79     112 ..      45     154 .. 0.54
   2 !   52.3   0.0   1.3e-17   5.9e-14       3     252 ..     161     383 ..     159     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.38
                                       SHHHHSSHHHHHHHHTTHHTSCHHHHH......H CS
                   Glycos_transf_3 189 ealeggepkenaeilkavlegkksaak......r 216
                                        ++e+     ++ ++++ l+g+k a++       
  gi|386002309|ref|YP_005920608.1|  79 VEVEVAPFPDSIYFIRNKLDGRKLAFDevleivE 112
                                       4445544455666666666666555443322221 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 1.3e-17
                                       TBEEEEESS-S.SSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEE CS
                   Glycos_transf_3   3 dlvDivgTGGd.gantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgf 78 
                                       ++vD+++ GG+ g++t   ++   ++vAaaG+ ++k + r+++s +G+aD  e l + + l+ ee+++++ee+g ++
  gi|386002309|ref|YP_005920608.1| 161 PIVDKHSIGGVpGDKT---TLLVVPLVAAAGLLIPKSSSRAITSPAGTADRAEVL-MPVGLDLEEMRSVVEEAGGCI 233
                                       79********978899...9999****************************9998.7889999************** PP

                                       EEHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHH CS
                   Glycos_transf_3  79 lfapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldev 155
                                       +   + h a    + vr e  +    ++  PL+ p        +++sk+ a +++ ++ +++++r++ v++    e+
  gi|386002309|ref|YP_005920608.1| 234 VWGGSVHLAPADDIFVRVEYPL----SI-DPLLLP--------SIISKKRAVGADLLVVDIPTGRGAKVKT--IGEA 295
                                       *****99999999999999999....66.799***........****************************..889* PP

                                       HHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTT CS
                   Glycos_transf_3 156 sllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlag 231
                                       +llak  +      g + + +++  +++++ra + ale    ke++e+l +   g+++   ++  ++ ag +l +ag
  gi|386002309|ref|YP_005920608.1| 296 NLLAKDFMEIGSrLGIRVQGAVTYGEQPIGRAIGPALEA---KEAMEVLMNR-PGPRDV--AEKATAIAGILLEMAG 366
                                       ******99999999************************9...9999999988.677775..5777778999999998 PP

                                       SSSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 232 kadslkegvakaeevidsGkA 252
                                            ++g a aee+++sGkA
  gi|386002309|ref|YP_005920608.1| 367 ----REDGKALAEELLRSGKA 383
                                       ....789*************9 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   6.6e-13     3e-09       5      69 ..     425     482 ..     423     487 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 6.6e-13
                                       E-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHH CS
                            PYNP_C   5 idareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklk 69 
                                       i++ +i+ +a+ +G        p d ++Gi l +k+Gd+V++G+pl+ti+a++ ++l++a+++l+
  gi|386002309|ref|YP_005920608.1| 425 INNSSIAEVARFAGC-------PKDEGAGILLARKIGDAVEEGDPLFTIFAERGNNLQRALDRLE 482
                                       677888888888888.......99************************************99986 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.2e-10   5.3e-07       3      63 .]      92     152 ..      91     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-10
                                       HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       +i+ ++dg +L  +e  +++++ +  +++d++i Af +Al+  G++ +E ++l  Am++ g
  gi|386002309|ref|YP_005920608.1|  92 FIRNKLDGRKLAFDEVLEIVEDTVAERLSDVEITAFVTALHSFGLDLDEATNLSLAMIKTG 152
                                       5899*****************************************************9865 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.2e-07    0.0041     177     250 ..     396     474 ..     371     490 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.2e-07
                           DUF2254 177 eeeeakdeeeseeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgee.. 245
                                        + e  +e+    + + ++r++rsG+l  i+ +++ ++a+      ++++ i l +++Gd v +g+pl++++ e+  
  gi|386002309|ref|YP_005920608.1| 396 GDPEVLPEDIAVGDHKFTVRSDRSGHLLWINNSSIAEVARfagcpkDEGAGILLARKIGDAVEEGDPLFTIFAERgn 472
                                       44455556667788999********************99633333378899********************998844 PP

                           DUF2254 246 ddeel 250
                                       +   l
  gi|386002309|ref|YP_005920608.1| 473 N---L 474
                                       2...2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3530.37
//
Query:       gi|386002310|ref|YP_005920609.1|  [L=158]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-05   24.7   2.1       0.43   11.2   0.1    3.1  2  Fer4_7     4Fe-4S dicluster domain
    3.4e-05   23.5  16.3     0.0022   17.7   1.1    3.8  4  Fer4       4Fe-4S binding domain
     0.0001   22.8   1.9     0.0001   22.8   1.9    2.4  1  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I
    0.00017   22.2   2.2    0.00017   22.2   2.2    2.8  2  Fer4_15    4Fe-4S single cluster domain
     0.0083   16.2   0.1      0.076   13.2   0.0    2.2  2  FYVE       FYVE zinc finger
     0.0087   16.2   5.1      0.015   15.4   0.1    2.8  3  Fer4_21    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   15.6   0.8      0.013   15.6   0.8    3.8  4  Fer4_2     4Fe-4S binding domain
      0.016   15.1   0.4      0.037   13.9   0.4    1.7  1  zf-C2HC_2  zinc-finger of a C2HC-type
       0.12   12.5   1.4       0.12   12.5   1.4    3.6  4  Fer4_6     4Fe-4S binding domain
       0.15   12.1   2.3        5.7    7.0   0.0    2.6  3  zf-FCS     MYM-type Zinc finger with FCS sequence motif
       0.22   12.5   0.0       0.22   12.5   0.0    2.3  2  zf-C2H2_4  C2H2-type zinc finger
       0.35   10.7   0.0       0.35   10.7   0.0    2.1  1  HNH_5      HNH endonuclease
       0.37   11.0   7.0        2.6    8.3   0.1    3.3  2  Fer4_9     4Fe-4S dicluster domain
       0.38   11.3   0.1       0.38   11.3   0.1    1.9  1  zf-C2H2    Zinc finger, C2H2 type
       0.76    9.9   8.0        1.8    8.7   4.1    3.0  2  Fer4_10    4Fe-4S dicluster domain
        2.3    9.2   6.5         29    5.7   1.7    3.2  2  Fer4_16    4Fe-4S double cluster binding domain
        3.3    8.8  11.6         20    6.4   0.2    3.4  3  Fer4_3     4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00041      0.43      32      46 ..      13      27 ..       2      35 .. 0.79
   2 !   10.0   0.4   0.00094      0.99       9      43 ..      65     101 ..      65     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                            Fer4_7 32 eidpekClgCgaCva 46
                                      ++d+++C+gC+aC +
  gi|386002310|ref|YP_005920609.1| 13 AVDEDECIGCRACSN 27
                                      678888888888865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00094
                            Fer4_7   9 vaaCpvkaieldeeenekgt..ekveidpekClgCga 43 
                                       v+aCp++ai++  +++ +g     +++++ +C  Cg+
  gi|386002310|ref|YP_005920609.1|  65 VEACPTGAISFGLADELPGEesFALTFEMVRCRICGR 101
                                       689*******998777776622445778889998874 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.1   2.1e-06    0.0022       3      15 ..      14      26 ..      12      28 .. 0.90
   2 !   10.9   0.1   0.00031      0.32      15      24 .]      65      74 ..      65      74 .. 0.92
   3 ?   -1.7   0.6       2.8     3e+03      10      14 ..      95      99 ..      94     101 .. 0.65
   4 ?    5.0   0.1     0.021        22       5      12 ..     130     137 ..     129     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                      EETTTSSS-THHH CS
                              Fer4  3 ideekCigCGaCv 15
                                      +de+ CigC aC 
  gi|386002310|ref|YP_005920609.1| 14 VDEDECIGCRACS 26
                                      9***********6 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00031
                                      HHHSTTTEEE CS
                              Fer4 15 vevCPvgAIt 24
                                      ve+CP+gAI+
  gi|386002310|ref|YP_005920609.1| 65 VEACPTGAIS 74
                                      89******96 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.8
                                      S-THH CS
                              Fer4 10 gCGaC 14
                                      +C +C
  gi|386002310|ref|YP_005920609.1| 95 RCRIC 99
                                      67777 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.021
                                       TTTSSS-T CS
                              Fer4   5 eekCigCG 12 
                                       +++C+gC 
  gi|386002310|ref|YP_005920609.1| 130 MDLCTGCR 137
                                       69*****6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.9   9.7e-08    0.0001       1      57 [.      14      74 ..      14      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.7e-08
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeed..deggasvvaeqpts..eeekadaeeAadaCPvesIg 57
                                      VD+d+Ci+c aC +l P++ +     + ga +  + p+s  e e   ae  ++aCP+ +I 
  gi|386002310|ref|YP_005920609.1| 14 VDEDECIGCRACSNLWPEISAAVglSDRGAKRTIRFPRSieEFEARIAEGLVEACPTGAIS 74
                                      9******************9875223567777888888753334555566679******96 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   2.2   1.6e-07   0.00017       3      65 ..      14      74 ..      12      75 .. 0.71
   2 ?   -0.0   0.2       1.5   1.5e+03       6      13 ..     131     138 ..     130     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-07
                           Fer4_15  3 vDrdaCigcglCvaeapev...feldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIr 65
                                      vD+d+Cigc +C  ++pe+   + l ++g ++++     +    +++ e   a+  ++aCP++AI+
  gi|386002310|ref|YP_005920609.1| 14 VDEDECIGCRACSNLWPEIsaaVGLSDRGAKRTI-----RFPRSIEEFEARIAEGLVEACPTGAIS 74
                                      9***************765111556666655444.....2234677777777777899******97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.5
                           Fer4_15   6 daCigcgl 13 
                                       d+C+gc +
  gi|386002310|ref|YP_005920609.1| 131 DLCTGCRQ 138
                                       89****86 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.41   4.3e+02      28      33 ..      22      27 ..      14      60 .. 0.76
   2 !   13.2   0.0   7.2e-05     0.076      17      66 ..      85     140 ..      61     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.41
                                      -TTT-- CS
                              FYVE 28 CrlCGk 33
                                      Cr+C +
  gi|386002310|ref|YP_005920609.1| 22 CRACSN 27
                                      444433 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.2e-05
                                       -B--SSS--EE-TTT--EE-STTS-EEE.EE......GGGTEEEEEEE-HHHHHHH CS
                              FYVE  17 kkFsllrrrhhCrlCGkvvCekCssklvall......ekeaeeksvrvCkeClael 66 
                                       ++F l+     Cr+CG+ + +k   + +++        + ++ + + +C+ C +++
  gi|386002310|ref|YP_005920609.1|  85 ESFALTFEMVRCRICGRPFATKKEMEYIRDRlpepvqARGSAASWMDLCTGCRQDV 140
                                       57888999999*********888877776666666655556667789999999886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.5e-05     0.015      33      52 ..      11      30 ..       4      36 .. 0.83
   2 ?   -2.0   0.0       3.9   4.1e+03      49      58 ..      66      74 ..      64      75 .. 0.70
   3 ?    2.0   0.6      0.22   2.3e+02      35      45 ..     127     137 ..      92     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                           Fer4_21 33 vlkvvedeCvGCnlCssvCP 52
                                      +l+v edeC+GC  Cs+  P
  gi|386002310|ref|YP_005920609.1| 11 ILAVDEDECIGCRACSNLWP 30
                                      56788999999999998777 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                           Fer4_21 49 svCPvedcie 58
                                      + CP+ ++i+
  gi|386002310|ref|YP_005920609.1| 66 EACPT-GAIS 74
                                      67995.7775 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.22
                           Fer4_21  35 kvvedeCvGCn 45 
                                       +   d C+GC 
  gi|386002310|ref|YP_005920609.1| 127 ASWMDLCTGCR 137
                                       45578999996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.8   1.2e-05     0.013       3      17 ..      12      26 ..      10      28 .. 0.87
   2 ?   -0.1   0.3       1.2   1.3e+03      17      22 .]      65      70 ..      65      70 .. 0.80
   3 ?   -0.2   0.8       1.3   1.3e+03      11      16 ..      94      99 ..      94     101 .. 0.85
   4 ?    3.0   0.4      0.12   1.2e+02       8      14 ..     131     137 ..     130     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            Fer4_2  3 vvvdtdrCigCgaCv 17
                                       +vd+d CigC+aC 
  gi|386002310|ref|YP_005920609.1| 12 LAVDEDECIGCRACS 26
                                      689***********5 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                            Fer4_2 17 vsaCPa 22
                                      v aCP+
  gi|386002310|ref|YP_005920609.1| 65 VEACPT 70
                                      579**7 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.3
                            Fer4_2 11 igCgaC 16
                                      ++C++C
  gi|386002310|ref|YP_005920609.1| 94 VRCRIC 99
                                      589999 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.12
                            Fer4_2   8 drCigCg 14 
                                       d C+gC+
  gi|386002310|ref|YP_005920609.1| 131 DLCTGCR 137
                                       78****7 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 ?   13.9   0.4   3.5e-05     0.037       1      15 [.      92     106 ..      92     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                         zf-C2HC_2   1 elvpCpkCgRsFnpd 15 
                                       e+v C++CgR F+++
  gi|386002310|ref|YP_005920609.1|  92 EMVRCRICGRPFATK 106
                                       79********99975 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   0.00011      0.12       3      15 ..      13      25 ..      11      27 .. 0.88
   2 ?    5.6   0.2     0.017        18      16      24 .]      65      73 ..      65      73 .. 0.90
   3 ?   -3.0   0.6       8.8   9.3e+03      11      15 ..      95      99 ..      94     100 .. 0.74
   4 ?    3.9   0.4     0.058        61       7      13 ..     131     137 ..     130     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            Fer4_6  3 eidpdkCigCgdC 15
                                      ++d+d CigC++C
  gi|386002310|ref|YP_005920609.1| 13 AVDEDECIGCRAC 25
                                      79*********** PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                            Fer4_6 16 vrvCPegai 24
                                      v +CP+gai
  gi|386002310|ref|YP_005920609.1| 65 VEACPTGAI 73
                                      689*****8 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.8
                            Fer4_6 11 gCgdC 15
                                       C+ C
  gi|386002310|ref|YP_005920609.1| 95 RCRIC 99
                                      58888 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.058
                            Fer4_6   7 dkCigCg 13 
                                       d+C+gC+
  gi|386002310|ref|YP_005920609.1| 131 DLCTGCR 137
                                       89****8 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.9   7.3e+03       6      10 ..      19      23 ..      17      24 .. 0.77
   2 ?    7.0   0.0    0.0054       5.7       3      23 ..      93     113 ..      91     115 .. 0.84
   3 ?    4.4   0.1     0.034        36       3      12 ..     130     139 ..     129     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                            zf-FCS  6 CwfCk 10
                                      C  C+
  gi|386002310|ref|YP_005920609.1| 19 CIGCR 23
                                      99997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0054
                            zf-FCS   3 kkrCwfCkkyikgkpeftyvl 23 
                                       + rC +C++ + +k+e+ y++
  gi|386002310|ref|YP_005920609.1|  93 MVRCRICGRPFATKKEMEYIR 113
                                       89************9986665 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.034
                            zf-FCS   3 kkrCwfCkky 12 
                                       ++ C+ C+++
  gi|386002310|ref|YP_005920609.1| 130 MDLCTGCRQD 139
                                       689*****98 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00021      0.22       2      16 ..      95     109 ..      94     112 .. 0.90
   2 ?   -1.9   0.1       8.3   8.8e+03       3       8 ..     133     138 ..     132     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                         zf-C2H2_4   2 kCpiCgksFsskkaL 16 
                                       +C+iCg++F +kk++
  gi|386002310|ref|YP_005920609.1|  95 RCRICGRPFATKKEM 109
                                       7***********986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.3
                         zf-C2H2_4   3 CpiCgk 8  
                                       C+ C++
  gi|386002310|ref|YP_005920609.1| 133 CTGCRQ 138
                                       999965 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034      0.35       1      47 [.      96     144 ..      96     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                             HNH_5   1 CiyCgkeiaekelseeHI...iP...eslGGkltisnlvtlCkkCNqkkgqkv 47 
                                       C +Cg+++a+ + ++e+I   +P   +++G   ++++l   C  C q  g++ 
  gi|386002310|ref|YP_005920609.1|  96 CRICGRPFAT-KKEMEYIrdrLPepvQARGSAASWMDL---CTGCRQDVGRNA 144
                                       99*****999.77999*94442333479*********9...******999886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0024       2.6      35      43 ..      18      26 ..       3      37 .. 0.74
   2 ?    1.1   3.4      0.43   4.6e+02      33      40 ..     119     137 ..      65     140 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                            Fer4_9 35 aCigCgaCv 43
                                      +CigC+aC 
  gi|386002310|ref|YP_005920609.1| 18 ECIGCRACS 26
                                      577777774 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.43
                            Fer4_9  33 e...........eaCigCg 40 
                                                   + C+gC+
  gi|386002310|ref|YP_005920609.1| 119 PvqargsaaswmDLCTGCR 137
                                       0222333334455677775 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00036      0.38       2      16 ..      95     109 ..      94     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                                       EETTTTEEESSHHHH CS
                           zf-C2H2   2 kCpdCgksFkrksnL 16 
                                       +C +Cg++F +k ++
  gi|386002310|ref|YP_005920609.1|  95 RCRICGRPFATKKEM 109
                                       7**********9876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.1    0.0017       1.8       4      22 ..      14      32 ..      11     104 .. 0.77
   2 ?    0.4   0.1      0.69   7.3e+02       7      13 ..     131     137 ..     125     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                           Fer4_10  4 idddtCirCgkCvkaCPad 22
                                      +d+d Ci+C++C +  P  
  gi|386002310|ref|YP_005920609.1| 14 VDEDECIGCRACSNLWPEI 32
                                      799*********9988773 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.69
                           Fer4_10   7 dtCirCg 13 
                                       d C++C+
  gi|386002310|ref|YP_005920609.1| 131 DLCTGCR 137
                                       6788886 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.075        79      53      62 ..      18      27 ..      10      31 .. 0.70
   2 ?    5.7   1.7     0.027        29       9      29 ..      65      85 ..      65     139 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.075
                           Fer4_16 53 aitgCdiCqd 62
                                      +++gC++C +
  gi|386002310|ref|YP_005920609.1| 18 ECIGCRACSN 27
                                      5677777754 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                           Fer4_16  9 aevCPtnaikekkekeieare 29
                                      +e+CPt+ai+   + e+  +e
  gi|386002310|ref|YP_005920609.1| 65 VEACPTGAISFGLADELPGEE 85
                                      589******987555554444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.7     0.021        22       1       8 [.      19      26 ..      19      28 .. 0.91
   2 ?    6.4   0.2     0.019        20       8      15 .]      65      72 ..      65      72 .. 0.93
   3 ?    1.7   0.2      0.62   6.6e+02       1       5 [.     133     137 ..     133     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                            Fer4_3  1 CtgCgaCv 8 
                                      C+gC+aC 
  gi|386002310|ref|YP_005920609.1| 19 CIGCRACS 26
                                      *******7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                            Fer4_3  8 vevCPvgA 15
                                      ve+CP+gA
  gi|386002310|ref|YP_005920609.1| 65 VEACPTGA 72
                                      89*****9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.62
                            Fer4_3   1 CtgCg 5  
                                       CtgC+
  gi|386002310|ref|YP_005920609.1| 133 CTGCR 137
                                       ****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1087.52
//
Query:       gi|386002311|ref|YP_005920610.1|  [L=154]
Description: Formate dehydrogenase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-13   49.7  10.6    3.1e-13   49.7  10.6    1.7  2  Fer4_11        4Fe-4S dicluster domain
    1.7e-11   43.7  32.9    1.6e-05   24.8   1.8    4.3  4  Fer4_6         4Fe-4S binding domain
    6.3e-11   41.6  37.9    6.9e-07   28.8   3.7    5.3  6  Fer4           4Fe-4S binding domain
    3.1e-10   40.5  29.4     0.0008   19.9  14.2    3.6  4  Fer4_7         4Fe-4S dicluster domain
    6.8e-09   35.8  26.7    0.00051   20.2   8.6    3.1  3  Fer4_9         4Fe-4S dicluster domain
    4.8e-07   30.6  23.2      0.015   16.2   3.9    4.3  4  Fer4_16        4Fe-4S double cluster binding domain
    6.4e-07   29.4  29.6    0.00027   21.0  12.4    3.3  3  Fer4_10        4Fe-4S dicluster domain
    6.9e-07   29.0  33.6    0.00012   21.9   2.2    4.3  4  Fer4_2         4Fe-4S binding domain
    4.2e-06   27.3  45.2     0.0044   17.8   5.9    4.3  4  Fer4_3         4Fe-4S binding domain
    4.4e-06   26.8  29.2     0.0047   17.3   3.3    4.3  4  Fer4_4         4Fe-4S binding domain
    0.00062   19.8  29.1      0.008   16.3  10.5    2.9  3  Fer4_21        4Fe-4S dicluster domain
     0.0011   19.5  24.3     0.0049   17.4   0.7    4.1  4  Fer4_17        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.1  30.9       0.96    9.9  12.0    3.7  2  Fer4_8         4Fe-4S dicluster domain
       0.21   11.7   0.6       0.57   10.3   0.6    1.7  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.6       1.7   2.2e+03      10      74 ..      13      19 ..       4      40 .. 0.57
   2 !   49.7  10.6   2.5e-16   3.1e-13       6     100 .]      40     126 ..      35     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                           Fer4_11 10 CrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmc 74
                                      Cr                                                          +C++ 
  gi|386002311|ref|YP_005920610.1| 13 CR----------------------------------------------------------ACEVA 19
                                      22..........................................................23333 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 2.5e-16
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p  C+hC+ +pC+ ++ps+a++++e    V ++  ++  ++  +v acP+ +v  + +++ v+kCd+c dr     
  gi|386002311|ref|YP_005920610.1|  40 VPVACHHCEAAPCALVCPSGALTQEE--AEVGFEAGKCT-RCGLCVVACPFGAVDLDPASM-VQKCDLCPDREV--- 109
                                       7999*******************998..78********8.****************99887.9*********86... PP

                           Fer4_11  83 lpacvescptgalnfgdr 100
                                        p cv +cp++al fgdr
  gi|386002311|ref|YP_005920610.1| 110 -PPCVLTCPAEALIFGDR 126
                                       .***************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.7   1.2e-05     0.016       2      20 ..       3      21 ..       2      29 .. 0.90
   2 !   11.3   4.3   0.00023      0.29       8      24 .]      43      61 ..      40      61 .. 0.91
   3 !   24.8   1.8   1.2e-08   1.6e-05       3      23 ..      69      89 ..      67      90 .. 0.89
   4 !    9.8   2.4   0.00065      0.84       7      24 .]      99     121 ..      96     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      + +d ++Ci C++C+++C 
  gi|386002311|ref|YP_005920610.1|  3 IYVDLERCIFCRACEVACE 21
                                      689***************6 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00023
                            Fer4_6  8 kCigCgd..CvrvCPegai 24
                                      +C +C++  C+ vCP ga+
  gi|386002311|ref|YP_005920610.1| 43 ACHHCEAapCALVCPSGAL 61
                                      8****999*********97 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.2e-08
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                       + + kC+ Cg Cv++CP+ga
  gi|386002311|ref|YP_005920610.1| 69 GFEAGKCTRCGLCVVACPFGA 89
                                      57788**************98 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00065
                            Fer4_6   7 dkCigC.gd....CvrvCPegai 24 
                                       +kC+ C ++    Cv  CP+ a+
  gi|386002311|ref|YP_005920610.1|  99 QKCDLCpDRevppCVLTCPAEAL 121
                                       69****8889**********996 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.5   1.7e-07   0.00021       1      18 [.       3      20 ..       3      22 .. 0.94
   2 ?   -0.8   0.1       1.2   1.5e+03       8      12 ..      44      48 ..      41      50 .. 0.60
   3 !    9.3   0.3    0.0008         1      14      24 .]      52      62 ..      51      62 .. 0.94
   4 !   28.8   3.7   5.4e-10   6.9e-07       5      23 ..      72      90 ..      68      91 .. 0.89
   5 ?   -2.1   0.4       3.1     4e+03       7      11 ..     100     104 ..      99     104 .. 0.64
   6 ?    5.0   0.5     0.019        24      14      23 ..     112     121 ..     112     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                                      EEEETTTSSS-THHHHHS CS
                              Fer4  1 vvideekCigCGaCvevC 18
                                      +++d e+Ci+C aC+ +C
  gi|386002311|ref|YP_005920610.1|  3 IYVDLERCIFCRACEVAC 20
                                      69**************** PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                      SSS-T CS
                              Fer4  8 CigCG 12
                                      C +C 
  gi|386002311|ref|YP_005920610.1| 44 CHHCE 48
                                      66664 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0008
                                      HHHHSTTTEEE CS
                              Fer4 14 CvevCPvgAIt 24
                                      C+ vCP gA+t
  gi|386002311|ref|YP_005920610.1| 52 CALVCPSGALT 62
                                      *********86 PP

  == domain 4  score: 28.8 bits;  conditional E-value: 5.4e-10
                                      TTTSSS-THHHHHSTTTEE CS
                              Fer4  5 eekCigCGaCvevCPvgAI 23
                                        kC++CG+Cv +CP+gA 
  gi|386002311|ref|YP_005920610.1| 72 AGKCTRCGLCVVACPFGAV 90
                                      679**************96 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 3.1
                                       TSSS- CS
                              Fer4   7 kCigC 11 
                                       kC  C
  gi|386002311|ref|YP_005920610.1| 100 KCDLC 104
                                       66666 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.019
                                       HHHHSTTTEE CS
                              Fer4  14 CvevCPvgAI 23 
                                       Cv  CP +A+
  gi|386002311|ref|YP_005920610.1| 112 CVLTCPAEAL 121
                                       ********97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   3.3    0.0001      0.13      30      48 ..       2      20 ..       1      23 [. 0.80
   2 !   19.9  14.2   6.3e-07    0.0008       1      52 []       9      60 ..       9      60 .. 0.78
   3 !   18.6  10.2   1.7e-06    0.0022       1      52 []      74     120 ..      74     120 .. 0.78
   4 ?    6.3   0.5     0.011        14       2      26 ..     101     130 ..     100     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            Fer4_7 30 kveidpekClgCgaCvavC 48
                                      ++++d e+C++C+aC+ +C
  gi|386002311|ref|YP_005920610.1|  2 EIYVDLERCIFCRACEVAC 20
                                      5678889999999999888 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.3e-07
                            Fer4_7  1 rCigCgaCvaaCp..vkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                      rCi C+aC++aC   +++ ++      + +++ + +p  C +C+a  C+ vCP+ga
  gi|386002311|ref|YP_005920610.1|  9 RCIFCRACEVACErvHGTSRIS----VEAVKDRASVPVACHHCEAapCALVCPSGA 60
                                      8***********9643333333....3344566889******************98 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.7e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                       +C+ Cg Cv+aCp +a++ld++       +++ + + C + ++  Cv +CP++a
  gi|386002311|ref|YP_005920610.1|  74 KCTRCGLCVVACPFGAVDLDPA-------SMVQKCDLCPDREVppCVLTCPAEA 120
                                       7*******************98.......3444555565555566999999876 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.011
                            Fer4_7   2 CigCg.....aCvaaCpvkaieldeeenek 26 
                                       C  C       Cv +Cp++a+ + ++ ++ 
  gi|386002311|ref|YP_005920610.1| 101 CDLCPdrevpPCVLTCPAEALIFGDRFEAT 130
                                       666633444479999999999887776554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  10.6   6.1e-07   0.00079       1      50 [.       9      60 ..       9      61 .. 0.82
   2 !   20.2   8.6     4e-07   0.00051       1      50 [.      74     120 ..      74     122 .. 0.89
   3 ?    5.6   1.3     0.014        18       1      17 [.     100     121 ..     100     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.1e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga..CveaCpkga 50
                                      +C+ C+aC+ aC+  + + + + + ++ ra    aC++C+a  C+ +Cp+ga
  gi|386002311|ref|YP_005920610.1|  9 RCIFCRACEVACERVHGTSRISVEAVKDRASVPVACHHCEAapCALVCPSGA 60
                                      5***********77776666666666666655689**************997 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                       kCt+Cg Cv aCp+g+v  d a    +        C  C +     Cv  Cp +a
  gi|386002311|ref|YP_005920610.1|  74 KCTRCGLCVVACPFGAVDLDPASMVQK--------CDLCPDrevppCVLTCPAEA 120
                                       7****************9999887765........888888889********876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.014
                            Fer4_9   1 kCtgCga.....CveaCpagvv 17 
                                       kC  C       Cv  Cpa++ 
  gi|386002311|ref|YP_005920610.1| 100 KCDLCPDrevppCVLTCPAEAL 121
                                       5777743345558888888765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.0     0.022        28       1      12 [.       9      20 ..       5      35 .. 0.79
   2 !   14.9   1.6     3e-05     0.039       2      23 ..      44      67 ..      43      73 .. 0.86
   3 !   16.2   3.9   1.2e-05     0.015       1      26 [.      74      99 ..      74     108 .. 0.83
   4 ?    4.9   0.6     0.041        52       8      27 ..     112     129 ..     100     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                           Fer4_16  1 rCgtCgkCaevC 12
                                      rC+ C++C  +C
  gi|386002311|ref|YP_005920610.1|  9 RCIFCRACEVAC 20
                                      466677777776 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3e-05
                           Fer4_16  2 CgtCgk..CaevCPtnaikekkek 23
                                      C+ C++  Ca vCP++a+++++++
  gi|386002311|ref|YP_005920610.1| 44 CHHCEAapCALVCPSGALTQEEAE 67
                                      *****999***********99543 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.2e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeie 26
                                      +C++Cg C+ +CP +a++ + + +++
  gi|386002311|ref|YP_005920610.1| 74 KCTRCGLCVVACPFGAVDLDPASMVQ 99
                                      6****************999655554 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.041
                           Fer4_16   8 CaevCPtnaikekkekeiea 27 
                                       C+ +CP++a+      ++ea
  gi|386002311|ref|YP_005920610.1| 112 CVLTCPAEALIFG--DRFEA 129
                                       99*******9877..34444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9  12.5     7e-05     0.089       2      56 .]       3      57 ..       2      57 .. 0.82
   2 !   21.0  12.4   2.1e-07   0.00027       7      56 .]      42      86 ..      38      86 .. 0.86
   3 !   17.3  10.0   3.1e-06    0.0039       4      56 .]      70     117 ..      67     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk..kvekCtgcg..aCveaCP 56
                                      +++d ++Ci C++C  aC    ++v ++  +s e++++   ++ +C++c+   C+ +CP
  gi|386002311|ref|YP_005920610.1|  3 IYVDLERCIFCRACEVAC----ERVHGTSRISVEAVKDRasVPVACHHCEaaPCALVCP 57
                                      67899*************....5777777777776666556899*****7669*****9 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                           Fer4_10  7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                        C +C+   C  +CP+        g+ ++eea+ +   +kCt+cg Cv aCP
  gi|386002311|ref|YP_005920610.1| 42 VACHHCEaaPCALVCPS--------GALTQEEAEVGfEAGKCTRCGLCVVACP 86
                                      57****9999*******........6666666666669**************9 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 3.1e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc...g..aCveaCP 56 
                                       +++ +C+rCg Cv aCP+             +      v+kC+ c   +   Cv  CP
  gi|386002311|ref|YP_005920610.1|  70 FEAGKCTRCGLCVVACPF----------GAVDLDPASMVQKCDLCpdrEvpPCVLTCP 117
                                       56789*************..........444444444577788885442669****99 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   2.4     6e-05     0.077       3      20 ..       3      20 ..       1      21 [. 0.94
   2 ?    4.9   3.6     0.025        32       9      21 ..      43      57 ..      34      58 .. 0.85
   3 !   21.9   2.2   9.5e-08   0.00012       4      21 ..      69      86 ..      66      87 .. 0.87
   4 !    6.8   2.5    0.0061       7.8       8      22 .]      99     118 ..      90     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-05
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      ++vd +rCi C+aC  aC
  gi|386002311|ref|YP_005920610.1|  3 IYVDLERCIFCRACEVAC 20
                                      79**************** PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.025
                            Fer4_2  9 rCigCg..aCvsaCP 21
                                      +C +C+  +C  +CP
  gi|386002311|ref|YP_005920610.1| 43 ACHHCEaaPCALVCP 57
                                      47789888******* PP

  == domain 3  score: 21.9 bits;  conditional E-value: 9.5e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       +++ +C++Cg Cv aCP
  gi|386002311|ref|YP_005920610.1| 69 GFEAGKCTRCGLCVVACP 86
                                      67888************* PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0061
                            Fer4_2   8 drCigC..g...aCvsaCPa 22 
                                       ++C  C  +   +Cv  CPa
  gi|386002311|ref|YP_005920610.1|  99 QKCDLCpdRevpPCVLTCPA 118
                                       689999653788*******8 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   4.4    0.0035       4.4       1      11 [.      10      20 ..      10      22 .. 0.97
   2 !   14.2   7.2   5.1e-05     0.065       1      15 []      44      60 ..      44      60 .. 0.90
   3 !   17.8   5.9   3.5e-06    0.0044       1      15 []      75      89 ..      75      89 .. 0.98
   4 ?    5.6   3.9     0.028        35       1      13 [.     101     118 ..     101     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+ C+aC+++C
  gi|386002311|ref|YP_005920610.1| 10 CIFCRACEVAC 20
                                      *********** PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.1e-05
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C++C+  +C  vCP+gA
  gi|386002311|ref|YP_005920610.1| 44 CHHCEaaPCALVCPSGA 60
                                      ****9556********9 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.5e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg+Cv++CP gA
  gi|386002311|ref|YP_005920610.1| 75 CTRCGLCVVACPFGA 89
                                      *************98 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.028
                            Fer4_3   1 CtgCg.....aCvevCPv 13 
                                       C+ C      +Cv  CP 
  gi|386002311|ref|YP_005920610.1| 101 CDLCPdrevpPCVLTCPA 118
                                       999*6567888******5 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.7   8.5e-05      0.11       2      15 ..       8      21 ..       7      31 .. 0.92
   2 !    7.5   1.4    0.0051       6.6       4      17 .]      44      59 ..      35      63 .. 0.88
   3 !   17.3   3.3   3.6e-06    0.0047       3      17 .]      74      88 ..      72      88 .. 0.92
   4 ?    5.3   1.1     0.026        34       3      16 ..     100     118 ..      99     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      erCi C++C+ aC+
  gi|386002311|ref|YP_005920610.1|  8 ERCIFCRACEVACE 21
                                      9************8 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                            Fer4_4  4 CigCgs..CvaaCPqg 17
                                      C +C +  C  +CP+g
  gi|386002311|ref|YP_005920610.1| 44 CHHCEAapCALVCPSG 59
                                      *****99*******75 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 3.6e-06
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C++Cg Cv aCP+g
  gi|386002311|ref|YP_005920610.1| 74 KCTRCGLCVVACPFG 88
                                      8************86 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.026
                            Fer4_4   3 rCigCgs.....CvaaCPq 16 
                                       +C  C+      Cv +CP 
  gi|386002311|ref|YP_005920610.1| 100 KCDLCPDrevppCVLTCPA 118
                                       788888556788******5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  10.5   6.2e-06     0.008       3      56 ..       5      60 ..       4      63 .. 0.79
   2 !   14.7   1.2   1.9e-05     0.025      38      57 ..      72      90 ..      59      92 .. 0.68
   3 !    8.4  10.6    0.0018       2.3       6      54 ..      73     119 ..      66     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                           Fer4_21  3 idedkCigCgkCliaCed.tshqaieidaktvlkvvedeCvGCnl..CssvCPvedc 56
                                      +d ++Ci C  C +aCe   ++  i+++a +  + v   C  C+   C+ vCP +++
  gi|386002311|ref|YP_005920610.1|  5 VDLERCIFCRACEVACERvHGTSRISVEAVKDRASVPVACHHCEAapCALVCP-SGA 60
                                      6889************9625677888888887788888899997555******.466 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                           Fer4_21 38 edeCvGCnlCssvCPvedci 57
                                      + +C+ C lC+  CP  +++
  gi|386002311|ref|YP_005920610.1| 72 AGKCTRCGLCVVACPF-GAV 90
                                      5578888888888885.554 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnl..CssvCPve 54 
                                        kC  Cg+C++aC+     a+++d++++++   d C   ++  C+  CP e
  gi|386002311|ref|YP_005920610.1|  73 GKCTRCGLCVVACP---FGAVDLDPASMVQK-CDLCPDREVppCVLTCPAE 119
                                       68999999999999...78888998888543.4666655544488888864 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.1    0.0014       1.8      44      57 ..       8      21 ..       2      27 .. 0.82
   2 !    8.5   1.3    0.0023         3       1      21 [.      43      65 ..      43      72 .. 0.86
   3 !   17.4   0.7   3.8e-06    0.0049      39      58 ..      68      87 ..      59      93 .. 0.77
   4 !    8.9   7.9    0.0017       2.2       1      27 [.      74      99 ..      74     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++Ci C+ Ce +C 
  gi|386002311|ref|YP_005920610.1|  8 ERCIFCRACEVACE 21
                                      68888888888885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0023
                           Fer4_17  1 rCiqCgy..ClpeCpsyeaydne 21
                                      +C++C++  C+ +Cps++ +++e
  gi|386002311|ref|YP_005920610.1| 43 ACHHCEAapCALVCPSGALTQEE 65
                                      5*****999*******9998876 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.8e-06
                           Fer4_17 39 keekaslCieCgeCerkCPq 58
                                         +a++C+ Cg+C+ +CP 
  gi|386002311|ref|YP_005920610.1| 68 VGFEAGKCTRCGLCVVACPF 87
                                      34689999999999999996 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0017
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllr 27
                                      +C++Cg C+ +Cp+++   + p+++++
  gi|386002311|ref|YP_005920610.1| 74 KCTRCGLCVVACPFGAVDLD-PASMVQ 99
                                      59999999999998877544.555555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  12.0   0.00075      0.96       2      64 ..       7      59 ..       6      60 .. 0.85
   2 ?    8.0  11.0     0.003       3.9       2      19 ..      72      89 ..      71     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                      le+Ci C aC+ aC  ++ t + + +a +++a       v        +C++c+a  C+ vCp g
  gi|386002311|ref|YP_005920610.1|  7 LERCIFCRACEVACERVHGTSRISVEAVKDRAS------V------PVACHHCEAapCALVCPSG 59
                                      79************9999998887777777666......3......569**************86 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                            Fer4_8  2 lekCieCgaCqsaCpvlr 19
                                      + kC++Cg+C  aCp+  
  gi|386002311|ref|YP_005920610.1| 72 AGKCTRCGLCVVACPFGA 89
                                      568999999999999654 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00045      0.57      32      67 ..      14      49 ..      12      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                                      CHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B CS
                     Fe_dep_repr_C 32 eaheeAerlEhalseelierldellgfpeecPhgdp 67
                                      +a+e A++  h +s+ ++e++ +  + p  c h + 
  gi|386002311|ref|YP_005920610.1| 14 RACEVACERVHGTSRISVEAVKDRASVPVACHHCEA 49
                                      69*****************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 951.44
//
Query:       gi|386002312|ref|YP_005920611.1|  [L=681]
Description: Formate dehydrogenase, subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete 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-82  277.1   0.0    3.3e-82  276.8   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.7e-29  101.4   0.0    4.5e-29  100.7   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
      7e-10   38.8   0.1    1.4e-09   37.7   0.1    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.8   0.0   5.5e-86   3.3e-82       1     430 [.      60     481 ..      60     483 .. 0.92

  Alignments for each domain:
  == domain 1  score: 276.8 bits;  conditional E-value: 5.5e-86
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl+ P+++      ++++r+sW+eAl+  a ++k+ti +ygp +  + +s + + +e+ ++++k+++llg+kn+ + 
  gi|386002312|ref|YP_005920611.1|  60 RLRFPLLK---A-GDGWRRISWEEALARLAGEIKETIRDYGPGALGFLGSAKCT-NEENYLFQKMARLLGSKNVDCC 131
                                       9*******...6.567**************************999988887777.9***************988888 PP

                                       ECCGGGTTHHHH..CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB- CS
                     Molybdopterin  78 dwyadlppasaq..qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigprya 152
                                          ++ p+   +  +++g+      +++np++dl+ns+ i+++GsN +e++p++ ar   +a+ ++  +iv +pr++
  gi|386002312|ref|YP_005920611.1| 132 ARRCHSPTIP-AlnRAFGA-----ACMTNPISDLANSGCIFAIGSNFAENHPLV-ARWALRAKDRGGFIIVADPRLT 201
                                       8888886644.34666666.....48899*************************.7887777777799********* PP

                                       HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHH CS
                     Molybdopterin 153 ellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelar 229
                                        ++  ad++l i+ gtd+al+++m++vi++e++++ +f++ +t+g+ee+++ +  +++e+++++++v a  + + ar
  gi|386002312|ref|YP_005920611.1| 202 PTAWLADLHLQINLGTDVALLNGMMNVIIEEGLYNSKFVEERTVGFEELADKVRWYTPERAAEITGVSASSILRAAR 278
                                       *7778************************************************************999999999998 PP

                                       HHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT CS
                     Molybdopterin 230 naaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke 306
                                        +a     s+i++ +g++++++g++++ a + Lal++g  g++g+g   l+Gq++++g a+++g l+  ++ + +++
  gi|386002312|ref|YP_005920611.1| 279 IYARSPA-SAILYSMGITQHSHGTDNVTACADLALICGHLGRSGAGLYPLRGQNNVQG-ACDMGVLADFYPGSVSVS 353
                                       8887777.**************************************************.**************9999 PP

                                       ....HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHH CS
                     Molybdopterin 307 ....ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltst 379
                                            +   +a++   l++  + ++  +  ++++++++ ly++g++ +++++  ++  ++l +ld++ v d+++t+t
  gi|386002312|ref|YP_005920611.1| 354 daegIRRLEVAWGGASLPKGMGMTAEAMPVAAGDGDLRLLYVMGEDIVNSDSASSRGRRELANLDFLAVQDIFMTET 430
                                       88753444467888889999999999999***************888888888888888999*************** PP

                                       HHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHH CS
                     Molybdopterin 380 alyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLa 430
                                       a++aD++LPaa+w Ek + yt++e+r+q   +a++ppgea+sd + +  La
  gi|386002312|ref|YP_005920611.1| 431 AEIADLVLPAAAWAEKAGSYTSTERRVQWSPRAIDPPGEARSDLSTIIRLA 481
                                       *******************************************98877776 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   7.5e-33   4.5e-29       1     110 [.     568     671 ..     568     672 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 7.5e-33
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l L+tgr++ +++++ +tr++l+l +++p  +ve+np dA + G+ dGdlVeve+rrG++ +ra+vt r  +Gv+fm
  gi|386002312|ref|YP_005920611.1| 568 LLLTTGRVVIHYNAGSMTRRSLSLMRRAPeLFVEVNPGDADQWGVVDGDLVEVETRRGEAWARARVTTRQERGVLFM 644
                                       689************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-E CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksv 110
                                       pf+++e       +N+lt+d +dp++++pefk++
  gi|386002312|ref|YP_005920611.1| 645 PFHFPE-------TNTLTSDVIDPVARIPEFKVA 671
                                       ******.......******************986 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   2.4e-13   1.4e-09       5      52 ..       8      54 ..       6      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.4e-13
                                      EEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4  5 ktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52
                                      +t+CpyC  gCg+ +    g    +e   dhp+neg lC+KG+++le 
  gi|386002312|ref|YP_005920611.1|  8 PTVCPYCALGCGFYIRKGEGGP-GIEYMLDHPTNEGALCPKGNAALEV 54
                                      79************99866666.8*******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 4294.73
//
Query:       gi|386002313|ref|YP_005920612.1|  [L=171]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.7  70.8    1.2e-06   29.0  12.2    3.4  5  Fer4_7    4Fe-4S dicluster domain
    6.5e-16   58.3  11.1    6.5e-16   58.3  11.1    2.0  2  Fer4_11   4Fe-4S dicluster domain
    5.4e-12   45.7  45.1    1.9e-05   24.7  10.9    2.9  3  Fer4_9    4Fe-4S dicluster domain
    1.6e-10   40.6  34.9      0.002   18.1   1.3    4.7  4  Fer4_6    4Fe-4S binding domain
    1.7e-10   40.3  39.1    0.00016   21.3   2.3    5.4  6  Fer4      4Fe-4S binding domain
    1.2e-09   39.0  21.9      0.017   16.1   2.0    4.3  4  Fer4_16   4Fe-4S double cluster binding domain
    1.7e-09   37.6  28.5    0.00058   19.9  12.4    3.2  3  Fer4_10   4Fe-4S dicluster domain
    3.3e-09   36.3  33.2     0.0088   16.1   2.2    4.3  4  Fer4_2    4Fe-4S binding domain
    6.1e-07   29.5  36.8     0.0075   16.7   4.0    4.4  4  Fer4_4    4Fe-4S binding domain
    0.00022   21.6  23.3     0.0026   18.2   6.5    3.3  4  Fer4_8    4Fe-4S dicluster domain
     0.0029   18.4  42.6      0.036   15.0   6.0    4.3  4  Fer4_3    4Fe-4S binding domain
     0.0044   17.1  32.0       0.11   12.6  11.6    3.8  3  Fer4_21   4Fe-4S dicluster domain
     0.0053   17.3  26.0       0.62   10.6   2.4    4.3  5  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.17   11.7  23.9       0.27   11.0   0.6    3.5  3  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.19   11.7   5.8        5.5    7.1   0.1    2.6  2  DUF4033   Domain of unknown function (DUF4033)


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   3.2   3.8e-05     0.046      30      50 ..       3      23 ..       1      25 [. 0.79
   2 !   29.0  12.2     1e-09   1.2e-06       1      52 []      10      77 ..      10      77 .. 0.66
   3 !   26.2  13.4   7.7e-09   9.2e-06       1      51 [.      60     107 ..      60     108 .. 0.92
   4 !   22.6  11.3     1e-07   0.00012       2      52 .]      94     140 ..      93     140 .. 0.88
   5 !   16.1   0.5   1.1e-05     0.013       1      27 [.     120     151 ..     119     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                            Fer4_7 30 kveidpekClgCgaCvavCPt 50
                                      ++ i+pe+C+gC++C+ +C +
  gi|386002313|ref|YP_005920612.1|  3 EILIRPERCMGCRSCEIACAV 23
                                      566889999999999999965 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaield.......eeenekgt......ekveid.pekClgCga..CvavCPtga 52
                                      rC+gC+ C+ aC v+  + +       e+  ++++      +++ i+ p+ C +C++  Cv+vCPtga
  gi|386002313|ref|YP_005920612.1| 10 RCMGCRSCEIACAVEHSQAKsllsavaERPAPRKRvyvefvPDYSISvPMACRHCEEapCVSVCPTGA 77
                                      8***********877777663333322222222222333345566644889*****99********98 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 7.7e-09
                            Fer4_7   1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       +C +C+   Cv++Cp++a++ de+     t+ v+++pe C+gC  C++vC +g
  gi|386002313|ref|YP_005920612.1|  60 ACRHCEeaPCVSVCPTGALRQDEV-----TRVVTHNPEGCIGCWTCASVCSYG 107
                                       5****7669**************9.....6789*****************987 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 1e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                       CigC  C+++C+++ i  + e      e+v+i+ ++C + ++  Cv++CPtga
  gi|386002313|ref|YP_005920612.1|  94 CIGCWTCASVCSYGMIGRNRE------ERVAIKCDRCPDLEVpaCVSACPTGA 140
                                       *****************9876......579*******7655444*******98 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 1.1e-05
                            Fer4_7   1 rCigCg.....aCvaaCpvkaieldeeenekg 27 
                                       +C  C      aCv+aCp++a+ ++e e+ ++
  gi|386002313|ref|YP_005920612.1| 120 KCDRCPdlevpACVSACPTGALVFKELEEFSE 151
                                       69999555666*************98765444 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5      0.29   3.5e+02       4      22 ..       5      21 ..       2      40 .. 0.62
   2 !   58.3  11.1   5.4e-19   6.5e-16       6      99 ..      57     145 ..      53     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.29
                           Fer4_11  4 lflpeqCrhCleppCvasa 22
                                      l+ pe C+ C +  C  ++
  gi|386002313|ref|YP_005920612.1|  5 LIRPERCMGCRS--CEIAC 21
                                      667888888864..32222 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 5.4e-19
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p  CrhC+e+pCv+++p++a+ +de t +V  +++ +  ++ +++++c y ++ +n+e+ ++ kCd c d      
  gi|386002313|ref|YP_005920612.1|  57 VPMACRHCEEAPCVSVCPTGALRQDEVTRVVTHNPEGCI-GCWTCASVCSYGMIGRNREERVAIKCDRCPDLEV--- 129
                                       799***********************************7.*****************************99865... PP

                           Fer4_11  83 lpacvescptgalnfgd 99 
                                        pacv++cptgal f +
  gi|386002313|ref|YP_005920612.1| 130 -PACVSACPTGALVFKE 145
                                       .***********99975 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   8.7   5.7e-08   6.8e-05       1      50 [.      10      77 ..      10      78 .. 0.85
   2 !   24.7  10.9   1.6e-08   1.9e-05       1      51 []      60     109 ..      60     109 .. 0.90
   3 !   23.1   9.5     5e-08     6e-05       2      50 ..      94     140 ..      93     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.7e-08
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase................eaCigCga..CveaCpkga 50
                                      +C+gC++C+ aC  ++ + ++    ++ r a                   aC +C++  Cv +Cp+ga
  gi|386002313|ref|YP_005920612.1| 10 RCMGCRSCEIACAVEHSQAKSLLSAVAERPAPRkrvyvefvpdysisvpMACRHCEEapCVSVCPTGA 77
                                      6***********888888887777777666555788889999999999999***************97 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.6e-08
                            Fer4_9   1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C  C +  Cv++Cp+g+ ++d+++r + ++ +    CigC +C+ +C  g+i
  gi|386002313|ref|YP_005920612.1|  60 ACRHCEEapCVSVCPTGALRQDEVTRVVTHNPE---GCIGCWTCASVCSYGMI 109
                                       599**8667********************9775...6***********99865 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 5e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                       C+gC +C ++C +g++ + + er a        +C  C +     Cv aCp+ga
  gi|386002313|ref|YP_005920612.1|  94 CIGCWTCASVCSYGMIGRNREERVAI-------KCDRCPDlevpaCVSACPTGA 140
                                       *******************9999999.......5*****9************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   6.6e-06    0.0079       4      20 ..       6      22 ..       3      28 .. 0.85
   2 !   15.0   4.2   1.6e-05      0.02       8      24 .]      60      78 ..      58      78 .. 0.93
   3 !   18.1   1.3   1.7e-06     0.002       1      24 []      86     109 ..      86     109 .. 0.96
   4 !    8.1   5.3    0.0025         3       8      24 .]     120     141 ..     119     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                            Fer4_6  4 idpdkCigCgdCvrvCP 20
                                      i p++C gC+ C+++C 
  gi|386002313|ref|YP_005920612.1|  6 IRPERCMGCRSCEIACA 22
                                      789*************7 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-05
                            Fer4_6  8 kCigCgd..CvrvCPegai 24
                                      +C +C++  Cv+vCP+ga+
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEEapCVSVCPTGAL 78
                                      6****999*********97 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.7e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       vv+++p+ CigC  C++vC +g+i
  gi|386002313|ref|YP_005920612.1|  86 VVTHNPEGCIGCWTCASVCSYGMI 109
                                       799*******************98 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0025
                            Fer4_6   8 kCigC.gd....CvrvCPegai 24 
                                       kC+ C +     Cv++CP+ga+
  gi|386002313|ref|YP_005920612.1| 120 KCDRCpDLevpaCVSACPTGAL 141
                                       577774447777********97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.8   3.8e-06    0.0046       3      18 ..       6      21 ..       4      21 .. 0.93
   2 ?   -1.0   0.3       1.5   1.8e+03      10      17 ..      60      67 ..      59      67 .. 0.72
   3 !   13.5   0.3   4.1e-05     0.049      14      24 .]      69      79 ..      68      79 .. 0.93
   4 !   21.3   2.3   1.4e-07   0.00016       2      23 ..      88     109 ..      87     110 .. 0.90
   5 ?   -1.7   0.7       2.4   2.9e+03      10      14 ..     120     124 ..     119     124 .. 0.51
   6 !   14.0   0.7   2.8e-05     0.033      13      23 ..     131     141 ..     131     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                                      EETTTSSS-THHHHHS CS
                              Fer4  3 ideekCigCGaCvevC 18
                                      i +e+C+gC  C+ +C
  gi|386002313|ref|YP_005920612.1|  6 IRPERCMGCRSCEIAC 21
                                      889************* PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                      S-THHHHH CS
                              Fer4 10 gCGaCvev 17
                                      +C  C+e+
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEEA 67
                                      68888876 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.1e-05
                                      HHHHSTTTEEE CS
                              Fer4 14 CvevCPvgAIt 24
                                      Cv+vCP+gA++
  gi|386002313|ref|YP_005920612.1| 69 CVSVCPTGALR 79
                                      *********85 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 1.4e-07
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       + ++e CigC +C++vC +g I
  gi|386002313|ref|YP_005920612.1|  88 THNPEGCIGCWTCASVCSYGMI 109
                                       689**************99877 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 2.4
                                       S-THH CS
                              Fer4  10 gCGaC 14 
                                       +C +C
  gi|386002313|ref|YP_005920612.1| 120 KCDRC 124
                                       55555 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 2.8e-05
                                       HHHHHSTTTEE CS
                              Fer4  13 aCvevCPvgAI 23 
                                       aCv++CP+gA+
  gi|386002313|ref|YP_005920612.1| 131 ACVSACPTGAL 141
                                       7*********8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.4    0.0027       3.2       1      14 [.      10      23 ..       4      44 .. 0.73
   2 !   16.1   2.0   1.4e-05     0.017       2      24 ..      61      85 ..      60      92 .. 0.82
   3 !   11.7   3.3   0.00033       0.4       2      28 ..      94     120 ..      93     130 .. 0.86
   4 !   13.1   0.8   0.00012      0.14       7      30 ..     131     154 ..     119     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                           Fer4_16  1 rCgtCgkCaevCPt 14
                                      rC +C+ C  +C +
  gi|386002313|ref|YP_005920612.1| 10 RCMGCRSCEIACAV 23
                                      35555555555554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.4e-05
                           Fer4_16  2 CgtCgk..CaevCPtnaikekkeke 24
                                      C  C++  C++vCPt+a+++++ ++
  gi|386002313|ref|YP_005920612.1| 61 CRHCEEapCVSVCPTGALRQDEVTR 85
                                      99**9999***********995444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00033
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                       C++C  Ca+vC  + i  ++e++++++
  gi|386002313|ref|YP_005920612.1|  94 CIGCWTCASVCSYGMIGRNREERVAIK 120
                                       *****************9988877665 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00012
                           Fer4_16   7 kCaevCPtnaikekkekeiearec 30 
                                       +C+++CPt+a+  k+ +e+   + 
  gi|386002313|ref|YP_005920612.1| 131 ACVSACPTGALVFKELEEFSESKR 154
                                       7***********996666654443 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   6.5e-06    0.0078       2      23 ..       4      23 ..       3      43 .. 0.74
   2 !   19.9  12.4   4.9e-07   0.00058       7      55 ..      59     104 ..      54     105 .. 0.93
   3 !   19.3  11.6   7.7e-07   0.00092       3      56 .]      88     137 ..      86     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.5e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      + i +++C++C+ C  aC a +
  gi|386002313|ref|YP_005920612.1|  4 ILIRPERCMGCRSCEIAC-A-V 23
                                      57899*************.3.2 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.9e-07
                           Fer4_10   7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                         C +C+   Cv++CP+     ga  +++   +v +++e C+gc  C+++C
  gi|386002313|ref|YP_005920612.1|  59 MACRHCEeaPCVSVCPT-----GALRQDEVTRVVTHNPEGCIGCWTCASVC 104
                                       68*****999*******.....999999999999***************** PP

  == domain 3  score: 19.3 bits;  conditional E-value: 7.7e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56 
                                        ++++ Ci+C +C ++C +    +g +  +++ee+v +k+++C++ +  aCv+aCP
  gi|386002313|ref|YP_005920612.1|  88 THNPEGCIGCWTCASVC-S----YGMI-GRNREERVAIKCDRCPDLEvpACVSACP 137
                                       6799*************.3....4444.456677788899999997777******9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.0   8.8e-06     0.011       5      20 ..       6      21 ..       2      23 .. 0.86
   2 !   16.1   2.2   7.4e-06    0.0088       9      22 .]      60      75 ..      46      75 .. 0.85
   3 !   11.3   3.1   0.00025      0.29       2      20 ..      86     104 ..      85     106 .. 0.89
   4 !   10.9   2.9   0.00032      0.39       9      22 .]     120     138 ..     112     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.8e-06
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                      + ++rC+gC++C  aC
  gi|386002313|ref|YP_005920612.1|  6 IRPERCMGCRSCEIAC 21
                                      569***********99 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7.4e-06
                            Fer4_2  9 rCigCg..aCvsaCPa 22
                                      +C +C+  +Cvs+CP+
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEeaPCVSVCPT 75
                                      7****889*******7 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00025
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       +v  +++ CigC +C s+C
  gi|386002313|ref|YP_005920612.1|  86 VVTHNPEGCIGCWTCASVC 104
                                       57889************** PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00032
                            Fer4_2   9 rCigCg.....aCvsaCPa 22 
                                       +C +C      aCvsaCP+
  gi|386002313|ref|YP_005920612.1| 120 KCDRCPdlevpACVSACPT 138
                                       79999445688*******7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.0   6.3e-06    0.0075       1      14 [.       8      21 ..       8      24 .. 0.91
   2 !   10.0   4.1   0.00089       1.1       3      17 .]      60      76 ..      58      76 .. 0.91
   3 !    9.2   3.1    0.0016       1.9       2      17 .]      92     107 ..      91     107 .. 0.89
   4 !   11.3   2.3   0.00035      0.42       3      17 .]     120     139 ..     115     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-06
                            Fer4_4  1 qerCigCgsCvaaC 14
                                      +erC gC+sC++aC
  gi|386002313|ref|YP_005920612.1|  8 PERCMGCRSCEIAC 21
                                      69************ PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00089
                            Fer4_4  3 rCigCgs..CvaaCPqg 17
                                       C +C    Cv++CP+g
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEEapCVSVCPTG 76
                                      6*****99*******86 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e CigC  C ++C++g
  gi|386002313|ref|YP_005920612.1|  92 EGCIGCWTCASVCSYG 107
                                       78***********975 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00035
                            Fer4_4   3 rCigCg.....sCvaaCPqg 17 
                                       +C +C+     +Cv+aCP+g
  gi|386002313|ref|YP_005920612.1| 120 KCDRCPdlevpACVSACPTG 139
                                       599999777777******86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   6.5   2.2e-06    0.0026       3      64 ..       9      76 ..       8      77 .. 0.81
   2 ?    6.2   2.9     0.012        15      49      62 ..      92     105 ..      79     108 .. 0.63
   3 !    6.6   2.5    0.0088        11       4      16 ..      93     105 ..      90     120 .. 0.74
   4 ?    6.4   0.4      0.01        13      10      33 ..     131     158 ..     118     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvlee......eealwsCttcga..CtevCpvg 64
                                      e+C++C  C+ aC v ++++k ll+a  e+ +     +        e           +C +c++  C++vCp+g
  gi|386002313|ref|YP_005920612.1|  9 ERCMGCRSCEIACAVEHSQAKSLLSAVAERPAprkrvY-------VEfvpdysISVPMACRHCEEapCVSVCPTG 76
                                      68***********9999999999999999999544331.......2234556688899******99*******87 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                            Fer4_8  49 wsCttcgaCtevCp 62 
                                       + C +c  C++vC 
  gi|386002313|ref|YP_005920612.1|  92 EGCIGCWTCASVCS 105
                                       55666666666664 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0088
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                        Ci+C  C s C 
  gi|386002313|ref|YP_005920612.1|  93 GCIGCWTCASVCS 105
                                       5888888888885 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.01
                            Fer4_8  10 aCqsaCp....vlrrtkkhlldargeaa 33 
                                       aC saCp    v+++  +++ ++r e a
  gi|386002313|ref|YP_005920612.1| 131 ACVSACPtgalVFKELEEFSESKRAESA 158
                                       7889999888777777788887777765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.0     0.079        94       1      11 [.      11      21 ..      11      25 .. 0.91
   2 !   15.0   6.0     3e-05     0.036       1      15 []      61      77 ..      61      77 .. 0.91
   3 ?    5.0   3.6     0.047        57       1      14 [.      94     107 ..      94     107 .. 0.88
   4 !   12.7   4.3   0.00016      0.19       1      15 []     121     140 ..     121     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.079
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+ C+ +C
  gi|386002313|ref|YP_005920612.1| 11 CMGCRSCEIAC 21
                                      *********** PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3e-05
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C +C+  +Cv vCP+gA
  gi|386002313|ref|YP_005920612.1| 61 CRHCEeaPCVSVCPTGA 77
                                      99**8778********9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.047
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gC +C  vC +g
  gi|386002313|ref|YP_005920612.1|  94 CIGCWTCASVCSYG 107
                                       ****77*****876 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00016
                            Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                       C+ C      aCv +CP+gA
  gi|386002313|ref|YP_005920612.1| 121 CDRCPdlevpACVSACPTGA 140
                                       99996678999********9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9  11.7   0.00033      0.39       3      56 ..       6      77 ..       4      80 .. 0.67
   2 !   12.6  11.6   9.5e-05      0.11       7      52 ..      60     105 ..      57     111 .. 0.79
   3 !    7.1  12.1    0.0048       5.8       5      55 ..      91     139 ..      90     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                           Fer4_21  3 idedkCigCgkCliaCedtshqai.........eidaktvl..............kvvedeCvGCnl..CssvCPvedc 56
                                      i +++C+gC +C iaC  +  qa                 +                v   C  C+   C+svCP+ ++
  gi|386002313|ref|YP_005920612.1|  6 IRPERCMGCRSCEIACAVEHSQAKsllsavaerP------AprkrvyvefvpdysISVPMACRHCEEapCVSVCPT-GA 77
                                      889*************999888875565544430......12222344555544244578999997455******6.55 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.5e-05
                           Fer4_21   7 kCigCgk..CliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCP 52 
                                        C +C++  C+ +C+   + a++ d+ t v+++  + C+GC  C+svC 
  gi|386002313|ref|YP_005920612.1|  60 ACRHCEEapCVSVCP---TGALRQDEVTrVVTHNPEGCIGCWTCASVCS 105
                                       588997555******...578888876515566799************6 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0048
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnl..CssvCPved 55 
                                       ++ CigC  C+ +C+   +  i  + ++++++  d+C   ++  C+s CP+ +
  gi|386002313|ref|YP_005920612.1|  91 PEGCIGCWTCASVCS---YGMIGRNREERVAIKCDRCPDLEVpaCVSACPT-G 139
                                       678***********9...899*99999999999****7765444******6.4 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   1.9    0.0015       1.8      44      57 ..       9      22 ..       2      26 .. 0.86
   2 !    9.0   1.2    0.0017       2.1       1      21 [.      60      82 ..      60      92 .. 0.80
   3 !   10.6   2.4   0.00052      0.62       2      25 ..      94     117 ..      93     122 .. 0.81
   4 ?    2.5   0.9      0.18   2.2e+02      48      58 ..     128     138 ..     109     141 .. 0.59
   5 ?    2.8   1.0      0.15   1.7e+02       7      16 ..     131     140 ..     119     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++C++C+ Ce +C 
  gi|386002313|ref|YP_005920612.1|  9 ERCMGCRSCEIACA 22
                                      79********9995 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                           Fer4_17  1 rCiqCgy..ClpeCpsyeaydne 21
                                      +C++C+   C+ +Cp+++ +++e
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEEapCVSVCPTGALRQDE 82
                                      5*****888******99887765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00052
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkl 25 
                                       Ci+C  C+ +C+++++ +n+++++
  gi|386002313|ref|YP_005920612.1|  94 CIGCWTCASVCSYGMIGRNREERV 117
                                       9**********9999977766665 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.18
                           Fer4_17  48 eCgeCerkCPq 58 
                                       e   C+++CP 
  gi|386002313|ref|YP_005920612.1| 128 EVPACVSACPT 138
                                       34457777775 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.15
                           Fer4_17   7 yClpeCpsye 16 
                                       +C+ +Cp+++
  gi|386002313|ref|YP_005920612.1| 131 ACVSACPTGA 140
                                       3777777644 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.2     0.017        20      21      51 ..       8      37 ..       1      48 [. 0.75
   2 ?    6.7   6.7    0.0049       5.8      23      56 ..      60      93 ..      38     111 .. 0.79
   3 ?   11.0   0.6   0.00023      0.27      14      58 ..     114     158 ..     106     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                                      HTT----TT-HHHHCSTT--.-HHHHHHHHHT CS
                           Fer4_20 21 AsRClqCkkapcvkgCPvei.dipefikkiae 51
                                       +RC+ C  + c+ +C ve  + ++ ++++ae
  gi|386002313|ref|YP_005920612.1|  8 PERCMGC--RSCEIACAVEHsQAKSLLSAVAE 37
                                      68*****..889999*9965155566666655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0049
                                      T----TT-HHHHCSTT---HHHHHHHHHTT-HHH CS
                           Fer4_20 23 RClqCkkapcvkgCPveidipefikkiaegnlee 56
                                       C +C++apcv+ CP+    ++ ++++ ++n e+
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEEAPCVSVCPTGALRQDEVTRVVTHNPEG 93
                                      6***************987777777777777665 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00023
                                       HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                           Fer4_20  14 eeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaa 58 
                                       ee+++ + +RC + + + cv++CP+   + + +++ +e++ +e+a
  gi|386002313|ref|YP_005920612.1| 114 EERVAIKCDRCPDLEVPACVSACPTGALVFKELEEFSESKRAESA 158
                                       4556667889999999*********99998888888776654443 PP

>> DUF4033  Domain of unknown function (DUF4033)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0046       5.5      32      45 ..      60      73 ..      36      78 .. 0.89
   2 ?    5.9   1.8      0.01        12      16      45 ..     107     136 ..      94     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0046
                           DUF4033 32 kCryLeesgCagvC 45
                                       Cr+ ee+ C++vC
  gi|386002313|ref|YP_005920612.1| 60 ACRHCEEAPCVSVC 73
                                      6************* PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                           DUF4033  16 aeslekkkeksgvkvkkCryLeesgCagvC 45 
                                       ++++++++e+ ++k ++C  Le   C++ C
  gi|386002313|ref|YP_005920612.1| 107 GMIGRNREERVAIKCDRCPDLEVPACVSAC 136
                                       567778888899999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1141.67
//
Query:       gi|386002314|ref|YP_005920613.1|  [L=625]
Description: Carbon-monoxide dehydrogenase, catalytic subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     4e-173  576.8   0.1   4.6e-173  576.6   0.1    1.0  1  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.6   0.1  2.6e-177  4.6e-173       1     510 [.      47     603 ..      47     604 .. 0.99

  Alignments for each domain:
  == domain 1  score: 576.6 bits;  conditional E-value: 2.6e-177
                                       -EE-SSTCT-ECSC....S.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHH CS
                                       xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   1 mfCrqCengpCrit....knkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddek 73 
                                       ++Cr+C++gpCri+    +++rGvCG++ad++var+ll+++++gaaah++har+++ ++++ a++++ + ++++d +
  gi|386002314|ref|YP_005920613.1|  47 VCCRNCNMGPCRIDpfgeGADRGVCGATADIIVARNLLRMIAAGAAAHSDHARDAVLAFKKMAEGEA-EGYQIKDGA 122
                                       6*****************************************************************9.********* PP

                                       HHHHHHHHHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane  74 klkrlaealgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflakt 150
                                       k+++la+++gi  e+++ ee+a ++a+v l++++k+e     +++ ++p++++ ++++ +i ++++d+e+ve++++t
  gi|386002314|ref|YP_005920613.1| 123 KMNALAAEYGISPEGRSPEEVALELANVLLSEFGKQE--GPITFTRRAPAKRQSVWEKAGIDPRGVDREIVECMHRT 197
                                       **********************************996..88999********************************* PP

                                       CCCTTSTHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 151 laglesdpldllskalrlGlld.lkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqt 226
                                       ++g+++dp++ll + lr++++d ++g++++++++++lfGtP+p+++e nlgvl+ d+vnI+v+GH++ ++e+++ ++
  gi|386002314|ref|YP_005920613.1| 198 HIGVDNDPVHLLLHGLRTSISDgWGGSMIATDVQDVLFGTPTPVMSESNLGVLKSDEVNIIVHGHEPILSEMIVAAA 274
                                       ***************************************************************************** PP

                                       CTTCCCCCCC.....GCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCE CS
                                       xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 227 egkglnvyth.....gemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktr 298
                                       e++++ + +      g+ + g+cct++++ +rh+++ +Gn++qqe+a++tgav+a+vvd++Ci+p l ++a +y+t+
  gi|386002314|ref|YP_005920613.1| 275 EDPEMVALAIemgakGISVSGICCTGNEVLMRHGIPTAGNFLQQELAVITGAVEAMVVDVQCIMPALGNLAGCYHTK 351
                                       ****99988778899************************************************************** PP

                                       EEEECTTB-.TTSEEE-.-CTTCHHHHHHHHHHHHCCHCCTTCGG.-............................HH CS
                                       xxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xx RF
                          Prismane 299 littsevak.pgakhie.eeekadkdaseiiekAielakareekkve............................id 345
                                       +i+ts++a  pg+ ++e +eeka ++a+ei++ A+e++++r++ +v+                            +d
  gi|386002314|ref|YP_005920613.1| 352 FISTSPKADfPGTLRMEyHEEKALETAREIVRAAVENYPNRDPGRVNipreksgcmvgfsaeailgalggtpqplVD 428
                                       *****************999999********************99999***************************** PP

                                       HHHTTSS-EEEEE-B---TTCGCC.HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHC......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                          Prismane 346 aiksGtIkgvvlvvGCdnakkgrd.yytelakelikrdvlvltaGCakyalnklglgtieaaelageg......... 412
                                       ai+sG Ikgv +vvGC+n+k ++d  +++l++eli++dvlv+t+GC+++a++k+gl+ +eaa+ ag+g         
  gi|386002314|ref|YP_005920613.1| 429 AIVSGSIKGVGAVVGCNNPKVQHDfGHVNLVRELIRNDVLVVTTGCNAIACAKAGLLLPEAAKEAGPGlrpicealg 505
                                       ***************************************************************************** PP

                                       EESEEEEESCCCHHHHHHHHHHHHHHTTSSGGGSSEEEEECC--SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 413 iPrvLdvGsCvdnyrivvialklaealgvdindLplaalalewyeqKAvailltllalGinihlgptlpafgspnvl 489
                                       +P+vL++GsCvd++ri+v+a++la++lgvdi+dLp a +a+ew+++KAv+i+++++a+G++++lg+++p++gsp+v+
  gi|386002314|ref|YP_005920613.1| 506 VPPVLHMGSCVDISRILVLAAALANHLGVDISDLPAAGAAPEWMSEKAVSIGAYVIASGVYTVLGTVPPVLGSPEVT 582
                                       ***************************************************************************** PP

                                       HHHHCHHHHHHCEEEECHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 490 kvlvedfedriggivtveedp 510
                                       +vl++ +e+ +g+ + ve+dp
  gi|386002314|ref|YP_005920613.1| 583 SVLTKGVEGVVGASFAVEPDP 603
                                       ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3850.66
//
Query:       gi|386002315|ref|YP_005920614.1|  [L=39]
Description: hypothetical protein Mhar_1631 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 262.30
//
Query:       gi|386002316|ref|YP_005920615.1|  [L=209]
Description: hypothetical protein Mhar_1632 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.3e-18   64.6  14.4    8.5e-18   64.4  14.4    1.0  1  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
          2    7.2  10.1        2.3    7.0  10.1    1.2  1  MFS_1_like  MFS_1 like family
        8.8    5.9   6.7         18    4.9   6.7    1.6  1  RTX         N-terminal domain in RTX protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4  14.4   1.4e-21   8.5e-18       3     187 ..      10     194 ..       8     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.4e-21
                             MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdr.fGrrrvlllglllfalg.l 76 
                                       ++ +++ ++++++ p+l + +     g +  ++g + tl+ ++ ++ +lp++r +d  +   r+l+lg +l a+  +
  gi|386002316|ref|YP_005920615.1|  10 ISDIFVLTGFGLIQPILAIfINEGVVGGTIFTAGVASTLFLVTKSLVQLPFARYVDGsVKKTRWLILGTVLIAIVpV 86 
                                       55678899999*******9555666999****************************745455588999999888855 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       ++++ + +++ ++++ vl G+g+g+++p+ + l ++  ++   g+  +++s++++lG++ ++++g+++as +g+ a+
  gi|386002316|ref|YP_005920615.1|  87 MYIF-IDHIYQVYLAEVLYGIGSGLAYPTWVCLWSRNLNPGSEGFEWSMYSTSTGLGTAATAAAGAAIASVAGFAAT 162
                                       5555.48888******************************************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkee 187
                                       f++ ++++l++  +++ll++++++++++  p++ 
  gi|386002316|ref|YP_005920615.1| 163 FVLTGLMCLVG--CGILLFLDRESPPEWRGPAPS 194
                                       ***********..777888888888887776665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.1   0.00038       2.3     236     382 ..      14     162 ..       1     165 [. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00038
                        MFS_1_like 236 ilgmswgiienFlflYLke..lgasntllGslva.lgvvaeiplfffaeklleklGhvklliiallayilrfllyai 309
                                       ++ + +g+i+  l ++++e  +g + +++G++ + + v  +++ + fa ++   +  ++ li++ +++++  ++y +
  gi|386002316|ref|YP_005920615.1|  14 FVLTGFGLIQPILAIFINEgvVGGTIFTAGVASTlFLVTKSLVQLPFARYVDGSVKKTRWLILGTVLIAIVPVMYIF 90 
                                       5555566666666666633124445555665544134556777777888888888889999**************** PP

                        MFS_1_like 310 ienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaifl 382
                                       i+    v ++evL+gi  gl + + v   s+   ++ e++  +++s+   glG+a  + +G ++    + + +
  gi|386002316|ref|YP_005920615.1|  91 IDHIYQVYLAEVLYGIGSGLAYPTWVCLWSRNLNPGSEGFEWSMYSTS-TGLGTAATAAAGAAIASVAGFAAT 162
                                       *********************************************975.9***99988877555455555555 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   6.7     0.003        18      65     112 ..     122     169 ..      39     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.003
                               RTX  65 elyrekktieaaltaistvldvvsavvsaaaaasgVGaPvallvalit 112
                                       +l  ++++ e +++++st l++ ++++++aa+as+ G   + +++++ 
  gi|386002316|ref|YP_005920615.1| 122 NLNPGSEGFEWSMYSTSTGLGTAATAAAGAAIASVAGFAATFVLTGLM 169
                                       566788999**************************9977666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1606.89
//
Query:       gi|386002317|ref|YP_005920616.1|  [L=320]
Description: ADP-ribosylglycohydrolase superfamily [Methanosaeta harundinacea 6Ac]
Scores for complete 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-63  214.2   6.1    3.7e-63  214.0   6.1    1.0  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.039   14.0   0.0    1.4  1  DUF531          Protein of unknown function (DUF531)


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.0   6.1   4.1e-67   3.7e-63       1     291 []      11     290 ..      11     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: 214.0 bits;  conditional E-value: 4.1e-67
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S.-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelge.tpdktgfghfglkpgewtddtqmalllleslleaggldpedla 76 
                                       G+llG+avGDAlG+pve+++ +eir+  ge  +   +  ++ h gl pg++tddt+++l l+e+l+eag +d e +a
  gi|386002317|ref|YP_005920616.1|  11 GSLLGLAVGDALGMPVEGMTAEEIRAGPGEVRDmIAPAADHFHSGLSPGQYTDDTEQTLILAETLIEAGSFDVERFA 87 
                                       89**********************9877777769899999************************************* PP

                                       HHHHH.HHT......T--SS--HHHHHHHHHTTTT-...-S-B...---BTTTGGG-HHHHHHTSS-HHHHHHHHHH CS
                    ADP_ribosyl_GH  77 rrflaeWlee.p.gdteprgignttrealrnlksgepppeaganangsagngalmRaaplgllyagdpeeaaelaee 151
                                       +r++  W ++ + + + +rg+g t ++a+++l  g  ++eag       ++g++mRaap+gl+y+ +++ +a++a  
  gi|386002317|ref|YP_005920616.1|  88 KRLAS-WGRCwTaDPRMNRGVGWTSKTAIQELLGGMAWREAGVA---TPTCGSAMRAAPIGLVYHCSLDLVARYADL 160
                                       **988.7777446779**************************98...9***************************** PP

                                       HHHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHH CS
                    ADP_ribosyl_GH 152 aarlTHnhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavd 228
                                       ++  TH++  a ag++a+a  +a  + g  +   l+ a  + a +  ++e+ ++l  a++l d d+       ea+ 
  gi|386002317|ref|YP_005920616.1| 161 QSLPTHSSAAARAGSVAVAVGVALSILGFAPLRVLEMA--ASASERVDREFGRRLLLAKELLDLDP------PEALA 229
                                       *************************9999999999999..78999999******************......9**** PP

                                       HH--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-HH CS
                    ADP_ribosyl_GH 229 elgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPee 291
                                       e+g++  + e+++aa+++ + +  ++eeal+aa++ GgDtdt+++iaGal+Ga  G e+iPe+
  gi|386002317|ref|YP_005920616.1| 230 EIGTSPMVGETVPAAFFCYIGF--EPEEALIAAASAGGDTDTIASIAGALAGAARGSEWIPER 290
                                       *********************5..6************************************96 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.4e-06     0.039       2      43 ..     149     190 ..     137     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-06
                            DUF531   2 ltlglvntYDkkklheaHkRaiARaapicyafdfnLalldFp 43 
                                       ++l lv  Y   + + +H  a ARa+++++a ++ L++l+F 
  gi|386002317|ref|YP_005920616.1| 149 CSLDLVARYADLQSLPTHSSAAARAGSVAVAVGVALSILGFA 190
                                       57889999*********************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2259.35
//
Query:       gi|386002318|ref|YP_005920617.1|  [L=341]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-32  111.4   0.0    5.8e-32  110.7   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    6.7e-24   85.0   0.0    8.7e-24   84.6   0.0    1.1  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
     0.0009   19.8   0.0     0.0022   18.5   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.031   15.1   0.0      0.066   14.0   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.16   12.6   0.1          7    7.3   0.1    2.5  2  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   1.6e-35   5.8e-32       1     116 [.       3     133 ..       3     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.6e-35
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCH CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpa 76 
                                       kv+ivG++Gy+G ellrlL+ hp +e v+++s++  +G+++ +++++l++++ l++e++++ e+ +++d+vf+a+p+
  gi|386002318|ref|YP_005920617.1|   3 KVGIVGGSGYTGGELLRLLSLHPGAEAVCITSRKL-EGRPVGDVHPHLRGISSLNFESPSASEVaERCDVVFTAVPH 78 
                                       7**********************************.**********************6666665************ PP

                                       HHHHHHHHHHHHTTSEEEESSSTTTTST...............TSEBE-HHHHGG CS
                    Semialdhyde_dh  77 gvskelapklaeagvkviDlssdfRlkd...............davyvlpevnre 116
                                       g++++++p+l++ag+kv+Dls+d+Rl                 +av+++pe+++e
  gi|386002318|ref|YP_005920617.1|  79 GTAMDWVPDLLDAGAKVVDLSADYRLPLevfertygmkhrafrEAVFGMPELHPE 133
                                       **************************889***********************998 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   2.4e-27   8.7e-24       2     184 .]     155     312 ..     154     312 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.4e-27
                                       HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHH CS
                   Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreel 78 
                                       +PL+ a g  erv++++++++SGaG++                 +++  ++ + a N+i+y+ + ++++  e+++el
  gi|386002318|ref|YP_005920617.1| 155 APLVGA-GLAERVVFDSKSGISGAGNA-----------------PSETSHYPNMAENVIAYKLT-THRHRAEVDQEL 212
                                       79***8.999****************7.................999999**************.************ PP

                                       HHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES.......SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSH CS
                   Semialdhyde_dhC  79 kavaetkkileftekvsatcvrVPvlrGhseavtiklk.......lkdveveeveellaaapevkvvvneeedrPtp 148
                                       + +     +++ft+      + VP++rG+++++++ +k       ++++e+++++  ++++ +++++  +   +P +
  gi|386002318|ref|YP_005920617.1| 213 SRLSP-GIRVSFTP------HVVPAIRGILTTAHLLVKdefigsiPDRDEISKIYRDFYRD-SPFIRLVP--GVPSL 279
                                       ****9.67899999......78***************************************.*******7..***** PP

                                       HHHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 149 aavaggtnsvsVGRirkdemgdeglklvvvgDNllk 184
                                        av+g +n++++G +++d +gd+ +++v+++DNl+k
  gi|386002318|ref|YP_005920617.1| 280 GAVRG-SNFCDIG-FEVDGSGDR-IVVVSAIDNLVK 312
                                       ****9.9******.********8.**********97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.2e-07    0.0022       1      96 [.       3     100 ..       3     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.2e-07
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHH..HHHHHHC....-EEECECHHHHHHH-SEEEE-S- CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekae..elaeelg....vkvtavdneeaaeeadvvvlavk 70 
                                       k+gi+ G+G  g  l++ l+ +   ++ ++ ++sr+ e +     + +l      + ++ +++e+ae++dvv+ av+
  gi|386002318|ref|YP_005920617.1|   3 KVGIVgGSGYTGGELLRLLSLHP-GAEAVC-ITSRKLEGRPvgDVHPHLRgissLNFESPSASEVAERCDVVFTAVP 77 
                                       799**99*****99999876653.477777.66999997641134444446666999999***************** PP

                                       HHHHHHHHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  71 pedveevlselakdalkgklvisvla 96 
                                          + + + +l   +++g  v++ +a
  gi|386002318|ref|YP_005920617.1|  78 HGTAMDWVPDL---LDAGAKVVDLSA 100
                                       ***99999999...888888888766 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.8e-05     0.066       1      89 [.       2      95 ..       2      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                      EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.....EESS..HHHHHTCTTESEEEE-S- CS
                      GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgve.....aysd..leelladpeidavivatp 71
                                      ++v+i+G+ G+ g + l  l   ++++e v++ +++ e       + ++       +++   +e+++  ++d+v+ a+p
  gi|386002318|ref|YP_005920617.1|  2 IKVGIVGGsGYTGGELL-RLLSLHPGAEAVCITSRKLEGRPVGDVHPHLRgisslNFESpsASEVAE--RCDVVFTAVP 77
                                      689****9777788888.555555*************999988777777733244444433333333..9********* PP

                                      GGGHHHHHHHHHHTT-EE CS
                      GFO_IDH_MocA 72 ngtheelakaaleagkhv 89
                                       gt ++ + ++l ag +v
  gi|386002318|ref|YP_005920617.1| 78 HGTAMDWVPDLLDAGAKV 95
                                      **************9987 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.069   2.5e+02      21      52 ..      69     100 ..      53     104 .. 0.76
   2 ?    7.3   0.1    0.0019         7      78      99 ..     282     304 ..     276     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.069
                                       -EEEEE-T.T-TTHHHHHHHHHHTT-EEEES-- CS
                        PGM_PMM_II  21 lkvvidpl.hGaggeilkellkelgvdvvelna 52 
                                         vv+++  hG++ +++++ll   g++vv l a
  gi|386002318|ref|YP_005920617.1|  69 CDVVFTAVpHGTAMDWVPDLLDA-GAKVVDLSA 100
                                       556666544************87.888887665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0019
                                       GGGGG-.SEEEEE-TTS-BEEEE CS
                        PGM_PMM_II  78 vkkega.dlglafDgDaDRlgvv 99 
                                       v+ +++ d+g+ +Dg +DR++vv
  gi|386002318|ref|YP_005920617.1| 282 VRGSNFcDIGFEVDGSGDRIVVV 304
                                       5555555**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2028.06
//
Query:       gi|386002319|ref|YP_005920618.1|  [L=161]
Description: Putative signal transduction protein with CBS domains [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-31  106.2   5.5    1.4e-17   63.9   0.4    2.3  3  CBS              CBS domain
  ------ inclusion threshold ------
      0.075   12.5   0.0      0.081   12.4   0.0    1.1  1  Aromatic_hydrox  Homotrimeric ring hydroxylase


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.3   1.2e-15   1.1e-11       1      55 [.       3      56 ..       3      58 .. 0.91
   2 ?   -3.8   0.0         2   1.8e+04      48      53 ..      77      82 ..      75      83 .. 0.70
   3 !   63.9   0.4   1.5e-21   1.4e-17       1      53 [.      98     149 ..      98     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.2e-15
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                                      ++d+m++++v +  ++ +++a++l+ +++ +s++PV+ e ++l G+v+++Dllr l
  gi|386002319|ref|YP_005920618.1|  3 IRDVMNSEPVAIQATEAVSDAVRLL-RTNeISGMPVL-EGDRLAGVVSESDLLRML 56
                                      58***********************.5555*******.6778***********976 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                                      HHHHHH CS
                               CBS 48 lrDllr 53
                                       rDl+r
  gi|386002319|ref|YP_005920618.1| 77 IRDLIR 82
                                      688887 PP

  == domain 3  score: 63.9 bits;  conditional E-value: 1.5e-21
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+++mt++v+tv+p++++e a+ +m++++++rlPV+ e+gklvGivt+ D++ 
  gi|386002319|ref|YP_005920618.1|  98 VSEVMTKKVFTVSPEDSIERAASMMVRHRINRLPVL-EEGKLVGIVTRGDIIA 149
                                       89**********************************.9*************95 PP

>> Aromatic_hydrox  Homotrimeric ring hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     9e-06     0.081      98     150 ..      33      86 ..       9     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9e-06
                   Aromatic_hydrox  98 htepvfea.tildksaregttyeaavgldvsiWlPgvlkvenfPypdmityely 150
                                        + pv+e+  ++++++  +      v  + ++WlP+ l+v ++P  d+i +e +
  gi|386002319|ref|YP_005920618.1|  33 SGMPVLEGdRLAGVVSESDLLRMLSVEREGGLWLPSPLEVLEVPIRDLIRWEKL 86 
                                       456777752466667777776777888999********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 999.79
//
Query:       gi|386002320|ref|YP_005920619.1|  [L=391]
Description: arginine biosynthesis protein ArgJ [Methanosaeta harundinacea 6Ac]
Scores for complete 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-132  440.3   1.8   5.4e-132  440.0   1.8    1.0  1  ArgJ      ArgJ family
     0.0087   15.8   0.2      0.046   13.5   0.0    2.4  3  TraD      Conjugal transfer protein TraD
  ------ inclusion threshold ------
      0.078   12.5   0.0       0.14   11.7   0.0    1.4  1  BID       BH3 interacting domain (BID)


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.0   1.8  9.1e-136  5.4e-132       6     376 .]      16     391 .]      11     391 .] 0.95

  Alignments for each domain:
  == domain 1  score: 440.0 bits;  conditional E-value: 9.1e-136
                                       XXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHS.EEEEEEEEEEXXXSXHHHHHHHHHHHHH CS
                              ArgJ   6 aagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkg.aravvvnsgnANavtgeqGledaeemae 81 
                                       a g+k+ k  +ali+++    aa+ fT+n+++Aap++v++e l ++ g +++v++nsg+ANa+tg +G+eda+ ma+
  gi|386002320|ref|YP_005920619.1|  16 ASGVKRGKYGVALIAASG--PAAGAFTTNRIRAAPLDVTSESLLASGGhLEGVIANSGCANAYTGPRGVEDARWMAD 90 
                                       67999999******9965..5799****************999777767**************************** PP

                                       HHHHHHTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETEEEEE CS
                              ArgJ  82 avaealgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgkevti 152
                                       ++a +lg+ +++v vasTGviG+ l+ e i   +e+++e+l+      eeaa+AimTTDt  K++ave      +++
  gi|386002320|ref|YP_005920619.1|  91 LLAGHLGVGADRVGVASTGVIGRYLDREVIAGLFEEAKERLRsdpgasEEAARAIMTTDTAVKEIAVEH---AGFRV 164
                                       ***************************************9977888889******************98...59*** PP

                                       EEEEEXSSSXXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHHH CS
                              ArgJ 153 agiaKGaGmihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedleef 229
                                       agi+KGaGmi+PnmaTmL+fi+tDa++s+e+l+e+l  avd+sFn++ vDgdtSTnD vl+ A+g++    +d+++f
  gi|386002320|ref|YP_005920619.1| 165 AGITKGAGMIEPNMATMLSFIYTDARISPEELRECLLGAVDESFNMLIVDGDTSTNDLVLVTATGKV---GADVDDF 238
                                       ******************************************************************9...78***** PP

                                       HHHHHHHHHHHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS-- CS
                              ArgJ 230 eealtevlqeLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagael 306
                                       +eal+ v  eLak++++DGEGatklve+ V+ga+++e+A+ +ak+v++ssLvKtA+fG+D+nwGRi+aa+G++gae+
  gi|386002320|ref|YP_005920619.1| 239 REALNYVSVELAKMMAKDGEGATKLVEMVVTGAREREDARLAAKTVMRSSLVKTAIFGNDPNWGRIVAAAGRSGAEV 315
                                       ***************************************************************************** PP

                                       -TTS-EE........TTEEEEETTEE----HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                              ArgJ 307 dpekvsv......llgevkvlekgepeevdeerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                       dpe++++      + +ev ++++g+ ++   ++a+e++k+ee+ i++dlg g+++a++++cDLsy+YvkiNadY+t
  gi|386002320|ref|YP_005920619.1| 316 DPERITLsisaadRDEEVFLVRRGKIVDGVLSEAEEVMKSEELLIKLDLGLGDATARAFGCDLSYDYVKINADYTT 391
                                       *******6665553346********99999********************************************98 PP

>> TraD  Conjugal transfer protein TraD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   7.7e-06     0.046      19      48 ..     106     137 ..     105     144 .. 0.85
   2 ?   -4.0   0.0       2.2   1.3e+04      15      24 ..     302     311 ..     301     319 .. 0.69
   3 ?   -3.8   0.0         2   1.2e+04      33      45 ..     344     356 ..     341     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-06
                              TraD  19 vkAG..lddldralLlGaLlelaellredeee 48 
                                       + +G   ++ldr++++G++ e++e+lr+d+++
  gi|386002320|ref|YP_005920619.1| 106 ASTGviGRYLDREVIAGLFEEAKERLRSDPGA 137
                                       556666689********************987 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.2
                              TraD  15 GgLVvkAGld 24 
                                       G +V++AG +
  gi|386002320|ref|YP_005920619.1| 302 GRIVAAAGRS 311
                                       6689999944 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2
                              TraD  33 GaLlelaellred 45 
                                       G+L e+ e+++++
  gi|386002320|ref|YP_005920619.1| 344 GVLSEAEEVMKSE 356
                                       8999999998876 PP

>> BID  BH3 interacting domain (BID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.3e-05      0.14      50     152 ..     125     226 ..     110     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                                       SXS.XSSXXX-S-S---TTT-STTS-HCHHHHHHHHHHHHHHHHHHHHCCSSTTSHHHHHHHHHCHCCCCCCCCHHH CS
                               BID  50 edkddeLqtDGnrashlqagrleadsesqeevirniarqLaqiGDeldksiqpklvneLaaqfvneslseedrrkkL 126
                                       e+  + L  D   +       + +d+  +e  +++   ++a i       i+p++   L+  +++++ s e+ r++L
  gi|386002320|ref|YP_005920619.1| 125 EEAKERLRSDPGASEEAARAIMTTDTAVKEIAVEHAGFRVAGITKG-AGMIEPNMATMLSFIYTDARISPEELRECL 200
                                       5556667777777777777778888888888888888899988755.568*************************** PP

                                       HHHHHHHHCTS--SSHCHHHHHHHHH CS
                               BID 127 aaaleqvmqtipkDlekekamLvltm 152
                                         a+++  + +  D +     Lvl+ 
  gi|386002320|ref|YP_005920619.1| 201 LGAVDESFNMLIVDGDTSTNDLVLVT 226
                                       *******9999999998888888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2593.66
//
Query:       gi|386002321|ref|YP_005920620.1|  [L=477]
Description: argininosuccinate lyase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-62  209.1   0.0    1.7e-61  208.3   0.0    1.4  1  Lyase_1   Lyase
    2.6e-15   56.9   0.1    2.6e-15   56.9   0.1    3.0  3  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.3   0.0   1.9e-65   1.7e-61      76     312 .]      72     292 ..      25     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 1.9e-65
                                       SSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT- CS
                           Lyase_1  76 qegsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdv 152
                                        e+ + a+++   e+i+    ++ ++ +  htg+S+nD v+T +r++l+ +l   L++++++L++al+e+a e++d+
  gi|386002321|ref|YP_005920620.1|  72 GEDVHEAIEA---ELIA----RVGAVGGRMHTGRSRNDEVATCIRIVLRGELLG-LMAEVNDLAEALVERAAENADT 140
                                       4566666666...4454....555****************************55.********************** PP

                                       EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST CS
                           Lyase_1 153 vkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp 229
                                       v +G+Thlq+A+P+tl++ l a+a+al rd  rl+++ +r++ ++lg+++ + tg+++d++   + a+ l+ ++g  
  gi|386002321|ref|YP_005920620.1| 141 VIPGFTHLQHAQPTTLAHHLLAHADALLRDFDRLQDSCQRVNRSPLGAAAFASTGFDIDRK---RTAELLG-FEG-- 211
                                       *************************************************************...99**9*9.999.. PP

                                       EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHH CS
                           Lyase_1 230 vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgv 306
                                          +ns++avs+rD+++e+l+a ++l+++ s++ae+l+l s++e+g+ el++  ++  SSiMP+K+NP+++El++g+
  gi|386002321|ref|YP_005920620.1| 212 -LVENSMDAVSTRDFLLEALSASAILMVNASRLAEELILWSTSEFGYLELDDLFTS-TSSIMPQKKNPDTAELIRGK 286
                                       .9**************************************************9999.8******************* PP

                                       HHHHHH CS
                           Lyase_1 307 agrvvG 312
                                        g v+G
  gi|386002321|ref|YP_005920620.1| 287 TGTVFG 292
                                       ****98 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.59   5.3e+03      42      63 ..      64      80 ..      11      84 .. 0.65
   2 ?   -1.5   0.2       0.5   4.5e+03       5      14 ..     124     133 ..     121     135 .. 0.83
   3 !   56.9   0.1   2.9e-19   2.6e-15       1      69 []     355     428 ..     355     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.59
                                      --HHHHHHH-TT--.GGGGGGSS CS
                            ASL_C2 42 ltleelkeisplle.edveeaLd 63
                                      ++l+      +l e edv+ea++
  gi|386002321|ref|YP_005920620.1| 64 IELA------ELGEgEDVHEAIE 80
                                      2222......3445566666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.5
                                       HHHHHHHHHC CS
                            ASL_C2   5 TdlADyLvrk 14 
                                        dlA++Lv++
  gi|386002321|ref|YP_005920620.1| 124 NDLAEALVER 133
                                       69*****986 PP

  == domain 3  score: 56.9 bits;  conditional E-value: 2.9e-19
                                       STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--.GGG--HHHHHHH-...TT...--.GGGGGGSSHHHHT CS
                            ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrlaeekgke.leeltleelkeis...pl...le.edveeaLdpeasV 68 
                                       FstAT++AD Lvrk  +pFR+AH+ivg+++++    g++ +e+l+ ++ + i+   p    +  e++++aLdp++ V
  gi|386002321|ref|YP_005920620.1| 355 FSTATEIADSLVRKtKIPFRTAHQIVGALAAKG---GTPaIEDLDEAAER-IAkfrPSergFGeEELAAALDPRRNV 427
                                       9*****************************993...33324444433333.32233334589989*********999 PP

                                       T CS
                            ASL_C2  69 a 69 
                                       a
  gi|386002321|ref|YP_005920620.1| 428 A 428
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2750.65
//
Query:       gi|386002322|ref|YP_005920621.1|  [L=115]
Description: hypothetical protein Mhar_1638 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.049   13.5   0.0    1.2  1  Cas_csx3  CRISPR-associated protein (Cas_csx3)


Domain annotation for each model (and alignments):
>> Cas_csx3  CRISPR-associated protein (Cas_csx3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-06     0.049      21      58 ..      71     108 ..      63     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-06
                                       .--TTSEEEEEESS-HHHHHHHHHHTTTSSEEEEEETT CS
                          Cas_csx3  21 eidlkqgvvisGrgPiWlygylvhelhetawiavydpr 58 
                                       ++ l++ +visG + +W+ g+++ +   ++w +  dpr
  gi|386002322|ref|YP_005920621.1|  71 KVALSSLLVISGEASFWVGGFILGREVVARWRGRLDPR 108
                                       5788999******************9999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 809.54
//
Query:       gi|386002323|ref|YP_005920622.1|  [L=503]
Description: hypothetical protein Mhar_1639 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0046   16.9   0.0       0.15   11.9   0.0    2.3  2  ATPase_2    ATPase domain predominantly from Archaea
     0.0068   15.9   0.0      0.027   13.9   0.0    1.8  2  SMC_N       RecF/RecN/SMC N terminal domain
     0.0092   16.4   0.0      0.032   14.6   0.0    1.7  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.043   13.6   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
      0.051   13.5   0.0       0.95    9.4   0.0    2.6  2  NACHT       NACHT domain
       0.11   12.8   0.0       0.23   11.7   0.0    1.5  1  AAA_22      AAA domain
       0.12   11.2   0.0       0.22   10.3   0.0    1.4  1  Adeno_IVa2  Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   5.9e-05      0.15      21      43 ..      47      69 ..      39      75 .. 0.85
   2 ?    2.3   0.0     0.052   1.3e+02      84     134 ..     153     206 ..     129     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiien 43
                                      +++++ Gp+gsGK+ L++ +i+ 
  gi|386002323|ref|YP_005920622.1| 47 SVILVIGPRGSGKSELFRAVIKL 69
                                      678889*************9985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.052
                          ATPase_2  84 iavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqklidlg 134
                                       +++    +++i++   + ++    a++ l +k++++ + i +  Del  l+   
  gi|386002323|ref|YP_005920622.1| 153 KDIDGGDIDKIYSvfkSLKNAPSLALDHLDAKLEREDRYIFVGYDELETLGAKN 206
                                       344444444444444277777899***********************9998444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     1e-05     0.027      18      44 ..      40      66 ..      32      69 .. 0.89
   2 ?   -1.6   0.0      0.59   1.5e+03     155     178 ..     169     192 ..     166     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                                      EEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 18 vilpfsksftaivGpNGSGKsnlldAi 44
                                       i  f++s+  ++Gp GSGKs l+ A+
  gi|386002323|ref|YP_005920622.1| 40 HIRAFDPSVILVIGPRGSGKSELFRAV 66
                                      56789*******************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.59
                                       CCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 155 kvkpaplyllDeidaaLDeknvkk 178
                                       + k ap   lD +da+L  + + +
  gi|386002323|ref|YP_005920622.1| 169 SLKNAPSLALDHLDAKLEREDRYI 192
                                       67889999*********9887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.3e-05     0.032      19      44 ..      41      66 ..      37      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrel 44
                                      +r+ +p+++l++G++G+GKs l r++
  gi|386002323|ref|YP_005920622.1| 41 IRAFDPSVILVIGPRGSGKSELFRAV 66
                                      5677899**************99987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.7e-05     0.043      19      45 ..      44      69 ..      36      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                            AAA_29 19 idlkgatlltGpsGsGKSTllDAiqal 45
                                      +d++ ++l++Gp GsGKS l+ A++ l
  gi|386002323|ref|YP_005920622.1| 44 FDPS-VILVIGPRGSGKSELFRAVIKL 69
                                      5655.59*************9998876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.14   3.6e+02      17      39 ..      14      35 ..      13      43 .. 0.85
   2 ?    9.4   0.0   0.00037      0.95       2      84 ..      48     149 ..      47     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                                      HHHHHHHHCTS-SCCCC-SEEEE CS
                             NACHT 17 lqklalawaegklpqgafklvFf 39
                                      l ++++awae++++++ f+  F+
  gi|386002323|ref|YP_005920622.1| 14 LSQIMVAWAEWEDEGK-FRKTFY 35
                                      578*********9997.888887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00037
                                       CEEEEC-TTTCHHHHHHHHHHH....HCTS-SCCCC-SEEEEEETTTTTTS-............-HCHHHCCCCTS- CS
                             NACHT   2 lvilqGeaGsGKTtLlqklala....waegklpqgafklvFflslrelsrsgna.........rsladllfsqlpep 65 
                                       ++++ G+ GsGK+ L + ++ +    + +++lp    +l+F  ++ +++++ +          + l ++l ++ p+p
  gi|386002323|ref|YP_005920622.1|  48 VILVIGPRGSGKSELFRAVIKLdlmpAIQRCLPD--ARLPF-KEMDRITWIAAYpaeshfpgtLELERFLIDDNPDP 121
                                       799**************99876222244555555..35554.45666666665577888888889999999999999 PP

                                       -SSS-C.........CHHHHCCSCCCEE CS
                             NACHT  66 aapvse.........vwavllelperlL 84 
                                       ++p+ e          w +l +  ++ L
  gi|386002323|ref|YP_005920622.1| 122 ERPPMEiwfaylvrfLWDHLSQEDQKSL 149
                                       9999997777777777777777777666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.2e-05      0.23       5      28 ..      46      69 ..      41      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.2e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                       ++++v+G+ G+GK+ l r + + 
  gi|386002323|ref|YP_005920622.1| 46 PSVILVIGPRGSGKSELFRAVIKL 69
                                      689**************9998765 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.6e-05      0.22      86     113 ..      45      72 ..      40      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.6e-05
                        Adeno_IVa2  86 qPviGviyGPtGsGksqllrnlisskli 113
                                       +P + ++ GP GsGks+l+r++i  +l+
  gi|386002323|ref|YP_005920622.1|  45 DPSVILVIGPRGSGKSELFRAVIKLDLM 72 
                                       57777889***************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.38s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 2643.45
//
Query:       gi|386002324|ref|YP_005920623.1|  [L=434]
Description: hypothetical protein Mhar_1640 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-06   27.3   0.0    3.7e-06   26.6   0.0    1.3  1  ParA            NUBPL iron-transfer P-loop NTPase
    1.4e-05   25.1   0.0    2.9e-05   24.1   0.0    1.7  1  AAA_31          AAA domain
    5.2e-05   23.3   0.0    7.6e-05   22.8   0.0    1.4  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0025   17.0   0.0     0.0045   16.2   0.0    1.3  1  ArsA_ATPase     Anion-transporting ATPase
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.029   13.6   0.0    1.3  1  MipZ            ATPase MipZ
      0.067   12.7   0.0       0.23   10.9   0.0    1.7  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
       0.17   11.1   0.0       0.33   10.2   0.0    1.4  1  VirC1           VirC1 protein
       0.18   10.7   0.1       0.29   10.1   0.1    1.2  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
        0.2   11.1   0.0       0.32   10.4   0.0    1.2  1  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
       0.21   11.5   0.0       0.37   10.7   0.0    1.3  1  Glyco_hydro_45  Glycosyl hydrolase family 45


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.1e-09   3.7e-06       5      56 ..     131     182 ..     129     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.1e-09
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56 
                                       +i+  S KGGVG+St  +++A++ +++g kv ++D D+  p i  ll ++++
  gi|386002324|ref|YP_005920623.1| 131 IIVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFDLDAPGIGVLLAADSK 182
                                       68889**************************************999988775 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.6e-08   2.9e-05       3      40 ..     131     168 ..     130     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.6e-08
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       +I+++ +KGGvG++T    +a   +++g+kv ++D+D 
  gi|386002324|ref|YP_005920623.1| 131 IIVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFDL 168
                                       89**********************************96 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.2e-08   7.6e-05       1      41 [.     132     172 ..     132     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.2e-08
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqann 41 
                                       i++ s+kGGvG +t + ++a+   r g +V ++D+D +a+ 
  gi|386002324|ref|YP_005920623.1| 132 IVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFDLDAPG 172
                                       6789**********************************985 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.5e-06    0.0045       3      38 ..     132     167 ..     131     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       +++ + KGGVG++t+ +++a++ +++g+kv +i  D
  gi|386002324|ref|YP_005920623.1| 132 IVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFD 167
                                       689999**************************9876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.029       2      39 ..     131     168 ..     130     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39 
                                       +iv+   kGG G+st     a+  +++G +v++id+dl
  gi|386002324|ref|YP_005920623.1| 131 IIVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFDL 168
                                       799999*****************************997 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.23       3      39 ..     131     167 ..     130     170 .. 0.92
   2 ?   -2.1   0.0       1.2   2.2e+03     109     129 ..     259     281 ..     221     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDls 39 
                                       ++++   +GGvG+++ l++ a++  ++ge+v viD+ 
  gi|386002324|ref|YP_005920623.1| 131 IIVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFD 167
                                       7888999****************************85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                          CBP_BcsQ 109 lkelk..eqyrwillDlpagasa 129
                                       l++++   + +w+l+D  ag s+
  gi|386002324|ref|YP_005920623.1| 259 LNQIRdeLKPDWLLIDARAGLSE 281
                                       44554334568999999887766 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00018      0.33       3      42 ..     131     170 ..     130     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                             VirC1   3 litfcslkGGaGkttalmglcsalasdgkrvalfeadenr 42 
                                       +i f s+kGG G++tal +   + +  g++v++ + d + 
  gi|386002324|ref|YP_005920623.1| 131 IIVFYSFKGGVGRSTALSSFAIQRTRMGEKVTVIDFDLDA 170
                                       5899**************9999999999999998877655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00016      0.29      39      70 ..     140     171 ..     126     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                       TSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB  39 GaGkstlvealglelrrrGkrvavlavDPssp 70 
                                       G+G+st+++ ++++ +r G++v+v+  D  +p
  gi|386002324|ref|YP_005920623.1| 140 GVGRSTALSSFAIQRTRMGEKVTVIDFDLDAP 171
                                       9************************9997666 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018      0.32       4      49 ..     133     179 ..     131     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                         Fer4_NifH   4 aiyG.kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllgg 49 
                                        +y  kGG+G+st+++  ++  ++mg+kv ++  D  a    +ll +
  gi|386002324|ref|YP_005920623.1| 133 VFYSfKGGVGRSTALSSFAIQRTRMGEKVTVIDFDLDAPGIGVLLAA 179
                                       566449*************************9999777766666655 PP

>> Glyco_hydro_45  Glycosyl hydrolase family 45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.37     108     160 ..     148     202 ..     132     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                    Glyco_hydro_45 108 kklivqvtnvggdlqdqnfdlqipgggl..gifdkgctaefgkeaalggdqyggv 160
                                         + +q t +g  +   +fdl  pg g+   +  kg ta +g+   +    yg v
  gi|386002324|ref|YP_005920623.1| 148 SSFAIQRTRMGEKVTVIDFDLDAPGIGVllAADSKGTTAPWGVLDYMLERPYGKV 202
                                       56779********************9973356789*******9877777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.67u 0.39s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 2232.79
//
Query:       gi|386002325|ref|YP_005920624.1|  [L=49]
Description: HEPN domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.82    9.2   2.7       0.39   10.2   0.5    1.6  2  DUF4462   Domain of unknown function (DUF4462)


Domain annotation for each model (and alignments):
>> DUF4462  Domain of unknown function (DUF4462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   2.2e-05      0.39       4      16 ..       4      16 ..       3      20 .. 0.80
   2 ?   -3.2   0.1      0.34   6.2e+03       2       5 ..      23      26 ..      22      26 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.2e-05
                           DUF4462  4 SrfnWNwLpRAGs 16
                                      Sr+ WN L+R ++
  gi|386002325|ref|YP_005920624.1|  4 SRSGWNTLIRYSP 16
                                      9********9655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.34
                           DUF4462  2 AKSr 5 
                                      AKS+
  gi|386002325|ref|YP_005920624.1| 23 AKSK 26
                                      8996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 297.01
//
Query:       gi|386002326|ref|YP_005920625.1|  [L=529]
Description: oligopeptide ABC transporter substrate-binding protein OppA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-12   45.0   0.0    2.7e-08   33.4   0.0    2.1  2  Peptidase_C25    Peptidase family C25
    2.7e-10   40.4   0.5    2.7e-10   40.4   0.5    1.9  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00017   21.5   0.0    0.00035   20.5   0.0    1.5  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
  ------ inclusion threshold ------
      0.048   13.7   0.0       0.12   12.4   0.0    1.6  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0001      0.45      42     118 ..     213     278 ..     166     322 .. 0.72
   2 !   33.4   0.0     6e-12   2.7e-08     241     377 ..     376     511 ..     363     512 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0001
                                       ........SHHHHHHHHHHHHHHHHTT--SEEEEES-T.............TTS--EE-.....TTT-SEESHHHHS CS
                     Peptidase_C25  42 Gek.....daaairnflkyayknwsasklkYllLvGdtsivvkvkspitksdliptyqiakslgnestiptDdyyas 113
                                       G +     d  +ir+ l ++ ++    ++ Y++L+G               +++p   + + +g+  ++ptD +y++
  gi|386002326|ref|YP_005920625.1| 213 GARvadptDWHEIRDALETISEET---GPAYIILLGGE-------------AVVPRPLTVTIDGRIWYLPTDAWYVD 273
                                       333332224556********9999...78899988888.............44554444444556667********* PP

                                       -T... CS
                     Peptidase_C25 114 ldgne 118
                                        d + 
  gi|386002326|ref|YP_005920625.1| 274 FDEDG 278
                                       **644 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 6e-12
                                       EEEEES-EETTEETTTT.E......EHHHHHT---TT--EEEEEESSSTT-TTSSS-.-HHHHHHHSTTSSEEEEEE CS
                     Peptidase_C25 241 fvnytGHGsetawades.l......stndisaltntnklpiaitaaCltgafdeetkrsfgeklvlnangGavayig 310
                                       +v ++GHGs++++++++ +      +++d++  tn +   i+  ++C tg + + +++sfg +++   ++Ga a+++
  gi|386002326|ref|YP_005920625.1| 376 YVVFMGHGSPDSFSTNDrVpifrveNVEDADLATNHP--VITGYVSCNTGLL-YRDRQSFGTEFL---RAGAAAFVA 446
                                       6889*********444432446667888888888866..888889*******.99988*******...99******9 PP

                                       ESS.---SS--SHHHHHHHHHHHHHHH......T-S-SS-HHHHHHH...............EEEEE-TT-- CS
                     Peptidase_C25 311 atr.lgysgvndrlsraffealfadaar...tlGealllaknelletglaqsiskgm.nkrtfnllGDPalr 377
                                        +   g++++   +   f +++ ++ ++   ++G+al + ++e ++  +    + +     +++++GDP+l+
  gi|386002326|ref|YP_005920625.1| 447 RNTeQGTPSH---FAALFPDYISGTGPQgtyRIGDALFELMRESVLRAG----DSEKpAAAQLSIYGDPTLK 511
                                       6641445444...444444444444444566***********9997643....233337888********97 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.5   5.9e-14   2.7e-10       3      59 ..      58     114 ..      56     158 .. 0.86
   2 ?   -4.2   0.0         4   1.8e+04      34      42 ..     468     476 ..     468     477 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.9e-14
                   CarboxypepD_reg   3 sGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGy 59 
                                       +GrVtd+ +g pi+g++Vt+ + d+  + ++tt+++G+fr++ +p g+ys    +  y
  gi|386002326|ref|YP_005920625.1|  58 EGRVTDEeTGDPIPGVAVTFLRGDDRRSWTATTGSSGSFRVA-VPEGSYSYITAHRDY 114
                                       7*****779*******************************97.******987655555 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4
                   CarboxypepD_reg  34 tdadGafrl 42 
                                       t+++G++r+
  gi|386002326|ref|YP_005920625.1| 468 TGPQGTYRI 476
                                       678899987 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 !   20.5   0.0   7.8e-08   0.00035       2      47 ..      58     106 ..      57     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.8e-08
                   CarbopepD_reg_2   2 sGtVvdketkeplpgatVyvkg....tkkgtvTdenGnFelknlpagkyt 47 
                                       +G+V+d+et++p+pg+ V++       +  ++T ++G+F++  +p+g y 
  gi|386002326|ref|YP_005920625.1|  58 EGRVTDEETGDPIPGVAVTFLRgddrRSWTATTGSSGSFRVA-VPEGSYS 106
                                       7*****************99552332468999*********5.****995 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 ?   12.4   0.0   2.6e-05      0.12      23      62 ..      65     104 ..      60     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                              bMG3  23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallar 62 
                                       ++g+P++g++V++l  +++  +++tT ++G  r+a ++ +
  gi|386002326|ref|YP_005920625.1|  65 ETGDPIPGVAVTFLRGDDRRSWTATTGSSGSFRVAVPEGS 104
                                       79*******************************9999443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3201.94
//
Query:       gi|386002327|ref|YP_005920626.1|  [L=1133]
Description: DNA polymerase II, large subunit DP2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1249.6   0.0          0 1248.4   0.0    1.5  2  PolC_DP2        DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.027   14.5  18.6       0.19   11.8   0.2    2.8  2  DZR             Double zinc ribbon
       0.15   12.3   5.8       0.58   10.4   0.1    2.6  2  DUF2072         Zn-ribbon containing protein
       0.69   10.0  11.8       0.14   12.3   7.1    2.1  2  TerY_C          TerY-C metal binding domain
        1.9    8.5  14.0       0.41   10.7   0.3    3.2  2  HypA            Hydrogenase/urease nickel incorporation, meta
        6.5    6.9  13.0         12    6.0   1.0    4.5  5  Nop10p          Nucleolar RNA-binding protein, Nop10p family


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1248.4   0.0         0         0       1     864 []       5     883 ..       5     883 .. 0.97
   2 ?   -2.0   0.0       0.2   6.1e+02     618     651 ..    1049    1086 ..    1022    1124 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1248.4 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirele.kelsreevalkiakei 76 
                                       eYfe le++l + +e+a +ar++g+dp+  vE+p+A dla+Rvekl+gi+g+a+r+rele + +sree+al+i++++
  gi|386002327|ref|YP_005920626.1|   5 EYFEVLEAGLASGMEVAGRARRQGKDPSLWVEVPTAVDLAERVEKLIGIEGIAARVRELEaEGMSREEAALAIGSDF 81 
                                       6***********************************************************788************** PP

                          PolC_DP2  77 aegkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaD 153
                                       a+g++g+++sk ea+d a+rt++alltegvvaAP+eGiakv+++knddgteylkvyyaGPiRsaGGtaqalsvLvaD
  gi|386002327|ref|YP_005920626.1|  82 AAGRIGSFSSKIEAIDGAIRTSVALLTEGVVAAPIEGIAKVDLGKNDDGTEYLKVYYAGPIRSAGGTAQALSVLVAD 158
                                       ***************************************************************************** PP

                          PolC_DP2 154 yvrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnr 230
                                       +vr+++g+drykpr +e+eRyveEi lY+rva+lqy psd+eir++v+n+p++i+Ge+te+eevsg+rdler+etnr
  gi|386002327|ref|YP_005920626.1| 159 CVRREVGIDRYKPRPDEVERYVEEIGLYRRVAGLQYAPSDDEIRTLVRNCPICIEGEPTEEEEVSGFRDLERIETNR 235
                                       ***************************************************************************** PP

                          PolC_DP2 231 vRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvlshps 307
                                       +RGG++lv aeGialk +K+kk+v+kl +egW+wl+el+++    kk+         ++ek+lrd+iaGRpv+shp+
  gi|386002327|ref|YP_005920626.1| 236 IRGGVALVSAEGIALKRPKLKKHVTKLAIEGWDWLDELASG---GKKDGGG------TSEKFLRDIIAGRPVFSHPH 303
                                       ****************************************9...3333333......468***************** PP

                          PolC_DP2 308 rkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddvee 384
                                       r+GGfRLrYGRsrntgla+ag+ Patm ll++fla+Gtq+kve PgKaaav pv+siegPtv+lknGd+vr+d++ee
  gi|386002327|ref|YP_005920626.1| 304 RPGGFRLRYGRSRNTGLAAAGFSPATMILLQDFLAAGTQVKVELPGKAAAVSPVSSIEGPTVRLKNGDLVRVDSAEE 380
                                       ***************************************************************************** PP

                          PolC_DP2 385 aleikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaeekpsaeealelseeldvpLhPk 461
                                       a  ++ ev++i+d+Ge+L+++G+flenn++L+p sy++eww++el++a+ + +  e+ps eea+e+s+++ vpLhP+
  gi|386002327|ref|YP_005920626.1| 381 AVLLRGEVAKIVDVGEVLISFGDFLENNRTLAPGSYCFEWWAAELAEAGGDPAGLEAPSGEEAIEISSRWRVPLHPA 457
                                       ***************************************************************************** PP

                          PolC_DP2 462 ytylwhdisveelekLaeavaekkkleeeklvleleeevkeiLekllvehkvkeekivieealallkslgldleeek 538
                                       +t+lwhd+s e + +L+eav++++++ +++l l+l  +vke Le+llv h+v+ee++++ + ++ll +lg+++e  +
  gi|386002327|ref|YP_005920626.1| 458 HTHLWHDLSPEGYLRLREAVSSAGEMGDGALSLPL--AVKEELETLLVLHRVREERLIVPDPAPLLLCLGVEAEGLR 532
                                       ************************99999999998..899********************************99999 PP

                          PolC_DP2 539 leke.eek.......................dalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfp 591
                                       l++    +                       ++l+lvn+++g++v+++aptr+g+RmGRPeKs++R+m+p++hvLfp
  gi|386002327|ref|YP_005920626.1| 533 LRELpG-EpvseiqdegadgdaivggepaprTSLDLVNQVAGIRVMARAPTRVGSRMGRPEKSDKREMRPPPHVLFP 608
                                       876651.244556788999********************************************************** PP

                          PolC_DP2 592 igeaggkrrsvkeaakk......kgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekce 662
                                        g+aggk+rsv e+ak+       g ie++i++r C++Cg+et+e+ C+ Cg++t +k +C+ c++   +ekc++c+
  gi|386002327|ref|YP_005920626.1| 609 TGDAGGKSRSVGECAKNhvgngkVGIIETSIGKRGCPQCGAETHEFLCR-CGAHTLPKRSCPVCHQPG-KEKCPRCG 683
                                       ****************55898877788**********************.**************9987.678***** PP

                          PolC_DP2 663 keakavkkkkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlp 739
                                       + ++a++++++d+kel+++al++l+e  +++e ++gv glts++k+pE+leKg+lRakh+v++fkdgtvRyD+tdlp
  gi|386002327|ref|YP_005920626.1| 684 RPTTAADEMRLDVKELYHRALAHLHE--REPELVRGVLGLTSRDKTPESLEKGVLRAKHGVYIFKDGTVRYDLTDLP 758
                                       **************************..56*********************************************** PP

                          PolC_DP2 740 lthfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnv 816
                                       lthfrp+e++ +v++lrelGY eDi+G+pl++e+q++el vqD++ls da+eyllkva+fvD++Lek+yglerfYn+
  gi|386002327|ref|YP_005920626.1| 759 LTHFRPREVHADVSRLRELGYAEDIYGEPLRDEEQVLELLVQDVILSFDAGEYLLKVAAFVDEELEKFYGLERFYNA 835
                                       ***************************************************************************** PP

                          PolC_DP2 817 ekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                       +  +dLiG l++glaPHtsagvl+R+iG+t+as+gy+hP+fHaakRRn
  gi|386002327|ref|YP_005920626.1| 836 RAPDDLIGCLLVGLAPHTSAGVLCRLIGYTTASAGYGHPFFHAAKRRN 883
                                       ***********************************************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.2
                          PolC_DP2  618 rrkCkkCgket....learCeeCgekteeklvCkkcee 651 
                                        + +C kCg++     l+  C++Cg ++  +++  ++++
  gi|386002327|ref|YP_005920626.1| 1049 KVRCVKCGAKFrrplLSDVCPKCGGRVILTVHEGSVRK 1086
                                        44566665543111134556666666555444433333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  13.0    0.0093        28       1      38 [.     644     686 ..     636     692 .. 0.68
   2 ?   11.8   0.2   6.3e-05      0.19      13      39 ..    1050    1076 ..    1043    1080 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0093
                               DZR   1 CpqCgee..........lppdarfCseCgtklkavaaedrCpsCgekv 38 
                                       CpqCg+e          ++  +r C+ C ++ k     ++Cp+Cg+++
  gi|386002327|ref|YP_005920626.1| 644 CPQCGAEtheflcrcgaHTLPKRSCPVCHQPGK-----EKCPRCGRPT 686
                                       888888866666666665556666666666665.....6777777665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.3e-05
                               DZR   13 rfCseCgtklkavaaedrCpsCgekvd 39  
                                          C +Cg+k +++  +d+Cp+Cg  v 
  gi|386002327|ref|YP_005920626.1| 1050 VRCVKCGAKFRRPLLSDVCPKCGGRVI 1076
                                        569999999998888999999997765 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   2.5     0.064   1.9e+02      19      33 ..     641     655 ..     634     685 .. 0.87
   2 ?   10.4   0.1   0.00019      0.58       3      47 ..    1051    1093 ..    1050    1129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.064
                           DUF2072  19 lkGCpsCGgkkFlyv 33 
                                       ++GCp+CG +  +++
  gi|386002327|ref|YP_005920626.1| 641 KRGCPQCGAETHEFL 655
                                       57*******998886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
                           DUF2072    3 kCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseeke 47  
                                        +C+kC+  f+     + + Cp+CGg+  l v+e + ++  + +++
  gi|386002327|ref|YP_005920626.1| 1051 RCVKCGAKFRR--PLLSDVCPKCGGRVILTVHEGSVRKYLEVSMK 1093
                                        7********75..55799************999987775544444 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   7.1   4.5e-05      0.14      72     115 ..     639     689 ..     621     698 .. 0.73
   2 ?   -1.6   0.1      0.89   2.7e+03     104     113 ..    1067    1076 ..    1047    1084 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                            TerY_C  72 eGapgCPhCgnalafavCeCgkll.....C..idgeeeatCpwCgkevkfg 115
                                       +G  gCP Cg+++   +C+Cg        C   ++++++ Cp+Cg+ ++ +
  gi|386002327|ref|YP_005920626.1| 639 IGKRGCPQCGAETHEFLCRCGAHTlpkrsCpvCHQPGKEKCPRCGRPTTAA 689
                                       7999*****************642222223324789999999999876654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.89
                            TerY_C  104 tCpwCgkevk 113 
                                        +Cp+Cg +v 
  gi|386002327|ref|YP_005920626.1| 1067 VCPKCGGRVI 1076
                                        4555554444 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   8.3      0.69   2.1e+03      87      97 ..     661     687 ..     621     699 .. 0.58
   2 ?   10.7   0.3   0.00014      0.41      69      97 ..    1048    1076 ..    1043    1087 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.69
                                       H................S-TTTSSS-E CS
                              HypA  87 l................rCpkCgsadv 97 
                                                        +Cp+Cg+  +
  gi|386002327|ref|YP_005920626.1| 661 HtlpkrscpvchqpgkeKCPRCGRPTT 687
                                       144555444445555557999998654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                        -EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA   69 vkvrCreCgkefeleekalrCpkCgsadv 97  
                                         kvrC +Cg++f+    +  CpkCg++ +
  gi|386002327|ref|YP_005920626.1| 1048 QKVRCVKCGAKFRRPLLSDVCPKCGGRVI 1076
                                        689*********96653457*****9743 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.18   5.3e+02      19      28 ..     643     652 ..     641     654 .. 0.84
   2 ?    0.2   0.2      0.27     8e+02      10      26 ..     657     674 ..     655     676 .. 0.81
   3 ?    6.0   1.0     0.004        12      17      40 ..     676     699 ..     666     703 .. 0.85
   4 ?    4.4   0.1     0.013        37      16      27 ..    1064    1075 ..    1049    1081 .. 0.83
   5 ?   -3.8   0.0       4.9   1.5e+04      39      48 ..    1101    1110 ..    1100    1111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                                       B-TTT-SB-B CS
                            Nop10p  19 vcpecggptk 28 
                                        cp+cg++t 
  gi|386002327|ref|YP_005920626.1| 643 GCPQCGAETH 652
                                       6******996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                                       TT--EESS.SB-TTT-SB CS
                            Nop10p  10 kcrvYTLk.kvcpecggp 26 
                                       +c+  TL   +cp c +p
  gi|386002327|ref|YP_005920626.1| 657 RCGAHTLPkRSCPVCHQP 674
                                       57889997699****876 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.004
                                       SSB-TTT-SB-B-SS--S--TT-T CS
                            Nop10p  17 kkvcpecggptksahPaRFSPdDk 40 
                                       k++cp+cg pt+ a   R +++  
  gi|386002327|ref|YP_005920626.1| 676 KEKCPRCGRPTTAADEMRLDVKEL 699
                                       799*********998777776655 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.013
                                        SSSB-TTT-SB- CS
                            Nop10p   16 Lkkvcpecggpt 27  
                                        L++vcp+cgg +
  gi|386002327|ref|YP_005920626.1| 1064 LSDVCPKCGGRV 1075
                                        89*******965 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 4.9
                                        -TTCHHHHHC CS
                            Nop10p   39 DkyskyRral 48  
                                        D y k+R +l
  gi|386002327|ref|YP_005920626.1| 1101 DDYTKQRLEL 1110
                                        99*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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):               6  [number of targets reported over threshold]
# CPU time: 0.84u 0.33s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 6681.13
//
Query:       gi|386002328|ref|YP_005920627.1|  [L=144]
Description: hypothetical protein Mhar_1643 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-19   70.8   0.1    1.4e-19   70.5   0.1    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.1   7.7e-24   1.4e-19       8     104 ..      18     121 ..      12     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 7.7e-24
                                       -TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-S-EEEEEEEEEEEE.TT...EEEEE CS
                            DUF296   8 epGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kllgrfeilslsGtilp.dg...lHlhv 73 
                                       ++G++iv++i+++a++ ++r ++v  aiGa++++t +++d+e+      +++ ++ei +l G+i+  dg   lH h+
  gi|386002328|ref|YP_005920627.1|  18 DHGSEIVASIIDLAERLEVRCGTV-AAIGALTEATlGFYDQEAheyrtiEIERPMEIAGLLGNISIrDGrpfLHAHA 93 
                                       68**********************.******************9999888889*************64489****** PP

                                       EEEETTSEEEEEEEEEE.EEEEEEEEEEEEE CS
                            DUF296  74 slagedgqvvgGhlaegplvaattvevvvae 104
                                       +la+++g v+gGhl +g +v  + +ev ++e
  gi|386002328|ref|YP_005920627.1|  94 TLADSKGDVMGGHLTRG-MV--FAAEVHLQE 121
                                       *****************.66..666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 966.98
//
Query:       gi|386002329|ref|YP_005920628.1|  [L=328]
Description: Asparagine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-35  123.5   3.5    1.5e-19   70.9   0.1    2.0  2  Asn_synthase   Asparagine synthase
     0.0029   16.8   0.1     0.0042   16.2   0.1    1.2  1  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.071   11.9   0.2        0.1   11.4   0.2    1.2  1  tRNA_Me_trans  tRNA methyl transferase
       0.28   10.6   0.1       0.46   10.0   0.1    1.3  1  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.1   3.3e-23   1.5e-19      22     144 ..     102     217 ..      85     228 .. 0.91
   2 !   53.4   0.6   7.1e-18   3.2e-14     223     307 ..     233     314 ..     224     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 3.3e-23
                      Asn_synthase  22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee. 97 
                                       + LSGG+DS+l+aala r+      ++ +g   +gs+++k a++v+++l ++  e  +++  +++al +v+ ++   
  gi|386002329|ref|YP_005920628.1| 102 VALSGGVDSALVAALAGRE------CVVVGV--EGSSDLKRARQVSDALDLQLEEALIDPGRIEEALAAVLPVIPSp 170
                                       67****************5......79****..*****************************************999 PP

                      Asn_synthase  98 .pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaals 144
                                        p+ ++ a  ly++++ a  +g   +L G+GaDElfgGY  +y ++  
  gi|386002329|ref|YP_005920628.1| 171 nPVDASIAATLYFVAEWASLRGHERILAGQGADELFGGYA-RYLETTT 217
                                       9**************************************9.9988754 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 7.1e-18
                      Asn_synthase 223 llrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpKegfsapvgewklkg 299
                                       l+r    +  +g+ +  P+lD r+v++a+++ppe+k+r+g  K+ LRe+++++lP e+++R+K+++++++g     +
  gi|386002329|ref|YP_005920628.1| 233 LVRDQAVAGLFGVRFSLPYLDVRVVRAAMAIPPEEKVREGVRKRPLREVAARHLPGEVAYREKKAMQYGSGVM---R 306
                                       55556667778999999**************************************************977766...5 PP

                      Asn_synthase 300 elrelaee 307
                                       e+++la++
  gi|386002329|ref|YP_005920628.1| 307 EVKRLARR 314
                                       77777765 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.3e-07    0.0042      20      68 ..     100     150 ..      83     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-07
                                       EEEEEE-SSHHHHHHHHHHHHHH...TCGEEEEEE--SSSTTHHHHHHHHHH CS
                      NAD_synthase  20 gvvlGlSGGvDSslvaalavkal...gkenvlalllPssvsseedvedalal 68 
                                       g v+ lSGGvDS+lvaala +     g e    l    +vs+  d++   al
  gi|386002329|ref|YP_005920628.1| 100 G-VVALSGGVDSALVAALAGRECvvvGVEGSSDLKRARQVSDALDLQLEEAL 150
                                       3.678*************9764322355555555555555555555555555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.3e-05       0.1       4      23 ..     101     120 ..      98     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.3e-05
                     tRNA_Me_trans   4 vvalSgGVDSsvaaallkeq 23 
                                       vvalSgGVDS+++aal  ++
  gi|386002329|ref|YP_005920628.1| 101 VVALSGGVDSALVAALAGRE 120
                                       79***********9986554 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0001      0.46       3      24 ..     101     122 ..      99     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                                       EEE--SSHHHHHHHHHHHHH-S CS
                              QueC   3 vvllSGGlDSttvlalakkegk 24 
                                       vv lSGG+DS+ v+ala +e+ 
  gi|386002329|ref|YP_005920628.1| 101 VVALSGGVDSALVAALAGRECV 122
                                       899*************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2037.39
//
Query:       gi|386002330|ref|YP_005920629.1|  [L=346]
Description: Periplasmic binding protein [Methanosaeta harundinacea 6Ac]
Scores for 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-27   94.2   0.0    1.1e-26   93.9   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0     6e-31   1.1e-26       1     234 [.      47     286 ..      47     289 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 6e-31
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl.gltdede 76 
                                       i+sl+p+ +e+ +alG++d++++v++ +  p    ++e   ++  +++e+d+E++ +  PDlvi+++g+   ++++e
  gi|386002330|ref|YP_005920629.1|  47 IISLTPAAAEVIYALGEADRLAAVSEDCISPPGLMAME---KVGESGREVDLERVMEIGPDLVIAKTGGlFSAEDEE 120
                                       89********************************9876...999*************************66666677 PP

                                       HHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..E CS
                      Peripla_BP_2  77 ellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggy 151
                                       +l   g+p++ ++  +  + l  +i  lg +lg+e+ea++++ +  +  + + ++++ +   ++p ++f++    ++
  gi|386002330|ref|YP_005920629.1| 121 RLKGYGVPVLRYRGLQI-DTLIPMIADLGLILGREEEAREMIGWARGYSDLVSARTAGIpeEERPRIYFMSMGHFDW 196
                                       777789*********97.***************************************99998999999999888889 PP

                                       EEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.........HHHT-S--HHHHT-SHH CS
                      Peripla_BP_2 152 vvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.........aeadnktgleflkenpl 219
                                       +   ++ +   +++ +g+enia++   +    +++E++l++dp+vi++s              +   + +++++ p+
  gi|386002330|ref|YP_005920629.1| 197 TAGFESAGHERIVE-AGGENIAEDL-PGKVPHVDMEWVLERDPEVIVYSIPtsqyagptpTLQEMADKRAEIMSLPA 271
                                       99999999999999.**********.9******************************66555555566678****** PP

                                       HHTSHHHHTT-EEEE CS
                      Peripla_BP_2 220 laelpAvkngrVyal 234
                                       + ++ Av++grVy  
  gi|386002330|ref|YP_005920629.1| 272 FDRIDAVETGRVYVA 286
                                       *************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2437.50
//
Query:       gi|386002331|ref|YP_005920630.1|  [L=274]
Description: hypothetical protein Mhar_1647 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 2017.33
//
Query:       gi|386002332|ref|YP_005920631.1|  [L=162]
Description: hypothetical protein Mhar_1648 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-32  111.7   0.0    2.5e-32  111.4   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   1.4e-36   2.5e-32       1     115 []      42     158 ..      42     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.4e-36
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTT.S..THHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnae.gpdnadaHlkss 75 
                                       d+t +v+++v+++g++ G+v+vf+  +t ++t+ E+ +p++ eD++ ale+++pe  eY hn+  g+ n+++H+++s
  gi|386002332|ref|YP_005920631.1|  42 DLTGKVAAIVERTGLSAGVVVVFASGATGAVTTIEY-EPGLVEDMKGALERIAPEGgEYAHNQRwGDGNGHSHIRAS 117
                                       789********************************9.*************************434555********* PP

                                       HH-SEEEEEEETTEE---TTEEEEEEESS.-SSEEEEEEEE CS
                           UPF0047  76 llgssltipvedgklalGtwqsiylveld.gpreRkvvvqv 115
                                       ++g+sl +p+  gkl lGtwq+i++++ld +pr R+vvvq+
  gi|386002332|ref|YP_005920631.1| 118 VIGPSLAVPFAGGKLLLGTWQQIVFLDLDnRPRYRRVVVQI 158
                                       *****************************667*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1147.50
//
Query:       gi|386002333|ref|YP_005920632.1|  [L=312]
Description: Protein with two GATE domains [Methanosaeta harundinacea 6Ac]
Scores for 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-05   24.3  22.5     0.0043   17.3   5.6    3.3  3  Gate             Nucleoside recognition
  ------ inclusion threshold ------
      0.076   12.6   0.1       0.23   11.1   0.1    1.8  1  RhodobacterPufX  Intrinsic membrane protein PufX


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.2     6e-07    0.0054       5      96 ..      16      98 ..      12     145 .. 0.89
   2 !   17.3   5.6   4.8e-07    0.0043       2     110 ..     180     281 ..     179     283 .. 0.84
   3 ?    0.3   0.5     0.092   8.2e+02       3      24 ..     283     304 ..     281     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6e-07
                              Gate  5 gpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpk 83
                                      + +i ++++  ++l++ +ll+ i+++ +p+f+     l+  ++ ++++++++  ++ g++++++        +g  +++
  gi|386002333|ref|YP_005920632.1| 16 LAMIGIGLFGAGVLTEMGLLQGISRIASPLFSFTR--LPDACASAFVVSLGSAVAANGMVARFR-------DEGCLNER 85
                                      6688899999***********************77..**************9999999999999.......99999999 PP

                              Gate 84 salafllfvllyt 96
                                      +++ + +++++ +
  gi|386002333|ref|YP_005920632.1| 86 EVILCAIMNSIPV 98
                                      9998888887765 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.8e-07
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       lk+  i l +++ +  l++ +++++++ l  p+   +g   + +++v+l+t +a+  v++++lg +        +++
  gi|386002333|ref|YP_005920632.1| 180 LKIAAIYLTMTAAVFALRDRGAFEAFSVL--PLAEIFG--IPPESIVPLTTYVASPIVGISLLGPMI-------HSN 245
                                       6788899999999999*********9999..*******..***********************9996.......889 PP

                              Gate  79 fdtpksal.afllfvllytpcvat...lavivrelg 110
                                         tp++a+ +++l ++++ p +a+   l+ +v+ +g
  gi|386002333|ref|YP_005920632.1| 246 GITPVQAMiVLMLGSMFMLPLFAArslLPRYVGLFG 281
                                       999999662666667777799988666666666666 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.092
                              Gate   3 kagpiillasiliwflssssll 24 
                                       ++g  i+l+s+ +++l   s+l
  gi|386002333|ref|YP_005920632.1| 283 RLGVGIVLFSTGMSILVRLSIL 304
                                       577889**********999887 PP

>> RhodobacterPufX  Intrinsic membrane protein PufX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.5e-05      0.23      24      64 ..     117     158 ..     111     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.5e-05
                   RhodobacterPufX  24 MlkGAgyAavfvlvllfllvalaliGrlL.PeqsrqtPdPvn 64 
                                       +l G +yA vf++  l+ + a+ +  r+L  e s   P+P+ 
  gi|386002333|ref|YP_005920632.1| 117 LLVGGFYAFVFIVTALVKISAVVILSRILlVERSCRVPEPIR 158
                                       67899********************99862688999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2139.33
//
Query:       gi|386002334|ref|YP_005920633.1|  [L=641]
Description: Alpha-amylase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-24   84.7   0.1    3.2e-17   63.1   0.0    3.9  3  Alpha-amylase    Alpha amylase, catalytic domain
      0.001   19.5   0.0     0.0043   17.5   0.0    2.0  2  Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.067   13.3   0.0    1.5  1  Malt_amylase_C   Maltogenic Amylase, C-terminal domain


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   5.3e-21   3.2e-17       7      83 ..     176     253 ..     170     287 .. 0.91
   2 !    4.3   0.0    0.0041        25     158     180 ..     294     317 ..     282     399 .. 0.81
   3 !   11.6   0.0   2.5e-05      0.15     278     330 ..     420     504 ..     409     508 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 5.3e-21
                                       HCTCCCCCCCT-SCEEE-B-CE.-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TTSC CS
                     Alpha-amylase   7 iekLdYlkeLGvtaiwlsPifk.spqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsdehe 82 
                                       +e+LdYl++LG++ i + P+ + s++ d g+    y  +d++fG   d+++ +++ah++gi vilD+V  Htsd++ 
  gi|386002334|ref|YP_005920633.1| 176 TERLDYLQDLGINCIEVMPVSNvSNTVDWGFLPIGYFGVDERFGKRCDMQRFVDAAHQRGIAVILDVVYGHTSDQFP 252
                                       89******************998999*************************************************98 PP

                                       C CS
                     Alpha-amylase  83 w 83 
                                       +
  gi|386002334|ref|YP_005920633.1| 253 Y 253
                                       8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0041
                                       CCCCCCTTT.-SEEEETTCCCTTT CS
                     Alpha-amylase 158 vvkfwlekg.idGfRlDvvkhvsk 180
                                       v ++wle   +dGfR D v+ +  
  gi|386002334|ref|YP_005920633.1| 294 VNHHWLEVYhVDGFRYDCVPNYWD 317
                                       7789**9888********998765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 2.5e-05
                                       TTCEEES--TTS--HHHHTTSSTTTT................................HHHHHHHHHCCCTSSSEEE CS
                     Alpha-amylase 278 eeavtflgnHDqeRilsrlgddsaea................................ekklklaaillltlrGvpv 322
                                       ++a  +l+nHD +R++  +g+                                     + k++ ++i ++  +G+p+
  gi|386002334|ref|YP_005920633.1| 420 KTALQYLENHDHPRLVCSFGNLPGGIdenlrllkernrdlcgaigsdlmalkdgdrslWYKVQPYLIGIFAAKGIPM 496
                                       567889*************9987544667899999999*************99999999999*************** PP

                                       EETTCCCT CS
                     Alpha-amylase 323 iYyGeEig 330
                                       i++G+E g
  gi|386002334|ref|YP_005920633.1| 497 IWQGQEFG 504
                                       ******98 PP

>> Alpha-amylase_C  Alpha amylase, C-terminal all-beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         2   1.2e+04      34      55 ..     329     350 ..     327     355 .. 0.77
   2 !   17.5   0.0   7.2e-07    0.0043       9      55 ..     569     614 ..     565     639 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                                       EECEEESSSS.SEEEEETTCTTS CS
                   Alpha-amylase_C  34 rqdyrvgvpa.agkyrdvlntda 55 
                                       +++y++ v+a ag +r ++++ +
  gi|386002334|ref|YP_005920633.1| 329 YETYNL-VKAkAGVWRRFFDGGS 350
                                       677888.6666999*99998766 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 7.2e-07
                                       SSEEEEEECTTT.EEEEEEE-SSSSEEECEEESSSSSEEEEETTCTTS CS
                   Alpha-amylase_C   9 nkviaFeRgdge.kllvvfNfhpsnsrqdyrvgvpaagkyrdvlntda 55 
                                       + v+ F+R dg+   lv++Nf++ + ++++++  p  g yr+ l+ ++
  gi|386002334|ref|YP_005920633.1| 569 RGVLLFSRDDGKrYSLVALNFTDRDQEVEFQF--PLSGDYREELHAKD 614
                                       789*****998889*********888888888..778*****996555 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.067      10      61 ..     568     620 ..     565     637 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                       -TTEEEEEEEETTEEEEEEEESS-EEEEE--G.GGTT-EEEETTTTEE----- CS
                    Malt_amylase_C  10 nrkvlaYlReyedetilvvaNrsaqaveldls.elagrvpvelfggeefpaig 61 
                                        r vl + R +++   lv++N++++++e++++  l+g    el  ++ +++++
  gi|386002334|ref|YP_005920633.1| 568 SRGVLLFSRDDGKRYSLVALNFTDRDQEVEFQfPLSGDYREELHAKDDLKDVA 620
                                       589******************66666666655558888777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3750.07
//
Query:       gi|386002335|ref|YP_005920634.1|  [L=234]
Description: hypothetical protein Mhar_1651 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1359.70
//
Query:       gi|386002336|ref|YP_005920635.1|  [L=250]
Description: hypothetical protein Mhar_1652 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1625.53
//
Query:       gi|386002337|ref|YP_005920636.1|  [L=271]
Description: hypothetical protein Mhar_1653 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1709.14
//
Query:       gi|386002338|ref|YP_005920637.1|  [L=377]
Description: hypothetical protein Mhar_1654 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-21   76.2   0.0    4.1e-21   75.3   0.0    1.4  1  SdrD_B           SdrD B-like domain
     0.0001   22.5   0.0    0.00028   21.1   0.0    1.7  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


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 !   75.3   0.0   4.6e-25   4.1e-21       3      87 ..     258     350 ..     256     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.6e-25
                            SdrD_B   3 iGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVef..ta.p...agy..t 71 
                                       iGdfVw D n+nGiqd+ge+gi gv+V L d+ g +    tTd  G+Y F +l++G+Y+V +  ++ p   +g    
  gi|386002338|ref|YP_005920637.1| 258 IGDFVWWDLNENGIQDDGEPGIPGVEVILFDDGGRQRGISTTDGRGYYYFGGLCSGHYHVWVkmSTlPelgEGArwW 334
                                       9**********************************************************988442234222233237 PP

                            SdrD_B  72 vtakkaGsddaldSda 87 
                                        t+ + G dd++dSd 
  gi|386002338|ref|YP_005920637.1| 335 PTEPNVGGDDSIDSDG 350
                                       899************7 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.2e-08   0.00028      10      56 ..     275     321 ..     271     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.2e-08
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsa 56 
                                          +i+g++V+++++++ ++   ttd  G++ + gl  g y v v +
  gi|386002338|ref|YP_005920637.1| 275 GEPGIPGVEVILFDDGGRQRGISTTDGRGYYYFGGLCSGHYHVWVKM 321
                                       44579********87777777789******************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2467.09
//
Query:       gi|386002339|ref|YP_005920638.1|  [L=156]
Description: von Willebrand factor, type A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.7   0.0    1.9e-10   41.4   0.0    1.1  1  VWA_2     von Willebrand factor type A domain
    9.2e-10   39.0   0.0    1.1e-09   38.8   0.0    1.1  1  VWA       von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.024   14.4   0.0        0.1   12.3   0.0    1.8  2  Ku_N      Ku70/Ku80 N-terminal alpha/beta domain
      0.098   12.6   0.0       0.14   12.1   0.0    1.2  1  VWA_3     von Willebrand factor type A domain
       0.12   11.7   0.0       0.17   11.2   0.0    1.4  1  VWA_CoxE  VWA domain containing CoxE-like protein


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   5.2e-14   1.9e-10       1     107 []       3     114 ..       3     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.2e-14
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgp..evlipltkdkakilnalrnleak... 72 
                                       +vf +D S+ m  +d +++rl a k+++++l ks   dr glv  +++    ++++lt+  ++i ++l++       
  gi|386002339|ref|YP_005920638.1|   3 VVFAIDYSNTMKISDPKNARLVATKEFIKNLNKS--SDRAGLVYWNNSIieSRVVNLTSEFDEIIAKLDKDISGrgv 77 
                                       79*************9999****99999999998..99*********976689999999888887777764444788 PP

                             VWA_2  73 ..gggtnlaaaLqlarkalkkrrkgekrvivlitDge 107
                                         +g t+++ aL+   +++++++k++k++i++++Dge
  gi|386002339|ref|YP_005920638.1|  78 spEGFTDFNRALNASIDMFSNKSKNTKKCIIFLSDGE 114
                                       899*****************999************96 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   3.1e-13   1.1e-09       2     134 ..       3     144 ..       2     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.1e-13
                                       EEEEEE-STTSCHHHHH.HHHHHHHHHHHHHTBTTTTEEEEEEEESSS..EEEEEETTSHCHHHHHHHHHHTG.... CS
                               VWA   2 ivfvlDgSgsmgeenfe.kvkefikklveklevgpegtrvglvqfsse..vktefslndysskeellsalnnl.... 71 
                                       +vf++D S+ m  ++ +  ++ + k+++++l+  + ++r glv  +++     +++l++  + +e++ +l++     
  gi|386002339|ref|YP_005920638.1|   3 VVFAIDYSNTMKISDPKnARLVATKEFIKNLN--KSSDRAGLVYWNNSiiESRVVNLTS--EFDEIIAKLDKDisgr 75 
                                       9**********888888567788999******..**************76566678887..4467777776643555 PP

                                       SGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS..........HTHHHHHHHHGCTEEE CS
                               VWA  72 kysgggttntgkalkyaleklfkssagaRenakkviilltdGksndg..........dpkeaaneakeqgikv 134
                                        +s+ g t+ + al++ ++ +f+ +++   n+kk ii+l+dG+++ +            + ++n+ak++gi++
  gi|386002339|ref|YP_005920638.1|  76 GVSPEGFTDFNRALNASID-MFSNKSK---NTKKCIIFLSDGEPKPQwipsiytppdGESSPVNRAKDAGIQI 144
                                       9999999999999998888.8888888...9*************66678888888877778888999888887 PP

>> Ku_N  Ku70/Ku80 N-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.2   7.2e+02       2      31 ..       3      31 ..       2      38 .. 0.68
   2 ?   12.3   0.0   2.9e-05       0.1      80     138 ..      59     118 ..      49     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.2
                                      EEEEEE-SHHHHCTTCCSCCHHHHHHHHHH CS
                              Ku_N  2 vvfviDvspaMfesskeeespfelalkcia 31
                                      vvf iD s +M  s ++    +  +++ i+
  gi|386002339|ref|YP_005920638.1|  3 VVFAIDYSNTMKISDPKNAR-LVATKEFIK 31
                                      89999999999766655544.555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.9e-05
                                       HHHHCCHHHCCHHHHC.CCTTSS-TTHHHHHHHHHHHHHHTTSSESEEEEEEEESSSSTC CS
                              Ku_N  80 kelkqivesedasveg.laedssqasllsaLivclellqkvgkklskkriflftdlddpf 138
                                        e+++i+ + d++  g  +++ +  ++  aL+++++++++ +k+++k +ifl + + +p+
  gi|386002339|ref|YP_005920638.1|  59 SEFDEIIAKLDKDISGrGVSPEGFTDFNRALNASIDMFSNKSKNTKKCIIFLSDGEPKPQ 118
                                       6777777777774433145677889**************888888888888877777776 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05      0.14       2     108 ..       2     115 ..       1     122 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                             VWA_3   2 evvivvDvsssmsaen..klvkdaLsvalrqLptnd.kiavllfgtkprplfpgsravsaaelqealqkike..... 70 
                                       evv+++D+s  m+ +   ++   a + +++ L+++  +  ++ +  +    +   +++  +e +e+ +k+++     
  gi|386002339|ref|YP_005920638.1|   2 EVVFAIDYSNTMKISDpkNARLVATKEFIKNLNKSSdRAGLVYWNNS---IIESRVVNLTSEFDEIIAKLDKdisgr 75 
                                       89*********9998887788889999*****998758888888887...88888888889**********999997 PP

                             VWA_3  71 .lelslgasnlegaLkealrqp..akpgevrsvilltDgss 108
                                         ++ +g ++  +aL++ ++ +  +++   + +i l+Dg +
  gi|386002339|ref|YP_005920638.1|  76 gVSP-EGFTDFNRALNASIDMFsnKSKNTKKCIIFLSDGEP 115
                                       7777.***********9999777567777888999999986 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.9e-05      0.17      97     161 ..      51     114 ..       1     118 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
                          VWA_CoxE  97 dtrlvdlTralrerDpaeaLarv.saavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDgl 161
                                       ++r+v+lT++++  +    L++  s +    +G T+ ++al++ +++++ ++ + + +++ +sDg+
  gi|386002339|ref|YP_005920638.1|  51 ESRVVNLTSEFD--EIIAKLDKDiSGRGVSPEGFTDFNRALNASIDMFSNKSKNTKKCIIFLSDGE 114
                                       57999*****99..555555443144444489*****************999999*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1230.56
//
Query:       gi|386002340|ref|YP_005920639.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002340|ref|YP_005920639.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002340|ref|YP_005920639.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002340|ref|YP_005920639.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002340|ref|YP_005920639.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002340|ref|YP_005920639.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2498.16
//
Query:       gi|386002341|ref|YP_005920640.1|  [L=560]
Description: von Willebrand factor, type A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.01   16.1   0.0       0.21   11.8   0.0    2.7  3  VWA            von Willebrand factor type A domain
        0.1   13.3   0.0       0.28   11.9   0.0    1.8  2  VWA_2          von Willebrand factor type A domain
       0.23   11.6   0.0       0.46   10.6   0.0    1.4  1  Thioredoxin_4  Thioredoxin


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 ?    0.1   0.0      0.14   8.5e+02     139     174 ..      10      46 ..       6      47 .. 0.69
   2 ?   -1.4   0.0       0.4   2.4e+03       3      13 ..     259     269 ..     257     294 .. 0.84
   3 ?   11.8   0.0   3.5e-05      0.21     104     161 ..     363     427 ..     313     440 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                       ESSSHHHHHHHHHSSSSC..HHCEEEESSHHHHHHHHH CS
                               VWA 139 vgnadekelLnkiasepg..eghvftvtdfeeleelfe 174
                                       ++nade+  L+++a+++g   +  +++t  ++++e+++
  gi|386002341|ref|YP_005920640.1|  10 IDNADEAR-LKEMAKTTGgnYTSSYNLTVQAAFREIYD 46 
                                       56788888.*******9954444466665556666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.4
                                       EEEEE-STTSC CS
                               VWA   3 vfvlDgSgsmg 13 
                                       v++ D+Sgsm+
  gi|386002341|ref|YP_005920640.1| 259 VLAFDVSGSMR 269
                                       8999******4 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 3.5e-05
                                       EEEEEEEESS--CSS...HTHHHHHHHHGCTEEEEEEEE......SSSHHHHHHHHHSSSSCHHCEE CS
                               VWA 104 kkviilltdGksndg...dpkeaaneakeqgikvfavGv......gnadekelLnkiasepgeghvf 161
                                          iil+ +G ++     ++++ a e+k++g+ ++ +G       +    ++ L ++a+++g g+++
  gi|386002341|ref|YP_005920640.1| 363 DGKIILFITGPDEFRpgeNLSDLAIELKRRGYAIYPIGAaideieSPLKYDN-LSRMAEMTG-GRFY 427
                                       556899999999884489**************************55555555.*******99.7776 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 ?   11.9   0.0   4.6e-05      0.28       2     104 ..     259     371 ..     258     375 .. 0.80
   2 ?   -3.9   0.0         3   1.8e+04      78     102 ..     437     459 ..     433     459 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsd.gp......evliplt...kdkakilnalrn 68 
                                       v+  D+SgSmr        +ea+++  +a +++   ++v+++  ++ g+       + +p+    ++++++l+al +
  gi|386002341|ref|YP_005920640.1| 259 VLAFDVSGSMRLV------YEAMREEDRAAFAEASFSNVSIIGWDEdGAegagedLLMVPPRplrEGRGELLAALAS 329
                                       6778********8......9*************99**********96454446433445553444************ PP

                             VWA_2  69 leak...gggtnlaaaLqlarkalkkrr...kgekrvivlit 104
                                       l      +++t +aa+Lq +r++ ++      g+ ++i++it
  gi|386002341|ref|YP_005920640.1| 330 LSGLceeTDQTVYAAGLQGVRDLDDDFGdhlGGDGKIILFIT 371
                                       *988999**************985332244578888888888 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                             VWA_2  78 laaaLqlarkalkkrrkgekrvivl 102
                                       l++aL+ a ++ + r   ++r+iv+
  gi|386002341|ref|YP_005920640.1| 437 LGEALRDAASHASGRV--APREIVV 459
                                       6789998888888774..7777775 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.7e-05      0.46      14      38 ..     193     218 ..     187     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.7e-05
                                       SEEEEEEE-TT-HHHHHHHHHHH.HH CS
                     Thioredoxin_4  14 pvtvieyedlrCphCakfeeeve.kl 38 
                                        ++++++ +++Cp C ++++e + k+
  gi|386002341|ref|YP_005920640.1| 193 EKVLYVFLNVTCPECSTWKTEDGsKI 218
                                       5689***************9876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3419.53
//
Query:       gi|386002342|ref|YP_005920641.1|  [L=840]
Description: hypothetical protein Mhar_1658 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-16   60.9   0.0    8.9e-08   32.6   0.0    2.5  2  VWA              von Willebrand factor type A domain
      8e-15   55.4   0.0    5.8e-09   36.6   0.0    2.6  2  VWA_2            von Willebrand factor type A domain
    4.9e-07   30.0   0.0     0.0001   22.5   0.0    2.3  2  vWA-TerF-like    vWA found in TerF C terminus
    5.2e-05   23.2   0.0      0.093   12.7   0.0    2.5  2  VWA_3            von Willebrand factor type A domain
     0.0001   21.9   4.1        6.9    6.1   0.0    4.3  4  NMT_C            Myristoyl-CoA:protein N-myristoyltransferase
     0.0016   18.7  34.6       0.48   10.8   1.1    5.2  4  DUF11            Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.067   13.4   0.0    1.7  2  GM_CSF           Granulocyte-macrophage colony-stimulating fa
      0.032   13.1   2.5         15    4.3   0.0    3.2  3  Branch_AA_trans  Branched-chain amino acid transport protein
      0.047   13.9   0.8    1.2e+02    2.8   0.0    4.0  4  PixA             Inclusion body protein
        1.2    7.7   9.9         18    3.8   0.1    3.9  4  Glt_symporter    Sodium/glutamate symporter


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 !   25.4   0.2   7.7e-09   1.4e-05       2     150 ..      35     190 ..      34     210 .. 0.76
   2 !   32.6   0.0   4.9e-11   8.9e-08       2     158 ..     640     804 ..     640     824 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.7e-09
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTB......TTTTEEEEEEEESSSEEEEEETTSHC..HHHHHHHHHHT CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklev......gpegtrvglvqfssevktefslndys..skeellsalnn 70 
                                       +++v+D+S smg+++ + ++++ ++++ + +v      ++   r+     +++ +++ ++ ++   +  e+l  ln+
  gi|386002342|ref|YP_005920641.1|  35 VILVIDNSASMGKSDENCIRNYTIRFFLEKIVnldcnnDEFALRIKDTFIGNKSHPINPVFSKDckNIVEVLGGLNR 111
                                       789**************666655555444443343344777777777888877666644444333488********* PP

                                       GSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS...HTHHHHHHHHGCTEEEEEEEESSSHH CS
                               VWA  71 lkysgggttntgkalkyaleklfkssagaRenakkviilltdGksndg...dpkeaaneakeqgikvfavGvgnade 144
                                       +  s+++  n +k lk+a++ + k+s++     + vi  ++dG + ++    ++ +++ ake+g+ + ++G+gn++e
  gi|386002342|ref|YP_005920641.1| 112 TICSSSEAINHDKILKNAVNDFSKASNN----KNYVIYYFSDGIEYSNrsrFLSSTLHLAKEKGVIINTIGFGNDTE 184
                                       99999999999*********88777777....67899999**999776678999*********************99 PP

                                       HHHHHH CS
                               VWA 145 kelLnk 150
                                         +L k
  gi|386002342|ref|YP_005920641.1| 185 GLKLLK 190
                                       766544 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 4.9e-11
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC.HHHHHHHHHHTG..SGGG CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndys.skeellsalnnl..kysg 75 
                                       +vf+lD+Sgsm ++  + + +   ++v+  +   e+  v++v+  +  +  f     + + + l++ l+nl  + ++
  gi|386002342|ref|YP_005920641.1| 640 VVFALDTSGSM-KKYYHLAPNESAEIVSGWS-AFENSTVSIVSWDHASELLFGPAPLKgNEDRLAEILDNLseMCIE 714
                                       79*********.99999************99.56667799999999988888777766566777777777766999* PP

                                       GSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS...HTHHHHHHHHGCTEEEEEEEE.......SSS CS
                               VWA  76 ggttntgkalkyaleklfkssagaRenakkviilltdGksndg...dpkeaaneakeqgikvfavGv.......gna 142
                                       ++ t+ +++l+  l +l + ++   +n +k+i++lt G+s+ +   +++e + ea e g kvf++G+        + 
  gi|386002342|ref|YP_005920641.1| 715 TDLTYYDQGLNGSLAELRDPASV-PPNSSKIIVFLT-GYSEFEageKLDEYISEANELGCKVFTIGIginesfeASK 789
                                       *******************9999.666666666555.999875579*********************9999998444 PP

                                       HHHHHHHHHSSSSCHH CS
                               VWA 143 dekelLnkiasepgeg 158
                                       + + +L+ki++ +g g
  gi|386002342|ref|YP_005920641.1| 790 NQHLNLTKISEGTG-G 804
                                       44444888888777.3 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 !   16.3   0.0   6.6e-06     0.012       1     106 [.      35     150 ..      35     152 .. 0.71
   2 !   36.6   0.0   3.2e-12   5.8e-09       1     105 [.     640     750 ..     640     753 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.6e-06
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.slpgdrvglv....tfsdgpevlipl.t...kdkakilnalrn 68 
                                       +++v+D+S+Sm+ +d +  r  +++ ++e++++ + ++d ++l       +++++ + p+ +   k+  ++l  l++
  gi|386002342|ref|YP_005920641.1|  35 VILVIDNSASMGKSDENCIRNYTIRFFLEKIVNlDCNNDEFALRikdtFIGNKSHPINPVfSkdcKNIVEVLGGLNR 111
                                       69************977777777888888888865578866664111033333333333244123666666666666 PP

                             VWA_2  69 leak.gggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       + ++ + + n ++ L+ a + ++k +++++ vi+ ++Dg
  gi|386002342|ref|YP_005920641.1| 112 TICSsSEAINHDKILKNAVNDFSKASNNKNYVIYYFSDG 150
                                       6666999***************999999999*******9 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 3.2e-12
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk...slpgdrvglvtfsdgpevlipl...tkdkakilnalrnlea 71 
                                       +vf lDtSgSm  +      ++ a +   ++++   ++ +++v++v+ ++ +e+l+++   + + +++ ++l+nl +
  gi|386002342|ref|YP_005920641.1| 640 VVFALDTSGSMKKY------YHLAPNESAEIVSgwsAFENSTVSIVSWDHASELLFGPaplKGNEDRLAEILDNLSE 710
                                       79***********8......999999999999977667999***************7644489*************9 PP

                             VWA_2  72 k...gggtnlaaaLqlarkalkkrr...kgekrvivlitD 105
                                       +   ++ t+++++L+   ++l++      + +++iv++t+
  gi|386002342|ref|YP_005920641.1| 711 McieTDLTYYDQGLNGSLAELRDPAsvpPNSSKIIVFLTG 750
                                       9**9*****************98889999********996 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.8e-08    0.0001       3     154 ..      34     194 ..      32     206 .. 0.81
   2 ?    5.1   0.0     0.012        21       2      19 ..     638     655 ..     637     661 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.8e-08
                     vWA-TerF-like   3 rVvlVlDasgSmskl....ykkgvvqavverllavaaqlDddg.elevwlfaskakrlpdvtladleeyvkeeeegl 74 
                                       +V+lV+D+s+Sm k+     ++ +++  +e+++ +  + D+ + +++  + ++k + +++v  +d+++ v+     +
  gi|386002342|ref|YP_005920641.1|  34 AVILVIDNSASMGKSdencIRNYTIRFFLEKIVNLDCNNDEFAlRIKDTFIGNKSHPINPVFSKDCKNIVEVLGGLN 110
                                       69**********764222278899999***********9997647899999*******************8776666 PP

                     vWA-TerF-like  75 lelkklggvneeapvleevlekvrkepaelptlvlFitDGgvkkk..keiekalreaskepiFwqFvglgkse..yg 147
                                       +++ + +++ +  ++l++ ++++ k ++++   + +++DG  +++  +  +++l+ a ++ +  + +g+g+     +
  gi|386002342|ref|YP_005920641.1| 111 RTICSSSEAINHDKILKNAVNDFSKASNNKNYVIYYFSDGIEYSNrsRFLSSTLHLAKEKGVIINTIGFGNDTegLK 187
                                       666666666788899999999999777776777778****887763356899******************9875677 PP

                     vWA-TerF-like 148 vLeklDd 154
                                       +L+ + +
  gi|386002342|ref|YP_005920641.1| 188 LLKYISE 194
                                       7776665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                     vWA-TerF-like   2 arVvlVlDasgSmsklyk 19 
                                       a Vv  lD+sgSm+k+y+
  gi|386002342|ref|YP_005920641.1| 638 ATVVFALDTSGSMKKYYH 655
                                       68999************7 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.2e-05     0.093       2     153 ..      34     200 ..      33     202 .. 0.73
   2 !    8.0   0.0    0.0014       2.5       3     136 ..     640     784 ..     638     806 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                             VWA_3   2 evvivvDvsssmsaen.klvkd.aLsvalrq....Lptndkiavllfgt....kprplfpgsravsaaelqealqki 68 
                                       +v++v+D s+sm ++  + +++ +++++l++    +  nd++a+++ +t    k  p  p + + + +   e+l  +
  gi|386002342|ref|YP_005920641.1|  34 AVILVIDNSASMGKSDeNCIRNyTIRFFLEKivnlDCNNDEFALRIKDTfignKSHPINPVFSKDC-KNIVEVLGGL 109
                                       799999999998777775555448999999988867788899999999955544444444444444.2222333333 PP

                             VWA_3  69 ke.lelslgasnlegaLkealrqp..akpgevrsvilltDgssaqgeervsdlisr.arek.irfhalglgsslsa. 139
                                       +  +  s+ a n  + Lk a+  +  a++     + +++Dg   +  +r+ ++    a+ek + + ++g+g+++   
  gi|386002342|ref|YP_005920641.1| 110 NRtICSSSEAINHDKILKNAVNDFskASNNKNYVIYYFSDGIEYSNRSRFLSSTLHlAKEKgVIINTIGFGNDTEGl 186
                                       334556699************9885577777777889*****977778887777763666679*********99966 PP

                             VWA_3 140 amlqaLAeasgGty 153
                                       ++l+ ++e +gGt 
  gi|386002342|ref|YP_005920641.1| 187 KLLKYISEFTGGTF 200
                                       9***********86 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0014
                             VWA_3   3 vvivvDvsssmsaenklvkdaLsvalrq..Lptndkiavllfgtkprplf.pgsravsaaelqealqkikelelslg 76 
                                       vv+++D+s sm++ ++l+ +    ++ +    +n  +++++++   + lf p   + +++ l e+l+ + e+  + +
  gi|386002342|ref|YP_005920641.1| 640 VVFALDTSGSMKKYYHLAPNESAEIVSGwsAFENSTVSIVSWDHASELLFgPAPLKGNEDRLAEILDNLSEMCIETD 716
                                       8999999999998774444444444444113467799*******999999999999999999999999999666556 PP

                             VWA_3  77 asnlegaLkealrqp.....akpgevrsvilltDgssaqgeervsdlisrar.ekirfhalglgs..s 136
                                        +   + L+  l+       ++p + + ++ lt+ s  +  e++ ++is+a     +++++g+g   s
  gi|386002342|ref|YP_005920641.1| 717 LTYYDQGLNGSLAELrdpasVPPNSSKIIVFLTGYSEFEAGEKLDEYISEANeLGCKVFTIGIGIneS 784
                                       666666666444322233568999999999999888877778******99874557788877775342 PP

>> NMT_C  Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.12   2.2e+02      77      94 ..     232     249 ..     224     254 .. 0.85
   2 !    6.1   0.0    0.0039       6.9      76      96 ..     338     358 ..     320     361 .. 0.88
   3 !    6.1   0.0     0.004       7.1      76      96 ..     445     465 ..     429     468 .. 0.89
   4 !    6.1   0.0     0.004       7.1      76      96 ..     552     572 ..     536     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                       TTTEEEEEEEETTS.EEE CS
                             NMT_C  77 eqvvwsYVvedeetkkit 94 
                                       ++v+w+YVv ++ + ++t
  gi|386002342|ref|YP_005920641.1| 232 DNVTWTYVVANRGNVNLT 249
                                       79********99887776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0039
                                       BTTTEEEEEEEETTS.EEEEE CS
                             NMT_C  76 eeqvvwsYVvedeetkkitDf 96 
                                       +++v+w+YVv+++ + ++tD+
  gi|386002342|ref|YP_005920641.1| 338 SDNVTWTYVVNNTGNVNLTDV 358
                                       789**********999***97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.004
                                       BTTTEEEEEEEETTS.EEEEE CS
                             NMT_C  76 eeqvvwsYVvedeetkkitDf 96 
                                       +++v+w+YVv+++ + ++tD+
  gi|386002342|ref|YP_005920641.1| 445 SDNVTWTYVVNNTGNVNLTDV 465
                                       689**********999***97 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.004
                                       BTTTEEEEEEEETTS.EEEEE CS
                             NMT_C  76 eeqvvwsYVvedeetkkitDf 96 
                                       +++v+w+YVv+++ + ++tD+
  gi|386002342|ref|YP_005920641.1| 552 SDNVTWTYVVNNTGNVNLTDV 572
                                       689**********999***97 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   3.5    0.0019       3.4       9      38 ..     227     256 ..     211     304 .. 0.74
   2 !    6.4   5.0    0.0063        11      10      37 ..     335     362 ..     318     405 .. 0.81
   3 !    9.4   2.3    0.0007       1.3      10      38 ..     442     470 ..     425     519 .. 0.76
   4 !   10.8   1.1   0.00027      0.48      10      39 ..     549     578 ..     532     664 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDt 38 
                                       e+  Gd+vt t +v N+g+++++ v v D 
  gi|386002342|ref|YP_005920641.1| 227 EIIVGDNVTWTYVVANRGNVNLTSVHVVDD 256
                                       7789******************99998884 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0063
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtD 37 
                                       ++  d+vt t +v Ntg++++++v v D
  gi|386002342|ref|YP_005920641.1| 335 LNLSDNVTWTYVVNNTGNVNLTDVYVVD 362
                                       57889****************9999888 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0007
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDt 38 
                                       ++  d+vt t +v Ntg++++++v v D 
  gi|386002342|ref|YP_005920641.1| 442 LNLSDNVTWTYVVNNTGNVNLTDVYVVDD 470
                                       57889****************99988884 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00027
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtl 39 
                                       ++  d+vt t +v Ntg++++++v v D  
  gi|386002342|ref|YP_005920641.1| 549 LNLSDNVTWTYVVNNTGNVNLTDVYVVDDI 578
                                       57889****************999888854 PP

>> GM_CSF  Granulocyte-macrophage colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       5.2   9.3e+03      17      44 ..     118     145 ..     115     149 .. 0.81
   2 ?   13.4   0.0   3.7e-05     0.067      44      77 ..     702     735 ..     692     744 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHH----HHHHTSEEEEES CS
                            GM_CSF  17 daikealsllnessdlaavlneevevvs 44 
                                       +ai+    l n  +d +   n++  v++
  gi|386002342|ref|YP_005920641.1| 118 EAINHDKILKNAVNDFSKASNNKNYVIY 145
                                       7889999999999999998888777765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.7e-05
                                       SS--BSSS--SHHHHHHHHHHT-SGGGGGGHHHH CS
                            GM_CSF  44 seefdlqeptclqtrlklykqGlrGsltklkgal 77 
                                       +e +d     c++t l  y qGl+Gsl++l+++ 
  gi|386002342|ref|YP_005920641.1| 702 AEILDNLSEMCIETDLTYYDQGLNGSLAELRDPA 735
                                       5667777889********************9875 PP

>> Branch_AA_trans  Branched-chain amino acid transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0083        15     173     213 ..     281     321 ..     261     332 .. 0.83
   2 ?    3.2   0.1     0.019        33     174     213 ..     389     428 ..     345     439 .. 0.83
   3 ?    4.0   0.1     0.011        19     173     216 ..     495     538 ..     452     639 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0083
                   Branch_AA_trans 173 easkayksaplikGfleGYlTmDalaslaFgiviveaiksk 213
                                       ++ ++y++ + ++G  +G + mD+  s  Fg++    i + 
  gi|386002342|ref|YP_005920641.1| 281 AVLGQYQNNATVNGTYNGTEVMDTDPSHYFGMILSIDIEKS 321
                                       34589**************************9987776655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.019
                   Branch_AA_trans 174 askayksaplikGfleGYlTmDalaslaFgiviveaiksk 213
                                       + + y++ +  +G  +G + mD+  s  Fg++    i + 
  gi|386002342|ref|YP_005920641.1| 389 VLGRYQNNATANGTYNGTEVMDTDPSHYFGMILSIDIEKS 428
                                       3589**************************9987766655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.011
                   Branch_AA_trans 173 easkayksaplikGfleGYlTmDalaslaFgiviveaikskgvk 216
                                       ++ + y++ +  +G  +G + mD+  s  Fg++    i +  + 
  gi|386002342|ref|YP_005920641.1| 495 AVLGRYQNNATANGTYNGTEVMDTDPSHYFGMILSIDIEKSTNG 538
                                       33589**************************9998777665544 PP

>> PixA  Inclusion body protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.68   1.2e+03     110     141 ..     214     249 ..     158     253 .. 0.70
   2 ?    2.8   0.0     0.065   1.2e+02     105     141 ..     320     356 ..     276     359 .. 0.82
   3 ?    2.8   0.0     0.067   1.2e+02     105     141 ..     427     463 ..     386     466 .. 0.84
   4 ?    2.7   0.0     0.072   1.3e+02     106     141 ..     535     570 ..     503     573 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.68
                                       GGSET.....-S-EEEEEEEEEEEEEB-SSEEEEEE CS
                              PixA 110 kenpe....glpptlqsekdyyweskvkktGtetyt 141
                                       + +++       p++    +++w+  v ++G++++t
  gi|386002342|ref|YP_005920641.1| 214 STDDDdadfPPGPEIIVGDNVTWTYVVANRGNVNLT 249
                                       3332234445567788889999*****999999987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.065
                                       EEE-GGGSET.-S-EEEEEEEEEEEEEB-SSEEEEEE CS
                              PixA 105 gpvpakenpeglpptlqsekdyyweskvkktGtetyt 141
                                       + ++ ++ + +  p+l+ + +++w+  v++tG++++t
  gi|386002342|ref|YP_005920641.1| 320 KSTNGEDADSAPGPILNLSDNVTWTYVVNNTGNVNLT 356
                                       44444444558899*******************9976 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.067
                                       EEE-GGGSET.-S-EEEEEEEEEEEEEB-SSEEEEEE CS
                              PixA 105 gpvpakenpeglpptlqsekdyyweskvkktGtetyt 141
                                       + ++ ++ + +  p+l+ + +++w+  v++tG++++t
  gi|386002342|ref|YP_005920641.1| 427 KSTNGEDADSAPGPILNLSDNVTWTYVVNNTGNVNLT 463
                                       44444444558899*******************9976 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.072
                                       EE-GGGSET.-S-EEEEEEEEEEEEEB-SSEEEEEE CS
                              PixA 106 pvpakenpeglpptlqsekdyyweskvkktGtetyt 141
                                        ++ ++ + +  p+l+ + +++w+  v++tG++++t
  gi|386002342|ref|YP_005920641.1| 535 STNGEDADSAPGPILNLSDNVTWTYVVNNTGNVNLT 570
                                       4444444558899*******************9976 PP

>> Glt_symporter  Sodium/glutamate symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3     0.026        47     104     138 ..     238     272 ..     228     293 .. 0.78
   2 ?    3.8   0.1     0.011        19     103     137 ..     344     378 ..     333     400 .. 0.82
   3 ?    3.8   0.1      0.01        18     103     137 ..     451     485 ..     440     507 .. 0.82
   4 ?    0.9   0.1     0.081   1.5e+02     103     137 ..     558     592 ..     547     610 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.026
                     Glt_symporter 104 iviqnlvGvslasllgldpllGllaGsislsGGhG 138
                                        v+ n   v l+s+  +d ++Gl+aG i+l  G  
  gi|386002342|ref|YP_005920641.1| 238 YVVANRGNVNLTSVHVVDDIIGLIAGPITLGAGEN 272
                                       56677778889999999*************87754 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                     Glt_symporter 103 liviqnlvGvslasllgldpllGllaGsislsGGh 137
                                         v+ n+  v l+ +  +d ++Gl+aG i+l  G 
  gi|386002342|ref|YP_005920641.1| 344 TYVVNNTGNVNLTDVYVVDDIIGLIAGPITLGAGE 378
                                       5678888899999******************8775 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.01
                     Glt_symporter 103 liviqnlvGvslasllgldpllGllaGsislsGGh 137
                                         v+ n+  v l+ +  +d ++Gl+aG i+l  G 
  gi|386002342|ref|YP_005920641.1| 451 TYVVNNTGNVNLTDVYVVDDIIGLIAGPITLGAGE 485
                                       5678888899999******************7764 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.081
                     Glt_symporter 103 liviqnlvGvslasllgldpllGllaGsislsGGh 137
                                         v+ n+  v l+ +  +d ++Gl+ G i+l  G 
  gi|386002342|ref|YP_005920641.1| 558 TYVVNNTGNVNLTDVYVVDDIIGLIVGPITLGAGE 592
                                       56788888999999*****************7764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (840 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 5428.77
//
Query:       gi|386002343|ref|YP_005920642.1|  [L=207]
Description: Ribonuclease HII [Methanosaeta harundinacea 6Ac]
Scores for complete 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-44  150.5   0.2    5.9e-44  150.3   0.2    1.0  1  RNase_HII  Ribonuclease HII
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.26   11.4   0.0    1.2  1  DUF4460    Domain of unknown function (DUF4460)


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.2   6.6e-48   5.9e-44       1     197 [.       1     198 [.       1     199 [. 0.88

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 6.6e-48
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH....HHTTT CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeiky...asene 74 
                                       +G DEaG+Gpv+G+++va+v+++++r   l +lgvkDSK L++ +re La  i+ ki  +  v+e   +   +  + 
  gi|386002343|ref|YP_005920642.1|   1 MGADEAGKGPVIGSMFVAGVVIDEDRLFDLAALGVKDSKLLAPARREALAIRIE-KIALDRYVLEVRPEvidELRKI 76 
                                       79****************************************************.5554443333222223377888 PP

                                       S-HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHH CS
                         RNase_HII  75 inlneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverde 151
                                       ++ nei + ++++v + l ++++ +d+ +v++ + + ++k+  ++   ++v++e++ad+ +++vaaASi+Akv+rd+
  gi|386002343|ref|YP_005920642.1|  77 MSMNEIMVRSFSKVLENLSADRAILDAADVKAERFARRVKEVSKTS--MEVVAEHRADRNHPVVAAASILAKVRRDL 151
                                       9******************************665555555555544..55*************************** PP

                                       HHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 152 elellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                        ++ ++++ g  ++gsGy+sd++t  +l++++ +   lp ++r s+kt
  gi|386002343|ref|YP_005920642.1| 152 SVREIEKAVG-REIGSGYPSDPATIRFLESWVGEhgDLPPVARQSWKT 198
                                       ********96.9********************99999**********8 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.26      11      54 ..      55      98 ..      46     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                           DUF4460 11 rnaLrpFYlavhPDlfgqyPkekkvNeeSLklLnsyleelkkee 54
                                      + aL ++ l+v+P+++ ++ k  ++Ne   + ++ +le+l+  +
  gi|386002343|ref|YP_005920642.1| 55 KIALDRYVLEVRPEVIDELRKIMSMNEIMVRSFSKVLENLSADR 98
                                      5689999*********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1235.82
//
Query:       gi|386002344|ref|YP_005920643.1|  [L=371]
Description: L-aspartate aminotransferase apoenzyme / phosphoserine aminotransferase apoenzyme [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-40  138.9   0.0    2.5e-40  138.6   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
     0.0038   16.6   0.0     0.0088   15.4   0.0    1.7  2  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.041   13.2   0.2       0.11   11.7   0.2    1.7  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.0   4.2e-44   2.5e-40       5     368 ..       2     338 ..       1     340 [. 0.91

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 4.2e-44
                                       TTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHH CS
                       Aminotran_5   5 saAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvals 80 
                                        +++ ++pq+Vl+a+++           +++h+++++ k++e++r+++++l+ +e+  e++++sG+++ ++++++ +
  gi|386002344|ref|YP_005920643.1|   2 IPGPVKVPQRVLRAMAKP----------MISHRSADFEKIYEDCRSRLKDLFDTEN--EVVVLSGSGTaGMEAAVGG 66 
                                       578999999999999999..........99*************************7..999999998879******* PP

                                       CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB-- CS
                       Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqp 157
                                       +   + +g+++v++++++ +++    el +r g  ++ + + ++   dl ++e++l++ +k++++ h++++ G+++p
  gi|386002344|ref|YP_005920643.1|  67 I---IGEGEKVVTVTNGKFGER--FTELGDRYGS-IVPLDFPWGTPFDLARIEAALEDGAKAITMVHNETSVGIVNP 137
                                       *...******************..*****99886.66**************************************** PP

                                       HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEE CS
                       Aminotran_5 158 veeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemvee 233
                                         e+gkla+k++a+++vD+ ++vg  ++ ++++g+D++  +++K l  P+G+ ++ v+k++   le  ++g ++  +
  gi|386002344|ref|YP_005920643.1| 138 AREVGKLARKYDAVFIVDGISSVGGNEFLTDEWGIDIAITGSQKcLAVPPGLAMVAVSKRAMDLLEEGKGGYYTDLK 214
                                       ********************************************8889*****************998888777777 PP

                                       EETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES..-B-CTCB CS
                       Aminotran_5 234 vsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlyg.pdkaerra 309
                                         l++++ +++p+     Tp v  + +l++al++ +e g+ + +++ ++la  ++++ ++l+   + +  +++  ++
  gi|386002344|ref|YP_005920643.1| 215 AHLKKASKNQTPY-----TPAVSLFFALQEALKMAAEEGFPERRARMAALAGGVRAAASALDIQLFPQvNEHTTYSN 286
                                       77799999*****.....**********************************9999999999888844133445566 PP

                                       SEEEEEE.TTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHH CS
                       Aminotran_5 310 sivsfnf.kgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeev 368
                                       +++++++  g++ ++++  ++++g+ v++G++ +          +++R++ + + te++v
  gi|386002344|ref|YP_005920643.1| 287 TVTAMKMpSGISDSQLRGGMRKRGVVVSGGQEGL--------KGKIFRIGTMGACTEADV 338
                                       7778888788999******************988........667777776555565555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-06    0.0088      14     168 ..      12     156 ..       7     269 .. 0.86
   2 ?   -3.4   0.0      0.78   4.6e+03     228     246 ..     301     317 ..     297     352 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-06
                                       HHHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES..-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTT CS
                   Beta_elim_lyase  14 msdaqaaamlGdesYgedktvnrLedavaelfgkeaalfvp..qGtaAnsillkillqrgeevivtepahihfdetg 88 
                                       + +a+a+ m+ + s   +k +++   ++++lf++e  + v   +Gta+ + ++  ++  ge+v+   ++ +  + t 
  gi|386002344|ref|YP_005920643.1|  12 VLRAMAKPMISHRSADFEKIYEDCRSRLKDLFDTENEVVVLsgSGTAGMEAAVGGIIGEGEKVVTVTNGKFGERFTE 88 
                                       67889999999999999999**************998877623699*******999988888888777777666666 PP

                                       HHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEE CS
                   Beta_elim_lyase  89 aiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplh 165
                                           ++++ + d++      +dl+++eaa+++ ga  + i ++  ++ +      v   +  rev ++a+ky+  ++
  gi|386002344|ref|YP_005920643.1|  89 LGDRYGSIVPLDFPWGT--PFDLARIEAALED-GA--KAITMVHNETSVG----IV---NPAREVGKLARKYDAVFI 153
                                       66778999777777666..9************.66..6777777666555....44...456999************ PP

                                       EEE CS
                   Beta_elim_lyase 166 lDg 168
                                       +Dg
  gi|386002344|ref|YP_005920643.1| 154 VDG 156
                                       **9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.78
                                       HHT---SSTHHHHH..HHH CS
                   Beta_elim_lyase 228 ylggglrqagvlaaleagi 246
                                       +l gg+r+ gv++    g 
  gi|386002344|ref|YP_005920643.1| 301 QLRGGMRKRGVVVS--GGQ 317
                                       56789999999887..444 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   1.9e-05      0.11      99     150 ..     107     161 ..      38     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                       B-GGGCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1  99 idpaaieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                        d a+ieaa++   kaI++Vh    +G v+   ++ ++a+k++ ++i D   ++G
  gi|386002344|ref|YP_005920643.1| 107 FDLARIEAALEDGAKAITMVHnetSVGIVNPAREVGKLARKYDAVFIVDGISSVG 161
                                       6999*****************44447999999***************99877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2355.50
//
Query:       gi|386002345|ref|YP_005920644.1|  [L=654]
Description: hypothetical protein Mhar_1661 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.9   0.2       0.67   10.2   0.0    2.1  2  FixG_C    IG-like fold at C-terminal of FixG, putative oxidor


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 ?   10.2   0.0   3.8e-05      0.67      35      86 ..      49     103 ..      48     111 .. 0.80
   2 ?   -0.3   0.1     0.065   1.2e+03       8      43 ..     462     498 ..     459     503 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.8e-05
                                       EEEEEEE-SSS-EEEEEEEES-S...S-EE.E.S--EEEE-TT-EEEEEEEEEE- CS
                            FixG_C  35 YtlkilNktekprrytlsveglp...glelagraekeitvapgekrkvpvfvrvp 86 
                                       Y ++++N  ++p+ry +++e  p   + + ++r ++ i++ + + ++v++ v  +
  gi|386002345|ref|YP_005920644.1|  49 YKIHLTNAMNSPMRYSVELEVGPdftDYTASKRYTTDISLTARSAQDVVFDVNFR 103
                                       9*******************54425555556677999999999999999988765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.065
                                       --SEEEEEEE-SS----.-----SEEEEEEEEEEE-S CS
                            FixG_C   8 replelnvlrdrgplyv.evsdgsieNsYtlkilNkt 43 
                                       +e++  nv++ rg++ v   s++  + +Yt++i N  
  gi|386002345|ref|YP_005920644.1| 462 KESITGNVTPARGVMQVfPDSNNLNRYVYTIHIENLG 498
                                       6778889999999999823444445667777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4639.27
//
Query:       gi|386002346|ref|YP_005920645.1|  [L=483]
Description: hypothetical protein Mhar_1662 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2669.42
//
Query:       gi|386002347|ref|YP_005920646.1|  [L=227]
Description: hypothetical protein Mhar_1663 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.3   3.3       0.11   12.7   0.5    2.1  2  DUF5367   Family of unknown function (DUF5367)
       0.54    9.0   2.8       0.33    9.7   0.9    1.6  1  DUF2207   Predicted membrane protein (DUF2207)
          1    9.0   9.7        5.6    6.6   0.6    2.3  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF5367  Family of unknown function (DUF5367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.31   1.8e+03      14      28 ..      95     108 ..      84     116 .. 0.51
   2 ?   12.7   0.5   1.8e-05      0.11      14      74 ..     141     201 ..     133     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.31
                           DUF5367  14 fllviplllvlllpv 28 
                                       ++ +++ll++  +++
  gi|386002347|ref|YP_005920646.1|  95 AVAAWMLLFAA-FAY 108
                                       33344333332.222 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.8e-05
                           DUF5367  14 fllviplllvlllpvykykklnkterlkaailialpgmllDvlilvfFeeifpnlqpeaas 74 
                                       f+l++  l++ ++p   y   + + ++k+ai++++p+++l ++  v    ifp  +p a +
  gi|386002347|ref|YP_005920646.1| 141 FVLLLAGLAAAFIPRELYGYYELSRKTKVAIMLTVPALALSIALSVQLGTIFPEVDPAARG 201
                                       455555555555565556666677899***************************9988765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.9   5.5e-05      0.33     368     437 ..      80     161 ..      38     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 5.5e-05
                           DUF2207 368 ergyfdkkgkkklkklsalglgliilglilillallllvll................lvfllilllillliaiivll 428
                                       + + f+++       ++a+++++++l+++++ ++ +l   +                l f+++ l++lll+++++++
  gi|386002347|ref|YP_005920646.1|  80 RDEMFTRQ----GSNFNAAAVAAWMLLFAAFAYFYFLTPEIfpghnyyqlptlssgpLGFAAFGLFVLLLAGLAAAF 152
                                       33444444....34566667777777776666665555555788**********99999999999999999999999 PP

                           DUF2207 429 lfsrllgrr 437
                                       +++ l g +
  gi|386002347|ref|YP_005920646.1| 153 IPRELYGYY 161
                                       998776654 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6   0.00094       5.6       5      53 ..      38     115 ..      30     129 .. 0.57
   2 ?    6.4   3.0     0.001       6.2       2      55 ..     132     194 ..     131     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00094
                           DUF4131   5 lalvllalllllllllllllrr.................................rprrrvllllllllllallgfa 48 
                                       l + ++++ll+  lll     r                                  + +  ++++ +ll++a+++f+
  gi|386002347|ref|YP_005920646.1|  38 LGVAIFIALLAGGLLLH----RlnmdrtyrnvaattrdgevspedlrdemftrqgSNFNAAAVAAWMLLFAAFAYFY 110
                                       34444444444444444....34455777776666666666666666666555443334447777777777777776 PP

                           DUF4131  49 lrapq 53 
                                       + +p+
  gi|386002347|ref|YP_005920646.1| 111 FLTPE 115
                                       66554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.001
                           DUF4131   2 glplalvllalllllllllllllrr.........rprrrvllllllllllallgfalrapqpn 55 
                                       +l++a++ l++lll+ l+++++ r+         +++  ++l++ +l+l ++l ++l +  p+
  gi|386002347|ref|YP_005920646.1| 132 PLGFAAFGLFVLLLAGLAAAFIPRElygyyelsrKTKVAIMLTVPALALSIALSVQLGTIFPE 194
                                       5789999999***********9999*****996555555566666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1289.25
//
Query:       gi|386002348|ref|YP_005920647.1|  [L=508]
Description: hypothetical protein Mhar_1664 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-08   34.7   0.2    4.5e-05   23.7   0.0    2.6  2  Tubulin    Tubulin/FtsZ family, GTPase domain
     0.0053   16.0   0.1      0.025   13.8   0.0    1.9  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0003       2.6       2      44 ..       3      64 ..       2      87 .. 0.70
   2 !   23.7   0.0     5e-09   4.5e-05     108     179 ..     152     223 ..     148     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0003
                                      EEEEEEHHHHHHHHHHHHH...HHHCH...........................HHHT.....TTE CS
                           Tubulin  2 iivigvGqcGnqignelwellakehgiqsdg.......................dslesfFsesgk 44
                                      ++++g+G+cG+++++++ +    ++ + + +                       ++ +sfF  +++
  gi|386002348|ref|YP_005920647.1|  3 LCIVGIGGCGGHLAERFLK----NQDVAPLKkslgehvsfggvkglwleadvqeTENQSFFGSHER 64
                                      579****************....3333322224566677777777777777776666666666554 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 5e-09
                                       HHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G-HHHHHHHHHHHHHHHH CS
                           Tubulin 108 kevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefsevvvepynailalkelie 179
                                       ke+ ++++ +g++++ slgGGTG+G+ + i+++++ e p  +v+   +l  e ++   + + a   l + i+
  gi|386002348|ref|YP_005920647.1| 152 KETGGSEMCDGILFIVSLGGGTGTGFVNPITRYIRGERPAYPVFVLGILTEEGTDPQQRAKEAKRDLGASIS 223
                                       66778888999**************************88888888888777555666666666665555544 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.058   5.2e+02       2      21 ..       5      24 ..       4      59 .. 0.74
   2 !   13.8   0.0   2.8e-06     0.025     139     183 ..     135     188 ..     120     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.058
                         Tubulin_2  2 viGLGGtGgkvlaelrrrlr 21
                                      ++G+GG Gg   +++ +   
  gi|386002348|ref|YP_005920647.1|  5 IVGIGGCGGHLAERFLKNQD 24
                                      79*******99888776654 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.8e-06
                         Tubulin_2 139 lrdaikrlrg........sageeegln.vfVvgSLaGGTGSGiflDvayllrki 183
                                       lr a++r+r+        + g++e+++ +  ++SL GGTG G + +++ ++r +
  gi|386002348|ref|YP_005920647.1| 135 LRAAWDRIRDyttlaaakETGGSEMCDgILFIVSLGGGTGTGFVNPITRYIRGE 188
                                       678888888888887765333366676578889******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2942.52
//
Query:       gi|386002349|ref|YP_005920648.1|  [L=193]
Description: hypothetical protein Mhar_1665 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1306.51
//
Query:       gi|386002350|ref|YP_005920649.1|  [L=337]
Description: hypothetical protein Mhar_1666 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-36  122.9   0.0    1.2e-35  122.4   0.0    1.3  1  DUF1722   Protein of unknown function (DUF1722)
    3.7e-32  111.2   0.0    6.5e-32  110.4   0.0    1.4  1  DUF523    Protein of unknown function (DUF523)


Domain annotation for each model (and alignments):
>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.0   1.3e-39   1.2e-35       1     117 []     202     318 ..     202     318 .. 1.00

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 1.3e-39
                           DUF1722   1 KyllmahsqkeyrelgrlvanakkepleelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqellel 77 
                                       K+ll+a++q+e r+lg + an++++p++e+a +Ye +l +al +  +++++invl+hi+g+fk +lsa ek+ +l+ 
  gi|386002350|ref|YP_005920649.1| 202 KMLLLAYHQAEARALGAIAANHDHRPFSEVAGDYEPHLAKALCRARRYTSNINVLMHIFGHFKGRLSAGEKAIFLDN 278
                                       9**************************************************************************** PP

                           DUF1722  78 iekYregkvplsvpltlLkhyarkydneylleqtylnpyP 117
                                       +++Yr+gk+++    t+Lk +++++++eyl +qt+++pyP
  gi|386002350|ref|YP_005920649.1| 279 VQRYRDGKITICPNTTILKAWVARFEDEYLGSQTFFEPYP 318
                                       ***************************************9 PP

>> DUF523  Protein of unknown function (DUF523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.0   7.3e-36   6.5e-32       1     137 []      17     160 ..      17     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 7.3e-36
                            DUF523   1 ilvSaCLlgekvrydgkakksevleeelkelvkeelvpvCPEvaggLptPRepael.......akr.vlkkegedvt 69 
                                       ++vS+C+  +++ry+g+  +s+++++ l+ +v  +++pvCPEv++gL++PR++++l       ++r v+ ++ +dvt
  gi|386002350|ref|YP_005920649.1|  17 VVVSRCIEVDHCRYNGQIISSDFVKS-LQPYV--QFLPVCPEVEIGLGVPRDSVRLvstnrekETRlVQPATDRDVT 90 
                                       79******************999988.*****..****************************977889********* PP

                            DUF523  70 ealekgaeealeelkeeeikgailkekSPSCGveki..Y..dgtfskklvegeGvfaallkeegievpseee 137
                                       ++++++a ++l+++   +++g+ilk+ SPSCG++++  Y  +g+    +++++G+f a++ ++++++++e+e
  gi|386002350|ref|YP_005920649.1|  91 AEMNTFAGSFLDAVG--DVDGFILKASSPSCGIRNTkvYptAGRSAALTRSASGLFGAAVLARHPHLAVEDE 160
                                       ************999..6***************999889765665555599****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2191.21
//
Query:       gi|386002351|ref|YP_005920650.1|  [L=450]
Description: hypothetical protein Mhar_1667 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0038   16.4   0.0      0.049   12.7   0.0    2.0  2  LpxK      Tetraacyldisaccharide-1-P 4'-kinase
  ------ inclusion threshold ------
      0.039   13.5   0.0      0.073   12.7   0.0    1.4  1  cobW      CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.5e-06     0.049      31      71 ..     117     156 ..      97     159 .. 0.89
   2 ?    1.3   0.0     0.016   1.4e+02     175     205 ..     260     290 ..     199     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-06
                                       B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK  31 erlpvpVivVGNitvGGtGKTPlvialvkllqarglkvgvl 71 
                                        ++ +pVi V  + + G+GK P++ ++ + ++ rgl+++v+
  gi|386002351|ref|YP_005920650.1| 117 LKSRLPVIAVTAVRT-GAGKSPAARYVSRIVRGRGLRPAVV 156
                                       56789******9998.58*********************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.016
                                       GGGG-SEEEE..........-TTTSSSS-EE CS
                              LpxK 175 rlkradlvilngakaeeeeaekaeeksipvl 205
                                       +l+rad+v++n+a+++ ++a ++ ++s++++
  gi|386002351|ref|YP_005920650.1| 260 NLRRADVVVINKARTAGSRAVAEIRESVRRV 290
                                       6999999999988877766655554444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.1e-06     0.073     133     175 ..     255     296 ..     228     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-06
                                       HHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-E CS
                              cobW 133 ekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakv 175
                                         ++  l  ad++v+nK+ ++ ++a  ++++e +r++np+a++
  gi|386002351|ref|YP_005920650.1| 255 YPGQVNLRRADVVVINKARTAGSRAV-AEIRESVRRVNPGART 296
                                       455667899***************65.************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2505.62
//
Query:       gi|386002352|ref|YP_005920651.1|  [L=262]
Description: Carbamate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-21   76.8   0.0    2.4e-21   76.4   0.0    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   1.3e-25   2.4e-21      37     240 ..       1     243 [.       1     244 [. 0.85

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 1.3e-25
                                       EEEEE--HHHHHHHHHH....TCCCCCHHHC....E..HHHHHHHHH..........HHHHHHHHHHHHHHHHTTHG CS
                         AA_kinase  37 lvvVhGggsftdgllal....ksglssgelaaglrstleeagevatr..........dalaslgerlvaallaaglp 99 
                                       +v+VhG+g+++ ++l +    +  +++++l+    +t+   g ++ r          + +a++ +++v    + +++
  gi|386002352|ref|YP_005920651.1|   1 MVLVHGNGPQVGMILLRieatRDRIPPEPLDVLVAETQGSIGYLLARtirsasahphQDVAAVMTQVVVDGSDPAFA 77 
                                       69***************766666666666664444444555555555887777777788888888888888888886 PP

                                       EEEE-GGGTCEECCCE.....................HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE... CS
                         AA_kinase 100 avglsaaaldateagr...................degsdgnvesvdaeaieelleagvvpvltgfigldeege... 154
                                           ++ ++ ++e+                      ++s++++e v+   i+e +++g++++ +g++g+++  +   
  gi|386002352|ref|YP_005920651.1|  78 RPTKPVGPFYSEEEALrlrekvgwdlapgakgwrrVVPSPRPREVVEMGVIREAVAEGHLVIAGGGGGVPVRRGrgr 154
                                       555555555555555568*************************************************9999999888 PP

                                       .....EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHH CS
                         AA_kinase 155 .....lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaa 226
                                             +++++D +++l A+ lgA++l+ilt+Vd Vy + + +   a+++p ++ +ea+++ + l  g+m +k++aa
  gi|386002352|ref|YP_005920651.1| 155 elfgvEAVVDKDLTSSLMAVGLGAERLVILTEVDAVYRDFGGEG--AEPIPHLRPEEARDILDLLPPGSMGPKVEAA 229
                                       9888877*********************************9887..******************************* PP

                                       HHHHHCTT-EEEEE CS
                         AA_kinase 227 laaarrggipvvIt 240
                                       la+a+  g  + It
  gi|386002352|ref|YP_005920651.1| 230 LAFAEATGRGALIT 243
                                       *****988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1755.65
//
Query:       gi|386002353|ref|YP_005920652.1|  [L=424]
Description: Sodium:neurotransmitter symporter family protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete 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-60  205.5  25.9    5.2e-32  111.2   6.4    2.2  2  SNF       Sodium:neurotransmitter symporter family
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.27   11.3   0.0    1.5  1  BiPBP_C   Penicillin-Binding Protein C-terminus Family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   6.4   5.8e-36   5.2e-32       2     114 ..       2     114 ..       1     128 [. 0.97
   2 !  100.2  11.7   1.3e-32   1.2e-28     182     448 ..     135     395 ..     120     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 5.8e-36
                               SNF   2 etwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkicP 78 
                                       e+ws++ +fil++vG+avg+gn+WRF  ++ +nGGGa+l+PYl++++   +Pl+ lela+G++ r   +t++ +  P
  gi|386002353|ref|YP_005920652.1|   2 ERWSSRTAFILASVGSAVGIGNIWRFSSVVGQNGGGAYLVPYLMAVFAFALPLMMLELAVGRRLRGDVVTAFGRARP 78 
                                       78*************************************************************************** PP

                               SNF  79 llkgiGyasivvalyvglyYnvilawalfYlfssft 114
                                       +++ +G++++ v++ +  yY v+ +w+l Y+  s+ 
  gi|386002353|ref|YP_005920652.1|  79 RFRPLGWVVCAVVFSILSYYLVVTGWTLAYVGFSIA 114
                                       ******************************998875 PP

  == domain 2  score: 100.2 bits;  conditional E-value: 1.3e-32
                               SNF 182 lcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllepkvWidaatqi 258
                                       ++ lv+  +v+l+i  G++ ++k++     f +++ll l   + +L+G   g ++++tpd++ l +p  W +a  q 
  gi|386002353|ref|YP_005920652.1| 135 ISALVMGAIVSLGIKDGIERATKLLIP---FSFLLLLGLAAFSSTLEGFGAGWRYLFTPDFSVLADPLLWAAAFGQA 208
                                       56678889***************9976...6789999**************************************** PP

                               SNF 259 ffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFiayp 335
                                       ffsl++g+G+l++++ Y +    + +++l++++++ ++ +laglv+F v+     e           G+ LaF + p
  gi|386002353|ref|YP_005920652.1| 209 FFSLSVGYGILLTYGDYLDEGIGILNSSLIITFADLAVAILAGLVIFPVVFTYGLE--------PAAGAELAFSTLP 277
                                       ************************************************98433322........3579********* PP

                               SNF 336 ealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavla......flvglllvte 406
                                       +a   +p+++ ++v FF  l  ++++s+++++e+  ++v+    +  rrr  + l+   +a      +  + + ++ 
  gi|386002353|ref|YP_005920652.1| 278 RAFEVMPYGSAFAVAFFALLFSAAMTSAVSMLEVGAASVAAATGI-SRRRVSFALTAGTIAlglpsaLSYSSAALEV 353
                                       **********************************99999999888.4455544443333320001002334456788 PP

                               SNF 407 gGiyvltlldkyaaslsllvvvlleaiavawvyglkkflddi 448
                                       gG+ vl+++d+ +  l+l++++ l a++ +w+   + + +++
  gi|386002353|ref|YP_005920652.1| 354 GGVRVLDIMDDTVGGLGLVLTATLIAVTFTWFMDGRALAEEM 395
                                       9******************************99888777665 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.1e-05      0.27      34      66 ..     370     403 ..     357     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
                           BiPBP_C  34 rlqlkarggeaplrWlldgepl.aetkrgrelaw 66 
                                        l+l+a   + +++W++dg+ l +e +rgr+la+
  gi|386002353|ref|YP_005920652.1| 370 GLVLTATLIAVTFTWFMDGRALaEEMGRGRRLAL 403
                                       567777777779**********888999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2647.41
//
Query:       gi|386002354|ref|YP_005920653.1|  [L=266]
Description: hypothetical protein Mhar_1670 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1490.30
//
Query:       gi|386002355|ref|YP_005920654.1|  [L=133]
Description: hypothetical protein Mhar_1672 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-05   24.5   3.4    4.2e-05   23.7   3.4    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
      4e-05   23.3   0.0    9.8e-05   22.0   0.0    1.7  1  HHH            Helix-hairpin-helix motif
     0.0082   16.6   0.0       0.01   16.3   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
     0.0097   16.5   0.1      0.059   14.0   0.0    2.0  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.22   11.5   0.0       0.29   11.1   0.0    1.1  1  DUF2400        Protein of unknown function (DUF2400)


Domain annotation for each model (and alignments):
>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   3.4   1.2e-08   4.2e-05       1      17 []     107     123 ..     107     123 .. 0.99

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.2e-08
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       C AR+P C+aC+La+ C
  gi|386002355|ref|YP_005920654.1| 107 CRARSPSCGACVLAEVC 123
                                       ***************** PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.7e-08   9.8e-05      13      30 .]      30      47 ..      27      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.7e-08
                                      HHTSTT-SHHHHHHHHHH CS
                               HHH 13 LlalPGVGpktAeaIlsy 30
                                      L++lPGVGpktA ++l +
  gi|386002355|ref|YP_005920654.1| 30 LVSLPGVGPKTAAVVLLF 47
                                      89*************976 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.8e-06      0.01      67     107 ..      48      88 ..      21      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                                       S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                       ++  +l +vD+hv r+ +rl+++ +  + +++e+ lee+ +
  gi|386002355|ref|YP_005920654.1|  48 AFRMPLLPVDTHVNRLSRRLGFVPAGASIEEAERILEEITP 88 
                                       44568999****************************88765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.6e-05     0.059      34      53 ..      23      46 ..       7      48 .. 0.70
   2 ?    0.1   0.0      0.36   1.3e+03      46      55 ..      77      86 ..      61      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                      HHH....HHTSTTS-HHHHHHHHH CS
                             HHH_5 34 vee....LakipGiGkktAeriil 53
                                      +ee    L ++pG+G+ktA  ++l
  gi|386002355|ref|YP_005920654.1| 23 AEEarqfLVSLPGVGPKTAAVVLL 46
                                      333335599999999999976665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                                      HHHHHHHHHH CS
                             HHH_5 46 ktAeriilel 55
                                      + Aeri++e+
  gi|386002355|ref|YP_005920654.1| 77 EEAERILEEI 86
                                      6799999985 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.2e-05      0.29     172     190 ..      53      71 ..      50      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                           DUF2400 172 iiPlDvHvarvarklgllk 190
                                       ++P+D+Hv+r++r+lg++ 
  gi|386002355|ref|YP_005920654.1|  53 LLPVDTHVNRLSRRLGFVP 71 
                                       58**************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 867.76
//
Query:       gi|386002356|ref|YP_005920655.1|  [L=149]
Description: DNA-(Apurinic or apyrimidinic site) lyase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-09   36.8   0.1    5.6e-09   36.4   0.1    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.18   11.6   0.0    1.4  1  Dimer_Tnp_hAT  hAT family C-terminal dimerisation region


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   6.2e-13   5.6e-09       1      66 [.      50     113 ..      50     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 6.2e-13
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv 66 
                                       v +ilsq+t+ +++ r++e+l+++   p  ++l++a++e+++ lir+ G+ + K ++ike+  +++
  gi|386002356|ref|YP_005920655.1|  50 VQTILSQNTTSANTHRAFESLKRA--YPAYQALLSAPDEEVAGLIRCGGLANIKTRRIKEALAMIQ 113
                                       689*********************..59*******************************9866666 PP

>> Dimer_Tnp_hAT  hAT family C-terminal dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.18      39      67 ..      49      77 ..      46      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                                      HHHHHHTS-S-TTTTHHHHHHTHHHHH-T CS
                     Dimer_Tnp_hAT 39 lardvLsipvssaasErsFstlgkvlles 67
                                      l++ +Ls+  +sa+++r+F  l++ +  +
  gi|386002356|ref|YP_005920655.1| 49 LVQTILSQNTTSANTHRAFESLKRAYPAY 77
                                      6789*******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1115.31
//
Query:       gi|386002357|ref|YP_005920656.1|  [L=425]
Description: hypothetical protein Mhar_1674 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-63  213.8  22.5    2.1e-63  213.8  22.5    2.8  3  DUF4010   Domain of unknown function (DUF4010)
    1.2e-14   54.7  11.8    1.2e-14   54.7  11.8    3.3  3  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.7  12.6         2   1.8e+04     134     195 ..      53     114 ..      10     138 .. 0.56
   2 ?   -7.6  12.0         2   1.8e+04      87     103 ..     109     135 ..      57     174 .. 0.38
   3 !  213.8  22.5   2.3e-67   2.1e-63       1     210 []     192     399 ..     192     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: -7.7 bits;  conditional E-value: 2
                           DUF4010 134 lfalilllakaaqeyfGdaglyalaalsGladvdAitlslarlaaegtlsaataalaillav 195
                                       l++l+  l++a+   +G a ++++ a  +l+ + + ++s+++l + +  s+ +aa+a +l++
  gi|386002357|ref|YP_005920656.1|  53 LITLLGTLSAAMAAEYGGAFIIVAFASFALMVAVGYAASATNLGRLDFTSEVAAAIAFILGA 114
                                       33333344444444445444444444445555555555555555433333333444433333 PP

  == domain 2  score: -7.6 bits;  conditional E-value: 2
                           DUF4010  87 a........lp..llalallallvaal 103
                                       a         p  ++++++la+l++++
  gi|386002357|ref|YP_005920656.1| 109 AfilgalcyHPdtVMLAIALAILGTVI 135
                                       122222222232222222222222222 PP

  == domain 3  score: 213.8 bits;  conditional E-value: 2.3e-67
                           DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivav 77 
                                       Vl+s i+++gYv++r++g+ rGl +tg lGGlvSStAv  ++a ++k+++e  +++++++++A+++m++r+ll v+v
  gi|386002357|ref|YP_005920656.1| 192 VLVSLIGYVGYVMIRIFGTDRGLSITGALGGLVSSTAVATTMAAEAKAHREVVPSAVFATTIASCTMFPRILLEVFV 268
                                       8**************************************************************************** PP

                           DUF4010  78 vnpallvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfGdagl 154
                                       vn++l+  l+lp++ ++++++++a+ll+r+re+ e++  ++l+ P++l++Alkf+++fal+ll++k+a+ yfG+ag 
  gi|386002357|ref|YP_005920656.1| 269 VNRDLFLPLLLPMASMTVAGVALALLLYRKRETIEAP--VNLTDPFRLSPALKFGAFFALVLLVSKVASIYFGEAGT 343
                                       *****************99999999999999999977..59************************************ PP

                           DUF4010 155 yalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalviG 210
                                       ya+++++GladvdAitlsla+la++ ++ +++a++ai+la+++ntlvK+++++v+G
  gi|386002357|ref|YP_005920656.1| 344 YAASLVAGLADVDAITLSLATLARTPAMGEEVAVAAITLAAMTNTLVKLAITFVLG 399
                                       *****************************************************987 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7  11.8   1.3e-18   1.2e-14       2     120 ..      20     144 ..      19     145 .. 0.85
   2 ?    0.3   1.4     0.094   8.5e+02      53      93 ..     193     233 ..     161     265 .. 0.53
   3 ?   -4.1   5.0         2   1.8e+04      94     107 ..     376     389 ..     320     424 .. 0.48

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.3e-18
                              MgtC   2 llAlllGlliGleRel.....rek..aaGlRTfaLvalgaalfvllslelaesrvaaqvvsgigflgagvilkekeg 71 
                                       l+++l+G+liG eRe+     + k  +aGlRTf+L++l+++l++ ++ e+  + ++  ++s   ++++g    + ++
  gi|386002357|ref|YP_005920656.1|  20 LISILIGALIGTERERdllekK-KrgVAGLRTFILITLLGTLSAAMAAEYGGAFIIVAFASFALMVAVGYAA-SATN 94 
                                       799*************888641.357********************88887777777777777777777776.3333 PP

                              MgtC  72 akvkglTTaaslwvtaaiGllvgl.glyllavvatvlvllllallreler 120
                                           ++T+++++ +++++G+l++  + ++la+++++l +++la++++ +r
  gi|386002357|ref|YP_005920656.1|  95 LGRLDFTSEVAAAIAFILGALCYHpDTVMLAIALAILGTVILAIKKTAHR 144
                                       499*******************9945699*****************9997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.094
                              MgtC  53 vvsgigflgagvilkekegakvkglTTaaslwvt.aaiGllv 93 
                                       +vs ig +g  +i     +++  ++T a + +v+ +a+ + +
  gi|386002357|ref|YP_005920656.1| 193 LVSLIGYVGYVMIR-IFGTDRGLSITGALGGLVSsTAVATTM 233
                                       45555555533322.233334444444444333212222222 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2
                              MgtC  94 glglyllavvatvl 107
                                       ++  ++la+++  l
  gi|386002357|ref|YP_005920656.1| 376 AVAAITLAAMTNTL 389
                                       22222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2707.32
//
Query:       gi|386002358|ref|YP_005920657.1|  [L=93]
Description: hypothetical protein Mhar_1675 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 747.73
//
Query:       gi|386002359|ref|YP_005920658.1|  [L=95]
Description: hypothetical protein Mhar_1676 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00044   20.9   1.3    0.00054   20.6   1.3    1.2  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.3     3e-08   0.00054       2      69 ..       3      74 ..       2      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3e-08
                          CxxCxxCC  2 CkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak.adgrCvfld..eetklCkiYe...eRpkicrlf 69
                                      C +Cg CC   +  + + + + +++ ++ +  + +  i+k a++rC++l   +e  lC i+     R + c  f
  gi|386002359|ref|YP_005920658.1|  3 CSRCGLCCI--NLDIFIINPRSIRPDGTLDPGDPEAMIRKpAGERCTHLAftGEVALCAIHDlpcYRGTPCDRF 74
                                      *********..7778888888999999999999999998899*****998435556****98666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 772.69
//
Query:       gi|386002360|ref|YP_005920659.1|  [L=271]
Description: putative inorganic polyphosphate/ATP-NAD kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.8e-54  182.8   0.0    9.9e-54  182.5   0.0    1.2  1  NAD_kinase  ATP-NAD kinase
     0.0028   17.3   0.0     0.0045   16.6   0.0    1.3  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   0.0   1.1e-57   9.9e-54      73     291 ..      49     256 ..      18     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 1.1e-57
                                       TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEE CS
                        NAD_kinase  73 afadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavim 149
                                       +  d++vd+i+ vGGDGT+l+  r +++   P+lg+n+G++gfl ++ep++a ++le++l  +++v +r++l++ ++
  gi|386002360|ref|YP_005920659.1|  49 RIEDMDVDFIVSVGGDGTILRTIRRMED-PRPILGINMGTLGFLVDVEPKDAVRTLERVLF-GFEVMERSRLSTRLN 123
                                       45688**********************7.99*****************************9.9**********6665 PP

                                       ETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT--- CS
                        NAD_kinase 150 rskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvla 226
                                                     + + ne+ +  +++++++e+e+ vd+ lle++++dgl+ +t+tGstay++saGgp+++P+v+a
  gi|386002360|ref|YP_005920659.1| 124 GVPL----------PPATNEIALLSASPAKMLEFEITVDDFLLESLRADGLLFATATGSTAYAMSAGGPIVDPRVDA 190
                                       5554..........568************************************************************ PP

                                       EEEEEESESSS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 227 ilivpicPhslssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                       +++vp+ P++ls+rp V++ +s +++ ++  ++eal+++dG+    +s++d +++++++k++++++
  gi|386002360|ref|YP_005920659.1| 191 VVLVPLAPFKLSARPWVLPAESVIKVDLElPEKEALVVIDGHNVATISKRDHITISRAEKPARFVK 256
                                       ****************************************************************97 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     5e-07    0.0045      31      87 ..      33      83 ..      12      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-07
                                      CEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEE CS
                          DAGK_cat 31 velelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgi 87
                                      +++e  + ++ g a++    +++ +vd+iv +GGDGt+   +  + +    +p lgi
  gi|386002360|ref|YP_005920659.1| 33 ITIEPETAKKLGFAETR---IEDMDVDFIVSVGGDGTILRTIRRMED---PRPILGI 83
                                      43333333333334333...4444569***********999999888...5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1975.93
//
Query:       gi|386002361|ref|YP_005920660.1|  [L=279]
Description: Inositol-1-monophosphatase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-29  103.5   0.0    1.7e-29  103.2   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
     0.0079   15.7   0.0      0.011   15.2   0.0    1.2  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0     2e-33   1.7e-29      39     257 ..      49     264 ..      17     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 2e-33
                                       HHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEET CS
                        Inositol_P  39 eedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllve 115
                                       +  + + +d+++e+++ ++l+ +  + +il+ee+++k+    +++ +++  +DP+DGT n + gip + Vsi  +  
  gi|386002361|ref|YP_005920660.1|  49 DGTPTKSIDQRAEDAVFAVLEGSGIDFAILSEEEGRKEI---GKCPSYFLHLDPLDGTFNAIAGIPFYSVSI-YISG 121
                                       4457899****************************9998...78888************************9.5667 PP

                                       TEEEEEEEEETTTTEEECEETTTEEEETC....EEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCH CS
                        Inositol_P 116 gkpvlGviaqPllgqlysaakgkGaflng....eklplsrappiseallvtlfavssrkdtseasllekvesavsae 188
                                        +  +G + + ++  +y a +g+Ga+++      +l++s++p+++++++      s+   +++++ +  +   v++ 
  gi|386002361|ref|YP_005920660.1| 122 PTSSFGYVSDLAHAARYFAERGRGAWSEAagrrARLRVSKTPTLQNFSV------SAYTLRPNTERIVPLGDVVRRI 192
                                       7888***********************9989888899999996666655......4555555545566665556555 PP

                                       EEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC.....SSSTTSSEEEEESCH CS
                        Inositol_P 189 gvrsvgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge.....grlllargiiaanqk 257
                                         r +gs+ ++l++va+G++da+++ +  +   D+AAG++i++eaGG+vtd  g+     g +++++++ia+n +
  gi|386002361|ref|YP_005920660.1| 193 --RTLGSTSAELCLVAAGRLDAFVDLRgGLRLVDVAAGSLIVQEAGGTVTDGWGDqigfnGDMWQKSEYIASN-G 264
                                       ..999*********************8889999******************9999999988888999999998.3 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-06     0.011      55     116 ..      47     105 ..      14     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
                            FBPase  55 NvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                                         +G   k +D +a++ ++++l+ s++  ++ SEEe   ++    k  +y + +DPlDG  n
  gi|386002361|ref|YP_005920660.1|  47 GADGTPTKSIDQRAEDAVFAVLEGSGIDFAILSEEEGRKEIG---KCPSYFLHLDPLDGTFN 105
                                       5678899***************************99887665...7789**********877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1956.31
//
Query:       gi|386002362|ref|YP_005920661.1|  [L=513]
Description: Na+/solute symporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-59  200.5  30.1    5.3e-59  200.1  30.1    1.2  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.1  30.1     3e-63   5.3e-59       1     406 []      35     453 ..      35     453 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 3e-63
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpd 73 
                                       y+lagr+l+ +v  + + as  s+  ++G +G+++  G  +++ ++ + l + + +ll++ +l     + g lT+ d
  gi|386002362|ref|YP_005920661.1|  35 YILAGRNLGFWVFTILIVASICSGMTILGTSGLGYVTGWPTIWEQVFVPLSAAVCILLFGTKLHaigrERGYLTVQD 111
                                       9***************************************9999999999999999*****999899999******* PP

                               SSF  74 ylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiq 150
                                       y+s Rf +k+ ++ lsa++ +lv  +++  ++v+  + +  ++G++y+ta+++ a++++ Y+++GGl Av +   iq
  gi|386002362|ref|YP_005920661.1| 112 YFSDRFYSKNGIRGLSAVTGILVSLIYMVGQFVAISMVLSWLFGISYHTALMISALIVTAYVIMGGLYAVAWSSLIQ 188
                                       **********9****************************************************************** PP

                               SSF 151 avlmlvgalilliivllevGgleslveklkeaapkvvdl........lt.pdslkllrdpltalslwlglvlGvagl 218
                                       +++++vg l+++  v+ ++Ggl ++   l+ ++p+ v+         +  p++   +  p++ ls+  +l +G+a +
  gi|386002362|ref|YP_005920661.1| 189 GLMLIVGVLLVAPAVVRSAGGLTHINAVLAGIDPNFVQPwypswypeMAgPYAGYAFATPIFLLSFFFLLAFGLASA 265
                                       **********************************99877788888883357777789******************** PP

                               SSF 219 philvRflaakdakailkgvlkltivlilvligmisiilfaiklagavp..kavgtevgvsniaypeLvvkllpnll 293
                                       ph++  ++aa da+  + + l +  v ++++ + i i  +a + + a +   + +++ + s+++++  +   +p+++
  gi|386002362|ref|YP_005920661.1| 266 PHVINNVFAARDARYFRWAPLAAFAVYVVIMYL-IKITGYAGRSMAAEGmiSLPTNVSNPSDYVFILGAEYAFPSII 341
                                       *****************************9999.777778888888888667777788889**************** PP

                               SSF 294 aGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklv 370
                                         ++  ++lAa+mst + l+l   + f  D+Yk+++r   a++  +  vsr++v   ++l +lla+ ++ + +++l+
  gi|386002362|ref|YP_005920661.1| 342 SVFIGVIVLAAVMSTTDRLMLTIGTYFGWDIYKRFLRPD-ARDPTITLVSRVAVAASAVLTLLLAWSKPPELLAWLI 417
                                       ***************************************.9*************************999888***** PP

                               SSF 371 elafaglasavlavillalfwkrvneqGAlagliiG 406
                                        + ++ + ++ +a +l +l+w r++++GA+ ++ +G
  gi|386002362|ref|YP_005920661.1| 418 WMGIGLMLACYVAPLLAGLYWRRATREGAIFSMGLG 453
                                       *******************************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 3133.47
//
Query:       gi|386002363|ref|YP_005920662.1|  [L=91]
Description: hypothetical protein Mhar_1681 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 625.71
//
Query:       gi|386002364|ref|YP_005920663.1|  [L=1375]
Description: Putative type II DNA modification enzyme [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-20   70.9   0.0    1.6e-19   70.2   0.0    1.4  1  TaqI_C    TaqI-like C-terminal specificity domain
    3.2e-13   50.1   0.0    8.6e-13   48.7   0.0    1.7  1  Eco57I    Eco57I restriction-modification methylase
    1.5e-07   31.0   0.0    2.6e-06   27.0   0.0    2.3  2  N6_Mtase  N-6 DNA Methylase


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 !   70.2   0.0   2.6e-23   1.6e-19       1     120 []    1031    1189 ..    1031    1189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.6e-23
                            TaqI_C    1 kpllkGkdikrysieikgnYldlikkklknek.................................a..kelfe.. 38  
                                        kp+l G+dikry++  +++Yl+l+++++++++                                 +  ++++e  
  gi|386002364|ref|YP_005920663.1| 1031 KPFLAGRDIKRYELPESDRYLILVPNGWTRAQssgaedpwgwfeakypavaahlaqfsdaaqkryDkgEYWWElr 1105
                                        79*****************************999999999999999999999988888777665516799999** PP

                            TaqI_C   39 ........ekpKilvrdiskkldaaydekayyvlntlylliakdelevslkyllgiLNSklikfyykkiystlrg 105 
                                                ek Ki++++i++++++++d ++ y++n++y+++        + yll++LNS+li  ++++  ++l+g
  gi|386002364|ref|YP_005920663.1| 1106 acdyydqfEKSKIFWPEIAGSARFTFDSNGLYANNKAYIIP------EATYYLLALLNSSLIRLFIQNSCTDLQG 1174
                                        *****************************************......4579************************ PP

                            TaqI_C  106 gysrlkrkeleklPi 120 
                                           +++   ++k Pi
  gi|386002364|ref|YP_005920663.1| 1175 NSFNFSAIFVDKTPI 1189
                                        999999999999887 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   1.4e-16   8.6e-13       4      98 ..     823     923 ..     820     927 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.4e-16
                            Eco57I   4 dviiGNPPYqeseakkelkaleek.......akdiyqkFvekalkle..dkylaliiparflasgkglkefrekllk 71 
                                       d+++GNPPY ++e   e k+   +        +d+y++Fve++ +l   +++ + i+ ++++ ++++++ +r+++  
  gi|386002364|ref|YP_005920663.1| 823 DAVVGNPPYVRQEGLGEFKGYFAEryrayhgVADLYVYFVELGASLLqkEGFFSYILANKWM-RANYGEPLRRWMK- 897
                                       99***********9999888776678999999*************99677899*********.9**********96. PP

                            Eco57I  72 dkklkklvefedskevFkdveikggil 98 
                                       ++ + ++v+f d   vF++++++ +il
  gi|386002364|ref|YP_005920663.1| 898 ERCIDEIVDFGDLP-VFPEATTYPCIL 923
                                       579***********.*********997 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.3e-10   2.6e-06      21     106 ..     514     644 ..     505     662 .. 0.91
   2 ?    1.2   0.0     0.029   1.7e+02     123     188 ..     819     884 ..     811     925 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.3e-10
                          N6_Mtase  21 egksgGeffTPrevsklivell....................epksgesvyDpacGsggllvqaekvlkee...... 71 
                                       e k +G ++TP  ++  ive +                    e     +v+Dpa+Gsg +lv a ++l  +      
  gi|386002364|ref|YP_005920663.1| 514 ERKATGSYYTPDYIVDYIVEKTvgpvvegrwkealleeqsliEATLAVKVLDPAMGSGHFLVGAVEFLAGKllraae 590
                                       67899**************998999************999998888889*******************9999***** PP

                          N6_Mtase  72 ...................dgktkelsiyGqeknettyrLakmNlllhgieykk 106
                                                          + +  +  iyG+++ne +++Lak+ l l  i+++k
  gi|386002364|ref|YP_005920663.1| 591 rdidwgwvedrgqftpewaKREVVARCIYGVDLNELAVELAKVSLWLSTIAKDK 644
                                       ****************99888899999*********************999886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.029
                          N6_Mtase 123 dkkfdvvvaNppfnqkewkektlekderfrea.vapksnadla..fllhiieslkpkGraavvlangvL 188
                                       +   d+vv Npp+  +e       k  +f+e+  a ++ adl   f+ +  + l+++G  + +lan  +
  gi|386002364|ref|YP_005920663.1| 819 NPGWDAVVGNPPYVRQE--GLGEFKG-YFAERyRAYHGVADLYvyFVELGASLLQKEGFFSYILANKWM 884
                                       5678*********9883..2222222.344443444455554444777777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.83u 0.27s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 8813.83
//
Query:       gi|386002365|ref|YP_005920664.1|  [L=163]
Description: N-acetyltransferase GCN5 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-13   50.2   0.0    2.5e-13   50.1   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.4e-09   37.0   0.0    5.8e-09   36.2   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.9e-08   33.6   0.0    6.6e-08   32.9   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.6e-05   22.3   0.0    0.00018   21.4   0.0    1.5  1  FR47             FR47-like protein
    0.00029   20.9   0.0      0.017   15.2   0.0    2.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0043   17.0   0.0     0.0076   16.2   0.0    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   8.3e-17   2.5e-13      19     127 .]      44     154 ..      10     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 8.3e-17
                   Acetyltransf_10  19 pealrerieegealllvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnas 94 
                                        e+l++ +++++  ++vae+ g +v v+  r ++ ++l+ V+p++++ Gig+ Ll+ +e+e++k g++  +l + ++
  gi|386002365|ref|YP_005920664.1|  44 GEQLSSDVNNSWQNMIVAEKAGVLVAVA-ARFDDLVGLVWVHPAHQRGGIGSVLLDIIETEIKKSGYGMaKLACFSD 119
                                       489999999*****************99.555568****************************************** PP

                   Acetyltransf_10  95 p.yavpfYeklGFkav.geeqeenGirfvpMekel 127
                                       +  a++fY   G+  + +e+ ee+G + + M+k+l
  gi|386002365|ref|YP_005920664.1| 120 NkRAIRFYLDKGWNLLsEEMNEEAGASEMIMTKML 154
                                       ****************9999***********9986 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   1.9e-12   5.8e-09      34     113 ..      57     128 ..      16     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.9e-12
                                       EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHH CS
                    Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaair 110
                                         +vae+ g l++ + ++ ++        +  ++V+p++++ G+Gs Ll+ +e + ++ g+    la+++dn++air
  gi|386002365|ref|YP_005920664.1|  57 NMIVAEKAGVLVAVA-ARFDDL-------VGLVWVHPAHQRGGIGSVLLDIIETEIKKSGYGMAKLACFSDNKRAIR 125
                                       455677777777777.444444.......6779********************888888774458999********* PP

                                       HHH CS
                    Acetyltransf_1 111 lYe 113
                                       +Y 
  gi|386002365|ref|YP_005920664.1| 126 FYL 128
                                       **4 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   2.2e-11   6.6e-08       4      73 ..      57     131 ..      54     133 .. 0.62

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.2e-11
                                       EEEEEEETTEEEEEEEEEEES.TCTEE.EEE-GGGTTSSHHHHHHHH...TT..SEEEEEEEEE....THHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld.aeitr.laVdpeyrgkGiGraLlea...ae..kgiileqlel....naekaikfY 69 
                                       +++Vae+ g  v  +a      +++ + ++V+p++++ GiG+ Ll++   ++  +g+ +   +l    ++++ai+fY
  gi|386002365|ref|YP_005920664.1|  57 NMIVAEKAGVLVAVAA----RfDDLVGlVWVHPAHQRGGIGSVLLDIietEIkkSGYGMA--KLacfsDNKRAIRFY 127
                                       5778877555555332....2223444599****************74441145442222..3334434459***** PP

                                       HHTT CS
                    Acetyltransf_7  70 eklG 73 
                                          G
  gi|386002365|ref|YP_005920664.1| 128 LDKG 131
                                       8766 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     6e-08   0.00018      24      80 ..      78     135 ..      56     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6e-08
                                       EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEE CS
                              FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfeki 80 
                                       +g + v+p h+r G gs+l   +  ei + g+ +  l    +N+++ir+y   G++++
  gi|386002365|ref|YP_005920664.1|  78 VGLVWVHPAHQRGGIGSVLLDIIETEIKKSGYGMAkLACFSDNKRAIRFYLDKGWNLL 135
                                       68999************************9997652677889********87777766 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.8e-06     0.017      75     126 ..      77     133 ..       5     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                                       EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                    Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                        v+ V v+p h++ g+ s Ll+   +e+++ g+ ++ l       ++i++Y  +G++
  gi|386002365|ref|YP_005920664.1|  77 LVGLVWVHPAHQRGGIGSVLLDIIETEIKKSGYGMAKLACfsdnkRAIRFYLDKGWN 133
                                       6999**********************************9977777678********7 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.6e-06    0.0076      10      32 ..      81     103 ..      78     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-06
                   Acetyltransf_13  10 iWvssshRrkgiAtkLldaaren 32 
                                       +Wv+++h+r gi + Lld++  +
  gi|386002365|ref|YP_005920664.1|  81 VWVHPAHQRGGIGSVLLDIIETE 103
                                       8*****************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1028.40
//
Query:       gi|386002366|ref|YP_005920665.1|  [L=454]
Description: hypothetical protein Mhar_1684 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-44  153.0   0.0    1.7e-44  152.4   0.0    1.1  1  Beta-lactamase   Beta-lactamase
     0.0012   18.5   0.0       0.21   11.1   0.0    2.4  2  Beta-lactamase2  Beta-lactamase enzyme family


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.0   1.9e-48   1.7e-44      47     307 ..     144     427 ..     131     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.9e-48
                                       TSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTST..........TCTTGGGTTEBHHHHHTTHSSCSSSSTST CS
                    Beta-lactamase  47 dtlfriaSvtKtftaaavlqlveeGkldLddpVskylP..........efagpgkgkiTlrdLltHtsGlpdlfasd 113
                                       d +f iaS+ K+fta++v +l+e+G+++Lddp+ +y P          e ++++++ +T+r+LltHtsG++d+  +d
  gi|386002366|ref|YP_005920665.1| 144 DVPFHIASIGKVFTATLVCMLAERGAVSLDDPIVDYMPesslenlfvfEEKDYAEQ-VTIRELLTHTSGVADY-VED 218
                                       779********************************************988888888.****************.999 PP

                                       TCTSHHHTH.............HHHHHHHH.HSBSSSSTTSCEE-SHHHHHHHHHHHHHHHTSHHHHHHHHHTTTTT CS
                    Beta-lactamase 114 lleeaaada.............aellrala.tlppkyapGtkwgYsntgygllgellekvtgrsleqllreeilrpL 176
                                        ++++  +              + ll++ + +++ +++pG  + Ys+tgy llg+++e+vt++++   l +e+++pL
  gi|386002366|ref|YP_005920665.1| 219 PVINGTLFLelilsnpdtywtpEMLLAFSRdNQHAVGKPGDLFHYSDTGYVLLGRIIENVTSKPFHVNLHDEFFKPL 295
                                       99999888889999999999966666655435677888*************************************** PP

                                       TSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHC.....TTTBEEEEHHHHHHHHHHHHHCCSSSSHHHHH CS
                    Beta-lactamase 177 gmkdtelgppesgdprdaagytgngpearappanlpaeae.....gagglistardlarflglalegglllsaetla 248
                                       +m+d +l   ++     a+ ++++++ +++++   + +       ++gg++st++dl+rf  +al++g+l s+  l 
  gi|386002366|ref|YP_005920665.1| 296 NMNDSYLMFRSEP----ANQPKKPVQKTWLSDTEISQFTSlssdwAGGGIVSTPADLLRFH-MALRDGQLISPDLLG 367
                                       ******9765555....333433334444444444444446667799**************.999999999999999 PP

                                       HHHHHHTSEEEECTTEEEECECSSEEEEECCH.......TEEEEEEESTEEEEEEEECGGTEEEEE CS
                    Beta-lactamase 249 qltaklssgttrpagiraglglGwvladktga.......pgtfghtGggygtyvfvdpeanlvvav 307
                                       q+      ++t+++  +  +g+G +  d +g        p+  gh G  +gt +f+d+ ++ ++++
  gi|386002366|ref|YP_005920665.1| 368 QM-----VTATNQFMPGIKYGMGMMEVDFQGLspmlsgfPTVTGHIG-IWGTHMFYDRTTDTYIII 427
                                       88.....7777777777788888888888888***************.***********9998876 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   2.4e-05      0.21      11      77 ..     143     211 ..     136     216 .. 0.85
   2 !    4.7   0.0    0.0022        19     116     158 ..     331     369 ..     314     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                                       TTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EE.EGGHHHHTSSSTSGGGST.TSEEEHHHHHHHHHH CS
                   Beta-lactamase2  11 adeefpaaStiKvpillalleavlegklslderl.tltaedivggsgilqklp.gktlslrdlltlmia 77 
                                       +d +f+ aS+ Kv+ +  ++  +++g +sld+++  + +e   +   ++++++   ++++r+llt +  
  gi|386002366|ref|YP_005920665.1| 143 KDVPFHIASIGKVFTATLVCMLAERGAVSLDDPIvDYMPESSLENLFVFEEKDyAEQVTIRELLTHTSG 211
                                       6889************888888889*******9625789999999999999996669999999998765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0022
                                       CCHHHTTSSTTEE-HHHHHHHHHHHHHTTSSHHHHHHHHHHT- CS
                   Beta-lactamase2 116 dleaadkdkrntttardlarllealargellspeelleilsnq 158
                                        l+  +++   ++t++dl r++ al  g+l+sp+    +l ++
  gi|386002366|ref|YP_005920665.1| 331 SLSSDWAGGGIVSTPADLLRFHMALRDGQLISPD----LLGQM 369
                                       4555566666789********************5....43332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3351.92
//
Query:       gi|386002367|ref|YP_005920666.1|  [L=156]
Description: hypothetical protein Mhar_1685 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1006.53
//
Query:       gi|386002368|ref|YP_005920667.1|  [L=127]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-10   40.9   0.0      2e-10   40.6   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    6.2e-09   36.0   0.0      1e-08   35.3   0.0    1.4  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   2.3e-14     2e-10       2      84 ..      44     124 ..      43     127 .] 0.94

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.3e-14
                                       STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHH CS
                           Polbeta   2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneappllly 78 
                                       +i +i+ k+ +++ + +FGS+a+g+a ++SD+Dl v   +  +l +   ++ ele + lg++vD+v  +  +  +++
  gi|386002368|ref|YP_005920667.1|  44 EILAIAAKY-GVRNVRIFGSVARGEADDRSDLDLLVEPLSGFTLIKNSAISRELEGL-LGRQVDVVSERGLRERIRQ 118
                                       68899****.***********************************************.9********9988899999 PP

                                       HHHHS- CS
                           Polbeta  79 eilkeg 84 
                                       ++lke 
  gi|386002368|ref|YP_005920667.1| 119 RVLKEA 124
                                       999975 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.1e-12     1e-08      10      88 ..      50     120 ..      34     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.1e-12
                                       HHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE....CEEECCCC CS
                      NTP_transf_2  10 elepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv....trekledp 82 
                                        +++v  v +fGS+arG+a   SD+Dllv   +         +l k++ i  +le llg++vd+v    +re ++ +
  gi|386002368|ref|YP_005920667.1|  50 AKYGVRNVRIFGSVARGEADDRSDLDLLVEPLSG-------FTLIKNSAISRELEGLLGRQVDVVsergLRERIR-Q 118
                                       4566999**********************97777.......568*********************6555555555.3 PP

                                       TEEEEE CS
                      NTP_transf_2  83 llvksi 88 
                                       +    +
  gi|386002368|ref|YP_005920667.1| 119 R----V 120
                                       3....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 842.46
//
Query:       gi|386002369|ref|YP_005920668.1|  [L=62]
Description: hypothetical protein Mhar_1687 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.6   1.0    2.2e-13   50.4   1.0    1.1  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   1.0   1.2e-17   2.2e-13       5      58 ..       3      54 ..       1      55 [. 0.91

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.2e-17
                            DUF104  5 IeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleell 58
                                      ++a+YEn vLKPLek+dLk+Ge v i+I++  + +++l g++k + ++ l+e++
  gi|386002369|ref|YP_005920668.1|  3 VKAIYENKVLKPLEKLDLKDGEVVDIEIRR--DAVDRLGGLVKISRRDWLDEVV 54
                                      79****************************..********99977777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 486.46
//
Query:       gi|386002370|ref|YP_005920669.1|  [L=165]
Description: hypothetical protein Mhar_1688 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-14   53.9   0.4    6.9e-14   52.4   0.4    1.7  1  PIN       PIN domain
    0.00092   19.7   0.1     0.0023   18.4   0.0    1.6  2  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   7.6e-18   6.9e-14       1     121 [.      11     159 ..      11     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 7.6e-18
                                       EEE-HHHHHHHHTTS.HHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS......................SCH CS
                               PIN   1 ivlDTsvliallrge.ekaeaarklleel....eelvtsalvlaEllyvlar......................rks 50 
                                       i++D+++++++++++   ae +  ll ++       v+s++vl E+ + ++                        + 
  gi|386002370|ref|YP_005920669.1|  11 IFIDANIFLYVIFDHwRYAEPCGNLLKDVnsgkRSAVSSIVVLGEVFHRVMVaevvekqnqnprqavrylkenpEEV 87 
                                       79**********55514555666666666888999*************************************99777 PP

                                       CHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  51 krekaaelvellll.lsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       k + aa    +++l  ++lki   + ei +  ++++++ygll+ Da+++At++e+ i+++a++D+df+rv++
  gi|386002370|ref|YP_005920669.1|  88 KNLSAAPSAIEKILeIENLKIARAGVEIMRLSLDFSKRYGLLSSDAIHLATMQEEEITALASNDSDFERVEW 159
                                       78888888888888899****************************************************986 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.6e-07    0.0023       1      95 [.      11     106 ..      11     125 .. 0.74
   2 ?   -1.1   0.0      0.26   2.3e+03     153     171 .]     135     154 ..     128     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-07
                            PIN_12   1 ifiDTnifld.effrlseeealkklleliesgkiklivpdivldEflknr.ekkieeskklekalks.lsklksakk 74 
                                       ifiD nifl   f + +++e + +ll++++sgk + + + +vl E+ + +   ++ e+   +++ ++ ++ lk++ +
  gi|386002370|ref|YP_005920669.1|  11 IFIDANIFLYvIFDHWRYAEPCGNLLKDVNSGKRSAVSSIVVLGEVFHRVmVAEVVEK--QNQNPRQaVRYLKENPE 85 
                                       9********763444445556************************9988875555555..23444447888888888 PP

                            PIN_12  75 klnekkkllslkeikkkieek 95 
                                       +++++++  s  e+  +ie+ 
  gi|386002370|ref|YP_005920669.1|  86 EVKNLSAAPSAIEKILEIENL 106
                                       888888776666666666554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.26
                            PIN_12 153 eyakknkek.vifvsrDkDf 171
                                       + a+  +e+   + s+D+Df
  gi|386002370|ref|YP_005920669.1| 135 HLATMQEEEiTALASNDSDF 154
                                       55664556667777888999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 937.83
//
Query:       gi|386002371|ref|YP_005920670.1|  [L=85]
Description: hypothetical protein Mhar_1689 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00013   22.1   0.2    0.00014   22.0   0.2    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0011   18.9   0.2     0.0015   18.5   0.2    1.2  1  YokU            YokU-like protein, putative antitoxin


Domain annotation for each model (and alignments):
>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.6e-08   0.00014       1      58 [.      11      68 ..      11      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.6e-08
                    MqsA_antitoxin  1 mkCpvCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseell 58
                                      m+C +C ++    +t  v++   g  +vik v ++ C++C e+++de+  ++l +++ 
  gi|386002371|ref|YP_005920670.1| 11 MRCLICKRGSTEPGTTTVTLERDGLIMVIKGVPAQVCENCAEAYVDEKVASELLTSAE 68
                                      9*********************************************997666554444 PP

>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.6e-07    0.0015       2      54 ..      13      63 ..      12      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-07
                              YokU  2 CewCeeeeakaststvyWelpdgtkaieiketPsieCseCglvyqeeevvkei 54
                                      C  C+  +++  t+tv  e  dg   + ik +P+ +C++C   y++e+v +e+
  gi|386002371|ref|YP_005920670.1| 13 CLICKRGSTEPGTTTVTLER-DGL-IMVIKGVPAQVCENCAEAYVDEKVASEL 63
                                      999**999999999999884.454.45689*******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 672.49
//
Query:       gi|386002372|ref|YP_005920671.1|  [L=56]
Description: hypothetical protein Mhar_1690 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-10   40.1   0.0    3.8e-10   40.0   0.0    1.1  1  DUF4258   Domain of unknown function (DUF4258)


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.1e-14   3.8e-10       4      37 ..      13      54 ..      10      56 .] 0.90

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.1e-14
                           DUF4258  4 HArermaeRgIseedieevlenGeiieeys........lvlg 37
                                      HA+erm eR+Is ed+++vl+ G +ie y+        l++g
  gi|386002372|ref|YP_005920671.1| 13 HAVERMFERDISVEDVRRVLLEGAVIEGYPedtpfpscLIFG 54
                                      ******************************888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 440.14
//
Query:       gi|386002373|ref|YP_005920672.1|  [L=76]
Description: hypothetical protein Mhar_1691 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.3   0.0      0.084   12.7   0.0    1.3  1  OST-HTH   OST-HTH/LOTUS domain


Domain annotation for each model (and alignments):
>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-06     0.084       6      40 ..      35      67 ..      30      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-06
                                      HHHHHHHHHHHTTTTSBEHHHHHHHHHHHHSST-S CS
                           OST-HTH  6 lkkeirelLrsdpdgwvslsrlgslykkkygksfd 40
                                       ++++ elL+s+pd  ++l +l+ +yk++   sf+
  gi|386002373|ref|YP_005920672.1| 35 AESNLAELLNSEPDI-YTLKDLKIDYKNMAA-SFR 67
                                      57899*********7.************998.886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.76
# Mc/sec: 301.66
//
Query:       gi|386002374|ref|YP_005920673.1|  [L=41]
Description: hypothetical protein Mhar_1692 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 295.94
//
Query:       gi|386002375|ref|YP_005920674.1|  [L=94]
Description: hypothetical protein Mhar_1693 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.034   14.1   0.3      0.062   13.3   0.3    1.4  1  Gin          Inhibitor of sigma-G Gin
       0.66    9.9   5.8       0.88    9.5   1.5    2.2  2  Stealth_CR3  Stealth protein CR3, conserved region 3


Domain annotation for each model (and alignments):
>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.9e-06     0.062      14      32 ..       6      24 ..       3      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-06
                                      SSS--EEHHHHHHHHHHS- CS
                               Gin 14 ilgkfICeeCekkivntev 32
                                      +++k+IC +C + iv+t+v
  gi|386002375|ref|YP_005920674.1|  6 LVDKIICIRCKHSIVSTSV 24
                                      6899*************97 PP

>> Stealth_CR3  Stealth protein CR3, conserved region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.5   9.8e-05      0.88       9      33 ..      34      59 ..      33      61 .. 0.90
   2 ?    2.5   0.2     0.015   1.4e+02       9      24 ..      63      78 ..      62      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 9.8e-05
                       Stealth_CR3  9 rsvlkelerr.fpeelartashrFRs 33
                                      r ++ e+++  +++e++rt+   +R+
  gi|386002375|ref|YP_005920674.1| 34 RRMMDEMSEVdWQAEIRRTVETMVRE 59
                                      78*******99********9988886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.015
                       Stealth_CR3  9 rsvlkelerrfpeela 24
                                      r +l   e+r+ e+++
  gi|386002375|ref|YP_005920674.1| 63 RMLLDRAEARWKEQVE 78
                                      557889999**99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 555.86
//
Query:       gi|386002376|ref|YP_005920675.1|  [L=136]
Description: hypothetical protein Mhar_1694 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-11   44.4   0.9    2.5e-11   44.2   0.9    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.9   1.4e-15   2.5e-11       2     118 ..       6     125 ..       5     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.4e-15
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEEE CS
                               PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....rkskrekaaelvellll.lsalkilp 72 
                                       vlD+sv+ a+++ ee + +a+++ +e  + vt +l++ E+ +v+ +     +++k  ++++l++ ++  ++ + +l+
  gi|386002376|ref|YP_005920675.1|   6 VLDSSVIAAIFFLEEASPRALARADE-CDPVTLDLAVPEVGNVAWKrvlfsGEDKGAALDALRDCREFiRETCTLLE 81 
                                       8**********888777555555554.899*********************999999*******9**9777777777 PP

                                       BCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  73 idaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                        +a+++eea eia + +++ +D l +A A+++g++l+ t D+++++
  gi|386002376|ref|YP_005920675.1|  82 -SADLLEEAFEIAVQDKISFYDSLFLAAAEKEGMPLL-TLDKKLYE 125
                                       .************************************.*****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 855.22
//
Query:       gi|386002377|ref|YP_005920676.1|  [L=116]
Description: Nucleotidyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-09   38.0   0.1    1.8e-09   37.7   0.1    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    1.6e-08   34.5   0.0    2.2e-08   34.1   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   2.1e-13   1.8e-09       2      56 ..      20      71 ..      19     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.1e-13
                                      HHHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHH CS
                      NTP_transf_2  2 kklleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeeglekl 56
                                      +++ ++  ++++  + +v+lfGS+arG a+++S+iD+lvv +ee       + ++kl
  gi|386002377|ref|YP_005920676.1| 20 EEFVKRATQRYGnrIRSVTLFGSVARGAAGEESEIDILVVIDEEDF-----RLRRKL 71
                                      5777888888889999****************************55.....334444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.4e-12   2.2e-08       7      67 ..      27      89 ..      21     116 .] 0.58

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.4e-12
                                      HHHH.HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH...SSSEEEEE CS
                           Polbeta  7 leke.keielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi..klgkkvDlv 67
                                       +++ + i+ + lFGS+a+g a eeS iD+ v+++e+ d+  + +l     di  ++g ++ + 
  gi|386002377|ref|YP_005920676.1| 27 TQRYgNRIRSVTLFGSVARGAAGEESEIDILVVIDEE-DFRLRRKLIGLSFDIllETGGDLSVK 89
                                      55554689*****************************.44443333333333322222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 677.27
//
Query:       gi|386002378|ref|YP_005920677.1|  [L=58]
Description: hypothetical protein Mhar_1696, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-09   37.6   0.3    3.3e-09   37.0   0.0    1.4  2  DUF4258   Domain of unknown function (DUF4258)


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.43   7.7e+03      15      21 ..      11      17 ..       8      22 .. 0.64
   2 !   37.0   0.0   1.8e-13   3.3e-09       1      33 [.      26      58 .]      26      58 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.43
                           DUF4258 15 seediee 21
                                       +ed++e
  gi|386002378|ref|YP_005920677.1| 11 EIEDVKE 17
                                      5677766 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 1.8e-13
                           DUF4258  1 fsaHArermaeRgIseedieevlenGeiieeys 33
                                      ++ HAr+rm+eRgI ++d+ ++++ G iie+y+
  gi|386002378|ref|YP_005920677.1| 26 ITFHARRRMDERGIYTDDLVNLILDGSIIEDYP 58
                                      689*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.33s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 346.83
//
Query:       gi|386002379|ref|YP_005920678.1|  [L=95]
Description: hypothetical protein Mhar_1697 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0019   18.3   0.0     0.0021   18.2   0.0    1.1  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito


Domain annotation for each model (and alignments):
>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-07    0.0021       5      62 ..      17      74 ..      14      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-07
                    MqsA_antitoxin  5 vCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseellefrk 62
                                       Cg++ l  +  d      g  +vik+v++  C  C e++++ + ++++ + +++fr+
  gi|386002379|ref|YP_005920678.1| 17 NCGRGRLAPGFTDYITRIDGSVLVIKNVRALICDVCDEAYITPDASREIDKIVRDFRE 74
                                      6**********************************************99999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 680.74
//
Query:       gi|386002380|ref|YP_005920679.1|  [L=104]
Description: DNA polymerase, beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00053   20.0   0.0    0.00075   19.5   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
     0.0042   17.3   0.1       0.01   16.1   0.1    1.6  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.4e-08   0.00075      15      90 ..      21     103 ..       9     104 .] 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.4e-08
                                       STTEEEEEE-S------EEEEEEEESS-........--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS CS
                           Polbeta  15 laylFGSrakgkareeSDiDlavllkek........ldleeelelaaelediklgkkvDlvdlneapplllyeilke 83 
                                        + + GS+a+g+  ++S iD ++ +  +            + ++l++el++i lg++v+lv  ++ +p ++  + k+
  gi|386002380|ref|YP_005920679.1|  21 RIAICGSFARGDEADDSGIDSGIEILIDllppgerpPLGLKWFRLEEELSRI-LGREVELVSERAMSPFVRPYVEKD 96 
                                       57788***************8887777777877766555669**********.9**********999****999999 PP

                                       -EEEES- CS
                           Polbeta  84 gkllysk 90 
                                         lly++
  gi|386002380|ref|YP_005920679.1|  97 MVLLYEE 103
                                       9999985 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-06      0.01      13      90 ..      17      95 ..       7     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                                      T.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH..HHHEHHHHHHHHCCCEEECTTEEEEEE...CEEECCCCTEE CS
                      NTP_transf_2 13 p.vakvvlfGSyarGtalkgSDiDllvvlpeevsre..kkeegleklaeiikfleellglevdlv...trekledpllv 85
                                      p   ++++ GS+arG+   +S iD  +    +   +  +++   +k  + +++l+++lg+ev lv    ++++     +
  gi|386002380|ref|YP_005920679.1| 17 PyARRIAICGSFARGDEADDSGIDSGIEILIDLL-PpgERPPLGLKWFRLEEELSRILGREVELVserAMSPFV----R 90
                                      556799******************8776655543.236567778999999**************9555444444....4 PP

                                      EEEEC CS
                      NTP_transf_2 86 ksile 90
                                       ++++
  gi|386002380|ref|YP_005920679.1| 91 PYVEK 95
                                      44333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 726.67
//
Query:       gi|386002381|ref|YP_005920680.1|  [L=158]
Description: hypothetical protein Mhar_1699 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   45.0   0.0    1.8e-11   44.2   0.0    1.4  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.021   14.8   0.3      0.051   13.5   0.3    1.6  1  DUF2095          Uncharacterized protein conserved in archaea
      0.064   13.2   0.0       0.12   12.3   0.0    1.4  1  BBS2_N           Ciliary BBSome complex subunit 2, N-terminal


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   3.1e-15   1.8e-11       3      83 ..      18     106 ..      16     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.1e-15
                   Acylphosphatase   3 llvtG.rVQgvgFRkfvrrlAkelglkGyvrNlsdg.....sVeivaegeeekvekfleelksgppk.arvdeveve 72 
                                       +++ G +V+gvg+R+f++++A+ lg++G++  ++ g     +V +++eg++e++ +f +  ++++p+ a+v+ev + 
  gi|386002381|ref|YP_005920680.1|  18 VEIIGpKVHGVGYRYFLMNQAMLLGVDGFAASNQAGidrqqKVLVLVEGSREALIDFSALAETEKPEeAEVSEVLIG 94 
                                       6788889**********************9999888888889*********************88888*****9987 PP

                   Acylphosphatase  73 eleeeeef.kdF 83 
                                       + +    + +dF
  gi|386002381|ref|YP_005920680.1|  95 DFDGFVPKmTDF 106
                                       766554444555 PP

>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   8.6e-06     0.051      38     116 ..      71     153 ..      58     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-06
                           DUF2095  38 eidairldeeevleeeee.egki.dfsgynptiidflrrcetde..ealeiinwmeergeithemakelrvvlvkkg 110
                                        id   l e e  ee e  e +i df g+ p + df     + +  +a+ ii+ +e + + t e  +e r+  +++ 
  gi|386002381|ref|YP_005920680.1|  71 LIDFSALAETEKPEEAEVsEVLIgDFDGFVPKMTDFAMVLTAGQivKAIPIIQEIESNTKETAESLREERLLRIEQD 147
                                       455556667777676665144334************87765554337899999999999999999999999999888 PP

                           DUF2095 111 vrafgp 116
                                       + a+  
  gi|386002381|ref|YP_005920680.1| 148 IHAIKA 153
                                       888765 PP

>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05      0.12       2      59 ..      93     153 ..      92     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                            BBS2_N   2 vgkfdgshp...claaattagkvlihnphekeqklkserlsasesevslLninkevtalaa 59 
                                       +g fdg  p     a++ tag+++   p  +e +++++++++s +e +lL+i++++ a++a
  gi|386002381|ref|YP_005920680.1|  93 IGDFDGFVPkmtDFAMVLTAGQIVKAIPIIQEIESNTKETAESLREERLLRIEQDIHAIKA 153
                                       799999877333668999**********999988888888899***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1067.01
//
Query:       gi|386002382|ref|YP_005920681.1|  [L=40]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 243.23
//
Query:       gi|386002383|ref|YP_005920682.1|  [L=49]
Description: DNA polymerase beta domain-containing protein region, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-09   37.6   0.0    2.2e-09   37.5   0.0    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
    2.1e-07   30.9   0.0    2.3e-07   30.8   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   2.4e-13   2.2e-09       4      41 ..      11      48 ..       8      49 .] 0.91

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.4e-13
                                      HHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEES CS
                      NTP_transf_2  4 lleelkelepvakvvlfGSyarGtalkgSDiDllvvlp 41
                                       +e+++++++++++++fGS+ r +++++SD+Dllv+++
  gi|386002383|ref|YP_005920682.1| 11 KIEDFCRRWKIKEMAIFGSALREDFGPESDLDLLVTFS 48
                                      5688999****************************997 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.6e-11   2.3e-07       1      41 [.      10      49 .]      10      49 .] 0.96

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.6e-11
                                      -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS CS
                           Polbeta  1 ekikeilekekeielaylFGSrakgkareeSDiDlavllke 41
                                      eki++++++  +i+ + +FGS +++++ +eSD+Dl v ++e
  gi|386002383|ref|YP_005920682.1| 10 EKIEDFCRRW-KIKEMAIFGSALREDFGPESDLDLLVTFSE 49
                                      89********.**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 330.42
//
Query:       gi|386002384|ref|YP_005920683.1|  [L=588]
Description: DNA polymerase I [Methanosaeta harundinacea 6Ac]
Scores for complete 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-68  229.6   0.0    8.6e-68  229.1   0.0    1.1  1  DNA_pol_A        DNA polymerase family A
  ------ inclusion threshold ------
       0.19   11.2   0.0       0.32   10.4   0.0    1.3  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme


Domain annotation for each model (and alignments):
>> DNA_pol_A  DNA polymerase family A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.1   0.0   9.5e-72   8.6e-68       8     374 ..     205     564 ..     199     565 .. 0.83

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 9.5e-72
                                       HHHHHHHHHHHHHHHHHHSS.C....-STTTCCCCHHHHTCCCCS.TTSBETTSBTTTCCHHHHHT.S....CHHHH CS
                         DNA_pol_A   8 seeleeeleeleeeiyelag.e....fnlnSpkqlaevLfeklklpekkktktgystdeevLekla.k...hplakl 75 
                                       se l++e +el++e+ ++a+ +    fn + p + ++v+   l+++        ++t++  Lek+  +   +++++l
  gi|386002384|ref|YP_005920683.1| 205 SESLGDEKAELTRELRSYAQsKgikdFNPKNPAHAKKVIK-SLGYHV-------EKTSAPFLEKMVrQhqaEEFINL 273
                                       6666666667777666666433445788888888888775.666533.......4588889999886334579**** PP

                                       HHHHHHHHHHHHHTTTTGGGCCBTTTSEE--EEESSSSSSSS-EEESS-GGGS-TTSCCHHHHHHTBCG.TTCCEEE CS
                         DNA_pol_A  76 ileyrelsklkstyvdallklinkktgrihtsfnqtvtatGrlsssepnlqnipirteegrriRkafvaeegghvll 152
                                       +l+yrel +lk+  +++ l +   ++gri+++++q + + Gr+++s+pn+q++p       r++++fva+++   l+
  gi|386002384|ref|YP_005920683.1| 274 LLKYREL-HLKEAHTKNWLVFS--EDGRIYPRLSQLGGRSGRITCSKPNIQQVPR----DPRLKSLFVASPN-MSLV 342
                                       *******.68888889998777..79***************************93....479*********5.66** PP

                                       EEEETTHHHHHHHHHCT.HHHHHHHHTTH-HHHHHHHHHCTS.GGGHHHHHHHHHHHHHHHHHTT--HHHHHHHH.T CS
                         DNA_pol_A 153 saDysqiELRilAhlsgdeklieafkegeDiHsktAsevfgvpveevtkeqRrqaKainfGiiYGagakgLaeql.g 228
                                       +aD+s iE+R+lA lsgde+lie+fk+g D H +tA+ +f++  ++++ e+R+ aK++n+G iYG g + +  ql  
  gi|386002384|ref|YP_005920683.1| 343 EADFSAIEMRLLAILSGDETLIETFKKGLDPHIQTAQAIFQK--SKISGEERQIAKTLNYGTIYGGGTNMVLSQLpD 417
                                       *****************************************9..9***********************999999978 PP

                                       SSHHHHHHHHHHHHHHSHHHHHHHHHHHHHC......CCE.CCEEETTCSEEEECTTT-CCHCCCHHHHHHHHHHHH CS
                         DNA_pol_A 229 iseeeAkefiekyferypgvksyleetleea......kek.gyvetllgrrrylpeiksknaalrekaeraavNapi 298
                                       ++e+eAkef+ +++++ypg++s+ +++ + a      +++ +  ++ lgr ry+      +     ++++a +N+p+
  gi|386002384|ref|YP_005920683.1| 418 LTEDEAKEFLYRFYRSYPGLRSWQQKVTNGApvltidRKTyKISRSALGRLRYI------D----PDQRNALINTPV 484
                                       **************************9987622222112223334444444444......2....22345669**** PP

                                       HHHHHHHHHHHHHHHHHHHHHTT-S.EEEEEEETTEEEEEEECCCHHHHHHHHHHHHHHHHH...SSS--EEEEEEE CS
                         DNA_pol_A 299 QGsAaDiiklamikieealkeeklk.arlllqvHDElvfevpeeeveevaelvkeamesave...ldvplkvevkvG 371
                                       Q ++aD+ k+a+ +++++l++ + +  +l+  vHD +++evp++++ e+a+l++++me+a       vp  +evkvG
  gi|386002384|ref|YP_005920683.1| 485 QATGADLQKIALGRLYRELTKPEHDaFNLVNAVHDSILLEVPDKRTGEAARLIQRVMEEAGGeilKVVPCLTEVKVG 561
                                       *******************8887752789****************************99987774489********* PP

                                       SSC CS
                         DNA_pol_A 372 knW 374
                                       k+W
  gi|386002384|ref|YP_005920683.1| 562 KDW 564
                                       *** PP

>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.6e-05      0.32      98     123 ..      82     107 ..      72     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.6e-05
                                       -EEEESS---HHHHHHHHHHHHHHCT CS
                   AICARFT_IMPCHas  98 aeqlqGkelsynNllDadaalelvke 123
                                       ++ l+G+ lsy Nl D+  a++l+++
  gi|386002384|ref|YP_005920683.1|  82 IRALKGRRLSYSNLWDTMLAWQLLRN 107
                                       5679******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 3645.42
//
Query:       gi|386002385|ref|YP_005920684.1|  [L=660]
Description: CRISPR-associated exonuclease, Cas4 family / CRISPR-associated protein, Cas1 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-94  315.0   0.0    5.1e-94  314.6   0.0    1.2  1  Cas_Cas1  CRISPR associated protein Cas1
    2.3e-22   79.8   0.0      4e-22   79.1   0.0    1.3  1  Cas_Cas4  Domain of unknown function DUF83
     0.0026   17.7   0.0     0.0046   16.9   0.0    1.4  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.6   0.0   8.6e-98   5.1e-94       1     282 [.     309     614 ..     309     615 .. 0.96

  Alignments for each domain:
  == domain 1  score: 314.6 bits;  conditional E-value: 8.6e-98
                                       EEEESTEEEEEEETTEEEEEE...SSE........................EEEEEECCCEEEEEEESTEEEEHHHH CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvek...ege........................ekkeiplediesivifgevslstkal 50 
                                       +yv  +g+++rkkg+rl++++     +                        ++ e +l++i+++ +fg v++st+al
  gi|386002385|ref|YP_005920684.1| 309 VYVVGHGHSVRKKGDRLEIRSikkG-DdedeekegsegrtgrgrgkgerdsAVVEARLREISQVNLFGGVEISTPAL 384
                                       69*******************7650.15567788888888888888888888888********************** PP

                                       HHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHH CS
                          Cas_Cas1  51 rllaekgipvvflsengkylgrlepeesgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeee 127
                                         l+++gipv+ +++ g+++g+ ++++++nvelr++Q+++a d++++l++a++iv+gk++n+r+ +rr+  ++    
  gi|386002385|ref|YP_005920684.1| 385 VDLMQRGIPVLHFTRGGWFQGMSVGHTHKNVELRMRQFAWAADRNRSLSIARSIVDGKIRNCRTQIRRNDPES---- 457
                                       ******************************************************************9999999.... PP

                                       HHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHHHHHHCS..CGGS-SS-SSSS-SSHHHHHHHHHHHHHHHH CS
                          Cas_Cas1 128 leeaieeleelleklekaesleeLrgiEGeaakaYfeafdkllk..eefefegRsrrppkDpvNalLsfgYtllyse 202
                                        ++a+++l++l +++++a+s+e+L+giEG+aa++Yf+ +++llk  + f+f +R+rrppkDpvNa+Ls++Y++l+++
  gi|386002385|ref|YP_005920684.1| 458 PKDALDRLSKLSKDAANASSMERLLGIEGAAAEIYFGRLEHLLKadQGFTFANRNRRPPKDPVNAVLSYLYAVLAKD 534
                                       99******************************************966****************************** PP

                                       HHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHH CS
                          Cas_Cas1 203 vlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfle 279
                                       v+ ++ avg+dPy+Gf+H++r+grp+LalD+mEefRp+++D++ ++l+n+r+l++kdF+k+  gv +++++++++l+
  gi|386002385|ref|YP_005920684.1| 535 VFVSLLAVGFDPYLGFYHRPRYGRPALALDMMEEFRPIIADSTTINLFNNRELTDKDFIKTGMGVSMKRQAKRTVLA 611
                                       ****************************************************************************9 PP

                                       HHH CS
                          Cas_Cas1 280 afe 282
                                        +e
  gi|386002385|ref|YP_005920684.1| 612 GYE 614
                                       998 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   6.7e-26     4e-22       5     162 .]      89     269 ..      86     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 6.7e-26
                          Cas_Cas4   5 iqyyliCkrklwlisheitleensetvelGkllhe..........esyerek.......kevelse.....sikiDv 59 
                                       +  +++C+r +++  ++ ++ ++ +tv+ G++ h           e     +       ++v+ls+     + +iD+
  gi|386002385|ref|YP_005920684.1|  89 LAEFAYCPRLCYMEWVGGEFVDSADTVD-GRFQHRrvdsevaradE-----DelqaihdRSVSLSGekvgvTCRIDL 159
                                       6789************************.******88876654331.....134556669999965699999***** PP

                          Cas_Cas4  60 vekekeklvvvEvKkskkk.....eeaa.klQllyYlllLekkgveikeGvleypkekkreevelteelreelekai 130
                                       +e e++++++vE+K++++      ++++ ++Ql+++ l+L+++g ++++G++++  ++kr+ v ++++l + + + i
  gi|386002385|ref|YP_005920684.1| 160 LEGEGRHVTPVEYKRGRAPcipggAYDSdRVQLCAQGLVLRENGYHCDNGIVYFAASRKRVPVDFDRDLVKLTLDLI 236
                                       ******************99999955555************************************************ PP

                          Cas_Cas4 131 keieeiisse.kppkvkkkkiCkkCayaelCli 162
                                       ++++++ +    pp+ +++++C +C++a +Cl+
  gi|386002385|ref|YP_005920684.1| 237 SDLRAVADGGaVPPPLQDSPKCVRCSMAGICLP 269
                                       ********996778889999***********86 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.7e-07    0.0046     124     254 ..     139     267 ..     108     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.7e-07
                          PDDEXK_1 124 g........gekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepaga 192
                                                gekv ++ riD+++ ++++++ ++yK g+ap  +   a  ++++Ql +  l+l+e+        + g+
  gi|386002385|ref|YP_005920684.1| 139 IhdrsvslsGEKVGVTCRIDLLEGEGRHVTPVEYKRGRAPCIPGG-AYDSDRVQLCAQGLVLRENGYHC----DNGI 210
                                       13344446479999********955556**********9977777.3344555************3222....899* PP

                          PDDEXK_1 193 lylrleepkvkdeevvkkmalteeeleallqeleelaeeilag.efparpskk..CeyCpyksvC 254
                                       +y+         +++  +++ +++    +l+ +++l +++++g  +p+   +   C +C+++ +C
  gi|386002385|ref|YP_005920684.1| 211 VYFAA-------SRKRVPVDFDRDLVKLTLDLISDL-RAVADGgAVPPPLQDSpkCVRCSMAGIC 267
                                       **999.......666677777787777777777776.777766577766555567********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3909.30
//
Query:       gi|386002386|ref|YP_005920685.1|  [L=98]
Description: CRISPR-associated protein, Cas2 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-14   53.6   0.0    2.5e-14   53.2   0.0    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.4e-18   2.5e-14       3      68 ..       7      70 ..       5      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.4e-18
                                      EEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEE CS
                       CRISPR_Cas2  3 vlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykl 68
                                      ++v+YDi  + +r++kv+k++k + +  v ySVF ++l+++   ++++ l  +i+++ed+++i+ l
  gi|386002386|ref|YP_005920685.1|  7 YVVSYDI-MEPRRLQKVHKMMKGF-GDPVHYSVFRCDLTPKGRVEMIAALTGLIKHDEDRVMIIDL 70
                                      89*****.****************.**************************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 659.10
//
Query:       gi|386002387|ref|YP_005920686.1|  [L=135]
Description: hypothetical protein Mhar_1705 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.7   0.0    1.6e-07   31.3   0.0    1.2  1  SAVED     SMODS-associated and fused to various effectors sen


Domain annotation for each model (and alignments):
>> SAVED  SMODS-associated and fused to various effectors sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   8.9e-12   1.6e-07     116     191 .]      47     117 ..       5     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 8.9e-12
                             SAVED 116 dairspedlealakavrdalrelkaehgvkriHlfaaaPaslafllGqrlnpralppvvvYeydrgsgkYepalsi 191
                                       d+   p+d  +++ +++  l++l  + gv+++ lf+a+P  la+ +G+rl+  ++ pv v+++++g+  Y+ +l++
  gi|386002387|ref|YP_005920686.1|  47 DTWLEPKDYPEVMVKING-LKDLAMKSGVTEVLLFYAGPIDLAIYIGTRLQ--NWVPVKVFNFEKGT--YRHSLTL 117
                                       556666666666666655.45555566************************..*********97776..9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 719.10
//
Query:       gi|386002388|ref|YP_005920687.1|  [L=102]
Description: CRISPR-associated protein, Csx3 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-21   76.2   0.2    1.6e-21   75.9   0.2    1.1  1  Cas_csx3    CRISPR-associated protein (Cas_csx3)
     0.0014   18.8   0.0       0.79    9.9   0.0    2.1  2  HAS-barrel  HAS barrel domain


Domain annotation for each model (and alignments):
>> Cas_csx3  CRISPR-associated protein (Cas_csx3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.2   1.8e-25   1.6e-21      13      79 .]      20      84 ..       9      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.8e-25
                                      GGT-----.--TTSEEEEEESS-HHHHHHHHHHTTTSSE..EEEEETTT.EEEEEEESS.SS-TT-EE- CS
                          Cas_csx3 13 LkklelPeeidlkqgvvisGrgPiWlygylvhelhetaw..iavydprLegavvvashtrevrvGqvik 79
                                      L+ l  P+ i + + vv++G++PiW+yg+ +h lh +++  ia ydprL gavvva+h+re  vG+v++
  gi|386002388|ref|YP_005920687.1| 20 LPPL--PK-IPRGSLVVVEGKAPIWRYGMALHLLHGSPAaaIAFYDPRL-GAVVVATHSREWAVGDVVD 84
                                      5555..88.*************************9876555********.*****************95 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00042       3.8      10      48 ..      10      51 ..       4      58 .. 0.84
   2 !    9.9   0.0   8.9e-05      0.79      21      55 ..      54      96 ..      49     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00042
                        HAS-barrel 10 ssslifrvegsk...dvkvGeyVeielpdgeivlGmvtdirr 48
                                      +s++i+ +e++    ++  G++V++e+    +++Gm + + +
  gi|386002388|ref|YP_005920687.1| 10 VSGPITSAEPLPplpKIPRGSLVVVEGKAPIWRYGMALHLLH 51
                                      578888888888888***********9999999999987766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.9e-05
                        HAS-barrel 21 k.......dvkvGeyVeielpdgeivlGmvtdirrgn..selsn 55
                                              d+++G  V++ +  +e+  G v+di   +  ++ s+
  gi|386002388|ref|YP_005920687.1| 54 PaaaiafyDPRLGAVVVATHS-REWAVGDVVDITLEGnpDQGSS 96
                                      3344555589***********.***********99666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 594.68
//
Query:       gi|386002389|ref|YP_005920688.1|  [L=327]
Description: hypothetical protein Mhar_1707 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.21   11.5   0.0    1.5  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)


Domain annotation for each model (and alignments):
>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.2e-05      0.21      67     128 ..     126     186 ..      95     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.2e-05
                       Cas_APE2256  67 eeFreglrnLveklarevknkkregekvlinaTgGfKpeiavltlvall.lade.vyYihEsfs 128
                                       ++F+++l  + + ++      ++ g++++ n++gG    +a ++++++l +a++  yY +E+  
  gi|386002389|ref|YP_005920688.1| 126 QDFKKALPVIYHTVNAL---GTKGGKELWANMVGGTNQINASILTAGSLsGAISrYYYYFEQDI 186
                                       44777777666666655...47999************************977651667788765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1882.68
//
Query:       gi|386002390|ref|YP_005920689.1|  [L=338]
Description: CRISPR-associated protein, Cmr6 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-13   51.4   2.7    6.4e-13   49.2   0.7    2.5  2  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.7   3.5e-17   6.4e-13       2     213 .]      83     253 ..      82     253 .. 0.74
   2 ?   -2.2   0.1      0.19   3.4e+03     121     148 ..     297     324 ..     271     335 .. 0.64

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.5e-17
                                       EEESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHH CS
                             RAMPs   2 letltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdlee 78 
                                       l+t  P  +G g ++++ e+  + + + g+Py+PGSS+kG++Rs++  ++++e++e                   ++
  gi|386002390|ref|YP_005920689.1|  83 LKTEGPFVTGLG-RNHPVENGFAWHQTLGTPYLPGSSVKGVVRSWAK-IWEEENDE------------------TIN 139
                                       899*********.*********************************5.65644432..................9** PP

                                       HHH--S....SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE..... CS
                             RAMPs  79 aiFGne.eeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngk.. 152
                                       +iFG +  + ++ g v+f Da p++                       +   + +h+   + +      + +  +  
  gi|386002390|ref|YP_005920689.1| 140 RIFGPRdSNTSSVGSVIFLDAIPISQV-------------------QLKADVMTPHYGPYYQGDEPPADWQSPVPvp 197
                                       ***9998899***********997631...................1222233333333333322222222222223 PP

                                       ....-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                             RAMPs 153 ....kkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                           + g+ f   + p       ++ r  ++ +++ ++l  +L+++     g G+++ +G+G++e
  gi|386002390|ref|YP_005920689.1| 198 flvvEAGQDFLFGVMPRR----PEDQRDGDDCKKAAEWLRVALNKI-----GGGAKTAVGYGRFE 253
                                       445544555666666666....999999999999***********9.....99*********996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.19
                                       EEEEEEEEEEEEEEEEE--SSS-EEEEE CS
                             RAMPs 121 klsgselrelldhsterrtrvaidrktk 148
                                         ++sel+e +    + r++  +dr+t+
  gi|386002390|ref|YP_005920689.1| 297 SIEDSELKEKILADIKARYGKLWDRPTG 324
                                       6677777777777777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1977.10
//
Query:       gi|386002391|ref|YP_005920690.1|  [L=119]
Description: Cmr5 family CRISPR-associated protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-25   88.6   0.1    4.1e-25   88.4   0.1    1.0  1  Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)


Domain annotation for each model (and alignments):
>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.1   2.3e-29   4.1e-25      21     121 ..       4     107 ..       1     108 [. 0.96

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 2.3e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC.......SSCCCHHHHHHHHHHHHHHHHCTSS...STTTCHHH CS
                          Cas_Cmr5  21 kkkekkykslvkklPalIltnGLgqalAfllskg.......kkkkedahkkllehlaewlkkeksaskkkkgendll 90 
                                       kk+ ++++s+v++lPa+I++nGLgqa+A  l+ +        +++e ahk l++ +++wl +     +  +g+  l+
  gi|386002391|ref|YP_005920690.1|   4 KKDYGNFGSYVQRLPATIVMNGLGQAMAGELAAArlakgdrMSADERAHKTLFDCVESWLFEC----EAYSGDGGLM 76 
                                       8999*************************9999999*****9********************9....8888999*** PP

                                       HHHHHSTHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Cas_Cmr5  91 kelleadlseymratreaLallnWlkRfAea 121
                                       ++++++++++y+ra++eaLa+l+Wlk+f++a
  gi|386002391|ref|YP_005920690.1|  77 AAIVNSSQENYVRAQAEALAYLDWLKKFSQA 107
                                       *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 701.01
//
Query:       gi|386002392|ref|YP_005920691.1|  [L=282]
Description: CRISPR-associated protein, Cmr4 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-23   82.6   0.1    7.1e-23   81.8   0.1    1.4  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.1   3.9e-27   7.1e-23       4     212 ..      10     275 ..       8     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 3.9e-27
                                       ESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHH CS
                             RAMPs   4 tltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeai 80 
                                       + tP+h G+g++++  +++ ++++ +++P+I GSSlkGal+  ++  + ++++e+++e    +          +e+ 
  gi|386002392|ref|YP_005920691.1|  10 AETPVHPGAGRSTGFVDLPVARESITEYPVIVGSSLKGALKDRARDKWPGKRSENGEEAAQSE---------EVERA 77 
                                       68*******************************************************999977.........9**** PP

                                       H--S...SS--SEEEEE............................................................ CS
                             RAMPs  81 FGneeeskiagrvffeDarpvkipgqileeskqikstpsp..................................... 120
                                       FG++   + ag ++++Dar++  p+++l + +++ ++p+                                      
  gi|386002392|ref|YP_005920691.1|  78 FGKQ---DGAGDLIVSDARLLLLPVRSLTGHYKWATCPNIlerlsrdihrsgfekklkipktdkkpengtvlgegsg 151
                                       ****...********************************************************************** PP

                                       .........................................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT- CS
                             RAMPs 121 .........................................klsgselrelldhsterrtrvaidrktktngkkkgg 156
                                                                                +ls+ +++ +   ++ +++r+ +d+ tkt+++    
  gi|386002392|ref|YP_005920691.1| 152 kifleerefkivetadksvieaidqlmpnrasaerlarqliVLSDDDFKWFASYGLPISARNVLDENTKTSKN---- 224
                                       ********************************************************************99877.... PP

                                       EEEEEEEESS..............HHHHHHHHHHHHHH...HHH---STTTTBTTT-E CS
                             RAMPs 157 lftleaipaerikfsgrirlenlsdeelgallklLdll..dlhflglGggkplGfGsv 212
                                       l+++e++ ++         + nl  e  +    l ++l  +  +l++Gg +++G G++
  gi|386002392|ref|YP_005920691.1| 225 LWYEETLAQD-------SLFYNLLMERGNGSIDLVKILvdERPYLQVGGNETVGQGWF 275
                                       9*********.......7777777777777777777777888**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1691.10
//
Query:       gi|386002393|ref|YP_005920692.1|  [L=378]
Description: CRISPR-associated protein, Cmr3 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-56  192.9   0.0    1.3e-56  192.7   0.0    1.0  1  Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)


Domain annotation for each model (and alignments):
>> Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.7   0.0     7e-61   1.3e-56       1     371 []       6     374 ..       6     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.7 bits;  conditional E-value: 7e-61
                          Cas_Cmr3   1 fllePlDplffrdgrpFedgeear..aasllfPlPsTlaGavrtalgekagldf.....gklleeekar..dgealg 68 
                                       ++l+P+ ++ffrdgrp+++ge++    +sl++P   T +Ga+r+ ++++++ d      g++ +e ka+  +g++l 
  gi|386002393|ref|YP_005920692.1|   6 YKLTPVGSWFFRDGRPYNQGESTLadIKSLFPPFAVTAVGAIRASFARDLARDQgwngkGDWPSEIKAKlgNGQKLA 82 
                                       689*****************9987779******************999999888778899999999999******** PP

                          Cas_Cmr3  69 eiavrGpllvrepdgkeellfPaPadllv...kekkeglvqllrlepr...dlpeglgplglpdreeveeprpkkkp 139
                                       ++++rGp+l re++g+ ++l+PaP++ll+   + ++++ ++l  l+p+   d ++g g ++lp++     ++ ++k+
  gi|386002393|ref|YP_005920692.1|  83 PLSFRGPYLLREKEGRSDFLVPAPLHLLGkesESDESKWEELCLLRPGeevDCDIGDG-VRLPSS-----KDAQGKK 153
                                       *****************************88877777788888888887444444444.444444.....3699*** PP

                          Cas_Cmr3 140 kplpaylsleglskwLrgelpesselvkeedlltkeeRigialdpetrtaeegalyqteglrlkedvrlallveldd 216
                                       + ++ yl+l++l+ +L g   ++  + k++dl+  e  +gia+d + rta eg ly+++ +rl ++v+la+ v++ +
  gi|386002393|ref|YP_005920692.1| 154 SLFGSYLTLKDLEVVLTGGDLSKISPIKAKDLWDFEFLVGIARDFKNRTALEGLLYSISRVRLMQGVSLAVEVDGIE 230
                                       *****************99999989999999******************************************9988 PP

                          Cas_Cmr3 217 paeeeklepailrLGGerrlalvee.elseelesvpeeveaaiaeggrlrlvLlTPaifakgwrpgwldkekelele 292
                                             + +++l++GGe+ la+ ++     ++++ +e +  + +   r++l++lTPa+f+  w pg++++     ++
  gi|386002393|ref|YP_005920692.1| 231 AGL---DLESTLPFGGEGGLAYADMmDGTIKIPDAAELIPSS-DGNIRFTLTHLTPAHFKCTW-PGPGEE-----VP 297
                                       776...679****************44444445544444444.77779***************.776644.....56 PP

                          Cas_Cmr3 293 elsae.lvaaavkrpvavSgwdlarkkpkptrravPaGsVyfleakeeeneeleelealtlsdaeqdrrdGfGlali 368
                                       +++++ +v+a+++rpv ++gwd ++++p p++++ P Gs++f+ea ++ +ee ++       ++++  + GfG+++i
  gi|386002393|ref|YP_005920692.1| 298 GITGSrVVSACLERPVWIGGWDSVNREPLPLKPFLPGGSTWFCEADGDRAEEIRKIGG---KKIGEYCEFGFGEIAI 371
                                       666656**********************************************999999...99************** PP

                          Cas_Cmr3 369 gvw 371
                                       g+w
  gi|386002393|ref|YP_005920692.1| 372 GSW 374
                                       *99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2174.42
//
Query:       gi|386002394|ref|YP_005920693.1|  [L=610]
Description: CRISPR-associated protein, Cmr2 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.5   0.0      4e-06   27.0   0.0    1.8  2  DUF3692   CRISPR-associated protein
      2e-05   24.9   0.0    5.5e-05   23.5   0.0    1.8  1  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> DUF3692  CRISPR-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.5e-10     4e-06      28     111 .]       1      80 [.       1      80 [. 0.94
   2 ?   -2.8   0.0       0.8   7.2e+03      79     108 ..     390     418 ..     336     420 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.5e-10
                                       HHHHHHHHHHHHHHHHT-GGGEEES--TT-HHHHHHTS---GGGGGSB---SEEEEEEE.TTTHHHHHHHHHHHHHH CS
                           DUF3692  28 llSylawkaikelvekyGpdvliyPslrgnplvdawllekleeeletalipnrfvlilpkeeeaeelaeeveealke 104
                                       +lSyl+  ai+e+++k G+  +  P++ ++pl++ + ++ + +++ +++ipnrf +i++++   + +a+++ + +++
  gi|386002394|ref|YP_005920693.1|   1 MLSYLSGCAISEVMDKGGQ--ITIPDVTDDPLLAWIRRSREGNAPIIGSIPNRFEAIVEDDP--KSVASSAAKMVQN 73 
                                       79****************9..99**********9999999999****************766..7999999****** PP

                                       HHHHHHH CS
                           DUF3692 105 awkeiae 111
                                       +w eiae
  gi|386002394|ref|YP_005920693.1|  74 RWMEIAE 80 
                                       ****985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.8
                                       SEEEEEEE.TTTHHHHHHHHHHHHHHHHHH CS
                           DUF3692  79 nrfvlilpkeeeaeelaeeveealkeawke 108
                                       + ++++lp   ea ++a+e+ e++++++++
  gi|386002394|ref|YP_005920693.1| 390 DDVLAMLP-MPEALKCAKELSESYEKRFED 418
                                       55666777.334556667766666666655 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   6.2e-09   5.5e-05       2     101 ..     341     441 ..     340     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.2e-09
                             mCpol   2 iaiDGDdiGkklealllsndeeeleklskevkeaikklkkllkdelgasvifaaGDsilaksslee..dllvelsrv 76 
                                       + +DGD+ Gk +  +  ++d+     + k + +++k +++++k   +   i+a+GD++la+ ++ e  + + els+ 
  gi|386002394|ref|YP_005920693.1| 341 LLMDGDNMGKLMGDYKDKEDL-----ITKALSAFTKDVRDIVKTR-EGVTIYAGGDDVLAMLPMPEalKCAKELSES 411
                                       5789***99988777555554.....789999*************.89999************98889889999999 PP

                             mCpol  77 yqkit.....gltvSiGvGktlrealiaLk 101
                                       y+k       +++++i++G  + +  i+L+
  gi|386002394|ref|YP_005920693.1| 412 YEKRFedvipEVKATISAGLVFSHYHIPLS 441
                                       999888889999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 3200.28
//
Query:       gi|386002395|ref|YP_005920694.1|  [L=394]
Description: CRISPR-associated protein, Cmr1 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-09   35.9   0.5    4.4e-08   33.4   0.4    2.3  2  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.4   2.5e-12   4.4e-08       1     212 [.       7     179 ..       7     180 .. 0.80
   2 ?   -2.5   0.0      0.24   4.3e+03     147     166 ..     331     353 ..     252     362 .. 0.56

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.5e-12
                                       EEEESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HH CS
                             RAMPs   1 kletltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdle 77 
                                       k+ ++tPl++ +                     ++  S+kG+lR+++++l+ ++++   + ++             e
  gi|386002395|ref|YP_005920694.1|   7 KFRVVTPLFMSGS--------------DKSQAELRVPSIKGVLRFWWRALALGRLGSVSRVRD------------EE 57 
                                       5789999999999..............9999999999***************99986654333............79 PP

                                       HHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-T CS
                             RAMPs  78 eaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkk 154
                                       ++iFG++ +++   +      +++++ gq+ ++ +++      +  g+  r+l  + +e  +  + + k ++     
  gi|386002395|ref|YP_005920694.1|  58 SHIFGSA-GRDVGQAKVHLSLKLDENIGQYKDPILKYANG---EPVGPGARYLGYGVVEAVPSRKRNTKEGQILR-- 128
                                       *******.7777777777778999*****99998887766...66666666777777776666666666555444.. PP

                                       T-EEE.EEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                             RAMPs 155 gglft.leaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                           + l++  ++      + ++++  d++ + +  +L ++ + f+glG +++ G+Gs+
  gi|386002395|ref|YP_005920694.1| 129 ----ScLKYPFDG---TLNLLFRNGTIDDDVENVTSALIAM-GLFGGLGSRSRKGYGSF 179
                                       ....445555555...77778899999999***********.****************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.24
                                       EEE......-TT-EEEEEEEESS CS
                             RAMPs 147 tktngk...kkgglftleaipae 166
                                       +  n++     +++f  e++p++
  gi|386002395|ref|YP_005920694.1| 331 QELNNGqyaAVPAIFPSEFLPPG 353
                                       22222224445555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2283.75
//
Query:       gi|386002396|ref|YP_005920695.1|  [L=331]
Description: hypothetical protein Mhar_1714 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1971.71
//
Query:       gi|386002397|ref|YP_005920696.1|  [L=1079]
Description: Carbamoyl-phosphate synthase, large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-96  321.2   1.4    1.4e-57  194.6   0.1    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.8e-27   95.5   0.0    1.4e-26   93.3   0.0    2.2  2  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    5.2e-25   88.0   0.2    6.4e-12   45.4   0.0    2.5  2  ATP-grasp        ATP-grasp domain
    1.5e-20   73.2   0.1    1.4e-19   70.1   0.1    2.7  3  MGS              MGS-like domain
    3.7e-16   59.3   0.3    3.4e-07   30.0   0.1    2.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    5.5e-13   48.8   0.0    1.8e-06   27.7   0.0    2.5  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      1e-08   35.4   0.1     0.0017   18.4   0.1    2.4  2  ATP-grasp_3      ATP-grasp domain
    4.3e-08   33.1   0.2      0.008   16.0   0.0    2.6  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    9.6e-07   28.5   0.0      0.055   12.9   0.0    2.7  2  ATP-grasp_5      ATP-grasp domain
    2.6e-06   27.2   0.0      0.011   15.3   0.1    2.6  2  ATP-grasp_2      ATP-grasp domain
     0.0043   16.3   0.0       0.66    9.2   0.0    2.7  3  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.017   15.1   0.0        1.2    9.2   0.0    2.5  2  DUF4176          Domain of unknown function (DUF4176)
       0.14   12.6   0.2        2.3    8.6   0.0    3.0  3  Jag_N            Jag N-terminus


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.6   0.1     1e-60   1.4e-57       1     210 [.     128     333 ..     128     334 .. 0.99
   2 !  125.7   0.2   1.2e-39   1.7e-36       1     210 [.     678     880 ..     678     881 .. 0.96

  Alignments for each domain:
  == domain 1  score: 194.6 bits;  conditional E-value: 1e-60
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+  +ke+++++++++ +s+a+   ++e+a ++a+++gyPv++++a+++GG+G+++++n eel+ ++++++a++   
  gi|386002397|ref|YP_005920696.1| 128 DRIIFKETMERLGIDMPKSTAV--YSVEDAEKVAADLGYPVVVRPAYTMGGTGGGLVYNVEELRTVASRGIAASL-- 200
                                       999******************9..************************************************995.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                           qvl+e+s+ g+ e+E+ev+rDak+ +itvc +en++++  +t+++   AP  t+++e   +l+  + ++v+++
  gi|386002397|ref|YP_005920696.1| 201 --IGQVLIEESVLGWEELELEVVRDAKNQMITVCFIENVDPMgvHTGDSYCTAPMLTISNELQARLQDYSYRIVEAI 275
                                       ..89************************************************************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                        v+g+ +v+f+ dpk+++ +viE+N+R s++sala+kaTG++++ ++ak+a g +L+e
  gi|386002397|ref|YP_005920696.1| 276 AVIGGTNVQFAHDPKTDRVVVIEINPRTSRSSALASKATGFPIALVSAKLACGLTLDE 333
                                       ********************************************************97 PP

  == domain 2  score: 125.7 bits;  conditional E-value: 1.2e-39
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+++++ +++k+++p+ +s  a  ++l+eal++a++igyP ++++++ lGG+Gm v+++ee l+  v++a++ ++  
  gi|386002397|ref|YP_005920696.1| 678 DRDRFRMMMEKMEIPMPESGMA--SNLDEALEVAARIGYPLMVRPSYVLGGRGMEVIYDEEMLERYVAAAVDVTP-- 750
                                       9******************999..**************************************************6.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         ++ +l++++l++  e E++ l+D + + +    +e + q   + +++  v P  t+ +++ ++++e ++k+++e+
  gi|386002397|ref|YP_005920696.1| 751 --ERPILIDRFLENALEAEADALSDGTSTFVPA-VMEHIEQAgvHSGDSACVIPPVTIPKRQIETIKEYTCKIAKEL 824
                                       ..99***********************999875.5888888888********************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       gvvg  ++++++ +  +  yv+E N+R s+  +l +k+  + ++ +a  + +g  L e
  gi|386002397|ref|YP_005920696.1| 825 GVVGLMNMQYAIAK--DVVYVLEANPRASRTVPLVSKVCNVSMARIATELMMGRGLAE 880
                                       ************95..999****************************99999998876 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.8   3.8e+03      28      49 ..      61      82 ..      53     102 .. 0.89
   2 !   93.3   0.0     1e-29   1.4e-26       2     122 .]     423     552 ..     422     552 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.8
                       CPSase_L_D3 28 heltkidpwFLekleelvelek 49
                                      +++t i+p  Le++ +++e e+
  gi|386002397|ref|YP_005920696.1| 61 ADVTYIEPLNLERMTQIIEKER 82
                                      6899*************99775 PP

  == domain 2  score: 93.3 bits;  conditional E-value: 1e-29
                       CPSase_L_D3   2 elkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkk.............eldeellre 65 
                                        lk p++eR f+i+ealr+g+sv+ei++lt+i+pwFL++++elvele+e+ + ++             +++++llr+
  gi|386002397|ref|YP_005920696.1| 423 MLKWPSSERQFIIYEALRKGASVQEISDLTRIKPWFLQQMKELVELEEEILSFRArtgegvaeadllsTIPDALLRR 499
                                       5889**********************************************999888999999999988888999*** PP

                       CPSase_L_D3  66 akklGfsDkqiaelleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       ak+ GfsDk++++ll+  +e+e+r+ rk+lgi   ++ v     e   + +Y+YstY
  gi|386002397|ref|YP_005920696.1| 500 AKEDGFSDKYLSKLLS-ISEREIRTRRKALGIVQGWEPVPVSGVE---DAAYYYSTY 552
                                       **************76.77888*********************99...999*****9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0     2e-13   2.8e-10       2     161 ..     137     304 ..     136     312 .. 0.89
   2 !   45.4   0.0   4.6e-15   6.4e-12       2     160 ..     687     850 ..     686     853 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2e-13
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       e+lg+ +p+ +av s e++e++a++lg+pvvv+ +     G G  +v + e+l+++++        ++v++Ee v  
  gi|386002397|ref|YP_005920696.1| 137 ERLGIDMPKSTAVYSVEDAEKVAADLGYPVVVR-PAYTMGGTGGGLVYNVEELRTVASRGiaasLIGQVLIEESVLG 212
                                       689******************************.999999*************999987666667799********* PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEEE...EEEECE.E-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgilr...lsvapa.evsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                         El + vvr+a+ ++ ++  +e+v   g+     ++ ap+ ++s++ q++ +++  +ive++ ++G   v +    
  gi|386002397|ref|YP_005920696.1| 213 WEELELEVVRDAKNQMITVCFIENVDPMGVHTgdsYCTAPMlTISNELQARLQDYSYRIVEAIAVIGGTNVQFAHDP 289
                                       **************************9999853337888863578889***********************988875 PP

                                       TCT.EEEEEEESS-- CS
                         ATP-grasp 148 dge.llvnElapRpH 161
                                       + + ++v E+ pR+ 
  gi|386002397|ref|YP_005920696.1| 290 KTDrVVVIEINPRTS 304
                                       5446*********85 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 4.6e-15
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       ek+++p+p+  ++++ +e+ e+a+++g+p++v+ +     G+G  v+ +ee le+ ++a+     e+++++  f + 
  gi|386002397|ref|YP_005920696.1| 687 EKMEIPMPESGMASNLDEALEVAARIGYPLMVR-PSYVLGGRGMEVIYDEEMLERYVAAAvdvtPERPILIDRFLEN 762
                                       6899*****************************.99999****************999998998999********99 PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                         E  + +  +    t + +v+e++++ g+       ++ p ++++++ ++++e++ ki++eLg+vG++ +   +  
  gi|386002397|ref|YP_005920696.1| 763 ALEAEADALSDGTS-TFVPAVMEHIEQAGVHsgdsACVIPPVTIPKRQIETIKEYTCKIAKELGVVGLMNMQYAIA- 837
                                       99988776654443.5555677899987654221168999*******************************99888. PP

                                       TCTEEEEEEESS- CS
                         ATP-grasp 148 dgellvnElapRp 160
                                       ++ ++v E  pR 
  gi|386002397|ref|YP_005920696.1| 838 KDVVYVLEANPRA 850
                                       3449999999985 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         4   5.5e+03       5      17 ..      33      45 ..      29      56 .. 0.81
   2 ?   -1.6   0.0       2.3   3.1e+03       4      20 ..     653     669 ..     626     694 .. 0.77
   3 !   70.1   0.1   9.9e-23   1.4e-19       2      95 .]     960    1045 ..     959    1045 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4
                                      HHHHHHHTTCEEE CS
                               MGS  5 lakklkelgfell 17
                                       +k+l+elg++++
  gi|386002397|ref|YP_005920696.1| 33 ACKALRELGYKIV 45
                                      5788888888886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHTTCEEEEEH CS
                               MGS   4 elakklkelgfellATg 20 
                                       ++a++l+e+g +++ T+
  gi|386002397|ref|YP_005920696.1| 653 NIARELEEAGARVIGTS 669
                                       56777777777777664 PP

  == domain 3  score: 70.1 bits;  conditional E-value: 9.9e-23
                                        HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH CS
                               MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatva 76  
                                        ++e ak+++++gf + AT+GT+++l+e+gi+  e++ k+ eg r++    i daikngei+lvint+ +++++  
  gi|386002397|ref|YP_005920696.1|  960 VLEAAKEFSRMGFAIRATRGTQEYLAENGIE-SELILKLTEG-RPN----IDDAIKNGEIQLVINTPIGKASQY- 1027
                                        6899***************************.**********.***....***********************9. PP

                                        CHHHHHHHHHHHTTSHEES CS
                               MGS   77 kdgykirraaenidIplpt 95  
                                         d+  ir+aa++++ p++t
  gi|386002397|ref|YP_005920696.1| 1028 -DDSYIRKAAIKYKLPYIT 1045
                                        .8999************98 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   2.5e-10   3.4e-07      26     174 ..     153     301 ..     141     307 .. 0.83
   2 !   26.5   0.0   2.9e-09     4e-06      27     174 ..     704     848 ..     687     857 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.5e-10
                                       HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHH..HHTT-SCEEEEE--.ESEEEEEEEEETSSCEEE CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaiee..afkydekvlvEeai.egreievavlgneklevs 99 
                                       e  ekv + lgypv+V+pa +    G   v ++eel+   ++  a++   +vl+Ee +   +e+e  v+ + k+++ 
  gi|386002397|ref|YP_005920696.1| 153 EDAEKVAADLGYPVVVRPAYTMGGTGGGLVYNVEELRTVASRgiAASLIGQVLIEESVlGWEELELEVVRDAKNQMI 229
                                       55799**************99999999***********999844677789*******9899*********9888888 PP

                                       EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEES CS
                   Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNt 174
                                       +v  i   + +      +++d+       ++++e ++++q+++ ++ +a+ + G + v f    +++++v+ E+N+
  gi|386002397|ref|YP_005920696.1| 230 TVCFIENVDPM----GVHTGDSYCTAPMLTISNELQARLQDYSYRIVEAIAVIGGTNVQFAHdPKTDRVVVIEINP 301
                                       87766554422....22233444455556789999***************************77899********6 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.9e-09
                                       HHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSS.CEEE CS
                   Dala_Dala_lig_C  27 llekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgnek.levs 99 
                                          +v +++gyp++V+p+      G++ +  ee l++++++a+  +  + +l+++++ ++ e e   l +++ + v 
  gi|386002397|ref|YP_005920696.1| 704 EALEVAARIGYPLMVRPSYVLGGRGMEVIYDEEMLERYVAAAVDVTpeRPILIDRFLeNALEAEADALSDGTsTFVP 780
                                       4568999***********999999******************98862267*******99*******99999834566 PP

                                       EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                        v e++ + g+       s+d+a +  p++++k + e+i+e+  k+ k l++ Gl  + + +  ++ +++ E N+
  gi|386002397|ref|YP_005920696.1| 781 AVMEHIEQAGVH------SGDSACVIPPVTIPKRQIETIKEYTCKIAKELGVVGLMNMQYAIA-KDVVYVLEANP 848
                                       678888888875......6799999**********************************9998.7899999*996 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.1e-06    0.0015      47     120 ..     262     338 ..     255     346 .. 0.82
   2 !   27.7   0.0   1.3e-09   1.8e-06      47     117 ..     811     882 ..     805     894 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepe 120
                                       ++l +++ r++e++++ g +nvQ+ +d ++   +++EiNpR s      s ++G  ++ +++kl+ gl  +e++ ++
  gi|386002397|ref|YP_005920696.1| 262 ARLQDYSYRIVEAIAVIGGTNVQFAHDPKTdrVVVIEINPRTSRSSAlASKATGFPIALVSAKLACGLTLDEIPYWR 338
                                       6788999******************9977766999*******96555156677999999999999998777776665 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.3e-09
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgleteeve 117
                                       e + e+++++a+e+g+ gl+n+Q+   +d  ++LE NpRas ++ + s +++v ++++a +l++g+  +e+ 
  gi|386002397|ref|YP_005920696.1| 811 ETIKEYTCKIAKELGVVGLMNMQYAIAKDVVYVLEANPRASRTVPLvSKVCNVSMARIATELMMGRGLAEIG 882
                                       677899**************************************8538899*************98666655 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.2e-06    0.0017       4     158 ..     129     303 ..     127     306 .. 0.70
   2 !   14.6   0.0   1.8e-05     0.025      10     158 ..     685     850 ..     676     853 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHTTT.S---.......-EESS--.......SSSEEEEESS-------B--SS--TTE............. CS
                       ATP-grasp_3   4 KlktykkLkeagvkvP...tkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                        + + + +++ g+ +P        +++e +        +++vv p++ +gg++  +v + ee+ +            
  gi|386002397|ref|YP_005920696.1| 129 RIIFKETMERLGIDMPkstA---VYSVEDAekvaadlGYPVVVRPAYTMGGTGGGLVYNVEELRTVASR-Giaasli 201
                                       556678889999****6552...333333334466789*********************9888754443.3478887 PP

                                       ...EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET......TEEEE.EEES----HHHHHHHHHHHHHTTSTT- CS
                       ATP-grasp_3  65 ...lvqefieG.kplSvsllsdgekvlvlavnrqliekaeke..fvyaG.nvtpietelkeevvelaeevveklegl 134
                                          l+ e + G ++l ++++ d+++  + ++  + ++  + +   +y+   +  i  el+ ++++   ++ve++  +
  gi|386002397|ref|YP_005920696.1| 202 gqvLIEESVLGwEELELEVVRDAKNQMITVCFIENVDPMGVHtgDSYCTaPMLTISNELQARLQDYSYRIVEAI-AV 277
                                       77777776667578999999987554443333333433222245444431466677799***************.88 PP

                                       -EEEEEEEEESS...SEEEEEEESS- CS
                       ATP-grasp_3 135 aGyvGvDlvlkd..eepyviEvNPRl 158
                                        G   v +      +  +viE+NPR 
  gi|386002397|ref|YP_005920696.1| 278 IGGTNVQFAHDPktDRVVVIEINPRT 303
                                       88888999854455799********6 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.8e-05
                                       HHTTT.S---.........-EESS--.......SSSEEEEESS-------B--SS--TTE...............EE CS
                       ATP-grasp_3  10 kLkeagvkvP.....tkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve........lv 66 
                                        +++ ++++P     +     +l+e+        ++l v p++  gg ++ v+ ++e +e+ ++           l+
  gi|386002397|ref|YP_005920696.1| 685 MMEKMEIPMPesgmaS-----NLDEAlevaariGYPLMVRPSYVLGGRGMEVIYDEEMLERYVAAAVdvtperpiLI 756
                                       5566688888665542.....3333333345559**********************99998888777899******* PP

                                       EE---SE.EEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHH...TTSTT--EEEE CS
                       ATP-grasp_3  67 qefieGk.plSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevv...ekleglaGyvG 139
                                        +f+e   ++ +++lsdg    ++    ++ie+a+ +   + +v+p  t  k++++++ e ++   ++l g++G++ 
  gi|386002397|ref|YP_005920696.1| 757 DRFLENAlEAEADALSDGTST-FVPAVMEHIEQAGVHSGDSACVIPPVTIPKRQIETIKEYTCkiaKEL-GVVGLMN 831
                                       ****9754899*****99444.44444444444444444444556655555555555544444000455.7777777 PP

                                       EEEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 140 vDlvlkdeepyviEvNPRl 158
                                           ++++  yv+E NPR 
  gi|386002397|ref|YP_005920696.1| 832 MQYAIAKDVVYVLEANPRA 850
                                       77779999**********6 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.7e-05     0.023       6     107 ..     132     229 ..     128     278 .. 0.80
   2 !   16.0   0.0   5.8e-06     0.008       7     186 ..     683     847 ..     678     852 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSS CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagek 82 
                                        k+ +++ gi  ++ +a+ ++e+a+++  +++ ++ Vv+++   +g g  ++ ++ee  ++++  +     G    +
  gi|386002397|ref|YP_005920696.1| 132 FKETMERLGIDMPKSTAVYSVEDAEKVAADLGYPV-VVRPAYTMGGTGGGLVYNVEELRTVASRGIAASLIG----Q 203
                                       5899*******************************.************************999999999999....9 PP

                                       EEEEE---S.EEEEEEEEECTTEEEE CS
                            GARS_A  83 vviEelleG.eEvsllalvdgktvkp 107
                                       v+iEe + G eE+ l ++ d k+ + 
  gi|386002397|ref|YP_005920696.1| 204 VLIEESVLGwEELELEVVRDAKNQMI 229
                                       ****9998846788888888776543 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.8e-06
                                       HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSE CS
                            GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekv 83 
                                       + +++k++ip +e    ++ +ea e+  + + +   v+++ + +g+g+ v  +ee   ++v+  ++     + ++ +
  gi|386002397|ref|YP_005920696.1| 683 RMMMEKMEIPMPESGMASNLDEALEVAARIGYPL-MVRPSYVLGGRGMEVIYDEEMLERYVAAAVD----VTPERPI 754
                                       679*******************************.99************************99997....45789** PP

                                       EEEE---S.EEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHH CS
                            GARS_A  84 viEelleG.eEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptveglk 159
                                       +i+ +le   E    al+dg+++  +p++ +h        g+  G   ++ p  ++++ ++e+ike        +++
  gi|386002397|ref|YP_005920696.1| 755 LIDRFLENaLEAEADALSDGTSTF-VPAVMEHIE----QAGVHSGDSACVIPPVTIPKRQIETIKE-----YTCKIA 821
                                       ******86269*********8764.555555542....3456666666666655555555555555.....222333 PP

                                       CTT---EEEEEEEEEEETTEEEEEEEE CS
                            GARS_A 160 kegipfkGvLyaglmlvedgpkvlefn 186
                                       ke    +G++  +  + +d  +vle n
  gi|386002397|ref|YP_005920696.1| 822 KE-LGVVGLMNMQYAIAKDVVYVLEAN 847
                                       33.444566666666666666666665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0     4e-05     0.055      16      52 ..     133     169 ..     128     174 .. 0.93
   2 !   12.4   0.0   5.9e-05     0.081      18      51 ..     685     718 ..     677     721 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                       ke +e +gi+++++  + s+e+a ++a+ +gypvv++
  gi|386002397|ref|YP_005920696.1| 133 KETMERLGIDMPKSTAVYSVEDAEKVAADLGYPVVVR 169
                                       677899*****************************96 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.9e-05
                       ATP-grasp_5  18 lleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                       ++e ++ip++e+ +as+ +ea+e+a++igyp  +
  gi|386002397|ref|YP_005920696.1| 685 MMEKMEIPMPESGMASNLDEALEVAARIGYPLMV 718
                                       68999**************************765 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   7.8e-06     0.011       8     120 ..     133     229 ..     131     236 .. 0.78
   2 !    8.9   0.0   0.00071      0.98      10      54 ..     685     728 ..     681     747 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-06
                                       HHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TT CS
                       ATP-grasp_2   8 keilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkq 84 
                                       ke +++ g+++p+++ + s e+ae++a++lg  + vv+    +GG G  gG  lv+++ee++++a++ + ++l+   
  gi|386002397|ref|YP_005920696.1| 133 KETMERLGIDMPKSTAVYSVEDAEKVAADLGYPV-VVRPAYTMGGTG--GG--LVYNVEELRTVASRGIAASLI--- 201
                                       788999**************************99.99*999***977..55..577888888888888887777... PP

                                       S-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEE CS
                       ATP-grasp_2  85 tgkeGkkvekvlveealdikkElYlsivlDraskkv 120
                                                +vl+ee++   +El l +v D +++++
  gi|386002397|ref|YP_005920696.1| 202 --------GQVLIEESVLGWEELELEVVRDAKNQMI 229
                                       ........3456666666666666666666665555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00071
                                       HHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCC CS
                       ATP-grasp_2  10 ilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRG 54 
                                       +++k ++++pe+ +a++ +ea e+a+++g    +v+     GGRG
  gi|386002397|ref|YP_005920696.1| 685 MMEKMEIPMPESGMASNLDEALEVAARIGYPL-MVRPSYVLGGRG 728
                                       799**************************998.88888889***9 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00048      0.66      20      88 ..     127     191 ..     120     203 .. 0.78
   2 ?   -3.0   0.0       2.5   3.5e+03      21      81 ..     678     734 ..     673     743 .. 0.65
   3 ?    3.8   0.0     0.021        29     197     268 ..     781     852 ..     770     861 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                       ATPgrasp_ST  20 ddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdyl 88 
                                       +d ++fke ++r g+++pk         +++++e++ ++l   vv++pa+++gG G   + ++e+ + +
  gi|386002397|ref|YP_005920696.1| 127 EDRIIFKETMERLGIDMPKST----AVYSVEDAEKVAADLGYPVVVRPAYTMGGTGGGLVYNVEELRTV 191
                                       7999***************43....346788888888888555************96666555555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                       ATPgrasp_ST  21 dKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvite 81 
                                       d   f+ ++++  +++p+  g+    ++++e+ ++ +++   ++++p +  gG+G+ vi +
  gi|386002397|ref|YP_005920696.1| 678 DRDRFRMMMEKMEIPMPE-SGMA---SNLDEALEVAARIGYPLMVRPSYVLGGRGMEVIYD 734
                                       555666666666777777.3333...34444444444443338999999999999999965 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.021
                       ATPgrasp_ST 197 alaavqtgeeieeHPdTgvklsglqiP..nweevlelaakaaeklpglgylGwDivldeekgplllElNarpgl 268
                                       a+ ++  ++   +  d+   +  ++iP  ++e++ e ++k+a++l  +g++ +  +++++  +++lE+N r + 
  gi|386002397|ref|YP_005920696.1| 781 AVMEH-IEQAGVHSGDSACVIPPVTIPkrQIETIKEYTCKIAKELGVVGLMNMQYAIAKDV-VYVLEANPRASR 852
                                       55555.555555666777777778887445899****************************.*******98765 PP

>> DUF4176  Domain of unknown function (DUF4176)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00089       1.2      13      38 ..       6      31 ..       4      35 .. 0.91
   2 ?    2.9   0.0     0.079   1.1e+02      13      38 ..     562     587 ..     560     591 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00089
                           DUF4176 13 gtkkvmiigrrqieeeekkiydYvgc 38
                                      + kk+miig  +i+ ++ + +dY+g 
  gi|386002397|ref|YP_005920696.1|  6 DIKKIMIIGSGPIVIGQACEFDYSGT 31
                                      679********************995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.079
                           DUF4176  13 gtkkvmiigrrqieeeekkiydYvgc 38 
                                       +++kvm++g  +++ +++  +dY+ +
  gi|386002397|ref|YP_005920696.1| 562 DRRKVMVLGGGPNRIGQGIEFDYCCV 587
                                       6789*******************965 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0016       2.3       3      21 ..     385     403 ..     383     407 .. 0.89
   2 ?   -2.8   0.1         6   8.3e+03       3      14 ..     699     710 ..     699     711 .. 0.84
   3 ?   -0.6   0.0       1.2   1.7e+03       5      17 ..    1003    1015 ..    1002    1018 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                             Jag_N   3 GkTveeAiekAlkeLgvsr 21 
                                       GkT +eA++kA++ L++ r
  gi|386002397|ref|YP_005920696.1| 385 GKTYKEALQKAIRSLEIGR 403
                                       9**************9876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6
                             Jag_N   3 GkTveeAiekAl 14 
                                       + +++eA+e A+
  gi|386002397|ref|YP_005920696.1| 699 ASNLDEALEVAA 710
                                       5789*****997 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                             Jag_N    5 TveeAiekAlkeL 17  
                                        ++++Ai+++  +L
  gi|386002397|ref|YP_005920696.1| 1003 NIDDAIKNGEIQL 1015
                                        79*******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1079 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.93u 0.36s 00:00:01.29 Elapsed: 00:00:00.58
# Mc/sec: 5603.70
//
Query:       gi|386002398|ref|YP_005920697.1|  [L=358]
Description: hypothetical protein Mhar_1716 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-39  135.9  38.3    2.5e-39  135.6  38.3    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
        5.3    7.1  10.3        2.9    8.0   4.0    3.0  2  DUF997           Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6  38.3   2.8e-43   2.5e-39       5     301 .]      18     330 ..      15     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 2.8e-43
                   LPG_synthase_TM   5 lalsalllall.lrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfv 80 
                                       l++++l+ +++ l++++l+++ a+l +++  ++ la+ll+ll v+++al W++l+r+l+++isl++++ +y+ ++f+
  gi|386002398|ref|YP_005920697.1|  18 LVVLGLFGYFAyLSHLGLGEVSASLVQVNLAVFGLAFLLSLLDVVFNALSWKTLVRELDHQISLLDVFLIYMSSIFL 94 
                                       5666666777789**************************************************************** PP

                   LPG_synthase_TM  81 nnvtPgalg.Gevvrayllkr.kegvslskalasvvverlldllalvllgllallllggllaegaavllllalalll 155
                                       nn++P++++ Ge +r+y+l++   + +l +++asv + r++  + +vl + ++l++l  + +  + ++l+  +++++
  gi|386002398|ref|YP_005920697.1|  95 NNLIPSGSVsGETARLYFLSKiAGNARLDSSTASVAATRIITAIPFVLGMSAGLAYLVLWYEVPS-WALTTCFSMIF 170
                                       *********************9999*********************************9877766.66666666666 PP

                   LPG_synthase_TM 156 lavlalllllllrrrlarlarvlkrlarllarfarklasakr...............klvlasprrlllafllslli 217
                                       l+v + +l+  + + + +l+  +  +    +++ +++    r                l++++ r l+++ ++ +  
  gi|386002398|ref|YP_005920697.1| 171 LMVSVGALFVGVCFSESWLSGAVNVVIDQVESLFKRSVN--RsfyssitrsfqqsmlLLLRNKNRPLVISSFWAFSG 245
                                       666665555555555555555555555554444433332..2346777889999**9999999999*********** PP

                   LPG_synthase_TM 218 wllealtlylllralgvdvslallllillaltlvgalp.plPgGlGvrEaalalllallGvsaaealaaallyrlit 293
                                       wl+  l++++ +r+lgv+v+++++++++ ++++++ lp +lPgG+G++E+++++l+ ++Gvs  +a+a+++l r+++
  gi|386002398|ref|YP_005920697.1| 246 WLSLNLVAFATFRSLGVEVPIFAIFAVYSVIMVFQNLPlILPGGVGIVEILMTALFTAVGVSLHDAAAVTILARVAQ 322
                                       *************************66666666666662689*********************************** PP

                   LPG_synthase_TM 294 lylllllG 301
                                       l++ ++lG
  gi|386002398|ref|YP_005920697.1| 323 LWFHTVLG 330
                                       *****998 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.0   0.00032       2.9      25      69 ..     140     186 ..     125     190 .. 0.81
   2 ?    1.3   0.4     0.038   3.4e+02      52      72 ..     264     284 ..     256     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00032
                            DUF997  25 Yglgskeveey..yilglPlWfflscillpilfivlvillvkfvFkd 69 
                                       ++lg + +  y      +P W ++ c+ +++l++ +  l v ++F++
  gi|386002398|ref|YP_005920697.1| 140 FVLGMSAGLAYlvLWYEVPSWALTTCFSMIFLMVSVGALFVGVCFSE 186
                                       66666666777767789************************999986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.038
                            DUF997  52 pilfivlvillvkfvFkdipL 72 
                                       +++f +++++ v +vF+++pL
  gi|386002398|ref|YP_005920697.1| 264 VPIFAIFAVYSVIMVFQNLPL 284
                                       567788888889999**9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1999.24
//
Query:       gi|386002399|ref|YP_005920698.1|  [L=362]
Description: hypothetical protein Mhar_1717 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-10   38.2   0.0    0.00096   18.5   0.0    2.1  2  Glyco_trans_1_3  Glycosyl transferase family 1
    4.7e-05   23.4   0.0    0.00012   22.1   0.0    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0005   20.1   0.0    0.00068   19.7   0.0    1.3  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.27   11.7   0.0    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
        0.2   11.7   0.0        0.4   10.7   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-07    0.0017      11      47 ..      12      49 ..       3      58 .. 0.89
   2 !   18.5   0.0   2.7e-07   0.00096     222     303 ..     235     319 ..     215     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-07
                   Glyco_trans_1_3 11 GaGhasRsrvvlehL.arghevkvvvsgraldvLekef 47
                                      G GhasR   +++ L  rgh+v v++sg al+ L++ef
  gi|386002399|ref|YP_005920698.1| 12 GLGHASRDIPIVRELlDRGHQVTVASSGNALELLRREF 49
                                      89*******999998689*****************998 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.7e-07
                   Glyco_trans_1_3 222 vYglrrd..teeekegnltykafseegFleDLataraviagagftLmtealyLkkPl.LavPvarqFeqvlnalyLe 295
                                       + g +++  t  e +g  +    s e  +e L +ar v++ +g+t m e   L+k   L +P  +q eq    +y  
  gi|386002399|ref|YP_005920698.1| 235 LLGSPQEsfTRREDDGTTVIAYASTEEKVELLNRARFVVSRSGYTTMMEVAELEKRHgLFIPTPGQTEQEYLSRYYR 311
                                       5555555445555666666667899999*************************99755************9999999 PP

                   Glyco_trans_1_3 296 rlgyGaav 303
                                       r g+    
  gi|386002399|ref|YP_005920698.1| 312 RRGWFLSR 319
                                       98876554 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.4e-08   0.00012      12     142 ..      23     160 ..      22     168 .. 0.79
   2 ?   -3.4   0.0       2.4   8.5e+03     115     125 ..     305     315 ..     290     326 .. 0.46

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.4e-08
                    Glyco_transf_4  12 araLarrGheVtvvtpgddgpleeev.........elvvrvprvplpllkrllrslafl........rrlrrllkre 71 
                                       +r+L +rGh+Vtv ++g   +l +++         e++ ++ +  +++l+++  +++ +        r l r+l ++
  gi|386002399|ref|YP_005920698.1|  23 VRELLDRGHQVTVASSGNALELLRREfpqcnfltfEDYPAPYSSTRFFLPKFTAYIPLMmkalvderRNLCRILSEG 99 
                                       799**************9999999999**999999555555555555555555444443233333337889999999 PP

                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSe 142
                                        +D + + +   + ++       + ip  +  H l     ++a+l+p ++l   +  +++++ d vi++ +
  gi|386002399|ref|YP_005920698.1| 100 SYDMIISDNRLGV-YS-------REIPSFFITHQLR--FSVPAYLWPVEILTLFVNGFFHSKYDGVIVPDN 160
                                       *****88885554.33.......59**********9..699***************************976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                    Glyco_transf_4 115 rlkplsrllra 125
                                       +l++++r++ +
  gi|386002399|ref|YP_005920698.1| 305 YLSRYYRRRGW 315
                                       33333333333 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.9e-07   0.00068      50     146 ..     246     338 ..     204     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.9e-07
                                       -TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--E.EEE--TT....S-HHHHHHHHHHHHHHSSE CS
                   Glyco_tran_28_C  50 veeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkpl.IlvplpeaaenhqdnNakelekagaalvle 125
                                       +e+++++v++++ +++ +e++ +a  v+sR+G +t +E++ l k + +++p p ++  +q++  ++  + g  l   
  gi|386002399|ref|YP_005920698.1| 246 REDDGTTVIAYASTEEKVELLNRARFVVSRSGYTTMMEVAELEKRHgLFIPTPGQT--EQEYLSRYYRRRGWFLSRS 320
                                       344456677888888999*************************98549******88..8877766666666666666 PP

                                       EEE-STTCHHHHHHHHCCS-- CS
                   Glyco_tran_28_C 126 qkeltpekLeeallelaaekl 146
                                       q++l   +L+e ++e ++ + 
  gi|386002399|ref|YP_005920698.1| 321 QYRL---DLAEDVDEAMEFSG 338
                                       6666...66666666666665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.5e-05      0.27      10      79 ..      22     106 ..      16     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                   Glyco_trans_4_4  10 laraLaarGheVtvltpapapgapeleedgvrvhrl...pvprrpspladlaal..............ralrrllrq 69 
                                       ++r+L +rGh+Vtv  ++ a +  ++e +++    +   p+p+++ ++  ++++              r l r+l  
  gi|386002399|ref|YP_005920698.1|  22 IVRELLDRGHQVTVASSGNALELLRREFPQCNFLTFedyPAPYSSTRFFLPKFTayiplmmkalvderRNLCRIL-- 96 
                                       689*******************99999999998866433799998767776666556666666677767777777.. PP

                   Glyco_trans_4_4  70 rrerpdvvha 79 
                                        +  +d +++
  gi|386002399|ref|YP_005920698.1|  97 SEGSYDMIIS 106
                                       7777777765 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 ?   10.7   0.0   0.00011       0.4       5      51 ..       6      58 ..       4     109 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                   Glyco_trans_4_2  5 lanlssv..h...tlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlk 51
                                      ++ l+++  h   ++ +++eL +rg++V+v+++++     + e +++++  ++
  gi|386002399|ref|YP_005920698.1|  6 VSPLNWGlgHasrDIPIVRELLDRGHQVTVASSGNALeLLRREFPQCNFLTFE 58
                                      56666653342223558****************77754445555566666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2144.93
//
Query:       gi|386002400|ref|YP_005920699.1|  [L=264]
Description: Methyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-24   85.4   0.0    1.1e-23   83.8   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    9.4e-23   80.7   0.0    1.6e-22   80.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.5e-22   79.3   0.0    3.4e-22   78.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.9e-18   66.4   0.0    4.4e-18   65.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.4e-15   57.6   0.0    2.1e-15   57.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.6e-14   52.3   0.0    6.5e-14   51.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.1e-08   32.7   0.0    8.5e-08   32.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    7.3e-08   32.1   0.0    1.1e-07   31.5   0.0    1.2  1  MTS              Methyltransferase small domain
    5.1e-07   29.3   0.0    7.4e-07   28.7   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    2.9e-06   26.9   0.0      5e-06   26.1   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
    4.7e-06   26.0   0.0    7.2e-06   25.4   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    8.3e-05   21.8   0.0    0.00011   21.3   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00023   20.4   0.0    0.00034   19.8   0.0    1.2  1  DREV             DREV methyltransferase
    0.00035   20.3   0.0    0.00047   19.8   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0057   16.7   0.0     0.0087   16.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0059   15.7   0.0      0.017   14.3   0.0    1.6  2  Fibrillarin      Fibrillarin
     0.0077   15.7   0.0      0.011   15.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.015   14.8   0.0    1.1  1  TehB             Tellurite resistance protein TehB
       0.03   13.9   0.0      0.055   13.1   0.0    1.5  1  MetW             Methionine biosynthesis protein MetW
      0.073   12.8   0.0        0.3   10.7   0.0    1.8  2  N6_N4_Mtase      DNA methylase
       0.15   11.8   0.0        1.4    8.7   0.0    2.0  2  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   1.2e-26   1.1e-23       1      97 []      35     129 ..      35     129 .. 0.96
   2 ?   -1.6   0.0       5.4   4.6e+03      21      55 ..     158     197 ..     137     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.2e-26
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vLd+GcG Gr+t+ +a+ +++++v+g+D s em++ are++  +g  n++f+ gda++l+fe+ +fDlvvs+ alh+
  gi|386002400|ref|YP_005920699.1|  35 VLDIGCGDGRITASIADLVPEGSVLGIDSSREMVRFAREKFPLQGHpNLSFQPGDARTLDFEE-EFDLVVSFAALHW 110
                                       9******************99********************998889**************97.9******877**9 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +   d++ +l+ i+r+LkpgG
  gi|386002400|ref|YP_005920699.1| 111 VG--DHRPVLRGIRRALKPGG 129
                                       88..7889************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                                       SSEEEEEESSHHHH..HHHHHHHHHTTT...TEEEEESBC CS
                   Methyltransf_25  21 kakvtgvDiseeml..eaareraeeegl...nvefvqgda 55 
                                       + ++ g+D+  ++   e+ r  +ee+gl   +ve++q+d+
  gi|386002400|ref|YP_005920699.1| 158 RRSFEGFDFRYGFFgaEEYRIWIEESGLvprRVELIQKDM 197
                                       4555555555555433445555566666666777777766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   1.8e-25   1.6e-22       1      95 [.      36     132 ..      36     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.8e-25
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+GcG Gr+++ +a+ +  ++v+g+D s em++ a+ek + +g+ +++f+ +da++l fe+  fDlvvs+ +lh+v
  gi|386002400|ref|YP_005920699.1|  36 LDIGCGDGRITASIADLVpeGSVLGIDSSREMVRFAREKFPLQGHpNLSFQPGDARTLDFEE-EFDLVVSFAALHWV 111
                                       8**************9999*****************************************99.9************* PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                        d++ +l+ i+R LkpgG+ +
  gi|386002400|ref|YP_005920699.1| 112 GDHRPVLRGIRRALKPGGRTF 132
                                       ******************976 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   3.9e-25   3.4e-22       2     110 ..      30     134 ..      29     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 3.9e-25
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       + + rvlD+GCG G++t  +a  l p++ v GiD s e++++Are+   +g  n++F+ gd+ +l+  +e e fDl+
  gi|386002400|ref|YP_005920699.1|  30 SGDERVLDIGCGDGRITASIA-DLVPEGSVLGIDSSREMVRFAREKFPLQGHPNLSFQPGDARTLD--FE-EEFDLV 102
                                       57899****************.77899***************************************..99.9***** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggillie 110
                                       +s+++l+ + d   +l++i r+lkpgg+  ++
  gi|386002400|ref|YP_005920699.1| 103 VSFAALHWVGDHRPVLRGIRRALKPGGRTFLQ 134
                                       ***************************97665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   5.1e-21   4.4e-18       1      98 [.      36     130 ..      36     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 5.1e-21
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+iGcG+G++++ +++  p+ +++g+D s++++  a+ek+  ++     n+ ++  d+  ld ++ fDlvv++ +lh
  gi|386002400|ref|YP_005920699.1|  36 LDIGCGDGRITASIADLVPEGSVLGIDSSREMVRFAREKFPLQGH---PNLSFQPGDARTLDFEEEFDLVVSFAALH 109
                                       8********************************999999998885...78999999999999999************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       ++ d r vl+ ir++LkpgGr
  gi|386002400|ref|YP_005920699.1| 110 WVGDHRPVLRGIRRALKPGGR 130
                                       ********************7 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   2.4e-18   2.1e-15      20     160 ..      29     185 ..       8     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.4e-18
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqg.... 81 
                                          + rvLdiGcG+G+ + ++++ +   sv g+D s+e+v  a+         +     +++          +    
  gi|386002400|ref|YP_005920699.1|  29 ISGDERVLDIGCGDGRITASIADLVPegSVLGIDSSREMVRFARekfplqghpN---LSFQPG---------Dartl 93 
                                       34567**********8888888887779*************9976654442221...222222.........23444 PP

                   Methyltransf_23  82 ....kfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi.........sf 145
                                            fdl+v++  l++v d+  +lr i++ lkpgG+ +l+  ++  +++ l+   +++++++r +          f
  gi|386002400|ref|YP_005920699.1|  94 dfeeEFDLVVSFAALHWVGDHRPVLRGIRRALKPGGRTFLQFGGRGNAALPLAIADEMIAEDSRRRsfegfdfryGF 170
                                       44559***********************************9977666555555555555555533312222233467 PP

                   Methyltransf_23 146 fsarslkelleeaGl 160
                                       f a++++ + ee+Gl
  gi|386002400|ref|YP_005920699.1| 171 FGAEEYRIWIEESGL 185
                                       777777777777776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   7.6e-17   6.5e-14      31     149 ..      15     131 ..      11     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 7.6e-17
                                       THHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--T CS
                   Ubie_methyltran  31 ihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqana 107
                                         rlW + +++       ++vlD+ +G g ++++++d v  +g v ++D + +m++ +++k   +g  n+ f  ++a
  gi|386002400|ref|YP_005920699.1|  15 AQRLWAEELIRKIEISGDERVLDIGCGDGRITASIADLV-PEGSVLGIDSSREMVRFAREKFPLQGHPNLSFQPGDA 90 
                                       5689999888877888889******************99.5799********************************* PP

                                       TT-TTS-T-EEEEEEES.-GGG-S-HHHHHHHHHHHEEEEEEE CS
                   Ubie_methyltran 108 eeLpfeddsfDvvtvsf.GlrnvtDklkaLkeayrvlkpGGrl 149
                                         L+fe+  fD+v vsf  l  v D+  +L+ ++r lkpGGr 
  gi|386002400|ref|YP_005920699.1|  91 RTLDFEE-EFDLV-VSFaALHWVGDHRPVLRGIRRALKPGGRT 131
                                       *****97.59987.66636999*******************96 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   9.9e-11   8.5e-08      55     135 ..      12      92 ..       6     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 9.9e-11
                                       EE--HHHHHH.HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEE CS
                              PCMT  55 tiSaphmval.alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvv 130
                                        +Sa  + a  ++  +e++  +rvL++G+G G  ta +a lv e g v++i+ ++e+v+ a+++   ++  n++++ 
  gi|386002400|ref|YP_005920699.1|  12 SSSAQRLWAEeLIRKIEISGDERVLDIGCGDGRITASIADLVPE-GSVLGIDSSREMVRFAREKFPLQGHPNLSFQP 87 
                                       566666666414566779999*********************65.66****************************** PP

                                       S-GGG CS
                              PCMT 131 gDGrk 135
                                       gD r+
  gi|386002400|ref|YP_005920699.1|  88 GDART 92 
                                       **874 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.3e-10   1.1e-07      23     106 ..      23     107 ..      15     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.3e-10
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-E CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkf 98 
                                       L+++++ + +++vlD+GcG G ++a++a+  pe +v  +d + + +++a+e +  +++  +++   d+     e++f
  gi|386002400|ref|YP_005920699.1|  23 LIRKIEISGDERVLDIGCGDGRITASIADLVPEGSVLGIDSSREMVRFAREKFPLQGHPnLSFQPGDARTLDFEEEF 99 
                                       555666667789******************************************9999889******9998888*** PP

                                       EEEEE--- CS
                               MTS  99 dlivsNPP 106
                                       dl+vs   
  gi|386002400|ref|YP_005920699.1| 100 DLVVSFAA 107
                                       ***98555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   8.7e-10   7.4e-07      44     163 ..      13     132 ..       5     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.7e-10
                                       HHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS.-EEEEE CS
                              CMAS  44 eeAqlaKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldler.kvevkl 118
                                        +Aq+   + +++k+e+   +++LdiGcG G ++   ++   + +v+g+  S+e  + a++++  ++  + + +   
  gi|386002400|ref|YP_005920699.1|  13 SSAQRLWAEELIRKIEISGDERVLDIGCGDGRITASIADLVpEGSVLGIDSSREMVRFAREKFPLQGHPNlSFQPGD 89 
                                       579999999************************999888753789******************99997652345555 PP

                                       S-GGG-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEE CS
                              CMAS 119 ldyedldekvdrvvsvgafehvgkenydtffkklkkllkedGlll 163
                                       +   d++e++d vvs+ a+  vg ++     + + ++lk++G+  
  gi|386002400|ref|YP_005920699.1|  90 ARTLDFEEEFDLVVSFAALHWVGDHR--PVLRGIRRALKPGGRTF 132
                                       56679999**************9865..45666777777777655 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   5.8e-09     5e-06       5      63 ..      35      92 ..      32     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.8e-09
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63
                                      vl+iGcG G+++  +A   P+ ++lGi+ ++++v+ + +k   ++  Nl    gda ++
  gi|386002400|ref|YP_005920699.1| 35 VLDIGCGDGRITASIADLVPEGSVLGIDSSREMVRFAREKFPLQGHPNLSFQPGDA-RT 92
                                      89*****************************************************9.44 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   8.5e-09   7.2e-06      44     162 ..      13     131 ..       7     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.5e-09
                                       HTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEES- CS
                    Methyltransf_2  44 qessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvgGd 119
                                       ++ ++l a++++++++++g ++++D+G G G + + i+ + P+ +v+  D + e v+ A+e++  + +++++f+ Gd
  gi|386002400|ref|YP_005920699.1|  13 SSAQRLWAEELIRKIEISGDERVLDIGCGDGRITASIADLVPEGSVLGIDSSrEMVRFAREKFPLQGHPNLSFQPGD 89 
                                       577899********************************************86379********************** PP

                                       TTTS---.--SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EE CS
                    Methyltransf_2 120 ffkdslP.eaDaillkrvlhDwsdekcvklLkrvkkalpagGkv 162
                                        +      e D+++    lh   d+  + +L+ +++al++gG+ 
  gi|386002400|ref|YP_005920699.1|  90 ARTLDFEeEFDLVVSFAALHWVGDH--RPVLRGIRRALKPGGRT 131
                                       **88887688999999999954444..6789***********86 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.3e-07   0.00011      19      93 ..      20      98 ..       8     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHH CS
                            RrnaAD 19 ineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpee 93
                                      ++e ++k++++ +  vl+ig G G  T+++a+ +   +v  + + ++++ + ++k+    +++l     D+ + ++ ee
  gi|386002400|ref|YP_005920699.1| 20 AEELIRKIEISGDERVLDIGCGDGRITASIADLVpeGSVLGIDSSREMVRFAREKFPlqGHPNLSFQPGDARTLDFEEE 98
                                      67889*****************************7666666777789********988899999999999999998875 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     4e-07   0.00034      94     186 ..      31     133 ..      14     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4e-07
                              DREV  94 edkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkkynvlsale..lq.....etdv..kldlilcln 159
                                        d+++ld+G GdG it  +a+ + e  v   + s +m  r+ + k+ + +  +  +q       d+  ++dl++++ 
  gi|386002400|ref|YP_005920699.1|  31 GDERVLDIGCGDGRITASIADLVPEgsVLGIDSSREMV-RFAREKFPLQGHPNlsFQpgdarTLDFeeEFDLVVSFA 106
                                       5899*******************999999999999995.5555566555443322331111133443379******* PP

                              DREV 160 lldrcfdplklledirsalepngrviv 186
                                        l    d   +l+ ir al+p gr  +
  gi|386002400|ref|YP_005920699.1| 107 ALHWVGDHRPVLRGIRRALKPGGRTFL 133
                                       *********************999765 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.6e-07   0.00047      46     140 ..      34     129 ..       6     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.6e-07
                              NodS  46 dalevGcaaGalterlapyckrltv..vdvveeaiararer..vkesshiswivsdvqqfstdekfdlivvaevlyy 118
                                        +l++Gc  G +t  +a +    +v  +d   e +  are+  ++  +++s+   d + ++ +e+fdl+v    l++
  gi|386002400|ref|YP_005920699.1|  34 RVLDIGCGDGRITASIADLVPEGSVlgIDSSREMVRFAREKfpLQGHPNLSFQPGDARTLDFEEEFDLVVSFAALHW 110
                                       58***************99887666336777888877777633689999**************************** PP

                              NodS 119 iedvaelraavrnlvsllapdg 140
                                       ++d       +r + + l+p+g
  gi|386002400|ref|YP_005920699.1| 111 VGDHRP---VLRGIRRALKPGG 129
                                       *99754...4555555555555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-05    0.0087      17      69 ..      24      73 ..      17      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                   Methyltransf_32 17 lkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaek 69
                                      +++  + sg+++v+D+G+G g  +  +a+      + +v+gid+++e+v+ a++
  gi|386002400|ref|YP_005920699.1| 24 IRK-IEISGDERVLDIGCGDGRITASIAD---LvPEGSVLGIDSSREMVRFARE 73
                                      455.4667899******************...5489**********99987765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.9e-05     0.017      63     109 ..      24      69 ..       3      75 .. 0.87
   2 ?   -2.1   0.0       1.9   1.6e+03      41      49 ..     172     180 ..     160     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHH CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlr 109
                                       ++++ i+ +++vL +G + G+  + ++D+v  eg v +++ s  ++r
  gi|386002400|ref|YP_005920699.1|  24 IRKIEISGDERVLDIGCGDGRITASIADLVP-EGSVLGIDSSREMVR 69 
                                       78899*************************9.********9998887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                       TTEEEEEE- CS
                       Fibrillarin  41 eeeEyRvWn 49 
                                       + eEyR+W 
  gi|386002400|ref|YP_005920699.1| 172 GAEEYRIWI 180
                                       568*****5 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.011     160     232 ..      30     104 ..      19     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                              PrmA 160 kegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk...eekadviv 231
                                        ++e+vlD+G+G G i a  a ++   +v+++D     v+ a+e + l +  + ++   +++++ +   ee++d++v
  gi|386002400|ref|YP_005920699.1|  30 SGDERVLDIGCGDGrITASIADLVPEGSVLGIDSSREMVRFAREKFPLQGHPNlSF---QPGDARTldfEEEFDLVV 103
                                       5789**********44444555667789******************9987776455...455555334678999998 PP

                              PrmA 232 a 232
                                       +
  gi|386002400|ref|YP_005920699.1| 104 S 104
                                       5 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.7e-05     0.015      20     128 ..      21     129 ..       2     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                       HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHT..T-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S CS
                              TehB  20 sevveavkivkpgkvldlgcgqgrnslylsll..gydvtawdknensiafleeikekenlknistalydineaklde 94 
                                        e++  ++i    +vld+gcg+gr +  ++ l     v  +d   + + f +e    +   n+s +  d  +++++e
  gi|386002400|ref|YP_005920699.1|  21 EELIRKIEISGDERVLDIGCGDGRITASIADLvpEGSVLGIDSSREMVRFAREKFPLQGHPNLSFQPGDARTLDFEE 97 
                                       4677888888899***********88877765124568999*********999999999999*************** PP

                                       -EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEE CS
                              TehB  95 rydfilstvvlmfleaeripsiienmqectkvgg 128
                                       ++d+++s   l ++  +r   +++ +++  k+gg
  gi|386002400|ref|YP_005920699.1|  98 EFDLVVSFAALHWVGDHR--PVLRGIRRALKPGG 129
                                       *******99888876654..35555666666665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.4e-05     0.055      11      54 ..      29      73 ..      21     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                              MetW 11 ikpgsrvldlGcGdGellellkeek.qvdgrGleldeegvaecva 54
                                      i    rvld+GcGdG +   +++   + +  G++ ++e v  + +
  gi|386002400|ref|YP_005920699.1| 29 ISGDERVLDIGCGDGRITASIADLVpEGSVLGIDSSREMVRFARE 73
                                      56678***********99888774313445677777777765554 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.91   7.8e+02     182     229 ..      21      71 ..      17      73 .. 0.66
   2 ?   10.7   0.0   0.00036       0.3      30      71 ..     109     150 ..      91     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.91
                                       HHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-E..EEEEESSHHHHHHH CS
                       N6_N4_Mtase 182 erlIklstkk.gdivlDpFaGSGtTavaakelgrk..fiGieieeeyvela 229
                                       e+lI+      ++ vlD  +G G + +  + l  +   +Gi+ ++e v+ a
  gi|386002400|ref|YP_005920699.1|  21 EELIRKIEISgDERVLDIGCGDGRITASIADLVPEgsVLGIDSSREMVRFA 71 
                                       6677666666255799*99***98655555543333378899998888755 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHH CS
                       N6_N4_Mtase  30 eyleflekvlkevrrvLkddgsifiniddseikkelkalade 71 
                                        ++  +++vl+ +rr Lk++g +f++++ +  +   +a+ade
  gi|386002400|ref|YP_005920699.1| 109 HWVGDHRPVLRGIRRALKPGGRTFLQFGGRGNAALPLAIADE 150
                                       699999***********************9988744555554 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0016       1.4      62      91 ..      22      50 ..      17      65 .. 0.79
   2 ?    0.7   0.0      0.46   3.9e+02     124     154 ..     100     131 ..      80     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                                      HHHHHHCTS-TTS-EEEES-TT-HHHHH-- CS
                    Methyltransf_8 62 viirklkkkkdnlvvadlGcGeakiaeavr 91
                                      ++irk++   ++  v d+GcG+ +i+ ++ 
  gi|386002400|ref|YP_005920699.1| 22 ELIRKIEIS-GDERVLDIGCGDGRITASIA 50
                                      566666654.455689*********98776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.46
                                       EEEEEES--.-SS-HHHHHHHHHHHEEEEEEE CS
                    Methyltransf_8 124 dvavfclsl.mgtnladflkeanrvlkvGGll 154
                                       d++v   +l  + + +  l+ ++r lk+GG  
  gi|386002400|ref|YP_005920699.1| 100 DLVVSFAALhWVGDHRPVLRGIRRALKPGGRT 131
                                       5555444441467888999**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1483.37
//
Query:       gi|386002401|ref|YP_005920700.1|  [L=203]
Description: DNA ligase D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-38  129.9   0.0    5.6e-38  129.4   0.0    1.2  1  LigD_N    DNA polymerase Ligase (LigD)


Domain annotation for each model (and alignments):
>> LigD_N  DNA polymerase Ligase (LigD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   0.0   3.1e-42   5.6e-38       1     104 [.      42     152 ..      42     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 3.1e-42
                                       EEEESSSEEEEEEEEETTEEEEEEETT---SSTTSEEEEEEEEEE-GGGGGEEEEE-TTSTT-EEEEEEEEEEEEE. CS
                            LigD_N   1 qeHdaprlHYDlrLeidevlsswavpkglpedpnskrlAvetedhpleyadfegliekgeygaGsvliwDtGtyev. 76 
                                       q+H+a+rlHYDlrLe+ +vl+swa+pkg++ d+++krlAv tedhpl+y+dfeg i++geygaGsv++wD Gtye+ 
  gi|386002401|ref|YP_005920700.1|  42 QKHRAKRLHYDLRLEVGGVLKSWAIPKGPSLDTKTKRLAVPTEDHPLDYIDFEGRIPEGEYGAGSVIVWDIGTYENt 118
                                       89*************************************************************************** PP

                                       ........-HHHHHHHTEEEEEEECSSSEEEEEE CS
                            LigD_N  77 ......eeklaealkkrkiklrLhGeklkgkyvl 104
                                                +aeal++++ ++ L+G+kl g y+l
  gi|386002401|ref|YP_005920700.1| 119 tradgaAVPIAEALERGHATFILSGKKLLGGYAL 152
                                       ***9998899**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 1136.41
//
Query:       gi|386002402|ref|YP_005920701.1|  [L=1348]
Description: Tetratricopeptide repeat family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.9e-213  681.1 115.6    6.9e-12   44.7   0.4   24.9 25  TPR_1            Tetratricopeptide repeat
   3.2e-174  564.4 142.1    1.9e-14   53.0   0.9   23.8 24  TPR_11           TPR repeat
   1.2e-167  530.9 109.6    1.5e-09   37.2   0.9   24.8 25  TPR_2            Tetratricopeptide repeat
   7.9e-139  440.6  97.3    1.5e-07   31.1   0.3   25.1 25  TPR_8            Tetratricopeptide repeat
   2.2e-131  428.2  88.9    1.1e-13   51.5   1.9   16.3 17  TPR_16           Tetratricopeptide repeat
   4.2e-122  390.1  88.5      6e-07   29.4   1.2   23.6 23  TPR_17           Tetratricopeptide repeat
     5e-100  319.6  61.1    0.00011   22.7   0.1   23.0 23  TPR_14           Tetratricopeptide repeat
    2.9e-74  245.4  75.0    3.9e-10   39.9   1.6   15.9 15  TPR_12           Tetratricopeptide repeat
    2.4e-71  236.2  66.7    5.3e-09   36.5   0.7   13.9 15  TPR_19           Tetratricopeptide repeat
    3.8e-61  203.3  47.1    2.7e-07   30.7   0.1   12.0 12  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    7.4e-60  199.0  33.8    1.3e-05   25.3   0.4   14.6 17  TPR_9            Tetratricopeptide repeat
    2.5e-47  156.4  69.4     0.0027   18.2   0.5   23.4 24  TPR_6            Tetratricopeptide repeat
    2.7e-44  146.0  50.9      0.024   14.6   0.1   20.0 19  TPR_7            Tetratricopeptide repeat
    1.2e-30  104.4  90.7      0.012   15.5   0.6   21.8 22  TPR_10           Tetratricopeptide repeat
    1.7e-29  103.1  27.5    0.00035   19.6   0.9   10.9 11  NARP1            NMDA receptor-regulated protein 1
    4.9e-25   88.7  25.8    0.00015   22.2   0.2   10.3 10  BTAD             Bacterial transcriptional activator domain
      1e-19   71.0  28.5       0.55   10.3   0.1   17.4 17  DUF3856          Domain of Unknown Function (DUF3856)
    5.2e-19   67.9  79.7      0.074   13.1   0.1   19.7 19  TPR_3            Tetratricopeptide repeat
    1.4e-16   60.3  36.2        4.2    7.5   0.5   19.1 18  ANAPC5           Anaphase-promoting complex subunit 5
    2.1e-13   50.1  88.3      0.099   12.7   0.3   19.5 20  MIT              MIT (microtubule interacting and transport) 
      3e-13   49.8  23.2    0.00042   20.3   0.1    9.7  9  SRP_TPR_like     Putative TPR-like repeat
    3.5e-13   49.7  66.1      0.074   12.7   0.7   15.3 15  TPR_21           Tetratricopeptide repeat-like domain
    1.2e-12   47.1   1.4         57    4.3   0.0   13.8 12  PPR              PPR repeat
    1.5e-12   46.9   0.1         36    5.4   0.2   11.6  9  TPR_4            Tetratricopeptide repeat
    3.9e-12   46.5  32.2      0.002   18.1   0.8   10.2  9  Wzy_C_2          Virulence factor membrane-bound polymerase, 
    1.1e-11   44.8   2.2        1.4    8.2   0.0    8.8  9  TPR_MalT         MalT-like TPR region
    3.1e-09   36.8  46.4       0.47   10.2   0.2   13.5 13  DUF5113          Domain of unknown function (DUF5113)
    3.1e-06   27.4  33.4          2    8.8   0.0   11.5 12  TPR_20           Tetratricopeptide repeat
    9.5e-05   22.6  19.6        1.9    8.8   0.1   12.8 14  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    0.00049   20.2  14.1         91    3.4   0.0   11.6 10  PPR_2            PPR repeat family
     0.0042   17.1   6.3         20    5.3   0.0    7.4  7  DUF627           Protein of unknown function (DUF627)
     0.0049   16.9  28.2         15    5.7   0.1   11.8  9  Ribosomal_S16    Ribosomal protein S16
     0.0055   16.7  44.1       0.33   11.1   0.1   13.9 12  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0079   16.0  25.7        1.9    8.2   0.4    9.4 12  TOM20_plant      Plant specific mitochondrial import receptor
  ------ inclusion threshold ------
      0.011   15.1  11.3      0.096   12.1   0.1    5.6  6  Coatomer_E       Coatomer epsilon subunit
      0.017   15.9   4.0         30    5.4   0.0    6.7  7  TetR_C_15        Tetracyclin repressor-like, C-terminal domai
      0.021   13.6   2.5         11    4.6   0.1    4.8  4  DUF3808          Protein of unknown function (DUF3808)
      0.051   13.2   0.1       0.51    9.9   0.0    2.6  2  CBAH             Linear amide C-N hydrolases, choloylglycine 
      0.067   12.3   3.4         10    5.1   0.1    4.5  5  Rota_NSP3        Rotavirus non-structural protein NSP3
      0.072   13.2   1.5         66    3.6   0.0    5.2  5  P2_Phage_GpR     P2 phage tail completion protein R (GpR)
       0.14   11.1   2.6         80    2.1   0.0    4.6  5  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
        0.3   11.2   2.0    1.9e+02    2.1   0.0    6.1  3  MAS20            MAS20 protein import receptor
        0.3   10.6   0.0        0.3   10.6   0.0   12.1 12  SHNi-TPR         SHNi-TPR
       0.43   10.4  16.5         23    4.9   0.0    9.0  9  BPS              BPS (Between PH and SH2)
       0.59    8.8  13.3       0.49    9.1   0.2    4.9  5  PknG_TPR         Protein kinase G tetratricopeptide repeat
        1.1    9.4   9.2    3.6e+02    1.4   0.0    7.8  7  YozE_SAM_like    YozE SAM-like fold
        6.1    6.0  30.4          6    6.0   1.3    8.5  5  FAT              FAT domain


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.8   2.9e-14   1.1e-11       2      34 .]      61      93 ..      60      93 .. 0.95
   2 !   44.7   0.4   1.8e-14   6.9e-12       4      34 .]      97     127 ..      94     127 .. 0.96
   3 !   37.8   5.0   2.6e-12   9.9e-10       1      34 []     128     161 ..     128     161 .. 0.97
   4 !   42.8   1.4     7e-14   2.7e-11       1      34 []     162     195 ..     162     195 .. 0.97
   5 !   30.9   0.0   3.9e-10   1.5e-07       4      34 .]     199     229 ..     197     229 .. 0.96
   6 !   28.7   0.1     2e-09   7.6e-07       3      34 .]     232     263 ..     231     263 .. 0.96
   7 !   38.6   0.2   1.5e-12   5.8e-10       2      34 .]     265     297 ..     264     297 .. 0.96
   8 !   33.3   0.2   6.9e-11   2.6e-08       1      34 []     298     331 ..     298     331 .. 0.98
   9 !   29.0   0.1   1.5e-09   5.9e-07       1      34 []     332     365 ..     332     365 .. 0.96
  10 !   36.4   0.0   7.5e-12   2.9e-09       1      34 []     366     399 ..     366     399 .. 0.97
  11 !   42.7   0.5   7.6e-14   2.9e-11       2      34 .]     401     433 ..     400     433 .. 0.96
  12 !   38.8   0.1   1.3e-12     5e-10       1      34 []     434     467 ..     434     467 .. 0.96
  13 !   35.9   0.1   1.1e-11   4.1e-09       1      34 []     468     501 ..     468     501 .. 0.97
  14 !   35.7   0.0   1.3e-11   4.8e-09       1      34 []     502     535 ..     502     535 .. 0.97
  15 !   13.5   0.1   0.00012     0.048       1      24 [.     536     559 ..     536     560 .. 0.92
  16 !   27.3   0.1   5.4e-09   2.1e-06       3      34 .]     586     617 ..     585     617 .. 0.96
  17 !   37.4   0.2   3.6e-12   1.4e-09       2      34 .]     619     651 ..     618     651 .. 0.95
  18 !   25.4   0.1   2.2e-08   8.3e-06       1      34 []     652     685 ..     652     685 .. 0.97
  19 ?   -0.0   0.2       2.3   8.9e+02      15      28 ..     700     713 ..     696     716 .. 0.78
  20 ?    1.5   0.0      0.79     3e+02      17      34 .]     716     733 ..     712     733 .. 0.91
  21 !   20.3   0.0   9.1e-07   0.00035       3      32 ..     750     779 ..     748     780 .. 0.95
  22 !   19.4   0.0   1.7e-06   0.00065       3      33 ..     784     814 ..     782     815 .. 0.92
  23 !   34.4   0.6   3.1e-11   1.2e-08       1      34 []     816     849 ..     816     849 .. 0.97
  24 !   39.3   0.7   8.6e-13   3.3e-10       2      32 ..     851     881 ..     850     883 .. 0.95
  25 !   10.8   0.2   0.00091      0.35       2      20 ..     885     903 ..     884     906 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.9e-14
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                      + ++n+G+a++ +g+ydeA+++y++A++l+P++
  gi|386002402|ref|YP_005920701.1| 61 DEWNNKGYALYLQGNYDEAIQDYKEAIRLDPEF 93
                                      78*****************************86 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 1.8e-14
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +yn+G+a+ k+gkydeA+++y++A++l+P++
  gi|386002402|ref|YP_005920701.1|  97 WYNKGLAFEKQGKYDEAIKAYNEAIRLDPEY 127
                                       *****************************86 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 2.6e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a+ n+G+a++ +gkydeA+++y++A++l+P++
  gi|386002402|ref|YP_005920701.1| 128 ANAWHNKGYALYLQGKYDEAIKAYNEAIRLYPEY 161
                                       79******************************86 PP

  == domain 4  score: 42.8 bits;  conditional E-value: 7e-14
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++ +G+a++++g+ydeA+++y++A++l+P++
  gi|386002402|ref|YP_005920701.1| 162 ANAWNSKGYALYSQGNYDEAIKAYNEAIRLDPEF 195
                                       79******************************86 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 3.9e-10
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + n+G ++f++gky+ A+ +y++A++lnP++
  gi|386002402|ref|YP_005920701.1| 199 WRNKGDTLFSQGKYELAIYAYDEAIRLNPED 229
                                       89***************************86 PP

  == domain 6  score: 28.7 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++ n+G+a+++lgkydeA+ + ++A++l+P+n
  gi|386002402|ref|YP_005920701.1| 232 SWINKGAALYRLGKYDEAIRASNEAIRLDPEN 263
                                       79****************************97 PP

  == domain 7  score: 38.6 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+ n+G+a+ ++gkydeA+++y++A++l P++
  gi|386002402|ref|YP_005920701.1| 265 YAWHNKGVALNSQGKYDEAIQAYDEAIRLSPEY 297
                                       79*****************************86 PP

  == domain 8  score: 33.3 bits;  conditional E-value: 6.9e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++++G a++++gkydeA+++ ++A++l+P+n
  gi|386002402|ref|YP_005920701.1| 298 ADAWNRKGEALLHQGKYDEAIQASNEAISLDPEN 331
                                       89******************************97 PP

  == domain 9  score: 29.0 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+ ++ +G+a+++ gk deA+++y++A++l P++
  gi|386002402|ref|YP_005920701.1| 332 ANGWNIKGVALYNRGKSDEAIKAYDEAIRLSPEY 365
                                       679*****************************86 PP

  == domain 10  score: 36.4 bits;  conditional E-value: 7.5e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++n+G+ + ++gkydeA++ +++ ++l+P++
  gi|386002402|ref|YP_005920701.1| 366 ADAWNNKGLSLKSQGKYDEAIQTFNETIRLDPEH 399
                                       89******************************86 PP

  == domain 11  score: 42.7 bits;  conditional E-value: 7.6e-14
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+yn+G+++ ++gkydeA++++++A++lnP++
  gi|386002402|ref|YP_005920701.1| 401 AAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEY 433
                                       69*****************************86 PP

  == domain 12  score: 38.8 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++a+y +Gna+ ++ +ydeA+++y+++++lnP++
  gi|386002402|ref|YP_005920701.1| 434 VDAWYSKGNALDSQSRYDEAIQAYDEVIKLNPEY 467
                                       58******************************86 PP

  == domain 13  score: 35.9 bits;  conditional E-value: 1.1e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++ +G a+ ++g+y+eA++++++A++ nP++
  gi|386002402|ref|YP_005920701.1| 468 ADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPEY 501
                                       89******************************86 PP

  == domain 14  score: 35.7 bits;  conditional E-value: 1.3e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++n+G+a+ +l ky+eA++++++A +lnP++
  gi|386002402|ref|YP_005920701.1| 502 ADAWNNKGVALVSLDKYEEAIQAFDEATRLNPED 535
                                       89******************************86 PP

  == domain 15  score: 13.5 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyy 24 
                                       a+a+  +G+a+++lgky+e ++ +
  gi|386002402|ref|YP_005920701.1| 536 ADAWLKKGVAFYHLGKYKETIQVC 559
                                       89*****************99866 PP

  == domain 16  score: 27.3 bits;  conditional E-value: 5.4e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       al  +G+a+  l ky++A+++y++A++lnP++
  gi|386002402|ref|YP_005920701.1| 586 ALMLKGLALETLDKYEDAVQAYDEAISLNPDD 617
                                       7899**************************96 PP

  == domain 17  score: 37.4 bits;  conditional E-value: 3.6e-12
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+ n+G+a+++lgkydeA+++y+++L+lnP++
  gi|386002402|ref|YP_005920701.1| 619 AAWENRGAALYSLGKYDEAVQAYDEVLRLNPED 651
                                       69*****************************86 PP

  == domain 18  score: 25.4 bits;  conditional E-value: 2.2e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+a++ +G+a+++l++++e +++ ++A++lnPn+
  gi|386002402|ref|YP_005920701.1| 652 ANAWKKKGYALHSLEEHEESVKALDEAIRLNPND 685
                                       79******************************97 PP

  == domain 19  score: -0.0 bits;  conditional E-value: 2.3
                                       T-HHHHHHHHHHHH CS
                             TPR_1  15 gkydeAleyyekAL 28 
                                       +kydeA+ + e+A+
  gi|386002402|ref|YP_005920701.1| 700 EKYDEAINASEEAI 713
                                       69****98866666 PP

  == domain 20  score: 1.5 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHHSTTH CS
                             TPR_1  17 ydeAleyyekALelnPnn 34 
                                       y+e +  ye+ ++lnP+n
  gi|386002402|ref|YP_005920701.1| 716 YNETITTYEEIVSLNPEN 733
                                       8999999*********97 PP

  == domain 21  score: 20.3 bits;  conditional E-value: 9.1e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                        +  +G ++ ++ +y+eA +++++A++lnP
  gi|386002402|ref|YP_005920701.1| 750 GWALKGIILGEQHEYNEAMQAFNEAVSLNP 779
                                       6999*************************9 PP

  == domain 22  score: 19.4 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++  +G  +  +gky eA+e+ + A++lnP+
  gi|386002402|ref|YP_005920701.1| 784 IWSFKGKYLNDQGKYYEAIEAIDMAISLNPE 814
                                       58889999**********************7 PP

  == domain 23  score: 34.4 bits;  conditional E-value: 3.1e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a++ +G+a++ +gk++eA+ +y++A++lnP++
  gi|386002402|ref|YP_005920701.1| 816 ALAWNYKGAALRGQGKHEEAILAYDEAIRLNPDD 849
                                       68******************************96 PP

  == domain 24  score: 39.3 bits;  conditional E-value: 8.6e-13
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +a++n+G+a++++g+y eA+++y++A+ ln 
  gi|386002402|ref|YP_005920701.1| 851 DAWNNKGLALYSQGNYSEAIQAYDRAIDLNS 881
                                       79***************************96 PP

  == domain 25  score: 10.8 bits;  conditional E-value: 0.00091
                                       HHHHHHHHHHHHTT-HHHH CS
                             TPR_1   2 kalynlGnayfklgkydeA 20 
                                       +a+yn+G a+  l+++ +A
  gi|386002402|ref|YP_005920701.1| 885 QAWYNKGDALDALKNFTQA 903
                                       79***************99 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.9   5.1e-17   1.9e-14       1      42 []      67     108 ..      67     108 .. 0.99
   2 !   45.2   5.0   1.4e-14   5.5e-12       6      42 .]     106     142 ..     106     142 .. 0.98
   3 !   40.7   8.8   3.6e-13   1.4e-10       1      42 []     135     176 ..     135     176 .. 0.99
   4 !   39.7   0.3   7.4e-13   2.8e-10       1      37 [.     169     205 ..     169     206 .. 0.95
   5 !   40.7   0.8   3.5e-13   1.3e-10       1      42 []     203     244 ..     203     244 .. 0.99
   6 !   33.8   0.7   5.2e-11     2e-08       1      42 []     237     278 ..     237     278 .. 0.95
   7 !   42.4   1.1   1.1e-13   4.2e-11       3      42 .]     273     312 ..     271     312 .. 0.95
   8 !   29.5   1.1   1.1e-09   4.3e-07       1      42 []     305     346 ..     305     346 .. 0.94
   9 !   35.0   0.7   2.1e-11   8.1e-09       3      37 ..     341     375 ..     339     377 .. 0.93
  10 !   32.1   0.0   1.8e-10   6.7e-08       1      42 []     373     414 ..     373     414 .. 0.94
  11 !   36.9   0.6   5.6e-12   2.1e-09       2      38 ..     408     444 ..     407     447 .. 0.91
  12 !   31.8   1.4   2.2e-10   8.5e-08       1      38 [.     441     478 ..     441     479 .. 0.94
  13 !   35.2   0.2   1.9e-11   7.1e-09       1      39 [.     475     513 ..     475     516 .. 0.94
  14 !   36.0   0.1   1.1e-11   4.1e-09       3      42 .]     511     550 ..     509     550 .. 0.95
  15 ?    2.0   0.0      0.43   1.7e+02      14      42 .]     563     591 ..     561     591 .. 0.84
  16 !   34.8   0.8   2.6e-11   9.8e-09       9      42 .]     599     632 ..     596     632 .. 0.97
  17 !   36.7   1.5   6.2e-12   2.4e-09       1      40 [.     625     664 ..     625     665 .. 0.95
  18 !   18.0   0.1   4.3e-06    0.0016       1      28 [.     659     686 ..     659     690 .. 0.95
  19 ?    0.6   0.2       1.2   4.5e+02       9      21 ..     701     713 ..     699     715 .. 0.77
  20 ?    0.3   0.1       1.5   5.5e+02      10      29 ..     716     735 ..     715     738 .. 0.88
  21 !    9.2   0.0    0.0024      0.92       7      26 ..     761     780 ..     756     781 .. 0.90
  22 !   17.9   1.2   4.8e-06    0.0018       2      42 .]     790     830 ..     789     830 .. 0.91
  23 !   42.5   1.3   9.8e-14   3.8e-11       1      42 []     823     864 ..     823     864 .. 0.95
  24 !   37.8   2.5   2.8e-12   1.1e-09       1      38 [.     857     894 ..     857     897 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.1e-17
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+y qG+y+eAi++Yk+A++ldP++++ +yn Gla+ kqG
  gi|386002402|ref|YP_005920701.1|  67 GYALYLQGNYDEAIQDYKEAIRLDPEFVWPWYNKGLAFEKQG 108
                                       99***************************************9 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1.4e-14
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +qGky+eAi+aY++A++ldP++a+a++n G+a+y qG
  gi|386002402|ref|YP_005920701.1| 106 KQGKYDEAIKAYNEAIRLDPEYANAWHNKGYALYLQG 142
                                       69*********************************99 PP

  == domain 3  score: 40.7 bits;  conditional E-value: 3.6e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+y qGky+eAi+aY++A++l P++a+a++  G+a+y qG
  gi|386002402|ref|YP_005920701.1| 135 GYALYLQGKYDEAIKAYNEAIRLYPEYANAWNSKGYALYSQG 176
                                       99***************************************9 PP

  == domain 4  score: 39.7 bits;  conditional E-value: 7.4e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G+a+y+qG+y+eAi+aY++A++ldP++ + + n G++
  gi|386002402|ref|YP_005920701.1| 169 GYALYSQGNYDEAIKAYNEAIRLDPEFMWPWRNKGDT 205
                                       99*****************************999975 PP

  == domain 5  score: 40.7 bits;  conditional E-value: 3.5e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       Gd +++qGkye Ai aY +A++l+P++ + + n G+a+y++G
  gi|386002402|ref|YP_005920701.1| 203 GDTLFSQGKYELAIYAYDEAIRLNPEDLNSWINKGAALYRLG 244
                                       99**************************************99 PP

  == domain 6  score: 33.8 bits;  conditional E-value: 5.2e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+y +Gky+eAi a ++A++ldP+n+ a++n G+a+  qG
  gi|386002402|ref|YP_005920701.1| 237 GAALYRLGKYDEAIRASNEAIRLDPENVYAWHNKGVALNSQG 278
                                       6799*********************************98887 PP

  == domain 7  score: 42.4 bits;  conditional E-value: 1.1e-13
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+ +qGky+eAi+aY +A++l+P++a+a++  G+a++ qG
  gi|386002402|ref|YP_005920701.1| 273 ALNSQGKYDEAIQAYDEAIRLSPEYADAWNRKGEALLHQG 312
                                       7899********************************9988 PP

  == domain 8  score: 29.5 bits;  conditional E-value: 1.1e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+  qGky+eAi+a ++A+ ldP+na+ ++  G+a+y+ G
  gi|386002402|ref|YP_005920701.1| 305 GEALLHQGKYDEAIQASNEAISLDPENANGWNIKGVALYNRG 346
                                       789999********************************9865 PP

  == domain 9  score: 35.0 bits;  conditional E-value: 2.1e-11
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       a+y +Gk +eAi+aY +A++l+P++a+a++n Gl 
  gi|386002402|ref|YP_005920701.1| 341 ALYNRGKSDEAIKAYDEAIRLSPEYADAWNNKGLS 375
                                       89******************************986 PP

  == domain 10  score: 32.1 bits;  conditional E-value: 1.8e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G  + +qGky+eAi+ +++ ++ldP+ + a+yn Gl++ +qG
  gi|386002402|ref|YP_005920701.1| 373 GLSLKSQGKYDEAIQTFNETIRLDPEHVAAWYNKGLTLNNQG 414
                                       667889******************************998887 PP

  == domain 11  score: 36.9 bits;  conditional E-value: 5.6e-12
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                         +  qGky+eAi+a+ +A++l+P++++a+y  G+a+
  gi|386002402|ref|YP_005920701.1| 408 LTLNNQGKYDEAIQAFDEAIRLNPEYVDAWYSKGNAL 444
                                       566779*****************************97 PP

  == domain 12  score: 31.8 bits;  conditional E-value: 2.2e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G+a+ +q +y+eAi+aY + +kl+P++a+a++  G a+
  gi|386002402|ref|YP_005920701.1| 441 GNALDSQSRYDEAIQAYDEVIKLNPEYADAWNSKGTAF 478
                                       899999**************************999775 PP

  == domain 13  score: 35.2 bits;  conditional E-value: 1.9e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       G a+ +qG+y+eAi+a+ +A++ +P++a+a++n G+a+ 
  gi|386002402|ref|YP_005920701.1| 475 GTAFNSQGRYNEAIKAFDEAIRRNPEYADAWNNKGVALV 513
                                       67999*******************************986 PP

  == domain 14  score: 36.0 bits;  conditional E-value: 1.1e-11
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a++++ kyeeAi+a+ +A +l+P++a+a+++ G+a+y +G
  gi|386002402|ref|YP_005920701.1| 511 ALVSLDKYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLG 550
                                       789999*******************************887 PP

  == domain 15  score: 2.0 bits;  conditional E-value: 0.43
                            TPR_11  14 ieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       i+aY   l+ +P++a+a +  G a++ +G
  gi|386002402|ref|YP_005920701.1| 563 IQAYDDDLRWNPEDANARLSKGIALMLKG 591
                                       66666668889*************99877 PP

  == domain 16  score: 34.8 bits;  conditional E-value: 2.6e-11
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       kye+A++aY +A+ l+Pd++ a+ n+G+a+y +G
  gi|386002402|ref|YP_005920701.1| 599 KYEDAVQAYDEAISLNPDDVAAWENRGAALYSLG 632
                                       8******************************998 PP

  == domain 17  score: 36.7 bits;  conditional E-value: 6.2e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       G a+y++Gky+eA++aY + l+l+P++a+a+ + G+a++ 
  gi|386002402|ref|YP_005920701.1| 625 GAALYSLGKYDEAVQAYDEVLRLNPEDANAWKKKGYALHS 664
                                       679**********************************986 PP

  == domain 18  score: 18.0 bits;  conditional E-value: 4.3e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                       G+a++++ + ee+++a+ +A++l+P++a
  gi|386002402|ref|YP_005920701.1| 659 GYALHSLEEHEESVKALDEAIRLNPNDA 686
                                       89************************98 PP

  == domain 19  score: 0.6 bits;  conditional E-value: 1.2
                            TPR_11   9 kyeeAieaYkkAl 21 
                                       ky+eAi+a ++A+
  gi|386002402|ref|YP_005920701.1| 701 KYDEAINASEEAI 713
                                       7999999877777 PP

  == domain 20  score: 0.3 bits;  conditional E-value: 1.5
                            TPR_11  10 yeeAieaYkkAlkldPdnae 29 
                                       y+e i+ Y++ + l+P+n +
  gi|386002402|ref|YP_005920701.1| 716 YNETITTYEEIVSLNPENST 735
                                       8999************9965 PP

  == domain 21  score: 9.2 bits;  conditional E-value: 0.0024
                            TPR_11   7 qGkyeeAieaYkkAlkldPd 26 
                                       q +y+eA++a+++A+ l+P 
  gi|386002402|ref|YP_005920701.1| 761 QHEYNEAMQAFNEAVSLNPA 780
                                       669***************95 PP

  == domain 22  score: 17.9 bits;  conditional E-value: 4.8e-06
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       + + +qGky eAiea   A+ l+P++a a++  G+a+  qG
  gi|386002402|ref|YP_005920701.1| 790 KYLNDQGKYYEAIEAIDMAISLNPESALAWNYKGAALRGQG 830
                                       55789******************************997776 PP

  == domain 23  score: 42.5 bits;  conditional E-value: 9.8e-14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a++ qGk eeAi aY +A++l+Pd+ +a++n Gla+y qG
  gi|386002402|ref|YP_005920701.1| 823 GAALRGQGKHEEAILAYDEAIRLNPDDEDAWNNKGLALYSQG 864
                                       567888***********************************9 PP

  == domain 24  score: 37.8 bits;  conditional E-value: 2.8e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G a+y+qG+y eAi+aY +A++l+++ + a+yn G+a+
  gi|386002402|ref|YP_005920701.1| 857 GLALYSQGNYSEAIQAYDRAIDLNSQLVQAWYNKGDAL 894
                                       899********************************996 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.4   4.5e-12   1.7e-09       2      33 ..      61      92 ..      60      93 .. 0.95
   2 !   35.5   0.6   1.4e-11   5.3e-09       4      34 .]      97     127 ..      95     127 .. 0.96
   3 !   35.3   4.3   1.6e-11     6e-09       1      34 []     128     161 ..     128     161 .. 0.96
   4 !   37.2   0.9   3.9e-12   1.5e-09       1      33 [.     162     194 ..     162     195 .. 0.96
   5 !   25.9   0.0   1.7e-08   6.4e-06       4      34 .]     199     229 ..     198     229 .. 0.97
   6 !   26.5   0.1   1.1e-08     4e-06       3      34 .]     232     263 ..     231     263 .. 0.96
   7 !   26.4   0.2   1.1e-08   4.3e-06       2      33 ..     265     296 ..     264     297 .. 0.95
   8 !   28.0   0.2   3.5e-09   1.3e-06       1      34 []     298     331 ..     298     331 .. 0.97
   9 !   26.2   0.1   1.4e-08   5.2e-06       1      33 [.     332     364 ..     332     365 .. 0.94
  10 !   27.5   0.0   5.3e-09     2e-06       1      34 []     366     399 ..     366     399 .. 0.97
  11 !   29.8   0.3   9.7e-10   3.7e-07       2      34 .]     401     433 ..     400     433 .. 0.95
  12 !   27.3   0.1     6e-09   2.3e-06       2      34 .]     435     467 ..     434     467 .. 0.96
  13 !   21.0   0.1     6e-07   0.00023       1      34 []     468     501 ..     468     501 .. 0.92
  14 !   29.6   0.1   1.1e-09   4.1e-07       1      34 []     502     535 ..     502     535 .. 0.97
  15 ?    6.9   0.0      0.02       7.5       1      19 [.     536     554 ..     536     569 .. 0.89
  16 !   23.8   0.1   7.7e-08   2.9e-05       3      34 .]     586     617 ..     584     617 .. 0.95
  17 !   33.3   0.3   7.3e-11   2.8e-08       2      34 .]     619     651 ..     618     651 .. 0.96
  18 !   20.7   0.2   7.8e-07    0.0003       1      34 []     652     685 ..     652     685 .. 0.96
  19 ?    1.5   0.2       1.1   4.3e+02      13      31 ..     698     716 ..     686     719 .. 0.75
  20 ?   -1.5   0.0       9.7   3.7e+03      23      34 .]     722     733 ..     716     733 .. 0.87
  21 !   16.9   0.0   1.3e-05    0.0049       3      32 ..     750     779 ..     748     780 .. 0.94
  22 !   10.9   0.0    0.0011      0.41       4      33 ..     785     814 ..     782     815 .. 0.85
  23 !   29.4   0.9   1.3e-09   4.8e-07       1      34 []     816     849 ..     816     849 .. 0.97
  24 !   30.9   0.5   4.1e-10   1.6e-07       2      32 ..     851     881 ..     850     883 .. 0.94
  25 ?    7.3   0.1     0.015       5.8       2      20 ..     885     903 ..     884     905 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.5e-12
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                      + ++n G+a+y +g+y+eA++++++A++ldP+
  gi|386002402|ref|YP_005920701.1| 61 DEWNNKGYALYLQGNYDEAIQDYKEAIRLDPE 92
                                      78*****************************7 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 1.4e-11
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +yn Gla +k+g+y+eA++a+++A++ldP++
  gi|386002402|ref|YP_005920701.1|  97 WYNKGLAFEKQGKYDEAIKAYNEAIRLDPEY 127
                                       9****************************85 PP

  == domain 3  score: 35.3 bits;  conditional E-value: 1.6e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a++n G+a+y +g+y+eA++a+++A++l+P++
  gi|386002402|ref|YP_005920701.1| 128 ANAWHNKGYALYLQGKYDEAIKAYNEAIRLYPEY 161
                                       689*****************************85 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 3.9e-12
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++  G+a+y +g+y+eA++a+++A++ldP+
  gi|386002402|ref|YP_005920701.1| 162 ANAWNSKGYALYSQGNYDEAIKAYNEAIRLDPE 194
                                       689*****************************7 PP

  == domain 5  score: 25.9 bits;  conditional E-value: 1.7e-08
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       + n G+ ++ +g+ye A+ a+++A++l+P++
  gi|386002402|ref|YP_005920701.1| 199 WRNKGDTLFSQGKYELAIYAYDEAIRLNPED 229
                                       89***************************86 PP

  == domain 6  score: 26.5 bits;  conditional E-value: 1.1e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        + n G a+y+lg+y+eA++a ++A++ldP+n
  gi|386002402|ref|YP_005920701.1| 232 SWINKGAALYRLGKYDEAIRASNEAIRLDPEN 263
                                       599***************************97 PP

  == domain 7  score: 26.4 bits;  conditional E-value: 1.1e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a++n G a+  +g+y+eA++a+++A++l P+
  gi|386002402|ref|YP_005920701.1| 265 YAWHNKGVALNSQGKYDEAIQAYDEAIRLSPE 296
                                       79*****************************8 PP

  == domain 8  score: 28.0 bits;  conditional E-value: 3.5e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a+++ G+a++++g+y+eA++a ++A++ldP+n
  gi|386002402|ref|YP_005920701.1| 298 ADAWNRKGEALLHQGKYDEAIQASNEAISLDPEN 331
                                       79******************************97 PP

  == domain 9  score: 26.2 bits;  conditional E-value: 1.4e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a +++  G a+y++g+ +eA++a+++A++l P+
  gi|386002402|ref|YP_005920701.1| 332 ANGWNIKGVALYNRGKSDEAIKAYDEAIRLSPE 364
                                       57899***************************8 PP

  == domain 10  score: 27.5 bits;  conditional E-value: 5.3e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++n Gl++  +g+y+eA++ f++ ++ldP++
  gi|386002402|ref|YP_005920701.1| 366 ADAWNNKGLSLKSQGKYDEAIQTFNETIRLDPEH 399
                                       79******************************86 PP

  == domain 11  score: 29.8 bits;  conditional E-value: 9.7e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+yn Gl + ++g+y+eA++af++A++l+P++
  gi|386002402|ref|YP_005920701.1| 401 AAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEY 433
                                       69*****************************85 PP

  == domain 12  score: 27.3 bits;  conditional E-value: 6e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+y  G+a+  + +y+eA++a++++++l+P++
  gi|386002402|ref|YP_005920701.1| 435 DAWYSKGNALDSQSRYDEAIQAYDEVIKLNPEY 467
                                       79*****************************85 PP

  == domain 13  score: 21.0 bits;  conditional E-value: 6e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++  G a   +g+y+eA++af++A++ +P++
  gi|386002402|ref|YP_005920701.1| 468 ADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPEY 501
                                       6899999999999*******************85 PP

  == domain 14  score: 29.6 bits;  conditional E-value: 1.1e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+a++n G a+  l++yeeA++af++A +l+P++
  gi|386002402|ref|YP_005920701.1| 502 ADAWNNKGVALVSLDKYEEAIQAFDEATRLNPED 535
                                       79******************************86 PP

  == domain 15  score: 6.9 bits;  conditional E-value: 0.02
                             TPR_2   1 aealynlGlayyklgdyee 19 
                                       a+a+   G a y+lg+y+e
  gi|386002402|ref|YP_005920701.1| 536 ADAWLKKGVAFYHLGKYKE 554
                                       789**************98 PP

  == domain 16  score: 23.8 bits;  conditional E-value: 7.7e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       al+  Gla++ l++ye+A++a+++A++l+P++
  gi|386002402|ref|YP_005920701.1| 586 ALMLKGLALETLDKYEDAVQAYDEAISLNPDD 617
                                       89999*************************97 PP

  == domain 17  score: 33.3 bits;  conditional E-value: 7.3e-11
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        a+ n+G a+y lg+y+eA++a++++l+l+P++
  gi|386002402|ref|YP_005920701.1| 619 AAWENRGAALYSLGKYDEAVQAYDEVLRLNPED 651
                                       69*****************************86 PP

  == domain 18  score: 20.7 bits;  conditional E-value: 7.8e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+   G+a+  l ++ee ++a+++A++l+Pn+
  gi|386002402|ref|YP_005920701.1| 652 ANAWKKKGYALHSLEEHEESVKALDEAIRLNPND 685
                                       689*****************************97 PP

  == domain 19  score: 1.5 bits;  conditional E-value: 1.1
                             TPR_2  13 klgdyeeAleafekAleld 31 
                                          +y+eA++a e+A++ +
  gi|386002402|ref|YP_005920701.1| 698 IIEKYDEAINASEEAIRAY 716
                                       5578999999999988765 PP

  == domain 20  score: -1.5 bits;  conditional E-value: 9.7
                             TPR_2  23 afekAleldPnn 34 
                                        +e+ ++l+P+n
  gi|386002402|ref|YP_005920701.1| 722 TYEEIVSLNPEN 733
                                       69********97 PP

  == domain 21  score: 16.9 bits;  conditional E-value: 1.3e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       ++   G ++ ++ +y+eA +af++A++l+P
  gi|386002402|ref|YP_005920701.1| 750 GWALKGIILGEQHEYNEAMQAFNEAVSLNP 779
                                       68899************************9 PP

  == domain 22  score: 10.9 bits;  conditional E-value: 0.0011
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +   G+ +  +g+y eA+ea + A++l+P+
  gi|386002402|ref|YP_005920701.1| 785 WSFKGKYLNDQGKYYEAIEAIDMAISLNPE 814
                                       6666777778*******************7 PP

  == domain 23  score: 29.4 bits;  conditional E-value: 1.3e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+++ G a++ +g++eeA+ a+++A++l+P++
  gi|386002402|ref|YP_005920701.1| 816 ALAWNYKGAALRGQGKHEEAILAYDEAIRLNPDD 849
                                       689*****************************97 PP

  == domain 24  score: 30.9 bits;  conditional E-value: 4.1e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +a++n Gla+y +g+y eA++a+++A+ l+ 
  gi|386002402|ref|YP_005920701.1| 851 DAWNNKGLALYSQGNYSEAIQAYDRAIDLNS 881
                                       69***************************96 PP

  == domain 25  score: 7.3 bits;  conditional E-value: 0.015
                             TPR_2   2 ealynlGlayyklgdyeeA 20 
                                       +a+yn G+a+ +l+++ +A
  gi|386002402|ref|YP_005920701.1| 885 QAWYNKGDALDALKNFTQA 903
                                       69**************998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.3   1.7e-08   6.5e-06       4      33 ..      63      92 ..      63      93 .. 0.97
   2 !   31.1   0.3   3.9e-10   1.5e-07       4      33 ..      97     126 ..      96     127 .. 0.97
   3 !   26.6   2.3   1.1e-08   4.1e-06       1      33 [.     128     160 ..     128     161 .. 0.95
   4 !   30.4   0.5   6.6e-10   2.5e-07       1      33 [.     162     194 ..     162     195 .. 0.96
   5 !   16.6   0.0   1.7e-05    0.0066       6      34 .]     201     229 ..     199     229 .. 0.95
   6 !   21.2   0.1   5.9e-07   0.00023       2      34 .]     231     263 ..     230     263 .. 0.95
   7 !   27.1   0.1   7.5e-09   2.8e-06       3      33 ..     266     296 ..     264     297 .. 0.95
   8 !   26.4   0.1   1.2e-08   4.6e-06       1      34 []     298     331 ..     298     331 .. 0.97
   9 !   19.3   0.1   2.3e-06   0.00089       2      33 ..     333     364 ..     332     365 .. 0.93
  10 !   24.7   0.0   4.3e-08   1.7e-05       1      34 []     366     399 ..     366     399 .. 0.97
  11 !   30.6   0.1   5.4e-10   2.1e-07       3      33 ..     402     432 ..     400     433 .. 0.95
  12 !   24.6   0.1   4.7e-08   1.8e-05       2      33 ..     435     466 ..     434     467 .. 0.96
  13 !   22.5   0.0   2.1e-07   8.1e-05       1      33 [.     468     500 ..     468     501 .. 0.96
  14 !   26.5   0.0   1.2e-08   4.4e-06       1      34 []     502     535 ..     502     535 .. 0.96
  15 ?    4.2   0.1      0.16        60       1      23 [.     536     558 ..     536     567 .. 0.89
  16 !   21.2   0.1   5.8e-07   0.00022       3      34 .]     586     617 ..     585     617 .. 0.95
  17 !   21.6   0.1   4.2e-07   0.00016       3      34 .]     620     651 ..     618     651 .. 0.94
  18 !   18.3   0.1   4.9e-06    0.0019       2      34 .]     653     685 ..     652     685 .. 0.92
  19 ?    3.6   0.3      0.24        92      12      31 ..     697     716 ..     686     719 .. 0.79
  20 ?    0.4   0.0       2.7     1e+03      17      34 .]     716     733 ..     714     733 .. 0.86
  21 !   14.0   0.0   0.00011     0.043       4      33 ..     751     780 ..     748     780 .. 0.94
  22 !   10.5   0.1    0.0016       0.6       4      33 ..     785     814 ..     784     815 .. 0.92
  23 !   16.7   0.1   1.6e-05    0.0061       3      34 .]     818     849 ..     816     849 .. 0.91
  24 !   23.3   0.4   1.2e-07   4.6e-05       2      32 ..     851     881 ..     850     883 .. 0.95
  25 !    8.8   0.1    0.0055       2.1       2      20 ..     885     903 ..     884     906 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.7e-08
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpd 33
                                      ++n+g+++  +g+y+eA++ y++a++ldp+
  gi|386002402|ref|YP_005920701.1| 63 WNNKGYALYLQGNYDEAIQDYKEAIRLDPE 92
                                      99***************************7 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.9e-10
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +yn+g++ +k+g+y+eA+++y++a++ldp+
  gi|386002402|ref|YP_005920701.1|  97 WYNKGLAFEKQGKYDEAIKAYNEAIRLDPE 126
                                       9****************************8 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 1.1e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a++n+g+++  +g+y+eA+++y++a++l p+
  gi|386002402|ref|YP_005920701.1| 128 ANAWHNKGYALYLQGKYDEAIKAYNEAIRLYPE 160
                                       679***************************997 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 6.6e-10
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a a++ +g+++ ++g+y+eA+++y++a++ldp+
  gi|386002402|ref|YP_005920701.1| 162 ANAWNSKGYALYSQGNYDEAIKAYNEAIRLDPE 194
                                       679*****************************7 PP

  == domain 5  score: 16.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       n+g++++++g+ye A+ +y +a++l+p++
  gi|386002402|ref|YP_005920701.1| 201 NKGDTLFSQGKYELAIYAYDEAIRLNPED 229
                                       89*************************86 PP

  == domain 6  score: 21.2 bits;  conditional E-value: 5.9e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        ++ n+g ++  lg+y+eA+ + ++a++ldp+n
  gi|386002402|ref|YP_005920701.1| 231 NSWINKGAALYRLGKYDEAIRASNEAIRLDPEN 263
                                       58*****************************86 PP

  == domain 7  score: 27.1 bits;  conditional E-value: 7.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++n+g ++ ++g+y+eA+++y +a++l+p+
  gi|386002402|ref|YP_005920701.1| 266 AWHNKGVALNSQGKYDEAIQAYDEAIRLSPE 296
                                       9*****************************7 PP

  == domain 8  score: 26.4 bits;  conditional E-value: 1.2e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a++++g ++l +g+y+eA+++ ++a++ldp+n
  gi|386002402|ref|YP_005920701.1| 298 ADAWNRKGEALLHQGKYDEAIQASNEAISLDPEN 331
                                       78******************************86 PP

  == domain 9  score: 19.3 bits;  conditional E-value: 2.3e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                         ++ +g ++ + g+ +eA+++y +a++l+p+
  gi|386002402|ref|YP_005920701.1| 333 NGWNIKGVALYNRGKSDEAIKAYDEAIRLSPE 364
                                       57999**************************7 PP

  == domain 10  score: 24.7 bits;  conditional E-value: 4.3e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a++n+g+ ++++g+y+eA++++++ ++ldp++
  gi|386002402|ref|YP_005920701.1| 366 ADAWNNKGLSLKSQGKYDEAIQTFNETIRLDPEH 399
                                       78******************************86 PP

  == domain 11  score: 30.6 bits;  conditional E-value: 5.4e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+yn+g+++ ++g+y+eA++++ +a++l+p+
  gi|386002402|ref|YP_005920701.1| 402 AWYNKGLTLNNQGKYDEAIQAFDEAIRLNPE 432
                                       9*****************************8 PP

  == domain 12  score: 24.6 bits;  conditional E-value: 4.7e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+y +g++++++ +y+eA+++y ++++l+p+
  gi|386002402|ref|YP_005920701.1| 435 DAWYSKGNALDSQSRYDEAIQAYDEVIKLNPE 466
                                       79*****************************8 PP

  == domain 13  score: 22.5 bits;  conditional E-value: 2.1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+a++ +g +  ++g+y+eA++++ +a++ +p+
  gi|386002402|ref|YP_005920701.1| 468 ADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPE 500
                                       78*****************************97 PP

  == domain 14  score: 26.5 bits;  conditional E-value: 1.2e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+a++n+g ++ +l +yeeA++++ +a++l+p++
  gi|386002402|ref|YP_005920701.1| 502 ADAWNNKGVALVSLDKYEEAIQAFDEATRLNPED 535
                                       78******************************85 PP

  == domain 15  score: 4.2 bits;  conditional E-value: 0.16
                                       CCHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkey 23 
                                       a+a++++g +   lg+y+e +++
  gi|386002402|ref|YP_005920701.1| 536 ADAWLKKGVAFYHLGKYKETIQV 558
                                       78****************97776 PP

  == domain 16  score: 21.2 bits;  conditional E-value: 5.8e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++++g+++++l +ye A+++y +a++l+pd+
  gi|386002402|ref|YP_005920701.1| 586 ALMLKGLALETLDKYEDAVQAYDEAISLNPDD 617
                                       6889**************************96 PP

  == domain 17  score: 21.6 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+ n g ++ +lg+y+eA+++y ++l+l+p++
  gi|386002402|ref|YP_005920701.1| 620 AWENRGAALYSLGKYDEAVQAYDEVLRLNPED 651
                                       899***************************86 PP

  == domain 18  score: 18.3 bits;  conditional E-value: 4.9e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        a+ ++g+++++l+++ee+++++ +a++l+p++
  gi|386002402|ref|YP_005920701.1| 653 NAWKKKGYALHSLEEHEESVKALDEAIRLNPND 685
                                       577789*************************96 PP

  == domain 19  score: 3.6 bits;  conditional E-value: 0.24
                                       HHTT-HHHHHHHHHHHHHHH CS
                             TPR_8  12 lklgdyeeAkeyyekaleld 31 
                                       l  ++y+eA+ + e+a+++ 
  gi|386002402|ref|YP_005920701.1| 697 LIIEKYDEAINASEEAIRAY 716
                                       56689***********9875 PP

  == domain 20  score: 0.4 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHH. CS
                             TPR_8  17 yeeAkeyyekaleldpdn 34 
                                       y+e + +ye+ ++l+p+n
  gi|386002402|ref|YP_005920701.1| 716 YNETITTYEEIVSLNPEN 733
                                       5667899*********86 PP

  == domain 21  score: 14.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       + ++g i+ ++ +y+eA++++++a++l+p+
  gi|386002402|ref|YP_005920701.1| 751 WALKGIILGEQHEYNEAMQAFNEAVSLNPA 780
                                       9999************************95 PP

  == domain 22  score: 10.5 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +  +g+ + ++g+y eA+e++  a++l+p+
  gi|386002402|ref|YP_005920701.1| 785 WSFKGKYLNDQGKYYEAIEAIDMAISLNPE 814
                                       6779999*********************97 PP

  == domain 23  score: 16.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++ +g +++ +g++eeA+ +y +a++l+pd+
  gi|386002402|ref|YP_005920701.1| 818 AWNYKGAALRGQGKHEEAILAYDEAIRLNPDD 849
                                       677789999*********************96 PP

  == domain 24  score: 23.3 bits;  conditional E-value: 1.2e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +a++n+g+++ ++g+y eA+++y +a++l+ 
  gi|386002402|ref|YP_005920701.1| 851 DAWNNKGLALYSQGNYSEAIQAYDRAIDLNS 881
                                       69***************************97 PP

  == domain 25  score: 8.8 bits;  conditional E-value: 0.0055
                                       CHHHHHHHHHHHTT-HHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeA 20 
                                       +a+yn+g++++ l+++ +A
  gi|386002402|ref|YP_005920701.1| 885 QAWYNKGDALDALKNFTQA 903
                                       89**************999 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.4e-05      0.02      37      65 ..      63      91 ..      56      92 .. 0.88
   2 !   51.5   1.9   2.9e-16   1.1e-13       1      65 [.      98     159 ..      98     159 .. 0.98
   3 !   51.5   2.8     3e-16   1.1e-13       2      65 ..     133     193 ..     132     194 .. 0.96
   4 !   36.0   0.2   2.1e-11     8e-09       2      66 ..     201     262 ..     200     264 .. 0.92
   5 !   45.4   1.4   2.4e-14     9e-12       9      67 ..     276     331 ..     268     332 .. 0.92
   6 !   43.6   0.0     9e-14   3.4e-11       4      66 ..     339     398 ..     338     400 .. 0.95
   7 !   44.4   0.0     5e-14   1.9e-11      10      65 ..     379     431 ..     377     433 .. 0.96
   8 !   50.2   0.3   7.7e-16   2.9e-13       1      66 [.     404     466 ..     404     470 .. 0.92
   9 !   44.2   0.4   5.8e-14   2.2e-11       1      66 [.     438     500 ..     438     503 .. 0.95
  10 !   41.3   0.6   4.6e-13   1.8e-10       6      60 ..     477     528 ..     472     531 .. 0.92
  11 !   36.0   0.0   2.1e-11     8e-09       4      66 ..     509     568 ..     507     569 .. 0.91
  12 !   37.8   2.7   5.7e-12   2.2e-09       3      60 ..     590     644 ..     588     645 .. 0.94
  13 !   37.0   1.8   1.1e-11     4e-09       4      68 .]     625     686 ..     624     686 .. 0.96
  14 ?   -0.7   0.0       6.4   2.4e+03      12      27 ..     701     716 ..     696     719 .. 0.86
  15 !   11.1   0.0    0.0012      0.48       4      60 ..     755     808 ..     752     809 .. 0.90
  16 !   34.0   0.7   8.7e-11   3.3e-08       5      68 .]     790     850 ..     788     850 .. 0.94
  17 !   36.0   1.3   2.1e-11     8e-09       2      55 ..     855     906 ..     854     907 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.4e-05
                            TPR_16 37 llllgdaalrqgrlaeAaalyraalraap 65
                                      ++++g a++ qg+++eA++ y++a+r +p
  gi|386002402|ref|YP_005920701.1| 63 WNNKGYALYLQGNYDEAIQDYKEAIRLDP 91
                                      88999*******************99998 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 2.9e-16
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++++a+ ++g+yd+A++a+++a+++d   P+ a A+ ++g a++ qg ++eA+ +y++a+r +p
  gi|386002402|ref|YP_005920701.1|  98 YNKGLAFEKQGKYDEAIKAYNEAIRLD---PEYANAWHNKGYALYLQGKYDEAIKAYNEAIRLYP 159
                                       789************************...********************************998 PP

  == domain 3  score: 51.5 bits;  conditional E-value: 3e-16
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++++a++ +g+yd+A++a+++a++++   P+ a A++ +g a++ qg+++eA+ +y++a+r +p
  gi|386002402|ref|YP_005920701.1| 133 NKGYALYLQGKYDEAIKAYNEAIRLY---PEYANAWNSKGYALYSQGNYDEAIKAYNEAIRLDP 193
                                       57899999******************...*******************************9998 PP

  == domain 4  score: 36.0 bits;  conditional E-value: 2.1e-11
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++++ ++ +g+y+ A+ a+++a++++   P++  ++ ++g a++r+g ++eA+ + ++a+r +p 
  gi|386002402|ref|YP_005920701.1| 201 NKGDTLFSQGKYELAIYAYDEAIRLN---PEDLNSWINKGAALYRLGKYDEAIRASNEAIRLDPE 262
                                       57999*********************...************************777777799986 PP

  == domain 5  score: 45.4 bits;  conditional E-value: 2.4e-14
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        +g+yd+A+ a+++a+++    P+ a+A++ +g+a+l+qg ++eA+++ ++a+  +p +
  gi|386002402|ref|YP_005920701.1| 276 SQGKYDEAIQAYDEAIRLS---PEYADAWNRKGEALLHQGKYDEAIQASNEAISLDPEN 331
                                       59*****************...************************9999998888866 PP

  == domain 6  score: 43.6 bits;  conditional E-value: 9e-14
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       + a++++g+ d+A++a+++a+++    P+ a+A++++g+++  qg ++eA++ +++ +r +p 
  gi|386002402|ref|YP_005920701.1| 339 GVALYNRGKSDEAIKAYDEAIRLS---PEYADAWNNKGLSLKSQGKYDEAIQTFNETIRLDPE 398
                                       5689********************...*****************************9999985 PP

  == domain 7  score: 44.4 bits;  conditional E-value: 5e-14
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +g+yd+A+  +++++++d   P++++A++++g+ +  qg ++eA++++++a+r  p
  gi|386002402|ref|YP_005920701.1| 379 QGKYDEAIQTFNETIRLD---PEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIRLNP 431
                                       9*****************...*******************************9988 PP

  == domain 8  score: 50.2 bits;  conditional E-value: 7.7e-16
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++++ + ++g+yd+A+ a+++a++++   P+ ++A++ +g+a+  q+r++eA+++y++ ++  p 
  gi|386002402|ref|YP_005920701.1| 404 YNKGLTLNNQGKYDEAIQAFDEAIRLN---PEYVDAWYSKGNALDSQSRYDEAIQAYDEVIKLNPE 466
                                       566777779******************...*****************************9988875 PP

  == domain 9  score: 44.2 bits;  conditional E-value: 5.8e-14
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       + +++a+  + +yd+A+ a+++++k++   P+ a+A++ +g a+  qgr+ eA+ ++++a+r  p 
  gi|386002402|ref|YP_005920701.1| 438 YSKGNALDSQSRYDEAIQAYDEVIKLN---PEYADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPE 500
                                       67899**********************...*******************************98886 PP

  == domain 10  score: 41.3 bits;  conditional E-value: 4.6e-13
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       a+  +g+y +A++a+++a++r+   P+ a+A++++g+a+  +  ++eA++++++a
  gi|386002402|ref|YP_005920701.1| 477 AFNSQGRYNEAIKAFDEAIRRN---PEYADAWNNKGVALVSLDKYEEAIQAFDEA 528
                                       55579*****************...***************************998 PP

  == domain 11  score: 36.0 bits;  conditional E-value: 2.1e-11
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       + a++ + +y++A+ a+++a++++   P++a+A+l +g+a++++g ++e +++++  ++a+ d
  gi|386002402|ref|YP_005920701.1| 509 GVALVSLDKYEEAIQAFDEATRLN---PEDADAWLKKGVAFYHLGKYKETIQVCNVSIQAYDD 568
                                       66888899****************...**********************99999998888876 PP

  == domain 12  score: 37.8 bits;  conditional E-value: 5.7e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       +++a+  + +y+dA+ a+++a+ ++   Pd+++A+ ++g a++ +g ++eA+++y++ 
  gi|386002402|ref|YP_005920701.1| 590 KGLALETLDKYEDAVQAYDEAISLN---PDDVAAWENRGAALYSLGKYDEAVQAYDEV 644
                                       6788889999***************...**************************9986 PP

  == domain 13  score: 37.0 bits;  conditional E-value: 1.1e-11
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       + a++ +g+yd+A+ a++++l+++   P++a A+  +g a+  + +++e + ++++a+r  p+++
  gi|386002402|ref|YP_005920701.1| 625 GAALYSLGKYDEAVQAYDEVLRLN---PEDANAWKKKGYALHSLEEHEESVKALDEAIRLNPNDA 686
                                       6799********************...***********************************985 PP

  == domain 14  score: -0.7 bits;  conditional E-value: 6.4
                            TPR_16  12 dyddAaaaleaalkrd 27 
                                       +yd+A++a e+a++++
  gi|386002402|ref|YP_005920701.1| 701 KYDEAINASEEAIRAY 716
                                       8999999999999987 PP

  == domain 15  score: 11.1 bits;  conditional E-value: 0.0012
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       + ++ ++ +y +A  a+++a+ ++   P+    + ++g  +  qg + eA+++++ a
  gi|386002402|ref|YP_005920701.1| 755 GIILGEQHEYNEAMQAFNEAVSLN---PAGSFIWSFKGKYLNDQGKYYEAIEAIDMA 808
                                       778899******************...66666*******************999876 PP

  == domain 16  score: 34.0 bits;  conditional E-value: 8.7e-11
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++ ++g+y +A++a + a+ ++   P+ a A++++g a+  qg ++eA+ +y++a+r  pd++
  gi|386002402|ref|YP_005920701.1| 790 KYLNDQGKYYEAIEAIDMAISLN---PESALAWNYKGAALRGQGKHEEAILAYDEAIRLNPDDE 850
                                       56669******************...***********************************985 PP

  == domain 17  score: 36.0 bits;  conditional E-value: 2.1e-11
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.a 55 
                                       ++++a++ +g+y +A+ a+++a++++   ++ ++A++++gda+ ++++++ Aa a
  gi|386002402|ref|YP_005920701.1| 855 NKGLALYSQGNYSEAIQAYDRAIDLN---SQLVQAWYNKGDALDALKNFTQAAmA 906
                                       5799**********************...*********************99966 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00029      0.11      11      34 .]      58      81 ..      55      81 .. 0.91
   2 !   25.5   0.0   2.8e-08   1.1e-05       2      34 .]      83     115 ..      82     115 .. 0.97
   3 !   29.4   1.2   1.6e-09     6e-07       1      34 []     116     149 ..     116     149 .. 0.96
   4 !   25.0   1.7     4e-08   1.5e-05       1      34 []     150     183 ..     150     183 .. 0.96
   5 !   15.6   0.0     4e-05     0.015       1      33 [.     184     216 ..     184     217 .. 0.95
   6 !   22.5   0.2   2.4e-07   9.3e-05       1      33 [.     218     250 ..     218     251 .. 0.96
   7 !   25.8   0.1   2.3e-08   8.6e-06       4      34 .]     255     285 ..     254     285 .. 0.97
   8 !   27.6   0.2   5.8e-09   2.2e-06       1      34 []     286     319 ..     286     319 .. 0.97
   9 !   20.1   0.1   1.5e-06   0.00056       4      34 .]     323     353 ..     322     353 .. 0.95
  10 !   27.1   0.2   8.9e-09   3.4e-06       1      34 []     354     387 ..     354     387 .. 0.97
  11 !   23.0   0.0   1.7e-07   6.5e-05       2      34 .]     389     421 ..     388     421 .. 0.95
  12 !   21.6   0.1   5.1e-07   0.00019       2      34 .]     423     455 ..     422     455 .. 0.96
  13 !   22.0   0.1   3.6e-07   0.00014       1      34 []     456     489 ..     456     489 .. 0.96
  14 !   24.4   0.1   6.3e-08   2.4e-05       2      34 .]     491     523 ..     490     523 .. 0.96
  15 !   16.2   0.0   2.6e-05    0.0099       2      31 ..     525     554 ..     524     557 .. 0.91
  16 ?    2.2   0.1      0.74   2.8e+02       6      32 ..     570     603 ..     565     605 .. 0.68
  17 !   24.6   0.1   5.2e-08     2e-05       1      34 []     606     639 ..     606     639 .. 0.97
  18 !   12.6   0.0   0.00036      0.14       1      31 [.     640     670 ..     640     673 .. 0.90
  19 ?    4.8   0.1      0.11        42       3      32 ..     676     705 ..     674     707 .. 0.82
  20 ?    1.5   0.0       1.2   4.8e+02       1      27 [.     722     748 ..     722     768 .. 0.86
  21 !   15.3   0.0     5e-05     0.019       5      33 ..     808     836 ..     805     836 .. 0.95
  22 !   26.0   0.4   1.9e-08   7.3e-06       1      34 []     838     871 ..     838     871 .. 0.97
  23 !   12.4   0.5   0.00042      0.16       1      32 [.     872     903 ..     872     907 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00029
                            TPR_17 11 nnadaynnLAelllknGdlmtArq 34
                                      +++d +nn++++l+ +G++++A+q
  gi|386002402|ref|YP_005920701.1| 58 SDPDEWNNKGYALYLQGNYDEAIQ 81
                                      68899*****************98 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 2.8e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y++a++ldP  +++++n++ +++k+G++++A++
  gi|386002402|ref|YP_005920701.1|  83 YKEAIRLDPEFVWPWYNKGLAFEKQGKYDEAIK 115
                                       9******************************85 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 1.6e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++ldP +a+a++n++++l+ +G++++A++
  gi|386002402|ref|YP_005920701.1| 116 AYNEAIRLDPEYANAWHNKGYALYLQGKYDEAIK 149
                                       599*****************************85 PP

  == domain 4  score: 25.0 bits;  conditional E-value: 4e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l+P +a+a+n ++++l+++G++++A++
  gi|386002402|ref|YP_005920701.1| 150 AYNEAIRLYPEYANAWNSKGYALYSQGNYDEAIK 183
                                       599*****************************85 PP

  == domain 5  score: 15.6 bits;  conditional E-value: 4e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a++ldP   +++ n++ +l ++G+++ A+
  gi|386002402|ref|YP_005920701.1| 184 AYNEAIRLDPEFMWPWRNKGDTLFSQGKYELAI 216
                                       599***************************997 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 2.4e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a++l+P + +++ n++ +l+++G++++A+
  gi|386002402|ref|YP_005920701.1| 218 AYDEAIRLNPEDLNSWINKGAALYRLGKYDEAI 250
                                       599*****************************7 PP

  == domain 7  score: 25.8 bits;  conditional E-value: 2.3e-08
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +a++ldP n++a++n++++l ++G++++A+q
  gi|386002402|ref|YP_005920701.1| 255 EAIRLDPENVYAWHNKGVALNSQGKYDEAIQ 285
                                       79***************************98 PP

  == domain 8  score: 27.6 bits;  conditional E-value: 5.8e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l P +ada+n ++e+ll++G++++A+q
  gi|386002402|ref|YP_005920701.1| 286 AYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQ 319
                                       599*****************************98 PP

  == domain 9  score: 20.1 bits;  conditional E-value: 1.5e-06
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +a+ ldP na+ +n ++++l+++G++++A++
  gi|386002402|ref|YP_005920701.1| 323 EAISLDPENANGWNIKGVALYNRGKSDEAIK 353
                                       79***************************85 PP

  == domain 10  score: 27.1 bits;  conditional E-value: 8.9e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l P +ada+nn++  l+++G++++A+q
  gi|386002402|ref|YP_005920701.1| 354 AYDEAIRLSPEYADAWNNKGLSLKSQGKYDEAIQ 387
                                       599*****************************98 PP

  == domain 11  score: 23.0 bits;  conditional E-value: 1.7e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + + ++ldP ++ a++n++ +l ++G++++A+q
  gi|386002402|ref|YP_005920701.1| 389 FNETIRLDPEHVAAWYNKGLTLNNQGKYDEAIQ 421
                                       7789***************************98 PP

  == domain 12  score: 21.6 bits;  conditional E-value: 5.1e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a++l+P ++da++ ++++l ++ ++++A+q
  gi|386002402|ref|YP_005920701.1| 423 FDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQ 455
                                       889****************************98 PP

  == domain 13  score: 22.0 bits;  conditional E-value: 3.6e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y ++++l+P +ada+n +++++ ++G++ +A++
  gi|386002402|ref|YP_005920701.1| 456 AYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIK 489
                                       599****************************985 PP

  == domain 14  score: 24.4 bits;  conditional E-value: 6.3e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       + +a++++P +ada+nn++++l ++ ++++A+q
  gi|386002402|ref|YP_005920701.1| 491 FDEAIRRNPEYADAWNNKGVALVSLDKYEEAIQ 523
                                       889****************************98 PP

  == domain 15  score: 16.2 bits;  conditional E-value: 2.6e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       + +a +l+P +ada+  ++++++++G++++
  gi|386002402|ref|YP_005920701.1| 525 FDEATRLNPEDADAWLKKGVAFYHLGKYKE 554
                                       78999**********************997 PP

  == domain 16  score: 2.2 bits;  conditional E-value: 0.74
                            TPR_17   6 leldPnnadaynnLAelll.......knGdlmtA 32 
                                       l+ +P +a+a   ++ +l         + ++++A
  gi|386002402|ref|YP_005920701.1| 570 LRWNPEDANARLSKGIALMlkglaleTLDKYEDA 603
                                       7789*********999998444444444456555 PP

  == domain 17  score: 24.6 bits;  conditional E-value: 5.2e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+ l+P+++ a+ n++ +l+++G++++A+q
  gi|386002402|ref|YP_005920701.1| 606 AYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQ 639
                                       599*****************************87 PP

  == domain 18  score: 12.6 bits;  conditional E-value: 0.00036
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y ++l+l+P +a+a+  ++++l+++ ++++
  gi|386002402|ref|YP_005920701.1| 640 AYDEVLRLNPEDANAWKKKGYALHSLEEHEE 670
                                       599********************99988776 PP

  == domain 19  score: 4.8 bits;  conditional E-value: 0.11
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                        +a++l+Pn+a  +  +   ll + ++++A
  gi|386002402|ref|YP_005920701.1| 676 DEAIRLNPNDAGCWLIKSFNLLIIEKYDEA 705
                                       78*********9998888888888877777 PP

  == domain 20  score: 1.5 bits;  conditional E-value: 1.2
                            TPR_17   1 lylkaleldPnnadaynnLAelllknG 27 
                                       +y++ + l+P n+ a n + ++l  +G
  gi|386002402|ref|YP_005920701.1| 722 TYEEIVSLNPENSTASNIKSRTLIAKG 748
                                       59999********99887777776665 PP

  == domain 21  score: 15.3 bits;  conditional E-value: 5e-05
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                       a+ l+P +a a+n+++ +l+ +G++++A+
  gi|386002402|ref|YP_005920701.1| 808 AISLNPESALAWNYKGAALRGQGKHEEAI 836
                                       899***********************996 PP

  == domain 22  score: 26.0 bits;  conditional E-value: 1.9e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a++l+P++ da+nn++ +l+++G++ +A+q
  gi|386002402|ref|YP_005920701.1| 838 AYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQ 871
                                       599*****************************97 PP

  == domain 23  score: 12.4 bits;  conditional E-value: 0.00042
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +a++l+   + a++n++ +l  ++++ +A
  gi|386002402|ref|YP_005920701.1| 872 AYDRAIDLNSQLVQAWYNKGDALDALKNFTQA 903
                                       59*********************998886665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   7.8e-05      0.03       8      40 ..      67      99 ..      60     103 .. 0.87
   2 !   22.7   0.1     3e-07   0.00011       4      42 ..      97     135 ..      94     137 .. 0.89
   3 !   20.2   0.3   1.8e-06   0.00069       2      38 ..     129     165 ..     128     171 .. 0.91
   4 !   21.9   0.1   5.3e-07    0.0002       2      42 ..     163     203 ..     162     205 .. 0.89
   5 !    9.7   0.0    0.0043       1.6       6      41 ..     201     236 ..     196     239 .. 0.85
   6 !   18.3   0.1   7.3e-06    0.0028       8      41 ..     237     270 ..     231     273 .. 0.90
   7 !   20.5   0.2   1.5e-06   0.00056      10      43 ..     273     306 ..     270     307 .. 0.91
   8 !   19.4   0.1   3.4e-06    0.0013       2      38 ..     299     335 ..     298     340 .. 0.92
   9 !   18.2   0.0   7.9e-06     0.003       9      39 ..     340     370 ..     333     375 .. 0.90
  10 !   13.6   0.0   0.00024     0.091      11      41 ..     376     406 ..     372     409 .. 0.90
  11 !   22.5   0.1   3.3e-07   0.00013       2      39 ..     401     438 ..     400     442 .. 0.94
  12 !   19.9   0.1   2.3e-06   0.00088       2      38 ..     435     471 ..     434     477 .. 0.95
  13 !   18.0   0.1   9.6e-06    0.0037       4      40 ..     471     507 ..     469     511 .. 0.87
  14 !   18.4   0.2   7.2e-06    0.0028      10      42 ..     511     543 ..     508     545 .. 0.91
  15 ?    4.7   0.0      0.18        67       2      37 ..     537     572 ..     536     579 .. 0.91
  16 !   22.2   0.6   4.3e-07   0.00016       4      42 ..     587     625 ..     585     627 .. 0.89
  17 !   22.2   0.2   4.1e-07   0.00016       7      42 ..     624     659 ..     623     661 .. 0.92
  18 !   18.4   0.0   6.8e-06    0.0026       2      39 ..     653     690 ..     652     694 .. 0.94
  19 ?   -0.1   0.0       6.3   2.4e+03      23      33 ..     708     718 ..     698     736 .. 0.50
  20 ?    5.7   0.0     0.086        33       4      33 ..     751     780 ..     749     785 .. 0.87
  21 !   16.1   0.0   3.7e-05     0.014       8      42 ..     789     823 ..     783     825 .. 0.90
  22 !   19.2   0.6   3.9e-06    0.0015       4      39 ..     819     854 ..     818     859 .. 0.88
  23 !   14.1   0.1   0.00017     0.065       9      42 ..     858     891 ..     856     893 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.8e-05
                            TPR_14  8 aeallalGdpdeAiallrralalaPddaeawll 40
                                      + al+ +G++deAi+ +++a++l+P++ + w+ 
  gi|386002402|ref|YP_005920701.1| 67 GYALYLQGNYDEAIQDYKEAIRLDPEFVWPWYN 99
                                      789999********************9988865 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 3e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++  + a++ +G++deAi+++++a++l+P+ a aw   +
  gi|386002402|ref|YP_005920701.1|  97 WYNKGLAFEKQGKYDEAIKAYNEAIRLDPEYANAWHNKG 135
                                       7778899****************************8765 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 1.8e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +a+   + al+ +G++deAi+++++a++l+P+ a aw
  gi|386002402|ref|YP_005920701.1| 129 NAWHNKGYALYLQGKYDEAIKAYNEAIRLYPEYANAW 165
                                       67888899**************************999 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 5.3e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +a+   + al+ +G++deAi+++++a++l+P++ + w+  +
  gi|386002402|ref|YP_005920701.1| 163 NAWNSKGYALYSQGNYDEAIKAYNEAIRLDPEFMWPWRNKG 203
                                       67778899************************999888765 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0043
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlll 41 
                                         ++ l+ +G+++ Ai ++++a++l+P+d+  w+  
  gi|386002402|ref|YP_005920701.1| 201 NKGDTLFSQGKYELAIYAYDEAIRLNPEDLNSWINK 236
                                       5678999**********************9877765 PP

  == domain 6  score: 18.3 bits;  conditional E-value: 7.3e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlll 41 
                                       ++al++lG++deAi++ ++a++l+P++  aw   
  gi|386002402|ref|YP_005920701.1| 237 GAALYRLGKYDEAIRASNEAIRLDPENVYAWHNK 270
                                       789****************************876 PP

  == domain 7  score: 20.5 bits;  conditional E-value: 1.5e-06
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawlllaq 43 
                                       al  +G++deAi+++++a++l P+ a+aw + ++
  gi|386002402|ref|YP_005920701.1| 273 ALNSQGKYDEAIQAYDEAIRLSPEYADAWNRKGE 306
                                       7889*************************98876 PP

  == domain 8  score: 19.4 bits;  conditional E-value: 3.4e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +a+ + +eall++G++deAi++ ++a++l+P++a  w
  gi|386002402|ref|YP_005920701.1| 299 DAWNRKGEALLHQGKYDEAIQASNEAISLDPENANGW 335
                                       799999**************************99766 PP

  == domain 9  score: 18.2 bits;  conditional E-value: 7.9e-06
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawl 39 
                                        al+++G+ deAi+++++a++l P+ a+aw 
  gi|386002402|ref|YP_005920701.1| 340 VALYNRGKSDEAIKAYDEAIRLSPEYADAWN 370
                                       6899*************************95 PP

  == domain 10  score: 13.6 bits;  conditional E-value: 0.00024
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlll 41 
                                       l  +G++deAi+ +++ ++l+P++ +aw+  
  gi|386002402|ref|YP_005920701.1| 376 LKSQGKYDEAIQTFNETIRLDPEHVAAWYNK 406
                                       7789************************875 PP

  == domain 11  score: 22.5 bits;  conditional E-value: 3.3e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +a++  +  l ++G++deAi+++++a++l+P+  +aw+
  gi|386002402|ref|YP_005920701.1| 401 AAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEYVDAWY 438
                                       7999999*****************************97 PP

  == domain 12  score: 19.9 bits;  conditional E-value: 2.3e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +a++  + al  + ++deAi++++++++l+P+ a+aw
  gi|386002402|ref|YP_005920701.1| 435 DAWYSKGNALDSQSRYDEAIQAYDEVIKLNPEYADAW 471
                                       79**********************************9 PP

  == domain 13  score: 18.0 bits;  conditional E-value: 9.6e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       +   + a+  +G++ eAi+++++a++++P+ a+aw  
  gi|386002402|ref|YP_005920701.1| 471 WNSKGTAFNSQGRYNEAIKAFDEAIRRNPEYADAWNN 507
                                       5556789999************************965 PP

  == domain 14  score: 18.4 bits;  conditional E-value: 7.2e-06
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                                       al  l++++eAi+++++a +l+P+da+awl  +
  gi|386002402|ref|YP_005920701.1| 511 ALVSLDKYEEAIQAFDEATRLNPEDADAWLKKG 543
                                       788999***********************9876 PP

  == domain 15  score: 4.7 bits;  conditional E-value: 0.18
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaea 37 
                                       +a+l+ + a+++lG+++e i++++  ++++ dd+++
  gi|386002402|ref|YP_005920701.1| 537 DAWLKKGVAFYHLGKYKETIQVCNVSIQAYDDDLRW 572
                                       79**********************999999999876 PP

  == domain 16  score: 22.2 bits;  conditional E-value: 4.3e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       l++ + al++l+++++A++++++a++l+Pdd +aw   +
  gi|386002402|ref|YP_005920701.1| 587 LMLKGLALETLDKYEDAVQAYDEAISLNPDDVAAWENRG 625
                                       5666899****************************8765 PP

  == domain 17  score: 22.2 bits;  conditional E-value: 4.1e-07
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +++al+ lG++deA+++++++l+l+P+da aw   +
  gi|386002402|ref|YP_005920701.1| 624 RGAALYSLGKYDEAVQAYDEVLRLNPEDANAWKKKG 659
                                       5889****************************8765 PP

  == domain 18  score: 18.4 bits;  conditional E-value: 6.8e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +a+++ + al  l++++e++++l++a++l+P+da  wl
  gi|386002402|ref|YP_005920701.1| 653 NAWKKKGYALHSLEEHEESVKALDEAIRLNPNDAGCWL 690
                                       79********************************9986 PP

  == domain 19  score: -0.1 bits;  conditional E-value: 6.3
                            TPR_14  23 llrralalaPd 33 
                                       + ++a++++ +
  gi|386002402|ref|YP_005920701.1| 708 ASEEAIRAYNE 718
                                       55555544333 PP

  == domain 20  score: 5.7 bits;  conditional E-value: 0.086
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPd 33 
                                       +++ + +l ++ ++ eA++++++a++l+P+
  gi|386002402|ref|YP_005920701.1| 751 WALKGIILGEQHEYNEAMQAFNEAVSLNPA 780
                                       6667788888999***************95 PP

  == domain 21  score: 16.1 bits;  conditional E-value: 3.7e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +++l  +G++ eAi++ + a++l+P++a aw + +
  gi|386002402|ref|YP_005920701.1| 789 GKYLNDQGKYYEAIEAIDMAISLNPESALAWNYKG 823
                                       788999*************************8766 PP

  == domain 22  score: 19.2 bits;  conditional E-value: 3.9e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +   ++al+ +G+++eAi ++++a++l+Pdd++aw 
  gi|386002402|ref|YP_005920701.1| 819 WNYKGAALRGQGKHEEAILAYDEAIRLNPDDEDAWN 854
                                       6667899****************************5 PP

  == domain 23  score: 14.1 bits;  conditional E-value: 0.00017
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                        al+ +G++ eAi++++ra++l+ +  +aw+  +
  gi|386002402|ref|YP_005920701.1| 858 LALYSQGNYSEAIQAYDRAIDLNSQLVQAWYNKG 891
                                       6899*******************99999998776 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.9   9.7e-10   3.7e-07       6      76 ..      63     125 ..      63     126 .. 0.92
   2 !   39.9   1.6     1e-12   3.9e-10       6      76 ..      97     159 ..      93     160 .. 0.93
   3 !   39.8   4.7   1.1e-12   4.2e-10       2      76 ..     127     193 ..     126     194 .. 0.94
   4 !   27.1   0.9   9.9e-09   3.8e-06       2      74 ..     161     225 ..     160     228 .. 0.91
   5 !   28.7   0.2   3.2e-09   1.2e-06       6      76 ..     199     261 ..     194     262 .. 0.90
   6 !   32.3   0.8   2.3e-10   8.8e-08       5      75 ..     266     328 ..     263     330 .. 0.91
   7 !   26.2   0.0   1.9e-08   7.4e-06       6      76 ..     335     397 ..     330     398 .. 0.89
   8 !   27.5   0.2   7.5e-09   2.9e-06       4      74 ..     401     463 ..     399     466 .. 0.89
   9 !   29.3   0.1     2e-09   7.6e-07       3      74 ..     468     531 ..     466     534 .. 0.89
  10 ?    0.5   0.0       1.9   7.3e+02       3      27 ..     536     560 ..     534     569 .. 0.79
  11 !   24.9   1.3   4.9e-08   1.9e-05      10      74 ..     584     647 ..     575     650 .. 0.72
  12 ?    6.6   1.9     0.024       9.1       3      76 ..     652     717 ..     650     725 .. 0.64
  13 ?    2.1   0.0      0.63   2.4e+02      52      74 ..     755     777 ..     752     780 .. 0.86
  14 !   16.3   1.1   2.3e-05    0.0087       9      74 ..     788     845 ..     783     848 .. 0.85
  15 !   17.4   1.4     1e-05     0.004       4      65 ..     851     904 ..     848     908 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 9.7e-10
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +nn + +l+ +g+ydeA++ +++a+++      p+    ++  +n g +++++g+y+eA+++++ea+++++
  gi|386002402|ref|YP_005920701.1|  63 WNNKGYALYLQGNYDEAIQDYKEAIRLD-----PE---FVWPWYNKGLAFEKQGKYDEAIKAYNEAIRLDP 125
                                       6899********************8888.....55...589999***********************9975 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1e-12
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++n +++  ++g+ydeA++ +++a+++      p+   +a++ +n g +++++g+y+eA+++++ea+++++
  gi|386002402|ref|YP_005920701.1|  97 WYNKGLAFEKQGKYDEAIKAYNEAIRLD-----PE---YANAWHNKGYALYLQGKYDEAIKAYNEAIRLYP 159
                                       6799********************7777.....76...6******************************97 PP

  == domain 3  score: 39.8 bits;  conditional E-value: 1.1e-12
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                        a+a++n + +l+ +g+ydeA++ +++a++++     p+   +a++ +  g +++ +g+y+eA+++++ea+++++
  gi|386002402|ref|YP_005920701.1| 127 YANAWHNKGYALYLQGKYDEAIKAYNEAIRLY-----PE---YANAWNSKGYALYSQGNYDEAIKAYNEAIRLDP 193
                                       589*************************9999.....87...5****************************9975 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 9.9e-09
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a+a+n  + +l+ +g+ydeA++ +++a+++      p+     +  rn g++++ +g+ye A++++ ea+++
  gi|386002402|ref|YP_005920701.1| 161 YANAWNSKGYALYSQGNYDEAIKAYNEAIRLD-----PE---FMWPWRNKGDTLFSQGKYELAIYAYDEAIRL 225
                                       5899*99*********************8887.....55...58999***********************998 PP

  == domain 5  score: 28.7 bits;  conditional E-value: 3.2e-09
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++n +++l+ +g+y+ A+  +++a+++      p+    +++ +n g ++++lg+y+eA+++ +ea+++++
  gi|386002402|ref|YP_005920701.1| 199 WRNKGDTLFSQGKYELAIYAYDEAIRLN-----PE---DLNSWINKGAALYRLGKYDEAIRASNEAIRLDP 261
                                       7799********************6666.....76...599**************************9975 PP

  == domain 6  score: 32.3 bits;  conditional E-value: 2.3e-10
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a++n +++l+ +g+ydeA++ +++a+++      p+   +a + +  g++++ +g+y+eA+++ +ea+ ++
  gi|386002402|ref|YP_005920701.1| 266 AWHNKGVALNSQGKYDEAIQAYDEAIRLS-----PE---YADAWNRKGEALLHQGKYDEAIQASNEAISLD 328
                                       689**********************8888.....77...59999999999999**************9876 PP

  == domain 7  score: 26.2 bits;  conditional E-value: 1.9e-08
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +n  +++l+ +g+ deA++ +++a+++      p+   +a + +n g  +  +g+y+eA++ ++e++++++
  gi|386002402|ref|YP_005920701.1| 335 WNIKGVALYNRGKSDEAIKAYDEAIRLS-----PE---YADAWNNKGLSLKSQGKYDEAIQTFNETIRLDP 397
                                       644899******************8888.....77...699*************************99875 PP

  == domain 8  score: 27.5 bits;  conditional E-value: 7.5e-09
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +a++n +++l+ +g+ydeA++ +++a+++      p+   ++ + +  g +++ + ry+eA++++ e++++
  gi|386002402|ref|YP_005920701.1| 401 AAWYNKGLTLNNQGKYDEAIQAFDEAIRLN-----PE---YVDAWYSKGNALDSQSRYDEAIQAYDEVIKL 463
                                       4677**********************6666.....76...589************************9987 PP

  == domain 9  score: 29.3 bits;  conditional E-value: 2e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a a+n  +++ + +gry eA++ +++a+++      p+   +a + +n g ++  l++yeeA++++ ea+++
  gi|386002402|ref|YP_005920701.1| 468 ADAWNSKGTAFNSQGRYNEAIKAFDEAIRRN-----PE---YADAWNNKGVALVSLDKYEEAIQAFDEATRL 531
                                       789988*********************3333.....65...79**************************997 PP

  == domain 10  score: 0.5 bits;  conditional E-value: 1.9
                            TPR_12   3 atalnnlaavlrrlgrydeAlelle 27 
                                       a a+ + +++ ++lg+y e ++ ++
  gi|386002402|ref|YP_005920701.1| 536 ADAWLKKGVAFYHLGKYKETIQVCN 560
                                       66787899999******99887665 PP

  == domain 11  score: 24.9 bits;  conditional E-value: 4.9e-08
                            TPR_12  10 aavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       + +l+  g   e l+ +e a++++ +++    +p+ +++  n g +++ lg+y+eA++++ e+l++
  gi|386002402|ref|YP_005920701.1| 584 GIALMLKGLALETLDKYEDAVQAYdEAI--SLNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLRL 647
                                       5555555555566666666666663333..44566799**************************98 PP

  == domain 12  score: 6.6 bits;  conditional E-value: 0.024
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+a+ + + +l+ l++++e+ + l++a+++      p+    a +    +  ++  ++y+eA+++ eea++++ 
  gi|386002402|ref|YP_005920701.1| 652 ANAWKKKGYALHSLEEHEESVKALDEAIRLN-----PND---AGCWLIKSFNLLIIEKYDEAINASEEAIRAYN 717
                                       7888889999999999999999999998887.....443...22333333333355555555555555555554 PP

  == domain 13  score: 2.1 bits;  conditional E-value: 0.63
                            TPR_12  52 grlyralgryeeAlelleealai 74 
                                       g+++ ++ +y eA ++++ea+ +
  gi|386002402|ref|YP_005920701.1| 755 GIILGEQHEYNEAMQAFNEAVSL 777
                                       788899999*********99865 PP

  == domain 14  score: 16.3 bits;  conditional E-value: 2.3e-05
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +  l+ +g+y eA+e  + a+ +      p++   a + +  g ++r +g++eeA+ ++ ea+++
  gi|386002402|ref|YP_005920701.1| 788 KGKYLNDQGKYYEAIEAIDMAISLN-----PES---ALAWNYKGAALRGQGKHEEAILAYDEAIRL 845
                                       56778999******99999997766.....776...778888899999***************997 PP

  == domain 15  score: 17.4 bits;  conditional E-value: 1e-05
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAl 65 
                                        a+nn +++l+ +g+y eA++ +++a+++ ++        ++++ +n g++++al+++ +A 
  gi|386002402|ref|YP_005920701.1| 851 DAWNNKGLALYSQGNYSEAIQAYDRAIDLNSQ--------LVQAWYNKGDALDALKNFTQAA 904
                                       5899**********************999833........6778888888888888888876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   9.3e-09   3.6e-06       1      61 [.      70     130 ..      70     135 .. 0.92
   2 !   31.7   1.0   4.3e-10   1.6e-07       1      56 [.     138     193 ..     138     195 .. 0.95
   3 !   21.8   0.2   5.4e-07   0.00021       1      58 [.     206     263 ..     206     269 .. 0.92
   4 !   36.5   0.7   1.4e-11   5.3e-09       4      62 ..     277     335 ..     274     339 .. 0.92
   5 !   24.7   0.1   6.6e-08   2.5e-05       4      60 ..     345     402 ..     342     406 .. 0.91
   6 !   32.2   0.6     3e-10   1.1e-07       4      62 ..     413     471 ..     410     475 .. 0.94
   7 !   34.5   0.5   5.6e-11   2.1e-08       4      63 ..     481     540 ..     479     544 .. 0.96
   8 !   17.9   0.1   8.7e-06    0.0033       6      59 ..     517     570 ..     516     574 .. 0.93
   9 !   27.7   2.7   7.7e-09   2.9e-06       6      64 ..     599     657 ..     596     661 .. 0.95
  10 !   22.1   0.5   4.1e-07   0.00016       4      59 ..     631     686 ..     628     693 .. 0.94
  11 ?    0.6   0.0       2.2   8.5e+02       7      40 ..     716     749 ..     696     750 .. 0.75
  12 ?    6.1   0.2     0.041        15       3      61 ..     760     818 ..     758     823 .. 0.86
  13 !   15.3   1.4   5.6e-05     0.021       3      62 ..     794     853 ..     792     859 .. 0.94
  14 !   26.0   1.9   2.5e-08   9.5e-06       1      55 [.     826     880 ..     826     888 .. 0.92
  15 !   16.9   1.2   1.7e-05    0.0066       1      44 [.     860     903 ..     860     905 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.3e-09
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       l+ +g+y+eA++ +++a+  dp+  + +++   a  ++g +deA+++ +++ + dp  a++
  gi|386002402|ref|YP_005920701.1|  70 LYLQGNYDEAIQDYKEAIRLDPEFVWPWYNKGLAFEKQGKYDEAIKAYNEAIRLDPEYANA 130
                                       5679***************************************************997444 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 4.3e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       l+ +g+y+eA++++ +a+  +p++a+a+     al+++g++deA+++ +++ + dp
  gi|386002402|ref|YP_005920701.1| 138 LYLQGKYDEAIKAYNEAIRLYPEYANAWNSKGYALYSQGNYDEAIKAYNEAIRLDP 193
                                       5679*******************************************999998887 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 5.4e-07
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       l+ +g+y+ A+ ++ +a+  +p++++ +++   al+ lg +deA+++ +++ + dp +
  gi|386002402|ref|YP_005920701.1| 206 LFSQGKYELAIYAYDEAIRLNPEDLNSWINKGAALYRLGKYDEAIRASNEAIRLDPEN 263
                                       678*******************************************999999999883 PP

  == domain 4  score: 36.5 bits;  conditional E-value: 1.4e-11
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +g+y+eA++++ +a+  +p++a+a+ +  eall +g +deA+++ +++   dp +a+ +
  gi|386002402|ref|YP_005920701.1| 277 QGKYDEAIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAISLDPENANGW 335
                                       9*******************************************999999999887766 PP

  == domain 5  score: 24.7 bits;  conditional E-value: 6.6e-08
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ar 60 
                                       +g+ +eA++++ +a+  +p++a+a+ +    l ++g +deA+++ ++  + dp + a+
  gi|386002402|ref|YP_005920701.1| 345 RGKSDEAIKAYDEAIRLSPEYADAWNNKGLSLKSQGKYDEAIQTFNETIRLDPEHvAA 402
                                       7999*******************************************99999986555 PP

  == domain 6  score: 32.2 bits;  conditional E-value: 3e-10
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +g+y+eA++++ +a+  +p++ +a++   +al ++ ++deA+++ d++ + +p  a+++
  gi|386002402|ref|YP_005920701.1| 413 QGKYDEAIQAFDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQAYDEVIKLNPEYADAW 471
                                       8***************************************************9976665 PP

  == domain 7  score: 34.5 bits;  conditional E-value: 5.6e-11
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                       +g+y eA++++ +a+  +p++a+a+ +   al++l  ++eA+++ d++ + +p da+++ 
  gi|386002402|ref|YP_005920701.1| 481 QGRYNEAIKAFDEAIRRNPEYADAWNNKGVALVSLDKYEEAIQAFDEATRLNPEDADAWL 540
                                       9******************************************************99985 PP

  == domain 8  score: 17.9 bits;  conditional E-value: 8.7e-06
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       +y+eA++++ +a   +p++a+a+l    a + lg ++e +++++   +++ dd 
  gi|386002402|ref|YP_005920701.1| 517 KYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKETIQVCNVSIQAYDDDL 570
                                       79*****************************************99999998875 PP

  == domain 9  score: 27.7 bits;  conditional E-value: 7.7e-09
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       +y++A++++ +a++ +p++ +a+ +   al++lg +deA ++ d++++ +p da++++ 
  gi|386002402|ref|YP_005920701.1| 599 KYEDAVQAYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLRLNPEDANAWKK 657
                                       79***************************************************998865 PP

  == domain 10  score: 22.1 bits;  conditional E-value: 4.1e-07
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                        g+y+eA++++ ++l  +p++a+a+     al +l + +e  ++Ld++ + +p+da
  gi|386002402|ref|YP_005920701.1| 631 LGKYDEAVQAYDEVLRLNPEDANAWKKKGYALHSLEEHEESVKALDEAIRLNPNDA 686
                                       69****************************************************87 PP

  == domain 11  score: 0.6 bits;  conditional E-value: 2.2
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgq 40 
                                       y e +  +e++ + +p+n+ a     + l+a g+
  gi|386002402|ref|YP_005920701.1| 716 YNETITTYEEIVSLNPENSTASNIKSRTLIAKGN 749
                                       5555667777888899999888888888888776 PP

  == domain 12  score: 6.1 bits;  conditional E-value: 0.041
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       ++  y eA++++ +a + +p  + ++    + l  +g + eA++++d +   +p +a +
  gi|386002402|ref|YP_005920701.1| 760 EQHEYNEAMQAFNEAVSLNPAGSFIWSFKGKYLNDQGKYYEAIEAIDMAISLNPESALA 818
                                       577899999*****999999999999999999999999999999999999988886554 PP

  == domain 13  score: 15.3 bits;  conditional E-value: 5.6e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       ++g+y eA+++   a++ +p++a a+ +   al  +g  +eA+ + d++ + +pdd++++
  gi|386002402|ref|YP_005920701.1| 794 DQGKYYEAIEAIDMAISLNPESALAWNYKGAALRGQGKHEEAILAYDEAIRLNPDDEDAW 853
                                       79*****************************************************98876 PP

  == domain 14  score: 26.0 bits;  conditional E-value: 2.5e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       l  +g+++eA+ ++ +a+  +p++++a+ +   al+++g++ eA+++ d++ + +
  gi|386002402|ref|YP_005920701.1| 826 LRGQGKHEEAILAYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQAYDRAIDLN 880
                                       568**********************************************998766 PP

  == domain 15  score: 16.9 bits;  conditional E-value: 1.7e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                                       l+ +g+y eA++++ +a++ + +   a+++  +al al+++++A
  gi|386002402|ref|YP_005920701.1| 860 LYSQGNYSEAIQAYDRAIDLNSQLVQAWYNKGDALDALKNFTQA 903
                                       678****************************************9 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1     2e-06   0.00075      29      81 ..      66     119 ..      55     120 .. 0.92
   2 !   29.4   7.2   1.8e-09     7e-07       2      81 ..     107     187 ..     106     188 .. 0.96
   3 !   28.0   0.1   5.1e-09     2e-06      31      78 ..     204     252 ..     199     256 .. 0.95
   4 !   20.0   0.3   1.6e-06   0.00059      22      78 ..     260     320 ..     253     324 .. 0.88
   5 !   24.3   0.2   7.2e-08   2.7e-05       2      81 ..     277     357 ..     276     358 .. 0.95
   6 !   30.7   0.1   7.2e-10   2.7e-07       6      81 ..     349     425 ..     344     426 .. 0.91
   7 !   26.1   0.2   1.9e-08   7.3e-06       2      81 ..     447     527 ..     446     528 .. 0.97
   8 ?    4.3   0.0      0.12        47      20      50 ..     533     564 ..     527     573 .. 0.76
   9 !   16.7   0.3   1.6e-05    0.0062      26      81 ..     587     643 ..     572     644 .. 0.92
  10 !   18.8   0.1   3.8e-06    0.0015      18      80 ..     647     710 ..     641     712 .. 0.87
  11 !    9.3   0.0    0.0035       1.3      35      80 ..     760     806 ..     753     808 .. 0.93
  12 !   28.6   0.8   3.2e-09   1.2e-06       2      77 ..     829     905 ..     828     907 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2e-06
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++++lyl+g+y++A++ +++a +l+++    +y ++ +  k++ky+eAi+a+ +
  gi|386002402|ref|YP_005920701.1|  66 KGYALYLQGNYDEAIQDYKEAiRLDPEFVWPWYNKGLAFEKQGKYDEAIKAYNE 119
                                       689***********************************************9876 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.8e-09
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       q++y++Ai  ++ +   ++e +++ + ++++lyl+g+y++A++ +++a +l+++  +++  ++ +l+ +++y+eAi+
  gi|386002402|ref|YP_005920701.1| 107 QGKYDEAIKAYNEAIRLDPEYANAWHNKGYALYLQGKYDEAIKAYNEAiRLYPEYANAWNSKGYALYSQGNYDEAIK 183
                                       899************999*********************************************************** PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       a+ +
  gi|386002402|ref|YP_005920701.1| 184 AYNE 187
                                       9876 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 5.1e-09
                                       HHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  31 lclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                        +l+++g+y+ A++ +++a +ln+++l++++ ++ +l+ L+ky+eAi+a
  gi|386002402|ref|YP_005920701.1| 204 DTLFSQGKYELAIYAYDEAiRLNPEDLNSWINKGAALYRLGKYDEAIRA 252
                                       689********************************************97 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 1.6e-06
                                       -HHHHHH...HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  22 spedayl...lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +pe++y+   ++ +l ++g+y++A++ +++a +l ++   ++  ++++ll ++ky+eAi+a
  gi|386002402|ref|YP_005920701.1| 260 DPENVYAwhnKGVALNSQGKYDEAIQAYDEAiRLSPEYADAWNRKGEALLHQGKYDEAIQA 320
                                       6777776444699**********************************************97 PP

  == domain 5  score: 24.3 bits;  conditional E-value: 7.2e-08
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       q++y++Ai  ++ +   ++e +++   ++++l+++g+y++A++  ++a  l++++ + + +++ +l+  +k +eAi+
  gi|386002402|ref|YP_005920701.1| 277 QGKYDEAIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAiSLDPENANGWNIKGVALYNRGKSDEAIK 353
                                       889************8888888888899************************************************* PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       a+++
  gi|386002402|ref|YP_005920701.1| 354 AYDE 357
                                       9986 PP

  == domain 6  score: 30.7 bits;  conditional E-value: 7.2e-10
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++Ai  ++ +   ++e +++   ++l+l ++g+y++A++ ++++ +l++++ +++y ++ +l  ++ky+eAi+a+++
  gi|386002402|ref|YP_005920701.1| 349 DEAIKAYDEAIRLSPEYADAWNNKGLSLKSQGKYDEAIQTFNETiRLDPEHVAAWYNKGLTLNNQGKYDEAIQAFDE 425
                                       789999999997778888888889**************************************************987 PP

  == domain 7  score: 26.1 bits;  conditional E-value: 1.9e-08
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       q +y++Ai  ++ + + ++e +++   ++ ++ ++g+y++A++ +++a + n++   ++  ++ +l+ L+kyeeAi+
  gi|386002402|ref|YP_005920701.1| 447 QSRYDEAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIKAFDEAiRRNPEYADAWNNKGVALVSLDKYEEAIQ 523
                                       889************************************************************************** PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       a+++
  gi|386002402|ref|YP_005920701.1| 524 AFDE 527
                                       *987 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.12
                                       H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.S CS
                            ANAPC3  20 tespedayllAlclylngqykrAyellrka.k 50 
                                       +e++++ + ++ ++y++g+yk+ +++++ + +
  gi|386002402|ref|YP_005920701.1| 533 PEDADAWLKKGVAFYHLGKYKETIQVCNVSiQ 564
                                       56666666679999********9999987755 PP

  == domain 9  score: 16.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  26 ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++l++l+l  + +y+ A + +++a  ln+ + +++   + +l+ L+ky+eA++a+++
  gi|386002402|ref|YP_005920701.1| 587 LMLKGLALETLDKYEDAVQAYDEAiSLNPDDVAAWENRGAALYSLGKYDEAVQAYDE 643
                                       7889999**********************************************9976 PP

  == domain 10  score: 18.8 bits;  conditional E-value: 3.8e-06
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                        ++e++++   ++++l +++++++  + l++a +ln+++ gc++++   ll ++ky+eAi+a e
  gi|386002402|ref|YP_005920701.1| 647 LNPEDANAWKKKGYALHSLEEHEESVKALDEAiRLNPNDAGCWLIKSFNLLIIEKYDEAINASE 710
                                       455666666667************************************************9865 PP

  == domain 11  score: 9.3 bits;  conditional E-value: 0.0035
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++ +y++A++ +++a  ln+    ++  +++ l +++ky eAi a++
  gi|386002402|ref|YP_005920701.1| 760 EQHEYNEAMQAFNEAvSLNPAGSFIWSFKGKYLNDQGKYYEAIEAID 806
                                       5789***************************************9986 PP

  == domain 12  score: 28.6 bits;  conditional E-value: 3.2e-09
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       q+++++Ai+ ++ +   +++++++   ++l+ly++g+y +A++ +++a +lns+  +++y ++ +l +Lk++ +A +
  gi|386002402|ref|YP_005920701.1| 829 QGKHEEAILAYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQAYDRAiDLNSQLVQAWYNKGDALDALKNFTQAAM 905
                                       789************8889888889999*********************************************9976 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00026     0.099      26      61 ..      57      92 ..      54      94 .. 0.93
   2 !   10.5   0.0    0.0014      0.54      23      62 ..      88     127 ..      87     132 .. 0.90
   3 !   17.4   0.1   9.7e-06    0.0037       6      62 ..     105     161 ..      99     166 .. 0.91
   4 !   16.1   0.1   2.5e-05    0.0094       9      61 ..     142     194 ..     136     205 .. 0.94
   5 !   16.0   0.0   2.5e-05    0.0097       7      62 ..     174     229 ..     168     232 .. 0.94
   6 !   15.9   0.1   2.8e-05     0.011       6      50 ..     207     251 ..     204     252 .. 0.93
   7 !   22.7   0.4   2.2e-07   8.3e-05       7      65 ..     242     300 ..     238     301 .. 0.93
   8 !   16.7   0.0   1.6e-05     0.006       4      65 ..     307     368 ..     305     369 .. 0.94
   9 !   22.1   0.0   3.3e-07   0.00013       8      64 ..     379     435 ..     374     437 .. 0.92
  10 !   18.4   0.0   4.6e-06    0.0018       8      65 ..     447     504 ..     442     506 .. 0.94
  11 !   15.5   0.0   3.7e-05     0.014       6      47 ..     513     554 ..     508     557 .. 0.90
  12 ?   -0.1   0.0       2.9   1.1e+03      22      40 ..     570     588 ..     561     591 .. 0.84
  13 !   22.9   0.3   1.9e-07   7.1e-05       4      52 ..     592     641 ..     589     643 .. 0.89
  14 !   19.8   0.1   1.7e-06   0.00067      11      63 ..     634     686 ..     633     693 .. 0.94
  15 ?   -1.4   0.0       7.1   2.7e+03      35      61 ..     754     780 ..     750     782 .. 0.86
  16 !   16.1   0.4   2.4e-05    0.0093      10      65 ..     797     852 ..     791     852 .. 0.95
  17 !   25.3   0.4   3.3e-08   1.3e-05       6      61 ..     827     882 ..     822     898 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00026
                             TPR_9 26 PddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                        dp+e+   G +l+ +G++ +A++d   +++l+p+
  gi|386002402|ref|YP_005920701.1| 57 ESDPDEWNNKGYALYLQGNYDEAIQDYKEAIRLDPE 92
                                      579******************************996 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                             TPR_9  23 llaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                        l+P+ +  ++  Gl+ +++G + +A+++ + +++l+p+ 
  gi|386002402|ref|YP_005920701.1|  88 RLDPEFVWPWYNKGLAFEKQGKYDEAIKAYNEAIRLDPEY 127
                                       588999999****************************975 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 9.7e-06
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                         + ++++a+++++  + l+P+ +  +   G +l+ +G + +A+++ + +++l p+ 
  gi|386002402|ref|YP_005920701.1| 105 EKQGKYDEAIKAYNEAIRLDPEYANAWHNKGYALYLQGKYDEAIKAYNEAIRLYPEY 161
                                       567899**********************************************99975 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 2.5e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++++a+++++  + l P+ +  +   G +l+ +G++ +A+++ + +++l+p+
  gi|386002402|ref|YP_005920701.1| 142 GKYDEAIKAYNEAIRLYPEYANAWNSKGYALYSQGNYDEAIKAYNEAIRLDPE 194
                                       6799**********************************************995 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 2.5e-05
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++ ++++a+++++  + l+P+    +r  G  l+ +G ++ A+ + + +++l+p++
  gi|386002402|ref|YP_005920701.1| 174 SQGNYDEAIKAYNEAIRLDPEFMWPWRNKGDTLFSQGKYELAIYAYDEAIRLNPED 229
                                       67889*************************************************87 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 2.8e-05
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                        ++ ++e a+ +++  + l+P+d   +   G +l++lG + +A++
  gi|386002402|ref|YP_005920701.1| 207 FSQGKYELAIYAYDEAIRLNPEDLNSWINKGAALYRLGKYDEAIR 251
                                       56788999***********************************97 PP

  == domain 7  score: 22.7 bits;  conditional E-value: 2.2e-07
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       r  ++++a+++++  + l+P+ ++ +   G++l  +G + +A+++ + +++l+p+ +da
  gi|386002402|ref|YP_005920701.1| 242 RLGKYDEAIRASNEAIRLDPENVYAWHNKGVALNSQGKYDEAIQAYDEAIRLSPEYADA 300
                                       66789*************************************************98776 PP

  == domain 8  score: 16.7 bits;  conditional E-value: 1.6e-05
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       +++ + ++++a+++++  + l+P+ +  +   G++l+ +G   +A+++ + +++l+p+ +da
  gi|386002402|ref|YP_005920701.1| 307 ALLHQGKYDEAIQASNEAISLDPENANGWNIKGVALYNRGKSDEAIKAYDEAIRLSPEYADA 368
                                       5688999**************************************************98776 PP

  == domain 9  score: 22.1 bits;  conditional E-value: 3.3e-07
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       + ++++a+++ +  + l+P+++  ++  Gl l  +G + +A+++++ +++l+p+  d
  gi|386002402|ref|YP_005920701.1| 379 QGKYDEAIQTFNETIRLDPEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEYVD 435
                                       678999**********************************************97655 PP

  == domain 10  score: 18.4 bits;  conditional E-value: 4.6e-06
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       + ++++a+++++ ++ l+P+ ++ +   G +   +G++++A+++++ +++ +p+ +da
  gi|386002402|ref|YP_005920701.1| 447 QSRYDEAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPEYADA 504
                                       7899*************************************************87776 PP

  == domain 11  score: 15.5 bits;  conditional E-value: 3.7e-05
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsa 47 
                                        + +++e+a+++ +    l+P+d++ ++  G++ ++lG +++
  gi|386002402|ref|YP_005920701.1| 513 VSLDKYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKE 554
                                       566899********************************9975 PP

  == domain 12  score: -0.1 bits;  conditional E-value: 2.9
                             TPR_9  22 lllaPddpeerrdRGllla 40 
                                       l ++P+d+  r+  G++l+
  gi|386002402|ref|YP_005920701.1| 570 LRWNPEDANARLSKGIALM 588
                                       89*************9986 PP

  == domain 13  score: 22.9 bits;  conditional E-value: 1.9e-07
                             TPR_9   4 ia.ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladL 52 
                                       +a    +++e a ++++  + l+Pdd+  +  RG +l+ lG + +A+++ 
  gi|386002402|ref|YP_005920701.1| 592 LAlETLDKYEDAVQAYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQAY 641
                                       55466799***************************************986 PP

  == domain 14  score: 19.8 bits;  conditional E-value: 1.7e-06
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +++a ++++ +l l+P+d+  +   G +l+ l+  ++ +++L+ +++l+p+++
  gi|386002402|ref|YP_005920701.1| 634 YDEAVQAYDEVLRLNPEDANAWKKKGYALHSLEEHEESVKALDEAIRLNPNDA 686
                                       789***********************************************886 PP

  == domain 15  score: -1.4 bits;  conditional E-value: 7.1
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapd 61 
                                        G++l ++  +++A+++++ +++l+p+
  gi|386002402|ref|YP_005920701.1| 754 KGIILGEQHEYNEAMQAFNEAVSLNPA 780
                                       6888889999***********999996 PP

  == domain 16  score: 16.1 bits;  conditional E-value: 2.4e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++ +a++++++ + l+P+++  +   G +l  +G  ++A+ + + +++l+pd++da
  gi|386002402|ref|YP_005920701.1| 797 KYYEAIEAIDMAISLNPESALAWNYKGAALRGQGKHEEAILAYDEAIRLNPDDEDA 852
                                       56689*************************************************97 PP

  == domain 17  score: 25.3 bits;  conditional E-value: 3.3e-08
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                         + ++e+a+ +++  + l+Pdd + +   Gl+l+ +G++s+A+++ +++++l+ +
  gi|386002402|ref|YP_005920701.1| 827 RGQGKHEEAILAYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQAYDRAIDLNSQ 882
                                       567899*********************************************99864 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2     0.005       1.9       7      31 ..      67      91 ..      65      92 .. 0.90
   2 !   16.4   0.2   2.7e-05      0.01       4      32 ..      98     126 ..      97     127 .. 0.93
   3 !   18.2   0.5     7e-06    0.0027       2      32 ..     130     160 ..     129     161 .. 0.91
   4 !   12.5   0.2   0.00046      0.18       7      31 ..     169     193 ..     168     194 .. 0.92
   5 ?    4.5   0.0      0.17        66       7      32 ..     203     228 ..     201     229 .. 0.89
   6 ?    5.6   0.0     0.078        30       7      32 ..     237     262 ..     234     263 .. 0.85
   7 !   10.9   0.1    0.0016       0.6       1      32 [.     265     296 ..     265     297 .. 0.89
   8 ?    5.6   0.0     0.074        28       6      32 ..     304     330 ..     300     331 .. 0.88
   9 ?    8.2   0.0     0.011       4.2       7      31 ..     339     363 ..     337     365 .. 0.88
  10 !   10.5   0.0    0.0021      0.81       7      32 ..     373     398 ..     371     399 .. 0.91
  11 !   13.8   0.1   0.00018     0.069       2      32 ..     402     432 ..     401     433 .. 0.94
  12 !   11.6   0.1   0.00094      0.36       1      32 [.     435     466 ..     435     467 .. 0.93
  13 !    9.3   0.1    0.0049       1.9       7      32 ..     475     500 ..     474     501 .. 0.88
  14 ?    3.7   0.0       0.3   1.1e+02       7      32 ..     509     534 ..     507     535 .. 0.85
  15 ?    2.9   0.0      0.52     2e+02       1      30 [.     537     566 ..     537     569 .. 0.84
  16 !   10.0   0.1    0.0031       1.2       2      32 ..     586     616 ..     585     617 .. 0.94
  17 !   12.5   0.1   0.00047      0.18       5      32 ..     623     650 ..     619     651 .. 0.89
  18 ?    1.9   0.0       1.1   4.3e+02       7      32 ..     659     684 ..     657     685 .. 0.86
  19 ?    0.6   0.0         3   1.2e+03      16      30 ..     709     723 ..     701     732 .. 0.76
  20 ?   -0.1   0.0       4.9   1.9e+03      15      31 ..     763     779 ..     755     780 .. 0.84
  21 ?    0.7   0.0       2.8   1.1e+03      10      33 .]     791     815 ..     791     815 .. 0.89
  22 ?    6.2   0.0     0.047        18       8      32 ..     824     848 ..     817     849 .. 0.83
  23 !   11.4   0.1     0.001      0.39       7      28 ..     857     878 ..     855     882 .. 0.91
  24 ?   -0.5   0.4       6.8   2.6e+03       1      20 [.     885     904 ..     885     906 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.005
                                      HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  7 alsyrklgdtdkAlealerlikeYP 31
                                      +++++ +g++d+A++ +++ i+  P
  gi|386002402|ref|YP_005920701.1| 67 GYALYLQGNYDEAIQDYKEAIRLDP 91
                                      89999999*************9888 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       y+ +l+++k+g++d+A++a+++ i+  P+
  gi|386002402|ref|YP_005920701.1|  98 YNKGLAFEKQGKYDEAIKAYNEAIRLDPE 126
                                       899*********************99885 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 7e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A  + +++++ +g++d+A++a+++ i+ YP+
  gi|386002402|ref|YP_005920701.1| 130 AWHNKGYALYLQGKYDEAIKAYNEAIRLYPE 160
                                       5667899***********************6 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00046
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       +++++++g++d+A++a+++ i+  P
  gi|386002402|ref|YP_005920701.1| 169 GYALYSQGNYDEAIKAYNEAIRLDP 193
                                       7899*****************9888 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +  ++++g+++ A+ a+++ i+  P+
  gi|386002402|ref|YP_005920701.1| 203 GDTLFSQGKYELAIYAYDEAIRLNPE 228
                                       66789999*************99996 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++++lg++d+A++a ++ i+  P+
  gi|386002402|ref|YP_005920701.1| 237 GAALYRLGKYDEAIRASNEAIRLDPE 262
                                       56788899********9999998886 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +A  + + ++ ++g++d+A++a+++ i+  P+
  gi|386002402|ref|YP_005920701.1| 265 YAWHNKGVALNSQGKYDEAIQAYDEAIRLSPE 296
                                       677888999999***************98885 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                        +++++ +g++d+A++a ++ i+  P+
  gi|386002402|ref|YP_005920701.1| 304 KGEALLHQGKYDEAIQASNEAISLDPE 330
                                       589999*9*********9999988876 PP

  == domain 9  score: 8.2 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + ++++ g++d+A++a+++ i+  P
  gi|386002402|ref|YP_005920701.1| 339 GVALYNRGKSDEAIKAYDEAIRLSP 363
                                       78999988***********999887 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       +ls++++g++d+A++++++ i+  P+
  gi|386002402|ref|YP_005920701.1| 373 GLSLKSQGKYDEAIQTFNETIRLDPE 398
                                       89999***************999886 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A y+ +l + ++g++d+A++a+++ i+  P+
  gi|386002402|ref|YP_005920701.1| 402 AWYNKGLTLNNQGKYDEAIQAFDEAIRLNPE 432
                                       89************************99996 PP

  == domain 12  score: 11.6 bits;  conditional E-value: 0.00094
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       dA y  + ++ ++ ++d+A++a++++ik  P+
  gi|386002402|ref|YP_005920701.1| 435 DAWYSKGNALDSQSRYDEAIQAYDEVIKLNPE 466
                                       789999999***99**************9996 PP

  == domain 13  score: 9.3 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++ ++g++ +A++a+++ i++ P+
  gi|386002402|ref|YP_005920701.1| 475 GTAFNSQGRYNEAIKAFDEAIRRNPE 500
                                       5667779****************996 PP

  == domain 14  score: 3.7 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++ +l+++++A++a+++  +  P+
  gi|386002402|ref|YP_005920701.1| 509 GVALVSLDKYEEAIQAFDEATRLNPE 534
                                       667778899**********9998885 PP

  == domain 15  score: 2.9 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeY 30 
                                       dA +k + +++ lg++ + ++  +  i+ Y
  gi|386002402|ref|YP_005920701.1| 537 DAWLKKGVAFYHLGKYKETIQVCNVSIQAY 566
                                       799*********99***9999877766666 PP

  == domain 16  score: 10.0 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       Al++ +l+++ l+++++A++a+++ i+  Pd
  gi|386002402|ref|YP_005920701.1| 586 ALMLKGLALETLDKYEDAVQAYDEAISLNPD 616
                                       89999******9****************998 PP

  == domain 17  score: 12.5 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                                       +++ ++++lg++d+A++a++++++  P+
  gi|386002402|ref|YP_005920701.1| 623 NRGAALYSLGKYDEAVQAYDEVLRLNPE 650
                                       6788999999**************9996 PP

  == domain 18  score: 1.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       ++++ +l +++++++al++ i+  P+
  gi|386002402|ref|YP_005920701.1| 659 GYALHSLEEHEESVKALDEAIRLNPN 684
                                       6777786799*************998 PP

  == domain 19  score: 0.6 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHH- CS
                             TPR_6  16 tdkAlealerlikeY 30 
                                       +++A++a+++ i+ Y
  gi|386002402|ref|YP_005920701.1| 709 SEEAIRAYNETITTY 723
                                       678888888887776 PP

  == domain 20  score: -0.1 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHHHH-T CS
                             TPR_6  15 dtdkAlealerlikeYP 31 
                                       ++ +A++a+++ ++  P
  gi|386002402|ref|YP_005920701.1| 763 EYNEAMQAFNEAVSLNP 779
                                       689*******9998777 PP

  == domain 21  score: 0.7 bits;  conditional E-value: 2.8
                                       HHH.HHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  10 yrk.lgdtdkAlealerlikeYPdS 33 
                                       y++ +g++ +A+ea +  i+  P+S
  gi|386002402|ref|YP_005920701.1| 791 YLNdQGKYYEAIEAIDMAISLNPES 815
                                       666689**************99998 PP

  == domain 22  score: 6.2 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   8 lsyrklgdtdkAlealerlikeYPd 32 
                                        ++r +g++++A+ a+++ i+  Pd
  gi|386002402|ref|YP_005920701.1| 824 AALRGQGKHEEAILAYDEAIRLNPD 848
                                       4455579****************98 PP

  == domain 23  score: 11.4 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       +l+++++g++++A++a++r i+
  gi|386002402|ref|YP_005920701.1| 857 GLALYSQGNYSEAIQAYDRAID 878
                                       89*****************997 PP

  == domain 24  score: -0.5 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAl 20 
                                       +A y+ + ++ +l++ ++A 
  gi|386002402|ref|YP_005920701.1| 885 QAWYNKGDALDALKNFTQAA 904
                                       68999999999999999996 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00038      0.15       3      33 ..      64      92 ..      62      94 .. 0.86
   2 !   14.6   0.1   6.3e-05     0.024       3      33 ..      98     126 ..      97     127 .. 0.91
   3 ?    7.0   0.2     0.017       6.6       1      28 [.     130     155 ..     130     160 .. 0.84
   4 !   11.8   0.0   0.00053       0.2       2      33 ..     165     194 ..     164     196 .. 0.85
   5 ?    6.2   0.0     0.032        12       4      34 ..     201     229 ..     199     231 .. 0.87
   6 ?    5.7   0.0     0.046        17       2      33 ..     233     262 ..     232     265 .. 0.78
   7 !   14.6   0.0   6.6e-05     0.025       1      32 [.     266     295 ..     266     296 .. 0.92
   8 ?    5.4   0.1     0.058        22       1      21 [.     300     320 ..     300     333 .. 0.79
   9 ?    4.6   0.0     0.098        38       6      32 ..     339     363 ..     335     364 .. 0.86
  10 !   10.8   0.0    0.0011       0.4       1      35 [.     368     400 ..     368     401 .. 0.92
  11 !    9.6   0.0    0.0025      0.97       1      32 [.     402     431 ..     402     432 .. 0.87
  12 !    8.1   0.0     0.008         3       1      29 [.     436     462 ..     436     466 .. 0.82
  13 ?    7.4   0.0     0.012       4.8       1      32 [.     470     499 ..     470     500 .. 0.88
  14 !   11.9   0.0   0.00046      0.18       1      35 [.     504     536 ..     504     537 .. 0.94
  15 ?    3.7   0.1       0.2        78       6      34 ..     591     617 ..     586     619 .. 0.78
  16 !   11.3   0.2   0.00076      0.29       2      35 ..     621     652 ..     620     653 .. 0.84
  17 ?   -0.2   0.0       3.5   1.3e+03       7      35 ..     660     686 ..     655     687 .. 0.87
  18 !    8.6   0.1    0.0054       2.1       1      33 [.     818     850 ..     818     852 .. 0.80
  19 !   11.9   0.2   0.00047      0.18       1      29 [.     852     878 ..     852     894 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00038
                             TPR_7  3 lnLarlysrlGdyeeAielyeqsLaltkdpe 33
                                      +n + +   +G+y+eAi+ y++  a++ dpe
  gi|386002402|ref|YP_005920701.1| 64 NNKGYALYLQGNYDEAIQDYKE--AIRLDPE 92
                                      6777787789************..9999986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.3e-05
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +n + +++++G+y+eAi+ y +  a++ dpe
  gi|386002402|ref|YP_005920701.1|  98 YNKGLAFEKQGKYDEAIKAYNE--AIRLDPE 126
                                       78899*****************..9998885 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.017
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n + +   +G+y+eAi+ y +  a+
  gi|386002402|ref|YP_005920701.1| 130 AWHNKGYALYLQGKYDEAIKAYNE--AI 155
                                       688999999999**********98..44 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00053
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++  + +  ++G+y+eAi+ y +  a++ dpe
  gi|386002402|ref|YP_005920701.1| 165 WNSKGYALYSQGNYDEAIKAYNE--AIRLDPE 194
                                       66667788899************..9999986 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.032
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       n +++ +++G+ye Ai  y +  a++  ped
  gi|386002402|ref|YP_005920701.1| 201 NKGDTLFSQGKYELAIYAYDE--AIRLNPED 229
                                       7799*****************..88888776 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.046
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       + n + +  rlG+y+eAi+   +  a++ dpe
  gi|386002402|ref|YP_005920701.1| 233 WINKGAALYRLGKYDEAIRASNE--AIRLDPE 262
                                       668899999*********97666..6666666 PP

  == domain 7  score: 14.6 bits;  conditional E-value: 6.6e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n +++  ++G+y+eAi+ y +  a++ +p
  gi|386002402|ref|YP_005920701.1| 266 AWHNKGVALNSQGKYDEAIQAYDE--AIRLSP 295
                                       799*********************..988887 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.058
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       a+++ +++   +G+y+eAi+ 
  gi|386002402|ref|YP_005920701.1| 300 AWNRKGEALLHQGKYDEAIQA 320
                                       678899*************85 PP

  == domain 9  score: 4.6 bits;  conditional E-value: 0.098
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       +++  ++G+ +eAi+ y +  a++ +p
  gi|386002402|ref|YP_005920701.1| 339 GVALYNRGKSDEAIKAYDE--AIRLSP 363
                                       6778889************..988887 PP

  == domain 10  score: 10.8 bits;  conditional E-value: 0.0011
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++n +    ++G+y+eAi+ + +   ++ dpe++
  gi|386002402|ref|YP_005920701.1| 368 AWNNKGLSLKSQGKYDEAIQTFNE--TIRLDPEHV 400
                                       6899999999**************..*****9986 PP

  == domain 11  score: 9.6 bits;  conditional E-value: 0.0025
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n + +  ++G+y+eAi+ + +  a++  p
  gi|386002402|ref|YP_005920701.1| 402 AWYNKGLTLNNQGKYDEAIQAFDE--AIRLNP 431
                                       688999999***************..777655 PP

  == domain 12  score: 8.1 bits;  conditional E-value: 0.008
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++  +++  ++ +y+eAi+ y +  ++ 
  gi|386002402|ref|YP_005920701.1| 436 AWYSKGNALDSQSRYDEAIQAYDE--VIK 462
                                       5677899***************99..544 PP

  == domain 13  score: 7.4 bits;  conditional E-value: 0.012
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++  + ++ ++G+y eAi+ + +  a+++ p
  gi|386002402|ref|YP_005920701.1| 470 AWNSKGTAFNSQGRYNEAIKAFDE--AIRRNP 499
                                       5677788999**************..999887 PP

  == domain 14  score: 11.9 bits;  conditional E-value: 0.00046
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++n +++ ++l +yeeAi+ + +  a++  peda
  gi|386002402|ref|YP_005920701.1| 504 AWNNKGVALVSLDKYEEAIQAFDE--ATRLNPEDA 536
                                       799*********************..***999986 PP

  == domain 15  score: 3.7 bits;  conditional E-value: 0.2
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       + + + l +ye+A++ y +  a+   p+d
  gi|386002402|ref|YP_005920701.1| 591 GLALETLDKYEDAVQAYDE--AISLNPDD 617
                                       667778999**********..88777766 PP

  == domain 16  score: 11.3 bits;  conditional E-value: 0.00076
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       + n + +  +lG+y+eA++ y +  +l+  peda
  gi|386002402|ref|YP_005920701.1| 621 WENRGAALYSLGKYDEAVQAYDE--VLRLNPEDA 652
                                       6688899999*************..888777775 PP

  == domain 17  score: -0.2 bits;  conditional E-value: 3.5
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltkdpeda 35 
                                        + ++l ++ee ++ + +  a++  p+da
  gi|386002402|ref|YP_005920701.1| 660 YALHSLEEHEESVKALDE--AIRLNPNDA 686
                                       5788999***********..999999886 PP

  == domain 18  score: 8.6 bits;  conditional E-value: 0.0054
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a+++ + + + +G++eeAi  y ++++l  d+e
  gi|386002402|ref|YP_005920701.1| 818 AWNYKGAALRGQGKHEEAILAYDEAIRLNPDDE 850
                                       678899999***************555555555 PP

  == domain 19  score: 11.9 bits;  conditional E-value: 0.00047
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++n + +  ++G+y+eAi+ y +  a++
  gi|386002402|ref|YP_005920701.1| 852 AWNNKGLALYSQGNYSEAIQAYDR--AID 878
                                       78999*******************..554 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   3.1e-05     0.012       6      30 ..      64      88 ..      64      89 .. 0.95
   2 ?    4.2   0.1      0.11        41      13      30 ..     105     122 ..      99     123 .. 0.84
   3 !   11.5   1.0   0.00055      0.21       6      32 ..     132     158 ..     128     158 .. 0.92
   4 !   10.8   0.4   0.00093      0.36       7      30 ..     167     190 ..     162     191 .. 0.88
   5 ?    2.1   0.1       0.5   1.9e+02       9      30 ..     203     224 ..     200     226 .. 0.88
   6 ?    6.1   0.2     0.027        10       7      29 ..     235     257 ..     233     259 .. 0.83
   7 !   13.8   0.1   0.00011     0.041       6      31 ..     268     293 ..     267     294 .. 0.93
   8 ?    3.5   0.1      0.18        68       9      29 ..     305     325 ..     299     327 .. 0.83
   9 !    9.0   0.0    0.0033       1.3       9      31 ..     339     361 ..     338     362 .. 0.94
  10 ?    4.7   0.0     0.075        29       6      23 ..     370     387 ..     366     395 .. 0.84
  11 !   11.3   0.1   0.00063      0.24       7      31 ..     405     429 ..     404     430 .. 0.91
  12 ?    5.8   0.0     0.035        13       9      30 ..     441     462 ..     440     464 .. 0.93
  13 ?    7.2   0.1     0.012       4.7       9      31 ..     475     497 ..     468     498 .. 0.86
  14 ?    4.0   0.1      0.12        48       6      28 ..     506     528 ..     502     532 .. 0.90
  15 ?    3.1   0.1      0.24        91       9      31 ..     591     613 ..     590     614 .. 0.86
  16 !   13.4   0.5   0.00014     0.053       7      30 ..     623     646 ..     622     648 .. 0.93
  17 ?    2.6   0.1      0.34   1.3e+02       9      31 ..     659     681 ..     659     682 .. 0.92
  18 ?    2.7   0.1      0.32   1.2e+02      17      34 ..     701     718 ..     700     730 .. 0.82
  19 ?    2.8   0.0       0.3   1.2e+02       9      30 ..     755     776 ..     755     778 .. 0.92
  20 ?   -1.2   0.0       5.6   2.1e+03      11      26 ..     791     806 ..     789     811 .. 0.76
  21 !    7.6   0.3    0.0095       3.6       9      30 ..     823     844 ..     819     846 .. 0.91
  22 !   14.1   0.4   8.4e-05     0.032       6      35 ..     854     883 ..     852     886 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
                            TPR_10  6 nNLanalrqrgrydeAealleeala 30
                                      nN + al+ +g+ydeA ++++ea++
  gi|386002402|ref|YP_005920701.1| 64 NNKGYALYLQGNYDEAIQDYKEAIR 88
                                      899********************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                            TPR_10  13 rqrgrydeAealleeala 30 
                                        ++g+ydeA + + ea++
  gi|386002402|ref|YP_005920701.1| 105 EKQGKYDEAIKAYNEAIR 122
                                       579*************97 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00055
                            TPR_10   6 nNLanalrqrgrydeAealleealair 32 
                                       +N + al+ +g+ydeA + + ea++++
  gi|386002402|ref|YP_005920701.1| 132 HNKGYALYLQGKYDEAIKAYNEAIRLY 158
                                       899*********************987 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00093
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                         + al+++g+ydeA + + ea++
  gi|386002402|ref|YP_005920701.1| 167 SKGYALYSQGNYDEAIKAYNEAIR 190
                                       5589******************97 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.5
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + +l+++g+y+ A   ++ea++
  gi|386002402|ref|YP_005920701.1| 203 GDTLFSQGKYELAIYAYDEAIR 224
                                       7799****************97 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.027
                            TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                       N ++al+++g+ydeA +   ea+
  gi|386002402|ref|YP_005920701.1| 235 NKGAALYRLGKYDEAIRASNEAI 257
                                       6699***********98766666 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 0.00011
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       +N ++al ++g+ydeA + ++ea+++
  gi|386002402|ref|YP_005920701.1| 268 HNKGVALNSQGKYDEAIQAYDEAIRL 293
                                       6889*******************986 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.18
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       + al ++g+ydeA +   ea+
  gi|386002402|ref|YP_005920701.1| 305 GEALLHQGKYDEAIQASNEAI 325
                                       78999********98766666 PP

  == domain 9  score: 9.0 bits;  conditional E-value: 0.0033
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       ++al++rg+ deA + ++ea+++
  gi|386002402|ref|YP_005920701.1| 339 GVALYNRGKSDEAIKAYDEAIRL 361
                                       79******************986 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.075
                            TPR_10   6 nNLanalrqrgrydeAea 23 
                                       nN +  l ++g+ydeA +
  gi|386002402|ref|YP_005920701.1| 370 NNKGLSLKSQGKYDEAIQ 387
                                       999*************76 PP

  == domain 11  score: 11.3 bits;  conditional E-value: 0.00063
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N + +l ++g+ydeA + ++ea+++
  gi|386002402|ref|YP_005920701.1| 405 NKGLTLNNQGKYDEAIQAFDEAIRL 429
                                       56899*****************985 PP

  == domain 12  score: 5.8 bits;  conditional E-value: 0.035
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +nal ++ rydeA + ++e++ 
  gi|386002402|ref|YP_005920701.1| 441 GNALDSQSRYDEAIQAYDEVIK 462
                                       899****************996 PP

  == domain 13  score: 7.2 bits;  conditional E-value: 0.012
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + a  ++gry+eA + ++ea+++
  gi|386002402|ref|YP_005920701.1| 475 GTAFNSQGRYNEAIKAFDEAIRR 497
                                       667789**************985 PP

  == domain 14  score: 4.0 bits;  conditional E-value: 0.12
                            TPR_10   6 nNLanalrqrgrydeAealleea 28 
                                       nN ++al ++ +y+eA + ++ea
  gi|386002402|ref|YP_005920701.1| 506 NNKGVALVSLDKYEEAIQAFDEA 528
                                       999****************9998 PP

  == domain 15  score: 3.1 bits;  conditional E-value: 0.24
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al  + +y++A++ ++ea+++
  gi|386002402|ref|YP_005920701.1| 591 GLALETLDKYEDAVQAYDEAISL 613
                                       567778899***********985 PP

  == domain 16  score: 13.4 bits;  conditional E-value: 0.00014
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++al+++g+ydeA++ ++e+l+
  gi|386002402|ref|YP_005920701.1| 623 NRGAALYSLGKYDEAVQAYDEVLR 646
                                       779*******************97 PP

  == domain 17  score: 2.6 bits;  conditional E-value: 0.34
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al+++ +++e+++ l+ea+++
  gi|386002402|ref|YP_005920701.1| 659 GYALHSLEEHEESVKALDEAIRL 681
                                       6799****************985 PP

  == domain 18  score: 2.7 bits;  conditional E-value: 0.32
                            TPR_10  17 rydeAealleealairrr 34 
                                       +ydeA +  eea++++ +
  gi|386002402|ref|YP_005920701.1| 701 KYDEAINASEEAIRAYNE 718
                                       688899999999888866 PP

  == domain 19  score: 2.8 bits;  conditional E-value: 0.3
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +++l ++ +y+eA++ + ea++
  gi|386002402|ref|YP_005920701.1| 755 GIILGEQHEYNEAMQAFNEAVS 776
                                       78999**************997 PP

  == domain 20  score: -1.2 bits;  conditional E-value: 5.6
                            TPR_10  11 alrqrgrydeAealle 26 
                                       +l ++g+y eA +  +
  gi|386002402|ref|YP_005920701.1| 791 YLNDQGKYYEAIEAID 806
                                       789********88655 PP

  == domain 21  score: 7.6 bits;  conditional E-value: 0.0095
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       ++alr +g+++eA   ++ea++
  gi|386002402|ref|YP_005920701.1| 823 GAALRGQGKHEEAILAYDEAIR 844
                                       89******************97 PP

  == domain 22  score: 14.1 bits;  conditional E-value: 8.4e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealairrrl 35 
                                       nN + al+++g+y eA + +++a+++  +l
  gi|386002402|ref|YP_005920701.1| 854 NNKGLALYSQGNYSEAIQAYDRAIDLNSQL 883
                                       899*********************986665 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0034       1.3     206     257 ..      74     125 ..      67     136 .. 0.92
   2 !    9.5   0.1     0.001       0.4     206     256 ..     142     192 ..     126     194 .. 0.92
   3 !    8.4   0.0    0.0023      0.88     206     259 ..     210     263 ..     205     270 .. 0.93
   4 !   18.5   0.1     2e-06   0.00077     203     257 ..     275     329 ..     261     332 .. 0.92
   5 !   12.2   0.0   0.00016     0.062     205     256 ..     345     396 ..     340     402 .. 0.93
   6 !   10.3   0.0   0.00062      0.24     202     255 ..     410     463 ..     398     466 .. 0.86
   7 !   10.1   0.1   0.00072      0.28     203     252 ..     445     494 ..     442     512 .. 0.88
   8 ?    3.7   0.0     0.061        23     205     251 ..     515     561 ..     510     572 .. 0.88
   9 !   19.6   0.9   9.2e-07   0.00035      13      99 ..     593     678 ..     583     735 .. 0.88
  10 !   13.0   0.1   9.5e-05     0.036     180     258 ..     772     850 ..     752     863 .. 0.79
  11 ?    3.8   0.1     0.058        22     206     257 ..     864     915 ..     853     919 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       g++++A++   +ai+ +p++v  +++K+  ++++G  ++A+++ +ea +lD 
  gi|386002402|ref|YP_005920701.1|  74 GNYDEAIQDYKEAIRLDPEFVWPWYNKGLAFEKQGKYDEAIKAYNEAIRLDP 125
                                       67899******************************************99995 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       g++++A++  ++ai+  p+  + +  K+  l  +G+ ++A+++ +ea +lD
  gi|386002402|ref|YP_005920701.1| 142 GKYDEAIKAYNEAIRLYPEYANAWNSKGYALYSQGNYDEAIKAYNEAIRLD 192
                                       6799*******************************************9999 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0023
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       g++e A+   d+ai+ +p+ ++ +++K+  l + G  ++A+++ +ea +lD + 
  gi|386002402|ref|YP_005920701.1| 210 GKYELAIYAYDEAIRLNPEDLNSWINKGAALYRLGKYDEAIRASNEAIRLDPEN 263
                                       678999********************************************9765 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 2e-06
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       +  g++++A++  d+ai+ +p+  + + +K++ l h+G  ++A+++ +ea +lD 
  gi|386002402|ref|YP_005920701.1| 275 NSQGKYDEAIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAISLDP 329
                                       67899************************************************95 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00016
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        g+ ++A++  d+ai+ +p+  + + +K+  lk +G  ++A+++ +e+ +lD
  gi|386002402|ref|YP_005920701.1| 345 RGKSDEAIKAYDEAIRLSPEYADAWNNKGLSLKSQGKYDEAIQTFNETIRLD 396
                                       467899*****************************************99999 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00062
                                       HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                        ++ g++++A++  d+ai+ +p+ v+ ++ K++ l  +   ++A+++ +e  kl
  gi|386002402|ref|YP_005920701.1| 410 LNNQGKYDEAIQAFDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQAYDEVIKL 463
                                       4568899******************************99999999999987666 PP

  == domain 7  score: 10.1 bits;  conditional E-value: 0.00072
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                       d   ++++A++  d+ i+ +p+  + +  K++ +  +G  ++A+++ +ea
  gi|386002402|ref|YP_005920701.1| 445 DSQSRYDEAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIKAFDEA 494
                                       6778899*****************************************99 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.061
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                       l ++e+A++  d+a + +p+  + +l K+  + h G  k+ ++v + 
  gi|386002402|ref|YP_005920701.1| 515 LDKYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKETIQVCNV 561
                                       56799**********************************99998764 PP

  == domain 9  score: 19.6 bits;  conditional E-value: 9.2e-07
                                       HHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-H CS
                             NARP1  13 iieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskede 89 
                                        +e  +k+e+A++  +e+ +   D +a  e+++  l  Lg+++eA ++y + l+ npe+ + +++   a++  +e +
  gi|386002402|ref|YP_005920701.1| 593 ALETLDKYEDAVQAYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLRLNPEDANAWKKKGYALHSLEE-H 668
                                       5677899*****************************************************999999999974444.5 PP

                                       HHHHHHHHHT CS
                             NARP1  90 eallalydel 99 
                                       e+ ++++de+
  gi|386002402|ref|YP_005920701.1| 669 EESVKALDEA 678
                                       5555555555 PP

  == domain 10  score: 13.0 bits;  conditional E-value: 9.5e-05
                                       .GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC. CS
                             NARP1 180 nedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl. 255
                                       ne  + +p+ +++w   f  ++ +  g++ +A+e id ai+ +p++   +  K+  l+ +G  ++A+ + +ea +l 
  gi|386002402|ref|YP_005920701.1| 772 NEAVSLNPAGSFIW--SFKGKYLNDQGKYYEAIEAIDMAISLNPESALAWNYKGAALRGQGKHEEAILAYDEAIRLn 846
                                       34456666677555..58899****************************************************9883 PP

                                       .TTT CS
                             NARP1 256 .Dla 258
                                        D +
  gi|386002402|ref|YP_005920701.1| 847 pDDE 850
                                       3444 PP

  == domain 11  score: 3.8 bits;  conditional E-value: 0.058
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       g++++A++  d+ai+ + +lv+ +++K+  l    ++++Aa +   +r+ D 
  gi|386002402|ref|YP_005920701.1| 864 GNYSEAIQAYDRAIDLNSQLVQAWYNKGDALDALKNFTQAAMAHSLGRERDM 915
                                       67899************************************99999999885 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.15        58      75     124 ..      73     122 ..      66     126 .. 0.90
   2 !   11.3   0.6   0.00089      0.34      71     124 ..     137     190 ..     119     195 .. 0.87
   3 !   15.1   0.1   6.1e-05     0.023      56     125 ..     224     293 ..     217     297 .. 0.87
   4 !   18.3   0.0   6.5e-06    0.0025      56     125 ..     292     361 ..     289     365 .. 0.91
   5 ?    2.3   0.0      0.56   2.1e+02      75     124 ..     379     428 ..     372     436 .. 0.87
   6 ?    6.8   0.0     0.023       8.7      70     124 ..     442     496 ..     425     501 .. 0.84
   7 ?    3.3   0.0      0.27     1e+02      71     142 ..     511     582 ..     500     586 .. 0.86
   8 !   14.2   1.5   0.00012     0.044      22     121 ..     574     677 ..     564     682 .. 0.79
   9 !   22.2   0.2   3.9e-07   0.00015      71     124 ..     825     878 ..     811     886 .. 0.90
  10 ?   -0.6   0.0       4.2   1.6e+03      99     128 ..     880     907 ..     878     916 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        G ++ea+++++++++++P   + +    +A  ++G+  eA+++Y+++ r
  gi|386002402|ref|YP_005920701.1|  73 QGNYDEAIQDYKEAIRLDPEFVWPWYNKGLAFEKQGKYDEAIKAYNEAIR 122
                                       58999****************************************99865 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00089
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a+   G+++ea++ ++++++++P   +++     Al+ +G+  eA+++Y+++ r
  gi|386002402|ref|YP_005920701.1| 137 ALYLQGKYDEAIKAYNEAIRLYPEYANAWNSKGYALYSQGNYDEAIKAYNEAIR 190
                                       566679********************************************9865 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       rl+ + l       +a+ rlG+++ea++  +++++++P +  ++     Al  +G+  eA+++Y+++ rl
  gi|386002402|ref|YP_005920701.1| 224 RLNPEDLNSWINKGAALYRLGKYDEAIRASNEAIRLDPENVYAWHNKGVALNSQGKYDEAIQAYDEAIRL 293
                                       555566666666778999***********************************************98765 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       rl+ +  +a  +  ea+l+ G+++ea++  +++++++P + + +     Al+  G+  eA+++Y+++ rl
  gi|386002402|ref|YP_005920701.1| 292 RLSPEYADAWNRKGEALLHQGKYDEAIQASNEAISLDPENANGWNIKGVALYNRGKSDEAIKAYDEAIRL 361
                                       56666677888999***************************************************98765 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.56
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                        G+++ea+++ ++ ++++P + +++    + l  +G+  eA+++++++ r
  gi|386002402|ref|YP_005920701.1| 379 QGKYDEAIQTFNETIRLDPEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIR 428
                                       68899999999999999999999999999999999999999999998765 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.023
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +a+ +  r++ea++ +++ ++++P   +++    +A   +Gr +eA+++++++ r
  gi|386002402|ref|YP_005920701.1| 442 NALDSQSRYDEAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIKAFDEAIR 496
                                       555566799*****************************************99865 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.27
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgpelralh 142
                                       a+++l ++eea++  +++++++P + +++ +   A +++G+  e ++v +   +  +++L   p+ +  +l 
  gi|386002402|ref|YP_005920701.1| 511 ALVSLDKYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKETIQVCNVSIQAYDDDLRWNPEDANARLS 582
                                       678999************************************999999888888888888888887766665 PP

  == domain 8  score: 14.2 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHTT.--SSTTGGGTT...STTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              BTAD  22 peeaaelleaAlal.wrGpaladlea...gewleaererleelrlealealaeaelrlGraeealaelealvaehPl 94 
                                       pe a ++l++++al  +G al+ l++      + +e+  l+ + ++a e + +a+ +lG+++ea++ +++ ++++P 
  gi|386002402|ref|YP_005920701.1| 574 PEDANARLSKGIALmLKGLALETLDKyedAVQAYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLRLNPE 650
                                       66677777777776247888888888432333446777899999999999999999999999999999999999999 PP

                                       -HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  95 rErlhrqlmrAlarsGrqaeALevYer 121
                                       + +++++   Al+ +++ +e  ++ ++
  gi|386002402|ref|YP_005920701.1| 651 DANAWKKKGYALHSLEEHEESVKALDE 677
                                       999999999999999998888777665 PP

  == domain 9  score: 22.2 bits;  conditional E-value: 3.9e-07
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       a+   G++eea+  ++++++++P +E+++    +Al+ +G+ +eA+++Y+r+ +
  gi|386002402|ref|YP_005920701.1| 825 ALRGQGKHEEAILAYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQAYDRAID 878
                                       556689********************************************9865 PP

  == domain 10  score: -0.6 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              BTAD  99 hrqlmrAlarsGrqaeALevYerlrrlLae 128
                                         ql +A +  G+  +AL+ + ++    a 
  gi|386002402|ref|YP_005920701.1| 880 NSQLVQAWYNKGDALDALKNFTQA--AMAH 907
                                       579999*************99876..4444 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.7   6.6e+02     105     127 ..      65      87 ..      63      94 .. 0.78
   2 ?    6.1   0.0     0.029        11     104     127 ..      98     121 ..      92     126 .. 0.89
   3 ?    3.3   0.0      0.21        80     102     129 ..     130     157 ..     125     163 .. 0.84
   4 ?    3.8   0.0      0.14        55     102     127 ..     164     189 ..     159     194 .. 0.85
   5 !   10.3   0.1    0.0014      0.55      62     128 ..     237     292 ..     216     304 .. 0.82
   6 ?    4.2   0.1      0.11        43      63     127 ..     306     359 ..     297     366 .. 0.69
   7 ?    2.9   0.0      0.28   1.1e+02     103     126 ..     369     392 ..     362     399 .. 0.86
   8 ?    7.2   0.0     0.013       5.1      99     127 ..     399     427 ..     383     433 .. 0.84
   9 ?    4.8   0.0     0.071        27      99     127 ..     433     461 ..     430     467 .. 0.87
  10 ?    4.8   0.0      0.07        27     103     126 ..     471     494 ..     464     505 .. 0.86
  11 ?    3.5   0.1      0.19        71     102     127 ..     504     529 ..     476     538 .. 0.64
  12 ?    6.8   0.1     0.017       6.6      60     126 ..     541     610 ..     526     614 .. 0.77
  13 ?    5.4   0.0     0.046        17     101     126 ..     619     644 ..     616     661 .. 0.80
  14 ?    4.0   0.0      0.12        47      45      86 ..     676     717 ..     668     721 .. 0.89
  15 ?   -1.5   0.0       6.2   2.4e+03      81     127 ..     767     809 ..     761     816 .. 0.63
  16 ?    3.0   0.1      0.25        97      91     127 ..     845     877 ..     815     883 .. 0.60
  17 ?    2.1   0.0      0.48   1.8e+02     106     128 ..     856     878 ..     852     919 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmag 127
                                       +++ al   G++dea++ ++ a 
  gi|386002402|ref|YP_005920701.1|  65 NKGYALYLQGNYDEAIQDYKEAI 87 
                                       67788888888888888888775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                                       HHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmag 127
                                       ++++ a+e+ G++dea+ka++ a 
  gi|386002402|ref|YP_005920701.1|  98 YNKGLAFEKQGKYDEAIKAYNEAI 121
                                       799*****************9886 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                       a  +++ al   G++dea+ka++ a  +
  gi|386002402|ref|YP_005920701.1| 130 AWHNKGYALYLQGKYDEAIKAYNEAIRL 157
                                       56789999**************998765 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a  s++ al + G++dea+ka++ a 
  gi|386002402|ref|YP_005920701.1| 164 AWNSKGYALYSQGNYDEAIKAYNEAI 189
                                       556899****************9885 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.0014
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                         al +lg+ydea++++++a+r       l+ ++   W     +++val++ G++dea++a+  a  
  gi|386002402|ref|YP_005920701.1| 237 GAALYRLGKYDEAIRASNEAIR-------LDPENVYAW----HNKGVALNSQGKYDEAIQAYDEAIR 292
                                       5789999999999999999997.......566665555....89*****************998865 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.11
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       eal++ g+ydea++++++a+        l+ ++ + W      ++val + G++dea+ka+  a 
  gi|386002402|ref|YP_005920701.1| 306 EALLHQGKYDEAIQASNEAIS-------LDPENANGWN----IKGVALYNRGKSDEAIKAYDEAI 359
                                       566666667766666666663.......4555555553....47888889999999998888775 PP

  == domain 7  score: 2.9 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrma 126
                                         +++ +l++ G++dea+++f+ +
  gi|386002402|ref|YP_005920701.1| 369 WNNKGLSLKSQGKYDEAIQTFNET 392
                                       56899****************875 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmag 127
                                        +aa ++++ +l++ G++dea++af  a 
  gi|386002402|ref|YP_005920701.1| 399 HVAAWYNKGLTLNNQGKYDEAIQAFDEAI 427
                                       478899*******************9886 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.071
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmag 127
                                       ++ a +s++ al++  r+dea++a+  + 
  gi|386002402|ref|YP_005920701.1| 433 YVDAWYSKGNALDSQSRYDEAIQAYDEVI 461
                                       677899******************98765 PP

  == domain 10  score: 4.8 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrma 126
                                         s+++a+++ Gr++ea+kaf  a
  gi|386002402|ref|YP_005920701.1| 471 WNSKGTAFNSQGRYNEAIKAFDEA 494
                                       568999*************99877 PP

  == domain 11  score: 3.5 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a  +++val +l +++ea++af  a+
  gi|386002402|ref|YP_005920701.1| 504 AWNNKGVALVSLDKYEEAIQAFDEAT 529
                                       44577888888888888888887776 PP

  == domain 12  score: 6.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH..H--TTSTHHHHHH.HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  60 glsealaklgrydealesadkalryfnr..rGeleqdeGklWi.aavfsravaleelGrkdealkafrma 126
                                           a+ +lg+y+e+++  + +++ ++   r + e+++ +l    a++ ++ ale l ++++a++a+  a
  gi|386002402|ref|YP_005920701.1| 541 KKGVAFYHLGKYKETIQVCNVSIQAYDDdlRWNPEDANARLSKgIALMLKGLALETLDKYEDAVQAYDEA 610
                                       5556999*************99998875226666666666643146788*****************9887 PP

  == domain 13  score: 5.4 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrma 126
                                       aa  +r++al +lG++dea++a+  +
  gi|386002402|ref|YP_005920701.1| 619 AAWENRGAALYSLGKYDEAVQAYDEV 644
                                       66678999999999999999998765 PP

  == domain 14  score: 4.0 bits;  conditional E-value: 0.12
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalryfn 86 
                                       +ea   +  da c+   s  l+ + +ydea++++++a+r +n
  gi|386002402|ref|YP_005920701.1| 676 DEAIRLNPNDAGCWLIKSFNLLIIEKYDEAINASEEAIRAYN 717
                                       67777888899999999999*******************998 PP

  == domain 15  score: -1.5 bits;  conditional E-value: 6.2
                                       HHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  81 alryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       a++ fn    l+ ++  +W      +++ l++ G++ ea++a  ma 
  gi|386002402|ref|YP_005920701.1| 767 AMQAFNEAVSLNPAGSFIWS----FKGKYLNDQGKYYEAIEAIDMAI 809
                                       55555555555555554442....36777788888888888877775 PP

  == domain 16  score: 3.0 bits;  conditional E-value: 0.25
                                       TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  91 leqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       l+ d+   W     +++ al + G+++ea++a+  a 
  gi|386002402|ref|YP_005920701.1| 845 LNPDDEDAW----NNKGLALYSQGNYSEAIQAYDRAI 877
                                       444444444....467888888888888888887765 PP

  == domain 17  score: 2.1 bits;  conditional E-value: 0.48
                                       HHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmage 128
                                       ++ al + G+++ea++a+  a +
  gi|386002402|ref|YP_005920701.1| 856 KGLALYSQGNYSEAIQAYDRAID 878
                                       55555556666666665555543 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00066      0.25       8      27 ..      67      84 ..      63      92 .. 0.86
   2 ?    4.8   0.1     0.073        28      13      26 ..     106     117 ..      97     126 .. 0.80
   3 !   12.9   1.2   0.00022     0.082       8      26 ..     135     151 ..     129     154 .. 0.89
   4 !   13.1   0.1   0.00019     0.074       8      26 ..     169     185 ..     163     194 .. 0.87
   5 ?    0.7   0.3       1.4   5.4e+02      10      25 ..     205     220 ..     204     229 .. 0.86
   6 ?    5.5   0.1     0.046        17       8      22 ..     237     251 ..     227     253 .. 0.87
   7 ?    7.4   0.2     0.012       4.5      13      25 ..     276     288 ..     265     290 .. 0.90
   8 ?    2.5   0.0       0.4   1.5e+02      14      23 ..     311     320 ..     309     330 .. 0.94
   9 ?    2.1   0.0      0.54     2e+02      10      25 ..     341     356 ..     339     358 .. 0.89
  10 ?    5.7   0.0     0.039        15      13      24 ..     378     389 ..     373     394 .. 0.90
  11 !    9.2   0.1    0.0032       1.2       9      25 ..     408     424 ..     402     426 .. 0.84
  12 ?    2.2   0.1      0.49   1.9e+02      14      25 ..     447     458 ..     435     460 .. 0.84
  13 ?    3.1   0.0      0.25        95      13      25 ..     480     492 ..     475     493 .. 0.87
  14 ?    3.3   0.0      0.22        83      15      30 ..     516     529 ..     512     535 .. 0.77
  15 ?    0.5   0.3       1.6   6.1e+02      15      25 ..     598     608 ..     596     610 .. 0.90
  16 !   12.3   0.3   0.00033      0.12       8      25 ..     625     642 ..     625     645 .. 0.91
  17 ?   -0.7   0.1       4.1   1.5e+03      15      23 ..     700     708 ..     700     709 .. 0.89
  18 ?    2.7   0.2      0.35   1.3e+02      13      23 ..     794     804 ..     791     809 .. 0.91
  19 !   10.9   0.3   0.00091      0.35       8      25 ..     857     874 ..     857     876 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00066
                                      HHHHHHTT-HHHHHHH..HH CS
                             TPR_3  8 AaefynkkkyqeArelfsYa 27
                                      ++++y++++y+eA++   Y+
  gi|386002402|ref|YP_005920701.1| 67 GYALYLQGNYDEAIQD--YK 84
                                      79************97..65 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.073
                                       HTT-HHHHHHH..H CS
                             TPR_3  13 nkkkyqeArelfsY 26 
                                        ++ky+eA+ +  Y
  gi|386002402|ref|YP_005920701.1| 106 KQGKYDEAIKA--Y 117
                                       59********9..5 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00022
                                       HHHHHHTT-HHHHHHH..H CS
                             TPR_3   8 AaefynkkkyqeArelfsY 26 
                                       ++++y+++ky+eA+ +  Y
  gi|386002402|ref|YP_005920701.1| 135 GYALYLQGKYDEAIKA--Y 151
                                       89************99..4 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00019
                                       HHHHHHTT-HHHHHHH..H CS
                             TPR_3   8 AaefynkkkyqeArelfsY 26 
                                       ++++y++++y+eA+ +  Y
  gi|386002402|ref|YP_005920701.1| 169 GYALYSQGNYDEAIKA--Y 185
                                       89*************9..5 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.4
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++++++ky+ A+ +++
  gi|386002402|ref|YP_005920701.1| 205 TLFSQGKYELAIYAYD 220
                                       5899*******99976 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.046
                                       HHHHHHTT-HHHHHH CS
                             TPR_3   8 AaefynkkkyqeAre 22 
                                       +a++y  +ky+eA+ 
  gi|386002402|ref|YP_005920701.1| 237 GAALYRLGKYDEAIR 251
                                       89***********95 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.012
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       +++ky+eA+++++
  gi|386002402|ref|YP_005920701.1| 276 SQGKYDEAIQAYD 288
                                       69*********87 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.4
                                       TT-HHHHHHH CS
                             TPR_3  14 kkkyqeArel 23 
                                       ++ky+eA+++
  gi|386002402|ref|YP_005920701.1| 311 QGKYDEAIQA 320
                                       8*******97 PP

  == domain 9  score: 2.1 bits;  conditional E-value: 0.54
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++yn +k +eA+ +++
  gi|386002402|ref|YP_005920701.1| 341 ALYNRGKSDEAIKAYD 356
                                       79************76 PP

  == domain 10  score: 5.7 bits;  conditional E-value: 0.039
                                       HTT-HHHHHHH. CS
                             TPR_3  13 nkkkyqeArelf 24 
                                       +++ky+eA+++f
  gi|386002402|ref|YP_005920701.1| 378 SQGKYDEAIQTF 389
                                       69********96 PP

  == domain 11  score: 9.2 bits;  conditional E-value: 0.0032
                                       HHHHHTT-HHHHHHH.. CS
                             TPR_3   9 aefynkkkyqeArelfs 25 
                                        ++ n++ky+eA+++f+
  gi|386002402|ref|YP_005920701.1| 408 LTLNNQGKYDEAIQAFD 424
                                       56669**********98 PP

  == domain 12  score: 2.2 bits;  conditional E-value: 0.49
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       + +y+eA+++++
  gi|386002402|ref|YP_005920701.1| 447 QSRYDEAIQAYD 458
                                       569*******87 PP

  == domain 13  score: 3.1 bits;  conditional E-value: 0.25
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       ++++y+eA+ +f+
  gi|386002402|ref|YP_005920701.1| 480 SQGRYNEAIKAFD 492
                                       79*********87 PP

  == domain 14  score: 3.3 bits;  conditional E-value: 0.22
                                       T-HHHHHHH..HHHHH CS
                             TPR_3  15 kkyqeArelfsYalla 30 
                                       +ky+eA+++f+   ++
  gi|386002402|ref|YP_005920701.1| 516 DKYEEAIQAFD--EAT 529
                                       8********98..555 PP

  == domain 15  score: 0.5 bits;  conditional E-value: 1.6
                                       T-HHHHHHH.. CS
                             TPR_3  15 kkyqeArelfs 25 
                                       +ky++A+++++
  gi|386002402|ref|YP_005920701.1| 598 DKYEDAVQAYD 608
                                       79*******77 PP

  == domain 16  score: 12.3 bits;  conditional E-value: 0.00033
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       +a++y+ +ky+eA+++++
  gi|386002402|ref|YP_005920701.1| 625 GAALYSLGKYDEAVQAYD 642
                                       799*************88 PP

  == domain 17  score: -0.7 bits;  conditional E-value: 4.1
                                       T-HHHHHHH CS
                             TPR_3  15 kkyqeArel 23 
                                       +ky+eA+++
  gi|386002402|ref|YP_005920701.1| 700 EKYDEAINA 708
                                       69*****97 PP

  == domain 18  score: 2.7 bits;  conditional E-value: 0.35
                                       HTT-HHHHHHH CS
                             TPR_3  13 nkkkyqeArel 23 
                                       +++ky+eA+e+
  gi|386002402|ref|YP_005920701.1| 794 DQGKYYEAIEA 804
                                       59*******97 PP

  == domain 19  score: 10.9 bits;  conditional E-value: 0.00091
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       + ++y++++y+eA+++++
  gi|386002402|ref|YP_005920701.1| 857 GLALYSQGNYSEAIQAYD 874
                                       5789************87 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.5   9.6e+02      55      70 ..      74      89 ..      68      92 .. 0.87
   2 ?    3.9   0.0      0.15        56      55      70 ..     108     123 ..      99     131 .. 0.85
   3 ?    4.4   0.0       0.1        39      53      70 ..     140     157 ..     124     166 .. 0.81
   4 ?    3.5   0.0      0.19        72      54      70 ..     175     191 ..     160     194 .. 0.88
   5 ?    5.7   0.0     0.041        16      49      73 ..     238     262 ..     230     266 .. 0.82
   6 ?    5.6   0.0     0.044        17      54      76 ..     277     299 ..     264     302 .. 0.85
   7 ?    3.3   0.0      0.23        87      53      75 ..     310     332 ..     306     340 .. 0.86
   8 ?    4.6   0.0     0.088        34      55      76 ..     346     367 ..     337     372 .. 0.88
   9 ?    2.4   0.0      0.44   1.7e+02      55      71 ..     380     396 ..     372     401 .. 0.86
  10 ?    5.8   0.0     0.038        15      55      73 ..     414     432 ..     400     437 .. 0.82
  11 ?   -0.1   0.0       2.5   9.7e+02      56      76 ..     449     469 ..     445     474 .. 0.87
  12 ?    7.5   0.5     0.011       4.2      39      76 ..     500     537 ..     465     546 .. 0.76
  13 ?    1.0   0.0       1.2   4.6e+02      49      70 ..     592     613 ..     566     617 .. 0.81
  14 ?    1.1   0.0       1.1   4.2e+02      52      73 ..     629     650 ..     620     655 .. 0.84
  15 ?    4.9   0.1     0.071        27      52      70 ..     663     681 ..     659     688 .. 0.87
  16 ?    1.5   0.1      0.82   3.1e+02      55      70 ..     700     715 ..     688     723 .. 0.79
  17 ?    1.9   0.0      0.61   2.3e+02      55      70 ..     762     777 ..     756     780 .. 0.89
  18 ?    2.2   0.1       0.5   1.9e+02      55      76 ..     830     851 ..     824     862 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.5
                            ANAPC5 55 ghneeAvkaleeairl 70
                                      g+++eA++  +eairl
  gi|386002402|ref|YP_005920701.1| 74 GNYDEAIQDYKEAIRL 89
                                      899***********97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       g+++eA+ka +eairl
  gi|386002402|ref|YP_005920701.1| 108 GKYDEAIKAYNEAIRL 123
                                       89************98 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.1
                            ANAPC5  53 dfghneeAvkaleeairl 70 
                                         g+++eA+ka +eairl
  gi|386002402|ref|YP_005920701.1| 140 LQGKYDEAIKAYNEAIRL 157
                                       5599************98 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.19
                            ANAPC5  54 fghneeAvkaleeairl 70 
                                        g+++eA+ka +eairl
  gi|386002402|ref|YP_005920701.1| 175 QGNYDEAIKAYNEAIRL 191
                                       589************97 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.041
                            ANAPC5  49 slhadfghneeAvkaleeairlAre 73 
                                          +++g+++eA++a +eairl  e
  gi|386002402|ref|YP_005920701.1| 238 AALYRLGKYDEAIRASNEAIRLDPE 262
                                       556899***************8655 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.044
                            ANAPC5  54 fghneeAvkaleeairlArenkD 76 
                                        g+++eA++a  eairl+ e +D
  gi|386002402|ref|YP_005920701.1| 277 QGKYDEAIQAYDEAIRLSPEYAD 299
                                       589**************999887 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.23
                            ANAPC5  53 dfghneeAvkaleeairlArenk 75 
                                       + g+++eA++a +eai+l  en+
  gi|386002402|ref|YP_005920701.1| 310 HQGKYDEAIQASNEAISLDPENA 332
                                       4599*************988876 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.088
                            ANAPC5  55 ghneeAvkaleeairlArenkD 76 
                                       g+ +eA+ka  eairl+ e +D
  gi|386002402|ref|YP_005920701.1| 346 GKSDEAIKAYDEAIRLSPEYAD 367
                                       7899************999888 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.44
                            ANAPC5  55 ghneeAvkaleeairlA 71 
                                       g+++eA+++++e+irl 
  gi|386002402|ref|YP_005920701.1| 380 GKYDEAIQTFNETIRLD 396
                                       899***********985 PP

  == domain 10  score: 5.8 bits;  conditional E-value: 0.038
                            ANAPC5  55 ghneeAvkaleeairlAre 73 
                                       g+++eA++a+ eairl  e
  gi|386002402|ref|YP_005920701.1| 414 GKYDEAIQAFDEAIRLNPE 432
                                       89*************9766 PP

  == domain 11  score: -0.1 bits;  conditional E-value: 2.5
                            ANAPC5  56 hneeAvkaleeairlArenkD 76 
                                        ++eA++a  e+i+l  e +D
  gi|386002402|ref|YP_005920701.1| 449 RYDEAIQAYDEVIKLNPEYAD 469
                                       689***********9888777 PP

  == domain 12  score: 7.5 bits;  conditional E-value: 0.011
                            ANAPC5  39 syqyalLnlaslhadfghneeAvkaleeairlArenkD 76 
                                       +y  a  n  +   +++++eeA++a+ ea+rl  e +D
  gi|386002402|ref|YP_005920701.1| 500 EYADAWNNKGVALVSLDKYEEAIQAFDEATRLNPEDAD 537
                                       45555566666667889999999999999999988887 PP

  == domain 13  score: 1.0 bits;  conditional E-value: 1.2
                            ANAPC5  49 slhadfghneeAvkaleeairl 70 
                                           +++++e+Av+a  eai+l
  gi|386002402|ref|YP_005920701.1| 592 LALETLDKYEDAVQAYDEAISL 613
                                       44567899************87 PP

  == domain 14  score: 1.1 bits;  conditional E-value: 1.1
                            ANAPC5  52 adfghneeAvkaleeairlAre 73 
                                       +++g+++eAv+a  e+ rl  e
  gi|386002402|ref|YP_005920701.1| 629 YSLGKYDEAVQAYDEVLRLNPE 650
                                       689*************998766 PP

  == domain 15  score: 4.9 bits;  conditional E-value: 0.071
                            ANAPC5  52 adfghneeAvkaleeairl 70 
                                       ++++++ee+vkal eairl
  gi|386002402|ref|YP_005920701.1| 663 HSLEEHEESVKALDEAIRL 681
                                       468999***********98 PP

  == domain 16  score: 1.5 bits;  conditional E-value: 0.82
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       ++++eA++a eeair 
  gi|386002402|ref|YP_005920701.1| 700 EKYDEAINASEEAIRA 715
                                       6789999999999985 PP

  == domain 17  score: 1.9 bits;  conditional E-value: 0.61
                            ANAPC5  55 ghneeAvkaleeairl 70 
                                       ++++eA++a++ea++l
  gi|386002402|ref|YP_005920701.1| 762 HEYNEAMQAFNEAVSL 777
                                       5799**********87 PP

  == domain 18  score: 2.2 bits;  conditional E-value: 0.5
                            ANAPC5  55 ghneeAvkaleeairlArenkD 76 
                                       g++eeA+ a  eairl  + +D
  gi|386002402|ref|YP_005920701.1| 830 GKHEEAILAYDEAIRLNPDDED 851
                                       789************9877666 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0068       2.6      17      33 ..      73      89 ..      72      89 .. 0.91
   2 !   11.4   0.6   0.00069      0.26      10      33 ..     100     123 ..      98     123 .. 0.87
   3 ?    6.8   1.3     0.018         7      17      33 ..     141     157 ..     139     163 .. 0.92
   4 !    8.8   0.8    0.0044       1.7      17      33 ..     175     191 ..     167     191 .. 0.90
   5 ?    3.7   0.4      0.17        66      17      33 ..     209     225 ..     208     225 .. 0.90
   6 ?   -0.9   0.0       4.8   1.8e+03      17      32 ..     243     258 ..     234     260 .. 0.75
   7 !   11.6   0.4   0.00057      0.22       9      33 ..     269     293 ..     265     294 .. 0.91
   8 ?   -0.1   0.0       2.6     1e+03      16      31 ..     310     325 ..     303     329 .. 0.75
   9 ?    5.4   0.1     0.052        20      14      33 ..     342     361 ..     338     362 .. 0.84
  10 ?    0.2   0.0       2.2   8.2e+02      16      31 ..     378     393 ..     370     395 .. 0.75
  11 ?    6.9   0.1     0.018       6.7      10      33 ..     406     429 ..     402     430 .. 0.86
  12 ?    3.8   0.3      0.16        62      13      29 ..     443     459 ..     438     463 .. 0.84
  13 ?    1.6   0.0      0.76   2.9e+02      16      31 ..     480     495 ..     473     497 .. 0.82
  14 ?    2.6   0.0      0.38   1.5e+02      24      45 ..     515     535 ..     506     547 .. 0.70
  15 !   10.2   0.3    0.0016      0.61       1      32 [.     581     612 ..     581     613 .. 0.95
  16 ?    1.4   0.2      0.89   3.4e+02      18      29 ..     632     643 ..     626     647 .. 0.86
  17 ?    0.3   0.1         2   7.5e+02      19      39 ..     708     728 ..     700     744 .. 0.62
  18 ?    0.2   0.0       2.1   8.1e+02      16      32 ..     760     776 ..     753     777 .. 0.84
  19 ?    1.9   0.1      0.62   2.4e+02      17      32 ..     829     844 ..     822     845 .. 0.90
  20 !   12.7   0.3   0.00026     0.099      16      49 ..     862     897 ..     855     908 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0068
                               MIT 17 agnyeeAlelYkealel 33
                                      +gny+eA++ Ykea++l
  gi|386002402|ref|YP_005920701.1| 73 QGNYDEAIQDYKEAIRL 89
                                      69************975 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00069
                               MIT  10 kAveeDnagnyeeAlelYkealel 33 
                                       k    +++g+y+eA+++Y ea++l
  gi|386002402|ref|YP_005920701.1| 100 KGLAFEKQGKYDEAIKAYNEAIRL 123
                                       566789***************975 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.018
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+y+eA+++Y ea++l
  gi|386002402|ref|YP_005920701.1| 141 QGKYDEAIKAYNEAIRL 157
                                       59************986 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0044
                               MIT  17 agnyeeAlelYkealel 33 
                                       +gny+eA+++Y ea++l
  gi|386002402|ref|YP_005920701.1| 175 QGNYDEAIKAYNEAIRL 191
                                       79************975 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.17
                               MIT  17 agnyeeAlelYkealel 33 
                                       +g+ye A+ +Y ea++l
  gi|386002402|ref|YP_005920701.1| 209 QGKYELAIYAYDEAIRL 225
                                       79************975 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 4.8
                               MIT  17 agnyeeAlelYkeale 32 
                                        g+y+eA+++  ea++
  gi|386002402|ref|YP_005920701.1| 243 LGKYDEAIRASNEAIR 258
                                       6899999998777775 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 0.00057
                               MIT   9 kkAveeDnagnyeeAlelYkealel 33 
                                       +k v + ++g+y+eA+++Y ea++l
  gi|386002402|ref|YP_005920701.1| 269 NKGVALNSQGKYDEAIQAYDEAIRL 293
                                       68899999**************975 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 2.6
                               MIT  16 nagnyeeAlelYkeal 31 
                                        +g+y+eA+++  ea+
  gi|386002402|ref|YP_005920701.1| 310 HQGKYDEAIQASNEAI 325
                                       6789999998766666 PP

  == domain 9  score: 5.4 bits;  conditional E-value: 0.052
                               MIT  14 eDnagnyeeAlelYkealel 33 
                                       + n+g+ +eA+++Y ea++l
  gi|386002402|ref|YP_005920701.1| 342 LYNRGKSDEAIKAYDEAIRL 361
                                       55899************975 PP

  == domain 10  score: 0.2 bits;  conditional E-value: 2.2
                               MIT  16 nagnyeeAlelYkeal 31 
                                       ++g+y+eA++ + e +
  gi|386002402|ref|YP_005920701.1| 378 SQGKYDEAIQTFNETI 393
                                       6899999999887655 PP

  == domain 11  score: 6.9 bits;  conditional E-value: 0.018
                               MIT  10 kAveeDnagnyeeAlelYkealel 33 
                                       k   + n+g+y+eA++++ ea++l
  gi|386002402|ref|YP_005920701.1| 406 KGLTLNNQGKYDEAIQAFDEAIRL 429
                                       5566789**************975 PP

  == domain 12  score: 3.8 bits;  conditional E-value: 0.16
                               MIT  13 eeDnagnyeeAlelYke 29 
                                        +D++  y+eA+++Y e
  gi|386002402|ref|YP_005920701.1| 443 ALDSQSRYDEAIQAYDE 459
                                       6899***********87 PP

  == domain 13  score: 1.6 bits;  conditional E-value: 0.76
                               MIT  16 nagnyeeAlelYkeal 31 
                                       ++g y eA++++ ea+
  gi|386002402|ref|YP_005920701.1| 480 SQGRYNEAIKAFDEAI 495
                                       7899*******99998 PP

  == domain 14  score: 2.6 bits;  conditional E-value: 0.38
                               MIT  24 lelYkealelLlqalkekneer 45 
                                       l++Y+ea++ + +a +  n+e+
  gi|386002402|ref|YP_005920701.1| 515 LDKYEEAIQAFDEATR-LNPED 535
                                       6778888888887776.34444 PP

  == domain 15  score: 10.2 bits;  conditional E-value: 0.0016
                               MIT   1 ldkAlelvkkAveeDnagnyeeAlelYkeale 32 
                                       l+k+++l  k   ++   +ye+A+++Y ea+ 
  gi|386002402|ref|YP_005920701.1| 581 LSKGIALMLKGLALETLDKYEDAVQAYDEAIS 612
                                       799***************************96 PP

  == domain 16  score: 1.4 bits;  conditional E-value: 0.89
                               MIT  18 gnyeeAlelYke 29 
                                       g+y+eA+++Y e
  gi|386002402|ref|YP_005920701.1| 632 GKYDEAVQAYDE 643
                                       8*********87 PP

  == domain 17  score: 0.3 bits;  conditional E-value: 2
                               MIT  19 nyeeAlelYkealelLlqalk 39 
                                         eeA+++Y e +    ++++
  gi|386002402|ref|YP_005920701.1| 708 ASEEAIRAYNETITTYEEIVS 728
                                       458899999888877766666 PP

  == domain 18  score: 0.2 bits;  conditional E-value: 2.1
                               MIT  16 nagnyeeAlelYkeale 32 
                                       ++++y eA++++ ea+ 
  gi|386002402|ref|YP_005920701.1| 760 EQHEYNEAMQAFNEAVS 776
                                       57899999999999985 PP

  == domain 19  score: 1.9 bits;  conditional E-value: 0.62
                               MIT  17 agnyeeAlelYkeale 32 
                                       +g+ eeA+ +Y ea++
  gi|386002402|ref|YP_005920701.1| 829 QGKHEEAILAYDEAIR 844
                                       5899**********97 PP

  == domain 20  score: 12.7 bits;  conditional E-value: 0.00026
                               MIT  16 nagnyeeAlelYkealelLlqalk.e.kneerrell 49 
                                       ++gny+eA+++Y  a++l +q+++   ++    ++l
  gi|386002402|ref|YP_005920701.1| 862 SQGNYSEAIQAYDRAIDLNSQLVQaWyNKGDALDAL 897
                                       589***************999999544443555555 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   3.0    0.0028       1.1       4      97 ..      82     184 ..      78     194 .. 0.69
   2 ?    6.5   0.0     0.021       8.1       4      42 ..     218     266 ..     215     289 .. 0.72
   3 ?    3.5   0.0      0.18        67       3      41 ..     285     325 ..     283     382 .. 0.79
   4 ?    0.7   0.1       1.3     5e+02       5      68 ..     355     423 ..     350     457 .. 0.55
   5 !   20.3   0.1   1.1e-06   0.00042      19      69 ..     498     560 ..     453     571 .. 0.80
   6 !    8.5   0.1    0.0052         2      20      67 ..     590     640 ..     575     644 .. 0.78
   7 !    9.4   0.2    0.0027         1       3      94 ..     605     705 ..     603     718 .. 0.74
   8 ?    2.7   0.1      0.32   1.2e+02       3      64 ..     639     705 ..     637     776 .. 0.74
   9 ?    1.9   0.1      0.55   2.1e+02       5      61 ..     839     900 ..     797     919 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0028
                      SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilkkveaee 75 
                                       +y++ +rl+ + +  +  k +a+ k +ky+ea+k+ +++  l+    +    k Y+lY   ky +a k  +++    
  gi|386002402|ref|YP_005920701.1|  82 DYKEAIRLDPEFVWPWynKGLAFEKQGKYDEAIKAYNEAIRLDpeyANAWHNKGYALYLQGKYDEAIKAYNEAIRLY 158
                                       566666666655555456888999999*******9999986662114567899*************99988765432 PP

                      SRP_TPR_like  76 ....kvkvlksqvlYrlgsyekAYkl 97 
                                           ++   k   lY  g+y++A k 
  gi|386002402|ref|YP_005920701.1| 159 peyaNAWNSKGYALYSQGNYDEAIKA 184
                                       21113334455678888888888544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.021
                      SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs........a 42 
                                       +y++ +rl+ + l+ +  k  al +l+ky+ea+++ +++         a
  gi|386002402|ref|YP_005920701.1| 218 AYDEAIRLNPEDLNSWinKGAALYRLGKYDEAIRASNEAIrldpenvyA 266
                                       69999999999999999999*************9988877444444440 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.18
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs 41 
                                       ++y++ +rl+ +  + +  k  al++ +ky+ea+++ +++ 
  gi|386002402|ref|YP_005920701.1| 285 QAYDEAIRLSPEYADAWnrKGEALLHQGKYDEAIQASNEAI 325
                                       6799999998877777777999************9987765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.3
                      SRP_TPR_like   5 yekilrlegkelkkf..kvvaliklekyeeaLkllkkgsals.edv..rfEkaYvlYklkkykkalkil 68 
                                       y++ +rl+ +  + +  k ++l + +ky+ea++  +++  l+ e+v   + k   l    ky +a + +
  gi|386002402|ref|YP_005920701.1| 355 YDEAIRLSPEYADAWnnKGLSLKSQGKYDEAIQTFNETIRLDpEHVaaWYNKGLTLNNQGKYDEAIQAF 423
                                       555566655555544446666666666666666666655333122211344444444444444444443 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 1.1e-06
                      SRP_TPR_like  19 f.........kvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilk 69 
                                                 k val++l+kyeea+++ +++  l+    d    k  ++Y+l kyk++ ++ +
  gi|386002402|ref|YP_005920701.1| 498 NpeyadawnnKGVALVSLDKYEEAIQAFDEATRLNpedADAWLKKGVAFYHLGKYKETIQVCN 560
                                       244444457799*******************977632257899**************999865 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.0052
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsalsed..vrfE.kaYvlYklkkykkalki 67 
                                       k +al +l+kye+a+++ +++ +l+ d    +E +  +lY l ky +a++ 
  gi|386002402|ref|YP_005920701.1| 590 KGLALETLDKYEDAVQAYDEAISLNPDdvAAWEnRGAALYSLGKYDEAVQA 640
                                       7789999************9998875422456636789********99875 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0027
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkilkkv... 71 
                                       ++y++ + l+ + +  +  +  al +l+ky+ea+++ ++   l+    +    k Y+l  l++ ++++k l+++   
  gi|386002402|ref|YP_005920701.1| 605 QAYDEAISLNPDDVAAWenRGAALYSLGKYDEAVQAYDEVLRLNpedANAWKKKGYALHSLEEHEESVKALDEAirl 681
                                       6788888888888877777999***************999877631134556899**************99875111 PP

                      SRP_TPR_like  72 eaee.kvkvlksqvlYrlgsyekA 94 
                                       + ++ ++  +ks  l  +++y++A
  gi|386002402|ref|YP_005920701.1| 682 NPNDaGCWLIKSFNLLIIEKYDEA 705
                                       334445666666666666666666 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.32
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykka 64 
                                       ++y+++lrl+ +  + +  k  al +le +ee++k+l+++  l+ +   +   k++ l  ++ky +a
  gi|386002402|ref|YP_005920701.1| 639 QAYDEVLRLNPEDANAWkkKGYALHSLEEHEESVKALDEAIRLNPNdagCWLIKSFNLLIIEKYDEA 705
                                       6788888887766665544667777788888877777776544322111444444444444444444 PP

  == domain 9  score: 1.9 bits;  conditional E-value: 0.55
                      SRP_TPR_like   5 yekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsedv...rfEkaYvlYklkky 61 
                                       y++ +rl+ +  + +  k +al + + y+ea+++ + +  l++++    + k  +l  lk++
  gi|386002402|ref|YP_005920701.1| 839 YDEAIRLNPDDEDAWnnKGLALYSQGNYSEAIQAYDRAIDLNSQLvqaWYNKGDALDALKNF 900
                                       33333333333333333444445555555555544444444433211134444444444444 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.23        89     152     174 ..      66      88 ..      61      93 .. 0.89
   2 !    8.8   3.2    0.0031       1.2     125     174 ..     106     156 ..     104     164 .. 0.80
   3 !    7.5   0.3    0.0078         3     149     174 ..     165     190 ..     159     194 .. 0.87
   4 ?    6.4   0.0     0.017       6.7     152     177 ..     202     227 ..     200     240 .. 0.89
   5 ?    6.8   0.7     0.013       4.8     150     174 ..     268     292 ..     238     299 .. 0.73
   6 !   10.4   1.0     0.001       0.4     125     178 ..     276     330 ..     274     335 .. 0.80
   7 !   12.7   0.7   0.00019     0.074     123     178 ..     308     364 ..     306     378 .. 0.82
   8 !    7.3   0.1    0.0093       3.5     125     175 ..     378     429 ..     374     439 .. 0.78
   9 ?    1.2   0.1      0.69   2.6e+02     152     174 ..     440     462 ..     435     468 .. 0.86
  10 ?    5.8   0.5     0.026       9.8     126     178 ..     447     500 ..     444     508 .. 0.77
  11 ?    5.3   0.2     0.036        14     126     180 ..     481     536 ..     478     545 .. 0.78
  12 ?    7.0   2.1     0.011       4.3     100     179 ..     571     651 ..     560     662 .. 0.74
  13 ?   -0.3   0.0         2   7.4e+02     151     176 ..     753     778 ..     750     790 .. 0.87
  14 !    9.1   0.4    0.0026      0.98     123     177 ..     792     847 ..     789     856 .. 0.82
  15 ?    4.3   0.3     0.076        29     151     177 ..     855     881 ..     849     895 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G +l+ qg+ deA + Y++A++
  gi|386002402|ref|YP_005920701.1|  66 KGYALYLQGNYDEAIQDYKEAIR 88 
                                       8999*****************96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0031
                            TPR_21 125 aekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       +++kydeA+k+ +++ + +   a +   +G +l+ qgk deA +aY++A++
  gi|386002402|ref|YP_005920701.1| 106 KQGKYDEAIKAYNEAiRLDPEYANAWHNKGYALYLQGKYDEAIKAYNEAIR 156
                                       6899******996651334444566678*********************97 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0078
                            TPR_21 149 aelrGDilvaqgkldeAraaYqaAla 174
                                        + +G +l++qg+ deA +aY++A++
  gi|386002402|ref|YP_005920701.1| 165 WNSKGYALYSQGNYDEAIKAYNEAIR 190
                                       5689********************96 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.017
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaale 177
                                       +GD l++qgk + A  aY++A++ + 
  gi|386002402|ref|YP_005920701.1| 202 KGDTLFSQGKYELAIYAYDEAIRLNP 227
                                       9********************98665 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.013
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAla 174
                                         +G +l +qgk deA +aY++A++
  gi|386002402|ref|YP_005920701.1| 268 HNKGVALNSQGKYDEAIQAYDEAIR 292
                                       569999*****************97 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.001
                            TPR_21 125 aekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                        ++kydeA+++ +++ + +   a + +++G++l+ qgk deA +a ++A++   e
  gi|386002402|ref|YP_005920701.1| 276 SQGKYDEAIQAYDEAIRlSPEYADAWNRKGEALLHQGKYDEAIQASNEAISLDPE 330
                                       6899*****9997665413344667789********************9986655 PP

  == domain 7  score: 12.7 bits;  conditional E-value: 0.00019
                            TPR_21 123 llaekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       ll ++kydeA+++  ea + +  +a   +++G +l+++gk deA +aY++A++   e
  gi|386002402|ref|YP_005920701.1| 308 LLHQGKYDEAIQASnEAISLDPENANGWNIKGVALYNRGKSDEAIKAYDEAIRLSPE 364
                                       7899*******988345566777889999**********************986655 PP

  == domain 8  score: 7.3 bits;  conditional E-value: 0.0093
                            TPR_21 125 aekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                        ++kydeA++t +++ + +  ++++   +G  l +qgk deA +a+++A++ 
  gi|386002402|ref|YP_005920701.1| 378 SQGKYDEAIQTFNETIRlDPEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIRL 429
                                       699*********77643133333344469********************975 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 0.69
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G++l +q + deA +aY++ ++
  gi|386002402|ref|YP_005920701.1| 440 KGNALDSQSRYDEAIQAYDEVIK 462
                                       8999999***********98765 PP

  == domain 10  score: 5.8 bits;  conditional E-value: 0.026
                            TPR_21 126 ekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                       +  ydeA+++ +++ + +   a + + +G ++ +qg+ +eA +a+++A++++ e
  gi|386002402|ref|YP_005920701.1| 447 QSRYDEAIQAYDEVIKlNPEYADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPE 500
                                       567888888887654313334556679**********************98765 PP

  == domain 11  score: 5.3 bits;  conditional E-value: 0.036
                            TPR_21 126 ekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka 180
                                       ++ y+eA+k+ +++ +++   a + + +G +lv+ +k +eA +a+++A + + e+a
  gi|386002402|ref|YP_005920701.1| 481 QGRYNEAIKAFDEAiRRNPEYADAWNNKGVALVSLDKYEEAIQAFDEATRLNPEDA 536
                                       889999999996651344445666778*********************98777665 PP

  == domain 12  score: 7.0 bits;  conditional E-value: 0.011
                            TPR_21 100 ewvlekakdeelkalarlRLarvllae.kkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       +w  e+a ++ l++ + l L  + l++ +ky++A+++ +++ + +  ++++ e rG +l++ gk deA +aY++ l+
  gi|386002402|ref|YP_005920701.1| 571 RWNPEDA-NARLSKGIALMLKGLALETlDKYEDAVQAYDEAISlNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLR 646
                                       5555555.45566666777777777644889999998865544155667788*********************9998 PP

                            TPR_21 175 aleek 179
                                        + e+
  gi|386002402|ref|YP_005920701.1| 647 LNPED 651
                                       76665 PP

  == domain 13  score: -0.3 bits;  conditional E-value: 2
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaal 176
                                       l+G il +q + +eA +a+++A++ +
  gi|386002402|ref|YP_005920701.1| 753 LKGIILGEQHEYNEAMQAFNEAVSLN 778
                                       78999999*************98765 PP

  == domain 14  score: 9.1 bits;  conditional E-value: 0.0026
                            TPR_21 123 llaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaale 177
                                       l +++ky eA+++++ + + +  +al+ + +G +l  qgk +eA  aY++A++ + 
  gi|386002402|ref|YP_005920701.1| 792 LNDQGKYYEAIEAIDMAISlNPESALAWNYKGAALRGQGKHEEAILAYDEAIRLNP 847
                                       5689999999999976554156678889***********************98655 PP

  == domain 15  score: 4.3 bits;  conditional E-value: 0.076
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaale 177
                                        +G +l++qg+  eA +aY++A++ ++
  gi|386002402|ref|YP_005920701.1| 855 NKGLALYSQGNYSEAIQAYDRAIDLNS 881
                                       58999*****************98765 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.15        57       9      28 ..     103     122 ..     103     124 .. 0.85
   2 ?    1.4   0.0       1.3   4.9e+02      13      27 ..     141     155 ..     137     157 .. 0.83
   3 ?    2.6   0.0      0.51   1.9e+02      10      28 ..     172     190 ..     170     192 .. 0.83
   4 ?   -0.5   0.0       4.9   1.9e+03       9      20 ..     239     250 ..     238     252 .. 0.86
   5 ?    1.4   0.0       1.2   4.6e+02      12      27 ..     276     291 ..     273     294 .. 0.82
   6 ?    0.9   0.0       1.9   7.1e+02      11      28 ..     343     360 ..     341     362 .. 0.82
   7 ?    2.7   0.0      0.48   1.8e+02      12      27 ..     378     393 ..     375     396 .. 0.83
   8 ?    2.6   0.0      0.53     2e+02      13      28 ..     413     428 ..     410     430 .. 0.86
   9 ?    3.6   0.0      0.25        96       9      29 ..     477     497 ..     471     498 .. 0.87
  10 ?    1.3   0.0       1.3   5.1e+02       9      26 ..     511     528 ..     510     532 .. 0.84
  11 ?    3.2   0.0      0.34   1.3e+02       9      28 ..     627     646 ..     626     648 .. 0.85
  12 ?   -1.4   0.0       9.6   3.7e+03      10      25 ..     860     875 ..     859     880 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++ k Gk++eA++ ++e ++
  gi|386002402|ref|YP_005920701.1| 103 AFEKQGKYDEAIKAYNEAIR 122
                                       57799**********99765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.3
                               PPR  13 nGkleeAlelfkeMk 27 
                                        Gk++eA++ ++e +
  gi|386002402|ref|YP_005920701.1| 141 QGKYDEAIKAYNEAI 155
                                       79********99965 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.51
                               PPR  10 ycknGkleeAlelfkeMke 28 
                                       + + G+++eA++ ++e ++
  gi|386002402|ref|YP_005920701.1| 172 LYSQGNYDEAIKAYNEAIR 190
                                       6789**********99765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 4.9
                               PPR   9 gycknGkleeAl 20 
                                       ++ + Gk++eA+
  gi|386002402|ref|YP_005920701.1| 239 ALYRLGKYDEAI 250
                                       6889*******8 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 1.2
                               PPR  12 knGkleeAlelfkeMk 27 
                                       + Gk++eA++ ++e +
  gi|386002402|ref|YP_005920701.1| 276 SQGKYDEAIQAYDEAI 291
                                       68*********99966 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.9
                               PPR  11 cknGkleeAlelfkeMke 28 
                                          Gk +eA++ ++e ++
  gi|386002402|ref|YP_005920701.1| 343 YNRGKSDEAIKAYDEAIR 360
                                       5689*********99665 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.48
                               PPR  12 knGkleeAlelfkeMk 27 
                                       + Gk++eA++ f+e +
  gi|386002402|ref|YP_005920701.1| 378 SQGKYDEAIQTFNETI 393
                                       67**********9955 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.53
                               PPR  13 nGkleeAlelfkeMke 28 
                                        Gk++eA++ f+e ++
  gi|386002402|ref|YP_005920701.1| 413 QGKYDEAIQAFDEAIR 428
                                       69**********9776 PP

  == domain 9  score: 3.6 bits;  conditional E-value: 0.25
                               PPR   9 gycknGkleeAlelfkeMkek 29 
                                       ++ + G++ eA++ f+e +++
  gi|386002402|ref|YP_005920701.1| 477 AFNSQGRYNEAIKAFDEAIRR 497
                                       67789************8887 PP

  == domain 10  score: 1.3 bits;  conditional E-value: 1.3
                               PPR   9 gycknGkleeAlelfkeM 26 
                                       ++++  k+eeA++ f+e 
  gi|386002402|ref|YP_005920701.1| 511 ALVSLDKYEEAIQAFDEA 528
                                       678899*********995 PP

  == domain 11  score: 3.2 bits;  conditional E-value: 0.34
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++ + Gk++eA++ ++e ++
  gi|386002402|ref|YP_005920701.1| 627 ALYSLGKYDEAVQAYDEVLR 646
                                       56789***********9877 PP

  == domain 12  score: -1.4 bits;  conditional E-value: 9.6
                               PPR  10 ycknGkleeAlelfke 25 
                                       + + G+++eA++ +++
  gi|386002402|ref|YP_005920701.1| 860 LYSQGNYSEAIQAYDR 875
                                       5678*******99987 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.35   1.3e+02       8      20 ..      67      79 ..      64      81 .. 0.89
   2 ?    3.8   0.0       0.3   1.2e+02       3      20 ..     130     147 ..     128     148 .. 0.90
   3 ?    0.3   0.0       4.2   1.6e+03       8      20 ..     169     181 ..     165     182 .. 0.90
   4 ?    4.3   0.0      0.22        83       5      20 ..     234     249 ..     231     252 .. 0.87
   5 ?    2.4   0.0      0.88   3.4e+02       2      23 ..     265     286 ..     264     289 .. 0.84
   6 ?    4.7   0.0      0.16        60       8      20 ..     305     317 ..     301     320 .. 0.92
   7 ?    2.6   0.0      0.75   2.9e+02       2      25 ..     401     424 ..     400     425 .. 0.85
   8 ?    5.4   0.2     0.094        36       2      25 ..     619     642 ..     618     643 .. 0.87
   9 ?   -0.2   0.1       5.8   2.2e+03       8      20 ..     823     835 ..     817     835 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.35
                             TPR_4  8 ArallalGdldeA 20
                                      + al+++G++deA
  gi|386002402|ref|YP_005920701.1| 67 GYALYLQGNYDEA 79
                                      789*********9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.3
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a ++ + al+++G +deA
  gi|386002402|ref|YP_005920701.1| 130 AWHNKGYALYLQGKYDEA 147
                                       778999***********9 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 4.2
                             TPR_4   8 ArallalGdldeA 20 
                                       + al+ +G++deA
  gi|386002402|ref|YP_005920701.1| 169 GYALYSQGNYDEA 181
                                       579999******9 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.22
                             TPR_4   5 laLArallalGdldeA 20 
                                       ++ + al++lG +deA
  gi|386002402|ref|YP_005920701.1| 234 INKGAALYRLGKYDEA 249
                                       67899**********9 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.88
                             TPR_4   2 rallaLArallalGdldeAral 23 
                                       +a ++ + al  +G +deA ++
  gi|386002402|ref|YP_005920701.1| 265 YAWHNKGVALNSQGKYDEAIQA 286
                                       578999*************766 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.16
                             TPR_4   8 ArallalGdldeA 20 
                                       ++all++G +deA
  gi|386002402|ref|YP_005920701.1| 305 GEALLHQGKYDEA 317
                                       79**********9 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.75
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       +a ++ + +l  +G +deA ++++
  gi|386002402|ref|YP_005920701.1| 401 AAWYNKGLTLNNQGKYDEAIQAFD 424
                                       688999*************77665 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.094
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                       +a  +++ al+ lG +deA ++ +
  gi|386002402|ref|YP_005920701.1| 619 AAWENRGAALYSLGKYDEAVQAYD 642
                                       57789**************99876 PP

  == domain 9  score: -0.2 bits;  conditional E-value: 5.8
                             TPR_4   8 ArallalGdldeA 20 
                                       + al  +G ++eA
  gi|386002402|ref|YP_005920701.1| 823 GAALRGQGKHEEA 835
                                       6899********9 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.8   5.2e-06     0.002     119     181 ..     103     166 ..      98     170 .. 0.89
   2 ?   -0.6   0.0       2.9   1.1e+03     121     181 ..     173     234 ..     168     241 .. 0.80
   3 !    9.3   0.2    0.0025      0.97     126     182 ..     246     303 ..     242     308 .. 0.87
   4 !    8.0   0.0    0.0064       2.4     123     182 ..     311     371 ..     305     377 .. 0.88
   5 ?    6.2   0.1     0.022       8.5     121     180 ..     377     437 ..     371     443 .. 0.85
   6 ?    0.2   0.0       1.6     6e+02     156     181 ..     447     472 ..     441     477 .. 0.86
   7 ?    6.0   0.1     0.026        10     120     180 ..     478     539 ..     473     544 .. 0.87
   8 ?    5.6   0.1     0.034        13     124     181 ..     598     656 ..     585     660 .. 0.82
   9 ?    7.0   0.1     0.013         5     122     182 ..     794     855 ..     787     861 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.2e-06
                           Wzy_C_2 119 lplspenlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakwv 181
                                       +  ++ ++++ +++++++i+l Pe a   ++  ++l l+G+ deA + + +a+ l+pe++ +w+
  gi|386002402|ref|YP_005920701.1| 103 AFEKQGKYDEAIKAYNEAIRLDPEYAnAWHNKGYALYLQGKYDEAIKAYNEAIRLYPEYANAWN 166
                                       556889999**************86527899********************************4 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
                           Wzy_C_2 121 lspenlaaklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakwv 181
                                        s+ n+++ +++++++i+l Pe     ++  + l  +G+ + A   +++a+ l pe+  +w+
  gi|386002402|ref|YP_005920701.1| 173 YSQGNYDEAIKAYNEAIRLDPEFMWpWRNKGDTLFSQGKYELAIYAYDEAIRLNPEDLNSWI 234
                                       57788899999999999999987653677778888899999999999999999999999995 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0025
                           Wzy_C_2 126 laaklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakwvq 182
                                       +++ + +++++i+l Pe     ++  ++l  +G+ deA q +++a+ l pe++ +w++
  gi|386002402|ref|YP_005920701.1| 246 YDEAIRASNEAIRLDPENVYaWHNKGVALNSQGKYDEAIQAYDEAIRLSPEYADAWNR 303
                                       678899999999999997542688899*****************************54 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0064
                           Wzy_C_2 123 penlaaklalarklihlsPepavierl.ilslallGdedeAeqilararalfpeedakwvq 182
                                       + ++++ +++++++i l Pe a   +   ++l   G+ deA + +++a+ l pe++ +w++
  gi|386002402|ref|YP_005920701.1| 311 QGKYDEAIQASNEAISLDPENANGWNIkGVALYNRGKSDEAIKAYDEAIRLSPEYADAWNN 371
                                       6789999*************99876662699999*************************65 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.022
                           Wzy_C_2 121 lspenlaaklalarklihlsPep.avierlilslallGdedeAeqilararalfpeedakw 180
                                       +s+ ++++ ++  +++i+l Pe  a  ++  l l  +G+ deA q  ++a+ l pe+  +w
  gi|386002402|ref|YP_005920701.1| 377 KSQGKYDEAIQTFNETIRLDPEHvAAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEYVDAW 437
                                       57788899999999999999985367889999999*********************99999 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 1.6
                           Wzy_C_2 156 lGdedeAeqilararalfpeedakwv 181
                                       + + deA q ++++++l pe++ +w+
  gi|386002402|ref|YP_005920701.1| 447 QSRYDEAIQAYDEVIKLNPEYADAWN 472
                                       5689*******************994 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.026
                           Wzy_C_2 120 plspenlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                        +s+  + + +++  ++i++ Pe a   ++  ++l+ l++ +eA q  ++a  l pe++ +w
  gi|386002402|ref|YP_005920701.1| 478 FNSQGRYNEAIKAFDEAIRRNPEYAdAWNNKGVALVSLDKYEEAIQAFDEATRLNPEDADAW 539
                                       56788888999999999999998653789999****************************99 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.034
                           Wzy_C_2 124 enlaaklalarklihlsPe.pavierlilslallGdedeAeqilararalfpeedakwv 181
                                       +++++ ++++ ++i l P   a  e+   +l  lG+ deA q ++++  l pe++ +w+
  gi|386002402|ref|YP_005920701.1| 598 DKYEDAVQAYDEAISLNPDdVAAWENRGAALYSLGKYDEAVQAYDEVLRLNPEDANAWK 656
                                       667788888888888888624778888899999*************************4 PP

  == domain 9  score: 7.0 bits;  conditional E-value: 0.013
                           Wzy_C_2 122 spenlaaklalarklihlsPepavierli.lslallGdedeAeqilararalfpeedakwvq 182
                                       ++ ++ + +++   +i l Pe a+  ++   +l ++G+++eA   +++a+ l p+++ +w++
  gi|386002402|ref|YP_005920701.1| 794 DQGKYYEAIEAIDMAISLNPESALAWNYKgAALRGQGKHEEAILAYDEAIRLNPDDEDAWNN 855
                                       6677778888888999999**99999997367899*************************54 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.048        18      47     110 ..      67     124 ..      65     131 .. 0.87
   2 !    8.2   0.0    0.0037       1.4      46     112 ..     100     160 ..      97     166 .. 0.85
   3 !    7.0   0.0    0.0087       3.3      47     113 ..     169     229 ..     162     245 .. 0.87
   4 !    7.7   0.0    0.0052         2      15     113 ..     244     331 ..     234     349 .. 0.76
   5 ?    3.8   0.0     0.079        30      47     111 ..     305     363 ..     301     367 .. 0.74
   6 ?    3.3   0.0      0.11        43      51     110 ..     377     430 ..     337     437 .. 0.68
   7 ?   -1.7   0.0       3.7   1.4e+03      47      92 ..     475     521 ..     470     533 .. 0.67
   8 ?    2.9   0.0      0.15        57      35     111 ..     579     649 ..     570     655 .. 0.75
   9 ?   -0.2   0.0       1.3   5.1e+02     284     319 ..     752     787 ..     746     790 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.048
                          TPR_MalT  47 GeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqla 110
                                       G+a  lqG+ ++A q ++ea++l       +  ++  +  +    +qG+ +eA++ y++a++l 
  gi|386002402|ref|YP_005920701.1|  67 GYALYLQGNYDEAIQDYKEAIRLD------PEFVWPWYNKGLAFEKQGKYDEAIKAYNEAIRLD 124
                                       788889999999999999999887......5579999999999******************985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0037
                          TPR_MalT  46 lGeasllqGdleaAlqalqeaekla.rqadslhvallallqqaeilvaqGrLheAletyeqalqlate 112
                                        G a+  qG+ ++A +a++ea++l    a+++h+  +al+        qG+ +eA++ y++a++l++e
  gi|386002402|ref|YP_005920701.1| 100 KGLAFEKQGKYDEAIKAYNEAIRLDpEYANAWHNKGYALY-------LQGKYDEAIKAYNEAIRLYPE 160
                                       599999*****************86377777887766666.......89999***********99876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0087
                          TPR_MalT  47 GeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateq 113
                                       G+a   qG+ ++A +a++ea++l       +  ++  +  +++l+ qG+ + A+  y +a++l +e 
  gi|386002402|ref|YP_005920701.1| 169 GYALYSQGNYDEAIKAYNEAIRLD------PEFMWPWRNKGDTLFSQGKYELAIYAYDEAIRLNPED 229
                                       888889999999999999999987......557*****************************98775 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0052
                          TPR_MalT  15 gdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaekla.rqadslhvallallqqaeil 90 
                                       g+ ++a++ +++A+ l pe+ + +      + G a   qG+ ++A qa+ ea++l+   ad+++       + +e l
  gi|386002402|ref|YP_005920701.1| 244 GKYDEAIRASNEAIRLDPENVYAW-----HNKGVALNSQGKYDEAIQAYDEAIRLSpEYADAWN-------RKGEAL 308
                                       667788888888888888877555.....4567777789999************9933344444.......678888 PP

                          TPR_MalT  91 vaqGrLheAletyeqalqlateq 113
                                        +qG+ +eA++  ++a+ l +e+
  gi|386002402|ref|YP_005920701.1| 309 LHQGKYDEAIQASNEAISLDPEN 331
                                       99999999999999999976654 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.079
                          TPR_MalT  47 GeasllqGdleaAlqalqeaekla.rqadslhvallallqqaeilvaqGrLheAletyeqalqlat 111
                                       Gea l+qG+ ++A qa +ea++l   +a+      + +   +  l  +G+ +eA++ y +a++l +
  gi|386002402|ref|YP_005920701.1| 305 GEALLHQGKYDEAIQASNEAISLDpENANG-----WNIK--GVALYNRGKSDEAIKAYDEAIRLSP 363
                                       889999999999999999998875244444.....4444..4445588888888888888888876 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.11
                          TPR_MalT  51 llqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqla 110
                                         qG+ ++A q+++e+++l       hva++  +  + +l  qG+ +eA++ + +a++l 
  gi|386002402|ref|YP_005920701.1| 377 KSQGKYDEAIQTFNETIRLD----PEHVAAW--YNKGLTLNNQGKYDEAIQAFDEAIRLN 430
                                       45778888888888887664....6665555..455778888899999999998888875 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 3.7
                          TPR_MalT  47 GeasllqGdleaAlqalqeaekla.rqadslhvallallqqaeilva 92 
                                       G+a+  qG+ ++A +a+ ea++     ad++++  +al+++ + + a
  gi|386002402|ref|YP_005920701.1| 475 GTAFNSQGRYNEAIKAFDEAIRRNpEYADAWNNKGVALVSLDKYEEA 521
                                       78888889999999999998876435666666666666666555555 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.15
                          TPR_MalT  35 dllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlat 111
                                       + l++++a+++ G a  +  + e+A+qa+ ea++l       +va++  +  +  l   G+ +eA++ y + l+l +
  gi|386002402|ref|YP_005920701.1| 579 ARLSKGIALMLKGLALETLDKYEDAVQAYDEAISLN----PDDVAAWENR--GAALYSLGKYDEAVQAYDEVLRLNP 649
                                       456789999999999999999999999999998875....3344566666..6666677888888888888887765 PP

  == domain 9  score: -0.2 bits;  conditional E-value: 1.3
                          TPR_MalT 284 iLqalalqaqgreeeAlaaLeqALeLAepegyirsF 319
                                        L  ++l +q++  eA++a  +A++L   + +i sF
  gi|386002402|ref|YP_005920701.1| 752 ALKGIILGEQHEYNEAMQAFNEAVSLNPAGSFIWSF 787
                                       567778888999999999999999998888888877 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.24        90      10      36 ..      62      88 ..      58     101 .. 0.90
   2 ?    5.7   0.9     0.031        12       7      37 ..     127     157 ..     117     161 .. 0.92
   3 ?    4.9   0.5     0.055        21       6      36 ..     160     190 ..     156     196 .. 0.91
   4 ?   -0.3   0.0       2.1   8.1e+02      11      37 ..     199     225 ..     194     255 .. 0.80
   5 !    8.1   0.2    0.0056       2.2      10      57 ..     266     312 ..     258     327 .. 0.80
   6 ?    4.0   0.0       0.1        38       7      47 ..     365     405 ..     355     407 .. 0.84
   7 !   10.2   0.2    0.0012      0.47      10      62 ..     402     453 ..     398     464 .. 0.81
   8 !   10.2   0.2    0.0012      0.47       7      64 ..     467     523 ..     457     541 .. 0.77
   9 ?   -0.5   0.1       2.6   9.8e+02      11      38 ..     621     648 ..     617     678 .. 0.70
  10 ?    0.7   0.1       1.1   4.1e+02      20      47 ..     698     725 ..     686     752 .. 0.85
  11 ?   -1.8   0.0       6.1   2.3e+03       5      36 ..     745     776 ..     741     780 .. 0.82
  12 ?    4.1   0.1     0.093        36      14      36 ..     788     810 ..     776     822 .. 0.88
  13 !    8.9   0.1    0.0032       1.2      10      62 ..     852     903 ..     848     928 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.24
                           DUF5113 10 dYanlayylnvegeyeeALeyldsale 36
                                      ++ n +y+l+ +g+y+eA++  ++a++
  gi|386002402|ref|YP_005920701.1| 62 EWNNKGYALYLQGNYDEAIQDYKEAIR 88
                                      78899****************999986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.031
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaley 37 
                                        an++ n +y+l+ +g+y+eA++  ++a+++
  gi|386002402|ref|YP_005920701.1| 127 YANAWHNKGYALYLQGKYDEAIKAYNEAIRL 157
                                       6999***********************9975 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.055
                           DUF5113   6 qiandYanlayylnvegeyeeALeyldsale 36 
                                       + an++ + +y+l+ +g+y+eA++  ++a++
  gi|386002402|ref|YP_005920701.1| 160 EYANAWNSKGYALYSQGNYDEAIKAYNEAIR 190
                                       5799**********************99986 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.1
                           DUF5113  11 YanlayylnvegeyeeALeyldsaley 37 
                                       ++n + +l+ +g+ye A+   d+a+++
  gi|386002402|ref|YP_005920701.1| 199 WRNKGDTLFSQGKYELAIYAYDEAIRL 225
                                       5788899999*************9986 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0056
                           DUF5113  10 dYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklk 57 
                                       ++ n + +ln +g+y+eA++  d+a+++  ++ + + +k  + l+++ 
  gi|386002402|ref|YP_005920701.1| 266 AWHNKGVALNSQGKYDEAIQAYDEAIRLSPEYADAWNRKG-EALLHQG 312
                                       46788999*******************9999988888887.5665544 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.1
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaleylNahyekYak 47 
                                        a+++ n +  l  +g+y+eA++++++ +++  +h   +++
  gi|386002402|ref|YP_005920701.1| 365 YADAWNNKGLSLKSQGKYDEAIQTFNETIRLDPEHVAAWYN 405
                                       57788899999*****************9998888887776 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0012
                           DUF5113  10 dYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmlleg 62 
                                       ++ n + +ln +g+y+eA++ +d+a+++  ++ + +++k  + ld++  ++e 
  gi|386002402|ref|YP_005920701.1| 402 AWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEYVDAWYSKG-NALDSQSRYDEA 453
                                       56788999******************98888888888887.688877666554 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.0012
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmllegeg 64 
                                        a+++ + +++ n +g+y+eA++ +d+a++   ++ + + +k    l +l  ++e  +
  gi|386002402|ref|YP_005920701.1| 467 YADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPEYADAWNNKGV-ALVSLDKYEEAIQ 523
                                       57888899*********************987777777777764.6666666666555 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 2.6
                           DUF5113  11 YanlayylnvegeyeeALeyldsaleyl 38 
                                       + n + +l+  g+y+eA++  d++l++ 
  gi|386002402|ref|YP_005920701.1| 621 WENRGAALYSLGKYDEAVQAYDEVLRLN 648
                                       5677778888899999999999999754 PP

  == domain 10  score: 0.7 bits;  conditional E-value: 1.1
                           DUF5113  20 vegeyeeALeyldsaleylNahyekYak 47 
                                       + ++y+eA++  ++a++  N+  ++Y +
  gi|386002402|ref|YP_005920701.1| 698 IIEKYDEAINASEEAIRAYNETITTYEE 725
                                       6789*****************9999976 PP

  == domain 11  score: -1.8 bits;  conditional E-value: 6.1
                           DUF5113   5 lqiandYanlayylnvegeyeeALeyldsale 36 
                                        ++ n +a  +  l  + ey+eA++ +++a++
  gi|386002402|ref|YP_005920701.1| 745 IAKGNGWALKGIILGEQHEYNEAMQAFNEAVS 776
                                       566677888888889999*********99986 PP

  == domain 12  score: 4.1 bits;  conditional E-value: 0.093
                           DUF5113  14 layylnvegeyeeALeyldsale 36 
                                        ++yln +g+y+eA+e +d a++
  gi|386002402|ref|YP_005920701.1| 788 KGKYLNDQGKYYEAIEAIDMAIS 810
                                       589******************97 PP

  == domain 13  score: 8.9 bits;  conditional E-value: 0.0032
                           DUF5113  10 dYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmlleg 62 
                                       ++ n + +l+ +g+y+eA++  d a+++  +  + +++k  d ld lk +++ 
  gi|386002402|ref|YP_005920701.1| 852 AWNNKGLALYSQGNYSEAIQAYDRAIDLNSQLVQAWYNKG-DALDALKNFTQA 903
                                       6788899999*****************999999*****98.9**999987765 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1         1     4e+02       6      47 ..     112     153 ..     107     164 .. 0.84
   2 ?    1.6   0.0      0.94   3.6e+02      10      44 ..     218     252 ..     213     262 .. 0.86
   3 ?    6.1   0.1     0.038        14       7      54 ..     249     296 ..     244     305 .. 0.83
   4 ?    1.8   0.2      0.81   3.1e+02       6      49 ..     282     325 ..     277     338 .. 0.83
   5 !    8.8   0.0    0.0052         2       6      54 ..     384     432 ..     379     442 .. 0.89
   6 ?    5.8   0.1     0.044        17       6      56 ..     418     468 ..     413     471 .. 0.90
   7 ?    5.4   0.1     0.061        23       6      57 ..     452     503 ..     447     515 .. 0.87
   8 ?    1.7   0.1      0.86   3.3e+02       6      43 ..     520     557 ..     515     581 .. 0.84
   9 ?    1.3   0.1       1.2   4.5e+02       7      38 ..     562     593 ..     557     605 .. 0.84
  10 !    8.1   0.3    0.0084       3.2       7      55 ..     603     651 ..     597     661 .. 0.86
  11 ?    1.7   0.0      0.84   3.2e+02       3      44 ..     667     708 ..     665     718 .. 0.89
  12 ?    5.8   0.7     0.044        17       5      44 ..     833     872 ..     829     904 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLle 47 
                                       + +++  +a+  +p+  +a ++   al+ +g+y+eA+++  e
  gi|386002402|ref|YP_005920701.1| 112 EAIKAYNEAIRLDPEYANAWHNKGYALYLQGKYDEAIKAYNE 153
                                       56788889999999999999999*************987655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.94
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleq 44 
                                       + ++a+  np+dl+  ++   al+  g+y+eA+ +
  gi|386002402|ref|YP_005920701.1| 218 AYDEAIRLNPEDLNSWINKGAALYRLGKYDEAIRA 252
                                       56789999************************976 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.038
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                        +++  +a+  +p+++ a ++   al+++g+y+eA+++  e ++   +
  gi|386002402|ref|YP_005920701.1| 249 AIRASNEAIRLDPENVYAWHNKGVALNSQGKYDEAIQAYDEAIRLSPE 296
                                       6788899999**************************987666665555 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.81
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                       + +++ ++a+  +p+  da     +all++g+y+eA+++  e +
  gi|386002402|ref|YP_005920701.1| 282 EAIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAI 325
                                       56888999999999999999999*************98755555 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0052
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       + ++++ +++  +p+ ++a ++  l l+ +g+y+eA++++ e ++ + +
  gi|386002402|ref|YP_005920701.1| 384 EAIQTFNETIRLDPEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPE 432
                                       6789999*******************************99888887665 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.044
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                       + ++++++a+  np+ +da +   +al +++ry+eA+++  e++k + +++
  gi|386002402|ref|YP_005920701.1| 418 EAIQAFDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQAYDEVIKLNPEYA 468
                                       67999*********************************9999998887775 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.061
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                       + +++ ++ ++ np+  da     +a +++gry eA++++ e ++r+ +++d
  gi|386002402|ref|YP_005920701.1| 452 EAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIKAFDEAIRRNPEYAD 503
                                       5678888889999999999999999**********************99965 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.86
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       + ++++++a   np+d da l+   a ++ g+y+e ++
  gi|386002402|ref|YP_005920701.1| 520 EAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKETIQ 557
                                       578999999999*******9999999999999998765 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 1.2
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagry 38 
                                       ++++ +++l  np+d +arl    al+ +g  
  gi|386002402|ref|YP_005920701.1| 562 SIQAYDDDLRWNPEDANARLSKGIALMLKGLA 593
                                       78999999************999999988755 PP

  == domain 10  score: 8.1 bits;  conditional E-value: 0.0084
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                        +++ ++a+  npdd++a  +   al++ g+y+eA+++  e+l+ + ++
  gi|386002402|ref|YP_005920701.1| 603 AVQAYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLRLNPED 651
                                       6889999*****************************9988888877665 PP

  == domain 11  score: 1.7 bits;  conditional E-value: 0.84
                            TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       ++++++++l++a+  np+d    l  +  ll  ++y+eA+++
  gi|386002402|ref|YP_005920701.1| 667 EHEESVKALDEAIRLNPNDAGCWLIKSFNLLIIEKYDEAINA 708
                                       578899****************99999999999999999986 PP

  == domain 12  score: 5.8 bits;  conditional E-value: 0.044
                            TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       ++ + + ++a+  npdd da  +  lal+++g+y eA+++
  gi|386002402|ref|YP_005920701.1| 833 EEAILAYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQA 872
                                       566777889999*************************975 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         5   1.9e+03      21      34 ..     107     120 ..     103     129 .. 0.85
   2 ?    1.1   0.1       1.3   4.8e+02      17      35 ..     137     155 ..     127     168 .. 0.80
   3 ?   -0.3   0.0       3.4   1.3e+03      13      35 ..     167     189 ..     160     197 .. 0.78
   4 ?    1.3   0.0       1.1     4e+02      14      34 ..     202     222 ..     198     232 .. 0.84
   5 ?   -0.6   0.0       4.1   1.6e+03      18      34 ..     240     256 ..     233     264 .. 0.79
   6 ?    0.5   0.0       1.9   7.4e+02      18      34 ..     274     290 ..     265     297 .. 0.81
   7 !    8.8   0.1    0.0049       1.9       8      34 ..     298     324 ..     292     331 .. 0.86
   8 ?   -0.2   0.0       3.1   1.2e+03      16      31 ..     374     389 ..     364     395 .. 0.77
   9 ?   -0.5   0.0       3.8   1.4e+03      20      34 ..     412     426 ..     405     434 .. 0.80
  10 ?    1.0   0.0       1.4   5.2e+02      13      35 ..     507     529 ..     499     537 .. 0.79
  11 ?    0.2   0.0       2.3   8.7e+02      12      33 ..     623     643 ..     614     675 .. 0.71
  12 ?    3.1   0.0       0.3   1.1e+02      17      69 ..     695     746 ..     691     752 .. 0.84
  13 ?   -1.6   0.1       8.5   3.3e+03      17      34 ..     825     842 ..     816     846 .. 0.76
  14 ?   -1.2   0.0       6.2   2.4e+03      18      37 ..     860     879 ..     853     888 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5
                         NRBF2_MIT  21 aGkyeeaischkka 34 
                                        Gky+eai  ++ a
  gi|386002402|ref|YP_005920701.1| 107 QGKYDEAIKAYNEA 120
                                       59******988876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.3
                         NRBF2_MIT  17 rllaaGkyeeaischkkaa 35 
                                        l   Gky+eai  ++ a 
  gi|386002402|ref|YP_005920701.1| 137 ALYLQGKYDEAIKAYNEAI 155
                                       56778*******9998876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.4
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkkaa 35 
                                        k   l + G y+eai  ++ a 
  gi|386002402|ref|YP_005920701.1| 167 SKGYALYSQGNYDEAIKAYNEAI 189
                                       566678899*******9988875 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.1
                         NRBF2_MIT  14 kadrllaaGkyeeaischkka 34 
                                       k d l++ Gkye ai  +  a
  gi|386002402|ref|YP_005920701.1| 202 KGDTLFSQGKYELAIYAYDEA 222
                                       7899***********887766 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 4.1
                         NRBF2_MIT  18 llaaGkyeeaischkka 34 
                                       l   Gky+eai   + a
  gi|386002402|ref|YP_005920701.1| 240 LYRLGKYDEAIRASNEA 256
                                       6678*******877665 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 1.9
                         NRBF2_MIT  18 llaaGkyeeaischkka 34 
                                       l + Gky+eai  +  a
  gi|386002402|ref|YP_005920701.1| 274 LNSQGKYDEAIQAYDEA 290
                                       6678*******988776 PP

  == domain 7  score: 8.8 bits;  conditional E-value: 0.0049
                         NRBF2_MIT   8 ahqqsrkadrllaaGkyeeaischkka 34 
                                       a   +rk + ll  Gky+eai   + a
  gi|386002402|ref|YP_005920701.1| 298 ADAWNRKGEALLHQGKYDEAIQASNEA 324
                                       66679****************987766 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 3.1
                         NRBF2_MIT  16 drllaaGkyeeaisch 31 
                                         l + Gky+eai   
  gi|386002402|ref|YP_005920701.1| 374 LSLKSQGKYDEAIQTF 389
                                       567789*******865 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 3.8
                         NRBF2_MIT  20 aaGkyeeaischkka 34 
                                         Gky+eai     a
  gi|386002402|ref|YP_005920701.1| 412 NQGKYDEAIQAFDEA 426
                                       67*******987766 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 1.4
                         NRBF2_MIT  13 rkadrllaaGkyeeaischkkaa 35 
                                        k   l++  kyeeai     a+
  gi|386002402|ref|YP_005920701.1| 507 NKGVALVSLDKYEEAIQAFDEAT 529
                                       5666788899******9988876 PP

  == domain 11  score: 0.2 bits;  conditional E-value: 2.3
                         NRBF2_MIT  12 srkadrllaaGkyeeaischkk 33 
                                       +r    l + Gky+ea+  +  
  gi|386002402|ref|YP_005920701.1| 623 NRG-AALYSLGKYDEAVQAYDE 643
                                       444.468899******987765 PP

  == domain 12  score: 3.1 bits;  conditional E-value: 0.3
                         NRBF2_MIT  17 rllaaGkyeeaischkkaaaylseamkltkseqaqlslelqreshikqllliq 69 
                                        ll   ky+eai   + a     e++  t  e   l  e    s ik   li 
  gi|386002402|ref|YP_005920701.1| 695 NLLIIEKYDEAINASEEAIRAYNETIT-TYEEIVSLNPENSTASNIKSRTLIA 746
                                       589999************999999875.7778888888999999999888875 PP

  == domain 13  score: -1.6 bits;  conditional E-value: 8.5
                         NRBF2_MIT  17 rllaaGkyeeaischkka 34 
                                        l   Gk+eeai  +  a
  gi|386002402|ref|YP_005920701.1| 825 ALRGQGKHEEAILAYDEA 842
                                       56778******9877655 PP

  == domain 14  score: -1.2 bits;  conditional E-value: 6.2
                         NRBF2_MIT  18 llaaGkyeeaischkkaaay 37 
                                       l + G y eai  + +a + 
  gi|386002402|ref|YP_005920701.1| 860 LYSQGNYSEAIQAYDRAIDL 879
                                       7789********99998765 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.24        91      13      28 ..     104     119 ..     100     122 .. 0.88
   2 ?    0.8   0.0       1.5   5.7e+02      16      28 ..     141     153 ..     136     156 .. 0.86
   3 ?    1.8   0.0      0.72   2.8e+02      12      28 ..     171     187 ..     168     190 .. 0.88
   4 ?   -0.9   0.0       5.3     2e+03      16      28 ..     277     289 ..     273     292 .. 0.87
   5 ?   -0.5   0.0       3.8   1.4e+03      12      24 ..     307     319 ..     306     323 .. 0.84
   6 ?    1.6   0.0      0.88   3.4e+02      12      28 ..     341     357 ..     335     361 .. 0.90
   7 ?    1.6   0.0      0.86   3.3e+02      15      28 ..     378     391 ..     373     394 .. 0.88
   8 ?    0.6   0.0       1.8   6.8e+02      15      28 ..     412     425 ..     407     430 .. 0.87
   9 ?    2.2   0.0      0.55   2.1e+02      15      33 ..     480     498 ..     475     500 .. 0.84
  10 ?   -0.5   0.0       3.9   1.5e+03      13      28 ..     628     643 ..     626     648 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.24
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       + k+gk++eA+k +ne
  gi|386002402|ref|YP_005920701.1| 104 FEKQGKYDEAIKAYNE 119
                                       669***********98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                             PPR_2  16 kgkveeAfklfne 28 
                                       +gk++eA+k +ne
  gi|386002402|ref|YP_005920701.1| 141 QGKYDEAIKAYNE 153
                                       89*********98 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.72
                             PPR_2  12 glckkgkveeAfklfne 28 
                                       +l+ +g+++eA+k +ne
  gi|386002402|ref|YP_005920701.1| 171 ALYSQGNYDEAIKAYNE 187
                                       46789**********98 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 5.3
                             PPR_2  16 kgkveeAfklfne 28 
                                       +gk++eA++ ++e
  gi|386002402|ref|YP_005920701.1| 277 QGKYDEAIQAYDE 289
                                       89*******9998 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 3.8
                             PPR_2  12 glckkgkveeAfk 24 
                                       +l+++gk++eA++
  gi|386002402|ref|YP_005920701.1| 307 ALLHQGKYDEAIQ 319
                                       789********97 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.88
                             PPR_2  12 glckkgkveeAfklfne 28 
                                       +l+++gk++eA+k ++e
  gi|386002402|ref|YP_005920701.1| 341 ALYNRGKSDEAIKAYDE 357
                                       57899**********98 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.86
                             PPR_2  15 kkgkveeAfklfne 28 
                                        +gk++eA++ fne
  gi|386002402|ref|YP_005920701.1| 378 SQGKYDEAIQTFNE 391
                                       48***********8 PP

  == domain 8  score: 0.6 bits;  conditional E-value: 1.8
                             PPR_2  15 kkgkveeAfklfne 28 
                                       ++gk++eA++ f+e
  gi|386002402|ref|YP_005920701.1| 412 NQGKYDEAIQAFDE 425
                                       69**********98 PP

  == domain 9  score: 2.2 bits;  conditional E-value: 0.55
                             PPR_2  15 kkgkveeAfklfneMkkrg 33 
                                        +g+++eA+k f+e  +r+
  gi|386002402|ref|YP_005920701.1| 480 SQGRYNEAIKAFDEAIRRN 498
                                       69***********987775 PP

  == domain 10  score: -0.5 bits;  conditional E-value: 3.9
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       l+  gk++eA++ ++e
  gi|386002402|ref|YP_005920701.1| 628 LYSLGKYDEAVQAYDE 643
                                       67789*********98 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.6   6.1e+02      62     103 ..     113     154 ..     110     158 .. 0.89
   2 ?   -0.3   0.0       2.8   1.1e+03      62     103 ..     147     188 ..     144     192 .. 0.78
   3 ?    2.4   0.0      0.39   1.5e+02      62     105 ..     283     326 ..     280     328 .. 0.93
   4 ?    1.7   0.0      0.65   2.5e+02      62     103 ..     351     392 ..     349     396 .. 0.91
   5 ?    5.3   0.0     0.051        20      62      99 ..     419     456 ..     416     464 .. 0.91
   6 ?   -0.3   0.0       2.8   1.1e+03      62      97 ..     603     645 ..     578     648 .. 0.77
   7 ?   -1.7   0.0       7.4   2.8e+03      62      92 ..     869     899 ..     858     910 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                       ++++++ea +l   yA+  ++ +  l  + +Y +a+k  ++a
  gi|386002402|ref|YP_005920701.1| 113 AIKAYNEAIRLDPEYANAWHNKGYALYLQGKYDEAIKAYNEA 154
                                       899*********************9999999*9999987766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.8
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                       ++++++ea +l   yA+     +  l s+  Y +a+k  ++a
  gi|386002402|ref|YP_005920701.1| 147 AIKAYNEAIRLYPEYANAWNSKGYALYSQGNYDEAIKAYNEA 188
                                       788888888888888888888888888888888888776665 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.39
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLs 105
                                       +++++ ea +ls  yA      ++ l  + +Y +a++ +++a+s
  gi|386002402|ref|YP_005920701.1| 283 AIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAIS 326
                                       89***********************************9999987 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.65
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakra 103
                                       +++++ ea +ls  yA    + +  l+s+ +Y +a++  +++
  gi|386002402|ref|YP_005920701.1| 351 AIKAYDEAIRLSPEYADAWNNKGLSLKSQGKYDEAIQTFNET 392
                                       899********************************9987665 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.051
                            DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkk 99 
                                       ++++f ea +l   y    +  ++ l+s++ Y +a++ 
  gi|386002402|ref|YP_005920701.1| 419 AIQAFDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQA 456
                                       89*********************************986 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 2.8
                            DUF627  62 svecfseavels.......rfyArsLfelasqlgsklyYkkav 97 
                                       +v+++ ea +l        +     L+ l++  + ++ Y +++
  gi|386002402|ref|YP_005920701.1| 603 AVQAYDEAISLNpddvaawENRGAALYSLGKYDEAVQAYDEVL 645
                                       7888888888888877777666677888888777777777765 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 7.4
                            DUF627  62 svecfseavelsrfyArsLfelasqlgskly 92 
                                       +++++ +a  l +   +  ++ ++ l+  + 
  gi|386002402|ref|YP_005920701.1| 869 AIQAYDRAIDLNSQLVQAWYNKGDALDALKN 899
                                       5555555555555555555555555555544 PP

>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.31   1.2e+02      25      58 ..     103     135 ..      98     137 .. 0.79
   2 ?    5.7   0.1     0.039        15      43      60 ..     210     239 ..     142     241 .. 0.75
   3 ?    4.2   0.0      0.12        45      28      58 ..     242     271 ..     239     274 .. 0.80
   4 ?    0.0   0.1       2.4   9.1e+02      21      58 ..     303     339 ..     279     342 .. 0.80
   5 ?    2.1   1.6      0.52     2e+02      58      58 ..     441     441 ..     365     546 .. 0.61
   6 ?    2.3   0.0      0.45   1.7e+02      25      60 ..     593     627 ..     589     628 .. 0.78
   7 ?    4.3   0.1      0.11        43      24      58 ..     626     659 ..     622     661 .. 0.79
   8 ?    0.0   0.0       2.4   9.2e+02      43      60 ..     794     825 ..     706     826 .. 0.71
   9 ?   -0.6   0.0       3.7   1.4e+03      29      58 ..     870     891 ..     837     892 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.31
                                       ESEEEEEEET.TTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  25 piEklGtYdP.lakkkekkevelneerikyWlgvG 58 
                                         Ek G Yd  ++  +e   ++l+ e ++ W ++G
  gi|386002402|ref|YP_005920701.1| 103 AFEKQGKYDEaIKAYNE--AIRLDPEYANAWHNKG 135
                                       578999***94554444..4***********9998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.039
                                       S............EEE-HHHHHHHHHTTEE CS
                     Ribosomal_S16  43 e............velneerikyWlgvGAq 60 
                                                    ++ln e ++ W+++GA 
  gi|386002402|ref|YP_005920701.1| 210 GkyelaiyaydeaIRLNPEDLNSWINKGAA 239
                                       04444445555559**************96 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.12
                                       EEEEEETTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  28 klGtYdPlakkkekkevelneerikyWlgvG 58 
                                       +lG Yd   + +++  ++l+ e +  W ++G
  gi|386002402|ref|YP_005920701.1| 242 RLGKYDEAIRASNE-AIRLDPENVYAWHNKG 271
                                       79****94444444.4*************99 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 2.4
                                       TTSSESEEEEEEET.TTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  21 rdgrpiEklGtYdP.lakkkekkevelneerikyWlgvG 58 
                                       r+g+ + + G Yd  ++  +++  ++l+ e ++ W  +G
  gi|386002402|ref|YP_005920701.1| 303 RKGEALLHQGKYDEaIQ-ASNE-AISLDPENANGWNIKG 339
                                       66666667799998444.4444.49*******9997777 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.52
                                       T CS
                     Ribosomal_S16  58 G 58 
                                       G
  gi|386002402|ref|YP_005920701.1| 441 G 441
                                       2 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.45
                                       ESEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTTEE CS
                     Ribosomal_S16  25 piEklGtYdPlakkkekkevelneerikyWlgvGAq 60 
                                        +E+l  Y+   +  ++  ++ln + +  W + GA 
  gi|386002402|ref|YP_005920701.1| 593 ALETLDKYEDAVQAYDE-AISLNPDDVAAWENRGAA 627
                                       68999999984444443.4***************96 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.11
                                       SESEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  24 rpiEklGtYdPlakkkekkevelneerikyWlgvG 58 
                                         +  lG Yd   +  + ++++ln e ++ W ++G
  gi|386002402|ref|YP_005920701.1| 626 AALYSLGKYDEAVQAYD-EVLRLNPEDANAWKKKG 659
                                       566789****9444433.47************999 PP

  == domain 8  score: 0.0 bits;  conditional E-value: 2.4
                                       S..............EEE-HHHHHHHHHTTEE CS
                     Ribosomal_S16  43 e..............velneerikyWlgvGAq 60 
                                                      ++ln e +  W  +GA 
  gi|386002402|ref|YP_005920701.1| 794 DqgkyyeaieaidmaISLNPESALAWNYKGAA 825
                                       03333333344444499*********999995 PP

  == domain 9  score: -0.6 bits;  conditional E-value: 3.7
                                       EEEEETTTTSSTS.SEEE-HHHHHHHHHTT CS
                     Ribosomal_S16  29 lGtYdPlakkkekkevelneerikyWlgvG 58 
                                       +  Yd          + ln + ++ W ++G
  gi|386002402|ref|YP_005920701.1| 870 IQAYDR--------AIDLNSQLVQAWYNKG 891
                                       333332........499*********9998 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.93   3.5e+02      10      34 ..      69      93 ..      67      94 .. 0.88
   2 ?    4.3   0.1      0.11        43       6      37 ..      99     130 ..      97     132 .. 0.86
   3 ?   -1.0   0.5       5.2     2e+03      10      35 ..     137     162 ..     134     165 .. 0.81
   4 ?    4.9   0.1     0.074        28       9      34 ..     170     195 ..     169     196 .. 0.91
   5 !   11.1   0.1   0.00085      0.33      10      34 ..     239     263 ..     237     266 .. 0.94
   6 ?   -0.2   0.0       2.8     1e+03      14      35 ..     277     298 ..     271     301 .. 0.85
   7 ?    2.5   0.0      0.39   1.5e+02      13      35 ..     310     332 ..     306     338 .. 0.89
   8 ?   -0.3   0.0       3.1   1.2e+03      14      34 ..     413     433 ..     404     436 .. 0.87
   9 ?   -1.3   0.1       6.5   2.5e+03      16      35 ..     449     468 ..     447     471 .. 0.87
  10 ?   -1.0   0.0       5.2     2e+03      15      35 ..     482     502 ..     480     505 .. 0.86
  11 !    8.0   0.1    0.0077       2.9      10      37 ..     627     654 ..     624     656 .. 0.90
  12 ?    2.6   0.1      0.39   1.5e+02       9      30 ..     858     879 ..     856     886 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.93
                                      HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C 10 GhyklgeYseArryvdalLeiEPen 34
                                      + y +g+Y+eA +  +  ++++Pe+
  gi|386002402|ref|YP_005920701.1| 69 ALYLQGNYDEAIQDYKEAIRLDPEF 93
                                      77889********999999999986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                                       HHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C   6 ylAlGhyklgeYseArryvdalLeiEPenrQa 37 
                                          l+  k+g+Y+eA +  +  ++++Pe  +a
  gi|386002402|ref|YP_005920701.1|  99 NKGLAFEKQGKYDEAIKAYNEAIRLDPEYANA 130
                                       55677789*******************98765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 5.2
                                       HHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenr 35 
                                       + y +g+Y+eA +  +  +++ Pe  
  gi|386002402|ref|YP_005920701.1| 137 ALYLQGKYDEAIKAYNEAIRLYPEYA 162
                                       778899*****999998888888765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.074
                                       HHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPen 34 
                                       ++ y +g+Y+eA +  +  ++++Pe+
  gi|386002402|ref|YP_005920701.1| 170 YALYSQGNYDEAIKAYNEAIRLDPEF 195
                                       578999******************97 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00085
                                       HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPen 34 
                                       + y+lg+Y+eA r  +  ++++Pen
  gi|386002402|ref|YP_005920701.1| 239 ALYRLGKYDEAIRASNEAIRLDPEN 263
                                       78**********************9 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 2.8
                                       HT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenr 35 
                                       +g+Y+eA +  d  +++ Pe  
  gi|386002402|ref|YP_005920701.1| 277 QGKYDEAIQAYDEAIRLSPEYA 298
                                       699*************999976 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.39
                                       HHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenr 35 
                                        +g+Y+eA +  +  ++++Pen 
  gi|386002402|ref|YP_005920701.1| 310 HQGKYDEAIQASNEAISLDPENA 332
                                       689*******************6 PP

  == domain 8  score: -0.3 bits;  conditional E-value: 3.1
                                       HT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                       +g+Y+eA +  d  +++ Pe 
  gi|386002402|ref|YP_005920701.1| 413 QGKYDEAIQAFDEAIRLNPEY 433
                                       799************999985 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 6.5
                                       -HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                       +Y+eA +  d ++++ Pe  
  gi|386002402|ref|YP_005920701.1| 449 RYDEAIQAYDEVIKLNPEYA 468
                                       7****************976 PP

  == domain 10  score: -1.0 bits;  conditional E-value: 5.2
                                       T-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenr 35 
                                       g+Y+eA +  d  ++  Pe  
  gi|386002402|ref|YP_005920701.1| 482 GRYNEAIKAFDEAIRRNPEYA 502
                                       89*********9999999875 PP

  == domain 11  score: 8.0 bits;  conditional E-value: 0.0077
                                       HHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPenrQa 37 
                                       + y lg+Y+eA +  d +L++ Pe  +a
  gi|386002402|ref|YP_005920701.1| 627 ALYSLGKYDEAVQAYDEVLRLNPEDANA 654
                                       7899*******************98776 PP

  == domain 12  score: 2.6 bits;  conditional E-value: 0.39
                                       HHHHHHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLei 30 
                                       l+ y +g+YseA +  d+ + +
  gi|386002402|ref|YP_005920701.1| 858 LALYSQGNYSEAIQAYDRAIDL 879
                                       78999********999987765 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.9   7.2e+02      52      76 ..     111     135 ..     101     184 .. 0.72
   2 ?   -2.2   0.0       7.8     3e+03      29      67 ..     234     262 ..     218     292 .. 0.58
   3 ?   -0.2   0.1       1.9   7.2e+02      14      43 ..     287     316 ..     279     343 .. 0.60
   4 ?   -0.4   0.0       2.2   8.4e+02      95     113 ..     381     399 ..     344     416 .. 0.64
   5 ?    6.7   0.0     0.014       5.3      52      85 ..     417     450 ..     409     453 .. 0.90
   6 ?    3.5   0.1      0.13        51      47      98 ..     446     493 ..     444     508 .. 0.80
   7 ?    1.8   0.0      0.45   1.7e+02      51     100 ..     484     529 ..     475     530 .. 0.70
   8 !    8.2   0.4    0.0049       1.9       7     111 ..     518     615 ..     512     622 .. 0.76
   9 ?    0.7   0.1      0.96   3.7e+02      21      72 ..     573     621 ..     568     644 .. 0.67
  10 ?    2.7   0.3      0.23        89      21     114 ..     648     734 ..     630     749 .. 0.51
  11 ?    2.7   0.2      0.24        93       9      73 ..     670     738 ..     662     785 .. 0.58
  12 ?    3.6   0.0      0.13        49      52     106 ..     833     887 ..     829     939 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHH-TT-HHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcig 76 
                                       ++ai  ++ea+ +dP+  +a    g
  gi|386002402|ref|YP_005920701.1| 111 DEAIKAYNEAIRLDPEYANAWHNKG 135
                                       6899999999999999888754444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.8
                                       HHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT CS
                       TOM20_plant  29 lrWggallelsqfqsvaeakqmiqdaiskleeallidPk 67 
                                       +  g al  l +++          +ai   +ea+ +dP+
  gi|386002402|ref|YP_005920701.1| 234 INKGAALYRLGKYD----------EAIRASNEAIRLDPE 262
                                       55555555555544..........344444444444444 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.9
                                       HHHHHHH-TT-HHHHHHHHHHHHHHHHHS- CS
                       TOM20_plant  14 aeatykknPldadnllrWggallelsqfqs 43 
                                        ++  +  P+ ad   r g+all   ++++
  gi|386002402|ref|YP_005920701.1| 287 YDEAIRLSPEYADAWNRKGEALLHQGKYDE 316
                                       444445566666666666666666555544 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHH-TT- CS
                       TOM20_plant  95 nfekatqffqqavdedPdn 113
                                       +++ a q f++++  dP+ 
  gi|386002402|ref|YP_005920701.1| 381 KYDEAIQTFNETIRLDPEH 399
                                       4455555555555555543 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafl 85 
                                       ++ai+ ++ea+ ++P+  da +  gna  s +++
  gi|386002402|ref|YP_005920701.1| 417 DEAIQAFDEAIRLNPEYVDAWYSKGNALDSQSRY 450
                                       69*************************9998776 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHH CS
                       TOM20_plant  47 akqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfek 98 
                                       ++   ++ai+ ++e + ++P+  da    g a+ s +++     ea + f+ 
  gi|386002402|ref|YP_005920701.1| 446 SQSRYDEAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYN----EAIKAFDE 493
                                       55667899*****************999999999999885....44444544 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHH CS
                       TOM20_plant  51 iqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekat 100
                                        ++ai  ++ea+  +P+  da    g a +s   +    eea + f+ at
  gi|386002402|ref|YP_005920701.1| 484 YNEAIKAFDEAIRRNPEYADAWNNKGVALVSLDKY----EEAIQAFDEAT 529
                                       68999999999999999999966666666554433....56666666665 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHH CS
                       TOM20_plant   7 feearkdaeatykknPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcignaytsfa 83 
                                       +eea +  ++  + nP+dad  l+ g a+  l ++++   + q+ + +i+ +++ l  +P+  +a    g a +   
  gi|386002402|ref|YP_005920701.1| 518 YEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKE---TIQVCNVSIQAYDDDLRWNPEDANARLSKGIALMLK- 590
                                       7888888899999*********************987...88999999999*********9998877666665432. PP

                                       HH---HHHHHHHHHHHHHHHHHHHHH-T CS
                       TOM20_plant  84 fltpdeeeakenfekatqffqqavdedP 111
                                              e+ +++e a q +++a+  +P
  gi|386002402|ref|YP_005920701.1| 591 ---GLALETLDKYEDAVQAYDEAISLNP 615
                                       ...2233444555555555555555555 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 0.96
                                       -TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHH CS
                       TOM20_plant  21 nPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdal 72 
                                       nP+da+  l  g al+ l  +    e+    +da++ ++ea+ ++P    a 
  gi|386002402|ref|YP_005920701.1| 573 NPEDANARLSKGIALM-LKGLAL--ETLDKYEDAVQAYDEAISLNPDDVAAW 621
                                       6777776666665554.444433..677778899999999999999765543 PP

  == domain 10  score: 2.7 bits;  conditional E-value: 0.23
                                       -TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHH....HHHHH---HHHHH CS
                       TOM20_plant  21 nPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcignayt....sfafltpdeeeak 93 
                                       nP+da+   + g al  l             ++++  l+ea+ ++P+ +   W+i    +     +    + +eea 
  gi|386002402|ref|YP_005920701.1| 648 NPEDANAWKKKGYALHSLEEH----------EESVKALDEAIRLNPN-DAGCWLIKSFNLliieKYDEAINASEEAI 713
                                       555555555555555444333..........2355556666666664.34456654332211113333444445555 PP

                                       HHHHHHHHHHHHHHHH-TT-H CS
                       TOM20_plant  94 enfekatqffqqavdedPdnd 114
                                       + ++ +   +++ v  +P+n 
  gi|386002402|ref|YP_005920701.1| 714 RAYNETITTYEEIVSLNPENS 734
                                       555555555555555555554 PP

  == domain 11  score: 2.7 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HH....HHHHHHHHHHHHHHHHHHH-TT-HHHHH CS
                       TOM20_plant   9 earkdaeatykknPldadnllrWggallelsqfqsva....eakqmiqdaiskleeallidPkkhdalW 73 
                                       e  k  ++  + nP da   l  +  ll + ++++ +    ea +  +++i+ +ee + ++P+   a  
  gi|386002402|ref|YP_005920701.1| 670 ESVKALDEAIRLNPNDAGCWLIKSFNLLIIEKYDEAInaseEAIRAYNETITTYEEIVSLNPENSTASN 738
                                       445555666667777777666666666666666543311113445567777777777777777666544 PP

  == domain 12  score: 3.6 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH CS
                       TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqa 106
                                       ++ai  ++ea+ ++P  +da    g a  s + +++  +   +  ++ +q+ q  
  gi|386002402|ref|YP_005920701.1| 833 EEAILAYDEAIRLNPDDEDAWNNKGLALYSQGNYSEAIQAYDRAIDLNSQLVQAW 887
                                       689999***********99988889998888888876666666666666666544 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.7   2.7e+02     215     258 ..     108     151 ..     101     194 .. 0.71
   2 ?    0.4   0.0      0.89   3.4e+02     206     258 ..     235     287 ..     207     303 .. 0.74
   3 ?    2.0   0.1      0.29   1.1e+02     181     258 ..     278     355 ..     265     390 .. 0.76
   4 ?   12.1   0.1   0.00025     0.096     177     255 ..     478     556 ..     442     577 .. 0.83
   5 ?   -2.1   0.2       5.3     2e+03     215     263 ..     598     646 ..     586     674 .. 0.58
   6 ?    1.9   0.0      0.32   1.2e+02      54     132 ..     698     778 ..     688     787 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                                       T-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsern 258
                                       g+y+eA +  +ea+  d++++++  N   a  + gk +e+++ +
  gi|386002402|ref|YP_005920701.1| 108 GKYDEAIKAYNEAIRLDPEYANAWHNKGYALYLQGKYDEAIKAY 151
                                       67777777777777777777777777777777777777766544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.89
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHH CS
                        Coatomer_E 206 gkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsern 258
                                        k ++   lg+y+eA    +ea+  d+++  +  N  va +  gk +e+++ +
  gi|386002402|ref|YP_005920701.1| 235 NKGAALYRLGKYDEAIRASNEAIRLDPENVYAWHNKGVALNSQGKYDEAIQAY 287
                                       44455567899999999999999999999999999999999999999988765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.29
                                       THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHH CS
                        Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevser 257
                                       +k+ +A   ++e     ++  +  n k  + l++g+y+eA +  +ea+  d+++++      va  + gk++e+++ 
  gi|386002402|ref|YP_005920701.1| 278 GKYDEAIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAISLDPENANGWNIKGVALYNRGKSDEAIKA 354
                                       67788888888877777777788888888899999999999999999999999999887788888888888888776 PP

                                       H CS
                        Coatomer_E 258 n 258
                                       +
  gi|386002402|ref|YP_005920701.1| 355 Y 355
                                       6 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00025
                                       HH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HH CS
                        Coatomer_E 177 avggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdae 253
                                       +++ +++++A   f+e   + ++  +  n k v+ + l++yeeA +   ea   +++d+++     va  hlgk +e
  gi|386002402|ref|YP_005920701.1| 478 FNSQGRYNEAIKAFDEAIRRNPEYADAWNNKGVALVSLDKYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKE 554
                                       44558899999999999999999999999999999999999999999999999999999999999999999999877 PP

                                       HH CS
                        Coatomer_E 254 vs 255
                                       ++
  gi|386002402|ref|YP_005920701.1| 555 TI 556
                                       65 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 5.3
                                       T-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsqlk 263
                                       ++ye+A +   ea+  ++ d  +  N   a   lgk +e+++ + + l+
  gi|386002402|ref|YP_005920701.1| 598 DKYEDAVQAYDEAISLNPDDVAAWENRGAALYSLGKYDEAVQAYDEVLR 646
                                       4555555555555555555555555555555555555555444433333 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.32
                                       HHHHS-TTS-HHHHHHHHHHHHHH-STTHHHHHHHHHHHHHS----S-HHHH.....HHHHHHHHHTT-HHHHHHHH CS
                        Coatomer_E  54 viseIkesaatelqAvrllaeylnspsrkeeilaelkeeladseiesnevlr.....llaaivflkegdfddalkll 125
                                        i++ +e+  ++  A+r++ e +++    eei++   e+ + s+i+s + ++      l +i++ ++ ++++a+++ 
  gi|386002402|ref|YP_005920701.1| 698 IIEKYDEAINASEEAIRAYNETITT---YEEIVSLNPENSTASNIKSRTLIAkgngwALKGIILGEQHEYNEAMQAF 771
                                       5666666778888999999999988...888888878888888887776654333335889**************99 PP

                                       TT--SHH CS
                        Coatomer_E 126 kksenLe 132
                                       ++  +L+
  gi|386002402|ref|YP_005920701.1| 772 NEAVSLN 778
                                       9887775 PP

>> TetR_C_15  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       4.7   1.8e+03       7      41 ..     111     146 ..     110     167 .. 0.76
   2 ?   -1.3   0.0       9.5   3.6e+03       7      47 ..     349     389 ..     348     397 .. 0.78
   3 ?    5.4   0.0     0.079        30       7      42 ..     417     453 ..     416     462 .. 0.82
   4 ?    0.6   0.0       2.5   9.7e+02       7      45 ..     451     489 ..     447     497 .. 0.75
   5 ?    1.2   0.0       1.6   6.1e+02       9      49 ..     487     527 ..     484     531 .. 0.76
   6 ?    0.2   0.1       3.3   1.3e+03       7      52 ..     635     680 ..     634     681 .. 0.90
   7 ?   -0.1   0.0         4   1.5e+03      31      57 ..    1230    1256 ..    1220    1260 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4.7
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elve 41 
                                       d+ + a+ +a r +p++  +++   ++l ++ + +e
  gi|386002402|ref|YP_005920701.1| 111 DEAIKAYNEAIRLDPEYANAWHNKGYALYLQgKYDE 146
                                       678999999999999999999988777766644444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 9.5
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeqri 47 
                                       d+ + a+ +a r  p++  ++     sl+ +   +++ q++
  gi|386002402|ref|YP_005920701.1| 349 DEAIKAYDEAIRLSPEYADAWNNKGLSLKSQGKYDEAIQTF 389
                                       78899***************999888888885555555555 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.079
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgel.elvea 42 
                                       d+ ++a+ +a r np++  ++++   +l+ + + +ea
  gi|386002402|ref|YP_005920701.1| 417 DEAIQAFDEAIRLNPEYVDAWYSKGNALDSQsRYDEA 453
                                       789********************99999888444444 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 2.5
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeq 45 
                                       d+ ++a+ ++ + np++  ++ +  ++ + + +  ++ +
  gi|386002402|ref|YP_005920701.1| 451 DEAIQAYDEVIKLNPEYADAWNSKGTAFNSQGRYNEAIK 489
                                       789******************999888777744333344 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 1.6
                         TetR_C_15   9 lvdallaahrenpalrrvlleeapslgelelvealeqriae 49 
                                        + a+ +a r+np++  ++     +l  l+  e++ q ++e
  gi|386002402|ref|YP_005920701.1| 487 AIKAFDEAIRRNPEYADAWNNKGVALVSLDKYEEAIQAFDE 527
                                       789***************99877777666666666665555 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 3.3
                         TetR_C_15   7 dalvdallaahrenpalrrvlleeapslgelelvealeqriaeala 52 
                                       d+ v+a+ ++ r np+   ++ +  ++l+ le++e+  + ++ea++
  gi|386002402|ref|YP_005920701.1| 635 DEAVQAYDEVLRLNPEDANAWKKKGYALHSLEEHEESVKALDEAIR 680
                                       789****************************999999888888775 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 4
                         TetR_C_15   31 apslgelelvealeqriaealaalLar 57  
                                          +l+   ++++++++++e++a+++a+
  gi|386002402|ref|YP_005920701.1| 1230 VLRLDPRYRHREFSKKLQEQIAEMIAQ 1256
                                        456666668999999999999999887 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.6   9.7e+02     286     295 ..     145     154 ..      99     194 .. 0.56
   2 ?    3.4   0.0     0.069        26     280     345 ..     377     438 ..     371     470 .. 0.80
   3 ?   -0.3   0.0      0.91   3.5e+02     276     338 ..     475     532 ..     471     534 .. 0.76
   4 ?    4.6   0.1     0.029        11     253     297 ..     766     810 ..     716     915 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                           DUF3808 286 deAlelleei 295
                                       deA+++++e+
  gi|386002402|ref|YP_005920701.1| 145 DEAIKAYNEA 154
                                       3333333322 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.069
                           DUF3808 280 slkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfleLlkls.kwSkalY 345
                                         +g+ deA+++++e i     +l   +    ++++ltl  + +y+ea+++f+e ++l+ ++  a+Y
  gi|386002402|ref|YP_005920701.1| 377 KSQGKYDEAIQTFNETI-----RLDPEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIRLNpEYVDAWY 438
                                       568999********877.....55555788999********************99999834566666 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.91
                           DUF3808 276 arieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfleLlkls 338
                                       +++   +g+ +eA+++++e+i   + e+ +       +++++lv l +y+ea+++f+e  +l+
  gi|386002402|ref|YP_005920701.1| 475 GTAFNSQGRYNEAIKAFDEAI-RRNPEYAD----AWNNKGVALVSLDKYEEAIQAFDEATRLN 532
                                       5566679999********999.45555443....34467889999999999999999877766 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.029
                           DUF3808 253 eleelLlksrkrfPksalwllfearieslkgnldeAlelleeiie 297
                                       e+ +++ ++ ++ P ++ +  f+++ +  +g+  eA+e+++++i+
  gi|386002402|ref|YP_005920701.1| 766 EAMQAFNEAVSLNPAGSFIWSFKGKYLNDQGKYYEAIEAIDMAIS 810
                                       555555555555555555555555555555555555555554442 PP

>> CBAH  Linear amide C-N hydrolases, choloylglycine hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0013      0.51      60     132 ..     359     433 ..     300     445 .. 0.84
   2 ?   -0.7   0.0       2.3   8.7e+02      51      78 ..     476     513 ..     435     544 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                                       SSSEEEESEEEETTS-EEE..EEE-TTT---BSS--TTSEEEEGGGHHHHHHHH-SSHHHHHHHHTTEEEB---C CS
                              CBAH  60 vesyPlfvdglNEkGlsia..glylaeyaeykkepkedkvniaagelirwvlenftsveevkeklkklkivneal 132
                                       +  +P ++d+ N kGls++  g y  ++++++++++ d  ++aa +     l+n  +++e++++  ++  +n+++
  gi|386002402|ref|YP_005920701.1| 359 IRLSPEYADAWNNKGLSLKsqGKYDEAIQTFNETIRLDPEHVAAWYNKGLTLNNQGKYDEAIQAFDEAIRLNPEY 433
                                       56689***********98532677799*************************************99988888776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                                       S..........-EEEEEEESSSEEEESEEEETTS-EEE CS
                              CBAH  51 d..........avvGmgtkvesyPlfvdglNEkGlsia 78 
                                                  a+      +   P ++d+ N kG  + 
  gi|386002402|ref|YP_005920701.1| 476 TafnsqgryneAIKAFDEAIRRNPEYADAWNNKGVALV 513
                                       12223333343444455555666677777777765443 PP

>> Rota_NSP3  Rotavirus non-structural protein NSP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.7   6.6e+02     220     252 ..      63      94 ..      58     121 .. 0.86
   2 ?    2.6   0.0      0.16        61     219     260 ..     164     204 ..     154     218 .. 0.88
   3 ?   -1.5   0.0       2.9   1.1e+03     218     250 ..     299     330 ..     247     356 .. 0.78
   4 ?   -0.2   0.0       1.1   4.2e+02     176     255 ..     325     403 ..     309     428 .. 0.77
   5 ?    5.1   0.1     0.027        10     218     261 ..     851     892 ..     790     906 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                         Rota_NSP3 220 yneklerlldvGsltsskeiieksieleiPiik 252
                                       +n+k+  l+  G++ ++++ ++ +i l+ P++ 
  gi|386002402|ref|YP_005920701.1|  63 WNNKGYALYLQGNYDEAIQDYKEAIRLD-PEFV 94 
                                       79999999999*****************.9985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                         Rota_NSP3 219 vyneklerlldvGsltsskeiieksieleiPiikadirnnes 260
                                        +n k+  l+  G++ ++++ ++ +i l+ P++   +rn+  
  gi|386002402|ref|YP_005920701.1| 164 AWNSKGYALYSQGNYDEAIKAYNEAIRLD-PEFMWPWRNKGD 204
                                       58999999*********************.***998888765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.9
                         Rota_NSP3 218 kvyneklerlldvGsltsskeiieksieleiPi 250
                                         +n k+e ll+ G++ ++++  + +i l+ P+
  gi|386002402|ref|YP_005920701.1| 299 DAWNRKGEALLHQGKYDEAIQASNEAISLD-PE 330
                                       568999999999999999999999999998.76 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.1
                         Rota_NSP3 176 l....ekykdivldldkmneevkldqnsisynsaailvstilgaelkvyneklerlldvGsltsskeiieksielei 248
                                       +    e  + + ++  ++ +  k+d+   +y++a  l           +n+k+  l   G++ ++++ ++ +i l+ 
  gi|386002402|ref|YP_005920701.1| 325 IsldpENANGWNIKGVALYNRGKSDEAIKAYDEAIRL----SPEYADAWNNKGLSLKSQGKYDEAIQTFNETIRLD- 396
                                       4456678888888888888888888888888887663....23345689999999999******************. PP

                         Rota_NSP3 249 Piikadi 255
                                       P+  a +
  gi|386002402|ref|YP_005920701.1| 397 PEHVAAW 403
                                       8866655 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.027
                         Rota_NSP3 218 kvyneklerlldvGsltsskeiieksieleiPiikadirnnesp 261
                                         +n+k+  l+  G++ ++++ + ++i+l+   ++a +  n+  
  gi|386002402|ref|YP_005920701.1| 851 DAWNNKGLALYSQGNYSEAIQAYDRAIDLNSQLVQAWY--NKGD 892
                                       679***************************99999988..4433 PP

>> P2_Phage_GpR  P2 phage tail completion protein R (GpR)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.4     9e+02      17      35 ..     222     240 ..     215     249 .. 0.81
   2 ?    3.6   0.0      0.17        66       9      49 ..     248     288 ..     242     295 .. 0.86
   3 ?   -1.0   0.0       4.6   1.8e+03      10      40 ..     385     415 ..     383     427 .. 0.80
   4 ?    2.3   0.0      0.45   1.7e+02      10      52 ..     419     461 ..     415     470 .. 0.85
   5 ?   -1.6   0.0       6.8   2.6e+03       9      35 ..     520     546 ..     514     565 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.4
                      P2_Phage_GpR  17 elaanpeklevfvdegelv 35 
                                         + npe l++++++g+  
  gi|386002402|ref|YP_005920701.1| 222 AIRLNPEDLNSWINKGAAL 240
                                       5688***********9866 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                      P2_Phage_GpR   9 aaLtaalpelaanpeklevfvdegelvatgaqslsfeyrYt 49 
                                       +a++a+ +  + +pe+++++ ++g   +++++++ +   Y+
  gi|386002402|ref|YP_005920701.1| 248 EAIRASNEAIRLDPENVYAWHNKGVALNSQGKYDEAIQAYD 288
                                       6899999******************9999888877777776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.6
                      P2_Phage_GpR  10 aLtaalpelaanpeklevfvdegelvatgaq 40 
                                       a+++  +  + +pe++ +++++g   +++++
  gi|386002402|ref|YP_005920701.1| 385 AIQTFNETIRLDPEHVAAWYNKGLTLNNQGK 415
                                       7888889999************988777544 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.45
                      P2_Phage_GpR  10 aLtaalpelaanpeklevfvdegelvatgaqslsfeyrYtlvl 52 
                                       a++a  +  + npe +++++ +g+   ++++++ +   Y+ v+
  gi|386002402|ref|YP_005920701.1| 419 AIQAFDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQAYDEVI 461
                                       56666677899*****************999999999998776 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 6.8
                      P2_Phage_GpR   9 aaLtaalpelaanpeklevfvdegelv 35 
                                       +a++a  + ++ npe  +++ ++g  +
  gi|386002402|ref|YP_005920701.1| 520 EAIQAFDEATRLNPEDADAWLKKGVAF 546
                                       67888888999***********99765 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.21        80     242     290 ..     204     252 ..     180     258 .. 0.86
   2 ?   -0.1   0.0      0.94   3.6e+02     243     292 ..     273     322 ..     248     327 .. 0.81
   3 ?    0.4   0.0      0.68   2.6e+02     219     271 ..     283     335 ..     272     356 .. 0.59
   4 ?    0.8   0.0       0.5   1.9e+02     218     289 ..     486     557 ..     446     568 .. 0.86
   5 ?    1.4   0.0      0.34   1.3e+02     211     289 ..     758     837 ..     750     843 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.21
                                       HHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             ChAPs 242 efllskkkeelAlevakravksaPsefktWalLvkvYikledienALlt 290
                                       + l s+ k+elA+ + ++a+++ P + + W+       +l+ +++A+ +
  gi|386002402|ref|YP_005920701.1| 204 DTLFSQGKYELAIYAYDEAIRLNPEDLNSWINKGAALYRLGKYDEAIRA 252
                                       5688999***********************9998888888888888766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.94
                                       HHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 243 fllskkkeelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                        l s+ k++ A+++ ++a++++P     W +  +  ++++ +++A+ + N
  gi|386002402|ref|YP_005920701.1| 273 ALNSQGKYDEAIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASN 322
                                       5678889999*************************999999999987766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.68
                                       HHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHH CS
                             ChAPs 219 avkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktW 271
                                       a++   e+++ +++ a+    + e ll++ k++ A++++++a+++ P + + W
  gi|386002402|ref|YP_005920701.1| 283 AIQAYDEAIRLSPEYADAWNRKGEALLHQGKYDEAIQASNEAISLDPENANGW 335
                                       33333444444444444444445555566666666666666666666666555 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.5
                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALl 289
                                       +a+k   e+++ +++ a+    +   l+s +k+e A+++ ++a+++ P +   W +    + +l+ +++ + 
  gi|386002402|ref|YP_005920701.1| 486 EAIKAFDEAIRRNPEYADAWNNKGVALVSLDKYEEAIQAFDEATRLNPEDADAWLKKGVAFYHLGKYKETIQ 557
                                       6888888999999999999999999999999***********************998888888888777665 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.34
                                       HHTT-HH.HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHH CS
                             ChAPs 211 lladeEv.davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledien 286
                                       l  ++E  +a++  ne+++ ++  + + + + ++l ++ k+  A+e+ + a+++ P     W +       ++  e+
  gi|386002402|ref|YP_005920701.1| 758 LGEQHEYnEAMQAFNEAVSLNPAGSFIWSFKGKYLNDQGKYYEAIEAIDMAISLNPESALAWNYKGAALRGQGKHEE 834
                                       5555554269999999999999999**********************************999887666666666666 PP

                                       HHH CS
                             ChAPs 287 ALl 289
                                       A+l
  gi|386002402|ref|YP_005920701.1| 835 AIL 837
                                       665 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.2   8.3e+02      81     107 ..     134     160 ..     130     163 .. 0.89
   2 ?    2.1   0.0      0.49   1.9e+02      81     107 ..     304     330 ..     302     333 .. 0.88
   3 ?    0.2   0.0         2   7.5e+02      81     106 ..     406     431 ..     371     435 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.2
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpq 107
                                       +G  l  qg+++ea+++   A++++p+
  gi|386002402|ref|YP_005920701.1| 134 KGYALYLQGKYDEAIKAYNEAIRLYPE 160
                                       67788999*****************96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.49
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcpq 107
                                       +GE ll qg+++ea+++   A+++ p+
  gi|386002402|ref|YP_005920701.1| 304 KGEALLHQGKYDEAIQASNEAISLDPE 330
                                       7***************99999988665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2
                             MAS20  81 lGEellaqgeeeeaaehlynAlkvcp 106
                                       +G +l +qg+++ea++++  A+++ p
  gi|386002402|ref|YP_005920701.1| 406 KGLTLNNQGKYDEAIQAFDEAIRLNP 431
                                       56677788999999999999998766 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00079       0.3      14      30 ..      73      89 ..      72      89 .. 0.89
   2 ?    0.9   0.0      0.81   3.1e+02      14      30 ..     107     123 ..     106     129 .. 0.89
   3 ?    3.9   0.1     0.098        37      14      36 ..     141     163 ..     140     164 .. 0.87
   4 ?    2.3   0.0      0.31   1.2e+02      14      30 ..     175     191 ..     174     191 .. 0.87
   5 ?    1.2   0.0      0.66   2.5e+02      14      30 ..     277     293 ..     276     297 .. 0.88
   6 ?   -0.2   0.0       1.8     7e+02      12      30 ..     309     327 ..     304     327 .. 0.82
   7 ?    0.3   0.1       1.3   4.9e+02      14      30 ..     413     429 ..     412     433 .. 0.87
   8 ?   -0.9   0.0       3.1   1.2e+03      14      26 ..     447     459 ..     446     464 .. 0.81
   9 ?   -2.0   0.0       6.5   2.5e+03      14      27 ..     481     494 ..     480     495 .. 0.84
  10 ?    1.5   0.1      0.53     2e+02      15      30 ..     598     613 ..     596     614 .. 0.91
  11 ?   -1.5   0.2       4.7   1.8e+03      13      30 ..     760     777 ..     760     777 .. 0.89
  12 ?    5.1   0.1      0.04        15      14      34 ..     863     883 ..     862     886 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00079
                          SHNi-TPR 14 nenFpqAveDlrkaLeL 30
                                      ++n+++A++D+++a+ L
  gi|386002402|ref|YP_005920701.1| 73 QGNYDEAIQDYKEAIRL 89
                                      68************865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.81
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386002402|ref|YP_005920701.1| 107 QGKYDEAIKAYNEAIRL 123
                                       579**********9866 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.098
                          SHNi-TPR  14 nenFpqAveDlrkaLeLreqllp 36 
                                       ++++++A++ +++a+ L+ ++ +
  gi|386002402|ref|YP_005920701.1| 141 QGKYDEAIKAYNEAIRLYPEYAN 163
                                       689*************9988765 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.31
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++n+++A++ +++a+ L
  gi|386002402|ref|YP_005920701.1| 175 QGNYDEAIKAYNEAIRL 191
                                       68***********9865 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.66
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386002402|ref|YP_005920701.1| 277 QGKYDEAIQAYDEAIRL 293
                                       689**********9866 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.8
                          SHNi-TPR  12 lEnenFpqAveDlrkaLeL 30 
                                       l ++++++A++  ++a+ L
  gi|386002402|ref|YP_005920701.1| 309 LHQGKYDEAIQASNEAISL 327
                                       6789*******99888876 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 1.3
                          SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                       ++++++A++ +++a+ L
  gi|386002402|ref|YP_005920701.1| 413 QGKYDEAIQAFDEAIRL 429
                                       579********999876 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 3.1
                          SHNi-TPR  14 nenFpqAveDlrk 26 
                                       ++++++A++ +++
  gi|386002402|ref|YP_005920701.1| 447 QSRYDEAIQAYDE 459
                                       79******98876 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 6.5
                          SHNi-TPR  14 nenFpqAveDlrka 27 
                                       ++++++A++ +++a
  gi|386002402|ref|YP_005920701.1| 481 QGRYNEAIKAFDEA 494
                                       689*****999887 PP

  == domain 10  score: 1.5 bits;  conditional E-value: 0.53
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       +++++Av+ +++a+ L
  gi|386002402|ref|YP_005920701.1| 598 DKYEDAVQAYDEAISL 613
                                       69***********987 PP

  == domain 11  score: -1.5 bits;  conditional E-value: 4.7
                          SHNi-TPR  13 EnenFpqAveDlrkaLeL 30 
                                       E++ +++A + +++a+ L
  gi|386002402|ref|YP_005920701.1| 760 EQHEYNEAMQAFNEAVSL 777
                                       78889*********9987 PP

  == domain 12  score: 5.1 bits;  conditional E-value: 0.04
                          SHNi-TPR  14 nenFpqAveDlrkaLeLreql 34 
                                       ++n+++A++ +++a++L  ql
  gi|386002402|ref|YP_005920701.1| 863 QGNYSEAIQAYDRAIDLNSQL 883
                                       68**************97776 PP

>> BPS  BPS (Between PH and SH2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.2   8.4e+02      21      41 ..     114     134 ..     106     137 .. 0.82
   2 ?    2.1   0.0      0.47   1.8e+02       9      42 ..     272     305 ..     268     309 .. 0.84
   3 ?    1.6   0.1      0.66   2.5e+02      19      41 ..     316     338 ..     310     345 .. 0.81
   4 ?   -1.7   0.0       6.9   2.6e+03      15      41 ..     346     372 ..     339     374 .. 0.80
   5 ?   -2.2   0.0       9.9   3.8e+03      24      43 ..     457     476 ..     452     478 .. 0.83
   6 ?    1.4   0.0      0.74   2.8e+02      24      42 ..     525     543 ..     518     546 .. 0.86
   7 ?   -2.1   0.0       9.3   3.5e+03      26      43 ..     609     626 ..     606     631 .. 0.85
   8 ?    4.9   0.0     0.061        23      25      42 ..     642     659 ..     632     664 .. 0.88
   9 ?    0.8   0.0       1.2   4.6e+02      21      42 ..     802     823 ..     795     827 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.2
                               BPS  21 IeNptEalsaaleegqaWRkk 41 
                                       I    Ea   ++e + aW  k
  gi|386002402|ref|YP_005920701.1| 114 IKAYNEAIRLDPEYANAWHNK 134
                                       66778*************988 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.47
                               BPS   9 VaMDFSGqkgrvIeNptEalsaaleegqaWRkks 42 
                                       Va+   G+    I    Ea    +e + aW +k 
  gi|386002402|ref|YP_005920701.1| 272 VALNSQGKYDEAIQAYDEAIRLSPEYADAWNRKG 305
                                       66666788888899999*************9996 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.66
                               BPS  19 rvIeNptEalsaaleegqaWRkk 41 
                                         I    Ea s ++e++  W  k
  gi|386002402|ref|YP_005920701.1| 316 EAIQASNEAISLDPENANGWNIK 338
                                       5678889*************766 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.9
                               BPS  15 GqkgrvIeNptEalsaaleegqaWRkk 41 
                                       G+    I    Ea    +e + aW  k
  gi|386002402|ref|YP_005920701.1| 346 GKSDEAIKAYDEAIRLSPEYADAWNNK 372
                                       55556677788999**********877 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 9.9
                               BPS  24 ptEalsaaleegqaWRkkss 43 
                                         E+   ++e + aW  k +
  gi|386002402|ref|YP_005920701.1| 457 YDEVIKLNPEYADAWNSKGT 476
                                       568999999******98876 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.74
                               BPS  24 ptEalsaaleegqaWRkks 42 
                                         Ea   ++e++ aW kk 
  gi|386002402|ref|YP_005920701.1| 525 FDEATRLNPEDADAWLKKG 543
                                       6799999*********996 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 9.3
                               BPS  26 EalsaaleegqaWRkkss 43 
                                       Ea s ++++  aW  + +
  gi|386002402|ref|YP_005920701.1| 609 EAISLNPDDVAAWENRGA 626
                                       99***********98876 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.061
                               BPS  25 tEalsaaleegqaWRkks 42 
                                        E+l  ++e++ aW+kk 
  gi|386002402|ref|YP_005920701.1| 642 DEVLRLNPEDANAWKKKG 659
                                       699*************96 PP

  == domain 9  score: 0.8 bits;  conditional E-value: 1.2
                               BPS  21 IeNptEalsaaleegqaWRkks 42 
                                       Ie    a s ++e ++aW  k 
  gi|386002402|ref|YP_005920701.1| 802 IEAIDMAISLNPESALAWNYKG 823
                                       77777899**********8776 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.17        64     134     231 ..      66     164 ..      55     184 .. 0.83
   2 ?    1.4   0.1      0.27     1e+02     120     241 ..     191     310 ..     171     322 .. 0.73
   3 ?    9.1   0.2    0.0013      0.49     119     231 ..     360     470 ..     340     498 .. 0.83
   4 ?   -0.4   0.0         1   3.8e+02     133     156 ..     507     530 ..     477     538 .. 0.67
   5 ?    0.4   0.2      0.54   2.1e+02     111     159 ..     601     649 ..     559     677 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---TT.-HHHHHHHH-TT-HHHHHHHHHHHHHTT CS
                          PknG_TPR 134 rglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetdee.kyYrtVwrtdrgvvsAaFGlaRqlaaag 209
                                       +g a  l+g+y+eA+++++e +++ p  + P      + E  g+ de+ k Y+   r d  +  A +    +l  +g
  gi|386002402|ref|YP_005920701.1|  66 KGYALYLQGNYDEAIQDYKEAIRLDPEFVWPWYNKGLAFEKQGKYDEAiKAYNEAIRLDPEYANAWHNKGYALYLQG 142
                                       57788899999999999999999999999999999999999999887559999999999999999999999999999 PP

                                       -HHHHHHHHHTS-TTSTTHHHH CS
                          PknG_TPR 210 draaAvaaLdeVpatSrhyttA 231
                                       + ++A++a +e  +    y++A
  gi|386002402|ref|YP_005920701.1| 143 KYDEAIKAYNEAIRLYPEYANA 164
                                       9999999988876666666665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                                       HHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---TT.-HHHHHHHH-TT-H CS
                          PknG_TPR 120 leeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetdee.kyYrtVwrtdrgvv 195
                                       l++e  + Wr    +g +  ++g+ye A+ ++de +++ p ++   +   a+  + g+ de+ +  +   r d   v
  gi|386002402|ref|YP_005920701.1| 191 LDPEFMWPWRN---KGDTLFSQGKYELAIYAYDEAIRLNPEDLNSWINKGAALYRLGKYDEAiRASNEAIRLDPENV 264
                                       45555555553...466667788888888888888888888888888888888887777764467777888888888 PP

                                       HHHHHHHHHHHHTT-HHHHHHHHHTS-TTSTTHHHHHHHHHHHCH- CS
                          PknG_TPR 196 sAaFGlaRqlaaagdraaAvaaLdeVpatSrhyttArltavlllls 241
                                        A +    +l  +g+ ++A++a de  + S  y+ A      +ll+
  gi|386002402|ref|YP_005920701.1| 265 YAWHNKGVALNSQGKYDEAIQAYDEAIRLSPEYADAWNRKGEALLH 310
                                       8888888889999999999999999999999999986555555555 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0013
                                       HHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---TT.-HHHHHHHH-TT- CS
                          PknG_TPR 119 eleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetdee.kyYrtVwrtdrgv 194
                                       +l++e+++ W     +gl+  ++g+y+eA+++F+e +++ p  +a       t    g+ de+ + ++   r +  +
  gi|386002402|ref|YP_005920701.1| 360 RLSPEYADAWN---NKGLSLKSQGKYDEAIQTFNETIRLDPEHVAAWYNKGLTLNNQGKYDEAiQAFDEAIRLNPEY 433
                                       45555666665...368888999*******************************999999975599*********** PP

                                       HHHHHHHHHHHHHTT-HHHHHHHHHTS-TTSTTHHHH CS
                          PknG_TPR 195 vsAaFGlaRqlaaagdraaAvaaLdeVpatSrhyttA 231
                                       v A +    +l  + + ++A++a deV +    y+ A
  gi|386002402|ref|YP_005920701.1| 434 VDAWYSKGNALDSQSRYDEAIQAYDEVIKLNPEYADA 470
                                       ***************************9999999887 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1
                                       HHHHHHHHHT-HHHHHHHHHHHHH CS
                          PknG_TPR 133 yrglaeLlegdyeeAaaeFdevla 156
                                        +g+a  + ++yeeA+++Fde  +
  gi|386002402|ref|YP_005920701.1| 507 NKGVALVSLDKYEEAIQAFDEATR 530
                                       368888999999999999998765 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHH---HHHHH.HHHHHHHHHT-HHHHHHHHHHHHHHST CS
                          PknG_TPR 111 eearelLdeleeeveedWrldW.yrglaeLlegdyeeAaaeFdevlaalp 159
                                       e+a++  de  + +++d    W  rg a  + g+y+eA++++devl++ p
  gi|386002402|ref|YP_005920701.1| 601 EDAVQAYDEAISLNPDDVA-AWeNRGAALYSLGKYDEAVQAYDEVLRLNP 649
                                       3444444443333333322.231345555556677777777777766544 PP

>> YozE_SAM_like  YozE SAM-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       3.4   1.3e+03      44      64 ..     138     158 ..     133     160 .. 0.91
   2 ?   -1.3   0.0       6.5   2.5e+03      44      61 ..     376     393 ..     375     395 .. 0.86
   3 ?    1.1   0.0       1.2   4.4e+02      44      62 ..     410     428 ..     408     429 .. 0.88
   4 ?    1.4   0.0      0.94   3.6e+02      44      62 ..     478     496 ..     465     497 .. 0.88
   5 ?    0.0   0.0       2.6   9.8e+02      46      61 ..     760     775 ..     758     777 .. 0.85
   6 ?    1.3   0.0         1     4e+02      42      62 ..     790     810 ..     789     811 .. 0.92
   7 ?   -1.3   0.0       6.9   2.6e+03      44      62 ..     860     878 ..     859     881 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.4
                                       HHTSHHHHTTHHHHHHHHHHH CS
                     YozE_SAM_like  44 LelnaeylssmeifdeaweeY 64 
                                       L+l+++y++++++ +ea+++Y
  gi|386002402|ref|YP_005920701.1| 138 LYLQGKYDEAIKAYNEAIRLY 158
                                       78899**************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.5
                                       HHTSHHHHTTHHHHHHHH CS
                     YozE_SAM_like  44 Lelnaeylssmeifdeaw 61 
                                       L+++++y++++++f+e +
  gi|386002402|ref|YP_005920701.1| 376 LKSQGKYDEAIQTFNETI 393
                                       67899*********9976 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.2
                                       HHTSHHHHTTHHHHHHHHH CS
                     YozE_SAM_like  44 Lelnaeylssmeifdeawe 62 
                                       L+++++y++++++fdea++
  gi|386002402|ref|YP_005920701.1| 410 LNNQGKYDEAIQAFDEAIR 428
                                       67799***********986 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.94
                                       HHTSHHHHTTHHHHHHHHH CS
                     YozE_SAM_like  44 Lelnaeylssmeifdeawe 62 
                                       ++++++y++++++fdea++
  gi|386002402|ref|YP_005920701.1| 478 FNSQGRYNEAIKAFDEAIR 496
                                       67899***********985 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 2.6
                                       TSHHHHTTHHHHHHHH CS
                     YozE_SAM_like  46 lnaeylssmeifdeaw 61 
                                       +++ey+++m++f+ea 
  gi|386002402|ref|YP_005920701.1| 760 EQHEYNEAMQAFNEAV 775
                                       6899*********996 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 1
                                       HHHHTSHHHHTTHHHHHHHHH CS
                     YozE_SAM_like  42 dYLelnaeylssmeifdeawe 62 
                                       +YL+ +++y +++e++d a++
  gi|386002402|ref|YP_005920701.1| 790 KYLNDQGKYYEAIEAIDMAIS 810
                                       6****************9986 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 6.9
                                       HHTSHHHHTTHHHHHHHHH CS
                     YozE_SAM_like  44 Lelnaeylssmeifdeawe 62 
                                       L+++++y++++++ d+a++
  gi|386002402|ref|YP_005920701.1| 860 LYSQGNYSEAIQAYDRAID 878
                                       7899************987 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.3     0.016         6     264     304 ..     106     152 ..      97     228 .. 0.78
   2 ?    2.0   2.3      0.25        95     268     291 ..     280     303 ..     170     405 .. 0.60
   3 ?    1.7   3.3      0.31   1.2e+02     268     307 ..     416     455 ..     378     615 .. 0.69
   4 ?    2.0   1.3      0.25        96     268     291 ..     518     541 ..     480     725 .. 0.61
   5 ?    2.6   0.4      0.16        63     266     301 ..     864     899 ..     822     939 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                                       S...-SSCCHHHHCCHHCTCCCHSTTCC......CCHHHHHCCHHHH CS
                               FAT 264 seekieeilqsysaateidpswykawht......walfnfevvskee 304
                                       ++ k +e+ ++y +a ++dp+ ++awh+      +   ++e+++++ 
  gi|386002402|ref|YP_005920701.1| 106 KQGKYDEAIKAYNEAIRLDPEYANAWHNkgyalyLQGKYDEAIKAYN 152
                                       455689*********************97766666666677777664 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                                       -SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 268 ieeilqsysaateidpswykawht 291
                                        +e+ q+y +a +++p+ ++aw++
  gi|386002402|ref|YP_005920701.1| 280 YDEAIQAYDEAIRLSPEYADAWNR 303
                                       555555555555555555555544 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.31
                                       -SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHS CS
                               FAT 268 ieeilqsysaateidpswykawhtwalfnfevvskeeeqk 307
                                        +e+ q++ +a +++p+  +aw++ + + + + +  e  +
  gi|386002402|ref|YP_005920701.1| 416 YDEAIQAFDEAIRLNPEYVDAWYSKGNALDSQSRYDEAIQ 455
                                       5555555555555555555555554444444444433322 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.25
                                       -SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 268 ieeilqsysaateidpswykawht 291
                                        ee+ q++ +at+++p+ ++aw +
  gi|386002402|ref|YP_005920701.1| 518 YEEAIQAFDEATRLNPEDADAWLK 541
                                       455555555555555555555544 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.16
                                       ..-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCH CS
                               FAT 266 ekieeilqsysaateidpswykawhtwalfnfevvs 301
                                        + +e+ q+y +a  ++ ++ +aw++ +++ +   +
  gi|386002402|ref|YP_005920701.1| 864 GNYSEAIQAYDRAIDLNSQLVQAWYNKGDALDALKN 899
                                       456788999999999999999999987777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 1.83u 0.41s 00:00:02.24 Elapsed: 00:00:00.89
# Mc/sec: 4556.77
//
Query:       gi|386002403|ref|YP_005920702.1|  [L=478]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-10   41.6   0.7    1.2e-09   38.8   0.7    2.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.045   13.6   0.0    1.5  1  NIL          NIL domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.7   1.3e-13   1.2e-09       4     166 ..     190     359 ..     187     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.3e-13
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                        rgC+ +C+fC+ ++      r+r l++e i++ + +++ ++g+k+v++       +++ ++ +++l  ++     +
  gi|386002403|ref|YP_005920702.1| 190 IRGCAVGCKFCQATS---FCSRPRPLPLEAIERVLSYYR-DQGIKVVVIEDESFGSDRRHADRVAELLDEHGMVWGC 262
                                       79************8...8*******************5.9999999999999999988889999999886556666 PP

                                       EEEECSSCHGHHHHHHHHHTT............-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                       xxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelg............vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrv 145
                                          + ++++  + ++++++++            +   ++g+e+++   vl+ + ++++  e+le++ekl+++g+  v
  gi|386002403|ref|YP_005920702.1| 263 MARADYLRDKVDEWAEMRRRPsrggggknpvrgFAGAAIGIESFHQQ-VLDGVAKREGAGEILETVEKLKSHGLGTV 338
                                       6666666655666666666669999*****9999*************.99999999********************* PP

                                       EEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGendeeleellel 166
                                        + ++g+p  + + ++e +e 
  gi|386002403|ref|YP_005920702.1| 339 GYYMIGFPTDTAASIREDVER 359
                                       ************999998775 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     5e-06     0.045      14      71 ..     167     231 ..     161     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-06
                                       S-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEE........ES-HHHHHHHHHHHHHTT-EE CS
                               NIL  14 ePllshlvrqlglevnIlqGsveriqgtpfGqlviel........sgsqesiaaalqylrkrnvdv 71 
                                        Pl+ hl++ +gl+ nI ++   +i+g ++G  + ++        +   e+i+++l y r+++++v
  gi|386002403|ref|YP_005920702.1| 167 PPLIEHLAAPFGLKLNIYGALF-TIRGCAVGCKFCQAtsfcsrprPLPLEAIERVLSYYRDQGIKV 231
                                       59**************966655.6*************55555553247789*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 2538.57
//
Query:       gi|386002404|ref|YP_005920703.1|  [L=278]
Description: Histone deacetylase family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-32  111.8   2.0    3.2e-24   86.0   0.1    3.1  3  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00016       2.8      27      53 ..      32      61 ..       7      64 .. 0.75
   2 !   86.0   0.1   1.8e-28   3.2e-24      85     179 ..      62     177 ..      59     187 .. 0.91
   3 !   17.6   0.0   1.2e-07    0.0021     235     294 ..     206     265 ..     197     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00016
                                      E....EE-----HHHHTTTS-HHHHHHHHC CS
                                      x...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 27 l...liqpseatkeellkvHskeYlelles 53
                                          +++p++a+ e++ ++Hs+e++e++++
  gi|386002404|ref|YP_005920703.1| 32 AgyeFVEPPQASLEDVSRIHSREHIERVRE 61
                                      03336899******************9976 PP

  == domain 2  score: 86.0 bits;  conditional E-value: 1.8e-28
                                       TTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                     Hist_deacetyl  85 pktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikyl................ 145
                                       +++l  alla+g++++a++  l+g  +aaf+lvrPpgHHa +++a G C++Nnvaia++ +                
  gi|386002404|ref|YP_005920703.1|  62 KGMLAPALLAAGGACRAAEIALRG--EAAFALVRPPGHHAASDHAWGMCYLNNVAIAVRMAldrmgggmggeaegpk 136
                                       678899****************99..9************************************************** PP

                                       .....HHCC-.SS.-EEEEE-SSS--HHHHHHCTT-TTEEE CS
                                       .....xxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 146 .....qakhe.lk.rvailDvDvHhGnGteeafysdpdvlt 179
                                            +++ +    rv+i+D+D+H+G+Gt ++f+ d++v +
  gi|386002404|ref|YP_005920703.1| 137 eaglgRRRGGgSGgRVLIVDIDLHFGDGTVSIFRWDERVRI 177
                                       *9998443442335********************9999966 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.2e-07
                                       CCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxx RF
                     Hist_deacetyl 235 eefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnle 294
                                       +e + dl+ vsaGfD++  d  g l+ls   y+e+ + l+e a++  + +  ++leGGY+++
  gi|386002404|ref|YP_005920703.1| 206 AESEFDLLAVSAGFDTYLLDWGGLLDLSD--YEEIGRILKEGAEERcSgRRFAVLEGGYHQD 265
                                       555668999************99998875..*************99988**********974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); 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: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1490.85
//
Query:       gi|386002405|ref|YP_005920704.1|  [L=40]
Description: Desulfoferrodoxin Dfx domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-17   61.3   7.9    4.9e-17   61.3   7.9    1.0  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
    0.00087   18.9   0.2     0.0012   18.5   0.2    1.2  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0069   16.1   0.3       0.12   12.1   0.7    2.0  2  A2L_zn_ribbon    A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.019   15.2   0.7       0.02   15.2   0.7    1.1  1  DUF1922          Domain of unknown function (DUF1922)
       0.14   11.9   0.1       0.15   11.9   0.1    1.1  1  DUF3449          Domain of unknown function (DUF3449)


Domain annotation for each model (and alignments):
>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   7.9   1.4e-20   4.9e-17       2      35 ..       3      36 ..       2      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.4e-20
                                      -TT-EEE-TTT--EEEECC--SS-EEETTEE-EE CS
                   Desulfoferrod_N  2 eklevYkCevCGniVeVleaGgGeLVCCgepMkl 35
                                      + +evY+CevCGn+V V eaG+G LVCCg+pM+l
  gi|386002405|ref|YP_005920704.1|  3 KVGEVYRCEVCGNVVLVQEAGAGMLVCCGKPMVL 36
                                      789*****************************87 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   3.4e-07    0.0012       6      24 ..       9      29 ..       7      29 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.4e-07
                           zf-RRN7  6 pCgvCgc.rsftl.ddGfyyC 24
                                      +C+vCg+ +++++  +G+ +C
  gi|386002405|ref|YP_005920704.1|  9 RCEVCGNvVLVQEaGAGMLVC 29
                                      7******88************ PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.7   3.4e-05      0.12       5      25 ..       9      30 ..       7      30 .. 0.89
   2 !    4.4   0.1    0.0091        33       9      18 ..      30      38 ..      28      40 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                     A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCi 25
                                       C+vCg+ ++++ +  g lvC+
  gi|386002405|ref|YP_005920704.1|  9 RCEVCGNVVLVQeAGAGMLVCC 30
                                      5**********88888999998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0091
                     A2L_zn_ribbon  9 Cggngilnse 18
                                      Cg++++l ++
  gi|386002405|ref|YP_005920704.1| 30 CGKPMVL-AK 38
                                      ******9.54 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.7   5.6e-06      0.02       3      32 ..       7      37 ..       6      40 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.6e-06
                                      EEEET.TS--EEEETT-SEEEETTTEEEE-- CS
                           DUF1922  3 ifRCd.CGRvlYakegaktrkCvCGktikvk 32
                                      ++RC+ CG v+ ++e  +     CGk + + 
  gi|386002405|ref|YP_005920704.1|  7 VYRCEvCGNVVLVQEAGAGMLVCCGKPMVLA 37
                                      7******************9999***88765 PP

>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.1e-05      0.15      86      99 ..       4      17 ..       1      22 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                                      XXXXXXXXXXXXXX CS
                           DUF3449 86 LgkeykCeiCgnav 99
                                      +g  y+Ce+Cgn+v
  gi|386002405|ref|YP_005920704.1|  4 VGEVYRCEVCGNVV 17
                                      6789********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.54
# Mc/sec: 224.01
//
Query:       gi|386002406|ref|YP_005920705.1|  [L=320]
Description: hypothetical protein Mhar_1724 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1860.01
//
Query:       gi|386002407|ref|YP_005920706.1|  [L=275]
Description: Triphosphoribosyl-dephospho-CoA protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-65  221.5   1.4    1.8e-65  221.4   1.4    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.4   1.4     1e-69   1.8e-65       8     281 .]       1     263 [.       1     263 [. 0.92

  Alignments for each domain:
  == domain 1  score: 221.4 bits;  conditional E-value: 1e-69
                                       XXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH...-- CS
                              CitG   8 lllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa...tg 81 
                                       +l E+s++pKPG+Vdr +++  + ++f++Fl Sa++++p+f++aa           +l ++G l+ +a+  +     
  gi|386002407|ref|YP_005920706.1|   1 MLIELSTSPKPGNVDRSHDF--EEVKFHHFLISAVSAYPAFRDAA----------LGLLPTGALIRRAVGSWrgwGL 65 
                                       789*****************..***********************..........7799*************99766 PP

                                       ----HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......---...... CS
                              CitG  82 gvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......eel...... 145
                                         NTh+G + ll++laaaagr          ++l+  +aevl+e+t+edav+f  a+++a +      + l      
  gi|386002407|ref|YP_005920706.1|  66 SQNTHFGSLTLLIPLAAAAGRG---------GDLRGSVAEVLEETTAEDAVEFyAAFEIAGArvaevaD-Lslkdpa 132
                                       89******************77.........79*****************************9987651.1566666 PP

                                       .HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--HHHHH CS
                              CitG 146 .kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDtnilr 221
                                        +d++++ ++ tl+e ++ls+ +d +++e++ gF+++f++a   l +++  + +lnd ++ ++l+ la++pD+++++
  gi|386002407|ref|YP_005920706.1| 133 sPDKIRS-EGKTLLELMRLSSAHDLVAREWSMGFERSFHLAR--LLAERVGELGLNDGVAITYLEALAAVPDSLVAS 206
                                       5667666.89*****************************555..44444455999********************** PP

                                       HHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                              CitG 222 rgGaegaeevqeeArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfla 281
                                       ++G e a+e++e+Ara+l     + e++l+ +eeldr +ve++i+PG++ADl+aa+lf+a
  gi|386002407|ref|YP_005920706.1| 207 KFGLERAKEASERARAILGF---EVEETLRLAEELDRMFVEEDINPGSTADLMAAALFIA 263
                                       ******************98...666799*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1575.61
//
Query:       gi|386002408|ref|YP_005920707.1|  [L=195]
Description: hypothetical protein Mhar_1726 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-47  160.2   0.1    4.6e-47  160.1   0.1    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.1   0.1   2.5e-51   4.6e-47       1     176 []      18     189 ..      18     189 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 2.5e-51
                                       EEEEEEEE-TT.-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETT CS
                            DUF447   1 yEvivtTksek.rpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetk 76 
                                       +E+i+tT +e+ + naaP+G+i+ g+++ +rlf g++T+eN+++ +++v+nv +Dp+lf+++algd+++++f +++ 
  gi|386002408|ref|YP_005920707.1|  18 NEIIATTVNEAgTHNAAPLGLIRTGETLSVRLFVGTHTYENIMSGKKFVANVSHDPILFVETALGDISDENFVERDG 94 
                                       7***********************************************************************99997 PP

                                       TCTT.EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCCSHHHHHHHHHH CS
                            DUF447  77 pakiavlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldiedkeklleeie 153
                                       +    +l++aeaw+ +++e      +    e+e vk e+le++++++nRg ++v+EaaV+atR+  ++ + +leei 
  gi|386002408|ref|YP_005920707.1|  95 EV---TLRDAEAWALFRCEPN--GLDIALPEVEFVKGEVLEREFRAVNRGINLVVEAAVAATRYVALKSDLYLEEIF 166
                                       54...**************75..56677789999******************************************* PP

                                       HHHHHHHHH--HHHHHHHHHHHH CS
                            DUF447 154 ylssvikktggerekealellke 176
                                       + +++++++gg+re+ea+++l+e
  gi|386002408|ref|YP_005920707.1| 167 KIRRIVNRCGGPREIEAMDRLEE 189
                                       ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1126.68
//
Query:       gi|386002409|ref|YP_005920708.1|  [L=221]
Description: DNA repair and recombination protein RadB [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-34  117.9   0.1    5.3e-34  117.6   0.1    1.1  1  Rad51           Rad51
    1.4e-09   37.8   0.2    1.9e-09   37.4   0.2    1.1  1  RecA            recA bacterial DNA recombination protein
    3.5e-09   36.3   4.3    9.7e-09   34.9   4.3    1.9  1  ATPase          KaiC
    5.9e-08   32.5   0.1    1.1e-07   31.6   0.1    1.4  1  AAA_25          AAA domain
    1.8e-07   31.0   0.0    2.1e-07   30.8   0.0    1.1  1  Zot             Zonular occludens toxin (Zot)
    8.4e-07   28.9   0.0    1.2e-06   28.3   0.0    1.2  1  AAA_24          AAA domain
    0.00041   20.8   0.1     0.0011   19.4   0.1    1.6  1  AAA             ATPase family associated with various cellula
     0.0025   17.2   0.1       0.43    9.9   0.0    2.3  2  DnaB_C          DnaB-like helicase C terminal domain
     0.0054   15.7   0.3     0.0098   14.8   0.2    1.5  2  TrwB_AAD_bind   Type IV secretion-system coupling protein DNA
  ------ inclusion threshold ------
      0.015   14.7   0.3       0.03   13.8   0.3    1.4  1  PhoH            PhoH-like protein
      0.016   15.1   0.0      0.023   14.6   0.0    1.3  1  ATPase_2        ATPase domain predominantly from Archaea
      0.016   15.5   0.0      0.027   14.7   0.0    1.4  1  AAA_22          AAA domain
      0.018   15.4   0.5      0.025   15.0   0.5    1.5  1  AAA_16          AAA ATPase domain
       0.02   14.5   0.1      0.039   13.6   0.1    1.4  1  SRP54           SRP54-type protein, GTPase domain
      0.029   14.4   0.6      0.034   14.2   0.6    1.4  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.031   14.0   0.5       0.13   11.9   0.2    1.9  2  IstB_IS21       IstB-like ATP binding protein
      0.038   13.2   0.2       0.11   11.7   0.1    1.6  2  DAP3            Mitochondrial ribosomal death-associated prot
      0.057   13.1   0.1      0.086   12.5   0.1    1.4  1  AAA_30          AAA domain
      0.072   13.3   0.8       0.39   11.0   0.4    2.1  2  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
       0.11   12.4   0.2       0.16   11.8   0.2    1.3  1  NTPase_1        NTPase
       0.11   12.1   0.0       0.19   11.3   0.0    1.4  1  CobU            Cobinamide kinase / cobinamide phosphate guan
       0.11   11.6   0.2       0.17   11.1   0.2    1.2  1  NB-ARC          NB-ARC domain
       0.18   11.0   0.0       0.31   10.2   0.0    1.3  1  DUF815          Protein of unknown function (DUF815)
       0.22   10.7   0.3       0.29   10.3   0.3    1.3  1  DUF2075         Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.1   7.2e-37   5.3e-34      18     252 ..       4     220 ..       2     221 .] 0.90

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 7.2e-37
                                       EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHH CS
                             Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaer 94 
                                       +l+ G++ lD+lLgGG e g it i+Ge ++Gkt +  + +v         G   k+++idteg f  er  +ia  
  gi|386002409|ref|YP_005920708.1|   4 RLSSGCEGLDRLLGGGYEPGIITQIYGEAGTGKTTIVLQAAV------GAVGRGLKVIFIDTEG-FSVERFRQIAG- 72 
                                       5899******************************87766655......568999*********6.9*********4. PP

                                       TT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHH CS
                             Rad51  95 ykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrk 171
                                            +e+  ++ +    + e+q++ ++ a +++a ++f+lli+Ds+t+lyR+ f+g ++   R   l+  l +L++
  gi|386002409|ref|YP_005920708.1|  73 --EGAKEIGAKIVVFEPLNLEQQHSSIKDA-TKIAGKEFGLLILDSATSLYRAAFEGDDNRPVRR-ALAAQLGELQE 145
                                       ..5789999****************99876.578999***********************99996.689999***** PP

                                       HHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEEEE CS
                             Rad51 172 ladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avfai 247
                                       +a ++++ vv+tnqv  ++++        + +P gG  + ha++t + + k+ + +R++++++  ++pe   a +++
  gi|386002409|ref|YP_005920708.1| 146 MARRHRIPVVVTNQVYMEIET-------GNLRPLGGMAMDHATKTAIFIEKRGEGKRLARLMKHRSMPEGGtAELQL 215
                                       ****************99998.......4568*******************999**************974156777 PP

                                       ETTEE CS
                             Rad51 248 geeGi 252
                                       + +G+
  gi|386002409|ref|YP_005920708.1| 216 TGKGV 220
                                       77776 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   2.6e-12   1.9e-09      33     194 ..       4     165 ..       2     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.6e-12
                                       EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GG... CS
                              RecA  33 tissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdid... 106
                                        +ssG  +ld  lG GG+  G i++iyG   +Gktt+ l+a + a  +g  + fid+e     ++ +  G   +   
  gi|386002409|ref|YP_005920708.1|   4 RLSSGCEGLDRLLG-GGYEPGIITQIYGEAGTGKTTIVLQAAVGAVGRGLKVIFIDTEGFSVERFRQIAGEGAKeig 79 
                                       689***********.******************************************97555555554444333111 PP

                                       .G-EEE--SSHHHHH.HHHHHH.HTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT- CS
                              RecA 107 .ellvsqpdtGeqal.eiadal.vrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksn 180
                                        +++v +p + eq    i da  +      l+++ds ++l  +a  eG+  d++     r ++  l  l+ + ++ +
  gi|386002409|ref|YP_005920708.1|  80 aKIVVFEPLNLEQQHsSIKDATkIAGKEFGLLILDSATSLY-RAAFEGD--DNRPV--RRALAAQLGELQEMARRHR 151
                                       256899999988765157765426667899******98885.8889998..44444..3557778999999999999 PP

                                       -EEEEEEE------ CS
                              RecA 181 tvvifinqirekiG 194
                                       + v+  nq+ + i 
  gi|386002409|ref|YP_005920708.1| 152 IPVVVTNQVYMEIE 165
                                       99999999999885 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   4.3   1.3e-11   9.7e-09       2      60 ..       6      63 ..       5     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.3e-11
                            ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa 60
                                      ++g eglD++l gG+  g ++ i+Ge+GtGKt+++lq ++  + + g +++f+ +e  +
  gi|386002409|ref|YP_005920708.1|  6 SSGCEGLDRLLGGGYEPGIITQIYGEAGTGKTTIVLQAAVGAVGR-GLKVIFIDTEGFS 63
                                      6899*********************************99999888.*******998655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   1.5e-10   1.1e-07      24     186 ..      14     157 ..       4     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.5e-10
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg.ealrd 99 
                                        l++g    g ++ ++G  gtGKtt++l+ a+  + G+           kV+++++E+      +R+r++  e +++
  gi|386002409|ref|YP_005920708.1|  14 RLLGGGYEPGIITQIYGEAGTGKTTIVLQAAVGAV-GR---------GLKVIFIDTEGFS---VERFRQIAgEGAKE 77 
                                       56666667899999******************999.44.........459*********9...67777755277666 PP

                            AAA_25 100 darllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdv.galveale 173
                                        +   v+     e+l+L   +++++ ++    + + +i   ++ +l+++D+ ++++++  + ++n+ v +al ++l 
  gi|386002409|ref|YP_005920708.1|  78 IGAKIVVF----EPLNL---EQQHSSIK----D-ATKIAG-KEFGLLILDSATSLYRAafEGDDNRPVrRALAAQLG 141
                                       66666665....56666...23333333....2.234555.56***************9999999998666666655 PP

                            AAA_25 174 ri...arrtgaavllv 186
                                       ++   arr+++ v+++
  gi|386002409|ref|YP_005920708.1| 142 ELqemARRHRIPVVVT 157
                                       5411167777777766 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.9e-10   2.1e-07       5     155 ..      28     190 ..      24     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.9e-10
                               Zot   5 vtGapGsgKtsgavkkdllpalkegRkiit.nidGlrlerieqvlgekvs..tarliridnpegaetlkefakwat. 77 
                                        +G+ G+gKt  +++  ++ a+  g k+i+ + +G+ +er++q+ ge  +   a+++  + p+  e+++++ k at 
  gi|386002409|ref|YP_005920708.1|  28 IYGEAGTGKTTIVLQA-AVGAVGRGLKVIFiDTEGFSVERFRQIAGEGAKeiGAKIVVFE-PLNLEQQHSSIKDATk 102
                                       58*************9.56666666666655***************99888988888877.7777776666665553 PP

                               Zot  78 id..kgallviDEcqeifpvrakegrkd......pevi.naftehRhlgwDivlltqdiskihk.evralaekavkl 144
                                       i+  + +ll++D +  ++ +  + + ++       + + +   ++R++   +v + q   +i+  ++r l ++a  +
  gi|386002409|ref|YP_005920708.1| 103 IAgkEFGLLILDSATSLYRAAFEGDDNRpvrralAAQLgELQEMARRHRIPVVVTNQVYMEIETgNLRPLGGMAMDH 179
                                       556578************99988655557777776666355567899999*******99999864899999999999 PP

                               Zot 145 krkaaigikgr 155
                                         k+ai i++r
  gi|386002409|ref|YP_005920708.1| 180 ATKTAIFIEKR 190
                                       99999988877 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.7e-09   1.2e-06       5      82 ..      26     124 ..      23     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.7e-09
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdieswedfldevvel.............. 59 
                                        +iyG++g+GKTt+++++       g k++fidte+ ++ +   + ++ ++   ++  ++v +              
  gi|386002409|ref|YP_005920708.1|  26 TQIYGEAGTGKTTIVLQAavgavgrGLKVIFIDTEGfSVERFRQIAGEGAK---EIGAKIVVFeplnleqqhssikd 99 
                                       58**********************************666666666666444...33333333344477778888888 PP

                            AAA_24  60 ..aaeladyktlviDtideleelcl 82 
                                         + + +++  l++D+++ l++ ++
  gi|386002409|ref|YP_005920708.1| 100 atKIAGKEFGLLILDSATSLYRAAF 124
                                       78889999************99876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.4e-06    0.0011       3     111 ..      28     159 ..      26     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS......................STTHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellsk......................yvgesekkirelfke 52 
                                       +yG  GtGKT+++ + a  +     +v f+ ++g ++                          ++++ ++i++  k 
  gi|386002409|ref|YP_005920708.1|  28 IYGEAGTGKTTIVLQAAVGAvgrglKVIFIDTEGFSVE-RfrqiagegakeigakivvfeplNLEQQHSSIKDATKI 103
                                       79**********99888885555224445555555544.35677777777788888875555555555555555555 PP

                                       HHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  53 akekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                       a ++     l++D + +l ++  +g++++  +r++++ l el+++ ++ +++  +++tn+
  gi|386002409|ref|YP_005920708.1| 104 AGKE--FGLLILDSATSLYRAAfEGDDNRPVRRALAAQLGELQEMARR-HRIP-VVVTNQ 159
                                       5444..4**************975555555555555555555555553.4344.455555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00057      0.43       2      57 ..       5      60 ..       5      75 .. 0.82
   2 ?    4.5   0.0     0.025        18     128     184 ..     106     166 ..      82     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00057
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESS CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfsle 57
                                      ls+g + LD+l++ G+++g ++ i + +++Gkt+++l+ a  a+  + l+v+++  e
  gi|386002409|ref|YP_005920708.1|  5 LSSGCEGLDRLLGgGYEPGIITQIYGEAGTGKTTIVLQAAVGAV-GRGLKVIFIDTE 60
                                      5789999**99862699999999***************998765.466778777666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.025
                                       TTEEEEEEEEGGGTBTS.CS.SSCC..CHHHHHHHHHHHHHHHHCTSXEEEEEEXSGGGCC CS
                                       xxxxxxxxxxxxxxxxx.xx.xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 128 kglgliviDyLqlmegs.ee.kenr..eqevseisrsLkalakelnvpvialsqLsraves 184
                                       k+ gl+++D    +  +  e ++nr  ++ +++   +L+++a+  ++pv++  q+  ++e+
  gi|386002409|ref|YP_005920708.1| 106 KEFGLLILDSATSLYRAaFEgDDNRpvRRALAAQLGELQEMARRHRIPVVVTNQVYMEIET 166
                                       66777777766555433222344552234566666789****************9888885 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.3e-05    0.0098      19      61 ..      27      69 ..      24      93 .. 0.87
   2 ?   -3.0   0.0       3.4   2.6e+03     133     158 ..     129     154 ..     111     163 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                     TrwB_AAD_bind 19 livGttGsGKtqalekllrairargdraivlDltGafvsrfyd 61
                                       i G +G+GKt+ + +   ++  rg ++i +D++G  v+rf +
  gi|386002409|ref|YP_005920708.1| 27 QIYGEAGTGKTTIVLQAAVGAVGRGLKVIFIDTEGFSVERFRQ 69
                                      689**************************************87 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                     TrwB_AAD_bind 133 aallralltadleeLkellagteaaa 158
                                       ++ +r+ l a+l eL+e+++++ +  
  gi|386002409|ref|YP_005920708.1| 129 NRPVRRALAAQLGELQEMARRHRIPV 154
                                       45566777778888888887776554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   4.1e-05      0.03      21      46 ..      25      50 ..      20      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                                      EEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkk 46
                                      i+ + G+aGtGKt + +++av a+ +
  gi|386002409|ref|YP_005920708.1| 25 ITQIYGEAGTGKTTIVLQAAVGAVGR 50
                                      67899****************98865 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.1e-05     0.023      18      83 ..      21     112 ..      15     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............ 82 
                                       ep  i  iYG  g GKt+++ +++      + +vi++ + ++ s +++++  +e  ++  ++ ++            
  gi|386002409|ref|YP_005920708.1|  21 EPGIITQIYGEAGTGKTTIVLQAAVGAVGRGLKVIFI-DTEGFSVERFRQIAGEGAKEIGAKIVVfeplnleqqhss 96 
                                       5677899********************9999999997.567777777777744333333222222444444444444 PP

                          ATPase_2  83 ...............g 83 
                                                       
  gi|386002409|ref|YP_005920708.1|  97 ikdatkiagkefgllI 112
                                       4444455555555441 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.7e-05     0.027       8     127 ..      26     156 ..      21     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka.erlsseellea 81 
                                       + ++Ge+GtGKTt + + +  ++ +      + +v+f++  + +    ++++ e ++++g +    e+l++e+  + 
  gi|386002409|ref|YP_005920708.1|  26 TQIYGEAGTGKTTIVLQAAVGAVGR------GLKVIFIDTEGFSveRFRQIAGEGAKEIGAKIVVfEPLNLEQQHSS 96 
                                       569***********99999999866......9999999999998666777777777777755555988888888888 PP

                            AAA_22  82 leqalrarav.ielliiDEaqhlr.....s..........eealeeLrsllnlsrkgvqliL 127
                                       + +a + +++  +lli+D a  l                 +++l eL +++   r+ +++++
  gi|386002409|ref|YP_005920708.1|  97 IKDATKIAGKeFGLLILDSATSLYraafeGddnrpvrralAAQLGELQEMAR--RHRIPVVV 156
                                       8888888888888999999999866655414455666677777777777777..77777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   3.3e-05     0.025      28      65 ..      27      66 ..      12     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                            AAA_16 28 llsGesGvGKsslvrellralekd..ggiflrgkcdqles 65
                                       ++Ge+G+GK+++v +++  + ++  ++if+ ++  + e+
  gi|386002409|ref|YP_005920708.1| 27 QIYGEAGTGKTTIVLQAAVGAVGRglKVIFIDTEGFSVER 66
                                      59************77776666663445555554444422 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.3e-05     0.039       6      92 ..      28     116 ..      24     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
                                       EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHH...TTEEEEESSTTSCHHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaek...lgvpvikkkeeadpaavakeaveka 79 
                                       + G  G+GKTt + + a     +g kv+++ +  f +  + Q++  + k   +++ v++  + +++ + +k+a + a
  gi|386002409|ref|YP_005920708.1|  28 IYGEAGTGKTTIVLQAAVGAVGRGLKVIFIDTEGFSVERFRQIAGEGAKeigAKIVVFEPLNLEQQHSSIKDATKIA 104
                                       7899**************************99999999999998766554444555677666677888899999888 PP

                                       HHTTSSEEEEEE- CS
                             SRP54  80 keekidvvlvDTa 92 
                                        + ++ ++++D+a
  gi|386002409|ref|YP_005920708.1| 105 GK-EFGLLILDSA 116
                                       77.7799999998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   4.6e-05     0.034       6      35 ..      30      59 ..      25     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                                      SSTTSSHHHHHHHHHHHHHHTT--EEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  6 tkGGvGKTtlaanLaralarrglrVllvDa 35
                                      +  G+GKTt+++  a+    rgl+V+ +D+
  gi|386002409|ref|YP_005920708.1| 30 GEAGTGKTTIVLQAAVGAVGRGLKVIFIDT 59
                                      678*************************96 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00018      0.13      52      85 ..      28      61 ..      24      82 .. 0.88
   2 ?   -0.5   0.0       1.2   8.9e+02      87     117 ..      85     116 ..      78     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                         IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrved 85
                                      + G +G+GK+ +    +v av +gl+v+f+ +e 
  gi|386002409|ref|YP_005920708.1| 28 IYGEAGTGKTTIVLQAAVGAVGRGLKVIFIDTEG 61
                                      78***************************99875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                         IstB_IS21  87 veelkrarrdgklaralkrllkv.dllilDdl 117
                                       +e l++++++ +++ a k   k   llilD  
  gi|386002409|ref|YP_005920708.1|  85 FEPLNLEQQHSSIKDATKIAGKEfGLLILDSA 116
                                       66788888888888888766554399999975 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00014      0.11      28      56 ..      28      56 ..      24      63 .. 0.89
   2 ?   -1.5   0.0       1.5   1.1e+03     140     162 ..     134     157 ..      86     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      EE-SSSSSTTTTHHHHHHHGGGS--EEEE CS
                              DAP3 28 ltGekgsGKSvlLlqalayAlekgwvvlh 56
                                      ++Ge g+GK++ +lqa   A+ +g  v+ 
  gi|386002409|ref|YP_005920708.1| 28 IYGEAGTGKTTIVLQAAVGAVGRGLKVIF 56
                                      89******************999877765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHTT.SS--EEEE CS
                              DAP3 140 dvfqallkeLkaqsk.grvpvlvt 162
                                        +++a l eL++ ++ +r+pv+vt
  gi|386002409|ref|YP_005920708.1| 134 RALAAQLGELQEMARrHRIPVVVT 157
                                       467888888888888778888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012     0.086      20      61 ..      25      66 ..      20     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv 61
                                      ++ + G AGtGKtt++ +++  +  +g +vi +  +g   ++
  gi|386002409|ref|YP_005920708.1| 25 ITQIYGEAGTGKTTIVLQAAVGAVGRGLKVIFIDTEGFSVER 66
                                      56688*********9877776666677888776665555555 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00052      0.39       5      36 ..      26      57 ..      22      65 .. 0.90
   2 ?    0.3   0.0         1   7.6e+02      95     110 ..     106     121 ..      79     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00052
                    CobA_CobO_BtuR  5 ihvytGdGKGKttAAlGlalRalgaglkvlvv 36
                                       ++y   G GKtt  l  a+ a+g+glkv+++
  gi|386002409|ref|YP_005920708.1| 26 TQIYGEAGTGKTTIVLQAAVGAVGRGLKVIFI 57
                                      4778888**********************997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1
                    CobA_CobO_BtuR  95 eeydlvvlDEinyalk 110
                                       +e+ l++lD  +  ++
  gi|386002409|ref|YP_005920708.1| 106 KEFGLLILDSATSLYR 121
                                       4555555555544433 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00022      0.16       4      50 ..      28      83 ..      25     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      EE--TTSSHHHHHHHHHHHH...GGGE.....EEEEEEEE-....------EEEEE CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkv.....gGfyteevr....eggrrigFkiv 50
                                      i G+ G+GKtT+v +++     +g+kv     +Gf +e+ r    eg + ig kiv
  gi|386002409|ref|YP_005920708.1| 28 IYGEAGTGKTTIVLQAAVGAVGRGLKVifidtEGFSVERFRqiagEGAKEIGAKIV 83
                                      669***********999998899988744444799999888666666677777776 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.19      63     131 ..      97     165 ..      86     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                              CobU  63 laealkeeek.kevvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvglgvv 131
                                       +++a k + k    +++D+ t +   ++  ++++ v+++l++++ el e++++++ +v +V+n v +++ 
  gi|386002409|ref|YP_005920708.1|  97 IKDATKIAGKeFGLLILDSATSLYRAAFEGDDNRPVRRALAAQLGELQEMARRHRIPV-VVTNQVYMEIE 165
                                       5555544444467899*************999888999********999999988875.69****99885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00023      0.17      17      40 ..      21      43 ..      10      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                      TSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                      e++ ++  ++G +G GKtt++ q+
  gi|386002409|ref|YP_005920708.1| 21 EPG-IITQIYGEAGTGKTTIVLQA 43
                                      667.8889************9876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00041      0.31      58     126 ..      28      98 ..      22     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                            DUF815  58 LwGarGtGKSslvkallneyaeegLrlieveke..dlkelpklvellrerperfilfvDDLsFeeeeeeyk 126
                                       ++G+ GtGK ++v  +   +  +gL++i ++ e  +++ + ++  + +++    i++   L  e++ ++ k
  gi|386002409|ref|YP_005920708.1|  28 IYGEAGTGKTTIVLQAAVGAVGRGLKVIFIDTEgfSVERFRQIAGEGAKEIGAKIVVFEPLNLEQQHSSIK 98 
                                       69***********999999999*****99988733577888888776666666666667777777776665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00039      0.29       6      37 ..      28      57 ..      24     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                           DUF2075  6 VtGvaGtGKtvvllnllaeleddeeertavyl 37
                                      + G+aGtGKt + l++++ +    ++ +++++
  gi|386002409|ref|YP_005920708.1| 28 IYGEAGTGKTTIVLQAAVGA--VGRGLKVIFI 57
                                      89************998876..5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1272.73
//
Query:       gi|386002410|ref|YP_005920709.1|  [L=341]
Description: hypothetical protein Mhar_1728 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.8   4.9        4.6    7.6   0.0    4.1  4  PFU       PFU (PLAA family ubiquitin binding)
       0.14   12.4   0.1        4.7    7.5   0.0    2.8  3  US22      US22 like
        3.3    8.1  13.1         46    4.5   0.0    5.4  6  Kelch_3   Galactose oxidase, central domain


Domain annotation for each model (and alignments):
>> PFU  PFU (PLAA family ubiquitin binding)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00076       4.6       9      36 ..      50      77 ..      44      88 .. 0.86
   2 ?    0.9   0.1     0.089   5.3e+02      19      36 ..     100     117 ..      96     127 .. 0.87
   3 ?    3.2   0.1     0.017     1e+02      13      38 ..     132     157 ..     124     173 .. 0.81
   4 ?    2.8   0.0     0.022   1.3e+02      17      33 ..     247     263 ..     235     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00076
                               PFU  9 vklvkeeegkveayqwsaaeekWekiGe 36
                                      v+++  ++++ e+y + +++++W+k+G+
  gi|386002410|ref|YP_005920709.1| 50 VRVFAVQSETGEIYRYAETTGEWTKVGN 77
                                      55666677899****************7 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.089
                               PFU  19 veayqwsaaeekWekiGe 36 
                                       + +y++s +  +W+++G 
  gi|386002410|ref|YP_005920709.1| 100 MGVYEFSGTAMEWTQVGG 117
                                       568*************95 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.017
                               PFU  13 keeegkveayqwsaaeekWekiGevv 38 
                                        + e+  e+y ++ +  +W++iGe  
  gi|386002410|ref|YP_005920709.1| 132 TNPEDGWEVYRYTGTPWEWVQIGERS 157
                                       56678899***************966 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.022
                               PFU  17 gkveayqwsaaeekWek 33 
                                       ++ e+y ws++ e+We+
  gi|386002410|ref|YP_005920709.1| 247 HTKELYRWSEDAESWER 263
                                       67899**********86 PP

>> US22  US22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00079       4.7      89     117 ..      48      76 ..      46      84 .. 0.89
   2 ?   -1.3   0.0      0.41   2.4e+03      90     117 ..      89     116 ..      77     117 .. 0.84
   3 ?    1.2   0.0     0.068     4e+02      90     113 ..     238     261 ..     236     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00079
                              US22  89 elgaVygydplddevyrlAasLseFlraG 117
                                        + +V+++  +++e+yr A++  e++++G
  gi|386002410|ref|YP_005920709.1|  48 YTVRVFAVQSETGEIYRYAETTGEWTKVG 76 
                                       6789*****************99999998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.41
                              US22  90 lgaVygydplddevyrlAasLseFlraG 117
                                       + + yg+dp+   vy+   + +e++++G
  gi|386002410|ref|YP_005920709.1|  89 DSRLYGLDPAGMGVYEFSGTAMEWTQVG 116
                                       6789******999999999998888877 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.068
                              US22  90 lgaVygydplddevyrlAasLseF 113
                                        gaVy+ d  ++e+yr  ++ + +
  gi|386002410|ref|YP_005920709.1| 238 AGAVYARDYHTKELYRWSEDAESW 261
                                       59**************99887665 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0077        46      17      37 ..      58      78 ..      55      98 .. 0.87
   2 ?    2.2   0.0     0.038   2.3e+02      21      35 ..     102     116 ..     101     125 .. 0.83
   3 ?    1.9   1.1     0.049   2.9e+02       6      40 ..     122     159 ..     121     164 .. 0.69
   4 ?   -2.8   0.0       1.5   8.9e+03       2      18 ..     168     184 ..     168     194 .. 0.70
   5 ?    3.4   0.1     0.017     1e+02      17      34 ..     247     264 ..     224     275 .. 0.87
   6 ?   -0.6   0.1      0.29   1.7e+03      20      36 ..     285     301 ..     273     316 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0077
                           Kelch_3 17 rlndvyvydldtntWaeiasl 37
                                       +++ y+y   t++W++++++
  gi|386002410|ref|YP_005920709.1| 58 ETGEIYRYAETTGEWTKVGNP 78
                                      67999************9886 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.038
                           Kelch_3  21 vyvydldtntWaeia 35 
                                       vy+++  + +W++++
  gi|386002410|ref|YP_005920709.1| 102 VYEFSGTAMEWTQVG 116
                                       89***********93 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.049
                           Kelch_3   6 ifGGlgd..dgqdrl.ndvyvydldtntWaeiaslppa 40 
                                       i+GG g+   +++ +  +vy+y    ++W +i++  p 
  gi|386002410|ref|YP_005920709.1| 122 IYGGGGFlyATNPEDgWEVYRYTGTPWEWVQIGERSPS 159
                                       677777776334444368999999989*****654443 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.5
                           Kelch_3   2 drlyifGGlgddgqdrl 18 
                                       d++   GG+ ++++ ++
  gi|386002410|ref|YP_005920709.1| 168 DYMASGGGYLAGMGFPY 184
                                       68888999988777666 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.017
                           Kelch_3  17 rlndvyvydldtntWaei 34 
                                       +++++y+ + d+++W++ 
  gi|386002410|ref|YP_005920709.1| 247 HTKELYRWSEDAESWERA 264
                                       4689***********975 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.29
                           Kelch_3  20 dvyvydldtntWaeias 36 
                                        +y +  d + W ++++
  gi|386002410|ref|YP_005920709.1| 285 LLYQLEEDGDLWMRDDT 301
                                       55555556665554422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1831.08
//
Query:       gi|386002411|ref|YP_005920710.1|  [L=138]
Description: CoA-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-29  102.1   0.0    2.8e-29  102.0   0.0    1.0  1  CoA_binding_2  CoA binding domain
    9.6e-05   23.0   0.0    0.00014   22.5   0.0    1.2  1  CoA_binding    CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   3.1e-33   2.8e-29       1     113 [.      18     132 ..      18     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.1e-33
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-..SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpke..eeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       rt+aVvG s+++g++++ v + +++ g++v+ +np +  eeilgekv  sl e pe++d+vdvf++pea++ +++ea
  gi|386002411|ref|YP_005920710.1|  18 RTVAVVGISPEEGRPSHFVSEVVKSYGFKVYLINPVHrgEEILGEKVLGSLREVPEKIDIVDVFRRPEAVAGLAEEA 94 
                                       79*********************************9999*************867********************** PP

                                       HHH--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHH CS
                     CoA_binding_2  76 lalgakavwlqpgsedeeaaelaeeagirvvgdrCilv 113
                                        ++g +++wlqpg+e+e ++e+++++g +vv   Ci+ 
  gi|386002411|ref|YP_005920710.1|  95 REKGFETFWLQPGTENEGVIEALDREGRTVVPGICIKT 132
                                       *******************************9999985 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.6e-08   0.00014       4      91 ..      18     103 ..      15     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.6e-08
                                       EEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding   4 tkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79 
                                         v+v+G++ +++    ++++  ++yg+k v+ +np + g+e+lg +v  s++e++ek  +d+  ++  +e+++  +
  gi|386002411|ref|YP_005920710.1|  18 RTVAVVGISPEEGRPShFVSEVVKSYGFK-VYLINPVHRGEEILGEKVLGSLREVPEK--IDIVDVFRRPEAVAGLA 91 
                                       689********999999999999999997.788*************************..99999999999999999 PP

                                       HHHHHTT-SEEE CS
                       CoA_binding  80 delveagikgiv 91 
                                       +e+ e+g ++ +
  gi|386002411|ref|YP_005920710.1|  92 EEAREKGFETFW 103
                                       999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 839.70
//
Query:       gi|386002412|ref|YP_005920711.1|  [L=720]
Description: Oligosaccharyl transferase, STT3 subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-25   90.0  16.8    2.7e-24   86.0  16.8    2.2  1  STT3      Oligosaccharyl transferase STT3 subunit
    1.8e-14   53.8   0.1    2.8e-14   53.2   0.1    1.3  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
    1.3e-10   41.7   8.4    1.3e-10   41.7   8.4    3.5  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
        2.1    7.8  12.5       0.02   14.5   4.1    2.0  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0  16.8   6.1e-28   2.7e-24      13     484 ..      27     507 ..      15     510 .. 0.76

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 6.1e-28
                                       CCCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHH CS
                              STT3  13 vavasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasa 89 
                                       +++a +   +++dg+ ++   D++Y  R ++++++n       ++ + wfd++  yP+G++++++pl   + ++ + 
  gi|386002412|ref|YP_005920711.1|  27 LYPARN---CIVDGRIVFFGYDSFYHIRRIAFTAEN-------FPATLWFDPYLNYPLGHPITWPPLFDQV-VAGAS 92 
                                       555555...8899***********************.......8***************************.77777 PP

                                       HHCCHHCHHHHHHHHCC.HHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHH CS
                              STT3  90 iinhsldvsirevclwl.pallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllf 165
                                       +++ + +    ev+ +l p++lgs ++ ++y l+r++++++ ++l+A++lai P  l+rt  Gf D+d++e +l+l 
  gi|386002412|ref|YP_005920711.1|  93 LLFGVPP----EVAGALaPPVLGSAAVLVVYVLARRTFGARVAVLSAFVLAIDPKHLARTHFGFVDHDALESLLILG 165
                                       8887777....777666378********************************************************* PP

                                       HHHHHHHHHHCCSTTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT..................... CS
                              STT3 166 vlffflkaiktksnkislaviaaliiflivlaWggyailiyallllfilalLiigr..................... 221
                                       ++ ++  a+   +++  l ++a+ +i+ + ++W+g  i ++a+l+  +l   +  r                     
  gi|386002412|ref|YP_005920711.1| 166 AILLLAYALTDRKRRLKLGAAAGALIAAVGYTWLGAPIYMVAILIYAVLQAALDLRdgndpsssilplaaafgvall 242
                                       ***********************************866666666555555544444899998888888777777777 PP

                                       ....S-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHH CS
                              STT3 222 ....felklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfislfq 294
                                           f   + +a  f+ +++ ++  ++  l+l +  ++  ++ + ++  + ++l a+   v++  + +++++  l+ 
  gi|386002412|ref|YP_005920711.1| 243 lflpFRGEAWLAPSFFGALGGIA--ALGALLLLSRLLRREGLAAPALLPAAAILGALALAVISPFWGESGIAALLTE 317
                                       76666777777779999999999..8888888888777777777788888888888888888888************ PP

                                       TT.HHHHTT--.GGGHHHHHHHHHHHHC....CCCCCTS---....--TTHHHHH..HHHHS---S--CCHHHCCSS CS
                              STT3 295 pgilsevlgli.gevvtalavlglialw....lgilyslldl....eyaklkiki..iilvsvwlpvgllaltkglr 360
                                       ++ ++ ++g++ g+ + a+ + +l  ++    lg+++ ll+l     +  l++ +  + l+ vw + +l+++ +  r
  gi|386002412|ref|YP_005920711.1| 318 GARYFFLGGVGeGRILEAVPIYRLLDPVslpaLGLFFLLLGLgtmiRMSRLSRRPgdMLLLIVWAAFTLALTAFQAR 394
                                       ***********999999998888888888888899999998887884444444434499999*************** PP

                                       ST.TTTCCCHHHCHHCCHHCTCHHHHHHHHHHHHHCCC-SCHCCCCCHH.HHHHHCCCHHHHHHHHCCHHHHHHHHH CS
                              STT3 361 fl.iftvPlgiifvgllleflavfvkiysvsqilfsgvvvillmltllp.vlallaavkiskifstykdekeakikv 435
                                       fl + ++  +i +v ll      ++ + +      +++ v ll+l+l p ++ ll  + ++   + +   +ea  +v
  gi|386002412|ref|YP_005920711.1| 395 FLyLSSLAGSI-SVALLFFWGSDRLVGRR--GPAPKAASVALLALLLFPnAVGLLEVIGAE--PEIKGGWIEALDWV 466
                                       **666666666.44444444444444444..223333334334443333145555544444..34455555666666 PP

                                       HHHHHHHHHCT.TTTTHHHTTHHHCHHHHHHHHHHHHHHHHHHHHHHHH CS
                              STT3 436 aakavaptksnglkeslewkantnrdsvvitwwdyghilaveadrpVtf 484
                                       a+       +  + e+ e     +    +++wwdyg  +   ++rpV++
  gi|386002412|ref|YP_005920711.1| 467 AE-------NTPQTEGFEDAFG-SPSYSIMSWWDYGNWILLQSRRPVVA 507
                                       44.......3345555555333.33344667777777777777777776 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1   6.3e-18   2.8e-14       1      92 []     627     716 ..     627     716 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 6.3e-18
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEE..... CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevta..... 72 
                                       GA+i+G+++ +    a++ + +nqgr f Y++ea   edG++e+tvPYst+gee      + +  gpY v       
  gi|386002412|ref|YP_005920711.1| 627 GARISGTTPYDGPMAAALVIASNQGRRFVYSNEA-MPEDGRYEITVPYSTDGEE------DARSIGPYLVGPmedlg 696
                                       9*********************************.6***************844......44445555554422222 PP

                                       TTEEEEE---HHHHHHT-EE CS
                           AglB_L1  73 gnvtaeveVpEeaVlsgetv 92 
                                       g+ ++eveV Ee+V  g++v
  gi|386002412|ref|YP_005920711.1| 697 GEGSREVEVAEEDVALGRVV 716
                                       88************999886 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   8.4   2.9e-14   1.3e-10       3     132 ..      81     215 ..      79     252 .. 0.85
   2 ?   -0.9   1.2      0.38   1.7e+03     123     155 ..     264     304 ..     239     314 .. 0.55
   3 ?   -3.0   4.1       1.7   7.6e+03     104     144 ..     353     398 ..     335     413 .. 0.44

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.9e-14
                             PMT_2   3 PPliawllalftklfgf.selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa..lftpda 76 
                                       PPl+  + a    lfg   e+a  l++ ++g+ ++l++y larr fg+r+a+l+a+ la+ p  +a ++   + +da
  gi|386002412|ref|YP_005920711.1|  81 PPLFDQVVAGASLLFGVpPEVAGALAPPVLGSAAVLVVYVLARRTFGARVAVLSAFVLAIDPKHLARTHfgFVDHDA 157
                                       999999**********99********************************************9999999899999** PP

                             PMT_2  77 plvllwalalylllrale..knklkywllagvlfGlgflsKytaallliaallyllis 132
                                       +  ll++ a++ll+ al+  k++lk  ++ag+l+++  ++   a ++++a+l+y++++
  gi|386002412|ref|YP_005920711.1| 158 LESLLILGAILLLAYALTdrKRRLKLGAAAGALIAAVGYTWLGAPIYMVAILIYAVLQ 215
                                       **************9999656669999*********9999999999999999998887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.38
                             PMT_2 123 iaall.yllis..arr.ilke....kkpylalllalllfsp 155
                                       iaal   ll+s   rr  l+     + + + ++lal+++sp
  gi|386002412|ref|YP_005920711.1| 264 IAALGaLLLLSrlLRReGLAApallPAAAILGALALAVISP 304
                                       44444322222342222333323333334455555555555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.7
                             PMT_2 104 agvlfGlgflsKytaalllia.allyllis....arrilkekkpyl 144
                                       + +l+Glg+++++  +   ++ +ll +++     a   ++ + +yl
  gi|386002412|ref|YP_005920711.1| 353 FFLLLGLGTMIRMSRLSRRPGdMLLLIVWAaftlALTAFQARFLYL 398
                                       4444555555554444433333222222221112222333344444 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.1   4.6e-06      0.02      63     194 ..      81     209 ..      14     249 .. 0.78
   2 ?   -3.6   1.3       1.5   6.8e+03      93     121 ..     382     410 ..     352     415 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                               PMT  63 dgnftfesigaeyypenvpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldsp 139
                                       ++ f+  ++ga+  ++  p+v+ +l + +lgs +v++vy ++++ +f  ++a+l+a+ +++++ +++ + +   d  
  gi|386002412|ref|YP_005920711.1|  81 PPLFDQVVAGASLLFGVPPEVAGALAPPVLGSAAVLVVYVLARR-TFGARVAVLSAFVLAIDPKHLARTHFGFVDHD 156
                                       678888999999999999*****************999999988.56699*******************99999975 PP

                               PMT 140 Ll.fftllsmyclvkferkapfsrswwlwllltgvalglavsvKwvglftvllvgl 194
                                        l   + l+ ++l+ +    + +++  +   ++g  ++ av+  w g+ +++++ l
  gi|386002412|ref|YP_005920711.1| 157 ALeSLLILGAILLLAYA--LTDRKRRLKLGAAAGALIA-AVGYTWLGAPIYMVAIL 209
                                       55144556777777774..3455666666666665555.55555777766633322 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.5
                               PMT  93 gslivplvyltllelgfskltallaallv 121
                                        +++++l+ + ++ l  s l++ ++++l+
  gi|386002412|ref|YP_005920711.1| 382 AAFTLALTAFQARFLYLSSLAGSISVALL 410
                                       33444455555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 4843.16
//
Query:       gi|386002413|ref|YP_005920712.1|  [L=406]
Description: phosphoserine phosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-18   67.8   0.3    3.4e-18   66.7   0.1    1.7  2  HAD              haloacid dehalogenase-like hydrolase
    6.9e-18   65.7   0.3    1.2e-17   64.9   0.3    1.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
      2e-13   50.1   2.3    1.3e-09   37.9   0.2    2.5  2  ACT_6            ACT domain
    1.8e-10   40.4   1.8    1.2e-05   24.9   0.4    2.7  2  ACT              ACT domain
    1.1e-09   38.4   1.8    7.4e-09   35.7   0.3    2.6  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    2.3e-09   37.0   0.0      3e-07   30.1   0.0    2.2  2  Put_Phosphatase  Putative Phosphatase
    5.9e-08   33.0   0.2    4.7e-07   30.1   0.2    2.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
    6.5e-08   33.1   2.0      0.018   15.7   0.1    3.1  3  ACT_4            ACT domain
  ------ inclusion threshold ------
        0.1   12.1   0.1        1.3    8.5   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
       0.22   11.0   0.0       0.37   10.2   0.0    1.3  1  YkuD_2           L,D-transpeptidase catalytic domain
       0.25   12.0   0.2        1.6    9.3   0.0    2.1  2  DUF3502          Domain of unknown function (DUF3502)


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.1   5.1e+03     143     172 ..     149     178 ..     110     181 .. 0.65
   2 !   66.7   0.1   2.1e-21   3.4e-18       1     186 [.     194     360 ..     194     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                               HAD 143 glegkpvrgegkvaalrewlaaegegidle 172
                                        +e  + +g+ +v++ re l+ae+e++ l+
  gi|386002413|ref|YP_005920712.1| 149 SIEFVMDFGALDVRREREELKAECEKLGLD 178
                                       444556677777777777777777777665 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 2.1e-21
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       ++fD+D T++d +++  +++  +++      r+++e ++ a+    ++ld  ++ +    ll+g + e+l++ ++ +
  gi|386002413|ref|YP_005920712.1| 194 IVFDMDSTIVDFETINQIAQ-AAGV-----DREVEEITKRAM---NGELDFVEALRSRVGLLRGTPvEALEEIAANI 261
                                       79******************.5555.....566777777777...55565556666677789999966666666666 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrge 152
                                       +        l+pg  el+++ ++ G++++++Sgg+ +++ +l ++lg+d+  a+ le +d  ltge  ++g ++  +
  gi|386002413|ref|YP_005920712.1| 262 Q--------LTPGSEELIHHLKEVGYKTALISGGFTYFTDILKERLGFDYTFANVLEIRDgLLTGE--IDGEIIDAA 328
                                       6........78********999********************************************..********* PP

                               HAD 153 gkvaalrewlaaegegidleevvayGDspsDlpl 186
                                       +k + +++   a+ egi+++++va+GD+ +D  +
  gi|386002413|ref|YP_005920712.1| 329 AKGRIVND--LARLEGISPDSIVAVGDGANDCLM 360
                                       ********..99999999999**********766 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.3   7.4e-21   1.2e-17       2     210 .]     192     365 ..     191     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 7.4e-21
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       +++vfD+d T+++ e     +i+++                     a+a ++  +++++++     +++ g+ ++++
  gi|386002413|ref|YP_005920712.1| 192 RLIVFDMDSTIVDFE-----TINQI---------------------AQAAGVDREVEEITK-----RAMNGELDFVE 237
                                       68*************.....*****.....................***************.....*********** PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       al               + r   l    + a+ +ia ++++ p+ +e++++Lk+ g++++l++g++  + + + ++l
  gi|386002413|ref|YP_005920712.1| 238 AL---------------RSRVGLLRGTPVEALEEIAANIQLTPGSEELIHHLKEVGYKTALISGGFTYFTDILKERL 299
                                       **...............66666666667777888888888******************************977777* PP

                                       T........GGGESEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x........xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G........ddyfdaviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       G         ++ d+ ++++i++    a ++ ++++ ++r  +++p  +++VGDg+nD  ++++Ag
  gi|386002413|ref|YP_005920712.1| 300 GfdytfanvLEIRDGLLTGEIDGeiiDAAAKGRIVNDLARLEGISPDSIVAVGDGANDCLMIQNAG 365
                                       *966665544444556666666677777778888888888889*********************98 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.2     8e-13   1.3e-09       4      75 ..      19      92 ..      17      92 .. 0.95
   2 !   11.5   0.1   0.00014      0.23       4      75 ..     110     181 ..     108     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8e-13
                             ACT_6  4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp..edalarlekaLlflakelgltvef 75
                                      +i+v+G+drpG++ ++++v a+  vni+D+ q ++ g ++  ++ +      a ++le  L +la++lg++v++
  gi|386002413|ref|YP_005920712.1| 19 VISVLGKDRPGIIRDILEVPAKMMVNIVDLDQRILQGIVVMSMVADFGkaTAAPKELEGSLQRLAADLGVEVSV 92
                                      8*********************************************997556******************9975 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                             ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLlflakelgltvef 75 
                                       ++t++  dr G++ +++s+ ae g+ni   ++   ++  s+  + +  + ++ r + +L   +++lgl+v++
  gi|386002413|ref|YP_005920712.1| 110 VVTILARDRVGIIYDVASLAAERGINIERAQVTARGELISIEFVMDFGALDVRREREELKAECEKLGLDVVI 181
                                       79*************************998777777777788888888888888899999999999998875 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.8e-05      0.03       2      51 ..      19      64 ..      18      76 .. 0.84
   2 !   24.9   0.4   7.6e-09   1.2e-05       2      65 ..     110     171 ..     109     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEE CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvd 51
                                      v++v+ +DrPG++ +++ + a++ +Ni+ + qr        iv++  v+d
  gi|386002413|ref|YP_005920712.1| 19 VISVLGKDRPGIIRDILEVPAKMMVNIVDLDQRILQG----IVVMSMVAD 64
                                      799****************************998854....666665555 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 7.6e-09
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       v+ ++++Dr+G++ +v+++ a+rgiNi++++++  ++     + +v   ++ d+    e+lk+ 
  gi|386002413|ref|YP_005920712.1| 110 VVTILARDRVGIIYDVASLAAERGINIERAQVTARGE--LISIEFVMDFGALDVRREREELKAE 171
                                       57899******************************99..8888888888888888888888876 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.29   4.7e+02       1      12 [.     194     212 ..     194     237 .. 0.65
   2 ?   -1.0   0.0      0.73   1.2e+03      13      55 ..     260     302 ..     257     308 .. 0.76
   3 !   35.7   0.3   4.6e-12   7.4e-09     186     254 ..     328     395 ..     322     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                                       EEEEIIIIIS-.......T CS
                       Hydrolase_3   1 ialDlDGTLln.......s 12 
                                       i++D+D T+++        
  gi|386002413|ref|YP_005920712.1| 194 IVFDMDSTIVDfetinqiA 212
                                       89*******9855444441 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.73
                                       TS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  13 dkkisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       + ++++ + e i+ lke g+k ++ +G  ++++  + e lg+d
  gi|386002413|ref|YP_005920712.1| 260 NIQLTPGSEELIHHLKEVGYKTALISGGFTYFTDILKERLGFD 302
                                       55778889999**********9999997666666666666655 PP

  == domain 3  score: 35.7 bits;  conditional E-value: 4.6e-12
                                       -SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 186 vsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVaka 254
                                       + Kg  +++la   +is++ ++a+GDg ND  M++ aglgvA  na+e +kk++d    + n  G++++
  gi|386002413|ref|YP_005920712.1| 328 AAKGRIVNDLARLEGISPDSIVAVGDGANDCLMIQNAGLGVAF-NAKEILKKVSDGSLSKENLIGLLNV 395
                                       67****************************************7.9********9988888777776666 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.8e-10     3e-07       2     119 ..     193     308 ..     192     311 .. 0.89
   2 ?    4.7   0.0     0.011        17     151     185 ..     330     360 ..     326     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.8e-10
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkglwnelmdrvlkelhe.qgvseadikkvlrsiplspglv 77 
                                       l+vfD D ti+d ++ n + ++++ +++ ee+ +   +g   ++++ +  +++  +g   + ++++  +i l+pg  
  gi|386002413|ref|YP_005920712.1| 193 LIVFDMDSTIVDFETINQIAQAAGVDREVEEITKRAMNGE-LDFVEALRSRVGLlRGTPVEALEEIAANIQLTPGSE 268
                                       89******************************99988554.667777777776525688899*************** PP

                   Put_Phosphatase  78 elikslakkkleldliiiSDaNsffieeileaagledlFsei 119
                                       eli++l  k+ ++   +iS   ++f + + e +g+   F+++
  gi|386002413|ref|YP_005920712.1| 269 ELIHHL--KEVGYKTALISGGFTYFTDILKERLGFDYTFANV 308
                                       ******..6889************************999987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                   Put_Phosphatase 151 KgkvleelvaeqaregveyerliYvGDganDlCpv 185
                                       Kg+++++l +    eg++ + ++ vGDganD C +
  gi|386002413|ref|YP_005920712.1| 330 KGRIVNDLARL---EGISPDSIVAVGDGAND-CLM 360
                                       77777777666...7999*************.444 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   2.9e-10   4.7e-07       1     175 [.     194     368 ..     194     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.9e-10
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkke 77 
                                       i+FD+D T++d      +++n++++  g++   ee  ++ ++ +l + ++ l ++     ++ + ++  +e   +  
  gi|386002413|ref|YP_005920712.1| 194 IVFDMDSTIVDF-----ETINQIAQAAGVDREVEEITKRAMNGEL-DFVEALRSRVG--LLRGTPVEALEEIAAN-- 260
                                       89*********5.....5567777777774444455555555555.89999999755..4777777888888877.. PP

                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsed.vekkKPdpeviekalekl..... 148
                                       +++ +g +el++ Lke gyk ++++ + +  ++   e+lg++  F  ++   d       d e+i +a +       
  gi|386002413|ref|YP_005920712.1| 261 IQLTPGSEELIHHLKEVGYKTALISGGFTYFTDILKERLGFDYTFANVLEIRDgLLTGEIDGEIIDAAAKGRivndl 337
                                       *********************************************98876655332333477777777777677777 PP

                             HAD_2 149 ....klkkeeviyvGDsptDieaakkagikv 175
                                           ++++++++ vGD  +D    ++ag+ v
  gi|386002413|ref|YP_005920712.1| 338 arleGISPDSIVAVGDGANDCLMIQNAGLGV 368
                                       7778***********************9866 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.1e-05     0.018       9      41 ..      20      52 ..      18      63 .. 0.85
   2 !   15.2   0.1   1.5e-05     0.025      10      52 ..     112     152 ..     109     156 .. 0.87
   3 ?   -1.4   0.0       2.2   3.6e+03      45      75 ..     313     343 ..     306     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                             ACT_4  9 leveaedrkglLaditqviseekanivsvnakt 41
                                      ++v ++dr+g+++di++v +++ +niv++  + 
  gi|386002413|ref|YP_005920712.1| 20 ISVLGKDRPGIIRDILEVPAKMMVNIVDLDQRI 52
                                      899************************998776 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                             ACT_4  10 eveaedrkglLaditqviseekanivsvnaktrkkdglaeiki 52 
                                       ++ a+dr g++ d++++ +e ++ni+  ++++r   +l +i++
  gi|386002413|ref|YP_005920712.1| 112 TILARDRVGIIYDVASLAAERGINIERAQVTAR--GELISIEF 152
                                       799**************************9995..55666665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.2
                             ACT_4  45 dglaeikitveVkdvehLsrviakLraipgV 75 
                                       dgl +++i+ e+ d++   r+++ L +++g+
  gi|386002413|ref|YP_005920712.1| 313 DGLLTGEIDGEIIDAAAKGRIVNDLARLEGI 343
                                       8899999999999999999999999999887 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.13   2.1e+02       2      26 ..     191     213 ..     190     232 .. 0.78
   2 ?    8.5   0.0   0.00077       1.3     163     208 ..     327     371 ..     323     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                                       SEEEEE-TBTTTB.S-HHHHHHHHH CS
                              S6PP   2 klllvsdLDntlvdgdnealarlne 26 
                                       k+l+v d+D+t+v  d e+++++ +
  gi|386002413|ref|YP_005920712.1| 191 KRLIVFDMDSTIV--DFETINQIAQ 213
                                       689**********..5555555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00077
                                       T-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT CS
                              S6PP 163 raskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgn 208
                                       +a kg+ ++ La+  ++ +++i+ +Gd  nD  ++++  lgV   n
  gi|386002413|ref|YP_005920712.1| 327 AAAKGRIVNDLARLEGISPDSIVAVGDGANDCLMIQNAGLGVAF-N 371
                                       688999999999999********************999999975.3 PP

>> YkuD_2  L,D-transpeptidase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.37      30      59 ..     179     208 ..     158     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                            YkuD_2  30 ltiiDfskpStekRlfviDlkkkkllletl 59 
                                       ++i D++k+ +ekRl v+D++++ + +et+
  gi|386002413|ref|YP_005920712.1| 179 VVIQDLDKSAKEKRLIVFDMDSTIVDFETI 208
                                       7899****************9988877764 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     0.001       1.6      91     125 ..     154     188 ..     147     191 .. 0.89
   2 ?   -0.1   0.0      0.84   1.4e+03     102     123 ..     205     226 ..     194     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                           DUF3502  91 letGlvDpeetlpkfneklkaaGidkviaelqkQl 125
                                       + +G++D+  + +++++++++ G+d vi+ l k +
  gi|386002413|ref|YP_005920712.1| 154 MDFGALDVRREREELKAECEKLGLDVVIQDLDKSA 188
                                       678**************************998865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.84
                           DUF3502 102 lpkfneklkaaGidkviaelqk 123
                                       ++++n+ ++aaG+d+ ++e++k
  gi|386002413|ref|YP_005920712.1| 205 FETINQIAQAAGVDREVEEITK 226
                                       467889999*****99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2455.61
//
Query:       gi|386002414|ref|YP_005920713.1|  [L=149]
Description: 30S ribosomal protein S19E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-56  188.4   0.0    5.1e-56  188.2   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.023   14.6   0.0       0.31   11.0   0.0    2.2  2  RuvB_C          RuvB C-terminal winged helix domain
      0.042   13.5   0.0      0.094   12.4   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
       0.12   12.4   0.0       0.22   11.5   0.0    1.5  1  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.2   0.0   1.1e-59   5.1e-56       1     135 [.       3     136 ..       3     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.2 bits;  conditional E-value: 1.1e-59
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       tv+dVp+++li+a+aeeLk+sgk+e+Pewa+++Ktg++ke++p ++dW++vR+As+lR++y++gpvGv+rlr++YGg
  gi|386002414|ref|YP_005920713.1|   3 TVYDVPPNHLIDAVAEELKSSGKIEPPEWAAFAKTGVNKEMPPVNPDWWFVRCASVLRRIYIDGPVGVSRLRSYYGG 79 
                                       79*************************************************************************** PP

                                       -------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
                    Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                                       k+rr++    f+k+sgsvir++lqqLe++g+vkk+ k gr+lt++Gq+++d+++++v+
  gi|386002414|ref|YP_005920713.1|  80 KHRRKTVTGSFAKGSGSVIREALQQLERAGYVKKM-KAGRQLTPAGQSFMDNLSHQVK 136
                                       ********************************999.55*****************996 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.052   2.3e+02      13      33 ..      57      77 ..      53      88 .. 0.82
   2 ?   11.0   0.0   6.9e-05      0.31      50      71 ..     107     128 ..      75     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.052
                                      HHHHHT.TT--B-HHHHHHHT CS
                            RuvB_C 13 kllkekfkggpvglktlaail 33
                                      ++l + + +gpvg++ l +  
  gi|386002414|ref|YP_005920713.1| 57 SVLRRIYIDGPVGVSRLRSYY 77
                                      6788999*******9997765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.9e-05
                                       HTTSEEEETTEEEE-HHHHHHH CS
                            RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                       + g++++ + GR+lT+ g +++
  gi|386002414|ref|YP_005920713.1| 107 RAGYVKKMKAGRQLTPAGQSFM 128
                                       789***************9886 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.1e-05     0.094      37      55 ..      94     112 ..      89     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       -HHHHHHHHHHHHHTTSEE CS
                              GntR  37 srttvReALrrLeaeglve 55 
                                       s +++ReAL++Le++g+v 
  gi|386002414|ref|YP_005920713.1|  94 SGSVIREALQQLERAGYVK 112
                                       6689************995 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.9e-05      0.22      35      64 ..      98     126 ..      92     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGle 64 
                                       +R  L+ le+ g++++  +agr+lt  G +
  gi|386002414|ref|YP_005920713.1|  98 IREALQQLERAGYVKKM-KAGRQLTPAGQS 126
                                       8999**********997.678****98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.37s 00:00:00.95 Elapsed: 00:00:00.58
# Mc/sec: 778.67
//
Query:       gi|386002415|ref|YP_005920714.1|  [L=117]
Description: hypothetical protein Mhar_1733 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-30  105.4  19.4    2.1e-30  105.3  19.4    1.0  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
       0.49    9.4   5.7       0.55    9.3   5.7    1.0  1  DUF945          Bacterial protein of unknown function (DUF945
       0.71   10.1  11.8       0.32   11.2   9.1    1.8  1  DUF4355         Domain of unknown function (DUF4355)
        2.9    8.3   6.9        3.4    8.1   6.6    1.3  1  DUF2924         Protein of unknown function (DUF2924)
        8.7    7.0  16.6        2.5    8.8  12.3    1.9  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3  19.4   5.8e-34   2.1e-30       1     110 [.      10     116 ..      10     117 .] 0.89

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 5.8e-34
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       ++++r++elq+q+ +s+  ++ ++ q++q +++ e++kqaiL++iL+peAreRLs+ir+++pe a+++e++L+ laq
  gi|386002415|ref|YP_005920714.1|  10 LKRKRIEELQRQQADSQMYSA-QRAQQEQMQQELEARKQAILRTILTPEARERLSSIRMARPEFASQIESQLVVLAQ 85 
                                       689**********99888664.444444455579******************************************* PP

                                       --SS-----HHHHHHHHHHHS---XXXXX..XX CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketkivisr 110
                                       sG+l+s +t+eqLk +L+q++ kk+e +i  +r
  gi|386002415|ref|YP_005920714.1|  86 SGRLQSAITDEQLKAILKQIQPKKREINI--TR 116
                                       *************************7777..54 PP

>> DUF945  Bacterial protein of unknown function (DUF945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.7   0.00015      0.55     282     378 ..       4     104 ..       1     110 [. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                            DUF945 282 elslnnLdaealkklqeaynqlqakala.kaeeqlqeqleeallealpkLlakgpeleiselslknpeGeltlnlsl 357
                                       + +l  L ++ +++lq++  + q+ + + +++eq+q++le++ ++ l+++l  +++ ++s++++  pe  ++++ +l
  gi|386002415|ref|YP_005920714.1|   4 DDELAELKRKRIEELQRQQADSQMYSAQrAQQEQMQQELEARKQAILRTILTPEARERLSSIRMARPEFASQIESQL 80 
                                       5578899999********9999999988999*****************************77777766666666555 PP

                            DUF945 358 dl...apedsaksdsenllqllkk 378
                                        +   +   + +  +e+l ++lk+
  gi|386002415|ref|YP_005920714.1|  81 VVlaqSGRLQSAITDEQLKAILKQ 104
                                       557665555566666666666666 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   9.1     9e-05      0.32      20      84 ..      11      67 ..       2      81 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9e-05
                           DUF4355 20 kknklekeledeikkeakklakmnaeekaeyeleklqkeleelkaelarkelkaearkvlaekki 84
                                      k++  e+       + ++   +m   ++a+   e++q+ele++k++  r  l+ ear+ l+   +
  gi|386002415|ref|YP_005920714.1| 11 KRKRIEEL------QRQQADSQMYSAQRAQ--QEQMQQELEARKQAILRTILTPEARERLSSIRM 67
                                      22222222......3444556677777777..9*************************9986555 PP

>> DUF2924  Protein of unknown function (DUF2924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.6   0.00094       3.4       2      75 ..       5      78 ..       4     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00094
                           DUF2924  2 aelaaLkelsvkeLkekwrelfgeeapklnkeflekrlayriqelaeggLseearrrleelaeekekkkkkakk 75
                                      +ela+Lk+ +++eL+++ ++    +a++ ++e ++++l  r q+     L+ ear+rl+++  ++ + +++ ++
  gi|386002415|ref|YP_005920714.1|  5 DELAELKRKRIEELQRQQADSQMYSAQRAQQEQMQQELEARKQAILRTILTPEARERLSSIRMARPEFASQIES 78
                                      689********************************************************998886655555555 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  12.3    0.0007       2.5      23      71 ..       5      52 ..       2      84 .. 0.75
   2 ?    0.9   0.3       0.2     7e+02      31      67 ..      75     111 ..      56     116 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0007
                    HIP1_clath_bdg 23 eeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarl 71
                                      +e++  k++  eel+r ++++ ++ + q+ + e++++elea+++ + r 
  gi|386002415|ref|YP_005920714.1|  5 DELAELKRKRIEELQRQQADS-QMYSAQRAQQEQMQQELEARKQAILRT 52
                                      788999999999999965555.5678899999***********987654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                    HIP1_clath_bdg  31 eleeelerlkeeaerkleeqkeelekLkreleakrae 67 
                                       ++e +l  l ++ + + +   e+l+++ ++++ k+ e
  gi|386002415|ref|YP_005920714.1|  75 QIESQLVVLAQSGRLQSAITDEQLKAILKQIQPKKRE 111
                                       4455555555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2772  (0.15461); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 721.30
//
Query:       gi|386002416|ref|YP_005920715.1|  [L=198]
Description: hypothetical protein Mhar_1734 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-06   26.3   0.2    0.00028   20.7   0.1    2.1  2  Asn_synthase     Asparagine synthase
    0.00081   18.9   0.0     0.0015   18.1   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.028   13.9   0.0    1.5  1  Diphthami_syn_2  Diphthamide synthase
      0.077   12.6   0.0        2.4    7.7   0.0    2.2  2  ThiI             Thiamine biosynthesis protein (ThiI)
      0.086   11.6   0.0       0.17   10.6   0.0    1.5  1  tRNA_Me_trans    tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   7.8e-08   0.00028      20      87 ..       3      66 ..       1      73 [. 0.85
   2 ?    3.6   0.0     0.012        43      30      78 ..     136     191 ..     133     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.8e-08
                      Asn_synthase 20 vGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeellda 87
                                      v +l+SGG DS+l + l+  +   ++   + +f  +++  a++a+e+ae+lg++h+++ ++   l++a
  gi|386002416|ref|YP_005920715.1|  3 VVVLFSGGKDSALASILLEPFF--DVELATFAF--RRHGTAEAAREAAEALGLPHRTITFEDGVLEEA 66
                                      7899******************..577777778..77788889***************9998766665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                      Asn_synthase  30 SSliaalaarqsk........splktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       S +i ala+r+ +        +p+  F +g+  ++ +e++ + +va+ +  +h + +
  gi|386002416|ref|YP_005920715.1| 136 SKTINALAKRYMEfvtlesglHPASDFEVGL-RRELEERHGQDAVARIFPANHMHTR 191
                                       77899*******9*******99*********.999************9999987655 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.2e-07    0.0015       1      60 [.       2      57 ..       2      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.2e-07
                                      EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE CS
                              QueC  1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkild 60
                                      k+vvl+SGG DS+ +  + ++ +  ve+ tf +   ++ + eaa++ a++lg+  h++++
  gi|386002416|ref|YP_005920715.1|  2 KVVVLFSGGKDSALAS-ILLEPFFDVELATFAFR--RHGTAEAAREAAEALGL-PHRTIT 57
                                      689*********9765.56788999******995..55667899999999999.777665 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.7e-06     0.028       1      17 [.       1      17 [.       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-06
                   Diphthami_syn_2  1 mkvavlysGGkDsilaL 17
                                      mkv+vl+sGGkDs+la 
  gi|386002416|ref|YP_005920715.1|  1 MKVVVLFSGGKDSALAS 17
                                      9************9995 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00066       2.4       5      46 ..       2      43 ..       1      54 [. 0.71
   2 ?    2.7   0.0     0.023        84     131     158 ..     118     145 ..     107     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00066
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlkne.pgtseeai 46
                                      kv++L SgG DS  a+  ll+  + v+l ++  +  gt+e+a+
  gi|386002416|ref|YP_005920715.1|  2 KVVVLFSGGKDSALASI-LLEPFFDVELATFAFRrHGTAEAAR 43
                                      79***********9975.6788888888877543033444444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.023
                              ThiI 131 visavvnllilrPLigldKeeiiklAke 158
                                        ++   ++  +rPL g+  + i +lAk+
  gi|386002416|ref|YP_005920715.1| 118 SLEDSRKVHYIRPLAGYGSKTINALAKR 145
                                       55666788899***************98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.8e-05      0.17       1      35 [.       1      34 [.       1      72 [. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.8e-05
                     tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqgyevigvflklw 35
                                      +kvvv++SgG DS++a +ll+  +++v+  ++++ 
  gi|386002416|ref|YP_005920715.1|  1 MKVVVLFSGGKDSALASILLE-PFFDVELATFAFR 34
                                      69*************988775.5666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1182.57
//
Query:       gi|386002417|ref|YP_005920716.1|  [L=49]
Description: 50S ribosomal protein L39e [Methanosaeta harundinacea 6Ac]
Scores for complete 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-20   72.6   7.1    1.7e-20   72.3   7.1    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   7.1   9.5e-25   1.7e-20       1      41 [.       8      48 ..       8      49 .] 0.97

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 9.5e-25
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkL 41
                                      kK+r aKa+ qNr+vP Wv++kt rkv ++pkrRhWRr+++
  gi|386002417|ref|YP_005920716.1|  8 KKIRHAKAFCQNRRVPGWVIIKTMRKVVSHPKRRHWRRSNI 48
                                      7*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 300.75
//
Query:       gi|386002418|ref|YP_005920717.1|  [L=90]
Description: 50S ribosomal protein L31e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-13   50.8   0.7    1.8e-13   50.5   0.7    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.7   9.8e-18   1.8e-13       5      70 ..       6      72 ..       3      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 9.8e-18
                    Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemg..tpdvridtrLnkavwakgirnvpyrirvrl 70
                                      r ytI   + ++++ + kr +rA+ e++k+ +k+m+  +++v+i  +Ln+a+wa+g +++p+r+rv+ 
  gi|386002418|ref|YP_005920717.1|  6 RVYTIP-LREVKKAPRWKRSKRAVYEVRKYLAKHMKtsIEEVKISRDLNEAIWARGSEKPPARVRVKA 72
                                      789**9.899**************************444799************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 541.05
//
Query:       gi|386002419|ref|YP_005920718.1|  [L=225]
Description: Translation initiation factor 6 (AeIF-6) [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-66  223.0   0.0    2.5e-66  222.8   0.0    1.0  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.8   0.0   1.4e-70   2.5e-66       1     197 []       9     203 ..       9     203 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 1.4e-70
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       rl+++gs  +Gvfar+t++ +lv+++++   ++a+e++L++  ++ t+ags++vGsl++gNs+g++++ +++dee++
  gi|386002419|ref|YP_005920718.1|   9 RLKVAGSALLGVFARCTETALLVAPETTPGAMAALEKHLGLAPFRGTLAGSSVVGSLACGNSRGFILTPHASDEEVA 85 
                                       7899**********************9*9************************************************ PP

                                       HHHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE CS
                             eIF-6  78 klkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllv 154
                                       +++     +v+rl+ k++A+GNvilaND++Alvhp ls++++e i+ +Lgvev rgti+g+ktvG+++v+tn+g+lv
  gi|386002419|ref|YP_005920718.1|  86 RVSAF--GKVARLSGKISAAGNVILANDTAALVHPGLSDRACESISRTLGVEVRRGTIGGLKTVGMTSVATNRGILV 160
                                       ***99..9********************************************************************* PP

                                       -TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 155 hpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       hp+++e el+e+e+l++++v++gTvN+Gs+lvgsg++aN++g+
  gi|386002419|ref|YP_005920718.1| 161 HPRISEAELAEVEDLFRLPVDVGTVNFGSPLVGSGILANSRGY 203
                                       ****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1287.05
//
Query:       gi|386002420|ref|YP_005920719.1|  [L=59]
Description: 50S ribosomal protein LX [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   38.3   0.1    1.4e-09   38.1   0.1    1.0  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
      0.047   12.4   0.1      0.047   12.4   0.1    1.0  1  DUF3808         Protein of unknown function (DUF3808)


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   1.5e-13   1.4e-09      69     121 .]       4      56 ..       2      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.5e-13
                                       ..........TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  69 ygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                       + i  +++ r++++ f + +++ +e++ave++Ys lgs+  +kr+ ++Ie+v+
  gi|386002420|ref|YP_005920719.1|   4 FEIKGKFKVRNSWQSFSQVVESNSEKNAVEKTYSLLGSKQGVKRNLVRIEEVK 56 
                                       6677799********************************************96 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.2e-06     0.047     117     146 ..       6      35 ..       1      56 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-06
                           DUF3808 117 iKgglklRkaYqiykeilkeikklekkkrs 146
                                       iKg +k+R+++q ++++ +  ++ +  +++
  gi|386002420|ref|YP_005920719.1|   6 IKGKFKVRNSWQSFSQVVESNSEKNAVEKT 35 
                                       9**************988776644433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 356.65
//
Query:       gi|386002421|ref|YP_005920720.1|  [L=145]
Description: Prefoldin, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-22   79.4   3.3    2.3e-22   79.1   3.3    1.1  1  Prefoldin      Prefoldin subunit
    3.2e-05   23.8   5.9      0.001   19.0   1.5    2.1  2  Prefoldin_2    Prefoldin subunit
     0.0078   15.7   6.5       0.14   11.8   0.2    2.6  2  Trimer_CC      Trimerisation motif
  ------ inclusion threshold ------
      0.027   13.5   0.2       0.03   13.3   0.2    1.0  1  Amidase        Amidase
      0.058   13.2   3.6       0.07   13.0   1.1    2.0  2  CdvA           CdvA-like coiled-coil domain
       0.12   12.8   7.2          2    8.8   1.5    2.5  2  V-SNARE        Vesicle transport v-SNARE protein N-terminus
       0.12   12.5   0.2       0.12   12.5   0.2    1.9  3  DUF5446        Family of unknown function (DUF5446)
       0.17   12.1   4.6       0.44   10.8   1.3    2.1  2  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
       0.24   11.9   5.6        9.6    6.8   0.1    2.4  2  MerR-DNA-bind  MerR, DNA binding
       0.52   10.8   8.4       0.41   11.2   1.6    2.0  2  APG6_N         Apg6 coiled-coil region
        0.6   10.3   9.7       0.16   12.1   0.9    2.6  3  T3SS_needle_E  Type III secretion system, cytoplasmic E compo


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   3.3   1.4e-25   2.3e-22       2     116 ..      24     138 ..      20     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.4e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeA 78 
                                       ++e+e++ ++l+  + ++e +ek+l++++ +++++e++e+lvp+g+g++v a++ ++dkv+v +Gag+++eks +eA
  gi|386002421|ref|YP_005920720.1|  24 QAEAEAIVQQLGIFQLSMEGCEKALAAVEAMDAAGEDQEILVPIGQGSFVHARLASKDKVVVGVGAGVSIEKSTQEA 100
                                       56788899999999999999********************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaq 116
                                       +e l +++++l+++  kl+++l  + +++ +++ ++a+
  gi|386002421|ref|YP_005920720.1| 101 KEALTQRKAQLSEATAKLNQALSRIEAEMGKIQSIAAE 138
                                       *****************************999999886 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.3    0.0022       3.7       4      43 ..      17      56 ..      14      84 .. 0.87
   2 !   19.0   1.5   6.2e-07     0.001      46      97 ..      82     134 ..      74     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                       Prefoldin_2  4 inkfqqlqqqlqqlaqqikqletqlkelelvleelellde 43
                                      ++ +qq q++ ++++qq+   +  ++ +e++l ++e +d 
  gi|386002421|ref|YP_005920720.1| 17 LMVYQQHQAEAEAIVQQLGIFQLSMEGCEKALAAVEAMDA 56
                                      6779****************************99999885 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 6.2e-07
                                       -EEEEET.TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  46 kvyklvG.dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelke 97 
                                       kv   vG +v ++++ +e+ke L +rk++l++  ++l++ l+++e+e+ ++++
  gi|386002421|ref|YP_005920720.1|  82 KVVVGVGaGVSIEKSTQEAKEALTQRKAQLSEATAKLNQALSRIEAEMGKIQS 134
                                       566666634678999*********************************99986 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.6    0.0033       5.4      25      39 ..      10      24 ..       9      28 .. 0.95
   2 !   11.8   0.2   8.5e-05      0.14       4      37 ..     105     138 ..     103     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0033
                                      HHHHHHHHHHHHHHH CS
                         Trimer_CC 25 EEelrkLqatVQelQ 39
                                      EEe+r+L  + Q++Q
  gi|386002421|ref|YP_005920720.1| 10 EEEIRRLLMVYQQHQ 24
                                      9*************9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.5e-05
                                       XXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHHH CS
                         Trimer_CC   4 srrratpeasgtpssdavSRLEEelrkLqatVQe 37 
                                       ++r+a+    ++  + a+SR+E e+ k+q +  e
  gi|386002421|ref|YP_005920720.1| 105 TQRKAQLSEATAKLNQALSRIEAEMGKIQSIAAE 138
                                       678888777789999**************98765 PP

>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.8e-05      0.03     182     275 ..      26     120 ..      14     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                       -SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----.HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHH CS
                           Amidase 182 alessldvvGplarsvedlalllrvilgedpkdstssvip.eesedlaeelkkslkglriGvvkedgvasldpevqr 257
                                       + e++ ++ G++  s e +  +l ++  +d +  ++  ++   ++++  ++  s++++++Gv    + ++ ++e ++
  gi|386002421|ref|YP_005920720.1|  26 EAEAIVQQLGIFQLSMEGCEKALAAVEAMDAAGEDQEILVpIGQGSFVHARLASKDKVVVGVGAGVSIEKSTQEAKE 102
                                       78999*************************9988887666656789999999999********************** PP

                                       HHHHHHHHHHCTT-EEEE CS
                           Amidase 258 avekalkaLeeaGhevve 275
                                       a+++ +++L+ea +++ +
  gi|386002421|ref|YP_005920720.1| 103 ALTQRKAQLSEATAKLNQ 120
                                       ***********9988866 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.28   4.6e+02      80     112 ..      23      55 ..       8      63 .. 0.52
   2 ?   13.0   1.1   4.3e-05      0.07      24      70 ..      97     143 ..      88     145 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.28
                              CdvA  80 Yksaieairellesaleekeeikklleklskle 112
                                       ++++ eai ++l   + ++e  +k+l+ +++++
  gi|386002421|ref|YP_005920720.1|  23 HQAEAEAIVQQLGIFQLSMEGCEKALAAVEAMD 55 
                                       344444444444444445555555555444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.3e-05
                              CdvA  24 kekleealkklkekakelkeklkkrlkeledqikslekalanlkisy 70 
                                        ++ +eal++ k++ +e   kl++ l+ +e ++ ++++  a  + ++
  gi|386002421|ref|YP_005920720.1|  97 TQEAKEALTQRKAQLSEATAKLNQALSRIEAEMGKIQSIAAEYERQF 143
                                       5688999999**************************99999888776 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4    0.0041       6.7      17      46 ..       6      36 ..       1      55 [. 0.87
   2 ?    8.8   1.5    0.0012         2      10      41 ..      95     125 ..      91     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0041
                           V-SNARE 17 slag.eerkaalreiekkldeaeelldqMel 46
                                       +++ ee +++l  +++++ eae +++q+ +
  gi|386002421|ref|YP_005920720.1|  6 AAPSeEEIRRLLMVYQQHQAEAEAIVQQLGI 36
                                      45665789999999**************976 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                           V-SNARE  10 sklarlsslageerkaalreiekkldeaeell 41 
                                       +  + ++ +a  +rka+l+e+ +kl++a + +
  gi|386002421|ref|YP_005920720.1|  95 KSTQEAK-EALTQRKAQLSEATAKLNQALSRI 125
                                       4444444.335799999999999999997655 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.3   3.8e+03      32      47 ..      16      31 ..       9      46 .. 0.60
   2 ?   -2.9   0.0       4.9     8e+03      22      27 ..      42      47 ..      25      55 .. 0.57
   3 ?   12.5   0.2   7.6e-05      0.12      16      56 ..      92     131 ..      77     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                           DUF5446 32 vneteaekeekeeerl 47
                                      +++  +  + + e+++
  gi|386002421|ref|YP_005920720.1| 16 LLMVYQQHQAEAEAIV 31
                                      3344444444444444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                           DUF5446 22 tevEke 27
                                      +  Ek+
  gi|386002421|ref|YP_005920720.1| 42 EGCEKA 47
                                      333333 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 7.6e-05
                           DUF5446  16 eiEeeltevEkelseavneteaekeekeeerldllekElkd 56 
                                        iE++ +e+ ++l+++  ++  e+  k ++ l+++e E+  
  gi|386002421|ref|YP_005920720.1|  92 SIEKSTQEAKEALTQRK-AQLSEATAKLNQALSRIEAEMGK 131
                                       69************995.5567999*************876 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1       0.1   1.7e+02      35      79 ..      10      54 ..       7      64 .. 0.66
   2 ?   10.8   1.3   0.00027      0.44      63     100 ..      95     132 ..      87     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHH CS
                      Seryl_tRNA_N 35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkel 79
                                      +e+ r+l    ++ qae  ++ ++ g    + e  e+ +a v+++
  gi|386002421|ref|YP_005920720.1| 10 EEEIRRLLMVYQQHQAEAEAIVQQLGIFQLSMEGCEKALAAVEAM 54
                                      577788888888888888888888776665554444444444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                                       CCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  63 kkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       k  +e +e+l ++ ++l+e +++l+++l+ +eae+ k+
  gi|386002421|ref|YP_005920720.1|  95 KSTQEAKEALTQRKAQLSEATAKLNQALSRIEAEMGKI 132
                                       44447888999999999999999999999999998776 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0059       9.6      18      36 ..      11      30 ..       9      40 .. 0.75
   2 ?    6.1   2.2    0.0098        16      32      63 ..      95     126 ..      92     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0059
                                      HHHHHHHHHHHS.TTTBHHH CS
                     MerR-DNA-bind 18 deIrelLalydd.rappcqd 36
                                      +eIr+lL +y++ +a + + 
  gi|386002421|ref|YP_005920720.1| 11 EEIRRLLMVYQQhQAEAEAI 30
                                      8********99944444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0098
                                       TBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  32 ppcqdvrallarklaeleeriaeLqalraeLa 63 
                                       ++ q++++ l ++ a+l e  a+L +   +++
  gi|386002421|ref|YP_005920720.1|  95 KSTQEAKEALTQRKAQLSEATAKLNQALSRIE 126
                                       5789********************99988776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.039        64      46      93 ..      10      57 ..       2      63 .. 0.56
   2 ?   11.2   1.6   0.00025      0.41      45      90 ..      97     142 ..      74     145 .] 0.61

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.039
                            APG6_N 46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93
                                      +ee+++l   +++ ++e e+ +++L   +   e  e++laa e+  +a
  gi|386002421|ref|YP_005920720.1| 10 EEEIRRLLMVYQQHQAEAEAIVQQLGIFQLSMEGCEKALAAVEAMDAA 57
                                      345555555566666666666666666666666666666666655555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00025
                            APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90 
                                       ++e  e+l ++ ++l+++ ++l + L ++e+e  ++++  a++e++
  gi|386002421|ref|YP_005920720.1|  97 TQEAKEALTQRKAQLSEATAKLNQALSRIEAEMGKIQSIAAEYERQ 142
                                       2345555555566666666666666666666665555555555554 PP

>> T3SS_needle_E  Type III secretion system, cytoplasmic E component of needle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.6     0.082   1.3e+02      43      59 ..      20      36 ..      14      42 .. 0.88
   2 ?   -1.8   0.0       2.2   3.6e+03      46      58 ..      37      49 ..      31      54 .. 0.72
   3 ?   12.1   0.9    0.0001      0.16       4      36 ..      93     124 ..      92     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.082
                                      HHHHHHHHHHHHHHHHH CS
                     T3SS_needle_E 43 YqqlqllaeAleaAeaI 59
                                      Yqq q +aeA+ +   I
  gi|386002421|ref|YP_005920720.1| 20 YQQHQAEAEAIVQQLGI 36
                                      ***********997766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                      HHHHHHHHHHHHH CS
                     T3SS_needle_E 46 lqllaeAleaAea 58
                                      +ql +e +e+A a
  gi|386002421|ref|YP_005920720.1| 37 FQLSMEGCEKALA 49
                                      6788888888875 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.0001
                                       HHHHHCCCCTHHHHHHHHHHHHHHHHHHHHHCC CS
                     T3SS_needle_E   4 LEdrLrhapgeqakelqdrLeaArarLkqalss 36 
                                       +E + ++a+ e++ +++++L++A a+L qals+
  gi|386002421|ref|YP_005920720.1|  93 IEKSTQEAK-EALTQRKAQLSEATAKLNQALSR 124
                                       677778888.9999****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1787  (0.0996709); expected 358.6 (0.02)
Passed bias filter:                      872  (0.0486363); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 923.36
//
Query:       gi|386002422|ref|YP_005920721.1|  [L=364]
Description: Signal recognition particle-docking protein FtsY [Methanosaeta harundinacea 6Ac]
Scores for complete 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-72  241.7   0.1    6.8e-72  241.2   0.1    1.2  1  SRP54            SRP54-type protein, GTPase domain
    4.8e-13   49.1   1.6    1.5e-12   47.5   1.6    1.9  1  SRP54_N          SRP54-type protein, helical bundle domain
    4.8e-07   30.3   0.6    1.2e-06   29.0   0.1    1.9  2  AAA_17           AAA domain
    6.3e-07   29.3   0.2    1.3e-06   28.3   0.2    1.5  1  AAA_30           AAA domain
    0.00024   20.4   0.1    0.00044   19.6   0.1    1.4  1  Zeta_toxin       Zeta toxin
    0.00029   20.0   0.8      0.026   13.6   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
    0.00035   20.3   0.1     0.0041   16.8   0.1    2.4  2  Thymidylate_kin  Thymidylate kinase
      0.002   18.1   0.0     0.0038   17.1   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
     0.0022   18.3   0.8     0.0043   17.3   0.0    1.9  1  AAA_28           AAA domain
     0.0024   17.8   0.9      0.015   15.2   0.1    2.4  3  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0024   18.3   0.1     0.0063   16.9   0.1    1.8  1  AAA              ATPase family associated with various cellul
     0.0026   17.8   0.0     0.0057   16.7   0.0    1.7  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0033   17.6   0.0     0.0067   16.6   0.0    1.6  1  AAA_33           AAA domain
     0.0046   17.3   0.2     0.0079   16.5   0.2    1.3  1  AAA_19           AAA domain
     0.0047   17.3   0.2     0.0047   17.3   0.2    2.3  1  AAA_16           AAA ATPase domain
     0.0051   17.1   0.0      0.012   15.9   0.0    1.6  1  AAA_22           AAA domain
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.017   14.2   0.0    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.011   15.7   0.7      0.027   14.4   0.1    1.9  2  NTPase_1         NTPase
      0.013   14.8   0.1      0.024   13.9   0.1    1.4  1  6PF2K            6-phosphofructo-2-kinase
      0.016   15.2   0.0      0.031   14.3   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.024   14.1   0.1      0.046   13.2   0.1    1.4  1  KTI12            Chromatin associated protein KTI12
      0.029   13.4   0.0      0.063   12.3   0.0    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.038   15.0   2.6      0.058   14.4   0.0    2.6  2  LytR_C           LytR cell envelope-related transcriptional a
      0.045   14.3   0.0       0.13   12.8   0.0    1.8  2  ABC_tran         ABC transporter
      0.054   13.0   0.0      0.095   12.2   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.06   13.4   0.4       0.24   11.5   0.4    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
      0.069   13.2   1.3       0.13   12.3   0.1    2.0  1  SurA_N           SurA N-terminal domain
       0.12   12.1   0.0       0.18   11.5   0.0    1.4  1  AAA_24           AAA domain
       0.13   12.3   0.0       0.41   10.6   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
       0.16   11.2   0.3       0.27   10.4   0.3    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2   0.1   1.1e-74   6.8e-72       2     196 .]     169     363 ..     168     363 .. 0.99

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 1.1e-74
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                         i++vG++G+GKTt++aK+a++lk++g++++l+a DtfRa+AveQ++++a+kl+v+++k++ ++dpaav+++ave 
  gi|386002422|ref|YP_005920721.1| 169 VKIVFVGVNGTGKTTSIAKVARYLKDRGYSIVLAAGDTFRAGAVEQIEVHANKLEVKLVKHRDGKDPAAVIFDAVEY 245
                                       5799************************************************************************* PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       ak+++ d+vl DTaGrl+++ +lm+++kki +vv+pd  ++v +a++g++av+ a+ F+eav i+g iltk D+dak
  gi|386002422|ref|YP_005920721.1| 246 AKAHHRDIVLADTAGRLHTNVNLMDQMKKIVRVVDPDLLIFVDEAIAGNDAVERARLFNEAVPIDGTILTKTDADAK 322
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gGaa+si++ +++P+ f+g+G+ + dl +f+pe+l++rllg
  gi|386002422|ref|YP_005920721.1| 323 GGAAISISSITGKPVLFLGIGQDYPDLVKFEPEWLLERLLG 363
                                       ***************************************95 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   1.6   2.5e-15   1.5e-12      15      75 .]      84     147 ..      74     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.5e-15
                                       SSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  15 kskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75 
                                         ++de+dl++ l+ele+aLle+DV+++v++ ++++vk + vg+kk     +++ v+++++ +L
  gi|386002422|ref|YP_005920721.1|  84 EVVLDEKDLKDPLWELEMALLESDVALPVAETIVASVKGELVGKKKkirADTGEIVEEALRSAL 147
                                       4479***************************************777988889999999999776 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       8.4     5e+03      37      72 ..     122     154 ..     116     167 .. 0.55
   2 !   29.0   0.1     2e-09   1.2e-06       1     109 [.     174     288 ..     174     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.4
                                       TTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSS CS
                            AAA_17  37 gglakardemrklpleekkelqkeaaekiaeeakkk 72 
                                       g+l+ +++++r    e+ +e ++ a  ++  e   +
  gi|386002422|ref|YP_005920721.1| 122 GELVGKKKKIRADTGEIVEEALRSALLQVLSE---N 154
                                       56666777777655555555555554444443...3 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 2e-09
                                       EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..H CS
                            AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrg.glakardemrklpleekkelqkeaaekiaeea..k 70 
                                       +G+ G GK+t ++k+++ +   g++ +l aGd +r+ a ++ +   ++ e++ +++++ k+  + + ++++ ++   
  gi|386002422|ref|YP_005920721.1| 174 VGVNGTGKTTSIAKVARYLkdrGYSiVLAAGDTFRAGAVEQiEVHANKLEVKLVKHRDGKDPAAVIFDAVEYAKahH 250
                                       79*************976666688735799******99999677888889999999999999999999886555337 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                       ++ vl d+  r+ ++  ++d+++k +++ ++pd++i+++
  gi|386002422|ref|YP_005920721.1| 251 RDIVLADTAGRLHTNVNLMDQMKK-IVRVVDPDLLIFVD 288
                                       788**********99999888885.89**********98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.2   2.2e-09   1.3e-06      22     113 ..     172     277 ..     159     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.2e-09
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grar 85 
                                       v +G+ GtGKtt+++++++ ++++g++++++A     A +++ +++++a+ ++  l +++             + a+
  gi|386002422|ref|YP_005920721.1| 172 VFVGVNGTGKTTSIAKVARYLKDRGYSIVLAAGDTFRAGAVE-QIEVHANKLEVKLVKHRdgkdpaavifdavEYAK 247
                                       679*****************************9999999998.8999**9999888888889999999999995567 PP

                            AAA_30  86 lepgtllivDEagmv..dtkqlaallkaae 113
                                        +++++++ D ag +  + + ++++ k+++
  gi|386002422|ref|YP_005920721.1| 248 AHHRDIVLADTAGRLhtNVNLMDQMKKIVR 277
                                       777788888888877332233444444333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.3e-07   0.00044      10     118 ..     162     273 ..     153     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.3e-07
                        Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilka..dpkkaseltqkdasel 83 
                                       + + e+P+ i+ +G  G GK++ +++++++l+ r+ ++v   +D++R+   e  e+ ++  ++k +     kd   +
  gi|386002422|ref|YP_005920721.1| 162 IAKAEKPVKIVFVGVNGTGKTTSIAKVARYLKdRGYSIVLAAGDTFRAGAVEQIEVHANklEVKLVKHRDGKDPAAV 238
                                       44569***************************67777788889****976444443332235555555555666667 PP

                        Zeta_toxin  84 vekllqeaiengyniivegtlrspdvvkklaealk 118
                                          ++++a  + ++i++  t    ++  +l++++k
  gi|386002422|ref|YP_005920721.1| 239 IFDAVEYAKAHHRDIVLADTAGRLHTNVNLMDQMK 273
                                       77777777777777777777777777766776666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.3e-05     0.026     101     180 ..     141     218 ..     105     229 .. 0.76
   2 ?    5.2   0.2     0.016       9.7     160     204 ..     236     285 ..     220     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                             T2SSE 101 keltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtv.EDpvEiqleganq 176
                                       ++l+ + l++  +++ +++e+++ka ++   i++ G  g+GKtt++  +  +++++   iv++  D+   +  +++q
  gi|386002422|ref|YP_005920721.1| 141 EALRSALLQVLSENRFDVDEFIAKA-EKPVKIVFVGVNGTGKTTSIAKVARYLKDRGYSIVLAaGDTF--RAGAVEQ 214
                                       556666667777777899*******.9999***********************999777776414553..4444555 PP

                             T2SSE 177 vqln 180
                                       ++++
  gi|386002422|ref|YP_005920721.1| 215 IEVH 218
                                       5555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                             T2SSE 160 ivtvEDpvEiqleganqvqlnak....kakvtfadllraaLRl.rPDrim 204
                                         ++ D+vE+  ++   + l +     +++v++ d +++++R  +PD ++
  gi|386002422|ref|YP_005920721.1| 236 AAVIFDAVEYAKAHHRDIVLADTagrlHTNVNLMDQMKKIVRVvDPDLLI 285
                                       56788*******9999999988889999**************55***754 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   6.9e-06    0.0041       3      30 ..     175     202 ..     173     228 .. 0.87
   2 ?    0.6   0.0      0.66     4e+02     110     137 ..     272     302 ..     260     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.9e-06
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvlt 30 
                                       G++G+GKtt +++++++lk++g+++vl 
  gi|386002422|ref|YP_005920721.1| 175 GVNGTGKTTSIAKVARYLKDRGYSIVLA 202
                                       9**********************97764 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.66
                                       HGGGTTS.E-SEEEEEE..SSHHHHHTSCCT CS
                   Thymidylate_kin 110 lnedvll.kPdltflld..vdpevalkRlak 137
                                       +++ v    Pdl +++d  +  + a++R++ 
  gi|386002422|ref|YP_005920721.1| 272 MKKIVRVvDPDLLIFVDeaIAGNDAVERARL 302
                                       444433359*******977788888888775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.4e-06    0.0038       2      48 ..     168     214 ..     167     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.4e-06
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkd 48 
                                       +v + + G+ g+GK+t   +++++L+++g+s++l  Gd+ R g  ++
  gi|386002422|ref|YP_005920721.1| 168 PVKIVFVGVNGTGKTTSIAKVARYLKDRGYSIVLAAGDTFRAGAVEQ 214
                                       67899************************************987665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.2e-06    0.0043       1      47 [.     170     220 ..     170     263 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.2e-06
                            AAA_28   1 kivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalp 47 
                                       kiv++G  +tGKTt +++ a+     gy++v  a+ ++     ++ e +++
  gi|386002422|ref|YP_005920721.1| 170 KIVFVGVNGTGKTTSIAKVARYlkdrGYSIVLAAGDTFRAGAVEQIEVHAN 220
                                       79**************9999544455***9977766666555554444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.6e-05     0.015       2      30 ..     171     199 ..     170     206 .. 0.93
   2 ?    0.0   0.1       1.2   7.4e+02      99     120 ..     207     228 ..     199     241 .. 0.61
   3 ?   -0.9   0.1       2.3   1.4e+03      24      40 ..     218     233 ..     212     285 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrv 30 
                                       + +vg +g+GKTt + k+ + lk+rg+++
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYLKDRGYSI 199
                                       679************************98 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                              MobB  99 fkkealpkievlraelgkeell 120
                                       f++ a+++iev+ ++l+ + + 
  gi|386002422|ref|YP_005920721.1| 207 FRAGAVEQIEVHANKLEVKLVK 228
                                       6777777777777776654332 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                              MobB  24 karglrvgtiKhahhgf 40 
                                       +a++l+v ++Kh     
  gi|386002422|ref|YP_005920721.1| 218 HANKLEVKLVKHRDG-K 233
                                       567777888887543.3 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.1e-05    0.0063       1      67 [.     171     243 ..     171     297 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                                       EEEESSTTSSHHHHHHHHHHHHT...HE...............EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.. CS
                               AAA   1 vllyGppGtGKTllakavakelg...ve...............fleisgsellskyvgesekkirelfkeakeka.. 57 
                                       ++++G  GtGKT+ +  va+ l+    +                +e+ + +l  k+v+++                 
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYLKdrgYSivlaagdtfragaveQIEVHANKLEVKLVKHR--------------Dgk 233
                                       5799*****************963333311111222222222144444444444433332..............122 PP

                                       TSEEEEEETG CS
                               AAA  58 kpsilfiDEi 67 
                                       +p  +++D +
  gi|386002422|ref|YP_005920721.1| 234 DPAAVIFDAV 243
                                       3333333333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.5e-06    0.0057       9      37 ..     178     206 ..     171     338 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.5e-06
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDp 37 
                                       G+GKTt  a+ ar+l++rg+ ++l   D+
  gi|386002422|ref|YP_005920721.1| 178 GTGKTTSIAKVARYLKDRGYSIVLAAGDT 206
                                       9*********************9976665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0067       2      79 ..     171     263 ..     171     306 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfg.....tdqqsktdytrvldrlyqilnelarkal 67 
                                       +++vG++G+GK+t + ++++ l+      vl + dt+r  +++      ++ + k    r  ++  + +++ ++ a 
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYLKdrgysIVLAAGDTFRAgAVEQievhaNKLEVKLVKHRDGKDPAAVIFDAVEYAK 247
                                       68**************9988888888977777888887744444543332222222222233334445567777777 PP

                            AAA_33  68 sagrnvildat....n 79 
                                       ++ r+++l  t     
  gi|386002422|ref|YP_005920721.1| 248 AHHRDIVLADTagrlH 263
                                       7777766655544442 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.3e-05    0.0079      12     111 ..     170     290 ..     159     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillv...aftgrAakelrerlaalgae................. 68 
                                        ++ ++  GtGKT+ + ++ ++l+++g     +i+l+   +f   A+++++   ++l+++                 
  gi|386002422|ref|YP_005920721.1| 170 KIVFVGVNGTGKTTSIAKVARYLKDRG----YSIVLAagdTFRAGAVEQIEVHANKLEVKlvkhrdgkdpaavifda 242
                                       34556789***************9999....444444222566667889988888888889999*******999999 PP

                            AAA_19  69 ...atTiH.rlalldfddlltealelleeaeeekklqeee.llivDEf 111
                                          a+  H  + l d+ ++l++ ++l+++ ++   + + + l++vDE+
  gi|386002422|ref|YP_005920721.1| 243 veyAKAHHrDIVLADTAGRLHTNVNLMDQMKKIVRVVDPDlLIFVDEA 290
                                       9998888844445677777777788877766666677888899****7 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   7.9e-06    0.0047      26      88 ..     170     233 ..     158     290 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.9e-06
                            AAA_16  26 lvllsGesGvGKsslvrellralekdg.giflrgkcdqlesa..ipysalaqalareellrqllde 88 
                                        ++++G  G+GK++ + +++r+l+++g  i + +  d ++++      + a+ l + +l++  + +
  gi|386002422|ref|YP_005920721.1| 170 KIVFVGVNGTGKTTSIAKVARYLKDRGySI-VLAAGDTFRAGavEQIEVHANKL-EVKLVKHRDGK 233
                                       57899***************9999996333.55555555222111112233333.22333333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-05     0.012       8     117 ..     171     280 ..     167     294 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.........erlss 75 
                                       +v +G  GtGKTt+++++++ l         +++ +++ l+++    +++   ++++++ +++          +++ 
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYL---------KDRGYSIVLAAGD---TFRAGAVEQIEVHANKlevklvkhrDGKDP 235
                                       6889******************.........6666655555555...455555555555555555555558866666 PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlrs.....eealeeLrslln 117
                                        +++    ++++a+++  +++ D a +l +     +++++++++ ++
  gi|386002422|ref|YP_005920721.1| 236 AAVIFDAVEYAKAHHR-DIVLADTAGRL-HtnvnlMDQMKKIVRVVD 280
                                       6666444445555555.58888888888.334556677666666665 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.9e-05     0.017      26      69 ..     160     200 ..     143     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                       TSS--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EE CS
                              LpxK  26 gllkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvg 69 
                                       +++ + + pv+++ VG   v GtGKT  ++ ++++l++rg+ ++
  gi|386002422|ref|YP_005920721.1| 160 EFIAKAEKPVKIVFVG---VNGTGKTTSIAKVARYLKDRGYSIV 200
                                       56778888*******9...99*******************9865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.5e-05     0.027       2      30 ..     171     199 ..     170     204 .. 0.91
   2 ?   -2.1   0.0       5.2   3.1e+03      93     124 ..     247     279 ..     234     302 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       ++  G  G+GKtT + kv++ lk++g+++
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYLKDRGYSI 199
                                       667799********************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.2
                                       H.HHH-EEEE---STTGGG-HHHHHHHHHHHT.T CS
                          NTPase_1  93 l.seadviviDEiGkmElkskkfkeaveevLk.s 124
                                         ++ d+++ D  G++  +++ +  +++++++  
  gi|386002422|ref|YP_005920721.1| 247 KaHHRDIVLADTAGRLHTNVNLMD-QMKKIVRvV 279
                                       446677777777777766665443.344444433 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     4e-05     0.024      10      43 ..     165     198 ..     158     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                                       ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT-- CS
                             6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvr 43 
                                        ++++ iv+vG   +gKt+   k+ rylk  g++
  gi|386002422|ref|YP_005920721.1| 165 AEKPVKIVFVGVNGTGKTTSIAKVARYLKDRGYS 198
                                       578999***********************65543 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.2e-05     0.031      21     141 ..     158     290 ..     130     306 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-05
                                       .........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEES CS
                            ResIII  21 s.......krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvs 90 
                                               ++  +++++   GtGKT  +ak++++l+  g+    ++l+ + +    + e+++  +++    ++ +++
  gi|386002422|ref|YP_005920721.1| 158 VdefiakaEKPVKIVFVGVNGTGKTTSIAKVARYLKDRGY---SIVLAAGDTFRAGAVEQIEVHANKLE--VKLVKH 229
                                       044444335666999*****************99999877...69999999999999998887777664..445555 PP

                                       SS-B--...............-SEEEE.EHHHHHHTH.........HHHTTT-SEEEEETG CS
                            ResIII  91 gdkkka........kekdstnkkilvt.tiqsldadseee.eeeseellrdrfdviiiDEa 141
                                        d+k++        +  ++++++i+++ t  +l+ + +   + ++     d  ++i++DEa
  gi|386002422|ref|YP_005920721.1| 230 RDGKDPaavifdavEYAKAHHRDIVLAdTAGRLHTNVNLMdQMKKIVRVVDPDLLIFVDEA 290
                                       5555555677777755556666666652455666666444333333344444447777776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.7e-05     0.046       4      91 ..     171     255 ..     170     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHH.HHHHTT.SEEEE-S- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsav.krdLskekvVIvDsl 79 
                                       +v+ G+  +GK+t  +++a++l+++++s+v+   ++++    +    + e ++ +   + v +rd +    VI D++
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYLKDRGYSIVLAAGDTFRAGAVE----QIEVHANKLEVKLVkHRDGKDPAAVIFDAV 243
                                       899*********************************9954444....333333333344440567777789****** PP

                                       --SHHHHHHHHH CS
                             KTI12  80 nyikgfRYeLyc 91 
                                        y k   +++  
  gi|386002422|ref|YP_005920721.1| 244 EYAKAHHRDIVL 255
                                       **9999888764 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011     0.063      20      64 ..     159     203 ..     145     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                       HHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEE CS
                              MeaB  20 erllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavla 64 
                                       ++ +aka +  ++ + Gv G+Gk t + +++  l++rG+ + + a
  gi|386002422|ref|YP_005920721.1| 159 DEFIAKAEKPVKIVFVGVNGTGKTTSIAKVARYLKDRGYSIVLAA 203
                                       56678888999999************************9987665 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       7.2   4.3e+03      18      35 ..      15      33 ..       9      67 .. 0.54
   2 ?   14.4   0.0   9.7e-05     0.058       7      39 ..     176     206 ..     176     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 7.2
                            LytR_C 18 rvadaLeerGf.tvgevgn 35
                                      +v+++ +e+G  ++ ++++
  gi|386002422|ref|YP_005920721.1| 15 AVSSKIQEKGEaQAEKAEA 33
                                      5555556665422222221 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.7e-05
                            LytR_C   7 lNgtgvsGlAarvadaLeerGftvgevgnagna 39 
                                       +Ngtg++   a+va++L++rG+ ++   +ag++
  gi|386002422|ref|YP_005920721.1| 176 VNGTGKTTSIAKVARYLKDRGYSIVL--AAGDT 206
                                       5*********************7665..23333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.3   4.3e+03      58      58 ..      74      74 ..      16     142 .. 0.59
   2 ?   12.8   0.0   0.00021      0.13      12      72 ..     169     235 ..     158     285 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.3
                                      C CS
                                      x RF
                          ABC_tran 58 r 58
                                      +
  gi|386002422|ref|YP_005920721.1| 74 S 74
                                      0 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG.....B-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke.....qeleslrkeigvlpqepqlfp 72 
                                        k+++vG nG+GK+t ++ +a+ lk+   +i l  g+ ++      +e +  + e++ +++ +  +p
  gi|386002422|ref|YP_005920721.1| 169 VKIVFVGVNGTGKTTSIAKVARYLKDRGYSIVLAaGDTFRAgaveqIEVHANKLEVKLVKHRDGKDP 235
                                       57899*************9999999877777555344444444433444444445555555555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016     0.095      34      64 ..     169     199 ..     158     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekyls 64 
                                        ++++vG  GtGKt+ i ++ + l+++ y++
  gi|386002422|ref|YP_005920721.1| 169 VKIVFVGVNGTGKTTSIAKVARYLKDRGYSI 199
                                       4679*****************9999887765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4    0.0004      0.24       1      84 [.     170     289 ..     170     307 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                                       EEEEEESTTSSHHHHHHHHHT..............STEEESSSTTSSSSEEEEEEEETTEE................ CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg..............ekaivsdkpgtTrdinegrvklkgke................ 47 
                                       ++++vG   +GK+t i +  +              +        +    +++++v+ +  +                
  gi|386002422|ref|YP_005920721.1| 170 KIVFVGVNGTGKTTSIAKVARylkdrgysivlaagD-------TFRAGAVEQIEVHAN--Klevklvkhrdgkdpaa 237
                                       589999999999999999996665554433333321.......233333333333311..11122222233344555 PP

                                       ...............EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEE CS
                          MMR_HSR1  48 ...............ielvDtpGliegaseekglgkaflalee...adlillvvd 84 
                                                      i+l+Dt+G ++   ++ +l ++++++ +    dl+++v +
  gi|386002422|ref|YP_005920721.1| 238 vifdaveyakahhrdIVLADTAGRLH---TNVNLMDQMKKIVRvvdPDLLIFVDE 289
                                       556666666666666********666...44455555555555311577777644 PP

>> SurA_N  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00022      0.13       7      95 ..      80     166 ..      78     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                            SurA_N   7 vvnddvvl.qseldervkevkkqlakqgkqlPpeavLerqvlerlilekiqlqeaektgirvddeelnqaiaeiAke 82 
                                       + +++vvl +++l++ + e+++ l +++ +lP ++++   v   l+ +k ++  a++   ++ +e+l+ a+ ++  e
  gi|386002422|ref|YP_005920721.1|  80 IFEQEVVLdEKDLKDPLWELEMALLESDVALPVAETIVASVKGELVGKKKKIR-ADTG--EIVEEALRSALLQVLSE 153
                                       567889884579**********************************9886664.4443..57799************ PP

                            SurA_N  83 Nkltldqlraala 95 
                                       N+ ++d++ a+ +
  gi|386002422|ref|YP_005920721.1| 154 NRFDVDEFIAKAE 166
                                       *******988765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0003      0.18       2      22 ..     168     188 ..     167     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                            AAA_24   2 klkiliyGpsgiGKTtlakel 22 
                                       ++ki+ +G +g+GKTt++++ 
  gi|386002422|ref|YP_005920721.1| 168 PVKIVFVGVNGTGKTTSIAKV 188
                                       689***************998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.7   2.8e+03      80      97 ..     142     159 ..     121     165 .. 0.81
   2 ?   10.6   0.0   0.00069      0.41       2      75 ..     171     244 ..     170     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHSSEEE.. CS
                             AAA_5  80 evlnsLlslleerrllle 97 
                                       +  ++Ll++l+e+r++++
  gi|386002422|ref|YP_005920721.1| 142 ALRSALLQVLSENRFDVD 159
                                       455689999999999876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00069
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                       ++ vG  GtgK++ + ++a+ l  r + +v+   dt ++  + ++e+   + + v+ +  r ++ ++ +++D ve
  gi|386002422|ref|YP_005920721.1| 171 IVFVGVNGTGKTTSIAKVARYLkDRGYSIVLAAGDTFRAGAVEQIEVHANKLE-VKLVKHRDGKDPAAVIFDAVE 244
                                       6789******************9999999999999999888888888443333.333334456666666666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00045      0.27       4     123 ..     172     280 ..     169     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke....ekkkkkeafeklssfinnlse 76 
                                       v+V Gv GtGKt    +++  l   +++ ++++l     +++   e+++ ++     k  k ++ ++++++i +   
  gi|386002422|ref|YP_005920721.1| 172 VFV-GVNGTGKTTSIAKVARYL---KDRGYSIVLAAGDTFRAGAVEQIEVHAnkleVKLVKHRDGKDPAAVIFD--- 241
                                       444.9****************9...6677778888888888888788877773333333344444555555554... PP

                           DUF2075  77 fkkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkr.a 123
                                          a e ++  + d+v+ D A rl t      + +  +q+k++++  +
  gi|386002422|ref|YP_005920721.1| 242 ---AVEYAKAHHRDIVLADTAGRLHT------NVNLMDQMKKIVRVvD 280
                                       ...55889999**************9......3333556666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.77u 0.41s 00:00:01.18 Elapsed: 00:00:00.59
# Mc/sec: 1862.76
//
Query:       gi|386002423|ref|YP_005920722.1|  [L=248]
Description: hypothetical protein Mhar_1741 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-89  298.6   0.0    2.2e-89  298.4   0.0    1.0  1  PIN_5     PINc domain ribonuclease


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.4   0.0   1.2e-93   2.2e-89       1     205 [.       8     223 ..       8     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 298.4 bits;  conditional E-value: 1.2e-93
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwl 76 
                                       rfvlDT+altd+ ++e  g+++++e+++++ld++aearl+lgiscyip psvy+E++ef+++++++e v++k+dtwl
  gi|386002423|ref|YP_005920722.1|   8 RFVLDTTALTDSLAWEGEGCTNICEGMNAILDCVAEARLHLGISCYIPyPSVYNEIREFVHHNGCDEAVLIKVDTWL 84 
                                       8**************************************************************************** PP

                             PIN_5  77 vkkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekee..........eeeevgelikklRe 143
                                       vk +pdryevkip++++yeyv ++r+rinkG++vaEea++ea+ ++ +++ ee          e+e vg +++k+Re
  gi|386002423|ref|YP_005920722.1|  85 VKMTPDRYEVKIPSKVFYEYVYYMRSRINKGMNVAEEAIWEAVGRCIAMSAEEgdlsafkdeiEREAVGGIVRKFRE 161
                                       ***********************************************99755557899999999************* PP

                             PIN_5 144 kYrealRkGilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeyl 205
                                       kYr+alR+GilDsa+D+d+llLAkEL+aav+s+D Gi++wae+lGlr++ea++fp ++keyl
  gi|386002423|ref|YP_005920722.1| 162 KYRSALRYGILDSAPDIDILLLAKELNAAVISQDLGIQRWAEQLGLRYLEARTFPVMIKEYL 223
                                       *************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1383.98
//
Query:       gi|386002424|ref|YP_005920723.1|  [L=241]
Description: hypothetical protein Mhar_1742 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-81  273.0   0.1    1.9e-81  272.9   0.1    1.0  1  NRD1_2    NrpR regulatory domains NRD1 and 2


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.9   0.1     1e-85   1.9e-81       3     237 ..       9     235 ..       7     236 .. 0.99

  Alignments for each domain:
  == domain 1  score: 272.9 bits;  conditional E-value: 1e-85
                                       -HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE........EEEE CS
                            NRD1_2   3 fviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegekelevpegkvgia 79 
                                       f +s+ie+l+++v+fdp++++G++i+N+sl+d + l+ +l+i+++vi+sgl+vs+++k++  g+k        ++i+
  gi|386002424|ref|YP_005920723.1|   9 FSLSRIENLMHQVSFDPRRMEGEIITNTSLVDLKMLDPTLRIFRDVIESGLAVSPYLKVETLGTK--------AKIM 77 
                                       889*************************************************************9........**** PP

                                       EE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEE CS
                            NRD1_2  80 tvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlR 156
                                         CSiti gvLlk+G+p++p+ GG++e+ d+epvrFt++++Y+ t+idP++v+is++lTsv e++etg+g+il+nl+
  gi|386002424|ref|YP_005920723.1|  78 SACSITISGVLLKAGVPIRPRGGGVIEVIDREPVRFTDMLMYWATTIDPIDVLISQELTSVVEMMETGSGRILGNLQ 154
                                       ***************************************************************************** PP

                                       EEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEG CS
                            NRD1_2 157 eipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidi 233
                                       e p++a e++ee l+ l +ag+sgvl++g+pn +vlgv+ve+++vg+ +vgG+n +aa+  +gi++e++++s+l++i
  gi|386002424|ref|YP_005920723.1| 155 EAPMIAAERIEERLDLLAEAGFSGVLDLGDPNMNVLGVSVERDHVGLSLVGGTNIVAAAMSHGIRIETESISSLTKI 231
                                       ***************************************************************************** PP

                                       GGSE CS
                            NRD1_2 234 selk 237
                                       +e++
  gi|386002424|ref|YP_005920723.1| 232 QEMT 235
                                       ***7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1354.20
//
Query:       gi|386002425|ref|YP_005920724.1|  [L=572]
Description: PHP C-terminal domain-containing protein, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-23   81.3   2.7    1.9e-22   79.4   0.3    3.0  3  HHH_8            Helix-hairpin-helix domain
    2.6e-20   72.3   0.0    6.7e-20   71.0   0.0    1.8  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    8.6e-12   45.5   1.9    3.3e-07   30.8   0.0    3.2  3  HHH_5            Helix-hairpin-helix domain
      2e-07   31.4   0.2    4.2e-07   30.4   0.2    1.5  1  PHP              PHP domain
    6.2e-06   25.8   3.4      0.032   14.1   0.2    3.7  4  HHH              Helix-hairpin-helix motif
    9.1e-06   25.9   0.0    2.3e-05   24.6   0.0    1.7  1  DNA_pol_B_palm   DNA polymerase beta palm
     0.0012   19.1   0.9        1.8    8.9   0.0    3.7  4  HHH_3            Helix-hairpin-helix motif
     0.0076   16.3   0.1       0.12   12.5   0.0    2.8  3  HHH_2            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.027   14.1   0.1    1.4  1  Cu-oxidase_4     Multi-copper polyphenol oxidoreductase lacca
      0.014   15.5   0.2        2.9    8.0   0.0    2.9  2  DUF3701          Phage integrase protein
      0.015   15.5   0.0        5.8    7.2   0.0    2.6  2  Cdd1             Pathogenicity locus
      0.028   14.2   0.0       0.22   11.4   0.0    2.4  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.098   13.0   0.0       0.33   11.3   0.0    1.9  2  NTP_transf_2     Nucleotidyltransferase domain
       0.11   12.4   0.1       0.56   10.1   0.0    2.0  2  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.3   1.5e-25   1.9e-22       1      68 []       3      72 ..       3      72 .. 0.96
   2 ?   -0.3   0.0       1.1   1.4e+03      46      62 ..      91     106 ..      76     111 .. 0.74
   3 ?   -2.2   0.0       4.3   5.5e+03      36      62 ..     117     141 ..     113     144 .. 0.64

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.5e-25
                                      HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH..TTHCTTSTT--HHHHHHHHHHHH CS
                             HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl..eeeltklpgiGkkiaakieeile 68
                                      N+e+a++L+e+ dllel+ge++f+v aYrrAar++e+++e+++ +  ++el+++pg+Gk+ia ki e+le
  gi|386002425|ref|YP_005920724.1|  3 NEEVARLLREMGDLLELRGESSFKVVAYRRAARTVESMKEDLEAIagRGELEAIPGVGKAIAGKISEFLE 72
                                      99*******************************************6555*******************97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                       TTHCTTSTT--HHHHHH CS
                             HHH_8  46 eeeltklpgiGkkiaak 62 
                                       + el ++ g+G+k+   
  gi|386002425|ref|YP_005920724.1|  91 A-ELLQISGLGPKTVSM 106
                                       3.4999******99765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.3
                                       CC-SS-HHHHTTHCTTSTT--HHHHHH CS
                             HHH_8  36 ealpeeitsleeeltklpgiGkkiaak 62 
                                       ++l+ + ++ + ++++lp +G+   + 
  gi|386002425|ref|YP_005920724.1| 117 AELEVAARE-H-RVRRLPRMGPTSEKN 141
                                       555544444.4.599999999876665 PP

>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   5.2e-23   6.7e-20       2      70 .]     254     315 ..     253     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 5.2e-23
                                       HHHHHS-HHHHHHHHHHHHCTTEEEETTEEE.......ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
                   DNA_pol_B_thumb   2 llyfTGsktFnrdlRrlakkkglkLnssglrdekgkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                       ++yfTGsk++n++lR+ a +kg++L+++ l+       + +dge + +++E+d++++Lg+++ipPe Re
  gi|386002425|ref|YP_005920724.1| 254 IQYFTGSKEHNVKLRHVALSKGYSLSEYSLT-------RLADGEELFFDREEDLYHHLGMDWIPPEIRE 315
                                       68*****************************.......9****************************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.2   0.00012      0.16      16      56 ..      28      72 ..      14      73 .. 0.66
   2 !   30.8   0.0   2.6e-10   3.3e-07       3      52 ..      92     143 ..      90     151 .. 0.86
   3 ?   -1.7   0.0       3.7   4.8e+03       4      11 ..     172     179 ..     165     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                      HHHHTTT--SHH....HHHH.S-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5 16 lallsaGiesve....dlaa.adveeLakipGiGkktAeriilelk 56
                                      +a  +a  ++ve    dl a a + eL +ipG+Gk  A +i + l+
  gi|386002425|ref|YP_005920724.1| 28 VAYRRA-ARTVEsmkeDLEAiAGRGELEAIPGVGKAIAGKISEFLE 72
                                      555555.5666633334444345789***************99885 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.6e-10
                                       HHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAerii 52 
                                       eLl++sG+Gpkt+  l+ + G+++v++l  a++ +++ ++p +G+   ++i+
  gi|386002425|ref|YP_005920724.1|  92 ELLQISGLGPKTVSMLHQKlGVSTVAELEVAAReHRVRRLPRMGPTSEKNIL 143
                                       8******************99*******87765269***************5 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.7
                                       HHTSTT-- CS
                             HHH_5   4 LlsvsGiG 11 
                                       L +v+GiG
  gi|386002425|ref|YP_005920724.1| 172 LRKVEGIG 179
                                       44566665 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2   3.3e-10   4.2e-07       1     119 [.     340     462 ..     340     503 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.3e-10
                                       EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT............HHHHHHHHHHHHTTTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf............gyvefykaakkkykagikpiiGle 65 
                                       dlHvH++ s    ++  ee+v++a+ lg++ +a+ Dh++              + +e ++ + ++ ++g+ +++G+e
  gi|386002425|ref|YP_005920724.1| 340 DLHVHSDWSDGRHSI--EEMVRAAQGLGYEYMAMCDHSHGLgianglaedrlrEKMELIRGL-NEAAEGFAILVGTE 413
                                       89*******443566..**********************999********888445555555.244689******** PP

                                       .......................E....EHHHHHHHHHHHHH..........HHHHHHS CS
                                       xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  66 ayvaddsekerpshl.....tllaknqeGyknllkllskaylegfyrkpridkellekh 119
                                       + +  d++ + p ++     +++a  ++Gy++  ++++++ +           ++ ++h
  gi|386002425|ref|YP_005920724.1| 414 VEIRADGKLDYPDEIlsecdVVVASVHSGYHQREREMTNRII----------SAMESEH 462
                                       ******995555554111123444445556655555555555..........4444444 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   2.5e-05     0.032      12      29 ..      52      69 ..      42      70 .. 0.92
   2 !   10.2   0.0   0.00043      0.55       7      25 ..      87     105 ..      81     109 .. 0.81
   3 ?   -1.0   0.0       1.5   1.9e+03      13      20 ..     172     179 ..     172     180 .. 0.89
   4 ?   -3.2   0.0       7.4   9.5e+03      20      28 ..     226     234 ..     226     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                                      HHHTSTT-SHHHHHHHHH CS
                               HHH 12 eLlalPGVGpktAeaIls 29
                                      eL+a+PGVG++ A++I +
  gi|386002425|ref|YP_005920724.1| 52 ELEAIPGVGKAIAGKISE 69
                                      9**************965 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                                       TSSHHHHHTSTT-SHHHHH CS
                               HHH   7 pasreeLlalPGVGpktAe 25 
                                       p  ++eLl+++G Gpkt  
  gi|386002425|ref|YP_005920724.1|  87 PPGLAELLQISGLGPKTVS 105
                                       66789************76 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.5
                                       HHTSTT-S CS
                               HHH  13 LlalPGVG 20 
                                       L +++G+G
  gi|386002425|ref|YP_005920724.1| 172 LRKVEGIG 179
                                       789****9 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 7.4
                                       SHHHHHHHH CS
                               HHH  20 GpktAeaIl 28 
                                       Gp +A +I 
  gi|386002425|ref|YP_005920724.1| 226 GPTKASVIV 234
                                       9****9997 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.8e-08   2.3e-05       8      55 ..     162     209 ..     155     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SEESSEEEEEEBTTBSTT CS
                    DNA_pol_B_palm   8 ealealvkkaakeldpevevivcGSYRRgaessGDvDvlitkkdakse 55 
                                         l++ +  ++++++   +++v+GS RRg+e+ GD+D+l t +  +++
  gi|386002425|ref|YP_005920724.1| 162 LPLAQEILGHLRKVEGIGDLNVAGSLRRGRETVGDIDILATSPAPEAA 209
                                       55677777888888888999*********************9987764 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.5     2e+03      29      45 ..      26      42 ..      18      52 .. 0.80
   2 !    8.9   0.0    0.0014       1.8      14      47 ..      51      83 ..      47      85 .. 0.86
   3 ?    5.9   0.0     0.012        16      44      63 ..      91     110 ..      89     111 .. 0.83
   4 ?   -2.1   0.0       3.7   4.7e+03      46      54 ..     172     180 ..     169     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                             HHH_3 29 nIvayReknGpfksree 45
                                      ++vayR +   ++s++e
  gi|386002425|ref|YP_005920724.1| 26 KVVAYRRAARTVESMKE 42
                                      789***99999999864 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                             HHH_3 14 eeLqklpGlgpklAknIvayReknGpfksreeLl 47
                                       eL+ +pG+g+++A +I ++  + G+++ r+ Ll
  gi|386002425|ref|YP_005920724.1| 51 GELEAIPGVGKAIAGKISEFL-ETGRIEARDRLL 83
                                      59*****************98.778888888876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.012
                             HHH_3  44 eeLlkvkglgpktfeqlagf 63 
                                        eLl+++glgpkt+  l ++
  gi|386002425|ref|YP_005920724.1|  91 AELLQISGLGPKTVSMLHQK 110
                                       699*********99887765 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.7
                             HHH_3  46 Llkvkglgp 54 
                                       L kv+g+g+
  gi|386002425|ref|YP_005920724.1| 172 LRKVEGIGD 180
                                       556666654 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   9.6e-05      0.12      32      57 ..      48      73 ..      32      78 .. 0.83
   2 ?   -0.3   0.0      0.94   1.2e+03      35      52 ..      91     108 ..      85     119 .. 0.80
   3 ?   -2.3   0.0       3.8   4.9e+03      35      45 ..     170     180 ..     164     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-05
                             HHH_2 32 asleeLlevddiGeeiAqsivefFen 57
                                      a   eL +++++G+ iA +i ef+e+
  gi|386002425|ref|YP_005920724.1| 48 AGRGELEAIPGVGKAIAGKISEFLET 73
                                      55679******************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.94
                             HHH_2  35 eeLlevddiGeeiAqsiv 52 
                                        eLl++ + G+++ +  +
  gi|386002425|ref|YP_005920724.1|  91 AELLQISGLGPKTVSMLH 108
                                       79********99866555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.8
                             HHH_2  35 eeLlevddiGe 45 
                                         L +v++iG+
  gi|386002425|ref|YP_005920724.1| 170 GHLRKVEGIGD 180
                                       56889999998 PP

>> Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.1e-05     0.027     104     208 ..     434     534 ..     428     543 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                       SEEEEEEE-HHHHHHTHHHHHHHHHCSTT--GGGEEEEE-SB--T.TT-EEE.HHHHHHHHHHSGGGGEEEEETTEE CS
                      Cu-oxidase_4 104 kvvaaaHaGwrGlvagvlektveamkelgakpedilaaiGPsIgp.ecyeVg.eevaeafeaadpeaaaaaeeegka 178
                                        vva +H+G      ++ +++++am++   + + i    G  Ig+ e+yeV+ e+v ea +++ +++   + +++  
  gi|386002425|ref|YP_005920724.1| 434 VVVASVHSGYHQREREMTNRIISAMES--EHVDVIGHPTGRKIGErEAYEVDlERVLEAAARTGTAM-EINAHPS-- 505
                                       58***********************88..5667777889****97369***8355566665444333.3333344.. PP

                                       EE-HHHHHHHHHHHTT-..SEEEE---BTT CS
                      Cu-oxidase_4 179 ylDLaalarlqLeeaGvkeenieasglCTv 208
                                        lDL     ++ +e+Gv + +i+   + T+
  gi|386002425|ref|YP_005920724.1| 506 RLDLNDRWSRRARELGV-KLAINTDAHSTC 534
                                       4****************.666777666665 PP

>> DUF3701  Phage integrase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0023       2.9      24      71 ..      28      73 ..      25      92 .. 0.80
   2 ?    4.4   0.0     0.031        40      22      65 ..     101     142 ..      96     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                           DUF3701 24 varrLaaagvktLaeLiarinrrgkrWwravprlGaakArrieafLaa 71
                                      va r aa+ v+ + e +++i  rg    +a+p++G+a A +i +fL++
  gi|386002425|ref|YP_005920724.1| 28 VAYRRAARTVESMKEDLEAIAGRG--ELEAIPGVGKAIAGKISEFLET 73
                                      566667778888888888888888..589*****************86 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                           DUF3701  22 prvarrLaaa.gvktLaeLiarinrrgkrWwravprlGaakArri 65 
                                       p++++ L+++ gv t+aeL ++ +  +    r +pr+G+++ ++i
  gi|386002425|ref|YP_005920724.1| 101 PKTVSMLHQKlGVSTVAELEVAAREHR---VRRLPRMGPTSEKNI 142
                                       77788887644********99988888...99******9987766 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.016        21       7      23 ..      52      68 ..      47      78 .. 0.86
   2 ?    7.2   0.0    0.0045       5.8       5      37 ..      90     123 ..      86     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                              Cdd1  7 elqdiPniGkalaedlv 23
                                      el+ iP++Gka+a ++ 
  gi|386002425|ref|YP_005920724.1| 52 ELEAIPGVGKAIAGKIS 68
                                      799**********9876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0045
                              Cdd1   5 lkelqdiPniGkalaedlv.elGirsveelkged 37 
                                       l+el +i + G+++ ++l+ +lG+++v+el+   
  gi|386002425|ref|YP_005920724.1|  90 LAELLQISGLGPKTVSMLHqKLGVSTVAELEVAA 123
                                       7899**************979********98665 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.3e+03       3      16 ..      53      66 ..      52      68 .. 0.83
   2 ?   11.4   0.0   0.00017      0.22       2      29 ..      92     120 ..      91     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                   DNA_pol_lambd_f  3 FtkvyGVGpktAkk 16
                                      +  + GVG ++A k
  gi|386002425|ref|YP_005920724.1| 53 LEAIPGVGKAIAGK 66
                                      66799*****9965 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                   DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyak.Girtledlr 29 
                                       +++++ G Gpkt +++++k G+ t+ +l 
  gi|386002425|ref|YP_005920724.1|  92 ELLQISGLGPKTVSMLHQKlGVSTVAELE 120
                                       689**********************9986 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.33       4      66 ..     168     223 ..     165     254 .. 0.73
   2 ?   -2.7   0.0         6   7.7e+03      32      74 ..     430     466 ..     429     485 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                       HHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEEC CS
                      NTP_transf_2   4 lleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleel 66 
                                       +l  l++ e++ ++ + GS +rG  +   DiD+l ++p++          ++ + i+ ++e l
  gi|386002425|ref|YP_005920724.1| 168 ILGHLRKVEGIGDLNVAGSLRRGRET-VGDIDILATSPAPE------AAIRAFVSIPVVEEVL 223
                                       556666666799999********955.38***********3......4445555555555544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                                       SSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE CS
                      NTP_transf_2  32 SDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv 74 
                                       S+ D++v + ++ +    ++++e   +ii++ e+    +vd++
  gi|386002425|ref|YP_005920724.1| 430 SECDVVVASVHSGY---HQREREMTNRIISAMES---EHVDVI 466
                                       56677777777766...34444444444444444...444444 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 ?   -1.0   0.0       1.1   1.4e+03      17      60 ..      22      65 ..      16      66 .. 0.69
   2 ?   10.1   0.0   0.00043      0.56      56      91 ..     427     464 ..     419     498 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                                      C-T-EEEEEETTHHHCHHHHCTTTCEEEE..--TT-CCHHHHHHTT CS
                    NAD_binding_10 17 rgghevtalvRnpeklaeleaeeglevve..gdvtdvedlaealkg 60
                                      ++ ++v+a+ R +  +++++  e le++   g+++    + +a++g
  gi|386002425|ref|YP_005920724.1| 22 ESSFKVVAYRRAARTVESMK--EDLEAIAgrGELEAIPGVGKAIAG 65
                                      44799****99999999887..556555422666666666666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00043
                                       HHHTT-SEEEES---TCC..HHHHHHHHHHHHHHCT-- CS
                    NAD_binding_10  56 ealkgadaVvsalggggk..deegaknivdaakeagvk 91 
                                       e l+ +d+Vv+++ +g    ++e++++i+ a++ ++v 
  gi|386002425|ref|YP_005920724.1| 427 EILSECDVVVASVHSGYHqrEREMTNRIISAMESEHVD 464
                                       67899*******966555448888**********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3326.84
//
Query:       gi|386002426|ref|YP_005920725.1|  [L=156]
Description: hypothetical protein Mhar_1744 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.099   12.7   0.1        0.2   11.8   0.1    1.4  2  I-set     Immunoglobulin I-set domain


Domain annotation for each model (and alignments):
>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.75   1.3e+04      12      27 ..      81      96 ..      80     100 .. 0.72
   2 ?   11.8   0.1   1.1e-05       0.2      63      90 .]     119     146 ..     117     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.75
                                      EETTS-EEEEEEEECS CS
                             I-set 12 vseGesvelectveGe 27
                                      v+ Ge   l+ +v+G+
  gi|386002426|ref|YP_005920725.1| 81 VRPGEGTVLRWRVSGV 96
                                      5667777788888876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.1e-05
                                       B-GGGGEEEEEEEEETSEEEEEEEEEEE CS
                             I-set  63 vevsDeGkYtckatnsagkaeakaeLkV 90 
                                       v+++++  Yt++a n ag++ea+a+++V
  gi|386002426|ref|YP_005920725.1| 119 VQPEETTVYTLTAINAAGEDEARATVEV 146
                                       8899999******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 922.69
//
Query:       gi|386002427|ref|YP_005920726.1|  [L=598]
Description: KamA family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-07   30.1   0.0    1.5e-06   28.7   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.036   14.2   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.7e-10   1.5e-06       3     147 ..     307     451 ..     305     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-10
                                       EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla... 74 
                                       ++  C++ C++C+r++   ++  ++++ s  ei   +++++ e+     v+++gg+pl+ +d   + + l +la   
  gi|386002427|ref|YP_005920726.1| 307 PYDSCPQICVYCQRNWEiTSPFMPSAMASEAEIDGALDWYA-EHEaMMDVLVTGGDPLVMADG-LIDKILGRLAemd 381
                                       6778*************99999******************7.4444*************9776.3333344444566 PP

                                       .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvd 147
                                           iri+  t+ t+p  ++ e+l e    +  lg  +++   ++ ++ +++   e++ea++++r +g++ v++
  gi|386002427|ref|YP_005920726.1| 382 hILSIRIATRTPVTVP-QRITEELCEIFASYHDLGRRSLSVV-THFMH-PREVTAETVEAIRRIRVLGMD-VYN 451
                                       7789999999999999.6666666665555557777777774.55555.889999999*****9999998.554 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     4e-06     0.036       7      88 ..     310     391 ..     307     411 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-06
                           Fer4_14   7 gCnlsCkgCdnketwks..elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       +C+  C+ C ++ +  s        +e +++  l d ++++ ++  + +tGG+PL  + +  ++k++ rl e  + +
  gi|386002427|ref|YP_005920726.1| 310 SCPQICVYCQRNWEITSpfMPSAMASEAEIDGAL-DWYAEHEAMMDVLVTGGDPL-VMADGLIDKILGRLAEMDHIL 384
                                       79999****9655444422445566667777777.55555555666*********.558899999999999998888 PP

                           Fer4_14  82 kiwletn 88 
                                       +i++ t 
  gi|386002427|ref|YP_005920726.1| 385 SIRIATR 391
                                       8888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 3557.54
//
Query:       gi|386002428|ref|YP_005920727.1|  [L=513]
Description: Extracellular solute-binding protein, family 5 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-77  259.5   0.1    8.2e-77  258.7   0.1    1.4  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.7   0.1   4.6e-81   8.2e-77       2     368 ..      76     422 ..      75     431 .. 0.92
   2 ?   -2.5   0.0       0.1   1.8e+03     277     330 ..     441     505 ..     423     510 .. 0.69

  Alignments for each domain:
  == domain 1  score: 258.7 bits;  conditional E-value: 4.6e-81
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       +vpaLAe+ we ++   +y+f+LR+gv+++DG+p++A+Dvvf+ e+++d+++++  +        i+++ea+dd+tv
  gi|386002428|ref|YP_005920727.1|  76 YVPALAER-WE-MEGDDVYIFHLRDGVTWHDGEPFNADDVVFTVEYTKDHPYQWVDSAI------IERAEALDDLTV 144
                                       79******.57.888889************************************99666......58********** PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTT.SE-BSSSEEEEE..EETTT.EEEEEE-TTSTTTSCSS CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtne.kpvgtGPYklke..fkpgq.kivlernpdYwgggkpk 151
                                       ++tl++p+a+fl  +  + + ++++ +++ dd+ ++  + ++vgtGPY+lk   +k  q + ++++ + Y+  g pk
  gi|386002428|ref|YP_005920727.1| 145 KLTLSAPYAPFLDQVGGTLPILPEHIWSEVDDPVNYREQdALVGTGPYTLKVedYKMAQgTYRYVAYDGYY-LGSPK 220
                                       ************************99999999999977615788****887655888776899*******9.***** PP

                                       SSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHH CS
                         SBP_bac_5 152 ldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAls 228
                                       ++++ f  i ++ ++aa+l++G +  +a++ p++i ql+ +  +      +  + + l++N++k+p++dkr+RqAl+
  gi|386002428|ref|YP_005920727.1| 221 VEELLFVKI-SAPNAAAELLQGRV-NMASIEPEMIGQLEGSFEILS--VPAHWWNYKLMINHQKEPLSDKRFRQALA 293
                                       *********.**************.999*********988888777..778888888******************** PP

                                       HHS-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEE CS
                         SBP_bac_5 229 yAiDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltllla 304
                                       yAiDre++v+++ +gy+ ++    +p+  +++++e++++y ++dp++A++lL++ Gy++++          + +l+ 
  gi|386002428|ref|YP_005920727.1| 294 YAIDREKLVEIAGRGYGLAGSPGfIPSDNDWYNPEMDDYY-PHDPAEAEELLADMGYDGRK----------IEVLIK 359
                                       ************9999988777658888899999988876.57*****************8..........****** PP

                                       TTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHH CS
                         SBP_bac_5 305 sgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnp 368
                                       +g++++++i eli ++l ++Gi+v+++t+++ ++ +++v ++dfd++++g g+  +dp++   +
  gi|386002428|ref|YP_005920727.1| 360 GGDTTAERIGELIEADLLAVGINVDLRTMES-KAVDSKVGEWDFDLAVSGHGGVIGDPNFLAGN 422
                                       *******************************.99999********************9987655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.1
                                       HHHHHTT-BCSSTSCEETC...........EEEEEEEEETTSHHHH.HHHHHHHHHHHHTTEEEEE CS
                         SBP_bac_5 277 klLkeaGykdgdggglrek...........klkltlllasgspaek.aiaeliqqqlkkiGikvev 330
                                       +lL+e   +++ ++ +re+           ++ ltl+++ +  a++ ++a +++ +  ++Gi + +
  gi|386002428|ref|YP_005920727.1| 441 ALLEEQVKETD-EDSRREMideaqvlyaedVPALTLFYTESFVAHDgQVALYYTHNGMALGIPIAL 505
                                       66666655554.566677777778888888888888888888888888888888888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3308.12
//
Query:       gi|386002429|ref|YP_005920728.1|  [L=180]
Description: hypothetical protein Mhar_1747 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-17   63.4   0.0    2.9e-17   63.1   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain
    3.2e-05   23.8   0.0    7.1e-05   22.7   0.0    1.5  1  DUF447         Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   3.2e-21   2.9e-17       4     134 ..      12     142 ..       7     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 3.2e-21
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTT.TEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS... CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldP.plvafslrlpsstadalkeagefvinllsesqealadafsqksg 79 
                                       ++ pv++++t  +++ +++a+    +++ l P   +a++  l+++t+d+++e+gefv+n+   + ++ ++ +++  +
  gi|386002429|ref|YP_005920728.1|  12 LPMPVVLISTVSKEGVRNAAPWGCIMPI-LRPlDEIAIASWLKRDTLDNIRETGEFVVNVPTLEMAEEVEICARSFP 87 
                                       799*******88899999*********9.9999***************************99999999999999777 PP

                                       SCCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEE CS
                     Flavin_Reduct  80 prtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavk 134
                                         ++d+++ agl++++s ++++p ++g++a++eC++v+++      l+ig+Vv  +
  gi|386002429|ref|YP_005920728.1|  88 -PEVDEFEEAGLSPHPStKVAPPGIAGCVAWMECELVEEILRERFSLIIGRVVFLE 142
                                       .9***************88999*****************9999*********9765 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.9e-09   7.1e-05       3      96 ..      17     124 ..      17     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.9e-09
                                       EEEEEE-TT.-EEEEEEEEEE....SSSEEEEEEETTSHHHHHHHHHSEEEEEE--.....-HHHHHHHHHS---GG CS
                            DUF447   3 vivtTksek.rpnaaPiGviv....kgdkvvlrlfkgsrTleNllengelvinvtd.....Dpllfakaalgdlees 69 
                                       v+++T s++ ++naaP G i+      d++ ++ + +  Tl+N++e+ge+v+nv +      + + a+++  +++e 
  gi|386002429|ref|YP_005920728.1|  17 VLISTVSKEgVRNAAPWGCIMpilrPLDEIAIASWLKRDTLDNIRETGEFVVNVPTlemaeEVEICARSFPPEVDEF 93 
                                       799***************99988888899************************964222214455555554444433 PP

                                       GEEEETT.TC.TT...EETT-SEEEEEEEEE CS
                            DUF447  70 dfdsetk.pa.kia..vlksaeawvevevee 96 
                                       +     + p  k+a   +++++aw+e+e+ e
  gi|386002429|ref|YP_005920728.1|  94 EEAGLSPhPStKVAppGIAGCVAWMECELVE 124
                                       2222222234445467777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1026.97
//
Query:       gi|386002430|ref|YP_005920729.1|  [L=140]
Description: hypothetical protein Mhar_1748 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-28   98.5   0.0    3.3e-28   98.3   0.0    1.1  1  TrmO         tRNA-methyltransferase O
  ------ inclusion threshold ------
       0.25   11.3   1.3        3.2    7.8   0.1    2.3  2  ADH_N_assoc  Alcohol dehydrogenase GroES-associated


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   3.6e-32   3.3e-28       2     119 .]      19     129 ..      18     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 3.6e-32
                                       S-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS CS
                              TrmO   2 iPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpn 78 
                                       +P q++ +    +e+e+++e+    +l ++e+++hl+ll ++++++ +k   k  pp  +g+e+ GvfatRsp+Rpn
  gi|386002430|ref|YP_005920729.1|  19 APFQGRHSV-EVCEVEVFEEF--LPGLADVEGCTHLFLLRWLDRAD-RK-MLKAFPP-HDGKEH-GVFATRSPNRPN 88 
                                       688888877.689********..99******************993.22.3444455.567677.************ PP

                                       -EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HHHH CS
                              TrmO  79 piglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                       pigl vv+l +v+g +l+v+++D+l+gtp+lDiKP ++++D
  gi|386002430|ref|YP_005920729.1|  89 PIGLGVVELLDVSGGRLRVRELDALEGTPLLDIKPRFSEVD 129
                                       ***********************************998887 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00036       3.2       6      18 ..      21      33 ..      21      33 .. 0.92
   2 ?    2.4   0.2     0.017   1.6e+02      13      21 ..     127     135 ..     127     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00036
                       ADH_N_assoc  6 yqGpkdVrVeeVP 18
                                      +qG+++V+V eV+
  gi|386002430|ref|YP_005920729.1| 21 FQGRHSVEVCEVE 33
                                      7********9996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.017
                       ADH_N_assoc  13 rVeeVPDPk 21 
                                       +V++ PD++
  gi|386002430|ref|YP_005920729.1| 127 EVDNIPDAT 135
                                       7******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 827.88
//
Query:       gi|386002431|ref|YP_005920730.1|  [L=114]
Description: hypothetical protein Mhar_1749 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.18   11.9   0.0    1.7  2  Cuticle_1  Crustacean cuticle protein repeat
       0.13   12.8   0.0       0.39   11.2   0.0    1.8  2  ImmE5      Colicin-E5 Imm protein


Domain annotation for each model (and alignments):
>> Cuticle_1  Crustacean cuticle protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18       6      19 ..      23      36 ..      22      47 .. 0.89
   2 ?   -2.9   0.0      0.85   7.7e+03      14      18 ..      98     102 ..      96     105 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                         Cuticle_1  6 itpDGtnvqfthgv 19
                                      ++pDG n++f+++ 
  gi|386002431|ref|YP_005920730.1| 23 VYPDGVNRHFPQDK 36
                                      89**********96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.85
                         Cuticle_1  14 qfthg 18 
                                       q++ g
  gi|386002431|ref|YP_005920730.1|  98 QLPDG 102
                                       55554 PP

>> ImmE5  Colicin-E5 Imm protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.4e-05      0.39      17      52 ..      36      74 ..      32      92 .. 0.75
   2 ?   -1.5   0.0      0.41   3.7e+03      40      55 ..      90     105 ..      85     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                             ImmE5 17 krnlfigriegGhwl...npGfrPdGnaswdgksklvde 52
                                      krnl+i ++  G+w    + G  Pd +++++ +  l de
  gi|386002431|ref|YP_005920730.1| 36 KRNLPIIMMANGDWTaeaVIGSPPDHDMEFKLYAILADE 74
                                      9*************8222458889999998877766655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                             ImmE5  40 naswdgksklvdeski 55 
                                       n sw g ++l d ++i
  gi|386002431|ref|YP_005920730.1|  90 NESWPGLEQLPDGAEI 105
                                       5677777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 643.07
//
Query:       gi|386002432|ref|YP_005920731.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002432|ref|YP_005920731.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002432|ref|YP_005920731.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002432|ref|YP_005920731.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002432|ref|YP_005920731.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002432|ref|YP_005920731.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1930.56
//
Query:       gi|386002433|ref|YP_005920732.1|  [L=124]
Description: erythromycin esterase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 798.53
//
Query:       gi|386002434|ref|YP_005920733.1|  [L=208]
Description: nicotinamidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-24   86.7   0.0    3.8e-24   85.8   0.0    1.4  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   2.1e-28   3.8e-24       2     175 .]       7     206 ..       6     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 2.1e-28
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvhe................leevkgdlde 62 
                                       +l+v+D+qndf+++g+ ++++ + +++ in   +++      v++t+d h+                 + +   + +
  gi|386002434|ref|YP_005920733.1|   7 VLIVVDVQNDFCPGGALQIKDGDSIIPLINGIMERFD----LVVATQDWHPknqvsfasnnpgkniyDQINISGIAQ 79 
                                       69**********************************6....499999999999999999999999877777778899 PP

                   Isochorismatase  63 rkaaphfkpgttgaelvpelaplegdvvvdKt......rfsaf......agtdldeiLkelgiktivlaGiatdvCV 127
                                         ++ h+++gt gae++++l   +   ++ K        +saf       +t+l  +Lk+l++++i ++G+atd+CV
  gi|386002434|ref|YP_005920733.1|  80 TLWPDHCIQGTKGAEFHDDLDLSKFSLILRKGmnplvdSYSAFiendrnTETGLAGYLKALKVREIFICGLATDYCV 156
                                       99*******************99999999999999999*************************************** PP

                   Isochorismatase 128 eatardaldlGyevvvvsDAvaalspel..hdaalkrlkqafatvitted 175
                                         +a+d l+ G+++ v+ DA+ +++       a + ++k+++  vi+++d
  gi|386002434|ref|YP_005920733.1| 157 YYSAMDSLRYGFRCNVIIDATRGVDLPKgsIGAVVSEMKDKGISVISSDD 206
                                       ************************95553577888999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1203.72
//
Query:       gi|386002435|ref|YP_005920734.1|  [L=958]
Description: leucyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for 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-57  192.7   0.0    1.3e-43  149.2   0.0    3.1  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    9.4e-23   80.6   0.1      2e-10   40.0   0.0    2.9  2  tRNA-synt_1g   tRNA synthetases class I (M)
    1.1e-21   77.4   0.0      2e-21   76.6   0.0    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
      1e-07   31.7   0.0    2.1e-07   30.6   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    2.2e-06   27.2   0.0      0.001   18.5   0.0    2.6  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.021   15.3   0.1      0.073   13.6   0.0    1.9  2  DUF406         Protein of unknown function (DUF406)
      0.028   13.3   0.1      0.081   11.8   0.0    1.9  2  tRNA-synt_1f   tRNA synthetases class I (K)
       0.07   13.3   0.0         11    6.3   0.0    2.7  2  DUF1858        Domain of unknown function (DUF1858)
      0.094   13.4   0.1       0.32   11.7   0.1    1.9  1  RsbRD_N        RsbT co-antagonist protein rsbRD N-terminal do


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.0   6.5e-47   1.3e-43       1     305 [.      13     323 ..      13     328 .. 0.87
   2 !   38.3   0.0   2.5e-13     5e-10     320     601 ..     391     667 ..     371     668 .. 0.81

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 6.5e-47
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai. 76 
                                       k+++kW e++vf +e     ek++f ++++ Py +G+lH Gh  + t+ d+v ry+rm+G++vl+ +G+   G +i 
  gi|386002435|ref|YP_005920734.1|  13 KWQQKWSEAGVFSAE---PSEKEKFFITIPYPYLNGNLHAGHTRTFTIGDVVARYRRMRGENVLFPMGFHVTGTPIv 86 
                                       589**********99...8889****************************************************994 PP

                       tRNA-synt_1  77 ..eakvekk.lg.akekkerkklgreefrekv..rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevf 147
                                            v+++    +k  ++ +++  e f   +  +++++++  e + +++ +G s+D+ re  T d+ +++ +++ +
  gi|386002435|ref|YP_005920734.1|  87 glSELVKNRdPEiEKVYTQHHDIPLEVFATLTtpQAIVDYFRRESKAAMESIGYSIDWRREFTTTDPAYKKFIEWQY 163
                                       43223332212203334577899999998765337899*************************************** PP

                       tRNA-synt_1 148 vrladkgliyrgkklvnwstklktalselEveykdkkda..lihvafpladkeevklviaTTtPeTllgdtavavnp 222
                                         l   g + +g+++v w+++ + ++ + ++ + ++     +  ++f +++  +  l  aT +PeT++g t + vnp
  gi|386002435|ref|YP_005920734.1| 164 FILRGLGYVSKGSHPVRWCPNDENPVEDHDILKGEEATIidFALIKFRFDG--K-ILPCATLRPETVFGVTNLWVNP 237
                                       ******************************966665543113344555444..3.5789****************** PP

                       tRNA-synt_1 223 eldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaP 296
                                       e+ ++   + +e++i+ +   ++l+  + + +   ++ g +L+gk+v++pl++ ++ i+   +vd ++G+G+V   P
  gi|386002435|ref|YP_005920734.1| 238 EVVHAvarVGDETWIVSQEAFEKLTFTDRTVERIGEVVGGDLIGKKVKNPLTGAEVLILPASFVDPDNGSGIVMSVP 314
                                       *8887899999*************99998888888999*************************************** PP

                       tRNA-synt_1 297 ahdedDyev 305
                                       ah + Dy +
  gi|386002435|ref|YP_005920734.1| 315 AHAPYDYLA 323
                                       *******65 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.5e-13
                       tRNA-synt_1 320 dgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalka 394
                                       +g+l+e +++++g  v + ++ ++++l + ++     +++ +  +c  +   ++ ++ +qWf + ++   +  + + 
  gi|386002435|ref|YP_005920734.1| 391 HGVLKERTGKYAGTAVSKIKDVLLADLIAGNVAEVFYEFSETPVICRCGTRCVVKMVRDQWFLNYSDpqWKGRVSQC 467
                                       6999*************************999999999999988999999999***********9876577777777 PP

                       tRNA-synt_1 395 vekvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkaleke 468
                                       + +++++p+  ++++++ +   +d +  R +  G+ +p    +  ++ ++ ++  +   l++  ++   ++ +l  e
  gi|386002435|ref|YP_005920734.1| 468 LAQMRLIPEEIRTEFENKVDWLKDKACARRKGLGTNLPWdqeWLIESLGDSTIYMSYYILAK-YVNAGLAIDNLVPE 543
                                       88************************************544466666666555334333333.33333444444445 PP

                       tRNA-synt_1 469 akdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgse 545
                                       + d +  +kg+   + d          +p  t++   + +e++   +p d+ ++G D +   +   +   +a+   +
  gi|386002435|ref|YP_005920734.1| 544 FFDFIFLGKGDAAAVADL-------TGMPEETVK---RIREDFVYWYPVDLRSSGKDLVANHLLFFLYHHVAIYPPS 610
                                       555555666666555554.......345555555...347899999***************9999999999999888 PP

                       tRNA-synt_1 546 Pf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                        + + + v+g+v   eG+KmSKs+g  +     +++ gad+ Rl+++ +++ ++d ++
  gi|386002435|ref|YP_005920734.1| 611 LWpRAMAVNGFVS-LEGKKMSKSKGPLLTLRRAVEANGADVTRLYILsNAEHTQDADW 667
                                       5537788999996.68******************************999999999877 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0     1e-13     2e-10       2      81 ..      35     117 ..      34     198 .. 0.83
   2 !   36.7   0.0     1e-12     2e-09     289     371 ..     588     672 ..     565     687 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1e-13
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH...HTTS-HHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe...kegvtpeelvekvheeik 75 
                                       ++t + pY ng+lH Gh ++  ++D++aRy+r+rge+vlf  g    Gtpi    e   +++ + e++ ++ h++  
  gi|386002435|ref|YP_005920734.1|  35 FITIPYPYLNGNLHAGHTRTFTIGDVVARYRRMRGENVLFPMGFHVTGTPIVGLSElvkNRDPEIEKVYTQHHDIPL 111
                                       89************************************************976544111344444566666666666 PP

                                       HHHHHT CS
                      tRNA-synt_1g  76 elfkkl 81 
                                       e+f++l
  gi|386002435|ref|YP_005920734.1| 112 EVFATL 117
                                       666554 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 1e-12
                                       EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS- CS
                      tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkD 363
                                       gkd +  H +f+     +       p+++++++++ +egkK+SkS+g + + + a+e   ad+ R y++++a++++D
  gi|386002435|ref|YP_005920734.1| 588 GKDLVANHLLFFLYHHVAiyPPSLWPRAMAVNGFVSLEGKKMSKSKGPLLTLRRAVEANGADVTRLYILSNAEHTQD 664
                                       9***********9999997666678**************************************************** PP

                                       EEE-HHHH CS
                      tRNA-synt_1g 364 ldfswedf 371
                                       +d++ + +
  gi|386002435|ref|YP_005920734.1| 665 ADWRNDGV 672
                                       **988765 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   9.9e-25     2e-21       1     125 [.     705     818 ..     705     842 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 9.9e-25
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+ s+l+k + e+tea+e  + ++a++++++ ++ndl +wy +   +              + l+ vl+ ++rl+
  gi|386002435|ref|YP_005920734.1| 705 DRWMESQLQKRIIETTEALEAVQTRRAVQSAFYHMINDL-RWYQRRGGK--------------NRLRSVLDVWVRLM 766
                                       9**************************************.999665322..............3499********** PP

                       Anticodon_1  78 aPfmPfitEelwqr....eeeelgkkesimlaewpe.kaeelekeleeeevel 125
                                       aPf+P+++Ee+w++    e++ +gk+  i++a wpe ++e+ ++ + e + +l
  gi|386002435|ref|YP_005920734.1| 767 APFTPHVCEEIWEEmagvEAKAFGKDAYISRARWPEaAPEKIDAGA-EMAEDL 818
                                       ************99***999999************97766665555.223333 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   1.1e-10   2.1e-07      12     126 ..     208     321 ..     203     327 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.1e-10
                     tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalape..hplveklaekkkelaafieevkkksesereletkekeGvftg 86 
                                       i+f+++++   l   t rp+t+fGvt + + pe  h +++   e+    ++  e+++ ++++ +++ +    G   g
  gi|386002435|ref|YP_005920734.1| 208 IKFRFDGK--ILPCATLRPETVFGVTNLWVNPEvvHAVARVGDETWIVSQEAFEKLTFTDRTVERIGE-VVGGDLIG 281
                                       55666654..3777899*************99844444444444444444444555555544444444.3578899* PP

                     tRNA-synt_1_2  87 lkaihPitgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                        k+ +P+tg ++ i  a +v  + g+g vm+vPah   D+
  gi|386002435|ref|YP_005920734.1| 282 KKVKNPLTGAEVLILPASFVDPDNGSGIVMSVPAHAPYDY 321
                                       ***********************************98887 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0037       7.3      21      50 ..      45      74 ..      27      81 .. 0.88
   2 !   18.5   0.0   5.1e-07     0.001     207     295 ..     581     671 ..     570     677 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0037
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                       + h Gh+R++ + D+++r+ +++g +v f
  gi|386002435|ref|YP_005920734.1| 45 GNLHAGHTRTFTIGDVVARYRRMRGENVLF 74
                                      678********************9999987 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.1e-07
                                       SEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                        +d+ s G+DL+  h    l  + a +  + + +    ng++++eg+kmsks + ++t++ +++   + + Rl++ls
  gi|386002435|ref|YP_005920734.1| 581 PVDLRSSGKDLVANHLLFFLYHHVAIYPpSLWPRAMAVNGFVSLEGKKMSKSKGPLLTLRRAVEANGADVTRLYILS 657
                                       5899999*****99999999999999996778999999**********************************99876 PP

                                       S.-TTS-EEE-HHH CS
                      tRNA-synt_1e 283 a.hyrsqldfkeel 295
                                       + ++ +  d++++ 
  gi|386002435|ref|YP_005920734.1| 658 NaEHTQDADWRNDG 671
                                       41566666666655 PP

>> DUF406  Protein of unknown function (DUF406)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       5.6   1.1e+04      17      54 ..     654     690 ..     643     700 .. 0.75
   2 ?   13.6   0.0   3.6e-05     0.073       6      76 ..     858     925 ..     854     931 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.6
                                       -SS--STTEEEEEEE-SSHHHHHHHHHHHHHHHHHH.S CS
                            DUF406  17 tiidnsdcvaeveivaaseaeaeaalakltekAkaves 54 
                                        i++n + + + +   +  ++ ++++ ++ ++A+++  
  gi|386002435|ref|YP_005920734.1| 654 YILSNAEHTQDADWRNDGVEATRQQVVRFYNLAREI-I 690
                                       578888888888888888888888999999999987.3 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.6e-05
                                       -SSS-----SS-SS--STTEEEEEEE-SSHHHHHHHHHHHHHHHHHH.STT-.EEEE----TT-SEEEEEE CS
                            DUF406   6 eeaagcavdvgtiidnsdcvaeveivaaseaeaeaalakltekAkavesepveisseieeaedgveLkarf 76 
                                       ee+  + +dvg+i++     ++++ va++++ea + +++l++ A a +s+p +i++  +   +   L+ +f
  gi|386002435|ref|YP_005920734.1| 858 EEKEAGSLDVGSIMKK---AMALPEVASHKKEAPKYAQRLMKGAHALNSDPLQIDEFETLSRERRYLERTF 925
                                       77888999******95...799*********************************9999888888777766 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.5   2.9e+03      35      62 ..      45      72 ..      44      74 .. 0.90
   2 ?   11.8   0.0   4.1e-05     0.081     273     315 ..     621     661 ..     580     727 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                      tRNA-synt_1f 35 GliHiGnlrevltadlvaralrkrgeev 62
                                      G +H G  r    +d+var  r rge+v
  gi|386002435|ref|YP_005920734.1| 45 GNLHAGHTRTFTIGDVVARYRRMRGENV 72
                                      899****************999998875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.1e-05
                      tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilrrkPkk 315
                                       +++l+g+ kms+SkG  ltl+ ++e    +v r++il+ + ++
  gi|386002435|ref|YP_005920734.1| 621 FVSLEGK-KMSKSKGPLLTLRRAVEANGADVTRLYILS-NAEH 661
                                       5666666.***************************998.4433 PP

>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0055        11       6      33 ..      56      85 ..      52      93 .. 0.90
   2 ?    4.0   0.0     0.029        57      21      58 ..     616     653 ..     606     653 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0055
                                      BHHHHHHH-GGGH..HHHHHTTGGGGGSCC CS
                           DUF1858  6 tIgelleeyPela..evLvelGfhclgcps 33
                                      tIg+++ +y  +   +vL+ +Gfh  g p+
  gi|386002435|ref|YP_005920734.1| 56 TIGDVVARYRRMRgeNVLFPMGFHVTGTPI 85
                                      9**********9999**********99998 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                                       HHHTTGGGGGSCCHHTTHHHHSBHHHHHHHHT--HHHH CS
                           DUF1858  21 LvelGfhclgcpsllktvakvetleqaakvhgidldeL 58 
                                       ++ +Gf  l+ +++ k+ ++ +tl+ a ++ g d+  L
  gi|386002435|ref|YP_005920734.1| 616 MAVNGFVSLEGKKMSKSKGPLLTLRRAVEANGADVTRL 653
                                       56679999999*********************999765 PP

>> RsbRD_N  RsbT co-antagonist protein rsbRD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00016      0.32      11      79 ..     702     767 ..     699     771 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                           RsbRD_N  11 ailekWleevlatypiesagllseaelreqlrelldallaalaseqldleseeeeelrealdelsrsRa 79 
                                       +++++W+e +l+ + ie+++ l+  ++r++++  + ++++ l+     +++  ++ lr++ld  +r++a
  gi|386002435|ref|YP_005920734.1| 702 ELIDRWMESQLQKRIIETTEALEAVQTRRAVQSAFYHMINDLRW---YQRRGGKNRLRSVLDVWVRLMA 767
                                       79****************99*******************55554...5568888899999998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (958 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 5401.87
//
Query:       gi|386002436|ref|YP_005920735.1|  [L=388]
Description: LL-diaminopimelate aminotransferase apoenzyme [Methanosaeta harundinacea 6Ac]
Scores for complete 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-63  213.6   0.0      5e-63  213.5   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5   0.0   2.8e-67     5e-63       2     362 ..      30     377 ..      29     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 2.8e-67
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvinLg+++++      t++ ++    + a+a + +++y+ ++g  e+++a+a+++++  k++l++e++v+ + G++
  gi|386002436|ref|YP_005920735.1|  30 DVINLGVGDPDLP----TPQIIIDSLCR-AAADPRNHQYPSYEGKIEFRTAVAEWYKETFKVDLDPESEVLALIGSK 101
                                       89**********9....9**********.****************************999***************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++i+ ++ ++ lnpg   lvpdp y+ yk++++ +gg  v  pl+ e++f  dl+++  ++++      k ++i+++
  gi|386002436|ref|YP_005920735.1| 102 EGIAHAPLAF-LNPGNLALVPDPAYPVYKTAVEFAGGVPVILPLKRENGFLPDLDSIPSDVAR------KARLIFLN 171
                                       **********.****************************************************......99****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                        p+NPtG+ a+l+  + l+d+a  +nl+++ D  Y++ +fg++++ + +++ve + +  +   slsK  +++G+RvG
  gi|386002436|ref|YP_005920735.1| 172 YPNNPTGACADLKFFKRLVDFAADNNLIVLHDNPYSEVYFGDERPPS-ILEVEGAREvAVEFHSLSKTCNMTGWRVG 247
                                       *****************************************999888.99999999977899*************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       +++g+ ++v  + ++++++ s    ++q a   al++a+++     +mr+++q+r + l+++L+++gl+v ++++++
  gi|386002436|ref|YP_005920735.1| 248 FVVGDREIVAGIGNVKSNIDSgnFGAVQDAGIVALKNAQKI---AADMRKTYQERVELLYAGLKKIGLEVEKPEATF 321
                                       ***************************************97...79******************************* PP

                                       EEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +l+  +     k+  +kL+++ g++ tpg  f+   +g +R++v + +++ + e+ve+
  gi|386002436|ref|YP_005920735.1| 322 YLWAWTGGR-SKDYTRKLIDQLGIVATPGVGFGDygEGYVRFSV-TQPTDRIAEAVER 377
                                       **9888877.89****************9999989*********.9999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2224.88
//
Query:       gi|386002437|ref|YP_005920736.1|  [L=717]
Description: Putative Ski2-type helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-22   77.6   0.0    2.2e-21   76.4   0.0    1.6  1  DEAD             DEAD/DEAH box helicase
    1.9e-09   38.0   1.5    9.2e-09   35.8   1.5    2.3  1  HHH_5            Helix-hairpin-helix domain
    2.2e-09   37.5   0.0    3.7e-09   36.8   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
    1.3e-06   28.8   0.0    1.4e-05   25.4   0.0    2.6  2  Helicase_C       Helicase conserved C-terminal domain
     0.0002   21.1   0.1     0.0019   18.0   0.0    2.6  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0006   19.9   0.1     0.0017   18.4   0.1    1.8  1  HHH_2            Helix-hairpin-helix motif
  ------ inclusion threshold ------
        0.2   11.6   0.8        1.3    9.0   0.0    2.7  2  HHH              Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   8.4e-25   2.2e-21       2     170 ..      37     193 ..      36     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 8.4e-25
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Qaea++  l +g+++lv+ +T++GKT+++ +++l++       +g + l+++P+r+La + +  +++f   ++++
  gi|386002437|ref|YP_005920736.1|  37 PPQAEAVEKGLlEGKSILVSVPTAAGKTMMAELAMLRAA-----LSGGRSLYIVPLRALASEKHAAFSRFSP-LGVK 107
                                       679999999887************************888.....5688*******************99988.6777 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       v +  g+ ++rd+   l  + +i+v+t ++ d+l+++g   ++++++lV+DE++ l + +++++++  +++l     
  gi|386002437|ref|YP_005920736.1| 108 VGVSSGDMERRDE--YL-GRNHIIVATSEKADSLIRNGARWIRDLSVLVVDEIHLLDSPNRGPTLEMTITKLL---- 177
                                       7755665555554..45.669**************999988*****************************994.... PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                       + + q q++ lSAT+ 
  gi|386002437|ref|YP_005920736.1| 178 RLNPQMQILGLSATVA 193
                                       3345677*******97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   1.5   3.6e-12   9.2e-09       4      56 ..     651     701 ..     648     703 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.6e-12
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       Ll+++G+G+++A++l++aG++s+e l++a +++La+i  +G+k A ++i +++
  gi|386002437|ref|YP_005920736.1| 651 LLDLKGVGRVRARKLHRAGYTSIERLKEAKAADLAEI--LGPKIAGKVIAQIR 701
                                       89***********************************..**********9987 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 !   36.8   0.0   1.4e-12   3.7e-09       3     169 ..      34     192 ..      27     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.4e-12
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       el++ Q+ea+e+ l      + k +l+  +T +GKT++a  ++ r + +g+  + l +vp ++l +    +f++f++
  gi|386002437|ref|YP_005920736.1|  34 ELYPPQAEAVEKGL-----LEGKSILVSVPTAAGKTMMAELAMLRAALSGG--RSLYIVPLRALASEKHAAFSRFSP 103
                                       57788888888887.....34679***************999999999999..9*********************** PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......T CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......s 149
                                         +  + ++ sgd +++  +    ++i+v+t +++d+ +      +         v+++DE H l + +       +
  gi|386002437|ref|YP_005920736.1| 104 LGV--KVGVSSGDMERR-DEYLGRNHIIVATSEKADSLI-----RNGARWIRDLSVLVVDEIHLLDSPNrgptlemT 172
                                       *99..677777777777.77889****************.....333333444459***********8466667779 PP

                                       THHHHHT---SEEEEEESS- CS
                            ResIII 150 wreilekfkeavllglTATp 169
                                       ++++l+ +++  +lgl+AT 
  gi|386002437|ref|YP_005920736.1| 173 ITKLLRLNPQMQILGLSATV 192
                                       9999999999*********7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.2   1.1e+04      14      53 ..      76     118 ..      65     133 .. 0.60
   2 !   25.4   0.0   5.3e-09   1.4e-05      39     111 .]     302     390 ..     238     390 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.2
                                       TTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHH CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekk...gikvavlhgelpqn 53 
                                        +gg++l +v+ +  +++    + +++   g+kv v  g+++ +
  gi|386002437|ref|YP_005920736.1|  76 LSGGRSLYIVPLRALASEkHAAF-SRFsplGVKVGVSSGDMERR 118
                                       46777777777777443322223.23345677777777776654 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 5.3e-09
                                       T.......TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS....SSH.....HH CS
                        Helicase_C  39 k.......gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp....rnv.....ts 99 
                                                  va +h+ l +++r  +   f++g+++ + +t  ++ G+++p  +++i         r++      +
  gi|386002437|ref|YP_005920736.1| 302 GrrladcvRSGVAFHHAGLLAEQRAVVEGGFRSGSIKAIASTPTLAAGLNLPARRVLIKSYRRyegsRGMvpipvME 378
                                       144455556788999*************************************99999954444332244245555** PP

                                       HHHHHTTSSSTT CS
                        Helicase_C 100 yiqriGRtgRag 111
                                       y q++GR+gR g
  gi|386002437|ref|YP_005920736.1| 379 YRQMAGRAGRPG 390
                                       **********75 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.67   1.7e+03      12      28 ..     133     149 ..     130     159 .. 0.87
   2 !   18.0   0.0   7.3e-07    0.0019       8      35 ..     656     684 ..     651     687 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.67
                   DNA_pol_lambd_f  12 ktAkkwyakGirtledl 28 
                                       ++A  ++++G r + dl
  gi|386002437|ref|YP_005920736.1| 133 EKADSLIRNGARWIRDL 149
                                       789*********99998 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 7.3e-07
                   DNA_pol_lambd_f   8 GVGpktAkkwyakGirtledlra.krakL 35 
                                       GVG+++A+k++++G++++e l++ k a+L
  gi|386002437|ref|YP_005920736.1| 656 GVGRVRARKLHRAGYTSIERLKEaKAADL 684
                                       9*********************9655665 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   6.7e-07    0.0017       6      52 ..     652     697 ..     647     703 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.7e-07
                             HHH_2   6 LGIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52 
                                       L ++ VG   A++L ++ + s+++Lk+a++ +L+e+   G++iA +++
  gi|386002437|ref|YP_005920736.1| 652 LDLKGVGRVRARKLHRAgYTSIERLKEAKAADLAEI--LGPKIAGKVI 697
                                       66899*********9866*****************9..6899998876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00051       1.3      13      28 ..     651     666 ..     650     668 .. 0.90
   2 ?   -0.6   0.3      0.57   1.4e+03       4      27 ..     675     696 ..     672     698 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                                       HHTSTT-SHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIl 28 
                                       Ll+l+GVG+ +A++ +
  gi|386002437|ref|YP_005920736.1| 651 LLDLKGVGRVRARKLH 666
                                       899**********987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                                       HHHTSSHHHHHTSTT-SHHHHHHH CS
                               HHH   4 glipasreeLlalPGVGpktAeaI 27 
                                       +l++a  ++L+++   Gpk A+++
  gi|386002437|ref|YP_005920736.1| 675 RLKEAKAADLAEI--LGPKIAGKV 696
                                       5555555555554..367777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 4193.06
//
Query:       gi|386002438|ref|YP_005920737.1|  [L=288]
Description: Anaerobic ribonucleoside-triphosphate reductase activating protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-17   64.2   0.0    3.3e-17   63.4   0.0    1.4  2  Radical_SAM  Radical SAM superfamily
    1.2e-08   35.3   0.0    1.7e-08   34.8   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
    7.7e-05   22.8   0.0    0.00013   22.1   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   5.5e-21   3.3e-17       1     154 [.      23     168 ..      23     178 .. 0.92
   2 ?   -3.3   0.0       1.7     1e+04      62      88 ..     240     264 ..     233     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 5.5e-21
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       v+++rgC+lrC++C++         + +  + +i+  ++e+     +  vil+ggepl++ +  ++++  +k+   g
  gi|386002438|ref|YP_005920737.1|  23 VIFMRGCPLRCPHCHNAL---LQTGESFEELADIKSRIDEAG-PF-ISAVILSGGEPLVQLKASREIAIHSKN--MG 92 
                                       689**************9...9*******************7.55.***************999999999998..8* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaadde.kvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                       +++ vet+g  p ++ + ++ +  vd v l+++ a  + ++   ++ ++   +v e+l+++ eag++   +r++++p
  gi|386002438|ref|YP_005920737.1|  93 LKVGVETSGRFP-DRLASLIEDGLVDMVFLDVKEALRDpEYAAATGQRDVAPRVAESLRLCLEAGVP-LEVRTTVFP 167
                                       ***********9.89999999955***********88888*****9889999***************.9*******9 PP

                                       T CS
                                       x RF
                       Radical_SAM 154 G 154
                                       +
  gi|386002438|ref|YP_005920737.1| 168 N 168
                                       5 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                                       THHHHHHHHHHTCCCTEEEEEEECSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  62 dfvellerlaklavpgiritvetngtl 88 
                                       +++ +l+++++l  ++++ +  ++g+ 
  gi|386002438|ref|YP_005920737.1| 240 PYQTELFQICQL--RKLHPRPASPGGS 264
                                       677889999999..6888877777766 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.8e-12   1.7e-08       7      95 ..      21     103 ..      14     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.8e-12
                           Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                        +++f+ gC+l+C+ C+n  ++     + f+  + ++  i+++  + i+ ++l+GGEPl+  + +a  e++ + k+ 
  gi|386002438|ref|YP_005920737.1|  21 AAVIFMRGCPLRCPHCHNALLQTG---ESFEeLADIKSRIDEA-GPFISAVILSGGEPLV--QLKASREIAIHSKNM 91 
                                       5699*************9877654...4444344566666776.8***************..999999999999999 PP

                           Fer4_12  83 kpekdiwlytgyt 95 
                                       ++ k+ ++++g+ 
  gi|386002438|ref|YP_005920737.1|  92 GL-KVGVETSGRF 103
                                       98.6888888865 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.1e-08   0.00013       2      90 ..      25     102 ..      23     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.1e-08
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       f+   gC+l C+ C n     ++ +  ++  ++++++  +++  + i+ + l+GGePL   + k+  ++  + k+ +
  gi|386002438|ref|YP_005920737.1|  25 FM--RGCPLRCPHCHNAL--LQTGESFEELADIKSRI--DEAGPF-ISAVILSGGEPL--VQLKASREIAIHSKNMG 92 
                                       66..8**********998..45566666778999999..555555.566*********..55666666655555555 PP

                           Fer4_14  79 pekkiwletngt 90 
                                         +k+ +et+g 
  gi|386002438|ref|YP_005920737.1|  93 --LKVGVETSGR 102
                                       ..8888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1768.04
//
Query:       gi|386002439|ref|YP_005920738.1|  [L=194]
Description: hypothetical protein Mhar_1757 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-14   54.2   0.0    3.2e-14   53.5   0.0    1.3  1  AAA_17         AAA domain
    3.2e-11   43.9   0.0    4.3e-11   43.5   0.0    1.2  1  AAA_18         AAA domain
    9.5e-09   35.6   0.0    1.2e-08   35.2   0.0    1.2  1  AAA_33         AAA domain
     0.0016   18.1   1.0     0.0029   17.3   0.4    1.6  1  PEP-utilizers  PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.025   14.3   0.1       0.14   11.8   0.0    2.0  2  CoaE           Dephospho-CoA kinase
      0.027   14.6   0.1       0.12   12.5   0.0    1.8  2  ADK            Adenylate kinase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.1e-17   3.2e-14       1     131 [.       7     129 ..       7     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.1e-17
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTS..HHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrkl..pleekkelqkeaaekiaeeakkkgvl 75 
                                       +G+PGsGK+ ++ +++++++++++ +Gd++reea+ +gl +++ ++  +  +l+e++  +++aa+ +a+ +      
  gi|386002439|ref|YP_005920738.1|   7 VGMPGSGKSAAA-EVAREMKIPVVVMGDVIREEAAACGLPPTDRNLGAVgnDLREREGPDAIAARCLAKIR------ 76 
                                       7********777.**************************88888888653366666666777777766654...... PP

                                       EEE-SEEEETTEEEESSHHHHHHHH...SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
                            AAA_17  76 vdghprikeqagfldglpkevleel.kpdaiilleadpeeilerrlkdrtrgrdddn 131
                                        +g p++   +g++++ +++ ++   +   +i +++++e  l+r ++   rgr+dd 
  gi|386002439|ref|YP_005920738.1|  77 ATGAPVV-VVEGIRSRSEVDLFRRSsNGFSLIEVYVPDEIRLARIAS---RGRSDDA 129
                                       4444443.345555555666665541445677899999877777765...7776664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   1.4e-14   4.3e-11       1     118 [.       4     128 ..       4     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.4e-14
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       ++  G+pG+GK+  a+  +++ ++     g+++r+ a+  gl  ++ +  a+ + +r++e+ ++ + ++l ++++  
  gi|386002439|ref|YP_005920738.1|   4 VGFVGMPGSGKSAAAEVAREM-KIpvvvmGDVIREEAAACGLPPTDRNLgAVGNDLREREGPDAIAARCLAKIRA-- 77 
                                       5678**************999.5777999******************99************************87.. PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeea 118
                                       + + ++v++g+++  e + +++       + +++++e++l R++ Rg++++
  gi|386002439|ref|YP_005920738.1|  78 TGAPVVVVEGIRSRSEVDLFRRSSNgfslIEVYVPDEIRLARIASRGRSDD 128
                                       777777************99988779*********************8874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   4.1e-12   1.2e-08       2     128 ..       4     132 ..       3     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.1e-12
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.avllssdtlrrrlfg.....tdqqsktdytrvldrlyq......ilnelarka 66 
                                       v +vG+pGsGKs  ae ++++ +  v++  d++r+  ++     t    ++++  v ++l++      i ++ ++k 
  gi|386002439|ref|YP_005920738.1|   4 VGFVGMPGSGKSAAAE-VAREMKiPVVVMGDVIREEAAAcglppT----DRNLGAVGNDLREregpdaIAARCLAKI 75 
                                       669*********9998.6778888***********7777644443....44333333332222223338889999** PP

                            AAA_33  67 lsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsev 128
                                       ++ g++v++  + +sr+e + f++  +  g  ++++ v +++e   +R+a R ++ d + + 
  gi|386002439|ref|YP_005920738.1|  76 RATGAPVVVVEGIRSRSEVDLFRRSSN--G--FSLIEVYVPDEIRLARIASRGRSDD-ANDC 132
                                       ********************9999998..5..779*******************754.4344 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   9.8e-07    0.0029      23      53 ..       2      32 ..       1      41 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.8e-07
                                      GEEEEEES--TTHHHHHHHHHHTT--EEE-- CS
                     PEP-utilizers 23 kaaGivterGGmtSHaAivArelgiPaVvgv 53
                                      k+ G+v   G+  S aA vAre++iP+Vv  
  gi|386002439|ref|YP_005920738.1|  2 KIVGFVGMPGSGKSAAAEVAREMKIPVVVMG 32
                                      57899999********************965 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.6e-05      0.14       2      37 ..       3      39 ..       2      63 .. 0.83
   2 ?    0.2   0.0      0.17   5.1e+02     126     163 ..     107     144 ..     102     169 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                                      EEEEEESTTSSHHHHHHHHHHTT-EEE.EHHHHHHHT CS
                              CoaE  2 ivgltGgiasGKstvanlfadlgvpiv.DaDlvArqv 37
                                      ivg  G  +sGKs++a++ +++++p+v   D++  ++
  gi|386002439|ref|YP_005920738.1|  3 IVGFVGMPGSGKSAAAEVAREMKIPVVvMGDVIREEA 39
                                      89**********************9871456665555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                                       EEEE--HHHHHHHHHHCCTSTHHHHHHHHHHS--HHHH CS
                              CoaE 126 lvvdvelelqveRlvardgvseeevkaiiaaQlseeer 163
                                       + v v+ e +++R+ +r   + ++  +  +a ++++ r
  gi|386002439|ref|YP_005920738.1| 107 IEVYVPDEIRLARIASRGRSDDANDCDLAKAVADRDAR 144
                                       56778888888888888655444444444443333333 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.12       2      36 ..       7      40 ..       6      44 .. 0.88
   2 ?   -0.6   0.0      0.43   1.3e+03     106     129 ..     106     139 ..      94     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                      +G Pg+GK   a++++++++++ +  Gd++R+e +
  gi|386002439|ref|YP_005920738.1|  7 VGMPGSGKSA-AAEVAREMKIPVVVMGDVIREEAA 40
                                      8*******86.55799***************9976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                                       EEEEE--HHHHHHHHHT..........GSHHHHH CS
                                       xxxxxxxxxxxxxxxxx..........xxxxxxx RF
                               ADK 106 vleldvpeevlveRltg..........Dneetvk 129
                                       ++e+ vp+e+ + R++           D +++v+
  gi|386002439|ref|YP_005920738.1| 106 LIEVYVPDEIRLARIASrgrsddandcDLAKAVA 139
                                       7889999999999998877887666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1126.85
//
Query:       gi|386002440|ref|YP_005920739.1|  [L=406]
Description: Signal recognition particle GTPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-10   41.0   0.0    3.8e-10   40.4   0.0    1.2  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.023   13.9   0.4        1.8    7.9   0.2    3.4  3  DUF3666     Ribose-5-phosphate isomerase
       0.63    9.2   3.3        1.4    8.1   3.3    1.7  1  KAP_NTPase  KAP family P-loop domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   6.4e-14   3.8e-10       3     147 ..      32     211 ..      30     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.4e-14
                            AAA_16   3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif...lrgkcdqlesaipysalaqal 76 
                                       v Re  +++ ++al+  +sgrp   l++G +G GKs+ +++l + le+d  i+   +r k   +  +i+ys ++ ++
  gi|386002440|ref|YP_005920739.1|  32 VRRESPIDRHANALR--SSGRPLKYLFVGSRGNGKSTELNRLSEILEDDLLIVpfsIRDKLNLY--DIEYSDILLII 104
                                       89************9..99************************888888566676678888877..9***9999999 PP

                            AAA_16  77 areellrqllde.....aesaeleawrekleeala..........................avpelagaea...... 116
                                       a+ e+++ + ++     + s+ l+ w+ek  e+ +                          a        +      
  gi|386002440|ref|YP_005920739.1| 105 AA-EIYERVSENvelssKLSDYLDSWSEKVIENEKsyglsaeakagfaafvfnitgkmkteA--------Strevtr 172
                                       66.88888888887766555567777777777666999999999999999999665555440........3445555 PP

                            AAA_16 117 .......srllellkrll.allsrderplvlvlDdlqwa 147
                                              s+l +++++++ +  ++ ++ +++++Ddl+++
  gi|386002440|ref|YP_005920739.1| 173 kviqpqlSDLIYAVNKIIiEAEEKLDKNILVIIDDLDKV 211
                                       6668888***********8888888999*********76 PP

>> DUF3666  Ribose-5-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.025   1.5e+02      20      31 ..      20      31 ..      19      33 .. 0.91
   2 ?   -4.0   0.0       1.5   9.2e+03      10      18 ..     287     295 ..     286     297 .. 0.83
   3 ?    7.9   0.2    0.0003       1.8       4      33 ..     347     382 ..     345     384 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.025
                                      HHT-STTHHHHH CS
                           DUF3666 20 gAisGerFqeyF 31
                                      +A+sGe+ +ey+
  gi|386002440|ref|YP_005920739.1| 20 EALSGETLKEYY 31
                                      7**********8 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.5
                                       HHHS-HHHH CS
                           DUF3666  10 LkaiDqdLv 18 
                                       Lk +D+ L+
  gi|386002440|ref|YP_005920739.1| 287 LKRMDESLI 295
                                       9999*9986 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0003
                                       --HHHHHHHS-HHHHHHH......T-STTHHHHHTT CS
                           DUF3666   4 kdlleiLkaiDqdLvkgA......isGerFqeyFFa 33 
                                       +d++ iL+  D +++k+       + Ge+Fq+++F 
  gi|386002440|ref|YP_005920739.1| 347 NDYIRILNPQDIEILKEVmktkgkVGGEKFQDLLFS 382
                                       58888888888888865322233399********95 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.3   0.00023       1.4     146     189 ..     175     215 ..      57     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00023
                        KAP_NTPase 146 eeaplkklqteveelladmektLdalqkrlVvviDdLDrcetee 189
                                        + +l +l   v++++ ++e++Ld+    ++v+iDdLD +  e+
  gi|386002440|ref|YP_005920739.1| 175 IQPQLSDLIYAVNKIIIEAEEKLDK---NILVIIDDLDKVNLEK 215
                                       4444444444555555555555555...**********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2399.13
//
Query:       gi|386002441|ref|YP_005920740.1|  [L=460]
Description: putative membrane protein, containing TPR repeats [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-53  174.4  20.0    4.3e-10   39.0   0.0    9.7 10  TPR_1            Tetratricopeptide repeat
      2e-46  152.4  25.3    3.3e-08   33.0   0.0    9.8 10  TPR_2            Tetratricopeptide repeat
    3.1e-44  145.5  23.9    2.1e-08   33.7   0.0    9.5 10  TPR_8            Tetratricopeptide repeat
    8.4e-43  143.8  18.6    9.6e-09   34.8   0.0    9.1  9  TPR_11           TPR repeat
      3e-39  130.6  12.6    5.5e-05   23.3   0.0    8.3  7  TPR_17           Tetratricopeptide repeat
    6.9e-34  116.0  31.2    2.7e-11   43.6   0.4    7.7  8  TPR_12           Tetratricopeptide repeat
    1.2e-25   89.8  25.3    9.3e-10   39.0   0.7    5.5  6  TPR_16           Tetratricopeptide repeat
    6.9e-25   85.6  30.4    7.6e-05   23.2   0.8    8.6  9  TPR_14           Tetratricopeptide repeat
    1.3e-21   76.5   9.3    1.3e-07   31.6   0.8    5.8  6  TPR_9            Tetratricopeptide repeat
    3.7e-19   69.0  23.1    8.4e-05   23.0   0.4    6.3  6  TPR_19           Tetratricopeptide repeat
    4.7e-17   61.4  13.3     0.0036   17.8   0.0    8.8  7  TPR_6            Tetratricopeptide repeat
    1.9e-16   58.8  11.2     0.0028   17.6   0.0    7.5  7  TPR_7            Tetratricopeptide repeat
    3.4e-16   58.5  23.4    0.00078   19.2   0.1    8.5  8  TPR_10           Tetratricopeptide repeat
    6.8e-13   49.3  10.7    0.00048   20.6   0.1    4.3  4  BTAD             Bacterial transcriptional activator domain
      1e-11   44.9   7.4    7.5e-06   26.1   0.2    4.1  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.5e-11   43.8  10.1    0.00049   20.2   0.1    6.2  5  DUF3856          Domain of Unknown Function (DUF3856)
    4.2e-10   39.2   7.2     0.0034   16.4   0.1    3.7  4  NARP1            NMDA receptor-regulated protein 1
    5.6e-09   35.6  13.8    6.3e-05   22.3   0.3    3.2  3  TPR_15           Tetratricopeptide repeat
    1.1e-06   28.7   7.5    0.00035   20.5   0.0    4.4  4  Wzy_C_2          Virulence factor membrane-bound polymerase, 
    4.6e-06   26.7   8.9        8.3    7.4   0.0    7.7  7  TPR_4            Tetratricopeptide repeat
    4.1e-05   23.8   7.4        1.5    9.1   0.0    4.9  6  TPR_5            Tetratrico peptide repeat
    0.00025   20.4   3.8       0.36   10.0   0.2    4.3  4  FAT              FAT domain
     0.0071   16.8   3.3        6.4    7.2   0.0    4.0  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0083   15.6   4.5        2.1    7.7   0.0    3.8  5  Coatomer_E       Coatomer epsilon subunit
  ------ inclusion threshold ------
      0.016   15.0   4.3        5.4    6.8   0.0    4.1  4  DUF5113          Domain of unknown function (DUF5113)
      0.017   14.2   0.4       0.65    8.9   0.1    2.7  3  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.033   14.3   2.5         21    5.2   0.1    4.4  4  ANAPC5           Anaphase-promoting complex subunit 5
      0.043   14.1   5.9         45    4.6   0.0    5.8  5  PPR              PPR repeat
       0.05   13.6   0.0       0.67   10.0   0.0    2.7  3  Paz_1            PAZ domain
      0.061   13.4   6.5        6.9    6.8   0.1    4.9  4  MIT              MIT (microtubule interacting and transport) 
      0.075   13.4   0.0         18    5.7   0.0    2.6  2  TruB_N           TruB family pseudouridylate synthase (N term
       0.21   11.3   5.4        5.9    6.6   0.0    4.2  5  RPN7             26S proteasome subunit RPN7
       0.29   11.5  12.7         13    6.2   1.1    5.0  5  TPR_20           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.18        96       3      19 ..      85     101 ..      83     104 .. 0.87
   2 ?   -2.5   0.0       9.8   5.3e+03      26      26 ..     148     148 ..     139     155 .. 0.48
   3 !   31.3   0.1   2.1e-10   1.1e-07       1      33 [.     157     189 ..     157     189 .. 0.94
   4 !   36.8   0.0   3.7e-12     2e-09       1      34 []     191     224 ..     191     224 .. 0.97
   5 !   19.6   0.8     1e-06   0.00055       1      33 [.     225     257 ..     225     257 .. 0.97
   6 !   11.5   0.0   0.00037       0.2       1      33 [.     259     291 ..     259     292 .. 0.96
   7 !   31.5   0.1   1.9e-10     1e-07       1      33 [.     293     325 ..     293     326 .. 0.96
   8 !   39.0   0.0   7.9e-13   4.3e-10       1      34 []     327     360 ..     327     360 .. 0.96
   9 ?    3.7   0.1      0.11        62      10      29 ..     370     389 ..     369     393 .. 0.88
  10 ?    3.2   0.0      0.16        86       4      30 ..     396     422 ..     393     425 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHTT-HHH CS
                             TPR_1   3 alynlGnayfklgkyde 19 
                                       ++  +++ y+kl ++d+
  gi|386002441|ref|YP_005920740.1|  85 IFMDIAVSYYKLDDLDK 101
                                       67789*********997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.8
                                       H CS
                             TPR_1  26 k 26 
                                       k
  gi|386002441|ref|YP_005920740.1| 148 K 148
                                       2 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 2.1e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a ++ nl+ ay+ lg+ d+ le+ +kA+el+P+
  gi|386002441|ref|YP_005920740.1| 157 ASTYENLAEAYRMLGQIDKSLECLDKAIELDPQ 189
                                       56799***************************6 PP

  == domain 4  score: 36.8 bits;  conditional E-value: 3.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a++++n+G+a+  lg+ deAl+++ekA+e +P++
  gi|386002441|ref|YP_005920740.1| 191 ARSWFNMGLALDDLGRKDEALKAFEKAIETDPED 224
                                       799*****************************86 PP

  == domain 5  score: 19.6 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a+ n G+a+++lg+ +e l++ ekA+e +P+
  gi|386002441|ref|YP_005920740.1| 225 AAAWANNGYALYYLGRIEESLKASEKAIEFDPQ 257
                                       78*****************************95 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+a+ n+  a+ ++g+ +e le+ ekA+ lnP+
  gi|386002441|ref|YP_005920740.1| 259 AEAWTNKSSALAQMGRIKESLEASEKAVNLNPK 291
                                       89******************************7 PP

  == domain 7  score: 31.5 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a a++n+G +++ l + +eA+e+ ++A+el+P+
  gi|386002441|ref|YP_005920740.1| 293 AMAWNNKGSVLYDLDRAEEAIEALDRAIELDPK 325
                                       679*****************************7 PP

  == domain 8  score: 39.0 bits;  conditional E-value: 7.9e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a+ n+G+a+ +lg+ ++Al++yekA+e++P++
  gi|386002441|ref|YP_005920740.1| 327 AMAWSNKGVALGSLGRMEDALDAYEKAIEHDPKD 360
                                       679*****************************86 PP

  == domain 9  score: 3.7 bits;  conditional E-value: 0.11
                                       HHHHTT-HHHHHHHHHHHHH CS
                             TPR_1  10 ayfklgkydeAleyyekALe 29 
                                       +y+klg+  + +e+++ A  
  gi|386002441|ref|YP_005920740.1| 370 LYRKLGREADSIEACKAARD 389
                                       6***************9865 PP

  == domain 10  score: 3.2 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                        yn++      g +d Al+  + ALe 
  gi|386002441|ref|YP_005920740.1| 396 EYNRACFEAVCGSPDAALALLRTALEN 422
                                       5899999999999************95 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.17        91       3      19 ..      85     101 ..      83     105 .. 0.85
   2 ?   -1.3   0.0       6.1   3.3e+03      26      33 ..     148     155 ..     137     156 .. 0.74
   3 !   28.5   0.1   1.7e-09   9.4e-07       3      33 ..     159     189 ..     157     190 .. 0.93
   4 !   33.0   0.0   6.1e-11   3.3e-08       1      34 []     191     224 ..     191     224 .. 0.96
   5 !   20.8   1.3     5e-07   0.00027       1      33 [.     225     257 ..     225     258 .. 0.96
   6 !   15.5   0.0   2.5e-05     0.014       1      33 [.     259     291 ..     259     292 .. 0.97
   7 !   28.2   0.1   2.2e-09   1.2e-06       1      33 [.     293     325 ..     293     326 .. 0.95
   8 !   26.7   0.0   6.3e-09   3.4e-06       1      34 []     327     360 ..     327     360 .. 0.95
   9 ?    4.1   0.1      0.11        62      10      30 ..     370     390 ..     363     393 .. 0.90
  10 ?    1.5   0.1      0.78   4.2e+02       5      29 ..     397     421 ..     394     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                             TPR_2   3 alynlGlayyklgdyee 19 
                                       + + ++ +yykl+d+++
  gi|386002441|ref|YP_005920740.1|  85 IFMDIAVSYYKLDDLDK 101
                                       66789*********997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.1
                             TPR_2  26 kAleldPn 33 
                                       k l+l+P+
  gi|386002441|ref|YP_005920740.1| 148 KLLKLNPT 155
                                       77888886 PP

  == domain 3  score: 28.5 bits;  conditional E-value: 1.7e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        + nl++ay+ lg+ ++ le+++kA+eldP+
  gi|386002441|ref|YP_005920740.1| 159 TYENLAEAYRMLGQIDKSLECLDKAIELDPQ 189
                                       689***************************7 PP

  == domain 4  score: 33.0 bits;  conditional E-value: 6.1e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ ++n+Gla+  lg+ +eAl+afekA+e dP++
  gi|386002441|ref|YP_005920740.1| 191 ARSWFNMGLALDDLGRKDEALKAFEKAIETDPED 224
                                       678*****************************86 PP

  == domain 5  score: 20.8 bits;  conditional E-value: 5e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+ n G+a+y+lg+ ee l+a ekA+e dP+
  gi|386002441|ref|YP_005920740.1| 225 AAAWANNGYALYYLGRIEESLKASEKAIEFDPQ 257
                                       689*****************************7 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 2.5e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       aea+ n   a++++g+ +e lea ekA+ l+P+
  gi|386002441|ref|YP_005920740.1| 259 AEAWTNKSSALAQMGRIKESLEASEKAVNLNPK 291
                                       89******************************7 PP

  == domain 7  score: 28.2 bits;  conditional E-value: 2.2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++n G ++y l++ eeA+ea+++A+eldP+
  gi|386002441|ref|YP_005920740.1| 293 AMAWNNKGSVLYDLDRAEEAIEALDRAIELDPK 325
                                       569*****************************7 PP

  == domain 8  score: 26.7 bits;  conditional E-value: 6.3e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a a+ n G a+  lg+ e+Al+a+ekA+e+dP++
  gi|386002441|ref|YP_005920740.1| 327 AMAWSNKGVALGSLGRMEDALDAYEKAIEHDPKD 360
                                       569*****************************86 PP

  == domain 9  score: 4.1 bits;  conditional E-value: 0.11
                             TPR_2  10 ayyklgdyeeAleafekAlel 30 
                                       +y+klg+ ++ +ea+++A  l
  gi|386002441|ref|YP_005920740.1| 370 LYRKLGREADSIEACKAARDL 390
                                       7***************99876 PP

  == domain 10  score: 1.5 bits;  conditional E-value: 0.78
                             TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                       yn+++  +  g ++ Al++++ Ale
  gi|386002441|ref|YP_005920740.1| 397 YNRACFEAVCGSPDAALALLRTALE 421
                                       67777777788899*********98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.22   1.2e+02       2      27 ..      84     109 ..      83     114 .. 0.86
   2 ?   -1.8   0.0       9.5   5.2e+03      23      32 ..     138     147 ..     135     155 .. 0.69
   3 !   22.9   0.1   1.1e-07   6.2e-05       1      33 [.     157     189 ..     157     189 .. 0.95
   4 !   33.7   0.0   3.8e-11   2.1e-08       1      34 []     191     224 ..     191     224 .. 0.96
   5 !   16.7   0.5   1.1e-05    0.0061       2      33 ..     226     257 ..     225     257 .. 0.94
   6 !   22.7   0.1   1.3e-07   7.2e-05       1      33 [.     259     291 ..     259     292 .. 0.97
   7 !   27.3   0.1   4.5e-09   2.4e-06       3      33 ..     295     325 ..     293     326 .. 0.97
   8 !   20.5   0.0   6.6e-07   0.00036       3      34 .]     329     360 ..     327     360 .. 0.95
   9 !    7.7   0.1    0.0088       4.8       3      27 ..     363     387 ..     361     391 .. 0.91
  10 ?   -0.9   0.0       4.9   2.6e+03      15      32 ..     407     424 ..     398     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                                       CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                       e+ + ++  y kl d+++   y +k 
  gi|386002441|ref|YP_005920740.1|  84 EIFMDIAVSYYKLDDLDKGDDYSRKS 109
                                       6778899***********99998886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.5
                                       HHHHHHHHHH CS
                             TPR_8  23 yyekaleldp 32 
                                        y+k+++l+ 
  gi|386002441|ref|YP_005920740.1| 138 QYRKVIQLSS 147
                                       5777777765 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.1e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+ y nl+ +y+ lg+++++ e++ ka+eldp+
  gi|386002441|ref|YP_005920740.1| 157 ASTYENLAEAYRMLGQIDKSLECLDKAIELDPQ 189
                                       57899**************************96 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 3.8e-11
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++++n+g+++++lg+++eA +++eka+e dp++
  gi|386002441|ref|YP_005920740.1| 191 ARSWFNMGLALDDLGRKDEALKAFEKAIETDPED 224
                                       79******************************85 PP

  == domain 5  score: 16.7 bits;  conditional E-value: 1.1e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        a+ n g+++  lg++ee+ ++ eka+e dp+
  gi|386002441|ref|YP_005920740.1| 226 AAWANNGYALYYLGRIEESLKASEKAIEFDPQ 257
                                       689999************************96 PP

  == domain 6  score: 22.7 bits;  conditional E-value: 1.3e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       aea+ n++s++ ++g+++e+ e+ eka+ l+p+
  gi|386002441|ref|YP_005920740.1| 259 AEAWTNKSSALAQMGRIKESLEASEKAVNLNPK 291
                                       79******************************7 PP

  == domain 7  score: 27.3 bits;  conditional E-value: 4.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++n+gs++ +l + eeA+e++ +a+eldp+
  gi|386002441|ref|YP_005920740.1| 295 AWNNKGSVLYDLDRAEEAIEALDRAIELDPK 325
                                       8*****************************7 PP

  == domain 8  score: 20.5 bits;  conditional E-value: 6.6e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a+ n+g ++ +lg++e A  +yeka+e dp++
  gi|386002441|ref|YP_005920740.1| 329 AWSNKGVALGSLGRMEDALDAYEKAIEHDPKD 360
                                       799************************99985 PP

  == domain 9  score: 7.7 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                        y  l ++y+klg+   ++e+++ a
  gi|386002441|ref|YP_005920740.1| 363 TYIALVRLYRKLGREADSIEACKAA 387
                                       589999***************9987 PP

  == domain 10  score: -0.9 bits;  conditional E-value: 4.9
                                       T-HHHHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekaleldp 32 
                                       g  ++A + ++ ale ++
  gi|386002441|ref|YP_005920740.1| 407 GSPDAALALLRTALENKE 424
                                       677899999999998665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.8     1e+03      15      25 ..     137     147 ..     137     149 .. 0.86
   2 !   12.1   0.0   0.00022      0.12      19      42 .]     148     171 ..     147     171 .. 0.91
   3 !   34.8   0.0   1.8e-11   9.6e-09       2      41 ..     165     204 ..     164     205 .. 0.92
   4 !   21.1   2.3   3.4e-07   0.00018       6      39 ..     203     236 ..     201     237 .. 0.95
   5 !   26.5   0.4   6.9e-09   3.7e-06       1      42 []     232     273 ..     232     273 .. 0.95
   6 !   20.0   0.0   7.6e-07   0.00041       3      41 ..     268     306 ..     266     307 .. 0.95
   7 !   31.9   0.0   1.4e-10   7.6e-08       1      42 []     300     341 ..     300     341 .. 0.96
   8 !   20.9   0.1   3.9e-07   0.00021       6      39 ..     339     372 ..     337     375 .. 0.86
   9 ?   -0.1   0.0       1.4   7.5e+02      11      28 ..     410     427 ..     406     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.8
                            TPR_11  15 eaYkkAlkldP 25 
                                       ++Y+k ++l++
  gi|386002441|ref|YP_005920740.1| 137 TQYRKVIQLSS 147
                                       69*******86 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                            TPR_11  19 kAlkldPdnaeayynLGlayykqG 42 
                                       k lkl+P+ a+ y nL++ay ++G
  gi|386002441|ref|YP_005920740.1| 148 KLLKLNPTTASTYENLAEAYRMLG 171
                                       679*****************8777 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 1.8e-11
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                        ay+ +G++++++e++ kA++ldP+ a+ ++n+Gla+  +
  gi|386002441|ref|YP_005920740.1| 165 EAYRMLGQIDKSLECLDKAIELDPQAARSWFNMGLALDDL 204
                                       5899*******************************98655 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 3.4e-07
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       ++G+ +eA++a++kA++ dP++a a+ n G+a+y
  gi|386002441|ref|YP_005920740.1| 203 DLGRKDEALKAFEKAIETDPEDAAAWANNGYALY 236
                                       57999***************************98 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 6.9e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+y +G++ee+++a +kA+++dP+ aea+ n   a++++G
  gi|386002441|ref|YP_005920740.1| 232 GYALYYLGRIEESLKASEKAIEFDPQAAEAWTNKSSALAQMG 273
                                       99*******************************999988887 PP

  == domain 6  score: 20.0 bits;  conditional E-value: 7.6e-07
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       a+ + G+++e++ea +kA++l+P+ a a++n G ++y +
  gi|386002441|ref|YP_005920740.1| 268 ALAQMGRIKESLEASEKAVNLNPKLAMAWNNKGSVLYDL 306
                                       7889********************************976 PP

  == domain 7  score: 31.9 bits;  conditional E-value: 1.4e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G ++y++ + eeAiea+ +A++ldP+ a a++n G+a+  +G
  gi|386002441|ref|YP_005920740.1| 300 GSVLYDLDRAEEAIEALDRAIELDPKLAMAWSNKGVALGSLG 341
                                       889**********************************99887 PP

  == domain 8  score: 20.9 bits;  conditional E-value: 3.9e-07
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       ++G+ e+A+ aY+kA++ dP++a  y +L  +y 
  gi|386002441|ref|YP_005920740.1| 339 SLGRMEDALDAYEKAIEHDPKDAITYIALVRLYR 372
                                       68***********************988855555 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 1.4
                            TPR_11  11 eeAieaYkkAlkldPdna 28 
                                       ++A++ +++Al+ +++ a
  gi|386002441|ref|YP_005920740.1| 410 DAALALLRTALENKEETA 427
                                       89*********9776665 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.4e-05      0.03       4      32 ..     148     176 ..     147     178 .. 0.92
   2 !   23.3   0.0     1e-07   5.5e-05       1      33 [.     179     211 ..     179     212 .. 0.95
   3 !   19.2   0.1     2e-06    0.0011       2      31 ..     214     243 ..     213     246 .. 0.90
   4 !   15.1   0.0   4.2e-05     0.023       3      32 ..     249     278 ..     248     280 .. 0.91
   5 !   18.6   0.1   3.2e-06    0.0017       3      34 .]     283     314 ..     282     314 .. 0.96
   6 !   17.3   0.0   8.2e-06    0.0045       2      32 ..     316     346 ..     315     348 .. 0.90
   7 !   23.1   0.0   1.1e-07     6e-05       1      31 [.     349     379 ..     349     384 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-05
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtA 32 
                                       k l+l+P+ a  y nLAe+++++G+ ++ 
  gi|386002441|ref|YP_005920740.1| 148 KLLKLNPTTASTYENLAEAYRMLGQIDKS 176
                                       789**********************9876 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ++ ka+eldP  a +++n++ +l  +G++++A+
  gi|386002441|ref|YP_005920740.1| 179 CLDKAIELDPQAARSWFNMGLALDDLGRKDEAL 211
                                       678****************************97 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 2e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                       ++ka+e dP +a a+ n +++l+ +G+ ++
  gi|386002441|ref|YP_005920740.1| 214 FEKAIETDPEDAAAWANNGYALYYLGRIEE 243
                                       9**********************9998776 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 4.2e-05
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +ka+e dP  a+a++n+  +l++ G+ ++ 
  gi|386002441|ref|YP_005920740.1| 249 EKAIEFDPQAAEAWTNKSSALAQMGRIKES 278
                                       79*********************9998765 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 3.2e-06
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +ka+ l+P+ a a+nn++ +l+ + + ++A++
  gi|386002441|ref|YP_005920740.1| 283 EKAVNLNPKLAMAWNNKGSVLYDLDRAEEAIE 314
                                       79***************************986 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 8.2e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + +a+eldP+ a a+ n++++l ++G+ ++A
  gi|386002441|ref|YP_005920740.1| 316 LDRAIELDPKLAMAWSNKGVALGSLGRMEDA 346
                                       579*********************9997777 PP

  == domain 7  score: 23.1 bits;  conditional E-value: 1.1e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y+ka+e+dP++a  y  L +l++k+G+ ++
  gi|386002441|ref|YP_005920740.1| 349 AYEKAIEHDPKDAITYIALVRLYRKLGREAD 379
                                       5**************************8655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.32   1.8e+02       7      36 ..      87     116 ..      82     134 .. 0.81
   2 !   26.3   0.1   1.2e-08   6.7e-06      26      76 ..     139     188 ..     136     189 .. 0.89
   3 !   43.6   0.4     5e-14   2.7e-11       2      75 ..     156     221 ..     155     223 .. 0.94
   4 !   18.8   1.6   2.7e-06    0.0015       3      74 ..     225     288 ..     223     291 .. 0.76
   5 !   27.3   0.7     6e-09   3.3e-06       2      76 ..     258     324 ..     257     325 .. 0.93
   6 !   34.1   0.4   4.6e-11   2.5e-08       2      75 ..     292     357 ..     291     359 .. 0.93
   7 !   23.4   0.6     1e-07   5.6e-05       2      73 ..     326     389 ..     325     393 .. 0.84
   8 !    7.4   1.4    0.0098       5.3       3      36 ..     361     394 ..     359     425 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.32
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrl 36 
                                         +a+ +++l ++d+  ++ +k++ i + l
  gi|386002441|ref|YP_005920740.1|  87 MDIAVSYYKLDDLDKGDDYSRKSMHIKELL 116
                                       56899*****************99887544 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.2e-08
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++k++++ ++ll + +p ta+t+ nL+++yr+lg+ ++ le l +a+++++
  gi|386002441|ref|YP_005920740.1| 139 YRKVIQLSSKLL-KLNPTTASTYENLAEAYRMLGQIDKSLECLDKAIELDP 188
                                       889999998887.6799******************************9976 PP

  == domain 3  score: 43.6 bits;  conditional E-value: 5e-14
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a+++ nla+++r lg+ d++le+l+ka+e+      p+   +a++ +n+g +++ lgr +eAl+++e+a++ +
  gi|386002441|ref|YP_005920740.1| 156 TASTYENLAEAYRMLGQIDKSLECLDKAIELD-----PQ---AARSWFNMGLALDDLGRKDEALKAFEKAIETD 221
                                       799*************************9999.....75...8***************************9965 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 2.7e-06
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a+a+ n + +l++lgr +e+l+  eka+e       p   ++a++  n + ++ ++gr +e le+ e+a+++
  gi|386002441|ref|YP_005920740.1| 225 AAAWANNGYALYYLGRIEESLKASEKAIEFD-----P---QAAEAWTNKSSALAQMGRIKESLEASEKAVNL 288
                                       5666699********************7777.....3...36777777777777777777777777777665 PP

  == domain 5  score: 27.3 bits;  conditional E-value: 6e-09
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a a++n  ++l+++gr  e+le  eka+++      p+   +a + +n g +++ l+r eeA+e+l +a+++++
  gi|386002441|ref|YP_005920740.1| 258 AAEAWTNKSSALAQMGRIKESLEASEKAVNLN-----PK---LAMAWNNKGSVLYDLDRAEEAIEALDRAIELDP 324
                                       7899************************7777.....64...9*****************************976 PP

  == domain 6  score: 34.1 bits;  conditional E-value: 4.6e-11
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a a+nn ++vl+ l r +eA+e l++a+e+      p+   +a +  n g ++  lgr e+Al+++e+a++ +
  gi|386002441|ref|YP_005920740.1| 292 LAMAWNNKGSVLYDLDRAEEAIEALDRAIELD-----PK---LAMAWSNKGVALGSLGRMEDALDAYEKAIEHD 357
                                       5889************************9999.....75...9***************************9976 PP

  == domain 7  score: 23.4 bits;  conditional E-value: 1e-07
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       +a a++n +++l  lgr+++Al+ +eka+e       p     a+t+++L rlyr+lgr ++ +e+ + a +
  gi|386002441|ref|YP_005920740.1| 326 LAMAWSNKGVALGSLGRMEDALDAYEKAIEHD-----P---KDAITYIALVRLYRKLGREADSIEACKAARD 389
                                       578999**********************6666.....5...4699999999999999999998887666655 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0098
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrl 36 
                                       a+++  l  ++r+lgr ++++e +++a+++++  
  gi|386002441|ref|YP_005920740.1| 361 AITYIALVRLYRKLGREADSIEACKAARDLIETE 394
                                       6788899999999999999999999999999655 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.7   5.8e-11   3.2e-08       2      67 ..     162     224 ..     161     228 .. 0.96
   2 !   17.5   0.1   9.2e-06     0.005       3      58 ..     231     283 ..     229     291 .. 0.90
   3 !   24.7   0.8     5e-08   2.7e-05       6      66 ..     268     325 ..     268     327 .. 0.95
   4 !   39.0   0.7   1.7e-12   9.3e-10       3      68 .]     299     361 ..     297     361 .. 0.96
   5 !   20.9   0.4   7.7e-07   0.00042       4      62 ..     334     389 ..     331     395 .. 0.92
   6 ?    4.0   0.3      0.14        79      11      33 ..     407     426 ..     397     432 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.8e-11
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +la a++ +g+ d+ ++ l+ a+++d   P+aa+++++ g+a+  +gr +eA+ ++++a++ +p +
  gi|386002441|ref|YP_005920740.1| 162 NLAEAYRMLGQIDKSLECLDKAIELD---PQAARSWFNMGLALDDLGRKDEALKAFEKAIETDPED 224
                                       58999999******************...**********************************987 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 9.2e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58 
                                        ++a++++g+ ++ ++a e a++ d   P+aaeA+ ++  a+++ gr +e +++ +
  gi|386002441|ref|YP_005920740.1| 231 NGYALYYLGRIEESLKASEKAIEFD---PQAAEAWTNKSSALAQMGRIKESLEASE 283
                                       699**********************...**********************996544 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 5e-08
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       a+++ g+  + ++a e a+ ++   P  a A++++g +++ + r +eA++++++a++ +p+
  gi|386002441|ref|YP_005920740.1| 268 ALAQMGRIKESLEASEKAVNLN---PKLAMAWNNKGSVLYDLDRAEEAIEALDRAIELDPK 325
                                       57899*****************...********************************9996 PP

  == domain 4  score: 39.0 bits;  conditional E-value: 1.7e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++  ++++ + ++A++al++a+++d   P  a A+ ++g+a+  +gr+++A+++y++a++++p+++
  gi|386002441|ref|YP_005920740.1| 299 KGSVLYDLDRAEEAIEALDRAIELD---PKLAMAWSNKGVALGSLGRMEDALDAYEKAIEHDPKDA 361
                                       67889********************...***********************************985 PP

  == domain 5  score: 20.9 bits;  conditional E-value: 7.7e-07
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       + a+  +g+ +dA+ a+e a++ d   P +a  + +l +++ ++gr a+ +++++aa +
  gi|386002441|ref|YP_005920740.1| 334 GVALGSLGRMEDALDAYEKAIEHD---PKDAITYIALVRLYRKLGREADSIEACKAARD 389
                                       5677889*****************...*****************************975 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.14
                            TPR_16  11 gdyddAaaaleaalkrdpssPda 33 
                                       g +d+A+a+l++al++     ++
  gi|386002441|ref|YP_005920740.1| 407 GSPDAALALLRTALENK---EET 426
                                       45778888888888877...444 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       2.1   1.2e+03      17      43 ..     139     165 ..     128     166 .. 0.85
   2 !   20.5   0.1   1.1e-06   0.00058       7      42 ..     163     198 ..     157     200 .. 0.93
   3 !   23.2   0.8   1.4e-07   7.6e-05       4      39 ..     194     229 ..     191     230 .. 0.91
   4 !   11.5   0.1   0.00078      0.43       9      40 ..     233     264 ..     232     267 .. 0.92
   5 ?    6.3   0.0     0.038        21       9      39 ..     267     297 ..     265     302 .. 0.91
   6 !   18.2   0.8   5.7e-06    0.0031       8      39 ..     300     331 ..     295     336 .. 0.89
   7 !   16.9   0.2   1.5e-05    0.0079      13      44 .]     339     370 ..     334     370 .. 0.91
   8 ?    6.7   0.1     0.029        16       4      30 ..     364     390 ..     362     405 .. 0.81
   9 ?    6.6   0.5     0.031        17      14      36 ..     406     429 ..     399     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.1
                            TPR_14  17 pdeAiallrralalaPddaeawlllaq 43 
                                       +++ i+l  ++l+l+P+ a ++  la+
  gi|386002441|ref|YP_005920740.1| 139 YRKVIQLSSKLLKLNPTTASTYENLAE 165
                                       66777888899***********99997 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.1e-06
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                                       laea++ lG+ d+++++l++a++l+P+ a+ w+ ++
  gi|386002441|ref|YP_005920740.1| 163 LAEAYRMLGQIDKSLECLDKAIELDPQAARSWFNMG 198
                                       8*****************************999886 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.4e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +  ++ al  lG+ deA++++++a++++P+da+aw 
  gi|386002441|ref|YP_005920740.1| 194 WFNMGLALDDLGRKDEALKAFEKAIETDPEDAAAWA 229
                                       7778999****************************5 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00078
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawll 40 
                                        al+ lG+ +e++++ ++a++ +P+ aeaw+ 
  gi|386002441|ref|YP_005920740.1| 233 YALYYLGRIEESLKASEKAIEFDPQAAEAWTN 264
                                       68899*************************85 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.038
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawl 39 
                                       +al++ G+ +e++++ ++a+ l+P+ a aw 
  gi|386002441|ref|YP_005920740.1| 267 SALAQMGRIKESLEASEKAVNLNPKLAMAWN 297
                                       6899************************996 PP

  == domain 6  score: 18.2 bits;  conditional E-value: 5.7e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       +++l+ l++ +eAi++l+ra++l+P+ a aw 
  gi|386002441|ref|YP_005920740.1| 300 GSVLYDLDRAEEAIEALDRAIELDPKLAMAWS 331
                                       7899*************************995 PP

  == domain 7  score: 16.9 bits;  conditional E-value: 1.5e-05
                            TPR_14  13 alGdpdeAiallrralalaPddaeawlllaql 44 
                                        lG+ ++A++++++a++++P+da ++++l++l
  gi|386002441|ref|YP_005920740.1| 339 SLGRMEDALDAYEKAIEHDPKDAITYIALVRL 370
                                       68999***********************9986 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.029
                            TPR_14   4 llalaeallalGdpdeAiallrralal 30 
                                       + al+++++ lG+ +++i+++++a +l
  gi|386002441|ref|YP_005920740.1| 364 YIALVRLYRKLGREADSIEACKAARDL 390
                                       5699*********99999999998665 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.031
                            TPR_14  14 lGdpdeAiallrrala.laPddae 36 
                                        G pd+A+allr al+ +  + ++
  gi|386002441|ref|YP_005920740.1| 406 CGSPDAALALLRTALEnKEETADW 429
                                       599************932333334 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.5e-05     0.013      11      63 ..     139     191 ..     136     193 .. 0.91
   2 !   27.4   0.9   4.9e-09   2.7e-06       8      65 ..     170     227 ..     163     231 .. 0.92
   3 !   13.6   0.0    0.0001     0.055      11      60 ..     241     290 ..     233     293 .. 0.90
   4 !   22.1   0.3   2.2e-07   0.00012       7      61 ..     271     325 ..     267     329 .. 0.90
   5 !   31.6   0.8   2.5e-10   1.3e-07       9      71 ..     307     369 ..     300     371 .. 0.92
   6 ?    2.1   0.1       0.4   2.2e+02      34      64 ..     398     428 ..     394     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       + + ++ +  ll l+P +++ +   + ++  lG++ + l++L+ +++l+p+a+
  gi|386002441|ref|YP_005920740.1| 139 YRKVIQLSSKLLKLNPTTASTYENLAEAYRMLGQIDKSLECLDKAIELDPQAA 191
                                       55667777889***************************************987 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.9e-09
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                         + ++ l++++  + l+P++++ ++  Gl+l  lG+  +Al+++e +++ +p++++a
  gi|386002441|ref|YP_005920740.1| 170 LGQIDKSLECLDKAIELDPQAARSWFNMGLALDDLGRKDEALKAFEKAIETDPEDAAA 227
                                       5678999**********************************************99987 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.0001
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        e+ l+++e  + ++P+++e +     +laq+G++++ l++ e ++ l+p
  gi|386002441|ref|YP_005920740.1| 241 IEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESLEASEKAVNLNP 290
                                       577899********************************999888887777 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 2.2e-07
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +  +  + l+++e  + l+P+ +  +   G +l+ l++ ++A+++L+++++l+p+
  gi|386002441|ref|YP_005920740.1| 271 QMGRIKESLEASEKAVNLNPKLAMAWNNKGSVLYDLDRAEEAIEALDRAIELDPK 325
                                       5566777899*******************************************96 PP

  == domain 5  score: 31.6 bits;  conditional E-value: 2.5e-10
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                       +++e+a+++++r + l+P+ +  +   G++l  lG+++ Al++ e +++++p+++  + +  +
  gi|386002441|ref|YP_005920740.1| 307 DRAEEAIEALDRAIELDPKLAMAWSNKGVALGSLGRMEDALDAYEKAIEHDPKDAITYIALVR 369
                                       789*************************************************99988776655 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.4
                             TPR_9  34 dRGlllaqlGclsaAladLeaylalapdapd 64 
                                        R+  +a  G + aAla L ++l++ ++ +d
  gi|386002441|ref|YP_005920740.1| 398 NRACFEAVCGSPDAALALLRTALENKEETAD 428
                                       677888888999***********99995544 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.9     1e+03      19      43 ..      77     101 ..      70     102 .. 0.87
   2 !   19.0   0.1   2.8e-06    0.0015       6      59 ..     138     191 ..     136     194 .. 0.90
   3 !   18.1   2.5   5.1e-06    0.0028       8      62 ..     208     262 ..     203     271 .. 0.90
   4 !   15.1   1.0   4.7e-05     0.026       1      57 [.     269     325 ..     269     331 .. 0.93
   5 !   23.0   0.4   1.5e-07   8.4e-05       5      61 ..     341     397 ..     339     401 .. 0.90
   6 ?    3.2   0.0      0.23   1.3e+02       5      23 ..     407     425 ..     406     432 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.9
                            TPR_19  19 qedpknaearllLAeallalgqlde 43 
                                       ++d + +e+ ++ A  +++l +ld+
  gi|386002441|ref|YP_005920740.1|  77 TDDYNKSEIFMDIAVSYYKLDDLDK 101
                                       6778899***************997 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.8e-06
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       +y   ++l +++l+ +p  a    +LAea+  lgq+d+  ++Ld++ e dp+ a
  gi|386002441|ref|YP_005920740.1| 138 QYRKVIQLSSKLLKLNPTTASTYENLAEAYRMLGQIDKSLECLDKAIELDPQAA 191
                                       56777888899999*************************************944 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 5.1e-06
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +eAl+++e+a++ dp++a+a+++   al+ lg+++e  ++ +++ e dp+ a+++
  gi|386002441|ref|YP_005920740.1| 208 DEALKAFEKAIETDPEDAAAWANNGYALYYLGRIEESLKASEKAIEFDPQAAEAW 262
                                       89*************************************9999999999976665 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 4.7e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l ++g+  e l++ e+a   +pk a a+ +   +l+ l + +eA+++Ld++ e dp+
  gi|386002441|ref|YP_005920740.1| 269 LAQMGRIKESLEASEKAVNLNPKLAMAWNNKGSVLYDLDRAEEAIEALDRAIELDPK 325
                                       57899**************************************************99 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 1.5e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       g+ ++Al+++e+a+++dpk+a   ++L++++ +lg+ ++ +++++a+ +    +++y
  gi|386002441|ref|YP_005920740.1| 341 GRMEDALDAYEKAIEHDPKDAITYIALVRLYRKLGREADSIEACKAARDLIETESEY 397
                                       7889*****************************************998876666665 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.23
                            TPR_19   5 gdyaeAlalleqalqedpk 23 
                                       g +++Alall+ al+ + +
  gi|386002441|ref|YP_005920740.1| 407 GSPDAALALLRTALENKEE 425
                                       6778888888888765544 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.64   3.5e+02       6      21 ..      89     104 ..      84     108 .. 0.81
   2 !   13.3   0.1   0.00018       0.1       5      32 ..     162     189 ..     160     190 .. 0.94
   3 !   17.8   0.0   6.7e-06    0.0036       3      32 ..     194     223 ..     192     224 .. 0.93
   4 ?    7.6   0.1     0.012       6.8       1      21 [.     233     253 ..     233     254 .. 0.94
   5 ?    7.8   0.2      0.01       5.5       9      32 ..     302     325 ..     266     326 .. 0.86
   6 !    9.4   0.0    0.0033       1.8       7      32 ..     334     359 ..     325     360 .. 0.77
   7 ?    3.1   0.1      0.32   1.8e+02       8      28 ..     369     392 ..     365     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAle 21 
                                       +a sy+kl+d dk  +
  gi|386002441|ref|YP_005920740.1|  89 IAVSYYKLDDLDKGDD 104
                                       89*****999998655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                                       +la++yr+lg+ dk+le l++ i+  P+
  gi|386002441|ref|YP_005920740.1| 162 NLAEAYRMLGQIDKSLECLDKAIELDPQ 189
                                       69******9***************9996 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                        ++++l++  lg++d+Al+a+e+ i+  P+
  gi|386002441|ref|YP_005920740.1| 194 WFNMGLALDDLGRKDEALKAFEKAIETDPE 223
                                       79********99**************9996 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAle 21 
                                       +Aly+l++  ++l+ ++kA+e
  gi|386002441|ref|YP_005920740.1| 233 YALYYLGRIEESLKASEKAIE 253
                                       8***********99*****97 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                        ++ l+++++A+eal+r i+  P+
  gi|386002441|ref|YP_005920740.1| 302 VLYDLDRAEEAIEALDRAIELDPK 325
                                       4555689************99886 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++ +lg+ ++Al+a+e+ i+  P+
  gi|386002441|ref|YP_005920740.1| 334 GVALGSLGRMEDALDAYEKAIEHDPK 359
                                       44555559*************99886 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.32
                                       HHHHHHHHHH...HHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtd...kAlealerlik 28 
                                       ++yrklg+ +   +A++a ++li+
  gi|386002441|ref|YP_005920740.1| 369 RLYRKLGREAdsiEACKAARDLIE 392
                                       689997644436688889998887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00016     0.088       1      33 [.     159     189 ..     159     192 .. 0.90
   2 !   17.6   0.0   5.1e-06    0.0028       1      35 [.     193     225 ..     193     226 .. 0.94
   3 ?   -0.6   0.0       3.2   1.7e+03       1      21 [.     234     254 ..     234     261 .. 0.82
   4 ?    0.1   0.0         2   1.1e+03       1      21 [.     268     288 ..     268     291 .. 0.90
   5 ?    6.4   0.1     0.019        10       1      32 [.     295     324 ..     295     327 .. 0.88
   6 !   16.3   0.0   1.3e-05     0.007       1      35 [.     329     361 ..     329     362 .. 0.93
   7 ?    4.7   0.4     0.065        36       1      27 [.     363     387 ..     363     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++ nLa++y+ lG+ ++ +e++ +  a++ dp+
  gi|386002441|ref|YP_005920740.1| 159 TYENLAEAYRMLGQIDKSLECLDK--AIELDPQ 189
                                       689*********************..8887775 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.1e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +++n++ +  +lG+ +eA++ +e+  a++ dpeda
  gi|386002441|ref|YP_005920740.1| 193 SWFNMGLALDDLGRKDEALKAFEK--AIETDPEDA 225
                                       689*********************..****99997 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.2
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       aL++L+r+ ++l   e+Aie+
  gi|386002441|ref|YP_005920740.1| 234 ALYYLGRIEESLKASEKAIEF 254
                                       789999998888888888886 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       aL +++r+ ++l   e+A+ l
  gi|386002441|ref|YP_005920740.1| 268 ALAQMGRIKESLEASEKAVNL 288
                                       7999*******9999999987 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.019
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n +++  +l + eeAie + +  a++ dp
  gi|386002441|ref|YP_005920740.1| 295 AWNNKGSVLYDLDRAEEAIEALDR--AIELDP 324
                                       78999*******************..777666 PP

  == domain 6  score: 16.3 bits;  conditional E-value: 1.3e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       a++n +++  +lG++e+A++ ye+  a++ dp da
  gi|386002441|ref|YP_005920740.1| 329 AWSNKGVALGSLGRMEDALDAYEK--AIEHDPKDA 361
                                       68999*******************..***999875 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.065
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                       ++ +L rly++lG+ ++ ie +++  a
  gi|386002441|ref|YP_005920740.1| 363 TYIALVRLYRKLGREADSIEACKA--A 387
                                       6889**********9999999998..3 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.4e-06   0.00078       1      30 [.     156     185 ..     156     186 .. 0.97
   2 !   15.5   0.0   2.1e-05     0.012       7      31 ..     196     220 ..     196     220 .. 0.96
   3 ?    4.9   0.1     0.046        25       9      30 ..     232     253 ..     228     254 .. 0.93
   4 ?    5.2   0.1     0.036        20       7      31 ..     264     288 ..     259     289 .. 0.88
   5 !   10.2   0.5     0.001      0.56       2      30 ..     293     321 ..     292     322 .. 0.93
   6 !   10.7   0.1   0.00067      0.37       2      30 ..     327     355 ..     326     355 .. 0.92
   7 ?    1.3   0.1      0.63   3.4e+02       4      28 ..     363     387 ..     361     394 .. 0.80
   8 ?    1.0   0.0      0.81   4.4e+02      16      30 ..     407     421 ..     398     426 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleeala 30 
                                       tAs++ NLa a+r +g+ d++++ l++a++
  gi|386002441|ref|YP_005920740.1| 156 TASTYENLAEAYRMLGQIDKSLECLDKAIE 185
                                       8***************************98 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.1e-05
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N++ al ++gr deA++ +e+a+++
  gi|386002441|ref|YP_005920740.1| 196 NMGLALDDLGRKDEALKAFEKAIET 220
                                       99*********************86 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.046
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + al+ +gr +e+++  e+a++
  gi|386002441|ref|YP_005920740.1| 232 GYALYYLGRIEESLKASEKAIE 253
                                       789*****************97 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.036
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N + al q+gr +e+++  e+a+++
  gi|386002441|ref|YP_005920740.1| 264 NKSSALAQMGRIKESLEASEKAVNL 288
                                       55789*****************985 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.001
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                                       A++ nN + +l+++ r +eA + l++a++
  gi|386002441|ref|YP_005920740.1| 293 AMAWNNKGSVLYDLDRAEEAIEALDRAIE 321
                                       8888***********************98 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00067
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                                       A++ +N ++al ++gr ++A++ +e+a++
  gi|386002441|ref|YP_005920740.1| 327 AMAWSNKGVALGSLGRMEDALDAYEKAIE 355
                                       7777899********************96 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.63
                            TPR_10   4 slnNLanalrqrgrydeAealleea 28 
                                       ++  L +++r++gr +++ + ++ a
  gi|386002441|ref|YP_005920740.1| 363 TYIALVRLYRKLGREADSIEACKAA 387
                                       7888999*******99888877766 PP

  == domain 8  score: 1.0 bits;  conditional E-value: 0.81
                            TPR_10  16 grydeAealleeala 30 
                                       g  d+A+all+ al+
  gi|386002441|ref|YP_005920740.1| 407 GSPDAALALLRTALE 421
                                       66799*******997 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   8.8e-07   0.00048      60     123 ..     155     218 ..     144     221 .. 0.91
   2 !   13.5   0.2   0.00014     0.074      71     121 ..     234     284 ..     223     289 .. 0.89
   3 !   15.2   0.3   4.1e-05     0.022      72     122 ..     303     353 ..     282     356 .. 0.90
   4 !   17.3   1.6     9e-06    0.0049      63     129 ..     328     394 ..     299     404 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.8e-07
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  60 lrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                          + +e laea   lG++++ l+ l+++++++P   r++  + +Al  +Gr+ eAL+++e++ 
  gi|386002441|ref|YP_005920740.1| 155 TTASTYENLAEAYRMLGQIDKSLECLDKAIELDPQAARSWFNMGLALDDLGRKDEALKAFEKAI 218
                                       556789******************************************************9875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       a+ +lGr+ee l+  e++++ +P   +++     Ala++Gr  e Le+ e+
  gi|386002441|ref|YP_005920740.1| 234 ALYYLGRIEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESLEASEK 284
                                       7789******************************************98655 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 4.1e-05
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       +  l raeea++ l+++++++P    ++     Al  +Gr ++AL +Ye++
  gi|386002441|ref|YP_005920740.1| 303 LYDLDRAEEAIEALDRAIELDPKLAMAWSNKGVALGSLGRMEDALDAYEKA 353
                                       56799*******************************************987 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 9e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                              BTAD  63 ealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaee 129
                                        a      a+ +lGr e+al+ +e++++++P +  ++ +l r ++++Gr+a+ +e+ + +r+l ++e
  gi|386002441|ref|YP_005920740.1| 328 MAWSNKGVALGSLGRMEDALDAYEKAIEHDPKDAITYIALVRLYRKLGREADSIEACKAARDLIETE 394
                                       3333334467778899999999999999999999999999999999999999999999999988876 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.8   2.1e+03      20      48 ..      79     108 ..      60     114 .. 0.64
   2 !   26.1   0.2   1.4e-08   7.5e-06       3      82 .]     137     217 ..     136     217 .. 0.90
   3 !   18.3   0.7   3.7e-06     0.002       5      81 ..     241     318 ..     233     319 .. 0.94
   4 ?    1.1   0.0      0.86   4.7e+02      68      82 .]     339     353 ..     323     385 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.8
                                       H--HHHHHH.HHHHHHHTT-HHHHHHHHHC CS
                            ANAPC3  20 tespedayl.lAlclylngqykrAyellrk 48 
                                        ++ + +++  A ++y++ + ++  ++ rk
  gi|386002441|ref|YP_005920740.1|  79 DYNKSEIFMdIAVSYYKLDDLDKGDDYSRK 108
                                       444445666448899998888776666666 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.4e-08
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                        +y++ i l+++ll+ ++  ++    lA+++  +gq ++ +e l+ka +l+++  ++++ ++ +l +L++ +eA++a
  gi|386002441|ref|YP_005920740.1| 137 TQYRKVIQLSSKLLKLNPTTASTYENLAEAYRMLGQIDKSLECLDKAiELDPQAARSWFNMGLALDDLGRKDEALKA 213
                                       689999********6666555555559************************************************** PP

                                       H-SS CS
                            ANAPC3  79 Lekl 82 
                                       +ek+
  gi|386002441|ref|YP_005920740.1| 214 FEKA 217
                                       *985 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +++ +  +e++ + +++ +e+   ++ +l ++g+ k+ +e  +ka +ln+k   ++  ++ +l++L++ eeAi aL+
  gi|386002441|ref|YP_005920740.1| 241 IEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESLEASEKAvNLNPKLAMAWNNKGSVLYDLDRAEEAIEALD 317
                                       6677888999999***************************************************************8 PP

                                       S CS
                            ANAPC3  81 k 81 
                                       +
  gi|386002441|ref|YP_005920740.1| 318 R 318
                                       7 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.86
                                       HTT-HHHHHHHH-SS CS
                            ANAPC3  68 kLkkyeeAiaaLekl 82 
                                        L+++e+A++a+ek+
  gi|386002441|ref|YP_005920740.1| 339 SLGRMEDALDAYEKA 353
                                       567777777777664 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1     9e-07   0.00049      55     128 ..     157     219 ..     151     223 .. 0.88
   2 ?    5.4   0.1     0.034        18      54      84 ..     224     254 ..     220     258 .. 0.89
   3 !    7.9   0.2    0.0054       2.9      45      83 ..     249     287 ..     247     325 .. 0.81
   4 !   11.6   0.1   0.00039      0.21      64     128 ..     295     355 ..     288     359 .. 0.79
   5 ?    5.6   0.0     0.028        15      45      81 ..     351     387 ..     349     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9e-07
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       a ++  l+ea+  lg+ d++le+ dka+       el+ +  + W    f+ + al++lGrkdealkaf++a e
  gi|386002441|ref|YP_005920740.1| 157 ASTYENLAEAYRMLGQIDKSLECLDKAI-------ELDPQAARSW----FNMGLALDDLGRKDEALKAFEKAIE 219
                                       5567889999999999999999999987.......8999999999....789*******************988 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  54 dalchaglsealaklgrydealesadkalry 84 
                                       da ++a    al  lgr +e+l++++ka+++
  gi|386002441|ref|YP_005920740.1| 224 DAAAWANNGYALYYLGRIEESLKASEKAIEF 254
                                       889999999999*************999875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0054
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalr 83 
                                       e a +++   a +++  s+ala++gr +e+le+++ka++
  gi|386002441|ref|YP_005920740.1| 249 EKAIEFDPQAAEAWTNKSSALAQMGRIKESLEASEKAVN 287
                                       6777888888999999*******************9975 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00039
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       a+ + g+    l  a++a++ ++r  el+      W     +++val +lGr ++al+a+++a e
  gi|386002441|ref|YP_005920740.1| 295 AWNNKGSVLYDLDRAEEAIEALDRAIELDPKLAMAW----SNKGVALGSLGRMEDALDAYEKAIE 355
                                       555555555667788888888888888887666666....69*******************9987 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.028
                                       TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadka 81 
                                       e a +h+  da+++ +l   + klgr  +++e+ + a
  gi|386002441|ref|YP_005920740.1| 351 EKAIEHDPKDAITYIALVRLYRKLGREADSIEACKAA 387
                                       7899**********************99999998776 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.2e-06    0.0034     188     259 ..     155     224 ..     108     226 .. 0.82
   2 !   14.9   0.3   1.7e-05    0.0092     180     255 ..     215     288 ..     203     293 .. 0.87
   3 !   13.1   0.2   6.3e-05     0.034     205     259 ..     306     360 ..     291     366 .. 0.90
   4 !    8.2   0.2    0.0019         1     205     258 ..     340     393 ..     336     437 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                       SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 188 esallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        +    ++  lA  y  lg+ +k+le++dkaie +p++   + + +  l   G  ++A ++ e+a + D +D
  gi|386002441|ref|YP_005920740.1| 155 TT--ASTYENLAEAYRMLGQIDKSLECLDKAIELDPQAARSWFNMGLALDDLGRKDEALKAFEKAIETDPED 224
                                       33..357888*******************************************************9999887 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-05
                                       .GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 180 nedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       ++  e++pe a  w+++  A +y  lg+ e++l+  +kaie +p++ e +++K+  l ++G +k+  e+ e+a +l
  gi|386002441|ref|YP_005920740.1| 215 EKAIETDPEDAAAWANNGYALYY--LGRIEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESLEASEKAVNL 288
                                       3456888999999***9999997..8999*****************************************999877 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 6.3e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       l + e+A+e +d+aie +p+l   + +K+  l   G +++A ++ e+a + D +D
  gi|386002441|ref|YP_005920740.1| 306 LDRAEEAIEALDRAIELDPKLAMAWSNKGVALGSLGRMEDALDAYEKAIEHDPKD 360
                                       445789*********************************************9999 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0019
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                       lg++e Al+  +kaieh+p+    y++  r++++ G   + +e+ + ar l + 
  gi|386002441|ref|YP_005920740.1| 340 LGRMEDALDAYEKAIEHDPKDAITYIALVRLYRKLGREADSIEACKAARDLIET 393
                                       678899*******************************************98655 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   1.2e-07   6.3e-05      68     182 ..     113     227 ..      95     231 .. 0.88
   2 !   17.3   4.3   3.9e-06    0.0021     126     249 ..     238     362 ..     228     367 .. 0.87
   3 ?    1.9   0.1      0.19     1e+02     119     177 ..     364     424 ..     359     432 .. 0.51

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
                            TPR_15  68 rqLlasgkaraedyerliel.lydaepkeaarlaekgwrrfrsprlLssalellerakdydriaellksleeeeaae 143
                                       ++Ll+ +k+ + +y+rli+  l + ++++ ++l+ k  +   +p   s + +l+e+ + + +i++ l+ l +  ++ 
  gi|386002441|ref|YP_005920740.1| 113 KELLNDEKGIILNYDRLIQVfLFKTQYRKVIQLSSKLLKL--NPTTASTYENLAEAYRMLGQIDKSLECLDKAIELD 187
                                       7899999999*********999************998765..55566667778888888999999999999999999 PP

                            TPR_15 144 .qsaafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                        q a+ ++ ++ +  + g++d+Al+++++A++ +p+++++
  gi|386002441|ref|YP_005920740.1| 188 pQAARSWFNMGLALDDLGRKDEALKAFEKAIETDPEDAAA 227
                                       88899******************************99876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.9e-06
                            TPR_15 126 ydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLre 201
                                       + ri+e lk  e+  ++  q a  +   +++  q g+ +++l++ ++A++l+p+ + + ++   +l Dl+r++e   
  gi|386002441|ref|YP_005920740.1| 238 LGRIEESLKASEKAIEFDpQAAEAWTNKSSALAQMGRIKESLEASEKAVNLNPKLAMAWNNKGSVLYDLDRAEE--- 311
                                       689*******9999999988899*******************************9999999999******9997... PP

                            TPR_15 202 llkawkaraesdasLwgpl...aaAlllLgrpkkALeylrkqakenrkdpl 249
                                       +++a+ ++ e d++L  +    + Al  Lgr + AL+ ++k  +  +kd+ 
  gi|386002441|ref|YP_005920740.1| 312 AIEALDRAIELDPKLAMAWsnkGVALGSLGRMEDALDAYEKAIEHDPKDAI 362
                                       888888888777777555522289******************999999875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
                            TPR_15 119 llerakdydriaellksleeeeaae..qsaafllaraelyrqegqtdaAlrdyreAlalap 177
                                       ++   + y+++++   s+e+ +aa+   +    + ra ++   g +daAl ++r Al+ + 
  gi|386002441|ref|YP_005920740.1| 364 YIALVRLYRKLGREADSIEACKAARdlIETESEYNRACFEAVCGSPDAALALLRTALENKE 424
                                       4444444444444444444333333222333334566666666777777777777776665 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.5e-07   0.00035     125     180 ..     138     194 ..     132     199 .. 0.90
   2 ?    3.6   0.1       0.1        54     152     181 ..     200     229 ..     196     235 .. 0.88
   3 ?    3.0   0.3      0.16        87     122     180 ..     271     330 ..     242     337 .. 0.61
   4 ?    2.2   0.0      0.28   1.5e+02     126     170 ..     343     388 ..     332     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.5e-07
                           Wzy_C_2 125 nlaaklalarklihlsPepa.vierlilslallGdedeAeqilararalfpeedakw 180
                                       ++ ++++l++kl++l P+ a ++e+l++++ +lG+ d+ +  l++a+ l p+++ +w
  gi|386002441|ref|YP_005920740.1| 138 QYRKVIQLSSKLLKLNPTTAsTYENLAEAYRMLGQIDKSLECLDKAIELDPQAARSW 194
                                       67899************865389**************************99999999 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                           Wzy_C_2 152 slallGdedeAeqilararalfpeedakwv 181
                                       +l  lG++deA++  ++a+   pe++a+w+
  gi|386002441|ref|YP_005920740.1| 200 ALDDLGRKDEALKAFEKAIETDPEDAAAWA 229
                                       66679************************5 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.16
                           Wzy_C_2 122 spenlaaklalarklihlsPepavi.erlilslallGdedeAeqilararalfpeedakw 180
                                       +   +++ l++++k++ l P+ a+  ++    l  l++ +eA   l+ra+ l p+ + +w
  gi|386002441|ref|YP_005920740.1| 271 QMGRIKESLEASEKAVNLNPKLAMAwNNKGSVLYDLDRAEEAIEALDRAIELDPKLAMAW 330
                                       444567777777777777777776513333445556777777777777777666666555 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.28
                           Wzy_C_2 126 laaklalarklihlsPepavie.rlilslallGdedeAeqilarar 170
                                       +++ l++++k+i++ P+ a+++  l  ++  lG+e++     + ar
  gi|386002441|ref|YP_005920740.1| 343 MEDALDAYEKAIEHDPKDAITYiALVRLYRKLGREADSIEACKAAR 388
                                       5788999*********999866257779999999988776666665 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.015       8.3       3      25 ..     159     181 ..     157     182 .. 0.86
   2 ?    6.6   0.0     0.028        15       1      21 [.     191     211 ..     191     216 .. 0.86
   3 ?    0.5   0.0       2.6   1.4e+03      16      24 ..     221     229 ..     221     245 .. 0.65
   4 ?    2.8   0.1      0.47   2.6e+02       7      26 .]     299     318 ..     293     318 .. 0.81
   5 ?    2.9   0.0      0.41   2.2e+02       2      25 ..     328     351 ..     327     352 .. 0.88
   6 ?   -0.4   0.0         5   2.7e+03       3      16 ..     363     376 ..     361     379 .. 0.84
   7 ?    3.4   0.1       0.3   1.6e+02      14      25 ..     406     417 ..     398     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       ++ +LA+a+  lG+ d  ++ l+
  gi|386002441|ref|YP_005920740.1| 159 TYENLAEAYRMLGQIDKSLECLD 181
                                       5679************9998886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.028
                             TPR_4   1 arallaLArallalGdldeAr 21 
                                       ar   +++ al +lG+ deA+
  gi|386002441|ref|YP_005920740.1| 191 ARSWFNMGLALDDLGRKDEAL 211
                                       577889**************8 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 2.6
                             TPR_4  16 dldeArall 24 
                                       d+++A+a++
  gi|386002441|ref|YP_005920740.1| 221 DPEDAAAWA 229
                                       566666665 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.47
                             TPR_4   7 LArallalGdldeAraller 26 
                                        + +l++l +++eA ++l+r
  gi|386002441|ref|YP_005920740.1| 299 KGSVLYDLDRAEEAIEALDR 318
                                       5668999*******999986 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.41
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                        a ++ + al  lG+ ++A+++ e
  gi|386002441|ref|YP_005920740.1| 328 MAWSNKGVALGSLGRMEDALDAYE 351
                                       688999**************9887 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 5
                             TPR_4   3 allaLArallalGd 16 
                                       +++aL r++  lG+
  gi|386002441|ref|YP_005920740.1| 363 TYIALVRLYRKLGR 376
                                       5799*********9 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.3
                             TPR_4  14 lGdldeAralle 25 
                                        G +d+A+all+
  gi|386002441|ref|YP_005920740.1| 406 CGSPDAALALLR 417
                                       6889*******9 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.6   1.9e+03      36      51 ..     138     152 ..     118     160 .. 0.74
   2 !    8.9   0.0    0.0031       1.7      43      97 ..     162     214 ..     154     221 .. 0.82
   3 ?    5.4   0.1     0.037        20       5      67 ..     195     254 ..     191     293 .. 0.66
   4 ?    0.5   0.1       1.3   6.9e+02      35      95 ..     256     314 ..     236     322 .. 0.65
   5 ?    5.0   0.0     0.052        28       7      59 ..     333     382 ..     327     396 .. 0.74
   6 !    9.1   0.0    0.0028       1.5       3      30 ..     395     422 ..     393     432 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.6
                             TPR_5  36 rrrratiqLassLRnl 51 
                                       +  r +iqL+s L  l
  gi|386002441|ref|YP_005920740.1| 138 QY-RKVIQLSSKLLKL 152
                                       44.568*****99665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0031
                             TPR_5  43 qLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsiv 97 
                                        La + R lG+++++l+ L++ +e  ++  +      + L+L dlgr+ ea++  
  gi|386002441|ref|YP_005920740.1| 162 NLAEAYRMLGQIDKSLECLDKAIELDPQAARSWF--NMGLALDDLGRKDEALKAF 214
                                       589999*************999998776655544..478999*********9876 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.037
                             TPR_5   5 FeragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraelea 67 
                                       F+ + a D  G++d+a + +++a++          a      +L  lG++ee+l+  ++ +e 
  gi|386002441|ref|YP_005920740.1| 195 FNMGLALDDLGRKDEALKAFEKAIETD---PEDAAAWANNGYALYYLGRIEESLKASEKAIEF 254
                                       777888899999999999999999864...444455666677777777777777766555554 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.3
                             TPR_5  35 arrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavs 95 
                                        ++  a    +s+L ++G+++e+l+  ++ ++  + +l  a +     vL dl+r +ea+ 
  gi|386002441|ref|YP_005920740.1| 256 PQAAEAWTNKSSALAQMGRIKESLEASEKAVNL-NPKLAMAWNN-KGSVLYDLDRAEEAIE 314
                                       566666677788888888888887755544443.2334444433.4456677777777765 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.052
                             TPR_5   7 ragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeeala 59 
                                       ++ a  s G+ + a   Y++a+++   + +     i L    R lG+ +++++
  gi|386002441|ref|YP_005920740.1| 333 KGVALGSLGRMEDALDAYEKAIEH---DPKDAITYIALVRLYRKLGREADSIE 382
                                       556778999999999999999996...55555666666666888888888775 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.0028
                             TPR_5   3 aaFeragarDstGhedkavplYrraLae 30 
                                       + ++ra+++   G +d+a  l r aL++
  gi|386002441|ref|YP_005920740.1| 395 SEYNRACFEAVCGSPDAALALLRTALEN 422
                                       5799**********************97 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00066      0.36     232     306 ..     144     211 ..     104     240 .. 0.73
   2 ?    2.5   0.1      0.13        68     267     291 ..     240     264 ..     234     284 .. 0.84
   3 ?    1.7   0.4      0.22   1.2e+02     245     291 ..     259     298 ..     246     312 .. 0.78
   4 ?    3.8   0.0      0.05        27     245     292 ..     293     340 ..     265     384 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00066
                                       ...........HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHH CS
                               FAT 232 keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeq 306
                                       + +++l +++   a +y  ++e  + l++       i++ l++  +a e+dp+ +  w++++l+ +   +k e  
  gi|386002441|ref|YP_005920740.1| 144 QLSSKLLKLNPTTASTYENLAEAYRMLGQ-------IDKSLECLDKAIELDPQAARSWFNMGLALDDLGRKDEAL 211
                                       56667777777778888888888888888.......888888888888888888888888888888776666555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                                       .-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 267 kieeilqsysaateidpswykawht 291
                                       +iee l++  +a e+dp+ ++aw +
  gi|386002441|ref|YP_005920740.1| 240 RIEESLKASEKAIEFDPQAAEAWTN 264
                                       48999******************87 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.22
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       a++ + k++ ++++++       i+e l++  +a+ ++p+++ aw++
  gi|386002441|ref|YP_005920740.1| 259 AEAWTNKSSALAQMGR-------IKESLEASEKAVNLNPKLAMAWNN 298
                                       6666666666666666.......999999999999999999999986 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.05
                                       HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC.......C CS
                               FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawht.......w 292
                                       a + + kG+ +  l +       +ee+ ++  +a e+dp+++ aw +       +
  gi|386002441|ref|YP_005920740.1| 293 AMAWNNKGSVLYDLDR-------AEEAIEALDRAIELDPKLAMAWSNkgvalgsL 340
                                       5555556665555555.......67777777777777777777777644444432 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.012       6.4      81     122 ..     135     176 ..     107     181 .. 0.89
   2 ?    6.3   0.4     0.023        13      78     125 ..     234     281 ..     189     294 .. 0.81
   3 ?    1.2   0.0      0.87   4.7e+02      83     122 ..     341     380 ..     296     389 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        + +yr +++l ++l+  +p+ a++ e +a+a++ lg+  +s
  gi|386002441|ref|YP_005920740.1| 135 FKTQYRKVIQLSSKLLKLNPTTASTYENLAEAYRMLGQIDKS 176
                                       5789*********************************98776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                       + +  g ++ +++  +++++ dp+ aea + k +al q+g+ +es  +
  gi|386002441|ref|YP_005920740.1| 234 ALYYLGRIEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESLEA 281
                                       45555677788888999999**********************999765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.87
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       g ++ a+   +++++ dp++a +  ++++ +++lg++a s
  gi|386002441|ref|YP_005920740.1| 341 GRMEDALDAYEKAIEHDPKDAITYIALVRLYRKLGREADS 380
                                       3344455555666666666666666666666666666665 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.65   3.5e+02     212     256 ..     168     212 ..     151     225 .. 0.78
   2 ?    0.7   0.0      0.52   2.8e+02     214     251 ..     204     241 ..     188     259 .. 0.83
   3 ?    1.4   0.1      0.32   1.8e+02     198     250 ..     290     342 ..     256     345 .. 0.73
   4 !    7.7   0.0    0.0038       2.1     209     256 ..     335     382 ..     327     397 .. 0.89
   5 ?    4.8   0.1     0.029        16     206     235 ..     398     427 ..     390     429 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.65
                                       HHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 212 lllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                        +lg+ ++  + L +a++ d++ +    N+  a  +lg+ +e+ +
  gi|386002441|ref|YP_005920740.1| 168 RMLGQIDKSLECLDKAIELDPQAARSWFNMGLALDDLGRKDEALK 212
                                       567888999999999999999999999999999999999977654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.52
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-- CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkd 251
                                       lgr +eA +  ++a++ d++d+ + +N   a   lg+ 
  gi|386002441|ref|YP_005920740.1| 204 LGRKDEALKAFEKAIETDPEDAAAWANNGYALYYLGRI 241
                                       67889*****************9999977666666655 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.32
                                       ---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT- CS
                        Coatomer_E 198 kstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgk 250
                                       ++  +  n k  v   l+r eeA + L  a++ d+k + + +N  va   lg+
  gi|386002441|ref|YP_005920740.1| 290 PKLAMAWNNKGSVLYDLDRAEEAIEALDRAIELDPKLAMAWSNKGVALGSLGR 342
                                       4556667888888889999*****************99999999888777776 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0038
                                       HHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 209 vvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       v+   lgr e+A    ++a+++d+kd+ t i lv +  +lg++a+++e
  gi|386002441|ref|YP_005920740.1| 335 VALGSLGRMEDALDAYEKAIEHDPKDAITYIALVRLYRKLGREADSIE 382
                                       5555789************************************99876 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.029
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-H CS
                        Coatomer_E 206 gkAvvslllgryeeAeslLkeaLdkdakde 235
                                        +A+ +   g++++A  lL++aL+ +++ +
  gi|386002441|ref|YP_005920740.1| 398 NRACFEAVCGSPDAALALLRTALENKEETA 427
                                       68999999****************998766 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0      0.01       5.4       7      36 ..     156     185 ..     152     189 .. 0.94
   2 ?    5.8   0.6      0.02        11      23     132 ..     206     321 ..     188     337 .. 0.56
   3 ?   -1.5   0.0       3.6     2e+03       8      36 ..     327     355 ..     324     365 .. 0.79
   4 ?   -0.5   0.0       1.8   9.6e+02       5      36 ..     391     421 ..     387     425 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.01
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                       +a++Y nla ++ + g+ +++Le+ld+a+e
  gi|386002441|ref|YP_005920740.1| 156 TASTYENLAEAYRMLGQIDKSLECLDKAIE 185
                                       699*************************97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                           DUF5113  23 eyeeALeyldsale........ylNahyekYakkk.adtldklkmllegegeaaelkWlkdekfktdyevildiRee 90 
                                       + +eAL+ +++a+e          N+ y  Y+  + +++l+  +   e + +aae +W ++    +    + +i+e 
  gi|386002441|ref|YP_005920740.1| 206 RKDEALKAFEKAIEtdpedaaaWANNGYALYYLGRiEESLKASEKAIEFDPQAAE-AWTNK---SSALAQMGRIKES 278
                                       5555555555544311111111456666666544414555555555555665555.68887...6777777788876 PP

                           DUF5113  91 lavayla..lkdkeaydYNnniYldllkllrqDksLesycrqle 132
                                       l ++  a  l+ k a  +Nn+  + l++l r  + +e+  r++e
  gi|386002441|ref|YP_005920740.1| 279 LEASEKAvnLNPKLAMAWNNKG-SVLYDLDRAEEAIEALDRAIE 321
                                       6555554114555566677664.567777777777776665555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.6
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       a ++ n + +l   g+ e+AL+  ++a+e
  gi|386002441|ref|YP_005920740.1| 327 AMAWSNKGVALGSLGRMEDALDAYEKAIE 355
                                       55677777778888999999999999987 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.8
                           DUF5113   5 lqiandYanlayylnvegeyeeALeyldsale 36 
                                        ++ ++Y n a++  v g+++ AL++l++ale
  gi|386002441|ref|YP_005920740.1| 391 IETESEY-NRACFEAVCGSPDAALALLRTALE 421
                                       5555666.445666788888999999988886 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0012      0.65     144     288 ..     134     279 ..      83     281 .. 0.85
   2 ?    2.6   0.2       0.1        55     239     291 ..     264     316 ..     243     320 .. 0.78
   3 ?    0.7   0.0      0.37     2e+02     251     282 ..     344     375 ..     333     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                                       THHHHTTCGGGG---TT-SS--SSSSHHHHHHHHHHHHHT-HHHHHHHHHHHHTT-GGGHHHHHHHHHHTT-...HH CS
                             ChAPs 144 afeklfekgvklgadsevqvptlvnNyLvetllklvrltkrydralellekLkeeepevvillarvlllade...Ev 217
                                       +f++ + k ++l+++    +pt+ + y  e l +  r+  ++d++le l+k +e +p+++     + l+ d+     
  gi|386002441|ref|YP_005920740.1| 134 LFKTQYRKVIQLSSKLLKLNPTTASTY--ENLAEAYRMLGQIDKSLECLDKAIELDPQAARSWFNMGLALDDlgrKD 208
                                       58999********************99..99****************************999999999888533366 PP

                                       HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                             ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                       +a+k  ++++e +++da+    +   l    + e  l+++++a+++ P + + W+  +    +++ i++ L
  gi|386002441|ref|YP_005920740.1| 209 EALKAFEKAIETDPEDAAAWANNGYALYYLGRIEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESL 279
                                       8***************999999888888888999999*****************99888888888777766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                                       HHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ChAPs 239 lqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALltL 291
                                        ++  l +  + +  le++++av++ P   + W     v  +l+  e+A+ +L
  gi|386002441|ref|YP_005920740.1| 264 NKSSALAQMGRIKESLEASEKAVNLNPKLAMAWNNKGSVLYDLDRAEEAIEAL 316
                                       555556666677788999****************9999999999999998877 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT CS
                             ChAPs 251 elAlevakravksaPsefktWalLvkvYikle 282
                                       e Al++ ++a++  P +  t++ Lv+ Y kl+
  gi|386002441|ref|YP_005920740.1| 344 EDALDAYEKAIEHDPKDAITYIALVRLYRKLG 375
                                       56889999********************9986 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.039        21      45      70 ..     195     220 ..      96     244 .. 0.91
   2 ?   -2.3   0.0       9.2     5e+03      52      69 ..     236     253 ..     225     258 .. 0.79
   3 ?    5.2   0.0     0.039        21      37      70 ..     289     322 ..     259     325 .. 0.81
   4 ?   -1.0   0.0       3.4   1.8e+03      44      67 ..     364     387 ..     359     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.039
                            ANAPC5  45 LnlaslhadfghneeAvkaleeairl 70 
                                       +n+     d+g ++eA+ka+e ai++
  gi|386002441|ref|YP_005920740.1| 195 FNMGLALDDLGRKDEALKAFEKAIET 220
                                       5666666789**************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.2
                            ANAPC5  52 adfghneeAvkaleeair 69 
                                       +++g  ee++ka e ai+
  gi|386002441|ref|YP_005920740.1| 236 YYLGRIEESLKASEKAIE 253
                                       567888899999888886 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.039
                            ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleeairl 70 
                                       + ++ +a  n  s+ +d++ +eeA++al  ai+l
  gi|386002441|ref|YP_005920740.1| 289 NPKLAMAWNNKGSVLYDLDRAEEAIEALDRAIEL 322
                                       677888999999999***************9986 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.4
                            ANAPC5  44 lLnlaslhadfghneeAvkaleea 67 
                                        ++l++l  ++g ++++++a + a
  gi|386002441|ref|YP_005920740.1| 364 YIALVRLYRKLGREADSIEACKAA 387
                                       578999999999988877776544 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.083        45       2      28 ..     159     185 ..     158     187 .. 0.87
   2 ?   -0.4   0.1       3.3   1.8e+03      14      25 ..     205     216 ..     204     219 .. 0.82
   3 ?   -0.2   0.0       2.8   1.5e+03       8      21 ..     267     280 ..     267     281 .. 0.89
   4 ?    4.5   0.0     0.088        48       9      28 ..     336     355 ..     335     357 .. 0.86
   5 ?    0.7   0.0       1.4   7.8e+02       1      15 [.     362     376 ..     362     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.083
                               PPR   2 tynslIsgycknGkleeAlelfkeMke 28 
                                       ty  l  +y   G++++ le++++ +e
  gi|386002441|ref|YP_005920740.1| 159 TYENLAEAYRMLGQIDKSLECLDKAIE 185
                                       8889999***************98665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.3
                               PPR  14 GkleeAlelfke 25 
                                       G+ +eAl+ f++
  gi|386002441|ref|YP_005920740.1| 205 GRKDEALKAFEK 216
                                       7889****9997 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.8
                               PPR   8 sgycknGkleeAle 21 
                                       s++++ G+++e le
  gi|386002441|ref|YP_005920740.1| 267 SALAQMGRIKESLE 280
                                       699********986 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.088
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                       ++++ G++e+Al+ +++ +e
  gi|386002441|ref|YP_005920740.1| 336 ALGSLGRMEDALDAYEKAIE 355
                                       68999********9998666 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.4
                               PPR   1 vtynslIsgycknGk 15 
                                       +ty +l++ y k G+
  gi|386002441|ref|YP_005920740.1| 362 ITYIALVRLYRKLGR 376
                                       699*********998 PP

>> Paz_1  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.8   3.7e+03      22      41 ..     199     218 ..     180     220 .. 0.81
   2 ?   10.0   0.0    0.0012      0.67      24      73 ..     235     285 ..     230     293 .. 0.84
   3 ?   -1.0   0.0       3.2   1.8e+03      20      42 ..     333     355 ..     313     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.8
                                       TT----EEEEEEEESGGSTT CS
                             Paz_1  22 igidfvgrvqdvfkakekge 41 
                                       + +d +gr ++ +ka ek  
  gi|386002441|ref|YP_005920740.1| 199 LALDDLGRKDEALKAFEKAI 218
                                       56788999999999999975 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                                       ----EEEEEEEESGGSTTHHHHHHHHH-SSHHHHHHHHHHHHS.HHHHHHS CS
                             Paz_1  24 idfvgrvqdvfkakekgeeffrlcmersthksskkaweellkn.relreka 73 
                                       + ++gr+++ +ka ek  ef   + e  t kss  a    +k+  e  eka
  gi|386002441|ref|YP_005920740.1| 235 LYYLGRIEESLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKEsLEASEKA 285
                                       5689*****************************998776666414666666 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.2
                                       EETT----EEEEEEEESGGSTTH CS
                             Paz_1  20 kpigidfvgrvqdvfkakekgee 42 
                                       k + +  +gr++d + a ek  e
  gi|386002441|ref|YP_005920740.1| 333 KGVALGSLGRMEDALDAYEKAIE 355
                                       66777889*********999765 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.046        25       3      32 ..     190     219 ..     173     220 .. 0.85
   2 ?   -0.8   0.1         3   1.6e+03       3      15 ..     311     323 ..     309     329 .. 0.75
   3 ?    6.8   0.1     0.013       6.9       6      33 ..     329     356 ..     325     356 .. 0.85
   4 ?   -2.0   0.1       7.1   3.9e+03       3      14 ..     411     422 ..     410     430 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.046
                               MIT   3 kAlelvkkAveeDnagnyeeAlelYkeale 32 
                                       +A + +++   +D  g  +eAl+++++a+e
  gi|386002441|ref|YP_005920740.1| 190 AARSWFNMGLALDDLGRKDEALKAFEKAIE 219
                                       556667788889999999999999999997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3
                               MIT   3 kAlelvkkAveeD 15 
                                       +A+e + +A+e+D
  gi|386002441|ref|YP_005920740.1| 311 EAIEALDRAIELD 323
                                       6788888888877 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.013
                               MIT   6 elvkkAveeDnagnyeeAlelYkealel 33 
                                       +  +k v + + g  e+Al++Y++a+e+
  gi|386002441|ref|YP_005920740.1| 329 AWSNKGVALGSLGRMEDALDAYEKAIEH 356
                                       5667888888999*************95 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.1
                               MIT   3 kAlelvkkAvee 14 
                                       +Al+l+++A e+
  gi|386002441|ref|YP_005920740.1| 411 AALALLRTALEN 422
                                       455555555443 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.044        24      78     124 ..     208     254 ..     166     270 .. 0.90
   2 ?    5.7   0.0     0.033        18      73     125 ..     271     323 ..     256     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.044
                                       HHHHHHC-EEE---------------------------------EEE CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvti 124
                                       +e+lk+f+ +ie  p   +A   nG  ly l r +e+++ +++ ++ 
  gi|386002441|ref|YP_005920740.1| 208 DEALKAFEKAIETDPEDAAAWANNGYALYYLGRIEESLKASEKAIEF 254
                                       6899******************************9999998888765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.033
                                       -HHHHHHHHHHC-EEE---------------------------------EEEE CS
                            TruB_N  73 teekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiy 125
                                       +  +++e l++ + +++  p    A + +G  ly+l r++e++e   r ++++
  gi|386002441|ref|YP_005920740.1| 271 QMGRIKESLEASEKAVNLNPKLAMAWNNKGSVLYDLDRAEEAIEALDRAIELD 323
                                       45678889999999999999999*********************999998876 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.011       5.9      35      65 ..     156     186 ..     151     201 .. 0.82
   2 ?   -1.4   0.0         3   1.6e+03      49      64 ..     204     219 ..     191     222 .. 0.86
   3 ?    2.6   0.2      0.18        99      32      62 ..     289     319 ..     237     348 .. 0.60
   4 ?    1.7   0.1      0.33   1.8e+02      16      65 ..     313     356 ..     305     361 .. 0.78
   5 ?   -2.2   0.0       5.2   2.8e+03      40      66 ..     365     391 ..     361     406 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC CS
                              RPN7  35 irrakldlaehYlkigdleeAlkaysrirey 65 
                                       ++ ++++lae Y + g+++++l+++ +++e 
  gi|386002441|ref|YP_005920740.1| 156 TASTYENLAEAYRMLGQIDKSLECLDKAIEL 186
                                       67899*********************97764 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                                       CT-HHHHHHHHHTCCC CS
                              RPN7  49 igdleeAlkaysrire 64 
                                        g ++eAlka+++++e
  gi|386002441|ref|YP_005920740.1| 204 LGRKDEALKAFEKAIE 219
                                       68999*****999876 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  32 keeirrakldlaehYlkigdleeAlkaysri 62 
                                         + ++a+++++   ++    eeA++a+ r+
  gi|386002441|ref|YP_005920740.1| 289 NPKLAMAWNNKGSVLYDLDRAEEAIEALDRA 319
                                       3344444455555555555555555555444 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC CS
                              RPN7  16 leeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrirey 65 
                                       +e+Ld+ ++       + + ++a+ +++    + g +e Al ay++++e+
  gi|386002441|ref|YP_005920740.1| 313 IEALDRAIE------LDPKLAMAWSNKGVALGSLGRMEDALDAYEKAIEH 356
                                       555555555......4777899999999999999***********99875 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 5.2
                                       HHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                              RPN7  40 ldlaehYlkigdleeAlkaysrireyc 66 
                                        +l + Y k g  + +++a++++r+  
  gi|386002441|ref|YP_005920740.1| 365 IALVRLYRKLGREADSIEACKAARDLI 391
                                       677888888888888888888888754 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0         1   5.6e+02      15      54 ..     150     189 ..     140     195 .. 0.81
   2 ?    6.2   1.1     0.024        13       4      44 ..     207     247 ..     204     261 .. 0.86
   3 ?    4.9   0.2     0.062        34       7      43 ..     244     280 ..     241     289 .. 0.93
   4 ?    0.7   0.2       1.3   6.9e+02       7      50 ..     278     321 ..     265     336 .. 0.67
   5 ?    5.0   0.3     0.055        30       7      44 ..     346     383 ..     341     432 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1
                            TPR_20  15 laanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       l+ np+   +  +lA+a+ + g+ +++le L + ++ d +
  gi|386002441|ref|YP_005920740.1| 150 LKLNPTTASTYENLAEAYRMLGQIDKSLECLDKAIELDPQ 189
                                       5668888899999***************999887776665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.024
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                       +++ l+++e+a++++p+d +a  +   al+  gr ee+l++
  gi|386002441|ref|YP_005920740.1| 207 KDEALKAFEKAIETDPEDAAAWANNGYALYYLGRIEESLKA 247
                                       567899****************************9999875 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.062
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAle 43 
                                       +l++ e+a++ +p+  +a  + + al++ gr +e+le
  gi|386002441|ref|YP_005920740.1| 244 SLKASEKAIEFDPQAAEAWTNKSSALAQMGRIKESLE 280
                                       688999****************************998 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.3
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       +l++ e+a++ np+   a  +   +l+   r eeA+e+L + ++
  gi|386002441|ref|YP_005920740.1| 278 SLEASEKAVNLNPKLAMAWNNKGSVLYDLDRAEEAIEALDRAIE 321
                                       45555556666666555555666666666777888887766655 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.055
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                        l++ e+a++ +p+d  + ++l +++ + gr+++++e+
  gi|386002441|ref|YP_005920740.1| 346 ALDAYEKAIEHDPKDAITYIALVRLYRKLGREADSIEA 383
                                       68899***********************9999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.59
# Mc/sec: 2364.71
//
Query:       gi|386002442|ref|YP_005920741.1|  [L=258]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for 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-37  126.5  14.0    1.2e-36  126.1  14.0    1.2  1  ABC2_membrane    ABC-2 type transporter
    8.6e-19   67.8  17.9    1.3e-18   67.3  17.9    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.3e-08   33.7  16.9    2.3e-08   33.7  16.9    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0064   16.5   8.1     0.0064   16.5   8.1    1.9  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1  14.0   2.7e-40   1.2e-36       4     209 ..      13     223 ..      10     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 2.7e-40
                     ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr.....pgllffsvlflafsaltsvapv 74 
                                       +a++  e+++  +d++ + ++r iqp+l++ vfg+v + +    ++g+ +     pg+l  s++f++   + ++ +v
  gi|386002442|ref|YP_005920741.1|  13 FAMIELEMRRLRHDRTEI-YTRAIQPILWLAVFGSVMSEVRgIPTGGIPYidyitPGVLLQSTIFVS--VFYGLTIV 86 
                                       678888999999999888.9******************96652333332256699************..999999** PP

                     ABC2_membrane  75 ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls....rfflflllllltalaassl 147
                                       +ere g+l+r+lv+p  s+sa v+++ +++ +++++qali++ ++++l g++       ++ ++++l+l++  + ++
  gi|386002442|ref|YP_005920741.1|  87 WERETGILKRLLVAPA-SRSATVIGRSIASGVRAVVQALIIFPVAILL-GVKFVpnpvYIVAAFIVLFLVSGGFAAI 161
                                       ****************.******************************9.777766454449999999999999**** PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       ++++++l+++ e ++ l++++++pl++ s +++pi+ mp  lq++a +nPltyav+a+r+ l
  gi|386002442|ref|YP_005920741.1| 162 SIFVASLMKTRERFMGLGQALIMPLFFASNALYPIELMPPALQYVALVNPLTYAVDAVRGLL 223
                                       **************************************77*******************976 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 !   67.3  17.9   2.8e-22   1.3e-18     161     343 ..      63     249 ..      51     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.8e-22
                   ABC2_membrane_3 161 sflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllil..llafglgip 234
                                       +++ + ++l   if++++     iv E+e++i++++lv++ s+++ ++++ +++++ +++q+l+i+  ++++g  + 
  gi|386002442|ref|YP_005920741.1|  63 DYITPgVLLQSTIFVSVF-YGLTIVWERETGILKRLLVAPASRSATVIGRSIASGVRAVVQALIIFpvAILLG--VK 136
                                       555552444445555555.5557****************************************9985468999..77 PP

                   ABC2_membrane_3 235 fg.nlglll...llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPff 307
                                       f  n ++++   ++++l +  ++a++ ++ sl+k+ e  ++l  ++i++l++++ +l+p+e +p al++++ ++P++
  gi|386002442|ref|YP_005920741.1| 137 FVpNPVYIVaafIVLFLVSGGFAAISIFVASLMKTRERFMGLGQALIMPLFFASNALYPIELMPPALQYVALVNPLT 213
                                       777666555433888888889999***************************************************** PP

                   ABC2_membrane_3 308 apglgllrl.itgdplweillsliilalfavvyllla 343
                                       +  ++   l i+gd l++++ ++++ ++f v+ +++a
  gi|386002442|ref|YP_005920741.1| 214 YAVDAVRGLlISGD-LSNLAVDVAAILVFDVLIFAVA 249
                                       *********55888.99***99999999999999887 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7  16.9   5.2e-12   2.3e-08      97     285 ..      85     255 ..      73     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.2e-12
                   ABC2_membrane_2  97 iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvllll 173
                                       i+ E+e g lk+lL  P+sR++ ++g  i++ +     +v +l+++ +a++    lg+ +    ++++++++vl+l+
  gi|386002442|ref|YP_005920741.1|  85 IVWERETGILKRLLVAPASRSATVIGRSIASGVR---AVVQALIIFPVAIL----LGVKFVPNPVYIVAAFIVLFLV 154
                                       777*******************************...66666666444343....3444444455555555554444 PP

                   ABC2_membrane_2 174 lvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneil 250
                                        + f+a++++++s+++++++ + l  +l++ l ++ +++ly++  ++   ++       + l++p  +   +++ +l
  gi|386002442|ref|YP_005920741.1| 155 SGGFAAISIFVASLMKTRERFMGLGQALIMPL-FFASNALYPIELMPPALQY-------VALVNPLTYAVDAVRGLL 223
                                       4478************9999999988887666.9999*****9887777777.......8*****999988888888 PP

                   ABC2_membrane_2 251 agsdlnalgstatnllilllllavllvlgyvlFkr 285
                                        ++d   l   a  ++++l+  +  ++++ v+Fk+
  gi|386002442|ref|YP_005920741.1| 224 ISGD---LSNLAVDVAAILVFDVLIFAVASVSFKK 255
                                       8886...3466777777778888888888899987 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   8.1   1.4e-06    0.0064      25     159 ..      36     167 ..      15     190 .. 0.70
   2 ?   -2.8   0.1       1.1   5.1e+03      57      69 ..     238     250 ..     227     256 .. 0.45

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                   ABC2_membrane_4  25 vpllallyfnllgk..tgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKl 99 
                                        p+l+l++f  + +  +g+ + +    + +  ++ll  ++ + ++ +  i  E++ + lk Ll+ P sr + +++  
  gi|386002442|ref|YP_005920741.1|  36 QPILWLAVFGSVMSevRGIPTGGIPYIDYITPGVLLQSTIFVSVFYGLTIVWERETGILKRLLVAPASRSATVIGRS 112
                                       455555555433222366666666555566667788888899999******************************** PP

                   ABC2_membrane_4 100 ivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialv 159
                                       i+  + +v+  l+ f +++l+++   fv+  v  v+ +++ +l+ g + +  ++ i++ +
  gi|386002442|ref|YP_005920741.1| 113 IASGVRAVVQALIIFPVAILLGV--KFVPNPVYIVAAFIVLFLVSGGFAA--IS-IFVAS 167
                                       ******99999998888777766..5666677777777777776666444..33.22222 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                   ABC2_membrane_4  57 llllplilgiias 69 
                                       +l++ +++  +as
  gi|386002442|ref|YP_005920741.1| 238 ILVFDVLIFAVAS 250
                                       2222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1571.55
//
Query:       gi|386002443|ref|YP_005920742.1|  [L=338]
Description: Daunorubicin resistance ATP-binding protein family [Methanosaeta harundinacea 6Ac]
Scores for 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-29  102.3   0.0    4.4e-29  101.7   0.0    1.3  1  ABC_tran      ABC transporter
    3.1e-13   50.2   0.0    3.8e-06   26.9   0.0    2.5  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.2e-07   30.1   0.0    1.2e-06   29.2   0.0    1.5  1  DUF4162       Domain of unknown function (DUF4162)
    0.00058   20.4   0.0    0.00098   19.7   0.0    1.3  1  AAA_23        AAA domain
    0.00074   19.2   0.0     0.0015   18.3   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0037   17.6   0.0      0.007   16.7   0.0    1.5  1  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.17   11.6   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.021   15.0   0.1      0.056   13.7   0.0    1.7  1  AAA_28        AAA domain
      0.026   14.1   0.0      0.047   13.3   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain
      0.027   14.9   0.0       0.16   12.4   0.0    2.1  1  AAA           ATPase family associated with various cellular 
      0.042   14.1   0.0      0.077   13.3   0.0    1.6  1  AAA_22        AAA domain
      0.045   14.1   0.0      0.094   13.1   0.0    1.6  1  AAA_16        AAA ATPase domain
       0.12   12.6   0.0       0.23   11.7   0.0    1.4  1  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.12   12.5   0.0       0.17   12.0   0.0    1.4  1  AAA_33        AAA domain
       0.13   11.9   0.0       0.21   11.3   0.0    1.3  1  AAA_30        AAA domain
       0.16   11.9   0.0       0.29   11.0   0.0    1.4  1  NACHT         NACHT domain
       0.27    9.8   0.0       0.33    9.6   0.0    1.1  1  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.0   4.2e-32   4.4e-29       1     136 [.      30     173 ..      30     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 4.2e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+l++ + e+ a++G+nG+GK+tL+++l+ + +pt+Ge +  g d+ + +  ++r+ ig++pqe++++ ++t r
  gi|386002443|ref|YP_005920742.1|  30 LDGVDLSVDQAEVFAFLGPNGSGKTTLMRILTTQFRPTSGEARAFGLDVVR-RGAEVRRMIGYVPQETSVWLDITGR 105
                                       789****************************************99***999.888999******************* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en              +++ ie+a+  +gl+e++++ v    +++SgG+ +r+++a+all kp++l+lDEpt
  gi|386002443|ref|YP_005920742.1| 106 ENllvyskiygvpkdRRKKSIEDAICAMGLEEVAERMV----KTYSGGMTRRLEIAAALLVKPRILFLDEPT 173
                                       ************87666666******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.9e-07   0.00031       2      36 ..      43      71 ..      42     100 .. 0.75
   2 !   26.9   0.0   3.6e-09   3.8e-06     238     297 ..     147     204 ..     134     208 .. 0.84
   3 ?   -2.8   0.0       4.1   4.3e+03     157     176 ..     255     277 ..     219     310 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.9e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdel 36
                                       ++ GpNgsGK++L+++l         ++++  e+
  gi|386002443|ref|YP_005920742.1| 43 FAFLGPNGSGKTTLMRILTTQ------FRPTSGEA 71
                                      6799**************544......44444444 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.6e-09
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       S G+ r l +++all  +   ++l++DEp  gL+P++ + ++e l + +r  g+ v++ TH
  gi|386002443|ref|YP_005920742.1| 147 SGGMTRRLEIAAALLVKP---RILFLDEPTIGLDPSARKAVWESLTAFKReCGTTVFFNTH 204
                                       666666669999999988...*********************99955555467899***** PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.1
                            AAA_21 157 lldglrke...rigllnifadyf 176
                                       +++g+ ++   ri+ l++++d +
  gi|386002443|ref|YP_005920742.1| 255 NHNGFDERalgRIRDLDLVRDAA 277
                                       22222222333444444444444 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.1e-09   1.2e-06       1      80 [.     228     325 ..     228     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.1e-09
                                       E-HHHHHTTS-SSEEEEE...........-------.............--.-EEEE-TTS-EEEEE--.------- CS
                           DUF4162   1 GtleeiKrsygknrieve...........adaeellee...........pg.veeveeeggelelkled.eeaanel 53 
                                       Gt+ e+Krs+ +++++++           +                    + v++    g++l + +ed e a + +
  gi|386002443|ref|YP_005920742.1| 228 GTPGELKRSLHGEILQLRfssnhhqnqnhN-------GfderalgrirdLDlVRDAALCGSRLDVFVEDgERALPLV 297
                                       9999**************997766643321.......0233442223223334444444588*******9******* PP

                                       ----.----EEEEEEEE---HHHHHHHH CS
                           DUF4162  54 lkal.tsgveirsFeeeePsLndIFiek 80 
                                       ++al ++gv+ ++++  +P+L+d+F+++
  gi|386002443|ref|YP_005920742.1| 298 IEALrSEGVTFERISTARPTLDDVFLRY 325
                                       ****88********************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.3e-07   0.00098      19      40 ..      40      61 ..      26      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.3e-07
                            AAA_23 19 kgltlItGpNGaGKTTildAik 40
                                        ++++ GpNG+GKTT+++ ++
  gi|386002443|ref|YP_005920742.1| 40 AEVFAFLGPNGSGKTTLMRILT 61
                                      4799**************9886 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.4e-06    0.0015      12      39 ..      30      57 ..      21      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      +dg ++++d+++++ + Gp+GsGK+Tl+
  gi|386002443|ref|YP_005920742.1| 30 LDGVDLSVDQAEVFAFLGPNGSGKTTLM 57
                                      678899999999***************8 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.6e-06     0.007       3      61 ..      45     105 ..      43     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-06
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl......klkkkdsvysrnpeddfwdgYtgqevvvidDfgqv 61 
                                       + Gp+g GK+tl++ L++++  ++      +     +v+ r++e   + gY  qe  v+ D+  +
  gi|386002443|ref|YP_005920742.1|  45 FLGPNGSGKTTLMRILTTQFRPTSgearafG----LDVVRRGAEVRRMIGYVPQETSVWLDITGR 105
                                       78*******************8884533330....345556777777777777777776666544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.17      23      44 ..      39      61 ..      28      79 .. 0.81
   2 ?    1.5   0.0      0.19     2e+02     323     364 ..     163     204 ..     155     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                            AAA_15 23 ee.ltvliGkNnsGKSsileald 44
                                         +  + G+N+sGK++++++l 
  gi|386002443|ref|YP_005920742.1| 39 QAeVFAFLGPNGSGKTTLMRILT 61
                                      334889**************995 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       k+ il+++EP + L p+a k ++++l    ++  t v++ TH
  gi|386002443|ref|YP_005920742.1| 163 KPRILFLDEPTIGLDPSARKAVWESLTAFKRECGTTVFFNTH 204
                                       5789*********************99998888888888888 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.3e-05     0.056       2      30 ..      43      71 ..      42      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                            AAA_28  2 ivitGgestGKTtlleaLaargypvvpEa 30
                                      ++++G+ ++GKTtl++ L+ +  p+  Ea
  gi|386002443|ref|YP_005920742.1| 43 FAFLGPNGSGKTTLMRILTTQFRPTSGEA 71
                                      689****************9877777664 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.047       2      44 ..      41      83 ..      40      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTH CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaA 44
                                      +v++++G++G+GKTt +  L  +++    ++    +D+ R +A
  gi|386002443|ref|YP_005920742.1| 41 EVFAFLGPNGSGKTTLMRILTTQFRPTSGEARAFGLDVVRRGA 83
                                      5889*********************999999999999999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.16       3      66 ..      45     171 ..      43     174 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       + Gp G GKT+l++ + +++  +                                                      
  gi|386002443|ref|YP_005920742.1|  45 FLGPNGSGKTTLMRILTTQFRPTsgearafgldvvrrgaevrrmigyvpqetsvwlditgrenllvyskiygvpkdr 121
                                       78**************9997422122223333333333334444444444444444444444444444444444444 PP

                                       ........EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 ........fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                               ++ + + e+ + +v+  +  +   ++ a +   kp ilf+DE
  gi|386002443|ref|YP_005920742.1| 122 rkksiedaICAMGLEEVAERMVKTYSGGMTRRLEIAAALLvKPRILFLDE 171
                                       44444444333333333333555555555555544444445566666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.3e-05     0.077       5      30 ..      40      65 ..      37     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                      a + +  G+ G+GKTtl+r l+ q+ 
  gi|386002443|ref|YP_005920742.1| 40 AEVFAFLGPNGSGKTTLMRILTTQFR 65
                                      5667788***************9984 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.9e-05     0.094      25      88 ..      41      95 ..      29     193 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                      e+  + G+ G+GK++l+r l ++++ +     +g+++ ++    ++++ + ++ ++ +  + +e
  gi|386002443|ref|YP_005920742.1| 41 EVFAFLGPNGSGKTTLMRILTTQFRPT-----SGEARAFG----LDVVRRGAEVRRMIGYVPQE 95
                                      677889**************9999987.....44444441....12233333333333333333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.23       4      74 ..      45     113 ..      43     120 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                       EESSTTSSHHHHHHCHCT-CCC-E..EETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEE.EE-SGGCTTTT-H CS
                               Roc   4 lvGdsgvGKtsllkrfvedkfsek..ekstigvdfltkevtkikgvendkkvkkvklniW.DtaGqerfrslhp 74 
                                       ++G +g+GKt+l++ ++  +f+++  e   +g+d++++ + +++ +     v   + ++W D+ G e+     +
  gi|386002443|ref|YP_005920742.1|  45 FLGPNGSGKTTLMRILT-TQFRPTsgEARAFGLDVVRRGA-EVRRMIG--YV-PQETSVWlDITGRENLLVYSK 113
                                       79**********98777.5555442267899999998765.4554321..12.234567778888877665555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.17       1      21 [.      42      62 ..      42     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                            AAA_33  1 lvllvGlpGsGKstlaerllk 21
                                      ++ + G++GsGK+tl + l  
  gi|386002443|ref|YP_005920742.1| 42 VFAFLGPNGSGKTTLMRILTT 62
                                      56799**********998843 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.21      17      43 ..      39      65 ..      33      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                            AAA_30 17 gdrvavltGpAGtGKttalkalreawe 43
                                      ++ v +  Gp G+GKtt+++ l+  ++
  gi|386002443|ref|YP_005920742.1| 39 QAEVFAFLGPNGSGKTTLMRILTTQFR 65
                                      55688899************9977665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.29       3      24 ..      43      64 ..      41      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                       +  G++GsGKTtL++ l ++ 
  gi|386002443|ref|YP_005920742.1| 43 FAFLGPNGSGKTTLMRILTTQF 64
                                      5678***********9887765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00031      0.33      22      39 ..      46      63 ..      38     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                            AAA_13 22 YGwNGaGKTtLSrllrsl 39
                                       G NG+GKTtL r+l  +
  gi|386002443|ref|YP_005920742.1| 46 LGPNGSGKTTLMRILTTQ 63
                                      59************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1998.77
//
Query:       gi|386002444|ref|YP_005920743.1|  [L=353]
Description: hypothetical protein Mhar_1762 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-21   76.1   0.0      7e-15   55.2   0.0    2.2  2  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.5e-08    0.0013      11      88 ..      39     128 ..      36     154 .. 0.79
   2 !   55.2   0.0   3.9e-19     7e-15       1      89 [.     181     289 ..     181     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.5e-08
                                       HHHHHHHHHHHCC....-TTSSSEEEEES-S..........TCHHHHHHHHCS--TTTTSEEE--...SS-SEEEEE CS
                              FmdE  11 lGyrmakaalkelgpkeeegdeelvaivetd..........sCldDAiqvltgctlGkgnlivmd...ygkkaltfk 74 
                                       lG  +a++a+ elg ++  gd+++ ++++             C  DA++ +tg ++Gk nli      +    + f+
  gi|386002444|ref|YP_005920743.1|  39 LGADAAEYAMAELGFVK--GDSNVLTLTNAGypvidgqttdLC-LDAVMETTGSSPGKENLINILsppWKPLWFGFY 112
                                       79999*********973..678888888888999999999555.59***************9886555777778*** PP

                                       ETTT-EEEEEEE-..C CS
                              FmdE  75 krktgkavrlklk..e 88 
                                       + +tg+av +k++   
  gi|386002444|ref|YP_005920743.1| 113 NSNTGEAVYMKVNadG 128
                                       ***********99441 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 3.9e-19
                                       HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--............ CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmd............ 65 
                                       +H+H+Cpg+ +G+  ak++ + l+++++ + + + +i+  ++C+dD +qv+++ct+Gk  l+v+             
  gi|386002444|ref|YP_005920743.1| 181 LHDHICPGVSSGFLLAKYMEETLPIEDPAN-QSYKVIACPNWCKDDYFQVAWDCTPGKSGLFVKYltadetaaltek 256
                                       5***********************998877.***************************9999999888888888888 PP

                                       SS-SEEEEEET.....TT-EEEEEEE-....CC CS
                              FmdE  66 ygkkaltfkkr.....ktgkavrlklk....ee 89 
                                       yg+ ++ +  r     k+g+++ l ++     +
  gi|386002444|ref|YP_005920743.1| 257 YGTRVAGIFIRwdaasKSGDGLVLGFDfdkaGN 289
                                       999999555555999999999999988655533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1940.65
//
Query:       gi|386002445|ref|YP_005920744.1|  [L=270]
Description: Putative methyltransferase mtx subunit X [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   10.8   0.0       0.34   10.2   0.0    1.3  1  PTA_PTB   Phosphate acetyl/butaryl transferase


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   1.9e-05      0.34     103     204 ..      66     162 ..      58     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.9e-05
                                       SHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEEETTEEEEEESSSS-SS--HHHHHH CS
                           PTA_PTB 103 datyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfimlledrlllfaDcavnvnPtaeelae 179
                                       d++   + l+++ge+Dg v G+ ++t+      +++i+   +v++   +++++l+d  +++a + + +  +  +  +
  gi|386002445|ref|YP_005920744.1|  66 DPASELVRLLEEGEVDGAVRGNLSATKV-----VRKIGRTFEVRVR-RLSLLALPDWSFFLAPVGIDEGDSISDRLS 136
                                       6666778899*************99876.....4567777767766.99999************************* PP

                                       HHHHHHHHHHHCC.SS--EEEEE-SS CS
                           PTA_PTB 180 ialesaktakalg.eeeprvAlLSyS 204
                                        a+  a  ++a+  e eprv +LS  
  gi|386002445|ref|YP_005920744.1| 137 LAVLGAGYIRAVDlETEPRVSILSGG 162
                                       *******9999853689*****9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1392.23
//
Query:       gi|386002446|ref|YP_005920745.1|  [L=320]
Description: AIR synthase related protein domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-16   59.3   0.4    7.3e-16   58.6   0.4    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
    1.1e-15   58.2   0.1    1.8e-15   57.4   0.1    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.4   8.1e-20   7.3e-16       1      92 [.      42     145 ..      42     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 8.1e-20
                                       SSSEE........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHH CS
                              AIRS   1 dDaav........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaa 66 
                                       +Daav        ++++d+  + +l ++ + +G+ av vn+ D+aamG+ P+a++++l+ +    +e+v++g+++++
  gi|386002446|ref|YP_005920745.1|  42 EDAAViddgeevmLLAADGIWSRLLEADAEWAGYCAVLVNVHDIAAMGGWPVAMVDVLSAGssdLAEAVLSGMRKGI 118
                                       6888545555555889999999999999999********************************999*********** PP

                                       HHTT-EEEEEEEEEESS.EEEEEEEEE CS
                              AIRS  67 eelgvplvgGdtsfsne.ptisvtavG 92 
                                       e+++vp+vgG+++ ++    + v+++G
  gi|386002446|ref|YP_005920745.1| 119 EKFKVPIVGGHLHPDTPySALDVAILG 145
                                       ************998654566777766 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1     2e-19   1.8e-15      46     150 ..     195     296 ..     159     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2e-19
                                       HHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHG CS
                            AIRS_C  46 tliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppe 122
                                       +++  +r+la++ glv+a +D+++ G lg+l ++++ s+ ga++dl+k+p  +    ++ ++   + G ++v+ +p+
  gi|386002446|ref|YP_005920745.1| 195 RQLGSMRELAER-GLVTAGKDISNPGMLGTLGMLLESSRAGAVVDLEKIPKPEGM--EMVVWQKMYPGMGFVVTAPA 268
                                       57788999***8.**********************************77776654..7889999999***9999999 PP

                                       GH.HHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C 123 ea.davlaileeeglpeaavIGevtakee 150
                                       ++ ++v  i++ +gl + avIG+vt++++
  gi|386002446|ref|YP_005920745.1| 269 AKaEEVAGIFRGRGL-TSAVIGRVTEERR 296
                                       999************.7*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1824.17
//
Query:       gi|386002447|ref|YP_005920746.1|  [L=327]
Description: PBS lyase HEAT domain-containing protein repeat-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-58  194.9  17.2    1.4e-22   79.9   1.6    5.0  5  HEAT_2        HEAT repeats
    6.3e-36  119.3   6.4    0.00019   21.4   0.0    9.5  9  HEAT          HEAT repeat
    1.2e-34  115.4  41.1    5.9e-07   29.6   0.3    9.3  9  HEAT_PBS      PBS lyase HEAT-like repeat
    1.5e-20   73.3  18.3     0.0065   17.0   0.0    8.7 10  HEAT_EZ       HEAT-like repeat
    5.3e-16   58.0   1.1      0.012   15.6   0.0    8.2  8  Arm           Armadillo/beta-catenin-like repeat
    5.6e-10   39.5   0.0    0.00028   21.0   0.0    4.0  4  Cnd1          non-SMC mitotic condensation complex subunit 1
    6.5e-05   21.7   0.0     0.0051   15.4   0.0    3.0  2  Adaptin_N     Adaptin N terminal region
  ------ inclusion threshold ------
       0.07   12.8   0.0         42    3.8   0.0    3.8  4  DUF4042       Domain of unknown function (DUF4042)
       0.11   12.5   0.1         11    6.0   0.1    3.5  5  DUF2019       Domain of unknown function (DUF2019)
        2.7    8.0   7.2         15    5.7   0.9    3.7  3  ALF           Short repeats of unknown function


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00092       1.6      31      69 ..       5      43 ..       1      45 [. 0.83
   2 !   79.9   1.6   7.8e-26   1.4e-22       1      88 []      37     125 ..      37     125 .. 0.95
   3 ?    5.6   0.1     0.011        20      32      65 ..     129     162 ..     126     167 .. 0.83
   4 !   49.2   0.3   2.8e-16   5.1e-13       5      64 ..     164     223 ..     160     229 .. 0.92
   5 !   64.5   0.4     5e-21   8.9e-18       8      87 ..     229     308 ..     224     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00092
                            HEAT_2 31 ealpaLvellededpavRraaaeaLgaigdpealpaLke 69
                                      e l  Lv+ l ded   R+ aa+ L++ g ++ +p+L++
  gi|386002447|ref|YP_005920746.1|  5 EPLSELVRSLGDEDYFKRQSAAWRLVEAGGEAIAPLLAA 43
                                      6788999999*******************9977777665 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 7.8e-26
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddd 76 
                                       +++Ll+al  dpdp+vr +a++aLg+ig+++ l+ L ++l ededpavR+ aa aL aigdp+a+p L ++l++d++
  gi|386002447|ref|YP_005920746.1|  37 IAPLLAALGGDPDPQVRFKAAWALGKIGDERGLEPLARALlEDEDPAVREWAASALEAIGDPRAVPPLSQSLATDPS 113
                                       579*****99**********************999999777************************************ PP

                            HEAT_2  77 dvvReaAaeaLa 88 
                                       ++vR ++  aL+
  gi|386002447|ref|YP_005920746.1| 114 REVRLRSSLALG 125
                                       ****99998885 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.011
                            HEAT_2  32 alpaLvellededpavRraaaeaLgaigdpealp 65 
                                       a++a+ +ll+  d + Rr+a+   g++++  + +
  gi|386002447|ref|YP_005920746.1| 129 AVEAFEDLLREGDLEARRMAVVGVGRLRSAGSME 162
                                       7899999999999999999999999998876655 PP

  == domain 4  score: 49.2 bits;  conditional E-value: 2.8e-16
                            HEAT_2   5 lqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpeal 64 
                                        + l+ d+dpe+rr+++++Lg++g  +alp+L+++l+d+ p vR++aa+a ++ig  +a+
  gi|386002447|ref|YP_005920746.1| 164 FAPLSGDADPELRRRVAWSLGEMGASDALPLLLPALKDDGPVVRMEAAKAVAKIGGADAC 223
                                       555889*************************************************99886 PP

  == domain 5  score: 64.5 bits;  conditional E-value: 5e-21
                            HEAT_2   8 lendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvReaA 83 
                                       l +dpdp vr  a+ +Lg+ig  eal+ Lve+l   +d+++R+ aa++Lg+igd +a++ L+e++   + + vRe+A
  gi|386002447|ref|YP_005920746.1| 229 LLEDPDPRVRLSAVTSLGEIGLAEALDRLVEVLfGEDDEEIRAWAAWSLGEIGDRRAIEPLQEACVKCP-PKVREKA 304
                                       459******************************99999***************************8776.6679999 PP

                            HEAT_2  84 aeaL 87 
                                       + +L
  gi|386002447|ref|YP_005920746.1| 305 LDSL 308
                                       9988 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0036       6.4       4      25 ..       9      30 ..       7      32 .. 0.86
   2 !   21.4   0.0   1.1e-07   0.00019       3      28 ..      39      64 ..      37      66 .. 0.86
   3 !   18.3   0.1   1.1e-06    0.0019       6      27 ..      74      95 ..      69      97 .. 0.80
   4 !   12.5   0.0   7.8e-05      0.14       2      28 ..     101     128 ..     100     131 .. 0.87
   5 !   10.6   0.0   0.00032      0.57       2      27 ..     161     186 ..     161     189 .. 0.90
   6 !   11.5   0.0   0.00016       0.3       2      27 ..     192     217 ..     191     219 .. 0.95
   7 !   18.5   0.0   8.8e-07    0.0016       7      27 ..     228     248 ..     224     250 .. 0.91
   8 !    9.9   0.0   0.00053      0.95       6      28 ..     258     281 ..     253     283 .. 0.78
   9 ?    2.1   0.0      0.17     3e+02      14      25 ..     298     309 ..     287     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                                      HHHHHHT-SSHHHHHHHHHHHH CS
                              HEAT  4 lllkllsDpspeVReaAakaLg 25
                                       l++ l D++ + R++Aa+ L+
  gi|386002447|ref|YP_005920746.1|  9 ELVRSLGDEDYFKRQSAAWRLV 30
                                      57889*************9875 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT  3 PlllkllsDpspeVReaAakaLgala 28
                                      Pll  l  Dp+p+VR  Aa+aLg++ 
  gi|386002447|ref|YP_005920746.1| 39 PLLAALGGDPDPQVRFKAAWALGKIG 64
                                      7777766****************995 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.1e-06
                                      HHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  6 lkllsDpspeVReaAakaLgal 27
                                        ll+D++p VRe Aa aL a+
  gi|386002447|ref|YP_005920746.1| 74 RALLEDEDPAVREWAASALEAI 95
                                      3457***************998 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkll.sDpspeVReaAakaLgala 28 
                                       +P+l + l +Dps eVR  + +aLga+ 
  gi|386002447|ref|YP_005920746.1| 101 VPPLSQSLaTDPSREVRLRSSLALGAFG 128
                                       688977777****************986 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00032
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                       + l+  l  D +pe R+ +a++Lg++
  gi|386002447|ref|YP_005920746.1| 161 MELFAPLSGDADPELRRRVAWSLGEM 186
                                       67889999****************98 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                       lPlll +l+D+ p VR+ Aaka++++
  gi|386002447|ref|YP_005920746.1| 192 LPLLLPALKDDGPVVRMEAAKAVAKI 217
                                       8*********************9987 PP

  == domain 7  score: 18.5 bits;  conditional E-value: 8.8e-07
                                       HHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   7 kllsDpspeVReaAakaLgal 27 
                                       +ll+Dp+p+VR +A+ +Lg++
  gi|386002447|ref|YP_005920746.1| 228 SLLEDPDPRVRLSAVTSLGEI 248
                                       689****************98 PP

  == domain 8  score: 9.9 bits;  conditional E-value: 0.00053
                                       HHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   6 lkll.sDpspeVReaAakaLgala 28 
                                       ++ l   ++ e+R+ Aa++Lg++ 
  gi|386002447|ref|YP_005920746.1| 258 VEVLfGEDDEEIRAWAAWSLGEIG 281
                                       4444477899************96 PP

  == domain 9  score: 2.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHH CS
                              HEAT  14 peVReaAakaLg 25 
                                       p+VRe A+ +L 
  gi|386002447|ref|YP_005920746.1| 298 PKVREKALDSLE 309
                                       78******9996 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   1.4    0.0022         4       2      25 ..      22      44 ..      21      46 .. 0.94
   2 !   25.2   0.3   8.6e-09   1.5e-05       1      26 [.      52      77 ..      52      78 .. 0.95
   3 !   23.3   0.1   3.5e-08   6.4e-05       1      26 [.      84     109 ..      84     110 .. 0.93
   4 ?    5.9   0.1     0.014        26       1      22 [.     116     137 ..     116     138 .. 0.88
   5 ?    0.2   0.1      0.94   1.7e+03       2      14 ..     145     157 ..     144     167 .. 0.89
   6 !   23.0   0.2   4.2e-08   7.5e-05       1      27 []     175     201 ..     175     201 .. 0.97
   7 ?    6.1   0.6     0.012        21       1      17 [.     206     222 ..     206     230 .. 0.88
   8 !   18.4   0.1   1.3e-06    0.0023       1      25 [.     237     261 ..     237     263 .. 0.96
   9 !   29.6   0.3   3.3e-10   5.9e-07       1      25 [.     269     293 ..     269     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                      HHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS  2 RraAakaLgqlgdeeaipaLleaL 25
                                      R +Aa+ L + g  eai++Ll+aL
  gi|386002447|ref|YP_005920746.1| 22 RQSAAWRLVEAGG-EAIAPLLAAL 44
                                      789**********.********99 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 8.6e-09
                                      HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLq 26
                                      vR  Aa+aLg++gde+ +++L +aL 
  gi|386002447|ref|YP_005920746.1| 52 VRFKAAWALGKIGDERGLEPLARALL 77
                                      899*********************95 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR +Aa aL ++gd++a+p+L + L+
  gi|386002447|ref|YP_005920746.1|  84 VREWAASALEAIGDPRAVPPLSQSLA 109
                                       9********************98875 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHCTSGGGHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLl 22 
                                       vR +   aLg++g+ ea + Ll
  gi|386002447|ref|YP_005920746.1| 116 VRLRSSLALGAFGAVEAFEDLL 137
                                       6778889************998 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.94
                                       HHHHHHHHHHCTS CS
                          HEAT_PBS   2 RraAakaLgqlgd 14 
                                       Rr A+ + g+l++
  gi|386002447|ref|YP_005920746.1| 145 RRMAVVGVGRLRS 157
                                       9**********97 PP

  == domain 6  score: 23.0 bits;  conditional E-value: 4.2e-08
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       +Rr+ a++Lg++g+ +a+p+Ll aL+d
  gi|386002447|ref|YP_005920746.1| 175 LRRRVAWSLGEMGASDALPLLLPALKD 201
                                       59***********************98 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHCTSGGG CS
                          HEAT_PBS   1 vRraAakaLgqlgdeea 17 
                                       vR +Aaka +++g  +a
  gi|386002447|ref|YP_005920746.1| 206 VRMEAAKAVAKIGGADA 222
                                       8************8554 PP

  == domain 8  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       vR +A+ +Lg++g  ea+++L+e+L
  gi|386002447|ref|YP_005920746.1| 237 VRLSAVTSLGEIGLAEALDRLVEVL 261
                                       8**********************98 PP

  == domain 9  score: 29.6 bits;  conditional E-value: 3.3e-10
                                       HHHHHHHHHHHCTSGGGHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                       +R++Aa++Lg++gd +ai++L+ea+
  gi|386002447|ref|YP_005920746.1| 269 IRAWAAWSLGEIGDRRAIEPLQEAC 293
                                       69*********************98 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         3   5.4e+03      27      50 ..       8      27 ..       5      29 .. 0.72
   2 !   17.0   0.0   3.6e-06    0.0065      28      55 .]      36      63 ..      34      63 .. 0.83
   3 !   13.6   0.1   4.1e-05     0.074      33      55 .]      72      95 ..      67      95 .. 0.84
   4 !    7.1   0.1    0.0043       7.7      27      54 ..      98     126 ..      98     127 .. 0.83
   5 ?   -2.9   0.0       5.9   1.1e+04      30      51 ..     130     151 ..     128     155 .. 0.61
   6 !    7.4   0.0    0.0034       6.2      30      55 .]     161     186 ..     156     186 .. 0.90
   7 !   11.8   0.2   0.00015      0.28      27      54 ..     189     216 ..     187     217 .. 0.90
   8 !    9.4   0.0   0.00084       1.5      35      55 .]     228     248 ..     225     248 .. 0.92
   9 !   10.7   0.0   0.00033       0.6      28      55 .]     252     280 ..     249     280 .. 0.76
  10 ?    1.3   0.0      0.29   5.1e+02      40      53 ..     296     309 ..     283     311 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3
                           HEAT_EZ 27 peilpaLlalLnddsdeV.RaaAag 50
                                      +e+++ L+     d+d   R+ Aa+
  gi|386002447|ref|YP_005920746.1|  8 SELVRSLG-----DEDYFkRQSAAW 27
                                      67788888.....887666777777 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.6e-06
                           HEAT_EZ 28 eilpaLlalLnddsdeVRaaAagaLgnl 55
                                      +i p+L+al  d+++ VR +Aa+aLg++
  gi|386002447|ref|YP_005920746.1| 36 AIAPLLAALGGDPDPQVRFKAAWALGKI 63
                                      456667777799999***********97 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 4.1e-05
                           HEAT_EZ 33 Ll.alLnddsdeVRaaAagaLgnl 55
                                      L+ alL+d++++VR+ Aa aL+++
  gi|386002447|ref|YP_005920746.1| 72 LArALLEDEDPAVREWAASALEAI 95
                                      554788***************986 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0043
                           HEAT_EZ  27 peilpaLlalL.nddsdeVRaaAagaLgn 54 
                                       p+++p+L + L +d+s eVR  +  aLg+
  gi|386002447|ref|YP_005920746.1|  98 PRAVPPLSQSLaTDPSREVRLRSSLALGA 126
                                       68999999888477777**********97 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 5.9
                           HEAT_EZ  30 lpaLlalLnddsdeVRaaAaga 51 
                                       + a+  lL+  + e R  A+  
  gi|386002447|ref|YP_005920746.1| 130 VEAFEDLLREGDLEARRMAVVG 151
                                       5566667766666886666654 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0034
                           HEAT_EZ  30 lpaLlalLnddsdeVRaaAagaLgnl 55 
                                       + ++++l  d ++e R  +a+ Lg +
  gi|386002447|ref|YP_005920746.1| 161 MELFAPLSGDADPELRRRVAWSLGEM 186
                                       7789999999999**********986 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.00015
                           HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgn 54 
                                       +++lp+Ll++L+dd + VR  Aa a ++
  gi|386002447|ref|YP_005920746.1| 189 SDALPLLLPALKDDGPVVRMEAAKAVAK 216
                                       589********************99776 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.00084
                           HEAT_EZ  35 alLnddsdeVRaaAagaLgnl 55 
                                       +lL+d++++VR  A+  Lg +
  gi|386002447|ref|YP_005920746.1| 228 SLLEDPDPRVRLSAVTSLGEI 248
                                       799***************986 PP

  == domain 9  score: 10.7 bits;  conditional E-value: 0.00033
                           HEAT_EZ  28 eilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       e+l+ L+  L  ++d e+Ra Aa+ Lg +
  gi|386002447|ref|YP_005920746.1| 252 EALDRLVEVLFGEDDeEIRAWAAWSLGEI 280
                                       677888877755555599*********86 PP

  == domain 10  score: 1.3 bits;  conditional E-value: 0.29
                           HEAT_EZ  40 dsdeVRaaAagaLg 53 
                                       ++++VR++A+  L+
  gi|386002447|ref|YP_005920746.1| 296 CPPKVREKALDSLE 309
                                       6779****998887 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     7e-06     0.012      13      39 ..      36      63 ..      35      65 .. 0.93
   2 ?    5.1   0.0     0.014        25      10      36 ..      65      92 ..      62      93 .. 0.87
   3 ?    3.2   0.0     0.057     1e+02       7      29 ..      94     117 ..      93     125 .. 0.77
   4 !    6.5   0.0    0.0052       9.3      11      37 ..     127     153 ..     119     157 .. 0.87
   5 ?    4.2   0.0     0.027        49      10      38 ..     157     185 ..     153     188 .. 0.82
   6 ?    3.2   0.0     0.055        99      11      36 ..     189     214 ..     185     218 .. 0.88
   7 ?    3.7   0.0     0.038        68      19      39 ..     228     248 ..     217     249 .. 0.86
   8 !    7.5   0.0    0.0024       4.3      12      39 ..     252     280 ..     251     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7e-06
                                      HHHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm 13 avppLvrLLs.sedeevqeeAawALsNL 39
                                      a+ pL++ L  ++d++v++ AawAL+ +
  gi|386002447|ref|YP_005920746.1| 36 AIAPLLAALGgDPDPQVRFKAAWALGKI 63
                                      799**********************965 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                                      HTTHHHHHHHHTT.TSSHHHHHHHHHHH CS
                               Arm 10 eaGavppLvrLLs.sedeevqeeAawAL 36
                                      +  +++pL r L  +ed+ v+e Aa+AL
  gi|386002447|ref|YP_005920746.1| 65 DERGLEPLARALLeDEDPAVREWAASAL 92
                                      66789999999999********999998 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.057
                                       HHHHTTHHHHHHHHTT.TSSHHHH CS
                               Arm   7 avieaGavppLvrLLs.sedeevq 29 
                                       a+ +  avppL + L  +++ ev+
  gi|386002447|ref|YP_005920746.1|  94 AIGDPRAVPPLSQSLAtDPSREVR 117
                                       788999*******99987776666 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0052
                                       TTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  11 aGavppLvrLLssedeevqeeAawALs 37 
                                        Gav+++ +LL+ +d e ++ A+  ++
  gi|386002447|ref|YP_005920746.1| 127 FGAVEAFEDLLREGDLEARRMAVVGVG 153
                                       69********************98776 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.027
                                       HTTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLssedeevqeeAawALsN 38 
                                       +aG ++ +  L  + d+e+++ +aw L+ 
  gi|386002447|ref|YP_005920746.1| 157 SAGSMELFAPLSGDADPELRRRVAWSLGE 185
                                       567777777777799***********986 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.055
                                       TTHHHHHHHHTTTSSHHHHHHHHHHH CS
                               Arm  11 aGavppLvrLLssedeevqeeAawAL 36 
                                       + a+p L+  L+++ + v+ eAa A+
  gi|386002447|ref|YP_005920746.1| 189 SDALPLLLPALKDDGPVVRMEAAKAV 214
                                       679*******************9887 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.038
                                       HHTTTSSHHHHHHHHHHHHHH CS
                               Arm  19 rLLssedeevqeeAawALsNL 39 
                                       +LL+++d++v+  A++ L+ +
  gi|386002447|ref|YP_005920746.1| 228 SLLEDPDPRVRLSAVTSLGEI 248
                                       79*************999876 PP

  == domain 8  score: 7.5 bits;  conditional E-value: 0.0024
                                       THHHHHHHHTT.TSSHHHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLs.sedeevqeeAawALsNL 39 
                                        a+++Lv+ L   +dee++  Aaw L+ +
  gi|386002447|ref|YP_005920746.1| 252 EALDRLVEVLFgEDDEEIRAWAAWSLGEI 280
                                       589***********************977 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   7.5e-05      0.13      26      86 ..      41      96 ..      29     109 .. 0.78
   2 ?   -2.5   0.0       2.6   4.6e+03      27      50 ..     134     157 ..     129     163 .. 0.75
   3 !   21.0   0.0   1.6e-07   0.00028      28      86 ..     197     249 ..     190     261 .. 0.90
   4 ?    0.8   0.0      0.25   4.4e+02      60      89 ..     254     284 ..     251     311 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                              Cnd1 26 LrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteis 86
                                      L +   D+dp+VR  aa ++ k+       e+g+    + lleDe+p V++ a +al+ i 
  gi|386002447|ref|YP_005920746.1| 41 LAALGGDPDPQVRFKAAWALGKIG-----DERGLEPLARALLEDEDPAVREWAASALEAIG 96
                                      4444479***********999864.....4566555556677**************99886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                              Cnd1  27 rkrLkDedpyVRktaaivvakLil 50 
                                       +  L+  d   R+ a+++v +L +
  gi|386002447|ref|YP_005920746.1| 134 EDLLREGDLEARRMAVVGVGRLRS 157
                                       567888888899999999999854 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 1.6e-07
                              Cnd1  28 krLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteis 86 
                                        +LkD+ p VR+ aa +vak+  +d +++        +lleD++prV+ +a+++l ei 
  gi|386002447|ref|YP_005920746.1| 197 PALKDDGPVVRMEAAKAVAKIGGADACRMAA------SLLEDPDPRVRLSAVTSLGEIG 249
                                       58*************************9876......99******************96 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.25
                              Cnd1  60 lselakll.eDenprVvanalaalteiseks 89 
                                       l++l + l  +++++++a a  +l ei ++ 
  gi|386002447|ref|YP_005920746.1| 254 LDRLVEVLfGEDDEEIRAWAAWSLGEIGDRR 284
                                       5677777767889999999999999999884 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.9e-06    0.0051     115     321 ..      37     270 ..      32     273 .. 0.66
   2 ?    3.4   0.0     0.013        23     414     478 ..     252     308 ..     249     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCC.HHH CS
                         Adaptin_N 115 lapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleeikkndrlll.kll 190
                                       +ap + +l  d++p+vr kAa a+ k+ +  +      l +    ll+d+dp v   A ++le i   +r+ +  l 
  gi|386002447|ref|YP_005920746.1|  37 IAPLLAALGGDPDPQVRFKAAWALGKIGD--ERG----LEPLARALLEDEDPAVREWAASALEAI-GDPRA-VpPLS 105
                                       55566666668888888888888777743..222....234466677888888888888888888.44443.22444 PP

                                       HHHHCCHHHHH..HCS-HHHHHHHHHHHCC---SSHHHH...................................... CS
                         Adaptin_N 191 pklvrrLcnll..teldpwlqvkiiklltrlarqepeer...................................... 227
                                       ++l++  ++ +   ++  ++    ++ + +l r+ + e+                                      
  gi|386002447|ref|YP_005920746.1| 106 QSLATDPSREVrlRSSLALGAFGAVEAFEDLLREGDLEArrmavvgvgrlrsagsmelfaplsgdadpelrrrvaws 182
                                       44444444433335555566667777777777777777778888888888888888888888888887777777666 PP

                                       .......HHHHHHHCGGCGCSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXX CS
                         Adaptin_N 228 .....skkellesllnllqssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkep 299
                                            + ++ l+ ll+ l+  ++ V +e+++++ ++  +++     ++   +ll+++d+ +r+ a+++l +i   e 
  gi|386002447|ref|YP_005920746.1| 183 lgemgA-SDALPLLLPALKDDGPVVRMEAAKAVAKIGGADA-----CRMAASLLEDPDPRVRLSAVTSLGEIGLAE- 252
                                       654432.6788888888888888888888888888877777.....555567888888888888888888887666. PP

                                       TTTTTTTCCCCSXXTTSXHHHH CS
                         Adaptin_N 300 kavqhldlkifllktdddvsir 321
                                            ld  ++ l  +dd++ir
  gi|386002447|ref|YP_005920746.1| 253 ----ALDRLVEVLFGEDDEEIR 270
                                       ....444445555555555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.013
                                       TCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTTXTT...HHHHHHCTTTTTTTSXHHHHHHHHHHH CS
                         Adaptin_N 414 eiiekLaellekieseearaaaiWllGeygelvsntesasdllrslaekfvlesekvklqiltal 478
                                       e++ +L+e+l   + ee+ra a+W lGe+g++          ++ l+e  v+++ kv+ ++l +l
  gi|386002447|ref|YP_005920746.1| 252 EALDRLVEVLFGEDDEEIRAWAAWSLGEIGDRRA--------IEPLQEACVKCPPKVREKALDSL 308
                                       577888999999999***************9866........45666666666666666666555 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.089   1.6e+02      41      67 ..      37      63 ..      28      69 .. 0.83
   2 ?   -1.4   0.0      0.93   1.7e+03      44      67 ..      72      95 ..      69     101 .. 0.83
   3 ?    1.1   0.0      0.15   2.7e+02      41      67 ..     191     217 ..     184     218 .. 0.85
   4 ?    3.8   0.0     0.023        42      44      66 ..     225     247 ..     215     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.089
                           DUF4042 41 eatLltillkDpspkvRaaalqvlaal 67
                                       a Ll  l  Dp p+vR  a+ +l ++
  gi|386002447|ref|YP_005920746.1| 37 IAPLLAALGGDPDPQVRFKAAWALGKI 63
                                      5678899999**********9999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.93
                           DUF4042 44 LltillkDpspkvRaaalqvlaal 67
                                      L   ll+D  p vR  a+++l a+
  gi|386002447|ref|YP_005920746.1| 72 LARALLEDEDPAVREWAASALEAI 95
                                      556789999******999998765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.15
                           DUF4042  41 eatLltillkDpspkvRaaalqvlaal 67 
                                       +  Ll  +lkD  p vR+ a++++a++
  gi|386002447|ref|YP_005920746.1| 191 ALPLLLPALKDDGPVVRMEAAKAVAKI 217
                                       55688899***************9986 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.023
                           DUF4042  44 LltillkDpspkvRaaalqvlaa 66 
                                       +   ll+Dp p+vR+ a+  l +
  gi|386002447|ref|YP_005920746.1| 225 MAASLLEDPDPRVRLSAVTSLGE 247
                                       556789***********988765 PP

>> DUF2019  Domain of unknown function (DUF2019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.19   3.4e+02      51      69 ..      41      59 ..      29      70 .. 0.84
   2 ?   -1.3   0.0       1.1     2e+03      53      78 ..      75     100 ..      60     112 .. 0.69
   3 ?   -2.3   0.0       2.3   4.2e+03      53      80 ..     107     134 ..      95     141 .. 0.72
   4 ?   -0.7   0.0      0.76   1.4e+03      51      73 ..     195     217 ..     188     226 .. 0.72
   5 ?    6.0   0.1    0.0061        11      46      82 ..     221     257 ..     206     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                                      GGGGGGSS-HHHHHHHHHT CS
                           DUF2019 51 LlsLyehpnvqvRlkAAka 69
                                      L +L   p  qvR kAA a
  gi|386002447|ref|YP_005920746.1| 41 LAALGGDPDPQVRFKAAWA 59
                                      556667899*******975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                       GGGGSS-HHHHHHHHHTTTTT-HHHH CS
                           DUF2019  53 sLyehpnvqvRlkAAkatLAvapaeA 78 
                                       +L+e     vR  AA a+ A+   +A
  gi|386002447|ref|YP_005920746.1|  75 ALLEDEDPAVREWAASALEAIGDPRA 100
                                       56777777788778777777765555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                                       GGGGSS-HHHHHHHHHTTTTT-HHHHHH CS
                           DUF2019  53 sLyehpnvqvRlkAAkatLAvapaeArk 80 
                                       sL   p  +vRl+   a+ A   +eA +
  gi|386002447|ref|YP_005920746.1| 107 SLATDPSREVRLRSSLALGAFGAVEAFE 134
                                       5667788899998877776666666654 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.76
                                       GGGGGGSS-HHHHHHHHHTTTTT CS
                           DUF2019  51 LlsLyehpnvqvRlkAAkatLAv 73 
                                       Ll+ ++     vR++AAka+  +
  gi|386002447|ref|YP_005920746.1| 195 LLPALKDDGPVVRMEAAKAVAKI 217
                                       666666677789****9987655 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.0061
                                       -GGGGGGGGGGSS-HHHHHHHHHTTTTT-HHHHHHHH CS
                           DUF2019  46 DqRraLlsLyehpnvqvRlkAAkatLAvapaeArkql 82 
                                       D  r+  sL+e p  +vRl+A +++  +  aeA   l
  gi|386002447|ref|YP_005920746.1| 221 DACRMAASLLEDPDPRVRLSAVTSLGEIGLAEALDRL 257
                                       77788999*************9988777777776555 PP

>> ALF  Short repeats of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.1   3.7e+03      21      29 ..      42      49 ..      42      54 .. 0.84
   2 ?    5.7   0.9    0.0083        15      13      30 ..      82     100 ..      73     101 .. 0.80
   3 ?    3.6   0.2     0.036        65       8      24 ..     199     215 ..     196     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                               ALF 21 aALdaGtpa 29
                                      aAL  G+p+
  gi|386002447|ref|YP_005920746.1| 42 AAL-GGDPD 49
                                      79*.59997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0083
                               ALF  13 paVraAAqaAL.daGtpaa 30 
                                       paVr+ A+ AL + G+p a
  gi|386002447|ref|YP_005920746.1|  82 PAVREWAASALeAIGDPRA 100
                                       9**********76788876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.036
                               ALF   8 latgGpaVraAAqaALd 24 
                                       l + Gp Vr +A++A +
  gi|386002447|ref|YP_005920746.1| 199 LKDDGPVVRMEAAKAVA 215
                                       5678***********84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1833.27
//
Query:       gi|386002448|ref|YP_005920747.1|  [L=1176]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-70  232.1   0.4    2.4e-14   53.4   0.0    8.7  8  PAS_3           PAS fold
    4.5e-66  220.0   4.0    6.4e-11   42.5   0.0    7.6  7  PAS_4           PAS fold
    9.1e-66  218.7   0.0    1.2e-12   48.0   0.0    7.1  7  PAS_9           PAS domain
    3.4e-55  184.9   0.8    9.2e-11   41.8   0.0    7.9  8  PAS             PAS fold
    2.5e-28   97.6   2.6      3e-07   30.3   0.1    6.3  6  PAS_8           PAS domain
    4.1e-22   78.8   0.0    5.1e-21   75.3   0.0    2.5  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    3.2e-13   49.5   0.8    1.9e-12   47.0   0.1    2.8  2  HisKA           His Kinase A (phospho-acceptor) domain
    7.4e-11   42.2   0.2      0.066   13.4   0.1    5.8  4  PAS_7           PAS fold
    2.6e-06   27.5   0.0      0.056   13.6   0.0    4.2  4  PAS_11          PAS domain
  ------ inclusion threshold ------
      0.018   14.7   0.2         13    5.4   0.0    3.3  3  PAS_12          UPF0242 C-terminal PAS-like domain
      0.058   13.3   0.1       0.56   10.1   0.0    2.3  2  MEKHLA          MEKHLA domain
       0.11   12.8   1.0        1.2    9.5   0.1    2.8  2  Rx_N            Rx N-terminal domain
       0.11   12.4   0.0       0.44   10.5   0.0    1.9  1  HATPase_c_5     GHKL domain
       0.15   12.7   0.0         16    6.1   0.0    4.1  5  PAS_10          PAS domain
       0.96   10.1   3.1        2.4    8.8   1.2    2.6  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        2.5    8.5   5.0         29    5.0   0.1    3.0  2  ATP-synt_DE     ATP synthase, Delta/Epsilon chain, long alpha


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 ?   -2.9   0.0       7.6   8.5e+03      29      50 ..       4      25 ..       2      29 .. 0.83
   2 !   44.1   0.0   1.6e-14   1.8e-11       2      88 ..      94     175 ..      93     176 .. 0.91
   3 !   42.7   0.0   4.7e-14   5.3e-11       5      89 .]     220     304 ..     216     304 .. 0.91
   4 !   53.4   0.0   2.1e-17   2.4e-14       3      89 .]     351     438 ..     349     438 .. 0.96
   5 !   40.7   0.0   1.9e-13   2.1e-10       2      89 .]     479     564 ..     478     564 .. 0.97
   6 !   16.8   0.0   5.3e-06     0.006       3      86 ..     606     690 ..     604     693 .. 0.82
   7 !   14.7   0.0   2.5e-05     0.028       4      87 ..     736     818 ..     733     819 .. 0.90
   8 !    7.4   0.0    0.0048       5.3       2      87 ..     857     934 ..     856     936 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.6
                             PAS_3 29 lvhpeDrervrealqealkkge 50
                                      ++  e++e++r+++ ++l++ +
  gi|386002448|ref|YP_005920747.1|  4 YILKEELEKARRQVRALLQEEC 25
                                      78899*********99997765 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 1.6e-14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                        y+s++ve+i+Gy + e++g+  ++ +++ peD  +++e l+ al +g     e R++ kdG++++v++++r+i   
  gi|386002448|ref|YP_005920747.1|  94 AYISPSVERIFGYPAGEVQGR--NVSQFLIPEDSRYLEERLKSAL-DGIFRVSELRFIAKDGSVHHVRTYGRPI--L 165
                                       69*******************..*******************999.7776699*********************..7 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g+   + g+
  gi|386002448|ref|YP_005920747.1| 166 EGHLRGIHGI 175
                                       7777777776 PP

  == domain 3  score: 42.7 bits;  conditional E-value: 4.7e-14
                             PAS_3   5 serveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvi.rden 79 
                                       ++r+ ei+G  p+e  +    w+  +hpeD++ v++al e++++++  ++ eyR   +  e  wv++r+ v+ rde+
  gi|386002448|ref|YP_005920747.1| 220 NRRYAEIVGTAPAEESDV-LAWKRSIHPEDLPSVERALREIAAGRTdLFDLEYRTTSAPAEA-WVHDRGLVVkRDES 294
                                       78999*******965554.59*************************788*****99998887.************** PP

                             PAS_3  80 gkpvrvigva 89 
                                       g+p+++ gv+
  gi|386002448|ref|YP_005920747.1| 295 GRPIKMAGVM 304
                                       ********96 PP

  == domain 4  score: 53.4 bits;  conditional E-value: 2.1e-17
                             PAS_3   3 yvserveeilGyspeellgk.veswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       +vse+v+++ Gy pe+++++  ++ ++lvhpeD+e v ++l + +++g+ ++ +e+R+++ +Ge+rw+ + + + rd
  gi|386002448|ref|YP_005920747.1| 351 FVSENVSQL-GYAPEDFYSRaASFDRNLVHPEDLELVVSELGRQIEEGSrSFFQEFRVLTSSGEVRWLASNVWISRD 426
                                       899999999.**********888889***********************9*************************** PP

                             PAS_3  78 engkpvrvigva 89 
                                       e g +++v g+a
  gi|386002448|ref|YP_005920747.1| 427 EAGAVTHVEGIA 438
                                       *********986 PP

  == domain 5  score: 40.7 bits;  conditional E-value: 1.9e-13
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       ++++++  e++Gy++++l+    ++ ++   eDre++++++q++l ++++++ ey  +rk G+++++  + r+i  +
  gi|386002448|ref|YP_005920747.1| 479 TFANQTAFELYGYDRQDLEVG-VNIFQVFAYEDREEMMKNFQRSLHDDKVFTYEYTGLRKEGTTFHLIVYSRPI-IR 553
                                       689******************.99**************************************************.99 PP

                             PAS_3  79 ngkpvrvigva 89 
                                       +g+pv + g++
  gi|386002448|ref|YP_005920747.1| 554 DGRPVGLRGTI 564
                                       ******99985 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 5.3e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD..rervrealqealkkgepyegeyRirrkdGeyrwveararvird 77 
                                        ++++ e+ lGys+ee+lg+ e++  l+ p+   r+++ ++l+e+  + ++     Ri+ k+Ge   +++++  + d
  gi|386002448|ref|YP_005920747.1| 606 LWNRASEKALGYSAEEVLGD-EEVWTLLFPDGeeRSEFLKTLDEIEMGLTAEGRRTRILAKSGEEKVISWSGIKLED 681
                                       69******************.9999999998756888888888775444444556*****************99999 PP

                             PAS_3  78 engkpvrvi 86 
                                        +g+ + ++
  gi|386002448|ref|YP_005920747.1| 682 GEGNGIGIV 690
                                       888877666 PP

  == domain 7  score: 14.7 bits;  conditional E-value: 2.5e-05
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirden 79 
                                        ++  e+++G+s+ e  g  ++++ +v   Dr  ++ a+  ++ +g+ + ++e  ++++ Ge + +++ ++++r++ 
  gi|386002448|ref|YP_005920747.1| 736 FNRGAEKVTGVSAKEAFGE-NFFMRFVAGADRRGFEMAVSSIF-EGKpAEQTEAAVVTRTGEPMAIQWGWSAVRSRT 810
                                       578899********99999.9******************9777.666256999************************ PP

                             PAS_3  80 gkpvrvig 87 
                                       g++ rvi+
  gi|386002448|ref|YP_005920747.1| 811 GEIERVIA 818
                                       *****996 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0048
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       ++++++  +++G++ ee +g+       +h + +  + e++  + ++++     + ++rkdG+++  + +  ++ ++
  gi|386002448|ref|YP_005920747.1| 857 LFANPALLDMFGFRLEEARGR-------LHQDFILDFGEDVSSSGEGNG-GRRRVTCVRKDGSTFPASISFAPVASS 925
                                       689999999999999999999.......566665566666654443333.467788899999999999999999999 PP

                             PAS_3  79 ngkpvrvig 87 
                                       +gkp   i 
  gi|386002448|ref|YP_005920747.1| 926 DGKPMATIV 934
                                       999887665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   5.7e-14   6.4e-11       2     109 ..      78     183 ..      77     184 .. 0.95
   2 !   20.5   0.1   3.9e-07   0.00044      21     108 ..     220     310 ..     205     312 .. 0.86
   3 !   20.9   0.0   2.9e-07   0.00032      27     109 ..     358     445 ..     347     446 .. 0.88
   4 !   36.1   0.0   5.6e-12   6.3e-09       2     110 .]     463     572 ..     462     572 .. 0.92
   5 !   35.1   0.0   1.1e-11   1.3e-08       7     107 ..     594     698 ..     589     701 .. 0.91
   6 !   25.2   0.0   1.3e-08   1.5e-05      10     106 ..     726     824 ..     719     827 .. 0.92
   7 !   33.3   0.0   4.2e-11   4.7e-08       2     107 ..     841     941 ..     840     944 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 5.7e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       +++  +++v+ + g++ y++++ +++fg+p+ e+ G+ + ++l +ed + le+ l+ +l+g  ++++l +   +g+ 
  gi|386002448|ref|YP_005920747.1|  78 ENVDGVIYVVETTGKIAYISPSVERIFGYPAGEVQGRNVSQFLIPEDSRYLEERLKSALDGIFRVSELRFIAKDGSV 154
                                       78888999*****************************************************999999999999**** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +h+ +  +P++  +G  +g+ +i++D+Te++
  gi|386002448|ref|YP_005920747.1| 155 HHVRTYGRPIL--EGHLRGIHGIMVDVTEQK 183
                                       **********5..59999***********97 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.9e-07
                             PAS_4  21 NaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelll.pgeerhy.elrllPlrdesG 93 
                                       N+++ae++g +p+e  +   +  +++pe d + +eralr+ ++g++ +++le++++  ++e ++ +  l+  rdesG
  gi|386002448|ref|YP_005920747.1| 220 NRRYAEIVGTAPAEESDVLAWkrSIHPE-DLPSVERALREIAAGRTDLFDLEYRTTsAPAEAWVhDRGLVVKRDESG 295
                                       999***************9998778887.9***************************5666655155568889**** PP

                             PAS_4  94 evigvlvisrDiTer 108
                                       ++i   ++++D+T +
  gi|386002448|ref|YP_005920747.1| 296 RPIKMAGVMQDVTWQ 310
                                       ************965 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.9e-07
                             PAS_4  27 lfgappeellGktla...ellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllPlrdesGevigv 98 
                                        +g++pe+++ +       l+ +ed + + + l r +e++ + +f+e+++l  +ge r++  ++   rde G v +v
  gi|386002448|ref|YP_005920747.1| 358 QLGYAPEDFYSRAASfdrNLVHPEDLELVVSELGRQIEEGSRSFFQEFRVLtsSGEVRWLASNVWISRDEAGAVTHV 434
                                       478899999999998854466666999*************************************999********** PP

                             PAS_4  99 lvisrDiTerr 109
                                        +i+ DiTer+
  gi|386002448|ref|YP_005920747.1| 435 EGIALDITERK 445
                                       **********8 PP

  == domain 4  score: 36.1 bits;  conditional E-value: 5.6e-12
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeel.lGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       d lp++++ +d  g+v++aN++a el+g+++++l +G   ++++  ed+++ + + +r l  +++ + + + l+ +g
  gi|386002448|ref|YP_005920747.1| 463 DTLPQPIFECDLAGKVTFANQTAFELYGYDRQDLeVGVNIFQVFAYEDREEMMKNFQRSLHDDKVFTYEYTGLRkEG 539
                                       789******************************966***************************99999999999666 PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        + h+ +  +P+  ++G+++g+ ++++DiTer+r
  gi|386002448|ref|YP_005920747.1| 540 TTFHLIVYSRPI-IRDGRPVGLRGTIVDITERKR 572
                                       666666666888.79*****************97 PP

  == domain 5  score: 35.1 bits;  conditional E-value: 1.1e-11
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlaellpee..daarleralrrvlegeepiefleelll....pge 77 
                                       +++v+d+d r+  +N+a+++ +g+++ee+lG      ++    d+++ ++ l+ + e e  ++ +  +++    +ge
  gi|386002448|ref|YP_005920747.1| 594 MIFVIDRDRRIFLWNRASEKALGYSAEEVLGDEEV--WTLLfpDGEERSEFLKTLDEIEMGLTAEGRRTRilakSGE 668
                                       89*****************************6544..444445999999999999999999999999999999**** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTe 107
                                       e++++++ + l+d +G  ig++++++D+Te
  gi|386002448|ref|YP_005920747.1| 669 EKVISWSGIKLEDGEGNGIGIVITAQDTTE 698
                                       *****************************9 PP

  == domain 6  score: 25.2 bits;  conditional E-value: 1.3e-08
                             PAS_4  10 vldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelll.pgeerhyelr 84 
                                        ldp gr++  N+ a+++ g++++e+ G+ ++  ++   d++++e a+    eg+ + +++  +++  ge+  +++ 
  gi|386002448|ref|YP_005920747.1| 726 GLDPRGRITLFNRGAEKVTGVSAKEAFGENFFmRFVAGADRRGFEMAVSSIFEGKPAEQTEAAVVTrTGEPMAIQWG 802
                                       35******************************8899999***************9888888888888********** PP

                             PAS_4  85 llPlrdesGevigvlvisrDiT 106
                                        + +r + Ge+  v+++++Di+
  gi|386002448|ref|YP_005920747.1| 803 WSAVRSRTGEIERVIAFGHDIS 824
                                       ********************97 PP

  == domain 7  score: 33.3 bits;  conditional E-value: 4.2e-11
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       +s++d++a++++  + l+aN+a  ++fg++ ee++G+  +++       ++ +++    eg+   +++++++ +g++
  gi|386002448|ref|YP_005920747.1| 841 ESSNDGIAIFGKSNHLLFANPALLDMFGFRLEEARGRLHQDFIL-----DFGEDVSSSGEGNGGRRRVTCVRKDGST 912
                                       89***************************************877.....699999999******************* PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTe 107
                                        + ++++ P+  ++G++++++v++rDi+e
  gi|386002448|ref|YP_005920747.1| 913 FPASISFAPVASSDGKPMATIVVARDISE 941
                                       ***************************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   1.1e-14   1.2e-11       3     104 .]      82     181 ..      80     181 .. 0.84
   2 ?   -0.0   0.0      0.94   1.1e+03      76     103 ..     280     308 ..     220     308 .. 0.74
   3 !    8.9   0.0    0.0016       1.7      11     104 .]     347     443 ..     337     443 .. 0.78
   4 !   48.0   0.0   1.1e-15   1.2e-12       2     104 .]     467     569 ..     466     569 .. 0.91
   5 !   31.1   0.0   1.9e-10   2.2e-07       3     104 .]     595     698 ..     593     698 .. 0.85
   6 !   31.7   0.0   1.2e-10   1.4e-07       4     103 ..     723     824 ..     720     824 .. 0.87
   7 !   43.8   0.0   2.2e-14   2.4e-11       2     104 .]     845     941 ..     844     941 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.1e-14
                             PAS_9   3 gil.idnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       g++ ++ + g+i y++++++r++Gy + ev g+++++++   pe+ + l++ l++  + ++r  e+ +i k+g+  +
  gi|386002448|ref|YP_005920747.1|  82 GVIyVVETTGKIAYISPSVERIFGYPAGEVQGRNVSQFL--IPEDSRYLEERLKSALDgIFRVSELRFIAKDGSVHH 156
                                       555358899*9****************************..66666666666666655667**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+   +p+ +++  l+gi +i++D+te
  gi|386002448|ref|YP_005920747.1| 157 VRTYGRPILEGH--LRGIHGIMVDVTE 181
                                       ********9666..66655*******8 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.94
                             PAS_9  76 fwvlltaspv.kdddgelvgiivilrDit 103
                                        wv+ +   v +d++g+ + ++++++D+t
  gi|386002448|ref|YP_005920747.1| 280 AWVHDRGLVVkRDESGRPIKMAGVMQDVT 308
                                       45443333334778999999*******99 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0016
                             PAS_9  11 grilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirkngetfwvlltas 83 
                                       g++++++e + +l Gy pe++  +  +     v++++ +  ++++ +q+++    + +e    +++ge  w   ++ 
  gi|386002448|ref|YP_005920747.1| 347 GPVEFVSENVSQL-GYAPEDFYSRAASFDRnlVHPEDLELVVSELGRQIEEgsRSFFQEFRVLTSSGEVRWLASNV- 421
                                       6889*********.**********9555554435555555555555555555599999*************55555. PP

                             PAS_9  84 pv.kdddgelvgiivilrDite 104
                                        + +d+ g ++++ +i  Dite
  gi|386002448|ref|YP_005920747.1| 422 WIsRDEAGAVTHVEGIALDITE 443
                                       555999*****999*******8 PP

  == domain 4  score: 48.0 bits;  conditional E-value: 1.1e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspee.vlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetf 76 
                                        +i+ ++  g++++aN++a +l+Gy++++  +g +i+++f   ++++e ++++ +++ + k++++e++  rk+g+tf
  gi|386002448|ref|YP_005920747.1| 467 QPIFECDLAGKVTFANQTAFELYGYDRQDlEVGVNIFQVF-AYEDREEMMKNFQRSLHDdKVFTYEYTGLRKEGTTF 542
                                       6788899*******************999789********.88888888888888888899**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +  +  +p++  dg+ vg+ ++++Dite
  gi|386002448|ref|YP_005920747.1| 543 HLIVYSRPIIR-DGRPVGLRGTIVDITE 569
                                       *********76.6788889********8 PP

  == domain 5  score: 31.1 bits;  conditional E-value: 1.9e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                        ++ ++ d ri  +N+a ++ lGys+eevlg    +++  +d e+++++ + l++++   +++ + + +  k+ge+ 
  gi|386002448|ref|YP_005920747.1| 595 IFV-IDRDRRIFLWNRASEKALGYSAEEVLGDEEVWTLlFPDGEERSEFLKTLDEIEMglTAEGRRTRILAKSGEEK 670
                                       455.559999*********************9944444447777777777777777778999999999999999999 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                        +  + + + d++g+ +gi+++ +D te
  gi|386002448|ref|YP_005920747.1| 671 VISWSGIKLEDGEGNGIGIVITAQDTTE 698
                                       99************************98 PP

  == domain 6  score: 31.7 bits;  conditional E-value: 1.2e-10
                             PAS_9   4 ili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                       +++  +p gri+ +N++a++++G s++e  g ++++ fv  ++++ ++ a+    +  ++++ e   ++++ge++ +
  gi|386002448|ref|YP_005920747.1| 723 FIVgLDPRGRITLFNRGAEKVTGVSAKEAFGENFFMRFVAGADRRGFEMAVSSIFEGkPAEQTEAAVVTRTGEPMAI 799
                                       455688********************************555555555555555555588****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       +   s+v++  ge+ ++i++ +Di+
  gi|386002448|ref|YP_005920747.1| 800 QWGWSAVRSRTGEIERVIAFGHDIS 824
                                       ************************7 PP

  == domain 7  score: 43.8 bits;  conditional E-value: 2.2e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       dgi+i  +++++l+aN+a+l+++G+  ee  g+   d++       ++ +++  +g+ +  ++ v+++rk+g+tf++
  gi|386002448|ref|YP_005920747.1| 845 DGIAIFGKSNHLLFANPALLDMFGFRLEEARGRLHQDFI------LDFGEDVSSSGEGNGGRRRVTCVRKDGSTFPA 915
                                       78999667777*********************9999999......444444444444489***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                        ++++pv ++dg+ ++ iv+ rDi+e
  gi|386002448|ref|YP_005920747.1| 916 SISFAPVASSDGKPMATIVVARDISE 941
                                       ************************98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   1.3e-13   1.4e-10       1     111 [.      71     177 ..      71     179 .. 0.87
   2 ?    1.0   0.0      0.35     4e+02       2     112 ..     195     306 ..     194     307 .. 0.63
   3 !    7.9   0.0    0.0027         3      48     113 .]     376     441 ..     326     441 .. 0.88
   4 !   32.5   0.0   6.1e-11   6.9e-08       2     112 ..     457     566 ..     456     567 .. 0.89
   5 !   36.8   0.0   2.8e-12   3.1e-09      12     112 ..     593     695 ..     585     696 .. 0.91
   6 !   41.8   0.0   8.2e-14   9.2e-11       4     113 .]     714     823 ..     711     823 .. 0.89
   7 !   13.4   0.0   5.2e-05     0.058       6     113 .]     839     939 ..     836     939 .. 0.82
   8 ?   -3.1   0.0       6.7   7.5e+03      60      90 ..    1123    1156 ..    1118    1157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.3e-13
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r ++e+ +  i vv   g+i y++++ e+++G+++ ev g++++ ++++ed+++l e+l+ +l    + +    
  gi|386002448|ref|YP_005920747.1|  71 ERYRCLVENVDGVIYVVETTGKIAYISPSVERIFGYPAGEVQGRNVSQFLIPEDSRYLEERLKSALDGIFRVSE--L 145
                                       68999*************************************************99999999999987655554..6 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlr 111
                                       +f  +dg++ h+++  +p++++  +  g+ g++ 
  gi|386002448|ref|YP_005920747.1| 146 RFIAKDGSVHHVRTYGRPILEGHLR--GIHGIMV 177
                                       666689********99999999765..6666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBG.GGGBSTTHHH.HHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgksl.ldliheedda.elaelleqlleqgeesrage 76 
                                       +l+  +e ++ +i+ +D ++  +  N+ ++e+ G ++ e +      ++ih+ed    + ++l++ ++ +++  + e
  gi|386002448|ref|YP_005920747.1| 195 RLKLAVEGADLAIWNRDLSTGEVVGNRRYAEIVGTAPAEESDVLAwKRSIHPED-LpSVERALREIAAGRTDLFDLE 270
                                       678889999999999998888888899999999999965555444044444444.3477777777777777666666 PP

                                       EEEECTTSSEEEEEEEE.EEEEETTEEEEEEEEEEEE CS
                               PAS  77 isfklrdgrpihlevra.spvrdaggeilgflgvlrd 112
                                        + +     + +++ r  +  rd++g+++   gv++d
  gi|386002448|ref|YP_005920747.1| 271 YRTTS-APAEAWVHDRGlVVKRDESGRPIKMAGVMQD 306
                                       66666.4444444444323445556666666666666 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0027
                                       GGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  48 dliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        l+h+ed + ++++l +++e+g++s  +e ++ +  g++++l  ++   rd+ g ++++ g++ di
  gi|386002448|ref|YP_005920747.1| 376 NLVHPEDLELVVSELGRQIEEGSRSFFQEFRVLTSSGEVRWLASNVWISRDEAGAVTHVEGIALDI 441
                                       46788888899***********************************************99988886 PP

  == domain 4  score: 32.5 bits;  conditional E-value: 6.1e-11
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHC.TTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreev.lgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++r++ ++lp pif  D  g+++++N++a el G++r+++ +g +++ ++  ed++e+ + +++ l++ + ++ + +
  gi|386002448|ref|YP_005920747.1| 457 RFREMADTLPQPIFECDLAGKVTFANQTAFELYGYDRQDLeVGVNIFQVFAYEDREEMMKNFQRSLHDDKVFTYEYT 533
                                       799**********************************77659************99999999999999999999999 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                        +++  g+++hl v  +p++  g  + g+ g++ d
  gi|386002448|ref|YP_005920747.1| 534 GLRK-EGTTFHLIVYSRPIIRDGR-PVGLRGTIVD 566
                                       9999.*******999999987744.4477777666 PP

  == domain 5  score: 36.8 bits;  conditional E-value: 2.8e-12
                                       SEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC...TTSS CS
                               PAS  12 dpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl...rdgr 85 
                                       ++ifv+D+d ri+++N+a e+ lG+s+eevlg   +  +  +d  e ++++++ l + e++ + e ++++   + g+
  gi|386002448|ref|YP_005920747.1| 593 PMIFVIDRDRRIFLWNRASEKALGYSAEEVLGDEEVWTLLFPDG-EERSEFLKTLDEIEMGLTAEGRRTRilaKSGE 668
                                       689*****************************999988888765.68888888888888888888888888999*** PP

                                       EEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  86 pihlevraspvrdaggeilgflgvlrd 112
                                       ++ +     ++ d++g+ +g++ +++d
  gi|386002448|ref|YP_005920747.1| 669 EKVISWSGIKLEDGEGNGIGIVITAQD 695
                                       *************************99 PP

  == domain 6  score: 41.8 bits;  conditional E-value: 8.2e-14
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisf 79 
                                       r i+e ++ +i+++D +gri+++N+ ae+ +G s++e+ g+++++ ++   d+  +  +++   e +  ++++   +
  gi|386002448|ref|YP_005920747.1| 714 RGIIEGADLFIVGLDPRGRITLFNRGAEKVTGVSAKEAFGENFFMRFVAGADRrGFEMAVSSIFEGKPAEQTEAAVV 790
                                       789****************************************9999887777577777777777777777777766 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++  g+p  ++  +s vr++ gei  ++ +++di
  gi|386002448|ref|YP_005920747.1| 791 TR-TGEPMAIQWGWSAVRSRTGEIERVIAFGHDI 823
                                       66.******************************8 PP

  == domain 7  score: 13.4 bits;  conditional E-value: 5.2e-05
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC. CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl. 81 
                                        +es+ d+i +  ++   l++N+a  +++G++ ee+ g+   d+i       + e ++   e +  +r      ++ 
  gi|386002448|ref|YP_005920747.1| 839 AIESSNDGIAIFGKSNHLLFANPALLDMFGFRLEEARGRLHQDFILD-----FGEDVSSSGEGNGGRRR---VTCVr 907
                                       589999*********************************99999963.....55554444444444444...22334 PP

                                       TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +dg+++++ +  +pv + +g++   ++v+rdi
  gi|386002448|ref|YP_005920747.1| 908 KDGSTFPASISFAPVASSDGKPMATIVVARDI 939
                                       69********************9999999998 PP

  == domain 8  score: -3.1 bits;  conditional E-value: 6.7
                                        HHHHHHHHHTT-ECCCCEEEEC...TTSSEEEEE CS
                               PAS   60 elleqlleqgeesrageisfkl...rdgrpihle 90  
                                        + +++l+++ge s +g  ++k+   ++g+ i++e
  gi|386002448|ref|YP_005920747.1| 1123 DPFTRLERSGEGSGIGLATVKKiveTCGGRIWAE 1156
                                        6789999999999999999999999999999986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     4e-05     0.045       1      62 [.      71     135 ..      71     140 .. 0.77
   2 ?   -1.2   0.0       2.1   2.3e+03       2      46 ..     195     238 ..     194     261 .. 0.53
   3 !   30.3   0.1   2.6e-10     3e-07       1      62 [.     456     517 ..     456     523 .. 0.82
   4 !   13.8   0.0   3.9e-05     0.044      13      56 ..     594     637 ..     585     650 .. 0.71
   5 !    9.9   0.0   0.00066      0.74       3      42 ..     713     753 ..     711     770 .. 0.81
   6 !   23.3   0.0   4.3e-08   4.8e-05       6      49 ..     839     883 ..     835     899 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg..qllpvlrplledaeql 62 
                                       er+r l+e+++  i vv  +g+ i ++ ++ ++++Gy+  ++ g  +    +++++r+l+e+++  
  gi|386002448|ref|YP_005920747.1|  71 ERYRCLVENVDGVIYVVEtTGK-IAYISPSVERIFGYPaGEVQGRNVSqfLIPEDSRYLEERLKSA 135
                                       6788889999999999995555.***************9999888886666666666666666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg 46 
                                       rl+ ++e ++ +i+  d   +  v  N++++e+ G +a+  ++++ 
  gi|386002448|ref|YP_005920747.1| 195 RLKLAVEGADLAIWNRDlSTG-EVVGNRRYAEIVG-TAPAEESDVL 238
                                       666666777777772222222.4446889999999.3223334443 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 2.6e-10
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.qllpvlrplle.daeql 62 
                                       +r+r + +++p++i+ +d +g+ ++++Nq+a el+Gy+    + ++g ++++v+ ++ + +++  
  gi|386002448|ref|YP_005920747.1| 456 RRFREMADTLPQPIFECDlAGK-VTFANQTAFELYGYD--RQDLEVGvNIFQVFAYEDReEMMKN 517
                                       59****************6666.*************99..5556677899999999988655544 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 3.9e-05
                             PAS_8  13 giavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpll 56 
                                        i+v+d+++ri  +N+a ++ lGys ++++g++  ++   +++++
  gi|386002448|ref|YP_005920747.1| 594 MIFVIDRDRRIFLWNRASEKALGYSaEEVLGDEE-VWTLLFPDGE 637
                                       5889**999****************777777555.3333333333 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00066
                             PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adlkg 42 
                                        r+++e ++  i+ +d +g+ i+  N+ a++ +G+s ++  g
  gi|386002448|ref|YP_005920747.1| 713 SRGIIEGADLFIVGLDpRGR-ITLFNRGAEKVTGVSaKEAFG 753
                                       588889999999999*6655.*************99655555 PP

  == domain 6  score: 23.3 bits;  conditional E-value: 4.3e-08
                             PAS_8   6 lfesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgqll 49 
                                       ++ess+dgia++   +  +++++N+a l+++G++ ++ +g l ++++
  gi|386002448|ref|YP_005920747.1| 839 AIESSNDGIAIFG--KsnHLLFANPALLDMFGFRlEEARGRLHQDFI 883
                                       69*********94..1446***************9999988887444 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.99   1.1e+03      64      97 ..     675     711 ..     649     727 .. 0.73
   2 !   75.3   0.0   4.6e-24   5.1e-21       4     110 ..    1068    1171 ..    1065    1173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.99
                                       HCSTCHTSTSSSHHHHHHHH.HHH..HTTTEEEEEEE CS
                         HATPase_c  64 ddstkrggggtGlGlsivkk.lve..lmgGeiwvese 97 
                                       ++ +  +g+g+G+G  i  +  +e  +m+ ei+ e e
  gi|386002448|ref|YP_005920747.1| 675 SGIKLEDGEGNGIGIVITAQdTTEyaKMEEEIRSERE 711
                                       5556677999999999999988884446666665444 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 4.6e-24
                                        HHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                         HATPase_c    4 krLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76  
                                        +r +q++snl++N++k+  +++ ie+e+ + +  d++++ v+D+G G +++  +k+f++f++    +r+g+g+G+
  gi|386002448|ref|YP_005920747.1| 1068 SRAKQVFSNLLENSLKY--SKDAIEIEVGSLDrgDEYEFWVKDDGLGFDMKYAEKIFDPFTR---LERSGEGSGI 1137
                                        6889************8..7899999988622469***************************...8899****** PP

                                        HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c   77 GlsivkklvelmgGeiwvesepgrGttftftlpl 110 
                                        Gl+ vkk+ve+ gG+iw es pgrG  f+ft+p+
  gi|386002448|ref|YP_005920747.1| 1138 GLATVKKIVETCGGRIWAESAPGRGAAFRFTIPK 1171
                                        *******************************997 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1         2   2.3e+03      33      58 ..      55      80 ..      27      81 .. 0.69
   2 !   47.0   0.1   1.7e-15   1.9e-12       2      65 ..     956    1021 ..     955    1023 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                                      -HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA 33 lteelkeyletiesearrldhlvedl 58
                                        eel+++ e ++++ +r + lve++
  gi|386002448|ref|YP_005920747.1| 55 EGEELAKANEALRRSLERYRCLVENV 80
                                      34788888888888888888888775 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 1.7e-15
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA    2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65  
                                        l+ f+ +++H+Lr PL +i+g+a aL+++  ++l e  ++yle+i   a+ +d+l+ dlLd+sri+
  gi|386002448|ref|YP_005920747.1|  956 LESFAYTISHDLRAPLRGIRGFALALQEDygDDLEEAGRKYLERIGAIAENMDRLILDLLDYSRIG 1021
                                        567999********************77779999999999************************97 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.5   5.6e+02       2      45 ..      78     120 ..      77     187 .. 0.57
   2 !   13.4   0.1   5.9e-05     0.066       4      59 ..     465     520 ..     463     575 .. 0.65
   3 !   12.9   0.0   8.3e-05     0.093       8     114 ..     595     703 ..     587     704 .. 0.76
   4 !    7.2   0.0     0.005       5.6       1      38 [.     840     877 ..     840     913 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.5
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                       en++  i v+  ++++  +   + +++++p++ v +g++++++l
  gi|386002448|ref|YP_005920747.1|  78 ENVDGVIYVVETTGKIAYISPSVERIFGYPAGEV-QGRNVSQFL 120
                                       6667777777777777777777777777777777.555555544 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.9e-05
                             PAS_7   4 msqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdv 59 
                                       ++q i   D ++++++ N+   el+++ ++ ++vgv++ ++++y  +++ +++ ++
  gi|386002448|ref|YP_005920747.1| 465 LPQPIFECDLAGKVTFANQTAFELYGYDRQDLEVGVNIFQVFAYEDREEMMKNFQR 520
                                       566777789999********************************977776663333 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 8.3e-05
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpd 84 
                                       i v+D+d r+ +wNr   + l++++e v      ee+   +   ge +++  +   e  +   ++g+++++  +  +
  gi|386002448|ref|YP_005920747.1| 595 IFVIDRDRRIFLWNRASEKALGYSAEEV---LGDEEVWTLLFPDGEERSEFLKTLDEIEMGLTAEGRRTRILAKSGE 668
                                       78**********************9999...444555555555555553333333333344567899999999999* PP

                             PAS_7  85 grvievrgnplpdg.....GfVttytDiTerrrae 114
                                       ++vi+  g +l+dg     G+V+t +D Te+ + e
  gi|386002448|ref|YP_005920747.1| 669 EKVISWSGIKLEDGegngiGIVITAQDTTEYAKME 703
                                       ****9999999665555559**********99877 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.005
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvg 38 
                                       +e+ ++Gi++f +++ L++ N   l+++++  e ++  
  gi|386002448|ref|YP_005920747.1| 840 IESSNDGIAIFGKSNHLLFANPALLDMFGFRLEEARGR 877
                                       577899**********************9876666555 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     5e-05     0.056       9      89 ..      88     163 ..      83     177 .. 0.91
   2 ?    4.6   0.0     0.031        35      37      64 ..     237     264 ..     223     283 .. 0.74
   3 ?   -0.7   0.0       1.4   1.5e+03      42      80 ..     376     414 ..     359     430 .. 0.81
   4 ?    3.0   0.0     0.097   1.1e+02       6      60 ..     470     522 ..     467     539 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                            PAS_11   9 didgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvkt 85 
                                        ++gkI  + +   + +   g++  e++gr + +++ p+d + l++ l+  +   g ++ s  R++++++ + +v+t
  gi|386002448|ref|YP_005920747.1|  88 ETTGKIAYISP---SVERIFGYPAGEVQGRNVSQFLIPEDSRYLEERLKSAL--DGIFRVSELRFIAKDGSVHHVRT 159
                                       689********...99999*********************************..99999999********9999999 PP

                            PAS_11  86 kskl 89 
                                        ++ 
  gi|386002448|ref|YP_005920747.1| 160 YGRP 163
                                       8776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.031
                            PAS_11  37 grsiydLchpqdlstlkshlrevissng 64 
                                        + +++ +hp+dl +++++lre+   + 
  gi|386002448|ref|YP_005920747.1| 237 VLAWKRSIHPEDLPSVERALREIAAGRT 264
                                       5689999****************93333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                            PAS_11  42 dLchpqdlstlkshlrevissngeatsslyRLrlsqdkf 80 
                                       +L+hp+dl+ + s l   i++  ++  + +R  +s++++
  gi|386002448|ref|YP_005920747.1| 376 NLVHPEDLELVVSELGRQIEEGSRSFFQEFRVLTSSGEV 414
                                       79*****99999988777768888888888888888766 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.097
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeel.vgrsiydLchpqdlstlkshlrevi 60 
                                       +  d+ gk++  ++    a    g+ +++l vg+ i++ +  +d++++++ ++  +
  gi|386002448|ref|YP_005920747.1| 470 FECDLAGKVTFANQ---TAFELYGYDRQDLeVGVNIFQVFAYEDREEMMKNFQRSL 522
                                       66789999999999...444444566655449*******************99866 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 ?   -0.7   0.0      0.88   9.8e+02      66      87 ..     475     496 ..     469     506 .. 0.87
   2 ?    4.7   0.0      0.02        22      57      91 ..     592     626 ..     576     638 .. 0.82
   3 ?    5.4   0.0     0.011        13      49      86 ..     838     873 ..     821     886 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.88
                            PAS_12  66 enkllfaNaqirallGwssdkf 87 
                                       + k+ faN+   +l G+  +++
  gi|386002448|ref|YP_005920747.1| 475 AGKVTFANQTAFELYGYDRQDL 496
                                       5699*************98876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                            PAS_12  57 gailvysqkenkllfaNaqirallGwssdkflqdf 91 
                                       + +++   ++++++  N+ +++ lG+s++++l d+
  gi|386002448|ref|YP_005920747.1| 592 SPMIFVIDRDRRIFLWNRASEKALGYSAEEVLGDE 626
                                       445566688999*****************998776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.011
                            PAS_12  49 DsLrsEnlgailvysqkenkllfaNaqirallGwssdk 86 
                                       D++ s n g i+++  k n+llfaN  + ++ G+  ++
  gi|386002448|ref|YP_005920747.1| 838 DAIESSNDG-IAIFG-KSNHLLFANPALLDMFGFRLEE 873
                                       666665555.66675.7899**************9886 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0005      0.56      50     114 ..     477     542 ..     445     546 .. 0.80
   2 ?   -0.2   0.0      0.78   8.7e+02      49      69 ..     854     874 ..     848     883 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                            MEKHLA  50 vfnyaNqaaldllettweel.tdlpsrksaepeekeeRealLekvaeqgfvenysGvrisstGrrf 114
                                         ++aNq+a++l+ ++ ++l + +   +++  e++ee  + +++  +++ v +y+   + ++G  f
  gi|386002448|ref|YP_005920747.1| 477 KVTFANQTAFELYGYDRQDLeVGVNIFQVFAYEDREEMMKNFQRSLHDDKVFTYEYTGLRKEGTTF 542
                                       468****************95689********************9999977666555555666655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.78
                            MEKHLA  49 pvfnyaNqaaldllettweel 69 
                                       + + +aN a ld++ +++ee 
  gi|386002448|ref|YP_005920747.1| 854 NHLLFANPALLDMFGFRLEEA 874
                                       6789************99986 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0011       1.2       7      73 ..      15      85 ..      10      92 .. 0.84
   2 ?    0.3   0.1      0.75   8.4e+02      30      66 ..     165     201 ..     164     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                              Rx_N  7 qkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqi....kdeavkeWlkelrdlaydaeDvlD 73
                                      +++ +ll+ee  +++g+ + le+l  +Le +++  e+a    +     +ea++  l++ r l+ +++ v+ 
  gi|386002448|ref|YP_005920747.1| 15 RQVRALLQEECPSIEGLSRGLEELSATLEELDGSAEEAWGEGEelakANEALRRSLERYRCLVENVDGVIY 85
                                      567899******************************99886663333699999999999999999988875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.75
                              Rx_N  30 lkdeLesiqavLedaeerqikdeavkeWlkelrdlay 66 
                                       l+  L+ i++++ d+ e++  +ea++e  ++l+ ++ 
  gi|386002448|ref|YP_005920747.1| 165 LEGHLRGIHGIMVDVTEQKKAEEALRESEERLKLAVE 201
                                       6788999*******************99999987665 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.44       9      90 ..    1073    1158 ..    1070    1167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                       HATPase_c_5    9 ilgnlLdNAieacskieeekrfIrltvrekkksliisieNs.......yegek.kklesskskkeehGiGlksir 75  
                                        +++nlL+N++  +++      +I++    + + + + ++         y++++ + +   ++++e  GiGl +++
  gi|386002448|ref|YP_005920747.1| 1073 VFSNLLENSLKYSKDAI----EIEVGSLDRGDEYEFWVKDDglgfdmkYAEKIfDPFTRLERSGEGSGIGLATVK 1143
                                        78888888887766644....35555555555566666555333322244555444445588999********** PP

                       HATPase_c_5   76 eivkkykgnlsieae 90  
                                        +iv++ +g ++ e +
  gi|386002448|ref|YP_005920747.1| 1144 KIVETCGGRIWAESA 1158
                                        ********9998765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.014        16       5     106 .]      77     180 ..      74     180 .. 0.89
   2 ?   -0.7   0.0         2   2.2e+03      56     106 .]     512     568 ..     482     568 .. 0.56
   3 ?   -1.2   0.0       2.6     3e+03      76     104 ..     667     695 ..     592     697 .. 0.63
   4 ?   -2.0   0.0         5   5.6e+03      12      35 ..     724     747 ..     717     751 .. 0.80
   5 ?   -0.9   0.0       2.3   2.5e+03      39      75 ..     926     962 ..     916     967 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                            PAS_10   5 LnstpieltflDdnlqirrFtpaakklfklipadv.Grpladihpkkavknveeviealrtgekdevevvv.pkngk 79 
                                        ++++  +  + ++ +i + +p+ +++f + +++v Gr+++++  ++    +ee +++  +g   ++e    +k+g 
  gi|386002448|ref|YP_005920747.1|  77 VENVDGVIYVVETTGKIAYISPSVERIFGYPAGEVqGRNVSQFLIPEDSRYLEERLKSALDGIFRVSELRFiAKDGS 153
                                       567777788899999*****************9998********999999999999999999998888776479999 PP

                            PAS_10  80 wvlvrylpyrdedgeiaGvvetfvDit 106
                                       ++ vr+      +g+ +G+  ++vD+t
  gi|386002448|ref|YP_005920747.1| 154 VHHVRTYGRPILEGHLRGIHGIMVDVT 180
                                       999999888889********9999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                            PAS_10  56 eeviealrtgekdevevvvp......kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                       ee++++++++  d + +  +      +  +++l+ y++    dg+  G+  t+vDit
  gi|386002448|ref|YP_005920747.1| 512 EEMMKNFQRSLHDDKVFTYEytglrkEGTTFHLIVYSRPIIRDGRPVGLRGTIVDIT 568
                                       333333333333222222222234423345567777777779999999999999996 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.6
                            PAS_10  76 kngkwvlvrylpyrdedgeiaGvvetfvD 104
                                        ++k++      ++d +g+  G+v+t +D
  gi|386002448|ref|YP_005920747.1| 667 GEEKVISWSGIKLEDGEGNGIGIVITAQD 695
                                       44555555566677778888888888888 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5
                            PAS_10  12 ltflDdnlqirrFtpaakklfkli 35 
                                       ++ lD   +i+ F++ a+k+  + 
  gi|386002448|ref|YP_005920747.1| 724 IVGLDPRGRITLFNRGAEKVTGVS 747
                                       56689999********99987655 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 2.3
                            PAS_10  39 vGrpladihpkkavknveeviealrtgekdevevvvp 75 
                                        G p+a+i+  + ++++ e  ++l t +++ +++  +
  gi|386002448|ref|YP_005920747.1| 926 DGKPMATIVVARDISEMIEYQQRLETLNRELESFAYT 962
                                       599********99999999999999999998887655 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.2    0.0021       2.4      29      93 ..       3      67 ..       1      72 [. 0.91
   2 ?   -1.2   0.0       2.9   3.3e+03      49      63 ..     944     958 ..     935     965 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                    HIP1_clath_bdg 29 kkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93
                                      +  l+eele+++++ +  l+e    +e L r le+ +a l++l +s e+   +ge+l++  +aL+
  gi|386002448|ref|YP_005920747.1|  3 RYILKEELEKARRQVRALLQEECPSIEGLSRGLEELSATLEELDGSAEEAWGEGEELAKANEALR 67
                                      66799*******************************************99999999998777775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                    HIP1_clath_bdg  49 eqkeelekLkrelea 63 
                                       e ++ le+L+rele+
  gi|386002448|ref|YP_005920747.1| 944 EYQQRLETLNRELES 958
                                       556788999999986 PP

>> ATP-synt_DE  ATP synthase, Delta/Epsilon chain, long alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.026        29      22      44 ..      52      74 ..      39      75 .. 0.81
   2 ?    3.0   1.6      0.11   1.2e+02       7      21 ..     184     198 ..     179     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                                      HHHHSS-HHHHHHHHHHHHHHHH CS
                       ATP-synt_DE 22 asddnidyarAqaaLrRAlaRlq 44
                                      a +++ ++a+A  aLrR l R +
  gi|386002448|ref|YP_005920747.1| 52 AWGEGEELAKANEALRRSLERYR 74
                                      4455699***********99976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHH CS
                       ATP-synt_DE   7 rAeeAkerAeerLee 21 
                                       +AeeA+++ eerL+ 
  gi|386002448|ref|YP_005920747.1| 184 KAEEALRESEERLKL 198
                                       677777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.98u 0.36s 00:00:01.34 Elapsed: 00:00:00.54
# Mc/sec: 6585.53
//
Query:       gi|386002449|ref|YP_005920748.1|  [L=388]
Description: Major facilitator superfamily MFS_1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-52  178.3  62.5    4.7e-33  114.6  26.9    2.0  2  MFS_1       Major Facilitator Superfamily
    3.5e-13   49.2  24.6    1.1e-07   31.0  10.3    2.0  2  MFS_1_like  MFS_1 like family
    1.2e-06   27.7  14.5    1.2e-06   27.7  14.5    2.6  2  Sugar_tr    Sugar (and other) transporter
    2.5e-05   22.9  28.5    0.00084   17.8  28.5    2.1  1  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
      0.033   13.5  31.9       0.32   10.2  31.4    2.7  1  MFS_4       Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6  26.9   1.3e-36   4.7e-33       1     233 [.      11     230 ..      11     230 .. 0.85
   2 !   69.4  31.2   6.9e-23   2.5e-19       8     174 ..     216     381 ..     209     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.3e-36
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l++++f ++l+ +i+ p+lp ++ae+lg+s+  igl+++++a++ a++++++Gr+sd  Gr++++++gll++al +l
  gi|386002449|ref|YP_005920748.1|  11 LFISVFAAMLGLGIVVPLLP-IYAEELGASGVWIGLIFSGFAVARAIFMPIVGRVSDEAGRKKFIVFGLLAYALLSL 86 
                                       799*****************.9*****************************************************44 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                         + a+++   l ++r+l G+++++++p+++a++ d++ + e g  +g ++++  lG   gpllgg+l +++g++++
  gi|386002449|ref|YP_005920748.1|  87 GYV-AAGSVySLTAVRFLHGIASAMVVPIAMAYVGDLSGRGEEGALMGKFQVSLFLGLGSGPLLGGVLNDAFGFSSA 162
                                       444.4444449****************************************************************** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg....l 226
                                       fy++a++s laf++++l+lpe + +++r +++           +p  +a++++     ++ia+ +    +s+    l
  gi|386002449|ref|YP_005920748.1| 163 FYAMAALSTLAFLVIVLFLPEAKGPSSRRRERLS---------IP--RAFRHPGAP--AVIAFTTH---NSIsrglL 223
                                       *************977888777777777766555.........33..444444422..33333333...33333468 PP

                             MFS_1 227 ltllply 233
                                       l+++ply
  gi|386002449|ref|YP_005920748.1| 224 LVFMPLY 230
                                       8888877 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 6.9e-23
                             MFS_1   8 salarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdr.fGrrrvlllglllfalg.lllllfa 82 
                                       ++++r++l++++p ++a +  isp e+g +lt+  +++a++++p+Gr++dr + + r++ +g++++a + +l+++ +
  gi|386002449|ref|YP_005920748.1| 216 NSISRGLLLVFMP-LYAPTISISPGEVGVILTFSIFLMAIFQVPMGRMADRgH-ALRMIAAGAVVSAGSlVLIPA-T 289
                                       5789999******.8999999******************************33.666999999999999444444.4 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                       +++w l+ + +  Glg+++++pa +a+++++  ++  g  +g +++++s+G+i +pllggl++++ + r vf++ ++
  gi|386002449|ref|YP_005920748.1| 290 NTFWELFMVAAANGLGSALILPALMAVTVKLGRRMGMGTSMGAYNTAMSFGMITAPLLGGLVMDLSSIRFVFILGGA 366
                                       889988888888***************************************************************** PP

                             MFS_1 160 vsllafvlfllllpe 174
                                       ++l afv ++ll ++
  gi|386002449|ref|YP_005920748.1| 367 AGLAAFVAVYLLTWR 381
                                       *******99999887 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0  10.3   3.2e-11   1.1e-07     230     384 ..      11     164 ..       4     165 .. 0.91
   2 !   25.3   8.4   1.7e-09   6.2e-06     180     384 ..     160     362 ..     156     363 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.2e-11
                        MFS_1_like 230 fllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfll 306
                                       +++ ++      gi+   l +Y +elgas+  +G +    +va  ++  +  ++ +  G  k ++++llay+l  l+
  gi|386002449|ref|YP_005920748.1|  11 LFISVFAAMLGLGIVVPLLPIYAEELGASGVWIGLIFSGFAVARAIFMPIVGRVSDEAGRKKFIVFGLLAYALLSLG 87 
                                       3444444445578999999********************************************************** PP

                        MFS_1_like 307 yaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                       y +  ++  +  + +Lhgi+ +++  +a+ yv ++ +++ e+ ++g ++   f lG ++G l+GG+l d ++   +F
  gi|386002449|ref|YP_005920748.1|  88 YVAAGSVYSLTAVRFLHGIASAMVVPIAMAYVGDLSGRGEEGALMGKFQVSLF-LGLGSGPLLGGVLNDAFGFSSAF 163
                                       ****9*****************************************9987755.88999**********99999998 PP

                        MFS_1_like 384 r 384
                                       +
  gi|386002449|ref|YP_005920748.1| 164 Y 164
                                       6 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.7e-09
                        MFS_1_like 180 sallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYLkelg 256
                                       s ++y +aal ++++lv++ +    k+++   ++ l ++ + +++p + +++++++   +s g++  F+ lY     
  gi|386002449|ref|YP_005920748.1| 160 SSAFYAMAALSTLAFLVIVLFLPEAKGPSSRRRERL-SIPRAFRHPGAPAVIAFTTHNSISRGLLLVFMPLYAPTIS 235
                                       6799999***99999998888878888887777655.5999************************************ PP

                        MFS_1_like 257 asntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaa 333
                                        s   +G+++++  ++  ++ + + ++ ++  + +++ ++ ++ +  ++l+ +++ +w ++++ + +g+  +l+  a
  gi|386002449|ref|YP_005920748.1| 236 ISPGEVGVILTFSIFLMAIFQVPMGRMADRGHALRMIAAGAVVSAGSLVLIPATNTFWELFMVAAANGLGSALILPA 312
                                       ******************************999******************************************** PP

                        MFS_1_like 334 aveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       ++ +  k+  +   +t +g ++++ +++G     l+GGl+ dl+s +f+F 
  gi|386002449|ref|YP_005920748.1| 313 LMAVTVKLGRRMGMGTSMGAYNTA-MSFGMITAPLLGGLVMDLSSIRFVFI 362
                                       *********************998.89*********************996 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7  14.5   3.3e-10   1.2e-06      14     194 ..       8     184 ..       6     186 .. 0.87
   2 ?   -2.2  15.7      0.38   1.4e+03      61     192 ..     251     381 ..     239     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.3e-10
                                       HHHHCGGGTHHHHHHHHTST.T--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                          Sugar_tr  14 Ydtgvigafltllkfaknfg.lsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvig 89 
                                       +d+ +i++f+++l+       l  + ++  +s v++gli+s f v ++i   ++g ++d  GRkk ++++ + +   
  gi|386002449|ref|YP_005920748.1|   8 FDVLFISVFAAMLGLGIVVPlLPIYAEELGASGVWIGLIFSGFAVARAIFMPIVGRVSDEAGRKKFIVFGLLAYALL 84 
                                       566667777666665554441445556666799******************************************** PP

                                       HHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS- CS
                          Sugar_tr  90 avlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn 166
                                       ++  +aa    sv+ l++ R+l Gi+  ++  ++  y++ ++     gal++ +q+++ +G   +  +g +ln+  +
  gi|386002449|ref|YP_005920748.1|  85 SLGYVAAG---SVYSLTAVRFLHGIASAMVVPIAMAYVGDLSGRGEEGALMGKFQVSLFLGLGSGPLLGGVLNDAFG 158
                                       ********...*************************************************99999999988877777 PP

                                       .TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 167 .adgwrillglqlvpallllilllflPES 194
                                        +     + +++++++l++l+++lflPE 
  gi|386002449|ref|YP_005920748.1| 159 fS---SAFYAMAALSTLAFLVIVLFLPEA 184
                                       32...4577888888999999******96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHH CS
                          Sugar_tr  61 iGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRg 137
                                       + ++f  ++g + +R  +l ++a+ +v++a   ++++++n+++ l++     G+g  l+       + ++   +  g
  gi|386002449|ref|YP_005920748.1| 251 LMAIFQVPMGRMADRGHALRMIAAGAVVSAGSLVLIPATNTFWELFMVAAANGLGSALILPALMAVTVKLGRRMGMG 327
                                       5567777888899999998888888888888888888779************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS- CS
                          Sugar_tr 138 alvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflP 192
                                       + ++ y++a++fG++ a  +g  + + s+  ++ + lg ++ +a ++++ ll+++
  gi|386002449|ref|YP_005920748.1| 328 TSMGAYNTAMSFGMITAPLLGGLVMDLSS-IRFVFILGGAAGLAAFVAVYLLTWR 381
                                       *********************99999999.8999999999999999999998886 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8  28.5   2.3e-07   0.00084      39     396 ..      35     381 ..       4     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-07
                             MFS_3  39 disasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligi 115
                                       ++ as + + l+    ++   ++  ++G ++D   r+k+++ + l  a     l +l ++   s+++l a+ +l gi
  gi|386002449|ref|YP_005920748.1|  35 ELGASGVWIGLIFSGFAVARAIFMPIVGRVSDEAGRKKFIVFGLLAYA-----LLSLGYVAAGSVYSLTAVRFLHGI 106
                                       667777888888887777777888889************998876544.....556778888899************ PP

                             MFS_3 116 GaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalaf.avnalsylalivallrwkr 191
                                        +a+  P   A vg+l  r +  a +    v + +    GP lgGvl  a+G   af a++als la +v++l    
  gi|386002449|ref|YP_005920748.1| 107 ASAMVVPIAMAYVGDLSGRGEEGALMGKFQVSLFLGLGSGPLLGGVLNDAFGFSSAFyAMAALSTLAFLVIVLFLPE 183
                                       ***********************9999*************************887753899**************** PP

                             MFS_3 192 evrksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillg.alGvGA 267
                                       ++ +ss  rE+l   +  ++R+  a      v++ ++   +s    l  +Pl a   ++  +   G++l+ ++ + A
  gi|386002449|ref|YP_005920748.1| 184 AKGPSSRRRERLS--IPRAFRHPGAPA----VIAFTTHNSISRGLLLVFMPLYAPT-ISISPGEVGVILTfSIFLMA 253
                                       **********985..556666654443....3333333344444467789999865.56677788888763677777 PP

                             MFS_3 268 ilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstl.nvavqlavPrWvvgR 343
                                       i+  + + r+ +r ++ r+++  av+ A  l+ +  +++ w +++v +  G +  + l  l  v+v+l   r   g 
  gi|386002449|ref|YP_005920748.1| 254 IFQ-VPMGRMADRGHALRMIAAGAVVSAGSLVLIPATNTFWELFMVAAANGLGSALILPALmAVTVKL-GRRMGMGT 328
                                       764.6678888999999********************************9988877776651555555.457779** PP

                             MFS_3 344 alavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklp 396
                                       ++  Y t+++ g+ +  ll G v +  s+++  ++++aa l+a ++++ll  +
  gi|386002449|ref|YP_005920748.1| 329 SMGAYNTAMSFGMITAPLLGGLVMDLSSIRFVFILGGAAGLAAFVAVYLLTWR 381
                                       ********99999999*****************99999988888888777655 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  31.4     9e-05      0.32      53     356 ..      65     370 ..      16     379 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9e-05
                             MFS_4  53 sagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslv....lahaaaarrervgallfa 124
                                       s +a R + +  glla +ll l  +++ s+  ++++Rfl G+asA+v  ++ + v     +  + a  ++ +  lf 
  gi|386002449|ref|YP_005920748.1|  65 SDEAGRKKfIVFGLLAYALLSLGYVAAGSVYSLTAVRFLHGIASAMVVPIAMAYVgdlsGRGEEGALMGKFQVSLFL 141
                                       445556667999*********************************986444444323114445556677888899** PP

                             MFS_4 125 GvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllp...raalreasaaaeaakaeqkslpllalll 198
                                       G G G +++g+l     + + + ss+ +a+a+ls +++l+++l lp     ++r  +  + +++  +  +p+++   
  gi|386002449|ref|YP_005920748.1| 142 GLGSGPLLGGVL-----NDAFGFSSAFYAMAALSTLAFLVIVLFLPeakGPSSRRRERLSIPRAFRHPGAPAVIAFT 213
                                       *****9999975.....3444555679*******************4321223333444455666777788888888 PP

                             MFS_4 199 aYglaGfGYiitatFlvaiardg..aggalleallWllvGlaaivgvlvwlrvakrsglrralaaallieavgvlls 273
                                       +   +  G+    +F++++a +   + g++   l  +++ +a++  +    r+a+r  + r++aa  ++ a +++l 
  gi|386002449|ref|YP_005920748.1| 214 THNSISRGLL--LVFMPLYAPTIsiSPGEVGVILTFSIFLMAIFQVPM--GRMADRGHALRMIAAGAVVSAGSLVLI 286
                                       8877888876..579999998865577888888999999888888775..577888889999999999999988888 PP

                             MFS_4 274 llspsplglivssvllGltflaitalvlqlarelappat.rrllglmTasfgigQilGpllasllaeatgslalall 349
                                        + ++   l + +   Gl    i +  ++++ +l       + +g+  ++   g i +pll +l+++ ++     +l
  gi|386002449|ref|YP_005920748.1| 287 PATNTFWELFMVAAANGLGSALILPALMAVTVKLGRRMGmGTSMGAYNTAMSFGMITAPLLGGLVMDLSSIRFVFIL 363
                                       7778877776666666655555555555554444443333778999999999999********99987665555555 PP

                             MFS_4 350 vaaaalv 356
                                        +aa l+
  gi|386002449|ref|YP_005920748.1| 364 GGAAGLA 370
                                       4444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.37s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 2114.72
//
Query:       gi|386002450|ref|YP_005920749.1|  [L=166]
Description: hypothetical protein Mhar_1768 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-06   28.2   0.3    6.6e-06   25.9   0.0    2.1  2  MarR_2           MarR family
      2e-05   24.3   0.1     0.0001   22.1   0.0    2.2  3  HTH_5            Bacterial regulatory protein, arsR family
    2.7e-05   24.0   0.1    0.00012   21.9   0.0    2.0  2  MarR             MarR family
     0.0003   20.5   0.1     0.0013   18.5   0.0    2.1  2  HTH_IclR         IclR helix-turn-helix domain
    0.00035   20.6   0.0    0.00079   19.5   0.0    1.6  1  DprA_WH          DprA winged helix domain
    0.00054   19.5   0.0     0.0018   17.8   0.0    2.0  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00084   19.4   0.7     0.0054   16.8   0.0    2.4  2  HTH_20           Helix-turn-helix domain
     0.0016   18.7   0.2      0.013   15.8   0.1    2.2  3  Penicillinase_R  Penicillinase repressor
     0.0018   18.1   0.7     0.0059   16.5   0.1    2.1  3  TrmB             Sugar-specific transcriptional regulator Trm
     0.0031   17.4   0.0     0.0065   16.4   0.0    1.5  1  HTH_36           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   16.0   0.1      0.048   14.2   0.0    1.9  2  HTH_27           Winged helix DNA-binding domain
      0.018   14.8   0.0      0.022   14.6   0.0    1.2  1  Haem_oxygenas_2  Iron-containing redox enzyme
      0.019   14.9   0.1      0.064   13.2   0.0    1.9  2  HTH_11           HTH domain
      0.035   13.8   0.0      0.051   13.3   0.0    1.2  1  AAA_30           AAA domain
      0.047   13.2   0.0       0.06   12.8   0.0    1.2  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
      0.061   13.0   0.2       0.19   11.3   0.0    1.7  2  RP-C             Replication protein C N-terminal domain
      0.072   13.5   0.0       0.22   11.9   0.0    1.8  2  Rrf2             Transcriptional regulator
        0.1   12.7   0.0       0.16   12.1   0.0    1.3  1  FUR              Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   6.6e-09   6.6e-06      14      61 ..      27      71 ..      19      71 .. 0.90
   2 ?   -0.4   0.0       1.1   1.1e+03      21      31 ..     144     154 ..     114     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.6e-09
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      L++ p+   ++  l++ +g+sks+vs   + L++ G v+r++ p+DkR
  gi|386002450|ref|YP_005920749.1| 27 LADQPR---SMDYLVEQTGYSKSTVSTNMAHLERMGIVRRVRLPGDKR 71
                                      555553...999***********************************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       EEEHHHHHHHH CS
                            MarR_2  21 dltvgelarrl 31 
                                       ++t++el + l
  gi|386002450|ref|YP_005920749.1| 144 RFTITELIDIL 154
                                       26666666665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     1e-07    0.0001       8      46 ..      24      62 ..      21      63 .. 0.95
   2 ?   -3.1   0.0       7.5   7.5e+03       6      21 ..      93     108 ..      92     110 .. 0.70
   3 ?   -1.5   0.0       2.4   2.4e+03      17      27 ..     146     156 ..     143     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1e-07
                                      HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + +La+++++   l+e++g s+stvS   + L+ +G+V+
  gi|386002450|ref|YP_005920749.1| 24 VLMLADQPRSMDYLVEQTGYSKSTVSTNMAHLERMGIVR 62
                                      579***********************************6 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.5
                                       HHHHHHTTSSEEHHHH CS
                             HTH_5   6 kILklLaegelcvcel 21 
                                       +I+++ a g +++ e+
  gi|386002450|ref|YP_005920749.1|  93 QIMQIIAAGAAKAQEI 108
                                       7888888777777666 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                                       EHHHHHHHHTS CS
                             HTH_5  17 cvcelaeelgl 27 
                                       +++el ++l+l
  gi|386002450|ref|YP_005920749.1| 146 TITELIDILKL 156
                                       78999999997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.2e-07   0.00012      23      57 ..      37      71 ..      29      73 .. 0.92
   2 ?   -1.0   0.0       1.7   1.7e+03      29      41 ..     142     154 ..     132     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                                      HHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 23 LakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      L ++ g skstv++   +Le+ G ++R + p+D+R
  gi|386002450|ref|YP_005920749.1| 37 LVEQTGYSKSTVSTNMAHLERMGIVRRVRLPGDKR 71
                                      7788899***************************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                                       S-HHHHHHHHHHH CS
                              MarR  29 vskstvtrvldrL 41 
                                       +++ t+t+++d L
  gi|386002450|ref|YP_005920749.1| 142 LDRFTITELIDIL 154
                                       5666777777766 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 !   18.5   0.0   1.3e-06    0.0013      13      50 ..      28      63 ..      24      65 .. 0.84
   2 ?   -1.6   0.0       2.5   2.5e+03      14      27 ..     131     144 ..     130     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      a +p+  +   l ++tg +kStv+  ++ L+++G+v++
  gi|386002450|ref|YP_005920749.1| 28 ADQPR--SMDYLVEQTGYSKSTVSTNMAHLERMGIVRR 63
                                      44444..467799***********************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                       TTBSS-BHHHHHHH CS
                          HTH_IclR  14 eapqeltlselArr 27 
                                       e+  +ltl++l +r
  gi|386002450|ref|YP_005920749.1| 131 ECSKALTLADLLDR 144
                                       56677888888776 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     8e-07   0.00079      21      57 ..      27      63 ..       9      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8e-07
                           DprA_WH 21 LgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      L+ +P+++D Lv++tg + ++vs+   +LE +G v+r
  gi|386002450|ref|YP_005920749.1| 27 LADQPRSMDYLVEQTGYSKSTVSTNMAHLERMGIVRR 63
                                      6899*****************************9998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.1     8e+03      22      30 ..       7      15 ..       7      17 .. 0.81
   2 !   17.8   0.0   1.8e-06    0.0018      20      48 .]      34      62 ..      25      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.1
                            HTH_24 22 eLAerlglS 30
                                      ++A +lg S
  gi|386002450|ref|YP_005920749.1|  7 QVATKLGYS 15
                                      579999988 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.8e-06
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +  L e++g S+stv++ +  Le++G+++
  gi|386002450|ref|YP_005920749.1| 34 MDYLVEQTGYSKSTVSTNMAHLERMGIVR 62
                                      556789*********************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.4e-06    0.0054      19      58 ..      27      65 ..      21      67 .. 0.90
   2 ?    0.5   0.2      0.64   6.4e+02      18      18 ..     126     126 ..      86     156 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.4e-06
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      L  +++++   l e+ + sk+t+s +++ Le+ g+v++vr
  gi|386002450|ref|YP_005920749.1| 27 L-ADQPRSMDYLVEQTGYSKSTVSTNMAHLERMGIVRRVR 65
                                      5.788888888889999*********************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.64
                                       H CS
                            HTH_20  18 a 18 
                                       a
  gi|386002450|ref|YP_005920749.1| 126 A 126
                                       1 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.3e-05     0.013      26      73 ..      36      85 ..      33      99 .. 0.79
   2 ?   -0.7   0.0       1.8   1.8e+03       6      26 ..      92     111 ..      88     123 .. 0.77
   3 ?   -0.5   0.0       1.5   1.5e+03      64      85 ..     126     147 ..     104     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                                      T--GGG---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXX CS
                   Penicillinase_R 26 eleeekelaysTVktllrrLvkKgllsreke..grafiYsplvseeeava 73
                                       l e++  ++sTV t + +L++ g+++r +    +++ Ys  +s +e ++
  gi|386002450|ref|YP_005920749.1| 36 YLVEQTGYSKSTVSTNMAHLERMGIVRRVRLpgDKRYYYSTIISIDEGTK 85
                                      67788899**********************98567777777777666555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                                       SHHHHHHHHHS-EEHHHHHHT CS
                   Penicillinase_R   6 aevmeilwekgeatvkevvee 26 
                                       +++m+i+ ++g a+++e+ e 
  gi|386002450|ref|YP_005920749.1|  92 RQIMQII-AAGAAKAQEILEG 111
                                       5899988.5688888888876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.5
                                       ----XXXXXXXXXXXXXXXXXX CS
                   Penicillinase_R  64 plvseeeavasavkqlldklfe 85 
                                       +lv+ee  +a ++ +lld++  
  gi|386002450|ref|YP_005920749.1| 126 ALVREECSKALTLADLLDRFTI 147
                                       6788888888888888888864 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.9e-06    0.0059      17      62 ..      26      74 ..      24      78 .. 0.84
   2 ?   -2.1   0.0       3.7   3.7e+03      32      43 ..      98     109 ..      88     111 .. 0.53
   3 ?   -2.3   0.0       4.2   4.2e+03      15      33 ..     125     143 ..     125     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-06
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklY 62
                                      +l+ +p ++d + e++g ++s+v   +  Le++G+V+r++     +++Y
  gi|386002450|ref|YP_005920749.1| 26 MLADQPRSMDYLVEQTGYSKSTVSTNMAHLERMGIVRRVRLPgdkRYYY 74
                                      568899999*****************************98555434444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                                       TTSSCHCHHHHH CS
                              TrmB  32 lgvprskvYevL 43 
                                       +    +k++e+L
  gi|386002450|ref|YP_005920749.1|  98 IAAGAAKAQEIL 109
                                       444444555554 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.2
                                       HHHHHHCCCHHCHHCCCTT CS
                              TrmB  15 laLlklgpatadeiaeelg 33 
                                       laL++++ ++a ++a  l+
  gi|386002450|ref|YP_005920749.1| 125 LALVREECSKALTLADLLD 143
                                       5899999999988887665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.6e-06    0.0065      27      55 .]      33      61 ..      29      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.6e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s+++l +++g sk+Tvs+  + Le+ G++
  gi|386002450|ref|YP_005920749.1| 33 SMDYLVEQTGYSKSTVSTNMAHLERMGIV 61
                                      89************************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.8e-05     0.048       9      59 ..      21      72 ..      13      80 .. 0.83
   2 ?   -1.4   0.0       3.5   3.5e+03      15      30 ..     141     156 ..     133     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-05
                            HTH_27  9 Lhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                      L+ + +  ++ +    l++ + +++s++s ++ +L+++G v r + + d+r+
  gi|386002450|ref|YP_005920749.1| 21 LRGVLMLADQPRSmDYLVEQTGYSKSTVSTNMAHLERMGIVRRVRLPGDKRY 72
                                      6666666666666566999***************************999997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                            HTH_27  15 rrrrkkladlcgrlnv 30 
                                        ++r ++++l++ l++
  gi|386002450|ref|YP_005920749.1| 141 LLDRFTITELIDILKL 156
                                       4566677777777765 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.022     106     173 ..      39     115 ..       5     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                   Haem_oxygenas_2 106 Ellv...sletlklaee.....lrelgldeeapeyfdlHvtiDna...Haamaleaviellateepeeqedvlegaw 171
                                       E++    s + + +a+      +r+++l+ ++++y++  ++iD+    H + ++ ++++ +a+   ++++++leg +
  gi|386002450|ref|YP_005920749.1|  39 EQTGyskSTVSTNMAHLermgiVRRVRLPGDKRYYYSTIISIDEGtkvHNENFR-QIMQIIAAGA-AKAQEILEGGE 113
                                       5554444555566666677777899****************************8.9999999986.99999999866 PP

                   Haem_oxygenas_2 172 rr 173
                                       + 
  gi|386002450|ref|YP_005920749.1| 114 EG 115
                                       65 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-05     0.064       9      46 ..      25      66 ..      21      75 .. 0.83
   2 ?   -2.0   0.0       3.6   3.5e+03      17      27 ..     137     147 ..     125     157 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpI 46
                                      L+ a++p s ++L e+++ S++tv   ++ Le +g    v++
  gi|386002450|ref|YP_005920749.1| 25 LMLADQPRSMDYLVEQTGYSKSTVSTNMAHLERMGivrrVRL 66
                                      67788999***************************6555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                            HTH_11  17 sgeeLAeeLnv 27 
                                       + ++L +++ +
  gi|386002450|ref|YP_005920749.1| 137 TLADLLDRFTI 147
                                       55555544444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.2e-05     0.051      46     118 ..      19     104 ..       4     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-05
                            AAA_30  46 g..grviglAptgkaAkvLaeelgieastiakllkrlk...........grarlepgtllivDEagmvdtkqlaall 109
                                       g  + v++lA + +  + L e++g   st+   +  l+           g +r+  +t++ +DE   v ++++++++
  gi|386002450|ref|YP_005920749.1|  19 GalRGVLMLADQPRSMDYLVEQTGYSKSTVSTNMAHLErmgivrrvrlpGDKRYYYSTIISIDEGTKVHNENFRQIM 95 
                                       3557799*****************98888888777777788********66899999******************** PP

                            AAA_30 110 kaaekagak 118
                                       +++++  ak
  gi|386002450|ref|YP_005920749.1|  96 QIIAAGAAK 104
                                       *99984444 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05      0.06      71     135 ..       4      69 ..       2     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                       Glu_dehyd_C  71 ptidlveelGatYvdsretpvdeipeaseemdlvvEaTGsakhafe.aiealapnGvaaLlGvped 135
                                        +i++  +lG      +   v  ++++ ++md++vE TG++k  +   + +l+  G++  + +p d
  gi|386002450|ref|YP_005920749.1|   4 ASIQVATKLGYSDAAGALRGVLMLADQPRSMDYLVEQTGYSKSTVStNMAHLERMGIVRRVRLPGD 69 
                                       5678888888888888889999999***************99866516999**9999866555554 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.19      75     114 ..      35      74 ..      31      78 .. 0.92
   2 ?   -1.2   0.0       1.3   1.3e+03     148     172 ..     113     137 ..      98     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                              RP-C  75 aqLsralglsestlrrhlaaLveaGliirrDspngkRyar 114
                                       + L +++g s+st++ ++a+L  +G++ r   p  kRy +
  gi|386002450|ref|YP_005920749.1|  35 DYLVEQTGYSKSTVSTNMAHLERMGIVRRVRLPGDKRYYY 74 
                                       6799**********************************76 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                              RP-C 148 aerralrrlrerltllrrdiaklie 172
                                       +e    r lr rl l+r +  k+++
  gi|386002450|ref|YP_005920749.1| 113 EEGDDARWLRSRLALVREECSKALT 137
                                       5667778899999999998888775 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.22      10      59 ..      20      65 ..      14      68 .. 0.88
   2 ?   -2.7   0.0       7.8   7.8e+03      28      47 ..      77      96 ..      71     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 10 alhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      al+ +l+La +++    s++ + e+++ s+s ++  +a+L++ g+v+ vr
  gi|386002450|ref|YP_005920749.1| 20 ALRGVLMLADQPR----SMDYLVEQTGYSKSTVSTNMAHLERMGIVRRVR 65
                                      7788888888888....68***************************9876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.8
                                      HHHHHHHHTS-HHHHHHHHH CS
                              Rrf2 28 seeiaerqnispsylekila 47
                                      + +i e ++++ +  ++i++
  gi|386002450|ref|YP_005920749.1| 77 IISIDEGTKVHNENFRQIMQ 96
                                      55677777888888888886 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.16      38      72 ..      41      75 ..      34     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEE CS
                               FUR 38 peislaTVYrtLklleeaglvkelefedgesryel 72
                                         s +TV  ++  le++g+v+++ + +++++y+ 
  gi|386002450|ref|YP_005920749.1| 41 TGYSKSTVSTNMAHLERMGIVRRVRLPGDKRYYYS 75
                                      56799**********************77776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 959.36
//
Query:       gi|386002451|ref|YP_005920750.1|  [L=775]
Description: Efflux transporter, putative, hydrophobe/amphiphile efflux-3 (HAE3) family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-52  176.4  25.7    1.6e-29  102.9   6.9    2.4  2  MMPL            MMPL family
    3.7e-10   39.8  12.0    1.6e-05   24.8   1.5    2.7  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    3.9e-10   39.4   6.1    3.9e-10   39.4   6.1    2.6  2  SecD_SecF       Protein export membrane protein
     0.0005   17.9  34.0      0.021   12.5  13.3    2.4  2  ACR_tran        AcrB/AcrD/AcrF family
    0.00078   17.7  12.7    0.00078   17.7  12.7    2.6  3  Patched         Patched family
  ------ inclusion threshold ------
      0.053   13.4   0.3      0.053   13.4   0.3    4.2  5  DUF3487         Protein of unknown function (DUF3487)
       0.61    9.6  16.4      0.048   13.2   1.7    3.6  3  Frag1           Frag1/DRAM/Sfk1 family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1  10.8   1.1e-25   2.9e-22     105     294 ..     171     359 ..      61     413 .. 0.76
   2 !  102.9   6.9   6.4e-33   1.6e-29      77     305 ..     524     751 ..     481     771 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.1e-25
                              MMPL 105 esvaai....raaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltv 177
                                       e+++a+    raav+ a+ ++g++  vtG  a+ ++++   + +++++ +++ ++ +v Ll+v+r +  +llpl  v
  gi|386002451|ref|YP_005920750.1| 171 ERIDAVlpvaRAAVKMAEFPAGADTIVTGEVALGDEIEREMNTSMGTLLLISGLLMVVALLLVFRHVNLPLLPLPIV 247
                                       3444431112667777779********************************************************** PP

                              MMPL 178 vvsllaalglvlilalllglelstfvlgl.lvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvta 253
                                        ++++ ++g++ +      l++  +++++ ++ +li+ G+DYa+ +  R+ ee ++g +  +a+i++v+ t+++v++
  gi|386002451|ref|YP_005920750.1| 248 FLGIIWTFGTMGF------LQVPLTMVSMaAFPILIGLGIDYAIQFQNRIEEEFKKGGSISTAAIDTVTHTAPAVLI 318
                                       **********444......44444444443899******************************************** PP

                              MMPL 254 aGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTl 294
                                       a ++  + +++L  +++p+++ +G+ + +G+++  l ++ +
  gi|386002451|ref|YP_005920750.1| 319 ALIITGAGFFSLFSSSVPMVRDFGLLCLIGIIMCYLSSVFV 359
                                       *********************************99987655 PP

  == domain 2  score: 102.9 bits;  conditional E-value: 6.4e-33
                              MMPL  77 aaafvSkDgkaaralvtlegdpgsteadesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklie 149
                                       a  f+  Dg+ +  ++   gd+++++++  ++++ + v++      p++g+ v  tG  a+++ +  a +  +  ++
  gi|386002451|ref|YP_005920750.1| 524 AVKFQYVDGHDTAQIILEIGDAFNNLGQVGIERLGEEVDRDLiwfgPPSGVSVTQTGEMAVMNTVIGALTTGRIRMT 600
                                       44566668888777777778*********************9*********************************** PP

                              MMPL 150 vvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRy 226
                                       +++lv+i++iL+++yr lv a+lp+l   + ++   g    + +++g++ + ++++l  +l+++vG+ Ya+l + R+
  gi|386002451|ref|YP_005920750.1| 601 LLGLVLIFIILMLIYRDLVKAVLPVLPMFIVIGWMGG----VMYISGMKYNPMTATLG-ALILGVGSEYAILTMERF 672
                                       ************************9876665555555....5899*****99999875.6789************** PP

                              MMPL 227 reelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllG 303
                                        ee ++ e+  ea+ +a +s+g +++a+Glt ++ + +L ++ +p+ +++G+   l+v++++++++T+ P ll  l 
  gi|386002451|ref|YP_005920750.1| 673 YEEKEKTENVMEALFKATGSIGAAIIASGLTTVFGFSALIASPFPMTSSFGTITVLSVIFALFATFTVFPVLLIRLE 749
                                       ***********************************************************************998777 PP

                              MMPL 304 ra 305
                                        +
  gi|386002451|ref|YP_005920750.1| 750 YW 751
                                       77 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   1.5   6.3e-09   1.6e-05      13     140 ..     244     371 ..     233     382 .. 0.85
   2 !   19.3   3.4   3.1e-07    0.0008      24     134 ..     636     746 ..     619     766 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.3e-09
                                       HHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHC CS
                    Sterol-sensing  13 viivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsillt 88 
                                       + iv l ++ ++g + +l+++lt++++  +P  ++  g+d    + + +++  ++    s     ++++++p++l+ 
  gi|386002451|ref|YP_005920750.1| 244 LPIVFLGIIWTFGTMGFLQVPLTMVSMAAFPI-LIGLGIDYAIQFQNRIEEEFKKGGSiSTAAIDTVTHTAPAVLIA 319
                                       668999*********************99995.579****999999999877666655699999************* PP

                                       CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                    Sterol-sensing  89 sltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre 140
                                       ++   + ++  ++++vp v+ F l + +++++ +l  +++ v+++   +r +
  gi|386002451|ref|YP_005920750.1| 320 LIITGAGFFSLFSSSVPMVRDFGLLCLIGIIMCYLSSVFVGVTIIQQMERGR 371
                                       *999999996679**********************99999888887666655 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 3.1e-07
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHCCCHHHHHHHHH CS
                    Sterol-sensing  24 lgllaylgltltliilevlPflvlavgvd.nifvlvkavqrtsrsldeseriaealgevgpsilltsltellalllg 99 
                                        g++++ g++++++++  l  l+l vg +  i+ + + +++ ++++++ e + +a g++g +i+++ lt ++ +   
  gi|386002451|ref|YP_005920750.1| 636 GGVMYISGMKYNPMTA-TLGALILGVGSEyAILTMERFYEEKEKTENVMEALFKATGSIGAAIIASGLTTVFGFSAL 711
                                       4899999999999999.9999********4578888889999999999************************99977 PP

                                       HHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHH CS
                    Sterol-sensing 100 altdvpavqeFclfaavavlvdFllqitfFvavLs 134
                                       +++ +p  ++F + ++++v++  +   t+F  +L 
  gi|386002451|ref|YP_005920750.1| 712 IASPFPMTSSFGTITVLSVIFALFATFTVFPVLLI 746
                                       78****************************88774 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   6.1   1.5e-13   3.9e-10      20     187 ..     202     368 ..     185     370 .. 0.92
   2 ?   -3.5  11.2       2.2   5.7e+03      19     175 ..     582     737 ..     572     750 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.5e-13
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTT CS
                         SecD_SecF  20 tvgpsvskelaekavlallialvliliyvalrFew.rvalaaiialvhDviitvgvlsllgievdlatvaalLtiiG 95 
                                       + g ++ +e+ ++    lli+ +l+++ + l F+  +++l  +  ++  +i t g +  l++++++ ++aa   +iG
  gi|386002451|ref|YP_005920750.1| 202 ALGDEIEREMNTSMGTLLLISGLLMVVALLLVFRHvNLPLLPLPIVFLGIIWTFGTMGFLQVPLTMVSMAAFPILIG 278
                                       56777888888899999999999**********96379*************************************** PP

                                       SSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTT CS
                         SecD_SecF  96 YSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgt 172
                                         ++  +   +r++e+++k    ++ +++ + +++t    +++ ++t    ++l+     +++df l  l+G+i+  
  gi|386002451|ref|YP_005920750.1| 279 LGIDYAIQFQNRIEEEFKK--GGSISTAAIDTVTHTAPAVLIALIITGAGFFSLFSSSVPMVRDFGLLCLIGIIMCY 353
                                       ****************999..88999999999******9999*9********************************* PP

                                       TTHHHHHHHHHHHHH CS
                         SecD_SecF 173 yssifiasplllllk 187
                                       +ss+f+  +++ +++
  gi|386002451|ref|YP_005920750.1| 354 LSSVFVGVTIIQQME 368
                                       *********999886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHH.HHHHHHHHHHHHHHHHHHHHHTT----HHH..HHHHHH CS
                         SecD_SecF  19 etvgpsvskelaekavlallialvliliyvalrFewrv.alaaiialvhDviitvgvlsllgievdlat..vaalLt 92 
                                        +v ++v   l++  +   l+ lvli+i ++l++++ v a+  ++ ++  +  + gv+ + g++ ++ t  ++al  
  gi|386002451|ref|YP_005920750.1| 582 MAVMNTVIGALTTGRIRMTLLGLVLIFIILMLIYRDLVkAVLPVLPMFIVIGWMGGVMYISGMKYNPMTatLGAL-- 656
                                       56667777788888888889999***********99874667777788888889999999999999865115665.. PP

                                       HTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTS CS
                         SecD_SecF  93 iiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGli 169
                                       i+G   +  ++ ++r  e+  k+k++++ e++ ++  +     i+  ltt++   al+  +  + ++f ++ ++ +i
  gi|386002451|ref|YP_005920750.1| 657 ILGVGSEYAILTMERFYEE--KEKTENVMEALFKATGSIGAAIIASGLTTVFGFSALIASPFPMTSSFGTITVLSVI 731
                                       788888999********99..66677888887777766666666667777777777777777888888888888887 PP

                                       TTTTTH CS
                         SecD_SecF 170 vgtyss 175
                                       +  + +
  gi|386002451|ref|YP_005920750.1| 732 FALFAT 737
                                       766655 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8  12.7   2.8e-05     0.071     337     482 ..     219     364 ..     173     369 .. 0.77
   2 !   12.5  13.3     8e-06     0.021     338     485 ..     601     744 ..     572     767 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 337 LleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnierkl 413
                                       Ll++ +L v+ ++l  + +   l p+ +v l ++ tf  + +l++ l + ++ +  + iGl +D Ai     ie++ 
  gi|386002451|ref|YP_005920750.1| 219 LLISGLLMVVALLLVFRHVNLPLLPLPIVFLGIIWTFGTMGFLQVPLTMVSMAAFPILIGLGIDYAIQFQNRIEEEF 295
                                       6788899999999999***************************************************9999999999 PP

                                       HHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHH....HHHHHHHHHHHHHHHCCH CS
                          ACR_tran 414 eeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfa....ltivlaillsvlvaltlt 482
                                       ++ g +   aa+ +++  + a++   ++  a f   ++l  +   + r+f+    + i+++ l sv+v +t++
  gi|386002451|ref|YP_005920750.1| 296 KK-GGSISTAAIDTVTHTAPAVLIALIITGAGF---FSLFSSSVPMVRDFGllclIGIIMCYLSSVFVGVTII 364
                                       99.666666666666665555544444444444...4444555566666652223578888888888888876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8e-06
                                       HHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHH..HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 338 leaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNll..tLfgLvlAiGlvvDdAiVvvEnierk 412
                                       l+++vL++++++l  ++l  ++ p++ + +++     v+++ g+  N +  tL++L l++G     Ai  +E  +++
  gi|386002451|ref|YP_005920750.1| 601 LLGLVLIFIILMLIYRDLVKAVLPVLPMFIVIGWMGGVMYISGMKYNPMtaTLGALILGVGS--EYAILTMERFYEE 675
                                       679*********************8765555544445777777777776337******9997..89********999 PP

                                       HHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          ACR_tran 413 leeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPal 485
                                        e+  e+ +ea +k+++ i+ a++a+ l+ +  f    +l  +   +  +f+   vl+++ +++   t+ P+l
  gi|386002451|ref|YP_005920750.1| 676 KEK-TENVMEALFKATGSIGAAIIASGLTTVFGF---SALIASPFPMTSSFGTITVLSVIFALFATFTVFPVL 744
                                       888.8888****************9988766544...444455666777777777777777777777777776 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.76     2e+03     499     538 ..      68     107 ..      20     117 .. 0.73
   2 ?   -2.8   5.1      0.48   1.2e+03     669     728 ..     224     284 ..     200     297 .. 0.83
   3 !   17.7  12.7     3e-07   0.00078     252     386 ..     616     751 ..     577     767 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.76
                           Patched 499 glqvevvvnNppdltikesrdrleelveefentpyalgkk 538
                                       g+q  vv      +t ++s + +e+l  ++e+++ +lg  
  gi|386002451|ref|YP_005920750.1|  68 GTQSIVVLVEGDSVTSPASLKAMERLTRQMETVEDVLGTV 107
                                       4454455555556788999999999999999999999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.48
                           Patched 669 cmfvvallfipelitvlvitlsivsidi.gviGflslWgvdLDpismitiimsiGfsvdls 728
                                       +++vvall++   + + +  l iv + i  ++G + +  v L  +sm++  + iG  +d++
  gi|386002451|ref|YP_005920750.1| 224 LLMVVALLLVFRHVNLPLLPLPIVFLGIiWTFGTMGFLQVPLTMVSMAAFPILIGLGIDYA 284
                                       6899999999999998888888888765158999*9***********************97 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 3e-07
                           Patched 252 skpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawk.rteaklsvkkrigealse 327
                                          + a+l vl  ++ i    G++++ G+++n ++     L+L++G   + l ++++  + e++++v + + +a   
  gi|386002451|ref|YP_005920750.1| 616 RDLVKAVLPVLPMFIVIGWMGGVMYISGMKYNPMTATLGALILGVGSEYAILTMERFYeEKEKTENVMEALFKATGS 692
                                       55677999999999999999****************************99998887650555666699999999999 PP

                           Patched 328 agvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaaka 386
                                        g ai    lT v+ F + + ++ p  + F  +t ++++f+ + ++t+f  +l   +  
  gi|386002451|ref|YP_005920750.1| 693 IGAAIIASGLTTVFGFSALIASPFPMTSSFGTITVLSVIFALFATFTVFPVLLIRLEYW 751
                                       9************************************************7666544433 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.2   4.0         7   1.8e+04      57      66 ..     225     234 ..     211     276 .. 0.52
   2 ?   13.4   0.3   2.1e-05     0.053      27      81 ..     321     373 ..     312     376 .. 0.82
   3 ?   -4.2   0.2       5.9   1.5e+04      46      64 ..     400     418 ..     394     421 .. 0.65
   4 ?   -5.2   5.5         7   1.8e+04      17      48 ..     589     620 ..     576     645 .. 0.46
   5 ?   -2.6   2.9       1.9   4.8e+03      30      69 ..     699     738 ..     692     749 .. 0.62

  Alignments for each domain:
  == domain 1  score: -5.2 bits;  conditional E-value: 7
                           DUF3487  57 alllvllvvl 66 
                                        ++++ll+v+
  gi|386002451|ref|YP_005920750.1| 225 LMVVALLLVF 234
                                       2222222222 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.1e-05
                           DUF3487  27 vlaglglvvglvlglllallvgslaliptialllvllvvlvggkllarlKRgkPd 81 
                                       ++ g+g+   +  +++++  +g  +l + ++++  l +v+vg ++++++ Rg+ d
  gi|386002451|ref|YP_005920750.1| 321 IITGAGFFSLFSSSVPMVRDFG--LLCLIGIIMCYLSSVFVGVTIIQQMERGRND 373
                                       4568888888899999988888..7777777888899***************965 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 5.9
                           DUF3487  46 lvgslaliptialllvllv 64 
                                       +++ +  i+t+a + ++++
  gi|386002451|ref|YP_005920750.1| 400 VISRWRAILTAATVFAVVG 418
                                       5666777777776666655 PP

  == domain 4  score: -5.2 bits;  conditional E-value: 7
                           DUF3487  17 frGltadEllvlaglglvvglvlglllallvg 48 
                                       ++ lt+  + ++++  ++++++l l+   lv+
  gi|386002451|ref|YP_005920750.1| 589 IGALTTGRIRMTLLGLVLIFIILMLIYRDLVK 620
                                       33344444433333333333333333333333 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 1.9
                           DUF3487  30 glglvvglvlglllallvgslaliptialllvllvvlvgg 69 
                                        +gl++ +  + l+a  + +   + ti++l+v++ ++ + 
  gi|386002451|ref|YP_005920750.1| 699 ASGLTTVFGFSALIASPFPMTSSFGTITVLSVIFALFATF 738
                                       4555666666666666666666666666666666655544 PP

>> Frag1  Frag1/DRAM/Sfk1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.8     0.031        79      92     175 ..     314     419 ..     213     426 .. 0.67
   2 ?    1.7   0.3      0.06   1.5e+02     152     182 ..     589     619 ..     574     646 .. 0.81
   3 ?   13.2   1.7   1.9e-05     0.048      15      82 ..     690     757 ..     681     770 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.031
                             Frag1  92 faalvlgligalglllvsifstaeyhsvHlvgavvffvfgflyvllqtalyykmgrhy................... 149
                                        a l+  +i   g + +   s     ++ l + + ++++++ +v++ + +  +m+r +                   
  gi|386002451|ref|YP_005920750.1| 314 PAVLIALIITGAGFFSLFSSSVPMVRDFGLLCLIGIIMCYLSSVFVGVTIIQQMERGRndrdhrtgasrkekaspig 390
                                       34444444433333333333444566666777777778888888777777778877778899*************** PP

                             Frag1 150 ...vwnkstisfrlkvvllilavvlailf 175
                                          v+  + ++ r++++l+++ v  ++++
  gi|386002451|ref|YP_005920750.1| 391 plvVKAVELVISRWRAILTAATVFAVVGL 419
                                       **99999********99988777766654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.06
                             Frag1 152 nkstisfrlkvvllilavvlailfgvffvrh 182
                                           +++r+++ ll l ++++il++++ +  
  gi|386002451|ref|YP_005920750.1| 589 IGALTTGRIRMTLLGLVLIFIILMLIYRDLV 619
                                       667788999***************9998875 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.9e-05
                             Frag1  15 gmliamlvcavvqgpvdyvfmh.keqflPyISdigatnpeslffslalnlglflvilvallrfqrlppl 82 
                                       ++ i + ++a  +  v   f +    ++P+ S+ g+ +  s +f+l++++++f+v+l+ l++++r ++ 
  gi|386002451|ref|YP_005920750.1| 690 TGSIGAAIIASGLTTV-FGFSAlIASPFPMTSSFGTITVLSVIFALFATFTVFPVLLIRLEYWRRTQRE 757
                                       4555555555555555.4455545778*************************************97764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.89u 0.36s 00:00:01.25 Elapsed: 00:00:00.58
# Mc/sec: 4051.79
//
Query:       gi|386002452|ref|YP_005920751.1|  [L=350]
Description: hypothetical protein Mhar_1770 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-05   22.6   0.1          1    9.7   0.0    3.1  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
  ------ inclusion threshold ------
       0.15   12.8   0.0       0.43   11.3   0.0    2.0  1  fn3_5            Fn3-like domain
        6.9    6.7   8.6      0.096   12.6   0.8    1.9  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.86   5.2e+03       3      17 ..      60      74 ..      58      75 .. 0.83
   2 !    9.5   0.0   0.00019       1.1      46      76 ..     132     164 ..     120     167 .. 0.74
   3 !    9.7   0.0   0.00017         1      39      79 .]     260     300 ..     223     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.86
                       NPCBM_assoc  3 pGetvtltltvtndg 17
                                      +Getvtl + +tn g
  gi|386002452|ref|YP_005920751.1| 60 RGETVTLFVDITNRG 74
                                      799999999999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                       NPCBM_assoc  46 slapGetve..atvkVtppagaaaGdyevtaka 76 
                                       +l+ Ge+ +    ++++++++a aG+y++++++
  gi|386002452|ref|YP_005920751.1| 132 ALRSGEKSRepLRFTIKISNRAPAGEYPLRLEL 164
                                       555555544225799***************987 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00017
                       NPCBM_assoc  39 vspasaaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                        + a + +l pGe+  + +k+ + ++a +  y +  ++++t
  gi|386002452|ref|YP_005920751.1| 260 DDQAYIGTLGPGEERAVRFKIDVDSDATPKPYSINSEIKYT 300
                                       56677789**************************9999986 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.43      67     114 ..     267     316 ..     200     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                             fn3_5  67 tvpAnssktvtvtldlpsdakkkngyfveGfvtlkdsedk...npelsvPY 114
                                       t+++++++ v++++d++sda+  + y + + ++ +d ++     +++++P+
  gi|386002452|ref|YP_005920751.1| 267 TLGPGEERAVRFKIDVDSDATP-KPYSINSEIKYTDHRGGtviSESMKIPV 316
                                       89**************999998.9999**********99988888999985 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   1.6       2.2   1.3e+04      21      31 ..      14      23 ..      10      26 .. 0.47
   2 ?   12.6   0.8   1.6e-05     0.096      17      40 ..     324     348 ..     323     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                                      XXXXXXXXXXX CS
                   Gram_pos_anchor 21 taaGllallgg 31
                                       a++ la +g+
  gi|386002452|ref|YP_005920751.1| 14 IALA-LASIGA 23
                                      3333.444444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       XXXXXXXXXXXXXXXXXX.XXXXXX CS
                   Gram_pos_anchor  17 nifltaaGllallggllL.lvkrRK 40 
                                       ++ l+a+++l+ll+g++  l++rRK
  gi|386002452|ref|YP_005920751.1| 324 SYTLPAVAVLILLAGGGAtLYRRRK 348
                                       6889****88888888888*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1898.33
//
Query:       gi|386002453|ref|YP_005920752.1|  [L=771]
Description: hypothetical protein Mhar_1771 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-52  178.7   0.3    2.5e-52  178.3   0.3    1.1  1  Peptidase_C25   Peptidase family C25
     0.0063   15.6   0.0      0.014   14.5   0.0    1.5  1  Propeptide_C25  Propeptide_C25
  ------ inclusion threshold ------
       0.58    9.9   2.3         10    5.9   0.7    2.3  2  Rep_2           Plasmid replication protein


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.3   4.2e-56   2.5e-52       1     376 [.     261     704 ..     261     706 .. 0.83

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 4.2e-56
                                       EEEEE-GGG.....HHHHHHHHHHHHHTTEEEEEEETTSTTT-S.......SHHHHHHHHHHHHHHHHTT--SEEEE CS
                     Peptidase_C25   1 yliItddel.....saaaerlaefrrskGldvkvvtveeiynefsaGek..daaairnflkyayknwsasklkYllL 70 
                                       y+iIt + l        +++la+++++kGl++++vtveeiy+ +++ +   d++ irnf+k+ayk++   + kYllL
  gi|386002453|ref|YP_005920752.1| 261 YVIITNQYLkdapgPYNFQALADHKKKKGLNAAIVTVEEIYAAYKYTYHrdDQEMIRNFIKDAYKHN---GIKYLLL 334
                                       89999999966665567****************************6655547777************...89***** PP

                                       ES-T..............................TTS--EE-.....TTT-SEESHHHHS-T............... CS
                     Peptidase_C25  71 vGdtsiv................vkv.kspitksdliptyqiakslgnestiptDdyyasldgneds.......... 120
                                       +Gd++                  +++ + p  ++  +p +++        +i++D yya+l+g  d           
  gi|386002453|ref|YP_005920752.1| 335 GGDGDGArvggetwdaivparllYAWaYEPDPDCCAVPKEKV--------GIASDVYYACLEGTFDGnnngiygept 403
                                       ****6559***********9999888999999999***9997........6***********977769********* PP

                                       ..TSSS-SSEEEEE--SSHHHHHHHHHHHHHHHCT--S-G....GGGEEEEEE--...................... CS
                     Peptidase_C25 121 ..ddltpdlavGRipvtsaaeaaavvnKiiaYerntengsaagqwrnkvlliagd....vvgew......eaad... 182
                                         ++++ d++vGR+pv++ ae++++v K+iaYe+  ++    + ++  + l++ +    +          e      
  gi|386002453|ref|YP_005920752.1| 404 dgVNFQADVYVGRAPVDNYAELSNFVRKTIAYEST-RA---DDPYLTAIWLVGEYlepmA---YlttnlsE--Iedh 471
                                       *********************************86.33...3569999999999975432...23444552..0446 PP

                                       ..........................HH.THHHHHHHHHHHTSSGGGT-SEEEEE-SS--.............TTTT CS
                     Peptidase_C25 183 ..........................gn.eiagttaettpseynvnklyadlaayeaetetevpaanqpllttqnll 232
                                                                 +   ++++++e  p+e+n+ +ly+    y   +  e ++ n   + ++ l+
  gi|386002453|ref|YP_005920752.1| 472 apeeqgcgdggcggggcggeggcldrWGgDYKDQIKEIIPEEFNIWTLYDR--DYRGGDC-EPDQHN---WPRSLLM 542
                                       66677788888888888888888888666**********************..5555555.223333...5588999 PP

                                       HHHH.H--SEEEEES-EETTEETTTTE....EHHHHHT---TT--EEEEEESSSTT-TTSSS-........-HHHHH CS
                     Peptidase_C25 233 kaln.qGvlfvnytGHGsetawadesl....stndisaltntnklpiaitaaCltgafdeetkr.......sfgekl 297
                                       ++++ +  + +n++G  +   +    +      n ++al+n +k+++ +++a +++ fd+ +++       s+ e++
  gi|386002453|ref|YP_005920752.1| 543 EKIDaNMIHAINHVGTANFCDIVA--YvmkmGYNHADALNN-SKYFFGYSQAGYAASFDNRDPEavylphdSVLEHF 616
                                       999955889999998555554422..1335699********.77**************999999************* PP

                                       HHSTTSSEEEEEEESS---SS-.......-SHHHHHHHHHHHHHHH.......T-S-SS-HHHHHHH.......... CS
                     Peptidase_C25 298 vlnangGavayigatrlgysgv.......ndrlsraffealfadaar....tlGealllaknelletglaqsiskgm 363
                                       v +a+gGa+a+ig++r g ++        ++++ +af+e++f++  +    ++G + + ++ +l+  g+  ++++  
  gi|386002453|ref|YP_005920752.1| 617 V-TAPGGAFAFIGNSRYGLIDLnsindspSQKFDKAFWEEIFNSSYTngnrSIGLVHQISRESLI--GGVLGADEMR 690
                                       *.**************9995555666667*************99997788899999999999999..4433333344 PP

                                       .....EEEEE-TT- CS
                     Peptidase_C25 364 .nkrtfnllGDPal 376
                                        +++++nllGDP++
  gi|386002453|ref|YP_005920752.1| 691 yCYFSINLLGDPET 704
                                       6***********97 PP

>> Propeptide_C25  Propeptide_C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.3e-06     0.014      39     179 ..      58     214 ..      34     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-06
                                       TTE...EEEEEE-TT-B----TTSB---BEEEEEE--SSEE.EEEEEEEEEEEEE-S--B-B---S-...BTTS-GG CS
                    Propeptide_C25  39 dkg...vfqrisitegeslsekGepelPilsksiavpetre.akvevvssktetlenvdiaPsksvv...veredpe 108
                                        +g   v+  ++i++      +Gep lP+++  i +p  +e  +v+v   + + l  v i P ++ v   + r+  +
  gi|386002453|ref|YP_005920752.1|  58 AEGsveVYDSVTIPGLHHRIVPGEPILPFRTARILIPYGQEvSEVKVFPGNERYLGRVSIRPGQTSVpigFTRNCTS 134
                                       4444446777788888888889***************8666268********************9996666667777 PP

                                       GS-B-..........--GG.GG--S-BS--SEEE---EEETTEEEEEEEE--EEEETTTTEEEEEEEEEEEEE.... CS
                    Propeptide_C25 109 kitYv..........lndslYsqnkslPseiatlsdpaylRdvrvqevnlaPlqYnPvtkelllykkikvaitfdrk 175
                                         + v           ++++Y+ + ++P+e   +         ++  vnl+P++Y P t e   y    v++t   +
  gi|386002453|ref|YP_005920752.1| 135 CHPEVnwtetpdlalRDEEIYESESPYPGEPSSILGVQKKNGYQILYVNLYPIRYIPKTGEAYSYGAFDVEVT-TAP 210
                                       7777788899999977889*********998888777777788999***************************.788 PP

                                       .EEE CS
                    Propeptide_C25 176 aeta 179
                                       aet+
  gi|386002453|ref|YP_005920752.1| 211 AETL 214
                                       8886 PP

>> Rep_2  Plasmid replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7    0.0017        10      76     117 ..     287     328 ..     274     333 .. 0.72
   2 ?    3.1   0.0     0.012        70     131     173 ..     544     586 ..     501     592 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0017
                             Rep_2  76 dklkevisekveslrnaysYliHednpeKaqYskkeiellng 117
                                       +k+ +     ve++ +ay+Y  H+d++e  +  +k+   +ng
  gi|386002453|ref|YP_005920752.1| 287 KKGLNAAIVTVEEIYAAYKYTYHRDDQEMIRNFIKDAYKHNG 328
                                       444455566788**************9977766666666655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.012
                             Rep_2 131 klleeiedlieendiielaelvdylreeesellivvvnntlyf 173
                                       k+  ++++ i++   ++++++v y+++ +++  + + n+ ++f
  gi|386002453|ref|YP_005920752.1| 544 KIDANMIHAINHVGTANFCDIVAYVMKMGYNHADALNNSKYFF 586
                                       344455566666666**************99998887776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.37s 00:00:01.14 Elapsed: 00:00:00.54
# Mc/sec: 4319.48
//
Query:       gi|386002454|ref|YP_005920753.1|  [L=294]
Description: Metallo-beta-lactamase superfamily protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-13   51.7   1.1    1.8e-13   50.9   0.8    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00012   21.6   0.1    0.00028   20.5   0.1    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.023   14.6   0.0      0.064   13.2   0.0    1.7  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.8     3e-17   1.8e-13       4      79 ..      35     107 ..      33     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3e-17
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                        p+ sy++e +g+ iL+D G+s  + + a   ++ g++++d+d+v+l+H+HlDH++glg lv+    ++++  +++
  gi|386002454|ref|YP_005920753.1|  35 EPGVSYYLEEGGKKILFDLGYSDLFIDNA---RKMGIDLLDLDYVVLSHGHLDHTWGLGPLVRLITEAKVEGVHHK 107
                                       5889************************9...6**************************99987655555544444 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   4.6e-08   0.00028      17      76 ..      64     118 ..      47     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.6e-08
                                       CGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEE.EEHHHHHHCCTTCGH CS
                     Lactamase_B_2  17 ralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklply.apkgvlavleanfvy 76 
                                       r++       +l ++d V+l+h+H DH+ gl  l + +++ k  +  ++ ++ a +++  v+
  gi|386002454|ref|YP_005920753.1|  64 RKM-----GIDLLDLDYVVLSHGHLDHTWGLGPLVRlITEAK--VEgVHHKTPALVAHPAVF 118
                                       333.....567889*****************99999655444..444677777777776665 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.064       9      50 ..      39      86 ..      37     118 .. 0.84
   2 ?   -1.8   0.0      0.43   2.6e+03     144     163 .]     247     266 ..     236     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                     Lactamase_B_3  9 sflletagarilvDPf......kanlgyeppaeeaDlvlisqaledHa 50
                                      s+ le +g++il D +      ++  +++++  + D v++s+++ dH 
  gi|386002454|ref|YP_005920753.1| 39 SYYLEEGGKKILFDLGysdlfiDNARKMGIDLLDLDYVVLSHGHLDHT 86
                                      7899**********886666654455666667***************5 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.43
                     Lactamase_B_3 144 qeealelakrLkpklvlPmh 163
                                        ee +++++r++p+ + P h
  gi|386002454|ref|YP_005920753.1| 247 LEETKRYLERVRPRRIHPCH 266
                                       57889999*******99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.39s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1598.16
//
Query:       gi|386002455|ref|YP_005920754.1|  [L=66]
Description: hypothetical protein Mhar_1773 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-16   59.6   8.7    2.4e-16   59.3   8.7    1.0  1  DUF378    Domain of unknown function (DUF378)


Domain annotation for each model (and alignments):
>> DUF378  Domain of unknown function (DUF378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   8.7   1.4e-20   2.4e-16       3      58 ..       7      60 ..       5      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.4e-20
                            DUF378  3 ldkialiLviiGalNWgliGlfdfdLVaalfggessllsriiYilVglaglylisl 58
                                      ld +a++Lv++G+lNWgl + f+f+LV++l+g  + +l++++Y+lV+la++yl +l
  gi|386002455|ref|YP_005920754.1|  7 LDLLAIVLVVVGGLNWGLYA-FGFNLVSILLG-WMPILEKVVYVLVALAAIYLAVL 60
                                      7899****************.9**********.78*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 382.69
//
Query:       gi|386002456|ref|YP_005920755.1|  [L=253]
Description: hypothetical protein Mhar_1774 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-66  222.6   2.8      5e-66  222.4   2.8    1.0  1  DUF1624        Protein of unknown function (DUF1624)
    1.9e-05   23.9  18.9    0.00058   19.0   8.1    2.7  2  Acyl_transf_3  Acyltransferase family


Domain annotation for each model (and alignments):
>> DUF1624  Protein of unknown function (DUF1624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.4   2.8   5.6e-70     5e-66       1     223 []       9     230 ..       9     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 5.6e-70
                           DUF1624   1 RieeiDalRGiAlilMiifHflfdLeffgylavslatsglwvvfarliaslFlfiaGvslvlahskslrwrkflkRg 77 
                                       R++eiD+lRG+A+++M+ fH l+dL+ff    v  + sg ++++a ++as+Fl+++Gvsl++++++     + l+Rg
  gi|386002456|ref|YP_005920755.1|   9 RYWEIDLLRGVAVLMMVGFHALYDLAFFSGARVVDLRSGGISLIAEATASIFLLLVGVSLAISTARDGGGLRLLRRG 85 
                                       9***************************999877666**************************************** PP

                           DUF1624  78 lkilaaallitaatylllpdsfivFGiLhlialalllallflrlpkalllllallilalglllreaifdlplllwlg 154
                                       + i+ +++ +t+ t+lll ++f+vFG+Lhli++ ++l ++++  p+ +l l++ +i a+gl+lr++++ +p+ll+lg
  gi|386002456|ref|YP_005920755.1|  86 IGIFSWGMGVTLSTLLLLGEGFVVFGVLHLIGITIILSIPLADRPRLALPLGVGAI-AAGLILRGQAVASPWLLPLG 161
                                       ***************************************************55555.569***************** PP

                           DUF1624 155 lssekfetndYvplfPWfgvvllGialgkllyekgkrrlklpslpkaklvrplallGrhsLliYlihqp 223
                                       l++ +f+++dY+p++PW gvvl+Gi+lg lly+ g+rr+ lp++p ++ +r ++ lGr sL+iYl+hqp
  gi|386002456|ref|YP_005920755.1| 162 LVPSGFYSVDYFPILPWSGVVLVGIFLGGLLYPGGERRCPLPKTPPPSPARGICALGRCSLPIYLLHQP 230
                                       ********************************************************************9 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   8.1   6.5e-08   0.00058       3     107 ..      12     124 ..      10     132 .. 0.74
   2 !    3.9   9.9    0.0025        23     199     310 ..     133     238 ..      88     244 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.5e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxx RF
                     Acyl_transf_3   3 ylDllRgiAillVvflHaliayspdagrgspiqasqssqiaflggfgvplFFllSGffla..........amlyrrr 69 
                                       ++DllRg+A+l++v +Hal+ +  + g     + s+ +   ++     ++F+ll G+ la          + l+r  
  gi|386002456|ref|YP_005920755.1|  12 EIDLLRGVAVLMMVGFHALYDLAFFSGARVVDLRSGGI--SLIAEATASIFLLLVGVSLAistardggglRLLRRGI 86 
                                       69******************555544444433333333..39*****************977777777777777777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3  70 glsklikrRilrlliplliwllliillialvaghiqan 107
                                       g +++ +   l  l+ l  + +++ +l+ ++++ i + 
  gi|386002456|ref|YP_005920755.1|  87 GIFSWGMGVTLSTLLLLGEGFVVFGVLHLIGITIILSI 124
                                       77777777777777777777777777777777666655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0025
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 199 llfflfGalladaddrdrnlsrglkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllllf 275
                                       +l++++Ga++a +  r++   + ++  l+l+l+   ++ + +f                +   +v++gi+l  ll  
  gi|386002456|ref|YP_005920755.1| 133 ALPLGVGAIAAGLILRGQAVASPWL--LPLGLVPSGFYSVDYFPIL-------------PWSGVVLVGIFLGGLLYP 194
                                       5555555555555555555533222..2222222222222222222.............223445555555555555 PP

                                       xxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 276 alpsrsafk.........llrylgkiSygiYliHlpllmllqkl 310
                                          +r              +  lg+ S+ iYl+H+p+l + + l
  gi|386002456|ref|YP_005920755.1| 195 GGERRCPLPktpppsparGICALGRCSLPIYLLHQPILIVSMEL 238
                                       5555554446777777777889****************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1470.11
//
Query:       gi|386002457|ref|YP_005920756.1|  [L=141]
Description: Exported lipoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-22   78.0   2.9    1.2e-11   44.0   0.2    2.1  2  Lipoprotein_15  Secreted repeat of unknown function


Domain annotation for each model (and alignments):
>> Lipoprotein_15  Secreted repeat of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   5.2e-13   9.4e-09       7      46 ..      39      77 ..      35      78 .. 0.90
   2 !   44.0   0.2   6.6e-16   1.2e-11       2      37 ..      95     130 ..      94     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.2e-13
                    Lipoprotein_15  7 dGtkqvaykGmPLYtFakDkkpgdktGdgvgaCagvWpvv 46
                                       G  +v+  G +LY+F++D  pg  t+ +  +C + Wp++
  gi|386002457|ref|YP_005920756.1| 39 LGDYLVDEGGYTLYYFSGDV-PGSGTSSCGETCIQYWPPF 77
                                      6999****************.66666************97 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 6.6e-16
                    Lipoprotein_15   2 tvtrddGtkqvaykGmPLYtFakDkkpgdktGdgvg 37 
                                       t+ r+dG  q++ykG+PLY+F +D  pgd +G+g +
  gi|386002457|ref|YP_005920756.1|  95 TIYREDGLAQTTYKGWPLYYFINDYRPGDIKGEGLD 130
                                       899*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 852.99
//
Query:       gi|386002458|ref|YP_005920757.1|  [L=139]
Description: hypothetical protein Mhar_1776 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-30  103.1   2.1    7.3e-16   57.4   0.6    2.2  2  Lipoprotein_15  Secreted repeat of unknown function


Domain annotation for each model (and alignments):
>> Lipoprotein_15  Secreted repeat of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0     3e-16   5.3e-12       7      46 ..      40      78 ..      35      78 .. 0.93
   2 !   57.4   0.6   4.1e-20   7.3e-16       3      46 ..      97     137 ..      95     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3e-16
                    Lipoprotein_15  7 dGtkqvaykGmPLYtFakDkkpgdktGdgvgaCagvWpvv 46
                                       G+ +v+ +Gm+LYtFa+D  ++++ ++++++Ca+ Wp++
  gi|386002458|ref|YP_005920757.1| 40 LGPFLVDGEGMTLYTFANDVPESGV-SACIDDCAERWPPF 78
                                      6999*********************.************96 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 4.1e-20
                    Lipoprotein_15   3 vtrddGtkqvaykGmPLYtFakDkkpgdktGdgvgaCagvWpvv 46 
                                       + r+dGt q++ykG+PLY++ +Dk+pgd+ G+g g   gvW vv
  gi|386002458|ref|YP_005920757.1|  97 IPREDGTFQTTYKGWPLYRYFEDKAPGDVLGQGLG---GVWSVV 137
                                       569********************************...****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); 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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 776.97
//
Query:       gi|386002459|ref|YP_005920758.1|  [L=151]
Description: hypothetical protein Mhar_1777 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-33  113.3   0.0    8.9e-33  113.0   0.0    1.1  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0     5e-37   8.9e-33       2     119 .]      20     133 ..      19     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 5e-37
                                       S-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS.-E.EGGGS--S-SS CS
                              TrmO   2 iPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggn.ervGvfatRsphRp 77 
                                        P +p++++++ +++e++++y   eal+g+e++ h+++++++h++   +  +++++p+ +++  + G+fatRsp Rp
  gi|386002459|ref|YP_005920758.1|  20 EPEDPKTMRNSLSTLEIDERY--LEALQGIERYRHVFVIYYIHRA--LG-YDLLVHPMGDESiPKRGLFATRSPRRP 91 
                                       6999*****************..********************99..56.5566666665544889*********** PP

                                       S-EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HHHH CS
                              TrmO  78 npiglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                       npigl+vv++ +veg++++v+g+D+ldg+p+lDiKPY +++D
  gi|386002459|ref|YP_005920758.1|  92 NPIGLTVVEVLNVEGRKITVTGLDALDGSPILDIKPYEEHFD 133
                                       *************************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.36s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 849.18
//
Query:       gi|386002460|ref|YP_005920759.1|  [L=143]
Description: hypothetical protein Mhar_1778 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 813.98
//
Query:       gi|386002461|ref|YP_005920760.1|  [L=65]
Description: hypothetical protein Mhar_1779 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-18   66.5   0.7    1.8e-18   66.2   0.7    1.0  1  DUF2116        Uncharacterized protein containing a Zn-ribbon
  ------ inclusion threshold ------
      0.012   15.3   0.6      0.017   14.8   0.6    1.3  1  zinc_ribbon_2  zinc-ribbon domain
       0.02   15.2   1.3      0.022   15.0   1.3    1.1  1  DUF4293        Domain of unknown function (DUF4293)
      0.035   14.1   1.1      0.043   13.8   1.1    1.3  1  DZR            Double zinc ribbon
        1.4    9.0   6.4        3.8    7.6   6.4    1.6  1  DHHC           DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.7     5e-22   1.8e-18       2      56 ..       6      60 ..       5      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 5e-22
                           DUF2116  2 pHkHCivCGkaIpldesfCsekCqeeyekkrkkvarsqqilfgililllavvlvl 56
                                       HkHCivCGk I+  e fC+e C+++y+++++++  +  +++g lil+l+v ++l
  gi|386002461|ref|YP_005920760.1|  6 SHKHCIVCGKTIDDAETFCDEVCESKYRSAQRRQTLFFLVFIGLLILMLIVPVIL 60
                                      6********************************7666666666666666666655 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6   4.8e-06     0.017       2      16 ..      10      24 ..       9      26 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFC 16
                                      C  CG++++d ++FC
  gi|386002461|ref|YP_005920760.1| 10 CIVCGKTIDDAETFC 24
                                      888************ PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.3   6.2e-06     0.022       2      28 ..      36      62 ..      35      65 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.2e-06
                           DUF4293  2 QRiQslyLllaailmaaflflplasiv 28
                                      QR Q+l++l+ + l++++l++p++ + 
  gi|386002461|ref|YP_005920760.1| 36 QRRQTLFFLVFIGLLILMLIVPVILKA 62
                                      9*********************98755 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   1.2e-05     0.043      25      47 ..       4      26 ..       1      38 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                               DZR 25 vaaedrCpsCgekvdpearfCpe 47
                                      ++++++C  Cg+ +d  ++fC+e
  gi|386002461|ref|YP_005920760.1|  4 APSHKHCIVCGKTIDDAETFCDE 26
                                      45578899999999999999975 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.4     0.001       3.8      15      65 ..       3      57 ..       1      62 [. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                              DHHC 15 kpprskHcrvCnrcvlrfDHhCpwlnnc....iGerNykyFllfllylllllila 65
                                      k p  kHc vC++ + +   +C  ++        +r   +Fl+f+  l+l+li+ 
  gi|386002461|ref|YP_005920760.1|  3 KAPSHKHCIVCGKTIDDAETFCDEVCESkyrsAQRRQTLFFLVFIGLLILMLIVP 57
                                      78899*************9999988765111133333334455555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.37s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 365.96
//
Query:       gi|386002462|ref|YP_005920761.1|  [L=582]
Description: Nitrous oxidase accessory protein-like protein [Methanosaeta harundinacea 6Ac]
Scores for 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-56  190.4  37.8    3.2e-29  101.9   9.6    3.1  3  NosD             Periplasmic copper-binding protein (NosD)
    4.4e-42  143.6  47.7      3e-19   69.4  13.3    3.3  3  Beta_helix       Right handed beta helix region
      1e-05   25.0  23.8      0.016   14.5   0.1    4.3  2  DUF1565          Protein of unknown function (DUF1565)
    0.00053   18.8   0.1      0.001   17.9   0.1    1.5  1  Pectinesterase   Pectinesterase
     0.0012   18.8   7.1     0.0012   18.8   7.1    3.1  3  Pectate_lyase_3  Pectate lyase superfamily protein
  ------ inclusion threshold ------
      0.056   13.1   0.0       0.14   11.8   0.0    1.7  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
       0.18   11.4   0.0       0.39   10.3   0.0    1.5  1  ArsA_HSP20       HSP20-like domain found in ArsA
        1.4    9.2   3.7         38    4.6   0.1    3.0  3  Pepsin-I3        Pepsin inhibitor-3-like repeated domain


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 !   43.5   1.0   9.7e-15   2.2e-11      24     105 ..     106     187 ..      58     198 .. 0.88
   2 !   56.9  12.4   7.9e-19   1.8e-15      40     200 ..     195     355 ..     189     361 .. 0.91
   3 !  101.9   9.6   1.4e-32   3.2e-29      12     210 ..     368     551 ..     347     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.7e-15
                              NosD  24 segseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNti 100
                                       ++g++i++ +is+      + ns++n+i +n++ ++ +Gi+l+++++n +e+n  ++ +sGi+l sss+nt+++N++
  gi|386002462|ref|YP_005920761.1| 106 ADGCRIEGLTISDFTGPGIYVNSQGNEIVKNVLVDNVHGIFLNGTSENLLEKNRQEGGYSGIVLLSSSQNTVTGNVA 182
                                       38999******99998888********************************************************** PP

                              NosD 101 snnen 105
                                       +++++
  gi|386002462|ref|YP_005920761.1| 183 KDCRG 187
                                       *9987 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 7.9e-19
                              NosD  40 gi.lldnssnntitgntienlryGihlenses.ntiedntlssnesGialmsssnntlenNtisnnenyGillsdss 114
                                       gi l+  ss+n+i g  i++++yG+ +e+ +s n +++  +++ + +ial s  +n +e+N++sn++n Gi + +ss
  gi|386002462|ref|YP_005920761.1| 195 GIrLVLGSSENEIIGGWINSCNYGVLVEGGSSaNAVREVLFDNVTTAIALNSVAKNLIEKNNVSNSTN-GIVVATSS 270
                                       566788999******************998887999999999999***********************.******** PP

                              NosD 115 nntisnNtisnnnkGifle.nsssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttk 190
                                       +n +++N+ s+ + +i+++ +s+ n++t N++e+  + Gi+ +++s+ n++ +N +++ +  ++ dgs+  ++++  
  gi|386002462|ref|YP_005920761.1| 271 ENVVAENRLSDLDLAIMISfGSTANVLTTNHVERA-NSGIV-ITESTANNFDENRLVGVRLGLSVDGSGAESFDNAI 345
                                       ******************8456*************.*****.****************9999999999999998887 PP

                              NosD 191 tsgtniiggp 200
                                       ++  +i g p
  gi|386002462|ref|YP_005920761.1| 346 PESNTIDGDP 355
                                       7777666655 PP

  == domain 3  score: 101.9 bits;  conditional E-value: 1.4e-32
                              NosD  12 vsargngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGial 87 
                                        +++   i+l + +++++ +  ++  +d+++  +s++++i +n++++  yG+ +  s++n  ++n++s+++  Gi+l
  gi|386002462|ref|YP_005920761.1| 368 ADRKLGHITLASCDNCTVDGCIVT--NDALFTHSSKGCRIVENVVSKA-YGMLIRRSDGNEFRGNQVSESRvGGIML 441
                                       3334447899999*****887776..688888***********88776.**********************9***** PP

                              NosD  88 msssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegnt 163
                                        +s +n+++ N++s+n   G ll++s++n +  Nt+  n+++Gi+l++s++ +i +N++ +n ++Gi  +s+s g  
  gi|386002462|ref|YP_005920761.1| 442 VESGGNVIKENNLSRNGWDGLLLRRSEKNRVLSNTAEaNQQAGIRLDGSNDAEIAENSVIGN-GVGIS-ISGSAGCI 516
                                       ******9999998888888*****************99************************.*****.******** PP

                              NosD 164 iynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdy 210
                                       +y+N++i+ns+++++dg+n   W               +gGNyWsd 
  gi|386002462|ref|YP_005920761.1| 517 VYRNNLIENSVQAEDDGENLWDWGA------------LKGGNYWSDH 551
                                       *****************66666644............66******95 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 !   52.0   8.1     3e-17   6.7e-14      25     154 ..     101     231 ..      60     235 .. 0.65
   2 !   37.2  14.3   1.1e-12   2.4e-09      20     149 ..     213     338 ..     212     351 .. 0.84
   3 !   69.4  13.3   1.3e-22     3e-19       3     157 ..     375     521 ..     373     523 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3e-17
                                       SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S CS
                        Beta_helix  25 GiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyss 101
                                       Gi +  ++ ++ie+ +i++ +g Giy+++ ++n i +n+  dn   gi l+g+s nl+e+n+ +   + Gi l +ss
  gi|386002462|ref|YP_005920761.1| 101 GIEVLADG-CRIEGLTISDFTGPGIYVNS-QGNEIVKNVLVDNV-HGIFLNGTSENLLEKNRQEGGYS-GIVLLSSS 173
                                       44444444.46666666666666777664.66666666666666.66777777777777776666655.66666666 PP

                                       --EEES-EEESTT......--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEE CS
                        Beta_helix 102 nntienNiidnna......gsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvr 154
                                       +nt+++N++++++      g+Gi +  +ss++++ + +i++++ +G+ v g+ss + vr
  gi|386002462|ref|YP_005920761.1| 174 QNTVTGNVAKDCRgskevpGAGIRLVLGSSENEIIGGWINSCN-YGVLVEGGSSANAVR 231
                                       6777777777776666666666666666666666666666665.676666666666655 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 1.1e-12
                                       S-SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SE CS
                        Beta_helix  20 nsggyGiylrgssn.vvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGi 95 
                                       ns++yG+ ++g+s+ + +++  + n  ++ i+++++++n i++n++s+++  gi +  +s n++  n+ +d +   i
  gi|386002462|ref|YP_005920761.1| 213 NSCNYGVLVEGGSSaNAVREVLFDN-VTTAIALNSVAKNLIEKNNVSNST-NGIVVATSSENVVAENRLSDLDL-AI 286
                                       4579999999999955555555555.9999*****************999.*********************87.99 PP

                                       E-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS CS
                        Beta_helix  96 yln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss 149
                                       +++ +s+ n+++ N+++  + sGivi++s   +++  N++++ +  G+ v gs++
  gi|386002462|ref|YP_005920761.1| 287 MISfGSTANVLTTNHVERAN-SGIVITEST-ANNFDENRLVGVR-LGLSVDGSGA 338
                                       99999999********9999.*********.7778999999887.8887777776 PP

  == domain 3  score: 69.4 bits;  conditional E-value: 1.3e-22
                                       EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S- CS
                        Beta_helix   3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasn 79 
                                       i + +++n+t+++++++n   ++++  +s++++i +n++++   +G+ i++s++n +++n++s++  ggi+l ++++
  gi|386002462|ref|YP_005920761.1| 375 ITLASCDNCTVDGCIVTN---DALFTHSSKGCRIVENVVSK--AYGMLIRRSDGNEFRGNQVSESRVGGIMLVESGG 446
                                       667899999*******99...899999999999*9999999..********************************** PP

                                       -EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                        Beta_helix  80 nlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                       n+i+ n+ ++ng +G+ l  s+ n++  N++++n+++Gi +d s+ + ++  N++ +n+ +Gi + gs++ + v++N
  gi|386002462|ref|YP_005920761.1| 447 NVIKENNLSRNGWDGLLLRRSEKNRVLSNTAEANQQAGIRLDGSN-DAEIAENSVIGNG-VGISISGSAG-CIVYRN 520
                                       ***********999*******************************.9999********7.*********9.777777 PP

                                       E CS
                        Beta_helix 157 t 157
                                       +
  gi|386002462|ref|YP_005920761.1| 521 N 521
                                       6 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0  20.8    0.0029       6.5      15     214 ..      46     278 ..      40     352 .. 0.67
   2 !   14.5   0.1   7.3e-06     0.016      95     195 ..     378     509 ..     339     533 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0029
                           DUF1565  15 fktiTkAlllakageviqlapGtYseatgEtFPlvi.pe.....gvnlvGneagKGlskslyagkkvgp.lis.ggg 83 
                                       ++ti  A+++ak g++i + +GtY e++  +  +++ p+      vnlvG+ +  G  ++l  g +++  +is ++g
  gi|386002462|ref|YP_005920761.1|  46 YRTIGEAIAVAKDGDTIYVKAGTYREHITLNNRIILmPPrgedgAVNLVGDGNDIGI-EVLADGCRIEGlTISdFTG 121
                                       9************************998766665552322333359**********9.7777666554446653555 PP

                           DUF1565  84 ddls.gvqnvtivlanea.tiaGvtitNp...........nilkgtgvliesasakianNtitgn.iadGievsiye 146
                                       + +  + q + iv +  + ++ G+ ++ +              ++  vl++s++ ++  N  +++ + + +  +   
  gi|386002462|ref|YP_005920761.1| 122 PGIYvNSQGNEIVKNVLVdNVHGIFLNGTsenlleknrqeG-GYSGIVLLSSSQNTVTGNVAKDCrGSKEVPGAGIR 197
                                       55443345555555544326888887777888887755321.22333666666888888888885134457777777 PP

                           DUF1565 147 aktgaggniisGnsilfeknGiaisgasaavenkien.................NiivkNli.....GvvanalalD 201
                                       ++ g+ +n i G  i + + G+  +g s a  n +++                 N+i kN+      G+v       
  gi|386002462|ref|YP_005920761.1| 198 LVLGSSENEIIGGWINSCNYGVLVEGGSSA--NAVREvlfdnvttaialnsvakNLIEKNNVsnstnGIV------- 265
                                       778877776666666666666666655554..22222222224444444333337777766533333433....... PP

                           DUF1565 202 lGsgsegsaGnNi 214
                                       + + se+ + +N 
  gi|386002462|ref|YP_005920761.1| 266 VATSSENVVAENR 278
                                       4444554444444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.3e-06
                           DUF1565  95 vlaneatiaGvtitNp......................................nilkgtgvliesa.sakianNti 132
                                          ++ t+ G  +tN                                       +  +  g+++ ++ + +i++N +
  gi|386002462|ref|YP_005920761.1| 378 ASCDNCTVDGCIVTNDalfthsskgcrivenvvskaygmlirrsdgnefrgnqvSESRVGGIMLVESgGNVIKENNL 454
                                       555555555555555555555555555555555555555555556666666544335778888877769999***** PP

                           DUF1565 133 tgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaavenkienNiivkNliGvva 195
                                       + n+ dG+  +  e k+ +  n++  n+    ++Gi  +g++ a    i +N ++ N  G+ +
  gi|386002462|ref|YP_005920761.1| 455 SRNGWDGLLLRRSE-KNRVLSNTAEANQ----QAGIRLDGSNDA---EIAENSVIGNGVGISI 509
                                       *******8887776.7777777765553....445555555555...5555555555555443 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.5e-07     0.001       3      49 ..      37      79 ..      35     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.5e-07
                                      EE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS CS
                    Pectinesterase  3 vvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkk 49
                                      +v +dg ++++ti ea+a +++       iyvkaG+Y+e+++++++ 
  gi|386002462|ref|YP_005920761.1| 37 IVDDDGFAQYRTIGEAIAVAKDGD----TIYVKAGTYREHITLNNRI 79
                                      6889*************9988655....59***********998753 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   7.1   5.2e-07    0.0012      19     214 ..      47     264 ..      34     265 .. 0.76
   2 ?   -1.1   0.6      0.61   1.4e+03     159     173 ..     381     397 ..     286     461 .. 0.50
   3 !    6.2   1.9    0.0036         8     143     210 ..     457     526 ..     422     533 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.2e-07
                                       HHHHHHH......HTSS-EEE-SEEEEESS-E..........EE-SSEEEEES-TTTEEEEE-TT-SS--SEEES-T CS
                   Pectate_lyase_3  19 aaiqkaiscasatttgavVYfPaGtYlvsspi..........ilksgvqLvGdgngrpvlkaaaafvgaglidgdpy 85 
                                         i +ai   +  ++g+++Y+ aGtY+ + ++               v+LvGdgn+  +  +a++ + +gl  +d +
  gi|386002462|ref|YP_005920761.1|  47 RTIGEAI---AVAKDGDTIYVKAGTYREHITLnnriilmpprGEDGAVNLVGDGNDIGIEVLADGCRIEGLTISDFT 120
                                       5677888...88999************999989999999997777789******************88888888888 PP

                                       TT-......-EEEEEEEEEEEGGGG-SS---S........SEEEES-E.EEEEEEEEEES-SSEEE-SSS---TT-- CS
                   Pectate_lyase_3  86 vsg..gs..ealiatnnfyrqirnlkiditav........apgatgih.wqtaqatslenvefemseasgtkhqgif 149
                                       + g  ++   + i +n++++++  + ++ t+         + g++gi    ++q+t   nv  + + +++  + gi+
  gi|386002462|ref|YP_005920761.1| 121 GPGiyVNsqGNEIVKNVLVDNVHGIFLNGTSEnlleknrqEGGYSGIVlLSSSQNTVTGNVAKDCRGSKEVPGAGIR 197
                                       86655224333344556666677777776666778775534444999978899999999998888877777888998 PP

                                       -SS--E..EEEES-EEES-SS-SEEE..S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEE CS
                   Pectate_lyase_3 150 iengsg..gflndlvfsglgdigiav..gnqqftvrnitfnnattgievlwgwgwtlknvkinncegGi 214
                                       +  gs+  +++   +++   ++g+ v  g+ + +vr++ f n tt+i +++  +  ++ ++++n+++Gi
  gi|386002462|ref|YP_005920761.1| 198 LVLGSSenEII-GGWINS-CNYGVLVegGSSANAVREVLFDNVTTAIALNSVAKNLIEKNNVSNSTNGI 264
                                       77777743333.223333.4566666415999999***************9777888899999999998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.61
                                       ES-EEES..-SS-SEEE CS
                   Pectate_lyase_3 159 ndlvfsg..lgdigiav 173
                                       ++++++g  + ++++ +
  gi|386002462|ref|YP_005920761.1| 381 DNCTVDGciVTNDALFT 397
                                       33333333322222222 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0036
                                       ---TT---SS--EEEE.ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E.EEEEEEEEESS CS
                   Pectate_lyase_3 143 tkhqgifiengsggfl.ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwg.wtlknvkinnc 210
                                       +  +g+++++++++ + ++    +  + gi++ g++++ + ++ + +++ gi+++ + g ++++n+ i+n+
  gi|386002462|ref|YP_005920761.1| 457 NGWDGLLLRRSEKNRVlSNTAEAN-QQAGIRLdGSNDAEIAENSVIGNGVGISISGSAGcIVYRNNLIENS 526
                                       445566666655544434444444.8999999988888888888888899999999999999999988776 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.3e-05      0.14      26      47 ..     357     379 ..     344     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.3e-05
                            PurK_C  26 lHlYgKe.earpgRKmGHitvvg 47 
                                       l+lYg + e+ + RK+GHit+ +
  gi|386002462|ref|YP_005920761.1| 357 LYLYGRSdEVVADRKLGHITLAS 379
                                       7899986368899*******976 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00018      0.39      17      40 ..      52      75 ..      50      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                        ArsA_HSP20 17 eidlsrsgdeLtIkignfrRqitL 40
                                       i ++++gd++ +k+g +r +itL
  gi|386002462|ref|YP_005920761.1| 52 AIAVAKDGDTIYVKAGTYREHITL 75
                                      689********************9 PP

>> Pepsin-I3  Pepsin inhibitor-3-like repeated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.017        38      16      31 ..     382     397 ..     368     401 .. 0.77
   2 ?   -1.6   0.0       1.4   3.1e+03      19      29 ..     400     410 ..     397     420 .. 0.81
   3 ?    4.3   0.1     0.021        47      15      33 ..     508     526 ..     496     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
                         Pepsin-I3  16 qyyfdGCvVqdNklyv 31 
                                           dGC+V++  l+ 
  gi|386002462|ref|YP_005920761.1| 382 NCTVDGCIVTNDALFT 397
                                       5568********9996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                         Pepsin-I3  19 fdGCvVqdNkl 29 
                                       ++GC +++N++
  gi|386002462|ref|YP_005920761.1| 400 SKGCRIVENVV 410
                                       78*******98 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.021
                         Pepsin-I3  15 tqyyfdGCvVqdNklyvgg 33 
                                       ++ +++GC+V  N l  + 
  gi|386002462|ref|YP_005920761.1| 508 SISGSAGCIVYRNNLIENS 526
                                       5789********9997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.58
# Mc/sec: 3040.82
//
Query:       gi|386002463|ref|YP_005920762.1|  [L=40]
Description: hypothetical protein Mhar_1781 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-12   46.1   0.0    3.9e-12   46.0   0.0    1.0  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   2.2e-16   3.9e-12       6      40 ..       1      35 [.       1      36 [. 0.93

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.2e-16
                                      XXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                        Sec61_beta  6 lryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                      +ry++ d+++ik++Pk+V+++s +++a+V++L++ 
  gi|386002463|ref|YP_005920762.1|  1 MRYFDADDTAIKLNPKTVIAISTGVGAAVMALNFS 35
                                      9****6668************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.36s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 229.73
//
Query:       gi|386002464|ref|YP_005920763.1|  [L=291]
Description: ApbC/Nbp35 iron-sulfur cluster carrier protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-97  325.1   0.0    3.1e-97  324.9   0.0    1.0  1  ParA             NUBPL iron-transfer P-loop NTPase
    1.3e-16   60.8   0.0    6.2e-16   58.6   0.0    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      2e-09   37.6   0.4    1.9e-08   34.4   0.4    2.1  1  AAA_31           AAA domain
    5.9e-09   35.6   0.0    1.2e-08   34.6   0.0    1.5  1  MipZ             ATPase MipZ
    6.4e-06   26.1   0.1      0.011   15.6   0.1    2.3  2  AAA_26           AAA domain
    4.9e-05   22.7   1.0     0.0016   17.7   0.3    2.5  2  ArsA_ATPase      Anion-transporting ATPase
    0.00012   21.2   0.4    0.00018   20.6   0.4    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00064   19.2   0.0     0.0018   17.8   0.0    1.7  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
     0.0015   18.4   0.1     0.0023   17.9   0.1    1.2  1  APS_kinase       Adenylylsulphate kinase
     0.0073   15.6   0.0      0.013   14.8   0.0    1.3  1  VirC1            VirC1 protein
  ------ inclusion threshold ------
      0.023   14.3   0.2      0.023   14.3   0.2    1.8  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.027   14.0   0.0      0.049   13.2   0.0    1.3  1  AAA_25           AAA domain
      0.041   13.4   0.3       0.28   10.6   0.2    1.9  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
      0.042   13.8   0.1      0.086   12.8   0.1    1.5  1  NTPase_1         NTPase
      0.065   13.0   0.0       0.12   12.2   0.0    1.4  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.068   12.9   0.4       0.11   12.2   0.4    1.3  1  AAA_30           AAA domain
      0.074   12.9   0.0       0.19   11.6   0.0    1.7  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.085   11.9   0.1       0.15   11.1   0.1    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.092   11.6   0.1       0.12   11.3   0.1    1.1  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.12   12.0   0.1       0.21   11.2   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
       0.13   11.6   0.2        0.2   10.9   0.2    1.2  1  DUF1611          Domain of unknown function (DUF1611_C) P-loo
       0.19   10.9   0.1       0.29   10.3   0.1    1.2  1  NB-ARC           NB-ARC domain
       0.21   11.9   0.0       0.45   10.8   0.0    1.5  1  AAA_22           AAA domain
       0.26   10.7   0.0       0.38   10.2   0.0    1.2  1  KTI12            Chromatin associated protein KTI12


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.9   0.0  4.1e-100   3.1e-97       2     245 ..      38     280 ..      37     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 324.9 bits;  conditional E-value: 4.1e-100
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSi 78 
                                       vk++i+++SgKGGVGKStvavnlA  L+++g++vg+lDaDi+Gps ++llgve+e+  +   ++ Pv++kg+kv+S+
  gi|386002464|ref|YP_005920763.1|  38 VKHKIMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTAKLLGVERERLLAGPGGIEPVDSKGLKVISM 114
                                       9*********************************************************9999*************** PP

                              ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvk 154
                                       +f l++ ++avvwrGpmk++aikq+l+dv+wg+lD+LiiDlPPGt+De l+v+q l +l+gaviVttpqeval d +
  gi|386002464|ref|YP_005920763.1| 115 AFALSDPSSAVVWRGPMKMAAIKQFLADVSWGDLDFLIIDLPPGTSDEPLSVVQLLpDLTGAVIVTTPQEVALLDSR 191
                                       ********************************************************889****************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe 231
                                       ka++m+k + v++lG+veNmsg+ cp+cge ++if++ggge++aeel vp+lg+ipldpei+  +deg  +v +  +
  gi|386002464|ref|YP_005920763.1| 192 KAVNMVKAMGVPLLGIVENMSGLRCPHCGEVIDIFKTGGGERAAEELAVPFLGAIPLDPEITPLGDEGVAFVDR--D 266
                                       *********************************************************************99866..5 PP

                              ParA 232 seaakaleeiaekv 245
                                       ++a++++e++++ +
  gi|386002464|ref|YP_005920763.1| 267 TAAKESFERVVDGI 280
                                       88899999988765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   8.3e-19   6.2e-16       1     119 [.      42     253 ..      42     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 8.3e-19
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+ias+kGGvGK+t+a+nLar l+ rg+rV ++DaD  ++++a l g+e +  +                       
  gi|386002464|ref|YP_005920763.1|  42 IMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTAKLLGVERE--Rllagpggiepvdskglkvismaf 116
                                       89****************************************944444444..3569******************** PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                               d  + 
  gi|386002464|ref|YP_005920763.1| 117 alsdpssavvwrgpmkmaaikqfladvswgdldfliidlppgtsdeplsvvqllpdltgavivttpqevallDSRKA 193
                                       *************************************9999999999999999999999999999999999988888 PP

                                       CHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC..........TS-EEEEEE--CCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry..........gvpvlgviprdeava 119
                                       +++++a+g +      ++g+v n+ + +    +  e ++  k  +          +vp+lg ip d +++
  gi|386002464|ref|YP_005920763.1| 194 VNMVKAMGVP------LLGIVENMSGLR--CPHCGEVIDIFK--TgggeraaeelAVPFLGAIPLDPEIT 253
                                       9999999965......899999988877..444444333322..12344555666888888888887775 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.4   2.6e-11   1.9e-08       3      49 ..      41      87 ..      39     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.6e-11
                            AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglg 49
                                       I ia  KGGvGK+T +vnla +l  +g +v + D+D  + +t +l 
  gi|386002464|ref|YP_005920763.1| 41 KIMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTAKLL 87
                                      68999********************************9999998543 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.6e-11   1.2e-08       1     112 [.      40     161 ..      40     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.6e-11
                                       EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHH..........HHHHT------EE CS
                              MipZ   1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraat..........aerkglsLplpea 67 
                                       h i+++  kGG Gkst+av +a  L ++G+rv+++d d+   + a+ l+  +++          +++kgl++    a
  gi|386002464|ref|YP_005920763.1|  40 HKIMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTAKLLGVERERllagpggiepVDSKGLKVISM-A 115
                                       6799******************************************99854443121222222257777776544.4 PP

                                       E-SSS-HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE--.SS-- CS
                              MipZ  68 lalseaeeaeveeeeeaevaeleelvadle.aeldfividtP.Gsds 112
                                       +als+ ++a v ++  +++a++++ +ad++  +ldf++id P G+ +
  gi|386002464|ref|YP_005920763.1| 116 FALSDPSSAVVWRGP-MKMAAIKQFLADVSwGDLDFLIIDLPpGTSD 161
                                       488887666666655.556899999999873579******8635433 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.5e-05     0.011       1      35 [.      40      74 ..      40      92 .. 0.93
   2 !    8.6   0.0     0.002       1.5     132     195 ..     177     253 ..     112     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                            AAA_26  1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyf 35
                                      ++i++++   gvGK++v+  L+r l+++g++vg++
  gi|386002464|ref|YP_005920763.1| 40 HKIMIASGKGGVGKSTVAVNLARVLQARGFRVGVL 74
                                      579*****************************986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk..vrnp..envetlekksg.........ipvlGvvPylpdle 195
                                       ++V+++++ ++ +   ++++++  +v++lG++ N   +r p   +v  ++k++g         +p lG++P +p+++
  gi|386002464|ref|YP_005920763.1| 177 VIVTTPQEVALLDSRKAVNMVKAMGVPLLGIVENMsgLRCPhcGEVIDIFKTGGgeraaeelaVPFLGAIPLDPEIT 253
                                       66777777777777778899999999999999886333333344555555555556666666699999999998876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   2.1e-06    0.0016       1      37 [.      40      76 ..      40      81 .. 0.87
   2 ?    2.8   0.0     0.075        56     204     243 ..     171     210 ..     160     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE- CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllist 37
                                      +k+++ +GKGGVGK+tv+  +a  l   g +v ++  
  gi|386002464|ref|YP_005920763.1| 40 HKIMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDA 76
                                      589999****************999988888877655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.075
                                       TTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                       ArsA_ATPase 204 pertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                       p+ t  ++V++p +++l ++++a++ +k +g+    ++ N
  gi|386002464|ref|YP_005920763.1| 171 PDLTGAVIVTTPQEVALLDSRKAVNMVKAMGVPLLGIVEN 210
                                       678999************************9988777755 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   2.5e-07   0.00018      19      73 ..      28      84 ..      16      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.5e-07
                                      HHHHGGG-S-S.EEEEE.EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-------- CS
                              MeaB 19 lerllakaGra.qvvGl.tGvPGaGkstlvealglelrrrGkrvavlavDPsspftG 73
                                      l++++a+ Gr  +++ +  G  G+Gkst+  +l+  l++rG rv+vl  D + p t 
  gi|386002464|ref|YP_005920763.1| 28 LRAVSARMGRVkHKIMIaSGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTA 84
                                      78899999996345555279****************************998888764 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.4e-06    0.0018       6      48 ..      46      88 ..      40      96 .. 0.86
   2 ?   -1.7   0.0       2.2   1.6e+03     195     215 ..     233     253 ..     191     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                         Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllg 48
                                       GkGG+Gkst + nl+  l+++g +v ++  D    st  llg
  gi|386002464|ref|YP_005920763.1| 46 SGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTAKLLG 88
                                      6***************************999999999987776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                         Fer4_NifH 195 kfaeelgtkvlevvPrdeivr 215
                                       + aeel+++ l ++P+d +++
  gi|386002464|ref|YP_005920763.1| 233 RAAEELAVPFLGAIPLDPEIT 253
                                       457788888888888888776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1     3e-06    0.0023       4      51 ..      42      89 ..      39      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-06
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51
                                      ++  +G  g GKst+a++l++ L+++g +v +Ld d       k Lg 
  gi|386002464|ref|YP_005920763.1| 42 IMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGPSTAKLLGV 89
                                      55678999**************************99766666666665 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.013       4      43 ..      42      81 ..      40      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                      i ++s kGG Gk+t  + l   l ++g rv++++ad   P
  gi|386002464|ref|YP_005920763.1| 42 IMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITGP 81
                                      67899*******************************7766 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.6       8.1   6.1e+03       8      12 ..       7      11 ..       7      12 .. 0.92
   2 ?   14.3   0.2     3e-05     0.023       8      25 ..     215     232 ..     209     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.1
                                      E-TTT CS
                   Desulfoferrod_N  8 kCevC 12
                                      kCe C
  gi|386002464|ref|YP_005920763.1|  7 KCEAC 11
                                      9***9 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3e-05
                                       E-TTT--EEEECC--SS- CS
                   Desulfoferrod_N   8 kCevCGniVeVleaGgGe 25 
                                       +C +CG+++ + + GgGe
  gi|386002464|ref|YP_005920763.1| 215 RCPHCGEVIDIFKTGGGE 232
                                       9****************7 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.6e-05     0.049      31      55 ..      38      62 ..      20      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                            AAA_25 31 pagelallaGapgtGKttlaldlal 55
                                      +++++ +  G +g+GK+t+a++la 
  gi|386002464|ref|YP_005920763.1| 38 VKHKIMIASGKGGVGKSTVAVNLAR 62
                                      379999*****************96 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00037      0.28      10      38 ..      48      76 ..      40      87 .. 0.89
   2 ?    0.5   0.0      0.48   3.6e+02     103     136 ..     134     168 ..     126     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                          CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDl 38
                                      +GGvG++++++ La+ l++ g +v v+D+
  gi|386002464|ref|YP_005920763.1| 48 KGGVGKSTVAVNLARVLQARGFRVGVLDA 76
                                      8***********************99997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.48
                          CBP_BcsQ 103 eallaalkelk.eqyrwillDlpagasaltrella 136
                                        a++++l+ ++ ++ +++++Dlp g+s+   ++++
  gi|386002464|ref|YP_005920763.1| 134 AAIKQFLADVSwGDLDFLIIDLPPGTSDEPLSVVQ 168
                                       567788888888999********998876555444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00011     0.086       4      31 ..      45      72 ..      41      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      EE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkvg 31
                                       +G+ GvGK+T+  +++++l+ +g++vg
  gi|386002464|ref|YP_005920763.1| 45 ASGKGGVGKSTVAVNLARVLQARGFRVG 72
                                      4799*********************996 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.12       1      33 [.      47      79 ..      47      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                      G+  +GKST+a +L+  +  +g ++ ++D+D+ 
  gi|386002464|ref|YP_005920763.1| 47 GKGGVGKSTVAVNLARVLQARGFRVGVLDADIT 79
                                      66789**************************85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00015      0.11      17      52 ..      39      74 ..      27      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                      +++++++ G  G GK+t+   l+++++a+g+rv +l
  gi|386002464|ref|YP_005920763.1| 39 KHKIMIASGKGGVGKSTVAVNLARVLQARGFRVGVL 74
                                      57799*************************999765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.19       4      34 ..      45      75 ..      42      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                              MobB  4 ivgksgsGKTtLleklipelkarglrvgtiK 34
                                        gk g GK t   +l ++l+arg+rvg++ 
  gi|386002464|ref|YP_005920763.1| 45 ASGKGGVGKSTVAVNLARVLQARGFRVGVLD 75
                                      458999**********************985 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00021      0.15      46      71 ..      49      74 ..      43      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                      S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                      GG GK  +++ l++ lqarg++vgvl
  gi|386002464|ref|YP_005920763.1| 49 GGVGKSTVAVNLARVLQARGFRVGVL 74
                                      9***********************98 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.12       5      51 ..      29      76 ..      25     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                     TrwB_AAD_bind  5 agvplpkeretqhili.vGttGsGKtqalekllrairargdraivlDl 51
                                       +v+ +  r +++i+i  G  G GK++++ +l r ++arg r+ vlD+
  gi|386002464|ref|YP_005920763.1| 29 RAVSARMGRVKHKIMIaSGKGGVGKSTVAVNLARVLQARGFRVGVLDA 76
                                      5667777777777777358899********************999875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.21       3      40 ..      42      79 ..      40      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                      +++  G  G+GK t +  La++l+++g +v +  aD+ 
  gi|386002464|ref|YP_005920763.1| 42 IMIASGKGGVGKSTVAVNLARVLQARGFRVGVLDADIT 79
                                      45567999************************999975 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00027       0.2       9      56 ..      37      83 ..      29      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                           DUF1611  9 evkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili 56
                                      +vk k++++ G +  vGK t a++l++ l++rG++++++  + tg  +
  gi|386002464|ref|YP_005920763.1| 37 RVKHKIMIASGKG-GVGKSTVAVNLARVLQARGFRVGVLDADITGPST 83
                                      5666666666665.69**********************9999998766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00039      0.29      15      41 ..      35      61 ..      25      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                                      TTTSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 15 kdelqslvvalvGmgGvGKttlakqil 41
                                      ++ ++  ++  +G+gGvGK+t+a +  
  gi|386002464|ref|YP_005920763.1| 35 MGRVKHKIMIASGKGGVGKSTVAVNLA 61
                                      56677889**************98765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0006      0.45       5      54 ..      40      85 ..      36      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstssk 54
                                      ++i++  G  G+GK+t++ +l++ l+++      r++v+  +++++++ k
  gi|386002464|ref|YP_005920763.1| 40 HKIMIASGKGGVGKSTVAVNLARVLQARG----FRVGVLDADITGPSTAK 85
                                      6899999****************997554....57777777777777665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005      0.38       5      41 ..      44      80 ..      42      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                      + +G   +GKst+a +La+ l++++ +v v+d +  g
  gi|386002464|ref|YP_005920763.1| 44 IASGKGGVGKSTVAVNLARVLQARGFRVGVLDADITG 80
                                      56788889**********************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 1617.21
//
Query:       gi|386002465|ref|YP_005920764.1|  [L=316]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-13   48.9   0.0    1.9e-12   47.9   0.0    1.6  1  Radical_SAM     Radical SAM superfamily
     0.0019   18.0   0.3      0.082   12.8   0.1    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0023   18.0   0.0       0.11   12.6   0.0    2.3  2  Fer4_14         4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.012   15.7   0.6      0.034   14.2   0.6    1.8  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
      0.017   15.2   4.7       0.26   11.4   0.8    3.1  3  HTH_20          Helix-turn-helix domain
      0.034   14.1   0.0       0.21   11.6   0.0    2.3  2  HRDC            HRDC domain
       0.13   12.5   0.1       0.65   10.3   0.1    2.1  1  Fer4_12         4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   7.4e-16   1.9e-12       3     159 ..      23     197 ..      21     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 7.4e-16
                                       EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE...................SSTGGG CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilg...................ggepll 59 
                                       +++ C+l+C++C+ + t   +  r++ +s+ e+lee+++l+ ekg + v  g                   +gepll
  gi|386002465|ref|YP_005920764.1|  23 PFKTCTLDCVYCQLGPTtCLTLAREERVSTAEVLEEIRSLS-EKGSDRVGHGdggagaagavefdyltlagSGEPLL 98 
                                       6789*************97778889999999*********5.8888888888899********************** PP

                                       STTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  60 ypdfvellerlaklavpgiritvetngtlpd.eeklerllelgvdrvslgleaadde.kvlklmnrghtfeevleal 134
                                       ++ + e+++ +++    +  +++ tngtl   ee+ ++ le+ +   sl++ +a  + ++ +++ +  +++++le+l
  gi|386002465|ref|YP_005920764.1|  99 HRGLDEIIRGAKEA--VDKPVALLTNGTLFFrEEVRREVLEADLIIPSLDAATAPTFkRINRPH-PDLSIDDLLEGL 172
                                       *************9..8************98888888999977777777777766666777777.99999******* PP

                                       HHHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 135 eklreagikrvvdrivglpGendee 159
                                        +lre    +++  +++++G nd e
  gi|386002465|ref|YP_005920764.1| 173 VRLREEFSGEIWLEVMLVKGINDGE 197
                                       ******5555*************88 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.047   1.2e+02      20      50 ..      36      66 ..      32      70 .. 0.92
   2 !   12.8   0.1   3.2e-05     0.082      16      62 ..     264     310 ..     255     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.047
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCT CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkG 50
                                      lgp t  ++a+e  v+ + v e +rsL++kG
  gi|386002465|ref|YP_005920764.1| 36 LGPTTCLTLAREERVSTAEVLEEIRSLSEKG 66
                                      68999999**********************9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                        Ll++ p t +e+++ +g+ r+ + ++L+ Le ++ ++r + + +lY
  gi|386002465|ref|YP_005920764.1| 264 DLLTRRPCTLEELSSLSGLHRNEILKYLEVLEAADEIRRLRHEGRLY 310
                                       699*******************************9999988775555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.048   1.2e+02       5      37 ..      24      59 ..      22      74 .. 0.67
   2 !   12.6   0.0   4.4e-05      0.11      48      93 ..      85     127 ..      77     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.048
                           Fer4_14  5 lsgCnlsCkgCd...nketwkselgkpqteelleqi 37
                                      +  C+l C+ C    ++     + + ++t e+le+i
  gi|386002465|ref|YP_005920764.1| 24 FKTCTLDCVYCQlgpTTCLTLAREERVSTAEVLEEI 59
                                      568********9775444444566666777777554 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.4e-05
                           Fer4_14  48 iqglvltG.GePLhyenkkellklvkrlkeeypekkiwletngtlei 93 
                                        + l+l G GePL++   + l+++++  ke + +k++ l tngtl  
  gi|386002465|ref|YP_005920764.1|  85 FDYLTLAGsGEPLLH---RGLDEIIRGAKEAV-DKPVALLTNGTLFF 127
                                       5789*********99...89999999999988.9*********9864 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   1.3e-05     0.034       7      42 ..     257     294 ..     252     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                    Sulfolobus_pRN   7 sekill..ilsrrcatleeleektGiekeellvyltrl 42 
                                       +  +l+   l+rr  tleel   +G++++e+l yl  l
  gi|386002465|ref|YP_005920764.1| 257 TTEVLIrdLLTRRPCTLEELSSLSGLHRNEILKYLEVL 294
                                       44555533699***********************9765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.023        59      23      51 ..      37      65 ..      29      66 .. 0.90
   2 ?   -1.9   0.0       1.5   3.7e+03      11      28 ..     131     151 ..     129     164 .. 0.59
   3 ?   11.4   0.8    0.0001      0.26      18      58 ..     264     304 ..     260     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.023
                                      TTB-HHHHHHHHTS-HHHHHHHHHHHHHC CS
                            HTH_20 23 egltaselaerldlskntlsyHLrvLeea 51
                                      ++ t+  la++ ++s +++   +r L+e 
  gi|386002465|ref|YP_005920764.1| 37 GPTTCLTLAREERVSTAEVLEEIRSLSEK 65
                                      799*******************9999985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                       HHHHHHHHH...STCTTB-HH CS
                            HTH_20  11 vRrrilraL...araegltas 28 
                                       vRr++l a    ++ +++ta+
  gi|386002465|ref|YP_005920764.1| 131 VRREVLEADliiPSLDAATAP 151
                                       677766552244444555555 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0001
                                       HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                        L ++++ t++el  + +l++n++ + L+vLe a+ +++ r
  gi|386002465|ref|YP_005920764.1| 264 DLLTRRPCTLEELSSLSGLHRNEILKYLEVLEAADEIRRLR 304
                                       45599*****************************9877766 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.96   2.5e+03      17      53 ..      46      63 ..      41      72 .. 0.54
   2 ?   11.6   0.0     8e-05      0.21      31      63 ..     261     293 ..     258     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.96
                                      HHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT- CS
                              HRDC 17 reedvppyvvfpdktLleiAeklPttleeLlqiegvg 53
                                      ree v                    t+e L++i+ ++
  gi|386002465|ref|YP_005920764.1| 46 REERV-------------------STAEVLEEIRSLS 63
                                      44433...................4455555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8e-05
                                       HHHHHHHH---SHHHHHTSTTT-HHHHHHHHHH CS
                              HRDC  31 tLleiAeklPttleeLlqiegvgkrklekygee 63 
                                        ++++  ++P tleeL++++g++++ + ky e 
  gi|386002465|ref|YP_005920764.1| 261 LIRDLLTRRPCTLEELSSLSGLHRNEILKYLEV 293
                                       589999*********************999874 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00025      0.65      12     100 ..      24     130 ..      14     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                           Fer4_12  12 vsgCnlsCkgCfnketwsfk...sgkeftkelleeiiedlkkesi.................egltllG.GEPllpe 67 
                                       ++ C+l C +C    t + +   +++  t e+leei    +k s+                 + ltl G GEPll  
  gi|386002465|ref|YP_005920764.1|  24 FKTCTLDCVYCQLGPTTCLTlarEERVSTAEVLEEIRSLSEKGSDrvghgdggagaagavefDYLTLAGsGEPLL-- 98 
                                       66788888888877777555332334446777777766666644445666677777777777899***99*****.. PP

                           Fer4_12  68 naeallelvkevkeekpekdiwlytgytleels 100
                                         + l e+++  ke+  +++ +l++g+ ++  +
  gi|386002465|ref|YP_005920764.1|  99 -HRGLDEIIRGAKEAVDKPVALLTNGTLFFREE 130
                                       .999***********************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1837.89
//
Query:       gi|386002466|ref|YP_005920765.1|  [L=282]
Description: hypothetical protein Mhar_1784 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-22   78.9  32.9    5.1e-22   78.7  32.9    1.0  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7  32.9   2.9e-26   5.1e-22       2     235 ..      47     275 ..      46     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.9e-26
                              TauE   2 llagllaGfvagllGiGggliavPlLllllppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGal 78 
                                       +l++++a +v  l+G+G +l+avPl  +ll +++av+  +++ v+ +l+ + +  rr  +d+ ++++ll+++l+G++
  gi|386002466|ref|YP_005920765.1|  47 FLIIFAAMLVRTLTGFGSALLAVPLRSILLGAKYAVPFIMVYEVLIYLMILGREGRRLGGDLVAAWPLLVAGLAGVP 123
                                       78899999****************9988779******************9999999966****************** PP

                              TauE  79 lGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvplll 155
                                       +Ga +l + +++llk  +g++l+++++l+l+  +      ++ r++ i++++ g+l+G+l G +G      ++p+ l
  gi|386002466|ref|YP_005920765.1| 124 IGAEVLMAASDRLLKGGMGIALIVFSILLLRDLG------AKLRRGGIASAASGLLAGFLCGSTGLP----GPPMAL 190
                                       ******************************9775......234455565555555566666666665....455555 PP

                              TauE 156 lll..glplkkavatslllilvislagalgyalagavdwpllll...llpgallGallGarlarrlsertlrrlfal 227
                                       ll+  g++  +++ + +l+ +++ l+++  +++ag +d +++     +lp+++lG + G r+  r++e+ +rrl ++
  gi|386002466|ref|YP_005920765.1| 191 LLRgqGFEKGEFRRLIVLFLTAVDLFAFGYFLWAGLIDKEMINNslfFLPAMVLGFIAGGRAFGRVDEASFRRLTLG 267
                                       55522666666*******************9*******664433445****************************** PP

                              TauE 228 lllvlgvk 235
                                       + l++gv 
  gi|386002466|ref|YP_005920765.1| 268 ITLAAGVL 275
                                       ****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1615.24
//
Query:       gi|386002467|ref|YP_005920766.1|  [L=1051]
Description: isoleucyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for 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-190  635.0   0.0   1.3e-190  634.7   0.0    1.1  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    4.3e-34  117.7   0.0    7.4e-34  116.9   0.0    1.4  1  Anticodon_1   Anticodon-binding domain of tRNA
    1.5e-24   86.5   1.1    5.6e-11   41.8   0.2    3.5  3  tRNA-synt_1g  tRNA synthetases class I (M)
    4.9e-06   26.1   0.0    0.00016   21.1   0.0    2.7  3  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
     0.0015   17.5   0.1     0.0055   15.7   0.0    1.9  3  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  634.7   0.0  3.5e-194  1.3e-190       4     601 ..      20     636 ..      17     637 .. 0.95

  Alignments for each domain:
  == domain 1  score: 634.7 bits;  conditional E-value: 3.5e-194
                       tRNA-synt_1   4 ekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                       ++We+ +++  +++++   ++f +vdgPPy tG++H+G a++k++kd + ryk+m+G+e + + GwD++Gl+ie kv
  gi|386002467|ref|YP_005920766.1|  20 KFWEDRGIYALARTTRAGGRKFFFVDGPPYTTGRIHLGTAWNKIIKDSILRYKSMNGFEIKDRAGWDMHGLPIEVKV 96 
                                       89**********999999*********************************************************** PP

                       tRNA-synt_1  81 ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliy 157
                                       e++lg k kke + +g+++f++k++e++  +++++++q++ lG+++D++++y+Tl++e+ ea +++++r  ++gl+ 
  gi|386002467|ref|YP_005920766.1|  97 EEHLGFKSKKEIEIYGVDRFIDKCKEFALSQKDQMTEQFRTLGAWLDWEDPYMTLKDEYLEAAWWTLKRANERGLLE 173
                                       ***************************************************************************** PP

                       tRNA-synt_1 158 rgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv....... 227
                                       rg ++vnw+++++ta++++Evey +++d++i+v+fp+ ++e++ ++i+TTtP+T++++++vav+p+++y+       
  gi|386002467|ref|YP_005920766.1| 174 RGFRVVNWCPRCETAIADAEVEYWEETDPSIYVKFPVVGEEKTFMMIWTTTPWTIPANVGVAVHPDFEYSrvrawkd 250
                                       **********************************************************************99*9988 PP

                       tRNA-synt_1 228 ..itkeklilaeallkslvkke..sekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVk 293
                                            e li+a+ l++ ++++   + ++il++  g+eLeg+e+e+pl        +   +i   d+v++e+ tG V+
  gi|386002467|ref|YP_005920766.1| 251 dpDGAEVLIIASPLVEGVLREGryKGYEILDRLGGAELEGLEYEHPLadlipaqGDIVHKIHLADFVTAEN-TGSVH 326
                                       8666799***********999865666********************888886444455677789**9986.***** PP

                       tRNA-synt_1 294 iaPahdedDyevgkkynlevinildedgtlteea.aefeglkvfdarkkvveelkekglllkaekiehsvpfcersk 369
                                       iaP+h+ +D+e+g   ++++ +++ edg++t ea ++++g +v +a++ v e+l  +glll + +i+h +++c+r k
  gi|386002467|ref|YP_005920766.1| 327 IAPGHGLEDFELGVAEGMPIFCPVGEDGRYTAEAgEKYAGKYVRAANEEVNEDLAGRGLLLAEGEISHRYGHCWRCK 403
                                       *******************************999789**************************************** PP

                       tRNA-synt_1 370 kpiiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvr 445
                                       +pii+ at+qWf ++++l++++l+++ kv+++p++ + +r+ +w+  ++dWciSRqr+WG ++p+++ ++ +e+ v 
  gi|386002467|ref|YP_005920766.1| 404 TPIIFIATPQWFLKISDLREDMLQEIAKVKWYPDWaGSARFRDWISGARDWCISRQRYWGIPLPIWICETCGEMEVI 480
                                       ***********************************99***************************************7 PP

                       tRNA-synt_1 446 eelkelvagreeeeaekkalekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadm 519
                                        +++el +    + +  ++l++ a+d +    +  ge+++++dv+DvWF+S+    +tl+yp   +++l++ +pad+
  gi|386002467|ref|YP_005920766.1| 481 GSMEELHQ---RSGSVVSELHRPAVDLVtikCTCGGEMRRVPDVFDVWFDSAVASWATLNYPRD-RRQLEEWWPADF 553
                                       77777776...45555566778888888763445689*************************99.9*********** PP

                       tRNA-synt_1 520 lleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdv 595
                                       ++eG D++rgW+++ +  s+  +g +P+++vl+hg+++d++G+KmSKs+gNv++p++v+ k gad lRl+++ ++  
  gi|386002467|ref|YP_005920766.1| 554 ITEGHDQTRGWFYSQLGASMVSFGVAPYRSVLMHGFTLDDKGKKMSKSIGNVVQPEEVVGKFGADTLRLYVLsSNAP 630
                                       ***********************************************************************966666 PP

                       tRNA-synt_1 596 grdinl 601
                                        +di++
  gi|386002467|ref|YP_005920766.1| 631 WEDIHF 636
                                       777765 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9   0.0   2.1e-37   7.4e-34       1     150 [.     685     837 ..     685     840 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 2.1e-37
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       drwils+ n+ ++ev++ +e y++++a +al +f+++dl++wy++lv+pr + e++++++  a++++ ev+ tl +l
  gi|386002467|ref|YP_005920766.1| 685 DRWILSRANSMAAEVEAGMETYQLHRATRALADFVLEDLSRWYIQLVRPRTWIETDDPDKLaAYATIMEVMATLAKL 761
                                       9******************************************************999977799************* PP

                       Anticodon_1  77 laPfmPfitEelwqr..eeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkv 150
                                       laPf+Pf++E+++q+  +++  g +es++l +w     +l ++ l e+e+ l++e+v+a+ ++r++ + k +++++ 
  gi|386002467|ref|YP_005920766.1| 762 LAPFAPFTAETIYQNlvRGTDPGAPESVHLHDWHRPRHDLiDEGL-EREMGLVREVVEAVSNARQKGGRKLRWPVSE 837
                                       ****************866667999********964444466666.89******************99999999654 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.5e-10     2e-06       8      64 ..      48     105 ..      43     196 .. 0.86
   2 !   14.2   0.0   3.7e-06     0.013     168     238 ..     398     467 ..     371     477 .. 0.86
   3 !   41.8   0.2   1.5e-14   5.6e-11     244     375 ..     521     645 ..     516     654 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.5e-10
                                       B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HH CS
                      tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpe 64 
                                       pY++g++HlG + + i+ D + Ryk ++g e+   +g D+hG pie+k e++ g + +
  gi|386002467|ref|YP_005920766.1|  48 PYTTGRIHLGTAWNKIIKDSILRYKSMNGFEIKDRAGWDMHGLPIEVKVEEHlGFKSK 105
                                       8***********************************************9875355554 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.7e-06
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       ++  +++  ++  t ++f+k+s++++++ + i++ +       +   ++w++   +d++isr+  wGip+P
  gi|386002467|ref|YP_005920766.1| 398 HCWRCKTPIIFIATPQWFLKISDLREDMLQEIAKVKWYPDWAGSARFRDWISG-ARDWCISRQRYWGIPLP 467
                                       677788888899999**********99999996666555666677889***86.9**************99 PP

  == domain 3  score: 41.8 bits;  conditional E-value: 1.5e-14
                                       EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHH..HHHTHHHHHHHHTT----S-EE CS
                      tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiik..FHtifwPaillgaelklpkkvv 316
                                       v+ VW+d  +   +++++      + ++ +e+W +        fi  g d ++  F +  + a + + ++   ++v 
  gi|386002467|ref|YP_005920766.1| 521 VFDVWFDSAVASWATLNYPR----DRRQLEEWWPA-------DFIteGHDQTRgwFYSQ-LGASMVSFGVAPYRSVL 585
                                       78899999999988888876....56799999*44.......55522555554323333.45666678999999*** PP

                                       EE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1g 317 ahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfverv 375
                                        h++ l  +gkK+SkS g+vv+++e++ ++ ad+lR y+++++   +D++fswe++ +++
  gi|386002467|ref|YP_005920766.1| 586 MHGFtLDDKGKKMSKSIGNVVQPEEVVGKFGADTLRLYVLSSNAPWEDIHFSWEEVANTN 645
                                       ***9456789*********************************************98753 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.25   8.9e+02      21      49 ..      52      80 ..      43      81 .. 0.89
   2 !   21.1   0.0   4.5e-08   0.00016     229     284 ..     572     628 ..     556     646 .. 0.81
   3 ?    1.0   0.0     0.059   2.1e+02     105     137 ..     927     959 ..     901     997 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.25
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                                        +hlG a + ++ D + r+  + g++++
  gi|386002467|ref|YP_005920766.1| 52 GRIHLGTAWNKIIKDSILRYKSMNGFEIK 80
                                      568*****************999999985 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.5e-08
                                       HHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                      tRNA-synt_1e 229 seaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                       s+  f+  ++    +h   l  +g+kmsks++n+++ ++v+ kf + +lRl++ls +
  gi|386002467|ref|YP_005920766.1| 572 SMVSFGvAPYRSVLMHGFTLDDKGKKMSKSIGNVVQPEEVVGKFGADTLRLYVLSSN 628
                                       6677776677788899999999*****************************998764 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-T CS
                      tRNA-synt_1e 105 vdeiielvekliekgyaYavsdgdvyfdvskke 137
                                       ++e++e++ek+ e+  a + s+g+vy dv+ ++
  gi|386002467|ref|YP_005920766.1| 927 LPEMVEFMEKVPENLVAAEFSSGTVYVDVTLTP 959
                                       69*************************997543 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       1.5   5.4e+03      34      53 ..      51      70 ..      40      83 .. 0.73
   2 ?   -3.0   0.1      0.75   2.7e+03     212     227 ..     424     439 ..     420     441 .. 0.81
   3 !   15.7   0.0   1.5e-06    0.0055     269     322 ..     585     639 ..     557     645 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.5
                      tRNA-synt_1f 34 SGliHiGnlrevltadlvar 53
                                       G+iH+G++ + +  d + r
  gi|386002467|ref|YP_005920766.1| 51 TGRIHLGTAWNKIIKDSILR 70
                                      58899998877666666655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.75
                      tRNA-synt_1f 212 diregngKLqWkvdwa 227
                                       d+ +  +K +W  dwa
  gi|386002467|ref|YP_005920766.1| 424 DMLQEIAKVKWYPDWA 439
                                       5667789********9 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.5e-06
                      tRNA-synt_1f 269 vvYelillkggekmssSkGnvltledwlevaepevlrflilrrk.Pkkakkldld 322
                                       ++  + l+++g+kms+S Gnv+ +e+++     ++lr+++l+++ P + ++++ +
  gi|386002467|ref|YP_005920766.1| 585 LMHGFTLDDKGKKMSKSIGNVVQPEEVVGKFGADTLRLYVLSSNaPWEDIHFSWE 639
                                       566788999999*************************999875426666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1051 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.90u 0.35s 00:00:01.25 Elapsed: 00:00:00.55
# Mc/sec: 5786.04
//
Query:       gi|386002468|ref|YP_005920767.1|  [L=153]
Description: hypothetical protein Mhar_1786 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-36  123.1   0.1    5.8e-36  123.0   0.1    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.1   3.3e-40   5.8e-36      10     126 ..      23     138 ..      11     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 3.3e-40
                                       TTTEEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEEEEE CS
                       DNase-RNase  10 ssqspvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtfyAelv 86 
                                       +  +pvvlL++e +r ++p+++g +ea +i  al+g+  pRP+thDL++s+le+lga++  vvI+dle g++yA+l 
  gi|386002468|ref|YP_005920767.1|  23 DLVAPVVLLEDEASR-IVPVFVGLSEAISIYSALSGAVSPRPTTHDLFISTLESLGARIAGVVIDDLEGGVYYARLS 98 
                                       33589********99.************************************************************* PP

                                       EEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-E CS
                       DNase-RNase  87 lrkeeeeleidaRpSDaiaLAlrtgapIyveeevleeasi 126
                                       ++ +++  e+daRpSD +aLAlr++apI ++e+v  ++++
  gi|386002468|ref|YP_005920767.1|  99 VSIDSGVREVDARPSDGMALALRAKAPIAIQERVAVQSAM 138
                                       **965459**************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 814.18
//
Query:       gi|386002469|ref|YP_005920768.1|  [L=1042]
Description: hypothetical protein Mhar_1787 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-62  209.3   0.0    1.3e-61  208.9   0.0    1.2  1  Peptidase_C25   Peptidase family C25
    1.7e-06   28.2   0.0    3.7e-06   27.1   0.0    1.5  1  CARDB           CARDB
    0.00092   18.4   0.0     0.0015   17.6   0.0    1.3  1  Propeptide_C25  Propeptide_C25


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   0.0   2.2e-65   1.3e-61       1     378 []     250     645 ..     250     645 .. 0.82

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 2.2e-65
                                       EEEEE-GGG.....HHHHHHHHHHHHHTTEEEEEEETTSTTT-S.....SHHHHHHHHHHHHHHHHTT--SEEEEES CS
                     Peptidase_C25   1 yliItddel.....saaaerlaefrrskGldvkvvtveeiynefsaGekdaaairnflkyayknwsasklkYllLvG 72 
                                       yliIt + l        +++l+ +++skG+ + +vtve+iy+ + +G +++++irnf+++ay      +  Y+lL+G
  gi|386002469|ref|YP_005920768.1| 250 YLIITNRGLknapvPYNFTDLVRWKSSKGVASTIVTVEDIYSAY-TGADEQEKIRNFIRDAYLYH---GITYVLLGG 322
                                       899999999555555579**************************.9*****************99...899****** PP

                                       -T.................TTS--EE-.......TTT-SEESHHHHS-T......................TSSS-S CS
                     Peptidase_C25  73 dtsivvkv....kspitksdliptyqiaks..lgnestiptDdyyasldgneds.................ddltpd 126
                                       d++            ++ +  +p+   ++   +     ip+D+yya+ldg+ ds                 +dl+ +
  gi|386002469|ref|YP_005920768.1| 323 DAD----GgrkgGEGWNSI--VPARGLWAWdyEATPPMIPSDLYYACLDGDYDSngngiygepedgpgggeVDLMAE 393
                                       **3....243223444444..66666665555445567************9999*********************** PP

                                       SEEEEE--SSHHHHHHHHHHHHHHHCT--S-G....GGGEEEEEE--...................HHTHHHHHHHH CS
                     Peptidase_C25 127 lavGRipvtsaaeaaavvnKiiaYerntengsaagqwrnkvlliagd....vvgew......eaadgneiagttaet 193
                                       ++vGR+pv+s ae++++v K+iaYe+    +   + +++kvll++ +    +v+ w      e++dg + +g  +++
  gi|386002469|ref|YP_005920768.1| 394 VYVGRAPVDSYAELSNFVRKTIAYESV---A--SDPYLEKVLLVGEYlgfgGVSDWggncldEIKDGSGSSGYNTTG 465
                                       *************************87...2..256***********766655555444443333333334444444 PP

                                       HHHTSSGGGT-SEEEEE-SS--.............TTTTHHHHH--SEEEEES-EETTEETTTTEEHHHHHT---TT CS
                     Peptidase_C25 194 tpseynvnklyadlaayeaetetevpaanqpllttqnllkalnqGvlfvnytGHGsetawadeslstndisaltntn 270
                                        p+ y+  +ly+                    +++ +l++ ++  v+ +n++GH s    +  + +++d+ +l+n +
  gi|386002469|ref|YP_005920768.1| 466 FPEDYQKSTLYDR--DRK--------------WDKAELMELIDGDVHSLNHLGHASVG--SAMKMNVEDVGRLKN-D 523
                                       4444444444443..222..............44568*********************..78999**********.7 PP

                                       --EEEEEESSSTT-TTSSS-........-HHHHHHHSTTSSEEEEEEESS---......SS--SHHHHHHHHHHHHH CS
                     Peptidase_C25 271 klpiaitaaCltgafdeetkr.......sfgeklvlnangGavayigatrlgy......sgvndrlsraffealfad 334
                                       + ++ ++++C++g fd+ +++       s+ e++v ++++Ga+a+ig++r+g+      +g ++r++r+f++a+f++
  gi|386002469|ref|YP_005920768.1| 524 RPFFGYSQGCYAGSFDNRDPDsvyspidSILEHFV-TEPHGAFAFIGNSRFGWgrrettDGPSQRYHRQFWDAVFGE 599
                                       8**************999999**************.*****************666554444*************** PP

                                       HH...T-S-SS-HHHHHHH................EEEEE-TT--- CS
                     Peptidase_C25 335 aartlGealllaknelletglaqsi.skgm.nkrtfnllGDPalrl 378
                                         r++G al+ ak ++l ++  ++  +    ++ ++nllGDP+++l
  gi|386002469|ref|YP_005920768.1| 600 GIRNIGRALQDAKEDNLGSIDKTTDgNVMRfCYYEINLLGDPETSL 645
                                       *****************65554444555558***********9875 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   6.2e-10   3.7e-06       4      85 ..     655     735 ..     652     748 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.2e-10
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEE CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtl 80 
                                       L+v     ps + + + +++++ vkN G +++ +++v+l+  + + ++  vp L +g+s++v+++w  + +eg + l
  gi|386002469|ref|YP_005920768.1| 655 LEVAGMDLPSYTKPDKPIEVRAVVKNRGIEDEWNVTVQLVEGDAVRDSEVVPHLPSGGSAEVRLSWSGA-AEGRYIL 730
                                       566666678889999************************998888888889*****************9.*****99 PP

                                       EEEES CS
                             CARDB  81 tvvvD 85 
                                       ++ v 
  gi|386002469|ref|YP_005920768.1| 731 EARVL 735
                                       99875 PP

>> Propeptide_C25  Propeptide_C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-07    0.0015      40     170 ..      64     195 ..      32     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-07
                                       TEEEEEEE-TT-B----TTSB---BEEEEEE--SSEE.EEEEEEEEEEEEE-S--B-B---S-BTTS-GGGS-B-.. CS
                    Propeptide_C25  40 kgvfqrisitegeslsekGepelPilsksiavpetre.akvevvssktetlenvdiaPsksvvveredpekitYv.. 113
                                       +   q i i++ e+   +Gep +P+++  i vp  +e  +++v+  + ++l  ++i P +  +      ++ + v  
  gi|386002469|ref|YP_005920768.1|  64 QNLTQSIRIPGLENRIIPGEPVVPFRTARILVPFGEEiQEIKVLPGEKKNLGKILIEPGQDPLPI--SFSGNRTVtp 138
                                       557899***************************6555167******************9887766..3444444445 PP

                                       --GG.GG--S-BS--SEEE---EEETTEEEEEEEE--EEEETTTTEEEEEEEEEEEE CS
                    Propeptide_C25 114 lndslYsqnkslPseiatlsdpaylRdvrvqevnlaPlqYnPvtkelllykkikvai 170
                                       ln+s Ys  +++P ++ t+         ++  +nl+P+ Y P tk    +    v++
  gi|386002469|ref|YP_005920768.1| 139 LNESTYSSLEPYPRDVFTVAGVQEKQGYKILLINLYPIMYIPKTKDTYYFGTFDVEV 195
                                       9*******************9999999*****************9887776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1042 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.85u 0.36s 00:00:01.21 Elapsed: 00:00:00.55
# Mc/sec: 5690.86
//
Query:       gi|386002470|ref|YP_005920769.1|  [L=255]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-15   55.0   2.7    1.2e-14   54.5   2.7    1.3  1  Beta_helix  Right handed beta helix region
    4.2e-14   52.4   4.6    5.2e-14   52.1   4.6    1.2  1  NosD        Periplasmic copper-binding protein (NosD)
      6e-09   35.6   9.1    7.9e-08   31.9   9.1    2.4  1  DUF1565     Protein of unknown function (DUF1565)


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   2.7     2e-18   1.2e-14      68     157 ..      80     181 ..      19     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2e-18
                                       -............SEEE-TT.--S--EEES-EEES-..SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EE CS
                        Beta_helix  68 n............gggialf.gasnnlienneitdn..ggsGiylnyssnntienNiidnnagsGividdsssnvtv 129
                                       +            g+g a+  +a++ ++e+  + +   g++Gi+++ s+ n i+nN +++n+ +Gi+++ds+ ++++
  gi|386002470|ref|YP_005920769.1|  80 KgsgegrpvidgnGVGSAVLlAADRITLEGFIVKNAgfGKAGIEVK-SDKNFIRNNLVTANRWYGISLSDSQ-ENVI 154
                                       23333333333333555554499999999999999988888**998.89***********************.999* PP

                                       ES-EEES-SSEEEE-TT-SS--EEES-E CS
                        Beta_helix 130 tnNtitnnkgaGiavvgsssnvtvrnNt 157
                                       t+N++++nk +Gi++ ++ss+ t+++N+
  gi|386002470|ref|YP_005920769.1| 155 TGNVVSSNK-YGIWISSGSSSSTIAQNQ 181
                                       ********9.*****************8 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   4.6   8.7e-18   5.2e-14      78     186 ..      89     198 ..      41     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 8.7e-18
                              NosD  78 lssnesGialmsssnn.tlenNtisnnen..yGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqk 150
                                       +++n+ G a+    ++ tle+ +++n     +Gi ++  + n i+nN ++ n  +Gi+l++s++n+itgN ++sn k
  gi|386002470|ref|YP_005920769.1|  89 IDGNGVGSAVLLAADRiTLEGFIVKNAGFgkAGIEVKSDK-NFIRNNLVTaNRWYGISLSDSQENVITGNVVSSN-K 163
                                       5566666655555555477665555554355676666555.4588888888888888888888888888888888.8 PP

                              NosD 151 iGilllsssegntiynNyFinnsenvkydgsnnneW 186
                                       +Gi++ s+s++ ti +N++ +n +  + d++  n W
  gi|386002470|ref|YP_005920769.1| 164 YGIWISSGSSSSTIAQNQLEKNANGNAVDAG-RNGW 198
                                       8888888888888888888666654444333.5555 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   9.1   1.3e-11   7.9e-08      13     192 ..      40     188 ..      28     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.3e-11
                           DUF1565  13 aPfktiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagkkvgplisgggddlsgv 89 
                                         + +i  A+ +a +g++i++  GtY+e+      +++ +   l G  +g G            p+i+g+g      
  gi|386002470|ref|YP_005920769.1|  40 CDYGSIQGAVEAADPGDTITVEGGTYKEN------VIVDKSLVLRGKGSGEGR-----------PVIDGNGVG---- 95 
                                       55667888888888888888888888876......466666666776666666...........889999877.... PP

                           DUF1565  90 qnvtivlaneatiaGvtitNpnilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGnsilfekn 166
                                         + ++ a++ t+ G+ ++N     + g+ ++s    i+nN +t+n   Gi+ s  +      +n+i+Gn + ++k 
  gi|386002470|ref|YP_005920769.1|  96 -SAVLLAADRITLEGFIVKNAGF-GKAGIEVKSDKNFIRNNLVTANRWYGISLSDSQ------ENVITGNVVSSNKY 164
                                       .47999***************55.7889***********************998875......9************* PP

                           DUF1565 167 GiaisgasaavenkienNiivkNliG 192
                                       Gi is  s +  + i +N + kN  G
  gi|386002470|ref|YP_005920769.1| 165 GIWISSGSSS--STIAQNQLEKNANG 188
                                       ****998888..56666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1544.11
//
Query:       gi|386002471|ref|YP_005920770.1|  [L=305]
Description: Ribonuclease Z [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-27   96.1   0.0    1.6e-13   50.7   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    3.6e-15   56.5   0.1    9.8e-13   48.5   0.0    2.4  2  Lactamase_B    Metallo-beta-lactamase superfamily
    8.3e-07   28.6   0.0    1.6e-06   27.7   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.21   11.5   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   3.5e-17   1.6e-13       3     133 ..      32     150 ..      31     158 .. 0.89
   2 !   43.5   0.0   5.5e-15   2.5e-11     132     201 .]     198     267 ..     185     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3.5e-17
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanf 74 
                                       +L+D+g ++  q++ra         + ++d +++th H+DH+ g++ l e   +++++  +++ +p+++++v+e  +
  gi|386002471|ref|YP_005920770.1|  32 LLFDCGEGTQRQMMRAK------TGMMSLDTIFITHHHADHILGIPGLLEtmaFQGRRdpVTIAGPPRTSEVVELFG 102
                                       69******988888886......5688************************996666678***************** PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECT CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegg 133
                                         +   ++++v++ el++g+ ++ +  g ei+a+  +h+ +          lG++++++
  gi|386002471|ref|YP_005920770.1| 103 RLCYYSRKFPVRALELEPGDVLRRD--GYEIEAVRTSHSIPS---------LGYCLRED 150
                                       ********99*************98..799********9998.........67766644 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 5.5e-15
                                       CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir...hmgHltpeeaveaaadlgakrlvliHi 201
                                       ++g++++y+gDt  +p e++e  +gadll++d+ + +   m +   +  H t +ea+++a+++ga+rlvl+Hi
  gi|386002471|ref|YP_005920770.1| 198 RPGRKIVYTGDTRPTP-EVEEASRGADLLIHDGSLDD--GMADwaaETMHTTAGEAARLAERAGARRLVLTHI 267
                                       589**********998.7789***********99554..4556778**************************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   2.2e-16   9.8e-13       3     140 ..      17     146 ..      15     151 .. 0.89
   2 !    5.4   0.1    0.0036        16     141     168 ..     199     225 ..     198     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.2e-16
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       +++ +++li  +g+++L+D+G +t++++++     ++ +   +d++++TH+H+DHi g +gl e+  +  +  + + 
  gi|386002471|ref|YP_005920770.1|  17 ERSPSAVLINREGELLLFDCGEGTQRQMMR-----AKTGMMSLDTIFITHHHADHILGIPGLLETMAFQGRRDPVTI 88 
                                       567899***********************8.....8************************************99998 PP

                                       HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE CS
                       Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey 140
                                       + +++  +  +       l ++s++ p++ +e ++g+++ r ++++    ++++++   ++
  gi|386002471|ref|YP_005920770.1|  89 AGPPRTSEVVELFGR---LCYYSRKFPVRALELEPGDVLRRDGYEIEAVRTSHSIPSLGYC 146
                                       888888886554444...6999*********************999999999998876665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0036
                                       TTCCEEEECTTTSSHHCCCCCC.TTCEE CS
                       Lactamase_B 141 gggkvlftGDallagetgridltlrgae 168
                                       +g+k+++tGD+ +++e ++ ++ + ++ 
  gi|386002471|ref|YP_005920770.1| 199 PGRKIVYTGDTRPTPEVEEASR-GADLL 225
                                       689*************999998.33333 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.5e-10   1.6e-06       6      62 ..      14      68 ..      10      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.5e-10
                     Lactamase_B_4  6 ptsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssig 62
                                      pt++ s + +l++ + +  lf ++gEgtQR ++  k+ +  l+ iF+t+ +  ++i 
  gi|386002471|ref|YP_005920770.1| 14 PTPERSPSAVLINREGELLLF-DCGEGTQRQMMRAKTGMMSLDTIFITHHH-ADHIL 68
                                      67777755555555559999*.***************************99.66665 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05      0.21       8     133 ..      21     226 ..      19     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                     Lactamase_B_3   8 nsflletagarilvDPfka.nlgyeppa....eeaDlvlisqaledHahletlkql..................... 58 
                                       +++l++ +g  +l D +++ + ++ + a     + D + i+++++dH     +++l                     
  gi|386002471|ref|YP_005920770.1|  21 SAVLINREGELLLFDCGEGtQRQMMR-AktgmMSLDTIFITHHHADHIL--GIPGLletmafqgrrdpvtiagpprt 94 
                                       57788888999999988753222222.23566899**********9963..55565566799997777777766555 PP

                     Lactamase_B_3  59 .................aenvkvleegeslevggleiravatsh................................. 85 
                                                          ++  le+g+ l+ +g ei+av+tsh                                 
  gi|386002471|ref|YP_005920770.1|  95 sevvelfgrlcyysrkfPVRALELEPGDVLRRDGYEIEAVRTSHsipslgyclredtrpgrfnrerasalgippgpl 171
                                       55555555555554433333333444888899999999999999888888888888888888888888888888888 PP

                     Lactamase_B_3  86 .........davggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                                 +vgg++ +++ +      g +i++ G++    + e  ++   +D+++
  gi|386002471|ref|YP_005920770.1| 172 fgrlqrggaVEVGGRTVRPEEVMGPPRPGRKIVYTGDTRP--TPEVEEASRGADLLI 226
                                       8877777766667777777777777777888888888775..445555555566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1702.27
//
Query:       gi|386002472|ref|YP_005920771.1|  [L=194]
Description: Two component transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0076   16.3   1.2       0.04   14.0   0.3    2.1  2  Ubiq_cyt_C_chap  Ubiquinol-cytochrome C chaperone


Domain annotation for each model (and alignments):
>> Ubiq_cyt_C_chap  Ubiquinol-cytochrome C chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   0.0    0.0069   1.2e+02      71      94 ..     101     124 ..      71     142 .. 0.82
   2 !   14.0   0.3   2.2e-06      0.04      51     113 ..     123     184 ..     119     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0069
                   Ubiq_cyt_C_chap  71 aeafygrllaydealgsddaaLaa 94 
                                        e +ygr+++  +alg  + +L++
  gi|386002472|ref|YP_005920771.1| 101 SEKMYGRAVSAGRALGLPSHQLER 124
                                       789*************99999986 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.2e-06
                   Ubiq_cyt_C_chap  51 eklreegvgdlsvpkrmkklaeafygrllaydealgsddaaLaaalwrnvykaslevdlekla 113
                                       e+l e gv   ++   +   + a+  ++l+++ al   d++La+ l+r++++++ e++++++a
  gi|386002472|ref|YP_005920771.1| 123 ERLFEAGVNHERRSMDLGRVGYALESVALSLENALIGRDDDLAEGLRRAMVEER-EKTMRRAA 184
                                       67888888888888999999999999****************************.99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1091.96
//
Query:       gi|386002473|ref|YP_005920772.1|  [L=301]
Description: Stationary phase survival protein SurE [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-49  168.9   0.2    1.3e-49  168.7   0.2    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7   0.2   7.1e-54   1.3e-49       1     192 [.      42     236 ..      42     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 7.1e-54
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iL+tNDDG+ ++gira v+ +   g ++ v+aP+ +rSg+g+++++ eplr+++++  ++ e+y+vsGtP+d v ++
  gi|386002473|ref|YP_005920772.1|  42 ILVTNDDGVYSAGIRAAVRGVVGLG-DLLVAAPSGQRSGVGRSISIFEPLRYNKVNL-DGVEAYEVSGTPTDSVIMG 116
                                       8*********************888.*************************996655.9****************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS.....SS-SSS---HHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk.....eeekkeedtfeaaakv 148
                                       +  llk k pdl vSGiN G+N++td+ ++SGT+gAaleaa  gipai  S+++ +     ++ ++++ +f+ a+++
  gi|386002473|ref|YP_005920772.1| 117 IFWLLKGKLPDLAVSGINIGENISTDTvTTSGTIGAALEAASYGIPAITASIQVIDqgdkfDNVNDQAYQFDVASAL 193
                                       ******99*******************9*************************99899999777778888******* PP

                                       HHHHHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCS CS
                              SurE 149 aaklveklieklllekvellnvNvPeleeeeikgvkvtrlgrrr 192
                                       +++++++++e+ l   v++ln+NvP + +ee ++v vtrl+r+ 
  gi|386002473|ref|YP_005920772.1| 194 VRRVAKNVLERGLPAGVDILNLNVPVNATEE-TEVVVTRLARKI 236
                                       *************************443344.447799999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1688.42
//
Query:       gi|386002474|ref|YP_005920773.1|  [L=315]
Description: hypothetical protein Mhar_1792 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1740.62
//
Query:       gi|386002475|ref|YP_005920774.1|  [L=380]
Description: DOMON domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for 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-55  185.0   1.0    1.2e-54  184.6   1.0    1.1  1  DUF2202       Uncharacterized protein domain (DUF2202)
    1.9e-28   99.1   0.0    2.8e-28   98.6   0.0    1.3  1  DOMON         DOMON domain
     0.0085   16.1   0.0      0.013   15.5   0.0    1.2  1  EB_dh         Ethylbenzene dehydrogenase
  ------ inclusion threshold ------
      0.033   14.6   0.8      0.067   13.6   0.8    1.5  1  Rubrerythrin  Rubrerythrin


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.6   1.0   2.6e-58   1.2e-54       1     160 [.     221     379 ..     221     380 .] 0.98

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 2.6e-58
                           DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       e++++l+++eeek+arD+Y elY  +kl++fl++ +seq+h+d+ k+l++kY+l  pv ++  G+f++++l +lY++
  gi|386002475|ref|YP_005920774.1| 221 EAEGVLFIWEEEKVARDLYAELYRATKLEVFLDLERSEQSHMDQAKTLVDKYHLVLPVGDE-PGAFSNQTLIDLYEE 296
                                       67999*****************************************************998.5************** PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseee 154
                                       L+++g +s edaL+v+a +e+++i+Dlek l++ +n+d+  v+++ll+Gsr+hlRs+vr+le++g+ Y pq++se e
  gi|386002475|ref|YP_005920774.1| 297 LLARGMRSEEDALRVAAAFEEISIMDLEKELEVAENEDVRVVFQGLLAGSRKHLRSYVRDLEDMGIMYAPQFLSERE 373
                                       ***************************************************************************** PP

                           DUF2202 155 fdeivs 160
                                       f+++++
  gi|386002475|ref|YP_005920774.1| 374 FEDVMK 379
                                       ***987 PP

>> DOMON  DOMON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   6.4e-32   2.8e-28       3     124 ..      65     183 ..      63     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 6.4e-32
                             DOMON   3 geykvswkvdgdgdeiefelsgkvntngyvaiGfsddgkMsnadvvvgwvdngrvyvqdyystggkgapriddt... 76 
                                       g++++sw+ d  ++ ++++l+g++   g+++iGf + ++M++ad+++g+vd+g+ +v d ystg +g p+ ddt   
  gi|386002475|ref|YP_005920774.1|  65 GDLEISWRSD--QEHLYMALKGRT--EGWISIGFDPLEWMKDADMIMGSVDGGKTTVLDLYSTGRYG-PHEDDTflg 136
                                       678899*999..999******988..5**********************************999999.********* PP

                             DOMON  77 gsqditllsgseengvttlkfrRkldtcdpkqdnkidldttvyviwaa 124
                                       g+ di    gsee+g+t ++f+Rkldt+d+  d+ + ++++v+viwa+
  gi|386002475|ref|YP_005920774.1| 137 GTYDILEFAGSEEDGYTVIEFKRKLDTGDE-FDKLLEPGESVSVIWAM 183
                                       *****************************9.****************8 PP

>> EB_dh  Ethylbenzene dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.8e-06     0.013     159     232 ..     100     179 ..      58     189 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                                       ........................................---EEEEEEETTEEEEEEEEES---TTS..---TTEE CS
                             EB_dh 159 ekdepaamf.skegfradd.enesvpfdp....ewkegdtadvkaeakykdGkWtVelvRpLkagnpldvalepgkv 229
                                        kd    m+ ++ g++++   ++++ + p    ++  g+   ++  ++ +dG+ ++e++R+L++g+++d+ lepg++
  gi|386002475|ref|YP_005920774.1| 100 MKDADMIMGsVDGGKTTVLdLYSTGRYGPheddTFLGGTYDILEFAGSEEDGYTVIEFKRKLDTGDEFDKLLEPGES 176
                                       444444455655555555554444444443333333344355566677788888889******************** PP

                                       EEE CS
                             EB_dh 230 ydv 232
                                       ++v
  gi|386002475|ref|YP_005920774.1| 177 VSV 179
                                       998 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   1.5e-05     0.067      10     133 ..     232     353 ..     229     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH CS
                      Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe 86 
                                       E  ar lY el++ +k       e+F++l + E+ H +  + l++k+ + l +    +  +++  ++ + ++++ L 
  gi|386002475|ref|YP_005920774.1| 232 EKVARDLYAELYRATK------LEVFLDLERSEQSHMDQAKTLVDKYHLVLPV---GDEPGAFSNQTLIDLYEELLA 299
                                       788999**********......68**********************9998883...444444444555555555555 PP

                                       .......HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  87 .......eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerl 133
                                              +a++ a a ee ++  +e+++e ++ne+++ +f+ l    +kH +++
  gi|386002475|ref|YP_005920774.1| 300 rgmrseeDALRVAAAFEEISIMDLEKELEVAENEDVRVVFQGLLAGSRKHLRSY 353
                                       66666669************************************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2202.12
//
Query:       gi|386002476|ref|YP_005920775.1|  [L=91]
Description: hypothetical protein Mhar_1794 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-10   39.5   1.1    5.8e-10   39.3   1.1    1.1  1  2TM       2TM domain
     0.0041   17.1   3.9      0.005   16.9   3.9    1.1  1  CrgA      Cell division protein CrgA


Domain annotation for each model (and alignments):
>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   1.1   6.4e-14   5.8e-10       6      54 ..      15      73 ..      10      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.4e-14
                               2TM  6 rvkeikgFyrhlvvYlivniflilinl.........gsswflw.pilfWgiglllhalk 54
                                      +++++k F +hl++Yl+vni+ ++in+            w  w   ++Wg+ +++h++ 
  gi|386002476|ref|YP_005920775.1| 15 QARMKKLFMTHLIIYLVVNIVWLAINYmmvmpanpnLPIWQPWySPIGWGLCIVIHYMT 73
                                      67899*********************999999999844444443779**********96 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.9   5.6e-07     0.005      22      84 ..      10      73 ..       2      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.6e-07
                              CrgA 22 vkakaakpsprwyvpvmlglmllGllwlvvyYlage.eipfmaelgawNlliGfgliivGllmt 84
                                       +++ +++ ++++++ ++  +++ ++wl ++Y++     p +  ++ w   iG gl iv   mt
  gi|386002476|ref|YP_005920775.1| 10 FRTAMQARMKKLFMTHLIIYLVVNIVWLAINYMMVMpANPNLPIWQPWYSPIGWGLCIVIHYMT 73
                                      45556778889999999999************99885567899***************988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 526.37
//
Query:       gi|386002477|ref|YP_005920776.1|  [L=219]
Description: Peroxiredoxin, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-30  105.4   0.0    2.5e-30  104.9   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    2.6e-11   43.2   0.1    5.2e-11   42.2   0.1    1.6  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
    6.2e-11   42.2   0.0    1.2e-10   41.3   0.0    1.4  2  Redoxin     Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   4.2e-34   2.5e-30       2     123 ..      13     140 ..      12     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 4.2e-34
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                       g+++pd+e+++++g+ +  +d++gk+ +lf +p+d++pvCtte  a++k+ +ef+++++ ++g+s+d+++sh k+ e
  gi|386002477|ref|YP_005920776.1|  13 GERVPDMEVQTTHGRMKIPADLSGKWFILFSHPGDFTPVCTTEFIAFQKMKKEFDDLNCALVGLSMDQVHSHMKWTE 89 
                                       899**********999999********************************************************** PP

                                       H-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  79 kes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                        ++      ++fp+++D +g+va ++g++++   + ++ra+fv+d++g ir 
  gi|386002477|ref|YP_005920776.1|  90 WIQekmdvkITFPIIAD-NGTVAGKLGMVHPGkGTNTVRAVFVVDPNGLIRL 140
                                       *****************.9**********999777899***********995 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   8.8e-15   5.2e-11       1      35 [.     161     199 ..     161     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 8.8e-15
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavk 35 
                                       ALQ +dk++va PAnW p     Gd+vi+pPp++e+ a  
  gi|386002477|ref|YP_005920776.1| 161 ALQISDKNKVALPANW-PnndlfGDEVIIPPPSDEKTAAT 199
                                       9***************.99****************98865 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0     2e-14   1.2e-10       3     130 ..      13     141 ..      11     156 .. 0.83
   2 ?   -3.0   0.0      0.91   5.5e+03      85     102 ..     186     203 ..     174     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2e-14
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...H CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...v 76 
                                       g+++Pd + ++  t+g     +++ gk  ++++ pg f+P+C++e ++++k ++++ + +   v++++d+       
  gi|386002477|ref|YP_005920776.1|  13 GERVPDMEVQT--THGRMKIPADLSGKWFILFSHPGDFTPVCTTEFIAFQKMKKEFDDLNCALVGLSMDQVHShmkW 87 
                                       8999**99877..9999999999***********************************************9995554 PP

                                       HHHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEE CS
                           Redoxin  77 kefwgk...eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvyl 130
                                       +e++ +    +++fp+++D  + ++ +lG+    +  +g    ++++v+d +g ++ +
  gi|386002477|ref|YP_005920776.1|  88 TEWIQEkmdVKITFPIIADN-GTVAGKLGMV--HPG-KGtNTVRAVFVVDPNGLIRLM 141
                                       44554498877788889996.99******55..433.33369***********88755 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.91
                                       -TSEEEE-TTSHHHHHTT CS
                           Redoxin  85 lkfpvlsDgsaaftkalG 102
                                       + +p  sD++ a t++ G
  gi|386002477|ref|YP_005920776.1| 186 VIIPPPSDEKTAATRKTG 203
                                       567778999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1239.31
//
Query:       gi|386002478|ref|YP_005920777.1|  [L=201]
Description: membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-06   28.9  21.5    4.9e-05   23.5   7.4    2.5  3  DUF4079         Protein of unknown function (DUF4079)
    7.4e-06   26.1   6.6    6.1e-05   23.2   7.1    1.9  2  Cytochrom_B561  Eukaryotic cytochrome b561
     0.0034   17.6   9.7       0.13   12.4   2.5    2.1  2  DUF2306         Predicted membrane protein (DUF2306)
  ------ inclusion threshold ------
      0.036   14.4   4.0       0.07   13.4   4.0    1.4  1  DUF420          Protein of unknown function (DUF420)
        1.8    8.3  10.3         24    4.7  10.3    2.2  1  DUF2157         Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2      0.01        36     100     131 ..      57      92 ..      46      97 .. 0.64
   2 !   18.2   6.1     6e-07    0.0021      57     135 ..      80     159 ..      70     164 .. 0.81
   3 !   23.5   7.4   1.4e-08   4.9e-05      48     139 ..     104     199 ..      96     201 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.01
                           DUF4079 100 alvpeiqkgks..taR..tlHialnvlalllfawqa 131
                                       al+++ ++g s   aR    H++l vla+ll++w +
  gi|386002478|ref|YP_005920777.1|  57 ALATSPNQGLSseIARlaPYHASLAVLAFLLLVWGM 92 
                                       44444444433325662246*************965 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6e-07
                           DUF4079  57 llllvvlgaigglvllylrrgklfpssHlyaGlavvvLlalsaalvpeiqkgks..taRtlHialnvlalllfawqa 131
                                       l +l++l+++ g+  +  r+g  +   H + G+  ++L + ++a++  + +  s   +R  H++l+++++ll+++  
  gi|386002478|ref|YP_005920777.1|  80 LAVLAFLLLVWGMT-VARRKGPGWLKKHRILGISGAALAVSAMAVAAYMVSAASqeHLRVPHAYLGSFIVLLLIVNP 155
                                       55666666666664.4578889***********9999999999988888766554589*****************99 PP

                           DUF4079 132 itGl 135
                                       + G+
  gi|386002478|ref|YP_005920777.1| 156 LLGF 159
                                       9987 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 1.4e-08
                           DUF4079  48 deHvklgslllllvvlgaigglvllylrrgklfpssHlyaGlavvvLlals...aalvpeiqkgks.taRtlHialn 120
                                       ++H  lg    +l+v +++++  ++ +  ++ + ++H y G  +v+Ll+++    +++  + ++   ++R++H  l+
  gi|386002478|ref|YP_005920777.1| 104 KKHRILGISGAALAVSAMAVAAYMVSAASQEHLRVPHAYLGSFIVLLLIVNpllGFIQLRVGTDLGrRMRRVHRFLG 180
                                       789999999999999999999999999999********************933223455555565568********* PP

                           DUF4079 121 vlalllfawqaitGlrill 139
                                        +alll+a+ ++ G+ i+ 
  gi|386002478|ref|YP_005920777.1| 181 RAALLLMALNILFGMIIVG 199
                                       ***************9985 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.054   1.9e+02     106     123 ..      72      89 ..      48     102 .. 0.66
   2 !   23.2   7.1   1.7e-08   6.1e-05      17     130 ..      81     195 ..      76     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHHH CS
                    Cytochrom_B561 106 lllplHvllGlvifvlai 123
                                       +l p+H+ l +++f+l +
  gi|386002478|ref|YP_005920777.1|  72 RLAPYHASLAVLAFLLLV 89 
                                       455666666666666543 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.7e-08
                                       HHTHHH.HS-.S...-HH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--SS-SHHHHHHHHHHHHHHHHHHH CS
                    Cytochrom_B561  17 aiLvyr.vss.trklskk..tkkllHlilqllalilavvgllavfksknekeianlyslHswlGlvtvilfllqlvl 89 
                                       a+L++   ++ +   ++k   +   H il + + +lav +++++ +  +++  ++l   H++lG   v+l++++ +l
  gi|386002478|ref|YP_005920777.1|  81 AVLAFLlLVWgMTVARRKgpGWLKKHRILGISGAALAVSAMAVAAYMVSAASQEHLRVPHAYLGSFIVLLLIVNPLL 157
                                       4555554444433334431134566999999999999999999999999999************************* PP

                                       HHHHHTSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Cytochrom_B561  90 GfvlfllpklskklralllplHvllGlvifvlaivtallGl 130
                                       Gf+ +    + ++l ++++++H++lG ++++l  +++l G+
  gi|386002478|ref|YP_005920777.1| 158 GFIQLR---VGTDLGRRMRRVHRFLGRAALLLMALNILFGM 195
                                       ***987...66778999*********************999 PP

>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.5   3.7e-05      0.13      67     144 ..      78     155 ..      46     158 .. 0.74
   2 !   10.7   1.5   0.00013      0.46       7      49 ..     150     194 ..     146     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                           DUF2306  67 lllallwlvftvlalvairrrd...faaHrawmirsYalalaavtlrlvllvlillvgedfetayavlsllawvpnl 140
                                       + la+l ++ +v++++ +rr+    +++Hr   i+ +ala++a+  +++++++     ++  ++++   +  +v +l
  gi|386002478|ref|YP_005920777.1|  78 ASLAVLAFLLLVWGMTVARRKGpgwLKKHRILGISGAALAVSAMAVAAYMVSAAS---QEHLRVPHAYLGSFIVLLL 151
                                       4588999999999999999998888999999999999999999999999777766...4444555555555555555 PP

                           DUF2306 141 vvae 144
                                       +v  
  gi|386002478|ref|YP_005920777.1| 152 IVNP 155
                                       5555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                           DUF2306   7 lalvalllGalqlv..krlrakrpklHrlaGrvyvlavllaalsg 49 
                                       l +v  llG +ql   + l ++ +++Hr +Gr+ +l++ l  l g
  gi|386002478|ref|YP_005920777.1| 150 LLIVNPLLGFIQLRvgTDLGRRMRRVHRFLGRAALLLMALNILFG 194
                                       556778999999972245667799***********9998876666 PP

>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.0     2e-05      0.07       3     128 ..      75     197 ..      73     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                            DUF420   3 alnavlnalaavllllglvaikk...gkieaHrklmll..afvlsalFlvlYllkhalagetkfggpeeegvirpvY 74 
                                         +a+l +la++ll++g+ ++++   g  ++Hr l ++  a+++sa+ ++ Y++  a +++ +         + ++Y
  gi|386002478|ref|YP_005920777.1|  75 PYHASLAVLAFLLLVWGMTVARRkgpGWLKKHRILGISgaALAVSAMAVAAYMVSAASQEHLR---------VPHAY 142
                                       5689999***************96666799***987651155555566666666655553333.........67788 PP

                            DUF420  75 laiLitHivLavvvvplvlvtlvlalkg...kfekHrkiaritvpiwlyvavtGvvv 128
                                       l  +i  ++L +v+  l +++l  +        + Hr ++r ++ ++ + ++ G+++
  gi|386002478|ref|YP_005920777.1| 143 LGSFI--VLLLIVNPLLGFIQLRVGTDLgrrMRRVHRFLGRAALLLMALNILFGMII 197
                                       77666..4566677777777777777656656778**********999999999886 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  10.3    0.0067        24      73     114 ..     115     199 ..      56     201 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0067
                           DUF2157  73 llllslllgavlwrdr.................................................rvpprlgealll 100
                                       +l++s++++      +                                                 rv+++lg+a+ll
  gi|386002478|ref|YP_005920777.1| 115 ALAVSAMAV------AaymvsaasqehlrvphaylgsfivlllivnpllgfiqlrvgtdlgrrmrRVHRFLGRAALL 185
                                       222222222......022222235677788888888888888888888888888888999***************** PP

                           DUF2157 101 laalllgaaialvg 114
                                       l al ++ ++++vg
  gi|386002478|ref|YP_005920777.1| 186 LMALNILFGMIIVG 199
                                       *******9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1139.23
//
Query:       gi|386002479|ref|YP_005920778.1|  [L=158]
Description: Integral membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-48  162.4  14.4    6.4e-48  162.2  14.4    1.0  1  TspO_MBR  TspO/MBR family


Domain annotation for each model (and alignments):
>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.2  14.4   3.6e-52   6.4e-48       4     135 .]      14     156 ..      11     156 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 3.6e-52
                                       HHHHHHHHHHHHHHHCCH.HHHHHS---TTS--HHHHTTHHHHHHHHHHHHHHHHHHH..........HHHHHHHHH CS
                          TspO_MBR   4 alpllvgllgglftksee.ewykslrkPpwaPpdwvfppvWtvlyilmgvaaylvwka..........lalyavqlv 69 
                                       + ++l++++g+lft  ++ +wy++l +P +aPpdwvf+pvWt+ly++mg++aylvw++          ++++++ql+
  gi|386002479|ref|YP_005920778.1|  14 GGCYLAAAIGSLFTTPNIpTWYATLSRPDFAPPDWVFGPVWTALYTMMGISAYLVWREgladpgvraaMGVFVLQLA 90 
                                       568899*********9999*************************************************99******* PP

                                       HHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHCHHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  70 lnllwsplffglkspvlalvdivallglvvalilafskvdklaallllpyllWllfatylnasiwr 135
                                       +n++ws +ffgl+sp+++l++i++l+gl+++ i +f+ ++++a++ll+pyllW++fa++ln++iwr
  gi|386002479|ref|YP_005920778.1|  91 FNVSWSAAFFGLRSPLAGLAVIIILWGLIALNIQRFRGISRTAGALLIPYLLWVSFAAVLNFEIWR 156
                                       *****************************************************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 943.93
//
Query:       gi|386002480|ref|YP_005920779.1|  [L=381]
Description: hypothetical protein Mhar_1798 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-05   23.9   0.0    0.00099   19.4   0.0    2.2  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.018   15.1   0.0        4.2    7.4   0.0    2.3  2  Glyoxalase_3  Glyoxalase-like domain
        0.2   11.6   0.0        0.3   10.9   0.0    1.3  1  DUF829        Eukaryotic protein of unknown function (DUF829)


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.034     2e+02      34      98 ..      90     162 ..      69     171 .. 0.67
   2 !   19.4   0.0   1.7e-07   0.00099       8      97 ..     231     330 ..     223     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.034
                                       TTTTEEEEEEEETTEEEEEEEESSTT.-THHH.........TS-EEEEEEEEES-HHHHHHHHCTTTEEEEEEEE CS
                      Glyoxalase_4  34 qevdlafallgsgsvqieLieplegp.eflae.........hgeglhhlaywvddldaavarleeqGfevvqkgv 98 
                                       q+++  +   gs    i + + l g+  fl++           + l  l ++++d+++ +   +++G+++++++ 
  gi|386002480|ref|YP_005920779.1|  90 QSMTAVLSNEGS--SDILVRSRLGGDnPFLRHnlhpksghlPNTRLETLVFRTKDIEELISIQRSRGVSFLSEDM 162
                                       555444444444..456666666655455555666677777888899999******************9998763 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.7e-07
                                       S-HHHHHHHHHH.TT-EESS--E.EE..........TTTTEEEEEEEETTEEEEEEEESSTT..-THHHTS-EEEEE CS
                      Glyoxalase_4   8 eDleaavarfsallGvgpwqryrdep..........qevdlafallgsgsvqieLieplegp..eflaehgeglhhl 72 
                                       eD  aa+++f  l ++ +   + +++          ++ + a++++++ s+++   e ++gp  +f+++ g+ +hhl
  gi|386002480|ref|YP_005920779.1| 231 EDRAAAMKEFLSLTNYCFDFAIYVRElnsitsvarfEGSKFAMVFTSGISPYVS--EEISGPteKFVHNYGARVHHL 305
                                       799999999999999887644444431111111111122334444444335554..5555556699*********** PP

                                       EEEES-HHHHHHHHCTTTEEEEEEE CS
                      Glyoxalase_4  73 aywvddldaavarleeqGfevvqkg 97 
                                       a+ ++++++++ +l   G+e++ + 
  gi|386002480|ref|YP_005920779.1| 306 AFQTEEIEETCSSLIGDGIEFLIAL 330
                                       *******************998654 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00071       4.2      76     129 ..     131     189 ..     108     241 .. 0.68
   2 ?    5.4   0.0    0.0029        17      73     101 ..     297     325 ..     279     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00071
                      Glyoxalase_3  76 eglhtlalrtddidataarlraaGvdeagrrvrpdggdlrwrllfladealpa......e 129
                                        +l tl++rt+di+++    r++Gv+ ++++   +g   ++ ++++++ +  +      +
  gi|386002480|ref|YP_005920779.1| 131 TRLETLVFRTKDIEELISIQRSRGVS-FLSEDMIEGDNCAFIQTVPSKYTGNSigfierG 189
                                       6899********************96.777666677778888888877432224455554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0029
                      Glyoxalase_3  73 akgeglhtlalrtddidataarlraaGvd 101
                                       ++g ++h+la++t++i++t   l   G++
  gi|386002480|ref|YP_005920779.1| 297 NYGARVHHLAFQTEEIEETCSSLIGDGIE 325
                                       5799***************9999988876 PP

>> DUF829  Eukaryotic protein of unknown function (DUF829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.1e-05       0.3     194     236 ..     139     181 ..     135     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                            DUF829 194 swrdveshaeeaeqrgvkvtakkfedspHvahmrkhperYvek 236
                                       + +d+e++++ +++rgv+  +++    +++a ++  p +Y+ +
  gi|386002480|ref|YP_005920779.1| 139 RTKDIEELISIQRSRGVSFLSEDMIEGDNCAFIQTVPSKYTGN 181
                                       679*************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2298.36
//
Query:       gi|386002481|ref|YP_005920780.1|  [L=390]
Description: Transporter, major facilitator family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-38  132.8  45.2    1.9e-19   69.8  13.5    2.1  2  MFS_1       Major Facilitator Superfamily
    7.7e-10   38.2  17.8      1e-06   27.9   0.2    2.1  2  Sugar_tr    Sugar (and other) transporter
    7.1e-05   21.8  14.7    0.00067   18.6   8.7    2.5  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
        1.1    7.6  25.6        0.1   11.0  10.0    4.2  4  MFS_3       Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8  13.5   4.2e-23   1.9e-19       2     179 ..      20     195 ..      19     233 .. 0.88
   2 !   65.3  27.7     1e-21   4.5e-18      15     173 ..     228     382 ..     212     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 4.2e-23
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.l 76 
                                        l+ +l+ +++ i+ p+lpl    +lg+ + +igl+ +l   + +++ l+ G++sdr+G+r+ ++ +g+ l+a+g l
  gi|386002481|ref|YP_005920780.1|  20 GLVSLLNDASSEIIQPILPL-FIASLGAGGLAIGLIGGLADGLPSLFKLLSGYWSDRMGARKpLVAAGYSLSAAGkL 95 
                                       57889999***********5.5589**************9999*******************9************55 PP

                             MFS_1  77 llllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWr 151
                                       ll+l  s  w  ++vl vl   g g+  +   a+ia+ +++e rgr++g+  a  s+Ga++g +l+ ll  +   +r
  gi|386002481|ref|YP_005920780.1|  96 LLAL--SATWqQVFVLKVLERSGKGIRSAPRDAIIAESASREGRGRGFGVHRALDSFGAVVGSALAYLLWqAGMDFR 170
                                       5555..66777***********************************************************44555** PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepper 179
                                        +f+++++v++la++    l+p+++ +r
  gi|386002481|ref|YP_005920780.1| 171 TIFLVAGAVAFLALL---PLVPVREGRR 195
                                       *************77...5555554444 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 1e-21
                             MFS_1  15 lgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllv 90 
                                       ++++  + + + dl     +  ll+ l+ l++ ++s+p G++sdr+Gr++vl lg+llfa+++l ++++ss ++l++
  gi|386002481|ref|YP_005920780.1| 228 FFILRAQgFFSGDLA--IGAPILLYILFNLVYTIFSIPSGAWSDRVGRKKVLTLGYLLFAVTSLGFALVSSAPVLIL 302
                                       444445555566644..4444579999***********************************66666658888**** PP

                             MFS_1  91 lrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                       l vl Gl  +++  a  al++d+   e rg ++g ++a+++++ai   l++g+l + +g +a+f++ a++++ a vl
  gi|386002481|ref|YP_005920780.1| 303 LFVLYGLVFALVDGAERALVSDLCGAEARGTGLGAYYAAVGVAAIASGLVAGALWQGIGPEATFLFGAAAAVAASVL 379
                                       **************************************************************************994 PP

                             MFS_1 168 fllllp 173
                                           ++
  gi|386002481|ref|YP_005920780.1| 380 ---IMR 382
                                       ...443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   2.3e-10     1e-06      64     190 ..      67     189 ..      65     195 .. 0.89
   2 !   13.3  12.4     6e-06     0.027     287     431 ..     244     378 ..     209     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.3e-10
                                       HHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHH CS
                          Sugar_tr  64 lfagllgdrfGRkkslli.aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgal 139
                                       l++g+++dr+G +k l++ +  l+ +g +l a++    ++++++v +vl   g G+ s+     i+E A  + Rg+ 
  gi|386002481|ref|YP_005920780.1|  67 LLSGYWSDRMGARKPLVAaGYSLSAAGKLLLALSA---TWQQVFVLKVLERSGKGIRSAPRDAIIAESASREGRGRG 140
                                       689********999998857789999*********...9************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                          Sugar_tr 140 vslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllf 190
                                        +++    +fG +v++ + + l +   +   +r  + ++ + a l l+ l+ 
  gi|386002481|ref|YP_005920780.1| 141 FGVHRALDSFGAVVGSALAYLLwQAGMD---FRTIFLVAGAVAFLALLPLVP 189
                                       **********************666666...999999999999666655555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6e-06
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHH CS
                          Sugar_tr 287 sksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialf 363
                                         ++l  i++  v +++++ +   +dr+GR+++l lG +  a+  + +     +lv++    + v+i +++l+  +f
  gi|386002481|ref|YP_005920780.1| 244 GAPILLYILFNLVYTIFSIPSGAWSDRVGRKKVLTLGYLLFAVTSLGF-----ALVSS----APVLILLFVLYGLVF 311
                                       55567778888888888888889**************98877766555.....47777....69************* PP

                                       HTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHH CS
                          Sugar_tr 364 algwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfii 431
                                       al  g     lvs+l   + R+++l   +a+  +a ++ +l+   + + ig   +fl+ a+ av++ +
  gi|386002481|ref|YP_005920780.1| 312 ALVDGAER-ALVSDLCGAEARGTGLGAYYAAVGVAAIASGLVAGALWQGIGPEATFLFGAAAAVAASV 378
                                       *9998888.788***************************************77777777777766554 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0015       6.8      17      80 ..      32      95 ..      19     106 .. 0.88
   2 !   18.6   8.7   1.5e-07   0.00067     280     385 .]     264     368 ..     210     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0015
                        MFS_1_like 17 sllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80
                                       ++P l +++ s g     ig+i  ++  +  l +++ g  +Dr+g+rk++v+++  lsa+  l
  gi|386002481|ref|YP_005920780.1| 32 IIQPILPLFIASLGAGGLAIGLIGGLADGLPSLFKLLSGYWSDRMGARKPLVAAGYSLSAAGKL 95
                                      578999999999999999************************************9999987666 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.5e-07
                        MFS_1_like 280 aeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsg 356
                                       +  + +++G  k+l+++ l+++++ l+ a++++a +++++ vL+g+ f+l+ +a    vs++ + ++++tg g + +
  gi|386002481|ref|YP_005920780.1| 264 SGAWSDRVGRKKVLTLGYLLFAVTSLGFALVSSAPVLILLFVLYGLVFALVDGAERALVSDLCGAEARGTGLGAYYA 340
                                       567789*********************************************************************98 PP

                        MFS_1_like 357 lyfglGralGsliGGllwdlksaiflFra 385
                                       + +g+      l++G+lw+  ++  +F +
  gi|386002481|ref|YP_005920780.1| 341 A-VGVAAIASGLVAGALWQGIGPEATFLF 368
                                       8.6777777778899*******9999976 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1    0.0045        20      38     107 ..      42     112 ..      36     134 .. 0.77
   2 ?    0.8   0.8     0.028   1.3e+02     226     245 ..     170     189 ..     164     201 .. 0.81
   3 ?   -0.2   0.1     0.055   2.4e+02     156     184 ..     203     231 ..     195     234 .. 0.85
   4 ?   11.0  10.0   2.2e-05       0.1      58     188 ..     257     382 ..     251     389 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0045
                             MFS_3  38 tdisasplmvAlvq.aaatLPifllsilaGalaDnfdrRkvlla.vqlllalvsvlltvlaalgllspwlll 107
                                       +++ a  l++ l+   a  LP  l+ +l+G  +D +  Rk l+a +++l a++ +ll+++a+ + + +  +l
  gi|386002481|ref|YP_005920780.1|  42 ASLGAGGLAIGLIGgLADGLPS-LFKLLSGYWSDRMGARKPLVAaGYSLSAAGKLLLALSATWQQVFVLKVL 112
                                       5666666677777524667886.689**********999988752678888888889888887776665554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.028
                             MFS_3 226 RaalFglsasavlaLLPlva 245
                                       R++   + a a laLLPlv 
  gi|386002481|ref|YP_005920780.1| 170 RTIFLVAGAVAFLALLPLVP 189
                                       6666678899********94 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.055
                             MFS_3 156 PAlgGvlvaavGaalafavnalsylaliv 184
                                       P l+  +v +vG a  fa+   sy++ i+
  gi|386002481|ref|YP_005920780.1| 203 PRLSPEIVPFVGVASLFALGNCSYMFFIL 231
                                       666777999****************9985 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 2.2e-05
                             MFS_3  58 ifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkr 134
                                         ++si++Ga +D + r+kvl  ++ll a++s+  ++++     +p+ l+ l +l g+ +al d a +A v++l  +
  gi|386002481|ref|YP_005920780.1| 257 YTIFSIPSGAWSDRVGRKKVLTLGYLLFAVTSLGFALVSS----APV-LILLFVLYGLVFALVDGAERALVSDLCGA 328
                                       5689************************999987776653....344.45556788999****************99 PP

                             MFS_3 135 rdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallr 188
                                       +   +        + +a  +   ++G l   +G+ ++f + a + +a  v ++r
  gi|386002481|ref|YP_005920780.1| 329 EARGTGLGAYYAAVGVAAIASGLVAGALWQGIGPEATFLFGAAAAVAASVLIMR 382
                                       9888777666666666666777899************99998888777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2101.42
//
Query:       gi|386002482|ref|YP_005920781.1|  [L=511]
Description: hypothetical protein Mhar_1800 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-38  131.6   0.0    6.7e-38  131.0   0.0    1.2  1  DUF87            Helicase HerA, central domain
    2.4e-05   23.2   0.0       0.05   12.2   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
      7e-05   21.9   0.0     0.0067   15.4   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.002   17.1   0.0     0.0048   15.9   0.0    1.6  2  AAA_10           AAA-like domain
     0.0096   14.8   0.0      0.014   14.2   0.0    1.2  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
  ------ inclusion threshold ------
      0.045   13.7   0.0       0.11   12.5   0.0    1.6  2  ResIII           Type III restriction enzyme, res subunit
      0.056   13.6   0.0       0.13   12.4   0.0    1.7  1  HAS-barrel       HAS barrel domain
       0.12   12.1   0.0          1    9.1   0.0    2.1  2  DEAD             DEAD/DEAH box helicase
       0.13   12.6   0.0        6.3    7.1   0.0    2.4  2  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.0   3.4e-41   6.7e-38       2     225 ..     111     326 ..     110     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 3.4e-41
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkv 78 
                                       +iG l +g +++v+ld++ lv++H+ il++TGsGKS+t+av leell +kg+ +li+DpHGEY+++++k+ ++++  
  gi|386002482|ref|YP_005920781.1| 111 YIGLL-EGHDLKVKLDADALVQKHCSILAKTGSGKSYTAAVVLEELL-EKGVALLIIDPHGEYASMKQKNSKGEFAR 185
                                       68877.99***************************************.*******************6666666666 PP

                             DUF87  79 itpspsa................kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklss 139
                                       +++sp                   d++l++n ++l+ +e+  +l+e   + ++ qr vl+ea++ ++   e +++  
  gi|386002482|ref|YP_005920781.1| 186 FDVSPRGydvtvyspassaaaphADRPLRFNGRNLTAREISAMLPE---DVTNSQRGVLYEAIKVLE--AEGGDYGL 257
                                       66665556666666666669**************************...66677**********998..99999999 PP

                             DUF87 140 depveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaq 216
                                       +e+++           +++k++++a+++l+ +le l + g++   ++t l +ll     + g+ +iid+ gv+ + q
  gi|386002482|ref|YP_005920781.1| 258 EEIIA-----------QAEKDSSKAKWGLIGHLEALADLGIFS-GKPTGLGDLL-----QRGRASIIDMTGVPPDLQ 317
                                       99999...........4678888********************.**********.....****************** PP

                             DUF87 217 qlvvsvilr 225
                                        ++v+ +l 
  gi|386002482|ref|YP_005920781.1| 318 GMIVAKLLS 326
                                       **9999986 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   2.5e-05      0.05      18      69 ..     128     179 ..     116     252 .. 0.86
   2 !    9.1   0.0   0.00022      0.43     284     353 ..     364     431 ..     300     464 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                            DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGe 69 
                                       +l+ +h  i   tG Gk  t  v+ e+l e Gv+ ++ d  G+ +++ +  +
  gi|386002482|ref|YP_005920781.1| 128 ALVQKHCSILAKTGSGKSYTAAVVLEELLEKGVALLIIDPHGEYASMKQKNS 179
                                       46789*************************************9999877654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00022
                            DUF853 284 vvrLi....rskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaite 353
                                       v+r i    r  G G+  ++q P+ + ++v++q  +  q  lr   p+d +a+ + ++++ ++    +ee i+ 
  gi|386002482|ref|YP_005920781.1| 364 VIRTIaaegRKFGLGLLVISQRPARVDKNVISQCNT--QIILRVTNPNDLRALSKGIEGMSSE----LEEEIKR 431
                                       4444422226679********************876..558*************999999764....4444444 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.4e-06    0.0067      14      57 ..     130     173 ..     122     180 .. 0.92
   2 !    4.1   0.0    0.0087        17     261     322 ..     365     418 ..     361     436 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-06
                     TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGafvs 57 
                                        ++h  i+  tGsGK+ ++   l+++ ++g   +++D++G++ s
  gi|386002482|ref|YP_005920781.1| 130 VQKHCSILAKTGSGKSYTAAVVLEELLEKGVALLIIDPHGEYAS 173
                                       689**************************************976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0087
                     TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsell 322
                                       + +++aegRkfG  + +  q  a++         ++++s +nt++ilrv++ +    ls+ +
  gi|386002482|ref|YP_005920781.1| 365 IRTIAAEGRKFGLGLLVISQRPARVD--------KNVISQCNTQIILRVTNPNDLRALSKGI 418
                                       56778888888877777777777775........5799999******999887777766665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.4e-06    0.0048      22      80 ..     132     188 ..     123     289 .. 0.60
   2 ?   -3.6   0.0         2     4e+03     265     292 ..     368     395 ..     362     429 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtL 80 
                                        ++ i+ ++G GKS++a ++   ++  g  +liiDp  e   +k++    ++++ + ++
  gi|386002482|ref|YP_005920781.1| 132 KHCSILAKTGSGKSYTAAVVLEELLEKGVALLIIDPHGEYASMKQKNS--KGEFARFDV 188
                                       689999*********************************666555432..244444444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                            AAA_10 265 lvRiGRsynaavylvtqsadDvlkeelk 292
                                       +   GR++   ++ ++q +  v+k+ ++
  gi|386002482|ref|YP_005920781.1| 368 IAAEGRKFGLGLLVISQRPARVDKNVIS 395
                                       5567888888888888888888777644 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.2e-06     0.014      44      90 ..     131     179 ..      93     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                   T4SS-DNA_transf  44 fehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgElaeltskiR 90 
                                       ++h ++ A t+sgK  +++vv+  ll ++ ++ ++Dp gE a +  k  
  gi|386002482|ref|YP_005920781.1| 131 QKHCSILAKTGSGKsyTAAVVLEELLEKGVALLIIDPHGEYASMKQKNS 179
                                       38************66689*********************999866654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05      0.11      24      53 ..     131     160 ..     118     184 .. 0.85
   2 ?   -3.5   0.0       4.6   9.2e+03     132     144 ..     338     350 ..     325     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgk 53 
                                       +k+  i + TG+GK+++aa + e+ll+kg 
  gi|386002482|ref|YP_005920781.1| 131 QKHCSILAKTGSGKSYTAAVVLEELLEKGV 160
                                       67778999******************9965 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.6
                                       T-SEEEEETGGGT CS
                            ResIII 132 rfdviiiDEaHrl 144
                                       +  ++++ EaH++
  gi|386002482|ref|YP_005920781.1| 338 NPGMVVVEEAHNY 350
                                       3449999999986 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.8e-05      0.13       5      57 ..       1      58 [.       1      83 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                        HAS-barrel  5 igestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn.......selsndl 57
                                      +ge+t+ ++ f   g  +   G+yV++++   ++   +v  + r n       ++++n  
  gi|386002482|ref|YP_005920781.1|  1 MGETTPFEFKFLMAG--EAPRGSYVKVKEGSKDWMVAQVMEVTRSNvayslsaIDEENPG 58
                                      699************..9**************************6665555443333333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0005         1      13      63 ..     130     175 ..     123     196 .. 0.76
   2 ?   -0.1   0.0      0.34   6.8e+02     108     136 ..     325     353 ..     316     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0005
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqt 63 
                                        ++++ + a+TGsGK+  +++ +  +++    ++g   li+ P  e a   
  gi|386002482|ref|YP_005920781.1| 130 VQKHCSILAKTGSGKSYTAAVVLE-ELL----EKGVALLIIDPHGEYASMK 175
                                       46788999********99877655.553....5788888888887766655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
                                       HHHHHHCTSSHCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 108 lddllstgklnlsqvrflVlDEadrlldq 136
                                       l dl++ +k    +  ++V+ Ea+++  +
  gi|386002482|ref|YP_005920781.1| 325 LSDLFEARKRGRVNPGMVVVEEAHNYIPE 353
                                       45566555544556689*******98766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0032       6.3       5      31 ..     131     157 ..     128     185 .. 0.81
   2 ?    2.8   0.0     0.067   1.3e+02      84     106 ..     327     359 ..     303     414 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0032
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqlde 31 
                                       ++++ + + +G+GK+++++ +le+l e
  gi|386002482|ref|YP_005920781.1| 131 QKHCSILAKTGSGKSYTAAVVLEELLE 157
                                       67889999************9999964 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.067
                            AAA_22  84 qalrarav....ielliiDEaqhlr....s..e 106
                                       + ++ar++    +++++++Ea++ +    s  +
  gi|386002482|ref|YP_005920781.1| 327 DLFEARKRgrvnPGMVVVEEAHNYIpergSgrA 359
                                       444444445568999*******95545542331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2735.58
//
Query:       gi|386002483|ref|YP_005920782.1|  [L=236]
Description: rhomboid family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-37  128.0  17.4    2.9e-37  128.0  17.4    1.5  2  Rhomboid  Rhomboid family
    3.2e-07   30.8   0.6    3.2e-07   30.8   0.6    2.5  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       0.4   3.6e+03     110     119 ..      62      71 ..      48      82 .. 0.48
   2 !  128.0  17.4   3.3e-41   2.9e-37       5     148 ..      89     230 ..      85     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.4
                                       CCCCCCCHHH CS
                          Rhomboid 110 fillnlvlgl 119
                                       ++l+ +v   
  gi|386002483|ref|YP_005920782.1|  62 CVLFYFVSVA 71 
                                       2333333222 PP

  == domain 2  score: 128.0 bits;  conditional E-value: 3.3e-41
                                       C-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHH CS
                          Rhomboid   5 gelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifg 81 
                                        + w+l+t++f+Ha+++HllfNm++l++fG++lerr+G++rfl ++++sgl+++++++++ +++   +vGaSGa+fg
  gi|386002483|ref|YP_005920782.1|  89 AHPWTLITHIFVHADMAHLLFNMIFLFFFGTELERRVGESRFLQIFIISGLVAAIGQMAVLPAG--SMVGASGALFG 163
                                       679*************************************************************..9********** PP

                                       HHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCCH CS
                          Rhomboid  82 llgallvlvprnrkllrkliiallllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllrr 148
                                       ++g+l+v  p+   ll+++i+  +  +++++  + ++++++a++++++AH++Gll+Gl++g +l  r
  gi|386002483|ref|YP_005920782.1| 164 VMGCLAVIAPEITVLLFFVIPLSIRAAVVLFAIIDFAFMGSADNIAHMAHIAGLLVGLAYGGILKDR 230
                                       ********************995555555555555566666677*****************999766 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       1.1     1e+04      64      70 ..      61      67 ..      52      80 .. 0.49
   2 !   30.8   0.6   3.6e-11   3.2e-07       1      75 [.      84     158 ..      84     178 .. 0.87
   3 ?    2.0   0.6     0.034   3.1e+02      48      93 ..     178     221 ..     172     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                           DUF1751 64 lltllly 70
                                      l+ l+++
  gi|386002483|ref|YP_005920782.1| 61 LCVLFYF 67
                                      2222222 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 3.6e-11
                           DUF1751   1 PgallpypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvtks 75 
                                       P+ l   pwtl+t+ fv + + ++l++++ l+++g+ lEr  g+  +l+ +++ ++++++  +++  + ++v +s
  gi|386002483|ref|YP_005920782.1|  84 PALLAAHPWTLITHIFVHADMAHLLFNMIFLFFFGTELERRVGESRFLQIFIISGLVAAIGQMAVLPAGSMVGAS 158
                                       7778889************************************99999999999999999887777766666555 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.034
                           DUF1751  48 lkFilvvnvitnllvvlltlllylvtkseelllvpisGlagilagf 93 
                                       l F+++  +i + + vl++++ ++++ s + + ++++  ag+l+g+
  gi|386002483|ref|YP_005920782.1| 178 LLFFVIPLSIRAAV-VLFAIIDFAFMGSADNI-AHMAHIAGLLVGL 221
                                       55666666665554.55555555555555533.4555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1432.17
//
Query:       gi|386002484|ref|YP_005920783.1|  [L=255]
Description: Hydrolase, TatD family [Methanosaeta harundinacea 6Ac]
Scores for complete 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-68  230.3   0.0    2.6e-68  230.1   0.0    1.0  1  TatD_DNase    TatD related DNase
    1.3e-05   25.1   1.7    9.6e-05   22.3   1.7    2.3  1  Amidohydro_2  Amidohydrolase
      6e-05   22.5   0.0    0.00057   19.3   0.0    2.4  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1   0.0   4.4e-72   2.6e-68       1     254 [.       9     253 ..       9     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 4.4e-72
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC..CCHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdea.sedllee 76 
                                       iD+HcHld+k+f++dr+e+++r ++agv+++++ g+++k++++ lela++y+  v+a+lG+ Pn + e  +e+++++
  gi|386002484|ref|YP_005920783.1|   9 IDTHCHLDFKNFNRDRDEVIQRGRKAGVTTMINSGIDLKTNRKSLELARRYDF-VFATLGLNPNGLGETtDEEVEAT 84 
                                       8***************************************************9.*************9856666699 PP

                                       HHHHHHCCCTSEEEEEEEEEET-CCCCCGH..HHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSE CS
                        TatD_DNase  77 lkelanvkhskvvaiGeiGLDyysreestk..eaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakak 151
                                       l+++  ++ +++v++Ge GLDyy r+++++  ++q+evF++ + lA+el+lp viH+r ae++  +++k+++    k
  gi|386002484|ref|YP_005920783.1|  85 LDQI-RAHAKEIVGVGEAGLDYY-RCPDERgrDRQREVFRKVVGLAEELDLPQVIHARLAEDEAFDVVKDLN----K 155
                                       9999.888899***********5.55555444**************************************84....7 PP

                                       EEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHH CS
                        TatD_DNase 152 vvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvv 228
                                       vv+H++sg++ ++k++l++g+yisl+ +++ ++  +++ l+++vpldrlLiETD+P+l+p   r+ rnepa+v   +
  gi|386002484|ref|YP_005920783.1| 156 VVFHCYSGTVGTMKEALDRGFYISLATVVCRSA--QHQVLARQVPLDRLLIETDSPFLSP---RKGRNEPAYVLDGL 227
                                       ******************************955..667777*******************...789*********** PP

                                       HHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 229 eklaelkaltleelaeitaeNakrlf 254
                                         +a++k+l++ee+ae+t++Na+++f
  gi|386002484|ref|YP_005920783.1| 228 HLIARIKGLPPEEVAEATTKNARKIF 253
                                       ************************99 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.7   1.6e-08   9.6e-05      91     291 .]      77     255 .]       9     255 .] 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-08
                                       CTSSHCHHHHHHHHHHHHTTECEEE...EESSTTTCCTTTCGGH...HHHHHHHHHHT-EEEEE....CHHHCHHHH CS
                      Amidohydro_2  91 vpldpedaaaeleraveelgfkGvr...lnphvggddllgdrld...rpifealeelglpvdihtGpspewlfggpq 161
                                       +++++e+++++++ ++  + ++Gv    l+    +d++ +dr+    r+++ ++eel+lp  ih             
  gi|386002484|ref|YP_005920783.1|  77 TDEEVEATLDQIRAHA--KEIVGVGeagLDYYRCPDERGRDRQRevfRKVVGLAEELDLPQVIH------------- 138
                                       5677777888888887..4454433322222222222222222234699***************............. PP

                                       HHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHH CS
                      Amidohydro_2 162 ettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspladppalarlie 238
                                              +l+ +++++   +l+ v+ H+  +   + ++ e+l+r+  +y+ l           +++ +      l  
  gi|386002484|ref|YP_005920783.1| 139 ------ARLAEDEAFDVVKDLNKVVFHCYSG--TVGTMKEALDRG--FYISL----------ATVVCRSAQHQVLAR 195
                                       ......7999999***************999..455555555544..58444..........678888888999999 PP

                                       HH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.......SSHHHHHHHHTHHHHHHCTB CS
                      Amidohydro_2 239 avgpdrilfGsDyPhptleaepealalldlval.......lsdeerekilggNAarlygl 291
                                        v+ dr+l  +D P+ +++  + + a + +  +       l++ee++    +NA++++gl
  gi|386002484|ref|YP_005920783.1| 196 QVPLDRLLIETDSPFLSPRKGRNEPAYVLDGLHliarikgLPPEEVAEATTKNARKIFGL 255
                                       9*****************9999999865543336899*********************97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.6e-08   0.00057       7     201 ..       9     182 ..       8     255 .] 0.59

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.6e-08
                                       EEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEES CS
                      Amidohydro_1   7 IDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggk 83 
                                       ID+H Hl +  ++++      + +e ++ + + g++t+++sG+    +            le a+++  ++ + + +
  gi|386002484|ref|YP_005920783.1|   9 IDTHCHLDFK-NFNR------DRDEVIQRGRKAGVTTMINSGIDLKTNR------KS---LELARRY--DFVFATLG 67 
                                       9******766.6677......9999999999999999999998643222......22...2333332..33344444 PP

                                       SEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH........HHHHHHHHHHHHTTEEEEEE CS
                      Amidohydro_1  84 vsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsde........elkealkeakkrdlpvaiHa 152
                                       ++++ g +et  +++e+ ++++    +++a+++v v+ a    + ++de          ++++ +a++ dlp +iHa
  gi|386002484|ref|YP_005920783.1|  68 LNPN-GLGETTDEEVEATLDQI----RAHAKEIVGVGEAGLDYYRCPDErgrdrqreVFRKVVGLAEELDLPQVIHA 139
                                       4444.44444444444444444....5555555555555555666666666666666999999************** PP

                                       ..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE.HH CS
                      Amidohydro_1 153 ..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt.pt 201
                                         +e+++  +d++++     +  +h +     g  +++k +l +g +++ +t
  gi|386002484|ref|YP_005920783.1| 140 rlAEDEA--FDVVKDLN---KVVFHCYS----GTVGTMKEALDRGFYISlAT 182
                                       7444444..48999999...44333333....55688899999999998433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1406.39
//
Query:       gi|386002485|ref|YP_005920784.1|  [L=542]
Description: 2-isopropylmalate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-83  279.2   2.9    5.7e-83  278.5   2.9    1.4  1  HMGL-like     HMGL-like
    1.7e-30  105.6   3.9    3.2e-30  104.7   3.9    1.5  1  LeuA_dimer    LeuA allosteric (dimerisation) domain
     0.0099   15.3   0.0       0.03   13.7   0.0    1.7  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.5   2.9   9.6e-87   5.7e-83       2     264 .]      43     301 ..      42     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 278.5 bits;  conditional E-value: 9.6e-87
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v+i+dttLRDGeq+++++l+ eek+ ia++Ld++gv++iE+gfp++s +dfe+vr +a+++ +a++++l+r   kdi
  gi|386002485|ref|YP_005920784.1|  43 VRIFDTTLRDGEQTPGVSLTPEEKIIIARQLDKLGVNVIEAGFPVSSRGDFEAVRMVAAEGLSAEVCGLARIMRKDI 119
                                       89*************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +aa +    ag+++vhvf++ts++++++ +kk+ree++++a+eav++++s+g  + +s++da+rt++ fl e+  a+
  gi|386002485|ref|YP_005920784.1| 120 DAALD----AGVDMVHVFVSTSDIQIQHTIKKSREEIVAQAVEAVEYVKSHGRTCLFSAMDATRTPVPFLKEIFGAV 192
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       e a +++ini+DtvGv+ P  +++l++++ + +k k+ + vHcHnd+GlAvan laA eaGa++v ++ nGlGeraG
  gi|386002485|ref|YP_005920784.1| 193 EGARCDIINIPDTVGVAIPTTFRQLVREICNSTK-KMVVDVHCHNDFGLAVANNLAAFEAGAREVQVAANGLGERAG 268
                                       **********************************.****************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                       na l e v+ l+ +  ++t + +  l ++a+lv
  gi|386002485|ref|YP_005920784.1| 269 NANLAETVMGLHSMYgAKTTIHTPYLFETAKLV 301
                                       ************986699999999999999887 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   3.9   5.4e-34   3.2e-30       3     132 ..     400     534 ..     398     535 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5.4e-34
                                       XXXXXXXXXXXXXXX...XX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHHT- CS
                        LeuA_dimer   3 tdedlealvkdelle...aeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgvdi 76 
                                       t +dl ++++ +++e    ++ + l++l+v++g++ +statv++ v  gee++ + +G+GpvdA+lnA+r +lg+++
  gi|386002485|ref|YP_005920784.1| 400 TGADLMTIAEVVIGElakDKQAVILKELAVMTGNTLTSTATVRAVV-RGEERVLADIGVGPVDAALNAVRGILGEET 475
                                       56666666666555555388**************************.9***************************55 PP

                                       ..EEEEEEEE--TT-TT--EEEEEEEE--G.GGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  77 ..kLldYsvhaitegtdaqaevrVelevdd.gkkvsgvGvdsdiveASlkAlisalnrl 132
                                         k+ d++++ait+g+da+aev + +e+   g+kv+++++++div+AS++Ali+a+nrl
  gi|386002485|ref|YP_005920784.1| 476 avKISDFRIEAITGGSDALAEVVIGVENGRlGRKVTARSAREDIVMASVEALINAINRL 534
                                       55*************************7335899***********************98 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.1e-06      0.03      27     121 ..      63     168 ..      46     175 .. 0.84
   2 ?   -2.7   0.0      0.53   3.2e+03     103     116 ..     379     392 ..     361     400 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC...........HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBC CS
                      AP_endonuc_2  27 deelrelrkaldelglriaslslftrfgypded...........erearreesvdalkraielaaaLGapllvlhpG 92 
                                       +ee   ++++ld+lg+++    ++  + +++e            e +       + +++ i++a + G+++++++++
  gi|386002485|ref|YP_005920784.1|  63 PEEKIIIARQLDKLGVNVIEAGFPVSSRGDFEAvrmvaaeglsaEVCGL----ARIMRKDIDAALDAGVDMVHVFVS 135
                                       55556688999999***99999999999999999999998766656666....899********************* PP

                                       C....GBCTTTSGHHHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  93 t....agagpkgseeeawerlaeslneladyae 121
                                       t      +  k+s+ee +++++e+++ +  +++
  gi|386002485|ref|YP_005920784.1| 136 TsdiqIQHTIKKSREEIVAQAVEAVEYVKSHGR 168
                                       *99997789999999999999999988887765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHH CS
                      AP_endonuc_2 103 eeawerlaeslnel 116
                                       +++++ + e++++l
  gi|386002485|ref|YP_005920784.1| 379 DDQLQEILERVKDL 392
                                       23334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3227.13
//
Query:       gi|386002486|ref|YP_005920785.1|  [L=251]
Description: Peptidylprolyl isomerase, FKBP-type [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-08   34.8   0.1      6e-08   32.9   0.1    1.9  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
     0.0055   16.8   0.0       0.01   15.9   0.0    1.5  1  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   6.7e-12     6e-08       5      77 ..       3      87 ..       1     111 [. 0.90
   2 ?   -0.8   0.0      0.21   1.9e+03      12      71 ..     126     187 ..     118     206 .. 0.58

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.7e-12
                                      B-TTCEEEEEEEEEETTSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGT CS
                            FKBP_C  5 akegdtVtvhykgkledgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippela 70
                                      +k+gd+++v+y+  + dg+v+ ++          ++   ++ p+ + vGsg+v+ Gf+e l g + G    +++ppe a
  gi|386002486|ref|YP_005920785.1|  3 VKDGDFIRVDYTESV-DGRVISTTdrdlamkndiYEegvEYGPALIIVGSGDVVAGFKEELIGKEIGASGSVEVPPEKA 80
                                      699************.999999998899988887557789*************************************** PP

                                      TTTTTBC CS
                            FKBP_C 71 Ygekgla 77
                                      Yg ++ +
  gi|386002486|ref|YP_005920785.1| 81 YGVRDPE 87
                                      **98874 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.21
                                       EEEEEEEETTSSEEEEHCCHTSEEEEETTSSS.SCHHHHHHHTT..SBTT-EEEEEEEGGGTT CS
                            FKBP_C  12 tvhykgkledgkvfdssrsrakplefkvGsgq.vikGfeealeg..mkvGekrtltippelaY 71 
                                       +++y+  l  +kv++ +++  + +e k+++ + +i+ f ++  +  +  G+ ++++ p e+ Y
  gi|386002486|ref|YP_005920785.1| 126 RIDYNHVL-ADKVVKYDYTIVERIEDKLEKLEgLIRIFAKIDLKaqILEGDVAEIESPWEMSY 187
                                       55555555.445555555555555555554333444443332222345566666666666666 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-06      0.01       3      70 ..     153     216 ..     151     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHH-TT--..--EEE.EETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEE CS
                          FKBP26_C   3 ekikelIkryiPnidlekfkie.iedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvde 70 
                                       ek+++lI  +  +id   +k + +e+ +++Ie p e++++ +  +++++IA+ +++ + + ++V + + 
  gi|386002486|ref|YP_005920785.1| 153 EKLEGLIRIF-AKID---LKAQiLEGDVAEIESPWEMSYYREWPMMRRGIAEMAMRLL-DLKEVRYLES 216
                                       7888888773.4565...444405788899**********************999888.******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1552.26
//
Query:       gi|386002487|ref|YP_005920786.1|  [L=156]
Description: Aspartate carbamoyltransferase, regulatory subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-35  118.8   0.6    1.2e-34  118.4   0.6    1.1  1  PyrI            Aspartate carbamoyltransferase regulatory cha
    6.7e-17   61.1   1.4    1.1e-16   60.4   1.4    1.3  1  PyrI_C          Aspartate carbamoyltransferase regulatory cha
  ------ inclusion threshold ------
      0.036   14.1   0.3       0.07   13.2   0.3    1.5  1  Dynamin_N       Dynamin family
      0.059   13.4   0.4        3.1    7.9   0.5    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.6   2.7e-38   1.2e-34       1      93 [.       8      99 ..       8     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.7e-38
                                      X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EE CS
                              PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnati 79
                                      l+v++i nG+ViDHI+ g+al+vl++L++d+ ++e+++++++nv+s++ gkKdi+k+e++el+eee++k++liap ati
  gi|386002487|ref|YP_005920786.1|  8 LRVTPIGNGTVIDHIPPGQALNVLRILGIDR-TTEATISVLMNVSSRRSGKKDIVKVEDRELKEEEVNKISLIAPGATI 85
                                      689***************************8.7777******************************************* PP

                                      EEEETTEEEEEE-- CS
                              PyrI 80 niIkdgevveKkkv 93
                                      niI+d++vveK++v
  gi|386002487|ref|YP_005920786.1| 86 NIIRDQRVVEKYTV 99
                                      ***********997 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   1.4   2.5e-20   1.1e-16       2      46 ..     105     150 ..     104     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.5e-20
                                       EESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEHH CS
                            PyrI_C   2 iegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeisee 46 
                                       i gv++CpNp CI+n+ ep++s+  v++k++v+l+C YCe++i e+
  gi|386002487|ref|YP_005920786.1| 105 IVGVVRCPNPSCISNTrEPIKSQILVKSKNPVILRCVYCEQPIAEK 150
                                       89**************99************************9986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.6e-05      0.07      82     160 ..      55     134 ..      36     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                       SSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHH.STTEEEEEEEETTS.-CCC-CHHHHHHHHST CS
                         Dynamin_N  82 ankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyi.kkadiilavtsanh.dlsnsealflarevdp 156
                                       ++k++  kv+  + ++  v++++l+  PG++ +  rdq++v++y  +  d+i+ v+ + + ++ ++ ++ +++++ +
  gi|386002487|ref|YP_005920786.1|  55 SGKKDIVKVEDRELKEEEVNKISLI-APGATINIIRDQRVVEKYTvDMPDLIVGVVRCPNpSCISNTREPIKSQILV 130
                                       3455555677788888888999999.8****************************9986637777799999999999 PP

                                       TBTT CS
                         Dynamin_N 157 kgkr 160
                                       k+k+
  gi|386002487|ref|YP_005920786.1| 131 KSKN 134
                                       8887 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5   0.00069       3.1      17      25 ..     108     116 ..     107     117 .. 0.91
   2 ?    2.7   0.0     0.029   1.3e+02       9      21 ..     129     141 ..     126     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00069
                    DNA_ligase_ZBD  17 iyRCtnlsC 25 
                                       + RC+n+sC
  gi|386002487|ref|YP_005920786.1| 108 VVRCPNPSC 116
                                       68******* PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.029
                    DNA_ligase_ZBD   9 vvReegeaiyRCt 21 
                                       +v+  + +i+RC+
  gi|386002487|ref|YP_005920786.1| 129 LVKSKNPVILRCV 141
                                       57778889****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 932.11
//
Query:       gi|386002488|ref|YP_005920787.1|  [L=306]
Description: aspartate carbamoyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-49  165.5   0.0    2.7e-48  163.8   0.0    1.7  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
      5e-30  104.7   0.0    6.5e-30  104.3   0.0    1.1  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.0     3e-52   2.7e-48       1     147 [.       5     145 ..       5     146 .. 0.94
   2 ?   -1.0   0.0      0.18   1.6e+03      50      80 ..     163     193 ..     147     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 3e-52
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       rh+ls++++s+eei+++ldla++l+    +  + + l+gk+lallF+epStRTr+Sfe+A+ rlGgk+l+l+ a   
  gi|386002488|ref|YP_005920787.1|   5 RHVLSMREFSREEIDSVLDLAEALEPYA-RGGRCDVLSGKILALLFFEPSTRTRLSFETAMMRLGGKTLNLGPA--- 77 
                                       8************************775.59999**************************************66... PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       + s+++kg  Esl+Dt+rv+++y+da+viRhp++ +++  a+++ vpv+Nagdg+g+HPtQ+L+Dl+tir
  gi|386002488|ref|YP_005920787.1|  78 EGSAIAKG--ESLADTIRVIGGYADALVIRHPKEGSARLAAQFSPVPVLNAGDGAGHHPTQTLLDLYTIR 145
                                       34666999..**********************77679999999**************************8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                                       -HHHHHHHHHHHHHTTSEEEEEESTTTSCT.T CS
                          OTCace_N  50 StRTrvSfevAakrlGgkvlslseaediql.s 80 
                                         RT  S   A +  G++ + +s + ++++ +
  gi|386002488|ref|YP_005920787.1| 163 YGRTVHSLAYALALYGADITLVSPP-TLEMpG 193
                                       5699999999999999999888844.555544 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.0   7.2e-34   6.5e-30       2     156 ..     152     300 ..     151     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 7.2e-34
                                       C.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   2 glkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +lkia+vGd k++++++sl+++la +g+d++lv+P++le+      ++k++ + +g  +  t+dle+++k++Dv+y 
  gi|386002488|ref|YP_005920787.1| 152 DLKIALVGDlKYGRTVHSLAYALALYGADITLVSPPTLEM----PGQIKADLAGKGTIVRETHDLESVIKEVDVLYV 224
                                       79***********************************988....34567888999********************** PP

                                       --SSETTCCGGHH....HHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekere....erlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhti 150
                                       ++++     +er+    e  k  k y++  e lk ak+ +i++H+LP  r +E++ eV+   ++v+f+q  +++ ++
  gi|386002488|ref|YP_005920787.1| 225 TRIQ-----RERFpdpyEYTKVAKSYRIAPESLKGAKEGLIIMHPLP--RVDEIAPEVDGTGHAVYFQQSFYGVPVR 294
                                       ****.....8888888555566666**********************..**************************** PP

                                       HHHHHH CS
                            OTCace 151 kAllvl 156
                                       +All +
  gi|386002488|ref|YP_005920787.1| 295 MALLKM 300
                                       ***976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1888.56
//
Query:       gi|386002489|ref|YP_005920788.1|  [L=256]
Description: hypothetical protein Mhar_1807 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-10   38.8   0.0    1.9e-07   31.3   0.0    2.5  2  Cas_Cas4  Domain of unknown function DUF83
    1.7e-09   38.0   0.1    5.3e-09   36.4   0.1    1.8  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
    1.2e-05   24.8   0.2    2.8e-05   23.6   0.2    1.6  1  Csa1      CRISPR-associated exonuclease Csa1


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0037        22       2      28 ..       7      33 ..       6      39 .. 0.85
   2 !   31.3   0.0   3.2e-11   1.9e-07      82     160 ..     167     245 ..     113     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0037
                          Cas_Cas4  2 gtkiqyyliCkrklwlisheitleens 28
                                      +++i+ yl C+r l++ +++ +++ + 
  gi|386002489|ref|YP_005920788.1|  7 ISEISLYLRCPRLLYFQAMGRRVHPEV 33
                                      6899************99998877665 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 3.2e-11
                          Cas_Cas4  82 aklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCaya 157
                                       ++l l  Y +lLe +   ++++G +ey+ + + +eve+ +++r+++ ++ +++++i +  k p   ++  C++C + 
  gi|386002489|ref|YP_005920788.1| 167 DRLRLAGYSMLLEeELEARVDRGLVEYLRSGEVREVEIRPTDRRRVLRIRDRVRSIREG-KLPDRPREAPCERCPVL 242
                                       5888999******99****************************************9998.6667777888*****99 PP

                          Cas_Cas4 158 elC 160
                                       e C
  gi|386002489|ref|YP_005920788.1| 243 ESC 245
                                       999 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   8.9e-13   5.3e-09       5     255 .]       8     246 ..       5     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.9e-13
                          PDDEXK_1   5 srletfleCplrfflryllgl..reeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeei 79 
                                       s+++ +l+Cp+  +++   +   +e e+ ++     l+ +++  ++e ++ ++edl e l+ea+e+++ e +   + 
  gi|386002489|ref|YP_005920788.1|   8 SEISLYLRCPRLLYFQAMGRRvhPEVETPKN----ILMREVALSLSEIGPEEGEDLGEWLREALERALVEVPAIYRE 80 
                                       88999*****999997666666666666666....678888877777444444466666666666555553333333 PP

                          PDDEXK_1  80 lessarlrylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriDrvd...dkeg..elriiDyKt 151
                                         + ++l+  ae++ +++++++ +++    + r++ p  +e+e  + ++ L Gr+Drv     ++g  +lri     
  gi|386002489|ref|YP_005920788.1|  81 RINPHDLQAAAEEVAAWAAEVAPKIQV---SLREINPSTVEVELRSDRLGLSGRVDRVVsrgAEDGsnHLRIPSILR 154
                                       334444444444444444444334444...33335555555444434677*******99998555577999998886 PP

                          PDDEXK_1 152 gsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleel 228
                                        + pp+     + +++l l+ Y ++l+e+  l+++ +++ + ylr         ++v++++  +++++++l +++++
  gi|386002489|ref|YP_005920788.1| 155 VDLPPEAGV--WRSDRLRLAGYSMLLEEE--LEARVDRGLVEYLRS--------GEVREVEIRPTDRRRVL-RIRDR 218
                                       665555555..899999************..444444888888888........56666666666665555.35666 PP

                          PDDEXK_1 229 aeeilagefparpskk.CeyCpyksvCr 255
                                       +++i++g+ p rp ++ Ce+Cp+ + C+
  gi|386002489|ref|YP_005920788.1| 219 VRSIREGKLPDRPREApCERCPVLESCE 246
                                       6779**********99**********95 PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   4.8e-09   2.8e-05     198     290 ..     160     246 ..      26     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.8e-09
                              Csa1 198 kvgsykeehelalaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidivekesDPG 274
                                         g ++++ +l laGY++ lE +le  vD G++ +++       +++ v i ++ R++ l  Rdr+   + +++ P 
  gi|386002489|ref|YP_005920788.1| 160 EAGVWRSD-RLRLAGYSMLLEEELEARVDRGLVEYLRSG-----EVREVEIRPTDRRRVLRIRDRVRS-IREGKLPD 229
                                       46777776.9**********************9988754.....45667888999**********865.68888898 PP

                              Csa1 275 lakkCs.skClflevCk 290
                                        +++ + + C+ le C+
  gi|386002489|ref|YP_005920788.1| 230 RPREAPcERCPVLESCE 246
                                       88876535799999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1364.03
//
Query:       gi|386002490|ref|YP_005920789.1|  [L=538]
Description: Deoxyribodipyrimidine photolyase-related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-53  181.7   0.0    2.9e-53  181.0   0.0    1.3  1  DPRP           Deoxyribodipyrimidine photo-lyase-related prot
    0.00021   20.8   0.0    0.00037   20.0   0.0    1.4  1  FAD_binding_7  FAD binding domain of DNA photolyase


Domain annotation for each model (and alignments):
>> DPRP  Deoxyribodipyrimidine photo-lyase-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   3.2e-57   2.9e-53       2     223 .]      42     257 ..      41     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 3.2e-57
                                       E--TT---TT-HHHCT--TTT-EEEEE--HCCCCSTTS-HHHHHHHHHHHHHHHHHHHHTT-EEEEE-TT-TT--SH CS
                              DPRP   2 lilgdqLskehsalkeadkkedrvlliEsaqeatyvrhHkqKlvlifaaMrhFaeeLrekgvevtylelddkenesl 78 
                                       +i++++L+++h++l++   + ++v+l+E+a+ +t  ++ k+Klvl++a+Mr ++e L e+g+ev+yle ++ke    
  gi|386002490|ref|YP_005920789.1|  42 VIFPHHLYRDHPSLRDP--ELSTVFLVEEARFFTDFNFNKKKLVLHRASMRGYQELLLERGLEVEYLEKRRKE---A 113
                                       79************987..7899**********************************************9654...5 PP

                                       HHHHHHHHHHH--SEEEEE--SSHHHHHHHHCHHHHCTSEEEEE--TTSSS-HHHHHHHHCC-SS--HHHHHHHHHH CS
                              DPRP  79 eeelealleelkieelevtepddkrleqrleelaeklelevevledehFltsreefkewakgrkklrmedFYremRk 155
                                         +l ++l+e +i  ++++e+ d++le+++ +  e+ ++++ev +++ Flt+r+  +++++gr+++ m++FYr++R 
  gi|386002490|ref|YP_005920789.1| 114 LPALFSALHESGIGIVRTAEIIDHPLEASFFKGLEAKGIRIEVDDSPGFLTTRALAHDLLRGRERISMASFYRRQRL 190
                                       6899999**********************99999998888888********************************** PP

                                       HHTTTEETTE.EGGGSS--GGGS-------TTS---------HHHHHHHHHHHHH-TTSSS--TT--- CS
                              DPRP 156 rlgiLmdedgkPvGGkWnfDaeNRkklpkklevpkplrfepdaitkevielvekrfadtfGsleefrw 223
                                       rl++L++ dg+P+GG+W+fD eNR+++pk++e+p+p+ +e++ i++e+ e+ve+rf+d++Gs++ f++
  gi|386002490|ref|YP_005920789.1| 191 RLKVLVE-DGRPLGGRWSFDPENRRRIPKEAEIPPPPALEESGIVREAKEYVEERFPDNPGSVDGFNF 257
                                       ******6.889******************************************************987 PP

>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.1e-08   0.00037       2     107 ..     334     433 ..     333     458 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-08
                                       HHHHH.HHHHHHHHHHCSTTTT.TSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHH CS
                     FAD_binding_7   2 lreLl.wrefyyallaaepela.eralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmi 76 
                                       +r+L+ wref++a+   e + + ++++  ++++ip          a  +G+TG+  vD ++     + + h+  R +
  gi|386002490|ref|YP_005920789.1| 334 IRQLIgWREFMRAAYLIEGDRErRSNFWGHHEKIPP---------ALYSGTTGISPVDQVVGRAIDHAYAHHIERLM 401
                                       555544888888877777666424455555555554.........6779**************************** PP

                                       HHHHHCTTT-B-HHHHHHHHHHH-TT.--CCH CS
                     FAD_binding_7  77 vasFltkdLlidWregeevFeellvD.adlas 107
                                       v   +++ + id  e  ++F+e ++D +d+a+
  gi|386002490|ref|YP_005920789.1| 402 VLGSFMNLCEIDPAEVYRWFMEIFIDsFDWAM 433
                                       999999********************447776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3270.06
//
Query:       gi|386002491|ref|YP_005920790.1|  [L=876]
Description: hypothetical protein Mhar_1809 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.7e-234  777.5   0.0   1.1e-233  777.3   0.0    1.0  1  DUF3160   Protein of unknown function (DUF3160)


Domain annotation for each model (and alignments):
>> DUF3160  Protein of unknown function (DUF3160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  777.3   0.0  6.2e-238  1.1e-233       2     631 .]      65     741 ..      64     741 .. 0.99

  Alignments for each domain:
  == domain 1  score: 777.3 bits;  conditional E-value: 6.2e-238
                           DUF3160   2 eeelalLkkngfvvieseke...eelvelYeslkekelPlfittDsvlhayHlfFdeiLkevEeeelapelkellka 75 
                                       e+++  L++ngfvvi ++ +   ee++ +Y+ lk+++lP+f+t+Ds+lh+yHl+F e+L++vEeee++++l++l+++
  gi|386002491|ref|YP_005920790.1|  65 EAAIMRLERNGFVVIVDPFSpvrEEVNPIYRILKNHDLPIFVTSDSLLHTYHLQFGETLRMVEEEEFYDDLWTLTEE 141
                                       788999*********98877888****************************************************** PP

                           DUF3160  76 lleelekqyesekseelkeaakrnvayfavArsLldekak................................evpee 120
                                       +l ++e+++ +++s+ ++eaa+rnva+f++A+sLl++k++                                evp +
  gi|386002491|ref|YP_005920790.1| 142 MLVRAEADH-EASSGLAREAARRNVAFFSTALSLLAPKEDqlcsggpqdcdegrfagtypyftpeeleaksfEVPPA 217
                                       *******99.89999************************************************************** PP

                           DUF3160 121 vkeeveeelelieaaeglaespifgyeekeDYSqYkpRGHYtksekLkrYFrammWlGrisfll......aesseee 191
                                       v+e ve+el+li +++g a+spifgy  +eDYSqY pRGHYt+se+Lk+YF am+W+Gr+sfll         seee
  gi|386002491|ref|YP_005920790.1| 218 VREVVEAELDLIYGQAGSATSPIFGY--DEDYSQYRPRGHYTRSERLKNYFMAMTWYGRMSFLLkgceggCLVSEEE 292
                                       **************************..************************************99999966899** PP

                           DUF3160 192 arrqteaallitellkedeellkkwkriyevtaflvGesDdlslyeyaellkkvkgkdaeelkldeeklkalkkela 268
                                       ar qt aa++i+++l ed+++++ w+ri +vt+f+vG+sDdl++y+y+e+++ ++g  ae  +l ee+l+ lk+ela
  gi|386002491|ref|YP_005920790.1| 293 ARVQTLAAAMIAQDLLEDPDTKELWDRISRVTSFYVGYSDDLGPYQYREAIDALFGPAAEARDLSEEELSILKAELA 369
                                       ***************************************************************************** PP

                           DUF3160 269 klkppqiigst......svpispleeeeeek.lketkgfrllGQRfvlDsyifqnlvsprvkentek.......... 328
                                       +++pp+i+g+t      +++++p+++ee++  l +t gfrl+GQRfv+Dsy f++lv+p+v+++t++          
  gi|386002491|ref|YP_005920790.1| 370 SYSPPRIYGGTgsdspaCIIQPPFTPEEADLcLAATAGFRLMGQRFVPDSYAFTRLVFPAVGGYTGEgeaftlgpyg 446
                                       ****************9999********999***********************************9********** PP

                           DUF3160 329 RalPkgLDvmaaLGserAeelLkkeleeteyenYkenleklkkevkaldeeawnknlYnswLyalrpllkekeegyP 405
                                       R +P+gLD+ma+LGserA+e+L +  e+++y nY+++ ++l +e+ +++ee+w++nlY+swL alrpll+e e+g P
  gi|386002491|ref|YP_005920790.1| 447 RSFPRGLDLMAVLGSERADEILVAL-EDSSYANYSARRAELGEEFFSISEEEWQRNLYWSWLFALRPLLQEPEAGAP 522
                                       ************************8.*************************************************** PP

                           DUF3160 406 tfmkteaWedkeLntalaSWteLrHDtiLYakqsyaemggggepeeekedrgYVEPnpefykrlaalteltaeglke 482
                                       +fm+t+aW+d++L+talaSWteLrHDtiLYak+sy+ +++g +pee+++++gYVEP+pe+y+rl++l ++ +++l+e
  gi|386002491|ref|YP_005920790.1| 523 AFMQTTAWQDRSLTTALASWTELRHDTILYAKESYTFVASGLPPEEMVAEAGYVEPVPEVYRRLRDLSRMSRQVLEE 599
                                       ********************************************9******************************** PP

                           DUF3160 483 relldeeskeklekleellerLkeisekelaneelteeeyefirsigeeleseleevderseeedekkkdaivADvh 559
                                       ++llde s+ +l +le++lerL+eise ela+++lt+ +++fir+ige+l++ l +vders      kk++ivADvh
  gi|386002491|ref|YP_005920790.1| 600 EGLLDEPSRGRLMSLEATLERLEEISEAELAGRKLTDGDLRFIRDIGERLDEALLGVDERS------KKTTIVADVH 670
                                       ***********************************************************99......9********* PP

                           DUF3160 560 TdpetgsvleegtGkvdlivvavpdadgklrlaaGpvfsyYefkqplseRLtdeeWremlkegkaperpeWt 631
                                       Tdp+t++vlee++G+v+++vva++++dg+++laaGpv+syYef qp+seRLtde Wre l  g++p++peWt
  gi|386002491|ref|YP_005920790.1| 671 TDPNTDMVLEEAVGYVRMMVVACHRPDGGVFLAAGPVYSYYEFLQPASERLTDEGWREILA-GDPPQDPEWT 741
                                       ************************************************************9.9********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.37s 00:00:01.16 Elapsed: 00:00:00.54
# Mc/sec: 4880.16
//
Query:       gi|386002492|ref|YP_005920791.1|  [L=643]
Description: S-layer protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-139  463.6   7.7    2.1e-70  236.7   2.8    2.0  2  S-layer   S-layer protein


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 !  229.7   0.2   1.7e-72     3e-68       7     258 .]      38     308 ..      33     308 .. 0.92
   2 !  236.7   2.8   1.2e-74   2.1e-70      10     257 ..     347     607 ..     339     608 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 1.7e-72
                           S-layer   7 seeltwtasnFsgfyydiddglssEsltlelesksdrtiee.gelvYsttpvekefefeewgsYevigflaekYfag 82 
                                        +++tw+++nF gf yd dd++ +E+ltl+++   +++++e  ++vY+tt++ ++f+fe+wg Y +i fl+e+ fag
  gi|386002492|ref|YP_005920791.1|  38 GATYTWDPQNFPGFSYDADDNICNERLTLTIT---GSSLDEpMGVVYETTAQLSDFDFEDWGMYYKISFLGEEQFAG 111
                                       6799*************************965...45555549********************************** PP

                           S-layer  83 y..dnsa..........etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkd 147
                                       y  +               s+d +l++ e+Lsk+lid+d+e+t+++   l L+egYel ik iD  g ++wleL+kd
  gi|386002492|ref|YP_005920791.1| 112 YagE--RyddwrqpylyDRSRDDNLMAGEELSKILIDDDQERTITKEAPLRLAEGYELGIKGIDAYG-SIWLELSKD 185
                                       *652..3345678898888999******************************************998.6******** PP

                           S-layer 148 geevdskvissska.....dstyvyekdlgdeddvviiavhvd.evfrgte...dslvviegifqisddvleieegd 215
                                       ge vds+ i +sk+     d+ty+y++dlg +  vv+iavh++  vf+gte   +++++++gi+qisd++++i eg 
  gi|386002492|ref|YP_005920791.1| 186 GEVVDSNLIAPSKDgatiaDKTYIYTRDLGISRGVVVIAVHFKgPVFHGTEgglQDAAIVNGIWQISDEAVSIGEGS 262
                                       ***********9999***************************846****99666789******************** PP

                           S-layer 216 efgkmevksvsen..eiemendds.itLsrdktieimddlkfkvaD 258
                                       +fgkm+++sv+ +  +i m+n+d+ i Ls++k+i +m++l++++aD
  gi|386002492|ref|YP_005920791.1| 263 SFGKMRISSVDAEsmRISMDNEDNrIVLSKNKEIPLMEELWIRTAD 308
                                       **********98755899***9988********************8 PP

  == domain 2  score: 236.7 bits;  conditional E-value: 1.2e-74
                           S-layer  10 ltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy.dn 85 
                                       +tw++snF+gfyyd+d++l++E lt +++  +++  e +++vY+t++++k+f+fe+wgsY +igfl+e+ fagy + 
  gi|386002492|ref|YP_005920791.1| 347 TTWESSNFAGFYYDVDNNLGTEALTTTIQ--GNSLEEPDGVVYTTSAQSKDFDFETWGSYWTIGFLGEEHFAGYaEG 421
                                       57************************975..6888888************************************855 PP

                           S-layer  86 sa......etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvi 156
                                       s+       +s+d +l++++ +s+vli +d+e tl+s   l+L+egYel++k iD   + v leL+k+ge +d   +
  gi|386002492|ref|YP_005920791.1| 422 SPydaplyYESSDPNLIAEDLISRVLISDDSEITLTSSRPLKLAEGYELSVKAIDQRTKIVSLELQKNGETIDVGTV 498
                                       557778988999***************************************************************** PP

                           S-layer 157 ssska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvsen 228
                                       ++sk+     ++ty+y+ +l++++dvv+iavh++++f++ ++ +v+++gi+qisd++++i+ g++f++m+v+ v+ +
  gi|386002492|ref|YP_005920791.1| 499 EPSKDgatiqEKTYTYKMTLNGAEDVVVIAVHFKDAFSNPDQAMVIVNGIWQISDSPIDIKVGTTFDRMKVQMVDPT 575
                                       **9999********************************************************************988 PP

                           S-layer 229 ..eiemendds.itLsrdktieimddlkfkva 257
                                         +i+m+n+++ i L ++++  +m+d+++k+a
  gi|386002492|ref|YP_005920791.1| 576 amSITMNNEKNkIGLYKNSDAALMGDIRVKTA 607
                                       669*****9877******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 3689.64
//
Query:       gi|386002493|ref|YP_005920792.1|  [L=280]
Description: Protease HtpX like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-40  137.5   0.0    4.5e-40  137.5   0.0    1.6  2  Peptidase_M48    Peptidase family M48
    2.6e-07   30.1   1.0    4.7e-07   29.3   0.1    1.9  2  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.044   14.0   0.0      0.085   13.1   0.0    1.4  1  DUF4157          Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.9         1     6e+03      93     132 ..      10      43 ..       1      46 [. 0.33
   2 !  137.5   0.0   7.6e-44   4.5e-40       2     196 .]      60     274 ..      59     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1
                                       HHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  93 llllglallisraeedaagafldalavliglliillflal 132
                                       l +++++++      + ag+    ++ +++++ +l+++++
  gi|386002493|ref|YP_005920792.1|  10 LVYMAFLAI---LAYQGAGM---VTMLAFVIIFMLVQYFF 43 
                                       222222222...22222222...22333344444444455 PP

  == domain 2  score: 137.5 bits;  conditional E-value: 7.6e-44
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikh 77 
                                       ++e++l++++ +l + a+l  p+++++vvn +  NAFa+g++  +  +++t+g++ + l+++el+aVl+HEl H+k+
  gi|386002493|ref|YP_005920792.1|  60 RDEPQLHQMITRLCALADL--PKPRIAVVNTSMPNAFATGRSPGNaVVAVTTGIM-RQLNPAELEAVLAHELTHVKN 133
                                       6799***************..*********************98889********.********************* PP

                                       THHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT..-..-S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  78 rhsvvslivsllasillllglallisraeedaaga..f..ldalavliglliillflalSRkrEyqADeagvellkr 150
                                       r+++v++i s l+++++++++  l+   ++  ++   +  +  + v++++ + ll  alSR+rE+ AD+ ++ ++ +
  gi|386002493|ref|YP_005920792.1| 134 RDVMVMTIASFLSTVAFFIVRYSLYFGGGGSSRNKggIwvAFFASVVVWIASSLLIRALSRYREFAADRGAAVITGQ 210
                                       *******************99887755544444430131123345666666777666******************** PP

                                       HHHHHHHHHHHHHHTT--S---HHHH..................HHS-SS--HHHHHHHHHH-X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 151 akdlvraliklakdlerqdvsaslrs..................ellstHPplleRiqalkele 196
                                       + +l++al+k++  + r ++++  r+                  +llstHPp ++R++al+ +e
  gi|386002493|ref|YP_005920792.1| 211 PSNLASALMKISGVMPRIPKEDLRRAegmnaffiipavsssslmKLLSTHPPVEKRLAALQGME 274
                                       *********************999999*********************************9885 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   7.9e-11   4.7e-07     178     227 ..     102     151 ..      18     152 .. 0.68
   2 ?   -1.8   0.1      0.23   1.4e+03     118     140 ..     174     197 ..     170     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7.9e-11
                     Peptidase_M56 178 kprIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclfwf 227
                                         ++ + + ++++l+ +ele +l+HEl+H+k++D++v  ++ +l+ + +f
  gi|386002493|ref|YP_005920792.1| 102 NAVVAVTTGIMRQLNPAELEAVLAHELTHVKNRDVMVMTIASFLSTVAFF 151
                                       4577888999***********************************99998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.23
                     Peptidase_M56 118 lyliaallvlkkr.fvrklgklra 140
                                       ++++ ++ ++ ++ ++r+l+++r+
  gi|386002493|ref|YP_005920792.1| 174 AFFASVVVWIASSlLIRALSRYRE 197
                                       344444444444445555555554 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.085      58      74 ..     117     133 ..      92     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                           DUF4157  58 saagrellaHELtHvvq 74 
                                        a+ +++laHELtHv  
  gi|386002493|ref|YP_005920792.1| 117 PAELEAVLAHELTHVKN 133
                                       456679*********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.37s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 1662.10
//
Query:       gi|386002494|ref|YP_005920793.1|  [L=190]
Description: hypothetical protein Mhar_1812 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1158.60
//
Query:       gi|386002495|ref|YP_005920794.1|  [L=92]
Description: hypothetical protein Mhar_1813 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 524.11
//
Query:       gi|386002496|ref|YP_005920795.1|  [L=231]
Description: phage shock protein A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-26   91.0  30.9    8.7e-26   90.9  30.9    1.0  1  PspA_IM30        PspA/IM30 family
    0.00045   20.2  12.6     0.0019   18.3   3.5    2.7  3  DUF1664          Protein of unknown function (DUF1664)
     0.0006   20.1   8.7       0.42   11.0   0.1    3.8  4  Flagellin_C      Bacterial flagellin C-terminal helical regio
     0.0066   16.2   0.1      0.032   14.0   0.0    2.1  2  NOG1             Nucleolar GTP-binding protein 1 (NOG1)
  ------ inclusion threshold ------
      0.036   13.8   3.3      0.036   13.8   3.3    3.8  3  DivIC            Septum formation initiator
       0.15    9.5  22.6      0.034   11.7  16.0    2.0  2  DUF3584          Protein of unknown function (DUF3584)
       0.16   12.1   7.4       0.27   11.4   6.0    2.1  2  COG5             Golgi transport complex subunit 5
       0.21   11.8  12.2       0.13   12.5   4.4    2.7  2  DUF5082          Domain of unknown function (DUF5082)
       0.24   11.5  15.5       0.63   10.2   1.1    2.8  3  GCN5L1           GCN5-like protein 1 (GCN5L1)
       0.26   10.6  21.1       0.16   11.2   7.5    2.3  2  DUF3450          Protein of unknown function (DUF3450)
       0.55    9.8  16.9       0.29   10.7  10.8    2.3  2  Snf7             Snf7
       0.68    9.9   7.7        1.7    8.6   1.3    2.3  2  DAP_B            D-aminopeptidase, domain B
       0.79   10.0  12.8         13    6.0  11.4    3.2  2  DUF3958          Protein of unknown function (DUF3958)
       0.82    9.7  19.3       0.13   12.3   1.0    4.1  4  DUF1515          Protein of unknown function (DUF1515)
        1.1    7.2   4.5        1.3    6.9   4.5    1.3  1  Prominin         Prominin
        1.3    7.8  23.6       0.47    9.3  11.5    2.1  2  Spc7             Spc7 kinetochore protein
        1.4    8.4  12.4        1.4    8.4   1.0    3.0  3  Fzo_mitofusin    fzo-like conserved region
        1.6    8.8  16.5       0.19   11.7   6.6    3.3  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        1.7    8.8  11.4        1.7    8.7   9.2    1.9  2  DUF1993          Domain of unknown function (DUF1993)
        1.8    7.1  11.1       0.54    8.8   5.8    1.9  2  FapA             Flagellar Assembly Protein A
        1.8    8.8  14.3        1.3    9.3   5.5    2.8  2  Spc24            Spc24 subunit of Ndc80
        2.6    8.6  30.8        0.7   10.4  22.0    3.3  2  APG6_N           Apg6 coiled-coil region
        3.1    7.8   6.9        7.4    6.6   0.9    3.2  4  SLIDE            SLIDE
        3.6    8.3  12.5    1.4e+03   -0.1   0.0    2.8  2  YabA             Initiation control protein YabA
        4.7    7.0  17.7        3.2    7.5   8.5    2.5  2  DUF724           Protein of unknown function (DUF724)
        4.8    7.6  20.6       0.11   12.8   2.8    4.3  4  CLZ              C-terminal leucine zipper domain of cyclic n
        5.1    7.5  16.6          8    6.8   7.0    2.4  2  YlqD             YlqD protein
        5.3    6.8   6.5          4    7.2   5.0    1.7  2  DUF3708          Phosphate ATP-binding cassette transporter
        6.2    6.7  18.0        7.8    6.4   6.2    2.9  3  Ax_dynein_light  Axonemal dynein light chain
        6.5    6.2  16.0         16    5.0  15.9    1.7  1  Exonuc_VII_L     Exonuclease VII, large subunit
        9.8    6.3  16.3        2.2    8.4   0.2    3.6  4  COG2             COG (conserved oligomeric Golgi) complex com


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9  30.9   1.5e-28   8.7e-26       1     219 [.       2     229 ..       2     231 .] 0.94

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.5e-28
                         PspA_IM30   1 gifkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaA 77 
                                       g+++r+++++ra+++ l+d +eDP+  l+   +   + l+++++ +a+v +++k+le + ++ + ++ +l ++A++A
  gi|386002496|ref|YP_005920795.1|   2 GLLNRMSTVVRAKMTTLMDRVEDPNETLDYSYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREA 78 
                                       689************************************************************************** PP

                         PspA_IM30  78 LtkgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqks 154
                                        ++ +e+LAr al++++ l+ +a+ l++q a ++   e+l++  ++l  k+e+++ kke++ka+ +aa aq +v++s
  gi|386002496|ref|YP_005920795.1|  79 VKADREDLARQALERKAALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVKVTES 155
                                       ***************************************************************************** PP

                         PspA_IM30 155 lgkls..tesatdslerieeKieerearadaaaelae........saqdldakleaagiqkevseqvlarlkaeq 219
                                       l ++s   ++   + er e+Kie + ar+ a  el e         + d + +l+ + + ++v e+ larlk+e+
  gi|386002496|ref|YP_005920795.1| 156 LTGISeeMADVGLAVERSEDKIETMRARSAALDELVErgtleefgGKDDVERELARVRARGSV-EADLARLKEEE 229
                                       *****5555556678*********************887776555444499999999999999.********987 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.4     0.013       7.4      51     115 ..       5      73 ..       3      80 .. 0.70
   2 ?    4.6   2.6     0.054        31      54     124 .]      47     115 ..      35     115 .. 0.57
   3 !   18.3   3.5   3.2e-06    0.0019      48     121 ..     109     181 ..      93     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                           DUF1664  51 eqvseslaatkrhLssrid....rvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +++s+ ++a    L++r++    ++d + ++q e+ +++k+ v+ev    ++++ +   + + + +l+ 
  gi|386002496|ref|YP_005920795.1|   5 NRMSTVVRAKMTTLMDRVEdpneTLDYSYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDD 73 
                                       566777777777888888622225667777888888888888888888888888777777777777765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.054
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve.svkeaveglesklerieekQ 124
                                        +++a+ k++L+ + +r+ +k+d+      + +e v++ redl++   + + ++     +l+++++++e++Q
  gi|386002496|ref|YP_005920795.1|  47 VAEVATSKKRLELQRARLASKMDQLD---DQAREAVKADREDLARQALERKaALAVEAASLDQQIADLEHEQ 115
                                       46677777777777777777776544...4455666666666655443333144555566666666666665 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3.2e-06
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        +le+ +e+l+at r+Lss+++    k +  k+  ++ +++v +v e l+ i+e++  v  ave  e k+e++ 
  gi|386002496|ref|YP_005920795.1| 109 ADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQV-KVTESLTGISEEMADVGLAVERSEDKIETMR 181
                                       4588889***********************999999999998.58999**********************9986 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.5     2e+03      14      34 ..      11      31 ..       4      37 .. 0.77
   2 ?    3.8   0.6      0.13        77       8      50 ..      40      82 ..      33      88 .. 0.76
   3 !    8.0   0.3    0.0062       3.6       4      44 ..     104     144 ..     101     148 .. 0.87
   4 !   11.0   0.1   0.00073      0.42       3      41 ..     151     189 ..     149     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                                      HHHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_C 14 vrselGavqnRlesaitnlka 34
                                      vr+++ + + R+e+ ++ l+ 
  gi|386002496|ref|YP_005920795.1| 11 VRAKMTTLMDRVEDPNETLDY 31
                                      688888999999998888875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHH CS
                       Flagellin_C  8 itdldkvrselGavqnRlesaitnlkaqsenlkaaesrledvD 50
                                      +++++   +e+ ++++Rle + ++l    + l+ + ++  ++D
  gi|386002496|ref|YP_005920795.1| 40 LQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKAD 82
                                      6677777788888888888888888888888888777666666 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHC CS
                       Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaes 44 
                                       +d++i dl+ ++ +l a + Rl+s +++    +e +ka+ s
  gi|386002496|ref|YP_005920795.1| 104 LDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYS 144
                                       78999999999999999999999999999999999999876 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00073
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHH CS
                       Flagellin_C   3 ivdeaitdldkvrselGavqnRlesaitnlkaqsenlka 41 
                                       +v+e +t+++++ +++G++ +R e+ i+ + a s  l++
  gi|386002496|ref|YP_005920795.1| 151 KVTESLTGISEEMADVGLAVERSEDKIETMRARSAALDE 189
                                       68999**************************99988875 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.6e-05     0.032      22      47 ..      24      49 ..      21      55 .. 0.90
   2 ?   -2.5   0.0       8.1   4.7e+03      30      42 ..     145     157 ..     140     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                              NOG1 22 DpseecgysleeQlsLleeikelfan 47
                                      Dp e+  ys ++Ql+Ll+++k  +a+
  gi|386002496|ref|YP_005920795.1| 24 DPNETLDYSYQKQLELLQNVKRGVAE 49
                                      9********************98875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.1
                              NOG1  30 sleeQlsLleeik 42 
                                         e Q+++ e++ 
  gi|386002496|ref|YP_005920795.1| 145 AAEAQVKVTESLT 157
                                       5688999998875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   5.9      0.31   1.8e+02      20      63 ..      34      77 ..      29      95 .. 0.65
   2 ?   13.8   3.3   6.3e-05     0.036      20      60 ..     102     142 ..      97     143 .. 0.91
   3 ?    2.4   0.2      0.23   1.3e+02      26      49 ..     170     193 ..     162     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXX CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARs 63
                                      +++ + ++  ++ +a++   +++Le + ++L s  d ++ +AR+
  gi|386002496|ref|YP_005920795.1| 34 QKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQARE 77
                                      44444455555566666666666666666666666666666664 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                             DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                        +l+q+ia+l++e +kl a++++L ++v+  +  ++ i+++
  gi|386002496|ref|YP_005920795.1| 102 ASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQ 142
                                       589***************************99999999875 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHCC CS
                             DivIC  26 iaalqaelaklkaeneeLeaevkd 49 
                                       +++ ++++++++a+ ++L++ v++
  gi|386002496|ref|YP_005920795.1| 170 VERSEDKIETMRARSAALDELVER 193
                                       678899*************99986 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  16.0     6e-05     0.034     643     749 ..      15     124 ..       1     131 [. 0.77
   2 ?    7.7   6.6   0.00093      0.54     813     909 ..      97     193 ..      96     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                           DUF3584 643 vaeaatalknardtlerlqnekesekdklek...aiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerl 716
                                       ++     ++  ++tl +  +++ ++ +++++    +a  k+  e q+  l+ +++ql+ q ++a ++ +edl  + l
  gi|386002496|ref|YP_005920795.1|  15 MTTLMDRVEDPNETLDYSYQKQLELLQNVKRgvaEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLARQAL 91 
                                       5555555566666666666665555555554111456678888999******************************* PP

                           DUF3584 717 ekkakwqevvgeldeqlaelkkaieaartqaka 749
                                       e+ka+++++ ++ld+q+a l+++ e+ ++ +++
  gi|386002496|ref|YP_005920795.1|  92 ERKAALAVEAASLDQQIADLEHEQEKLEATERR 124
                                       ************************999987766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00093
                           DUF3584 813 laeerpalkeqveelesaaeeleqeltrliedtklerkkle..kerkalekqldqldenlrklrdllskl.aelkld 886
                                       la e + l +q ++le+++e+le   +rl++++++ r k e  k++ ++ +++++++e+l+++  ++  +  +++ +
  gi|386002496|ref|YP_005920795.1|  97 LAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKEtiKAQYSAAEAQVKVTESLTGISEEMADVgLAVERS 173
                                       56678889999999999999999999999999998876655114555667778899999999999999993333333 PP

                           DUF3584 887 adaeqaegelaerlaaleelkrk 909
                                       +d  + e ++  r aal+el ++
  gi|386002496|ref|YP_005920795.1| 174 ED--KIE-TMRARSAALDELVER 193
                                       33..333.456666666666554 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.5   8.4e+02      70      91 ..      35      57 ..       3      60 .. 0.49
   2 ?   11.4   6.0   0.00046      0.27      26      93 ..      52     120 ..      38     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                                      XXX.XXXXXXXXXXXXXXXXXXX CS
                              COG5 70 lss.vlselksslesLsasyerl 91
                                      ++  +l+++k  ++++  s +rl
  gi|386002496|ref|YP_005920795.1| 35 KQLeLLQNVKRGVAEVATSKKRL 57
                                      22235566666666666666665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00046
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX- CS
                              COG5  26 dteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlks 93 
                                       +++  l+ +++rl + +++ld++ r+ +++  ++L  ++ ++k + +    +l++++++L+   e+l+ 
  gi|386002496|ref|YP_005920795.1|  52 TSKKRLELQRARLASKMDQLDDQAREAVKADREDLARQALERKAALAvEAASLDQQIADLEHEQEKLEA 120
                                       567788999******************************9999999978999********999999975 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.0      0.16        91      21      76 ..      32      87 ..      26      92 .. 0.80
   2 ?   12.5   4.4   0.00023      0.13       4      90 ..      93     181 ..      90     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                           DUF5082 21 aleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnle 76
                                      ++++++e L+ +k+ + ++  s k  + + +  + +++ +  ++++ ++ +r++l 
  gi|386002496|ref|YP_005920795.1| 32 SYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLA 87
                                      57888999999999888888888888888888888888888888888888887765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00023
                           DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs...nles 77 
                                       ++++l  ++a+l ++ia+le   e+L+++ ++ls++ e++  kk+ ++ +    e+ + k +++  gi +   ++  
  gi|386002496|ref|YP_005920795.1|  93 RKAALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEA-QVKVTESLTGISEemaDVGL 168
                                       67888899999999******999***********9999999999999888777753.44445555555444479999 PP

                           DUF5082  78 syqtyvdkldeli 90 
                                       ++++++dk++++ 
  gi|386002496|ref|YP_005920795.1| 169 AVERSEDKIETMR 181
                                       9999999999875 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1    0.0011      0.63      32      72 ..      37      77 ..      12      81 .. 0.87
   2 ?    7.3   7.0    0.0088       5.1       8      85 ..      75     151 ..      72     156 .. 0.79
   3 ?   -1.3   0.0         4   2.3e+03      21      59 ..     174     212 ..     168     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                            GCN5L1 32 ealvdklnsgvaeayanqkklekeakalqanvakfakqtdq 72
                                       +l++++++gvae+ + +k+le +  +l+++++++  q+++
  gi|386002496|ref|YP_005920795.1| 37 LELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQARE 77
                                      57899******************************999865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0088
                            GCN5L1   8 kqaerreeqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsal 84 
                                       +++  +++ e + ++a+e  aal+ +   +l++++a + ++q+kle+  ++l+++v++f+ + +   a +++ + ++
  gi|386002496|ref|YP_005920795.1|  75 AREAVKADREDLARQALERKAALAVE-AASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQV 150
                                       44555666777777777666666554.5789****************************999888888887777766 PP

                            GCN5L1  85 k 85 
                                       k
  gi|386002496|ref|YP_005920795.1| 151 K 151
                                       6 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4
                            GCN5L1  21 keaiesaaaltealvdklnsgvaeayanqkklekeakal 59 
                                       ++ ie+++a + al + +++g  e +  +  +e e+ ++
  gi|386002496|ref|YP_005920795.1| 174 EDKIETMRARSAALDELVERGTLEEFGGKDDVERELARV 212
                                       555677777777888888888888887777777776655 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.4     0.019        11      48     130 ..      14      96 ..       8      98 .. 0.85
   2 ?   11.2   7.5   0.00028      0.16       6      64 ..      96     154 ..      94     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveldlPflleeR 124
                                       ++   + ++++ +e l+   +++ +l++++++ +a++ ++++++e  +++l   ++++ d+ ++ v++d   l+ + 
  gi|386002496|ref|YP_005920795.1|  14 KMTTLMDRVEDPNETLDYSYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLARQA 90 
                                       56666788888899999999999999*****************************************9988777766 PP

                           DUF3450 125 qarlak 130
                                        +r a 
  gi|386002496|ref|YP_005920795.1|  91 LERKAA 96 
                                       666555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00028
                           DUF3450   6 alllasgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeelesle 64 
                                       al++ +++l+++++++++e+ek  a++++ ++k+++   +k++++a+y a++++++ +e
  gi|386002496|ref|YP_005920795.1|  96 ALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVKVTE 154
                                       6677777779****************************************999987655 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  10.8    0.0005      0.29       6      79 ..      50     123 ..      45     144 .. 0.90
   2 ?    2.0   3.1      0.24   1.4e+02      53     149 ..     115     212 ..     113     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   6 LrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlks 79 
                                       + +++++l+ ++ +l  k  +l+ ++++  k  ++d a+++L +k  +  + ++ld+q a le  ++++e +++
  gi|386002496|ref|YP_005920795.1|  50 VATSKKRLELQRARLASKMDQLDDQAREAVKADREDLARQALERKAALAVEAASLDQQIADLEHEQEKLEATER 123
                                       5678899*************************************************************998876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHHHHHHHHHHTCHHHHHHH CS
                              Snf7  53 yekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkvdidkidklmdeiedqmekaeeisEalsr 129
                                       +ek+ +     ++++e+ + + e+ k++ + ++a  ++++ +  +++++   ++    +  ed++e ++  s al++
  gi|386002496|ref|YP_005920795.1| 115 QEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVKVTESLTGISEEMA--DVGLAVERSEDKIETMRARSAALDE 189
                                       55666666667888889999999999999999999999999999999988..8888888888888888888888888 PP

                                       HHTT-...GGTTHHHHHHHHHHH CS
                              Snf7 130 sldda...deedEeeleaeLdaL 149
                                        ++ +   +    +++e+eL ++
  gi|386002496|ref|YP_005920795.1| 190 LVERGtleEFGGKDDVERELARV 212
                                       88777664444567888888766 PP

>> DAP_B  D-aminopeptidase, domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7     0.042        25      18      86 ..      17      84 ..      13      93 .. 0.84
   2 ?    8.6   1.3    0.0029       1.7      50     106 ..      95     153 ..      86     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.042
                             DAP_B 18 qLlvtvekgekgkvkvtYaksaeelkltseteaesksvvaeiegdelrierlkenrtlkarrvkeaeka 86
                                      +L+ +ve+ ++  +  +Y+k+ e l+ ++   ae ++ + ++e +  r++ + +++  +ar   +a+++
  gi|386002496|ref|YP_005920795.1| 17 TLMDRVEDPNET-LDYSYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADRE 84
                                      566667666665.999***************************************99999988777665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                             DAP_B  50 aesksvvaeiegdelrierlkenrtlkarrvkeaekal..dkaelaGeyrceelestle 106
                                       a  +  +a+++++   +e ++e+++ + rr++++ +a   +k++++++y ++e + +++
  gi|386002496|ref|YP_005920795.1|  95 AALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAFrvKKETIKAQYSAAEAQVKVT 153
                                       55555678999********************8876554449999********9887765 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.4     0.023        13      63     105 ..      96     137 ..      32     139 .. 0.66
   2 ?   -1.3   0.0       4.4   2.6e+03       8      40 ..     161     193 ..     154     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                           DUF3958  63 klrdevqrlsrklredLEeeeeeLkrekrqLedqeeelyyekr 105
                                       +l  e+++l++++ +dLE e+e+L+  +r+L++++e++ ++k 
  gi|386002496|ref|YP_005920795.1|  96 ALAVEAASLDQQI-ADLEHEQEKLEATERRLSSKVEAFRVKKE 137
                                       4566899999998.69*********************999885 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.4
                           DUF3958   8 qelrelaekqeenekelkkqeqlkeeyeehfnq 40 
                                       +e+ ++   +e+ e ++ + + + ++++e+ ++
  gi|386002496|ref|YP_005920795.1| 161 EEMADVGLAVERSEDKIETMRARSAALDELVER 193
                                       555666666777777888888888887777666 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.17        98      31      73 ..       8      50 ..       5      54 .. 0.81
   2 ?    5.6   1.3     0.027        15       8      48 ..      34      74 ..      29      85 .. 0.84
   3 ?    1.7   0.6      0.44   2.5e+02       4      38 ..     102     136 ..      98     155 .. 0.86
   4 ?   12.3   1.0   0.00022      0.13       6      53 ..     152     198 ..     146     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                           DUF1515 31 sdasrakmyrkmdelvervtalegsvvklkaditsvkevtedv 73
                                      s + rakm+  md + +  ++l+ s  k  + + +vk   ++v
  gi|386002496|ref|YP_005920795.1|  8 STVVRAKMTTLMDRVEDPNETLDYSYQKQLELLQNVKRGVAEV 50
                                      7899*********999999999999888877788887766666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                           DUF1515  8 qqlgtllaevkelredlkrsedrsdasrakmyrkmdelver 48
                                      q+  +ll++vk    ++  s++r + +ra++  kmd+l ++
  gi|386002496|ref|YP_005920795.1| 34 QKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQ 74
                                      666678888888888999******************99765 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.44
                           DUF1515   4 agvlqqlgtllaevkelredlkrsedrsdasrakm 38 
                                       a++ qq+ +l  e ++l    +r   + +a r+k 
  gi|386002496|ref|YP_005920795.1| 102 ASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKK 136
                                       7899999****999999999999999999999875 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00022
                           DUF1515   6 vlqqlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtale 53 
                                       v ++l  +  e+ ++  ++ rsed+ +++ra+    +delver t  e
  gi|386002496|ref|YP_005920795.1| 152 VTESLTGISEEMADVGLAVERSEDKIETMRARS-AALDELVERGTLEE 198
                                       556677788999999999*************86.579******76554 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.5    0.0022       1.3     620     698 ..      55     133 ..       4     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                          Prominin 620 kltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikk 696
                                       k  +++   la+k+++l ++  ++ k  ++ l ++a + +a  +  +  l++++++l+++ +kl+++++ l+++++ 
  gi|386002496|ref|YP_005920795.1|  55 KRLELQRARLASKMDQLDDQAREAVKADREDLARQALERKAALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEA 131
                                       22233333455555555555555545566666666666666666666666666666666666666666666666654 PP

                          Prominin 697 ll 698
                                       + 
  gi|386002496|ref|YP_005920795.1| 132 FR 133
                                       43 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  17.5     0.019        11     139     254 ..      38     147 ..      11     150 .. 0.54
   2 ?    9.3  11.5   0.00081      0.47     143     273 ..     103     227 ..      89     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                              Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLe........elree 207
                                       +L +              ++++  +e+ + +++le ++a+l +++++l ++a+e  + d+e+L+        +l  e
  gi|386002496|ref|YP_005920795.1|  38 ELLQ--------------NVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLArqalerkaALAVE 100
                                       3333..............34444455555566666666666666666666666666666555532111111123333 PP

                              Spc7 208 laelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                        a+l+++i+ ++ e ++l++   +l++k+e+ + +k++++++ ++ae
  gi|386002496|ref|YP_005920795.1| 101 AASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAE 147
                                       44455555555555555555555566666666666666666666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00081
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieek 218
                                       +l++++++le+++e+Le+ e  l++ +++++ +k+++++++   ++++      +  e+L  + ee+a++   +e+ 
  gi|386002496|ref|YP_005920795.1| 103 SLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQV------KvTESLTGISEEMADVGLAVERS 173
                                       455555555555555555555555555555555555555555555544......33889****************** PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlke 273
                                       ++++++++++ ++l+e +e  + +    +++++  e  + + +g+ e ++ rlke
  gi|386002496|ref|YP_005920795.1| 174 EDKIETMRARSAALDELVERGTLEEFGGKDDVE-RELARVRARGSVEADLARLKE 227
                                       ***************999998776655555555.333344456666667777665 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.0    0.0024       1.4      90     138 ..      30      78 ..      25      84 .. 0.90
   2 ?    4.5   3.7     0.039        22      99     144 ..      79     124 ..      73     149 .. 0.71
   3 ?    0.8   0.4      0.55   3.2e+02      66     131 ..     123     187 ..     119     196 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                     Fzo_mitofusin  90 ncshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkka 138
                                       + s q q el + ++r  ++v +++k le + ++l +++++l++  ++a
  gi|386002496|ref|YP_005920795.1|  30 DYSYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREA 78 
                                       67889999***********************************988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.039
                     Fzo_mitofusin  99 lsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnk 144
                                       ++   + l +q  e ++ l  e ++l+++i+ le+ q+k+++   +
  gi|386002496|ref|YP_005920795.1|  79 VKADREDLARQALERKAALAVEAASLDQQIADLEHEQEKLEATERR 124
                                       5566677888888999999999999999999999988877654332 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.55
                     Fzo_mitofusin  66 ralKrQfveyatekLrlivsltsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekl 131
                                       r+l +    +  +k    +++ +a+ + +v++ l+   +++  +v  + +  e++i++++++ ++l
  gi|386002496|ref|YP_005920795.1| 123 RRLSSKVEAFRVKKETIKAQYSAAEAQVKVTESLTGISEEMA-DVGLAVERSEDKIETMRARSAAL 187
                                       444444444444444444445555555555555555544442.34444444444444444444444 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.5      0.73   4.2e+02      42      71 ..      47      76 ..      27      82 .. 0.49
   2 ?    1.1   0.5      0.71   4.1e+02      22      46 ..      55      79 ..      46      98 .. 0.64
   3 ?   11.7   6.6   0.00033      0.19      11      58 ..     105     152 ..      96     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.73
                        TMF_DNA_bd 42 nkelekeikelkkkleklekeleeleerlk 71
                                      ++e  ++ k+l+ + ++l +++++l + ++
  gi|386002496|ref|YP_005920795.1| 47 VAEVATSKKRLELQRARLASKMDQLDDQAR 76
                                      334444444444444444444444444444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.71
                        TMF_DNA_bd 22 ekLskkelklnntikkLrkknkele 46
                                      ++L+ +  +l  ++++L+ +++e+ 
  gi|386002496|ref|YP_005920795.1| 55 KRLELQRARLASKMDQLDDQAREAV 79
                                      4455566666666666666666665 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00033
                        TMF_DNA_bd  11 DeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkklek 58 
                                       D+qIa L  E ekL+++e++l+ ++   r k +    + +  + +++ 
  gi|386002496|ref|YP_005920795.1| 105 DQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVKV 152
                                       9************************99998877666555555444444 PP

>> DUF1993  Domain of unknown function (DUF1993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   9.2     0.003       1.7      14     125 ..      38     152 ..      27     161 .. 0.67
   2 ?    0.7   0.1      0.86     5e+02      58     113 ..     147     208 ..     140     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHCCHHHHC..HHHHHT--SSTTS--HHHHHHHHHHHHHHHHCHHCT-GS----S.-SSHHHHHHHHH CS
                           DUF1993  14 knlsalLkkaeahaaakkidpeellearLapDMlpLsfQvqiatdtakkavarlagkeppsledeektfadlraria 90 
                                       + l+++ k++ a+ a++k +  el  arLa  M +L  Q + a+++ ++ +ar a +   +l  e  ++++ +a ++
  gi|386002496|ref|YP_005920795.1|  38 ELLQNV-KRGVAEVATSK-KRLELQRARLASKMDQLDDQAREAVKADREDLARQALERKAALAVEAASLDQQIADLE 112
                                       444443.33333333333.46789*****************************999988888777888888888888 PP

                                       HHHHHHHCS-GGGHCCCC.....CEEEE.C.CCCCEEEEH CS
                           DUF1993  91 ktialLesvdpekldake.....ekevelklggkeleftg 125
                                       +  + Le+++++   + e     +++++ +++  e+++++
  gi|386002496|ref|YP_005920795.1| 113 HEQEKLEATERRLSSKVEafrvkKETIKAQYSAAEAQVKV 152
                                       8888888877663333331112244444444555555554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.86
                                       HHHHHHHCHHCT-GS-......---S.-SSHHHHHHHHHHHHHHHHCS-GGGHCCCCCEEEE CS
                           DUF1993  58 dtakkavarlagkepp......sledeektfadlrariaktialLesvdpekldakeekeve 113
                                       ++  k+++ l+g + +      ++e++e++++ +rar a+  +l+e+ + e++ +k++ e e
  gi|386002496|ref|YP_005920795.1| 147 EAQVKVTESLTGISEEmadvglAVERSEDKIETMRARSAALDELVERGTLEEFGGKDDVERE 208
                                       44555555665553334455555677888999999999988888888888888777765554 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.8   0.00093      0.54     333     415 ..      41     122 ..      27     133 .. 0.83
   2 ?    0.6   0.2      0.28   1.6e+02     309     365 ..     137     196 ..     129     230 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00093
                              FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       +++k+ ++e+ +  ++le +  +l +k+++l++ +a++++++++++   ++le k +l  e ++l++++++l++e e
  gi|386002496|ref|YP_005920795.1|  41 QNVKRGVAEVATSKKRLELQRARLASKMDQLDD-QAREAVKADREDLARQALERKAALAVEAASLDQQIADLEHEQE 116
                                       577788888888888888888888888******.99**************************************999 PP

                              FapA 410 skkeea 415
                                       + ++ +
  gi|386002496|ref|YP_005920795.1| 117 KLEATE 122
                                       984443 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                              FapA 309 kevkakklGselgtkteiev.gldepelkekl..keleeeleeleeeleklkkkikklpk 365
                                       +++ka+  ++e+++k + ++ g++e  ++  l  ++ e+++e ++++   l++ +++   
  gi|386002496|ref|YP_005920795.1| 137 ETIKAQYSAAEAQVKVTESLtGISEEMADVGLavERSEDKIETMRARSAALDELVERGTL 196
                                       566777667777777777777777666666667777777777777766666666544444 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.0      0.11        63       7      44 ..      41      80 ..      35      94 .. 0.71
   2 ?    9.3   5.5    0.0023       1.3       5      67 ..      93     161 ..      89     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                             Spc24  7 friakelsdleselesleselaelkeeleeleeesee..k 44
                                      +++   + ++ ++ ++le + a+l +++++l+++  e  k
  gi|386002496|ref|YP_005920795.1| 41 QNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREavK 80
                                      5566667788888889999999999999999988888431 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0023
                             Spc24   5 ekfriakelsdleselesleselaelkeeleeleeesee...keser.ve.detllklklYrsL.Giel 67 
                                       +k ++a e+ +l++++ +le+e+++l+++ + l+++ e+   k++++ ++  ++  ++k+ +sL Gi+ 
  gi|386002496|ref|YP_005920795.1|  93 RKAALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAfrvKKETIkAQySAAEAQVKVTESLtGISE 161
                                       577889999999999999999999999999999999888887333332444666688888888888865 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  22.0    0.0012       0.7      10     130 ..      39     154 ..      11     157 .. 0.80
   2 ?   -0.8   1.9       3.6   2.1e+03     103     103 ..     196     196 ..     154     231 .] 0.51

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                            APG6_N  10 LleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaa 86 
                                       Ll+++++ ++++   ++ +e   ++l ++ ++      ++++ e   ++ e+  +++le  ++l  e ++l++++a+
  gi|386002496|ref|YP_005920795.1|  39 LLQNVKRGVAEVATSKKRLELQRARLASKMDQL-----DDQAREAVKADREDLARQALERKAALAVEAASLDQQIAD 110
                                       555555555566666666665555555554442.....4445555567788888999999999************** PP

                            APG6_N  87 leeelealeeeeerfwreynelqlelleleeeldsleaqyehaq 130
                                       le e e+le+ e+r  ++  +++++++  + +  + eaq++ ++
  gi|386002496|ref|YP_005920795.1| 111 LEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVKVTE 154
                                       ***************************************99876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.6
                            APG6_N 103 r 103
                                        
  gi|386002496|ref|YP_005920795.1| 196 L 196
                                       1 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         6   3.5e+03      26      43 ..      17      34 ..       6      50 .. 0.66
   2 ?   -1.1   0.1       3.2   1.9e+03      14      37 ..      54      77 ..      39      89 .. 0.70
   3 ?    6.6   0.9     0.013       7.4       5      47 ..     106     148 ..     104     155 .. 0.88
   4 ?    2.8   0.0       0.2   1.1e+02       7      30 ..     170     193 ..     167     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6
                             SLIDE 26 kkveqyknplqelkikyp 43
                                        ++++++p + l+ +y+
  gi|386002496|ref|YP_005920795.1| 17 TLMDRVEDPNETLDYSYQ 34
                                      455666666666665554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.2
                             SLIDE 14 ieklkelkellkkkveqyknplqe 37
                                       ++l+ +++ l++k++q+++  +e
  gi|386002496|ref|YP_005920795.1| 54 KKRLELQRARLASKMDQLDDQARE 77
                                      345556667788888887776655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                             SLIDE   5 kqIekgekkieklkelkellkkkveqyknplqelkikyppsnk 47 
                                       +qI   e+++ekl+  ++ l +kve+++   + +k +y+++++
  gi|386002496|ref|YP_005920795.1| 106 QQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEA 148
                                       689999***************************9999976554 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.2
                             SLIDE   7 Iekgekkieklkelkellkkkveq 30 
                                       +e++e+kie ++   ++l++ ve+
  gi|386002496|ref|YP_005920795.1| 170 VERSEDKIETMRARSAALDELVER 193
                                       89*****************99986 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0  12.0       4.8   2.8e+03      70      70 ..      88      88 ..      14     190 .. 0.62
   2 ?   -0.1   0.0       2.5   1.4e+03      19      52 ..     158     191 ..     144     228 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.8
                                      X CS
                              YabA 70 k 70
                                      +
  gi|386002496|ref|YP_005920795.1| 88 R 88
                                      1 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  19 elleeleelkeelaelleenaeLeleneklrerl 52 
                                        ++ee++++  ++++  ++ +++++    l e++
  gi|386002496|ref|YP_005920795.1| 158 GISEEMADVGLAVERSEDKIETMRARSAALDELV 191
                                       3334444444444444444444444443333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.5    0.0056       3.2     103     184 ..      32     118 ..      15     120 .. 0.82
   2 ?    6.6   8.2     0.011       6.2     111     185 ..      83     154 ..      75     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0056
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk.....ekkeaadkeiarlkseaekleeel 174
                                       +++k le ++++++ ++e +++k++le + + l +k+ +l  q+  +          +a ++ a+l +ea++l++++
  gi|386002496|ref|YP_005920795.1|  32 SYQKQLELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVkadreDLARQALERKAALAVEAASLDQQI 108
                                       67888999999999**************************9998776656655334455667788999999999999 PP

                            DUF724 175 edveqeFeav 184
                                        d e+e e++
  gi|386002496|ref|YP_005920795.1| 109 ADLEHEQEKL 118
                                       9999987765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                            DUF724 111 rkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeava 185
                                       r++l ++  e    k+ l  e + l+++i++le +++ l + + + ++++ + ++++e+++ +++++e +++ + 
  gi|386002496|ref|YP_005920795.1|  83 REDLARQALER---KAALAVEAASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVKVTE 154
                                       44444444444...4456678889999*****9999999999999999999999999999999999999998775 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6      0.63   3.6e+02      37      62 ..      34      58 ..       1      66 [. 0.71
   2 ?    1.7   0.8      0.58   3.3e+02      10      31 ..      66      88 ..      62      98 .. 0.71
   3 ?   12.8   2.8   0.00019      0.11      15      62 ..     104     151 ..     101     161 .. 0.94
   4 ?    2.0   0.1      0.47   2.7e+02      24      50 ..     161     187 ..     153     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.63
                               CLZ 37 essLeaLqtrlarLlaeyessqrkLk 62
                                      +++Le Lq+ ++r +ae+ +s+++L+
  gi|386002496|ref|YP_005920795.1| 34 QKQLELLQN-VKRGVAEVATSKKRLE 58
                                      567777775.7888888888888876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.58
                               CLZ 10 lKdglLDeeaakag.aeqkelee 31
                                       K++ LD +a++a  a++++l +
  gi|386002496|ref|YP_005920795.1| 66 SKMDQLDDQAREAVkADREDLAR 88
                                      59999*99954443377776654 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00019
                               CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                       LD++ a+ + eq++le   +rL s++ea+  + + + a+y++++++ k
  gi|386002496|ref|YP_005920795.1| 104 LDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQYSAAEAQVK 151
                                       9****************************************9998876 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.47
                               CLZ  24 aeqkeleekverLessLeaLqtrlarL 50 
                                       +e  ++   ver e ++e++  r a L
  gi|386002496|ref|YP_005920795.1| 161 EEMADVGLAVERSEDKIETMRARSAAL 187
                                       556677778999999999999999987 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.3     0.082        48      20      79 ..      38      97 ..      33     102 .. 0.80
   2 ?    6.8   7.0     0.014         8      23      73 ..     102     151 ..      82     199 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.082
                              YlqD 20 elqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkql 79
                                      el+q++++ + ++ +  ++Le+q  rl +++ + + q+ e++++  e   ++ le+k+ l
  gi|386002496|ref|YP_005920795.1| 38 ELLQNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLARQALERKAAL 97
                                      678888888888888889999999999999998888888888888888888888887765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                              YlqD  23 qqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserl 73 
                                       ++l++qi  l++e ++Le  ++rl ++++   + ++e+i++q+++ +++++
  gi|386002496|ref|YP_005920795.1| 102 ASLDQQIADLEHEQEKLEATERRLSSKVEAFRV-KKETIKAQYSAAEAQVK 151
                                       234444444444444444444444444443332.55555555554444332 PP

>> DUF3708  Phosphate ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.0    0.0069         4      92     149 ..      62     119 ..       8     134 .. 0.76
   2 ?   -1.8   0.0       4.1   2.4e+03     118     118 ..     148     148 ..     112     191 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0069
                           DUF3708  92 rniaegldaLsaaeaealkatadeirallaavgvalgtevtpavvaaaahlrarqrve 149
                                        ++a+ +d+L+++ +ea+ka+++++++ + +  +al++e++++  ++a    + +++e
  gi|386002496|ref|YP_005920795.1|  62 ARLASKMDQLDDQAREAVKADREDLARQALERKAALAVEAASLDQQIADLEHEQEKLE 119
                                       468888888***********9999999999999****998887777665444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.1
                           DUF3708 118 a 118
                                       a
  gi|386002496|ref|YP_005920795.1| 148 A 148
                                       1 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.9     0.034        19     108     166 ..      30      85 ..       6      96 .. 0.71
   2 ?    6.4   6.2     0.013       7.8     120     162 ..     100     142 ..      84     154 .. 0.65
   3 ?    3.0   1.1      0.15        87     102     165 ..     125     193 ..     120     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.034
                   Ax_dynein_light 108 aFgmrkalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekk 166
                                        +  +k+l+     +++++ ++e+ + k++le q a l +k+++l+ ++ e  +++++ 
  gi|386002496|ref|YP_005920795.1|  30 DYSYQKQLELL---QNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADRED 85 
                                       55566666444...356666777888888888888888888888888888877766554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                   Ax_dynein_light 120 gkselekkikeLeeekeelekqvaelkaklealekrekerrqe 162
                                       + + l+++i++Le+e+e+le     l +k+ea + +++  +++
  gi|386002496|ref|YP_005920795.1| 100 EAASLDQQIADLEHEQEKLEATERRLSSKVEAFRVKKETIKAQ 142
                                       4566778888888888888888888888888776665554444 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.15
                   Ax_dynein_light 102 lyessvaFgmrkal.qaeqgkselekkike....Leeekeelekqvaelkaklealekrekerrqeeek 165
                                       l  +  aF ++k++ +a+   +e + k++e    + ee ++    v+  + k+e++++r++   +  e+
  gi|386002496|ref|YP_005920795.1| 125 LSSKVEAFRVKKETiKAQYSAAEAQVKVTEsltgISEEMADVGLAVERSEDKIETMRARSAALDELVER 193
                                       555566788888765666666666666444444478888888888888888888888888776666665 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  15.9     0.027        16     146     258 ..      19     127 ..       3     199 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.027
                      Exonuc_VII_L 146 eeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl. 221
                                        +++e+ ++ l+ + +++le   q++++   ++++++++le +r rl +  ++l+ + ++++k+ re+l + +  l 
  gi|386002496|ref|YP_005920795.1|  19 MDRVEDPNETLDYSYQKQLELL-QNVKRGVAEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLARQA--Le 92 
                                       4444444444444444444322.22222233345566666666666666666666666666666666666655..21 PP

                      Exonuc_VII_L 222 k...............ekleekkerlkklkerlelleekkerleeleeklea 258
                                       +               +                  le+++e+le+ e++l++
  gi|386002496|ref|YP_005920795.1|  93 RkaalaveaasldqqiA-----------------DLEHEQEKLEATERRLSS 127
                                       12223322322222222.................333333333333333322 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.3      0.53   3.1e+02      72     104 ..      38      69 ..       4      78 .. 0.47
   2 ?    2.3   2.6       0.3   1.7e+02      76     115 ..      48      87 ..      31     103 .. 0.67
   3 ?   -2.2   8.5       7.2   4.2e+03      70     104 ..      96     130 ..      47     149 .. 0.50
   4 ?    8.4   0.2    0.0038       2.2      58     101 ..     150     193 ..     143     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.53
                              COG2  72 eevesplaaarkkvesvreklsereeeveskle 104
                                       e ++ ++++ + +v   ++ l+ +++++ sk++
  gi|386002496|ref|YP_005920795.1|  38 ELLQ-NVKRGVAEVATSKKRLELQRARLASKMD 69 
                                       2222.2333333333333333333333333333 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.3
                              COG2  76 splaaarkkvesvreklsereeeveskleeakeleekrel 115
                                        ++a+ +k++e  r+ l+ ++ +++++ +ea ++ ++   
  gi|386002496|ref|YP_005920795.1|  48 AEVATSKKRLELQRARLASKMDQLDDQAREAVKADREDLA 87 
                                       3566677888888888888888888888887777666544 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.2
                              COG2  70 eleevesplaaarkkvesvreklsereeeveskle 104
                                       +l     +l +   ++e  +ekl+++e++++sk+e
  gi|386002496|ref|YP_005920795.1|  96 ALAVEAASLDQQIADLEHEQEKLEATERRLSSKVE 130
                                       33333344555555566666666666666666665 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0038
                              COG2  58 vslSghLvglqeeleevesplaaarkkvesvreklsereeeves 101
                                       v++ ++L+g+ ee+  v   +++  +k+e +r+  ++  e ve 
  gi|386002496|ref|YP_005920795.1| 150 VKVTESLTGISEEMADVGLAVERSEDKIETMRARSAALDELVER 193
                                       89******************************999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1929  (0.107591); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.83u 0.36s 00:00:01.19 Elapsed: 00:00:00.53
# Mc/sec: 1301.62
//
Query:       gi|386002497|ref|YP_005920796.1|  [L=187]
Description: hypothetical protein Mhar_1815 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1089.68
//
Query:       gi|386002498|ref|YP_005920797.1|  [L=742]
Description: hypothetical protein Mhar_1816 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-32  112.6   0.0    3.9e-32  111.8   0.0    1.4  1  Helicase_C_2  Helicase C-terminal domain
    8.7e-12   45.0   0.0    1.5e-11   44.2   0.0    1.4  1  DEAD_2        DEAD_2
    6.8e-06   26.2   0.0     0.0035   17.4   0.0    2.6  2  ResIII        Type III restriction enzyme, res subunit
    1.1e-05   25.9   0.1      0.011   16.1   0.0    3.3  4  AAA_16        AAA ATPase domain
    7.5e-05   22.5   0.0     0.0002   21.1   0.0    1.8  1  HBB           Helical and beta-bridge domain
     0.0069   16.7   0.3       0.49   10.7   0.0    3.2  3  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.028   14.2   0.1       0.18   11.5   0.0    2.2  2  DEAD          DEAD/DEAH box helicase
       0.13   13.0   0.0       0.28   11.9   0.0    1.5  1  Herpes_U15    Human herpesvirus U15 protein


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0   1.7e-35   3.9e-32       3     169 ..     544     715 ..     542     717 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.7e-35
                      Helicase_C_2   3 ellevvpggvlvffpSyklleevverlkeeleskkieifvee.keesrekvleeykek.kkkgaillavcrGklsEG 77 
                                        ++e v g+v vff+Sy+++ +   + k+     ++ +f+e+ ++e+  ++l+++ ++ k++ga+ll+v +Gkl EG
  gi|386002498|ref|YP_005920797.1| 544 AVIEEVSGNVAVFFTSYSMMSQYEPFCKAAARGVGKLLFTEPrNSEDLPAILDDFFKAgKRQGAVLLGVSGGKLAEG 620
                                       578999************************999999****9989999********9966****************** PP

                      Helicase_C_2  78 idfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeR 154
                                       id+++++l+ v +vglP+  +++ + e  + y++++g+kn+   +y+ +a+++  Qa+GR+iR++ ++g+i+++D+R
  gi|386002498|ref|YP_005920797.1| 621 IDYKGEALNGVAVVGLPLGFYNEIQREVNQYYVRKYGQKNGILIAYTLPAINRGLQAAGRVIRDASERGVILFCDRR 697
                                       **************************************999************************************ PP

                      Helicase_C_2 155 fakee...ireklpkwlr 169
                                       f++e    + + lpkw++
  gi|386002498|ref|YP_005920797.1| 698 FREEGrggVFSFLPKWIQ 715
                                       **9762224455668887 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   6.6e-15   1.5e-11       3     165 ..      96     296 ..      94     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 6.6e-15
                                       ESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH......... CS
                            DEAD_2   3 sRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek......... 70 
                                       +RT+sq++ +++e++k+ s +  +++  ++ + +++++C    + +e ++++v + C +l++ ++++          
  gi|386002498|ref|YP_005920797.1|  96 VRTVSQIDVYLDEMEKIWSKT--SHRPTITYMVGKQKICP---IADEFSGESVYAGCARLREWTKRRMiarlgevgg 167
                                       7****************7544..47788999********4...345555788999****999888877999****** PP

                                       ..................TTTTTT-SCCCCHHHH....HHHHHHC---C.HHHHH........HHHHCT--HHHHHH CS
                            DEAD_2  71 ..................eekCsffenleelkkl....kkllleevvdi.edlve........lgeklklCPYylsr 116
                                                          + C+++  ++e+ +l    + +   +v+d+ ++l e          e  ++CPY ++ 
  gi|386002498|ref|YP_005920797.1| 168 kfydpsqdrnapqsvpgyRTFCPYYMMTREVFELsgkpHFRHSGKVLDLvDELREgirspdrfQKECREVCPYEVMS 244
                                       ******************999****99966666555456666677777536777799999996666779******** PP

                                       HHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHH CS
                            DEAD_2 117 elledadiiilpYqyLldekireslk...gislknsivilDEAhNiedvcee 165
                                         ++  d++il Y+ L++++  e +    +++ +   + +DEAhN+ d ++ 
  gi|386002498|ref|YP_005920797.1| 245 LSAKGSDVVILNYSHLFSPEFQEIIFdwlELERESLTLFVDEAHNLGDAVRA 296
                                       ***********************98777778888889999*******99876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06    0.0035       3      50 ..      43      90 ..      42     141 .. 0.75
   2 !    6.0   0.0    0.0049        11     100     147 ..     246     293 ..     209     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                      EE-HHHHHHHHHHT......TTSEEE.EEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  3 elreyQeeaienlleklkskrdkrgl.ikmaTGtGKTlvaaklierllk 50
                                      +lr+yQ  +++++  ++   +d+ +l i ++TG+GKT ++a++ ++   
  gi|386002498|ref|YP_005920797.1| 43 SLRPYQDAMLDDVYGTVR-AGDHGVLmIDAPTGSGKTSCIAAALAAAPG 90
                                      59************9999.77776555************9887766554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0049
                                       ....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                            ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                       +++ +++++ +++ l +++ +e   +   l+ +++ +++DEaH+lg++
  gi|386002498|ref|YP_005920797.1| 246 SAKGSDVVILNYSHLFSPEFQEIIFDWLELERESLTLFVDEAHNLGDA 293
                                       55677888888888888887777777778888888**********984 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.1e-06     0.011      10      54 ..      50      94 ..      45     137 .. 0.85
   2 !    5.6   0.0    0.0083        19     106     159 ..     239     303 ..     207     314 .. 0.74
   3 ?   -2.9   0.0       3.4   7.5e+03      57      87 ..     378     402 ..     344     456 .. 0.59
   4 ?   -1.5   0.0       1.3   2.9e+03     106     106 ..     600     600 ..     524     696 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.1e-06
                            AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggi 54
                                      ++L +++++vr+g+ +++++  + G+GK+s + ++l a+ ++ ++
  gi|386002498|ref|YP_005920797.1| 50 AMLDDVYGTVRAGDHGVLMIDAPTGSGKTSCIAAALAAAPGKIAV 94
                                      789*******************************99988888233 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0083
                            AAA_16 106 a.avpelagaea........srllellkrll.allsrderplvlvlDdlqwadeaslql.laaLl 159
                                         +v +l+++++        + +  ++++++ + l+ +++ l l++D+++ + +a ++l +++L 
  gi|386002498|ref|YP_005920797.1| 239 PyEVMSLSAKGSdvvilnysHLFSPEFQEIIfDWLELERESLTLFVDEAHNLGDAVRALnMRLLT 303
                                       366666666666777777777788899****9999996667****************99887775 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.4
                            AAA_16  57 rgkcdqlesaipysalaqalareellrqlld 87 
                                       ++ +d+ e+       ++a+++  l+  +l+
  gi|386002498|ref|YP_005920797.1| 378 YQGFDDIEE------ALSAATEVALMVSELE 402
                                       444444422......2333323222222222 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.3
                            AAA_16 106 a 106
                                       +
  gi|386002498|ref|YP_005920797.1| 600 K 600
                                       1 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.7e-08    0.0002     118     187 ..     451     525 ..     414     528 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.7e-08
                                       T..EECCCCS-TCCHHH.HHHHCHCCCCCCTS-SSHHHHHH.HHT....EEE...S..S.GGHCCCCCCCCCSHT CS
                               HBB 118 g.esLeavcldPskalr.flkerlssllmsgtltpleeysd.iiGleaklkkf..pspfpkEnlivlfatdVsTk 187
                                           Le   +dP+  +r    ++  +++ sgtl+ple+y+  i+G + + kk+  p+pfp+E ++  +a+  +T+
  gi|386002498|ref|YP_005920797.1| 451 RrAWLEVNNVDPAPLVRrITDNINATVMLSGTLSPLEAYELyILGERGRAKKIslPNPFPQEHRLLMVAKAATTQ 525
                                       247899999***9887615567889999***********95267777666665449*************999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00022      0.49       4      46 ..      63     105 ..      59     131 .. 0.76
   2 ?    1.6   0.1      0.14   3.1e+02      94     110 ..     281     295 ..     269     312 .. 0.72
   3 ?   -0.5   0.0      0.63   1.4e+03      22      91 ..     519     604 ..     517     610 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46 
                                       ++g+l++ +++G+GKT +++  l  ++  ++ + + ++++ v+
  gi|386002498|ref|YP_005920797.1|  63 DHGVLMIDAPTGSGKTSCIAAALAAAPGKIAVTVRTVSQIDVY 105
                                       6799****************99999876655555555555444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                            AAA_22  94 lliiDEaqhlrseeale 110
                                        l +DEa++l   +a++
  gi|386002498|ref|YP_005920797.1| 281 TLFVDEAHNLG--DAVR 295
                                       689*******3..3333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.63
                            AAA_22  22 lrrlleqldeeakaee...............erpevvfvtlpsst.sskdllrellralglelkaerlsseelleal 82 
                                       ++  + ql+++++a +                +   vf+t  s +   + ++++ +r +g  l +e+ +se+l + l
  gi|386002498|ref|YP_005920797.1| 519 AKAATTQLEKREEAGNrreieehvravieevSGNVAVFFTSYSMMsQYEPFCKAAARGVGKLLFTEPRNSEDLPAIL 595
                                       55556666666666556666655665665333333335555555557777899999999988888888888888877 PP

                            AAA_22  83 eqalrarav 91 
                                        + ++a ++
  gi|386002498|ref|YP_005920797.1| 596 DDFFKAGKR 604
                                       777776665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.2e-05      0.18       3      36 ..      47      86 ..      45     127 .. 0.79
   2 ?   -0.2   0.0      0.33   7.5e+02     124     138 ..     281     295 ..     235     320 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                                      HHHHHHHHHH......TTCEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  3 iQaeaiplil......gggdvlvaaeTGsGKTlaflipvl 36
                                      +Q+++++ ++      + g +++ a+TGsGKT + + ++ 
  gi|386002498|ref|YP_005920797.1| 47 YQDAMLDDVYgtvragDHGVLMIDAPTGSGKTSCIAAALA 86
                                      56666666664443323367889**********9877665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                                       EEEEETHHHHHHTTT CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldqgf 138
                                       +l +DEa++l d  +
  gi|386002498|ref|YP_005920797.1| 281 TLFVDEAHNLGDAVR 295
                                       3678*****999754 PP

>> Herpes_U15  Human herpesvirus U15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.28      10      46 ..     232     267 ..     225     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                        Herpes_U15  10 qecrelcplpvlmslsnllskieivyvkylfkmdfst 46 
                                       +ecre+cp  v msls   s++ i+   +lf  +f  
  gi|386002498|ref|YP_005920797.1| 232 KECREVCPYEV-MSLSAKGSDVVILNYSHLFSPEFQE 267
                                       59******975.9*************9****998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 4385.55
//
Query:       gi|386002499|ref|YP_005920798.1|  [L=128]
Description: hypothetical protein Mhar_1817 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-45  153.4   0.0    2.2e-45  153.1   0.0    1.1  1  DUF555       Protein of unknown function (DUF555)
  ------ inclusion threshold ------
      0.055   12.9   0.0      0.097   12.1   0.0    1.3  1  zf-ribbon_3  zinc-ribbon domain
       0.06   13.6   0.1       0.12   12.6   0.1    1.5  1  Dodecin      Dodecin


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.0   3.7e-49   2.2e-45       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 3.7e-49
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkv 76 
                                       +++v le+aw+vrdvks+ddAig+Aiseagkrln++ ld+ve+evg+t cP+cge+l+++++va+talvgll+e++v
  gi|386002499|ref|YP_005920798.1|   3 NFKVLLEGAWLVRDVKSADDAIGVAISEAGKRLNSKkLDYVEVEVGQTVCPACGESLDGVFMVAGTALVGLLFEIRV 79 
                                       799********************************99**************************************** PP

                            DUF555  77 fnaeseEhaeriakseigkaledvP 101
                                       ++ae eEha riaks+igkal  vP
  gi|386002499|ref|YP_005920798.1|  80 YDAEGEEHAFRIAKSTIGKALGAVP 104
                                       ***********************99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.6e-05     0.097      13      24 ..      46      57 ..      44      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                       zf-ribbon_3 13 ssddnvCpyCGt 24
                                      + +++vCp CG+
  gi|386002499|ref|YP_005920798.1| 46 EVGQTVCPACGE 57
                                      67999*****97 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     2e-05      0.12      13      38 ..      18      45 ..      17      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                      S-HHHHHHHHHHHHHHH-..SSEEEEEE CS
                           Dodecin 13 kSwedAiqnAiaeAsktl..rnirwveV 38
                                      kS +dAi  Ai+eA k l  ++++ veV
  gi|386002499|ref|YP_005920798.1| 18 KSADDAIGVAISEAGKRLnsKKLDYVEV 45
                                      799*************993346777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 766.84
//
Query:       gi|386002500|ref|YP_005920799.1|  [L=167]
Description: hypothetical protein Mhar_1818 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 964.19
//
Query:       gi|386002501|ref|YP_005920800.1|  [L=735]
Description: RNA binding S1 domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-64  215.8   0.1    3.4e-63  212.6   0.1    2.1  2  Tex_N     Tex-like protein N-terminal domain
    2.4e-44  150.8   0.0    4.8e-44  149.8   0.0    1.5  1  Tex_YqgF  Tex protein YqgF-like domain
    1.9e-29  101.7   0.0    3.8e-29  100.7   0.0    1.6  1  HHH_3     Helix-hairpin-helix motif
    1.2e-20   73.6   0.4    2.4e-20   72.7   0.4    1.5  1  S1        S1 RNA binding domain
    2.8e-20   73.0   0.1    8.9e-20   71.4   0.1    1.9  1  HHH_9     HHH domain
    4.1e-09   35.9   0.2     0.0022   17.8   0.0    3.0  2  HHH       Helix-hairpin-helix motif
      5e-07   29.6   0.0    9.5e-07   28.7   0.0    1.4  1  YqgF      Holliday-junction resolvase-like of SPT6
      6e-05   23.3   0.0    0.00012   22.4   0.0    1.4  1  HHH_7     Helix-hairpin-helix motif
    0.00031   20.7   0.0    0.00091   19.2   0.0    1.7  1  PsbU      Photosystem II 12 kDa extrinsic protein (PsbU)
    0.00072   20.1   0.0       0.18   12.5   0.0    3.1  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.081   13.2   0.0    2.2  1  HHH_6     Helix-hairpin-helix motif
      0.046   13.8   0.0       0.32   11.1   0.0    2.3  2  HHH_2     Helix-hairpin-helix motif
      0.054   13.5   0.4       0.16   12.0   0.4    1.7  1  CARD      Caspase recruitment domain
       0.13   11.7   0.0       0.21   11.0   0.0    1.3  1  T2SSK     Type II secretion system (T2SS), protein K


Domain annotation for each model (and alignments):
>> Tex_N  Tex-like protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.6   0.1   2.7e-66   3.4e-63       2     182 .]      20     203 ..      19     203 .. 0.98
   2 ?    0.7   0.0      0.29   3.7e+02     116     159 ..     588     627 ..     579     645 .. 0.73

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 2.7e-66
                             Tex_N   2 aeelslkekqveavveLldegatvPFIARYRkeatggldeeqlreieerleylrelekrkeevlksieeqgklteeL 78 
                                        +el+l+ekqv+a+++Ll++g+t+PFIARYRkeatgglde++l ++++r e +rel++r++++l+s++e++ lteeL
  gi|386002501|ref|YP_005920800.1|  20 GRELGLREKQVHAALALLEDGKTIPFIARYRKEATGGLDEVALAAVRDRAELIRELDRRRSSILRSLREREVLTEEL 96 
                                       5799************************************************************************* PP

                             Tex_N  79 kkkieaaktleeledlylpYkpkrkTkatiArekGLeplAelileqksl.aeeeaakyvn..kevksaeealegard 152
                                       +k+i +a t++ ledlylp++pkr+T+a++Are+GL plA+ i++q +  + +eaak+++  +ev s++eal+gard
  gi|386002501|ref|YP_005920800.1|  97 EKRILEAPTIAVLEDLYLPFRPKRRTRASVARERGLLPLADRIFDQGEIdPGAEAAKFLDpeREVGSVDEALAGARD 173
                                       *********************************************9977779********99*************** PP

                             Tex_N 153 Iiaeeisedaelrkklrellkkegvivskv 182
                                       Iiae+ised+ +r+++r+l+ +eg+++skv
  gi|386002501|ref|YP_005920800.1| 174 IIAERISEDPGARSRIRDLFLREGILRSKV 203
                                       **************************9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                             Tex_N 116 plAelileqksl.aeeeaakyvnkevksaeealegardIiaeeis 159
                                         +e ++ +++l ++ ea++yv     ++++ l  +rdI+ae ++
  gi|386002501|ref|YP_005920800.1| 588 ATVEDLIRDPHLqERIEAERYV-----TEKAGLPTIRDILAELAK 627
                                       5566666666553457788884.....7899999*******9765 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   3.7e-47   4.8e-44       2     126 .]     332     454 ..     331     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 3.7e-47
                                       -EEEEE--STT-EEEEEE-TTS-EEEEEEE--STTT--HHHHHHHHHHHHHHTT--EEEEESSTTHHHHHHHHHHHH CS
                          Tex_YqgF   2 vvlglDPgyrtGcKlavvdetgkvletaviyphepkkkveeakkklkklvkkykveliaiGnGtasreteklvaeli 78 
                                       +v+++DPg+rtGcK++++d++g++l+++vi+ph p + v+ea++k+ +l++++ ve+ia+GnGta+rete++++ l 
  gi|386002501|ref|YP_005920800.1| 332 TVMAIDPGFRTGCKVVILDRSGSLLAKEVIFPHPPPRAVQEAERKILDLCERFGVEFIAVGNGTAGRETEEFLRGLG 408
                                       79************************************************************************987 PP

                                       HHGGG--EEEEE--TTHHHHHHSHHHHHH-TTS-HHHHHHHHHHHHHH CS
                          Tex_YqgF  79 keeelkvkyvivsEaGaSvYSaselaaeEfpdldvslrgavsiarrlq 126
                                            +v +v+v+EaGaSvYS+s+ a+eEfp+ d ++r+a+si+rrlq
  gi|386002501|ref|YP_005920800.1| 409 IP--GDVPIVMVDEAGASVYSTSRAAREEFPEEDATIRSAISIGRRLQ 454
                                       54..589****************************************9 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0     3e-32   3.8e-29       1      65 []     494     558 ..     494     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 3e-32
                             HHH_3   1 vnavgvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpktfeqlagflr 65 
                                       vnavgvd+NtAs e+L++++GlgpklA+ Iv yRe+nGpf++reeL+kv+glgp +feq+agflr
  gi|386002501|ref|YP_005920800.1| 494 VNAVGVDLNTASIELLSRVAGLGPKLARSIVLYREENGPFRTREELKKVPGLGPRAFEQAAGFLR 558
                                       79*************************************************************97 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.4   1.8e-23   2.4e-20       4      75 .]     653     723 ..     650     723 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.8e-23
                                       TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                        g  + G+Vt+v  +GafV++g +++g+v++sel+++  v+dp ev++v+++v+v vlkvd +r+ri+ls++
  gi|386002501|ref|YP_005920800.1| 653 PGMSLPGTVTNVAAFGAFVDVGVHQDGLVHKSELADR-FVRDPAEVVRVHQKVEVTVLKVDLERKRISLSMR 723
                                       688899*******************************.********************************97 PP

>> HHH_9  HHH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.1   6.9e-23   8.9e-20       1      70 []     564     633 ..     564     633 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 6.9e-23
                             HHH_9   1 npLDnTavHPEsYalakkllkklgldlkeligeeallkkldkkklaeeevgeptleDIleeLakPgrDpR 70 
                                       +pLD +avHPEs  ++++++ +lg+++++li++  l+++++++++++e++g+pt++DIl+eLakPgrDpR
  gi|386002501|ref|YP_005920800.1| 564 DPLDGSAVHPESSGIVEAMAGDLGATVEDLIRDPHLQERIEAERYVTEKAGLPTIRDILAELAKPGRDPR 633
                                       69*******************************************************************9 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0022       5      30 .]     501     526 ..     499     526 .. 0.93
   2 !   15.0   0.0   1.3e-05     0.017       2      21 ..     528     547 ..     527     548 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                       HHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   5 lipasreeLlalPGVGpktAeaIlsy 30 
                                       l++as+e L  + G Gpk A++I  y
  gi|386002501|ref|YP_005920800.1| 501 LNTASIELLSRVAGLGPKLARSIVLY 526
                                       89*********************987 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHTSSHHHHHTSTT-SH CS
                               HHH   2 leglipasreeLlalPGVGp 21 
                                        e+   ++reeL+++PG Gp
  gi|386002501|ref|YP_005920800.1| 528 EENGPFRTREELKKVPGLGP 547
                                       578899*************9 PP

>> YqgF  Holliday-junction resolvase-like of SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   7.5e-10   9.5e-07      99     147 ..     413     461 ..     409     464 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.5e-10
                                       --EEE---TTHHHHHTSHHHHHHSTT--HHHHHHHHHHHHHH-HHHHHH CS
                              YqgF  99 vgvilvddevailYqnskkaeaefrdkPpllkyavalaRkiqdPLleya 147
                                       v++++vd+  a  Y  s+ a +ef++  + ++ a+++ R++qdPL e  
  gi|386002501|ref|YP_005920800.1| 413 VPIVMVDEAGASVYSTSRAAREEFPEEDATIRSAISIGRRLQDPLAELV 461
                                       89*******************************************9976 PP

>> HHH_7  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     9e-08   0.00012       6     103 ..     468     559 ..     464     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9e-08
                                       S---TTGGGS-HHHHHHHHHHHHHHH.HHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHHHC-S----TT CS
                             HHH_7   6 lsfhPlqellskeellkaletalvdi.vnlvgvdvnkavankyeaallkyiaGlGprkatdllkklkrlnerlears 81 
                                       + +  +q+ + ++ l   l+ ++v+i vn vgvd+n a     + +ll  +aGlGp+ a  ++   ++ n+++ +r+
  gi|386002501|ref|YP_005920800.1| 468 IGVGQYQHDVDEKALKMKLD-EVVEIsVNAVGVDLNTA-----SIELLSRVAGLGPKLARSIV-LYREENGPFRTRE 537
                                       55667899999999988887.56665389*******99.....5679**********999987.468899******* PP

                                       HHHHTTSS-HHHHHHHCCCEE- CS
                             HHH_7  82 qlitkqilskkvflncagflki 103
                                       +l     l+++ f  +agfl i
  gi|386002501|ref|YP_005920800.1| 538 ELKKVPGLGPRAFEQAAGFLRI 559
                                       ********************98 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.1e-07   0.00091      14      59 ..     498     547 ..     486     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.1e-07
                                       SEETTTS-GGGGGGSTTTTTHHHHHHH....HS---SSGGGGGG-TT--H CS
                              PsbU  14 kvDlnnanvrafrqlrGlyPtlakkiv....knaPYdsvedvlniPgLse 59 
                                        vDln a++    ++ Gl P+la  iv    +n+P+ + e++ ++PgL  
  gi|386002501|ref|YP_005920800.1| 498 GVDLNTASIELLSRVAGLGPKLARSIVlyreENGPFRTREELKKVPGLGP 547
                                       59************************9666669**************975 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00014      0.18      28      53 ..     500     525 ..     491     529 .. 0.86
   2 ?    4.1   0.0     0.058        74      35      46 ..     537     548 ..     534     552 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                       HHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5  28 dlaaadveeLakipGiGkktAeriil 53 
                                       dl  a++e L+++ G+G+k+A++i+l
  gi|386002501|ref|YP_005920800.1| 500 DLNTASIELLSRVAGLGPKLARSIVL 525
                                       5567899999***********99987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.058
                                       HHHHTSTTS-HH CS
                             HHH_5  35 eeLakipGiGkk 46 
                                       eeL k+pG+G++
  gi|386002501|ref|YP_005920800.1| 537 EELKKVPGLGPR 548
                                       677777777765 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.3e-05     0.081      29      61 ..     509     541 ..     461     555 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                             HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlar 61 
                                       L+ + glg + a++iv  Re++gpf++ e+l +
  gi|386002501|ref|YP_005920800.1| 509 LSRVAGLGPKLARSIVLYREENGPFRTREELKK 541
                                       899***********************9998865 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.32      29      54 ..     501     526 ..     499     531 .. 0.90
   2 ?   -1.3   0.0       1.8   2.3e+03      33      46 ..     535     548 ..     534     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                             HHH_2  29 LkkasleeLlevddiGeeiAqsivef 54 
                                       L +as+e L+ v + G++ A+siv +
  gi|386002501|ref|YP_005920800.1| 501 LNTASIELLSRVAGLGPKLARSIVLY 526
                                       899********************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                             HHH_2  33 sleeLlevddiGee 46 
                                       + eeL +v++ G++
  gi|386002501|ref|YP_005920800.1| 535 TREELKKVPGLGPR 548
                                       679*********97 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00012      0.16       7      44 ..      67     105 ..      64     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       THHHHHHHSS.HHHHHHHHHHHTTSS-HHHHHHHHTSSS CS
                              CARD   7 nrkrLverlk.slsglldyLlekkVLteeeeekikaktt 44 
                                        r +L+++l    s +l  L+e++VLtee e +i++ +t
  gi|386002501|ref|YP_005920800.1|  67 DRAELIRELDrRRSSILRSLREREVLTEELEKRILEAPT 105
                                       7999******99999******************998877 PP

>> T2SSK  Type II secretion system (T2SS), protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00016      0.21     181     233 ..     495     547 ..     479     560 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                             T2SSK 181 ektkiNiNtasaevLaAlveglslsqaqrllaaRpea.gfrsvadflaasalsg 233
                                        ++ +++Ntas e+L+ +   l  + a++++  R+e+ +fr+ +++++ + l+ 
  gi|386002501|ref|YP_005920800.1| 495 NAVGVDLNTASIELLSRVAG-LGPKLARSIVLYREENgPFRTREELKKVPGLGP 547
                                       67889**********99887.9************99989******999866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (735 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 4238.78
//
Query:       gi|386002502|ref|YP_005920801.1|  [L=232]
Description: HD domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-12   47.4   0.7    3.6e-12   46.6   0.7    1.4  1  HD        HD domain
     0.0037   17.3   0.1      0.006   16.6   0.1    1.3  1  ProSAAS   ProSAAS precursor


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.7   4.1e-16   3.6e-12       3     121 ..      46     147 ..      45     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 4.1e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.. CS
                                HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.. 77 
                                        H l+V+++ar ++e +g  +d+ ++ laaLlHD + g   +         e+ ++ e+ g ei++++ kr g++  
  gi|386002502|ref|YP_005920801.1|  46 SHALRVYRIARAIGEAEG--ADSMIVALAALLHDAASGSKLR---------ERSEEAEERGLEIIQDIMKRWGYPde 111
                                       7*****************..*******************443.........3445689***************99** PP

                                       .HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  78 .ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                        +  v+++++ h+ s  ++         + +lea+++++aDrl+a
  gi|386002502|ref|YP_005920801.1| 112 vIGGVLRAVEVHSYSRGIE---------PATLEAMVLQDADRLDA 147
                                       *999************866.........***************98 PP

>> ProSAAS  ProSAAS precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.6e-07     0.006      37     117 ..      29     110 ..      20     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-07
                           ProSAAS  37 vkeprglgaasaplaetgvprrl.rravargeaagavqelaralahll.eaerqeraraeaqeaedqqarvlaqllr 111
                                       +ke  +l     p  + + ++r+ r a a gea ga   +  ala ll +a    + r  ++eae++   ++ ++++
  gi|386002502|ref|YP_005920801.1|  29 IKEIGALYEGKDPAHDLSHALRVyRIARAIGEAEGAD-SMIVALAALLhDAASGSKLRERSEEAEERGLEIIQDIMK 104
                                       6777777777788888888877615577889988875.5666777776368899999******************** PP

                           ProSAAS 112 vwgspr 117
                                        wg p 
  gi|386002502|ref|YP_005920801.1| 105 RWGYPD 110
                                       ***995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1301.39
//
Query:       gi|386002503|ref|YP_005920802.1|  [L=396]
Description: Xaa-Pro dipeptidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-35  123.1   0.0    1.7e-35  122.6   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24
    1.7e-14   54.6   0.0    3.6e-14   53.5   0.0    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.0   1.9e-39   1.7e-35       2     209 .]     147     380 ..     146     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 1.9e-39
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTT...............TCEESSSSEEEEGGGGGSTT CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhg...............arglafppivasgenaavlh 63 
                                       lir+aari +a +  v +++++g+ e elaa++ea+ +++ g                      +   +g+ aa++ 
  gi|386002503|ref|YP_005920802.1| 147 LIRAAARILDAGIGSVPDHLEEGMAEIELAAKLEAE-MRALGhsgslrfrrfnqelpM------GHLMAGPSAAYPS 216
                                       79********************************99.555555677777765444440......5555566666655 PP

                                       TBCSSSB................--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-S CS
                     Peptidase_M24  64 ytpndrv................lkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavk 124
                                       ++++ +                 +++++++l+d+g++y+gy++D tr +++G+ ++e +e+++a+le+ + + + ++
  gi|386002503|ref|YP_005920802.1| 217 FVASPTGgigpsllqpqgpgfrkIRKNEPILVDYGGVYNGYIADETRIFSLGPLSKELEEAHAAALEVERGIAESLR 293
                                       54422222233333333334444**********************************************9999**** PP

                                       TTSBHHHHHHHHHHHHHHTTB........CCGBSS...CSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEE CS
                     Peptidase_M24 125 pGvtlseidaaarevlesagl........akffph...glGHgvGlevhdegpsvsresndgrkleeGmvftiEpgi 190
                                       pG++++ei+++ +++ e+ g+        +        ++GHgvGle+ +  p +   +  ++++ ++m++++Ep++
  gi|386002503|ref|YP_005920802.1| 294 PGNSGREIYEISEALGEELGYrdrlggpvG----AkcgFVGHGVGLEIDEY-PVLG--P-VDHEILPNMTVAVEPKM 362
                                       ******************999888865432....23559**********98.*987..3.4899***********77 PP

                                       EEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 191 yfapgeggvriedtvlvte 209
                                          pg+g+v iedt+l t+
  gi|386002503|ref|YP_005920802.1| 363 I-YPGVGVVGIEDTFLTTD 380
                                       7.69***********9985 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0     4e-18   3.6e-14       1     132 []      18     139 ..      18     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 4e-18
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd 76 
                                       R+erl+ +me  gl ++++++  ++ Y++G+   +++ +++++  ++ + + +v+     +a+ees  + +v + + 
  gi|386002503|ref|YP_005920802.1|  18 RVERLQSRME--GLTGAIIFQAVDMLYFSGT---AQEGLVYVPADPEAEaVVMVR-KSLDRAREES--PLDVSPLK- 85 
                                       8999999995..9******************...777777776766666445555.9999999999..77777666. PP

                                       HSSHHHHHHHHHHHHT.-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                      Creatinase_N  77 pvealadllkellese.krvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                          ++ +l ++l+  e  ++g+eld+l+++ ye++k+alpdae++d+se i+ +R v
  gi|386002503|ref|YP_005920802.1|  86 ---SMKSLKADLAIPEgAKIGLELDVLPFNNYERVKAALPDAEFKDVSEPIRMVRSV 139
                                       ...78888888888788************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2246.84
//
Query:       gi|386002504|ref|YP_005920803.1|  [L=287]
Description: hypothetical protein Mhar_1822 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-06   26.4   0.0    7.4e-06   25.9   0.0    1.2  1  dCache_1  Cache domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.036   14.0   0.0    1.4  1  CHASE     CHASE domain


Domain annotation for each model (and alignments):
>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   8.2e-10   7.4e-06      54     237 ..      71     284 ..      40     287 .] 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8.2e-10
                          dCache_1  54 easreslqallksilksnpdisgvylvdadGqviassdpssppnleg.....tddpadrdwykealaggggkpvisd 125
                                        +  + +++ l+ +l+ n+d+ +   ++++G+++++         eg     ++d++ ++ + ++l +++  ++ ++
  gi|386002504|ref|YP_005920803.1|  71 GLEGDGAREVLRGLLAENSDLVEAVTFSEEGKILVA-------ECEGceggeGEDISGQEHIAQILRTKN-PTFSGQ 139
                                       44455678999********996665569*****996.......5555666779****************5.444444 PP

                          dCache_1 126 pyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlqd.lls.niklgetgyvfi.......vdsdGniiahpdk 193
                                       +    ++g + ++ia p+ ++ gkfiG + a l++++l+d l+  +++++ + +  i       +  dG+i ++ d+
  gi|386002504|ref|YP_005920803.1| 140 FLL--VEGYHGTAIAYPVISPEGKFIGGISAILKPEELMDaLVApKLRFDTSTRSNItdysfwsMHLDGLIAYDRDE 214
                                       442..35999***********9******************888866666665565554444444888********** PP

                          dCache_1 194 dllgknlrdelkaq..........................ealekalakiesgvssvklngeeylvayap 237
                                       +++gk l++    q                          + ++ ++  +es +++v+l+g+e+ + +++
  gi|386002504|ref|YP_005920803.1| 215 SQIGKLLFEDPLYQpfsslldlgerivaeraghgyytfqvTEEDERVVTKESYWTTVGLHGREWRIIVTR 284
                                       *********99999*********99999999999999999999999999999999999999999777665 PP

>> CHASE  CHASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     4e-06     0.036      91     164 ..     123     183 ..     119     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-06
                             CHASE  91 ealerardtgrpvlsgpvrLvqededgqagfllylPvyrkegpetveerraallGfvyavfriddlleklllql 164
                                       e +++ ++t++p+ sg + Lv+    g  g+ +  Pv ++         + +++G ++a+++ ++l+++l+  +
  gi|386002504|ref|YP_005920803.1| 123 EHIAQILRTKNPTFSGQFLLVE----GYHGTAIAYPVISP---------EGKFIGGISAILKPEELMDALVAPK 183
                                       678999***************8....9***********99.........336****************777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.74
# Mc/sec: 1177.47
//
Query:       gi|386002505|ref|YP_005920804.1|  [L=329]
Description: Cache, type 2 domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-37  127.9   0.0    1.3e-21   77.0   0.0    2.1  2  sCache_2    Single Cache domain 2
    4.1e-27   95.1   0.0    9.8e-14   51.2   0.0    2.1  2  dCache_2    Cache domain
  ------ inclusion threshold ------
      0.099   12.7   0.0       0.18   11.9   0.0    1.4  1  COPI_assoc  COPI associated protein


Domain annotation for each model (and alignments):
>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   2.2e-25   1.3e-21      38     153 ..      80     200 ..      63     202 .. 0.85
   2 !   49.0   0.0   9.3e-17   5.6e-13      54     143 ..     238     326 ..     208     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.2e-25
                          sCache_2  38 qeevkel.vnglkfgdG.....kgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvt 108
                                       qe+ +e+ +++  +++G     + Y++++d +gt+++hPf+p+++G++ +n +D+nG+ +ir+lv++a+ +g gf++
  gi|386002505|ref|YP_005920804.1|  80 QEKGREAaLEEFSKKNGsfvrgELYIYAYDFNGTNIAHPFKPDWIGESKINETDSNGVLYIRNLVNAAR-PGYGFTY 155
                                       444444314444555556666689*********************************************.******* PP

                          sCache_2 109 ylwkkpge.geveeklayvkyfepWdwvigtgvylddinkavekil 153
                                       + +++p++ g+ e k+ y++++   +w++g+g yl ++++ +++  
  gi|386002505|ref|YP_005920804.1| 156 FIFPNPADgGRDEFKIGYAMKVDD-GWWLGSGLYLPEVSASFDQEE 200
                                       ********999999********98.9**************998875 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 9.3e-17
                          sCache_2  54 kgYffvldedgtllvhPfnpqleGknasnlkDanGkyiirelvkeakkkgggfvtylwkkpge.geveeklayvkyf 129
                                         Y+f++d+dg +l+ P +p+l G+++++  D+ G+++ire +++a+  g g+++y +++ +   ++  kl+yv  +
  gi|386002505|ref|YP_005920804.1| 238 GRYIFAYDYDGVTLALPHQPELLGSSRIEASDPIGVRFIREAIETAS-LGRGYIYYIYPDSSRgMRPALKLSYVSDV 313
                                       67*********************************************.*************9989***********9 PP

                          sCache_2 130 epWdwvigtgvyld 143
                                        +  w++g+g+y +
  gi|386002505|ref|YP_005920804.1| 314 DG-SWFLGSGIYAE 326
                                       98.8*******975 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   1.6e-17   9.8e-14      89     197 ..      97     204 ..      63     233 .. 0.85
   2 !   42.3   0.0   8.6e-15   5.1e-11     204     292 ..     237     325 ..     224     327 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.6e-17
                          dCache_2  89 rydggegyyfiidskgtlilhpdspsleGknlldlkdkdGryiiremiklakkkgeGfveytwpkp.dekkprkkis 164
                                       ++++ge y++++d +gt+i+hp++p+  G + ++  d++G  +ir+++++a + g Gf  + +p+p d ++++ ki+
  gi|386002505|ref|YP_005920804.1|  97 SFVRGELYIYAYDFNGTNIAHPFKPDWIGESKINETDSNGVLYIRNLVNAA-RPGYGFTYFIFPNPaDGGRDEFKIG 172
                                       3889**********************************************9.8899********************* PP

                          dCache_2 165 yvkyfepldwiIGtgaylddieeelkqellktl 197
                                       y+ +    +w +G+g yl ++ +  +qe ++ l
  gi|386002505|ref|YP_005920804.1| 173 YAMKVDD-GWWLGSGLYLPEVSASFDQEERDGL 204
                                       *****98.9***********9999997766665 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 8.6e-15
                          dCache_2 204 nngyifiydtdgniilhplkkelngknllevkdkkgkl.lqelleaakkkgegfveYkwpkpsgd.kerkKisyvry 278
                                       +++yif+yd+dg++++ p+++el g  ++e +d+ g+  ++e +e a  + +g++ Y++p++s++ ++  K+syv+ 
  gi|386002505|ref|YP_005920804.1| 237 DGRYIFAYDYDGVTLALPHQPELLGSSRIEASDPIGVRfIREAIETASLG-RGYIYYIYPDSSRGmRPALKLSYVSD 312
                                       679*********************************99999999988865.59************************ PP

                          dCache_2 279 fppwdWiigtgvyl 292
                                       +    W++g+g+y 
  gi|386002505|ref|YP_005920804.1| 313 VDG-SWFLGSGIYA 325
                                       *99.********96 PP

>> COPI_assoc  COPI associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.18      69     103 ..       7      41 ..       6      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                        COPI_assoc  69 GRGlfyillgllvsyggvlsilialllflvGLvyi 103
                                       GRG f++++++lv      +il+a+++flvG + +
  gi|386002505|ref|YP_005920804.1|   7 GRGWFCTVVSMLVLDMNSKNILLAIFFFLVGAALL 41 
                                       9*********99988889*************7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1835.61
//
Query:       gi|386002506|ref|YP_005920805.1|  [L=111]
Description: hypothetical protein Mhar_1824 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 677.06
//
Query:       gi|386002507|ref|YP_005920806.1|  [L=417]
Description: DOMON domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-41  141.8   0.0    2.3e-41  141.3   0.0    1.2  1  DUF2202       Uncharacterized protein domain (DUF2202)
      2e-18   66.8   0.0    2.7e-18   66.4   0.0    1.2  1  DOMON         DOMON domain
  ------ inclusion threshold ------
      0.028   14.8   0.1      0.079   13.4   0.0    1.8  2  Rubrerythrin  Rubrerythrin


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   0.0   3.9e-45   2.3e-41       3     160 ..     262     416 ..     260     417 .] 0.96

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 3.9e-45
                           DUF2202   3 dsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnkLv 79 
                                       +++ ++ eee++arD+YlelY+ ++l ifl++a+se+th+ ++ +l+++ +l+ p +    G++ de+lq++Y++L+
  gi|386002507|ref|YP_005920806.1| 262 QGMAFILEEERMARDLYLELYKTTRLPIFLDVARSEETHIASILTLMKRRGLSAPPEAP--GVYADETLQKIYEDLL 336
                                       67999************************************************998777..**************** PP

                           DUF2202  80 ekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseeefd 156
                                       + ++   + aL ++a++e+ +++Dl+k ++   + d+++vY +l+ Gs++hlR+fvr leerg eY+p  +s+eefd
  gi|386002507|ref|YP_005920806.1| 337 SGADGP-VVALGAAAQVEEASVHDLRKEIEGALEPDLISVYGGLMVGSEKHLRTFVRALEERGGEYNPMILSQEEFD 412
                                       977776.88******************************************************************** PP

                           DUF2202 157 eivs 160
                                       +iv+
  gi|386002507|ref|YP_005920806.1| 413 RIVR 416
                                       **96 PP

>> DOMON  DOMON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   4.5e-22   2.7e-18       3     124 ..     104     222 ..     102     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 4.5e-22
                             DOMON   3 geykvswkvdgdgdeiefelsgkvntngyvaiGfsddgkMsnadvvvgwvdngrvyvqdyystggkgapriddt... 76 
                                       g+++v+w++d  ++ ++++l+g++  +g++aiGf ++++ ++ dvv+g v +  + v+d y  + +g p+i d    
  gi|386002507|ref|YP_005920806.1| 104 GDLEVFWRTD--DEHLYMALRGET--TGWLAIGFYPREWKKGGDVVIGRVNGRDAVVEDQYIIDFFG-PHIPDVels 175
                                       5789******..888******876..7**********************************899999.88877779* PP

                             DOMON  77 gsqditllsgseengvttlkfrRkldtcdpkqdnkidldttvyviwaa 124
                                       g++di    g e++gvt ++frR+ldt+d+  d++i++++ + +iw +
  gi|386002507|ref|YP_005920806.1| 176 GTDDILEFGGLEKGGVTVIEFRRRLDTGDE-FDRAITPGEDLPIIWSI 222
                                       *****************************9.***************76 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.079       9      59 ..     270     314 ..     263     368 .. 0.87
   2 ?   -2.8   0.0       1.3   7.8e+03      43      65 ..     384     407 ..     382     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTT CS
                      Rubrerythrin   9 gEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepe 59 
                                        E +ar lY el++ ++  +p    +F+++A+ E+ H + +  l++ + ++
  gi|386002507|ref|YP_005920806.1| 270 EERMARDLYLELYKTTR--LP----IFLDVARSEETHIASILTLMKRRGLS 314
                                       466899***********..88....********************998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHCSTTHH..B.S CS
                      Rubrerythrin  43 reHakilnklleklepele.levk 65 
                                       ++H + + ++le++ +e++ ++ +
  gi|386002507|ref|YP_005920806.1| 384 EKHLRTFVRALEERGGEYNpMILS 407
                                       578899999999999988855555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2478.87
//
Query:       gi|386002508|ref|YP_005920807.1|  [L=159]
Description: hypothetical protein Mhar_1826 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   13.4   0.0      0.048   12.7   0.0    1.3  1  RELT      Tumour necrosis factor receptor superfamily member 


Domain annotation for each model (and alignments):
>> RELT  Tumour necrosis factor receptor superfamily member 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-06     0.048      15      35 ..      61      81 ..      58      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-06
                              RELT 15 LlGvLiChvLkkKGYrCttek 35
                                      L Gv+iC    ++GYr t ++
  gi|386002508|ref|YP_005920807.1| 61 LYGVVICEEWTRRGYRDTCKE 81
                                      89**************77655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 984.31
//
Query:       gi|386002509|ref|YP_005920808.1|  [L=237]
Description: type 12 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-16   61.2   0.0    2.2e-16   60.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.4e-16   61.0   0.0    2.1e-16   60.5   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.5e-15   57.6   0.0    2.6e-15   56.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    6.8e-13   48.8   0.0    9.7e-13   48.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    6.8e-12   45.4   0.0    8.5e-12   45.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.9e-07   29.0   0.0    1.2e-06   28.2   0.0    1.5  1  MTS              Methyltransferase small domain
      9e-07   28.5   0.0    1.5e-06   27.7   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.3e-05   24.6   0.0    1.8e-05   24.2   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00022   20.5   0.0    0.00038   19.7   0.0    1.3  1  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
    0.00043   19.7   0.0    0.00063   19.2   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0025   17.2   0.0     0.0047   16.2   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.021   14.3   0.0       0.03   13.8   0.0    1.1  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
      0.078   12.7   0.1       0.18   11.5   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.12   11.7   0.0       0.17   11.3   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.15   12.5   0.0       0.27   11.7   0.0    1.3  1  LIAS_N           N-terminal domain of lipoyl synthase of Radi


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   1.8e-19   2.2e-16       1      97 []      49     151 ..      49     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.8e-19
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT......TEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl......nvefvqgdaedlpfedgsfDlvvss 71 
                                       vLdlGcGtG+ ++a++kr ++a++  +D s++m+ aa+e++++ ++      +v  + ++  dl +++++fD+vvs+
  gi|386002509|ref|YP_005920808.1|  49 VLDLGCGTGNASAAILKRSPAAEIFLLDGSASMVVAAKEKIAAISPgsvigsRVADIAAEGWDLGLASSEFDAVVST 125
                                       9*****************889********************9955566343344444444466889**********8 PP

                                       STGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  72 galhhlsdedlekalkeiarvLkpgG 97 
                                        +l+hl+ e ++ a+ +++++LkpgG
  gi|386002509|ref|YP_005920808.1| 126 LVLEHLDFESYRSAIGKCFQLLKPGG 151
                                       88***********************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   1.7e-19   2.1e-16       1      99 []      50     153 ..      50     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.7e-19
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg...ssfDlvvasn 74 
                                       L++GcGtG+ ++a+l++ p +e+  +D s+s++++akek+a++++ ++   ++ ++ ++  d g   s fD+vv+  
  gi|386002509|ref|YP_005920808.1|  50 LDLGCGTGNASAAILKRSPAAEIFLLDGSASMVVAAKEKIAAISPGSVIGSRVADIAAEGWDLGlasSEFDAVVSTL 126
                                       8*******************************************999888888877777666669************ PP

                   Methyltransf_12  75 vlhhl..kdirevldnirklLkpgGrl 99 
                                       vl+hl  +  r+++ ++ +lLkpgG+l
  gi|386002509|ref|YP_005920808.1| 127 VLEHLdfESYRSAIGKCFQLLKPGGWL 153
                                       *************************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   2.2e-18   2.6e-15       1      95 [.      50     154 ..      50     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.2e-18
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECC....CTSS-TT-EEEEEEES CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadae....klpfednsfDlvvsse 69 
                                       Ld+GcGtG  ++a+ kr   a+++ +D s+ m+ +akek+    +   +  +vad+     +l ++++ fD+vvs+ 
  gi|386002509|ref|YP_005920808.1|  50 LDLGCGTGNASAAILKRSpaAEIFLLDGSASMVVAAKEKIAAISPgsVIGSRVADIAaegwDLGLASSEFDAVVSTL 126
                                       8**************88889*****************9999988899666677777754557*************** PP

                                       -CCC-..CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  70 vlhhv..edpekalkeiaRvLkpgGllv 95 
                                       vl+h+  e  ++a+ ++ ++LkpgG+l+
  gi|386002509|ref|YP_005920808.1| 127 VLEHLdfESYRSAIGKCFQLLKPGGWLI 154
                                       *****999******************98 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   8.2e-16   9.7e-13      18     163 ..      40     220 ..      18     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 8.2e-16
                   Methyltransf_23  18 pk.lraggrvLdiGcGtGillevl.rengf.svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqg. 81 
                                       ++ l +  rvLd+GcGtG+ +  + ++ ++ ++ + D s  +v  a+         + + +              + 
  gi|386002509|ref|YP_005920808.1|  40 ERlLGSAPRVLDLGCGTGNASAAIlKRSPAaEIFLLDGSASMVVAAKekiaaispgSVIGS--------------Rv 102
                                       33345667**********7666553777767*********999988754444333311111..............02 PP

                   Methyltransf_23  82 ...............kfdlIvlrevlehvp..dppellrqiatllkpgGylllse.plasl.............ked 127
                                                       fd +v++ vleh++  ++ +++ + ++llkpgG+l+  e +++               +++
  gi|386002509|ref|YP_005920808.1| 103 adiaaegwdlglassEFDAVVSTLVLEHLDfeSYRSAIGKCFQLLKPGGWLIAVEgYAE-EesdmvvwfselmeARR 178
                                       222333344445555***************878*******************9995333.22456666666664233 PP

                   Methyltransf_23 128 rllld......wlylvpagrhisffsarslkelleeaGlevv 163
                                       +l++d      +  l+ ++++ ++    + + +++eaG++ v
  gi|386002509|ref|YP_005920808.1| 179 ELIDDpelsdfVSGLRAKDEVHHYAGKAQKAGWWREAGFDRV 220
                                       333335555445555666677777777777777777777655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   7.1e-15   8.5e-12       3     120 ..      45     171 ..      43     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 7.1e-15
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre.naqklgldnveFeqgdiee.lekl.ledekfD 76 
                                       ++ rvlDlGCGtG+ + ++  +  p ae++++D s+ ++  A+e +a+    + +  +++di +    l l+ + fD
  gi|386002509|ref|YP_005920808.1|  45 SAPRVLDLGCGTGNASAAIL-KRSPAAEIFLLDGSASMVVAAKEkIAAISPGSVIGSRVADIAAeGWDLgLASSEFD 120
                                       7789****************.7789*******************44444444478888899988433445666**** PP

                   Methyltransf_31  77 lilsnevl..naladpdkileeiervlkpggilliedprllaelp.....a 120
                                        ++s  vl   ++ +  +++++ +++lkpgg l++ +  +++e +      
  gi|386002509|ref|YP_005920808.1| 121 AVVSTLVLehLDFESYRSAIGKCFQLLKPGGWLIAVEGYAEEESDmvvwfS 171
                                       ********99999**********************9999555554444442 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0     1e-09   1.2e-06      31      82 ..      45      98 ..      30     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1e-09
                                      TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..E CS
                               MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..v 82
                                       + +vlDlGcG+G  +aa++k+sp ae+ l+d +a  + +ake ++a      +
  gi|386002509|ref|YP_005920808.1| 45 SAPRVLDLGCGTGNASAAILKRSPAAEIFLLDGSASMVVAAKEKIAAISPGsvI 98
                                      4557**************************************999887654442 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.3e-09   1.5e-06      50     157 ..      48     161 ..      14     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.....TEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.....nieflqanaeeLpfeddsfDvvt 121
                                       +vlD+ +Gtg+ ++++++      ++ +lD +++m+  +++k+   +       ++  + a++ +L      fD v 
  gi|386002509|ref|YP_005920808.1|  48 RVLDLGCGTGNASAAILKRS-PAAEIFLLDGSASMVVAAKEKIAAISPGsvigsRVADIAAEGWDLGLASSEFDAVV 123
                                       79**************9975.6789*****************9876543336889*******************986 PP

                                       EES-GG..G-S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran 122 vsfGlr..nvtDklkaLkeayrvlkpGGrlvvlefskv 157
                                        +  l   ++  +  a+ + ++ lkpGG l+ +e    
  gi|386002509|ref|YP_005920808.1| 124 STLVLEhlDFESYRSAIGKCFQLLKPGGWLIAVEGYAE 161
                                       555554227899*******************9996554 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.5e-08   1.8e-05      64     164 ..      47     155 ..      34     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.5e-08
                                       -EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-S.....SS-EEEEES-GG.G---.--SEEE CS
                              CMAS  64 mtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldl.....erkvevklldye.dlde.kvdrvv 132
                                        ++Ld+GcG G+      +r   ++++ l  S+     ak++++++       +r +++   ++   l+  ++d+vv
  gi|386002509|ref|YP_005920808.1|  47 PRVLDLGCGTGNASAAILKRSpAAEIFLLDGSASMVVAAKEKIAAISPgsvigSRVADIAAEGWDlGLASsEFDAVV 123
                                       589*********9999988862578999999999999******9986411222577899999997345557****** PP

                                       EES-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 133 svgafehvgkenydtffkklkkllkedGllll 164
                                       s  ++eh+ +e+y   + k+++llk++G l+ 
  gi|386002509|ref|YP_005920808.1| 124 STLVLEHLDFESYRSAIGKCFQLLKPGGWLIA 155
                                       ****************************9864 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.1e-07   0.00038     157     200 ..     117     158 ..     100     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
                                       ..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEEE CS
                    NNMT_PNMT_TEMT 157 kkadvvvtifcleaacedleeylralrnlasllkpGGhlvlggv 200
                                       +++d+vv+++ le    d+e+y+ a+ +  +llkpGG l+ ++ 
  gi|386002509|ref|YP_005920808.1| 117 SEFDAVVSTLVLEHL--DFESYRSAIGKCFQLLKPGGWLIAVEG 158
                                       469**********85..9**********************8765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.2e-07   0.00063      31     148 ..      46     171 ..      16     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.2e-07
                                       S-EEEEES-TTSHHHHHHH..HTT-EEEEEES-H.HHHHHHHHHHHHTT-TTEEEEE--GGG----.....S-EEEE CS
                              TehB  31 pgkvldlgcgqgrnslyls..llgydvtawdkne.nsiafleeikekenlknistalydineakld.....erydfi 99 
                                         +vldlgcg g  s  +       ++  +d  + + +a  e+i+ +   + i +++ di +   d      ++d +
  gi|386002509|ref|YP_005920808.1|  46 APRVLDLGCGTGNASAAILkrSPAAEIFLLDGSAsMVVAAKEKIAAISPGSVIGSRVADIAAEGWDlglasSEFDAV 122
                                       5689********99875540144677888887651667888999999999999*******9865432222279**** PP

                                       EEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB--SSS--SS--S CS
                              TehB 100 lstvvlmfleaeripsiienmqectkvggynlivaamstddvpctvpfs 148
                                       +st+vl  l+ e+  s i    +  k+gg+ + v     ++    v fs
  gi|386002509|ref|YP_005920808.1| 123 VSTLVLEHLDFESYRSAIGKCFQLLKPGGWLIAVEGYAEEESDMVVWFS 171
                                       ******************************9999999888888888777 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     4e-06    0.0047      57     172 ..      40     163 ..      21     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4e-06
                                       SS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE.-HHHHHHHHHHS----.....-TTEEEEES-TTTS---. CS
                    Methyltransf_2  57 afdleglkslvDvGGGtGalakaivsayPtikvivfD.lpeVveaAkehlsage.....eervefvgGdffkdslP. 126
                                       +  l + ++++D+G GtG + +ai +  P  ++ ++D  ++ v aAke++ a        +rv+ ++ + ++  l  
  gi|386002509|ref|YP_005920808.1|  40 ERLLGSAPRVLDLGCGTGNASAAILKRSPAAEIFLLDgSASMVVAAKEKIAAISpgsviGSRVADIAAEGWDLGLAs 116
                                       4446677899***************************4467888999987443201111344444444444444443 PP

                                       .--SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TT CS
                    Methyltransf_2 127 .eaDaillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgad 172
                                        e Da++ + vl   + e+ +  + ++ + l++gG +i ve   +++
  gi|386002509|ref|YP_005920808.1| 117 sEFDAVVSTLVLEHLDFESYRSAIGKCFQLLKPGGWLIAVEGYAEEE 163
                                       37799999999998889999999999999999999999998776655 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.5e-05      0.03      57     170 ..      47     166 ..      32     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                   Methyltransf_PK  57 kvaldcGaGiGrvtknlLlkl.lskvDlvepvekflekakeelae......ekkkvgkvyvvglqeftPeegrYdli 126
                                        ++ld G+G G  +  +L +  ++++ l++  ++++ +ake++a         ++v+++   g  +   ++ ++d +
  gi|386002509|ref|YP_005920808.1|  47 PRVLDLGCGTGNASAAILKRSpAAEIFLLDGSASMVVAAKEKIAAispgsvIGSRVADIAAEGW-DLGLASSEFDAV 122
                                       5789**************986379********************96554333344444444443.33445999**** PP

                   Methyltransf_PK 127 WiqWcvghLtDedlvaflkrckkalkpnGlivvkenvakeekde 170
                                           ++ hL  e + + + +c + lkp+G ++  e  a+ee d+
  gi|386002509|ref|YP_005920808.1| 123 VSTLVLEHLDFESYRSAIGKCFQLLKPGGWLIAVEGYAEEESDM 166
                                       ********************************999999999865 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.18      64     126 ..      37      97 ..       8     156 .. 0.69
   2 ?   -2.5   0.0         3   3.6e+03     134     147 ..     208     221 ..     190     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                       HHHHHTT...--TT-EEEEES-TTSHHHH.HHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSE CS
                              PCMT  64 lalelle...lkkgarvLevGsGsGylta.vlarlvgekgrvvsierikelveeakrnlkkldlenv 126
                                       l+        l    rvL++G+G+G  +a +l r   + + +  ++ ++++v +ak+++ +    +v
  gi|386002509|ref|YP_005920808.1|  37 LI----GerlLGSAPRVLDLGCGTGNASAaILKRS--PAAEIFLLDGSASMVVAAKEKIAAISPGSV 97 
                                       33....234478889**********8755055553..344567888899999999988887776644 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3
                                       GGTTGGG-SEEEEE CS
                              PCMT 134 rkGyeekaPYdaih 147
                                       + G+  +a +d++h
  gi|386002509|ref|YP_005920808.1| 208 KAGWWREAGFDRVH 221
                                       469999*****998 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.17     158     269 ..      42     167 ..      31     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLg.akkvvavDiDevAvkvakeNaelN........kveaklevalseellk.. 223
                                       l+ +  +vlD+G+G+G  + a +k   a++++ +D     v +ake ++          +    +   +++e  +  
  gi|386002509|ref|YP_005920808.1|  42 LLGSAPRVLDLGCGTGNASAAILKRSpAAEIFLLDGSASMVVAAKEKIAAIspgsvigsR----V-ADIAAEGWDlg 113
                                       4555669**************998653899***************998876333221111....1.12223332233 PP

                              PrmA 224 ..eekadvivaNILaevl.....ielaedikklvkeggllil.SGilkekaeev 269
                                         ++++d +v+  + e l      + + +  +l+k+gg+li+  G  +e +++v
  gi|386002509|ref|YP_005920808.1| 114 laSSEFDAVVSTLVLEHLdfesyRSAIGKCFQLLKPGGWLIAvEGYAEEESDMV 167
                                       446889999998888877333323567777888888888774256666666666 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.27      27      65 ..     172     208 ..     159     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                            LIAS_N  27 sltdekkelleeGPdlqDFvsgdkedkseweeykgnlkr 65 
                                       +l  e ++ l + P+l+DFvsg  ++  e ++y+g++++
  gi|386002509|ref|YP_005920808.1| 172 EL-MEARRELIDDPELSDFVSGLRAKD-EVHHYAGKAQK 208
                                       44.4566667788*********98776.99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1295.19
//
Query:       gi|386002510|ref|YP_005920809.1|  [L=109]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-13   48.7   0.5    8.2e-13   48.5   0.5    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    1.6e-12   47.4   0.1      2e-12   47.0   0.1    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.14   11.9   0.1       0.18   11.5   0.1    1.2  1  MdcG          Phosphoribosyl-dephospho-CoA transferase MdcG


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.5   1.4e-16   8.2e-13       6      91 ..      28     105 ..      17     109 .] 0.88

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.4e-16
                                       HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCC CS
                      NTP_transf_2   6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledp 82 
                                         l e+++v+++ +fGS +rG+a+++SD+D+lv ++e          l++ +  ++ l+ ll ++vdlvt+  l+  
  gi|386002510|ref|YP_005920809.1|  28 PVLAERYKVKSLGVFGSQVRGEARRDSDVDILVEFEET-------PDLFRFMDLEDDLVALLRRRVDLVTKRALK-G 96 
                                       56889999******************************.......5689********************999888.6 PP

                                       TEEEEEECE CS
                      NTP_transf_2  83 llvksilee 91 
                                        + k il+e
  gi|386002510|ref|YP_005920809.1|  97 NIGKRILSE 105
                                       666666655 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   3.3e-16     2e-12       7      82 ..      31     104 ..      19     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3.3e-16
                                       HHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHH CS
                           Polbeta   7 lekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilk 82 
                                       +e++ +++ + +FGS+++g+ar++SD+D+ v ++e+ dl + ++l+++l  + l+++vDlv+ ++ +  + ++il+
  gi|386002510|ref|YP_005920809.1|  31 AERY-KVKSLGVFGSQVRGEARRDSDVDILVEFEETPDLFRFMDLEDDLVAL-LRRRVDLVTKRALKGNIGKRILS 104
                                       4455.9**********************************************.99******988877777777765 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.1e-05      0.18     127     163 ..      51      88 ..      35      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
                              MdcG 127 hesSDLDLlirvasalqlarlldllaaleaaa.vrlDg 163
                                       + +SD+D+l+++++  +l r++dl ++l a+   r+D+
  gi|386002510|ref|YP_005920809.1|  51 RRDSDVDILVEFEETPDLFRFMDLEDDLVALLrRRVDL 88 
                                       789***********************999985599996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 644.16
//
Query:       gi|386002511|ref|YP_005920810.1|  [L=96]
Description: hypothetical protein Mhar_1829 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-26   92.6   0.0    1.8e-26   92.3   0.0    1.0  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0   9.9e-31   1.8e-26       5     111 ..       2      86 ..       1      90 [. 0.98

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 9.9e-31
                                       HHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHHHH CS
                             DUF86   5 leklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepwrk 81 
                                       +ek++efte+l+ eef+++e+ y av+r+l+v+gEaa++++ +                      v+ ++pe+pw++
  gi|386002511|ref|YP_005920810.1|   2 IEKVEEFTEDLSLEEFEESEMVYFAVIRALEVMGEAAKQVPTE----------------------VKRRYPEVPWSR 56 
                                       799****************************************......................************ PP

                                       HHCCHHHHHT-CCCTTHHHHHHHHHHTCHH CS
                             DUF86  82 miglRNrLvHgYlgidpeivwsiikenlpd 111
                                       m+g+R++++HgY+g+d+ ivw+++++ +p 
  gi|386002511|ref|YP_005920810.1|  57 MAGMRDKMIHGYFGVDLHIVWETATRSIPN 86 
                                       **************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 527.75
//
Query:       gi|386002512|ref|YP_005920811.1|  [L=431]
Description: ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-06   28.6   0.0    3.6e-06   26.9   0.0    1.8  2  AAA_3      ATPase family associated with various cellular act
     0.0025   17.8   0.0     0.0045   17.0   0.0    1.4  1  AAA_5      AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
       0.34   11.1   1.5        1.4    9.2   0.1    2.7  4  DnaB_bind  DnaB-helicase binding domain of primase


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.48   2.9e+03       3      23 ..      53      73 ..      52      82 .. 0.74
   2 !   26.9   0.0     6e-10   3.6e-06      68     129 ..     138     197 ..     134     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.48
                             AAA_3  3 llegvPGlaktllvkalakal 23
                                      ll g  G  kt+lv+ l++a+
  gi|386002512|ref|YP_005920811.1| 53 LLYGGMGANKTTLVNLLGSAF 73
                                      667778999*****9998765 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 6e-10
                             AAA_3  68 adeinrappktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrf 129
                                        +einr p+  q  +le ++ r++ ++get +l ++   +at nP + + typl ea ldr 
  gi|386002512|ref|YP_005920811.1| 138 INEINRFPSGKQNLFLELLQKRKIGYAGETLELGDTC-YFATMNP-DFSATYPLDEALLDRI 197
                                       58*******************************9985.57*****.899************7 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.5e-07    0.0045       3     137 ..      53     196 ..      51     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.5e-07
                                       EEE--SSSSHHHHHHHGGGGB......S--EEEEE--TT--HHHHH--B--....................------ CS
                             AAA_5   3 lLvGppGtgKselaerlaaal......nreveyvqltrdtteedlkgrreik...........ngttslvdsplvra 62 
                                       lL G  G  K++l+  l +a+      + e +++ ++   tee+++g ++++           +g++    ++l + 
  gi|386002512|ref|YP_005920811.1|  53 LLYGGMGANKTTLVNLLGSAFtglsfdEVENLMITGHPEQTEEKIVGFIDPRqwsclphpsgsPGEEPSPIQVLWTP 129
                                       89******************999999999999******************877777777766666666666666666 PP

                                       --G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  63 aregeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                         +++  v++E++r +s  +n +l ll +r++     ge            +  +at+np      +l++al++R
  gi|386002512|ref|YP_005920811.1| 130 WARSRWKVINEINRFPSGKQNLFLELLQKRKIG--YAGETLELGD------TCYFATMNPDFSATYPLDEALLDR 196
                                       66*******************************..6666665555......78899**99999999999999999 PP

>> DnaB_bind  DnaB-helicase binding domain of primase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.86   5.1e+03      42      54 ..     318     330 ..     316     332 .. 0.86
   2 ?   -2.0   0.0      0.71   4.2e+03      14      31 ..     329     346 ..     324     346 .. 0.84
   3 ?   -2.3   0.0      0.86   5.2e+03      19      28 ..     367     376 ..     364     378 .. 0.75
   4 ?    9.2   0.1   0.00023       1.4      25      49 ..     405     429 ..     404     431 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHT-- CS
                         DnaB_bind  42 lYirrlAerlgid 54 
                                        Y+r +A +lg+d
  gi|386002512|ref|YP_005920811.1| 318 SYTRAVALLLGLD 330
                                       5999999999997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.71
                                       TTSHHHHHHHHHHHHHHH CS
                         DnaB_bind  14 lstpegkaravrealpll 31 
                                       l+  +g ++ +r+++p +
  gi|386002512|ref|YP_005920811.1| 329 LDGSDGLIEVMRAVAPYV 346
                                       5567899999*****986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.86
                                       HHHHHHHHHH CS
                         DnaB_bind  19 gkaravreal 28 
                                       g+ ++vr ++
  gi|386002512|ref|YP_005920811.1| 367 GRLQYVRDLV 376
                                       7888888876 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00023
                                       HHHHHHHTTSSSHHHHHHHHHHHHH CS
                         DnaB_bind  25 realpllaripdpieRdlYirrlAe 49 
                                       +eal+ l++++dpi R  Y++ l +
  gi|386002512|ref|YP_005920811.1| 405 QEALEELSKSDDPIARLDYVKALER 429
                                       69*******************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2334.80
//
Query:       gi|386002513|ref|YP_005920812.1|  [L=278]
Description: Formylmethanofuran dehydrogenase, subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete 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-06   28.3  25.2     0.0012   18.5   2.7    2.8  2  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.7   6.8e-08    0.0012     130     162 ..     130     162 ..     127     174 .. 0.87
   2 !   14.2  15.1   1.4e-06     0.025      91     159 ..     184     253 ..     164     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.8e-08
                                       SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEE CS
                             GXGXG 130 dhgceYmtGGvvvvLgktgrnfaaGmsgGiayv 162
                                       +h++e m GG++vvLg  g+++++ m gG +  
  gi|386002513|ref|YP_005920812.1| 130 HHLGERMSGGRLVVLGGAGDYLGQEMRGGGIVA 162
                                       799*************************98765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-06
                                       S-SSTTTT--SEEEEESSB--SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEE CS
                             GXGXG  91 vGnvvlygatgGklfirgkageRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGi 159
                                       +Gn ++ g  gG++ ++g ag R++  ++   + ++g  g++++  m GG + v g  g   +  m+gG+
  gi|386002513|ref|YP_005920812.1| 184 AGNYLAVGNSGGRVVVKGGAGARSGWLMRSGRIRIGGDaGEYLGLMMRGGEISVGGGAGARAGWRMKGGL 253
                                       4777777777777777777777777777555555555557777777777777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1536.44
//
Query:       gi|386002514|ref|YP_005920813.1|  [L=514]
Description: hypothetical protein Mhar_1832 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00054   20.6   0.0    0.00093   19.8   0.0    1.4  1  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.093   12.1   0.0       0.15   11.4   0.0    1.3  1  VWA_CoxE  VWA domain containing CoxE-like protein


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     1e-07   0.00093       1      64 [.     326     389 ..     326     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
                             VWA_2   1 lvfvlDtSgSmrngdy.gptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakiln 64 
                                       l++vlD+SgSm +    ++t  ++++++  +++++ +g  v+ ++fsd++  + ++t+d a+++ 
  gi|386002514|ref|YP_005920813.1| 326 LLVVLDSSGSMDGHRRgTKTHAATLAAFKASIFAHSRGAEVAAISFSDRMV-IQKWTRDIAAVEM 389
                                       689********8875515777777788888899999***********9975.5677777776655 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05      0.15      53      99 ..     320     374 ..     285     430 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                          VWA_CoxE  53 rerkprelvllvDvSgSmaay...saiflallhAllqqlp......rtevfaFdtr 99 
                                        er p +l++++D SgSm+ +   ++ ++a l+A  +++       ++ ++ F++r
  gi|386002514|ref|YP_005920813.1| 320 SERVP-DLLVVLDSSGSMDGHrrgTKTHAATLAAFKASIFahsrgaEVAAISFSDR 374
                                       46778.9***********98622223333333333333212222455555556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2909.16
//
Query:       gi|386002515|ref|YP_005920814.1|  [L=204]
Description: Multimeric flavodoxin WrbA [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-17   61.6   0.1    1.3e-16   60.7   0.1    1.4  1  FMN_red       NADPH-dependent FMN reductase
    3.4e-09   36.7   0.0    4.3e-09   36.4   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
      1e-05   25.8   0.0      0.088   13.0   0.0    2.2  2  Flavodoxin_5  Flavodoxin domain
    1.2e-05   25.6   0.1      0.001   19.3   0.0    2.1  2  Flavodoxin_1  Flavodoxin
  ------ inclusion threshold ------
      0.032   14.6   0.3      0.072   13.5   0.3    1.6  1  YCII          YCII-related domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1   3.6e-20   1.3e-16       1     144 [.       1     146 [.       1     154 [. 0.80

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 3.6e-20
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T..T-CEEEEETTTS..--..---HCHGHT..CGGSHHHHHHHHHHHH- CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkea.gaevelidladl.ilpcalcdkdlese..gqtsddvaellekiaaa 73 
                                       mk+lv++ + +  + t +lae++ae + +  ga+ve+ ++ +       l   +   e  +  s+     +e +a+a
  gi|386002515|ref|YP_005920814.1|   1 MKVLVLYYTMN--GHTHRLAEAVAEGAHQVkGAKVEMRRVPETlSEA-ELARRGASAEaaEIFSEVPVCRVEELAEA 74 
                                       89999999986..**************77668888888877763222.233322221133556666666789***** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHH.HHHHHTT-EEEE CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlr.qvlaelgaivvp 144
                                       da++++tP Y g++ g++ ++lD ++  ++++ l gK++++++ +g+++gg++a+  ++ + l +lg+ivv+
  gi|386002515|ref|YP_005920814.1|  75 DAIVFGTPSYLGNMAGQMRSFLDSTGDLWRNNLLVGKVGGVFVSSGSQHGGQEAAILAFiPTLLHLGMIVVG 146
                                       ***************************************************99987655166669****997 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.2e-12   4.3e-09       1     137 [.       1     122 [.       1     149 [. 0.75

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.2e-12
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC..HHHHTT..CHHHHHHHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak..layeek..padveseqie 73 
                                       mk+L+++   ++   ++++la+a++e++++ + ++v+ r + ++    l+++ la    +a++ +  +       +e
  gi|386002515|ref|YP_005920814.1|   1 MKVLVLYYTMNG---HTHRLAEAVAEGAHQVKGAKVEMRRVPET----LSEAELARRgaSAEAAEifSEVPVCR-VE 69 
                                       9*********98...68*************98888********7....66666665322233332322222333.58 PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS- CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgp 137
                                       +l++adaiv+++P +  ++  ++  ++D     g           r ++L gk   v v++G+ 
  gi|386002515|ref|YP_005920814.1|  70 ELAEADAIVFGTPSYLGNMAGQMRSFLDST---GDLW--------RNNLLVGKVGGVFVSSGSQ 122
                                       9***************************96...4443........4577778888888888777 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00013      0.47       1      35 [.       4      39 ..       4      48 .. 0.86
   2 !   13.0   0.0   2.4e-05     0.088      33      68 ..      64      98 ..      45     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                      Flavodoxin_5  1 lilYsSrdGqTkkiaeriaeelree.gelvdvedve 35
                                      l+lY +  G+T++ ae++ae   +  g+ v+++ v 
  gi|386002515|ref|YP_005920814.1|  4 LVLYYTMNGHTHRLAEAVAEGAHQVkGAKVEMRRVP 39
                                      79******************9997789999999884 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.4e-05
                      Flavodoxin_5 33 dvekesedlesydavvigasvyygkllpelakFvek 68
                                      +v +  e+l+++da+v+g++ y g++ +++++F++ 
  gi|386002515|ref|YP_005920814.1| 64 PV-CRVEELAEADAIVFGTPSYLGNMAGQMRSFLDS 98
                                      44.56789*************************986 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.8e-07     0.001       1      43 [.       5      45 ..       5      52 .. 0.87
   2 !    5.4   0.0    0.0053        19      18      79 ..      49     106 ..      44     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-07
                                      EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGG CS
                      Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslsei 43
                                      +lY+++ G+t  lA+++ae++++  ++   v+++++ e+lse 
  gi|386002515|ref|YP_005920814.1|  5 VLYYTMNGHTHRLAEAVAEGAHQ--VKGAKVEMRRVPETLSEA 45
                                      89*******************75..778999****99886655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0053
                                       HHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHCHH CS
                      Flavodoxin_1  18 aeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppengesffqdllelkgde 79 
                                       ++++++++  a+++s   + + ++e+ e + ++++t+ +  G +  +++sf ++  +l++++
  gi|386002515|ref|YP_005920814.1|  49 RRGASAEA--AEIFSEVPVCR-VEELAEADAIVFGTPSY-LGNMAGQMRSFLDSTGDLWRNN 106
                                       44444322..34444444444.799***9********55.5****9*999999999999654 PP

>> YCII  YCII-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     2e-05     0.072      10      81 ..      10      84 ..       1      90 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                      -TTGHHHHHHHHHHHHHHHHHHHHTTGEEEE..............EEEECSCSSSSCGGCEEEEEEEEEESSHHHHHHH CS
                              YCII 10 kpasleeraallaahlayleelkkeGvllaa..............GpklvidGpfaetkeqlgGfyiveaadldeaiei 74
                                      + ++             +l e  +eG   +                ++l+++G  ae++e++  + +++++ l+ea +i
  gi|386002515|ref|YP_005920814.1| 10 MNGH-----------THRLAEAVAEGAHQVKgakvemrrvpetlsEAELARRGASAEAAEIFSEVPVCRVEELAEADAI 77
                                      4443...........33333333333333333333344456677789999***************************** PP

                                      HHT-HHH CS
                              YCII 75 aardPfv 81
                                      + + P +
  gi|386002515|ref|YP_005920814.1| 78 VFGTPSY 84
                                      **99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.40s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1081.82
//
Query:       gi|386002516|ref|YP_005920815.1|  [L=192]
Description: rubrerythrin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-31  109.5   5.9    2.1e-31  109.1   5.9    1.2  1  Rubrerythrin  Rubrerythrin
    1.1e-10   41.6   0.4    1.4e-10   41.2   0.4    1.1  1  Ferritin      Ferritin-like domain
     0.0097   15.9   0.4      0.017   15.2   0.1    1.6  2  HypA          Hydrogenase/urease nickel incorporation, metall
  ------ inclusion threshold ------
      0.019   14.8   0.3      0.019   14.8   0.3    2.5  3  HalOD2        Halobacterial output domain 2
       0.11   12.6   3.0       0.26   11.4   3.0    1.6  1  Zn-ribbon_8   Zinc ribbon domain
       0.12   12.3   1.3       0.82    9.6   0.1    2.3  2  TFIIS_C       Transcription factor S-II (TFIIS)
       0.16   12.0   2.4          1    9.4   0.1    2.1  2  DUF892        Domain of unknown function (DUF892)
        7.4    6.4   7.3        1.1    9.0   0.5    2.2  2  Rubredoxin_2  Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   5.9   9.5e-35   2.1e-31       2     136 ..      12     139 ..      11     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 9.5e-35
                                       HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       ++ +A+agEs+ar++Y+++a++ak egy+qi+++F e+A++E+eHak+l+k+l +  + +          + +++  
  gi|386002516|ref|YP_005920815.1|  12 NILTAFAGESQARNRYNFFASQAKkEGYEQISAIFAETADNEKEHAKRLFKFLVEGGEAEV--------RASFPAGV 80 
                                       7789***************************************************666666........899999** PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                       +  t +nL++a++g+ +e++emy++++  a+ eg++e++++++++a aE +He+r+ +l
  gi|386002516|ref|YP_005920815.1|  81 IGPTVENLRAAAAGEKHEYSEMYPEFAAKADAEGFPEVAETMRNIAAAEVGHEKRFLAL 139
                                       ********************************************************998 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.4   6.3e-14   1.4e-10       6     139 ..      15     143 ..      10     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6.3e-14
                                       HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCS.SH CS
                          Ferritin   6 eqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefg.sv 81 
                                        ++a e +a + y  +a+ +k +g+e++++ f e a+ e eha++l++++ + G+      ae+ +  +    g +v
  gi|386002516|ref|YP_005920815.1|  15 TAFAGESQARNRYNFFASQAKKEGYEQISAIFAETADNEKEHAKRLFKFLVEGGE------AEVRASFPAGVIGpTV 85 
                                       67899***********************************************886......6666655555568799 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  82 eevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                       e+  +aa   + + +e++ e ++ a++eg p  a+ + ++ + ++ he+ + al +++
  gi|386002516|ref|YP_005920815.1|  86 ENLRAAAAGEKHEYSEMYPEFAAKADAEGFPEVAETMRNIAAAEVGHEKRFLALAKNI 143
                                       999999999999***************************************9998887 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.7   8.2e+03      12      19 ..      44      52 ..      31      71 .. 0.48
   2 !   15.2   0.1   7.4e-06     0.017      69      96 ..     155     182 ..     120     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.7
                                      HHHHHHH.C CS
                              HypA 12 evveeea.k 19
                                       +  e+a +
  gi|386002516|ref|YP_005920815.1| 44 AIFAETAdN 52
                                      333333322 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.4e-06
                                       -EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsad 96 
                                       v+ rCr+Cg+  e +e+ ++Cp+C++++
  gi|386002516|ref|YP_005920815.1| 155 VSWRCRNCGYIHEGAEAPEECPACEHER 182
                                       789*******9997765568****9976 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.2   7.3e+03      20      29 ..      35      44 ..      31      45 .. 0.73
   2 ?   14.8   0.3   8.6e-06     0.019      21      46 ..     146     171 ..     143     173 .. 0.86
   3 ?    2.0   0.9     0.089     2e+02       2      10 ..     172     180 ..     171     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                            HalOD2 20 lGeGyrqLGa 29
                                        eGy+q+ a
  gi|386002516|ref|YP_005920815.1| 35 KKEGYEQISA 44
                                      5579999865 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.6e-06
                            HalOD2  21 GeGyrqLGayvWkCtrCGevqaaAdp 46 
                                       G  +++ G   W+C +CG +  +A++
  gi|386002516|ref|YP_005920815.1| 146 GTVFKREGVVSWRCRNCGYIHEGAEA 171
                                       66677889999************987 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.089
                            HalOD2   2 PekCseCsl 10 
                                       Pe+C++C+ 
  gi|386002516|ref|YP_005920815.1| 172 PEECPACEH 180
                                       9******85 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.0   0.00012      0.26       7      34 ..     158     180 ..     156     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       rC++Cg  +e      +a +++CP+C +
  gi|386002516|ref|YP_005920815.1| 158 RCRNCGYIHEGA----EA-PEECPACEH 180
                                       9*****999933....33.466****87 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.14   3.2e+02      30      36 ..     158     164 ..     154     166 .. 0.76
   2 ?    9.6   0.1   0.00037      0.82       2      13 ..     174     185 ..     173     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                           TFIIS_C  30 kCtkCgh 36 
                                       +C +Cg+
  gi|386002516|ref|YP_005920815.1| 158 RCRNCGY 164
                                       7888886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00037
                           TFIIS_C   2 kCpkCgsreayf 13 
                                       +Cp C +++ayf
  gi|386002516|ref|YP_005920815.1| 174 ECPACEHERAYF 185
                                       7**********9 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00045         1     111     155 ..      25      69 ..       5      73 .. 0.85
   2 ?    2.7   0.3     0.051   1.2e+02     100     152 ..      92     142 ..      70     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 111 AsYgtLialAeqlgekeaaklLeqtleeekatdekltelaeslvn 155
                                        +Y+  ++ A++ g++++ +++ +t ++ek+ +++l +++ ++ +
  gi|386002516|ref|YP_005920815.1|  25 NRYNFFASQAKKEGYEQISAIFAETADNEKEHAKRLFKFLVEGGE 69 
                                       58999999****************************998876655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.051
                                       .HHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 100 aaaqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdekltelaes 152
                                       aa+ + e+ E+  Y   +a A++ g +e+a++++++ + e   +++  +la++
  gi|386002516|ref|YP_005920815.1|  92 AAGEKHEYSEM--YPEFAAKADAEGFPEVAETMRNIAAAEVGHEKRFLALAKN 142
                                       24555555554..99999999************99999999888888888765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0005       1.1       1       9 [.     157     165 ..     155     167 .. 0.80
   2 ?    0.4   1.2      0.25   5.5e+02      17      22 ..     175     180 ..     174     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0005
                      Rubredoxin_2   1 YvCsqCGfe 9  
                                       ++C++CG+ 
  gi|386002516|ref|YP_005920815.1| 157 WRCRNCGYI 165
                                       788999885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
                      Rubredoxin_2  17 CpsCgs 22 
                                       Cp+C +
  gi|386002516|ref|YP_005920815.1| 175 CPACEH 180
                                       ****75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1056.53
//
Query:       gi|386002517|ref|YP_005920816.1|  [L=340]
Description: Restriction endonuclease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-09   38.3   0.0    1.8e-09   37.6   0.0    1.3  1  Mrr_cat      Restriction endonuclease
     0.0071   16.3   0.6       0.42   10.6   0.0    2.5  2  HSDR_N_2     Type I restriction enzyme R protein N terminus (
  ------ inclusion threshold ------
       0.09   12.8   0.1       0.21   11.6   0.1    1.6  1  DBD_Tnp_Mut  MuDR family transposase


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 !   37.6   0.0     3e-13   1.8e-09      26     106 ..      17      99 ..       1     106 [. 0.81

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3e-13
                                       E---B-T.TSSB--EEEETTEEEEEEEEEEE--T...S-B-HHHHHHHHHHCTTS..SEEEEEESS-B-HHHHHHHH CS
                           Mrr_cat  26 eltgrsg.DggiDliakkdplgserilvqaKryk...nkvgvkeVqeligalkkrgadkgifvttsdftkaAreeae 98 
                                       +l +++g  ++iD++++ ++++ +r+lv++K  +    k+g + ++++ +++++ + d +i+ t+ +ft++A+ +a+
  gi|386002517|ref|YP_005920816.1|  17 RLIRDTGvKHQIDVTINNNDNK-RRVLVECKDFNlsgEKIGLPIIRDFWAVVDDIKPDDAIVLTCTGFTRDAILFAK 92 
                                       44444443678******98855.**********65558*************************************** PP

                                       TT--EEEE CS
                           Mrr_cat  99 elnkieLl 106
                                         ++i+L 
  gi|386002517|ref|YP_005920816.1|  93 M-KGIRLA 99 
                                       9.999986 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0     7e-05      0.42      34      63 ..      23      52 ..      11      66 .. 0.84
   2 ?    3.3   0.2     0.013        79      10      46 ..     190     229 ..     185     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7e-05
                          HSDR_N_2 34 skkkraDivvykkdkkpllivecKapsvki 63
                                      + k ++D+ + ++d+k +++vecK  +++ 
  gi|386002517|ref|YP_005920816.1| 23 GVKHQIDVTINNNDNKRRVLVECKDFNLSG 52
                                      67899*******************998765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.013
                          HSDR_N_2  10 ikyLveelgypkeliavekelqlg...skkkraDivvykk 46 
                                         yL +e++y +++i  ++e q++   + k  +D ++ ++
  gi|386002517|ref|YP_005920816.1| 190 YLYLKTEKNYSATKIYSDVEFQIEdlpQHKIHIDEIILED 229
                                       5799***********9888888776656777788877665 PP

>> DBD_Tnp_Mut  MuDR family transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.6e-05      0.21      15      46 ..      14      46 ..       4      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                       DBD_Tnp_Mut 15 elrkalkkyaIahhrefrvvksd.ksrytvrCe 46
                                        r+ ++ + ++h+  + ++++d k+r+ v+C+
  gi|386002517|ref|YP_005920816.1| 14 HNRRLIRDTGVKHQIDVTINNNDnKRRVLVECK 46
                                      568999*****************999******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1923.41
//
Query:       gi|386002518|ref|YP_005920817.1|  [L=82]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-07   31.8   0.2    1.3e-07   31.6   0.2    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    0.00011   22.4   0.2    0.00013   22.2   0.2    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.031   14.1   0.1      0.031   14.1   0.1    1.2  1  MdcG          Phosphoribosyl-dephospho-CoA transferase MdcG


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.2   2.2e-11   1.3e-07      28      89 ..       2      62 ..       1      66 [. 0.94

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.2e-11
                                      ----EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EEEES CS
                           Polbeta 28 reeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkegkllys 89
                                       eeSDiD+ + ++  ++  + + l++eled+  +++vDl+++++ +  l+ +il+e + +++
  gi|386002518|ref|YP_005920817.1|  2 DEESDIDILIEFEGIRSHLDFAHLKNELEDA-VNRRVDLLTCKSLHARLKDRILAEQIPILK 62
                                      589****************************.9**********************9998875 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   2.1e-08   0.00013      29      90 ..       2      55 ..       1      61 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.1e-08
                                      CTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEEEEEEC CS
                      NTP_transf_2 29 lkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpllvksile 90
                                       ++SDiD+l+ ++         ++ ++ a    +le    ++vdl+t+++l+  +l++ il 
  gi|386002518|ref|YP_005920817.1|  2 DEESDIDILIEFEGI-------RSHLDFAHLKNELEDAVNRRVDLLTCKSLH-ARLKDRILA 55
                                      689************.......6678899999999999999***********.666666654 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.2e-06     0.031     127     163 ..       2      39 ..       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-06
                              MdcG 127 hesSDLDLlirvasalqlarlldllaaleaa.avrlDg 163
                                        e+SD+D+li+++  +++ ++++l ++le+a + r+D+
  gi|386002518|ref|YP_005920817.1|   2 DEESDIDILIEFEGIRSHLDFAHLKNELEDAvNRRVDL 39 
                                       689**************************99559**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.37s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 448.06
//
Query:       gi|386002519|ref|YP_005920818.1|  [L=86]
Description: hypothetical protein Mhar_1838 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-11   43.8   0.0      3e-11   43.5   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0033   17.4   0.0     0.0045   16.9   0.0    1.2  1  DUF1902          Domain of unknown function (DUF1902)


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   3.4e-15     3e-11       1      47 [.      32      78 ..      32      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 3.4e-15
                   HicB_lk_antitox  1 ypiaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhleg 47
                                      + +++e+ded  y  +vP lpGc++ +++l+e ++ akeaiel+le 
  gi|386002519|ref|YP_005920818.1| 32 FNVLVERDEDGYYVATVPSLPGCHTQAKSLDELMERAKEAIELYLEV 78
                                      6799*****************************************96 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-07    0.0045       9      44 ..      39      73 ..      31      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-07
                                      ETTTTEEEEE-SSSTT---EESSHHHHHHHHHHHHH CS
                           DUF1902  9 DeeAgVWvaesddipGlvteaetleeLlkkleamip 44
                                      D e g +va+   +pG  t+a++l+eL+++ + +i 
  gi|386002519|ref|YP_005920818.1| 39 D-EDGYYVATVPSLPGCHTQAKSLDELMERAKEAIE 73
                                      4.55999***********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 502.04
//
Query:       gi|386002520|ref|YP_005920819.1|  [L=649]
Description: Acetyl-CoA hydrolase/transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-60  201.5   0.0    9.8e-60  201.0   0.0    1.3  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    6.9e-39  133.9   0.0    1.3e-38  133.0   0.0    1.4  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    1.7e-11   45.0   0.0    3.1e-11   44.1   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.4e-08   34.2   0.1    6.1e-08   32.9   0.0    1.7  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    8.2e-08   32.2   0.2    7.3e-07   29.2   0.2    2.4  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.3e-05   24.8   0.1    6.1e-05   23.4   0.1    1.8  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.1e-05   23.8   0.0      7e-05   23.0   0.0    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
      8e-05   22.1   0.0       0.34   10.3   0.0    3.0  3  CoA_trans        Coenzyme A transferase
    0.00077   17.9   0.1       0.42    8.9   0.0    2.2  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans
     0.0019   18.1   0.1     0.0044   17.0   0.1    1.5  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.022   14.5   0.1    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.016   15.1   0.0      0.077   12.9   0.0    2.0  3  DeoRC            DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.0   6.5e-63   9.8e-60       1     154 []     288     441 ..     288     441 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 6.5e-63
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHST CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalsk 77 
                                       Gs + y++ld+np +e+r+++y+n+p via+n+++++insale+dl Gq+++esl g+++sG+Ggq dF+rg+ ls+
  gi|386002520|ref|YP_005920819.1| 288 GSAETYRYLDDNPLVEFRSIDYTNSPLVIAKNRRMTAINSALEIDLSGQATAESLAGSHYSGIGGQADFMRGSVLSQ 364
                                       8999************************************************************************* PP

                                       T-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                   AcetylCoA_hyd_C  78 ggksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                        g+si+alpSta+ g++SrIvp+l++g++vt +r dv+yvvTEyGia+L+ k++rera  li+iAhpdfr++L+eea
  gi|386002520|ref|YP_005920819.1| 365 AGRSILALPSTADGGRTSRIVPTLRPGSGVTLSRGDVHYVVTEYGIAYLHAKNVRERALDLIAIAHPDFRPQLIEEA 441
                                       **************************************************************************997 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0   0.0   8.7e-42   1.3e-38       5     189 ..      12     195 ..       8     200 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 8.7e-42
                   AcetylCoA_hydro   5 yekklke.peeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekd 80 
                                       +e + k  p+++ +   +++ i+ +++++vgt +++p+ l+   + +++ ++++l  +++  v+++g  ++  ee++
  gi|386002520|ref|YP_005920819.1|  12 LEAMKKRwPKKFWPETAIFERIHPGDRIFVGTGCGEPQHLVGALKRYVEKRPNSLTGAEMIHVWTLG-IAPCAEEQF 87 
                                       566666678999999999*************************************************.********* PP

                   AcetylCoA_hydro  81 avlyrpapkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEva 157
                                         ++r ++++vg+  r ain g +++++++lsevp ++ +g +piDval++++++d++Gyl lG++v+++K+++E a
  gi|386002520|ref|YP_005920819.1|  88 RENFRLNSFFVGSRSRDAINRGDADYTPIFLSEVPALFRHGAIPIDVALVQTSPPDRHGYLRLGISVDIVKAAVEAA 164
                                       ***************************************************************************** PP

                   AcetylCoA_hydro 158 elvvivvkknpPrvngydelialdkvdyivvd 189
                                       e+v+++++  +Pr+ g d++  +++vd +v  
  gi|386002520|ref|YP_005920819.1| 165 EIVIAQINPRMPRIPG-DGFVSVEEVDHLVFC 195
                                       ****************.*********987754 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   2.1e-14   3.1e-11       2     137 ..     477     616 ..     477     617 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.1e-14
                    Acetyltransf_3   2 LlLrplteeDlealfel...rsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivl.kdtg...viGsvg 70 
                                       +lLrp++ +D + l e+   +sd     r++++  + e ++ wl+++   ++ ++ + +a v+ ++ g   viG+  
  gi|386002520|ref|YP_005920819.1| 477 ILLRPVKITDEPLLKEFfhqLSDDSlYSRFMTT--KKELSHPWLQEFSVVDYSKKMVILATVEdRPAGretVIGIGQ 551
                                       68********33333542336666657787654..66999*****99555555566554444455555454688888 PP

                    Acetyltransf_3  71 lrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       +  l e+   ae+ y+++++++++G+++e ++ l+++a +++g++ +va++  +N + +r ++k+Gf
  gi|386002520|ref|YP_005920819.1| 552 YGLLGESMM-AEVAYVVRDDYHRQGVGRELLARLTHLA-RKQGVQGFVAEVLSTNVRIFRMFQKMGF 616
                                       887777766.****************************.8888***********************9 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.9   8.8e+03      16      48 ..      19      55 ..      10      81 .. 0.56
   2 !   32.9   0.0   4.1e-11   6.1e-08      41     117 .]     538     616 ..     491     616 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.9
                                      HHHHHHHHHHHHHHSTTC.EEEE...EEETTEEEEEE CS
                    Acetyltransf_1 16 nedaseeefeesfsleae.gllv...aeedgeliGfi 48
                                      +++++  e +++ +++++ +++v   + e + l+G +
  gi|386002520|ref|YP_005920819.1| 19 WPKKFWPETAIFERIHPGdRIFVgtgCGEPQHLVGAL 55
                                      4555555555555567776666655333334466655 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 4.1e-11
                                       T.....TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHH CS
                    Acetyltransf_1  41 d.....geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlY 112
                                       d     +++iG  ++    +     ++   ++V+ +y+++G+G++Ll  l + ar++g++  v++v ++n++  r++
  gi|386002520|ref|YP_005920819.1| 538 DrpagrETVIGIGQYGLLGE---SMMAEVAYVVRDDYHRQGVGRELLARLTHLARKQGVQGFVAEVLSTNVRIFRMF 611
                                       25665677888888888888...6777789*****************************99999************* PP

                                       HHTTE CS
                    Acetyltransf_1 113 eklGF 117
                                       +k+GF
  gi|386002520|ref|YP_005920819.1| 612 QKMGF 616
                                       ****9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   1.7e+03      19      72 ..     205     264 ..     190     278 .. 0.72
   2 !   29.2   0.2   4.9e-10   7.3e-07      57     110 ..     565     620 ..     522     630 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                   Acetyltransf_10  19 p..ealrerieegealllvaeeggkiv.Gvielrdgs.....hisllfVdpeyrgqGigkaL 72 
                                       p  ++++++i  ge++  ++e+g +i  G++++ +       +  +l V+ e    Gi+  +
  gi|386002520|ref|YP_005920819.1| 205 PapDEIARKI--GEYVARIVEDGSTIQvGYGSVPNAVlaclgEKKHLGVHTELFTDGIADLM 264
                                       4447888888..88888888888777449988877666666677788888888888888655 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 4.9e-10
                   Acetyltransf_10  57 lfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavg 110
                                        +V+++y++qG+g++Ll ++ + a+k+g +    +v +++    ++++k+GF++ +
  gi|386002520|ref|YP_005920819.1| 565 YVVRDDYHRQGVGRELLARLTHLARKQGVQGfVAEVLSTNvRIFRMFQKMGFVVEK 620
                                       489*************************************9***********9765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   4.1e-08   6.1e-05      15      75 ..     547     617 ..     523     618 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.1e-08
                                       EEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHH.H....TTSEEE...EEEEEETHH.HHHHHHHHTTEE CS
                    Acetyltransf_7  15 vGfialslld...aeitrlaVdpeyrgkGiGraLle.a....aekgii...leqlelnae.kaikfYeklGFe 75 
                                       +G   + ll+     +   +V+ +y+++G+Gr+Ll+ +    +++g++        l+++ +  ++++k+GF+
  gi|386002520|ref|YP_005920819.1| 547 IGIGQYGLLGesmMAEVAYVVRDDYHRQGVGRELLArLthlaRKQGVQgfvA--EVLSTNvRIFRMFQKMGFV 617
                                       44333333322232233366***************85344542255442222..23333224455*******8 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   4.7e-08     7e-05      58     138 ..     544     620 ..     509     631 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.7e-08
                    Acetyltransf_4  58 drivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGF 134
                                       ++++G+ ++g +   +++  ae+ + + + d   +g+grel++ l   +++q+++ ++ae+ s+n     +++++GF
  gi|386002520|ref|YP_005920819.1| 544 ETVIGIGQYGLL---GESMMAEVAYVV-RDDYHRQGVGRELLARLTHLARKQGVQGFVAEVLSTNVRIFRMFQKMGF 616
                                       455666666622...468888888777.5799********************************************* PP

                    Acetyltransf_4 135 elvg 138
                                        +++
  gi|386002520|ref|YP_005920819.1| 617 VVEK 620
                                       7765 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00023      0.34       6      40 ..      27      59 ..      25      86 .. 0.81
   2 ?   -0.5   0.0      0.45   6.8e+02     146     190 ..     129     171 ..     126     173 .. 0.82
   3 !    7.8   0.0    0.0013         2       4      67 ..     214     271 ..     211     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                                      HHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHT CS
                         CoA_trans  6 eavakeikdGmtvavGGFgligiPealiaalarsg 40
                                       a+ ++i+ G+ ++vG  +++g+P++l+ al r  
  gi|386002520|ref|YP_005920819.1| 27 TAIFERIHPGDRIFVG--TGCGEPQHLVGALKRYV 59
                                      688899**********..**********9998865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.45
                                       SSSEEEEEEECCEEETTCSEESSGGGHTTHSHHHHHHEEEEEEEE CS
                         CoA_trans 146 alkadvalikaskadeegnlvfeksagnfnkpaiaeaakvtilev 190
                                       a+  dval++ s  d++g+l+   s+   +  a+  aa+++i+++
  gi|386002520|ref|YP_005920819.1| 129 AIPIDVALVQTSPPDRHGYLRLGISVDIVK-AAVE-AAEIVIAQI 171
                                       66679***************9999888888.4444.899999987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0013
                                       HHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEE CS
                         CoA_trans   4 aaeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllngsvkk 67 
                                       + e va+ ++dG+t+ vG     g  P +++ a +    k++  ++ e  + g+  l+++g v++
  gi|386002520|ref|YP_005920819.1| 214 IGEYVARIVEDGSTIQVG----YGsVP-NAVLACLGE--KKHLGVHTELFTDGIADLMKSGAVDN 271
                                       668899************....88799.777777766..89999999998899999999999987 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00028      0.42     139     207 ..     133     198 ..     123     208 .. 0.80
   2 !    6.7   0.0    0.0013       1.9     450     482 ..     398     429 ..     389     432 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                   Mal_decarbox_Al 139 nvalvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdklprvd.iPadwvdfvveadkp 207
                                       +valv ++  dr+G l  G + +   a vea+     iviaq+n  + ++p    +  + vd +v +d+p
  gi|386002520|ref|YP_005920819.1| 133 DVALVQTSPPDRHGYLRLGISVDIVKAAVEAA----EIVIAQINPRMPRIPGDGfVSVEEVDHLVFCDEP 198
                                       69*******************99777777776....69******98877775432566777777777776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0013
                   Mal_decarbox_Al 450 gddvthvvteeGiayllkaesleereqairava 482
                                         dv +vvte Giayl+ a+++ er   + a+a
  gi|386002520|ref|YP_005920819.1| 398 RGDVHYVVTEYGIAYLH-AKNVRERALDLIAIA 429
                                       579************97.567777776666665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     3e-06    0.0044      28      80 ..     566     619 ..     558     624 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                                       EE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE.EETT-HHHHHHHHHHT-EEE CS
                              FR47  28 qvlpehrrrGlgsrlvkalakeiaergktvllv.vvasNtpsirlyeklGfeki 80 
                                        v+++  r+G g+ l + l++  +++g + ++  v  +N +  r+++k+Gf + 
  gi|386002520|ref|YP_005920819.1| 566 VVRDDYHRQGVGRELLARLTHLARKQGVQGFVAeVLSTNVRIFRMFQKMGFVVE 619
                                       699************************9987762677899***********764 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.5e-05     0.022      89     143 ..     569     622 ..     564     623 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                                       HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                        +++++g++++ll +l+h++ ++ +++  v+E   +N r+ r+++k+Gf+ ek +
  gi|386002520|ref|YP_005920819.1| 569 DDYHRQGVGRELLARLTHLARKQ-GVQGFVAEVLSTNVRIFRMFQKMGFVVEKVW 622
                                       567899***********988777.**************************99865 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.8   7.1e+03      14      28 ..      30      44 ..      28      49 .. 0.85
   2 ?   -2.7   0.0       3.4   5.1e+03      84     104 ..      84     104 ..      75     108 .. 0.81
   3 ?   12.9   0.0   5.1e-05     0.077       7      49 ..     212     254 ..     209     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.8
                             DeoRC 14 aeliedgdtifldaG 28
                                       e i++gd if+++G
  gi|386002520|ref|YP_005920819.1| 30 FERIHPGDRIFVGTG 44
                                      57799******9988 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                             DeoRC  84 aeealrqfnvdkaflgangid 104
                                        e++ ++f+++ +f+g ++ d
  gi|386002520|ref|YP_005920819.1|  84 EEQFRENFRLNSFFVGSRSRD 104
                                       5778899********998765 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 5.1e-05
                             DeoRC   7 rrIAkaAaeliedgdtifldaGtTtlelaraLaekknltvvTn 49 
                                       r+I++++a+++edg+ti ++ G+   ++   L ekk+l v T 
  gi|386002520|ref|YP_005920819.1| 212 RKIGEYVARIVEDGSTIQVGYGSVPNAVLACLGEKKHLGVHTE 254
                                       79************************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.78u 0.37s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 3453.29
//
Query:       gi|386002521|ref|YP_005920820.1|  [L=688]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-14   53.8   0.0    4.9e-14   52.9   0.0    1.4  1  VWA_2          von Willebrand factor type A domain
    3.8e-13   50.1   0.0    1.3e-12   48.3   0.0    1.8  1  VWA            von Willebrand factor type A domain
      0.001   19.2   0.1      0.019   15.1   0.1    2.3  1  vWA-TerF-like  vWA found in TerF C terminus


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   8.2e-18   4.9e-14       1     106 [.     280     412 ..     280     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 8.2e-18
                             VWA_2   1 lvfvlDtSgSmrng..dy.................gptrleaakdaveallkslp.gdrvglvtfsdgpevliplt. 56 
                                       lv+vlD SgSm+++  +y                 +++++e+a +av +ll++l  +dr+glv+fsd+++++ plt 
  gi|386002521|ref|YP_005920820.1| 280 LVVVLDYSGSMGSPfnEYyydrfgsrvdvevdsglSKSKMEIADRAVVELLGHLEvEDRFGLVVFSDEAYLVDPLTr 356
                                       79*********998654489*************999******************99*******************88 PP

                             VWA_2  57 ...kdkakilnalrnleakgggtnlaaaLqlarkalkkrr....kgekrvivlitDg 106
                                          kd +++++a+ ++e++ ggtn++a++ + ++a+ k      + e+++i++itD+
  gi|386002521|ref|YP_005920820.1| 357 iddKDLDALKAAIIEIEEY-GGTNMEAGMMKGTAAFGKYGeidpAEEENRIIFITDA 412
                                       87899************96.****************88878999************6 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.2e-16   1.3e-12       1     171 [.     279     474 ..     279     478 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.2e-16
                                       EEEEEEE-STTS........................CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEE CS
                               VWA   1 DivfvlDgSgsm........................geenfekvkefikklveklevgpegtrvglvqfssevktef 53 
                                       ++v+vlD Sgsm                        +++++e + +++ +l+++le     +r+glv fs+e++ + 
  gi|386002521|ref|YP_005920820.1| 279 NLVVVLDYSGSMgspfneyyydrfgsrvdvevdsglSKSKMEIADRAVVELLGHLE---VEDRFGLVVFSDEAYLVD 352
                                       799**********************999999999999*******************...****************** PP

                                       ETTSHC..HHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEES.....S--CSSHTHHH CS
                               VWA  54 slndys..skeellsalnnlkysgggttntgkalkyaleklfkssagaRenakkviilltd.....Gksndgdpkea 123
                                       +l++    + ++l+ a+ ++  ++ggt+ +++++ +++  + k  +   ++ ++ ii++td     G++ +g +++ 
  gi|386002521|ref|YP_005920820.1| 353 PLTRIDdkDLDALKAAIIEI-EEYGGTN-MEAGMMKGTAAFGKYGEIDPAEEENRIIFITDampnlGETGEGGLLRI 427
                                       ****6634668888888886.5555565.********997777766677789*********9999999988899999 PP

                                       HHHHHGCTEEEEEEEESSSHHHHHHHHHSSSSCHHCEEEESSHHHHHH CS
                               VWA 124 aneakeqgikvfavGvgnadekelLnkiasepgeghvftvtdfeelee 171
                                       ++e  ++gi +  +Gvg + ++el+++i++  g  +++ v++ +e+ee
  gi|386002521|ref|YP_005920820.1| 428 LRENARKGIYTTFIGVGVDFNTELVEEISKVRG-ANYYSVHSAKEFEE 474
                                       999999***********************9999.99999999997765 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.2e-06     0.019      26     144 ..     321     446 ..     277     476 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-06
                     vWA-TerF-like  26 vver.llavaaqlDddgelevwlfaskakrlpdvtladleeyvkeeeegllelkklggvneeapvle..evlekvrk 99 
                                       +++r ++ +  +l+ + +   ++f+++a  ++++t  d ++  +  ++ ++e++++gg+n+ea +++  + + k+ +
  gi|386002521|ref|YP_005920820.1| 321 IADRaVVELLGHLEVEDRFGLVVFSDEAYLVDPLTRIDDKDL-DALKAAIIEIEEYGGTNMEAGMMKgtAAFGKYGE 396
                                       233312233344444444444555555555555554444443.67888999***************82245567888 PP

                     vWA-TerF-like 100 .epaelptlvlFitDG....gvkkkkeiekalreaskepiFwqFvglgks 144
                                        +pae    ++FitD     g + +    ++lre +++ i+  F+g+g  
  gi|386002521|ref|YP_005920820.1| 397 iDPAEEENRIIFITDAmpnlGETGEGGLLRILRENARKGIYTTFIGVGVD 446
                                       899999*********83333445567889******************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 3725.85
//
Query:       gi|386002522|ref|YP_005920821.1|  [L=316]
Description: hypothetical protein Mhar_1841 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-64  216.7   0.0    1.2e-63  215.3   0.0    1.5  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.3   0.0   6.9e-68   1.2e-63       1     213 [.      47     304 ..      47     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 6.9e-68
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl+g +a+++++ +v+g++g l+YRGydi +L+ ++s+feev ylLl+g+lPt++el++f+++l+e+r+lp+++ ++
  gi|386002522|ref|YP_005920821.1|  47 GLEGAIACKSRVGFVNGSEGTLIYRGYDIFDLC-AHSTFEEVSYLLLYGDLPTESELASFESRLNEYRFLPNTL-RT 121
                                       799******************************.7************************************888.88 PP

                                       HHCSS.TTS-HHHHHHHHHHH....................HHHHSTT............................. CS
                      Citrate_synt  78 lealp.kdahpmavlraavsa....................lsaddee............................. 104
                                       l+++p + ++pma+lr ++++                    +                                   
  gi|386002522|ref|YP_005920821.1| 122 LMNAPvERMNPMAALRLGTNLmhqrqtwrdsedarpsledaI-----Asdedsipmetrptgerhaiyefqrrhlrr 193
                                       8889999**********9999666666655555555555543.....045555888888888888888888888855 PP

                                       ..CTCHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHHHSS---HHHHHHHHHH CS
                      Citrate_synt 105 ..seakee....seeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflymlrgkkpdeeeaklldla 175
                                              +     + + +++++ liA ++t+aaai r r+gr p+epd++l +a+n+lym++g++p++ e++++d+ 
  gi|386002522|ref|YP_005920821.1| 194 ptD----PrlapDDAESMDSCIHLIAGMATLAAAIGRLRRGRLPIEPDPELGHAANLLYMMTGRRPTPVEERVMDVS 266
                                       442....245567888999***********************9*****99*************************** PP

                                       HHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHT CS
                      Citrate_synt 176 lvlhaDHelnaSTfaarvvaStladlysaiaagigalk 213
                                       l+lhaDH++naSTfa+ vvaSt++d+y+++ agigal+
  gi|386002522|ref|YP_005920821.1| 267 LILHADHGMNASTFACLVVASTMSDIYFSVDAGIGALY 304
                                       ************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.38s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1687.01
//
Query:       gi|386002523|ref|YP_005920822.1|  [L=438]
Description: IS66 family element, transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-49  166.7   0.0    7.7e-49  166.7   0.0    1.7  2  DDE_Tnp_IS66    Transposase IS66 family
    6.5e-07   29.6   3.3    1.4e-06   28.5   3.3    1.6  1  zf-IS66         zinc-finger binding domain of transposase IS6
    0.00013   22.2   0.1    0.00047   20.4   0.0    1.9  2  DDE_Tnp_IS240   DDE domain
     0.0035   17.3   0.1     0.0071   16.3   0.1    1.5  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.048   14.0   0.0    2.0  1  DUF5623         Domain of unknown function (DUF5623)
      0.013   15.5   4.6      0.048   13.7   3.0    2.4  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
      0.027   14.8   5.2      0.064   13.6   5.2    1.6  1  DUF737          Protein of unknown function (DUF737)
      0.052   13.6   1.8       0.16   12.0   1.8    1.9  1  MCC-bdg_PDZ     PDZ domain of MCC-2 bdg protein for Usher syn
      0.056   12.9   2.2        5.9    6.4   0.1    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.074   12.8   2.1        3.2    7.6   0.3    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.084   13.1   0.3        1.7    8.9   0.2    2.5  2  MazG            MazG nucleotide pyrophosphohydrolase domain
       0.11   13.0   8.6      0.073   13.5   3.1    3.0  2  ZapB            Cell division protein ZapB
       0.14   12.3   4.1       0.19   11.8   1.9    2.1  2  DivIVA          DivIVA protein
       0.14   12.3   0.5         22    5.3   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.21   11.4   4.0       0.68    9.7   4.0    1.8  1  DivIC           Septum formation initiator
        0.3   10.6   1.8       0.36   10.4   0.6    1.7  2  TMCO5           TMCO5 family
        0.4   10.7   2.9         17    5.5   0.3    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.79    9.1   3.2         15    5.0   0.3    2.5  2  zf-TFIIB        Transcription factor zinc-finger
        1.4    8.5   4.3        1.2    8.7   1.4    2.2  3  Snf7            Snf7
        1.4    9.0   3.8         16    5.7   0.1    2.4  2  UPF0547         Uncharacterised protein family UPF0547
        1.9    7.3   5.8        0.8    8.5   2.0    2.0  2  XRCC4           DNA double-strand break repair and V(D)J reco
        4.9    7.3   9.2       0.96    9.6   1.9    3.1  3  bZIP_1          bZIP transcription factor


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.5       3.2   2.6e+03     185     223 ..       8      44 ..       2      54 .. 0.66
   2 !  166.7   0.0   9.5e-52   7.7e-49       2     280 ..     149     408 ..     148     410 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.2
                      DDE_Tnp_IS66 185 reareaeaeerlalrqeesrpllaeleawleeqlkkvlp 223
                                       ++++   ++erl++++e +r+ +a+lea l + ++ ++p
  gi|386002523|ref|YP_005920822.1|   8 KQLK--AENERLKRENEFQREQIAKLEARLAKYENAHTP 44 
                                       3333..247888888888888888888877766644444 PP

  == domain 2  score: 166.7 bits;  conditional E-value: 9.5e-52
                      DDE_Tnp_IS66   2 slagpsllAeilvlkyadhlPlyRqeeilarl.GvelsrgtlanwvkraaelleplvealkaallasevihaDETtl 77 
                                       +++g++++A++++lky+d lP ++++++l+rl G++++++t+ ++++raa++++  ++a+ + +++++++ +DET++
  gi|386002523|ref|YP_005920822.1| 149 GRFGNNVIAQTTLLKYEDRLPHRKIQNALKRLhGLTICAATVLDLTRRAADAVQSQYDAILNSVRNAPILYVDETSI 225
                                       789************************************************************************** PP

                      DDE_Tnp_IS66  78 rvlkpgrgkgkksylWvyvtdkrkpavlfeyspsRggevaealLag.fkGvlvsDgyagYnklaeeqvthalCwaHl 153
                                       +       +g+++++Wv+ t      ++  + +sRg++v  ++L+  f G++v+Dg+++Y k++    +++ CwaHl
  gi|386002523|ref|YP_005920822.1| 226 K------VQGERHWIWVFTTPS---ETFVVIRKSRGMKVLMEVLTRrFDGIIVCDGWKPYAKFT---KRLQRCWAHL 290
                                       *......89***********88...9*****************9999****************5...899******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakkksqaaaealarigklyaierear.eaeaeerlalrqeesrpllaeleawleeqlkkvlpksklgk 229
                                       +R+ +d+ ++      ++ea+   g+l+++ +e++ + e++   ++r    +   ++l++w+ +       ++k++k
  gi|386002523|ref|YP_005920822.1| 291 LRESKDLADK------IEEAVPLHGDLKDLYEELTdALENDPPPEVRMGLLEMARSKLHQWIMK----EYMSEKVKK 357
                                       *******975......556666666666666666532356777888888888899999999986....468999*** PP

                      DDE_Tnp_IS66 230 airyllkrweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                       +i ++ +  e  ++f+ ++ v+++NN+aERa+R  v+ RK+ +++++e+G 
  gi|386002523|ref|YP_005920822.1| 358 LIGKISNGFEYWFTFIIQPAVEPTNNRAERALREHVVLRKIIGTLRNEKGT 408
                                       ************************************************996 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   3.3   1.8e-09   1.4e-06       3      45 ..      91     134 ..      90     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.8e-09
                           zf-IS66   3 tCpcCGg.llkpigedrvreeldip.PakfrViehirpkyaCpcC 45 
                                        Cp+CG+ l +pi ++    + +ip P+ ++V+e+ +  y+Cp+C
  gi|386002523|ref|YP_005920822.1|  91 LCPDCGAkLGDPIRKE-SKIIEEIPePQPIIVTEYKIAHYRCPSC 134
                                       5******888899999.89******9999**************** PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.7e-07   0.00047       6     100 ..     220     302 ..     217     324 .. 0.75
   2 ?   -2.8   0.0       8.1   6.6e+03      95     129 ..     381     421 ..     361     423 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.7e-07
                     DDE_Tnp_IS240   6 vDETyvkikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkreg. 81 
                                       vDET +k++G+ ++++           ++++k R++k    +l++ ++        iv D+ + ya+  k+l+r   
  gi|386002523|ref|YP_005920822.1| 220 VDETSIKVQGERHWIWVFTTPSETF--VVIRKSRGMKVLMEVLTRRFDGI------IVCDGWKPYAKFTKRLQRCWa 288
                                       9***************987665554..578999**999999999988888......****************99543 PP

                     DDE_Tnp_IS240  82 elfdevshvqvkylnnriE 100
                                       +l++     ++k l + iE
  gi|386002523|ref|YP_005920822.1| 289 HLLR-----ESKDLADKIE 302
                                       3333.....3444444444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.1
                     DDE_Tnp_IS240  95 lnnriEs...dhrtlKkrl...rptrgfkslksaaktlagf 129
                                        nnr E+   +h  l+k +   r  +g    +++ ++la++
  gi|386002523|ref|YP_005920822.1| 381 TNNRAERalrEHVVLRKIIgtlRNEKGTSIHERIMTVLATW 421
                                       57777752224555665544335555555555555555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.7e-06    0.0071      13      39 ..      90     139 ..      81     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.7e-06
                               DZR  13 rfCseCgtklkavaa.......................edrCpsCgekvd 39 
                                         C++Cg+kl  + +                       ++rCpsC+++v 
  gi|386002523|ref|YP_005920822.1|  90 DLCPDCGAKLGDPIRkeskiieeipepqpiivteykiaHYRCPSCQKEVV 139
                                       58*******9766668899***************************9953 PP

>> DUF5623  Domain of unknown function (DUF5623)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.9e-05     0.048      12      59 ..     306     356 ..     301     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                           DUF5623  12 evHqevgrllkellesvarskg...vssrlsavrstLddWlemEyseeeld 59 
                                        +H ++  l +el+++++++         l+++rs+L++W+ +Ey +e+++
  gi|386002523|ref|YP_005920822.1| 306 PLHGDLKDLYEELTDALENDPPpevRMGLLEMARSKLHQWIMKEYMSEKVK 356
                                       56778888888888888887774423345799*************888766 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.0   5.9e-05     0.048      11      48 ..       4      41 ..       3      49 .. 0.92
   2 ?    0.1   0.0         1   8.2e+02      42      72 ..     287     317 ..     279     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                        TMF_DNA_bd 11 DeqIaqLmeEGekLskkelklnntikkLrkknkeleke 48
                                      +e+I+qL++E e+L+ ++  ++++i kL + +++ e+ 
  gi|386002523|ref|YP_005920822.1|  4 EEIIKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41
                                      699***************************99998875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                        TMF_DNA_bd  42 nkelekeikelkkkleklekeleeleerlke 72 
                                        ++l  e k+l +k+e+ +     l+++++e
  gi|386002523|ref|YP_005920822.1| 287 WAHLLRESKDLADKIEEAVPLHGDLKDLYEE 317
                                       5667788899999999999999988888765 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.2   7.9e-05     0.064     147     180 ..       4      37 ..       1      43 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-05
                            DUF737 147 erkarqLeekekeLkkqdafYkeqlakLeeknae 180
                                       e  ++qL + ++ Lk+ ++f +eq+akLe++ a+
  gi|386002523|ref|YP_005920822.1|   4 EEIIKQLKAENERLKRENEFQREQIAKLEARLAK 37 
                                       5679***************************987 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.8    0.0002      0.16       6      41 ..       7      41 ..       4      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                       MCC-bdg_PDZ  6 IeeLkaqnelLsltleerkqqseeLsldlgkaEsna 41
                                      I +Lka ne+L++  e  ++q ++L  +l k+E na
  gi|386002523|ref|YP_005920822.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKYE-NA 41
                                      899******************************.55 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.012       9.5      19      26 .]      92      99 ..      90      99 .. 0.82
   2 ?    6.4   0.1    0.0073       5.9       2      15 ..     128     142 ..     127     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                       zf-ribbon_3 19 CpyCGtkl 26
                                      Cp CG+kl
  gi|386002523|ref|YP_005920822.1| 92 CPDCGAKL 99
                                      99999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0073
                       zf-ribbon_3   2 tvrCPnCGa.plssd 15 
                                       ++rCP+C + +++sd
  gi|386002523|ref|YP_005920822.1| 128 HYRCPSCQKeVVASD 142
                                       79*****98887776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.004       3.2       2      11 ..      92     101 ..      91     102 .. 0.83
   2 ?    4.6   0.1     0.034        28       1      10 [.     130     139 ..     130     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                     zinc_ribbon_2   2 CpnCGaelqd 11 
                                       Cp CGa+l d
  gi|386002523|ref|YP_005920822.1|  92 CPDCGAKLGD 101
                                       9999999865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.034
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +Cp+C +e+ 
  gi|386002523|ref|YP_005920822.1| 130 RCPSCQKEVV 139
                                       6******986 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.48   3.9e+02      51      73 ..     149     171 ..     142     172 .. 0.85
   2 ?    8.9   0.2    0.0021       1.7       6      37 ..     286     322 ..     281     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                                       H---HHHHHHHHHHHHHHH-GGG CS
                              MazG  51 ggidledvaetileKlerRhphv 73 
                                       g++  + +a+t+l K+e R ph+
  gi|386002523|ref|YP_005920822.1| 149 GRFGNNVIAQTTLLKYEDRLPHR 171
                                       6667777899***********97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHT.....T-HHHHHHHHHHHH CS
                              MazG   6 llaylleEvgEvaeaIkk.....edrdeleeELGDvL 37 
                                         a+ll E + +a++I++     +d ++l eEL D L
  gi|386002523|ref|YP_005920822.1| 286 CWAHLLRESKDLADKIEEavplhGDLKDLYEELTDAL 322
                                       66899*************99*99************87 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.1   8.9e-05     0.073      20      54 ..       7      41 ..       5      48 .. 0.88
   2 ?    1.0   0.3      0.74     6e+02      54      69 ..     347     362 ..     280     364 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                              ZapB 20 itlLqmeieeLkeeneelkeenreleeeneqlkee 54
                                      i++L+ e+e+Lk+ene   e++++le+ + + ++ 
  gi|386002523|ref|YP_005920822.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41
                                      899***********************988887655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.74
                              ZapB  54 ereawqerlkkLLgkl 69 
                                        +e + e++kkL+gk+
  gi|386002523|ref|YP_005920822.1| 347 MKEYMSEKVKKLIGKI 362
                                       3555667777777776 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   0.00024      0.19      25      62 ..       5      42 ..       4      44 .. 0.92
   2 ?   -0.7   0.0       1.7   1.4e+03      35      68 ..     288     321 ..     277     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXX CS
                            DivIVA 25 eFLdqvakdyeallkeneelkekvkeleeklkeykele 62
                                      e+++q+  + e+l +ene ++e++++le +l++y++++
  gi|386002523|ref|YP_005920822.1|  5 EIIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42
                                      67899999**************************9975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXX CS
                            DivIVA  35 eallkeneelkekvkeleeklkeykeleetLkkt 68 
                                         ll+e+++l +k++e+     + k+l e+L ++
  gi|386002523|ref|YP_005920822.1| 288 AHLLRESKDLADKIEEAVPLHGDLKDLYEELTDA 321
                                       5789999999999999877777777777766665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.042        34      27      35 ..      89      98 ..      80     100 .. 0.79
   2 ?    5.3   0.0     0.026        22       6      14 ..     129     137 ..     126     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.042
                       Zn-ribbon_8 27 ta.CPeCgse 35
                                      ++ CP+Cg++
  gi|386002523|ref|YP_005920822.1| 89 IDlCPDCGAK 98
                                      566*****86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.026
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       YrC +C++e
  gi|386002523|ref|YP_005920822.1| 129 YRCPSCQKE 137
                                       888888865 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.0   0.00084      0.68      19      50 ..       7      38 ..       3      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                      +kqlk+e ++l++e++ +++++++Lea+++++
  gi|386002523|ref|YP_005920822.1|  7 IKQLKAENERLKRENEFQREQIAKLEARLAKY 38
                                      57888888888888888888888888888777 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00044      0.36      61     101 ..       2      42 ..       1      63 [. 0.87
   2 ?   -2.0   0.0       2.6   2.1e+03     164     183 ..     321     344 ..     278     370 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                             TMCO5  61 ekedalkeLeletaklekkneiLlkevveLqkkisrkeskq 101
                                       ++e+  k+L+ e  +l+++ne+  +++++L+ ++ + e+ +
  gi|386002523|ref|YP_005920822.1|   2 HEEEIIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42 
                                       679999****************************9998654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                             TMCO5 164 kmee....eketlllekevsklqs 183
                                        +e+    e  + lle   skl +
  gi|386002523|ref|YP_005920822.1| 321 ALENdpppEVRMGLLEMARSKLHQ 344
                                       222233333333344444444333 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.038        31       2       9 ..      92      99 ..      92     106 .. 0.91
   2 ?    5.5   0.3     0.021        17       1      11 [.     130     140 ..     130     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                    DNA_ligase_ZBD  2 CPvCGsav 9 
                                      CP CG+++
  gi|386002523|ref|YP_005920822.1| 92 CPDCGAKL 99
                                      *****997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+C  +vv 
  gi|386002523|ref|YP_005920822.1| 130 RCPSCQKEVVA 140
                                       5*******995 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.019        15      16      26 ..      86      96 ..      82      96 .. 0.89
   2 ?    3.9   0.2     0.041        33       2      14 ..     131     143 ..     130     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.019
                          zf-TFIIB 16 gveidyCpqCr 26
                                      +v id Cp+C+
  gi|386002523|ref|YP_005920822.1| 86 EVAIDLCPDCG 96
                                      699*******7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                          zf-TFIIB   2 CPkCqdeleeser 14 
                                       CP+Cq e + s++
  gi|386002523|ref|YP_005920822.1| 131 CPSCQKEVVASDH 143
                                       *****99887765 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.4    0.0015       1.2       2      38 ..       6      42 ..       5      62 .. 0.84
   2 ?   -3.0   0.0       5.8   4.7e+03       6      26 ..     283     303 ..     279     323 .. 0.66
   3 ?   -0.9   0.0       1.3   1.1e+03      29      62 ..     353     404 ..     332     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                              Snf7  2 airsLrkaerkldkkqeslekkikkleaelkklakkg 38
                                       i++L+ + ++l+++ e+ +++i+klea l+k+    
  gi|386002523|ref|YP_005920822.1|  6 IIKQLKAENERLKRENEFQREQIAKLEARLAKYENAH 42
                                      6899****************************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.8
                                       HHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   6 Lrkaerkldkkqeslekkikk 26 
                                       L+++   l ++++ l +ki++
  gi|386002523|ref|YP_005920822.1| 283 LQRCWAHLLRESKDLADKIEE 303
                                       556666666666666666654 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                       HHHHHHHCTT-..................HHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7  29 aelkklakkgn..................kdralllLKqkkryekqldqldn 62 
                                       +++kkl+ k++                  + ra ++L++ + ++k +  l n
  gi|386002523|ref|YP_005920822.1| 353 EKVKKLIGKISngfeywftfiiqpaveptNNRAERALREHVVLRKIIGTLRN 404
                                       4556666665566667777777777777789999999999999998877766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.02        16       7      21 ..      82      96 ..      82      97 .. 0.91
   2 ?    3.8   0.7     0.074        60       2      10 ..     130     138 ..     130     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                           UPF0547  7 eakvPvaaqfCphCG 21
                                      +++v va   Cp+CG
  gi|386002523|ref|YP_005920822.1| 82 DRQVEVAIDLCPDCG 96
                                      68999999******9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.074
                           UPF0547   2 vCPeCeakv 10 
                                       +CP C+ +v
  gi|386002523|ref|YP_005920822.1| 130 RCPSCQKEV 138
                                       6*****998 PP

>> XRCC4  DNA double-strand break repair and V(D)J recombination protein XRCC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.0   0.00098       0.8     137     173 ..       5      41 ..       1      44 [. 0.90
   2 ?   -0.3   0.1      0.47   3.8e+02     147     184 ..     281     317 ..     274     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00098
                             XRCC4 137 dqiaelqakNehLqkENerLlrdwsdvterlekyvka 173
                                       + i++l+a+Ne+L++ENe  +++  ++++rl ky +a
  gi|386002523|ref|YP_005920822.1|   5 EIIKQLKAENERLKRENEFQREQIAKLEARLAKYENA 41 
                                       578899***************************9876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                             XRCC4 147 ehLqkENerLlrdwsdvterlekyvkakEeleadLYkr 184
                                       ++Lq+   +Llr+ +d+ +++e+ v    +l+ dLY+ 
  gi|386002523|ref|YP_005920822.1| 281 KRLQRCWAHLLRESKDLADKIEEAVPLHGDLK-DLYEE 317
                                       679999999***************99999985.88875 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.9    0.0012      0.96      35      61 ..       7      33 ..       4      36 .. 0.89
   2 ?   -1.0   0.1       2.3   1.9e+03      18      27 ..      48      57 ..      46      62 .. 0.82
   3 ?    0.1   0.0       1.1     9e+02      29      51 ..     281     303 ..     278     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 35 vkaLekeNksLkseleelkkevekLks 61
                                       k+L++eN+ Lk e+e  +++++kL+ 
  gi|386002523|ref|YP_005920822.1|  7 IKQLKAENERLKRENEFQREQIAKLEA 33
                                      699********************9975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                      HHHHHHHHHH CS
                            bZIP_1 18 rrsRqRKqae 27
                                      rr R+RK+ +
  gi|386002523|ref|YP_005920822.1| 48 RRGRKRKKGY 57
                                      7889***977 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkselee 51 
                                       ++L+r  + L  e k+L++++ee
  gi|386002523|ref|YP_005920822.1| 281 KRLQRCWAHLLRESKDLADKIEE 303
                                       77888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      871  (0.0485805); expected 358.6 (0.02)
Passed Vit filter:                       147  (0.00819901); 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):              22  [number of targets reported over threshold]
# CPU time: 0.77u 0.37s 00:00:01.14 Elapsed: 00:00:00.56
# Mc/sec: 2367.52
//
Query:       gi|386002524|ref|YP_005920823.1|  [L=139]
Description: 2-methylcitrate synthase/citrate synthase II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-42  144.7   0.0    4.1e-42  144.5   0.0    1.0  1  Citrate_synt    Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.15   12.5   0.0    1.2  1  Transglut_core  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   0.0   4.6e-46   4.1e-42     239     361 .]       2     122 ..       1     122 [. 0.95

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 4.6e-46
                                       HHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTC.HTHHHHHHHHHHHHHHHHHHHHCHHGCT-EB-T CS
                      Citrate_synt 239 eeylekvlakekerlpGfGHrvykksDpRakilkelaeelaee.kgkdpllklaeeleevapevlkekeeknlypNv 314
                                       +e+++++ +++ +++pGfGHrvy+++DpRa++l  la  +ae   ++d+++ +a++lee + ++l   e k+++pNv
  gi|386002524|ref|YP_005920823.1|   2 KEWYNTARSSG-RKVPGFGHRVYRTYDPRARVLGPLAGMMAESnPNCDKMYSIAKRLEEEVVSDLGM-E-KKIFPNV 75 
                                       68888998875.*****************************99999**************9999984.5.79***** PP

                                       HHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 315 DfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                       D+ysg++y+a+g+p +l+tvlfa+sRvaGw+A+++e+l++n+i+RPr
  gi|386002524|ref|YP_005920823.1|  76 DYYSGIVYHAMGVPGDLYTVLFAVSRVAGWTARVMEYLENNRIFRPR 122
                                       ************************************99********8 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05      0.15       9      80 ..      45     114 ..      38     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                    Transglut_core   9 agakdplekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgyls 80 
                                       ++ ++ +  ak+++e+v +  + + ++  p  +  + ++ +  G+  d  +++ a+ R +G  aRv+  yl+
  gi|386002524|ref|YP_005920823.1|  45 PNCDKMYSIAKRLEEEVVSDLGME-KKIFPNVDYYSGIVYHAMGVPGDLYTVLFAVSRVAGWTARVME-YLE 114
                                       667888999999999999999999.888888888999999*************************984.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.38s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 775.73
//
Query:       gi|386002525|ref|YP_005920824.1|  [L=594]
Description: Alkyl sulfatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-36  125.4   0.0    3.7e-36  124.6   0.0    1.3  1  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    2.3e-13   50.6   1.8    3.8e-13   49.9   0.7    2.0  2  Lactamase_B      Metallo-beta-lactamase superfamily
    1.1e-08   35.4   0.0    2.5e-08   34.3   0.0    1.6  1  Alkyl_sulf_C     Alkyl sulfatase C-terminal
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.038   14.5   0.0    1.6  1  SCP2             SCP-2 sterol transfer family
       0.02   14.4   0.1      0.036   13.6   0.1    1.5  1  Lactamase_B_2    Beta-lactamase superfamily domain
      0.032   14.7   0.0      0.091   13.2   0.0    1.7  1  MycE_N           MycE methyltransferase N-terminal


Domain annotation for each model (and alignments):
>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   0.0   1.2e-39   3.7e-36       1     135 [.     331     465 ..     331     468 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 1.2e-39
                                       -CCCHHHC----HHHHTSGGGSSSSS-HHHHHHHHHHHHH-S--S-GGGTS---HHHHHHHHHHHTTSHHHHHHHHH CS
                   Alkyl_sulf_dimr   1 tpdeiaekvklPeslanepylreyYGtvehnvraiyqrylGWfdgnPanLnplppeekakrlvelmGgaekvlekak 77 
                                       tp ei+e ++lP++la++p+l+ey+G+++ ++ +i+q+y+GWf g+ ++++p++p+e+a++++ l+Gg++ ++ekak
  gi|386002525|ref|YP_005920824.1| 331 TPGEIIEVLELPPHLAEDPNLQEYFGEMDRDIFQIFQQYMGWFTGRSRDIFPTSPREEAEKMAYLAGGVDGLAEKAK 407
                                       788************************************************************************** PP

                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsgake 135
                                       ++l+egd++wa+ + +h++  dpen ea+e+k +++  l++++++a++Rn+ ls+  e
  gi|386002525|ref|YP_005920824.1| 408 ASLDEGDVKWAMIFSDHVLLLDPENVEAREVKNSSMLYLAEETKNAQVRNYILSEYLE 465
                                       *****************************************************99776 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.7   1.3e-16   3.8e-13       5     195 ..      73     290 ..      69     292 .. 0.88
   2 ?   -2.6   0.0       1.5   4.5e+03      58      87 ..     396     425 ..     396     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.3e-16
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSG....GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEH CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglk....pkdvdavilTHlHlDHiGglgglveatdvpvgavae 77 
                                        +n +lieg +g+i+iD+G st  a ++++ + ++l+     k+v+a+i+TH+H  Hi g+  ++      v+a++ 
  gi|386002525|ref|YP_005920824.1|  73 RANPVLIEGTDGLIVIDPGESTTSAEMVKAAYNEHLDdifsRKPVKAIIYTHHHDCHINGASVFAGNDSPEVIAHET 149
                                       57899************************77777765222279********************************** PP

                                       HHHCCHCHHHHHHHHHCCHH............................TTCHCGCCEEEEETTTEECCCTEEEEEHE CS
                       Lactamase_B  78 eapalfmeeaddaasrkgll............................lagvsadkpdvdeeeldgnaggrralyvt 126
                                        +++lf++ +  ++ +                                + +    +p  +  e+ ++   ++ l ++
  gi|386002525|ref|YP_005920824.1| 150 FEEHLFGPREVVSQIFPIKVyravkyagirfqndpgyfvnggifpfsvPGPSGYLPPTLTVGERLETNIAGVNLTIV 226
                                       **********88777766669**************************977777777777788888888888899999 PP

                                       CTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE CS
                       Lactamase_B 127 ggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp 195
                                       + p+ + +   v+++++kv++    ++    +  +l         + d  +y++s++++++l+ae++v+
  gi|386002525|ref|YP_005920824.1| 227 HAPAETTDINYVWLPDKKVIVQIGIFYKSFPAINTL-----RGASHRDPLNYIASIDDMRTLDAEYMVL 290
                                       99*************************999999999.....7788888888888889999*****9997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                       HTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                       Lactamase_B  58 iGglgglveatdvpvgavaeeapalfmeea 87 
                                       +Gg++gl+e++++   +   ++++ f +++
  gi|386002525|ref|YP_005920824.1| 396 AGGVDGLAEKAKASLDEGDVKWAMIFSDHV 425
                                       699999999999988888888777776665 PP

>> Alkyl_sulf_C  Alkyl sulfatase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   8.2e-12   2.5e-08       4     103 ..     482     581 ..     479     594 .] 0.87

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 8.2e-12
                                       -HHCCCCS-HHHHHHHHHHHB-HHHHTT-EEEEEEEETTTTE..EEEEEEETTEEEE.ECT---TTSSEEEEE-HHH CS
                      Alkyl_sulf_C   4 spdvlaalsleqlfDylAirvdgpkaadkdltinlvvtDvde..kyllrlsngvLthtrkaaqaddadltvtltreq 78 
                                       + +++  +++  +f  +A++++++ka d+++++ l ++D  e  +y l ++ g++   +++ + +d+++t+ ++   
  gi|386002525|ref|YP_005920824.1| 482 DENIVVYMPMATIFRIMAVSLNATKALDEEYAVGLSLSDDSEsaEYALYVRRGIVEV-QEGVP-EDPKFTIDTDSLS 556
                                       56778889******************************996556*************.88777.9************ PP

                                       HHHHHTTSS-HHHHHHTTTEEEEE- CS
                      Alkyl_sulf_C  79 LvalllgkatlgkevaagklkieGd 103
                                       + +l+lgk +++++va g +++ G 
  gi|386002525|ref|YP_005920824.1| 557 MKNLVLGKLNPEEAVAGGAVEVGGA 581
                                       **********************775 PP

>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.038      17      88 ..     505     580 ..     485     583 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       HCCH-E..EEEEEECTC.T..EEEEEETTSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEEC CS
                              SCP2  17 lkklag..vlrfdltdlkg..sltldlkegqldvaakdegkadvtlslsledllelaegklnpqkafmqgkLkieG 88 
                                        k+l +   + ++l+d  +  ++ l +  g ++v+++  +++++t+  ++  ++ l+ gklnp +a   g +++ G
  gi|386002525|ref|YP_005920824.1| 505 TKALDEeyAVGLSLSDDSEsaEYALYVRRGIVEVQEGVPEDPKFTIDTDSLSMKNLVLGKLNPEEAVAGGAVEVGG 580
                                       5666665555566666666777888888888999988889***************************999988766 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.036       3      72 ..      86     156 ..      85     292 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       EEES--TTHHHH..HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCT CS
                     Lactamase_B_2   3 iLiDagpdlrqq..alral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavlea 72 
                                       i+iD+g ++      + a  +      + +p++a+++th H  H++g+  ++       +++a++   ++l  
  gi|386002525|ref|YP_005920824.1|  86 IVIDPGESTTSAemVKAAYnEHLDDIFSRKPVKAIIYTHHHDCHINGASVFAGNDS--PEVIAHETFEEHLFG 156
                                       789999995444432333323333444558*****************999999433..369999999998854 PP

>> MycE_N  MycE methyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.091      46     104 ..     507     567 ..     493     572 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                            MycE_N  46 v..devsvqlalsaggeelsvlvaVgkggpvveagesaaaaatveqdleelvralfGPvre 104
                                       +  +e  v+l+ls++ e++++ ++V+ g ++v++g  ++++ t+  d   +   ++G +++
  gi|386002525|ref|YP_005920824.1| 507 AldEEYAVGLSLSDDSESAEYALYVRRGIVEVQEGVPEDPKFTIDTDSLSMKNLVLGKLNP 567
                                       366799**************************************99987777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 3317.20
//
Query:       gi|386002526|ref|YP_005920825.1|  [L=376]
Description: Nonspecific acid phosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-16   60.7   0.0    3.3e-16   60.2   0.0    1.2  1  HAD        haloacid dehalogenase-like hydrolase
    3.1e-05   24.4   0.0    0.00036   20.9   0.0    2.0  1  Hydrolase  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   3.7e-20   3.3e-16       1     188 []     113     317 ..     113     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.7e-20
                               HAD   1 alfDfDgTLldgdsle....lllrfllrrga.prlwralreklllal....frellrldraglaelleallagls.e 67 
                                       a fD+DgTL+ + +++    +++++++ + + +++w   +++   ++       +++++  ++ e + a+ + ++ e
  gi|386002526|ref|YP_005920825.1| 113 ATFDNDGTLWCEYPNYvpylFIFDRVYDMASyHPEWNSTEPF--SSIlsgeRTGAGSFSPGEVLEIYVATSSNMTaE 187
                                       78**********888889985555444443303334444444..333444468888899999999999********* PP

                               HAD  68 elaaelerfvaevirpk........lldpgalellaahraaGdrvvvvSgglrplvepll.aelg..adevlatele 133
                                       e  a +++++++  +p         ++   +lell+  r++G++v++v+gg + +v+++  + +g  +++v+++ ++
  gi|386002526|ref|YP_005920825.1| 188 EYMALARDWLDRSSHPDhglpytecVY-KPMLELLSYLRSQGFKVYIVTGGDQDFVRAFSqEVYGipPEQVIGSAVK 263
                                       **********99999999977665334.68888888888*********************88999*********544 PP

                               HAD 134 vdd.rltge...lglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       ++   ++g    ++l++  v  +g+v+a +    ++  g+++  + ayG+s +D+p+l+
  gi|386002526|ref|YP_005920825.1| 264 HQFiEVDGNtsvVKLPEVQVVTDGRVKAEQI---QQIVGLRP--ILAYGNSDGDIPMLK 317
                                       4447666665557777777666666644444...33333333..*************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     4e-08   0.00036     104     209 ..     200     319 ..     111     320 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4e-08
                                       TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT.......GGGESEEEEHHCES.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.......xxxxxxxxxxxxxx.. RF
                         Hydrolase 104 qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lG.......ddyfdaviasdiet.. 170
                                       + + ++ +   +   v++ + e++ +L+++g++v+++tg+++ ++++  ++ +G           +av  + ie+  
  gi|386002526|ref|YP_005920825.1| 200 SSHPDHGLPYTEC--VYKPMLELLSYLRSQGFKVYIVTGGDQDFVRAFSQEvYGippeqviG---SAVKHQFIEVdg 271
                                       4444455555556..99999**************************9999999999955541...333333333334 PP

                                       ......STTT......SHHHHHHHHHHH.TSTGGGEEEEESSHHHHHHHHHT CS
                                       ......xxxx......xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 171 ......vakp......spegkvaaireL.qgkpeevamVGDgvnDaaalaaA 209
                                                p      + + k + i+++ + +p  +++ G +  D+++l+ A
  gi|386002526|ref|YP_005920825.1| 272 ntsvvkL--PevqvvtDGRVKAEQIQQIvGLRP--ILAYGNSDGDIPMLKFA 319
                                       3353333..144666777777777777744777..9******99**999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2110.11
//
Query:       gi|386002527|ref|YP_005920826.1|  [L=389]
Description: Toxic anion resistance protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-74  250.9  11.7    2.2e-74  250.5  11.7    1.1  1  TelA       Toxic anion resistance protein (TelA)
  ------ inclusion threshold ------
       0.11   12.7   0.4       0.11   12.7   0.4    3.3  4  DUF148     Domain of unknown function DUF148
       0.13   12.4  11.7        1.6    8.9   0.5    3.8  4  Fib_alpha  Fibrinogen alpha/beta chain family
        2.3    8.6   8.4        5.8    7.3   0.5    3.1  3  KxDL       Uncharacterized conserved protein


Domain annotation for each model (and alignments):
>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.5  11.7     5e-78   2.2e-74      14     330 ..      72     383 ..      65     384 .. 0.97

  Alignments for each domain:
  == domain 1  score: 250.5 bits;  conditional E-value: 5e-78
                              TelA  14 nsilqfGaeaqkkiakfsdrlLe......svktkdlgevgklLseLvkelkeldpdelkeekklgllplfkkaknki 84 
                                       +si +fG e+++  a+ +++lL+          ++ g v+  L eL++el++ldp+ ++ +k  g+l+   k+ +++
  gi|386002527|ref|YP_005920826.1|  72 QSIESFGGESMATSAA-KNSLLQvtvgnlARDGDEGGVVARGLMELNRELRDLDPSLIDFTKT-GILG---KVFDPV 143
                                       79*******9999888.**********998899***********************9966655.9887...9***** PP

                              TelA  85 eklfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpeleakaea 161
                                       +++fa+Y+ka + i +I+ +Le+g+  l++dn++L+ ++++++   k+L k i++G +    +d+ ++ e+ea++++
  gi|386002527|ref|YP_005920826.1| 144 RAYFARYQKADSAIADIIASLERGKAILRNDNTTLEIEQQALRSLTKKLMKEIQLGIL----MDRSIEMEIEAAKAR 216
                                       **********************************************************....*************** PP

                              TelA 162 sgdpedaqalrdleealdrleqrvqDLelaravsiQtapqirlvqknnkeLiekiqsaittTiplwknqlvvalalk 238
                                       ++dpe+++ + +  e+l++l+qr++D+e++  v++Q+++++++v +nn+eLi+++++a t+Ti+++++ ++va al+
  gi|386002527|ref|YP_005920826.1| 217 NEDPEKVRFVAE--EILFPLRQRIMDMEQMVVVNQQGVMAMEVVIRNNRELIRGVDRAKTVTISALRTSVTVAGALY 291
                                       ************..*************************************************************** PP

                              TelA 239 rqklaleaqkavndtTnellkknAemlkqqsieiakeaergivdietLkkafetlietidevdqiqeegrekrkeae 315
                                       +qk al++++ +ndtTn +++ +++mlk+q +ei++ +  +++++e +k+af++++e++++++++++e++  +++++
  gi|386002527|ref|YP_005920826.1| 292 HQKVALKKIEMLNDTTNGIIRGTSQMLKDQGAEIQRRSMATSISVEGMKAAFADVMEALESISTYKQEALPIMRDTI 368
                                       ***************************************************************************** PP

                              TelA 316 keLeeleeelkkkLl 330
                                       ++++el ++ +++++
  gi|386002527|ref|YP_005920826.1| 369 NQFKELAAKGEEEIQ 383
                                       ********9999886 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.066     3e+02      29      59 ..      27      57 ..      23      72 .. 0.87
   2 ?   12.7   0.4   2.3e-05      0.11      53      99 ..     151     197 ..     148     203 .. 0.91
   3 ?   -1.4   0.1      0.54   2.4e+03      57      89 ..     295     327 ..     279     347 .. 0.77
   4 ?   -0.5   0.4      0.29   1.3e+03      62      89 ..     343     370 ..     298     387 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.066
                            DUF148 29 ekygvtdeykefeakvkaqkeevkknvtavi 59
                                       k++v+++++   ++v + ++ ++knv++++
  gi|386002527|ref|YP_005920826.1| 27 IKKEVQEQVEPAPEEVGELQALAEKNVAQIL 57
                                      5788999999999999999999999999987 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.3e-05
                            DUF148  53 knvtavisnLssvqekleaIldnkslTrkeqkeaieelkkqypkevs 99 
                                       ++++++i+ + +  e+ +aIl n++ T + +++a+++l+k++ ke++
  gi|386002527|ref|YP_005920826.1| 151 QKADSAIADIIASLERGKAILRNDNTTLEIEQQALRSLTKKLMKEIQ 197
                                       67788899999999999*************************99975 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.54
                            DUF148  57 avisnLssvqekleaIldnkslTrkeqkeaiee 89 
                                        ++++++  ++  + I+  +s+  k+q ++i++
  gi|386002527|ref|YP_005920826.1| 295 VALKKIEMLNDTTNGIIRGTSQMLKDQGAEIQR 327
                                       567777888888888888888888888888886 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.29
                            DUF148  62 LssvqekleaIldnkslTrkeqkeaiee 89 
                                       +++v e le+I   k+     +++ i++
  gi|386002527|ref|YP_005920826.1| 343 FADVMEALESISTYKQEALPIMRDTINQ 370
                                       4444444555544444444444444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.027   1.2e+02      90     128 ..      24      66 ..       3      69 .. 0.73
   2 ?   -0.6   0.1      0.31   1.4e+03      52     113 ..     151     191 ..     135     209 .. 0.50
   3 ?    4.9   1.6    0.0063        28      70     119 ..     217     267 ..     182     278 .. 0.77
   4 ?    8.9   0.5   0.00035       1.6      44     123 ..     297     387 ..     280     388 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.027
                                       CCHHHHHHHCCH....HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  90 ilrlketidaqe....snirvLqnvlesneqkiqkLeqdidqk 128
                                        + +k+++++q+    +++ +Lq + e+n+ +i  L  d++ k
  gi|386002527|ref|YP_005920826.1|  24 EAAIKKEVQEQVepapEEVGELQALAEKNVAQILTLDLDVAPK 66 
                                       556666666665322368999***************9999866 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                         Fib_alpha  52 keaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                       ++a++ + +i  sl++ ++  + ndn++ ++                    + ++L+++ ++
  gi|386002527|ref|YP_005920826.1| 151 QKADSAIADIIASLERGKAILR-NDNTTLEI--------------------EQQALRSLTKK 191
                                       3444444444444433333333.23333222....................22333333333 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0063
                                       HHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  70 kskkdn.dnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiq 119
                                       ++++++   v +++   l+++i+++++ ++ + + + ++  v+++n++ i 
  gi|386002527|ref|YP_005920826.1| 217 NEDPEKvRFVAEEILFPLRQRIMDMEQMVVVNQQGVMAMEVVIRNNRELIR 267
                                       333333366677777789****************************99876 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00035
                                       CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHH CS
                         Fib_alpha  44 leeisnstkeaeelvkeikdslrekqkskkd...........ndnvikksskeleeeilrlketidaqe.snirvLq 108
                                       l++i+  + +++ +++ ++++l+++ ++ +             + ++ ++ + le  i+++k++    +  +i++ +
  gi|386002527|ref|YP_005920826.1| 297 LKKIEMLNDTTNGIIRGTSQMLKDQGAEIQRrsmatsisvegMKAAFADVMEALE-SISTYKQEALPIMrDTINQFK 372
                                       4444444444444444444444444444433333333333226999999******.9****999999999******* PP

                                       HHHHHHHHHHHHHHH CS
                         Fib_alpha 109 nvlesneqkiqkLeq 123
                                       ++  + e++iqkLe+
  gi|386002527|ref|YP_005920826.1| 373 ELAAKGEEEIQKLEK 387
                                       *************96 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   4.7e+03      30      44 ..      40      54 ..      26      73 .. 0.55
   2 ?    5.0   0.6    0.0065        29      37      80 ..     151     194 ..     149     196 .. 0.91
   3 ?    7.3   0.5    0.0013       5.8       9      68 ..     295     354 ..     290     385 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                              KxDL 30 reLlelnalsqerla 44
                                      +e+ el+al+++ +a
  gi|386002527|ref|YP_005920826.1| 40 EEVGELQALAEKNVA 54
                                      344444444444433 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0065
                              KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       +++++  a++ a +++g+  l++ +  Le  ++ +rsl++kl+k
  gi|386002527|ref|YP_005920826.1| 151 QKADSAIADIIASLERGKAILRNDNTTLEIEQQALRSLTKKLMK 194
                                       5677888999999****************************987 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0013
                              KxDL   9 edldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesif 68 
                                       ++l++i  l   t g +  ++++L+++ a+ q+r   ++  ++  + +  +v + Lesi 
  gi|386002527|ref|YP_005920826.1| 295 VALKKIEMLNDTTNGIIRGTSQMLKDQGAEIQRRSMATSISVEGMKAAFADVMEALESIS 354
                                       6788899999999999********************999999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2238.33
//
Query:       gi|386002528|ref|YP_005920827.1|  [L=553]
Description: hypothetical protein Mhar_1847 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-19   68.5   0.1    1.6e-18   67.6   0.1    1.4  1  VWA           von Willebrand factor type A domain
    7.1e-12   45.9   0.0    2.2e-11   44.4   0.0    1.8  2  VWA_2         von Willebrand factor type A domain
    1.6e-09   37.9   0.0    2.4e-09   37.3   0.0    1.2  1  SBP_bac_11    Bacterial extracellular solute-binding protein
     0.0057   16.2   0.0      0.011   15.3   0.0    1.3  1  Citrate_bind  ATP citrate lyase citrate-binding


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 !   67.6   0.1   3.6e-22   1.6e-18       3     166 ..     378     539 ..     378     550 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 3.6e-22
                                       EEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC..HHHHHHHHHHTGSGGGGS CS
                               VWA   3 vfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndys..skeellsalnnlkysggg 77 
                                       vfv+D+Sgsm+++ +++ k+ +++    +    e+  +glv++s++v +  +++++   +++++  a+++l ++ggg
  gi|386002528|ref|YP_005920827.1| 378 VFVVDVSGSMEGRPLNNLKRSLIDGQYYIG---ENNLIGLVSYSNDVNIDLPISKFDlkQRASFVGAVDEL-QAGGG 450
                                       8******************99877555555...7888******************998888*********6.99999 PP

                                       SC-HHHHHHHHHHHHHHHHGT..SST.TSEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHH CS
                               VWA  78 ttntgkalkyaleklfkssag..aRe.nakkviilltdGksndg.dpkeaaneakeqgikvfavGvgnadekelLnk 150
                                       t+ t +a++ a++ l++++a    ++ n k  i +l+dG++n+g ++++  + + + gi ++++G+ na+ k+ Ln 
  gi|386002528|ref|YP_005920827.1| 451 TA-TFDAIAVAMKMLIDQKAAgpDKDpNLKPRIFVLSDGETNKGhSLNDIRDIVEDLGIPIYTIGY-NANIKA-LNA 524
                                       99.****************99663337****************86777777777777********8.677888.999 PP

                                       HSSSSCHHCEEEESSH CS
                               VWA 151 iasepgeghvftvtdf 166
                                       i++ ++    ++++++
  gi|386002528|ref|YP_005920827.1| 525 ISNINE-AASINADTE 539
                                       988777.444444444 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 ?   -2.8   0.0       2.2     1e+04      94     106 ..     344     356 ..     319     357 .. 0.72
   2 !   44.4   0.0   4.9e-15   2.2e-11       2     107 .]     378     489 ..     377     489 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
                             VWA_2  94 kgekrvivlitDg 106
                                       + +++++vl++Dg
  gi|386002528|ref|YP_005920827.1| 344 EEYQSEAVLVSDG 356
                                       4577999999998 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 4.9e-15
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsdgpevliplt....kdkakilnalrnleakg 73 
                                       vfv+D+SgSm+++      l  +k+ +++    +  ++ +glv++s+++++ +p +    k +a++  a+++l+a g
  gi|386002528|ref|YP_005920827.1| 378 VFVVDVSGSMEGR-----PLNNLKRSLIDGQYYIGeNNLIGLVSYSNDVNIDLPISkfdlKQRASFVGAVDELQA-G 448
                                       8***********9.....79999988888777776488****************97777889************9.6 PP

                             VWA_2  74 ggtnlaaaLqlarkalkkrr.......kgekrvivlitDge 107
                                       ggt + +a+  a+k+l +++        + k +i++++Dge
  gi|386002528|ref|YP_005920827.1| 449 GGTATFDAIAVAMKMLIDQKaagpdkdPNLKPRIFVLSDGE 489
                                       ****************555556778889***********96 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   5.3e-13   2.4e-09       6     229 ..      94     340 ..      92     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5.3e-13
                                       -SSTHHHHHHHHHHH.HH..H.H-..--EEEEESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGGGG-EE CS
                        SBP_bac_11   6 agslaaalrelaaaF.ea..h.tg..vkvevsaggsgklarqiadga.rpDvwipassawlellaaaglvqaesavp 75 
                                       ++++  +l+e+a++F  a  +  g  v v+++a +sg  a+ i++g+  p+++ p +  w e+++++g+ ++  +  
  gi|386002528|ref|YP_005920827.1|  94 GSGTDGWLTEVAEDFnNAgiKiDGkpVSVRLRAIPSGLGADYITSGKyMPEAYTPSNDFWGEMIISKGVDAELVEGR 170
                                       667789*********66644344499***************************************9998888899** PP

                                       EEEEEEEEEESTT-.........TT---S.HHHHHHSS--EEEE--T-TTTTH....H.HHHHGGG--.....HHHH CS
                        SBP_bac_11  76 lassplviavpkgn.........pkkikg.wadLlkpglklavadPttspsGl....aalalleaaga.....qell 133
                                       l+++   i+  k++         + + k+ ++++++++l +++++P +s++Gl     +l +++++        + +
  gi|386002528|ref|YP_005920827.1| 171 LVGNVAGILLTKSKkdelerkygAINTKTiVDAVANQELAIGYTNPLASSTGLnfliSTLYAFDKSDLlsdkaVAGF 247
                                       *************977666665434555548999999****************655544555554433666667779 PP

                                       HHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE-.-TTT--...EEEEEEEE-TT--HHHH CS
                        SBP_bac_11 134 kalekkvvklgessrqlltaveageadagivyeseakaaengdkleavyl.peglnldpldypaavlkkaakreaAr 209
                                       ++++ +++  + ++ q+ +a+++g  + ++   +  +   n ++++ ++  p g+  d   y+++ l+++ +++   
  gi|386002528|ref|YP_005920827.1| 248 ESFQANIPLVAYTTLQMRDAAKSGFLEGFVLEYQTYL---NDPDIRHYNFtPFGVRHDNPIYAIGELSGE-ESRILN 320
                                       ********999999**********9999998888888...799***996626666657799999999988.788*** PP

                                       HHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 210 aFlafLrspeaqailrkyGf 229
                                       +F++f ++++ q++++kyGf
  gi|386002528|ref|YP_005920827.1| 321 EFVKFSQQEKYQNLAAKYGF 340
                                       *******************9 PP

>> Citrate_bind  ATP citrate lyase citrate-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-06     0.011      95     170 ..     445     521 ..     430     526 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-06
                      Citrate_bind  95 liiGggianftnvaatfkgiiraleelksklkehkvkiyvrr.ggpnyqeglkamkelgeelglpikvfgpethita 170
                                       l  Ggg a f  +a ++k +i++     +k  + k +i+v   g +n  ++l+ ++++ e+lg+pi+  g +++i a
  gi|386002528|ref|YP_005920827.1| 445 LQAGGGTATFDAIAVAMKMLIDQKAAGPDKDPNLKPRIFVLSdGETNKGHSLNDIRDIVEDLGIPIYTIGYNANIKA 521
                                       667*************************************87356688899*****************999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 3161.75
//
Query:       gi|386002529|ref|YP_005920828.1|  [L=243]
Description: hypothetical protein Mhar_1848 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.054   12.8   3.2      0.074   12.3   3.2    1.2  1  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
        2.2    8.8   5.0         27    5.3   1.0    2.6  3  NPV_P10         Nucleopolyhedrovirus P10 protein
        2.4    6.9   5.0        4.7    5.9   0.4    2.7  3  DUF4781         Domain of unknown function (DUF4781)


Domain annotation for each model (and alignments):
>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.2   1.2e-05     0.074     101     238 ..      86     221 ..      69     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                    ALIX_LYPXL_bnd 101 klqenkedlelL.sgpeeeleaa..lpssssaaasesveeqirklrsllekldelkaer.eqllkdlkekaendDit 173
                                       +l+ ++++++l+  +  + l+++  +  +   ++ +s+e + +k+   +++++++     ++++++l     ++D  
  gi|386002529|ref|YP_005920828.1|  86 ELKTFEKTIDLMlDQ-IDRLQKKnkIIREILLQIFSSSEISYQKFDGVISEVERIFFMNmRSIINKLDA-FDEEDY- 159
                                       555566666666333.22222222233111112345778888899999999999987551679999975.555544. PP

                    ALIX_LYPXL_bnd 174 pklltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksdseq 238
                                         ++++k++ ++ +  e++++e++e y+++++ ++++ ++ e++l +++++  e++   +++s+q
  gi|386002529|ref|YP_005920828.1| 160 -NFIRNKSNSGDFS--EQFMDEKIEVYNKYITFVKEAAEDNEAILLKLDKLLLELSGLNSVESGQ 221
                                       .89******66644..599******************************9998888888777765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.0    0.0045        27      18      65 ..      69     115 ..      68     125 .. 0.80
   2 ?   -0.5   0.0      0.31   1.8e+03       5      47 ..     114     154 ..     111     157 .. 0.64
   3 ?    4.4   0.1    0.0085        51      16      56 ..     176     216 ..     174     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0045
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       +k+  +++ +d +++  ++++  ++ +d + +q++ l++k + I +iL
  gi|386002529|ref|YP_005920828.1|  69 QKIMTVEDYIDALKD-RRELKTFEKTIDLMLDQIDRLQKKNKIIREIL 115
                                       677778888888876.44557788999999999999999999999998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.31
                           NPV_P10   5 iLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaq 47 
                                       iLl+I +  +   +k d + ++v+++     ++  + +kLda 
  gi|386002529|ref|YP_005920828.1| 114 ILLQIFSSSEISYQKFDGVISEVERIFF--MNMRSIINKLDAF 154
                                       7777777666666777777777766643..3445577788875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0085
                           NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                       +d+k+++ ++ ++ v+e  +d + +  kLd++  +L  l++
  gi|386002529|ref|YP_005920828.1| 176 MDEKIEVYNKYITFVKEAAEDNEAILLKLDKLLLELSGLNS 216
                                       699****************************9999888876 PP

>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.048   2.8e+02     201     224 ..      37      60 ..      29      70 .. 0.82
   2 ?    5.9   0.4   0.00079       4.7     267     309 ..      73     114 ..      64     115 .. 0.87
   3 ?    1.1   0.3     0.023   1.4e+02      15      43 ..     164     192 ..     155     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.048
                           DUF4781 201 ginvssivisgtgvansvydlvlk 224
                                       ++ ++ i++sg+g++++ y l+  
  gi|386002529|ref|YP_005920828.1|  37 AFGIAFIFLSGAGLIYGNYRLLAE 60 
                                       5667889***********999865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.00079
                           DUF4781 267 kikdyretlrsnrsrkaFkkilketakkneekeskkldiirtl 309
                                       +++dy ++l+++r+ k+F+k+++    + +  + kk +iir++
  gi|386002529|ref|YP_005920828.1|  73 TVEDYIDALKDRRELKTFEKTIDLMLDQIDRLQ-KKNKIIREI 114
                                       6789*******************9999999655.799****87 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.023
                           DUF4781  15 eeknseeccmiyiDetgRVYknwedyven 43 
                                       +++ns +  + + De+  VY+++  +v++
  gi|386002529|ref|YP_005920828.1| 164 NKSNSGDFSEQFMDEKIEVYNKYITFVKE 192
                                       34566667789*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1332.86
//
Query:       gi|386002530|ref|YP_005920829.1|  [L=842]
Description: sulfatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-88  296.8   0.0    2.6e-88  296.4   0.0    1.2  1  Sulfatase     Sulfatase
      8e-05   22.4   0.1     0.0083   15.7   0.0    2.3  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
      0.026   13.1   0.0      0.037   12.6   0.0    1.1  1  DUF229        Protein of unknown function (DUF229)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.4   0.0   4.3e-92   2.6e-88       1     308 [.     145     554 ..     145     555 .. 0.97

  Alignments for each domain:
  == domain 1  score: 296.4 bits;  conditional E-value: 4.3e-92
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.. CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg.. 75 
                                       pnvv+i++dd+g+g++g++gg++  tpn+drla  glr++nf+++a +csp+ra+lltgr++h++gv+++ e +   
  gi|386002530|ref|YP_005920829.1| 145 PNVVFIVLDDVGFGQIGCFGGPID-TPNIDRLAVGGLRYNNFHTTA-MCSPTRACLLTGRNHHSVGVGAVIELPAgy 219
                                       9**********************9.9******************98.************************99999* PP

                                       ....HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC.....CTTTSEEEETSSSCHHTCCCCCCCCCECT CS
                         Sulfatase  76 ....gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyk.....nrgfdrflgfptgsaalkdpekseyngev 143
                                             l ++ atLpe+l e G+nt a+gkwhl+ + + +++      +rgf++++gf++ ++++++p+ ++++++v
  gi|386002530|ref|YP_005920829.1| 220 pgysMTLSKNAATLPEILLESGFNTFAVGKWHLSDHLNAAGPFdnwptGRGFEKYYGFIGSETNQWYPDLVSGTTRV 296
                                       *9*999***************************977777754479*****************************988 PP

                                       CCC..TTTTCSHHHHHHHHHHHHH...HCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH...... CS
                         Sulfatase 144 lrv..ppeggysddrlldealefl...larn.dkpfflylatlapHappeapdeyakkyatffddgseaar...... 208
                                        ++  p+eg++ +++l+d+a++f+   +a++ + p flyl++ a+Hap++ap+e  ++y+++fd+g+++ r      
  gi|386002530|ref|YP_005920829.1| 297 DPPktPEEGYHISEDLVDRAIGFIksqQAAEpGHPYFLYLSFGACHAPHHAPKEQIDMYKGRFDQGWDEVRnetlar 373
                                       877***********************955556*************************************88889999 PP

                                       ...................................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSS CS
                         Sulfatase 209 ...................................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhg 250
                                                                          +  e+y+++++ +D +igr+l+ Le+ g+l++tl+v +SD+g
  gi|386002530|ref|YP_005920829.1| 374 qkamgivpedaelpprnpdipawvdlsedqqrvfaREQEVYAGFLTHTDAQIGRFLDHLEDMGQLNDTLIVLISDNG 450
                                       9999999999******************************************************************* PP

                                       SCCCG.............................................HHTTSSSCTTCSSSHHHHBEEEEEEET CS
                         Sulfatase 251 aslee.............................................sngplrggkganayeggtrvPllvwwp 282
                                       as e+                                             +n+p++ +k+ n++egg+++P+++++p
  gi|386002530|ref|YP_005920829.1| 451 ASREGgfngtsnnylyfnriiqnvtsvlahidelggtetwnhyaegwamaGNTPFKRYKQ-NTHEGGIHDPMIIYYP 526
                                       ************************************************************.**************** PP

                                       TTSHC..EEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 283 gekap..rvseelvshiDlfptildlag 308
                                         ++   r++e++++++D++pt+l+l+g
  gi|386002530|ref|YP_005920829.1| 527 ALIEDggRIREQYTHAVDIVPTVLELLG 554
                                       **************************99 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.1    0.0037        22       1      63 [.     147     209 ..     147     251 .. 0.87
   2 !   15.7   0.0   1.4e-06    0.0083     197     254 ..     414     481 ..     285     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0037
                                       EEEEEETT-BTTHHHHHGS..TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS- CS
                      Phosphodiest   1 vlvislDGlradlldrlae..llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGi 63 
                                       v++i+lD + +  +  + +  ++pn+++La  g+++ n +++  ++  p  a+l+TG++  + G+
  gi|386002530|ref|YP_005920829.1| 147 VVFIVLDDVGFGQIGCFGGpiDTPNIDRLAVGGLRYNNFHTT--AMCSPTRACLLTGRNHHSVGV 209
                                       6888888888888888764589***************85554..567799999999998777665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEH.T....TSEEEGGGTSTGGH.....G CS
                      Phosphodiest 197 vedalrrvDkaigdLlealderglsaetniilvSDHGmadvs.d....dkvielndlleekg.....l 254
                                        +  l   D+ ig++l+ l+++g  ++t i+l SD G++    +    ++ +++n+++++ +     +
  gi|386002530|ref|YP_005920829.1| 414 YAGFLTHTDAQIGRFLDHLEDMGQLNDTLIVLISDNGASREGgFngtsNNYLYFNRIIQNVTsvlahI 481
                                       56678889*******************************99765677666777777777766664441 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-06     0.037     309     344 ..     416     451 ..     409     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-06
                            DUF229 309 nllealDedllkylkklekkgllentlvlllsDHGl 344
                                        +l+++D ++ ++l +le++g+l++tl++l+sD G 
  gi|386002530|ref|YP_005920829.1| 416 GFLTHTDAQIGRFLDHLEDMGQLNDTLIVLISDNGA 451
                                       58999****************************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (842 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.36s 00:00:01.17 Elapsed: 00:00:00.55
# Mc/sec: 4608.70
//
Query:       gi|386002531|ref|YP_005920830.1|  [L=507]
Description: sulfatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-72  244.7   0.0    1.8e-72  244.4   0.0    1.1  1  Sulfatase     Sulfatase
    1.6e-06   28.8   0.0    3.2e-06   27.9   0.0    1.5  1  Sulfatase_C   C-terminal region of aryl-sulfatase
    6.8e-05   22.6   0.1      0.033   13.8   0.0    2.3  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.031   14.2   0.0    1.7  1  DUF4994       Domain of unknown function


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.4   0.0     4e-76   1.8e-72       1     306 [.      56     377 ..      56     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 244.4 bits;  conditional E-value: 4e-76
                                       EEEEEEEESSE-TTGSGGGTTTSCS...SHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTT CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktat...tpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevg 74 
                                       pn+v+ lad +g++d g+ygg       tp++d++a+eglr+t+fys  + c+p+raa+ltgr p+++g+a  +e g
  gi|386002531|ref|YP_005920830.1|  56 PNIVIMLADNMGYMDPGCYGGGAVLgapTPRMDQMAKEGLRLTSFYSE-TQCTPTRAAMLTGRLPIRTGMALASETG 131
                                       9*********************977777******************88.5************************999 PP

                                       T.HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC.... CS
                         Sulfatase  75 g.gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv.... 146
                                          g+ ++e tL+++l +aGYnta++gkwhlg + ++  ++n gfd+f+g     + ++++e + ++++++      
  gi|386002531|ref|YP_005920830.1| 132 SnAGISPEERTLARVLSDAGYNTAIFGKWHLGDIRESE-PQNMGFDEFFGLLYHLNSYTQSE-RIGFDPRWEAgepl 206
                                       9*******************************996666.68*********777666666655.666778888899** PP

                                       ..................TTTTCSHHHHHHHHHHHHH.HCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCC CS
                         Sulfatase 147 ..................ppeggysddrlldealefl.larn.dkpfflylatlapHappeapdeyakkyatffddg 203
                                                           +  y d++ +++al ++  ++  ++pff+y+ +  +H+p   ++++a+k        
  gi|386002531|ref|YP_005920830.1| 207 glveakkgenltevsplnVSSLAYVDEQSMERALAYIkSQSSsADPFFVYIPFVRTHFPSVQNPRWAGK-------- 275
                                       *****************9999****************966666**************************........ PP

                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG....HHTTSSSCTTCSSSHHHHBEE CS
                         Sulfatase 204 seaarqlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgaslee....sngplrggkganayeggtrvP 276
                                            ++ + y++ + ++D+++g vl++L+e+g  +nt+vv tSD+g+ l++    +  p+rgg g ++yegg+rvP
  gi|386002531|ref|YP_005920830.1| 276 -----SSKGPYGDGLMEMDHHVGMVLDTLKELGIENNTIVVLTSDNGPTLDQwpdsGFSPFRGGIG-TTYEGGVRVP 346
                                       .....99************************************************9999*******.********** PP

                                       EEEEETTTSHC.EEECSEEEGGGHHHHHHHH CS
                         Sulfatase 277 llvwwpgekap.rvseelvshiDlfptildl 306
                                       ++ wwpg +++ r s+e++   Dlf+t++ l
  gi|386002531|ref|YP_005920830.1| 347 CIFWWPGMIEAgRSSDEIICTLDLFTTLAVL 377
                                       ***************************9866 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   7.2e-10   3.2e-06       3     103 ..     406     498 ..     404     504 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 7.2e-10
                                       -SEEEEEETTE......ECEEEETTEEEECEE--GCGTT-GGGTTTSSSTT-EEECCEEEEETTT-TT--S-TTSTT CS
                       Sulfatase_C   3 heflfhYcgae......lhAvRlgkyKahfvtpsfdpegaegcygsecvekvtehdpPllFdlerDpsEkyplsaes 73 
                                       +e +++Y g+       + AvR++++K+h           ++ +g e      + + P ++++e Dp+E+++++   
  gi|386002531|ref|YP_005920830.1| 406 REWVVWYIGTGsaantiPAAVRWHQFKVHTRA-------YDSFQGPE----SYYGQIPAVYNIEMDPREEHNIA--- 468
                                       5556666666444556699**********666.......44445555....777888*****************... PP

                                       CCHHHHHHHHHHHHHHHCCC------TCCH CS
                       Sulfatase_C  74 peykevlkeikkaveehkktlkpvpnqlak 103
                                        e++ v+++ +k+++ + +++ ++pn+ ++
  gi|386002531|ref|YP_005920830.1| 469 GEHDFVISAFTKIYRGLVASMIEYPNTPSR 498
                                       8********************999998665 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0013       5.7      20      63 ..      83     124 ..      78     134 .. 0.85
   2 !   13.8   0.0   7.4e-06     0.033     199     233 ..     283     317 ..     260     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0013
                                       TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS- CS
                      Phosphodiest  20 llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGi 63 
                                       ++p ++++akeg++ +    +  t+  p  a+++TG+ P  +G+
  gi|386002531|ref|YP_005920830.1|  83 PTPRMDQMAKEGLRLT--SFYSETQCTPTRAAMLTGRLPIRTGM 124
                                       69***********888..3333466689***************9 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 199 dalrrvDkaigdLlealderglsaetniilvSDHG 233
                                       d l + D+++g  l+ l+e g++++t ++l+SD G
  gi|386002531|ref|YP_005920830.1| 283 DGLMEMDHHVGMVLDTLKELGIENNTIVVLTSDNG 317
                                       78999****************************87 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.9e-06     0.031       1      96 [.     382     480 ..     382     482 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.9e-06
                           DUF4994   1 lPkgeapDSenvlkallGkd.kkdReyvi...eqaanktlsvrkkkWkyiePskgpalikltkielGnskepqLydl 73 
                                       +P++   D  ++ + +lG++ +++Re+v+     ++  +    + +W   + ++  a+ +++  e  + + p  y++
  gi|386002531|ref|YP_005920830.1| 382 VPADRPIDGIDQSEFILGRQeNSNREWVVwyiGTGSAANTIPAAVRWHQFKVHT-RAYDSFQGPESYYGQIPAVYNI 457
                                       68999999**********751679****83222333333333566788877665.6788889999999999****** PP

                           DUF4994  74 kkdegekenvaekhpekvkelke 96 
                                       + d+ e++n+a +h  +++++++
  gi|386002531|ref|YP_005920830.1| 458 EMDPREEHNIAGEHDFVISAFTK 480
                                       *************9988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2884.69
//
Query:       gi|386002532|ref|YP_005920831.1|  [L=498]
Description: hypothetical protein Mhar_1851 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.7   0.0      0.086   12.7   0.0    1.4  1  UPF0728   Uncharacterised protein family UPF0728


Domain annotation for each model (and alignments):
>> UPF0728  Uncharacterised protein family UPF0728
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-06     0.086      32      65 ..      71     103 ..      66     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-06
                           UPF0728  32 avlkkdGheveLektedynvvelvvngetvfqCk 65 
                                       ++l++dG++v+L + +  nv  lv n+ +vf+C+
  gi|386002532|ref|YP_005920831.1|  71 EALEEDGFTVQLGELKTQNVFDLV-NEGIVFSCN 103
                                       689******************995.777*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2763.78
//
Query:       gi|386002533|ref|YP_005920832.1|  [L=458]
Description: Anaerobic sulfatase-maturating enzyme [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-13   51.3   0.0    2.8e-13   50.6   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    3.4e-11   42.8   6.7    6.8e-11   41.9   6.7    1.6  1  SEC-C        SEC-C motif
    9.8e-10   38.8   0.1    2.4e-09   37.6   0.1    1.7  1  SPASM        Iron-sulfur cluster-binding domain
    0.00075   19.8   0.0     0.0018   18.6   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.082   13.1   0.0       0.15   12.2   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   7.7e-17   2.8e-13       4     167 .]      18     187 ..      16     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 7.7e-17
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHH.HHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileev.kelk.aekg.vkevilgggepllypdfvellerlakla... 74 
                                       +  Cnl+C++C + +++  +++g ++  +e+le   +++  a k+   +v + ggep+l   ++++ + +  ++   
  gi|386002533|ref|YP_005920832.1|  18 GAICNLGCRYCFFLSKKNLYPDGSFRMSDEVLESYiRQYIeAQKNpSVTVAWQGGEPTLMG-LEFFRRSIEVEEkyr 93 
                                       578*************7777777777777777655144445555569999999******63.333333333333578 PP

                                       ..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ..vpgiritvetngtlpdeeklerllelgvdrvslgleaadde....kvlklmnrghtfeevlealeklreagikrv 145
                                            + +t+ tng+l+d+e+ e + e     + l+l+ + +     +v k   +g+tf++v++a ++lr+++++  
  gi|386002533|ref|YP_005920832.1|  94 qpGISFQNTMQTNGILLDDEWCEFFSEND-FLIGLSLDGPRELhdayRVDKA--GGPTFDRVMRAARLLRKHRVE-- 165
                                       66667889*******************77.************9865555555..679***************999.. PP

                                       EEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 146 vdrivglpGendeeleellell 167
                                       ++++  ++  n ++  +++++l
  gi|386002533|ref|YP_005920832.1| 166 FNILATVHAANQDHPLDVYRFL 187
                                       7777777778888888888875 PP

>> SEC-C  SEC-C motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   6.7   1.9e-14   6.8e-11       1      19 []     410     428 ..     410     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.9e-14
                             SEC-C   1 RNdpCPCGSGkKYKkCCgp 19 
                                       RNdpCPCGSG+K+KkC+g+
  gi|386002533|ref|YP_005920832.1| 410 RNDPCPCGSGLKFKKCHGR 428
                                       9****************97 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   6.7e-13   2.4e-09       4      68 .]     271     332 ..     265     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 6.7e-13
                             SPASM   4 psrslfInsdGdVvpCcvdkktyvee.lklGnireesleeIwnseeyqefrkskkfplielCrnCp 68 
                                         ++++ +++GdV+ C    +++ve+ + lGni+e +l++I  s + ++f ++k + l+e+Cr+C+
  gi|386002533|ref|YP_005920832.1| 271 CGTAMVMEHNGDVYSC----DHFVEPkYLLGNIHERPLASIAGSAKQRRFGREKLDLLPEYCRRCE 332
                                       46899***********....4555556***************999*****9667777889*****6 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.9e-07    0.0018      15     115 ..      21     125 ..      17     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.9e-07
                           Fer4_12  15 CnlsCkgCfnketw..sfksgkeftkelleeiiedlkk.esi..egltllGGEPllpena..eallelvkevkeekp 84 
                                       Cnl C++Cf  + +   ++++  +++e+le  i++  + +++    +   GGEP l+     +  +e+ ++ ++ ++
  gi|386002533|ref|YP_005920832.1|  21 CNLGCRYCFFLSKKnlYPDGSFRMSDEVLESYIRQYIEaQKNpsVTVAWQGGEPTLMGLEffRRSIEVEEKYRQPGI 97 
                                       ********965555236778888877777766665554245522456668****99432222444455555555544 PP

                           Fer4_12  85 .ekdiwlytgytleelskkekeellkeidvlv 115
                                         ++ + ++g  l+    +e+ e+ +e d+l+
  gi|386002533|ref|YP_005920832.1|  98 sFQNTMQTNGILLD----DEWCEFFSENDFLI 125
                                       33344444444444....45667777777766 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05      0.15       7      61 ..      20      77 ..      17     128 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                           Fer4_14  7 gCnlsCkgCdnketwks..elgkpqteelleqilk.dlkkseikiqglvltGGePLhy 61
                                       Cnl C+ C+  ++++   +     ++e+le+ ++   ++++     +   GGeP + 
  gi|386002533|ref|YP_005920832.1| 20 ICNLGCRYCFFLSKKNLypDGSFRMSDEVLESYIRqYIEAQKNPSVTVAWQGGEPTLM 77
                                      5*********55544443355666666666666664455555545568899****633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2762.20
//
Query:       gi|386002534|ref|YP_005920833.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002534|ref|YP_005920833.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002534|ref|YP_005920833.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002534|ref|YP_005920833.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002534|ref|YP_005920833.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002534|ref|YP_005920833.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2253.60
//
Query:       gi|386002535|ref|YP_005920834.1|  [L=469]
Description: hypothetical protein Mhar_1854 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-29   99.4  18.3      2e-06   27.3   0.1    7.9  8  TPR_1       Tetratricopeptide repeat
    3.3e-28   95.5   8.9    9.1e-06   25.4   0.0    7.5  7  TPR_2       Tetratricopeptide repeat
    8.8e-17   59.9  15.1     0.0022   18.1   0.0    6.9  7  TPR_8       Tetratricopeptide repeat
    3.1e-14   53.0   0.2    0.00029   21.1   0.0    5.2  5  TPR_12      Tetratricopeptide repeat
    5.4e-14   51.6  13.7    0.00054   19.6   0.0    6.8  7  TPR_11      TPR repeat
    2.7e-13   49.6   1.7        2.2    9.1   0.1    7.5  7  TPR_6       Tetratricopeptide repeat
    2.8e-12   47.0   0.0      0.008   16.7   0.0    4.3  4  TPR_19      Tetratricopeptide repeat
    4.5e-11   42.3   1.1        1.7    9.2   0.0    6.4  6  TPR_17      Tetratricopeptide repeat
    4.3e-10   39.5   1.3    8.4e-10   38.6   0.5    1.9  1  DUF3883     Domain of unknown function (DUF3883)
    1.2e-08   35.5   0.0      0.023   15.3   0.0    5.0  5  TPR_16      Tetratricopeptide repeat
    2.5e-08   34.0   0.0     0.0037   17.4   0.0    3.2  3  TPR_9       Tetratricopeptide repeat
    8.4e-08   32.4   0.0       0.46   11.4   0.0    6.4  7  TPR_14      Tetratricopeptide repeat
    1.1e-07   32.0   4.8     0.0022   18.2   0.2    4.1  5  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    5.7e-07   29.1   3.2        3.1    8.1   0.0    6.9  7  TPR_7       Tetratricopeptide repeat
    1.5e-06   28.1   4.8      0.085   12.9   0.3    4.2  4  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
     0.0015   18.4   2.3        4.9    7.2   0.1    4.6  5  TPR_10      Tetratricopeptide repeat
     0.0089   15.0   0.7       0.31    9.9   0.0    2.8  3  NARP1       NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.022   14.2   0.8       0.29   10.5   0.1    2.7  4  Coatomer_E  Coatomer epsilon subunit
       0.12   11.0   0.0       0.52    9.0   0.0    2.0  2  PknG_TPR    Protein kinase G tetratricopeptide repeat
        0.2   12.4   0.0        0.2   12.4   0.0    2.7  1  Sel1        Sel1 repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0029       2.6      16      28 ..       4      16 ..       4      21 .. 0.89
   2 !   21.3   0.0   1.8e-07   0.00016       3      34 .]      25      56 ..      23      56 .. 0.95
   3 !   18.3   0.0   1.6e-06    0.0014       1      32 [.      57      88 ..      57      90 .. 0.87
   4 ?    2.7   0.0      0.14   1.3e+02       5      25 ..      95     115 ..      93     121 .. 0.87
   5 !    6.9   0.0    0.0065       5.8      10      33 ..     135     158 ..     133     159 .. 0.87
   6 !   27.3   0.1   2.3e-09     2e-06       2      33 ..     161     192 ..     160     193 .. 0.96
   7 !   21.0   0.3   2.3e-07    0.0002       9      34 .]     202     227 ..     202     227 .. 0.96
   8 ?   -0.9   0.0       1.9   1.7e+03      16      24 ..     240     248 ..     240     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                                      -HHHHHHHHHHHH CS
                             TPR_1 16 kydeAleyyekAL 28
                                      +y+ A++y+++A+
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAI 16
                                      6***********9 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                      al +++ ++f l+ky+e  +yy+ +L ++Pn+
  gi|386002535|ref|YP_005920834.1| 25 ALIGKAFCLFDLKKYEESDKYYDMVLVIDPNH 56
                                      7899**************************97 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnP 32
                                      a al ++G +++++ ++++A+ey+ kA   +P
  gi|386002535|ref|YP_005920834.1| 57 ASALVGKGKIFYEKRDLNKAIEYFTKASNSDP 88
                                      67999*********************965555 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHTT-HHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyye 25 
                                        n+ +++++lg++d A ++y+
  gi|386002535|ref|YP_005920834.1|  95 LNKIYVFQELGEHDRANACYN 115
                                       688899**********88887 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0065
                                       HHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPn 33 
                                        + ++ ++++A++ y++ ++ +Pn
  gi|386002535|ref|YP_005920834.1| 135 ELCENDRFEDAIDIYSEIVQKDPN 158
                                       5667889****************9 PP

  == domain 6  score: 27.3 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        a+ n+G++y+ lg y++  +++++A+ ++P+
  gi|386002535|ref|YP_005920834.1| 161 SAWINMGLIYYLLGIYEKSNACCNRAIAIDPK 192
                                       59*****************************7 PP

  == domain 7  score: 21.0 bits;  conditional E-value: 2.3e-07
                                       HHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   9 nayfklgkydeAleyyekALelnPnn 34 
                                       ++y+k++++++  eyy+++Le++Pn+
  gi|386002535|ref|YP_005920834.1| 202 VIYYKQNEFNKSNEYYQRVLEIDPNF 227
                                       58**********************97 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 1.9
                                       -HHHHHHHH CS
                             TPR_1  16 kydeAleyy 24 
                                       k+++A+ey+
  gi|386002535|ref|YP_005920834.1| 240 KHNKAVEYF 248
                                       689999999 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.022        19      16      29 ..       4      17 ..       2      21 .. 0.89
   2 !   16.2   0.0   8.8e-06    0.0079       3      34 .]      25      56 ..      24      56 .. 0.94
   3 !   16.3   0.0   8.7e-06    0.0078       2      33 ..      58      89 ..      57      90 .. 0.90
   4 ?    2.0   0.1      0.32   2.8e+02      11      27 ..     101     117 ..      99     124 .. 0.80
   5 !    7.8   0.0    0.0043       3.8      10      33 ..     135     158 ..     133     159 .. 0.89
   6 !   25.4   0.0     1e-08   9.1e-06       3      33 ..     162     192 ..     160     193 .. 0.96
   7 !   20.2   0.1   4.8e-07   0.00043      10      33 ..     203     226 ..     202     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                             TPR_2 16 dyeeAleafekAle 29
                                      +ye A+++f++A+ 
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAIN 17
                                      69**********96 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.8e-06
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                      al   + +++ l++yee  ++++ +l +dPn+
  gi|386002535|ref|YP_005920834.1| 25 ALIGKAFCLFDLKKYEESDKYYDMVLVIDPNH 56
                                      67889*************************97 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 8.7e-06
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                       al   G++ y++ d+++A+e+f kA   dP+
  gi|386002535|ref|YP_005920834.1| 58 SALVGKGKIFYEKRDLNKAIEYFTKASNSDPK 89
                                      688899********************988886 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.32
                             TPR_2  11 yyklgdyeeAleafekA 27 
                                         +lg++++A ++++  
  gi|386002535|ref|YP_005920834.1| 101 FQELGEHDRANACYNNI 117
                                       6789**********875 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0043
                             TPR_2  10 ayyklgdyeeAleafekAleldPn 33 
                                        + +++++e+A++ + + ++ dPn
  gi|386002535|ref|YP_005920834.1| 135 ELCENDRFEDAIDIYSEIVQKDPN 158
                                       577899*****************9 PP

  == domain 6  score: 25.4 bits;  conditional E-value: 1e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+ n+Gl+yy lg ye+  +++++A+++dP+
  gi|386002535|ref|YP_005920834.1| 162 AWINMGLIYYLLGIYEKSNACCNRAIAIDPK 192
                                       8*****************************7 PP

  == domain 7  score: 20.2 bits;  conditional E-value: 4.8e-07
                             TPR_2  10 ayyklgdyeeAleafekAleldPn 33 
                                       +yyk++++++  e+++++le+dPn
  gi|386002535|ref|YP_005920834.1| 203 IYYKQNEFNKSNEYYQRVLEIDPN 226
                                       8**********************9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.018        16      17      29 ..       5      17 ..       4      21 .. 0.90
   2 !    9.7   0.0    0.0012         1       7      34 .]      29      56 ..      25      56 .. 0.85
   3 !   18.1   0.0   2.4e-06    0.0022       1      33 [.      57      89 ..      57      90 .. 0.93
   4 ?    0.1   0.0       1.4   1.2e+03      11      25 ..     101     115 ..      99     120 .. 0.87
   5 !   17.5   0.1   3.6e-06    0.0032       2      33 ..     161     192 ..     160     193 .. 0.96
   6 !   12.9   0.1   0.00011     0.099      10      33 ..     203     226 ..     202     227 .. 0.95
   7 ?   -2.1   0.0       7.4   6.6e+03      17      24 ..     241     248 ..     240     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                                      HHHHHHHHHHHHH CS
                             TPR_8 17 yeeAkeyyekale 29
                                      ye+A++y+ +a+ 
  gi|386002535|ref|YP_005920834.1|  5 YENAIQYFDEAIN 17
                                      9**********96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                                      HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  7 lgsiylklgdyeeAkeyyekaleldpdn 34
                                      ++ ++++l++yee+ +yy  +l +dp++
  gi|386002535|ref|YP_005920834.1| 29 KAFCLFDLKKYEESDKYYDMVLVIDPNH 56
                                      67789*************9888888876 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 2.4e-06
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+a++ +g+i  ++ d+++A+ey+ ka   dp+
  gi|386002535|ref|YP_005920834.1| 57 ASALVGKGKIFYEKRDLNKAIEYFTKASNSDPK 89
                                      578999*************************98 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.4
                                       HHHTT-HHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyye 25 
                                        ++lg+++ A ++y+
  gi|386002535|ref|YP_005920834.1| 101 FQELGEHDRANACYN 115
                                       679*******99997 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 3.6e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+ n+g+iy  lg ye++ +++++a+ +dp+
  gi|386002535|ref|YP_005920834.1| 161 SAWINMGLIYYLLGIYEKSNACCNRAIAIDPK 192
                                       69*****************************8 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00011
                                       HHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleldpd 33 
                                       iy k+++++++ eyy+++le+dp+
  gi|386002535|ref|YP_005920834.1| 203 IYYKQNEFNKSNEYYQRVLEIDPN 226
                                       8**********************8 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 7.4
                                       HHHHHHHH CS
                             TPR_8  17 yeeAkeyy 24 
                                       +++A+ey+
  gi|386002535|ref|YP_005920834.1| 241 HNKAVEYF 248
                                       78999998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.086        77      19      35 ..       5      21 ..       4      24 .. 0.81
   2 !   21.1   0.0   3.2e-07   0.00029       5      73 ..      25      85 ..      22      89 .. 0.92
   3 ?    0.0   0.0       1.2     1e+03      12      27 ..     100     115 ..      93     123 .. 0.65
   4 !   13.8   0.0   6.2e-05     0.055      26      76 ..     142     191 ..     136     192 .. 0.88
   5 !   17.2   0.1   5.1e-06    0.0046       4      76 ..     161     225 ..     158     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.086
                            TPR_12 19 ydeAlellekaleiarr 35
                                      y+ A++++++a++++r+
  gi|386002535|ref|YP_005920834.1|  5 YENAIQYFDEAINRHRK 21
                                      88999999999988876 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.2e-07
                            TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73
                                      al   a +l+ l++y+e+ ++++ +l i      p+h   a++l + g ++++  ++ +A+e++++a +
  gi|386002535|ref|YP_005920834.1| 25 ALIGKAFCLFDLKKYEESDKYYDMVLVID-----PNH---ASALVGKGKIFYEKRDLNKAIEYFTKASN 85
                                      55689********************9999.....999...9*************************976 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.2
                            TPR_12  12 vlrrlgrydeAlelle 27 
                                       v ++lg++d A ++++
  gi|386002535|ref|YP_005920834.1| 100 VFQELGEHDRANACYN 115
                                       5566666666655554 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 6.2e-05
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +e a++i++++   + p+++++ +n+g +y++lg ye+  +  ++a+ai++
  gi|386002535|ref|YP_005920834.1| 142 FEDAIDIYSEIV-QKDPNLISAWINMGLIYYLLGIYEKSNACCNRAIAIDP 191
                                       788999998885.56799***********************9999999976 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 5.1e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +a+ n++++++ lg y+++ +++++a++i      p++  t + ++   ++y +++++ +  e+++++l+i++
  gi|386002535|ref|YP_005920834.1| 161 SAWINMGLIYYLLGIYEKSNACCNRAIAID-----PKS--TMALYCKRVIYY-KQNEFNKSNEYYQRVLEIDP 225
                                       6899**************************.....*99..********9998.888**************976 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.37   3.3e+02       9      22 ..       4      17 ..       4      19 .. 0.88
   2 !   11.7   0.0   0.00018      0.16       4      40 ..      33      69 ..      32      70 .. 0.95
   3 !    7.9   0.0    0.0027       2.4       1      26 [.      64      89 ..      64      96 .. 0.94
   4 ?   -0.7   0.1       1.4   1.2e+03       5      18 ..     102     115 ..      99     116 .. 0.84
   5 !   19.6   0.0     6e-07   0.00054       4      42 .]     136     174 ..     133     174 .. 0.94
   6 !    9.3   0.2   0.00099      0.89       3      32 ..     169     198 ..     169     200 .. 0.90
   7 !   16.5   0.2   5.6e-06     0.005       3      30 ..     203     230 ..     203     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.37
                            TPR_11  9 kyeeAieaYkkAlk 22
                                      +ye+Ai+ + +A++
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAIN 17
                                      69999999999985 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00018
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                      ++++ kyee+ + Y   l +dP+ a+a+ + G+++y+
  gi|386002535|ref|YP_005920834.1| 33 LFDLKKYEESDKYYDMVLVIDPNHASALVGKGKIFYE 69
                                      68999******************************98 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0027
                            TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPd 26
                                      G+++ye+ ++++Aie + kA + dP+
  gi|386002535|ref|YP_005920834.1| 64 GKIFYEKRDLNKAIEYFTKASNSDPK 89
                                      99*******************99997 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.4
                            TPR_11   5 yeqGkyeeAieaYk 18 
                                        e+G+ + A ++Y+
  gi|386002535|ref|YP_005920834.1| 102 QELGEHDRANACYN 115
                                       589**********8 PP

  == domain 5  score: 19.6 bits;  conditional E-value: 6e-07
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++e  ++e+Ai  Y++ ++ dP+  +a+ n+Gl+yy +G
  gi|386002535|ref|YP_005920834.1| 136 LCENDRFEDAIDIYSEIVQKDPNLISAWINMGLIYYLLG 174
                                       778889******************************998 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00099
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       +yy +G ye++ ++ ++A+++dP++  a+y
  gi|386002535|ref|YP_005920834.1| 169 IYYLLGIYEKSNACCNRAIAIDPKSTMALY 198
                                       79*********************9876666 PP

  == domain 7  score: 16.5 bits;  conditional E-value: 5.6e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaea 30 
                                       +yy+q++++++ e Y++ l++dP++ ++
  gi|386002535|ref|YP_005920834.1| 203 IYYKQNEFNKSNEYYQRVLEIDPNFFSL 230
                                       7***********************9876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.068        61      15      33 .]       4      22 ..       1      22 [. 0.87
   2 ?    5.7   0.0     0.029        26       5      33 .]      28      56 ..      25      56 .. 0.87
   3 !    7.9   0.0    0.0059       5.2       2      31 ..      59      88 ..      58      89 .. 0.87
   4 ?    2.8   0.0      0.25   2.2e+02       9      28 ..     100     119 ..      94     121 .. 0.84
   5 ?    4.6   0.0     0.068        61      15      32 ..     141     158 ..     135     159 .. 0.89
   6 ?    6.1   0.0     0.023        20       3      33 .]     163     193 ..     161     193 .. 0.92
   7 !    9.1   0.1    0.0024       2.2       9      32 ..     203     226 ..     202     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.068
                                      HHHHHHHHHHHHHHH-TT- CS
                             TPR_6 15 dtdkAlealerlikeYPdS 33
                                      ++++A++++++ i+++ +S
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAINRHRKS 22
                                      799***********98665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                                      HHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  5 klalsyrklgdtdkAlealerlikeYPdS 33
                                        a +++ l++++++ ++++ ++   P++
  gi|386002535|ref|YP_005920834.1| 28 GKAFCLFDLKKYEESDKYYDMVLVIDPNH 56
                                      56899***99************9999985 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0059
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYP 31
                                      Al   ++ +++  d  kA+e++ +  ++ P
  gi|386002535|ref|YP_005920834.1| 59 ALVGKGKIFYEKRDLNKAIEYFTKASNSDP 88
                                      788889999*977**********9988887 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealerlik 28 
                                        +++lg++d+A + +++++k
  gi|386002535|ref|YP_005920834.1| 100 VFQELGEHDRANACYNNIRK 119
                                       577899*********99987 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHHHHH-TT CS
                             TPR_6  15 dtdkAlealerlikeYPd 32 
                                       + ++A++++ +++++ P+
  gi|386002535|ref|YP_005920834.1| 141 RFEDAIDIYSEIVQKDPN 158
                                       789*************98 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPdS 33 
                                         +++l y+ lg ++k+ +  +r i   P+S
  gi|386002535|ref|YP_005920834.1| 163 WINMGLIYYLLGIYEKSNACCNRAIAIDPKS 193
                                       5689******99**************99998 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                        y+k+++  k+ e+++r+++  P+
  gi|386002535|ref|YP_005920834.1| 203 IYYKQNEFNKSNEYYQRVLEIDPN 226
                                       69***9**************9997 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00026      0.23       6      62 ..       4      58 ..       2      64 .. 0.90
   2 !   10.2   0.0   0.00092      0.82       2      57 ..      68     123 ..      67     130 .. 0.91
   3 !   16.7   0.0     9e-06     0.008       3      60 ..     138     194 ..     136     202 .. 0.93
   4 ?    6.9   0.0      0.01       9.1      16      57 ..     185     226 ..     183     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                            TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                       y++A++++ +a+    k+  a+++ A +l+ l+ ++e  +  d ++  dp++  ++
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAINRHRKSIMALIGKAFCLFDLKKYEESDKYYDMVLVIDPNH--AS 58
                                      599************************************99999999999994..44 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00092
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++  d+  A++++++a   dpk    +l+ + +  +lg+ d A a+ + + ++d++
  gi|386002535|ref|YP_005920834.1|  68 YEKRDLNKAIEYFTKASNSDPKFMVPLLNKIYVFQELGEHDRANACYNNIRKSDKK 123
                                       57789*****************9999999**********************99987 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 9e-06
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       ++ ++++A+++++++ q+dp+   a++++  +++ lg +++  a+++++ + dp+ + 
  gi|386002535|ref|YP_005920834.1| 138 ENDRFEDAIDIYSEIVQKDPNLISAWINMGLIYYLLGIYEKSNACCNRAIAIDPK-ST 194
                                       6789*************************************************99.54 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.01
                            TPR_19  16 qalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       +a++ dpk+  a++    ++++++++++  +  ++++e dp+
  gi|386002535|ref|YP_005920834.1| 185 RAIAIDPKSTMALYCKRVIYYKQNEFNKSNEYYQRVLEIDPN 226
                                       789999********99***********************998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.9   1.7e+03       2      31 ..      12      41 ..      11      43 .. 0.88
   2 !    9.0   0.0    0.0023         2       2      34 .]      46      78 ..      45      78 .. 0.91
   3 ?    2.8   0.0       0.2   1.8e+02       2      32 ..      80     110 ..      79     110 .. 0.93
   4 !    9.2   0.0    0.0019       1.7       2      28 ..     149     175 ..     148     179 .. 0.86
   5 !    7.1   0.1    0.0089         8       1      27 [.     182     208 ..     182     213 .. 0.82
   6 ?    5.9   0.0     0.022        20       1      13 [.     216     228 ..     216     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmt 31
                                      + +a+ ++ ++  a+  +A +l  ++++++
  gi|386002535|ref|YP_005920834.1| 12 FDEAINRHRKSIMALIGKAFCLFDLKKYEE 41
                                      7899999999999********999998876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      y  +l +dPn+a a+  ++++++++ dl +A++
  gi|386002535|ref|YP_005920834.1| 46 YDMVLVIDPNHASALVGKGKIFYEKRDLNKAIE 78
                                      6778899********************999986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       ++ka   dP+  +++ n+ +++ ++G++++A
  gi|386002535|ref|YP_005920834.1|  80 FTKASNSDPKFMVPLLNKIYVFQELGEHDRA 110
                                       8899999*********************998 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0019
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                       y + +++dPn   a+ n++ +++ +G 
  gi|386002535|ref|YP_005920834.1| 149 YSEIVQKDPNLISAWINMGLIYYLLGI 175
                                       6677899****************9985 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0089
                            TPR_17   1 lylkaleldPnnadaynnLAelllknG 27 
                                       ++ +a+++dP++  a++ + ++++k++
  gi|386002535|ref|YP_005920834.1| 182 CCNRAIAIDPKSTMALYCKRVIYYKQN 208
                                       799*************98766666666 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.022
                            TPR_17   1 lylkaleldPnna 13 
                                       +y+++le+dPn +
  gi|386002535|ref|YP_005920834.1| 216 YYQRVLEIDPNFF 228
                                       6**********75 PP

>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.5   9.4e-13   8.4e-10       1      88 [.     330     420 ..     330     424 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 9.4e-13
                           DUF3883   1 gEklvlealkekekeeg...vewvnedvedglgYDiesvdkedgeerfIEVKtta.kgkkdfelsrnElefaqekgd 73 
                                       gEk+v ++l++ e++ +     wv+++     ++D+ +++  + + ++I +K+t+ + +++f+ls+nEle  +  + 
  gi|386002535|ref|YP_005920834.1| 330 GEKYVNNYLTQLERNGSikrFCWVSDQH-ATSPFDFYVIN-DNLDVILIDIKSTNnHFNNKFYLSSNELEQIASSEY 404
                                       6999999*99999999988899999999.99********9.6888**********999******************* PP

                           DUF3883  74 kYwlyrVfnagkep.k 88 
                                       +Y +yr++++++++ k
  gi|386002535|ref|YP_005920834.1| 405 EYRIYRIYEMSDSTaK 420
                                       **********887645 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0      0.01       9.1      13      67 ..       5      56 ..       4      57 .. 0.89
   2 !   15.3   0.0   2.6e-05     0.023       7      60 ..      33      83 ..      33      88 .. 0.94
   3 ?    2.5   0.0      0.25   2.3e+02       3      29 ..      97     123 ..      95     127 .. 0.85
   4 ?    6.8   0.0     0.012        11       9      66 ..     138     192 ..     133     194 .. 0.91
   5 ?    2.9   0.0       0.2   1.8e+02       6      31 ..     203     225 ..     202     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                            TPR_16 13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                      y+ A+ ++++a+ r+        Al +++ +++ ++ ++e   +y+  l  +p++
  gi|386002535|ref|YP_005920834.1|  5 YENAIQYFDEAINRH---RKSIMALIGKAFCLFDLKKYEESDKYYDMVLVIDPNH 56
                                      899************...77888*****************999999988888875 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.6e-05
                            TPR_16  7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60
                                      ++++++y++  ++++ +l  d   P +a Al ++g +++++ +l +A++++ +a
  gi|386002535|ref|YP_005920834.1| 33 LFDLKKYEESDKYYDMVLVID---PNHASALVGKGKIFYEKRDLNKAIEYFTKA 83
                                      68999****************...***************************986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.25
                            TPR_16   3 laraalragdyddAaaaleaalkrdps 29 
                                       + + + ++g+ d+A a ++  +k+d++
  gi|386002535|ref|YP_005920834.1|  97 KIYVFQELGEHDRANACYNNIRKSDKK 123
                                       5667899****************9965 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.012
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ +++dA+  + + + +d   P    A+ + g++++ +g +++  a +++a++ +p+
  gi|386002535|ref|YP_005920834.1| 138 ENDRFEDAIDIYSEIVQKD---PNLISAWINMGLIYYLLGIYEKSNACCNRAIAIDPK 192
                                       5779***************...*********************999999999998886 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.2
                            TPR_16   6 aalragdyddAaaaleaalkrdpssP 31 
                                       ++++++++ +  ++++++l+ d   P
  gi|386002535|ref|YP_005920834.1| 203 IYYKQNEFNKSNEYYQRVLEID---P 225
                                       599****************987...4 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00032      0.29      16      60 ..      44      88 ..      33      92 .. 0.89
   2 !   17.4   0.0   4.1e-06    0.0037       7      62 ..     138     193 ..     136     201 .. 0.94
   3 ?    0.5   0.0      0.74   6.7e+02       3      27 ..     202     226 ..     200     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                             TPR_9 16 avverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60
                                      ++++++l+++P++++ +   G + ++  +l++A++ +  +   +p
  gi|386002535|ref|YP_005920834.1| 44 KYYDMVLVIDPNHASALVGKGKIFYEKRDLNKAIEYFTKASNSDP 88
                                      799********************************9988776666 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.1e-06
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +++++e a+ ++  +++ +P+ ++ +   Gl+++ lG +++  a+ ++++a++p+ 
  gi|386002535|ref|YP_005920834.1| 138 ENDRFEDAIDIYSEIVQKDPNLISAWINMGLIYYLLGIYEKSNACCNRAIAIDPKS 193
                                       689**************************************************976 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.74
                             TPR_9   3 aiaireedweralavverllllaPd 27 
                                        i+  ++++ +  ++++r+l ++P+
  gi|386002535|ref|YP_005920834.1| 202 VIYYKQNEFNKSNEYYQRVLEIDPN 226
                                       5677788888888888999988886 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.26   2.3e+02      16      43 ..       4      31 ..       3      32 .. 0.87
   2 ?    3.4   0.0      0.19   1.7e+02      11      42 ..      33      64 ..      28      66 .. 0.85
   3 ?   -0.4   0.0       3.2   2.9e+03       9      33 ..      65      89 ..      63      97 .. 0.79
   4 ?   -0.0   0.0       2.5   2.2e+03       9      26 ..      99     116 ..      93     124 .. 0.81
   5 !   11.4   0.0   0.00051      0.46      13      42 ..     138     167 ..     133     169 .. 0.90
   6 ?    3.6   0.0      0.17   1.5e+02       4      39 ..     163     198 ..     161     200 .. 0.82
   7 ?    2.5   0.0      0.38   3.4e+02      11      34 ..     204     227 ..     196     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.26
                            TPR_14 16 dpdeAiallrralalaPddaeawlllaq 43
                                      +++ Ai+++++a+ ++ ++  a++  a+
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAINRHRKSIMALIGKAF 31
                                      5789**********99999999887776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.19
                            TPR_14 11 llalGdpdeAiallrralalaPddaeawllla 42
                                      l+ l +++e+ ++++ +l  +P++a a+   +
  gi|386002535|ref|YP_005920834.1| 33 LFDLKKYEESDKYYDMVLVIDPNHASALVGKG 64
                                      56788999999**************9997766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 3.2
                            TPR_14  9 eallalGdpdeAiallrralalaPd 33
                                      +++++ +d+ +Ai+++ +a   +P+
  gi|386002535|ref|YP_005920834.1| 65 KIFYEKRDLNKAIEYFTKASNSDPK 89
                                      5677889999******999666665 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 2.5
                            TPR_14   9 eallalGdpdeAiallrr 26 
                                        ++ +lG++d+A a+++ 
  gi|386002535|ref|YP_005920834.1|  99 YVFQELGEHDRANACYNN 116
                                       577899******888875 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00051
                            TPR_14  13 alGdpdeAiallrralalaPddaeawllla 42 
                                       +++++++Ai+++ ++++++P+   aw+ ++
  gi|386002535|ref|YP_005920834.1| 138 ENDRFEDAIDIYSEIVQKDPNLISAWINMG 167
                                       5789**********************9987 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.17
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +  ++ +++ lG ++++ a+++ra+a +P++  a++
  gi|386002535|ref|YP_005920834.1| 163 WINMGLIYYLLGIYEKSNACCNRAIAIDPKSTMALY 198
                                       66677788888888999999**********998875 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.38
                            TPR_14  11 llalGdpdeAiallrralalaPdd 34 
                                       ++ + ++ ++ ++++r+l+ +P++
  gi|386002535|ref|YP_005920834.1| 204 YYKQNEFNKSNEYYQRVLEIDPNF 227
                                       777888899999**********86 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.5e-06    0.0022      38      74 ..       4      41 ..       2      49 .. 0.95
   2 ?    3.3   0.0      0.11        97      19      52 ..      53      87 ..      42      95 .. 0.79
   3 ?    1.7   0.1      0.34     3e+02       2      64 ..      70     129 ..      69     151 .. 0.71
   4 ?    4.1   0.0      0.06        54      33      74 ..     136     178 ..     110     182 .. 0.86
   5 ?    4.3   0.5     0.053        47      11      49 ..     182     220 ..     176     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                                      -HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3 38 qykrAyellrka.klnskslgcrylfAqcllkLkkyee 74
                                      +y+ A++++++a +   ks+ +++ +A cl++Lkkyee
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAiNRHRKSIMALIGKAFCLFDLKKYEE 41
                                      79***********************************9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                                      HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHH CS
                            ANAPC3 19 etespedayllAlclylngqykrAyellrka.kln 52
                                      ++++++++  +++ +y+  + ++A+e++ ka +++
  gi|386002535|ref|YP_005920834.1| 53 DPNHASALVGKGKIFYEKRDLNKAIEYFTKAsNSD 87
                                      566777777789*****************995544 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.34
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAq 64 
                                       ++++++Ai ++ ++ +++++    ++ + +++ ++g+++rA   +++     ks +  yl+ +
  gi|386002535|ref|YP_005920834.1|  70 KRDLNKAIEYFTKASNSDPKFMVPLLNKIYVFQELGEHDRANACYNNI---RKSDKKFYLLSK 129
                                       567788888888888877877777888889999999999999998888...555555566654 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.06
                                       HHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3  33 lylngqykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                                       l++n +++ A++++++  +++++ + +++ ++  ++ L+ ye+
  gi|386002535|ref|YP_005920834.1| 136 LCENDRFEDAIDIYSEIvQKDPNLISAWINMGLIYYLLGIYEK 178
                                       7889999999999999999999999999999999999999975 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.053
                                       HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka 49 
                                       +++r+ a +++s  ++y +   +y+++++++  e++++ 
  gi|386002535|ref|YP_005920834.1| 182 CCNRAIAIDPKSTMALYCKRVIYYKQNEFNKSNEYYQRV 220
                                       789999999*********************988888776 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.077        69      15      28 ..       5      16 ..       4      29 .. 0.62
   2 ?    2.2   0.0      0.25   2.2e+02      10      34 ..      34      56 ..      24      58 .. 0.77
   3 !    8.1   0.0    0.0034       3.1       2      32 ..      60      88 ..      59      91 .. 0.84
   4 ?   -0.1   0.1       1.4   1.2e+03       9      22 ..     101     114 ..      99     116 .. 0.83
   5 ?   -0.5   0.0       1.9   1.7e+03      13      22 ..     140     149 ..     136     158 .. 0.80
   6 ?    0.3   0.0         1   9.4e+02       1      27 [.     162     188 ..     162     193 .. 0.78
   7 ?    6.1   0.0     0.015        13       7      30 ..     202     225 ..     201     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.077
                             TPR_7 15 yeeAielyeqsLal 28
                                      ye+Ai+++ +  a+
  gi|386002535|ref|YP_005920834.1|  5 YENAIQYFDE--AI 16
                                      6677777666..33 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                             TPR_7 10 srlGdyeeAielyeqsLaltkdped 34
                                      ++l +yee  ++y    +l  dp++
  gi|386002535|ref|YP_005920834.1| 34 FDLKKYEESDKYYDM--VLVIDPNH 56
                                      45889**********..77766666 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0034
                             TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32
                                      L+  + ++ + +d  +Aie++++  a  +dp
  gi|386002535|ref|YP_005920834.1| 60 LVGKGKIFYEKRDLNKAIEYFTK--ASNSDP 88
                                      55668899999************..888877 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.4
                             TPR_7   9 ysrlGdyeeAiely 22 
                                       +++lG++++A  +y
  gi|386002535|ref|YP_005920834.1| 101 FQELGEHDRANACY 114
                                       899******97666 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.9
                             TPR_7  13 GdyeeAiely 22 
                                        ++e+Ai++y
  gi|386002535|ref|YP_005920834.1| 140 DRFEDAIDIY 149
                                       689*****99 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                       a+ n++ +y  lG ye+   ++ +++a
  gi|386002535|ref|YP_005920834.1| 162 AWINMGLIYYLLGIYEKSNACCNRAIA 188
                                       6789*****999999998888877444 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.015
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltk 30 
                                       ++y +++++ +  e+y+++L+++ 
  gi|386002535|ref|YP_005920834.1| 202 VIYYKQNEFNKSNEYYQRVLEIDP 225
                                       6899**************888764 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.6   2.3e+03      16      28 ..       4      16 ..       3      21 .. 0.83
   2 !    9.6   0.0    0.0011      0.96      14      37 ..      36      59 ..      30      66 .. 0.89
   3 ?    4.5   0.0     0.041        37      11      34 ..     170     193 ..     166     203 .. 0.88
   4 !   12.9   0.3   9.4e-05     0.085      11      34 ..     204     227 ..     196     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                                      -HHHHHHHHHHHH CS
                        Fis1_TPR_C 16 eYseArryvdalL 28
                                      eY++A +y d  +
  gi|386002535|ref|YP_005920834.1|  4 EYENAIQYFDEAI 16
                                      8*******99776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                                      HT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQa 37
                                      l++Y+e+ +y d++L i+P+   a
  gi|386002535|ref|YP_005920834.1| 36 LKKYEESDKYYDMVLVIDPNHASA 59
                                      89*****************98776 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.041
                                       HHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPen 34 
                                       +y lg Y+++  ++++ ++i+P+ 
  gi|386002535|ref|YP_005920834.1| 170 YYLLGIYEKSNACCNRAIAIDPKS 193
                                       678999****************85 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 9.4e-05
                                       HHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPen 34 
                                       +yk+ e++++ +y +++Lei+P++
  gi|386002535|ref|YP_005920834.1| 204 YYKQNEFNKSNEYYQRVLEIDPNF 227
                                       8*********************96 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0054       4.9      16      34 ..       3      21 ..       2      23 .. 0.92
   2 ?   -1.3   0.0       2.5   2.3e+03      12      28 ..      33      49 ..      33      52 .. 0.83
   3 ?    0.5   0.0      0.68   6.1e+02      25      39 ..     142     156 ..     136     158 .. 0.79
   4 ?   -2.2   0.0       4.8   4.3e+03       7      30 ..     165     188 ..     164     189 .. 0.75
   5 ?    5.8   0.0     0.014        13      11      31 ..     203     223 ..     202     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0054
                            TPR_10 16 grydeAealleealairrr 34
                                      ++y+ A ++++ea++++r+
  gi|386002535|ref|YP_005920834.1|  3 YEYENAIQYFDEAINRHRK 21
                                      689**************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                            TPR_10 12 lrqrgrydeAealleea 28
                                      l+++++y+e+ ++++ +
  gi|386002535|ref|YP_005920834.1| 33 LFDLKKYEESDKYYDMV 49
                                      67899******999766 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.68
                            TPR_10  25 leealairrrllGpd 39 
                                       +e+a++i+ +++  d
  gi|386002535|ref|YP_005920834.1| 142 FEDAIDIYSEIVQKD 156
                                       799999999988776 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 4.8
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N++ +++ +g y+++ a + +a+a
  gi|386002535|ref|YP_005920834.1| 165 NMGLIYYLLGIYEKSNACCNRAIA 188
                                       899999998877777777777776 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.014
                            TPR_10  11 alrqrgrydeAealleealai 31 
                                       +++++++++++ ++++++l+i
  gi|386002535|ref|YP_005920834.1| 203 IYYKQNEFNKSNEYYQRVLEI 223
                                       7******************97 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.38   3.4e+02     207     233 ..       4      30 ..       2      57 .. 0.73
   2 !    9.9   0.0   0.00034      0.31     205     290 ..      70     156 ..      64     174 .. 0.78
   3 ?    1.8   0.0       0.1        91     203     256 ..     171     224 ..     150     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.38
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKa 233
                                       ++e+A++y d+ai+++ +++   + Ka
  gi|386002535|ref|YP_005920834.1|   4 EYENAIQYFDEAINRHRKSIMALIGKA 30 
                                       567788888888888777777776666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00034
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHH..HHHHTT-HHHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcak..ymLradeveeA 279
                                        ++ +kA+ey  ka +++p+++   l+K  +++  G+ ++A ++ ++ rk D++  y+ sk +    +  +d+ e A
  gi|386002535|ref|YP_005920834.1|  70 KRDLNKAIEYFTKASNSDPKFMVPLLNKIYVFQELGEHDRANACYNNIRKSDKK-FYLLSKIVDgiELCENDRFEDA 145
                                       46889***********************************************87.5777777652234566677777 PP

                                       HHHHTTTS-TT CS
                             NARP1 280 eetvslFtree 290
                                        ++ s   +++
  gi|386002535|ref|YP_005920834.1| 146 IDIYSEIVQKD 156
                                       76666666655 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.1
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                         lg +ek+  + ++ai+ +p+++   + K  i+ ++ +++k  e  ++  ++D
  gi|386002535|ref|YP_005920834.1| 171 YLLGIYEKSNACCNRAIAIDPKSTMALYCKRVIYYKQNEFNKSNEYYQRVLEID 224
                                       45677999999***********************99999999988877666655 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00032      0.29     183     239 ..       5      61 ..       3      63 .. 0.93
   2 ?   -0.8   0.0       0.9   8.1e+02     222     256 ..      78     112 ..      61     150 .. 0.56
   3 ?    0.6   0.0      0.34     3e+02     215     244 ..     140     169 ..      93     218 .. 0.68
   4 ?   -3.5   0.0         6   5.4e+03      52      74 ..     257     279 ..     250     302 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHH CS
                        Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLi 239
                                       +++A   f+e  +++ +  + l gkA +   l++yee ++     L  d++++ +L+
  gi|386002535|ref|YP_005920834.1|   5 YENAIQYFDEAINRHRKSIMALIGKAFCLFDLKKYEESDKYYDMVLVIDPNHASALV 61 
                                       6788889***************************************99999999885 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.9
                                       HHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 222 slLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       +   +a ++d+k    L N + + q+lg  + + +
  gi|386002535|ref|YP_005920834.1|  78 EYFTKASNSDPKFMVPLLNKIYVFQELGEHDRANA 112
                                       55555666666666666666666666665543322 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.34
                                       T-HHHHHHHHHHHHHH-TT-HHHHHHHHHH CS
                        Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvva 244
                                       +r+e+A  +  e  +kd++   + iN+   
  gi|386002535|ref|YP_005920834.1| 140 DRFEDAIDIYSEIVQKDPNLISAWINMGLI 169
                                       355555555555555555555555555444 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6
                                       HHHHHHS-TTS-HHHHHHHHHHH CS
                        Coatomer_E  52 qiviseIkesaatelqAvrllae 74 
                                       +i i+ I+++a+++ q +rl   
  gi|386002535|ref|YP_005920834.1| 257 NIIIKIINSTASSDAQLLRLQQS 279
                                       45666676666777766665433 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00058      0.52     143     227 ..       4      89 ..       1     109 [. 0.77
   2 ?   -2.1   0.0       1.4   1.2e+03     164     196 ..     191     229 ..     188     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00058
                                       -HHHHHHHHHHHHHHSTT-SHHHHHHHHHH.HHHT---TT-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                          PknG_TPR 143 dyeeAaaeFdevlaalpGEiaPklaLAata.ElagetdeekyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaL 218
                                       +ye+A++ Fde ++     i   ++ A+   +l + +++ kyY++V   d +  sA  G  +   ++ d ++A++  
  gi|386002535|ref|YP_005920834.1|   4 EYENAIQYFDEAINRHRKSIMALIGKAFCLfDLKKYEESDKYYDMVLVIDPNHASALVGKGKIFYEKRDLNKAIEYF 80 
                                       67777777777776666666656665654314555666789*********************************988 PP

                                       HTS-TTSTT CS
                          PknG_TPR 219 deVpatSrh 227
                                        + +++  +
  gi|386002535|ref|YP_005920834.1|  81 TKASNSDPK 89 
                                       777666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHH...T---T....T-HHHHHHHH-TT-HH CS
                          PknG_TPR 164 PklaLAataEla...getde....ekyYrtVwrtdrgvvs 196
                                       Pk  +A  + ++   + ++e    ++yY+ V   d +  s
  gi|386002535|ref|YP_005920834.1| 191 PKSTMALYCKRViyyK-QNEfnksNEYYQRVLEIDPNFFS 229
                                       7777788777775531.222333379*****999998766 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00023       0.2      15      35 ..      63      85 ..      59      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                              Sel1 15 nGl.g.vpkDpekAiewyekAAe 35
                                      +G+   +++D +kAie++ kA +
  gi|386002535|ref|YP_005920834.1| 63 KGKiFyEKRDLNKAIEYFTKASN 85
                                      566633889************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2612.17
//
Query:       gi|386002536|ref|YP_005920835.1|  [L=93]
Description: hypothetical protein Mhar_1855 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 596.32
//
Query:       gi|386002537|ref|YP_005920836.1|  [L=981]
Description: Type I site-specific deoxyribonuclease chain R [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-28   99.8   3.1    5.7e-28   98.1   3.1    1.8  1  SWI2_SNF2      SWI2/SNF2 ATPase
    4.3e-19   69.2   0.2    1.6e-18   67.3   0.0    2.2  2  HSDR_N         Type I restriction enzyme R protein N terminus
    6.2e-15   55.6   0.1    1.5e-14   54.4   0.1    1.7  1  ResIII         Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   3.1   9.5e-32   5.7e-28       1     211 [.     277     527 ..     277     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 9.5e-32
                         SWI2_SNF2   1 qQyravekavervke.gdrkgGviWHtqGSGKsltmvflakklle.e...elknpkvvvvtDRkdLdkQlsktfaka 72 
                                       +Q+  v+k+++++++ g  k  +i H  GSGKs + ++la++l+  e   ++    ++vvtDR+ LdkQ+++t++++
  gi|386002537|ref|YP_005920836.1| 277 HQLDVVRKLLASAQHrGAGKRYLIQHSAGSGKSNSIAWLAHQLIGlErdgKTIFDSIIVVTDRRVLDKQIKDTIKQF 353
                                       7999999999999886778999*********************98532223355689******************98 PP

                         SWI2_SNF2  73 ..geekpkqaesrkeLkellekesekiifttiqKfeeeekeklevlsereniivlvDEaHRsqyg............ 135
                                          ++++ +ae++++L++ l +  +kii+tt+qKf    k ++   ++ + + +++DEaH sq g            
  gi|386002537|ref|YP_005920836.1| 354 aqVSATVGHAERSADLRQYL-AGGKKIIITTVQKFPVVLK-AIGDEHRGHSFAIIIDEAHSSQGGrtsakmsmvlsk 428
                                       433455569***********.679***********74333.5777788889************************** PP

                         SWI2_SNF2 136 ..............elakklrkalpnaafigFTGTPilkkdkktkevFg...........eyidkYtikeaveDgav 187
                                                     +   + rk+l na++++FT TP +    kt e+Fg           +  ++Yt+k+a++ g +
  gi|386002537|ref|YP_005920836.1| 429 eggekeaetpedriNRIMESRKMLSNASYFAFTATPKN----KTLEIFGeaymegddvkhRPFHSYTMKQAIQEGFI 501
                                       ***********95544445589**************66....588888866666666665799************** PP

                         SWI2_SNF2 188 vpil..Yesrlaklelkeeekldeef 211
                                       +++l  Y+   +  +l ++ + d ef
  gi|386002537|ref|YP_005920836.1| 502 LDVLknYTPVDSYYRLVKKVEDDPEF 527
                                       *9862244444444444444444444 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   2.7e-22   1.6e-18       3     191 ..       7     206 ..       5     209 .. 0.73
   2 ?   -3.5   0.1       1.4   8.4e+03      48      71 ..     883     914 ..     876     955 .. 0.47

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.7e-22
                                       SHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH..........-HHHHHHHH. CS
                            HSDR_N   3 sEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln..........ikkltkrla. 68 
                                       sE+ le   + +l+ e+Gy   + kd   +     v  +   + le  l +q +a n          ++++ +rl+ 
  gi|386002537|ref|YP_005920836.1|   7 SEKNLESLIVQSLISEAGYVEGDSKDYDRDH---AVDLI---KLLEFLLSTQPQAVNqlgldgeglkLQQFLARLQg 77 
                                       7888888555555588998876666544222...22222...44555666666777777788888886677666665 PP

                                       ..TT--HHHHHHHHHTS.-EEEE..TS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTEEEEEEE CS
                            HSDR_N  69 ..lsdgnkefyellkeg.kvkfk..egrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvnglplvviE 139
                                         +  g  ++++   +  + +++   g++   +L   +  ++N f+v++Q+ ++ ++++   D++lf+nglp++++E
  gi|386002537|ref|YP_005920836.1|  78 eiAKRGVIDVLRNGINHgPAHIDvfYGTPSPGNLKAAELFAANVFSVTRQLHYSkDETQLAFDLCLFINGLPIATFE 154
                                       544444444444433333555334656666656666666777************999999***************** PP

                                       E--T...T-HHHHHHHHTSS---.---SSSGGGGG-..-EEEEE-SS-EEEEE--SS CS
                            HSDR_N 140 lKrp...gtieeAinQikryrkeksdvsipqlfrYl..qfgvisngketrfyaktkr 191
                                       lK++   +t+e+A++Q+kr+r++      + lf++   +++++++++e+r+++  ++
  gi|386002537|ref|YP_005920836.1| 155 LKNSltkQTVEDAVQQYKRDRNP-----RELLFQFGrcAVHFAVDDHEVRMCTHLQG 206
                                       ****9966*************99.....7***********************98765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHH...-HHHHHHHH.....TT- CS
                            HSDR_N  48 eknlreqlgaln...ikkltkrla.....lsd 71 
                                        k +++q+g+++   i+ ++k ++       +
  gi|386002537|ref|YP_005920836.1| 883 IKAFNDQFGNIEwkdIDRIHKIISeeipaKVS 914
                                       55566666655555533333333222222112 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 !   54.4   0.1   2.5e-18   1.5e-14       4     170 ..     274     465 ..     271     466 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.5e-18
                                       E-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHHHHG CS
                            ResIII   4 lreyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtleef 74 
                                       +r++Q +++++ll++ ++    kr+li++  G+GK+  +a l+ +l   ++        ++++ +r+ l +q ++++
  gi|386002537|ref|YP_005920836.1| 274 PRYHQLDVVRKLLASAQHrGAGKRYLIQHSAGSGKSNSIAWLAHQLIGLERDGktifdSIIVVTDRRVLDKQIKDTI 350
                                       79***********9998623345***********************9976555889999****************** PP

                                       GGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS..... CS
                            ResIII  75 kkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak.... 147
                                       k+f++  ++    + s d +   ++ +  kki++tt+q++   +    ++  +  r+++  iiiDEaH +++     
  gi|386002537|ref|YP_005920836.1| 351 KQFAQVSATVGHAERSADLR---QYLAGGKKIIITTVQKFPVVL----KAIGDEHRGHSFAIIIDEAHSSQGGrtsa 420
                                       *****997543333333333...4589*****************....6666677777779***********98877 PP

                                       ........T...........TTHHH...HHT---SEEEEEESS-S CS
                            ResIII 148 ........k...........swrei...lekfkeavllglTATpe 170
                                               +            +++i    +++++a  +++TATp+
  gi|386002537|ref|YP_005920836.1| 421 kmsmvlskEggekeaetpedRINRImesRKMLSNASYFAFTATPK 465
                                       6666666505556666777788888555667799**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (981 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.88u 0.32s 00:00:01.20 Elapsed: 00:00:00.53
# Mc/sec: 5525.58
//
Query:       gi|386002538|ref|YP_005920837.1|  [L=333]
Description: hypothetical protein Mhar_1857 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-119  396.8   6.2   4.6e-119  396.3   6.2    1.1  1  Virulence_RhuM  Virulence protein RhuM family
  ------ inclusion threshold ------
      0.025   14.7   0.1      0.025   14.7   0.1    2.5  4  Mrr_N           Mrr N-terminal domain
       0.13   12.3   0.0       0.23   11.4   0.0    1.4  1  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Virulence_RhuM  Virulence protein RhuM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.3   6.2  7.6e-123  4.6e-119       1     249 [.      57     305 ..      57     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.3 bits;  conditional E-value: 7.6e-123
                    Virulence_RhuM   1 avvkkfrtvakegkreverevklynLdaiiavGyrvkskratqFRkWatkvlkeylikGfvldderlkngkklgkdy 77 
                                       a+++kfr v++eg+r+ver+v++ynL++i+a+Gyrv+s+r++qFR+Wat++l+ey++kGfvldderlk +++lg+dy
  gi|386002538|ref|YP_005920837.1|  57 ATTRKFRLVQTEGSRQVERRVDFYNLEMILAIGYRVRSHRGVQFRRWATERLREYIVKGFVLDDERLKGERALGADY 133
                                       689************************************************************************** PP

                    Virulence_RhuM  78 fdellerirdiRasErrfyqkvtdiyatsiDYdkkseatkeFfatvqnklhyavtgktaaeliveradaekenmgLt 154
                                       fdellerirdiRasE+rfyqkv+diya+siDYd+++++t+eFf+ vqnklh+a+tg+taaeli erada+k+nmgLt
  gi|386002538|ref|YP_005920837.1| 134 FDELLERIRDIRASEKRFYQKVRDIYALSIDYDSRAQSTQEFFRIVQNKLHWAITGHTAAELISERADASKPNMGLT 210
                                       ***************************************************************************** PP

                    Virulence_RhuM 155 twkgakvlksdvtiakNYLseeelkeLnrivsayldlaelqakrrkeltmedwaekldeflelndkevLkdaGkisa 231
                                       +wkgakv+++dv +akNYL ++e+ +Lnr+v+++ld+ae+qa+rrk++ m+dw+ekld+fl++n++ +L+++G+is+
  gi|386002538|ref|YP_005920837.1| 211 AWKGAKVRQADVLVAKNYLLADEIGQLNRLVTMWLDYAEDQANRRKPVCMKDWREKLDAFLQFNQRAILEHSGRISM 287
                                       ***************************************************************************** PP

                    Virulence_RhuM 232 eqakekaekeyekfkkqr 249
                                       e+ak+ a ++y++f+++r
  gi|386002538|ref|YP_005920837.1| 288 EEAKRLALEQYQAFNQRR 305
                                       ***************776 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.69   4.1e+03      43      58 ..      66      81 ..      27      98 .. 0.56
   2 ?   -3.2   0.0       1.6   9.5e+03      21      37 ..     106     122 ..     102     124 .. 0.72
   3 ?   14.7   0.1   4.1e-06     0.025       4      70 ..     133     199 ..     131     204 .. 0.79
   4 ?   -3.1   0.1       1.5     9e+03      31      43 ..     317     326 ..     293     330 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.69
                             Mrr_N 43 psgkqtrfknrvgWar 58
                                      ++  ++ +++rv +++
  gi|386002538|ref|YP_005920837.1| 66 QTEGSRQVERRVDFYN 81
                                      3333556777777765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                             Mrr_N  21 keirervaerfglseee 37 
                                       + +re++ + f l++e 
  gi|386002538|ref|YP_005920837.1| 106 ERLREYIVKGFVLDDER 122
                                       56788888888888886 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4.1e-06
                             Mrr_N   4 lmlplLealadgsehrlkeirervaerfgls..eeeraellpsgkq..trfknrvgWartyLkkagllesp 70 
                                       ++ +lLe ++d +++  k  +++v++ + ls   + ra+ +   ++  ++++n+++Wa+t  + a+l+++ 
  gi|386002538|ref|YP_005920837.1| 133 YFDELLERIRDIRASE-KRFYQKVRDIYALSidYDSRAQST---QEffRIVQNKLHWAITGHTAAELISER 199
                                       8899*******99999.99********96662044444444...34568******************9875 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.5
                             Mrr_N  31 fglseeeraellp 43 
                                       f   eee++++lp
  gi|386002538|ref|YP_005920837.1| 317 F---EEEVKRMLP 326
                                       2...555555555 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.9e-05      0.23      21      46 ..      19      44 ..      16      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
                            HTH_36 21 nggcfpsqetlakrlglsknTvsrai 46
                                      +g ++ sq+ la+++ +s +T+s +i
  gi|386002538|ref|YP_005920837.1| 19 DGTVWLSQRLLAELYQVSTRTISEHI 44
                                      4569*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2096.86
//
Query:       gi|386002539|ref|YP_005920838.1|  [L=474]
Description: Restriction modification system DNA specificity domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-07   29.7   0.0     0.0066   16.7   0.0    2.4  2  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   2.5e-05      0.44     135     155 ..     161     181 ..     104     195 .. 0.83
   2 !   16.7   0.0   3.7e-07    0.0066       1     163 [.     230     408 ..     230     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.5e-05
                                       EE--HHHHHHHHHHHHHHHHH CS
                       Methylase_S 135 plPpleeQkkIakiLsqldnt 155
                                        lPpl+eQ  I+++L+ +d  
  gi|386002539|ref|YP_005920838.1| 161 ILPPLPEQAAIVRFLDHIDGR 181
                                       59****************983 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.7e-07
                                       ETT-EEEEHHHHEEEEE-----TT..GGTTT--EEEE-HH.HCCT.........EE-HHHHCCTT---B-TT-EEEE CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkk..elkengkypyirag.ilnn.........kvvkdglgykkkyilpkgdilis 65 
                                       p+ w+vv L  ++e+k g+ +  +  e  +   +p + ++ + ++         +  kd  + ++  + + gd+l s
  gi|386002539|ref|YP_005920838.1| 230 PVHWNVVPLRKLVEVKDGTHDTPSyvEPSDTS-FPLVMSKdFGPSsicfdnvnhISAKDHFEIVERSNTKRGDVLMS 305
                                       67899999999999955554444441555544.488777767777899999999999999999999999*9999999 PP

                                       -S.SSTT-EEEESS-.BEE-TTEEEEEEST.TT--HHHHHHHHH..HCHHHHHHHCCSSTTT---HHHHCC-EE.EE CS
                       Methylase_S  66 sr.atiGkvayrdkk.yylnqsvivlipkn.kkkineflylyll..lklkklkslsvgstqpkltkenlkkikI.pl 136
                                       ++ ++iGk+ + d +  +  ++v  ++  n +++  +f+++yl   l+  ++  ls+g++q+ l + +++++ + ++
  gi|386002539|ref|YP_005920838.1| 306 MIgGNIGKALIVDTNrEFSIKNVALFKTCNsSHLA-RFILYYLRsgLLDIQIAMLSKGGAQGFLALGQIRNLSFlKI 381
                                       999*********99535777888888888856666.********543333555559****************97266 PP

                                       --HHHHHHHHHHHHHHHH.HHHHHHHHH CS
                       Methylase_S 137 PpleeQkkIakiLsqldn.tielekkik 163
                                       P  +e + I+++L+q  +   +l+++  
  gi|386002539|ref|YP_005920838.1| 382 P-ANEMELIVETLDQKLAvHDALIAAAS 408
                                       6.78899******997776666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2842.96
//
Query:       gi|386002540|ref|YP_005920839.1|  [L=711]
Description: type I restriction-modification system specificity subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-54  183.0   0.0    1.2e-53  182.4   0.0    1.2  1  N6_Mtase  N-6 DNA Methylase
    4.2e-22   79.3   0.2    2.4e-21   76.8   0.1    2.3  2  HsdM_N    HsdM N-terminal domain
  ------ inclusion threshold ------
      0.088   12.5   0.0       0.29   10.8   0.0    1.8  1  UPF0020   Putative RNA methylase family UPF0020
       0.59   10.0   2.3        1.2    9.0   0.1    2.5  3  Tma16     Translation machinery-associated protein 16


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.4   0.0   2.8e-57   1.2e-53       3     283 ..     171     485 ..     169     501 .. 0.85

  Alignments for each domain:
  == domain 1  score: 182.4 bits;  conditional E-value: 2.8e-57
                          N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivell........epksgesvyDpacGsggllvqaekvlkee 71 
                                       ++++G ++E l+r+f ee+ +++Ge fTPr+v++l+++l+        e+      yD acG+gg+l  a++ lk+ 
  gi|386002540|ref|YP_005920839.1| 171 NHAIGTIFEELIRRFNEENNEEAGEHFTPRDVVRLMADLVilpiadkiESA-TYLLYDGACGTGGMLTIADERLKQI 246
                                       6899***********************************999998764333.3469*************99988764 PP

                          N6_Mtase  72 ...dgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew..... 140
                                          +gk  +++++Gqe+n++ty+++k  ll++g   +     lg+tl+++ f   ++fd++++Npp++++ w     
  gi|386002540|ref|YP_005920839.1| 247 aqeHGKDVSIHLFGQEVNPETYAITKADLLIKGEGDEAEYFFLGSTLSQDAFA-SREFDFMLSNPPYGKS-Wkadme 321
                                       4337777788888********************99998889************.****************.*98887 PP

                          N6_Mtase 141 ..kektlekderfrea.........vapksnadlafllhiieslkpk....GraavvlangvLfr...ggkegkIrk 199
                                           k  + d rf            +  +s  +++fl  +++++k++     r+a v +  +Lf    g  e +Ir+
  gi|386002540|ref|YP_005920839.1| 322 rmGGKADILDLRFVIEhagdpdfklITRSSDGQMMFLVNMLSKMKHQtplgSRIAEVHNGSSLFTgdaGQGESNIRR 398
                                       765566667779987778999999999999**********99988753332599**********944456789**** PP

                          N6_Mtase 200 alvekdlveavialpeklFyntsiptcilvlkkekae.rkgkvlfidaseefkkkd....rkknklteediekildt 271
                                        ++e+d +ea+ialp ++Fynt+i+t i+vl+  k++ rkgkv +ida++ fk       +k+ +l++edi++i+d 
  gi|386002540|ref|YP_005920839.1| 399 WIIENDWLEAIIALPLNMFYNTGIATYIWVLTNRKPDhRKGKVQLIDATSWFKPLRknlgKKNCELSAEDIQRIVDL 475
                                       *********************************99998***********998743323668999************* PP

                          N6_Mtase 272 ykekskevdkfs 283
                                       + ++++  +++s
  gi|386002540|ref|YP_005920839.1| 476 FLSFQE--SEQS 485
                                       **9932..2222 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.1   5.3e-25   2.4e-21       1     137 []       9     145 ..       9     145 .. 0.91
   2 ?   -1.4   0.0      0.75   3.4e+03      83     110 ..     170     197 ..     164     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 5.3e-25
                                       HHHHHHHHH.HHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC............--..--------....S-C CS
                            HsdM_N   1 lesklwkaa.diLRgkvdaseykeyilgLlFlKrlddveeereeklleeyken.....aleeleeklkskeafyipe 71 
                                       +++++w +a d LR+ + + +y+++il++++++rld+v+e++++ +l+ +k+       +++ + +++s++afy+++
  gi|386002540|ref|YP_005920839.1|   9 ITNFIWGIAdDVLRDIYVRGKYRDVILPMTVIRRLDAVLEPTKQSVLDLKKQLdeagiTNQDAALRQASGQAFYNTS 85 
                                       679******999**668*****************************988444334565337889999999******* PP

                                       CCSHHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS......S-----SSHHHHHHHHHHH CS
                            HsdM_N  72 elrWkelakkkdddelgenlnkafpaleelnkslkgvfmkddfnafalgeitkkspalLskviekf 137
                                       ++ +++l++++++++l+++l++++++++ +   +++++   d+++f++++ t+ + + L  +iekf
  gi|386002540|ref|YP_005920839.1|  86 PFLLRDLKARPKAQQLKADLEAYLDGFSPN---VQDIL---DKFKFRNQIPTLVEADILGYLIEKF 145
                                       **********99999**************9...*****...68*********************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.75
                                       -HHHHHHHHHHCHHHHCT--STHHHHHH CS
                            HsdM_N  83 dddelgenlnkafpaleelnkslkgvfm 110
                                       d+ ++g  ++++++ ++e+n++ +g+++
  gi|386002540|ref|YP_005920839.1| 170 DNHAIGTIFEELIRRFNEENNEEAGEHF 197
                                       4556899999999999999986555444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.4e-05      0.29      75     137 ..     254     318 ..     219     323 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.4e-05
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--...STTS---EEEE---------- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr...lkegevdvivtnpPYGerlgs 137
                                       + ++l+g + +++  + ++  +   g gd+ e+  +  + L     ++ e+d +++npPYG++ ++
  gi|386002540|ref|YP_005920839.1| 254 VSIHLFGQEVNPETYAITKADLLIKGEGDEAEYFFLGST-LSqdaFASREFDFMLSNPPYGKSWKA 318
                                       444455555555555555555555554444444332222.2222224559************9765 PP

>> Tma16  Translation machinery-associated protein 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.37   1.7e+03      56      84 ..     168     196 ..     136     201 .. 0.83
   2 ?    9.0   0.1   0.00026       1.2      26      81 ..     430     488 ..     428     512 .. 0.82
   3 ?   -2.8   0.4       1.1     5e+03      80     106 ..     557     583 ..     554     587 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
                             Tma16  56 plsleelkeliekylkRndeeleelkser 84 
                                       pl++  +  + e+ ++R++ee +e+  e+
  gi|386002540|ref|YP_005920839.1| 168 PLDNHAIGTIFEELIRRFNEENNEEAGEH 196
                                       67778888899999999999999987665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00026
                             Tma16  26 akkkkerakkkssllervkffqealde...ekkplsleelkeliekylkRndeeleelk 81 
                                       +++k +++k k +l++  ++f+   ++   ++ +ls e+++++++ +l+ +++e +++ 
  gi|386002540|ref|YP_005920839.1| 430 TNRKPDHRKGKVQLIDATSWFKPLRKNlgkKNCELSAEDIQRIVDLFLSFQESEQSKIF 488
                                       678899999************9775555559999**************99988887765 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.1
                             Tma16  80 lkserrkgrpkskreelleekkereee 106
                                       +++++++g + +++ ++l ++  +e++
  gi|386002540|ref|YP_005920839.1| 557 EQRAKKQGIKITAKRQKLIQTALAEKD 583
                                       455667776666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 4188.66
//
Query:       gi|386002541|ref|YP_005920840.1|  [L=255]
Description: hypothetical protein Mhar_1860 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1560.68
//
Query:       gi|386002542|ref|YP_005920841.1|  [L=320]
Description: GTP cyclohydrolase mptA [Methanosaeta harundinacea 6Ac]
Scores for 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-83  277.8   0.6      1e-82  277.6   0.6    1.0  1  GCHY-1          Type I GTP cyclohydrolase folE2
    0.00038   21.0   0.9     0.0083   16.7   0.2    2.8  2  FolB            Dihydroneopterin aldolase
  ------ inclusion threshold ------
      0.026   14.5   0.2      0.038   14.0   0.2    1.2  1  EspB            Enterobacterial EspB protein
       0.19   11.8   1.3        9.8    6.3   0.1    2.4  2  MPTase-PolyVal  Metallopeptidase superfamily domain


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.6   0.6   2.3e-86     1e-82       1     259 []       4     293 ..       4     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 277.6 bits;  conditional E-value: 2.3e-86
                                       .XXXXXXXXXX----SEEEEEEEEEEEEE--TTT.S-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG. CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdkek.kaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee. 74 
                                       lpDvq+ ++e++i+l+rVG++gvk++vkv ++++ +++ l++++++fvdLp+++kG+++SR++ev++   ee+++e 
  gi|386002542|ref|YP_005920841.1|   4 LPDVQACQPEYPINLTRVGLTGVKKLVKVLREDEeRPIVLISNFEVFVDLPSDRKGANLSRNFEVIDeVLEEAINEp 80 
                                       79***************************998762669*****************************6666777768 PP

                                       .GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE CS
                            GCHY-1  75 .kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvttl 146
                                        + +ee    i++++l+k+eya+raev++k+ey++e+++pv+++ g+e +++++ea ++   +v++ vg+ev+++t+
  gi|386002542|ref|YP_005920841.1|  81 vYVIEElcgeIARRVLSKHEYATRAEVKMKSEYIVERSSPVTKTAGQEVVDIFAEAVARA-GTVRKLVGAEVVGMTA 156
                                       8455555556************************************************65.37************** PP

                                       -HHHHHHS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S- CS
                            GCHY-1 147 CPCskeisrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyel 202
                                       CPC++ei+r+l+                     ++++HnQR++  +++++  +++ v+++d+i+++e+s+ss+v+ l
  gi|386002542|ref|YP_005920841.1| 157 CPCAQEIMRDLVrrelstlglgpeeardfaarlPVATHNQRGRGMISIQVC-DRRCVSLDDIIRIIERSMSSRVFGL 232
                                       **********99*************************************75.8899********************* PP

                                       --HHHHHHHHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 203 lKReDEkavtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       lKR+DE+ v+++a++npkFvED+vR++a+++     ve+f          +++ neESiH+Hna+A
  gi|386002542|ref|YP_005920841.1| 233 LKRPDEALVVQRAHSNPKFVEDCVRTMAQKV-----VESFkdlpddavvVLKQVNEESIHQHNAFA 293
                                       *******************************.....555555599999999**************8 PP

>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.9e-06    0.0083      27      95 ..      45     111 ..      32     129 .. 0.75
   2 ?    1.5   0.0     0.092   4.1e+02      58      84 ..     242     267 ..     202     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                                       EEEEEEE-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHHHCHST.ESEEEEEEEE CS
                              FolB  27 vdleleldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaealleefp.vekvevrveK 95 
                                        ++e+ +dl +  +  +l  + +++ + + ++e +++ ++  +E l+ +ia+++l++++ ++++ev+++ 
  gi|386002542|ref|YP_005920841.1|  45 SNFEVFVDLPSDRKGANL--SRNFEVIDEVLEEAINE-PVYVIEELCGEIARRVLSKHEyATRAEVKMKS 111
                                       556666665544454444..56777777777777777.*****************999999999999976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.092
                                       HHHHHSSEES-HHHHHHHHHHHHHCHS CS
                              FolB  58 kelvesssfkllEalaeriaealleef 84 
                                       ++ + s + k +E  ++  a++++e+f
  gi|386002542|ref|YP_005920841.1| 242 VQRAHS-NPKFVEDCVRTMAQKVVESF 267
                                       333323.55666666666666665555 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   8.6e-06     0.038     100     187 ..      92     285 ..      74     300 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.6e-06
                              EspB 100 aksVntasEvsvkAlvk.asEsiadaagetvgklqqgiasvaaaaktr............................. 146
                                       a++V ++ E ++ A vk  sE i++ ++ +  ++ q+++ + a+a +r                             
  gi|386002542|ref|YP_005920841.1|  92 ARRVLSKHEYATRAEVKmKSEYIVERSSPVTKTAGQEVVDIFAEAVARagtvrklvgaevvgmtacpcaqeimrdlv 168
                                       899***********777369**********************9999999**************************** PP

                              EspB 147 ............................................................................n 147
                                                                                                                    
  gi|386002542|ref|YP_005920841.1| 169 rrelstlglgpeeardfaarlpvathnqrgrgmisiqvcdrrcvslddiiriiersmssrvfgllkrpdealvvqrA 245
                                       *************************************************************************9988 PP

                              EspB 148 eqrakavedlqesnleeykktvresqDkiasvlqdlrsta 187
                                         + k ved +  ++++  +  +   D+++ vl+++ +  
  gi|386002542|ref|YP_005920841.1| 246 HSNPKFVEDCVRTMAQKVVESFKDLPDDAVVVLKQVNEES 285
                                       888999****************************998764 PP

>> MPTase-PolyVal  Metallopeptidase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.01        46      65     106 ..      72     114 ..      63     120 .. 0.76
   2 ?    6.3   0.1    0.0022       9.8      67      95 ..     289     317 ..     281     320 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.01
                    MPTase-PolyVal  65 dlskrfgseayarEElvAelgaaflcae.lgiepevrdhaaYi 106
                                        l++ +++  y  EEl+ e++  +l ++    ++ev+ +++Yi
  gi|386002542|ref|YP_005920841.1|  72 VLEEAINEPVYVIEELCGEIARRVLSKHeYATRAEVKMKSEYI 114
                                       5677888999***********9888765144555666777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0022
                    MPTase-PolyVal  67 skrfgseayarEElvAelgaaflcaelgi 95 
                                       ++ f +++ ++ El+Aelga  l a++++
  gi|386002542|ref|YP_005920841.1| 289 HNAFAERSATMGELRAELGAEALSASCEV 317
                                       578999999*************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2051.01
//
Query:       gi|386002543|ref|YP_005920842.1|  [L=213]
Description: RNA 2'-phosphotransferase, Tpt1 / KptA family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.8e-24   84.5   0.0      1e-23   84.3   0.0    1.1  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family


Domain annotation for each model (and alignments):
>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   5.8e-28     1e-23       2     180 ..      30     194 ..      29     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 5.8e-28
                         PTS_2-RNA   2 revqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelveleelliranq 78 
                                       r+++l++ ++  LRh +++ gL +++ G+v+++ l e   ++ + ++ + + ++V+s++K+R+e+    e  ira+ 
  gi|386002543|ref|YP_005920842.1|  30 RSERLGRLVAGALRHFPDDLGLVMDPRGWVDLDALSEAIGTRYRWANKRLVIALVQSDPKERYEIR---EGKIRAKY 103
                                       67899******************************997777776699999**************44...467***** PP

                         PTS_2-RNA  79 ghsi.kkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrksaevl 154
                                       ghs+ ++       l+  ++   l + +++g + ++ ++il + gLk ++++++hl+t+ p+++  +   r+++  +
  gi|386002543|ref|YP_005920842.1| 104 GHSVgVS-------LDYPKNR--L-AALYYGANEEEADRIL-EVGLKAATQRYVHLSTT-PEKAWHVGTFRTNSPRV 168
                                       ***6222.......5553332..3.459*************.99**************7.766667777999***** PP

                         PTS_2-RNA 155 iyidvekaladgikfyvsengviLte 180
                                       i +d+e+a+++g+k+++ + +++++e
  gi|386002543|ref|YP_005920842.1| 169 IRVDAEAAMRAGVKMMTVSPDIVISE 194
                                       ****************9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1493.85
//
Query:       gi|386002544|ref|YP_005920843.1|  [L=203]
Description: Di-trans,poly-cis-decaprenylcistransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-21   75.2   0.0    1.3e-20   73.9   0.0    1.6  2  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0     0.084   1.5e+03      28      46 ..      40      58 ..      37      60 .. 0.84
   2 !   73.9   0.0   7.1e-25   1.3e-20     116     224 .]      97     202 ..      69     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.084
                                      HHHHHHHHHHTT-SEEEEE CS
                      Prenyltransf 28 lkeilelclelgvkvvtvY 46
                                      + e+  +c++lgv+   ++
  gi|386002544|ref|YP_005920843.1| 40 VGEVAGWCTSLGVREAAIF 58
                                      678999*******998887 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 7.1e-25
                                       SEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT CS
                      Prenyltransf 116 klvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlay 191
                                        l+l++    g+r+e++ a+r+l++e+     + e++de+++e++l    +   pDlliR +  + lS+F++wq+ay
  gi|386002544|ref|YP_005920843.1|  97 PLHLVVSAGPGGREEVTGAIRSLLEEVRVGLLDpEAVDEAAIEARLRL--K-LRPDLLIRLG-PRELSDFMIWQSAY 169
                                       3889999999*************99997666554566899*******8..4.68******97.566*********** PP

                                       -EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 192 selyfldvlWPdfskedllealleyqkrerrfg 224
                                       selyf+d  W  ++k d+l a+++yq+rerrfg
  gi|386002544|ref|YP_005920843.1| 170 SELYFIDRSWEGLKKVDFLLAVRDYQRRERRFG 202
                                       *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1199.46
//
Query:       gi|386002545|ref|YP_005920844.1|  [L=409]
Description: membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-52  176.3  15.2    6.3e-52  176.3  15.2    2.1  2  DUF92     Integral membrane protein DUF92
  ------ inclusion threshold ------
        4.8    7.3   5.3       0.73    9.9   0.4    2.2  2  DHHC      DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.9      0.35   3.2e+03     151     151 ..      93      93 ..      39     147 .. 0.55
   2 !  176.3  15.2     7e-56   6.3e-52       2     235 ..     184     398 ..     183     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.35
                             DUF92 151 a 151
                                       a
  gi|386002545|ref|YP_005920844.1|  93 A 93 
                                       0 PP

  == domain 2  score: 176.3 bits;  conditional E-value: 7e-56
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       ++l+l++ a+r k+ + +++++ v++++l+++    + +fllll F+llgs +t++k+++K+  +++++++g R+++
  gi|386002545|ref|YP_005920844.1| 184 FALALGIGAYRMKAADAEAVISEVIICLLVIFF-ADIFWFLLLLSFYLLGSGFTRYKYAKKQelRIAQARGGVRGYK 259
                                       68999***********************99999.8889************************88888888999**** PP

                             DUF92  77 qVlanslvalllally..lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGlla 151
                                       +V +nslv+l++a+ly  ++sdl+++++++s+A++++DTlaSE+G++ + skp +it+l++v+pG++GgV+llG +a
  gi|386002545|ref|YP_005920844.1| 260 NVYSNSLVPLAMAVLYgvYGSDLFAFAFLGSVATATGDTLASEIGETAR-SKPKMITNLRSVEPGVDGGVTLLGEAA 335
                                       ****************76559************************7775.5************************** PP

                             DUF92 152 sllGalliall.avlllllellillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlLdNnaV 227
                                       sl+Gal+ + l ++++++ +  +++++l G+lG+++DSlLGatlq++                       lL+Nn+V
  gi|386002545|ref|YP_005920844.1| 336 SLFGALFTGGLaIATGMAGCGGFAAALLGGFLGTNFDSLLGATLQSR----------------------GLLSNNGV 390
                                       *********66255555556699999999******************......................79999999 PP

                             DUF92 228 Nllsallt 235
                                       Nl+++l++
  gi|386002545|ref|YP_005920844.1| 391 NLFATLFG 398
                                       99999987 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.5       0.5   4.5e+03      57      66 ..      54      63 ..      14     110 .. 0.59
   2 ?    9.9   0.4   8.1e-05      0.73      83     133 ..     193     243 ..     154     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.5
                              DHHC 57 ylllllilal 66
                                      + l ++ + l
  gi|386002545|ref|YP_005920844.1| 54 FALEATSFHL 63
                                      2222222222 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.1e-05
                              DHHC  83 seflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtieamkk 133
                                        ++ a++    + ++++++l ++f+ ++++lll ++yl+  ++T++ ++kk
  gi|386002545|ref|YP_005920844.1| 193 YRMKAADAEAVISEVIICLLVIFFADIFWFLLLLSFYLLGSGFTRYKYAKK 243
                                       3333333333366788888889999999999999*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2384.88
//
Query:       gi|386002546|ref|YP_005920845.1|  [L=221]
Description: hypothetical protein Mhar_1865 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.5   1.2       0.28   11.4   1.2    1.6  1  DIM       DIM protein


Domain annotation for each model (and alignments):
>> DIM  DIM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   1.6e-05      0.28       4      30 ..      36      60 ..      34      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
                               DIM  4 LsLlaflllllalaaanalpGkViING 30
                                      Ls+  fl +ll+ aaa+a + +V+  G
  gi|386002546|ref|YP_005920845.1| 36 LSI--FLAGLLLAAAASAAGENVTLGG 60
                                      666..****9*************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1538.36
//
Query:       gi|386002547|ref|YP_005920846.1|  [L=496]
Description: Aspartate aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-48  166.1   0.0    1.5e-48  165.8   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8   0.0   8.4e-53   1.5e-48       3     346 ..     104     448 ..     102     460 .. 0.88

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 8.4e-53
                                       EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                       v nLg ++ ++     +++ v+ a +       + + y+p +glp+l+ea+a+f++r+ +++  +e +v+vg+G+++
  gi|386002547|ref|YP_005920846.1| 104 VANLGLGQSPFP----VPTPVVNALRL----YASEKDYLPVKGLPALREAVADFHRRKDGVSASPE-NVLVGPGSKE 171
                                       567777777777....66666666655....566789*****************************.********** PP

                                       HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE.TEEEEEEE CS
                     Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk.ktkvilve 155
                                       l  +l  +       ei+vp+p + sy + +++ g +v+  +++  +++h++ e l + l+   e+++ ++++++++
  gi|386002547|ref|YP_005920846.1| 172 LMFLLQLVYY----GEIIVPTPAWVSYVPQAQILGKKVRLLHTTFDDKWHITSERLARFLEG--EQDVyRPRILVLN 242
                                       *999999995....58******************************************9998..445569******* PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTT.STT.EEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranvee.epn.llivgslsKafGlaGeRv 230
                                        p NP+G  +++eele+++++a++y+l+l++De+Y+ +    +     ++ v++ +p+ ++i ++lsK  G+ G+R+
  gi|386002547|ref|YP_005920846.1| 243 YPGNPDGLTYSPEELEEIASVAREYELVLLSDEIYGQLHHRGE-----HVSVARfYPEgTIISSGLSKWCGAGGWRL 314
                                       ***************************************9954.....444444255578***************** PP

                                       EEEEEEH...HHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECC CS
                     Aminotran_1_2 231 Gyilgna...avvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlas 302
                                       G ++  +   +++++++ +++  +   s++ q a+++a +    ++++l  +r+ l ++  e+++ L+e+g  v a+
  gi|386002547|ref|YP_005920846.1| 315 GTFTFPPdmdWLLEAMAAVASETYTsvSAPIQFAAVQAFRGGIAIERYLWHARRILSTLGSEFYAVLREAGARVHAP 391
                                       *****76699**********999999*************************************************** PP

                                       SCSSEEEEEETHHCHHHHHHH...........HHHTCTEEEEEGGGGTS...TTEEEE CS
                     Aminotran_1_2 303 qsgmflltdlsaetakelskk...........Lleevgvyvtpgtsftv...pgrlRi 346
                                       ++g++l++dls++ a+ ls+            Ll   +v+++pg+ f+    + + Ri
  gi|386002547|ref|YP_005920846.1| 392 EGGFYLFVDLSPL-ADRLSRRgiqdgatlcerLLADRKVAILPGSAFGRpnrELSARI 448
                                       *************.66666667777777777755555**********99554445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2986.36
//
Query:       gi|386002548|ref|YP_005920847.1|  [L=542]
Description: SecD/SecF/SecDF export membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-15   57.5  10.5    2.6e-15   56.3  10.5    1.5  1  SecD_SecF  Protein export membrane protein
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.34   10.5   0.0    1.7  1  Sec_GG     SecD/SecF GG Motif
       0.54    9.1  24.5      0.017   14.1  18.4    1.6  2  MMPL       MMPL family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3  10.5   4.4e-19   2.6e-15      12     173 ..     366     524 ..     358     526 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 4.4e-19
                                       -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH.HHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                         SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewr.valaaiialvhDviitvgvlsllgievdlatv 87 
                                       ++e+i    v + +++++++++++a +ia++++ ++++ r++++ + +  +++ ++ v++++++ +ll+ ++dla++
  gi|386002548|ref|YP_005920847.1| 366 NVEIIGSGQVTAALGDQFKKQVLIAGIIAILAVGLVIYYRYRDPrIVIPMVATSFSEVLMMLALAALLKWQLDLAAI 442
                                       6788888899********************************861555566669*********************** PP

                                       HHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHH CS
                         SecD_SecF  88 aalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalal 164
                                       a+++ +iG  v+  v+++d +  +     +++  +i    l++ +   +++ +tt+++++ l+ +g ++ k+fal+ 
  gi|386002548|ref|YP_005920847.1| 443 AGIIAVIGTGVDHLVIITDELLYE----GKMPSGKIYLARLSSAFGIIMAAAATTIVAMLPLFAMGFGAFKSFALVT 515
                                       *******************98877....56888899999999999988999999*********************** PP

                                       HHHTSTTTT CS
                         SecD_SecF 165 lvGlivgty 173
                                       + G+++g++
  gi|386002548|ref|YP_005920847.1| 516 IAGVLIGVL 524
                                       *******96 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.7e-05      0.34       4      23 ..      33      52 ..      33      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.7e-05
                                      HHC--EE-TTTS-EEEEEEE CS
                            Sec_GG  4 ftkGlNLGlDFtGGthielq 23
                                      f+  l++GlD+ GG+ ++l+
  gi|386002548|ref|YP_005920847.1| 33 FHSRLKYGLDLEGGSWLQLK 52
                                      56789*********977766 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.4       1.2   7.1e+03     147     160 ..      11      24 ..       3      25 .. 0.54
   2 ?   14.1  18.4   2.8e-06     0.017     122     292 ..     364     527 ..     324     538 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 1.2
                              MMPL 147 lievvtlvvilviL 160
                                       +i +v+++ +lviL
  gi|386002548|ref|YP_005920847.1|  11 MIFFVAVAAALVIL 24 
                                       44455555555554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.8e-06
                              MMPL 122 glkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllgle 198
                                       +++ve+ G++ ++a l d +++++ ++++++++ + ++    yr + +++ +++t   ++l+ l+l+++l+    l+
  gi|386002548|ref|YP_005920847.1| 364 PVNVEIIGSGQVTAALGDQFKKQVLIAGIIAILAVGLVIYYRYRDPRIVIPMVATSFSEVLMMLALAALLKWQ--LD 438
                                       57899********************999999999999999999999998888888888888888885544443..23 PP

                              MMPL 199 lstfvlgllvvlliavGtDYallLvsRyreelaagedree.aviravastgkvvtaaGltvaiamlgLvvarlpvla 274
                                       l+  +    ++ +i++G+D  ++++      l +g+      +   + s+ + ++aa++t ++aml L ++ +++++
  gi|386002548|ref|YP_005920847.1| 439 LAAIA---GIIAVIGTGVDHLVIITDE---LLYEGKMPSGkIYLARLSSAFGIIMAAAATTIVAMLPLFAMGFGAFK 509
                                       33333...345578******9998765...55555555440455669999*************************** PP

                              MMPL 275 qvGvaialGvlvdvlivl 292
                                       +++++   Gvl+ vli++
  gi|386002548|ref|YP_005920847.1| 510 SFALVTIAGVLIGVLIAR 527
                                       ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 3120.10
//
Query:       gi|386002549|ref|YP_005920848.1|  [L=297]
Description: SecD/SecF/SecDF export membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  101.9   8.7    2.7e-29  101.9   8.7    1.4  2  SecD_SecF        Protein export membrane protein
    3.7e-06   26.2   0.0    8.1e-06   25.2   0.0    1.6  1  Sec_GG           SecD/SecF GG Motif
      0.004   17.2   2.4      0.004   17.2   2.4    3.0  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.022   12.9  11.6      0.032   12.3  11.6    1.2  1  Patched          Patched family
        6.7    5.5  17.4      0.073   12.0   8.7    1.8  2  MMPL             MMPL family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.4       1.4     5e+03      82      96 ..      18      32 ..      15      36 .. 0.69
   2 !  101.9   8.7   7.6e-33   2.7e-29       7     187 ..     100     284 ..      94     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                                      --HHHHHHHHHHTTS CS
                         SecD_SecF 82 vdlatvaalLtiiGY 96
                                      ++la++a  L+i+G+
  gi|386002549|ref|YP_005920848.1| 18 ISLAVLAVALSILGF 32
                                      666777777777776 PP

  == domain 2  score: 101.9 bits;  conditional E-value: 7.6e-33
                                       --SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHH.HHHHHHHHHHHHHHHHHHHHHTT--- CS
                         SecD_SecF   7 kevdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrv.alaaiialvhDviitvgvlsllgiev 82 
                                       + +++++e  +++  gp +s +l+e+a   + +++++++++++l+F+ ++ al +i+a+++D++it++++ + g+++
  gi|386002549|ref|YP_005920848.1| 100 AMIEAEYEEPEIKYMGPVYSTRLQEQAKKYIPLSFLFMAVVIFLIFRTPFvALTVILAAFSDIMITAACMNIAGVKL 176
                                       4556689999*************************************98637888888******************* PP

                                       -HHHHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHH.HHHHHHHHHHHHHHHTTHH..HHHHHHHHHHHHTTT CS
                         SecD_SecF  83 dlatvaalLtiiGYSvndtvvvfdrvrenlrkkkratlke.iinlslnqtLtrtiltslt..tllvvvallllggds 156
                                       +l tvaalL++iGYSv++++++ +rv ++  +++++ +    +  ++++t   +i +     t+ ++v+  +   ++
  gi|386002549|ref|YP_005920848.1| 177 SLGTVAALLMLIGYSVDSNILLNNRVLKRKGRTEDKVVGAfRTGIAMTSTTFSAIFALFLvsTFSYLVSSSFTQINI 253
                                       ****************************96665555543314566777777778888654459999999999999** PP

                                       THHHHHHHHHHTSTTTTTHHHHHHHHHHHHH CS
                         SecD_SecF 157 lkdfalallvGlivgtyssifiasplllllk 187
                                       l d++++ll+Gl++g ++++ ++s+ l ++ 
  gi|386002549|ref|YP_005920848.1| 254 LFDISTVLLFGLLAGLMNTWVMNSNALRWYL 284
                                       *************************999985 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.3e-09   8.1e-06       6      25 ..      39      58 ..      37      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.3e-09
                                      C--EE-TTTS-EEEEEEEE- CS
                            Sec_GG  6 kGlNLGlDFtGGthielqfd 25
                                       ++NLG++FtGGt+i++ + 
  gi|386002549|ref|YP_005920848.1| 39 SPVNLGVEFTGGTIITVPVA 58
                                      699**************986 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.12   4.3e+02      72      95 ..      16      39 ..      13      43 .. 0.68
   2 !   17.2   2.4   1.1e-06     0.004      26      88 ..     122     190 ..     118     201 .. 0.74
   3 !    6.1   0.4     0.003        11      35      85 ..     214     272 ..     206     289 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                   Phage_holin_3_6 72 vaavllvlagvlalvglkklkkak 95
                                      va+ l+vla++l ++g   lk  +
  gi|386002549|ref|YP_005920848.1| 16 VAISLAVLAVALSILGFTYLKTGS 39
                                      666677777777777777776655 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.1e-06
                   Phage_holin_3_6  26 lkeeakragsgagllgaagvlallalllllval.alala.a.lwlaaliva...avllvlagvlalvgl 88 
                                       l+e+ak+ + +  l++a ++++++  +++ +++ ++a++ +   +a++ +a   + l  +a++l+l+g+
  gi|386002549|ref|YP_005920848.1| 122 LQEQAKKYIPLSFLFMAVVIFLIFRTPFVALTViLAAFSdImITAACMNIAgvkLSLGTVAALLMLIGY 190
                                       89***************************9999556666566333333344011555566677777776 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.003
                   Phage_holin_3_6  35 sgagllgaagvlallalllllvala...lala.a...lwlaali.vaavllvlagvlal 85 
                                       +ga   g+a+  + ++++++l+++    ++++       + + i + +++ +lag++  
  gi|386002549|ref|YP_005920848.1| 214 VGAFRTGIAMTSTTFSAIFALFLVStfsYLVSsSftqINILFDIsTVLLFGLLAGLMNT 272
                                       56666777777777777777777732333332223553334444134555555555544 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  11.6   8.8e-06     0.032     665     800 ..     132     270 ..     120     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-06
                           Patched 665 lallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsekd 741
                                       l++l m+vv +l+   ++++l ++l+  s  + ++  + + gv+L   ++++++m iG+svd       +  + ++ 
  gi|386002549|ref|YP_005920848.1| 132 LSFLFMAVVIFLIFRTPFVALTVILAAFSDIMITAACMNIAGVKLSLGTVAALLMLIGYSVDSNILLNNRVLKRKG- 207
                                       6899*************************9999*****************************99999999888888. PP

                           Patched 742 dakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvL.....vvvigllHgLl 800
                                        ++++vv a  + g  +     S i +++++ +    +   F +  +L     v+++gll gL+
  gi|386002549|ref|YP_005920848.1| 208 RTEDKVVGAFRT-GIAMTSTTFSAIFALFLVSTFSYLVSSSFTQINILfdistVLLFGLLAGLM 270
                                       9999*****986.888888888877776665544444444566554443333356666666665 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.4      0.31   1.1e+03     250     286 ..      17      53 ..      13      59 .. 0.67
   2 ?   12.0   8.7     2e-05     0.073     143     285 ..     124     266 ..     117     296 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.31
                              MMPL 250 vvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlv 286
                                       ++  a l va+++lg++ ++ ++  ++Gv    G ++
  gi|386002549|ref|YP_005920848.1|  17 AISLAVLAVALSILGFTYLKTGSPVNLGVEFTGGTII 53 
                                       5666667777777777777777777777766666555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2e-05
                              MMPL 143 rdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYa 219
                                       +++k+ + ++++  +v+ ++++r +  al ++l +  +++++ +      +++g++ls  +++ + ++li+ ++D +
  gi|386002549|ref|YP_005920848.1| 124 EQAKKYIPLSFLFMAVVIFLIFRTPFVALTVILAAFSDIMITAAC----MNIAGVKLSLGTVA-ALLMLIGYSVDSN 195
                                       667777888889999**************************9999....66777777776665.556789******* PP

                              MMPL 220 llLvsRyreelaagedreeavira....vastgkvvtaaGltvaiamlgL...vvarlpvlaqvGvaialGvl 285
                                       +lL  R   + ++ ed+  ++ r+      +t ++++a  l ++ ++  L   +++++++l  + +++  G+l
  gi|386002549|ref|YP_005920848.1| 196 ILLNNRVLKRKGRTEDKVVGAFRTgiamTSTTFSAIFA--LFLVSTFSYLvssSFTQINILFDISTVLLFGLL 266
                                       *******9999999999666665411102223333332..333333333311134444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1912.67
//
Query:       gi|386002550|ref|YP_005920849.1|  [L=442]
Description: 3-hexulose-6-phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-44  150.5   1.1    3.8e-44  150.5   1.1    2.1  3  RraA-like       Aldolase/RraA
    5.1e-21   75.3   5.4    1.3e-20   73.9   5.4    1.7  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    1.6e-06   27.7   0.2    4.7e-06   26.2   0.1    1.8  2  His_biosynth    Histidine biosynthesis protein
    3.7e-06   26.9   3.3    0.00042   20.3   0.2    3.3  3  ADH_zinc_N      Zinc-binding dehydrogenase
    2.3e-05   23.7   2.9    6.4e-05   22.2   1.6    2.1  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
      7e-05   22.5   2.7    0.00025   20.7   0.4    2.1  2  HMGL-like       HMGL-like
    0.00012   21.4   2.2    0.00035   19.9   0.2    2.6  3  TMP-TENI        Thiamine monophosphate synthase
    0.00023   20.6   3.6     0.0004   19.8   3.6    1.4  1  ThiG            Thiazole biosynthesis protein ThiG
    0.00037   20.0   1.9      0.038   13.4   0.1    2.5  2  PEP_mutase      Phosphoenolpyruvate phosphomutase
    0.00039   20.1   1.3     0.0013   18.3   0.9    1.8  2  Peripla_BP_4    Periplasmic binding protein domain
     0.0032   16.6   0.1     0.0066   15.6   0.1    1.4  1  Dus             Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.024   13.9   1.1      0.024   13.9   1.1    2.1  2  DHO_dh          Dihydroorotate dehydrogenase
      0.031   13.1   3.5       0.12   11.1   0.9    2.6  3  Trp_syntA       Tryptophan synthase alpha chain
      0.039   13.1   0.2       0.13   11.5   0.1    2.0  2  DUF561          Protein of unknown function (DUF561)
      0.054   13.3   2.0       0.22   11.3   0.5    2.4  2  DUF3983         Protein of unknown function (DUF3983)
      0.058   13.5   0.0       0.11   12.5   0.0    1.4  1  CryBP1          CryBP1 protein
       0.16   11.2   2.4       0.88    8.7   0.2    2.9  3  PEP_hydrolase   Phosphoenolpyruvate hydrolase-like
       0.22   10.5   8.0          2    7.3   8.0    2.3  1  IMPDH           IMP dehydrogenase / GMP reductase domain
       0.67    8.9   9.2       0.65    9.0   4.4    2.1  2  FMN_dh          FMN-dependent dehydrogenase
        1.4    8.3   3.7        9.6    5.5   3.6    2.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.8e+03      28      57 ..      96     124 ..      58     163 .. 0.69
   2 ?   -2.5   0.1       5.7   5.1e+03      46      62 ..     190     206 ..     168     231 .. 0.57
   3 !  150.5   1.1   4.2e-47   3.8e-44       1     150 []     251     397 ..     251     397 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                                       EEEEEEESS.BGHHHHHHHTS--TTEEEEE CS
                         RraA-like  28 pavTvkvveadnslvkealeeagpgdvlVv 57 
                                       ++v + +   d+s+v++al +a++  v V+
  gi|386002550|ref|YP_005920849.1|  96 NIVAILASS-DDSTVHDALRAARKYGVEVM 124
                                       344444444.66788888887777666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                                       HTS--TTEEEEEESTT. CS
                         RraA-like  46 leeagpgdvlVvdgggd 62 
                                        e++ +g+ +V+ gg+ 
  gi|386002550|ref|YP_005920849.1| 190 AEAIAAGASIVIVGGSV 206
                                       44445555555554444 PP

  == domain 3  score: 150.5 bits;  conditional E-value: 4.2e-47
                                       HHHHHHHCEE-SSBSTB.TT.EE.S.EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHH CS
                         RraA-like   1 tadvsDalkklggrsggirpler.s.fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGglla 75 
                                       t+++sDa++  +g  +++ p+++ + +vG+avTv+++e+d+++  ea++ agp+dv+V+ +g+  +  +++ Ggl +
  gi|386002550|ref|YP_005920849.1| 251 TPNISDAMH-RKGAMRDVLPINPgQkIVGRAVTVQTFEGDWAKSVEAIDLAGPEDVIVIYNGS--RYVSCW-GGLAT 323
                                       789******.444444799999965899********************************888..558999.***** PP

                                       HHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                         RraA-like  76 taakangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                       +++k +gvaGvv+dGavRD++e+re+++p+fa  +tp++ + k g ge+n ++++gg++v+pgdliv+D++Gvvv
  gi|386002550|ref|YP_005920849.1| 324 QSCKIKGVAGVVIDGAVRDLDEIREMGYPIFASSITPMAGEPK-GMGEINAEITCGGLSVRPGDLIVGDDSGVVV 397
                                       **************************************96666.******************************8 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   5.4   1.5e-23   1.3e-20       3     224 ..      19     218 ..      17     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.5e-23
                                       EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHH CS
                         OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqa 76 
                                       L++alD+ + ++++++a ++ +  +++++ +++l++++g     ++++++++k    ++i++D+K++D G+ + ++a
  gi|386002550|ref|YP_005920849.1|  19 LQVALDLLELDRAIQIALEAADgGADWIEAGTPLIKSEG-----MDAVRELKKALpaKKIVADMKTVDTGAMEVEMA 90 
                                       9**************************************.....**********889******************** PP

                                       HSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHH CS
                         OMPdecase  77 tagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkae 149
                                             +k++a+iv + a  ++++v  +++aa+k+g    ++++ + s++  ++ +  +  g+++ cv+   +++  
  gi|386002550|ref|YP_005920849.1|  91 ------AKAGANIVAILASSDDSTVHDALRAARKYG--VEVMVDLLGSPDPVTRSRemEalGVDYICVHVGIDQQ-- 157
                                       ......69***************************9..9**************99986379************99.. PP

                                       TTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 150 dfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                         +mG  a             +  +   +++   ++++g+    + ++i  aga+i+ivG ++ +++d  +  ++
  gi|386002550|ref|YP_005920849.1| 158 --MMGRRAIDF----------LDEILGHVKI-PVAVAGGIDAPSAAEAIA-AGASIVIVGGSVARSPDVTASGRK 218
                                       ..455554444..........4456667777.8999*****998888877.99***************9988776 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.8   1.7e+03      95     132 ..      42      81 ..      31     116 .. 0.63
   2 !   26.2   0.1   5.2e-09   4.7e-06      29     115 ..     131     216 ..     109     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                                       T-SEEEESHHHHH-..THHHHHHHHHHCGGGEEEEEEEEE CS
                      His_biosynth  95 gadkviigtaavkn..pelikelaekfgsqkivvaiDarr 132
                                       gad +  gt  +k+   + ++el ++ +++kiv+   + +
  gi|386002550|ref|YP_005920849.1|  42 GADWIEAGTPLIKSegMDAVRELKKALPAKKIVADMKTVD 81 
                                       5666666666665522455677777777766666554444 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.2e-09
                                       TSHHHHHHHHHHHT-SEEEE.EEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHH CS
                      His_biosynth  29 gdpvelakryeeegadelhv.vDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigta 104
                                        dpv   ++ e+ g+d+++v v +d  + gr + +d + ei+ +v+ipv v GGI   + ++e++ aga+ vi+g +
  gi|386002550|ref|YP_005920849.1| 131 PDPVTRSREMEALGVDYICVhVGIDQQMMGR-RAIDFLDEILGHVKIPVAVAGGIDAPS-AAEAIAAGASIVIVGGS 205
                                       6899999999999999998867899888666.5799********************999.99999************ PP

                                       HHH-THHHHHH CS
                      His_biosynth 105 avknpelikel 115
                                       ++++p++  + 
  gi|386002550|ref|YP_005920849.1| 206 VARSPDVTASG 216
                                       *****997654 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   4.7e-07   0.00042       3      70 ..      83     156 ..      82     169 .. 0.84
   2 ?    3.2   0.1     0.092        83      61      91 ..     176     207 ..     162     246 .. 0.74
   3 ?    2.5   0.0      0.15   1.4e+02       3      35 ..     319     351 ..     318     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHHHHTT-EEEE.EESSHH.....HHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHH CS
                        ADH_zinc_N   3 GlaavqlAkalGaevia.vdssee.....klelakklGadevinykea.dlverikeltggegvdvvfecvGsga 70 
                                       G + v++A+ +Ga+++a  +ss++      l+ a+k+G+++ ++     d+v r +e+    gvd++  +vG+ +
  gi|386002550|ref|YP_005920849.1|  83 GAMEVEMAAKAGANIVAiLASSDDstvhdALRAARKYGVEVMVDLLGSpDPVTRSREME-ALGVDYICVHVGIDQ 156
                                       78899********999954444445666677**************8888**********.89**********655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.092
                                       EEEESSCSHHHHHHHHHCEEEEEEEEECSC..T CS
                        ADH_zinc_N  61 vvfecvGsgatleaalkllkpgGrlvvvGg..g 91 
                                       + + ++G g   ++a ++++ g  +v+vGg   
  gi|386002550|ref|YP_005920849.1| 176 IPVAVAG-GIDAPSAAEAIAAGASIVIVGGsvA 207
                                       5555667.88889999*************9532 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTE CS
                        ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakklGa 35 
                                       G +a q +k+ G+  +++d+  + l+  +++G 
  gi|386002550|ref|YP_005920849.1| 319 GGLATQSCKIKGVAGVVIDGAVRDLDEIREMGY 351
                                       6789**************************995 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.6   7.1e-08   6.4e-05      43     183 ..      74     213 ..      43     223 .. 0.73
   2 ?   -0.0   0.0      0.47   4.3e+02     160     183 ..     324     347 ..     303     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.1e-08
                                       -TTS---BS-SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHHH....HHHHHHTT-SE CS
                              NanE  43 lpdsevritatlkdideLaaagadiialDatdrerpvtieelikkikekyqllmaDistlee....glvakklGvdi 115
                                       + d +   t  + +++  a+aga+i+a+ a + +   t+++ +++ ++ ++ +m D+    +    +   ++lGvd+
  gi|386002550|ref|YP_005920849.1|  74 VADMKTVDTGAM-EVEMAAKAGANIVAILASSDD--STVHDALRAARKYGVEVMVDLLGSPDpvtrSREMEALGVDY 147
                                       344554445554.8999***********999876..577899**************86544411114456789**** PP

                                       EE-TTTTSSTTS-..SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHH CS
                              NanE 116 vGttlsGytkeeek.aepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeia 183
                                       +   + G  ++       Df l + l + ++ v + G i++P   ++ai  G+  v+vG++++r  +++
  gi|386002550|ref|YP_005920849.1| 148 ICVHV-GIDQQMMGrRAIDF-LDEILGHVKIPVAVAGGIDAPSA-AEAIAAGASIVIVGGSVARSPDVT 213
                                       *8765.65555554244444.55667899*************85.578899*************98887 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.47
                                       HHHHTT--SEEEE-HHHH-HHHHH CS
                              NanE 160 kkaieiGvdavvvGsaitrleeia 183
                                       +++   Gv+ vv+ +a+  l+ei 
  gi|386002550|ref|YP_005920849.1| 324 QSCKIKGVAGVVIDGAVRDLDEIR 347
                                       445556777777777777776664 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   2.8e-07   0.00025      14     122 ..      20     127 ..      19     130 .. 0.86
   2 ?    1.8   0.1      0.16   1.5e+02      30     123 ..     138     230 ..     130     258 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                                       HTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT- CS
                         HMGL-like  14 qalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgaga 90 
                                       q + + l++++ ++ia + ++ g d iE+g p    + +++vr+++ka++ ++i+a ++ ++    + ve + +aga
  gi|386002550|ref|YP_005920849.1|  20 QVALDLLELDRAIQIALEAADGGADWIEAGTPLIKSEGMDAVRELKKALPAKKIVADMKTVDTGA-MEVEMAAKAGA 95 
                                       5566778999*******************************************999888877664.34555677*** PP

                                       SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHH CS
                         HMGL-like  91 krvhvfiatselhlkaklkkdreevakkaeea 122
                                       ++v +  +  +  ++  l+  r++ ++ ++++
  gi|386002550|ref|YP_005920849.1|  96 NIVAILASSDDSTVHDALRAARKYGVEVMVDL 127
                                       *******9999999999999998887777765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                                       HHHHHHT-SEE--....TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HH CS
                         HMGL-like  30 kaLdeagvdeiEv....gfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatsel 102
                                       ++++++gvd+i v       +++   ++++ +i  +vk++ + +    +    + a++    aga +v v  ++   
  gi|386002550|ref|YP_005920849.1| 138 REMEALGVDYICVhvgiDQQMMGRRAIDFLDEILGHVKIP-VAVAGGIDAPSAAEAIA----AGASIVIVGGSVARS 209
                                       5778999999998773334579999************999.55555555555555555....777777777666664 PP

                                       HHHHHHSSTHHHHHHHHHHHH CS
                         HMGL-like 103 hlkaklkkdreevakkaeeav 123
                                          +  ++ + e++++a+e v
  gi|386002550|ref|YP_005920849.1| 210 PDVTASGRKIREAMDRAHEGV 230
                                       455555555555555555544 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.3   1.2e+03     149     149 ..      74      74 ..      30     103 .. 0.44
   2 ?   -0.4   0.1      0.69   6.2e+02      13      61 ..      81     124 ..      71     128 .. 0.57
   3 !   19.9   0.2   3.9e-07   0.00035     110     177 ..     138     202 ..     129     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                          TMP-TENI 149 l 149
                                       +
  gi|386002550|ref|YP_005920849.1|  74 V 74 
                                       2 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.69
                          TMP-TENI  13 eellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpli 61 
                                       ++ +  ve a+k+g+++v + + + d++++ +      +++rkygv+++
  gi|386002550|ref|YP_005920849.1|  81 DTGAMEVEMAAKAGANIVAILASS-DDSTVHDAL----RAARKYGVEVM 124
                                       555667788888888887776655.444443333....33444555444 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 3.9e-07
                          TMP-TENI 110 eeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevleagadgvav 177
                                       +e+ealg+dYi+v   +     ++   + +++l e+  +++iPv + GGi++ ++ae+++aga+ v v
  gi|386002550|ref|YP_005920849.1| 138 REMEALGVDYICV---HVGIDQQMMGRRAIDFLDEILGHVKIPVAVAGGIDAPSAAEAIAAGASIVIV 202
                                       6788999999986...3356667778999**********************************99977 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   3.6   4.4e-07    0.0004     114     225 ..     111     224 ..      83     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                                       HHHHHHHHTT-EEEEEE..-S-HHH.HHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SH CS
                              ThiG 114 kaaeiLvkeGFevlpYv..sdDlvl.arrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigsp 187
                                       +a ++  k G ev++ +  s+D+v+ +r +e +G+  +          +G ++  +l  i+ ++k+Pv v  Gi  p
  gi|386002550|ref|YP_005920849.1| 111 DALRAARKYGVEVMVDLlgSPDPVTrSREMEALGVDYICVHVGIDQQMMGRRAIDFLDEILGHVKIPVAVAGGIDAP 187
                                       556666667777777542367777536778888888887666666667888999999999***************99 PP

                                       HHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 188 sdaaqamelGadavllntavaeakdpvamArafklave 225
                                       s aa+a+  Ga+ v++  +va++ d  a  r ++ a++
  gi|386002550|ref|YP_005920849.1| 188 S-AAEAIAAGASIVIVGGSVARSPDVTASGRKIREAMD 224
                                       8.789********************9998888877765 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   4.3e-05     0.038     163     228 ..      88     159 ..      73     171 .. 0.79
   2 !    5.9   0.1    0.0083       7.5     184     226 ..     167     209 ..     158     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                        PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaav.dvplnvvp.l..kgt..lsvaelaelGvarislgnhllraal 228
                                       ++ a+AGA+ v +   ++d+++++ ++a  +  + v++ l  +++  +  +e+++lGv  i ++  + ++++
  gi|386002550|ref|YP_005920849.1|  88 EMAAKAGANIVAILASSDDSTVHDALRAArKYGVEVMVdLlgSPDpvTRSREMEALGVDYICVHVGIDQQMM 159
                                       6789******************99999985655555553333333558999**********99988777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0083
                        PEP_mutase 184 iaelvaavdvplnvvplkgtlsvaelaelGvarislgnhllra 226
                                       + e++ +v++p+ v  + +++s ae  ++G++++++g +++r+
  gi|386002550|ref|YP_005920849.1| 167 LDEILGHVKIPVAVAGGIDAPSAAEAIAAGASIVIVGGSVARS 209
                                       56777888899999998778******************99986 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.9   1.5e-06    0.0013      43     149 ..      85     201 ..      55     230 .. 0.67
   2 ?   -0.7   0.0      0.94   8.4e+02     132     160 ..     251     284 ..     213     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHTT-SEEE.E--SSHHHHHHHHHHHHHTT-EEEE..............ESTTGCTTT-CEE...EEE CS
                      Peripla_BP_4  43 eQvaqiedaiakgvdgii.vapvdstalapalkkakaaGIpVva..............fdsddapsgerla...yvg 101
                                        +   +e a ++g++ ++ +a+ d +++ +al +a++ G+ V++              + ++    +   +   +vg
  gi|386002550|ref|YP_005920849.1|  85 ME---VEMAAKAGANIVAiLASSDDSTVHDALRAARKYGVEVMVdllgspdpvtrsreMEAL--GVD---YicvHVG 153
                                       44...455555689966537778889999***********9888776666664322222222..333...2556*** PP

                                       C-HHHHHHHHHHHHHHHCTTH.EEEEEETSCCCHHHHHHHHHHHHHHH CS
                      Peripla_BP_4 102 fdneaaGelqaeylaeklggkkgkvvilaGspgdpnaeeriegfrkvl 149
                                       +d++ +G+ + + l e lg+ k+ v++  G    ++ae+ ++g+  v+
  gi|386002550|ref|YP_005920849.1| 154 IDQQMMGRRAIDFLDEILGHVKIPVAVAGGIDAPSAAEAIAAGASIVI 201
                                       *******************99777777666666666666677776555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.94
                                       CCCHHHHHHHHHHHHHHHHH-TTCEECC.....E CS
                      Peripla_BP_4 132 spgdpnaeeriegfrkvlkeypgikiva.....e 160
                                       +p+ ++a  r  ++r+vl   pg kiv+     +
  gi|386002550|ref|YP_005920849.1| 251 TPNISDAMHRKGAMRDVLPINPGQKIVGravtvQ 284
                                       5666677778889999987788999999665321 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.3e-06    0.0066     145     266 ..     138     266 ..     129     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.3e-06
                                       HHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTT CS
                               Dus 145 kiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPw 221
                                       + +ea G++ + vH    +q+  g+  ++   e+  +v+ipv + G+I  +++a+ai +  Ga  v++g    + P 
  gi|386002550|ref|YP_005920849.1| 138 REMEALGVDYICVHVGIDQQMM-GRRAIDFLDEILGHVKIPVAVAGGIDAPSAAEAIAA--GASIVIVGGSVARSPD 211
                                       6789999*******98776665.6677999************************99976..5*************** PP

                                       HHHHHHHHHHSC------.HHHH........HHHHHH.HHHHCHHTTCCCCCCHH CS
                               Dus 222 lfaestavktgeaepapp.laee........aeivee.hlkkleeelgedkglrk 266
                                       + a+  ++++  ++ +   +++e        +ei++e   +++ + ++++ ++r+
  gi|386002550|ref|YP_005920849.1| 212 VTASGRKIREAMDRAHEGvIRRErksmdeemFEIFREvSTPNISDAMHRKGAMRD 266
                                       *997556666544444443444434444445555554234555555655555555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.34   3.1e+02     259     293 ..      35      70 ..      32     103 .. 0.78
   2 ?   13.9   1.1   2.6e-05     0.024     224     276 ..     157     206 ..     148     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.34
                                       HHHHHHHTECEEEESHHHHH.HGTCHHHHHHHHHHH CS
                            DHO_dh 259 alekieaGAslvqvytalvf.egpkiakkikkelee 293
                                       ale +  GA  +  +t l++ eg+ +++++kk l++
  gi|386002550|ref|YP_005920849.1|  35 ALEAADGGADWIEAGTPLIKsEGMDAVRELKKALPA 70 
                                       788888888888888888763577777777777754 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.6e-05
                                       GGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 224 kalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       + + ++a+ ++ e+  ++k  ip+   GGi +   a e i aGAs+v v+  +
  gi|386002550|ref|YP_005920849.1| 157 QMMGRRAIDFLDEILGHVK--IPVAVAGGIDA-PSAAEAIAAGASIVIVGGSV 206
                                       667789*************..*********86.5689**********999766 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.21   1.9e+02      22      47 ..      27      52 ..      18      59 .. 0.85
   2 ?   -0.9   0.0      0.65   5.8e+02     116     164 ..      69     117 ..      51     129 .. 0.69
   3 ?   11.1   0.9   0.00014      0.12     188     232 ..     165     209 ..     147     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.21
                                      -HHHHHHHHHHHHHCT-SSEEEE--- CS
                         Trp_syntA 22 dleqsleilkalekagadviElGlpf 47
                                      +l++ ++i  + +++gad iE G p 
  gi|386002550|ref|YP_005920849.1| 27 ELDRAIQIALEAADGGADWIEAGTPL 52
                                      5778889999999**********995 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.65
                                       EEEEEETTSBCCCHHHH.HHHHHHTT-EEEEEE-TTS-HHHHHHHHHH-- CS
                         Trp_syntA 116 vdglivpDlPleeaeel.veaakkkglelvflvapttsderlkevveqae 164
                                        +  iv+D+ + +   + ve+a k+g ++v ++a  ++d++++  +++a+
  gi|386002550|ref|YP_005920849.1|  69 PAKKIVADMKTVDTGAMeVEMAAKAGANIVAILAS-SDDSTVHDALRAAR 117
                                       44557788877776666357788888888888887.77777776666665 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00014
                                       HHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHH CS
                         Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkk 232
                                       +++ ++  + + Pvav  Gi +++ ++++a++a+ vivG  + + 
  gi|386002550|ref|YP_005920849.1| 165 DFLDEILGHVKIPVAVAGGIDAPSAAEAIAAGASIVIVGGSVARS 209
                                       567777788899***************************988775 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.13     180     225 ..     169     214 ..     128     229 .. 0.85
   2 ?   -3.3   0.0       4.3   3.9e+03     206     226 ..     329     349 ..     317     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                            DUF561 180 eiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeee 225
                                       ei  +v++Pv  a G+   ++  a+++gas + +g +v +  d ++
  gi|386002550|ref|YP_005920849.1| 169 EILGHVKIPVAVAGGIDAPSAAEAIAAGASIVIVGGSVARSPDVTA 214
                                       677899**************************99999998777665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                            DUF561 206 lgasGiGigsavsklndeeem 226
                                        g +G+ i  av+ l+++ em
  gi|386002550|ref|YP_005920849.1| 329 KGVAGVVIDGAVRDLDEIREM 349
                                       47889999999*999999998 PP

>> DUF3983  Protein of unknown function (DUF3983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.78     7e+02       3      11 ..     217     225 ..     216     230 .. 0.86
   2 ?   11.3   0.5   0.00025      0.22       9      18 ..     406     415 ..     404     417 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.78
                           DUF3983   3 RKvRKAIAR 11 
                                       RK+R A+ R
  gi|386002550|ref|YP_005920849.1| 217 RKIREAMDR 225
                                       9*****977 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
                           DUF3983   9 IARRAKdVEK 18 
                                       IARRAK+VEK
  gi|386002550|ref|YP_005920849.1| 406 IARRAKEVEK 415
                                       9********9 PP

>> CryBP1  CryBP1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.11      19      93 ..     296     375 ..     283     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            CryBP1  19 evdieeleelklifntdkleccld.kedeeciidnvgdievdvevlklvGaiey.....ilnatpavrgdkvgrGef 89 
                                       ++d    e++ +i+n  +   c     +++c+i++v+ + +d+ v  l    e          tp + g++ g Ge 
  gi|386002550|ref|YP_005920849.1| 296 AIDLAGPEDVIVIYNGSRYVSCWGgLATQSCKIKGVAGVVIDGAVRDLDEIREMgypifASSITP-MAGEPKGMGEI 371
                                       4588899********99988887626899****************88866555333632223356.89999999999 PP

                            CryBP1  90 diev 93 
                                       + e+
  gi|386002550|ref|YP_005920849.1| 372 NAEI 375
                                       9886 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.9   1.7e+03      25      43 ..      85     103 ..      60     106 .. 0.62
   2 ?    8.7   0.2   0.00098      0.88     161     229 ..     136     212 ..     126     223 .. 0.67
   3 ?    0.3   0.0      0.37   3.3e+02      32      46 ..     300     314 ..     270     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                     PEP_hydrolase  25 lsakaaeaggaDliliyns 43 
                                       +   +a+++ga+++ i+ s
  gi|386002550|ref|YP_005920849.1|  85 MEVEMAAKAGANIVAILAS 103
                                       5567777888888888776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00098
                     PEP_hydrolase 161 earamaeaGadvivahlGlttggsigaktalsleeavelvqeia.........daakevnpdvivlvhGGpiaeped 228
                                        +r+m + G+d i++h+G+ ++ ++g +    l+e   +v+  +         +aa+++     +++ GG +a+  d
  gi|386002550|ref|YP_005920849.1| 136 RSREMEALGVDYICVHVGIDQQ-MMGRRAIDFLDEILGHVKIPVavaggidapSAAEAIAAGASIVIVGGSVARSPD 211
                                       5799**************9865.678888877777776666433000111111445555566666666777766666 PP

                     PEP_hydrolase 229 a 229
                                       +
  gi|386002550|ref|YP_005920849.1| 212 V 212
                                       5 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.37
                     PEP_hydrolase  32 aggaDliliynsGrf 46 
                                       ag  D+i+iyn  r+
  gi|386002550|ref|YP_005920849.1| 300 AGPEDVIVIYNGSRY 314
                                       57789******9999 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.0    0.0023         2     195     254 ..     163     221 ..      53     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgevilieg 254
                                       A+    e+  + ++pv   GGi      + A+aaGa++v++G  +a+  +  ++   i++
  gi|386002550|ref|YP_005920849.1| 163 AIDFLDEILGHVKIPVAVAGGIDAP-SAAEAIAAGASIVIVGGSVARSPDVTASGRKIRE 221
                                       5555566777789999999999876.5689999999999999999987655444433333 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.073        66      80     156 ..      64     140 ..      52     149 .. 0.78
   2 ?    9.0   4.4   0.00073      0.65     252     303 ..     158     206 ..     136     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.073
                                       HHHHHHHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHH CS
                            FMN_dh  80 laraaakagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRerdl 156
                                       l +a  + +i+  + tv + ++e  +aa+ g  ++ +  ++d++++ + l+ a++ g++++v  +  p +  R r++
  gi|386002550|ref|YP_005920849.1|  64 LKKALPAKKIVADMKTVDTGAMEVEMAAKAGANIVAILASSDDSTVHDALRAARKYGVEVMVDLLGSPDPVTRSREM 140
                                       5566666777777778877777766666667999999999*******************999777777666666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00073
                                       TT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 252 dgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                            +id L ei  +v+  i+v v gGi   s ++ A+a GA++v++G  +
  gi|386002550|ref|YP_005920849.1| 158 MMGRRAIDFLDEILGHVK--IPVAVAGGIDAPS-AAEAIAAGASIVIVGGSV 206
                                       455679*********997..*********8876.89*************876 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.6     0.011       9.6     136     196 ..     150     205 ..      55     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                                       S-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 136 vePgfgGQkFipevlekikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsa 196
                                       v  g + Q      ++ + ++        +++ + v GG+++ +++++++aga ++++g  
  gi|386002550|ref|YP_005920849.1| 150 VHVGIDQQMMGRRAIDFLDEILGH-----VKIPVAVAGGIDAPSAAEAIAAGASIVIVGGS 205
                                       455555554444444444443333.....457899*******************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3134.65
//
Query:       gi|386002551|ref|YP_005920850.1|  [L=304]
Description: diaminopimelate epimerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-54  183.0   0.6    3.1e-31  108.1   0.0    2.1  2  DAP_epimerase  Diaminopimelate epimerase
  ------ inclusion threshold ------
       0.01   14.9   0.2      0.087   11.9   0.0    2.0  2  Pro_racemase   Proline racemase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   3.4e-35   3.1e-31       1     118 [.      27     148 ..      27     150 .. 0.95
   2 !   73.6   0.1   1.6e-24   1.4e-20       2     119 ..     175     285 ..     174     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 3.4e-35
                                       EEEECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvr 74 
                                       f+k +Gn+nd+v++d+ ++ +v       ++ + c+r++g+g+dgvlf  +s+ +d+++r f  dgseaemCGnGvr
  gi|386002551|ref|YP_005920850.1|  27 FTKLQGNGNDFVLIDEQDGVKVADplkGSFAVQCCHRNFGVGGDGVLFLGASEHADLRMRLFQPDGSEAEMCGNGVR 103
                                       7999***************77777666899*********************************************** PP

                                       HHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS..EEEEEE-- CS
                     DAP_epimerase  75 vfaaylreggletkkevtvetlgGeleievkddgek..vkvdmGka 118
                                       + a+y++++g++  ++++vetl+G +++ v+  g     +vdmG +
  gi|386002551|ref|YP_005920850.1| 104 CLAKYAWDSGMV-GESFEVETLAGIIPLMVRGIGGDfwARVDMGVP 148
                                       **********88.*********************999999***976 PP

  == domain 2  score: 73.6 bits;  conditional E-value: 1.6e-24
                                       EEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETT.TEEESTTHCC.HHHH CS
                     DAP_epimerase   2 akshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklryfnrd.gseaemCGnG.vrvf 76 
                                       a+++G+p++v++v+d+ +  ++e   ++ + +   +p++ +v+fv     + +++r+f+r+ ++e+ +CG+G v+ +
  gi|386002551|ref|YP_005920850.1| 175 AVNTGVPHAVIFVEDLLNLPLEE--VAPHIRRSSLFPEGANVNFVRI--GDAFQVRTFERGvEGETLSCGTGsVASA 247
                                       79***************988888..*********************6..999****7666439*********88888 PP

                                       HHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--E CS
                     DAP_epimerase  77 aaylreggletkkevtvetlgGeleievkddgekvkvdmGkas 119
                                       a++ r g     +ev vet+gG+l i+   d +   ++ G+a 
  gi|386002551|ref|YP_005920850.1| 248 AVARRMGM--VGDEVFVETRGGPLLITFDGDRA---YMDGPAA 285
                                       88777775..48****************99985...9999986 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.8e-06     0.087      59     122 ..      73     132 ..      67     153 .. 0.77
   2 ?    0.7   0.1     0.024   2.2e+02      80     101 ..     236     257 ..     231     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-06
                                       EE--SSTTSSEEEEEEESSSB-.SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEE CS
                      Pro_racemase  59 lvppkepdadlgvifletsgyl.pmcGsntigvvtvlletGlvevqepetklsletpaGlvevta 122
                                       l+   +++adl + +++++g    mcG+++ ++++ + ++G+v         ++et aG++   +
  gi|386002551|ref|YP_005920850.1|  73 LFLGASEHADLRMRLFQPDGSEaEMCGNGVRCLAKYAWDSGMVGESF-----EVETLAGIIPLMV 132
                                       566677899999999999997527*******************8553.....4577777766655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.024
                                       -SSTHHHHHHHHHHHHHTTSS- CS
                      Pro_racemase  80 lpmcGsntigvvtvlletGlve 101
                                       + +cG ++++ ++v+   G+v 
  gi|386002551|ref|YP_005920850.1| 236 TLSCGTGSVASAAVARRMGMVG 257
                                       5579999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 2143.01
//
Query:       gi|386002552|ref|YP_005920851.1|  [L=144]
Description: hypothetical protein Mhar_1871 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.55
# Mc/sec: 788.76
//
Query:       gi|386002553|ref|YP_005920852.1|  [L=476]
Description: Phosphoesterase, RecJ domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-19   68.4   0.9    8.1e-19   68.4   0.9    2.2  3  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.032   14.5   0.0      0.057   13.7   0.0    1.4  1  DHH       DHH family
       0.12   12.6   0.0       0.36   11.0   0.0    1.7  2  bPH_2     Bacterial PH domain
       0.21   11.4   0.3        8.1    6.3   0.0    2.3  2  RF3_C     Class II release factor RF3, C-terminal domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.6   7.1e+03      56      80 ..      16      41 ..       9      57 .. 0.60
   2 ?   -1.5   0.4       0.7   3.1e+03     100     114 ..     145     158 ..     142     178 .. 0.65
   3 !   68.4   0.9   1.8e-22   8.1e-19      40     138 .]     368     470 ..     336     470 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                      HHHHHHHHHTHGBT.TCEEEEEEEEC CS
                             DHHA1 56 lgiaadklksklkk.pvivfvakeeg 80
                                      l+ + ++  + + + +++v+++  + 
  gi|386002553|ref|YP_005920852.1| 16 LARISERAAESIIRqKEVVVASHVDA 41
                                      45555555565555566666665554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.7
                                       HHHHHHHTTCCEEEE CS
                             DHHA1 100 akeaaaklgggGGGH 114
                                       a++  a   g+GGG 
  gi|386002553|ref|YP_005920852.1| 145 ARA-LAGAVGSGGGN 158
                                       444.55666667776 PP

  == domain 3  score: 68.4 bits;  conditional E-value: 1.8e-22
                                       CEEEEEECHCCHHHHHHHHHHHHHHTHG.BT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCC CS
                             DHHA1  40 vkvlvaevgeewdagalgiaadklkskl.kk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklggg 110
                                       +  ++ ++ + +  +++gi+a++  ++   + p+i+f+a+e+g + kvsar ++d    g++++e++ +aa+++gg 
  gi|386002553|ref|YP_005920852.1| 368 HIQYFDAK-DRILDTIVGIVAGMSFQTAdRRkPIIAFAAAEDG-RLKVSARGTQDlvraGLNLAEAIFRAAEEVGGV 442
                                       33444444.45556689999999888777667***********.********************************* PP

                                       EEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1 111 GGGHdlAaGagipaekleealealeeai 138
                                       GGGH+ AaGa+ip+e   e+le+l++++
  gi|386002553|ref|YP_005920852.1| 443 GGGHNVAAGATIPPEARAEFLEFLDAIV 470
                                       ************************9875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.057       2      56 ..      33     115 ..      32     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                       EEEE-ECSSSHHHHHHHHHHHH.................................CECS--TCGGCGCCHHCCCSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan.................................llvDhneksqavegeakeeaed 45 
                                       +++    + D+D+++Sa  ++                                  +  D ++  qa++    e +  
  gi|386002553|ref|YP_005920852.1|  33 VVV--ASHVDADGLTSAGIISIaldragvdrktlffrqldlpaleeiadlgpdlvIFTDLGSGMQAEIL---EMGLS 104
                                       444..899********77777766889999999999999988888888888888889999999999976...***** PP

                                       EEEEE-S---S CS
                                       xxxxxxxxxxx RF
                               DHH  46 viiiDHHrlge 56 
                                        ++ DHHr++ 
  gi|386002553|ref|YP_005920852.1| 105 AVVADHHRPQG 115
                                       ********975 PP

>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.8   8.3e+03      47      78 ..      48      79 ..      47      80 .. 0.79
   2 ?   11.0   0.0   8.1e-05      0.36      21      71 ..     358     407 ..     357     410 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                             bPH_2 47 glgtivietaggsraevelplrsvpdaeelae 78
                                      g+ +i+++ ag +r+   ++ +++p  ee+a+
  gi|386002553|ref|YP_005920852.1| 48 GIISIALDRAGVDRKTLFFRQLDLPALEEIAD 79
                                      56678888888888888888888888888876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.1e-05
                             bPH_2  21 lrktldiplerIqavsleqsllqrrlgl.gtivietaggsraevelplrsvp 71 
                                        +++ ++pl++Iq  + ++ +l+ + g+ + ++++ta+  +  + +++   +
  gi|386002553|ref|YP_005920852.1| 358 VKEEGIVPLSHIQYFDAKDRILDTIVGIvAGMSFQTADRRK--PIIAFAAAE 407
                                       68899*********************************997..777776655 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.021        96      51      60 ..     165     174 ..     157     183 .. 0.77
   2 ?    6.3   0.0    0.0018       8.1      22      67 ..     347     397 ..     338     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                                       EEEEESSTHH CS
                             RF3_C  51 lilgaVGqLQ 60 
                                       +i+gaVG LQ
  gi|386002553|ref|YP_005920852.1| 165 AIVGAVGDLQ 174
                                       7********* PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0018
                                       GHHHHHHHHHHHHHCTS.....SEEEEET.TSS-EEEEESSTHHHHHHHHH CS
                             RF3_C  22 krkqlrkgleqLaeEGa.....vqvfkeeeageelilgaVGqLQfeVveeR 67 
                                       +r++l +gl+ ++eEG+     +q f  +++  ++i+g V  + f+    R
  gi|386002553|ref|YP_005920852.1| 347 HRQNLVNGLKLVKEEGIvplshIQYFDAKDRILDTIVGIVAGMSFQTADRR 397
                                       578899**********833333599999988899******99999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3039.12
//
Query:       gi|386002554|ref|YP_005920853.1|  [L=376]
Description: Transposase, IS605 OrfB family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-23   80.2   0.1    2.1e-22   78.8   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.2e-21   76.3   0.0    5.2e-21   75.1   0.0    1.6  1  OrfB_IS605      Probable transposase
    6.5e-17   60.7   2.9    1.4e-16   59.6   2.9    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
    0.00081   19.0   0.3     0.0013   18.3   0.3    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.001   18.5   0.3       0.28   10.7   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0019   18.2   0.4     0.0033   17.4   0.4    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.019   15.5   0.8        3.2    8.4   0.2    2.8  3  FeoB_Cyto       FeoB cytosolic helical domain
      0.022   14.3   0.7          1    9.0   0.1    3.0  3  RecR            RecR protein
      0.051   13.3   0.5        4.3    7.2   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
       0.09   12.4   0.3        1.1    9.0   0.1    2.6  2  GATA            GATA zinc finger


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 !   78.8   0.1   1.2e-25   2.1e-22       5      68 ..     295     358 ..     291     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.2e-25
                    OrfB_Zn_ribbon   5 keqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                           +yka+ +G kv++v+p++TS+ Cs+Cg k++++ls+r+++Cp+Cg+++drD nAaiNil+
  gi|386002554|ref|YP_005920853.1| 295 VITTSYKAESAGSKVVLVDPRNTSQLCSRCGLKVNKSLSDRVHECPQCGLVMDRDENAAINILR 358
                                       55568*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   2.9e-24   5.2e-21       3     117 ..     165     277 ..     163     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.9e-24
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve++++ +p+ k + +agiD+G++ +at+++++   ++ ++r+++s++k+lak++++l++  k++  + ka + ++
  gi|386002554|ref|YP_005920853.1| 165 SVEIDDPpKPPWKDGLMAGIDVGLESFATLSNGE---KIDNPRFFRSEEKALAKAQRRLSKYEKGTPERWKALKVVQ 238
                                       678777746677999*******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                         h+++++rr +++h+++++l+++   ++ e+L + nm 
  gi|386002554|ref|YP_005920853.1| 239 QTHERIANRRYDFAHQVSHNLVERFGLIAFEDLSITNML 277
                                       *************************************97 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 !   59.6   2.9   8.1e-20   1.4e-16       1      47 []       1      46 [.       1      46 [. 0.99

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 8.1e-20
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lka+kyr+yPT+ Q+ k+++t++ +R+ YN  La+rk+  e+egk
  gi|386002554|ref|YP_005920853.1|  1 M-LKAFKYRIYPTKAQRSKMEQTLELCRWTYNETLAYRKNSFEQEGK 46
                                      8.*******************************************98 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   7.4e-07    0.0013       2      30 ..     317     345 ..     316     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.4e-07
                     zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                       t++ C+rCG ++ ++  ++   Cp+Cgl 
  gi|386002554|ref|YP_005920853.1| 317 TSQLCSRCGLKVNKSLSDRVHECPQCGLV 345
                                       789************************85 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00016      0.28       8      30 ..     307     329 ..     305     335 .. 0.84
   2 !    5.6   0.1    0.0063        11      22      31 ..     339     348 ..     337     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                       CEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   8 stnlveDpergelvCtdCGlVle 30 
                                       s+ +++Dp ++  +C++CGl + 
  gi|386002554|ref|YP_005920853.1| 307 SKVVLVDPRNTSQLCSRCGLKVN 329
                                       444799**************986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0063
                                       ESSSSBEEEE CS
                      TF_Zn_Ribbon  22 CtdCGlVled 31 
                                       C+ CGlV++ 
  gi|386002554|ref|YP_005920853.1| 339 CPQCGLVMDR 348
                                       *******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   1.8e-06    0.0033      10      44 ..     316     352 ..     312     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + ++ Cs+Cg k+++  +   + Cp+Cg  +d +++ 
  gi|386002554|ref|YP_005920853.1| 316 NTSQLCSRCGLKVNKSLSdrVHECPQCGLVMDRDENA 352
                                       6789*********9877799********999999875 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.5   1.2e+04      47      67 ..      63      83 ..      53      91 .. 0.63
   2 ?    8.4   0.2    0.0018       3.2       6      36 ..     210     238 ..     209     242 .. 0.93
   3 ?    5.3   0.0     0.016        29      69      90 ..     239     260 ..     237     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.5
                         FeoB_Cyto 47 edpelraeveearkeleaelg 67
                                      ++pel++   ++ ++++++ +
  gi|386002554|ref|YP_005920853.1| 63 NKPELTEVFSQTLQNVQERVD 83
                                      446777777777777776654 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0018
                         FeoB_Cyto   6 EkaiekleellkesnlkaklppRwlAlklLe 36 
                                       Eka++k ++ l+++  ++  p+Rw Alk+ +
  gi|386002554|ref|YP_005920853.1| 210 EKALAKAQRRLSKY--EKGTPERWKALKVVQ 238
                                       89***********9..************865 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.016
                         FeoB_Cyto  69 dledvIvdarykfiegilrevv 90 
                                       ++ + I++ ry+f+++++   v
  gi|386002554|ref|YP_005920853.1| 239 QTHERIANRRYDFAHQVSHNLV 260
                                       67789************98766 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.56     1e+03       4      16 ..      70      82 ..      68      84 .. 0.86
   2 ?    1.8   0.1     0.099   1.8e+02      13      23 ..     315     325 ..     310     326 .. 0.75
   3 ?    9.0   0.1   0.00058         1      12      29 ..     332     349 ..     330     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.56
                                      HHHHHHHHHHHH- CS
                              RecR  4 eLaeaLqeakekv 16
                                       ++++Lq++ e+v
  gi|386002554|ref|YP_005920853.1| 70 VFSQTLQNVQERV 82
                                      599*******998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.099
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +++ + CsrCg
  gi|386002554|ref|YP_005920853.1| 315 RNTSQLCSRCG 325
                                       666789****8 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00058
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + ++v+ C++Cg + ++d
  gi|386002554|ref|YP_005920853.1| 332 LSDRVHECPQCGLVMDRD 349
                                       679*********998886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.024        44      11      20 ..     316     325 ..     315     328 .. 0.77
   2 ?    7.2   0.1    0.0024       4.3       7      20 ..     330     343 ..     329     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                     zinc_ribbon_2  11 dnakFCpyCG 20 
                                       ++++ C++CG
  gi|386002554|ref|YP_005920853.1| 316 NTSQLCSRCG 325
                                       5678899998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2   7 aelqdnakFCpyCG 20 
                                       + l+d++  Cp+CG
  gi|386002554|ref|YP_005920853.1| 330 KSLSDRVHECPQCG 343
                                       679999*******9 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00059       1.1      16      31 ..     314     329 ..     312     333 .. 0.86
   2 ?   -0.1   0.0      0.41   7.4e+02      21      28 ..     337     344 ..     334     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00059
                              GATA  16 pdgnksLCnaCGlyyk 31 
                                       p+++ +LC  CGl+  
  gi|386002554|ref|YP_005920853.1| 314 PRNTSQLCSRCGLKVN 329
                                       89999********865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                              GATA  21 sLCnaCGl 28 
                                       + C +CGl
  gi|386002554|ref|YP_005920853.1| 337 HECPQCGL 344
                                       57999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2370.26
//
Query:       gi|386002555|ref|YP_005920854.1|  [L=72]
Description: hypothetical protein Mhar_1874 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-27   93.8   0.6    5.9e-27   93.7   0.6    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.6   3.3e-31   5.9e-27       1      64 []       5      68 ..       5      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 3.3e-31
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE-S CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrle 64
                                      VyK++elvGsSp+SwedA+++Ai++A+k+lr++r++eV e+++++e+gki+ Y+++++v+F++e
  gi|386002555|ref|YP_005920854.1|  5 VYKIVELVGSSPTSWEDAAKSAIEKAAKSLRDLRVAEVRELDVKLEGGKIVAYRAKVRVSFKIE 68
                                      9*************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 498.46
//
Query:       gi|386002556|ref|YP_005920855.1|  [L=153]
Description: Thioredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-20   72.3   0.0    3.3e-20   72.0   0.0    1.1  1  Thioredoxin    Thioredoxin
    2.7e-06   27.8   0.1      1e-05   25.9   0.1    1.8  1  Thioredoxin_2  Thioredoxin-like domain
      4e-06   27.1   0.1    7.3e-05   23.0   0.1    2.1  2  Thioredoxin_4  Thioredoxin
    0.00012   22.1   0.0    0.00018   21.5   0.0    1.4  1  Thioredoxin_3  Thioredoxin domain
    0.00046   20.1   0.0    0.00058   19.8   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    0.00055   20.2   0.0     0.0017   18.6   0.0    1.8  2  Thioredoxin_8  Thioredoxin-like
     0.0015   18.4   0.0     0.0019   18.1   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0022   17.8   0.0     0.0033   17.3   0.0    1.2  1  DUF2847        Protein of unknown function (DUF2847)
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.02   14.6   0.0    1.2  1  Redoxin        Redoxin
      0.023   14.9   0.1      0.039   14.2   0.1    1.4  1  Glutaredoxin   Glutaredoxin
      0.066   13.4   0.0       0.09   13.0   0.0    1.2  1  Thioredoxin_7  Thioredoxin-like


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0     2e-23   3.3e-20       2     101 ..      30     129 ..      29     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2e-23
                                       EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78 
                                       +++ t+ ++ee v+ +  + lv F +p C+hC+++ P +e+ a+e+++kvk+++++v en+ ++++y+v + Pt+kl
  gi|386002556|ref|YP_005920855.1|  30 IVEATDISWEEVVERSVGPTLVMFHSPACPHCRMMMPSFEEYAREFEGKVKFVRINVMENSFTPERYGVMATPTFKL 106
                                       57788999********************************************************************* PP

                                       EETTEEEEEEESS-HHHHHHHHH CS
                       Thioredoxin  79 fkngkevkkyegarekeklaafl 101
                                       f  g+ v +++ga+  + l++++
  gi|386002556|ref|YP_005920855.1| 107 FCGGRPVLEMVGAAGPSLLKKMV 129
                                       *************9877777666 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   6.2e-09     1e-05       6     106 ..      47     126 ..      42     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.2e-09
                     Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                        p+lv+f++p Cp C+ ++  ++e+           ++ +++++ +++  +   +             ++ygv +tP
  gi|386002556|ref|YP_005920855.1|  47 GPTLVMFHSPACPHCRMMMPSFEEY---ARE-----FEGKVKFVRINVMENSFTP-------------ERYGVMATP 102
                                       79***********************...333.....6777888888888888887.............88******* PP

                     Thioredoxin_2  83 tivfldgkeivarlpGyvpaeele 106
                                       t+ ++ g ++v++++G+  +  l+
  gi|386002556|ref|YP_005920855.1| 103 TFKLFCGGRPVLEMVGAAGPSLLK 126
                                       *99777777999999998666555 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   4.5e-08   7.3e-05      16      58 ..      49      89 ..      45      94 .. 0.91
   2 ?    4.5   0.0     0.021        34     126     146 ..      86     106 ..      83     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                                      EEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..- CS
                     Thioredoxin_4 16 tvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpld 58
                                      t++ +++ +CphC+ +  + e+  +e+  +Gkvkf+ ++++ +
  gi|386002556|ref|YP_005920855.1| 49 TLVMFHSPACPHCRMMMPSFEEYAREF--EGKVKFVRINVMEN 89
                                      899************************..*******9998654 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHT--SS-EEEE CS
                     Thioredoxin_4 126 veaeskeakkagiestPtfii 146
                                       v+++s + ++ g+ +tPtf +
  gi|386002556|ref|YP_005920855.1|  86 VMENSFTPERYGVMATPTFKL 106
                                       89999999***********86 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.1e-07   0.00018       7      53 ..      55     104 ..      49     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                       SSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHH...HHCT-SSSSEE CS
                     Thioredoxin_3   7 gpgCakCpklekavkeaaaekgikaevekvtdfeei...ekygVmsvPal 53 
                                       +p C++C+ ++  ++e+a e + k+++++++ +e+    e+ygVm++P+ 
  gi|386002556|ref|YP_005920855.1|  55 SPACPHCRMMMPSFEEYAREFEGKVKFVRINVMENSftpERYGVMATPTF 104
                                       789*****************9777766666444433359*********85 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.6e-07   0.00058      25      67 ..      47      86 ..      23     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                                      TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES CS
                          AhpC-TSA 25 gkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv 67
                                      g p++++f++   cp+C+  +p++++++ ef+  +v+ + ++v
  gi|386002556|ref|YP_005920855.1| 47 G-PTLVMFHSP-ACPHCRMMMPSFEEYAREFE-GKVKFVRINV 86
                                      4.999999999.9******************9.4577776665 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0017       4      45 ..      49      88 ..      47     100 .. 0.92
   2 ?   -0.8   0.0       1.2     2e+03      75      86 ..      93     104 ..      85     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                      EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
                     Thioredoxin_8  4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldk 45
                                      +l++f++  cp+c+ ++p+  e+ ++++   kv++v +++ +
  gi|386002556|ref|YP_005920855.1| 49 TLVMFHSPACPHCRMMMPSFEEYAREFE--GKVKFVRINVME 88
                                      89*************************9..9*****999866 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       TT-S--TT-SEE CS
                     Thioredoxin_8  75 kkkynvkaiPtl 86 
                                        ++y+v+a Pt+
  gi|386002556|ref|YP_005920855.1|  93 PERYGVMATPTF 104
                                       579*******97 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.2e-06    0.0019     133     199 ..      50     107 ..      44     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                              TraF 133 LlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlv 199
                                       L++F+++ cp c++++p+ ++ a++++ +v++V ++   +  +p+         r+gv  tP++ l+
  gi|386002556|ref|YP_005920855.1|  50 LVMFHSPACPHCRMMMPSFEEYAREFEGKVKFVRINVMENSFTPE---------RYGVMATPTFKLF 107
                                       99*********************************9887765666.........9999999998775 PP

>> DUF2847  Protein of unknown function (DUF2847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     2e-06    0.0033       8      61 ..      37      89 ..      31      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                           DUF2847  8 qleeileeskekpvlifKhstrcsiSaealkelekeleeeeeevkvylldvies 61
                                       +ee++e+s   p+l++ hs +c+  ++++  +e++++e e +vk++ ++v+e+
  gi|386002556|ref|YP_005920855.1| 37 SWEEVVERSVG-PTLVMFHSPACPHCRMMMPSFEEYAREFEGKVKFVRINVMEN 89
                                      68999999998.999999*******************************99986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05      0.02      30      75 ..      49      91 ..      24     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      EEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                           Redoxin 30 kvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75
                                      ++v   + +  cP C+  +p +e++a++  e+ v++v +++ +++f
  gi|386002556|ref|YP_005920855.1| 49 TLV--MFHSPACPHCRMMMPSFEEYARE-FEGKVKFVRINVMENSF 91
                                      333..333446**************999.6888********99998 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.4e-05     0.039       2      35 ..      51      90 ..      50     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                      EEEESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSH CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelg......vkfeeidvdkde 35
                                      v+f +p Cp+C+++   ++e+       vkf  i+v++++
  gi|386002556|ref|YP_005920855.1| 51 VMFHSPACPHCRMMMPSFEEYArefegkVKFVRINVMENS 90
                                      89************99998888777788889999998885 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.5e-05      0.09      19      63 ..      48      89 ..      40     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                                      -EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S CS
                     Thioredoxin_7 19 pvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvter 63
                                      p lv+f++  c++C+ +   f++    ++ + +k+ ++r++v e+
  gi|386002556|ref|YP_005920855.1| 48 PTLVMFHSPACPHCRMMMPSFEEY--ARE-FEGKVKFVRINVMEN 89
                                      78*****************99877..777.999999999998443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 971.61
//
Query:       gi|386002557|ref|YP_005920856.1|  [L=112]
Description: hypothetical protein Mhar_1876 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   10.9   0.0       0.15   10.6   0.0    1.1  1  Adenylate_cycl  Adenylate cyclase, class-I


Domain annotation for each model (and alignments):
>> Adenylate_cycl  Adenylate cyclase, class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.6e-06      0.15     168     216 ..      52     100 ..      44     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.6e-06
                    Adenylate_cycl 168 sYrnLiqfarknkisesispedigiLtRkLyaaFeelpgkvellnpqis 216
                                        Yr L++  +++ +s+s s  d+ iL+R+L    +e ++ +  + +++ 
  gi|386002557|ref|YP_005920856.1|  52 TYRDLMEIVAEFLFSSSYSRRDLRILMRRLGVEDSEMQKNLIYMARSWH 100
                                       6*****************************9888888888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:01.15
# Mc/sec: 293.73
//
Query:       gi|386002558|ref|YP_005920857.1|  [L=920]
Description: alanyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-126  423.2   0.0   1.9e-126  422.8   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    5.9e-20   72.1   7.9    1.3e-19   70.9   7.9    1.6  1  DHHA1         DHHA1 domain
    2.9e-13   49.7   0.6    2.9e-13   49.7   0.6    1.9  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.18   11.2   0.5         33    3.9   0.1    3.1  3  DUF4926       Domain of unknown function (DUF4926)


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.8   0.0  4.2e-130  1.9e-126       1     549 [.      63     597 ..      63     600 .. 0.94

  Alignments for each domain:
  == domain 1  score: 422.8 bits;  conditional E-value: 4.2e-130
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e+re++l+fFe kgHt++k+++v++++++++++++A++a+f+p+++++e  p++++++ sQ+ciR++    Dl++VG
  gi|386002558|ref|YP_005920857.1|  63 EMREHYLSFFEGKGHTRIKRYPVIARWRDDIYLTIASIADFQPFITSGEVPPPANPLTVSQPCIRLD----DLDSVG 135
                                       89*****************************************************************....****** PP

                                       TSSS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGE CS
                      tRNA-synt_2c  78 ktarHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeeri 147
                                       + +rH+T FeM++++ f+     +Y+k+ +++++ ell   lg d+  ++++++++++  +a++  e ++g+ e ++
  gi|386002558|ref|YP_005920857.1| 136 RSGRHLTTFEMMAHHVFNtpeeeIYWKDRTVALCDELLL-GLGADPLAITYKESPWAGggNAGPSVEVMMGGLELAT 211
                                       ***************************************.9****************999***************** PP

                                       EEE-HHHHEEESSSS......EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST....TSHE CS
                      tRNA-synt_2c 148 lrfgekdnfwemgdt......gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree....dgtl 214
                                       l+f ++++    g++      +  ++++++++++g e++++++ + ++++d+++ +++ ++   ++ ++    ++  
  gi|386002558|ref|YP_005920857.1| 212 LVF-MDMKLSPRGEHlikgerYDRMDNYIVDTGYGLERFVWASRGSPTIYDAIFPDVVATITDLAGLQSsvsdEERA 287
                                       ***.99888877777777777*********************************99999998866665555559999 PP

                                       EEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT-- CS
                      tRNA-synt_2c 215 kpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvv 291
                                       ++L+ +++ +Gm + +  a L+++r +++++++++ +++ e i++          e+++++aDH+r+la++l+dG++
  gi|386002558|ref|YP_005920857.1| 288 RILASNARLAGMVDLED-ATLRDLRGRVAKEIGISAEKLDEIITP---------LERIYAVADHTRCLAYMLGDGII 354
                                       ************99987.57*************************.........799******************** PP

                                       SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHH CS
                      tRNA-synt_2c 292 psnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlkl 368
                                       psn+++gY++R+++Rr++r +k+L ++ + l++lv+++++ l+  y++l+ +  ++ ei+++Eeer+a+Tle+G++l
  gi|386002558|ref|YP_005920857.1| 355 PSNVKAGYLARLVIRRTLRQMKDLSIEVP-LSDLVSMQISRLD--YTDLDGRLGTIVEILDQEEERYAETLEKGRRL 428
                                       *****************************.************9..******************************** PP

                                       HHHHHHHCCC.CSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXX CS
                      tRNA-synt_2c 369 leelikklkk.kkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvea 444
                                       +++ ++   k ++++++++++ Lyd++G+P+++ +e a e+g++v+ ++++++++++ + + ++ ++++       +
  gi|386002558|ref|YP_005920857.1| 429 VKRIAEGRGKrGETIPLSEMISLYDSHGIPPEIAREAALEEGVEVELPDNFYSRVASTHIKAEKLEKEE-------S 498
                                       ******98777************************************************9955555544.......6 PP

                                       TTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEE CS
                      tRNA-synt_2c 445 lkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvq 521
                                         +l++t+  l+ye+            +++f+++v    +++vvLd+T fY+e+GGq gD+Gli+k ++ frv+dvq
  gi|386002558|ref|YP_005920857.1| 499 KIDLPETRR-LFYER----------PFERKFQARVLGLVDGAVVLDQTLFYPEGGGQPGDRGLIRKGSGAFRVVDVQ 564
                                       678999888.99999..........56799*********************************************** PP

                                       EETTEEEEEXSS.XSX.....XXTTSEEEEEEX CS
                      tRNA-synt_2c 522 kakgvvlhkgkleegk.....lkvgdkvkaevd 549
                                        a+ vvlh++  ee +     ++ gd +++evd
  gi|386002558|ref|YP_005920857.1| 565 AAGRVVLHRIAEEESEaaaaeVRPGDFIEGEVD 597
                                       ********9988765423333777888888877 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   7.9     3e-23   1.3e-19       4     133 ..     780     909 ..     777     912 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 3e-23
                                       HCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEEC CS
                             DHHA1   4 lneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeeg 80 
                                       + ee+k+l+ke ++lke+la+++ e+l ++a e+ + kv+va + e++d   l  aa+++    k+ v+++ +++eg
  gi|386002558|ref|YP_005920857.1| 780 FFEEWKDLKKEAARLKEELARAQVESLTSRAIEAGDLKVVVATL-ENADVEELIKAASMISG--KDYVAILGSEKEG 853
                                       789******************************99*********.*****************..9977777777777 PP

                                       TEEEEEEEESSH..SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHH CS
                             DHHA1  81 dkvkvsarskkd..gvdagelakeaaaklgggGGGH.dlAaGagipaekleealea 133
                                        k+   ++ ++   g+ age++k+a + +gggGGG+ + A+G+g  ae+l ealea
  gi|386002558|ref|YP_005920857.1| 854 AKIVAAVGKTGLarGLAAGEIVKAATKVVGGGGGGKpEIAQGGGPRAERLSEALEA 909
                                       4555555555449*****************************************96 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.9   1.3e+04      24      36 ..     487     499 ..     486     499 .. 0.87
   2 !   49.7   0.6   6.4e-17   2.9e-13       1      44 []     699     741 ..     699     741 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                                       GC-SEEEECCECC CS
                          tRNA_SAD  24 eIgafkilseesi 36 
                                       +I+a k+ +ees+
  gi|386002558|ref|YP_005920857.1| 487 HIKAEKLEKEESK 499
                                       7999999999986 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 6.4e-17
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +rvv++G+ +ve+C GtH+ nTg++g +k+l+ e++++g+ RI+
  gi|386002558|ref|YP_005920857.1| 699 IRVVQMGT-DVEACAGTHCTNTGMVGPIKVLRTERVQDGVERIE 741
                                       7******6.**********************************7 PP

>> DUF4926  Domain of unknown function (DUF4926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1    0.0074        33      31      48 ..       4      21 ..       2      23 .. 0.82
   2 ?    3.8   0.0    0.0082        37      19      34 ..     402     418 ..     386     419 .. 0.83
   3 ?   -2.2   0.0       0.6   2.7e+03      33      57 ..     470     494 ..     466     495 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0074
                           DUF4926 31 geaYeVEFsdddGeTlal 48
                                      ++aY  EF+ d+G T + 
  gi|386002558|ref|YP_005920857.1|  4 EDAYHLEFFKDEGFTRKT 21
                                      469**********99766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0082
                           DUF4926  19 GqvGTvVevy.eegeaY 34 
                                       G  GT+Ve++ +e+e Y
  gi|386002558|ref|YP_005920857.1| 402 GRLGTIVEILdQEEERY 418
                                       999*******6555665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.6
                           DUF4926  33 aYeVEFsdddGeTlalltLseeqle 57 
                                       + eVE  d+    +a+  +++e+le
  gi|386002558|ref|YP_005920857.1| 470 GVEVELPDNFYSRVASTHIKAEKLE 494
                                       6899999999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (920 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 5434.27
//
Query:       gi|386002559|ref|YP_005920858.1|  [L=92]
Description: hypothetical protein Mhar_1878 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   46.5   0.2    5.8e-12   46.2   0.2    1.1  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.2   3.2e-16   5.8e-12       3      76 .]      18      89 ..      17      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.2e-16
                            MJ1316  3 taqdvlnRirWdkeldkskfvvgyldR..fkgikevpleeiswiedflleeeegelaIPlHRiryikrkgevvWdR 76
                                      + +++ln i+W   ld+++ ++ +l+R  +k+ ++ +++eis  + f++ +e   ++IP+HRi +i+++g+ v++R
  gi|386002559|ref|YP_005920858.1| 18 HPREILNEIKWRG-LDMERCEIEVLHRgaPKDRITLKGSEISLGRSFFARGE---TMIPYHRILRIWYDGRTVYSR 89
                                      5689*******86.5****************************888555555...59*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 676.09
//
Query:       gi|386002560|ref|YP_005920859.1|  [L=344]
Description: hypothetical protein Mhar_1879 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-18   65.8   0.0    4.4e-18   65.3   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
    1.5e-10   40.9   0.0      3e-10   40.0   0.0    1.5  1  Dimerisation2    Dimerisation domain
    9.9e-08   32.0   0.0    1.5e-07   31.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.2e-06   28.3   0.0    5.9e-06   26.9   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
      2e-05   25.2   0.0    6.8e-05   23.5   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
    0.00012   21.7   0.0    0.00018   21.1   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00035   20.3   0.0    0.00052   19.8   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
  ------ inclusion threshold ------
      0.014   15.5   0.2       0.12   12.5   0.1    2.6  3  HTH_20           Helix-turn-helix domain
      0.041   13.4   0.1       0.07   12.6   0.1    1.3  1  Methyltransf_19  S-adenosyl methyltransferase
      0.058   14.4   0.0       0.17   12.9   0.0    1.9  1  Methyltransf_24  Methyltransferase domain
       0.13   12.6   4.5       0.69   10.2   1.7    2.9  2  TetR_C_11        Tetracyclin repressor-like, C-terminal domai
       0.62   10.6   4.1        2.1    8.8   4.1    1.9  1  DUF802           Domain of unknown function (DUF802)


Domain annotation for each model (and alignments):
>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0     3e-21   4.4e-18      60     184 ..     170     295 ..     135     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 3e-21
                                       GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS.-----TTEEEEES-TTTS---.--SEEEEE CS
                    Methyltransf_2  60 leglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl.sageeervefvgGdffkdslP.eaDaillk 134
                                         ++++++D+GGG G +  a+v+a+P+++++vfDlp V+eaA++++ +a+ e rve+v+Gdf +d++  e D+il +
  gi|386002560|ref|YP_005920859.1| 170 APSFRRMLDLGGGPGLISVAVVAAHPEMRGVVFDLPPVAEAAERFVrEAEMEGRVEVVAGDFSQDPIGgEYDLILAS 246
                                       5679******************************************999******************9777887777 PP

                                       SSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHH CS
                    Methyltransf_2 135 rvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdl 184
                                         l+  s ++   l+k+v +al++gG  +     l a+++++++ +l  l
  gi|386002560|ref|YP_005920859.1| 247 ASLY-SSRGRLDPLMKKVLDALNPGGVFVSLHDGLTAERTKPTAMKLGWL 295
                                       7777.5899*****************999888888888888887776544 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0     2e-13     3e-10      11      89 ..      27      98 ..      17      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2e-13
                     Dimerisation2 11 aSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLvsssp 89
                                       ++ L t  eLgvFd L e    s+ee+ae lg s++ t+++ld ++a++L  +e     ++lY+n+ +a ++L++++p
  gi|386002560|ref|YP_005920859.1| 27 KTRLLLTGIELGVFDHLGE--RRSSEELAEILGGSPETTRIFLDGLAAFDLVVKE-----EGLYQNSGIAANHLARDGP 98
                                      67889************99..8999***************************955.....47*************9987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0     1e-10   1.5e-07       8     164 ..     159     324 ..     147     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1e-10
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae...........kakkaqkdqf 71 
                                        +++++ +l++  ++  r Ld+G G G i   v ++++    +++Dl p+a +  +           +     +   
  gi|386002560|ref|YP_005920859.1| 159 MVARAIGELPE-APSFRRMLDLGGGPGlISVAVVAAHPEmRGVVFDLPPVAEAAERfvreaemegrvEVVAGDF--- 231
                                       34455555543.78888**********7766667777656*******998777654555554442222222222... PP

                   Methyltransf_23  72 deqeaaepqgkfdlIvlrevlehvp.dppellrqiatllkpgGylllseplaslkedrllldwlylvpag..rhisf 145
                                          + ++  g +dlI ++ +l++ +  +  l++++ + l+pgG+++ +  +  +++++     l + pa+  r    
  gi|386002560|ref|YP_005920859.1| 232 ---SQDPIGGEYDLILASASLYSSRgRLDPLMKKVLDALNPGGVFVSLHDGLTAERTKPTAMKLGWLPAEllRGEIA 305
                                       ...3346677***************7799***************998887666544444333345555543345567 PP

                   Methyltransf_23 146 fsarslkelleeaGlevve 164
                                       f++ +++  +++aG++ ++
  gi|386002560|ref|YP_005920859.1| 306 FDRGEIASSMKRAGFRSIS 324
                                       899************9765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     4e-09   5.9e-06       2      97 .]     177     271 ..     176     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4e-09
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       LdlG G+G ++ a+ ++ ++ + + +D+ + + eaa++ ++e+++  +ve+v gd+++ p   g++Dl+++s +l +
  gi|386002560|ref|YP_005920859.1| 177 LDLGGGPGLISVAVVAAHPEMRGVVFDLPPVA-EAAERFVREAEMegRVEVVAGDFSQDPIG-GEYDLILASASL-Y 250
                                       9************9999879999999997655.55666666655667***********9975.6*******8665.5 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                        s+ +l+ ++k++ ++L+pgG
  gi|386002560|ref|YP_005920859.1| 251 SSRGRLDPLMKKVLDALNPGG 271
                                       578899**************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.7   8.6e+03      75      95 ..     105     125 ..     102     126 .. 0.81
   2 !   23.5   0.0   4.6e-08   6.8e-05       1      99 []     177     273 ..     177     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.7
                   Methyltransf_12  75 vlhhlkdirevldnirklLkp 95 
                                       +l+++++i+++l+++ +l++ 
  gi|386002560|ref|YP_005920859.1| 105 LLEVWRQIESALEEMPRLVVE 125
                                       688999999999999888765 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 4.6e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+G G ++ a+ +++p+ + ++ D+ p a   a+e++ ++  +   +ve+ a d ++++ g+ +Dl++as  l 
  gi|386002560|ref|YP_005920859.1| 177 LDLGGGPGLISVAVVAAHPEMRGVVFDLPPVAE--AAERFVREA-EMEGRVEVVAGDFSQDPIGGEYDLILASASLY 250
                                       8****************9*********999988..888887766.4678999999999988888*********6666 PP

                   Methyltransf_12  78 hl.kdirevldnirklLkpgGrl 99 
                                            ++ +++++ ++L+pgG++
  gi|386002560|ref|YP_005920859.1| 251 SSrGRLDPLMKKVLDALNPGGVF 273
                                       6659999**************86 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.2e-07   0.00018      27     104 ..     167     246 ..     156     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                       CHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEE CS
                               MTS  27 lpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdl 100
                                       lp++   +++lDlG G G++++a+ +++pe++ +++d    A e+a++ +++ ++e  vevva d  ++   +++dl
  gi|386002560|ref|YP_005920859.1| 167 LPEApSFRRMLDLGGGPGLISVAVVAAHPEMRGVVFDLPPVA-EAAERFVREAEMEgrVEVVAGDFSQDPIGGEYDL 242
                                       555556688***********************99***99988.677777888888889***********999***** PP

                                       EEE- CS
                               MTS 101 ivsN 104
                                       i+  
  gi|386002560|ref|YP_005920859.1| 243 ILAS 246
                                       *975 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.5e-07   0.00052      16     146 ..     138     266 ..     132     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.5e-07
                   Methyltransf_16  16 sigrkvWdaavvlvkylekklake......lganelsklsvlELGsGtGlvGlavaellpeakviltDleellellk 86 
                                       s ++  W aav+  +y    +a+          ++ s +++l+LG G Gl+ +av ++ pe++ ++ Dl+ + e  +
  gi|386002560|ref|YP_005920859.1| 138 SSAADRWAAAVA--EYQRAGVAEMvaraigELPEAPSFRRMLDLGGGPGLISVAVVAAHPEMRGVVFDLPPVAEAAE 212
                                       667777888887..6655443333666666446788999****************9999****************** PP

                   Methyltransf_16  87 knielnknalkskvkvevLdWgeeleedllekeevDlilaaDcvYled.slelLvkvLkel 146
                                       + +  +   ++ +v+v + d  +    d +   e+Dlila+  +Y     l++L+k + + 
  gi|386002560|ref|YP_005920859.1| 213 RFVREA--EMEGRVEVVAGDFSQ----DPI-GGEYDLILASASLYSSRgRLDPLMKKVLDA 266
                                       ***995..5*****999988866....445.4569**********8652566666554444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.8e-05      0.12      12      54 ..      36      76 ..      27      81 .. 0.84
   2 ?   -2.7   0.0       4.4   6.5e+03      13      20 ..     110     127 ..     108     141 .. 0.60
   3 ?   -1.6   0.0       1.9   2.9e+03       9      20 ..     257     275 ..     256     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                       ++++++L  +e ++ +elae l++s+ t +  L+ L+  +Lv
  gi|386002560|ref|YP_005920859.1| 36 ELGVFDHL--GERRSSEELAEILGGSPETTRIFLDGLAAFDLV 76
                                      589*****..*****************9999888888888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.4
                                       HHHHHHH..........S CS
                            HTH_20  13 rrilraL..........a 20 
                                       r i++aL          +
  gi|386002560|ref|YP_005920859.1| 110 RQIESALeemprlvvegP 127
                                       678888844444444444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.9
                                       -HHHHHHHHHH.......S CS
                            HTH_20   9 hPvRrrilraL.......a 20 
                                       +P   ++l+aL       +
  gi|386002560|ref|YP_005920859.1| 257 DPLMKKVLDALnpggvfvS 275
                                       6777899999954444444 PP

>> Methyltransf_19  S-adenosyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.7e-05      0.07      35     133 ..     140     233 ..     132     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                   Methyltransf_19  35 aaeallkalpelvkvaranRaflrRavrvlaeeaGirqflDiGtGlPtednvHqvaqrvaPesRvvYvDnDPivlah 111
                                       aa++ ++a++e +++     ++++Ra+  l e    r +lD+G G P    v  va    Pe R v  D  P++ a 
  gi|386002560|ref|YP_005920859.1| 140 AADRWAAAVAEYQRAGV--AEMVARAIGELPEAPSFRRMLDLGGG-PGLISVAVVA--AHPEMRGVVFDLPPVAEAA 211
                                       44444444444443333..35789*******************98.7777776665..57******99*99998888 PP

                   Methyltransf_19 112 arallestpeGatdyieaDlrd 133
                                        r + e + eG+ +++++D+ +
  gi|386002560|ref|YP_005920859.1| 212 ERFVREAEMEGRVEVVAGDFSQ 233
                                       888888899**********865 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.17      12     102 ..     188     274 ..     133     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                   Methyltransf_24  12 lwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaaeavled. 87 
                                       +++++a  +   +r v++d  p ae+a++++rea+++ rv+++ +d+++       g++Dl++  ++   ++ + d 
  gi|386002560|ref|YP_005920859.1| 188 VAVVAAHPE---MRGVVFDLPPVAEAAERFVREAEMEGRVEVVAGDFSQD--PIG-GEYDLILASASLYSSRGRLDp 258
                                       444433333...444788888889999********************999..455.89*******998775444444 PP

                   Methyltransf_24  88 .leallprlapggvvl 102
                                        ++ +l+ l+pggv++
  gi|386002560|ref|YP_005920859.1| 259 lMKKVLDALNPGGVFV 274
                                       48999********876 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.24   3.5e+02      81     100 ..      17      36 ..       9      40 .. 0.86
   2 ?   10.2   1.7   0.00046      0.69      37      93 ..     133     187 ..     106     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                         TetR_C_11  81 lvldlllgpllyrllltgep 100
                                        + dll++p+  rllltg +
  gi|386002560|ref|YP_005920859.1|  17 ELYDLLIAPIKTRLLLTGIE 36 
                                       678*************9865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00046
                         TetR_C_11  37 eaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlllgpllyr 93 
                                       +a++   +a++  +++ e +ra ++++++rA+  Gel++    +++ldl  gp l  
  gi|386002560|ref|YP_005920859.1| 133 AAEATSSAADRWAAAVAEYQRAGVAEMVARAI--GELPEAPSFRRMLDLGGGPGLIS 187
                                       4555777899999***************9998..7****9999*****999987655 PP

>> DUF802  Domain of unknown function (DUF802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.1    0.0014       2.1       7      28 ..     135     156 ..     133     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                            DUF802   7 ataaavAaaWraALaeQqqaqe 28 
                                        +++++A+ W aA ae q+a+ 
  gi|386002560|ref|YP_005920859.1| 135 EATSSAADRWAAAVAEYQRAGV 156
                                       699****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2232.76
//
Query:       gi|386002561|ref|YP_005920860.1|  [L=148]
Description: hypothetical protein Mhar_1880 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-16   60.4   0.6    2.3e-16   60.1   0.1    1.4  2  PEMT        Phospholipid methyltransferase
    3.8e-05   24.0   0.0    5.7e-05   23.5   0.0    1.4  1  ICMT        Isoprenylcysteine carboxyl methyltransferase (ICM
    6.1e-05   22.7   0.0    7.8e-05   22.3   0.0    1.1  1  DUF1295     Protein of unknown function (DUF1295)
     0.0017   17.9   0.1     0.0022   17.5   0.1    1.1  1  NnrU        NnrU protein
     0.0026   17.1   1.3     0.0033   16.7   1.3    1.1  1  SLAC1       Voltage-dependent anion channel
  ------ inclusion threshold ------
      0.042   12.6   0.0      0.056   12.2   0.0    1.2  1  ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.8   1.1e+04      59      68 ..      12      21 ..       7      27 .. 0.47
   2 !   60.1   0.1   7.8e-20   2.3e-16       4     106 .]      37     137 ..      35     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                              PEMT 59 stlgflGlaL 68
                                        l +l +aL
  gi|386002561|ref|YP_005920860.1| 12 AALLVLSAAL 21
                                      3333333333 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 7.8e-20
                              PEMT   4 ilGlllialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllal 80 
                                       ++G+lli lg++l+l++ + +++ +t++     e  ++lv sG++r++++P+y+g+ +++lG a ++gs+a++ + l
  gi|386002561|ref|YP_005920860.1|  37 FVGFLLIGLGVILNLWADSLFKRRKTTVKPR--EMPTALVISGPFRISRHPMYLGMAAILLGEAVVFGSLASFSFPL 111
                                       57*************************9997..6667**************************************** PP

                              PEMT  81 lvllvylialkfvEephlakiYgkre 106
                                       +++ ++ ++ ++ Ee++l++ +g+++
  gi|386002561|ref|YP_005920860.1| 112 IFAGLMEALFIRREEEMLEEAFGEEY 137
                                       **9999999999***********976 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.9e-08   5.7e-05      32      93 ..      70     130 ..      39     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                              ICMT  32 dhklvksglykylrHPnYllfvilelatllLlcnakltalvllalvalllf..vRikeEekaLa 93 
                                        + lv sg++++ rHP Yl+  ++ l+  ++++    +a + ++l  + l+    i+ Ee++L 
  gi|386002561|ref|YP_005920860.1|  70 PTALVISGPFRISRHPMYLGMAAILLG-EAVVFGS--LASFSFPLIFAGLMeaLFIRREEEMLE 130
                                       467999**************5555555.5555555..577777777777765667888888875 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.6e-08   7.8e-05     100     234 ..      14     143 ..       7     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.6e-08
                           DUF1295 100 lvalpvllaaa.skeeqalkaldviglalwlvgivlealaDqQlsafkkd..pankgk.vldsGLwrysRHPNYfge 172
                                       l++l+  l  + + ++ a   ++++g  l+ +g++l+  aD   ++ k++  p+     ++ sG +r sRHP Y+g 
  gi|386002561|ref|YP_005920860.1|  14 LLVLSAALHYSyPTRQVADPPWAFVGFLLIGLGVILNLWADSLFKRRKTTvkPREMPTaLVISGPFRISRHPMYLGM 90 
                                       444444333330223334478********************977776665115544445999*************** PP

                           DUF1295 173 aliWwglflialealeglealaiagpllltlllvfvsgipllEkkalkkykdkeeyreYqkk 234
                                       a i +g  ++ + +l++ ++ +i++ l+  l++      +  E++  + ++  eey  Y+++
  gi|386002561|ref|YP_005920860.1|  91 AAILLGEAVV-FGSLASFSFPLIFAGLMEALFI------RREEEMLEEAFG--EEYLDYRRR 143
                                       **99997665.4455666788888877766654......333434444444..666666655 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.4e-07    0.0022      44     155 ..      11     124 ..       9     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.4e-07
                              NnrU  44 lglvlliigfgaarye.vllWeppawlrhlalllmlvafillaaallpgnplsvglka...dlaetgivritrHPml 116
                                        ++ l++ +++++ y   ++ +pp +     l+   v + l+a +l++ +++ v  ++    l   g +ri rHPm 
  gi|386002561|ref|YP_005920860.1|  11 FAALLVLSAALHYSYPtRQVADPPWAFVGFLLIGLGVILNLWADSLFKRRKTTVKPREmptALVISGPFRISRHPMY 87 
                                       56677778888888886666666666666666666677778999******9999888888888889*********** PP

                              NnrU 117 lgvaiWAlaHllanGdlasvllfgglllwalvgviaidr 155
                                       lg+a   l+  ++ G+las+  +  l++  l++ ++i+r
  gi|386002561|ref|YP_005920860.1|  88 LGMAAILLGEAVVFGSLASF--SFPLIFAGLMEALFIRR 124
                                       ****9999999999999986..34444444555555544 PP

>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.3   1.1e-06    0.0033     142     231 ..      10     101 ..       7     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                             SLAC1 142 vvgllvvallgallaesqnpslqll..gilvvslllwglGlllalvlfvlylyrlithklppaelrptlfiplGplg 216
                                       +++ l+v +++ ++     p +q++  ++++v++ll+glG++l l+  +l+  r  t    +++ +pt  +  Gp+ 
  gi|386002561|ref|YP_005920860.1|  10 IFAALLVLSAALHY---SYPTRQVAdpPWAFVGFLLIGLGVILNLWADSLFKRRKTTV---KPREMPTALVISGPFR 80 
                                       44555555555444...33444455789**************************8887...45679**********7 PP

                             SLAC1 217 q......galallllgkaapk 231
                                       +       ++a++llg+a+  
  gi|386002561|ref|YP_005920860.1|  81 IsrhpmyLGMAAILLGEAVVF 101
                                       766666666666678777744 PP

>> ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05     0.056     349     424 ..      71     145 ..      55     148 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                        ERG4_ERG24 349 skLlvsGWyglarkinYlgDwlqslswsLatgfqsvlpyfyvlyFlvlLvhR.elRDeekCkkkYGedweeYkkkvp 424
                                       + L++sG ++++r++ Ylg   + l  +  + f s+ ++ ++l F+ l+      R+ee  ++ +Ge++  Y+++v+
  gi|386002561|ref|YP_005920860.1|  71 TALVISGPFRISRHPMYLGMAAILLGEA--VVFGSLASFSFPLIFAGLMEALfIRREEEMLEEAFGEEYLDYRRRVR 145
                                       689****************776666655..567788888899999988755414567888999***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 981.12
//
Query:       gi|386002562|ref|YP_005920861.1|  [L=146]
Description: hypothetical protein Mhar_1881 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-20   71.6   0.3    8.5e-20   71.2   0.3    1.1  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.3   4.7e-24   8.5e-20      14     107 ..      49     136 ..      34     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 4.7e-24
                               LTD  14 medgagnnanefvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngskasssavwn 89 
                                                 e+ve+ N +++a dL+gw+l+d++++ ytfp+g  +l  g +v+v++g g ++a++ + + +s++wn
  gi|386002562|ref|YP_005920861.1|  49 SWVD------EWVEISNLGEAAQDLTGWTLKDEQNHtYTFPEGF-VLMEGVSVLVHTGVGDDTATDLYMDLASPIWN 118
                                       3333......*********************************9.***************99*****9888****** PP

                               LTD  90 nggdavaLydasgevvds 107
                                       nggd ++L+d++g+v+++
  gi|386002562|ref|YP_005920861.1| 119 NGGDVATLLDPDGNVIST 136
                                       ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1013.52
//
Query:       gi|386002563|ref|YP_005920862.1|  [L=138]
Description: Competence-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-15   56.6   0.1    3.6e-15   56.3   0.1    1.1  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1     2e-19   3.6e-15      17     108 ..      48     134 ..      34     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2e-19
                               LTD  17 gagnnan.efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngskasssavwnng 91 
                                             + e+ve++N++ ++ d + w+led++++ y fp+g  +l +g+ v v++g g+++ ++ ++++ ++vw+++
  gi|386002563|ref|YP_005920862.1|  48 D-----DdEWVEVVNPGMASQDFTFWTLEDENNNtYLFPEGF-VLLPGAAVKVHTGMGNATETDLYWGRDDLVWDDE 118
                                       2.....23************************99*******9.*******************************984 PP

                               LTD  92 gdava.Lydasgevvdsv 108
                                         +va L++a+ge+v+++
  gi|386002563|ref|YP_005920862.1| 119 --EVAtLKNAAGEIVARY 134
                                       ..5555*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 812.04
//
Query:       gi|386002564|ref|YP_005920863.1|  [L=727]
Description: Cytochrome c class I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-36  122.7  18.6    1.1e-05   25.1   0.0    8.9  9  PQQ       PQQ enzyme repeat
    3.2e-34  118.6   7.0    1.4e-15   57.5   0.5    4.5  4  PQQ_2     PQQ-like domain
    5.9e-25   87.9   0.0    9.2e-25   87.3   0.0    1.3  1  DOMON     DOMON domain
    2.9e-12   46.7  46.3     0.0065   16.9   0.0   10.4  9  PQQ_3     PQQ-like domain
  ------ inclusion threshold ------
      0.042   13.8   0.0      0.084   12.8   0.0    1.5  2  EB_dh     Ethylbenzene dehydrogenase
       0.24   11.3   2.0        9.4    6.2   0.0    3.9  5  DUF4905   Domain of unknown function (DUF4905)


Domain annotation for each model (and alignments):
>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   4.2e+03      22      30 ..      73      81 ..      72      82 .. 0.82
   2 !   17.3   0.0   1.1e-06    0.0032       1      25 [.      97     121 ..      97     131 .. 0.93
   3 !   21.9   0.1   3.7e-08   0.00011       1      29 [.     140     168 ..     140     171 .. 0.93
   4 !   23.6   0.1   1.1e-08   3.4e-05       7      34 ..     202     229 ..     195     233 .. 0.81
   5 ?   -0.2   0.0      0.39   1.2e+03      14      34 ..     246     266 ..     246     268 .. 0.82
   6 !    9.4   0.0   0.00034         1      12      32 ..     286     306 ..     282     309 .. 0.86
   7 !   15.7   0.1   3.5e-06      0.01       4      25 ..     331     353 ..     329     356 .. 0.83
   8 !   14.4   0.1   8.8e-06     0.026       9      24 ..     421     436 ..     419     438 .. 0.92
   9 !   25.1   0.0   3.7e-09   1.1e-05       2      37 ..     454     489 ..     453     490 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                                      EEEEEESSS CS
                               PQQ 22 vlWrfktgg 30
                                      v+W+f+++g
  gi|386002564|ref|YP_005920863.1| 73 VVWSFPIPG 81
                                      799999876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.1e-06
                                       TEEEEEETTSEEEEEETTTCCEEEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWr 25 
                                       +vvy  +   +++AlD++TG+ +W+
  gi|386002564|ref|YP_005920863.1|  97 DVVYFQDLRCNVFALDLETGDPIWS 121
                                       689999999***************7 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 3.7e-08
                                       TEEEEEETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktg 29 
                                       g+v+++ + +++ AlDa TG+++W+++++
  gi|386002564|ref|YP_005920863.1| 140 GKVFVAKDLYNVTALDAGTGEEVWTTRLS 168
                                       79***********************9986 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 1.1e-08
                                       ETTSEEEEEETTTCCEEEEEESSSCGSS CS
                               PQQ   7 sadGylyAlDadTGkvlWrfktggpvls 34 
                                          G++ AlDa+TG+++W+f t++ ++ 
  gi|386002564|ref|YP_005920863.1| 202 GGIGVISALDAETGDIVWEFSTVDSPDL 229
                                       55699*****************998875 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.39
                                       EEETTTCCEEEEEESSSCGSS CS
                               PQQ  14 AlDadTGkvlWrfktggpvls 34 
                                       A+D++TG   W + +++p  +
  gi|386002564|ref|YP_005920863.1| 246 AVDVETGITFWGTGNPAPFPG 266
                                       89*****99998888877665 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.00034
                                       EEEEETTTCCEEEEEESSSCG CS
                               PQQ  12 lyAlDadTGkvlWrfktggpv 32 
                                       l+AlD +TG+++W +++ +++
  gi|386002564|ref|YP_005920863.1| 286 LVALDHATGDMIWYHQVLPHD 306
                                       89***********99987776 PP

  == domain 7  score: 15.7 bits;  conditional E-value: 3.5e-06
                                       EEE.ETTSEEEEEETTTCCEEEE CS
                               PQQ   4 ylg.sadGylyAlDadTGkvlWr 25 
                                       ++g  + G++yA+D+++G++lW+
  gi|386002564|ref|YP_005920863.1| 331 VYGaGKMGKVYAFDRTSGELLWS 353
                                       44447789**************8 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 8.8e-06
                                       TSEEEEEETTTCCEEE CS
                               PQQ   9 dGylyAlDadTGkvlW 24 
                                        G l+A+Da+TGk+lW
  gi|386002564|ref|YP_005920863.1| 421 TGELVAIDASTGKILW 436
                                       599************* PP

  == domain 9  score: 25.1 bits;  conditional E-value: 3.7e-09
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                        v+++ +dG++ A+ a+TG+++W+ ++++ ++++p+
  gi|386002564|ref|YP_005920863.1| 454 LVFAAEYDGTIHAFRAETGEEVWEMRAPAGINGWPA 489
                                       69999*****************************97 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.5e-05     0.044     115     148 ..      89     122 ..      69     129 .. 0.88
   2 !   39.2   0.6   1.9e-13   5.5e-10      28     104 ..     131     223 ..     126     233 .. 0.85
   3 !   21.0   0.1   6.7e-08    0.0002       4      62 ..     285     354 ..     245     359 .. 0.85
   4 !   57.5   0.5   4.7e-19   1.4e-15       1     136 [.     336     509 ..     336     522 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                             PQQ_2 115 saspavagdtvvvgessgklvaldpkdGkvlWer 148
                                       ++ p+++gd+v++++ + ++ ald+++G+++W+r
  gi|386002564|ref|YP_005920863.1|  89 ASNPIIVGDVVYFQDLRCNVFALDLETGDPIWSR 122
                                       6789999*************************98 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.9e-13
                             PQQ_2  28 gvsravlsggtlfvatgggrlvaldaatGkvlWettl.egpvvga...plvaegrvvvva..........sdg..ql 88 
                                       g++++ ++ g++fva +  +++alda tG+++W+t+l e+ + g+   p v  g v+v +          ++g  ++
  gi|386002564|ref|YP_005920863.1| 131 GPNGPAVGWGKVFVAKDLYNVTALDAGTGEEVWTTRLsEVATTGIdiqPSVYAGLVYVSTvpgtgdvfyaPGGigVI 207
                                       777888899****************************65555555899************99999999885556699 PP

                             PQQ_2  89 ialdaedGkrlWstqq 104
                                       +aldae+G+ +W++  
  gi|386002564|ref|YP_005920863.1| 208 SALDAETGDIVWEFST 223
                                       99***********544 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 6.7e-08
                             PQQ_2   4 vvsaldaatGaelWrvdlar...........plgggvsravlsggtlfvatgggrlvaldaatGkvlWet 62 
                                       +++ald atG  +W   + +           p+ ++++ +  s+++++ a+++g+++a+d+++G++lW++
  gi|386002564|ref|YP_005920863.1| 285 SLVALDHATGDMIWYHQVLPhdlfdhdfqisPILAERDSGGRSQKVVYGAGKMGKVYAFDRTSGELLWSA 354
                                       56799*9*******995544445555666665888888888899999999******************86 PP

  == domain 4  score: 57.5 bits;  conditional E-value: 4.7e-19
                             PQQ_2   1 degvvsaldaatGaelWrvdlar...................p........................lgggvsravl 34 
                                       ++g v+a+d+++G++lW+  ++r                   +                         ++ +  ++l
  gi|386002564|ref|YP_005920863.1| 336 KMGKVYAFDRTSGELLWSAVVGRydeaaqldvlpegttriypGvlggvetpmaysdgvlyvpvvnlfTDWTP--TSL 410
                                       5899***************55555555567667666666665144444444555555556666666666666..667 PP

                             PQQ_2  35 sggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepae 111
                                       + +t+   +g+g+lva+da+tGk+lW +++e  ++g  +v ++ v+++  dg++ a+ ae+G+++W+  ++      
  gi|386002564|ref|YP_005920863.1| 411 DTSTIDFNNGTGELVAIDASTGKILWIRSFETMALGGATVINDLVFAAEYDGTIHAFRAETGEEVWE-MRAP----- 481
                                       777777777*********************99999999*****************************.4444..... PP

                             PQQ_2 112 lrssaspavagdtvvvges...sgklva 136
                                       ++ ++ pavag+t+v +     + klva
  gi|386002564|ref|YP_005920863.1| 482 AGINGWPAVAGETIVWPAGvgaDPKLVA 509
                                       7788999999999887655444555555 PP

>> DOMON  DOMON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   3.1e-28   9.2e-25       3     124 ..     586     704 ..     584     705 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 3.1e-28
                             DOMON   3 geykvswkvdgdgdeiefelsgkvntngyvaiGfsddgkMsnadvvvgwvdngrvyvqdyystggkgapriddt..g 77 
                                       g+y vsw+ d  g+++++ l g+++  g+vaiGf +++ M++ad+v+gwv++g ++v d ystg +g  ++d++  g
  gi|386002564|ref|YP_005920863.1| 586 GRYVVSWRND--GETLYMGLAGQAE--GFVAIGFEPTQAMKDADMVMGWVSGGEATVLDLYSTGVYGPHPPDEElgG 658
                                       689****888..*********9995..****************************************6667766*** PP

                             DOMON  78 sqditllsgseengvttlkfrRkldtcdpkqdnkidldttvyviwaa 124
                                       ++di +  g+e +g t ++f+R+ dt+d+  d+++ +++tv++iw +
  gi|386002564|ref|YP_005920863.1| 659 TDDILSFGGREADGWTVIEFERRMDTGDR-FDQAFRPGETVNIIWSI 704
                                       *****************************.***************86 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.4e-06     0.016       3      40 .]      73     115 ..      72     115 .. 0.84
   2 ?    2.4   0.8     0.082   2.5e+02       1      40 []     116     158 ..     116     158 .. 0.78
   3 !   12.9   3.0   3.9e-05      0.12       1      40 []     159     214 ..     159     214 .. 0.68
   4 ?    0.1   1.3      0.41   1.2e+03       1      19 [.     215     247 ..     215     261 .. 0.61
   5 ?    5.2   0.0      0.01        31      23      39 ..     330     346 ..     315     347 .. 0.81
   6 !    7.5   3.4     0.002       6.1       2      40 .]     349     431 ..     348     431 .. 0.70
   7 !   16.9   0.0   2.2e-06    0.0065       1      40 []     432     471 ..     432     471 .. 0.93
   8 !    6.9   0.6     0.003       8.9       1      36 [.     472     510 ..     472     513 .. 0.79
   9 ?   -3.6   0.0         6   1.8e+04      20      27 ..     595     602 ..     588     606 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-06
                             PQQ_3   3 vlWsvqlpg.pvnssp....avdgglvyvgtgdGtlyAlDaet 40 
                                       v+Ws+++pg  +++++     ++g++vy+ +   +++AlD et
  gi|386002564|ref|YP_005920863.1|  73 VVWSFPIPGiGAYGAAasnpIIVGDVVYFQDLRCNVFALDLET 115
                                       79******975544446677888******************98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.082
                             PQQ_3   1 GevlWsv.....qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G+++Ws+     ++ gp   +pav+ g+v+v+ +  +++AlDa t
  gi|386002564|ref|YP_005920863.1| 116 GDPIWSRfynvtEVVGP--NGPAVGWGKVFVAKDLYNVTALDAGT 158
                                       88899999954444445..78999999999998889999999987 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3.9e-05
                             PQQ_3   1 GevlWsvqlpgpvnssp....avdgglvyvgtg............dGtlyAlDaet 40 
                                       Ge++W+++l + ++++      v+ glvyv+t              G + AlDaet
  gi|386002564|ref|YP_005920863.1| 159 GEEVWTTRLSEVATTGIdiqpSVYAGLVYVSTVpgtgdvfyapggIGVISALDAET 214
                                       99*****66664444555555666666666666666666666666*********98 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.41
                             PQQ_3   1 GevlWsv..............qlpgpvnsspav 19 
                                       G+++W++              + +g ++++pav
  gi|386002564|ref|YP_005920863.1| 215 GDIVWEFstvdspdlwgnpgvNSGGGAWYPPAV 247
                                       899999965544444444433334455555555 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.01
                             PQQ_3  23 lvyvgtgdGtlyAlDae 39 
                                       +vy ++  G++yA+D +
  gi|386002564|ref|YP_005920863.1| 330 VVYGAGKMGKVYAFDRT 346
                                       6888888********87 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.002
                             PQQ_3   2 evlWsv.......................qlpgpvnsspavdgglvyvgtg.....................dGtly 34 
                                       e+lWs                        ++ g v +++a+++g++yv                         G l+
  gi|386002564|ref|YP_005920863.1| 349 ELLWSAvvgrydeaaqldvlpegttriypGVLGGVETPMAYSDGVLYVPVVnlftdwtptsldtstidfnngTGELV 425
                                       555555555555555555554443333333445677777**********9999999999999999999999999999 PP

                             PQQ_3  35 AlDaet 40 
                                       A+Da t
  gi|386002564|ref|YP_005920863.1| 426 AIDAST 431
                                       999977 PP

  == domain 7  score: 16.9 bits;  conditional E-value: 2.2e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G++lW +++   + ++++v ++lv+++ +dGt++A+ aet
  gi|386002564|ref|YP_005920863.1| 432 GKILWIRSFETMALGGATVINDLVFAAEYDGTIHAFRAET 471
                                       999****9999666999*********************98 PP

  == domain 8  score: 6.9 bits;  conditional E-value: 0.003
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg...dGtlyAl 36 
                                       Ge++W+ + p+ +n+ pav+g +++  +g   d +l+A+
  gi|386002564|ref|YP_005920863.1| 472 GEEVWEMRAPAGINGWPAVAGETIVWPAGvgaDPKLVAF 510
                                       9**********999889****998755555556666665 PP

  == domain 9  score: -3.6 bits;  conditional E-value: 6
                             PQQ_3  20 dgglvyvg 27 
                                       dg ++y+g
  gi|386002564|ref|YP_005920863.1| 595 DGETLYMG 602
                                       56777777 PP

>> EB_dh  Ethylbenzene dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.8   8.4e+03     185     208 ..     369     396 ..     331     399 .. 0.58
   2 ?   12.8   0.0   2.8e-05     0.084     193     232 ..     660     700 ..     519     705 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.8
                                       ............---EEEEEEETTEEEE CS
                             EB_dh 185 p....ewkegdtadvkaeakykdGkWtV 208
                                       p    ++++g +++v++ + y+dG  +V
  gi|386002564|ref|YP_005920863.1| 369 PegttRIYPGVLGGVETPMAYSDGVLYV 396
                                       1233345555559999999999998777 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.8e-05
                                       ---EEEEEEETTEEEE.EEEEES---TTS..---TTEEEEE CS
                             EB_dh 193 advkaeakykdGkWtV.elvRpLkagnpldvalepgkvydv 232
                                        d+ + +  + + WtV e+ R++++g+++d+a++pg+++++
  gi|386002564|ref|YP_005920863.1| 660 DDILSFGGREADGWTViEFERRMDTGDRFDQAFRPGETVNI 700
                                       6666667778899*9868********************986 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.1   1.2e+04      24      35 ..     110     121 ..     103     124 .. 0.64
   2 ?   -1.8   0.1         1     3e+03      71      83 .]     207     219 ..     204     219 .. 0.87
   3 ?    0.8   0.1      0.16   4.7e+02      70      83 .]     285     298 ..     280     298 .. 0.92
   4 ?   -0.6   0.0      0.43   1.3e+03      69      83 .]     338     352 ..     333     352 .. 0.85
   5 ?    6.2   0.0    0.0031       9.4      69      83 .]     422     436 ..     417     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.1
                           DUF4905  24 aldletgkllfe 35 
                                       aldletg  +++
  gi|386002564|ref|YP_005920863.1| 110 ALDLETGDPIWS 121
                                       566666666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                           DUF4905  71 liaiDiktgkllW 83 
                                       + a+D++tg ++W
  gi|386002564|ref|YP_005920863.1| 207 ISALDAETGDIVW 219
                                       5599********9 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
                           DUF4905  70 gliaiDiktgkllW 83 
                                        l+a+D  tg ++W
  gi|386002564|ref|YP_005920863.1| 285 SLVALDHATGDMIW 298
                                       69************ PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.43
                           DUF4905  69 kgliaiDiktgkllW 83 
                                        ++ a+D  +g+llW
  gi|386002564|ref|YP_005920863.1| 338 GKVYAFDRTSGELLW 352
                                       5778*********** PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.0031
                           DUF4905  69 kgliaiDiktgkllW 83 
                                        +l+aiD+ tgk+lW
  gi|386002564|ref|YP_005920863.1| 422 GELVAIDASTGKILW 436
                                       689************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (727 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 4145.26
//
Query:       gi|386002565|ref|YP_005920864.1|  [L=160]
Description: Activator of Hsp90 ATPase 1 family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-12   46.0   0.3    7.7e-12   45.7   0.3    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.5e-06   27.7   0.0    2.9e-06   27.5   0.0    1.1  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
    1.1e-05   25.6   0.0    1.2e-05   25.5   0.0    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.3   1.3e-15   7.7e-12       2     131 ..       4     128 ..       3     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.3e-15
                                       EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEE.CCCS.SEEEEEEEEEETTTTEEE CS
                   Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvr.vggr.gtvreelvevdpegrlls 76 
                                       v+++++v+i  +pe+Vw++++dfe+++ W p+++ v ++  +g+  + + ++r  ggr    r ++++v   gr l+
  gi|386002565|ref|YP_005920864.1|   4 VEIRDEVEIRGSPEEVWRILTDFEAYRDWNPFIRPVVGVASEGA--RLRVQIRpPGGRaMAFRPRVTRVAR-GRELR 77 
                                       678999****************************9988876777..666899956666755********87.***** PP

                                       EEEE..SSS-TSEEEEEEEEECC.ETEEEEEEEEEEEE--TT--HHHHHHHHHHHHH CS
                   Polyketide_cyc2  77 yriv.kpvpvanyvatwtvtpdg.ggtrvtwtgefdagplggpfekpaaakavkgdl 131
                                       + ++    ++ +++  ++++p g +  r++ +  f      g++  p+a+  ++++ 
  gi|386002565|ref|YP_005920864.1|  78 WLGRlWLPGILDGEHIFEIEPLGpDRVRLVQREIFS-----GLL-VPLARGRIREET 128
                                       *9977778999************4446644333244.....332.455555555543 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   4.8e-10   2.9e-06       3     123 ..      15     142 ..      13     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.8e-10
                                       -HHHHHHHHH-HHHHHHHEEEEEEEE--.STTEEEEE.EETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEEEE CS
                             AHSA1   3 pperVfraltdpellkrWftlteaemdl.rpGgkfrl.rdspdgkefgnegeylevvpperlvytwrledepeeees 77 
                                       +pe+V+r ltd e+ + W    +  + +  +G + r+  + p g+++ ++ +++ v + ++l +  rl  ++   + 
  gi|386002565|ref|YP_005920864.1|  15 SPEEVWRILTDFEAYRDWNPFIRPVVGVaSEGARLRVqIRPPGGRAMAFRPRVTRVARGRELRWLGRLWLPG-ILDG 90 
                                       89****************433444444436799*****888************************8887555.8899 PP

                                       EEEEEEEE.ETTEEEEEEEE......EEEEHCHHHHHHHHHHHHHHHHHHHHH CS
                             AHSA1  78 tvtielee.egggTrltlth......tglprkqkeeegveeGweqsldqLkal 123
                                       +  +e+e+  ++ +rl+ ++        l+r++ +ee + +G++++ + Lk+ 
  gi|386002565|ref|YP_005920864.1|  91 EHIFEIEPlGPDRVRLVQREifsgllVPLARGRIREE-TIAGFREMDRALKER 142
                                       *******************999888878888888887.999999998888876 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     2e-09   1.2e-05       4      49 ..      15      56 ..      12     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2e-09
                                      -HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSS CS
                    Polyketide_cyc  4 padqvyalvadvesypeflphcssvevleeaesglsadlevgfggl 49
                                      ++++v+++++d+e y +++p+++ v+ ++ +++    +l+v+  + 
  gi|386002565|ref|YP_005920864.1| 15 SPEEVWRILTDFEAYRDWNPFIRPVVGVASEGA----RLRVQIRPP 56
                                      79**********************999999996....333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1238.34
//
Query:       gi|386002566|ref|YP_005920865.1|  [L=572]
Description: hypothetical protein Mhar_1885 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-16   59.8   0.0    1.5e-06   28.4   0.0    2.8  2  DUF11       Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.024   14.9   0.0        1.4    9.3   0.0    2.5  2  Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
      0.025   13.6   0.0      0.041   12.9   0.0    1.3  1  DUF4929     Domain of unknown function (DUF4929)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.6e-10   1.5e-06      16      83 ..     324     393 ..     317     401 .. 0.86
   2 !   28.4   0.0   2.5e-10   1.5e-06      11      82 ..     443     516 ..     434     522 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.6e-10
                             DUF11  16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatlsftvrvtrtaa 83 
                                        +y++t+ N g+++++ v v+D+ P+g  +v++s +    +  a++s + L +g ++ +++ + vt+   
  gi|386002566|ref|YP_005920865.1| 324 ARYVITLENDGGKTLEPVLVRDVFPPGGIFVRSSLRptLTSDGANWSLTHLSPGDEREIELVLDVTNFRG 393
                                       58**********************************775666678888************9999987655 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.5e-10
                             DUF11  11 rpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrta 82 
                                       + G  v ytl v N g +++  + vtD lP g++++ +s     +  + a+++  +L++ge  t+++ v++  ++
  gi|386002566|ref|YP_005920865.1| 443 AVGNRVWYTLEVENLGDRPL-VANVTDRLPDGMRLIYSSPIfasYEDGVATWNLVDLAPGEVETVAYGVEALWSG 516
                                       57999***************.****************998844455555666669************99987665 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.027   1.6e+02      28      85 ..     326     382 ..     318     387 .. 0.84
   2 ?    9.3   0.0   0.00023       1.4      13      83 ..     433     504 ..     427     511 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.027
                        Chlam_OMP6  28 ypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekski 85 
                                       y i +   g k    v++ + +p    fvrs    t t+dg   w +  l  g+   i
  gi|386002566|ref|YP_005920865.1| 326 YVITLENDGGKTLEPVLVRDVFPPGGIFVRSSLRPTLTSDGA-NWSLTHLSPGDEREI 382
                                       6777777788888889999999999****************7.599999998887766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00023
                        Chlam_OMP6  13 eisqavpeyatvgs..pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgeks 83 
                                        is+a     +vg    y +e+   g +  v   +t++lp  + ++ s p  +   dg   w++  l  ge  
  gi|386002566|ref|YP_005920865.1| 433 SISKAGDVDEAVGNrvWYTLEVENLGDRPLVAN-VTDRLPDGMRLIYSSPIFASYEDGVATWNLVDLAPGEVE 504
                                       5555544444455411699*********99976.599***************************999999865 PP

>> DUF4929  Domain of unknown function (DUF4929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-06     0.041     167     196 ..      28      57 ..      18      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-06
                           DUF4929 167 rsfegksvitLsekAtadkPvLkmidnplG 196
                                          +gks it+sek t+ +PvL +   ++G
  gi|386002566|ref|YP_005920865.1|  28 AGQDGKSSITVSEKSTVHRPVLNISAASFG 57 
                                       5679*******************9988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3512.26
//
Query:       gi|386002567|ref|YP_005920866.1|  [L=205]
Description: hypothetical protein Mhar_1886 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-15   57.5   0.6    9.5e-11   42.1   0.0    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-06   28.3   0.1    1.9e-06   27.6   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.6e-05   23.7   0.0    5.2e-05   23.2   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.083   13.2   0.0       0.25   11.7   0.0    1.9  1  TAL_effector   TAL effector repeat


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   2.1e-14   9.5e-11       6      67 ..      27      86 ..      22      91 .. 0.93
   2 !   13.9   0.2   8.9e-06      0.04     120     197 .]     111     190 ..      95     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 2.1e-14
                                      SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                       Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                       +++l+e +g+ +L D+G ++   + a  l+ +gl p d+d +++TH+HlDH  +l+ +++a
  gi|386002567|ref|YP_005920866.1| 27 PSTVLLEEPGRRVLADPGADGKSLLSA--LRERGLSPSDIDLIFVTHGHLDHLLNLRLFPDA 86
                                      5789999******************98..8****************************9987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.9e-06
                                       EEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS..SHHCCCCCC..TTCEEE-SHCHHHHHHHHHHHHHHHCHSEE CS
                       Lactamase_B 120 rralyvtggpghghghgvveygggkvlftGDall..agetgridl.tlrgaevrdpsdaekyldsllklaglkaevl 193
                                         ++ +t+g+++ h ++ v +g +++l++GD++    g  +r+dl  l ++e+  + d e +++s +++   +a v+
  gi|386002567|ref|YP_005920866.1| 111 EIEVLPTPGHAPDHASLLVPSGKETWLVAGDLFWwrDGAVPRTDLpSLLDLEDELATDPEALRRSRIEAL-RRATVV 186
                                       4566788888888888888899999********9887778888887566666666666666665555442.355556 PP

                                       EESS CS
                       Lactamase_B 194 vpgH 197
                                       +pgH
  gi|386002567|ref|YP_005920866.1| 187 IPGH 190
                                       6698 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   4.2e-10   1.9e-06       1      48 [.      37      81 ..      37      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.2e-10
                                      SEEEES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGG CS
                     Lactamase_B_2  1 rriLiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlagll 48
                                      rr+L D+g d   l    l+al  +e+  ++++id++++th+H DHl +l 
  gi|386002567|ref|YP_005920866.1| 37 RRVLADPGADgksL----LSAL--RERGLSPSDIDLIFVTHGHLDHLLNLR 81
                                      8*********4432....4444..12356788***************8876 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.2e-08   5.2e-05       8      51 ..      28      78 ..      26     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.2e-08
                     Lactamase_B_3  8 nsflletagarilvDPf.......kanlgyeppa......eeaDlvlisqaledHah 51
                                      +++lle +g r+l DP+       +a       +       ++Dl+ +++++ dH  
  gi|386002567|ref|YP_005920866.1| 28 STVLLEEPGRRVLADPGadgksllSAL------RerglspSDIDLIFVTHGHLDHLL 78
                                      899**************5554443112......1345555***************75 PP

>> TAL_effector  TAL effector repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05      0.25      13      27 ..      50      64 ..      48      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                                      HHHHHHHTT--HHHH CS
                      TAL_effector 13 hgpaLrqrGfSradI 27
                                      ++ aLr+rG+S+ dI
  gi|386002567|ref|YP_005920866.1| 50 LLSALRERGLSPSDI 64
                                      678***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1284.41
//
Query:       gi|386002568|ref|YP_005920867.1|  [L=188]
Description: hypothetical protein Mhar_1887 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.5   4.1      0.005   16.7   4.1    1.9  1  Nudix_N_2        Nudix N-terminal
     0.0043   16.9   0.0     0.0073   16.2   0.0    1.3  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
       0.01   15.2   1.7       0.18   11.2   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.018   15.4   0.5      0.044   14.2   0.5    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.022   14.8   0.4      0.036   14.1   0.4    1.3  1  DZR              Double zinc ribbon
      0.028   14.3   1.1       0.94    9.4   0.1    2.6  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.042   14.0   0.8        8.3    6.6   0.1    2.7  3  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
      0.059   12.9   6.4        0.1   12.2   0.7    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.062   13.0   2.2        0.8    9.5   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.073   12.8   1.5        1.4    8.6   0.2    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.087   12.8   0.9        7.7    6.6   0.4    2.8  3  FliMN_C          Type III flagellar switch regulator (C-ring)
       0.15   12.0   1.0       0.28   11.1   1.0    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.26   10.9   0.9         22    4.7   0.1    2.5  2  RecR             RecR protein
        0.3   11.0   1.3        5.4    7.0   0.1    2.6  2  zinc_ribbon_4    zinc-ribbon domain
       0.38   10.5   4.7        5.9    6.6   4.7    2.3  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.41   10.9   5.6         12    6.1   0.9    3.0  2  zf-RING_7        C4-type zinc ribbon domain
       0.68   10.6   3.6        4.3    8.1   3.0    2.5  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.78    9.9   4.0        3.1    8.0   4.0    2.0  1  Zn-ribbon_8      Zinc ribbon domain
        3.3    7.7   5.2         11    6.1   5.2    1.7  1  Prok-RING_1      Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.1   5.3e-06     0.005       2      32 ..       6      36 ..       6      36 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.3e-06
                                      B-TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgtih 32
                                      FC++CG+ +e+ + + + ++  +C+aCgt+h
  gi|386002568|ref|YP_005920867.1|  6 FCPECGEVTEHGTVKLGREHLVRCEACGTVH 36
                                      9**************999999*********9 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.7e-06    0.0073       2      32 ..       5      37 ..       5      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                      EBESTTTSBEEEEECSCCCE..EEESSSS-EEE CS
                    RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegkn..feCrqCgYeep 32
                                      +FCp+Cg   +  + k+g+   + C  Cg + p
  gi|386002568|ref|YP_005920867.1|  5 IFCPECGEVTEHGTVKLGREhlVRCEACGTVHP 37
                                      7*****************99*********9988 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00019      0.18       2      11 ..       4      13 ..       3      17 .. 0.76
   2 ?    3.0   0.1     0.074        70       3      10 ..      27      34 ..      26      38 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                       zf-ribbon_3  2 tvrCPnCGap 11
                                      +++CP+CG++
  gi|386002568|ref|YP_005920867.1|  4 EIFCPECGEV 13
                                      7889999987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.074
                       zf-ribbon_3  3 vrCPnCGa 10
                                      vrC +CG+
  gi|386002568|ref|YP_005920867.1| 27 VRCEACGT 34
                                      68999997 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   4.6e-05     0.044       6      41 ..       7      39 ..       5      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgastpwf 41
                                      CP Cg+  ++++ ++++++    v C+ Cg ++p+ 
  gi|386002568|ref|YP_005920867.1|  7 CPECGEVTEHGTVKLGREH---LVRCEACGTVHPHQ 39
                                      *****************99...********976664 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   3.9e-05     0.036      11      38 ..       3      36 ..       1      41 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-05
                               DZR 11 darfCseCgtklkavaa.......edrCpsCgekv 38
                                      + +fC+eCg+  +   +         rC +Cg+  
  gi|386002568|ref|YP_005920867.1|  3 EEIFCPECGEVTEH-GTvklgrehLVRCEACGTVH 36
                                      679******99863.3368899999*******975 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       0.1        98      27      32 ..       6      11 ..       4      14 .. 0.65
   2 ?    9.4   0.1   0.00099      0.94      13      24 ..      28      38 ..      25      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.1
                           DUF35_N 27 vCphCg 32
                                      +Cp Cg
  gi|386002568|ref|YP_005920867.1|  6 FCPECG 11
                                      577776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00099
                           DUF35_N 13 rCpdCGtvqfPP 24
                                      rC +CGtv +P 
  gi|386002568|ref|YP_005920867.1| 28 RCEACGTV-HPH 38
                                      9*******.675 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0088       8.3      22      33 ..       3      14 ..       1      16 [. 0.82
   2 ?    5.1   0.0     0.026        25       5      19 ..      23      37 ..      19      44 .. 0.79
   3 ?   -2.4   0.0       5.7   5.4e+03      53      67 ..     125     139 ..     119     142 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0088
                      NOB1_Zn_bind 22 tkkFCpkCGnkt 33
                                      +  FCp+CG+ t
  gi|386002568|ref|YP_005920867.1|  3 EEIFCPECGEVT 14
                                      568******865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                      NOB1_Zn_bind  5 kswvlrChaCfkvtk 19
                                      +++++rC aC +v +
  gi|386002568|ref|YP_005920867.1| 23 REHLVRCEACGTVHP 37
                                      8899******99875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.7
                      NOB1_Zn_bind  53 knfqlnlrGtkyslp 67 
                                          q + r t + +p
  gi|386002568|ref|YP_005920867.1| 125 VSVQRRGRTTSFDVP 139
                                       333444444555555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   0.00011       0.1      16      31 ..       1      16 [.       1      26 [. 0.81
   2 ?    3.6   0.6      0.05        47      21      28 ..      28      35 ..      22      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                      STTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlVled 31
                                      ++ e++C++CG+V e 
  gi|386002568|ref|YP_005920867.1|  1 MQEEIFCPECGEVTEH 16
                                      6789*********996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.05
                                      EESSSSBE CS
                      TF_Zn_Ribbon 21 vCtdCGlV 28
                                      +C++CG+V
  gi|386002568|ref|YP_005920867.1| 28 RCEACGTV 35
                                      7*****98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00085       0.8      14      21 ..       5      12 ..       2      13 .. 0.75
   2 ?    3.1   0.2     0.088        83      16      21 ..      29      34 ..      27      37 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00085
                     zinc_ribbon_2 14 kFCpyCGt 21
                                       FCp+CG+
  gi|386002568|ref|YP_005920867.1|  5 IFCPECGE 12
                                      68888886 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.088
                     zinc_ribbon_2 16 CpyCGt 21
                                      C+ CGt
  gi|386002568|ref|YP_005920867.1| 29 CEACGT 34
                                      777776 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.096        91      16      24 ..       3      11 ..       1      14 [. 0.84
   2 ?    8.6   0.2    0.0015       1.4      10      24 ..      19      33 ..      15      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.096
                                      S----SSS- CS
                    DNA_RNApol_7kD 16 dpiRCkeCG 24
                                      + i C eCG
  gi|386002568|ref|YP_005920867.1|  3 EEIFCPECG 11
                                      6788****9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                                      ----SSS----SSS- CS
                    DNA_RNApol_7kD 10 vslkkgdpiRCkeCG 24
                                      v+l ++  +RC  CG
  gi|386002568|ref|YP_005920867.1| 19 VKLGREHLVRCEACG 33
                                      789999********9 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.8   3.6e+03      39      56 ..      13      30 ..      12      32 .. 0.81
   2 ?    6.6   0.4    0.0082       7.7      27      56 ..      71     100 ..      59     103 .. 0.90
   3 ?    3.6   0.0      0.07        66      28      63 ..     106     157 ..     100     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.8
                                      GGGCEEEEETTEEEEEEE CS
                           FliMN_C 39 adepvevyvngkpiarGe 56
                                      ++e+ +v+ +   + r+e
  gi|386002568|ref|YP_005920867.1| 13 VTEHGTVKLGREHLVRCE 30
                                      578889999999999998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0082
                                       HHTTSEEE--TTGGGCEEEEETTEEEEEEE CS
                           FliMN_C  27 LkvGdvipLdkpadepvevyvngkpiarGe 56 
                                       L+vGd i +d  +++ v v v   ++a+G+
  gi|386002568|ref|YP_005920867.1|  71 LAVGDEILVDDGIGDVVMVEVTSLELAEGR 100
                                       89************************9996 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.07
                                       HTTSEEE--TTGGGCEEEEET................TEEEEEEEEEEETTE CS
                           FliMN_C  28 kvGdvipLdkpadepvevyvn................gkpiarGelgvvggr 63 
                                       k+G v +L ++a ++v v+v                 + p+a Ge+ + +gr
  gi|386002568|ref|YP_005920867.1| 106 KAGEVMTLWTRAVDEVVVKVSvqrrgrttsfdvpargDEPFAVGEVRTADGR 157
                                       8999****99999999999987777777777777777777777777777665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0   0.00029      0.28      31      56 ..       7      36 ..       5      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                    OrfB_Zn_ribbon 31 CseCgsknke....alsgrtfkCpnCgfea 56
                                      C+eCg++ ++       + +++C++Cg+++
  gi|386002568|ref|YP_005920867.1|  7 CPECGEVTEHgtvkLGREHLVRCEACGTVH 36
                                      **********99866677889******986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.023        22      18      28 ..       6      16 ..       1      19 [. 0.87
   2 ?    4.4   0.1     0.028        27      13      25 ..      23      35 ..      20      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                                      E-TTT--EESS CS
                              RecR 18 hCsrCgnltee 28
                                      +C++Cg +te+
  gi|386002568|ref|YP_005920867.1|  6 FCPECGEVTEH 16
                                      8********97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.028
                                      HHH-EE-TTT--E CS
                              RecR 13 kekvrhCsrCgnl 25
                                      +e++ +C+ Cg++
  gi|386002568|ref|YP_005920867.1| 23 REHLVRCEACGTV 35
                                      78999******97 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.21     2e+02       4       9 ..       6      11 ..       4      15 .. 0.63
   2 ?    7.0   0.1    0.0057       5.4      25      34 ..      26      35 ..      19      37 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                     zinc_ribbon_4  4 tCpsCk 9 
                                       Cp+C+
  gi|386002568|ref|YP_005920867.1|  6 FCPECG 11
                                      466665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0057
                     zinc_ribbon_4 25 kvrCskCghv 34
                                       vrC +Cg+v
  gi|386002568|ref|YP_005920867.1| 26 LVRCEACGTV 35
                                      5888888876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.7    0.0062       5.9       5      31 ..       6      36 ..       6      36 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0062
                     zf-NADH-PPase  5 FCgrCGapte...paeg.gwarvCpaCgleh 31
                                      FC+ CG  te   ++ g ++  +C+aCg+ h
  gi|386002568|ref|YP_005920867.1|  6 FCPECGEVTEhgtVKLGrEHLVRCEACGTVH 36
                                      9*****777533334444999*******988 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9     0.013        12      23      30 ..       4      11 ..       2      11 .. 0.84
   2 ?    5.9   0.1     0.016        15      23      30 ..      26      33 ..      18      42 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                       ++CpeCG
  gi|386002568|ref|YP_005920867.1|  4 EIFCPECG 11
                                      59*****9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                      +v+C+ CG
  gi|386002568|ref|YP_005920867.1| 26 LVRCEACG 33
                                      66666665 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.0    0.0046       4.3       3      28 ..       5      32 ..       3      36 .. 0.70
   2 ?    1.4   0.5      0.54   5.1e+02       3      12 ..      27      36 ..      25      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0046
                           zf-ISL3  3 hrCPnCgsktv..vkhgkkerrvrhlpi 28
                                      + CP+Cg++t   +++  +e  vr + +
  gi|386002568|ref|YP_005920867.1|  5 IFCPECGEVTEhgTVKLGREHLVRCEAC 32
                                      78*******7633444447888886655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.54
                           zf-ISL3  3 hrCPnCgskt 12
                                       rC  Cg ++
  gi|386002568|ref|YP_005920867.1| 27 VRCEACGTVH 36
                                      58*****984 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.0    0.0033       3.1       8      34 ..       7      34 ..       3      40 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                       Zn-ribbon_8  8 CeeCghefe.vlqsisdapltaCPeCgs 34
                                      C eCg++ e   ++  ++ l+ C +Cg 
  gi|386002568|ref|YP_005920867.1|  7 CPECGEVTEhGTVKLGREHLVRCEACGT 34
                                      *****99997555566777888****97 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.2     0.011        11       6      30 ..       6      36 ..       2      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                       Prok-RING_1  6 kCpvCgkelkee......dDiVvCpeCgtpy 30
                                       Cp Cg+  +++      + +V C +Cgt++
  gi|386002568|ref|YP_005920867.1|  6 FCPECGEVTEHGtvklgrEHLVRCEACGTVH 36
                                      6999*999999999999999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1096.61
//
Query:       gi|386002569|ref|YP_005920868.1|  [L=200]
Description: protein-L-isoaspartate O-methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-68  231.2   0.0    1.2e-68  231.0   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    8.8e-16   58.0   0.0    1.1e-15   57.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.5e-09   37.7   0.0      4e-09   37.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    9.3e-09   35.3   0.0    1.2e-08   35.0   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    8.7e-07   29.5   0.0    1.7e-06   28.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    9.2e-06   25.3   0.0    1.2e-05   24.9   0.0    1.2  1  MTS              Methyltransferase small domain
    3.4e-05   23.3   0.0    4.5e-05   22.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.9e-05   23.1   0.0    7.3e-05   22.5   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00014   21.3   0.0    0.00019   20.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00015   21.1   0.0    0.00018   20.9   0.0    1.1  1  GidB             rRNA small subunit methyltransferase G
     0.0002   20.5   0.0    0.00028   20.0   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00044   19.5   0.0    0.00057   19.1   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    0.00051   19.6   0.0    0.00081   18.9   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
     0.0012   18.0   0.0     0.0019   17.3   0.0    1.2  1  Fibrillarin      Fibrillarin
     0.0042   16.5   0.0     0.0051   16.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0061   16.4   0.0     0.0071   16.2   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.046   13.7   0.0    1.8  2  Methyltransf_32  Methyltransferase domain
      0.028   14.4   0.0      0.041   13.8   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.056   12.9   0.0      0.081   12.4   0.0    1.1  1  Methyltransf_5   MraW methylase family
      0.072   12.4   0.1       0.11   11.8   0.1    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.086   12.6   0.0       0.12   12.1   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
       0.14   11.9   0.0       0.19   11.4   0.0    1.1  1  Met_10           Met-10+ like-protein


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.0   0.0   1.5e-71   1.2e-68      17     207 ..       6     194 ..       2     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.0 bits;  conditional E-value: 1.5e-71
                                       --HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHH CS
                              PCMT  17 ksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlar 93 
                                       +sd+v+ea+e+++Re fvp+  +++aY+d pl+ig ++tiSaphmva++++ll+l +g+rvL+vG+GsGy++av+a+
  gi|386002569|ref|YP_005920868.1|   6 VSDRVLEAMEDTPRELFVPNRVRQMAYQDHPLPIGDGQTISAPHMVAIMCDLLDLGEGMRVLDVGTGSGYHAAVMAK 82 
                                       69*************************************************************************** PP

                                       HHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEEEEEEE CS
                              PCMT  94 lvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLkeGGrlv 170
                                       lvg++g+v sier++ lv+ a++nl + ++env+vv+gDG  G +++aP+d+i v+a+ap++Pe+l  QLk GG+lv
  gi|386002569|ref|YP_005920868.1|  83 LVGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRGLPDHAPFDRINVAATAPKVPEPLQAQLKVGGKLV 159
                                       ***************************************************************************** PP

                                       EEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BC CS
                              PCMT 171 vPvgeeeeQvlklvdkkadgkvvikkleevrfvpltd 207
                                       +Pvg +  Q+l lv +++ + +++++   v+fvpl +
  gi|386002569|ref|YP_005920868.1| 160 IPVG-TCYQELLLVVRTE-EGFEMEQHGGVVFVPLIG 194
                                       ****.999******9999.889************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   1.4e-18   1.1e-15       3      90 ..      62     147 ..      60     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.4e-18
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDli 78 
                                       +g+rvlD+G+G+G+ + ++a+++gp+++v++i++ ++ + +Ar+n+++ g++nv++ +gd    l+ +   ++fD i
  gi|386002569|ref|YP_005920868.1|  62 EGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRgLPDH---APFDRI 135
                                       79****************************************************************77...99***9 PP

                   Methyltransf_31  79 lsnevlnaladp 90 
                                       +  ++   +++p
  gi|386002569|ref|YP_005920868.1| 136 NVAATAPKVPEP 147
                                       987666444433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   4.9e-12     4e-09       1      71 [.      66     138 ..      66     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.9e-12
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvss 71 
                                       vLd+G+G+G +++ +ak +g +++v+ ++  +++++ ar++++e+g+ nv++v+gd ++ lp +++ fD + ++
  gi|386002569|ref|YP_005920868.1|  66 VLDVGTGSGYHAAVMAKLVGpEGHVYSIERVATLVAFARKNLSEAGIeNVTVVEGDGSRgLP-DHAPFDRINVA 138
                                       9******************66************************************77366.56699998775 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.5e-11   1.2e-08      29      97 ..      51     119 ..      42     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-11
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvt 97 
                                       ++++   L+l +G +v++ GtGsg  +  +a+ v+P Gh++++e  ++ + +ar+++ e ++++++ v+
  gi|386002569|ref|YP_005920868.1|  51 VAIMCDLLDLGEGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVE 119
                                       56677789******************************************************8766554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     2e-09   1.7e-06       1      79 [.      67     149 ..      67     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2e-09
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvssevlh 72 
                                       LdvG+G+G++a+ +ak +   ++v+ ++  +++++ a+++ se+g+ +v++v++d ++  ++d + fD + +  +  
  gi|386002569|ref|YP_005920868.1|  67 LDVGTGSGYHAAVMAKLVgpeGHVYSIERVATLVAFARKNLSEAGIeNVTVVEGDGSR-GLPDhAPFDRINVAATAP 142
                                       8**************8888**************************************9.888856899998888877 PP

                                       C-CCHHH CS
                   Methyltransf_11  73 hvedpek 79 
                                        v++p +
  gi|386002569|ref|YP_005920868.1| 143 KVPEPLQ 149
                                       7766655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.5e-08   1.2e-05      25      96 ..      56     129 ..      50     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.5e-08
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle.vevvasdvleeveek 96 
                                       + l+  +  +vlD+G+G G+ +a++ak   pe +v  ++  a  +++a++nl++ ++e v+vv+ d+   ++++
  gi|386002569|ref|YP_005920868.1|  56 DLLDLGEGMRVLDVGTGSGYHAAVMAKLvGPEGHVYSIERVATLVAFARKNLSEAGIEnVTVVEGDGSRGLPDH 129
                                       5566667789*************99997258889********************************99998853 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.5e-08   4.5e-05      46     126 ..      61     141 ..      49     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.5e-08
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                        +g +vlDv +G+g  a+ +++ vg +g+v  ++  ++++  ++k l e g  n+  + +++ +   +   fD + v
  gi|386002569|ref|YP_005920868.1|  61 GEGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRGLPDHAPFDRINV 137
                                       4789*********************************************************9886666788998888 PP

                                       ES-G CS
                   Ubie_methyltran 123 sfGl 126
                                       +   
  gi|386002569|ref|YP_005920868.1| 138 AATA 141
                                       7544 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     9e-08   7.3e-05       3      85 ..      57     137 ..      55     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9e-08
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       lL++ e+ ++lD+ ++ G   + +a+l+ ++g+v+ +++ ++ +    +nl+  g++n++v+e+D+++   + +   
  gi|386002569|ref|YP_005920868.1|  57 LLDLGEGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRGLPDHA--P 131
                                       68889999**********************************************************99855555..5 PP

                                       EEEEEE CS
                   Methyltr_RsmB-F  80 fDriLl 85 
                                       fDri +
  gi|386002569|ref|YP_005920868.1| 132 FDRINV 137
                                       999966 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.4e-07   0.00019      52     131 ..      52     135 ..      44     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.4e-07
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG--- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde 126
                                        ++++ l+l +Gm++Ld+G+G G+ +  +++  +   +v ++   +   + a+k++ e+++e+ + v+  + + l++
  gi|386002569|ref|YP_005920868.1|  52 AIMCDLLDLGEGMRVLDVGTGSGYHAAVMAKLVGpeGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRGLPD 128
                                       6789*******************9999888876522679999999999999*********99999999999999998 PP

                                       ..--SEE CS
                              CMAS 127 ..kvdrv 131
                                         ++dr+
  gi|386002569|ref|YP_005920868.1| 129 haPFDRI 135
                                       8899998 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.2e-07   0.00018      51     120 ..      65     136 ..      47     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-07
                                       .EEEETSTTTTTH.HHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEE CS
                              GidB  51 kviDvGsGaGlPG.ipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvt 120
                                       +v+DvG+G G  + ++ +++ pe +++ +e+    +aF ++  +e ++env++ve +       + ++d + 
  gi|386002569|ref|YP_005920868.1|  65 RVLDVGTGSGYHAaVMAKLVGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRgLPDHAPFDRIN 136
                                       5*********97616667************************************988666545555566555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.5e-07   0.00028      24      85 ..      56     122 ..      44     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                                       HHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                            RrnaAD  24 dklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                       d l+l e + vl++g+G G   + +ak +    +v ++E    L+++ +k+ls    e+++vv+ D+
  gi|386002569|ref|YP_005920868.1|  56 DLLDLGEGMRVLDVGTGSGYHAAVMAKLVgpeGHVYSIERVATLVAFARKNLSeaGIENVTVVEGDG 122
                                       668899*************************88899*****************88889******996 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     7e-07   0.00057      42     110 ..      57     124 ..      16     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7e-07
                                       HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHH CS
                    Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalk 110
                                       L++l +  rvl++G+  Gy +  +a  + ++G++ +i+     ++ a+k +  ag+++ + + egd+ +
  gi|386002569|ref|YP_005920868.1|  57 LLDLGEGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVATLVAFARKNLSEAGIEN-VTVVEGDGSR 124
                                       78999999***********************************************975.7777887765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.9e-07   0.00081       4      66 ..      65     128 ..      62     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.9e-07
                                       EEEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHH CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvlle 66 
                                        vl++G+G+G +   +Ak   P+  +  iE   ++va + k+  + +++N+ +++gd  + l++
  gi|386002569|ref|YP_005920868.1|  65 RVLDVGTGSGYHAAVMAKLvGPEGHVYSIERVATLVAFARKNLSEAGIENVTVVEGDGSRGLPD 128
                                       589**************9637************************************9877765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.4e-06    0.0019      66     105 ..      58      97 ..      48     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                                       -S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
                       Fibrillarin  66 lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                                       l + +g +vL +G++sG  ++ ++ +vg+eg vy++e   
  gi|386002569|ref|YP_005920868.1|  58 LDLGEGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVA 97 
                                       56789*******************************9754 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.3e-06    0.0051     161     228 ..      62     133 ..      51     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.3e-06
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevA..vkvakeNaelNkveakleva..lseellkeekad 228
                                       eg +vlDvGtGSG  a + akL   + + + i+ vA  v  a++N++  ++e+   v    s+ l++++++d
  gi|386002569|ref|YP_005920868.1|  62 EGMRVLDVGTGSGYHAAVMAKLVGPEGHVYSIERVAtlVAFARKNLSEAGIENVTVVEgdGSRGLPDHAPFD 133
                                       4669**********9999999988888888888888446678999999999886645311344444556666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.7e-06    0.0071      21      58 ..      61     101 ..       9     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-06
                   Methyltransf_23  21 raggrvLdiGcGtGillevlre.ngf..svtgvDlspeave 58 
                                        +g+rvLd+G+G+G+ + v+++  g   +v+ ++    +v+
  gi|386002569|ref|YP_005920868.1|  61 GEGMRVLDVGTGSGYHAAVMAKlVGPegHVYSIERVATLVA 101
                                       4678***********99999552466455555555444444 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-05     0.046      16      75 ..      57     111 ..      46     128 .. 0.78
   2 ?   -0.7   0.0       1.6   1.3e+03     139     155 ..     153     169 ..     144     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                   Methyltransf_32  16 llkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75 
                                       ll    +  + ++v+DvG G gY + v+a   +  + +v++i+  + lv+ a+k  ++ g
  gi|386002569|ref|YP_005920868.1|  57 LL----DLGEGMRVLDVGTGSGYHAAVMAK-LVGPEGHVYSIERVATLVAFARKNLSEAG 111
                                       33....4477899****************9.55689*******99999988887666555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                   Methyltransf_32 139 ekeakllvlvpCCyhel 155
                                       +   kl++ v+ Cy+el
  gi|386002569|ref|YP_005920868.1| 153 KVGGKLVIPVGTCYQEL 169
                                       556689999******98 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     5e-05     0.041      14      88 ..      62     137 ..      52     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvk.egkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvvi 88 
                                       +g rv+D+Gt  gy ++ ++k  g   +v+ ++  +  ++ a++n+++ag+e +++v+ +dG   l ++  +d + +
  gi|386002569|ref|YP_005920868.1|  62 EGMRVLDVGTGSGYHAAVMAKlVGPEGHVYSIERVATLVAFARKNLSEAGIE-NVTVVEGDGSRGLPDHApFDRINV 137
                                       5679******988877777652588899**********************96.69*******999987666776655 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.9e-05     0.081       8      75 ..      50     119 ..      45     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                       TTHHHHHHT---TT-EEEES--TTSHHHHHHHTT--TT.EEEEEES-HHHHHHHTT.....-.--EEEEE CS
                    Methyltransf_5   8 LlqevvellepkedgvyiDaTlGaggHsealLeqlsel.rligidrDksalarakerLkefe.krltlvk 75 
                                       ++  +++ll+ +e+   +D+  G+g H+  + + +  + ++++i+r  + +a a+++L+e   +++t+v+
  gi|386002569|ref|YP_005920868.1|  50 MVAIMCDLLDLGEGMRVLDVGTGSGYHAAVMAKLVGPEgHVYSIERVATLVAFARKNLSEAGiENVTVVE 119
                                       6777899*************************9998888*******************987635577776 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00014      0.11      59     121 ..      59     123 ..      43     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                       -GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHH...HHHHHHHS-----TTEEEEES-TT CS
                    Methyltransf_2  59 dleglkslvDvGGGtGalakaivsayPtikvivfDlpeV...veaAkehlsageeervefvgGdff 121
                                       dl +  +++DvG G+G  a+ +++   + ++ v+ + +V   v+ A++ ls +  e+v++v+Gd  
  gi|386002569|ref|YP_005920868.1|  59 DLGEGMRVLDVGTGSGYHAAVMAK-LVGPEGHVYSIERVatlVAFARKNLSEAGIENVTVVEGDGS 123
                                       555566889*******98765555.55666666666544222899*****999999*******965 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.12      26      54 ..      63      91 ..      48     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            DUF938 26 tervLEiasGtGqHAvffApalpnlkwqp 54
                                      + rvL++++G+G HA+ +A+++ +  +  
  gi|386002569|ref|YP_005920868.1| 63 GMRVLDVGTGSGYHAAVMAKLVGPEGHVY 91
                                      349****************9987665544 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.19      99     172 ..      61     135 ..      53     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                       -TT-EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEE CS
                            Met_10  99 eegevVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrv 172
                                        eg +V+dv  G G++a ++ak+ + +  v++i+   + v + ++n+    +e+v  ++++Dg   ++ +  +dr+
  gi|386002569|ref|YP_005920868.1|  61 GEGMRVLDVGTGSGYHAAVMAKLvGPEGHVYSIERVATLVAFARKNLSEAGIENVT-VVEGDGSRGLPdHAPFDRI 135
                                       57889***********9999987256789***********************9976.8999987665535556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1322.38
//
Query:       gi|386002570|ref|YP_005920869.1|  [L=504]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-83  277.9   0.0    6.3e-83  277.5   0.0    1.2  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    4.4e-78  262.1   0.0    5.1e-78  261.9   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    7.7e-06   25.5   0.0      2e-05   24.2   0.0    1.7  2  Sulfatase      Sulfatase
      9e-05   22.2   0.0    0.00015   21.4   0.0    1.3  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
      0.025   14.7   0.1      0.052   13.6   0.1    1.5  1  PglZ           PglZ domain


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.5   0.0   1.8e-86   6.3e-83       1     215 []      80     290 ..      80     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 277.5 bits;  conditional E-value: 1.8e-86
                                       HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT CS
                            iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapk 77 
                                       in aiedg++f n++l ea++ a+++g++lHl+GLlSdGgVHSh+ hl+all+la+++g+ +v++ha+lDGRD++p+
  gi|386002570|ref|YP_005920869.1|  80 INLAIEDGTFFANPNLAEAVDLARDRGGTLHLMGLLSDGGVHSHQAHLFALLRLARDRGLGRVRIHAILDGRDVPPR 156
                                       899************************************************************************** PP

                                       -HHHHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG-- CS
                            iPGM_N  78 saleyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefve 154
                                       sal+y +elee + + g gk+a+v GRyy+MDRd+rwer+e ay+a+++geg + a+s++ea++++y++ge Defv 
  gi|386002570|ref|YP_005920869.1| 157 SALGYFRELEEVMGSFGLGKVATVAGRYYSMDRDRRWERTELAYRAMTSGEGLR-ADSPAEAVQAAYDRGEDDEFVR 232
                                       **************************************************9977.789******************* PP

                                       -EEE...TCCGGS--TT-EEEE----CCCCHHHHHHHHSTTHHCC..--TT-EEEESS-S-T CS
                            iPGM_N 155 ptviaeegkkegtikdgDaviffNFRaDRareltraltdkefkefe.kakklklvtmteYde 215
                                       ptvi    +++g ++dgD++iffNFR+DRar++t+a+  ++f ef+ ++ ++++v+mt+Y+e
  gi|386002570|ref|YP_005920869.1| 233 PTVI----DPDGLVRDGDSLIFFNFRPDRARQITKAFLLPDFCEFDrRKVEVHFVCMTQYQE 290
                                       ****....899**********************************86677889*******85 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.9   0.0   1.4e-81   5.1e-78       1     247 [.       2     490 ..       2     491 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.9 bits;  conditional E-value: 1.4e-81
                                       -EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.......... 67 
                                       k+v l+++DG+Ge+ + e nai  A+tPt+d+Lk ++P + +i+a g++vglp ++mgnsevgHl+l          
  gi|386002570|ref|YP_005920869.1|   2 KPVTLIIMDGFGESGEVEGNAIAAARTPTIDRLKGSYPFT-TIGAAGLDVGLPPGQMGNSEVGHLNLgagrivyqdy 77 
                                       6899************************************.9*********************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|386002570|ref|YP_005920869.1|  78 trinlaiedgtffanpnlaeavdlardrggtlhlmgllsdggvhshqahlfallrlardrglgrvrihaildgrdvp 154
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|386002570|ref|YP_005920869.1| 155 prsalgyfreleevmgsfglgkvatvagryysmdrdrrwertelayramtsgeglradspaeavqaaydrgeddefv 231
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|386002570|ref|YP_005920869.1| 232 rptvidpdglvrdgdsliffnfrpdrarqitkafllpdfcefdrrkvevhfvcmtqyqesigapiafpadhltetlg 308
                                       ***************************************************************************** PP

                                       ..........HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.CC.-SE CS
                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ..........lrisetvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldailsgkfdl 134
                                                 lri+et+k+ahvtff+nggr+++ ++ e+r  ips++v+t+d +pem+a ev+++++++i  g++dl
  gi|386002570|ref|YP_005920869.1| 309 evvsraglrqLRIAETEKYAHVTFFFNGGREEPSPG-EDRLLIPSPKVATYDRKPEMSAFEVTDAVVEKIRGGAYDL 384
                                       ************************************.**************************************** PP

                                       EEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS.........-----EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                     Metalloenzyme 135 vvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk.qplTsHtlepVPil 210
                                       +v+n++n DmvGHtg +ea+++a+ea+D +v+++++++ + +g +++t+DHgnae+m +r++ q +T+Ht++ VP+ 
  gi|386002570|ref|YP_005920869.1| 385 IVLNYANSDMVGHTGIFEAAVEAVEAVDDCVGRVVSEVLARGGAVLLTSDHGNAEQMEDRKTgQHHTAHTTNRVPFG 461
                                       ***********************************************************9889*************9 PP

                                       EESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 211 ivgkglapdkvkegakfrekggLanvaatllnllgle 247
                                       ++g + +p       ++re+g La+va+t+l+llgl 
  gi|386002570|ref|YP_005920869.1| 462 LIGGK-RP-------RLREDGILADVAPTVLDLLGLP 490
                                       88886.34.......699****************985 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.63   2.3e+03       5      33 ..       6      35 ..       4      38 .. 0.75
   2 !   24.2   0.0   5.5e-09     2e-05     209     308 ..     399     488 ..     346     489 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.63
                                      EEEESSE-TTGSGGGTTTSCS..SHHHHHHH CS
                         Sulfatase  5 liladdlgagdlglyggktat..tpnldrla 33
                                      li++d +g +  ++ g+ +a+  tp++drl 
  gi|386002570|ref|YP_005920869.1|  6 LIIMDGFGES-GEVEGNAIAAarTPTIDRLK 35
                                      8999999875.466777776666*****985 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 5.5e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTS CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgek 285
                                          ea   +ve vDd++grv+ ++    l++   v+ tSDhg +    +   r + ++ + +   rvP+ + +  +k
  gi|386002570|ref|YP_005920869.1| 399 GIFEAAVEAVEAVDDCVGRVVSEV----LARGGAVLLTSDHGNAE---QMEDRKTGQHHTAHTTNRVPFGLIG--GK 466
                                       667788899***************....**************944...4455555555888888999997765..55 PP

                                       HCEEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 286 aprvseelvshiDlfptildlag 308
                                       +p +  e   + D++pt+ldl+g
  gi|386002570|ref|YP_005920869.1| 467 RP-RLREDGILADVAPTVLDLLG 488
                                       55.445666678*********99 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.3e-08   0.00015     163     238 ..     371     441 ..     334     470 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.3e-08
                                       SHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEH CS
                      Phosphodiest 163 kvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmadvs 238
                                       ++v+ek   + +dl+++++ + D vgH  G+ +    +a++ vD+++g+ ++++  r      +++l+SDHG a+  
  gi|386002570|ref|YP_005920869.1| 371 DAVVEKIRgGAYDLIVLNYANSDMVGH-TGIFEA-AVEAVEAVDDCVGRVVSEVLAR----GGAVLLTSDHGNAEQM 441
                                       334444447999***************.666665.5689******************....779********87654 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.4e-05     0.052     111     169 ..     381     437 ..     359     443 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                              PglZ 111 dkevvyivhnkvDalgdkasteqksfeaveeslkelkelvkslleengykvlltaDHGf 169
                                        ++++++   + D++g+  + e +  eave     + ++v+++l + g  vllt+DHG+
  gi|386002570|ref|YP_005920869.1| 381 AYDLIVLNYANSDMVGHTGIFEAA-VEAVEAVDDCVGRVVSEVLAR-GGAVLLTSDHGN 437
                                       456667766677899995554433.345554444677778888888.***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3224.99
//
Query:       gi|386002571|ref|YP_005920870.1|  [L=196]
Description: hypothetical protein Mhar_1890 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-18   65.9  15.9    3.7e-12   46.6   6.2    2.0  2  VIT1      VIT family


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   1.0   2.4e-10   4.3e-06       2      61 ..      23      82 ..      22      98 .. 0.90
   2 !   46.6   6.2   2.1e-16   3.7e-12     117     211 ..      91     188 ..      82     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.4e-10
                              VIT1  2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserd 61
                                      r +v+ a DG+++ +++v+G   ++l+++++v+ aG+ +++A  iS    +Yl+ ++er 
  gi|386002571|ref|YP_005920870.1| 23 RLFVMNAFDGILTLMGVVIGAHFSGLSNPEVVIKAGIGGIIALGISGMSSAYLAERAERR 82
                                      568999***************************************************985 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 2.1e-16
                              VIT1 117 lmlreelgpsa.seelasplkaAlssalsfliGgliPllpylfve..svglalvvsiavtllalllfGavkalltgs 190
                                       +ml++ +  +  + ++   +  Al+ ++s ++Gg+i ++py+fv+  ++  a+++s+a+ ll+l+++G++ a++++ 
  gi|386002571|ref|YP_005920870.1|  91 AMLKDLKRSQFaRASEFATVVVALVNGISPALGGMILVIPYFFVPaiDMEAAFRASLALGLLCLFVLGIFLARISSE 167
                                       4555333222213333567899***********************8889**************************** PP

                              VIT1 191 sklvsalrmlliGalAaaaay 211
                                       +++vs++rm+l+G+l+ a+  
  gi|386002571|ref|YP_005920870.1| 168 RMIVSGVRMILVGLLTIAIVS 188
                                       ***************988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1079.32
//
Query:       gi|386002572|ref|YP_005920871.1|  [L=538]
Description: Peptidase, ArgE/DapE family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-38  130.4   0.0    1.1e-37  129.8   0.0    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.7e-22   78.7   0.0    5.7e-22   77.7   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
    3.9e-05   23.4   0.0    5.7e-05   22.9   0.0    1.2  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.0   1.8e-41   1.1e-37       2     205 ..     199     514 ..     198     516 .. 0.85

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 1.8e-41
                                       EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.T CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.g 76 
                                       ++ HlDvVp++e   w++ pf+l+++dG++yGrG++d kg v+a+++alra++++g +p++++ +l+++dEEgg+ +
  gi|386002572|ref|YP_005920871.1| 199 IYTHLDVVPAGEG--WSKdPFALDIRDGRIYGRGVADSKGAVAALIAALRAIEATG-RPQRNLLVLLTTDEEGGGyS 272
                                       899******6655..************************************99997.99*************98899 PP

                                       HHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                     Peptidase_M20  77 Gakallegleerekvdavfelhieepgileagklaigvv...................................... 115
                                       G  ++++    +  v++ + ++++++   +     + ++                                      
  gi|386002572|ref|YP_005920871.1| 273 GLCYFAD----EGLVKGDV-MLCMDSFSDD-----VIIGsngiitweatvrgkaahsgasflgenaiekalpvieal 339
                                       9999999....44444444.2233333333.....112233444555555566677777788888888888889999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|386002572|ref|YP_005920871.1| 340 ldlkgrvearrstlrasseleehgvdfvrpmlnvtvirggikenivpdrcvlrgdrrvipeermeeaaaeleremaa 416
                                       999999999999999999999999999999999999999999999999***************************** PP

                                       .EEEEEEE..EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEE.EEEESS.GGCTT CS
                                       .xxxxxxx..xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxx.xxxxx RF
                     Peptidase_M20 116 .kvevell..eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agiptv.mifgpg.sglaH 183
                                         v++e++  +g++p++++ d+p+v+ +++a+e + g++++l   + ++ d +++    gipt+ +++g+  +++ H
  gi|386002572|ref|YP_005920871.1| 417 lPVDLEWRswMGYPPMRIDpDHPWVAEVRRALEGASGRSPRLAGAQ-YSLDQAYVaevTGIPTCvYGVGRQtDSNPH 492
                                       9788888888************************99*999999888.********777777966256995537**** PP

                                       STTTEEEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 184 spnEyvdledlekgikvlarll 205
                                       +p+E+v ledl  ++++la+l+
  gi|386002572|ref|YP_005920871.1| 493 GPDENVTLEDLSIYARFLAALI 514
                                       *******************998 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   9.5e-26   5.7e-22       1     103 [.     300     416 ..     300     421 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 9.5e-26
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC...................TCCTCCCCCEEC CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..............eerslprttlnvtgi 63 
                                       ig  G+++++ tv+gka+Hsga   g+NAiek+  ++++l d++g+++              ++ ++ r+ lnvt+i
  gi|386002572|ref|YP_005920871.1| 300 IGSNGIITWEATVRGKAAHSGASFLGENAIEKALPVIEALLDLKGRVEarrstlrasseleeHGVDFVRPMLNVTVI 376
                                       5789************************************************************************* PP

                                       CE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  64 egGsaknvipdeaeakidiRllpgedpeevleeieeilek 103
                                       +gG + n++pd++ +  d+R+ p+e  ee+ +e+e  +++
  gi|386002572|ref|YP_005920871.1| 377 RGGIKENIVPDRCVLRGDRRVIPEERMEEAAAELEREMAA 416
                                       **********************************988766 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   9.6e-09   5.7e-05       1      98 [.     184     292 ..     184     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.6e-09
                                       EEEEEESTTCESEEEEEEEE--B-TTT.............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEE CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg.............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgv 63 
                                       N+ a+l  +a +e++++  H+D v+ g             +g     G+ D+   vaal+  +r+++a g rp+r++
  gi|386002572|ref|YP_005920871.1| 184 NLWARLDVGA-EETMVIYTHLDVVPAGegwskdpfaldirDGRiYGRGVADSKGAVAALIAALRAIEATG-RPQRNL 258
                                       7889999999.99*************9***98888888764445567********************988.****** PP

                                       EEEEESSCSGSSHHHHHHHHHHCCCTTEEEEEEEC CS
                     Peptidase_M28  64 rflffdaEEagllGSkafakakpelkkiaavlnlD 98 
                                        +l+++ EE g +    ++ a++ l k +++l +D
  gi|386002572|ref|YP_005920871.1| 259 LVLLTTDEEGGGYSGLCYF-ADEGLVKGDVMLCMD 292
                                       *********9766555555.455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 3212.15
//
Query:       gi|386002573|ref|YP_005920872.1|  [L=143]
Description: molybdopterin-guanine dinucleotide biosynthesis protein MobB [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-17   62.5   0.1    4.5e-17   62.2   0.1    1.1  1  MobB           Molybdopterin guanine dinucleotide synthesis p
  ------ inclusion threshold ------
      0.039   13.7   0.1      0.058   13.1   0.1    1.3  1  AAA_29         P-loop containing region of AAA domain
      0.063   13.3   0.1       0.09   12.8   0.1    1.3  1  AAA_14         AAA domain
       0.08   12.3   0.3       0.12   11.7   0.3    1.2  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.11   12.6   0.3       0.15   12.2   0.3    1.4  1  MMR_HSR1       50S ribosome-binding GTPase
       0.12   12.4   0.0       0.17   11.9   0.0    1.2  1  Dynamin_N      Dynamin family
       0.18   12.3   0.0       0.18   12.2   0.0    1.1  1  AAA_23         AAA domain
       0.25   11.1   0.3       0.34   10.7   0.3    1.1  1  ATP_bind_1     Conserved hypothetical ATP binding protein
        0.3   10.0   0.1       0.48    9.3   0.1    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.1   2.3e-20   4.5e-17       1     109 [.       3     107 ..       3     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2.3e-20
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleea 77 
                                       v+++vg+++sGKTtL+e ++++l+ rg rvgtiK    g+ v++ g D+ rh +AGA+ v+ +++er+    ++   
  gi|386002573|ref|YP_005920872.1|   3 VISVVGTKKSGKTTLVEAMVRALRGRG-RVGTIKNMP-GHPVEDRG-DTRRHFEAGADVVVGVGSERILFKVSRG-- 74 
                                       689***********************9.9*****865.66777777.*************999999998888863.. PP

                              MobB  78 elsleellarlse..vDlvlvEGfkkealpkiev 109
                                          lee l+ l++  v + +vEGfk++ lpki++
  gi|386002573|ref|YP_005920872.1|  75 -GGLEEALEELRAsgVEFAIVEGFKTSGLPKIVL 107
                                       .47888888884446*****************86 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.9e-05     0.058      26      50 ..       5      29 ..       1      33 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                            AAA_29 26 lltGpsGsGKSTllDAiqalLvpak 50
                                       ++G+  sGK+Tl+ A+   L ++ 
  gi|386002573|ref|YP_005920872.1|  5 SVVGTKKSGKTTLVEAMVRALRGRG 29
                                      589**************99987765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.5e-05      0.09       3      26 ..       2      25 ..       1      44 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikel 26
                                      k++ ++G +++GKTtl++ +++ l
  gi|386002573|ref|YP_005920872.1|  2 KVISVVGTKKSGKTTLVEAMVRAL 25
                                      7899*************9998766 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   6.2e-05      0.12      44      62 ..       6      24 ..       3      27 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                                      EE--TTSSHHHHHHHHHHH CS
                      FtsK_SpoIIIE 44 vaGatgsGKStalntLilS 62
                                      v+G+++sGK+t + +++ +
  gi|386002573|ref|YP_005920872.1|  6 VVGTKKSGKTTLVEAMVRA 24
                                      9***************976 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   7.4e-05      0.15       2      29 ..       4      34 ..       3      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                                      EEEEESTTSSHHHHHHHHHTS...TEEESSS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge...kaivsdk 29
                                      + +vG   +GK+tL+ a++++   + +v+ +
  gi|386002573|ref|YP_005920872.1|  4 ISVVGTKKSGKTTLVEAMVRAlrgRGRVGTI 34
                                      789****************855444444433 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.7e-05      0.17       1      20 [.       4      23 ..       4      30 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                                      EEEEEBTTTTHHHHHHHHHT CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                      i vvG+ +sGK+++++a+++
  gi|386002573|ref|YP_005920872.1|  4 ISVVGTKKSGKTTLVEAMVR 23
                                      78***************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.3e-05      0.18      24      52 ..       6      33 ..       2     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                            AAA_23 24 ItGpNGaGKTTildAiklaLygetprlsr 52
                                      ++G   +GKTT+++A+  aL g+ +r ++
  gi|386002573|ref|YP_005920872.1|  6 VVGTKKSGKTTLVEAMVRALRGR-GRVGT 33
                                      678888**************995.33333 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00017      0.34       1      30 [.       6      35 ..       6      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavv 30
                                      vvG+  sGKtt+v+a++  l+ rgr   + 
  gi|386002573|ref|YP_005920872.1|  6 VVGTKKSGKTTLVEAMVRALRGRGRVGTIK 35
                                      89****************999998866655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00024      0.48      18      49 ..       4      35 ..       2      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivl 49
                                      i +vGt  sGKt+ +e+++ra+r rg    + 
  gi|386002573|ref|YP_005920872.1|  4 ISVVGTKKSGKTTLVEAMVRALRGRGRVGTIK 35
                                      5689*********************9765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1006.77
//
Query:       gi|386002574|ref|YP_005920873.1|  [L=218]
Description: hypothetical protein Mhar_1893 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1371.03
//
Query:       gi|386002575|ref|YP_005920874.1|  [L=325]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-11   43.3   0.0    2.1e-10   41.3   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.035   14.4   0.0       0.11   12.9   0.0    1.8  1  CbiX         CbiX


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   2.3e-14   2.1e-10       1     162 [.      95     249 ..      95     254 .. 0.81
   2 ?    1.3   0.0     0.043   3.9e+02      89     140 ..     247     296 ..     243     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.3e-14
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vp 76 
                                       ++v++ C ++C+fCa+p+  + +++++++ ve++++ ++++      + + l++g      ++v  ++++++     
  gi|386002575|ref|YP_005920874.1|  95 ITVSERCIYDCKFCAVPK-LSGGVKPKERVVEMVAQALDSGE----LEAISLTSGVERTPEEEVARVAEIVRALrRF 166
                                       67999************9.48888888888888888888886....9999999776666555555555555544445 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivg 151
                                       ++ i v++ + +      ++l e+g d +  ++e +d+  + + + +g +++++++al  ++++ + r  v++++++
  gi|386002575|ref|YP_005920874.1| 167 DLPIGVSVTPARG---SSKALQEAGADEIKYNVECLDPVLFGRVC-PGASLDKIKAALADAAAR-FGRnrVFSNVIV 238
                                       6666666666665...77***************************.*****************9.55559******* PP

                                       BTTTSHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeelee 162
                                       + Ge++  l+e
  gi|386002575|ref|YP_005920874.1| 239 GLGESEPSLRE 249
                                       ****9988877 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.043
                                       HGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  89 pdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklrea 140
                                       + +e +e+l+e+g     + +  +++ +v +  + ++++e++l++ + lr+a
  gi|386002575|ref|YP_005920874.1| 247 L-REGIEELAEMG-VLPVIRAVYPHPLRVGEVEMVRPSPERLLDLSRHLRRA 296
                                       4.78899999999.77777777778878888888889999999999999987 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05      0.11       2      55 ..     210     262 ..     210     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                                       STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEE CS
                              CbiX   2 GSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkri 55 
                                       G+++++ +++++++a+++ +++ f  v +g  e +epsl+e+++elae+gv  +
  gi|386002575|ref|YP_005920874.1| 210 GASLDKIKAALADAAARFGRNRVFSNVIVGLGE-SEPSLREGIEELAEMGVLPV 262
                                       6677888999*********************99.9**************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2155.97
//
Query:       gi|386002576|ref|YP_005920875.1|  [L=148]
Description: hypothetical protein Mhar_1895 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.6   0.0       0.32   11.0   0.0    1.3  1  RNHCP     RNHCP domain


Domain annotation for each model (and alignments):
>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.8e-05      0.32      44      76 ..      32      63 ..      21      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.8e-05
                             RNHCP 44 seCkglmepiavevkkkkewvivhrCekCgelk 76
                                      + C+g +++++   ++ ++w +  rC+ Cg++ 
  gi|386002576|ref|YP_005920875.1| 32 AGCGGELSSLGCY-STPGGWLVASRCRGCGSIV 63
                                      68*********97.669************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 972.42
//
Query:       gi|386002577|ref|YP_005920876.1|  [L=257]
Description: Dihydrodipicolinate reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-42  141.9   0.0    1.3e-41  141.4   0.0    1.2  1  DapB_C        Dihydrodipicolinate reductase, C-terminus
    8.9e-26   90.4   0.0    1.6e-25   89.7   0.0    1.4  1  DapB_N        Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.014   15.0   0.2      0.035   13.8   0.1    1.5  1  Peripla_BP_6  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   2.2e-45   1.3e-41       1     121 []     124     254 ..     124     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 2.2e-45
                                       HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH.................-S-ETTCCCEEE CS
                            DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia....egke.........arkkkeigihsv 64 
                                       Gvnl+ +l+e+aa  l++ yd+e+iE+Hh+kK+DaPSGTA++ ++ +a       +           + +eig+h+v
  gi|386002577|ref|YP_005920876.1| 124 GVNLFWRLIEDAAISLEG-YDIEVIEAHHRKKMDAPSGTAAEAVRVLAgvtgR--DavvygregqGLRGDEIGVHAV 197
                                       9***************99.*****************************77650..245555434344458******* PP

                                       ETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                            DapB_C  65 RgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                       R+g++vg+h+vlfag ge++eikh+a+sr+ Fa+Ga++aa+w+a++ +g+y+m +vL
  gi|386002577|ref|YP_005920876.1| 198 RAGDIVGDHTVLFAGPGERLEIKHQAHSRQAFATGAVRAARWVASATPGIYTMAEVL 254
                                       *******************************************9999********98 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   2.6e-29   1.6e-25       1     124 []       3     121 ..       3     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2.6e-29
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliD 73 
                                       +++av+G +GrmG+ +++ + + edl lva++d  +       +ge lg    gv+v+   dl+evl++  a+vliD
  gi|386002577|ref|YP_005920876.1|   3 VRIAVAGSRGRMGQLLIEEIGRFEDLSLVAGFDLVG-------VGEPLGG---GVFVSdpRDLAEVLRSsgAQVLID 69 
                                       69********************************99.......5655554...89999788*******99******* PP

                                       -S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHH.HTTTSEEEE-S-- CS
                            DapB_N  74 FTtpeavlenlklalekgvklViGTTGlseeelaelee.lakkigvviapNf 124
                                       FT+p+a++en+++a+++gv+lV+GTTGls+ ++ e++  +  k+++vi+pN+
  gi|386002577|ref|YP_005920876.1|  70 FTAPAATVENVRVAADRGVNLVVGTTGLSDPQRREIAGsIEGKVAAVISPNY 121
                                       ************************************9945566********7 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.8e-06     0.035     162     246 ..      32     115 ..      25     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-06
                                       CTEEEEEEEEE-TTH....HHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHHHHH CS
                      Peripla_BP_6 162 aGgevvgeepvplgt....tdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsgseedlka 234
                                       aG+++vg +  plg+    +d+  ++  ++++ga++++  +++a+++  ++ aa+ G++     ++++++s+++ + 
  gi|386002577|ref|YP_005920876.1|  32 AGFDLVG-VGEPLGGgvfvSDPRDLAEVLRSSGAQVLIDFTAPAATVENVRVAADRGVNL---VVGTTGLSDPQRRE 104
                                       5777664.33355555688999999**********************************5...688999***99999 PP

                                       HHHHHHTTEEEE CS
                      Peripla_BP_6 235 lggeaaegvlav 246
                                       ++g + eg +a+
  gi|386002577|ref|YP_005920876.1| 105 IAG-SIEGKVAA 115
                                       998.78885554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1496.41
//
Query:       gi|386002578|ref|YP_005920877.1|  [L=287]
Description: Dihydrodipicolinate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-95  317.7   0.0    4.9e-95  317.5   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.5   0.0   2.8e-99   4.9e-95       6     286 ..       2     280 ..       1     283 [. 0.98

  Alignments for each domain:
  == domain 1  score: 317.5 bits;  conditional E-value: 2.8e-99
                                       EEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSH CS
                             DHDPS   6 italvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnst 82 
                                       ++a++tpf edg++d+e lr ++e+  ++gv g+v +GttGEsatl+ ee++ +veiave a  r++v+ag+Gsn+t
  gi|386002578|ref|YP_005920877.1|   2 LPAIITPFREDGEVDEEGLRGNVEYFSAAGVAGIVPCGTTGESATLNFEEHKRVVEIAVESA--RVKVVAGTGSNNT 76 
                                       789*********************************************************87..8************ PP

                                       HHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEE CS
                             DHDPS  83 seaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivg 159
                                       +ea++l+k+ae+aGad++l++tPYYnkp+ +g+  hf+a++e+ dlp+ilYnvp+rt  +l+pe v++La+len++g
  gi|386002578|ref|YP_005920877.1|  77 REAVELTKHAEDAGADAALLITPYYNKPNDRGMLAHFRAVAESSDLPLILYNVPGRTSINLKPELVAELAKLENVIG 153
                                       ***************************************************************************** PP

                                       EEE-SS-CTHHHHHHCCCS.TTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                             DHDPS 160 vKeavgdleevikikkevg.kdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnek 235
                                       +Kea+g+l+++  i++ ++ +++ ++sGdd l+l+++ lG++Gvisv +++a+++m ++++a+ +Gdl++a+ l+  
  gi|386002578|ref|YP_005920877.1| 154 IKEASGNLSQISAIIEMTRdEEFFVLSGDDGLTLPIMALGGKGVISVVADVAPRKMVAMVDAMLKGDLEKARRLHYI 230
                                       *************999886258******************************************************* PP

                                       HHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHH CS
                             DHDPS 236 llplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleall 286
                                       l pl+ +lf e+n+i+vkta  ++Gl +++ lr Pl+p++e+++ +l++++
  gi|386002578|ref|YP_005920877.1| 231 LSPLVSALFLETNPIPVKTATGMIGLAAGP-LRLPLAPMAEKNEMRLKEAV 280
                                       ******************************.***********999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1911.15
//
Query:       gi|386002579|ref|YP_005920878.1|  [L=63]
Description: 30S ribosomal protein S17e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-11   43.3   0.4    3.4e-11   43.1   0.4    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.4   1.9e-15   3.4e-11       1      56 [.       1      56 [.       1      61 [. 0.97

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.9e-15
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHH CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvth 56
                                      mg v+ + +K  a  +++ y   ++ndF++nk +++e + i++k +rn++aGy+t+
  gi|386002579|ref|YP_005920878.1|  1 MGSVKPNYIKNFADDLMKAYQGVFNNDFEHNKDMVSEYTDIKNKTIRNRVAGYITR 56
                                      899***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 430.40
//
Query:       gi|386002580|ref|YP_005920879.1|  [L=461]
Description: Phosphomethylpyrimidine kinase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-78  261.7   0.1    7.1e-78  261.4   0.1    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    1.9e-58  196.7   0.0    2.8e-58  196.2   0.0    1.3  1  ThiP_synth    Thiamine-phosphate synthase
    2.8e-08   33.4   1.4    5.1e-08   32.6   1.4    1.3  1  PfkB          pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.4   0.1   1.2e-81   7.1e-78       1     246 []      12     251 ..      12     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 1.2e-81
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       DssGGAGiqAD+ktf alg++g+s+ita+taqnt gv ev+p+p+e v +ql a++ed++++a+K+Gml+s+e++  
  gi|386002580|ref|YP_005920879.1|  12 DSSGGAGIQADIKTFGALGCHGTSAITAVTAQNTLGVLEVYPMPPEAVISQLAALAEDFEISAAKTGMLSSREVVLE 88 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       va +++++++p+V+DPV+ a+ g +ll++ea+ +l e+L+pla v+tPN++EaeaL+g ++++e ++ +a++++l+l
  gi|386002580|ref|YP_005920879.1|  89 VAGFFEREEIPLVVDPVVEAEAGGRLLDPEALGLLVERLIPLARVVTPNIFEAEALTGIRVTDEGSALRAGEAILDL 165
                                       ***************************************************************************** PP

                                       T-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvtea 231
                                       ga+a +++Gghl g      d+l++ +++ ++++er++   +hG GCt+s+a aa la g+++eeA + Ak++   +
  gi|386002580|ref|YP_005920879.1| 166 GAEAAVVTGGHLAG-----DDLLVTAKGYCIIRGERVP-GGNHGVGCTYSAATAAFLAGGRDIEEAARLAKAFAAGS 236
                                       ***********933.....49*****************.99************************************ PP

                                       HHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 232 ikealelgkgagpvn 246
                                       +++++++g+ga pvn
  gi|386002580|ref|YP_005920879.1| 237 VRKSIAVGRGASPVN 251
                                       *************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.2   0.0   4.7e-62   2.8e-58       2     164 ..     269     447 ..     268     448 .. 0.95

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 4.7e-62
                                       HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC- CS
                        ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfd 78 
                                       +++++e+l +e+++ +liPevg N+++a+ +A+++eDvaav+GR+vr+++rv+++g+++fgas+hvar++laam+fd
  gi|386002580|ref|YP_005920879.1| 269 VSDGVEALLSEPALVDLIPEVGLNLGMAIFGASGPEDVAAVEGRLVRAGRRVRACGSVRFGASRHVARIILAAMSFD 345
                                       67889************************************************************************ PP

                                       TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC......S...........-ECEEE CS
                        ThiP_synth  79 pevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel......e...........vpdviy 138
                                       p +raa+n+r+ e++lea+ +lgl++++f+reeepe+ ++tm+wg+ eai++       +           vp+vi+
  gi|386002580|ref|YP_005920879.1| 346 PGARAAMNLRFGEDVLEAALALGLSASDFSREEEPEG-EKTMSWGTGEAIRRFrsgskeGgatdpgrlerpVPQVIW 421
                                       *************************************.8***********999887765055667778889****** PP

                                       E--BCTB--EEEEEESSHHHHHHHHH CS
                        ThiP_synth 139 deGgvGkEpmiyvlgkdaeevvekvl 164
                                       d+Gg GkEpm+++lg++a ev++ ++
  gi|386002580|ref|YP_005920879.1| 422 DRGGPGKEPMLRLLGRSAGEVADLAV 447
                                       **********************9876 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   1.4   8.5e-12   5.1e-08     177     293 ..     124     240 ..     109     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.5e-12
                                       HHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGG.GEEEEEETTEEEEEEE.SSSS-S CS
                              PfkB 177 llellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGk.eGalvvekdgelkvpavpkvkvv 252
                                       +++l++la +++pn  E+ealtg   +d+ +al+a+++++  ga+  vvt G   G  +  + + +++ +  ++ + 
  gi|386002580|ref|YP_005920879.1| 124 VERLIPLARVVTPNIFEAEALTGIRVTDEGSALRAGEAILDLGAEAAVVTGGHlAGDDLLVTAKGYCIIR-GERVPG 199
                                       6899************************************************845666666888888888.67999* PP

                                       BGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSS CS
                              PfkB 253 DttGAGDsfvggflaallegksleealrfanavAalvvqkk 293
                                          G G ++ ++ +a l+ g ++eea+r+a a+Aa +v+k+
  gi|386002580|ref|YP_005920879.1| 200 GNHGVGCTYSAATAAFLAGGRDIEEAARLAKAFAAGSVRKS 240
                                       ***********************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2913.92
//
Query:       gi|386002581|ref|YP_005920880.1|  [L=186]
Description: hypothetical protein Mhar_1900 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-06   27.8   7.0        0.5   10.3   0.0    5.0  5  Clathrin_H_link  Clathrin-H-link


Domain annotation for each model (and alignments):
>> Clathrin_H_link  Clathrin-H-link
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   2.8e-05       0.5      10      28 ..      10      28 ..       6      31 .. 0.92
   2 !    4.6   0.0    0.0017        31       7      30 ..      41      64 ..      38      67 .. 0.90
   3 !    3.7   0.2    0.0033        59      10      30 ..      78      98 ..      71     109 .. 0.86
   4 !    2.7   0.1    0.0067   1.2e+02       8      31 ..     110     133 ..     104     136 .. 0.86
   5 !    6.4   0.1   0.00047       8.5      11      42 ..     147     180 ..     143     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.8e-05
                   Clathrin_H_link 10 vqqFeqllaqgnykeAakv 28
                                      ++ Fe+ +aqg+y+eAak+
  gi|386002581|ref|YP_005920880.1| 10 IRLFEERMAQGRYREAAKI 28
                                      578***************8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0017
                   Clathrin_H_link  7 dlyvqqFeqllaqgnykeAakvAa 30
                                      d + ++++++l  g+y+ Aa++A 
  gi|386002581|ref|YP_005920880.1| 41 DAVRREYSRVLGIGEYSLAAELAK 64
                                      77899****************996 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0033
                   Clathrin_H_link 10 vqqFeqllaqgnykeAakvAa 30
                                       ++F + +  ++yk+Aa+ A 
  gi|386002581|ref|YP_005920880.1| 78 SRSFVRKVDGEQYKAAAEFAK 98
                                      6789999999*******9985 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.0067
                   Clathrin_H_link   8 lyvqqFeqllaqgnykeAakvAae 31 
                                         ++ +++ +  g  k+Aa +A+ 
  gi|386002581|ref|YP_005920880.1| 110 AAIRAYNKSMDFGLAKNAADIAVD 133
                                       568899****************86 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.00047
                   Clathrin_H_link  11 qqFeqllaqgnykeAakvAae..spqgiLRtpet 42 
                                       + F   + +g y++A kvA e     ++LR +et
  gi|386002581|ref|YP_005920880.1| 147 KAFAAHMDSGLYNKALKVAREygLSPDLLREAET 180
                                       67999**************873323447777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1277.31
//
Query:       gi|386002582|ref|YP_005920881.1|  [L=137]
Description: hypothetical protein Mhar_1901 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-44  149.2   0.3    6.4e-44  149.0   0.3    1.0  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.3   3.6e-48   6.4e-44       3     127 .]       8     132 ..       6     132 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 3.6e-48
                                       ---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE.. CS
                             DUF61   3 ilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelgesv 79 
                                       ++ k+++s+n+hlP +rk+L+elL+eekp +++kd++++++dk+el+ ++e +p++lwd+l+LPIl+em p++g++ 
  gi|386002582|ref|YP_005920881.1|   8 LIVKTVQSMNQHLPGRRKRLTELLQEEKPGVRGKDNTFFIMDKKELKVISEAVPKYLWDRLRLPILIEMAPQYGSGS 84 
                                       6889************************************************************************* PP

                                       EEEES-HHHHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TEE CS
                             DUF61  80 ylvrgkaevkvvskilgkereeedelviykpevrelrrklptatqliF 127
                                       ++v+g+ae  +v+k+l++er  ++ ++iy+pe+relrr+lpt++q++F
  gi|386002582|ref|YP_005920881.1|  85 ARVQGEAEGILVRKLLKIERGDRKMVIIYMPEIRELRRNLPTTSQYAF 132
                                       ***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 944.99
//
Query:       gi|386002583|ref|YP_005920882.1|  [L=395]
Description: Metal dependent phosphohydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   46.7   2.6    5.2e-12   46.1   1.1    2.2  2  HD        HD domain
  ------ inclusion threshold ------
       0.09   12.2   0.0       0.17   11.4   0.0    1.4  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   1.1   5.8e-16   5.2e-12       1     121 [.      50     162 ..      50     163 .. 0.71
   2 ?   -2.5   0.0      0.63   5.7e+03      21      35 ..     363     380 ..     348     389 .. 0.68

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 5.8e-16
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH......HHHCTCCHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk......eeefekflaHekvgaeilrev 70 
                                       r+eHsl+ ++la+ l ++lg+ e+d   +++aaLlHD+G+gpf++  e+       e    +   He+++ ++ r +
  gi|386002583|ref|YP_005920882.1|  50 RFEHSLGSYHLAGLLSRHLGLdEADGTEIQAAALLHDVGHGPFSHVTERVlssylrE----E---HEDIADRLRRGE 119
                                       79*******************************************999997655431....2...444433333333 PP

                                       HHHHHHH....HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  71 ekrlgld....ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +++   d       +++lir  +               q  + + +v+++D+l +
  gi|386002583|ref|YP_005920882.1| 120 LGDVLRDrglqPHRIQRLIRGETPLG------------QVVSGEVDVDRMDYLTR 162
                                       33321112222456777777766666............67788888888888776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.63
                                       H...HHHHHHHHHHHHHT CS
                                HD  21 e...eedrellllaaLlH 35 
                                           ee r++++ aa  H
  gi|386002583|ref|YP_005920882.1| 363 IyttEEHRDRVRRAATSH 380
                                       133477777777777766 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.9e-05      0.17      96     149 ..      51     106 ..      41     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHHHHHHTT-S-H..HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHH CS
                              HDOD  96 wehslavAlvarelaeelgledp..eeaflaGLLhdiGklvllsllpeeleellek 149
                                        ehsl +  +a  l ++lgl+++   e+  a+LLhd+G   + ++ +  l+  l++
  gi|386002583|ref|YP_005920882.1|  51 FEHSLGSYHLAGLLSRHLGLDEAdgTEIQAAALLHDVGHGPFSHVTERVLSSYLRE 106
                                       58999999**************76899***********999999988888777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2367.81
//
Query:       gi|386002584|ref|YP_005920883.1|  [L=192]
Description: hypothetical protein Mhar_1903 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1274.94
//
Query:       gi|386002585|ref|YP_005920884.1|  [L=621]
Description: Cell surface protein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-28   98.0   0.3    8.5e-28   97.2   0.3    1.3  1  NosD             Periplasmic copper-binding protein (NosD)
    4.2e-09   36.4   4.1    4.2e-09   36.4   4.1    2.0  2  Beta_helix       Right handed beta helix region
  ------ inclusion threshold ------
        0.1   12.4   0.9        0.3   10.9   0.6    1.7  2  Pectate_lyase_3  Pectate lyase superfamily protein


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 !   97.2   0.3   1.4e-31   8.5e-28      71     239 ..     121     315 ..      83     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 1.4e-31
                              NosD  71 ntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNries 147
                                         ++++  +++++G+ +  +  +t+e+N +s+n++ Gill+  ++  i+nN + nn+ G+ le+s +n+i gNri++
  gi|386002585|ref|YP_005920884.1| 121 FLVTGSGSEEMDAGVRVLGEG-CTVEDNLLSGNRI-GILLQSVTGGAIRNNSVENNGIGLLLERSWDNEIAGNRIAE 195
                                       556666777778888888887.9999999999999.99999999999999999999999999999999999999999 PP

                              NosD 148 nqkiGil.....................................llsssegntiynNyFinnsenvkydgsnnneWn 187
                                       n ++Gi                                      +  + ++n+iy+N +++n en+ +dg  +n W+
  gi|386002585|ref|YP_005920884.1| 196 N-GVGIKavrqnasesitasdsggvsikyrpkteaatlevskigFAGGLKENRIYGNELLDNGENALDDG--ENLWD 269
                                       9.99999999999999999999999999*************99999999*********************..9**** PP

                              NosD 188 ttktsgtniiggpylgGNyWsdydg.....eDadgDGigDtpYeindgv.iDylplvn 239
                                                      gGN+++d+d      +D+ +DG++D p +i++g  +D+ p ++
  gi|386002585|ref|YP_005920884.1| 270 DGR------------GGNHFDDFDAieegcRDRERDGLCDAPRKIPGGPsVDERPIAS 315
                                       ***............*******************************988799999765 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 !   36.4   4.1     7e-13   4.2e-09      22     137 ..     105     214 ..      89     233 .. 0.81
   2 ?    0.1   0.1      0.11   6.3e+02      76      94 ..     242     260 ..     210     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7e-13
                                       SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT...-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SE CS
                        Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgs...snntisnntisdnngggialfgasnnlienneitdnggsGi 95 
                                       +g+G++l+g++  +i++  +++++ + ++       +++t+++n  s+n   gi l+   +  i+nn +++ng  G+
  gi|386002585|ref|YP_005920884.1| 105 SGSGVTLQGDGA-RIQGFLVTGSGSEEMDAGVRvlgEGCTVEDNLLSGNR-IGILLQSVTGGAIRNNSVENNGI-GL 178
                                       7999*******9.99999999955555555444555**************.*********************76.** PP

                                       E-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES- CS
                        Beta_helix  96 ylnyssnntienNiidnnagsGividdsssnvtvtnNtitnn 137
                                        l+ s +n i +N+i +n+  Gi    ++        +it +
  gi|386002585|ref|YP_005920884.1| 179 LLERSWDNEIAGNRIAENG-VGIKAVRQN-----ASESITAS 214
                                       *******************.999988888.....23333333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                                       --S--EEES-EEES-SS-S CS
                        Beta_helix  76 gasnnlienneitdnggsG 94 
                                       g + n i++ne  dng++ 
  gi|386002585|ref|YP_005920884.1| 242 GLKENRIYGNELLDNGENA 260
                                       5567778888888877653 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.32   1.9e+03      21      73 ..      60     105 ..      58     130 .. 0.58
   2 ?   10.9   0.6   5.1e-05       0.3     153     215 .]     139     201 ..     110     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.32
                                       HHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-TTTEEEEE-TT CS
                   Pectate_lyase_3  21 iqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvGdgngrpvlkaaaa 73 
                                       iq+a+   ++ ++g+ V +  G Y+ +  +    g+ L+G g  rp++ a ++
  gi|386002585|ref|YP_005920884.1|  60 IQAAL---DEARSGDAVLVEGGVYRERLVV--SEGIALQGIG--RPQIDAGGS 105
                                       77888...6777777788888888644443..4444444444..344433332 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.1e-05
                                       --EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEEE CS
                   Pectate_lyase_3 153 gsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinncegGid 215
                                       g+g +++d   sg  +igi + +    ++rn+ ++n++ g  ++++w+  +++++i + ++Gi+
  gi|386002585|ref|YP_005920884.1| 139 GEGCTVEDNLLSG-NRIGILLqSVTGGAIRNNSVENNGIGLLLERSWDNEIAGNRIAENGVGIK 201
                                       5667889******.*******8899999****************************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4328.64
//
Query:       gi|386002586|ref|YP_005920885.1|  [L=265]
Description: 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-62  210.4   0.1    3.7e-62  210.0   0.1    1.1  1  DeoC          DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.013   15.0   0.2        2.1    7.7   0.0    2.6  3  PEP_mutase    Phosphoenolpyruvate phosphomutase
      0.033   13.8   0.1      0.082   12.5   0.0    1.6  2  Peripla_BP_4  Periplasmic binding protein domain
       0.44   10.4   2.2         11    5.9   0.0    2.7  3  DUF2862       Protein of unknown function (DUF2862)


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   0.1   8.2e-66   3.7e-62       1     235 []      21     237 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 8.2e-66
                                       EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTT CS
                              DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskq 77 
                                       +vi+++D++++ +++++        +l ++v++++++ga+avl ++g++ +++++y++di+l+v+++++t l ++++
  gi|386002586|ref|YP_005920885.1|  21 TVIIPMDHGISVGPVKGL------VNLSEMVDRVAEGGANAVLQQKGMVKHGHRGYGSDIGLIVHMSASTALGPDPN 91 
                                       69****************......9***************************************************9 PP

                                       EEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  78 rdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                        +v  v++veea++ GAdav+v++++   gse+e+ +l++++ v+e+c+ +g+pli+++y+r+++i d +   d+v 
  gi|386002586|ref|YP_005920885.1|  92 NKVQ-VCQVEEALKVGADAVSVHINI---GSETEADQLKKLGSVAERCDFWGMPLIAMMYPRGDKIADPN-GVDVVS 163
                                       9999.*********************...***************************************99.999*** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvls 228
                                        Aar++aelGaDiiK++++        +d e+f++v++++pvp vv++GG+   ++e+fle+++ A+ +ag+ Gv++
  gi|386002586|ref|YP_005920885.1| 164 LAARAGAELGADIIKTNYT--------GDPETFREVVAGCPVP-VVIAGGPkteTDEEFLEMIRGAI-DAGGRGVAI 230
                                       *******************........****************.********999************.********* PP

                                       SHHHHTT CS
                              DeoC 229 GRaifqk 235
                                       GR++fq+
  gi|386002586|ref|YP_005920885.1| 231 GRNVFQH 237
                                       *****97 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1   4.7e+03     117     130 ..      39      52 ..      23      58 .. 0.59
   2 ?    4.7   0.0    0.0041        18     165     220 ..     102     165 ..      97     169 .. 0.75
   3 ?    7.7   0.0   0.00047       2.1     163     211 ..     167     215 ..     165     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                        PEP_mutase 117 ldieefaekiaaar 130
                                       +++ e+++++a++ 
  gi|386002586|ref|YP_005920885.1|  39 VNLSEMVDRVAEGG 52 
                                       44444444444433 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0041
                        PEP_mutase 165 YaeAGAdgvfvpgl..........qkdaeiaelvaavdvplnvvplkgtlsvaelae.lGvarislg 220
                                        ++ GAd+v v+            +k  ++ae ++ +++pl++++    +  +++a+  Gv ++sl+
  gi|386002586|ref|YP_005920885.1| 102 ALKVGADAVSVHINigseteadqlKKLGSVAERCDFWGMPLIAMM---YPRGDKIADpNGVDVVSLA 165
                                       5789********99999999888677777888898889******9...4444444441457777765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00047
                        PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsvaelae 211
                                       ra ae GAd +      ++++ +e+va ++vp+++  +++t + +e+ e
  gi|386002586|ref|YP_005920885.1| 167 RAGAELGADIIKTNYTGDPETFREVVAGCPVPVVIAGGPKTETDEEFLE 215
                                       667899*****************************99887777777655 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.74   3.3e+03     219     239 ..      41      60 ..      30      65 .. 0.73
   2 ?   12.5   0.0   1.8e-05     0.082      38     178 ..      89     250 ..      79     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.74
                                       HHHHHHHHHTTSSEEEEE--H CS
                      Peripla_BP_4 219 tpealeaikdGtidatvaqdp 239
                                        +e+++++++G  + +v+q+ 
  gi|386002586|ref|YP_005920885.1|  41 LSEMVDRVAEGGAN-AVLQQK 60 
                                       56888888888877.666654 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.8e-05
                                       TT-HHHHHHHHHHHHHTT-SEEEE--SSH........HHHHHHHHHHHHTT-EEEEESTT...GCTTT-CEEEEEC- CS
                      Peripla_BP_4  38 endaaeQvaqiedaiakgvdgiivapvds........talapalkkakaaGIpVvafdsd...dapsgerlayvgfd 103
                                       +++++ Qv q+e a++ g+d++ v+ + +        + l ++ +++   G+p +a+  +    +++ +++ +v+  
  gi|386002586|ref|YP_005920885.1|  89 DPNNKVQVCQVEEALKVGADAVSVHINIGseteadqlKKLGSVAERCDFWGMPLIAMMYPrgdKIADPNGVDVVSLA 165
                                       678899*****************988877666677778888999999999******666666999999999999999 PP

                                       HHHHHHHHHHHHHHHCTTH............EEEEEETSCCCHHHHHHHHHHHHHHHHH-T.TCEECCEEESTTTCH CS
                      Peripla_BP_4 104 neaaGelqaeylaeklggk...........kgkvvilaGspgdpnaeeriegfrkvlkeyp.gikivaevaganwda 168
                                         a +el a+ ++ +  g+           +  vv +aG p +  +ee++e +r ++++ + g+ i   v +  +++
  gi|386002586|ref|YP_005920885.1| 166 ARAGAELGADIIKTNYTGDpetfrevvagcPVPVV-IAGGPKTETDEEFLEMIRGAIDAGGrGVAIGRNVFQ-HENP 240
                                       99999999999999999999999999988666666.6799999999***99999999995545555443334.6999 PP

                                       HHHHHHHHHH CS
                      Peripla_BP_4 169 ekaqqaleal 178
                                       +k ++a++a+
  gi|386002586|ref|YP_005920885.1| 241 TKMTRAISAI 250
                                       9998888877 PP

>> DUF2862  Protein of unknown function (DUF2862)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.013        58       1      18 [.       4      21 ..       4      29 .. 0.89
   2 ?    5.9   0.0    0.0025        11       5      51 ..      39      84 ..      34      86 .. 0.85
   3 ?   -3.7   0.0       2.5   1.1e+04       4      13 ..      93     102 ..      92     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                                      TT-EEEE----S---TTH CS
                           DUF2862  1 iGqkvkverlrdrvskel 18
                                      iG++v++er+ dr s ++
  gi|386002586|ref|YP_005920885.1|  4 IGKRVRMERIIDRNSGNT 21
                                      9************88776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0025
                                      EEE----S---TTHHHHBT-..EEEEEEEEE-SSSSEEEEEEETTS- CS
                           DUF2862  5 vkverlrdrvskelveklkkepvgtikdfKmtDGsgiGvvvkledgt 51
                                      v ++++ drv +  ++++ + + g++k      Gs+iG++v+++ +t
  gi|386002586|ref|YP_005920885.1| 39 VNLSEMVDRVAEGGANAVLQ-QKGMVKHGHRGYGSDIGLIVHMSAST 84
                                      56788889999999999888.799999999999*********98765 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.5
                                       EEEE----S- CS
                           DUF2862   4 kvkverlrdr 13 
                                       kv+v+++++ 
  gi|386002586|ref|YP_005920885.1|  93 KVQVCQVEEA 102
                                       8999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1566.62
//
Query:       gi|386002587|ref|YP_005920886.1|  [L=74]
Description: hypothetical protein Mhar_1907 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   43.7   0.2    1.9e-11   43.4   0.2    1.1  1  PC4       Transcriptional Coactivator p15 (PC4)


Domain annotation for each model (and alignments):
>> PC4  Transcriptional Coactivator p15 (PC4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.2     1e-15   1.9e-11       4      52 .]      13      61 ..      10      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1e-15
                                      TCCEEEEEEEETTEEEEEEEEEEECTTEEEEEEEEEEEEHHHHHHHHHH CS
                               PC4  4 skkrrvtvrefkGktlvdIReyyekdgelkPgkKGIsLtleqweaLkka 52
                                      + +  v+ +ef+G++ +dIRey++ d  +  +k+GI +++eqw+ ++++
  gi|386002587|ref|YP_005920886.1| 13 TTELVVRRTEFRGSAGIDIREYVTSDRYTGWSKNGIRIPVEQWRSFREI 61
                                      56678999****************98777789**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 493.09
//
Query:       gi|386002588|ref|YP_005920887.1|  [L=252]
Description: hypothetical protein Mhar_1908 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.25   11.6   0.0    1.3  1  TOPRIM_C  C-terminal associated domain of TOPRIM


Domain annotation for each model (and alignments):
>> TOPRIM_C  C-terminal associated domain of TOPRIM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.4e-05      0.25      40     119 ..      86     166 ..      79     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                          TOPRIM_C  40 kYYkGLgtstskeakeyfsnldkhlkefkleee.edkeaielaFskkkaderkewlkklepgtyldkkkkkisysdF 115
                                        Y++GL+ s  +  +ey++ +++++ e+ le+e e  ++ + aF + +  +  e l+  +  ++   kk +is++d 
  gi|386002588|ref|YP_005920887.1|  86 YYFRGLWFSLISLNSEYLRRVSDRVLEYALEHEfEMGRLYQQAFVEMRKLSPGEKLEISQLAHQTSVKKARISLEDL 162
                                       499***************************9994556999****887766655555555555555545567****** PP

                          TOPRIM_C 116 vnke 119
                                       +++e
  gi|386002588|ref|YP_005920887.1| 163 IDEE 166
                                       *988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1716.96
//
Query:       gi|386002589|ref|YP_005920888.1|  [L=400]
Description: translation initiation factor 2 subunit gamma [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-31  107.2   0.1    8.8e-31  106.0   0.1    1.7  1  eIF2_C          Initiation factor eIF2 gamma, C terminal
    1.4e-27   96.5   0.8    1.6e-26   93.0   0.8    2.1  1  GTP_EFTU        Elongation factor Tu GTP binding domain
    1.1e-07   32.1   0.5    3.6e-07   30.5   0.5    2.0  1  GTP_EFTU_D2     Elongation factor Tu domain 2
    3.3e-05   23.9   0.4    0.00076   19.4   0.1    2.3  2  RsgA_GTPase     RsgA GTPase
      0.004   17.2   0.3     0.0079   16.2   0.3    1.4  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
      0.007   16.4   0.4      0.013   15.5   0.4    1.4  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
  ------ inclusion threshold ------
      0.018   14.6   0.0       0.21   11.2   0.0    2.2  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.032   14.3   0.0       0.08   13.0   0.0    1.8  1  MMR_HSR1        50S ribosome-binding GTPase
      0.087   12.8   0.0       0.18   11.8   0.0    1.4  1  zinc-ribbons_6  zinc-ribbons
      0.096   12.3   0.2        0.2   11.2   0.1    1.6  2  Ras             Ras family
       0.18   11.6   0.5        6.8    6.4   0.0    2.7  3  PduV-EutP       Ethanolamine utilisation - propanediol utilis


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.1   5.4e-34   8.8e-31       2      86 .]     313     398 ..     312     398 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 5.4e-34
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESS.EEEEEEEEEEE-STTEEEEEEEEETTS CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkd.eakvkLkkPvcaekgekialsRrvekr 77 
                                       +++++++ller+vg+++e +ve+++++E+Lmln+G+a+t+gvv+s+++  +++v+L++Pvca  g+++a+sRrv++r
  gi|386002589|ref|YP_005920888.1| 313 SFTMKIRLLERVVGATDEADVEPIHTSEPLMLNVGTATTVGVVSSAREGgMVEVQLRRPVCAAAGDRVAVSRRVGAR 389
                                       589*********************************************55*************************** PP

                                       EEEEEEEEE CS
                            eIF2_C  78 WrLiGwGei 86 
                                       WrLiG+G+i
  gi|386002589|ref|YP_005920888.1| 390 WRLIGVGTI 398
                                       *******98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.8     1e-29   1.6e-26       9     193 ..       2     188 ..       1     189 [. 0.90

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1e-29
                                       EESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..................... CS
                          GTP_EFTU   9 ighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..................... 64 
                                       +ghvDhGKtTL+ +L    g              +D+++eE +rgi+i    +                        
  gi|386002589|ref|YP_005920888.1|   2 VGHVDHGKTTLVRALS---G------------VWTDQHSEEIKRGISIRLGYADATfrkcpncpapeaytvektcpg 63 
                                       8************998...2............2478999999******9999988888999************9*99 PP

                                       ...TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST. CS
                          GTP_EFTU  65 ...ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl. 135
                                           ++  ++++++D+PGH+  + ++  g++++Dgavl+++a+e  ++pqt+e+l  +   g+  i+++ NK+D + 
  gi|386002589|ref|YP_005920888.1|  64 cgsPSEVLRTVSFVDSPGHETLMATMLSGAAIMDGAVLIIAASEPcPQPQTKEHLMALDITGIDrIVIVQNKIDLVs 140
                                       985488899**********************************9879*****************788888******9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       k++l e  +e+k k+      ++  +++   + p+v++Sa ++ +v+ ++ea+ e +p
  gi|386002589|ref|YP_005920888.1| 141 KERLIEHYNEIK-KF------VKGTVAE---NAPIVPISAQQNVNVDMVIEAIEETIP 188
                                       99999******9.77......4444444...57********************99988 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.5   2.2e-10   3.6e-07       1      72 [.     220     300 ..     220     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.2e-10
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS..GS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikgled..ai 67 
                                       G+v++g++ +G+l+++d ++i +  ++ ++e       i t++++l +  ++++ea +g+ +Gv++ +++  +  ++
  gi|386002589|ref|YP_005920888.1| 220 GGVIGGTLTQGVLQPDDPIEIKPgRSV-ESEgrkqwvpIDTKVTALMAGGGPQEEATPGGLIGVGTQLDPALTksDL 295
                                       89*******************996655.6668***********************************9987766667 PP

                                       STTCE CS
                       GTP_EFTU_D2  68 ivGdt 72 
                                       +vG++
  gi|386002589|ref|YP_005920888.1| 296 LVGQV 300
                                       77776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.094   1.5e+02     105     136 ..       2      30 ..       1      34 [. 0.70
   2 !   19.4   0.1   4.6e-07   0.00076      13      99 ..      93     185 ..      70     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.094
                                       ECSTTSSHHHHHHHHCTT-----S-------- CS
                       RsgA_GTPase 105 vGqSGvGKStLinallpelelktgevseklgr 136
                                       vG+   GK+tL+ al +     t + se+ +r
  gi|386002589|ref|YP_005920888.1|   2 VGHVDHGKTTLVRALSGV---WTDQHSEEIKR 30 
                                       788889*********995...44444444444 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 4.6e-07
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       +a +d ++++++++ep  ++++ +  L+++  +gi ++viv nKiDl+++e+      e++++ + + a + +++ +
  gi|386002589|ref|YP_005920888.1|  93 AAIMDGAVLIIAASEPCPQPQT-KEHLMALDITGIdRIVIVQNKIDLVSKERliehynEIKKFVKGTVAENAPIVPI 168
                                       8889**********88777766.667888899999789999**********99997777888888888889999999 PP

                                       -TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  83 saktkegleelkellkd 99 
                                       sa+++ +++ + e++++
  gi|386002589|ref|YP_005920888.1| 169 SAQQNVNVDMVIEAIEE 185
                                       99999999988887776 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   4.8e-06    0.0079      58     100 ..     129     183 ..     126     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                        ++v NKiDl+s+e l e ++e              +v+iSa++++n+d + e+i
  gi|386002589|ref|YP_005920888.1| 129 IVIVQNKIDLVSKERLIEHYNEikkfvkgtvaenAPIVPISAQQNVNVDMVIEAI 183
                                       57899*****99998877766556778889987668999************9988 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   8.1e-06     0.013       5      28 ..      43      69 ..      40      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.1e-06
                                      -EE-TTT-...-EESSSB-TTT-SB-B CS
                            Nop10p  5 lrkcgkcr...vYTLkkvcpecggptk 28
                                       rkc++c     YT +k+cp cg+p +
  gi|386002589|ref|YP_005920888.1| 43 FRKCPNCPapeAYTVEKTCPGCGSPSE 69
                                      58899987777************9876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.19   3.1e+02       6      21 ..       2      17 ..       1      30 [. 0.72
   2 ?   11.2   0.0   0.00013      0.21     103     169 ..      87     155 ..      58     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                                      EESTTCCHHHHHHHHH CS
                              cobW  6 tGflGsGKTtLlnhll 21
                                      +G +  GKTtL+++l 
  gi|386002589|ref|YP_005920888.1|  2 VGHVDHGKTTLVRALS 17
                                      577778******9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                       SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEE..E-HHHHCHC..HHHHHHHHHHH CS
                              cobW 103 eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvl..nKtDlldeeallekleerlrql 169
                                       ++ l+ ++ +d+ v ++ a++   + +++e+++   ++  d +v+  nK+Dl+++e+l+e+ +e+ + +
  gi|386002589|ref|YP_005920888.1|  87 ATMLSGAAIMDGAVLIIAASEPCPQPQTKEHLMALDITGIDRIVIvqNKIDLVSKERLIEHYNEIKKFV 155
                                       556777888999999999999989999999999999**999877666*********9999998877655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05      0.08       5      96 ..       2     116 ..       1     168 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                       EESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE............................EEE CS
                          MMR_HSR1   5 vGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke............................iel 50 
                                       vG+   GK+tL++al+g  + + s++    + i+ g  +  ++  +                            + +
  gi|386002589|ref|YP_005920888.1|   2 VGHVDHGKTTLVRALSGVwTDQHSEEIKRGISIRLGYADatFR--KcpncpapeaytvektcpgcgspsevlrtVSF 76 
                                       9***************976445555554444454444432233..12346666666777777777777777777*** PP

                                       EECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT...TTCSHHHHHH CS
                          MMR_HSR1  51 vDtpGliegaseekglgkaflalee.adlillvvdas...eeklkpldee 96 
                                       vD pG  e       l  ++l+    +d ++l++ as       +p+ +e
  gi|386002589|ref|YP_005920888.1|  77 VDSPG-HE------TLMATMLSGAAiMDGAVLIIAASepcP---QPQTKE 116
                                       *****.44......677777776665688888887773330...333333 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.18      17      44 ..      44      73 ..      27      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      EE-TTT--..EEEEEEE-SSS-S---EEEE CS
                    zinc-ribbons_6 17 yhCeaCqe..dlkkealCpeCeqelevlka 44
                                       +C +C +   +++e++Cp C+++ evl+ 
  gi|386002589|ref|YP_005920888.1| 44 RKCPNCPApeAYTVEKTCPGCGSPSEVLRT 73
                                      57999*87779****************987 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.1   3.5e+03       4      17 ..       1      14 [.       1      31 [. 0.78
   2 ?   11.2   0.1   0.00012       0.2     106     160 ..     128     187 ..     114     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                      EEESTTSSHHHHHH CS
                               Ras  4 lvGdsavGKtslll 17
                                      +vG    GKt+l+ 
  gi|386002589|ref|YP_005920888.1|  1 MVGHVDHGKTTLVR 14
                                      5899999***9985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                                       EEEEEEETTTGGG.G-SS-.HHHHHHHHH...HHTSEEEEEBTTTTCTHHHHHHHHHHHH CS
                               Ras 106 pivLvGnKvDlee.kravs.teegeelak...elglkfletSAktnenveeafeellrei 160
                                        iv+v nK+Dl + +r ++ ++e +++ k     +++ + +SA++n nv+ ++e++ ++i
  gi|386002589|ref|YP_005920888.1| 128 RIVIVQNKIDLVSkERLIEhYNEIKKFVKgtvAENAPIVPISAQQNVNVDMVIEAIEETI 187
                                       589*******9873566652567788876222456999***************9998876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0042       6.8       6      23 ..       1      18 [.       1      29 [. 0.88
   2 ?    2.4   0.2     0.075   1.2e+02      94     142 ..     131     184 ..      71     185 .. 0.52
   3 ?   -2.2   0.0         2   3.2e+03      98     136 ..     327     365 ..     311     368 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0042
                         PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                      ++G+v+ GKttL +al+g
  gi|386002589|ref|YP_005920888.1|  1 MVGHVDHGKTTLVRALSG 18
                                      68**************97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.075
                         PduV-EutP  94 Giitkidlaedeeniea...veelLks..aGaekifevsavekegieellkyle 142
                                        +  kidl+++e  ie     ++++k   a  + i  +sa ++++++ +++ +e
  gi|386002589|ref|YP_005920888.1| 131 IVQNKIDLVSKERLIEHyneIKKFVKGtvAENAPIVPISAQQNVNVDMVIEAIE 184
                                       233688888777666651113344443113445589999999999999998886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                         PduV-EutP  98 kidlaedeenieaveelLksaGaeki.fevsavekegiee 136
                                        +d a d e i+++e l+ ++G ++    vs+ ++ g+ e
  gi|386002589|ref|YP_005920888.1| 327 ATDEA-DVEPIHTSEPLMLNVGTATTvGVVSSAREGGMVE 365
                                       45555.6677888888888888665415666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2613.16
//
Query:       gi|386002590|ref|YP_005920889.1|  [L=127]
Description: Nucleotide binding protein, PINc [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-39  133.1   0.1    6.3e-39  132.9   0.1    1.0  1  PIN_9     PIN like domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.1   3.5e-43   6.3e-39       1     116 []       3     116 ..       3     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 3.5e-43
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkg.kertaakvalsLaerceiveaeeeka 76 
                                       v+lDtnaLm+p qfgvd+fe le+l g  el+vp++vl+EL++la  +++ ++rtaa+++l+La rcei+ea+ e+a
  gi|386002590|ref|YP_005920889.1|   3 VLLDTNALMVPGQFGVDLFEGLEEL-GFRELLVPRPVLRELAALACLAESrRDRTAARIGLALAGRCEILEAS-EEA 77 
                                       89***********************.******************99887769*********************.*** PP

                             PIN_9  77 DdailelakeldaavlvTnDreLkkrllekgipvilLRqk 116
                                       Dda+++la + +aav+ TnD+eLkk+l ++g++vi+LRq+
  gi|386002590|ref|YP_005920889.1|  78 DDALVDLALKSGAAVF-TNDKELKKKLSTRGVTVIHLRQR 116
                                       ****************.**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 851.94
//
Query:       gi|386002591|ref|YP_005920890.1|  [L=190]
Description: DNA-directed RNA polymerase subunit E' [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-18   66.2   0.0    3.9e-18   65.6   0.0    1.3  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    6.4e-14   52.0   0.1    1.3e-13   51.0   0.1    1.5  1  S1             S1 RNA binding domain
  ------ inclusion threshold ------
      0.017   15.4   0.3      0.081   13.2   0.3    1.9  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   6.6e-22   3.9e-18       3      70 .]      10      77 ..       8      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 6.6e-22
                                      EEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  3 tvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +vr++P ++g++le+a++ +l++kye +v++ lG +vavl + +++eg++l g+G+vy+++ f+a+vF
  gi|386002591|ref|YP_005920890.1| 10 IVRIPPGQMGDPLEEAVEMALRNKYEARVDKTLGTVVAVLGVDDIGEGRILAGDGAVYYDANFDAIVF 77
                                      8******************************************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.1   2.2e-17   1.3e-13       1      69 [.      78     155 ..      78     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.2e-17
                                       HSTTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTT CS
                                S1   1 kpekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdr 67 
                                       kpe  e+veGeV++++k+Gaf+ +g + +g++++s++ ++             +d+++ l +Gd+v+++++ +  ++
  gi|386002591|ref|YP_005920890.1|  78 KPEMQEIVEGEVVEIVKFGAFIGIG-PFDGLLHVSQITNEyisydeknsrLASKDSNKSLGEGDRVRARIIAISLNE 153
                                       678889*******************.************************99*******************998877 PP

                                       TE CS
                                S1  68 rr 69 
                                       ++
  gi|386002591|ref|YP_005920890.1| 154 KE 155
                                       76 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.4e-05     0.081       1      91 [.      79     166 ..      79     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P ++e+++g + +  + g ++ +g fd ++   +   e+ ++de+++       ++++  l  g+++r r+  ++ +
  gi|386002591|ref|YP_005920890.1|  79 PEMQEIVEGEVVEIVKFGAFIGIGPFDGLLHVSQITNEYISYDEKNSRLAS---KDSNKSLGEGDRVRARIIAISLN 152
                                       7789************************9999999*********9997654...55778899**************9 PP

                                       ------HHHHHCHH CS
                     RNA_pol_Rbc25  78 dvkpkspkeaelee 91 
                                       +++p+++k   + +
  gi|386002591|ref|YP_005920890.1| 153 EKEPRESKIGLTMR 166
                                       99998877554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1189.15
//
Query:       gi|386002592|ref|YP_005920891.1|  [L=61]
Description: DNA-directed RNA polymerase subunit E'' [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-14   53.1   0.1    3.2e-14   52.8   0.1    1.1  1  Spt4          Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
      0.012   15.2   1.6      0.016   14.7   1.6    1.2  1  RecR          RecR protein
      0.019   14.6   2.6       0.18   11.5   0.1    2.2  2  zf-RRN7       Zinc-finger of RNA-polymerase I-specific TFIIB,
      0.023   14.1   1.4      0.041   13.3   0.1    1.9  2  zf-ribbon_3   zinc-ribbon domain
      0.031   13.8   0.3       0.15   11.6   0.0    2.0  2  TF_Zn_Ribbon  TFIIB zinc-binding
      0.075   12.7   0.1      0.078   12.7   0.1    1.0  1  DTW           DTW domain
       0.19   11.9   2.5       0.72   10.0   2.5    1.9  1  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.1   1.3e-17   3.2e-14       2      77 .]       4      61 .]       3      61 .] 0.97

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.3e-17
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      +AC++C+++++        Cp+C           +s ++s++++G+v+i+dp++S+vAk+  l+ + pg YAlkv+
  gi|386002592|ref|YP_005920891.1|  4 QACRECHRIVEGLV-----CPIC-----------GSASLSKDWTGYVVIIDPKESEVAKK--LGITLPGRYALKVR 61
                                      8**********999.....****...........**************************..************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.6   6.3e-06     0.016      18      36 ..       5      23 ..       4      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                                      E-TTT--EESSSS-CCCCS CS
                              RecR 18 hCsrCgnlteedlCaICsd 36
                                       C++C+ + e  +C+IC +
  gi|386002592|ref|YP_005920891.1|  5 ACRECHRIVEGLVCPICGS 23
                                      5****************76 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4     0.022        57      24      28 ..       6      10 ..       6      14 .. 0.85
   2 ?   11.5   0.1   7.1e-05      0.18       4      15 ..      15      30 ..      13      31 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.022
                           zf-RRN7 24 CrrCh 28
                                      Cr+Ch
  gi|386002592|ref|YP_005920891.1|  6 CRECH 10
                                      ***** PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.1e-05
                           zf-RRN7  4 gppCgvCgc....rsf 15
                                      g +C++Cg+    +++
  gi|386002592|ref|YP_005920891.1| 15 GLVCPICGSaslsKDW 30
                                      78*******7766666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.35   8.9e+02      17      22 ..       4       9 ..       2       9 .. 0.77
   2 ?   13.3   0.1   1.6e-05     0.041       4      17 ..      17      31 ..      14      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.35
                       zf-ribbon_3 17 nvCpyC 22
                                      ++C  C
  gi|386002592|ref|YP_005920891.1|  4 QACREC 9 
                                      679988 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.6e-05
                       zf-ribbon_3  4 rCPnCGa.plssddn 17
                                       CP CG+  ls+d++
  gi|386002592|ref|YP_005920891.1| 17 VCPICGSaSLSKDWT 31
                                      5******99***996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.2     5e+02       3       7 ..       6      10 ..       4      14 .. 0.76
   2 ?   11.6   0.0   5.9e-05      0.15       2      14 ..      17      29 ..      16      44 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                                      ETTTT CS
                      TF_Zn_Ribbon  3 CPnCg 7 
                                      C +C+
  gi|386002592|ref|YP_005920891.1|  6 CRECH 10
                                      99997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.9e-05
                                      EETTTTCEECHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                      +CP+Cgs +l  D
  gi|386002592|ref|YP_005920891.1| 17 VCPICGSASLSKD 29
                                      8******998443 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     3e-05     0.078       2      39 ..       4      43 ..       3      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                               DTW  2 elCerCllpaevclcsslpp..leklpikvlilqhpkEkk 39
                                      + C +C++ +e ++c    +  l k ++ ++++  pkE +
  gi|386002592|ref|YP_005920891.1|  4 QACRECHRIVEGLVCPICGSasLSKDWTGYVVIIDPKESE 43
                                      67****************99999**************954 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.5   0.00028      0.72       8      38 ..       6      28 ..       3      30 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.evrr 38
                                      C+eC++  e l+         CP Cgs  + +
  gi|386002592|ref|YP_005920891.1|  6 CRECHRIVEGLV---------CPICGSaSLSK 28
                                      999999999777.........******88877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 417.69
//
Query:       gi|386002593|ref|YP_005920892.1|  [L=178]
Description: hypothetical protein Mhar_1913 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-40  136.5   0.1    4.4e-40  136.2   0.1    1.1  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.1   2.5e-44   4.4e-40       5     125 ..      55     174 ..      50     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 2.5e-44
                            DUF359   5 llkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDL 81 
                                       l ++g+kPd++ivD+ktkR +v ++ ++ +   ++e+++iev Npa+t+t+el+++i+e l+ + +v+i+VdGEEDL
  gi|386002593|ref|YP_005920892.1|  55 LSSSGRKPDICIVDHKTKRMPVPDHVQQGI-GDRDEYDTIEVYNPAATLTQELVDVIRERLAGNGRVKIVVDGEEDL 130
                                       56789*****************99555555.56999***************************************** PP

                            DUF359  82 avlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                       a+lpail+ap gs+vvYGqp+eG v+v vt e ke+a+++++k+
  gi|386002593|ref|YP_005920892.1| 131 ATLPAILYAPLGSTVVYGQPNEGSVAVVVTPERKEYAKSIMDKM 174
                                       ******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1047.80
//
Query:       gi|386002594|ref|YP_005920893.1|  [L=101]
Description: 30S ribosomal protein S24e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-24   83.5   0.1    9.5e-24   83.2   0.1    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.1   5.3e-28   9.5e-24       1      75 [.      20      93 ..      20      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 5.3e-28
                                      EEEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS- CS
                    Ribosomal_S24e  1 vvdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglae 75
                                      ++ v H+g +tps+++i +k+a+ ++++  lv+v++++++fG+++t G+akiY+++e+ak++E+ h+++Rn +a 
  gi|386002594|ref|YP_005920893.1| 20 KFVVSHDG-PTPSRKSIIDKIAATMNSKVGLVMVDSLKSEFGKRETIGYAKIYENEERAKEVERAHVIERNVPAP 93
                                      589*****.**************************************************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 688.71
//
Query:       gi|386002595|ref|YP_005920894.1|  [L=49]
Description: 30S ribosomal protein S27ae [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-19   67.8   1.7    7.3e-19   67.7   1.7    1.0  1  Ribosomal_S27    Ribosomal protein S27a
    5.1e-06   26.3   0.8      0.017   15.0   0.0    2.1  2  Nudix_N_2        Nudix N-terminal
    0.00093   19.3   1.7     0.0011   19.1   1.7    1.1  1  Ribosomal_L37e   Ribosomal protein L37e
  ------ inclusion threshold ------
      0.017   15.1   2.9      0.028   14.4   2.9    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.02   14.9   0.5      0.021   14.9   0.5    1.0  1  DUF1451          Zinc-ribbon containing domain
      0.023   14.9   0.1      0.023   14.9   0.1    1.1  1  IBR              IBR domain, a half RING-finger domain
      0.026   14.4   2.8      0.076   12.9   2.8    1.7  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.034   14.5   1.4      0.049   14.0   1.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.035   14.1   1.3      0.057   13.4   1.3    1.3  1  DZR              Double zinc ribbon
      0.059   13.1   4.1        1.2    9.0   0.4    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.085   12.8   1.3       0.11   12.4   1.3    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.13   12.4   3.3        0.7   10.1   0.5    2.2  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.15   11.8   0.0       0.15   11.8   0.0    1.1  1  DUF4100          Protein of unknown function (DUF4100)
       0.31   11.3   2.8       0.59   10.4   0.4    2.0  2  zinc_ribbon_9    zinc-ribbon
       0.32   10.7   4.6        1.3    8.7   0.4    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.45   10.0   7.4        7.5    6.1   7.4    2.1  1  zf-ribbon_3      zinc-ribbon domain
       0.46   10.7   4.2        6.8    6.9   4.2    2.0  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   1.7   6.9e-22   7.3e-19       3      45 .]       5      45 ..       3      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 6.9e-22
                                      SSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  3 kyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      ++Y + + + ++r+r+ Cpr CG+Gvf++ehkdR +CGkCg+T
  gi|386002595|ref|YP_005920894.1|  5 EFYDLAG-DAIKRKRQICPR-CGNGVFLGEHKDRLACGKCGYT 45
                                      7999999.9***********.*********************9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00047      0.49      19      29 ..      15      25 ..       9      26 .. 0.87
   2 !   15.0   0.0   1.6e-05     0.017      17      32 ..      31      46 ..      27      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
                                      SS-EEEETTTT CS
                         Nudix_N_2 19 nreRlvCpaCg 29
                                      +r R +Cp+Cg
  gi|386002595|ref|YP_005920894.1| 15 KRKRQICPRCG 25
                                      589*******9 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-05
                                      T-SS-EEEETTTTEEE CS
                         Nudix_N_2 17 gDnreRlvCpaCgtih 32
                                      g+++ Rl C +Cg++ 
  gi|386002595|ref|YP_005920894.1| 31 GEHKDRLACGKCGYTE 46
                                      99***********975 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.7     1e-06    0.0011      16      43 ..      18      48 ..      10      49 .] 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                    Ribosomal_L37e 16 HilCrrCgkrsy...hvqkktCascGypsak 43
                                        +C rCg+  +   h  +  C++cGy + k
  gi|386002595|ref|YP_005920894.1| 18 RQICPRCGNGVFlgeHKDRLACGKCGYTEFK 48
                                      468*********887888889******7654 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 ?   14.4   2.9   2.6e-05     0.028      17      46 .]      17      45 ..       7      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrkayriktrglfqCkeCrkq 46
                                       +++CP+Cg+  +    +  ++ C +C+++
  gi|386002595|ref|YP_005920894.1| 17 KRQICPRCGNGVFLGEHK-DRLACGKCGYT 45
                                      5689*****885544444.7*******985 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   1.9e-05     0.021     106     144 ..      10      48 ..       2      49 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                           DUF1451 106 sGevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                                       +G+ +   + +C +Cg+ + l + +   +C kCg teF+
  gi|386002595|ref|YP_005920894.1|  10 AGDAIKRKRQICPRCGNGVFLGEHKDRLACGKCGYTEFK 48 
                                       7899999999****************9***********7 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.1e-05     0.023      15      46 ..      15      44 ..       4      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                               IBR 15 dpnlkwCprpdCeaiieksegcksvtCskCgf 46
                                      +++++ Cp   C++ +   e+++++ C kCg+
  gi|386002595|ref|YP_005920894.1| 15 KRKRQICP--RCGNGVFLGEHKDRLACGKCGY 44
                                      456889**..9**********9999*****97 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.8   7.2e-05     0.076       4      31 ..      21      46 ..      19      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                                      ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                      Cp CgN     e k    ++C +CgY e
  gi|386002595|ref|YP_005920894.1| 21 CPRCGNGVFLGEHKDR--LACGKCGYTE 46
                                      ******9888888877..88******75 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.4   4.7e-05     0.049       6      36 ..      21      44 ..      17      49 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga 36
                                      CP Cg+   l++++++        +C +Cg+
  gi|386002595|ref|YP_005920894.1| 21 CPRCGNGVFLGEHKDRL-------ACGKCGY 44
                                      *************8886.......5999*99 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.3   5.4e-05     0.057       7      36 ..      13      44 ..      10      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                               DZR  7 elppdarfCseCgtk..lkavaa..edrCpsCge 36
                                      +++ + + C++Cg+   l +  +    +C +Cg+
  gi|386002595|ref|YP_005920894.1| 13 AIKRKRQICPRCGNGvfLGE--HkdRLACGKCGY 44
                                      67888999999999944444..345999999997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0011       1.2       2       7 ..      21      26 ..      17      28 .. 0.70
   2 ?    5.9   0.3      0.01        11      16      21 ..      39      44 ..      33      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp+CG+
  gi|386002595|ref|YP_005920894.1| 21 CPRCGN 26
                                      777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|386002595|ref|YP_005920894.1| 39 CGKCGY 44
                                      888886 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3   0.00011      0.11      29      55 ..      19      45 ..      18      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfe 55
                                      + C++Cg  +    +++++ C +Cg++
  gi|386002595|ref|YP_005920894.1| 19 QICPRCGNGVFLGEHKDRLACGKCGYT 45
                                      78******999999***********97 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.086        90       2       8 ..      21      27 ..      20      35 .. 0.83
   2 ?   10.1   0.5   0.00066       0.7      37      46 ..      38      47 ..      32      49 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.086
                    zinc_ribbon_13  2 CpKCgnt 8 
                                      Cp+Cgn 
  gi|386002595|ref|YP_005920894.1| 21 CPRCGNG 27
                                      9***986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00066
                    zinc_ribbon_13 37 sCknCgYtel 46
                                       C +CgYte+
  gi|386002595|ref|YP_005920894.1| 38 ACGKCGYTEF 47
                                      7********8 PP

>> DUF4100  Protein of unknown function (DUF4100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.15     110     129 ..       2      21 ..       1      31 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                           DUF4100 110 aKkeFheviidsiKrkrqlt 129
                                       a  eF+++  d+iKrkrq+ 
  gi|386002595|ref|YP_005920894.1|   2 AANEFYDLAGDAIKRKRQIC 21 
                                       678***************86 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00056      0.59      21      30 ..      19      27 ..      10      32 .. 0.71
   2 ?    2.1   0.1      0.23   2.4e+02      16      28 ..      32      43 ..      28      47 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00056
                     zinc_ribbon_9 21 dvlCPhCggg 30
                                      ++ CP+Cg+g
  gi|386002595|ref|YP_005920894.1| 19 QI-CPRCGNG 27
                                      45.****875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                     zinc_ribbon_9 16 pdedsdvlCPhCg 28
                                      +++d+ + C  Cg
  gi|386002595|ref|YP_005920894.1| 32 EHKDRLA-CGKCG 43
                                      5556666.*9998 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4    0.0013       1.3       4      10 ..      19      25 ..      16      33 .. 0.78
   2 ?    4.2   0.4     0.034        35       6      10 ..      39      43 ..      38      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                     zf-NADH-PPase  4 rFCgrCG 10
                                      + C+rCG
  gi|386002595|ref|YP_005920894.1| 19 QICPRCG 25
                                      7899999 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.034
                     zf-NADH-PPase  6 CgrCG 10
                                      Cg+CG
  gi|386002595|ref|YP_005920894.1| 39 CGKCG 43
                                      99998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.4    0.0072       7.5       4      24 ..      20      44 ..      17      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0072
                       zf-ribbon_3  4 rCPnCGa.p.lss..ddnvCpyCGt 24
                                       CP+CG+ + l +  d  +C +CG+
  gi|386002595|ref|YP_005920894.1| 20 ICPRCGNgVfLGEhkDRLACGKCGY 44
                                      7******998874338899999997 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.2    0.0065       6.8       1      33 [.      14      46 ..      14      49 .] 0.62

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0065
                      NOB1_Zn_bind  1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnkt 33
                                      ikr ++   rC   + + +++++  C kCG   
  gi|386002595|ref|YP_005920894.1| 14 IKRKRQICPRCGNGVFLGEHKDRLACGKCGYTE 46
                                      556666666666666666777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 355.79
//
Query:       gi|386002596|ref|YP_005920895.1|  [L=258]
Description: hypothetical protein Mhar_1916 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-36  124.1   2.2    8.4e-36  123.6   2.2    1.1  1  Band_7           SPFH domain / Band 7 family
    6.5e-06   26.0   0.1    9.7e-06   25.4   0.1    1.3  1  Band_7_1         SPFH domain-Band 7 family
  ------ inclusion threshold ------
       0.11   12.6   1.0        2.2    8.4   0.0    2.5  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   2.2   1.4e-39   8.4e-36       5     177 ..      28     194 ..      25     195 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 1.4e-39
                            Band_7   5 egevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaa 81 
                                       e e++v++r G++s++++pGl +i+P +++  ++++rv+t+dv++ + v+tkD++ v +d++++yrv   + ++v +
  gi|386002596|ref|YP_005920895.1|  28 EYERLVIFRLGRYSGIKGPGLTIIIPVIDKAMTIDLRVVTIDVQK-QAVITKDNVTVAVDAILYYRV-VEPDRAVIQ 102
                                       789******************************************.*********************.********* PP

                            Band_7  82 veresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqala 158
                                       v    +n++   + +++ +lr v++e +l++lls+reel+ +l++ l  q + +G+ ++ v+++d+++p+   +a+a
  gi|386002596|ref|YP_005920895.1| 103 V----ENYKVATSLLAQTTLRDVLGEIELDDLLSKREELNVKLQEILDRQTDPWGIKITAVTLRDVSLPESMLRAIA 175
                                       *....************************************************************************ PP

                            Band_7 159 akqaaeaeaqaeiaraeae 177
                                       + ++ae+e++ +i  ae+e
  gi|386002596|ref|YP_005920895.1| 176 KQAEAEREKRSRIILAEGE 194
                                       ***************9987 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.6e-09   9.7e-06     142     209 ..     115     180 ..      75     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-09
                          Band_7_1 142 vtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       +t+l dvl+e  i + dl +k eel  kl+e l+ + +  G+++++++++++slpe++ +a+ k+a++
  gi|386002596|ref|YP_005920895.1| 115 QTTLRDVLGE--IELDDLLSKREELNVKLQEILDRQTDPWGIKITAVTLRDVSLPESMLRAIAKQAEA 180
                                       4456677765..67789***********************************************9976 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.027   1.6e+02      76     105 ..     121     150 ..      78     155 .. 0.78
   2 ?    8.4   0.0   0.00037       2.2      93     119 ..     163     189 ..     153     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.027
                   HicB_lk_antitox  76 alvdvdlskldgkaeriNitlpervlkriD 105
                                       +l +++l+ l +k e +N+ l e + ++ D
  gi|386002596|ref|YP_005920895.1| 121 VLGEIELDDLLSKREELNVKLQEILDRQTD 150
                                       56689999************9988877766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00037
                   HicB_lk_antitox  93 NitlpervlkriDaavkaagesRSgfl 119
                                        ++lpe++l+ i ++++a++e RS  +
  gi|386002596|ref|YP_005920895.1| 163 DVSLPESMLRAIAKQAEAEREKRSRII 189
                                       59**********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1571.95
//
Query:       gi|386002597|ref|YP_005920896.1|  [L=454]
Description: Nodulation efficiency protein NfeD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-13   49.0   0.1    2.1e-12   47.2   0.1    2.0  1  NfeD            NfeD-like C-terminal, partner-binding
    0.00054   19.9   0.1    0.00088   19.2   0.1    1.3  1  CLP_protease    Clp protease
      0.002   17.3   0.0     0.0066   15.5   0.0    1.5  1  FMN_dh          FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.097   13.2   0.2       0.18   12.4   0.2    1.3  1  EF-G-binding_N  Elongation factor G-binding protein, N-termin
       0.27   10.5   1.0        1.8    7.8   0.0    2.2  2  ECH_1           Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.1   5.9e-16   2.1e-12       3      84 .]     374     452 ..     371     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.9e-16
                                       XXXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SS CS
                              NfeD   3 avvsvlllvllrplllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsegeiekgerVrVveveGl 78 
                                       +v+++ ++++l++++  +++     t +e +  +++++l++i+ +G+v+++Ge+W a++e++ie+ge V+Vv+ e +
  gi|386002597|ref|YP_005920896.1| 374 IVIGAFFVFALYKVAEARRRP----TYSEMMEAEVAEALDRIDpRGHVMYNGEYWVAEAEEPIEAGEMVEVVGKERM 446
                                       677778888888888887744....8888999**********558******************************** PP

                                       SEEEEE CS
                              NfeD  79 tliVep 84 
                                        l+V++
  gi|386002597|ref|YP_005920896.1| 447 VLKVRR 452
                                       ****96 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.4e-07   0.00088      47     178 ..      85     215 ..      57     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
                                       S-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE..E.EEETHHHHHHHTS-TTGEEEETTEEEEES-TEEEEEE CS
                      CLP_protease  47 kdillyinspGGsvtaglaIydtmqyikpdvsticl..G.laaSmgslllaagekgkRfalpnarimihqPlggaqg 120
                                       + +++ +++pGG +t++ +I  +++  + +v+ ++   G +a S+g+++l++ +    +++p + i   qP++    
  gi|386002597|ref|YP_005920896.1|  85 EALVITLDTPGGGLTETKEITGLIERTSLPVIGYVYpsGaTAWSAGTIILLSSDIA--AMVPGTIIGSAQPVQIGPT 159
                                       678999*********************9999877765563578*************..89***********988777 PP

                                       EHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE CS
                      CLP_protease 121 qasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidev 178
                                        ++ + ++++ ++ + + ++e  a++ +++    ++ +  +  l+ae+A++yG i++v
  gi|386002597|ref|YP_005920896.1| 160 GMEAV-NDTKVINAVVALVEE-KARNNNRNTTAAREFVLSNLNLNAEDALRYGVIEHV 215
                                       44444.556777777665555.455566666777778888899*************99 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-06    0.0066     119     167 ..      66     114 ..      59     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                                       CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHCT--BSTT-T CS
                            FMN_dh 119 pkdrelteellkraeaagykalvltvDtpvlgkRerdlrngfslppklk 167
                                       p ++++++e +++ae  g++alv+t+Dtp  g  e ++ +g+   ++l 
  gi|386002597|ref|YP_005920896.1|  66 PASDDIVREAIAEAEGRGCEALVITLDTPGGGLTETKEITGLIERTSLP 114
                                       678899**************************99999888776665554 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   4.9e-05      0.18      22      68 ..     162     206 ..     159     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                    EF-G-binding_N  22 rsvnDkkvveavkalaaekIlelfpelseeqkelLeqiddik.tkeka 68 
                                       ++vnD+kv++av al++ek ++     +++++e++  +++ + + e+a
  gi|386002597|ref|YP_005920896.1| 162 EAVNDTKVINAVVALVEEKARNNN-RNTTAAREFV--LSNLNlNAEDA 206
                                       68********************64.5566667776..66666666666 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.8      0.11   4.1e+02      94     114 ..      44      64 ..      32      72 .. 0.86
   2 ?    7.8   0.0   0.00049       1.8     147     176 ..     189     218 ..     183     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                                       EE-SEEETHHHHHHHHSSEEE CS
                             ECH_1  94 avnGaaigGGlelalacDivi 114
                                       a+ G a+g G+++++a D +i
  gi|386002597|ref|YP_005920896.1|  44 ALAGSAAGQGCVMVVALDGAI 64 
                                       678*************99877 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHT-EEEHHHHHHCTSSSEEESG CS
                             ECH_1 147 skAeeilllgkkisaqealkvGlvdkvvpe 176
                                        +A+e +l   +++a++al+ G++++v p 
  gi|386002597|ref|YP_005920896.1| 189 TAAREFVLSNLNLNAEDALRYGVIEHVSPS 218
                                       5799***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2736.34
//
Query:       gi|386002598|ref|YP_005920897.1|  [L=110]
Description: UspA domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-17   63.9   2.4    2.8e-17   63.6   2.4    1.2  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.083   13.2   0.1       0.11   12.9   0.1    1.5  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   2.4   3.1e-21   2.8e-17      34     140 ..       2     109 ..       1     110 [] 0.85

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 3.1e-21
                                       EEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEE CS
                               Usp  34 illhvidprasgavsdadeeaeeeeleleeaeleada...akaaaeaggvkvevvveegdpaeeilevaeeedadli 107
                                       ++l+v++p   + vs    +        ++++ +++a    +++a+a+gv  e +++eg pae+ile+    + d +
  gi|386002598|ref|YP_005920897.1|   2 TVLYVVEPVVITDVSHNIVDDVVVGMRRSRMKDAEKAtnsVEELAKAAGVPAEKKIVEGYPAEVILEIS--TGMDVV 76 
                                       67888888877777766666666666666666666666788999**********************995..679*** PP

                                       EEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp 108 VvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       VvGs gr+gl r+llGSv+e+v+r++++pV++V
  gi|386002598|ref|YP_005920897.1|  77 VVGSMGRTGLTRFLLGSVAEKVVRNSEVPVMIV 109
                                       ********************************9 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.2e-05      0.11      41      71 ..      58      89 ..      11     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                                      CSSTHHHHHHHH.TT-SEEEESSSCHHHHHHH CS
                     Nitro_FeMo-Co 41 ggggklaqllae.egvdvvivgkiGpralakl 71
                                       +g+ ++ +l+   g+dvv+vg++G+  l+++
  gi|386002598|ref|YP_005920897.1| 58 VEGYPAEVILEIsTGMDVVVVGSMGRTGLTRF 89
                                      4555556666669************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 726.66
//
Query:       gi|386002599|ref|YP_005920898.1|  [L=115]
Description: Nodulation efficiency protein NfeD, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-14   54.1   0.1    2.2e-14   53.6   0.1    1.2  1  NfeD       NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
      0.052   13.0   0.1      0.059   12.9   0.1    1.1  1  DUF1129    Protein of unknown function (DUF1129)
       0.16   12.0   0.6        7.7    6.5   0.0    2.1  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.1   3.7e-18   2.2e-14       4      84 .]      33     113 ..      30     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 3.7e-18
                                       XXXXXXXXXXX...XXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE- CS
                              NfeD   4 vvsvlllvllr...plllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsegeiekgerVrVveve 76 
                                       ++ v  l++++   +++  ++ +   +t + ++  +++++l++i+ +G+v+++Ge+W a++e++ie+ge V+Vv+ e
  gi|386002599|ref|YP_005920898.1|  33 LAIVFGLFFVFaisKVAEARR-R---PTYSAKMEAEVAEALDRIDpRGHVMYNGEYWAAEAEEPIEAGEMVEVVGKE 105
                                       444444444441114444444.2...36666899**********558****************************** PP

                                       SSSEEEEE CS
                              NfeD  77 GltliVep 84 
                                        + l+V++
  gi|386002599|ref|YP_005920898.1| 106 RMVLKVRR 113
                                       ******96 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.8e-06     0.059      91     136 ..       6      50 ..       1      66 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-06
                           DUF1129  91 lfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltr 136
                                       ++ + +g   +f+++  +++  litl+ +a+v+Gl++v+    + +
  gi|386002599|ref|YP_005920898.1|   6 VLLVTIGSPEWFTPADYETD-ALITLFALAIVFGLFFVFAISKVAE 50 
                                       56667788889999888888.*****************99888764 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1    0.0064        38      80     121 ..       9      54 ..       1      63 [. 0.44
   2 ?    6.5   0.0    0.0013       7.7      41      65 ..      86     110 ..      78     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0064
                         RseC_MucC  80 lgallgsall...gssellaalgall...glvlgflivrllskrlkkk 121
                                       +++   ++++    ++++l  l+al+   gl++ f i ++ + r  ++
  gi|386002599|ref|YP_005920898.1|   9 VTIGSPEWFTpadYETDALITLFALAivfGLFFVFAISKVAEAR--RR 54 
                                       44444444446654444444444443000334444444444333..44 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0013
                         RseC_MucC  41 eveneigakvGdkVevgieeksllk 65 
                                        +e e ++++G++Vev  +e+++lk
  gi|386002599|ref|YP_005920898.1|  86 AAEAEEPIEAGEMVEVVGKERMVLK 110
                                       5677889999************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 762.45
//
Query:       gi|386002600|ref|YP_005920899.1|  [L=454]
Description: putative membrane protein, containing TPR repeats [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29   99.5  15.9    4.8e-07   29.3   0.0    9.5  9  TPR_1      Tetratricopeptide repeat
    5.5e-25   85.4  13.2    0.00098   19.1   0.1    9.5  9  TPR_2      Tetratricopeptide repeat
    2.4e-21   74.5   1.4      4e-05   23.7   0.0    6.4  6  TPR_17     Tetratricopeptide repeat
    1.8e-17   62.0   9.1    0.00041   20.3   0.0    7.7  9  TPR_8      Tetratricopeptide repeat
    2.9e-13   49.2  19.9    0.00048   19.7   0.0    7.5  9  TPR_11     TPR repeat
    4.8e-13   49.5   0.1    0.00018   22.0   0.0    3.7  5  TPR_16     Tetratricopeptide repeat
    4.5e-09   36.4   0.4        2.7    9.0   0.1    6.5  6  TPR_14     Tetratricopeptide repeat
    4.6e-09   36.4   3.4        0.2   12.0   0.1    5.0  6  TPR_12     Tetratricopeptide repeat
      5e-09   36.5   0.4      0.012   16.1   0.0    4.7  5  TPR_19     Tetratricopeptide repeat
    1.7e-08   33.9   0.5      0.021   13.8   0.0    4.0  4  NARP1      NMDA receptor-regulated protein 1
      3e-06   27.3   0.0        1.6    8.9   0.0    4.3  4  TPR_9      Tetratricopeptide repeat
    1.4e-05   25.3   2.5       0.35   11.1   0.0    4.3  4  ANAPC3     Anaphase-promoting complex, cyclosome, subunit 3
    3.2e-05   24.0   4.2       0.31   11.1   0.1    4.2  4  DUF3856    Domain of Unknown Function (DUF3856)
    0.00057   19.2   0.7          3    7.0   0.0    4.2  5  TPR_15     Tetratricopeptide repeat
    0.00089   19.0   4.5        4.3    7.3   0.0    4.6  5  TPR_10     Tetratricopeptide repeat
     0.0018   18.1   0.7        4.4    7.0   0.0    3.6  3  TPR_21     Tetratricopeptide repeat-like domain
  ------ inclusion threshold ------
      0.013   14.4   2.1      0.017   14.0   2.1    1.1  1  EcsB       Bacterial ABC transporter protein EcsB
      0.033   12.4   6.2       0.05   11.9   6.2    1.2  1  YfhO       Bacterial membrane protein YfhO
       0.14   12.9   3.8         82    4.2   0.0    5.2  5  TPR_6      Tetratricopeptide repeat
       0.28   11.1   0.6       0.59   10.1   0.6    1.5  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
        2.8    7.5  10.6        0.4   10.3   3.0    2.3  2  Wzy_C      O-Antigen ligase


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   4.3e-05     0.037       2      31 ..      97     126 ..      96     128 .. 0.94
   2 ?    1.3   0.2      0.39   3.4e+02       6      16 ..     135     145 ..     130     170 .. 0.58
   3 ?   -0.6   0.0       1.6   1.3e+03      19      32 ..     229     242 ..     228     244 .. 0.83
   4 !   26.1   0.1   5.9e-09   5.1e-06       3      30 ..     251     278 ..     249     280 .. 0.95
   5 !   29.3   0.0   5.6e-10   4.8e-07       2      33 ..     284     315 ..     283     316 .. 0.93
   6 !   11.2   0.0    0.0003      0.25       3      31 ..     319     347 ..     317     348 .. 0.93
   7 ?    1.1   0.0      0.47     4e+02       2      14 ..     352     364 ..     351     366 .. 0.79
   8 !   10.2   0.1    0.0006      0.51      18      34 .]     404     420 ..     403     420 .. 0.92
   9 !    7.4   0.0    0.0049       4.2       4      30 ..     424     450 ..     421     452 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       + ++ +G  ++k+++y +A ++++k + l+
  gi|386002600|ref|YP_005920899.1|  97 DYWNTRGIDHRKNKEYYDAFQAFDKGIHLD 126
                                       57*************************998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.39
                                       HHHHHHHHTT- CS
                             TPR_1   6 nlGnayfklgk 16 
                                       n++na+ ++gk
  gi|386002600|ref|YP_005920899.1| 135 NKANALCQKGK 145
                                       56666555554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHST CS
                             TPR_1  19 eAleyyekALelnP 32 
                                       eAl   ekA+  +P
  gi|386002600|ref|YP_005920899.1| 229 EALHTIEKAIATYP 242
                                       89999999998777 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 5.9e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       a+  +G a++kl kyd+A+e+++kA++l
  gi|386002600|ref|YP_005920899.1| 251 AYATKGTALYKLSKYDDAIEACDKAVKL 278
                                       7999*********************998 PP

  == domain 5  score: 29.3 bits;  conditional E-value: 5.6e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                         +  +Gna+ ++g++  A+++++kA+el P+
  gi|386002600|ref|YP_005920899.1| 284 LGWAIKGNALESKGNHWAAIKDFNKAIELKPD 315
                                       578899*************************8 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                        +y +G+  + lg+   Al +y+kA+e +
  gi|386002600|ref|YP_005920899.1| 319 FWYSKGQSIRALGDNLLALHAYDKAIEFD 347
                                       5999***********************87 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHT CS
                             TPR_1   2 kalynlGnayfkl 14 
                                       +a++++G+a f l
  gi|386002600|ref|YP_005920899.1| 352 DAWNQRGMAMFDL 364
                                       8******986655 PP

  == domain 8  score: 10.2 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHHHHSTTH CS
                             TPR_1  18 deAleyyekALelnPnn 34 
                                       + Al  +++A+ +nPn+
  gi|386002600|ref|YP_005920899.1| 404 NNALNSFDRAIDINPND 420
                                       68*************97 PP

  == domain 9  score: 7.4 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALel 30 
                                       + n+G ++ +lg+  eA e+y kA el
  gi|386002600|ref|YP_005920899.1| 424 WVNKGRVLSELGRTTEANEAYAKAREL 450
                                       99*********************9886 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   8.4e-05     0.072       2      32 ..      97     127 ..      96     129 .. 0.93
   2 ?    0.4   0.0       1.1     9e+02      17      33 ..     153     169 ..     131     170 .. 0.66
   3 ?    1.4   0.0      0.54   4.6e+02      18      33 ..     228     243 ..     225     244 .. 0.88
   4 !   19.1   0.1   1.2e-06   0.00098       3      30 ..     251     278 ..     249     280 .. 0.93
   5 !   15.9   0.0   1.2e-05    0.0099       2      33 ..     284     315 ..     283     316 .. 0.93
   6 !   10.6   0.0   0.00061      0.52       3      31 ..     319     347 ..     317     350 .. 0.92
   7 ?    2.8   0.0      0.18   1.6e+02       2      15 ..     352     365 ..     351     368 .. 0.90
   8 !    8.0   0.0    0.0041       3.5      18      34 .]     404     420 ..     400     420 .. 0.90
   9 !   13.0   0.0   9.9e-05     0.085       3      30 ..     423     450 ..     421     452 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ++++ +G  ++k+++y +A +af+k + ld 
  gi|386002600|ref|YP_005920899.1|  97 DYWNTRGIDHRKNKEYYDAFQAFDKGIHLDN 127
                                       68***********************999985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                             TPR_2  17 yeeAleafekAleldPn 33 
                                       +eeAl+  + A+++ P+
  gi|386002600|ref|YP_005920899.1| 153 LEEALKTIDYAISIGPK 169
                                       57777777777777665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.54
                             TPR_2  18 eeAleafekAleldPn 33 
                                       +eAl+  ekA++ +P 
  gi|386002600|ref|YP_005920899.1| 228 NEALHTIEKAIATYPP 243
                                       69**********9996 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 1.2e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       a+   G a+ykl +y++A+ea++kA++l
  gi|386002600|ref|YP_005920899.1| 251 AYATKGTALYKLSKYDDAIEACDKAVKL 278
                                       78999*********************98 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.2e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++   G+a++ +g++  A+++f+kA+el P+
  gi|386002600|ref|YP_005920899.1| 284 LGWAIKGNALESKGNHWAAIKDFNKAIELKPD 315
                                       678999*************************8 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.00061
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                        +y  G++ ++lgd   Al+a++kA+e d
  gi|386002600|ref|YP_005920899.1| 319 FWYSKGQSIRALGDNLLALHAYDKAIEFD 347
                                       5999**********************987 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.18
                             TPR_2   2 ealynlGlayyklg 15 
                                       +a++++G+a + lg
  gi|386002600|ref|YP_005920899.1| 352 DAWNQRGMAMFDLG 365
                                       79*********999 PP

  == domain 8  score: 8.0 bits;  conditional E-value: 0.0041
                             TPR_2  18 eeAleafekAleldPnn 34 
                                       + Al+ f++A+ ++Pn+
  gi|386002600|ref|YP_005920899.1| 404 NNALNSFDRAIDINPND 420
                                       679************97 PP

  == domain 9  score: 13.0 bits;  conditional E-value: 9.9e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                        + n G+++ +lg+  eA ea+ kA el
  gi|386002600|ref|YP_005920899.1| 423 FWVNKGRVLSELGRTTEANEAYAKAREL 450
                                       699**********************987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.21   1.8e+02       2      28 ..     119     145 ..     118     150 .. 0.86
   2 !    9.2   0.1    0.0019       1.7       3      34 .]     235     270 ..     233     270 .. 0.80
   3 ?   -0.7   0.1       2.9   2.5e+03      17      33 ..     287     303 ..     277     304 .. 0.83
   4 !   14.0   0.0   5.7e-05     0.049       2      29 ..     306     333 ..     305     337 .. 0.89
   5 !   16.8   0.0   7.6e-06    0.0065       1      27 [.     339     365 ..     339     371 .. 0.89
   6 !   23.7   0.0   4.7e-08     4e-05       2      32 ..     410     440 ..     409     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                       + k + ld  + + + n+A++l+++G+
  gi|386002600|ref|YP_005920899.1| 119 FDKGIHLDNRSTKCLVNKANALCQKGK 145
                                       67888888899999*********9985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                            TPR_17   3 lkaleld.Pnn...adaynnLAelllknGdlmtArq 34 
                                       +ka++ + Pnn   + ay  ++++l+k+ ++++A++
  gi|386002600|ref|YP_005920899.1| 235 EKAIATYpPNNpqlPGAYATKGTALYKLSKYDDAIE 270
                                       67777763333666********************86 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.9
                            TPR_17  17 nnLAelllknGdlmtAr 33 
                                         ++++l+++G++  A+
  gi|386002600|ref|YP_005920899.1| 287 AIKGNALESKGNHWAAI 303
                                       557999999**999997 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 5.7e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdl 29 
                                       + ka+el P+++++++ +++  + +Gd 
  gi|386002600|ref|YP_005920899.1| 306 FNKAIELKPDSSVFWYSKGQSIRALGDN 333
                                       78******************99999986 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 7.6e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknG 27 
                                       +y ka+e d+ ++da+n+++ ++  +G
  gi|386002600|ref|YP_005920899.1| 339 AYDKAIEFDKLDSDAWNQRGMAMFDLG 365
                                       59******************9877665 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 4.7e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + +a++++Pn++ ++ n++++l+++G++ +A
  gi|386002600|ref|YP_005920899.1| 410 FDRAIDINPNDSMFWVNKGRVLSELGRTTEA 440
                                       789************************9887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.2   3.6e+03      11      31 ..     106     126 ..      97     128 .. 0.77
   2 ?   -2.4   0.0       9.1   7.8e+03      13      25 ..     149     161 ..     137     169 .. 0.56
   3 ?   -2.3   0.0       8.7   7.4e+03      19      29 ..     229     239 ..     227     243 .. 0.67
   4 !   14.2   0.1   4.5e-05     0.039       3      30 ..     251     278 ..     249     279 .. 0.95
   5 !   20.3   0.0   4.8e-07   0.00041       4      33 ..     286     315 ..     283     316 .. 0.94
   6 !    7.3   0.1    0.0073       6.3       4      31 ..     320     347 ..     318     348 .. 0.93
   7 ?   -1.9   0.0       6.3   5.4e+03       2      15 ..     352     365 ..     351     365 .. 0.84
   8 ?    5.5   0.0     0.028        24      17      34 .]     403     420 ..     402     420 .. 0.91
   9 !   12.3   0.0   0.00019      0.16       4      27 ..     424     447 ..     423     450 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.2
                                       HHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyyekaleld 31 
                                       ++k ++y  A +++ k + ld
  gi|386002600|ref|YP_005920899.1| 106 HRKNKEYYDAFQAFDKGIHLD 126
                                       567888999999999987665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.1
                                       HTT-HHHHHHHHH CS
                             TPR_8  13 klgdyeeAkeyye 25 
                                       +   +eeA +++ 
  gi|386002600|ref|YP_005920899.1| 149 DESSLEEALKTID 161
                                       5555666666655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHH CS
                             TPR_8  19 eAkeyyekale 29 
                                       eA  ++eka+ 
  gi|386002600|ref|YP_005920899.1| 229 EALHTIEKAIA 239
                                       67777777774 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                       ay  +g ++ kl +y+ A+e++ ka++l
  gi|386002600|ref|YP_005920899.1| 251 AYATKGTALYKLSKYDDAIEACDKAVKL 278
                                       89************************97 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 4.8e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +  +g++++++g++ +A++ ++ka+el+pd
  gi|386002600|ref|YP_005920899.1| 286 WAIKGNALESKGNHWAAIKDFNKAIELKPD 315
                                       8899*************************8 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                       +y +g+  + lgd   A  +y ka+e d
  gi|386002600|ref|YP_005920899.1| 320 WYSKGQSIRALGDNLLALHAYDKAIEFD 347
                                       9999**********************88 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 6.3
                                       CHHHHHHHHHHHTT CS
                             TPR_8   2 eayynlgsiylklg 15 
                                       +a+++ g++ ++lg
  gi|386002600|ref|YP_005920899.1| 352 DAWNQRGMAMFDLG 365
                                       79*****9988876 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHH. CS
                             TPR_8  17 yeeAkeyyekaleldpdn 34 
                                       +++A  ++ +a++++p++
  gi|386002600|ref|YP_005920899.1| 403 LNNALNSFDRAIDINPND 420
                                       689*************96 PP

  == domain 9  score: 12.3 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyeka 27 
                                       ++n+g+++++lg+  eA e+y ka
  gi|386002600|ref|YP_005920899.1| 424 WVNKGRVLSELGRTTEANEAYAKA 447
                                       99*******************998 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.2   1.9e+03       7      41 ..     109     143 ..     106     144 .. 0.69
   2 ?    0.5   0.1      0.58   4.9e+02       6      28 ..     149     171 ..     137     173 .. 0.77
   3 ?   -1.9   0.3       3.4   2.9e+03       7      22 ..     187     202 ..     185     203 .. 0.81
   4 ?   -2.9   0.1       6.7   5.7e+03      10      17 ..     234     241 ..     234     241 .. 0.87
   5 !    8.9   0.1    0.0013       1.1       1      23 [.     256     278 ..     256     280 .. 0.93
   6 !   19.7   0.0   5.7e-07   0.00048       1      36 [.     290     325 ..     290     331 .. 0.91
   7 !   16.1   0.0   7.5e-06    0.0064       2      42 .]     325     365 ..     324     365 .. 0.92
   8 !   12.0   0.0   0.00015      0.13      10      42 .]     403     435 ..     403     435 .. 0.89
   9 ?    3.5   0.1     0.068        58       1      22 [.     428     449 ..     428     452 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.2
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                         +y +A +a+ k + ld+ +   + n ++a+ ++
  gi|386002600|ref|YP_005920899.1| 109 NKEYYDAFQAFDKGIHLDNRSTKCLVNKANALCQK 143
                                       56778888899999999887766666666666555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.58
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdna 28 
                                       +   +eeA++    A+ + P+++
  gi|386002600|ref|YP_005920899.1| 149 DESSLEEALKTIDYAISIGPKYP 171
                                       55678999998888888888887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.4
                            TPR_11   7 qGkyeeAieaYkkAlk 22 
                                        ++ e Ai+ Y +Alk
  gi|386002600|ref|YP_005920899.1| 187 ENQEEMAIQGYANALK 202
                                       5666889**9*99997 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 6.7
                            TPR_11  10 yeeAieaY 17 
                                       +e+Ai+ Y
  gi|386002600|ref|YP_005920899.1| 234 IEKAIATY 241
                                       599***99 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0013
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G a+y++ ky++Aiea  kA+kl
  gi|386002600|ref|YP_005920899.1| 256 GTALYKLSKYDDAIEACDKAVKL 278
                                       679*************9999997 PP

  == domain 6  score: 19.7 bits;  conditional E-value: 5.7e-07
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+a+ ++G+  +Ai++++kA++l+Pd+  ++y  G+
  gi|386002600|ref|YP_005920899.1| 290 GNALESKGNHWAAIKDFNKAIELKPDSSVFWYSKGQ 325
                                       89999*********************9999998886 PP

  == domain 7  score: 16.1 bits;  conditional E-value: 7.5e-06
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +  +++G++  A+ aY kA+++d  + +a++ +G a++ +G
  gi|386002600|ref|YP_005920899.1| 325 QSIRALGDNLLALHAYDKAIEFDKLDSDAWNQRGMAMFDLG 365
                                       56688999999**************************9998 PP

  == domain 8  score: 12.0 bits;  conditional E-value: 0.00015
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +++A++++ +A++++P++  ++ n G ++ ++G
  gi|386002600|ref|YP_005920899.1| 403 LNNALNSFDRAIDINPNDSMFWVNKGRVLSELG 435
                                       589***************999999998887776 PP

  == domain 9  score: 3.5 bits;  conditional E-value: 0.068
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G+++ e+G+ +eA eaY kA +
  gi|386002600|ref|YP_005920899.1| 428 GRVLSELGRTTEANEAYAKARE 449
                                       788899***********99965 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00021      0.18      24      65 ..     239     280 ..     228     283 .. 0.75
   2 !   22.0   0.0   2.2e-07   0.00018       3      67 ..     255     316 ..     253     317 .. 0.92
   3 !   13.5   0.0    0.0001     0.086       4      62 ..     290     345 ..     289     353 .. 0.85
   4 ?    3.2   0.1      0.16   1.4e+02       8      45 ..     328     362 ..     321     365 .. 0.70
   5 !   18.2   0.0   3.4e-06    0.0029      16      64 ..     406     451 ..     403     454 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                            TPR_16  24 lkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                         + p  P+ + A+  +g a+++++ +++A++++++a++ + 
  gi|386002600|ref|YP_005920899.1| 239 ATYPPNNPQLPGAYATKGTALYKLSKYDDAIEACDKAVKLGR 280
                                       455677788889999999999999999999999999987665 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.2e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++a++++ +yddA++a + a+k++      a  +  +g+a+  +g++ +A+  +++a++  pd+
  gi|386002600|ref|YP_005920899.1| 255 KGTALYKLSKYDDAIEACDKAVKLG---RYEALGWAIKGNALESKGNHWAAIKDFNKAIELKPDS 316
                                       799**********************...555669999***************9999999****97 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.0001
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       ++a+   g+  +A++ ++ a+++ p+s++   +++ +g++  ++g+  +A+ +y++a++
  gi|386002600|ref|YP_005920899.1| 290 GNALESKGNHWAAIKDFNKAIELKPDSSV---FWYSKGQSIRALGDNLLALHAYDKAIE 345
                                       677888888899************77777...*******************88877774 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.16
                            TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                       +++gd   A++a++ a++ d    ++ +A++ +g a +
  gi|386002600|ref|YP_005920899.1| 328 RALGDNLLALHAYDKAIEFD---KLDSDAWNQRGMAMF 362
                                       67888889999999999999...555557777776655 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 3.4e-06
                            TPR_16  16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       A++ +++a++ +   P +  ++ ++g+++ ++gr +eA ++y++a + +
  gi|386002600|ref|YP_005920899.1| 406 ALNSFDRAIDIN---PNDSMFWVNKGRVLSELGRTTEANEAYAKARELG 451
                                       99**********...99999*******************9999997655 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       4.4   3.7e+03       7      28 ..     102     123 ..      97     131 .. 0.79
   2 !    9.0   0.1    0.0032       2.7       2      38 ..     250     286 ..     249     289 .. 0.85
   3 !    8.1   0.0    0.0065       5.5       4      43 ..     286     325 ..     283     327 .. 0.89
   4 ?    1.0   0.1       1.2     1e+03      14      38 ..     330     354 ..     326     361 .. 0.57
   5 ?    7.1   0.0     0.013        11      20      43 ..     406     429 ..     402     430 .. 0.90
   6 ?    3.0   0.1      0.27   2.3e+02       8      29 ..     428     449 ..     427     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.4
                            TPR_14   7 laeallalGdpdeAiallrral 28 
                                       ++  ++ + ++ +A +++++ +
  gi|386002600|ref|YP_005920899.1| 102 RGIDHRKNKEYYDAFQAFDKGI 123
                                       666688899999*****99886 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0032
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                        a++  + al+ l ++d+Ai+++++a++l+  +a  w
  gi|386002600|ref|YP_005920899.1| 250 GAYATKGTALYKLSKYDDAIEACDKAVKLGRYEALGW 286
                                       68889999*******************9887666555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0065
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++  + al+  G++ +Ai+ +++a++l Pd+ ++w+  +q
  gi|386002600|ref|YP_005920899.1| 286 WAIKGNALESKGNHWAAIKDFNKAIELKPDSSVFWYSKGQ 325
                                       666789999999999********************87665 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.2
                            TPR_14  14 lGdpdeAiallrralalaPddaeaw 38 
                                       lGd   A+ ++++a++ +  d +aw
  gi|386002600|ref|YP_005920899.1| 330 LGDNLLALHAYDKAIEFDKLDSDAW 354
                                       3444445556666666666555555 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.013
                            TPR_14  20 AiallrralalaPddaeawlllaq 43 
                                       A++ ++ra++ +P+d  +w   ++
  gi|386002600|ref|YP_005920899.1| 406 ALNSFDRAIDINPNDSMFWVNKGR 429
                                       8999***************98876 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.27
                            TPR_14   8 aeallalGdpdeAiallrrala 29 
                                       +++l +lG++ eA +++ +a +
  gi|386002600|ref|YP_005920899.1| 428 GRVLSELGRTTEANEAYAKARE 449
                                       6899*************99976 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.74   6.3e+02       7      28 ..     100     121 ..      96     159 .. 0.76
   2 !    9.4   0.1    0.0014       1.2      24      72 ..     232     276 ..     211     280 .. 0.68
   3 !   11.2   0.1   0.00041      0.35       9      74 ..     255     312 ..     247     315 .. 0.70
   4 !   12.0   0.1   0.00023       0.2       9      67 ..     289     346 ..     281     349 .. 0.92
   5 ?    5.9   0.0     0.018        16       8      52 ..     322     365 ..     315     366 .. 0.69
   6 !   10.4   0.0   0.00074      0.63      42      74 ..     418     450 ..     401     453 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.74
                            TPR_12   7 nnlaavlrrlgrydeAlellek 28 
                                       n ++  +r+ ++y +A++ ++k
  gi|386002600|ref|YP_005920899.1| 100 NTRGIDHRKNKEYYDAFQAFDK 121
                                       4578889999999999999887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                            TPR_12  24 ellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                          eka++    ++ p++p++  ++ + g+++++l +y++A+e+  +a+
  gi|386002600|ref|YP_005920899.1| 232 HTIEKAIA----TYPPNNPQLPGAYATKGTALYKLSKYDDAIEACDKAV 276
                                       44444433....3457777777777777777777777777777655554 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00041
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +++l++l +yd+A+e ++ka+ + r      ++++ ++    g +++  g++ +A++ +++a+++
  gi|386002600|ref|YP_005920899.1| 255 KGTALYKLSKYDDAIEACDKAVKLGR------YEALGWA--IKGNALESKGNHWAAIKDFNKAIEL 312
                                       7999*****************77773......3223333..3366666777777777777777766 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00023
                            TPR_12   9 laavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                        +++l   g++  A++ ++ka+e+   ++    ++   ++ r+Lg+ ++al  y++A+e+
  gi|386002600|ref|YP_005920899.1| 289 KGNALESKGNHWAAIKDFNKAIELKpDSS--VFWYSKGQSIRALGDNLLALHAYDKAIEF 346
                                       58999999*****************7777..99************************997 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.018
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLg 52 
                                         ++  r+lg+   Al  ++ka+e   +l  + + +   ++++Lg
  gi|386002600|ref|YP_005920899.1| 322 SKGQSIRALGDNLLALHAYDKAIEFD-KLDSDAWNQRGMAMFDLG 365
                                       56777788888888888888888877.555566666666666665 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00074
                            TPR_12  42 pltattlrnLgrlyralgryeeAlelleealai 74 
                                       p+ +    n gr++++lgr+ eA e++ +a ++
  gi|386002600|ref|YP_005920899.1| 418 PNDSMFWVNKGRVLSELGRTTEANEAYAKAREL 450
                                       555666677888999999999999999888875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         8   6.8e+03       5      39 ..     110     144 ..     107     145 .. 0.79
   2 ?    1.2   0.0      0.64   5.5e+02       4      29 ..     150     175 ..     149     177 .. 0.87
   3 !    7.3   0.1     0.008       6.9       9      53 ..     229     277 ..     227     290 .. 0.76
   4 ?    5.3   0.0     0.032        28       5      46 ..     297     345 ..     294     346 .. 0.80
   5 !   16.1   0.0   1.4e-05     0.012       8      52 ..     404     448 ..     403     451 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalg 39 
                                       + y +A +++ + +  d+ +   + + A+al + g
  gi|386002600|ref|YP_005920899.1| 110 KEYYDAFQAFDKGIHLDNRSTKCLVNKANALCQKG 144
                                       56778888888888888888888888999998887 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.64
                            TPR_19   4 egdyaeAlalleqalqedpknaearl 29 
                                       e  ++eAl+   +a++  pk++ a l
  gi|386002600|ref|YP_005920899.1| 150 ESSLEEALKTIDYAISIGPKYPPAIL 175
                                       56789****************99987 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.008
                            TPR_19   9 eAlalleqalqe....dpknaearllLAeallalgqldeAealLdalpe 53 
                                       eAl   e+a++     +p+ + a +    al++l  +d+A++++d++ +
  gi|386002600|ref|YP_005920899.1| 229 EALHTIEKAIATyppnNPQLPGAYATKGTALYKLSKYDDAIEACDKAVK 277
                                       67777777765545556666777777799***************99866 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.032
                            TPR_19   5 gdyaeAlalleqalqedpknaearl.......lLAeallalgqldeAea 46 
                                       g++ +A++ + +a++ +p+++  ++       +L + llal  +d+A++
  gi|386002600|ref|YP_005920899.1| 297 GNHWAAIKDFNKAIELKPDSSVFWYskgqsirALGDNLLALHAYDKAIE 345
                                       677799**********999555555555555579*************87 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 1.4e-05
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                        +Al+ + +a++ +p+++  + +  ++l +lg+++eA ++ +++ 
  gi|386002600|ref|YP_005920899.1| 404 NNALNSFDRAIDINPNDSMFWVNKGRVLSELGRTTEANEAYAKAR 448
                                       68***********************************99988775 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.15   1.3e+02     184     225 ..     126     170 ..      89     204 .. 0.69
   2 !    6.3   0.2    0.0045       3.8     200     255 ..     217     278 ..     173     282 .. 0.71
   3 !    7.6   0.0    0.0018       1.5     210     259 ..     301     350 ..     289     352 .. 0.91
   4 !   13.8   0.0   2.5e-05     0.021     190     255 ..     385     450 ..     365     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                                       ----SSHHHHHHHHHHHHHHHHT-SH...HHHHHHHHHHHH-TT- CS
                             NARP1 184 ekepesallwvlyflAqhydklgsre...kAleyidkaiehtptl 225
                                        +++ ++l+   + l q   + g+ +   +Al++id ai+  p+ 
  gi|386002600|ref|YP_005920899.1| 126 DNRSTKCLVNKANALCQKGKRFGDESsleEALKTIDYAISIGPKY 170
                                       345555666666666666666555333337777777777777765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0045
                                       HHHHHHT-..SHHHHHHHHHHHHH....-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 200 qhydklgs..rekAleyidkaieh....tptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       +h  +  +  r++Al++i+kai+     +p+l   y tK++ l +    ++A+e+ ++a kl
  gi|386002600|ref|YP_005920899.1| 217 KHAGEQIDelRNEALHTIEKAIATyppnNPQLPGAYATKGTALYKLSKYDDAIEACDKAVKL 278
                                       4443332233569*********963333689**************************99887 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 210 kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        A++  +kaie +p +  +++ K++ ++  Gd   A ++ ++a ++D+ D
  gi|386002600|ref|YP_005920899.1| 301 AAIKDFNKAIELKPDSSVFWYSKGQSIRALGDNLLALHAYDKAIEFDKLD 350
                                       79999******************************************977 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 190 allwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                        l+w ++  A + +     ++Al+  d+ai+ +p+   ++++K+r+l   G  ++A e+  +ar+l
  gi|386002600|ref|YP_005920899.1| 385 ELFWLNTDSAVYGEFNYYLNNALNSFDRAIDINPNDSMFWVNKGRVLSELGRTTEANEAYAKAREL 450
                                       466666666666666667789*******************************************98 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.57   4.9e+02       9      34 ..     151     176 ..     148     177 .. 0.84
   2 !    8.0   0.0    0.0038       3.2      10      62 ..     264     316 ..     229     319 .. 0.94
   3 ?    3.3   0.0       0.1        89      10      45 ..     332     367 ..     326     369 .. 0.91
   4 !    8.9   0.0    0.0019       1.6      13      52 ..     405     444 ..     402     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.57
                             TPR_9   9 edweralavverllllaPddpeerrd 34 
                                          e+al++++  + + P+ p  ++ 
  gi|386002600|ref|YP_005920899.1| 151 SSLEEALKTIDYAISIGPKYPPAILT 176
                                       56799*************98877765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0038
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +++ a+++++  + l   ++  +   G +l+  G+  aA++d++ +++l pd 
  gi|386002600|ref|YP_005920899.1| 264 KYDDAIEACDKAVKLGRYEALGWAIKGNALESKGNHWAAIKDFNKAIELKPDS 316
                                       7899999********************************************96 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.1
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGcl 45 
                                       d+  al +++  + ++  d + +  RG++ + lGc 
  gi|386002600|ref|YP_005920899.1| 332 DNLLALHAYDKAIEFDKLDSDAWNQRGMAMFDLGCK 367
                                       78899*****************************96 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0019
                             TPR_9  13 ralavverllllaPddpeerrdRGlllaqlGclsaAladL 52 
                                        al   +r + ++P+d   +   G++l +lG++ +A ++ 
  gi|386002600|ref|YP_005920899.1| 405 NALNSFDRAIDINPNDSMFWVNKGRVLSELGRTTEANEAY 444
                                       589999***************************9998765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0075       6.4      33      68 ..     106     142 ..      98     149 .. 0.89
   2 !   11.1   0.0   0.00041      0.35      42      81 ..     237     274 ..     227     275 .. 0.72
   3 ?    1.2   0.1      0.52   4.4e+02      35      70 ..     295     331 ..     272     346 .. 0.61
   4 ?    1.9   0.0      0.31   2.6e+02       6      79 ..     404     444 ..     400     453 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0075
                                       HHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHH CS
                            ANAPC3  33 lylngqykrAyellrka.klnskslgcrylfAqcllk 68 
                                       + +n++y+ A++ ++k   l+++s +c++ +A +l +
  gi|386002600|ref|YP_005920899.1| 106 HRKNKEYYDAFQAFDKGiHLDNRSTKCLVNKANALCQ 142
                                       789**************************99987765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00041
                                       HHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  42 AyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       A+  + ++  n++ +g+  +++ +l+kL+ky++Ai a +k
  gi|386002600|ref|YP_005920899.1| 237 AIATYPPN--NPQLPGAYATKGTALYKLSKYDDAIEACDK 274
                                       44444444..677778888899999999999999988665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.52
                                       HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT CS
                            ANAPC3  35 lngqykrAyellrka.klnskslgcrylfAqcllkLk 70 
                                       + g++  A++ ++ka +l++ s   +y ++q+  +L+
  gi|386002600|ref|YP_005920899.1| 295 SKGNHWAAIKDFNKAiELKPDSSVFWYSKGQSIRALG 331
                                       5666666777777777777777766666665543333 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +nA+  ++                                  +a ++n+++   ++ ++++l +L++  eA  a+
  gi|386002600|ref|YP_005920899.1| 404 NNALNSFD----------------------------------RAiDINPNDSMFWVNKGRVLSELGRTTEANEAY 444
                                       44444444..................................444555555555555555555555555554443 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.8   2.4e+03      71     121 ..     112     158 ..      98     165 .. 0.55
   2 !    8.9   0.1    0.0017       1.5      57     128 ..     251     311 ..     249     316 .. 0.66
   3 ?    4.7   0.0     0.034        29      80     128 ..     301     345 ..     277     359 .. 0.69
   4 !   11.1   0.1   0.00036      0.31      78     129 ..     403     450 ..     389     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           DUF3856  71 ydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealk 121
                                       y +a+++ dk+++  nr  +   ++     +a++++++ + +  + +ealk
  gi|386002600|ref|YP_005920899.1| 112 YYDAFQAFDKGIHLDNRSTKCLVNK----ANALCQKGKRFGDESSLEEALK 158
                                       5555555555555555544332222....2344555555555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  57 chaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       ++a+   al kl +yd+a+e+ dka++         + e   W      ++ ale+ G++  a+k f++a e
  gi|386002600|ref|YP_005920899.1| 251 AYATKGTALYKLSKYDDAIEACDKAVKL-------GRYEALGWA----IKGNALESKGNHWAAIKDFNKAIE 311
                                       5899999******************863.......233333342....245555555555555555555554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.034
                                       HHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  80 kalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                        a++ fn+  el+ d    W    +s+++++  lG +  al+a+ +a e
  gi|386002600|ref|YP_005920899.1| 301 AAIKDFNKAIELKPDSSVFW----YSKGQSIRALGDNLLALHAYDKAIE 345
                                       36667777777777777777....5677777777777777777777666 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                        ++al+ f+r  +++ ++   W+    ++++ l+elGr+ ea +a+ +a e+
  gi|386002600|ref|YP_005920899.1| 403 LNNALNSFDRAIDINPNDSMFWV----NKGRVLSELGRTTEANEAYAKAREL 450
                                       5789******************6....8********************9986 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         3   2.6e+03      41      68 ..      93     120 ..      68     132 .. 0.53
   2 ?    1.4   0.1      0.18   1.5e+02     158     235 ..     186     270 ..     172     280 .. 0.69
   3 !    7.0   0.0    0.0035         3     145     180 ..     282     317 ..     274     319 .. 0.91
   4 ?    5.2   0.0     0.013        11     144     181 ..     315     352 ..     311     356 .. 0.89
   5 ?    2.9   0.0     0.063        54     137     172 ..     411     447 ..     396     452 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3
                            TPR_15  41 skdteyWrtladLAwalqqedearkAyr 68 
                                       + +t+yW t++   ++++++ +a +A  
  gi|386002600|ref|YP_005920899.1|  93 EIQTDYWNTRGIDHRKNKEYYDAFQAFD 120
                                       4445555555544444444444444443 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                            TPR_15 158 qegqtdaAlrdyreAlalapd....sselraallWlliDlgrraeLrellkawkaraesdasLwgplaa...AlllL 227
                                       qe+q++ A++ y +Al+ + d     ++lr+++    iD  r++ L  + ka   +  ++++L+g++a+   Al +L
  gi|386002600|ref|YP_005920899.1| 186 QENQEEMAIQGYANALKSKCDilihLADLREKHAGEQIDELRNEALHTIEKAIATYPPNNPQLPGAYATkgtALYKL 262
                                       67777777777777777776622223566666666677777666666666666666699999999998533377777 PP

                            TPR_15 228 grpkkALe 235
                                       ++++ A e
  gi|386002600|ref|YP_005920899.1| 263 SKYDDAIE 270
                                       77777765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0035
                            TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       +a+ +++ +++ + +g++ aA++d+ +A++l+pdss
  gi|386002600|ref|YP_005920899.1| 282 EALGWAIKGNALESKGNHWAAIKDFNKAIELKPDSS 317
                                       67789999**************************87 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.013
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                       +s+ f++  +++ r+ g++  Al++y +A++ +  +s+
  gi|386002600|ref|YP_005920899.1| 315 DSSVFWYSKGQSIRALGDNLLALHAYDKAIEFDKLDSD 352
                                       799***************************98877776 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.063
                            TPR_15 137 eeeeaae.qsaafllaraelyrqegqtdaAlrdyreA 172
                                        +  + + ++++f++  +++ ++ g+t +A ++y +A
  gi|386002600|ref|YP_005920899.1| 411 DRAIDINpNDSMFWVNKGRVLSELGRTTEANEAYAKA 447
                                       4444545578889999999999999999998888877 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.8   8.4e+03       9      26 ..     103     120 ..     100     123 .. 0.77
   2 !    7.3   0.0     0.005       4.3       4      31 ..     132     159 ..     130     160 .. 0.93
   3 ?   -2.4   0.1       5.7   4.9e+03      19      32 ..     228     241 ..     227     241 .. 0.78
   4 ?    4.9   0.1      0.03        26       9      31 ..     256     278 ..     250     285 .. 0.85
   5 ?    5.1   0.1     0.025        21       7      29 ..     426     448 ..     425     450 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.8
                            TPR_10   9 analrqrgrydeAealle 26 
                                       ++ +r+ ++y +A + ++
  gi|386002600|ref|YP_005920899.1| 103 GIDHRKNKEYYDAFQAFD 120
                                       888999999999988765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.005
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                       +l N anal+q g++ + e  leeal +
  gi|386002600|ref|YP_005920899.1| 132 CLVNKANALCQKGKRFGDESSLEEALKT 159
                                       78899********************976 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.7
                            TPR_10  19 deAealleealair 32 
                                       +eA+   e+a+a++
  gi|386002600|ref|YP_005920899.1| 228 NEALHTIEKAIATY 241
                                       67777789999997 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.03
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al+++ +yd+A + +++a+ +
  gi|386002600|ref|YP_005920899.1| 256 GTALYKLSKYDDAIEACDKAVKL 278
                                       899*****************987 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.025
                            TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                       N +++l+++gr +eA + + +a 
  gi|386002600|ref|YP_005920899.1| 426 NKGRVLSELGRTTEANEAYAKAR 448
                                       6699***********99999985 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0063       5.4     125     176 ..     261     313 ..     257     323 .. 0.86
   2 ?   -1.3   0.0       1.8   1.5e+03     152     174 ..     323     345 ..     318     359 .. 0.82
   3 !    7.0   0.0    0.0051       4.4     152     174 ..     427     449 ..     419     454 .] 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                            TPR_21 125 aekkydeAlktL.eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       +  kyd+A+++  +a+k   ++al   ++G++l ++g+   A + +++A++ +
  gi|386002600|ref|YP_005920899.1| 261 KLSKYDDAIEACdKAVKLGRYEALGWAIKGNALESKGNHWAAIKDFNKAIELK 313
                                       56799*****9944567789*****************************9865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G  + a g++  A +aY++A++
  gi|386002600|ref|YP_005920899.1| 323 KGQSIRALGDNLLALHAYDKAIE 345
                                       7888889999999999**99986 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0051
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G +l++ g+++eA +aY +A +
  gi|386002600|ref|YP_005920899.1| 427 KGRVLSELGRTTEANEAYAKARE 449
                                       899*****************976 PP

>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.1   1.9e-05     0.017     126     208 ..       5      86 ..       1     124 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                              EcsB 126 glsiaelllllllllllkllnlllkweelrlqgkkkrridrlirlllnalllylllalapllalllilllllvllll 202
                                       ++++++++l++++l+++ +++  l+w+ ++     +r    ++ ++ ++l+ +++++ ++++ ++ i++ l++l++ 
  gi|386002600|ref|YP_005920899.1|   5 QHDFGNIFLIVAVLFVVLCWWNRLNWNGIKAYIYVYRF-TIIFGVISAILIGFYIYYEKSWSEIASIAIGLVALIIA 80 
                                       788999************************88866665.56888888888877777777777777776666666655 PP

                              EcsB 203 lkrkkk 208
                                       l+ ++ 
  gi|386002600|ref|YP_005920899.1|  81 LISLES 86 
                                       555443 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.2   5.8e-05      0.05     309     386 ..      12      86 ..       5     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.8e-05
                              YfhO 309 fallllllilsfllpplnlvwhgfqaPvgfpyRfsfilsflllllaaealkelkqlkklkllaailllvlllliill 385
                                       f+++ +l+++ ++++ ln  w+g +a   ++yRf  i+  ++++l+   + + k+++++  +a+ l+++ ++li+l 
  gi|386002600|ref|YP_005920899.1|  12 FLIVAVLFVVLCWWNRLN--WNGIKAYI-YVYRFTIIFGVISAILIGFYIYYEKSWSEIASIAIGLVALIIALISLE 85 
                                       445555566666666665..******99.*********************999999766666666665555555543 PP

                              YfhO 386 l 386
                                        
  gi|386002600|ref|YP_005920899.1|  86 S 86 
                                       3 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.6   2.3e+03      17      31 ..     228     242 ..     208     243 .. 0.73
   2 ?    3.8   0.2      0.12   1.1e+02       7      28 ..     256     277 ..     251     278 .. 0.88
   3 ?   -1.0   0.0       4.4   3.7e+03      18      33 .]     301     316 ..     289     316 .. 0.70
   4 ?   -0.5   0.0         3   2.5e+03      18      32 ..     405     419 ..     403     420 .. 0.88
   5 ?    4.2   0.0     0.096        82       7      27 ..     428     448 ..     424     450 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHH-T CS
                             TPR_6  17 dkAlealerlikeYP 31 
                                        +Al + e+ i  YP
  gi|386002600|ref|YP_005920899.1| 228 NEALHTIEKAIATYP 242
                                       388889999999999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       + +++kl ++d+A+ea ++ +k
  gi|386002600|ref|YP_005920899.1| 256 GTALYKLSKYDDAIEACDKAVK 277
                                       78999999********998876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHH-TT- CS
                             TPR_6  18 kAlealerlikeYPdS 33 
                                       +A++ +++ i+  PdS
  gi|386002600|ref|YP_005920899.1| 301 AAIKDFNKAIELKPDS 316
                                       5999999999988887 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3
                                       HHHHHHHHHHHH-TT CS
                             TPR_6  18 kAlealerlikeYPd 32 
                                       +Al  ++r i+  P+
  gi|386002600|ref|YP_005920899.1| 405 NALNSFDRAIDINPN 419
                                       69999******9998 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.096
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerli 27 
                                       ++ + +lg+t++A ea+ + +
  gi|386002600|ref|YP_005920899.1| 428 GRVLSELGRTTEANEAYAKAR 448
                                       78888999*********9976 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   0.00069      0.59      63     119 ..      32      92 ..      29      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00069
                         RseC_MucC  63 llkaallvYllPllllilgallgsall....gssellaalgallglvlgflivrllskrlk 119
                                        +ka ++vY + +++ +++a+l+ +        se+++++++l++l+++++ ++  +++lk
  gi|386002600|ref|YP_005920899.1|  32 GIKAYIYVYRFTIIFGVISAILIGFYIyyekSWSEIASIAIGLVALIIALISLESSTSQLK 92 
                                       6899999999999999998888888888999999************999999888777766 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   2.8      0.69   5.9e+02      18      49 ..       9      40 ..       5      46 .. 0.76
   2 ?   10.3   3.0   0.00047       0.4      18      71 ..      44      96 ..      37     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.69
                             Wzy_C 18 giigllvalivlliifykrripfllllg.ilvg 49
                                      g i l+va++++++ +++r+  + ++++ i+v 
  gi|386002600|ref|YP_005920899.1|  9 GNIFLIVAVLFVVLCWWNRLN-WNGIKAyIYVY 40
                                      567888899999998888888.99998866664 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00047
                             Wzy_C 18 giigllvalivlliifykrripfllllgilvgvilliilfvlstnletlknitk 71
                                       i g++ a+++++ i+y++ +   + ++++ +v+l+i+l++l+++  +lk i+ 
  gi|386002600|ref|YP_005920899.1| 44 IIFGVISAILIGFYIYYEKSW-SEIASIAIGLVALIIALISLESSTSQLKEIQT 96
                                      57899****************.88888888888899999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 2414.97
//
Query:       gi|386002601|ref|YP_005920900.1|  [L=689]
Description: Minichromosome maintenance protein MCM [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-97  325.3   0.0    1.8e-97  324.9   0.0    1.2  1  MCM              MCM P-loop domain
    4.1e-35  120.4   0.0    6.7e-35  119.7   0.0    1.3  1  MCM_OB           MCM OB domain
    4.5e-28   97.5   0.0    8.7e-28   96.6   0.0    1.5  1  MCM_lid          MCM AAA-lid domain
    5.3e-09   35.8   0.1    9.9e-07   28.3   0.1    2.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.4e-08   34.9   0.0    3.3e-08   33.6   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00012   22.0   0.0    0.00042   20.2   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
     0.0022   18.6   0.1      0.013   16.1   0.0    2.3  2  MCM_N            MCM N-terminal domain
     0.0039   16.9   0.0      0.047   13.4   0.0    2.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.009   16.4   0.4      0.058   13.8   0.1    2.5  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
       0.11   12.2   0.1        1.1    9.0   0.1    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.14   12.6   0.0       0.45   10.9   0.0    2.0  1  AAA              ATPase family associated with various cellul
       0.51   10.5   4.3        1.2    9.3   4.3    1.6  1  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.9   0.0  1.2e-100   1.8e-97       2     221 ..     260     480 ..     259     483 .. 0.97

  Alignments for each domain:
  == domain 1  score: 324.9 bits;  conditional E-value: 1.2e-100
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       ++ i+el+++++i+e++ ksiapsiyg+e+vk+a++lqlf+gv+k l+d+t++rgdi++llvgdpg+aKsqlL+y++
  gi|386002601|ref|YP_005920900.1| 260 ERLIRELSTDPHIYENIRKSIAPSIYGYEEVKEALALQLFSGVSKGLPDGTRIRGDIHILLVGDPGIAKSQLLRYIS 336
                                       5679************************************************************************* PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEES CS
                               MCM  79 klapravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaK 154
                                       kl+pr++ytsgk+s++agLta+ v+de  +  + +eaGalvladkG++ciDe+dkm++edrsalhEamEqqtis+aK
  gi|386002601|ref|YP_005920900.1| 337 KLSPRGIYTSGKSSTSAGLTATAVKDELGDGrWSIEAGALVLADKGIACIDEMDKMRSEDRSALHEAMEQQTISVAK 413
                                       **************************986555********************************************* PP

                                       SSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHH CS
                               MCM 155 aGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehiv 221
                                       aG++atL++r+++laAanpk+gr+dk + +a++inls+al+srFDlifvl D++++ +D+++a+hi 
  gi|386002601|ref|YP_005920900.1| 414 AGVMATLKSRCALLAAANPKFGRFDKYEGIAQQINLSPALMSRFDLIFVLTDEPSDARDSQIARHIG 480
                                       *****************************************************************95 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   4.5e-38   6.7e-35       4     125 ..      96     222 ..      93     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 4.5e-38
                                       G--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEE CS
                            MCM_OB   4 dlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfv 75 
                                       +lrs+hig+l+ +eG+v +++ev+pk+++a+fec++cg+         +++eP  C++++C++++pfkl  ++s+fv
  gi|386002601|ref|YP_005920900.1|  96 ELRSDHIGRLIALEGLVRTVTEVRPKVVSAAFECQRCGHLFYKeqttsKFQEPYDCPNEACDRRGPFKLLLDRSRFV 172
                                       79************************************95443456778999************************* PP

                                       EEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                            MCM_OB  76 dfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                       d q++++QEspee+  Ge P++l+v leddl   + PGdrv + G++r++
  gi|386002601|ref|YP_005920900.1| 173 DAQNVRVQESPEELRGGEQPQTLDVQLEDDLSGIIYPGDRVVINGVLRSY 222
                                       **********************************************9986 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   5.8e-31   8.7e-28       1      86 [.     513     597 ..     513     598 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 5.8e-31
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       e+lrkYiayar++++P+ls+ a+e l+++Yv+lRk+ +d  +k +p+t+RqLe+l RLse++A+lrls+++t  d+e
  gi|386002601|ref|YP_005920900.1| 513 EVLRKYIAYARKNVFPVLSDGARERLESYYVNLRKQGQDG-NKPVPVTARQLEALFRLSESSARLRLSDEITGGDAE 588
                                       68*********************************99655.9*********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  78 eairllkes 86 
                                       ++ir+++++
  gi|386002601|ref|YP_005920900.1| 589 RVIRIVEAC 597
                                       ******987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   6.6e-10   9.9e-07      92     163 ..     365     436 ..     311     469 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.6e-10
                      Mg_chelatase  92 Gggs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgk 163
                                       G g+ +++ G++ la +G+  +DE+ +++++   +L e +e++++++++a   ++  +r+ l+aa+Np   g+
  gi|386002601|ref|YP_005920900.1| 365 GDGRwSIEAGALVLADKGIACIDEMDKMRSEDRSALHEAMEQQTISVAKAGVMATLKSRCALLAAANPK-FGR 436
                                       55555999***********************************************************94.344 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 !   33.6   0.0   2.2e-11   3.3e-08       1     138 []     317     457 ..     317     457 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.2e-11
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEE...EE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnrevey...vqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                       ++lLvG+pG++Ks+l ++++++  r + +      ++++t++ +k ++   +g+ s + ++lv     + i+++DE 
  gi|386002601|ref|YP_005920900.1| 317 HILLVGDPGIAKSQLLRYISKLSPRGIYTsgkSSTSAGLTATAVKDELG--DGRWSIEAGALV--LADKGIACIDEM 389
                                       79*********************66555512246778888888888888..9999********..88999******* PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..........-TT-TTHHHHTT- CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.........rslnelspalrsRf 138
                                       ++++se  ++L+  +e++++++++ g     k+        ++a+anp            ++ +lspal sRf
  gi|386002601|ref|YP_005920900.1| 390 DKMRSEDRSALHEAMEQQTISVAKAGVMATLKSR-----CALLAAANPKFgrfdkyegiAQQINLSPALMSRF 457
                                       *********************9988888877775.....8999999998666667666667777888888887 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.8e-07   0.00042       1     112 [.     317     432 ..     317     442 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.8e-07
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqft.pdllPsdilGtevfeeke.kefefkkGpvf.an..llladein 72 
                                       h+ll g PG+ak +l + ++k        i         + ++ t v +e    ++++++G+++ a+  +   de++
  gi|386002601|ref|YP_005920900.1| 317 HILLVGDPGIAKSQLLRYISKLSPRG---IYTSgKSSTSAGLTATAVKDELGdGRWSIEAGALVlADkgIACIDEMD 390
                                       9***************9999865443...33221344667888898888754499******976343338889**** PP

                             AAA_3  73 rappktqsalleameerqvtveg..ethklpepflvlatqnP 112
                                       +  +  +sal eame+++++v++     +l++   +la+ nP
  gi|386002601|ref|YP_005920900.1| 391 KMRSEDRSALHEAMEQQTISVAKagVMATLKSRCALLAAANP 432
                                       *****************99987511577999**********9 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.4e-06     0.013       8      74 ..      13      69 ..       6      83 .. 0.86
   2 ?   -3.1   0.0         8   1.2e+04      58      85 ..     520     547 ..     504     568 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.4e-06
                             MCM_N  8 LeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealke 74
                                      +++             Y d+l e+a+    +++L +++ d+  +d+e+a+++le+p   l++ e al e
  gi|386002601|ref|YP_005920900.1| 13 IRS------------RYWDELLELADSypLRRSLSIKFPDIDRYDPEFADELLEKPGPLLEAAETALLE 69
                                      443............49999999999855679******************************9999866 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8
                             MCM_N  58 lenpkeylplleealkevvkklepsykd 85 
                                           k + p+l+++++e +++++ +  +
  gi|386002601|ref|YP_005920900.1| 520 AYARKNVFPVLSDGARERLESYYVNLRK 547
                                       4455667788888888877777665444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.2e-05     0.047      82     144 ..     369     433 ..     309     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       SS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS- CS
                   Sigma54_activat  82 ekekkGlfekadgGtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatned 144
                                        + ++G++  ad+G+  +De+ ++  e  + L ++++++++   + G  ++ k  + ++aa+n +
  gi|386002601|ref|YP_005920900.1| 369 WSIEAGALVLADKGIACIDEMDKMRSEDRSALHEAMEQQTIsvAKAGVMATLKSRCALLAAANPK 433
                                       45678********************************997622699999**********999865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         5   7.5e+03      67     101 ..     147     181 ..     111     207 .. 0.60
   2 !   13.8   0.1   3.9e-05     0.058      26     125 ..     317     406 ..     289     430 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5
                            AAA_16  67 ipysalaqalareellrqlldeaesaeleawrekl 101
                                        py+   +a++r++ ++ lld+++  +++  r + 
  gi|386002601|ref|YP_005920900.1| 147 EPYDCPNEACDRRGPFKLLLDRSRFVDAQNVRVQE 181
                                       45666667777888888888887766666555543 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.9e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde...aesaeleawre 99 
                                        +ll+G++G+ Ks l+r +   l+ + gi+++gk   +            l++ + ++++l +   + +a +   ++
  gi|386002601|ref|YP_005920900.1| 317 HILLVGDPGIAKSQLLRYIS-KLSPR-GIYTSGKSSTS----------AGLTA-TAVKDELGDgrwSIEAGALVLAD 380
                                       699*****************.68888.78888888887..........55544.66666666645533333344444 PP

                            AAA_16 100 kleealaavpelagaeasrllellkr 125
                                       k  + + + ++++++++s+l+e++ +
  gi|386002601|ref|YP_005920900.1| 381 KGIACIDEMDKMRSEDRSALHEAMEQ 406
                                       44444445666666666666666654 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00072       1.1      34     115 ..     316     411 ..     277     427 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00072
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl....k.itsg.....Pvlekagd....laalltnleekdvlfideihrl 96 
                                        h+ll+G PG+ k+ l + i+k     +    k +ts+      v ++ gd    + a    l +k +  ide+ ++
  gi|386002601|ref|YP_005920900.1| 316 IHILLVGDPGIAKSQLLRYISKLSPRGIytsgKsSTSAgltatAVKDELGDgrwsIEAGALVLADKGIACIDEMDKM 392
                                       59************999988864333221111212222111103333334433335555566888899999999999 PP

                            RuvB_N  97 sraveevlysamedfrldi 115
                                       +++    l+ ame  ++ +
  gi|386002601|ref|YP_005920900.1| 393 RSEDRSALHEAMEQQTISV 411
                                       9999999999999988876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.45       1     124 [.     318     437 ..     318     463 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS........TSEEEEEETGGG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka........kpsilfiDEida 69 
                                       +ll+G pG+ K+ l + + k  + + + +sg++ +s   g ++  +++ + + + +         ++ i  iDE+d+
  gi|386002601|ref|YP_005920900.1| 318 ILLVGDPGIAKSQLLRYISKL-SPRGIYTSGKSSTS--AGLTATAVKDELGDGRWSIeagalvlaDKGIACIDEMDK 391
                                       69***************9887.55666677777773..444444444444443221122336676679********* PP

                                       HHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHHS.TTS CS
                               AAA  70 laksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpallr.gRf 124
                                       + +++            ++L +++++++ + +k  v+++ ++    l  a  + gRf
  gi|386002601|ref|YP_005920900.1| 392 MRSED-----------RSALHEAMEQQTISVAKAGVMATLKSrCALLAAANPKfGRF 437
                                       *8888...........66677777777666444444433333233333333344444 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.3   0.00082       1.2       6      31 ..     127     153 ..     126     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00082
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdaplta.CPe 31 
                                       ++C++Cgh f + q+ s+  ++  CP+
  gi|386002601|ref|YP_005920900.1| 127 FECQRCGHLFYKEQTTSKFQEPYdCPN 153
                                       99************9997778888*95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 3999.13
//
Query:       gi|386002602|ref|YP_005920901.1|  [L=103]
Description: hypothetical protein Mhar_1922 [Methanosaeta harundinacea 6Ac]
Scores for 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-27   93.2   0.1      1e-26   93.0   0.1    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.1   5.8e-31     1e-26       1      92 []      13     103 .]      13     103 .] 0.99

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 5.8e-31
                                       EEETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG CS
                            DUF424   1 yrtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpds 77 
                                       +r++++ ++vavcd+ellgktf+eg l+l+v+e f+g+e+a+  e+ ++L+ a+iaN+vge+av++ ++   +d  +
  gi|386002602|ref|YP_005920901.1|  13 HRIRGE-VMVAVCDSELLGKTFDEGALSLTVEEAFFGEEVATVREVAEALAGASIANMVGEKAVACGIETKCIDGRN 88 
                                       7999**.********************************************************************** PP

                                       -EEETTEEEEEEEE- CS
                            DUF424  78 Vlvidgvphaqigkl 92 
                                       +l+idgvp aq++++
  gi|386002602|ref|YP_005920901.1|  89 ILKIDGVPTAQMVRM 103
                                       *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 666.69
//
Query:       gi|386002603|ref|YP_005920902.1|  [L=355]
Description: NMD3 family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-45  153.3   0.0    8.7e-45  153.1   0.0    1.1  1  NMD3         NMD3 family
  ------ inclusion threshold ------
       0.11   12.7   9.3       0.43   10.7   0.8    3.3  3  Zn-ribbon_8  Zinc ribbon domain
       0.57   10.3   4.0       0.21   11.7   1.2    1.6  2  TerY_C       TerY-C metal binding domain
        1.2    8.8   6.3        2.6    7.7   0.7    3.2  3  RecR         RecR protein
        3.4    7.8   7.5         10    6.3   3.6    2.7  2  DZR          Double zinc ribbon


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.0   2.4e-48   8.7e-45       1     243 []       7     237 ..       7     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 2.4e-48
                              NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                       C+rCG ++  l  glC++C l+e  ++e+ +++ev+ C+ Cg  + +g+W     ++  +++e++ ++v  g+ +++
  gi|386002603|ref|YP_005920902.1|   7 CPRCGGPSA-L--GLCSRCRLEEATLLEVSDHAEVTACPVCGFQRVQGRW----RDTGGTVEEMIFEAVAGGIALHR 76 
                                       ********5.6..9*******************************999**....6789999999999999******* PP

                              NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                       ++e+ +v+ ++ +   + + s+++ ++v+v+g++ g+     ++e +v+ + +r +C+rCsr+ag+yyea++Q+R++
  gi|386002603|ref|YP_005920902.1|  77 DLEDPQVD-ISIS---KLN-STQYLATVRVSGTFGGL---AASEERTVRATAERATCERCSRMAGNYYEATIQLRGT 145
                                       *******9.6666...555.88899*********885...347********************************** PP

                              NMD3 155 .relteeehkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvse 226
                                          +  +e ++  +++e++     +++d+ +fi+++k vk G+D+ +gs++++r +++++++++gg++ es kl+++
  gi|386002603|ref|YP_005920902.1| 146 aGPPGPAELDEGRKIAEDVTkscfERGDRLSFIQETKAVKGGIDLVVGSTQQGRAIARAIHERFGGSTLESFKLAGT 222
                                       *******************999999**************************************************** PP

                              NMD3 227 dkksgkevyrltysvrl 243
                                        ++ g++vyr++++vrl
  gi|386002603|ref|YP_005920902.1| 223 -RD-GRNVYRTSILVRL 237
                                       .88.***********97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0064        23      27      35 ..       5      13 ..       1      15 [. 0.74
   2 ?   10.7   0.8   0.00012      0.43       8      35 ..      19      48 ..      18      51 .. 0.81
   3 ?    0.3   0.1      0.21   7.7e+02      24      33 ..     120     129 ..     110     132 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0064
                       Zn-ribbon_8 27 taCPeCgse 35
                                       +CP+Cg++
  gi|386002603|ref|YP_005920902.1|  5 SVCPRCGGP 13
                                      46*****94 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.e 35
                                      C +C  e   l ++sd ++++ CP Cg  +
  gi|386002603|ref|YP_005920902.1| 19 CSRCRLEEATLLEVSDHAEVTaCPVCGFqR 48
                                      9999988888889998888888****9655 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.21
                       Zn-ribbon_8  24 apltaCPeCg 33 
                                       a+  +C +C 
  gi|386002603|ref|YP_005920902.1| 120 AERATCERCS 129
                                       3345599995 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   5.9e-05      0.21      76     113 ..       6      49 ..       2      61 .. 0.73
   2 ?   -3.3   0.1       2.5   8.9e+03     101     111 ..     121     131 ..     118     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                            TerY_C  76 gCPhCgnalafavCe.C....gkllCidg.eeeatCpwCgkevk 113
                                        CP Cg   a+ +C+ C      ll +++ +e ++Cp Cg +  
  gi|386002603|ref|YP_005920902.1|   6 VCPRCGGPSALGLCSrCrleeATLLEVSDhAEVTACPVCGFQRV 49 
                                       7*************735333335666776366778****97755 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                            TerY_C 101 eeatCpwCgke 111
                                       e+atC +C + 
  gi|386002603|ref|YP_005920902.1| 121 ERATCERCSRM 131
                                       67888888764 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.7   0.00072       2.6      19      35 ..       7      23 ..       5      26 .. 0.91
   2 ?    2.0   0.0     0.043   1.6e+02      15      23 ..      37      45 ..      29      48 .. 0.83
   3 ?   -0.2   0.1      0.22   7.7e+02      27      35 ..     121     129 ..     117     132 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00072
                                      -TTT--EESSSS-CCCC CS
                              RecR 19 CsrCgnlteedlCaICs 35
                                      C+rCg  +   lC+ C+
  gi|386002603|ref|YP_005920902.1|  7 CPRCGGPSALGLCSRCR 23
                                      ****************7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.043
                                      H-EE-TTT- CS
                              RecR 15 kvrhCsrCg 23
                                      +v+ C++Cg
  gi|386002603|ref|YP_005920902.1| 37 EVTACPVCG 45
                                      688999998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.22
                                       SSSS-CCCC CS
                              RecR  27 eedlCaICs 35 
                                       e+  C+ Cs
  gi|386002603|ref|YP_005920902.1| 121 ERATCERCS 129
                                       555566665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.6    0.0028        10       1      38 [.       7      49 ..       4      54 .. 0.67
   2 ?    1.7   0.1     0.073   2.6e+02      23      38 ..     117     132 ..     109     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0028
                               DZR  1 CpqCgeelppdarfCseCgtk......lkavaa...edrCpsCgek.v 38
                                      Cp+Cg +  +    Cs+C+ +      ++   +    ++Cp Cg + v
  gi|386002603|ref|YP_005920902.1|  7 CPRCGGP--SALGLCSRCRLEeatlleVS---DhaeVTACPVCGFQrV 49
                                      8888877..44458888887766653333...2455999999997655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.073
                               DZR  23 kavaaedrCpsCgekv 38 
                                       +a+a+  +C +C++++
  gi|386002603|ref|YP_005920902.1| 117 RATAERATCERCSRMA 132
                                       4555577888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2234.81
//
Query:       gi|386002604|ref|YP_005920903.1|  [L=435]
Description: hypothetical protein Mhar_1924 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-12   48.1   0.3    3.1e-12   46.8   0.2    1.8  2  Toprim_4  Toprim domain
    8.5e-07   29.3   0.0      2e-06   28.1   0.0    1.6  1  Toprim_2  Toprim-like
    0.00013   22.1   0.5     0.0008   19.6   0.1    2.5  2  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.3   1.4e+04      25      44 ..      83     102 ..      79     116 .. 0.73
   2 !   46.8   0.2   5.2e-16   3.1e-12       2      82 ..     172     264 ..     171     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                          Toprim_4  25 avlggalspldgirpeklkt 44 
                                       a+l +al++ d ++p   ++
  gi|386002604|ref|YP_005920903.1|  83 AILASALETIDRVGPCIARI 102
                                       67888888888888766555 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 5.2e-16
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                       +i +VEg+aDvl+l ++gikn+vav g+++ p+  +++ ++k  +++++    +e +vke++++ d D+     eG+
  gi|386002604|ref|YP_005920903.1| 172 AILVVEGRADVLNLLRYGIKNAVAVGGTNV-PPTIAELCSKKVvTAFTDgdrgGELIVKELLQVADIDYvarapEGK 247
                                       799***************************.999999999999999999********************88888887 PP

                          Toprim_4  69 ataerlae...llleeg 82 
                                        + ++  +   + l+++
  gi|386002604|ref|YP_005920903.1| 248 CVEDMSQKeivRALRQK 264
                                       77777666555444555 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.3e-10     2e-06       2      69 ..     175     236 ..     174     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.3e-10
                          Toprim_2   2 vfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellr 69 
                                       v+Eg  D+l l+++gik   n+va+gGt+++++ ++l +++    v   +D D+ G+  +k+l +++ 
  gi|386002604|ref|YP_005920903.1| 175 VVEGRADVLNLLRYGIK---NAVAVGGTNVPPTIAELCSKK---VVTAFTDGDRGGELIVKELLQVAD 236
                                       9***************9...********6666666665555...46666************9998884 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.58   3.5e+03      30      30 ..      65      65 ..      20     135 .. 0.51
   2 !   19.6   0.1   1.3e-07    0.0008       2      91 ..     173     240 ..     172     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.58
                                      S CS
                            Toprim 30 G 30
                                      G
  gi|386002604|ref|YP_005920903.1| 65 G 65
                                      3 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.3e-07
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEE.CSSSHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiila.tDpDreGe 77 
                                       + +vEg +d+ ++ ++   g ++++a+ G+ +  +                    +el    ++++ a tD+Dr Ge
  gi|386002604|ref|YP_005920903.1| 173 ILVVEGRADVLNLLRY---GIKNAVAVGGTNVPPTI-------------------AELC-S-KKVVTAfTDGDRGGE 225
                                       78**************...9**********997665...................5554.4.4555555******** PP

                                       HHHHHHHHHHT.HHH CS
                            Toprim  78 aiawellevlk.ell 91 
                                        i +ell+v++ +++
  gi|386002604|ref|YP_005920903.1| 226 LIVKELLQVADiDYV 240
                                       *******99985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2668.57
//
Query:       gi|386002605|ref|YP_005920904.1|  [L=122]
Description: hypothetical protein Mhar_1925 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-36  123.3   0.1    6.5e-36  123.2   0.1    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.1   3.6e-40   6.5e-36       2     116 ..      12     121 ..      11     122 .] 0.97

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 3.6e-40
                                       EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SE CS
                              PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpa 78 
                                       k++++vr+DLk+s Gk+a+q+ahAav +++++ k+     ++++W+eegq+kivlk++  ++  +l+++a+++g++a
  gi|386002605|ref|YP_005920904.1|  12 KQCIIVREDLKLSSGKLAVQVAHAAVLAMERADKR-----IVRDWKEEGQRKIVLKARTLQDVFRLRDEAERAGVAA 83 
                                       9*****************************98885.....89*********************************** PP

                                       EEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB CS
                              PTH2  79 alirDagrtqiepgtkTvlaigPapksivdkvtgkLkl 116
                                       a++ Dag t+i+pgt+T+l++gPap+ ++d++tg Lkl
  gi|386002605|ref|YP_005920904.1|  84 AIVIDAGLTEIPPGTVTALGLGPAPEAQIDRITGGLKL 121
                                       *************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 875.08
//
Query:       gi|386002606|ref|YP_005920905.1|  [L=425]
Description: tRNA pseudouridine synthase D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-155  517.6   0.0   2.4e-155  517.5   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)
  ------ inclusion threshold ------
       0.18   11.7   3.0       0.46   10.3   0.1    2.6  3  DUF5559   Family of unknown function (DUF5559)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.5   0.0  2.6e-159  2.4e-155       2     416 .]      11     422 ..      10     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 517.5 bits;  conditional E-value: 2.6e-159
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaG 78 
                                       lg+ely+t+++g+gGrlr++ eDF VeE+   + +++  +g+ylv++vek +w+t++lvr+l+r+l+is+kr+++aG
  gi|386002606|ref|YP_005920905.1|  11 LGMELYATSSPGCGGRLRAEVEDFAVEEL---APDQRYGRGRYLVVEVEKAGWETHHLVRDLSRQLQISQKRFSWAG 84 
                                       89***************************...55567999************************************* PP

                              TruD  79 tKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileel 154
                                       tKDk+AvT+Q +si+++e+ el ++++++v+++ +gr++r+++lGdL GN+F++r+r++  ++ eaa+r+e+++ e+
  gi|386002606|ref|YP_005920905.1|  85 TKDKNAVTRQRMSIYGLEEGELVRANLPGVRIRALGRSDRPVSLGDLRGNRFAVRIREIdLDDAEAARRLEAVTGEI 161
                                       ************************************************************99*************** PP

                              TruD 155 eekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpksl 231
                                       ++ gg+PNyfGvQRFG++rpvthlvG+a+v+gd e+A+++y++ pf+ e+e+tr+are +  ++d++ al+e+p +l
  gi|386002606|ref|YP_005920905.1| 162 RALGGLPNYFGVQRFGEVRPVTHLVGEALVRGDPEGAAMIYLALPFPGEPESTRAARERLLADRDFSLALKEYPLRL 238
                                       ***************************************************************************** PP

                              TruD 232 ryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrl 308
                                       ryEra++ rL+e ++d+++++ +l +nL+rlFvhAyqS l+Nr+ls+R+++glpl ++veGDvv+f+++ lp++d+l
  gi|386002606|ref|YP_005920905.1| 239 RYERAMMARLQE-EGDFARSFDVLAENLRRLFVHAYQSLLYNRILSRRMKSGLPLGRAVEGDVVCFSKDGLPNPDKL 314
                                       ************.**************************************************************** PP

                              TruD 309 qlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrv 385
                                       q+v+ +n  +v+rl++rgrafvt+pl+G+ +e+a g +geier+vl+eeg+el+dF++ + p+l+s G+rRa+llrv
  gi|386002606|ref|YP_005920905.1| 315 QAVDGSNLSAVNRLADRGRAFVTLPLFGYGSEFAGGLPGEIERAVLAEEGVELSDFRVDANPGLGSPGSRRAALLRV 391
                                       ***************************************************************************** PP

                              TruD 386 edlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       + + + +e+++++l+F Lp+GsYATvvlrE+
  gi|386002606|ref|YP_005920905.1| 392 DPVVVVEEGSSALLKFDLPPGSYATVVLREY 422
                                       *9999999**********************8 PP

>> DUF5559  Family of unknown function (DUF5559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.046   4.1e+02      98     147 ..      82     130 ..      70     134 .. 0.70
   2 ?   10.3   0.1   5.1e-05      0.46     106     150 ..     134     178 ..     128     185 .. 0.87
   3 ?   -2.6   0.0      0.47   4.3e+03     129     150 ..     328     349 ..     319     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.046
                           DUF5559  98 wvggegwgevgglrlskvgrrdrevgrglrapagrgramggmprmgtvgd 147
                                       w g +    v   r+s  g  + e+ r    p  r ra+g   r  ++gd
  gi|386002606|ref|YP_005920905.1|  82 WAGTKDKNAVTRQRMSIYGLEEGELVRA-NLPGVRIRALGRSDRPVSLGD 130
                                       7777777777777777777777777765.457777777777777766666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.1e-05
                           DUF5559 106 evgglrlskvgrrdrevgrglrapagrgramggmprmgtvgdfgq 150
                                       +   +r+ ++   d e  r l a +g  ra+gg+p    v  fg+
  gi|386002606|ref|YP_005920905.1| 134 NRFAVRIREIDLDDAEAARRLEAVTGEIRALGGLPNYFGVQRFGE 178
                                       5556888999999***********************999999997 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.47
                           DUF5559 129 pagrgramggmprmgtvgdfgq 150
                                        a rgra+  +p +g   +f  
  gi|386002606|ref|YP_005920905.1| 328 LADRGRAFVTLPLFGYGSEFAG 349
                                       5889999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2968.92
//
Query:       gi|386002607|ref|YP_005920906.1|  [L=297]
Description: Putative methanogenesis marker protein 11 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-10   39.7   0.2      5e-07   29.8   0.0    3.3  2  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.8e-11     5e-07       1     113 [.     151     239 ..     151     242 .. 0.93
   2 !    2.6   0.1    0.0073   1.3e+02       1      11 [.     273     283 ..     273     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.8e-11
                                       TTHHHHHHHHHH-..-TT....S-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTS CS
                           DUF1743   1 grgiiGAtaalganiale....dstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpd 73 
                                       +++++GAt++l++nia +    +++y                                     +sh lv+l+P +p+
  gi|386002607|ref|YP_005920906.1| 151 DSKTEGATWSLVHNIAAKvdrpEARY-------------------------------------VSHALVQLFP-VPT 189
                                       7899***********98776666666.....................................9*********.*** PP

                                       S........EEEEEEES-HHHHHHHHHCSEE..S-EEC..EEEEEESTTS CS
                           DUF1743  74 p........vlfGirgedpeallkaakeilskeeesee..mavfrtnqgt 113
                                       +        v+f+  + +++ +l++++++l+++++see  mav+r+++++
  gi|386002607|ref|YP_005920906.1| 190 KtqncvstvVEFAALPGKADPMLAEFRDLLERYTVSEEtgMAVYRGFDPS 239
                                       **********************************************9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0073
                                       TTHHHHHHHHH CS
                           DUF1743   1 grgiiGAtaal 11 
                                       grg+iGA+aa+
  gi|386002607|ref|YP_005920906.1| 273 GRGLIGALAAI 283
                                       89********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2030.26
//
Query:       gi|386002608|ref|YP_005920907.1|  [L=531]
Description: Indolepyruvate ferredoxin oxidoreductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-07   31.6   0.2    2.9e-07   30.4   0.2    1.7  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    0.00085   19.0   1.0      0.056   13.0   0.7    2.8  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
  ------ inclusion threshold ------
       0.14   10.0   0.3       0.24    9.2   0.3    1.3  1  DUF3367       Alpha-(1->3)-arabinofuranosyltransferase


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2   4.9e-11   2.9e-07      28      94 ..     415     477 ..     397     520 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.9e-11
                                       S-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHH CS
                      TPP_enzyme_C  28 gtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggqqep 94 
                                         +G ++++A+G        + va++GD +++++ l  l+ av+++  ++v++l+N++ +mtggq  p
  gi|386002608|ref|YP_005920907.1| 415 YGLGSSVAVASGFGE-----KGVALIGDYALAHSgLLGLIDAVNNRREVLVLLLDNGVAAMTGGQGVP 477
                                       457777777777764.....78******************************************9443 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.7   9.4e-06     0.056       5     100 ..      41     132 ..      38     186 .. 0.79
   2 ?   -1.2   0.0      0.23   1.4e+03      83     106 ..     271     294 ..     261     311 .. 0.76
   3 ?    2.5   0.0     0.016        97      78     135 ..     443     498 ..     419     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-06
                                       HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-C.HHHHHHCH CS
                      TPP_enzyme_N   5 ealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvts.gpGatnal 80 
                                       e+l  +L++l+v++ + vpG  i++ + al e       +a +E +a   A g + a+g++++vlv + g++++   
  gi|386002608|ref|YP_005920907.1|  41 EVLKGCLEELNVQVRIYVPGYPITEAVPALGEGA----EMATNEKVALEVALGSS-ASGRRAIVLVKHlGINLLADP 112
                                       677789**************99999999999984....6789***********95.5567777777666******** PP

                                       HHHHHHHHHT--EEEEEEE- CS
                      TPP_enzyme_N  81 talaeAkvdriPllvlsgdr 100
                                        a+a  ++ +  l+vl+g+ 
  gi|386002608|ref|YP_005920907.1| 113 LAIAPTHTIGAGLVVLAGED 132
                                       *****************974 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.23
                                       HHHHHHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrg 106
                                       +  A+++ +Pllv+  ++p  l+ 
  gi|386002608|ref|YP_005920907.1| 271 AGYASKTDLPLLVVGFSHPLPLEA 294
                                       56799999*******999988776 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.016
                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGG CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspee 135
                                       ++l +l++A  +r  +lvl  d++++     + q++ d + ++r ++ +a++++ pe+
  gi|386002608|ref|YP_005920907.1| 443 SGLLGLIDAVNNRREVLVLLLDNGVAAMT--GGQGVPDLSPVLRTIVPDARTIDLPED 498
                                       678899*******************9999..6777999******99999999998875 PP

>> DUF3367  Alpha-(1->3)-arabinofuranosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   4.1e-05      0.24     269     320 ..     430     481 ..     418     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 4.1e-05
                           DUF3367 269 epvlvlatalvaalGLaGLarrdlparrllllillvgvvllaagyagelgsp 320
                                       + v+++   ++a  GL+GL  +    r++l+l+l  gv++++ g      sp
  gi|386002608|ref|YP_005920907.1| 430 KGVALIGDYALAHSGLLGLIDAVNNRREVLVLLLDNGVAAMTGGQGVPDLSP 481
                                       668889999********************************99876655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3660.87
//
Query:       gi|386002609|ref|YP_005920908.1|  [L=280]
Description: Beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-11   43.1   1.7    6.8e-11   42.5   0.9    1.7  2  Lactamase_B    Metallo-beta-lactamase superfamily
    9.4e-07   28.5   0.0    1.4e-06   27.9   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.9   7.5e-15   6.8e-11       6      98 ..      28     139 ..      25     202 .. 0.75
   2 ?   -2.8   0.0      0.59   5.3e+03     181     197 .]     235     251 ..     217     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 7.5e-15
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       ++s ++e +++ +++D+G +t a   a   +alg++++ v  + l+H+H+DH+Gglg l+e+t+ ++++ + + ++ 
  gi|386002609|ref|YP_005920908.1|  28 GFSAYLEFGDSRVIFDAGQTTTAVSNA---RALGIDLEGVP-IALSHGHYDHTGGLGSLIEKTGPVPVYAHPDVFVS 100
                                       57888999******************8...59999999998.789******************************** PP

                                       HCHHHHHHHHHCCHH.......................T CS
                       Lactamase_B  83 fmeeaddaasrkgll.......................l 98 
                                       ++  +++a    g++                       +
  gi|386002609|ref|YP_005920908.1| 101 RYTRRGGALRQIGIPfrrgdleaagarfelsrraeeifP 139
                                       *****9999998776766666433333333332222220 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.59
                                       HHHHHHHHCHSEEEESS CS
                       Lactamase_B 181 sllklaglkaevlvpgH 197
                                       +++ l+ l+ evl+p+H
  gi|386002609|ref|YP_005920908.1| 235 TIEALRSLDLEVLAPSH 251
                                       67788899999999998 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.6e-10   1.4e-06       2      67 ..      39      98 ..      38     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.6e-10
                                      EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHH CS
                     Lactamase_B_2  2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvl 67
                                      r+++Dag  + +   +ral       +l+ +  + l+h+HyDH+ gl +l e ++  +p+ya+++v 
  gi|386002609|ref|YP_005920908.1| 39 RVIFDAGQTTTAVsNARAL-----GIDLEGVP-IALSHGHYDHTGGLGSLIEKTG-PVPVYAHPDVF 98
                                      7889999885444335554.....77888888.99*****************554.3******9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1717.09
//
Query:       gi|386002610|ref|YP_005920909.1|  [L=660]
Description: Cation transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-49  166.4  14.4    1.2e-39  136.2   7.2    4.0  4  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0     0.055   9.9e+02     404     436 ..      45      75 ..      40      88 .. 0.82
   2 !    5.5   0.0   0.00028       4.9      64      82 ..      98     116 ..      84     136 .. 0.72
   3 !  136.2   7.2   6.5e-44   1.2e-39      91     420 ..     198     495 ..     165     503 .. 0.88
   4 !   25.9   0.0   1.8e-10   3.3e-06     431     491 ..     593     654 ..     589     659 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.055
                              TrkH 404 lvdlwslflvlliilileglklsdvqepdfsff 436
                                       l +l+ ++++ll +++ e ++l++  +  f ++
  gi|386002610|ref|YP_005920909.1|  45 LPALFTFAIGLLMAILGEEEVLTNREG--FALV 75 
                                       6689******************99987..5544 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.00028
                              TrkH  64 ldalfeavsgltttglsvi 82 
                                       +dalfe++sg+tttg+s  
  gi|386002610|ref|YP_005920909.1|  98 IDALFESMSGFTTTGASIL 116
                                       4566666666666666655 PP

  == domain 3  score: 136.2 bits;  conditional E-value: 6.5e-44
                              TrkH  91 sgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvv 167
                                         l++r ++q++Gg+g++vl  ++lp lg  + +l ++e++++  ++   ++++e++kil+ +y++++++ f+ll  
  gi|386002610|ref|YP_005920909.1| 198 GLLFWRCFTQWLGGMGIIVLFIAILPNLGVAGRQLFKAEVPGPS-EDLIRPRIRETAKILWGVYMVITAAEFLLL-- 271
                                       4689************************************9996.67889*************************.. PP

                              TrkH 168 liytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasf....nknivillvaiifiilGnigFpillrv 240
                                                + +      p ++a+++++S+++++Gfs  ++S+a++     ++++i++++i+f+++++ +F +++r+
  gi|386002610|ref|YP_005920909.1| 272 -------MLARM------PAYDAVCTTFSTVSTGGFSPRADSIAYYggpdYNAPFIEVIVIVFMFISGASFALHYRT 335
                                       .......78889......***************************94443255**********************98 PP

                              TrkH 241 iiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfilldegslvvksipkgsrvl 317
                                       +                  s++ d+++r+  Ll++  +++++l+  +     d  +         + +   +g+r +
  gi|386002610|ref|YP_005920909.1| 336 MYVNRT-------------SLIEDPEFRFYSLLVGAVILIVVLIGGV-----DGSFLGD---SPEAEGVGLAGQRLR 391
                                       765433.............5788*******99998877777777633.....4333222...222333344699*** PP

                              TrkH 318 kalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskks 393
                                       +a+Fq vs  t  GF+++d++ ++   k++l++ m+ g+++gSt gg++ ++v+  ++  ++e+ +  +pkav  ++
  gi|386002610|ref|YP_005920909.1| 392 AAAFQTVSIVTStGFATADYDLWSSPAKLILLFLMFTGACAGSTSGGMKLVRVLLSVRYCRRELFRTLHPKAVMAVK 468
                                       ***********99**************************************************************** PP

                              TrkH 394 idgkhlerqllvdlwslflvlliilil 420
                                       ++   +++++l+++  ++ ++++i+ +
  gi|386002610|ref|YP_005920909.1| 469 LKASPVREDVLHSIMVFMALYILIFAV 495
                                       **************9999999888765 PP

  == domain 4  score: 25.9 bits;  conditional E-value: 1.8e-10
                              TrkH 431 pdfsffdiLfevvSaygtvGLSlGa.knaslsaqlttisklvlialmirGrlrglpvlldra 491
                                        d++++ +  +v+Sa+g+vG+ +     +    +++ i+kl+li+ m++Grl+ l+vl++ +
  gi|386002610|ref|YP_005920909.1| 593 SDMDVISAASAVASALGNVGPAFHRyGPTDNYSEVPGIGKLILIVCMWIGRLELLTVLVLLV 654
                                       579999999*************9744677777899***********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 4029.44
//
Query:       gi|386002611|ref|YP_005920910.1|  [L=618]
Description: Cation transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-48  163.6  18.4    4.7e-39  134.2   6.0    4.5  4  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1     0.026   4.6e+02     403     436 ..      41      72 ..      35      85 .. 0.83
   2 !    6.0   0.8   0.00019       3.3     189     209 ..      96     116 ..      69     147 .. 0.74
   3 !  134.2   6.0   2.6e-43   4.7e-39      72     420 ..     175     492 ..     138     500 .. 0.85
   4 !   26.3   0.1   1.3e-10   2.3e-06     434     490 ..     554     611 ..     548     616 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.026
                              TrkH 403 llvdlwslflvlliilileglklsdvqepdfsff 436
                                       ll +l+ ++++ll +++ e ++l++  +  f ++
  gi|386002611|ref|YP_005920910.1|  41 LLPALFTFAIGLLMAILGEEEVLTNKEG--FALV 72 
                                       67899*******************9987..5554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00019
                              TrkH 189 waffhsmSafnnlGfsltpnS 209
                                       +a+f smS+f++ G s++++S
  gi|386002611|ref|YP_005920910.1|  96 DALFESMSGFTTTGASILSES 116
                                       566666666666666666655 PP

  == domain 3  score: 134.2 bits;  conditional E-value: 2.6e-43
                              TrkH  72 sgltttglsvivveesl.prsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslseli 147
                                       +gl+ +g++++ ++ +   r  l++r ++++iGg+g++vl  ++lp lg  + +l ++e++++  ++   +++++++
  gi|386002611|ref|YP_005920910.1| 175 GGLSGSGTNLTSNLIEPtYRGLLFWRCFTNWIGGMGIIVLFIAILPNLGVAGRQLFNAEVPGPT-EDLIRPRIKQTA 250
                                       466666776666655552566799************************************9996.67889******* PP

                              TrkH 148 kilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnkn....ivil 220
                                       kil+ +y++l+++ f+ll           + +      p ++a+++++S++ ++Gfs  ++S+a++       ++i+
  gi|386002611|ref|YP_005920910.1| 251 KILWGVYMVLTAAEFLLL---------MLAKM------PAYDAICTTFSTVATGGFSPRAESIAYYSGPdyngPLIE 312
                                       ******************.........88889......****************************7544448**** PP

                              TrkH 221 lvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilf 297
                                       +v+i+f+++ + +F +++r++    k+              ++d ++++  L++  ++++++l+          i  
  gi|386002611|ref|YP_005920910.1| 313 VVVILFMFVCGANFALHYRTMYVSRKSL-------------IKDAEFKFYSLIVLASILVITLIG--------GIDE 368
                                       *******************987666555.............679999999655444444444444........3334 PP

                              TrkH 298 illdegslvvksipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeef 373
                                        l +eg  + +   +  r + a+Fq vs  t+ GF+++d++ ++   k++l++ m+ gg++gStag ++ ++++ + 
  gi|386002611|ref|YP_005920910.1| 369 SLPPEGPDLEGFDLASHRLRTAAFQTVSIITTtGFATADYDLWSSPAKLILLFLMFTGGCAGSTAGAMKVVRILLAL 445
                                       556677666665556789************999******************************************** PP

                              TrkH 374 slgkyeieqekepkavskksidgkhlerqllvdlwslflvlliilil 420
                                       +  ++e+ +  +pkav  ++++g+ +++++l+++  ++ ++++i+ +
  gi|386002611|ref|YP_005920910.1| 446 QCCRRELFRTLHPKAVMAVKLKGAPVREDVLRSILIFMAIYILIFAI 492
                                       ***********************************999999988754 PP

  == domain 4  score: 26.3 bits;  conditional E-value: 1.3e-10
                              TrkH 434 sffdiLfevvSaygtvGLSlGa.knaslsaqlttisklvlialmirGrlrglpvlldr 490
                                       +++ +  +v+ ++g+vG++l     +  + +++ i+kl+li+ m++Grl++l+vl++ 
  gi|386002611|ref|YP_005920910.1| 554 DMISACSAVATCLGNVGPGLHRfGPTDNFSEVPGIGKLILILCMWMGRLEVLTVLVLL 611
                                       56677789***********986578889999***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 4229.39
//
Query:       gi|386002612|ref|YP_005920911.1|  [L=393]
Description: 2-isopropylmalate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-82  276.2   0.9    3.6e-82  275.9   0.9    1.1  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.9   0.9     2e-86   3.6e-82       2     264 .]      20     276 ..      19     276 .. 0.99

  Alignments for each domain:
  == domain 1  score: 275.9 bits;  conditional E-value: 2e-86
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       ++++d+tLRDGeq +++ ++ +ek+ ia +Lde+gv+ iE+gfp+ se ++ +vr + + + +++i +l r++ kd+
  gi|386002612|ref|YP_005920911.1|  20 IEVCDVTLRDGEQMPGVVFRPDEKIDIAIKLDEVGVEIIEAGFPVVSEAEMRAVRDVSNLGLDSKISVLSRSVPKDV 96 
                                       789************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +aa +    + +++v vfiats+lhlk+kl+++ ee++k+a e v++a+++g  v++s+eda+rt+ + l +++++a
  gi|386002612|ref|YP_005920911.1|  97 DAALA----CDVDMVSVFIATSDLHLKYKLHMTCEEAIKSALETVEYAKDHGLIVRFSAEDATRTEFNLLKRLYKKA 169
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       ee  a++++iaDtvG+++P+ ++ l++++k++vk  +++ +HcH+dlGlA+antlaA+eaGa+++ +tvnG+Ger+G
  gi|386002612|ref|YP_005920911.1| 170 EECRADYVSIADTVGIMNPRTVYFLVREIKKVVK--IPICMHCHDDLGLALANTLAAAEAGAKQLHTTVNGIGERSG 244
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealgvdtgldlqklrsiaalv 264
                                       n++leel++al++      +d++kl+++++lv
  gi|386002612|ref|YP_005920911.1| 245 NTPLEELMVALRVHYSVDRYDTTKLTDLSKLV 276
                                       ***************99***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2669.19
//
Query:       gi|386002613|ref|YP_005920912.1|  [L=353]
Description: Cell surface protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-24   84.6  14.7    6.2e-24   84.6  14.7    1.9  2  Beta_helix       Right handed beta helix region
    9.8e-21   74.1  11.1    1.4e-20   73.6  11.1    1.3  1  NosD             Periplasmic copper-binding protein (NosD)
    1.3e-06   28.4   5.1    2.1e-06   27.7   5.1    1.3  1  Pectate_lyase_3  Pectate lyase superfamily protein
    0.00016   21.1  13.2    0.00067   19.1  13.2    2.2  1  DUF1565          Protein of unknown function (DUF1565)
  ------ inclusion threshold ------
      0.031   14.2   0.6       0.13   12.2   0.2    2.1  2  DUF4957          Domain of unknown function (DUF4957)


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.017        62      27      91 ..     128     208 ..     125     217 .. 0.55
   2 !   84.6  14.7   1.7e-27   6.2e-24       3     157 ..     190     347 ..     188     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                                       EE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---...................SEEE-TT--S--EEES CS
                        Beta_helix  27 ylrgssnvvienneiannsgsGiyilgssnntisnntisdnn...................gggialfgasnnlien 84 
                                       +l+g+s ++i+   i    g+G  ++     t ++n+i d                     +g + l +as++ +e+
  gi|386002613|ref|YP_005920912.1| 128 CLNGCSYTTIQ-AAIDA-AGEGDVVEV-GSGTYRENVIVDKRvtirgvntgegvpvvdaqgNGSAVLLKASGVFLEG 201
                                       55555555555.55555.444444443.4444444444333333333334444567777755677777999999999 PP

                                       -EEES-S CS
                        Beta_helix  85 neitdng 91 
                                        +it+ g
  gi|386002613|ref|YP_005920912.1| 202 LTITNAG 208
                                       9999885 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 1.7e-27
                                       EEE-SS-E.EEESEEEES-...SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT- CS
                        Beta_helix   3 isingssnvtiknntisns...ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfg 76 
                                       ++++ s++  +++ ti+n+   +++Gi + + ++ v+ ++ + n++  Giy++gs+n+t+s++  s+n+++gi +f 
  gi|386002613|ref|YP_005920912.1| 190 VLLKASGV-FLEGLTITNAgpyPSAGIEVVSRDS-VVAGCAVMNSNWAGIYLKGSANTTVSRCISSNNGNDGILVFR 264
                                       55666666.99***********************.9999************************************** PP

                                       -S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS.... CS
                        Beta_helix  77 asnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss.... 149
                                       a +nli+ + +++n ++Gi l +s++n+ie+N + nn+  Gi++d+s+ n +vt+N+++ n+ +Gi + +s+     
  gi|386002613|ref|YP_005920912.1| 265 ATGNLISESVVSNNLDDGIALLSSDDNRIEGNLVANNTDVGIFLDNSK-NAVVTGNVLSYNA-KGISLLNSGIdrvg 339
                                       ************************************************.999*********9.99999888765555 PP

                                       --EEES-E CS
                        Beta_helix 150 nvtvrnNt 157
                                        + + nNt
  gi|386002613|ref|YP_005920912.1| 340 PNRFFNNT 347
                                       56666666 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6  11.1   3.8e-24   1.4e-20      27     177 ..     202     351 ..     156     353 .] 0.84

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 3.8e-24
                              NosD  27 seisnneisnsrdgilldnssnntitgn.tienlryGihlensesntiedntlssne.sGialmsssnntlenNtis 101
                                        +i  n+   +++gi +  s +  + g+ +++++ +Gi+l++s ++t++ ++ s+n+ +Gi++ + ++n ++ +++s
  gi|386002613|ref|YP_005920912.1| 202 LTI-TNAGPYPSAGIEV-VSRDSVVAGCaVMNSNWAGIYLKGSANTTVSRCISSNNGnDGILVFRATGNLISESVVS 276
                                       444.4555566777744.45555566662666679****************************************** PP

                              NosD 102 nnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvk 177
                                       nn + Gi l  s++n i++N +  n++ Gifl+ns++ ++tgN +++n   Gi  l +s   ++  N F+nn++n++
  gi|386002613|ref|YP_005920912.1| 277 NNLDDGIALLSSDDNRIEGNLVAnNTDVGIFLDNSKNAVVTGNVLSYN-AKGIS-LLNSGIDRVGPNRFFNNTVNLE 351
                                       **********************99************************.*****.8899999***********9975 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   5.1   5.9e-10   2.1e-06      20     213 ..     136     327 ..     133     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.9e-10
                                       HHHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-..TTTEEEEE-TT-SS--SEEES-TT.T-..-EE CS
                   Pectate_lyase_3  20 aiqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvGdg..ngrpvlkaaaafvgaglidgdpyv.sggseal 93 
                                        iq+ai   +a  +g+vV + +GtY+ +      + v++ G     g+pv+ a+++   a l++++ +  +g     
  gi|386002613|ref|YP_005920912.1| 136 TIQAAI---DAAGEGDVVEVGSGTYRENVI--VDKRVTIRGVNtgEGVPVVDAQGNGS-AVLLKASGVFlEG--LT- 203
                                       59****...99**************95554..59999999965226667777766432.2333333333344..22. PP

                                       EEEEEEEEE..GGGG-SS---S.....SEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EE CS
                   Pectate_lyase_3  94 iatnnfyrq..irnlkiditav.....apgatgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvf 163
                                       i+++  y +  i  +  d+  +     +++ +gi  + + +t+++++ + ++++    ++gi++ +  g+ ++++v+
  gi|386002613|ref|YP_005920912.1| 204 ITNAGPYPSagIEVVSRDSVVAgcavmNSNWAGIYLKGSANTTVSRC-ISSNNG----NDGILVFRATGNLISESVV 275
                                       2222333222377777776655666456666****************.333333....46***************** PP

                                       ES-SS-SEEE.S-EEEEE.ES-EEE-S--SEEE-TT-EEEEEEEEEESSSEE CS
                   Pectate_lyase_3 164 sglgdigiav.gnqqftv.rnitfnnattgievlwgwgwtlknvkinncegG 213
                                       s++ d+gia+ ++++  +  n++ nn+  gi ++ +++ ++ ++ ++   +G
  gi|386002613|ref|YP_005920912.1| 276 SNNLDDGIALlSSDDNRIeGNLVANNTDVGIFLDNSKNAVVTGNVLSYNAKG 327
                                       **********9865555538999999********988877766666555555 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  13.2   1.9e-07   0.00067      15     217 ..     134     345 ..     128     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-07
                           DUF1565  15 fktiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagk.............kvgpl 78 
                                       + ti  A+ +a  g+v+++  GtY e+      +++ + v++ G ++g G   ++ a+                g +
  gi|386002613|ref|YP_005920912.1| 134 YTTIQAAIDAAGEGDVVEVGSGTYREN------VIVDKRVTIRGVNTGEGV-PVVDAQGngsavllkasgvfLEGLT 203
                                       789*********************997......689999999999999999.3333333233444432333322333 PP

                           DUF1565  79 isgggddlsgvqnvti.vlaneatiaGvtitNpnilkgtgvliesa.sakianNtitgniadGiev........... 142
                                       i  +g+       + i v+   + +aG  + N n     g++++++ +++++    ++n++dGi v           
  gi|386002613|ref|YP_005920912.1| 204 ITNAGPYP----SAGIeVVSRDSVVAGCAVMNSNW---AGIYLKGSaNTTVSRCISSNNGNDGILVfratgnlises 273
                                       33344333....35553677889999*****9955...899999987888888888889999977766666555443 PP

                           DUF1565 143 ...siyeaktgagg.........niisGnsilfekn.GiaisgasaavenkienNiivkNliGvvanalalDlGsgs 206
                                          +      +  +         n i Gn ++++++ Gi  +++++a    +  N+++ N +G+     +       
  gi|386002613|ref|YP_005920912.1| 274 vvsN------NLDDgiallssddNRIEGNLVANNTDvGIFLDNSKNA---VVTGNVLSYNAKGISLLNSGI------ 335
                                       3321......1111122233333669999999999989999888888...68999*****99998555443...... PP

                           DUF1565 207 egsaGnNifsn 217
                                        + +G N f n
  gi|386002613|ref|YP_005920912.1| 336 -DRVGPNRFFN 345
                                       .3455555555 PP

>> DUF4957  Domain of unknown function (DUF4957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.6e-05      0.13       1     134 [.     155     278 ..     155     279 .. 0.77
   2 ?    0.3   0.1      0.17     6e+02      53      79 ..     276     302 ..     268     339 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                           DUF4957   1 GtYtlsgeidfskkvtirgvdkanhpki..tlgkgnasistgasLkiknldldgsasdssfialsetpdetikdtlt 75 
                                       GtY    ++ + k+vtirgv+  ++  +    g+g+a + ++ +  ++ l++      +    +  +  e +  + +
  gi|386002613|ref|YP_005920912.1| 155 GTYR--ENVIVDKRVTIRGVNTGEGVPVvdAQGNGSAVLLKASGVFLEGLTITN---AG---PYPSAGIEVVSRDSV 223
                                       6676..89999*********9998755546666667777777788888888873...23...355555555556667 PP

                           DUF4957  76 iqnCeikdvnkgliydnnkkyviesivinnclvkniessggdiidfkkgfinnltvknS 134
                                       + +C + + n   iy        ++ ++++c+ +n++ +g  +++     i +  v+n+
  gi|386002613|ref|YP_005920912.1| 224 VAGCAVMNSNWAGIYLKG----SANTTVSRCISSNNGNDGILVFRATGNLISESVVSNN 278
                                       9**************887....6899************998888777777877777775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                           DUF4957  53 sasdssfialsetpdetikdtltiqnC 79 
                                       s++ ++ ial  ++d+ i+++l+ +n 
  gi|386002613|ref|YP_005920912.1| 276 SNNLDDGIALLSSDDNRIEGNLVANNT 302
                                       344445555555666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2507.75
//
Query:       gi|386002614|ref|YP_005920913.1|  [L=271]
Description: Glutamine cyclotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-96  321.4   0.0    4.5e-96  321.1   0.0    1.0  1  Glu_cyclase_2  Glutamine cyclotransferase
  ------ inclusion threshold ------
       0.85   10.2   5.1        3.8    8.1   0.0    3.3  4  PQQ_3          PQQ-like domain


Domain annotation for each model (and alignments):
>> Glu_cyclase_2  Glutamine cyclotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.1   0.0  5.1e-100   4.5e-96      22     251 .]      39     267 ..      19     267 .. 0.95

  Alignments for each domain:
  == domain 1  score: 321.1 bits;  conditional E-value: 5.1e-100
                     Glu_cyclase_2  22 saaeelkvevvaeyphdpeaftqGLefedgelyestGlegksslrkvdletgkvlkeaeldeelFgEGitvlgdkly 98 
                                        a++++ ++vva yphdpeaftqGL f+dg lye+tGl+g+s++r++ letg+ ++++ l+++lFgEGi++++d+l+
  gi|386002614|ref|YP_005920913.1|  39 MAPPVYGYRVVAAYPHDPEAFTQGLAFRDGLLYEGTGLYGRSEIRETVLETGEEIRSRGLPPSLFGEGIALIDDELL 115
                                       37899************************************************************************ PP

                     Glu_cyclase_2  99 qltwkegvafvydaetleeigrvsyegeGWGlttdgkrlvmsdGsstltfldpktfaetksvevtkdgkevsklNEL 175
                                       qltw++gv++v+d e+++ +g +sy +eGWG+t+dg+rl+msdGsstl+fldp+tf++t+s+ev++dgk++  lNEL
  gi|386002614|ref|YP_005920913.1| 116 QLTWRSGVGLVWDLESFTVVGAFSYPTEGWGITADGQRLIMSDGSSTLRFLDPETFEVTGSLEVEADGKPLLGLNEL 192
                                       ***************************************************************************** PP

                     Glu_cyclase_2 176 eyvkgeiyaNvwqtdrilridpatGkvtgvidlsalreeaekaakedVlNGiAydpetdrlfvTGKlWpklfevkl 251
                                       e+v+g iyaNvw+ d+i++i+p +G+v+g+idl++l +e+e++   dVlNGiAydp+++rlfvTGKlWp +fe+++
  gi|386002614|ref|YP_005920913.1| 193 EWVDGLIYANVWKADEIAIISPGSGRVVGWIDLAGLLSEEERERG-DVLNGIAYDPASGRLFVTGKLWPWVFEIEV 267
                                       ***************************************999865.****************************86 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.015   1.3e+02      12      29 ..      58      75 ..      43      83 .. 0.84
   2 ?    8.1   0.0   0.00043       3.8      13      40 .]     144     170 ..     118     170 .. 0.85
   3 ?   -3.6   0.0         2   1.8e+04      21      26 ..     196     201 ..     194     201 .. 0.68
   4 ?   -2.5   0.1      0.94   8.5e+03      13      27 ..     239     255 ..     236     256 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.015
                             PQQ_3 12 pvnsspavdgglvyvgtg 29
                                      + + ++a+ +gl+y gtg
  gi|386002614|ref|YP_005920913.1| 58 AFTQGLAFRDGLLYEGTG 75
                                      556688********9997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00043
                             PQQ_3  13 vnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       ++ + ++dg ++ +++g  tl+ lD+et
  gi|386002614|ref|YP_005920913.1| 144 GW-GITADGQRLIMSDGSSTLRFLDPET 170
                                       33.4699*******************98 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2
                             PQQ_3  21 gglvyv 26 
                                       +gl+y+
  gi|386002614|ref|YP_005920913.1| 196 DGLIYA 201
                                       788875 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.94
                             PQQ_3  13 vnsspavd..gglvyvg 27 
                                       v  + a+d   g+++v+
  gi|386002614|ref|YP_005920913.1| 239 VLNGIAYDpaSGRLFVT 255
                                       55566666333677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1721.51
//
Query:       gi|386002615|ref|YP_005920914.1|  [L=120]
Description: hypothetical protein Mhar_1935 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00047   20.0   0.0    0.00072   19.4   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.063   13.5   0.0       0.11   12.7   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
      0.066   13.2   0.0       0.15   12.0   0.0    1.6  1  PadR      Transcriptional regulator PadR-like family
      0.066   13.0   0.0       0.07   12.9   0.0    1.3  1  BamHI     Restriction endonuclease BamHI


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 !   19.4   0.0   1.6e-07   0.00072      16      64 ..      30      85 ..      15      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-07
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYra 64
                                      +L + ++a+ ++i   +++ ++ v  ++rsL d G+V  ++ r        k+Y+ 
  gi|386002615|ref|YP_005920914.1| 30 YLANVEEASSRDIEMGSNLRQPEVSIAMRSLRDNGWVSEKEVRrggkgrpMKVYSL 85
                                      5778899*******************************999887888884447765 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05      0.11       5      54 ..      27      76 ..      25      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkk 54
                                      +++yLa v+ea+ +++    ++ + + s+ ++ L ++g+++ +   +g+k
  gi|386002615|ref|YP_005920914.1| 27 LITYLANVEEASSRDIEMGSNLRQPEVSIAMRSLRDNGWVSEKEVRRGGK 76
                                      689*************************************8766665544 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05      0.15      37      65 ..      56      85 ..      45      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                                      HHHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                              PadR 37 aLkrLekeglvesewees.gegpprkyYrl 65
                                      a+++L+++g+v++++++  g+g+p k+Y l
  gi|386002615|ref|YP_005920914.1| 56 AMRSLRDNGWVSEKEVRRgGKGRPMKVYSL 85
                                      5789************9999********87 PP

>> BamHI  Restriction endonuclease BamHI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.6e-05      0.07      55      95 ..      50      91 ..      15     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                             BamHI 55 kPikeelmirlkedgwklekrlalkaeakPGkvdav.klieg 95
                                      +P   + m  l+++gw  ek+++ +++ +P kv  +   i++
  gi|386002615|ref|YP_005920914.1| 50 QPEVSIAMRSLRDNGWVSEKEVRRGGKGRPMKVYSLlTPIDE 91
                                      5667789***********************999766344554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 714.25
//
Query:       gi|386002616|ref|YP_005920915.1|  [L=90]
Description: FeoA domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-15   55.5   0.0    5.6e-15   55.4   0.0    1.1  1  FeoA       FeoA domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.025   14.7   0.1    1.2  1  PCSK9_C1   Proprotein convertase subtilisin-like/kexin type 9
      0.028   14.5   0.1      0.046   13.7   0.1    1.4  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   9.4e-19   5.6e-15       3      73 ..       4      73 ..       2      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 9.4e-19
                                      GGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  3 LsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      L+ ++ +   ei++++d+    ++rL++mG+++G+r++ +a +pfggp+v+++g+  v++gr++A++I Ve
  gi|386002616|ref|YP_005920915.1|  4 LTKAPCNLVLEIKSFADS-FGWAKRLESMGIRKGQRVRKIACQPFGGPVVIEIGGCCVSMGRGIASKIDVE 73
                                      556666667899999998.88***********************************************998 PP

>> PCSK9_C1  Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.1e-06     0.025      36      81 ..      13      61 ..       2      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-06
                          PCSK9_C1 36 lsCssfsrs.G.krrGerievreGrke.CvahnafgGegvyavarCCll 81
                                      l   sf++s G  +r e++ +r+G+++  +a + fgG  v  +  CC+ 
  gi|386002616|ref|YP_005920915.1| 13 LEIKSFADSfGwAKRLESMGIRKGQRVrKIACQPFGGPVVIEIGGCCVS 61
                                      55567776642257889*******99725899***************85 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.8e-06     0.046       9      39 ..      59      89 ..      52      90 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
                                      EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE- CS
                         ETF_alpha  9 vvsgGrGlkskenlelleelaealgaavgas 39
                                       vs+GrG++sk ++e++ e a++ +a  ga 
  gi|386002616|ref|YP_005920915.1| 59 CVSMGRGIASKIDVEVVSEAADQREAPTGAL 89
                                      69***********************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 630.72
//
Query:       gi|386002617|ref|YP_005920916.1|  [L=270]
Description: Imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-80  268.1   0.0    6.4e-80  267.9   0.0    1.0  1  His_biosynth  Histidine biosynthesis protein
    6.8e-08   32.0   0.0    0.00041   19.5   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    7.3e-07   28.9   2.0     0.0037   16.7   0.2    2.1  2  NMO           Nitronate monooxygenase
    9.3e-06   25.1   0.1     0.0023   17.3   0.1    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
    4.5e-05   22.8   0.1       0.03   13.5   0.1    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
      6e-05   22.5   0.2     0.0033   16.9   0.1    2.1  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    0.00027   20.3   0.2       0.18   11.2   0.1    2.1  2  TMP-TENI      Thiamine monophosphate synthase
     0.0085   15.1   0.3       0.71    8.8   0.1    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.028   13.9   0.1    1.3  1  PcrB          PcrB family
      0.049   13.5   0.6       0.13   12.1   0.0    1.9  2  TRI9          TRI9 protein
      0.078   11.8   0.1       0.12   11.2   0.1    1.2  1  Trp_syntA     Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.9   0.0   3.9e-83   6.4e-80       1     227 [.       5     251 ..       5     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 267.9 bits;  conditional E-value: 3.9e-83
                                       EEEEEEEE....ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S CS
                      His_biosynth   1 riipalDl....kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf 73 
                                       riip+lD+     +G+vV   kG +f+e ryag p+ela+ry+eegade++++D++a++e re+++++++++a++vf
  gi|386002617|ref|YP_005920916.1|   5 RIIPCLDCdlavPQGRVV---KGIEFKEIRYAGVPWELATRYYEEGADEIVFLDITASSERRETMKNVIRATAKNVF 78 
                                       8******877778*****...******************************************************** PP

                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE....C............. CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr....g............. 133
                                       ip+ vGGGIr +edv+++++agadkv ++taa+k+p li+e+a ++gsq++vvaiDa+r    g             
  gi|386002617|ref|YP_005920916.1|  79 IPLAVGGGIRAVEDVRAVFQAGADKVTVNTAALKRPGLISEIAGEYGSQACVVAIDAKRrdgpGegrisvstpegds 155
                                       ***********************************************************88661557777888899* PP

                                       .EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHH CS
                      His_biosynth 134 .ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkel 209
                                        ++  ++g+re +g+da+ +a ++e+lgageillt++drdGt +G+d++lt++++++v+ipviasGG+g+++++ e+
  gi|386002617|ref|YP_005920916.1| 156 wFEASFYGGREFSGVDAIAWAMEAERLGAGEILLTSMDRDGTYDGFDVPLTDAVSRRVRIPVIASGGCGNPDHILEV 232
                                       99*************************************************************************** PP

                                       H.HTTCSEEEESHHHHTTS CS
                      His_biosynth 210 k.segvdavivgsalyege 227
                                       + ++g++a++++s++++ge
  gi|386002617|ref|YP_005920916.1| 233 FsKTGASAALAASIFHYGE 251
                                       *77788***********97 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.5e-07   0.00041     174     225 ..      69     119 ..      38     134 .. 0.85
   2 !   10.4   0.0   0.00015      0.24     177     212 ..     208     243 ..     200     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                                       HHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                               Dus 174 aIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                        I++  ++v ip+ + G+I+ +ed++a+ +  Gad v +  +al++P l+ e
  gi|386002617|ref|YP_005920916.1|  69 VIRATAKNVFIPLAVGGGIRAVEDVRAVFQA-GADKVTVNTAALKRPGLISE 119
                                       4777788888*******************99.*****************985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                       HHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                               Dus 177 evkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                       +v ++v+ipvia G++ +++ + ++ ++tGa + ++
  gi|386002617|ref|YP_005920916.1| 208 AVSRRVRIPVIASGGCGNPDHILEVFSKTGASAALA 243
                                       68899**************************99776 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.3e-06    0.0037     182     226 ..      67     111 ..      55     113 .. 0.82
   2 !   12.0   0.1   6.2e-05       0.1     184     225 ..     205     247 ..     159     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                               NMO 182 faLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                        +++   ++ v iP+   GGi   ++v a++ +GA  v + t+ L
  gi|386002617|ref|YP_005920916.1|  67 KNVIRATAKNVFIPLAVGGGIRAVEDVRAVFQAGADKVTVNTAAL 111
                                       346666677777*****************************9966 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.2e-05
                               NMO 184 LvpqvldavdiPviAaGGiidrrgvaaaLa.lGAsgvqigtrf 225
                                       L + v   v iPviA GG  +   +  +++  GAs++  ++ f
  gi|386002617|ref|YP_005920916.1| 205 LTDAVSRRVRIPVIASGGCGNPDHILEVFSkTGASAALAASIF 247
                                       6677777777***************999983688888766655 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.4e-06    0.0023     134     207 ..      37     110 ..      21     138 .. 0.87
   2 !    5.9   0.0    0.0043         7     169     204 ..     208     244 ..     196     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
                              ThiG 134 lvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntav 207
                                         la r  e G+  ++ l     s +  + k++++   +++ +P+ v  Gi+  +d+ ++++ Gad v +nta 
  gi|386002617|ref|YP_005920916.1|  37 WELATRYYEEGADEIVFLDITASSERRETMKNVIRATAKNVFIPLAVGGGIRAVEDVRAVFQAGADKVTVNTAA 110
                                       56788888889998888888889999999999****************************************95 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0043
                                       HHHHH-SS-BEEES---SHHHHHHHH.HTT-SEEEES CS
                              ThiG 169 iiieeakvPvivDAGigspsdaaqam.elGadavlln 204
                                        + +++++Pvi   G g+p ++ +++ + Ga+a l +
  gi|386002617|ref|YP_005920916.1| 208 AVSRRVRIPVIASGGCGNPDHILEVFsKTGASAALAA 244
                                       567789*****************99835788888876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.8e-05      0.03     232     279 ..      68     113 ..      61     125 .. 0.83
   2 !    7.3   0.0    0.0015       2.4     240     291 ..     212     261 ..     205     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                       +vir+ +k++   ip+   GGi + eD+   ++aGA  v v ta  ++
  gi|386002617|ref|YP_005920916.1|  68 NVIRATAKNVF--IPLAVGGGIRAVEDVRAVFQAGADKVTVNTAALKR 113
                                       67888888888..9**99*************************98554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0015
                                       HTTT.S-EEEESS--SHHHHHHHH.HHTECEEEESHHHHHHGTCHHHHHHHHH CS
                            DHO_dh 240 rlkkeipiIgvGGiesgeDaleki.eaGAslvqvytalvfegpkiakkikkel 291
                                       r+  +ip+I++GG    +  le + + GAs+    + +++ g + + ++k  l
  gi|386002617|ref|YP_005920916.1| 212 RV--RIPVIASGGCGNPDHILEVFsKTGASAALAASIFHY-GEWGVGEVKSRL 261
                                       44..5*****************87469***9888888766.455555666555 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     2e-06    0.0033     126     170 ..      65     109 ..      64     111 .. 0.92
   2 ?    3.5   0.0     0.026        43     132     163 ..     207     239 ..     202     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                                       GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                      G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                       ++++vi+++ k++ ip+  GG i+  edv+++++aGa+ v++ + 
  gi|386002617|ref|YP_005920916.1|  65 TMKNVIRATAKNVFIPLAVGGGIRAVEDVRAVFQAGADKVTVNTA 109
                                       5889************************************98765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                       CTSTTS...EEEEESS--SHHHHHHHCTT..SS CS
                      G3P_antiterm 132 keikkelkipiiaGGLietkedveealka.Gai 163
                                       ++++++++ip+ia+G   + +++ e++++ Ga+
  gi|386002617|ref|YP_005920916.1| 207 DAVSRRVRIPVIASGGCGNPDHILEVFSKtGAS 239
                                       678999*********999999998887541555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00011      0.18     140     179 ..      68     108 ..      37     110 .. 0.73
   2 !    7.4   0.0    0.0015       2.5     114     172 ..     176     238 ..     168     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                          TMP-TENI 140 eglkelaealeiPvvaiGGitl.envaevleagadgvavvs 179
                                       + ++++a+++ iP+ + GGi++ e+v +v++agad v v +
  gi|386002617|ref|YP_005920916.1|  68 NVIRATAKNVFIPLAVGGGIRAvEDVRAVFQAGADKVTVNT 108
                                       56788888888*********96599************9866 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                          TMP-TENI 114 algadYigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGi.tlenvaevl.eaga 172
                                       a+ a  +g+G i  T+   d   +  ++ +  +++++++iPv+a GG  +++++ ev+ ++ga
  gi|386002617|ref|YP_005920916.1| 176 AMEAERLGAGEILLTSMDRDGtyDGFDVPLTDAVSRRVRIPVIASGGCgNPDHILEVFsKTGA 238
                                       667778899999999998888456667778999**************8457778777744444 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00043      0.71     113     172 ..      44     106 ..      32     110 .. 0.61
   2 !    4.4   0.0    0.0095        15     202     239 ..     209     247 ..     195     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00043
                                       HHTT-S.EEEEE-STS..SSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                       xxxxxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 113 veagvd.vlvvdsahg..hsekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                        e+g+d ++++d++      e++ +++++  k+v     ++G +   e ++a+++agad v v
  gi|386002617|ref|YP_005920916.1|  44 YEEGADeIVFLDITASseRRETMKNVIRATAKNVFIPLAVGGGIRAVEDVRAVFQAGADKVTV 106
                                       566776244456433200233344444444444432235789999999999999999998877 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0095
                                       HHCTCT-EEEEES---SHHHHHHHHH.TT-SEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             IMPDH 202 aakkagvpviaDGGikysgdivkAla.aGadavmlGsll 239
                                       + ++  +pvia GG  +  +i   ++  Ga+a +  s++
  gi|386002617|ref|YP_005920916.1| 209 VSRRVRIPVIASGGCGNPDHILEVFSkTGASAALAASIF 247
                                       567889****************99974699988877776 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.7e-05     0.028     157     210 ..      52     109 ..      41     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                       EEEE-TTSSS-H...HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CH CS
                              PcrB 157 iYlEasGaledv...eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnv 210
                                       ++l+    +e     ++vi+  +k   + l vGGGir  E+ + v +a AD + v ++
  gi|386002617|ref|YP_005920916.1|  52 VFLDITASSERRetmKNVIRATAKNVFIPLAVGGGIRAVEDVRAVFQAgADKVTVNTA 109
                                       5555544444440014444445555556788********************9988765 PP

>> TRI9  TRI9 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       2.8   4.6e+03      18      27 ..     155     164 ..     154     175 .. 0.63
   2 ?   12.1   0.0   8.1e-05      0.13      20      37 ..     230     247 ..     225     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.8
                              TRI9  18 sWLevFaYsG 27 
                                       sW e   Y G
  gi|386002617|ref|YP_005920916.1| 155 SWFEASFYGG 164
                                       6777666654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.1e-05
                              TRI9  20 LevFaYsGvsaaLCatiW 37 
                                       LevF+  G saaL a i+
  gi|386002617|ref|YP_005920916.1| 230 LEVFSKTGASAALAASIF 247
                                       9**************996 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.2e-05      0.12     179     229 ..      59     110 ..      55     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                                       TSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHH CS
                         Trp_syntA 179 enavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSal 229
                                       +++  +++++++++  k    P+avG Gi++ e+v++v  ++ad v v  a 
  gi|386002617|ref|YP_005920916.1|  59 SSERRETMKNVIRATAKNVFIPLAVGGGIRAVEDVRAVFqAGADKVTVNTAA 110
                                       45667788999999999999******************999***99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1723.78
//
Query:       gi|386002618|ref|YP_005920917.1|  [L=200]
Description: Imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-22   77.6   0.0    1.2e-21   77.4   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.7e-08   33.4   0.0    6.7e-08   32.6   0.0    1.3  1  SNO            SNO glutamine amidotransferase family
    2.2e-06   27.4   0.0    2.7e-06   27.1   0.0    1.1  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.4e-05   25.0   0.3     0.0023   17.7   0.1    2.2  2  Peptidase_C26  Peptidase C26
    0.00012   21.9   0.0    0.00022   21.1   0.0    1.4  1  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
       0.22   10.6   0.0       0.43    9.6   0.0    1.5  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0     4e-25   1.2e-21       2     186 ..       5     194 ..       4     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 4e-25
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS- CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiP 73 
                                       ++D++ ++  ++ +al ++g+  ++       ee    l ++dgi+v+ G+gs g           a++ea+e++ P
  gi|386002618|ref|YP_005920917.1|   5 VVDYGVGNLFSIYNALERIGAGPKIATEP---EE----LAGFDGIVVP-GVGSFGrcmrqLSRFEPALREALEEGRP 73 
                                       57888888888888888888888887733...33....579***9985.788888887888888999********** PP

                                       EEEETHHHHHHHHHTTT...........EEE...EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGC CS
                            GATase  74 iLGICLGmQllaiefgr...........kvv...kekekehhggtmrlgddetallyglknevierhrHryevnpke 136
                                       iLGIC GmQ+l++ + +           +vv        +++g++    ++e ++l g +++   ++ H+y + p  
  gi|386002618|ref|YP_005920917.1|  74 ILGICVGMQVLFERSEEspeeglgwidgEVVrlpASVLVPQMGWNTLSIKREVEILDGISDDDFFYFVHSYHCVP-- 148
                                       *****************88888888888666776556689**********************************9.. PP

                                       HHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
                            GATase 137 lepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnf 186
                                          +g +v+a+++ +++++++i  ++ +++vQFHPE++  ++g ++l+nf
  gi|386002618|ref|YP_005920917.1| 149 --GDGRVVAATCDYGQKIAAAISVES-LFAVQFHPEKSG-EKGLSILRNF 194
                                       ..9999*******************9.*********865.5559999987 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.2e-11   6.7e-08      11     173 ..      16     184 ..      10     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHH.HHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEET CS
                               SNO  11 hveaikkclaenktvkrkedlaevdaliiPGGestamskli.ertglyedllefvknsekvvlGtCaGlillskele 86 
                                         +a+++ +a  k   ++e+la+ d++++PG  s   ++ + +   + ++l+e ++++ +++lG C G+ +l ++ e
  gi|386002618|ref|YP_005920917.1|  16 IYNALERIGAGPKIATEPEELAGFDGIVVPGVGSF--GRCMrQLSRFEPALREALEEG-RPILGICVGMQVLFERSE 89 
                                       568999999999*******************8774..444404456778999999999.***************999 PP

                                       TBSS-SS--CCEEEET.......TTT-SCCGEEEEEEEETTTC.SEEEEEESS--EEEEE-.TTTCEEEEECTT.EE CS
                               SNO  87 nelvktlellkvkvkr.......nafGrqvdsfekeldfknli.ekftavfiraPvieeilddeavkvlyeldg.ei 154
                                       ++  + l+ ++ +v r          G    s ++e+++ + i ++    f+ + +    +d  +v    +  g +i
  gi|386002618|ref|YP_005920917.1|  90 ESPEEGLGWIDGEVVRlpasvlvPQMGWNTLSIKREVEILDGIsDDDFFYFVHSYHCVP-GDGRVVAATCDY-GqKI 164
                                       9999999999988877333222245899999*******987665555557887766532.333333333333.6366 PP

                                       EEEE.ETTEEEESS-GGGST CS
                               SNO 155 vvak.qkkilatsfhPelae 173
                                        +a   + ++a+ fhPe + 
  gi|386002618|ref|YP_005920917.1| 165 AAAIsVESLFAVQFHPEKSG 184
                                       5555455999*******875 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   9.2e-10   2.7e-06      18     115 ..      19     103 ..       2     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 9.2e-10
                          GATase_3  18 pLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeied 94 
                                       +Le+ ++  +  +  + e+l+   d +++pG  +  + +   + s+++ a++ea+e+g+p+lgiC G+q+L e+ e+
  gi|386002618|ref|YP_005920917.1|  19 ALERIGA--GPKIATEPEELAG-FDGIVVPGVGSFGRCM--RQLSRFEPALREALEEGRPILGICVGMQVLFERSEE 90 
                                       4444442..2233336788855.9999999988877665..45566**************************99876 PP

                          GATase_3  95 pegvegeageveglglLdiet 115
                                       +          eglg++d e+
  gi|386002618|ref|YP_005920917.1|  91 SP--------EEGLGWIDGEV 103
                                       54........35777777666 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   7.7e-07    0.0023      98     118 ..      64      84 ..      54      86 .. 0.90
   2 !    5.4   0.0    0.0047        14     198     216 .]     167     181 ..     139     181 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.7e-07
                     Peptidase_C26  98 iraalergvPilgiCrGlqll 118
                                       +r+ale+g PilgiC G+q+l
  gi|386002618|ref|YP_005920917.1|  64 LREALEEGRPILGICVGMQVL 84 
                                       689****************98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0047
                     Peptidase_C26 198 aieseeakafvlgvQwHPE 216
                                       ai++e     +++vQ+HPE
  gi|386002618|ref|YP_005920917.1| 167 AISVE----SLFAVQFHPE 181
                                       33333....489******9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   7.4e-08   0.00022      60     109 ..      37      86 ..      27      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.4e-08
                                       CG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  60 aeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                       a +D +v+pG  +   ++r+ +++   ++e++e+g+++  IC g q+L +
  gi|386002618|ref|YP_005920917.1|  37 AGFDGIVVPGVGSFGRCMRQLSRFEPALREALEEGRPILGICVGMQVLFE 86 
                                       569*******9999*********************************986 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00014      0.43      43     105 ..      35      86 ..       9      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                          GATase_5  43 slddfqilalpGGfsygDelgsgkgwakslllneklrealekflnredtlaLGiCnGfqlLvk 105
                                       +l+ f ++++pG  s       g+ + +  +++++lreal    ++ +  +LGiC G+q+L++
  gi|386002618|ref|YP_005920917.1|  35 ELAGFDGIVVPGVGSF------GRCMRQLSRFEPALREAL----EE-GRPILGICVGMQVLFE 86 
                                       5556666666665555......355666666666666666....55.999**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1275.94
//
Query:       gi|386002619|ref|YP_005920918.1|  [L=140]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-08   34.1  13.0     0.0015   19.1   2.1    2.8  2  Fer4_7      4Fe-4S dicluster domain
    5.3e-08   32.8   8.4    5.3e-08   32.8   8.4    2.5  3  Fer4_10     4Fe-4S dicluster domain
    6.2e-07   29.0   6.2    2.7e-05   23.8   1.0    3.7  4  Fer4        4Fe-4S binding domain
    1.5e-06   28.2   8.7    1.5e-06   28.2   8.7    2.4  2  Fer4_9      4Fe-4S dicluster domain
    1.9e-06   28.7  10.9     0.0071   17.3   2.7    2.5  2  Fer4_16     4Fe-4S double cluster binding domain
      7e-05   22.9   8.7      7e-05   22.9   8.7    2.2  3  Fer4_21     4Fe-4S dicluster domain
    0.00027   20.9  21.1    0.00035   20.5   1.1    3.6  4  Fer4_6      4Fe-4S binding domain
    0.00034   20.5   1.2    0.00034   20.5   1.2    3.9  4  Fer4_2      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.013   15.4   0.0    3.0  3  zf-C2HC_2   zinc-finger of a C2HC-type
      0.016   15.0   0.1      0.016   15.0   0.1    2.5  3  zf-C2H2_11  zinc-finger C2H2-type
       0.14   12.7   1.2       0.14   12.7   1.2    3.1  4  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
       0.65   10.6  22.3        0.2   12.2   2.0    3.7  3  Fer4_4      4Fe-4S binding domain
        1.9    9.5   0.0        1.9    9.5   0.0    3.7  4  zf-C2H2_4   C2H2-type zinc finger
        4.4    7.8  21.5         11    6.6  13.1    3.2  2  Fer4_8      4Fe-4S dicluster domain
        4.7    7.8  22.3       0.91   10.1   3.1    3.4  3  Fer4_17     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.1   1.3e-06    0.0015       2      27 ..       9      34 ..       8      42 .. 0.83
   2 !   17.4   5.6   4.1e-06    0.0049       2      43 ..      40      82 ..      39     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekg 27
                                      CigC  C ++Cp++ i  +e ++e++
  gi|386002619|ref|YP_005920918.1|  9 CIGCLSCSNVCPSQNILRTETAEERR 34
                                      ************99998888766654 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.1e-06
                            Fer4_7  2 Ci.gCgaCvaaCpvkaieldeeenekgtekveidpekClgCga 43
                                      C  +C  Cv+ Cp++a++l +++++ + +++ +d   C  Cg+
  gi|386002619|ref|YP_005920918.1| 40 CReECDLCVEHCPARALSLVPFDEAVPEPEASFDLVACRICGR 82
                                      5548******************999999***********9974 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   8.4   4.5e-11   5.3e-08       2      56 .]       2      52 ..       1      52 [. 0.94
   2 ?    4.1  11.6     0.043        51       8      24 ..      39      87 ..      38     121 .. 0.62
   3 ?    1.0   0.2      0.39   4.7e+02      17      23 ..     107     113 ..     102     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.5e-11
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.cgaCveaCP 56
                                      ++id   Ci+C  C ++CP+     +++  ++  e+ r+  ++C + c  Cve+CP
  gi|386002619|ref|YP_005920918.1|  2 IRIDLRLCIGCLSCSNVCPS-----QNILRTETAEERRILWKRCREeCDLCVEHCP 52
                                      789*****************.....9999999999999999***988********9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.043
                           Fer4_10  8 tCi.rCgkCvkaCPadl...............................t 24
                                      +C  +C  Cv+ CPa +                               +
  gi|386002619|ref|YP_005920918.1| 39 RCReECDLCVEHCPARAlslvpfdeavpepeasfdlvacricgrryatE 87
                                      68449**********8877777776666666666666666666666663 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.39
                           Fer4_10  17 kaCPadl 23 
                                       +aCP++ 
  gi|386002619|ref|YP_005920918.1| 107 RACPTCR 113
                                       4666633 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.0   2.2e-08   2.7e-05       2      20 ..       3      21 ..       2      24 .. 0.89
   2 !   14.4   0.4   2.1e-05     0.026      11      23 ..      44      56 ..      42      57 .. 0.90
   3 ?   -1.7   0.6       2.4   2.9e+03      10      14 ..      76      80 ..      75      82 .. 0.70
   4 ?    0.6   0.2      0.48   5.7e+02      15      20 ..     106     111 ..     106     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.2e-08
                                      EEETTTSSS-THHHHHSTT CS
                              Fer4  2 videekCigCGaCvevCPv 20
                                       id  +CigC  C +vCP 
  gi|386002619|ref|YP_005920918.1|  3 RIDLRLCIGCLSCSNVCPS 21
                                      79999*************7 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.1e-05
                                      -THHHHHSTTTEE CS
                              Fer4 11 CGaCvevCPvgAI 23
                                      C +Cve CP  A+
  gi|386002619|ref|YP_005920918.1| 44 CDLCVEHCPARAL 56
                                      **********998 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.4
                                      S-THH CS
                              Fer4 10 gCGaC 14
                                      +C +C
  gi|386002619|ref|YP_005920918.1| 76 ACRIC 80
                                      68777 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.48
                                       HHHSTT CS
                              Fer4  15 vevCPv 20 
                                       v +CP+
  gi|386002619|ref|YP_005920918.1| 106 VRACPT 111
                                       78***7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   8.7   1.3e-09   1.5e-06       2      50 ..       9      55 ..       8      56 .. 0.88
   2 ?    0.5   1.5      0.58   6.9e+02      24      40 ..      99     113 ..      62     118 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCpkga 50
                                      C+gC +C ++Cp++ + + + ++++r+ ++   +C  +C  Cve+Cp  a
  gi|386002619|ref|YP_005920918.1|  9 CIGCLSCSNVCPSQNILRTETAEERRILWK---RCrEECDLCVEHCPARA 55
                                      ****************99999999998654...7*667*********875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.58
                            Fer4_9  24 rkarlraase....eaCigCg 40 
                                       +        +     aC +C+
  gi|386002619|ref|YP_005920918.1|  99 QSQ------NpewvRACPTCR 113
                                       222......133344577775 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.6   2.5e-05      0.03       2      28 ..       9      33 ..       8      43 .. 0.78
   2 !   17.3   2.7     6e-06    0.0071       4      61 ..      43     113 ..      39     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiear 28
                                      C++C  C +vCP++ i  +  +++e r
  gi|386002619|ref|YP_005920918.1|  9 CIGCLSCSNVCPSQNILRT--ETAEER 33
                                      ***************9988..444444 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6e-06
                           Fer4_16   4 tCgkCaevCPtnaikekkekeiearecisy.............ntaekkdlaedeekckkqeaitgCdiCq 61 
                                       +C  C+e CP++a++     e+ ++ + s              ++++ ++++ +  + ++ e++  C +C 
  gi|386002619|ref|YP_005920918.1|  43 ECDLCVEHCPARALSLVPFDEAVPEPEASFdlvacricgrryaTEPMLRRVEASLPQSQNPEWVRACPTCR 113
                                       6**************8866666555544445577777777787888899999999999999999***9997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   8.7   5.9e-08     7e-05       2      53 ..       3      53 ..       2      58 .. 0.87
   2 !    6.5   4.4    0.0076         9      10      47 ..      43      80 ..      34      83 .. 0.71
   3 ?   -2.6   0.1       5.4   6.5e+03      50      54 ..     108     112 ..     105     117 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.9e-08
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCv.GCnlCssvCPv 53
                                      rid   CigC +C  +C+  s + +++++++  +++ ++C   C+lC++ CP 
  gi|386002619|ref|YP_005920918.1|  3 RIDLRLCIGCLSCSNVCP--SQNILRTETAEERRILWKRCReECDLCVEHCPA 53
                                      699999************..67788999999999999999637*********5 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0076
                           Fer4_21 10 gCgkCliaCedtshqaieidaktvlkvvedeCvGCnlC 47
                                      +C +C+  C+  +   + +d++   +  + + v+C +C
  gi|386002619|ref|YP_005920918.1| 43 ECDLCVEHCPARALSLVPFDEAVPEPEASFDLVACRIC 80
                                      57777777777777777777777667777777777777 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.4
                           Fer4_21  50 vCPve 54 
                                        CP+ 
  gi|386002619|ref|YP_005920918.1| 108 ACPTC 112
                                       34442 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.1   2.9e-07   0.00035       2      24 .]       2      24 ..       1      24 [. 0.90
   2 !   11.4   2.8   0.00022      0.26       8      24 .]      39      56 ..      38      56 .. 0.83
   3 ?   -1.8   0.1       3.2   3.9e+03      12      15 ..      77      80 ..      71      82 .. 0.69
   4 ?    1.0   0.2      0.42     5e+02      16      21 ..     106     111 ..     106     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      ++id  +CigC  C +vCP + i
  gi|386002619|ref|YP_005920918.1|  2 IRIDLRLCIGCLSCSNVCPSQNI 24
                                      789999*************9865 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00022
                            Fer4_6  8 kCi.gCgdCvrvCPegai 24
                                      +C   C+ Cv +CP+ a+
  gi|386002619|ref|YP_005920918.1| 39 RCReECDLCVEHCPARAL 56
                                      57646**********986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.2
                            Fer4_6 12 CgdC 15
                                      C+ C
  gi|386002619|ref|YP_005920918.1| 77 CRIC 80
                                      6666 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.42
                            Fer4_6  16 vrvCPe 21 
                                       vr+CP+
  gi|386002619|ref|YP_005920918.1| 106 VRACPT 111
                                       789996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.2   2.9e-07   0.00034       4      21 ..       3      20 ..       1      21 [. 0.90
   2 !   10.3   1.4   0.00052      0.63       9      22 .]      39      53 ..      33      53 .. 0.87
   3 ?   -0.3   0.6       1.2   1.4e+03      12      16 ..      76      80 ..      75      83 .. 0.84
   4 ?    0.1   0.6      0.93   1.1e+03      18      22 .]     107     111 ..     106     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       +d + CigC +C ++CP
  gi|386002619|ref|YP_005920918.1|  3 RIDLRLCIGCLSCSNVCP 20
                                      58999************* PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00052
                            Fer4_2  9 rCi.gCgaCvsaCPa 22
                                      rC  +C  Cv  CPa
  gi|386002619|ref|YP_005920918.1| 39 RCReECDLCVEHCPA 53
                                      89757*********8 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.2
                            Fer4_2 12 gCgaC 16
                                      +C++C
  gi|386002619|ref|YP_005920918.1| 76 ACRIC 80
                                      79999 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.93
                            Fer4_2  18 saCPa 22 
                                        aCP+
  gi|386002619|ref|YP_005920918.1| 107 RACPT 111
                                       57775 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 ?   -3.2   1.3       7.3   8.7e+03       4       8 ..      43      47 ..      41      51 .. 0.69
   2 ?   15.4   0.0   1.1e-05     0.013       2      16 ..      74      88 ..      73      90 .. 0.91
   3 ?    1.3   1.5      0.28   3.3e+02       4      10 ..     108     114 ..     107     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.3
                         zf-C2HC_2  4 pCpkC 8 
                                      +C  C
  gi|386002619|ref|YP_005920918.1| 43 ECDLC 47
                                      67777 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                         zf-C2HC_2  2 lvpCpkCgRsFnpdr 16
                                      lv C++CgR++++++
  gi|386002619|ref|YP_005920918.1| 74 LVACRICGRRYATEP 88
                                      99*********9986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.28
                         zf-C2HC_2   4 pCpkCgR 10 
                                        Cp C R
  gi|386002619|ref|YP_005920918.1| 108 ACPTCRR 114
                                       6****98 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   1.3       8.2   9.8e+03       7      10 ..      12      15 ..      10      19 .. 0.85
   2 ?   -3.5   2.5       8.1   9.6e+03       6      13 ..      39      47 ..      38      47 .. 0.68
   3 ?   15.0   0.1   1.3e-05     0.016       7      22 ..      77      92 ..      75      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.2
                        zf-C2H2_11  7 CleC 10
                                      Cl C
  gi|386002619|ref|YP_005920918.1| 12 CLSC 15
                                      9999 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.1
                        zf-C2H2_11  6 qCl.eCGlc 13
                                      +C+ eC lc
  gi|386002619|ref|YP_005920918.1| 39 RCReECDLC 47
                                      676358888 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.3e-05
                        zf-C2H2_11  7 CleCGlcftSqlsLsR 22
                                      C+ CG+ ++ +++L+R
  gi|386002619|ref|YP_005920918.1| 77 CRICGRRYATEPMLRR 92
                                      ***************9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   0.00012      0.14       1      18 [.       4      21 ..       4      22 .. 0.91
   2 ?    3.5   1.9     0.091   1.1e+02       8      18 ..      43      53 ..      38      54 .. 0.88
   3 ?   -2.5   0.1       6.8   8.1e+03       8      13 ..      76      81 ..      75      88 .. 0.75
   4 ?   -2.1   0.2         5   5.9e+03      50      53 ..     108     111 ..     106     116 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D   Ci+c +C +++P 
  gi|386002619|ref|YP_005920918.1|  4 IDLRLCIGCLSCSNVCPS 21
                                      68889************5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.091
                           Fer4_13  8 acgaCvelaPd 18
                                      +c++Cve +P 
  gi|386002619|ref|YP_005920918.1| 43 ECDLCVEHCPA 53
                                      6*********5 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.8
                           Fer4_13  8 acgaCv 13
                                      ac +C+
  gi|386002619|ref|YP_005920918.1| 76 ACRICG 81
                                      788886 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 5
                           Fer4_13  50 aCPv 53 
                                       aCP+
  gi|386002619|ref|YP_005920918.1| 108 ACPT 111
                                       4554 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.0   0.00017       0.2       4      17 .]       9      22 ..       6      23 .. 0.92
   2 ?   10.2   1.3   0.00078      0.94       2      16 ..      38      53 ..      37      61 .. 0.90
   3 ?    2.4   0.3      0.24   2.9e+02       6      12 ..     108     114 ..     106     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      CigC sC ++CP++
  gi|386002619|ref|YP_005920918.1|  9 CIGCLSCSNVCPSQ 22
                                      ************75 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00078
                            Fer4_4  2 erCi.gCgsCvaaCPq 16
                                      +rC  +C+ Cv  CP 
  gi|386002619|ref|YP_005920918.1| 38 KRCReECDLCVEHCPA 53
                                      79988**********6 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.24
                            Fer4_4   6 gCgsCva 12 
                                        C+ C++
  gi|386002619|ref|YP_005920918.1| 108 ACPTCRR 114
                                       4888876 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4       1.7   2.1e+03       3      16 ..      12      25 ..      10      27 .. 0.78
   2 ?   -0.2   0.4       2.2   2.6e+03       2       7 ..      43      48 ..      42      57 .. 0.73
   3 ?    9.5   0.0    0.0016       1.9       2      18 ..      76      92 ..      75      92 .. 0.87
   4 ?   -0.5   0.2       2.7   3.2e+03       2       8 ..     108     114 ..     107     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.7
                         zf-C2H2_4  3 CpiCgksFsskkaL 16
                                      C  C+ +++s++ L
  gi|386002619|ref|YP_005920918.1| 12 CLSCSNVCPSQNIL 25
                                      88999998888755 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.2
                         zf-C2H2_4  2 kCpiCg 7 
                                      +C++C 
  gi|386002619|ref|YP_005920918.1| 43 ECDLCV 48
                                      599993 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0016
                         zf-C2H2_4  2 kCpiCgksFsskkaLlr 18
                                       C+iCg+++ +   L+r
  gi|386002619|ref|YP_005920918.1| 76 ACRICGRRYATEPMLRR 92
                                      6*********9988875 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.7
                         zf-C2H2_4   2 kCpiCgk 8  
                                        Cp C++
  gi|386002619|ref|YP_005920918.1| 108 ACPTCRR 114
                                       6**9*65 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  13.1    0.0089        11       2      63 ..       6      53 ..       5      55 .. 0.67
   2 ?   -2.6  11.9       6.6   7.9e+03       7      17 ..      43      76 ..      38     134 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0089
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC.ttcgaCtevCpv 63
                                      l+ Ci+C  C + Cp+ +  + +  +a+++++   +           ++C  +c  C+e Cp 
  gi|386002619|ref|YP_005920918.1|  6 LRLCIGCLSCSNVCPSQNILRTE--TAEERRIL--W-----------KRCrEECDLCVEHCPA 53
                                      678************88888654..33333333..2...........3343568888888885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                            Fer4_8  7 eCgaCqsaCp.......................v 17
                                      eC +C ++Cp                       +
  gi|386002619|ref|YP_005920918.1| 43 ECDLCVEHCParalslvpfdeavpepeasfdlvA 76
                                      6999999998555544444444444444444441 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.1   0.00076      0.91      44      58 ..       7      21 ..       3      24 .. 0.80
   2 ?    3.1  13.6      0.12   1.4e+02       2      58 ..       9      53 ..       8      56 .. 0.69
   3 ?    1.0   1.5      0.53   6.4e+02      41      50 ..     104     113 ..      74     131 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00076
                           Fer4_17 44 slCieCgeCerkCPq 58
                                       lCi+C  C+ +CP+
  gi|386002619|ref|YP_005920918.1|  7 RLCIGCLSCSNVCPS 21
                                      579999999999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCi.eCgeCerkCPq 58
                                      Ci+C  C ++Cps ++ ++e ++             e++  +++C  eC +C++ CP+
  gi|386002619|ref|YP_005920918.1|  9 CIGCLSCSNVCPSQNILRTETAE-------------ERRILWKRCReECDLCVEHCPA 53
                                      99999999999998886664332.............2234566664258888888885 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.53
                           Fer4_17  41 ekaslCieCg 50 
                                       e +  C +C+
  gi|386002619|ref|YP_005920918.1| 104 EWVRACPTCR 113
                                       4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 880.57
//
Query:       gi|386002620|ref|YP_005920919.1|  [L=145]
Description: 4Fe-4S binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-13   48.6  31.0    4.7e-06   26.4   1.1    4.2  4  Fer4_6        4Fe-4S binding domain
    1.5e-10   40.4  35.3    7.6e-08   31.9   1.3    5.6  5  Fer4          4Fe-4S binding domain
    1.6e-10   41.4  28.6    3.2e-05   24.4  10.6    3.7  3  Fer4_7        4Fe-4S dicluster domain
    5.3e-10   39.3  10.7    5.3e-10   39.3  10.7    1.7  2  Fer4_11       4Fe-4S dicluster domain
    2.6e-08   33.5  34.1    1.2e-05   25.1   1.5    4.2  4  Fer4_2        4Fe-4S binding domain
    7.5e-08   32.4  27.5     0.0025   17.9   9.1    3.3  4  Fer4_9        4Fe-4S dicluster domain
    5.1e-06   27.0  42.4     0.0078   17.1   4.7    4.2  4  Fer4_3        4Fe-4S binding domain
    1.8e-05   24.8  26.3    0.00045   20.3   8.2    3.4  3  Fer4_21       4Fe-4S dicluster domain
    3.1e-05   24.0  32.6      0.013   15.6  12.4    3.6  4  Fer4_10       4Fe-4S dicluster domain
    8.8e-05   22.7  35.4     0.0069   16.8   3.1    4.6  4  Fer4_4        4Fe-4S binding domain
    0.00082   19.9  28.0      0.012   16.1   1.4    4.3  4  Fer4_17       4Fe-4S dicluster domain
     0.0063   17.4  30.3      0.085   13.8   1.6    4.6  5  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.011   16.2  32.5       0.48   10.9  23.2    4.1  2  Fer4_8        4Fe-4S dicluster domain
      0.095   13.6   1.4      0.095   13.6   1.4    3.7  4  Fer4_22       4Fe-4S dicluster domain
       0.16   12.5  20.1       0.26   11.9   3.2    3.3  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
        2.2    9.1  23.5        9.2    7.1   7.1    3.2  2  Fer4_15       4Fe-4S single cluster domain
        8.8    6.6  17.8        7.3    6.8   0.3    2.9  2  Fer4_18       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.3   3.7e-06    0.0039       2      20 ..       3      21 ..       2      25 .. 0.91
   2 !    7.2   2.3    0.0052       5.5       8      24 .]      44      62 ..      44      62 .. 0.89
   3 !   26.4   1.1   4.5e-09   4.7e-06       4      23 ..      71      90 ..      70      91 .. 0.93
   4 !   14.9   2.1     2e-05     0.021       7      24 .]      98     120 ..      94     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      v +d  +CigC+ C+++C 
  gi|386002620|ref|YP_005920919.1|  3 VYVDIRRCIGCRSCEVACE 21
                                      789999************6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0052
                            Fer4_6  8 kCigCgd..CvrvCPegai 24
                                      +C +C++  C+++C  ga+
  gi|386002620|ref|YP_005920919.1| 44 LCHHCEEasCAAACFSGAL 62
                                      6****999******88875 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 4.5e-09
                            Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                      +d +kC+gCg C  +CP+g+
  gi|386002620|ref|YP_005920919.1| 71 FDVEKCTGCGLCSLACPFGV 90
                                      99***************997 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 2e-05
                            Fer4_6   7 dkCigC.gd....CvrvCPegai 24 
                                        kC+ C g+    Cv+ CP++a+
  gi|386002620|ref|YP_005920919.1|  98 HKCDLCeGRaeptCVTTCPANAL 120
                                       69****999************97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   4.4   8.4e-06    0.0088       1      18 [.       3      20 ..       3      22 .. 0.92
   2 ?    1.2   2.7      0.34   3.6e+02      13      23 ..      52      62 ..      43      63 .. 0.83
   3 !   31.9   1.3   7.2e-11   7.6e-08       3      22 ..      71      90 ..      69      92 .. 0.91
   4 ?   -0.1   0.2      0.89   9.4e+02       7      11 ..      99     103 ..      94     105 .. 0.68
   5 !    9.7   0.4   0.00074      0.78      13      24 .]     110     121 ..     110     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.4e-06
                                      EEEETTTSSS-THHHHHS CS
                              Fer4  1 vvideekCigCGaCvevC 18
                                      v++d  +CigC  C+ +C
  gi|386002620|ref|YP_005920919.1|  3 VYVDIRRCIGCRSCEVAC 20
                                      689999************ PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.34
                                      HHHHHSTTTEE CS
                              Fer4 13 aCvevCPvgAI 23
                                       C+ +C  gA+
  gi|386002620|ref|YP_005920919.1| 52 SCAAACFSGAL 62
                                      59999998886 PP

  == domain 3  score: 31.9 bits;  conditional E-value: 7.2e-11
                                      EETTTSSS-THHHHHSTTTE CS
                              Fer4  3 ideekCigCGaCvevCPvgA 22
                                      +d ekC+gCG+C  +CP+g+
  gi|386002620|ref|YP_005920919.1| 71 FDVEKCTGCGLCSLACPFGV 90
                                      799***************97 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.89
                                       TSSS- CS
                              Fer4   7 kCigC 11 
                                       kC  C
  gi|386002620|ref|YP_005920919.1|  99 KCDLC 103
                                       66666 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00074
                                       HHHHHSTTTEEE CS
                              Fer4  13 aCvevCPvgAIt 24 
                                       +Cv  CP +A+t
  gi|386002620|ref|YP_005920919.1| 110 TCVTTCPANALT 121
                                       5*********86 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2  14.4    0.0002      0.21       1      52 []       9      61 ..       9      61 .. 0.72
   2 !   24.4  10.6   3.1e-08   3.2e-05       2      52 .]      45      90 ..      44      90 .. 0.86
   3 !   12.1   0.6   0.00022      0.23       1      22 [.      99     125 ..      99     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                            Fer4_7  1 rCigCgaCvaaCp.vkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                      rCigC+ C++aC  v+  + + + ++  + + + +p  C +C++  C+a+C +ga
  gi|386002620|ref|YP_005920919.1|  9 RCIGCRSCEVACErVHGGRGHVH-VH-FVGDSASVPILCHHCEEasCAAACFSGA 61
                                      8***********94333333222.22.22566778999****9999*****9887 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.1e-08
                            Fer4_7  2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C +C+   C+aaC ++a+  +         ++++d ekC+gCg C  +CP+g+
  gi|386002620|ref|YP_005920919.1| 45 CHHCEeaSCAAACFSGALHKEG-------SRTAFDVEKCTGCGLCSLACPFGV 90
                                      8999666999999999998755.......5799******************96 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00022
                            Fer4_7   1 rCigCg.....aCvaaCpvkaieldee 22 
                                       +C  C+      Cv +Cp++a+++d +
  gi|386002620|ref|YP_005920919.1|  99 KCDLCEgraepTCVTTCPANALTTDFD 125
                                       688886667779**********99853 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4       2.4   2.6e+03      69      75 ..      14      20 ..       3      33 .. 0.59
   2 !   39.3  10.7     5e-13   5.3e-10       6      96 ..      41     121 ..      37     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.4
                           Fer4_11 69 ekCdmcl 75
                                      + C++  
  gi|386002620|ref|YP_005920919.1| 14 RSCEVAC 20
                                      2333333 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 5e-13
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       +p  C+hC+e++C+a++ s+a++k+       +d +++  ++  +  acP+ +v +   ++ ++kCd+c  r e   
  gi|386002620|ref|YP_005920919.1|  41 VPILCHHCEEASCAAACFSGALHKEG--SRTAFDVEKCT-GCGLCSLACPFGVVWT---EKIAHKCDLCEGRAE--- 108
                                       6889*******************998..56679999998.************9865...56778*********9... PP

                           Fer4_11  83 lpacvescptgaln 96 
                                        p+cv++cp++al+
  gi|386002620|ref|YP_005920919.1| 109 -PTCVTTCPANALT 121
                                       .********99875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.5   4.3e-06    0.0045       3      20 ..       3      20 ..       1      21 [. 0.92
   2 ?    0.0   3.0       1.1   1.1e+03      10      20 ..      45      57 ..      39      57 .. 0.74
   3 !   25.1   1.5   1.1e-08   1.2e-05       4      21 ..      70      87 ..      67      88 .. 0.92
   4 !    9.1   3.1    0.0014       1.5       9      22 .]      99     117 ..      94     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      v+vd +rCigC++C  aC
  gi|386002620|ref|YP_005920919.1|  3 VYVDIRRCIGCRSCEVAC 20
                                      78999************* PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                            Fer4_2 10 CigCg..aCvsaC 20
                                      C +C+  +C  aC
  gi|386002620|ref|YP_005920919.1| 45 CHHCEeaSCAAAC 57
                                      5567666888888 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 1.1e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      ++d ++C+gCg C  aCP
  gi|386002620|ref|YP_005920919.1| 70 AFDVEKCTGCGLCSLACP 87
                                      79**************** PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0014
                            Fer4_2   9 rCigCg.....aCvsaCPa 22 
                                       +C  C+     +Cv+ CPa
  gi|386002620|ref|YP_005920919.1|  99 KCDLCEgraepTCVTTCPA 117
                                       68889667889*******8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   9.1   2.4e-06    0.0025       1      50 [.       9      61 ..       9      62 .. 0.82
   2 !   17.9  11.1   2.4e-06    0.0025       5      49 ..      45      89 ..      43      91 .. 0.67
   3 !   15.1  11.4   1.9e-05      0.02       1      50 [.      75     119 ..      75     120 .. 0.81
   4 !    7.0   2.6     0.006       6.3       1      19 [.      99     122 ..      99     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-06
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.eaCigCga..CveaCpkga 50
                                      +C+gC++C+ aC+  +  + +++     + as    C++C++  C++aC +ga
  gi|386002620|ref|YP_005920919.1|  9 RCIGCRSCEVACERVHGGRGHVHVHFVGDSASVpILCHHCEEasCAAACFSGA 61
                                      6***********887777777777777766655789*****999*****8876 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.4e-06
                            Fer4_9  5 CgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C+ C+ea C a  +++   ++  r    + e+C+gCg C  aCp g
  gi|386002620|ref|YP_005920919.1| 45 CHHCEEAsCAAACFSGALHKEGSRTAF-DVEKCTGCGLCSLACPFG 89
                                      666655446666666666666666533.3358************87 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.9e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                       kCtgCg C  aCp+gvv  ++ + k          C  C+      Cv  Cp +a
  gi|386002620|ref|YP_005920919.1|  75 KCTGCGLCSLACPFGVVWTEKIAHK----------CDLCEGraeptCVTTCPANA 119
                                       7***************966655544..........77787777888999999876 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.006
                            Fer4_9   1 kCtgC.....gaCveaCpagvvve 19 
                                       kC  C      +Cv+ Cpa++ + 
  gi|386002620|ref|YP_005920919.1|  99 KCDLCegraePTCVTTCPANALTT 122
                                       577785443334888888888765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   4.8    0.0068       7.2       1      11 [.      10      20 ..      10      23 .. 0.96
   2 !   11.0   5.6   0.00063      0.67       1      15 []      45      61 ..      45      61 .. 0.91
   3 !   17.1   4.7   7.4e-06    0.0078       1      14 [.      76      89 ..      76      90 .. 0.95
   4 !   10.0   3.6    0.0014       1.5       1      15 []     100     119 ..     100     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0068
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+ C+++C
  gi|386002620|ref|YP_005920919.1| 10 CIGCRSCEVAC 20
                                      *********** PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00063
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C++C+   C  +C++gA
  gi|386002620|ref|YP_005920919.1| 45 CHHCEeaSCAAACFSGA 61
                                      ****8667********9 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 7.4e-06
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      CtgCg+C  +CP g
  gi|386002620|ref|YP_005920919.1| 76 CTGCGLCSLACPFG 89
                                      ************87 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0014
                            Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                       C+ C+     +Cv  CP +A
  gi|386002620|ref|YP_005920919.1| 100 CDLCEgraepTCVTTCPANA 119
                                       ****8798888******987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.6   2.4e-05     0.025       3      20 ..       5      22 ..       3      35 .. 0.88
   2 !   20.3   8.2   4.3e-07   0.00045      11      53 ..      45      88 ..      38      93 .. 0.65
   3 ?    0.5   3.1      0.63   6.6e+02      46      56 ..     110     119 ..      90     122 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                           Fer4_21  3 idedkCigCgkCliaCed 20
                                      +d  +CigC +C +aCe 
  gi|386002620|ref|YP_005920919.1|  5 VDIRRCIGCRSCEVACER 22
                                      67789***********94 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.3e-07
                           Fer4_21 11 CgkCl.iaCedtsh.qaieidaktvlkvvedeCvGCnlCssvCPv 53
                                      C +C   +C  ++   a++++  ++++   ++C+GC lCs  CP 
  gi|386002620|ref|YP_005920919.1| 45 CHHCEeASCAAACFsGALHKE-GSRTAFDVEKCTGCGLCSLACPF 88
                                      444431234444440455554.445578899*************5 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.63
                           Fer4_21  46 lCssvCPvedc 56 
                                        C++ CP  ++
  gi|386002620|ref|YP_005920919.1| 110 TCVTTCPA-NA 119
                                       68999995.55 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  14.0     0.012        13       2      55 ..       3      57 ..       2      58 .. 0.67
   2 !   13.4  13.0   5.8e-05     0.061       8      56 .]      44      87 ..      39      87 .. 0.89
   3 !   15.6  12.4   1.2e-05     0.013       4      56 .]      71     116 ..      68     116 .. 0.73
   4 !    8.6   2.3    0.0019         2       7      23 ..      98     119 ..      93     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaC 55
                                      v++d  +Ci+C+ C  aC   +++ ++       +    ++  C++c+  +C++aC
  gi|386002620|ref|YP_005920919.1|  3 VYVDIRRCIGCRSCEVAC-ERVHGGRGHVHVHFVGDSASVPILCHHCEeaSCAAAC 57
                                      678889************.5444444444444444444456667777555899999 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.8e-05
                           Fer4_10  8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       C +C+   C +aC +        +  +e+++   +vekCtgcg C  aCP
  gi|386002620|ref|YP_005920919.1| 44 LCHHCEeaSCAAAC-F------SGALHKEGSRTAFDVEKCTGCGLCSLACP 87
                                      6****9999*****.5......58888888999999**************9 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.2e-05
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg.....aCveaCP 56 
                                       +d ++C++Cg C  aCP+              e++     kC+ c+      Cv  CP
  gi|386002620|ref|YP_005920919.1|  71 FDVEKCTGCGLCSLACPF---------GVVWTEKI---AHKCDLCEgraepTCVTTCP 116
                                       6899**************.........33334444...4456666444478******9 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0019
                           Fer4_10   7 dtCirCg.....kCvkaCPadl 23 
                                        +C  C+     +Cv+ CPa++
  gi|386002620|ref|YP_005920919.1|  98 HKCDLCEgraepTCVTTCPANA 119
                                       5677777777788999999865 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   3.1   6.5e-06    0.0069       3      15 ..       9      21 ..       8      30 .. 0.94
   2 ?    3.3   2.9      0.14   1.4e+02       4      14 ..      45      57 ..      42      58 .. 0.89
   3 !   15.8   2.4   1.3e-05     0.014       2      17 .]      74      89 ..      74      89 .. 0.94
   4 ?    3.8   3.8     0.094        99       6      16 ..     107     117 ..      97     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.5e-06
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      rCigC+sC+ aC+
  gi|386002620|ref|YP_005920919.1|  9 RCIGCRSCEVACE 21
                                      8***********8 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                            Fer4_4  4 CigCg..sCvaaC 14
                                      C +C   sC aaC
  gi|386002620|ref|YP_005920919.1| 45 CHHCEeaSCAAAC 57
                                      999*9767***** PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.3e-05
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e+C+gCg C  aCP+g
  gi|386002620|ref|YP_005920919.1| 74 EKCTGCGLCSLACPFG 89
                                      79************86 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.094
                            Fer4_4   6 gCgsCvaaCPq 16 
                                         + Cv +CP 
  gi|386002620|ref|YP_005920919.1| 107 AEPTCVTTCPA 117
                                       3458******6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   1.7   0.00034      0.36      43      57 ..       7      21 ..       3      23 .. 0.86
   2 !    6.8   1.5    0.0095        10       2      20 ..      45      65 ..      44      72 .. 0.83
   3 !   16.1   1.4   1.1e-05     0.012      41      60 ..      71      90 ..      63      91 .. 0.80
   4 ?    3.0   1.1      0.14   1.5e+02       2      18 ..     100     121 ..      98     143 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                           Fer4_17 43 aslCieCgeCerkCP 57
                                      + +Ci+C+ Ce +C 
  gi|386002620|ref|YP_005920919.1|  7 IRRCIGCRSCEVACE 21
                                      679999999999996 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0095
                           Fer4_17  2 CiqCgy..ClpeCpsyeaydn 20
                                      C++C+   C+++C+s++ +++
  gi|386002620|ref|YP_005920919.1| 45 CHHCEEasCAAACFSGALHKE 65
                                      ****9777******9998876 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.1e-05
                           Fer4_17 41 ekaslCieCgeCerkCPqgl 60
                                        +++C++Cg+C+ +CP g+
  gi|386002620|ref|YP_005920919.1| 71 FDVEKCTGCGLCSLACPFGV 90
                                      46899************875 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                           Fer4_17   2 CiqCgy.....ClpeCpsyeay 18 
                                       C  C+      C+  Cp ++ +
  gi|386002620|ref|YP_005920919.1| 100 CDLCEGraeptCVTTCPANALT 121
                                       5555533334488888877664 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.4     0.059        62       1      12 [.       9      20 ..       6      22 .. 0.78
   2 !    7.3   1.5    0.0086       9.1       2      20 ..      45      65 ..      44      75 .. 0.81
   3 !   13.8   1.6     8e-05     0.085      51      66 ..      73      88 ..      63      89 .. 0.77
   4 ?   -0.7   0.1       2.7   2.9e+03      55      61 ..      98     104 ..      89     107 .. 0.75
   5 !    8.7   1.5    0.0032       3.3       7      27 ..     110     128 ..      99     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.059
                           Fer4_16  1 rCgtCgkCaevC 12
                                      rC++C+ C  +C
  gi|386002620|ref|YP_005920919.1|  9 RCIGCRSCEVAC 20
                                      588888888887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0086
                           Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                      C+ C++  Ca +C ++a++++
  gi|386002620|ref|YP_005920919.1| 45 CHHCEEasCAAACFSGALHKE 65
                                      99**9888**********988 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 8e-05
                           Fer4_16 51 qeaitgCdiCqdvCPa 66
                                       e++tgC+ C  +CP+
  gi|386002620|ref|YP_005920919.1| 73 VEKCTGCGLCSLACPF 88
                                      5789999999999998 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.7
                           Fer4_16  55 tgCdiCq 61 
                                       + Cd C+
  gi|386002620|ref|YP_005920919.1|  98 HKCDLCE 104
                                       7888886 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0032
                           Fer4_16   7 kCaevCPtnaikekkekeiea 27 
                                        C+ +CP+na++++  + + +
  gi|386002620|ref|YP_005920919.1| 110 TCVTTCPANALTTD--FDLLS 128
                                       5**********998..54444 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  23.2   0.00045      0.48       2      65 .]       7      90 ..       6      90 .. 0.71
   2 ?    8.1  11.6    0.0035       3.7       2      22 ..      73      93 ..      72     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaae...................dvqeeqvlee........eealwsCt 52
                                      +++Ci+C  C+ aC  ++  + + + +  g+ a                             +        +  +++Ct
  gi|386002620|ref|YP_005920919.1|  7 IRRCIGCRSCEVACERVHGGRgHVHVHFVGDSASvpilchhceeascaaacfsG--------AlhkegsrtAFDVEKCT 77
                                      689***********9888877565666666655578887766555566555551........034444444788***** PP

                            Fer4_8 53 tcgaCtevCpvgi 65
                                      +cg C+ +Cp g+
  gi|386002620|ref|YP_005920919.1| 78 GCGLCSLACPFGV 90
                                      **********875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0035
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk 22
                                      +ekC++Cg+C  aCp+   + 
  gi|386002620|ref|YP_005920919.1| 73 VEKCTGCGLCSLACPFGVVWT 93
                                      789***********9655444 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.4     0.018        19      81      93 ..       9      21 ..       2      24 .. 0.67
   2 ?   -1.9   2.5       6.1   6.4e+03       5      19 ..      45      59 ..      42      69 .. 0.64
   3 ?   13.6   1.4     9e-05     0.095      73      94 ..      67      88 ..      60      90 .. 0.82
   4 ?    0.2   0.3       1.4   1.4e+03       7      14 ..     110     117 ..      94     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                           Fer4_22 81 gCvGCgRCieacp 93
                                       C+GC  C+ ac 
  gi|386002620|ref|YP_005920919.1|  9 RCIGCRSCEVACE 21
                                      6777777776665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.1
                           Fer4_22  5 CgaCtlvCptCsCfd 19
                                      C +C  +  +  Cf+
  gi|386002620|ref|YP_005920919.1| 45 CHHCEEASCAAACFS 59
                                      666666555556654 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 9e-05
                           Fer4_22 73 fkekfgesgCvGCgRCieacpv 94
                                       ++ f+ ++C+GCg C+ acp 
  gi|386002620|ref|YP_005920919.1| 67 SRTAFDVEKCTGCGLCSLACPF 88
                                      4567899*************96 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.4
                           Fer4_22   7 aCtlvCpt 14 
                                       +C ++Cp+
  gi|386002620|ref|YP_005920919.1| 110 TCVTTCPA 117
                                       34444444 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.2   0.00024      0.26       1      47 [.       5      51 ..       5      63 .. 0.85
   2 ?   10.9   1.5   0.00048      0.51       2      17 ..      72      87 ..      72      88 .. 0.92
   3 ?    0.1   1.2       1.2   1.2e+03      11      18 ..     110     117 ..      99     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeA 47
                                      VD  +Ci+c +C  ++  v     +   ++v +  + + + +++eeA
  gi|386002620|ref|YP_005920919.1|  5 VDIRRCIGCRSCEVACERVHGGRGHVHVHFVGDSASVPILCHHCEEA 51
                                      78899**************9999999999999999998888888887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00048
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++C++cg+C  ++P
  gi|386002620|ref|YP_005920919.1| 72 DVEKCTGCGLCSLACP 87
                                      5689***********9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                           Fer4_13  11 aCvelaPd 18 
                                       +Cv ++P 
  gi|386002620|ref|YP_005920919.1| 110 TCVTTCPA 117
                                       67777774 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.1    0.0087       9.2       1      30 [.       3      31 ..       3      57 .. 0.71
   2 ?    5.9   8.5      0.02        21       3      19 ..      71      87 ..      70     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0087
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedgla 30
                                      V+vD  +Cigc  C  ++++v      +++
  gi|386002620|ref|YP_005920919.1|  3 VYVDIRRCIGCRSCEVACERVHGGR-GHVH 31
                                      89****************8655444.3443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      +D ++C+gcglC  ++p
  gi|386002620|ref|YP_005920919.1| 71 FDVEKCTGCGLCSLACP 87
                                      7999************8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0069       7.3      84     101 ..       9      26 ..       2      35 .. 0.81
   2 ?    2.5  11.1      0.15   1.6e+02      48      89 ..      63     104 ..      46     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0069
                           Fer4_18  84 eciscllcidacdkvmek 101
                                        ci c  c  ac++v + 
  gi|386002620|ref|YP_005920919.1|   9 RCIGCRSCEVACERVHGG 26 
                                       5***********999765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                           Fer4_18  48 kekeerkekgagdcidcescvkvcPtgidirkGlqleciscl 89 
                                       +++ +r++ ++ +c+ c+ c   cP g+   + +  +c  c 
  gi|386002620|ref|YP_005920919.1|  63 HKEGSRTAFDVEKCTGCGLCSLACPFGVVWTEKIAHKCDLCE 104
                                       5566777888999***************99999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 804.74
//
Query:       gi|386002621|ref|YP_005920920.1|  [L=678]
Description: Formate dehydrogenase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete 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-88  297.1   0.0    2.7e-88  296.8   0.0    1.0  1  Molybdopterin    Molybdopterin oxidoreductase
    1.1e-27   96.2   0.0    3.2e-27   94.8   0.0    1.8  2  Molydop_binding  Molydopterin dinucleotide binding domain
    6.9e-15   54.8   0.2    1.5e-14   53.7   0.2    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.8   0.0   4.5e-92   2.7e-88       1     429 [.      60     480 ..      60     483 .. 0.94

  Alignments for each domain:
  == domain 1  score: 296.8 bits;  conditional E-value: 4.5e-92
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl++P+ R   rgeG Fvr+sW+eAl lia+ l  +i   gp  va f +++ + +e+ ++l+kl++llg +    +
  gi|386002621|ref|YP_005920920.1|  60 RLTTPLRR---RGEG-FVRISWEEALGLIARGLGDVIRRDGPGGVA-FLASSKCTNEENYLLQKLARLLGTP---HV 128
                                       9*******...9777.**************************9999.56666677****************7...67 PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d++a+l++a  +    +t+g+       ++np+ d+  s+ i+++GsN++e++p+  ar   +a +++a viv +pr
  gi|386002621|ref|YP_005920920.1| 129 DNCARLCHAPSVvglnRTLGAA-----GMTNPIPDIGSSKCIFIIGSNLAENHPVI-ARWVHRAHEDGAVVIVADPR 199
                                       8999999999876666666554.....6789*************************.99999999999********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                        + ++  ad+ l ++pgtd+al+ +m+hvi++e++ d + +++ t g+e +++ +   ++e+ +++++v+ + + + 
  gi|386002621|ref|YP_005920920.1| 200 ETPTTWMADLFLQLTPGTDVALLSGMAHVIIAEGLIDGDYIARNTRGFEALRESVRSSSPERISEITGVPPDDIVRA 276
                                       ***7788*********************************************************************9 PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       ar +a+    s i++ +g+++++ g+++++a+ nLal++g  g+pg+g+  l+Gq++++g a+++gal+  ++ +  
  gi|386002621|ref|YP_005920920.1| 277 ARAYASSPA-SSILYSMGITQHSTGTDNVQAISNLALITGHLGRPGTGVMPLRGQNNVQG-ACDMGALAEFYPGYGR 351
                                       999988888.88999*********************************************.*******999998888 PP

                                       TT....HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSS CS
                     Molybdopterin 305 ke....ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlt 377
                                              + +  a++   l++ p+ +++e++ ++ s++++++y+lg++p +++++ ++v++ale+ldl+vv d+++t
  gi|386002621|ref|YP_005920920.1| 352 SDdpetIRRFSSAWGVPALPKGPGLTATEMICAAASGDIRAMYILGEDPANSDPCSQKVHQALEDLDLLVVQDIFMT 428
                                       87897656666899999************************************************************ PP

                                       HHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHH CS
                     Molybdopterin 378 stalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaL 429
                                        ta+ aD++LP+a w Eke+ +tn+e+r+q  ++av+ppgea sd +I+ a+
  gi|386002621|ref|YP_005920920.1| 429 ATARLADVVLPGAVWAEKEGSFTNTERRVQWSSKAVDPPGEALSDLEIIAAV 480
                                       *************************************************997 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   7.2e+03      60      77 ..     428     445 ..     427     447 .. 0.87
   2 !   94.8   0.0   5.3e-31   3.2e-27       1     109 [.     567     669 ..     567     671 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                       EEEEEEESSB-TTEEEEE CS
                   Molydop_binding  60 evrakvtervrpGvvfmp 77 
                                       ++ a++ + v pG v+++
  gi|386002621|ref|YP_005920920.1| 428 TATARLADVVLPGAVWAE 445
                                       78999**********987 PP

  == domain 2  score: 94.8 bits;  conditional E-value: 5.3e-31
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l L+tgr+  +++++ +tr++++l ++ep  +veinp+dA  l i+ Gd V ve++rG +e+ a++t+rv++Gvvfm
  gi|386002621|ref|YP_005920920.1| 567 LLLTTGRVAVHHNAGSMTRRSPSLLRREPdLFVEINPADAFPLRIAGGDPVLVETPRGGAEALARLTDRVKRGVVFM 643
                                       68*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefks 109
                                       pf+++        +N+lt++atdp +++pefk+
  gi|386002621|ref|YP_005920920.1| 644 PFHFPG-------TNRLTSEATDPEARIPEFKV 669
                                       ******.......******************97 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.2   2.4e-18   1.5e-14       4      53 ..       6      55 ..       4      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.4e-18
                                      EEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCC CS
                    Molybdop_Fe4S4  4 vktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllerv 53
                                      v+t+CpyCg gCg+ v+v+ gk v +e  p hpv+eg lC KG+++le++
  gi|386002621|ref|YP_005920920.1|  6 VPTVCPYCGAGCGFFVSVERGKAVGMEYMPGHPVSEGALCSKGNAALEFL 55
                                      89********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3912.56
//
Query:       gi|386002622|ref|YP_005920921.1|  [L=270]
Description: Glutamate synthase, alpha subunit domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-34  117.4   5.4    7.8e-34  116.9   5.4    1.1  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9   5.4   4.4e-38   7.8e-34      13     185 ..      51     221 ..      30     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 4.4e-38
                                       HHHHHHHHHHTTT---....-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GG CS
                             GXGXG  13 ilsneiakrygeeglpe...dtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkae 86 
                                        + n++++ry+ + l +    +++i++ G+aG++l+afl  G ++ ++G+a+d vG++++ G++++++ +       
  gi|386002622|ref|YP_005920921.1|  51 SIRNVCGQRYIGTRLYTpqgLRMEIEVFGTAGNDLAAFL-YGHRIAVHGNAQDGVGNTMDAGEVIVRGRA------- 119
                                       5778888888888875522245999**************.9*****************************....... PP

                                       GSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B.....-SSBT CS
                             GXGXG  87 eniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt.....grnfa 152
                                            G+v+ ++++gG++++r+  g+R+a ++     + +++vv+g   d+++eYm+GGvv+vL        ++ ++
  gi|386002622|ref|YP_005920921.1| 120 -----GDVLGFSMRGGEIYVRDGCGYRAALHMkeyegKRPVLVVGGRsQDFLGEYMAGGVVIVLDLAgeshdAHFIG 191
                                       .....***************************9999999********99***************999555555679* PP

                                       TT--EEEEEEE-SSSTHHHHB-TTT-EEEES-S CS
                             GXGXG 153 aGmsgGiayvldedekfekklnkelvelekved 185
                                       +Gm+gG++y++ + e+  ++++ + ve++ v+d
  gi|386002622|ref|YP_005920921.1| 192 TGMHGGVIYLRGSVEE--SQVG-DQVEISPVDD 221
                                       **********954444..2443.4456666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1830.38
//
Query:       gi|386002623|ref|YP_005920922.1|  [L=504]
Description: Glutamate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.9e-139  462.9   0.0   7.9e-139  462.9   0.0    1.4  2  Glu_synthase     Conserved region in glutamate synthase
    3.7e-16   59.4   0.0    9.4e-09   35.2   0.0    2.2  2  Glu_syn_central  Glutamate synthase central domain
    5.5e-09   35.5   6.2      7e-08   31.8   3.7    2.6  3  IMPDH            IMP dehydrogenase / GMP reductase domain
    4.3e-08   32.6   5.2    8.6e-08   31.6   2.6    2.4  3  FMN_dh           FMN-dependent dehydrogenase
    1.5e-06   28.2  19.9      2e-06   27.9  11.3    2.5  2  Fer4_9           4Fe-4S dicluster domain
      2e-06   27.8  14.6    0.00042   20.4   0.5    3.4  3  Fer4_10          4Fe-4S dicluster domain
    8.9e-05   22.0   1.5    0.00018   21.0   1.5    1.4  1  NMO              Nitronate monooxygenase
    0.00012   22.1   8.5    0.00012   22.1   8.5    2.4  2  Fer4_21          4Fe-4S dicluster domain
    0.00016   22.2  18.3    0.00051   20.6  11.7    2.7  2  Fer4_7           4Fe-4S dicluster domain
    0.00025   20.7   2.3    0.00025   20.7   2.3    3.7  3  Fer4             4Fe-4S binding domain
     0.0004   19.7   0.1     0.0041   16.4   0.2    2.1  2  DHO_dh           Dihydroorotate dehydrogenase
    0.00045   21.1   0.4    0.00045   21.1   0.4    3.5  3  Fer4_16          4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.022   14.2   0.1      0.053   13.0   0.1    1.5  1  His_biosynth     Histidine biosynthesis protein
      0.028   14.9   2.6      0.028   14.9   2.6    3.8  3  Fer4_4           4Fe-4S binding domain
       0.09   12.9  22.9      0.076   13.1   3.1    3.5  3  Fer4_6           4Fe-4S binding domain
       0.23   11.3   1.6        0.5   10.2   1.6    1.5  1  zf_PR_Knuckle    PR zinc knuckle motif
        8.5    6.7  24.5       0.21   11.8   2.3    3.8  3  Fer4_2           4Fe-4S binding domain
        9.3    6.8  21.6         25    5.4  13.9    3.2  2  Fer4_8           4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.7       5.5   5.5e+03     312     333 ..      18      38 ..      16      48 .. 0.83
   2 !  462.9   0.0  7.9e-142  7.9e-139       4     368 .]     108     472 ..     105     472 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.5
                                       --S---GGGT--TTSSS---HH CS
                      Glu_synthase 312 CimarvChtntCpvGvatqdpe 333
                                       C ++r C   +C+ G  t dp 
  gi|386002623|ref|YP_005920922.1|  18 CGQCRGCE-RQCAFGTHTYDPA 38 
                                       99999996.58******99996 PP

  == domain 2  score: 462.9 bits;  conditional E-value: 7.9e-142
                                       -HHHHHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGEEE--SS--.--GGGS--HHHHHTTEE---B-TTTS-H CS
                      Glu_synthase   4 eievikllqkavqveskesidkyrekleerevlkakrdlleldaaeealikleevepalkikkriltsamSyGalse 80 
                                       +i++++++ +a+qv +++s+d +re++e r++l++k+d+++++a+   ++  +e+ p+l ++++il+samSyGa+s 
  gi|386002623|ref|YP_005920922.1| 108 RIYWDHIVLNASQV-TNPSLDPLREPMELRTFLGRKPDMMDISADSGEVEIRTELSPNLVVETPILFSAMSYGAISY 183
                                       6899**********.*****************************99999999************************* PP

                                       HHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS--EE-GG CS
                      Glu_synthase  81 eahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeGgqlpge 157
                                       +a ++la+a+ + +t +ntGEGG+++e +++    ai+QvasgrFG+++eyLn a+a+eik++QGakpg+Gg+lpge
  gi|386002623|ref|YP_005920922.1| 184 NAFKSLATAACKSKTYFNTGEGGLPREMREEFGRCAIVQVASGRFGIDAEYLNIAQAVEIKVGQGAKPGIGGHLPGE 260
                                       ***************************************************************************** PP

                                       G--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEE CS
                      Glu_synthase 158 KvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevn.keakvsvKlvaeagvetiaagvakanadiili 233
                                       Kvs ++a++R+i++g+d+iSPaphhdiysiedl+ li++Lke++ +e+++svK++a ++  +ia+g+++a+adii+i
  gi|386002623|ref|YP_005920922.1| 261 KVSLSVAETRMIPQGTDAISPAPHHDIYSIEDLSTLITALKEATnYEKPISVKIAAVHNFAAIASGIVRAGADIIAI 337
                                       *******************************************99******************************** PP

                                       E-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHHT CS
                      Glu_synthase 234 dGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaalial 310
                                       dGl+GGTGA+pk +++++G+P+ela++  d++l+eeg+r+r s+i +Gg++++ dv+ka+alGAdav+ig+aalia+
  gi|386002623|ref|YP_005920922.1| 338 DGLRGGTGAAPKAIRDNVGIPTELAISSLDRRLREEGIRNRCSIISAGGIRCSSDVIKAIALGADAVYIGSAALIAM 414
                                       ***************************************************************************** PP

                                       T--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                      Glu_synthase 311 gCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368
                                       gC+ +++C+t++C++G++tqdp+L  rl+ve + er+ n+i a+++e+re+l+ +gin
  gi|386002623|ref|YP_005920922.1| 415 GCTLCQKCYTGKCNWGICTQDPRLSGRLNVEIASERLSNLISAWSHEIREMLGGMGIN 472
                                       *******************************************************986 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   8.1e-08     8e-05      53     105 ..     116     175 ..      77     225 .. 0.76
   2 !   35.2   0.0   9.4e-12   9.4e-09     134     270 ..     314     480 ..     266     489 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.1e-08
                                       E----SSS----TTTTGGG-B--EEES----SSS.........--GGGG-EEEESSSB--HH CS
                   Glu_syn_central  53 qlfAqVTNPpiDpiREelvmsletllGkegnlle.........eeeeqakrlklesPiLtee 105
                                        + +qVTNP++Dp+RE   m l+t+lG+++++++          ++e   +l++e+PiL ++
  gi|386002623|ref|YP_005920922.1| 116 LNASQVTNPSLDPLREP--MELRTFLGRKPDMMDisadsgeveIRTELSPNLVVETPILFSA 175
                                       5668************6..89***********996554443322224446777777777654 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 9.4e-12
                                       HHHHHHHHHHHHHHHHTT-SEEEEESS........--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--S CS
                   Glu_syn_central 134 eealerlceeaeeavregaeilvLsDr........kvseervpipslLavgavhhhLvrkglrtkvslvvesgeare 202
                                        +a+++ ++ a+  vr+ga+i+ ++          k+ +++v ip+ La+++++++L ++g r+++s++  +g +r 
  gi|386002623|ref|YP_005920922.1| 314 IAAVHNFAAIASGIVRAGADIIAIDGLrggtgaapKAIRDNVGIPTELAISSLDRRLREEGIRNRCSII-SAGGIRC 389
                                       4678888888999999999999998876777666667789***************************87.6788*** PP

                                       HHHHHHHHHTT-SEEEEHHHHHHH......HHHHTTT..................S-...----HHHHHHHHHHHHH CS
                   Glu_syn_central 203 vhhfavllgyGadavnPylaleti......eklveeg..................al...aeeeleknyrkavekGl 252
                                         +++  +++Gadav+   a  ++      +    +                   +l    ++e  +n+++a ++ +
  gi|386002623|ref|YP_005920922.1| 390 SSDVIKAIALGADAVYIGSAALIAmgctlcQ----KCytgkcnwgictqdprlsgRLnveIASERLSNLISAWSHEI 462
                                       ***************8655544443333331....2244445555555444444411432233334*********** PP

                                       HHHHHHTT--BHHHHHHS CS
                   Glu_syn_central 253 lKimskmGistlqSYkga 270
                                          +  mGi  l+S +g 
  gi|386002623|ref|YP_005920922.1| 463 REMLGGMGINALESLRGN 480
                                       **************9986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.043        43      17      43 ..     151     177 ..     142     186 .. 0.84
   2 !   31.8   3.7     7e-11     7e-08     156     238 ..     321     409 ..     286     417 .. 0.77
   3 ?   -2.7   0.0       2.3   2.3e+03     298     328 ..     450     480 ..     446     485 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.043
                                       -GGGSB--EESSTTEEESSSEEE-SST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  17 lpkevdlktkltkkiklniPlvsaamd 43 
                                        + ev+++t+l+ ++ +++P++ +am 
  gi|386002623|ref|YP_005920922.1| 151 DSGEVEIRTELSPNLVVETPILFSAMS 177
                                       4559********************996 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 7e-11
                                       HHHHHHHHHTT-SEEEE.-SS-STTBHHHHH.CSB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                             IMPDH 156 aegakaLieagadavkv.GiGpGsiCttrvv.agvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAl 226
                                       a+ a+ +++agad++ + G+  G     + +   vG+p   A+++  +  ++ g      +i+ GGi+ s d++kA+
  gi|386002623|ref|YP_005920922.1| 321 AAIASGIVRAGADIIAIdGLRGGTGAAPKAIrDNVGIPTELAISSLDRRLREEGirnrCSIISAGGIRCSSDVIKAI 397
                                       334566899******9988877776666655268*****************999555568***************** PP

                                       HTT-SEEEESCC CS
                                       xxxxxxxxxxxx RF
                             IMPDH 227 aaGadavmlGsl 238
                                       a+Gadav +Gs 
  gi|386002623|ref|YP_005920922.1| 398 ALGADAVYIGSA 409
                                       **********85 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.3
                                       -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 298 svkevveqlvgglrsgmgylGaktieelkek 328
                                       +++++++   +++r+ +g +G + +e+l+ +
  gi|386002623|ref|YP_005920922.1| 450 RLSNLISAWSHEIREMLGGMGINALESLRGN 480
                                       578889999999*************999876 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.1   4.1e+03      57      84 ..     167     194 ..     151     200 .. 0.71
   2 !   31.6   2.6   8.6e-11   8.6e-08     267     308 ..     374     415 ..     310     418 .. 0.84
   3 ?    0.5   0.0      0.25   2.5e+02     313     342 ..     449     478 ..     445     485 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.1
                                       ESSSEEE--BSTGGGTSTTHHHHHHHHH CS
                            FMN_dh  57 lslPvliaPvglaklahpdgelalaraa 84 
                                       +++P+l++++++  +  +  +  ++ a+
  gi|386002623|ref|YP_005920922.1| 167 VETPILFSAMSYGAISYNAFKSLATAAC 194
                                       6789999999999888755444434444 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 8.6e-11
                                       HH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                            FMN_dh 267 avggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                        +++r+ ++  gGir  sDv+kA+alGAdav +G ++l ++ 
  gi|386002623|ref|YP_005920922.1| 374 GIRNRCSIISAGGIRCSSDVIKAIALGADAVYIGSAALIAMG 415
                                       45789*******************************999875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 313 eGvervleilraelertmallGvksvaeld 342
                                       e+++++++ +++e+++ +  +G++ +++l+
  gi|386002623|ref|YP_005920922.1| 449 ERLSNLISAWSHEIREMLGGMGINALESLR 478
                                       6778999*******************9985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9  11.3     2e-09     2e-06       1      51 []      17      64 ..      17      64 .. 0.94
   2 ?    5.1   1.3     0.025        25       2      16 ..     416     431 ..     387     447 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC +C+ C+++C +g++++d a+     + +   +C gC++Cv  Cpk+ai
  gi|386002623|ref|YP_005920922.1| 17 KCGQCRGCERQCAFGTHTYDPAADRLVSDDR---KCAGCQRCVIFCPKDAI 64
                                      7*********************999998775...8*************997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.025
                            Fer4_9   2 CtgCgaCvea.Cpagv 16 
                                       Ct C++C +  C+ g+
  gi|386002623|ref|YP_005920922.1| 416 CTLCQKCYTGkCNWGI 431
                                       6666666332255554 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.4   0.00047      0.47       2      19 ..      11      28 ..      10      40 .. 0.86
   2 !   20.4   0.5   4.3e-07   0.00042       2      24 ..      42      76 ..      41     103 .. 0.70
   3 ?    4.9   0.7     0.029        29       8      19 ..     415     427 ..     409     459 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      v++d+++C +C+ C + C
  gi|386002623|ref|YP_005920922.1| 11 VIRDEEKCGQCRGCERQC 28
                                      6899************** PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4.3e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl............t 24
                                      +v dd +C +C++Cv +CP d+            +
  gi|386002623|ref|YP_005920922.1| 42 LVSDDRKCAGCQRCVIFCPKDAievrpspsfyrpN 76
                                      5789***************9875555555555550 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.029
                           Fer4_10   8 tCirCgkCvka.C 19 
                                        C+ C+kC +  C
  gi|386002623|ref|YP_005920922.1| 415 GCTLCQKCYTGkC 427
                                       5999999998657 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.5   1.8e-07   0.00018     150     232 ..     325     417 ..     294     422 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                               NMO 150 rkvearGaDalivqGpeaG.GhqGtpevgd.kglfaLvpqvldavd...........iPviAaGGiidrrgvaaaLa 213
                                         + ++GaD++ ++G  +G G  +  ++ d +g     + + + +d             +i aGGi    +v  a+a
  gi|386002623|ref|YP_005920922.1| 325 SGIVRAGADIIAIDGLRGGtGAAP-KAIRDnVGI--PTELAISSLDrrlreegirnrCSIISAGGIRCSSDVIKAIA 398
                                       334567899999999988844455.333333221..11222223333444678888899****************** PP

                               NMO 214 lGAsgvqigtrfLltkesd 232
                                       lGA +v+ig++ L++  ++
  gi|386002623|ref|YP_005920922.1| 399 LGADAVYIGSAALIAMGCT 417
                                       *************998776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   8.5   1.2e-07   0.00012       4      58 ..      14      65 ..      11      66 .. 0.80
   2 ?    1.0   3.2      0.47   4.7e+02      17      47 ..     388     422 ..     377     428 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidaktvlkv.vedeCvGCnlCssvCPvedcie 58
                                      de+kC +C  C   C  ++h+   +d+++   v  + +C GC+ C++ CP +d+ie
  gi|386002623|ref|YP_005920922.1| 14 DEEKCGQCRGCERQCAFGTHT---YDPAADRLVsDDRKCAGCQRCVIFCP-KDAIE 65
                                      799*************76654...5655544441678*************.79998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                           Fer4_21  17 aCedtshqaieidaktvl....kvvedeCvGCnlC 47 
                                        C+   ++ai + a++v+    ++++  C+ C+ C
  gi|386002623|ref|YP_005920922.1| 388 RCSSDVIKAIALGADAVYigsaALIAMGCTLCQKC 422
                                       57777777777666554423224455555555555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  11.7   5.1e-07   0.00051       1      52 []      17      63 ..      17      63 .. 0.95
   2 ?    4.7   0.5     0.047        47      30      51 ..     408     430 ..     387     431 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.1e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C +C+ C++ C  ++ ++d++      ++++ d +kC gC++Cv  CP++a
  gi|386002623|ref|YP_005920922.1| 17 KCGQCRGCERQCAFGTHTYDPA-----ADRLVSDDRKCAGCQRCVIFCPKDA 63
                                      7*******************98.....5789******************987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.047
                            Fer4_7  30 kveidpekClgCgaCva.vCPtg 51 
                                       ++++ ++ C+ C++C +  C +g
  gi|386002623|ref|YP_005920922.1| 408 SAALIAMGCTLCQKCYTgKCNWG 430
                                       556677899****9998667776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   3.2     0.003         3       2      18 ..      12      28 ..      11      30 .. 0.93
   2 !   20.7   2.3   2.5e-07   0.00025       4      24 .]      45      65 ..      42      65 .. 0.91
   3 ?    0.3   1.4      0.72   7.2e+02       8      15 ..     416     423 ..     412     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.003
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      + deekC  C  C+  C
  gi|386002623|ref|YP_005920922.1| 12 IRDEEKCGQCRGCERQC 28
                                      67************999 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.5e-07
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                      d  kC gC +Cv  CP +AI+
  gi|386002623|ref|YP_005920922.1| 45 DDRKCAGCQRCVIFCPKDAIE 65
                                      778*****************6 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.72
                                       SSS-THHH CS
                              Fer4   8 CigCGaCv 15 
                                       C+ C +C+
  gi|386002623|ref|YP_005920922.1| 416 CTLCQKCY 423
                                       99999997 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.29   2.9e+02     147     180 ..     291     324 ..     283     345 .. 0.75
   2 !   16.4   0.2   4.1e-06    0.0041     241     285 ..     375     420 ..     360     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHH.SSEEEEEE-SSSSHHHHHH CS
                            DHO_dh 147 eelkaillkvvkevs.kvpvlvKlaPdltdeekkd 180
                                       e+l++ +++ +++++ ++p+ vK+a  + +++ ++
  gi|386002623|ref|YP_005920922.1| 291 EDLSTLITALKEATNyEKPISVKIAA-VHNFAAIA 324
                                       789999999998887799******97.66555544 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.1e-06
                                       TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH.HHHHGTCHHH CS
                            DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvyta.lvfegpkiak 285
                                       ++++  iI+ GGi  + D++  i  GA +v +++a l+  g ++++
  gi|386002623|ref|YP_005920922.1| 375 IRNRCSIISAGGIRCSSDVIKAIALGADAVYIGSAaLIAMGCTLCQ 420
                                       567889***************************9724556666665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.5     0.072        72       1      14 [.      17      30 ..      13      41 .. 0.83
   2 !   21.1   0.4   4.5e-07   0.00045       1      57 [.      48     101 ..      48     103 .. 0.66
   3 ?   -0.8   2.3       3.2   3.2e+03       2       8 ..     416     422 ..     402     435 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                           Fer4_16  1 rCgtCgkCaevCPt 14
                                      +Cg+C+ C   C  
  gi|386002623|ref|YP_005920922.1| 17 KCGQCRGCERQCAF 30
                                      59999999999965 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.5e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgC 57 
                                       +C +C++C+  CP +ai+ + ++++  r + s++ ++ +dl+ ++e+      +tgC
  gi|386002623|ref|YP_005920922.1|  48 KCAGCQRCVIFCPKDAIEVRPSPSFY-RPNASWSREKIEDLKRQAETGG--VLLTGC 101
                                       5*****************99878775.4444554455555555544433..334666 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.2
                           Fer4_16   2 CgtCgkC 8  
                                       C+ C+kC
  gi|386002623|ref|YP_005920922.1| 416 CTLCQKC 422
                                       4445555 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.3e-05     0.053      75     106 ..     380     411 ..     367     417 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaav 106
                                        +   GGIr  +dv +++ +gad v ig+aa+
  gi|386002623|ref|YP_005920922.1| 380 SIISAGGIRCSSDVIKAIALGADAVYIGSAAL 411
                                       45556777777777777777777777777765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   5.3      0.17   1.7e+02       2      15 ..      16      29 ..      15      31 .. 0.86
   2 ?   14.9   2.6   2.9e-05     0.028       3      16 ..      48      61 ..      46      71 .. 0.92
   3 ?    0.2   3.8       1.5   1.5e+03       4      12 ..     416     424 ..     413     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e+C +C+ C++ C 
  gi|386002623|ref|YP_005920922.1| 16 EKCGQCRGCERQCA 29
                                      7899*********5 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.9e-05
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +C gC +Cv++CP 
  gi|386002623|ref|YP_005920922.1| 48 KCAGCQRCVIFCPK 61
                                      6************5 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.5
                            Fer4_4   4 CigCgsCva 12 
                                       C+ C +C+ 
  gi|386002623|ref|YP_005920922.1| 416 CTLCQKCYT 424
                                       9******95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.7   0.00023      0.23       4      22 ..      13      31 ..      11      33 .. 0.89
   2 ?   13.1   3.1   7.7e-05     0.076       5      24 .]      45      64 ..      42      64 .. 0.91
   3 ?   -1.3   3.1       2.7   2.7e+03       9      17 ..     416     424 ..     416     430 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            Fer4_6  4 idpdkCigCgdCvrvCPeg 22
                                       d++kC +C+ C+r C +g
  gi|386002623|ref|YP_005920922.1| 13 RDEEKCGQCRGCERQCAFG 31
                                      59**************875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d+ kC gC +Cv+ CP +ai
  gi|386002623|ref|YP_005920922.1| 45 DDRKCAGCQRCVIFCPKDAI 64
                                      788*************9998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.7
                            Fer4_6   9 CigCgdCvr 17 
                                       C+ C +C++
  gi|386002623|ref|YP_005920922.1| 416 CTLCQKCYT 424
                                       999999997 PP

>> zf_PR_Knuckle  PR zinc knuckle motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.6    0.0005       0.5      10      24 ..     413     427 ..     408     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                     zf_PR_Knuckle  10 siWCtLCeksYpSdC 24 
                                       ++ CtLC+k Y+  C
  gi|386002623|ref|YP_005920922.1| 413 AMGCTLCQKCYTGKC 427
                                       667**********99 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.4     0.013        13       5      20 ..      13      28 ..      10      30 .. 0.86
   2 ?   11.8   2.3   0.00021      0.21       6      21 ..      45      60 ..      40      61 .. 0.87
   3 ?   -0.6   4.6       1.8   1.8e+03      10      20 ..     416     427 ..     411     434 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                       d+++C +C+ C   C
  gi|386002623|ref|YP_005920922.1| 13 RDEEKCGQCRGCERQC 28
                                      599******99*8877 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      d ++C gC  Cv  CP
  gi|386002623|ref|YP_005920922.1| 45 DDRKCAGCQRCVIFCP 60
                                      6689***********9 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.8
                            Fer4_2  10 CigCgaCvsa.C 20 
                                       C+ C +C++  C
  gi|386002623|ref|YP_005920922.1| 416 CTLCQKCYTGkC 427
                                       999999987556 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  13.9     0.025        25       3      64 ..      16      62 ..      14      63 .. 0.77
   2 ?    4.0   0.8     0.068        68      49      59 ..     414     424 ..     377     460 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ekC++C  C+ +C +      h +d+  ++    +++++        +C +c++C+  Cp++
  gi|386002623|ref|YP_005920922.1| 16 EKCGQCRGCERQCAFG----THTYDPAADR---LVSDDR--------KCAGCQRCVIFCPKD 62
                                      69***********654....4556666663...345555........8************86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.068
                            Fer4_8  49 wsCttcgaCte 59 
                                         Ct c++C +
  gi|386002623|ref|YP_005920922.1| 414 MGCTLCQKCYT 424
                                       45666666632 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2968.43
//
Query:       gi|386002624|ref|YP_005920923.1|  [L=441]
Description: Glutamine amidotransferase, class-II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-16   59.5   0.0    3.8e-12   45.6   0.0    2.1  2  GATase_2  Glutamine amidotransferases class-II
    2.4e-08   34.3   0.0    4.6e-07   30.1   0.0    2.4  2  GATase_6  Glutamine amidotransferase domain
    6.4e-06   26.1   0.0      0.011   15.6   0.0    2.4  2  GATase_7  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   6.4e-16   3.8e-12      32     242 ..      87     294 ..      77     301 .. 0.81
   2 !   11.7   0.0   1.3e-05     0.077     272     371 ..     307     408 ..     298     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 6.4e-16
                                       S-B-TTSSSBSEEEEEEE--HHHHHHH.....HHHTT-----GGG-EEEEEEE-SSHHHHHHHHHHHHHHHHHTT-E CS
                          GATase_2  32 GavgadektGDGaGillqiPdeflrke.....akekgielpeageyavgmlflpkdeekaeeakkileeiveeegle 103
                                       Ga++ d +   G G++ +i +  +r +     +++ gi  ++++ ya+  +f   +++++++akk++e+ ++ + ++
  gi|386002624|ref|YP_005920923.1|  87 GAMNRDGDRFTGEGVMKAIANMHVRGNglgggFAAYGIYPEHRDCYALHLMFTGPSPQAKKDAKKEFEAFLS-RRFD 162
                                       566666666667777777777776654222225566777788899**********************98876.5799 PP

                                       EEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT---HHHHHHHHHHHHHHHGGG.....-BTTBEEEEEESSEEEE CS
                          GATase_2 104 vlgwRevpvdksvlgeaakesePsieqvfvekkedlseeelerklyviRkriekeiakkkaekefYicslssrtivY 180
                                       +    e+p+d+ v      +  P i + fv  + d   +e e+  y++R  +e +     + ++ Yi s  ++   +
  gi|386002624|ref|YP_005920923.1| 163 LFFDEEIPTDEAV----PVRDPPLIWRYFVLPRID-PASEEEEGDYIVRSIMEVNG----KIENAYIFSSGKNMGCF 230
                                       999*******975....67889********99985.455557778****9888775....57899************ PP

                                       EESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SS....EEEEE--TTHHHHH CS
                          GATase_2 181 kglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRl....laHnGEintlrGnk 242
                                       kg+  +e+++e++  + d++++++   vH Rf tnt   W  a+P+ l    + HnGEi     n+
  gi|386002624|ref|YP_005920923.1| 231 KGVGYPEEIGEYF--MLDRTYRAHTWTVHGRFPTNTQAWWGGAHPFSLldttIVHNGEISSYGTNR 294
                                       *************..5899***************************86222268*****8764443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.3e-05
                                       S-HHHHHHHHHHHHHHTT--HHHHH.HHHS----TT-GGGTHHHHHHHHHHTTT---..--SSEEEEE.E-SSEEEE CS
                          GATase_2 272 gsDsasldnvlellvlsgrslaeal.mlliPeawennksldkekkafyeyasalmep..WDGPalivf.tdGkvvga 344
                                       + D++ +  + +ll++  r + e +  +l P+ w++ +++ ++ + ++    ++  p   +GP ++++ + G+++g 
  gi|386002624|ref|YP_005920923.1| 307 QTDTEVIAYAADLLMRRQRLPIEVVaKILAPPIWNSIDRMPEKERRLFTTLRMVYGPllMNGPFAVIIgQTGRMIGL 383
                                       57899999999****999887776626999*****************99999999994459**77666267999986 PP

                                       EE-TT--S--EEEEETT--EEEESSTT CS
                          GATase_2 345 vLDRnGLRPaRylvtkddlvvlasEvG 371
                                       + DR  LRP     t+ ++++++sE  
  gi|386002624|ref|YP_005920923.1| 384 T-DRIRLRPLT-AATSGEMFYISSEEA 408
                                       5.*******86.567777888888754 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   7.7e-11   4.6e-07      10      88 ..     249     330 ..     241     346 .. 0.82
   2 ?    1.3   0.0     0.061   3.7e+02     101     134 .]     373     406 ..     364     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.7e-11
                          GATase_6  10 vedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall..... 81 
                                       ++++++ +H R  ++  a   ga+Pf  +    ++vhNGei+ y++ r  l+   g+a+  ++Dtev++ ++     
  gi|386002624|ref|YP_005920923.1| 249 YRAHTWTVHGRFPTNTQAWWGGAHPF--SLLDTTIVHNGEISSYGTNRWYLEM-YGYACTLQTDTEVIAYAAdllmr 322
                                       55667788999999999988999***..99999************88888888.****************8856666 PP

                          GATase_6  82 .eelGeev 88 
                                        ++l+ ev
  gi|386002624|ref|YP_005920923.1| 323 rQRLPIEV 330
                                       66655554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.061
                          GATase_6 101 wdkrentlilardrlgvkplyyavdesglafase 134
                                       +  +++++i ++dr+  +pl+ a++++ ++++se
  gi|386002624|ref|YP_005920923.1| 373 IIGQTGRMIGLTDRIRLRPLTAATSGEMFYISSE 406
                                       444678888899*******************998 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.9e-06     0.011      13      61 ..     271     316 ..     264     334 .. 0.84
   2 !    7.9   0.0   0.00045       2.7      74     120 ..     366     409 ..     362     411 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                          GATase_7  13 aQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllal 61 
                                       a P++     + +iv+nGei  y   r  Le  g++++ ++Dtev++ +
  gi|386002624|ref|YP_005920923.1| 271 AHPFS---LLDTTIVHNGEISSYGTNRWYLEMYGYACTLQTDTEVIAYA 316
                                       55665...24579********************************9544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00045
                          GATase_7  74 lnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelka 120
                                       +nG fA++i ++ +  ++   Dr+  +PL  +++ g+ ++++Se  +
  gi|386002624|ref|YP_005920923.1| 366 MNGPFAVIIGQTGR--MIGLTDRIRLRPLTAATS-GEMFYISSEEAS 409
                                       68999999987766..******************.89******9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2498.92
//
Query:       gi|386002625|ref|YP_005920924.1|  [L=78]
Description: hypothetical protein Mhar_1945 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.51
# Mc/sec: 464.39
//
Query:       gi|386002626|ref|YP_005920925.1|  [L=475]
Description: hypothetical protein Mhar_1946 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.6   0.0    8.7e-11   42.1   0.0    3.0  3  HSDR_N    Type I restriction enzyme R protein N terminus (HSD
    3.2e-10   40.0   0.2    2.4e-09   37.2   0.0    2.5  3  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD
    0.00047   20.1   0.2      0.004   17.1   0.0    2.5  3  SeqA      SeqA protein C-terminal domain
  ------ inclusion threshold ------
       0.19   11.5   0.1       0.27   11.0   0.1    1.2  1  DUF2855   Protein of unknown function (DUF2855)


Domain annotation for each model (and alignments):
>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   2.9e-05      0.13       2      38 ..      22      59 ..      21      64 .. 0.87
   2 !   42.1   0.0   1.9e-14   8.7e-11     110     193 ..      49     126 ..      48     127 .. 0.86
   3 ?   -1.5   0.1      0.46   2.1e+03     147     155 ..     208     216 ..     152     262 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                                      SSHHHHHH.HHHHHHHHTT-EE................ CS
                            HSDR_N  2 lsEaeleqelidellrelGyqvlskkdveiegrrpe.v 38
                                      ++E+++++ l+++++ +lGy+v ++++v +e +++  +
  gi|386002626|ref|YP_005920925.1| 22 QTEEATKNALVLPFITALGYNVFDPTEVVPEFTADVgT 59
                                      89**************************9999887753 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 1.9e-14
                                       EEE----S..SSS---EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---SSSGGGGG-.....-EEEEE- CS
                            HSDR_N 110 vvnQvtvt..gnqkrrpDivlfvnglplvviElKrpgtieeAinQikryrkeksdvsipqlfrYl.....qfgvisn 179
                                       vv ++t +   ++ +++D+ ++ ng+p++++E+K  g+         + +ke+    + ql+rY+     +fgv++n
  gi|386002626|ref|YP_005920925.1|  49 VVPEFTADvgTKKGEKVDYAILMNGKPIILFECKWCGS---------DLEKEH----ASQLYRYFsvtdgRFGVLTN 112
                                       667777778788999********************653.........223333....9******************* PP

                                       SS-EEEEE--SSSG CS
                            HSDR_N 180 gketrfyaktkrre 193
                                       g  +rfy++ ++++
  gi|386002626|ref|YP_005920925.1| 113 GIIYRFYSDLEKQN 126
                                       ********999987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.46
                                       HHHHHHHTS CS
                            HSDR_N 147 eeAinQikr 155
                                       +e + Qi++
  gi|386002626|ref|YP_005920925.1| 208 REQFYQITK 216
                                       222223222 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   5.4e-13   2.4e-09       2     102 ..      24     127 ..      23     135 .. 0.87
   2 ?   -1.5   0.1      0.54   2.4e+03      20      77 ..     242     302 ..     226     308 .. 0.56
   3 ?   -2.5   0.0       1.1   4.9e+03      12      28 ..     458     474 ..     454     475 .] 0.80

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.4e-13
                          HSDR_N_2   2 EEwvRqklikyLveelgyp...keliavekelqlg.skkkraDivvykkdkkpllivecKapsvkiseevleqlksY 74 
                                       EE +   l+  +++ lgy+    +++  e++  +g +k +++D+++  +  kp+++ ecK     +++e+ +ql +Y
  gi|386002626|ref|YP_005920925.1|  24 EEATKNALVLPFITALGYNvfdPTEVVPEFTADVGtKKGEKVDYAILMNG-KPIILFECKWCGSDLEKEHASQLYRY 99 
                                       8889999999999999996333799*********9556667*****9988.************************** PP

                          HSDR_N_2  75 lealkaeylvvtNglehivykvdkkkkk 102
                                        +++  +++v+tNg    +y   +k++k
  gi|386002626|ref|YP_005920925.1| 100 FSVTDGRFGVLTNGIIYRFYSDLEKQNK 127
                                       **************99999885555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.54
                          HSDR_N_2  20 pkeliavekelqlg..skkkraDivvykkd.kkpllivecKapsvkiseevleqlksYlea 77 
                                        ++++ ++++++    +k++   i+  +++ + ++++  + ++ +  +  ++  +ksY+++
  gi|386002626|ref|YP_005920925.1| 242 SEGEMIRNEPIEQIiiEKQPGEEIITTEEEyEGYYIVKTILRSFIDPKRVTIRDVKSYCNV 302
                                       5555555555553323444444555555552334444444555555577777777777776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                          HSDR_N_2  12 yLveelgypkeliavek 28 
                                        ++  +gy++e+++ve+
  gi|386002626|ref|YP_005920925.1| 458 NIIILFGYNEEDLSVEI 474
                                       6677789******9997 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.84   3.8e+03      28      65 ..     210     246 ..     202     254 .. 0.69
   2 ?   -1.4   0.0       0.5   2.2e+03      49      72 ..     314     337 ..     306     339 .. 0.83
   3 !   17.1   0.0   8.8e-07     0.004      23      63 ..     395     434 ..     385     449 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.84
                              SeqA  28 alyradpeaFakatekvkGrtRvYfakdeetllasgks 65 
                                       ++y+++++a ++ + + k ++R+ +a  ee ++++g+ 
  gi|386002626|ref|YP_005920925.1| 210 QFYQITKKALKQFI-NDKINERLKYALVEERVISEGEM 246
                                       56777777777777.56667777777777777777765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.5
                              SeqA  49 RvYfakdeetllasgkstkpkqip 72 
                                       R+Yf ++++ l   +k+ + + +p
  gi|386002626|ref|YP_005920925.1| 314 RLYFNTSQKYLGLFDKNKNEQSVP 337
                                       99******9998888887777766 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 8.8e-07
                              SeqA  23 lliLsalyradpeaFakatekvkGrtRvYfakdeetllasg 63 
                                       l + +++ + ++++F++++ +++Gr+R Yf+kd ++l +s+
  gi|386002626|ref|YP_005920925.1| 395 LKVCEIMQTSHKDEFEQVL-SLTGRKRPYFTKDPDQLRSSE 434
                                       556789999**********.*************99987654 PP

>> DUF2855  Protein of unknown function (DUF2855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     6e-05      0.27     246     315 ..     166     236 ..     118     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6e-05
                           DUF2855 246 sthkvksseelqeakaaaaala..kpvqffapevidkrieelgaeeyferlaaawkrfleeaavkekklvrv 315
                                       +++ ++++e  +  ++++++ +  + v ffa++v + r+++  +e++++ +++a+k+f+++   ++ k+  v
  gi|386002626|ref|YP_005920925.1| 166 ASELKYTKEIKKIIEEQTKD-PsdEFVKFFASQVYSGRMTQPVREQFYQITKKALKQFINDKINERLKYALV 236
                                       44444444332222222222.124889*********************************997777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2787.93
//
Query:       gi|386002627|ref|YP_005920926.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002627|ref|YP_005920926.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002627|ref|YP_005920926.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002627|ref|YP_005920926.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002627|ref|YP_005920926.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002627|ref|YP_005920926.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2252.47
//
Query:       gi|386002628|ref|YP_005920927.1|  [L=187]
Description: hypothetical protein Mhar_1948 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1104.42
//
Query:       gi|386002629|ref|YP_005920928.1|  [L=112]
Description: Nitrogen regulatory protein P-II [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-36  124.3   0.1    2.8e-36  124.2   0.1    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.2   0.1   1.6e-40   2.8e-36       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 1.6e-40
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       +eaiirpe+l++v+e+L+k g++g+++te+kGrG+qkg     r   y+ve+lpkvkle+vv+d d++++v+ i++a
  gi|386002629|ref|YP_005920928.1|   4 VEAIIRPERLSAVREVLDKNGFPGMSATEIKGRGRQKGVSLQWRAGDYKVEFLPKVKLEVVVEDGDADRIVDLICDA 80 
                                       79*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tge GDGkiFv+pv +v+r+rt+
  gi|386002629|ref|YP_005920928.1|  81 AHTGEAGDGKIFVYPVVDVVRVRTK 105
                                       ***********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 610.84
//
Query:       gi|386002630|ref|YP_005920929.1|  [L=454]
Description: Ammonium transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     4e-115  384.7  39.8   5.1e-115  384.4  39.8    1.1  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.4  39.8  2.8e-119  5.1e-115       1     399 []      64     453 ..      64     453 .. 0.99

  Alignments for each domain:
  == domain 1  score: 384.4 bits;  conditional E-value: 2.8e-119
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-......TT CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign......lg 71 
                                       a++l+saalv++m +g++l+++g+vr+kn++++++ ++  ++ ++l+++l+Gy+lafg +  v+g+ig       +g
  gi|386002630|ref|YP_005920929.1|  64 AWVLFSAALVLLMIPGVGLFYGGMVRKKNAISTMIFSFAIMGTISLQWILLGYTLAFGPD--VGGVIGGldhlglRG 138
                                       79********************************************************99..******99**99999 PP

                                       TTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--. CS
                   Ammonium_transp  72 lsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvli 148
                                       ++  +++ ++++++ f++fq++fa++++++++g+ +erikfs++l+fs+ ++tlvy p+ahwvwg gg+l+++gvl 
  gi|386002630|ref|YP_005920929.1| 139 VGMEAMEGQSIPALTFMIFQAMFAVITVSLITGSYVERIKFSSFLVFSLAWATLVYDPIAHWVWG-GGFLSEMGVL- 213
                                       9999*************************************************************.**********. PP

                                       -SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHH CS
                   Ammonium_transp 149 DfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaav 225
                                       DfAg++vVH+ +gv++La+a+v+g r+g +    + +++hn+p +vlG+ lLwfgWfgFNaGsal+a+++a++ a+v
  gi|386002630|ref|YP_005920929.1| 214 DFAGGIVVHISAGVSALAIAMVIGARRGFG---RDPMEPHNIPTTVLGASLLWFGWFGFNAGSALAADGIAAN-AFV 286
                                       ****************************99...899*************************************.*** PP

                                       HHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC- CS
                   Ammonium_transp 226 tTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkid 302
                                       +T+++aaa+a t++++s+ +   ++ lg++ G++AGl+AiT+a+++v+p++A+ iG+ A+++ ++++ +++   k+d
  gi|386002630|ref|YP_005920929.1| 287 ATNTSAAAAATTWMILSWRD-RAPSALGIVTGAVAGLAAITPAAGFVTPIAAVPIGVGAAIVGYYAILFIRGGKKVD 362
                                       *******************9.99****************************************************** PP

                                       CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB CS
                   Ammonium_transp 303 DsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLr 379
                                       Dsldv+a Hg+g++wG++a+gifa         ++gll g+ +ql vq+++++++ +y+fvvt+ +++ +++++gLr
  gi|386002630|ref|YP_005920929.1| 363 DSLDVLACHGIGSTWGVVATGIFASIG------ATGLLAGNPSQLAVQAAAAAFVWIYSFVVTFGIAKAVDAAMGLR 433
                                       *************************98......579***************************************** PP

                                       --HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 380 vseeeeevglDvaehgetay 399
                                       v  +ee vglD+++hge ay
  gi|386002630|ref|YP_005920929.1| 434 VGTDEEAVGLDISQHGEGAY 453
                                       *****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2812.93
//
Query:       gi|386002631|ref|YP_005920930.1|  [L=503]
Description: Glutamine synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   9.6e-128  426.0   0.0   1.1e-127  425.7   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
      1e-31  108.5   0.0    1.5e-30  104.7   0.0    2.6  2  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.34   10.8   0.0    1.9  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.0  1.9e-131  1.1e-127       2     345 .]     166     499 ..     165     499 .. 0.97

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 1.9e-131
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBH.CCCCCTCCHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsv.apvdeaedlrre 77 
                                       +dPR+ lkr la l+e+G++++vgpElE+f f++++ +e                 +kggyf+  +++d+a++lrr+
  gi|386002631|ref|YP_005920930.1| 166 GDPRYALKRNLAALKEMGYDYYVGPELEYFYFKDDKGTE---------------ILDKGGYFDAmTTMDAASNLRRD 227
                                       69*******************************998744...............5789****961667899****** PP

                                       HHHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEE CS
                        Gln-synt_C  78 ivealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhl 154
                                        + +le++gi+ve shhEva++Q+Ei+l++++alk+aD v+t++ vvke+A++hg++atFmpKp++g+nG+gmHvh+
  gi|386002631|ref|YP_005920930.1| 228 TILTLESMGINVEYSHHEVAPSQHEIDLRYQEALKMADIVMTYRIVVKEIAQQHGYYATFMPKPIFGENGTGMHVHQ 304
                                       ***************************************************************************** PP

                                       EEEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE- CS
                        Gln-synt_C 155 SlwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa 231
                                       S++ k ++n+f+d++d y+ls++++h+i+Gllk a+ +ta+t+++vnSYkRlvpgyeaPv+++w+ rNRsal+R+p+
  gi|386002631|ref|YP_005920930.1| 305 SIF-KGKRNAFFDPGDGYHLSDFGKHYIAGLLKNAPVITAVTNQWVNSYKRLVPGYEAPVYISWARRNRSALVRMPM 380
                                       ***.999********************************************************************** PP

                                       ...TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHH CS
                        Gln-synt_C 232 ...skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlea 303
                                          +ke+a+rvE+R+pd+ aNPYLa++++laAg+dG++nk+e++epve+d+++++++e+   gi++lP sl eAl  
  gi|386002631|ref|YP_005920930.1| 381 ykpGKENATRVEYRSPDPGANPYLAFSVMLAAGMDGVKNKYELPEPVERDIFKMTEAEKekVGIRSLPGSLIEALML 457
                                       *999****************************************************9998899************** PP

                                       HHCSHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 304 leedellkevlgeevieaylalkraEleeleeevsdwelery 345
                                        e+++l++e+lg++++ +++a k+ E++e+++ vs+we+e+y
  gi|386002631|ref|YP_005920930.1| 458 TEKSDLIREALGDHIFTNFIASKKVEWDEFRTDVSRWEIEKY 499
                                       ***************************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   2.6e-34   1.5e-30       2      83 .]      77     159 ..      76     159 .. 0.98
   2 ?    0.5   0.0     0.083     5e+02      29      55 ..     438     465 ..     414     490 .. 0.80

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 2.6e-34
                                       --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEEE CS
                        Gln-synt_N   2 vkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktarv 76 
                                       vkfv+l+FtDi g +k+++i+ +el e a+eeg++FDGSsi+gfa+ieeSDm+ kPd++t++i+P+r+++  ++ r+
  gi|386002631|ref|YP_005920930.1|  77 VKFVRLWFTDILGLPKSFAISPSEL-EGAFEEGMGFDGSSIQGFARIEESDMVAKPDPETFTILPWRAKEgqNVGRM 152
                                       8************************.******************************************99999**** PP

                                       EEEEE-T CS
                        Gln-synt_N  77 icdvydp 83 
                                       +cd+++p
  gi|386002631|ref|YP_005920930.1| 153 FCDILEP 159
                                       ****987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.083
                                       HTTTT-E.EEETTSSTTT------EEEE CS
                        Gln-synt_N  29 daleegv.sFDGSsiegfaeieeSDmlL 55 
                                       +  + g+ s+ GS ie     e+SD++ 
  gi|386002631|ref|YP_005920930.1| 438 EKEKVGIrSLPGSLIEALMLTEKSDLIR 465
                                       45567888999**************985 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.6e-05      0.34       4      86 ..      66     139 ..      63     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.6e-05
                                       .......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-G CS
                      Gln-synt_N_2   4 eavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpdP 80 
                                        +v e +e k v+++++ ++d  G+ +  a++ ++Le  + +G+G+    ++++    i+e++ ++        pdP
  gi|386002631|ref|YP_005920930.1|  66 DKVFEAIESKGVKFVRLWFTDILGLPKSFAISPSELEGAFEEGMGFDG--SSIQGFARIEESDMVA-------KPDP 133
                                       6899*****************************************964..3445555555544332.......3555 PP

                                       GG-EEE CS
                      Gln-synt_N_2  81 asaval 86 
                                        ++  l
  gi|386002631|ref|YP_005920930.1| 134 ETFTIL 139
                                       555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 3338.85
//
Query:       gi|386002632|ref|YP_005920931.1|  [L=603]
Description: translation initiation factor aIF-2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-33  115.7   0.0    5.7e-32  110.8   0.0    2.7  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.4e-29  101.8   5.5    1.4e-29  101.8   5.5    2.8  3  GTP_EFTU_D4  Elongation factor Tu domain 4
      7e-21   74.3   1.8    1.1e-20   73.7   0.1    2.3  3  IF-2         Translation-initiation factor 2
    1.4e-09   38.2   0.0    1.4e-09   38.2   0.0    3.5  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.6e-06   28.1   0.0    5.2e-06   26.5   0.0    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.063   13.3   0.0          3    7.9   0.0    3.0  3  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   1.9e-35   5.7e-32       4     190 ..      22     227 ..      19     231 .. 0.82
   2 ?   -1.6   0.0      0.55   1.7e+03      98     136 ..     336     379 ..     328     440 .. 0.58

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.9e-35
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         ++++ghvDhGKtTL+d++  +t a+ ++g+ ++        ++E    +  +++   +  + +   + +iDtPGH
  gi|386002632|ref|YP_005920931.1|  22 PIVCVMGHVDHGKTTLLDKIRGTTIADGEAGAITQ-----HIGATEIPLAVITEVCGPLFRGDFQIPGLLFIDTPGH 93 
                                       579******************77777666444443.....4455555555444555555555999************ PP

                                       GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHH CS
                          GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveev 146
                                        +F++  +rg + +D+avl+vd++eG +pqt e +++++++++p++v+ NK+Dr+            a+lk + e v
  gi|386002632|ref|YP_005920931.1|  94 HSFTSLRSRGGSLADLAVLIVDVNEGFQPQTIESINILKRYRTPFVVAANKIDRIsgwlpvegaplAATLKAQSERV 170
                                       **************************************************************999977777777777 PP

                                       HHHHHHH....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 147 kqklsrk....eeklekygekge.........kevpvvfgSalkgegvktllealve 190
                                       + +l+++     ++l k+g++++         k++ vv++S+++gegv +ll +l  
  gi|386002632|ref|YP_005920931.1| 171 RGDLDNRiyelVGELYKQGFNSDrydrisdftKNIGVVPISSISGEGVADLLMVLLG 227
                                       7777666555555555665555588889999999*****************988765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.55
                                       EEEEETTTBSTHHHHHHHHHHHHTTTE..EEEEEESCGST...H CS
                          GTP_EFTU  98 vlvvdaveGvepqteevlrlalkegvp..iivfiNKmDrl...k 136
                                       + vv+ +e+v +  +e+   + + ++    + +i K D +   +
  gi|386002632|ref|YP_005920931.1| 336 IRVVSEDEDVDAVAQEIRSELETARIDteNVGVIIKTDTIgslE 379
                                       66777777777777777777777777666777777777774331 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.52   1.5e+03      35      53 ..     238     255 ..     224     258 .. 0.80
   2 ?   -2.0   0.1       1.2   3.5e+03      30      30 ..     352     352 ..     315     377 .. 0.54
   3 !  101.8   5.5   4.7e-33   1.4e-29       1      86 []     475     560 ..     475     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.52
                                       EEEETTE.EEEEEEEEEET CS
                       GTP_EFTU_D4  35 klikedGrevGeilqiqdk 53 
                                       k+ +++G  vG+il+++++
  gi|386002632|ref|YP_005920931.1| 238 KV-RASGPGVGTILEVKEE 255
                                       44.889999******9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                       E CS
                       GTP_EFTU_D4  30 i 30 
                                       i
  gi|386002632|ref|YP_005920931.1| 352 I 352
                                       2 PP

  == domain 3  score: 101.8 bits;  conditional E-value: 4.7e-33
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr 77 
                                       rPg i+i+p++vfr+s+pa+vGv+v+gG+i+ gv+l++edG  +G+++ +q +g+++  a+ G+eva+si+g++vGr
  gi|386002632|ref|YP_005920931.1| 475 RPGMIRIIPDYVFRQSKPAVVGVQVVGGQITNGVTLMREDGAVIGTVKGVQASGENVGSASVGKEVAVSIDGPTVGR 551
                                       7**************************************************************************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       qi+eg+ily
  gi|386002632|ref|YP_005920931.1| 552 QIHEGEILY 560
                                       ********9 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.2   9.5e+03      82     102 ..     163     183 ..     160     185 .. 0.80
   2 !   73.7   0.1   3.6e-24   1.1e-20       6     104 ..     357     454 ..     350     455 .. 0.90
   3 ?   -3.4   0.2       3.6   1.1e+04      35      63 ..     529     562 ..     516     572 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.2
                                       HCCCCCTSEEEEESSHHHHHH CS
                              IF-2  82 klaekegvkirlynvIYklid 102
                                        +a++e v+  l n IY+l+ 
  gi|386002632|ref|YP_005920931.1| 163 LKAQSERVRGDLDNRIYELVG 183
                                       578889999999999999986 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 3.6e-24
                                       HCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST....EEEEEESSSCTH CS
                              IF-2   6 eeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn....aiiigFnvkvsk 78 
                                       e+   ++++++viik+D+ GsleAl   Le+      ++++  ++vG+it++Dv  a+a +    + ++gFnvk+ +
  gi|386002632|ref|YP_005920931.1| 357 ETARIDTENVGVIIKTDTIGSLEALVGELESK-----EIPIHAADVGPITRRDVIRAAAIQdplySAVLGFNVKILP 428
                                       444555699**********************8.....5*******************99555888************ PP

                                       HHHHCCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  79 kakklaekegvkirlynvIYkliddv 104
                                       +a ++++k++v i+l++vIY+l++++
  gi|386002632|ref|YP_005920931.1| 429 DALTEVQKSDVPIFLSEVIYNLLENY 454
                                       ***********************986 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.6
                                       HCTT.....SSTEEEECEEEESS.B-HHHHHHHH CS
                              IF-2  35 ekles....eevkvkvihsgvGa.itesDvelas 63 
                                       e+++s    +ev v++    vG  i+e ++ +++
  gi|386002632|ref|YP_005920931.1| 529 ENVGSasvgKEVAVSIDGPTVGRqIHEGEILYVN 562
                                       4444444456777777777777447777666655 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   4.5e-13   1.4e-09       1      73 [.     259     336 ..     259     337 .. 0.92
   2 ?    3.7   0.2     0.027        82      16      65 ..     333     377 ..     333     384 .. 0.76
   3 ?    0.4   4.1       0.3     9e+02       3      74 .]     494     560 ..     493     560 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.5e-13
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE.........ETTSEEEEEEEESSCCSGSS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea.........vaganaGvivaikgledaii 68 
                                       Gt+ ++++y+G+++ Gd++++   +t k++ivt+i++l+++++  ++           + a+ Gv+v ++++e+a +
  gi|386002632|ref|YP_005920931.1| 259 GTTLDVILYDGEFRSGDTIVV---GTLKEPIVTKIRALLKPRPLSEIRseerflpvkHVAAASGVKVSAPKIESA-L 331
                                       89*******************...467889***********775555599************************8.* PP

                                       TTCEE CS
                       GTP_EFTU_D2  69 vGdtl 73 
                                       +G+t+
  gi|386002632|ref|YP_005920931.1| 332 AGSTI 336
                                       ****8 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.027
                                       TEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
                       GTP_EFTU_D2  16 GdevrilgndtskkeivtrissletfhededeavaganaGvivaikgled 65 
                                       G ++r+  ++ +++   ++  + e   e e+  ++ +n+Gvi++ + + +
  gi|386002632|ref|YP_005920931.1| 333 GSTIRV--VSEDED---VDAVAQEIRSELETARIDTENVGVIIKTDTIGS 377
                                       678888..665566...7777777777888888**********9988876 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.3
                                       EEEEEEEESEEETTEEEEEECTCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskke.ivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       v+++ v+ G++  G +++    d    +  ++++++++++ e++  a +g  + v + ++ +   i  G++l+
  gi|386002632|ref|YP_005920931.1| 494 VVGVQVVGGQITNGVTLMR--ED----GaVIGTVKGVQASGENVGSASVGKEVAVSIDGPTVGRQIHEGEILY 560
                                       6667777777777766655..43....2489**************************9999999999998886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.7e-09   5.2e-06       2     114 .]      24     144 ..      23     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.7e-09
                                       EEEEESTTSSHHHHHHHHHT......STEEESSSTTSSSSEEEEEEE.....ETTEE.......EEEEECGGCSSHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg......ekaivsdkpgtTrdinegrvk.....lkgke.......ielvDtpGliega 60 
                                       v+++G+   GK+tL+ ++ g      e+  ++++ g+T  +     +     +   +       + ++DtpG  +  
  gi|386002632|ref|YP_005920931.1|  24 VCVMGHVDHGKTTLLDKIRGttiadgEAGAITQHIGATEIPLAVITEvcgplF---RgdfqipgLLFIDTPG-HH-- 94 
                                       89****************98333322244556666666666666555444441...044444449*******.44.. PP

                                       HHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  61 seekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                           +++    +  + adl++l+vd++ e+++p+  e  ++l++ + p+++++nk
  gi|386002632|ref|YP_005920931.1|  95 ----SFTSLRSRGGSlADLAVLIVDVN-EGFQPQTIESINILKRYRTPFVVAANK 144
                                       ....2222222222348********87.88*****9*99**99999*****9998 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.001         3       1      33 [.      24      56 ..      24      62 .. 0.87
   2 ?    0.9   0.0      0.14     4e+02      99     113 ..      81      95 ..      75     124 .. 0.87
   3 ?   -0.4   0.0      0.35   1.1e+03      59      81 ..     339     361 ..     305     399 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                      ++v+G++ +GK+++l+++ g  i   +++ +T+
  gi|386002632|ref|YP_005920931.1| 24 VCVMGHVDHGKTTLLDKIRGTTIADGEAGAITQ 56
                                      78******************9998777777776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                       TS-SEEEEE---B-S CS
                         Dynamin_N  99 lvkgltlvDlPGlds 113
                                       + +gl ++D+PG +s
  gi|386002632|ref|YP_005920931.1|  81 QIPGLLFIDTPGHHS 95 
                                       568999******987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.35
                                       T-EB--CHHHHHHHHHHHHHHHT CS
                         Dynamin_N  59 ekkledfsevreeieketekiag 81 
                                        +++ed+++v++ei++e e++  
  gi|386002632|ref|YP_005920931.1| 339 VSEDEDVDAVAQEIRSELETARI 361
                                       56789999999999998887653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 3354.09
//
Query:       gi|386002633|ref|YP_005920932.1|  [L=143]
Description: nucleoside diphosphate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-55  185.1   0.0    6.1e-55  184.9   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9   0.0   3.4e-59   6.1e-55       6     134 ..       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 3.4e-59
                                       EE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHH CS
                               NDK   6 liKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiek 82 
                                       +iKPd+v+rgl+g+i++r+e+kglkiva+km +l ++ a+ehYaeh++kpff +lv+f+tsgp v +v+eg+dai++
  gi|386002633|ref|YP_005920932.1|   1 MIKPDGVQRGLVGRIVQRIEAKGLKIVAMKMRTLPQDVAREHYAEHSQKPFFGDLVSFITSGPSVPMVVEGKDAISE 77 
                                       8**************************************************************************** PP

                                       HHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGG CS
                               NDK  83 vreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeee 134
                                       +r++ Gatnp++a+pgtiR+dfg+++g+N++HgSds+esa+rei+l F e e
  gi|386002633|ref|YP_005920932.1|  78 MRKMNGATNPTKAQPGTIRGDFGLDMGRNVIHGSDSPESAKREIALHFGEAE 129
                                       ************************************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 862.70
//
Query:       gi|386002634|ref|YP_005920933.1|  [L=57]
Description: 50S ribosomal protein L24e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-18   64.5   1.3    8.4e-18   64.4   1.3    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    7.1e-06   25.9   2.2    9.6e-06   25.5   2.2    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
     0.0029   17.7   1.9     0.0038   17.3   1.9    1.1  1  YHS             YHS domain
     0.0054   16.2   4.1     0.0099   15.3   4.1    1.4  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
  ------ inclusion threshold ------
      0.073   11.9   0.1      0.076   11.8   0.1    1.0  1  SerH            Cell surface immobilisation antigen SerH
       0.45   10.4   6.5          1    9.3   6.5    1.5  1  VATC            Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   1.3   2.8e-21   8.4e-18       1      52 [.       1      53 [.       1      56 [. 0.95

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.8e-21
                                      XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTS CS
                    Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWT 52
                                      m+ +kCsF+ +ki+ G+Gk++ ++Dg+v+ F+ssKc ++++   r Pr+++W 
  gi|386002634|ref|YP_005920933.1|  1 MEERKCSFCNRKIEAGTGKIYAKKDGTVYYFCSSKCeKNMIGLGRVPRRVEWA 53
                                      7889********************************778999**********6 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   2.2   3.2e-09   9.6e-06       4      37 ..       4      36 ..       2      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.2e-09
                            zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                      ++C+fC+++i+ ++   ++  +dg v++FCS+ C
  gi|386002634|ref|YP_005920933.1|  4 RKCSFCNRKIEAGT-GKIYAKKDGTVYYFCSSKC 36
                                      69************.79***************99 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.9   1.3e-06    0.0038       6      34 ..       9      37 ..       8      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCk 34
                                      c  k++ ++ + + + +G+ YyFcS +C+
  gi|386002634|ref|YP_005920933.1|  9 CNRKIEAGTGKIYAKKDGTVYYFCSSKCE 37
                                      66778888888889999***********8 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   4.1   3.3e-06    0.0099      14      48 ..       4      41 ..       4      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                            zf-FLZ 14 saCflCkkkLgegk.DiymYrGdka..FCSeeCRqqqi 48
                                      ++C++C++k++ g   iy  +  +   FCS+ C ++ i
  gi|386002634|ref|YP_005920933.1|  4 RKCSFCNRKIEAGTgKIYAKKDGTVyyFCSSKCEKNMI 41
                                      58**********998999988655345******88876 PP

>> SerH  Cell surface immobilisation antigen SerH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.5e-05     0.076     158     192 ..       4      38 ..       1      46 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                              SerH 158 anCaaCattaspkgknvfAnsaGsaCvassasCgs 192
                                        +C+ C+   ++ + +++A ++G+     s+ C+ 
  gi|386002634|ref|YP_005920933.1|   4 RKCSFCNRKIEAGTGKIYAKKDGTVYYFCSSKCEK 38 
                                       56777777777777777777777777777777764 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.5   0.00034         1       4      31 ..       4      36 ..       2      39 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00034
                              VATC  4 lrCsiCgesle...gkvyFek..fdfrYCstkC 31
                                      ++Cs+C++++e   gk+y +k    + +Cs kC
  gi|386002634|ref|YP_005920933.1|  4 RKCSFCNRKIEagtGKIYAKKdgTVYYFCSSKC 36
                                      79*********65557777774445889***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 414.95
//
Query:       gi|386002635|ref|YP_005920934.1|  [L=71]
Description: 30S ribosomal protein S28e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-31  106.3   0.2    6.5e-31  106.1   0.2    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.2   3.6e-35   6.5e-31       3      64 .]       7      68 ..       5      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 3.6e-35
                                      -EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  3 aklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                       ++AeVi+++g+tG++Ge+tq+++++leg++kgrii+Rn++GP+r+GD+L+LlEt+rEA++L
  gi|386002635|ref|YP_005920934.1|  7 GVPAEVIEIIGNTGMHGEATQIKCRILEGSNKGRIITRNCMGPIRMGDVLMLLETAREAKKL 68
                                      689*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 503.27
//
Query:       gi|386002636|ref|YP_005920935.1|  [L=122]
Description: 50S ribosomal protein L7Ae [Methanosaeta harundinacea 6Ac]
Scores for 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-26   89.4   0.3    1.1e-25   89.2   0.3    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    0.00029   20.7   0.0     0.0004   20.2   0.0    1.2  1  PELOTA_1        PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.3   1.2e-29   1.1e-25       4      93 ..      20     109 ..      17     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 1.2e-29
                                       HHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSEC CS
                    Ribosomal_L7Ae   4 eevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpv 80 
                                        e++++a+++g+l++G++e+tka+erg aklv++ edvep+e++++++ lc+ek+ py++vk + e+G ++g ++ +
  gi|386002636|ref|YP_005920935.1|  20 LEAIELARDTGRLKKGTNETTKAIERGVAKLVVVGEDVEPPEIVAHIPPLCEEKKTPYIYVKKQSEIGSACGMRVKS 96 
                                       68999************************************************************************ PP

                                       SEEEEEESTTTHH CS
                    Ribosomal_L7Ae  81 salaikdegdskd 93 
                                       +a+ai ++g+ kd
  gi|386002636|ref|YP_005920935.1|  97 AAVAILEPGKGKD 109
                                       ********98776 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.5e-08    0.0004      17      71 ..      27      83 ..      16      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.5e-08
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                      +d+ + K g  E+T+++ R v + v+v ++ e  + +ah+  L++ek++p+  v+++
  gi|386002636|ref|YP_005920935.1| 27 RDTGRLKKGTNETTKAIERGVAKLVVVGEDVEppEIVAHIPPLCEEKKTPYIYVKKQ 83
                                      688899*********************9988865679************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 858.14
//
Query:       gi|386002637|ref|YP_005920936.1|  [L=267]
Description: hypothetical protein Mhar_1957 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1873.38
//
Query:       gi|386002638|ref|YP_005920937.1|  [L=506]
Description: Dihydropteroate synthase-related protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-09   36.8   0.0      9e-09   35.4   0.0    1.8  1  DUF4346      Domain of unknown function (DUF4346)
      1e-08   35.2   0.4    4.1e-08   33.2   0.1    2.1  2  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0     1e-12     9e-09      61     118 .]     444     498 ..     424     498 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1e-12
                           DUF4346  61 kreaekvyrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                        r+ + +  g +a+ l  +i+ +     vt+ldhaaYlGRel rae+a+  g++Y qD
  gi|386002638|ref|YP_005920937.1| 444 VRHDAVTLVGTSARGLLGEIVSR---GLVTRLDHAAYLGRELERAEIAIGLGRSYSQD 498
                                       56666777888888887777765...67*****************************9 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.21   1.8e+03      55      77 ..      75      97 ..      73      98 .. 0.81
   2 !   33.2   0.1   4.6e-12   4.1e-08      18     123 ..     148     242 ..     141     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind 55 eeelervvpvlealrdeadvpis 77
                                      + +l+rv+p+l++++  ++vp +
  gi|386002638|ref|YP_005920937.1| 75 AVDLRRVLPLLDEVELSTTVPAC 97
                                      5799********99887777765 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 4.6e-12
                                       THHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHC.TSEEEEE-S-HHHHHHHHHTT CS
                       Pterin_bind  18 edldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdea.dvpisiDttkaevaeaAlkag 93 
                                       +d ++  +++r   +eGAd++D+g              +e + v+  +  +++ea  +p+s+D+ +++ ++a+++ag
  gi|386002638|ref|YP_005920937.1| 148 LDDAALAEKVRHYEREGADMIDLGIPLD----------AEPAAVARAVI-VAKEAtSLPVSVDSLRPDLLKAGIEAG 213
                                       4667778999*************97544..........44455555554.44456589******************* PP

                                       SEEEEETTTTSSSTTHHHHHHHHT-EEEEE CS
                       Pterin_bind  94 adivNdvsgeerdpkmlelvaeagaavvvm 123
                                        d+v +  g +  +++ +l+a ag++ vv+
  gi|386002638|ref|YP_005920937.1| 214 CDLVLSLDGSN-LEEVGPLAASAGVPAVVL 242
                                       ***********.9***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 3192.56
//
Query:       gi|386002639|ref|YP_005920938.1|  [L=112]
Description: hypothetical protein Mhar_1959 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 769.63
//
Query:       gi|386002640|ref|YP_005920939.1|  [L=164]
Description: hypothetical protein Mhar_1960 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1005.90
//
Query:       gi|386002641|ref|YP_005920940.1|  [L=154]
Description: hypothetical protein Mhar_1961 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-38  130.8   0.0    3.2e-38  130.6   0.0    1.0  1  DUF2299   Uncharacterized conserved protein (DUF2299)


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0   1.8e-42   3.2e-38       2     138 .]      13     149 ..      12     149 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 1.8e-42
                                       HHHHHHHTT-EEEE---TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHH CS
                           DUF2299   2 ikeWLkeeGlkveevpdanaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkefls 78 
                                       i++W++++G++++e +   ++f+++ ++ ++  +++++i+p++ +++vvv+++v+vs +h++alss++ ++r+ef++
  gi|386002641|ref|YP_005920940.1|  13 IHNWMADRGYFIKEGDFIGYRFEFIGKFGND--THFSIIQPESLPRAVVVVSNVSVSAAHYDALSSMELKDREEFIW 87 
                                       89****************************9..******************************************** PP

                                       HHHHHHTTTT-EEEEE-TTS--...-EEEEEEEEEGGG--HHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2299  79 elkrdLlrlcvdfqlipqdeel..pqsiqvskeiykdgltknelldavkrvrnakllviwll 138
                                       +lkr++++l+ +f++ p+ e+l  p+siq+skei  d+lt+ +l++av++ ++++l+viw++
  gi|386002641|ref|YP_005920940.1|  88 DLKREFIFLPSSFTFDPSFEQLgiPKSIQFSKEISYDELTEGRLHEAVDYNSRCVLWVIWVF 149
                                       ************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1012.60
//
Query:       gi|386002642|ref|YP_005920941.1|  [L=471]
Description: Amidophosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-22   79.7   0.0    2.4e-22   79.1   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    8.9e-22   77.7   0.0      2e-21   76.6   0.0    1.6  1  GATase_6      Glutamine amidotransferase domain
    3.2e-08   32.8   0.0    1.2e-06   27.6   0.0    2.2  2  GATase_4      Glutamine amidotransferases class-II
    1.6e-05   24.4   0.1    3.4e-05   23.4   0.1    1.5  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0069   15.1   0.3        2.3    6.8   0.1    2.2  2  GATase_2      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   6.7e-26   2.4e-22      10     122 ..      88     207 ..      77     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 6.7e-26
                          GATase_7  10 eagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnG 76 
                                        +++QP++   ++ +++i++nG ++N  +l+eeLea+g  f+++sDtev+++l+ +         e ++e++++  G
  gi|386002642|ref|YP_005920941.1|  88 LKNSQPILVkYKESSVAIAHNGNLVNAGKLKEELEAEGEVFHSTSDTEVMARLFVRammvredpaEAVREIMRKAVG 164
                                       5689**998789999**************************************9889******************** PP

                          GATase_7  77 mfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       +++++++  ++  +++aRD+lGikPL +g+++ + +++aSe  a+ 
  gi|386002642|ref|YP_005920941.1| 165 SYSIVLLMGNT--VIAARDPLGIKPLCVGKTD-TDVIVASESAAID 207
                                       ********999..******************6.79******99985 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   5.6e-25     2e-21      12     134 .]      71     202 ..      50     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 5.6e-25
                          GATase_6  12 devalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.... 81 
                                       + ++++HvR +++g++   ++ qP+  + +++ ++++hNG   n+++l+eel+a +g  f s+sDtev+++l+    
  gi|386002642|ref|YP_005920941.1|  71 GPTGVGHVRYSTTGES-ALKNsQPIlvKYKESSVAIAHNGNLVNAGKLKEELEA-EGEVFHSTSDTEVMARLFvram 145
                                       4589***********9.55555***87777788*********************.****************998877 PP

                          GATase_6  82 ..eelG....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                         +e +     e +++++G +++  +    nt+i ard lg+kpl+++ ++  +++ase
  gi|386002642|ref|YP_005920941.1| 146 mvREDPaeavREIMRKAVGSYSI--VLLMGNTVIAARDPLGIKPLCVGKTDTDVIVASE 202
                                       77333322334455566665544..44569999999**********************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 !   27.6   0.0   3.4e-10   1.2e-06      10     118 ..      18     121 ..       8     179 .. 0.75
   2 ?    3.0   0.0     0.011        40     221     256 ..     194     233 ..     188     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.4e-10
                          GATase_4  10 nvptdisfsftgfaarggltdahadGwGiafyegkaarvfkdpepsaesplaelvreypiksk...nvvaHiRkatq 83 
                                       nv  +i + + ++++rg++        Gi+ y+gk +r+ k     a   +ae+ ++  i++      v H+R  t+
  gi|386002642|ref|YP_005920941.1|  18 NVAKSIYYALYALQHRGQE------SAGISVYDGKVVRTHK-----AMGLVAEVFNNPRIEALggpTGVGHVRYSTT 83 
                                       5666777777777777766......5699999999999755.....5678999998877887533378********* PP

                          GATase_4  84 GevklenthpFvRelwgrewifAHnGdlke...ykpkl 118
                                       Ge +l+n++p   ++++ +  +AHnG+l +   +k++l
  gi|386002642|ref|YP_005920941.1|  84 GESALKNSQPILVKYKESSVAIAHNGNLVNagkLKEEL 121
                                       ****************************6622334444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.011
                          GATase_4 221 drvavvatepLt....rdetWkklepGellvfrdGalvat 256
                                       d+ ++va+e       + +  ++++pGe++v +dG+++  
  gi|386002642|ref|YP_005920941.1| 194 DTDVIVASESAAidtlNGKLVRDVRPGEMVVAKDGDVRFY 233
                                       556666666655333344567899************9876 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   9.4e-09   3.4e-05      15     120 ..     270     379 ..     260     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.4e-09
                                       EEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE...............EE-- CS
                      Pribosyltran  15 varlaaeileeyngkpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdes.......rlle 83 
                                       + +++ae ++    + d+v +++  G++fa  ++++ ++++   + k +y + +   ++ +   e+       +  +
  gi|386002642|ref|YP_005920941.1| 270 IGSILAEEHSL---EADTVTPVPDSGITFAIGYHQRSNIKYReCLMKNRYIGRTFI-MPGQELREIavrlkmnTIRP 342
                                       55566666666...8999*******************9997735555555555554.44555555569999999*** PP

                                       --TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  84 dpagkkVliVDDildtGgTllaalelLkekgpeevri 120
                                       +++g+++++VDD +  G+T +++++ +++ g++ev++
  gi|386002642|ref|YP_005920941.1| 343 NIEGNRIIMVDDSIVRGTTSRRIVDMVRSTGAKEVHV 379
                                       **********************************985 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0   0.00093       3.3      10      89 ..      12      90 ..       5     115 .. 0.78
   2 !    6.8   0.1   0.00064       2.3     330     394 ..     164     225 ..     155     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00093
                                      SS--BSHHHHHHHHHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEEEE-SSHHHHHH CS
                          GATase_2 10 kgkkshkivekalealenleHRGavgadektGDGaGillqiPdeflrkeakekgielpeageyavgmlflpkdeekaee 88
                                      + ++ +++ ++   al  l+HRG  +a  +  DG  + +++   ++++++++  ie    g ++vg++  ++  e+a +
  gi|386002642|ref|YP_005920941.1| 12 SADPCRNVAKSIYYALYALQHRGQESAGISVYDGKVVRTHKAMGLVAEVFNNPRIEALG-GPTGVGHVRYSTTGESALK 89
                                      45567888899999************************************999999865.8999998876665544443 PP

                                      H CS
                          GATase_2 89 a 89
                                       
  gi|386002642|ref|YP_005920941.1| 90 N 90
                                      3 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00064
                                       SSEEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEE CS
                          GATase_2 330 GPalivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllv 394
                                       G  +iv+  G++v a  D  G++P     t+   v++asE+  +d  + ++v+   ++PG+m++ 
  gi|386002642|ref|YP_005920941.1| 164 GSYSIVLLMGNTVIAARDPLGIKPLCVGKTD-TDVIVASESAAIDTLNGKLVRD--VRPGEMVVA 225
                                       556799999***************8776665.55789********999999986..56***9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3102.50
//
Query:       gi|386002643|ref|YP_005920942.1|  [L=60]
Description: 50S ribosomal protein L37e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-23   81.4  12.6    4.1e-23   81.3  12.6    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.033   14.2   0.5      0.035   14.1   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.25   11.0   1.3        0.4   10.3   1.3    1.4  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
       0.52    9.8   4.3        2.3    7.7   4.1    1.9  2  zf-ribbon_3     zinc-ribbon domain
        0.6    9.7   4.5        2.5    7.7   0.3    2.4  2  zn-ribbon_14    Zinc-ribbon
        3.4    7.7   6.5        4.8    7.3   0.5    2.2  2  YhfH            YhfH-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3  12.6   1.4e-26   4.1e-23       1      51 [.       2      52 ..       2      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.4e-26
                    Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsa 51
                                      tkGt+s+Gkr +kktH++CrrCgk s+++++ktCascG+ +s++lr y W++
  gi|386002643|ref|YP_005920942.1|  2 TKGTPSMGKR-HKKTHVKCRRCGKVSFNYRTKTCASCGFgRSKRLRGYVWQK 52
                                      8*********.999************************************97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   1.2e-05     0.035      66      98 ..      12      43 ..       4      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      EE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 66 evpvkvrCreCgkefeleekalrCpkCgsadve 98
                                      +++ +v+Cr+Cgk    + ++ +C +Cg  + +
  gi|386002643|ref|YP_005920942.1| 12 HKKTHVKCRRCGKVSF-NYRTKTCASCGFGRSK 43
                                      56889*******5444.434568****976655 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00013       0.4       2       8 ..       3       9 ..       3       9 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                         MraY_sig1 2 kGTPTMG 8
                                     kGTP+MG
  gi|386002643|ref|YP_005920942.1| 3 KGTPSMG 9
                                     8*****9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3    0.0041        12      16      24 ..      16      24 ..       9      26 .. 0.62
   2 ?    7.7   4.1   0.00078       2.3       2      24 ..      16      39 ..      15      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0041
                       zf-ribbon_3 16 dnvCpyCGt 24
                                       ++C  CG+
  gi|386002643|ref|YP_005920942.1| 16 HVKCRRCGK 24
                                      566777775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00078
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGt 24
                                      +v+C +CG+     + ++C++CG 
  gi|386002643|ref|YP_005920942.1| 16 HVKCRRCGKvSFNYRTKTCASCGF 39
                                      68999****769999********5 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3   0.00084       2.5       2      10 ..      18      26 ..      17      29 .. 0.87
   2 ?    3.6   0.4     0.016        47       2       8 ..      33      39 ..      32      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00084
                      zn-ribbon_14  2 kCerCGylS 10
                                      kC+rCG +S
  gi|386002643|ref|YP_005920942.1| 18 KCRRCGKVS 26
                                      8*****998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.016
                      zn-ribbon_14  2 kCerCGy 8 
                                      +C  CG+
  gi|386002643|ref|YP_005920942.1| 33 TCASCGF 39
                                      8*****8 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.6     0.014        41      15      22 ..      18      25 ..      13      29 .. 0.87
   2 ?    7.3   0.5    0.0016       4.8      13      20 ..      31      38 ..      25      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                              YhfH 15 kCteCGke 22
                                      kC  CGk+
  gi|386002643|ref|YP_005920942.1| 18 KCRRCGKV 25
                                      7*****95 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                              YhfH 13 kKkCteCG 20
                                      +K+C++CG
  gi|386002643|ref|YP_005920942.1| 31 TKTCASCG 38
                                      7******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 405.23
//
Query:       gi|386002644|ref|YP_005920943.1|  [L=72]
Description: Small nuclear ribonucleoprotein, LSM family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-24   83.0   0.2    9.2e-24   82.9   0.2    1.0  1  LSM       LSM domain
     0.0022   18.1   0.0     0.0023   18.0   0.0    1.1  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.2     1e-27   9.2e-24       3      67 .]       9      72 .]       7      72 .] 0.97

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1e-27
                                      HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                      l++++n  v+v+lk+gr +rG L+g+D +mNlvL+++ee+++++  ++klg+v++RG+n+v+is+
  gi|386002644|ref|YP_005920943.1|  9 LNESLNGPVIVKLKDGRAFRGELQGYDIHMNLVLDNTEEIREGE-DSKKLGTVVVRGDNVVYISP 72
                                      8999**************************************99.******************96 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-07    0.0023      15      55 ..      16      55 ..       4      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-07
                                      EEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS..... CS
                            SM-ATX 15 evevtvknGevyeGifstvslekdfsvvLkmarkvkk.ansk 55
                                      +v v++k+G  ++G +++++    +++vL+++ ++++ ++sk
  gi|386002644|ref|YP_005920943.1| 16 PVIVKLKDGRAFRGELQGYDI--HMNLVLDNTEEIREgEDSK 55
                                      699******************..**************32222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 452.21
//
Query:       gi|386002645|ref|YP_005920944.1|  [L=159]
Description: PUA domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-18   64.4   0.6    9.8e-18   63.9   0.6    1.3  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.036   14.4   0.0       0.07   13.4   0.0    1.5  1  DUF1947   Domain of unknown function (DUF1947)
      0.039   14.2   0.0      0.056   13.7   0.0    1.2  1  UPF0113   UPF0113 PUA domain
       0.25   12.0   0.1       0.97   10.2   0.1    1.8  1  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.6   2.2e-21   9.8e-18       3      73 ..      80     150 ..      78     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.2e-21
                                       EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                       vvvd gAv+++ +ga+++apG+ve ++++ +gd V+iv e  ++++avG+a++ + e++   g+ ++ +++v
  gi|386002645|ref|YP_005920944.1|  80 VVVDSGAVRFIINGADVMAPGIVESDEKIAPGDPVVIVEERhRKPIAVGIALLPGPEMRGS-GKAVRSVHHV 150
                                       8***************************************88****************877.6777777765 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.6e-05      0.07       1      55 [.       5      62 ..       5      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                      --EE--HHHHHHHHHHHHTTT---TT--...-EEEE-S.S-EEEEETTEEEEEE.SSS CS
                           DUF1947  1 kRHfLSkKeakeileklkekyisislesdk.iEieeek.keklYlingvpilfe.eek 55
                                      +RH L+  e+k+i + ++ + ++ s      +E++e++ ++ l+l  g+p+++  e++
  gi|386002645|ref|YP_005920944.1|  5 SRHHLKGSESKRIQSAIEPFLEDPSPLRGLtLEVAETDqDFDLILLKGRPVFMMvEDR 62
                                      6********************9987766666*****9989************988876 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.056       2      54 ..      80     133 ..      79     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvV.lnengeplGiGkirkd 54 
                                       vvv+  a + ++ G dv+  +i++ +e++  ++ vv+     ++p+++G++   
  gi|386002645|ref|YP_005920944.1|  80 VVVDSGAVRFIINGADVMAPGIVESDEKIAPGDPVVIvEERHRKPIAVGIALLP 133
                                       5677667777788*****************777666515666899999998654 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00022      0.97       6      26 ..       2      22 ..       1      70 [. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                           Pre-PUA  6 kvksntqlksSdrrkLrakll 26
                                      k+ks+++lk+S+ +++++ + 
  gi|386002645|ref|YP_005920944.1|  2 KIKSRHHLKGSESKRIQSAIE 22
                                      79***************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1015.28
//
Query:       gi|386002646|ref|YP_005920945.1|  [L=300]
Description: membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0078   16.1  15.1     0.0078   16.1  15.1    3.0  3  DUF4013         Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
      0.035   13.7  19.7       0.12   12.0   8.9    2.6  2  SUR7            SUR7/PalI family
       0.77    8.7   3.9        1.4    7.8   1.4    2.3  2  SHR3_chaperone  ER membrane protein SH3
       0.84    9.1   0.0       0.84    9.1   0.0    3.7  3  DUF3169         Protein of unknown function (DUF3169)
        3.8    7.6  12.3         10    6.2   1.7    3.2  3  DHHC            DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  15.1   2.2e-06    0.0078      38     165 ..       5     154 ..       2     158 .. 0.73
   2 ?    2.3  15.0     0.036   1.3e+02      90     164 ..     174     243 ..     149     247 .. 0.70
   3 ?   -0.8   0.3      0.34   1.2e+03      87     114 ..     254     273 ..     240     290 .. 0.43

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                           DUF4013  38 ddwgkllvdGlk......afvvslvYllipliialltllvalaslaagdsaagallvlall................ 92 
                                       +d+g+ll++G+        ++v +v++++ +++ l++ +v+++++  ++s+   +  ++ l                
  gi|386002646|ref|YP_005920945.1|   5 EDIGTLLRRGFEtwrgnlNLAVPFVLTIVAIML-LTVAMVLAVMYPLITSSPDLFSTAGDLedpqelmeflqgagnl 80 
                                       489999999999777775477777777666666.5555555555555555555555555557777777777777777 PP

                           DUF4013  93 ..glllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigivlsllail 165
                                         +++++l+++l+++l ++ +++++++ +a+  +ls    +k +++  ++ ++++++a ++++v+++v  l+++l
  gi|386002646|ref|YP_005920945.1|  81 glAAAIILIAILAMAL-LSSFFTAGAIGMAKVATLSGKTTLKDMWSSGRRHFIRLFLAEVVMMVVILVGVLVLTL 154
                                       6544444445566666.888889***********************99988899999999999998887777765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.036
                           DUF4013  90 allglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigivlsllai 164
                                       +  +l +all ++++l+ +++ll +   +++ +g l+    +k+ +++ +++  ++++++++++++++++++la+
  gi|386002646|ref|YP_005920945.1| 174 L--ILWIALL-IAFSLI-ISILLAMVPYALVVDG-LGPIGAIKAGIAFFRSNKMDVFLIWLVVMAVSVAIQFLAA 243
                                       2..2222222.334445.7888878888888888.999999********9999******************9975 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.34
                           DUF4013  87 lvlallglllalllvllllllfglllpv 114
                                       ++  l g++ +l+        ++ l++v
  gi|386002646|ref|YP_005920945.1| 254 AFSSLSGVVSILI--------VAPLTTV 273
                                       3333333333333........2222222 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0   0.00034       1.2     115     177 ..      27     117 ..      17     137 .. 0.67
   2 ?   12.0   8.9   3.2e-05      0.12     113     208 ..     139     236 ..     127     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00034
                              SUR7 115 lfilhiialvlsfislvvgllaic..vspdnsr...........l...............lsflnlllsvlsflatl 163
                                        f+l i+a++l ++++v++++  +  +spd  +           +               +++  l +++ls ++t+
  gi|386002646|ref|YP_005920945.1|  27 PFVLTIVAIMLLTVAMVLAVMYPLitSSPDLFStagdledpqelMeflqgagnlglaaaiILIAILAMALLSSFFTA 103
                                       699***************99988634233333344444444444044444444444444488888899999999999 PP

                              SUR7 164 laalldtllfvfvr 177
                                        a +++ ++    +
  gi|386002646|ref|YP_005920945.1| 104 GAIGMAKVATLSGK 117
                                       99998766665555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.2e-05
                              SUR7 113 kalfilhiialvlsfislvvgllaicvspdnsrllsflnlllsvlsflatllaalldtllfvfvrkkin...lkefg 186
                                        ++++++++++   ++ ++  l++ +    n++ +  l l++++l++++++++ ll+++ +++v   +    + ++g
  gi|386002646|ref|YP_005920945.1| 139 VVMMVVILVGVLVLTLPFIADLMGAF--ETNEPEFGPLILWIALLIAFSLIISILLAMVPYALVVDGLGpigAIKAG 213
                                       5799**********************..888888999*************************9999999999999** PP

                              SUR7 187 ikaslglkflaf.aWlalaaall 208
                                       i ++ + k+  f +Wl+++a+ +
  gi|386002646|ref|YP_005920945.1| 214 IAFFRSNKMDVFlIWLVVMAVSV 236
                                       ********988526777766544 PP

>> SHR3_chaperone  ER membrane protein SH3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.056     2e+02       9      76 ..      35     101 ..      28     112 .. 0.80
   2 ?    7.8   1.4    0.0004       1.4     114     148 ..     119     152 ..      95     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.056
                    SHR3_chaperone   9 liigstsFflGvlfanfpyDynlLwssesteeafdaalehykflhaspplikrilhiviglgliglli 76 
                                       + + +++ +l+v++  ++   + L+s++   e  ++++e+++   +   +   il ++++++l+ ++ 
  gi|386002646|ref|YP_005920945.1|  35 IMLLTVAMVLAVMYPLITS-SPDLFSTAGDLEDPQELMEFLQGAGNLGLAAAIILIAILAMALLSSFF 101
                                       5566677778888876654.567899999999999999999999999999999999999999998875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0004
                    SHR3_chaperone 114 vtegawgevdredslkvlaasntilalvLvGVlvL 148
                                       + ++ w+  +r++ ++   a  ++++++LvGVlvL
  gi|386002646|ref|YP_005920945.1| 119 TLKDMWS-SGRRHFIRLFLAEVVMMVVILVGVLVL 152
                                       3444444.5888999999999*************9 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.2  10.8         5   1.8e+04     211     220 ..      87      96 ..      13     153 .. 0.58
   2 ?   -8.3  11.3         5   1.8e+04     112     112 ..     149     149 ..      84     203 .. 0.47
   3 ?    9.1   0.0   0.00023      0.84     102     173 ..     225     296 ..     218     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: -8.2 bits;  conditional E-value: 5
                           DUF3169 211 llillivlfl 220
                                       +li++++++l
  gi|386002646|ref|YP_005920945.1|  87 ILIAILAMAL 96 
                                       2222222222 PP

  == domain 2  score: -8.3 bits;  conditional E-value: 5
                           DUF3169 112 i 112
                                       +
  gi|386002646|ref|YP_005920945.1| 149 V 149
                                       1 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00023
                           DUF3169 102 iglilssvslilsfllilasyslkiyeeesssklvlifliaivlfliilflkiiiqvrivklikkmnPekkg 173
                                       + ++l+++++ +++ +++a +s++ +++++ s+l+ ++ i iv+ l+++ ++ ++ +r  k+  +  P++ g
  gi|386002646|ref|YP_005920945.1| 225 FLIWLVVMAVSVAIQFLAAPFSGSEAASAAFSSLSGVVSILIVAPLTTVWWTRLYMTRAGKMAEAETPRDEG 296
                                       5689999999999***********99999999999999**********************999998887766 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5     0.003        11      51     129 ..      28     121 ..      15     126 .. 0.54
   2 ?    6.2   1.7    0.0028        10      49     111 ..     133     193 ..     127     203 .. 0.67
   3 ?    1.2   0.1       0.1   3.7e+02      55     120 ..     226     280 ..     216     294 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.003
                              DHHC  51 Fllfllylllllilalvlllialvklveeekkseflavtllkk................llsilllvlsllfllllg 111
                                       F+l +++++ll++ ++++ ++ l++  ++   +     + + +                ++ i +l+++ll  ++++
  gi|386002646|ref|YP_005920945.1|  28 FVLTIVAIMLLTVAMVLAVMYPLITSSPDLFSTAGDLEDPQ-ElmeflqgagnlglaaaIILIAILAMALLSSFFTA 103
                                       65555555555555555444444444444433333322222.25677778899877665555555555566666666 PP

                              DHHC 112 llllfhlylilrnlTtie 129
                                         + +  + +l ++Tt  
  gi|386002646|ref|YP_005920945.1| 104 GAIGMAKVATLSGKTTLK 121
                                       666666666666666655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0028
                              DHHC  49 kyFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllg 111
                                       + Fl+ +++++++l+ +lvl+l ++ +l+   +++e +  +l+  l+  ll+++sl++ +ll+
  gi|386002646|ref|YP_005920945.1| 133 RLFLAEVVMMVVILVGVLVLTLPFIADLMGAFETNEPEFGPLI--LWIALLIAFSLIISILLA 193
                                       6788888888888888888999999998888888877766553..344444444444444443 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.1
                              DHHC  55 llylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlyl 120
                                       l++l+++++ +   ++++l   ++ +++ ++        ++s l+ v+s+l+++ l+ +  ++ly+
  gi|386002646|ref|YP_005920945.1| 226 LIWLVVMAVSV---AIQFLAAPFSGSEAASA--------AFSSLSGVVSILIVAPLTTVWWTRLYM 280
                                       33333332222...22223333333322222........223444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 1981.23
//
Query:       gi|386002647|ref|YP_005920946.1|  [L=69]
Description: hypothetical protein Mhar_1967 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.23   11.5   0.5       0.23   11.5   0.5    1.9  2  Bee_toxin  Honey bee toxin


Domain annotation for each model (and alignments):
>> Bee_toxin  Honey bee toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2     0.091   1.6e+03       8      20 ..      21      33 ..      16      40 .. 0.70
   2 ?   11.5   0.5   1.3e-05      0.23      10      27 ..      43      60 ..      40      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.091
                         Bee_toxin  8 iflFlsviLitsY 20
                                      +f+Fl   L   Y
  gi|386002647|ref|YP_005920946.1| 21 LFFFLVYALYLDY 33
                                      6899876665555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.3e-05
                         Bee_toxin 10 lFlsviLitsYFVtPtms 27
                                      lF + i  tsYFVt t+ 
  gi|386002647|ref|YP_005920946.1| 43 LFAAGIFATSYFVTSTIV 60
                                      788889********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 543.30
//
Query:       gi|386002648|ref|YP_005920947.1|  [L=400]
Description: Potassium channel protein [Methanosaeta harundinacea 6Ac]
Scores for 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-27   95.7   0.1    3.5e-13   49.2   0.0    2.4  2  TrkA_C        TrkA-C domain
    2.1e-15   57.0  16.5    1.9e-08   34.7   5.2    2.3  2  PhoU          PhoU domain
    0.00012   21.9   0.0       0.34   10.6   0.0    2.4  2  Cupin_6       Cupin
  ------ inclusion threshold ------
      0.077   13.0   1.2       0.86    9.6   0.4    2.4  2  Dicistro_VP4  Cricket paralysis virus, VP4


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   7.7e-17   3.5e-13       3      67 ..     122     188 ..     120     190 .. 0.95
   2 !   44.3   0.0   2.6e-15   1.1e-11       2      66 ..     321     387 ..     320     391 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 7.7e-17
                                       EEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       + +v+++s++ G++l e+ ++++ g  v+airRg  +++ p + tv+ +GD+l+  g+++++  + e
  gi|386002648|ref|YP_005920947.1| 122 RAVVGSDSKVTGRSLEEISFETEaGMSVIAIRRGeSWIYDPEPGTVIVAGDILFARGHDEGVPLFLE 188
                                       679**********************************************************999876 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 2.6e-15
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       ++v++++g+ ++G tl++l+l+++ g+ v+a++Rg  + ++p +  +L +GD+++  gs+s+ + l 
  gi|386002648|ref|YP_005920947.1| 321 TRVEIAPGAEMDGETLGDLDLETEtGIYVMAVKRGgRWTYNPKPKVTLAAGDLIFARGSKSGEELLL 387
                                       799*********************************************************9987766 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   5.2   4.2e-12   1.9e-08       1      88 [.      15      98 ..      15      99 .. 0.91
   2 !   28.0   3.5     5e-10   2.2e-06       2      88 ..     216     298 ..     215     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.2e-12
                                      HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERig 79
                                      l +m++++e m+d+ ++a+  +d++la evi++++++d + + ++ +++ a+ + +    d ++l+++l+ia+  E i+
  gi|386002648|ref|YP_005920947.1| 15 LVEMKDTSELMVDLGYSAVLYDDEDLAMEVIRLEEKMDVYDYHVQMAAMLAARTVE----DAEALSGVLQIASAAEIIS 89
                                      579*****************************************999887775443....58899************** PP

                                      HHHHHHHHH CS
                              PhoU 80 Dhavniaer 88
                                        a +ia +
  gi|386002648|ref|YP_005920947.1| 90 NAAGDIASI 98
                                      *******87 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 5e-10
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        +m++ +e ++ +a++a+  + +e a ev   ++e+d++ ++++r +l+a+++ +     ++ l +ll++a + E i
  gi|386002648|ref|YP_005920947.1| 216 VEMKNRSELAVGLAYTAVLFDSEEVAIEVEVIEEEMDEMKYDLQRWVLRAAKHVDD----IENLRGLLHLAVSTEII 288
                                       69***************777777***********************9999977664....5556669********** PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                       +D a +ia+ 
  gi|386002648|ref|YP_005920947.1| 289 SDAALKIANV 298
                                       ********86 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   7.6e-05      0.34      27      70 ..     140     181 ..     122     231 .. 0.77
   2 !    9.0   0.0   0.00024       1.1      26      68 ..     339     379 ..     307     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.6e-05
                           Cupin_6  27 slrfpaglalhvvlrGscwlidpasgepvrLsagdvvllpggep 70 
                                       s++ +ag++++++ rG+ w+ dp+      + agd+++ +g ++
  gi|386002648|ref|YP_005920947.1| 140 SFETEAGMSVIAIRRGESWIYDPE--PGTVIVAGDILFARGHDE 181
                                       455577799************888..44899********99743 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00024
                           Cupin_6  26 wslrfpaglalhvvlrGscwlidpasgepvrLsagdvvllpgg 68 
                                        +l+ + g+ +++v rG  w   p+    v+L+agd+++ +g 
  gi|386002648|ref|YP_005920947.1| 339 LDLETETGIYVMAVKRGGRWTYNPK--PKVTLAAGDLIFARGS 379
                                       4556666799************888..78**********9875 PP

>> Dicistro_VP4  Cricket paralysis virus, VP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00019      0.86      36      54 ..      80      98 ..      69      99 .. 0.93
   2 ?    1.3   0.0     0.075   3.3e+02      38      53 ..     282     297 ..     272     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00019
                                      -SSSS-TT----HHHHHHH CS
                      Dicistro_VP4 36 eiakateivAdkvgsvAkL 54
                                      +ia+a ei+++++g++A++
  gi|386002648|ref|YP_005920947.1| 80 QIASAAEIISNAAGDIASI 98
                                      589**************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.075
                                       SSS-TT----HHHHHH CS
                      Dicistro_VP4  38 akateivAdkvgsvAk 53 
                                       a  tei++d++ ++A 
  gi|386002648|ref|YP_005920947.1| 282 AVSTEIISDAALKIAN 297
                                       5579*******99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2386.67
//
Query:       gi|386002649|ref|YP_005920948.1|  [L=160]
Description: hypothetical protein Mhar_1969 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-72  242.0   0.0    2.2e-72  241.9   0.0    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.9   0.0   1.2e-76   2.2e-72       1     154 []       6     159 ..       6     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 241.9 bits;  conditional E-value: 1.2e-76
                                       EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvf 77 
                                       v++++p++ nvilg shfikt edlyea++ ++p+ +fg+af+Easg++Lvr+egnd+el+++a+++al +g+gh+f
  gi|386002649|ref|YP_005920948.1|   6 VRMKIPQDSNVILGMSHFIKTAEDLYEAIAGTAPRSRFGIAFSEASGPCLVRCEGNDPELIDAAKEAALGLGCGHTF 82 
                                       789************************************************************************** PP

                                       EEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                     Adenosine_kin  78 villknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                       v+l+++afPinvlnaik+v+ev+ if+Atanplev+vaeteqgrg++gv+DG+spkg e+ +d+++r+ +lrk+gYk
  gi|386002649|ref|YP_005920948.1|  83 VVLIRDAFPINVLNAIKAVQEVCGIFCATANPLEVVVAETEQGRGIMGVIDGSSPKGAETASDVSDRRGMLRKFGYK 159
                                       ****************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1028.35
//
Query:       gi|386002650|ref|YP_005920949.1|  [L=445]
Description: Dihydroorotase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-24   86.9   0.0    2.1e-24   86.5   0.0    1.2  1  Amidohydro_1  Amidohydrolase family
    1.8e-16   60.7   0.5    6.4e-10   39.1   0.1    2.6  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   2.4e-28   2.1e-24       1     320 [.      50     374 ..      50     407 .. 0.77

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 2.4e-28
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       ivlPG +D+HvH++             +p+ t++e  e+g + a+ +G+ttv d ++t+++     + +  le ae+
  gi|386002650|ref|YP_005920949.1|  50 IVLPGAVDLHVHFR-------------DPGYTYKEDWETGSTSAVAGGVTTVVDQPNTDPPtlderSYRMKLETAER 113
                                       79***********9.............*******************************8888777655556666666 PP

                                       SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEE CS
                      Amidohydro_1  73 lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpva 149
                                                 + ++d ++ +  + ++++l++               +a+++ + ++ sd+ l+ +l+e ++ +l  +
  gi|386002650|ref|YP_005920949.1| 114 ----------RSVVD-FCLNGGPGRMKRLAELG------------ASAIGEIFTYEHSDDDLRRILEETARSGLLPT 167
                                       ..........45555.99999999999997764............2899**************************** PP

                                       EEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEE.....EHCTCEEEHH.HHHHHHHHHHHHCEE.... CS
                      Amidohydro_1 150 iHaletkgevedaeaafgetiehgthlevaeslglldeikli.....lahgvhltpt.eaellkerlkeagva.... 216
                                       iHa e+ g + +  a   ++   + +   +  l+ ++ i ++     +ah++hl+ +  +ell++++++ + +    
  gi|386002650|ref|YP_005920949.1| 168 IHA-EDGGVIRENTAPLRDRRDPELYSMARPNLAEAKAIEMVlkmteRAHICHLSTSeGLELLRAAKRGGKRVscev 243
                                       ***.88999999999999999998898888999999999999999**********6655555555555555552555 PP

                                       ...HHHHHHHH...............SEHHHHHHHHHHHHTSCEEEEEECT.................TSSCCGGHH CS
                      Amidohydro_1 217 ...hcpfsnsi...............lrsgrealrkaldeGvkvglgtDga.................asgnslnll 258
                                          h+ f+ +                   + +al++ l++G + ++++D+a                   g + ++ 
  gi|386002650|ref|YP_005920949.1| 244 aphHLLFTKRDwqrqgtllkmnpplrDFRDKDALWEGLRKGQIDAIASDHAphlpeekrdeiwdappgVPG-VETM- 318
                                       565444444448999999999999553345568****************9988887766655554432111.1123. PP

                                       HHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC....C CS
                      Amidohydro_1 259 eelrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl....d 320
                                         + l+l          +    lsl + +++ +  +A++lgl+ ++G i+ GkdADl+++d+     
  gi|386002650|ref|YP_005920949.1| 319 --MPLLL--------IaVRSNLLSLGRMVDALSRRPAEILGLS-TKGGIARGKDADLAIIDPraasE 374
                                       ..22222........2223666********************7.****************9865432 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.2e-08   0.00047       1      84 [.      42     109 ..      42     117 .. 0.79
   2 !   39.1   0.1   7.2e-14   6.4e-10     402     473 .]     325     408 ..     142     408 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.2e-08
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfp 77 
                                       e iD +G++vlPG vD H H    g+ + + +++  + ++++g  t+v dq +t            d + ++e++++
  gi|386002650|ref|YP_005920949.1|  42 EAIDGRGMIVLPGAVDLHVHFRDPGYTYKE-DWETGSTSAVAGGVTTVVDQPNT------------DPPTLDERSYR 105
                                       679**********************77755.55555799999999999999998............67777666654 PP

                      Amidohydro_3  78 yalaeld 84 
                                          + l+
  gi|386002650|ref|YP_005920949.1| 106 ---MKLE 109
                                       ...5554 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 7.2e-14
                      Amidohydro_3 402 lrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear............vrlt 465
                                       + +++ lsl  ++++++r+pA++lgl+++ G+++ G+dADl+++d +++ ++ +++l++              ++ t
  gi|386002650|ref|YP_005920949.1| 325 AVRSNLLSLGRMVDALSRRPAEILGLSTK-GGIARGKDADLAIIDpRAASEIRADRLHSGAewtpyqgrraifPKIT 400
                                       556789**********************8.***************99999999999988779999999999999999 PP

                      Amidohydro_3 466 vvdGrvvy 473
                                       +++G+vvy
  gi|386002650|ref|YP_005920949.1| 401 MIRGEVVY 408
                                       99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2889.22
//
Query:       gi|386002651|ref|YP_005920950.1|  [L=144]
Description: Heat shock protein Hsp20 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-12   47.0   0.0      3e-12   46.6   0.0    1.2  1  HSP20       Hsp20/alpha crystallin family
    2.5e-08   33.4   0.1    3.7e-08   32.8   0.1    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
  ------ inclusion threshold ------
       0.08   14.0   0.0       0.12   13.5   0.0    1.2  1  CS          CS domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   4.9e-16     3e-12       1     101 [.      48     143 ..      48     144 .] 0.94

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 4.9e-16
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       d+++++ee  + +d+pg k+e +++ v+++ v++++  e     +++l +er + +  r+++L  +v++++v+a ++
  gi|386002651|ref|YP_005920950.1|  48 DVVDSPEEVVLYIDLPGTKRELIDLGVTEDAVTIRARFE--PPPGNYLQRERPEAEMGRRIKLAAEVKPEQVRARYE 122
                                       678999*******************************99..99999******************************* PP

                                       TTEEEEEEEBSS--..-------- CS
                             HSP20  78 dGvLtvtvpkkepekkkkerkiqi 101
                                       dGvL v +pk       k+ +++i
  gi|386002651|ref|YP_005920950.1| 123 DGVLVVRLPKLIVV---KPHSVPI 143
                                       **********9998...5566665 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   6.2e-12   3.7e-08       3      63 .]      55     130 ..      53     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.2e-12
                        ArsA_HSP20   3 eyvlkldLPfvdkeeidlsrsgdeLtIkig................nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       e+vl +dLP+ ++e idl  ++d  tI++                    R+i L   ++ ++v +A++edgvL++r+
  gi|386002651|ref|YP_005920950.1|  55 EVVLYIDLPGTKRELIDLGVTEDAVTIRARfepppgnylqrerpeaEMGRRIKLAAEVKPEQV-RARYEDGVLVVRL 130
                                       789*******************************************99***************.***********96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-05      0.12       8      76 .]      52     132 ..      47     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                       ETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETSCEEEEECE................BSS-BETTTEEEEEETT CS
                                CS   8 tldeVvvtiyvkkvnikkkdvkvefkerslkvkigkeklliege................LfgpIdpeesswtiesk 68 
                                       +++eVv++i +++   k + +++  +e+ +++      ++ +g+                L+++++pe+ + + e+ 
  gi|386002651|ref|YP_005920950.1|  52 SPEEVVLYIDLPGT--KRELIDLGVTEDAVTIRA-R-FEPPPGNylqrerpeaemgrrikLAAEVKPEQVRARYEDG 124
                                       689**********8..999999999999977776.3.233467778888**********************999999 PP

                                       EEEEEEEB CS
                                CS  69 kveitLkK 76 
                                        + + L K
  gi|386002651|ref|YP_005920950.1| 125 VLVVRLPK 132
                                       88888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1018.32
//
Query:       gi|386002652|ref|YP_005920951.1|  [L=410]
Description: hypothetical protein Mhar_1972 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-13   49.2   0.0    9.9e-13   48.3   0.0    1.5  1  DUF4139   Domain of unknown function (DUF4139)
    1.1e-06   29.0   1.5    2.5e-06   27.8   0.3    2.2  2  DUF4140   N-terminal domain of unknown function (DUF4140)
  ------ inclusion threshold ------
      0.082   12.5   0.1        0.2   11.2   0.1    1.7  1  AIRC      AIR carboxylase
       0.24   12.3   0.7         16    6.5   0.0    2.9  3  DUF756    Domain of unknown function (DUF756)


Domain annotation for each model (and alignments):
>> DUF4139  Domain of unknown function (DUF4139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.2e-16   9.9e-13       4     205 ..     113     401 ..     110     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.2e-16
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139   4 syvvsea.gWsPlYdlrldtakeevqltykAkvyQktgeDWknvnLtLstakpnrggsppelspwylrvvnevtegg 79 
                                        y+++ a +W+P Y ++l+++   v ++++A v+++ geD + v+L+L ++ p+ +  +  l      +   + +++
  gi|386002652|ref|YP_005920951.1| 113 AYLMTMAgQWRPIYSVHLEEES--VIVSAQAIVRNNFGEDLEGVRLKLVSGPPQVAPLEKYLAVGGFAM--RAVAEE 185
                                       565555416*********9887..9*****************************998888775444444..555666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                           DUF4139  80 tsvtfeipkkvsipsdgeetkvt...................................................... 102
                                        ++ ++ p+ + +p+ ge  ++                                                       
  gi|386002652|ref|YP_005920951.1| 186 EAMDYA-PAAAPVPATGELETLYiyelsgrkdlgmgkevgfplleeaapilrsylweayrnsegpvtevvranntmk 261
                                       778888.88899999888888888999999999999999999*********************************** PP

                                       ...................................xxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxx RF
                           DUF4139 103 ...................................Gvdpkikverkllkkkksetgli...........gsqrrvey 133
                                                                          G+  ++kv+rk  + +++ + +             +++++++
  gi|386002652|ref|YP_005920951.1| 262 dpwpagsallyrngeyvsgveipftpvgteaeivvGSSADLKVSRKMASYTTE-EEISqvpgadnatsaVKTTTETW 337
                                       ************************************************99999.5555568999999988999**** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4139 134 aytitvkNtksepvtlkvedqvPvSrdeeikveledaepskaevdkdtgilewklklapgekkkiefsyevk 205
                                       +y + +k + ++ +t++v d  P+    e++   +d+ep++++  ++   lew+l+l p++++ ie++y + 
  gi|386002652|ref|YP_005920951.1| 338 TYLLNIKSNLDRNATVEVSDTKPLRA--EVVS--ADPEPKETT--AT--GLEWELSLTPRQEASIEYTYVII 401
                                       ***********************954..4444..566666333..33..57******************986 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.3   5.6e-10   2.5e-06       1      52 [.      40      90 ..      40      97 .. 0.92
   2 ?   -1.8   0.0      0.98   4.4e+03      32      61 ..     345     375 ..     324     393 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.6e-10
                           DUF4140  1 Vtvypdr.AevtreikvelkaGtnevtiegLpptldedSlrVegagaatildv 52
                                      Vt+ypd+ A+v+r++++e+++G +++++  Lp++++ dS+r e+++ at+  v
  gi|386002652|ref|YP_005920951.1| 40 VTIYPDGiATVRRTGEMEVTEGVHRLVL-ALPASVKVDSVRFEATN-ATVEKV 90
                                      9*************************99.9*************987.576655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.98
                           DUF4140  32 ptlde.dSlrVegagaatildvqvervpnre 61 
                                       ++ld   ++ V+ +++++   v+ + +p ++
  gi|386002652|ref|YP_005920951.1| 345 SNLDRnATVEVSDTKPLRAEVVSADPEPKET 375
                                       4555434666666666555555555444444 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.6e-05       0.2       4      52 ..     294     345 ..     291     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.6e-05
                                       EEESSGGGHHHHHHHHHHHHH...TT-EEEEEE--TTTSHHHHHHHHHHCHT CS
                              AIRC   4 iimGSdsDlevmkkaaeilke...lgveyevrvvSahrtpeelleyaeeaee 52 
                                       i++GS+ Dl+v +k+a+  +e    +v+   + +Sa +t++e+ +y+ ++++
  gi|386002652|ref|YP_005920951.1| 294 IVVGSSADLKVSRKMASYTTEeeiSQVPGADNATSAVKTTTETWTYLLNIKS 345
                                       9****************99994555568899************999877665 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0037        16      26      64 ..      78     113 ..      50     117 .. 0.76
   2 ?    2.9   0.0     0.046   2.1e+02      31      56 ..     243     268 ..     236     272 .. 0.82
   3 ?   -2.1   0.0       1.7   7.6e+03      42      50 ..     341     349 ..     321     391 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0037
                            DUF756  26 arftVydnakapwtytveagdqledhwklassg.gwYdlt 64 
                                       +rf  ++    ++  +v +gd+le++++++s+g +++dl+
  gi|386002652|ref|YP_005920951.1|  78 VRFEATN----ATVEKVVRGDNLEYTLNVSSTGvQRFDLA 113
                                       3444433....45566779*******************96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.046
                            DUF756  31 ydnakapwtytveagdqledhwklas 56 
                                       y n + p t  v+a+++++d w++ s
  gi|386002652|ref|YP_005920951.1| 243 YRNSEGPVTEVVRANNTMKDPWPAGS 268
                                       55543499**************9875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                            DUF756  42 veagdqled 50 
                                       +  +++l+ 
  gi|386002652|ref|YP_005920951.1| 341 LNIKSNLDR 349
                                       333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2439.63
//
Query:       gi|386002653|ref|YP_005920952.1|  [L=566]
Description: arginyl-tRNA synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-35  121.0   0.0    6.8e-35  120.6   0.0    1.1  1  tRNA-synt_1d     tRNA synthetases class I (R)
    8.1e-30  103.4   0.0    2.8e-29  101.7   0.0    1.9  2  DALR_1           DALR anticodon binding domain
    1.8e-08   34.8   0.0    4.3e-08   33.6   0.0    1.7  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    8.2e-07   28.3   0.0     0.0045   16.0   0.0    2.2  2  tRNA-synt_1f     tRNA synthetases class I (K)
    0.00025   19.9   0.0       0.11   11.2   0.1    2.2  2  tRNA-synt_1g     tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.034   12.4   0.0      0.049   11.9   0.0    1.1  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0   2.3e-38   6.8e-35      18     349 .]     117     439 ..     104     439 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 2.3e-38
                                       ST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS---- CS
                      tRNA-synt_1d  18 ekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqel 94 
                                        +++v+v+++s n   ++hvGh+r  +iGd+++r+l  +G  v    +v D G+q  +++ +  ++  +    +++ 
  gi|386002653|ref|YP_005920952.1| 117 MNERVIVEHTSANPNGPLHVGHIRNSVIGDTLVRILRRAGCRVEAQYYVNDMGRQIAIVVWGCGRYPLDG---SKPD 190
                                       5789********************************************************9999998887...5677 PP

                                       -SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..CCCC CS
                      tRNA-synt_1d  95 qdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..lyke 168
                                         + ++y +a+kd++   +++e     ++  ++gd+++   ++  v+++    +++  rl++t    r es  + + 
  gi|386002653|ref|YP_005920952.1| 191 HAIAKVYIQANKDLAAAPELKEGVDRLMQLYEGGDPETAAKFREAVEYALSGIDETLRRLNITHDSrRWESefVRDG 267
                                       78899********************************999999999*****************86557888857778 PP

                                       CHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHH CS
                      tRNA-synt_1d 169 slneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslh 245
                                       s  +++k l++ gl + ++G l ++l+  g +  +v+++sDG+ lytt+D+a   +r + +  d+++ v+ +  +l 
  gi|386002653|ref|YP_005920952.1| 268 STAGVLKALEATGLTEWEEGSLQLDLSGDGFEKKLVLKRSDGTSLYTTRDLA--YHRWKAESSDRMIDVLGADHKLI 342
                                       99************************9777777889**************97..68999****************** PP

                                       HHHHHHHHHCTT.SSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHC CS
                      tRNA-synt_1d 246 lqqiflilkkig.yvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadele 321
                                         q+ ++l+ +g  +pe +  e  ++         +++tr+G+ +  ++lLde   +a + ++ + ++     + + 
  gi|386002653|ref|YP_005920952.1| 343 SGQLRAALRLMGvREPEIVIFEFVSL------PTGSMSTRRGKFISTDELLDEVEAQAYREVTARRPE--EGEEFRR 411
                                       ************55566555444333......5569**************************999999..6667788 PP

                                       HHHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 322 kvaeavgvgaikyaDlsknrindyifdw 349
                                       +va  v++ga++y  ++    +  +fdw
  gi|386002653|ref|YP_005920952.1| 412 AVAREVALGAVRYDVVRVSPEKATVFDW 439
                                       99***********988777777777777 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   3.5e+03     103     117 ..     345     359 ..     340     360 .. 0.83
   2 !  101.7   0.0   9.3e-33   2.8e-29       1     119 []     453     566 .]     453     566 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHTT----S CS
                            DALR_1 103 vLangLdlLGieape 117
                                        L+ +L+l+G++ pe
  gi|386002653|ref|YP_005920952.1| 345 QLRAALRLMGVREPE 359
                                       5899*******9886 PP

  == domain 2  score: 101.7 bits;  conditional E-value: 9.3e-33
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       +qy+haR++sil ka++ g    + + +ll+++ee eL+k++ qf  ++  +a+el+ph la+y+ eLa+ f++fY+
  gi|386002653|ref|YP_005920952.1| 453 IQYSHARACSILDKAGAVG----GFDPHLLSSPEEVELVKKISQFDLAIDLSARELKPHLLATYARELAEIFNQFYR 525
                                       7***************988....3445556999******************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       + +vl+++  ++ +aRLaLv+a+r+ L+++Ld LGi+a+e m
  gi|386002653|ref|YP_005920952.1| 526 ASPVLEADPGVR-EARLALVEAARNCLRSTLDTLGIPALESM 566
                                       **********99.***************************99 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.4e-11   4.3e-08       3      84 ..       9      94 ..       7      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.4e-11
                                      HHHHHHHHHHHHHSS-HHHHGGG-E-.....SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEE CS
                   Arg_tRNA_synt_N  3 lkeaiaealkkaagadleeeeiviekp....knpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvev 75
                                      +++++++al+++  ++l   + ++e +      + ++D+a+ + ++la  l+k P ei  +i e++  ++   ++++e+
  gi|386002653|ref|YP_005920952.1|  9 VEALLRDALDRCG-FPLPQADGKVEGNelllEMSPHADLASTISFRLAPILRKGPAEISRKIQEAVVLDGKgtVDRAEA 86
                                      678999******5.555555666663224446789*****************************887776556****** PP

                                      ETT.EEEEE CS
                   Arg_tRNA_synt_N 76 agpGFiNff 84
                                       gp ++Nff
  gi|386002653|ref|YP_005920952.1| 87 MGP-YLNFF 94
                                      ***.****9 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   8.5e-05      0.25      23      71 ..     120     168 ..     101     171 .. 0.82
   2 !   16.0   0.0   1.5e-06    0.0045     229     319 ..     322     409 ..     231     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.5e-05
                      tRNA-synt_1f  23 devvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                         +v  + + p G++H+G +r+ + +d ++r lr+ g +v+  ++++dm
  gi|386002653|ref|YP_005920952.1| 120 RVIVEHTSANPNGPLHVGHIRNSVIGDTLVRILRRAGCRVEAQYYVNDM 168
                                       3444568899******************************999999998 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-06
                      tRNA-synt_1f 229 rWaalgVd..fEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepe 302
                                       rW+a++ d  +   G Dh     S +   + a +++g+++Pe v++e+++l  g  ms  +G++++ +++l+ +e +
  gi|386002653|ref|YP_005920952.1| 322 RWKAESSDrmIDVLGADHKL--ISGQ--LRAAlRLMGVREPEIVIFEFVSLPTG-SMSTRRGKFISTDELLDEVEAQ 393
                                       78887665447889999999..3333..3334499*****************99.9********************* PP

                      tRNA-synt_1f 303 vlrflilrrkPkkakkl 319
                                         r +++r +P++  ++
  gi|386002653|ref|YP_005920952.1| 394 AYREVTAR-RPEEGEEF 409
                                       99999999.88876665 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   3.8e-05      0.11      10      38 ..     130     158 ..     121     170 .. 0.87
   2 !    6.5   0.0   0.00099         3     307     356 ..     353     401 ..     311     414 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-E CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgee 38 
                                       +ng+lH+Gh+++ +++D ++R  r  g  
  gi|386002653|ref|YP_005920952.1| 130 PNGPLHVGHIRNSVIGDTLVRILRRAGCR 158
                                       79**********************98865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00099
                                       TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHH CS
                      tRNA-synt_1g 307 aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaa 356
                                        +++ p+ +v  e++ +  + +S+ rg ++ ++e+l++++a++ R + a+
  gi|386002653|ref|YP_005920952.1| 353 MGVREPE-IVIFEFVSLPTGSMSTRRGKFISTDELLDEVEAQAYREVTAR 401
                                       5566664.7789*****************************999966655 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.6e-05     0.049      32      66 ..     128     162 ..     114     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                       tRNA-synt_1  32 PyvtGslHiGhalaktlkdivirykrmkGkevlyv 66 
                                        + +G lH+Gh+ ++++ d+++r+ r  G +v+ +
  gi|386002653|ref|YP_005920952.1| 128 ANPNGPLHVGHIRNSVIGDTLVRILRRAGCRVEAQ 162
                                       5789*************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 3235.27
//
Query:       gi|386002654|ref|YP_005920953.1|  [L=316]
Description: hypothetical protein Mhar_1974 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1754.42
//
Query:       gi|386002655|ref|YP_005920954.1|  [L=261]
Description: Tryptophan synthase, alpha subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-83  279.6   0.0    1.8e-83  279.4   0.0    1.0  1  Trp_syntA     Tryptophan synthase alpha chain
    2.4e-05   23.9   0.0    3.8e-05   23.3   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
    0.00014   21.4   0.1     0.0029   17.1   0.1    2.1  2  PcrB          PcrB family
     0.0097   15.1   0.1       0.02   14.1   0.1    1.5  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.056   12.7   0.2      0.056   12.7   0.2    1.7  2  ThiG          Thiazole biosynthesis protein ThiG
      0.081   12.1   0.0       0.11   11.7   0.0    1.2  1  DHO_dh        Dihydroorotate dehydrogenase
        0.4   10.7   0.2        0.4   10.7   0.2    2.8  3  ALF           Short repeats of unknown function


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.4   0.0   6.9e-87   1.8e-83       8     236 ..       9     234 ..       3     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 279.4 bits;  conditional E-value: 6.9e-87
                                       TB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHH CS
                         Trp_syntA   8 nraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkk 84 
                                        r  +++y+ agdp+ e ++e+ + l++agadv+ElGlp sdP+adGPvIqaa++ra+++g++++  +e+ +++r  
  gi|386002655|ref|YP_005920954.1|   9 RRPLLIAYICAGDPSPEATVEVAELLARAGADVVELGLPHSDPIADGPVIQAAAQRAIEAGMNTDVYFETASRIR-- 83 
                                       6789***********************************************************************.. PP

                                       CSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHH CS
                         Trp_syntA  85 evevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevve 161
                                         ++P+v+++y+n+++++g e+f  ++   g++glivpDlP+eea +l++a+++++l+l++l+ap+t+ er+  ++e
  gi|386002655|ref|YP_005920954.1|  84 -AKIPLVFMGYYNMIYQRGLEKFAGDCGASGITGLIVPDLPPEEAGPLRAACRRADLDLISLIAPNTPAERIPLIAE 159
                                       .9*************************************************************************** PP

                                       H--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC.T CS
                         Trp_syntA 162 qaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkiee.e 236
                                       +++gf Y+v+raGvTga+++v +++++l+er+++  ++P avGFGist+eq+++v+ ++ad++ivGSa v+ i +  
  gi|386002655|ref|YP_005920954.1| 160 NSSGFLYLVARAGVTGARSEVLQSTKALIERVNS--ELPRAVGFGISTPEQAAEVIrAGADAAIVGSACVDLISKgD 234
                                       ********************************86..68******************9****************9633 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.5e-08   3.8e-05      59     107 ..     182     228 ..     150     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                       +  ++l+e++ +e  +p  vG GI++ e+++e+++agad  i+g+a v+
  gi|386002655|ref|YP_005920954.1| 182 QSTKALIERVNSE--LPRAVGFGISTPEQAAEVIRAGADAAIVGSACVD 228
                                       4567889999999..******************************9986 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.047   1.2e+02       8      37 ..      16      45 ..       7      53 .. 0.88
   2 !   17.1   0.1   1.1e-06    0.0029     158     211 ..     166     226 ..     161     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.047
                                      EEEEE-TTSS-CHHHHHHHHCTT-SEEEEE CS
                              PcrB  8 hltklDPeeenpdEiveiviesgtDavmig 37
                                      ++   DP  e + E++e +++ g+D v +g
  gi|386002655|ref|YP_005920954.1| 16 YICAGDPSPEATVEVAELLARAGADVVELG 45
                                      777789*******************99766 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-06
                                       EEE-.TTSSS-H....HHHHHHHHHHS.SSEEEEESS--SHHHHHHHHCC.SSEEEE-CHH CS
                              PcrB 158 YlEa.sGaledv....eevialkkkle.karlivGGGirsaEkAkevvea.ADvivvGnvv 211
                                       Yl a +G+++      + ++al  +++ +    vG Gi  +E+A+ev++a AD+ +vG + 
  gi|386002655|ref|YP_005920954.1| 166 YLVArAGVTGARsevlQSTKALIERVNsELPRAVGFGISTPEQAAEVIRAgADAAIVGSAC 226
                                       6655555555542004445554444431334589************************875 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   7.9e-06      0.02     152     176 ..     202     226 ..     170     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.9e-06
                                       ---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 152 rintPekakkaieiGvdavvvGsai 176
                                        i tPe+a+++i+ G+da +vGsa 
  gi|386002655|ref|YP_005920954.1| 202 GISTPEQAAEVIRAGADAAIVGSAC 226
                                       489********************96 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.72   1.8e+03     110     127 ..      25      42 ..      21      72 .. 0.56
   2 ?   12.7   0.2   2.2e-05     0.056     168     207 ..     185     226 ..     167     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHHTT-EEE CS
                              ThiG 110 vetlkaaeiLvkeGFevl 127
                                         t++ ae+L++ G  v+
  gi|386002655|ref|YP_005920954.1|  25 EATVEVAELLARAGADVV 42 
                                       555666666666555543 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.2e-05
                                       HHHHHH-..SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
                              ThiG 168 kiiieea..kvPvivDAGigspsdaaqamelGadavllntav 207
                                       k +ie++  ++P  v  Gi +p++aa+++  Gada ++ +a 
  gi|386002655|ref|YP_005920954.1| 185 KALIERVnsELPRAVGFGISTPEQAAEVIRAGADAAIVGSAC 226
                                       56667665589***************************9985 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.11     193     276 ..     144     226 ..     115     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                       EEE...BSEE--CTTCCGCCCCTT.SSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTEC CS
                            DHO_dh 193 iivtNttvqrlaidlkseknvkan.ktGGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAs 268
                                       +i+ Nt  +r  +  ++ +         G+ G+  ++  l+   +l +r+++e+p     Gi++ e a e i+aGA 
  gi|386002655|ref|YP_005920954.1| 144 LIAPNTPAERIPLIAENSSGFLYLvARAGVTGA--RSEVLQSTKALIERVNSELPRAVGFGISTPEQAAEVIRAGAD 218
                                       555566555554444444444443433447776..56677888899999999999755559**************** PP

                                       EEEESHHH CS
                            DHO_dh 269 lvqvytal 276
                                       +  v++a 
  gi|386002655|ref|YP_005920954.1| 219 AAIVGSAC 226
                                       ****9987 PP

>> ALF  Short repeats of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.28   7.1e+02       2      15 ..      28      41 ..      28      44 .. 0.86
   2 ?   10.7   0.2   0.00016       0.4      12      26 ..      55      69 ..      52      74 .. 0.88
   3 ?   -2.2   0.8       1.7   4.3e+03      15      26 ..     213     223 ..     207     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.28
                               ALF  2 vavarllatgGpaV 15
                                      v+va+lla +G  V
  gi|386002655|ref|YP_005920954.1| 28 VEVAELLARAGADV 41
                                      79******999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                               ALF 12 GpaVraAAqaALdaG 26
                                      Gp  +aAAq+A++aG
  gi|386002655|ref|YP_005920954.1| 55 GPVIQAAAQRAIEAG 69
                                      9***********988 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.7
                               ALF  15 VraAAqaALdaG 26 
                                        ra A aA+  G
  gi|386002655|ref|YP_005920954.1| 213 IRAGADAAI-VG 223
                                       466666776.36 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1633.69
//
Query:       gi|386002656|ref|YP_005920955.1|  [L=405]
Description: Tryptophan synthase subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-36  126.0   2.7    2.5e-36  125.6   2.7    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   2.7   1.4e-40   2.5e-36       3     284 ..      61     379 ..      59     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 1.4e-40
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallG 78 
                                       ++ +pTPl  +++ls+elg++++lK+E+l ++g++K++ +    +   + g +++ ++e+++G+hg+a A+++a lG
  gi|386002656|ref|YP_005920955.1|  61 YAGRPTPLYLARALSRELGQKVYLKREDLVHGGAHKLNNVLGQALVaKAIG-KTRLIAETGAGQHGVASAMVGANLG 136
                                       5789************************************95555514555.9************************ PP

                                       -EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTT.......SHH...HHHH CS
                              PALP  79 lkvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfd.......npt...vieg 142
                                       l+ ++++ + +    + +v +++llGa+v+ v ++  + ++a++e+ +++ g y + ++        +p+   v e 
  gi|386002656|ref|YP_005920955.1| 137 LETEVYMGEVDIerqKMNVYRMELLGARVIPVRSGSRTLKDAINEAMRDWAGSYETTHYLmgtvagpHPYplmVREL 213
                                       ******99999955569********************************9999999999988888775558866666 PP

                                       HHTHHHHHHHHTT....TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCC...S..S.SS..B CS
                              PALP 143 ygtiglEileqlg....gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarsl...ragrrvtvpv 212
                                       ++ ig E  eq+     + pdav ++vGgG++++Gi  g+ +   ++r+i+ve+     +++++   ++g       
  gi|386002656|ref|YP_005920955.1| 214 QSVIGTEAREQILaaegRLPDAVAACVGGGSNAMGIFSGFLK--DETRLIAVEAG-GRGITSGRkiaDHG------- 280
                                       ********866555666************************9..568*****987.33333333112333....... PP

                                       .............................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB CS
                              PALP 213 s............................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregi 261
                                       +                             ++a gl+ + ++++   l++    +    +de+al ++r+l   egi
  gi|386002656|ref|YP_005920955.1| 281 AclnfgdegvlhgamtkilqdpygqilesYSLAAGLDYPGVGPELAHLAEVGRVTPAVADDETALLGLRRLSVLEGI 357
                                       245555669999999999**********9**********88888888888888888999****************** PP

                                       -B-HHHHHHHHHHHHHHHHCCTT CS
                              PALP 262 vvepssaaalaalklreagelke 284
                                       ++   s +a+  + lr+  +l+e
  gi|386002656|ref|YP_005920955.1| 358 IPALESSHAVGYA-LRNPDALGE 379
                                       ****888888888.777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2826.08
//
Query:       gi|386002657|ref|YP_005920956.1|  [L=265]
Description: Indole-3-glycerol phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-52  177.6   0.0    3.2e-52  177.2   0.0    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.021   14.6   0.0    1.2  1  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
       0.11   11.5   0.0       0.18   10.8   0.0    1.2  1  FMN_dh        FMN-dependent dehydrogenase
       0.15   11.2   0.0       0.21   10.8   0.0    1.3  1  DHO_dh        Dihydroorotate dehydrogenase
       0.17   11.4   0.0       0.27   10.6   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.2   0.0   8.9e-56   3.2e-52      22     245 ..      21     239 ..       3     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 177.2 bits;  conditional E-value: 8.9e-56
                                       GCCCCG..-S..S-SS-HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC-- CS
                              IGPS  22 adleaavkla..kpkrsfaeaLresekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqG 96 
                                        +l + +++a  ++  + a+aLr+ +    +iaE+K     + l+ e+  +a iA+ ye+     iSVLt++ yF G
  gi|386002657|ref|YP_005920956.1|  21 PSLASPIRVAdpRDLPGRARALRS-RGISPIIAEIKPRILKRPLLSEE--VATIAQRYEADAGCGISVLTQPTYFLG 94 
                                       355555433200333344556666.88899*******99999888888..789*******98899************ PP

                                       -CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHH CS
                              IGPS  97 sledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeler 173
                                       s e+ r +r++ +lp+lrKdFi+de q++    +  d++LLi+++ +   le l+eaa   +le+LvEvh+e+el+ 
  gi|386002657|ref|YP_005920956.1|  95 SPENARVARRSSALPILRKDFILDERQLD---EVATDLVLLIAAFSS--PLEGLVEAALARDLEPLVEVHTEAELDL 166
                                       *****************************...6889******99855..468************************* PP

                                       HHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-T CS
                              IGPS 174 alklgakiiGvNnRnLktlevdlntteeLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrqe 245
                                       alk +a+i+G+NnR+L tl+v+l t+e L +l++++  ++vaeSG++tr dv +++e+g++a+LvG+slm+++
  gi|386002657|ref|YP_005920956.1| 167 ALKTEARIVGINNRDLSTLKVSLATFEGLGPLAKNSgLFVVAESGVETRRDVLRMEEAGADAILVGTSLMEEP 239
                                       **********************************8889********************************986 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.9e-06     0.021      80     157 ..     151     234 ..     133     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                                       TSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT......SEEEEESS--TTTHHHHHCTT-S CS
                         QRPTase_C  80 evkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr......vlievSGgvtlenveeyaksgvd 150
                                        ++  vev++++el+ +l++ea i+ + n +  +lk  + + +   +       +++  SG  t  +v  + + g d
  gi|386002657|ref|YP_005920956.1| 151 DLEPLVEVHTEAELDLALKTEARIVGINNRDLSTLKVSLATFEGLGPLaknsglFVVAESGVETRRDVLRMEEAGAD 227
                                       45568******************************999988776655556678899999**99************** PP

                                       EEEECHH CS
                         QRPTase_C 151 visvgal 157
                                       +i vg+ 
  gi|386002657|ref|YP_005920956.1| 228 AILVGTS 234
                                       ***9985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     5e-05      0.18     224     302 ..     158     234 ..     155     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5e-05
                                       E-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEES CS
                            FMN_dh 224 vltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllG 300
                                       v t+++ ++a++  + ++ + N     l  + at++ L  ++++ g  + v++ +G+ +  Dvl+    GAda+l+G
  gi|386002657|ref|YP_005920956.1| 158 VHTEAELDLALKTEARIVGINNRDLSTLKVSLATFEGLGPLAKNSG--LFVVAESGVETRRDVLRMEEAGADAILVG 232
                                       6677778888888888888888888888899999999999988888..99**************************9 PP

                                       HH CS
                            FMN_dh 301 Rp 302
                                         
  gi|386002657|ref|YP_005920956.1| 233 TS 234
                                       76 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.8e-05      0.21     241     277 ..     202     236 ..     140     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                                       TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                           + +++  G+e+ +D+l + eaGA ++ v+t l+
  gi|386002657|ref|YP_005920956.1| 202 SG--LFVVAESGVETRRDVLRMEEAGADAILVGTSLM 236
                                       33..7899999***********************994 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.6e-05      0.27      74     111 ..     204     241 ..     189     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.6e-05
                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THH CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpel 111
                                       + v   +G+ +  dv ++ eagad + +gt+ +++p l
  gi|386002657|ref|YP_005920956.1| 204 LFVVAESGVETRRDVLRMEEAGADAILVGTSLMEEPGL 241
                                       44555667777777777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1693.95
//
Query:       gi|386002658|ref|YP_005920957.1|  [L=121]
Description: Anthranilate synthase component II [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  103.4   0.0    1.4e-29  103.2   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.6e-14   54.2   0.3    8.2e-13   48.6   0.3    2.0  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.6e-33   1.4e-29      67     186 ..       3     115 ..       1     118 [. 0.95

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.6e-33
                                       HCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEE CS
                            GATase  67 arenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepagle 143
                                       a+e ++ iLG+CLG+Q++ +++g+++ +    + hg+ +++ +d++++++gl+++++  ++H+++v++   +   l+
  gi|386002658|ref|YP_005920957.1|   3 AFE-GTAILGVCLGHQAINLAYGGTINRTA--PVHGKASEIFHDGRGIFRGLQSPLKGGRYHSLAVED---LAPPLR 73 
                                       677.999******************99877..9**********************************9...9999** PP

                                       EEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
                            GATase 144 vtakseddeelmeiiekknpfvgvQFHPEststpegpellfnf 186
                                       +ta+++d+  +m++++++ p+ gvQFHPEs++tpeg++l++n 
  gi|386002658|ref|YP_005920957.1|  74 ITATTSDG-VVMGVRHRSLPVEGVQFHPESVLTPEGKRLIANW 115
                                       *****887.9*****************************9986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.3   9.2e-17   8.2e-13     106     216 .]       7     101 ..       3     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 9.2e-17
                     Peptidase_C26 106 vPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikela 182
                                       + ilg+C+G+q +n a+GGt+++ +        h ++       ++  +  +++  l + +  +   +H+ a+++la
  gi|386002658|ref|YP_005920957.1|   7 TAILGVCLGHQAINLAYGGTINRTAPV------HGKA------SEIFHDGRGIFRGL-Q-SPLKGGRYHSLAVEDLA 69 
                                       669*******************99994......3233......33434445555555.4.5889999********** PP

                     Peptidase_C26 183 eelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       + lr++A+++Dgv+  +++++   +v gvQ+HPE
  gi|386002658|ref|YP_005920957.1|  70 PPLRITATTSDGVVMGVRHRS--LPVEGVQFHPE 101
                                       ****************99999..67********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 820.11
//
Query:       gi|386002659|ref|YP_005920958.1|  [L=502]
Description: Anthranilate synthase, component I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-95  319.0   0.0    1.3e-91  306.8   0.0    3.0  3  Chorismate_bind  chorismate binding enzyme
    4.1e-28   98.4   0.0    4.4e-26   91.8   0.0    2.9  3  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0   0.00054       4.8      40      90 ..      32      85 ..      19      88 .. 0.69
   2 ?    1.7   0.0     0.017   1.5e+02     159     181 ..     111     133 ..     109     135 .. 0.95
   3 !  306.8   0.0   1.4e-95   1.3e-91       5     258 .]     239     490 ..     236     490 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00054
                                      HHHHHHHHHCTBSSSEEEEE...EETT......EEEEEEESSEEEEEETTSEEEEECEEE CS
                   Chorismate_bind 40 plalyralrarnpapysfll...eled......sellgaSPElllkveggrrietepiaG 90
                                      pl+ly+alr    + y fll   e  +      ++++gaSP  ++kv+g+ r+e+++  G
  gi|386002659|ref|YP_005920958.1| 32 PLSLYSALRG---EGYPFLLesvE--KsgqrarFSFVGASPAAVVKVRGR-RFEVQVFDG 85
                                      5666666665...55566664331..1334566899************65.999988766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.017
                                       EEEEESTT--HHHHHHHCSS-CC CS
                   Chorismate_bind 159 iegelkedvslldllkalfPtga 181
                                       i+ge++++ +l+dll++ +P+g+
  gi|386002659|ref|YP_005920958.1| 111 ISGEIRPERDLFDLLRSAIPAGT 133
                                       89*******************98 PP

  == domain 3  score: 306.8 bits;  conditional E-value: 1.4e-95
                                       HHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTS CS
                   Chorismate_bind   5 YaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggr 81 
                                       ++e+v+++ke+i agd+++vvlsrr++++l  + dp+ lyr+lr+ np+py++++e++d++l+gaSPE+l++++ +r
  gi|386002659|ref|YP_005920958.1| 239 FEESVRRAKEHILAGDIFQVVLSRRTRVRLG-RPDPVVLYRRLREINPSPYTYIFEFGDHSLVGASPETLFSLS-DR 313
                                       899**************************66.669***************************************.55 PP

                                       EEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEE CS
                   Chorismate_bind  82 rietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvst 158
                                        ++t+piaGT +rg + eed  l++++ledeKeraEh+m+vdl rnd+++v+k+gs+kv+++++v rys+v+h+ +t
  gi|386002659|ref|YP_005920958.1| 314 VVTTNPIAGTCPRGGSREEDDLLAAKMLEDEKERAEHVMLVDLGRNDVRSVSKAGSIKVEDFMAVLRYSHVQHIETT 390
                                       ***************************************************************************** PP

                                       EEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEE CS
                   Chorismate_bind 159 iegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelr 235
                                       ++g+l+e+++++d+ +a+fP+g+++GaPk rameiid+lE ++Rg+Y+G vgy+++dg+a++a++IR++v++ + + 
  gi|386002659|ref|YP_005920958.1| 391 VRGTLREGCDSFDAARAIFPAGTLSGAPKLRAMEIIDDLEGRERGIYGGGVGYFSSDGSADFAIAIRSVVLEGDLAV 467
                                       *************************************************************************99** PP

                                       EEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 236 lgaGaGIvadSdpeaEyeEtlaK 258
                                       ++aGaGIvadSdp++E+ Et+ K
  gi|386002659|ref|YP_005920958.1| 468 VQAGAGIVADSDPHREFLETERK 490
                                       ********************998 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   4.9e-30   4.4e-26       4     141 ..      31     190 ..      28     191 .. 0.92
   2 ?   -0.3   0.0      0.12   1.1e+03       5      65 ..     273     334 ..     271     355 .. 0.63
   3 ?    2.6   0.0     0.015   1.4e+02      88     101 ..     434     447 ..     358     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 4.9e-30
                     Anth_synt_I_N   4 tplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg......................... 55 
                                       +pls+y +l++e+++flLeS+e++g+++r+Sf+g++p++++k++++++ev++                         
  gi|386002659|ref|YP_005920958.1|  31 APLSLYSALRGEGYPFLLESVEKSGQRARFSFVGASPAAVVKVRGRRFEVQVfdgaggliellrrrllasavidgpg 107
                                       7**************************************************************************** PP

                     Anth_synt_I_N  56 ...pegeeleeeepldalrellerfrsaedseptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydt 129
                                            ge + e +++d+lr  +      ++++ +   f gG +Gyl+YDlv e  + p    +  + pda + ++d+
  gi|386002659|ref|YP_005920958.1| 108 gygISGEIRPERDLFDLLRSAIPAGT-GPSKF-GRQAFLGGGIGYLAYDLVAERIDRP----KASDKPDAVFGIFDK 178
                                       ***999********************.54555.5556*************88776555....44557********** PP

                     Anth_synt_I_N 130 livfDhkerrly 141
                                       ++vfDh+++++ 
  gi|386002659|ref|YP_005920958.1| 179 CFVFDHLTGKVC 190
                                       *******99985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                     Anth_synt_I_N   5 plsvylklaeee...hkflLeSaeneggegrySfigldpflelkskngeveveg.....pegeeleeee 65 
                                       p+ +y++l+e +   +++++e ++        S++g++p   +   ++ v+++      p g+ +ee +
  gi|386002659|ref|YP_005920958.1| 273 PVVLYRRLREINpspYTYIFEFGD-------HSLVGASPETLFSLSDRVVTTNPiagtcPRGGSREEDD 334
                                       666777777766666666666554.......78999999777777777777666666665555555555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.015
                     Anth_synt_I_N  88 lpfvgGlvGylgYD 101
                                         ++gG vGy++ D
  gi|386002659|ref|YP_005920958.1| 434 RGIYGGGVGYFSSD 447
                                       4589*******977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3174.39
//
Query:       gi|386002660|ref|YP_005920959.1|  [L=213]
Description: N-(5'-phosphoribosyl)anthranilate isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-31  109.5   0.0    1.9e-31  109.3   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase
  ------ inclusion threshold ------
      0.017   14.5   2.7      0.017   14.5   2.7    1.8  2  NMO       Nitronate monooxygenase
       0.06   12.7   0.1       0.13   11.6   0.1    1.7  1  TMP-TENI  Thiamine monophosphate synthase
       0.11   12.4   0.7       0.29   11.1   0.0    2.0  2  DUF3606   Protein of unknown function (DUF3606)
       0.18   12.0   0.0        0.4   10.9   0.0    1.6  1  UPF0180   Uncharacterised protein family (UPF0180)
       0.23   11.0   4.9        1.6    8.3   1.2    2.7  2  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.0   6.5e-35   1.9e-31       1     192 [.       4     204 ..       4     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 6.5e-35
                                       TCE----SHHHHHHHHHHTSSEEEEE.--TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECE CS
                              PRAI   1 akicgltrasdvkaavkagadelgli.faesskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldv 74 
                                       akicg++++    aav +gad++g++ + + s+r++ +++a++l+   p+    V V   ++++e  ++a + g +v
  gi|386002660|ref|YP_005920959.1|   4 AKICGIRDPGARDAAVASGADAVGFVvEISRSRRSIGRKEAKSLIGGLPPFvsSVIVVEPKSAAEAASLALDTGAEV 80 
                                       69**********************972567899****************763467777778888999999999**** PP

                                       EEE-CGG.-HHHHHHHHHHS-TTSEEEEEEE-SSS--S-SSTT-.SEEEEE....SSS-SSSXXXXGGGGTTSXX.. CS
                              PRAI  75 vQLHGdedeqeyeellktelpvikalkvaesvdevkearradhv.dllllD....sgaGGtGelldwsliskllks. 145
                                       +Q+ G     e   +l++ +p      v++ +   +earr   v d+ll+D     + GGtG+  dw+l ++l k+ 
  gi|386002660|ref|YP_005920959.1|  81 LQVNGTL-GFEDLAALREMVPAKLVATVPARAGALEEARRLAGVaDALLVDshegGKLGGTGTVHDWNLTAELVKKv 156
                                       *******.7777778888999999999999999***********9******655555678**************99* PP

                                       .TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHH CS
                              PRAI 146 .lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfv 192
                                         +viLAGGL+peNvaeai+  g+++vDvssGVEt G kD +ki++f+
  gi|386002660|ref|YP_005920959.1| 157 gAPVILAGGLSPENVAEAIRAVGPYAVDVSSGVETGGRKDPAKIAAFL 204
                                       *********************************************997 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.38   1.1e+03     137     165 ..      58      86 ..      55      91 .. 0.83
   2 ?   14.5   2.7   5.8e-06     0.017     142     222 ..     110     186 ..     101     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.38
                               NMO 137 vvliptissvkearkvearGaDalivqGp 165
                                       v+++   s++++a  +   Ga +l v+G 
  gi|386002660|ref|YP_005920959.1|  58 VIVVEPKSAAEAASLALDTGAEVLQVNGT 86 
                                       56666679999999999999999999997 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.8e-06
                               NMO 142 tissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsg 218
                                        +++ +ear ++   aDal v+   +GG  G   +g++   +L ++ ++ v  Pvi aGG+  ++  +a+ a+G  +
  gi|386002660|ref|YP_005920959.1| 110 RAGALEEARRLAG-VADALLVDSH-EGGKLG--GTGTVHDWNLTAELVKKVGAPVILAGGLSPENVAEAIRAVGPYA 182
                                       4677777777754.49*****965.567777..5778899*********************9999999999999999 PP

                               NMO 219 vqig 222
                                       v + 
  gi|386002660|ref|YP_005920959.1| 183 VDVS 186
                                       8876 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.3e-05      0.13     136     170 ..     143     177 ..      70     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                          TMP-TENI 136 plgleglkelaealeiPvvaiGGitlenvaevlea 170
                                       + ++++ +el++++  Pv+  GG+++envae+++a
  gi|386002660|ref|YP_005920959.1| 143 VHDWNLTAELVKKVGAPVILAGGLSPENVAEAIRA 177
                                       66899999**********************99864 PP

>> DUF3606  Protein of unknown function (DUF3606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.6   4.9e+03      37      43 ..     151     157 ..     150     158 .. 0.82
   2 ?   11.1   0.0   9.8e-05      0.29      29      49 ..     165     185 ..     164     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                           DUF3606  37 aAVraVG 43 
                                       + V++VG
  gi|386002660|ref|YP_005920959.1| 151 ELVKKVG 157
                                       689***9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.8e-05
                           DUF3606  29 gvteeqLraAVraVGnsakkV 49 
                                       g+++e +++A+raVG+ a +V
  gi|386002660|ref|YP_005920959.1| 165 GLSPENVAEAIRAVGPYAVDV 185
                                       689*************88887 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013       0.4      44      75 ..     145     176 ..     115     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                           UPF0180  44 dtnvmgiedtetkapvInAsgktaeeIlqeve 75 
                                       d n+ ++  ++ +apvI A g+++e++ + ++
  gi|386002660|ref|YP_005920959.1| 145 DWNLTAELVKKVGAPVILAGGLSPENVAEAIR 176
                                       445555555899****************9997 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.029        87      88     103 ..      17      32 ..      14      45 .. 0.87
   2 ?    8.3   1.2   0.00053       1.6     148     215 ..      61     176 ..      42     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.029
                                       HHHHTT-SEEEEEEEE CS
                              DeoC  88 eakalGAdavkvvvyy 103
                                       +a+a GAdav++vv +
  gi|386002660|ref|YP_005920959.1|  17 AAVASGADAVGFVVEI 32 
                                       699**********977 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00053
                                       CHHHHHHHHHHHHTCCT-SEEEE--S.................................................SC CS
                              DeoC 148 vdpdlvaeAarvsaelGaDiiKvevp.................................................ke 175
                                       v+p+  aeAa+++ + Ga ++ v+ +                                                 k 
  gi|386002660|ref|YP_005920959.1|  61 VEPKSAAEAASLALDTGAEVLQVNGTlgfedlaalremvpaklvatvparagaleearrlagvadallvdsheggKL 137
                                       56888899999999999999999999999999999999999999999999999999999999999999999888888 PP

                                       C.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHH CS
                              DeoC 176 vvnateedaevfkdvikaapvpgvvlsGGvseedfletve 215
                                       +   t  d +   +++k++  p v+l+GG s e+++e+++
  gi|386002660|ref|YP_005920959.1| 138 GGTGTVHDWNLTAELVKKVGAP-VILAGGLSPENVAEAIR 176
                                       8888889999999999999999.99999998777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1457.95
//
Query:       gi|386002661|ref|YP_005920960.1|  [L=341]
Description: anthranilate phosphoribosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-90  300.6   0.1    1.5e-89  299.9   0.1    1.3  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    3.4e-15   55.6   0.5    6.7e-15   54.7   0.5    1.5  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.9   0.1   1.7e-93   1.5e-89       3     253 .]      72     321 ..      70     321 .. 0.99

  Alignments for each domain:
  == domain 1  score: 299.9 bits;  conditional E-value: 1.7e-93
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       +lvD++gTGGdg nt+N+Staaaiv+A+ G+ vakhgn +vss +Gsa vL +lgv++   pe+v +++e+ g+gf+
  gi|386002661|ref|YP_005920960.1|  72 PLVDTCGTGGDGTNTINVSTAAAIVAASSGAFVAKHGNYAVSSACGSANVLAELGVEVAPGPERVCQAIETLGIGFM 148
                                       68*************************************************************************** PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHH CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevs 156
                                       +ap +h++mk va +rrel +rTvfn+LGPL+npa +  q++gvy++ l+ kla +lk lg+eralvvhg+Glde++
  gi|386002661|ref|YP_005920960.1| 149 LAPVFHPSMKRVASIRRELATRTVFNILGPLTNPAGAPFQVMGVYDPRLCDKLALALKILGTERALVVHGSGLDEIT 225
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSS CS
                   Glycos_transf_3 157 llakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagka 233
                                        ++ t + el+ g +++yt++p++fg   a+ e+++gg+p+ena  l ++l+g+k+   rd+v++n gaal++ag a
  gi|386002661|ref|YP_005920960.1| 226 NTGPTRISELDRGALKSYTVTPQEFGYPLARIEEIRGGSPEENAGRLVEILSGAKGPG-RDVVAMNSGAALYVAGIA 301
                                       ********************************************************97.****************** PP

                                       SSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 234 dslkegvakaeevidsGkAl 253
                                       +sl +g++ aee+idsG Al
  gi|386002661|ref|YP_005920960.1| 302 ESLFDGARMAEESIDSGRAL 321
                                       *****************995 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.5   7.5e-19   6.7e-15       4      61 ..       4      60 ..       2      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 7.5e-19
                                      HHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHH CS
                   Glycos_trans_3N  4 ikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmre 61
                                      ++++++g +L+ +e+++++ ++++g +tdaqi+A+L+Al++kGe + Eia+la+Amr+
  gi|386002661|ref|YP_005920960.1|  4 LQQVLEGRDLSVSEAEALLGEVFNG-ATDAQIGALLVALKMKGEAVSEIAGLARAMRA 60
                                      7899********************8.79****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2351.24
//
Query:       gi|386002662|ref|YP_005920961.1|  [L=295]
Description: hypothetical protein Mhar_1982 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1905.13
//
Query:       gi|386002663|ref|YP_005920962.1|  [L=642]
Description: Glycogen debranching enzyme, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.9e-111  372.1   0.0   3.8e-111  371.7   0.0    1.1  1  GDE_C           Amylo-alpha-1,6-glucosidase
    7.2e-67  225.0   0.0    9.7e-67  224.6   0.0    1.1  1  GDE_N           Glycogen debranching enzyme N terminal
  ------ inclusion threshold ------
      0.063   12.0   0.0      0.092   11.5   0.0    1.1  1  Glyco_hydro_63  Glycosyl hydrolase family 63 C-terminal domai


Domain annotation for each model (and alignments):
>> GDE_C  Amylo-alpha-1,6-glucosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.7   0.0  6.4e-115  3.8e-111       3     383 .]     275     627 ..     273     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: 371.7 bits;  conditional E-value: 6.4e-115
                             GDE_C   3 sdqflvrrkseslkeeekgvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegq 79 
                                       +dqflvrr          g+s+iAG+pwF+dWGRD++IaL+GllL+tgrfe+A ++l tFa+++++Gl+PN +    
  gi|386002663|ref|YP_005920962.1| 275 ADQFLVRRG--------DGKSIIAGYPWFNDWGRDAMIALPGLLLTTGRFEDAGTVLATFAGAMKDGLLPNDFG--- 340
                                       566666654........799*****************************************************5... PP

                             GDE_C  80 ealyntvdaslwlieaiekYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakv 156
                                          ynt+da+lw+  a++kY +y+gd e++r+ +p+l+ i ++y+  t    + d  dgli  +     lTWmDakv
  gi|386002663|ref|YP_005920962.1| 341 AEGYNTIDAALWFFWAVYKYWSYSGDLELVRQLLPTLRAICRRYAGETP-GSYSD-GDGLIASKP---GLTWMDAKV 412
                                       457*****************************************98887.88888.9*****999...9******** PP

                             GDE_C 157 kgepvtPRdGkaveinaLwyaaLkileelaekalge.akkssykelaekikesfekkFwdeaaaavakreilaDvlk 232
                                        +e vtPR+Gka+einaLwy+ Lk++e + e+  +e a++  y  lae++ es++k Fw+      +++++l+D+++
  gi|386002663|ref|YP_005920962.1| 413 GEEFVTPRAGKACEINALWYNGLKVMELFTERLGDEvAEEVVYPDLAERVGESYSK-FWN------PEEGCLYDLID 482
                                       *******************************7666688999**************9.***......9*********9 PP

                             GDE_C 233 sseekdlslRpNflialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvW 309
                                            d  +RpN++ia sl++++l++   + v+e+a+eeLltp+Gl+tL+p+dp+Y g+Y+g   +rd aYHqGtvW
  gi|386002663|ref|YP_005920962.1| 483 G---IDPAIRPNQVIAASLPFTPLDASMVRGVVETATEELLTPYGLRTLSPRDPAYLGRYEGGPAERDRAYHQGTVW 556
                                       8...799********************************************************************** PP

                             GDE_C 310 vwllgsyveallkfgeklgkskealeevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                       +wl+g y++a+l++g +   +k++ e + +lL+ l +   + g+g++ E+fdgd+++ p gci+QAWSv+e++r
  gi|386002663|ref|YP_005920962.1| 557 PWLMGPYITARLRAGGN---TKKEREAAGELLRPLIDLEGQIGVGTICEVFDGDGPHRPGGCITQAWSVGEVMR 627
                                       ***************98...6677777889999999999999*****************************987 PP

>> GDE_N  Glycogen debranching enzyme N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.6   0.0   1.6e-70   9.7e-67       1     212 [.      18     226 ..      18     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 224.6 bits;  conditional E-value: 1.6e-70
                             GDE_N   1 REwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLe 77 
                                       REwl+TNglGGYas+tv+ antR+yhGlLvaal+pp+gRtllls++de+l+ +g +++L++++ypg+i+p+G+++L+
  gi|386002663|ref|YP_005920962.1|  18 REWLVTNGLGGYASSTVIAANTRSYHGLLVAALTPPTGRTLLLSSIDEELIADGVSCHLACHQYPGTIYPQGFRHLQ 94 
                                       9**************************************************************************** PP

                             GDE_N  78 sFelepvptwtyrvgdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqe.... 150
                                       +F+  pvpt+ yr +++++ek+++m++gent++i+Y++e+      +r +pl+++R+fh ++ a +++q++ +    
  gi|386002663|ref|YP_005920962.1|  95 EFRRYPVPTFLYRTEGMEVEKRVFMVYGENTTVIRYDIEG---VGLFRAVPLVSCRSFHVASGAPPMDQSRLSvegp 168
                                       ****************************************...679*****************98887777556665 PP

                             GDE_N 151 eglveiqaseaepslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfevelk 212
                                        g+v+    ++++ +++ ++ ++++ +e+ wy+ +ey++E++rGl++red +spg+fe+e++
  gi|386002663|ref|YP_005920962.1| 169 GGGVR---LRSDCDFSIVSD-GARYLREDLWYHSLEYEVERRRGLQWREDAFSPGRFEAEVD 226
                                       33332...234556666666.999**********************************9986 PP

>> Glyco_hydro_63  Glycosyl hydrolase family 63 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.5e-05     0.092     375     411 ..     516     556 ..     498     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.5e-05
                                       TTTTEETTEEBSB-TTSTTTT-.........TT-SSSS-B- CS
                    Glyco_hydro_63 375 peelwsdyGlrslskksslygkrn....tehdenYWrgpiW 411
                                       +eel ++yGlr ls +++ y  r     +e d +Y +g++W
  gi|386002663|ref|YP_005920962.1| 516 TEELLTPYGLRTLSPRDPAYLGRYeggpAERDRAYHQGTVW 556
                                       589****************98774334479**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4692.29
//
Query:       gi|386002664|ref|YP_005920963.1|  [L=538]
Description: Alpha-amylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-53  180.9   0.0    4.8e-53  180.5   0.0    1.2  1  Glyco_hydro_57   Glycosyl hydrolase family 57
  ------ inclusion threshold ------
      0.065   13.1   0.0       0.13   12.2   0.0    1.5  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   0.0   5.4e-57   4.8e-53       2     325 .]       6     300 ..       5     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 5.4e-57
                                       EEEEE-----TTS-...SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHH CS
                    Glyco_hydro_57   2 fvfhqHqplykkpg...kgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpate 75 
                                       + f++Hqpl+ +++   +g   ++  r    + Y++++ +  +f +v+                    +k+ylpa++
  gi|386002664|ref|YP_005920963.1|   6 LCFEVHQPLRLRRDffwSGSPMRRIERDLLSDFYFDDPENRRIFDRVA--------------------EKCYLPANQ 62 
                                       6799*******9996666666666777777788***************....................********* PP

                                       HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHH CS
                    Glyco_hydro_57  76 ellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsed 152
                                       ++le ie+  ++ + +k       ++++sg +l q++++ n+evl++f  l+++g vE+l ++y+H+l++l++d  +
  gi|386002664|ref|YP_005920963.1|  63 VILEEIERHRDSERPFK------AAYSFSGVFLDQAERY-NPEVLDSFARLVDTGMVEVLEQTYHHSLASLYEDGRE 132
                                       *****************......****************.************************************* PP

                                       HHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS..-EE CS
                    Glyco_hydro_57 153 ieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllkngg.iav 228
                                       + +qv+++re + + fg +Pr f ++El+++++i++i++ +G+  +f+++       +    p+++y+++  + i++
  gi|386002664|ref|YP_005920963.1| 133 FAEQVRMHRERVWDAFGTRPRIFENTELLYDDRIAKIVEGMGYAGIFAEGI----VAH----PNWVYRPEGCDrISL 201
                                       *************************************************94....334....8999**999999*** PP

                                       EE--CHH-TTTSGGG-................TTSB...........-TT---TTT-..-BB-TT-S---HHHHHHH CS
                    Glyco_hydro_57 229 ffRdreLsddigFrys....eqypleavddfinwlk.kvkkaksevvtialdgEnwg..hypetgkkeFleklyeel 298
                                       ++Rd+++ dd+gFr+s    + ypl ++++++ w+  kv    +++v+i+ d+E++g  +++ tg++eFl+ l++++
  gi|386002664|ref|YP_005920963.1| 202 LLRDYQITDDMGFRFSarwwKEYPL-TAEKYASWIAaKV----GDCVNIFCDYETFGehQWADTGIFEFLRHLPRKI 273
                                       *******************999***.**********565....********************************** PP

                                       HHHHHHHHHHHHHHHHHHSS-EEEEEE CS
                    Glyco_hydro_57 299 eenglielvtpsefikklkpkgliklp 325
                                        +  ++++ tps+++++++p +++++p
  gi|386002664|ref|YP_005920963.1| 274 LRWDHLRFATPSDVVRDHPPLQTLSVP 300
                                       *******************99988775 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.13      49     122 ..     101     176 ..      61     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHTT.EEEEE--SS--EG.GGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT.E CS
                   Polysacc_deac_1  49 devremaasG.veignHtinhsnl.krlseeevrreierakdalrkalgreprlfryPygsasatvlevarelgfa 122
                                       d   ++++ G ve+   t++hs     +  +e+++++ + ++ + +a+g +pr f    + +++++ ++++ +g+a
  gi|386002664|ref|YP_005920963.1| 101 DSFARLVDTGmVEVLEQTYHHSLAsLYEDGREFAEQVRMHRERVWDAFGTRPRIFENTELLYDDRIAKIVEGMGYA 176
                                       677899*************9997634445559***************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 3078.81
//
Query:       gi|386002665|ref|YP_005920964.1|  [L=443]
Description: N-acetyltransferase GCN5 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-15   54.8   0.1    1.5e-14   54.1   0.1    1.3  1  Acetyltransf_9  Acetyltransferase (GNAT) domain
     0.0037   17.2   0.0      0.033   14.1   0.0    2.2  2  FR47            FR47-like protein
     0.0078   16.4   0.3      0.015   15.5   0.3    1.5  1  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   2.6e-18   1.5e-14       2     126 ..      19     146 ..      18     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.6e-18
                                       EEEE-.GGGHHHHHHHHHHHTT----H...HHHHHHHHHHTTSEEEEEEE..TTEEEEEEEEEEEEEEETTEEEEEE CS
                    Acetyltransf_9   2 irelt.eedldevlellkyaFqdeespl.eeireyfrklleesrvlgaed..ngelvgqlallplelnvpGktlkaa 74 
                                       ir+++ ++d  +  +++++ F  ee     e  ++  + ++++r ++a +   ge+++ +al+p+++ + G +lk+a
  gi|386002665|ref|YP_005920964.1|  19 IRRAEsPDDAGKLRHHFDRIFLPEEVGEfAETVFSHLPGMKNERWFIAVEeeTGEIASAFALIPWTWEMAGIRLKVA 95 
                                       6677657889999999999999999887546778888888998888887767999********************** PP

                                       EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT-E CS
                    Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGye 126
                                         + V++   hr+rg+++ L +++ + ++eeg  l++  ++ +++YrrfGy 
  gi|386002665|ref|YP_005920964.1|  96 EMGIVGTGEGHRNRGLMRLLYREFEATLAEEGFDLAVVQGI-PGFYRRFGYY 146
                                       *****************************************.********95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.6e-06     0.033      17      60 ..      90     133 ..      84     145 .. 0.92
   2 ?    0.2   0.0      0.13   7.7e+02      35      52 ..     245     263 ..     242     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-06
                                       EE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE CS
                              FR47  17 lrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllv 60 
                                       +r+++ e+g + + + hr+rGl ++l ++  + +ae+g ++ +v
  gi|386002665|ref|YP_005920964.1|  90 IRLKVAEMGIVGTGEGHRNRGLMRLLYREFEATLAEEGFDLAVV 133
                                       68899*********************************998877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
                                       SSSHH.HHHHHHHHHHHHH CS
                              FR47  35 rrGlg.srlvkalakeiae 52 
                                       r+G+g +++v++++++i+ 
  gi|386002665|ref|YP_005920964.1| 245 RQGFGaGLIVSEVSEGISD 263
                                       889973577999**99987 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   2.5e-06     0.015      31     117 .]      59     145 ..      28     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                                       TTCEEEEEEET..TEEEEEEEEEEEET......TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE CS
                    Acetyltransf_1  31 eaegllvaeed..geliGfisllkipd......ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl 99 
                                        +e++++a e+  ge++    l + ++      +  +va++  +   + +r++Gl ++L+++ e  + eeg+    l
  gi|386002665|ref|YP_005920964.1|  59 KNERWFIAVEEetGEIASAFALIPWTWemagirL--KVAEMGIVGTGEGHRNRGLMRLLYREFEATLAEEGF---DL 130
                                       4556666555524555555544444445888543..8999999999************************99...55 PP

                                       EEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1 100 aveedndaairlYeklGF 117
                                       av    ++  ++Y+++G+
  gi|386002665|ref|YP_005920964.1| 131 AV---VQGIPGFYRRFGY 145
                                       55...4566789977997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2704.87
//
Query:       gi|386002666|ref|YP_005920965.1|  [L=268]
Description: Putative circadian clock protein, KaiC [Methanosaeta harundinacea 6Ac]
Scores for complete 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-47  162.0   0.2    1.7e-47  161.7   0.2    1.0  1  ATPase           KaiC
    4.3e-05   23.4   0.0    6.7e-05   22.8   0.0    1.2  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
    5.6e-05   22.8   0.0    0.00012   21.8   0.0    1.5  1  AAA_25           AAA domain
     0.0036   16.7   0.0     0.0067   15.8   0.0    1.5  2  DnaB_C           DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.015   14.5   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.029   13.6   0.1      0.053   12.8   0.1    1.3  1  Rad51            Rad51
      0.033   13.7   0.5       0.36   10.2   0.0    2.1  2  PhoH             PhoH-like protein
      0.046   13.8   0.0      0.084   12.9   0.0    1.5  1  AAA_14           AAA domain
      0.054   13.2   0.0      0.078   12.7   0.0    1.2  1  IstB_IS21        IstB-like ATP binding protein
      0.055   13.2   0.1      0.094   12.4   0.1    1.3  1  Sigma54_activat  Sigma-54 interaction domain
        0.1   11.7   0.0       0.18   10.9   0.0    1.3  1  DAP3             Mitochondrial ribosomal death-associated pro
       0.21   11.8   0.4       0.39   11.0   0.3    1.7  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.7   0.2   1.1e-50   1.7e-47       1     227 [.      37     262 ..      37     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.7 bits;  conditional E-value: 1.1e-50
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlek 76 
                                       v++gI+g+D++++gG+ +++v  +tG++GtGKt+fa qF+ +g+++ ge+g+++   e+ae l+++ + s+ wd+ k
  gi|386002666|ref|YP_005920965.1|  37 VPSGIPGFDDLVNGGFHRRTVNTVTGSSGTGKTVFASQFIHEGIKN-GEKGMIIMPSESAEYLKRELHsSFRWDFWK 112
                                       79********************************************.******************99879******* PP

                            ATPase  77 leeegklaiidasesaeesaeekdkedleelieelaeai....keikakrvviDsitgl.ayeekeavaReilrqlv 148
                                       leeegkl+i+d++    +  +++ ++d+ e++ ++++ +    +e k +rv+iD + ++ +  e++ v+R+  + l+
  gi|386002666|ref|YP_005920965.1| 113 LEEEGKLVIVDVTDPVLR-LQKSIETDPVEFLINFRKLVdkkvREEKPQRVLIDDLMAFfTAVESPFVMRSLADDLF 188
                                       ***********9988765.55577777777777777665111166677***********999*************** PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                         l+ lgvTa+++       ea+g  ++ e+ +d   +L++++i +++vR++ i+kmRg+++s+ + +++I++eg  
  gi|386002666|ref|YP_005920965.1| 189 GDLRSLGVTAVITIG-----EAFGMTQIMEYGADSCTILKRERIGNNMVRSIYIMKMRGSRISNSIRVLDISDEGMA 260
                                       **************9.....89****************************************************998 PP

                            ATPase 226 vl 227
                                       v 
  gi|386002666|ref|YP_005920965.1| 261 VS 262
                                       85 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.5e-08   6.7e-05      17     103 ..      72     161 ..      69     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.5e-08
                              MEDS  17 lvpfikaglargekvlyvasastldelrealrka.gldvdaalesgqleildaeety...lrgggfdpermlealrr 89 
                                       +++fi++g+++gek ++++++++ + l+++l++    d  +++e+g+l i+d ++      ++ + dp ++l ++r+
  gi|386002666|ref|YP_005920965.1|  72 ASQFIHEGIKNGEKGMIIMPSESAEYLKRELHSSfRWDFWKLEEEGKLVIVDVTDPVlrlQKSIETDPVEFLINFRK 148
                                       679****************************8852344445**************9977777888999********* PP

                              MEDS  90 alakal.adgyaglr 103
                                        ++k + ++  +  r
  gi|386002666|ref|YP_005920965.1| 149 LVDKKVrEE--KPQR 161
                                       ***998444..3444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.8e-08   0.00012      11     157 ..      33     173 ..      25     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.8e-08
                            AAA_25  11 svadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedel 86 
                                       s +++ + +p  ++lv g   + +++ ++G +gtGKt++a++  ++    G++  g         ++   E +e  l
  gi|386002666|ref|YP_005920965.1|  33 SYEKVPSGIPGFDDLVNGGFHRRTVNTVTGSSGTGKTVFASQFIHEGIkNGEK--G--------MIIMPSESAE-YL 98 
                                       55666777888899***9889*************************9955553..2........2233333333.55 PP

                            AAA_25  87 rrRlravgeal....rddarllvldlagveslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsralgg 157
                                       +r l+  ++      ++ ++l ++d+ +   l+L +++  +++  l  + + ++++++e e+++ v iD l +++ +
  gi|386002666|ref|YP_005920965.1|  99 KRELHSSFRWDfwklEEEGKLVIVDVTD-PVLRLQKSIETDPVefLINFRKLVDKKVRE-EKPQRVLIDDLMAFFTA 173
                                       5555554433334448889******977.699999999999888888888889999999.99********9998865 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.5e-06    0.0067       3      74 ..      38     108 ..      37     170 .. 0.74
   2 ?   -3.7   0.0       3.9   5.9e+03     202     236 ..     213     242 ..     210     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-06
                                       XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTX CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaei 74 
                                       ++g   +D+l+ +G+++ ++  + + +++Gkt++a +++++  ++ +++++++  e  + + ++R l s  + 
  gi|386002666|ref|YP_005920965.1|  38 PSGIPGFDDLVnGGFHRRTVNTVTGSSGTGKTVFASQFIHEGIKNGEKGMIIMPSE--SAEYLKRELHSSFRW 108
                                       67777788766268*************************99888777776665444..344556666555555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                                       CCCXSEEEEEEECCHHHHHHCHHCEEEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 202 eqdADvvlflyrdeyykedseekgkaeiiiaKhRn 236
                                       e  AD  ++l r+++ ++      +  i+i+K R 
  gi|386002666|ref|YP_005920965.1| 213 EYGADSCTILKRERIGNNM-----VRSIYIMKMRG 242
                                       5567777777777665532.....34677777765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     1e-05     0.015       2      40 ..      56      91 ..      55     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvN 40
                                      +v  VtG +GtGKtv ++++++e     ++ ++ +++  
  gi|386002666|ref|YP_005920965.1| 56 TVNTVTGSSGTGKTVFASQFIHEG---IKNGEKGMIIMP 91
                                      5778*****************997...344444444444 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.5e-05     0.053      14      56 ..      32      74 ..      20      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                                      HSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51 14 sellqlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                      ++  ++  G   +D+l++GG++  ++  + G +++Gkt ++ +
  gi|386002666|ref|YP_005920965.1| 32 KSYEKVPSGIPGFDDLVNGGFHRRTVNTVTGSSGTGKTVFASQ 74
                                      555567788899**************************99876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00024      0.36      19      54 ..      55      90 ..      47     102 .. 0.83
   2 ?    1.5   0.1      0.12   1.7e+02      99     126 ..     226     253 ..     208     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                      -SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                              PhoH 19 ndivfaiGpaGtGKtylavalavealkkkkvkriil 54
                                       ++ +++G++GtGKt +a +   e +k+++   ii+
  gi|386002666|ref|YP_005920965.1| 55 RTVNTVTGSSGTGKTVFASQFIHEGIKNGEKGMIIM 90
                                      678899************999888888887777765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.12
                                       HHHTTSEEEEEGGGGTT--B-SEEEEE- CS
                              PhoH  99 llekgkievaplaymRGrTlndafvilD 126
                                        + +++++ + +  mRG  +++++ +lD
  gi|386002666|ref|YP_005920965.1| 226 RIGNNMVRSIYIMKMRGSRISNSIRVLD 253
                                       56678888999999*********99998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.6e-05     0.084       3      71 ..      56     123 ..      54     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeekktylflD 71 
                                        + ++tG   +GKT+++ q+i+e +   ++ ++ +  ++ ++ k++  +++   + ++ +e + ++++ D
  gi|386002666|ref|YP_005920965.1|  56 TVNTVTGSSGTGKTVFASQFIHEGIkNGEKGMIIMPSESAEYLKRELHSSFRWDFWKL-EE-EGKLVIVD 123
                                       6789*****************9999888888999999998888776555555555553.33.56666666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.2e-05     0.078      38      79 ..      47      87 ..      31     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                         IstB_IS21 38 LatlsfiekkenivllGpsGvGKshlaialgveavraglsvl 79
                                      L+++ f ++  n  ++G sG+GK+ +a  + +e++++g + +
  gi|386002666|ref|YP_005920965.1| 47 LVNGGFHRRTVN-TVTGSSGTGKTVFASQFIHEGIKNGEKGM 87
                                      556666666655.579********************998755 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.3e-05     0.094      26      55 ..      59      89 ..      50     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                                      EEECSTTSSHHHHHHH.HHHHSTTTTS-EEE CS
                   Sigma54_activat 26 litGesGtGKellara.iheaskrkekpfva 55
                                       +tG sGtGK+++a++ ihe  k+ ek ++ 
  gi|386002666|ref|YP_005920965.1| 59 TVTGSSGTGKTVFASQfIHEGIKNGEKGMII 89
                                      589**********965289877777766654 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.18      28      63 ..      60      98 ..      46     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                      EE-SSSSSTTTTHHHHHHHGGGS...--EEEEES-GGGG CS
                              DAP3 28 ltGekgsGKSvlLlqalayAlek...gwvvlhvpeaedl 63
                                      +tG  g+GK+v  +q ++ ++++   g++++   +ae l
  gi|386002666|ref|YP_005920965.1| 60 VTGSSGTGKTVFASQFIHEGIKNgekGMIIMPSESAEYL 98
                                      89*******************987768888877777655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00026      0.39       5      28 ..      55      78 ..      52     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                            AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                      +++ +vtG sGtGKT+ + ++ ++
  gi|386002666|ref|YP_005920965.1| 55 RTVNTVTGSSGTGKTVFASQFIHE 78
                                      56678************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1843.22
//
Query:       gi|386002667|ref|YP_005920966.1|  [L=612]
Description: Glycogen synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.0   0.0    1.3e-06   27.3   0.0    2.8  2  Glycogen_syn     Glycogen synthase
    0.00014   21.9   0.0      0.013   15.5   0.0    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4
    0.00093   18.8   0.0      0.002   17.7   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.068   13.6   0.1       0.23   11.9   0.0    1.9  2  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.9e-10   1.3e-06       6     336 ..      16     400 ..      11     407 .. 0.74
   2 !   26.3   0.0   5.9e-10   2.7e-06     441     577 ..     451     591 ..     439     607 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.9e-10
                                       TTS-SSCHHHHHHHHHHHHH.....H..HHGGGEEEEEE-........-TTGGG.GTEEE---..-SHHHHHHHHHH CS
                      Glycogen_syn   6 vankvGGiytvlkskakvtt.....e..elGdnytllGpl........keqkar.teveelea..enealkkalksl 64 
                                       v+nk+GGi+ v+ + a++ +     +  e   + ++ Gp+        ++ kar t+v  l+a   n++l +al++l
  gi|386002667|ref|YP_005920966.1|  16 VCNKMGGIWDVIDAEARTLArlaarKeiECDLKILVAGPYyptagadwNKGKARvTDVSGLDAldMNDELTSALDQL 92 
                                       7899999999998877654311111211233345566887333332222333332567777762235669******* PP

                                       GGGT--EEEEEESSTT--E.EEEE-G...........GGGSTTHHHHHHHHHHHH-----TT-H.....HHHHHHHH CS
                      Glycogen_syn  65 rekGvkvlyGrwlieGapk.vilfdl...........dsaavkldewkaelwekvkigipeedr.....etndaiil 124
                                       +++G++v+  +  + G p   +lf++           ++ ++  +  kae w+  ++ + + +r     e  + + l
  gi|386002667|ref|YP_005920966.1|  93 KAEGIDVVAAQTEVAGVPIgYLLFNTayydsiiktlyGTKMTLANAIKAEAWQLSRLDSMQFERapygpEYTHYLGL 169
                                       ****************9963577775222111111112333445889999999999988776653333377788999 PP

                                       HHHHHHHHHHHHCT--....................--EEEEEEETGGGHHHHHHHHHTT-SEEEEEEESS-HHHHH CS
                      Glycogen_syn 125 Gflvalflkefrelee....................kkavvahfhewlaGvgliltrkrkldvatvftthatllGry 181
                                        + v++f++ +++l e                    k +v  h he+ +  +l  ++   ++v t+ t hat+ Gr 
  gi|386002667|ref|YP_005920966.1| 170 SYAVSQFVHYLVSLGEerakkygdeaisefarsvmpKMRVSLHCHEFPTFYALARLKCLGVPVRTMATLHATVPGRS 246
                                       99999999988877666778899999****999998889999*********************************96 PP

                                       HHHTT---TTSTTS--HHHHHHHTT-HHHHHHHHHHHHHSSEEEESSHHHHHHHHHHSS---SEE----B-GGGT-- CS
                      Glycogen_syn 182 lcagavdfynnldkfdvdkeaGkrqiyhrycleraaahtadvfttvseitaleaehllkrkpdvvlpnGlnvkkfsa 258
                                               y  l+k + ++ + + ++        + a+ adv + v + t  ea  l+++   +v+ nG+++     
  gi|386002667|ref|YP_005920966.1| 247 S------GYRSLEKVAKNDGTWDPNVPVGMATLESLAKYADVVSFVGDSTMREAM-LFHKLNGIVIRNGIELDVRRI 316
                                       3......4999999998888888899888877788999************99985.45556778999**98765554 PP

                                       TTTHHHHHHHHHHHHHHHHHH...HTTT---S-GGGEEEEEEESSS-TTTTTHHHHHHHHHHHHHHHHC---..... CS
                      Glycogen_syn 259 lhefqnlhalkkekindfvrG...hfyGhldfdldktlyffiaGryefsnkGadifieslarlnyllkveks..... 327
                                         + +n     + ki+ f+       yG    d ++ l +f+  r e +nkG   +++sl   n+ll++++      
  gi|386002667|ref|YP_005920966.1| 317 DWDKKN---ACRRKIQRFLSEglhRVYGGEVIDPEEILPVFTISRLELENKGYPQLLDSLLLQNHLLRHRRMdhrfa 390
                                       444444...4577999998742324789999*************************************987634444 PP

                                       .T-EEEEEEE CS
                      Glycogen_syn 328 .kktvvafli 336
                                        k+ vv++li
  gi|386002667|ref|YP_005920966.1| 391 eKMRVVCLLI 400
                                       3555666655 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 5.9e-10
                                       SEEEEEE-S---TTSSSS---HHHHHHH-SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHHH-T.TGGG CS
                      Glycogen_syn 441 rvkvvfhpeflsstspllgldyeefvrGchlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfmeelie.dakd 516
                                       +v  +++p++    +  + +  +e + Gc  G+fps yep+  t  e    G ps+ +   Gf   +++     +  
  gi|386002667|ref|YP_005920966.1| 451 QVSAILYPQWAGPDDGGMRMGVDEIMAGCVAGIFPSQYEPFLLTGLEAGREGTPSIVSRACGFSDALKKVERlVTGL 527
                                       577788999999999999999******************************************99887654423445 PP

                                       GTEEEE--SSS-HHHHHHHHHHHHHHHHT--HHHHHHHHHHHH...HHGGGGBHHHHTHHHHHH CS
                      Glycogen_syn 517 yGiyivdrrfkslddsveqlaqflyefvkksrrqriiqrnrte...rlsdlldwkrlGlyyvka 577
                                        G+ +vd    sl++ + + a  l  f+      ++  r   e    l++l++w +  l+y k 
  gi|386002667|ref|YP_005920966.1| 528 GGVVVVDNIEASLQEMILDYALALDYFTWTYLEDQVKYRLLCEesfALAKLMNWTEPVLEYYKN 591
                                       6899*************99999888888888777777776555222699999999887777664 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.01        47      25      86 ..      50     110 ..      21     127 .. 0.73
   2 !   15.5   0.0   2.9e-06     0.013      76     169 ..     211     312 ..     203     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                    Glyco_transf_4  25 vtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalga 86 
                                       ++ g+  p++ + ++ +   rv  ++  ++l +   l ++  +lk+e++Dvv a++++a++ 
  gi|386002667|ref|YP_005920966.1|  50 LVAGPYYPTAGA-DWNKGKARVTDVSGLDALDMNDELTSALDQLKAEGIDVVAAQTEVAGVP 110
                                       455555555555.56666666666777788888888999999**************988754 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.9e-06
                    Glyco_transf_4  76 vHahspaalgaallalrr.rlgiplVltvHglye...........krllkarlkplsrllralerrllrradrviav 140
                                       +H+h ++++ +al++l+     +++ +t+H + +                + + p  ++  a ++ l++ ad v  v
  gi|386002667|ref|YP_005920966.1| 211 LHCHEFPTF-YALARLKClGVPVRTMATLHATVPgrssgyrslekVAKNDGTWDPNVPVGMATLESLAKYADVVSFV 286
                                       49**98776.6666666634555569*********99999888774455667778999999999999********** PP

                    Glyco_transf_4 141 SeatadelrerygvppekitVipnGvDle 169
                                        ++t +e +  ++++     Vi nG+ l+
  gi|386002667|ref|YP_005920966.1| 287 GDSTMREAMLFHKLNG---IVIRNGIELD 312
                                       *******999666776...8******998 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-07     0.002      86     143 ..     472     535 ..     467     550 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-07
                                       HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT CS
                   Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpn 143
                                       ++e++  + + ++ps++E+f ++ lEA   g+p i+s a+g+++ +k+ e       G++v  n
  gi|386002667|ref|YP_005920966.1| 472 VDEIMAGCVAGIFPSQYEPFLLTGLEAGREGTPSIVSRACGFSDALKKVErlvtglGGVVVVDN 535
                                       567788888889**********************************999988855444444444 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 ?   -3.3   0.0       2.5   1.1e+04      84     109 ..     269     295 ..     264     310 .. 0.52
   2 ?   11.9   0.0   5.1e-05      0.23      66     116 ..     472     524 ..     459     546 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                                       SHHHHHHHHTT-EEEE-TGG.GTTT-- CS
                   Glyco_trans_1_4  84 glkllEamaaglpvVatdvg.giaevv 109
                                       g+++lE++a    vV++     ++e++
  gi|386002667|ref|YP_005920966.1| 269 GMATLESLAKYADVVSFVGDsTMREAM 295
                                       555666666555555552221344444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.1e-05
                                       HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE- CS
                   Glyco_trans_1_4  66 laellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.gengllv 116
                                       ++e++a +   ++Ps  e f l+ lEa   g+p +++++ g+++++ ++   lv
  gi|386002667|ref|YP_005920966.1| 472 VDEIMAGCVAGIFPSqyEPFLLTGLEAGREGTPSIVSRACGFSDALkKV-ERLV 524
                                       7899999999*****999*******************999999988532.2232 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (612 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4604.78
//
Query:       gi|386002668|ref|YP_005920967.1|  [L=408]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-33  114.8   0.0      4e-33  114.4   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.4e-22   80.5   0.1    2.5e-22   79.8   0.1    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.2e-21   75.7   0.0    1.2e-20   74.2   0.0    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.9e-19   70.6   0.0    6.2e-19   69.0   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.3e-09   38.1   0.0    4.7e-08   33.0   0.0    2.6  1  Glyco_transf_5   Starch synthase catalytic domain
    1.7e-06   28.3   0.0    3.9e-06   27.2   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00096   17.9   0.0     0.0045   15.7   0.0    1.8  2  Glyco_transf_20  Glycosyltransferase family 20
     0.0071   16.4   0.0      0.024   14.7   0.0    1.8  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.14   10.7   0.0       0.21   10.1   0.0    1.2  1  Glycogen_syn     Glycogen synthase
       0.17   12.0   0.0        4.5    7.4   0.0    2.6  3  DUF2325          Uncharacterized protein conserved in bacteri


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 !  114.4   0.0   2.2e-36     4e-33       3     171 ..     209     381 ..     207     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 2.2e-36
                                       HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflg 79 
                                       e+ ++++ ++e++++il+vgrle++Kgv  l++a++++ ++ +p++kl+++G+g+ e +++++ae+l+ s +v ++ 
  gi|386002668|ref|YP_005920967.1| 209 EELQERYSLKEEDEVILFVGRLEPVKGVIPLLEAMPKVLQE-HPRAKLLVVGKGTLEGRVRSMAEALGGSVKV-VTD 283
                                       6778889999****************************976.***************************9998.789 PP

                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTT....SEEEE-TT-HHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdge....tGllvkpnnaealae 150
                                       +++ e +++ +  ad+ v+ps +E+fGiv +EA a   p+++ +  ++g++e+v d      tG++v p ++ ++a 
  gi|386002668|ref|YP_005920967.1| 284 FLDLESKIHHYALADLCVFPSLYEPFGIVGVEAAAMERPAVVGAsgVSGLREIVDDPSaerpTGVHVNPRDPGDIAW 360
                                       99989999*********************************9997899********999****************** PP

                                       HHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 151 airklledeelrerlgenark 171
                                       +i+ +l+d+e+r+++g+n+r 
  gi|386002668|ref|YP_005920967.1| 361 GINLVLDDPERRREWGRNGRA 381
                                       *******************96 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 !   79.8   0.1   1.4e-25   2.5e-22       2     134 .]     222     368 ..     221     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.4e-25
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---...HHHHHHHTT-T.TEEEE---...THHHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgp.rpeeleelaagleerveftGfv...edlaellaa 72 
                                        vilfvGrl e+vkgv  llea+p++++++  ++l++vG+g+ +  +++++a+ l  +v+++      e++  ++a 
  gi|386002668|ref|YP_005920967.1| 222 EVILFVGRL-EPVKGVIPLLEAMPKVLQEHprAKLLVVGKGTlE-GRVRSMAEALGGSVKVVTDFldlESKIHHYAL 296
                                       58*******.889**************88447*********955.599988876667777666554878899***** PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGG..GTTT--.....T.TSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvg..giaevv.....g.engllvppgdpealaeailrLled 134
                                       ad++v+Ps  e fg++ +Ea+a+++p V+ + g  g++e+v     +  +g+ v+p+dp ++a  i  +l+d
  gi|386002668|ref|YP_005920967.1| 297 ADLCVFPSlyEPFGIVGVEAAAMERPAVVGASGvsGLREIVddpsaErPTGVHVNPRDPGDIAWGINLVLDD 368
                                       ****************************88753339*****9765414689************999888876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   6.6e-24   1.2e-20       1     169 [.      15     196 ..      15     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 6.6e-24
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev...................elvvrvprvplpllkrllrsl 58 
                                       +GG ++++  ++++La +G e++v+t gd+   ++e                    + +++ + + +    ++l++l
  gi|386002668|ref|YP_005920967.1|  15 FGGLGVYADSISKELASLGQEISVFTMGDGSLKRREKargisvfretpapmrdgweP-FISDRTRAWGEGVDFLFDL 90 
                                       59***************************9999999987776666666555544421.1111112222222333333 PP

                    Glyco_transf_4  59 aflrrl.rrllkre.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrr 133
                                        ++ +l  + l+++  +D+  ah++  l  ++la++r lg+pl+++vH+l+    +++   p  +++  le + +  
  gi|386002668|ref|YP_005920967.1|  91 LSYNQLaVASLRENgPFDLAVAHDWLGL-PGGLAAKRVLGVPLIFHVHSLE----VGRETAPNPQIV-DLELKGAGL 161
                                       333333134444447*********9886.788888888*************....555555555555.5788899** PP

                    Glyco_transf_4 134 adrviavSeatadelrerygvppekitVipnGvDle 169
                                       ad vi+vS+a++++l   +gvp++ki+V ++Gv +e
  gi|386002668|ref|YP_005920967.1| 162 ADGVITVSKAMKEQLSG-LGVPEDKIEVSYHGVEPE 196
                                       *****************.***************987 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 !   69.0   0.0   3.4e-22   6.2e-19       1     156 [.      16     188 ..      16     192 .. 0.78
   2 ?   -1.2   0.0       1.4   2.5e+03      81      81 ..     260     260 ..     191     345 .. 0.57

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 3.4e-22
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhr.lpvprrp.s.plad.........laalral.. 63 
                                       gG g+y+  ++++La +G e+ v+t ++    +++ ++g+ v r  p+p r  + p+ +         +++l++l  
  gi|386002668|ref|YP_005920967.1|  16 GGLGVYADSISKELASLGQEISVFTMGDGSLKRREKARGISVFReTPAPMRDgWePFISdrtrawgegVDFLFDLls 92 
                                       8************************9888888889999999986246665542222211222222344445544433 PP

                   Glyco_trans_4_4  64 ......rrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavl 134
                                             ++l  ++  ++d+ +ah++++ + +++a+r  g+pl++++h+l++ r+ ++ ++++  le   +  ad+v+
  gi|386002668|ref|YP_005920967.1|  93 ynqlavASL--RENGPFDLAVAHDWLGLPGGLAAKRVLGVPLIFHVHSLEVGRETAPNPQIV-DLELKGAGLADGVI 166
                                       322111444..59************8888888888667************999988888888.8999********** PP

                   Glyco_trans_4_4 135 vvseaeaeelralgvpadrvvv 156
                                       +vs a+ e+l  lgvp d+++v
  gi|386002668|ref|YP_005920967.1| 167 TVSKAMKEQLSGLGVPEDKIEV 188
                                       ********************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                   Glyco_trans_4_4  81 s 81 
                                        
  gi|386002668|ref|YP_005920967.1| 260 K 260
                                       1 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 !   33.0   0.0   2.6e-11   4.7e-08       1     228 [.       2     175 ..       2     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.6e-11
                    Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkva 77 
                                       ki + + E++p    GGL+  +++++k+La lg++++v++ + g++k+++ ++                        
  gi|386002668|ref|YP_005920967.1|   2 KIAYYSLEFPP-RIFGGLGVYADSISKELASLGQEISVFTMGDGSLKRRE-KA------------------------ 52 
                                       79999******.*******************************9999976.22........................ PP

                    Glyco_transf_5  78 klkkdgvdvyfldnpeffdreglYgdk.gedyednaerfa...lfsraalelleklgwkpdvihahDWhtalvpall 150
                                           +g++v+      + d ++++ ++  + + +  + +     +++ a++ l++ +  +d+ +ahDW     ++ +
  gi|386002668|ref|YP_005920967.1|  53 ----RGISVFRETPAPMRDGWEPFISDrTRAWGEGVDFLFdllSYNQLAVASLRE-NGPFDLAVAHDWLGLPGGLAA 124
                                       ....255555544444444444555444444444444433333444555555566.457**********99999999 PP

                    Glyco_transf_5 151 kel.ykerglfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflk.agivyadavttVSpty 225
                                       k +          ++++f++H+l+  +   +++                     ++  l+  g  +ad v+tVS+ +
  gi|386002668|ref|YP_005920967.1| 125 KRVlG--------VPLIFHVHSLEVGRETAPNP---------------------QIVDLElKGAGLADGVITVSKAM 172
                                       99955........*************8887543.....................34444447888888888888888 PP

                    Glyco_transf_5 226 akE 228
                                       +++
  gi|386002668|ref|YP_005920967.1| 173 KEQ 175
                                       776 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 !   27.2   0.0   2.2e-09   3.9e-06       3      91 ..     301     397 ..     299     398 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.2e-09
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltdda..egleelftpgk....evilfe..dleelaekiryllanpeerraiae 71 
                                       ++ps +e +  + +Eaaa+ ++a++ ++  +gl+e++++      +++ +   d+ ++a  i+ +l++pe+rr+ ++
  gi|386002668|ref|YP_005920967.1| 301 VFPSLYEPFGIVGVEAAAMERPAVVGASgvSGLREIVDDPSaerpTGVHVNprDPGDIAWGINLVLDDPERRREWGR 377
                                       56888888999999************88*********9999999988888889************************ PP

                   Glyco_trans_1_2  72 aarervlaehtydhraeqll 91 
                                       ++r+++l+ +++ ++a++ l
  gi|386002668|ref|YP_005920967.1| 378 NGRAKCLRIFNWPRAARETL 397
                                       ****************9876 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-06    0.0045     260     309 ..     203     254 ..     170     262 .. 0.79
   2 ?   -0.4   0.0      0.19   3.4e+02     357     398 ..     281     322 ..     276     380 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHHT...TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGT CS
                   Glyco_transf_20 260 svsekvkelkerf..enkkklilgvDrlDyikGvkqkllaferfLeeypelr 309
                                       + +++++el+er+  +++ ++il v rl+ +kGv   l+a+ + L+e+p  +
  gi|386002668|ref|YP_005920967.1| 203 TKRRRIEELQERYslKEEDEVILFVGRLEPVKGVIPLLEAMPKVLQEHPRAK 254
                                       33567888888873334569*****************************865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                                       EES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTT CS
                   Glyco_transf_20 357 lersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqe 398
                                       ++  ld e +i  +a ad+++  sl +   +v  e  ++++ 
  gi|386002668|ref|YP_005920967.1| 281 VTDFLDLESKIHHYALADLCVFPSLYEPFGIVGVEAAAMERP 322
                                       5666888999999************99999999999988776 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 !   14.7   0.0   1.3e-05     0.024      16     116 ..      25     146 ..      19     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                   Glyco_trans_4_2  16 lakeLakrgyeVhvitpkkga.kdeleaegihvhrl.kvd...................rkgpleylkafkl.kkli 70 
                                       + keLa+ g e++v+t+++g+ k++++a gi v r  + +                   + + + +l++++l ++ +
  gi|386002668|ref|YP_005920967.1|  25 ISKELASLGQEISVFTMGDGSlKRREKARGISVFREtPAPmrdgwepfisdrtrawgegVDFLFDLLSYNQLaVASL 101
                                       6799*************99998*********9888753335556777777777777766777999999877765666 PP

                   Glyco_trans_4_2  71 kkikP.Dvvhahyakpygllgslaar.lsgvipvvlsvwGldvlkfpk 116
                                       ++++P D+  ah  + +gl g+laa+  +g +p+++ v+ l v ++  
  gi|386002668|ref|YP_005920967.1| 102 RENGPfDLAVAHD-W-LGLPGGLAAKrVLG-VPLIFHVHSLEVGRETA 146
                                       6665449999999.4.57999999994555.********999954433 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00012      0.21     470     503 ..     298     333 ..     285     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                       SEEE---SSBSS-HHHHHHHHTT--EEEE..TTBHH CS
                      Glycogen_syn 470 hlGvfpsyyepwGytpaectvmGipsvtt..nlsGf 503
                                        l vfps yep+G    e + m  p+v     +sG+
  gi|386002668|ref|YP_005920967.1| 298 DLCVFPSLYEPFGIVGVEAAAMERPAVVGasGVSGL 333
                                       689**********************99641134544 PP

>> DUF2325  Uncharacterized protein conserved in bacteria (DUF2325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.2   3.5e+02       4      35 ..      14      45 ..      13      55 .. 0.86
   2 ?   -3.0   0.0       4.6   8.2e+03      23      54 ..     192     227 ..     187     229 .. 0.57
   3 ?    7.4   0.0    0.0025       4.5       3      44 ..     255     291 ..     254     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
                           DUF2325  4 ivGGddrmeeqyrklleklggklkvfdgrkek 35
                                      i GG   +  +++k l +lg ++ vf+ ++++
  gi|386002668|ref|YP_005920967.1| 14 IFGGLGVYADSISKELASLGQEISVFTMGDGS 45
                                      689999999******************99884 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.6
                           DUF2325  23 ggklkvfdgrkekkkk..kles..kigkaDlvvlft 54 
                                       g++ +vf+   +k+++  +l++   +++ D v+lf+
  gi|386002668|ref|YP_005920967.1| 192 GVEPEVFSPSATKRRRieELQErySLKEEDEVILFV 227
                                       556666666666555444333311567778888876 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0025
                           DUF2325   3 livGGddrmeeqyrklleklggklkvfdgrkekkkkkleski 44 
                                       l+v G+  +e+++r ++e+lgg++kv++     ++     ki
  gi|386002668|ref|YP_005920967.1| 255 LLVVGKGTLEGRVRSMAEALGGSVKVVTDFLDLES-----KI 291
                                       68999***********************9887333.....33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2623.15
//
Query:       gi|386002669|ref|YP_005920968.1|  [L=320]
Description: sulfate adenylyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-14   51.4   0.0    1.7e-12   46.9   0.0    2.6  2  DUF4921          Domain of unknown function (DUF4921)
    7.4e-13   49.3   0.0    4.4e-12   46.8   0.0    2.0  1  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    1.2e-05   24.8   0.0    8.7e-05   21.9   0.0    2.2  3  DUF4931          Domain of unknown function (DUF4931)
    0.00026   20.8   0.0    0.00035   20.3   0.0    1.2  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
  ------ inclusion threshold ------
       0.11   13.2   0.0        1.7    9.4   0.0    2.1  2  HIT              HIT domain
       0.35   11.1   2.2       0.37   11.0   0.1    2.1  2  zf-RING_7        C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF4921  Domain of unknown function (DUF4921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.053   1.6e+02      41      63 ..      32      54 ..      14      86 .. 0.74
   2 !   46.9   0.0   5.6e-16   1.7e-12     216     389 ..     139     313 ..     109     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.053
                           DUF4921 41 edreeacafcedrkletpPekar 63
                                      ++  ++c fc  +   tpP  a 
  gi|386002669|ref|YP_005920968.1| 32 RSDPKTCPFCPGNEEMTPPAVAA 54
                                      445689*************8665 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 5.6e-16
                           DUF4921 216 krnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeiarlrenPnl.ynelavdyaakhnlviaendhav 291
                                        +++ v Yv++f+nW + aGas+ h h qlva+  +      e++ + + P   y +l v+  a+ + +i en   v
  gi|386002669|ref|YP_005920968.1| 139 IADPGVGYVSIFKNWGRVAGASLSHTHSQLVALPIVPPALLRELEAIGRSPRCpYCSL-VEREAASDRLIFENGRFV 214
                                       4578899********************************************9846665.55555555556799**** PP

                           DUF4921 292 afagfGhryptlevysksatkePweqseeevravsdlvhalhaaagad..vpcneeWhhrpidv.dvpmpwrilikw 365
                                        +a f    p  e +   + + P  +   + r++ dl  al  a   +  + +   ++++  ++ d      + i  
  gi|386002669|ref|YP_005920968.1| 215 LIAPFFSEAP-YETWILPKGHAPSLEGL-DPRGLEDLAEALGEALRRQdrLLSGPAYNYTIRQLpDRRYHLNLRIHP 289
                                       *****98877.58899988899977654.57899****999988765422556666666554442445555566677 PP

                           DUF4921 366 rvstlaGfeggtkiylntisPael 389
                                        +s+laGfe +t i++n++ P++ 
  gi|386002669|ref|YP_005920968.1| 290 AISALAGFERNTGIFINSVPPEAA 313
                                       8******************99865 PP

>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.5e-15   4.4e-12      19     184 .]       6     175 ..       1     175 [. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.5e-15
                   GalP_UDP_transf  19 ltgewvlvsphrtkrpwqgqqekiskdtlpekDklkcyLcPgnsrangefnpky..k....stfvftndFpalseds 89 
                                       +++e+ +++++r+krp   ++e+      ++ D  +c++cPgn++++    + y  +    + ++   d+ a s  +
  gi|386002669|ref|YP_005920968.1|   6 FLEEYCIIAAERKKRPSDFRRERG----RERSDPKTCPFCPGNEEMTPPAVAAYtvDgvgpDGVERVRDWWARSFPN 78 
                                       5678888999*****999998888....67777668**********9999888853222222344445555555555 PP

                   GalP_UDP_transf  90 nyikteaiakn...ilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvlifENkG 163
                                        y++ +a   +   +++ a+ a+G  evii s++h+   ++ s +++++ v  +++++a+  a  ++ +v if N G
  gi|386002669|ref|YP_005920968.1|  79 LYPAVTADP-EpptREWVADRARGFHEVIIESPDHDADPSEFSRQELERLVTIYRDRYASHIADPGVGYVSIFKNWG 154
                                       555553332.134589********************************************9999************* PP

                   GalP_UDP_transf 164 aamgvsnphPHgqiwaeehlp 184
                                          g+s+ h H+q+ a +++p
  gi|386002669|ref|YP_005920968.1| 155 RVAGASLSHTHSQLVALPIVP 175
                                       *************99888776 PP

>> DUF4931  Domain of unknown function (DUF4931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.84   2.5e+03      18      26 ..      36      44 ..      28      48 .. 0.75
   2 !   21.9   0.0   2.9e-08   8.7e-05      52     121 ..     102     171 ..      98     177 .. 0.93
   3 ?   -0.7   0.0      0.24   7.3e+02      16      42 ..     187     217 ..     180     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.84
                           DUF4931 18 tacPfcdre 26
                                      ++cPfc  +
  gi|386002669|ref|YP_005920968.1| 36 KTCPFCPGN 44
                                      68****654 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.9e-08
                           DUF4931  52 lqtvlietdeceedistyseehlrellrfgvkhwlelekseeyksvllfknhGPlsGGsikhahmqivGl 121
                                       +  v+ie+ + + d s++s++ l++l++   +++     +     v +fkn+G ++G s+ h+h q+v l
  gi|386002669|ref|YP_005920968.1| 102 FHEVIIESPDHDADPSEFSRQELERLVTIYRDRYASHIADPGVGYVSIFKNWGRVAGASLSHTHSQLVAL 171
                                       5679******************************9999999999999*********************88 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.24
                           DUF4931  16 ketacPfc...drekltd.ildeegslillk 42 
                                       ++  cP+c   +re  +d ++ e+g ++l+ 
  gi|386002669|ref|YP_005920968.1| 187 RSPRCPYCslvEREAASDrLIFENGRFVLIA 217
                                       5678999955568988884566788888865 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07   0.00035      25      91 ..     199     265 ..     146     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                                       HHHH-TTEEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCT CS
                     GalP_UDP_tr_C  25 elaekervvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnlfe 91 
                                         a+ +r++ ++  f+ ++p++   P+e+ +l+k + +sl  l     edla +l + +r++d l +
  gi|386002669|ref|YP_005920968.1| 199 REAASDRLIFENGRFVLIAPFFSEAPYETWILPKGHAPSLEGLDPRGLEDLAEALGEALRRQDRLLS 265
                                       34567899999999*************************************************9977 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.17     5e+02      70      90 ..     146     166 ..     104     171 .. 0.80
   2 ?    9.4   0.0   0.00058       1.7       5      77 ..     203     275 ..     199     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                                       CEEEEEEESGGGT-SSSS-EE CS
                               HIT  70 glrvvinngahagqsvahlHi 90 
                                        + +++n g+ ag s  h H 
  gi|386002669|ref|YP_005920968.1| 146 YVSIFKNWGRVAGASLSHTHS 166
                                       467999**************5 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00058
                                       -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEE CS
                               HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinn 77 
                                        +++++e+ +++++   +++ap  + ++pk h++ l+ l++  l +l +a  +  +   + ++  +++++i +
  gi|386002669|ref|YP_005920968.1| 203 SDRLIFENGRFVLIAPFFSEAPYETWILPKGHAPSLEGLDPRGLEDLAEALGEALRRQDRLLSGPAYNYTIRQ 275
                                       67899******************************************99999999888888888888887766 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 ?   -1.6   0.2       1.1   3.3e+03      25      29 ..      37      41 ..      25      41 .. 0.85
   2 ?   11.0   0.1   0.00012      0.37       9      30 ..     174     195 ..     173     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                      E-TTT CS
                         zf-RING_7 25 tCpeC 29
                                      tCp C
  gi|386002669|ref|YP_005920968.1| 37 TCPFC 41
                                      9**99 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                                       --CCHHHHHCCSTB-EE-TTT- CS
                         zf-RING_7   9 lppqvlselragdevvtCpeCG 30 
                                       +pp++l+el a +  ++Cp+C+
  gi|386002669|ref|YP_005920968.1| 174 VPPALLRELEAIGRSPRCPYCS 195
                                       8********************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2016.60
//
Query:       gi|386002670|ref|YP_005920969.1|  [L=383]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-32  111.9   0.0    3.5e-32  111.3   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-30  106.8   0.4    2.1e-30  106.0   0.4    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    7.7e-26   91.1   0.0    1.2e-25   90.5   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.2e-24   85.3   0.0      1e-23   84.5   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.7e-15   56.3   1.0    1.3e-06   28.3   0.4    2.2  2  Glyco_transf_5   Starch synthase catalytic domain
    5.9e-10   39.3   0.0    8.5e-10   38.8   0.0    1.2  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    2.5e-09   37.4   0.0    4.8e-09   36.5   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.22   12.0   0.0          1    9.9   0.0    2.0  2  Poxvirus_B22R_N  Poxvirus B22R protein N-terminal


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   1.6e-35   3.5e-32      11     172 .]     202     358 ..     195     358 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.6e-35
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                       +    +++l+ gr++++Kg+  l++a++++ ++ + ++k+v++G+ge+++e +++a el+++  +iflg+++ + +e
  gi|386002670|ref|YP_005920969.1| 202 IHPLAPVVLFCGRMNYQKGPCILVEAIPSILAR-HWDAKFVFIGDGEMRAECERQARELGVEGSCIFLGYIPSNVKE 277
                                       5555799************************98.**************************************999** PP

                                       HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
                   Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                       e+++++d+++lps++E+fGiv+lE   ag+pvia+ a     ++k+ e+Gll     +e++a  i++ll+d+++ er
  gi|386002670|ref|YP_005920969.1| 278 EWMNACDMVCLPSRNEPFGIVVLEGWDAGKPVIATEA---VSIIKNFEDGLLAYIQ-PESIAWCINRLLDDPQEMER 350
                                       ***********************************84...689*********9887.******************** PP

                                       HHHHHHHH CS
                   Glycos_transf_1 165 lgenarkr 172
                                       lg+++r+r
  gi|386002670|ref|YP_005920969.1| 351 LGRAGRER 358
                                       *****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 !  106.0   0.4   9.3e-34   2.1e-30       1     166 [.      12     182 ..      12     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 9.3e-34
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrl.rrllkre..... 71 
                                       vGGv+ hv e+++aLarrGheV+v+t+++d  +++e      v++ + + +  ++ +la + r+  ++++r+     
  gi|386002670|ref|YP_005920969.1|  12 VGGVAPHVSEISEALARRGHEVHVFTRRGDFGSYDEI---NGVHYQR-VDSDLAGDILAQMDRMsDAIFDRFwhvqk 84 
                                       7***********************************3...3333333.33333333333333320222233344445 PP

                    Glyco_transf_4  72 ...kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl..lrradrviavSea 143
                                          k+DvvH h+++++  al +++++++ip+V+t+H+++ +++ +++ +  ++ ++   r +     a  vi++++ 
  gi|386002670|ref|YP_005920969.1|  85 lfgKFDVVHGHDWHPV-TALNKIKAAYRIPYVITLHSTE-WGRCGNNFSTDYIPREIAHREWlaGYEAAMVITTTQR 159
                                       559************8.566666668*************.67776666655555555555554677999******** PP

                    Glyco_transf_4 144 tadelrerygvppekitVipnGv 166
                                       ++del+ +y++ppeki++ipnG 
  gi|386002670|ref|YP_005920969.1| 160 MKDELMMLYQIPPEKIEIIPNGL 182
                                       **********************5 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 !   90.5   0.0   5.5e-29   1.2e-25       2     134 .]     207     344 ..     206     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 5.5e-29
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---...HHHHHHHT..T-T.TEEEE---.TH.HHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgp.rpeeleelaa..gleerveftGfv.ed.laella 71 
                                       pv+lf+Gr+   +kg  +l+ea+p +++++  +++v++Gdg+ r +e+e++a+  g+e +++f+G++ ++ ++e+++
  gi|386002670|ref|YP_005920969.1| 207 PVVLFCGRM-NYQKGPCILVEAIPSILARHwdAKFVFIGDGEmR-AECERQARelGVEGSCIFLGYIpSNvKEEWMN 281
                                       89*******.567**************99545**********55.69*999977999999*******73369***** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       a+d++++Ps  e fg+++lE   ag+pv+at++     ++   e+gll+   +pe++a  i rLl+d
  gi|386002670|ref|YP_005920969.1| 282 ACDMVCLPSrnEPFGIVVLEGWDAGKPVIATEAVS---IIknFEDGLLAY-IQPESIAWCINRLLDD 344
                                       *********999*******************8744...4442599*9996.47************97 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   4.6e-27     1e-23       1     160 []      13     181 ..      13     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 4.6e-27
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaal........ralrrllrq 69 
                                       gG++ +v e+++aLa+rGheV+v+t++++ g++  e +gv++ r++   +++ la ++++        + ++ l   
  gi|386002670|ref|YP_005920969.1|  13 GGVAPHVSEISEALARRGHEVHVFTRRGDFGSY-DEINGVHYQRVDSDLAGDILAQMDRMsdaifdrfWHVQKL--- 85 
                                       8*************************9999998.7899*******98878877777665544334333444555... PP

                   Glyco_trans_4_4  70 rrerpdvvhahsptaglaarlarrrrgiplvvtlhg.lllrrgsgavrrly.ral.errllrr..adavlvvseaea 141
                                          ++dvvh h+++   a   ++++ +ip+v+tlh+  ++r g+ ++  ++ r++ +r  l++  a+ v+++++ + 
  gi|386002670|ref|YP_005920969.1|  86 -FGKFDVVHGHDWHPVTALNKIKAAYRIPYVITLHStEWGRCGNNFSTDYIpREIaHREWLAGyeAAMVITTTQRMK 161
                                       .5***********9777777777699*********736699999999999886665554444445999********* PP

                   Glyco_trans_4_4 142 eelra.lgvpadrvvvvpng 160
                                       +el   + +p+++++++png
  gi|386002670|ref|YP_005920969.1| 162 DELMMlYQIPPEKIEIIPNG 181
                                       *****888***********8 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 !   26.6   0.0   1.9e-09   4.3e-06       4      43 ..       1      40 [.       1      61 [. 0.87
   2 !   28.3   0.4   5.9e-10   1.3e-06     117     180 ..      70     129 ..      45     169 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.9e-09
                    Glyco_transf_5  4 fvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry 43
                                      ++++E     k+GG+a +v+++++aLa++gh+v+v++ r 
  gi|386002670|ref|YP_005920969.1|  1 MLSWESLYSTKVGGVAPHVSEISEALARRGHEVHVFTRRG 40
                                      79****999***************************9875 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 5.9e-10
                    Glyco_transf_5 117 lfsraalellekl..gw.kpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpk 180
                                        +s a+ +  +++   + k+dv+h hDWh + +   +k++y+       i++v+t+H++++ ++ ++
  gi|386002670|ref|YP_005920969.1|  70 RMSDAIFDRFWHVqkLFgKFDVVHGHDWHPVTALNKIKAAYR-------IPYVITLHSTEWGRCGNN 129
                                       5555666655565433336**************999999984.......*************99883 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 !   38.8   0.0   3.8e-13   8.5e-10      11     110 ..      17     122 ..       7     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.8e-13
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg....pleylk..af.klkklikki.kPDvvh 79 
                                       +h++++ ++La rg+eVhv+t++++   ++e +g+h +r+++d +g    ++  ++  +f +++ + k + k+Dvvh
  gi|386002670|ref|YP_005920969.1|  17 PHVSEISEALARRGHEVHVFTRRGDFGSYDEINGVHYQRVDSDLAGdilaQMDRMSdaIFdRFWHVQKLFgKFDVVH 93 
                                       79********************9999***************9966654445555533246788888887657***** PP

                   Glyco_trans_4_2  80 ahyakpygllgslaarlsgvipvvlsvwGld 110
                                        h   p+  l ++    +  ip+v++ + + 
  gi|386002670|ref|YP_005920969.1|  94 GHDWHPVTALNKIK--AAYRIPYVITLHSTE 122
                                       *******9999994..4444*******9775 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   2.2e-12   4.8e-09       2      89 ..     286     371 ..     285     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.2e-12
                   Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervl 78 
                                       v  psr+e +  +++E   +G ++++++a ++ + f++g  ++ +  +e++a  i++ll++p+e +++++a+rer +
  gi|386002670|ref|YP_005920969.1| 286 VCLPSRNEPFGIVVLEGWDAGKPVIATEAVSIIKNFEDG--LLAYIQPESIAWCINRLLDDPQEMERLGRAGRERLE 360
                                       5579***********************999999999999..77778******************************* PP

                   Glyco_trans_1_2  79 aehtydhraeq 89 
                                       +e+t+d  a++
  gi|386002670|ref|YP_005920969.1| 361 REFTWDEIARE 371
                                       ******99987 PP

>> Poxvirus_B22R_N  Poxvirus B22R protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   3.5e+03      55      68 ..     271     284 ..     269     286 .. 0.88
   2 ?    9.9   0.0   0.00046         1      32      64 ..     345     377 ..     340     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                   Poxvirus_B22R_N  55 ikeevkeeFkskCe 68 
                                       i ++vkee+ ++C+
  gi|386002670|ref|YP_005920969.1| 271 IPSNVKEEWMNACD 284
                                       7789*********8 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00046
                   Poxvirus_B22R_N  32 vkyldsvekaeaelleekfnWtkikeevkeeFk 64 
                                       +++++ + +a +e+le +f W++i+ e +e +k
  gi|386002670|ref|YP_005920969.1| 345 PQEMERLGRAGRERLEREFTWDEIARETEEVYK 377
                                       57888999999***************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2491.28
//
Query:       gi|386002671|ref|YP_005920970.1|  [L=251]
Description: hypothetical protein Mhar_1991 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-07   31.6   0.1    2.5e-07   30.8   0.1    1.3  1  bPH_2     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   1.4e-11   2.5e-07       2      58 ..     135     191 ..     134     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.4e-11
                             bPH_2   2 rattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietagg 58 
                                       r+++y it+ r+++ sG l+  ++++ +++I ++ +eqs+ ++ +++gti+  ta+g
  gi|386002671|ref|YP_005920970.1| 135 RSHRYYITNWRLIMESGHLGVHRRTLLYKNINDLVVEQSFPGKVFNFGTIIPITASG 191
                                       7899**********************************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1730.18
//
Query:       gi|386002672|ref|YP_005920971.1|  [L=540]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-50  169.0   0.0      1e-49  168.3   0.0    1.3  1  AAA              ATPase family associated with various cellul
    1.3e-25   89.4   1.0    1.2e-24   86.3   0.1    3.0  3  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.2e-13   50.6   0.3      3e-13   49.3   0.2    1.8  1  AAA_lid_3        AAA+ lid domain
    1.5e-12   47.1   0.0    5.4e-12   45.3   0.0    2.0  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.5e-09   37.8   0.0    3.2e-09   36.7   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.5e-08   33.1   0.0    9.6e-08   32.3   0.0    1.3  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.6e-07   31.4   0.1    1.1e-06   28.7   0.1    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    4.8e-07   30.3   0.1    1.5e-06   28.7   0.1    1.7  1  AAA_16           AAA ATPase domain
    2.3e-06   27.9   0.0    4.2e-06   27.0   0.0    1.4  1  AAA_33           AAA domain
    1.8e-05   25.0   0.1     0.0007   19.9   0.0    2.2  2  AAA_22           AAA domain
    9.9e-05   22.4   0.0    0.00016   21.7   0.0    1.3  1  AAA_14           AAA domain
    0.00018   20.8   0.0     0.0004   19.7   0.0    1.5  1  TIP49            TIP49 P-loop domain
    0.00081   19.7   0.0     0.0016   18.7   0.0    1.5  1  AAA_28           AAA domain
     0.0019   17.6   0.2       0.88    8.9   0.0    2.6  2  ATPase           KaiC
     0.0022   18.5   0.0     0.0048   17.5   0.0    1.6  1  AAA_18           AAA domain
      0.003   17.2   1.0       0.57    9.7   0.1    2.5  2  AAA_25           AAA domain
     0.0032   17.2   0.0     0.0068   16.2   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0039   17.6   0.0     0.0067   16.8   0.0    1.4  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.014   14.8   0.1      0.026   13.9   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.016   15.0   0.0      0.025   14.3   0.0    1.2  1  AAA_11           AAA domain
       0.02   14.6   0.0       0.12   12.0   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
      0.021   14.9   0.0      0.054   13.5   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.022   14.6   0.0      0.051   13.4   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
      0.023   14.5   0.0      0.078   12.8   0.0    1.8  2  Bac_DnaA         Bacterial dnaA  protein
      0.033   13.7   0.0      0.061   12.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.036   13.5   0.0       0.22   11.0   0.0    2.1  2  PhoH             PhoH-like protein
      0.036   14.0   0.0      0.091   12.7   0.0    1.7  1  NACHT            NACHT domain
      0.088   12.0   0.0       0.12   11.5   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
        0.1   11.9   0.0        0.2   10.9   0.0    1.4  1  Zeta_toxin       Zeta toxin
        0.1   12.7   0.0       0.22   11.6   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.17   11.6   0.0       0.31   10.7   0.0    1.4  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.0   1.8e-52     1e-49       1     131 [.     215     344 ..     215     345 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 1.8e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTlla+a+a+e++++f ++sg+e++sky gese+++re+fkea+e+a psi+fiDEid++a++r++ 
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNSHFQTLSGPEIMSKYYGESEERLREIFKEAEEEA-PSIIFIDEIDSIAPKREEV 290
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+r+v+qLl+++dg++++ +kv+vigatnrpd+ldpal+r gRfdr+iei+
  gi|386002672|ref|YP_005920971.1| 291 TGEVERRIVAQLLAVMDGLESR-GKVVVIGATNRPDSLDPALRRpGRFDREIEIG 344
                                       *********************6.77***************************996 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.1     2e-27   1.2e-24       1      82 [.       6      87 ..       6      91 .. 0.94
   2 ?   -2.0   0.1       7.2   4.2e+03      29      44 ..     122     138 ..     120     153 .. 0.67
   3 ?   -1.1   0.0       3.7   2.1e+03       4      27 ..     408     430 ..     405     438 .. 0.77

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2e-27
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L+V ea+++dvgrgi+r+d++++ + g++ gdv+ i+gk+kT+a+ +p++ped+g+gi+r+dg++R+nagvsi+d+  
  gi|386002672|ref|YP_005920971.1|  6 TLKVGEARPSDVGRGIARVDQAVIYNAGWQAGDVLSISGKKKTAALLLPGYPEDTGTGIVRLDGNIRRNAGVSIDDRAP 84
                                      69**************************************************************************966 PP

                                      EEE CS
                           CDC48_N 80 Vrk 82
                                      V+ 
  gi|386002672|ref|YP_005920971.1| 85 VKV 87
                                      654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.2
                                       S-TTSEEEEEC.CCCEE CS
                           CDC48_N  29 lepgdvveieg.krkTv 44 
                                       l +gdv+ei+   rk+ 
  gi|386002672|ref|YP_005920971.1| 122 LTRGDVIEISVmGRKIE 138
                                       56899999987555544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.7
                                       EECCSS-CSSTTEEEE-HHHHHHH CS
                           CDC48_N   4 Vaeapqedvgrgivridpedmeel 27 
                                       V+ +p  +  ++iv+++++ +++l
  gi|386002672|ref|YP_005920971.1| 408 VESIPV-EILNKIVVVNEDFVDAL 430
                                       666663.4899*******998876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.2   5.3e-16     3e-13       1      37 [.     367     403 ..     367     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 5.3e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                       dv l++LA  T+G++GADlaal reA+++Alrr  +e
  gi|386002672|ref|YP_005920971.1| 367 DVKLEKLADITHGFVGADLAALAREAGMRALRRIVPE 403
                                       8********************************7665 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   9.3e-15   5.4e-12       2      63 ..     106     167 ..     105     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 9.3e-15
                                       .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCC.SCEEECTSCCEEESTTCC CS
                           CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkg.pvgitetTeielgtkpve 63 
                                       i g+ ++yl+r + gr++t Gd++ ++++g+ i+lv+++++P+  +v+i + T ie+++kp++
  gi|386002672|ref|YP_005920971.1| 106 ITGG-EEYLRRLLDGRVLTRGDVIEISVMGRKIELVATKITPAAeAVIIGDRTGIEISEKPAK 167
                                       7788.88************************************99****************98 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   5.5e-12   3.2e-09      31     104 ..     210     291 ..     188     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 5.5e-12
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsra 99 
                                       ea   vll+GpPG Gkt la+ +a+e ++++++ sgP +      e +  l  ++++ ee+   ++fidei  ++++
  gi|386002672|ref|YP_005920971.1| 210 EAPKGVLLHGPPGTGKTLLARALASETNSHFQTLSGPEImskyygESEERLREIFKEAEEEapSIIFIDEIDSIAPK 286
                                       566789*******************************994433333456799999888765337************* PP

                            RuvB_N 100 veevl 104
                                        eev 
  gi|386002672|ref|YP_005920971.1| 287 REEVT 291
                                       **986 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.7e-10   9.6e-08       6     105 ..     215     308 ..     212     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.7e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+la+ala+  +    +++ ++   e++     + + ++++  ++  ++aee+   i+++DEid i
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETN----SHFQTLSGPEIMS----KYYGESEERLREIFKEAEEEApsIIFIDEIDSI 283
                                       5789*****************99....59***********....9999****************999********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v r  V   LL +++g
  gi|386002672|ref|YP_005920971.1| 284 APKrEEVTGEVERRIV-AQLLAVMDG 308
                                       **99999999988755.557888887 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 !   28.7   0.1   1.9e-09   1.1e-06       1     136 [.     214     333 ..     214     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.9e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ la+ +n+ +++  +++ +++             +++   ++ ++a+   ++i+++DE++
  gi|386002672|ref|YP_005920971.1| 214 GVLLHGPPGTGKTLLARALASETNSHFQTLSGPEIMSKYYGES--------EERL-REIFKEAEeeAPSIIFIDEID 281
                                       59*******************************9777543222........2333.4444455557899******** PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        +     ev++++ + +  + l +++g e  ++        + vi+++n++d    +l+palr+
  gi|386002672|ref|YP_005920971.1| 282 SIApkrEEVTGEVERRIVAQLLAVMDGLESRGK--------VVVIGATNRPD----SLDPALRR 333
                                       997333578888888888888888887777765........99*********....99999987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   2.5e-09   1.5e-06      16     140 ..     204     318 ..     199     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.5e-09
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaes 91 
                                       +er+    p  vll+G++G+GK+ l+r+l+ + + + + +l+g    +     y+    + l r e++++ ++e   
  gi|386002672|ref|YP_005920971.1| 204 FERLGVEAPKGVLLHGPPGTGKTLLARALASETNSH-FQTLSGPEIMS----KYYGeSEERL-R-EIFKEAEEE--- 270
                                       66666667899*******************533333.44455544444....3323255555.4.555555555... PP

                            AAA_16  92 aeleawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       a    + +++++ +    e++g+ ++r+ ++l + ++ l+++++ +v++
  gi|386002672|ref|YP_005920971.1| 271 APSIIFIDEIDSIAPKREEVTGEVERRIVAQLLAVMDGLESRGK-VVVI 318
                                       5556666667777778888888888***********99999888.6654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   7.3e-09   4.2e-06       2      80 ..     215     323 ..     215     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7.3e-09
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll+G+pG+GK+ la+ l+ ++   +++ls ++++++++g+ +++++                              
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNshFQTLSGPEIMSKYYGESEERLReifkeaeeeapsiifideidsiapkreeVT 291
                                       799****************99999****************8888887777777777788888888888877655433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnl 80 
                                        +v+ r+ ++l ++ +   s+g+ v++ atn+
  gi|386002672|ref|YP_005920971.1| 292 GEVERRIVAQLLAVMDGLESRGKVVVIGATNR 323
                                       34666677777777777777777788888775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.2e-06    0.0007       8      59 ..     215     266 ..     210     271 .. 0.75
   2 ?    4.8   0.0     0.057        33      73     129 ..     255     319 ..     244     325 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                       ++++G++GtGKT+l+r l+++ + + +++  +pe++ +++  s++ ++++++e
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNSH-FQTLSGPEIMsKYYGESEERLREIFKE 266
                                       689*****************98544.445567777767777777777777665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.057
                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvG 129
                                        s+e+l+e + +a +++    ++ iDE++ +   +         +++ +L   ++  ++  +++++G
  gi|386002672|ref|YP_005920971.1| 255 ESEERLREIFKEAEEEAPS--IIFIDEIDSIApkReevtgeveRRIVAQLLAVMDGLESRGKVVVIG 319
                                       5566666666666666655..*********9875323333333333333333333355555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.7e-07   0.00016       4      88 ..     214     307 ..     211     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.7e-07
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev... 76 
                                        +++ G+  +GKT l++ l++e     +++  ++  +   k + ++e +l e+++e  +ee  +++f+DEi  +   
  gi|386002672|ref|YP_005920971.1| 214 GVLLHGPPGTGKTLLARALASETN---SHFQTLSGPEIMSKYYGESEeRLREIFKEA-EEEAPSIIFIDEIDSIapk 286
                                       5899****************9988...999999999988877776652555555554.55699*********99666 PP

                            AAA_14  77 .........pewekalkslvd 88 
                                                +++   l  ++d
  gi|386002672|ref|YP_005920971.1| 287 reevtgeveRRIVAQLLAVMD 307
                                       555555555444444444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     7e-07    0.0004      50      97 ..     212     257 ..     206     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                        ++vLl Gp+gtGkt la a++ e +   +f +lsg e+ s     +e
  gi|386002672|ref|YP_005920971.1| 212 PKGVLLHGPPGTGKTLLARALASETN--SHFQTLSGPEIMSKYYGESE 257
                                       599********************987..79*********998776654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.7e-06    0.0016       2      49 ..     215     267 ..     214     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                                       + + G+++tGKT l++aLa++    ++++  pE++ +++ e  ++ +++ +++
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASEtnsHFQTLsgPEIMSKYYGESEERLREIFKEA 267
                                       6799***************6556667777789999999988887777666554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0015      0.88      15      38 ..     208     231 ..     201     242 .. 0.81
   2 ?    6.1   0.0      0.01         6     108     154 ..     257     309 ..     231     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       G+   + vl+ G pGtGKt++a  
  gi|386002672|ref|YP_005920971.1| 208 GVEAPKGVLLHGPPGTGKTLLARA 231
                                       55566779*************975 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                            ATPase 108 ieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                        e+l+e+ ke ++   + + iD i+++    +e + +v R+i+ ql+ v+ +l
  gi|386002672|ref|YP_005920971.1| 257 EERLREIFKEAEEeapSIIFIDEIDSIapkREEVTGEVERRIVAQLLAVMDGL 309
                                       556666666666544466777777777432455666789**********9876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.2e-06    0.0048       1      27 [.     215     259 ..     215     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.2e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................gvn 27 
                                       +ll G+pG+GKt la++L++++++                   ++
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNShfqtlsgpeimskyygesEER 259
                                       7899**************999866666666665555555555333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00098      0.57      36      56 ..     215     235 ..     208     244 .. 0.89
   2 ?    5.5   0.1     0.019        11     128     175 ..     258     305 ..     246     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00098
                            AAA_25  36 allaGapgtGKttlaldlala 56 
                                       +ll G+pgtGKt la  la +
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASE 235
                                       69*************999875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeri 175
                                       + ++++ +++ee e +  + iD ++++ +  e+   +v +++v++l  +
  gi|386002672|ref|YP_005920971.1| 258 ERLREIFKEAEE-EAPSIIFIDEIDSIAPKREEVTGEVeRRIVAQLLAV 305
                                       456788899999.88***************9999999989999998766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0068      44      71 ..     209     236 ..     199     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       +e+ ++++l Gp+G+GK+ la al+ e+
  gi|386002672|ref|YP_005920971.1| 209 VEAPKGVLLHGPPGTGKTLLARALASET 236
                                       5677899*****************9875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-05    0.0067       1      36 [.     215     250 ..     215     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++l+Gp+g+GK++la+ La++  +++++ + ++++s
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNSHFQTLSGPEIMS 250
                                       689********************9997776666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.5e-05     0.026      25      43 ..     215     233 ..     208     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt+la++l+
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALA 233
                                       89**************997 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.4e-05     0.025      17      44 ..     212     239 ..     202     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                            AAA_11  17 seitliqGPPGtgKTktivellsqllsr 44 
                                       ++ +l++GPPGtgKT    +l s+ +s+
  gi|386002672|ref|YP_005920971.1| 212 PKGVLLHGPPGTGKTLLARALASETNSH 239
                                       55689**********9999999999755 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.12      21      48 ..     211     238 ..     198     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskr 48 
                                        +  vl++G  GtGK+llara+ ++++ 
  gi|386002672|ref|YP_005920971.1| 211 APKGVLLHGPPGTGKTLLARALASETNS 238
                                       56789****************9876554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.4e-05     0.054      11      47 ..     204     241 ..     189     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-05
                                       HHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--.- CS
                              TsaE  11 gkklakalgdvilLeGdLGaGKTtlvrglakalgve.e 47 
                                        ++l+ ++ + +lL+G+ G+GKT l+r+la++ + + +
  gi|386002672|ref|YP_005920971.1| 204 FERLGVEAPKGVLLHGPPGTGKTLLARALASETNSHfQ 241
                                       44555544567*******************99877653 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.8e-05     0.051       2      30 ..     215     243 ..     214     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktll++ala+  + +f+ +
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNSHFQTL 243
                                       89*********************999865 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.078      37     179 ..     215     359 ..     210     390 .. 0.76
   2 ?   -1.9   0.0       4.2   2.4e+03     184     210 ..     406     438 ..     379     445 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       ++++g+ G Gkt L +a++ e+ ++++      l++ e +++     +++  e fke   ++  ++ iD+i  +a k
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETNSHFQ-----TLSGPEIMSKYYGESEERLREIFKEAEEEApSIIFIDEIDSIAPK 286
                                       79**************99988877765.....5789999999999999999999**98885527899*******988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkki 179
                                                 ++  +l+ +++ l   gk vv+ +   P +l+    r   rf++   ++i  p++e rl++l+ ++
  gi|386002672|ref|YP_005920971.1| 287 ReevtgeverRIVAQLLAVMDGLESRGKVVVIGATNRPDSLDPAL-RRPGRFDRE--IEIGVPNREARLEVLQIHA 359
                                       52222211113445678888999999************9886644.335688775..5666789999999987554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.2
                                       --...--TTHHH...HHHHH--S-HHHHHHHHH CS
                          Bac_DnaA 184 le...vpeevle...fiaervtdnvRelegaln 210
                                       l+   +p e+l+    + e + d +Rele +  
  gi|386002672|ref|YP_005920971.1| 406 LDvesIPVEILNkivVVNEDFVDALRELEPSAM 438
                                       444457788877222456788888999986544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.061      30      64 ..     209     242 ..     202     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       +++ k vll Gp GtGKt++++ l ++ + +++++
  gi|386002672|ref|YP_005920971.1| 209 VEAPKGVLLHGPPGTGKTLLARALASETN-SHFQT 242
                                       677899****************9999888.55554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.9   1.1e+03     135     163 ..     136     164 ..     132     172 .. 0.83
   2 ?   11.0   0.0   0.00037      0.22      22      43 ..     215     236 ..     205     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                       HHHHHHTTB-TT-EEEEEE---------- CS
                              PhoH 135 qmkmfltRlGenskvvvtGdvtqidlpkg 163
                                       +++ + t++   + +v+ Gd t i++ ++
  gi|386002672|ref|YP_005920971.1| 136 KIELVATKITPAAEAVIIGDRTGIEISEK 164
                                       678899999999********999987754 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                                       EEEE--TTSSTTHHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                       v   Gp GtGKt+la ala e 
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASET 236
                                       6789************999765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016     0.091       3      25 ..     215     237 ..     213     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       v+l+G++G GKT L++ la++  
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASETN 237
                                       79****************99865 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.12       4      35 ..     215     239 ..     212     296 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertav 35 
                                       vl +G +GtGKt+++ +l+ e        +++
  gi|386002672|ref|YP_005920971.1| 215 VLLHGPPGTGKTLLARALASET-------NSH 239
                                       6889**************9998.......222 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034       0.2      14      41 ..     210     237 ..     201     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdele 41 
                                       e Pk +ll G pG GK+ la++l+ e++
  gi|386002672|ref|YP_005920971.1| 210 EAPKGVLLHGPPGTGKTLLARALASETN 237
                                       89*********************99985 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00038      0.22      22      50 ..     213     241 ..     202     291 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                                       S-EEEEEETT--HHHHHHCC--TTS-EE- CS
                   Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgpwle 50 
                                         v+l G++G+gk+l Ar+L+++     +
  gi|386002672|ref|YP_005920971.1| 213 KGVLLHGPPGTGKTLLARALASETNSHFQ 241
                                       569*****************987665443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00054      0.31       4      76 ..     214     282 ..     211     293 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                            AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                        +l+ Gp+g+GKT la+ l  ++   ++t  G   +    ++   s e +++ ++e ++e +  ++++iD id 
  gi|386002672|ref|YP_005920971.1| 214 GVLLHGPPGTGKTLLARALaSETNSHFQTLSGPEIMSKYYGE---SEERLREIFKEAEEEAP--SIIFIDEIDS 282
                                       5899************99954444444444444333333333...66666666666666666..6677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 3398.25
//
Query:       gi|386002673|ref|YP_005920972.1|  [L=187]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-24   85.8   0.0      5e-24   85.2   0.0    1.3  1  AAA        ATPase family associated with various cellular act
    1.5e-14   53.5   0.1      3e-14   52.6   0.1    1.5  1  AAA_lid_3  AAA+ lid domain
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.23   11.5   0.0    1.5  1  PapB       Adhesin biosynthesis transcription regulatory prot
       0.18   11.8   0.0       0.39   10.8   0.0    1.5  1  Vps4_C     Vps4 C terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   1.1e-27     5e-24      47     131 ..       2      87 ..       1      88 [. 0.95

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 1.1e-27
                                       HHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS CS
                               AAA  47 relfkeakekakpsilfiDEidalaksr..sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr 121
                                       re+f++a++ a p++lf+DE+da+a++r   +s++ ++erv++q+l+e+dg++   ++v+v++atnrpd +dpallr
  gi|386002673|ref|YP_005920972.1|   2 RETFRKARQAA-PTVLFFDEMDAIAPARggGTSDTHVTERVISQILSEMDGLEAL-HNVVVVAATNRPDIIDPALLR 76 
                                       899*******9.****************98778999******************7.66******************* PP

                                       .TTSSEEEETT CS
                               AAA 122 .gRfdrkieie 131
                                        gRfdr iei+
  gi|386002673|ref|YP_005920972.1|  77 pGRFDRMIEIG 87 
                                       ********996 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   6.6e-18     3e-14       1      44 [.     110     166 ..     110     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 6.6e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...........gik..e.itmedfe 44 
                                       d+dl ++ +rT+GySGADla++c+eA++lA+r+                  i+ ++f+
  gi|386002673|ref|YP_005920972.1| 110 DIDLVAISKRTDGYSGADLASVCNEAVMLAIREyvlagrpqeeeE-IakYrIESKHFD 166
                                       89******************************9666655554331.133357777776 PP

>> PapB  Adhesin biosynthesis transcription regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.1e-05      0.23      33      78 ..     127     173 ..     125     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                              PapB  33 eissirSekvinalrdylVkGvsr.kevCeryevnqgYlsislkrlq 78 
                                       ++ s++ e v+ a+r+y+  G+ +  e   +y + +  +  +lk+++
  gi|386002673|ref|YP_005920972.1| 127 DLASVCNEAVMLAIREYVLAGRPQeEEEIAKYRIESKHFDEALKKVK 173
                                       7899*****************976156799*********99999986 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.7e-05      0.39      21      44 ..     152     175 ..     148     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.7e-05
                            Vps4_C  21 sdkllePpvtlkDflkalkkarpt 44 
                                       ++++ +  ++ k+f++alkk++p+
  gi|386002673|ref|YP_005920972.1| 152 EEEIAKYRIESKHFDEALKKVKPS 175
                                       68899999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1274.35
//
Query:       gi|386002674|ref|YP_005920973.1|  [L=141]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-14   51.2   0.3    1.3e-13   50.5   0.3    1.4  1  AAA_lid_3  AAA+ lid domain
    4.2e-09   36.9   0.0    7.4e-09   36.1   0.0    1.4  1  AAA        ATPase family associated with various cellular act
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.22   11.6   0.0    1.4  1  Vps4_C     Vps4 C terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.3   2.2e-17   1.3e-13       1      45 []      64     121 ..      64     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.2e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...........gik..e.itmedfee 45 
                                       dvdl+++ +rT+G SGADla++ +eAa+lA+r+                  i+ ++fee
  gi|386002674|ref|YP_005920973.1|  64 DVDLAAISKRTDGRSGADLANVTNEAAMLAIREyvlagrpqeddE-IakYrIESKHFEE 121
                                       9********************************777777776532.2333699999986 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 !   36.1   0.0   1.2e-12   7.4e-09      92     131 ..       2      41 ..       1      42 [. 0.92

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.2e-12
                                       HHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  92 eldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       e+dg++   ++v+vi+atnrpd +dpallr gRfdr +ei+
  gi|386002674|ref|YP_005920973.1|   2 EMDGLEAF-HNVLVIAATNRPDIIDPALLRpGRFDRMVEIG 41 
                                       79999997.66*************************99986 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.7e-05      0.22      21      44 ..     106     129 ..     102     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                            Vps4_C  21 sdkllePpvtlkDflkalkkarpt 44 
                                        d++ +  ++ k+f++alkk++p+
  gi|386002674|ref|YP_005920973.1| 106 DDEIAKYRIESKHFEEALKKVKPS 129
                                       6899999****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 931.48
//
Query:       gi|386002675|ref|YP_005920974.1|  [L=314]
Description: transposase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-22   77.4   0.1    1.5e-21   76.2   0.1    1.6  1  DUF772     Transposase domain (DUF772)
    2.1e-14   53.7   0.4    5.3e-14   52.4   0.4    1.7  1  DDE_Tnp_1  Transposase DDE domain
    0.00018   21.2   0.0    0.00039   20.1   0.0    1.6  1  DDE_Tnp_4  DDE superfamily endonuclease


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 !   76.2   0.1   2.4e-25   1.5e-21       1      72 [.      51     122 ..      51     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                            DUF772   1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee...lerlfee 72 
                                       Grp++++ lmlk+lllq++yglSd e+e+++++++sf+ flg+    d++pd +t++ fR+r+++   +e ++ee
  gi|386002675|ref|YP_005920974.1|  51 GRPNFDVILMLKVLLLQQWYGLSDLETEKQISDRISFMKFLGFP---DSIPDSRTIWLFRERMAQtgkDESVWEE 122
                                       9*****************************************95...99****************9887777665 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.4   8.8e-18   5.3e-14       3     212 ..     134     298 ..     132     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.8e-18
                         DDE_Tnp_1   3 krevlivDattvrvpgtk..............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskgl 65 
                                       +++++i Dat++++   +               d+ w +kg + ++gyklh  vd   gli s++ t+++vhds++ 
  gi|386002675|ref|YP_005920974.1| 134 VKRGTIQDATFIEADPGGskkprretartrrsRDGTWAKKGEELHFGYKLHSKVDIDYGLIRSIESTTASVHDSRVD 210
                                       689999********88889*************99999999**********************************985 PP

                         DDE_Tnp_1  66 kqlldelrprkgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrr 141
                                          +      +g +vl+D+GY+  ++   +                              ++++  +++l+  +k+r
  gi|386002675|ref|YP_005920974.1| 211 LS-V------EGEVVLRDKGYFgVKAKGNDFT----------------------------MKRAAAGHPLSDLDKLR 252
                                       55.2......89**********4466666666............................9**************** PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       n+                          +++lR   Er F+ +kr+f+  ++ + +  rv+ +++++++a+
  gi|386002675|ref|YP_005920974.1| 253 NR-------------------------LISKLRFPGERQFAVIKRVFRSAHVMVTTIPRVHVKMVFTAFAF 298
                                       **.........................**************************************999986 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00039      73     141 ..     213     284 ..     158     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                         DDE_Tnp_4  73 kpgdvilaDkgFklse.kl..lvpykkkkkkqlseeevefnraiasarihvErvigrlkgrfrilrsrlrik 141
                                        +g+v+l Dkg+ + + k    ++++   +++ls  ++ +nr i++ r   Er ++ +k+ fr  ++ +   
  gi|386002675|ref|YP_005920974.1| 213 VEGEVVLRDKGYFGVKaKGndFTMKRAAAGHPLSDLDKLRNRLISKLRFPGERQFAVIKRVFRSAHVMVTTI 284
                                       35899******98655322326777779***********************************998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2316.22
//
Query:       gi|386002676|ref|YP_005920975.1|  [L=149]
Description: hypothetical protein Mhar_1996, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-23   82.4   0.0    3.8e-23   82.1   0.0    1.0  1  Phage_integrase  Phage integrase family
    0.00025   21.2   0.0    0.00046   20.3   0.0    1.4  1  Integrase_1      Integrase


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   4.3e-27   3.8e-23      25     156 ..      12     143 ..       2     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 4.3e-27
                                       HHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHH..CHCCTTTSBSSB CS
                   Phage_integrase  25 lllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellska..leeaeksellfa 99 
                                       ++ +l+  +GlR  E+++L+++d+dle++ i+v ++ + ++k+r+v  +e + e+++e+l+++  l +++++++ +a
  gi|386002676|ref|YP_005920975.1|  12 IIWQLMALCGLRSVEAVNLTYGDIDLERRLIHVGKTSSNSGKSRTVIYPECLQEVIEEQLDRHrhLYRKNEHNYFIA 88 
                                       56799*****************************9*****************************9999999999999 PP

                                       ETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT CS
                   Phage_integrase 100 skrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllG 156
                                           +pls+++vr af+++   agie   +pH+lRh +a  L+++gvdl+++ k lG
  gi|386002676|ref|YP_005920975.1|  89 GW-WSPLSTRAVRYAFQKYSDMAGIE-GYSPHSLRHFYAESLVRKGVDLDTIRKNLG 143
                                       88.9**********************.**************************9998 PP

>> Integrase_1  Integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.2e-08   0.00046      35     148 ..      12     126 ..       3     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.2e-08
                       Integrase_1  35 avlqLarvlGLRseEAvqlakslktWkkaLergeerlrvvfG.TKGgrpRevtilerealksavalaikvaeernGk 110
                                       ++ qL ++ GLRs EAv+l         +++ ++  ++v    +  g++R+  ++  e l+++++++     +r+ +
  gi|386002676|ref|YP_005920975.1|  12 IIWQLMALCGLRSVEAVNLT------YGDIDLERRLIHVGKTsSNSGKSRT--VIYPECLQEVIEEQL----DRHRH 76 
                                       677999*************8......4555556666777554156788886..567889999999986....78889 PP

                       Integrase_1 111 Lidkpdlslipd.............ryreilrrlgltgessphslRyayaq 148
                                       L +k++ +  ++             ++++    +g++  +sphslR+ ya+
  gi|386002676|ref|YP_005920975.1|  77 LYRKNEHNYFIAgwwsplstravryAFQKYSDMAGIE-GYSPHSLRHFYAE 126
                                       9999999988888999999998844344443334644.589********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1100.42
//
Query:       gi|386002677|ref|YP_005920976.1|  [L=99]
Description: hypothetical protein Mhar_1997 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 770.43
//
Query:       gi|386002678|ref|YP_005920977.1|  [L=297]
Description: Cation periplasmic solute binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-68  228.4   0.0    1.1e-67  228.1   0.0    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.1   0.0   6.4e-72   1.1e-67       1     251 [.      40     289 ..      40     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 228.1 bits;  conditional E-value: 6.4e-72
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvev 77 
                                       Vva+t plg + + v+Gd vev vLvppga+pH++eptp++++++aeA+l++ ng++lE w++++++++    r+ v
  gi|386002678|ref|YP_005920977.1|  40 VVASTVPLGTFSSMVGGDLVEVAVLVPPGASPHTFEPTPSKLAEVAEAELYIKNGAGLEIWMERMIQANR---RMLV 113
                                       9*****************************************************************8886...4466 PP

                                       EETTTTCCSEBCSS..........ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  78 idlsegveeeeeee..........DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeire 144
                                       +d+s+gve  e +           DpHiWlspkna+ +ve+i d+Lve+dp+na++y++n ++y  +Leeld+e+++
  gi|386002678|ref|YP_005920977.1| 114 VDTSTGVELIETAGsschekiltaDPHIWLSPKNAMIIVEEICDGLVEVDPENAEAYRRNRDDYLLRLEELDRELES 190
                                       777777643333335555566777***************************************************** PP

                                       HHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 145 elaeipeekrklvtthdafgylarayglevagiagiste..aaqiaalieeikeagvkaifveplaspklaetlaee 219
                                       +++   +++r +++ h+a++y+ar+y l +++i + ++e  ++ +a+++e ++e+++++ifv+p++spk+ae +a e
  gi|386002678|ref|YP_005920977.1| 191 AFS--GASRREFIVLHPAWSYFARDYALVQVAILEGDKEpgPRYLAEIVEVAREENLTTIFVDPNFSPKSAEIIAGE 265
                                       ***..556778*********************996666679************************************ PP

                                       HT-EEEEE-STSSSTSTTSTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 220 agvkvatlysldslgdegsaetYidmmranle 251
                                       +g +v++l++l +        +Yi+ mra  +
  gi|386002678|ref|YP_005920977.1| 266 IGGRVVPLDPLAE--------DYIENMRAVSR 289
                                       **********333........9*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1916.09
//
Query:       gi|386002679|ref|YP_005920978.1|  [L=251]
Description: Cation ABC transporter, ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-29  100.9   0.0    1.2e-28  100.4   0.0    1.3  1  ABC_tran   ABC transporter
    5.5e-13   49.4   1.5    1.4e-05   25.1   0.0    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    3.3e-07   30.0   0.0    5.6e-07   29.2   0.0    1.3  1  SMC_N      RecF/RecN/SMC N terminal domain
    0.00099   18.8   0.0     0.0021   17.7   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
     0.0026   18.3   0.1     0.0049   17.4   0.1    1.4  1  AAA_23     AAA domain
     0.0057   16.4   0.1     0.0099   15.6   0.1    1.6  1  AAA_30     AAA domain
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.048   13.4   0.0    1.6  2  AAA_15     AAA ATPase domain
      0.025   14.3   0.1        3.6    7.3   0.0    2.2  2  IstB_IS21  IstB-like ATP binding protein
      0.031   14.5   0.3       0.94    9.8   0.2    2.3  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
      0.051   13.2   0.0      0.091   12.3   0.0    1.3  1  AAA_27     AAA domain
      0.062   12.9   0.2       0.13   11.9   0.2    1.5  1  cobW       CobW/HypB/UreG, nucleotide-binding domain
       0.08   13.4   0.1       0.36   11.3   0.0    2.0  2  AAA        ATPase family associated with various cellular act
      0.094   13.1   0.1       0.13   12.6   0.1    1.5  1  AAA_16     AAA ATPase domain
       0.11   12.4   0.0       0.27   11.2   0.0    1.6  2  NACHT      NACHT domain
       0.15   12.3   0.0       0.35   11.1   0.0    1.6  1  AAA_28     AAA domain
       0.15   11.0   0.0       0.23   10.5   0.0    1.2  1  T2SSE      Type II/IV secretion system protein
       0.16   11.7   0.0       0.25   11.0   0.0    1.2  1  DUF460     Protein of unknown function (DUF460)
       0.17   10.9   0.0       0.25   10.3   0.0    1.2  1  MeaB       Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.18   11.0   0.0       0.26   10.4   0.0    1.2  1  PIF1       PIF1-like helicase
        0.2   12.0   0.3       0.67   10.2   0.1    1.9  2  AAA_22     AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   1.3e-31   1.2e-28       1     136 [.      22     167 ..      22     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 1.3e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++v+l++keg  ++++G+nG GK+tLl++++gl+kp  G++ + g +      e +r ++g+lpq++ ++++  +r
  gi|386002679|ref|YP_005920978.1|  22 LEEVNLEVKEGDFLGLIGPNGGGKTTLLRAILGLVKPSRGRVAVFGMS-----PEAARCRVGYLPQKSLFDQRFPIR 93 
                                       689***************************************666554.....566***********8888888787 PP

                                       HH...................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                                            e++e +  al+ +g+ +lkd+ +      LSgGq+qrv +aral+++p+llllDEp
  gi|386002679|ref|YP_005920978.1|  94 ALevvlmgrrgrmglfdhyssEDREAALSALKAVGMLDLKDREI----GALSGGQQQRVFVARALVSEPDLLLLDEP 166
                                       7789*************987555555889999999999999999....***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                        
  gi|386002679|ref|YP_005920978.1| 167 A 167
                                       6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.5   4.4e-08     4e-05       2      22 ..      35      55 ..      34      86 .. 0.81
   2 !   25.1   0.0   1.5e-08   1.4e-05     228     299 ..     131     198 ..      87     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.4e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +liGpNg GK++LL+a+ +l
  gi|386002679|ref|YP_005920978.1| 35 LGLIGPNGGGKTTLLRAILGL 55
                                      68****************887 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.5e-08
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       d +++ +  lS G+++  +++ al + +   +lll+DEp +g++ ++ r+++ell +l++ +  +i+++H+ 
  gi|386002679|ref|YP_005920978.1| 131 DLKDREIGALSGGQQQRVFVARALVSEP---DLLLLDEPATGIDSARRREFYELLGDLNE-NMTIIMVSHDI 198
                                       4566678889999999988888888888...9***********************77777.7********96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.2e-10   5.6e-07      25     204 ..      33     203 ..      19     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.2e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEET..TEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdne..dkklkiekeevsi 99 
                                        f  ++GpNG GK+ ll Ai   LG      ++ ++ +  ++    ++++ +++v  + +++  d++++i++ ev++
  gi|386002679|ref|YP_005920978.1|  33 DFLGLIGPNGGGKTTLLRAI---LGL-----VKPSRGRVAVFG--MSPEAARCRVGYLPQKSlfDQRFPIRALEVVL 99 
                                       58889***************...993.....566777777776..78999999999987665447779******999 PP

                                       EEEEETTSE.EEEEETTEEE-HHHHHH..HHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkge.seykingkevtkkevse..llesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                       + r  r g   +y  +++e+  + ++   +l  ++ ++ +LSgG+++ v +    A   v+   l llDe +  +D 
  gi|386002679|ref|YP_005920978.1| 100 MGRRGRMGLfDHYSSEDREAALSALKAvgMLDLKDREIGALSGGQQQRVFV----ARALVSEPDLLLLDEPATGIDS 172
                                       999999998578888999999988875336888888899******985544....44455777799*********** PP

                                       HHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkeksknaQfivislreemlek 204
                                       ++++++ ell   ++n+ +i++s++   ++ 
  gi|386002679|ref|YP_005920978.1| 173 ARRREFYELLGDLNENMTIIMVSHDISAVST 203
                                       ************************9777665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.4e-06    0.0021      16      50 ..      26      60 ..      16      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       +e+++ ++  l+Gp+G GK+Tll Ai  l  p++
  gi|386002679|ref|YP_005920978.1| 26 NLEVKEGDFLGLIGPNGGGKTTLLRAILGLVKPSR 60
                                      56666555888****************99999987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.4e-06    0.0049      22      39 ..      35      52 ..      20      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.4e-06
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                        ++GpNG GKTT+l+Ai
  gi|386002679|ref|YP_005920978.1| 35 LGLIGPNGGGKTTLLRAI 52
                                      5689*************9 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-05    0.0099      20      60 ..      34      74 ..      25     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAk 60
                                      +  l Gp G GKtt+l+a+  +++ + grv+++  + +aA+
  gi|386002679|ref|YP_005920978.1| 34 FLGLIGPNGGGKTTLLRAILGLVKPSRGRVAVFGMSPEAAR 74
                                      67799********************9888888877777775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-05     0.048      16      48 ..      24      57 ..      21      85 .. 0.85
   2 ?   -2.1   0.0       2.7   2.4e+03     323     364 ..     157     196 ..     151     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      +v ++++e  +  liG+N+ GK+++l+a+  + +
  gi|386002679|ref|YP_005920978.1| 24 EVNLEVKEGdFLGLIGPNGGGKTTLLRAILGLVK 57
                                      5566666667899****************76666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++++ll++EP + +     +++++ll +l ++    +i+ +H
  gi|386002679|ref|YP_005920978.1| 157 EPDLLLLDEPATGIDSARRREFYELLGDLNENMT--IIMVSH 196
                                       6789999999999999999999999999988874..777777 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.021        19      47      67 ..      32      52 ..      19      66 .. 0.84
   2 ?    7.3   0.0     0.004       3.6     104     148 ..     153     196 ..     139     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.021
                         IstB_IS21 47 kenivllGpsGvGKshlaial 67
                                       + + l+Gp G GK+ l  a+
  gi|386002679|ref|YP_005920978.1| 32 GDFLGLIGPNGGGKTTLLRAI 52
                                      566779*********998775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.004
                         IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                       + + ++dll+lD+ ++  +d+a +++++e++ +  e+ +ii+ s 
  gi|386002679|ref|YP_005920978.1| 153 ALVSEPDLLLLDEPAT-GIDSARRREFYELLGDLNENMTIIMVSH 196
                                       445678*******986.79******************99998875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0011      0.94      28      88 ..     135     182 ..     130     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       r++g+lSGG++q ++  a     +al+s+       ++l++LDE   ++D+ ++++  ell
  gi|386002679|ref|YP_005920978.1| 135 REIGALSGGQQQRVFV-A-----RALVSE-------PDLLLLDEPATGIDSARRREFYELL 182
                                       6788888888855442.2.....333444.......89999***99999999999988886 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001     0.091      17      49 ..      23      55 ..       9      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      ++++++ +e d+  ++GpN  GK+t+lrAi  l
  gi|386002679|ref|YP_005920978.1| 23 EEVNLEVKEGDFLGLIGPNGGGKTTLLRAILGL 55
                                      567888889999999**************9876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00014      0.13       4      31 ..      36      65 ..      33      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      EEEESTTCCHHHHHHHHH..CT--SS-EEE CS
                              cobW  4 vltGflGsGKTtLlnhll..enraglklav 31
                                      +l G+ G GKTtLl+++l   + +  ++av
  gi|386002679|ref|YP_005920978.1| 36 GLIGPNGGGKTTLLRAILglVKPSRGRVAV 65
                                      789**************9876777777776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0004      0.36       3      22 ..      37      56 ..      35      94 .. 0.85
   2 ?   -0.2   0.0       1.4   1.3e+03      58      67 ..     157     166 ..     117     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      l+Gp G GKT+l +a+   +
  gi|386002679|ref|YP_005920978.1| 37 LIGPNGGGKTTLLRAILGLV 56
                                      89*************98765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                                       TSEEEEEETG CS
                               AAA  58 kpsilfiDEi 67 
                                       +p  l++DE 
  gi|386002679|ref|YP_005920978.1| 157 EPDLLLLDEP 166
                                       4677777773 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014      0.13      26      57 ..      34      66 ..      19     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggif.lr 57
                                       + l+G+ G GK++l+r++l  ++ ++g + + 
  gi|386002679|ref|YP_005920978.1| 34 FLGLIGPNGGGKTTLLRAILGLVKPSRGRVaVF 66
                                      46689***************7777664444222 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.27       5      28 ..      37      60 ..      33      96 .. 0.76
   2 ?   -2.0   0.0       3.3     3e+03      72     112 ..     148     185 ..     140     222 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                      EEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  5 lqGeaGsGKTtLlqklalawaegk 28
                                      l G++G GKTtLl+ +  + + ++
  gi|386002679|ref|YP_005920978.1| 37 LIGPNGGGKTTLLRAILGLVKPSR 60
                                      78*************987776655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                                       CHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHH CS
                             NACHT  72 vwavllelperlLlilDglDelvtdlgqkekqpvrtlLsel 112
                                       v++ ++ + e  Ll+lD   e +t  + +++++  +lL++l
  gi|386002679|ref|YP_005920978.1| 148 VFVARALVSEPDLLLLD---EPATGIDSARRREFYELLGDL 185
                                       55555555555555555...333333333444445555444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.35       4      32 ..      37      74 ..      35      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                            AAA_28  4 itGgestGKTtlleaLa.....argypvv....pEaar 32
                                      ++G+ ++GKTtll+a+      +rg + v    pEaar
  gi|386002679|ref|YP_005920978.1| 37 LIGPNGGGKTTLLRAILglvkpSRGRVAVfgmsPEAAR 74
                                      79************987566555554433355566666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00026      0.23     133     160 ..      36      63 ..       7      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                             T2SSE 133 lvsGgTgsGKttllyallkeinksderi 160
                                        + G+ g GKttll a+l  ++ s  r+
  gi|386002679|ref|YP_005920978.1|  36 GLIGPNGGGKTTLLRAILGLVKPSRGRV 63 
                                       467******************9987776 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00028      0.25      54     115 ..     168     229 ..     160     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                            DUF460  54 lalkssreldreevieliselGkpvivAtDvspppetvkklarslkavlyvPeedlsveeKe 115
                                         ++s r+ +  e++  ++e  + ++v+ D+s ++ +vkk+a   +   y+ +++l +ee e
  gi|386002679|ref|YP_005920978.1| 168 TGIDSARRREFYELLGDLNENMTIIMVSHDISAVSTYVKKIACVSRRLFYHSSKELFAEEIE 229
                                       567899999999999999999999*******************9999999999999888755 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.25      16      70 ..      19      73 ..      12      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                                      HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 16 kellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      +++le++  +  +   +Gl G  G Gk tl+ a+   ++    rvav  + P + 
  gi|386002679|ref|YP_005920978.1| 19 RTVLEEVNLEVKEGDFLGLIGPNGGGKTTLLRAILGLVKPSRGRVAVFGMSPEAA 73
                                      6788888888888999*****************9998888888*****9999765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029      0.26       8      59 ..      20      69 ..      15      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                      HHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESS CS
                              PIF1  8 kvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAss 59
                                      +v++++   +  ++g ++ + G  G gKt l++a+l  +++++  v++   s
  gi|386002679|ref|YP_005920978.1| 20 TVLEEV--NLEVKEGDFLGLIGPNGGGKTTLLRAILGLVKPSRGRVAVFGMS 69
                                      556666..556699**************************998888876555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00075      0.67       5      26 ..      32      53 ..      27      75 .. 0.87
   2 ?   -1.4   0.0         3   2.7e+03      85     114 ..     153     184 ..     130     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00075
                            AAA_22  5 agilvvtGesGtGKTtllrrll 26
                                        +l ++G+ G GKTtllr +l
  gi|386002679|ref|YP_005920978.1| 32 GDFLGLIGPNGGGKTTLLRAIL 53
                                      567889************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                            AAA_22  85 alrarav...ielliiDEaqh.lr...seealeeLrs 114
                                       a         + ll++DE    ++   + e +e L +
  gi|386002679|ref|YP_005920978.1| 153 A-----LvsePDLLLLDEPATgIDsarRREFYELLGD 184
                                       3.....2344558888886665654433555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1485.85
//
Query:       gi|386002680|ref|YP_005920979.1|  [L=264]
Description: Cation ABC-3 transport family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-76  255.1  30.0    7.9e-76  255.0  30.0    1.0  1  ABC-3     ABC 3 transport family
    2.1e-08   33.6  34.2    3.9e-08   32.7  34.2    1.5  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.0  30.0   8.8e-80   7.9e-76       2     256 ..       7     261 ..       6     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 255.0 bits;  conditional E-value: 8.8e-80
                             ABC-3   2 yeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrkt 78 
                                       yef+qral+a+++ ++ c+++g++v+l+r++++g++++H a++G++l+yllg+ +ll a+l++l+aa+++++++ + 
  gi|386002680|ref|YP_005920979.1|   7 YEFMQRALAAGLIAAVLCGVIGVYVILNRIVFIGGGIAHTAFGGIGLGYLLGTDPLLFAVLFSLAAALGIGAISDRP 83 
                                       9**************************************************************************** PP

                             ABC-3  79 klkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfde 155
                                       +++edtaig+ +++++alg+v++sl+++++ dl+ yLfGnil++s  d++li+++++++l l+ l++k+ll+++fd+
  gi|386002680|ref|YP_005920979.1|  84 RVSEDTAIGVFWAAGMALGIVFISLSHGYAPDLFDYLFGNILAVSWGDVLLISVLTLLILGLVALLYKDLLILSFDP 160
                                       ***************************************************************************** PP

                             ABC-3 156 elAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllS 232
                                        + ++ gl+++ l+llll+++al+vvv +++vG+iLviall+iP+a+ r+ ++sl+ ++++Aillg  +v++Gl++S
  gi|386002680|ref|YP_005920979.1| 161 GYGEAVGLPTRGLRLLLLCMVALSVVVLIKIVGIILVIALLTIPGAIGRQHSSSLKGIMALAILLGGAFVLVGLVVS 237
                                       ***************************************************************************** PP

                             ABC-3 233 yyldlatGavivlvatllfllall 256
                                       y+l++++Ga+i+l a+  fl++ l
  gi|386002680|ref|YP_005920979.1| 238 YQLNIPSGATIILAAAGSFLASTL 261
                                       ********************9976 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  34.2   4.4e-12   3.9e-08      96     303 ..      54     255 ..       9     264 .] 0.79

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.4e-12
                             FecCD  96 gslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGsls 172
                                       g l     +l+a+l++l+a+l + +++  r + s  +   +G+  +a ++  + ++  l +   + ++  +l+G++ 
  gi|386002680|ref|YP_005920979.1|  54 GYLLGTDPLLFAVLFSLAAALGIGAIS-DRPRVSEDTA--IGVFWAAGMALGIVFIS-L-SHGYAPDLFDYLFGNIL 125
                                       444556778999999999999999999.5555555544..36666665544444444.3.3567799********** PP

                             FecCD 173 gaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLi. 248
                                        +sw +vll++vl+ll+l l++ll+++l +l+++    +++G++++ +rllll++val + v + +vG+i  ++L+ 
  gi|386002680|ref|YP_005920979.1| 126 AVSWGDVLLISVLTLLILGLVALLYKDLLILSFDPGYGEAVGLPTRGLRLLLLCMVALSVVVLIKIVGIILVIALLt 202
                                       **************************************************************************874 PP

                             FecCD 249 vPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGa 303
                                       +P  + +  +++ + ++ l++llG++++l+  +++  l  p+   + i++a+ G 
  gi|386002680|ref|YP_005920979.1| 203 IPGAIGRQHSSSLKGIMALAILLGGAFVLVGLVVSYQLNIPSG--ATIILAAAGS 255
                                       79999999999*******************9999988854444..5555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1576.57
//
Query:       gi|386002681|ref|YP_005920980.1|  [L=336]
Description: hypothetical protein Mhar_2001 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.4e-06   25.8   0.1     0.0039   17.4   0.1    3.2  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
      0.063   13.5   0.0          1    9.7   0.0    2.2  2  CARDB        CARDB


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.76   6.8e+03       2      17 ..      53      68 ..      52      71 .. 0.87
   2 !    4.4   0.0     0.005        45      40      74 ..     117     150 ..     113     155 .. 0.82
   3 !   17.4   0.1   4.3e-07    0.0039       2      73 ..     201     271 ..     200     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.76
                       NPCBM_assoc  2 epGetvtltltvtndg 17
                                      +pG   tl+l ++ndg
  gi|386002681|ref|YP_005920980.1| 53 SPGTGGTLRLILANDG 68
                                      789999******9998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.005
                       NPCBM_assoc  40 spasaaslapGetveatvkVtppagaaaGdyevta 74 
                                        p ++++l pGet   ++++ + +ga+ G   + +
  gi|386002681|ref|YP_005920980.1| 117 GPVQIDRLGPGETSPLEFEIEIEEGAE-GPILLSL 150
                                       688999******************999.5555555 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 4.3e-07
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslsl.PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevt 73 
                                       +pGe+ ++ l++ n g+a+a+n   +l + P+   v  +   ++ +++pG t+ a ++V +  +a aG+y+v 
  gi|386002681|ref|YP_005920980.1| 201 SPGEEGEISLVLGNAGKATARNCTARLVAaPPFIPV--SNISRLGDIPPGGTAVARFEVAVEGSARAGEYRVG 271
                                       799********************9999887887664..4456889*************************995 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.041   3.7e+02      50      87 ..     117     155 ..     103     161 .. 0.85
   2 ?    9.7   0.0   0.00011         1       9      78 ..     194     268 ..     179     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.041
                                       EEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEEEESTT CS
                             CARDB  50 gtvtvpsLaagesttvsftwtte.ategevtltvvvDpd 87 
                                       g v++  L +ge++  +f + +e  +eg + l+++v+ +
  gi|386002681|ref|YP_005920980.1| 117 GPVQIDRLGPGETSPLEFEIEIEeGAEGPILLSLQVEYE 155
                                       567899**************9999899999888888765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE...SEE-CTEEEEEEEEEE-S..-S-CEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv...psLaagesttvsftwtte..ategev 78 
                                       +++ s +++gee +i++ + N G+a++++++++l++       +++     + +g+++  +f + +e  a +ge+
  gi|386002681|ref|YP_005920980.1| 194 ISTRSGLSPGEEGEISLVLGNAGKATARNCTARLVAAPPFIPVSNIsrlGDIPPGGTAVARFEVAVEgsARAGEY 268
                                       567788899***************************999885555533367778888888888877755555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2155.93
//
Query:       gi|386002682|ref|YP_005920981.1|  [L=307]
Description: ABC transporter ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-28   99.2   0.0    3.8e-28   98.7   0.0    1.2  1  ABC_tran  ABC transporter
    1.2e-12   48.3   0.4    1.4e-05   25.1   0.1    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      8e-06   26.5   0.0    1.6e-05   25.5   0.0    1.5  1  DUF4162   Domain of unknown function (DUF4162)
    0.00087   19.8   0.1      0.002   18.7   0.1    1.6  1  AAA_23    AAA domain
     0.0012   18.7   0.1        1.3    8.7   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0021   17.7   0.0     0.0039   16.9   0.0    1.3  1  AAA_29    P-loop containing region of AAA domain
     0.0069   15.1   0.0        0.3    9.7   0.0    2.1  2  AAA_13    AAA domain
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.041   13.6   0.0    1.4  1  AAA_30    AAA domain
      0.029   14.4   0.0       0.36   10.8   0.0    2.4  2  AAA_5     AAA domain (dynein-related subfamily)
      0.029   14.0   0.1        1.5    8.4   0.0    2.3  2  cobW      CobW/HypB/UreG, nucleotide-binding domain
      0.031   14.1   0.0      0.048   13.5   0.0    1.2  1  MukB      MukB N-terminal
       0.12   11.4   0.0       0.23   10.4   0.0    1.4  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.15   12.1   0.0        4.7    7.2   0.0    2.3  2  AAA_14    AAA domain
       0.18   11.5   0.0       0.35   10.6   0.0    1.5  1  AAA_24    AAA domain
       0.19   11.1   0.0        1.5    8.2   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   3.1e-31   3.8e-28       1     137 []      23     167 ..      23     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 3.1e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vsl ++ege+ +i+G+nGaGK+tL+++++ l +p+eG++++ g +  + +++  r++i + + +p++   ltvr
  gi|386002682|ref|YP_005920981.1|  23 LHQVSLAIEEGEVFGILGPNGAGKTTLMSIFSTLIRPDEGRLEVLGLNALR-DTHAIRERINISSGNPNFPWSLTVR 98 
                                       789****************************************99888888.89*********************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en             +  + +e a+s+++l+     +v+s+ ++LS G kqrv+la+++l++p++l+lDEpt+
  gi|386002682|ref|YP_005920981.1|  99 ENlnhsamlyglygrDLARSVEGAISTFDLEA----HVDSKFETLSTGLKQRVSLAKSILNRPEILFLDEPTS 167
                                       ****9999999888777777999999999888....555666*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.6e-07   0.00019       2      63 ..      36     111 ..      35     138 .. 0.76
   2 !   25.1   0.1   1.2e-08   1.4e-05     236     298 ..     138     198 ..     135     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl..............drdvegltdelsggggirkipslldlydpeipfefeie 63 
                                        ++ GpNg+GK++L+ +++ l r               d++++++ ++ s+g+++  ++   +++   +++ ++++
  gi|386002682|ref|YP_005920981.1|  36 FGILGPNGAGKTTLMSIFSTLIRPdegrlevlglnalrDTHAIRERINISSGNPNFPWSLTVRENLNHSAMLYGLY 111
                                       689******************9989988888887777777777777777777777777777777777666666665 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.2e-08
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkll...rrllellkelsrngaQviltTHS 298
                                        lS G k+   l+ ++l ++    +l++DEp +gL+P +    r l+  + ++++    v+ltTH 
  gi|386002682|ref|YP_005920981.1| 138 TLSTGLKQRVSLAKSILNRP---EILFLDEPTSGLDPDMAmktRALIHRIYREEE--MTVVLTTHY 198
                                       57888888889999***999...9*************887788999999999999..9*******5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.3e-08   1.6e-05       1      80 [.     221     305 ..     221     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-08
                                       E-HHHHHTTS.-SSEEEEE....-------..---EEEE-TTS-EEEEE--.---------------EEEEEEEE-- CS
                           DUF4162   1 GtleeiKrsy.gknrieve....adaeelleepgveeveeeggelelkled.eeaanellkaltsgveirsFeeeeP 71 
                                       Gt+ e+Kr++  ++ri +e     d+ +l+ +pgv +v+   g++e+  +  + a  ++++a  +++ei ++ +e+P
  gi|386002682|ref|YP_005920981.1| 221 GTPGELKRALkIGDRIFIEyegeIDPISLRIIPGVMDVRPSAGRVEVVFDRsDGALGRIIRAF-DRAEILEMGLEKP 296
                                       9999******6689999**8755558999999******************88***********.************* PP

                                       -HHHHHHHH CS
                           DUF4162  72 sLndIFiek 80 
                                        L+d+F+e+
  gi|386002682|ref|YP_005920981.1| 297 DLEDVFLEL 305
                                       *******97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.7e-06     0.002      19      37 ..      33      51 ..      11      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                            AAA_23 19 kgltlItGpNGaGKTTild 37
                                        ++ I GpNGaGKTT++ 
  gi|386002682|ref|YP_005920981.1| 33 GEVFGILGPNGAGKTTLMS 51
                                      5699*************85 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0018       2.2      25      49 ..      35      59 ..      22      85 .. 0.81
   2 !    8.7   0.0    0.0011       1.3     317     364 ..     146     197 ..     118     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnn 49
                                      +  + G+N++GK++++ ++  ++  
  gi|386002682|ref|YP_005920981.1| 35 VFGILGPNGAGKTTLMSIFSTLIRP 59
                                      55688*************9988775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                            AAA_15 317 k....dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +    +++ +++ il+++EP   L p++ +    l+ ++ +++++ v++tTH
  gi|386002682|ref|YP_005920981.1| 146 RvslaKSILNRPEILFLDEPTSGLDPDMAMKTRALIHRIYREEEMTVVLTTH 197
                                       23344556678899************************************** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.2e-06    0.0039      13      50 ..      24      61 ..      20      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++ ++ i++ +++ + Gp+G+GK+Tl+  +++l+ p++
  gi|386002682|ref|YP_005920981.1| 24 HQVSLAIEEGEVFGILGPNGAGKTTLMSIFSTLIRPDE 61
                                      55666777555999*************98899888875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00025       0.3      21      39 ..      38      56 ..      34      69 .. 0.88
   2 ?    3.4   0.0      0.02        24     521     569 ..     151     197 ..     108     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NGaGKTtL ++++ l
  gi|386002682|ref|YP_005920981.1| 38 ILGPNGAGKTTLMSIFSTL 56
                                      679************9987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.02
                            AAA_13 521 dseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTH 569
                                       +s ++  +i ++D P S LD ++ +    li   +  +++   + + TH
  gi|386002682|ref|YP_005920981.1| 151 KSILNRPEILFLDEPTSGLDPDMAMKTRALIHRIY--REEEMTVVLTTH 197
                                       44557899***********************9998..455556677777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.4e-05     0.041      14      53 ..      30      68 ..      23      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                            AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglA 53
                                      +++g  v  + Gp G+GKtt+++    +++ ++gr+ +l 
  gi|386002682|ref|YP_005920981.1| 30 IEEG-EVFGILGPNGAGKTTLMSIFSTLIRPDEGRLEVLG 68
                                      4444.59999***************999998865555544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.36       4      54 ..      38      91 ..      36     231 .. 0.82
   2 ?    0.9   0.0      0.34   4.1e+02      20      72 ..     181     239 ..     172     255 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                      EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--....... CS
                             AAA_5  4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttsl 54
                                      ++Gp G gK++l+  ++ ++   + ++e+  l++   +  ++ r++i++g+  +
  gi|386002682|ref|YP_005920981.1| 38 ILGPNGAGKTTLMSIFSTLIrpdEGRLEVLGLNALRDTHAIRERINISSGNPNF 91
                                      68*******************988888888888888889999999998766555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                       GGGB..S--EEEEE--TT--H.HHHH--B--............--------G-SEEEEE CS
                             AAA_5  20 aaal..nreveyvqltrdtte.edlkgrreik...ngttslvdsplvraaregeilvlD 72 
                                        +++  + e+++v+ t +++e e+l  r+ +       +  ++++l+ra + g+ ++++
  gi|386002682|ref|YP_005920981.1| 181 IHRIyrEEEMTVVLTTHYMPEaEELCDRIAFLregRLIALGTPGELKRALKIGDRIFIE 239
                                       44446777778888888886525688888777643334445788889888888877775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0013       1.5       2      18 ..      35      51 ..      34      79 .. 0.82
   2 ?    3.7   0.0     0.035        42      76      99 ..     226     249 ..     170     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                                      EEEEEESTTCCHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLln 18
                                      v+++ G+ G+GKTtL++
  gi|386002682|ref|YP_005920981.1| 35 VFGILGPNGAGKTTLMS 51
                                      67899**********86 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.035
                                       HHHHHTT-SEEEEEECTTTTHHHH CS
                              cobW  76 leereerldviliEttGlaePapv 99 
                                       l++  ++ d+i+iE  G  +P  +
  gi|386002682|ref|YP_005920981.1| 226 LKRALKIGDRIFIEYEGEIDPISL 249
                                       44444899*********9999887 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.048      28      59 ..      35      66 ..      14      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                                      HHHHHS--SHHHHHHHHHHHHHHS--TTT--- CS
                              MukB 28 vttlsGgnGaGksttmaafvtaliPdlsllhf 59
                                      v  + G nGaGk+t m  f t + Pd  +l+ 
  gi|386002682|ref|YP_005920981.1| 35 VFGILGPNGAGKTTLMSIFSTLIRPDEGRLEV 66
                                      5567799*******************999976 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002      0.23      15      63 ..      19      67 ..       6      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                      HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                       ke+l++++    + +v G+ G  GaGk tl++ + + +r    r  vl
  gi|386002682|ref|YP_005920981.1| 19 KKEVLHQVSLAIEEGEVFGILGPNGAGKTTLMSIFSTLIRPDEGRLEVL 67
                                      68999999999999*********************99998777777776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.004       4.7       3      26 ..      34      56 ..      32      82 .. 0.80
   2 ?    2.5   0.0      0.11   1.4e+02      35      97 ..     125     194 ..     105     197 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.004
                            AAA_14  3 kilvitGaRrvGKTtllkqlikel 26
                                      ++  i G+  +GKTtl+  ++++l
  gi|386002682|ref|YP_005920981.1| 34 EVFGILGPNGAGKTTLMS-IFSTL 56
                                      67889***********84.44455 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                            AAA_14  35 yinldderdkkladpekllelilek..lke....ekktylflDEiqev......pewekalkslvdegknldviv 97 
                                        ++l+ + d+k+++   l + ++++  l +    ++ ++lflDE           + +  + ++++e+ ++ v++
  gi|386002682|ref|YP_005920981.1| 125 TFDLEAHVDSKFET---LSTGLKQRvsL-AksilNRPEILFLDEPTSGldpdmaMKTRALIHRIYREE-EMTVVL 194
                                       55555555544443...34444444221.1245568999*****765544444355555555555555.556655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.35       5      30 ..      36      59 ..      32      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfid 30
                                      + i Gp+g+GKTtl++ +  ++l+  
  gi|386002682|ref|YP_005920981.1| 36 FGILGPNGAGKTTLMSIF--STLIRP 59
                                      6799***********999..555544 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0013       1.5      25      41 ..      34      50 ..      13      57 .. 0.79
   2 ?    0.3   0.0      0.33   3.9e+02     158     203 ..     156     201 ..     123     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++  i+GpNG+GK+ l+
  gi|386002682|ref|YP_005920981.1| 34 EVFGILGPNGAGKTTLM 50
                                      35679*********998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.33
                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                       +  + +lDe  + LD     k   l+++   +  + v+  ++ m e
  gi|386002682|ref|YP_005920981.1| 156 RPEILFLDEPTSGLDPDMAMKTRALIHRIYREEEMTVVLTTHYMPE 201
                                       444678999999**99988888888886655555555444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1957.99
//
Query:       gi|386002683|ref|YP_005920982.1|  [L=261]
Description: ABC transporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-10   40.4  23.9    2.1e-10   40.4  23.9    1.6  2  ABC2_membrane    ABC-2 type transporter
      0.008   15.3  31.6       0.01   15.0  31.6    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4  23.9   2.3e-14   2.1e-10       9     208 ..      16     217 ..       9     218 .. 0.80
   2 ?   -1.7   0.2      0.17   1.6e+03     107     127 ..     227     247 ..     222     259 .. 0.48

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.3e-14
                     ABC2_membrane   9 reflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr..pgllffsvlflafsaltsvapvferergvle 83 
                                       ++++  +r+ ++  +  ++ p++ +l +g++   l+  +d +++  +g+++ s+l ++ ++  + +++f+   ++++
  gi|386002683|ref|YP_005920982.1|  16 KNWIISKRNVFTV-FELIFWPFISLLSIGLLTRFLEVADDMVAFvlVGAIALSILQIS-QIDVAYILLFDLWSKSIK 90 
                                       5565555555444.66666666666666666666552344444456************.5555555*********** PP

                     ABC2_membrane  84 relvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rf...flflllllltalaasslgllisalap 156
                                       + +v+p+ +    vl+ +l+ ++++ ++ +i+ + + +l+g+d    +   +l++l+ ++++ a++++ ++is+l+ 
  gi|386002683|ref|YP_005920982.1|  91 QTFVAPV-RGYHLVLGAMLFGVARGSAVFIILAAASRYLFGFDFLaGGaatVLIFLAGIFVTAASIGMVVCISILLF 166
                                       *******.************************************973355688888888888888889999999988 PP

                     ABC2_membrane 157 sfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                        ++  +  +s +  +++l+sG+++p++ +p  lq +++  Plty++e +rs+
  gi|386002683|ref|YP_005920982.1| 167 GQRADVAAWS-LSGIMMLVSGVYYPVSILPWPLQILSKSIPLTYFLEFYRSA 217
                                       7776666665.567789************9789***************9987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.17
                     ABC2_membrane 107 vsllqalifllivyflvgldl 127
                                       +++++al++++ ++++++l +
  gi|386002683|ref|YP_005920982.1| 227 LGMALALLYFAASLLILNLAI 247
                                       334444444444444444443 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 !   15.0  31.6   1.1e-06      0.01     156     342 ..      52     242 ..      17     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                   ABC2_membrane_3 156 lsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...la 228
                                       +++++ f+++ +i++ ++ i+ + +a+ ++++  s+ +++ +v++v+ + ++l+ +l+ ++ +  +++++ +   ++
  gi|386002683|ref|YP_005920982.1|  52 ADDMVAFVLVgAIALSILQISQIDVAYILLFDLWSKSIKQTFVAPVRGYHLVLGAMLFGVARGSAVFIILAAasrYL 128
                                       455555555515555555555555566669************************************99999955559 PP

                   ABC2_membrane_3 229 fglgipfgnlglllllfllfgl....ayialgyllssl.fknsetaqilifivilllsgffgglfpledlpsalkwi 300
                                       fg  ++f   g++ +l++l g+    a+i ++  +s l f + +++  +++ ++ ++++++g+ +p++ lp +l+++
  gi|386002683|ref|YP_005920982.1| 129 FG--FDFLAGGAATVLIFLAGIfvtaASIGMVVCISILlFGQRADV--AAWSLSGIMMLVSGVYYPVSILPWPLQIL 201
                                       99..888866666655555555122244444445555555555553..344444479999***************** PP

                   ABC2_membrane_3 301 fsiiPffapglgllrlitgdplweillsliilalfavvylll 342
                                       +  iP++++ ++  +  +g+   ++ll +++ +l +++ ll+
  gi|386002683|ref|YP_005920982.1| 202 SKSIPLTYFLEFYRSA-YGYGSHQVLLGMALALLYFAASLLI 242
                                       *******988877555.5554589887777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1788.90
//
Query:       gi|386002684|ref|YP_005920983.1|  [L=409]
Description: Dihydropteroate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-53  180.6   0.0    5.1e-53  180.2   0.0    1.1  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.2   0.0   2.9e-57   5.1e-53       1     244 []      21     258 ..      21     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 2.9e-57
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHH.HC.TSE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrd.ea.dvp 75 
                                       mg++N++ +sf++++    +d++l +a +  eeGA++lD+g+ st Pg+  ++eeee +r+ p lea+ d    +v 
  gi|386002684|ref|YP_005920983.1|  21 MGVINLSRESFYEESY-AGIDAVLGRALAFAEEGAEVLDLGAVSTAPGSPSIPEEEERRRLFPALEAVLDgLGeEVV 96 
                                       9************765.5****************************************************53479** PP

                                       EEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHH CS
                       Pterin_bind  76 isiDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflea 152
                                       +s+Dt +a+va +Al+aga  +Ndvsg+  dp+m+++va+++  +++m+++++p       g+  d+  ++ a l +
  gi|386002684|ref|YP_005920983.1|  97 VSVDTQRASVADDALSAGAGCINDVSGLH-DPAMAKTVADHDGSLIIMASKERP-------GDILDMR-DIVANLGE 164
                                       *****************************.*********************333.......4444443.44455666 PP

                                       HHHHHHHTT--GGGEEEETTTTS...STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHH CS
                       Pterin_bind 153 rveaaeeaGvaperillDpgigf...gkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagt 226
                                       rv+aa eaGva+e++ +Dpgig     k + h+l++l+ l++l + l+ pv+ +vSrksf+g++le  ++++R  g+
  gi|386002684|ref|YP_005920983.1| 165 RVRAAWEAGVAAEKVTVDPGIGRwtpPKGPGHDLAILDGLERL-RVLKRPVMAAVSRKSFIGAVLERPSPSDRLPGS 240
                                       8999999**************99888999**************.99999**************997667******** PP

                                       HHHHHHHHHTT-SEEEES CS
                       Pterin_bind 227 aaflalaaaaGadivrVh 244
                                       +a++a a+ +Ga+ vr+h
  gi|386002684|ref|YP_005920983.1| 241 LAAAAVAVYNGAHLVRTH 258
                                       *****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2576.50
//
Query:       gi|386002685|ref|YP_005920984.1|  [L=137]
Description: Cytidine deaminase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-23   81.2   0.0    8.1e-23   81.0   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   4.5e-27   8.1e-23       1     138 [.       9     122 ..       9     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 4.5e-27
                                       -..-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..... CS
                       F420_ligase   1 giktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrn 77 
                                       gikt+l++ g+dl+e ++  ++++gl l dgD++vv+e++va+aeg +v+l++++p+++A+e+aek+ ++dp     
  gi|386002685|ref|YP_005920984.1|   9 GIKTNLVRAGEDLVEALLGGMERSGLALADGDVLVVAESAVATAEGGVVDLSEVTPGPRARELAEKY-EKDP----- 79 
                                       89*****************************************************************.****..... PP

                                       .............HHHHHHHHTEEEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TT CS
                       F420_ligase  78 rfsliLkalakatrkvevvlsepsdevgn...qlidekytdevlvklGllgsnagidesnveeg 138
                                                    r++e++l  +++++g    +++++k         G+l+ nagid+sn++ +
  gi|386002685|ref|YP_005920984.1|  80 -------------REMELILASSDRIMGGipgVVLTVK--------DGFLYPNAGIDHSNAPPA 122
                                       .............***************9988777777........5*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 790.02
//
Query:       gi|386002686|ref|YP_005920985.1|  [L=261]
Description: Cytidine deaminase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-26   91.0   0.1    1.2e-25   90.3   0.1    1.4  1  F420_ligase      F420-0:Gamma-glutamyl ligase
    8.3e-15   54.5   0.3    1.5e-14   53.7   0.3    1.4  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.1e-08   35.4   0.4    1.7e-08   34.7   0.4    1.3  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
     0.0054   16.4   1.5       0.69    9.5   0.2    2.2  2  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.1   2.7e-29   1.2e-25     155     244 .]       2      89 ..       1      89 [. 0.98

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2.7e-29
                                       HHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC- CS
                       F420_ligase 155 kkklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsG 231
                                       +++++e+tgk+++V+i   D+++++++l++++va++++g+ +++d rg+kdl+g++l +t +av+d+l s+a+Lv+G
  gi|386002686|ref|YP_005920985.1|   2 RRRMEEATGKRIGVVI--GDSRTHPLRLGCVGVALACDGILPVEDARGQKDLYGRPLLVTRKAVADNLVSAAELVMG 76 
                                       789*************..*********************************************************** PP

                                       SSSS---EEEEES CS
                       F420_ligase 232 sadegtPvvlvrg 244
                                       ++deg+P+v++rg
  gi|386002686|ref|YP_005920985.1|  77 EGDEGVPAVIIRG 89 
                                       ************8 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.3   3.3e-18   1.5e-14       5      95 ..     129     224 ..     127     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 3.3e-18
                                       HHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE... CS
                   dCMP_cyt_deam_1   5 ekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv... 77 
                                        +l+e a +a+++a+ ++s f+VGa+++ +g +++ ++n e+a++   i+AE+ A++kaa++g+ ++ +a  +v   
  gi|386002686|ref|YP_005920985.1| 129 DRLIESAREAMERAYaPYSGFRVGAALLAKGGRVYSAANVENASSGAAICAERAAMAKAASEGEREF-EALAVVaet 204
                                       578999*******************************************************975566.333333687 PP

                                       ..EE--BHHHHHHHHHHT-S CS
                   dCMP_cyt_deam_1  78 ..tlePCsmCakaiiqsgik 95 
                                          + PC+ C++ +i++g +
  gi|386002686|ref|YP_005920985.1| 205 vePVAPCGICRQSLIEFGDE 224
                                       778899***********954 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.4   3.8e-12   1.7e-08      44     112 ..     128     197 ..      95     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.8e-12
                                       S-HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHH.TT--GGG CS
                   dCMP_cyt_deam_2  44 ddelkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvl.ggkefee 112
                                        d+l e+A +a++++yapys    G aL  k g+vy+   +E+a     + + +aA+ ++   g++efe 
  gi|386002686|ref|YP_005920985.1| 128 YDRLIESAREAMERAYAPYSGFRVGAALLAKGGRVYSAANVENASSGAAICAERAAMAKAASeGEREFEA 197
                                       46799******************************************************99944455554 PP

>> LmjF365940-deam  A distinct subfamily of CDD/CDA-like deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00015      0.69      59      89 ..     161     190 ..      85     205 .. 0.82
   2 !    7.0   0.1   0.00088       3.9     148     175 ..     202     226 ..     190     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                   LmjF365940-deam  59 elvrgvNlEvSmPtGSlCsErnaigkalasd 89 
                                       +++ + N+E        C+Er+a++ka + +
  gi|386002686|ref|YP_005920985.1| 161 RVYSAANVENASSGAAICAERAAMAKAAS-E 190
                                       48999****9999999**********644.3 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00088
                   LmjF365940-deam 148 arksnPLkPCGaCeewLkkiaevnpdfk 175
                                       a++  P+ PCG+C++ L    e + ++k
  gi|386002686|ref|YP_005920985.1| 202 AETVEPVAPCGICRQSLI---EFGDEIK 226
                                       55669********99874...4455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1557.27
//
Query:       gi|386002687|ref|YP_005920986.1|  [L=282]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for 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-06   25.7   0.0    1.3e-05   25.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0021   18.7   0.0      0.003   18.2   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
     0.0043   17.7   0.0     0.0071   17.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.029   14.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      0.058   14.1   0.0        0.1   13.4   0.0    1.5  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.7e-09   1.3e-05      78     164 ..     111     196 ..      59     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.7e-09
                   Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkel 154
                                       e ++ fdl+++++++ehvp p++ l++i +  k g ++  +e + ++  ++   d + + + ++hi+f++ +++ +l
  gi|386002687|ref|YP_005920986.1| 111 ETEDIFDLVTMFDLIEHVPEPEMFLSSISERAKFGLLMTPMETGGDWFGAKP-PDKQGDHHPDGHINFYTPKNYLKL 186
                                       45668*************************9997766666777777664444.5568889999************** PP

                   Methyltransf_23 155 leeaGlevve 164
                                       l + G+e++e
  gi|386002687|ref|YP_005920986.1| 187 LDDGGWELIE 196
                                       ******9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.5e-07     0.003       5      90 ..      59     139 ..      53     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.5e-07
                                       T-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                   Methyltransf_25   5 GcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                       G G   +++++ k+ g   +   ++++++++ + r+ +    + ++f+qg++ ++++ ++ fDlv+++  ++h++++
  gi|386002687|ref|YP_005920986.1|  59 GFGANSMAFQINKHQGhYPRTSVFELASNFVIIGRQLY----PYINFIQGSILEYKETEDIFDLVTMFDLIEHVPEP 131
                                       44555556666666544778888999999999999999....89***********************877***9976 PP

                                       HHHHHHHHHH CS
                   Methyltransf_25  81 dlekalkeia 90 
                                       +   +l+ i+
  gi|386002687|ref|YP_005920986.1| 132 E--MFLSSIS 139
                                       6..6677665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     2e-06    0.0071       2      85 ..      53     139 ..      52     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                       EET-TTSHHHHHHH.....HTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-C CS
                   Methyltransf_11   2 dvGcGtGrlaeala.....krg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevl 71 
                                       d+G + G  a+ +a     ++g   r+  ++l+ +++ + ++ ++     ++f+++++ + +  ++ fDlv+++  +
  gi|386002687|ref|YP_005920986.1|  53 DIGGCFGFGANSMAfqinkHQGhyPRTSVFELASNFVIIGRQLYPY----INFIQGSILEYKETEDIFDLVTMFDLI 125
                                       6666666666666666655444556777777777777666666655....779*******988888*********** PP

                                       CC-CCHHHHHHHHH CS
                   Methyltransf_11  72 hhvedpekalkeia 85 
                                       +hv++pe +l+ i 
  gi|386002687|ref|YP_005920986.1| 126 EHVPEPEMFLSSIS 139
                                       *********99886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.2e-06     0.029      56     102 ..      99     143 ..      91     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-06
                   Methyltransf_31  56 veFeqgdiee.leklledekfDlilsnevlnaladpdkileeiervlk 102
                                       ++F qg+i e +e+   ++ fDl++ ++++ ++++p+ +l +i++  k
  gi|386002687|ref|YP_005920986.1|  99 INFIQGSILEyKET---EDIFDLVTMFDLIEHVPEPEMFLSSISERAK 143
                                       78********6663...49*********************99987666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05       0.1      52      93 ..     100     142 ..      61     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                   Methyltransf_12  52 elealdlldldgg.ssfDlvvasnvlhhlkdirevldnirklL 93 
                                       ++ + ++l+ ++  + fDlv+++++++h+++++ +l++i +  
  gi|386002687|ref|YP_005920986.1| 100 NFIQGSILEYKETeDIFDLVTMFDLIEHVPEPEMFLSSISERA 142
                                       5555555555555679********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1880.10
//
Query:       gi|386002688|ref|YP_005920987.1|  [L=236]
Description: Glycosyl transferase family 2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-19   69.7   0.0    4.5e-19   69.0   0.0    1.3  1  Glyco_tranf_2_5  Glycosyltransferase like family
     0.0038   17.0   0.0      0.021   14.7   0.0    1.9  2  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0     5e-23   4.5e-19       1     180 [.      17     191 ..      17     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5e-23
                   Glyco_tranf_2_5   1 afivcvnneelyeeclsylenlevpegyeveiiairna....ksiaeaynkalsasdakykvYlhqDvliinkdfik 73 
                                       +++v +nn+++++    ++++l+  +  e e+i+++n     ks  ea n +  ++  +y +++hqDv +  + +++
  gi|386002688|ref|YP_005920987.1|  17 SVVVVYNNKHIFNS--VLMRSLKD-QTAEFELISLDNTrgefKSASEALNYGGLRATGRYIMFVHQDVDLGIETWLE 90 
                                       68999********9..77788875.669**********9************************************** PP

                   Glyco_tranf_2_5  74 dlleiFkkdkkiGmiGvvGakslpesgvwweskkkvgkvietskeeakelraeeeeseyeeVeaidGllmatqydv. 149
                                       ++ +i++  +++G+ Gv+G ++  +s      ++++g++ ++      e + ++e ++ eeV+++d ll+++ ++  
  gi|386002688|ref|YP_005920987.1|  91 EVEKILDGIPDLGIAGVAGMSEAGRSF----AERQRGHISNS-----GEIW-GREMEKEEEVQTLDELLLIIPRSQf 157
                                       *******************88776665....44578888877.....4444.55667889***********977766 PP

                   Glyco_tranf_2_5 150 ...pwredlftgfhfYdvsqslefekagykvvVp 180
                                          +++e+ f+++h+Y ++ +l++++ag k +V 
  gi|386002688|ref|YP_005920987.1| 158 ektQFDEKTFDHWHCYGADYCLSVKRAGLKAYVI 191
                                       889**************************99883 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 ?   -0.1   0.0     0.078     7e+02       3      36 ..      18      50 ..      17      55 .. 0.73
   2 !   14.7   0.0   2.3e-06     0.021      68     133 ..      59     132 ..      51     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.078
                                      EEEESS-TTTHHHHH.HHHHHHGGCCEEEEEEEEE CS
                   Glycos_transf_2  3 viptyNeektlletl.esllaqdpypdfeiivvDD 36
                                      v+++yN ++    +l +sl++q    +fe+i +D+
  gi|386002688|ref|YP_005920987.1| 18 VVVVYNNKHIFNSVLmRSLKDQ--TAEFELISLDN 50
                                      6777887666665542677777..99999999997 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHH--SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.......E CS
                   Glycos_transf_2  68 agalnaglraatgdyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernkrv.......g 133
                                       + aln g  +atg+yi+f+ +D+    + wle++ + l+  ++ +++g    ++ ++ + er++++       +
  gi|386002688|ref|YP_005920987.1|  59 SEALNYGGLRATGRYIMFVHQDVDLGIEtWLEEVEKILDGIPDLGIAGVAGMSEAGRSFAERQRGHisnsgeiW 132
                                       689************************99***********9999999999999999999999998877665431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1598.28
//
Query:       gi|386002689|ref|YP_005920988.1|  [L=151]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-05   24.4   0.0      0.001   19.7   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
     0.0079   16.9   0.1      0.014   16.1   0.0    1.5  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.096   12.7   0.3       0.13   12.2   0.3    1.2  1  DUF371           Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.7e-07     0.001      32      91 ..      10      66 ..       1      71 [. 0.81
   2 ?    3.0   0.0     0.027   1.6e+02       4      37 ..      83     116 ..      81     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.7e-07
                                      HHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEE CS
                   Methyltransf_11 32 klakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpekalkeiaRvLkpg 91
                                      + +k++++++     ++++ +e + f+ +sfD+v+s e+ +++  e++++++ ++ R+ ++ 
  gi|386002689|ref|YP_005920988.1| 10 ESVKKCIHDQ-----YIRSKIELVAFKPKSFDAVISIESTDNLseEERRRLVYQMERWARKK 66
                                      4556666665.....599****99*******************999***********98876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.027
                                       T-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHH CS
                   Methyltransf_11   4 GcGtGrlaealakrgarvvgvDlskemlklakek 37 
                                       G G G ++++l+k g +++g+  + ++  + k++
  gi|386002689|ref|YP_005920988.1|  83 GEGWGWNLRYLEKIGFKIYGICGWRRLGIYDKKN 116
                                       6799****************98777665444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-06     0.014      30      95 ..       4      65 ..       1      66 [. 0.82
   2 ?   -3.2   0.0       2.5   1.5e+04       5      26 ..      83     102 ..      83     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                                      SHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEE CS
                   Methyltransf_25 30 seemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkp 95
                                      s++ l++  +++    ++ ++++ ++e + f+ +sfD+v+s+ +   ls+e++++++ ++ r+ ++
  gi|386002689|ref|YP_005920988.1|  4 SDSNLDESVKKC----IHDQYIRSKIELVAFKPKSFDAVISIESTDNLSEEERRRLVYQMERWARK 65
                                      555555555555....466899999999*************988****************998775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.5
                                       T-TTSHHHHHHHCTSTSSEEEE CS
                   Methyltransf_25   5 GcGtGrltlalakrlgkakvtg 26 
                                       G G G ++++l k  g  k++g
  gi|386002689|ref|YP_005920988.1|  83 GEGWGWNLRYLEKI-G-FKIYG 102
                                       56889999988876.3.66666 PP

>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   2.2e-05      0.13      42     113 ..       6      80 ..       1      82 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                       GGS-HHHHHHHS----EEEEEEE-...SS-EEEEEEE--TT-----SSEEEEESSS---TTEEEBS-S--GGGS- CS
                            DUF371  42 adlseelkealkeeeatitvtlev...geledeitgrGspkltlenerdlvvRkSdyvddrTllvkadkaaadld 113
                                       ++l+e++k+ ++++  + +++l +   ++    i  + +++l+ e+ r+lv+    +  ++ ++v+ ++a+++++
  gi|386002689|ref|YP_005920988.1|   6 SNLDESVKKCIHDQYIRSKIELVAfkpKSFDAVISIESTDNLSEEERRRLVYQMERWARKKVIIVSKNRASQEIE 80 
                                       789*********99987777777655344556666788899******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 929.04
//
Query:       gi|386002690|ref|YP_005920989.1|  [L=505]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-26   91.3   0.0    7.5e-25   87.7   0.0    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
    6.6e-19   68.7   0.0    1.1e-18   68.0   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.3e-10   41.0   0.2    8.2e-10   39.2   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    2.4e-09   37.3   0.0    4.4e-09   36.4   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    2.4e-07   30.7   0.4    2.1e-06   27.6   0.0    2.5  3  Methyltransf_31  Methyltransferase domain
     0.0001   23.0   0.3    0.00038   21.1   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    0.00038   21.1   0.1     0.0013   19.4   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
    0.00083   18.8   0.0     0.0014   18.0   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0037   17.2   0.0     0.0063   16.4   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0082   15.6   0.0      0.016   14.7   0.0    1.5  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.012   15.3   0.1       0.06   13.0   0.0    2.3  2  Glyco_tranf_2_5  Glycosyltransferase like family
      0.063   12.4   0.0       0.13   11.3   0.0    1.5  1  DREV             DREV methyltransferase
      0.085   13.4   0.0        0.2   12.2   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.11   13.2   0.0       0.25   12.0   0.0    1.6  1  DUF4864          Domain of unknown function (DUF4864)


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 ?    1.1   0.0      0.24     3e+02      95     151 ..      86     142 ..      78     146 .. 0.70
   2 !   87.7   0.0   5.9e-28   7.5e-25       1     129 [.     199     321 ..     199     366 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.24
                                       THHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..EEEECCHCCCCHCCCCCCS CS
                   Glycos_transf_2  95 dwleklvealekdgadvvlgqrprifgetdeiernkrv..generlyfkerkrslkgnl 151
                                       + le++ + ++ d    v+ ++p+++++  +i +++r   +en++ yf+e+    ++ +
  gi|386002690|ref|YP_005920989.1|  86 KVLEEIWRVAKPDA--TVYITVPYCQSSGAFIDPTHRSffNENSMDYFEEYTDLPNWYS 142
                                       56666666666633..4778888888888888888777789999999988887777755 PP

  == domain 2  score: 87.7 bits;  conditional E-value: 5.9e-28
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s+++   N  k   e++esl +  +yp++eii+vD+gStD+++e ++e    +p+v ++++e n G+a++l +g+++
  gi|386002690|ref|YP_005920989.1| 199 SIIVLNWNGLKDTMECIESLENL-TYPNYEIILVDNGSTDGSQEAVKER---FPDVVLVQNEMNLGFAAGLGEGIKH 271
                                       8999999****************.*************************...69*********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiern 129
                                       ++++yi+fl+ D+++d+ wl +l++++  + +   +g++  + ++ + ++  
  gi|386002690|ref|YP_005920989.1| 272 TSSEYIAFLNNDTVVDRRWLDELIRPFLTTKD--EIGATSSTIMSYGDRKEV 321
                                       ****************************9766..555555554444444443 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 !   68.0   0.0   8.7e-22   1.1e-18       1     216 [.     196     409 ..     196     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 8.7e-22
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       p  ++++V ++n  ++  e++esl + +yp++e+++v+++s+++  e ++e   ++pdv  ++v+n++nlg+   + 
  gi|386002690|ref|YP_005920989.1| 196 PK-VSIIVLNWNGLKDTMECIESLENLTYPNYEIILVDNGSTDGSQEAVKE---RFPDV--VLVQNEMNLGF---AA 263
                                       55.9****************************************8887776...****6..999****9995...88 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqff.ltp.kvgavgtpvflln.rstl....vsalgalefaerhlr 147
                                       +l e++++++s+++++++ Dtvv+ + l+ l + f  t+ ++ga     +++  r+ +     s+l+   f+++ ++
  gi|386002690|ref|YP_005920989.1| 264 GLGEGIKHTSSEYIAFLNNDTVVDRRWLDELIRPFlTTKdEIGATSSTIMSYGdRKEVqyggDSRLNI--FGQTRAS 338
                                       99*********************************744436666665555554144444443344444..7888889 PP

                   Glyco_tranf_2_3 148 flaarralgvltlnGsgslirrevlkelegldp..lflltdDyelglrlrragfrtayvpgaavrevfpss 216
                                       + + r  + + t++G+ +++ rev + le +     f  ++ ++l+ rl ++g++  y pg++v++  + +
  gi|386002690|ref|YP_005920989.1| 339 NKVERGIKETGTISGASFMMKREVIDGLEEFLCpeYFAYFEEIDLSWRLVNRGYKLIYSPGSVVYHKGGMT 409
                                       9999999999999****************87765789999**************************97644 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.6   4.7e+03       1       7 [.      29      35 ..      29      43 .. 0.87
   2 !   39.2   0.0   6.4e-13   8.2e-10      48      95 ..      54     102 ..      41     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                                      EEET-TT CS
                   Methyltransf_11  1 LdvGcGt 7 
                                      Ld+GcG+
  gi|386002690|ref|YP_005920989.1| 29 LDIGCGN 35
                                      8*****7 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 6.4e-13
                                       TTEECCC.TSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  48 vvadaek.lpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllv 95 
                                       + ad++k +pf+dn fD +++++vl+h++dp k+l+ei+Rv kp+ +++
  gi|386002690|ref|YP_005920989.1|  54 IIADMSKrFPFKDNIFDEIYCHHVLEHFQDPIKVLEEIWRVAKPDATVY 102
                                       456777648***********************************98876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   3.5e-12   4.4e-09      26     135 ..      28     128 ..       6     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.5e-12
                   Methyltransf_23  26 vLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppell 102
                                        LdiGcG   +  ++   ++ ++ vD+   ++++          +f       +++ fd I++ +vleh++dp ++l
  gi|386002690|ref|YP_005920989.1|  28 KLDIGCGNKKNEGCIGIDQVRLEPVDIIADMSKR---------FPF-------KDNIFDEIYCHHVLEHFQDPIKVL 88 
                                       59*************999*********8777665.........455.......7799******************** PP

                   Methyltransf_23 103 rqiatllkpgGylllseplasl.......kedrllldwly 135
                                         i++  kp++ +++++p + +        +++ + ++ +
  gi|386002690|ref|YP_005920989.1|  89 EEIWRVAKPDATVYITVPYCQSsgafidpTHRSFFNENSM 128
                                       *****************84333566666423333444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.1   1.4e+03       8      14 ..      29      35 ..      23      42 .. 0.86
   2 !   27.6   0.0   1.7e-09   2.1e-06      52     112 ..      43     106 ..      34     144 .. 0.82
   3 ?   -0.7   0.0      0.89   1.1e+03      84     111 ..     203     232 ..     181     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                   Methyltransf_31  8 lDlGCGt 14
                                      lD+GCG+
  gi|386002690|ref|YP_005920989.1| 29 LDIGCGN 35
                                      9*****8 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.7e-09
                   Methyltransf_31  52 gldnveFeqgdiee.lekl..ledekfDlilsnevlnaladpdkileeiervlkpggilliedp 112
                                       g+d v++e  di + ++k   ++d+ fD i ++ vl ++ dp k+leei rv kp+  + i+ p
  gi|386002690|ref|YP_005920989.1|  43 GIDQVRLEPVDIIAdMSKRfpFKDNIFDEIYCHHVLEHFQDPIKVLEEIWRVAKPDATVYITVP 106
                                       6777777777776666666669*********************************998888755 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.89
                   Methyltransf_31  84 l..naladpdkileeiervlkpggillied 111
                                       l  n l+d  +++e++e++  p+ ++++ d
  gi|386002690|ref|YP_005920989.1| 203 LnwNGLKDTMECIESLENLTYPNYEIILVD 232
                                       255778888888888888888888877665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.3   4.2e+03       2       8 ..      29      35 ..      29      39 .. 0.92
   2 !   21.1   0.0     3e-07   0.00038      52      96 ..      55      98 ..      35      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.3
                                      EEET-TT CS
                   Methyltransf_25  2 LdlGcGt 8 
                                      Ld+GcG+
  gi|386002690|ref|YP_005920989.1| 29 LDIGCGN 35
                                      8*****6 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3e-07
                                      ESBC.CGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25 52 qgda.edlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpg 96
                                       +d+ +++pf+d+ fD +++ ++l+h++d    k+l+ei+rv kp+
  gi|386002690|ref|YP_005920989.1| 55 IADMsKRFPFKDNIFDEIYCHHVLEHFQD--PIKVLEEIWRVAKPD 98
                                      35563669************877****95..569**********96 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.6   7.2e+03       1       7 [.      29      35 ..      29      38 .. 0.91
   2 !   19.4   0.0     1e-06    0.0013      50      98 ..      46     100 ..      35     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.6
                   Methyltransf_12  1 LeiGcGt 7 
                                      L+iGcG+
  gi|386002690|ref|YP_005920989.1| 29 LDIGCGN 35
                                      8****95 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1e-06
                   Methyltransf_12  50 nvelealdlldldgg......ssfDlvvasnvlhhlkdirevldnirklLkpgGr 98 
                                       +v+le  d++ + ++      + fD +++++vl+h++d+ +vl++i ++ kp++ 
  gi|386002690|ref|YP_005920989.1|  46 QVRLEPVDIIADMSKrfpfkdNIFDEIYCHHVLEHFQDPIKVLEEIWRVAKPDAT 100
                                       55555555555555566668889*****************************975 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0014      84     151 ..      28     103 ..      12     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHTSS........TEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran  84 mLkvgekklkeegki........nieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        L++g    k+eg i         ++ +   ++++pf+d+ fD +   + l  + D  k+L+e++rv kp  ++++
  gi|386002690|ref|YP_005920989.1|  28 KLDIGCGNKKNEGCIgidqvrlePVDIIADMSKRFPFKDNIFDEIYCHHVLEHFQDPIKVLEEIWRVAKPDATVYI 103
                                       556665556666655455444446778888999*************************************999876 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 !   16.4   0.0     5e-06    0.0063       1     144 [.     276     430 ..     276     471 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaa.elaspevaivqgpvlvm..nvanwleelaalf...faedhgkdilvrealgrvvp 71 
                                       +i++l  Dtv+++  l e+++ +l++ +  i+ + +++m  + ++ ++   +++   f  +   +  v  +++++ +
  gi|386002690|ref|YP_005920989.1| 276 YIAFLNNDTVVDRRWLDELIRpFLTT-KDEIGATSSTIMsyGDRKEVQYGGDSRlniFG-QTRASNKVERGIKETGT 350
                                       79999************999856664.44555566555554888888888888834332.2333456778******* PP

                   Glyco_trans_2_3  72 svGsgaflrrsalqevg..gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeksplt...lraalr...QrkRw 140
                                       + G+ ++  r++++ +    ++   ++  E  d++ rl  +Gy++++ p+s+v+ k+  t   + +++r    r ++
  gi|386002690|ref|YP_005920989.1| 351 ISGASFMMKREVIDGLEefLCP-EYFAYFEEIDLSWRLVNRGYKLIYSPGSVVYHKGGMTsskISDRMRindVRNKY 426
                                       ************9977764444.5789*************************9999888766655555544444444 PP

                   Glyco_trans_2_3 141 ayGc 144
                                       +  +
  gi|386002690|ref|YP_005920989.1| 427 LTFY 430
                                       4443 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 !   14.7   0.0   1.2e-05     0.016      16      94 ..     212     286 ..     184     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                   Glyco_tranf_2_2  16 eerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDa 90 
                                       +e +  l++ +y  ++ e+i+vd+gS++   e v+       lv  ++      + aa    G++++ s+++ Fl+ 
  gi|386002690|ref|YP_005920989.1| 212 MECIesLENLTY--PNYEIILVDNGSTDGSQEAVKERFPDVVLVQ-NE---MNLGFAAGLGEGIKHTSSEYIAFLNN 282
                                       555544444455..9**************9999998776666665.34...47899999*****************9 PP

                   Glyco_tranf_2_2  91 Dcfi 94 
                                       D  +
  gi|386002690|ref|YP_005920989.1| 283 DTVV 286
                                       9865 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       8.4   1.1e+04     148     162 ..      61      75 ..      52      79 .. 0.78
   2 ?   13.0   0.0   4.7e-05      0.06      32      86 ..     250     306 ..     200     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 8.4
                   Glyco_tranf_2_5 148 dvpwredlftgfhfY 162
                                        +p+++++f++ ++ 
  gi|386002690|ref|YP_005920989.1|  61 RFPFKDNIFDEIYCH 75 
                                       469999999999876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.7e-05
                   Glyco_tranf_2_5  32 iiairna..ksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFk.kdkkiG 86 
                                       ++ ++n+     a++  +++++++ +y  +l++D++ + ++++ +l++ F   +++iG
  gi|386002690|ref|YP_005920989.1| 250 VVLVQNEmnLGFAAGLGEGIKHTSSEYIAFLNNDTV-VDRRWLDELIRPFLtTKDEIG 306
                                       5566666556789*********************96.7999******99851445555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.13     151     192 ..      68     107 ..      54     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                              DREV 151 kldlilclnlldrcfdplklledirsalepngrvivalvlPv 192
                                        +d i c  +l+   dp+k+le+i+ + +p++ v ++  +P+
  gi|386002690|ref|YP_005920989.1|  68 IFDEIYCHHVLEHFQDPIKVLEEIWRVAKPDATVYIT--VPY 107
                                       5899**************************9887665..344 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015       0.2      11      51 ..     215     258 ..     208     296 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                   Glyco_tranf_2_4  11 lahhlalgf..drilvydndstDgtrailkel.pevkllhvdks 51 
                                       ++ +++l +   +i+++dn+stDg+ + +ke  p+v l++++ +
  gi|386002690|ref|YP_005920989.1| 215 IESLENLTYpnYEIILVDNGSTDGSQEAVKERfPDVVLVQNEMN 258
                                       4555566553236****************997699999888743 PP

>> DUF4864  Domain of unknown function (DUF4864)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.25      30      82 ..     376     428 ..     368     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                           DUF4864  30 akfgtaerFlemVrqaYpavyrprsvaflkletkeggvvqevlivdsdgkalt 82 
                                       a f++ +   + V+++Y+ +y+p sv ++k  ++  ++  + +i d  +k lt
  gi|386002690|ref|YP_005920989.1| 376 AYFEEIDLSWRLVNRGYKLIYSPGSVVYHKGGMTSSKISDRMRINDVRNKYLT 428
                                       667777788899********************************998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3154.99
//
Query:       gi|386002691|ref|YP_005920990.1|  [L=343]
Description: LPS glycosyltransferase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-18   66.6   0.0    4.6e-18   65.9   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
      6e-16   58.4   0.0    2.4e-15   56.5   0.0    2.0  2  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   5.1e-22   4.6e-18       3     131 ..     176     301 ..     174     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 5.1e-22
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleerveftGfvedlaellaaadvfv 77 
                                       +++ vG+    +kg+d+ll+a++++r++  d +l+i+G+g  pe+ + ++    ++v++ G+v+dl +++++a++fv
  gi|386002691|ref|YP_005920990.1| 176 IVMSVGSG--TYKGMDILLDAFKKVRNEvpDSELYIIGGG-HPERWN-ET----KGVHVEGHVSDLIPYFNSASLFV 244
                                       67888887..56**************99745*******88.664665.33....69********************* PP

                                       E--..---SHHHHHHHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHHHHHHH CS
                   Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevv...gengllvppgdpealaeailrL 131
                                         s   +f+++ lE++ ag+p+ +td  g++evv   g+    v   d+ ++ae ilr 
  gi|386002691|ref|YP_005920990.1| 245 QSSraDTFPVSSLESLRAGVPTMVTDKTGTKEVVselGT--EFVRRVDEGDIAEGILRY 301
                                       ***7669*******************99******74433..345556899999999875 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.53   4.8e+03     127     144 ..      43      60 ..      39      61 .. 0.83
   2 !   56.5   0.0   2.7e-19   2.4e-15      12     170 ..     171     317 ..     165     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.53
                                       HCHHCHTTTSEEEE-TT- CS
                   Glycos_transf_1 127 paevvkdgetGllvkpnn 144
                                       +++++k  ++G+l++ ++
  gi|386002691|ref|YP_005920990.1|  43 YPKMIKIFVNGALIPDYD 60 
                                       788999999****99886 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 2.7e-19
                                       TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHH CS
                   Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredlee 88 
                                       + +k+i+ svg  ++ Kg d l++af++++  + p+  l i+G+g+  +   ++    +  + v++ g+vs  dl+ 
  gi|386002691|ref|YP_005920990.1| 171 KLQKNIVMSVGSGTY-KGMDILLDAFKKVRN-EVPDSELYIIGGGHP-E---RW----NETKGVHVEGHVS--DLIP 235
                                       5689999****9888.*************75.6**********5544.2...33....33467899*****..**** PP

                                       HHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH.HHHHH CS
                   Glycos_transf_1  89 llknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede.elrer 164
                                       ++++a++fv++s+ + f+++ lE++ ag+p+ +++  g +evv +  t  +v  ++  ++ae+i ++ + e e+r +
  gi|386002691|ref|YP_005920990.1| 236 YFNSASLFVQSSRADTFPVSSLESLRAGVPTMVTDKTGTKEVVSELGT-EFVRRVDEGDIAEGILRYFDLEeEKRLA 311
                                       ***********************************************8.6677788***********9999788888 PP

                                       HHHHHH CS
                   Glycos_transf_1 165 lgenar 170
                                       l+++a+
  gi|386002691|ref|YP_005920990.1| 312 LSNKAK 317
                                       887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2454.75
//
Query:       gi|386002692|ref|YP_005920991.1|  [L=313]
Description: Glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-32  112.8   0.1    3.1e-32  111.7   0.0    1.6  2  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-23   83.8   0.0    2.3e-23   83.3   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.9e-17   63.0   0.1    2.2e-08   33.9   0.0    2.0  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
      0.009   15.9   0.0      0.014   15.3   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
      0.061   13.2   0.0       0.18   11.7   0.0    1.9  1  DUF5348          Domain of unknown function (DUF5348)
       0.11   11.3   0.0       0.18   10.5   0.0    1.3  1  GNT-I            GNT-I family


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.0     1e-35   3.1e-32       1     120 [.      11     128 ..      11     167 .. 0.90
   2 ?   -2.2   0.0       1.1   3.2e+03     102     148 ..     203     252 ..     192     269 .. 0.45

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 1e-35
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       sv+iptyN+++++ ++++s+l+q  y+dfe+ivvD +S Det+e++ ++  +d r+r++  + ++G+++a+n g+r 
  gi|386002692|ref|YP_005920991.1|  11 SVIIPTYNRPSLVGRAIKSVLSQ-SYQDFELIVVDGSSDDETKEVVMDF--GDRRIRYVSETGKRGLSNARNMGIRS 84 
                                       8**********************.*************************..79************************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH..TTCEEEEEEEEEE CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekd.gadvvlgqrprif 120
                                       + gdyi++lD+Dde+ p +le  v+ l++  ++ +v+++ +r++
  gi|386002692|ref|YP_005920991.1|  85 SMGDYIALLDDDDEWLPCKLEMQVDLLDRLpEEYGVVYSGYRTE 128
                                       *****************************834445555555554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHH.TTCEEEEEEEEEECCCCCCCHC-SS...EEEECCHCCCCHCCCC CS
                   Glycos_transf_2 102 ealekdgadvvlgqrprifgetdeiernkrv...generlyfkerkrslk 148
                                       + ++ +g+++ + q ++i g ++  +++++    ++++   ++++ + l+
  gi|386002692|ref|YP_005920991.1| 203 AVYHIHGDQMTFDQSRFIVGVEGVLKKHHEDfsrNRKSLAEQYRYLGVLY 252
                                       44444444444444444444444333333333444444444444444444 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 !   83.3   0.0   7.8e-27   2.3e-23       2     213 ..       8     208 ..       7     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 7.8e-27
                   Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++++v++pt+n+++ +g+ + s+l+q+y ++e++vv+  sd+et ev++     ++d r+r+v    + g++g s+a
  gi|386002692|ref|YP_005920991.1|   8 PHVSVIIPTYNRPSLVGRAIKSVLSQSYQDFELIVVDGSSDDETKEVVMD----FGDRRIRYVS---ETGKRGLSNA 77 
                                       47**********************************************96....9******993...357899**** PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarr 153
                                        n ++r   +d+++l+DdD+ + P+ l++++ ++  l +++g+v+   +++++ + v  ++  e ++ ++r+ +   
  gi|386002692|ref|YP_005920991.1|  78 RNMGIRSSMGDYIALLDDDDEWLPCKLEMQVDLLdrLPEEYGVVYSGYRTERDGNIVGEYYPAERGDVYARM-LKGS 153
                                       **********************************98888*******************99998866666633.3334 PP

                   Glyco_tranf_2_3 154 algvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaa.vrevf 213
                                        l+v+     +  i r++++  + +d+     +D++++ rl + +++  yvp+ + v++ +
  gi|386002692|ref|YP_005920991.1| 154 ILSVP-----TIIISRSCFEVVGYFDEELPSCEDWDMWIRLAK-EYKFEYVPEILaVYHIH 208
                                       55555.....59***************77888********976.68999999876566655 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 !   33.9   0.0   7.3e-12   2.2e-08       1     106 [.      11     111 ..      11     133 .. 0.85
   2 !   27.4   0.1   7.3e-10   2.2e-06     167     223 ..     159     213 ..     141     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 7.3e-12
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                       sv+ip ++      +   ++   ++  +++elivvd+ S +++ e+v  + d + +  ++++     +l+ arN G+
  gi|386002692|ref|YP_005920991.1|  11 SVIIPTYNRPSL--VGRAIKSVLSQSYQDFELIVVDGSSDDETKEVVMDFGDRRIRY-VSETG--KRGLSNARNMGI 82 
                                       789999887766..777775555555579*********************9988764.45653..5688889***** PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilkli 106
                                         + +d++  lD D+ + + k+e ++ l+
  gi|386002692|ref|YP_005920991.1|  83 RSSMGDYIALLDDDDEWLPCKLEMQVDLL 111
                                       ***********************999875 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 7.3e-10
                   Glyco_tranf_2_2 167 silinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykaraksls 223
                                       +i+i r  f  vG +DE++  ++ ED+d+ +Rlak +k+  ++     y+ +  +++
  gi|386002692|ref|YP_005920991.1| 159 TIIISRSCFEVVGYFDEEL--PSCEDWDMWIRLAKEYKFEYVPEILAVYHIHGDQMT 213
                                       699****************..*****************9877777778888888887 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.6e-06     0.014       1     124 [.      89     206 ..      89     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelas.p.evaivqgpvlvm..nvanwleelaalffaedhgkdilvrealgrvvpsv 73 
                                       +i+llD+D+   p  l+  +++l++ p e+++v   ++++  + +n++ e + +++ +        r+  g+ ++++
  gi|386002692|ref|YP_005920991.1|  89 YIALLDDDDEWLPCKLEMQVDLLDRlPeEYGVV--YSGYRteRDGNIVGEYYPAERGD-----VYARMLKGSILSVP 158
                                       799999999999999999999999877355544..44443348899999999999954.....44566667777777 PP

                   Glyco_trans_2_3  74 Gsgaflrrsalqevggwdgdessvs.EDfdmglrlqrkGyrvrfvpes.lvke 124
                                       +  ++++rs ++ vg++d  e+  s ED+dm++rl+++ y++ +vpe  +v+ 
  gi|386002692|ref|YP_005920991.1| 159 T--IIISRSCFEVVGYFD--EELPScEDWDMWIRLAKE-YKFEYVPEIlAVYH 206
                                       6..78999**********..555544*********987.******99866655 PP

>> DUF5348  Domain of unknown function (DUF5348)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.1e-05      0.18      26      46 ..      86     107 ..      62     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                           DUF5348  26 cGeslevlved.eWvptriEmd 46 
                                        G+ + +l +d eW+p+++Em 
  gi|386002692|ref|YP_005920991.1|  86 MGDYIALLDDDdEWLPCKLEMQ 107
                                       699999999999*********7 PP

>> GNT-I  GNT-I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.2e-05      0.18      93     153 ..       8      67 ..       2      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.2e-05
                             GNT-I  93 dviavlvlacsradavrrtvekllkyrpsaekfPlivsqdcsneevkkevlsygdk.vtyik 153
                                       + ++v++ + +r + v r+++++l    s + f liv   +s++e+k+ v+ +gd+ + y+ 
  gi|386002692|ref|YP_005920991.1|   8 PHVSVIIPTYNRPSLVGRAIKSVLS--QSYQDFELIVVDGSSDDETKEVVMDFGDRrIRYVS 67 
                                       5688999999*************97..57789**********************95367765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1879.65
//
Query:       gi|386002693|ref|YP_005920992.1|  [L=317]
Description: Glycosyl transferase family 2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-27   94.8   0.0    1.3e-26   93.4   0.0    1.7  2  Glycos_transf_2  Glycosyl transferase family 2
    1.5e-15   57.7   0.0    2.6e-15   56.9   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-13   50.8   0.0    4.2e-13   49.4   0.0    1.6  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00094   18.7   0.0     0.0016   17.9   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.056   13.4   0.0    1.7  1  Glyco_trans_2_3  Glycosyl transferase family group 2
      0.028   14.5   0.0      0.076   13.1   0.0    1.7  2  Peptidase_C42    Beet yellows virus-type papain-like endopept
       0.04   13.6   0.0       0.08   12.6   0.0    1.4  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase


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 !   93.4   0.0     5e-30   1.3e-26       1     133 [.       7     138 ..       7     175 .. 0.86
   2 ?   -1.8   0.0      0.94   2.4e+03      92     104 ..     243     255 ..     242     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 5e-30
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svvip yN  + + ++l+s+l+q + +dfe++vv  gS De +++++++   d r+ ++ +e ++G ++a+n+++++
  gi|386002693|ref|YP_005920992.1|   7 SVVIPLYNKGPHIGRALRSVLNQ-TFQDFEVVVVEGGSADEGPAVVRSF--DDSRISLFYQE-GTGVSTARNQAVER 79 
                                       8**********************.*************************..58*********.66************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS...E CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv...g 133
                                       ++ d+++flDaDde+ p++le +++   k+++++ +++ +r + +++e + ++     +
  gi|386002693|ref|YP_005920992.1|  80 SKADLVAFLDADDEWMPEHLETILRLRGKHPEAGMYATAYRVQAMDGEVRSAEYReipE 138
                                       **********************************9999999999998888776444451 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.94
                                       E-TTHHHHHHHHH CS
                   Glycos_transf_2  92 pdpdwleklveal 104
                                       ++pd le+l+e++
  gi|386002693|ref|YP_005920992.1| 243 VPPDLLEPLIEYI 255
                                       689********98 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 !   56.9   0.0     1e-18   2.6e-15       1     190 [.       4     189 ..       4     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1e-18
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       p  ++v++p +n  + +g+ l+s+l+q+  ++evvvv  +s +e  +v++     ++d r+++  + +  g tg s+
  gi|386002693|ref|YP_005920992.1|   4 PE-ISVVIPLYNKGPHIGRALRSVLNQTFQDFEVVVVEGGSADEGPAVVRS----FDDSRISLFYQ-E--G-TGVST 71 
                                       55.9*******************************************9996....9******7533.3..5.57888 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvflln.rstlvsalgal..efaerhl.rfl 149
                                       a n+a+++ k dlv+++D+D+ ++P+ l+ +l++  ++p++g+  t  +++  +  + sa ++   e+  + l  + 
  gi|386002693|ref|YP_005920992.1|  72 ARNQAVERSKADLVAFLDADDEWMPEHLETILRLRgKHPEAGMYATAYRVQAmDGEVRSAEYREipEPPWEGLmPNY 148
                                       99************************************************974666666554422233323332444 PP

                   Glyco_tranf_2_3 150 aarralgvltlnGsgslirrevlkelegldplfllt.dDyel 190
                                       + + alg  ++ +sg++++ ++++e +g+   ++ + +D++l
  gi|386002693|ref|YP_005920992.1| 149 FKSAALGENPVITSGMAVPKSIFEEVGGFPI-GYWWgEDADL 189
                                       4457888899999*************99999.6666699876 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 !   49.4   0.0   1.6e-16   4.2e-13       1     204 [.       7     198 ..       7     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.6e-16
                   Glyco_tranf_2_2   1 svviplraseerhyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarN 74 
                                       svvipl+++    +i   +   l+++++   ++e++vv++gS+++   +v+s+ d +   ++++      + + arN
  gi|386002693|ref|YP_005920992.1|   7 SVVIPLYNKGP--HIGRALrsvLNQTFQ---DFEVVVVEGGSADEGPAVVRSFDDSRISLFYQEG----TGVSTARN 74 
                                       89*****9654..477766444888888...9****************************87776....689999** PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledll 151
                                       + ++++++dlv FlDaD+ + ++++e il+      lr     a +++  + +++    ++  e+  +     e l+
  gi|386002693|ref|YP_005920992.1|  75 QAVERSKADLVAFLDADDEWMPEHLETILR------LRGKHPEAGMYATAYRVQAMDGEVRSAEYREIPEPPWEGLM 145
                                       ****************************99......55444444456666666666666777777777777776777 PP

                   Glyco_tranf_2_2 152 aakstlvk..ffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaik 204
                                         +   +        +s + + +  f evGG+   +     ED dl+ ++a++++
  gi|386002693|ref|YP_005920992.1| 146 PNYFKSAAlgENPVITSGMAVPKSIFEEVGGFPIGY--WWGEDADLFGKIALKYP 198
                                       644333221122223466777888888888887777..66788888888887776 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.4e-07    0.0016      23     130 ..      74     187 ..      70     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.4e-07
                   Glyco_transf_21  23 lqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaaleaafl......ntlagvlq 92 
                                       +qa+e+ k+dl+ ++D+d    p+ Le++l+   + p++g+   ++++ + +g  +  e   +      + ++++++
  gi|386002693|ref|YP_005920992.1|  74 NQAVERSKADLVAFLDADDEWMPEHLETILRLRGKhPEAGMYATAYRVQAMDGEVRSAEYREIpeppweGLMPNYFK 150
                                       58999*************************976555***********999999888888888776777667799999 PP

                   Glyco_transf_21  93 aklsglgfavGksmalrreaLeaiGGfealadeLAeDy 130
                                       +++ g + ++ + ma+ ++++e++GGf +++++  eD+
  gi|386002693|ref|YP_005920992.1| 151 SAALGENPVITSGMAVPKSIFEEVGGF-PIGYWWGEDA 187
                                       97788999999***************9.4588888886 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 ?   13.4   0.0   2.2e-05     0.056       2     108 ..      85     194 ..      84     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaela.spevaivqgpvlvmnvanwleelaalf.....faedhgkdilvrealgrvvps 72 
                                       +++lDaD+   p+ l+ i+++   +pe++++ + + v++    ++     +     +    +   + ++alg+  p+
  gi|386002693|ref|YP_005920992.1|  85 VAFLDADDEWMPEHLETILRLRGkHPEAGMYATAYRVQAMDGEVRSAEYREipeppWE-GLMPNYFKSAALGE-NPV 159
                                       789******9999*******99978********9888633333334444441123342.23333333346666.489 PP

                   Glyco_trans_2_3  73 vGsgaflrrsalqevggwdgdessvsEDfdmglrlq 108
                                        +sg++++ s ++evgg++      +ED d+  +++
  gi|386002693|ref|YP_005920992.1| 160 ITSGMAVPKSIFEEVGGFP-IGYWWGEDADLFGKIA 194
                                       9*****************9.7799999999866665 PP

>> Peptidase_C42  Beet yellows virus-type papain-like endopeptidase C42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.1   1.1e+04      30      42 ..     111     123 ..     105     124 .. 0.75
   2 ?   13.1   0.0     3e-05     0.076      47      74 ..     189     216 ..     171     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.1
                     Peptidase_C42  30 alGafPtvaklka 42 
                                       + G++ t+ +++a
  gi|386002693|ref|YP_005920992.1| 111 EAGMYATAYRVQA 123
                                       5689999888876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3e-05
                     Peptidase_C42  47 eyGkealklglrGaytsrsvfHCdydss 74 
                                        +Gk alk+++  +++++ ++HCd  + 
  gi|386002693|ref|YP_005920992.1| 189 LFGKIALKYPVAFSWVAGVIYHCDASNR 216
                                       79*********************98765 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.1e-05      0.08      24      57 ..     164     195 ..     152     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                   Glyco_transf_7C  24 lalrkedfekiNGfsntfwgWGgEDdelyaRlak 57 
                                       +a+ k+ fe+++Gf+  +w WG ED +l+ ++a 
  gi|386002693|ref|YP_005920992.1| 164 MAVPKSIFEEVGGFPIGYW-WG-EDADLFGKIAL 195
                                       78999*************9.75.9****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1928.55
//
Query:       gi|386002694|ref|YP_005920993.1|  [L=427]
Description: Polysaccharide pyruvyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-38  132.3   0.0    5.1e-38  131.6   0.0    1.3  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase


Domain annotation for each model (and alignments):
>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.6   0.0   2.9e-42   5.1e-38       1     285 [.      28     357 ..      28     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 2.9e-42
                                       -HHHHHHHHHHHHHHHHTT-EEEEEESSTTT--HHHHHHHHHTS-GGGEE........................... CS
                    PS_pyruv_trans   1 NyGDelilealvklLrelgpdaeiivltpdpsetkkllkvktpilkklskvllkrlrkkdi................ 61 
                                       N G e+i+ ++vk+Lre++  + +i ++  +s+ +++      + + + +          +                
  gi|386002694|ref|YP_005920993.1|  28 NRGCEAIVRGTVKILREHFKGPRFICISRFSSDEQFNRQQTGERDEAITH----------Lqtrgrmsreqalrnfw 94 
                                       89**************************5555555554444333333332..........02223334444566667 PP

                                       ...................................EEE--E....EEEETT-HHH.HHHHHHHHHHS-SSEEEE-SE CS
                    PS_pyruv_trans  62 ..............................ddaddviivGgdgtlgndgdlsrlp.dalrllflakkagkpviilgq 107
                                                                     dda+ v+ vGg     n+  ++  p  + +l+ +a  +++p++++g+
  gi|386002694|ref|YP_005920993.1|  95 rpytwsyvhkryfrpemlkyleyqkmiphlDDAAAVLSVGG----DNYSLDYGVPtLFTDLDDIAIEKRRPIVLWGA 167
                                       77777777777777888888*********************....8888888899999******************* PP

                                       EE...-S-HHHHHHHHHHHHHTTEEEESSHHHHH.HHHHHHTT-EEE---GGGGG---HHHHHHS-.........-- CS
                    PS_pyruv_trans 108 giGp.flnealrkllkkilakadlisvRdelSaelleslglkrnveltpDpaflleqlapseilet.........dk 174
                                       ++Gp  + ++++ ++++ l+ ++ i++R+  + ++l+  g+ +nv+ + Dpaf +++ +p++i+++         ++
  gi|386002694|ref|YP_005920993.1| 168 SVGPfDKIPEYEGYMARHLREVTGIFARESVTIDYLRGIGVVENVYPVSDPAFMMDPEKPAGIEDEisieedsigIN 244
                                       *****************************************99*************************999998867 PP

                                       ----------SS--EE---SSS---HH.................................HH-TTS-HHHHHHHHHH CS
                    PS_pyruv_trans 175 rkylrvakssekdledleellakvydllle.kgarllllpivkkdglelddlyllllra.aakkekvtildrfaspe 249
                                          l +     +dl+ + el+a ++  ++   g+r++ +p+v ++++++ + + +   +  + +ek+t++++ +s++
  gi|386002694|ref|YP_005920993.1| 245 LSPLMANYVTGGDLDRWTELAASIVAGVAArTGMRVYMIPHVTVPDSNDYEFMSRAVARiRDGREKITLVPPRYSAA 321
                                       7777777777789999************************************************************* PP

                                       HHHHHHHTSSEEEE--HHHHHHHHHHT--EEEE--S CS
                    PS_pyruv_trans 250 ellsliaradfvitsRlHglifalsfgvPvigisyd 285
                                       e +++i+++ ++ + R H++++als+gvP++ ++y+
  gi|386002694|ref|YP_005920993.1| 322 ETKWIIGKMAVFAGARTHATVAALSSGVPTLSFAYS 357
                                       **********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2707.62
//
Query:       gi|386002695|ref|YP_005920994.1|  [L=463]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-27   96.5   0.0    2.1e-27   95.9   0.0    1.2  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.3e-15   57.2   0.0    3.2e-15   56.0   0.0    1.7  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    4.6e-09   36.3   4.5    4.6e-09   36.3   4.5    2.3  2  Fer4_21      4Fe-4S dicluster domain
    1.5e-07   30.9   2.3    1.5e-07   30.9   2.3    3.4  4  Fer4         4Fe-4S binding domain
    1.9e-07   30.8  15.0    4.4e-05   23.4   1.6    3.3  3  Fer4_6       4Fe-4S binding domain
    2.3e-07   31.3   9.1    3.5e-07   30.7   6.2    2.6  2  Fer4_7       4Fe-4S dicluster domain
    8.2e-05   22.7   6.3    8.2e-05   22.7   6.3    2.7  2  Fer4_9       4Fe-4S dicluster domain
    0.00021   21.7   3.6       0.36   11.3   0.6    3.2  3  Fer4_8       4Fe-4S dicluster domain
    0.00044   20.3  15.1     0.0012   18.9   9.6    3.5  4  Fer4_10      4Fe-4S dicluster domain
     0.0021   18.8   7.6     0.0031   18.2   1.3    2.9  2  Fer4_15      4Fe-4S single cluster domain
     0.0034   18.3  13.1      0.041   14.8   2.2    3.1  3  Fer4_16      4Fe-4S double cluster binding domain
     0.0072   16.4   1.8     0.0072   16.4   1.8    3.5  4  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   16.4   1.5       0.01   16.4   1.5    2.8  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
      0.031   14.8   0.5      0.031   14.8   0.5    3.3  2  Fer4_4       4Fe-4S binding domain
      0.053   14.1  13.6       0.23   12.0   2.2    3.3  4  Fer4_17      4Fe-4S dicluster domain
       0.11   13.4   0.5       0.11   13.4   0.5    2.7  2  Fer4_22      4Fe-4S dicluster domain
        2.6    7.6   5.9         11    5.6   0.5    2.7  2  DUF3343      Protein of unknown function (DUF3343)
        7.5    7.7  28.6        0.3   12.1   4.0    3.4  2  Fer4_3       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   2.1e-30   2.1e-27       3     147 ..     178     339 ..     177     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 2.1e-30
                       FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk..kklkekilltiglfCggnfspealrklleelgvdpedvkklefr.........gkg 68 
                                       ++av+G+PC i+a+r +qk  +kl  ++++t+gl+Cg+ +s+ +++ ++   g+   +vk++++r         +  
  gi|386002695|ref|YP_005920994.1| 178 RYAVTGLPCYIKAIRLAQKkdPKLSARVVVTVGLVCGQLKSRPFTEYIASLAGLV-GEVKGVRYRgksqeqpatN-- 251
                                       89*******************************************9999999976.59*******6554443322.. PP

                       FrhB_FdhB_C  69 kfrvelkd...........ekeislk........elee.....firpsCkvCkdktaelADisvGdvwgpekkgddd 121
                                                                k        e        f++++C++C+d +ae+AD++++d+w+p+++ +d 
  gi|386002695|ref|YP_005920994.1| 252 -------YhyaftstagdeR-----KifwndgiaE--AwtnrwFTPRACNYCDDVFAECADVTFMDAWLPDYS-KDY 313
                                       .......2223233333331.....1223344441..144566******************************.6** PP

                       FrhB_FdhB_C 122 egvstvlvrtekgeellekaveagel 147
                                       +g+++v+vr+  +e+l+++ v +g l
  gi|386002695|ref|YP_005920994.1| 314 RGTNLVVVRSPLIEDLIRRGVRDGGL 339
                                       *****************999888765 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   3.2e-18   3.2e-15       4      77 ..      97     169 ..      94     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 3.2e-18
                       FrhB_FdhB_N   4 ArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwr.pkpviattkeellaaaGskYtlspnlklL 77 
                                       +++ ++  r  ++sGG++t+ll++lL egi+d v++vap+ dp r +   +  ++  ++a aGs Y++++++ ++
  gi|386002695|ref|YP_005920994.1|  97 GHADEH--RSAGASGGMATWLLERLLAEGIVDHVVCVAPTGDPERlFSFSVFDDPPAVRAGAGSAYCPVEMSGAI 169
                                       555555..********************************999999************************99877 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   4.5   4.7e-12   4.6e-09       2      54 ..       9      62 ..       8      65 .. 0.85
   2 ?   -2.3   0.3       5.1   5.1e+03       8      18 ..     286     296 ..     282     302 .. 0.56

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.7e-12
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCv.GCnlCssvCPve 54
                                      ++d++ CigCg+C+  C++++ +       ++ ++  + C+ GC lC++vCP  
  gi|386002695|ref|YP_005920994.1|  9 VVDHELCIGCGLCAALCPEEALEMTWNRYGEYNPLEIEPCTrGCGLCLKVCPFA 62
                                      589***************977776666666777888899988**********76 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                           Fer4_21   8 CigCgkCliaC 18 
                                       C  C   +  C
  gi|386002695|ref|YP_005920994.1| 286 CNYCDDVFAEC 296
                                       44444444445 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   2.3   1.5e-10   1.5e-07       2      24 .]       9      31 ..       8      31 .. 0.94
   2 !   12.5   1.5   9.6e-05     0.096      10      20 ..      51      61 ..      50      62 .. 0.94
   3 ?   -3.3   0.1        10   9.9e+03      17      21 ..     160     164 ..     159     164 .. 0.77
   4 ?   -2.8   0.1       6.7   6.7e+03       7      11 ..     285     289 ..     283     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.5e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+d e+CigCG+C+  CP +A++
  gi|386002695|ref|YP_005920994.1|  9 VVDHELCIGCGLCAALCPEEALE 31
                                      79*******************85 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.6e-05
                                      S-THHHHHSTT CS
                              Fer4 10 gCGaCvevCPv 20
                                      gCG+C +vCP+
  gi|386002695|ref|YP_005920994.1| 51 GCGLCLKVCPF 61
                                      9*********7 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 10
                                       HSTTT CS
                              Fer4  17 vCPvg 21 
                                        CPv+
  gi|386002695|ref|YP_005920994.1| 160 YCPVE 164
                                       6**85 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 6.7
                                       TSSS- CS
                              Fer4   7 kCigC 11 
                                        C +C
  gi|386002695|ref|YP_005920994.1| 285 ACNYC 289
                                       46666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.6   4.4e-08   4.4e-05       3      24 .]       9      30 ..       9      30 .. 0.94
   2 !   14.4   2.2     3e-05      0.03       7      21 ..      46      61 ..      45      67 .. 0.90
   3 ?   -2.2   0.1       5.4   5.4e+03      17      21 ..     382     386 ..     382     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.4e-08
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                      ++d ++CigCg C++ CPe a+
  gi|386002695|ref|YP_005920994.1|  9 VVDHELCIGCGLCAALCPEEAL 30
                                      699****************996 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3e-05
                            Fer4_6  7 dkCi.gCgdCvrvCPe 21
                                      ++C+ gCg C +vCP+
  gi|386002695|ref|YP_005920994.1| 46 EPCTrGCGLCLKVCPF 61
                                      689989*********7 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.4
                            Fer4_6  17 rvCPe 21 
                                       rvCP+
  gi|386002695|ref|YP_005920994.1| 382 RVCPA 386
                                       79**7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   6.2   3.5e-10   3.5e-07       2      50 ..      15      61 ..      14      62 .. 0.83
   2 ?   -0.3   0.0       1.7   1.7e+03      35      44 ..     283     292 ..     249     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.5e-10
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekCl.gCgaCvavCPt 50
                                      CigCg C+a Cp +a+e++        e+  ++ e C+ gCg C +vCP+
  gi|386002695|ref|YP_005920994.1| 15 CIGCGLCAALCPEEALEMTWNR---YGEYNPLEIEPCTrGCGLCLKVCPF 61
                                      ******************8762...2244457899**758*********7 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                            Fer4_7  35 pekClgCgaC 44 
                                       p+ C +C+  
  gi|386002695|ref|YP_005920994.1| 283 PRACNYCDDV 292
                                       5667777653 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   6.3   8.3e-08   8.2e-05       2      47 ..      15      60 ..      14      64 .. 0.81
   2 ?   -0.7   0.0       1.6   1.6e+03      34      46 ..     284     296 ..     261     308 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.3e-08
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCp 47
                                      C+gCg C + Cp ++ ++ ++++   +  +  e C  gCg C+++Cp
  gi|386002695|ref|YP_005920994.1| 15 CIGCGLCAALCPEEALEMTWNRYGEYNPLE-IEPCtRGCGLCLKVCP 60
                                      ***************988887776555443.358*556********9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                            Fer4_9  34 eaCigCgaCveaC 46 
                                        aC  C + ++ C
  gi|386002695|ref|YP_005920994.1| 284 RACNYCDDVFAEC 296
                                       4566665533333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   0.00037      0.36       4      16 ..      14      26 ..      11      42 .. 0.77
   2 !    9.2   0.0    0.0017       1.7       5      21 ..      48      65 ..      44     113 .. 0.83
   3 ?   -0.9   0.0       2.3   2.3e+03       4      29 ..     285     314 ..     283     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                            Fer4_8  4 kCieCgaCqsaCp 16
                                       Ci+Cg+C + Cp
  gi|386002695|ref|YP_005920994.1| 14 LCIGCGLCAALCP 26
                                      5999999999998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
                            Fer4_8  5 Ci.eCgaCqsaCpvlrrt 21
                                      C+ +Cg+C + Cp++ ++
  gi|386002695|ref|YP_005920994.1| 48 CTrGCGLCLKVCPFADHE 65
                                      6526*********88765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                            Fer4_8   4 kCieCgaCqsaCp...vlrrtk.khlldar 29 
                                       +C+ C   +++C    ++ ++  + ++d r
  gi|386002695|ref|YP_005920994.1| 285 ACNYCDDVFAECAdvtFMDAWLpDYSKDYR 314
                                       566666666888433355555544444444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   9.6   1.2e-06    0.0012       3      56 .]       9      60 ..       7      60 .. 0.86
   2 !   12.8   0.8   9.8e-05     0.098       8      33 ..      47      70 ..      42      81 .. 0.70
   3 ?   -1.9   0.2       3.7   3.7e+03      43      50 ..     284     291 ..     273     299 .. 0.59
   4 ?   -1.7   0.0       3.2   3.2e+03      17      23 ..     382     388 ..     381     406 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.cgaCveaCP 56
                                      v+d + Ci+Cg C + CP    +      + ++e +   +e Ct+ cg C ++CP
  gi|386002695|ref|YP_005920994.1|  9 VVDHELCIGCGLCAALCPE---EALEMTWNRYGEYNPLEIEPCTRgCGLCLKVCP 60
                                      67999**************...666667777777777799****88********9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.8e-05
                           Fer4_10  8 tCi.rCgkCvkaCPadltsvgakgeas 33
                                       C+ +Cg C k+CP+   ++  ++e +
  gi|386002695|ref|YP_005920994.1| 47 PCTrGCGLCLKVCPF---ADHEEDEGT 70
                                      68769*********9...444444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.7
                           Fer4_10  43 ekCtgcga 50 
                                        +C  c  
  gi|386002695|ref|YP_005920994.1| 284 RACNYCDD 291
                                       55555542 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.2
                           Fer4_10  17 kaCPadl 23 
                                       ++CPa  
  gi|386002695|ref|YP_005920994.1| 382 RVCPARE 388
                                       68**933 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.3   3.1e-06    0.0031       2      20 ..       9      27 ..       9      31 .. 0.94
   2 ?    2.8   0.6       0.2     2e+02      10      26 ..      51      65 ..      44      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      vvD+++CigcglC+a++pe
  gi|386002695|ref|YP_005920994.1|  9 VVDHELCIGCGLCAALCPE 27
                                      69***************97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                           Fer4_15 10 gcglCvaeapevfelde 26
                                      gcglC++++p  f  +e
  gi|386002695|ref|YP_005920994.1| 51 GCGLCLKVCP--FADHE 65
                                      9********9..44333 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.2   4.1e-05     0.041       2      20 ..      15      33 ..      14      48 .. 0.84
   2 !    8.8   2.0    0.0032       3.1      54      66 ..      48      61 ..      39      62 .. 0.73
   3 ?   -2.3   0.1       9.2   9.1e+03      55      63 ..     284     292 ..     257     297 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg Ca  CP++a++++
  gi|386002695|ref|YP_005920994.1| 15 CIGCGLCAALCPEEALEMT 33
                                      ****************987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                           Fer4_16 54 i.tgCdiCqdvCPa 66
                                      +  gC+ C +vCP+
  gi|386002695|ref|YP_005920994.1| 48 CtRGCGLCLKVCPF 61
                                      43789999999987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.2
                           Fer4_16  55 tgCdiCqdv 63 
                                         C+ C dv
  gi|386002695|ref|YP_005920994.1| 284 RACNYCDDV 292
                                       456666654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.8   7.2e-06    0.0072       4      22 .]       9      27 ..       8      27 .. 0.89
   2 !   13.4   2.0   6.3e-05     0.062       8      21 ..      46      60 ..      40      61 .. 0.86
   3 ?   -1.1   0.5       2.6   2.6e+03       5      13 ..     281     289 ..     279     299 .. 0.64
   4 ?   -2.7   0.2       8.2   8.2e+03      19      22 .]     383     386 ..     382     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.2e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      vvd + CigCg C   CP+
  gi|386002695|ref|YP_005920994.1|  9 VVDHELCIGCGLCAALCPE 27
                                      57899********999**5 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.3e-05
                            Fer4_2  8 drCi.gCgaCvsaCP 21
                                      + C+ gCg C+++CP
  gi|386002695|ref|YP_005920994.1| 46 EPCTrGCGLCLKVCP 60
                                      569868********* PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.6
                            Fer4_2   5 vdtdrCigC 13 
                                       + +++C+ C
  gi|386002695|ref|YP_005920994.1| 281 FTPRACNYC 289
                                       556777777 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 8.2
                            Fer4_2  19 aCPa 22 
                                       +CPa
  gi|386002695|ref|YP_005920994.1| 383 VCPA 386
                                       8**8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4   1.5     1e-05      0.01       1      18 [.      10      27 ..      10      28 .. 0.96
   2 ?    2.4   0.7      0.24   2.4e+02       8      18 ..      51      61 ..      45      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD + Ci+cg+C++l+P+
  gi|386002695|ref|YP_005920994.1| 10 VDHELCIGCGLCAALCPE 27
                                      89***************7 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                           Fer4_13  8 acgaCvelaPd 18
                                      +cg+C +++P 
  gi|386002695|ref|YP_005920994.1| 51 GCGLCLKVCPF 61
                                      7*********5 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   3.1e-05     0.031       2      16 ..      13      27 ..      12      37 .. 0.91
   2 ?    8.4   1.9    0.0035       3.5       3      16 ..      47      61 ..      45      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e CigCg C a CP 
  gi|386002695|ref|YP_005920994.1| 13 ELCIGCGLCAALCPE 27
                                      67************4 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0035
                            Fer4_4  3 rCi.gCgsCvaaCPq 16
                                       C+ gCg C  +CP+
  gi|386002695|ref|YP_005920994.1| 47 PCTrGCGLCLKVCPF 61
                                      5877**********6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   0.00023      0.23      44      59 ..      13      28 ..       3      30 .. 0.86
   2 ?    5.0   9.9     0.036        36       2      57 ..      15      60 ..      14      62 .. 0.58
   3 ?    8.1   0.7     0.004         4       3      18 ..      50      65 ..      47      80 .. 0.79
   4 ?   -1.4   0.1       3.5   3.5e+03       4      12 ..     285     296 ..     284     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      +lCi+Cg+C++ CP++
  gi|386002695|ref|YP_005920994.1| 13 ELCIGCGLCAALCPEE 28
                                      6899999999999986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.036
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCi.eCgeCerkCP 57
                                      Ci+Cg C++ Cp  +   +    + r       +e  +  +++ C+ +Cg+C ++CP
  gi|386002695|ref|YP_005920994.1| 15 CIGCGLCAALCPEEALEMT----WNRY------GE-YNPLEIEPCTrGCGLCLKVCP 60
                                      8888888888887665222....2222......12.233466777645777777777 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.004
                           Fer4_17  3 iqCgyClpeCpsyeay 18
                                      ++Cg Cl++Cp+    
  gi|386002695|ref|YP_005920994.1| 50 RGCGLCLKVCPFADHE 65
                                      4899999999987664 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.5
                           Fer4_17   4 qCgyClp...eC 12 
                                        C yC +   eC
  gi|386002695|ref|YP_005920994.1| 285 ACNYCDDvfaEC 296
                                       588887744455 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   0.00011      0.11      71      95 ..       4      28 ..       1      29 [. 0.82
   2 ?    3.6   0.5      0.12   1.2e+02      82      93 ..      48      60 ..      33      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                           Fer4_22 71 sefkekfgesgCvGCgRCieacpvk 95
                                      + ++e ++++ C+GCg C + cp++
  gi|386002695|ref|YP_005920994.1|  4 NIVTEVVDHELCIGCGLCAALCPEE 28
                                      5566778999************975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                           Fer4_22 82 Cv.GCgRCieacp 93
                                      C+ GCg C ++cp
  gi|386002695|ref|YP_005920994.1| 48 CTrGCGLCLKVCP 60
                                      5449999999998 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.7     0.043        43      37      53 ..      16      33 ..      12      47 .. 0.82
   2 ?    5.6   0.5     0.011        11      36      52 ..      49      66 ..      42      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.043
                           DUF3343 37 agCGlalrv.needieea 53
                                       gCGl+  + +ee +e+ 
  gi|386002695|ref|YP_005920994.1| 16 IGCGLCAALcPEEALEMT 33
                                      69*******999999986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                           DUF3343 36 sagCGlalrv.neediee 52
                                      ++gCGl+l+v + +d ee
  gi|386002695|ref|YP_005920994.1| 49 TRGCGLCLKVcPFADHEE 66
                                      58*******977777665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.5   0.00045      0.45       1      15 []      15      29 ..      15      29 .. 0.93
   2 ?   12.1   4.0    0.0003       0.3       1      12 [.      48      60 ..      48      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg+C   CP+ A
  gi|386002695|ref|YP_005920994.1| 15 CIGCGLCAALCPEEA 29
                                      ************866 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0003
                            Fer4_3  1 Ct.gCgaCvevCP 12
                                      Ct gCg+C++vCP
  gi|386002695|ref|YP_005920994.1| 48 CTrGCGLCLKVCP 60
                                      8879********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3060.52
//
Query:       gi|386002696|ref|YP_005920995.1|  [L=515]
Description: Polysaccharide biosynthesis protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-11   43.7  27.9    2.1e-11   43.7  27.9    2.5  3  Polysacc_synt  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7  27.9   1.2e-15   2.1e-11       4     270 ..      16     295 ..      13     298 .. 0.77
   2 ?   -3.2  15.3      0.24   4.2e+03      76     215 ..     314     460 ..     309     481 .. 0.74
   3 ?    0.2   1.7     0.022     4e+02     147     189 ..     446     491 ..     438     512 .. 0.51

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.2e-15
                     Polysacc_synt   4 gvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.........k 71 
                                       + + +++  l++ +++ + ++y+  +lg + +Gl  la++i+++  i++++ ln+ ++r+     ++          
  gi|386002696|ref|YP_005920995.1|  16 NLLANIAYFLFSVGIGVLLVPYFISTLGVAAYGLIPLAASITGYVAIFVQS-LNTVVTRFLTVDLQRgdyalanrtF 91 
                                       6666677778888999*********************************96.************9999977766432 PP

                     Polysacc_synt  72 elvslillnvllvll.vlvllfllllliaaflglpelavlylilalmll.llvg.vasfrrglfqglermkyaavsq 145
                                       ++ + +l++++l+++ v+++++ + ++i+++  ++e   ++l+l ++ + ll + +  f ++lf +++r   + + +
  gi|386002696|ref|YP_005920995.1|  92 NTAFFGLSALVLLMVpVVLVVAWFVPTIFDVPAGEENGAVILFLGVSAAfLLSSwNGNFTVQLF-AFNRLDLQNLVN 167
                                       2222222222222221344455567777777777777777777776666544440445555554.677777777777 PP

                     Polysacc_synt 146 vveqlsrvilvliavflfld.ivaavlgavlaalvggivslavlrkkf.r..prfvilslklvrellsfsapltiss 218
                                       +++ l+ + l+l++++l ++ ++ ++++++++a ++++vs+++ r+   +  ++   ++  +vr+l  +++++++++
  gi|386002696|ref|YP_005920995.1| 168 LASLLVQTGLILLLFTLCGPsLALVGGAYLSGAAAASVVSFILARRVCpHlrVSIQYFDHVRVRDLCGMGWWVVVNQ 244
                                       77777777777777777777699999999****************88884557777777****************** PP

                     Polysacc_synt 219 laillytyidsillglllgaeavGiYnaayqllvaisgllapivtaalfPvf 270
                                       +++ll+     i+  ll ga+++G Y    ql+++++ ++    + +l+P++
  gi|386002696|ref|YP_005920995.1| 245 IGTLLFHSAALIVVNLLFGATSAGLYAIPLQLVLLLQAVAGILSG-VLVPTI 295
                                       ********************************9999987776666.****98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.24
                     Polysacc_synt  76 lillnvllvllvlvllfllllliaaflglpelavlylilalmll...llvgvasfrr..glfqglermkyaavsqvv 147
                                         +l+ l + l   l++ +++ i ++  +p++avl +++ l      l ++v  +++    +++++    +++ + v
  gi|386002696|ref|YP_005920995.1| 314 AVKLMGLAMALPIGLVCGFAPQILTVWVGPQFAVLAPLILLLTFhlsLNLAVLPLFSinVAYNQVRVPGVVTMLMGV 390
                                       5678889999999999999999999********99987666555245555555555411345555555666666666 PP

                     Polysacc_synt 148 eqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr..prfvils.lklvrellsfsaplt 215
                                        +++ ++++ +++ +++ + +a++ga + +l +g++  ++ +k ++  +++ ++s l+ ++ ++++++   
  gi|386002696|ref|YP_005920995.1| 391 VNITLAVALPLLTGWGY-YGVAAAGAIVLTLKNGFFTPWYATKVLGvdVQTFTPSiLSGIFATILVGVAAG 460
                                       66666666666666666.999*********************99966777778888999999999998655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.022
                     Polysacc_synt 147 veqlsrvilvliavflfld...ivaavlgavlaalvggivslavlr 189
                                       ++ ++ +ilv++a    +    i+++ +  v +++v++ ++l+v++
  gi|386002696|ref|YP_005920995.1| 446 LSGIFATILVGVAAGALNTlfdIASLSMLVVYGTVVSLAYLLLVYK 491
                                       3334444444444433332222666555666666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 2725.90
//
Query:       gi|386002697|ref|YP_005920996.1|  [L=354]
Description: glycosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-36  125.0   1.0    4.5e-36  124.4   1.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
      3e-29  101.7   0.0    6.6e-29  100.6   0.0    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    3.7e-25   89.2   0.2      7e-25   88.3   0.2    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.8e-23   82.8   0.1    3.7e-22   79.2   0.0    2.2  2  Glyco_trans_1_4  Glycosyl transferases group 1
    3.2e-08   33.7   0.0    6.7e-08   32.7   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0015   18.3   1.7        1.3    8.7   0.0    2.8  3  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
      0.022   15.2   0.3       0.13   12.6   0.3    2.4  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   1.0   1.8e-39   4.5e-36       1     169 [.      14     175 ..      14     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 1.8e-39
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                       vGGverhv e+a++Lar+ heV+v++ +  g l+++   v+ +++v ++ +  ++  +  ++++r  lk++++DvvH
  gi|386002697|ref|YP_005920996.1|  14 VGGVERHVQEIAERLARK-HEVEVISADLVGGLPRR--EVIKGVKVTRFRSFSPGDAYFVAPQIRSYLKKGGFDVVH 87 
                                       7*****************.******66666555555..48888888888899999999999**************** PP

                    Glyco_transf_4  78 ahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygv 154
                                       ah+++a+ a l+al+   + +lV+t H +       + ++ l+r +r+l  r++  adr+i+vS+++++ +++ +g+
  gi|386002697|ref|YP_005920996.1|  88 AHNYHAFPALLAALAC-NREKLVFTPHYHG--VGSTPLRNILNRPYRRLGSRIFEGADRIICVSHYERRLVARDFGF 161
                                       ****999777666666.999*****99888..567889999999999999*************************** PP

                    Glyco_transf_4 155 ppekitVipnGvDle 169
                                       + eki+VipnG++l+
  gi|386002697|ref|YP_005920996.1| 162 E-EKIEVIPNGINLD 175
                                       9.8**********98 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   2.6e-32   6.6e-29       4     153 ..     176     323 ..     174     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2.6e-32
                                       HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflge 80 
                                       ++++ +++  + ++il++grl+++K+vd++++a+++l+    +++++ i G g +++ lk++ae l+l d+v++lg+
  gi|386002697|ref|YP_005920996.1| 176 DIKRAEPFEVEGRLILYIGRLDRYKNVDRVVEAMEHLP----EDFRFFIGGTGIYQNDLKRMAERLNLTDRVKLLGF 248
                                       567788888999*************************7....68********************************* PP

                                       CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT...-HHHHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn...naealaeair 153
                                       vs+ed+  ++k++d+fv  s  E+fG+++lEA+aa  p+++  agg+ e  +    G+l   +   ++e+la  +r
  gi|386002697|ref|YP_005920996.1| 249 VSEEDKYRWMKSCDLFVNLSSVEAFGMTVLEALAAAAPAVVNSAGGLGEFAERFG-GVLAVRPediSPEELAHSMR 323
                                       *************************************************999998.77766665777888887765 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 !   88.3   0.2   2.7e-28     7e-25       1     160 []      15     171 ..      15     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 2.7e-28
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape.leedgvrvhrlpvprrpspladlaa.lralrrllrqrrerpd 75 
                                       gG++r+v+e+a++La+  heV+v+ ++  +g p+ ++  gv v+r++       ++d+ + +++ r++l  ++ ++d
  gi|386002697|ref|YP_005920996.1|  15 GGVERHVQEIAERLARK-HEVEVISADLVGGLPRrEVIKGVKVTRFRSFS----PGDAYFvAPQIRSYL--KKGGFD 84 
                                       8**************99.******987777755427889******88663....456665268******..****** PP

                   Glyco_trans_4_4  76 vvhahsptaglaarlarrrrgiplvvtlhgll..lrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgv 149
                                       vvhah+++a +a ++a +  + +lv+t+h +    ++    + r yr+l +r++ +ad++++vs++e++++++ +g+
  gi|386002697|ref|YP_005920996.1|  85 VVHAHNYHAFPALLAALACNREKLVFTPHYHGvgSTPLRNILNRPYRRLGSRIFEGADRIICVSHYERRLVARdFGF 161
                                       *******86655555543358899999996551144445556666689999**********************5665 PP

                   Glyco_trans_4_4 150 padrvvvvpng 160
                                         ++++v+png
  gi|386002697|ref|YP_005920996.1| 162 -EEKIEVIPNG 171
                                       .59*******8 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 ?    1.1   0.0      0.19   4.9e+02       9      59 ..       9      56 ..       2      81 .. 0.68
   2 !   79.2   0.0   1.4e-25   3.7e-22       3     128 ..     189     322 ..     187     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                                      ---GG.GTHHHHHHHH.HHHH.H.H...EEEEEES---..HHHHHHHTT-T.TEEE CS
                   Glyco_trans_1_4  9 rleenvkgvdllleav.pllrkk.d...vrlvivGdgprpeeleelaagleervef 59
                                      r+++nv gv+  ++++ ++l++k +   +   +vG+ pr+ e+   +    ++v++
  gi|386002697|ref|YP_005920996.1|  9 RYSPNVGGVERHVQEIaERLARKhEvevISADLVGGLPRR-EV---I----KGVKV 56
                                      5567999999999999888887743567788999944443.22...2....23444 PP

  == domain 2  score: 79.2 bits;  conditional E-value: 1.4e-25
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                        il++Grl +++k+vd ++ea+++l  +d+r+ i G g  + ++l+++a+  +l++rv+++Gfv  ed+ ++++++d
  gi|386002697|ref|YP_005920996.1| 189 LILYIGRL-DRYKNVDRVVEAMEHLP-EDFRFFIGGTGIyQ-NDLKRMAErlNLTDRVKLLGFVseEDKYRWMKSCD 262
                                       69******.678**************.66*******99855.6999888668999*********9889********* PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSS.EE--TT-..HHHHHHHH CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv.geng.llvppgd..pealaeai 128
                                       +fv+ s  e fg+++lEa+aa+ p V+ ++gg+ e+     g l v p+d  pe+la  +
  gi|386002697|ref|YP_005920996.1| 263 LFVNLSsvEAFGMTVLEALAAAAPAVVNSAGGLGEFAeRFGGvLAVRPEDisPEELAHSM 322
                                       *****999************************9998853445466699988899999765 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.6e-11   6.7e-08      11     138 ..      19     147 ..      10     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.6e-11
                   Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitp..kkgakdeleaegihvhrlkvdrkgpleylk.af.klkklikkikPDvvhahya 83 
                                        h+ ++a+ La   +eV+vi+    +g  ++++ +g++v r++   +++ +++  ++ ++++ +kk ++Dvvhah+ 
  gi|386002697|ref|YP_005920996.1|  19 RHVQEIAERLAR-KHEVEVISAdlVGGLPRREVIKGVKVTRFR---SFSPGDAYfVApQIRSYLKKGGFDVVHAHNY 91 
                                       488888888887.9*******96445559*************9...553333333444******************8 PP

                   Glyco_trans_4_2  84 kpy.gllgslaarlsgvipvvlsvwGldvlkfpkksklkklllklalk...katkvist 138
                                           +ll++la   ++  ++v++ +  +v ++p ++ l +++ +l  +    a+++i+ 
  gi|386002697|ref|YP_005920996.1|  92 HAFpALLAALA---CNREKLVFTPHYHGVGSTPLRNILNRPYRRLGSRifeGADRIICV 147
                                       76546666666...666789*99999999999999888888777754444488888875 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 !    8.4   0.0   0.00061       1.6       1      51 [.       2      51 ..       2      71 .. 0.80
   2 !    8.7   0.0    0.0005       1.3     130     178 ..      80     118 ..      58     160 .. 0.74
   3 ?   -3.4   0.1       2.4   6.2e+03      14      30 ..     291     307 ..     283     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00061
                    Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry.gaikeek.k 51
                                      +i  v+  ++p   +GG+ ++v+++++ La++ h+v+vi+ +  g +++++  
  gi|386002697|ref|YP_005920996.1|  2 RIAQVCHRYSP--NVGGVERHVQEIAERLARK-HEVEVISADLvGGLPRREvI 51
                                      57778888888..9***************997.8******9998888887642 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0005
                    Glyco_transf_5 130 gwkpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrf 178
                                       + ++dv+hah +h+  + + + +++       + k+vft H   y+g+ 
  gi|386002697|ref|YP_005920996.1|  80 KGGFDVVHAHNYHAFPALLAALACN-------REKLVFTPH---YHGVG 118
                                       2369*********987755544444.......368999988...55555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.4
                    Glyco_transf_5  14 ktGGLadvvgaLpkaLa 30 
                                        +GGL+++++ +   La
  gi|386002697|ref|YP_005920996.1| 291 SAGGLGEFAERFGGVLA 307
                                       579***99998877776 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   5.2e-05      0.13       2      38 ..     264     300 ..     263     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                   Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelft 38 
                                       ++n+s  e + + ++Ea+a+ a+a++++a gl+e+ +
  gi|386002697|ref|YP_005920996.1| 264 FVNLSSVEAFGMTVLEALAAAAPAVVNSAGGLGEFAE 300
                                       67899999*******************99***99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2038.96
//
Query:       gi|386002698|ref|YP_005920997.1|  [L=303]
Description: Glycosyl transferase family 2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-24   84.4   0.0    1.1e-23   83.9   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.2e-18   67.0   0.0    8.7e-18   65.0   0.0    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.7e-12   47.7   0.0    2.3e-12   47.3   0.0    1.1  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    7.8e-12   45.0   0.0    1.2e-11   44.4   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00018   21.1   0.0    0.00026   20.5   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   3.2e-27   1.1e-23       1     169 [.       4     167 ..       4     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 3.2e-27
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnag 74 
                                       s+viptyNeekt+l+ le  l+  +p++d+e+ivvD +S D+t++i+ee     ++ r+++ + ee++G+  +ln+g
  gi|386002698|ref|YP_005920997.1|   4 SIVIPTYNEEKTILKKLENTLDLnYPKKDMELIVVD-CSDDRTPNIVEERLGgrGEIRLILDHEEERRGLPYSLNKG 79 
                                       8**********************9999999999985.888************7777777777899999********* PP

                                       HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCS CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnl 151
                                        ++atgd+++  D D   d+d l+  v  +e+d+ ++v g  +  ++ + ei r ++        +     s+ +++
  gi|386002698|ref|YP_005920997.1|  80 YSMATGDIVVKTDCDAMLDRDALKSAVSSFEEDRIGCVTGRAVPMGSRSEEIYRGLN-------MKIQLLESRIDST 149
                                       ********************************9999999999999999999999864.......3445555555677 PP

                                       TTCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 152 sfeigsaallrrealeel 169
                                        + +g+++++rr +l+++
  gi|386002698|ref|YP_005920997.1| 150 IIAHGPFTAFRRPLLQKI 167
                                       889999999999999875 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 !   65.0   0.0   2.4e-21   8.7e-18       4     215 ..       3     203 ..       2     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.4e-21
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalp.dvrvrvvvnarnlgstgksr 77 
                                       +++++pt+nee+++++ le++l   yp    e+ +vvd sd+ t + +ee   +l+ + ++r++ + ++ +++g  +
  gi|386002698|ref|YP_005920997.1|   3 ISIVIPTYNEEKTILKKLENTLDLNYPKkdMEL-IVVDCSDDRTPNIVEE---RLGgRGEIRLILD-HEEERRGLPY 74 
                                       79************************8842343.4457899999**9998...8887789**9866.657889**** PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpv.fllnrs.tlvsalgalefaerhlrflaar 152
                                       +ln +++++++d+v+  D D+ ++ d+lk+++  f+ +++g+v+++   +  rs    +          ++++ ++ 
  gi|386002698|ref|YP_005920997.1|  75 SLNKGYSMATGDIVVKTDCDAMLDRDALKSAVSSFEEDRIGCVTGRAvPMGSRSeEIYR--------GLNMKIQLLE 143
                                       ***********************************999******755244344313333........4455666666 PP

                   Glyco_tranf_2_3 153 ralg.vltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfps 215
                                        +++ +++ +G ++++rr +l+ +   d+  +l+dD el+l +rr+g+r+   p+++ +e + +
  gi|386002698|ref|YP_005920997.1| 144 SRIDsTIIAHGPFTAFRRPLLQKI---DE-DSLADDSELSLKIRRQGYRSILNPEVIFYEKTSE 203
                                       6666368889**************...88.88*******************9999998877543 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 !   47.3   0.0   6.4e-16   2.3e-12       2     190 ..      88     254 ..      87     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 6.4e-16
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaf 78 
                                       ++  D+D +l++d l+ +++ +++++++ v+g  ++m+  +  ee++        +k++l  +++ +++  +G  ++
  gi|386002698|ref|YP_005920997.1|  88 VVKTDCDAMLDRDALKSAVSSFEEDRIGCVTGRAVPMG--SRSEEIYRG----LNMKIQLLESRIDSTIIAHGPFTA 158
                                       6778*******************99************4..445555553....34689999999************* PP

                   Glyco_trans_2_3  79 lrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGceleklillvrl 155
                                       +rr +lq++   d  e+s+++D +++l+++r+Gyr ++ pe++++ek++     +  Q++R a G      +    +
  gi|386002698|ref|YP_005920997.1| 159 FRRPLLQKI---D--EDSLADDSELSLKIRRQGYRSILNPEVIFYEKTSE--EGREEQKTRRASGL-----V----R 219
                                       *********...8..9********************************99..55677999999993.....2....3 PP

                   Glyco_trans_2_3 156 lgylgsllwsalplhlallllfsllalalvlllll 190
                                       l +  + l+ +    l++ll+f+++ +a v+l+ll
  gi|386002698|ref|YP_005920997.1| 220 LMWRNKTLFLNPKYGLYGLLVFPFNFTAIVILPLL 254
                                       34444444433334444444444444444443333 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   3.4e-15   1.2e-11      21     156 ..      75     202 ..      58     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.4e-15
                   Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVts..lpvgsdakglaaaleaaflntlagvlqakl 95 
                                        l+++++ a  d++v  D+d+++++d+L++ + ++e++++g+Vt+  +p+gs+ + +++ l     n+  ++l ++ 
  gi|386002698|ref|YP_005920997.1|  75 SLNKGYSMATGDIVVKTDCDAMLDRDALKSAVSSFEEDRIGCVTGraVPMGSRSEEIYRGL-----NMKIQLLESRI 146
                                       68999***************************************86677888888888855.....66666666667 PP

                   Glyco_transf_21  96 sglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvp 156
                                         + +a G + a+rr  L++i    +  d LA+D +l+  +r++G++ +l p++i+ ++++
  gi|386002698|ref|YP_005920997.1| 147 DSTIIAHGPFTAFRRPLLQKI---DE--DSLADDSELSLKIRRQGYRSILNPEVIFYEKTS 202
                                       7799*****************...44..99***********************99865554 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 !   20.5   0.0   7.3e-08   0.00026       1     103 [.       4     106 ..       4     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.3e-08
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqka.kyy.deeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarN 74 
                                       s+vip +++e++  i  ++ +     y  +++elivvd  S + + + v+     ++++  + d +++  +l  + N
  gi|386002698|ref|YP_005920997.1|   4 SIVIPTYNEEKT--ILKKLENTLdLNYpKKDMELIVVD-CSDDRTPNIVEERLGGRGEIrLILDHEEERRGLPYSLN 77 
                                       79**********..999995543133448899*99997.6999999***********9974455557789******* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekil 103
                                       +G s a +d+v+  D D +   D ++  +
  gi|386002698|ref|YP_005920997.1|  78 KGYSMATGDIVVKTDCDAMLDRDALKSAV 106
                                       *********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1890.51
//
Query:       gi|386002699|ref|YP_005920998.1|  [L=440]
Description: Peptidase U62, modulator of DNA gyrase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-61  207.3   1.7    5.4e-61  206.9   1.7    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.9   1.7     3e-65   5.4e-61       5     279 .]       8     293 ..       5     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 206.9 bits;  conditional E-value: 3e-65
                                       EEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-...... CS
                         PmbA_TldD   5 rleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea...... 75 
                                       r+ +++ t v ++nge++++s+s  +g+++r++ gg++gf++t +++  +l   +era ++a+  + d++       
  gi|386002699|ref|YP_005920998.1|   8 RVIRGKATRVVLDNGELDEISESFFEGAAIRALAGGSWGFVQTESLD--DLSGDLERARRAARRIAGDENLdlapsi 82 
                                       6789999*********************************9978777..77777777777777777888878899** PP

                                       .............GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEE CS
                         PmbA_TldD  76 .............eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtr 139
                                                    +++s eek++ll+e+e+a+ +++         ++s+++a ++++  ++ +a+S+G d+e + tr
  gi|386002699|ref|YP_005920998.1|  83 pgksgkvpvkkdpASLSLEEKVDLLREIEAAA-KVS---------GVSSTQAVYNEVLVKTNYASSDGRDLEAEATR 149
                                       *****************************883.332.........799***************************** PP

                                       EEEEEEEEE..STCSET.EEEEEEEE...SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHG CS
                         PmbA_TldD 140 vslslsvia.ddggsgd.gmgggsgy...edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllhe 211
                                       v+++++++a ++g + + gm+++ g+   e +e+ d+  +a++a e+a+a+l+ak++  g ypVv + e  g+++he
  gi|386002699|ref|YP_005920998.1| 150 VGFYVTAVAsRAGLY-QaGMESRAGScglELFEDVDAVGLARRAGETAVALLDAKAPRGGVYPVVVDQELGGVFVHE 225
                                       *********554333.22455555556668888899999************************************** PP

                                       HHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 212 avghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                       avgha+ead vleg S+l++k+Ge+++sel+t+ ddp    +g+ypfDdEG  + +tvl+e+GvL++y
  gi|386002699|ref|YP_005920998.1| 226 AVGHAAEADIVLEGGSILEGKIGERIGSELVTVKDDPSLPLYGFYPFDDEGSGSGETVLVEDGVLTSY 293
                                       ******************88*****************6599*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2679.10
//
Query:       gi|386002700|ref|YP_005920999.1|  [L=640]
Description: ATP-dependent protease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-33  115.9   1.7    2.6e-33  115.3   1.7    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    2.4e-28   99.2   0.0    5.3e-22   78.3   0.0    2.4  2  AAA_32           AAA domain
    1.7e-15   56.9   0.0    3.1e-08   33.2   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.2e-14   53.5   0.0    1.9e-08   34.2   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    1.1e-10   41.6   0.1     0.0011   18.9   0.0    3.7  3  AAA_5            AAA domain (dynein-related subfamily)
    1.3e-09   38.0   0.8    2.5e-09   37.0   0.8    1.5  1  ChlI             Subunit ChlI of Mg-chelatase
    2.8e-06   26.6   0.2       0.02   14.0   0.0    2.9  4  MCM              MCM P-loop domain
    1.5e-05   25.4   0.0       0.24   11.8   0.0    3.2  2  AAA              ATPase family associated with various cellul
    4.5e-05   23.7   0.0      0.005   17.1   0.0    2.9  2  AAA_22           AAA domain
    0.00082   19.7   0.2     0.0057   17.0   0.2    2.3  1  AAA_19           AAA domain
     0.0017   18.5   0.0       0.63   10.2   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0025   17.6   0.0       0.11   12.2   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.003   17.1   0.0      0.016   14.8   0.0    2.0  2  AAA_7            P-loop containing dynein motor region
     0.0055   17.1   0.2        0.3   11.5   0.0    2.9  2  AAA_16           AAA ATPase domain
     0.0079   15.4   0.0        2.6    7.2   0.0    2.4  2  TIP49            TIP49 P-loop domain
  ------ inclusion threshold ------
      0.013   15.4   0.0        7.5    6.4   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
      0.014   15.4   0.3      0.048   13.7   0.2    1.9  1  DUF1676          Protein of unknown function (DUF1676)
      0.019   15.5   0.0      0.065   13.8   0.0    1.9  1  AAA_18           AAA domain
      0.019   14.7   0.0      0.078   12.7   0.0    2.0  2  AAA_30           AAA domain
      0.071   13.2   0.0        3.7    7.7   0.0    2.5  2  MMR_HSR1         50S ribosome-binding GTPase
       0.14   12.6   0.0       0.82   10.2   0.0    2.2  3  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   1.7     3e-36   2.6e-33      11     202 ..     416     604 ..     406     607 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 3e-36
                                       H-S-SS--SSSSS--BSSEEEEEEEETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS-GG CS
                             Lon_C  11 lGkkrfrseeaekedqvGvvtGlawtevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsraee 83 
                                       l +++  s  +++  ++G v Gla     G +l i a ++p     +gk++ tG+l ++ ke++q   +++++    
  gi|386002700|ref|YP_005920999.1| 416 LERRKDYSMFKNSGAEIGRVNGLAVVGDSGIVLPIMAEVTPaqskEEGKVIATGRLQEIAKEAVQNVSALIKKFL-- 490
                                       4444444444567789*******************99888732224689****************9988887543.. PP

                                       GSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHH CS
                             Lon_C  84 lgidkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakr 160
                                        g d    ++kd+hi +       +G sa +++ata++s+l  +++++++amtG +++rG vlp+GG+ +k+ aa +
  gi|386002700|ref|YP_005920999.1| 491 -GED---ITNKDVHIQFIGTYEGVEGDSASISIATAVISALESVPIKQNIAMTGSLSVRGDVLPVGGVTQKIEAAAQ 563
                                       .333...5689******9999999***************************************************** PP

                                       TT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHH CS
                             Lon_C 161 agikkvilPkenekdlediPeevreeleiilveevdevlkaa 202
                                       agi++v++Pk+ne d+  i e+ r+ ++ii+v++++ev++  
  gi|386002700|ref|YP_005920999.1| 564 AGITTVLIPKSNEGDVL-IDETFRDRIKIIPVTSISEVFEYS 604
                                       ***************95.99******************9976 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.8e-07   0.00075       7      91 ..      35     114 ..      30     130 .. 0.81
   2 !   78.3   0.0   6.2e-25   5.3e-22     281     509 ..     175     402 ..     170     406 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.8e-07
                            AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpa 83 
                                       ++++igq+ Ave ++ + +   +  ++ ++G++gtG+++l + +  e    e+  +D++  nn +++++Pk+  +pa
  gi|386002700|ref|YP_005920999.1|  35 IDQVIGQDEAVEVIRKAAH---QRRHVMLIGSPGTGKSMLGRAMS-ELLPVED-LQDVLVYNNPEENNNPKIRVVPA 106
                                       5899***********8865...5569***********98766655.5555544.67888889*************** PP

                            AAA_32  84 GkGkelkk 91 
                                       G+G++  +
  gi|386002700|ref|YP_005920999.1| 107 GRGRQIVD 114
                                       ****9754 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 6.2e-25
                            AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkieyesemg..alvtdftlIkaGaLhkAnGGyLildaedlLeeplaWeaL 355
                                       ++lvdns++++aP v  +  +  +L+G + ++  +     +  ++++++Ga+h+A+ G+L +d  + L+ + + ++L
  gi|386002700|ref|YP_005920999.1| 175 KLLVDNSKQKKAPYVDATGAHAGSLLGDVRHDPFQSggLETPSHERVESGAIHRAHKGVLFIDEVNTLRLE-SQQSL 250
                                       79****************************99754333555689**********************99865.67999 PP

                            AAA_32 356 kraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteene 432
                                         +L+++e  i       + +s    + +p+p+d   i  G+ +    ++ +     k +  ++ + d+m+ t en 
  gi|386002700|ref|YP_005920999.1| 251 LTSLQEGEYPITGQ---SERSSGALVRTDPVPCDFVMIAAGNLDAMAGMHPALRSRIKGYGYEVYMRDTMDDTLENR 324
                                       9***********53...446788899*********99999999999888888888889999**************** PP

                            AAA_32 433 kkyarfiasivkke.kllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekAl 508
                                       +k++rf+a+ v+++ k+++f+r+ava++++++ r a+++ +l++ ++++  l+r A  +a++ega + e +hV +A 
  gi|386002700|ref|YP_005920999.1| 325 EKLVRFVAQEVNRDgKIPHFTRDAVAEIVREAKRRAGRKGHLTLLLRDLGGLIRVAGDVARSEGAALTEMRHVLEAK 401
                                       *******9987655289********************************************************9996 PP

                            AAA_32 509 e 509
                                       +
  gi|386002700|ref|YP_005920999.1| 402 K 402
                                       5 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   3.7e-11   3.1e-08       3      55 ..      36      88 ..      34     102 .. 0.92
   2 !   21.1   0.0   1.9e-07   0.00016      96     158 ..     220     290 ..     211     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.7e-11
                      Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                       +v+Gq+ea ++++ aa  + +++l+G+pG+GK+ml +++++llp  + +++l
  gi|386002700|ref|YP_005920999.1| 36 DQVIGQDEAVEVIRKAAHQRRHVMLIGSPGTGKSMLGRAMSELLPVEDLQDVL 88
                                      689******************************************98887776 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.9e-07
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakv........efparfqlvaamNp 158
                                       +++ G+i +ah+GvLf+DE+  ++ +  ++L + l++ge  i+ ++++           p++f ++aa N+
  gi|386002700|ref|YP_005920999.1| 220 RVESGAIHRAHKGVLFIDEVNTLRLESQQSLLTSLQEGEYPITGQSERSsgalvrtdPVPCDFVMIAAGNL 290
                                       6789********************************99988864433320111221235777777777775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.8e-06     0.005      10      46 ..      43      79 ..      35      98 .. 0.86
   2 !   34.2   0.0   2.2e-11   1.9e-08      83     130 ..     218     267 ..     170     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheas 46
                                      e++e i+k+a+++ +v++ G  GtGK++l ra+ e  
  gi|386002700|ref|YP_005920999.1| 43 EAVEVIRKAAHQRRHVMLIGSPGTGKSMLGRAMSELL 79
                                      68899***************************98855 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.2e-11
                                       S-BE..HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  83 kekk..GlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       +e+   G++++a++G+lf+De+++l le Q+ Ll+ lqege+   G+s+ 
  gi|386002700|ref|YP_005920999.1| 218 HERVesGAIHRAHKGVLFIDEVNTLRLESQQSLLTSLQEGEYPITGQSER 267
                                       443335************************************99998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     3e-06    0.0026       1      24 [.      57      84 ..      57     126 .. 0.84
   2 !   18.9   0.0   1.3e-06    0.0011      65     137 ..     230     303 ..     160     304 .. 0.81
   3 ?    0.3   0.1      0.75   6.4e+02      64     108 ..     362     415 ..     342     521 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-06
                                      EEEEE--SSSSHHHHHHHGGGGB....S CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal....n 24
                                      +v+L+G pGtgKs+l + ++++l     
  gi|386002700|ref|YP_005920999.1| 57 HVMLIGSPGTGKSMLGRAMSELLpvedL 84
                                      79********************964442 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.3e-06
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnelspalr 135
                                       ++ +l++DEv++++ e ++sLl+ l e ++++    e+ + +      +      f  ia++n      + + palr
  gi|386002700|ref|YP_005920999.1| 230 HKGVLFIDEVNTLRLESQQSLLTSLQEGEYPITGQSERSSGALVR---TdpvpcdFVMIAAGNLDA--MAGMHPALR 301
                                       788****************************87777777776632...2457999*******9888..788889**9 PP

                                       TT CS
                             AAA_5 136 sR 137
                                       sR
  gi|386002700|ref|YP_005920999.1| 302 SR 303
                                       99 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.75
                                       -...........G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---. CS
                             AAA_5  64 r...........egeilvlDEveraesevlnsLlslleerrllleeggelvkaknd 108
                                       r            g i v ++v r e ++l ++  +le +++    + e++ a+ +
  gi|386002700|ref|YP_005920999.1| 362 RkghltlllrdlGGLIRVAGDVARSEGAALTEMRHVLEAKKMA--RSVEQQLADMY 415
                                       2555555555667778888888888888888888888888887..44444444444 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.8     3e-12   2.5e-09      12     121 .]     465     575 ..     453     575 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3e-12
                              ChlI  12 ftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGe 87 
                                       +  +G +++  ke+ + v + +k+  g ++ +k + +         eG + +++iA ++++ale+++ ++++ + G 
  gi|386002700|ref|YP_005920999.1| 465 VIATGRLQEIAKEAVQNVSALIKKfLGEDITNKDVHIQFIGTYEGVEGDSASISIATAVISALESVPIKQNIAMTGS 541
                                       55578899999************989*************************************************** PP

                              ChlI  88 LsldGslrpvkgvlpialaakkegikkvivpken 121
                                       Ls  G++ pv gv++ + aa+++gi++v++pk+n
  gi|386002700|ref|YP_005920999.1| 542 LSVRGDVLPVGGVTQKIEAAAQAGITTVLIPKSN 575
                                       *******************************998 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00063      0.54      52      82 ..      50      80 ..      25      86 .. 0.75
   2 !   14.0   0.0   2.4e-05      0.02      82     145 ..     184     254 ..     175     262 .. 0.76
   3 ?   -3.6   0.0       5.7   4.8e+03      20      51 ..     483     514 ..     471     527 .. 0.66
   4 ?   -2.9   0.0       3.5     3e+03     104     127 ..     573     581 ..     528     602 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00063
                                      SBBCSS-EEEEEESSTSTHHHHHHHHHHHSS CS
                               MCM 52 tklrgdinvllvgdpgtaKsqlLkyveklap 82
                                      +    + +v+l+g pgt+Ks l +++++l+p
  gi|386002700|ref|YP_005920999.1| 50 KAAHQRRHVMLIGSPGTGKSMLGRAMSELLP 80
                                      4466778**************9999988877 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.4e-05
                                       SSEEEEESSSSSSSHSSSEEEEESSSSS.......EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHH CS
                               MCM  82 pravytsgkgssaagLtaavvrdeetge.......fvleaGalvladkGvcciDefdkmkeedrsalhEam 145
                                       ++a y+ ++g+ a  L   v++d+ ++          +e+Ga+  a+kGv+ iDe++  + e +++l+  +
  gi|386002700|ref|YP_005920999.1| 184 KKAPYVDATGAHAGSLLGDVRHDPFQSGgletpshERVESGAIHRAHKGVLFIDEVNTLRLESQQSLLTSL 254
                                       56667777777777777777777766544444444579**********************99999998766 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.7
                                       HHSSTTSSS-HHHHHHHHHHHH---EBBBSSS CS
                               MCM  20 ksiapsiyghedvkkaillqlfggvkkkledk 51 
                                       ++++++ +g++   k + +q +g+++  + d+
  gi|386002700|ref|YP_005920999.1| 483 SALIKKFLGEDITNKDVHIQFIGTYEGVEGDS 514
                                       45666777777777778888877777665554 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.5
                                       ESSSSSEEEEETHHHHTTTSEEEE CS
                               MCM 104 deetgefvleaGalvladkGvcci 127
                                       +               +++G ++i
  gi|386002700|ref|YP_005920999.1| 573 K---------------SNEGDVLI 581
                                       2...............33444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00028      0.24       1      22 [.      58      79 ..      58     129 .. 0.81
   2 !    9.8   0.0    0.0012      0.99      58     124 ..     230     304 ..     215     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      v+l+G pGtGK++l +a+ + l
  gi|386002700|ref|YP_005920999.1| 58 VMLIGSPGTGKSMLGRAMSELL 79
                                      68**************998766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGG CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdk 114
                                       ++ +lfiDE+  l  ++           ++ Llt l++ +                      ++++i+a+n   +  
  gi|386002700|ref|YP_005920999.1| 230 HKGVLFIDEVNTLRLES-----------QQSLLTSLQEGEYPitgqserssgalvrtdpvPCDFVMIAAGNLdaMAG 295
                                       359**********8888...........9999999999999999999999999***9999667********999999 PP

                                       STHHHHSTTS CS
                               AAA 115 ldpallrgRf 124
                                       + pal+ +R+
  gi|386002700|ref|YP_005920999.1| 296 MHPALR-SRI 304
                                       999999.897 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.8e-06     0.005       4      38 ..      54      96 ..      49     133 .. 0.77
   2 ?    3.2   0.0      0.12        98      85     108 ..     225     250 ..     197     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee........e 38
                                      ++++++++G +GtGK++l r + e l+ e  ++         +
  gi|386002700|ref|YP_005920999.1| 54 QRRHVMLIGSPGTGKSMLGRAMSELLPVEDLQDVlvynnpeeN 96
                                      899**********************987655544555555442 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                            AAA_22  85 alraravielliiDEaqhlr..s.eea 108
                                       a++++++ ++l iDE+  lr  s + +
  gi|386002700|ref|YP_005920999.1| 225 AIHRAHK-GVLFIDEVNTLRleSqQSL 250
                                       4566666.***********66532333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   6.7e-06    0.0057       6     126 ..      50     255 ..      41     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                            AAA_19   6 e.alkekvllvtaGpGtGKTrvlkhivallvelggvkp..........eeillvaftgrAakelrerlaalgaeatT 71 
                                       + a++++++++++ pGtGK+ + +++ +ll  +  +++          ++ + v ++gr  + +     ++ ++++T
  gi|386002700|ref|YP_005920999.1|  50 KaAHQRRHVMLIGSPGTGKSMLGRAMSELLPVEDLQDVlvynnpeennNPKIRVVPAGRGRQIVDAHKMEARKKTQT 126
                                       347999*************9988888777766665555789999999888899999999988888776555556666 PP

                            AAA_19  72 iHrlal....................................................................... 77 
                                          + +                                                                       
  gi|386002700|ref|YP_005920999.1| 127 RNMFFMlimmgllvyayymgqllfgiiaaalifltmrylipkddsmvpkllvdnskqkkapyvdatgahagsllgdv 203
                                       65554488899999999999999999999999999999999999999999988888888888777777777766664 PP

                            AAA_19  78 ....ldfddlltealelle.........eaeeekkl.qeee.llivDEfqdvd.elqyrLlkall 126
                                                         +         e+ e+  + ++++ +l++DE+  +  e q++Ll  l 
  gi|386002700|ref|YP_005920999.1| 204 rhdpF-------------QsggletpshERVESGAIhRAHKgVLFIDEVNTLRlESQQSLLTSLQ 255
                                       44332.............0333335555333333331445579*****************99887 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.019        16      14      43 ..      48      77 ..      42      92 .. 0.87
   2 !   10.2   0.0   0.00073      0.63      62      97 ..     223     258 ..     169     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                                      HHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                   Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhk 43
                                      + +aa++   v l+G +G+gk++  r++++
  gi|386002700|ref|YP_005920999.1| 48 IRKAAHQRRHVMLIGSPGTGKSMLGRAMSE 77
                                      678999999**************9998876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00073
                                       HHHHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHT CS
                   Sigma54_activ_2  62 ldlleqakggtLylkdiadlskaeqkeLlellakae 97 
                                       +  + +a+ g+L++ +++ l  + q+ Ll  l+++e
  gi|386002700|ref|YP_005920999.1| 223 SGAIHRAHKGVLFIDEVNTLRLESQQSLLTSLQEGE 258
                                       4456679**************************954 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00013      0.11       6      55 ..      35      77 ..      30      85 .. 0.77
   2 ?    2.7   0.0      0.11        97      84     110 ..     230     256 ..     224     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            RuvB_N  6 leeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiak 55
                                      +++ igq++    ++++ +aa++r+    hv+l+G+PG Gk+ l + +++
  gi|386002700|ref|YP_005920999.1| 35 IDQVIGQDE---AVEVIRKAAHQRR----HVMLIGSPGTGKSMLGRAMSE 77
                                      466777765...4567778888885....9************99988776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                            RuvB_N  84 ekdvlfideihrlsraveevlysamed 110
                                       +k vlfide+  l+ + ++ l +++++
  gi|386002700|ref|YP_005920999.1| 230 HKGVLFIDEVNTLRLESQQSLLTSLQE 256
                                       578********9998888888777765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05     0.016      26      62 ..      48      84 ..      42      95 .. 0.84
   2 ?   -1.2   0.0       1.5   1.3e+03     100     115 ..     230     245 ..     227     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkldkeky 62
                                      +++  +++++v+l+G+ GtGK+++ + + + l+ e++
  gi|386002700|ref|YP_005920999.1| 48 IRKAAHQRRHVMLIGSPGTGKSMLGRAMSELLPVEDL 84
                                      6778899****************99988888776665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                             AAA_7 100 kklvvFvDDlnmpake 115
                                       +k v+F+D++n  + e
  gi|386002700|ref|YP_005920999.1| 230 HKGVLFIDEVNTLRLE 245
                                       5789*******98776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00035       0.3      13      46 ..      49      77 ..      37     120 .. 0.77
   2 ?    2.2   0.0      0.25   2.2e+02     132     158 ..     227     254 ..     218     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                            AAA_16 13 lsalervrsgrpelvllsGesGvGKsslvrellr 46
                                      +     + +++ + v+l+G +G+GKs l r+  +
  gi|386002700|ref|YP_005920999.1| 49 RK----A-AHQRRHVMLIGSPGTGKSMLGRAMSE 77
                                      33....3.334499*************9888775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                            AAA_16 132 rderplvlvlDdlqwadeaslql.laaL 158
                                       +++++ vl++D++  ++ +s+q  l +L
  gi|386002700|ref|YP_005920999.1| 227 HRAHKGVLFIDEVNTLRLESQQSlLTSL 254
                                       447779************9999945444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0     0.003       2.6      40      74 ..      45      79 ..      17      90 .. 0.75
   2 !    5.5   0.0    0.0098       8.4     279     304 ..     231     256 ..     219     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.003
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 40 velikekklaGravLlaGpsgtGktalaiaiskel 74
                                      ve+i++     r v+l G +gtGk+ l  a+s+ l
  gi|386002700|ref|YP_005920999.1| 45 VEVIRKAAHQRRHVMLIGSPGTGKSMLGRAMSELL 79
                                      5677777777799**************99999866 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0098
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnrales 304
                                       +GvlfiDev+ l +e+   l  +l +
  gi|386002700|ref|YP_005920999.1| 231 KGVLFIDEVNTLRLESQQSLLTSLQE 256
                                       7*************997766666655 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.013        11       1      24 [.      57      80 ..      57      87 .. 0.91
   2 ?    6.4   0.0    0.0088       7.5      63      98 ..     231     266 ..     214     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                             AAA_3  1 hvllegvPGlaktllvkalakald 24
                                      hv+l g PG++k +l +a+++ l 
  gi|386002700|ref|YP_005920999.1| 57 HVMLIGSPGTGKSMLGRAMSELLP 80
                                      9******************99875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0088
                             AAA_3  63 anllladeinrappktqsalleameerqvtvegeth 98 
                                       + +l+ de+n     +q +ll +++e +  ++g++ 
  gi|386002700|ref|YP_005920999.1| 231 KGVLFIDEVNTLRLESQQSLLTSLQEGEYPITGQSE 266
                                       46899*********************9988877654 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.7e-05     0.048     109     149 ..     110     155 ..      74     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                           DUF1676 109 e........egRkkkkkkkklkkmllplllalk.lklklLlplalgllal 149
                                                e+R    kk + ++m+ +l++++  + +  ++ l++g++a 
  gi|386002700|ref|YP_005920999.1| 110 RqivdahkmEAR----KKTQTRNMFFMLIMMGLlVYAYYMGQLLFGIIAA 155
                                       022222334666....445677888888888888***********99986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.6e-05     0.065       1      50 [.      58     111 ..      58     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.....aldesk 50 
                                       ++l G pG+GK+ l+++ s++l  ++ l+dv+  n++++ ++p+     a +  +
  gi|386002700|ref|YP_005920999.1|  58 VMLIGSPGTGKSMLGRAMSELL-PVEDLQDVLVYNNPEENNNPKirvvpAGRGRQ 111
                                       789*****************95.37888888888888888887754444333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.2e-05     0.078       8      43 ..      46      80 ..      39      95 .. 0.74
   2 ?   -2.2   0.0       3.4   2.9e+03      87     114 ..     229     256 ..     201     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-05
                            AAA_30  8 aavealltsgdrvavltGpAGtGKttalkalreawe 43
                                      ++++++++++ r ++l G +GtGK+++ +a+ e++ 
  gi|386002700|ref|YP_005920999.1| 46 EVIRKAAHQR-RHVMLIGSPGTGKSMLGRAMSELLP 80
                                      3455555555.6999*************99999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                            AAA_30  87 epgtllivDEagmvdtkqlaallkaaek 114
                                       +++ +l +DE+  +  ++ ++ll+++++
  gi|386002700|ref|YP_005920999.1| 229 AHKGVLFIDEVNTLRLESQQSLLTSLQE 256
                                       4557999999999999999999888765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0044       3.7       2      36 ..      58      99 ..      57     140 .. 0.75
   2 ?    2.8   0.0      0.14   1.2e+02      23      69 ..     335     390 ..     326     434 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0044
                                      EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdi 36
                                      v+++G p +GKS L +a+++       + + v + p    ++
  gi|386002700|ref|YP_005920999.1| 58 VMLIGSPGTGKSMLGRAMSEllpvedlQDVLVYNNPEENNNP 99
                                      89***************9875555443355666666555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                                       TEEESSSTTSSSSEEEEEEE...ETTEE........EEEEECGGCSS.....HHHHHHHHHHH CS
                          MMR_HSR1  23 kaivsdkpgtTrdinegrvk...lkgke........ielvDtpGlie.....gaseekglgka 69 
                                       + + +++p  Trd + + v+       +        + l D+ Gli            ++g a
  gi|386002700|ref|YP_005920999.1| 335 VNRDGKIPHFTRDAVAEIVReakR---RagrkghltLLLRDLGGLIRvagdvAR----SEGAA 390
                                       556689999*****9999984440...2444455559999****9852221111....11111 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00096      0.82      10      36 ..      54      80 ..      47     130 .. 0.82
   2 ?   -2.0   0.0       5.5   4.7e+03      41      41 ..     389     389 ..     309     485 .. 0.58
   3 ?   -1.7   0.0       4.5   3.8e+03      36      80 ..     455     511 ..     425     544 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00096
                                      TTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagllk 36
                                      + + v ++G+ G+GKS L +++++ll 
  gi|386002700|ref|YP_005920999.1| 54 QRRHVMLIGSPGTGKSMLGRAMSELLP 80
                                      567899****************99875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.5
                                       E CS
                                       x RF
                          ABC_tran  41 e 41 
                                        
  gi|386002700|ref|YP_005920999.1| 389 A 389
                                       0 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.5
                                       --....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...........H CS
                                       xx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                          ABC_tran  36 kp....teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...........e 80 
                                       +p    +eG++ +    l+e+ +e +++  + l ++ +l +++t+++            e
  gi|386002700|ref|YP_005920999.1| 455 TPaqskEEGKV-IATGRLQEIAKEAVQNV-SALIKK-FLGEDITNKDVhiqfigtyegvE 511
                                       44344477777.55555555444444433.333333.45566655555555555544441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      815  (0.0454571); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 3804.22
//
Query:       gi|386002701|ref|YP_005921000.1|  [L=720]
Description: AAA ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-95  315.1   0.0      5e-47  159.6   0.0    2.7  2  AAA              ATPase family associated with various cellul
    1.7e-28   98.1   0.5    1.7e-13   50.1   0.2    2.7  2  AAA_lid_3        AAA+ lid domain
    6.6e-27   93.5   0.1    2.7e-26   91.6   0.5    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.8e-15   56.0   0.0    2.8e-07   30.4   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.2e-13   48.3   0.1    1.4e-12   47.2   0.1    1.6  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
      3e-12   47.2   0.3    3.2e-05   24.4   0.0    3.2  2  AAA_16           AAA ATPase domain
    6.3e-12   45.9   0.0    7.8e-06   26.1   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    4.5e-11   42.9   0.7    0.00021   21.3   0.1    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-10   39.7   0.0    0.00012   21.4   0.0    2.4  2  TIP49            TIP49 P-loop domain
    5.5e-10   39.7   0.8     0.0031   17.8   0.1    3.9  3  AAA_22           AAA domain
    1.3e-08   35.0   0.0     0.0027   17.7   0.0    2.3  2  AAA_14           AAA domain
    1.8e-08   34.7   0.0     0.0067   16.6   0.0    2.5  2  AAA_33           AAA domain
    1.1e-07   31.7   0.0      0.015   15.1   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
    5.3e-07   30.2   0.0      0.034   14.7   0.0    2.6  2  AAA_18           AAA domain
    6.2e-07   29.2   4.0        1.8    8.1   0.2    4.3  4  AAA_25           AAA domain
      2e-06   27.3   2.5      0.045   13.1   0.1    3.0  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.1e-06   26.0   0.0       0.12   12.6   0.0    2.6  2  AAA_28           AAA domain
    1.6e-05   24.7   0.1       0.44   10.2   0.0    3.5  2  Sigma54_activat  Sigma-54 interaction domain
    2.4e-05   23.8   0.6       0.18   11.1   0.0    3.2  3  ATPase           KaiC
    4.7e-05   23.4   0.2       0.22   11.5   0.1    2.9  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    4.9e-05   22.9   0.1       0.21   11.0   0.0    2.3  2  PhoH             PhoH-like protein
    6.9e-05   22.4   0.0       0.28   10.7   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    7.3e-05   23.1   0.0       0.66   10.4   0.0    2.4  2  RNA_helicase     RNA helicase
    8.5e-05   23.1   0.0       0.46   11.0   0.0    2.4  2  ABC_tran         ABC transporter
    0.00011   22.1   0.0       0.44   10.4   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00016   21.5   0.0       0.54    9.9   0.0    2.4  2  AAA_24           AAA domain
    0.00073   18.9   0.0       0.92    8.7   0.0    2.4  2  Zeta_toxin       Zeta toxin
    0.00091   19.7   0.0        0.8   10.1   0.0    2.7  2  AAA_17           AAA domain
     0.0011   18.9   0.1        5.6    6.8   0.0    3.6  4  Rad17            Rad17 P-loop domain
     0.0012   18.6   0.3        2.1    8.0   0.0    3.0  2  AAA_30           AAA domain
     0.0018   18.6   1.2        2.1    8.7   0.1    2.9  2  AAA_19           AAA domain
      0.002   18.2   0.0        2.1    8.4   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0027   17.9   0.0        1.2    9.2   0.0    2.4  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0028   16.9   0.0        1.4    8.0   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
     0.0029   17.5   0.2        2.7    7.9   0.1    3.5  4  NACHT            NACHT domain
     0.0035   16.7   0.0        1.3    8.1   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0035   16.5   0.0        1.6    7.8   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0046   16.4   0.0        2.6    7.4   0.0    2.3  2  IPT              Isopentenyl transferase
  ------ inclusion threshold ------
       0.01   15.6   0.0        4.4    7.0   0.0    2.2  2  AAA_11           AAA domain
      0.012   15.4   0.1        3.8    7.2   0.0    2.3  2  Cytidylate_kin   Cytidylate kinase
      0.034   14.0   0.0        2.2    8.1   0.0    2.6  2  Bac_DnaA         Bacterial dnaA  protein
      0.036   14.0   0.3         20    5.1   0.0    3.3  3  NTPase_1         NTPase
      0.038   14.1   0.1         11    6.1   0.0    2.4  2  SKI              Shikimate kinase
      0.043   13.0   0.0          9    5.4   0.0    2.4  2  NB-ARC           NB-ARC domain
      0.072   12.5   0.0        7.7    5.9   0.0    2.8  2  TniB             Bacterial TniB protein
      0.094   12.6   0.1         30    4.4   0.0    3.2  3  ATPase_2         ATPase domain predominantly from Archaea
       0.14   11.5   0.0         26    4.2   0.0    2.9  3  SRPRB            Signal recognition particle receptor beta su
       0.15   11.8   0.0         18    5.2   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
       0.18   11.5   0.1         26    4.5   0.0    3.2  4  Guanylate_kin    Guanylate kinase
       0.25   11.1   0.0        3.8    7.2   0.0    2.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   0.0   1.4e-49     5e-47       1     131 [.     212     341 ..     212     342 .. 0.98
   2 !  152.7   0.0   1.9e-47     7e-45       1     131 [.     484     614 ..     484     615 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 1.4e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +ll+GppGtGKTl+a+ava+e++++f++isg+e++sk+ gesek++re+f+ea+++a psi+fiDEid++a++r++ 
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANFISISGPEITSKFYGESEKRLREIFEEAERSA-PSIVFIDEIDSIAPKREEV 287
                                       69******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + + e+rvv+qLl+ +dg+  + ++vivi+atnrp++ldpa++r gRfdr++ei+
  gi|386002701|ref|YP_005921000.1| 288 AGDLERRVVAQLLSLMDGLAYR-GEVIVIAATNRPNSLDPAIRRgGRFDREMEIG 341
                                       *********************7.66**************************9986 PP

  == domain 2  score: 152.7 bits;  conditional E-value: 1.9e-47
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vll+GppGtGKTllakava+e+gv+f++++g+ellsk+vgese+ +re+f++ak+ a ps +f+DE+da++++r sg
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGVNFISVKGPELLSKWVGESERAVREVFRKAKQAA-PSLIFFDEVDAVVPARgSG 559
                                       79******************************************************9.****************888 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +s  +ervv+q+lteldgv +  ++v+v++atnrpd ldp llr gRfdr i+i+
  gi|386002701|ref|YP_005921000.1| 560 LDSHATERVVSQFLTELDGVVEL-KDVVVLAATNRPDLLDPSLLRpGRFDRLIRIP 614
                                       8*********************7.55**************************9987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.2   4.8e-16   1.7e-13       1      36 [.     364     399 ..     364     422 .. 0.90
   2 !   45.5   0.0   1.3e-14   4.6e-12       1      35 [.     637     671 ..     637     692 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 4.8e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                       dvdl+ +AerT+G++GADla+lc+eAa+++l+  i+
  gi|386002701|ref|YP_005921000.1| 364 DVDLEGIAERTHGFVGADLASLCKEAAMHTLKGLIP 399
                                       9******************************97655 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 1.3e-14
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgi 35 
                                       dv+ ++LAe TeG++GAD++ lcreA++ Alr++i
  gi|386002701|ref|YP_005921000.1| 637 DVSASRLAEVTEGWTGADIETLCREAGMTALREKI 671
                                       8999*****************************97 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.5   7.4e-29   2.7e-26       1      84 [.       6      88 ..       6      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 7.4e-29
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +LrVaea+++dvgrgi+r+ ++ +++lg+e g vvei+g+r+++a++w+a p++  k++Ir+dg++R+n+gv+i+d+Vt
  gi|386002701|ref|YP_005921000.1|  6 TLRVAEAYHRDVGRGIARLAQDLISDLGVEGGAVVEIQGRRTAYAVAWQASPKEA-KDVIRIDGNLRSNLGVGIDDRVT 83
                                      69***************************************999*********77.*********************** PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      Vrk e
  gi|386002701|ref|YP_005921000.1| 84 VRKSE 88
                                      **976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   7.8e-10   2.8e-07      36     103 ..     212     287 ..     205     295 .. 0.83
   2 !   22.1   0.0   2.8e-07    0.0001      36      69 ..     484     517 ..     478     602 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 7.8e-10
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                       +ll+GpPG Gkt +a+ +a+e ++++ + sgP +      e ++ l  ++ + e++   ++fidei  ++++ eev
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANFISISGPEItskfygESEKRLREIFEEAERSapSIVFIDEIDSIAPKREEV 287
                                       79*******************************93333333456788888887654337************99997 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.8e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       vll+GpPG Gkt lak +a+e gv++ +  gP l
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGVNFISVKGPEL 517
                                       9******************************986 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.1   3.8e-15   1.4e-12       7      59 ..     109     161 ..     104     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 3.8e-15
                                       CHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEES CS
                           CDC48_2   7 maylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgt 59 
                                       ++yl r +lgrp++kG+++ +e  + ++ +vVvst Pkgpv++  +Tei++ +
  gi|386002701|ref|YP_005921000.1| 109 PQYLLRTLLGRPIVKGEQLKIEMISSALGFVVVSTAPKGPVVVAAETEIKILK 161
                                       689**********************************************9974 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   8.8e-08   3.2e-05      19     137 ..     204     312 ..     179     316 .. 0.71
   2 !   18.6   0.1   5.2e-06    0.0018      22      63 ..     479     517 ..     471     577 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 8.8e-08
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaele 95 
                                       +    p+ +ll G++G+GK+ ++r+++ + e++   f++    + +s      +    ++ +l +  +++++sa   
  gi|386002701|ref|YP_005921000.1| 204 LGIRPPQGLLLFGPPGTGKTLIARAVASETEAN---FISISGPEITS-----KFYGESEK-RLREIFEEAERSAPSI 271
                                       44444599*******************877766...66666666622.....34444423.5555555556667777 PP

                            AAA_16  96 awrekleealaavpelagaeasrllellkrllallsrderpl 137
                                        + +++++ +    e+ag++++r+ ++l +l++ l+ +++ +
  gi|386002701|ref|YP_005921000.1| 272 VFIDEIDSIAPKREEVAGDLERRVVAQLLSLMDGLAYRGE-V 312
                                       78888888888999******************66655455.3 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.2e-06
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                         p+ vll G++G+GK+ l++++++   ++g+ f++ k  +l
  gi|386002701|ref|YP_005921000.1| 479 RPPRGVLLFGPPGTGKTLLAKAVAT---ESGVNFISVKGPEL 517
                                       44699*******************6...66677888888877 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.2e-08   7.8e-06       6     105 ..     212     305 ..     207     310 .. 0.87
   2 !   17.2   0.0   1.2e-05    0.0041       6     104 ..     484     577 ..     479     583 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.2e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++a+a+a+  ++    ++i +   e++     + + ++++  ++   +ae +   iv++DEid i
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEA----NFISISGPEITS----KFYGESEKRLREIFEEAERSApsIVFIDEIDSI 280
                                       5788****************9985....************....99999999999999999999899********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+   d  r  V+  LL +++g
  gi|386002701|ref|YP_005921000.1| 281 APKrEEVAGDLERR-VVAQLLSLMDG 305
                                       **977777777775.77778889887 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.2e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a    v    ++i +   ell     + + +++   ++   +a++     +++DE+d +
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGV----NFISVKGPELLS----KWVGESERAVREVFRKAKQAApsLIFFDEVDAV 552
                                       6788******************98....************....66666677777777777777799********** PP

                                       ---.---------HHHHHHHHHHHH CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqile 104
                                        p  +s       e V+  +L  l+
  gi|386002701|ref|YP_005921000.1| 553 VPArGSGLDSHATERVVSQFLTELD 577
                                       **95555555677778877776666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   5.8e-07   0.00021       2     136 ..     212     330 ..     211     331 .. 0.70
   2 !   17.2   0.1   1.1e-05    0.0039       1     129 [.     483     596 ..     483     605 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.8e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ +a+ +a+ +++++  + +++ t+  ++ g+ e        +  ++ ++a+   ++i+++DE++ 
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANFISISGPEITS--KFYGESE-------KRLREIFEEAErsAPSIVFIDEIDS 279
                                       89*****************************99665..4556555.......3445555566557899********9 PP

                                       --...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  77 ae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                       +     ev++ L +    + l+l++g  + ++        + via++n+++    +l+pa+r+
  gi|386002701|ref|YP_005921000.1| 280 IApkrEEVAGDLERRVVAQLLSLMDGLAYRGE--------VIVIAATNRPN----SLDPAIRR 330
                                       88222345555544444444444444333332........89999999988....88888775 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.1e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a   + ++  v +++      l+ ++    g+ ++   ++ r+a+   ++++++DEv+
  gi|386002701|ref|YP_005921000.1| 483 GVLLFGPPGTGKTLLAKAVATESGVNFISVKGPE------LLSKWV---GESERAVREVFRKAKqaAPSLIFFDEVD 550
                                       59*****************999999999998887......777777...4555555666666665788899999999 PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslne 129
                                        + ++  + L s   er ++   ++el ++ +   l+++ v+a++n++d     
  gi|386002701|ref|YP_005921000.1| 551 AVVPARGSGLDSHATERVVS-QFLTELDGVVE---LKDVVVLAATNRPD----L 596
                                       88888888888888888777.33333333322...23388888888888....4 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-05     0.007      51      93 ..     210     250 ..     206     280 .. 0.78
   2 !   21.4   0.0   3.3e-07   0.00012      51     106 ..     482     536 ..     479     539 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                       +++Ll Gp+gtGkt +a a++ e      f+++sg e+ s   
  gi|386002701|ref|YP_005921000.1| 210 QGLLLFGPPGTGKTLIARAVASETE--ANFISISGPEITSKFY 250
                                       579******************9965..89******99977533 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r+vLl Gp+gtGkt la a++ e g  v f++++g e+ s  v  +e ++ + +rk+
  gi|386002701|ref|YP_005921000.1| 482 RGVLLFGPPGTGKTLLAKAVATESG--VNFISVKGPELLSKWVGESErAVREVFRKA 536
                                       89********************987..9***************99985688999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   8.8e-06    0.0031       8      68 ..     212     268 ..     206     317 .. 0.64
   2 !   14.5   0.1   8.8e-05     0.032       8      29 ..     484     505 ..     479     523 .. 0.81
   3 ?   -1.3   0.0       6.9   2.5e+03      82     103 ..     532     552 ..     523     578 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.8e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglel 68 
                                       l+++G++GtGKT+ +r ++++          ++ ++     ++t +  ++s++ lre++++ ++++
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASET---------EANFIsisgpEITSKFYGESEKRLREIFEEAERSA 268
                                       89******************98.........44555223333333333355555555555555544 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       ++++G++GtGKT+l++ ++ + 
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATES 505
                                       689**************99876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.9
                            AAA_22  82 leqalrarav..ielliiDEaqhl 103
                                       + + ++      ++l+  DE++ +
  gi|386002701|ref|YP_005921000.1| 532 VFRKAK---QaaPSLIFFDEVDAV 552
                                       333334...34459*******986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.6e-06    0.0027       5      76 ..     212     280 ..     209     319 .. 0.80
   2 !   14.9   0.0   5.6e-05      0.02       5      76 ..     484     552 ..     481     597 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.6e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       l++ G+  +GKT +++ +++e      +++ i+  + + k + ++ek l++i+e+++++  +++f+DEi  +
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETE---ANFISISGPEITSKFYGESEKRLREIFEEAERSAPSIVFIDEIDSI 280
                                       67899**************9988...9******9999998777777666666666556699********987 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k ++ e+      + +i+++ +++  k   ++e+  +++++k+k+   +++f+DE+  v
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESG-----VNFISVKGPELlsKWVGESERAVREVFRKAKQAAPSLIFFDEVDAV 552
                                       6899***************8888.....66666666666224444555555555555555689********988 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.6e-05     0.013       3      47 ..     213     259 ..     212     334 .. 0.77
   2 !   16.6   0.0   1.9e-05    0.0067       2      41 ..     484     525 ..     484     593 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktd 47 
                                       ll G+pG+GK+  a+ ++ ++   ++ +s +++ ++ +g+ ++++++
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASETEanFISISGPEITSKFYGESEKRLRE 259
                                       789***************99998899999999999999977777663 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.9e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtd 41 
                                       vll G+pG+GK+ la+ ++ + g  ++ +  ++l+++ +g+ 
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGvnFISVKGPELLSKWVGES 525
                                       7899*******************8888888888777777643 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.6e-05     0.027      47      71 ..     209     233 ..     201     277 .. 0.89
   2 !   15.1   0.0   4.1e-05     0.015      48      71 ..     482     505 ..     477     549 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.6e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                        ++++l+Gp+G+GK+ +a a++ e+
  gi|386002701|ref|YP_005921000.1| 209 PQGLLLFGPPGTGKTLIARAVASET 233
                                       5889****************99876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.1e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                        +++l+Gp+G+GK+ la a+++e 
  gi|386002701|ref|YP_005921000.1| 482 RGVLLFGPPGTGKTLLAKAVATES 505
                                       5799***************98765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0    0.0003      0.11       2      25 ..     213     244 ..     212     319 .. 0.74
   2 !   14.7   0.0   9.4e-05     0.034       1      39 [.     484     520 ..     484     580 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0003
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf.......g 25 
                                       ll G+pG+GKt +a+++++++ ++        
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASETeANfisisgpE 244
                                       689**************888744356666663 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 9.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglll 39 
                                       +ll G+pG+GKt lak+++ +   gvn ++v   + l+ 
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATES--GVNFISVKGPELLSK 520
                                       799***************9987..887777655544444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.012       4.3      37      54 ..     213     230 ..     204     234 .. 0.85
   2 ?    6.7   0.0     0.014       4.9     130     186 ..     257     315 ..     246     322 .. 0.81
   3 !    8.1   0.2     0.005       1.8      36      54 ..     484     502 ..     477     513 .. 0.87
   4 ?    5.2   0.1      0.04        14     128     184 ..     527     588 ..     520     591 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                            AAA_25  37 llaGapgtGKttlaldla 54 
                                       ll+G+pgtGKt +a  +a
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVA 230
                                       89**********997766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                            AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar..rtgaavllv 186
                                       ++++ +++e+   +  v iD ++++ +  e+ + d  +++v++l ++ +  +++  v+++
  gi|386002701|ref|YP_005921000.1| 257 LREIFEEAER-SAPSIVFIDEIDSIAPKREEVAGDLeRRVVAQLLSLMDglAYRGEVIVI 315
                                       5667777777.55***************999999977*******9998755666666665 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.005
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt la  +a
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVA 502
                                       68***********997665 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.04
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg.....densnsdv.galvealeriarrtgaavl 184
                                       ++v+++ +++++ + + l+ +D +++++++     d+++ + v +++++ l+ + + +++ vl
  gi|386002701|ref|YP_005921000.1| 527 RAVREVFRKAKQ-AAPSLIFFDEVDAVVPArgsglDSHATERVvSQFLTELDGVVELKDVVVL 588
                                       6899999*****.66***********9999884444444444457777777777777777776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00015     0.054      25      43 ..     212     230 ..     209     236 .. 0.91
   2 ?   -2.8   0.0       9.6   3.4e+03     108     157 ..     270     319 ..     263     322 .. 0.70
   3 !   13.1   0.1   0.00012     0.045      25      43 ..     484     502 ..     476     504 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       lll+GppG+GKt++a++++
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVA 230
                                       89*************9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.6
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevt.israkakvefparfqlvaamN 157
                                        ++f+DE+  +  k  ev    le++ v+ +      + +  ++ ++aa+N
  gi|386002701|ref|YP_005921000.1| 270 SIVFIDEIDSIAPKREEV-AGDLERRVVAqLLSLMDGLAYRGEVIVIAATN 319
                                       578999999888876554.56677777742555666778888888888888 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00012
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVA 502
                                       89*************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0013      0.45       4      45 ..     214     260 ..     212     290 .. 0.72
   2 !   12.6   0.0   0.00034      0.12       2      32 ..     484     515 ..     483     547 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                            AAA_28   4 itGgestGKTtlleaLaar....gypvv.pEaareileeklakgeda 45 
                                       ++G+++tGKT +++a a++     +++  pE+  +++ e  ++ +++
  gi|386002701|ref|YP_005921000.1| 214 LFGPPGTGKTLIARAVASEteanFISISgPEITSKFYGESEKRLREI 260
                                       89***************544442344446777666665555555544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00034
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaar 32 
                                       + ++G+++tGKT l++a a + g++ +   + 
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATEsGVNFISVKGP 515
                                       6799***************7666665533333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0012      0.44      24      61 ..     211     245 ..     203     332 .. 0.70
   2 !    9.4   0.0    0.0022       0.8      24      46 ..     483     505 ..     474     595 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                        +l+ G  GtGK+l+ara+ +++   e++f+++   +i
  gi|386002701|ref|YP_005921000.1| 211 GLLLFGPPGTGKTLIARAVASET---EANFISISGPEI 245
                                       5799**************97655...466777665544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                                       -EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheas 46 
                                        vl+ G  GtGK+lla+a+ ++s
  gi|386002701|ref|YP_005921000.1| 483 GVLLFGPPGTGKTLLAKAVATES 505
                                       69****************98766 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0088       3.2      14      37 ..     204     227 ..     198     244 .. 0.83
   2 ?    2.0   0.0      0.31   1.1e+02     110     153 ..     256     305 ..     228     319 .. 0.65
   3 !   11.1   0.0   0.00049      0.18       8      40 ..     473     502 ..     467     515 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0088
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   +  l+ G pGtGKt++a 
  gi|386002701|ref|YP_005921000.1| 204 LGIRPPQGLLLFGPPGTGKTLIAR 227
                                       4777788899***********986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.31
                            ATPase 110 elaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkk 153
                                       +l+e+ +e +    + v iD i+++    +e   ++ R+ + ql++ + +
  gi|386002701|ref|YP_005921000.1| 256 RLREIFEEAERsapSIVFIDEIDSIapkREEVAGDLERRVVAQLLSLMDG 305
                                       44444444433233778888888882113333445578888888888865 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00049
                            ATPase   8 lDeilkgGipegrvvlitGepGtGKtifalqFl 40 
                                       +D i   Gi   r vl+ G pGtGKt++a+  +
  gi|386002701|ref|YP_005921000.1| 473 FDSI---GIRPPRGVLLFGPPGTGKTLLAKAVA 502
                                       4555...8999999**************98755 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0062       2.2      20      49 ..     210     241 ..     180     252 .. 0.79
   2 ?   -1.7   0.0       7.7   2.8e+03      82     105 ..     448     471 ..     442     482 .. 0.70
   3 !   11.5   0.1   0.00062      0.22      21      51 ..     483     515 ..     454     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0062
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                       + +lL G+ G+GKT ++r++a++ + +  +++
  gi|386002701|ref|YP_005921000.1| 210 QGLLLFGPPGTGKTLIARAVASETEANfiSIS 241
                                       4599*****************99887655555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.7
                                       HCTTCCCCSTSCEEEEETGGGGCC CS
                              TsaE  82 elgleeyleeeavvlvEWpeklee 105
                                       e+g  +  +e+ v +vEWp k+ e
  gi|386002701|ref|YP_005921000.1| 448 EVGGLDRAKEDLVEAVEWPLKYPE 471
                                       555555555667999***988544 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00062
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        +lL G+ G+GKT l++++a + gv+  +vk P
  gi|386002701|ref|YP_005921000.1| 483 GVLLFGPPGTGKTLLAKAVATESGVNfiSVKGP 515
                                       399*********************998888877 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.002       0.7      23      42 ..     213     232 ..     206     238 .. 0.86
   2 !   11.0   0.0   0.00058      0.21      22      42 ..     484     504 ..     477     510 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                                       EEE--TTSSTTHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalave 42 
                                         +Gp GtGKt++a a+a e
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASE 232
                                       579***********999865 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00058
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v  +Gp GtGKt+la a+a e
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATE 504
                                       6789************99976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00077      0.28      35      63 ..     211     238 ..     200     287 .. 0.76
   2 !    8.9   0.0    0.0027      0.99      34      55 ..     482     503 ..     475     513 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00077
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkekyl 63 
                                        +ll Gp GtGKt+i++ + ++ +  +++
  gi|386002701|ref|YP_005921000.1| 211 GLLLFGPPGTGKTLIARAVASETE-ANFI 238
                                       689**************9999888.4443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
                             AAA_7  34 kpvllvGptGtGKtviikdllk 55 
                                       + vll Gp GtGKt+++k + +
  gi|386002701|ref|YP_005921000.1| 482 RGVLLFGPPGTGKTLLAKAVAT 503
                                       569*************998655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0018      0.66       2      26 ..     213     237 ..     212     287 .. 0.78
   2 !   10.4   0.0    0.0019      0.67       1      21 [.     484     504 ..     484     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0018
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                       +l+Gp+g+GK+++a+ +a++ + ++
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASETEANF 237
                                       79**************999988776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0019
                      RNA_helicase   1 iwlyGpsgeGKStlakeLaka 21 
                                       ++l+Gp+g+GK++lak +a++
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATE 504
                                       679*************98776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0013      0.46       7      68 ..     205     265 ..     203     312 .. 0.80
   2 !    9.6   0.0    0.0034       1.2       8      65 ..     478     533 ..     474     591 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0013
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.p 68 
                                        +++ + + ++G+ G+GK+ +++++a +++  +  i + g +++++   +++k+++ +++e +
  gi|386002701|ref|YP_005921000.1| 205 GIRPPQGLLLFGPPGTGKTLIARAVASETE--ANFISISGPEITSKFYGESEKRLREIFEEaE 265
                                       567777889******************986..6788889999999888888888888887733 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0034
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlp 65 
                                       +++ + v ++G+ G+GK+ L+k++a ++      i ++g +l ++   ++++ ++ ++
  gi|386002701|ref|YP_005921000.1| 478 IRPPRGVLLFGPPGTGKTLLAKAVATESGV--NFISVKGPELLSKWVGESERAVREVF 533
                                       66667789****************998753..45555666666655555555554444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0     0.003       1.1       2      30 ..     212     240 ..     211     297 .. 0.86
   2 !   10.4   0.0    0.0012      0.44       2      89 ..     484     567 ..     483     599 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++ktl+++a+a+  +++f  i
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANFISI 240
                                       58899*****************9999765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappkt 78 
                                       vll g PG++ktll+ka+a+  +++f  ++  p+ll    +G +   ++ +e+  k+     +l++ de++   p  
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGVNFISVK-GPELLSK-WVGESE--RAVREVFRKAKQAAPSLIFFDEVDAVVPAR 556
                                       7999******************99998886.5677644.344432..222222222223334566666666666655 PP

                             AAA_3  79 qsalleameer 89 
                                        s l     er
  gi|386002701|ref|YP_005921000.1| 557 GSGLDSHATER 567
                                       55555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0029         1       5      33 ..     212     235 ..     209     290 .. 0.60
   2 !    9.9   0.0    0.0015      0.54       5      22 ..     484     501 ..     481     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtek 33 
                                       +l++Gp+g+GKT +a+          te+
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAV-----ASETEA 235
                                       689*********999887.....344444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l++Gp+g+GKT lak  
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAV 501
                                       79*************987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0026      0.92      16      51 ..     209     242 ..     200     262 .. 0.88
   2 !    7.4   0.0    0.0065       2.3      16      50 ..     481     513 ..     474     518 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       P  +ll G pG GK+ +a++++ e+  + n++ +++
  gi|386002701|ref|YP_005921000.1| 209 PQGLLLFGPPGTGKTLIARAVASET--EANFISISG 242
                                       7778999*****************9..899999876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0065
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       P  +ll G pG GK+ la+++++e   + n++ ++
  gi|386002701|ref|YP_005921000.1| 481 PRGVLLFGPPGTGKTLLAKAVATES--GVNFISVK 513
                                       77799******************98..77877765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.024       8.7       1      26 [.     215     240 ..     215     286 .. 0.88
   2 !   10.1   0.0    0.0022       0.8       1      32 [.     487     519 ..     487     599 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.024
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ ++ + +  ++s 
  gi|386002701|ref|YP_005921000.1| 215 FGPPGTGKTLIARAVASETEANFISI 240
                                       6**************99987777765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0022
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllre 32 
                                       +G+PG GK+ +++ ++ + g+ ++s  G  l +
  gi|386002701|ref|YP_005921000.1| 487 FGPPGTGKTLLAKAVATESGVNFISVkGPELLS 519
                                       6*****************999998865544444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       7.1   2.6e+03     107     136 ..     162     191 ..     151     197 .. 0.85
   2 ?    4.7   0.0     0.071        25      43      71 ..     207     235 ..     199     243 .. 0.79
   3 ?    3.0   0.0      0.24        85     135     178 ..     237     280 ..     230     286 .. 0.75
   4 ?    6.8   0.0     0.016       5.6      45      82 ..     481     518 ..     471     556 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.1
                             Rad17 107 esfkeleLkdakylklqklGddlrtdkkli 136
                                       ++ +e+ ++d  y  +  lG+++r  +++i
  gi|386002701|ref|YP_005921000.1| 162 DTLEEMAVRDVSYEDIGGLGKEIRMVREMI 191
                                       67899999*************999988877 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.071
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgi 71 
                                       r+ + LL+ GP+G gk+ + + ++ e   
  gi|386002701|ref|YP_005921000.1| 207 RPPQGLLLFGPPGTGKTLIARAVASETEA 235
                                       566779***********999988877655 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.24
                             Rad17 135 lilve..dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                       +i +   ++ +kfy++s ++lre+  ++ rs  +   i+ i ei+s+
  gi|386002701|ref|YP_005921000.1| 237 FISISgpEITSKFYGESeKRLREIFEEAERSAPS---IVFIDEIDSI 280
                                       5555333799*****9999******999877655...6677888875 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.016
                             Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvsl 82 
                                        r +L+ GP+G gk+   k ++ e g++++    p +l
  gi|386002701|ref|YP_005921000.1| 481 PRGVLLFGPPGTGKTLLAKAVATESGVNFISVKGPELL 518
                                       5567899*******************999988777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.006       2.1      22      44 ..     213     235 ..     203     247 .. 0.86
   2 ?    7.2   0.0      0.01       3.7      21      39 ..     484     502 ..     471     508 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.006
                            AAA_30  22 vltGpAGtGKttalkalreawea 44 
                                       +l Gp+GtGKt + +a++   ea
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASETEA 235
                                       678************99876665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.01
                            AAA_30  21 avltGpAGtGKttalkalr 39 
                                       ++l Gp+GtGKt + ka++
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVA 502
                                       6789*********999986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0058       2.1      12      34 ..     211     233 ..     206     269 .. 0.79
   2 ?    7.3   0.1     0.015       5.5      12      30 ..     483     501 ..     476     518 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0058
                            AAA_19  12 vllvtaGpGtGKTrvlkhivall 34 
                                        ll+ ++pGtGKT + +++ ++ 
  gi|386002701|ref|YP_005921000.1| 211 GLLLFGPPGTGKTLIARAVASET 233
                                       5799*********9988776655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.015
                            AAA_19  12 vllvtaGpGtGKTrvlkhi 30 
                                        +l+ ++pGtGKT + k++
  gi|386002701|ref|YP_005921000.1| 483 GVLLFGPPGTGKTLLAKAV 501
                                       5899*********877665 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0059       2.1      24      81 ..     212     280 ..     206     288 .. 0.62
   2 ?    7.0   0.0     0.017         6      24      47 ..     484     507 ..     479     562 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0059
                                       EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp.........ldlleqa...kggtLylkdiadl 81 
                                       ++l G++G+gk+l+Ar+ +++ + + ++i   e  +             +++e+a    + + ++ +i+++
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANfISISGPEITS--KfygesekrlREIFEEAersAPSIVFIDEIDSI 280
                                       89***************9987765312232222222..122333334455555543336777777777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l A++ + +sg 
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGV 507
                                       9****************9988775 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.027       9.8       8      56 ..     218     267 ..     214     316 .. 0.77
   2 !    9.2   0.0    0.0033       1.2       8      64 ..     490     545 ..     486     589 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.027
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde..rsrl 56 
                                        G+g++ i++a+A + + +f++   +e ++k  g se+ + e ++e  r  +
  gi|386002701|ref|YP_005921000.1| 218 PGTGKTLIARAVASETEANFISISGPEITSKFYGESEKRLrEIFEEaeR--S 267
                                       59*************************************9777777432..2 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0033
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevdersrlssflskll 64 
                                        G+g++ +++a+A++ g++f++ + +e ++k  g se  v+ev  +++ +++ s ++
  gi|386002701|ref|YP_005921000.1| 490 PGTGKTLLAKAVATESGVNFISVKGPELLSKWVGESERAVREVFRKAK-QAAPSLIF 545
                                       59***********************************99966555333.33333333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.016       5.9      54     115 ..     210     276 ..     203     324 .. 0.67
   2 !    8.0   0.0     0.004       1.4      22      77 ..     441     505 ..     422     544 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDD 115
                                       + +LL+G  GtGK  + +a+ +e++++ + +   e++ +   e +k ++++    er+   i+f+D 
  gi|386002701|ref|YP_005921000.1| 210 QGLLLFGPPGTGKTLIARAVASETEANFISISgpEITSKFYGESEKRLREIFeeaERSAPSIVFIDE 276
                                       678*******************999988665323555544433333333332111333445666665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
                            DUF815  22 vdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallney 77 
                                       v ev++ ++ g+d+ ke+lve +e  l+          +p + vLL+G  GtGK  l ka+ +e 
  gi|386002701|ref|YP_005921000.1| 441 VAEVHWYEVGGLDRAKEDLVEAVEWPLKYpeafdsigiRPPRGVLLFGPPGTGKTLLAKAVATES 505
                                       5566666777777777777777664444300011111145577*****************98764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.062        22       4      23 ..     213     232 ..     210     237 .. 0.87
   2 ?   -1.0   0.0       4.2   1.5e+03      64     128 ..     252     318 ..     246     333 .. 0.66
   3 !    7.9   0.1    0.0077       2.7       3      23 ..     484     504 ..     482     508 .. 0.89
   4 ?   -1.9   0.0       7.5   2.7e+03      57     109 ..     517     573 ..     515     596 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.062
                                       EEEC-TTTCHHHHHHHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqklala 23 
                                       +l G++G GKT  ++ +a++
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASE 232
                                       788************99987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.2
                                       S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEE CS
                             NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvr 128
                                       e++++ +e++++  + + ++++ +D +D ++ + ++   + +++v   L +l+ +   ++  ++++++
  gi|386002701|ref|YP_005921000.1| 252 ESEKRLREIFEEAERSAPSIVF-IDEIDSIAPKREEvagDLERRVVAQLLSLMDGLAYRGEVIVIAAT 318
                                       5666677766666666666666.599999998887788844455555555787776666655555443 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0077
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT L++ +a++
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATE 504
                                       7899************99975 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 7.5
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............H CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlL 109
                                       ll +   e++++v+ev+   ++++   L+ +D +D +v   g      ++++ v + L
  gi|386002701|ref|YP_005921000.1| 517 LLSKWVGESERAVREVFRK-AKQAAPSLIFFDEVDAVVPARGSgldshATERVVSQFL 573
                                       5556666777778885544.56777778889999998887777655554444444444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0037       1.3       7      44 ..     215     245 ..     210     291 .. 0.68
   2 ?    6.3   0.0     0.014         5       6      25 ..     486     505 ..     482     540 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                           DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                        G +GtGKt+++ +++ e        +a+++s ++p++
  gi|386002701|ref|YP_005921000.1| 215 FGPPGTGKTLIARAVASET-------EANFISISGPEI 245
                                       599*********9999998.......555555555554 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                         G +GtGKt+++ ++++e 
  gi|386002701|ref|YP_005921000.1| 486 LFGPPGTGKTLLAKAVATES 505
                                       5699*********9999886 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.012       4.4     117     136 ..     212     231 ..     206     235 .. 0.88
   2 !    7.8   0.0    0.0044       1.6     117     136 ..     484     503 ..     478     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       ++++Gp+ tGkt +a+a a 
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVAS 231
                                       5799************9986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0044
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v+++Gp+ tGkt la+a a+
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVAT 503
                                       7899*************997 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.014       5.1       5      32 ..     213     240 ..     210     245 .. 0.92
   2 !    7.4   0.0    0.0071       2.6       5      32 ..     485     512 ..     482     534 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l+fG+ +tGKt  a ++a et a  i++
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASETEANFISI 240
                                       89*******************9998875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0071
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l+fG+ +tGKt  a ++a e g+  i++
  gi|386002701|ref|YP_005921000.1| 485 LLFGPPGTGKTLLAKAVATESGVNFISV 512
                                       89********************999875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.012       4.4      21      41 ..     213     233 ..     199     271 .. 0.79
   2 ?    6.3   0.0      0.02       7.1      20      37 ..     484     501 ..     472     542 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                            AAA_11  21 liqGPPGtgKTktivellsql 41 
                                       l+ GPPGtgKT    ++ s+ 
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASET 233
                                       788********8877777665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                            AAA_11  20 tliqGPPGtgKTktivel 37 
                                       +l+ GPPGtgKT    ++
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAV 501
                                       5889********554444 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.011       3.8       5      28 ..     216     239 ..     213     245 .. 0.92
   2 ?    5.7   0.0     0.029        11       5      28 ..     488     511 ..     484     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                                       -STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                       GP g+GK  +ara+a++ ++++++
  gi|386002701|ref|YP_005921000.1| 216 GPPGTGKTLIARAVASETEANFIS 239
                                       9******************99986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                                       -STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                       GP g+GK  +a+a+a++ g+++++
  gi|386002701|ref|YP_005921000.1| 488 GPPGTGKTLLAKAVATESGVNFIS 511
                                       9*****************999986 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.006       2.2      37     175 ..     212     352 ..     207     378 .. 0.74
   2 ?    2.8   0.0      0.26        92      37      58 ..     484     505 ..     479     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.006
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       l+++g+ G Gkt + +a++ e+++n+     + +++ e ++++    +++  e f e  r++  ++ iD+i  +a k
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANF-----ISISGPEITSKFYGESEKRLREIFEEAERSApSIVFIDEIDSIAPK 283
                                       89**********99999998887766.....568899999999999999999999999996527899******9988 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlail 175
                                                 ++  +l+ +++ l   g+ +v+++   P++l+    r   rf++ + + i  pd++ rl+il
  gi|386002701|ref|YP_005921000.1| 284 ReevagdlerRVVAQLLSLMDGLAYRGEVIVIAATNRPNSLDPAI-RRGGRFDREMEIGI--PDKNGRLEIL 352
                                       522222111134456777778888889999999999998887654.33567777655544..6777777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.26
                                       EEEE-SSSSSHHHHHHHHHHHH CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignev 58 
                                       ++++g+ G Gkt L ka++ e 
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATES 505
                                       799***************9875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.055        20       3      32 ..     213     242 ..     211     258 .. 0.83
   2 ?   -1.2   0.0       4.7   1.7e+03      82     105 ..     254     278 ..     247     296 .. 0.73
   3 ?    5.1   0.0     0.055        20       2      26 ..     484     508 ..     483     549 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.055
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       ++ GppG+GKt + + v+++ + + ++++G
  gi|386002701|ref|YP_005921000.1| 213 LLFGPPGTGKTLIARAVASETEANFISISG 242
                                       677************999999887777777 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHH.HHH-EEEE---S CS
                          NTPase_1  82 eelalealrkal.seadviviDEiG 105
                                       e+   e++++a  s + ++ iDEi 
  gi|386002701|ref|YP_005921000.1| 254 EKRLREIFEEAErSAPSIVFIDEID 278
                                       555566677776466779*****95 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.055
                                       EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                       v++ GppG+GKt l k v+ +   +
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATESGVN 508
                                       6788********9999998776444 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.032        11       1      23 [.     218     240 ..     218     268 .. 0.72
   2 ?    5.7   0.0     0.041        15       1      23 [.     490     512 ..     490     540 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.032
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ +++++A + + +fi +
  gi|386002701|ref|YP_005921000.1| 218 PGTGKTLIARAVASETEANFISI 240
                                       69******************976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.041
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A + g++fi +
  gi|386002701|ref|YP_005921000.1| 490 PGTGKTLLAKAVATESGVNFISV 512
                                       69******************965 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.025         9      23      43 ..     212     232 ..     199     246 .. 0.84
   2 ?    4.9   0.0     0.034        12      23      43 ..     484     504 ..     480     510 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       + l G +G GKt +a+ + ++
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASE 232
                                       6789************99988 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l G +G GKt lak +  +
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATE 504
                                       6689************99876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.021       7.7      35      59 ..     209     233 ..     191     242 .. 0.83
   2 ?    3.1   0.0      0.15        55      35      56 ..     481     502 ..     454     509 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                              TniB  35 mpnlllvGdsnnGKtmivekFarlh 59 
                                       ++ lll+G++ +GKt i++  a++ 
  gi|386002701|ref|YP_005921000.1| 209 PQGLLLFGPPGTGKTLIARAVASET 233
                                       5899*************99877665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                              TniB  35 mpnlllvGdsnnGKtmivekFa 56 
                                       ++ +ll+G++ +GKt +++  a
  gi|386002701|ref|YP_005921000.1| 481 PRGVLLFGPPGTGKTLLAKAVA 502
                                       3689***********9998655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.084        30      22      51 ..     211     239 ..     199     317 .. 0.56
   2 ?    3.7   0.0      0.14        51      23      43 ..     484     504 ..     479     513 .. 0.85
   3 ?   -1.7   0.0       6.4   2.3e+03     103     131 ..     526     553 ..     503     562 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.084
                          ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyv 51 
                                        ++++Gp g GKt + + ++++ e  ++  
  gi|386002701|ref|YP_005921000.1| 211 GLLLFGPPGTGKTLIARAVASETEA-NFIS 239
                                       5789999999999888887777643.4433 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                          ATPase_2  23 yfiYGpegsGKtaLlkeiien 43 
                                       ++++Gp g GKt L k ++++
  gi|386002701|ref|YP_005921000.1| 484 VLLFGPPGTGKTLLAKAVATE 504
                                       689***********9998876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.4
                          ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqkli 131
                                       ++a+    +++ +k+k+     i++De+  ++
  gi|386002701|ref|YP_005921000.1| 526 ERAV----REVFRKAKQaapSLIFFDEVDAVV 553
                                       4444....44555555555478999**98765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.9   1.4e+03      77     107 ..     134     164 ..     124     171 .. 0.81
   2 ?    4.2   0.0     0.071        26       6      49 ..     212     255 ..     209     261 .. 0.76
   3 ?    3.5   0.0      0.12        42       5      27 ..     483     505 ..     480     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.9
                                       EEEEEEEETTS-HHHHHHHHHHHHHHHHHHH CS
                             SRPRB  77 kglvfvvDStidpkevkevAEllyeillite 107
                                        +l fvv St+ +  v   AE  ++il +t 
  gi|386002701|ref|YP_005921000.1| 134 SALGFVVVSTAPKGPVVVAAETEIKILKDTL 164
                                       57789******9999**9***9999999886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.071
                                       EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGT CS
                             SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgs 49 
                                       +ll G+  +GKT++   +   +++   +S+  ++++ k+ +e ++
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVA-SETEANFISIsGPEITSKFYGESEK 255
                                       7999********8866655.5567778888899999998655554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                                       EEEEE-STTSSHHHHHHHHHHSS CS
                             SRPRB   5 avllvGlsdsGKTslftrLttds 27 
                                        vll G+  +GKT+l + + t+s
  gi|386002701|ref|YP_005921000.1| 483 GVLLFGPPGTGKTLLAKAVATES 505
                                       599************98888775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.13        45      21      38 ..     209     225 ..     201     231 .. 0.78
   2 ?    5.2   0.0     0.049        18      21      42 ..     481     501 ..     471     503 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                            AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                       ++g  ll Gp G+GK+ +
  gi|386002701|ref|YP_005921000.1| 209 PQG-LLLFGPPGTGKTLI 225
                                       355.9**********755 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.049
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       ++g +ll Gp G+GK+ l  A+
  gi|386002701|ref|YP_005921000.1| 481 PRG-VLLFGPPGTGKTLLAKAV 501
                                       356.9**********8776555 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.072        26       5      39 ..     212     247 ..     209     254 .. 0.87
   2 ?    0.0   0.0       1.6   5.8e+02      74      95 ..     245     266 ..     242     284 .. 0.79
   3 ?    2.6   0.0      0.27        96       3      30 ..     482     509 ..     480     514 .. 0.85
   4 ?   -2.0   0.0       6.9   2.5e+03      78      96 ..     521     539 ..     516     543 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.072
                                       EEEESTTTSSHHHHHHHHHHHSTTTE.EE--EEESS CS
                     Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekf.gvsvshtTr 39 
                                       + l gp g+Gk  +  a+ se + +f ++s +++T 
  gi|386002701|ref|YP_005921000.1| 212 LLLFGPPGTGKTLIARAVASETEANFiSISGPEITS 247
                                       6899**********************5588888875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.6
                                       ETTEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  74 fsgnlygtsveaieevlekgki 95 
                                        +++ yg+s +  +e++e++  
  gi|386002701|ref|YP_005921000.1| 245 ITSKFYGESEKRLREIFEEAER 266
                                       57899************99865 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.27
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r v l gp g+Gk  l ka+ +e   +f
  gi|386002701|ref|YP_005921000.1| 482 RGVLLFGPPGTGKTLLAKAVATESGVNF 509
                                       6789***************988877666 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6.9
                                       EEEEEHHHHHHHHHTTSEE CS
                     Guanylate_kin  78 lygtsveaieevlekgkiv 96 
                                         g+s  a++ev+ k+k++
  gi|386002701|ref|YP_005921000.1| 521 WVGESERAVREVFRKAKQA 539
                                       6799***********9986 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.56     2e+02       4      71 ..     215     277 ..     212     282 .. 0.66
   2 ?    7.2   0.0     0.011       3.8       4      71 ..     487     549 ..     484     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.56
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ + r ++++   ++ +++   e+ ++   +++++  + +++++ ++       i+++DE+
  gi|386002701|ref|YP_005921000.1| 215 FGPPGTGKTLIARAVASETeANFISISG-PEITSKFYGESEKRLREIFEEAERSAP-----SIVFIDEI 277
                                       588*******999999986755555554.444444446666666666665555543.....48888886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++ +s +++ +++   ell++++ ++++   + ++++ +a+ +     ++++DE 
  gi|386002701|ref|YP_005921000.1| 487 FGPPGTGKTLLAKAVATESgVNFISVKG-PELLSKWVGESERAVREVFRKAKQAA-P----SLIFFDEV 549
                                       588*************999*88877777.9******9776666555555555544.3....38888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 4418.78
//
Query:       gi|386002702|ref|YP_005921001.1|  [L=230]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-13   49.4   6.9      2e-11   43.8   0.0    2.8  3  HTH_20          Helix-turn-helix domain
    6.9e-11   41.8   0.0    4.2e-08   32.9   0.0    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
    2.7e-07   30.4   5.8    0.00039   20.2   0.0    3.4  4  MarR_2          MarR family
    3.9e-07   29.9   0.0     0.0012   18.6   0.0    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
    2.4e-06   27.0   2.9     0.0075   15.8   0.0    3.9  4  HTH_24          Winged helix-turn-helix DNA-binding
    7.7e-06   25.9   5.4      0.003   17.6   0.0    2.8  2  DprA_WH         DprA winged helix domain
    0.00026   20.7   0.1      0.016   15.0   0.0    2.5  2  LexA_DNA_bind   LexA DNA binding domain
    0.00028   21.2   0.0        1.2    9.5   0.0    2.5  2  Rrf2            Transcriptional regulator
     0.0026   18.2   1.2       0.87   10.1   0.0    3.3  3  HTH_27          Winged helix DNA-binding domain
     0.0054   16.5   0.8       0.53   10.1   0.2    2.8  2  HTH_IclR        IclR helix-turn-helix domain
     0.0059   16.6   1.0          1    9.4   0.0    2.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0065   16.1   0.0        1.2    8.7   0.0    2.7  3  DDRGK           DDRGK domain
  ------ inclusion threshold ------
      0.023   14.6   0.1       0.18   11.8   0.0    2.3  2  MarR            MarR family
      0.024   14.7   0.1       0.72   10.0   0.0    2.7  3  DUF2250         Uncharacterized protein conserved in archaea 
      0.028   14.1   0.2       0.83    9.3   0.3    2.6  2  GntR            Bacterial regulatory proteins, gntR family
      0.077   13.0   0.0       0.32   11.0   0.0    2.1  1  PadR            Transcriptional regulator PadR-like family
        0.1   12.8   0.0         20    5.5   0.0    2.4  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.11   12.3   0.0        9.7    6.1   0.0    2.5  2  HTH_10          HTH DNA binding domain
       0.16   12.0   0.0         11    6.2   0.0    2.4  2  FeoC            FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   2.1e-14     2e-11       2      58 ..       5      60 ..       4      63 .. 0.96
   2 ?   -2.6   0.4       6.6   6.2e+03      44      52 ..     138     146 ..     137     160 .. 0.69
   3 !    9.4   0.2    0.0011         1      10      61 .]     178     228 ..     169     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.1e-14
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +i+++L+++ Rrril++L + +++ ++e a+rldl ++ + +HL+ Le+agL+e  r
  gi|386002702|ref|YP_005921001.1|  5 EILDILGNENRRRILQLL-SCRPFYFNEMAKRLDLGPKAVIDHLEMLERAGLIECYR 60
                                      799***************.***********************************877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                                       HHHHHHHCT CS
                            HTH_20  44 HLrvLeeag 52 
                                       +Lr+Lee  
  gi|386002702|ref|YP_005921001.1| 138 RLRELEEER 146
                                       577777644 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       ++ ++il aL   +    ++la+rl+++ + +  +Lr L+  g v  ++e++
  gi|386002702|ref|YP_005921001.1| 178 EMEAEILTAL-LSGDSGSEALAARLGIPAAVVEERLRGLAAQGKVQKRGERW 228
                                       5566677777.333444579********************999999998886 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 !   32.9   0.0   4.5e-11   4.2e-08       1      46 [.      12      57 ..      12      57 .. 0.97
   2 !    6.5   0.0    0.0078       7.4       6      45 ..     182     221 ..     177     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.5e-11
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++R++IL+lL+ ++ ++ e a+ l+l + +v  HL +L+ aGL+e
  gi|386002702|ref|YP_005921001.1| 12 NENRRRILQLLSCRPFYFNEMAKRLDLGPKAVIDHLEMLERAGLIE 57
                                      589*****************************************96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0078
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       +IL +L +g   +  la+ lg++ + v + L+ L  +G V
  gi|386002702|ref|YP_005921001.1| 182 EILTALLSGDSGSEALAARLGIPAAVVEERLRGLAAQGKV 221
                                       8******************************999888865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.1e-07   0.00039       7      62 .]      15      65 ..      12      65 .. 0.95
   2 ?   -0.9   0.1       1.7   1.6e+03      44      61 ..     146     164 ..     145     165 .. 0.78
   3 ?   -2.1   0.0         4   3.8e+03      47      57 ..     167     177 ..     161     180 .. 0.76
   4 !   10.8   0.5   0.00038      0.35      25      54 ..     195     224 ..     177     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.1e-07
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                       +r+L  L +rp   +  +e a+rl+l + av  +l+ L++aGL+e  ++  D+R+
  gi|386002702|ref|YP_005921001.1| 15 RRRILQLLSCRP---FYFNEMAKRLDLGPKAVIDHLEMLERAGLIECYRD--DRRR 65
                                      589*********...9******************************9999..9996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                       HHHHTTSEEEEESSS.SSS CS
                            MarR_2  44 rLvaaGLverrpgpe.DkR 61 
                                       rL  +GL+e+ +++e ++R
  gi|386002702|ref|YP_005921001.1| 146 RLRLRGLLEEIASEEmAAR 164
                                       7778999999988887776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4
                                       HTTSEEEEESS CS
                            MarR_2  47 aaGLverrpgp 57 
                                       a GL+++++++
  gi|386002702|ref|YP_005921001.1| 167 ATGLIVESASD 177
                                       67999999874 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00038
                                       HHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  25 gelarrlglsksavsrilkrLvaaGLverr 54 
                                        +la+rlg++ + v  +l+ L a+G v++r
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQKR 224
                                       689**********************98876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0017       1.6      16      62 ..      20      67 ..      18      72 .. 0.82
   2 !   18.6   0.0   1.3e-06    0.0012       8      58 ..     178     227 ..     177     230 .] 0.94

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklY 62
                                       Ll+  p   +e a++l++    v + L+ Le++Gl+e  +   +++Y
  gi|386002702|ref|YP_005921001.1| 20 QLLSCRPFYFNEMAKRLDLGPKAVIDHLEMLERAGLIECYRDDrRRKY 67
                                      588888889999*************************97764434444 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.3e-06
                                       HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       e+Ea++ +aLl +g +  + +a +lg+p + v e Lr L   G V+++ +r
  gi|386002702|ref|YP_005921001.1| 178 EMEAEILTALL-SGDSGSEALAARLGIPAAVVEERLRGLAAQGKVQKRGER 227
                                       79*********.99********************************98765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.14   1.3e+02       2      13 ..      12      23 ..      11      26 .. 0.88
   2 !   15.8   0.0     8e-06    0.0075      21      48 .]      30      57 ..      29      57 .. 0.96
   3 ?   -1.6   0.4       2.1     2e+03      37      44 ..     138     145 ..     137     147 .. 0.85
   4 !    6.8   0.0    0.0053         5      22      47 ..     196     221 ..     178     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                            HTH_24  2 detdrkILelLq 13
                                      +e++r+IL+lL 
  gi|386002702|ref|YP_005921001.1| 12 NENRRRILQLLS 23
                                      799******995 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8e-06
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e A+rl+l p +v  +l+ Le++GlI+
  gi|386002702|ref|YP_005921001.1| 30 NEMAKRLDLGPKAVIDHLEMLERAGLIE 57
                                      699************************7 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.1
                            HTH_24  37 rlkrLeee 44 
                                       rl++Leee
  gi|386002702|ref|YP_005921001.1| 138 RLRELEEE 145
                                       99****97 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0053
                            HTH_24  22 eLAerlglSpstvnrrlkrLeeeGlI 47 
                                        LA rlg++ + v +rl+ L  +G +
  gi|386002702|ref|YP_005921001.1| 196 ALAARLGIPAAVVEERLRGLAAQGKV 221
                                       69***************988888876 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.2e-06     0.003      12      57 ..      13      58 ..       7      61 .. 0.95
   2 !    9.5   1.2    0.0011         1       8      55 ..     174     221 ..     162     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-06
                           DprA_WH 12 dlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      + +rr+L++L+  P  + + ++r+ l + +v  +L +LE aGl+e 
  gi|386002702|ref|YP_005921001.1| 13 ENRRRILQLLSCRPFYFNEMAKRLDLGPKAVIDHLEMLERAGLIEC 58
                                      679*****************************************85 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                           DprA_WH   8 pplddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlv 55 
                                        ++d+ e+ +L+aL +     ++L++r+g+paa+v   L  L  +G+v
  gi|386002702|ref|YP_005921001.1| 174 SASDEMEAEILTALLSGDSGSEALAARLGIPAAVVEERLRGLAAQGKV 221
                                       567999999**9999999999**************9888777666666 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.016      29      59 ..      30      59 ..      26      65 .. 0.89
   2 ?    3.1   0.1     0.089        84      32      57 ..     198     222 ..     194     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierd 59
                                       e+a++l l  p+av  hL+ Ler G+ie  
  gi|386002702|ref|YP_005921001.1| 30 NEMAKRLDLG-PKAVIDHLEMLERAGLIECY 59
                                      69*******9.*****************975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.089
                                       HHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind  32 aralglkSpsaveehLkaLerKGyie 57 
                                       a +lg+  ++ vee+L+ L+  G ++
  gi|386002702|ref|YP_005921001.1| 198 AARLGIP-AAVVEERLRGLAAQGKVQ 222
                                       6788888.8899*********99886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0013       1.2      26      58 ..      27      59 ..      18      60 .. 0.89
   2 !    9.1   0.0    0.0017       1.6      26      56 ..     192     222 ..     179     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksv 58
                                      +  +e+a+r ++ p+ +   l++L++agl++  
  gi|386002702|ref|YP_005921001.1| 27 FYFNEMAKRLDLGPKAVIDHLEMLERAGLIECY 59
                                      56789*************************965 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  26 vsseeiaerqnispsylekilakLrkaglvk 56 
                                         se++a+r +i++ ++e  l+ L+ +g v+
  gi|386002702|ref|YP_005921001.1| 192 SGSEALAARLGIPAAVVEERLRGLAAQGKVQ 222
                                       4799************************987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00092      0.87      25      64 ..      33      70 ..      30      73 .. 0.82
   2 ?    0.7   0.1      0.83   7.8e+02      38      54 ..     138     159 ..     125     180 .. 0.68
   3 ?    4.5   0.0     0.054        51       5      52 ..     180     225 ..     176     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00092
                            HTH_27 25 cgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                      ++rl+++  +++  l+ L+++GL+e   ++ drr+k +r+
  gi|386002702|ref|YP_005921001.1| 33 AKRLDLGPKAVIDHLEMLERAGLIEC--YRDDRRRKYFRI 70
                                      678999999999************54..555699999997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.83
                            HTH_27  38 slkkLtek.....GLvertgde 54 
                                        l++L+e      GL+e+ ++e
  gi|386002702|ref|YP_005921001.1| 138 RLRELEEErlrlrGLLEEIASE 159
                                       4555555544444777666665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.054
                            HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                       +a +L  +    + +  ++l+ rl + ++ + + l+ L ++G v++ g
  gi|386002702|ref|YP_005921001.1| 180 EAEILTALL--SGDSGSEALAARLGIPAAVVEERLRGLAAQGKVQKRG 225
                                       666666666..55566689***********************997665 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 ?    4.0   0.0     0.046        44       7      49 ..       5      57 ..       4      58 .. 0.80
   2 !   10.1   0.2   0.00057      0.53       7      51 ..     182     224 ..     181     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.046
                                      HHHCT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iLd+l+ ++++            + e+A+r++l + +v  +L  L++ G++e
  gi|386002702|ref|YP_005921001.1|  5 EILDILGNENRRrilqllscrpFYFNEMAKRLDLGPKAVIDHLEMLERAGLIE 57
                                      57777777777777777776665689999999999999999999999999986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00057
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       +iL al +++ +     lA+r+g+p + v   L+ L  +G v++ 
  gi|386002702|ref|YP_005921001.1| 182 EILTALLSGDSG--SEALAARLGIPAAVVEERLRGLAAQGKVQKR 224
                                       688888888886..899***********************98875 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 !    9.4   0.0    0.0011         1      25      54 ..      30      63 ..       8      75 .. 0.82
   2 ?    5.1   0.1     0.023        22      25      58 ..     195     229 ..     164     230 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE..E..T CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis..r..g 54
                                       e+A +l l +  v   l  L+r+gli+  r  +
  gi|386002702|ref|YP_005921001.1| 30 NEMAKRLDLGPKAVIDHLEMLERAGLIEcyRddR 63
                                      69**************************864332 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                                       HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEE CS
                         HTH_Crp_2  25 eelAsmlGltretvsrilseLkreglis.rgrrir 58 
                                       e lA++lG+    v   l+ L  +g ++ rg r +
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQkRGERWT 229
                                       78**************************5553355 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0013       1.2     117     158 ..      30      72 ..      25      84 .. 0.85
   2 ?   -0.9   0.1       1.1   1.1e+03     133     149 ..     138     155 ..     131     185 .. 0.56
   3 ?    3.8   0.0      0.04        38     117     144 ..     195     222 ..     193     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                                       HHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT-.-EEE--- CS
                             DDRGK 117 eelavkfklktqevierikeLeeqgsltGvlDdrG.kyiyitd 158
                                       +e+a +++l  + vi+ ++ Le  g ++   Ddr  ky  i +
  gi|386002702|ref|YP_005921001.1|  30 NEMAKRLDLGPKAVIDHLEMLERAGLIECYRDDRRrKYFRIAE 72 
                                       79*****************************997426766665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHS.SS-EEE-T CS
                             DDRGK 133 rikeLeeqg.sltGvlDd 149
                                       r++eLee+  +l G+l +
  gi|386002702|ref|YP_005921001.1| 138 RLRELEEERlRLRGLLEE 155
                                       555554443234444433 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.04
                                       HHHHHHH-S-HHHHHHHHHHHHHHSSS- CS
                             DDRGK 117 eelavkfklktqevierikeLeeqgslt 144
                                       e la+++++ + +v er++ L +qg+++
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQ 222
                                       679**********************985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.18      17      57 ..      26      64 ..      12      66 .. 0.83
   2 ?   -0.2   0.0         1   9.7e+02      21      48 ..     195     222 ..     189     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      p +  e+ak+l + + +v   l  Le++Glie +++  DrR
  gi|386002702|ref|YP_005921001.1| 26 PFYFNEMAKRLDLGPKAVIDHLEMLERAGLIECYRD--DRR 64
                                      456789***************************999..777 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  21 seLakklgvskstvtrvldrLekkGlie 48 
                                         La +lg+  + v + l+ L  +G ++
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQ 222
                                       579*******999999999999998776 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 ?   10.0   0.0   0.00076      0.72      20      56 ..      24      60 ..       9      69 .. 0.84
   2 ?   -1.1   0.1       2.2   2.1e+03      44      58 ..     145     159 ..     131     165 .. 0.74
   3 ?    1.2   0.0      0.43     4e+02      26      54 ..     195     223 ..     173     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                           DUF2250 20 anvdYaksiakeleipleevrellkkLeelGLlerve 56
                                        + Y   +ak+l++  + v + l+ Le++GL+e + 
  gi|386002702|ref|YP_005921001.1| 24 CRPFYFNEMAKRLDLGPKAVIDHLEMLERAGLIECYR 60
                                      55668899*************************9875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                           DUF2250  44 kkLeelGLlervegk 58 
                                       ++L+  GLle+  ++
  gi|386002702|ref|YP_005921001.1| 145 ERLRLRGLLEEIASE 159
                                       467778999997765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.43
                           DUF2250  26 ksiakeleipleevrellkkLeelGLler 54 
                                         +a +l ip   v+e l+ L   G +++
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQK 223
                                       5678999***************9998887 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.24   2.3e+02      28      55 ..      30      57 ..      29      62 .. 0.84
   2 ?    9.3   0.3   0.00088      0.83      28      58 ..     195     225 ..     172     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglve 55
                                      +e a++++ +   v   L +Le++gl+e
  gi|386002702|ref|YP_005921001.1| 30 NEMAKRLDLGPKAVIDHLEMLERAGLIE 57
                                      577888888888888889********98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00088
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR  28 reLaaefgVsrttvReALrrLeaeglverrq 58 
                                       ++Laa++g+ + +v e Lr L+a+g v+ r 
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQKRG 225
                                       68*************************9775 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.32      36      67 ..      45      72 ..      18      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTd 67
                                      + L+ Le+ gl+e ++++    ++rky+r+++
  gi|386002702|ref|YP_005921001.1| 45 DHLEMLERAGLIECYRDD----RRRKYFRIAE 72
                                      57999**********887....7******987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.031        30      27      53 ..      31      57 ..      19      63 .. 0.91
   2 ?    5.5   0.0     0.021        20      26      53 ..     195     222 ..     183     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.031
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyve 53
                                      ++a+rL+  p  V   l+ Le++G++e
  gi|386002702|ref|YP_005921001.1| 31 EMAKRLDLGPKAVIDHLEMLERAGLIE 57
                                      78***********************97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  26 kdlaerLnvspssVsemlkkLekdGyve 53 
                                         la rL++ ++ V e l+ L+ +G v+
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQ 222
                                       579*********************9776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.066        62      27      48 ..      30      51 ..      25      53 .. 0.87
   2 ?    6.1   0.0      0.01       9.7      26      45 ..     194     213 ..     191     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.066
                            HTH_10 27 keLAkelGIskstlsehLrkae 48
                                      +e+Ak+l++ + ++ +hL+  e
  gi|386002702|ref|YP_005921001.1| 30 NEMAKRLDLGPKAVIDHLEMLE 51
                                      79****************8655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                            HTH_10  26 lkeLAkelGIskstlsehLr 45 
                                       +++LA +lGI ++ ++e+Lr
  gi|386002702|ref|YP_005921001.1| 194 SEALAARLGIPAAVVEERLR 213
                                       689****************9 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.011        11      17      47 ..      29      59 ..      23      65 .. 0.91
   2 ?    3.2   0.0     0.099        94      18      47 ..     195     224 ..     188     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                              FeoC 17 lkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      ++e++++++  p+a+ + Le+++r G +e+ 
  gi|386002702|ref|YP_005921001.1| 29 FNEMAKRLDLGPKAVIDHLEMLERAGLIECY 59
                                      89************************99875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.099
                              FeoC  18 keLsrhfkaspealeamLeqwvrkGrvekv 47 
                                       + L+ ++ + ++ +e  L  + + G+v+k+
  gi|386002702|ref|YP_005921001.1| 195 EALAARLGIPAAVVEERLRGLAAQGKVQKR 224
                                       57999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1492.07
//
Query:       gi|386002703|ref|YP_005921002.1|  [L=437]
Description: hypothetical protein Mhar_2023 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-44  152.0   1.5    1.8e-44  151.5   1.5    1.1  1  DUF21      Cyclin M transmembrane N-terminal domain
    2.8e-23   81.7   0.4    1.3e-22   79.6   0.0    2.1  2  CorC_HlyC  Transporter associated domain
    5.5e-11   42.8   1.4    3.3e-08   33.8   0.1    2.7  3  CBS        CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   1.5     3e-48   1.8e-44       2     176 .]       7     198 ..       6     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 3e-48
                             DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvel 78 
                                       ++ ll++++++f++aE+A+vs +r+rl+elae g+ +a  +l+l ++p  +Lst++ig+tlv +l++a+++a++++ 
  gi|386002703|ref|YP_005921002.1|   7 VLTLLIIINGLFAMAEIAVVSSRRSRLQELAEGGDGGAGVALDLAEEPTAFLSTIQIGITLVGTLAGAYGGATVAKE 83 
                                       568999*******************************************************************9999 PP

                             DUF21  79 lae............galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllsklln 143
                                       la             + +++ i+++++t+ +l++gE++Pk+ al+ +e+ia+++a plr++++  +Plv+lls ++n
  gi|386002703|ref|YP_005921002.1|  84 LAGrleavpalaphsTFIGFGIVVIAITYTMLILGELVPKRAALNDPERIASIVASPLRLFSRAASPLVFLLSGSTN 160
                                       9889999******9999999********************************************************* PP

                             DUF21 144 lil.....esesepavseeelkklveeseeegvieeee 176
                                       +++     + +++p+v+eee+k l+++++ +gv+e+ e
  gi|386002703|ref|YP_005921002.1| 161 VVIralgiKPNNGPPVTEEEIKILIDLGAGAGVFEKAE 198
                                       **********************************9976 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.23   1.4e+03      10      29 ..     318     337 ..     312     343 .. 0.67
   2 !   79.6   0.0   2.2e-26   1.3e-22       2      80 ..     348     428 ..     347     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.23
                                       EETT-BHHHHHHHHTSTTHH CS
                         CorC_HlyC  10 vdGslpldeleeelglelpe 29 
                                       v+G ++l +l e++  ++p 
  gi|386002703|ref|YP_005921002.1| 318 VEGLVTLTDLLEAIVGDIPH 337
                                       67777777777776666665 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 2.2e-26
                                       EECTTEEEEETT-BHHHHHHHHTS.TTHHCT...-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEE CS
                         CorC_HlyC   2 eldegsylvdGslpldeleeelgl.elpeed...yeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkk 74 
                                       ++++gs+lvdG +++d+++e +++ ++peed   y+TlgG+ + +++riP  g+   +d++glrf+V++md +r++k
  gi|386002703|ref|YP_005921002.1| 348 QRGDGSWLVDGMISIDDFKENFDVeKMPEEDagvYQTLGGFAIMQFERIPHSGD--HFDWGGLRFEVMDMDYNRVDK 422
                                       689*********************77***9888899******************..99999**************** PP

                                       EEEEE- CS
                         CorC_HlyC  75 vrvekl 80 
                                       + +++l
  gi|386002703|ref|YP_005921002.1| 423 LLITPL 428
                                       ***985 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0   0.00099       5.9       8      53 ..     222     268 ..     213     271 .. 0.75
   2 !   33.8   0.1   5.5e-12   3.3e-08       8      56 ..     284     332 ..     273     333 .. 0.87
   3 ?   -3.9   0.1         3   1.8e+04      42      50 ..     355     364 ..     350     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00099
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllr 53 
                                       ++v +   +t   + e++  ++++ +PV   d d+ + G+v+ +Dll 
  gi|386002703|ref|YP_005921002.1| 222 EIVWLGARETPDMIKEKISGRAYTLFPVCngDLDD-VMGVVHAKDLLF 268
                                       77777777888888889944449777**9877777.**********95 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 5.5e-12
                                       SCEEEETTSBHHHHHHHHHHHTSS.EEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvs.rlPVVdedgklvGivtlrDllrall 56 
                                       ++++vp+++   ++le+++e+g++ ++ VVde g++ G+vtl+Dll+a++
  gi|386002703|ref|YP_005921002.1| 284 PPLFVPESMRGLKVLERFKETGIHlAI-VVDEFGRVEGLVTLTDLLEAIV 332
                                       678999999999******999995344.89******************97 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3
                                       EE.EEEEHHH CS
                               CBS  42 lv.GivtlrD 50 
                                       lv G+++  D
  gi|386002703|ref|YP_005921002.1| 355 LVdGMISIDD 364
                                       4559999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2893.47
//
Query:       gi|386002704|ref|YP_005921003.1|  [L=267]
Description: HtpX protease, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-38  130.4   0.0    8.9e-38  130.0   0.0    1.1  1  Peptidase_M48  Peptidase family M48
    0.00039   19.7   0.1    0.00067   18.9   0.1    1.3  1  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.078   13.2   0.1       0.19   12.0   0.1    1.7  1  DUF4157        Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0   1.5e-41   8.9e-38       2     196 .]      55     267 .]      54     267 .] 0.83

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.5e-41
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikh 77 
                                       ++++ l  +v+ l+++a++  p++kvy+v+ p  NAFa+g+  ++  ++ t+g++ + l+++el+aV++HEl+H+k+
  gi|386002704|ref|YP_005921003.1|  55 SEAPALYGIVRGLVDRAQM--PMPKVYIVDTPMPNAFATGRDPQHaAVAATTGIM-RILDKDELEAVMAHELAHVKN 128
                                       667788889999*******..*********************9999*********.********************* PP

                                       THHHHHHHHHHHHHHHHHHHH...HHHTT-SHHHHHTT--S..---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  78 rhsvvslivsllasillllgl...allisraeedaagafld..alavliglliillflalSRkrEyqADeagvellk 149
                                       r++++s + +++a ++ ++++     li   ++d+ag +++  a a+l+ +  ++ ++a+SR+rE+ AD+ g+el+ 
  gi|386002704|ref|YP_005921003.1| 129 RDTLISSVAATIAGVITFMASmaqWSLIFGGRDDDAGSIVGviAMAILAPIAAMIIQMAISRSREFGADAGGAELCG 205
                                       ******6666666666665551114566666666666665511555555667778888******************* PP

                                       .HHHHHHHHHHHHHHTT--S---HHHH...............HHS-SS--HHHHHHHHHH-X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 150 rakdlvraliklakdlerqdvsaslrs...............ellstHPplleRiqalkele 196
                                       r+ +l++al kl   + r++ +  + +                l+stHP+++eRi++l+e++
  gi|386002704|ref|YP_005921003.1| 206 RPMALASALSKLEGAAGRVQADVNPSTahmfivnplkgkklaSLFSTHPSTQERIARLSEMK 267
                                       *************99999766666555779999999999999*****************985 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.1e-07   0.00067     187     221 ..     106     140 ..      96     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-07
                     Peptidase_M56 187 flkklsdeeleyillHElaHlkrkDllvnllvavl 221
                                       +++ l+++ele +++HElaH+k++D+l+  ++a +
  gi|386002704|ref|YP_005921003.1| 106 IMRILDKDELEAVMAHELAHVKNRDTLISSVAATI 140
                                       5667899********************99887654 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.2e-05      0.19      38      74 ..      99     128 ..      86     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                           DUF4157  38 AqAfTlgndivfaageyqpesaagrellaHELtHvvq 74 
                                       A A T+g   ++       ++ + ++++aHEL+Hv  
  gi|386002704|ref|YP_005921003.1|  99 AVAATTGIMRIL-------DKDELEAVMAHELAHVKN 128
                                       555555555555.......4556689*********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1692.31
//
Query:       gi|386002705|ref|YP_005921004.1|  [L=660]
Description: Tetratricopeptide TPR_2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-143  460.9  37.6      2e-10   40.1   0.3   17.5 18  TPR_1            Tetratricopeptide repeat
   9.4e-127  403.2  56.8    5.8e-09   35.4   0.5   17.3 17  TPR_2            Tetratricopeptide repeat
   1.4e-107  343.1  14.1    6.7e-07   29.0   0.0   17.2 17  TPR_8            Tetratricopeptide repeat
   2.2e-107  350.5  47.4    4.6e-10   39.0   0.5   17.1 17  TPR_11           TPR repeat
    8.9e-93  298.2  30.1    3.9e-07   30.0   0.0   17.1 17  TPR_17           Tetratricopeptide repeat
    2.8e-79  261.5  87.6    2.9e-12   47.0   1.2   11.2 12  TPR_16           Tetratricopeptide repeat
    7.4e-63  203.8  84.6    0.00036   21.1   0.0   17.2 17  TPR_14           Tetratricopeptide repeat
      5e-62  206.2  62.7    2.6e-09   37.2   1.7   12.6 14  TPR_12           Tetratricopeptide repeat
    1.7e-52  175.5  62.2    1.8e-08   34.4   3.1   10.8 13  TPR_9            Tetratricopeptide repeat
    7.4e-51  170.5  49.4    9.1e-09   35.7   0.1   10.7 11  TPR_19           Tetratricopeptide repeat
    5.5e-41  135.6  44.2     0.0048   16.8   0.0   16.9 17  TPR_7            Tetratricopeptide repeat
    6.3e-29   98.7  24.2       0.11   13.1   0.1   16.3 16  TPR_6            Tetratricopeptide repeat
    1.7e-22   78.6  78.0      0.035   14.0   0.4   16.7 17  TPR_10           Tetratricopeptide repeat
    3.7e-22   78.4   4.8     0.0046   17.1   0.0    7.2  7  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    5.3e-20   72.3  42.9     0.0053   17.2   2.2    8.8  9  BTAD             Bacterial transcriptional activator domain
    2.4e-15   56.8  21.0      0.057   13.5   0.1   10.8 10  DUF3856          Domain of Unknown Function (DUF3856)
    4.1e-12   45.8   1.7       0.76    8.6   0.1    8.2  9  NARP1            NMDA receptor-regulated protein 1
    5.5e-12   45.5  29.6    0.00084   18.6   0.7    7.5  8  TPR_15           Tetratricopeptide repeat
      1e-10   41.4   0.2        1.5    8.0   0.0    8.5  8  FAT              FAT domain
    1.9e-09   37.2  93.6       0.86   10.4   0.0   16.9 16  TPR_4            Tetratricopeptide repeat
    3.7e-06   26.6   0.7        2.8    7.3   0.1    5.8  6  Coatomer_E       Coatomer epsilon subunit
    1.6e-05   24.7   8.6        7.9    6.6   0.0    7.7  6  TPR_3            Tetratricopeptide repeat
    6.7e-05   22.7  26.7       0.13   12.0   0.1    9.1 11  TPR_21           Tetratricopeptide repeat-like domain
    0.00016   21.5   0.2       0.18   11.6   0.0    4.6  4  Imm31            Immunity protein 31
    0.00022   21.2  17.4        2.8    8.1   0.1    8.6  9  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
      0.003   17.8  15.8      0.041   14.1   1.1    6.8  5  TPR_5            Tetratrico peptide repeat
     0.0047   16.6   2.3         22    4.7   0.0    6.3  9  RPN7             26S proteasome subunit RPN7
     0.0076   15.9   0.9        1.8    8.4   0.0    5.0  3  PPTA             Protein prenyltransferase alpha subunit repe
  ------ inclusion threshold ------
      0.012   15.9  17.8        1.7    9.0   0.0    7.7 10  TPR_20           Tetratricopeptide repeat
      0.013   15.9   0.0         41    4.5   0.0    4.2  6  TruB_N           TruB family pseudouridylate synthase (N term
      0.013   14.6   0.0       0.41    9.7   0.0    2.9  3  Rota_NSP3        Rotavirus non-structural protein NSP3
      0.014   14.9   0.1        3.4    7.0   0.0    3.2  4  EST1_DNA_bind    Est1 DNA/RNA binding domain
      0.015   15.1   3.3         94    2.8   0.0    6.6  8  DUF5113          Domain of unknown function (DUF5113)
       0.13   12.4  30.3         20    5.3   0.1   11.3 12  MIT              MIT (microtubule interacting and transport) 
        1.4    9.4   6.6    2.3e+02    2.2   0.0    5.4  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
        5.4    6.3  10.8        2.1    7.7   0.1    5.1  5  SNAP             Soluble NSF attachment protein, SNAP
        6.6    6.3  12.0         12    5.5   0.1    6.3  7  SHNi-TPR         SHNi-TPR
        6.6    7.3  12.5         21    5.7   0.3    4.9  3  HEAT_EZ          HEAT-like repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.011       5.1      11      33 ..      75      97 ..      65      98 .. 0.92
   2 !   11.1   0.0   0.00058      0.27      16      34 .]     115     133 ..      99     133 .. 0.84
   3 !   32.2   0.0   1.3e-10   6.1e-08       3      34 .]     136     167 ..     135     167 .. 0.97
   4 !   31.7   0.0   1.8e-10   8.7e-08       2      33 ..     169     200 ..     168     201 .. 0.96
   5 !   32.4   0.3   1.1e-10   5.1e-08       1      32 [.     202     233 ..     202     235 .. 0.95
   6 ?   -0.8   0.1       3.3   1.6e+03       4      21 ..     239     256 ..     238     257 .. 0.83
   7 !   26.3   0.0   9.5e-09   4.5e-06       3      34 .]     272     303 ..     271     303 .. 0.96
   8 !   34.9   0.0   1.7e-11   8.2e-09       3      34 .]     306     337 ..     305     337 .. 0.97
   9 !   37.3   0.2   3.1e-12   1.4e-09       1      32 [.     338     369 ..     338     371 .. 0.95
  10 !   38.1   0.5   1.7e-12     8e-10       1      34 []     372     405 ..     372     405 .. 0.96
  11 !   26.5   0.0   7.7e-09   3.6e-06       3      33 ..     408     438 ..     407     439 .. 0.97
  12 !   36.5   0.0   5.5e-12   2.6e-09       1      32 [.     440     471 ..     440     473 .. 0.97
  13 !   27.1   0.1     5e-09   2.4e-06       1      34 []     474     507 ..     474     507 .. 0.97
  14 !   27.8   0.0     3e-09   1.4e-06       4      33 ..     511     540 ..     509     541 .. 0.96
  15 !   29.7   0.0   7.7e-10   3.6e-07       1      30 [.     542     571 ..     542     572 .. 0.96
  16 !   32.4   0.0   1.1e-10   5.1e-08       1      32 [.     576     607 ..     576     609 .. 0.96
  17 !   40.1   0.3   4.1e-13     2e-10       1      33 [.     610     642 ..     610     643 .. 0.95
  18 ?   -1.6   0.1       6.1   2.9e+03       1      14 [.     644     657 ..     644     658 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                                      HHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1 11 yfklgkydeAleyyekALelnPn 33
                                      y++ g  d Al   ++ L l+P+
  gi|386002705|ref|YP_005921004.1| 75 YRQEGAIDLALSSLDRSLALDPD 97
                                      9999******************8 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00058
                                       -HHHHHHHHHHHHHHSTTH CS
                             TPR_1  16 kydeAleyyekALelnPnn 34 
                                       + + A+e++e+AL ++P++
  gi|386002705|ref|YP_005921004.1| 115 DREMAVEAFERALGIDPED 133
                                       6699*************86 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 1.3e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++y lGna+  lg+ deAl++y++ L+++P+n
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQAYNRSLTIDPEN 167
                                       7*****************************97 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       ka++n+G+++  lg+y+eA   +e+A++ +P+
  gi|386002705|ref|YP_005921004.1| 169 KAWNNRGLILGALGRYEEAASSFERAISSDPD 200
                                       7***************************9998 PP

  == domain 5  score: 32.4 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a a+ n+Gna++ lg+++eAle+y  AL ++ 
  gi|386002705|ref|YP_005921004.1| 202 AAAWQNRGNALRALGRPEEALECYASALAIDS 233
                                       78***************************995 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHTT-HHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAl 21 
                                       +++ + +++ lg+ +eAl
  gi|386002705|ref|YP_005921004.1| 239 WKGAAELLRALGRDEEAL 256
                                       666688999********8 PP

  == domain 7  score: 26.3 bits;  conditional E-value: 9.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a++ +G+++  lg+y+eA+e ++ AL+ +P +
  gi|386002705|ref|YP_005921004.1| 272 AWNDRGLILGVLGRYEEAVESFDAALRADPGY 303
                                       9****************************975 PP

  == domain 8  score: 34.9 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a++n+G+a+ +lg+ +eAle y++ + ++P++
  gi|386002705|ref|YP_005921004.1| 306 AWNNRGLALANLGRSEEALESYNRSIDIDPSF 337
                                       9*****************************96 PP

  == domain 9  score: 37.3 bits;  conditional E-value: 3.1e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a a+yn+G a+f l++ydeA+e+y+ ALe++P
  gi|386002705|ref|YP_005921004.1| 338 ALAWYNRGRALFDLERYDEAVEAYDSALEVEP 369
                                       68****************************99 PP

  == domain 10  score: 38.1 bits;  conditional E-value: 1.7e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a a++n+G+a+  lg+ +eAle y++ALe++P +
  gi|386002705|ref|YP_005921004.1| 372 ALAWNNRGAALAALGREEEALESYDRALEIDPGY 405
                                       68******************************76 PP

  == domain 11  score: 26.5 bits;  conditional E-value: 7.7e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+yn+G +++  g+y +A++++++A++ nP+
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDEAIRFNPT 438
                                       9*****************************7 PP

  == domain 12  score: 36.5 bits;  conditional E-value: 5.5e-12
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+a+  +G+a++++ ++ eAl +yekALel+P
  gi|386002705|ref|YP_005921004.1| 440 ADAWHSKGHALYQMRRPGEALVCYEKALELDP 471
                                       89****************************** PP

  == domain 13  score: 27.1 bits;  conditional E-value: 5e-09
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a+++  +G+a+  l++  eA e++++ALel+P++
  gi|386002705|ref|YP_005921004.1| 474 AETWHHRGVALADLNRAAEAAEAFDRALELDPEY 507
                                       799*****************************86 PP

  == domain 14  score: 27.8 bits;  conditional E-value: 3e-09
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +y++G + ++ g+++eAl+++ +A el+P 
  gi|386002705|ref|YP_005921004.1| 511 WYRKGILAYSSGRPEEALAHFTRAAELDPG 540
                                       9****************************7 PP

  == domain 15  score: 29.7 bits;  conditional E-value: 7.7e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+a++n+G ++f lg+ deAle  ++ALe 
  gi|386002705|ref|YP_005921004.1| 542 AEAWNNRGWILFTLGDTDEALESIDRALEA 571
                                       89**************************95 PP

  == domain 16  score: 32.4 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                       a+ ++n+G+++  lgk +eAle+y++ + ++P
  gi|386002705|ref|YP_005921004.1| 576 AEGWNNRGVVLTALGKNEEALEAYNRTIDIDP 607
                                       799****************************9 PP

  == domain 17  score: 40.1 bits;  conditional E-value: 4.1e-13
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++a++n+G+ +++lg+y eA ++y +ALel+P 
  gi|386002705|ref|YP_005921004.1| 610 PRAWNNKGASLYHLGRYREAADCYGRALELDPA 642
                                       58******************************5 PP

  == domain 18  score: -1.6 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHT CS
                             TPR_1   1 akalynlGnayfkl 14 
                                       a+a  n+++a+++l
  gi|386002705|ref|YP_005921004.1| 644 ADARANRAAALQRL 657
                                       78999*****9876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00048      0.23       1      33 [.      65      97 ..      65      98 .. 0.96
   2 !   13.0   0.0   0.00018     0.083      10      34 .]     109     133 ..      99     133 .. 0.86
   3 !   26.8   0.0   7.2e-09   3.4e-06       3      34 .]     136     167 ..     135     167 .. 0.97
   4 !   28.8   0.0   1.6e-09   7.4e-07       2      33 ..     169     200 ..     168     201 .. 0.96
   5 !   28.3   0.7   2.4e-09   1.1e-06       1      31 [.     202     232 ..     202     235 .. 0.94
   6 ?    3.4   0.0      0.21     1e+02       4      25 ..     239     260 ..     237     269 .. 0.78
   7 !   24.8   0.1     3e-08   1.4e-05       3      33 ..     272     302 ..     271     303 .. 0.95
   8 !   27.6   0.0   3.9e-09   1.8e-06       3      33 ..     306     336 ..     304     337 .. 0.96
   9 !   31.0   0.8   3.2e-10   1.5e-07       1      32 [.     338     369 ..     338     371 .. 0.95
  10 !   31.8   1.4   1.7e-10   8.1e-08       1      33 [.     372     404 ..     372     405 .. 0.96
  11 !   29.9   0.0   7.2e-10   3.4e-07       3      33 ..     408     438 ..     406     439 .. 0.96
  12 !   29.8   0.1   7.8e-10   3.7e-07       1      33 [.     440     472 ..     440     473 .. 0.96
  13 !   28.6   0.9   1.9e-09     9e-07       1      34 []     474     507 ..     474     507 .. 0.96
  14 !   28.5   0.0     2e-09   9.4e-07       4      34 .]     511     541 ..     509     541 .. 0.97
  15 !   26.2   0.0   1.1e-08   5.1e-06       1      31 [.     542     572 ..     542     574 .. 0.96
  16 !   25.2   0.0   2.2e-08     1e-05       1      34 []     576     609 ..     576     609 .. 0.96
  17 !   35.4   0.5   1.2e-11   5.8e-09       1      33 [.     610     642 ..     610     643 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPn 33
                                      ae++ + ++ y++ g  + Al  ++++l+ldP+
  gi|386002705|ref|YP_005921004.1| 65 AEGWLEEAERYRQEGAIDLALSSLDRSLALDPD 97
                                      799*****************************8 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00018
                             TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                                       a+y+l d e A+eafe+Al +dP++
  gi|386002705|ref|YP_005921004.1| 109 ALYNLTDREMAVEAFERALGIDPED 133
                                       799********************86 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 7.2e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++y+lG+a+  lg+ +eAl+a++++l +dP+n
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQAYNRSLTIDPEN 167
                                       6*****************************97 PP

  == domain 4  score: 28.8 bits;  conditional E-value: 1.6e-09
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +a++n+Gl++ +lg+yeeA+  fe+A++ dP+
  gi|386002705|ref|YP_005921004.1| 169 KAWNNRGLILGALGRYEEAASSFERAISSDPD 200
                                       79****************************98 PP

  == domain 5  score: 28.3 bits;  conditional E-value: 2.4e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a a+ n+G+a+++lg++eeAle++  Al++d
  gi|386002705|ref|YP_005921004.1| 202 AAAWQNRGNALRALGRPEEALECYASALAID 232
                                       689**************************98 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.21
                             TPR_2   4 lynlGlayyklgdyeeAleafe 25 
                                       +   ++++++lg+ eeAl+ ++
  gi|386002705|ref|YP_005921004.1| 239 WKGAAELLRALGRDEEALARLD 260
                                       6678999**********98655 PP

  == domain 7  score: 24.8 bits;  conditional E-value: 3e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++ +Gl++  lg+yeeA+e f++Al+ dP+
  gi|386002705|ref|YP_005921004.1| 272 AWNDRGLILGVLGRYEEAVESFDAALRADPG 302
                                       8*****************************7 PP

  == domain 8  score: 27.6 bits;  conditional E-value: 3.9e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++n+Gla+++lg+ eeAle +++++ +dP 
  gi|386002705|ref|YP_005921004.1| 306 AWNNRGLALANLGRSEEALESYNRSIDIDPS 336
                                       9*****************************6 PP

  == domain 9  score: 31.0 bits;  conditional E-value: 3.2e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a a+yn+G+a++ l +y+eA+ea++ Ale +P
  gi|386002705|ref|YP_005921004.1| 338 ALAWYNRGRALFDLERYDEAVEAYDSALEVEP 369
                                       689**************************999 PP

  == domain 10  score: 31.8 bits;  conditional E-value: 1.7e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a++n+G a+++lg+ eeAle +++Ale+dP+
  gi|386002705|ref|YP_005921004.1| 372 ALAWNNRGAALAALGREEEALESYDRALEIDPG 404
                                       689*****************************7 PP

  == domain 11  score: 29.9 bits;  conditional E-value: 7.2e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+yn+G ++y  g+y +A++af++A++ +P+
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDEAIRFNPT 438
                                       9*****************************8 PP

  == domain 12  score: 29.8 bits;  conditional E-value: 7.8e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a++  G a+y++ ++ eAl ++ekAleldP+
  gi|386002705|ref|YP_005921004.1| 440 ADAWHSKGHALYQMRRPGEALVCYEKALELDPG 472
                                       79******************************6 PP

  == domain 13  score: 28.6 bits;  conditional E-value: 1.9e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ae ++ +G a++ l++ +eA+eaf++AleldP++
  gi|386002705|ref|YP_005921004.1| 474 AETWHHRGVALADLNRAAEAAEAFDRALELDPEY 507
                                       799*****************************85 PP

  == domain 14  score: 28.5 bits;  conditional E-value: 2e-09
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +y+ G ++y +g++eeAl++f +A eldP++
  gi|386002705|ref|YP_005921004.1| 511 WYRKGILAYSSGRPEEALAHFTRAAELDPGH 541
                                       9****************************86 PP

  == domain 15  score: 26.2 bits;  conditional E-value: 1.1e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       aea++n+G++++ lgd +eAle  ++Ale d
  gi|386002705|ref|YP_005921004.1| 542 AEAWNNRGWILFTLGDTDEALESIDRALEAD 572
                                       89**************************976 PP

  == domain 16  score: 25.2 bits;  conditional E-value: 2.2e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ae+++n+G ++ +lg+ eeAlea+++ + +dP +
  gi|386002705|ref|YP_005921004.1| 576 AEGWNNRGVVLTALGKNEEALEAYNRTIDIDPAH 609
                                       799*****************************75 PP

  == domain 17  score: 35.4 bits;  conditional E-value: 1.2e-11
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++a++n G ++y+lg+y eA++++ +AleldP 
  gi|386002705|ref|YP_005921004.1| 610 PRAWNNKGASLYHLGRYREAADCYGRALELDPA 642
                                       589*****************************5 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.21     1e+02       6      33 ..      70      97 ..      65      98 .. 0.84
   2 !   20.4   0.0   8.4e-07    0.0004       1      34 []      99     133 ..      99     133 .. 0.94
   3 !   24.2   0.0   4.9e-08   2.3e-05       3      34 .]     136     167 ..     135     167 .. 0.97
   4 !   29.0   0.0   1.4e-09   6.7e-07       2      33 ..     169     200 ..     168     201 .. 0.96
   5 !   19.4   0.1   1.8e-06   0.00083       1      31 [.     202     232 ..     202     234 .. 0.94
   6 ?    0.8   0.0       1.6   7.6e+02       8      32 ..     243     267 ..     239     269 .. 0.82
   7 !   19.5   0.0   1.6e-06   0.00078       3      32 ..     272     301 ..     271     303 .. 0.95
   8 !   25.6   0.0   1.8e-08   8.3e-06       3      33 ..     306     336 ..     304     337 .. 0.96
   9 !   27.1   0.1   5.8e-09   2.7e-06       3      33 ..     340     370 ..     338     371 .. 0.95
  10 !   22.9   0.2   1.3e-07   6.1e-05       3      32 ..     374     403 ..     372     405 .. 0.95
  11 !   13.8   0.0   0.00011     0.052       3      33 ..     408     438 ..     407     439 .. 0.96
  12 !   24.1   0.0   5.3e-08   2.5e-05       1      32 [.     440     471 ..     440     473 .. 0.97
  13 !   21.4   0.0     4e-07   0.00019       1      33 [.     474     506 ..     474     507 .. 0.96
  14 !   14.2   0.0   8.1e-05     0.038       4      33 ..     511     540 ..     508     541 .. 0.94
  15 !   24.4   0.0   4.3e-08     2e-05       1      31 [.     542     572 ..     542     574 .. 0.96
  16 !   19.4   0.0   1.7e-06   0.00081       1      34 []     576     609 ..     576     609 .. 0.96
  17 !   21.8   0.0   2.9e-07   0.00014       2      33 ..     611     642 ..     610     643 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.21
                                      HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  6 nlgsiylklgdyeeAkeyyekaleldpd 33
                                        +  y++ g ++ A +++ + l ldpd
  gi|386002705|ref|YP_005921004.1| 70 EEAERYRQEGAIDLALSSLDRSLALDPD 97
                                      5555699********************7 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 8.4e-07
                                       CCHHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiy.lklgdyeeAkeyyekaleldpdn 34 
                                       aea+++ g i   +l d e+A+e++e+al +dp++
  gi|386002705|ref|YP_005921004.1|  99 AEAWVLRGEIAlYNLTDREMAVEAFERALGIDPED 133
                                       79******8888*********************86 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 4.9e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++y lg++++ lg+ +eA ++y++ l++dp+n
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQAYNRSLTIDPEN 167
                                       7*****************************86 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 1.4e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n g+i+  lg+yeeA +++e+a++ dpd
  gi|386002705|ref|YP_005921004.1| 169 KAWNNRGLILGALGRYEEAASSFERAISSDPD 200
                                       79*****************************7 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 1.8e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a a++n g++++ lg+ eeA e+y  al +d
  gi|386002705|ref|YP_005921004.1| 202 AAAWQNRGNALRALGRPEEALECYASALAID 232
                                       579*************************998 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.6
                                       HHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldp 32 
                                       + +++ lg+ eeA + +  a+ +dp
  gi|386002705|ref|YP_005921004.1| 243 AELLRALGRDEEALARLDGAVGADP 267
                                       78999********987777777777 PP

  == domain 7  score: 19.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a++  g+i+  lg+yeeA+e++  al++dp
  gi|386002705|ref|YP_005921004.1| 272 AWNDRGLILGVLGRYEEAVESFDAALRADP 301
                                       89***************************9 PP

  == domain 8  score: 25.6 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++n g+++ +lg+ eeA e+y++ +++dp+
  gi|386002705|ref|YP_005921004.1| 306 AWNNRGLALANLGRSEEALESYNRSIDIDPS 336
                                       8*****************************6 PP

  == domain 9  score: 27.1 bits;  conditional E-value: 5.8e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+yn g+++++l++y+eA+e+y  ale +p+
  gi|386002705|ref|YP_005921004.1| 340 AWYNRGRALFDLERYDEAVEAYDSALEVEPA 370
                                       8***************************997 PP

  == domain 10  score: 22.9 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a++n g ++  lg+ eeA e+y +ale+dp
  gi|386002705|ref|YP_005921004.1| 374 AWNNRGAALAALGREEEALESYDRALEIDP 403
                                       8****************************9 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a+yn gs++   g+y  A++++ +a++ +p+
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDEAIRFNPT 438
                                       8***************************996 PP

  == domain 12  score: 24.1 bits;  conditional E-value: 5.3e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a++ +g+++ ++ +  eA  +yekaleldp
  gi|386002705|ref|YP_005921004.1| 440 ADAWHSKGHALYQMRRPGEALVCYEKALELDP 471
                                       78*****************************9 PP

  == domain 13  score: 21.4 bits;  conditional E-value: 4e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ae +++ g ++ +l++  eA e++ +aleldp+
  gi|386002705|ref|YP_005921004.1| 474 AETWHHRGVALADLNRAAEAAEAFDRALELDPE 506
                                       799*****************************8 PP

  == domain 14  score: 14.2 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +y++g +  + g+ eeA + + +a eldp 
  gi|386002705|ref|YP_005921004.1| 511 WYRKGILAYSSGRPEEALAHFTRAAELDPG 540
                                       9***************************96 PP

  == domain 15  score: 24.4 bits;  conditional E-value: 4.3e-08
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       aea++n g+i+++lgd +eA e++ +ale+d
  gi|386002705|ref|YP_005921004.1| 542 AEAWNNRGWILFTLGDTDEALESIDRALEAD 572
                                       79***************************98 PP

  == domain 16  score: 19.4 bits;  conditional E-value: 1.7e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ae ++n g ++  lg+ eeA e+y++ +++dp++
  gi|386002705|ref|YP_005921004.1| 576 AEGWNNRGVVLTALGKNEEALEAYNRTIDIDPAH 609
                                       689*****************************86 PP

  == domain 17  score: 21.8 bits;  conditional E-value: 2.9e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n+g  +  lg+y eA  +y +aleldp+
  gi|386002705|ref|YP_005921004.1| 611 RAWNNKGASLYHLGRYREAADCYGRALELDPA 642
                                       89*****************************7 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-06    0.0011       3      36 ..      74     107 ..      72     113 .. 0.93
   2 !   12.5   0.0   0.00018     0.087      11      38 ..     117     144 ..     109     145 .. 0.93
   3 !   27.8   0.0   3.1e-09   1.5e-06       7      42 .]     147     182 ..     147     182 .. 0.96
   4 !   24.9   0.1   2.5e-08   1.2e-05       6      42 .]     180     216 ..     177     216 .. 0.93
   5 !   17.9   0.1   3.8e-06    0.0018       1      25 [.     209     233 ..     209     235 .. 0.97
   6 !    7.9   0.0    0.0053       2.5       3      38 ..     245     280 ..     243     281 .. 0.92
   7 !   25.9   0.3   1.2e-08   5.7e-06       7      42 .]     283     318 ..     282     318 .. 0.97
   8 !   32.5   0.1   1.1e-10   5.1e-08       7      40 ..     317     350 ..     314     351 .. 0.93
   9 !   39.0   0.5   9.8e-13   4.6e-10       1      42 []     345     386 ..     345     386 .. 0.98
  10 !   32.9   0.7   7.8e-11   3.7e-08       4      40 ..     382     418 ..     381     420 .. 0.92
  11 !   31.7   0.0   1.9e-10   9.1e-08       1      41 [.     413     453 ..     413     453 .. 0.97
  12 !   20.9   0.0   4.4e-07   0.00021      12      40 ..     458     486 ..     457     488 .. 0.94
  13 !   15.1   0.5   2.8e-05     0.013       4      40 ..     484     520 ..     483     522 .. 0.87
  14 !   21.6   0.0   2.6e-07   0.00012       5      42 .]     519     556 ..     515     556 .. 0.94
  15 !   16.1   0.0   1.4e-05    0.0068       3      42 .]     551     590 ..     549     590 .. 0.93
  16 !   33.1   0.2     7e-11   3.3e-08       4      42 .]     586     624 ..     585     624 .. 0.95
  17 !   32.5   1.2   1.1e-10   5.1e-08       3      41 ..     619     657 ..     617     658 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                        y++ G ++ A+ ++ + l+ldPd aea+  +G+
  gi|386002705|ref|YP_005921004.1|  74 RYRQEGAIDLALSSLDRSLALDPDLAEAWVLRGE 107
                                       7****************************99997 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
                            TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlay 38 
                                       e A+ea+++Al +dP++  ++y+LG+a+
  gi|386002705|ref|YP_005921004.1| 117 EMAVEAFERALGIDPEDGVVWYELGNAL 144
                                       569***********************96 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 3.1e-09
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+ +eA++aY++ l +dP+n  a++n+Gl++ ++G
  gi|386002705|ref|YP_005921004.1| 147 LGRVDEALQAYNRSLTIDPENGKAWNNRGLILGALG 182
                                       69*****************************99988 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 2.5e-08
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++G+yeeA  ++++A+  dPd a a+ n+G+a+ ++G
  gi|386002705|ref|YP_005921004.1| 180 ALGRYEEAASSFERAISSDPDLAAAWQNRGNALRALG 216
                                       68******************************97776 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 3.8e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                       G+a++++G+ eeA+e+Y  Al++d+
  gi|386002705|ref|YP_005921004.1| 209 GNALRALGRPEEALECYASALAIDS 233
                                       9**********************95 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0053
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +++++G+ eeA++++  A+  dP +  a++ +Gl++
  gi|386002705|ref|YP_005921004.1| 245 LLRALGRDEEALARLDGAVGADPGDKAAWNDRGLIL 280
                                       6899**************************999975 PP

  == domain 7  score: 25.9 bits;  conditional E-value: 1.2e-08
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+yeeA+e++ +Al+ dP +  a++n+Gla++++G
  gi|386002705|ref|YP_005921004.1| 283 LGRYEEAVESFDAALRADPGYLLAWNNRGLALANLG 318
                                       69*******************************998 PP

  == domain 8  score: 32.5 bits;  conditional E-value: 1.1e-10
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       +G+ eeA+e+Y++ +++dP++a a+yn+G a++ 
  gi|386002705|ref|YP_005921004.1| 317 LGRSEEALESYNRSIDIDPSFALAWYNRGRALFD 350
                                       7999*************************99986 PP

  == domain 9  score: 39.0 bits;  conditional E-value: 9.8e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a++++ +y+eA+eaY  Al+  P +a a++n+G+a++++G
  gi|386002705|ref|YP_005921004.1| 345 GRALFDLERYDEAVEAYDSALEVEPAFALAWNNRGAALAALG 386
                                       99************************************9998 PP

  == domain 10  score: 32.9 bits;  conditional E-value: 7.8e-11
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       + ++G+ eeA+e+Y +Al++dP +  a+yn+G ++y 
  gi|386002705|ref|YP_005921004.1| 382 LAALGREEEALESYDRALEIDPGYEIAWYNRGSVLYL 418
                                       6789******************************996 PP

  == domain 11  score: 31.7 bits;  conditional E-value: 1.9e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       G ++y  G+y +Ai+a+ +A++++P++a+a++  G+a+y++
  gi|386002705|ref|YP_005921004.1| 413 GSVLYLEGRYFDAIKAFDEAIRFNPTSADAWHSKGHALYQM 453
                                       889************************************96 PP

  == domain 12  score: 20.9 bits;  conditional E-value: 4.4e-07
                            TPR_11  12 eAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       eA+ +Y+kAl+ldP  ae ++++G+a++ 
  gi|386002705|ref|YP_005921004.1| 458 EALVCYEKALELDPGRAETWHHRGVALAD 486
                                       8*************************976 PP

  == domain 13  score: 15.1 bits;  conditional E-value: 2.8e-05
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       + ++++  eA ea+ +Al+ldP++   +y  G + y 
  gi|386002705|ref|YP_005921004.1| 484 LADLNRAAEAAEAFDRALELDPEYEPPWYRKGILAYS 520
                                       67899999*****************999999987665 PP

  == domain 14  score: 21.6 bits;  conditional E-value: 2.6e-07
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       y+ G+ eeA++++ +A +ldP  aea++n+G +++ +G
  gi|386002705|ref|YP_005921004.1| 519 YSSGRPEEALAHFTRAAELDPGHAEAWNNRGWILFTLG 556
                                       899****************************9998887 PP

  == domain 15  score: 16.1 bits;  conditional E-value: 1.4e-05
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +++ +G+ +eA+e+  +Al+ d   ae ++n+G+++ ++G
  gi|386002705|ref|YP_005921004.1| 551 ILFTLGDTDEALESIDRALEADTALAEGWNNRGVVLTALG 590
                                       7899*******************************98777 PP

  == domain 16  score: 33.1 bits;  conditional E-value: 7e-11
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++++Gk+eeA+eaY++ +++dP  ++a++n G+ +y +G
  gi|386002705|ref|YP_005921004.1| 586 LTALGKNEEALEAYNRTIDIDPAHPRAWNNKGASLYHLG 624
                                       789********************************9887 PP

  == domain 17  score: 32.5 bits;  conditional E-value: 1.1e-10
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                        +y +G+y eA  +Y +Al+ldP +a+a  n+++a++++
  gi|386002705|ref|YP_005921004.1| 619 SLYHLGRYREAADCYGRALELDPAFADARANRAAALQRL 657
                                       6899********************************987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00061      0.29       3      32 ..      89     119 ..      88     121 .. 0.82
   2 !   23.5   0.0   9.9e-08   4.7e-05       2      34 .]     123     155 ..     122     155 .. 0.96
   3 !   23.7   0.1   8.2e-08   3.9e-05       1      32 [.     156     187 ..     156     188 .. 0.97
   4 !   23.8   0.0   7.8e-08   3.7e-05       2      34 .]     191     223 ..     190     223 .. 0.96
   5 ?    2.3   0.0      0.56   2.6e+02       1      33 [.     224     256 ..     224     257 .. 0.90
   6 !    8.0   0.0    0.0089       4.2       9      34 .]     266     291 ..     262     291 .. 0.93
   7 !   20.5   0.2   8.6e-07    0.0004       2      34 .]     293     325 ..     292     325 .. 0.94
   8 !   23.5   0.0     1e-07   4.8e-05       2      34 .]     327     359 ..     326     359 .. 0.96
   9 !   17.7   0.2   6.8e-06    0.0032       2      34 .]     361     393 ..     360     393 .. 0.94
  10 !   19.4   0.0   1.9e-06   0.00092       2      33 ..     395     426 ..     394     427 .. 0.95
  11 !   17.8   0.0   6.5e-06     0.003       2      32 ..     429     459 ..     428     460 .. 0.91
  12 !   21.6   0.1     4e-07   0.00019       1      32 [.     462     493 ..     462     495 .. 0.95
  13 !   15.2   0.0   4.3e-05      0.02       2      33 ..     497     528 ..     496     529 .. 0.95
  14 !   30.0   0.0   8.3e-10   3.9e-07       2      34 .]     531     563 ..     530     563 .. 0.95
  15 !   12.5   0.0   0.00032      0.15       3      34 .]     566     597 ..     565     597 .. 0.94
  16 !   18.5   0.1     4e-06    0.0019       1      32 [.     598     629 ..     598     631 .. 0.96
  17 !   13.2   0.1   0.00019     0.091       1      25 [.     632     656 ..     632     658 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00061
                            TPR_17   3 lkaleldPnnadaynnLAel.llknGdlmtA 32 
                                        ++l+ldP+ a+a+ +++e+ l+++ d ++A
  gi|386002705|ref|YP_005921004.1|  89 DRSLALDPDLAEAWVLRGEIaLYNLTDREMA 119
                                       699****************736687776666 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9.9e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +++al +dP + +++++L+++l+ +G+ ++A+q
  gi|386002705|ref|YP_005921004.1| 123 FERALGIDPEDGVVWYELGNALSFLGRVDEALQ 155
                                       89*****************************97 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 8.2e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y ++l +dP n +a+nn++ +l  +G++++A
  gi|386002705|ref|YP_005921004.1| 156 AYNRSLTIDPENGKAWNNRGLILGALGRYEEA 187
                                       59****************************98 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 7.8e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +++a+  dP+ a a++n++++l+ +G++++A++
  gi|386002705|ref|YP_005921004.1| 191 FERAISSDPDLAAAWQNRGNALRALGRPEEALE 223
                                       89*****************************85 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.56
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y  al++d   + ++   Aell+ +G+ ++A+
  gi|386002705|ref|YP_005921004.1| 224 CYASALAIDSGLVGSWKGAAELLRALGRDEEAL 256
                                       6778999999999999999***********997 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0089
                            TPR_17   9 dPnnadaynnLAelllknGdlmtArq 34 
                                       dP +  a+n ++ +l  +G++++A++
  gi|386002705|ref|YP_005921004.1| 266 DPGDKAAWNDRGLILGVLGRYEEAVE 291
                                       89999******************975 PP

  == domain 7  score: 20.5 bits;  conditional E-value: 8.6e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +  al+ dP +  a+nn++ +l+++G++++A++
  gi|386002705|ref|YP_005921004.1| 293 FDAALRADPGYLLAWNNRGLALANLGRSEEALE 325
                                       6789***************************85 PP

  == domain 8  score: 23.5 bits;  conditional E-value: 1e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +++++dP+ a a++n++++l  + ++++A++
  gi|386002705|ref|YP_005921004.1| 327 YNRSIDIDPSFALAWYNRGRALFDLERYDEAVE 359
                                       99****************************975 PP

  == domain 9  score: 17.7 bits;  conditional E-value: 6.8e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y  ale +P  a a+nn++ +l+ +G+ ++A++
  gi|386002705|ref|YP_005921004.1| 361 YDSALEVEPAFALAWNNRGAALAALGREEEALE 393
                                       888**************************9975 PP

  == domain 10  score: 19.4 bits;  conditional E-value: 1.9e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +ale+dP +  a++n++ +l+  G++ +A+
  gi|386002705|ref|YP_005921004.1| 395 YDRALEIDPGYEIAWYNRGSVLYLEGRYFDAI 426
                                       99*************************99997 PP

  == domain 11  score: 17.8 bits;  conditional E-value: 6.5e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + +a++ +P++ada++ ++ +l++  ++++A
  gi|386002705|ref|YP_005921004.1| 429 FDEAIRFNPTSADAWHSKGHALYQMRRPGEA 459
                                       889*******************999888887 PP

  == domain 12  score: 21.6 bits;  conditional E-value: 4e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y+kaleldP  a+ ++ ++++l+ +++ ++A
  gi|386002705|ref|YP_005921004.1| 462 CYEKALELDPGRAETWHHRGVALADLNRAAEA 493
                                       8***************************9988 PP

  == domain 13  score: 15.2 bits;  conditional E-value: 4.3e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +aleldP + ++++ ++ l ++ G++++A+
  gi|386002705|ref|YP_005921004.1| 497 FDRALELDPEYEPPWYRKGILAYSSGRPEEAL 528
                                       89****************************97 PP

  == domain 14  score: 30.0 bits;  conditional E-value: 8.3e-10
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +++a+eldP +a+a+nn++++l  +Gd+++A++
  gi|386002705|ref|YP_005921004.1| 531 FTRAAELDPGHAEAWNNRGWILFTLGDTDEALE 563
                                       89*****************************85 PP

  == domain 15  score: 12.5 bits;  conditional E-value: 0.00032
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                        +ale d   a+ +nn++++l  +G+ ++A++
  gi|386002705|ref|YP_005921004.1| 566 DRALEADTALAEGWNNRGVVLTALGKNEEALE 597
                                       599**************************985 PP

  == domain 16  score: 18.5 bits;  conditional E-value: 4e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y + +++dP ++ a+nn++  l+++G++++A
  gi|386002705|ref|YP_005921004.1| 598 AYNRTIDIDPAHPRAWNNKGASLYHLGRYREA 629
                                       599***************************98 PP

  == domain 17  score: 13.2 bits;  conditional E-value: 0.00019
                            TPR_17   1 lylkaleldPnnadaynnLAelllk 25 
                                       +y +aleldP  ada  n+A +l +
  gi|386002705|ref|YP_005921004.1| 632 CYGRALELDPAFADARANRAAALQR 656
                                       799*****************99975 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.0   1.4e-05    0.0064       2      45 ..      70     110 ..      69     112 .. 0.94
   2 !   28.7   0.0   3.2e-09   1.5e-06       6      66 ..     109     166 ..     108     168 .. 0.91
   3 !   37.8   3.9   4.6e-12   2.2e-09       3      65 ..     174     233 ..     172     236 .. 0.94
   4 !   23.3   5.5   1.6e-07   7.6e-05       3      67 ..     208     269 ..     207     270 .. 0.97
   5 !   28.8   6.5   3.1e-09   1.5e-06       3      66 ..     242     302 ..     240     303 .. 0.96
   6 !   41.7   0.7   2.9e-13   1.4e-10       2      65 ..     275     335 ..     274     336 .. 0.95
   7 !   43.5   9.1   7.8e-14   3.7e-11       1      67 [.     342     405 ..     342     406 .. 0.98
   8 !   15.0   0.0   6.2e-05     0.029      36      67 ..     408     439 ..     406     440 .. 0.94
   9 !   34.4   4.5   5.2e-11   2.5e-08       3      66 ..     446     506 ..     444     508 .. 0.96
  10 !   47.0   1.2   6.2e-15   2.9e-12       1      64 [.     512     572 ..     512     576 .. 0.95
  11 !   36.0   0.9   1.7e-11     8e-09       9      65 ..     588     641 ..     580     642 .. 0.92
  12 !   12.4   6.2    0.0004      0.19       7      44 ..     620     654 ..     619     659 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-05
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                       ++a  +++ g  d A+  l++ l++d   Pd aeA+ l+g++al
  gi|386002705|ref|YP_005921004.1|  70 EEAERYRQEGAIDLALSSLDRSLALD---PDLAEAWVLRGEIAL 110
                                       6899999*******************...************996 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.2e-09
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       a++++ d + A++a+e+al  d   P++   +++lg+a+  +gr++eA+++y++ l+ +p 
  gi|386002705|ref|YP_005921004.1| 109 ALYNLTDREMAVEAFERALGID---PEDGVVWYELGNALSFLGRVDEALQAYNRSLTIDPE 166
                                       6788888899************...66666**************************99996 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 4.6e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       +++++ ++g+y++Aa  +e+a+ +d   Pd a+A+ ++g+a+ ++gr +eA++ y++al+ ++
  gi|386002705|ref|YP_005921004.1| 174 RGLILGALGRYEEAASSFERAISSD---PDLAAAWQNRGNALRALGRPEEALECYASALAIDS 233
                                       789999*******************...*****************************998776 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 1.6e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++a++++g++++A++ +  al+ d   +  + ++ + ++++ ++gr +eA+a ++ a++a+p++
  gi|386002705|ref|YP_005921004.1| 208 RGNALRALGRPEEALECYASALAID---SGLVGSWKGAAELLRALGRDEEALARLDGAVGADPGD 269
                                       79***********************...***********************************97 PP

  == domain 5  score: 28.8 bits;  conditional E-value: 3.1e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +a +++++g+ ++A+a+l+ a+ +d   P + +A++ +g+++ ++gr++eA++ ++aalra+p+
  gi|386002705|ref|YP_005921004.1| 242 AAELLRALGRDEEALARLDGAVGAD---PGDKAAWNDRGLILGVLGRYEEAVESFDAALRADPG 302
                                       68899999*****************...***********************************8 PP

  == domain 6  score: 41.7 bits;  conditional E-value: 2.9e-13
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++++++  +g+y++A++ ++aal++d   P    A++++g+a++ +gr +eA++ y++ ++ +p
  gi|386002705|ref|YP_005921004.1| 275 DRGLILGVLGRYEEAVESFDAALRAD---PGYLLAWNNRGLALANLGRSEEALESYNRSIDIDP 335
                                       57889999******************...*****************************999998 PP

  == domain 7  score: 43.5 bits;  conditional E-value: 7.8e-14
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++ra++++ +yd+A++a++ al+     P+ a A++++g a++++gr +eA++ y++al+ +p++
  gi|386002705|ref|YP_005921004.1| 342 YNRGRALFDLERYDEAVEAYDSALEVE---PAFALAWNNRGAALAALGREEEALESYDRALEIDPGY 405
                                       799************************...***********************************96 PP

  == domain 8  score: 15.0 bits;  conditional E-value: 6.2e-05
                            TPR_16  36 AllllgdaalrqgrlaeAaalyraalraapda 67 
                                       A++++g +++  gr+ +A+ ++++a+r  p +
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDEAIRFNPTS 439
                                       9*************************999976 PP

  == domain 9  score: 34.4 bits;  conditional E-value: 5.2e-11
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++a+++ +++ +A+  +e al++d   P +ae + ++g+a++ ++r aeAa+++++al+ +p 
  gi|386002705|ref|YP_005921004.1| 446 KGHALYQMRRPGEALVCYEKALELD---PGRAETWHHRGVALADLNRAAEAAEAFDRALELDPE 506
                                       79***********************...*********************************996 PP

  == domain 10  score: 47.0 bits;  conditional E-value: 6.2e-15
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       + ++ +a+ +g++++A+a +++a ++d   P +aeA++++g++++ +g+ +eA++ +++al+a+
  gi|386002705|ref|YP_005921004.1| 512 YRKGILAYSSGRPEEALAHFTRAAELD---PGHAEAWNNRGWILFTLGDTDEALESIDRALEAD 572
                                       67899**********************...*******************************886 PP

  == domain 11  score: 36.0 bits;  conditional E-value: 1.7e-11
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       ++g+ ++A++a++++++ d   P++++A++++g +++++gr+ eAa+ y +al+ +p
  gi|386002705|ref|YP_005921004.1| 588 ALGKNEEALEAYNRTIDID---PAHPRAWNNKGASLYHLGRYREAADCYGRALELDP 641
                                       689****************...************************98888888888 PP

  == domain 12  score: 12.4 bits;  conditional E-value: 0.0004
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                       ++ +g+y++Aa  + +al++d   P+ a+A+ +++ a+
  gi|386002705|ref|YP_005921004.1| 620 LYHLGRYREAADCYGRALELD---PAFADARANRAAAL 654
                                       5668*****************...**********9997 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.8   1.4e-05    0.0065       2      43 ..      66     107 ..      65     109 .. 0.94
   2 !   11.4   0.0   0.00097      0.46      17      42 ..     116     141 ..     105     143 .. 0.86
   3 !   21.1   0.0   7.6e-07   0.00036       3      39 ..     136     172 ..     135     177 .. 0.93
   4 !   15.4   0.1   5.4e-05     0.025      11      40 ..     178     207 ..     173     210 .. 0.88
   5 !   15.5   1.2   4.9e-05     0.023       2      30 ..     203     231 ..     202     234 .. 0.93
   6 !   13.2   1.6   0.00026      0.12       4      38 ..     239     273 ..     236     279 .. 0.92
   7 !   15.1   0.7   6.6e-05     0.031       4      39 ..     273     308 ..     272     313 .. 0.83
   8 !   19.5   0.1   2.5e-06    0.0012       4      42 ..     307     345 ..     305     346 .. 0.91
   9 !   20.8   3.0   9.7e-07   0.00046       3      39 ..     340     376 ..     338     380 .. 0.94
  10 !   19.1   0.6   3.3e-06    0.0016       7      41 ..     378     412 ..     375     415 .. 0.91
  11 !   18.4   0.0   5.7e-06    0.0027       3      39 ..     408     444 ..     406     447 .. 0.95
  12 !   19.5   0.3   2.5e-06    0.0012       2      42 ..     441     481 ..     440     483 .. 0.93
  13 !   15.8   2.6   3.7e-05     0.018       2      42 ..     475     515 ..     474     517 .. 0.91
  14 !   20.0   0.2   1.7e-06   0.00081       4      38 ..     511     545 ..     509     549 .. 0.94
  15 !   16.3   0.2   2.6e-05     0.012       2      38 ..     543     579 ..     542     585 .. 0.89
  16 !   15.7   0.0     4e-05     0.019       6      40 ..     581     615 ..     576     619 .. 0.87
  17 !   15.0   1.9   6.8e-05     0.032       9      42 ..     618     651 ..     616     653 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       e +l+ ae +++ G  d A+  l+r lal+Pd aeaw l ++
  gi|386002705|ref|YP_005921004.1|  66 EGWLEEAERYRQEGAIDLALSSLDRSLALDPDLAEAWVLRGE 107
                                       779999*******************************99886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00097
                            TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                                        + A+++++ral  +P+d ++w++l+
  gi|386002705|ref|YP_005921004.1| 116 REMAVEAFERALGIDPEDGVVWYELG 141
                                       5669********************98 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 7.6e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ++++l+ al  lG+ deA+++++r l  +P++  aw 
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQAYNRSLTIDPENGKAWN 172
                                       59******************************99995 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 5.4e-05
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawll 40 
                                       l alG+++eA+  ++ra++ +Pd a+aw  
  gi|386002705|ref|YP_005921004.1| 178 LGALGRYEEAASSFERAISSDPDLAAAWQN 207
                                       5589************************86 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 4.9e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       +a++ ++ al+alG+p+eA++++  ala 
  gi|386002705|ref|YP_005921004.1| 203 AAWQNRGNALRALGRPEEALECYASALAI 231
                                       79************************996 PP

  == domain 6  score: 13.2 bits;  conditional E-value: 0.00026
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       ++ +ae+l+alG+ +eA+a l+ a+ ++P+d +aw
  gi|386002705|ref|YP_005921004.1| 239 WKGAAELLRALGRDEEALARLDGAVGADPGDKAAW 273
                                       8889******************************9 PP

  == domain 7  score: 15.1 bits;  conditional E-value: 6.6e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       + +++ +l  lG+++eA++ +++al+++P+ + aw 
  gi|386002705|ref|YP_005921004.1| 273 WNDRGLILGVLGRYEEAVESFDAALRADPGYLLAWN 308
                                       66666667779***********************94 PP

  == domain 8  score: 19.5 bits;  conditional E-value: 2.5e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +  ++ al++lG+ +eA++ ++r ++ +P++a aw+  +
  gi|386002705|ref|YP_005921004.1| 307 WNNRGLALANLGRSEEALESYNRSIDIDPSFALAWYNRG 345
                                       666899*****************************9876 PP

  == domain 9  score: 20.8 bits;  conditional E-value: 9.7e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a++ +++al+ l+++deA+++++ al+  P++a aw 
  gi|386002705|ref|YP_005921004.1| 340 AWYNRGRALFDLERYDEAVEAYDSALEVEPAFALAWN 376
                                       8**********************************95 PP

  == domain 10  score: 19.1 bits;  conditional E-value: 3.3e-06
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +++al+alG+ +eA++ ++ral+ +P+ + aw+  
  gi|386002705|ref|YP_005921004.1| 378 RGAALAALGREEEALESYDRALEIDPGYEIAWYNR 412
                                       689****************************9865 PP

  == domain 11  score: 18.4 bits;  conditional E-value: 5.7e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a++ ++++l+  G++ +Ai+++++a++ +P++a+aw 
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDEAIRFNPTSADAWH 444
                                       89*********************************96 PP

  == domain 12  score: 19.5 bits;  conditional E-value: 2.5e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +a+   ++al++ ++p eA+ ++++al+l+P+ ae+w + +
  gi|386002705|ref|YP_005921004.1| 441 DAWHSKGHALYQMRRPGEALVCYEKALELDPGRAETWHHRG 481
                                       789999*******************************9876 PP

  == domain 13  score: 15.8 bits;  conditional E-value: 3.7e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       e +  ++ al+ l + +eA+++++ral+l+P+ +  w++ +
  gi|386002705|ref|YP_005921004.1| 475 ETWHHRGVALADLNRAAEAAEAFDRALELDPEYEPPWYRKG 515
                                       78999***************************998888765 PP

  == domain 14  score: 20.0 bits;  conditional E-value: 1.7e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       +++ + + + +G+p+eA+a++ ra +l+P++aeaw
  gi|386002705|ref|YP_005921004.1| 511 WYRKGILAYSSGRPEEALAHFTRAAELDPGHAEAW 545
                                       89999999**************************9 PP

  == domain 15  score: 16.3 bits;  conditional E-value: 2.6e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       ea+  ++++l++lGd+deA++  +ral+++ + ae w
  gi|386002705|ref|YP_005921004.1| 543 EAWNNRGWILFTLGDTDEALESIDRALEADTALAEGW 579
                                       89999***********************998888877 PP

  == domain 16  score: 15.7 bits;  conditional E-value: 4e-05
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawll 40 
                                        ++ +l alG+ +eA+++++r ++ +P++++aw  
  gi|386002705|ref|YP_005921004.1| 581 NRGVVLTALGKNEEALEAYNRTIDIDPAHPRAWNN 615
                                       57889****************************65 PP

  == domain 17  score: 15.0 bits;  conditional E-value: 6.8e-05
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                       + l++lG+++eA++++ ral+l+P++a+a+   a
  gi|386002705|ref|YP_005921004.1| 618 ASLYHLGRYREAADCYGRALELDPAFADARANRA 651
                                       56899*******************9999997766 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.68   3.2e+02      57      76 ..      58      77 ..      49      78 .. 0.81
   2 !    8.8   0.9     0.004       1.9      13      75 ..      75     130 ..      72     132 .. 0.85
   3 !   31.5   0.2   3.5e-10   1.6e-07       5      73 ..     136     196 ..     132     200 .. 0.93
   4 !   37.2   1.7   5.5e-12   2.6e-09       4      75 ..     169     232 ..     167     234 .. 0.92
   5 !   29.7   3.2   1.2e-09   5.9e-07       2      64 ..     201     262 ..     200     265 .. 0.91
   6 !   29.1   0.3   1.8e-09   8.7e-07       5      76 ..     272     335 ..     270     336 .. 0.86
   7 !   17.2   0.2     1e-05    0.0047       3      32 ..     338     367 ..     336     368 .. 0.90
   8 !   19.1   0.9   2.6e-06    0.0012       3      32 ..     372     401 ..     370     406 .. 0.90
   9 !   27.8   0.1     5e-09   2.4e-06       4      75 ..     407     470 ..     404     471 .. 0.90
  10 !   27.4   1.7   6.6e-09   3.1e-06       3      76 ..     440     505 ..     438     506 .. 0.93
  11 !   30.6   0.1   6.3e-10     3e-07       7      75 ..     512     572 ..     510     574 .. 0.91
  12 !   29.3   0.1   1.6e-09   7.8e-07       3      76 ..     542     607 ..     542     608 .. 0.91
  13 !   33.3   0.6   9.5e-11   4.5e-08       3      76 ..     576     641 ..     572     642 .. 0.93
  14 !   18.6   1.4   3.6e-06    0.0017       4      50 ..     611     656 ..     609     657 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.68
                            TPR_12 57 algryeeAlelleealaiae 76
                                      alg+ e A+ +leea + ++
  gi|386002705|ref|YP_005921004.1| 58 ALGDEESAEGWLEEAERYRQ 77
                                      7999**********998776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.004
                            TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +r+ g  d Al+ l+++l++      pd  ++a++lr+   ly ++ + e A+e++e+al i+
  gi|386002705|ref|YP_005921004.1|  75 YRQEGAIDLALSSLDRSLALD-----PDL-AEAWVLRGEIALYNLT-DREMAVEAFERALGID 130
                                       788888899999999998888.....875.8899999988888888.************9876 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 3.5e-10
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       ++++l+++l  lgr deAl+ ++++l i      p++     + +n g ++ algryeeA + +e+a+ 
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQAYNRSLTID-----PEN---GKAWNNRGLILGALGRYEEAASSFERAIS 196
                                       6789*************************.....887...7799***********************85 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 5.5e-12
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a+nn++++l +lgry+eA + +e+a   +        p++a++ +n g ++ralgr+eeAle +  alai+
  gi|386002705|ref|YP_005921004.1| 169 KAWNNRGLILGALGRYEEAASSFERA---I-----SSDPDLAAAWQNRGNALRALGRPEEALECYASALAID 232
                                       5899**********************...3.....345669*****************************95 PP

  == domain 5  score: 29.7 bits;  conditional E-value: 1.2e-09
                            TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeA 64 
                                       +a+a+ n++++lr+lgr +eAle++  al+i + l G  + ++a+ lr+Lgr  +al r++ A
  gi|386002705|ref|YP_005921004.1| 201 LAAAWQNRGNALRALGRPEEALECYASALAIDSGLVGS-WKGAAELLRALGRDEEALARLDGA 262
                                       6777779*************************999875.99************9999999988 PP

  == domain 6  score: 29.1 bits;  conditional E-value: 1.8e-09
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+n ++++l  lgry+eA e +++al++      p    ++ + +n g ++  lgr eeAle ++++++i++
  gi|386002705|ref|YP_005921004.1| 272 AWNDRGLILGVLGRYEEAVESFDAALRAD-----PG---YLLAWNNRGLALANLGRSEEALESYNRSIDIDP 335
                                       68789********************9999.....64...45677777777777****************976 PP

  == domain 7  score: 17.2 bits;  conditional E-value: 1e-05
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       a a++n++ +l+ l+rydeA e ++ ale+
  gi|386002705|ref|YP_005921004.1| 338 ALAWYNRGRALFDLERYDEAVEAYDSALEV 367
                                       67899*********************9996 PP

  == domain 8  score: 19.1 bits;  conditional E-value: 2.6e-06
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                       a a+nn++a+l++lgr +eAle +++alei
  gi|386002705|ref|YP_005921004.1| 372 ALAWNNRGAALAALGREEEALESYDRALEI 401
                                       678999999999999999999999999998 PP

  == domain 9  score: 27.8 bits;  conditional E-value: 5e-09
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a++n+++vl+  gry +A++ +++a++     ++p+    a + +  g +++++ r+ eAl  +e+al+++
  gi|386002705|ref|YP_005921004.1| 407 IAWYNRGSVLYLEGRYFDAIKAFDEAIR-----FNPT---SADAWHSKGHALYQMRRPGEALVCYEKALELD 470
                                       6899**********************33.....3476...599**************************986 PP

  == domain 10  score: 27.4 bits;  conditional E-value: 6.6e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a++  +++l+++ r  eAl ++ekale+      p     a+t +  g ++  l+r +eA e++ +al++++
  gi|386002705|ref|YP_005921004.1| 440 ADAWHSKGHALYQMRRPGEALVCYEKALELD-----PG---RAETWHHRGVALADLNRAAEAAEAFDRALELDP 505
                                       789999*************************.....53...7*****************************976 PP

  == domain 11  score: 30.6 bits;  conditional E-value: 6.3e-10
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       ++ + + +  gr +eAl+++ +a e+      p h   a++ +n g++++ lg+++eAle   +al+++
  gi|386002705|ref|YP_005921004.1| 512 YRKGILAYSSGRPEEALAHFTRAAELD-----PGH---AEAWNNRGWILFTLGDTDEALESIDRALEAD 572
                                       567888999**************9999.....777...99**************************986 PP

  == domain 12  score: 29.3 bits;  conditional E-value: 1.6e-09
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a a+nn++ +l+ lg+ deAle  ++ale+ ++l        a+  +n g ++ alg+ eeAle+++++++i++
  gi|386002705|ref|YP_005921004.1| 542 AEAWNNRGWILFTLGDTDEALESIDRALEADTAL--------AEGWNNRGVVLTALGKNEEALEAYNRTIDIDP 607
                                       67999**********************9999666........5558************************9975 PP

  == domain 13  score: 33.3 bits;  conditional E-value: 9.5e-11
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a  +nn+++vl++lg+ +eAle +++ ++i      p hp    + +n g  ++ lgry+eA + + +al++++
  gi|386002705|ref|YP_005921004.1| 576 AEGWNNRGVVLTALGKNEEALEAYNRTIDID-----PAHPR---AWNNKGASLYHLGRYREAADCYGRALELDP 641
                                       56789**************************.....99955...8**************************975 PP

  == domain 14  score: 18.6 bits;  conditional E-value: 3.6e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrn 50 
                                       +a+nn +a l++lgry eA +++ +ale+   ++ + +++ a++l+ 
  gi|386002705|ref|YP_005921004.1| 611 RAWNNKGASLYHLGRYREAADCYGRALELD-PAFADARANRAAALQR 656
                                       6899************************99.5566778888888775 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.7   9.1e-08   4.3e-05       3      63 ..      73     134 ..      72     136 .. 0.94
   2 !   31.0   0.1   4.6e-10   2.1e-07      10      65 ..     149     204 ..     143     208 .. 0.94
   3 !   11.1   0.7   0.00072      0.34      25      60 ..     198     233 ..     196     251 .. 0.83
   4 !    9.9   1.8    0.0017       0.8       9      64 ..     216     271 ..     209     272 .. 0.91
   5 !   16.9   2.7   1.1e-05    0.0054      11      60 ..     252     301 ..     242     306 .. 0.88
   6 !   14.0   0.4   9.2e-05     0.043      21      61 ..     296     336 ..     294     340 .. 0.90
   7 !   23.7   4.0   8.4e-08     4e-05       6      61 ..     315     370 ..     310     385 .. 0.87
   8 !   21.1   4.1   5.4e-07   0.00025       6      61 ..     349     404 ..     344     408 .. 0.92
   9 !   18.3   0.7     4e-06    0.0019       8      65 ..     385     442 ..     378     446 .. 0.92
  10 !   26.9   3.3   8.6e-09   4.1e-06       7      61 ..     452     506 ..     446     510 .. 0.92
  11 !   16.3   0.6   1.8e-05    0.0083      19      63 ..     498     542 ..     498     544 .. 0.93
  12 !   23.4   0.3   1.1e-07     5e-05       6      59 ..     519     572 ..     514     577 .. 0.91
  13 !   34.4   3.1   3.8e-11   1.8e-08      10      67 ..     591     652 ..     585     658 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.1e-08
                             TPR_9   3 aiaireedweralavverllllaPddpeerrdRG.lllaqlGclsaAladLeaylalapdap 63 
                                       +++ +e   + al  ++r l+l+Pd +e +  RG ++l+ l + + A++++e++l ++p++ 
  gi|386002705|ref|YP_005921004.1|  73 ERYRQEGAIDLALSSLDRSLALDPDLAEAWVLRGeIALYNLTDREMAVEAFERALGIDPEDG 134
                                       5899******************************5579*********************986 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 4.6e-10
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       + ++al++++r l ++P+    +  RGl+l  lG++++A+  +e++++ +pd ++a
  gi|386002705|ref|YP_005921004.1| 149 RVDEALQAYNRSLTIDPENGKAWNNRGLILGALGRYEEAASSFERAISSDPDLAAA 204
                                       6789***********************************************97765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00072
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +Pd +  +  RG +l  lG++++Al++   +la++ 
  gi|386002705|ref|YP_005921004.1| 198 DPDLAAAWQNRGNALRALGRPEEALECYASALAIDS 233
                                       799****************************99876 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0017
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        + e+al+++ + l++++  ++ +   + ll  lG+ ++Ala L+ ++  +p + +
  gi|386002705|ref|YP_005921004.1| 216 GRPEEALECYASALAIDSGLVGSWKGAAELLRALGRDEEALARLDGAVGADPGDKA 271
                                       57899****************************************99999997765 PP

  == domain 5  score: 16.9 bits;  conditional E-value: 1.1e-05
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        e+ala ++  +  +P d   + dRGl+l  lG++++A++ ++a+l+ +p
  gi|386002705|ref|YP_005921004.1| 252 DEEALARLDGAVGADPGDKAAWNDRGLILGVLGRYEEAVESFDAALRADP 301
                                       567788888888889*******************************9998 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 9.2e-05
                             TPR_9  21 llllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        l  +P     +  RGl+la lG+ ++Al+  ++ ++++p+
  gi|386002705|ref|YP_005921004.1| 296 ALRADPGYLLAWNNRGLALANLGRSEEALESYNRSIDIDPS 336
                                       57778999999*************************99995 PP

  == domain 7  score: 23.7 bits;  conditional E-value: 8.4e-08
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++  ++e+al+ ++r + ++P  +  ++ RG++l+ l+++ +A+++ + +l+++p+
  gi|386002705|ref|YP_005921004.1| 315 ANLGRSEEALESYNRSIDIDPSFALAWYNRGRALFDLERYDEAVEAYDSALEVEPA 370
                                       677899************************************************93 PP

  == domain 8  score: 21.1 bits;  conditional E-value: 5.4e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                          e++++a +++++ l + P  +  +  RG +la lG+ ++Al+  +++l+++p 
  gi|386002705|ref|YP_005921004.1| 349 FDLERYDEAVEAYDSALEVEPAFALAWNNRGAALAALGREEEALESYDRALEIDPG 404
                                       56799************************************************995 PP

  == domain 9  score: 18.3 bits;  conditional E-value: 4e-06
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                         + e+al+ ++r l ++P     ++ RG +l+  G++  A+++++ +++ +p  +da
  gi|386002705|ref|YP_005921004.1| 385 LGREEEALESYDRALEIDPGYEIAWYNRGSVLYLEGRYFDAIKAFDEAIRFNPTSADA 442
                                       567799***********************************************99887 PP

  == domain 10  score: 26.9 bits;  conditional E-value: 8.6e-09
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + ++  +al ++e  l l+P ++e +  RG++la l++ ++A+++++++l+l+p+
  gi|386002705|ref|YP_005921004.1| 452 QMRRPGEALVCYEKALELDPGRAETWHHRGVALADLNRAAEAAEAFDRALELDPE 506
                                       5677889**********************************************96 PP

  == domain 11  score: 16.3 bits;  conditional E-value: 1.8e-05
                             TPR_9  19 erllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +r l l+P+    ++  G+l + +G++++Ala + ++++l+p  +
  gi|386002705|ref|YP_005921004.1| 498 DRALELDPEYEPPWYRKGILAYSSGRPEEALAHFTRAAELDPGHA 542
                                       799***************************************554 PP

  == domain 12  score: 23.4 bits;  conditional E-value: 1.1e-07
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                        ++ + e+ala   r   l+P ++e +  RG +l+ lG++ +Al+  +++l+ +
  gi|386002705|ref|YP_005921004.1| 519 YSSGRPEEALAHFTRAAELDPGHAEAWNNRGWILFTLGDTDEALESIDRALEAD 572
                                       5677899*******************************************9865 PP

  == domain 13  score: 34.4 bits;  conditional E-value: 3.8e-11
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap....dapdaea 67 
                                       ++e+al++++r + ++P +p+ +   G  l++lG++++A+++  ++l+l+p    +++ ++a
  gi|386002705|ref|YP_005921004.1| 591 KNEEALEAYNRTIDIDPAHPRAWNNKGASLYHLGRYREAADCYGRALELDPafadARANRAA 652
                                       789************************************************66443333333 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.1     0.041        19      24      65 ..      64     105 ..      52     110 .. 0.71
   2 !   25.8   0.0   2.5e-08   1.2e-05      10      57 ..     119     166 ..     114     177 .. 0.91
   3 !   24.0   0.7   8.6e-08   4.1e-05       5      53 ..     182     230 ..     178     234 .. 0.93
   4 !   22.3   1.2   2.9e-07   0.00013       2      61 ..     213     272 ..     212     278 .. 0.92
   5 !   20.3   0.3   1.3e-06   0.00061       5      57 ..     284     336 ..     283     342 .. 0.94
   6 !   25.5   2.8   2.9e-08   1.4e-05       2      57 ..     349     404 ..     348     410 .. 0.94
   7 !   18.4   0.2     5e-06    0.0023       4      62 ..     385     443 ..     382     448 .. 0.90
   8 !    9.8   0.0    0.0024       1.1       2      45 ..     417     460 ..     416     462 .. 0.93
   9 !   24.3   0.7     7e-08   3.3e-05       1      57 [.     450     506 ..     450     514 .. 0.94
  10 !   35.7   0.1   1.9e-11   9.1e-09       2      56 ..     519     573 ..     518     580 .. 0.93
  11 !   18.5   2.0   4.5e-06    0.0021       3      62 ..     588     647 ..     586     657 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.041
                            TPR_19  24 naearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       +ae +l  Ae + + g +d A   Ld+ ++ dpd a+++ L+
  gi|386002705|ref|YP_005921004.1|  64 SAEGWLEEAERYRQEGAIDLALSSLDRSLALDPDLAEAWVLR 105
                                       666667777777888888888888888888888877666554 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.5e-08
                            TPR_19  10 AlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       A++++e+al  dp+++ +++ L +al  lg++deA ++ ++ +  dp 
  gi|386002705|ref|YP_005921004.1| 119 AVEAFERALGIDPEDGVVWYELGNALSFLGRVDEALQAYNRSLTIDPE 166
                                       99**************************************99998887 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 8.6e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       g+y+eA++ +e+a++ dp+ a+a+ +  +al alg+++eA ++ + +++
  gi|386002705|ref|YP_005921004.1| 182 GRYEEAASSFERAISSDPDLAAAWQNRGNALRALGRPEEALECYASALA 230
                                       9*****************************************9988776 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 2.9e-07
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                        a g+++eAl+ +++al+ d +    + + Ae+l alg+ +eA a Ld +  +dp d ++
  gi|386002705|ref|YP_005921004.1| 213 RALGRPEEALECYASALAIDSGLVGSWKGAAELLRALGRDEEALARLDGAVGADPGDKAA 272
                                       6779***************************************************99444 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 1.3e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       g+y+eA++ + +al +dp+++ a+ +   al +lg+ +eA +  ++  + dp 
  gi|386002705|ref|YP_005921004.1| 284 GRYEEAVESFDAALRADPGYLLAWNNRGLALANLGRSEEALESYNRSIDIDPS 336
                                       89*******************************************99999987 PP

  == domain 6  score: 25.5 bits;  conditional E-value: 2.9e-08
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       ++ ++y+eA++++ +al+ +p  a a+ +   al alg+ +eA +  d+++e dp 
  gi|386002705|ref|YP_005921004.1| 349 FDLERYDEAVEAYDSALEVEPAFALAWNNRGAALAALGREEEALESYDRALEIDPG 404
                                       67789***********************************************9997 PP

  == domain 7  score: 18.4 bits;  conditional E-value: 5e-06
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                        g+ +eAl+ + +al+ dp+++ a+++   +l+  g++ +A+++ d++ + +p +a+++
  gi|386002705|ref|YP_005921004.1| 385 LGREEEALESYDRALEIDPGYEIAWYNRGSVLYLEGRYFDAIKAFDEAIRFNPTSADAW 443
                                       57779********************************************9999985554 PP

  == domain 8  score: 9.8 bits;  conditional E-value: 0.0024
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       + eg+y +A++++ +a+  +p +a+a+     al+++ ++ eA 
  gi|386002705|ref|YP_005921004.1| 417 YLEGRYFDAIKAFDEAIRFNPTSADAWHSKGHALYQMRRPGEAL 460
                                       679************************************99997 PP

  == domain 9  score: 24.3 bits;  conditional E-value: 7e-08
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l+++ ++ eAl  +e+al+ dp+ ae +     al  l++ +eA ++ d+++e dp 
  gi|386002705|ref|YP_005921004.1| 450 LYQMRRPGEALVCYEKALELDPGRAETWHHRGVALADLNRAAEAAEAFDRALELDPE 506
                                       6899***************************************************98 PP

  == domain 10  score: 35.7 bits;  conditional E-value: 1.9e-11
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       + +g+++eAla++++a + dp++aea+ +   +l+ lg++deA + +d+++e+d 
  gi|386002705|ref|YP_005921004.1| 519 YSSGRPEEALAHFTRAAELDPGHAEAWNNRGWILFTLGDTDEALESIDRALEADT 573
                                       568*************************************************996 PP

  == domain 11  score: 18.5 bits;  conditional E-value: 4.5e-06
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       a g+ +eAl+++ + ++ dp +++a+ +    l+ lg++ eA ++  +++e dp  a+++
  gi|386002705|ref|YP_005921004.1| 588 ALGKNEEALEAYNRTIDIDPAHPRAWNNKGASLYHLGRYREAADCYGRALELDPAFADAR 647
                                       568899************************************************944444 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.83   3.9e+02       9      32 ..      75      98 ..      69     101 .. 0.82
   2 !    7.9   0.0    0.0074       3.5      11      33 ..     112     134 ..     101     136 .. 0.81
   3 !    9.8   0.0    0.0018      0.87       2      31 ..     137     166 ..     136     169 .. 0.86
   4 !   16.8   0.0     1e-05    0.0048       1      33 [.     170     200 ..     170     203 .. 0.92
   5 !   15.5   0.1   2.7e-05     0.013       1      30 [.     204     233 ..     204     235 .. 0.91
   6 ?    3.1   0.1      0.25   1.2e+02       6      34 ..     243     269 ..     238     271 .. 0.82
   7 !    8.2   0.0    0.0059       2.8      12      32 ..     283     301 ..     275     302 .. 0.91
   8 !    9.1   0.0     0.003       1.4       1      29 [.     306     334 ..     306     338 .. 0.86
   9 !   14.9   0.2   4.1e-05     0.019       1      31 [.     340     368 ..     340     372 .. 0.86
  10 !    9.0   0.2    0.0031       1.5       1      29 [.     374     402 ..     374     407 .. 0.89
  11 ?   -0.3   0.0       2.9   1.4e+03       1      29 [.     408     434 ..     408     440 .. 0.77
  12 ?    7.2   0.0     0.012       5.7       2      34 ..     443     473 ..     442     475 .. 0.82
  13 !    7.6   0.1    0.0093       4.4       2      32 ..     477     505 ..     476     509 .. 0.83
  14 !    8.0   0.0    0.0066       3.1      11      36 .]     520     543 ..     511     543 .. 0.84
  15 !   11.3   0.1   0.00061      0.29       1      28 [.     544     571 ..     544     577 .. 0.87
  16 !    7.6   0.0    0.0089       4.2       2      35 ..     579     610 ..     579     611 .. 0.89
  17 !   15.7   0.2   2.3e-05     0.011       1      31 [.     612     642 ..     612     647 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.83
                             TPR_7  9 ysrlGdyeeAielyeqsLaltkdp 32
                                      y+++G  + A++ + +sLal+ d 
  gi|386002705|ref|YP_005921004.1| 75 YRQEGAIDLALSSLDRSLALDPDL 98
                                      778888888999999999999886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0074
                             TPR_7  11 rlGdyeeAielyeqsLaltkdpe 33 
                                       +l d+e A+e +e++L+++ +++
  gi|386002705|ref|YP_005921004.1| 112 NLTDREMAVEAFERALGIDPEDG 134
                                       688***********999887776 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0018
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       ++ L+++ s lG+ +eA++ y +sL ++ +
  gi|386002705|ref|YP_005921004.1| 137 WYELGNALSFLGRVDEALQAYNRSLTIDPE 166
                                       678********************7777654 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 1e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++n + +  +lG+yeeA++ +e+  a+ +dp+
  gi|386002705|ref|YP_005921004.1| 170 AWNNRGLILGALGRYEEAASSFER--AISSDPD 200
                                       7899********************..9999986 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 2.7e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       a+ n +++ ++lG+ eeA+e+y  +La+++
  gi|386002705|ref|YP_005921004.1| 204 AWQNRGNALRALGRPEEALECYASALAIDS 233
                                       67899*******************999875 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.25
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       a+l ++lG+ eeA+  +    a+  dp+d
  gi|386002705|ref|YP_005921004.1| 243 AELLRALGRDEEALARLDG--AVGADPGD 269
                                       8999*********998888..77777776 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.0059
                             TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                       lG+yeeA+e + +  al+ dp
  gi|386002705|ref|YP_005921004.1| 283 LGRYEEAVESFDA--ALRADP 301
                                       7************..888887 PP

  == domain 8  score: 9.1 bits;  conditional E-value: 0.003
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++n + +  +lG+ eeA+e y +s+ ++
  gi|386002705|ref|YP_005921004.1| 306 AWNNRGLALANLGRSEEALESYNRSIDID 334
                                       799*******************9965554 PP

  == domain 9  score: 14.9 bits;  conditional E-value: 4.1e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n +r+ ++l +y+eA+e y    al+ +
  gi|386002705|ref|YP_005921004.1| 340 AWYNRGRALFDLERYDEAVEAYDS--ALEVE 368
                                       789*********************..55544 PP

  == domain 10  score: 9.0 bits;  conditional E-value: 0.0031
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++n + +  +lG+ eeA+e y ++L+++
  gi|386002705|ref|YP_005921004.1| 374 AWNNRGAALAALGREEEALESYDRALEID 402
                                       789*********************77765 PP

  == domain 11  score: -0.3 bits;  conditional E-value: 2.9
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++n +++   +G+y +Ai+ + +  a++
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDE--AIR 434
                                       677888888888999999999988..665 PP

  == domain 12  score: 7.2 bits;  conditional E-value: 0.012
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       ++  +++  ++++  eA+ +ye+  al+ dp+ 
  gi|386002705|ref|YP_005921004.1| 443 WHSKGHALYQMRRPGEALVCYEK--ALELDPGR 473
                                       677788999999999********..88888776 PP

  == domain 13  score: 7.6 bits;  conditional E-value: 0.0093
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++  +++  +l++ +eA+e + ++L+l+  p
  gi|386002705|ref|YP_005921004.1| 477 WHHRGVALADLNRAAEAAEAFDRALELD--P 505
                                       778899*****************55554..4 PP

  == domain 14  score: 8.0 bits;  conditional E-value: 0.0066
                             TPR_7  11 rlGdyeeAielyeqsLaltkdpedae 36 
                                       + G+ eeA+ ++++  a + dp++ae
  gi|386002705|ref|YP_005921004.1| 520 SSGRPEEALAHFTR--AAELDPGHAE 543
                                       56************..9999999875 PP

  == domain 15  score: 11.3 bits;  conditional E-value: 0.00061
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n + + + lGd++eA+e   ++L+ 
  gi|386002705|ref|YP_005921004.1| 544 AWNNRGWILFTLGDTDEALESIDRALEA 571
                                       799*********************6654 PP

  == domain 16  score: 7.6 bits;  conditional E-value: 0.0089
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       ++n +++  +lG+ eeA+e y +   ++ dp ++
  gi|386002705|ref|YP_005921004.1| 579 WNNRGVVLTALGKNEEALEAYNR--TIDIDPAHP 610
                                       6899******************9..998888776 PP

  == domain 17  score: 15.7 bits;  conditional E-value: 2.3e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       a++n +     lG+y+eA+++y ++L+l+ +
  gi|386002705|ref|YP_005921004.1| 612 AWNNKGASLYHLGRYREAADCYGRALELDPA 642
                                       577788888889************7777655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.054        26       2      31 ..     101     131 ..     100     133 .. 0.75
   2 ?    7.3   0.0     0.017         8       3      31 ..     137     165 ..     135     167 .. 0.86
   3 !    9.1   0.0    0.0047       2.2       6      32 ..     174     200 ..     173     201 .. 0.91
   4 ?    5.6   0.2     0.059        28       5      27 ..     207     229 ..     203     231 .. 0.86
   5 ?    0.5   0.1       2.5   1.2e+03       6      23 ..     242     259 ..     241     268 .. 0.84
   6 ?    3.6   0.0      0.27   1.3e+02      12      31 ..     282     301 ..     273     303 .. 0.82
   7 ?    7.0   0.0     0.022        10       6      31 ..     310     335 ..     309     336 .. 0.88
   8 !   13.1   0.1   0.00024      0.11       2      28 ..     340     366 ..     339     370 .. 0.90
   9 ?    6.4   0.1     0.034        16       7      31 ..     379     403 ..     377     405 .. 0.86
  10 !    9.4   0.0    0.0036       1.7       2      33 .]     408     439 ..     407     439 .. 0.90
  11 ?    1.5   0.0       1.2   5.9e+02       7      31 ..     447     471 ..     441     472 .. 0.83
  12 ?    6.3   0.0     0.037        17       6      32 ..     480     506 ..     475     507 .. 0.87
  13 ?    4.5   0.0      0.14        64       4      32 ..     512     540 ..     511     541 .. 0.84
  14 ?    5.0   0.0     0.094        44       6      27 ..     548     569 ..     544     571 .. 0.87
  15 ?    6.3   0.0     0.037        18       7      31 ..     583     607 ..     581     609 .. 0.84
  16 ?    6.0   0.1     0.046        22       7      31 ..     617     641 ..     615     642 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.054
                                       HHHHHH.HHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 Alykla.lsyrklgdtdkAlealerlikeYP 31 
                                       A  +++  ++++l+d + A+ea+er +   P
  gi|386002705|ref|YP_005921004.1| 101 AWVLRGeIALYNLTDREMAVEAFERALGIDP 131
                                       66666734566799***********986665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlikeYP 31 
                                        y l+ ++  lg+ d+Al+a++r ++  P
  gi|386002705|ref|YP_005921004.1| 137 WYELGNALSFLGRVDEALQAYNRSLTIDP 165
                                       799999999999**********9777666 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       ++l + +lg++++A   +er i++ Pd
  gi|386002705|ref|YP_005921004.1| 174 RGLILGALGRYEEAASSFERAISSDPD 200
                                       688888999***************998 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerli 27 
                                       +++ ++r+lg++++Ale + + +
  gi|386002705|ref|YP_005921004.1| 207 NRGNALRALGRPEEALECYASAL 229
                                       68999***99********98765 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAleal 23 
                                       +a+++r+lg+ ++Al+ l
  gi|386002705|ref|YP_005921004.1| 242 AAELLRALGRDEEALARL 259
                                       589999999*****9877 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  12 klgdtdkAlealerlikeYP 31 
                                        lg++++A+e ++  ++  P
  gi|386002705|ref|YP_005921004.1| 282 VLGRYEEAVESFDAALRADP 301
                                       479**********9998877 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       ++l++ +lg++++Ale ++r i+  P
  gi|386002705|ref|YP_005921004.1| 310 RGLALANLGRSEEALESYNRSIDIDP 335
                                       7999***99**********9888766 PP

  == domain 8  score: 13.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       A y+++++++ l ++d+A+ea+++ ++
  gi|386002705|ref|YP_005921004.1| 340 AWYNRGRALFDLERYDEAVEAYDSALE 366
                                       89*********88*********99887 PP

  == domain 9  score: 6.4 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + ++ +lg+ ++Ale ++r ++  P
  gi|386002705|ref|YP_005921004.1| 379 GAALAALGREEEALESYDRALEIDP 403
                                       67788899************99888 PP

  == domain 10  score: 9.4 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       A y+++  ++  g++ +A++a+++ i+  P+S
  gi|386002705|ref|YP_005921004.1| 408 AWYNRGSVLYLEGRYFDAIKAFDEAIRFNPTS 439
                                       88****8888878*************988876 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + +++++ ++ +Al  +e+ ++  P
  gi|386002705|ref|YP_005921004.1| 447 GHALYQMRRPGEALVCYEKALELDP 471
                                       66888888999********999877 PP

  == domain 12  score: 6.3 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       ++ ++  l+++++A ea++r ++  P+
  gi|386002705|ref|YP_005921004.1| 480 RGVALADLNRAAEAAEAFDRALELDPE 506
                                       788899999*************99885 PP

  == domain 13  score: 4.5 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       y+ + + ++ g++++Al+ + r  +  P+
  gi|386002705|ref|YP_005921004.1| 512 YRKGILAYSSGRPEEALAHFTRAAELDPG 540
                                       88887788766***********9998886 PP

  == domain 14  score: 5.0 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                       +++ ++ lgdtd+Ale  +r +
  gi|386002705|ref|YP_005921004.1| 548 RGWILFTLGDTDEALESIDRAL 569
                                       7999**999******9888776 PP

  == domain 15  score: 6.3 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       +  + +lg+ ++Alea++r i+  P
  gi|386002705|ref|YP_005921004.1| 583 GVVLTALGKNEEALEAYNRTIDIDP 607
                                       66677889************99888 PP

  == domain 16  score: 6.0 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       + s++ lg++++A + + r ++  P
  gi|386002705|ref|YP_005921004.1| 617 GASLYHLGRYREAADCYGRALELDP 641
                                       66889999***********999777 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       9.1   4.3e+03      15      28 ..      59      72 ..      58      78 .. 0.78
   2 ?    0.4   0.0       1.4   6.7e+02      11      30 ..     109     128 ..     108     132 .. 0.74
   3 !   11.3   0.1   0.00052      0.25       7      31 ..     139     163 ..     138     163 .. 0.92
   4 !   11.5   0.1   0.00045      0.21       6      30 ..     172     196 ..     171     197 .. 0.96
   5 !   14.0   0.4   7.4e-05     0.035       7      31 ..     207     231 ..     201     237 .. 0.90
   6 ?    2.6   0.6      0.29   1.4e+02       9      28 ..     243     262 ..     242     265 .. 0.83
   7 ?    5.2   0.1     0.042        20       7      30 ..     275     298 ..     273     299 .. 0.85
   8 ?    6.7   0.4     0.014       6.7       6      30 ..     308     332 ..     306     333 .. 0.91
   9 !   11.0   0.4   0.00062      0.29       7      31 ..     343     367 ..     342     368 .. 0.93
  10 !   10.4   2.2   0.00098      0.46       6      31 ..     376     401 ..     372     401 .. 0.95
  11 ?    2.2   0.0      0.38   1.8e+02       7      30 ..     411     434 ..     410     435 .. 0.90
  12 !   11.3   0.1   0.00053      0.25       9      30 ..     447     468 ..     440     469 .. 0.92
  13 ?    6.1   1.1     0.023        11       6      30 ..     478     502 ..     473     503 .. 0.89
  14 ?    3.3   0.0      0.17        82       9      30 ..     515     536 ..     515     537 .. 0.85
  15 !    8.0   0.1    0.0057       2.7       6      30 ..     546     570 ..     542     574 .. 0.92
  16 !    9.2   0.1    0.0025       1.2       6      31 ..     580     605 ..     580     605 .. 0.92
  17 !   10.6   0.5   0.00085       0.4       6      30 ..     614     638 ..     612     639 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.1
                            TPR_10 15 rgrydeAealleea 28
                                      +g+ + Ae +leea
  gi|386002705|ref|YP_005921004.1| 59 LGDEESAEGWLEEA 72
                                      57778899999987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.4
                            TPR_10  11 alrqrgrydeAealleeala 30 
                                       al+++ +++ A++ +e+al 
  gi|386002705|ref|YP_005921004.1| 109 ALYNLTDREMAVEAFERALG 128
                                       67777778888888888874 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00052
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                        L+nal+ +gr deA++ + ++l i
  gi|386002705|ref|YP_005921004.1| 139 ELGNALSFLGRVDEALQAYNRSLTI 163
                                       59****************9999875 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00045
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN + +l ++gry+eA   +e+a++
  gi|386002705|ref|YP_005921004.1| 172 NNRGLILGALGRYEEAASSFERAIS 196
                                       999********************96 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 7.4e-05
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N +nalr++gr +eA++ +  alai
  gi|386002705|ref|YP_005921004.1| 207 NRGNALRALGRPEEALECYASALAI 231
                                       88*********************97 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.29
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       a +lr++gr +eA+a l+ a
  gi|386002705|ref|YP_005921004.1| 243 AELLRALGRDEEALARLDGA 262
                                       6689*********9977655 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.042
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       + + +l  +gry+eA++ ++ al+
  gi|386002705|ref|YP_005921004.1| 275 DRGLILGVLGRYEEAVESFDAALR 298
                                       567888889********9999996 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.014
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN + al ++gr +eA++ + ++++
  gi|386002705|ref|YP_005921004.1| 308 NNRGLALANLGRSEEALESYNRSID 332
                                       99***************99988876 PP

  == domain 9  score: 11.0 bits;  conditional E-value: 0.00062
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++al+++ rydeA++ ++ al++
  gi|386002705|ref|YP_005921004.1| 343 NRGRALFDLERYDEAVEAYDSALEV 367
                                       779*******************985 PP

  == domain 10  score: 10.4 bits;  conditional E-value: 0.00098
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN ++al ++gr +eA++ +++al+i
  gi|386002705|ref|YP_005921004.1| 376 NNRGAALAALGREEEALESYDRALEI 401
                                       9***********************97 PP

  == domain 11  score: 2.2 bits;  conditional E-value: 0.38
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N + +l+  gry +A + ++ea++
  gi|386002705|ref|YP_005921004.1| 411 NRGSVLYLEGRYFDAIKAFDEAIR 434
                                       668899999*************96 PP

  == domain 12  score: 11.3 bits;  conditional E-value: 0.00053
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       ++al+q++r  eA+  +e+al+
  gi|386002705|ref|YP_005921004.1| 447 GHALYQMRRPGEALVCYEKALE 468
                                       89*******************8 PP

  == domain 13  score: 6.1 bits;  conditional E-value: 0.023
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       ++ ++al +++r +eA + +++al+
  gi|386002705|ref|YP_005921004.1| 478 HHRGVALADLNRAAEAAEAFDRALE 502
                                       56699******************98 PP

  == domain 14  score: 3.3 bits;  conditional E-value: 0.17
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       +++ ++ gr +eA+a++ +a +
  gi|386002705|ref|YP_005921004.1| 515 GILAYSSGRPEEALAHFTRAAE 536
                                       5677999*********998875 PP

  == domain 15  score: 8.0 bits;  conditional E-value: 0.0057
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN + +l+ +g+ deA++  ++al+
  gi|386002705|ref|YP_005921004.1| 546 NNRGWILFTLGDTDEALESIDRALE 570
                                       9*****************9999997 PP

  == domain 16  score: 9.2 bits;  conditional E-value: 0.0025
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN +++l+++g+ +eA++ + ++++i
  gi|386002705|ref|YP_005921004.1| 580 NNRGVVLTALGKNEEALEAYNRTIDI 605
                                       99****************99988865 PP

  == domain 17  score: 10.6 bits;  conditional E-value: 0.00085
                            TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                       nN ++ l+++gry eA + + +al+
  gi|386002705|ref|YP_005921004.1| 614 NNKGASLYHLGRYREAADCYGRALE 638
                                       899********************98 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.013       6.4      32      80 ..     109     158 ..      77     160 .. 0.86
   2 !    7.8   0.0    0.0079       3.7       8      81 ..     119     193 ..     111     194 .. 0.79
   3 !    9.3   0.1    0.0028       1.3       3      80 ..     182     260 ..     180     262 .. 0.85
   4 !   17.0   0.1   1.1e-05    0.0052      29      80 ..     310     362 ..     282     364 .. 0.79
   5 !   17.1   0.0   9.9e-06    0.0046       7      81 ..     390     465 ..     385     466 .. 0.83
   6 !    7.6   0.0    0.0093       4.4       4      81 ..     489     567 ..     483     568 .. 0.85
   7 !   15.0   0.0   4.4e-05     0.021      32      81 ..     585     635 ..     569     636 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                                       HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       +ly++ + + A e +++a ++++++  ++y ++ +l  L++++eA++a+ 
  gi|386002705|ref|YP_005921004.1| 109 ALYNLTDREMAVEAFERAlGIDPEDGVVWYELGNALSFLGRVDEALQAYN 158
                                       689999999*************************************9986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0079
                                       HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       A+  +er+l  ++e+    y l+ +l  +g+ ++A++ ++++  +++++ +++   +  l +L++yeeA + +e+
  gi|386002705|ref|YP_005921004.1| 119 AVEAFERALGIDPEDGVVWYELGNALSFLGRVDEALQAYNRSlTIDPENGKAWNNRGLILGALGRYEEAASSFER 193
                                       555666777444555555666799999999999999999999999999999999999999999999999988876 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0028
                                       T-HHHHHHHHHHHH.HHH--HHHHHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayll.AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       ++y++A   +er+  ++  ++ +a    + +l  +g+ ++A+e + +a  ++s   g++  +A+ l +L++ eeA+a
  gi|386002705|ref|YP_005921004.1| 182 GRYEEAASSFERAI-SSDPDLAAAWQNrGNALRALGRPEEALECYASAlAIDSGLVGSWKGAAELLRALGRDEEALA 257
                                       57999999999999.4443444444436********************99999999********************9 PP

                                       HH- CS
                            ANAPC3  78 aLe 80 
                                        L+
  gi|386002705|ref|YP_005921004.1| 258 RLD 260
                                       886 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                        +l+l ++g+ ++A+e ++++ +++++   ++y  +++l++L++y+eA+ a++
  gi|386002705|ref|YP_005921004.1| 310 RGLALANLGRSEEALESYNRSiDIDPSFALAWYNRGRALFDLERYDEAVEAYD 362
                                       389999*******************************************9986 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 9.9e-06
                                       HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +A+  ++r+l+ ++  + + y  + +lyl g+y  A++ +++a + n++s  ++  ++++l+++ +  eA+ ++ek
  gi|386002705|ref|YP_005921004.1| 390 EALESYDRALEIDPGYEIAWYNRGSVLYLEGRYFDAIKAFDEAiRFNPTSADAWHSKGHALYQMRRPGEALVCYEK 465
                                       5666667777444444444444599***********************************************9998 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0093
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +  +A   ++r+l+ ++e +   y ++   y++g+ ++A+  + +a +l++ + +++   +  l+ L+  +eA+  +
  gi|386002705|ref|YP_005921004.1| 489 RAAEAAEAFDRALELDPEYEPPWYRKGILAYSSGRPEEALAHFTRAaELDPGHAEAWNNRGWILFTLGDTDEALESI 565
                                       556677777777777777777777778889****************9**************************9987 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       ++
  gi|386002705|ref|YP_005921004.1| 566 DR 567
                                       65 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 4.4e-05
                                       HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +l  +g+ ++A+e ++++ ++++ +++++  ++ +l+ L++y eA +++++
  gi|386002705|ref|YP_005921004.1| 585 VLTALGKNEEALEAYNRTiDIDPAHPRAWNNKGASLYHLGRYREAADCYGR 635
                                       566789999**************************************9986 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3    0.0002     0.092      62     121 ..      99     159 ..      56     163 .. 0.83
   2 !   16.0   0.6   2.6e-05     0.012      73     122 ..     179     228 ..     169     233 .. 0.92
   3 !    9.4   0.2    0.0028       1.3      68     122 ..     242     296 ..     230     298 .. 0.91
   4 !   14.3   0.4   8.8e-05     0.042      74     121 ..     282     329 ..     271     333 .. 0.92
   5 !   17.2   2.2   1.1e-05    0.0053      64     123 ..     340     399 ..     332     407 .. 0.91
   6 !    9.2   0.0    0.0033       1.6      75     122 ..     419     466 ..     408     475 .. 0.91
   7 !   12.9   1.0   0.00023      0.11      62     123 ..     474     535 ..     466     538 .. 0.84
   8 !    8.5   0.2    0.0055       2.6      61     122 ..     541     602 ..     532     605 .. 0.87
   9 !    9.1   1.5    0.0036       1.7      69     122 ..     583     636 ..     548     659 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0002
                                       HHHHHHHHH.HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  62 lealealae.aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                        ea   + e a+  l ++e a++  e+++  +P +   + +l  Al  +Gr  eAL++Y+r
  gi|386002705|ref|YP_005921004.1|  99 AEAWVLRGEiALYNLTDREMAVEAFERALGIDPEDGVVWYELGNALSFLGRVDEALQAYNR 159
                                       555666666455667899999**************************************98 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.6e-05
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        +lGr+eea++  e++++ +P   ++++    Al+++Gr +eALe Y ++
  gi|386002705|ref|YP_005921004.1| 179 GALGRYEEAASSFERAISSDPDLAAAWQNRGNALRALGRPEEALECYASA 228
                                       589********************************************876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0028
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        ae++ +lGr eeala+l+++v ++P + +++    + l  +Gr +eA e ++ +
  gi|386002705|ref|YP_005921004.1| 242 AAELLRALGRDEEALARLDGAVGADPGDKAAWNDRGLILGVLGRYEEAVESFDAA 296
                                       5788899****************************999**********9999765 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 8.8e-05
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                        lGr+eea++  +a+++++P    ++    +Ala +Gr +eALe Y+r
  gi|386002705|ref|YP_005921004.1| 282 VLGRYEEAVESFDAALRADPGYLLAWNNRGLALANLGRSEEALESYNR 329
                                       58********************************************98 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       a   + +a++ l+r++ea++ ++++++ +P    ++    +Ala++Gr++eALe Y+r+ 
  gi|386002705|ref|YP_005921004.1| 340 AWYNRGRALFDLERYDEAVEAYDSALEVEPAFALAWNNRGAALAALGREEEALESYDRAL 399
                                       566788999***********************************************9984 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0033
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        Gr+ +a++  +++++ +P+  +++     Al+++ r +eAL  Ye++
  gi|386002705|ref|YP_005921004.1| 419 EGRYFDAIKAFDEAIRFNPTSADAWHSKGHALYQMRRPGEALVCYEKA 466
                                       589999***************************************987 PP

  == domain 7  score: 12.9 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        e    +  a++ l+ra+ea++  +++++++P  E  +       + sGr +eAL+ + r+ 
  gi|386002705|ref|YP_005921004.1| 474 AETWHHRGVALADLNRAAEAAEAFDRALELDPEYEPPWYRKGILAYSSGRPEEALAHFTRAA 535
                                       5566677778999**********************9876665556789**********9975 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  61 rlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                         ea   +   +++lG+ +eal+  +++++++    + +      l ++G+++eALe+Y+r+
  gi|386002705|ref|YP_005921004.1| 541 HAEAWNNRGWILFTLGDTDEALESIDRALEADTALAEGWNNRGVVLTALGKNEEALEAYNRT 602
                                       56677777788899**********************************************97 PP

  == domain 9  score: 9.1 bits;  conditional E-value: 0.0036
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                          +++lG+ eeal+ +++ ++ +P + r++    + l+++Gr  eA   Y r+
  gi|386002705|ref|YP_005921004.1| 583 GVVLTALGKNEEALEAYNRTIDIDPAHPRAWNNKGASLYHLGRYREAADCYGRA 636
                                       336789999999999999999999999999999999999999999999998776 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   0.00012     0.057      68     126 ..     140     194 ..     119     197 .. 0.82
   2 ?    5.8   0.0     0.028        13     101     126 ..     203     228 ..     200     245 .. 0.86
   3 !    9.9   0.1    0.0015      0.73      68     126 ..     283     330 ..     276     335 .. 0.79
   4 !   10.3   0.3    0.0012      0.56      62     128 ..     345     400 ..     331     403 .. 0.69
   5 ?   -1.8   0.0       6.3     3e+03     104     126 ..     410     432 ..     407     438 .. 0.77
   6 ?    0.1   0.0       1.6   7.5e+02     104     128 ..     444     468 ..     414     479 .. 0.73
   7 ?    4.4   0.1     0.078        37      99     129 ..     477     503 ..     431     509 .. 0.73
   8 ?    4.3   0.1     0.083        39      79     128 ..     525     570 ..     517     577 .. 0.76
   9 ?    5.4   0.2     0.039        18      67     126 ..     554     602 ..     532     606 .. 0.71
  10 !    8.0   0.1    0.0058       2.7      60     128 ..     574     638 ..     570     641 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                                       TT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  68 lgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       lg+  + l  +d+al+ +nr   ++ ++Gk W     +r+  l  lGr++ea  +f+ a
  gi|386002705|ref|YP_005921004.1| 140 LGNALSFLGRVDEALQAYNRSLTIDPENGKAW----NNRGLILGALGRYEEAASSFERA 194
                                       4444455666788888899999**********....58*****************9987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 101 aavfsravaleelGrkdealkafrma 126
                                       aa  +r+ al  lGr +eal+ +  a
  gi|386002705|ref|YP_005921004.1| 203 AAWQNRGNALRALGRPEEALECYASA 228
                                       56679****************99877 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0015
                                       TT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  68 lgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       lgry+ea+es d alr          d G   + a  +r+ al++lGr++eal++++ +
  gi|386002705|ref|YP_005921004.1| 283 LGRYEEAVESFDAALR---------ADPGY--LLAWNNRGLALANLGRSEEALESYNRS 330
                                       6777777777777764.........56664..467889*****************9876 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0012
                                       HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                         al  l rydea+e+ d+al+       +e +       a  +r++al+ lGr++eal+++  a e
  gi|386002705|ref|YP_005921004.1| 345 GRALFDLERYDEAVEAYDSALE-------VEPAFA----LAWNNRGAALAALGREEEALESYDRALE 400
                                       5666666666666666666663.......333333....3446899999999999999999999887 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 6.3
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                       ++r+  l   Gr+ +a+kaf  a
  gi|386002705|ref|YP_005921004.1| 410 YNRGSVLYLEGRYFDAIKAFDEA 432
                                       67888888888888888888766 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.6
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmage 128
                                        s+++al ++ r  eal  +++a e
  gi|386002705|ref|YP_005921004.1| 444 HSKGHALYQMRRPGEALVCYEKALE 468
                                       4666666666666677666666666 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  99 WiaavfsravaleelGrkdealkafrmagem 129
                                       W     +r+val++l r +ea +af  a e+
  gi|386002705|ref|YP_005921004.1| 477 W----HHRGVALADLNRAAEAAEAFDRALEL 503
                                       3....579999**********9999999886 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.083
                                       HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       ++al +f r  el+    + W     +r+  l  lG +deal++   a e
  gi|386002705|ref|YP_005921004.1| 525 EEALAHFTRAAELDPGHAEAW----NNRGWILFTLGDTDEALESIDRALE 570
                                       678888888888887777777....5788888888888888887776655 PP

  == domain 9  score: 5.4 bits;  conditional E-value: 0.039
                                       HTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  67 klgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                        lg+ deales+d+al+      +   +eG  W     +r+v l  lG+++eal+a++ +
  gi|386002705|ref|YP_005921004.1| 554 TLGDTDEALESIDRALEA-----DTALAEG--W----NNRGVVLTALGKNEEALEAYNRT 602
                                       566666666666666642.....2233333..4....57899999999999999998865 PP

  == domain 10  score: 8.0 bits;  conditional E-value: 0.0058
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  60 glsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                       +l+e + + g   +al   ++al+ +nr  +++ +  + W     +++++l  lGr+ ea + +  a e
  gi|386002705|ref|YP_005921004.1| 574 ALAEGWNNRGVVLTALGKNEEALEAYNRTIDIDPAHPRAW----NNKGASLYHLGRYREAADCYGRALE 638
                                       567777777777889999999*******999999999999....58999***********999988877 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.098        46     200     259 ..      73     133 ..      70     158 .. 0.88
   2 ?   -1.3   0.0       1.7   7.9e+02      45      73 ..     141     169 ..     132     176 .. 0.83
   3 !    6.2   0.0    0.0088       4.1     205     256 ..     181     232 ..     176     234 .. 0.68
   4 ?    3.3   0.0     0.065        30      12      68 ..     244     300 ..     242     328 .. 0.83
   5 ?    2.7   0.1       0.1        48      17      70 ..     317     370 ..     309     401 .. 0.62
   6 ?    0.2   0.1      0.59   2.8e+02      42      69 ..     376     403 ..     353     417 .. 0.71
   7 ?    5.0   0.0      0.02       9.4     208     256 ..     422     470 ..     405     474 .. 0.91
   8 ?    5.3   0.0     0.017       7.9     207     257 ..     523     573 ..     512     576 .. 0.79
   9 !    8.6   0.1    0.0016      0.76     205     273 ..     589     659 ..     584     660 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.098
                                       HHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHH.HHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 200 qhydklgsrekAleyidkaiehtptlvelyltKaril.khaGdlkkAaevmeearklDlaD 259
                                         y + g  + Al+ +d+ ++ +p l e ++ +++i      d + A+e+ e+a  +D +D
  gi|386002705|ref|YP_005921004.1|  73 ERYRQEGAIDLALSSLDRSLALDPDLAEAWVLRGEIAlYNLTDREMAVEAFERALGIDPED 133
                                       66778888999************************96256799999999999999999887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                       HHHHHHTT-HHHHHHHHHHHHHH-TT-CH CS
                             NARP1  45 aelllkLgrkeeAeatyeaLlernpensk 73 
                                       ++ l  Lgr +eA ++y++ l+  pen k
  gi|386002705|ref|YP_005921004.1| 141 GNALSFLGRVDEALQAYNRSLTIDPENGK 169
                                       5667789***********99999999965 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0088
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       lg++e+A +  ++ai+++p l   ++++++ l+  G +++A e+  +a ++D
  gi|386002705|ref|YP_005921004.1| 181 LGRYEEAASSFERAISSDPDLAAAWQNRGNALRALGRPEEALECYASALAID 232
                                       5667777777777777777777777777777777777777777766666655 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.065
                                       HHHHHHTHHHHHHHHHHH.HGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH- CS
                             NARP1  12 qiieeagkleeAlehLee.kekqivDklavketkaelllkLgrkeeAeatyeaLlern 68 
                                        +++  g+ eeAl++L+  +  +  Dk a++  ++ +l  Lgr+eeA + + a l+  
  gi|386002705|ref|YP_005921004.1| 244 ELLRALGRDEEALARLDGaVGADPGDKAAWN-DRGLILGVLGRYEEAVESFDAALRAD 300
                                       578889999*******974677778888776.699**************999887765 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.1
                                       HTHHHHHHHHHHH.HGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                             NARP1  17 agkleeAlehLee.kekqivDklavketkaelllkLgrkeeAeatyeaLlernpe 70 
                                        g+ eeAle  ++  + +    la+  ++++ l+ L+r++eA ++y + le  p 
  gi|386002705|ref|YP_005921004.1| 317 LGRSEEALESYNRsIDIDPSFALAW-YNRGRALFDLERYDEAVEAYDSALEVEPA 370
                                       5666666666554122222333333.46888899999999999999888877665 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.59
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                             NARP1  42 etkaelllkLgrkeeAeatyeaLlernp 69 
                                       ++++  l +Lgr+eeA + y + le  p
  gi|386002705|ref|YP_005921004.1| 376 NNRGAALAALGREEEALESYDRALEIDP 403
                                       4577777888888888888877777665 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.02
                                       SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       +  A++  d+ai+ +pt+ + +  K++ l ++  + +A  + e+a +lD
  gi|386002705|ref|YP_005921004.1| 422 YFDAIKAFDEAIRFNPTSADAWHSKGHALYQMRRPGEALVCYEKALELD 470
                                       5589****************************9999**99999999999 PP

  == domain 8  score: 5.3 bits;  conditional E-value: 0.017
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       + e+Al    +a e +p   e + +++ il   Gd ++A e +++a + D+
  gi|386002705|ref|YP_005921004.1| 523 RPEEALAHFTRAAELDPGHAEAWNNRGWILFTLGDTDEALESIDRALEADT 573
                                       456788888888888888888888888888888888888888888888877 PP

  == domain 9  score: 8.6 bits;  conditional E-value: 0.0016
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT..T-HHHHHHHHHHHHHT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl..aDRyiNskcakymLra 273
                                       lg+ e+Ale  ++ i+ +p     + +K+  l h G  ++Aa++  +a +lD   aD   N  +a + L+a
  gi|386002705|ref|YP_005921004.1| 589 LGKNEEALEAYNRTIDIDPAHPRAWNNKGASLYHLGRYREAADCYGRALELDPafADARANRAAALQRLQA 659
                                       67899***********************************************6225777777777776665 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.7   1.8e-06   0.00084     143     244 ..      62     164 ..      46     173 .. 0.79
   2 !    6.8   0.1    0.0072       3.4     146     176 ..     202     232 ..     177     237 .. 0.76
   3 !    7.5   0.5    0.0043         2     149     242 ..     239     332 ..     236     341 .. 0.81
   4 !    7.5   3.8    0.0045       2.1     141     242 ..     296     400 ..     288     409 .. 0.76
   5 ?    5.3   1.9      0.02       9.5     140     178 ..     363     404 ..     336     469 .. 0.59
   6 ?    5.6   0.1     0.017       7.9     141     201 ..     434     495 ..     420     510 .. 0.78
   7 !   15.4   1.6   1.8e-05    0.0084     148     244 ..     510     606 ..     483     613 .. 0.80
   8 ?    0.9   0.0      0.44   2.1e+02     149     184 ..     613     648 ..     607     650 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-06
                            TPR_15 143 eqsaafllaraelyrqegqtdaAlrdyreAlalapdssel...r.aallWlliDlgrraeLrellkawkaraesdas 215
                                       e+sa  +l  ae yrqeg+ d Al  + + lal+pd +e+   r +  l++l D++ + e   + ++  +   +d +
  gi|386002705|ref|YP_005921004.1|  62 EESAEGWLEEAERYRQEGAIDLALSSLDRSLALDPDLAEAwvlRgEIALYNLTDREMAVE---AFERALGIDPEDGV 135
                                       689999******************************776422232335777877775554...555555666***** PP

                            TPR_15 216 LwgplaaAlllLgrpkkALeylrkqaken 244
                                        w  l+ Al++Lgr ++AL+ +++ +   
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQAYNRSLTID 164
                                       **********************9987655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0072
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlala 176
                                       aa ++ r+++ r+ g++++Al++y  Ala +
  gi|386002705|ref|YP_005921004.1| 202 AAAWQNRGNALRALGRPEEALECYASALAID 232
                                       6889999*****************9999876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0043
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselra.allWlliDlgrraeLrellkawkaraesdasLwgpl...a 221
                                       +   ael r+ g+ ++Al  +  A+ ++p+++++ + + l l + lgr++e   +++ + a+ ++d+ + ++    +
  gi|386002705|ref|YP_005921004.1| 239 WKGAAELLRALGRDEEALARLDGAVGADPGDKAAWNdRGLILGV-LGRYEE---AVESFDAALRADPGYLLAWnnrG 311
                                       777899************************99986514444445.8*9997...99999999999998855543338 PP

                            TPR_15 222 aAlllLgrpkkALeylrkqak 242
                                        Al+ Lgr+++ALe +++  +
  gi|386002705|ref|YP_005921004.1| 312 LALANLGRSEEALESYNRSID 332
                                       9*************9998765 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0045
                            TPR_15 141 aaeqsaaflla...raelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesda 214
                                       a++ ++ +lla   r+ +  + g++++Al+ y + ++ +p  + +  +   +l Dl+r++e   +++a+  + e ++
  gi|386002705|ref|YP_005921004.1| 296 ALRADPGYLLAwnnRGLALANLGRSEEALESYNRSIDIDPSFALAWYNRGRALFDLERYDE---AVEAYDSALEVEP 369
                                       55566665554333788889999*****************97776666667899******7...8999988885555 PP

                            TPR_15 215 sL...wgplaaAlllLgrpkkALeylrkqak 242
                                       +    w+  +aAl++Lgr+++ALe + + ++
  gi|386002705|ref|YP_005921004.1| 370 AFalaWNNRGAALAALGREEEALESYDRALE 400
                                       5411267779**************9988765 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.02
                            TPR_15 140 eaaeqsaaf...llaraelyrqegqtdaAlrdyreAlalapd 178
                                       +a+e ++af   +  r+++  + g++++Al+ y +Al+ +p+
  gi|386002705|ref|YP_005921004.1| 363 SALEVEPAFalaWNNRGAALAALGREEEALESYDRALEIDPG 404
                                       334433333222566666666667777777777777766666 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.017
                            TPR_15 141 aae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLre 201
                                       +++  sa  +   + +  q  ++ +Al +y++Al+l+p+ +e       +l Dl+r+ae+ e
  gi|386002705|ref|YP_005921004.1| 434 RFNpTSADAWHSKGHALYQMRRPGEALVCYEKALELDPGRAETWHHRGVALADLNRAAEAAE 495
                                       5555678888889999999999****************998877777777777777777555 PP

  == domain 7  score: 15.4 bits;  conditional E-value: 1.8e-05
                            TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAl 224
                                        +++ + l+   g++++Al  + +A +l+p+ +e+ ++  W+l  lg ++e+ e + +  ++  + a+ w+  +  l
  gi|386002705|ref|YP_005921004.1| 510 PWYRKGILAYSSGRPEEALAHFTRAAELDPGHAEAWNNRGWILFTLGDTDEALESIDRALEADTALAEGWNNRGVVL 586
                                       488888889999**************************************94444433333335566668888999* PP

                            TPR_15 225 llLgrpkkALeylrkqaken 244
                                        +Lg++++ALe +++  +  
  gi|386002705|ref|YP_005921004.1| 587 TALGKNEEALEAYNRTIDID 606
                                       ************99987655 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.44
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselra 184
                                       +   +++    g+  +A  +y +Al+l+p+ +++ra
  gi|386002705|ref|YP_005921004.1| 613 WNNKGASLYHLGRYREAADCYGRALELDPAFADARA 648
                                       666666677789999**************9999887 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.46   2.2e+02     144     178 ..      62      96 ..       4     111 .. 0.84
   2 !    8.0   0.0    0.0031       1.5     260     335 ..     149     234 ..     134     247 .. 0.68
   3 ?    3.3   0.0     0.081        38     251     298 ..     310     350 ..     305     372 .. 0.82
   4 ?    3.4   0.0      0.08        38     250     291 ..     377     411 ..     360     417 .. 0.86
   5 ?    1.9   0.0      0.21     1e+02     270     291 ..     424     445 ..     419     455 .. 0.87
   6 ?    4.1   0.0     0.047        22     266     296 ..     454     488 ..     445     498 .. 0.80
   7 ?    4.0   0.0     0.051        24     266     294 ..     522     552 ..     513     561 .. 0.85
   8 ?    2.4   0.0      0.15        73     242     291 ..     573     615 ..     555     630 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.46
                                       S-STTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT CS
                               FAT 144 gvkaemwlkfanlarksgrlslAekaLkelleedp 178
                                       + +ae wl+ a+  r+ g ++lA ++L + l  dp
  gi|386002705|ref|YP_005921004.1|  62 EESAEGWLEEAERYRQEGAIDLALSSLDRSLALDP 96 
                                       55688899999999999999999999999988888 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0031
                                       CCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHSSSS...................S-TCC.H CS
                               FAT 260 kldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeqkeeee..................pedlq.e 317
                                       +       ++e+lq+y ++  idp+  kaw++ +l      + ee  ++ e+                         
  gi|386002705|ref|YP_005921004.1| 149 R-------VDEALQAYNRSLTIDPENGKAWNNRGLILGALGRYEEAASSFERaissdpdlaaawqnrgnaL-R-AlG 216
                                       3.......89*********************9666555555555544444434445555777777765421.2.224 PP

                                       HHHCCT..CCHHHHTTTS CS
                               FAT 318 yvvpavkgflksislsse 335
                                        +++a++++  +++  s+
  gi|386002705|ref|YP_005921004.1| 217 RPEEALECYASALAIDSG 234
                                       677788888877776665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.081
                                       CCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHH CS
                               FAT 251 kGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfe 298
                                       +G  +++l++       +ee+l+sy ++  idps + aw++ +++ f 
  gi|386002705|ref|YP_005921004.1| 310 RGLALANLGR-------SEEALESYNRSIDIDPSFALAWYNRGRALFD 350
                                       5666777777.......9**********************97776665 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.08
                                       TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 250 kkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                        +G  ++al++        ee+l+sy +a eidp+ + aw++
  gi|386002705|ref|YP_005921004.1| 377 NRGAALAALGR-------EEEALESYDRALEIDPGYEIAWYN 411
                                       56777888888.......89***************999**86 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.21
                                       SCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 270 eilqsysaateidpswykawht 291
                                       ++ +++ +a +++p++++awh+
  gi|386002705|ref|YP_005921004.1| 424 DAIKAFDEAIRFNPTSADAWHS 445
                                       6789*****************8 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.047
                                       ..-SSCCHHHHCCHHCTCCCHSTTCC....CCHHH CS
                               FAT 266 ekieeilqsysaateidpswykawht....walfn 296
                                       +++ e+l +y +a e+dp+ +++wh+    +a++n
  gi|386002705|ref|YP_005921004.1| 454 RRPGEALVCYEKALELDPGRAETWHHrgvaLADLN 488
                                       56889********************9665566555 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.051
                                       ..-SSCCHHHHCCHHCTCCCHSTTCC..CCH CS
                               FAT 266 ekieeilqsysaateidpswykawht..wal 294
                                        ++ee+l+++++a+e+dp+ ++aw++  w l
  gi|386002705|ref|YP_005921004.1| 522 GRPEEALAHFTRAAELDPGHAEAWNNrgWIL 552
                                       4689********************9855555 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.15
                                       .HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 242 kllarcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       + la+  + +G  ++al+k       +ee+l++y +   idp    aw++
  gi|386002705|ref|YP_005921004.1| 573 TALAEGWNNRGVVLTALGK-------NEEALEAYNRTIDIDPAHPRAWNN 615
                                       4557777889999999999.......9*********************86 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.9       3.8   1.8e+03       7      26 .]      52      71 ..      51      71 .. 0.82
   2 ?    1.4   0.2       1.5   7.1e+02       7      18 ..      98     109 ..      97     110 .. 0.88
   3 !    9.1   0.0    0.0049       2.3       3      23 ..     136     156 ..     134     159 .. 0.86
   4 ?    7.8   0.1     0.013       6.2       6      26 .]     173     193 ..     170     193 .. 0.85
   5 !    9.9   1.6    0.0027       1.3       6      23 ..     207     224 ..     201     227 .. 0.88
   6 ?    1.5   5.6       1.4   6.7e+02       7      25 ..     242     260 ..     241     260 .. 0.92
   7 ?    3.7   0.1      0.26   1.2e+02       6      22 ..     275     291 ..     271     295 .. 0.81
   8 !    9.4   0.2     0.004       1.9       4      22 ..     307     325 ..     304     329 .. 0.87
   9 ?    7.9   0.4     0.012       5.7       2      24 ..     339     361 ..     338     363 .. 0.89
  10 ?    7.5   3.1     0.016       7.6       3      25 ..     374     396 ..     372     397 .. 0.84
  11 ?    5.2   4.4     0.089        42       3      26 .]     476     499 ..     474     499 .. 0.88
  12 ?    4.7   0.0      0.12        59      10      24 ..     517     531 ..     512     533 .. 0.82
  13 !   10.4   0.0    0.0018      0.86       2      25 ..     543     566 ..     542     567 .. 0.85
  14 ?    2.7   0.1      0.54   2.6e+02       6      23 ..     581     598 ..     574     601 .. 0.87
  15 ?    6.5   0.0     0.032        15       1      23 [.     610     632 ..     610     635 .. 0.86
  16 ?   -1.1   2.0       9.5   4.5e+03       3      14 ..     646     657 ..     644     658 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.8
                             TPR_4  7 LArallalGdldeAraller 26
                                      LA a  alGd + A+ +le+
  gi|386002705|ref|YP_005921004.1| 52 LALADPALGDEESAEGWLEE 71
                                      56666699**********97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.5
                             TPR_4   7 LArallalGdld 18 
                                       LA+a+ ++G+ +
  gi|386002705|ref|YP_005921004.1|  98 LAEAWVLRGEIA 109
                                       9********976 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0049
                             TPR_4   3 allaLArallalGdldeAral 23 
                                       + + L+ al  lG+ deA+++
  gi|386002705|ref|YP_005921004.1| 136 VWYELGNALSFLGRVDEALQA 156
                                       56889*************987 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.013
                             TPR_4   6 aLArallalGdldeAraller 26 
                                       +++  l alG+++eA+  +er
  gi|386002705|ref|YP_005921004.1| 173 NRGLILGALGRYEEAASSFER 193
                                       78999**********987775 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0027
                             TPR_4   6 aLArallalGdldeAral 23 
                                       +++ al alG+++eA++ 
  gi|386002705|ref|YP_005921004.1| 207 NRGNALRALGRPEEALEC 224
                                       7999***********986 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 1.4
                             TPR_4   7 LArallalGdldeAralle 25 
                                        A++l alG+ +eA+a l+
  gi|386002705|ref|YP_005921004.1| 242 AAELLRALGRDEEALARLD 260
                                       69**************986 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.26
                             TPR_4   6 aLArallalGdldeAra 22 
                                       +++  l  lG+++eA +
  gi|386002705|ref|YP_005921004.1| 275 DRGLILGVLGRYEEAVE 291
                                       67889999*******87 PP

  == domain 8  score: 9.4 bits;  conditional E-value: 0.004
                             TPR_4   4 llaLArallalGdldeAra 22 
                                         +++ al+ lG+++eA++
  gi|386002705|ref|YP_005921004.1| 307 WNNRGLALANLGRSEEALE 325
                                       5689*************97 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.012
                             TPR_4   2 rallaLArallalGdldeArall 24 
                                        a ++++ral++l ++deA ++ 
  gi|386002705|ref|YP_005921004.1| 339 LAWYNRGRALFDLERYDEAVEAY 361
                                       689****************9875 PP

  == domain 10  score: 7.5 bits;  conditional E-value: 0.016
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                       a  +++ al+alG+ +eA++  +
  gi|386002705|ref|YP_005921004.1| 374 AWNNRGAALAALGREEEALESYD 396
                                       66799*************98665 PP

  == domain 11  score: 5.2 bits;  conditional E-value: 0.089
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       + + ++ al++l +++eA+++++r
  gi|386002705|ref|YP_005921004.1| 476 TWHHRGVALADLNRAAEAAEAFDR 499
                                       66889**************99886 PP

  == domain 12  score: 4.7 bits;  conditional E-value: 0.12
                             TPR_4  10 allalGdldeArall 24 
                                       +++  G+++eA+a++
  gi|386002705|ref|YP_005921004.1| 517 LAYSSGRPEEALAHF 531
                                       56668********95 PP

  == domain 13  score: 10.4 bits;  conditional E-value: 0.0018
                             TPR_4   2 rallaLArallalGdldeAralle 25 
                                        a  ++++ l+ lGd deA++  +
  gi|386002705|ref|YP_005921004.1| 543 EAWNNRGWILFTLGDTDEALESID 566
                                       56779**************98665 PP

  == domain 14  score: 2.7 bits;  conditional E-value: 0.54
                             TPR_4   6 aLArallalGdldeAral 23 
                                       +++ +l alG  +eA+++
  gi|386002705|ref|YP_005921004.1| 581 NRGVVLTALGKNEEALEA 598
                                       7999***********987 PP

  == domain 15  score: 6.5 bits;  conditional E-value: 0.032
                             TPR_4   1 arallaLArallalGdldeAral 23 
                                       +ra  + +  l++lG++ eA++ 
  gi|386002705|ref|YP_005921004.1| 610 PRAWNNKGASLYHLGRYREAADC 632
                                       678888999***********986 PP

  == domain 16  score: -1.1 bits;  conditional E-value: 9.5
                             TPR_4   3 allaLArallal 14 
                                       a++++A al++l
  gi|386002705|ref|YP_005921004.1| 646 ARANRAAALQRL 657
                                       899****99986 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.02       9.4     213     262 ..     180     229 ..     151     234 .. 0.87
   2 ?    2.5   0.0      0.17        82     214     256 ..     283     325 ..     274     334 .. 0.87
   3 ?   -0.3   0.0       1.2   5.5e+02     214     255 ..     351     392 ..     343     412 .. 0.62
   4 ?    1.4   0.0      0.37   1.7e+02     208     256 ..     447     495 ..     418     509 .. 0.75
   5 !    7.3   0.1    0.0059       2.8     211     256 ..     552     597 ..     517     609 .. 0.87
   6 ?    0.8   0.0      0.55   2.6e+02     206     247 ..     615     656 ..     607     660 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.02
                                       HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsql 262
                                       +lgryeeA s+ + a+ +d+  + +  N   a   lg+++e+ e + s l
  gi|386002705|ref|YP_005921004.1| 180 ALGRYEEAASSFERAISSDPDLAAAWQNRGNALRALGRPEEALECYASAL 229
                                       689************************************99988776665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       lgryeeA ++   aL  d+ +  +  N   a  +lg+++e+ e
  gi|386002705|ref|YP_005921004.1| 283 LGRYEEAVESFDAALRADPGYLLAWNNRGLALANLGRSEEALE 325
                                       79*******************9999999999999999988765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.2
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                       l+ry+eA +   +aL+ ++  + +  N   a   lg+++e+ 
  gi|386002705|ref|YP_005921004.1| 351 LERYDEAVEAYDSALEVEPAFALAWNNRGAALAALGREEEAL 392
                                       566677766666666666666555555555555555555443 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.37
                                       HHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 208 AvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                         +  ++ r+ eA    ++aL+ d+  +et     va  +l++ ae+ e
  gi|386002705|ref|YP_005921004.1| 447 GHALYQMRRPGEALVCYEKALELDPGRAETWHHRGVALADLNRAAEAAE 495
                                       4455678999999999999999999999999888888888888777654 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0059
                                       HHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 211 slllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                         +lg+ +eA +++  aL+ d+  +e   N  v+ + lgk++e+ e
  gi|386002705|ref|YP_005921004.1| 552 LFTLGDTDEALESIDRALEADTALAEGWNNRGVVLTALGKNEEALE 597
                                       5678999**********************************99865 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.55
                                       HHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHH CS
                        Coatomer_E 206 gkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqh 247
                                        k +   +lgry eA      aL+ d+  +++ +N   a q 
  gi|386002705|ref|YP_005921004.1| 615 NKGASLYHLGRYREAADCYGRALELDPAFADARANRAAALQR 656
                                       555666799***********************9998777665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.24   1.1e+02      15      36 .]     148     167 ..     137     167 .. 0.88
   2 ?    1.3   0.0      0.78   3.7e+02      15      31 ..     284     296 ..     283     300 .. 0.81
   3 ?    6.6   0.0     0.017       7.9      10      25 ..     347     362 ..     340     366 .. 0.85
   4 ?    3.9   0.0      0.11        54       8      25 ..     413     430 ..     408     432 .. 0.87
   5 ?   -0.2   0.0       2.2     1e+03      16      35 ..     489     506 ..     479     506 .. 0.79
   6 ?    6.2   0.0     0.023        11       8      33 ..     617     640 ..     617     642 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.24
                                       T-HHHHHHH..HHHHHHH-TT- CS
                             TPR_3  15 kkyqeArelfsYallaildken 36 
                                       ++ +eA+++  Y  + ++d+en
  gi|386002705|ref|YP_005921004.1| 148 GRVDEALQA--YNRSLTIDPEN 167
                                       7889*****..77*******99 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.78
                                       T-HHHHHHH..HHHHHH CS
                             TPR_3  15 kkyqeArelfsYallai 31 
                                       ++y+eA+e f+    a+
  gi|386002705|ref|YP_005921004.1| 284 GRYEEAVESFD----AA 296
                                       89******998....44 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.017
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++++ ++y+eA+e+++
  gi|386002705|ref|YP_005921004.1| 347 ALFDLERYDEAVEAYD 362
                                       678999********87 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.11
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       + ++y+ ++y +A+ +f+
  gi|386002705|ref|YP_005921004.1| 413 GSVLYLEGRYFDAIKAFD 430
                                       889************987 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.2
                                       -HHHHHHH..HHHHHHH-TT CS
                             TPR_3  16 kyqeArelfsYallaildke 35 
                                       +  eA+e+f+   +  ld+e
  gi|386002705|ref|YP_005921004.1| 489 RAAEAAEAFD--RALELDPE 506
                                       7789****98..88888875 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.023
                                       HHHHHHTT-HHHHHHH..HHHHHHH- CS
                             TPR_3   8 AaefynkkkyqeArelfsYallaild 33 
                                       +a++y  ++y eA++   Y+ +  ld
  gi|386002705|ref|YP_005921004.1| 617 GASLYHLGRYREAADC--YGRALELD 640
                                       799*************..88887777 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.3   1.1e+03     125     174 ..      77     128 ..      72     140 .. 0.72
   2 ?    1.5   0.0      0.43     2e+02     153     178 ..     141     166 ..     138     177 .. 0.85
   3 ?    0.8   0.0      0.74   3.5e+02     146     175 ..     168     197 ..     147     202 .. 0.65
   4 ?    5.6   0.1     0.024        12     125     174 ..     180     230 ..     175     235 .. 0.77
   5 ?    2.2   0.2      0.27   1.3e+02     120     176 ..     243     300 ..     242     307 .. 0.81
   6 ?   -1.3   0.0       3.3   1.5e+03     151     174 ..     309     332 ..     305     338 .. 0.87
   7 !    7.5   1.7    0.0063         3     121     174 ..     346     400 ..     320     406 .. 0.83
   8 ?    1.9   0.0      0.33   1.5e+02     122     174 ..     415     468 ..     407     477 .. 0.55
   9 ?    0.8   0.1      0.73   3.4e+02     151     177 ..     479     505 ..     473     518 .. 0.83
  10 !   12.0   0.1   0.00027      0.13     122     175 ..     551     605 ..     548     615 .. 0.83
  11 ?   -2.5   0.0       7.4   3.5e+03     152     175 ..     616     639 ..     610     655 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                            TPR_21 125 aekkydeAlktLeakke.eafaalvaelrGDi.lvaqgkldeAraaYqaAla 174
                                       +e+++d Al+ L+++ + +   a++  lrG+i l++  +++ A +a+++Al 
  gi|386002705|ref|YP_005921004.1|  77 QEGAIDLALSSLDRSLAlDPDLAEAWVLRGEIaLYNLTDREMAVEAFERALG 128
                                       6788888888887665413334556668999834678999999999999985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.43
                            TPR_21 153 GDilvaqgkldeAraaYqaAlaalee 178
                                       G++l+  g+ deA +aY+++l+   e
  gi|386002705|ref|YP_005921004.1| 141 GNALSFLGRVDEALQAYNRSLTIDPE 166
                                       8889999************9986655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.74
                            TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       +++ + rG il a g+ +eA + +++A+++
  gi|386002705|ref|YP_005921004.1| 168 GKAWNNRGLILGALGRYEEAASSFERAISS 197
                                       455566888888888888888888888765 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.024
                            TPR_21 125 aekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       a + y+eA +  e++ + +   a++ + rG++l a g+ +eA + Y  Ala
  gi|386002705|ref|YP_005921004.1| 180 ALGRYEEAASSFERAISsDPDLAAAWQNRGNALRALGRPEEALECYASALA 230
                                       5677888888886654403445666788*********************97 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.27
                            TPR_21 120 arvllaekkydeAlktLeakkeeaf.aalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       a++l a +  +eAl++L+++  +   + ++ + rG il   g+ +eA + ++aAl+a 
  gi|386002705|ref|YP_005921004.1| 243 AELLRALGRDEEALARLDGAVGADPgDKAAWNDRGLILGVLGRYEEAVESFDAALRAD 300
                                       66788889999******98876654144445669********************9986 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 3.3
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAla 174
                                        rG +l++ g+ +eA + Y+++++
  gi|386002705|ref|YP_005921004.1| 309 NRGLALANLGRSEEALESYNRSID 332
                                       589999*************99886 PP

  == domain 7  score: 7.5 bits;  conditional E-value: 0.0063
                            TPR_21 121 rvllaekkydeAlktLeak..keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       r l++ + ydeA+++ +++   e af al+ + rG +l+a g+ +eA + Y++Al+
  gi|386002705|ref|YP_005921004.1| 346 RALFDLERYDEAVEAYDSAleVEPAF-ALAWNNRGAALAALGREEEALESYDRALE 400
                                       56788899999999997751145566.5666789********************97 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.33
                            TPR_21 122 vllaekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       vl  e+ y +A+k+ +++ + +  +a +   +G +l+++ +  eA   Y++Al+
  gi|386002705|ref|YP_005921004.1| 415 VLYLEGRYFDAIKAFDEAiRFNPTSADAWHSKGHALYQMRRPGEALVCYEKALE 468
                                       344444444444444322022333444445566666666666666666666665 PP

  == domain 9  score: 0.8 bits;  conditional E-value: 0.73
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaale 177
                                        rG +l+  ++ +eA +a+++Al+   
  gi|386002705|ref|YP_005921004.1| 479 HRGVALADLNRAAEAAEAFDRALELDP 505
                                       689999999*************98655 PP

  == domain 10  score: 12.0 bits;  conditional E-value: 0.00027
                            TPR_21 122 vllaekkydeAlktLeakkeea.faalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       +l+  +++deAl+ ++++ e+    a+  + rG +l+a gk++eA +aY++ ++ 
  gi|386002705|ref|YP_005921004.1| 551 ILFTLGDTDEALESIDRALEADtALAEGWNNRGVVLTALGKNEEALEAYNRTIDI 605
                                       5677899********9876654045777889*******************98875 PP

  == domain 11  score: -2.5 bits;  conditional E-value: 7.4
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaa 175
                                       +G  l+  g+  eA + Y +Al+ 
  gi|386002705|ref|YP_005921004.1| 616 KGASLYHLGRYREAADCYGRALEL 639
                                       777888889999999999998875 PP

>> Imm31  Immunity protein 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00039      0.18      12      66 ..     161     218 ..     155     225 .. 0.87
   2 ?   -1.7   0.0       5.9   2.8e+03      15      32 ..     266     283 ..     261     296 .. 0.71
   3 ?   -0.5   0.0       2.4   1.1e+03      13      65 ..     366     421 ..     361     425 .. 0.71
   4 ?    3.2   0.0      0.17        80      10      34 ..     567     591 ..     561     633 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                             Imm31  12 lstdailaelhGerGvvl...GrseddqGefeyavfiyadeniCWsleedeleaeGek 66 
                                       l+ d++ ++ + +rG +l   Gr e+    fe a+    d    W+   + l+a G+ 
  gi|386002705|ref|YP_005921004.1| 161 LTIDPENGKAWNNRGLILgalGRYEEAASSFERAISSDPDLAAAWQNRGNALRALGRP 218
                                       789*************972225889999**************************9985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.9
                             Imm31  15 dailaelhGerGvvlGrs 32 
                                       d+     + +rG +lG  
  gi|386002705|ref|YP_005921004.1| 266 DPGDKAAWNDRGLILGVL 283
                                       555666799999999864 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.4
                             Imm31  13 stdailaelhGerGvv...lGrseddqGefeyavfiyadeniCWsleedeleaeGe 65 
                                        +++  a  + +rG+    lGr e+    ++ a+ i    +i W      l  eG+
  gi|386002705|ref|YP_005921004.1| 366 EVEPAFALAWNNRGAAlaaLGREEEALESYDRALEIDPGYEIAWYNRGSVLYLEGR 421
                                       56677777888888642226888888888988888865444888887777777777 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.17
                             Imm31  10 rvlstdailaelhGerGvvlGrsed 34 
                                       r l +d+ lae + +rGvvl   + 
  gi|386002705|ref|YP_005921004.1| 567 RALEADTALAEGWNNRGVVLTALGK 591
                                       778999************9754333 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.6   1.2e+03       9      33 ..     108     132 ..     107     134 .. 0.91
   2 ?    2.2   0.0      0.42     2e+02      15      36 ..     148     169 ..     138     172 .. 0.86
   3 ?   -0.9   0.0       3.8   1.8e+03      14      33 ..     181     200 ..     180     204 .. 0.89
   4 ?    4.7   0.0     0.067        32      14      33 ..     283     302 ..     282     306 .. 0.93
   5 ?   -2.1   0.0       9.1   4.3e+03       9      34 ..     312     337 ..     310     338 .. 0.85
   6 !    8.1   0.1    0.0059       2.8      10      34 ..     347     371 ..     340     374 .. 0.84
   7 ?    1.3   0.0      0.79   3.7e+02      18      34 ..     389     405 ..     379     408 .. 0.83
   8 ?   -1.1   0.1       4.4   2.1e+03      18      34 ..     491     507 ..     478     508 .. 0.79
   9 ?    7.1   0.2     0.012       5.5      12      38 ..     621     647 ..     618     656 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.6
                                       HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                       ++ y l + ++A +  ++ L i+Pe
  gi|386002705|ref|YP_005921004.1| 108 IALYNLTDREMAVEAFERALGIDPE 132
                                       688999999***************8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.42
                                       T-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQ 36 
                                       g+ +eA++  ++ L i+Pen  
  gi|386002705|ref|YP_005921004.1| 148 GRVDEALQAYNRSLTIDPENGK 169
                                       66689***************65 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.8
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+Y+eA    ++ ++ +P+
  gi|386002705|ref|YP_005921004.1| 181 LGRYEEAASSFERAISSDPD 200
                                       799*****999999999997 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.067
                                       HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                       lg+Y+eA +  da L+ +P+
  gi|386002705|ref|YP_005921004.1| 283 LGRYEEAVESFDAALRADPG 302
                                       79****************97 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 9.1
                                       HHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPen 34 
                                       l+ + lg+ +eA++  ++ + i+P++
  gi|386002705|ref|YP_005921004.1| 312 LALANLGRSEEALESYNRSIDIDPSF 337
                                       67888999999999999999999975 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0059
                                       HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPen 34 
                                       + + l +Y+eA +  d  Le+EP +
  gi|386002705|ref|YP_005921004.1| 347 ALFDLERYDEAVEAYDSALEVEPAF 371
                                       6667899****************86 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  18 seArryvdalLeiEPen 34 
                                       +eA++  d+ Lei+P+ 
  gi|386002705|ref|YP_005921004.1| 389 EEALESYDRALEIDPGY 405
                                       79*************85 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  18 seArryvdalLeiEPen 34 
                                        eA +  d+ Le++Pe 
  gi|386002705|ref|YP_005921004.1| 491 AEAAEAFDRALELDPEY 507
                                       678899999******85 PP

  == domain 9  score: 7.1 bits;  conditional E-value: 0.012
                                       HHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaq 38 
                                       y lg+Y+eA  +  + Le++P +  a+
  gi|386002705|ref|YP_005921004.1| 621 YHLGRYREAADCYGRALELDPAFADAR 647
                                       89********************99887 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.38   1.8e+02      42      94 ..     138     188 ..     113     199 .. 0.58
   2 !   14.1   1.1   8.6e-05     0.041       6      97 ..     207     293 ..     202     301 .. 0.82
   3 ?    0.4   0.1       1.5   7.2e+02      82      95 ..     312     325 ..     283     365 .. 0.68
   4 ?    2.9   0.1      0.26   1.2e+02       6      29 ..     377     400 ..     372     405 .. 0.86
   5 ?    1.1   0.6      0.92   4.4e+02      26      26 ..     601     601 ..     511     637 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.38
                             TPR_5  42 iqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereav 94 
                                         L  +L  lG+++eal+  +  l+  +++ + a    + L+L +lgr +ea 
  gi|386002705|ref|YP_005921004.1| 138 YELGNALSFLGRVDEALQAYNRSLTIDPENGK-A-WNNRGLILGALGRYEEAA 188
                                       45566666666666666666665554333222.2.334556666666666665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.6e-05
                             TPR_5   6 eragarDstGhedkavplYrraLa..eGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaafl 80 
                                       +r+ a    G++++a + Y  aLa   GL g+ ++ a +     LR lG+ eeala L++ + a  d  d+a    +
  gi|386002705|ref|YP_005921004.1| 207 NRGNALRALGRPEEALECYASALAidSGLVGSWKGAAEL-----LRALGRDEEALARLDGAVGA--DPGDKAAWNDR 276
                                       577788899***********9985338*****9998765.....9*************998765..44567888999 PP

                             TPR_5  81 aLvLsdlgrereavsiv 97 
                                        L+L  lgr +eav   
  gi|386002705|ref|YP_005921004.1| 277 GLILGVLGRYEEAVESF 293
                                       9***********99865 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                             TPR_5  82 LvLsdlgrereavs 95 
                                       L+L++lgr +ea+ 
  gi|386002705|ref|YP_005921004.1| 312 LALANLGRSEEALE 325
                                       45555555555543 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.26
                             TPR_5   6 eragarDstGhedkavplYrraLa 29 
                                       +r++a    G+e++a + Y raL+
  gi|386002705|ref|YP_005921004.1| 377 NRGAALAALGREEEALESYDRALE 400
                                       6788888999**********9997 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.92
                             TPR_5  26 r 26 
                                       r
  gi|386002705|ref|YP_005921004.1| 601 R 601
                                       1 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.19        88      29      61 ..      58      90 ..      52      97 .. 0.89
   2 ?   -2.3   0.0       6.5   3.1e+03      49      62 ..     147     160 ..     137     168 .. 0.78
   3 ?   -1.1   0.0       2.7   1.3e+03     119     138 ..     174     193 ..     168     198 .. 0.84
   4 ?   -1.7   0.0       4.3     2e+03      34      63 ..     200     229 ..     191     234 .. 0.84
   5 ?   -0.9   0.0       2.5   1.2e+03      25      62 ..     326     364 ..     308     374 .. 0.67
   6 ?   -1.1   0.1       2.9   1.4e+03      30      64 ..     366     400 ..     339     401 .. 0.71
   7 ?    2.0   0.0      0.31   1.4e+02      36      68 ..     542     574 ..     531     577 .. 0.87
   8 ?    4.7   0.0     0.046        22      16      64 ..     562     604 ..     550     609 .. 0.80
   9 ?   -1.8   0.0       4.7   2.2e+03      38      63 ..     612     637 ..     605     639 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.19
                                      TT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHT CS
                              RPN7 29 nlgkeeirrakldlaehYlkigdleeAlkaysr 61
                                       lg+ee ++++l+ ae+Y + g ++ Al  + r
  gi|386002705|ref|YP_005921004.1| 58 ALGDEESAEGWLEEAERYRQEGAIDLALSSLDR 90
                                      589*************************99887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.5
                                       CT-HHHHHHHHHTC CS
                              RPN7  49 igdleeAlkaysri 62 
                                        g ++eAl+ay+r 
  gi|386002705|ref|YP_005921004.1| 147 LGRVDEALQAYNRS 160
                                       6899*******994 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.7
                                       HHHHHHHTT-HHHHHHHHCT CS
                              RPN7 119 eGlallairkfkeAaellld 138
                                        Gl+l a ++++eAa+ +  
  gi|386002705|ref|YP_005921004.1| 174 RGLILGALGRYEEAASSFER 193
                                       58999999*******99865 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  34 eirrakldlaehYlkigdleeAlkaysrir 63 
                                       + ++a++++++     g  eeAl++y+ ++
  gi|386002705|ref|YP_005921004.1| 200 DLAAAWQNRGNALRALGRPEEALECYASAL 229
                                       6778888899999999999*******9865 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 2.5
                                       HHH.HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7  25 dak.enlgkeeirrakldlaehYlkigdleeAlkaysri 62 
                                        +  +  ++ + + a++++++  ++   ++eA++ay  +
  gi|386002705|ref|YP_005921004.1| 326 SYNrSIDIDPSFALAWYNRGRALFDLERYDEAVEAYDSA 364
                                       333344566666677777777777777777777777666 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 2.9
                                       T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       +++   + a+++++   +  g  eeAl+ y r++e
  gi|386002705|ref|YP_005921004.1| 366 EVEPAFALAWNNRGAALAALGREEEALESYDRALE 400
                                       45556677778888888888999999999998875 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--S CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrireycts 68 
                                       ++a+++++   ++ gd++eAl+   r++e  t 
  gi|386002705|ref|YP_005921004.1| 542 AEAWNNRGWILFTLGDTDEALESIDRALEADTA 574
                                       577888889999**************9998776 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  16 leeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       le +d+ l+       ++  ++++++++   +  g+ eeAl+ay+r+++
  gi|386002705|ref|YP_005921004.1| 562 LESIDRALEA------DTALAEGWNNRGVVLTALGKNEEALEAYNRTID 604
                                       4555555554......78889999999999999************9976 PP

  == domain 9  score: -1.8 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrir 63 
                                       a+++++   +  g ++eA  +y r++
  gi|386002705|ref|YP_005921004.1| 612 AWNNKGASLYHLGRYREAADCYGRAL 637
                                       66677777777888888888887776 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.7   1.8e+03      11      22 ..     163     174 ..     159     179 .. 0.74
   2 ?    0.7   0.0         1   4.8e+02      18      22 ..     476     480 ..     464     481 .. 0.77
   3 !    8.4   0.0    0.0038       1.8       7      27 ..     533     553 ..     530     554 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.7
                                       H-TT-CHHHHHH CS
                              PPTA  11 kdpkNYsaWnyR 22 
                                        dp N  aWn R
  gi|386002705|ref|YP_005921004.1| 163 IDPENGKAWNNR 174
                                       56777669**99 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                                       HHHHH CS
                              PPTA  18 aWnyR 22 
                                       +W++R
  gi|386002705|ref|YP_005921004.1| 476 TWHHR 480
                                       7***9 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0038
                                       HHHHH-TT-CHHHHHHHHHHC CS
                              PPTA   7 kliekdpkNYsaWnyRrwlle 27 
                                        ++e+dp +  aWn R w+l 
  gi|386002705|ref|YP_005921004.1| 533 RAAELDPGHAEAWNNRGWILF 553
                                       68899**************96 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.029        14       7      53 ..     119     165 ..     114     197 .. 0.76
   2 ?    2.4   0.1      0.41     2e+02       8      49 ..     188     229 ..     183     236 .. 0.85
   3 ?    9.0   0.0    0.0037       1.7       4      55 ..     252     303 ..     249     329 .. 0.89
   4 ?    2.6   0.1      0.36   1.7e+02       7      47 ..     289     329 ..     287     346 .. 0.86
   5 ?    0.6   0.1       1.5   7.1e+02       9      50 ..     359     400 ..     344     413 .. 0.70
   6 ?    1.4   0.0      0.87   4.1e+02       6      53 ..     390     437 ..     386     452 .. 0.85
   7 ?   -1.0   0.1       4.7   2.2e+03      12      56 ..     464     508 ..     454     521 .. 0.70
   8 ?   -0.4   0.2       3.3   1.5e+03       9      50 ..     495     536 ..     487     571 .. 0.65
   9 ?    1.2   0.2         1   4.8e+02       8      80 ..     528     598 ..     522     604 .. 0.64
  10 ?   -0.4   0.1       3.1   1.5e+03       6      59 ..     594     647 ..     589     656 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.029
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                        ++++e+al  +p+d    ++l +al   gr++eAl++  + l  d 
  gi|386002705|ref|YP_005921004.1| 119 AVEAFERALGIDPEDGVVWYELGNALSFLGRVDEALQAYNRSLTIDP 165
                                       68999*******************************98777776655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.41
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                        +++e+a+ ++pd  +a  +  +al a gr eeAle   + l
  gi|386002705|ref|YP_005921004.1| 188 ASSFERAISSDPDLAAAWQNRGNALRALGRPEEALECYASAL 229
                                       567899*****************************9655555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0037
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                       d++ la l+ a+ a+p d +a  d  l l   gryeeA+e + + l++d ++
  gi|386002705|ref|YP_005921004.1| 252 DEEALARLDGAVGADPGDKAAWNDRGLILGVLGRYEEAVESFDAALRADPGY 303
                                       6678999999*******************************99999999776 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.36
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLle 47 
                                        +++++aal a+p  l a  +  lal+  gr eeAle   +
  gi|386002705|ref|YP_005921004.1| 289 AVESFDAALRADPGYLLAWNNRGLALANLGRSEEALESYNR 329
                                       5788999*****************************97655 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.5
                            TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       ++ ++al+ +p+   a  +   al+a gr+eeAle   + l+
  gi|386002705|ref|YP_005921004.1| 359 EAYDSALEVEPAFALAWNNRGAALAALGREEEALESYDRALE 400
                                       555555555555555556667788888999999987555555 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.87
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                       + l++ ++al+ +p    a ++   +l+ +gry +A++++ e ++ + 
  gi|386002705|ref|YP_005921004.1| 390 EALESYDRALEIDPGYEIAWYNRGSVLYLEGRYFDAIKAFDEAIRFNP 437
                                       567778889999999999999999*************99988888775 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 4.7
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                       e+al+ +p   ++ +    al+  +r +eA+e++ + l+ d ++e
  gi|386002705|ref|YP_005921004.1| 464 EKALELDPGRAETWHHRGVALADLNRAAEAAEAFDRALELDPEYE 508
                                       566777777777777777777777777777777766666666665 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 3.3
                            TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                       +++++al+ +p+     +    + ++ gr eeAl+++ +  +
  gi|386002705|ref|YP_005921004.1| 495 EAFDRALELDPEYEPPWYRKGILAYSSGRPEEALAHFTRAAE 536
                                       555555566666656666666677778888888887766554 PP

  == domain 9  score: 1.2 bits;  conditional E-value: 1
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvak 80 
                                       la + +a++ +p   +a  +    l+  g+ +eAle + + l++d + +++   + +  +++alg+++++ ++
  gi|386002705|ref|YP_005921004.1| 528 LAHFTRAAELDPGHAEAWNNRGWILFTLGDTDEALESIDRALEADTALAEGWNNRGV--VLTALGKNEEALEA 598
                                       556666677777777777777777777788888888887777777777665444433..35555555555554 PP

  == domain 10  score: -0.4 bits;  conditional E-value: 3.1
                            TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwedda 59 
                                       + l++  +++  +p+   a  +    l++ gry+eA++   + l+ d +++d +
  gi|386002705|ref|YP_005921004.1| 594 EALEAYNRTIDIDPAHPRAWNNKGASLYHLGRYREAADCYGRALELDPAFADAR 647
                                       556777777788888888888888888888999999887777777777666555 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.97   4.6e+02      77     126 ..     184     233 ..     134     247 .. 0.88
   2 ?    0.8   0.0       1.2   5.7e+02      78     132 ..     287     341 ..     284     352 .. 0.84
   3 ?    2.6   0.0      0.33   1.6e+02      78     135 ..     321     378 ..     312     386 .. 0.87
   4 ?    2.3   0.0      0.41   1.9e+02      73     125 ..     350     402 ..     341     420 .. 0.88
   5 ?    4.5   0.0     0.087        41      79     117 ..     424     462 ..     417     485 .. 0.85
   6 ?   -1.8   0.0       7.4   3.5e+03      78     113 ..     593     628 ..     583     639 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.97
                                       HHHHHHHC-EEE---------------------------------EEEEE CS
                            TruB_N  77 leevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiye 126
                                        ee++++f+ +i+  p   +A + +G+ l  l r +e++e  +    i++
  gi|386002705|ref|YP_005921004.1| 184 YEEAASSFERAISSDPDLAAAWQNRGNALRALGRPEEALECYASALAIDS 233
                                       688999****************************9999999888887776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                                       HHHHHHC-EEE---------------------------------EEEEEEEEEEE CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelellev 132
                                       ee++++f  +++  p    A + +G  l +l r++e++e  +r++ i+    l++
  gi|386002705|ref|YP_005921004.1| 287 EEAVESFDAALRADPGYLLAWNNRGLALANLGRSEEALESYNRSIDIDPSFALAW 341
                                       78999999999999*******************************9986554444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.33
                                       HHHHHHC-EEE---------------------------------EEEEEEEEEEEEEE CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep 135
                                       ee+l++++ +i+  p+   A   +G+ l++l r +e+ve      +++    l+++++
  gi|386002705|ref|YP_005921004.1| 321 EEALESYNRSIDIDPSFALAWYNRGRALFDLERYDEAVEAYDSALEVEPAFALAWNNR 378
                                       7899999999*999*************************9999999987777777665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.41
                                       -HHHHHHHHHHC-EEE---------------------------------EEEE CS
                            TruB_N  73 teekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiy 125
                                       + e+ +e+++++ +++e  p    A + +G  l  l re+e++e   r  +i+
  gi|386002705|ref|YP_005921004.1| 350 DLERYDEAVEAYDSALEVEPAFALAWNNRGAALAALGREEEALESYDRALEID 402
                                       5677899999999999*9***99*********************999999986 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.087
                                       HHHHHC-EEE----------------------------- CS
                            TruB_N  79 evlkkftGeieqvppmySAvkvnGkrlyelaregeever 117
                                       +++k+f  +i+  p    A + +G+ ly++ r ge++  
  gi|386002705|ref|YP_005921004.1| 424 DAIKAFDEAIRFNPTSADAWHSKGHALYQMRRPGEALVC 462
                                       578999999*************************98765 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 7.4
                                       HHHHHHC-EEE------------------------- CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelarege 113
                                       ee+l++++ +i+  p    A + +G  ly+l r  e
  gi|386002705|ref|YP_005921004.1| 593 EEALEAYNRTIDIDPAHPRAWNNKGASLYHLGRYRE 628
                                       778888889999999999999999999999988665 PP

>> Rota_NSP3  Rotavirus non-structural protein NSP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.66   3.1e+02     220     263 ..     307     349 ..     302     374 .. 0.67
   2 ?   -0.6   0.0       1.3   5.9e+02     221     258 ..     342     377 ..     338     396 .. 0.83
   3 ?    9.7   0.0   0.00087      0.41     218     261 ..     611     652 ..     597     658 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.66
                         Rota_NSP3 220 yneklerlldvGsltsskeiieksieleiPiikadirnnespdf 263
                                       +n+++  l ++G   ++ e +++si+++ P +   + n     f
  gi|386002705|ref|YP_005921004.1| 307 WNNRGLALANLGRSEEALESYNRSIDID-PSFALAWYNRGRALF 349
                                       6777777777888888888888888888.777655545444433 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                         Rota_NSP3 221 neklerlldvGsltsskeiieksieleiPiikadirnn 258
                                        ++++ l+d+  + +++e +  ++e+e P +   + nn
  gi|386002705|ref|YP_005921004.1| 342 YNRGRALFDLERYDEAVEAYDSALEVE-PAFALAW-NN 377
                                       467999*********************.9997766.44 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00087
                         Rota_NSP3 218 kvyneklerlldvGsltsskeiieksieleiPiikadirnnesp 261
                                       + +n+k+  l+++G + ++ + + +++el+ P + ad r n + 
  gi|386002705|ref|YP_005921004.1| 611 RAWNNKGASLYHLGRYREAADCYGRALELD-PAF-ADARANRAA 652
                                       679***************************.998.788888765 PP

>> EST1_DNA_bind  Est1 DNA/RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0073       3.4       1      55 [.     153     207 ..     153     221 .. 0.87
   2 ?   -2.9   0.0       7.9   3.7e+03       1      35 [.     391     425 ..     391     426 .. 0.79
   3 ?    2.8   0.0      0.15        69       1      42 [.     459     500 ..     459     501 .. 0.84
   4 ?    1.8   0.0      0.29   1.4e+02       1      55 [.     493     547 ..     493     547 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHHHHHHHBSB--.TTHHHH CS
                     EST1_DNA_bind   1 AlrYYllAaellPsnGepyNQlgviaiysedkldavYyylRSllssnpf.ptAkeN 55 
                                       Al+ Y++  ++ P+nG++ N  g+i  + ++  +a+  + R++ ss+p   +A++N
  gi|386002705|ref|YP_005921004.1| 153 ALQAYNRSLTIDPENGKAWNNRGLILGALGRYEEAASSFERAI-SSDPDlAAAWQN 207
                                       6778***************************************.555554888877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.9
                                       HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHH CS
                     EST1_DNA_bind   1 AlrYYllAaellPsnGepyNQlgviaiysedklda 35 
                                       Al+ Y++A e+ P++  +    g + + +++ +da
  gi|386002705|ref|YP_005921004.1| 391 ALESYDRALEIDPGYEIAWYNRGSVLYLEGRYFDA 425
                                       7899*********9988877777777777777777 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                     EST1_DNA_bind   1 AlrYYllAaellPsnGepyNQlgviaiysedkldavYyylRS 42 
                                       Al +Y++A el P+  e+ ++ gv   + ++  +a+  + R+
  gi|386002705|ref|YP_005921004.1| 459 ALVCYEKALELDPGRAETWHHRGVALADLNRAAEAAEAFDRA 500
                                       788********************9888877777777666665 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHHHHHHHHHHBSB--TTHHHH CS
                     EST1_DNA_bind   1 AlrYYllAaellPsnGepyNQlgviaiysedkldavYyylRSllssnpfptAkeN 55 
                                       A++ +++A el P++  p    g++a++s++  +a  +++R+   +  +  A++N
  gi|386002705|ref|YP_005921004.1| 493 AAEAFDRALELDPEYEPPWYRKGILAYSSGRPEEALAHFTRAAELDPGHAEAWNN 547
                                       5666899**********************************98766666666666 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.2        94       7      36 ..     201     230 ..     199     232 .. 0.91
   2 ?    0.5   0.0      0.97   4.6e+02      17      36 ..     279     298 ..     271     332 .. 0.84
   3 ?    0.4   0.1         1   4.9e+02      12      37 ..     342     367 ..     336     385 .. 0.76
   4 ?   -0.2   0.1       1.7   7.9e+02      10      36 ..     374     400 ..     361     410 .. 0.77
   5 ?    1.6   0.0      0.44   2.1e+02      11      37 ..     409     435 ..     395     455 .. 0.83
   6 ?   -0.8   0.0       2.5   1.2e+03       8      37 ..     440     469 ..     436     496 .. 0.84
   7 ?   -0.1   0.0       1.5   6.9e+02       8      36 ..     542     570 ..     540     575 .. 0.87
   8 ?   -1.8   0.0       4.9   2.3e+03       8      48 ..     576     616 ..     570     634 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsale 36 
                                        a ++ n +++l + g++eeALe+ +sal 
  gi|386002705|ref|YP_005921004.1| 201 LAAAWQNRGNALRALGRPEEALECYASALA 230
                                       57889999********************96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.97
                           DUF5113  17 ylnvegeyeeALeyldsale 36 
                                        l v g+yeeA+e +d al+
  gi|386002705|ref|YP_005921004.1| 279 ILGVLGRYEEAVESFDAALR 298
                                       56678999999999999996 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1
                           DUF5113  12 anlayylnvegeyeeALeyldsaley 37 
                                        n + +l+  ++y+eA+e  dsale+
  gi|386002705|ref|YP_005921004.1| 342 YNRGRALFDLERYDEAVEAYDSALEV 367
                                       56666677777888888888888875 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.7
                           DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                       ++ n + +l + g+ eeALe  d ale
  gi|386002705|ref|YP_005921004.1| 374 AWNNRGAALAALGREEEALESYDRALE 400
                                       556777788888888888888888886 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.44
                           DUF5113  11 YanlayylnvegeyeeALeyldsaley 37 
                                       + n ++ l+ eg+y +A++ +d+a+++
  gi|386002705|ref|YP_005921004.1| 409 WYNRGSVLYLEGRYFDAIKAFDEAIRF 435
                                       457788999***************975 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.5
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaley 37 
                                       a+++ + + +l+  +++ eAL + ++ale+
  gi|386002705|ref|YP_005921004.1| 440 ADAWHSKGHALYQMRRPGEALVCYEKALEL 469
                                       78899999999999*************985 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 1.5
                           DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                       a+++ n +  l++ g+ +eALe +d ale
  gi|386002705|ref|YP_005921004.1| 542 AEAWNNRGWILFTLGDTDEALESIDRALE 570
                                       678888999999999999******99997 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 4.9
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakk 48 
                                       a+ + n +  l + g+ eeALe  +  +++  ah + + +k
  gi|386002705|ref|YP_005921004.1| 576 AEGWNNRGVVLTALGKNEEALEAYNRTIDIDPAHPRAWNNK 616
                                       56667777777777888888887777777666666655555 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.2   1.5e+03      18      31 ..     148     161 ..     147     163 .. 0.83
   2 ?    0.7   0.0       1.2   5.7e+02      23      39 ..     180     196 ..     173     214 .. 0.72
   3 ?    2.0   0.2      0.46   2.2e+02      19      31 ..     217     229 ..     214     231 .. 0.84
   4 ?    1.0   0.0      0.94   4.4e+02      18      31 ..     284     297 ..     282     300 .. 0.69
   5 ?    3.8   0.0      0.13        61      15      32 ..     315     332 ..     309     333 .. 0.84
   6 ?    5.3   0.1     0.042        20      18      32 ..     352     366 ..     350     367 .. 0.89
   7 ?    3.3   0.2      0.18        85      17      32 ..     385     400 ..     372     401 .. 0.80
   8 ?   -2.0   0.0       8.5     4e+03      19      32 ..     421     434 ..     419     446 .. 0.59
   9 ?    0.3   0.0       1.5   7.3e+02      22      33 ..     458     469 ..     455     469 .. 0.90
  10 ?   -0.3   0.3       2.4   1.1e+03       2      17 ..     559     574 ..     558     576 .. 0.89
  11 ?    0.8   0.0       1.1   5.2e+02      17      32 ..     589     604 ..     581     605 .. 0.79
  12 ?    3.4   0.2      0.17        82      18      33 ..     624     639 ..     615     656 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.2
                               MIT  18 gnyeeAlelYkeal 31 
                                       g  +eAl++Y  +l
  gi|386002705|ref|YP_005921004.1| 148 GRVDEALQAYNRSL 161
                                       5679******9987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                               MIT  23 AlelYkealelLlqalk 39 
                                       Al  Y+ea   +  a++
  gi|386002705|ref|YP_005921004.1| 180 ALGRYEEAASSFERAIS 196
                                       77777777777777776 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.46
                               MIT  19 nyeeAlelYkeal 31 
                                         eeAle+Y +al
  gi|386002705|ref|YP_005921004.1| 217 RPEEALECYASAL 229
                                       569********98 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.94
                               MIT  18 gnyeeAlelYkeal 31 
                                       g yeeA+e +  al
  gi|386002705|ref|YP_005921004.1| 284 GRYEEAVESFDAAL 297
                                       56777777777766 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.13
                               MIT  15 DnagnyeeAlelYkeale 32 
                                        n g  eeAle Y  +++
  gi|386002705|ref|YP_005921004.1| 315 ANLGRSEEALESYNRSID 332
                                       678999*********998 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.042
                               MIT  18 gnyeeAlelYkeale 32 
                                       + y+eA+e+Y +ale
  gi|386002705|ref|YP_005921004.1| 352 ERYDEAVEAYDSALE 366
                                       57***********98 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.18
                               MIT  17 agnyeeAlelYkeale 32 
                                        g  eeAle Y  ale
  gi|386002705|ref|YP_005921004.1| 385 LGREEEALESYDRALE 400
                                       67789*********98 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 8.5
                               MIT  19 nyeeAlelYkeale 32 
                                        y +A++++ ea++
  gi|386002705|ref|YP_005921004.1| 421 RYFDAIKAFDEAIR 434
                                       45555555555553 PP

  == domain 9  score: 0.3 bits;  conditional E-value: 1.5
                               MIT  22 eAlelYkealel 33 
                                       eAl +Y++alel
  gi|386002705|ref|YP_005921004.1| 458 EALVCYEKALEL 469
                                       89*******996 PP

  == domain 10  score: -0.3 bits;  conditional E-value: 2.4
                               MIT   2 dkAlelvkkAveeDna 17 
                                       d+Ale + +A e+D a
  gi|386002705|ref|YP_005921004.1| 559 DEALESIDRALEADTA 574
                                       78************87 PP

  == domain 11  score: 0.8 bits;  conditional E-value: 1.1
                               MIT  17 agnyeeAlelYkeale 32 
                                        g+ eeAle+Y   ++
  gi|386002705|ref|YP_005921004.1| 589 LGKNEEALEAYNRTID 604
                                       6899*******98766 PP

  == domain 12  score: 3.4 bits;  conditional E-value: 0.17
                               MIT  18 gnyeeAlelYkealel 33 
                                       g y eA ++Y  alel
  gi|386002705|ref|YP_005921004.1| 624 GRYREAADCYGRALEL 639
                                       89************95 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.4   6.4e+02      70     108 ..      66     104 ..      58     125 .. 0.82
   2 ?    2.2   0.0      0.49   2.3e+02      83     122 ..     182     221 ..     144     229 .. 0.87
   3 ?   -1.1   0.0       5.1   2.4e+03      83     122 ..     284     323 ..     236     329 .. 0.65
   4 ?    1.2   0.1         1   4.8e+02      75     122 ..     344     391 ..     339     396 .. 0.90
   5 ?   -1.1   0.0         5   2.3e+03      82     125 ..     555     598 ..     540     604 .. 0.82
   6 ?    2.1   0.1      0.51   2.4e+02      77     117 ..     618     658 ..     609     660 .] 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHH CS
                   Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpenaeakel 108
                                       e  le+a+++++eg + +a++ l+  ++ dp+ aea  l
  gi|386002705|ref|YP_005921004.1|  66 EGWLEEAERYRQEGAIDLALSSLDRSLALDPDLAEAWVL 104
                                       5568999999999********999999999998888766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.49
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       g y+ aa+  + ++ +dp+ a+a + + +al++lg+ +e+
  gi|386002705|ref|YP_005921004.1| 182 GRYEEAASSFERAISSDPDLAAAWQNRGNALRALGRPEEA 221
                                       6799999999999999999999999999999999998876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.1
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       g y+ a+e  + ++ adp    a + +  al +lg+ +e+
  gi|386002705|ref|YP_005921004.1| 284 GRYEEAVESFDAALRADPGYLLAWNNRGLALANLGRSEEA 323
                                       4488888888888888888888888877788888777776 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       + ++ ++ + y  a+e  + +++ +p  a a + + +al +lg+++e+
  gi|386002705|ref|YP_005921004.1| 344 RGRALFDLERYDEAVEAYDSALEVEPAFALAWNNRGAALAALGREEEA 391
                                       6778899999*********************************99986 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 5
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHH CS
                   Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatw 125
                                        gd   a+e ++ +++ad   ae  + +  +l++lg+ +e+  +
  gi|386002705|ref|YP_005921004.1| 555 LGDTDEALESIDRALEADTALAEGWNNRGVVLTALGKNEEALEA 598
                                       57788899999999999999999999999999999999887665 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.51
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlg 117
                                        + +  g yr aa     +++ dp  a+a++ +a+al++l 
  gi|386002705|ref|YP_005921004.1| 618 ASLYHLGRYREAADCYGRALELDPAFADARANRAAALQRLQ 658
                                       56678899*****************************9885 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.3   4.4e+03     122     142 ..     107     127 ..     104     129 .. 0.76
   2 ?    7.7   0.1    0.0044       2.1      58     122 ..     184     251 ..     178     297 .. 0.86
   3 ?   -0.1   0.2         1   4.8e+02     129     143 ..     352     366 ..     345     402 .. 0.53
   4 ?    0.0   0.2      0.98   4.6e+02      85     110 ..     451     474 ..     420     537 .. 0.57
   5 ?   -0.5   0.6       1.4   6.8e+02     119     119 ..     574     574 ..     490     638 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.3
                                       HHHHHTT--HHHHHHHHHHHH CS
                              SNAP 122 elyekelgdlekAieaYekAa 142
                                       e+   +l d e A+ea+e+A 
  gi|386002705|ref|YP_005921004.1| 107 EIALYNLTDREMAVEAFERAL 127
                                       666667788899999999986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHH.TT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHH.HHHTT-HHHHHHHHHHHHH CS
                              SNAP  58 flkaAecqek.lkekdeaanayveAakcykkv.speeAvealekAiei.ytekgrfrraAklkkeiae 122
                                       +++aA+  e+ ++++ + a a+++ +++++   +peeA e++ +A +i     g+++ aA+l + ++ 
  gi|386002705|ref|YP_005921004.1| 184 YEEAASSFERaISSDPDLAAAWQNRGNALRALgRPEEALECYASALAIdSGLVGSWKGAAELLRALGR 251
                                       8888888877799999**************988*************9955567899999988887775 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
                                       --HHHHHHHHHHHHH CS
                              SNAP 129 gdlekAieaYekAae 143
                                       +++++A+eaY+ A e
  gi|386002705|ref|YP_005921004.1| 352 ERYDEAVEAYDSALE 366
                                       345555555555544 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.98
                                       HHHT-HHHHHHHHHHHHHHHHHTT-H CS
                              SNAP  85 ykkvspeeAvealekAieiytekgrf 110
                                       y++ +p eA  ++ekA e+  + gr 
  gi|386002705|ref|YP_005921004.1| 451 YQMRRPGEALVCYEKALEL--DPGRA 474
                                       5555666666666666553..33333 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.4
                                       H CS
                              SNAP 119 e 119
                                        
  gi|386002705|ref|YP_005921004.1| 574 A 574
                                       1 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.7   2.7e+03      18      30 ..     151     163 ..     151     163 .. 0.88
   2 ?   -1.0   0.0       2.7   1.3e+03      16      28 ..     183     195 ..     182     196 .. 0.87
   3 ?    1.2   0.0      0.54   2.5e+02      16      28 ..     285     297 ..     284     298 .. 0.91
   4 ?    5.5   0.1     0.024        12      15      29 ..     352     366 ..     350     367 .. 0.96
   5 ?   -0.3   0.1       1.5   7.3e+02      18      30 ..     389     401 ..     389     401 .. 0.92
   6 ?   -0.1   0.1       1.4   6.4e+02      19      36 ..     492     509 ..     491     510 .. 0.82
   7 ?   -2.0   0.0       5.5   2.6e+03      16      30 ..     625     639 ..     624     639 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.7
                          SHNi-TPR  18 pqAveDlrkaLeL 30 
                                       ++A++ ++++L +
  gi|386002705|ref|YP_005921004.1| 151 DEALQAYNRSLTI 163
                                       6899******986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                          SHNi-TPR  16 nFpqAveDlrkaL 28 
                                       ++++A++ +++a+
  gi|386002705|ref|YP_005921004.1| 183 RYEEAASSFERAI 195
                                       8******999996 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.54
                          SHNi-TPR  16 nFpqAveDlrkaL 28 
                                       ++++Ave +++aL
  gi|386002705|ref|YP_005921004.1| 285 RYEEAVESFDAAL 297
                                       9**********98 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.024
                          SHNi-TPR  15 enFpqAveDlrkaLe 29 
                                       e++++Ave +++aLe
  gi|386002705|ref|YP_005921004.1| 352 ERYDEAVEAYDSALE 366
                                       9*************8 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.5
                          SHNi-TPR  18 pqAveDlrkaLeL 30 
                                       ++A+e +++aLe+
  gi|386002705|ref|YP_005921004.1| 389 EEALESYDRALEI 401
                                       68*********98 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.4
                          SHNi-TPR  19 qAveDlrkaLeLreqllp 36 
                                       +A+e +++aLeL  +++p
  gi|386002705|ref|YP_005921004.1| 492 EAAEAFDRALELDPEYEP 509
                                       79999******9777666 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 5.5
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++ +A+  + +aLeL
  gi|386002705|ref|YP_005921004.1| 625 RYREAADCYGRALEL 639
                                       677888888888887 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5     0.059        28       1      17 [.     205     221 ..     205     230 .. 0.74
   2 ?    0.8   0.1       1.6   7.7e+02       1      15 [.     307     321 ..     307     327 .. 0.80
   3 ?    5.7   0.3     0.045        21       1      20 [.     375     397 ..     375     401 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.059
                           HEAT_EZ   1 wrvRraAawaLGrlagg 17 
                                       w++R +A++aLGr+++ 
  gi|386002705|ref|YP_005921004.1| 205 WQNRGNALRALGRPEEA 221
                                       99*********996633 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.6
                           HEAT_EZ   1 wrvRraAawaLGrla 15 
                                       w++R  A+++LGr +
  gi|386002705|ref|YP_005921004.1| 307 WNNRGLALANLGRSE 321
                                       99**********833 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.045
                           HEAT_EZ   1 wrvRraAawaLGr...laggepe 20 
                                       w++R aA++aLGr   +++  ++
  gi|386002705|ref|YP_005921004.1| 375 WNNRGAALAALGReeeALESYDR 397
                                       99**********97776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 1.09u 0.30s 00:00:01.39 Elapsed: 00:00:00.69
# Mc/sec: 2904.29
//
Query:       gi|386002706|ref|YP_005921005.1|  [L=122]
Description: hypothetical protein Mhar_2026 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.9e-32  107.5   0.0    7.9e-09   35.0   0.0    4.0  4  TPR_1        Tetratricopeptide repeat
    4.2e-26   88.9   0.1    1.7e-07   30.8   0.0    4.0  4  TPR_2        Tetratricopeptide repeat
    3.3e-24   84.3   0.9    2.5e-09   36.7   0.0    4.0  4  TPR_11       TPR repeat
    1.7e-22   77.7   0.0    3.7e-06   26.7   0.0    3.8  4  TPR_8        Tetratricopeptide repeat
    2.1e-18   65.3   0.0    6.5e-05   23.0   0.0    3.8  4  TPR_17       Tetratricopeptide repeat
    1.7e-17   63.3   0.7    1.2e-08   35.0   0.3    2.1  2  TPR_9        Tetratricopeptide repeat
    2.9e-17   63.0   1.3    6.8e-11   42.6   0.4    2.7  3  TPR_16       Tetratricopeptide repeat
    1.9e-16   60.1   6.8    9.9e-07   29.0   0.4    3.2  3  TPR_12       Tetratricopeptide repeat
    3.3e-14   52.4   1.7    2.4e-05   24.8   0.3    4.0  4  TPR_14       Tetratricopeptide repeat
    1.2e-11   44.9   0.0    0.00013   22.4   0.0    2.1  2  TPR_19       Tetratricopeptide repeat
    2.4e-11   42.8   0.1     0.0021   18.0   0.0    3.7  4  TPR_7        Tetratricopeptide repeat
      3e-09   36.9   0.1      0.014   16.0   0.0    3.6  4  TPR_6        Tetratricopeptide repeat
    1.4e-05   24.8   1.3      0.014   15.3   0.1    3.5  4  TPR_10       Tetratricopeptide repeat
    0.00018   21.9   0.6      0.074   13.5   0.2    2.2  3  BTAD         Bacterial transcriptional activator domain
     0.0024   18.0   0.1        4.5    7.3   0.0    2.9  3  DUF3856      Domain of Unknown Function (DUF3856)
     0.0025   17.1   0.0      0.072   12.3   0.0    2.5  1  TPR_15       Tetratricopeptide repeat
     0.0073   16.5   0.3        1.5    9.2   0.0    3.4  4  PPR          PPR repeat
     0.0084   15.8   0.3          2    8.1   0.0    2.5  3  TPR_21       Tetratricopeptide repeat-like domain
     0.0095   16.0   0.2         17    5.6   0.0    3.6  4  MIT          MIT (microtubule interacting and transport) doma
  ------ inclusion threshold ------
      0.022   13.7   0.0          1    8.2   0.0    2.1  2  NARP1        NMDA receptor-regulated protein 1
      0.029   14.6   0.1        0.6   10.4   0.0    2.1  2  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
      0.031   14.4   0.3        6.9    6.8   0.0    3.0  3  Fis1_TPR_C   Fis1 C-terminal tetratricopeptide repeat
      0.045   13.5   0.0        9.7    5.9   0.0    2.1  2  TOM20_plant  Plant specific mitochondrial import receptor sub
      0.055   13.2   0.0       0.66    9.7   0.0    2.2  2  RPN7         26S proteasome subunit RPN7
        0.1   12.9   0.1        7.1    6.9   0.0    2.5  3  TPR_5        Tetratrico peptide repeat
       0.18   10.9   0.0       0.29   10.2   0.0    1.2  1  Rota_NSP3    Rotavirus non-structural protein NSP3


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0059       4.1      14      33 ..       1      20 [.       1      21 [. 0.84
   2 !   35.0   0.0   1.1e-11   7.9e-09       3      32 ..      24      53 ..      22      55 .. 0.96
   3 !   30.0   0.0   4.2e-10   2.9e-07       1      33 [.      56      88 ..      56      89 .. 0.96
   4 !   30.6   0.0   2.9e-10     2e-07       1      30 [.      90     119 ..      90     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0059
                                      TT-HHHHHHHHHHHHHHSTT CS
                             TPR_1 14 lgkydeAleyyekALelnPn 33
                                      ++++ eAl++y+ A  ++P+
  gi|386002706|ref|YP_005921005.1|  1 MKRPSEALDCYDVAAGIDPT 20
                                      7899*******977777776 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.1e-11
                                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1  3 alynlGnayfklgkydeAleyyekALelnP 32
                                      ++ n+G ++++lg+++eA+e y++AL ++P
  gi|386002706|ref|YP_005921005.1| 24 VWRNRGTILQSLGRLEEAVESYDRALAIDP 53
                                      799**************************9 PP

  == domain 3  score: 30.0 bits;  conditional E-value: 4.2e-10
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPn 33
                                      a+ +y +G a+  l +++eA+e y+ AL +nP 
  gi|386002706|ref|YP_005921005.1| 56 ADLWYIRGTALDGLMRHEEAIESYDSALAINPG 88
                                      799*****************************7 PP

  == domain 4  score: 30.6 bits;  conditional E-value: 2.9e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a++++++G a++klg++ +A+e+y+k +el
  gi|386002706|ref|YP_005921005.1|  90 ARSWNRKGDAFYKLGQHRKAVECYDKFIEL 119
                                       799**********************97666 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.011       7.7      15      34 .]       2      21 ..       1      21 [. 0.90
   2 !   30.8   0.0   2.4e-10   1.7e-07       3      33 ..      24      54 ..      22      55 .. 0.95
   3 !   20.6   0.0   4.5e-07   0.00031       1      34 []      56      89 ..      56      89 .. 0.96
   4 !   26.2   0.1   7.4e-09   5.1e-06       1      31 [.      90     120 ..      90     122 .] 0.94

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                             TPR_2 15 gdyeeAleafekAleldPnn 34
                                      +++ eAl++++ A  +dP++
  gi|386002706|ref|YP_005921005.1|  2 KRPSEALDCYDVAAGIDPTD 21
                                      7899**********999986 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.4e-10
                             TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                      ++ n+G ++  lg++eeA+e +++Al++dP 
  gi|386002706|ref|YP_005921005.1| 24 VWRNRGTILQSLGRLEEAVESYDRALAIDPA 54
                                      8*****************************5 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 4.5e-07
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      a+++y +G a+  l ++eeA+e ++ Al+++P++
  gi|386002706|ref|YP_005921005.1| 56 ADLWYIRGTALDGLMRHEEAIESYDSALAINPGD 89
                                      789*****************************86 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 7.4e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                       a+ +++ G+a yklg++ +A+e+++k +el 
  gi|386002706|ref|YP_005921005.1|  90 ARSWNRKGDAFYKLGQHRKAVECYDKFIELS 120
                                       678*************************996 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0005      0.35      12      42 .]       6      36 ..       3      36 .. 0.95
   2 !   36.7   0.0   3.7e-12   2.5e-09       3      37 ..      31      65 ..      29      67 .. 0.90
   3 !   31.0   0.2   2.1e-10   1.4e-07      10      42 .]      72     104 ..      71     104 .. 0.97
   4 !   17.8   0.0   2.8e-06    0.0019       1      24 [.      97     120 ..      97     122 .] 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                            TPR_11 12 eAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      eA+ +Y  A  +dP++  ++ n+G +++ +G
  gi|386002706|ref|YP_005921005.1|  6 EALDCYDVAAGIDPTDGAVWRNRGTILQSLG 36
                                      9***********************9999887 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 3.7e-12
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37
                                      ++ ++G++eeA+e+Y +Al++dP +a+++y +G a
  gi|386002706|ref|YP_005921005.1| 31 ILQSLGRLEEAVESYDRALAIDPASADLWYIRGTA 65
                                      66689*************************99976 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 2.1e-10
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        eeAie+Y  Al+++P +a+ ++  G+a+yk+G
  gi|386002706|ref|YP_005921005.1|  72 HEEAIESYDSALAINPGDARSWNRKGDAFYKLG 104
                                       79*****************************99 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 2.8e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                       Gda+y++G+  +A+e+Y k ++l+
  gi|386002706|ref|YP_005921005.1|  97 GDAFYKLGQHRKAVECYDKFIELS 120
                                       9*****************988886 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.1   7.6e+02      14      33 ..       1      20 [.       1      21 [. 0.85
   2 !   25.5   0.0   1.3e-08     9e-06       6      33 ..      27      54 ..      23      55 .. 0.92
   3 !   20.0   0.0   7.8e-07   0.00054       1      33 [.      56      88 ..      56      89 .. 0.95
   4 !   26.7   0.0   5.4e-09   3.7e-06       1      31 [.      90     120 ..      90     122 .] 0.96

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                                      TT-HHHHHHHHHHHHHHHHH CS
                             TPR_8 14 lgdyeeAkeyyekaleldpd 33
                                      +++  eA  +y  a  +dp+
  gi|386002706|ref|YP_005921005.1|  1 MKRPSEALDCYDVAAGIDPT 20
                                      578889*****999999997 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1.3e-08
                                      HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  6 nlgsiylklgdyeeAkeyyekaleldpd 33
                                      n g i+++lg++eeA+e+y +al +dp+
  gi|386002706|ref|YP_005921005.1| 27 NRGTILQSLGRLEEAVESYDRALAIDPA 54
                                      899************************7 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 7.8e-07
                                      CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      a+++y  g +++ l ++eeA+e+y  al ++p 
  gi|386002706|ref|YP_005921005.1| 56 ADLWYIRGTALDGLMRHEEAIESYDSALAINPG 88
                                      689****************************96 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 5.4e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a++++++g++  klg++ +A+e+y k +el+
  gi|386002706|ref|YP_005921005.1|  90 ARSWNRKGDAFYKLGQHRKAVECYDKFIELS 120
                                       79***************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.5e-07   0.00052       1      34 []      10      43 ..      10      43 .. 0.90
   2 !   17.2   0.0   6.7e-06    0.0046       2      33 ..      45      76 ..      44      77 .. 0.90
   3 !   23.0   0.0   9.4e-08   6.5e-05       2      34 .]      79     111 ..      78     111 .. 0.94
   4 ?   -0.4   0.0       2.9     2e+03       1       8 [.     112     119 ..     112     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.5e-07
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      +y  a+ +dP++  ++ n++++l ++G+l++A++
  gi|386002706|ref|YP_005921005.1| 10 CYDVAAGIDPTDGAVWRNRGTILQSLGRLEEAVE 43
                                      56677779***********************975 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.7e-06
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                      y +al++dP +ad+++ ++++l  + ++++A+
  gi|386002706|ref|YP_005921005.1| 45 YDRALAIDPASADLWYIRGTALDGLMRHEEAI 76
                                      99********************9888887776 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 9.4e-08
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y  al+++P +a ++n ++ +++k+G++++A++
  gi|386002706|ref|YP_005921005.1|  79 YDSALAINPGDARSWNRKGDAFYKLGQHRKAVE 111
                                       7789**************************975 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.9
                            TPR_17   1 lylkalel 8  
                                       +y k++el
  gi|386002706|ref|YP_005921005.1| 112 CYDKFIEL 119
                                       8*****97 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.3   1.7e-11   1.2e-08      10      65 ..       3      58 ..       2      66 .. 0.93
   2 !   26.9   0.0   5.9e-09   4.1e-06      10      59 ..      71     120 ..      69     122 .] 0.96

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.7e-11
                             TPR_9 10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      + ++al +++    ++P d   +r RG +l+ lG+l++A++  +++la++p+ +d 
  gi|386002706|ref|YP_005921005.1|  3 RPSEALDCYDVAAGIDPTDGAVWRNRGTILQSLGRLEEAVESYDRALAIDPASADL 58
                                      5679***********************************************99886 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 5.9e-09
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                       ++e+a++ +++ l+++P d++ +   G + ++lG+ ++A+++ + +++l+
  gi|386002706|ref|YP_005921005.1|  71 RHEEAIESYDSALAINPGDARSWNRKGDAFYKLGQHRKAVECYDKFIELS 120
                                       6899*******************************************986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         3   2.1e+03      49      67 ..       3      21 ..       2      22 .. 0.78
   2 !   42.6   0.4   9.9e-14   6.8e-11       2      68 .]      27      90 ..      26      90 .. 0.97
   3 !   25.4   0.0   2.4e-08   1.6e-05      13      59 ..      72     115 ..      70     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3
                            TPR_16 49 rlaeAaalyraalraapda 67
                                      r  eA++ y+ a++ +p +
  gi|386002706|ref|YP_005921005.1|  3 RPSEALDCYDVAAGIDPTD 21
                                      6778888899999988875 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 9.9e-14
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68
                                      ++++++  +g+ ++A++ +++al+ d   P+ a+ ++ +g a+  + r++eA++ y++al+  p+++
  gi|386002706|ref|YP_005921005.1| 27 NRGTILQSLGRLEEAVESYDRALAID---PASADLWYIRGTALDGLMRHEEAIESYDSALAINPGDA 90
                                      579999********************...***********************************986 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 2.4e-08
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                        ++A++ ++ al+ +   P +a++++ +gda++++g + +A++ y++
  gi|386002706|ref|YP_005921005.1|  72 HEEAIESYDSALAIN---PGDARSWNRKGDAFYKLGQHRKAVECYDK 115
                                       699************...***********************988776 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   2.8e-07   0.00019       5      32 ..      24      51 ..       1      54 [. 0.64
   2 !   29.0   0.4   1.4e-09   9.9e-07       5      74 ..      24      85 ..      20      87 .. 0.88
   3 !   23.9   0.1   5.5e-08   3.8e-05       6      72 ..      59     117 ..      54     122 .] 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-07
                            TPR_12  5 alnnlaavlrrlgrydeAlellekalei 32
                                      +++n++++l+ lgr++eA e +++al+i
  gi|386002706|ref|YP_005921005.1| 24 VWRNRGTILQSLGRLEEAVESYDRALAI 51
                                      4455555555555555555555555554 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.4e-09
                            TPR_12  5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                      +++n++++l+ lgr++eA e +++al+i      p     a   +  g++++ l r+eeA+e +  alai
  gi|386002706|ref|YP_005921005.1| 24 VWRNRGTILQSLGRLEEAVESYDRALAID-----PA---SADLWYIRGTALDGLMRHEEAIESYDSALAI 85
                                      788**************************.....75...4777888888888777*************98 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 5.5e-08
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++ ++++l  l r++eA+e ++ al+i      p     a++ +  g+++++lg++++A+e + + +
  gi|386002706|ref|YP_005921005.1|  59 WYIRGTALDGLMRHEEAIESYDSALAIN-----PG---DARSWNRKGDAFYKLGQHRKAVECYDKFI 117
                                       5556777778889999999999999999.....43...69**********************98755 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.07        49      16      42 ..       3      29 ..       1      31 [. 0.89
   2 !   24.8   0.3   3.4e-08   2.4e-05       3      39 ..      24      60 ..      22      66 .. 0.91
   3 !   19.6   0.1   1.6e-06    0.0011       2      42 ..      57      97 ..      56      99 .. 0.92
   4 !    9.2   0.0    0.0034       2.4       4      29 ..      93     118 ..      90     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.07
                            TPR_14 16 dpdeAiallrralalaPddaeawllla 42
                                      +p eA+++++ a   +P+d ++w+  +
  gi|386002706|ref|YP_005921005.1|  3 RPSEALDCYDVAAGIDPTDGAVWRNRG 29
                                      799********************9765 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 3.4e-08
                            TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawl 39
                                      +++ ++ +l  lG+++eA++ ++rala +P++a++w+
  gi|386002706|ref|YP_005921005.1| 24 VWRNRGTILQSLGRLEEAVESYDRALAIDPASADLWY 60
                                      68889999***************************96 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.6e-06
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42
                                      ++++ ++ al  l +++eAi+ ++ ala +P+da+ w + +
  gi|386002706|ref|YP_005921005.1| 57 DLWYIRGTALDGLMRHEEAIESYDSALAINPGDARSWNRKG 97
                                      789*******************************9998776 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0034
                            TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                       + + ++a++ lG++++A++++++ ++
  gi|386002706|ref|YP_005921005.1|  93 WNRKGDAFYKLGQHRKAVECYDKFIE 118
                                       677899***************99877 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.2e-07   0.00043       5      62 ..       2      59 ..       1      64 [. 0.92
   2 !   22.4   0.0   1.9e-07   0.00013       6      49 ..      71     114 ..      67     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.2e-07
                            TPR_19  5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      +++ eAl+ +  a   dp +++++ +   +l +lg+l+eA +  d++++ dp +a+++
  gi|386002706|ref|YP_005921005.1|  2 KRPSEALDCYDVAAGIDPTDGAVWRNRGTILQSLGRLEEAVESYDRALAIDPASADLW 59
                                      678899999999****************************************988776 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.9e-07
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                       +++eA++ + +al+ +p++a+ + +  +a ++lgq  +A ++ d
  gi|386002706|ref|YP_005921005.1|  71 RHEEAIESYDSALAINPGDARSWNRKGDAFYKLGQHRKAVECYD 114
                                       689*************************************9987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.2   2.2e+03      16      25 ..       5      14 ..       3      22 .. 0.71
   2 !   18.0   0.0     3e-06    0.0021       4      30 ..      27      53 ..      24      58 .. 0.85
   3 ?    5.8   0.0     0.023        16      14      33 ..      71      88 ..      63      91 .. 0.78
   4 !   14.6   0.0   3.5e-05     0.024       1      28 [.      92     119 ..      92     122 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.2
                             TPR_7 16 eeAielyeqs 25
                                      +eA+++y  +
  gi|386002706|ref|YP_005921005.1|  5 SEALDCYDVA 14
                                      6999999764 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltk 30
                                      n + + ++lG+ eeA+e y ++La++ 
  gi|386002706|ref|YP_005921005.1| 27 NRGTILQSLGRLEEAVESYDRALAIDP 53
                                      7899*****************887764 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.023
                             TPR_7 14 dyeeAielyeqsLaltkdpe 33
                                      ++eeAie y    al+  p+
  gi|386002706|ref|YP_005921005.1| 71 RHEEAIESYDS--ALAINPG 88
                                      689********..5555444 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.5e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       ++++ ++++ +lG++++A+e+y + ++l
  gi|386002706|ref|YP_005921005.1|  92 SWNRKGDAFYKLGQHRKAVECYDKFIEL 119
                                       57889*****************986655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         6   4.1e+03      14      25 ..       2      13 ..       1      20 [. 0.77
   2 !    9.8   0.0     0.002       1.4       6      33 .]      28      55 ..      26      55 .. 0.88
   3 ?    6.8   0.0     0.017        12       3      31 ..      59      87 ..      57      89 .. 0.86
   4 !   16.0   0.0     2e-05     0.014       7      28 ..      97     118 ..      95     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6
                                      HHHHHHHHHHHH CS
                             TPR_6 14 gdtdkAlealer 25
                                      +++++Al+ ++ 
  gi|386002706|ref|YP_005921005.1|  2 KRPSEALDCYDV 13
                                      578899999976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                                      HHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  6 lalsyrklgdtdkAlealerlikeYPdS 33
                                      ++  +++lg+ ++A+e ++r +   P S
  gi|386002706|ref|YP_005921005.1| 28 RGTILQSLGRLEEAVESYDRALAIDPAS 55
                                      678889999************9998876 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                                      HHHHHHHHHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  3 lyklalsyrk.lgdtdkAlealerlikeYP 31
                                       y ++ ++   + ++++A+e +++ +   P
  gi|386002706|ref|YP_005921005.1| 59 WYIRGTALDGlM-RHEEAIESYDSALAINP 87
                                      588999999879.**********9998888 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                       + +++klg+++kA+e ++++i+
  gi|386002706|ref|YP_005921005.1|  97 GDAFYKLGQHRKAVECYDKFIE 118
                                       899***99************97 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.2   2.2e+03      20      35 ..       6      14 ..       1      21 [. 0.53
   2 !   15.3   0.1     2e-05     0.014       7      31 ..      27      51 ..      26      51 .. 0.94
   3 ?    3.5   0.0       0.1        72      11      31 ..      65      85 ..      63      86 .. 0.81
   4 ?    2.6   0.0      0.19   1.3e+02      11      27 ..      99     115 ..      90     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.2
                            TPR_10 20 eAealleealairrrl 35
                                      eA+       +++  +
  gi|386002706|ref|YP_005921005.1|  6 EAL-------DCYDVA 14
                                      555.......554444 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2e-05
                            TPR_10  7 NLanalrqrgrydeAealleealai 31
                                      N + +l+++gr++eA++ +++alai
  gi|386002706|ref|YP_005921005.1| 27 NRGTILQSLGRLEEAVESYDRALAI 51
                                      7799*******************97 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                            TPR_10 11 alrqrgrydeAealleealai 31
                                      al  + r++eA + ++ alai
  gi|386002706|ref|YP_005921005.1| 65 ALDGLMRHEEAIESYDSALAI 85
                                      66667799****999999997 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.19
                            TPR_10  11 alrqrgrydeAeallee 27 
                                       a +++g++ +A++ +++
  gi|386002706|ref|YP_005921005.1|  99 AFYKLGQHRKAVECYDK 115
                                       66889999999999876 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.026        18      85     122 ..      11      48 ..       2      56 .. 0.69
   2 !   13.5   0.2   0.00011     0.074      68     122 ..      28      82 ..      23      85 .. 0.91
   3 !   12.9   0.0   0.00016      0.11      75     125 ..      69     119 ..      60     122 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.026
                                       HHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  85 lealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       ++ ++  +P++ + +r   + l  +Gr +eA e Y+r+
  gi|386002706|ref|YP_005921005.1|  11 YDVAAGIDPTDGAVWRNRGTILQSLGRLEEAVESYDRA 48 
                                       55566677777777777777777888888888888776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00011
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       +   + +lGr eea++ +++++a +P   +l+    +Al  + r +eA+e Y+++
  gi|386002706|ref|YP_005921005.1|  28 RGTILQSLGRLEEAVESYDRALAIDPASADLWYIRGTALDGLMRHEEAIESYDSA 82 
                                       5666779*********************************************986 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00016
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       l r+eea++ +++++a +P + r++     A +++G+  +A e Y+++ +l
  gi|386002706|ref|YP_005921005.1|  69 LMRHEEAIESYDSALAINPGDARSWNRKGDAFYKLGQHRKAVECYDKFIEL 119
                                       559******************************************998765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0066       4.5     104     126 ..      26      48 ..       6      55 .. 0.83
   2 ?    5.8   0.0     0.019        13     105     126 ..      61      82 ..      56      87 .. 0.81
   3 ?    1.0   0.0      0.57   3.9e+02     105     126 ..      95     116 ..      89     121 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                                       HHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrma 126
                                        +r++ l++lGr +ea++++  a
  gi|386002706|ref|YP_005921005.1|  26 RNRGTILQSLGRLEEAVESYDRA 48 
                                       57999999999999999999876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                                       HHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrma 126
                                        r++al++l r++ea++++  a
  gi|386002706|ref|YP_005921005.1|  61 IRGTALDGLMRHEEAIESYDSA 82 
                                       5889999999999999998776 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.57
                                       HHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrma 126
                                       +++ a+ +lG++ +a++ + + 
  gi|386002706|ref|YP_005921005.1|  95 RKGDAFYKLGQHRKAVECYDKF 116
                                       4555666666666666666554 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00011     0.072     147     182 ..      23      58 ..       6     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                       a++  r+ + +  g+ ++A++ y +Ala +p+s++l
  gi|386002706|ref|YP_005921005.1|  23 AVWRNRGTILQSLGRLEEAVESYDRALAIDPASADL 58 
                                       566666666666666666666666666666665554 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.4   1.7e+03      15      24 ..       3      12 ..       1      13 [. 0.83
   2 ?    2.4   0.0      0.32   2.2e+02      13      24 ..      35      46 ..      32      49 .. 0.83
   3 ?   -1.6   0.0       6.2   4.3e+03      15      21 ..      71      77 ..      64      81 .. 0.62
   4 !    9.2   0.0    0.0022       1.5       8      28 ..      98     118 ..      97     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.4
                               PPR 15 kleeAlelfk 24
                                      +++eAl++++
  gi|386002706|ref|YP_005921005.1|  3 RPSEALDCYD 12
                                      799***9986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.32
                               PPR 13 nGkleeAlelfk 24
                                       G+leeA+e ++
  gi|386002706|ref|YP_005921005.1| 35 LGRLEEAVESYD 46
                                      69*****99766 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.2
                               PPR 15 kleeAle 21
                                      ++eeA+e
  gi|386002706|ref|YP_005921005.1| 71 RHEEAIE 77
                                      4566655 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0022
                               PPR   8 sgycknGkleeAlelfkeMke 28 
                                       +++ k G++++A+e++++ +e
  gi|386002706|ref|YP_005921005.1|  98 DAFYKLGQHRKAVECYDKFIE 118
                                       6899*************9876 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0     0.003         2     151     179 ..      27      55 ..      18      70 .. 0.85
   2 ?   -0.2   0.0         1   7.1e+02     151     177 ..      61      87 ..      55      95 .. 0.77
   3 ?    5.1   0.0     0.024        17     147     171 ..      91     115 ..      89     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.003
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleek 179
                                        rG il + g+l+eA + Y++Ala   ++
  gi|386002706|ref|YP_005921005.1|  27 NRGTILQSLGRLEEAVESYDRALAIDPAS 55 
                                       69********************9876655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaale 177
                                       +rG +l    + +eA + Y+ Ala + 
  gi|386002706|ref|YP_005921005.1|  61 IRGTALDGLMRHEEAIESYDSALAINP 87 
                                       577777777888999999999997655 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.024
                            TPR_21 147 lvaelrGDilvaqgkldeAraaYqa 171
                                       +  +++GD++++ g+  +A + Y++
  gi|386002706|ref|YP_005921005.1|  91 RSWNRKGDAFYKLGQHRKAVECYDK 115
                                       56689****************9987 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.4   9.9e+02      21      31 ..       5      15 ..       2      17 .. 0.80
   2 ?    4.7   0.0     0.046        32      18      31 ..      36      49 ..      29      51 .. 0.87
   3 ?    5.6   0.0     0.025        17      17      31 ..      69      83 ..      62      85 .. 0.80
   4 ?    0.2   0.0       1.2   8.3e+02      18      29 ..     104     115 ..     102     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                               MIT 21 eeAlelYkeal 31
                                      +eAl++Y  a 
  gi|386002706|ref|YP_005921005.1|  5 SEALDCYDVAA 15
                                      69*****8775 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.046
                               MIT 18 gnyeeAlelYkeal 31
                                      g  eeA+e Y  al
  gi|386002706|ref|YP_005921005.1| 36 GRLEEAVESYDRAL 49
                                      789********998 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.025
                               MIT 17 agnyeeAlelYkeal 31
                                          eeA+e Y +al
  gi|386002706|ref|YP_005921005.1| 69 LMRHEEAIESYDSAL 83
                                      55789********98 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.2
                               MIT  18 gnyeeAlelYke 29 
                                       g+  +A+e+Y +
  gi|386002706|ref|YP_005921005.1| 104 GQHRKAVECYDK 115
                                       788899999987 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0015         1     209     258 ..       5      54 ..       1      81 [. 0.70
   2 ?    3.2   0.0     0.048        33      42      66 ..      94     118 ..      71     122 .] 0.61

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                             NARP1 209 ekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                       ++Al++ d a   +pt   ++ ++++il+  G l++A+e  ++a ++D a
  gi|386002706|ref|YP_005921005.1|   5 SEALDCYDVAAGIDPTDGAVWRNRGTILQSLGRLEEAVESYDRALAIDPA 54 
                                       57788888888888888888888888888888888888888888888854 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.048
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                             NARP1  42 etkaelllkLgrkeeAeatyeaLle 66 
                                       + k++   kLg++ +A + y + +e
  gi|386002706|ref|YP_005921005.1|  94 NRKGDAFYKLGQHRKAVECYDKFIE 118
                                       4566777777777777777776665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.026        18      32      80 ..      31      80 ..      18      82 .. 0.88
   2 ?   10.4   0.0   0.00088       0.6       4      51 ..      71     119 ..      69     122 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.026
                                      HHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3 32 clylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                       l ++g+ ++A e +++a  +++ s   +y+ + +l  L ++eeAi  ++
  gi|386002706|ref|YP_005921005.1| 31 ILQSLGRLEEAVESYDRAlAIDPASADLWYIRGTALDGLMRHEEAIESYD 80
                                      6788999999********9999************9999*******98765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00088
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.kl 51 
                                       ++++Ai  ++ +la ++ ++ +   ++ ++y++gq+ +A e ++k+ +l
  gi|386002706|ref|YP_005921005.1|  71 RHEEAIESYDSALAINPGDARSWNRKGDAFYKLGQHRKAVECYDKFiEL 119
                                       68999999999999999999999999***************99998554 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.13        92      14      33 ..      35      54 ..      34      58 .. 0.91
   2 ?    0.6   0.0      0.87     6e+02      14      33 ..      69      88 ..      56      90 .. 0.76
   3 ?    6.8   0.0      0.01       6.9      11      30 ..     100     119 ..      99     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                                      HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                                      lg+ +eA +  d+ L+i+P 
  gi|386002706|ref|YP_005921005.1| 35 LGRLEEAVESYDRALAIDPA 54
                                      78999*************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.87
                                      HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                                      l +++eA +  d  L+i P+
  gi|386002706|ref|YP_005921005.1| 69 LMRHEEAIESYDSALAINPG 88
                                      56788888888888988886 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.01
                                       HHHHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLei 30 
                                        yklg++++A ++ d ++e+
  gi|386002706|ref|YP_005921005.1| 100 FYKLGQHRKAVECYDKFIEL 119
                                       6**************99885 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.015        10      44      75 ..      31      61 ..      27      68 .. 0.81
   2 ?    5.9   0.0     0.014       9.7       3      46 ..      68     111 ..      66     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                                      HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHH CS
                       TOM20_plant 44 vaeakqmiqdaiskleeallidPkkhdalWci 75
                                      + ++   +++a+  ++ al idP   d lW i
  gi|386002706|ref|YP_005921005.1| 31 ILQSLGRLEEAVESYDRALAIDPASAD-LWYI 61
                                      667777899**************9887.5655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHHS-HHH CS
                       TOM20_plant   3 rlllfeearkdaeatykknPldadnllrWggallelsqfqsvae 46 
                                        l+  eea ++ ++  + nP da    r g+a+  l q ++  e
  gi|386002706|ref|YP_005921005.1|  68 GLMRHEEAIESYDSALAINPGDARSWNRKGDAFYKLGQHRKAVE 111
                                       56777888888888899999999999999999999999887666 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.31   2.2e+02      44      63 ..      30      49 ..      23      56 .. 0.79
   2 ?    9.7   0.0   0.00096      0.66      36      64 ..      90     118 ..      69     122 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.31
                                      HHHHHCT-HHHHHHHHHTCC CS
                              RPN7 44 ehYlkigdleeAlkaysrir 63
                                          + g leeA++ y r++
  gi|386002706|ref|YP_005921005.1| 30 TILQSLGRLEEAVESYDRAL 49
                                      55667899********9975 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00096
                                       HHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  36 rrakldlaehYlkigdleeAlkaysrire 64 
                                       +r ++++++ ++k g++++A+++y + +e
  gi|386002706|ref|YP_005921005.1|  90 ARSWNRKGDAFYKLGQHRKAVECYDKFIE 118
                                       567899******************99766 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0      0.01       7.1       6      29 ..      27      50 ..      13      54 .. 0.87
   2 ?    3.4   0.0      0.13        87       5      30 ..      60      85 ..      56      99 .. 0.84
   3 ?   -1.7   0.0       4.7   3.2e+03      11      26 ..     100     115 ..      91     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                             TPR_5  6 eragarDstGhedkavplYrraLa 29
                                      +r+++  s G+ ++av+ Y raLa
  gi|386002706|ref|YP_005921005.1| 27 NRGTILQSLGRLEEAVESYDRALA 50
                                      578888999999999999999997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                             TPR_5  5 FeragarDstGhedkavplYrraLae 30
                                      + r++a D   ++++a++ Y  aLa 
  gi|386002706|ref|YP_005921005.1| 60 YIRGTALDGLMRHEEAIESYDSALAI 85
                                      5688999999999**********985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.7
                             TPR_5  11 rDstGhedkavplYrr 26 
                                       +   G++ kav+ Y +
  gi|386002706|ref|YP_005921005.1| 100 FYKLGQHRKAVECYDK 115
                                       4556788888888865 PP

>> Rota_NSP3  Rotavirus non-structural protein NSP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00042      0.29     178     247 ..      55     120 ..      30     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                         Rota_NSP3 178 kykdivldldkmneevkldqnsisynsaailvstilgaelkvyneklerlldvGsltsskeiieksiele 247
                                         + + +   ++++ ++ ++   sy+sa +    i   + + +n k++  +++G+  +++e + k iel 
  gi|386002706|ref|YP_005921005.1|  55 SADLWYIRGTALDGLMRHEEAIESYDSALA----INPGDARSWNRKGDAFYKLGQHRKAVECYDKFIELS 120
                                       455688999999***************999....8899******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 714.62
//
Query:       gi|386002707|ref|YP_005921006.1|  [L=949]
Description: Tetratricopeptide TPR_2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.8e-221  705.8  47.0    1.1e-11   44.1   0.2   26.0 26  TPR_1            Tetratricopeptide repeat
   2.5e-196  620.5  60.4    2.7e-10   39.6   0.2   26.0 26  TPR_2            Tetratricopeptide repeat
   1.2e-175  569.0  66.2    7.2e-13   48.0   0.1   25.5 26  TPR_11           TPR repeat
   7.5e-151  478.1  29.0    7.8e-08   31.9   0.0   26.0 26  TPR_8            Tetratricopeptide repeat
   1.7e-124  406.2  69.7    5.1e-12   46.2   1.4   14.8 17  TPR_16           Tetratricopeptide repeat
   9.2e-122  389.0  23.1    5.2e-07   29.6   0.2   25.4 26  TPR_17           Tetratricopeptide repeat
   3.9e-103  329.2  73.6    2.7e-06   27.7   0.6   24.6 25  TPR_14           Tetratricopeptide repeat
    1.5e-94  310.5  24.0      2e-10   41.0   2.9   15.0 17  TPR_19           Tetratricopeptide repeat
    4.4e-93  305.7  68.2    3.8e-10   39.9   0.3   19.3 20  TPR_12           Tetratricopeptide repeat
    2.7e-89  293.4  67.5      1e-09   38.4   1.1   17.4 21  TPR_9            Tetratricopeptide repeat
    6.1e-65  210.6  59.7    0.00032   20.5   0.1   24.5 24  TPR_7            Tetratricopeptide repeat
    4.4e-59  193.3  45.5     0.0016   18.9   0.1   23.8 24  TPR_6            Tetratricopeptide repeat
    1.7e-49  165.9  10.2    2.2e-06   27.8   0.1   11.7 12  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.8e-36  122.4  84.4     0.0011   18.7   0.4   23.7 25  TPR_10           Tetratricopeptide repeat
    1.8e-35  122.5  31.2     0.0013   19.2   0.1   13.1 13  BTAD             Bacterial transcriptional activator domain
    2.6e-29  102.6   0.0     0.0051   15.8   0.0   11.4 12  NARP1            NMDA receptor-regulated protein 1
    1.3e-27   96.7  22.4       0.37   10.9   0.0   17.9 19  DUF3856          Domain of Unknown Function (DUF3856)
    1.1e-25   87.5  74.0       0.11   13.2   2.8   20.5 20  TPR_4            Tetratricopeptide repeat
    2.7e-25   88.2  31.7    0.00068   19.7   0.1   17.1 18  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    6.4e-20   70.8  15.8        0.5   10.4   0.0   17.0 18  TPR_3            Tetratricopeptide repeat
    1.5e-18   66.9   0.0     0.0066   16.5   0.1    7.7  8  SRP_TPR_like     Putative TPR-like repeat
    4.7e-13   49.0  11.3       0.21   10.7   1.1    8.1  8  TPR_15           Tetratricopeptide repeat
    1.9e-12   47.3   2.3       0.66   10.4   0.3    9.0 10  TPR_20           Tetratricopeptide repeat
    1.2e-08   34.7  32.1        2.8    8.4   0.0   16.7 16  PPR              PPR repeat
    1.4e-08   34.9  24.3        6.5    7.0   0.0   14.5 15  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
    1.9e-06   27.6   0.0       0.13   11.7   0.0    4.7  5  Coatomer_E       Coatomer epsilon subunit
    6.2e-06   26.2  49.5        1.3    9.2   0.8   16.4 16  MIT              MIT (microtubule interacting and transport) 
      7e-05   22.4   0.0       0.25   10.7   0.2    5.8  5  TPR_MalT         MalT-like TPR region
    7.8e-05   22.0   0.0         11    5.2   0.0    6.5  7  FAT              FAT domain
    0.00017   22.0   0.0         20    5.6   0.0    6.4  6  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00022   21.0  28.0        2.3    7.9   0.1   11.0 12  TPR_21           Tetratricopeptide repeat-like domain
    0.00033   19.9   0.0        2.6    7.1   0.0    3.9  3  Rota_NSP3        Rotavirus non-structural protein NSP3
      0.001   18.6  15.3        4.4    6.6   0.0    8.5  8  SNAP             Soluble NSF attachment protein, SNAP
     0.0016   18.6  20.2        9.5    6.5   0.0   10.4 10  TPR_5            Tetratrico peptide repeat
  ------ inclusion threshold ------
      0.032   14.3   0.0         13    6.0   0.0    4.6  4  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
      0.044   12.8   0.0        5.8    5.8   0.0    3.3  4  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
      0.048   12.4  10.4        1.5    7.5   0.1    5.9  7  PknG_TPR         Protein kinase G tetratricopeptide repeat
       0.53    9.9   7.0         98    2.6   0.3    6.6  5  HTH_Bact         Helix-turn-helix bacterial domain
        2.2    7.8   6.0         14    5.3   0.0    5.6  4  SHNi-TPR         SHNi-TPR
        3.6    7.3  19.8         29    4.3   0.1    9.3  8  RPN7             26S proteasome subunit RPN7
        5.6    7.4   6.1         66    4.0   0.0    5.3  5  Aida_N           Aida N-terminus


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0077       3.4       4      33 ..      28      57 ..      27      58 .. 0.91
   2 !   32.3   0.0   1.2e-10   5.4e-08       1      34 []      59      92 ..      59      92 .. 0.96
   3 !   26.5   0.0   8.5e-09   3.7e-06       3      32 ..      95     124 ..      93     125 .. 0.94
   4 !   25.3   0.0     2e-08   8.8e-06       2      32 ..     128     158 ..     127     159 .. 0.94
   5 !   27.7   0.0   3.5e-09   1.5e-06       2      33 ..     162     193 ..     161     194 .. 0.94
   6 !   31.5   0.1   2.3e-10     1e-07       1      33 [.     195     227 ..     195     228 .. 0.95
   7 !   34.8   0.2   2.1e-11     9e-09       2      32 ..     230     260 ..     229     262 .. 0.97
   8 !   40.4   0.0   3.6e-13   1.6e-10       3      33 ..     265     295 ..     263     296 .. 0.96
   9 !   43.2   0.1   4.4e-14   1.9e-11       2      34 .]     298     330 ..     297     330 .. 0.95
  10 !   30.4   0.0     5e-10   2.2e-07       4      33 ..     334     363 ..     331     364 .. 0.96
  11 !   44.1   0.2   2.4e-14   1.1e-11       2      34 .]     366     398 ..     365     398 .. 0.97
  12 !   31.0   0.1   3.3e-10   1.4e-07       2      29 ..     400     427 ..     399     431 .. 0.94
  13 !   15.7   0.0   2.2e-05    0.0095       2      34 .]     434     466 ..     433     466 .. 0.94
  14 !   27.0   0.4     6e-09   2.6e-06       2      31 ..     468     497 ..     467     499 .. 0.94
  15 !   15.3   0.0   2.9e-05     0.013       2      33 ..     502     533 ..     501     534 .. 0.94
  16 !   31.5   0.0   2.2e-10   9.6e-08       2      34 .]     536     568 ..     535     568 .. 0.96
  17 !   30.5   0.0   4.5e-10     2e-07       4      33 ..     572     601 ..     571     602 .. 0.94
  18 !   34.8   0.0     2e-11   8.7e-09       3      32 ..     605     634 ..     603     635 .. 0.94
  19 !   33.1   0.1   6.9e-11     3e-08       5      32 ..     635     662 ..     634     662 .. 0.95
  20 !   34.0   0.1   3.7e-11   1.6e-08       1      34 []     665     698 ..     665     698 .. 0.97
  21 !   21.6   0.0     3e-07   0.00013       5      34 .]     703     732 ..     700     732 .. 0.94
  22 !    9.5   0.0     0.002      0.89       6      29 ..     738     761 ..     734     766 .. 0.89
  23 !   25.8   0.0   1.4e-08   6.2e-06       3      33 ..     769     799 ..     768     800 .. 0.95
  24 !   15.6   0.0   2.4e-05     0.011       4      33 ..     804     833 ..     802     834 .. 0.93
  25 !   26.1   0.0   1.2e-08     5e-06       1      33 [.     835     867 ..     835     868 .. 0.96
  26 !   18.4   0.0   3.2e-06    0.0014       3      32 ..     871     900 ..     869     900 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0077
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALelnPn 33
                                      + +++  +++++ yd Al y +k L ++P 
  gi|386002707|ref|YP_005921006.1| 28 WLGKAIGFYSNESYDLALLYVNKSLDIDPA 57
                                      78889999*********************5 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.2e-10
                                      HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                      ++a+  +G+++  lg++deAl ++++ Le++P++
  gi|386002707|ref|YP_005921006.1| 59 PDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQD 92
                                      68******************************86 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 8.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       ++y +G +++ lg ydeA+++y++A e n 
  gi|386002707|ref|YP_005921006.1|  95 IWYSKGFVLYGLGIYDEAIDCYDRAMEFNS 124
                                       6************************99985 PP

  == domain 4  score: 25.3 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       + +  +G+a+++lg+y+eA+  y++A+  +P
  gi|386002707|ref|YP_005921006.1| 128 DLWRARGLALYSLGRYEEAVRSYDEAIVFDP 158
                                       78999**********************9998 PP

  == domain 5  score: 27.7 bits;  conditional E-value: 3.5e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       + +y++G+a+  lg+y++A+e y+ A++++ +
  gi|386002707|ref|YP_005921006.1| 162 DLWYQKGLALCGLGRYEKAIESYDFAITIDGD 193
                                       68***************************976 PP

  == domain 6  score: 31.5 bits;  conditional E-value: 2.3e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       a ++ ++++a+++lg+ +eA+++y++A+ ++P+
  gi|386002707|ref|YP_005921006.1| 195 AASWHGKALALYSLGRAEEAIDCYDRAIDIDPS 227
                                       678*****************************7 PP

  == domain 7  score: 34.8 bits;  conditional E-value: 2.1e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       +++yn+G a++ lg+++eA ++y+ A+e++P
  gi|386002707|ref|YP_005921006.1| 230 DVWYNKGIALYALGRHEEAFKCYDAAVEIDP 260
                                       68****************************9 PP

  == domain 8  score: 40.4 bits;  conditional E-value: 3.6e-13
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++n+G+a+++lg+ +eA+++y++A+ ++P+
  gi|386002707|ref|YP_005921006.1| 265 AWFNKGLAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       9*****************************7 PP

  == domain 9  score: 43.2 bits;  conditional E-value: 4.4e-14
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +++n+Gna++ lg++deA e+y++A+e++P++
  gi|386002707|ref|YP_005921006.1| 298 AVWNNKGNALYALGRFDEAQECYRRAVEIDPEY 330
                                       58*****************************86 PP

  == domain 10  score: 30.4 bits;  conditional E-value: 5e-10
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +ynlG+++++lg+ +eAle+y++ +e++Pn
  gi|386002707|ref|YP_005921006.1| 334 WYNLGVVLQRLGRGEEALEAYDRLIEIDPN 363
                                       *****************************9 PP

  == domain 11  score: 44.1 bits;  conditional E-value: 2.4e-14
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +a+yn+G+a+++lg+ydeA  +y+++Le++P+n
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYDRVLEIDPEN 398
                                       8******************************97 PP

  == domain 12  score: 31.0 bits;  conditional E-value: 3.3e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                       +++y +++a+ +lg+y+eAl++y++ALe
  gi|386002707|ref|YP_005921006.1| 400 DVWYDKALALGSLGRYEEALDCYDEALE 427
                                       68*************************9 PP

  == domain 13  score: 15.7 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++l+n+ n++++l++y+e + +y  ++ ++P +
  gi|386002707|ref|YP_005921006.1| 434 EVLNNRCNILYSLERYNESVGCYGDVIGIDPGY 466
                                       89****************************975 PP

  == domain 14  score: 27.0 bits;  conditional E-value: 6e-09
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       +a+yn+G+a++ lg+y+eA + y +A  ln
  gi|386002707|ref|YP_005921006.1| 468 NAWYNRGVALYTLGRYEEASASYGEAAALN 497
                                       59************************9998 PP

  == domain 15  score: 15.3 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                       +a+ ++G a+   g yd A+e+y+ A+ l+P 
  gi|386002707|ref|YP_005921006.1| 502 DAWVGMGDAFAAAGIYDRAVEAYDGAIALYPG 533
                                       8****************************997 PP

  == domain 16  score: 31.5 bits;  conditional E-value: 2.2e-10
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        ++yn+G+++++  +++eA+e +++++e++P++
  gi|386002707|ref|YP_005921006.1| 536 AVWYNRGLLLYNASRLEEAVESFDEVIEIDPSY 568
                                       68*****************************97 PP

  == domain 17  score: 30.5 bits;  conditional E-value: 4.5e-10
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +  +G+a++ lg+ deA+++y++ALe+ P+
  gi|386002707|ref|YP_005921006.1| 572 WRLKGLALYALGRSDEAIDCYDEALEISPS 601
                                       7889************************96 PP

  == domain 18  score: 34.8 bits;  conditional E-value: 2e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                        +yn+G+++f+lg+y eA+e y++++el+ 
  gi|386002707|ref|YP_005921006.1| 605 LWYNRGVVLFSLGRYGEAIESYDRVIELDR 634
                                       7***************************95 PP

  == domain 19  score: 33.1 bits;  conditional E-value: 6.9e-11
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALelnP 32 
                                       y +G a+++lg+ydeA+e+yek+Le+ P
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLEVSP 662
                                       889**********************988 PP

  == domain 20  score: 34.0 bits;  conditional E-value: 3.7e-11
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       aka+y++G+a++ lg+y+   e+y++++e++P +
  gi|386002707|ref|YP_005921006.1| 665 AKAWYQKGLAHQILGDYERSAECYDRVVEIDPGY 698
                                       89******************************76 PP

  == domain 21  score: 21.6 bits;  conditional E-value: 3e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALelnPnn 34 
                                        ++G ++++lg+yd Al+ y+ AL+ +P++
  gi|386002707|ref|YP_005921006.1| 703 LRRGFVLLRLGDYDGALASYDLALQEDPDD 732
                                       589*************************96 PP

  == domain 22  score: 9.5 bits;  conditional E-value: 0.002
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALe 29 
                                       ++G a++ lg+++eA + +++ L 
  gi|386002707|ref|YP_005921006.1| 738 GRGEALLALGRFEEASATFDRILA 761
                                       69***************9999886 PP

  == domain 23  score: 25.8 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a+ ++G+a+  l +ydeA++ y++A+ +n +
  gi|386002707|ref|YP_005921006.1| 769 AWHGRGLALAGLLRYDEAIDSYDRAIAINSS 799
                                       8****************************87 PP

  == domain 24  score: 15.6 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       + ++G ++ + g++++A++ +++A+ l+ +
  gi|386002707|ref|YP_005921006.1| 804 WIGRGGVLEEAGRLEDAVASFDRAIALDQE 833
                                       999*************************87 PP

  == domain 25  score: 26.1 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                       ++a+  +G a++k g++++A + +++A+ l+P+
  gi|386002707|ref|YP_005921006.1| 835 PEAWSMRGRALMKAGRLEDAAASFDRAIALDPS 867
                                       58******************************7 PP

  == domain 26  score: 18.4 bits;  conditional E-value: 3.2e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a  ++G ++  +g+ +eA+ +ye A+ l+P
  gi|386002707|ref|YP_005921006.1| 871 AQRGRGSVFEAQGRAEEAIGCYEAAIALDP 900
                                       55689************************9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0       0.1        45       4      33 ..      28      57 ..      26      58 .. 0.87
   2 !   27.7   0.0   3.8e-09   1.6e-06       1      34 []      59      92 ..      59      92 .. 0.96
   3 !   22.5   0.0   1.7e-07   7.5e-05       3      31 ..      95     123 ..      93     125 .. 0.92
   4 !   27.6   0.1   4.3e-09   1.9e-06       1      32 [.     127     158 ..     127     160 .. 0.94
   5 !   18.4   0.0   3.8e-06    0.0017       2      31 ..     162     191 ..     161     194 .. 0.86
   6 !   26.6   0.1   8.4e-09   3.7e-06       1      33 [.     195     227 ..     195     228 .. 0.94
   7 !   31.4   0.2   2.4e-10   1.1e-07       2      32 ..     230     260 ..     229     262 .. 0.95
   8 !   31.6   0.0   2.2e-10   9.8e-08       3      33 ..     265     295 ..     263     296 .. 0.96
   9 !   37.6   0.2   2.5e-12   1.1e-09       2      34 .]     298     330 ..     297     330 .. 0.95
  10 !   28.4   0.0   2.3e-09     1e-06       4      33 ..     334     363 ..     331     364 .. 0.96
  11 !   39.6   0.2   6.1e-13   2.7e-10       2      34 .]     366     398 ..     365     398 .. 0.97
  12 !   25.3   0.3   2.3e-08     1e-05       2      32 ..     400     430 ..     399     432 .. 0.93
  13 !   11.9   0.0   0.00043      0.19       1      33 [.     433     465 ..     433     466 .. 0.92
  14 !   26.1   0.8   1.2e-08   5.4e-06       3      31 ..     469     497 ..     467     499 .. 0.95
  15 !   18.2   0.0   4.3e-06    0.0019       2      34 .]     502     534 ..     501     534 .. 0.95
  16 !   26.4   0.0     1e-08   4.4e-06       2      33 ..     536     567 ..     535     568 .. 0.95
  17 !   27.7   0.0   3.9e-09   1.7e-06       3      33 ..     571     601 ..     570     602 .. 0.95
  18 !   28.1   0.0   2.8e-09   1.2e-06       3      31 ..     605     633 ..     603     635 .. 0.95
  19 !   28.4   0.1   2.4e-09     1e-06       5      32 ..     635     662 ..     634     663 .. 0.95
  20 !   28.6   0.1     2e-09   8.6e-07       1      33 [.     665     697 ..     665     698 .. 0.96
  21 !   23.3   0.0   9.6e-08   4.2e-05       5      34 .]     703     732 ..     699     732 .. 0.93
  22 !   12.6   0.2   0.00027      0.12       3      30 ..     735     762 ..     733     766 .. 0.87
  23 !   21.6   0.0   3.4e-07   0.00015       3      32 ..     769     798 ..     767     800 .. 0.94
  24 !   16.8   0.0   1.2e-05    0.0053       3      33 ..     803     833 ..     801     834 .. 0.93
  25 !   30.2   0.0     6e-10   2.6e-07       1      33 [.     835     867 ..     835     868 .. 0.96
  26 !   20.2   0.0     1e-06   0.00044       2      32 ..     870     900 ..     869     901 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldPn 33
                                      +   +   y +  y+ Al + +k+l +dP 
  gi|386002707|ref|YP_005921006.1| 28 WLGKAIGFYSNESYDLALLYVNKSLDIDPA 57
                                      6667888899999****************6 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 3.8e-09
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                                      ++a+   G+++  lg+++eAl +f+++le+dP++
  gi|386002707|ref|YP_005921006.1| 59 PDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQD 92
                                      689*****************************86 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.7e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       ++y  G ++y lg y+eA++++++A e +
  gi|386002707|ref|YP_005921006.1|  95 IWYSKGFVLYGLGIYDEAIDCYDRAMEFN 123
                                       7************************9977 PP

  == domain 4  score: 27.6 bits;  conditional E-value: 4.3e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       ++++ ++Gla+y lg+yeeA++ +++A+  dP
  gi|386002707|ref|YP_005921006.1| 127 PDLWRARGLALYSLGRYEEAVRSYDEAIVFDP 158
                                       579*************************9998 PP

  == domain 5  score: 18.4 bits;  conditional E-value: 3.8e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       +++y+ Gla+  lg+ye+A+e ++ A+ +d
  gi|386002707|ref|YP_005921006.1| 162 DLWYQKGLALCGLGRYEKAIESYDFAITID 191
                                       68*********************8666666 PP

  == domain 6  score: 26.6 bits;  conditional E-value: 8.4e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a  ++  +la+y lg+ eeA++++++A+ +dP 
  gi|386002707|ref|YP_005921006.1| 195 AASWHGKALALYSLGRAEEAIDCYDRAIDIDPS 227
                                       5789****************************6 PP

  == domain 7  score: 31.4 bits;  conditional E-value: 2.4e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +++yn G a+y+lg++eeA +++++A+e+dP
  gi|386002707|ref|YP_005921006.1| 230 DVWYNKGIALYALGRHEEAFKCYDAAVEIDP 260
                                       68****************************9 PP

  == domain 8  score: 31.6 bits;  conditional E-value: 2.2e-10
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++n Gla y lg+ eeA++++++A+ +dP 
  gi|386002707|ref|YP_005921006.1| 265 AWFNKGLAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       8*****************************6 PP

  == domain 9  score: 37.6 bits;  conditional E-value: 2.5e-12
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +++n G+a+y+lg+++eA e++++A+e+dP++
  gi|386002707|ref|YP_005921006.1| 298 AVWNNKGNALYALGRFDEAQECYRRAVEIDPEY 330
                                       68*****************************85 PP

  == domain 10  score: 28.4 bits;  conditional E-value: 2.3e-09
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                       +ynlG ++ +lg+ eeAlea+++ +e+dPn
  gi|386002707|ref|YP_005921006.1| 334 WYNLGVVLQRLGRGEEALEAYDRLIEIDPN 363
                                       9****************************9 PP

  == domain 11  score: 39.6 bits;  conditional E-value: 6.1e-13
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ea+yn+Gla+y lg+y+eA+ +++++le+dP+n
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYDRVLEIDPEN 398
                                       8******************************97 PP

  == domain 12  score: 25.3 bits;  conditional E-value: 2.3e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +++y  +la+  lg+yeeAl+++++Ale  P
  gi|386002707|ref|YP_005921006.1| 400 DVWYDKALALGSLGRYEEALDCYDEALEAGP 430
                                       68*************************9876 PP

  == domain 13  score: 11.9 bits;  conditional E-value: 0.00043
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +e+l+n+ +++y l +y+e + ++  ++ +dP+
  gi|386002707|ref|YP_005921006.1| 433 PEVLNNRCNILYSLERYNESVGCYGDVIGIDPG 465
                                       689*********************999999886 PP

  == domain 14  score: 26.1 bits;  conditional E-value: 1.2e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       a+yn+G a+y lg+yeeA + + +A +l+
  gi|386002707|ref|YP_005921006.1| 469 AWYNRGVALYTLGRYEEASASYGEAAALN 497
                                       9**************************98 PP

  == domain 15  score: 18.2 bits;  conditional E-value: 4.3e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +a+  +G+a +++g y++A+ea++ A++l+P++
  gi|386002707|ref|YP_005921006.1| 502 DAWVGMGDAFAAAGIYDRAVEAYDGAIALYPGD 534
                                       79*****************************86 PP

  == domain 16  score: 26.4 bits;  conditional E-value: 1e-08
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++yn+Gl++y++ ++eeA+e f++++e+dP 
  gi|386002707|ref|YP_005921006.1| 536 AVWYNRGLLLYNASRLEEAVESFDEVIEIDPS 567
                                       79*****************************7 PP

  == domain 17  score: 27.7 bits;  conditional E-value: 3.9e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++   Gla+y+lg+ +eA++++++Ale+ P 
  gi|386002707|ref|YP_005921006.1| 571 VWRLKGLALYALGRSDEAIDCYDEALEISPS 601
                                       6999************************995 PP

  == domain 18  score: 28.1 bits;  conditional E-value: 2.8e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       ++yn+G +++ lg+y eA+e +++++eld
  gi|386002707|ref|YP_005921006.1| 605 LWYNRGVVLFSLGRYGEAIESYDRVIELD 633
                                       7***************************9 PP

  == domain 19  score: 28.4 bits;  conditional E-value: 2.4e-09
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                       y+ G+a+y lg+y+eA+e++ek+le  P
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLEVSP 662
                                       789**********************988 PP

  == domain 20  score: 28.6 bits;  conditional E-value: 2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+a+y+ Gla+  lgdye+ +e++++++e+dP+
  gi|386002707|ref|YP_005921006.1| 665 AKAWYQKGLAHQILGDYERSAECYDRVVEIDPG 697
                                       79******************************7 PP

  == domain 21  score: 23.3 bits;  conditional E-value: 9.6e-08
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldPnn 34 
                                        ++G ++++lgdy+ Al+ ++ Al+ dP++
  gi|386002707|ref|YP_005921006.1| 703 LRRGFVLLRLGDYDGALASYDLALQEDPDD 732
                                       69**************************97 PP

  == domain 22  score: 12.6 bits;  conditional E-value: 0.00027
                             TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                       a   +G+a+++lg++eeA + f++ l+ 
  gi|386002707|ref|YP_005921006.1| 735 AARGRGEALLALGRFEEASATFDRILAN 762
                                       66789******************99975 PP

  == domain 23  score: 21.6 bits;  conditional E-value: 3.4e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       a++ +Gla++ l +y+eA++ +++A++++ 
  gi|386002707|ref|YP_005921006.1| 769 AWHGRGLALAGLLRYDEAIDSYDRAIAINS 798
                                       8**************************996 PP

  == domain 24  score: 16.8 bits;  conditional E-value: 1.2e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       ++  +G +++++g++e+A++ f++A++ld +
  gi|386002707|ref|YP_005921006.1| 803 LWIGRGGVLEEAGRLEDAVASFDRAIALDQE 833
                                       7999************************976 PP

  == domain 25  score: 30.2 bits;  conditional E-value: 6e-10
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +ea+ ++G+a++k+g++e+A++ f++A++ldP 
  gi|386002707|ref|YP_005921006.1| 835 PEAWSMRGRALMKAGRLEDAAASFDRAIALDPS 867
                                       69******************************6 PP

  == domain 26  score: 20.2 bits;  conditional E-value: 1e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea   +G + +++g+ eeA+ ++e+A++ldP
  gi|386002707|ref|YP_005921006.1| 870 EAQRGRGSVFEAQGRAEEAIGCYEAAIALDP 900
                                       678899************************9 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.5    0.0006      0.26       4      42 .]      35      73 ..      35      73 .. 0.85
   2 !   33.4   0.0   5.9e-11   2.6e-08       1      42 []      66     107 ..      66     107 .. 0.97
   3 !   26.5   0.0   8.8e-09   3.8e-06       8      42 .]     107     141 ..     106     141 .. 0.96
   4 !   34.3   0.1   3.1e-11   1.4e-08       1      41 [.     134     174 ..     134     175 .. 0.94
   5 !   26.4   0.2     9e-09   3.9e-06       1      42 []     168     209 ..     168     209 .. 0.96
   6 !   41.5   0.2   1.8e-13   7.9e-11       3      42 .]     204     243 ..     202     243 .. 0.97
   7 !   30.6   0.2   4.6e-10     2e-07       3      42 .]     238     277 ..     238     277 .. 0.98
   8 !   45.5   0.1   9.7e-15   4.2e-12       1      42 []     270     311 ..     270     311 .. 0.98
   9 !   48.0   0.1   1.6e-15   7.2e-13       1      42 []     304     345 ..     304     345 .. 0.99
  10 !   34.1   0.3   3.7e-11   1.6e-08       7      42 .]     344     379 ..     343     379 .. 0.95
  11 !   32.3   0.1   1.3e-10   5.6e-08       1      42 []     372     413 ..     372     413 .. 0.96
  12 !   19.8   0.4   1.1e-06   0.00046       6      39 ..     411     444 ..     406     444 .. 0.90
  13 !   28.2   0.1   2.5e-09   1.1e-06       2      42 .]     441     481 ..     440     481 .. 0.98
  14 !   22.3   0.5   1.7e-07   7.5e-05       3      42 .]     476     515 ..     476     515 .. 0.94
  15 !   26.6   1.8   8.3e-09   3.6e-06       1      40 [.     508     547 ..     508     549 .. 0.97
  16 !   21.6   0.1   2.9e-07   0.00013       9      42 .]     550     583 ..     546     583 .. 0.96
  17 !   40.2   0.0   4.4e-13   1.9e-10       1      42 []     576     617 ..     576     617 .. 0.98
  18 !   18.5   0.0   2.7e-06    0.0012       3      24 ..     612     633 ..     610     634 .. 0.93
  19 !   36.8   0.3   5.2e-12   2.3e-09       1      39 [.     638     676 ..     638     679 .. 0.95
  20 !   18.5   0.0   2.7e-06    0.0012       7      42 .]     678     713 ..     677     713 .. 0.97
  21 !   21.1   0.3   4.2e-07   0.00018       4      42 .]     709     747 ..     706     747 .. 0.94
  22 ?    4.2   0.0     0.078        34       1      37 [.     740     776 ..     740     780 .. 0.74
  23 !   16.0   0.1   1.6e-05     0.007       9      40 ..     782     813 ..     782     815 .. 0.86
  24 !   26.7   0.0   7.7e-09   3.4e-06       6      42 .]     813     849 ..     808     849 .. 0.94
  25 !   27.6   0.0   3.9e-09   1.7e-06       1      42 []     842     883 ..     842     883 .. 0.98
  26 !   18.1   0.1   3.7e-06    0.0016       1      28 [.     876     903 ..     876     904 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                      +y+   y+ A+   +k l++dP +++a++  G+++  +G
  gi|386002707|ref|YP_005921006.1| 35 FYSNESYDLALLYVNKSLDIDPAYPDAWSLKGYILSDLG 73
                                      57777777787777999***************9988776 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 5.9e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+++ ++G+++eA+ ++++ l++dP+++ ++y  G+++y +G
  gi|386002707|ref|YP_005921006.1|  66 GYILSDLGRLDEALSCFNRSLEIDPQDPHIWYSKGFVLYGLG 107
                                       88999**********************************998 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 8.8e-09
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G y+eAi +Y +A +++++ ++++ ++Gla+y +G
  gi|386002707|ref|YP_005921006.1| 107 GIYDEAIDCYDRAMEFNSTGPDLWRARGLALYSLG 141
                                       66******************************998 PP

  == domain 4  score: 34.3 bits;  conditional E-value: 3.1e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       G a+y++G+yeeA+ +Y +A+ +dP + +++y  Gla+  +
  gi|386002707|ref|YP_005921006.1| 134 GLALYSLGRYEEAVRSYDEAIVFDPAQGDLWYQKGLALCGL 174
                                       899*********************************98665 PP

  == domain 5  score: 26.4 bits;  conditional E-value: 9e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a++ +G+ye+Aie+Y  A+ +d d+a  +++ +la+y +G
  gi|386002707|ref|YP_005921006.1| 168 GLALCGLGRYEKAIESYDFAITIDGDDAASWHGKALALYSLG 209
                                       7789999********************************998 PP

  == domain 6  score: 41.5 bits;  conditional E-value: 1.8e-13
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+y++G+ eeAi +Y +A+++dP+  +++yn G a+y++G
  gi|386002707|ref|YP_005921006.1| 204 ALYSLGRAEEAIDCYDRAIDIDPSLTDVWYNKGIALYALG 243
                                       89************************************98 PP

  == domain 7  score: 30.6 bits;  conditional E-value: 4.6e-10
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+y++G+ eeA ++Y +A+++dP +  a++n Gla+y +G
  gi|386002707|ref|YP_005921006.1| 238 ALYALGRHEEAFKCYDAAVEIDPLYHPAWFNKGLAFYSLG 277
                                       69***********************************998 PP

  == domain 8  score: 45.5 bits;  conditional E-value: 9.7e-15
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+y++G+ eeAi +Y +A+++dP+ + +++n G+a+y++G
  gi|386002707|ref|YP_005921006.1| 270 GLAFYSLGRVEEAIDCYDRAIDIDPSLVAVWNNKGNALYALG 311
                                       89**************************************98 PP

  == domain 9  score: 48.0 bits;  conditional E-value: 1.6e-15
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+y++G+++eA e+Y++A+++dP++ + +ynLG++++++G
  gi|386002707|ref|YP_005921006.1| 304 GNALYALGRFDEAQECYRRAVEIDPEYSNPWYNLGVVLQRLG 345
                                       9***************************************98 PP

  == domain 10  score: 34.1 bits;  conditional E-value: 3.7e-11
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+ eeA+eaY + +++dP+  ea+yn+Gla+y +G
  gi|386002707|ref|YP_005921006.1| 344 LGRGEEALEAYDRLIEIDPNLSEAWYNRGLALYSLG 379
                                       6888*****************************998 PP

  == domain 11  score: 32.3 bits;  conditional E-value: 1.3e-10
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+y++G+y+eA  +Y + l++dP+n +++y  +la+  +G
  gi|386002707|ref|YP_005921006.1| 372 GLALYSLGRYDEAAGCYDRVLEIDPENGDVWYDKALALGSLG 413
                                       899**********************************98887 PP

  == domain 12  score: 19.8 bits;  conditional E-value: 1.1e-06
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       ++G+yeeA+ +Y +Al+  P  +e+++n+ +++y
  gi|386002707|ref|YP_005921006.1| 411 SLGRYEEALDCYDEALEAGPRRPEVLNNRCNILY 444
                                       79*************************9977765 PP

  == domain 13  score: 28.2 bits;  conditional E-value: 2.5e-09
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +++y++ +y+e++ +Y   + +dP + +a+yn+G+a+y +G
  gi|386002707|ref|YP_005921006.1| 441 NILYSLERYNESVGCYGDVIGIDPGYENAWYNRGVALYTLG 481
                                       89************************************998 PP

  == domain 14  score: 22.3 bits;  conditional E-value: 1.7e-07
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       a+y +G+yeeA ++Y +A +l+ + ++a+ ++G+a+++ G
  gi|386002707|ref|YP_005921006.1| 476 ALYTLGRYEEASASYGEAAALNGSRVDAWVGMGDAFAAAG 515
                                       6899*******************************98766 PP

  == domain 15  score: 26.6 bits;  conditional E-value: 8.3e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       Gda+ + G y+ A+eaY  A++l P ++ ++yn+Gl++y+
  gi|386002707|ref|YP_005921006.1| 508 GDAFAAAGIYDRAVEAYDGAIALYPGDPAVWYNRGLLLYN 547
                                       9************************************996 PP

  == domain 16  score: 21.6 bits;  conditional E-value: 2.9e-07
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       ++eeA+e++ + +++dP++  ++   Gla+y++G
  gi|386002707|ref|YP_005921006.1| 550 RLEEAVESFDEVIEIDPSYEGVWRLKGLALYALG 583
                                       89******************************98 PP

  == domain 17  score: 40.2 bits;  conditional E-value: 4.4e-13
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G a+y++G+ +eAi +Y +Al+++P+ ++++yn+G++++ +G
  gi|386002707|ref|YP_005921006.1| 576 GLALYALGRSDEAIDCYDEALEISPSEVSLWYNRGVVLFSLG 617
                                       899************************************998 PP

  == domain 18  score: 18.5 bits;  conditional E-value: 2.7e-06
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkld 24 
                                       +++++G+y eAie+Y + ++ld
  gi|386002707|ref|YP_005921006.1| 612 VLFSLGRYGEAIESYDRVIELD 633
                                       79*******************9 PP

  == domain 19  score: 36.8 bits;  conditional E-value: 5.2e-12
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       G a+y++G+y+eAie+Y+k l+ +P  a a+y  Gla++
  gi|386002707|ref|YP_005921006.1| 638 GEALYSLGRYDEAIECYEKVLEVSPLEAKAWYQKGLAHQ 676
                                       89***********************************98 PP

  == domain 20  score: 18.5 bits;  conditional E-value: 2.7e-06
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +G+ye + e+Y + +++dP + e+ + +G++++++G
  gi|386002707|ref|YP_005921006.1| 678 LGDYERSAECYDRVVEIDPGYEEVILRRGFVLLRLG 713
                                       7********************************998 PP

  == domain 21  score: 21.1 bits;  conditional E-value: 4.2e-07
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +  +G+y++A+++Y  Al+ dPd+ ea  ++G+a++++G
  gi|386002707|ref|YP_005921006.1| 709 LLRLGDYDGALASYDLALQEDPDDLEAARGRGEALLALG 747
                                       6679*******************************9998 PP

  == domain 22  score: 4.2 bits;  conditional E-value: 0.078
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G a+ ++G++eeA + + + l+  +++  a++++Gla
  gi|386002707|ref|YP_005921006.1| 740 GEALLALGRFEEASATFDRILANASEDGGAWHGRGLA 776
                                       8899*********999887666666666666666655 PP

  == domain 23  score: 16.0 bits;  conditional E-value: 1.6e-05
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       +y+eAi +Y +A+++++++  ++ ++G ++ +
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAIAINSSDNLLWIGRGGVLEE 813
                                       7*****************98888888877665 PP

  == domain 24  score: 26.7 bits;  conditional E-value: 7.7e-09
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       e G++e+A++++ +A++ld++++ea++ +G a++k G
  gi|386002707|ref|YP_005921006.1| 813 EAGRLEDAVASFDRAIALDQEDPEAWSMRGRALMKAG 849
                                       67******************************99977 PP

  == domain 25  score: 27.6 bits;  conditional E-value: 3.9e-09
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+a+++ G++e+A +++ +A++ldP++ ea  ++G ++ +qG
  gi|386002707|ref|YP_005921006.1| 842 GRALMKAGRLEDAAASFDRAIALDPSSGEAQRGRGSVFEAQG 883
                                       89**************************************99 PP

  == domain 26  score: 18.1 bits;  conditional E-value: 3.7e-06
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdna 28 
                                       G ++ +qG+ eeAi +Y++A++ldP  +
  gi|386002707|ref|YP_005921006.1| 876 GSVFEAQGRAEEAIGCYEAAIALDPPTP 903
                                       566779*******************766 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.59   2.6e+02      15      33 ..      39      57 ..      35      58 .. 0.88
   2 !   27.5   0.0   4.7e-09   2.1e-06       2      34 .]      60      92 ..      59      92 .. 0.96
   3 !   12.5   0.0    0.0003      0.13       2      31 ..      94     123 ..      93     125 .. 0.93
   4 !   13.7   0.0   0.00013     0.056       6      32 ..     132     158 ..     127     160 .. 0.87
   5 !   18.0   0.0   5.4e-06    0.0024       2      33 ..     162     193 ..     161     194 .. 0.93
   6 !   23.7   0.1     8e-08   3.5e-05       2      33 ..     196     227 ..     195     228 .. 0.95
   7 !   25.4   0.0   2.2e-08   9.6e-06       2      32 ..     230     260 ..     229     260 .. 0.97
   8 !   27.9   0.0   3.4e-09   1.5e-06       2      33 ..     264     295 ..     263     296 .. 0.96
   9 !   31.9   0.0   1.8e-10   7.8e-08       3      33 ..     299     329 ..     297     330 .. 0.95
  10 !   20.8   0.0   6.5e-07   0.00028       4      33 ..     334     363 ..     331     364 .. 0.96
  11 !   26.4   0.1   1.1e-08   4.8e-06       2      34 .]     366     398 ..     365     398 .. 0.96
  12 !   21.2   0.0     5e-07   0.00022       2      30 ..     400     428 ..     399     431 .. 0.94
  13 ?    3.7   0.0       0.2        90       3      32 ..     435     464 ..     433     466 .. 0.87
  14 !   18.4   0.3   3.9e-06    0.0017       3      31 ..     469     497 ..     467     499 .. 0.92
  15 ?    6.5   0.0     0.026        11       2      32 ..     502     532 ..     501     534 .. 0.92
  16 !   21.1   0.0   5.3e-07   0.00023       3      33 ..     537     567 ..     535     568 .. 0.95
  17 !   20.5   0.0   8.3e-07   0.00036       6      33 ..     574     601 ..     570     602 .. 0.92
  18 !   25.5   0.0   2.1e-08   9.3e-06       2      32 ..     604     634 ..     603     635 .. 0.95
  19 !   25.5   0.1   2.1e-08   9.2e-06       5      32 ..     635     662 ..     634     662 .. 0.95
  20 !   28.0   0.0   3.4e-09   1.5e-06       1      32 [.     665     696 ..     665     698 .. 0.96
  21 !   12.1   0.0   0.00043      0.19       4      34 .]     702     732 ..     699     732 .. 0.90
  22 ?    5.7   0.0     0.046        20       8      28 ..     740     760 ..     738     766 .. 0.86
  23 !   11.9   0.0   0.00049      0.21       3      33 ..     769     799 ..     767     800 .. 0.93
  24 !    9.0   0.0    0.0042       1.8       4      33 ..     804     833 ..     803     834 .. 0.87
  25 !   17.8   0.0   6.2e-06    0.0027       2      33 ..     836     867 ..     835     868 .. 0.96
  26 !   12.3   0.0   0.00037      0.16       8      32 ..     876     900 ..     874     902 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.59
                                      T-HHHHHHHHHHHHHHHHH CS
                             TPR_8 15 gdyeeAkeyyekaleldpd 33
                                      + y+ A  y +k l++dp+
  gi|386002707|ref|YP_005921006.1| 39 ESYDLALLYVNKSLDIDPA 57
                                      67999*************7 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 4.7e-09
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                      +a+ ++g+i+++lg+++eA +++++ le+dp++
  gi|386002707|ref|YP_005921006.1| 60 DAWSLKGYILSDLGRLDEALSCFNRSLEIDPQD 92
                                      79*****************************86 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0003
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       +++y +g ++  lg y+eA+ +y +a e +
  gi|386002707|ref|YP_005921006.1|  94 HIWYSKGFVLYGLGIYDEAIDCYDRAMEFN 123
                                       68************************9977 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                         g+++ +lg+yeeA+ +y +a+  dp
  gi|386002707|ref|YP_005921006.1| 132 ARGLALYSLGRYEEAVRSYDEAIVFDP 158
                                       5799******************97776 PP

  == domain 5  score: 18.0 bits;  conditional E-value: 5.4e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++y++g+++  lg+ye+A+e+y  a+++d d
  gi|386002707|ref|YP_005921006.1| 162 DLWYQKGLALCGLGRYEKAIESYDFAITIDGD 193
                                       68***********************9999976 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 8e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +++ +++++ +lg+ eeA+ +y +a+++dp+
  gi|386002707|ref|YP_005921006.1| 196 ASWHGKALALYSLGRAEEAIDCYDRAIDIDPS 227
                                       68****************************96 PP

  == domain 7  score: 25.4 bits;  conditional E-value: 2.2e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +++yn+g ++  lg++eeA ++y  a+e+dp
  gi|386002707|ref|YP_005921006.1| 230 DVWYNKGIALYALGRHEEAFKCYDAAVEIDP 260
                                       69****************************9 PP

  == domain 8  score: 27.9 bits;  conditional E-value: 3.4e-09
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++n+g++  +lg+ eeA+ +y +a+++dp+
  gi|386002707|ref|YP_005921006.1| 264 PAWFNKGLAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       79****************************96 PP

  == domain 9  score: 31.9 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +++n+g+++  lg+++eA+e+y++a+e+dp+
  gi|386002707|ref|YP_005921006.1| 299 VWNNKGNALYALGRFDEAQECYRRAVEIDPE 329
                                       8*****************************8 PP

  == domain 10  score: 20.8 bits;  conditional E-value: 6.5e-07
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +ynlg +++ lg+ eeA e+y + +e+dp+
  gi|386002707|ref|YP_005921006.1| 334 WYNLGVVLQRLGRGEEALEAYDRLIEIDPN 363
                                       9****************************8 PP

  == domain 11  score: 26.4 bits;  conditional E-value: 1.1e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ea+yn g+++ +lg+y+eA  +y ++le+dp+n
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYDRVLEIDPEN 398
                                       8******************************86 PP

  == domain 12  score: 21.2 bits;  conditional E-value: 5e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                       +++y +++++ +lg+yeeA  +y +ale+
  gi|386002707|ref|YP_005921006.1| 400 DVWYDKALALGSLGRYEEALDCYDEALEA 428
                                       68*************************95 PP

  == domain 13  score: 3.7 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +++n  +i+ +l++y+e++ +y  ++ +dp
  gi|386002707|ref|YP_005921006.1| 435 VLNNRCNILYSLERYNESVGCYGDVIGIDP 464
                                       5666668999*******************9 PP

  == domain 14  score: 18.4 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+yn g ++ +lg+yeeA ++y +a  l+
  gi|386002707|ref|YP_005921006.1| 469 AWYNRGVALYTLGRYEEASASYGEAAALN 497
                                       9*********************9998776 PP

  == domain 15  score: 6.5 bits;  conditional E-value: 0.026
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +a++ +g++    g y+ A+e+y  a+ l p
  gi|386002707|ref|YP_005921006.1| 502 DAWVGMGDAFAAAGIYDRAVEAYDGAIALYP 532
                                       79999**********************9998 PP

  == domain 16  score: 21.1 bits;  conditional E-value: 5.3e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++yn g+++ +  ++eeA+e++ +++e+dp+
  gi|386002707|ref|YP_005921006.1| 537 VWYNRGLLLYNASRLEEAVESFDEVIEIDPS 567
                                       8*****************************7 PP

  == domain 17  score: 20.5 bits;  conditional E-value: 8.3e-07
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++g+++  lg+ +eA+ +y +ale++p+
  gi|386002707|ref|YP_005921006.1| 574 LKGLALYALGRSDEAIDCYDEALEISPS 601
                                       799***********************96 PP

  == domain 18  score: 25.5 bits;  conditional E-value: 2.1e-08
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +++yn g ++++lg+y eA+e+y +++eld+
  gi|386002707|ref|YP_005921006.1| 604 SLWYNRGVVLFSLGRYGEAIESYDRVIELDR 634
                                       68***************************96 PP

  == domain 19  score: 25.5 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                       y +g ++ +lg+y+eA+e+yek+le +p
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLEVSP 662
                                       789**********************998 PP

  == domain 20  score: 28.0 bits;  conditional E-value: 3.4e-09
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       a+a+y++g++++ lgdye + e+y +++e+dp
  gi|386002707|ref|YP_005921006.1| 665 AKAWYQKGLAHQILGDYERSAECYDRVVEIDP 696
                                       79*****************************9 PP

  == domain 21  score: 12.1 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        ++ g ++l lgdy+ A ++y  al+ dpd+
  gi|386002707|ref|YP_005921006.1| 702 ILRRGFVLLRLGDYDGALASYDLALQEDPDD 732
                                       5688999**********************96 PP

  == domain 22  score: 5.7 bits;  conditional E-value: 0.046
                                       HHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekal 28 
                                       g ++l lg++eeA +++ + l
  gi|386002707|ref|YP_005921006.1| 740 GEALLALGRFEEASATFDRIL 760
                                       8899***********998766 PP

  == domain 23  score: 11.9 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++  g+++  l +y+eA+ +y +a+ ++ +
  gi|386002707|ref|YP_005921006.1| 769 AWHGRGLALAGLLRYDEAIDSYDRAIAINSS 799
                                       8999***********************9975 PP

  == domain 24  score: 9.0 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +   g ++++ g++e A++++ +a+ ld++
  gi|386002707|ref|YP_005921006.1| 804 WIGRGGVLEEAGRLEDAVASFDRAIALDQE 833
                                       56677889999****************987 PP

  == domain 25  score: 17.8 bits;  conditional E-value: 6.2e-06
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ea+ + g++++k g++e A +++ +a+ ldp+
  gi|386002707|ref|YP_005921006.1| 836 EAWSMRGRALMKAGRLEDAAASFDRAIALDPS 867
                                       89****************************96 PP

  == domain 26  score: 12.3 bits;  conditional E-value: 0.00037
                                       HHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldp 32 
                                       gs+ + +g+ eeA+ +ye a+ ldp
  gi|386002707|ref|YP_005921006.1| 876 GSVFEAQGRAEEAIGCYEAAIALDP 900
                                       89999*******************9 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   9.4e-08   4.1e-05       4      68 .]      32      93 ..      29      93 .. 0.93
   2 !   28.8   0.0   3.4e-09   1.5e-06       3      60 ..      65     119 ..      63     127 .. 0.92
   3 !   23.2   0.4   1.8e-07     8e-05       7      66 ..     103     159 ..      97     162 .. 0.89
   4 !   29.9   0.1   1.5e-09   6.7e-07       1      66 [.     165     227 ..     165     229 .. 0.95
   5 !   39.7   0.0   1.3e-12   5.5e-10       1      66 [.     233     295 ..     233     296 .. 0.97
   6 !   40.8   0.2     6e-13   2.6e-10       2      66 ..     302     363 ..     301     365 .. 0.97
   7 !   43.0   0.4   1.2e-13   5.3e-11       1      66 [.     335     397 ..     335     398 .. 0.96
   8 !   42.0   1.9   2.5e-13   1.1e-10       1      68 []     369     433 ..     369     433 .. 0.97
   9 !   23.2   0.1   1.9e-07   8.3e-05       1      53 [.     403     452 ..     403     467 .. 0.90
  10 !   19.2   0.2   3.2e-06    0.0014       5      60 ..     441     494 ..     437     504 .. 0.89
  11 !   34.8   7.0   4.4e-11   1.9e-08       1      68 []     471     535 ..     471     535 .. 0.97
  12 !   40.3   1.3   8.4e-13   3.7e-10       3      67 ..     507     568 ..     505     569 .. 0.95
  13 !   39.3   0.0   1.8e-12   7.7e-10       3      64 ..     575     633 ..     573     637 .. 0.93
  14 !   37.2   0.0   7.5e-12   3.3e-09       1      67 [.     635     698 ..     635     699 .. 0.97
  15 !   29.5   6.6   1.9e-09   8.5e-07       7      66 ..     709     765 ..     703     767 .. 0.94
  16 !   29.6   1.5   1.9e-09   8.2e-07       3      68 .]     773     835 ..     771     837 .. 0.93
  17 !   46.2   1.4   1.2e-14   5.1e-12       2      66 ..     840     901 ..     839     903 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.4e-08
                            TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68
                                      a  ++ +  yd A+ + +  l+ d   P+ ++A+ l+g ++  +grl+eA+  +++ l+ +p++p
  gi|386002707|ref|YP_005921006.1| 32 AIGFYSNESYDLALLYVNKSLDID---PAYPDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQDP 93
                                      556788899*****999*******...************************************98 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 3.4e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       +++++ ++g+ d+A+  +++ l+ d   P++++ ++ +g +++ +g ++eA++ y++a
  gi|386002707|ref|YP_005921006.1|  65 KGYILSDLGRLDEALSCFNRSLEID---PQDPHIWYSKGFVLYGLGIYDEAIDCYDRA 119
                                       5788999******************...************************999997 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.8e-07
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ +g yd+A+  +++a + ++  Pd    + ++g+a++ +gr++eA+  y++a+  +p 
  gi|386002707|ref|YP_005921006.1| 103 LYGLGIYDEAIDCYDRAMEFNSTGPD---LWRARGLALYSLGRYEEAVRSYDEAIVFDPA 159
                                       677888***************77777...*******************999999977774 PP

  == domain 4  score: 29.9 bits;  conditional E-value: 1.5e-09
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++++a+  +g+y++A++ ++ a+  d    d+a+++ ++++a++ +gr +eA++ y++a++ +p+
  gi|386002707|ref|YP_005921006.1| 165 YQKGLALCGLGRYEKAIESYDFAITID---GDDAASWHGKALALYSLGRAEEAIDCYDRAIDIDPS 227
                                       678899999******************...99******************************9995 PP

  == domain 5  score: 39.7 bits;  conditional E-value: 1.3e-12
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++++ a++++g+ ++A + ++aa++ d   P+ + A++++g+a++ +gr++eA++ y++a++ +p+
  gi|386002707|ref|YP_005921006.1| 233 YNKGIALYALGRHEEAFKCYDAAVEID---PLYHPAWFNKGLAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       7899***********************...********************************9995 PP

  == domain 6  score: 40.8 bits;  conditional E-value: 6e-13
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++++a++++g++d+A++ +++a++ d   P+    +++lg+++ r+gr +eA+++y+++++ +p+
  gi|386002707|ref|YP_005921006.1| 302 NKGNALYALGRFDEAQECYRRAVEID---PEYSNPWYNLGVVLQRLGRGEEALEAYDRLIEIDPN 363
                                       579***********************...********************************9997 PP

  == domain 7  score: 43.0 bits;  conditional E-value: 1.2e-13
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++l+  + r+g+ ++A++a++++++ d   P   eA++++g+a++ +gr++eAa  y++ l+ +p 
  gi|386002707|ref|YP_005921006.1| 335 YNLGVVLQRLGRGEEALEAYDRLIEID---PNLSEAWYNRGLALYSLGRYDEAAGCYDRVLEIDPE 397
                                       789999*********************...*******************************99996 PP

  == domain 8  score: 42.0 bits;  conditional E-value: 2.5e-13
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++++a++ +g+yd+Aa  ++++l+ d   P++ + ++ +++a+  +gr++eA++ y++al+a+p  p
  gi|386002707|ref|YP_005921006.1| 369 YNRGLALYSLGRYDEAAGCYDRVLEID---PENGDVWYDKALALGSLGRYEEALDCYDEALEAGPRRP 433
                                       789************************...**********************************9765 PP

  == domain 9  score: 23.2 bits;  conditional E-value: 1.9e-07
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                                       +++a+a+  +g+y++A+  +++al+++   P+++e l+++ ++++ + r+ e 
  gi|386002707|ref|YP_005921006.1| 403 YDKALALGSLGRYEEALDCYDEALEAG---PRRPEVLNNRCNILYSLERYNES 452
                                       799************************...***************99999765 PP

  == domain 10  score: 19.2 bits;  conditional E-value: 3.2e-06
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraa 60 
                                       ++++ + +y + +  +  ++  d   P    A++++g+a++ +gr++eA   + +aa
  gi|386002707|ref|YP_005921006.1| 441 NILYSLERYNESVGCYGDVIGID---PGYENAWYNRGVALYTLGRYEEASaSYGEAA 494
                                       5789999****************...***********************86666665 PP

  == domain 11  score: 34.8 bits;  conditional E-value: 4.4e-11
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++++ a++ +g+y++A a + +a +++     +++A+ + gda++++g +++A+++y+ a++ +p++p
  gi|386002707|ref|YP_005921006.1| 471 YNRGVALYTLGRYEEASASYGEAAALN---GSRVDAWVGMGDAFAAAGIYDRAVEAYDGAIALYPGDP 535
                                       78899**********************...99**********************************98 PP

  == domain 12  score: 40.3 bits;  conditional E-value: 8.4e-13
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +++a+++ag yd+A++a++ a++++   P +++ ++++g++++ ++rl+eA++ +++ ++ +p++
  gi|386002707|ref|YP_005921006.1| 507 MGDAFAAAGIYDRAVEAYDGAIALY---PGDPAVWYNRGLLLYNASRLEEAVESFDEVIEIDPSY 568
                                       6999*********************...88888***************************99976 PP

  == domain 13  score: 39.3 bits;  conditional E-value: 1.8e-12
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       +++a++++g+ d+A+  +++al+     P  +  ++++g++++ +gr+ eA++ y++ ++ +
  gi|386002707|ref|YP_005921006.1| 575 KGLALYALGRSDEAIDCYDEALEIS---PSEVSLWYNRGVVLFSLGRYGEAIESYDRVIELD 633
                                       699**********************...***************************9988665 PP

  == domain 14  score: 37.2 bits;  conditional E-value: 7.5e-12
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++++ a++ +g+yd+A++ +e +l+     P+ a A++ +g+a+  +g++++ a+ y++ ++ +p++
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLEVS---PLEAKAWYQKGLAHQILGDYERSAECYDRVVEIDPGY 698
                                       67899**********************...***********************************96 PP

  == domain 15  score: 29.5 bits;  conditional E-value: 1.9e-09
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +lr+gdyd A+a ++ al  d   Pd+ eA+ ++g+a+l++gr++eA a +++ l++a+ 
  gi|386002707|ref|YP_005921006.1| 709 LLRLGDYDGALASYDLALQED---PDDLEAARGRGEALLALGRFEEASATFDRILANASE 765
                                       89*******************...******************************999875 PP

  == domain 16  score: 29.6 bits;  conditional E-value: 1.9e-09
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       +++a++ + +yd+A+  +++a++ +   + +   + ++g ++ ++grl++A+a +++a++ +  +p
  gi|386002707|ref|YP_005921006.1| 773 RGLALAGLLRYDEAIDSYDRAIAIN---SSDNLLWIGRGGVLEEAGRLEDAVASFDRAIALDQEDP 835
                                       6899999******************...99999*************************98877665 PP

  == domain 17  score: 46.2 bits;  conditional E-value: 1.2e-14
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++ra+++ag+ +dAaa +++a+++d   P   eA+ ++g ++ +qgr +eA+  y+aa++ +p 
  gi|386002707|ref|YP_005921006.1| 840 MRGRALMKAGRLEDAAASFDRAIALD---PSSGEAQRGRGSVFEAQGRAEEAIGCYEAAIALDPP 901
                                       78************************...99999**************************99997 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.9e-06    0.0034       4      33 ..      50      79 ..      47      80 .. 0.95
   2 !   16.0   0.0   2.6e-05     0.011       1      33 [.      81     113 ..      81     114 .. 0.95
   3 !   16.1   0.0   2.4e-05      0.01       1      33 [.     115     147 ..     115     148 .. 0.97
   4 !   15.1   0.0   5.1e-05     0.022       2      34 .]     150     182 ..     149     182 .. 0.96
   5 !   10.2   0.0    0.0018      0.79       5      33 ..     187     215 ..     184     216 .. 0.94
   6 !   24.6   0.0   4.8e-08   2.1e-05       1      32 [.     217     248 ..     217     250 .. 0.96
   7 !   19.3   0.0   2.3e-06     0.001       1      33 [.     251     283 ..     251     284 .. 0.96
   8 !   27.8   0.0   4.3e-09   1.9e-06       1      34 []     285     318 ..     285     318 .. 0.98
   9 !   26.2   0.0   1.4e-08   6.3e-06       1      33 [.     319     351 ..     319     352 .. 0.94
  10 !   29.6   0.2   1.2e-09   5.2e-07       1      32 [.     353     384 ..     353     385 .. 0.97
  11 !   26.0   0.0   1.7e-08   7.4e-06       1      33 [.     387     419 ..     387     420 .. 0.97
  12 ?    4.1   0.1      0.16        72       1      30 [.     421     450 ..     421     453 .. 0.89
  13 !   15.1   0.0   5.2e-05     0.023       1      32 [.     455     486 ..     455     488 .. 0.91
  14 ?    2.1   0.0      0.73   3.2e+02       2      34 .]     490     522 ..     489     522 .. 0.89
  15 !   18.3   0.1   4.7e-06     0.002       2      34 .]     524     556 ..     523     556 .. 0.93
  16 !   12.9   0.0   0.00025      0.11       2      33 ..     558     589 ..     557     590 .. 0.95
  17 !   21.8   0.0   3.7e-07   0.00016       1      34 []     591     624 ..     591     624 .. 0.97
  18 ?    4.0   0.0      0.18        77      17      34 .]     635     652 ..     634     652 .. 0.92
  19 !   17.6   0.0   7.9e-06    0.0035       1      31 [.     653     683 ..     653     686 .. 0.96
  20 !   13.7   0.0   0.00014     0.063       1      33 [.     687     719 ..     687     720 .. 0.96
  21 !    8.5   0.0    0.0067       2.9       2      32 ..     722     752 ..     721     754 .. 0.93
  22 ?   -0.2   0.0       3.9   1.7e+03       2      33 ..     756     787 ..     755     788 .. 0.83
  23 ?    2.3   0.0      0.62   2.7e+02       2      33 ..     790     821 ..     789     822 .. 0.94
  24 !   15.7   0.0   3.2e-05     0.014       2      32 ..     824     854 ..     823     856 .. 0.95
  25 !    8.3   0.0    0.0076       3.3       2      33 ..     858     889 ..     857     890 .. 0.95
  26 ?   -0.3   0.1       4.1   1.8e+03       1      10 [.     891     900 ..     891     901 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.9e-06
                            TPR_17  4 kaleldPnnadaynnLAelllknGdlmtAr 33
                                      k+l++dP ++da+ +++++l+ +G+l++A+
  gi|386002707|ref|YP_005921006.1| 50 KSLDIDPAYPDAWSLKGYILSDLGRLDEAL 79
                                      99**************************96 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.6e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ++ ++le+dP ++  ++ ++ +l+ +G +++A+
  gi|386002707|ref|YP_005921006.1|  81 CFNRSLEIDPQDPHIWYSKGFVLYGLGIYDEAI 113
                                       799************************999997 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.4e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a+e + + +d++  ++ +l+++G++++A+
  gi|386002707|ref|YP_005921006.1| 115 CYDRAMEFNSTGPDLWRARGLALYSLGRYEEAV 147
                                       8******************************96 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 5.1e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +a+  dP   d++++++ +l+ +G++++A++
  gi|386002707|ref|YP_005921006.1| 150 YDEAIVFDPAQGDLWYQKGLALCGLGRYEKAIE 182
                                       99*****************************86 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0018
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                       a+ +d ++a +++ +A +l+++G+ ++A+
  gi|386002707|ref|YP_005921006.1| 187 AITIDGDDAASWHGKALALYSLGRAEEAI 215
                                       78999**********************97 PP

  == domain 6  score: 24.6 bits;  conditional E-value: 4.8e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y +a+++dP+  d+++n++ +l+ +G++++A
  gi|386002707|ref|YP_005921006.1| 217 CYDRAIDIDPSLTDVWYNKGIALYALGRHEEA 248
                                       8****************************999 PP

  == domain 7  score: 19.3 bits;  conditional E-value: 2.3e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y  a+e+dP + +a++n++ +++++G+ ++A+
  gi|386002707|ref|YP_005921006.1| 251 CYDAAVEIDPLYHPAWFNKGLAFYSLGRVEEAI 283
                                       8*****************************997 PP

  == domain 8  score: 27.8 bits;  conditional E-value: 4.3e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +a+++dP+ + ++nn++++l+ +G++++A++
  gi|386002707|ref|YP_005921006.1| 285 CYDRAIDIDPSLVAVWNNKGNALYALGRFDEAQE 318
                                       8*******************************96 PP

  == domain 9  score: 26.2 bits;  conditional E-value: 1.4e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y++a+e+dP ++++++nL+++l ++G+ ++A+
  gi|386002707|ref|YP_005921006.1| 319 CYRRAVEIDPEYSNPWYNLGVVLQRLGRGEEAL 351
                                       8**************************988886 PP

  == domain 10  score: 29.6 bits;  conditional E-value: 1.2e-09
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y + +e+dPn ++a++n++ +l+++G++++A
  gi|386002707|ref|YP_005921006.1| 353 AYDRLIEIDPNLSEAWYNRGLALYSLGRYDEA 384
                                       59****************************98 PP

  == domain 11  score: 26.0 bits;  conditional E-value: 1.7e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y ++le+dP n d+++ +A +l ++G++++A+
  gi|386002707|ref|YP_005921006.1| 387 CYDRVLEIDPENGDVWYDKALALGSLGRYEEAL 419
                                       8******************************96 PP

  == domain 12  score: 4.1 bits;  conditional E-value: 0.16
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                       +y +ale  P  ++++nn+ ++l+++ ++ 
  gi|386002707|ref|YP_005921006.1| 421 CYDEALEAGPRRPEVLNNRCNILYSLERYN 450
                                       8******************99998887775 PP

  == domain 13  score: 15.1 bits;  conditional E-value: 5.2e-05
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       +y  ++ +dP + +a++n++++l+ +G++++A
  gi|386002707|ref|YP_005921006.1| 455 CYGDVIGIDPGYENAWYNRGVALYTLGRYEEA 486
                                       57777889**********************98 PP

  == domain 14  score: 2.1 bits;  conditional E-value: 0.73
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y +a++l+ + +da+  ++ +++ +G +++A++
  gi|386002707|ref|YP_005921006.1| 490 YGEAAALNGSRVDAWVGMGDAFAAAGIYDRAVE 522
                                       667888899999*****************9975 PP

  == domain 15  score: 18.3 bits;  conditional E-value: 4.7e-06
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       y  a++l+P ++ +++n++ ll+++ +l++A++
  gi|386002707|ref|YP_005921006.1| 524 YDGAIALYPGDPAVWYNRGLLLYNASRLEEAVE 556
                                       7789**************************975 PP

  == domain 16  score: 12.9 bits;  conditional E-value: 0.00025
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +++e+dP++  ++ +++ +l+ +G++++A+
  gi|386002707|ref|YP_005921006.1| 558 FDEVIEIDPSYEGVWRLKGLALYALGRSDEAI 589
                                       6789**************************97 PP

  == domain 17  score: 21.8 bits;  conditional E-value: 3.7e-07
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y +ale+ P+ + +++n++++l ++G++++A++
  gi|386002707|ref|YP_005921006.1| 591 CYDEALEISPSEVSLWYNRGVVLFSLGRYGEAIE 624
                                       8*******************************86 PP

  == domain 18  score: 4.0 bits;  conditional E-value: 0.18
                            TPR_17  17 nnLAelllknGdlmtArq 34 
                                       ++++e+l+++G++++A++
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIE 652
                                       889*************86 PP

  == domain 19  score: 17.6 bits;  conditional E-value: 7.9e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                       +y+k+le  P  a+a+++++ ++  +Gd+++
  gi|386002707|ref|YP_005921006.1| 653 CYEKVLEVSPLEAKAWYQKGLAHQILGDYER 683
                                       8****************************97 PP

  == domain 20  score: 13.7 bits;  conditional E-value: 0.00014
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +++e+dP + ++   ++ +ll++Gd++ A+
  gi|386002707|ref|YP_005921006.1| 687 CYDRVVEIDPGYEEVILRRGFVLLRLGDYDGAL 719
                                       8*****************************997 PP

  == domain 21  score: 8.5 bits;  conditional E-value: 0.0067
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y  al+ dP++ +a   ++e+ll +G++++A
  gi|386002707|ref|YP_005921006.1| 722 YDLALQEDPDDLEAARGRGEALLALGRFEEA 752
                                       666999*********************9998 PP

  == domain 22  score: -0.2 bits;  conditional E-value: 3.9
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + + l++   +  a++ ++ +l+ + ++++A+
  gi|386002707|ref|YP_005921006.1| 756 FDRILANASEDGGAWHGRGLALAGLLRYDEAI 787
                                       6788899999999********99887777775 PP

  == domain 23  score: 2.3 bits;  conditional E-value: 0.62
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +a++++ ++  ++  ++ +l+++G+l++A+
  gi|386002707|ref|YP_005921006.1| 790 YDRAIAINSSDNLLWIGRGGVLEEAGRLEDAV 821
                                       99**************************9996 PP

  == domain 24  score: 15.7 bits;  conditional E-value: 3.2e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + +a++ld  +++a+ +++++l k+G+l++A
  gi|386002707|ref|YP_005921006.1| 824 FDRAIALDQEDPEAWSMRGRALMKAGRLEDA 854
                                       789*************************998 PP

  == domain 25  score: 8.3 bits;  conditional E-value: 0.0076
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + +a++ldP++ +a   ++ +++ +G+ ++A+
  gi|386002707|ref|YP_005921006.1| 858 FDRAIALDPSSGEAQRGRGSVFEAQGRAEEAI 889
                                       789**************************996 PP

  == domain 26  score: -0.3 bits;  conditional E-value: 4.1
                            TPR_17   1 lylkaleldP 10 
                                       +y+ a++ldP
  gi|386002707|ref|YP_005921006.1| 891 CYEAAIALDP 900
                                       8********9 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.34   1.5e+02       4      42 ..      28      66 ..      26      68 .. 0.86
   2 !   20.3   0.0   1.5e-06   0.00067       1      39 [.      59      97 ..      59     102 .. 0.93
   3 ?    2.6   0.0      0.73   3.2e+02       3      27 ..      95     119 ..      93     125 .. 0.84
   4 !   22.7   0.7   2.6e-07   0.00011       1      42 [.     127     168 ..     127     170 .. 0.94
   5 !    8.9   0.1    0.0066       2.9       3      41 ..     163     201 ..     161     204 .. 0.91
   6 !   17.2   0.1   1.5e-05    0.0065       4      41 ..     198     235 ..     195     238 .. 0.88
   7 !   19.6   0.0   2.5e-06    0.0011       3      41 ..     231     269 ..     229     272 .. 0.91
   8 !   15.2   0.0   6.7e-05     0.029       5      38 ..     267     300 ..     264     304 .. 0.87
   9 !   19.7   0.1   2.4e-06     0.001       8      42 ..     304     338 ..     298     339 .. 0.89
  10 !   19.4   0.1     3e-06    0.0013       4      40 ..     334     370 ..     331     373 .. 0.93
  11 !   25.0   0.2   4.7e-08   2.1e-05       2      42 ..     366     406 ..     365     408 .. 0.93
  12 !   17.3   0.3   1.3e-05    0.0059       3      38 ..     401     436 ..     400     440 .. 0.93
  13 !   14.4   0.3   0.00012     0.051       2      43 ..     468     509 ..     467     510 .. 0.95
  14 !   21.1   0.3   8.3e-07   0.00036       2      41 ..     502     541 ..     501     544 .. 0.93
  15 !   17.6   0.0   1.1e-05    0.0048       1      42 [.     535     576 ..     535     578 .. 0.94
  16 !   20.8   0.0     1e-06   0.00045       4      40 ..     572     608 ..     570     611 .. 0.91
  17 !   11.5   0.0     0.001      0.45       3      31 ..     605     633 ..     603     636 .. 0.92
  18 !   22.3   0.1   3.5e-07   0.00015       5      42 ..     635     672 ..     633     674 .. 0.92
  19 !   16.9   0.0   1.9e-05    0.0083       2      42 ..     666     706 ..     665     708 .. 0.93
  20 !   22.5   0.9   2.9e-07   0.00013       3      40 ..     701     738 ..     699     741 .. 0.90
  21 !   15.0   2.0   7.6e-05     0.033       2      39 ..     734     771 ..     733     778 .. 0.89
  22 !    9.3   0.1    0.0052       2.3       3      39 ..     769     805 ..     768     808 .. 0.86
  23 !   21.9   0.4   4.5e-07    0.0002       4      42 ..     804     842 ..     801     843 .. 0.92
  24 !   27.7   0.6   6.2e-09   2.7e-06       1      40 [.     835     874 ..     835     877 .. 0.94
  25 !   18.1   0.1   7.7e-06    0.0034       2      32 ..     870     900 ..     869     905 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.34
                            TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawllla 42
                                      +l  a  ++ ++ +d A+ + ++ l+ +P+ ++aw l +
  gi|386002707|ref|YP_005921006.1| 28 WLGKAIGFYSNESYDLALLYVNKSLDIDPAYPDAWSLKG 66
                                      6667788899999**********************7665 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.5e-06
                            TPR_14  1 peallalaeallalGdpdeAiallrralalaPddaeawl 39
                                      p+a+ + + +l  lG++deA+ +++r l+ +P+d+ +w+
  gi|386002707|ref|YP_005921006.1| 59 PDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQDPHIWY 97
                                      789********************************9997 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.73
                            TPR_14   3 allalaeallalGdpdeAiallrra 27 
                                        ++  + +l+ lG +deAi++++ra
  gi|386002707|ref|YP_005921006.1|  95 IWYSKGFVLYGLGIYDEAIDCYDRA 119
                                       67778888999999**********9 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 2.6e-07
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       p++++a++ al+ lG+++eA++ +++a+  +P++ ++w++ +
  gi|386002707|ref|YP_005921006.1| 127 PDLWRARGLALYSLGRYEEAVRSYDEAIVFDPAQGDLWYQKG 168
                                       789*******************************99998765 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0066
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       ++++ + al  lG++++Ai+ ++ a+  + dda+ w   
  gi|386002707|ref|YP_005921006.1| 163 LWYQKGLALCGLGRYEKAIESYDFAITIDGDDAASWHGK 201
                                       89******************************9988655 PP

  == domain 6  score: 17.2 bits;  conditional E-value: 1.5e-05
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +   a al+ lG+ +eAi++++ra++ +P+  ++w+  
  gi|386002707|ref|YP_005921006.1| 198 WHGKALALYSLGRAEEAIDCYDRAIDIDPSLTDVWYNK 235
                                       6667899**********************999999865 PP

  == domain 7  score: 19.6 bits;  conditional E-value: 2.5e-06
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +++  + al+alG+++eA +++++a++ +P    aw+  
  gi|386002707|ref|YP_005921006.1| 231 VWYNKGIALYALGRHEEAFKCYDAAVEIDPLYHPAWFNK 269
                                       6888899************************99999865 PP

  == domain 8  score: 15.2 bits;  conditional E-value: 6.7e-05
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeaw 38 
                                          + a++ lG+ +eAi++++ra++ +P+  ++w
  gi|386002707|ref|YP_005921006.1| 267 FNKGLAFYSLGRVEEAIDCYDRAIDIDPSLVAVW 300
                                       55678999*********************99998 PP

  == domain 9  score: 19.7 bits;  conditional E-value: 2.4e-06
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       + al+alG++deA +++rra++ +P+    w+ l+
  gi|386002707|ref|YP_005921006.1| 304 GNALYALGRFDEAQECYRRAVEIDPEYSNPWYNLG 338
                                       789**********************9988887775 PP

  == domain 10  score: 19.4 bits;  conditional E-value: 3e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       ++ l+ +l +lG+ +eA+++++r+++ +P+  eaw+ 
  gi|386002707|ref|YP_005921006.1| 334 WYNLGVVLQRLGRGEEALEAYDRLIEIDPNLSEAWYN 370
                                       8999*******************************86 PP

  == domain 11  score: 25.0 bits;  conditional E-value: 4.7e-08
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ea++ ++ al+ lG++deA+ +++r+l+ +P++ ++w+  a
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYDRVLEIDPENGDVWYDKA 406
                                       89**********************************97665 PP

  == domain 12  score: 17.3 bits;  conditional E-value: 1.3e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       ++++ a al  lG+++eA++++++al+++P  +e++
  gi|386002707|ref|YP_005921006.1| 401 VWYDKALALGSLGRYEEALDCYDEALEAGPRRPEVL 436
                                       799***************************999875 PP

  == domain 13  score: 14.4 bits;  conditional E-value: 0.00012
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +a++ ++ al++lG+++eA a + +a al+ +  +aw  +++
  gi|386002707|ref|YP_005921006.1| 468 NAWYNRGVALYTLGRYEEASASYGEAAALNGSRVDAWVGMGD 509
                                       69***********************************99986 PP

  == domain 14  score: 21.1 bits;  conditional E-value: 8.3e-07
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                       +a+  +++a++a+G +d+A+++++ a+al+P+d+++w+  
  gi|386002707|ref|YP_005921006.1| 502 DAWVGMGDAFAAAGIYDRAVEAYDGAIALYPGDPAVWYNR 541
                                       799**********************************876 PP

  == domain 15  score: 17.6 bits;  conditional E-value: 1.1e-05
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       p++++ ++ +l+++ +++eA++ ++++++ +P+ + +w+l +
  gi|386002707|ref|YP_005921006.1| 535 PAVWYNRGLLLYNASRLEEAVESFDEVIEIDPSYEGVWRLKG 576
                                       689***********************************9875 PP

  == domain 16  score: 20.8 bits;  conditional E-value: 1e-06
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       +++ + al+alG+ deAi+++++al+  P++  +w+ 
  gi|386002707|ref|YP_005921006.1| 572 WRLKGLALYALGRSDEAIDCYDEALEISPSEVSLWYN 608
                                       888899**************************99986 PP

  == domain 17  score: 11.5 bits;  conditional E-value: 0.001
                            TPR_14   3 allalaeallalGdpdeAiallrralala 31 
                                       +++ ++ +l+ lG++ eAi+ ++r+++l+
  gi|386002707|ref|YP_005921006.1| 605 LWYNRGVVLFSLGRYGEAIESYDRVIELD 633
                                       7999*********************9975 PP

  == domain 18  score: 22.3 bits;  conditional E-value: 3.5e-07
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++ +eal+ lG++deAi++++++l+  P +a aw++ +
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLEVSPLEAKAWYQKG 672
                                       7789******************************9865 PP

  == domain 19  score: 16.9 bits;  conditional E-value: 1.9e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +a+++ + a+  lGd+++++++++r+++ +P+ +e+ l+ +
  gi|386002707|ref|YP_005921006.1| 666 KAWYQKGLAHQILGDYERSAECYDRVVEIDPGYEEVILRRG 706
                                       79********************************9988876 PP

  == domain 20  score: 22.5 bits;  conditional E-value: 2.9e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       + l+++ +ll+lGd+d+A+a ++ al+ +Pdd+ea + 
  gi|386002707|ref|YP_005921006.1| 701 VILRRGFVLLRLGDYDGALASYDLALQEDPDDLEAARG 738
                                       5689999**************************99875 PP

  == domain 21  score: 15.0 bits;  conditional E-value: 7.6e-05
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       ea + ++eallalG+++eA a ++r+la a +d  aw 
  gi|386002707|ref|YP_005921006.1| 734 EAARGRGEALLALGRFEEASATFDRILANASEDGGAWH 771
                                       678889***********************999999995 PP

  == domain 22  score: 9.3 bits;  conditional E-value: 0.0052
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       a+  ++ al+ l ++deAi+ ++ra+a + +d  +w+
  gi|386002707|ref|YP_005921006.1| 769 AWHGRGLALAGLLRYDEAIDSYDRAIAINSSDNLLWI 805
                                       67778888888889**************999888886 PP

  == domain 23  score: 21.9 bits;  conditional E-value: 4.5e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       +  ++ +l+++G++++A+a ++ra+al+ +d+eaw + +
  gi|386002707|ref|YP_005921006.1| 804 WIGRGGVLEEAGRLEDAVASFDRAIALDQEDPEAWSMRG 842
                                       777999*****************************8876 PP

  == domain 24  score: 27.7 bits;  conditional E-value: 6.2e-09
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       pea+ ++++al+ +G++++A+a ++ra+al+P++ ea++ 
  gi|386002707|ref|YP_005921006.1| 835 PEAWSMRGRALMKAGRLEDAAASFDRAIALDPSSGEAQRG 874
                                       79********************************999875 PP

  == domain 25  score: 18.1 bits;  conditional E-value: 7.7e-06
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP 32 
                                       ea++ ++++++a+G+ +eAi ++++a+al+P
  gi|386002707|ref|YP_005921006.1| 870 EAQRGRGSVFEAQGRAEEAIGCYEAAIALDP 900
                                       688999***********************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.5e-08   1.1e-05       4      62 ..      38      96 ..      35     100 .. 0.94
   2 !   13.6   0.0   0.00016     0.072       5      50 ..     107     152 ..     103     160 .. 0.90
   3 !   17.0   0.1   1.4e-05    0.0061       5      62 ..     141     199 ..     140     206 .. 0.91
   4 !   20.6   0.0     1e-06   0.00046       5      57 ..     175     227 ..     171     233 .. 0.94
   5 !   21.0   0.0   8.2e-07   0.00036       4      60 ..     208     265 ..     205     269 .. 0.91
   6 !   15.5   0.0   4.2e-05     0.018       1      57 [.     239     295 ..     239     303 .. 0.94
   7 !   19.0   0.0   3.4e-06    0.0015       5      47 ..     277     319 ..     273     322 .. 0.94
   8 !   33.0   0.1   1.5e-10   6.4e-08       1      61 [.     307     367 ..     307     373 .. 0.94
   9 !   32.3   0.1   2.4e-10     1e-07       4      61 ..     378     435 ..     375     439 .. 0.93
  10 !   13.5   0.0   0.00018     0.077      14      48 ..     456     490 ..     443     503 .. 0.82
  11 !   27.7   0.0   6.4e-09   2.8e-06       3      65 ..     513     575 ..     511     577 .. 0.94
  12 !   22.2   0.0   3.4e-07   0.00015       1      56 [.     579     634 ..     579     644 .. 0.93
  13 !   11.0   0.0     0.001      0.46      30      59 ..     636     665 ..     634     673 .. 0.79
  14 !   15.6   0.0   3.8e-05     0.017       5      47 ..     679     721 ..     677     723 .. 0.95
  15 !   41.0   2.9   4.7e-13     2e-10       1      58 [.     709     766 ..     709     780 .. 0.91
  16 !   24.9   0.1   4.9e-08   2.1e-05       6      66 ..     782     842 ..     772     844 .. 0.95
  17 !   23.1   0.1   1.8e-07   7.9e-05       1      59 [.     845     903 ..     845     907 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.5e-08
                            TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      ++ y+ Al +  + l+ dp +++a+ l   +l  lg+ldeA  + ++ +e dp+d+ ++
  gi|386002707|ref|YP_005921006.1| 38 NESYDLALLYVNKSLDIDPAYPDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQDPHIW 96
                                      788999*************************************************9876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00016
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       g y+eA++ + +a++ +   ++++ +   al++lg+++eA +  d+
  gi|386002707|ref|YP_005921006.1| 107 GIYDEAIDCYDRAMEFNSTGPDLWRARGLALYSLGRYEEAVRSYDE 152
                                       559*************************************988776 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.4e-05
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                       g+y+eA++ + +a+  dp +++++++   al  lg++++A++  d +   d dd a ++
  gi|386002707|ref|YP_005921006.1| 141 GRYEEAVRSYDEAIVFDPAQGDLWYQKGLALCGLGRYEKAIESYDFAITIDGDDaASWH 199
                                       89*****************************************9999999999866666 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 1e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       g+y+ A++ +  a++ d ++a+ + + A al++lg+ +eA+++ d++ + dp 
  gi|386002707|ref|YP_005921006.1| 175 GRYEKAIESYDFAITIDGDDAASWHGKALALYSLGRAEEAIDCYDRAIDIDPS 227
                                       99*********************************************999997 PP

  == domain 5  score: 21.0 bits;  conditional E-value: 8.2e-07
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ar 60 
                                        g+ +eA++ + +a++ dp   +++++  +al+alg+ +eA ++ da+ e dp   ++
  gi|386002707|ref|YP_005921006.1| 208 LGRAEEAIDCYDRAIDIDPSLTDVWYNKGIALYALGRHEEAFKCYDAAVEIDPLYhPA 265
                                       5999**********************************************99984355 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 4.2e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       l+a g+++eA + + +a + dp +  a+ +   a ++lg+++eA+++ d++ + dp 
  gi|386002707|ref|YP_005921006.1| 239 LYALGRHEEAFKCYDAAVEIDPLYHPAWFNKGLAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       6788***********************************************999997 PP

  == domain 7  score: 19.0 bits;  conditional E-value: 3.4e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       g+ +eA++ + +a++ dp   +++ +  +al+alg++deA+++
  gi|386002707|ref|YP_005921006.1| 277 GRVEEAIDCYDRAIDIDPSLVAVWNNKGNALYALGRFDEAQEC 319
                                       8999*************************************98 PP

  == domain 8  score: 33.0 bits;  conditional E-value: 1.5e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       l+a g+++eA++ +++a + dp++++ +++L  +l  lg+ +eA ++ d+l e dp+ +++
  gi|386002707|ref|YP_005921006.1| 307 LYALGRFDEAQECYRRAVEIDPEYSNPWYNLGVVLQRLGRGEEALEAYDRLIEIDPNLSEA 367
                                       6788****************************************************96554 PP

  == domain 9  score: 32.3 bits;  conditional E-value: 2.4e-10
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                        g+y+eA+  + ++l+ dp+n++++++ A al +lg+++eA ++ d+++e+ p  +++
  gi|386002707|ref|YP_005921006.1| 378 LGRYDEAAGCYDRVLEIDPENGDVWYDKALALGSLGRYEEALDCYDEALEAGPRRPEV 435
                                       69************************************************99987765 PP

  == domain 10  score: 13.5 bits;  conditional E-value: 0.00018
                            TPR_19  14 leqalqedpknaearllLAeallalgqldeAealL 48 
                                       +  ++  dp++++a+++   al+ lg+++eA a  
  gi|386002707|ref|YP_005921006.1| 456 YGDVIGIDPGYENAWYNRGVALYTLGRYEEASASY 490
                                       5567788************************9875 PP

  == domain 11  score: 27.7 bits;  conditional E-value: 6.4e-09
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       a+g y++A++++  a++ +p++++++++   +l+++ +l+eA +  d++ e dp  + +++L+
  gi|386002707|ref|YP_005921006.1| 513 AAGIYDRAVEAYDGAIALYPGDPAVWYNRGLLLYNASRLEEAVESFDEVIEIDPSYEGVWRLK 575
                                       7888**************************************************988888886 PP

  == domain 12  score: 22.2 bits;  conditional E-value: 3.4e-07
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                       l+a g+ +eA++ + +al+ +p    ++++   +l++lg++ eA++  d++ e d+
  gi|386002707|ref|YP_005921006.1| 579 LYALGRSDEAIDCYDEALEISPSEVSLWYNRGVVLFSLGRYGEAIESYDRVIELDR 634
                                       67889*********************************************999876 PP

  == domain 13  score: 11.0 bits;  conditional E-value: 0.001
                            TPR_19  30 lLAeallalgqldeAealLdalpeedpdda 59 
                                          eal++lg++deA+++ ++++e  p +a
  gi|386002707|ref|YP_005921006.1| 636 EKGEALYSLGRYDEAIECYEKVLEVSPLEA 665
                                       557899999999999999999998888754 PP

  == domain 14  score: 15.6 bits;  conditional E-value: 3.8e-05
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       gdy++ ++ + ++ + dp+++e+ l+   +ll lg++d A a 
  gi|386002707|ref|YP_005921006.1| 679 GDYERSAECYDRVVEIDPGYEEVILRRGFVLLRLGDYDGALAS 721
                                       899*************************************875 PP

  == domain 15  score: 41.0 bits;  conditional E-value: 4.7e-13
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       ll  gdy+ Ala +  alqedp+++ea+ +  eallalg+++eA a+ d++++ +  d
  gi|386002707|ref|YP_005921006.1| 709 LLRLGDYDGALASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRILANASED 766
                                       5778***********************************************9988766 PP

  == domain 16  score: 24.9 bits;  conditional E-value: 4.9e-08
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                                       +y+eA++ + +a++ +  +  ++++   +l ++g+l++A a  d++ + d+ d++++s ++
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAIAINSSDNLLWIGRGGVLEEAGRLEDAVASFDRAIALDQEDPEAWSMRG 842
                                       79******************************************************99865 PP

  == domain 17  score: 23.1 bits;  conditional E-value: 1.8e-07
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                       l+++g++++A+a + +a++ dp ++ea+ +   +  a+g+ +eA+ + +a+ + dp ++
  gi|386002707|ref|YP_005921006.1| 845 LMKAGRLEDAAASFDRAIALDPSSGEAQRGRGSVFEAQGRAEEAIGCYEAAIALDPPTP 903
                                       799***********************************************999999864 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         2   8.8e+02      57      75 ..      37      55 ..      30      57 .. 0.76
   2 !   14.2   0.0     9e-05     0.039       5      32 ..      61      88 ..      58      94 .. 0.82
   3 !   24.2   0.1   7.1e-08   3.1e-05       5      72 ..      95     154 ..      91     154 .. 0.90
   4 !   30.6   0.2   7.1e-10   3.1e-07       5      76 ..     163     226 ..     160     227 .. 0.93
   5 !   30.7   0.1   6.7e-10   2.9e-07       5      76 ..     231     294 ..     228     295 .. 0.90
   6 !   34.4   0.1   4.7e-11   2.1e-08       6      76 ..     266     328 ..     261     329 .. 0.93
   7 !   39.7   0.3   9.9e-13   4.3e-10       4      74 ..     298     360 ..     295     361 .. 0.93
   8 !   39.9   0.3   8.8e-13   3.8e-10       4      76 ..     332     396 ..     329     397 .. 0.93
   9 !   15.3   0.3   4.1e-05     0.018       6      32 ..     402     428 ..     397     433 .. 0.85
  10 !   15.6   1.1   3.3e-05     0.015       5      73 ..     435     495 ..     431     497 .. 0.81
  11 !   17.9   2.5   6.3e-06    0.0027       4      75 ..     468     531 ..     465     533 .. 0.85
  12 !   13.0   0.1   0.00021     0.092       5      76 ..     503     566 ..     499     567 .. 0.83
  13 !   25.7   0.1   2.4e-08     1e-05       5      75 ..     537     599 ..     533     601 .. 0.87
  14 !   17.5   0.0   8.9e-06    0.0039       4      36 ..     604     636 ..     601     639 .. 0.86
  15 !   29.3   0.6   1.8e-09   7.7e-07       8      75 ..     636     695 ..     634     697 .. 0.93
  16 !   24.6   1.7   5.4e-08   2.3e-05       5      75 ..     702     763 ..     698     765 .. 0.89
  17 !   19.7   2.9   1.8e-06   0.00079       5      74 ..     735     796 ..     731     799 .. 0.83
  18 !   18.4   0.7   4.6e-06     0.002       5      75 ..     769     831 ..     765     832 .. 0.90
  19 !   20.8   0.2   8.2e-07   0.00036       6      76 ..     804     866 ..     799     867 .. 0.90
  20 !   11.1   0.1   0.00086      0.38       5      32 ..     871     898 ..     867     899 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2
                            TPR_12 57 algryeeAlelleealaia 75
                                        + y+ Al + +++l+i+
  gi|386002707|ref|YP_005921006.1| 37 SNESYDLALLYVNKSLDID 55
                                      5567889999999999886 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9e-05
                            TPR_12  5 alnnlaavlrrlgrydeAlellekalei 32
                                      a++  + +l  lgr+deAl++++++lei
  gi|386002707|ref|YP_005921006.1| 61 AWSLKGYILSDLGRLDEALSCFNRSLEI 88
                                      5667888899999999999999999988 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 7.1e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       +++  + vl+ lg ydeA++++++a+e    + Gpd        r+ g +++ lgryeeA++ + ea+
  gi|386002707|ref|YP_005921006.1|  95 IWYSKGFVLYGLGIYDEAIDCYDRAMEFN--STGPDL------WRARGLALYSLGRYEEAVRSYDEAI 154
                                       67789************************..457774......8999*****************9995 PP

  == domain 4  score: 30.6 bits;  conditional E-value: 7.1e-10
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++++ +++l+ lgry++A+e ++ a+ i      +d    a++ ++ + +++ lgr eeA++ + +a++i++
  gi|386002707|ref|YP_005921006.1| 163 LWYQKGLALCGLGRYEKAIESYDFAITID-----GDD---AASWHGKALALYSLGRAEEAIDCYDRAIDIDP 226
                                       57799********************9999.....775...99***************************976 PP

  == domain 5  score: 30.7 bits;  conditional E-value: 6.7e-10
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +++n + +l++lgr++eA++++++a+ei       +hp    + +n g +++ lgr eeA++ + +a++i++
  gi|386002707|ref|YP_005921006.1| 231 VWYNKGIALYALGRHEEAFKCYDAAVEID-P---LYHP----AWFNKGLAFYSLGRVEEAIDCYDRAIDIDP 294
                                       678**************************.3...3564....59************************9975 PP

  == domain 6  score: 34.4 bits;  conditional E-value: 4.7e-11
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       + n +++ + lgr +eA++++++a++i      p +  ++++ +n g +++algr++eA+e +++a++i++
  gi|386002707|ref|YP_005921006.1| 266 WFNKGLAFYSLGRVEEAIDCYDRAIDID-----P-S--LVAVWNNKGNALYALGRFDEAQECYRRAVEIDP 328
                                       558999******************9999.....7.4..9*****************************986 PP

  == domain 7  score: 39.7 bits;  conditional E-value: 9.9e-13
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +++nn +++l++lgr+deA+e++++a+ei      p+   +++  +nLg ++++lgr eeAle++ + ++i
  gi|386002707|ref|YP_005921006.1| 298 AVWNNKGNALYALGRFDEAQECYRRAVEID-----PE---YSNPWYNLGVVLQRLGRGEEALEAYDRLIEI 360
                                       6899**************************.....77...58899*********************99987 PP

  == domain 8  score: 39.9 bits;  conditional E-value: 8.8e-13
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       + ++nl++vl+rlgr +eAle +++ +ei      p+   ++++ +n g +++ lgry+eA   + ++l+i++
  gi|386002707|ref|YP_005921006.1| 332 NPWYNLGVVLQRLGRGEEALEAYDRLIEID-----PN---LSEAWYNRGLALYSLGRYDEAAGCYDRVLEIDP 396
                                       5688**************************.....75...99****************************986 PP

  == domain 9  score: 15.3 bits;  conditional E-value: 4.1e-05
                            TPR_12   6 lnnlaavlrrlgrydeAlellekalei 32 
                                       ++  a++l  lgry+eAl+++++ale+
  gi|386002707|ref|YP_005921006.1| 402 WYDKALALGSLGRYEEALDCYDEALEA 428
                                       667889999999999999999999986 PP

  == domain 10  score: 15.6 bits;  conditional E-value: 3.3e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       +lnn+ ++l+ l+ry e+  ++  ++ i    +G     + ++ +n g +++ lgryeeA + + ea a
  gi|386002707|ref|YP_005921006.1| 435 VLNNRCNILYSLERYNESVGCYGDVIGID---PG-----YENAWYNRGVALYTLGRYEEASASYGEAAA 495
                                       67888899999999999999999997777...44.....445889999999999999999999999876 PP

  == domain 11  score: 17.9 bits;  conditional E-value: 6.3e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +a++n++++l+ lgry+eA + + +a ++      + +   + +  ++g+++ a+g y+ A+e++  a+a++
  gi|386002707|ref|YP_005921006.1| 468 NAWYNRGVALYTLGRYEEASASYGEAAALN-----G-S--RVDAWVGMGDAFAAAGIYDRAVEAYDGAIALY 531
                                       7899**********************7777.....4.3..67788888888888888888888888888887 PP

  == domain 12  score: 13.0 bits;  conditional E-value: 0.00021
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a++ ++++ +++g yd A e ++ a++++     p  p+   + +n g l++ + r+eeA+e + e+++i++
  gi|386002707|ref|YP_005921006.1| 503 AWVGMGDAFAAAGIYDRAVEAYDGAIALY-----PGDPA---VWYNRGLLLYNASRLEEAVESFDEVIEIDP 566
                                       67788888888899999999999998888.....54544...799*****99999************99975 PP

  == domain 13  score: 25.7 bits;  conditional E-value: 2.4e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +++n++++l+ + r++eA e +++++ei      p +++   + r  g +++algr +eA++ + eal+i 
  gi|386002707|ref|YP_005921006.1| 537 VWYNRGLLLYNASRLEEAVESFDEVIEID-----PSYEG---VWRLKGLALYALGRSDEAIDCYDEALEIS 599
                                       688**************************.....76655...46777777779****************96 PP

  == domain 14  score: 17.5 bits;  conditional E-value: 8.9e-06
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrl 36 
                                       ++++n+++vl+ lgry eA+e +++++e+ r  
  gi|386002707|ref|YP_005921006.1| 604 SLWYNRGVVLFSLGRYGEAIESYDRVIELDRYE 636
                                       5678************************98755 PP

  == domain 15  score: 29.3 bits;  conditional E-value: 1.8e-09
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       + +++l+ lgrydeA+e++ek+le+      p   l+a + +  g +++ lg+ye   e + ++++i+
  gi|386002707|ref|YP_005921006.1| 636 EKGEALYSLGRYDEAIECYEKVLEVS-----P---LEAKAWYQKGLAHQILGDYERSAECYDRVVEID 695
                                       5799******************9999.....5...79***************************9996 PP

  == domain 16  score: 24.6 bits;  conditional E-value: 5.4e-08
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       +l +++ vl+rlg+yd Al+ ++ al+       pd    +++ r+ g++++algr+eeA + + + la a
  gi|386002707|ref|YP_005921006.1| 702 IL-RRGFVLLRLGDYDGALASYDLALQED-----PDD---LEAARGRGEALLALGRFEEASATFDRILANA 763
                                       45.89********************6666.....775...99************************99976 PP

  == domain 17  score: 19.7 bits;  conditional E-value: 1.8e-06
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       a++ ++++l++lgr++eA + +++ l+ a++  G+       + ++ g ++  l ry+eA++ + +a+ai
  gi|386002707|ref|YP_005921006.1| 735 AARGRGEALLALGRFEEASATFDRILANASED-GG-------AWHGRGLALAGLLRYDEAIDSYDRAIAI 796
                                       55589************************554.33.......4578888888777999999999999998 PP

  == domain 18  score: 18.4 bits;  conditional E-value: 4.6e-06
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       a++ ++++l+ l rydeA++ +++a++i   +   d+  +    ++ g +++++gr+e+A++ + +a+a++
  gi|386002707|ref|YP_005921006.1| 769 AWHGRGLALAGLLRYDEAIDSYDRAIAIN--S--SDN--L--LWIGRGGVLEEAGRLEDAVASFDRAIALD 831
                                       688999*******************9999..3..566..2..589***********************986 PP

  == domain 19  score: 20.8 bits;  conditional E-value: 8.2e-07
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +  ++ vl ++gr+++A + +++a+++ ++   p    +a+++r+ + +  ++gr+e+A + + +a+a+++
  gi|386002707|ref|YP_005921006.1| 804 WIGRGGVLEEAGRLEDAVASFDRAIALDQED--P----EAWSMRGRALM--KAGRLEDAAASFDRAIALDP 866
                                       55899***********************866..6....79*********..7***************9975 PP

  == domain 20  score: 11.1 bits;  conditional E-value: 0.00086
                            TPR_12   5 alnnlaavlrrlgrydeAlellekalei 32 
                                       a++ +++v  ++gr +eA+ ++e+a+++
  gi|386002707|ref|YP_005921006.1| 871 AQRGRGSVFEAQGRAEEAIGCYEAAIAL 898
                                       5556777888888888888888877765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.2e-07   0.00018       7      64 ..      37      94 ..      33      95 .. 0.96
   2 !   31.1   0.0   4.3e-10   1.9e-07       9      62 ..      73     126 ..      66     128 .. 0.90
   3 !   30.8   0.5   5.4e-10   2.3e-07      11      63 ..     109     161 ..     108     163 .. 0.93
   4 !   19.1   0.1   2.5e-06    0.0011      12      64 ..     144     196 ..     143     198 .. 0.94
   5 !   19.0   0.1   2.7e-06    0.0012      11      62 ..     177     228 ..     177     232 .. 0.94
   6 !   21.9   0.5   3.4e-07   0.00015       9      60 ..     209     260 ..     201     266 .. 0.92
   7 !   26.2   0.1   1.5e-08   6.5e-06       9      61 ..     243     295 ..     235     300 .. 0.93
   8 !   20.1   0.1   1.2e-06   0.00053      10      61 ..     278     329 ..     277     333 .. 0.95
   9 !   15.6   0.3   3.1e-05     0.014       9      51 ..     311     353 ..     304     354 .. 0.93
  10 !   38.4   1.1   2.3e-12     1e-09       5      64 ..     341     400 ..     337     401 .. 0.93
  11 !   28.5   1.0   2.9e-09   1.3e-06      12      65 ..     382     435 ..     381     437 .. 0.95
  12 !   11.4   0.0    0.0006      0.26      25      65 ..     463     503 ..     442     505 .. 0.86
  13 !   25.2   0.2   3.1e-08   1.3e-05      11      61 ..     517     567 ..     510     578 .. 0.91
  14 !   28.5   0.0   2.8e-09   1.2e-06       9      60 ..     583     634 ..     574     643 .. 0.90
  15 !   24.6   0.1   4.8e-08   2.1e-05       9      60 ..     645     696 ..     638     701 .. 0.93
  16 !   26.2   2.0   1.4e-08   6.3e-06      10      67 ..     680     737 ..     678     740 .. 0.95
  17 !   24.4   3.1   5.4e-08   2.3e-05       5      62 ..     709     766 ..     703     769 .. 0.94
  18 !   17.6   0.5   7.1e-06    0.0031       6      61 ..     744     799 ..     740     803 .. 0.91
  19 !   19.6   2.4   1.7e-06   0.00073      10      69 ..     782     841 ..     775     843 .. 0.94
  20 !   28.5   2.8   2.9e-09   1.3e-06       5      66 ..     811     872 ..     807     874 .. 0.93
  21 !   20.2   0.9   1.1e-06    0.0005       7      64 ..     847     904 ..     845     907 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.2e-07
                             TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64
                                      ++e ++ al +v+  l ++P  p+ +   G +l  lG+l +Al ++++ l+++p++p 
  gi|386002707|ref|YP_005921006.1| 37 SNESYDLALLYVNKSLDIDPAYPDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQDPH 94
                                      57999**************************************************996 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 4.3e-10
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                        + ++al + +r l ++P+dp+ ++  G++l+ lG + +A+++ +++++ +   
  gi|386002707|ref|YP_005921006.1|  73 GRLDEALSCFNRSLEIDPQDPHIWYSKGFVLYGLGIYDEAIDCYDRAMEFNSTG 126
                                       6789******************************************99877655 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 5.4e-10
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                       +++a+ +++r + +++  p+++r RGl+l+ lG++++A++  + ++  +p+  
  gi|386002707|ref|YP_005921006.1| 109 YDEAIDCYDRAMEFNSTGPDLWRARGLALYSLGRYEEAVRSYDEAIVFDPAQG 161
                                       579***************************************99998888765 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 2.5e-06
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       e+a + ++  ++++P + ++++  Gl+l  lG++++A++  + ++ +++d+++
  gi|386002707|ref|YP_005921006.1| 144 EEAVRSYDEAIVFDPAQGDLWYQKGLALCGLGRYEKAIESYDFAITIDGDDAA 196
                                       789999***************************************99998875 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 2.7e-06
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       +e+a++ ++  + ++ dd+  +   +l+l+ lG+ ++A+++ +++++++p+ 
  gi|386002707|ref|YP_005921006.1| 177 YEKAIESYDFAITIDGDDAASWHGKALALYSLGRAEEAIDCYDRAIDIDPSL 228
                                       5899*********************************************975 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 3.4e-07
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        ++e+a+ +++r + ++P   + ++  G++l+ lG+ ++A ++ +a+++++p
  gi|386002707|ref|YP_005921006.1| 209 GRAEEAIDCYDRAIDIDPSLTDVWYNKGIALYALGRHEEAFKCYDAAVEIDP 260
                                       6899*********************************************999 PP

  == domain 7  score: 26.2 bits;  conditional E-value: 1.5e-08
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        ++e+a ++++  + ++P  +  ++  Gl+ + lG++++A+++ +++++++p+
  gi|386002707|ref|YP_005921006.1| 243 GRHEEAFKCYDAAVEIDPLYHPAWFNKGLAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       689************************************************96 PP

  == domain 8  score: 20.1 bits;  conditional E-value: 1.2e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       + e+a+ +++r + ++P  +  +   G +l+ lG++ +A ++  ++++++p+
  gi|386002707|ref|YP_005921006.1| 278 RVEEAIDCYDRAIDIDPSLVAVWNNKGNALYALGRFDEAQECYRRAVEIDPE 329
                                       5689**********************************************96 PP

  == domain 9  score: 15.6 bits;  conditional E-value: 3.1e-05
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAlad 51 
                                        ++++a +++ r + ++P+    ++  G++l++lG+ ++Al++
  gi|386002707|ref|YP_005921006.1| 311 GRFDEAQECYRRAVEIDPEYSNPWYNLGVVLQRLGRGEEALEA 353
                                       58999***********************************986 PP

  == domain 10  score: 38.4 bits;  conditional E-value: 2.3e-12
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       ++r  + e+al++++rl+ ++P+  e ++ RGl+l+ lG++ +A+ + ++ l+++p++ d
  gi|386002707|ref|YP_005921006.1| 341 LQRLGRGEEALEAYDRLIEIDPNLSEAWYNRGLALYSLGRYDEAAGCYDRVLEIDPENGD 400
                                       567778899***********************************************9887 PP

  == domain 11  score: 28.5 bits;  conditional E-value: 2.9e-09
                             TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       ++a  +++r+l ++P+  + ++d +l+l  lG++++Al++ + +l+  p +p++
  gi|386002707|ref|YP_005921006.1| 382 DEAAGCYDRVLEIDPENGDVWYDKALALGSLGRYEEALDCYDEALEAGPRRPEV 435
                                       78999********************************************99976 PP

  == domain 12  score: 11.4 bits;  conditional E-value: 0.0006
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       +P     ++ RG++l+ lG++++A a    ++al++++ da
  gi|386002707|ref|YP_005921006.1| 463 DPGYENAWYNRGVALYTLGRYEEASASYGEAAALNGSRVDA 503
                                       5555678*******************999999999988776 PP

  == domain 13  score: 25.2 bits;  conditional E-value: 3.1e-08
                             TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++ra ++++  ++l P dp  ++ RGlll+   +l++A++ ++  ++++p+
  gi|386002707|ref|YP_005921006.1| 517 YDRAVEAYDGAIALYPGDPAVWYNRGLLLYNASRLEEAVESFDEVIEIDPS 567
                                       79**********************************************997 PP

  == domain 14  score: 28.5 bits;  conditional E-value: 2.8e-09
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        ++++a+ +++  l + P ++++++ RG++l+ lG++ +A++  ++ ++l+ 
  gi|386002707|ref|YP_005921006.1| 583 GRSDEAIDCYDEALEISPSEVSLWYNRGVVLFSLGRYGEAIESYDRVIELDR 634
                                       6899******************************************999875 PP

  == domain 15  score: 24.6 bits;  conditional E-value: 4.8e-08
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                        ++++a++++e +l + P ++  ++  Gl+++ lG+++  +++ ++ ++++p
  gi|386002707|ref|YP_005921006.1| 645 GRYDEAIECYEKVLEVSPLEAKAWYQKGLAHQILGDYERSAECYDRVVEIDP 696
                                       6899*********************************************999 PP

  == domain 16  score: 26.2 bits;  conditional E-value: 1.4e-08
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaea 67 
                                       d+er  ++++r++ ++P   e ++ RG++l +lG++ +Ala  + +l+ +pd+ +a++
  gi|386002707|ref|YP_005921006.1| 680 DYERSAECYDRVVEIDPGYEEVILRRGFVLLRLGDYDGALASYDLALQEDPDDLEAAR 737
                                       899*************************************************988875 PP

  == domain 17  score: 24.4 bits;  conditional E-value: 5.4e-08
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++r  d++ ala +++ l+ +Pdd e  r RG +l  lG++++A a +++ la+a ++
  gi|386002707|ref|YP_005921006.1| 709 LLRLGDYDGALASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRILANASED 766
                                       68899***********************************************999876 PP

  == domain 18  score: 17.6 bits;  conditional E-value: 7.1e-06
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       +   ++e+a a+ +r+l+ a++d + +  RGl+la l ++ +A++  ++++a++ +
  gi|386002707|ref|YP_005921006.1| 744 LALGRFEEASATFDRILANASEDGGAWHGRGLALAGLLRYDEAIDSYDRAIAINSS 799
                                       666799********************************************998765 PP

  == domain 19  score: 19.6 bits;  conditional E-value: 1.7e-06
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       ++++a+  ++r +++++ d  ++  RG +l++ G+l+ A+a +++++al+ ++p+a  +r
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAIAINSSDNLLWIGRGGVLEEAGRLEDAVASFDRAIALDQEDPEAWSMR 841
                                       6899**************************************************997666 PP

  == domain 20  score: 28.5 bits;  conditional E-value: 2.9e-09
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       + ++ + e a a  +r ++l+ +dpe +  RG++l++ G+l+ A+a +++++al+p+  +a 
  gi|386002707|ref|YP_005921006.1| 811 LEEAGRLEDAVASFDRAIALDQEDPEAWSMRGRALMKAGRLEDAAASFDRAIALDPSSGEAQ 872
                                       56788999************************************************988775 PP

  == domain 21  score: 20.2 bits;  conditional E-value: 1.1e-06
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                        + + e a a  +r ++l+P + e  r RG + + +G+ ++A+ + ea++al+p  p+
  gi|386002707|ref|YP_005921006.1| 847 KAGRLEDAAASFDRAIALDPSSGEAQRGRGSVFEAQGRAEEAIGCYEAAIALDPPTPE 904
                                       6778999***********************************************6665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00031      0.14       2      32 ..      62      92 ..      61      95 .. 0.84
   2 ?    5.5   0.0     0.046        20      15      27 ..     109     121 ..     104     128 .. 0.81
   3 !    9.4   0.1    0.0026       1.1       6      32 ..     134     160 ..     129     163 .. 0.79
   4 ?    7.5   0.1      0.01       4.4       4      23 ..     166     185 ..     163     205 .. 0.85
   5 !    9.2   0.1    0.0029       1.3       6      32 ..     202     226 ..     197     231 .. 0.75
   6 ?    4.0   0.1      0.14        59       2      31 ..     232     259 ..     231     261 .. 0.83
   7 !   14.1   0.0   8.3e-05     0.036       1      33 [.     265     295 ..     265     298 .. 0.88
   8 !   14.8   0.0     5e-05     0.022       2      32 ..     300     328 ..     299     332 .. 0.86
   9 !   13.9   0.0   9.4e-05     0.041       2      30 ..     334     362 ..     334     366 .. 0.86
  10 !   18.0   0.1   4.7e-06    0.0021       1      34 [.     367     400 ..     367     401 .. 0.88
  11 !   13.1   0.2   0.00017     0.075       8      33 ..     408     434 ..     402     437 .. 0.81
  12 ?    4.9   0.4     0.073        32       1      28 [.     469     496 ..     469     500 .. 0.87
  13 ?    4.8   0.0     0.077        34       1      28 [.     503     530 ..     503     536 .. 0.83
  14 ?    0.9   0.0       1.4   6.1e+02       2      30 ..     538     566 ..     537     571 .. 0.79
  15 !    9.5   0.0    0.0024         1       9      33 ..     579     601 ..     574     604 .. 0.75
  16 !   14.0   0.0   8.8e-05     0.038       2      33 ..     606     635 ..     604     639 .. 0.85
  17 !   20.5   0.1   7.4e-07   0.00032       6      35 ..     638     665 ..     635     666 .. 0.86
  18 !   10.1   0.1    0.0016      0.68       2      31 ..     668     695 ..     667     700 .. 0.79
  19 !    7.7   0.1     0.009       3.9      10      34 ..     710     732 ..     706     735 .. 0.86
  20 ?    3.9   0.1      0.14        63       6      34 ..     740     768 ..     739     769 .. 0.87
  21 ?    4.7   0.0     0.085        37      14      32 ..     782     800 ..     776     802 .. 0.88
  22 ?    5.8   0.1     0.035        16       9      35 ..     811     835 ..     807     836 .. 0.83
  23 !    7.8   0.0    0.0087       3.8       2      33 ..     838     867 ..     837     871 .. 0.82
  24 !   15.1   0.0   4.1e-05     0.018       6      33 ..     876     901 ..     875     904 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00031
                             TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32
                                      ++  + + s+lG+ +eA++++ +sL+++ ++
  gi|386002707|ref|YP_005921006.1| 62 WSLKGYILSDLGRLDEALSCFNRSLEIDPQD 92
                                      5667889****************99998665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.046
                             TPR_7  15 yeeAielyeqsLa 27 
                                       y+eAi++y ++++
  gi|386002707|ref|YP_005921006.1| 109 YDEAIDCYDRAME 121
                                       9*********554 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0026
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       + +  +lG+yeeA++ y ++++++ ++
  gi|386002707|ref|YP_005921006.1| 134 GLALYSLGRYEEAVRSYDEAIVFDPAQ 160
                                       567779*************77666665 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.01
                             TPR_7   4 nLarlysrlGdyeeAielye 23 
                                       + + + + lG+ye+Aie y 
  gi|386002707|ref|YP_005921006.1| 166 QKGLALCGLGRYEKAIESYD 185
                                       56788999*********995 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0029
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdp 32 
                                       a +  +lG+ eeAi++y +  a++ dp
  gi|386002707|ref|YP_005921006.1| 202 ALALYSLGRAEEAIDCYDR--AIDIDP 226
                                       6677799************..555444 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.14
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       ++n + +  +lG++eeA ++y +  a++ d
  gi|386002707|ref|YP_005921006.1| 232 WYNKGIALYALGRHEEAFKCYDA--AVEID 259
                                       6788999999***********99..66555 PP

  == domain 7  score: 14.1 bits;  conditional E-value: 8.3e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       a++n + ++ +lG+ eeAi++y +  a++ dp+
  gi|386002707|ref|YP_005921006.1| 265 AWFNKGLAFYSLGRVEEAIDCYDR--AIDIDPS 295
                                       68999*******************..8877765 PP

  == domain 8  score: 14.8 bits;  conditional E-value: 5e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++n +++  +lG+++eA e+y++  a++ dp
  gi|386002707|ref|YP_005921006.1| 300 WNNKGNALYALGRFDEAQECYRR--AVEIDP 328
                                       7999*******************..665554 PP

  == domain 9  score: 13.9 bits;  conditional E-value: 9.4e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       ++nL+++ +rlG+ eeA+e y ++++++ 
  gi|386002707|ref|YP_005921006.1| 334 WYNLGVVLQRLGRGEEALEAYDRLIEIDP 362
                                       68*********************767764 PP

  == domain 10  score: 18.0 bits;  conditional E-value: 4.7e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++n + +  +lG+y+eA+++y ++L+++ + +d
  gi|386002707|ref|YP_005921006.1| 367 AWYNRGLALYSLGRYDEAAGCYDRVLEIDPENGD 400
                                       6899999*****************9998877665 PP

  == domain 11  score: 13.1 bits;  conditional E-value: 0.00017
                             TPR_7   8 lysrlGdyeeAielyeqsL.altkdpe 33 
                                       +  +lG+yeeA+++y ++L a  ++pe
  gi|386002707|ref|YP_005921006.1| 408 ALGSLGRYEEALDCYDEALeAGPRRPE 434
                                       66689************8877666665 PP

  == domain 12  score: 4.9 bits;  conditional E-value: 0.073
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++n +++   lG+yeeA   y ++ al
  gi|386002707|ref|YP_005921006.1| 469 AWYNRGVALYTLGRYEEASASYGEAAAL 496
                                       68999*************9999996665 PP

  == domain 13  score: 4.8 bits;  conditional E-value: 0.077
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       a++ +++++ + G y++A+e y  ++al
  gi|386002707|ref|YP_005921006.1| 503 AWVGMGDAFAAAGIYDRAVEAYDGAIAL 530
                                       57789*****************995554 PP

  == domain 14  score: 0.9 bits;  conditional E-value: 1.4
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       ++n + l  +  + eeA+e + ++++++ 
  gi|386002707|ref|YP_005921006.1| 538 WYNRGLLLYNASRLEEAVESFDEVIEIDP 566
                                       57778888889999********9766665 PP

  == domain 15  score: 9.5 bits;  conditional E-value: 0.0024
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdpe 33 
                                         +lG+ +eAi++y ++L++  +p+
  gi|386002707|ref|YP_005921006.1| 579 LYALGRSDEAIDCYDEALEI--SPS 601
                                       5579************5554..444 PP

  == domain 16  score: 14.0 bits;  conditional E-value: 8.8e-05
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++n +++ ++lG+y eAie y +  +++ d +
  gi|386002707|ref|YP_005921006.1| 606 WYNRGVVLFSLGRYGEAIESYDR--VIELDRY 635
                                       5899*******************..6666665 PP

  == domain 17  score: 20.5 bits;  conditional E-value: 7.4e-07
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +++  +lG+y+eAie+ye+  +l+ +p++a
  gi|386002707|ref|YP_005921006.1| 638 GEALYSLGRYDEAIECYEK--VLEVSPLEA 665
                                       677889*************..999988876 PP

  == domain 18  score: 10.1 bits;  conditional E-value: 0.0016
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       +++ + +++ lGdye+ +e+y +  +++ d
  gi|386002707|ref|YP_005921006.1| 668 WYQKGLAHQILGDYERSAECYDR--VVEID 695
                                       6677888999************9..55444 PP

  == domain 19  score: 7.7 bits;  conditional E-value: 0.009
                             TPR_7  10 srlGdyeeAielyeqsLaltkdped 34 
                                        rlGdy+ A+  y    al +dp+d
  gi|386002707|ref|YP_005921006.1| 710 LRLGDYDGALASYDL--ALQEDPDD 732
                                       69*************..88888876 PP

  == domain 20  score: 3.9 bits;  conditional E-value: 0.14
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       +++  +lG++eeA   + + La ++++++
  gi|386002707|ref|YP_005921006.1| 740 GEALLALGRFEEASATFDRILANASEDGG 768
                                       678899*************9998888776 PP

  == domain 21  score: 4.7 bits;  conditional E-value: 0.085
                             TPR_7  14 dyeeAielyeqsLaltkdp 32 
                                       +y+eAi+ y +++a+ +++
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAIAINSSD 800
                                       7**********88887766 PP

  == domain 22  score: 5.8 bits;  conditional E-value: 0.035
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkdpeda 35 
                                        ++ G+ e+A+  + +  a++ d+ed+
  gi|386002707|ref|YP_005921006.1| 811 LEEAGRLEDAVASFDR--AIALDQEDP 835
                                       6789************..888888776 PP

  == domain 23  score: 7.8 bits;  conditional E-value: 0.0087
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       ++  +r+  + G+ e+A+  + +  a++ dp+
  gi|386002707|ref|YP_005921006.1| 838 WSMRGRALMKAGRLEDAAASFDR--AIALDPS 867
                                       56679******************..6666654 PP

  == domain 24  score: 15.1 bits;  conditional E-value: 4.1e-05
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                       +++++++G+ eeAi++ye+  a++ dp 
  gi|386002707|ref|YP_005921006.1| 876 GSVFEAQGRAEEAIGCYEA--AIALDPP 901
                                       7899***************..8887775 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.9   8.5e+02       8      31 ..      67      90 ..      41      92 .. 0.78
   2 ?    0.8   0.0       2.1   9.4e+02       9      26 ..     102     119 ..      96     121 .. 0.79
   3 ?    6.8   0.0     0.027        12       6      27 ..     133     154 ..     132     158 .. 0.91
   4 ?    4.3   0.1      0.17        76       3      24 ..     164     185 ..     162     190 .. 0.86
   5 !   10.3   0.0     0.002       0.9       7      31 ..     202     226 ..     197     227 .. 0.91
   6 ?    8.0   0.0     0.011       4.8       1      31 [.     230     260 ..     230     261 .. 0.91
   7 !   13.7   0.0   0.00018     0.077       2      31 ..     265     294 ..     264     295 .. 0.94
   8 !    9.7   0.1    0.0032       1.4       7      32 ..     304     329 ..     302     330 .. 0.90
   9 !   15.6   0.0   4.2e-05     0.019       4      32 ..     335     363 ..     334     364 .. 0.95
  10 !   18.9   0.1   3.7e-06    0.0016       1      32 [.     366     397 ..     366     398 .. 0.95
  11 ?    5.2   0.2     0.089        39       2      28 ..     401     427 ..     400     428 .. 0.86
  12 ?    5.8   0.5     0.055        24       2      25 ..     469     492 ..     468     495 .. 0.90
  13 !   13.2   0.1   0.00024      0.11       1      32 [.     502     533 ..     502     534 .. 0.95
  14 !   11.4   0.0   0.00094      0.41       2      31 ..     537     566 ..     536     568 .. 0.92
  15 !    8.3   0.0    0.0087       3.8       7      31 ..     576     600 ..     574     601 .. 0.90
  16 !    9.4   0.0    0.0041       1.8       4      28 ..     607     631 ..     604     633 .. 0.93
  17 !   14.8   0.0   7.7e-05     0.034       4      28 ..     635     659 ..     634     663 .. 0.90
  18 !    8.7   0.0    0.0065       2.8       2      31 ..     667     696 ..     666     698 .. 0.89
  19 !   10.6   0.0    0.0017      0.76       2      32 ..     701     731 ..     700     732 .. 0.93
  20 ?    5.8   0.1     0.058        25       6      29 ..     739     762 ..     734     765 .. 0.90
  21 ?    3.4   0.0      0.32   1.4e+02       5      28 ..     772     795 ..     769     798 .. 0.83
  22 ?    1.1   0.0       1.8   7.7e+02      10      27 ..     811     828 ..     806     830 .. 0.83
  23 ?    7.9   0.1     0.012       5.1       5      33 .]     840     868 ..     836     868 .. 0.90
  24 ?    5.6   0.0     0.063        28       6      31 ..     875     900 ..     870     902 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6  8 lsyrklgdtdkAlealerlikeYP 31
                                      + +  lg+ d+Al  ++r ++  P
  gi|386002707|ref|YP_005921006.1| 67 YILSDLGRLDEALSCFNRSLEIDP 90
                                      4444569*********99887777 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealerl 26 
                                        ++ lg +d+A++ ++r 
  gi|386002707|ref|YP_005921006.1| 102 VLYGLGIYDEAIDCYDRA 119
                                       5667789********986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                       ++l++++lg++++A++ +++ i
  gi|386002707|ref|YP_005921006.1| 133 RGLALYSLGRYEEAVRSYDEAI 154
                                       599****99*********9876 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAleale 24 
                                        y+ +l++  lg+++kA+e ++
  gi|386002707|ref|YP_005921006.1| 164 WYQKGLALCGLGRYEKAIESYD 185
                                       589999999999*******996 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       al++++lg++++A++ ++r i+  P
  gi|386002707|ref|YP_005921006.1| 202 ALALYSLGRAEEAIDCYDRAIDIDP 226
                                       89****99*************9887 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       d+ y+ + ++++lg++++A + ++  ++  P
  gi|386002707|ref|YP_005921006.1| 230 DVWYNKGIALYALGRHEEAFKCYDAAVEIDP 260
                                       678*********99*********99998766 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       A ++ +l++++lg+ ++A++ ++r i+  P
  gi|386002707|ref|YP_005921006.1| 265 AWFNKGLAFYSLGRVEEAIDCYDRAIDIDP 294
                                       889********99*************9887 PP

  == domain 8  score: 9.7 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       + ++++lg+ d+A e ++r ++  P+
  gi|386002707|ref|YP_005921006.1| 304 GNALYALGRFDEAQECYRRAVEIDPE 329
                                       78999*99*************99885 PP

  == domain 9  score: 15.6 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       y+l+  +++lg+ ++Alea++rli+  P+
  gi|386002707|ref|YP_005921006.1| 335 YNLGVVLQRLGRGEEALEAYDRLIEIDPN 363
                                       9********99**************9998 PP

  == domain 10  score: 18.9 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       +A y+++l++++lg++d+A   ++r+++  P+
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYDRVLEIDPE 397
                                       79**********99**************9996 PP

  == domain 11  score: 5.2 bits;  conditional E-value: 0.089
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       + y  al++ +lg++++Al+ +++ ++
  gi|386002707|ref|YP_005921006.1| 401 VWYDKALALGSLGRYEEALDCYDEALE 427
                                       6788899999999*********98875 PP

  == domain 12  score: 5.8 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                       A y+++ +++ lg++++A + + +
  gi|386002707|ref|YP_005921006.1| 469 AWYNRGVALYTLGRYEEASASYGE 492
                                       89*********99*****998865 PP

  == domain 13  score: 13.2 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       dA   ++ ++ ++g +d+A+ea++  i  YP+
  gi|386002707|ref|YP_005921006.1| 502 DAWVGMGDAFAAAGIYDRAVEAYDGAIALYPG 533
                                       78999*******99*****************6 PP

  == domain 14  score: 11.4 bits;  conditional E-value: 0.00094
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       + y+++l+++++ + ++A+e ++++i+  P
  gi|386002707|ref|YP_005921006.1| 537 VWYNRGLLLYNASRLEEAVESFDEVIEIDP 566
                                       57*********99*************9988 PP

  == domain 15  score: 8.3 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                       +l++++lg++d+A++ +++ ++  P
  gi|386002707|ref|YP_005921006.1| 576 GLALYALGRSDEAIDCYDEALEISP 600
                                       89****99**********9998776 PP

  == domain 16  score: 9.4 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlik 28 
                                       y+++  +++lg++ +A+e ++r+i+
  gi|386002707|ref|YP_005921006.1| 607 YNRGVVLFSLGRYGEAIESYDRVIE 631
                                       99*******99************97 PP

  == domain 17  score: 14.8 bits;  conditional E-value: 7.7e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlik 28 
                                       y  ++++++lg++d+A+e +e++++
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLE 659
                                       7889*****99************98 PP

  == domain 18  score: 8.7 bits;  conditional E-value: 0.0065
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       A y+ +l+++ lgd++++ e ++r+++  P
  gi|386002707|ref|YP_005921006.1| 667 AWYQKGLAHQILGDYERSAECYDRVVEIDP 696
                                       8899999999677*************9988 PP

  == domain 19  score: 10.6 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       + ++++  +++lgd+d Al+ ++  ++e Pd
  gi|386002707|ref|YP_005921006.1| 701 VILRRGFVLLRLGDYDGALASYDLALQEDPD 731
                                       67999******99*****************9 PP

  == domain 20  score: 5.8 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                       +++++++lg+ ++A ++++r++ +
  gi|386002707|ref|YP_005921006.1| 739 RGEALLALGRFEEASATFDRILAN 762
                                       699****99***********9987 PP

  == domain 21  score: 3.4 bits;  conditional E-value: 0.32
                                       HHHHHHHH.HHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrk.lgdtdkAlealerlik 28 
                                        ++l++   l ++d+A++ ++r i 
  gi|386002707|ref|YP_005921006.1| 772 GRGLALAGlL-RYDEAIDSYDRAIA 795
                                       6788899768.**********9985 PP

  == domain 22  score: 1.1 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerli 27 
                                       ++++g+ ++A++ ++r i
  gi|386002707|ref|YP_005921006.1| 811 LEEAGRLEDAVASFDRAI 828
                                       46678**********998 PP

  == domain 23  score: 7.9 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   5 klalsyrklgdtdkAlealerlikeYPdS 33 
                                       ++++++ k+g+ ++A + ++r i   P S
  gi|386002707|ref|YP_005921006.1| 840 MRGRALMKAGRLEDAAASFDRAIALDPSS 868
                                       789*****99**************99987 PP

  == domain 24  score: 5.6 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                       ++  ++++g++++A+  +e  i   P
  gi|386002707|ref|YP_005921006.1| 875 RGSVFEAQGRAEEAIGCYEAAIALDP 900
                                       67889999***********9998766 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.7e-07   7.6e-05       2      81 ..      38     118 ..      37     119 .. 0.96
   2 !    8.5   0.0    0.0055       2.4      30      79 ..     134     184 ..     126     187 .. 0.87
   3 !   21.4   0.1   4.8e-07   0.00021      24      80 ..     194     253 ..     188     255 .. 0.91
   4 !   12.7   0.0   0.00027      0.12      29      80 ..     269     321 ..     262     323 .. 0.92
   5 !   27.8   0.1   4.9e-09   2.2e-06       6      81 ..     348     424 ..     345     425 .. 0.96
   6 !   18.6   0.0   3.7e-06    0.0016       3      81 ..     413     492 ..     411     493 .. 0.96
   7 !   17.1   0.0   1.1e-05    0.0046      23      81 ..     535     594 ..     511     595 .. 0.84
   8 !   14.7   0.0   5.9e-05     0.026      28      80 ..     574     627 ..     573     629 .. 0.94
   9 !   17.6   0.0   7.5e-06    0.0033      26      81 ..     604     656 ..     595     657 .. 0.90
  10 !   18.7   0.1   3.5e-06    0.0015       3      78 ..     645     721 ..     643     723 .. 0.95
  11 !   11.4   0.0   0.00065      0.29       4      81 ..     714     792 ..     711     793 .. 0.91
  12 ?    6.7   0.0     0.019       8.4       3      80 ..     815     893 ..     796     895 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-07
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       ++ y+ A+++ ++ l  ++  p++  l+++ l  +g+ ++A+  ++++ +++++++ ++y ++ +l+ L+ y+eAi+
  gi|386002707|ref|YP_005921006.1|  38 NESYDLALLYVNKSLDIDPAYPDAWSLKGYILSDLGRLDEALSCFNRSlEIDPQDPHIWYSKGFVLYGLGIYDEAID 114
                                       688999*********999*********************************************************** PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       ++++
  gi|386002707|ref|YP_005921006.1| 115 CYDR 118
                                       9876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0055
                                       HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +l+ly++g+y++A + +++a   ++     +y ++ +l  L++ye+Ai  +
  gi|386002707|ref|YP_005921006.1| 134 GLALYSLGRYEEAVRSYDEAiVFDPAQGDLWYQKGLALCGLGRYEKAIESY 184
                                       689*****************6666666699*****************9876 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 4.8e-07
                                       HHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  24 edayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++a ++  Al+ly++g+ ++A++ +++a +++++   ++y ++ +l++L+++eeA ++++
  gi|386002707|ref|YP_005921006.1| 194 DAASWHgkALALYSLGRAEEAIDCYDRAiDIDPSLTDVWYNKGIALYALGRHEEAFKCYD 253
                                       67778666***********************************************99876 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00027
                                       HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       ++l++y++g+ ++A++ +++a +++++  +++  ++ +l++L++++eA  ++ 
  gi|386002707|ref|YP_005921006.1| 269 KGLAFYSLGRVEEAIDCYDRAiDIDPSLVAVWNNKGNALYALGRFDEAQECYR 321
                                       5899********************************************88765 PP

  == domain 5  score: 27.8 bits;  conditional E-value: 4.9e-09
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++A+  ++rl + +++ +e+ y  +l+ly++g+y++A   +++  ++++++  ++y +A +l  L++yeeA++++++
  gi|386002707|ref|YP_005921006.1| 348 EEALEAYDRLIEIDPNLSEAWYNRGLALYSLGRYDEAAGCYDRVlEIDPENGDVWYDKALALGSLGRYEEALDCYDE 424
                                       689999*****999***********************************************************9986 PP

  == domain 6  score: 18.6 bits;  conditional E-value: 3.7e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++y++A+ +++ +l+a +++pe +   +  ly++++y++    + +  ++++  ++++y  + +l+ L++yeeA a 
  gi|386002707|ref|YP_005921006.1| 413 GRYEEALDCYDEALEAGPRRPEVLNNRCNILYSLERYNESVGCYGDViGIDPGYENAWYNRGVALYTLGRYEEASAS 489
                                       68************************************************************************998 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       +++
  gi|386002707|ref|YP_005921006.1| 490 YGE 492
                                       876 PP

  == domain 7  score: 17.1 bits;  conditional E-value: 1.1e-05
                                       HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  23 pedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       p  a ++  +l ly++++ ++A e +++  +++++ +g++ l++ +l++L++ +eAi+++++
  gi|386002707|ref|YP_005921006.1| 535 P--AVWYnrGLLLYNASRLEEAVESFDEViEIDPSYEGVWRLKGLALYALGRSDEAIDCYDE 594
                                       4..4555559************************************************9986 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3  28 llAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       l++l+ly +g+ ++A++ +++a ++ ++    +y  + +l+ L++y eAi  ++
  gi|386002707|ref|YP_005921006.1| 574 LKGLALYALGRSDEAIDCYDEAlEISPSEVSLWYNRGVVLFSLGRYGEAIESYD 627
                                       5789******************99999999********************9876 PP

  == domain 9  score: 17.6 bits;  conditional E-value: 7.5e-06
                                       HHHH..HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  26 ayll..AlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       ++++  + +l+++g+y +A+e +++       +  ry ++++l+ L++y+eAi ++ek
  gi|386002707|ref|YP_005921006.1| 604 SLWYnrGVVLFSLGRYGEAIESYDRV-----IELDRYEKGEALYSLGRYDEAIECYEK 656
                                       56777789******************.....7889********************998 PP

  == domain 10  score: 18.7 bits;  conditional E-value: 3.5e-06
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       ++y++Ai ++e++l+ ++  +++ y ++l++  +g+y+r  e +++  ++++  +++ +  + +ll L+ y+ A+a 
  gi|386002707|ref|YP_005921006.1| 645 GRYDEAIECYEKVLEVSPLEAKAWYQKGLAHQILGDYERSAECYDRVvEIDPGYEEVILRRGFVLLRLGDYDGALAS 721
                                       68**********************************************************************99986 PP

  == domain 11  score: 11.4 bits;  conditional E-value: 0.00065
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +y+ A+  ++++l+ +++++e+a   +++l+ +g++++A   +++    +s++ g++   + +l  L +y+eAi+ +
  gi|386002707|ref|YP_005921006.1| 714 DYDGALASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRIlANASEDGGAWHGRGLALAGLLRYDEAIDSY 790
                                       79999999*****8889999999999********************77777777********************988 PP

                                       -S CS
                            ANAPC3  80 ek 81 
                                       ++
  gi|386002707|ref|YP_005921006.1| 791 DR 792
                                       75 PP

  == domain 12  score: 6.7 bits;  conditional E-value: 0.019
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++++A+  ++r+ a ++e+pe+  + + +l ++g+ + A   +++a  l+++s ++    + +  ++++ eeAi +
  gi|386002707|ref|YP_005921006.1| 815 GRLEDAVASFDRAIALDQEDPEAWSMRGRALMKAGRLEDAAASFDRAiALDPSSGEAQRGRGSVFEAQGRAEEAIGC 891
                                       57788999999999999999999999999999999999999988888777777777666666666666666666666 PP

                                       H- CS
                            ANAPC3  79 Le 80 
                                       +e
  gi|386002707|ref|YP_005921006.1| 892 YE 893
                                       65 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.027        12       9      31 ..      66      88 ..      66      88 .. 0.90
   2 ?    0.6   0.0       1.3   5.6e+02      15      30 ..     106     121 ..     100     127 .. 0.61
   3 !   10.4   0.2    0.0011      0.47       9      29 ..     134     154 ..     133     155 .. 0.94
   4 ?   -0.5   0.0       2.9   1.3e+03       9      23 ..     168     182 ..     168     189 .. 0.84
   5 ?    7.1   0.1     0.012       5.2       9      31 ..     202     224 ..     196     224 .. 0.94
   6 !   13.1   0.1   0.00015     0.065       7      31 ..     234     258 ..     233     258 .. 0.93
   7 ?    5.5   0.0     0.036        16       9      31 ..     270     292 ..     268     292 .. 0.89
   8 !   18.7   0.4   2.6e-06    0.0011       6      31 ..     301     326 ..     301     326 .. 0.97
   9 !   14.4   0.3   5.9e-05     0.026       7      31 ..     336     360 ..     335     360 .. 0.94
  10 !   11.5   0.2   0.00048      0.21       7      31 ..     370     394 ..     369     394 .. 0.94
  11 !   11.2   0.3    0.0006      0.26       9      30 ..     406     427 ..     404     429 .. 0.93
  12 ?   -0.1   0.0       2.1   9.3e+02       5      29 ..     436     460 ..     434     462 .. 0.81
  13 !    8.2   0.8    0.0053       2.3       7      30 ..     472     495 ..     471     497 .. 0.90
  14 ?   -1.2   0.1       4.9   2.1e+03      18      31 ..     517     530 ..     507     531 .. 0.62
  15 ?    4.6   0.1     0.073        32       7      31 ..     540     564 ..     539     564 .. 0.93
  16 !    9.6   0.1    0.0019      0.82       9      31 ..     576     598 ..     576     599 .. 0.94
  17 !    7.8   0.0    0.0073       3.2       7      31 ..     608     632 ..     607     634 .. 0.92
  18 !   14.0   0.1   8.1e-05     0.035       9      31 ..     638     660 ..     636     661 .. 0.93
  19 ?    2.2   0.0      0.41   1.8e+02       9      31 ..     672     694 ..     666     696 .. 0.75
  20 ?    2.5   0.1      0.33   1.4e+02       9      30 ..     706     727 ..     705     727 .. 0.87
  21 ?    0.5   0.1       1.4   6.2e+02       9      23 ..     740     754 ..     738     761 .. 0.82
  22 ?    4.0   0.2      0.11        48       9      31 ..     774     796 ..     772     797 .. 0.91
  23 ?    3.3   0.1      0.18        78      11      31 ..     810     830 ..     808     833 .. 0.85
  24 ?    4.3   0.2     0.086        38       9      30 ..     842     863 ..     839     864 .. 0.93
  25 ?    3.3   0.1      0.19        82      14      30 ..     881     897 ..     869     901 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                            TPR_10  9 analrqrgrydeAealleealai 31
                                      + +l+++gr+deA+  + ++l+i
  gi|386002707|ref|YP_005921006.1| 66 GYILSDLGRLDEALSCFNRSLEI 88
                                      6789**********999999986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.3
                            TPR_10  15 rgrydeAealleeala 30 
                                       +g ydeA + +++a++
  gi|386002707|ref|YP_005921006.1| 106 LGIYDEAIDCYDRAME 121
                                       5556666666666654 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0011
                            TPR_10   9 analrqrgrydeAealleeal 29 
                                       + al+++gry+eA++ ++ea+
  gi|386002707|ref|YP_005921006.1| 134 GLALYSLGRYEEAVRSYDEAI 154
                                       789****************97 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.9
                            TPR_10   9 analrqrgrydeAea 23 
                                       + al+ +gry++A +
  gi|386002707|ref|YP_005921006.1| 168 GLALCGLGRYEKAIE 182
                                       6789999****9976 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.012
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a al+++gr +eA + +++a++i
  gi|386002707|ref|YP_005921006.1| 202 ALALYSLGRAEEAIDCYDRAIDI 224
                                       789*****************986 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 0.00015
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++al+++gr++eA + ++ a++i
  gi|386002707|ref|YP_005921006.1| 234 NKGIALYALGRHEEAFKCYDAAVEI 258
                                       669*******************997 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.036
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + a +++gr +eA + +++a++i
  gi|386002707|ref|YP_005921006.1| 270 GLAFYSLGRVEEAIDCYDRAIDI 292
                                       78889***************986 PP

  == domain 8  score: 18.7 bits;  conditional E-value: 2.6e-06
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nN +nal+++gr+deA + +++a++i
  gi|386002707|ref|YP_005921006.1| 301 NNKGNALYALGRFDEAQECYRRAVEI 326
                                       899*********************97 PP

  == domain 9  score: 14.4 bits;  conditional E-value: 5.9e-05
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       NL+++l+++gr++eA++ +++ ++i
  gi|386002707|ref|YP_005921006.1| 336 NLGVVLQRLGRGEEALEAYDRLIEI 360
                                       9******************998876 PP

  == domain 10  score: 11.5 bits;  conditional E-value: 0.00048
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N + al+++grydeA   ++++l+i
  gi|386002707|ref|YP_005921006.1| 370 NRGLALYSLGRYDEAAGCYDRVLEI 394
                                       7799******************997 PP

  == domain 11  score: 11.2 bits;  conditional E-value: 0.0006
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       a al ++gry+eA++ ++eal+
  gi|386002707|ref|YP_005921006.1| 406 ALALGSLGRYEEALDCYDEALE 427
                                       78999****************8 PP

  == domain 12  score: -0.1 bits;  conditional E-value: 2.1
                            TPR_10   5 lnNLanalrqrgrydeAealleeal 29 
                                       lnN  n+l+++ ry+e++  + +++
  gi|386002707|ref|YP_005921006.1| 436 LNNRCNILYSLERYNESVGCYGDVI 460
                                       6777799*********998887766 PP

  == domain 13  score: 8.2 bits;  conditional E-value: 0.0053
                            TPR_10   7 NLanalrqrgrydeAealleeala 30 
                                       N ++al+ +gry+eA a + ea a
  gi|386002707|ref|YP_005921006.1| 472 NRGVALYTLGRYEEASASYGEAAA 495
                                       779**************9999987 PP

  == domain 14  score: -1.2 bits;  conditional E-value: 4.9
                            TPR_10  18 ydeAealleealai 31 
                                       yd+A++ ++ a+a+
  gi|386002707|ref|YP_005921006.1| 517 YDRAVEAYDGAIAL 530
                                       56666666666665 PP

  == domain 15  score: 4.6 bits;  conditional E-value: 0.073
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N + +l++  r++eA++ ++e+++i
  gi|386002707|ref|YP_005921006.1| 540 NRGLLLYNASRLEEAVESFDEVIEI 564
                                       67999*****************997 PP

  == domain 16  score: 9.6 bits;  conditional E-value: 0.0019
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al+++gr deA + ++eal+i
  gi|386002707|ref|YP_005921006.1| 576 GLALYALGRSDEAIDCYDEALEI 598
                                       789******************98 PP

  == domain 17  score: 7.8 bits;  conditional E-value: 0.0073
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N +++l+++gry eA + +++++++
  gi|386002707|ref|YP_005921006.1| 608 NRGVVLFSLGRYGEAIESYDRVIEL 632
                                       7799*****************9986 PP

  == domain 18  score: 14.0 bits;  conditional E-value: 8.1e-05
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al+++grydeA + +e++l++
  gi|386002707|ref|YP_005921006.1| 638 GEALYSLGRYDEAIECYEKVLEV 660
                                       679******************96 PP

  == domain 19  score: 2.2 bits;  conditional E-value: 0.41
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + a++ +g+y+++ + ++++++i
  gi|386002707|ref|YP_005921006.1| 672 GLAHQILGDYERSAECYDRVVEI 694
                                       56777777777777777777765 PP

  == domain 20  score: 2.5 bits;  conditional E-value: 0.33
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       + +l ++g+yd+A+a ++ al+
  gi|386002707|ref|YP_005921006.1| 706 GFVLLRLGDYDGALASYDLALQ 727
                                       668999*********9988875 PP

  == domain 21  score: 0.5 bits;  conditional E-value: 1.4
                            TPR_10   9 analrqrgrydeAea 23 
                                       + al ++gr++eA a
  gi|386002707|ref|YP_005921006.1| 740 GEALLALGRFEEASA 754
                                       67999********76 PP

  == domain 22  score: 4.0 bits;  conditional E-value: 0.11
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       + al  + rydeA + +++a+ai
  gi|386002707|ref|YP_005921006.1| 774 GLALAGLLRYDEAIDSYDRAIAI 796
                                       67889999*************98 PP

  == domain 23  score: 3.3 bits;  conditional E-value: 0.18
                            TPR_10  11 alrqrgrydeAealleealai 31 
                                       +l + gr+++A+a +++a+a+
  gi|386002707|ref|YP_005921006.1| 810 VLEEAGRLEDAVASFDRAIAL 830
                                       67789**************97 PP

  == domain 24  score: 4.3 bits;  conditional E-value: 0.086
                            TPR_10   9 analrqrgrydeAealleeala 30 
                                       ++al + gr+++A a +++a+a
  gi|386002707|ref|YP_005921006.1| 842 GRALMKAGRLEDAAASFDRAIA 863
                                       899*****************98 PP

  == domain 25  score: 3.3 bits;  conditional E-value: 0.19
                            TPR_10  14 qrgrydeAealleeala 30 
                                       ++gr +eA   +e a+a
  gi|386002707|ref|YP_005921006.1| 881 AQGRAEEAIGCYEAAIA 897
                                       56666666666666665 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.45     2e+02      73     124 ..      70     121 ..      63     126 .. 0.93
   2 !   15.7   0.1   3.5e-05     0.015      66     120 ..     131     185 ..     128     190 .. 0.93
   3 ?    4.0   0.1      0.15        64     104     123 ..     203     222 ..     196     227 .. 0.85
   4 !   16.3   0.0   2.2e-05    0.0098      71     123 ..     238     290 ..     235     295 .. 0.94
   5 !   19.2   0.1     3e-06    0.0013      65     123 ..     300     358 ..     291     361 .. 0.91
   6 !   18.0   0.1   6.7e-06    0.0029      68     122 ..     371     425 ..     363     429 .. 0.92
   7 !   10.4   0.0    0.0015      0.65      61     122 ..     432     493 ..     428     502 .. 0.93
   8 !   16.3   0.0   2.2e-05    0.0097      75     125 ..     548     598 ..     536     611 .. 0.89
   9 ?    3.9   0.1      0.15        67     104     124 ..     639     659 ..     609     665 .. 0.73
  10 ?    5.6   0.2     0.047        20      70     123 ..     639     692 ..     634     697 .. 0.77
  11 ?    0.1   0.0       2.3     1e+03      74     122 ..     677     725 ..     666     733 .. 0.83
  12 !    9.2   0.6    0.0035       1.5      61     123 ..     732     794 ..     705     800 .. 0.91
  13 !   11.1   0.7   0.00089      0.39      52     122 ..     825     895 ..     803     898 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.45
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       + lGr +eal+  ++ ++ +P +   +      l+ +G   eA+  Y+r+++
  gi|386002707|ref|YP_005921006.1|  70 SDLGRLDEALSCFNRSLEIDPQDPHIWYSKGFVLYGLGIYDEAIDCYDRAME 121
                                       679*********************************************9986 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                              BTAD  66 ealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                       +a+  a+ +lGr+eea++ +++++  +P + +l+ q  +Al+ +Gr ++A+e Y+
  gi|386002707|ref|YP_005921006.1| 131 RARGLALYSLGRYEEAVRSYDEAIVFDPAQGDLWYQKGLALCGLGRYEKAIESYD 185
                                       56777999**********************************************7 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.15
                                       HHHHHTT-HHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlr 123
                                       +Al+ +Gr +eA+  Y+r+ 
  gi|386002707|ref|YP_005921006.1| 203 LALYSLGRAEEAIDCYDRAI 222
                                       799***********999975 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.2e-05
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       a+ +lGr+eea + ++a+v+ +Pl   ++    +A + +Gr +eA+  Y+r+ 
  gi|386002707|ref|YP_005921006.1| 238 ALYALGRHEEAFKCYDAAVEIDPLYHPAWFNKGLAFYSLGRVEEAIDCYDRAI 290
                                       5679*********************************************9985 PP

  == domain 5  score: 19.2 bits;  conditional E-value: 3e-06
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  65 lealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                            +a+ +lGr +ea++ ++++v+ +P   + +  l   l r+Gr +eALe+Y+rl 
  gi|386002707|ref|YP_005921006.1| 300 WNNKGNALYALGRFDEAQECYRRAVEIDPEYSNPWYNLGVVLQRLGRGEEALEAYDRLI 358
                                       556678999***********************************************986 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       +  a+ +lGr++ea++ +++ ++ +P + + +    +Al  +Gr +eAL  Y+++
  gi|386002707|ref|YP_005921006.1| 371 RGLALYSLGRYDEAAGCYDRVLEIDPENGDVWYDKALALGSLGRYEEALDCYDEA 425
                                       6668899*********************************************987 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  61 rlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       r e+l  +++ + +l+r++e ++ + + +  +P  E+++     Al+ +Gr +eA + Y ++
  gi|386002707|ref|YP_005921006.1| 432 RPEVLNNRCNILYSLERYNESVGCYGDVIGIDPGYENAWYNRGVALYTLGRYEEASASYGEA 493
                                       557899999*************************************************9877 PP

  == domain 8  score: 16.3 bits;  conditional E-value: 2.2e-05
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                         r eea++  ++ ++ +P  E  +r+  +Al+++Gr  eA+  Y+++ ++
  gi|386002707|ref|YP_005921006.1| 548 ASRLEEAVESFDEVIEIDPSYEGVWRLKGLALYALGRSDEAIDCYDEALEI 598
                                       56899*****************************************98776 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.15
                                       HHHHHTT-HHHHHHHHHHHHH CS
                              BTAD 104 rAlarsGrqaeALevYerlrr 124
                                       +Al+ +Gr  eA+e Ye++ +
  gi|386002707|ref|YP_005921006.1| 639 EALYSLGRYDEAIECYEKVLE 659
                                       688999999999999988755 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.047
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                       ea+ +lGr++ea++ +e+ ++  Pl  +++ q  +A   +G+ +   e Y+r++
  gi|386002707|ref|YP_005921006.1| 639 EALYSLGRYDEAIECYEKVLEVSPLEAKAWYQKGLAHQILGDYERSAECYDRVV 692
                                       677888888888888888888888888888888888777777777777777765 PP

  == domain 11  score: 0.1 bits;  conditional E-value: 2.3
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                        lG++e+ ++ +++ v+ +P  E+        l r+G+   AL+ Y+ +
  gi|386002707|ref|YP_005921006.1| 677 ILGDYERSAECYDRVVEIDPGYEEVILRRGFVLLRLGDYDGALASYDLA 725
                                       5788999999999999999999999988888999999999999999765 PP

  == domain 12  score: 9.2 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                              BTAD  61 rlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                        lea + + ea+l+lGr eea a+ ++++a+   +  ++    +Ala + r  eA+  Y+r+ 
  gi|386002707|ref|YP_005921006.1| 732 DLEAARGRGEALLALGRFEEASATFDRILANASEDGGAWHGRGLALAGLLRYDEAIDSYDRAI 794
                                       6899999****************************************************9986 PP

  == domain 13  score: 11.1 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  52 aererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       +++ +l+++  ea   + +a+++ Gr e+a+a  ++++a++P   ++ r       ++Gr +eA++ Ye +
  gi|386002707|ref|YP_005921006.1| 825 DRAIALDQEDPEAWSMRGRALMKAGRLEDAAASFDRAIALDPSSGEAQRGRGSVFEAQGRAEEAIGCYEAA 895
                                       4566788888899999999**************************9999999999999*******999986 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05    0.0051     205     262 ..      38      95 ..      32      99 .. 0.94
   2 ?    4.8   0.0     0.024        11     204     259 ..     139     194 ..     113     196 .. 0.90
   3 !   12.1   0.0   0.00015     0.065     204     256 ..     207     259 ..     197     261 .. 0.92
   4 !   10.8   0.0   0.00038      0.17     204     256 ..     275     327 ..     265     330 .. 0.89
   5 !    6.9   0.0    0.0056       2.5      21     102 ..     348     428 ..     339     432 .. 0.64
   6 ?    2.5   0.0      0.13        55      16      77 ..     411     474 ..     401     500 .. 0.76
   7 ?   -2.5   0.0         4   1.8e+03     206     256 ..     515     565 ..     509     568 .. 0.82
   8 !    6.5   0.0    0.0077       3.3     205     257 ..     582     634 ..     570     637 .. 0.91
   9 ?    5.0   0.1     0.022       9.6      44     244 ..     637     683 ..     634     697 .. 0.53
  10 !   10.9   0.0   0.00035      0.15       5      71 ..     700     766 ..     696     773 .. 0.91
  11 !    7.9   0.0    0.0029       1.3     206     280 ..     781     855 ..     776     858 .. 0.88
  12 ?    3.8   0.0     0.051        22     205     256 ..     848     899 ..     842     901 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHH CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyi 262
                                        +s++ Al y++k ++ +p   + +  K+ il   G l++A ++ +++ ++D +D +i
  gi|386002707|ref|YP_005921006.1|  38 NESYDLALLYVNKSLDIDPAYPDAWSLKGYILSDLGRLDEALSCFNRSLEIDPQDPHI 95 
                                       57899**************************************************887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        lg++e+A++  d+ai  +p   +l+++K+  l   G  +kA+e  + a  +D  D
  gi|386002707|ref|YP_005921006.1| 139 SLGRYEEAVRSYDEAIVFDPAQGDLWYQKGLALCGLGRYEKAIESYDFAITIDGDD 194
                                       5789*******************************************999999887 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00015
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        lg+ e+A+++ d+ai+ +p+l++++++K+  l   G  ++A ++ + a ++D
  gi|386002707|ref|YP_005921006.1| 207 SLGRAEEAIDCYDRAIDIDPSLTDVWYNKGIALYALGRHEEAFKCYDAAVEID 259
                                       478899******************************************99988 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00038
                                       HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        lg++e+A+++ d+ai+ +p+lv ++ +K++ l   G +++A e+  +a ++D
  gi|386002707|ref|YP_005921006.1| 275 SLGRVEEAIDCYDRAIDIDPSLVAVWNNKGNALYALGRFDEAQECYRRAVEID 327
                                       5788999************************************9999998888 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHH CS
                             NARP1  21 eeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalyd 97 
                                       eeAle  ++  +   +  +   +++  l  Lgr++eA+  y + le  pen + + +   a++ s +  e+ l++yd
  gi|386002707|ref|YP_005921006.1| 348 EEALEAYDRLIEIDPNLSEAWYNRGLALYSLGRYDEAAGCYDRVLEIDPENGDVWYDKALALG-SLGRYEEALDCYD 423
                                       555544444333333333445578888999999999999999999999999876655555555.3445677888888 PP

                                       HTTTS CS
                             NARP1  98 elaek 102
                                       e+ e+
  gi|386002707|ref|YP_005921006.1| 424 EALEA 428
                                       77665 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.13
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T..T-CHHHHH CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernp..enskYyeg 77 
                                         g++eeAl+  +e+ +    + +v++++ ++l  L+r++e+   y + +   p  en  Y +g
  gi|386002707|ref|YP_005921006.1| 411 SLGRYEEALDCYDEALEAGPRRPEVLNNRCNILYSLERYNESVGCYGDVIGIDPgyENAWYNRG 474
                                       5688899999999988888899999999999999999999999999998877653355555555 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 4
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       g +++A+e  d ai+  p    ++++++ +l  a  l++A+e  +e  ++D
  gi|386002707|ref|YP_005921006.1| 515 GIYDRAVEAYDGAIALYPGDPAVWYNRGLLLYNASRLEEAVESFDEVIEID 565
                                       567889999999999999999999999999999999999999888877776 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.0077
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                                       lg+ ++A+++ d+a+e +p+ v l+++++ +l   G   +A+e  ++  +lD+
  gi|386002707|ref|YP_005921006.1| 582 LGRSDEAIDCYDEALEISPSEVSLWYNRGVVLFSLGRYGEAIESYDRVIELDR 634
                                       68899*****************************************9999996 PP

  == domain 9  score: 5.0 bits;  conditional E-value: 0.022
                                       HHHHHHHTT-HHHHHHHHHHHHHH-T.T-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SHHHHTHHHH--H CS
                             NARP1  44 kaelllkLgrkeeAeatyeaLlernp.enskYyeglekakklskedeeallalydelaekyprsdaprRlpLdfleG 119
                                       k+e l  Lgr++eA + ye+ le  p e +++y+                                           
  gi|386002707|ref|YP_005921006.1| 637 KGEALYSLGRYDEAIECYEKVLEVSPlEAKAWYQ------------------------------------------- 670
                                       6677777777777777777777776633344333........................................... PP

                                       HHHHHHHHHHHHHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTTTTSSSSTTGG.GSS----SSHHHHHHH CS
                             NARP1 120 eeFkelvdkYlrkaLrkgvPslfanlksLYedkeKvkileelvegyvkslktsgklsesdnedsekepesallwvly 196
                                                                                                                    
  gi|386002707|ref|YP_005921006.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHH CS
                             NARP1 197 flAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkk 244
                                                                          K+  ++  Gd ++
  gi|386002707|ref|YP_005921006.1| 671 -----------------------------------KGLAHQILGDYER 683
                                       ...................................3333333333333 PP

  == domain 10  score: 10.9 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                             NARP1   5 ellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                       e++L +  ++   g+++ Al+  + + ++  D l+    ++e ll+Lgr+eeA+at+ ++l   +e+
  gi|386002707|ref|YP_005921006.1| 700 EVILRRGFVLLRLGDYDGALASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRILANASED 766
                                       67777888899999***********99*********************************9988875 PP

  == domain 11  score: 7.9 bits;  conditional E-value: 0.0029
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHTT-HHHHH CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcakymLradeveeAe 280
                                        ++++A++  d+ai+ + +   l++ ++ +l+ aG l++A++  ++a +lD++D    s   + +++a++ e A+
  gi|386002707|ref|YP_005921006.1| 781 LRYDEAIDSYDRAIAINSSDNLLWIGRGGVLEEAGRLEDAVASFDRAIALDQEDPEAWSMRGRALMKAGRLEDAA 855
                                       67999**********9999999********************************888888888888888877775 PP

  == domain 12  score: 3.8 bits;  conditional E-value: 0.051
                                       HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                        g+ e A    d+ai+ +p++ e +  ++ +++ +G  ++A+ + e a +lD
  gi|386002707|ref|YP_005921006.1| 848 AGRLEDAAASFDRAIALDPSSGEAQRGRGSVFEAQGRAEEAIGCYEAAIALD 899
                                       5678899999************************************999998 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00084      0.37      76     129 ..      73     122 ..      59     125 .. 0.90
   2 !   10.8   0.0   0.00089      0.39      64     126 ..     136     187 ..     129     190 .. 0.85
   3 ?    6.6   0.0     0.017       7.6      64     127 ..     170     222 ..     168     227 .. 0.74
   4 !   10.2   0.0    0.0013      0.58      66     129 ..     206     258 ..     188     260 .. 0.69
   5 ?    4.7   0.0     0.067        29     102     127 ..     265     290 ..     259     294 .. 0.88
   6 ?    7.1   0.0     0.012       5.2     100     129 ..     297     326 ..     293     332 .. 0.88
   7 !    8.1   0.0    0.0061       2.7      77     129 ..     346     394 ..     330     405 .. 0.75
   8 !    7.7   0.0    0.0077       3.4     105     128 ..     404     427 ..     393     442 .. 0.62
   9 ?    4.1   0.0       0.1        45     102     127 ..     469     494 ..     465     503 .. 0.86
  10 ?   -0.8   0.0       3.4   1.5e+03      55      83 ..     501     529 ..     489     533 .. 0.76
  11 ?   -1.9   0.0       7.3   3.2e+03     102     129 ..     537     564 ..     535     571 .. 0.86
  12 ?    3.5   0.0      0.16        70     106     129 ..     575     598 ..     570     601 .. 0.89
  13 ?    5.5   0.0     0.038        17     103     136 ..     606     639 ..     601     640 .. 0.88
  14 ?    5.9   0.0     0.029        13     104     128 ..     635     659 ..     633     666 .. 0.86
  15 ?    2.1   0.2      0.44   1.9e+02      66      83 ..     710     727 ..     702     774 .. 0.68
  16 ?    3.3   0.1      0.18        81      98     126 ..     769     793 ..     731     797 .. 0.57
  17 ?    6.7   0.1     0.016       7.1      63     127 ..     775     828 ..     764     835 .. 0.76
  18 ?    3.8   0.2      0.13        55      79     127 ..     818     862 ..     810     873 .. 0.84
  19 ?    1.3   0.2      0.75   3.3e+02     106     127 ..     841     862 ..     829     898 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  76 esadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                          d+al  fnr  e++ ++ ++W    +s++  l +lG +dea++ +  a e 
  gi|386002707|ref|YP_005921006.1|  73 GRLDEALSCFNRSLEIDPQDPHIW----YSKGFVLYGLGIYDEAIDCYDRAMEF 122
                                       56799*******************....79*******************99985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00089
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       al  lgry+ea++s d+a+ +       + ++G lW    ++++ al +lGr+++a++++  a
  gi|386002707|ref|YP_005921006.1| 136 ALYSLGRYEEAVRSYDEAIVF-------DPAQGDLW----YQKGLALCGLGRYEKAIESYDFA 187
                                       7899**************987.......55677788....68999999999999999999876 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.017
                                       HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       al++lgry++a+es d a+        ++ d+   W      +a al +lGr +ea++ +  a 
  gi|386002707|ref|YP_005921006.1| 170 ALCGLGRYEKAIESYDFAIT-------IDGDDAASW----HGKALALYSLGRAEEAIDCYDRAI 222
                                       67778888888888777774.......566676667....568999999999999999888775 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0013
                                       HHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  66 aklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         lgr       a++a+  ++r  +++      W    ++++ al  lGr++ea+k +  a+e+
  gi|386002707|ref|YP_005921006.1| 206 YSLGR-------AEEAIDCYDRAIDIDPSLTDVW----YNKGIALYALGRHEEAFKCYDAAVEI 258
                                       44444.......4444444555556666666666....89*******************99985 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a f+++ a+ +lGr +ea++ +  a 
  gi|386002707|ref|YP_005921006.1| 265 AWFNKGLAFYSLGRVEEAIDCYDRAI 290
                                       679*****************999886 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 100 iaavfsravaleelGrkdealkafrmagem 129
                                       +a+  +++ al  lGr dea + +r a+e+
  gi|386002707|ref|YP_005921006.1| 297 VAVWNNKGNALYALGRFDEAQECYRRAVEI 326
                                       566779*********************997 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0061
                                       HHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856  77 sadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                         ++al+ ++r  e++ +  + W    ++r+ al +lGr+dea   +  + e+
  gi|386002707|ref|YP_005921006.1| 346 RGEEALEAYDRLIEIDPNLSEAW----YNRGLALYSLGRYDEAAGCYDRVLEI 394
                                       55667777777777777666666....89*****************9999885 PP

  == domain 8  score: 7.7 bits;  conditional E-value: 0.0077
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkafrmage 128
                                       ++a al +lGr++eal+ +  a e
  gi|386002707|ref|YP_005921006.1| 404 DKALALGSLGRYEEALDCYDEALE 427
                                       566666666666666666655554 PP

  == domain 9  score: 4.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                       a ++r+val  lGr++ea  ++  a+
  gi|386002707|ref|YP_005921006.1| 469 AWYNRGVALYTLGRYEEASASYGEAA 494
                                       6689**************99997765 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalr 83 
                                         ++ g+ +a+a  g yd a+e+ d a+ 
  gi|386002707|ref|YP_005921006.1| 501 VDAWVGMGDAFAAAGIYDRAVEAYDGAIA 529
                                       45678899999999999999999888765 PP

  == domain 11  score: -1.9 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                       + ++r+  l +  r +ea+++f  + e+
  gi|386002707|ref|YP_005921006.1| 537 VWYNRGLLLYNASRLEEAVESFDEVIEI 564
                                       5689999999999*******99988875 PP

  == domain 12  score: 3.5 bits;  conditional E-value: 0.16
                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmagem 129
                                       ++ al  lGr+dea++ +  a e+
  gi|386002707|ref|YP_005921006.1| 575 KGLALYALGRSDEAIDCYDEALEI 598
                                       7899**************999885 PP

  == domain 13  score: 5.5 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S- CS
                           DUF3856 103 vfsravaleelGrkdealkafrmagemiaerkGe 136
                                        ++r+v l +lGr+ ea++++  + e+    kGe
  gi|386002707|ref|YP_005921006.1| 606 WYNRGVVLFSLGRYGEAIESYDRVIELDRYEKGE 639
                                       589**********************998888887 PP

  == domain 14  score: 5.9 bits;  conditional E-value: 0.029
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 104 fsravaleelGrkdealkafrmage 128
                                       ++++ al +lGr+dea++ ++++ e
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLE 659
                                       5789999999999999999998877 PP

  == domain 15  score: 2.1 bits;  conditional E-value: 0.44
                                       HHTT-HHHHHHHHHHHHH CS
                           DUF3856  66 aklgrydealesadkalr 83 
                                       ++lg+yd al s d al+
  gi|386002707|ref|YP_005921006.1| 710 LRLGDYDGALASYDLALQ 727
                                       678888888888887775 PP

  == domain 16  score: 3.3 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  98 lWiaavfsravaleelGrkdealkafrma 126
                                        W      r+ al++l r+dea++++  a
  gi|386002707|ref|YP_005921006.1| 769 AW----HGRGLALAGLLRYDEAIDSYDRA 793
                                       34....34566666666666666655544 PP

  == domain 17  score: 6.7 bits;  conditional E-value: 0.016
                                       HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                        ala+l rydea+ s d+a+        +++ +  lWi     r+  lee Gr ++a+ +f  a 
  gi|386002707|ref|YP_005921006.1| 775 LALAGLLRYDEAIDSYDRAI-------AINSSDNLLWIG----RGGVLEEAGRLEDAVASFDRAI 828
                                       47788888888888877776.......467788889984....8899999999999999988775 PP

  == domain 18  score: 3.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                       + a+  f+r   l+q++ + W      r++al + Gr ++a  +f  a 
  gi|386002707|ref|YP_005921006.1| 818 EDAVASFDRAIALDQEDPEAWS----MRGRALMKAGRLEDAAASFDRAI 862
                                       5678889999999999999994....699************99998875 PP

  == domain 19  score: 1.3 bits;  conditional E-value: 0.75
                                       HHHHHHHTT-HHHHHHHHHHHH CS
                           DUF3856 106 ravaleelGrkdealkafrmag 127
                                       r++al + Gr ++a  +f  a 
  gi|386002707|ref|YP_005921006.1| 841 RGRALMKAGRLEDAAASFDRAI 862
                                       5566666666666666665543 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.14        59       5      23 ..      63      81 ..      59      84 .. 0.78
   2 ?    7.3   0.1     0.021         9       5      24 ..     131     150 ..     127     152 .. 0.85
   3 ?    4.3   0.3      0.19        84       3      23 ..     197     217 ..     195     220 .. 0.80
   4 ?    7.6   0.0     0.016       6.9       5      20 ..     233     248 ..     231     248 .. 0.90
   5 ?   -0.9   0.0       8.9   3.9e+03       6      23 ..     268     285 ..     264     288 .. 0.73
   6 !   12.3   0.0   0.00048      0.21       7      26 .]     303     322 ..     298     322 .. 0.89
   7 !   13.0   0.1    0.0003      0.13       5      26 .]     335     356 ..     333     356 .. 0.91
   8 !    9.5   0.1    0.0039       1.7       3      22 ..     367     386 ..     365     390 .. 0.86
   9 ?    6.3   0.0     0.043        19       5      25 ..     403     423 ..     400     424 .. 0.85
  10 !    9.0   0.0    0.0057       2.5       3      21 ..     469     487 ..     468     492 .. 0.90
  11 ?   -0.7   0.0       7.7   3.4e+03       1      23 [.     535     557 ..     535     560 .. 0.83
  12 ?    6.7   0.0     0.031        14       8      22 ..     576     590 ..     571     594 .. 0.82
  13 ?    3.7   0.0      0.29   1.3e+02       4      20 ..     606     622 ..     603     628 .. 0.86
  14 ?    5.0   0.0      0.11        49       7      24 ..     637     654 ..     634     656 .. 0.81
  15 ?   -0.3   0.0       5.8   2.5e+03       4      25 ..     668     689 ..     665     690 .. 0.78
  16 ?    7.8   0.1     0.014       6.2       7      22 ..     705     720 ..     703     723 .. 0.88
  17 !   13.2   2.8   0.00026      0.11       2      26 .]     734     758 ..     733     758 .. 0.91
  18 ?    2.9   0.3      0.54   2.4e+02       5      26 .]     805     826 ..     802     826 .. 0.82
  19 !   10.6   0.3    0.0018      0.77       1      26 []     835     860 ..     835     860 .. 0.89
  20 ?    1.3   0.1       1.7   7.4e+02       3      20 ..     871     888 ..     869     893 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.14
                             TPR_4  5 laLArallalGdldeAral 23
                                      ++ +  l +lG+ldeA+  
  gi|386002707|ref|YP_005921006.1| 63 SLKGYILSDLGRLDEALSC 81
                                      566778999*******975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.021
                             TPR_4   5 laLArallalGdldeArall 24 
                                        a++ al+ lG+++eA +  
  gi|386002707|ref|YP_005921006.1| 131 RARGLALYSLGRYEEAVRSY 150
                                       6899************9865 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.19
                             TPR_4   3 allaLArallalGdldeAral 23 
                                         ++ A al+ lG+++eA + 
  gi|386002707|ref|YP_005921006.1| 197 SWHGKALALYSLGRAEEAIDC 217
                                       567789************665 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.016
                             TPR_4   5 laLArallalGdldeA 20 
                                       ++ + al+alG+++eA
  gi|386002707|ref|YP_005921006.1| 233 YNKGIALYALGRHEEA 248
                                       78899**********9 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 8.9
                             TPR_4   6 aLArallalGdldeAral 23 
                                       + + a + lG+ +eA + 
  gi|386002707|ref|YP_005921006.1| 268 NKGLAFYSLGRVEEAIDC 285
                                       566777789*****9665 PP

  == domain 6  score: 12.3 bits;  conditional E-value: 0.00048
                             TPR_4   7 LArallalGdldeAraller 26 
                                        + al+alG++deA++  +r
  gi|386002707|ref|YP_005921006.1| 303 KGNALYALGRFDEAQECYRR 322
                                       588*************9997 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 0.0003
                             TPR_4   5 laLArallalGdldeAraller 26 
                                       ++L+ +l++lG+ +eA+++ +r
  gi|386002707|ref|YP_005921006.1| 335 YNLGVVLQRLGRGEEALEAYDR 356
                                       89***************99876 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0039
                             TPR_4   3 allaLArallalGdldeAra 22 
                                       a ++++ al+ lG++deA+ 
  gi|386002707|ref|YP_005921006.1| 367 AWYNRGLALYSLGRYDEAAG 386
                                       889***************85 PP

  == domain 9  score: 6.3 bits;  conditional E-value: 0.043
                             TPR_4   5 laLArallalGdldeAralle 25 
                                       ++ A al  lG+++eA++  +
  gi|386002707|ref|YP_005921006.1| 403 YDKALALGSLGRYEEALDCYD 423
                                       66799************9876 PP

  == domain 10  score: 9.0 bits;  conditional E-value: 0.0057
                             TPR_4   3 allaLArallalGdldeAr 21 
                                       a ++++ al+ lG+++eA 
  gi|386002707|ref|YP_005921006.1| 469 AWYNRGVALYTLGRYEEAS 487
                                       679***************5 PP

  == domain 11  score: -0.7 bits;  conditional E-value: 7.7
                             TPR_4   1 arallaLArallalGdldeAral 23 
                                       +++ ++++ +l+ + +l+eA + 
  gi|386002707|ref|YP_005921006.1| 535 PAVWYNRGLLLYNASRLEEAVES 557
                                       5678999999999999***9875 PP

  == domain 12  score: 6.7 bits;  conditional E-value: 0.031
                             TPR_4   8 ArallalGdldeAra 22 
                                       + al+alG++deA +
  gi|386002707|ref|YP_005921006.1| 576 GLALYALGRSDEAID 590
                                       88***********65 PP

  == domain 13  score: 3.7 bits;  conditional E-value: 0.29
                             TPR_4   4 llaLArallalGdldeA 20 
                                        ++++ +l+ lG++ eA
  gi|386002707|ref|YP_005921006.1| 606 WYNRGVVLFSLGRYGEA 622
                                       689*************9 PP

  == domain 14  score: 5.0 bits;  conditional E-value: 0.11
                             TPR_4   7 LArallalGdldeArall 24 
                                        ++al+ lG++deA +  
  gi|386002707|ref|YP_005921006.1| 637 KGEALYSLGRYDEAIECY 654
                                       589***********7665 PP

  == domain 15  score: -0.3 bits;  conditional E-value: 5.8
                             TPR_4   4 llaLArallalGdldeAralle 25 
                                        +  + a++ lGd+++ ++  +
  gi|386002707|ref|YP_005921006.1| 668 WYQKGLAHQILGDYERSAECYD 689
                                       56678999******99877665 PP

  == domain 16  score: 7.8 bits;  conditional E-value: 0.014
                             TPR_4   7 LArallalGdldeAra 22 
                                       ++ +ll+lGd+d A+a
  gi|386002707|ref|YP_005921006.1| 705 RGFVLLRLGDYDGALA 720
                                       6889**********98 PP

  == domain 17  score: 13.2 bits;  conditional E-value: 0.00026
                             TPR_4   2 rallaLArallalGdldeAraller 26 
                                        a+ ++++allalG+++eA a+++r
  gi|386002707|ref|YP_005921006.1| 734 EAARGRGEALLALGRFEEASATFDR 758
                                       58899**************999886 PP

  == domain 18  score: 2.9 bits;  conditional E-value: 0.54
                             TPR_4   5 laLArallalGdldeAraller 26 
                                       ++++ +l ++G+l++A a ++r
  gi|386002707|ref|YP_005921006.1| 805 IGRGGVLEEAGRLEDAVASFDR 826
                                       567778999*******997765 PP

  == domain 19  score: 10.6 bits;  conditional E-value: 0.0018
                             TPR_4   1 arallaLArallalGdldeAraller 26 
                                       + a ++++ral  +G+l++A+a ++r
  gi|386002707|ref|YP_005921006.1| 835 PEAWSMRGRALMKAGRLEDAAASFDR 860
                                       57899****************97765 PP

  == domain 20  score: 1.3 bits;  conditional E-value: 1.7
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a+ +++ +  a+G+++eA
  gi|386002707|ref|YP_005921006.1| 871 AQRGRGSVFEAQGRAEEA 888
                                       66677777789******9 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00034      0.15       8      44 ..      32      68 ..      31      74 .. 0.94
   2 ?    1.6   0.0      0.66   2.9e+02      14      33 ..      72      91 ..      70      93 .. 0.92
   3 ?   -1.7   0.0       7.1   3.1e+03      12      29 ..     104     121 ..     103     123 .. 0.85
   4 ?    3.0   0.0      0.24   1.1e+02       9      32 ..     135     158 ..     133     160 .. 0.82
   5 ?    0.8   0.0       1.2   5.2e+02       3      25 ..     163     185 ..     162     194 .. 0.80
   6 ?    0.1   0.0         2   8.5e+02       8      33 ..     202     227 ..     201     231 .. 0.92
   7 !    9.5   0.1    0.0022      0.98       2      34 ..     230     262 ..     229     266 .. 0.90
   8 ?   -1.6   0.0       6.9     3e+03       9      33 ..     271     295 ..     267     296 .. 0.88
   9 ?    4.7   0.1     0.072        32      10      34 ..     306     330 ..     304     333 .. 0.91
  10 ?    6.6   0.0     0.019       8.3       5      36 ..     335     366 ..     331     368 .. 0.89
  11 !   19.7   0.1   1.6e-06   0.00068       2      35 ..     366     399 ..     365     402 .. 0.93
  12 ?    5.7   0.1     0.037        16       8      33 ..     406     431 ..     399     437 .. 0.82
  13 ?    2.8   0.1      0.28   1.2e+02       4      20 ..     470     486 ..     467     489 .. 0.89
  14 ?   -0.4   0.0       2.9   1.3e+03      12      41 ..     546     575 ..     538     584 .. 0.82
  15 ?   -0.6   0.0       3.4   1.5e+03       9      33 ..     577     601 ..     574     602 .. 0.90
  16 ?    6.2   0.0     0.026        11      10      32 ..     640     662 ..     635     668 .. 0.91
  17 !   10.6   0.0     0.001      0.45       4      35 ..     668     699 ..     665     702 .. 0.90
  18 !    8.2   0.0     0.006       2.6      12      38 ..     710     736 ..     708     737 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                                      HHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
                        Fis1_TPR_C  8 AlGhyklgeYseArryvdalLeiEPenrQaqsLkeli 44
                                      A+G y    Y+ A+ yv+  L i+P    a sLk +i
  gi|386002707|ref|YP_005921006.1| 32 AIGFYSNESYDLALLYVNKSLDIDPAYPDAWSLKGYI 68
                                      8999******************************998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.66
                                      HT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                                      lg+ +eA+ + ++ Lei+P+
  gi|386002707|ref|YP_005921006.1| 72 LGRLDEALSCFNRSLEIDPQ 91
                                      7899***************8 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.1
                                       HHHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLe 29 
                                       y lg Y+eA  + d+ +e
  gi|386002707|ref|YP_005921006.1| 104 YGLGIYDEAIDCYDRAME 121
                                       78999****999999886 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.24
                                       HHHHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEP 32 
                                       l+ y lg+Y+eA r  d  +  +P
  gi|386002707|ref|YP_005921006.1| 135 LALYSLGRYEEAVRSYDEAIVFDP 158
                                       899**********98887766555 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHT-HHHHHHHHH CS
                        Fis1_TPR_C   3 clYylAlGhyklgeYseArryvd 25 
                                         Y+  l+   lg+Y++A +  d
  gi|386002707|ref|YP_005921006.1| 163 LWYQKGLALCGLGRYEKAIESYD 185
                                       5699999***********87665 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 2
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPe 33 
                                       Al+ y lg+ +eA  + d+ + i+P+
  gi|386002707|ref|YP_005921006.1| 202 ALALYSLGRAEEAIDCYDRAIDIDPS 227
                                       8999********************97 PP

  == domain 7  score: 9.5 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPen 34 
                                       +  Y   ++ y lg+++eA ++ da  ei+P  
  gi|386002707|ref|YP_005921006.1| 230 DVWYNKGIALYALGRHEEAFKCYDAAVEIDPLY 262
                                       6779999************************76 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 6.9
                                       HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                       l+ y lg+ +eA  + d+ + i+P+
  gi|386002707|ref|YP_005921006.1| 271 LAFYSLGRVEEAIDCYDRAIDIDPS 295
                                       788999999*************996 PP

  == domain 9  score: 4.7 bits;  conditional E-value: 0.072
                                       HHHHHT-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEPen 34 
                                       + y lg+++eA ++ ++  ei+Pe 
  gi|386002707|ref|YP_005921006.1| 306 ALYALGRFDEAQECYRRAVEIDPEY 330
                                       6789*******************96 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPenrQ 36 
                                       Y l +   +lg+ +eA++  d+l+ei+P+ + 
  gi|386002707|ref|YP_005921006.1| 335 YNLGVVLQRLGRGEEALEAYDRLIEIDPNLSE 366
                                       88888899********************9765 PP

  == domain 11  score: 19.7 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPenr 35 
                                       e  Y   l+ y lg+Y+eA  + d++Lei+Pen 
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYDRVLEIDPENG 399
                                       67899***************************95 PP

  == domain 12  score: 5.7 bits;  conditional E-value: 0.037
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPe 33 
                                       Al+   lg+Y+eA+ + d  Le  P+
  gi|386002707|ref|YP_005921006.1| 406 ALALGSLGRYEEALDCYDEALEAGPR 431
                                       6777779**************99886 PP

  == domain 13  score: 2.8 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHT-HHHH CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseA 20 
                                        Y   ++ y lg+Y+eA
  gi|386002707|ref|YP_005921006.1| 470 WYNRGVALYTLGRYEEA 486
                                       6999************9 PP

  == domain 14  score: -0.4 bits;  conditional E-value: 2.9
                                       HHHT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaqsLk 41 
                                       y   + +eA +  d ++ei+P+ + +  Lk
  gi|386002707|ref|YP_005921006.1| 546 YNASRLEEAVESFDEVIEIDPSYEGVWRLK 575
                                       6677889999999********988777776 PP

  == domain 15  score: -0.6 bits;  conditional E-value: 3.4
                                       HHHHHHT-HHHHHHHHHHHHHHTTS CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                       l+ y lg+ +eA  + d  Lei P+
  gi|386002707|ref|YP_005921006.1| 577 LALYALGRSDEAIDCYDEALEISPS 601
                                       788999999*************995 PP

  == domain 16  score: 6.2 bits;  conditional E-value: 0.026
                                       HHHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiEP 32 
                                       + y lg+Y+eA ++ + +Le+ P
  gi|386002707|ref|YP_005921006.1| 640 ALYSLGRYDEAIECYEKVLEVSP 662
                                       6799*****************99 PP

  == domain 17  score: 10.6 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPenr 35 
                                        Y+  l+h  lg+Y+++ ++ d++ ei+P+ +
  gi|386002707|ref|YP_005921006.1| 668 WYQKGLAHQILGDYERSAECYDRVVEIDPGYE 699
                                       588999***********************976 PP

  == domain 18  score: 8.2 bits;  conditional E-value: 0.006
                                       HHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaq 38 
                                       ++lg+Y+ A+   d  L+ +P+   a+
  gi|386002707|ref|YP_005921006.1| 710 LRLGDYDGALASYDLALQEDPDDLEAA 736
                                       69********************99885 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.092        40       4      25 ..      96     117 ..      95     119 .. 0.92
   2 ?    3.6   0.0      0.15        67       8      24 ..     134     150 ..     132     154 .. 0.87
   3 ?    6.7   0.0     0.016         7      15      33 ..     175     191 ..     173     194 .. 0.87
   4 ?    6.3   0.0     0.022       9.8       4      25 ..     198     219 ..     196     225 .. 0.89
   5 ?    3.6   0.0      0.15        67       8      25 ..     270     287 ..     266     293 .. 0.91
   6 ?    2.3   0.0       0.4   1.8e+02      10      34 ..     306     328 ..     304     329 .. 0.84
   7 ?    6.1   0.0     0.025        11       2      34 ..     332     362 ..     331     364 .. 0.85
   8 !   10.4   0.0    0.0012       0.5       2      28 ..     366     391 ..     365     398 .. 0.79
   9 ?    1.4   0.1      0.76   3.3e+02      13      25 ..     411     423 ..     400     426 .. 0.77
  10 ?   -0.1   0.1       2.2   9.5e+02       5      20 ..     471     486 ..     468     496 .. 0.78
  11 ?   -1.9   0.4         8   3.5e+03      15      25 ..     515     525 ..     510     531 .. 0.72
  12 ?   -2.0   0.0       8.9   3.9e+03       8      25 ..     542     559 ..     538     559 .. 0.82
  13 ?    1.0   0.0         1   4.5e+02       8      25 ..     576     593 ..     573     598 .. 0.87
  14 ?    1.5   0.0      0.68     3e+02       8      25 ..     610     627 ..     606     629 .. 0.84
  15 !    7.5   0.0    0.0091         4      10      25 ..     640     655 ..     638     658 .. 0.86
  16 ?   -1.0   0.1       4.3   1.9e+03      15      29 ..     713     725 ..     711     727 .. 0.84
  17 ?   -0.8   0.1       3.7   1.6e+03      16      25 ..     782     791 ..     782     799 .. 0.86
  18 ?    1.1   0.0      0.96   4.2e+02      13      33 ..     881     899 ..     876     900 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHTT-HHHHHHH.. CS
                             TPR_3   4 lysyAaefynkkkyqeArelfs 25 
                                       +ys ++++y  + y+eA++ ++
  gi|386002707|ref|YP_005921006.1|  96 WYSKGFVLYGLGIYDEAIDCYD 117
                                       788899*************976 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.15
                                       HHHHHHTT-HHHHHHH. CS
                             TPR_3   8 AaefynkkkyqeArelf 24 
                                       + ++y+ ++y+eA+  +
  gi|386002707|ref|YP_005921006.1| 134 GLALYSLGRYEEAVRSY 150
                                       5789*********9775 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.016
                                       T-HHHHHHH..HHHHHHH- CS
                             TPR_3  15 kkyqeArelfsYallaild 33 
                                       ++y++A+e ++  ++ ++d
  gi|386002707|ref|YP_005921006.1| 175 GRYEKAIESYD--FAITID 191
                                       89*******77..*99998 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHTT-HHHHHHH.. CS
                             TPR_3   4 lysyAaefynkkkyqeArelfs 25 
                                       +++ A ++y+ ++ +eA++ ++
  gi|386002707|ref|YP_005921006.1| 198 WHGKALALYSLGRAEEAIDCYD 219
                                       667799*************976 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.15
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       + +fy+ ++ +eA++ ++
  gi|386002707|ref|YP_005921006.1| 270 GLAFYSLGRVEEAIDCYD 287
                                       679************976 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.4
                                       HHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3  10 efynkkkyqeArelfsYallaildk 34 
                                       ++y  ++++eA e   Y+ +  +d+
  gi|386002707|ref|YP_005921006.1| 306 ALYALGRFDEAQEC--YRRAVEIDP 328
                                       689**********9..988877776 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHTT-HHHHHHH..HHHHHHH-T CS
                             TPR_3   2 dylysyAaefynkkkyqeArelfsYallaildk 34 
                                       + +y ++ +++  ++ +eA+e+++   l  +d+
  gi|386002707|ref|YP_005921006.1| 332 NPWYNLGVVLQRLGRGEEALEAYD--RLIEIDP 362
                                       67********************77..6666665 PP

  == domain 8  score: 10.4 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHTT-HHHHHHH..HHH CS
                             TPR_3   2 dylysyAaefynkkkyqeArelfsYal 28 
                                       + +y  + ++y+ ++y+eA++ ++ ++
  gi|386002707|ref|YP_005921006.1| 366 EAWYNRGLALYSLGRYDEAAGCYD-RV 391
                                       66777899**************88.44 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.76
                                       HTT-HHHHHHH.. CS
                             TPR_3  13 nkkkyqeArelfs 25 
                                       + ++y+eA++ ++
  gi|386002707|ref|YP_005921006.1| 411 SLGRYEEALDCYD 423
                                       679*******976 PP

  == domain 10  score: -0.1 bits;  conditional E-value: 2.2
                                       HHHHHHHHHTT-HHHH CS
                             TPR_3   5 ysyAaefynkkkyqeA 20 
                                       y  + ++y  ++y+eA
  gi|386002707|ref|YP_005921006.1| 471 YNRGVALYTLGRYEEA 486
                                       5557789********9 PP

  == domain 11  score: -1.9 bits;  conditional E-value: 8
                                       T-HHHHHHH.. CS
                             TPR_3  15 kkyqeArelfs 25 
                                       + y+ A+e+++
  gi|386002707|ref|YP_005921006.1| 515 GIYDRAVEAYD 525
                                       55888888866 PP

  == domain 12  score: -2.0 bits;  conditional E-value: 8.9
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       +  +yn  +++eA+e f+
  gi|386002707|ref|YP_005921006.1| 542 GLLLYNASRLEEAVESFD 559
                                       67899999******9876 PP

  == domain 13  score: 1.0 bits;  conditional E-value: 1
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       + ++y  ++ +eA++ ++
  gi|386002707|ref|YP_005921006.1| 576 GLALYALGRSDEAIDCYD 593
                                       568999*********976 PP

  == domain 14  score: 1.5 bits;  conditional E-value: 0.68
                                       HHHHHHTT-HHHHHHH.. CS
                             TPR_3   8 AaefynkkkyqeArelfs 25 
                                       + ++++ ++y eA+e ++
  gi|386002707|ref|YP_005921006.1| 610 GVVLFSLGRYGEAIESYD 627
                                       668999*********976 PP

  == domain 15  score: 7.5 bits;  conditional E-value: 0.0091
                                       HHHHTT-HHHHHHH.. CS
                             TPR_3  10 efynkkkyqeArelfs 25 
                                       ++y+ ++y+eA+e + 
  gi|386002707|ref|YP_005921006.1| 640 ALYSLGRYDEAIECYE 655
                                       68***********943 PP

  == domain 16  score: -1.0 bits;  conditional E-value: 4.3
                                       T-HHHHHHH..HHHH CS
                             TPR_3  15 kkyqeArelfsYall 29 
                                       ++y+ A+  ++  l+
  gi|386002707|ref|YP_005921006.1| 713 GDYDGALASYD--LA 725
                                       89*****9976..87 PP

  == domain 17  score: -0.8 bits;  conditional E-value: 3.7
                                       -HHHHHHH.. CS
                             TPR_3  16 kyqeArelfs 25 
                                       +y+eA++ ++
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYD 791
                                       7******976 PP

  == domain 18  score: 1.1 bits;  conditional E-value: 0.96
                                       HTT-HHHHHHH..HHHHHHH- CS
                             TPR_3  13 nkkkyqeArelfsYallaild 33 
                                        +++ +eA++   Y+ + +ld
  gi|386002707|ref|YP_005921006.1| 881 AQGRAEEAIGC--YEAAIALD 899
                                       69*********..88888887 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.045        20      20      97 ..      31     115 ..      23     126 .. 0.67
   2 !    8.1   0.0    0.0057       2.5      13      66 ..     126     182 ..     114     217 .. 0.79
   3 ?    6.0   0.0     0.026        11       5      68 ..     184     252 ..     181     263 .. 0.77
   4 !    8.9   0.0    0.0034       1.5      19      98 ..     232     320 ..     212     332 .. 0.74
   5 !   15.6   0.0   2.8e-05     0.012       3      94 ..     352     452 ..     349     468 .. 0.78
   6 !   11.2   0.0   0.00063      0.28       4      74 ..     387     462 ..     385     506 .. 0.67
   7 ?    1.4   0.0      0.73   3.2e+02      20      37 ..     473     490 ..     462     591 .. 0.70
   8 !   16.5   0.1   1.5e-05    0.0066       3      88 ..     590     671 ..     588     695 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.045
                      SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveaee....kvkvlksqvlYrlg 89 
                                       k++ + + e y+ aL +++k         d    k Y+l  l ++ +al+ +++  + +    ++   k  vlY lg
  gi|386002707|ref|YP_005921006.1|  31 KAIGFYSNESYDLALLYVNKSLdidPAYPDAWSLKGYILSDLGRLDEALSCFNRSLEIDpqdpHIWYSKGFVLYGLG 107
                                       56666677778888888887762222234555668899999999999999998754433311445555777888888 PP

                      SRP_TPR_like  90 syekAYkl 97 
                                        y++A ++
  gi|386002707|ref|YP_005921006.1| 108 IYDEAIDC 115
                                       88888554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0057
                      SRP_TPR_like  13 gkelkkfkvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalk 66 
                                       g+ l + + +al +l++yeea++  +++      ++d+ + k  +l  l +y+ka +
  gi|386002707|ref|YP_005921006.1| 126 GPDLWRARGLALYSLGRYEEAVRSYDEAIvfdPAQGDLWYQKGLALCGLGRYEKAIE 182
                                       5677788999*************9999875556789999999999999999999975 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.026
                      SRP_TPR_like   5 yekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkil 68 
                                       y+  + ++g+    +  k++al +l++ eea+   + +        dv + k  +lY l + ++a k  
  gi|386002707|ref|YP_005921006.1| 184 YDFAITIDGDDAASWhgKALALYSLGRAEEAIDCYDRAIdidPSLTDVWYNKGIALYALGRHEEAFKCY 252
                                       55566666666666666999***********999887762323447899***************99875 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0034
                      SRP_TPR_like  19 f..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveaee.kvkvl...ksqvlY 86 
                                       +  k +al  l+++eea k  + +     l +   f k  ++Y l + ++a    +++ + +  +  +   k   lY
  gi|386002707|ref|YP_005921006.1| 232 WynKGIALYALGRHEEAFKCYDAAVeidPLYHPAWFNKGLAFYSLGRVEEAIDCYDRAIDIDpSLVAVwnnKGNALY 308
                                       35599**************9887763446778889******************999987776533332233678999 PP

                      SRP_TPR_like  87 rlgsyekAYklL 98 
                                        lg +++A ++ 
  gi|386002707|ref|YP_005921006.1| 309 ALGRFDEAQECY 320
                                       999999996655 PP

  == domain 5  score: 15.6 bits;  conditional E-value: 2.8e-05
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveae 74 
                                       e+y+++++++ +  + +  + +al +l++y+ea    +        ++dv ++ka +l  l +y++al   +++ + 
  gi|386002707|ref|YP_005921006.1| 352 EAYDRLIEIDPNLSEAWynRGLALYSLGRYDEAAGCYDRVLeidPENGDVWYDKALALGSLGRYEEALDCYDEALEA 428
                                       6788888887766666567999**********9877665542226789*********************99886554 PP

                      SRP_TPR_like  75 e..kvkvlk..sqvlYrlgsyekA 94 
                                          + +vl+    +lY l+ y++ 
  gi|386002707|ref|YP_005921006.1| 429 GprRPEVLNnrCNILYSLERYNES 452
                                       445777776224679******986 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.00063
                      SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveae 74 
                                       +y+++l+++ ++ + +  k++al +l++yeeaL   +++        +v   +  +lY l++y++++     v + 
  gi|386002707|ref|YP_005921006.1| 387 CYDRVLEIDPENGDVWydKALALGSLGRYEEALDCYDEALeagPRRPEVLNNRCNILYSLERYNESVGCYGDVIGI 462
                                       5888888887777766779999999999999999888766444345667778888888888888877655555444 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.73
                      SRP_TPR_like  20 kvvaliklekyeeaLkll 37 
                                       + val +l++yeea    
  gi|386002707|ref|YP_005921006.1| 473 RGVALYTLGRYEEASASY 490
                                       345555555555554333 PP

  == domain 8  score: 16.5 bits;  conditional E-value: 1.5e-05
                      SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkveaeekv 77 
                                       ++y++ l+++ +e++ +  + v l +l++y ea++  +      e  r+Ek  +lY l +y +a +  +kv ++   
  gi|386002707|ref|YP_005921006.1| 590 DCYDEALEISPSEVSLWynRGVVLFSLGRYGEAIESYDRVI---ELDRYEKGEALYSLGRYDEAIECYEKVLEV--- 660
                                       578999999988888777799************99988877...7789****************9998887655... PP

                      SRP_TPR_like  78 kvlksqvlYrl 88 
                                       + l+++  Y +
  gi|386002707|ref|YP_005921006.1| 661 SPLEAKAWYQK 671
                                       55555555555 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00052      0.23     148     237 ..      61     150 ..      55     170 .. 0.92
   2 !    7.0   0.1    0.0069         3     144     274 ..     193     323 ..     173     326 .. 0.87
   3 !    6.8   0.0     0.008       3.5     149     251 ..     334     436 ..     328     452 .. 0.88
   4 ?   -0.2   0.0       1.1   4.7e+02     142     177 ..     531     566 ..     476     571 .. 0.72
   5 ?    3.9   0.0     0.061        27     127     181 ..     549     604 ..     537     616 .. 0.79
   6 !   10.7   1.1   0.00049      0.21     146     268 ..     699     821 ..     616     823 .. 0.87
   7 !   10.4   0.2   0.00064      0.28     124     183 ..     812     872 ..     809     875 .. 0.90
   8 ?   -1.1   0.0       1.9   8.4e+02     153     178 ..     876     901 ..     873     904 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                            TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgpla 221
                                        +++ + + ++ g+ d+Al ++ + l+ +p++  +     ++l  lg ++e   ++  + ++    ++ ++Lw + +
  gi|386002707|ref|YP_005921006.1|  61 AWSLKGYILSDLGRLDEALSCFNRSLEIDPQDPHIWYSKGFVLYGLGIYDE---AIDCYDRAMefnSTGPDLWRARG 134
                                       68888999999***************************************7...999999887888999******** PP

                            TPR_15 222 aAlllLgrpkkALeyl 237
                                        Al  Lgr+++A + +
  gi|386002707|ref|YP_005921006.1| 135 LALYSLGRYEEAVRSY 150
                                       ************8766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgpl 220
                                       ++aa +   a +    g+ ++A+ +y +A++ +p  +++  +   +l  lgr +e   + k + a+ e d+ ++++ 
  gi|386002707|ref|YP_005921006.1| 193 DDAASWHGKALALYSLGRAEEAIDCYDRAIDIDPSLTDVWYNKGIALYALGRHEE---AFKCYDAAVEIDPLYHPAW 266
                                       789999999999999**********************998888778888999997...9999999999999998887 PP

                            TPR_15 221 ...aaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrlRrqv 274
                                          + A   Lgr ++A + + +  +  ++ +++      al++ gr+deA++  r++
  gi|386002707|ref|YP_005921006.1| 267 fnkGLAFYSLGRVEEAIDCYDRAIDIDPSLVAVWNNKGNALYALGRFDEAQECYRRA 323
                                       455779999****************99999999999999***********9876665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.008
                            TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAll 225
                                       ++ ++ + ++ g+ ++Al++y + ++ +p+ se+  +   +l  lgr++e+     +  +   ++ + w   a Al 
  gi|386002707|ref|YP_005921006.1| 334 WYNLGVVLQRLGRGEEALEAYDRLIEIDPNLSEAWYNRGLALYSLGRYDEAAGCYDRVLEIDPENGDVWYDKALALG 410
                                       77778889999*******************999988888888889*****9999999999999999*********** PP

                            TPR_15 226 lLgrpkkALeylrkqakenrkdplwl 251
                                        Lgr+++AL+ +   +++ ++ p +l
  gi|386002707|ref|YP_005921006.1| 411 SLGRYEEALDCYDEALEAGPRRPEVL 436
                                       **********9999888887777665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.1
                            TPR_15 142 aeqsaafllaraelyrqegqtdaAlrdyreAlalap 177
                                       + +++a+++ r+ l  ++++ ++A++ + e+++ +p
  gi|386002707|ref|YP_005921006.1| 531 YPGDPAVWYNRGLLLYNASRLEEAVESFDEVIEIDP 566
                                       447888888888888888888888888887777766 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.061
                            TPR_15 127 driaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                       +r++e ++s  e  +   + + ++ + + +  + g++d+A+ +y eAl+ +p + +
  gi|386002707|ref|YP_005921006.1| 549 SRLEEAVESFDEVIEIDpSYEGVWRLKGLALYALGRSDEAIDCYDEALEISPSEVS 604
                                       45555555555555555455789999999999*******************98766 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00049
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaa 222
                                       + + l+r+ + ++ g+ d Al  y  Al+ +pd+ e+  +   +l+ lgr +e+ ++  +  a+a++d   w   + 
  gi|386002707|ref|YP_005921006.1| 699 EEVILRRGFVLLRLGDYDGALASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRILANASEDGGAWHGRGL 775
                                       4577889999999**************************************************************** PP

                            TPR_15 223 AlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAw 268
                                       Al+ L r+++A + + +  + n++d l  +    +le agr + A 
  gi|386002707|ref|YP_005921006.1| 776 ALAGLLRYDEAIDSYDRAIAINSSDNLLWIGRGGVLEEAGRLEDAV 821
                                       ***************************999*9********999885 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.00064
                            TPR_15 124 kdydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselr 183
                                       +++ r+++ ++s  +  a+  +++  +++r+++  ++g+ ++A   + +A+al+p s e++
  gi|386002707|ref|YP_005921006.1| 812 EEAGRLEDAVASFDRAIALDqEDPEAWSMRGRALMKAGRLEDAAASFDRAIALDPSSGEAQ 872
                                       67789999999999999987589********************************998876 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 1.9
                            TPR_15 153 aelyrqegqtdaAlrdyreAlalapd 178
                                       +++ +++g+ ++A+ +y+ A+al+p 
  gi|386002707|ref|YP_005921006.1| 876 GSVFEAQGRAEEAIGCYEAAIALDPP 901
                                       6677899****************995 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.2   1.4e+03       8      43 ..     147     182 ..     142     191 .. 0.86
   2 ?   -0.6   0.1       3.8   1.7e+03      14      43 ..     187     216 ..     178     230 .. 0.84
   3 ?   -1.1   0.0       5.6   2.4e+03      12      43 ..     219     250 ..     210     262 .. 0.82
   4 ?   -1.7   0.0       8.6   3.8e+03      12      43 ..     253     284 ..     243     285 .. 0.86
   5 ?    0.8   0.0       1.4   6.1e+02       7      42 ..     350     385 ..     345     392 .. 0.88
   6 ?    4.2   0.0      0.12        53      15      43 ..     392     420 ..     388     428 .. 0.91
   7 !    9.4   0.0    0.0029       1.3       8      63 ..     521     575 ..     517     592 .. 0.82
   8 ?    1.0   0.0       1.2   5.4e+02       8      55 ..     589     636 ..     583     643 .. 0.83
   9 !   10.4   0.3    0.0015      0.66       9      55 ..     720     766 ..     715     795 .. 0.80
  10 ?    7.3   0.1     0.013       5.8       7      76 ..     820     887 ..     816     893 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.2
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAle 43 
                                       +++ ++a+  +p+  d+ ++  lal   grye+A+e
  gi|386002707|ref|YP_005921006.1| 147 VRSYDEAIVFDPAQGDLWYQKGLALCGLGRYEKAIE 182
                                       556677778899999999****************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.8
                            TPR_20  14 alaanpddldarldlAlallaagryeeAle 43 
                                       a++ + dd +  +  Alal++ gr eeA++
  gi|386002707|ref|YP_005921006.1| 187 AITIDGDDAASWHGKALALYSLGRAEEAID 216
                                       566677888888999*************97 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.6
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAle 43 
                                       ++a+  +p+  d  ++   al+a gr+eeA++
  gi|386002707|ref|YP_005921006.1| 219 DRAIDIDPSLTDVWYNKGIALYALGRHEEAFK 250
                                       56677788888888999999**********86 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 8.6
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAle 43 
                                       +aa++ +p  + a ++  la ++ gr+eeA++
  gi|386002707|ref|YP_005921006.1| 253 DAAVEIDPLYHPAWFNKGLAFYSLGRVEEAID 284
                                       678889999999999999999*********97 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.4
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAl 42 
                                        l++ ++ ++ +p+  +a ++  lal++ gry+eA+
  gi|386002707|ref|YP_005921006.1| 350 ALEAYDRLIEIDPNLSEAWYNRGLALYSLGRYDEAA 385
                                       5777788899999999*****************996 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.12
                            TPR_20  15 laanpddldarldlAlallaagryeeAle 43 
                                       l+ +p++ d  +d Alal + gryeeAl+
  gi|386002707|ref|YP_005921006.1| 392 LEIDPENGDVWYDKALALGSLGRYEEALD 420
                                       6789***********************98 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0029
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkq 63 
                                       +++ + a+a  p d +  ++  l+l+ a+r eeA+e + e+++ d ++ ++  r +
  gi|386002707|ref|YP_005921006.1| 521 VEAYDGAIALYPGDPAVWYNRGLLLYNASRLEEAVESFDEVIEIDPSY-EGVWRLK 575
                                       66777789999**********************************999.5555555 PP

  == domain 8  score: 1.0 bits;  conditional E-value: 1.2
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                       ++  ++al+ +p+++ + ++   +l++ gry eA+e   ++++ dr +
  gi|386002707|ref|YP_005921006.1| 589 IDCYDEALEISPSEVSLWYNRGVVLFSLGRYGEAIESYDRVIELDRYE 636
                                       5566789999*************************9887777777655 PP

  == domain 9  score: 10.4 bits;  conditional E-value: 0.0015
                            TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                       a+ + al+++pddl+a+    +alla gr eeA + + +il++ +++
  gi|386002707|ref|YP_005921006.1| 720 ASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRILANASED 766
                                       5666789**************************99988888766554 PP

  == domain 10  score: 7.3 bits;  conditional E-value: 0.013
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdp 76 
                                        +a++++a+a + +d +a     +al++agr e+A++ + + ++ d +   ++a++    +fea g +++
  gi|386002707|ref|YP_005921006.1| 820 AVASFDRAIALDQEDPEAWSMRGRALMKAGRLEDAAASFDRAIALDPSS--GEAQRGRGSVFEAQGRAEE 887
                                       57889999*****************************999999866665..7777777888888887766 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.13        57      11      25 ..      70      84 ..      68      88 .. 0.85
   2 ?    0.0   0.0         3   1.3e+03      10      25 ..     137     152 ..     136     155 .. 0.81
   3 ?    0.2   0.1       2.7   1.2e+03       9      21 ..     170     182 ..     170     185 .. 0.86
   4 ?    1.6   0.0      0.96   4.2e+02      10      25 ..     205     220 ..     204     224 .. 0.84
   5 ?    1.1   0.1       1.3   5.8e+02      12      24 ..     241     253 ..     238     257 .. 0.84
   6 ?    3.7   0.0       0.2        88      10      25 ..     273     288 ..     272     292 .. 0.86
   7 ?    2.4   0.0       0.5   2.2e+02       9      26 ..     306     323 ..     305     327 .. 0.82
   8 ?    3.3   0.0      0.26   1.1e+02      12      28 ..     343     359 ..     340     361 .. 0.89
   9 ?    1.0   0.0       1.5   6.6e+02      10      27 ..     375     392 ..     374     395 .. 0.82
  10 !    8.4   0.0    0.0065       2.8       9      30 ..     408     429 ..     407     430 .. 0.90
  11 ?    0.3   0.0       2.4     1e+03      13      28 ..     548     563 ..     545     565 .. 0.84
  12 ?    2.0   0.0       0.7   3.1e+02      12      26 ..     581     595 ..     578     598 .. 0.82
  13 ?   -1.5   0.0       9.3   4.1e+03      11      28 ..     614     631 ..     612     633 .. 0.80
  14 ?    4.8   0.1     0.091        40       9      27 ..     640     658 ..     639     660 .. 0.85
  15 ?    0.9   0.0       1.5   6.6e+02      10      27 ..     743     760 ..     741     762 .. 0.82
  16 ?    0.7   0.0       1.9   8.1e+02       8      23 ..     843     858 ..     837     862 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                               PPR 11 cknGkleeAlelfke 25
                                      +  G+l+eAl++f++
  gi|386002707|ref|YP_005921006.1| 70 SDLGRLDEALSCFNR 84
                                      568**********97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 3
                               PPR  10 ycknGkleeAlelfke 25 
                                       + + G++eeA++ ++e
  gi|386002707|ref|YP_005921006.1| 137 LYSLGRYEEAVRSYDE 152
                                       5678******987776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.7
                               PPR   9 gycknGkleeAle 21 
                                       ++c  G++e+A+e
  gi|386002707|ref|YP_005921006.1| 170 ALCGLGRYEKAIE 182
                                       68999******98 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.96
                               PPR  10 ycknGkleeAlelfke 25 
                                       + + G+ eeA++++++
  gi|386002707|ref|YP_005921006.1| 205 LYSLGRAEEAIDCYDR 220
                                       5678*********997 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 1.3
                               PPR  12 knGkleeAlelfk 24 
                                         G++eeA+++++
  gi|386002707|ref|YP_005921006.1| 241 ALGRHEEAFKCYD 253
                                       579*******997 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.2
                               PPR  10 ycknGkleeAlelfke 25 
                                       + + G++eeA++++++
  gi|386002707|ref|YP_005921006.1| 273 FYSLGRVEEAIDCYDR 288
                                       6789*********997 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.5
                               PPR   9 gycknGkleeAlelfkeM 26 
                                       ++   G+++eA e++++ 
  gi|386002707|ref|YP_005921006.1| 306 ALYALGRFDEAQECYRRA 323
                                       67789*********9985 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.26
                               PPR  12 knGkleeAlelfkeMke 28 
                                       + G+ eeAle +++++e
  gi|386002707|ref|YP_005921006.1| 343 RLGRGEEALEAYDRLIE 359
                                       78***********9987 PP

  == domain 9  score: 1.0 bits;  conditional E-value: 1.5
                               PPR  10 ycknGkleeAlelfkeMk 27 
                                       + + G+++eA  ++++ +
  gi|386002707|ref|YP_005921006.1| 375 LYSLGRYDEAAGCYDRVL 392
                                       5678********999876 PP

  == domain 10  score: 8.4 bits;  conditional E-value: 0.0065
                               PPR   9 gycknGkleeAlelfkeMkekG 30 
                                       ++++ G++eeAl++++e +e G
  gi|386002707|ref|YP_005921006.1| 408 ALGSLGRYEEALDCYDEALEAG 429
                                       68999************88876 PP

  == domain 11  score: 0.3 bits;  conditional E-value: 2.4
                               PPR  13 nGkleeAlelfkeMke 28 
                                       + +leeA+e f+e +e
  gi|386002707|ref|YP_005921006.1| 548 ASRLEEAVESFDEVIE 563
                                       5689********9876 PP

  == domain 12  score: 2.0 bits;  conditional E-value: 0.7
                               PPR  12 knGkleeAlelfkeM 26 
                                         G+ +eA+++++e 
  gi|386002707|ref|YP_005921006.1| 581 ALGRSDEAIDCYDEA 595
                                       579*********995 PP

  == domain 13  score: -1.5 bits;  conditional E-value: 9.3
                               PPR  11 cknGkleeAlelfkeMke 28 
                                        + G++ eA+e +++ +e
  gi|386002707|ref|YP_005921006.1| 614 FSLGRYGEAIESYDRVIE 631
                                       5789******99888765 PP

  == domain 14  score: 4.8 bits;  conditional E-value: 0.091
                               PPR   9 gycknGkleeAlelfkeMk 27 
                                       ++ + G+++eA+e++++ +
  gi|386002707|ref|YP_005921006.1| 640 ALYSLGRYDEAIECYEKVL 658
                                       56789**********9865 PP

  == domain 15  score: 0.9 bits;  conditional E-value: 1.5
                               PPR  10 ycknGkleeAlelfkeMk 27 
                                       +   G++eeA   f++++
  gi|386002707|ref|YP_005921006.1| 743 LLALGRFEEASATFDRIL 760
                                       5568**********9875 PP

  == domain 16  score: 0.7 bits;  conditional E-value: 1.9
                               PPR   8 sgycknGkleeAlelf 23 
                                       +++ k+G+le+A   f
  gi|386002707|ref|YP_005921006.1| 843 RALMKAGRLEDAAASF 858
                                       6899*******97655 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         9     4e+03      21      34 ..      72      85 ..      66      88 .. 0.82
   2 ?    3.5   0.0       0.2        87      20      39 ..     105     124 ..      98     140 .. 0.84
   3 ?   -1.0   0.0         5   2.2e+03      18      34 ..     137     153 ..     130     156 .. 0.77
   4 ?    2.8   0.0      0.33   1.4e+02      14      35 ..     201     222 ..     195     233 .. 0.85
   5 ?    1.5   0.1      0.81   3.5e+02      18      35 ..     239     256 ..     232     259 .. 0.85
   6 ?    1.1   0.0       1.1   4.6e+02      21      35 ..     276     290 ..     269     297 .. 0.86
   7 ?    5.9   0.0     0.033        14      12      36 ..     301     325 ..     293     330 .. 0.87
   8 ?    0.1   0.0       2.2   9.8e+02      17      33 ..     374     390 ..     360     397 .. 0.79
   9 ?    3.2   0.0      0.24   1.1e+02      17      34 ..     408     425 ..     403     430 .. 0.79
  10 ?    0.2   0.0         2   8.9e+02      18      36 ..     477     495 ..     471     500 .. 0.83
  11 ?    0.8   0.0       1.4     6e+02      18      36 ..     579     597 ..     574     605 .. 0.84
  12 ?    7.0   0.0     0.015       6.5      14      35 ..     637     658 ..     628     678 .. 0.87
  13 ?    3.6   0.0      0.18        80      14      33 ..     739     758 ..     728     766 .. 0.79
  14 ?   -1.6   0.0       7.4   3.2e+03      14      35 ..     841     862 ..     837     866 .. 0.77
  15 ?    2.5   0.1      0.39   1.7e+02      16      35 ..     877     896 ..     867     899 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 9
                         NRBF2_MIT 21 aGkyeeaischkka 34
                                       G+ +ea+sc +++
  gi|386002707|ref|YP_005921006.1| 72 LGRLDEALSCFNRS 85
                                      5999******9875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.2
                         NRBF2_MIT  20 aaGkyeeaischkkaaayls 39 
                                         G y+eai c+ +a ++ s
  gi|386002707|ref|YP_005921006.1| 105 GLGIYDEAIDCYDRAMEFNS 124
                                       5699***********98866 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 5
                         NRBF2_MIT  18 llaaGkyeeaischkka 34 
                                       l + G+yeea+  +  a
  gi|386002707|ref|YP_005921006.1| 137 LYSLGRYEEAVRSYDEA 153
                                       6678******9877655 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.33
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaa 35 
                                       ka  l + G+ eeai c+ +a 
  gi|386002707|ref|YP_005921006.1| 201 KALALYSLGRAEEAIDCYDRAI 222
                                       66778899**********9986 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.81
                         NRBF2_MIT  18 llaaGkyeeaischkkaa 35 
                                       l a G++eea  c+  a 
  gi|386002707|ref|YP_005921006.1| 239 LYALGRHEEAFKCYDAAV 256
                                       8899*********98876 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 1.1
                         NRBF2_MIT  21 aGkyeeaischkkaa 35 
                                        G+ eeai c+ +a 
  gi|386002707|ref|YP_005921006.1| 276 LGRVEEAIDCYDRAI 290
                                       699********9986 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.033
                         NRBF2_MIT  12 srkadrllaaGkyeeaischkkaaa 36 
                                       + k + l a G+++ea  c+++a +
  gi|386002707|ref|YP_005921006.1| 301 NNKGNALYALGRFDEAQECYRRAVE 325
                                       678899****************987 PP

  == domain 8  score: 0.1 bits;  conditional E-value: 2.2
                         NRBF2_MIT  17 rllaaGkyeeaischkk 33 
                                        l + G+y+ea  c+ +
  gi|386002707|ref|YP_005921006.1| 374 ALYSLGRYDEAAGCYDR 390
                                       57788*********976 PP

  == domain 9  score: 3.2 bits;  conditional E-value: 0.24
                         NRBF2_MIT  17 rllaaGkyeeaischkka 34 
                                        l + G+yeea+ c+  a
  gi|386002707|ref|YP_005921006.1| 408 ALGSLGRYEEALDCYDEA 425
                                       455679********9887 PP

  == domain 10  score: 0.2 bits;  conditional E-value: 2
                         NRBF2_MIT  18 llaaGkyeeaischkkaaa 36 
                                       l + G+yeea + +  aaa
  gi|386002707|ref|YP_005921006.1| 477 LYTLGRYEEASASYGEAAA 495
                                       6778*******99999987 PP

  == domain 11  score: 0.8 bits;  conditional E-value: 1.4
                         NRBF2_MIT  18 llaaGkyeeaischkkaaa 36 
                                       l a G+ +eai c+  a +
  gi|386002707|ref|YP_005921006.1| 579 LYALGRSDEAIDCYDEALE 597
                                       7899*********998865 PP

  == domain 12  score: 7.0 bits;  conditional E-value: 0.015
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaa 35 
                                       k + l + G+y+eai c++k  
  gi|386002707|ref|YP_005921006.1| 637 KGEALYSLGRYDEAIECYEKVL 658
                                       7789999***********9975 PP

  == domain 13  score: 3.6 bits;  conditional E-value: 0.18
                         NRBF2_MIT  14 kadrllaaGkyeeaischkk 33 
                                       + + lla G++eea +   +
  gi|386002707|ref|YP_005921006.1| 739 RGEALLALGRFEEASATFDR 758
                                       6799**********987665 PP

  == domain 14  score: -1.6 bits;  conditional E-value: 7.4
                         NRBF2_MIT  14 kadrllaaGkyeeaischkkaa 35 
                                       +   l+ aG+ e+a +   +a 
  gi|386002707|ref|YP_005921006.1| 841 RGRALMKAGRLEDAAASFDRAI 862
                                       5566889999999998887775 PP

  == domain 15  score: 2.5 bits;  conditional E-value: 0.39
                         NRBF2_MIT  16 drllaaGkyeeaischkkaa 35 
                                         + a G+ eeai c++ a 
  gi|386002707|ref|YP_005921006.1| 877 SVFEAQGRAEEAIGCYEAAI 896
                                       556689*********98775 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.6   2.5e+03     214     234 ..      72      92 ..      30      95 .. 0.56
   2 ?   -0.2   0.0       1.2   5.2e+02     205     254 ..     199     248 ..     192     252 .. 0.91
   3 !    8.8   0.0    0.0022      0.97     199     256 ..     295     352 ..     270     365 .. 0.83
   4 !   11.7   0.0   0.00029      0.13     181     251 ..     379     449 ..     359     456 .. 0.80
   5 ?   -2.1   0.0       4.6     2e+03     212     237 ..     710     735 ..     703     762 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.6
                                       TT-HHHHHHHHHHHHHH-TT- CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakd 234
                                       lgr +eA s  + +L+ d++d
  gi|386002707|ref|YP_005921006.1|  72 LGRLDEALSCFNRSLEIDPQD 92 
                                       445555555555555555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHH CS
                        Coatomer_E 205 ngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaev 254
                                        gkA +   lgr eeA      a+d d+   ++  N  +a   lg+ +e+
  gi|386002707|ref|YP_005921006.1| 199 HGKALALYSLGRAEEAIDCYDRAIDIDPSLTDVWYNKGIALYALGRHEEA 248
                                       6999********************************99999999998776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0022
                                       --HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 199 stplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       s  ++ n k  +  +lgr++eA++  + a + d+++ +   Nl v+ q lg+ +e+ e
  gi|386002707|ref|YP_005921006.1| 295 SLVAVWNNKGNALYALGRFDEAQECYRRAVEIDPEYSNPWYNLGVVLQRLGRGEEALE 352
                                       5556777778888899***********************************9988765 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00029
                                       THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-- CS
                        Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkd 251
                                       +++ +A   ++ + e  +++ ++   kA +   lgryeeA     eaL+  ++ +e+L N       l++ 
  gi|386002707|ref|YP_005921006.1| 379 GRYDEAAGCYDRVLEIDPENGDVWYDKALALGSLGRYEEALDCYDEALEAGPRRPEVLNNRCNILYSLERY 449
                                       56677777777777777888899999999999****************************87766666655 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 4.6
                                       HHTT-HHHHHHHHHHHHHH-TT-HHH CS
                        Coatomer_E 212 lllgryeeAeslLkeaLdkdakdeet 237
                                       l lg+y+ A  +   aL+ d+ d e+
  gi|386002707|ref|YP_005921006.1| 710 LRLGDYDGALASYDLALQEDPDDLEA 735
                                       66778888888888888888777765 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.25   1.1e+02      20      32 ..     109     121 ..     106     124 .. 0.89
   2 ?    4.7   0.0     0.073        32      18      31 ..     141     154 ..     139     156 .. 0.91
   3 ?    1.2   0.0      0.88   3.9e+02      18      31 ..     175     188 ..     174     190 .. 0.86
   4 ?    4.7   0.1     0.073        32      11      32 ..     202     223 ..     193     224 .. 0.80
   5 ?    3.3   0.1      0.19        85      18      32 ..     243     257 ..     234     258 .. 0.87
   6 ?    3.9   0.0      0.13        56      18      32 ..     277     291 ..     272     298 .. 0.91
   7 ?    1.5   0.0      0.72   3.1e+02      18      32 ..     311     325 ..     309     326 .. 0.89
   8 !    9.2   0.8    0.0029       1.3      10      32 ..     405     427 ..     403     428 .. 0.86
   9 ?   -0.8   0.3       3.7   1.6e+03      17      31 ..     480     494 ..     472     496 .. 0.83
  10 ?   -1.5   0.2       6.1   2.7e+03      17      32 ..     514     529 ..     512     530 .. 0.83
  11 ?    3.5   0.0      0.17        75      18      32 ..     583     597 ..     581     598 .. 0.87
  12 ?    0.2   0.0       1.9   8.2e+02      18      31 ..     617     630 ..     609     632 .. 0.83
  13 ?    3.9   0.2      0.13        57      18      31 ..     645     658 ..     639     660 .. 0.85
  14 ?    0.7   0.0       1.3   5.6e+02      16      32 ..     711     727 ..     702     728 .. 0.85
  15 ?    2.2   0.0      0.44   1.9e+02      19      31 ..     782     794 ..     780     796 .. 0.89
  16 ?    2.9   0.1      0.26   1.1e+02      15      32 ..     880     897 ..     875     898 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.25
                               MIT  20 yeeAlelYkeale 32 
                                       y+eA+++Y  a+e
  gi|386002707|ref|YP_005921006.1| 109 YDEAIDCYDRAME 121
                                       9*********987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.073
                               MIT  18 gnyeeAlelYkeal 31 
                                       g yeeA++ Y ea+
  gi|386002707|ref|YP_005921006.1| 141 GRYEEAVRSYDEAI 154
                                       89***********8 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.88
                               MIT  18 gnyeeAlelYkeal 31 
                                       g ye+A+e Y  a+
  gi|386002707|ref|YP_005921006.1| 175 GRYEKAIESYDFAI 188
                                       78********9887 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.073
                               MIT  11 AveeDnagnyeeAlelYkeale 32 
                                       A  + + g  eeA+++Y  a++
  gi|386002707|ref|YP_005921006.1| 202 ALALYSLGRAEEAIDCYDRAID 223
                                       5556667899**********98 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.19
                               MIT  18 gnyeeAlelYkeale 32 
                                       g  eeA+++Y  a+e
  gi|386002707|ref|YP_005921006.1| 243 GRHEEAFKCYDAAVE 257
                                       789**********98 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.13
                               MIT  18 gnyeeAlelYkeale 32 
                                       g  eeA+++Y  a++
  gi|386002707|ref|YP_005921006.1| 277 GRVEEAIDCYDRAID 291
                                       6789*********98 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.72
                               MIT  18 gnyeeAlelYkeale 32 
                                       g ++eA e+Y+ a+e
  gi|386002707|ref|YP_005921006.1| 311 GRFDEAQECYRRAVE 325
                                       7899*********98 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0029
                               MIT  10 kAveeDnagnyeeAlelYkeale 32 
                                       kA  + + g yeeAl++Y eale
  gi|386002707|ref|YP_005921006.1| 405 KALALGSLGRYEEALDCYDEALE 427
                                       666777889************98 PP

  == domain 9  score: -0.8 bits;  conditional E-value: 3.7
                               MIT  17 agnyeeAlelYkeal 31 
                                        g yeeA   Y ea 
  gi|386002707|ref|YP_005921006.1| 480 LGRYEEASASYGEAA 494
                                       589********9996 PP

  == domain 10  score: -1.5 bits;  conditional E-value: 6.1
                               MIT  17 agnyeeAlelYkeale 32 
                                       ag y+ A+e+Y  a+ 
  gi|386002707|ref|YP_005921006.1| 514 AGIYDRAVEAYDGAIA 529
                                       67799******98885 PP

  == domain 11  score: 3.5 bits;  conditional E-value: 0.17
                               MIT  18 gnyeeAlelYkeale 32 
                                       g  +eA+++Y eale
  gi|386002707|ref|YP_005921006.1| 583 GRSDEAIDCYDEALE 597
                                       5679*********98 PP

  == domain 12  score: 0.2 bits;  conditional E-value: 1.9
                               MIT  18 gnyeeAlelYkeal 31 
                                       g y eA+e Y   +
  gi|386002707|ref|YP_005921006.1| 617 GRYGEAIESYDRVI 630
                                       89********8755 PP

  == domain 13  score: 3.9 bits;  conditional E-value: 0.13
                               MIT  18 gnyeeAlelYkeal 31 
                                       g y+eA+e+Y++ l
  gi|386002707|ref|YP_005921006.1| 645 GRYDEAIECYEKVL 658
                                       89********9865 PP

  == domain 14  score: 0.7 bits;  conditional E-value: 1.3
                               MIT  16 nagnyeeAlelYkeale 32 
                                       + g+y+ Al  Y  al+
  gi|386002707|ref|YP_005921006.1| 711 RLGDYDGALASYDLALQ 727
                                       569**********9997 PP

  == domain 15  score: 2.2 bits;  conditional E-value: 0.44
                               MIT  19 nyeeAlelYkeal 31 
                                        y+eA++ Y  a+
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAI 794
                                       69*********98 PP

  == domain 16  score: 2.9 bits;  conditional E-value: 0.26
                               MIT  15 DnagnyeeAlelYkeale 32 
                                       + +g  eeA+ +Y+ a+ 
  gi|386002707|ref|YP_005921006.1| 880 EAQGRAEEAIGCYEAAIA 897
                                       678999**********96 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   5.3e+02      87     124 ..      66     102 ..      53     124 .. 0.76
   2 ?    0.8   0.0      0.57   2.5e+02      74     108 ..     293     325 ..     265     359 .. 0.63
   3 ?   -0.4   0.0       1.3   5.8e+02     284     310 ..     573     599 ..     568     603 .. 0.85
   4 !   10.7   0.2   0.00056      0.25      21     132 ..     739     852 ..     731     888 .. 0.77
   5 ?    1.8   0.1      0.28   1.2e+02      47     108 ..     842     897 ..     836     911 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                          TPR_MalT  87 aeilvaqGrLheAletyeqalqlateqglqqlplvgfl 124
                                       + il   GrL+eAl  ++++l+ ++ q+ + +   gf+
  gi|386002707|ref|YP_005921006.1|  66 GYILSDLGRLDEALSCFNRSLE-IDPQDPHIWYSKGFV 102
                                       6788888999999999999888.555555555555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.57
                          TPR_MalT  74 dslhvallallqqaeilvaqGrLheAletyeqalq 108
                                       d + va++     ++ l a Gr++eA e y++a +
  gi|386002707|ref|YP_005921006.1| 293 DPSLVAVWNNK--GNALYALGRFDEAQECYRRAVE 325
                                       34444444433..6666666677777776666655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                          TPR_MalT 284 iLqalalqaqgreeeAlaaLeqALeLA 310
                                        L  lal+a+gr++eA++  ++ALe+ 
  gi|386002707|ref|YP_005921006.1| 573 RLKGLALYALGRSDEAIDCYDEALEIS 599
                                       5788999*********99999999875 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00056
                          TPR_MalT  21 lelArqALallpeddl.lariaatavl.GeasllqGdleaAlqalqeaekl...arqadslhvallallqqaeilva 92 
                                       +  A  AL +++e    + ri+a+a+  G+a++ +G   a+l ++ ea++    a +++s+++ l+  +  + +l +
  gi|386002707|ref|YP_005921006.1| 739 RGEALLALGRFEEASAtFDRILANASEdGGAWHGRGLALAGLLRYDEAIDSydrAIAINSSDNLLWIGR--GGVLEE 813
                                       556778888888765415678888774499******9999******99976344777788888888766..888999 PP

                          TPR_MalT  93 qGrLheAletyeqalqlateqglqqlplvgfllvlladll 132
                                        GrL++A+  + +a++l +e  ++ + + g +l + ++l 
  gi|386002707|ref|YP_005921006.1| 814 AGRLEDAVASFDRAIALDQEDPEA-WSMRGRALMKAGRLE 852
                                       9***************87776666.999999988877764 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.28
                          TPR_MalT  47 GeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalq 108
                                       G+a + +G+le+A +++  a++l  + +       a ++ + +  aqGr +eA+  ye a++
  gi|386002707|ref|YP_005921006.1| 842 GRALMKAGRLEDAAASFDRAIALDPSSG------EAQRGRGSVFEAQGRAEEAIGCYEAAIA 897
                                       4444444444444444444443332222......2223444444445555555555554444 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.1     4e+03     258     290 ..      72      97 ..      64      98 .. 0.79
   2 ?    0.4   0.0      0.67   2.9e+02     267     291 ..     210     234 ..     199     243 .. 0.87
   3 ?    2.4   0.0      0.17        73     259     291 ..     243     268 ..     233     282 .. 0.79
   4 ?    5.2   0.0     0.024        11     250     296 ..     302     341 ..     291     348 .. 0.83
   5 ?    3.4   0.0     0.081        35     268     292 ..     347     373 ..     338     407 .. 0.84
   6 ?   -2.0   0.0       3.6   1.6e+03     250     291 ..     574     608 ..     554     618 .. 0.83
   7 ?   -0.2   0.0         1   4.5e+02     252     296 ..     638     675 ..     632     807 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.1
                                       CCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 258 lqkldwseekieeilqsysaateidpswykawh 290
                                       l++        +e+l+++ ++ eidp+  + w+
  gi|386002707|ref|YP_005921006.1|  72 LGR-------LDEALSCFNRSLEIDPQDPHIWY 97 
                                       555.......799************99998886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.67
                                       .-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 267 kieeilqsysaateidpswykawht 291
                                       ++ee+ ++y +a  idps+++ w++
  gi|386002707|ref|YP_005921006.1| 210 RAEEAIDCYDRAIDIDPSLTDVWYN 234
                                       489*******************986 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.17
                                       CCCT.S...-SSCCHHHHCCHHCTCCCHS.TTCC CS
                               FAT 259 qkldwseekieeilqsysaateidpswyk.awht 291
                                       ++        ee++++y aa+eidp +y+ aw++
  gi|386002707|ref|YP_005921006.1| 243 GR-------HEEAFKCYDAAVEIDP-LYHpAWFN 268
                                       44.......89**************.55559987 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.024
                                       TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHH CS
                               FAT 250 kkGewqealqkldwseekieeilqsysaateidpswykawhtwalfn 296
                                        kG  + al++       ++e+ ++y++a+eidp+  + w++++ + 
  gi|386002707|ref|YP_005921006.1| 302 NKGNALYALGR-------FDEAQECYRRAVEIDPEYSNPWYNLGVVL 341
                                       56666666777.......99**********************98766 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.081
                                       -SSCCHHHHCCHHCTCCCHSTTCC..C CS
                               FAT 268 ieeilqsysaateidpswykawht..w 292
                                        ee+l++y +  eidp++ +aw++  +
  gi|386002707|ref|YP_005921006.1| 347 GEEALEAYDRLIEIDPNLSEAWYNrgL 373
                                       689*******************98443 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 3.6
                                       TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                               FAT 250 kkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                       +kG  + al++       ++e+ ++y +a ei+ps    w++
  gi|386002707|ref|YP_005921006.1| 574 LKGLALYALGR-------SDEAIDCYDEALEISPSEVSLWYN 608
                                       56777777777.......99************9998888876 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 1
                                       CCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHH CS
                               FAT 252 Gewqealqkldwseekieeilqsysaateidpswykawhtwalfn 296
                                       Ge + +l++        +e+ ++y +  e++p  +kaw++ +l++
  gi|386002707|ref|YP_005921006.1| 638 GEALYSLGR-------YDEAIECYEKVLEVSPLEAKAWYQKGLAH 675
                                       555555555.......67777777777777777777777644444 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.6   1.6e+03      76     122 ..      32      78 ..      28      84 .. 0.87
   2 ?    0.4   0.0       1.9   8.3e+02      83     122 ..     175     214 ..     162     217 .. 0.91
   3 ?    1.9   0.0      0.64   2.8e+02      78     122 ..     374     418 ..     365     422 .. 0.88
   4 ?   -0.2   0.0       2.9   1.3e+03      77     122 ..     543     588 ..     521     591 .. 0.84
   5 ?    5.6   0.0     0.046        20      67     134 ..     697     764 ..     670     766 .. 0.86
   6 ?    2.1   0.0      0.57   2.5e+02      74     122 ..     840     888 ..     814     892 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.6
                                       HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  76 akealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       a   ++++ y +a+  +n+ +  dp   +a +lk  +l  lg+  e+
  gi|386002707|ref|YP_005921006.1|  32 AIGFYSNESYDLALLYVNKSLDIDPAYPDAWSLKGYILSDLGRLDEA 78 
                                       556688999*****************************999998776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.9
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       g y+ a+e  +++++ d ++a+  + ka al +lg+++e+
  gi|386002707|ref|YP_005921006.1| 175 GRYEKAIESYDFAITIDGDDAASWHGKALALYSLGRAEEA 214
                                       78999*******************************9986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.64
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       + ++ g y  aa   + +++ dpen +    ka al +lg+ +e+
  gi|386002707|ref|YP_005921006.1| 374 ALYSLGRYDEAAGCYDRVLEIDPENGDVWYDKALALGSLGRYEEA 418
                                       5677899999******************************98876 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.9
                                       HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                          +++  ++ a+e  + +++ dp+ +   +lk  al +lg+  e+
  gi|386002707|ref|YP_005921006.1| 543 LLLYNASRLEEAVESFDEVIEIDPSYEGVWRLKGLALYALGRSDEA 588
                                       55678899999**********************9999999998775 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.046
                                       TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  67 GgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsgak 134
                                       G +e +l++    l+ gdy  a+   + ++++dp++ ea + + +al +lg+++e+ ++    l+ a+
  gi|386002707|ref|YP_005921006.1| 697 GYEEVILRRGFVLLRLGDYDGALASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRILANAS 764
                                       5567777888888899**************************************99887666666665 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.57
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                        + ++ +k+g ++ aa   + +++ dp+  ea++ + +++e+ g+++e+
  gi|386002707|ref|YP_005921006.1| 840 MRGRALMKAGRLEDAAASFDRAIALDPSSGEAQRGRGSVFEAQGRAEEA 888
                                       5678899***********************************9999886 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.8   1.6e+03     151     175 ..      64      88 ..      41     103 .. 0.87
   2 ?   -1.0   0.0       2.8   1.2e+03     124     174 ..      70     121 ..      66     131 .. 0.74
   3 ?   -1.2   0.0       3.3   1.4e+03     152     175 ..     133     156 ..     109     171 .. 0.85
   4 ?   -1.9   0.1       5.4   2.3e+03     152     174 ..     235     257 ..     233     259 .. 0.90
   5 !    7.3   0.0    0.0082       3.6     150     176 ..     301     327 ..     296     346 .. 0.87
   6 ?   -2.3   0.0         7   3.1e+03     158     179 ..     411     432 ..     408     441 .. 0.80
   7 ?   -0.9   2.8       2.5   1.1e+03     153     174 ..     508     529 ..     475     535 .. 0.82
   8 ?    4.2   0.0     0.073        32     150     176 ..     573     599 ..     543     612 .. 0.81
   9 ?    1.3   0.0      0.56   2.5e+02     152     174 ..     637     659 ..     632     675 .. 0.87
  10 !    7.9   0.1    0.0053       2.3     120     178 ..     706     765 ..     679     778 .. 0.81
  11 ?    2.4   0.7      0.25   1.1e+02     145     176 ..     834     865 ..     782     873 .. 0.70
  12 ?    4.7   0.8     0.051        22     145     175 ..     868     898 ..     843     905 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.8
                            TPR_21 151 lrGDilvaqgkldeAraaYqaAlaa 175
                                       l+G il+  g+ldeA + ++++l+ 
  gi|386002707|ref|YP_005921006.1|  64 LKGYILSDLGRLDEALSCFNRSLEI 88 
                                       89*************9999998875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.8
                            TPR_21 124 laekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        + + +deAl+  +++ e +  + ++   +G +l+  g  deA + Y++A++
  gi|386002707|ref|YP_005921006.1|  70 SDLGRLDEALSCFNRSLEiDPQDPHIWYSKGFVLYGLGIYDEAIDCYDRAME 121
                                       5666677777777554332566777777899999999999999999999997 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.3
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaa 175
                                       rG +l++ g+ +eA   Y++A+  
  gi|386002707|ref|YP_005921006.1| 133 RGLALYSLGRYEEAVRSYDEAIVF 156
                                       888999999*********999865 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.4
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G +l+a g+ +eA + Y+aA++
  gi|386002707|ref|YP_005921006.1| 235 KGIALYALGRHEEAFKCYDAAVE 257
                                       788999**************986 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0082
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaal 176
                                       + +G++l+a g++deA++ Y++A++  
  gi|386002707|ref|YP_005921006.1| 301 NNKGNALYALGRFDEAQECYRRAVEID 327
                                       579********************9865 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 7
                            TPR_21 158 aqgkldeAraaYqaAlaaleek 179
                                       + g+ +eA + Y++Al+a+  +
  gi|386002707|ref|YP_005921006.1| 411 SLGRYEEALDCYDEALEAGPRR 432
                                       56899999999****9998765 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 2.5
                            TPR_21 153 GDilvaqgkldeAraaYqaAla 174
                                       GD+++a g  d A +aY+ A+a
  gi|386002707|ref|YP_005921006.1| 508 GDAFAAAGIYDRAVEAYDGAIA 529
                                       9999999999999999999886 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.073
                            TPR_21 150 elrGDilvaqgkldeAraaYqaAlaal 176
                                        l+G +l+a g+ deA + Y++Al+  
  gi|386002707|ref|YP_005921006.1| 573 RLKGLALYALGRSDEAIDCYDEALEIS 599
                                       48999******************9865 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 0.56
                            TPR_21 152 rGDilvaqgkldeAraaYqaAla 174
                                       +G++l++ g+ deA + Y++ l+
  gi|386002707|ref|YP_005921006.1| 637 KGEALYSLGRYDEAIECYEKVLE 659
                                       8******************9887 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.0053
                            TPR_21 120 arvllaekkydeAlktLeakkeeafaa.lvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                         vll  ++yd Al+  + + +e  +  ++a  rG++l+a g+++eA a +++ la+ +e
  gi|386002707|ref|YP_005921006.1| 706 GFVLLRLGDYDGALASYDLALQEDPDDlEAARGRGEALLALGRFEEASATFDRILANASE 765
                                       5589999*******9998777666655145677****************99998887766 PP

  == domain 11  score: 2.4 bits;  conditional E-value: 0.25
                            TPR_21 145 aalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                       + ++  +rG +l++ g+l++A a +++A+a  
  gi|386002707|ref|YP_005921006.1| 834 DPEAWSMRGRALMKAGRLEDAAASFDRAIALD 865
                                       34445689999999999999999999998755 PP

  == domain 12  score: 4.7 bits;  conditional E-value: 0.051
                            TPR_21 145 aalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       +++++  rG ++ aqg+ +eA   Y+aA+a 
  gi|386002707|ref|YP_005921006.1| 868 SGEAQRGRGSVFEAQGRAEEAIGCYEAAIAL 898
                                       5677788*********************975 PP

>> Rota_NSP3  Rotavirus non-structural protein NSP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.006       2.6     217     252 ..     297     331 ..     281     338 .. 0.89
   2 ?    4.1   0.0     0.049        21     213     247 ..     599     633 ..     584     636 .. 0.89
   3 ?    3.7   0.0     0.066        29     222     260 ..     636     674 ..     634     696 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.006
                         Rota_NSP3 217 lkvyneklerlldvGsltsskeiieksieleiPiik 252
                                       + v+n+k++ l+ +G + +++e + +++e++ P++ 
  gi|386002707|ref|YP_005921006.1| 297 VAVWNNKGNALYALGRFDEAQECYRRAVEID-PEYS 331
                                       789****************************.9875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.049
                         Rota_NSP3 213 lgaelkvyneklerlldvGsltsskeiieksiele 247
                                         +e+ ++ +++  l+ +G + +++e + ++iel+
  gi|386002707|ref|YP_005921006.1| 599 SPSEVSLWYNRGVVLFSLGRYGEAIESYDRVIELD 633
                                       5678999999************************9 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.066
                         Rota_NSP3 222 eklerlldvGsltsskeiieksieleiPiikadirnnes 260
                                       ek+e l+ +G + +++e +ek++e+   + ka +++  +
  gi|386002707|ref|YP_005921006.1| 636 EKGEALYSLGRYDEAIECYEKVLEVSPLEAKAWYQKGLA 674
                                       7999*********************96678888866555 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.1   4.9e+02      89     101 ..     142     154 ..     107     189 .. 0.49
   2 ?    6.6   0.0      0.01       4.4      69     103 ..     190     224 ..     175     229 .. 0.85
   3 ?   -0.4   0.1       1.4   6.1e+02      89     101 ..     278     290 ..     233     325 .. 0.69
   4 ?    3.1   0.0      0.12        53      80     179 ..     352     457 ..     273     463 .. 0.67
   5 ?    3.8   0.1     0.076        33     108     181 ..     481     561 ..     449     569 .. 0.64
   6 ?    4.5   0.1     0.045        20      89     182 ..     599     692 ..     580     699 .. 0.68
   7 ?   -0.2   0.0       1.2   5.4e+02     166     190 ..     778     802 ..     739     815 .. 0.58
   8 ?   -0.2   0.1       1.2   5.2e+02     124     176 ..     811     863 ..     806     865 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHHHH CS
                              SNAP  89 speeAvealekAi 101
                                       + eeAv+++++Ai
  gi|386002707|ref|YP_005921006.1| 142 RYEEAVRSYDEAI 154
                                       3333333333333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                                       T-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHH CS
                              SNAP  69 kekdeaanayveAakcykkvspeeAvealekAiei 103
                                        + d+aa+ + +A   y+  ++eeA++++++Ai+i
  gi|386002707|ref|YP_005921006.1| 190 IDGDDAASWHGKALALYSLGRAEEAIDCYDRAIDI 224
                                       4679*****************************87 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                                       -HHHHHHHHHHHH CS
                              SNAP  89 speeAvealekAi 101
                                       ++eeA++++++Ai
  gi|386002707|ref|YP_005921006.1| 278 RVEEAIDCYDRAI 290
                                       3333333333333 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.12
                                       HHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--..HHHHHHH.....HHHHHHHHHHTT CS
                              SNAP  80 eAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgd..lekAiea.....YekAaelyeqee 149
                                       eA+  + + +p+ + + +++  ++y + gr ++aA  +  + e+  ++ gd  ++kA++      Ye+A + y++  
  gi|386002707|ref|YP_005921006.1| 352 EAYDRLIEIDPNLSEAWYNRGLALY-SLGRYDEAAGCYDRVLEIDPEN-GDvwYDKALALgslgrYEEALDCYDEAL 426
                                       4444444456666666666666655.4577777777777777776655.5555555544333333777777766554 PP

                                       .-HHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                              SNAP 150 .akalankcllkvAelsaelekyekAieiye 179
                                        a  +  ++l +  ++  +le+y++++  y 
  gi|386002707|ref|YP_005921006.1| 427 eAGPRRPEVLNNRCNILYSLERYNESVGCYG 457
                                       3555555555555566666666666666665 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.076
                                       T-HHHHHHHHHHHHHHHHHTT--.............HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-H CS
                              SNAP 108 grfrraAklkkeiaelyekelgd.............lekAieaYekAaelyeqeeakalankcllkvAelsaeleky 171
                                       gr ++a+  + e a l  + ++              +++A+eaY+ A  ly ++ a      +ll  A       ++
  gi|386002707|ref|YP_005921006.1| 481 GRYEEASASYGEAAALNGSRVDAwvgmgdafaaagiYDRAVEAYDGAIALYPGDPAVWYNRGLLLYNA------SRL 551
                                       55566666666666655555422333333444444489999999999999998887666655555444......344 PP

                                       HHHHHHHHHH CS
                              SNAP 172 ekAieiyekv 181
                                       e+A+e +++v
  gi|386002707|ref|YP_005921006.1| 552 EEAVESFDEV 561
                                       4455554444 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.045
                                       -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHH CS
                              SNAP  89 speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqee.akalankcllkvAel 164
                                       sp+e    +++ + +  + gr  +a + +  + el   e g+   ++  Y++A e ye+   ++ l  k++ +    
  gi|386002707|ref|YP_005921006.1| 599 SPSEVSLWYNRGVVL-FSLGRYGEAIESYDRVIELDRYEKGEALYSLGRYDEAIECYEKVLeVSPLEAKAWYQKGLA 674
                                       555555555555543.3567777777777777787777777777777888888888887654666677777777777 PP

                                       HHHTT-HHHHHHHHHHHH CS
                              SNAP 165 saelekyekAieiyekva 182
                                       +  l++ye+++e y++v 
  gi|386002707|ref|YP_005921006.1| 675 HQILGDYERSAECYDRVV 692
                                       777788888888888775 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 1.2
                                       HHTT-HHHHHHHHHHHHHTTSS-TT CS
                              SNAP 166 aelekyekAieiyekvakkslennl 190
                                       a l +y++Ai+ y++ +    + nl
  gi|386002707|ref|YP_005921006.1| 778 AGLLRYDEAIDSYDRAIAINSSDNL 802
                                       3444667777777665555555444 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 1.2
                                       HHHTT--HHHHHHHHHHHHHHHHHTT.-HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SNAP 124 yekelgdlekAieaYekAaelyeqee.akalankcllkvAelsaelekyekAie 176
                                       +e++ g+le+A++++++A  l +++  a +    +l+k+  l+   +++++Ai+
  gi|386002707|ref|YP_005921006.1| 811 LEEA-GRLEDAVASFDRAIALDQEDPeAWSMRGRALMKAGRLEDAAASFDRAIA 863
                                       5555.8899999999999988777765666677777777788888778887775 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.022       9.5       7      96 ..     133     217 ..     127     241 .. 0.82
   2 ?    2.7   0.0      0.32   1.4e+02       3      29 ..     265     291 ..     263     294 .. 0.92
   3 ?    2.4   0.0      0.39   1.7e+02      13      93 ..     309     384 ..     298     388 .. 0.74
   4 ?    5.7   0.0     0.039        17       4      32 ..     402     430 ..     399     447 .. 0.87
   5 ?    1.3   0.0      0.89   3.9e+02      13      29 ..     581     597 ..     575     607 .. 0.85
   6 ?    0.9   0.0       1.2   5.1e+02       5      29 ..     635     659 ..     631     669 .. 0.86
   7 ?   -1.0   0.1       4.4   1.9e+03      50      79 ..     711     740 ..     665     766 .. 0.53
   8 ?   -1.3   0.1       5.7   2.5e+03      15      63 ..     713     758 ..     700     795 .. 0.53
   9 ?   -1.3   0.1       5.5   2.4e+03       7      30 ..     807     830 ..     804     864 .. 0.73
  10 ?    0.6   0.0       1.5   6.5e+02       6      29 ..     874     897 ..     869     904 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                             TPR_5   7 ragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLv 83 
                                       r+ a  s G+ ++av  Y +a+   + +  ++ +  q   +L  lG+ e+a++  +  ++  +d  d+a     aL+
  gi|386002707|ref|YP_005921006.1| 133 RGLALYSLGRYEEAVRSYDEAI---VFDPAQGDLWYQKGLALCGLGRYEKAIESYDFAITIDGD--DAASWHGKALA 204
                                       5556678899999999999998...567888899999999999999999999887777666555..67888899*** PP

                             TPR_5  84 Lsdlgrereavsi 96 
                                       L +lgr +ea+  
  gi|386002707|ref|YP_005921006.1| 205 LYSLGRAEEAIDC 217
                                       **********976 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.32
                             TPR_5   3 aaFeragarDstGhedkavplYrraLa 29 
                                       a F+++ a+ s G+ ++a+  Y ra++
  gi|386002707|ref|YP_005921006.1| 265 AWFNKGLAFYSLGRVEEAIDCYDRAID 291
                                       6799999******************86 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.39
                             TPR_5  13 stGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgr 89 
                                         G+ d+a + Yrra++    +    +    L   L  lG+ eeal+  + ++e  + +l++a    + L+L +lgr
  gi|386002707|ref|YP_005921006.1| 309 ALGRFDEAQECYRRAVEI---DPEYSNPWYNLGVVLQRLGRGEEALEAYDRLIEIDP-NLSEAWY-NRGLALYSLGR 380
                                       678999999999999985...566667778888889999999999988887776654.4666654.46777778877 PP

                             TPR_5  90 erea 93 
                                         ea
  gi|386002707|ref|YP_005921006.1| 381 YDEA 384
                                       7776 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.039
                             TPR_5   4 aFeragarDstGhedkavplYrraLaeGL 32 
                                        +++a a  s G+ ++a   Y +aL++G 
  gi|386002707|ref|YP_005921006.1| 402 WYDKALALGSLGRYEEALDCYDEALEAGP 430
                                       578999999*****************995 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.89
                             TPR_5  13 stGhedkavplYrraLa 29 
                                         G++d+a+  Y +aL+
  gi|386002707|ref|YP_005921006.1| 581 ALGRSDEAIDCYDEALE 597
                                       56999999999999997 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.2
                             TPR_5   5 FeragarDstGhedkavplYrraLa 29 
                                       +e++ a  s G+ d+a++ Y++ L+
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLE 659
                                       7888888999***********9997 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 4.4
                             TPR_5  50 nlGeaeealaLLraeleapsdelddalaaf 79 
                                        lG+ + ala  +  l++ +d+l++a    
  gi|386002707|ref|YP_005921006.1| 711 RLGDYDGALASYDLALQEDPDDLEAARGRG 740
                                       456666666666666666666666554433 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 5.7
                             TPR_5  15 GhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLra 63 
                                       G+ d a   Y  aL+e  ++  + r       +L  lG+ eea a  + 
  gi|386002707|ref|YP_005921006.1| 713 GDYDGALASYDLALQEDPDDLEAARGR---GEALLALGRFEEASATFDR 758
                                       444444444555554444443333322...2334444444444444444 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 5.5
                             TPR_5   7 ragarDstGhedkavplYrraLae 30 
                                       r+g+ +  G+ + av  + ra+a 
  gi|386002707|ref|YP_005921006.1| 807 RGGVLEEAGRLEDAVASFDRAIAL 830
                                       666777777777777777777653 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 1.5
                             TPR_5   6 eragarDstGhedkavplYrraLa 29 
                                        r+++++  G+ ++a+  Y+ a+a
  gi|386002707|ref|YP_005921006.1| 874 GRGSVFEAQGRAEEAIGCYEAAIA 897
                                       6899999*************9986 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.6   1.6e+03      12      32 ..     133     153 ..      99     188 .. 0.79
   2 ?   -1.4   0.0         6   2.6e+03      11      42 ..     370     401 ..     367     428 .. 0.66
   3 ?    6.0   0.0     0.029        13      11      52 ..     540     581 ..     538     604 .. 0.79
   4 ?    0.9   0.0       1.1   4.8e+02      10      35 ..     635     660 ..     629     682 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.6
                          Rapsyn_N  12 kGLklyesndtekalrvWrkv 32 
                                       +GL ly     e+a+r + ++
  gi|386002707|ref|YP_005921006.1| 133 RGLALYSLGRYEEAVRSYDEA 153
                                       677777777777777766655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6
                          Rapsyn_N  11 ekGLklyesndtekalrvWrkvLkktsdregk 42 
                                       ++GL ly     ++a   + +vL+   ++++ 
  gi|386002707|ref|YP_005921006.1| 370 NRGLALYSLGRYDEAAGCYDRVLEIDPENGDV 401
                                       57888888888888888888887766555554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.029
                          Rapsyn_N  11 ekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLita 52 
                                       ++GL ly+    e+a++ + +v++     eg +r+ G  + a
  gi|386002707|ref|YP_005921006.1| 540 NRGLLLYNASRLEEAVESFDEVIEIDPSYEGVWRLKGLALYA 581
                                       69********************************99975544 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.1
                          Rapsyn_N  10 iekGLklyesndtekalrvWrkvLkk 35 
                                        ekG  ly     ++a++ + kvL+ 
  gi|386002707|ref|YP_005921006.1| 635 YEKGEALYSLGRYDEAIECYEKVLEV 660
                                       68999999999999999999999985 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.4   3.2e+03     248     273 ..     209     234 ..     201     251 .. 0.78
   2 ?    5.8   0.0     0.013       5.8     251     289 ..     314     352 ..     279     356 .. 0.88
   3 ?    2.6   0.0      0.12        54     249     281 ..     584     616 ..     553     627 .. 0.83
   4 ?   -1.8   0.0       2.7   1.2e+03     244     273 ..     641     670 ..     637     683 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.4
                                       S--HHHHHHHHHHHHH-TT-HHHHHH CS
                             ChAPs 248 kkeelAlevakravksaPsefktWal 273
                                        + e A+++ +ra+++ Ps    W+ 
  gi|386002707|ref|YP_005921006.1| 209 GRAEEAIDCYDRAIDIDPSLTDVWYN 234
                                       56678999****************96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                             ChAPs 251 elAlevakravksaPsefktWalLvkvYikledienALl 289
                                       + A+e+ +rav++ P  +++W+ L  v  +l+  e+AL 
  gi|386002707|ref|YP_005921006.1| 314 DEAQECYRRAVEIDPEYSNPWYNLGVVLQRLGRGEEALE 352
                                       679*************************99999999985 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.12
                                       --HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHT CS
                             ChAPs 249 keelAlevakravksaPsefktWalLvkvYikl 281
                                       +++ A+++ ++a +++Pse + W+    v  +l
  gi|386002707|ref|YP_005921006.1| 584 RSDEAIDCYDEALEISPSEVSLWYNRGVVLFSL 616
                                       5677999****************9866655555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.7
                                       HHHSS--HHHHHHHHHHHHH-TT-HHHHHH CS
                             ChAPs 244 llskkkeelAlevakravksaPsefktWal 273
                                       l s  +++ A+e+ ++  +++P e k W++
  gi|386002707|ref|YP_005921006.1| 641 LYSLGRYDEAIECYEKVLEVSPLEAKAWYQ 670
                                       556678899*******************97 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.5     2e+03     135     154 ..     134     153 ..     121     228 .. 0.59
   2 ?   -2.0   0.0       2.6   1.1e+03     131     155 ..     231     256 ..     200     260 .. 0.66
   3 ?    4.4   0.0     0.029        13      98     157 ..     337     394 ..     297     428 .. 0.76
   4 ?   -0.1   0.0      0.67   2.9e+02     131     157 ..     537     564 ..     479     569 .. 0.72
   5 ?   -0.2   0.0      0.73   3.2e+02     122     162 ..     566     603 ..     550     641 .. 0.59
   6 ?    7.5   0.1    0.0034       1.5     107     221 ..     644     759 ..     636     765 .. 0.74
   7 ?   -1.4   0.1       1.7   7.5e+02     110     156 ..     817     863 ..     810     871 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.5
                                       HHHHHHHT-HHHHHHHHHHH CS
                          PknG_TPR 135 glaeLlegdyeeAaaeFdev 154
                                       gla  + g+yeeA+ ++de 
  gi|386002707|ref|YP_005921006.1| 134 GLALYSLGRYEEAVRSYDEA 153
                                       55555555555555555542 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                                       HHH.HHHHHHHHT-HHHHHHHHHHHH CS
                          PknG_TPR 131 dWy.rglaeLlegdyeeAaaeFdevl 155
                                        Wy +g+a  + g+ eeA++++d+ +
  gi|386002707|ref|YP_005921006.1| 231 VWYnKGIALYALGRHEEAFKCYDAAV 256
                                       588459999999*********99865 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.029
                                       HHHHHHHHHCT-HH.HHHHHHHHHHHHH---HHHHHH.HHHHHHHHT-HHHHHHHHHHHHHH CS
                          PknG_TPR  98 LaevrahldlGdve.earelLdeleeeveedWrldWy.rglaeLlegdyeeAaaeFdevlaa 157
                                       L  v  +l  G+ + ea ++L e++++ +e W    y rgla  + g+y+eAa ++d+vl++
  gi|386002707|ref|YP_005921006.1| 337 LGVVLQRLGRGEEAlEAYDRLIEIDPNLSEAW----YnRGLALYSLGRYDEAAGCYDRVLEI 394
                                       55555666666543356666666666666655....538********************986 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.67
                                       HHH.HHHHHHHHT-HHHHHHHHHHHHHH CS
                          PknG_TPR 131 dWy.rglaeLlegdyeeAaaeFdevlaa 157
                                        Wy rgl    + ++eeA+++Fdev+++
  gi|386002707|ref|YP_005921006.1| 537 VWYnRGLLLYNASRLEEAVESFDEVIEI 564
                                       4774678878889999999999999875 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.73
                                       HHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-S CS
                          PknG_TPR 122 eeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEi 162
                                       +++e+ Wrl+   gla  + g+ +eA++++de l++ p E+
  gi|386002707|ref|YP_005921006.1| 566 PSYEGVWRLK---GLALYALGRSDEAIDCYDEALEISPSEV 603
                                       4455555553...5555555555555555555555555554 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.0034
                                       CT-HHHHHHHHHHHHHHH---HHHHHH.HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---.TT CS
                          PknG_TPR 107 lGdveearelLdeleeeveedWrldWy.rglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetd.ee 181
                                       lG  +ea e  +++ e ++ + +  Wy +gla+ + gdye+ a+++d+v+++ pG     l   ++  + g+ d + 
  gi|386002707|ref|YP_005921006.1| 644 LGRYDEAIECYEKVLEVSPLEAK-AWYqKGLAHQILGDYERSAECYDRVVEIDPGYEEVILRRGFVLLRLGDYDgAL 719
                                       56666666666666666666655.46636899999999999999999999999998888888888888888877345 PP

                                       -HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS CS
                          PknG_TPR 182 kyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeV 221
                                         Y+   + d   + Aa G   +l a g+ ++A a+ d +
  gi|386002707|ref|YP_005921006.1| 720 ASYDLALQEDPDDLEAARGRGEALLALGRFEEASATFDRI 759
                                       7888888888888888888888888888888888888776 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 1.7
                                       HHHHHHHHHH...HHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHH CS
                          PknG_TPR 110 veearelLde...leeeveedWrldWyrglaeLlegdyeeAaaeFdevla 156
                                        e+a++ +d+   l++e +e W +   rg a + +g++e Aaa+Fd+ +a
  gi|386002707|ref|YP_005921006.1| 817 LEDAVASFDRaiaLDQEDPEAWSM---RGRALMKAGRLEDAAASFDRAIA 863
                                       555555555411145555556654...78899999999999999998665 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0         1   4.5e+02       2      15 ..      41      54 ..      40      55 .. 0.88
   2 ?    2.6   0.3      0.22        98      26      48 ..     161     183 ..     160     188 .. 0.87
   3 ?   -1.7   0.0         5   2.2e+03       1      14 [.     414     427 ..     414     429 .. 0.84
   4 ?   -0.1   0.0       1.7   7.3e+02       1      16 [.     646     661 ..     646     664 .. 0.92
   5 ?    2.3   0.0      0.28   1.2e+02       1      16 [.     782     797 ..     782     807 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                                      HHHHHHHHHHHHHH CS
                          HTH_Bact  2 YeeaLeqvnkAiei 15
                                      Y+ aL +vnk + i
  gi|386002707|ref|YP_005921006.1| 41 YDLALLYVNKSLDI 54
                                      9*********9865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHTT--HHHHHH CS
                          HTH_Bact  26 GQLyYqkgecleklgfseeeIke 48 
                                       G L+Yqkg  l  lg  e+ I++
  gi|386002707|ref|YP_005921006.1| 161 GDLWYQKGLALCGLGRYEKAIES 183
                                       88******999999988888876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5
                                       -HHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAie 14 
                                       rYeeaL   + A+e
  gi|386002707|ref|YP_005921006.1| 414 RYEEALDCYDEALE 427
                                       79999999988886 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.7
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rY+ea+e  +k +e+S
  gi|386002707|ref|YP_005921006.1| 646 RYDEAIECYEKVLEVS 661
                                       7*********999988 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.28
                                       -HHHHHHHHHHHHHHH CS
                          HTH_Bact   1 rYeeaLeqvnkAieiS 16 
                                       rY+ea+   ++Ai+i 
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAIAIN 797
                                       7************985 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.031        14      15      30 ..     311     326 ..     310     333 .. 0.88
   2 ?   -2.6   0.0       8.7   3.8e+03      16      29 ..     414     427 ..     413     427 .. 0.78
   3 ?   -0.5   0.1         2   8.7e+02       1      10 [.     685     694 ..     685     695 .. 0.89
   4 ?   -2.0   0.0       5.8   2.5e+03      16      30 ..     782     796 ..     782     796 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.031
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       ++F++A+e +r+a+e+
  gi|386002707|ref|YP_005921006.1| 311 GRFDEAQECYRRAVEI 326
                                       59*************8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.7
                          SHNi-TPR  16 nFpqAveDlrkaLe 29 
                                       ++++A+  +++aLe
  gi|386002707|ref|YP_005921006.1| 414 RYEEALDCYDEALE 427
                                       78888888888886 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2
                          SHNi-TPR   1 AdvydlLGEi 10 
                                       A++yd+  Ei
  gi|386002707|ref|YP_005921006.1| 685 AECYDRVVEI 694
                                       9*****9998 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5.8
                          SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                       ++++A+  +++a+++
  gi|386002707|ref|YP_005921006.1| 782 RYDEAIDSYDRAIAI 796
                                       79********99976 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.1   1.8e+03     118     133 ..     132     147 ..     107     154 .. 0.63
   2 ?   -0.5   0.0         2   8.6e+02      42      64 ..     201     223 ..     174     232 .. 0.79
   3 ?    0.2   0.1       1.2   5.2e+02      33      64 ..     226     257 ..     210     259 .. 0.80
   4 ?    2.9   0.0      0.18        79      41      64 ..     268     291 ..     263     301 .. 0.83
   5 ?    3.2   0.0      0.15        64      37      64 ..     298     325 ..     291     330 .. 0.86
   6 ?   -1.3   0.0       3.4   1.5e+03      40      64 ..     403     427 ..     393     430 .. 0.77
   7 ?    4.3   0.1     0.065        29      35      64 ..     630     659 ..     620     662 .. 0.85
   8 ?   -1.5   0.0       4.2   1.8e+03     122     141 ..     742     761 ..     734     767 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.1
                                       HHHHHHHHTT-HHHHH CS
                              RPN7 118 yeGlallairkfkeAa 133
                                       + Glal + ++++eA+
  gi|386002707|ref|YP_005921006.1| 132 ARGLALYSLGRYEEAV 147
                                       4555555555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                                       HHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  42 laehYlkigdleeAlkaysrire 64 
                                       +a   ++ g  eeA+ +y r+++
  gi|386002707|ref|YP_005921006.1| 201 KALALYSLGRAEEAIDCYDRAID 223
                                       56666789999********9877 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  33 eeirrakldlaehYlkigdleeAlkaysrire 64 
                                        +  + +++++   +  g +eeA+k+y +++e
  gi|386002707|ref|YP_005921006.1| 226 PSLTDVWYNKGIALYALGRHEEAFKCYDAAVE 257
                                       55666777788888899999999999998765 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  41 dlaehYlkigdleeAlkaysrire 64 
                                       +++  +++ g +eeA+ +y r+++
  gi|386002707|ref|YP_005921006.1| 268 NKGLAFYSLGRVEEAIDCYDRAID 291
                                       6788899**************987 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  37 rakldlaehYlkigdleeAlkaysrire 64 
                                       + ++++++  +  g ++eA+++y+r++e
  gi|386002707|ref|YP_005921006.1| 298 AVWNNKGNALYALGRFDEAQECYRRAVE 325
                                       5678999999***************976 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 3.4
                                       HHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  40 ldlaehYlkigdleeAlkaysrire 64 
                                       +d+a    + g +eeAl +y +++e
  gi|386002707|ref|YP_005921006.1| 403 YDKALALGSLGRYEEALDCYDEALE 427
                                       5566666678999*******99986 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.065
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  35 irrakldlaehYlkigdleeAlkaysrire 64 
                                       i    ++++e  ++ g ++eA+++y++++e
  gi|386002707|ref|YP_005921006.1| 630 IELDRYEKGEALYSLGRYDEAIECYEKVLE 659
                                       555678999*****************9986 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 4.2
                                       HHHHTT-HHHHHHHHCTS-G CS
                              RPN7 122 allairkfkeAaellldils 141
                                       alla ++f+eA+ ++  il+
  gi|386002707|ref|YP_005921006.1| 742 ALLALGRFEEASATFDRILA 761
                                       56777777777777655554 PP

>> Aida_N  Aida N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.15        66       8      29 ..     267     288 ..     263     297 .. 0.90
   2 ?   -1.3   0.0       6.6   2.9e+03      18      31 ..     345     358 ..     336     392 .. 0.80
   3 ?   -1.4   0.2       7.1   3.1e+03       8      29 ..     403     424 ..     401     428 .. 0.88
   4 ?   -1.4   0.0       7.2   3.1e+03      16      31 ..     615     630 ..     606     635 .. 0.77
   5 ?    0.6   0.1       1.7   7.5e+02       7      31 ..     634     658 ..     631     676 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.15
                            Aida_N   8 lkkavdfdsWGqlveAvdeYer 29 
                                       ++k++ f s G + eA+d Y+r
  gi|386002707|ref|YP_005921006.1| 267 FNKGLAFYSLGRVEEAIDCYDR 288
                                       8999****************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.6
                            Aida_N  18 GqlveAvdeYerla 31 
                                       G   eA+++Y+rl 
  gi|386002707|ref|YP_005921006.1| 345 GRGEEALEAYDRLI 358
                                       55678999999884 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.1
                            Aida_N   8 lkkavdfdsWGqlveAvdeYer 29 
                                       ++ka+   s G   eA+d Y++
  gi|386002707|ref|YP_005921006.1| 403 YDKALALGSLGRYEEALDCYDE 424
                                       7899999999**********86 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 7.2
                            Aida_N  16 sWGqlveAvdeYerla 31 
                                       s G   eA++ Y+r+ 
  gi|386002707|ref|YP_005921006.1| 615 SLGRYGEAIESYDRVI 630
                                       668889*******985 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.7
                            Aida_N   7 slkkavdfdsWGqlveAvdeYerla 31 
                                       +++k+    s G   eA++ Ye++ 
  gi|386002707|ref|YP_005921006.1| 634 RYEKGEALYSLGRYDEAIECYEKVL 658
                                       5677777778899*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (949 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 1.44u 0.35s 00:00:01.79 Elapsed: 00:00:00.88
# Mc/sec: 3267.29
//
Query:       gi|386002708|ref|YP_005921007.1|  [L=178]
Description: N-acetyltransferase, GNAT family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-13   49.5   0.1    5.3e-13   49.2   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.6e-10   41.0   0.0    2.1e-10   40.6   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      3e-09   36.7   0.2    4.9e-09   36.0   0.2    1.3  1  FR47             FR47-like protein
    3.1e-08   33.9   0.2    4.2e-08   33.5   0.2    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.1e-05   24.6   0.0       0.01   15.9   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.019   15.1   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
        0.1   12.7   0.1       0.18   12.0   0.1    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
        0.2   11.3   0.0        0.3   10.7   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   2.4e-16   5.3e-13       8     117 .]      18     119 ..      11     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.4e-16
                                       HHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHH CS
                    Acetyltransf_1   8 lvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlea 84 
                                       ++++f+p+   + e + + +    ae + ++ e+g ++Gf+ ++ +       + +  l V pe rg+G+G++L+ a
  gi|386002708|ref|YP_005921007.1|  18 ERACFPPEVAFPAETV-ALI---LAEATALVAEGGSIVGFVAGFARGG----WGKVLTLEVLPEGRGRGVGRRLMVA 86 
                                       5555544333333333.222...34444456799************99....89999******************** PP

                                       HHHHHHHTTESEEEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  85 leerareegikkivlaveedndaairlYek.lGF 117
                                       lee++ ++g+k+  l+v++ n++a++lY   lG+
  gi|386002708|ref|YP_005921007.1|  87 LEEELASQGAKAALLEVSAENERAVALY-AgLGY 119
                                       **********99888*************.65997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   9.4e-14   2.1e-10      32     108 ..      41     121 ..      21     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.4e-14
                   Acetyltransf_10  32 lllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYek 103
                                       + lva egg+ivG+++   +g+  ++  l V pe rg+G+g++L+ a+eee+  +g k   l+v a +  av++Y  
  gi|386002708|ref|YP_005921007.1|  41 TALVA-EGGSIVGFVAGfARGGwgKVLTLEVLPEGRGRGVGRRLMVALEEELASQGAKAaLLEVSAENeRAVALYAG 116
                                       44555.789******665777779***************************99999999****************** PP

                   Acetyltransf_10 104 lGFka 108
                                       lG+ +
  gi|386002708|ref|YP_005921007.1| 117 LGYGK 121
                                       **976 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.2   2.2e-12   4.9e-09      14      79 ..      55     121 ..      45     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.2e-12
                                       EEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-E.EEEEETT-HHHHHHHHHHT-EE CS
                              FR47  14 awilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktv.llvvvasNtpsirlyeklGfek 79 
                                       a+  r   g +  l+vlpe r+rG g+rl  al +e+a +g ++ ll v a+N+++ +ly  lG+ k
  gi|386002708|ref|YP_005921007.1|  55 AGFARGGWGKVLTLEVLPEGRGRGVGRRLMVALEEELASQGAKAaLLEVSAENERAVALYAGLGYGK 121
                                       5666666799999**************************99765166799***************87 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.2   1.9e-11   4.2e-08       5      74 ..      42     119 ..      32     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.9e-11
                                       EEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEE...EEEEEETHHHHHHHHHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea..ae...kgii...leqlelnaekaikfYek 71 
                                        +Va ++g ivGf+a   ++  +    l V+pe rg+G+Gr+L+ a  +e   +g +   le +  ++e+a+++Y+ 
  gi|386002708|ref|YP_005921007.1|  42 ALVA-EGGSIVGFVAGFARGgwGKVLTLEVLPEGRGRGVGRRLMVAleEElasQGAKaalLE-VSAENERAVALYAG 116
                                       4555.67999***9999987433344488***************875422566663332222.2334449******* PP

                                       TTE CS
                    Acetyltransf_7  72 lGF 74 
                                       lG+
  gi|386002708|ref|YP_005921007.1| 117 LGY 119
                                       **9 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.003       6.7       1      59 [.       2      56 ..       2      60 .. 0.79
   2 !   15.9   0.0   4.5e-06      0.01      80     127 ..      69     121 ..      62     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                                      .EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEE CS
                    Acetyltransf_9  1 eirelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlal 59
                                      +ir+ ++ dl+ vl+l +++F  e        e +  +l e+ +l+ae +g +vg +a 
  gi|386002708|ref|YP_005921007.1|  2 RIRRGRPGDLPTVLALERACFPPEVAFP---AETVALILAEATALVAE-GGSIVGFVAG 56
                                      69**********************9986...35666677776666665.8899987765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.5e-06
                                       EE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  80 avapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                        v pe rgrgv ++L+ ++ ee++++g++ +ll       +++++Y  +Gy++
  gi|386002708|ref|YP_005921007.1|  69 EVLPEGRGRGVGRRLMVALEEELASQGAKAALLEVsaeneRAVALYAGLGYGK 121
                                       588******************************99666665679999999987 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   8.7e-06     0.019      89     144 ..      74     129 ..      39     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.7e-06
                    Acetyltransf_4  89 nnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkci 144
                                        + +g+gr l+ ale+ l+ q+ +  l e+ ++ne ++++++ lG+ ++g +++++
  gi|386002708|ref|YP_005921007.1|  74 GRGRGVGRRLMVALEEELASQGAKAALLEVSAENERAVALYAGLGYGKAGLLRGYY 129
                                       67899*********************************************999875 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.9e-05      0.18      30      60 ..      68      98 ..      50     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                   Acetyltransf_CG 30 TeVpeelrGkGiAkkLvkaalddareeglkv 60
                                       eV +e rG+G++++L+ a  ++  ++g k 
  gi|386002708|ref|YP_005921007.1| 68 LEVLPEGRGRGVGRRLMVALEEELASQGAKA 98
                                      5899***************999999988875 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014       0.3      89     141 ..      72     123 ..      70     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                       HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                       +e rg+g++++l+ al + l ++ +++  ++E +++Nera++l++ +G+ k++
  gi|386002708|ref|YP_005921007.1|  72 PEGRGRGVGRRLMVALEEELASQ-GAKAALLEVSAENERAVALYAGLGYGKAG 123
                                       56799*********999998887.99**********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1220.99
//
Query:       gi|386002709|ref|YP_005921008.1|  [L=126]
Description: hypothetical protein Mhar_2029 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  111.6   3.8    2.3e-32  110.9   3.8    1.3  1  DUF2111        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.048   13.6   0.0    1.1  1  Ntox46         Bacterial toxin 46
      0.073   13.1   1.6       0.12   12.4   1.6    1.3  1  Phage_holin_8  Putative phage holin


Domain annotation for each model (and alignments):
>> DUF2111  Uncharacterized protein conserved in archaea (DUF2111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   3.8   3.9e-36   2.3e-32       1      83 []      22     103 ..      22     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3.9e-36
                           DUF2111   1 vhelvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaai 77 
                                       v++++g lPvt+rs   +Gvr+e gkv+d+ Ytgp+Leev+++gk+++++pk+G+Y+Gvpv vaPi ++eg viaa+
  gi|386002709|ref|YP_005921008.1|  22 VNQILG-LPVTMRSLRVPGVRVEGGKVLDDGYTGPILEEVIASGKAVRAIPKSGVYQGVPVSVAPIVHSEGGVIAAM 97 
                                       689999.********************************************************************** PP

                           DUF2111  78 GvVDit 83 
                                       GvVD++
  gi|386002709|ref|YP_005921008.1|  98 GVVDVV 103
                                       ****96 PP

>> Ntox46  Bacterial toxin 46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.1e-06     0.048      51     115 ..      52     117 ..      44     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.1e-06
                                       SSS--EEEEE-TT-EEEEEE-TT----SEEBS-TT--TGGGTS-SEEEETTTTEEE.E-EEEEEEE CS
                            Ntox46  51 ftqpvrvetlargktlwqyqvpgarqgnwyslspdvvptelginplgtirkaetiv.pkvlnvyrs 115
                                       +t p+  e +a gk++      g  qg   s++p v      i  +g +    ti  p v  +y  
  gi|386002709|ref|YP_005921008.1|  52 YTGPILEEVIASGKAVRAIPKSGVYQGVPVSVAPIVHSEGGVIAAMGVVDVVGTIDiPAVFGAYAG 117
                                       789*********************************9999999*******9999954888888865 PP

>> Phage_holin_8  Putative phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6     2e-05      0.12      12      40 ..      91     119 ..      79     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                     Phage_holin_8  12 aaavtgvglagllpgidadvvlGAfaGav 40 
                                       ++ ++++g++ ++  id ++v+GA+aG v
  gi|386002709|ref|YP_005921008.1|  91 GGVIAAMGVVDVVGTIDIPAVFGAYAGVV 119
                                       5788999********************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 769.09
//
Query:       gi|386002710|ref|YP_005921009.1|  [L=390]
Description: argininosuccinate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     7e-164  545.7   0.0     8e-164  545.5   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
     0.0052   15.9   0.0      0.011   14.9   0.0    1.4  1  NAD_synthase     NAD synthase
  ------ inclusion threshold ------
      0.095   12.2   0.0       0.19   11.2   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.5   0.0  1.3e-167    8e-164       1     386 [.       6     386 ..       6     388 .. 0.99

  Alignments for each domain:
  == domain 1  score: 545.5 bits;  conditional E-value: 1.3e-167
                   Arginosuc_synth   1 vLaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikana 76 
                                       vLaysGGlDtsv+i+ll+e++g e vi+v+ dvGq++ed+++ +++a+kl++ +++v+Dakeefv dyifpaikan+
  gi|386002710|ref|YP_005921009.1|   6 VLAYSGGLDTSVCIPLLRERYGfERVITVLTDVGQPKEDIERGNKRAEKLSD-EHYVIDAKEEFVTDYIFPAIKANG 81 
                                       8*********************999**************************9.************************ PP

                   Arginosuc_synth  77 lYedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeiey 153
                                        Ye+ Y+lgta+aRPlia+k veva++ ga+a+ hGctG+GnDq+Rfe+++r+++  l v+aP+R+lel+Re+ei+y
  gi|386002710|ref|YP_005921009.1|  82 SYEG-YVLGTAIARPLIARKTVEVAERLGADALGHGCTGRGNDQLRFEAIFRATE--LRVVAPMRDLELSREWEIDY 155
                                       ****.************************************************99..******************** PP

                   Arginosuc_synth 154 akekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeel 230
                                       a+++gi+v+vt+++p+siDenl++rsie+g Ledp ++ppe+iy++tk+p++   +p++v+ief +GvP+aldge++
  gi|386002710|ref|YP_005921009.1| 156 ARDHGIDVPVTRERPWSIDENLWSRSIEGGLLEDPFFEPPEEIYAWTKPPERGL-APQKVDIEFSAGVPIALDGERM 231
                                       ****************************************************99.9********************* PP

                   Arginosuc_synth 231 svlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvY 307
                                         +elie+ln+ ag+hGvGR+D++edR++glk+Re+Ye+paa+vL++ah+dle+l+l+r +++fk +v++ ++el Y
  gi|386002710|ref|YP_005921009.1| 232 GGVELIENLNRTAGEHGVGRTDMIEDRVLGLKARENYEHPAATVLLTAHRDLERLVLSRAELRFKASVDDAWSELAY 308
                                       ***************************************************************************** PP

                   Arginosuc_synth 308 kGlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqa 384
                                        Gl+++Pl+++l+af++++q+rv+G vr+kl  G++  +gR+s+ ++Yd+e++s+d ++++ q++ eGf+k+hg+qa
  gi|386002710|ref|YP_005921009.1| 309 MGLVNDPLYSDLSAFVDQSQKRVNGVVRMKLSCGRAFSVGRRSPDAIYDQEMVSFD-SKTLSQRDSEGFAKYHGFQA 384
                                       ********************************************************.9******************9 PP

                   Arginosuc_synth 385 kl 386
                                       + 
  gi|386002710|ref|YP_005921009.1| 385 RF 386
                                       85 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-06     0.011      21      83 ..       5      66 ..       2      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                                      EEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase 21 vvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                      +vl  SGG+D s+   l ++  g e+v+++l  ++ +++ed+e   + ae+l++e  +id k+
  gi|386002710|ref|YP_005921009.1|  5 IVLAYSGGLDTSVCIPLLRERYGFERVITVLT-DVGQPKEDIERGNKRAEKLSDEHYVIDAKE 66
                                      69999************************998.999********************9999876 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.19       3      59 ..       6      62 ..       4      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                                      EEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEE CS
                              QueC  3 vvllSGGlDSttvlalakkeg..kevealtfdYgqr.hkkeleaakkiakelgveehkil 59
                                      v+  SGGlD ++++ l ++++  ++v+++  d gq  +++e    +k a++l   eh ++
  gi|386002710|ref|YP_005921009.1|  6 VLAYSGGLDTSVCIPLLRERYgfERVITVLTDVGQPkEDIE--RGNKRAEKLSD-EHYVI 62
                                      6678**********9999987669**********9734444..34444444443.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2605.84
//
Query:       gi|386002711|ref|YP_005921010.1|  [L=366]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for 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-18   65.3   0.1    1.5e-17   64.4   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    2.4e-07   31.1   0.0    4.3e-07   30.3   0.0    1.4  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
        0.1   12.8   0.0       0.25   11.6   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
       0.17   12.1   0.1         16    5.8   0.0    2.4  2  DUF1611_N    Domain of unknown function (DUF1611_N) Rossmann-


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.1   3.4e-21   1.5e-17       1     165 [.      91     243 ..      91     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 3.4e-21
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++vtr+C  rC +C ++e       + +l++eei++ v+e+  e g+  ++++ g+pll++d+ +l+++   +    
  gi|386002711|ref|YP_005921010.1|  91 IEVTRACGCRCDHCLIKE------GEGELDTEEIKRVVDEA-LELGASIITFTEGDPLLRDDILDLIRHVDPE---R 157
                                       689**************7......68999999*********.8999*****************9999999998...9 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                         + + t+g+  ++e +++l+++g+  + +g+ + d+  v+++++   +  ++ ++a++++ eag+ ++ +++v + 
  gi|386002711|ref|YP_005921010.1| 158 AVVNLFTPGLEMTPERAKELKDAGLYNILIGVYSRDPS-VHDRIRgVEGAHQKAIAAIKMALEAGLLVTMSTHVKGD 233
                                       **************************************.99999999999****************95555555555 PP

                                       TTSHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 154 Gendeeleelle 165
                                       G   +e  +l++
  gi|386002711|ref|YP_005921010.1| 234 G--VSETLDLYD 243
                                       5..444455555 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   9.6e-11   4.3e-07       1      47 [.     304     344 ..     304     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 9.6e-11
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse 47 
                                       C+a++r l I +dG V pC +       + ++G++re +l+eIw+  
  gi|386002711|ref|YP_005921010.1| 304 CMAGRRWLHIGVDGGVRPCPYL------DEVVGDVRERPLKEIWKAV 344
                                       99*****************333......689*************543 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05      0.25      14      83 ..      96     157 ..      88     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                           Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                        C  +C+ C    +   +++ e ++e ++++++++ +   + +t++ G+Pll   ++++l+l+++v  e 
  gi|386002711|ref|YP_005921010.1|  96 ACGCRCDHCL---I--KEGEGELDTEEIKRVVDEALELGASIITFTEGDPLL---RDDILDLIRHVDPER 157
                                       5777888887...3..33455677888999999999999*************...99999***9997665 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0035        16      43      65 ..     111     134 ..     106     143 .. 0.86
   2 ?    3.7   0.1     0.017        74      46      85 ..     207     249 ..     202     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0035
                         DUF1611_N  43 gklp.eswreavkeAleaGldvvs 65 
                                       g l+ e+ +++v+eAle+G ++++
  gi|386002711|ref|YP_005921010.1| 111 GELDtEEIKRVVDEALELGASIIT 134
                                       566658999*************96 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.017
                         DUF1611_N  46 peswreavkeAleaGldvvsGlHer...Lsddpelaalakkkg 85 
                                       +++  +a+k AleaGl v  + H +   +s+  +l +la++ g
  gi|386002711|ref|YP_005921010.1| 207 HQKAIAAIKMALEAGLLVTMSTHVKgdgVSETLDLYDLAAELG 249
                                       5677899***********9999974233666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2161.25
//
Query:       gi|386002712|ref|YP_005921011.1|  [L=211]
Description: GTP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-16   59.9   0.0    2.8e-16   59.6   0.0    1.1  1  MMR_HSR1      50S ribosome-binding GTPase
      3e-14   53.0   0.1    4.5e-06   26.3   0.0    3.0  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    6.6e-06   26.1   0.1      0.028   14.3   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
    9.9e-06   25.2   0.1    3.2e-05   23.5   0.1    1.8  1  FeoB_N        Ferrous iron transport protein B
    2.1e-05   24.0   0.0      0.036   13.5   0.0    2.4  2  Arf           ADP-ribosylation factor family
    9.7e-05   22.6   0.0       0.03   14.6   0.0    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase
    0.00068   19.1   0.0       0.14   11.6   0.0    2.3  2  SRPRB         Signal recognition particle receptor beta subun
    0.00072   19.2   0.0       0.11   12.1   0.0    2.5  2  Ras           Ras family
    0.00085   19.1   0.0     0.0015   18.3   0.0    1.5  1  AAA_24        AAA domain
     0.0017   17.7   0.0     0.0025   17.2   0.0    1.2  1  Septin        Septin
     0.0029   18.0   0.0     0.0062   17.0   0.0    1.7  1  AAA           ATPase family associated with various cellular 
     0.0038   17.8   0.0      0.011   16.2   0.0    1.8  1  AAA_18        AAA domain
     0.0046   16.9   0.0     0.0067   16.4   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0081   16.1   0.0      0.011   15.6   0.0    1.3  1  NTPase_1      NTPase
     0.0083   15.1   0.0        2.6    7.0   0.0    2.6  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
  ------ inclusion threshold ------
      0.013   15.5   0.0       0.02   14.9   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.019   14.1   0.1      0.029   13.5   0.1    1.2  1  Parvo_NS1     Parvovirus non-structural protein NS1
      0.028   14.7   0.0       0.22   11.8   0.0    2.3  2  AAA_22        AAA domain
      0.043   14.1   0.0      0.065   13.5   0.0    1.3  1  AAA_28        AAA domain
      0.044   14.2   0.0      0.082   13.3   0.0    1.5  1  RNA_helicase  RNA helicase
      0.051   12.8   0.0      0.097   11.8   0.0    1.4  1  NB-ARC        NB-ARC domain
      0.054   13.1   0.1       0.23   11.0   0.1    2.1  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.089   12.8   0.0         16    5.5   0.0    2.3  2  Dynamin_N     Dynamin family
      0.093   12.7   0.0        6.9    6.8   0.0    2.2  2  MOEP19        KH-like RNA-binding domain
       0.12   12.3   0.0       0.42   10.5   0.0    1.8  2  NACHT         NACHT domain
       0.13   11.7   0.0        3.1    7.2   0.0    2.5  3  TniB          Bacterial TniB protein
       0.17   12.4   0.0       0.24   11.9   0.0    1.3  1  ABC_tran      ABC transporter
        0.2   12.0   0.0       0.29   11.5   0.0    1.4  1  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   4.4e-19   2.8e-16       1     114 []      25     168 ..      25     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4.4e-19
                                       EEEEEESTTSSHHHHHHHHHT.....STEEESSSTTSSSSEEEEEEE...ETT..EEEEEEECGGC........... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg.....ekaivsdkpgtTrdinegrvk...lkg..keielvDtpGl........... 56 
                                       +++i+G pN+GK+tL n++++     e+  +s++p  Tr   +        +g   e+ +vDtpG+           
  gi|386002712|ref|YP_005921011.1|  25 RIGIYGPPNAGKTTLANRIVKdwsgmEVGGISNIPHETRRAMRTDGVvinANGssVELDIVDTPGMatkidfrefma 101
                                       69******************95544336799********9966652223333334779*******877767666655 PP

                                       ..S..S....HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 ..i..e....gaseek.glgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                         +  e    +a+e   g+ +a++ le+ d +llv+d++e+ +++++ ++   +e +k pl++v+nk
  gi|386002712|ref|YP_005921011.1| 102 ygLeeEeakrRAKEATeGVIEAIKWLEDLDGVLLVMDSTEDPYTQVNVTVVGNMEARKLPLLIVANK 168
                                       4424313333222222578888887889*********8888*********9999999********98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-07   8.4e-05       4      81 ..      24      91 ..      21     109 .. 0.81
   2 !   26.3   0.0     7e-09   4.5e-06      86     191 ..     122     209 ..     117     211 .] 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                                      EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSG CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHv 81
                                        igi g  ++GKtTL  r++++ + ++      +    + + ++E +r +  +  +i+ +  +++ ++ ++DtPG +
  gi|386002712|ref|YP_005921011.1| 24 ARIGIYGPPNAGKTTLANRIVKDWSGMEV-----G---GISNIPHETRRAMRTDGVVINAN--GSSVELDIVDTPGMA 91
                                      679******************87776544.....3...48999******999999999999..*************64 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 7e-09
                                       HHHHHHHT-SEEEEEEETTTBSTHHHH.HHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqte.evlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekyg 161
                                       e i+ l+ lDg++lv+d++e++ +q + +v+  + ++++p+ ++ NKmD +ka+ ++i+ +  q             
  gi|386002712|ref|YP_005921011.1| 122 EAIKWLEDLDGVLLVMDSTEDPYTQVNvTVVGNMEARKLPLLIVANKMDLPKASPSRIKAAFPQ------------- 185
                                       55666899*************9999754999********************9999988776653............. PP

                                       HTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 162 ekgekevpvvfgSalkgegvktllealvel 191
                                              p+v +Sal+g ++++l  a+ ++
  gi|386002712|ref|YP_005921011.1| 186 ------HPLVSVSALEGSNIDELYAAIARH 209
                                       ......356777777777777777777666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.4e-05     0.028     104     162 ..      28      91 ..      18      96 .. 0.78
   2 !    9.9   0.0   0.00099      0.63      16      98 ..     130     207 ..     112     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                                       EECSTTSSHHHHHHHHCT.T-----S--------------SEEEEEETT....TEEEESS-SSS CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallp.elelktgevseklgrGkhTTtavellelae....gglliDtPGfr 162
                                       + G+  +GK+tL n+++     +++g +s+  ++ +   ++  ++  a+    +  ++DtPG+ 
  gi|386002712|ref|YP_005921011.1|  28 IYGPPNAGKTTLANRIVKdWSGMEVGGISNIPHETRRAMRTDGVVINANgssvELDIVDTPGMA 91 
                                       6788999**********944589******9999888888777666555512234468*****96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00099
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHH CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkeglee 92 
                                       +d +l+v+  +e+ +++  +  ++  +e+++++++iv nK+Dl + +   +++k+++ +   +++ vsa ++++++e
  gi|386002712|ref|YP_005921011.1| 130 LDGVLLVMDSTEDPYTQVNV-TVVGNMEARKLPLLIVANKMDLPKASP--SRIKAAFPQH--PLVSVSALEGSNIDE 201
                                       56777777665444444333.477899****************99988..6777777666..888888888999998 PP

                                       HHHHCT CS
                       RsgA_GTPase  93 lkellk 98 
                                       l ++++
  gi|386002712|ref|YP_005921011.1| 202 LYAAIA 207
                                       887765 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   4.9e-08   3.2e-05       3     156 .]      26     206 ..      24     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.9e-08
                                       EEEEESTTSSHHHHHHHHHT..TSEEEE...ESTTSSSEEEE..E.EEEETT..EEEEEEE----...........S CS
                            FeoB_N   3 valvGnpnvGkttlfnaltg..akqkvg...NwpGvtvekke..g.klklkg..keveivDlPGi...........Y 58 
                                       + + G pn+Gkttl n++ +  +  +vg   N p  t    +  g  ++ +g   e++ivD PG+           Y
  gi|386002712|ref|YP_005921011.1|  26 IGIYGPPNAGKTTLANRIVKdwSGMEVGgisNIPHETRRAMRtdGvVINANGssVELDIVDTPGMatkidfrefmaY 102
                                       7789**************8733345665122666666433221121334444337889*******888888777777 PP

                                       SS.......SSSSHHHHHHHHHHHCTSSSEEEEEEEGGG...HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE CS
                            FeoB_N  59 sl.......sayseeekvardflleeepdvvvnvvdatn...lernLyLtlqllelgvpvvlalnmideaekkgiei 125
                                        l        a    e v + +   e+ d v+ v+d+t+    + n++++ ++   ++p++++ n++d  +++  +i
  gi|386002712|ref|YP_005921011.1| 103 GLeeeeakrRAKEATEGVIEAIKWLEDLDGVLLVMDSTEdpyTQVNVTVVGNMEARKLPLLIVANKMDLPKASPSRI 179
                                       776655433333344555555555899**********974435667777777778889*************999999 PP

                                       -HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 126 dlkkLsekLgvpvvktsakkkegieellkai 156
                                        ++      + p v++sa ++++i+el +ai
  gi|386002712|ref|YP_005921011.1| 180 KAAFP----QHPLVSVSALEGSNIDELYAAI 206
                                       87644....4688999999999999998765 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0021       1.4       8      37 ..      18      46 ..      11      54 .. 0.84
   2 !   13.5   0.0   5.7e-05     0.036      80     132 ..     128     176 ..     118     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                                      GTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                               Arf  8 lklkkkelrilllGLDnaGKtTilkklkle 37
                                      +++ kk +ri + G  naGKtT+ +++ ++
  gi|386002712|ref|YP_005921011.1| 18 IFG-KKRARIGIYGPPNAGKTTLANRIVKD 46
                                      556.899****************9998765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.7e-05
                                       TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS- CS
                               Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpeals 132
                                       e+ d+v+ v+Ds++    +       +++ + e ++ +ll++aNK+Dlp+a  
  gi|386002712|ref|YP_005921011.1| 128 EDLDGVLLVMDSTEDPYTQVN----VTVVGNMEARKLPLLIVANKMDLPKASP 176
                                       667777777777765433322....3466777999**************9854 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.6e-05      0.03       2      66 ..      26      90 ..      25     102 .. 0.89
   2 ?    6.0   0.0     0.021        13      79     120 .]     129     171 ..     122     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                      + + G  ++GKt+l++r+v+d    +   +  +   t+++++++gv  + + ++v+l+i Dt G 
  gi|386002712|ref|YP_005921011.1| 26 IGIYGPPNAGKTTLANRIVKDWSGMEVGGISNIPHETRRAMRTDGVVINANGSSVELDIVDTPGM 90
                                      56789**************999999999999999999999999**9999999*********9985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.021
                                       TSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TTT CS
                               Roc  79 eaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiDl 120
                                       + + ++lv+ds+++   +  ++ + ++   k p+++v+nk+Dl
  gi|386002712|ref|YP_005921011.1| 129 DLDGVLLVMDSTEDPYTQVNVTVVGNMEArKLPLLIVANKMDL 171
                                       55778999999999888888899988755166*********95 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00022      0.14       3      59 ..      23      90 ..      21     111 .. 0.69
   2 ?    5.3   0.0     0.019        12      67     134 ..     121     180 ..     115     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                      --EEEEE-STTSSHHHHHHHHHHS.....S---B---SS-EEETTG............GGTT-SEEEETT- CS
                             SRPRB  3 kpavllvGlsdsGKTslftrLttd.....svkktvtSqessaalkv.........ksekgskltliDfPGh 59
                                      + ++ + G+ ++GKT+l +r+ +d           +S  ++ + +           +    +l+++D PG 
  gi|386002712|ref|YP_005921011.1| 23 RARIGIYGPPNAGKTTLANRIVKDwsgmeV---GGISNIPHETRRAmrtdgvvinANGSSVELDIVDTPGM 90
                                      5677899*****************774430...33444444443333335555333555666778999995 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                       HHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHH CS
                             SRPRB  67 leklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklik 134
                                       +e +k  + l g++ v+DSt dp    +v     +++ ++e    ++++li  nK +l  a  p+ ik
  gi|386002712|ref|YP_005921011.1| 121 IEAIKWLEDLDGVLLVMDSTEDPYTQVNV-----TVVGNME--ARKLPLLIVANKMDLPKAS-PSRIK 180
                                       67888889999999999999999765554.....3444444..6788999999999998874.45565 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.039        25       6      57 ..      30      89 ..      25     102 .. 0.62
   2 !   12.1   0.0   0.00017      0.11      70     159 ..     128     209 ..     122     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.039
                                      ESTTSSHHHHHHHHHHSSCSSSC..TTTSSEEEEEEEEEET.......TEEEEEEEEEETT CS
                               Ras  6 GdsavGKtslllrfvkdkFkeey..esTigvdfytkeievd.......gkevkleiwDTAG 57
                                      G  + GKt+l +r vkd    e   +s i   ++++ +++d       g++v+l+i DT G
  gi|386002712|ref|YP_005921011.1| 30 GPPNAGKTTLANRIVKDWSGMEVggISNIPH-ETRRAMRTDgvvinanGSSVELDIVDTPG 89
                                      6667788888888887654433311444422.22333333334444559999999999988 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                                       TTESEEEEEEETTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTT CS
                               Ras  70 rdaegillvyditsresfenvk.kwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAkt 145
                                       +d +g+llv d t ++ +++v+ + v +   +  +++p+++v+nK+Dl +        ++  a   + + + +SA +
  gi|386002712|ref|YP_005921011.1| 128 EDLDGVLLVMDST-EDPYTQVNvTVVGN---MEARKLPLLIVANKMDLPKASP-----SRIKAAFPQHPLVSVSALE 195
                                       5667888888855.56788887344443...333469***********97333.....3333455678999****** PP

                                       TCTHHHHHHHHHHH CS
                               Ras 146 nenveeafeellre 159
                                         n++e++ +++r+
  gi|386002712|ref|YP_005921011.1| 196 GSNIDELYAAIARH 209
                                       ******99999885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.4e-06    0.0015       2      59 ..      23     103 ..      22     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                            AAA_24   2 klkiliyGpsgiGKTtlakel.......................gpkplfidtekGlksldadkfpdieswedflde 55 
                                        ++i iyGp+ +GKTtla+++                         + ++i+ ++++ +ld  + p + + +df+++
  gi|386002712|ref|YP_005921011.1|  23 RARIGIYGPPNAGKTTLANRIvkdwsgmevggisniphetrramRTDGVVINANGSSVELDIVDTPGMATKIDFREF 99 
                                       579****************9977777777777777777766666666677777777777777777777777777777 PP

                            AAA_24  56 vvel 59 
                                       +++ 
  gi|386002712|ref|YP_005921011.1| 100 MAYG 103
                                       6665 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.9e-06    0.0025       9      79 ..      28      97 ..      24     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                                      EEEBTTSSCCCCCCTTSSSS----.--------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHH CS
                            Septin  9 vvGesglGkttlintlfetdliee.ekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdns 79
                                      + G    Gkttl n ++++    e   +++    +++   +++  vvi+ +g  ++l ++Dtpg   ++d +
  gi|386002712|ref|YP_005921011.1| 28 IYGPPNAGKTTLANRIVKDWSGMEvGGISNI--PHETRRAMRTDGVVINANGSSVELDIVDTPGMATKIDFR 97
                                      5688889*********987665542444433..555667788999********************9999965 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.6e-06    0.0062       3      38 ..      28     101 ..      26     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.6e-06
                                       EESSTTSSHHHHHHHHHHHHT.HE....................EEEEETTTCSSS.................S CS
                               AAA   3 lyGppGtGKTllakavakelg.ve....................fleisgsellsk.................y 38 
                                       +yGpp  GKT+la+ ++k+++ +e                    +++ +gs++  +                  
  gi|386002712|ref|YP_005921011.1|  28 IYGPPNAGKTTLANRIVKDWSgMEvggisniphetrramrtdgvVINANGSSVELDivdtpgmatkidfrefmA 101
                                       7******************7322233333444555555555555555555555433344444444444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-05     0.011       1      25 [.      26      78 ..      26     150 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf...........................g 25
                                      I++ G+p +GKttla+++ k   g+                           +
  gi|386002712|ref|YP_005921011.1| 26 IGIYGPPNAGKTTLANRIVKDWsGMevggisniphetrramrtdgvvinangS 78
                                      89****************98866666666666666666666667444444441 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0067      21      67 ..      24      70 ..      15     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesisklde 67
                                        + iYGp + GKt+L ++i++  +  +   i  i+ ++++  ++d 
  gi|386002712|ref|YP_005921011.1| 24 ARIGIYGPPNAGKTTLANRIVKDWSGMEVGGISNIPHETRRAMRTDG 70
                                      5567*****************99877777766666666666666655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.011       2      35 ..      26      57 ..      25     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                      + i Gpp  GKtTl +++++    sg++vgG+  
  gi|386002712|ref|YP_005921011.1| 26 IGIYGPPNAGKTTLANRIVKDW--SGMEVGGISN 57
                                      7899****************99..8******964 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0041       2.6      30      51 ..      24      45 ..      17      59 .. 0.87
   2 ?    5.6   0.0      0.01       6.5     204     229 ..     185     210 ..     132     211 .] 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0041
                                      EEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 30 qvvGltGvPGaGkstlvealgl 51
                                       ++G+ G P aGk tl ++++ 
  gi|386002712|ref|YP_005921011.1| 24 ARIGIYGPPNAGKTTLANRIVK 45
                                      69***************99876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                                       --EEEEEBCCCTBSHHHHHHHHHHHH CS
                              MeaB 204 rpkvlktsavegeGidelvdaieehr 229
                                       + +++ +sa+eg  idel +ai +h+
  gi|386002712|ref|YP_005921011.1| 185 QHPLVSVSALEGSNIDELYAAIARHF 210
                                       568999*****************996 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.2e-05      0.02      56     102 ..     160     208 ..     136     211 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                      MMR_HSR1_Xtn  56 ipclyvlNKiDl..isleeldelarepnsvviSaekelnldeLkekiwe 102
                                       +p l+v NK+Dl  +s + +++   ++  v +Sa ++ n+deL  +i +
  gi|386002712|ref|YP_005921011.1| 160 LPLLIVANKMDLpkASPSRIKAAFPQHPLVSVSALEGSNIDELYAAIAR 208
                                       689*********6666677777666788999************998865 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.5e-05     0.029     112     136 ..      21      45 ..       9      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
                         Parvo_NS1 112 gkrntvwfyGpantGktnlaeaIak 136
                                        kr  +++yGp+n Gkt la+ I+k
  gi|386002712|ref|YP_005921011.1|  21 KKRARIGIYGPPNAGKTTLANRIVK 45 
                                       47888****************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.22      10      80 ..      28     118 ..      21     142 .. 0.66
   2 ?   -0.3   0.0       1.9   1.2e+03      32      65 ..     178     211 .]     164     211 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.........................erpevv...fvtlpsstsskdllr 58 
                                       ++G++ +GKTtl++r+++         +                         ++++ v    v+ p+  +  d+++
  gi|386002712|ref|YP_005921011.1|  28 IYGPPNAGKTTLANRIVKDWS---G--MevggisniphetrramrtdgvvinaNGSS-VeldIVDTPGMATKIDFRE 98 
                                       89*************988642...2..123556777788888876666666643333.2366777777778888888 PP

                            AAA_22  59 ellralglelkaerlsseelle 80 
                                        ++  l++e  +   + +e  e
  gi|386002712|ref|YP_005921011.1|  99 FMAYGLEEEEAK--RRAKEATE 118
                                       777777777777..44444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                            AAA_22  32 eakaeeerpevvfvtlpsstsskdllrellralg 65 
                                       ++ka+ ++ ++v+v + ++++ ++l+ +++r +g
  gi|386002712|ref|YP_005921011.1| 178 RIKAAFPQHPLVSVSALEGSNIDELYAAIARHFG 211
                                       4555557888999999999999999999998775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001     0.065       1      57 [.      25     101 ..      25     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                            AAA_28   1 kivitGgestGKTtlleaLaar.......gypvv.pEaareileeklakgedalpwv.e...........dllafae 57 
                                       +i i G++ +GKTtl++++ ++       g++ + +E+ r + +++   + + +  + +           d+ +f +
  gi|386002712|ref|YP_005921011.1|  25 RIGIYGPPNAGKTTLANRIVKDwsgmevgGISNIpHETRRAMRTDGVVINANGSSVElDivdtpgmatkiDFREFMA 101
                                       5789***************9777877778888888999999988888555544443222455566665554444432 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00013     0.082       3      24 ..      28      49 ..      26      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                      RNA_helicase  3 lyGpsgeGKStlakeLakallk 24
                                      +yGp++ GK+tla++++k++++
  gi|386002712|ref|YP_005921011.1| 28 IYGPPNAGKTTLANRIVKDWSG 49
                                      8***************999874 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015     0.097      21      45 ..      24      48 ..      12      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      EEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnksd 45
                                        ++++G +  GKttla+ i+++ +
  gi|386002712|ref|YP_005921011.1| 24 ARIGIYGPPNAGKTTLANRIVKDWS 48
                                      4699******************966 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00036      0.23       3      35 ..      26      58 ..      24     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNe 35
                                      +++ G++ +GKTtL n+++++ +g+++  i N 
  gi|386002712|ref|YP_005921011.1| 26 IGIYGPPNAGKTTLANRIVKDWSGMEVGGISNI 58
                                      57899**************99999999888884 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.026        17       1      20 [.      26      45 ..      26      59 .. 0.90
   2 ?    5.5   0.0     0.024        16     102     155 ..      81     156 ..      56     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                                      EEEEEBTTTTHHHHHHHHHT CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                      i + G  ++GK++++n +++
  gi|386002712|ref|YP_005921011.1| 26 IGIYGPPNAGKTTLANRIVK 45
                                      6788999***********97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                                       SEEEEE---B-SSSGTTS......................HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHS CS
                         Dynamin_N 102 gltlvDlPGldsvnkrdq......................elvkeyikkadiilavtsanhdlsnsealflarevd 155
                                       +l +vD+PG+    + ++                        + + +++ d +l+v+++  d  ++ +  +  +++
  gi|386002712|ref|YP_005921011.1|  81 ELDIVDTPGMATKIDFREfmaygleeeeakrrakeategvIEAIKWLEDLDGVLLVMDSTEDPYTQVNVTVVGNME 156
                                       6889*****9876665555777777777777776666544223334566666666666666655555555555555 PP

>> MOEP19  KH-like RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0       0.1        64      49      69 ..      16      36 ..       9      41 .. 0.79
   2 ?    6.8   0.0     0.011       6.9      34      69 ..     123     159 ..     120     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                            MOEP19 49 kaldseglaeilifGrprykk 69
                                      k+++ +++a+i i+G+p++ k
  gi|386002712|ref|YP_005921011.1| 16 KWIFGKKRARIGIYGPPNAGK 36
                                      667778899999999998755 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                            MOEP19  34 ripeiEqvsqtllevkalds.eglaeilifGrprykk 69 
                                        i+ +E    +ll +++ +    ++ ++++G+ +++k
  gi|386002712|ref|YP_005921011.1| 123 AIKWLEDLDGVLLVMDSTEDpYTQVNVTVVGNMEARK 159
                                       577788888999***999876************9997 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00066      0.42       5      26 ..      28      49 ..      24      59 .. 0.87
   2 ?   -0.8   0.0       1.9   1.2e+03      82      99 ..     132     149 ..     107     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                                      EEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  5 lqGeaGsGKTtLlqklalawae 26
                                      + G++  GKTtL+ +++ +w  
  gi|386002712|ref|YP_005921011.1| 28 IYGPPNAGKTTLANRIVKDWSG 49
                                      7899999*************75 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                                       CEEEEEE-STT-SS-TCH CS
                             NACHT  82 rlLlilDglDelvtdlgq 99 
                                        +Ll++D+ ++  t+ + 
  gi|386002712|ref|YP_005921011.1| 132 GVLLVMDSTEDPYTQVNV 149
                                       577888887776665554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0048       3.1      36      58 ..      24      46 ..       9      60 .. 0.84
   2 ?   -1.4   0.0       2.1   1.3e+03      92     126 ..     105     138 ..      62     150 .. 0.56
   3 ?    1.6   0.0      0.25   1.6e+02      61      92 ..     177     208 ..     148     211 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0048
                              TniB 36 pnlllvGdsnnGKtmivekFarl 58
                                        + ++G++n GKt+++++  ++
  gi|386002712|ref|YP_005921011.1| 24 ARIGIYGPPNAGKTTLANRIVKD 46
                                      55789************997765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                              TniB  92 ealgaplkararvskleqqvlrllrelkvrvLiiD 126
                                       e+ +a+ +a++ ++    ++++ l++l+  +L++D
  gi|386002712|ref|YP_005921011.1| 105 EEEEAKRRAKEATE-GVIEAIKWLEDLDGVLLVMD 138
                                       33333322222222.22334566677777777776 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.25
                              TniB  61 pekdedaekvpvlvvqappkpdekrlyaaiLe 92 
                                       ++ ++   + p++ v+a + ++ ++lyaai +
  gi|386002712|ref|YP_005921011.1| 177 SRIKAAFPQHPLVSVSALEGSNIDELYAAIAR 208
                                       4445566789******************9966 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00038      0.24      11      42 ..      23      55 ..      20     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00038
                                      TSEEEEEESTTSSHHHHHHHHTTSS--.SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllkp.teGei 42
                                        +++i G+  aGK+tL++ + +  +  + G i
  gi|386002712|ref|YP_005921011.1| 23 RARIGIYGPPNAGKTTLANRIVKDWSGmEVGGI 55
                                      6789***************99987665455666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00045      0.29      29     107 ..      28     131 ..      21     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00045
                            AAA_16  29 lsGesGvGKsslvrellralekd..................ggiflrgkcdqlesaipysa.laqalareellrqll 86 
                                       ++G++  GK++l++++ + +++                   +g++++++  + e +i   +  a+ ++++e+++  l
  gi|386002712|ref|YP_005921011.1|  28 IYGPPNAGKTTLANRIVKDWSGMevggisniphetrramrtDGVVINANGSSVELDIVDTPgMATKIDFREFMAYGL 104
                                       89***************999999888888888888888877677766666666445333455888888888888888 PP

                            AAA_16  87 deaesaeleawrekleeala........a 107
                                       +e+e++  ++++e+ e++++        +
  gi|386002712|ref|YP_005921011.1| 105 EEEEAK--RRAKEATEGVIEaikwledlD 131
                                       775553..333333444444344444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1175.85
//
Query:       gi|386002713|ref|YP_005921012.1|  [L=115]
Description: hypothetical protein Mhar_2033 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-44  147.5   3.5    1.1e-43  147.3   3.5    1.0  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   3.5   6.3e-48   1.1e-43       1     105 []       9     112 ..       9     112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 6.3e-48
                           DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkes 77 
                                       le+m+smekirlil kvk+g+ivvlE gLtpeee klie+tm+ei+ deFsGieie+yp k++ +++l+k+lgk+  
  gi|386002713|ref|YP_005921012.1|   9 LESMSSMEKIRLILSKVKRGNIVVLELGLTPEEEVKLIEMTMTEIRLDEFSGIEIESYPVKNE-STFLNKILGKSGI 84 
                                       799***********************************************************9.9************ PP

                           DUF2073  78 eerltvigPanqlktlkkdkdlisalvs 105
                                       ++r+tvigPanql+t++kdk  is+ vs
  gi|386002713|ref|YP_005921012.1|  85 KTRMTVIGPANQLRTVEKDKYQISTKVS 112
                                       ************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 728.94
//
Query:       gi|386002714|ref|YP_005921013.1|  [L=183]
Description: hypothetical protein Mhar_2034 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-27   95.7   0.1    4.2e-26   91.8   0.1    2.0  1  DUF2072   Zn-ribbon containing protein


Domain annotation for each model (and alignments):
>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.1   2.3e-30   4.2e-26      17     133 .]       2     179 ..       1     179 [. 0.77

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 2.3e-30
                           DUF2072  17 eilkGCpsCGgkkFlyvkeeekkedvseeke.......elvaeaeee.............................. 56 
                                       ++l+GCp+CG+kkFl+vk +ek ++v  + +               e                              
  gi|386002714|ref|YP_005921013.1|   2 DVLEGCPVCGWKKFLFVKSKEKIKEVRGALNaseiggpC-------Epwpegddalrkilkapphqppnmepantet 71 
                                       689******************999888776632233320.......2566666776666667776666666555555 PP

                           DUF2072  57 .......ieevldaeeteeeklekk.........................................ekekaekekee 85 
                                                                                                         e e+++++ +e
  gi|386002714|ref|YP_005921013.1|  72 akrepprK----------------GrkgrsrrsaegrekqketpkpkgtlgffdldstrgreppppEGESKNHRIDE 132
                                       55555540................044445555555555566667789****************98888899999** PP

                           DUF2072  86 edrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlkk 133
                                       ++ +es+r+ epG+YelNl++L+erdelvmalk+ g+Y++dl+s++kk
  gi|386002714|ref|YP_005921013.1| 133 GKMLESIRMSEPGTYELNLSSLFERDELVMALKD-GTYFIDLSSAFKK 179
                                       *******************************987.**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1238.46
//
Query:       gi|386002715|ref|YP_005921014.1|  [L=54]
Description: hypothetical protein Mhar_2035 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 386.16
//
Query:       gi|386002716|ref|YP_005921015.1|  [L=131]
Description: hypothetical protein Mhar_2036 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.027   14.7   0.0    1.4  1  Reo_sigmaC  Reovirus sigma C capsid protein C-terminal domain


Domain annotation for each model (and alignments):
>> Reo_sigmaC  Reovirus sigma C capsid protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-06     0.027      48      96 ..      11      59 ..       4      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-06
                        Reo_sigmaC 48 vslvfeldkitklpsdlsrlvpsagfqaasfpvdvsftrdsathayqvy 96
                                      ++l   l   +k p dls l  +a ++a++ pv +s+tr++   + ++ 
  gi|386002716|ref|YP_005921015.1| 11 AMLLVGLGVAAKTPIDLSTLGKKAEMKASTTPVVISYTREAPRTTTNAV 59
                                      56777889999****************************9865555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 795.56
//
Query:       gi|386002717|ref|YP_005921016.1|  [L=272]
Description: hypothetical protein Mhar_2037 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.22   11.1   0.0    1.2  1  DUF953    Eukaryotic protein of unknown function (DUF953)


Domain annotation for each model (and alignments):
>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.2e-05      0.22      36      64 ..     166     194 ..     163     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                                       BSSHHHHHHHHHHHHHHHH-SS-EEEEEE CS
                            DUF953  36 sWCPdCvkaepvieealkeapedvklvrv 64 
                                       s CP C + e  i+ +l+++  +v+ + v
  gi|386002717|ref|YP_005921016.1| 166 SNCPACLQQESAIRRVLEDLGDEVVYLDV 194
                                       88*********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1911.29
//
Query:       gi|386002718|ref|YP_005921017.1|  [L=330]
Description: Rhodanese domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-16   60.0   0.0    4.9e-11   43.1   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-06     0.035      26      99 ..     127     202 ..     105     204 .. 0.81
   2 !   43.1   0.0   2.7e-15   4.9e-11      11      94 ..     243     322 ..     234     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-06
                         Rhodanese  26 ekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggr..aaaaaallkklGyknvsv 96 
                                       e++ I+gA+++      ++ + e+ +l+ p+e+++     gi +++++v+y d+      ++a + +k+lG++++ +
  gi|386002718|ref|YP_005921017.1| 127 EASYIEGAIHL----PLDQVFAEDGSLKSPAEISAIfgaaGIAEEDPLVIYSDSFFNgfDTFAFWVMKYLGHQELLL 199
                                       6789*******....6667778888888888888888889***********998766345666889999**666999 PP

                         Rhodanese  97 ldG 99 
                                       l+G
  gi|386002718|ref|YP_005921017.1| 200 LEG 202
                                       988 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 2.7e-15
                         Rhodanese  11 kgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallk 87 
                                       +   +++D+R+peeY++gh++gA+n+   ++ ++ +  a +++l e+++ l  d++ +vvvy  +gg a+ ++++l 
  gi|386002718|ref|YP_005921017.1| 243 D--LQIVDARSPEEYSAGHLEGARNI-DSSKVMGAEGLAGDQALGEAFSGL--DKDVPVVVYSTKGGVASMVWYALL 314
                                       3..34*********************.777888888888888888888888..**********99999888899999 PP

                         Rhodanese  88 klGykn.v 94 
                                         G++  +
  gi|386002718|ref|YP_005921017.1| 315 DQGFTPrM 322
                                       89985545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2165.04
//
Query:       gi|386002719|ref|YP_005921018.1|  [L=594]
Description: TrkA-C domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-47  162.0  30.7    4.4e-47  160.7  30.7    1.7  1  CitMHS         Citrate transporter
    1.5e-20   72.8   0.9    1.7e-09   37.4   0.1    2.4  2  TrkA_C         TrkA-C domain
    5.2e-18   65.3  33.4    7.3e-10   38.5  15.3    2.6  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7  30.7   7.3e-51   4.4e-47       1     300 []      18     541 ..      18     541 .. 0.88

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 7.3e-51
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                       l+l+i+++ r d+va+++l+++    v+   ea++g+a p+++++++  i+++al  +G++d + + + +   + ++
  gi|386002719|ref|YP_005921018.1|  18 LLLFIWGRWRYDLVAIIALLVAtisgVVPWSEAFTGFAHPAVVTVGAILIVSRALLNSGIVDLIQKSITSPKDS-TK 93 
                                       589*************8888889***************************************999999854443.34 PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 .llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglsl 148
                                         +  l  l+ +ls+f++n+g+++i++p+ l++ +r +++pp+ ll+pla+a+ +gg+lt+iGtp            
  gi|386002719|ref|YP_005921018.1|  94 rQVRSLTGLVSILSGFMNNVGALAILLPVSLRVSRR-TGNPPSlLLMPLAFASLLGGLLTLIGTP------------ 157
                                       356679999**************************9.9999999*********************............ PP

                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                            CitMHS 149 pnlll.....................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv.... 200
                                       pn+++                      ++ll+gl+++++++                          ++l p+    
  gi|386002719|ref|YP_005921018.1| 158 PNIIVasyraevlgepfrmfdftpvgGGVLLAGLIFIWFFG--------------------------WKLTPKrkgg 208
                                       *****999999999999999999888888************..........................5555555555 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|386002719|ref|YP_005921018.1| 209 sskedlfkienyiteiwvssrsklvgkrlrvlkeppvsdmqilglvrgdlripmptgdeilepgdilavetsaenik 285
                                       55555555555555556677899999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|386002719|ref|YP_005921018.1| 286 yilkwrglellggmkvgkkallskdvglieavvaadspmvgetarsltlgrrydmnliavarrgevlaerlgdiafq 362
                                       999999999999999999999999999999999999999************************************** PP

                                       .....................................................................xxxxxxx. RF
                            CitMHS 201 .....................................................................atillla. 207
                                                                                                            +++   + 
  gi|386002719|ref|YP_005921018.1| 363 pgdvllmqgpsgtipevleslgclplaergmklgrrqksppvpllifggalaataagllpveiafasaaVGM---Vl 436
                                       *****************************************9999999998888888888888887666333...13 PP

                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..x.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 208 .........ykkveWsvlllfaGvfllvgaleqtGilealadll.ga..g.gplvalalvlgliallsafisnvava 271
                                                y++++W++++l+++++++++ale tG +e++++++ +a  + + +v+la++l+ +++l+++i+n+a+a
  gi|386002719|ref|YP_005921018.1| 437 agvltiheaYESIDWPIIFLLGALIPVGAALESTGGAETISAAIlQAlsPfPAVVILAALLAWTMILTNIINNAAAA 513
                                       4578899****************************9999998885668545776777777888888*********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 272 almapialgmapalgllspsplalalavg 300
                                       ++mapia+++a +l  lsp+p+++a avg
  gi|386002719|ref|YP_005921018.1| 514 VIMAPIAFNAALVLD-LSPDPFLMAVAVG 541
                                       *********999877.99*********98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1   3.4e-12     2e-08       2      67 ..     222     289 ..     221     292 .. 0.91
   2 !   37.4   0.1   2.8e-13   1.7e-09       1      69 [.     313     383 ..     313     384 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.4e-12
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       +e+ v++ s+lvGk+l+ l+ +   +  +++++Rg  ++++p+gd +Le+GD+l v +s ++++ + +
  gi|386002719|ref|YP_005921018.1| 222 TEIWVSSRSKLVGKRLRVLKEPPVsDMQILGLVRGdLRIPMPTGDEILEPGDILAVETSAENIKYILK 289
                                       577799************8877779**********999************************998766 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 2.8e-13
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       l+e +v+a+sp+vG t + l l +r + +++a+ rRg++l    gd  +++GDvll  g++ ++ e+ e l
  gi|386002719|ref|YP_005921018.1| 313 LIEAVVAADSPMVGETARSLTLGRRyDMNLIAVaRRGEVLAERLGDIAFQPGDVLLMQGPSGTIPEVLESL 383
                                       6899*****************************888899999999*********************99876 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   7.7   1.9e-12   1.2e-08     265     434 ..       3     164 ..       1     198 [. 0.88
   2 ?   -2.3   0.0      0.28   1.7e+03     257     289 ..     291     323 ..     273     333 .. 0.71
   3 !   38.5  15.3   1.2e-13   7.3e-10     304     467 ..     434     593 ..     404     594 .] 0.85

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.9e-12
                     Na_sulph_symp 265 ltarekallilfvlllllWifgeslnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllers 341
                                       +t+ +  + +++ l+lll i g         vai++l +  ++ v+ W        a   ++  g+++ +++ l +s
  gi|386002719|ref|YP_005921018.1|   3 MTTDQLLIFAILGLALLLFIWGRWR---YDLVAIIALLVATISGVVPWS-EAFTGFAHPAVVTVGAILIVSRALLNS 75 
                                       7778888888888888888888755...578******************.55567899999**************** PP

                     Na_sulph_symp 342 gliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatsla 418
                                       g+++ + +++t+  +  s +  +   l+ +v +   f  ++   a+llp+ l v+  + g pp l+ ++la+a+ l+
  gi|386002719|ref|YP_005921018.1|  76 GIVDLIQKSITSPKD--STKRQVRS-LTGLVSILSGFMNNVGALAILLPVSLRVSRRT-GNPPSLLLMPLAFASLLG 148
                                       **********99998..55555554.45567777899*********************.****************** PP

                     Na_sulph_symp 419 gfllpyatgpnpivfg 434
                                       g+l+ ++t+pn iv +
  gi|386002719|ref|YP_005921018.1| 149 GLLTLIGTPPNIIVAS 164
                                       *************976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.28
                     Na_sulph_symp 257 telkelGpltarekallilfvlllllWifgesl 289
                                       ++l++lG ++  +kall   v+l+   +  +s+
  gi|386002719|ref|YP_005921018.1| 291 RGLELLGGMKVGKKALLSKDVGLIEAVVAADSP 323
                                       6899***********998877777666666555 PP

  == domain 3  score: 38.5 bits;  conditional E-value: 1.2e-13
                     Na_sulph_symp 304 llllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaS 380
                                       ++l  vl+ +    +   W +++llg+li +   le +g  e ++ ++ + ls   pav+i++ l+++ ++ + +  
  gi|386002719|ref|YP_005921018.1| 434 MVLAGVLTIH-EAYESIDWPIIFLLGALIPVGAALESTGGAETISAAILQALS-PFPAVVILAALLAWTMILTNIIN 508
                                       4455577766.4566789*********************99999988888887.55666666667777999999*** PP

                     Na_sulph_symp 381 atAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiiglli 457
                                       ++A  ++++pi   +a ++    p  + +++a+  s a fl+p++   n +v g g  +  dywrlG++ls++  l 
  gi|386002719|ref|YP_005921018.1| 509 NAAAAVIMAPIAFNAALVL-DLSPDPFLMAVAVGASCA-FLTPIGHQSNTLVMGPGGYQFGDYWRLGLPLSLVATLA 583
                                       *******************.555777888999999999.************************************** PP

                     Na_sulph_symp 458 llllgalwwk 467
                                        l l+ + w 
  gi|386002719|ref|YP_005921018.1| 584 ALPLILWIWP 593
                                       **99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4072.25
//
Query:       gi|386002720|ref|YP_005921019.1|  [L=636]
Description: TrkA-C domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-58  198.9  69.1    2.2e-45  155.1  37.3    1.9  2  CitMHS         Citrate transporter
    2.7e-17   62.3   0.1    2.9e-10   39.8   0.0    2.4  2  TrkA_C         TrkA-C domain
    2.5e-15   56.5  28.5    1.3e-11   44.2  10.8    2.4  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
  ------ inclusion threshold ------
        0.8    9.1   0.0        0.8    9.1   0.0    2.7  3  MttA_Hcf106    mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.1  37.3     5e-49   2.2e-45       1     300 []      59     581 ..      59     581 .. 0.83
   2 !   58.2  23.8   1.7e-19   7.5e-16       8     168 ..     462     631 ..     452     634 .. 0.85

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 5e-49
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                       l+l+i+++ r dvv+ll+l+++    ++  ++a+ g++ p++++++++ + +++l  +G++d +a +l r++  +++
  gi|386002720|ref|YP_005921019.1|  59 LILFIWGRWRYDVVSLLALLAAtvtgLVPWDQAFLGFGHPAVITVAAVLVASRGLLNSGVVDVMAGWLSRAGD-SPT 134
                                       58**************999999*99999999**************************************8777.688 PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 .llvllvlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslp 149
                                         ++ l  l+ +ls+f++n+g++++++p+ +++a r +++p +ll+pla ++ +gg+lt+iGtp            p
  gi|386002720|ref|YP_005921019.1| 135 rQVASLTGLVTILSGFMNNVGAMALLLPVGIRMAIRSGNSPSILLMPLASGSLLGGLLTLIGTP------------P 199
                                       89999*******************************6666666*********************............* PP

                                       xxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                            CitMHS 150 nlll.....................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv..... 200
                                       n+++                     l+++l g+l++ l++                          ++l+pv     
  gi|386002720|ref|YP_005921019.1| 200 NIIIatfraesvgdpfgmfdftpvgLGVALSGFLFISLIG--------------------------WRLVPVrksps 250
                                       *********************999999999999*******..........................44444444444 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|386002720|ref|YP_005921019.1| 251 skerlfeienyltevlipegarmagktlqevreaskadfqvlgllsgetrlaspsifhplmpgeillvesdadelki 327
                                       44444444444444566667777777777777777777777777777777777777777777777777777777777 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|386002720|ref|YP_005921019.1| 328 flddtgfqlgeekkvgeealssgdmgiveavvktdsrllgrtarsaslrwrygvnlvgvarhgiqlqkrlgqvrfqa 404
                                       77777777777777777777778888888888888888888888888888888888888888888888888888888 PP

                                       ................................................................xxxxxxx...... RF
                            CitMHS 201 ................................................................atillla...... 207
                                                                                                             a      
  gi|386002720|ref|YP_005921019.1| 405 gdvlllqgprehlpeilntmgclplaerglrlghprriilsvaifgsailavavgllpvqialvS-----Aavamvm 476
                                       88888888888888888888888888888888888888888888876666555555555554441.....1556668 PP

                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 208 .........ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlgliallsafisnvava 271
                                                y +++W+v++l++++++++ ale tG + ++a+++ +   g +p+v+la++l+++++ls +++n+a+a
  gi|386002720|ref|YP_005921019.1| 477 gglmnlrevYTSIDWPVIILLGAMIPVGRALETTGGAGLIAESILSlsgGyPPIVSLAMLLVITMFLSDIVNNAAAA 553
                                       999********************************99999988855676469*9*********************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 272 almapialgmapalgllspsplalalavg 300
                                       +lmapi lg+a+ ++ lsp+p+++a a+g
  gi|386002720|ref|YP_005921019.1| 554 VLMAPIGLGIASFMN-LSPDPFLMAVAIG 581
                                       ************777.88*********98 PP

  == domain 2  score: 58.2 bits;  conditional E-value: 1.7e-19
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xx RF
                            CitMHS   8 klrldvvallvlvll..vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd..llvl.lv 79 
                                        + +++v+  v++++  ++ + e+++ i++p+i+ll++++ +g+ale tG++  +a+ +l+l+gg +    l + l 
  gi|386002720|ref|YP_005921019.1| 462 PVQIALVSAAVAMVMggLMNLREVYTSIDWPVIILLGAMIPVGRALETTGGAGLIAESILSLSGGYPPivSL-AmLL 537
                                       377888888888888999***********************************************9885334.3599 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                            CitMHS  80 lltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglslpnlll.. 153
                                       ++t++ls +v+n +++++m+pi l +a   ++l+p  +l+++a++a+    ltpiG               n l+  
  gi|386002720|ref|YP_005921019.1| 538 VITMFLSDIVNNAAAAVLMAPIGLGIAS-FMNLSPDpFLMAVAIGASCAF-LTPIGHQ------------SNTLVmg 600
                                       9**************************9.58888888************9.*****99............8888878 PP

                                       .................xxxxxxxxxxxxxxx RF
                            CitMHS 154 .................lalllvgllplvllf 168
                                                        l++++v  +pl+++f
  gi|386002720|ref|YP_005921019.1| 601 pggyqfgdywrmglpmeLVIAVV-SIPLIVIF 631
                                       87888888777777676555555.68888887 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.2e-08   0.00037       1      62 [.     262     325 ..     262     330 .. 0.89
   2 !   39.8   0.0   6.4e-14   2.9e-10       1      68 [.     354     423 ..     354     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.2e-08
                                       CEEEEEE--GGGTTSBHHHHTHHHH...S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar...gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdl 62 
                                       l+ev +p+g++++Gktl+e  +r+    ++ v+++  g  +l +ps    L++G +llv ++ ++l
  gi|386002720|ref|YP_005921019.1| 262 LTEVLIPEGARMAGKTLQE--VREAskaDFQVLGLLSGeTRLASPSIFHPLMPGEILLVESDADEL 325
                                       579****************..7777779*******88879999999999**********8888876 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 6.4e-14
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       +ve +v+ +s+l G+t + + lr r gv++v++ r+g +l    g  ++++GDvll+ g++++l e+ + 
  gi|386002720|ref|YP_005921019.1| 354 IVEAVVKTDSRLLGRTARSASLRWRyGVNLVGVaRHGIQLQKRLGQVRFQAGDVLLLQGPREHLPEILNT 423
                                       5899*****************************666677888888*******************998876 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   9.7   3.8e-07    0.0017     269     439 ..      48     210 ..      19     243 .. 0.80
   2 !   44.2  10.8   2.9e-15   1.3e-11     296     467 ..     465     633 ..     415     635 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-07
                     Na_sulph_symp 269 ekallilfvlllllWifgeslnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersglie 345
                                         ++ ++++l l+l i g        +v++++l    ++ ++ W+       +   ++  +++++ +++l +sg+++
  gi|386002720|ref|YP_005921019.1|  48 LAMIFGVLLLTLILFIWGRWR---YDVVSLLALLAATVTGLVPWD-QAFLGFGHPAVITVAAVLVASRGLLNSGVVD 120
                                       556777777777787777644...4678899999999999****9.44455666788888999999*********** PP

                     Na_sulph_symp 346 wlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfll 422
                                        ++  l+   +  sp+  ++ +   +v++   f  ++  +a llp+ + +a    g  p ++ ++la  + l+g+l+
  gi|386002720|ref|YP_005921019.1| 121 VMAGWLSRAGD--SPTRQVASLT-GLVTILSGFMNNVGAMALLLPVGIRMAIRS-GNSPSILLMPLASGSLLGGLLT 193
                                       ******99888..9999887765.5677788999*******************9.888999**************** PP

                     Na_sulph_symp 423 pyatgpnpivfgagylk 439
                                        ++t+pn i+  +   +
  gi|386002720|ref|YP_005921019.1| 194 LIGTPPNIIIATFRAES 210
                                       *********97765544 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 2.9e-15
                     Na_sulph_symp 296 vaivvlvillllr........vldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavai 364
                                       +a+v                 +++    v     W +++llg++i + + le +g    +++++ +++ g+ p v +
  gi|386002720|ref|YP_005921019.1| 465 IALVS-------AavamvmggLMNLR-EVYTSIDWPVIILLGAMIPVGRALETTGGAGLIAESILSLSGGYPPIVSL 533
                                       33333.......33333333588888.5667789******************************************* PP

                     Na_sulph_symp 365 iiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvk 441
                                       +++l++ +++      ++A  + ++pi l +a  + +  p  + +++a+  s a fl+p++   n +v g g  +  
  gi|386002720|ref|YP_005921019.1| 534 AMLLVITMFLSDI-VNNAAAAVLMAPIGLGIASFMNLS-PDPFLMAVAIGASCA-FLTPIGHQSNTLVMGPGGYQFG 607
                                       9999998877655.567777889************555.777788999999999.********************** PP

                     Na_sulph_symp 442 dywrlGfilsiigllillllgalwwk 467
                                       dywr+G+++ ++  ++ + l++++w 
  gi|386002720|ref|YP_005921019.1| 608 DYWRMGLPMELVIAVVSIPLIVIFWP 633
                                       *************************6 PP

>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3      0.73   3.3e+03       1      16 [.      93     108 ..      93     108 .. 0.88
   2 ?    9.1   0.0   0.00018       0.8      22      43 ..     267     288 ..     266     325 .. 0.91
   3 ?   -3.6   1.1       1.6   7.3e+03       2      14 ..     613     625 ..     612     631 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.73
                                       S-HHHHHHHHHHHHHH CS
                       MttA_Hcf106   1 lgapelliIlvValll 16 
                                       lg+ + ++I v a+l+
  gi|386002720|ref|YP_005921019.1|  93 LGFGHPAVITVAAVLV 108
                                       5889999****99997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                       MttA_Hcf106  22 LPEvaraLGktLreFkkavkel 43 
                                       +PE ar +GktL+e ++a k +
  gi|386002720|ref|YP_005921019.1| 267 IPEGARMAGKTLQEVREASKAD 288
                                       8*****************9976 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.6
                                       -HHHHHHHHHHHH CS
                       MttA_Hcf106   2 gapelliIlvVal 14 
                                       g+p  l+I+vV +
  gi|386002720|ref|YP_005921019.1| 613 GLPMELVIAVVSI 625
                                       7777899999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3767.84
//
Query:       gi|386002721|ref|YP_005921020.1|  [L=93]
Description: Peptidyl-prolyl cis-trans isomerase C [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  101.0   0.1    6.4e-29  100.8   0.1    1.1  1  Rotamase       PPIC-type PPIASE domain
    2.1e-28   99.2   0.2    2.7e-28   98.8   0.2    1.2  1  Rotamase_3     PPIC-type PPIASE domain
    5.2e-13   49.9   0.2      6e-13   49.7   0.2    1.0  1  Rotamase_2     PPIC-type PPIASE domain
  ------ inclusion threshold ------
      0.071   12.8   0.0      0.091   12.5   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal


Domain annotation for each model (and alignments):
>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.1   1.4e-32   6.4e-29      17      96 ..      13      90 ..       2      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.4e-32
                                      HHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHHCCS-CT-B-S-EEETTEEEEEEE CS
                          Rotamase 17 eakakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefekaafslkkGeisepvetkfGfhiikl 95
                                      ++++ka+e+le++++ge+ F+e+ArkyS d++s kn+Gdlgw++kg+++pefe+aaf+++kG++++pv+t+fG+h+ik+
  gi|386002721|ref|YP_005921020.1| 13 KTEKKAKEVLEKISKGES-FAEMARKYS-DCPSSKNKGDLGWFAKGKMVPEFERAAFEAEKGKVVGPVKTDFGYHLIKI 89
                                      5789************99.*********.*************************************************9 PP

                                      E CS
                          Rotamase 96 e 96
                                      +
  gi|386002721|ref|YP_005921020.1| 90 I 90
                                      7 PP

>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.2     6e-32   2.7e-28      14     116 .]       3      93 .]       1      93 [] 0.92

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 6e-32
                        Rotamase_3  14 dsvkvshIlistkgkesrseeeakakadsllaalkegadFaalAkeySdDpaskenGGelgwftkgqmvkeFedavf 90 
                                       ++v+++hIl++t           ++ka ++l+++ +g++Fa++A++ySd p+ ++n G+lgwf kg+mv+eFe a+f
  gi|386002721|ref|YP_005921020.1|   3 KQVHAAHILVKT-----------EKKAKEVLEKISKGESFAEMARKYSDCPS-SKNKGDLGWFAKGKMVPEFERAAF 67 
                                       578889999975...........689***********************998.56668******************* PP

                        Rotamase_3  91 slkkgeiskvvktdfGyHiikvtdkk 116
                                       +++kg++ ++vktdfGyH+ik++dkk
  gi|386002721|ref|YP_005921020.1|  68 EAEKGKVVGPVKTDFGYHLIKIIDKK 93 
                                       ***********************997 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.2   1.3e-16     6e-13      24     109 ..       6      93 .]       2      93 .] 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.3e-16
                        Rotamase_2  24 tlelavvkdqvaaeaalalakagaekdfaalakgnskkaadlg.....ifesasnlpeelakaafalkpgevsgpve 95 
                                       + +++ vk++++a+ +l++  +g  ++fa++a+++s+++++++     +f++ + +p e++ aaf++++g+v+gpv+
  gi|386002721|ref|YP_005921020.1|   6 HAAHILVKTEKKAKEVLEKISKG--ESFAEMARKYSDCPSSKNkgdlgWFAKGKMVP-EFERAAFEAEKGKVVGPVK 79 
                                       4568999**************99..59*******99885555555555**9999777.******************* PP

                        Rotamase_2  96 tdngyyivkvtevk 109
                                       td+gy+++k++++k
  gi|386002721|ref|YP_005921020.1|  80 TDFGYHLIKIIDKK 93 
                                       **********9975 PP

>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05     0.091      73     111 ..       5      39 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                                       HHHHHHHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH. CS
                     Ribo_biogen_C  73 laaalyilglkeeaeellskfkwgeeFlelnkelleeYa 111
                                       + aa +++ ++++a+e+l+k + ge+F e+ ++    Y+
  gi|386002721|ref|YP_005921020.1|   5 VHAAHILVKTEKKAKEVLEKISKGESFAEMARK----YS 39 
                                       5689999*********************99875....44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 775.68
//
Query:       gi|386002722|ref|YP_005921021.1|  [L=692]
Description: Multi-sensor signal transduction histidine kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-41  139.1   0.1    3.1e-26   91.5   0.1    3.4  3  PAS_3         PAS fold
    6.9e-26   90.5   0.0      2e-13   50.5   0.0    3.6  3  PAS_9         PAS domain
    2.4e-24   85.5   0.0    2.5e-08   33.9   0.0    3.9  3  PAS           PAS fold
    1.7e-22   79.7   0.0    6.6e-22   77.8   0.0    2.1  2  Response_reg  Response regulator receiver domain
    7.2e-20   71.3   1.2    1.7e-10   41.1   0.0    4.4  5  PAS_4         PAS fold
    4.4e-13   48.9   0.0    0.00019   21.4   0.0    3.7  3  PAS_8         PAS domain
    3.5e-07   30.6   0.0    9.2e-07   29.2   0.0    1.8  1  GAF_2         GAF domain
    0.00034   20.7   0.0      0.027   14.6   0.0    2.8  3  PAS_11        PAS domain
     0.0044   17.6   0.0       0.01   16.5   0.0    1.6  1  GAF           GAF domain
  ------ inclusion threshold ------
      0.059   14.0   0.0       0.15   12.7   0.0    1.7  1  PAS_10        PAS domain


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 !   28.9   0.0   5.9e-10   1.1e-06       2      88 ..     323     407 ..     322     408 .. 0.95
   2 !   14.7   0.0   1.5e-05     0.027       3      43 ..     450     489 ..     448     512 .. 0.85
   3 !   91.5   0.1   1.7e-29   3.1e-26       4      89 .]     576     663 ..     575     663 .. 0.98

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.9e-10
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +  s+  e+i+Gy++ e+ g+   +  l  peD + + e + ++ ++g+ ++g   ++rk+Ge +    ++++++de
  gi|386002722|ref|YP_005921021.1| 323 LEFSPGAEKIFGYRRREMVGN--PVSRLHLPEDVALFPEVHRQMREGGRGFSGLTTLVRKNGEKFPAIFSTYPLFDE 397
                                       56899****************..****************************************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g+    +gv
  gi|386002722|ref|YP_005921021.1| 398 SGQMRAALGV 407
                                       ***9888776 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-05
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealq 43 
                                        v+ + e ++G  p+e++gk  +w +++  eDre +++ + 
  gi|386002722|ref|YP_005921021.1| 450 KVNSESEALFGRPPQEVEGK-MRWDEFISEEDREDLWDLFR 489
                                       589999**************.99*********999888776 PP

  == domain 3  score: 91.5 bits;  conditional E-value: 1.7e-29
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvi.rde 78 
                                        s+++ eilGyspeel+ ++  w +lvhp+Dr+rv++al+++l++ +py e+e+R+r kdG+++w+  r++v+ +de
  gi|386002722|ref|YP_005921021.1| 576 FSDKWGEILGYSPEELKTHLGIWDSLVHPDDRARVKQALMDHLEGLTPYcEIEHRMRSKDGGWVWILGRGKVVsWDE 652
                                       6899************************************************************************* PP

                             PAS_3  79 ngkpvrvigva 89 
                                        g+pvr+ gv+
  gi|386002722|ref|YP_005921021.1| 653 RGRPVRMTGVI 663
                                       *********96 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.1e-16     2e-13       3     104 .]     309     413 ..     307     413 .. 0.86
   2 !   21.6   0.0   1.1e-07   0.00019       3     104 .]     438     538 ..     436     538 .. 0.79
   3 !   14.2   0.0   2.2e-05     0.039      16      99 ..     576     663 ..     571     668 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.1e-16
                             PAS_9   3 gili...dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirknge 74 
                                       +++i    +pd ++l ++++a++++Gy ++e++g +++ l    pe+   + ++ +q+r+    +++ ++l+rknge
  gi|386002722|ref|YP_005921021.1| 309 SFVItdgSDPDPTVLEFSPGAEKIFGYRRREMVGNPVSRLH--LPEDVALFPEVHRQMREggRGFSGLTTLVRKNGE 383
                                       66765556677799***************************..55555555555555555567************** PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +f++ ++ +p++d++g +++++++++Dite
  gi|386002722|ref|YP_005921021.1| 384 KFPAIFSTYPLFDESGQMRAALGVSVDITE 413
                                       *****************************8 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.1e-07
                             PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgks.itdlfvtdpeanerlraaleqgrk....kerevevvlirkng 73 
                                       +++i+ +dg ++ ++N   + l+G  p+ev gk  +++++  ++e++e+l+++++ g++    +  ++e +li++ g
  gi|386002722|ref|YP_005921021.1| 438 AMAIVEEDG-LIsKVNSESEALFGRPPQEVEGKMrWDEFI--SEEDREDLWDLFRKGQRrlktPTAQYEADLIDRWG 511
                                       688999***.666********************7588888..****************99*9999999999999977 PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDite 104
                                       +    l++as +  +    + ++v +++ite
  gi|386002722|ref|YP_005921021.1| 512 GIKRGLFRASIIPRT----KQYVVSVTNITE 538
                                       555555555444322....224556666665 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.2e-05
                             PAS_9  16 aNeaalrllGyspeevlgks.itdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvlltaspv.kdd 88 
                                       +++++ ++lGyspee+  +  i+d +v+++++++ ++a+++ ++   + +e e  ++ k+g+ +w+l +   v +d+
  gi|386002722|ref|YP_005921021.1| 576 FSDKWGEILGYSPEELKTHLgIWDSLVHPDDRARVKQALMDHLEGltPYCEIEHRMRSKDGGWVWILGRGKVVsWDE 652
                                       688999*********7665568888878888888888888888889999******************9999995555 PP

                             PAS_9  89 dgelvgiivil 99 
                                        g+ v++ +++
  gi|386002722|ref|YP_005921021.1| 653 RGRPVRMTGVI 663
                                       88877776666 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.2e-11   1.1e-07       3     109 ..     299     407 ..     297     411 .. 0.91
   2 !   33.9   0.0   1.4e-11   2.5e-08       2      65 ..     427     491 ..     426     503 .. 0.84
   3 !   15.2   0.0   8.9e-06     0.016      13      98 ..     563     650 ..     551     666 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.2e-11
                                       HHHHHHHSSSEEEEEE...TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCC CS
                               PAS   3 lraileslpdpifvvD...edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrage 76 
                                       l ai+e++ +  +++D    d  +l++++ ae+++G++r e++g ++++l  +ed a ++e  +q +e g+ +++  
  gi|386002722|ref|YP_005921021.1| 299 LLAIFETAEVSFVITDgsdPDPTVLEFSPGAEKIFGYRRREMVGNPVSRLHLPEDVALFPEVHRQMREGGRGFSGLT 375
                                       6688888888888888777999********************************99999999999999999999999 PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgv 109
                                       + +++ +g+++++   + p++d++g+++ +lgv
  gi|386002722|ref|YP_005921021.1| 376 TLVRK-NGEKFPAIFSTYPLFDESGQMRAALGV 407
                                       99999.*********************999997 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 1.4e-11
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHH CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleql 65 
                                        +rai+e++ +++ +v edg i+ vN++ e l+G +++ev gk+  d+++ e+d+ +l +l+++ 
  gi|386002722|ref|YP_005921021.1| 427 YYRAIFENSGTAMAIVEEDGLISKVNSESEALFGRPPQEVEGKMRWDEFISEEDReDLWDLFRKG 491
                                       79**********************************************99997654444444443 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 8.9e-06
                                       EEEEEETTSBEEEECHHHHHHHSSTHHHC.TTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEE CS
                               PAS  13 pifvvDedgrilyvNaaaeellGlsreev.lgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpi 87 
                                       +i+ ++  +    +++++ e+lG+s+ee+  +  + d+++++dd+  ++++l  +le  ++ +  e++ + +dg+ +
  gi|386002722|ref|YP_005921021.1| 563 GIWDWNLETGEGSFSDKWGEILGYSPEELkTHLGIWDSLVHPDDRaRVKQALMDHLEGLTPYCEIEHRMRSKDGGWV 639
                                       788888666666789***********99945778999999999998******************************* PP

                                       EEEEEEEEEEE CS
                               PAS  88 hlevraspvrd 98 
                                       +++ r + v +
  gi|386002722|ref|YP_005921021.1| 640 WILGRGKVVSW 650
                                       **999887765 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   3.7e-25   6.6e-22       1     109 [.       4     114 ..       4     117 .. 0.93
   2 ?   -4.1   0.0       9.7   1.7e+04      31      50 ..     295     314 ..     290     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 3.7e-25
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH..HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell..keekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vlivdDdp+++el + +le++g  +v+ +e+++e le l   e+++++++ D  mpgmdG+ +lk +r ++ e+p i
  gi|386002722|ref|YP_005921021.1|   4 VLIVDDDPAILELAALFLERSGDIQVDPTETAAEGLERLegGERNYHVVVSDYAMPGMDGIAFLKAVRSRKLEIPFI 80 
                                       8******************66655***************655677******************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHHHHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpeeLlk 109
                                       ++t++s ee+++eal+ gad +l+K+ +p+ L +
  gi|386002722|ref|YP_005921021.1|  81 LFTGKSREEVVIEALNSGADYYLQKDGNPKILFA 114
                                       **************************99987765 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 9.7
                                       SHHHHHHHHHHHHESEEEEE CS
                      Response_reg  31 dgkealellkeekvdlillD 50 
                                       + +++l+++++ +v  +++D
  gi|386002722|ref|YP_005921021.1| 295 SEEQLLAIFETAEVSFVITD 314
                                       56788888888888888888 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.4   1.5e+04      47      62 ..     111     126 ..     108     130 .. 0.80
   2 ?   -0.4   0.0      0.74   1.3e+03      84     102 ..     240     257 ..     220     262 .. 0.80
   3 !   41.1   0.0   9.7e-14   1.7e-10      12     110 .]     317     416 ..     303     416 .. 0.91
   4 !   19.5   0.0   4.8e-07   0.00087       1     108 [.     432     539 ..     432     541 .. 0.70
   5 !    5.7   0.1    0.0095        17      42     107 ..     600     668 ..     577     671 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.4
                             PAS_4  47 edaarleralrrvleg 62 
                                        + a+l++++r+++e+
  gi|386002722|ref|YP_005921021.1| 111 ILFAELSHQIRQAAES 126
                                       5678999999999985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.74
                             PAS_4  84 rllPlrdesGevigvlvis 102
                                        ++P+r ++Gevig++ ++
  gi|386002722|ref|YP_005921021.1| 240 AVVPIR-HEGEVIGYYSVG 257
                                       469998.6******99776 PP

  == domain 3  score: 41.1 bits;  conditional E-value: 9.7e-14
                             PAS_4  12 dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllP 87 
                                       dpd +vl  ++ a+++fg+++ e++G ++  l+ +ed a + +  r++ eg++  + l++l++ +ge  +  ++ +P
  gi|386002722|ref|YP_005921021.1| 317 DPDPTVLEFSPGAEKIFGYRRREMVGNPVSRLHLPEDVALFPEVHRQMREGGRGFSGLTTLVRkNGEKFPAIFSTYP 393
                                       99******************************999988888888888889*************************** PP

                             PAS_4  88 lrdesGevigvlvisrDiTerrr 110
                                       l+desG+ +++l++s+DiTe++r
  gi|386002722|ref|YP_005921021.1| 394 LFDESGQMRAALGVSVDITEQKR 416
                                       ********************986 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 4.8e-07
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralr...rvlegeepiefleell 73 
                                       ++++  a a++ +dg +  +N ++++lfg+pp+e+ Gk  + e+ +eed+++l +  r   r l++ +++++++  +
  gi|386002722|ref|YP_005921021.1| 432 FENSGTAMAIVEEDGLISKVNSESEALFGRPPQEVEGKMRWdEFISEEDREDLWDLFRkgqRRLKTPTAQYEADLID 508
                                       7899999*******************************88878*****99988766651114555555555555555 PP

                             PAS_4  74 l..pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                       +  + ++  +  +++P  +       ++v ++ iTe+
  gi|386002722|ref|YP_005921021.1| 509 RwgGIKRGLFRASIIPRTK------QYVVSVTNITEQ 539
                                       5544444444444455432......555555555555 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0095
                             PAS_4  42 ellpeedaarleralrrvlegeepiefleelll..pgeerhyelrl..lPlrdesGevigvlvisrDiTe 107
                                       +l+ ++d+ar+ +al   leg +p+ + e++ +  +g++++++ r   + + de+G+++   ++++++ +
  gi|386002722|ref|YP_005921021.1| 600 SLVHPDDRARVKQALMDHLEGLTPYCEIEHRMRskDGGWVWILGRGkvVSW-DERGRPVRMTGVIQEMRA 668
                                       566667***********************9999999999999988887888.899999998888887765 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0023       2      47 ..     298     349 ..     297     371 .. 0.77
   2 !   21.4   0.0     1e-07   0.00019       1      63 [.     426     488 ..     426     493 .. 0.70
   3 ?    5.3   0.0     0.012        21      26      63 ..     576     614 ..     551     619 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                             PAS_8   2 rlralfesspdgiavvd..lgd..rivdvNqaalellGys.adlkgellg..q 47 
                                       +l a+fe++ ++ +++d  +    ++++  + a++++Gy+  ++ g ++    
  gi|386002722|ref|YP_005921021.1| 298 QLLAIFETAEVSFVITDgsD-PdpTVLEFSPGAEKIFGYRrREMVGNPVSrlH 349
                                       56689***********9653.2579***************9999998885432 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1e-07
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle..daeqll 63 
                                       e++ra+fe+s  ++a+v ++++i  vN   + l+G + +++ g +   +++++ ++++  d+++l+
  gi|386002722|ref|YP_005921021.1| 426 EYYRAIFENSGTAMAIVEEDGLISKVNSESEALFGRPpQEVEG-K--MRWDEFISEEDreDLWDLF 488
                                       79****************7777999**********66444333.3..3333333333324665555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.012
                             PAS_8  26 vNqaalellGys.adlkgellgqllpvlrplledaeqll 63 
                                         +++ e+lGys ++lk+ l  ++  v+++ +++ +q l
  gi|386002722|ref|YP_005921021.1| 576 FSDKWGEILGYSpEELKTHLGIWDSLVHPDDRARVKQAL 614
                                       678899************999777777777666777766 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.1e-10   9.2e-07       2     137 ..     147     283 ..     146     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.1e-10
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndlee 76 
                                       ++l+  l+l++ +++ +   ++g i+l++   g + l+++ +  +e  ++++r+ ++  +  + r ++p+++ + ++
  gi|386002722|ref|YP_005921021.1| 147 TSLSAALSLCVGAAIAVSeTDCGTIYLLERSSGsFILSHSQGFSPEYVEEISRRRRNPSTSLISRAQEPIYIRH-QD 222
                                       7899999*********95499******996555466666766777777777554433347789999******99.44 PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                          + + + +++glr++++vP+++eg+v+G  +++++  ++  +e ++ Le++a+    ai
  gi|386002722|ref|YP_005921021.1| 223 RGLPLQKAREREGLRAMAVVPIRHEGEVIGYYSVGTHTFDEIPPEGRSGLETIAAMTENAI 283
                                       45666666899**********************9888888888888888888888777766 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       8.3   1.5e+04      64      84 ..     165     185 ..     162     188 .. 0.81
   2 ?    2.6   0.0     0.081   1.5e+02      29      73 ..     334     377 ..     317     386 .. 0.85
   3 !   14.6   0.0   1.5e-05     0.027      39      89 ..     597     647 ..     583     655 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.3
                            PAS_11  64 geatsslyRLrlsqdkfvkvk 84 
                                       ++ + ++y L  s++ f+  +
  gi|386002722|ref|YP_005921021.1| 165 ETDCGTIYLLERSSGSFILSH 185
                                       567899999999999999766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.081
                            PAS_11  29 glekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRL 73 
                                       g+ + e+vg  + +L+ p+d+    + +r++  + g++ s l  L
  gi|386002722|ref|YP_005921021.1| 334 GYRRREMVGNPVSRLHLPEDVALFPEVHRQMR-EGGRGFSGLTTL 377
                                       89999**************************9.999888766555 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.5e-05
                            PAS_11  39 siydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktkskl 89 
                                       ++  L+hp+d+ ++k++l++ ++     ++   R+r++++ +v++  ++k+
  gi|386002722|ref|YP_005921021.1| 597 IWDSLVHPDDRARVKQALMDHLEGLTPYCEIEHRMRSKDGGWVWILGRGKV 647
                                       6999******************999999****************9777776 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.6e-06      0.01      18     108 ..     165     257 ..     148     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.6e-06
                                       TESEEEEEE.EEETTEEECEEEEECC.........EEEET.TSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHH CS
                               GAF  18 gadrvalyl.pdydGlhydipqasrw.........lfmkn.grgicgqvlatgqplvipdstpdprfaqynrrdlle 83 
                                       + d +++yl ++++G+   +++++ +          +++n  ++++    + ++p+ i    + +r ++   ++  e
  gi|386002722|ref|YP_005921021.1| 165 ETDCGTIYLlERSSGSFI-LSHSQGFspeyveeisRRRRNpSTSLI---SRAQEPIYIR---HQDRGLP--LQKARE 232
                                       567777877644555333.333344443333333322222133323...3457899999...7777666..667889 PP

                                       HTTESEEEEEEEEETTEEEEEEEEE CS
                               GAF  84 nmgirsslvvPlvndgelwGllvlh 108
                                       + g r+++vvP++++ge++G  ++ 
  gi|386002722|ref|YP_005921021.1| 233 REGLRAMAVVPIRHEGEVIGYYSVG 257
                                       9*******************76665 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.3e-05      0.15      18     106 .]     319     412 ..     300     412 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                            PAS_10  18 nlqirrFtpaakklfk.lipadvGrpladihpkkavknveeviealrtgekdevevvv..p.kngkw.vlvrylpyr 89 
                                       +  ++ F+p a+k+f  ++++ vG+p++ +h ++ v  + ev  ++r+g +  +        + +k+  +  + p+ 
  gi|386002722|ref|YP_005921021.1| 319 DPTVLEFSPGAEKIFGyRRREMVGNPVSRLHLPEDVALFPEVHRQMREGGRGFSGLTTlvRkNGEKFpAIFSTYPLF 395
                                       557899***9999997266788***************************9965443321131445554677888999 PP

                            PAS_10  90 dedgeiaGvvetfvDit 106
                                       de g+++ ++ + vDit
  gi|386002722|ref|YP_005921021.1| 396 DESGQMRAALGVSVDIT 412
                                       99999888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 3751.97
//
Query:       gi|386002723|ref|YP_005921022.1|  [L=384]
Description: Myo-inositol-1-phosphate synthase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-32  111.4   0.0    8.5e-32  109.7   0.0    1.8  2  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
    0.00016   21.2   0.0    0.00043   19.8   0.0    1.6  2  NAD_binding_5   Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.34     3e+03      48      77 ..     109     141 ..     101     152 .. 0.66
   2 !  109.7   0.0   9.4e-36   8.5e-32       1     109 []     196     304 ..     196     304 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHSS--EEE.......EEEEE-GG CS
                    Inos-1-P_synth  48 isKssvvddivkanelly...vdhevvikYvpy 77 
                                        sK+ vv+d    + + +      ev i+Y+p+
  gi|386002723|ref|YP_005921022.1| 109 DSKTFVVSDREPCDVVREldeSGAEVLINYMPV 141
                                       567777766644444433444556799999986 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 9.4e-36
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kY 74 
                                       G+T+++++La+l+ +rg+k++++++lN +Gn+D++n+ +++r+ksK+isK+++v+++++  +l+     ++i   +Y
  gi|386002723|ref|YP_005921022.1| 196 GATIVHRTLAKLFNDRGCKLDRTYQLNTGGNTDFLNMLSQDRLKSKRISKTEAVQSVLDV-PLMA--DDIHIgpsDY 269
                                       9*********************************************************98.5443..4699999*** PP

                                       -GGGTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  75 vpylgDsKvaldeieseiflggkntielkleceDS 109
                                       vp+ +D+K+++ ++e++if+++++++el+l++eDS
  gi|386002723|ref|YP_005921022.1| 270 VPWQKDNKICFLRMEGRIFGDVPINLELRLSVEDS 304
                                       **********************************9 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.23   2.1e+03      61      96 ..      32      68 ..       8      79 .. 0.66
   2 !   19.8   0.0   4.8e-08   0.00043     205     260 ..     146     260 ..     117     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.23
                                      xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 61 dvyvpikdllplvnpndl.vfgGwDisslnlaeamer 96
                                      +    +++ +  + p d+ v+ ++Di + ++ + +++
  gi|386002723|ref|YP_005921022.1| 32 NWIGLMHRSVGGYRPGDIeVVAAFDIDERKVGKDVSE 68
                                      3444566666777788887778888887777766655 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 4.8e-08
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx............................. RF
                     NAD_binding_5 205 pstiyavAailegvpyingsPqntl.vpglvelAekkgvfiaGdDfKt............................. 251
                                       +s  ya Aa+ +gv y+n  P      p+  +  e+ g++i+GdD+K+                             
  gi|386002723|ref|YP_005921022.1| 146 ASRFYAQAALDAGVGYVNCMPVFIAsDPAWAKKFEEAGIPIVGDDVKSqigativhrtlaklfndrgckldrtyqln 222
                                       7999******************99989*********************99999999988888888888888888888 PP

                                       .............................xxxxxxxxx RF
                     NAD_binding_5 252 .............................lLAaPlilD 260
                                                                    +L  Pl+ D
  gi|386002723|ref|YP_005921022.1| 223 tggntdflnmlsqdrlkskriskteavqsVLDVPLMAD 260
                                       88888888888888888888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2414.06
//
Query:       gi|386002724|ref|YP_005921023.1|  [L=267]
Description: Prephenate dehydratase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-56  191.1   0.0    1.9e-56  190.8   0.0    1.1  1  PDT       Prephenate dehydratase
    2.1e-12   46.6   0.0    4.6e-12   45.5   0.0    1.6  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.0   2.1e-60   1.9e-56       1     181 [.       2     175 ..       2     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 2.1e-60
                                       EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEE CS
                               PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgE 77 
                                       +++lGpegt+s++Aa+++   +++e+  ++ +eev++ave g+ad++vvP+ENs+eGsV  tlD Ll+ +d++ivgE
  gi|386002724|ref|YP_005921023.1|   2 IGVLGPEGTFSEKAARRLS--PGAEIRYFRDFEEVISAVEVGDADLGVVPLENSLEGSVGATLDSLLR-HDVEIVGE 75 
                                       789*************998..***********************************************.99****** PP

                                       EEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHH CS
                               PDT  78 vvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaae 154
                                       + l+i+hcLl++ +   e ++ ++Shpqal+Qcr ++++++p++e +++ st++Aa+   a++  ++aaia ++aa 
  gi|386002724|ref|YP_005921023.1|  76 INLRIRHCLLGRGGA--EGVRVILSHPQALAQCRGYIKRRFPEAELRTTGSTSHAARL--AQEFPEMAAIADAEAAG 148
                                       ************999..99***************************************..999************** PP

                                       HTT-EEEECS-SS-S--EEEEEEEEET CS
                               PDT 155 lyglkvleeniedkknntTRFlvlake 181
                                       +ygl v+e++++d+++n+TRF v+++ 
  gi|386002724|ref|YP_005921023.1| 149 RYGLAVIERDVQDSDENVTRFAVVGRS 175
                                       ************************986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   5.1e-16   4.6e-12       9      65 ..     194     250 ..     186     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 5.1e-16
                                       SSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   9 DrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                        +PG+L +v+g +a rgiN+++ie+r+s++ +++++f++++++++++++v+eal ++
  gi|386002724|ref|YP_005921023.1| 194 TEPGALWEVLGEFATRGINLTKIESRPSRRALGDYYFFIDLEGHASDPQVKEALARI 250
                                       58****************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1777.54
//
Query:       gi|386002725|ref|YP_005921024.1|  [L=418]
Description: Hydroxymethylglutaryl-CoA reductase, degradative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.1e-111  372.5   6.6   2.5e-111  372.3   6.6    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
       0.55   10.5   3.9        3.4    8.0   0.3    3.4  3  GARS_C       Phosphoribosylglycinamide synthetase, C domain


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.3   6.6  2.8e-115  2.5e-111       4     367 .]      16     378 ..      13     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 372.3 bits;  conditional E-value: 2.8e-115
                                       HHHHHHHH...S-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHHH CS
                       HMG-CoA_red   4 eRrkllee...lteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrga 77 
                                       +R+k+++e   l+e+e+e++++ +l+ ++adkm+Env+G +q+PlG+a+++li+g+e+lvPmAteE+s++A+as+ga
  gi|386002725|ref|YP_005921024.1|  16 DRLKMVAEnsgLSEAEVEAIGSLGLSLDQADKMVENVVGLFQIPLGIATNFLIDGREVLVPMATEEPSVIAAASNGA 92 
                                       7999999989999**************************************************************** PP

                                       HHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-...S CS
                       HMG-CoA_red  78 kainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla...g 147
                                       +++ ++gG+ +t++++ ++ra ++++  v+d+  ++ +i +++ e+ + an+ +++  s+ggg+  +e+ v++   g
  gi|386002725|ref|YP_005921024.1|  93 RMALAGGGF-VTSSTEPVMRALIQVT-GVDDPWGTRLAIlARSGEIAARANEKDPMlvSHGGGVVGVEAeVVEtrkG 167
                                       *********.9999999*********.******************************************77779999 PP

                                       SEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHH CS
                       HMG-CoA_red 148 rlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevv 224
                                       ++vv++l vd++DAmGaN+vn+++ea+a++iee++g++++l+i sNl++ ++a+a+++++ +++        g+evv
  gi|386002725|ref|YP_005921024.1| 168 PMVVVHLLVDCRDAMGANAVNTMAEALAPFIEEITGGRVYLRIISNLADLRLARARAVFKAEEI-------GGAEVV 237
                                       9***********************************************************9999.......9***** PP

                                       HHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT..........SEEETTT CS
                       HMG-CoA_red 225 ekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa..........leevedg 291
                                       + i+ asa a+ d++ra  +t+nkGi       +Ng++Av +AtG+D++a+e+++h +aa           e+ +dg
  gi|386002725|ref|YP_005921024.1| 238 DGIVLASALAESDPYRA--ATHNKGI-------MNGVTAVTMATGNDTRAIEAGAHSYAArggmyrslsvYEKNRDG 305
                                       *****************..*******.......********************************995554444888 PP

                                       EEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 292 dlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       dl+gs++lP ++VGtvGG+t+++p a+++ ++lg+++a+   +L +i+a+vgLAq+++alrALa+eg+q+gHm+lh+
  gi|386002725|ref|YP_005921024.1| 306 DLVGSIELP-VAVGTVGGATRVHPVARAAvRVLGLRSAD---DLGRILASVGLAQNFAALRALATEGIQRGHMSLHA 378
                                       9********.*****************************...*********************************96 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.16   1.5e+03      34      47 ..     133     159 ..      76     167 .. 0.69
   2 ?    1.1   0.0     0.054   4.8e+02      37      66 ..     201     231 ..     179     237 .. 0.80
   3 ?    8.0   0.3   0.00038       3.4      37      74 ..     343     379 ..     272     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.16
                                       E.............EEE-SSEEEEEEE CS
                            GARS_C  34 k.............lvtsGGRvlavva 47 
                                       +             lv++GG v++v a
  gi|386002725|ref|YP_005921024.1| 133 SgeiaaranekdpmLVSHGGGVVGVEA 159
                                       044444555567778999999988866 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.054
                                       E-SSEE.EEEEEEESSHHHHHHHHHHHHTTC CS
                            GARS_C  37 tsGGRv.lavvavgetleeArakayeavkki 66 
                                        +GGRv l +++  ++l+ Ara+a  ++++i
  gi|386002725|ref|YP_005921024.1| 201 ITGGRVyLRIISNLADLRLARARAVFKAEEI 231
                                       689**95567888899999999998777665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00038
                                       E-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE-- CS
                            GARS_C  37 tsGGRvlavvavgetleeArakayeavkkikfeglfyR 74 
                                        + GR+la v++++++++ ra a e++++ ++ +l+ R
  gi|386002725|ref|YP_005921024.1| 343 DDLGRILASVGLAQNFAALRALATEGIQRGHM-SLHAR 379
                                       456*************************9988.56655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2716.50
//
Query:       gi|386002726|ref|YP_005921025.1|  [L=505]
Description: Beta-ribofuranosylaminobenzene 5'-phosphate synthase family [Methanosaeta harundinacea 6Ac]
Scores for 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-30  103.9   0.0    1.3e-29  103.1   0.0    1.3  1  DUF98           p-hydroxybenzoic acid synthase
    7.5e-07   29.3   0.3    2.5e-06   27.6   0.3    2.0  1  GHMP_kinases_N  GHMP kinases N terminal domain
    9.3e-07   29.1   0.2      3e-06   27.5   0.2    1.9  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.025   14.4   0.3      0.047   13.5   0.3    1.5  1  UTRA            UTRA domain


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.0   2.8e-33   1.3e-29       1     143 [.      25     176 ..      24     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 2.8e-33
                                       HH--S-HHHHHHHHHSS-EEEEEEEEEEEE--HHHHHHHTS-TT-EEEEEEEEEEE..TTEEEEEEEEEEEGGGS-H CS
                             DUF98   1 LlgDGsvTrhlelltqekveveliemeaeeseeeeapkeveelkkpllrRqVwlra..ngqklayAeSwwneeelek 75 
                                       L +DGsvT  le++t+++ve+e++ +++++++e++a + + e ++++++R+V l++  +g++l++A+S +++++le+
  gi|386002726|ref|YP_005921025.1|  25 LGTDGSVTCLLEVVTGSPVEIETLVQRVVAADEATARELEIEAGDEVNYRVVKLKSsaSGETLIHAASLTPIKRLED 101
                                       568****************************************************9999****************** PP

                                       HHHH....SSS-HHHHHHHTT--BEEEE.EEEEEEE--HHHHHHT..SS-EEEEEEEEEEETTEEEEEEEEEEEG CS
                             DUF98  76 ylke....kdqpiwksLtkerlelfRei.rglalgeadeLeeafg..ekgpfwsRhYrlfhkgkpltvirEvFsp 143
                                        +k     +d+pi+++L+++r+e++R++ r  al+ea  L+  fg  +k p++sR+Y+++++g+pl+ i+E+F+ 
  gi|386002726|ref|YP_005921025.1| 102 RFKTdlmrADMPIGTILKRHRIESRRDLlRFRALKEAADLRGIFGvlSKEPLLSREYKIIRHGRPLMAITETFPY 176
                                       **9989999******************82555678888******98889************************97 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.3   5.6e-10   2.5e-06       1      65 [.     257     317 ..     257     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.6e-10
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyG 65 
                                       di+i+s    + GLG+++ la a+++Al++l+g s      a e+ +++ +g +sg+ vaa+  G
  gi|386002726|ref|YP_005921025.1| 257 DIRIRSSYQQHVGLGGGTQLAMAVAKALCELYGRSP----PAREIAKAVERGGTSGIGVAAFEGG 317
                                       6899****************************9763....37777777777*********98665 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.2   6.8e-10     3e-06       1      84 [.     404     484 ..     404     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.8e-10
                    GHMP_kinases_C   1 llealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqva 76 
                                       +++a+ +g +e +g ++n+ q++  ++ +v+   p +++l e+++e+G  +a+   +++Gptv+a++  ++++ +++
  gi|386002726|ref|YP_005921025.1| 404 MMPAVMTGEIEGFGAAVNRIQALgFKRVEVELQDPLVRRLMEEMREAG--AAGSGLSSFGPTVYAVA--DSGVREIE 476
                                       678888999***************9999********************..888888888********..99999999 PP

                    GHMP_kinases_C  77 ralreefe 84 
                                        a re +e
  gi|386002726|ref|YP_005921025.1| 477 AAAREVME 484
                                       99999886 PP

>> UTRA  UTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.1e-05     0.047       6     140 ..      43     179 ..      39     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                       EEEEEEEEEEEE--HHHHHHHTS-TTSEE.EEEEEE.EEETTEEEEEEEEEEEGGGTTTCHHHHHH..CS-HHHHHH CS
                              UTRA   6 pktevlsleevpasaeiaeaLglpagepv.lrieRl.rladgepvaleesylpaslvpdlleedle..egslyayle 78 
                                       ++ e+l  ++v a+++ a++L+++ag++v +r++ l   a ge ++++ s  p ++++d  + dl   + ++  +l+
  gi|386002726|ref|YP_005921025.1|  43 VEIETLVQRVVAADEATARELEIEAGDEVnYRVVKLkSSASGETLIHAASLTPIKRLEDRFKTDLMraDMPIGTILK 119
                                       67899***********************855555552567*********************9999655777777776 PP

                                       HHHTTSEEEEEEEEEEEE--HHHHHHHTSTTT-EEEEEEEEEEETTSCEEEEEEEEEETTTE CS
                              UTRA  79 erlgvpitraeetiearladaeeaelLgisagspvLviervtydadgrpveysrsyyrgdrf 140
                                       + + ++ +r   +++a    a+   ++g+ + +p+L+ e       grp+   +++++ ++f
  gi|386002726|ref|YP_005921025.1| 120 R-HRIESRRDLLRFRALKEAADLRGIFGVLSKEPLLSREYKIIRH-GRPLMAITETFPYHKF 179
                                       6.6666666666666666688999999999999999998888877.8888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 2690.42
//
Query:       gi|386002727|ref|YP_005921026.1|  [L=357]
Description: Peptidase M42 family protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-103  345.7   0.2   1.9e-103  345.5   0.2    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    3.5e-10   39.9   0.2    6.5e-10   39.1   0.2    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
  ------ inclusion threshold ------
      0.047   13.4   0.0        3.8    7.1   0.0    2.4  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.5   0.2  3.1e-107  1.9e-103       1     292 []      51     342 ..      51     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: 345.5 bits;  conditional E-value: 3.1e-107
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gnl+a+++g   +p+vmiaAH+DeiG+m k ++e+Gf+rf ++GG+ +++l +qrv i+ ++g i GvigskppH++
  gi|386002727|ref|YP_005921026.1|  51 GNLVATRRG--RRPSVMIAAHIDEIGLMTKYVDEKGFIRFVTIGGWFDQTLLNQRVIIHADSGPIWGVIGSKPPHVM 125
                                       9********..99**************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       ++e+rkk++e+k++f+D+g +s+eea  lGi++G+++++d++f++la++++++ka+D+ragv++++e+lk+ ++e+ 
  gi|386002727|ref|YP_005921026.1| 126 TPEDRKKPIEVKDMFVDAGCESQEEALGLGIKPGTPMSIDRTFARLAGDRVTGKAFDNRAGVVMMIEALKRTRTES- 201
                                       ************************************************************************9985. PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpklr 226
                                         t+++v+tvqEEvGl+Ga+tsa+ ++pd+a+a Dvt+ gd+pg ++k++   +gkGpv+++ Das   +i+  k++
  gi|386002727|ref|YP_005921026.1| 202 --TIFAVGTVQEEVGLKGARTSAFGLSPDVALATDVTIPGDHPGIDKKDSPleIGKGPVVIIADASgrgIITTSKVV 276
                                       ..***********************************************9899************999899****** PP

                                       HHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 227 kkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       ++l e+Ak+ +ip+q+ev  gg+tDA+ai+lt+eg+ t++is++tryiHspvev++l+d++a+++L
  gi|386002727|ref|YP_005921026.1| 277 SWLAETAKEFEIPVQMEVSGGGTTDATAIQLTREGIHTGVISVATRYIHSPVEVLSLKDVDACAEL 342
                                       ***************************************************************987 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.2   1.1e-13   6.5e-10      31     206 ..     177     348 ..     163     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.1e-13
                                       ESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEE..EEEEESSSBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                     Peptidase_M20  31 yGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavf..elhieepgil 105
                                        G  a d+ +gv++++eal++ + e      ti  + ++ EE+g +Ga+  + gl     +d ++  ++ i  ++++
  gi|386002727|ref|YP_005921026.1| 177 TGK-AFDNRAGVVMMIEALKRTRTES-----TIFAVGTVQEEVGLKGARTSAFGLS----PDVALatDVTIP-GDHP 242
                                       455.89*************9977776.....***********88899999999665....333331133333.2222 PP

                                       CHST....ETEEEE....EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH....TTTE CS
                                       xxxx....xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                     Peptidase_M20 106 eagk....laigvv....kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff....agip 170
                                         +k    l          v +    +g+   +  s++v +lae+a+e+    v+++vsg g+tda  +    +gi 
  gi|386002727|ref|YP_005921026.1| 243 GIDKkdspL----EigkgPVVIIADASGRGIITT-SKVVSWLAETAKEF-EIPVQMEVSGGGTTDATAIqltrEGIH 313
                                       222212233....144546777767888888888.9************6.777888866669*******87777776 PP

                                       EEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 171 tvmifgpgsglaHspnEyvdledlekgikvlarlle 206
                                       t +i +     +Hsp E ++l+d+ ++++++ar+le
  gi|386002727|ref|YP_005921026.1| 314 TGVISVAT-RYIHSPVEVLSLKDVDACAELIARALE 348
                                       77665545.89**********************986 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0057        34       1      26 [.      52      75 ..      52      86 .. 0.81
   2 ?    7.1   0.0   0.00064       3.8      35      82 ..     180     222 ..     165     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0057
                                      EEEEEESTTCESEEEEEEEE--B-TT CS
                     Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgv 26
                                      N++at +g+     ++++AH+D +g 
  gi|386002727|ref|YP_005921026.1| 52 NLVATRRGRR--PSVMIAAHIDEIGL 75
                                      7888888777..58********9886 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00064
                                       TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHH CS
                     Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafa 82 
                                       A Dn +gv++++e ++   +     + ++  + +  EE gl G++  a
  gi|386002727|ref|YP_005921026.1| 180 AFDNRAGVVMMIEALKRTRT-----ESTIFAVGTVQEEVGLKGARTSA 222
                                       889*********99887776.....7899999************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1919.84
//
Query:       gi|386002728|ref|YP_005921027.1|  [L=143]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-37  126.6   7.1    1.1e-36  126.4   7.1    1.0  1  Usp             Universal stress protein family
     0.0069   16.0   0.8     0.0088   15.6   0.8    1.2  1  AAA_25          AAA domain
  ------ inclusion threshold ------
      0.014   15.5   0.2      0.017   15.2   0.2    1.2  1  UPF0172         Uncharacterised protein family (UPF0172)
      0.025   15.4   0.1      0.043   14.6   0.1    1.4  1  Histone_HNS     H-NS histone family
      0.063   14.3   0.2       0.12   13.4   0.2    1.5  1  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon
      0.077   13.8   0.0       0.13   13.1   0.0    1.4  1  CTD_bind        RNA polymerase II-binding domain.
       0.14   12.4   0.7         18    5.7   0.1    2.7  2  IF3_N           Translation initiation factor IF-3, N-termina


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   7.1   4.4e-40   1.1e-36       1     141 []       1     143 []       1     143 [] 0.87

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 4.4e-40
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCC.CCHHHHHHHHHHHHHHHHHHHH.HHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavs.dadeeaeeeeleleeaeleada.akaaa 75 
                                       my+rIlVa+Dgs  sk A+e+A++laka+ga+l  ++++ +   +++  ++  + +e e++l++  ++a a  k++a
  gi|386002728|ref|YP_005921027.1|   1 MYDRILVATDGSAKSKVAVEHAVDLAKATGAKLLGVYIVNEVVVASAVrQLGADKKEIEAKLQASGEKAVAdIKKMA 77 
                                       9************************************998877666551444444444444444444444478**** PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +++gv+ve+ v++g pa +i+++a+ e++dliV+Gs+g+sg+ +ll+GSv ++vl  a+cpVlvVr
  gi|386002728|ref|YP_005921027.1|  78 DEAGVAVETMVRSGAPANAIVDLARTEEVDLIVMGSHGESGVTKLLIGSVVQKVLYWASCPVLVVR 143
                                       *****************************************************************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.8   3.4e-06    0.0088      37     147 ..       5     110 ..       4     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.4e-06
                            AAA_25  37 llaGapgtGKttlaldlalava..tGkpwlg.....pvapeqgkVlyvsaEdsedelrrRlravgeal.......rd 99 
                                       +l++  g+ K+ +a++ a+++a  tG ++lg     + ++   +V  + a+ +e  ++ +l+a ge++       +d
  gi|386002728|ref|YP_005921027.1|   5 ILVATDGSAKSKVAVEHAVDLAkaTGAKLLGvyivnE-VVVASAVRQLGADKKE--IEAKLQASGEKAvadikkmAD 78 
                                       89******************************85532.3455555555555555..*********998666644422 PP

                            AAA_25 100 darllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvv 147
                                        a+++v + ++            +    a  +a+ + ++  e+v+l+v
  gi|386002728|ref|YP_005921027.1|  79 EAGVAVETMVR------------SG---APANAIVDLART-EEVDLIV 110
                                       22222222111............11...111223333333.5555555 PP

>> UPF0172  Uncharacterised protein family (UPF0172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   6.6e-06     0.017      58     111 ..      15      71 ..       8     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.6e-06
                           UPF0172  58 levAlaqvesyakekglvivGyYqanerlsdtelsslaek...iadkiaenfsdavl 111
                                        +vA++++   ak++g +++G+Y+ ne +  +++ +l+     i  k++++ ++av+
  gi|386002728|ref|YP_005921027.1|  15 SKVAVEHAVDLAKATGAKLLGVYIVNEVVVASAVRQLGADkkeIEAKLQASGEKAVA 71 
                                       579***************************999999653213488888887777665 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.7e-05     0.043      10      48 ..      55      93 ..      48     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXX----SSS----- CS
                       Histone_HNS 10 ekqeealeaeerkealaeirelaaeyGltleelaaeakk 48
                                      +k++ea+ +++ ++a+a+i+++a+e G+ +e + ++++ 
  gi|386002728|ref|YP_005921027.1| 55 KKEIEAKLQASGEKAVADIKKMADEAGVAVETMVRSGAP 93
                                      7899999999*********************99877554 PP

>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.5e-05      0.12       1      50 [.      56     103 ..      56     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                    HK97-gp10_like   1 dklakkleklserevekaikkalkkaAkevldkakkrtpsvdtggdLrds 50 
                                       +++++kl++  e ++   ikk++ +a+  v++++++ +p  + + dL++ 
  gi|386002728|ref|YP_005921027.1|  56 KEIEAKLQASGE-KAVADIKKMADEAGVAVETMVRSGAP-ANAIVDLART 103
                                       68999******9.6*************************.6776667665 PP

>> CTD_bind  RNA polymerase II-binding domain.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05      0.13       1      44 [.      32      79 ..      32      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                          CTD_bind  1 kLnllYLaNdvlqnskrkq....kdefapaFapvlpeafadaykkape 44
                                      kL ++Y++N+v+  s+ +q    k e+  ++++  ++a+ad++k a+e
  gi|386002728|ref|YP_005921027.1| 32 KLLGVYIVNEVVVASAVRQlgadKKEIEAKLQASGEKAVADIKKMADE 79
                                      8999**********9777878988999999999999999999986665 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.017        42      12      43 ..       6      37 ..       4      64 .. 0.85
   2 ?    5.7   0.1    0.0071        18      26      54 ..      95     123 ..      39     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                                      EE-SSS-EEEEEEHHHHHHHHHHHTSEEEEEE CS
                             IF3_N 12 lvdedGeqlGvistreAlrlaeekgldLVevs 43
                                      lv  dG   + + ++ A++la+  g +L  v 
  gi|386002728|ref|YP_005921027.1|  6 LVATDGSAKSKVAVEHAVDLAKATGAKLLGVY 37
                                      7889999999***************9998775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0071
                                       HHHHHHHHHHTSEEEEEESSSSS-EEEEE CS
                             IF3_N  26 reAlrlaeekgldLVevspnaepPVcrim 54 
                                       + +++la+ +++dL+ +    e  V +++
  gi|386002728|ref|YP_005921027.1|  95 NAIVDLARTEEVDLIVMGSHGESGVTKLL 123
                                       567899999999*9999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 830.41
//
Query:       gi|386002729|ref|YP_005921028.1|  [L=146]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-30  106.0   0.4    2.6e-30  105.8   0.4    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.4   1.5e-34   2.6e-30       1     141 []       1     146 []       1     146 [] 0.98

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 1.5e-34
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....ak 72 
                                       my++Il+a+Dgs +s +  + +++lak+ g+e+ +l+vi ++a + v +++   +  +++l++a ++ ++      +
  gi|386002729|ref|YP_005921028.1|   1 MYEKILIATDGSAASMNSSRSGIKLAKSLGSEVLVLYVINEMAISRVIASMIGRGFRQEDLRRALKASAEkvvseVT 77 
                                       9**************************************************999999999999988888899***** PP

                                       HHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  73 aaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++ ea+gv ve +++egdpa  ile+ae e++dli++Gs+g++g+s  l+GSv+e+vl+ ++ pV++Vr
  gi|386002729|ref|YP_005921028.1|  78 KMGEAAGVRVEPIIKEGDPASRILETAEIEGVDLILMGSHGEGGISSKLIGSVAEKVLNWSTAPVMIVR 146
                                       ********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 927.83
//
Query:       gi|386002730|ref|YP_005921029.1|  [L=133]
Description: phosphoribosylaminoimidazole carboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-44  149.5   0.1    5.4e-44  149.4   0.1    1.0  1  AIRC      AIR carboxylase
  ------ inclusion threshold ------
      0.034   14.0   0.1        3.4    7.6   0.1    2.2  2  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.4   0.1     6e-48   5.4e-44       2     131 ..       4     129 ..       3     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 6e-48
                                       EEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS CS
                              AIRC   2 VgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttl 78 
                                       +++i GS+sD +v++k+ ++l e gv+y+ rv+Sahr+p +l+ y++e +    kv+Ia+AG +a+Lpg++as t+ 
  gi|386002730|ref|YP_005921029.1|   4 IAVISGSKSDRPVVEKVLRVLVEKGVDYDERVLSAHRNPLDLELYIKETD---AKVFIAVAGLSAALPGFIASRTDR 77 
                                       89********************************************9876...58********************** PP

                                       -EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT- CS
                              AIRC  79 PVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkd 131
                                       PVigvPv++ +l gld+ll+i qmP+gvpva+v+i+ ++n allA++il++k+
  gi|386002730|ref|YP_005921029.1|  78 PVIGVPVSA-KLGGLDALLAISQMPPGVPVACVGIDAGENGALLAVRILGAKE 129
                                       *********.9**************************************9986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00038       3.4      28      51 ..       6      29 ..       1      35 [. 0.84
   2 ?    4.5   0.0    0.0036        32       4      35 ..      47      78 ..      43      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00038
                                      HCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB 28 iaeelgvprskvYevLrsLedkGl 51
                                      + + ++ +r+ v +vLr L++kG+
  gi|386002730|ref|YP_005921029.1|  6 VISGSKSDRPVVEKVLRVLVEKGV 29
                                      56678899***************6 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0036
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSS CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvp 35
                                      l ++e++akv++a+  l  a    ia+++++p
  gi|386002730|ref|YP_005921029.1| 47 LYIKETDAKVFIAVAGLSAALPGFIASRTDRP 78
                                      5589*********9988888777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 728.57
//
Query:       gi|386002731|ref|YP_005921030.1|  [L=97]
Description: Chorismate mutase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-13   49.2   3.5    5.8e-13   49.0   3.5    1.1  1  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   3.5   3.3e-17   5.8e-13       1      75 []      10      88 ..      10      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.3e-17
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHHH CS
                              CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralqk 75
                                      R+e+ ++D++i++L+ eR +la+++ e+K++ g  ++d+++e+ v++r  + a    ld+ a+++if  +i++s++ q+
  gi|386002731|ref|YP_005921030.1| 10 RAEVQKVDRDIIALIYERVRLAEDIFEAKRALGVGIEDKNQEKLVMKRALDMAtelgLDAGAVKEIFAILIRMSLEKQH 88
                                      99*************************************************556678******************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 555.93
//
Query:       gi|386002732|ref|YP_005921031.1|  [L=286]
Description: shikimate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-12   46.2   5.2    6.4e-12   45.5   1.7    2.3  2  GHMP_kinases_N  GHMP kinases N terminal domain
      0.008   16.5   0.0      0.023   15.0   0.0    1.8  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.036   3.3e+02      18      58 ..      13      54 ..       6      58 .. 0.70
   2 !   45.5   1.7   7.2e-16   6.4e-12       2      66 .]      76     144 ..      75     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.036
                                      HHHHHHHHHHHHHHTTEHHHH.HHHHHHHHHHHHHHHHHSHH CS
                    GHMP_kinases_N 18 AAlavalvaAllallglslee.aklaleaerlaqggngsggD 58
                                      A++  a++    +++g++l++ a+  l+   ++ g +++++D
  gi|386002732|ref|YP_005921031.1| 13 ATVLNAVANWKGSAFGVDLKTsAEVVLDESPAVKGDVPGIDD 54
                                      445555555556666777866688888888888888888887 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 7.2e-16
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH...HHHHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl...eeaklaleaerlaqggngsggDv.aasvyGg 66 
                                       ++++s+iP+++GL SS+A+a a+v+A l++lg +l   e  ++++ a r a+++ ++ +D+ +as++Gg
  gi|386002732|ref|YP_005921031.1|  76 VRTWSDIPLARGLKSSSAAANAAVLATLDALGEDLdplEATRIGVAAARDAGVTITGAFDDaSASMLGG 144
                                       5789***************************999753355********************999999998 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.6e-06     0.023      43      79 ..     228     261 ..     205     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-06
                    GHMP_kinases_C  43 lselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                       +++ Ga +a+lsG+  Gp+ +al+ ++++ ++v+ a+
  gi|386002732|ref|YP_005921031.1| 228 ALASGARSASLSGT--GPAYAALV-EDENIDDVEAAW 261
                                       5688999*******..********.888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 2085.83
//
Query:       gi|386002733|ref|YP_005921032.1|  [L=198]
Description: hypothetical protein Mhar_2053 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1338.46
//
Query:       gi|386002734|ref|YP_005921033.1|  [L=101]
Description: hypothetical protein Mhar_2054 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-15   55.9   0.0    4.3e-15   55.7   0.0    1.1  1  DUF3467   Protein of unknown function (DUF3467)


Domain annotation for each model (and alignments):
>> DUF3467  Protein of unknown function (DUF3467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   2.4e-19   4.3e-15       9      91 .]       4      85 ..       1      85 [. 0.94

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.4e-19
                           DUF3467  9 gkkiralrievdesvaggsYsngaivmtspsEfiidFlqlvpgrpearvksrvvlspaaakqlvaaLqknldlyetrfG 87
                                      +k i++l+++++e   + +Y+n++ + + + E+++ Fl+ +p+ + a+ +  v ++p++ak+l++aL+ nl++ye+++G
  gi|386002734|ref|YP_005921033.1|  4 KKRIEQLGVRIPE-RLEPVYANLIKISHADDEVTLTFLHKIPETNLAQGRAIVTITPQHAKRLLRALSANLKRYEATYG 81
                                      5678999999999.89***********************9999998999999*************************** PP

                           DUF3467 88 eikl 91
                                      eikl
  gi|386002734|ref|YP_005921033.1| 82 EIKL 85
                                      **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 650.99
//
Query:       gi|386002735|ref|YP_005921034.1|  [L=386]
Description: hypothetical protein Mhar_2055 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-08   34.8   1.8    1.2e-08   34.8   1.8    1.9  1  FAD_oxidored    FAD dependent oxidoreductase
    5.1e-07   29.1   0.3    5.9e-06   25.6   0.0    2.0  2  Lycopene_cycl   Lycopene cyclase protein
    0.00012   21.4   0.2      0.015   14.5   0.0    3.0  3  Thi4            Thi4 family
    0.00027   20.3   0.2    0.00051   19.4   0.0    1.6  2  FAD_binding_3   FAD binding domain
    0.00056   18.7   0.4    0.00085   18.1   0.4    1.2  1  HI0933_like     HI0933-like protein
      0.001   18.3   0.5     0.0039   16.3   0.2    2.1  2  FAD_binding_2   FAD binding domain
     0.0014   17.9   0.5     0.0062   15.8   0.2    2.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0022   17.2   0.1     0.0022   17.2   0.1    2.0  1  GIDA            Glucose inhibited division protein A
     0.0027   17.0   0.1      0.029   13.6   0.1    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0032   16.4   0.8      0.014   14.3   0.0    1.9  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.021   15.0   0.1    2.9  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.033   13.2   0.0      0.043   12.8   0.0    1.2  1  DUF1424         Putative rep protein (DUF1424)


Domain annotation for each model (and alignments):
>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   1.8   7.9e-12   1.2e-08       1     154 [.       4     154 ..       4     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 7.9e-12
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee..qvvtgiareflerlrq...rgg 72 
                                       Dv+VvG+ p+G+aAA ++a+aGa+v+L++++  +GG +   + + ++g+  ++  +v +  + + le +r     g+
  gi|386002735|ref|YP_005921034.1|   4 DVLVVGASPSGIAAATSSAKAGAEVILLDKD--MGGSFGHPANTFFDGMFRRAglAVEREYVLHDLEGMRIispAGH 78 
                                       9***************************987..7********99999988666777777777777777766332122 PP

                      FAD_oxidored  73 arlkkrskwn.....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       a  +           + +   + a++ +  ++agv++l +   +++  +    + v++       +i A+v+iDA+g
  gi|386002735|ref|YP_005921034.1|  79 A-VE-----IpaagrFIDRGRFDALYLDRAEGAGVELLRGVARSAPLAD--SGRRVETD----AGEIGARVVIDASG 143
                                       1.22.....0223338*************************99999998..34677774....689**********9 PP

                      FAD_oxidored 145 .dGdlaalaGv 154
                                        dG +a + G 
  gi|386002735|ref|YP_005921034.1| 144 vDGAIARKEGL 154
                                       78999887775 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     4e-09   5.9e-06       1     143 [.       4     145 ..       4     158 .. 0.85
   2 ?    1.5   0.1      0.08   1.2e+02     257     325 ..     265     334 ..     244     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4e-09
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvliea..spsllfpnnyvWsdefedlga..leecvehsWsgtivylddgk 73 
                                       Dv+v+Ga p g++ A  +  ak+g +v+l++   + s  +p+n      f+ +g     e v h  +g+++  ++g+
  gi|386002735|ref|YP_005921034.1|   4 DVLVVGASPSGIAAATSS--AKAGAEVILLDKdmGGSFGHPANTFFDGMFRRAGLavEREYVLHDLEGMRIISPAGH 78 
                                       9**************999..99********862256666788887777777777332468999999*********** PP

                     Lycopene_cycl  74 killgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                        +++  a + + + r+ +  l r   +gv+ll++ + s+  ++   ++v +++g +i ar+v+da+g   
  gi|386002735|ref|YP_005921034.1|  79 AVEIPAAGRFIDRGRFDALYLDRAEGAGVELLRGVARSAPLADS-GRRVETDAG-EIGARVVIDASG-VD 145
                                       **********************************9999988877.788888888.6***********.44 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.08
                     Lycopene_cycl 257 kvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....slsarawatlwprerkrqreffrllgla 325
                                       + +a Gaaag+      Y + r+   a  +a+  aaa++ s    s++ r w++  + e ++ r+ +  lg++
  gi|386002735|ref|YP_005921034.1| 265 SLMATGAAAGMSG--IAYAI-RAGTMAGEVAAGAAAAGDVSirglSPYVRRWRREFGLEYRMGRASLLTLGRM 334
                                       4678888888864..33655.344445556666666666668999999*************999988788876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     1e-05     0.015      17      54 ..       2      36 ..       1      67 [. 0.85
   2 ?    1.5   0.0       0.1   1.5e+02     153     173 ..     129     149 ..     111     153 .. 0.85
   3 ?    1.5   0.0     0.096   1.4e+02     185     222 ..     235     273 ..     209     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                      + Dv++vGa +sG++aa   ak+ + +v++l++ +  G
  gi|386002735|ref|YP_005921034.1|  2 NCDVLVVGASPSGIAAATSSAKA-GAEVILLDKDM--G 36
                                      68********************9.9*****99976..3 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                       B-EEEEEEEEEE--GSSSTTT CS
                              Thi4 153 DPlvirakvvvdatGhdgeiv 173
                                       D   i a+vv+da+G dg i 
  gi|386002735|ref|YP_005921034.1| 129 DAGEIGARVVIDASGVDGAIA 149
                                       6667899**********9885 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.096
                                       TTS-----ECB-HHHHHHHHHHHECEEE.TTEEE-THHH CS
                              Thi4 185 kiekvkgeksldaekaedaivkktrevv.pnlyvaGmev 222
                                        + +v+++k + ++++ dai     e+v + l+++G ++
  gi|386002735|ref|YP_005921034.1| 235 ADYDVSDMKIVSVNRGGDAIATLPGEIVaDSLMATGAAA 273
                                       4568999*************9999998824566666543 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.4e-07   0.00051       2      33 ..       3      34 ..       2      57 .. 0.92
   2 ?   -3.7   0.0       3.6   5.4e+03     149     182 ..     130     163 ..     124     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.4e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +dVl+VGa+p+G+ +a+  ++aG +v+l++k 
  gi|386002735|ref|YP_005921034.1|  3 CDVLVVGASPSGIAAATSSAKAGAEVILLDKD 34
                                      9*****************************97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.6
                                       EEEEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEE CS
                     FAD_binding_3 149 eeetvrakYlvGaDGgrStvrktlgie.fegeetv 182
                                       +  ++ a+ ++ a G+ ++++++ g++ ++ +e+v
  gi|386002735|ref|YP_005921034.1| 130 AG-EIGARVVIDASGVDGAIARKEGLSpLKHPEDV 163
                                       44.78899999999999999999888855555544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   5.7e-07   0.00085       2      32 ..       4      34 ..       3      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.7e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      dv+v+G+ ++G+ aA s ak+g++V+ll+k 
  gi|386002735|ref|YP_005921034.1|  4 DVLVVGASPSGIAAATSSAKAGAEVILLDKD 34
                                      8****************************96 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   2.6e-06    0.0039       1      31 [.       4      34 ..       4      47 .. 0.93
   2 ?   -1.2   0.0      0.53     8e+02     166     200 ..     136     175 ..      87     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                      Dv+V+G+  +G aAA++ a+aG++v++++k 
  gi|386002735|ref|YP_005921034.1|  4 DVLVVGASPSGIAAATSSAKAGAEVILLDKD 34
                                      9***************************996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.53
                                       EEEECTTEEEEEEEEET.....TTTCEEEEEESEEEE--- CS
                     FAD_binding_2 166 eLivedgrvtGavvenp.....esgrevrirakavvlatg 200
                                       +++++  +v Ga+++++     + +++v+ +a avv  +g
  gi|386002735|ref|YP_005921034.1| 136 RVVIDASGVDGAIARKEglsplKHPEDVAWAAEAVVELAG 175
                                       4555666777777776677777777777777777776555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   4.2e-06    0.0062       2      31 ..       4      33 ..       3      49 .. 0.86
   2 ?   -1.2   0.0      0.64   9.5e+02     184     240 ..      93     147 ..      78     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvel 31
                                      dv+v+G+ p G+aaa+  a+aga+v+l+++
  gi|386002735|ref|YP_005921034.1|  4 DVLVVGASPSGIAAATSSAKAGAEVILLDK 33
                                      89*************************962 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrps 240
                                       ++ a + ++ e  Gve+  g    +  +  ++ + v++d  ei a+ v+ a Gv   
  gi|386002735|ref|YP_005921034.1|  93 RFDALYLDRAEGAGVELLRGVA--RSAPLADSGRRVETDAGEIGARVVIDASGVDGA 147
                                       5677788888888999885544..444444434688899999999999999998765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.5e-06    0.0022       1      34 [.       4      37 ..       4      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34
                                      dv V+G+  +G++AA  +a++Ga+v+L+ ++++ 
  gi|386002735|ref|YP_005921034.1|  4 DVLVVGASPSGIAAATSSAKAGAEVILLDKDMGG 37
                                      79*************************9666554 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.9e-05     0.029     166     196 ..       4      34 ..       1      45 [. 0.86
   2 ?    0.9   0.0      0.15   2.2e+02     111     133 ..     121     143 ..     110     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrg 196
                                       +v+V+G++ S++ aA+  +++gaeV +++++
  gi|386002735|ref|YP_005921034.1|   4 DVLVVGASPSGIAAATSSAKAGAEVILLDKD 34 
                                       7999999999999999999999999999876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                       Pyr_redox_3 111 degfevetsketyeAkkviiAtG 133
                                       d+g +vet+ +++ A+ vi A G
  gi|386002735|ref|YP_005921034.1| 121 DSGRRVETDAGEIGARVVIDASG 143
                                       67889**************9999 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.17   2.5e+02       1      34 [.       4      34 ..       4      40 .. 0.86
   2 !   14.3   0.0   9.4e-06     0.014     151     216 ..      89     151 ..      74     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      ++++vG+ ++G  aA+  aka+   +ev l++++
  gi|386002735|ref|YP_005921034.1|  4 DVLVVGASPSGIAAATSSAKAG---AEVILLDKD 34
                                      699*************999999...788888776 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.4e-06
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieq 216
                                       +d+++++ +  + ae +Gv+ ++g   ++ l ++gr  +++++ g+ + a+ +iD+sG  g +  +
  gi|386002735|ref|YP_005921034.1|  89 IDRGRFDALYLDRAEGAGVELLRGVARSAPLADSGR--RVETDAGE-IGARVVIDASGVDGAIARK 151
                                       79******************************9996..78887776.************9988765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.4e-05     0.021       1      28 [.       7      34 ..       7      56 .. 0.91
   2 ?   -2.5   0.0       4.1   6.2e+03      15      35 ..      89     109 ..      84     130 .. 0.59
   3 ?   -1.5   1.1       2.1   3.1e+03       4      14 ..     273     283 ..     272     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vGa  sG +aA   akag++v ll+k 
  gi|386002735|ref|YP_005921034.1|  7 VVGASPSGIAAATSSAKAGAEVILLDKD 34
                                      8*************************95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                                       HHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  15 LakagfdvlllekrdrlGGra 35 
                                       + + +fd l l+++++ G  +
  gi|386002735|ref|YP_005921034.1|  89 IDRGRFDALYLDRAEGAGVEL 109
                                       555577888888888888433 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.1
                                       -SHHHHHHHHH CS
                     NAD_binding_8   4 aGlsGlvaAyl 14 
                                       aG+sG ++A +
  gi|386002735|ref|YP_005921034.1| 273 AGMSGIAYAIR 283
                                       8******9976 PP

>> DUF1424  Putative rep protein (DUF1424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.9e-05     0.043     115     185 ..     155     223 ..     121     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                           DUF1424 115 pllehlrdllesweavrdalarvledrefey.laileptepagngpagyvhihlgvfvkgpvvaeqfedvld 185
                                        +l+h +d+  + eav + la   e+r fey l  + p   a+ +p g     lgvfv+g     + ++ ld
  gi|386002735|ref|YP_005921034.1| 155 SPLKHPEDVAWAAEAVVE-LAGLGEERRFEYfLGSISPGWKATFSPGGGDLATLGVFVRGHG--RDVRPFLD 223
                                       468999999999999976.89999******95789************************963..44555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.19s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 3078.01
//
Query:       gi|386002736|ref|YP_005921035.1|  [L=76]
Description: hypothetical protein Mhar_2056 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-12   45.5   0.1    6.4e-12   45.3   0.1    1.1  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   3.6e-16   6.4e-12       4      57 ..      12      66 ..       9      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.6e-16
                                      HHHHHHH.TT-EEEEEETTEEEEE-..TTSS-EEEEE.S-SSS--CCCHHHHHHHCC CS
                        HicA_toxin  4 viklLek.lGfevvrqkGSHvrfkh..pdkrgivtvppHpgkelkpgtlksIlkqaG 57
                                      ++k+L k + fe+ +++GSHvr+ +  pd++  ++vp+H  +elk gtlk +lk a+
  gi|386002736|ref|YP_005921035.1| 12 AVKILCKkFDFEISGRTGSHVRLSKmtPDGKVGTVVPMH--RELKMGTLKGVLKLAK 66
                                      57888777******99*********99999999******..*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 493.57
//
Query:       gi|386002737|ref|YP_005921036.1|  [L=55]
Description: hypothetical protein Mhar_2057 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0021   18.2   0.0     0.0023   18.0   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.3e-07    0.0023      22      56 ..       8      42 ..       3      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-07
                   HicB_lk_antitox 22 Gcfsagdtleeaianakeaielhlegliedgeeip 56
                                      G  s g+t eea++n kea el+le+   ++++ p
  gi|386002737|ref|YP_005921036.1|  8 GTVSQGKTPEEAVDNLKEATELYLEEFPLEEKKRP 42
                                      999**********************9876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 407.87
//
Query:       gi|386002738|ref|YP_005921037.1|  [L=108]
Description: hypothetical protein Mhar_2058 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 727.94
//
Query:       gi|386002739|ref|YP_005921038.1|  [L=453]
Description: hypothetical protein Mhar_2059 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-12   47.1   0.0    4.6e-12   46.2   0.0    1.4  1  NACHT            NACHT domain
    2.1e-05   24.8   0.0    0.00012   22.4   0.0    2.2  3  AAA_22           AAA domain
    5.1e-05   23.7   0.0    0.00035   21.0   0.0    2.3  1  AAA_16           AAA ATPase domain
    0.00048   20.5   0.0     0.0048   17.3   0.0    2.2  2  AAA_19           AAA domain
     0.0012   19.2   0.0     0.0065   16.9   0.0    2.1  2  AAA              ATPase family associated with various cellul
     0.0019   18.7   0.0     0.0061   17.1   0.0    1.9  2  AAA_18           AAA domain
     0.0061   16.0   0.0      0.019   14.4   0.0    1.7  1  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.024   15.1   0.0    1.6  1  ABC_tran         ABC transporter
      0.012   15.2   0.0      0.022   14.3   0.0    1.5  1  AAA_25           AAA domain
      0.042   13.6   0.0      0.071   12.9   0.0    1.3  1  AAA_11           AAA domain
       0.05   13.3   0.0      0.086   12.6   0.0    1.4  1  AAA_30           AAA domain
      0.051   13.3   0.0       0.08   12.6   0.0    1.3  1  AAA_24           AAA domain
      0.062   12.6   0.1       0.29   10.4   0.0    1.9  2  Zeta_toxin       Zeta toxin
      0.084   13.0   0.0       0.21   11.6   0.0    1.6  1  DUF87            Helicase HerA, central domain
       0.13   11.4   0.0        0.2   10.8   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.15   11.6   0.0       0.27   10.7   0.0    1.4  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
       0.17   11.6   0.0       0.31   10.7   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.18   11.7   0.0       0.34   10.8   0.0    1.4  1  Rad17            Rad17 P-loop domain
       0.25    9.9   0.0       0.38    9.3   0.0    1.2  1  GvpD             GvpD gas vesicle protein


Domain annotation for each model (and alignments):
>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   4.9e-15   4.6e-12       2     161 ..     120     269 ..     119     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4.9e-15
                                       CEEEEC-TTTCHHHHHHHHHHHH..CTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalaw..aegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavl 76 
                                        +++ Ge+G GKTt l +la+++  ++g++p+++ ++vF ls+ +++++     +ad l+++l ++   +++ +a +
  gi|386002739|ref|YP_005921038.1| 120 SLLILGEPGAGKTTTLLELAREMidRAGEDPSEKIPVVFNLSSWTDPKQ--P--IADWLTEELRAKYNIPKK-IAAR 191
                                       689******************9933345555655555555555555554..4..899999999888776666.9999 PP

                                       CCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCC CS
                             NACHT  77 lelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfses 153
                                       +   ++lLl+lDg+De++     +++++  + ++  +++     ++l++ +r +    l   l  +  + +++++ +
  gi|386002739|ref|YP_005921038.1| 192 WVENDSLLLLLDGFDEVAP----ERREACIEAINVFLEE---HFVPLVVCCRKEEYDALDGRLNLQSAVLLQPLTPE 261
                                       ******************9....4556999999999999...999***********99*999999999********* PP

                                       HHHHHHHH CS
                             NACHT 154 rrkqlvrk 161
                                       +++ ++++
  gi|386002739|ref|YP_005921038.1| 262 QIDGYLER 269
                                       ***99987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.1   3.9e+03      54      84 ..      24      57 ..      16      63 .. 0.70
   2 !   22.4   0.0   1.2e-07   0.00012       5      96 ..     118     233 ..     115     248 .. 0.68
   3 ?   -2.7   0.0       6.9   6.5e+03      80     101 ..     355     375 ..     310     392 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.1
                            AAA_22 54 kdllrellralglelka...erlsseellealeq 84
                                      + llr+ll+++++e ++      +++++l+++++
  gi|386002739|ref|YP_005921038.1| 24 DALLRKLLSKYTSEDERsarDAFNRQAMLTRVRD 57
                                      5678889999988887766656666666666655 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.2e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsst.sskdllrellralglelka....... 70 
                                        ++l++ Ge+G+GKTt+l +l+++   +   +     ++  v ++l+s t   + ++ +l ++l  + +        
  gi|386002739|ref|YP_005921038.1| 118 GRSLLILGEPGAGKTTTLLELAREMIDR---AGedpSEKIPVVFNLSSWTdPKQPIADWLTEELRAKYNIpkkiaar 191
                                       5789*******************98333...3332333333356666666344445777777777544447777777 PP

                            AAA_22  71 .................erlsseellealeqalraravielli 96 
                                                        ++ ++e+++ea++  l++++v +l++
  gi|386002739|ref|YP_005921038.1| 192 wvendsllllldgfdevAPERREACIEAINVFLEEHFV-PLVV 233
                                       77777777777777777777777777777777777776.5544 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.9
                            AAA_22  80 ealeqalraravielliiDEaq 101
                                       + l q +++++   +++i+ +q
  gi|386002739|ref|YP_005921038.1| 355 SWLGQKMSEHGQ-TVFLIERMQ 375
                                       344444444444.555555444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.7e-07   0.00035      14      88 ..     112     185 ..     108     235 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.7e-07
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekd.........ggif.lrgkcdqlesaipysalaqalaree 80 
                                       +++erv    ++++l+ Ge+G GK++ + el+r++ ++          ++f l+ ++d        +++a+ l++ e
  gi|386002739|ref|YP_005921038.1| 112 DVFERV----GRSLLILGEPGAGKTTTLLELAREMIDRagedpsekiPVVFnLSSWTDPK------QPIADWLTE-E 177
                                       444444....489***************99999888887888888765666777777777......668888844.6 PP

                            AAA_16  81 llrqllde 88 
                                       l ++ + +
  gi|386002739|ref|YP_005921038.1| 178 LRAKYNIP 185
                                       66655555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     5e-06    0.0048       9      49 ..     117     157 ..     111     165 .. 0.85
   2 ?    0.3   0.0      0.83   7.9e+02      56      92 ..     331     371 ..     288     393 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5e-06
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillva 49 
                                         + ll+++ pG GKT++l +  ++++++ g++p e + v 
  gi|386002739|ref|YP_005921038.1| 117 VGRSLLILGEPGAGKTTTLLELAREMIDRAGEDPSEKIPVV 157
                                       56789***********************9999997766655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.83
                            AAA_19  56 kelrerlaalgae...........atTiHrlalldfddlltealelle 92 
                                       +++ e       +            +TiH l+ l+ +  ++ +  +l 
  gi|386002739|ref|YP_005921038.1| 331 DRMFE-------RtgrtdpkrytkEKTIHWLSWLGQKMSEHGQTVFLI 371
                                       33333.......144455678888899999988777776666555554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.3   2.1e+03      33      52 ..      29      48 ..      19      54 .. 0.83
   2 !   16.9   0.0   6.9e-06    0.0065       1      90 [.     121     224 ..     121     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                                      TCSSSSTTHHHHHHHHHHHH CS
                               AAA 33 ellskyvgesekkirelfke 52
                                      +llsky +e e++ r+ f++
  gi|386002739|ref|YP_005921038.1| 29 KLLSKYTSEDERSARDAFNR 48
                                      68899999999999999987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.9e-06
                                       EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS......STTHHHHHHHHHHHHHHHTS...T CS
                               AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellsk......yvgesekkirelfkeakeka...k 58 
                                       +l+ G pG GKT++   +a+e+          ++  + +++s+ ++       ++ e  +   ++ k++ +     +
  gi|386002739|ref|YP_005921038.1| 121 LLILGEPGAGKTTTLLELAREMidragedpseKI-PVVFNLSSWTDPkqpiadWLTEELRAKYNIPKKIAARWvenD 196
                                       5899*****************8776665553222.366666776633478777777777776677766533335544 PP

                                       SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  59 psilfiDEidalaksrsgseseeeervvnqLl 90 
                                          l++D +d++a++r    +e   +++n++l
  gi|386002739|ref|YP_005921038.1| 197 SLLLLLDGFDEVAPER----REACIEAINVFL 224
                                       59999*********99....444444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0        10   9.4e+03      45      69 ..      44      68 ..      25      87 .. 0.59
   2 !   17.1   0.0   6.4e-06    0.0061       2      85 ..     122     208 ..     121     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 10
                            AAA_18 45 aldeskrldedkldklldaleenss 69
                                      +  + + + + ++d +++++ ens 
  gi|386002739|ref|YP_005921038.1| 44 DAFNRQAMLTRVRDFWVKGVLENSL 68
                                      4445556666666666666666654 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.4e-06
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.......gvnlrdvakenglllevdpe.....aldeskrldedkldklldalee 66 
                                       l+ G pG+GKtt   eL++++ +       ++++  v+  + + ++   +     +l e++r++ +  +k+   + e
  gi|386002739|ref|YP_005921038.1| 122 LILGEPGAGKTTTLLELAREM-IdragedpSEKIPVVFNLSSWTDP---KqpiadWLTEELRAKYNIPKKIAARWVE 194
                                       689**************9997.355986653333333333333333...3444888888888888888888888888 PP

                            AAA_18  67 nssaleegknlvidghlae 85 
                                       n+s       l++dg+ + 
  gi|386002739|ref|YP_005921038.1| 195 NDS-----LLLLLDGFDEV 208
                                       877.....66677776654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     2e-05     0.019      36     170 ..     119     244 ..     113     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                              TniB  36 pnlllvGdsnnGKtmivekFarlhppekded.aekvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqv 111
                                       ++ll++G++  GKt+ + + ar+  ++  ed +ek+pv+      +  ++ + + + e+l+a+++  +++++   + 
  gi|386002739|ref|YP_005921038.1| 119 RSLLILGEPGAGKTTTLLELAREMIDRAGEDpSEKIPVVFNLSSWTDPKQPIADWLTEELRAKYNIPKKIAARWVEN 195
                                       69******************9999888765537899**998888888889999999999999998888777766665 PP

                              TniB 112 lrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealralr 170
                                              +  +L++D ++++     ++++++++a+  + +e  +p+v++  +e ++al+
  gi|386002739|ref|YP_005921038.1| 196 -------DSLLLLLDGFDEVA---PERREACIEAINVFLEEHFVPLVVCCRKEEYDALD 244
                                       .......44468899999888...88888899999999999999999988888888775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-05     0.024      11      42 ..     118     149 ..     115     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei 42 
                                       g+ + i+Ge GaGK+t l  la+++ + +Ge 
  gi|386002739|ref|YP_005921038.1| 118 GRSLLILGEPGAGKTTTLLELAREMIDRAGED 149
                                       67789********************9999986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.022      33      76 ..     118     158 ..     101     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                            AAA_25  33 gelallaGapgtGKttlaldlalava..tGkpwlgpvapeqgkVly 76 
                                       g   l+ G pg+GKtt +l+la ++         g+ ++e+++V++
  gi|386002739|ref|YP_005921038.1| 118 GRSLLILGEPGAGKTTTLLELAREMIdrA-----GEDPSEKIPVVF 158
                                       5567899******************9443.....434568888887 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05     0.071      20      44 ..     121     145 ..     110     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                            AAA_11  20 tliqGPPGtgKTktivellsqllsr 44 
                                        li G PG gKT+t++el ++++ r
  gi|386002739|ref|YP_005921038.1| 121 LLILGEPGAGKTTTLLELAREMIDR 145
                                       5899*****************9754 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.1e-05     0.086      20      46 ..     120     147 ..     110     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.1e-05
                            AAA_30  20 vavltGpAGtGKttalkal.reaweaag 46 
                                         ++ G +G+GKtt+l +l re++++ag
  gi|386002739|ref|YP_005921038.1| 120 SLLILGEPGAGKTTTLLELaREMIDRAG 147
                                       56899********998777699999887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.5e-05      0.08       3      22 ..     119     138 ..     117     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                       +++li G++g+GKTt+++el
  gi|386002739|ref|YP_005921038.1| 119 RSLLILGEPGAGKTTTLLEL 138
                                       6799*************999 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00031      0.29      19      41 ..     121     143 ..     116     149 .. 0.86
   2 ?   -0.9   0.0      0.91   8.6e+02      52      98 ..     320     368 ..     316     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                        Zeta_toxin  19 illgGqpGAGKselaellkdele 41 
                                       +l+ G pGAGK++++ +l++e+ 
  gi|386002739|ref|YP_005921038.1| 121 LLILGEPGAGKTTTLLELAREMI 143
                                       5788***************9996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.91
                        Zeta_toxin  52 DdlRelhPeyeeilka..dpkkaseltqkdaselvekllqeaiengyni 98 
                                       D+ R l+  y + + +    ++  ++t++ +  +   l q+  e+g+ +
  gi|386002739|ref|YP_005921038.1| 320 DHRRHLFKTYVDRMFErtGRTDPKRYTKEKTIHWLSWLGQKMSEHGQTV 368
                                       6777777777665443236778889999999999999999999999876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.21      20      49 ..     115     144 ..     110     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                             DUF87  20 klvtrHlAilgsTGsGKSntvavLleelle 49 
                                       + v r+l+ilg+ G+GK++t   L +e++ 
  gi|386002739|ref|YP_005921038.1| 115 ERVGRSLLILGEPGAGKTTTLLELAREMID 144
                                       5689***********************995 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022       0.2       4      26 ..     121     148 ..     118     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                           DUF2075   4 vlVtGvaGtGKtvvllnllael.....e 26 
                                       +l+ G++G+GKt  ll+l+ e+     e
  gi|386002739|ref|YP_005921038.1| 121 LLILGEPGAGKTTTLLELAREMidragE 148
                                       7899****************99443322 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.27      10      47 ..     115     152 ..     108     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                       HS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGG CS
                     UvrD-helicase  10 aslggpilveAsAGsGKTfvlaerilrlikeeeiepdr 47 
                                       + +g ++l++  +G+GKT++l e+  ++i+ ++ +p++
  gi|386002739|ref|YP_005921038.1| 115 ERVGRSLLILGEPGAGKTTTLLELAREMIDRAGEDPSE 152
                                       557899************************99999877 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 ?   10.7   0.0   0.00033      0.31       2      41 ..     122     156 ..     121     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpk 41 
                                       ++ G pG+GK+t + +l+r+     ++ ++ e+ +e  p 
  gi|386002739|ref|YP_005921038.1| 122 LILGEPGAGKTTTLLELARE-----MIDRAGEDPSEKIPV 156
                                       78999**************9.....556656666665555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.34      42      70 ..     116     143 ..     109     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                             Rad17  42 srkkriLLisGPsGCgkstvvkvLskelg 70 
                                       +   r LLi G +G gk+t++ +L++e+ 
  gi|386002739|ref|YP_005921038.1| 116 RV-GRSLLILGEPGAGKTTTLLELAREMI 143
                                       44.56799*****************9976 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0004      0.38       7      29 ..     115     137 ..     110     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0004
                              GvpD   7 geaGktllikGaPGtGktlftlr 29 
                                       +++G++lli G+PG+Gkt+  l+
  gi|386002739|ref|YP_005921038.1| 115 ERVGRSLLILGEPGAGKTTTLLE 137
                                       589***************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2892.41
//
Query:       gi|386002740|ref|YP_005921039.1|  [L=246]
Description: hypothetical protein Mhar_2060 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-61  204.4   0.0      1e-60  204.1   0.0    1.1  1  YhcG_C     YhcG PDDEXK nuclease domain
    3.3e-16   59.7   0.2      5e-16   59.1   0.2    1.3  1  DUF1016_N  DUF1016 N-terminal domain
  ------ inclusion threshold ------
      0.056   13.4   0.0        0.1   12.6   0.0    1.4  1  HSDR_N_2   Type I restriction enzyme R protein N terminus (HS
        0.1   13.1   0.8       0.31   11.6   0.8    1.9  1  Rnk_N      Rnk N-terminus


Domain annotation for each model (and alignments):
>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.1   0.0   2.3e-64     1e-60       2     155 .]      76     230 ..      75     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 2.3e-64
                            YhcG_C   2 eilkdpyvldflelkeeykErelekalieklkkfllelGkgFafvgrqyrleveekefyidLlfYhlklkcyvvieL 78 
                                       eilkdpy +dfl+l e+ +Er+l+++l+ +l++fl+elG gFafvg++++lev++++f+idLlfYhl+l+cyvv+eL
  gi|386002740|ref|YP_005921039.1|  76 EILKDPYSFDFLSLGERASERDLHRSLLAHLRDFLIELGVGFAFVGSEHPLEVGGQDFRIDLLFYHLRLRCYVVVEL 152
                                       89*************************************************************************** PP

                            YhcG_C  79 KvgefkpedagklnlYlsaldeelkk.eednptiGiilckekdktvveyalkeinkpigvseYelpkelpeelkekl 154
                                       K+g+f pe++gkln+Ylsa+d+ +++ ++d ptiGi+lck+k+++++eyal++ nkp+g+s+Y+l+k l+ e+k++l
  gi|386002740|ref|YP_005921039.1| 153 KIGDFAPEQVGKLNFYLSAVDDLIREaDHDGPTIGILLCKTKNRVIAEYALRDLNKPVGISSYRLEKALAGEMKRNL 229
                                       ***********************987256********************************************9998 PP

                            YhcG_C 155 p 155
                                       p
  gi|386002740|ref|YP_005921039.1| 230 P 230
                                       6 PP

>> DUF1016_N  DUF1016 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.2   1.1e-19     5e-16      84     137 .]       1      54 [.       1      54 [. 0.98

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.1e-19
                         DUF1016_N  84 lqqlvaqlsWshnllllekvkdeeerefYleeaieegWsrreLerqiksklyer 137
                                       +qq+ aq++W hn+++l+k+kd+ ere+Y++e++++gWsr++L +qi+s+l++r
  gi|386002740|ref|YP_005921039.1|   1 MQQVAAQIPWFHNCVILDKLKDRAEREWYVRETVNNGWSRNVLVHQIESDLFRR 54 
                                       589*************************************************98 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05       0.1      16      72 ..     112     166 ..     104     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                          HSDR_N_2  16 elgypkeliavekelqlgskkkraDivvykkdkkpllivecKapsvkiseevleqlk 72 
                                       elg+    +  e +l++g++  r+D+++y  + + +++ve+K  + + ++  +  l+
  gi|386002740|ref|YP_005921039.1| 112 ELGVGFAFVGSEHPLEVGGQDFRIDLLFYHLRLRCYVVVELKIGDFAPEQ--VGKLN 166
                                       566666778899******************************98887754..55555 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   6.9e-05      0.31      12      36 ..     216     240 ..     215     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHCTTTTSSTTHHHHHHHHH CS
                             Rnk_N  12 RLeaLldsladrdppaaeaLeaELd 36 
                                       RLe+ l++++ r+ p++e+LeaEL 
  gi|386002740|ref|YP_005921039.1| 216 RLEKALAGEMKRNLPTIEELEAELS 240
                                       99999999****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.27s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1442.41
//
Query:       gi|386002741|ref|YP_005921040.1|  [L=258]
Description: ribosomal RNA large subunit methyltransferase E [Methanosaeta harundinacea 6Ac]
Scores for 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-57  195.1   0.0    1.2e-57  194.9   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
    3.5e-05   23.7   0.0    7.7e-05   22.6   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    8.7e-05   22.4   0.0     0.0029   17.4   0.0    2.1  1  Methyltransf_31  Methyltransferase domain
      0.002   17.4   0.0       0.19   10.9   0.0    2.1  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
     0.0068   17.1   0.2       0.11   13.3   0.2    2.5  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.0   3.3e-61   1.2e-57       1     177 []      18     191 ..      18     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 3.3e-61
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetie 77 
                                       yr+Rsa+KL++i+++f+l+++g++v+DlgaaPGgw qv+ +    +g+vv+vDl  ++p++gvtti++dit pet e
  gi|386002741|ref|YP_005921040.1|  18 YRARSAFKLQQINQRFRLIRRGDAVLDLGAAPGGWLQVAKEIS--GGRVVGVDLLAIEPIDGVTTIKADITAPETLE 92 
                                       9**************************************9995..49****************************** PP

                                       HHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEE CS
                              FtsJ  78 kikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFek 154
                                       +i eal++ k+d+v++D ap+ sg+++ld++++++L ++al++a ++lkpgg+f++k+f+g+ + ++l++++  F++
  gi|386002741|ref|YP_005921040.1|  93 LIVEALGG-KADVVICDAAPNLSGNWTLDHARSIDLSRSALRVAESVLKPGGNFLVKVFQGDTFLDYLSEVRVRFRR 168
                                       ******77.******************************************************************** PP

                                       EEEEE-SS--CCG-EEEEEEEEC CS
                              FtsJ 155 vsvvkPkssrsesseeflvcrgf 177
                                        + + P++sr+es+e+++v +gf
  gi|386002741|ref|YP_005921040.1| 169 AQSHSPAASRKESAEMYVVGQGF 191
                                       ********************997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.2e-08   7.7e-05      15     124 ..      31     154 ..      15     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.2e-08
                   Methyltransf_23  15 rllpklraggrvLdiGcGtGillevlren.gfsvtgvDlspeaveiae...kakkaqkdqfdeqeaae.pqgkfdlI 86 
                                       + +   r+g  vLd+G++ G +l+v++e  g  v+gvDl    +e +    ++k  +  ++  + + e   gk d++
  gi|386002741|ref|YP_005921040.1|  31 QRFRLIRRGDAVLDLGAAPGGWLQVAKEIsGGRVVGVDLLA--IEPIDgvtTIKADITAPETLELIVEaLGGKADVV 105
                                       44444688999***************776477*******75..45544333333333333322222224677***** PP

                   Methyltransf_23  87 vlrevlehvpdpp...........ellrqiatllkpgGylllseplasl 124
                                       ++    +   +++           ++lr + + lkpgG++l+ ++  + 
  gi|386002741|ref|YP_005921040.1| 106 ICDAAPNLSGNWTldharsidlsrSALRVAESVLKPGGNFLVKVFQGDT 154
                                       *99998888898899999999999******************9986554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     8e-07    0.0029       3     114 ..      38     158 ..      36     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8e-07
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled......e 73 
                                       +g  vlDlG++ G  + ++    +++++vvG+D       lA e      +d v+  ++di++ e+ le        
  gi|386002741|ref|YP_005921040.1|  38 RGDAVLDLGAAPGGWLQVAK--EISGGRVVGVDL------LAIE-----PIDGVTTIKADITAPET-LELivealgG 100
                                       56789999999988877666..567899999997......5555.....57788888889988444.344556799* PP

                   Methyltransf_31  74 kfDlilsnevl...........naladpdkileeiervlkpggilliedpr......l 114
                                       k D+++++++              +  + ++l+ +e+vlkpgg +l+  ++       
  gi|386002741|ref|YP_005921040.1| 101 KADVVICDAAPnlsgnwtldhaRSIDLSRSALRVAESVLKPGGNFLVKVFQgdtfldY 158
                                       ********777888888888888999999*****************998884444442 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   5.2e-05      0.19      25      68 ..       9      50 ..       3      64 .. 0.80
   2 !    4.5   0.0    0.0049        17     163     198 ..     114     148 ..      78     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                                      HCSTTTTSTCCCCHHHHHHHHHHHHHHTSSS-ECEEEEET-TT- CS
                    NNMT_PNMT_TEMT 25 yykkasedaaeeqvvlfaLknllqtlatgekkgdtllDiGaGPT 68
                                      +y ka+ +   +  + f+L+ + q+++   + gd +lD+Ga P 
  gi|386002741|ref|YP_005921040.1|  9 FYRKAKAEGY-RARSAFKLQQINQRFRLIRR-GDAVLDLGAAPG 50
                                      5555555555.56789***********7776.*********996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0049
                                       EEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEE CS
                    NNMT_PNMT_TEMT 163 vtifcleaacedleeylralrnlasllkpGGhlvlg 198
                                       +   +l+ a ++++  + alr + s+lkpGG +++ 
  gi|386002741|ref|YP_005921040.1| 114 SGNWTLDHA-RSIDLSRSALRVAESVLKPGGNFLVK 148
                                       445566654.67788899*************99864 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2     3e-05      0.11       1      97 []      42     143 ..      42     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE....... CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs....... 70 
                                       vLdlG+ +G +++ + +  g ++v+gvD+ +       + ++++    e ++  +e+l    g+ D+v++       
  gi|386002741|ref|YP_005921040.1|  42 VLDLGAAPGGWLQVAKEISG-GRVVGVDLLAIEPIDGVTTIKADITAPETLELIVEAL---GGKADVVICdaapnls 114
                                       9********99887776656.*******976444333344432222334444444444...4778888887666665 PP

                                       .ESTGGG.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  71 .sgalhh.lsdedlekalkeiarvLkpgG 97 
                                        + +l h  s +  + al+ + +vLkpgG
  gi|386002741|ref|YP_005921040.1| 115 gNWTLDHaRSIDLSRSALRVAESVLKPGG 143
                                       43345573444445779999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1545.41
//
Query:       gi|386002742|ref|YP_005921041.1|  [L=428]
Description: Phosphoglucomutase/phosphomannomutase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-26   90.6   0.0    9.9e-26   90.1   0.0    1.3  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    6.3e-18   65.3   0.0    1.3e-17   64.3   0.0    1.5  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    9.9e-16   58.0   0.0    1.7e-15   57.2   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.2e-10   39.4   0.0    1.4e-09   37.9   0.0    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   2.2e-29   9.9e-26       9     129 ..       1     115 [.       1     124 [. 0.92

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 2.2e-29
                                       EEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHH CS
                         PGM_PMM_I   9 lRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfa 85 
                                       +Rg++g +elt e + ++g+a+++yl++    +++++GrDtRvs++ +++a++ g++++G++v ++g+lp+ ++sf 
  gi|386002742|ref|YP_005921041.1|   1 MRGVFG-TELTGEIANRVGKALGSYLAN----GRIALGRDTRVSGPAVERAFLDGVLSTGCSVERYGVLPISMISFE 72 
                                       69****.77******************8....9******************************************** PP

                                       HHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHH CS
                         PGM_PMM_I  86 irklkadagimitaSHnppeyngiKvylsnGgpispeveekIea 129
                                       + + +++a+ +i+aSHnppeyngi++ +s+G+ +  + e+++ +
  gi|386002742|ref|YP_005921041.1|  73 TWRGGYNAAAYISASHNPPEYNGIRFRTSEGYGMLYH-ETEMMN 115
                                       *******************************987765.445555 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 !   64.3   0.0   2.9e-21   1.3e-17       3     103 .]     141     235 ..     138     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.9e-21
                                       HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGG CS
                        PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvk 79 
                                       Y + ++     + + +++l++v+d ++Ga+ ++++ l ++lg+d    n epd+ fp++ p p+e e+l++++++v 
  gi|386002742|ref|YP_005921041.1| 141 YADYVE----GKLTFGRPLRIVLDMGNGAACGTFP-LYQRLGFDCRVTNGEPDGLFPGRGPAPTE-ESLRDAARMVV 211
                                       444444....445589****************997.89***************************.*********** PP

                                       GGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  80 kegadlglafDgDaDRlgvvderG 103
                                       +++ad g+ fD+DaDR  v+d+rG
  gi|386002742|ref|YP_005921041.1| 212 ETEADYGVGFDPDADRGLVIDDRG 235
                                       *********************998 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   3.7e-19   1.7e-15       2     110 ..     240     343 ..     239     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.7e-19
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                       +++++++lak+  +    pg +vv+ + +s+++er +  lg ++++ +vGd +v++++keegavlG E S+h+++++
  gi|386002742|ref|YP_005921041.1| 240 PEKVAVILAKERYA----PGDKVVAGFDCSMIVERELLPLGFEVIRERVGDVFVANRVKEEGAVLGVERSAHLFIPE 312
                                       67899999998865....5556******************************************************* PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleel 110
                                       ++  +D   ++l++ ei+++ g+ lsel++++
  gi|386002742|ref|YP_005921041.1| 313 FQLSDDPFAMSLALGEIVSR-GERLSELADAI 343
                                       ******************87.78*****9554 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 !   37.9   0.0   3.2e-13   1.4e-09      23      60 ..     369     412 ..     337     420 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.2e-13
                                       H......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHH CS
                        PGM_PMM_IV  23 a......sikeglkilledGrrlavRpSGTepllrvyvEak.sde 60 
                                              ++ +glki++ed ++l +RpS+T+pl+r+yvE+  +d 
  gi|386002742|ref|YP_005921041.1| 369 DlaplepDTTDGLKITTEDYTVL-IRPSNTQPLIRLYVETAgTDV 412
                                       1334455799*************.****************96554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2767.78
//
Query:       gi|386002743|ref|YP_005921042.1|  [L=305]
Description: glycosyl transferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-15   56.8   0.0    3.4e-15   56.2   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.1e-07   32.0   0.0    1.5e-07   31.6   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00028   21.4   0.0    0.00043   20.7   0.0    1.3  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.013   14.4   0.3      0.016   14.0   0.3    1.1  1  AA_permease_2    Amino acid permease
      0.019   15.3   0.0      0.076   13.4   0.0    1.7  2  NTP_transf_3     MobA-like NTP transferase domain
      0.056   13.1   0.6      0.074   12.7   0.6    1.1  1  Tetraspanin      Tetraspanin family
       0.12   12.8   0.4       0.35   11.3   0.4    1.8  2  MFS_MOT1         Molybdate transporter of MFS superfamily


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.3e-18   3.4e-15       1     164 [.       7     158 ..       7     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.3e-18
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ ipt Nee+ ++ ++   +++     ++++v+D  S+D+t+e +ee+     + rv+ +  + Gk+ al ++++ 
  gi|386002743|ref|YP_005921042.1|   7 CILIPTLNEEDAIAGVIGEFKRM---GFDDLLVIDGHSQDRTRERAEEA-----GARVVVQRGR-GKGQALKEAFSL 74 
                                       699********************...99999999999************.....99*****955.************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                          + i+ +D D ++ p+ +  l+e+  ++ ad v+g+r+ +       + n+     +rl ++  +  ++  ls++
  gi|386002743|ref|YP_005921042.1|  75 IEAEQIVMIDGDGTYLPGEVGHLLEPVLAGKADHVMGNRFGNLEPGALTRLNSA---GNRLINFFFRLIYDVPLSDI 148
                                       *****************************************9999999999986...56666665555566666665 PP

                                       STCCCEEEEH CS
                   Glycos_transf_2 155 igsaallrre 164
                                         +++++ re
  gi|386002743|ref|YP_005921042.1| 149 LTGYRAFTRE 158
                                       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 !   31.6   0.0   5.7e-11   1.5e-07       3     133 ..       5     122 ..       3     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 5.7e-11
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       d+ +l+pt+need +  v+ ++ +   + +++ v++  s++ t+e+aee+       + rvvv+ r  g +gk +al
  gi|386002743|ref|YP_005921042.1|   5 DVCILIPTLNEEDAIAGVIGEFKR--MGFDDLLVIDGHSQDRTRERAEEA-------GARVVVQ-R--G-RGKGQAL 68 
                                       689*******************99..566999999************993.......5566655.5..5.6****** PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlv 133
                                       +ea++ ++ + ++++D+D    P+ +  ll  +l+ k+++v +++f + +  ++
  gi|386002743|ref|YP_005921042.1|  69 KEAFSLIEAEQIVMIDGDGTYLPGEVGHLLEPVLAGKADHVMGNRFGNLEPGAL 122
                                       *************************99999999999999999999877655544 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.7e-07   0.00043       2      47 ..      14      60 ..      13      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkllh 47
                                      ne+d++  +++  +++gfd++lv+d +s+D+tr+  +e  ++v + +
  gi|386002743|ref|YP_005921042.1| 14 NEEDAIAGVIGEFKRMGFDDLLVIDGHSQDRTRERAEEAgARVVVQR 60
                                      9**********************************998635555554 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   6.4e-06     0.016     182     244 ..     221     282 ..     187     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-06
                     AA_permease_2 182 ffpngwpgvllgllivlwsfdGfesaanvsee.vkk..kdvpkaifigllivlvlyllvniaflgv 244
                                       + ++ +p++ +gl+++++ ++Gf    +v++e + +    +p++i  +lli++++ l++    +g+
  gi|386002743|ref|YP_005921042.1| 221 MAKTHNPLFYFGLMGSFFGTAGFILGLYVLREwITTrtEHIPLTILTALLIIVGFQLFF----MGI 282
                                       4566789999**********************95552357**********999998876....444 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05     0.076      21     102 ..      13      93 ..       9     111 .. 0.85
   2 ?   -0.8   0.0      0.68   1.7e+03       9      45 ..     111     151 ..     100     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                       CCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT CS
                      NTP_transf_3  21 lggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacD 95 
                                       l+++  ++ v+  ++++g+d+++v+ g+  +  ++++++ g+rvv+++  g+g +++l+ a + + +a++++++ +D
  gi|386002743|ref|YP_005921042.1|  13 LNEEDAIAGVIGEFKRMGFDDLLVIDGHsqDRTRERAEEAGARVVVQR--GRGKGQALKEAFSLI-EAEQIVMIDGD 86 
                                       4777788899999************999666788999**********9..89999*******998.89****99999 PP

                                       -TT--HH CS
                      NTP_transf_3  96 mPlltpe 102
                                         +l+ e
  gi|386002743|ref|YP_005921042.1|  87 GTYLPGE 93 
                                       8887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.68
                                       -TTTTT..THHHHCC..CCCCHHHHHHHHHCTT.-CEEEEE CS
                      NTP_transf_3   9 SsRmgg..dKallpl..ggkpllervldalraagvdevvvv 45 
                                       + R+g   + al +l  +g +l+   ++ + ++++++++  
  gi|386002743|ref|YP_005921042.1| 111 GNRFGNlePGALTRLnsAGNRLINFFFRLIYDVPLSDILTG 151
                                       78888666889988888899999999999999988886544 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   2.9e-05     0.074       5      75 ..     228     292 ..     225     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   5 lfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalken 75 
                                       lf f l+   +g + +++G++++     ++   ++ ++  + +il+ lli+vG+ lf++g+lG   a   +
  gi|386002743|ref|YP_005921042.1| 228 LFYFGLMGSFFGTAGFILGLYVL----REWI--TTRTEHIPLTILTALLIIVGFQLFFMGILGDAVASMHR 292
                                       788999999999999****9993....2333..344667788899999***************65555444 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   4.6e+03      38      54 ..     132     148 ..      94     161 .. 0.77
   2 ?   11.3   0.4   0.00014      0.35      72     111 .]     235     277 ..     207     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                          MFS_MOT1  38 lmnlltglfggvPmchg 54 
                                       l+n++  l+++vP++ +
  gi|386002743|ref|YP_005921042.1| 132 LINFFFRLIYDVPLSDI 148
                                       78888888999998744 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00014
                          MFS_MOT1  72 gillGlvllllgltg...llerllrliPksvlgglllgaGleL 111
                                       g ++G + ++lgl     ++++ +++iP ++l +ll+++G++L
  gi|386002743|ref|YP_005921042.1| 235 GSFFGTAGFILGLYVlreWITTRTEHIPLTILTALLIIVGFQL 277
                                       56778888888888877899999999***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1951.29
//
Query:       gi|386002744|ref|YP_005921043.1|  [L=283]
Description: Oxidoreductase FAD/NAD(P)-binding domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-12   46.6   0.0    6.9e-12   46.0   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    6.7e-10   38.6   2.5    1.3e-09   37.7   2.5    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0045   17.3   0.0     0.0081   16.5   0.0    1.4  1  FAD_binding_6    Oxidoreductase FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   1.2e-15   6.9e-12       3     108 ..     131     229 ..     129     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.2e-15
                                       EEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHH CS
                     NAD_binding_1   3 agGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqd 79 
                                       +gG+G+a +rs+++ i++  +d ++v++vyG+rt +dl++  e  +++++  +   v  +v+  +a+w+g+ g v+ 
  gi|386002744|ref|YP_005921043.1| 131 GGGSGFATLRSLINYIADHRDDYREVTVVYGARTPQDLYFTSEYGSWQAADIE---VGITVDMMDASWKGNVGLVTS 204
                                       79*********************************************666655...55555999***********98 PP

                                       HHHHHHHHHSSTTEEEEEECSHHHHHHHH CS
                     NAD_binding_1  80 alleellslkkeethvyvCGppgMikavr 108
                                        l  e+++   +   + +CGpp Mi+av+
  gi|386002744|ref|YP_005921043.1| 205 LL-SEIDP---APGAAALCGPPMMIRAVA 229
                                       87.78888...7788899********997 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   2.5   2.1e-13   1.3e-09       1      41 [.     247     279 ..     247     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.1e-13
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e++M+CGvG C +C++           +vC+dGP+F +d+v
  gi|386002744|ref|YP_005921043.1| 247 ERHMKCGVGKCEHCTMGP--------YHVCTDGPIFSYDRV 279
                                       89****************........79***********98 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-06    0.0081       4      96 ..      26     115 ..      23     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                                       EEEEEECCTTEEEEEE...EESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHH CS
                     FAD_binding_6   4 ltekeevsedtrifrf...klpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsq 77 
                                       +++    s +t  +++   + ++e+ ++++ +Gq++++++   ge    + +++ss++ +  l++ v+  + G+++q
  gi|386002744|ref|YP_005921043.1|  26 VVDIDVESTNTYLLSLrpiDDEDETVEIDYSPGQFLMVSVFGLGE---CPISIASSPT-REPLQICVR--EAGRITQ 96 
                                       56666667777777773112344556789************8888...4566555554.445666666..79***** PP

                                       HHHCS-TT-EEEEEEEE-S CS
                     FAD_binding_6  78 aLdelkigdtleikGPlGk 96 
                                        +  +++gd+l i+GP+G+
  gi|386002744|ref|YP_005921043.1|  97 GMMAARVGDVLGIRGPFGN 115
                                       *****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1733.94
//
Query:       gi|386002745|ref|YP_005921044.1|  [L=334]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-28   97.3   7.6    7.1e-28   97.3   7.6    1.7  2  Fer4_22   4Fe-4S dicluster domain
    3.2e-07   30.8   3.8      0.002   18.6   0.2    2.4  2  Fer4_17   4Fe-4S dicluster domain
    1.8e-06   28.3   7.9    1.3e-05   25.5   8.1    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00081   19.5  14.3      0.009   16.1   3.9    2.5  2  Fer4_21   4Fe-4S dicluster domain
    0.00089   19.8  13.8      0.016   15.8   0.4    2.7  2  Fer4_7    4Fe-4S dicluster domain
      0.001   19.2  11.0       0.14   12.3   1.6    2.7  3  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.7  16.3       0.14   12.3   2.2    3.4  3  Fer4_2    4Fe-4S binding domain
      0.077   12.8  20.3        0.3   11.0   3.8    2.5  2  Fer4      4Fe-4S binding domain
      0.093   12.9   4.0        3.8    7.7   0.7    2.3  2  Fer4_18   4Fe-4S dicluster domain
       0.16   12.9  11.0       0.36   11.8   0.2    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
        1.2   10.2  21.6        1.5    9.9   4.5    3.5  3  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.5       4.7   7.7e+03       7      19 ..     128     140 ..     125     144 .. 0.83
   2 !   97.3   7.6   4.3e-31   7.1e-28       1      95 [.     231     322 ..     231     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
                           Fer4_22   7 aCtlvCptCsCfd 19 
                                       +Ct+    C+C +
  gi|386002745|ref|YP_005921044.1| 128 NCTTPGERCFCAS 140
                                       6999999999986 PP

  == domain 2  score: 97.3 bits;  conditional E-value: 4.3e-31
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekf 77 
                                       rClsCg C+lvCp C+Cf+v d+      +ger+r+ dsC+l++f+++++g+n+r++ +erlr+++l+k+ ++ ek+
  gi|386002745|ref|YP_005921044.1| 231 RCLSCGGCSLVCPVCHCFTVIDQGV---PDGERLRCRDSCTLAGFSRMTSGANPRPSLGERLRHWYLDKFVYIPEKT 304
                                       7*********************984...579********************************************** PP

                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       g  gCvGCgRC+++c ++
  gi|386002745|ref|YP_005921044.1| 305 GLFGCVGCGRCSRVCLSD 322
                                       ***************865 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5   7.6e-05      0.12      35      57 ..     221     243 ..     192     246 .. 0.72
   2 !   18.6   0.2   1.2e-06     0.002       8      61 .]     263     324 ..     260     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-05
                           Fer4_17  35 eeaekeekaslCieCgeCerkCP 57 
                                       ee+  e + s+C++Cg+C+ +CP
  gi|386002745|ref|YP_005921044.1| 221 EETDWEVAGSRCLSCGGCSLVCP 243
                                       33334445699***********9 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                           Fer4_17   8 ClpeCpsyea....ydnepk....kllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       C+++C          + +p+    + lr ++l ++ ++ +++    C++Cg+C+r+C +++d
  gi|386002745|ref|YP_005921044.1| 263 CRDSCTLAGFsrmtSGANPRpslgERLRHWYLDKFVYIPEKTGLFGCVGCGRCSRVCLSDVD 324
                                       888888533322222223333344567778888999998999***************99987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.7   0.00015      0.24      45      63 ..     226     244 ..     187     246 .. 0.71
   2 !   25.5   8.1   8.2e-09   1.3e-05       3      62 ..     230     320 ..     228     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                            Fer4_8  45 eealwsCttcgaCtevCpv 63 
                                       e a  +C++cg C+ vCpv
  gi|386002745|ref|YP_005921044.1| 226 EVAGSRCLSCGGCSLVCPV 244
                                       4467889999999999996 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 8.2e-09
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee...............................eea 47 
                                       ++C  Cg C   Cpv++++   +   + ge+    ++++ l +                               +++
  gi|386002745|ref|YP_005921044.1| 230 SRCLSCGGCSLVCPVCHCFTvIDQGVPDGERLR-CRDSCTLAGfsrmtsganprpslgerlrhwyldkfvyipeKTG 305
                                       69****************997788888888888.6666665556667777777788888888888889999999*** PP

                            Fer4_8  48 lwsCttcgaCtevCp 62 
                                       l+ C++cg+C++vC 
  gi|386002745|ref|YP_005921044.1| 306 LFGCVGCGRCSRVCL 320
                                       **************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.9   5.5e-06     0.009      30      58 ..     221     249 ..     212     250 .. 0.86
   2 !    8.4   2.7    0.0014       2.4      41      51 ..     309     319 ..     303     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.5e-06
                           Fer4_21  30 aktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       ++t ++v  ++C  C  Cs vCPv  c +
  gi|386002745|ref|YP_005921044.1| 221 EETDWEVAGSRCLSCGGCSLVCPVCHCFT 249
                                       567789999***************99976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                           Fer4_21  41 CvGCnlCssvC 51 
                                       CvGC  Cs vC
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVC 319
                                       99999999999 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   9.6e-06     0.016      27      50 ..     221     244 ..     193     245 .. 0.82
   2 !   11.1   3.1   0.00029      0.48      38      50 ..     309     321 ..     261     323 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-06
                            Fer4_7  27 gtekveidpekClgCgaCvavCPt 50 
                                       +  ++e+  ++Cl+Cg C  vCP+
  gi|386002745|ref|YP_005921044.1| 221 EETDWEVAGSRCLSCGGCSLVCPV 244
                                       4467899999*************7 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
                            Fer4_7  38 ClgCgaCvavCPt 50 
                                       C+gCg+C +vC +
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVCLS 321
                                       7777777777755 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.6   8.7e-05      0.14      32      48 ..     224     244 ..     192     248 .. 0.76
   2 !   10.3   2.6   0.00037      0.61      34      48 ..     307     321 ..     259     324 .. 0.61
   3 !   10.3   2.0   0.00038      0.62       2      16 ..     309     323 ..     308     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.7e-05
                            Fer4_9  32 se....eaCigCgaCveaCpk 48 
                                       ++    ++C++Cg C  +Cp 
  gi|386002745|ref|YP_005921044.1| 224 DWevagSRCLSCGGCSLVCPV 244
                                       22567789***********96 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00037
                            Fer4_9  34 eaCigCgaCveaCpk 48 
                                         C+gCg+C  +C +
  gi|386002745|ref|YP_005921044.1| 307 FGCVGCGRCSRVCLS 321
                                       567777777777754 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00038
                            Fer4_9   2 CtgCgaCveaCpagv 16 
                                       C+gCg+C ++C ++v
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVCLSDV 323
                                       899999999997766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   8.7e-05      0.14       9      21 ..     231     243 ..     223     244 .. 0.90
   2 ?   -0.7   0.2       1.2   1.9e+03      16      20 ..     263     267 ..     260     270 .. 0.57
   3 ?   11.3   1.8   0.00018       0.3      10      20 ..     309     319 ..     296     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.7e-05
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       rC++Cg C  +CP
  gi|386002745|ref|YP_005921044.1| 231 RCLSCGGCSLVCP 243
                                       8************ PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                            Fer4_2  16 CvsaC 20 
                                       C+++C
  gi|386002745|ref|YP_005921044.1| 263 CRDSC 267
                                       55555 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00018
                            Fer4_2  10 CigCgaCvsaC 20 
                                       C+gCg C  +C
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVC 319
                                       *********** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.8   0.00019       0.3       6      20 ..     230     244 ..     227     244 .. 0.94
   2 ?    7.2   8.6    0.0029       4.8       8      18 ..     309     319 ..     308     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                       TTSSS-THHHHHSTT CS
                              Fer4   6 ekCigCGaCvevCPv 20 
                                       ++C  CG C  vCPv
  gi|386002745|ref|YP_005921044.1| 230 SRCLSCGGCSLVCPV 244
                                       69************7 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0029
                                       SSS-THHHHHS CS
                              Fer4   8 CigCGaCvevC 18 
                                       C+gCG+C  vC
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVC 319
                                       *********** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.7    0.0023       3.8      51      74 ..     222     245 ..     190     271 .. 0.68
   2 ?    6.0   0.1    0.0084        14      59      76 ..     307     324 ..     294     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0023
                           Fer4_18  51 eerkekgagdcidcescvkvcPtg 74 
                                       e+  e + + c++c+ c  vcP+ 
  gi|386002745|ref|YP_005921044.1| 222 ETDWEVAGSRCLSCGGCSLVCPVC 245
                                       3344556678************73 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0084
                           Fer4_18  59 gdcidcescvkvcPtgid 76 
                                         c+ c+ c +vc  ++d
  gi|386002745|ref|YP_005921044.1| 307 FGCVGCGRCSRVCLSDVD 324
                                       57***********99998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00022      0.36      39      66 ..     217     244 ..     194     245 .. 0.77
   2 ?    3.6   5.8     0.077   1.3e+02      54      64 ..     309     319 ..     262     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                           Fer4_16  39 kdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       k+++e++  +  + ++  C+ C  vCP+
  gi|386002745|ref|YP_005921044.1| 217 KRAIEETDWEVAGSRCLSCGGCSLVCPV 244
                                       5666666667778899999999999996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.077
                           Fer4_16  54 itgCdiCqdvC 64 
                                       + gC++C +vC
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVC 319
                                       55666666665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.9     0.024        39       1      13 [.     232     244 ..     232     247 .. 0.93
   2 ?    0.1   0.7       1.3   2.1e+03       1      11 [.     245     267 ..     245     269 .. 0.72
   3 ?    9.9   4.5   0.00092       1.5       1      12 [.     309     320 ..     309     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg C  vCPv
  gi|386002745|ref|YP_005921044.1| 232 CLSCGGCSLVCPV 244
                                       999*********7 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                            Fer4_3   1 CtgCg.............aCvevC 11 
                                       C +C              +C ++C
  gi|386002745|ref|YP_005921044.1| 245 C-HCFtvidqgvpdgerlRCRDSC 267
                                       6.8866667777777777798888 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00092
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+gCg+C +vC 
  gi|386002745|ref|YP_005921044.1| 309 CVGCGRCSRVCL 320
                                       ***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2169.13
//
Query:       gi|386002746|ref|YP_005921045.1|  [L=675]
Description: Formate dehydrogenase subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete 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-82  276.1   0.0    6.1e-82  275.9   0.0    1.0  1  Molybdopterin    Molybdopterin oxidoreductase
    2.4e-30  104.8   0.0    5.1e-30  103.8   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.4e-17   62.2   0.6    7.4e-17   61.1   0.6    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.9   0.0     1e-85   6.1e-82       1     430 [.      58     479 ..      58     481 .. 0.94

  Alignments for each domain:
  == domain 1  score: 275.9 bits;  conditional E-value: 1e-85
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl+ P++R   r  G+ vr+sW+eAl++ a++lk+++++ gp +v +  s + + +e+ ++++kl+++  +  ++++
  gi|386002746|ref|YP_005921045.1|  58 RLRAPLIR---R-GGRMVRSSWEEALTATAERLKEIREEAGPGAVGVLTSAKGT-NEENYLFAKLARAGLR--TNNV 127
                                       9*******...9.9********************************98888888.899999**********..9*** PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HC CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryael 154
                                       d+ a+l++a  +  +g+ +  + +++np+ +l  sd+i++ GsN  e +p++ a i+ a++++ a +iv +pr +++
  gi|386002746|ref|YP_005921045.1| 128 DHVARLCHAPSVAGLGAALG-SGAMTNPIRGLLSSDAILVTGSNTTEQHPLVAATILEAQSRG-AALIVADPRRTQI 202
                                       *********99955555443.456788*************************99999999996.99**********9 PP

                                       GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHH CS
                     Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarna 231
                                       ++ ad  la++ gtd+a ++++ + il+ ++ d+ef+r +t g++ +++ ++++++e ++k+++++ r   e a+ a
  gi|386002746|ref|YP_005921045.1| 203 ASLADHRLAPRLGTDVAWINGLLNLILEGGLADEEFIRERTAGFDALKDSVSKYTPEVVEKISGIPPR-DLEAAAAA 278
                                       999******************************************************55555555555.55677777 PP

                                       HHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT.. CS
                     Molybdopterin 232 aktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke.. 306
                                       + +a+++++++ +g +++++g++++ a++nL+l++gn g++g+g   l+G  +++g a+++galp  +s ++ +e  
  gi|386002746|ref|YP_005921045.1| 279 FGEAPRAAVVYAMGTTQHSNGTENVLALANLVLATGNLGREGTGICPLRGHQNVQG-ACDMGALPNVYSGYQKVEdp 354
                                       888889*************************************************9.*******************9 PP

                                       .HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHT CS
                     Molybdopterin 307 .ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstaly 382
                                         + ++ a +  +l+  p+ ++ve+++++k++ +k l++ g+np+++ +d+++v +ale+l+++ v +++ t+t   
  gi|386002746|ref|YP_005921045.1| 355 aARGRMEAAWGTDLPPAPGLTAVEMMEAAKEGRLKGLFISGENPMMSYPDRGLVGRALESLEFLAVAEIFPTETTAL 431
                                       98888888888899999************************************************************ PP

                                       SSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHH CS
                     Molybdopterin 383 aDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLa 430
                                       aD++LPaa++ Ek++++t++e+r+q+ ++av+ppgea+++ ++  aL 
  gi|386002746|ref|YP_005921045.1| 432 ADVVLPAASFAEKDGTFTSTERRVQRVRRAVPPPGEARPEVEVAAALL 479
                                       *******************************************99996 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0   8.6e-34   5.1e-30       1     111 []     561     667 ..     561     667 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 8.6e-34
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l L+tgrsl ++h++ +tr+++ l ++ p + ve+npedAaalG++ G  V+ves+ Gs+ev+a++t++v+pG+vf 
  gi|386002746|ref|YP_005921045.1| 561 LLLTTGRSLFHFHTGSMTRRTPLLDRELPkPAVEMNPEDAAALGVRSGGGVVVESASGSLEVEARTTDSVPPGTVFF 637
                                       68***********************999999********************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksva 111
                                       pf++ e     ++aN lt++++dp s++pefk ++
  gi|386002746|ref|YP_005921045.1| 638 PFHFAE-----APANLLTAADLDPRSKIPEFKRTP 667
                                       ****99.....*********************975 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.6   1.2e-20   7.4e-17       2      55 .]       2      55 ..       1      55 [. 0.95

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.2e-20
                                      EEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                    Molybdop_Fe4S4  2 kvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55
                                      + + t+C yCg+gCgl +hv+dg+ v v ++p hp+++grlCvKG  ++++v++
  gi|386002746|ref|YP_005921045.1|  2 EMIATTCVYCGCGCGLFIHVEDGRAVGVSPNPAHPISRGRLCVKGWLAADFVHH 55
                                      6689*****************************************999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 4026.27
//
Query:       gi|386002747|ref|YP_005921046.1|  [L=419]
Description: hypothetical protein Mhar_2067 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2746.94
//
Query:       gi|386002748|ref|YP_005921047.1|  [L=127]
Description: hypothetical protein Mhar_2068 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.56
# Mc/sec: 686.68
//
Query:       gi|386002749|ref|YP_005921048.1|  [L=1021]
Description: hypothetical protein Mhar_2069 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1021 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 5782.84
//
Query:       gi|386002750|ref|YP_005921049.1|  [L=295]
Description: hypothetical protein Mhar_2070 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1766.50
//
Query:       gi|386002751|ref|YP_005921050.1|  [L=363]
Description: hypothetical protein Mhar_2071 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2431.97
//
Query:       gi|386002752|ref|YP_005921051.1|  [L=297]
Description: hypothetical protein Mhar_2072 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.066   13.6   0.0       0.67   10.4   0.1    2.3  2  GLEYA     GLEYA domain


Domain annotation for each model (and alignments):
>> GLEYA  GLEYA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   3.8e-05      0.67       3      36 ..      11      45 ..       9      81 .. 0.86
   2 ?    0.3   0.0     0.053   9.5e+02       4      22 ..     115     133 ..     109     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                                      EEEEEEE--SSSEEEEEEE.EEESEEEEEESBT.T CS
                             GLEYA  3 lelrGYfyapktgtYtfslsnaDdiallwlGdk.A 36
                                      l l G +      +Ytf + n+ d  ++w+  + A
  gi|386002752|ref|YP_005921051.1| 11 LLLAGLISSASAASYTFGVYNVTDGSYFWISRQsA 45
                                      5667777788899*****************98744 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.053
                                       EEEEEE--SSSEEEEEEE. CS
                             GLEYA   4 elrGYfyapktgtYtfsls 22 
                                       + r Yf +  +  +t++l+
  gi|386002752|ref|YP_005921051.1| 115 VNRSYFKPAGSDVWTITLE 133
                                       5689999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1900.78
//
Query:       gi|386002753|ref|YP_005921052.1|  [L=337]
Description: GTP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-15   56.5   0.0    3.8e-15   56.0   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    2.6e-12   46.5   0.1    1.3e-11   44.2   0.1    1.8  1  FeoB_N       Ferrous iron transport protein B
  ------ inclusion threshold ------
       0.02   14.8   0.0        0.1   12.5   0.0    1.9  2  RsgA_GTPase  RsgA GTPase
      0.053   14.0   0.1       0.11   13.0   0.1    1.4  1  ABC_tran     ABC transporter
      0.063   13.1   0.1        0.1   12.4   0.1    1.3  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.087   12.9   0.0        4.1    7.4   0.1    2.2  2  Dynamin_N    Dynamin family
       0.16   12.2   0.0        0.3   11.3   0.0    1.5  1  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.16   11.5   0.0        4.1    6.9   0.0    2.3  2  GTP_EFTU     Elongation factor Tu GTP binding domain
       0.17   11.7   0.0       0.27   11.0   0.0    1.3  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
       0.18   11.5   0.0        0.4   10.4   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
       0.22   10.9   0.0       0.38   10.2   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
       0.23   11.1   0.1        3.1    7.4   0.1    2.1  2  Ras          Ras family


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   2.5e-18   3.8e-15       1      87 [.     145     241 ..     145     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2.5e-18
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS.HHHHHHHHHHHHHH.... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie.gaseekglgkafla.... 72 
                                       e++++Gr+NvGKStL++ ltg++++v+++pg+T  + ++     g  ++ vD+pG +  ++  e+g+++  ++    
  gi|386002753|ref|YP_005921052.1| 145 EIVLIGRSNVGKSTLFRLLTGKRVRVGRRPGVTVGPARALA---G-AVTYVDMPG-YGyMKGAERGVQEGTKDfivr 216
                                       699***********************************955...3.8********.754333333333333333333 PP

                                       ..HHCTSEEEEEEETT........T CS
                          MMR_HSR1  73 ..leeadlillvvdas........e 87 
                                          e+ad ill v++          
  gi|386002753|ref|YP_005921052.1| 217 ylEEKADEILLAVQVIdaasfieiA 241
                                       4234477777666532222444440 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1     9e-15   1.3e-11       2     127 ..     145     286 ..     144     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 9e-15
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSS.SSSSHHHHHHHHHHH.. CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYsl.sayseeekvardfll.. 75 
                                       +++l+G  nvGk+tlf  ltg++ +vg  pGvtv  +++        v+ vD+PG   +  a    ++ ++df++  
  gi|386002753|ref|YP_005921052.1| 145 EIVLIGRSNVGKSTLFRLLTGKRVRVGRRPGVTVGPARALAG----AVTYVDMPGYGYMkGAERGVQEGTKDFIVry 217
                                       699*******************************99998888....999******8555233444455566666555 PP

                                       .CTSSSEE...EEEEEGGGH.........HHHHHHHHHHHH....TTSSEEEEEETHHHHHHTTEEE-H CS
                            FeoB_N  76 .eeepdvv...vnvvdatnl.........ernLyLtlqlle....lgvpvvlalnmideaekkgieidl 127
                                        ee++d +   v+v+da+++         + ++ L ++l+e    l++ v +a n++d++e++  ++d+
  gi|386002753|ref|YP_005921052.1| 218 lEEKADEIllaVQVIDAASFieiadrwegRGEIPLEVELFEfltdLDLAVAVAANKMDKVEDRDATLDA 286
                                       555555432337889987642223222213467777776652222678899999********9999985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.8e-05       0.1     102     125 ..     146     168 ..     138     174 .. 0.84
   2 ?   -0.7   0.0      0.76   1.1e+03      45      65 ..     263     284 ..     256     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                                       EEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelel 125
                                       +vl+G S vGKStL   l+++ ++
  gi|386002753|ref|YP_005921052.1| 146 IVLIGRSNVGKSTLFRLLTGK-RV 168
                                       79**************99987.44 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.76
                                       TT-EEEEEEE-GGG--HHH.HH CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeee.el 65 
                                        ++ + ++ nK+D +e+++ +l
  gi|386002753|ref|YP_005921052.1| 263 LDLAVAVAANKMDKVEDRDaTL 284
                                       567888999*****99998333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.4e-05      0.11      13      34 ..     145     166 ..     141     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-05
                                       EEEEEESTTSSHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagl 34 
                                        ++++G++  GKStL++ll+g+
  gi|386002753|ref|YP_005921052.1| 145 EIVLIGRSNVGKSTLFRLLTGK 166
                                       579****************997 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.8e-05       0.1       1      26 [.     150     175 ..     150     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpv 26 
                                       G +++GKSTl rlL  + +r gr+p 
  gi|386002753|ref|YP_005921052.1| 150 GRSNVGKSTLFRLLTGKRVRVGRRPG 175
                                       789********************986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0027       4.1       1      25 [.     146     170 ..     146     182 .. 0.84
   2 ?    3.2   0.0     0.053        80      99     136 ..     184     229 ..     177     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                                       EEEEEBTTTTHHHHHHHHHTS--S- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilp 25 
                                       i+++G  + GKS++   L+g+++ +
  gi|386002753|ref|YP_005921052.1| 146 IVLIGRSNVGKSTLFRLLTGKRVRV 170
                                       89*******************9865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.053
                                       TS-SEEEEE---B-SSSGTTS.......HHHHHHH.STTEEEEEEE CS
                         Dynamin_N  99 lvkgltlvDlPGldsvnkrdq.......elvkeyi.kkadiilavt 136
                                       l   +t vD+PG+  ++  +        + + +y+ +kad il+ +
  gi|386002753|ref|YP_005921052.1| 184 LAGAVTYVDMPGYGYMKGAERgvqegtkDFIVRYLeEKADEILLAV 229
                                       5667999*****9988777777889999999999998888777644 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002       0.3       2      25 ..     146     169 ..     145     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                       EEEESSTTSSHHHHHHCHCT-CCC CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfs 25 
                                       +vl+G s+vGK++l++ ++ ++++
  gi|386002753|ref|YP_005921052.1| 146 IVLIGRSNVGKSTLFRLLTGKRVR 169
                                       89*************999887765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.059        88       5      26 ..     145     166 ..     142     196 .. 0.85
   2 ?    6.9   0.0    0.0028       4.1     106     141 ..     248     286 ..     202     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.059
                                       EEEEEESTTSSHHHHHHHHHHH CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyk 26 
                                        i++ig  + GK+TL   L+ k
  gi|386002753|ref|YP_005921052.1| 145 EIVLIGRSNVGKSTLFRLLTGK 166
                                       58899**********9877655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                       BSTHHHHHHHHHHHHTTTEEEEEEESCGST...HHHHHH CS
                          GTP_EFTU 106 GvepqteevlrlalkegvpiivfiNKmDrl...kaelke 141
                                       G  p   e+++ + ++++ + v+ NKmD++   +a+l+ 
  gi|386002753|ref|YP_005921052.1| 248 GEIPLEVELFEFLTDLDLAVAVAANKMDKVedrDATLDA 286
                                       45556668888999999*************665555554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.27       3      20 ..     147     164 ..     146     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                            AAA_21   3 vliGpNgsGKSnLLdald 20 
                                       vliG+ ++GKS+L+++l 
  gi|386002753|ref|YP_005921052.1| 147 VLIGRSNVGKSTLFRLLT 164
                                       9**************995 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027       0.4      24      39 ..     145     160 ..     136     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                        ++l+G+s +GKSTl+
  gi|386002753|ref|YP_005921052.1| 145 EIVLIGRSNVGKSTLF 160
                                       4799**********98 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00025      0.38       4      29 ..     144     169 ..     141     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                       -EEEEE-STTSSHHHHHHHHHHSS-- CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvk 29 
                                         ++l+G s+ GK +lf +Lt + v+
  gi|386002753|ref|YP_005921052.1| 144 SEIVLIGRSNVGKSTLFRLLTGKRVR 169
                                       6799****************988765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0021       3.1       2      18 ..     146     162 ..     145     179 .. 0.84
   2 ?    1.5   0.0      0.13     2e+02      70     119 ..     220     279 ..     207     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                                       EEEEESTTSSHHHHHHH CS
                               Ras   2 lvlvGdsavGKtslllr 18 
                                       +vl+G s+vGK++l   
  gi|386002753|ref|YP_005921052.1| 146 IVLIGRSNVGKSTLFRL 162
                                       89***********9765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                       TTESEEEEEEETTBHHHHHTHH.HHHH..HHHHHST.......TTSEEEEEEETTTGGGG CS
                               Ras  70 rdaegillvyditsresfenvk.kwve..eikrvae.......envpivLvGnKvDleek 119
                                       ++a+ ill  ++ +++sf +++ +w    ei   +e        ++++++ +nK+D  e+
  gi|386002753|ref|YP_005921052.1| 220 EKADEILLAVQVIDAASFIEIAdRWEGrgEIPLEVElfefltdLDLAVAVAANKMDKVED 279
                                       5688999999999*****999977743124444444555555545677777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2185.08
//
Query:       gi|386002754|ref|YP_005921053.1|  [L=383]
Description: Transporter, small conductance mechanosensitive ion channel (MscS) family [Methanosaeta harundinacea 6Ac]
Scores for complete 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-46  157.9   0.1    2.5e-46  157.9   0.1    1.4  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.0   2.8         1   1.8e+04       3      15 ..      84      96 ..      79     101 .. 0.51
   2 !  157.9   0.1   1.4e-50   2.5e-46       8     206 .]     140     336 ..     134     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: -6.0 bits;  conditional E-value: 1
                                      HHHHHHHHHHHHH CS
                        MS_channel  3 ilkiliivvgili 15
                                      ilk+lii++++++
  gi|386002754|ref|YP_005921053.1| 84 ILKVLIIIIITYL 96
                                      3444444444433 PP

  == domain 2  score: 157.9 bits;  conditional E-value: 1.4e-50
                                       HHHHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                        MS_channel   8 iivvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                       i+v g+l+v+ ++        +lla++G++gla+g+a++d++snl++Gi+l + +pf++GD+v++++  G++ed++l
  gi|386002754|ref|YP_005921053.1| 140 IYVAGFLMVIYQIPTLssiSVTLLAGAGVAGLAIGFAAQDSLSNLISGIFLAIFHPFRVGDFVDFKGEYGQIEDLTL 216
                                       5566666666665554333668******************************************************* PP

                                       SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEE CS
                        MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellv 158
                                       r t+i+t+dgr +++Pns + ++ i+N+s +++    +v++g+ ys+d   +++++e+++e+++++p vlkd + +v
  gi|386002754|ref|YP_005921053.1| 217 RHTTIKTWDGRRIFVPNSLMGSQPIINWSITDPVITWRVDVGIGYSAD---IDRAREIMLEVARRHPLVLKDHDITV 290
                                       ************************************************...************************** PP

                                       EEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 159 vldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       ++++++d ++n++++v v+    +  +s+  ++++ ikk ++eegiei
  gi|386002754|ref|YP_005921053.1| 291 RITDLADFAVNMRLTVDVPH--RDVAYSTACDLREAIKKRFDEEGIEI 336
                                       ********************..89**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2658.32
//
Query:       gi|386002755|ref|YP_005921054.1|  [L=311]
Description: putative secreted protein, NosD family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-53  182.0  41.8    1.4e-39  135.9  24.9    2.0  2  NosD             Periplasmic copper-binding protein (NosD)
    5.3e-38  130.4  62.7    1.4e-21   76.9  20.9    2.1  2  Beta_helix       Right handed beta helix region
    1.6e-06   27.7  27.8    3.3e-06   26.6  12.2    2.2  2  DUF1565          Protein of unknown function (DUF1565)
  ------ inclusion threshold ------
      0.023   14.5  23.1       0.23   11.2   4.0    3.1  3  Pectate_lyase_3  Pectate lyase superfamily protein


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 !   55.3  10.9   1.2e-18   5.3e-15      44     131 ..      39     127 ..      20     128 .. 0.92
   2 !  135.9  24.9     3e-43   1.4e-39      55     240 ..     118     303 ..     117     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.2e-18
                              NosD  44 dnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisn 120
                                         s++nti++n ++ ++yGi+l+++ +n + +n + +n+ Gi+l+ss+++t+  N++ nn+  Gills+++nnti+n
  gi|386002755|ref|YP_005921054.1|  39 AISKENTIRNNMVTGNEYGIVLDGAARNSVLKNFVCKNDVGISLYSSERCTIVENEACNNTFGGILLSRANNNTIRN 115
                                       56899************************************************************************ PP

                              NosD 121 Ntis.nnnkGif 131
                                       N++s n  +Gi 
  gi|386002755|ref|YP_005921054.1| 116 NNASqNRWAGII 127
                                       ****99999987 PP

  == domain 2  score: 135.9 bits;  conditional E-value: 3e-43
                              NosD  55 tienlryGihlensesntiedntlssne.sGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGi 130
                                       + +n  +Gi l ++++nt+++n++++n+ +Gi+l +ss+nt+++N+++ n ++G+ l +ss n i+ Nti nn +G+
  gi|386002755|ref|YP_005921054.1| 118 ASQNRWAGIILGECSDNTVSNNVVRQNDnQGIWLLRSSANTIRGNRVRFNYIFGVRLLYSSRNAITSNTIRNNLDGV 194
                                       5567789********************************************************************** PP

                              NosD 131 flensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylg..GN 205
                                       +le+s++n++ gN+++ n ++G++ +++s +n+iy N++i+n++++   +s  n+Wn+t+  ++ ++g +y +  GN
  gi|386002755|ref|YP_005921054.1| 195 SLESSNGNVLAGNNLSIN-EYGVY-VDNSFNNRIYMNNLIGNNNDAHSWNS-TNYWNSTELLKYIYNGVQYRRyvGN 268
                                       ******************.*****.*******************9999876.********99*************** PP

                              NosD 206 yWsdydgeDadgDGigDtpYeindgviDylplvnp 240
                                       yWs y g D  gDG+ D p+ +++   Dy pl +p
  gi|386002755|ref|YP_005921054.1| 269 YWSGYFGPDPFGDGLVDRPHAVSGRERDYNPLKKP 303
                                       ********************************998 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 !   76.9  20.9   3.2e-25   1.4e-21       2     157 ..      10     163 ..       9     164 .. 0.96
   2 !   66.8  33.8   4.2e-22   1.9e-18       2     140 ..     102     238 ..     102     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.2e-25
                                       SEEE-SS-E.EEESEEEES-....SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-T CS
                        Beta_helix   2 gisingssnvtiknntisns....ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggial 74 
                                       +++i+ +++  +++++++ns    +++Gi++ + +n +i+nn +++ +++Gi + g+++n + +n +  n  +gi l
  gi|386002755|ref|YP_005921054.1|  10 AVVISADEV-LFEGFDVTNSgklwKDAGIKAISKEN-TIRNNMVTG-NEYGIVLDGAARNSVLKNFVCKND-VGISL 82 
                                       688888888.**************************.*********.**********99999999999999.***** PP

                                       T--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS-- CS
                        Beta_helix  75 fgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnv 151
                                       + + + +i  ne  +n   Gi l+ ++nnti+nN+++ n+ +Gi + + s ++tv+nN++ +n++ Gi++ +ss+ +
  gi|386002755|ref|YP_005921054.1|  83 YSSERCTIVENEACNNTFGGILLSRANNNTIRNNNASQNRWAGIILGECS-DNTVSNNVVRQNDNQGIWLLRSSA-N 157
                                       ****************999*******************************.************************.* PP

                                       EEES-E CS
                        Beta_helix 152 tvrnNt 157
                                       t+r+N 
  gi|386002755|ref|YP_005921054.1| 158 TIRGNR 163
                                       *****7 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 4.2e-22
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgas 78 
                                       gi++++ +n ti+nn+ s + ++Gi l+++s+++++nn++ +n   Gi++l+ss nti++n+++ n+ +g+ l ++s
  gi|386002755|ref|YP_005921054.1| 102 GILLSRANNNTIRNNNASQNRWAGIILGECSDNTVSNNVVRQNDNQGIWLLRSSANTIRGNRVRFNYIFGVRLLYSS 178
                                       89999999********************************************************************* PP

                                       --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-S.SE CS
                        Beta_helix  79 nnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnk.ga 140
                                       +n i  n+i++n + G++l++s+ n++ +N+++ n+ +G+++d+s  n+++  N++ +n+ +a
  gi|386002755|ref|YP_005921054.1| 179 RNAITSNTIRNNLD-GVSLESSNGNVLAGNNLSINE-YGVYVDNSF-NNRIYMNNLIGNNnDA 238
                                       ************99.*********************.*********.6666555555444144 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6  12.2   7.3e-10   3.3e-06      92     233 ..      10     159 ..       2     168 .. 0.73
   2 !    6.0   9.4    0.0015       6.7     101     190 ..     158     236 ..     153     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.3e-10
                           DUF1565  92 vtivlaneatiaGvtitNpni.lkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGnsil..... 162
                                       + ++ a+e+   G+ +tN  +  k+ g+   s   +i+nN +tgn + Gi  +   a++++ +n +  n +      
  gi|386002755|ref|YP_005921054.1|  10 AVVISADEVLFEGFDVTNSGKlWKDAGIKAISKENTIRNNMVTGN-EYGIVLDGA-ARNSVLKNFVCKNDVGislys 84 
                                       55778899999********7768*********************7.99****888.588888888766664433433 PP

                           DUF1565 163 feknGiaisgasaave.....nkienNiivkNliGvvanalalDlGsgsegsaGnNifsnnaeaDinisaaktqkl 233
                                       +e   i++++a +        ++ +nN+i +N+   + +  +  lG+ s++++ nN+++ n ++ i+    +++++
  gi|386002755|ref|YP_005921054.1|  85 SERCTIVENEACNNTFggillSRANNNTIRNNNASQN-RWAGIILGECSDNTVSNNVVRQNDNQGIWLLRSSANTI 159
                                       2222444444444322344446666666666665433.344456**********************9966665554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0015
                           DUF1565 101 tiaGvtitNpnilkgtgvliesasakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaav 177
                                       ti+G +++   i   +  l++s+   i +Nti +n  dG++ +        +gn+ +Gn++  ++ G+  +   ++ 
  gi|386002755|ref|YP_005921054.1| 158 TIRGNRVRFNYIFGVR--LLYSSRNAITSNTIRNN-LDGVSLESS------NGNVLAGNNLSINEYGVYVD---NSF 222
                                       5666666555342222..56777899******997.799998877......59**************9865...456 PP

                           DUF1565 178 enki.enNiivkNl 190
                                       +n+i  nN+i +N+
  gi|386002755|ref|YP_005921054.1| 223 NNRIyMNNLIGNNN 236
                                       68997888888775 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   6.2e-05      0.28     153     214 ..      41     103 ..      10     104 .. 0.79
   2 ?   11.2   4.0   5.2e-05      0.23     131     213 ..     109     193 ..     106     195 .. 0.79
   3 ?    2.9   7.1     0.019        83     138     195 ..     185     242 ..     177     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                                       --EEEEES-EEES-SS-SEEE.S.-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEE.ESSSEEE CS
                   Pectate_lyase_3 153 gsggflndlvfsglgdigiav.g.nqqftvrnitfnnattgievlwgwgwtlknvki.nncegGi 214
                                       ++++++++  ++g  ++gi + g   +++++n +++n   gi++ ++++ t++ ++  nn+ gGi
  gi|386002755|ref|YP_005921054.1|  41 SKENTIRNNMVTG-NEYGIVLdGaARNSVLKNFVCKN-DVGISLYSSERCTIVENEAcNNTFGGI 103
                                       3457999999999.9******768999999*******.******999998888775559999998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.2e-05
                                       ES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE.-S--SEEE-TT-EEEEEEE CS
                   Pectate_lyase_3 131 envefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfn.nattgievlwgwgwtlknv 205
                                        n+++++++as++   gi++ + s +++++ v+++++++gi + ++ + t+r + +  n   g+++l++++  + ++
  gi|386002755|ref|YP_005921054.1| 109 NNNTIRNNNASQNRWAGIILGECSDNTVSNNVVRQNDNQGIWLlRSSANTIRGNRVRfNYIFGVRLLYSSRNAITSN 185
                                       6899*******99999************88888888*******8877777755544313377888888777777777 PP

                                       EEESSSEE CS
                   Pectate_lyase_3 206 kinncegG 213
                                       +i n  +G
  gi|386002755|ref|YP_005921054.1| 186 TIRNNLDG 193
                                       87776666 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.019
                                       E-SSS---TT---SS--EEEE..ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE- CS
                   Pectate_lyase_3 138 seasgtkhqgifiengsggfl..ndlvfsglgdigiavgnqqftvrnitfnnattgievl 195
                                       ++   ++ +g+ +e+++g++l  n+l ++ +g +  +  n+ ++++n+  nn + + + +
  gi|386002755|ref|YP_005921054.1| 185 NTIR-NNLDGVSLESSNGNVLagNNLSINEYGVYVDNSFNNRIYMNNLIGNN-NDAHSWN 242
                                       3333.78889********************555555555********99888.5554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2091.08
//
Query:       gi|386002756|ref|YP_005921055.1|  [L=412]
Description: proteasome-activating nucleotidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-43  146.8   0.2    1.2e-42  145.5   0.0    1.8  1  AAA              ATPase family associated with various cellul
    1.7e-12   46.9   0.1    4.4e-12   45.6   0.1    1.7  1  AAA_lid_3        AAA+ lid domain
    4.7e-05   23.4   1.1    0.00028   20.9   0.1    2.7  1  AAA_5            AAA domain (dynein-related subfamily)
    5.6e-05   23.3   0.2    0.00022   21.4   0.0    2.1  1  AAA_2            AAA domain (Cdc48 subfamily)
    9.4e-05   22.2   0.0    0.00029   20.6   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00015   22.2   0.3     0.0012   19.2   0.3    2.2  1  AAA_16           AAA ATPase domain
    0.00025   21.3   0.1      0.029   14.6   0.0    2.5  2  AAA_22           AAA domain
     0.0017   17.6   0.0     0.0044   16.3   0.0    1.6  1  TIP49            TIP49 P-loop domain
     0.0037   17.3   0.0      0.012   15.7   0.0    1.8  1  AAA_14           AAA domain
     0.0041   16.9   0.0     0.0088   15.8   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0064   16.9   0.2       0.14   12.6   0.0    2.5  2  AAA_17           AAA domain
  ------ inclusion threshold ------
       0.01   16.4   0.4      0.045   14.3   0.0    2.2  2  AAA_18           AAA domain
       0.01   15.2   0.1      0.021   14.2   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.015   15.7   0.0       0.03   14.7   0.0    1.5  1  RNA_helicase     RNA helicase
      0.016   15.3   2.7      0.026   14.7   2.7    1.3  1  DUF3340          C-terminal domain of tail specific protease 
      0.017   14.9   0.0      0.092   12.5   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
       0.02   14.4   0.0       0.04   13.4   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.021   15.1   0.1      0.092   13.0   0.0    2.1  2  AAA_28           AAA domain
      0.031   14.4   0.1        0.1   12.8   0.0    2.0  2  AAA_33           AAA domain
      0.036   14.3   5.9      0.098   12.9   5.9    1.7  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.04   14.0   0.2       0.35   11.0   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.046   13.2   0.0       0.16   11.4   0.0    1.9  1  PhoH             PhoH-like protein
      0.051   13.3   0.0       0.15   11.7   0.0    1.9  1  AAA_30           AAA domain
      0.069   12.9   2.5       0.16   11.8   2.5    1.6  1  SKA2             Spindle and kinetochore-associated protein 2
      0.074   12.1   0.2       0.18   10.9   0.0    1.6  2  Parvo_NS1        Parvovirus non-structural protein NS1
       0.09   12.5   0.1        0.2   11.4   0.1    1.7  1  AAA_24           AAA domain
        0.1   11.3   2.7       0.15   10.8   2.7    1.2  1  Caldesmon        Caldesmon
       0.11   12.3   1.5        1.4    8.7   0.0    2.3  2  AAA_11           AAA domain
       0.17   11.4   1.2        1.1    8.8   0.1    2.3  2  AAA_25           AAA domain
       0.27   11.6   0.1       0.27   11.6   0.1    2.1  2  AAA_19           AAA domain
       0.35   10.5   8.3       0.54    9.8   0.6    2.3  2  NRBF2            Nuclear receptor-binding factor 2, autophagy
       0.36   11.4   1.3       0.76   10.3   0.0    2.1  2  ABC_tran         ABC transporter
       0.58   10.2   9.2       0.27   11.3   2.9    2.3  2  CtIP_N           Tumour-suppressor protein CtIP N-terminal do
       0.92    9.4   7.8        1.7    8.5   7.8    1.4  1  Ax_dynein_light  Axonemal dynein light chain
        1.1    9.7   4.3          5    7.6   2.1    2.5  2  FlaC_arch        Flagella accessory protein C (FlaC)
        1.4    9.4   8.5        2.5    8.6   8.5    1.3  1  APG6_N           Apg6 coiled-coil region
        5.3    7.2  11.6       0.39   10.8   3.6    2.3  2  bZIP_1           bZIP transcription factor


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.0   2.4e-45   1.2e-42       1     131 [.     191     323 ..     191     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 2.4e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vll+GppGtGKTl+akava+++ ++f+ +sgsel+ k++ge+++ +r++f+ a+ ka p i+fiDEid++++ r   
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHSRATFIHMSGSELVHKFIGEGAQLVRDIFQMARDKA-PAIVFIDEIDSVGSIRthd 266
                                       79******************************************************9.****************987 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        ++ s e +r++ qLl+eldg++ + ++v vi+atnr+d ldpallr gRfdr+iei+
  gi|386002756|ref|YP_005921055.1| 267 GTTGSAEVNRTMMQLLAELDGFRAR-GDVKVIAATNRIDILDPALLRpGRFDRIIEIP 323
                                       66789999****************7.66****************************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1     9e-15   4.4e-12       2      44 ..     347     389 ..     346     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 9e-15
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       vdl  +A++TeG SGADl+++  eA+++A+rr  +++t edf+
  gi|386002756|ref|YP_005921055.1| 347 VDLRVIAKETEGASGADLKSIAVEAGMMAIRRRGTAVTPEDFK 389
                                       9*****************************************7 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   5.7e-07   0.00028       1     133 [.     190     309 ..     190     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.7e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK+ +a+ +a+  ++++  + +++      l+ +    +g +  +d   +   + ++i+++DE++ +
  gi|386002756|ref|YP_005921055.1| 190 GVLLFGPPGTGKTLIAKAVAHHSRATFIHMSGSE------LVHKFI-GEGAQLVRDIFQMARDKAPAIVFIDEIDSV 259
                                       59*******************9998887766655......776666.355566777777777779999999999988 PP

                                       -.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHH CS
                             AAA_5  78 e.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspa 133
                                           + +      e +r ++  + el ++++ +   ++ via++n+ d     l+pa
  gi|386002756|ref|YP_005921055.1| 260 GsIRTHDGTTGSAEVNRTMMQLLAELDGFRARG---DVKVIAATNRID----ILDPA 309
                                       755666777777777777766666666666532...477777777777....55555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.6e-07   0.00022       6     103 ..     191     282 ..     187     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.6e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a + ++    ++i +  sel      + + +  +  ++  + a ++   iv++DEid +
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHSRA----TFIHMSGSELVH----KFIGEGAQLVRDIFQMARDKApaIVFIDEIDSV 259
                                       5677******************96....999999999999....66666666667776666666677********** PP

                                       ------------HHHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLLqil 103
                                        + ++      + +V r ++q+l
  gi|386002756|ref|YP_005921055.1| 260 GSIRTHDGTTGSAEVNRTMMQLL 282
                                       *9866666677889999999998 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.9e-07   0.00029      33      95 ..     188     258 ..     180     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.9e-07
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihr 95 
                                          vll+GpPG Gkt +ak +a+   +++ + sg  l ++  g+ a l+ ++      ++  ++fidei  
  gi|386002756|ref|YP_005921055.1| 188 PKGVLLFGPPGTGKTLIAKAVAHHSRATFIHMSGSELVHKfiGEGAQLVRDIfqmardKAPAIVFIDEIDS 258
                                       5679**********************999888888765543345555544432112213346999999975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   2.5e-06    0.0012      24      95 ..     188     249 ..     158     293 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.5e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaele 95 
                                       p  vll G++G+GK+ ++++++++ +++ +i ++g    +         + + +   +l+r++ ++a++++++
  gi|386002756|ref|YP_005921055.1| 188 PKGVLLFGPPGTGKTLIAKAVAHHSRAT-FIHMSGSELVH-------KfIGEGA---QLVRDIFQMARDKAPA 249
                                       389*******************877666.33344444444.......2244444...6666666665554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     6e-05     0.029       8      41 ..     191     215 ..     186     227 .. 0.81
   2 ?    3.8   0.0      0.13        65      78     126 ..     235     297 ..     230     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                       ++++G++GtGKT+ ++ +++           r++
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHS---------RAT 215
                                       689**************99976.........444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                            AAA_22  78 llealeqalraravielliiDEaqhlr....s..........eealeeLrsllnl.srkgvqli 126
                                       l++ + q +r++a  +++ iDE++ +     +           ++++ L +l  + +r +v++i
  gi|386002756|ref|YP_005921055.1| 235 LVRDIFQMARDKAP-AIVFIDEIDSVGsirtHdgttgsaevnRTMMQLLAELDGFrARGDVKVI 297
                                       55555566666666.9*********976654155566677777777777666666667777766 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.1e-06    0.0044      51      90 ..     189     226 ..     185     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                       ++vLl Gp+gtGkt +a a++++  +   f+++sgse+  
  gi|386002756|ref|YP_005921055.1| 189 KGVLLFGPPGTGKTLIAKAVAHH--SRATFIHMSGSELVH 226
                                       89*******************97..5689*******9865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.4e-05     0.012       5      79 ..     191     262 ..     188     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                       +++ G+  +GKT ++k +++++      ++ ++  +   k + + ++l + i+++++++   ++f+DEi  v ++
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHSR---ATFIHMSGSELVHKFIGEGAQLVRDIFQMARDKAPAIVFIDEIDSVGSI 262
                                       7899**************98888...8889998888777666665678888888866678999******998554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-05    0.0088      45      71 ..     186     212 ..     159     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                       e  ++++l+Gp+G+GK+ +a a++++ 
  gi|386002756|ref|YP_005921055.1| 186 EPPKGVLLFGPPGTGKTLIAKAVAHHS 212
                                       556789****************99865 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.85   4.1e+02      39     109 ..      53     123 ..      26     137 .. 0.67
   2 !   12.6   0.0   0.00029      0.14       1      37 [.     194     232 ..     194     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.85
                                       SHSSHHHHCTS.HHHHHHHHHHHH...HHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  39 lakardemrkl.pleekkelqkea...aekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                       l++++++mr++  l+++++l++++    +++ e+ +++ vl+  h    ++++f+ +   e+ e l+p++ + ++
  gi|386002756|ref|YP_005921055.1|  53 LISNKKYMREEeRLKKENALLRRMplfLATVVEM-GEDYVLLRQHG---NNQEFITTTSPEMMEALEPNTRVAIN 123
                                       5677788885413333444444431113344443.77778888887...45677777777888999998877776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00029
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTT CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrg 37 
                                       +G+PG GK+ +++ ++++    f h+s ++l+ + + +g
  gi|386002756|ref|YP_005921055.1| 194 FGPPGTGKTLIAKAVAHHSraTFIHMSGSELVHKFIGEG 232
                                       6***********999987644788888788776666444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       3.4   1.6e+03      31      69 ..      16      58 ..      10     101 .. 0.60
   2 ?   14.3   0.0   9.3e-05     0.045       1      25 [.     191     223 ..     191     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.4
                            AAA_18 31 vakenglllevdpe....aldeskrldedkldklldaleenss 69
                                      ++ ++ + le++++    +++  + ++ed ++kl+++l  n +
  gi|386002756|ref|YP_005921055.1| 16 LHLKRITALENENKrlseEIETLRMEKEDTRAKLVETLISNKK 58
                                      4445555555555544433344444444455555555555544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.3e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.........g 25 
                                       +ll G+pG+GKt +ak+++ +             
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHS-RatfihmsgsE 223
                                       799***************7773.12245555442 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.4e-05     0.021      24      43 ..     190     209 ..     178     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                        +ll+GppG+GKt++ak+++
  gi|386002756|ref|YP_005921055.1| 190 GVLLFGPPGTGKTLIAKAVA 209
                                       689*************9875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.3e-05      0.03       1      67 [.     191     248 ..     191     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenp 67 
                                       ++l+Gp+g+GK+++ak     +      +++  ++++ + ++ ++++ g+ + ++ D+ q+  ++ p
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKA----V-----AHHSRATFIHMSGSELVHKFIGEGAQLVRDIFQMARDKAP 248
                                       689**************....3.....4555777889999999999999999999999999876433 PP

>> DUF3340  C-terminal domain of tail specific protease (DUF3340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.7   5.4e-05     0.026      30     100 ..       5      76 ..       2     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-05
                           DUF3340  30 kiaallpkLkkksekRiakdp.eFklleediawlkerkekktvsLnekkrkaereeqeakrlarenerekak 100
                                       +i+++ + +++ + kRi + + e k l e+i++l+ +ke++   L e+   +++  +e++rl++en+  +++
  gi|386002756|ref|YP_005921055.1|   5 TITPDQESIQELHLKRITALEnENKRLSEEIETLRMEKEDTRAKLVETLISNKKYMREEERLKKENALLRRM 76 
                                       567888999********987637899****************************************987754 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019     0.092      23      47 ..     189     213 ..     173     230 .. 0.81
   2 ?   -1.6   0.0       4.1     2e+03     133     143 ..     292     302 ..     288     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         vl+ G  GtGK+l+a+a+ ++s+
  gi|386002756|ref|YP_005921055.1| 189 KGVLLFGPPGTGKTLIAKAVAHHSR 213
                                       679****************987775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                                       --EEEEEEESS CS
                   Sigma54_activat 133 vdvriiaatne 143
                                        dv++iaatn+
  gi|386002756|ref|YP_005921055.1| 292 GDVKVIAATNR 302
                                       589******97 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.2e-05      0.04      28      58 ..     183     213 ..     173     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkld 58 
                                         ++  k vll Gp GtGKt+i+k + ++  
  gi|386002756|ref|YP_005921055.1| 183 IGVEPPKGVLLFGPPGTGKTLIAKAVAHHSR 213
                                       55667789***************99877655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         6   2.9e+03     117     117 ..      56      56 ..       9      99 .. 0.52
   2 ?   13.0   0.0   0.00019     0.092       2      35 ..     191     225 ..     190     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6
                            AAA_28 117 p 117
                                       +
  gi|386002756|ref|YP_005921055.1|  56 N 56 
                                       1 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00019
                            AAA_28   2 ivitGgestGKTtlleaLaargypvv.pEaareil 35 
                                       + ++G+++tGKT +++a a +   ++ + ++ e++
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHSRATFiHMSGSELV 225
                                       6799***************9954433254554444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.8   3.3e+03      15      15 ..      92      92 ..      25     143 .. 0.62
   2 ?   12.8   0.0   0.00021       0.1       2      32 ..     191     223 ..     191     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.8
                            AAA_33 15 l 15
                                      l
  gi|386002756|ref|YP_005921055.1| 92 L 92
                                      1 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt 32 
                                       vll G+pG+GK+  a+ ++ +    +++ s  +
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHSRatFIHMSGSE 223
                                       7899*************9766664466666655 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 ?   12.9   5.9    0.0002     0.098       9      73 ..       8      73 ..       1      87 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                       TMF_TATA_bd  9 psvqlverls.seirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekel 73
                                      p+++ +++l  ++i  lE+E + l ee+e+l  e++++r+ +v+ + +n +  +++++l++ ++ l
  gi|386002756|ref|YP_005921055.1|  8 PDQESIQELHlKRITALENENKRLSEEIETLRMEKEDTRAKLVETLISNKKYMREEERLKKENALL 73
                                      5555666665357999*****************************************999877655 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       2.2   1.1e+03      73     121 ..      16      67 ..       9      79 .. 0.70
   2 ?   11.0   0.0   0.00072      0.35      24      79 ..     191     257 ..     185     263 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.2
                                       EEEEE-TT--HHHHHHHHHHHHH....HTTTT-EEEEEEEE-TTT..----HH CS
                   Sigma54_activ_2  73 LylkdiadlskaeqkeLlellak....aeksslrlVstsskdleqlleagafd 121
                                       L lk i  l+++  k+L e ++     +e  +++lV t  ++ +++ e+ +++
  gi|386002756|ref|YP_005921055.1|  16 LHLKRITALENE-NKRLSEEIETlrmeKEDTRAKLVETLISNKKYMREEERLK 67 
                                       566667776544.4677777776665577889999998888888877776665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00072
                                       EEEEEETT--HHHHHHCC--TTS-.EE--SSTTHHHH-H........HHHHHHT...TTSEEEEEE-T CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp.wleifvverlaklp........ldlleqa...kggtLylkdia 79 
                                       v+l G++G+gk+l+A++ ++ s    +++    +l++           d+++ a    +++ ++ +i+
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHSRAtFIHMSGS-ELVHKFigegaqlvRDIFQMArdkAPAIVFIDEID 257
                                       9***************9977665403333222.22221123333333555555433355566666665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.16      22      42 ..     191     211 ..     174     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v  +Gp GtGKt++a a+a +
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHH 211
                                       7889***********999865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00031      0.15       6      44 ..     176     214 ..     171     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreawea 44 
                                       Q ++++++  ++ + ++l Gp+GtGKt + ka++++ +a
  gi|386002756|ref|YP_005921055.1| 176 QPELFAEIGVEPPKGVLLFGPPGTGKTLIAKAVAHHSRA 214
                                       6666777777777778999************99887665 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.5   0.00033      0.16      44      87 ..      18      61 ..       4      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                              SKA2 44 lerlkkvkeelqaLkeqceellaekkelidkirttlvanrellq 87
                                      l+r++++ +e + L+e++e l  ek+++  k+  tl++n++ ++
  gi|386002756|ref|YP_005921055.1| 18 LKRITALENENKRLSEEIETLRMEKEDTRAKLVETLISNKKYMR 61
                                      79*************************************99875 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.4   3.1e+03       7      31 ..      44      68 ..      34      75 .. 0.68
   2 ?   10.9   0.0   0.00037      0.18     117     138 ..     191     212 ..     185     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.4
                         Parvo_NS1  7 dkiknlveelvekgivteedWaaid 31
                                      d   +lve+l+ +++  +e+ + ++
  gi|386002756|ref|YP_005921055.1| 44 DTRAKLVETLISNKKYMREEERLKK 68
                                      4557889999977777666655555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v+++Gp+ tGkt +a+a a+ +
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHS 212
                                       899****************976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00041       0.2       5      31 ..     191     219 ..     188     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidt 31 
                                       +l++Gp+g+GKT +ak      ++ fi +
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVahHSRATFIHM 219
                                       89*************99877777777655 PP

>> Caldesmon  Caldesmon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.7   0.00031      0.15     298     344 ..      10      57 ..       3      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                         Caldesmon 298 kkrkqeeaerkv.reeeekrkmkeeiErRRaEAaEkrqkvedtvdgeg 344
                                       ++  qe++ +++   e+e +++ eeiE  R+E  + r k+ +t+ +++
  gi|386002756|ref|YP_005921055.1|  10 QESIQELHLKRItALENENKRLSEEIETLRMEKEDTRAKLVETLISNK 57 
                                       66778899888878899***********************99986665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.7      0.24   1.2e+02     160     195 ..      21      56 ..       2     134 .. 0.55
   2 ?    8.7   0.0    0.0028       1.4      20      41 ..     191     212 ..     176     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                            AAA_11 160 kskleqerrklkkerkelskeleeaeesleeevlde 195
                                          le+e++ l++e+++l+ e e ++++l e+++++
  gi|386002756|ref|YP_005921055.1|  21 ITALENENKRLSEEIETLRMEKEDTRAKLVETLISN 56 
                                       222223333333333333333333333333222222 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l+ GPPGtgKT    ++ ++ 
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHHS 212
                                       6899********6655555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0022       1.1      36      56 ..     191     211 ..     184     215 .. 0.89
   2 ?    0.6   0.1      0.72   3.5e+02     131     184 ..     237     297 ..     211     300 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0022
                            AAA_25  36 allaGapgtGKttlaldlala 56 
                                       +ll+G+pgtGKt +a  +a++
  gi|386002756|ref|YP_005921055.1| 191 VLLFGPPGTGKTLIAKAVAHH 211
                                       69************9888875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.72
                            AAA_25 131 daleaaieevegvrlvviDplsralgg...densnsd.....vgalvealeriarrtgaavl 184
                                       +++ + +++ + ++ v iD ++++ +    d +  s+     + +l++ l+ +++r ++ v+
  gi|386002756|ref|YP_005921055.1| 237 RDIFQMARD-KAPAIVFIDEIDSVGSIrthDGTTGSAevnrtMMQLLAELDGFRARGDVKVI 297
                                       344444444.4488999998888766644432222223444367888888888888887776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.5       9.5   4.6e+03      31      31 ..      87      87 ..      19     156 .. 0.56
   2 ?   11.6   0.1   0.00056      0.27      11      35 ..     189     213 ..     182     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.5
                            AAA_19 31 v 31
                                       
  gi|386002756|ref|YP_005921055.1| 87 G 87
                                      0 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00056
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                       k +l+ ++pGtGKT + k++ ++  
  gi|386002756|ref|YP_005921055.1| 189 KGVLLFGPPGTGKTLIAKAVAHHSR 213
                                       56899*********98887776654 PP

>> NRBF2  Nuclear receptor-binding factor 2, autophagy regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   3.1     0.062        30      85     121 ..      10      47 ..       3      52 .. 0.77
   2 ?    9.8   0.6    0.0011      0.54      93     143 ..      48      92 ..      42     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.062
                             NRBF2  85 atkiadLk.rlvelLlaenerLrkenkqLkaekaRLqk 121
                                       +  i++L+ + +  L +en+rL +e + L+ ek   ++
  gi|386002756|ref|YP_005921055.1|  10 QESIQELHlKRITALENENKRLSEEIETLRMEKEDTRA 47 
                                       45677776357999****************99976555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                             NRBF2  93 rlvelLlaenerLrkenkqLkaekaRLqkeplekeldvdaDfvekseLWgL 143
                                       +lve+L+  n++ ++e ++Lk e+a L++ pl       a  ve  e ++L
  gi|386002756|ref|YP_005921055.1|  48 KLVETLIS-NKKYMREEERLKKENALLRRMPLFL-----ATVVEMGEDYVL 92 
                                       78999986.88899999************99644.....556666666654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.7       5.4   2.6e+03      52      69 ..      26      43 ..       2     143 .. 0.61
   2 ?   10.3   0.0    0.0016      0.76       8      37 ..     185     214 ..     181     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.4
                                      B-HHHCCHCEEEE-SS-- CS
                                      xxxxxxxxxxxxxxxxxx RF
                          ABC_tran 52 qeleslrkeigvlpqepq 69
                                      +e ++l++ei++l  e++
  gi|386002756|ref|YP_005921055.1| 26 NENKRLSEEIETLRMEKE 43
                                      233333333333333222 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0016
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                       +++ + v ++G+ G+GK+ ++k++a++++ 
  gi|386002756|ref|YP_005921055.1| 185 VEPPKGVLLFGPPGTGKTLIAKAVAHHSRA 214
                                       67777899****************999875 PP

>> CtIP_N  Tumour-suppressor protein CtIP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.9   0.00056      0.27      87     118 ..      10      41 ..       2      43 .. 0.87
   2 ?    2.5   0.9       0.3   1.4e+02      32      58 ..      45      71 ..      39      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00056
                            CtIP_N  87 fessklqslqlitiLtnEmntLkeenkkLkee 118
                                        es +   l++it L+nE+++L ee ++L+ e
  gi|386002756|ref|YP_005921055.1|  10 QESIQELHLKRITALENENKRLSEEIETLRME 41 
                                       4677778899*******************977 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                            CtIP_N 32 ldaqrleelfsknqqlreqqkalkeni 58
                                      ++a+ +e+l+s ++ +re+++ +ken 
  gi|386002756|ref|YP_005921055.1| 45 TRAKLVETLISNKKYMREEERLKKENA 71
                                      568889999999999999999988874 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.8    0.0036       1.7     125     182 ..      18      74 ..       5      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                   Ax_dynein_light 125 ekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqqlk 182
                                        k+i++Le+e+++l +++++l+ + e+++++  e + +++k  + e e lkk+n  l+
  gi|386002756|ref|YP_005921055.1|  18 LKRITALENENKRLSEEIETLRMEKEDTRAKLVETLISNKKY-MREEERLKKENALLR 74 
                                       4789************************99999988766555.555689999998886 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.1      0.01         5       1      29 [.      20      48 ..      20      56 .. 0.87
   2 ?    1.3   0.0      0.94   4.6e+02      15      31 ..     155     171 ..     142     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                         FlaC_arch  1 ridelEnklsklsteletvkkeneelsks 29
                                      ri  lEn+ ++ls e+et++ e e+ + +
  gi|386002756|ref|YP_005921055.1| 20 RITALENENKRLSEEIETLRMEKEDTRAK 48
                                      8999*****************99988765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.94
                         FlaC_arch  15 eletvkkeneelsksve 31 
                                       +++ +++++ e+s++ve
  gi|386002756|ref|YP_005921055.1| 155 QVGGLEDQIREVSETVE 171
                                       67788999999999987 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   8.5    0.0052       2.5      50     107 ..      15      72 ..       2      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0052
                            APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne 107
                                       e   +++ +le+e ++l ee++ l  e+e+ +a+l +     ++  +eeer  +e   
  gi|386002756|ref|YP_005921055.1|  15 ELHLKRITALENENKRLSEEIETLRMEKEDTRAKLVETLISNKKYMREEERLKKENAL 72 
                                       3334669999999999999999999999999999998888888888888887777654 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.6   0.00081      0.39      25      57 ..      10      43 ..      10      50 .. 0.82
   2 ?    0.6   1.3       1.3   6.4e+02      42      60 ..      56      74 ..      45      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00081
                                      HHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 25 qaeieeLe.rrvkaLekeNksLkseleelkkeve 57
                                      q++i+eL  +r  aLe+eNk L++e+e+l+ e e
  gi|386002756|ref|YP_005921055.1| 10 QESIQELHlKRITALENENKRLSEEIETLRMEKE 43
                                      677788864789*****************97766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 42 NksLkseleelkkevekLk 60
                                      Nk++  e e+lkke++ L+
  gi|386002756|ref|YP_005921055.1| 56 NKKYMREEERLKKENALLR 74
                                      7888888899999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1274  (0.0710581); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                       152  (0.00847788); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 2494.48
//
Query:       gi|386002757|ref|YP_005921056.1|  [L=366]
Description: Methionine adenosyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.9e-115  384.0   0.1   8.2e-115  383.8   0.1    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
     0.0086   16.1   0.1       0.67   10.0   0.0    2.6  2  bact-PGI_C       Bacterial phospho-glucose isomerase C-termin
  ------ inclusion threshold ------
      0.022   14.8   0.2       0.21   11.6   0.0    2.4  2  Nup35_RRM_2      Nup53/35/40-type RNA recognition motif
       0.09   13.5   0.2        0.4   11.4   0.0    2.2  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
       0.12   12.8   0.0       0.45   10.9   0.0    1.9  2  NolB             Nodulation protein NolB


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.8   0.1  2.3e-118  8.2e-115      14     395 ..       9     361 ..       2     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 383.8 bits;  conditional E-value: 2.3e-118
                                       TTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE-EEEEEEEE CS
                   AdoMet_Synthase  14 eeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGeviepieillsgr 90 
                                       +  ++E+vErKG+GHPD++aDgi+ea+s++ls+ yle+fg+ilhhn+Dkvl++aG++e +fgGG+v+ep +++++gr
  gi|386002757|ref|YP_005921056.1|   9 RPLTFEVVERKGLGHPDTLADGISEAISMELSRSYLEEFGEILHHNVDKVLITAGRVEVEFGGGRVLEPPTVIVGGR 85 
                                       55689************************************************************************ PP

                                       EEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEEEES-- CS
                   AdoMet_Synthase  91 atkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvgyapls 167
                                       at  +++   ++e ++ + a ++lk++l +l  +    +d +++ gs +L+++++r       aNDtS+gvg+apl 
  gi|386002757|ref|YP_005921056.1|  86 ATPPAGE---DLEGLIARVASDHLKRSLANLLEH---RIDARVRGGSPELVSLMRR------GANDTSIGVGFAPLN 150
                                       **98766...5899***************88544...789**************99......69************* PP

                                       HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHHHHHHH CS
                   AdoMet_Synthase 168 eleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeeveelakkl 244
                                        +e+lvle+e+ ++       +  vGeD Kvm++R +++++l va+a+v+++v+++eeY evke+++e++++ a   
  gi|386002757|ref|YP_005921056.1| 151 PTEELVLELEERVRM------VRGVGEDTKVMAVRIRDRLNLVVAAAIVSKFVSSMEEYREVKERVRETIATAAD-- 219
                                       ***********9985......789***************************************999998876554.. PP

                                       STTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHHH CS
                   AdoMet_Synthase 245 tkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvlan 321
                                             ev+vN+aD    ++++lt+tG+s+E+gDdG++GRGNR  Glitp+rpms+EA aGKNPv+HvGKiYnv+a 
  gi|386002757|ref|YP_005921056.1| 220 -----AEVAVNAAD--GGNNIFLTLTGSSIEMGDDGATGRGNRGSGLITPMRPMSIEAIAGKNPVNHVGKIYNVVAG 289
                                       .....6899*****..8899********************************************************* PP

                                       HHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT CS
                   AdoMet_Synthase 322 eiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteelieg 395
                                       + a+ei+e ++gv+e+yv+l+s+iG p+ ePl+ +v++  +++ +    e+++eei+d++l+ i +++e++++g
  gi|386002757|ref|YP_005921056.1| 290 RAAAEIAE-LDGVEEAYVTLVSRIGAPLTEPLLRAVEIRGDERPD-GGAERRIEEIVDRHLQGIGDLVEDFVAG 361
                                       *****986.9****************************7776655.5669*******************99987 PP

>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00019      0.67       3      38 ..     150     185 ..     149     209 .. 0.90
   2 ?    3.0   0.0     0.026        94      11      39 ..     270     297 ..     268     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                       -HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHH CS
                        bact-PGI_C   3 npakqlAlelagklpviygssellevaArRfknqln 38 
                                       np ++l lel++++ ++ g++e ++v+A+R+++ ln
  gi|386002757|ref|YP_005921056.1| 150 NPTEELVLELEERVRMVRGVGEDTKVMAVRIRDRLN 185
                                       8999*****************************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.026
                                       HHTTSEEEEE-..TT-THHHHHHHHHHHH CS
                        bact-PGI_C  11 elagklpviygssellevaArRfknqlne 39 
                                       ++agk pv    ++ ++v+A R++ +++e
  gi|386002757|ref|YP_005921056.1| 270 AIAGKNPVNHV-GKIYNVVAGRAAAEIAE 297
                                       68999999999.9**************98 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05      0.21      17      33 ..      40      56 ..      30      70 .. 0.81
   2 ?   -0.3   0.0       0.3   1.1e+03      14      29 ..     341     356 ..     335     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                       Nup35_RRM_2 17 VlehFasfGeIvkhyvp 33
                                       + ++++fGeI +h+v+
  gi|386002757|ref|YP_005921056.1| 40 SRSYLEEFGEILHHNVD 56
                                      466*************8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.3
                       Nup35_RRM_2  14 ielVlehFasfGeIvk 29 
                                       +e+V +h++ +G  v+
  gi|386002757|ref|YP_005921056.1| 341 EEIVDRHLQGIGDLVE 356
                                       467778******9886 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011       0.4      10      25 ..      20      35 ..      11      67 .. 0.85
   2 ?   -1.8   0.1       1.5   5.3e+03      56      72 ..     199     215 ..     172     226 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                   S-AdoMet_synt_N 10 seGHPDkvadqisdai 25
                                        GHPD +ad is+ai
  gi|386002757|ref|YP_005921056.1| 20 GLGHPDTLADGISEAI 35
                                      46************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                   S-AdoMet_synt_N  56 ttkakvdiekivrevik 72 
                                       + + + ++++ vre+i 
  gi|386002757|ref|YP_005921056.1| 199 SMEEYREVKERVRETIA 215
                                       33344566677777665 PP

>> NolB  Nodulation protein NolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   5.4e+03     104     118 ..      86     100 ..      81     103 .. 0.84
   2 ?   10.9   0.0   0.00012      0.45      83     139 ..     147     200 ..     135     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                              NolB 104 gvpqggkdfeamiae 118
                                       + p++g+d e +ia 
  gi|386002757|ref|YP_005921056.1|  86 ATPPAGEDLEGLIAR 100
                                       689********9996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                              NolB  83 alpgPaqklpleadaaGaeasgvpqggkdfeamiaeLRdlYngvtqvaLvskgvsgi 139
                                       a+  P+++l le +    ++  v+ +g+d ++m   +Rd  n v+  a+vsk vs++
  gi|386002757|ref|YP_005921056.1| 147 APLNPTEELVLELE-E--RVRMVRGVGEDTKVMAVRIRDRLNLVVAAAIVSKFVSSM 200
                                       55677777777777.3..4445999*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2409.37
//
Query:       gi|386002758|ref|YP_005921057.1|  [L=102]
Description: hypothetical protein Mhar_2078 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28   99.9   0.1    1.4e-28   99.8   0.1    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.1   7.7e-33   1.4e-28       3     103 .]       2      97 ..       1      97 [. 0.97

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 7.7e-33
                                       EE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHH CS
                           DUF5611   3 eYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaaldtv 79 
                                       eY++KrGf +e+ er+++ lee f++e++eeg+ l  s+ga+k++ev+i   +kkl+v+te++d    +de++ldt+
  gi|386002758|ref|YP_005921057.1|   2 EYSFKRGFGPEL-ERIRSALEEEFPTEIREEGGRLLLSYGALKSIEVSI--VGKKLLVTTESTD--GVTDEVILDTN 73 
                                       9***********.************************************..9**********77..69********* PP

                                       HHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  80 kkfndFLeeaTGydaKeRkkkakk 103
                                       k+f+dFLe+aTGy+aK+R ++akk
  gi|386002758|ref|YP_005921057.1|  74 KRFRDFLERATGYTAKQRLQQAKK 97 
                                       **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 701.50
//
Query:       gi|386002759|ref|YP_005921058.1|  [L=418]
Description: enolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.2e-108  360.5   0.1   7.8e-108  360.2   0.1    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.3e-57  192.3   0.2    2.5e-56  189.4   0.0    2.1  2  Enolase_N  Enolase, N-terminal domain
    5.7e-05   22.8   0.0    8.7e-05   22.2   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.026   13.7   0.0    1.4  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.2   0.1  1.7e-111  7.8e-108       2     288 ..     141     416 ..     140     418 .] 0.98

  Alignments for each domain:
  == domain 1  score: 360.2 bits;  conditional E-value: 1.7e-111
                                       -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                         Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                       ++lPvP+lnv+nGG+hagn+la+qefmilP gas f+e lr+ ae+yh l ++l+ +yg  atnvG eGG+aP l++
  gi|386002759|ref|YP_005921058.1| 141 TTLPVPSLNVLNGGQHAGNDLAIQEFMILPKGASCFSEGLRMAAETYHALGKILRGRYGVGATNVGYEGGYAPPLNK 217
                                       58*************************************************************************** PP

                                       HHHHHHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  79 nkealdliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       +++ald +++a++++Gy++++ i++d+a+s f+  +++ y +d+k+        l+  +++d+y +lv+ yPi+ ie
  gi|386002759|ref|YP_005921058.1| 218 TADALDSLMSALDATGYDKEIGIGMDAAASSFF--ENGSYAIDGKK--------LSGGEMVDFYADLVSTYPIILIE 284
                                       *********************************..778****9998........9********************** PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dp++e+ +  ++ lt++l     ivGdd++vtn++rl+++ie ka+nalllk+nqiG+++e+++a+++a ++g+ v+
  gi|386002759|ref|YP_005921058.1| 285 DPFEEEAFGDFAALTARLP-GTIIVGDDIYVTNVQRLAKGIEMKATNALLLKLNQIGTVSEAFDAARMAFRNGFKVM 360
                                       ******************9.567****************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE- CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakya 288
                                        shrs eted+ +ad++v+l a  +ktGaparser akynqllriee+lg++a ya
  gi|386002759|ref|YP_005921058.1| 361 ASHRSAETEDSALADVTVALGAEMLKTGAPARSERNAKYNQLLRIEEALGSAASYA 416
                                       *******************************************************8 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4   0.0   5.6e-60   2.5e-56       1     131 []       5     135 ..       5     135 .. 0.98
   2 ?    0.3   0.1      0.17   7.5e+02      84     105 ..     219     240 ..     215     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 5.6e-60
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I++++areildSrGnpTvev+v+t  g +graavpsGaStg++ealelrDg ++ry+gkgv++av+nvn++i p+li
  gi|386002759|ref|YP_005921058.1|   5 IENIHAREILDSRGNPTVEVDVWTCCG-FGRAAVPSGASTGTHEALELRDG-DDRYGGKGVLQAVKNVNDVIGPKLI 79 
                                       89**********************877.8*********************9.79**********************9 PP

                                       ..TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 ..gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                         g+ +++q+++D+++++lDgt++ks+lGaNail+vSl vakaaA+++ +ply+yl
  gi|386002759|ref|YP_005921058.1|  80 esGITALEQRAVDNFMLALDGTSHKSNLGANAILGVSLGVAKAAADELAIPLYQYL 135
                                       7789***************************************************8 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHH-STT-TTT-H CS
                         Enolase_N  84 qeeiDkllielDgtenksklGa 105
                                         ++D+l+ +lD t   +++G 
  gi|386002759|ref|YP_005921058.1| 219 ADALDSLMSALDATGYDKEIGI 240
                                       5689**********99998885 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.9e-08   8.7e-05      28     156 ..     219     363 ..     192     402 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.9e-08
                                       HHHHHHHHHHHHHHTTTSTSEEEEE-TTTS..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHH CS
                          MR_MLE_C  28 aedvervravreavgpgddvdlmvDanqaw..............dlatAirvarelee.ldllwlEEPvppeddleg 89 
                                       a+ ++ +  + +a+g ++++ + +Da ++               +  + + +   l + + + ++E+P+  e    +
  gi|386002759|ref|YP_005921058.1| 219 ADALDSLMSALDATGYDKEIGIGMDAAASSffengsyaidgkklSGGEMVDFYADLVStYPIILIEDPFEEE-AFGD 294
                                       5666666667777788888888888777744566666777776677788888888866699*********95.6*** PP

                                       HHHHHHHH.SSEEEEST.TSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  90 laelrara.sipiaagE.slysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                        a+l+ar  ++ i+++  ++++++++++ +e +a  ++ ++++++g ++ea + a++a  +g +v+  +
  gi|386002759|ref|YP_005921058.1| 295 FAALTARLpGTIIVGDDiYVTNVQRLAKGIEMKATNALLLKLNQIGTVSEAFDAARMAFRNGFKVMASH 363
                                       *****64454444444325667****************************************9987655 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-06     0.026     133     217 ..     298     383 ..     267     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-06
                            MAAL_C 133 lkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarv 208
                                       l+++     +v D+ +  +++ + + ++ +a++++ +k   +G+++++ +a  ++ ++g +++    + et+ sa +
  gi|386002759|ref|YP_005921058.1| 298 LTARLPGTIIVGDDiYVTNVQRLAKGIEMKATNALLLKLNQIGTVSEAFDAARMAFRNGFKVMASHRSAETEDSALA 374
                                       556666677777663677788999999*************************************************9 PP

                            MAAL_C 209 svhvalatr 217
                                        v val ++
  gi|386002759|ref|YP_005921058.1| 375 DVTVALGAE 383
                                       999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2449.60
//
Query:       gi|386002760|ref|YP_005921059.1|  [L=1232]
Description: WD repeat protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-118  383.1  24.5    3.4e-08   34.0   0.1   14.5 14  WD40           WD domain, G-beta repeat
    3.7e-35  121.3   0.0    5.6e-35  120.7   0.0    1.2  1  NB-ARC         NB-ARC domain
    3.5e-30  105.0   0.0    3.2e-29  101.9   0.0    2.8  2  TIR_2          TIR domain
    5.3e-15   55.6   0.0    1.3e-14   54.3   0.0    1.7  1  APAF1_C        APAF-1 helical domain
    7.4e-15   54.6   0.0       0.02   13.6   0.0    6.0  6  Nucleoporin_N  Nup133 N terminal like
    7.6e-15   55.0   8.6          1    9.7   0.0    8.5 11  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma
    1.4e-13   50.3  24.7       0.36    9.4   0.0   12.1 13  Nup160         Nucleoporin Nup120/160
    1.1e-11   44.4   2.2       0.56    9.4   0.0    8.2 11  120_Rick_ant   120 KDa Rickettsia surface antigen
    5.4e-11   41.6   4.6      0.013   14.1   0.0    5.3  5  Cytochrom_D1   Cytochrome D1 heme domain
    4.3e-06   26.2   0.2        6.9    6.4   0.0    5.2  7  Nudix_N        Hydrolase of X-linked nucleoside diphosphate N
    7.5e-06   26.0  18.4         14    5.7   0.2    9.3 11  DUF5570        Family of unknown function (DUF5570)
     0.0011   18.8   0.0    2.8e+02    1.5   0.0    6.9  7  HIRA_B         HIRA B motif
     0.0078   16.0   0.0      0.018   14.8   0.0    1.5  1  TIR            TIR domain
  ------ inclusion threshold ------
       0.02   15.3   0.0      0.066   13.6   0.0    2.0  1  AAA_16         AAA ATPase domain
      0.036   13.8   1.0         77    3.1   0.0    5.6  7  DUF4597        Domain of unknown function (DUF4597)
      0.044   14.3   0.0         88    3.7   0.0    4.7  3  UN_NPL4        Nuclear pore localisation protein NPL4
      0.044   13.6   0.0         18    5.2   0.0    4.8  6  RVT_thumb      Reverse transcriptase thumb domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   5.3e-10   5.6e-07       3      38 .]     647     683 ..     645     683 .. 0.91
   2 !   31.1   0.0   2.7e-10   2.9e-07       1      38 []     687     725 ..     687     725 .. 0.96
   3 !   33.1   0.0   6.3e-11   6.6e-08       1      38 []     729     767 ..     729     767 .. 0.96
   4 !   25.5   0.0   1.5e-08   1.6e-05       1      38 []     771     809 ..     771     809 .. 0.93
   5 !   26.5   0.1   7.6e-09     8e-06       1      38 []     813     851 ..     813     851 .. 0.92
   6 !   29.2   0.1   1.1e-09   1.1e-06       2      38 .]     856     893 ..     855     893 .. 0.92
   7 !   28.2   0.0   2.2e-09   2.3e-06       2      38 .]     898     935 ..     897     935 .. 0.92
   8 !   31.5   0.0     2e-10   2.1e-07       2      38 .]     940     977 ..     939     977 .. 0.94
   9 !   34.0   0.1   3.2e-11   3.4e-08       2      38 .]     982    1019 ..     981    1019 .. 0.95
  10 !   27.4   0.0   3.8e-09     4e-06       2      38 .]    1024    1061 ..    1023    1061 .. 0.93
  11 !   33.5   0.0   4.7e-11     5e-08       2      38 .]    1066    1103 ..    1065    1103 .. 0.95
  12 !   24.2   0.0     4e-08   4.2e-05       1      38 []    1107    1145 ..    1107    1145 .. 0.93
  13 !   28.4   0.0   1.9e-09     2e-06       1      38 []    1149    1187 ..    1149    1187 .. 0.92
  14 ?    4.2   0.1     0.086        91       2      32 ..    1192    1222 ..    1191    1226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.3e-10
                                       EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       +lr+l+GH +sv+++a+ pdg+  +s+s D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 647 LLRILKGHsDSVRAVAVTPDGRRAVSASGDRTLKVWD 683
                                       699*****777************998877*******9 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.7e-10
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ lrtl GH +sv+++a+ pdg   +s+sdD t+r+Wd
  gi|386002760|ref|YP_005921059.1| 687 GEELRTLIGHsNSVRAVAVTPDGLRAVSASDDSTLRVWD 725
                                       5789******999*************************9 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 6.3e-11
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ lrtl+GH +sv+++a+ pdg+  +s+s+D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 729 GEELRTLEGHsNSVSAVAVTPDGRRAVSASRDRTLKVWD 767
                                       5789******999*************************9 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 1.5e-08
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ lrtl+GH +sv+++a+ pdg   +s+s D t+++Wd
  gi|386002760|ref|YP_005921059.1| 771 GEELRTLKGHsNSVSAVAVTPDGLRAVSASGDLTLKVWD 809
                                       5789******999************998877*******9 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 7.6e-09
                                       TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       g+ lrtl GH ++v+++++ p+g   +s+s D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 813 GEELRTLIGHsCWVNAVKVTPNGLRAVSASGDQTLKVWD 851
                                       5789******777************998877*******9 PP

  == domain 6  score: 29.2 bits;  conditional E-value: 1.1e-09
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       + l tl+GH s+v+++   pdg+  +s+sdD+t+++Wd
  gi|386002760|ref|YP_005921059.1| 856 EMLLTLKGHsSWVNAVTLTPDGRRAVSASDDQTLKVWD 893
                                       56889****777*************************9 PP

  == domain 7  score: 28.2 bits;  conditional E-value: 2.2e-09
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       + l tl+GH s+v+ +a+ pdg   +s+sdD+t+++Wd
  gi|386002760|ref|YP_005921059.1| 898 EMLLTLKGHsSWVNEVAVTPDGLRAVSASDDQTLKVWD 935
                                       56889****777*************************9 PP

  == domain 8  score: 31.5 bits;  conditional E-value: 2e-10
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                       + l tl+GH ++v+++a  pdg+ ++s+s+D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 940 EMLLTLKGHyCWVNAVALTPDGRRVVSASRDKTLKVWD 977
                                       56889****999*************************9 PP

  == domain 9  score: 34.0 bits;  conditional E-value: 3.2e-11
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40    2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38  
                                        + lrtl+GH ++v+++a+ pdg+  +s+sdD+t+++Wd
  gi|386002760|ref|YP_005921059.1|  982 EELRTLKGHsNWVSAVAVTPDGRRAVSASDDHTLKVWD 1019
                                        579******999*************************9 PP

  == domain 10  score: 27.4 bits;  conditional E-value: 3.8e-09
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40    2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38  
                                        + lrtl+GH +sv+++a+ pdg   +s+s D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 1024 EELRTLKGHsDSVSAVAVTPDGLRAVSASFDQTLKVWD 1061
                                        579******777************999999*******9 PP

  == domain 11  score: 33.5 bits;  conditional E-value: 4.7e-11
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40    2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38  
                                        + lrtl+GH +sv+++a+ pdg+  +s+s+D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 1066 EELRTLKGHsNSVRAVAVTPDGRRAVSASRDRTLKVWD 1103
                                        579******999*************************9 PP

  == domain 12  score: 24.2 bits;  conditional E-value: 4e-08
                                        TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40    1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38  
                                        g+ lrtl+GH ++v+++a  pdg   +s+s D t+++Wd
  gi|386002760|ref|YP_005921059.1| 1107 GEELRTLKGHsNWVNAVAATPDGLRAVSASGDLTLKVWD 1145
                                        5789******999************998877*******9 PP

  == domain 13  score: 28.4 bits;  conditional E-value: 1.9e-09
                                        TEEEEEEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40    1 gqclrtltGHss.vtslafspdgawlasGsdDgtvriWd 38  
                                        g+ lrtl+GHs  v+++a+ pdg+  +s+s D+t+++Wd
  gi|386002760|ref|YP_005921059.1| 1149 GEELRTLKGHSYwVRAVAVTPDGRKAVSSSFDQTLKVWD 1187
                                        5789******446************999999*******9 PP

  == domain 14  score: 4.2 bits;  conditional E-value: 0.086
                                        EEEEEEESSSSEEEEEEETTSSEEEEE.ETTS CS
                              WD40    2 qclrtltGHssvtslafspdgawlasG.sdDg 32  
                                        + + t+t+ +s++++   pdg  +++G s  g
  gi|386002760|ref|YP_005921059.1| 1192 EIVATFTADGSIRCCTIGPDGVTIVAGeS-SG 1222
                                        56788987778**************9965.55 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   5.4e-38   5.6e-35      23     252 .]     203     422 ..     197     422 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 5.4e-38
                                       EEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslseddleekeeveslkrklvr 98 
                                       v++ GmgG+GK++la+ + ++ d v+  F+ ++ w+++++   + ++l+ i  +L +   d + +e+ ++ k+kl +
  gi|386002760|ref|YP_005921059.1| 203 VGVQGMGGIGKSVLAAVVARD-DGVRLAFPdGIFWLSIGRDIREADLLQ-IQSKLARILGDESVFENLNDGKEKLLE 277
                                       89*******************.*******77*****************9.*****************999******* PP

                                       HCCCTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS- CS
                            NB-ARC  99 lLltkrfllvlDDVweeedwdkigvvlparenrlrvllTTRdeevanavsatsekievelLekdeawellenkvfek 175
                                       lL +k  ll+lDDVw+  d      ++ +    +r+l+TTR+ ++  + ++      + lLe  +a++ll   +   
  gi|386002760|ref|YP_005921059.1| 278 LLADKVCLLILDDVWKARDA----GAFDSLGPNCRMLITTRNADIITNLGG--SEYSLDLLEVPKALKLLADWAGID 348
                                       *****************997....68899999*************999999..778999*************99988 PP

                                       GGCHH..CHHHHHHHHHHCTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHHCTGCC.TS--S.SSSSSSHHHHHHHHH CS
                            NB-ARC 176 kleekesleevakeivekckGlPlalkvlggllstkktveewkkvleklesklle.vekst.skslesvasilqlsy 250
                                        ++    l++ a+eiv++c+ lPlal+++g++l+  k +++wk+vl+kl+s  l  +e    ++ +  + + +q+s+
  gi|386002760|ref|YP_005921059.1| 349 ADS----LPREANEIVQECGRLPLALAIIGAMLQ-GKPLNRWKNVLHKLQSTDLDkIERDFpHYPYHDLLKTIQVSV 420
                                       887....999*******************98888.6789**************998877662578999*******99 PP

                                       HT CS
                            NB-ARC 251 en 252
                                       en
  gi|386002760|ref|YP_005921059.1| 421 EN 422
                                       96 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0     3e-32   3.2e-29       1     115 [.       4     122 ..       4     125 .. 0.92
   2 ?   -2.1   0.0       5.4   5.7e+03       6      38 ..     493     525 ..     492     539 .. 0.69

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 3e-32
                             TIR_2   1 VFiSyssedkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaale 77 
                                       +FiSy+ +dkewae++a++Le+ g++++++ wd++pg++++ e+++a ++ +++++vlsp+yle  +++ e+ aa++
  gi|386002760|ref|YP_005921059.1|   4 FFISYTKADKEWAEWIAWHLEETGYSTVIQVWDFRPGSNFVLEMDKASRETERTIAVLSPNYLEAFYTQPEWAAAFK 80 
                                       6**************************9************************************************* PP

                             TIR_2  78 aaeegkkr.lipvllepekpp..laslqyidlskk.de.eale 115
                                       ++++g+k  l+pv+++++kp+  l+ + yidl  + de  a++
  gi|386002760|ref|YP_005921059.1|  81 KDPKGEKGsLLPVRVRECKPGglLGPIVYIDLV-GlDEkIAMD 122
                                       999999889*******88887767********9.545535555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.4
                             TIR_2   6 ssedkewaeklaeaLeaagirvwldrwdlkpge 38 
                                        +++ e +++l+++L +a  r  ld w+  p +
  gi|386002760|ref|YP_005921059.1| 493 VRKQVEDVTELHNRLLEAYRRKCLDGWHTGPDD 525
                                       5666688999****9777333347999876655 PP

>> APAF1_C  APAF-1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   1.3e-17   1.3e-14       2      74 ..     501     571 ..     500     584 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.3e-17
                           APAF1_C   2 qdLHkklveryekkykeeelskldkddlywysyleyHlakanlveelkallldldwieakvkltgpsslledy 74 
                                       ++LH++l+e+y++k+ +  +  + +dd y++++l+ Hl++a++ +el+++lld++wi+ak+++t  ssl++dy
  gi|386002760|ref|YP_005921059.1| 501 TELHNRLLEAYRRKCLDGWH--TGPDDGYIFQHLARHLIEAGRKDELRNILLDFNWIRAKLETTDVSSLVADY 571
                                       79***************976..55799999999***************************************9 PP

>> Nucleoporin_N  Nup133 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00041      0.43     199     295 ..     653     753 ..     630     755 .. 0.83
   2 !    8.2   0.0   0.00088      0.93     201     274 ..     739     811 ..     730     839 .. 0.79
   3 !    5.4   0.0    0.0063       6.6     202     295 ..     782     879 ..     773     882 .. 0.81
   4 !    6.2   0.0    0.0035       3.7     214     274 ..     878     937 ..     859     964 .. 0.78
   5 !   12.0   0.0     6e-05     0.063     214     296 ..     962    1048 ..     951    1061 .. 0.87
   6 !   13.6   0.0   1.9e-05      0.02     200     293 ..    1074    1171 ..    1063    1185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00041
                                       --GG-EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEEE CS
                     Nucleoporin_N 199 sereeivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildisp 275
                                         ++++ ++++ +  r+ +++s +++++v+dl+  ++ ++l ++ +  ++++ + + +l+a + + +++l+++d++ 
  gi|386002760|ref|YP_005921059.1| 653 GHSDSVRAVAVTPDGRRAVSASGDRTLKVWDLERGEELRTLIGHSNSVRAVAVT-PDGLRAVSASDDSTLRVWDLVR 728
                                       468899999999999******************555577777777766666655.9******************987 PP

                                       S-TT.....TSSCEEEEEEECSSSE CS
                     Nucleoporin_N 276 vsae.....essllhlvaitsngvr 295
                                        ++      +s+ + +va+t +g+r
  gi|386002760|ref|YP_005921059.1| 729 GEELrtlegHSNSVSAVAVTPDGRR 753
                                       6665777778999999999999988 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00088
                                       GG-EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEE CS
                     Nucleoporin_N 201 reeivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildis 274
                                       ++++ ++++ +  r+ +++s++++++v+dl+  ++ ++lk++ +  ++++ + + +l+a + +++ +lk++d++
  gi|386002760|ref|YP_005921059.1| 739 SNSVSAVAVTPDGRRAVSASRDRTLKVWDLERGEELRTLKGHSNSVSAVAVT-PDGLRAVSASGDLTLKVWDLE 811
                                       6788999999999******************555577777777777777755.999999999999999999986 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0063
                                       G-EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEEES-T CS
                     Nucleoporin_N 202 eeivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildispvsa 278
                                       +++ ++++ +   + +++s + +++v+dl+  ++ ++l ++  + ++++ + +++l+a + +++ +lk++d++  ++
  gi|386002760|ref|YP_005921059.1| 782 NSVSAVAVTPDGLRAVSASGDLTLKVWDLERGEELRTLIGHSCWVNAVKVT-PNGLRAVSASGDQTLKVWDLKSGEM 857
                                       5566666666666778899999********6666999***********988.*******************997766 PP

                                       T.....TSSCEEEEEEECSSSE CS
                     Nucleoporin_N 279 e.....essllhlvaitsngvr 295
                                             +ss++ +v +t +g+r
  gi|386002760|ref|YP_005921059.1| 858 LltlkgHSSWVNAVTLTPDGRR 879
                                       6666668888888888888877 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0035
                                       CEEEEEETTSEEEEEEEETTCE.E-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEE CS
                     Nucleoporin_N 214 rilytlsskgvirvydlsasng.esslksdidirqilleaitesliasaplaskslkildis 274
                                       r+ +++s + +++v+dl+ +++   +lk++ ++ ++++ + + +l+a + + + +lk++d++
  gi|386002760|ref|YP_005921059.1| 878 RRAVSASDDQTLKVWDLE-RGEmLLTLKGHSSWVNEVAVT-PDGLRAVSASDDQTLKVWDLE 937
                                       77899*************.66669**************88.*******************87 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 6e-05
                                        CEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEEES-TT.....TSSC CS
                     Nucleoporin_N  214 rilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildispvsae.....essl 283 
                                        r+++++s++++++v+dl+  ++ ++lk++ ++ ++++ + + + +a + + + +lk++d++  ++      +s+ 
  gi|386002760|ref|YP_005921059.1|  962 RRVVSASRDKTLKVWDLERYEELRTLKGHSNWVSAVAVT-PDGRRAVSASDDHTLKVWDLERYEELrtlkgHSDS 1035
                                        899***************666699*************88.99999999************999887888889999 PP

                                        EEEEEEECSSSEE CS
                     Nucleoporin_N  284 lhlvaitsngvrl 296 
                                        + +va+t +g r+
  gi|386002760|ref|YP_005921059.1| 1036 VSAVAVTPDGLRA 1048
                                        9999999998775 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 1.9e-05
                                        -GG-EEEEEEECCTCEEEEEETTSEEEEEEEETTCEE-EEEEEEEHHHHHHHH.HHSCHTTTCGCTTT-EEEEEE CS
                     Nucleoporin_N  200 ereeivqlridssrrilytlsskgvirvydlsasngesslksdidirqilleaitesliasaplaskslkildis 274 
                                         ++++ ++++ +  r+ +++s++++++v+dl+  ++ ++lk++ ++ ++++ + + +l+a + +++ +lk++d++
  gi|386002760|ref|YP_005921059.1| 1074 HSNSVRAVAVTPDGRRAVSASRDRTLKVWDLERGEELRTLKGHSNWVNAVAAT-PDGLRAVSASGDLTLKVWDLE 1147
                                        67889999999999******************66669**************66.*******************97 PP

                                        ES-TT.....TSSCEEEEEEECSS CS
                     Nucleoporin_N  275 pvsae.....essllhlvaitsng 293 
                                          ++      +s ++ +va+t +g
  gi|386002760|ref|YP_005921059.1| 1148 KGEELrtlkgHSYWVRAVAVTPDG 1171
                                        554445555566666666666665 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.018        19      37      84 ..     654     700 ..     648     706 .. 0.87
   2 ?    4.0   0.0     0.057        60      38      85 ..     697     743 ..     693     746 .. 0.89
   3 !    9.7   0.0   0.00099         1      28      86 ..     722     786 ..     711     791 .. 0.86
   4 ?    4.7   0.0     0.035        37      19      77 ..     755     820 ..     745     834 .. 0.72
   5 ?    2.9   0.0      0.13   1.3e+02      37      81 ..     822     866 ..     804     875 .. 0.81
   6 !    8.3   0.1    0.0027       2.9      29      81 ..     849     908 ..     836     914 .. 0.80
   7 ?    5.1   0.1     0.026        27      29      79 ..     891     948 ..     883     958 .. 0.79
   8 ?    5.0   0.1     0.028        30      28      81 ..     941     992 ..     919    1000 .. 0.77
   9 !    7.7   0.1    0.0041       4.3      19      87 ..     965    1039 ..     954    1044 .. 0.87
  10 !    8.8   0.0    0.0019         2      28      81 ..    1058    1118 ..    1049    1126 .. 0.86
  11 !    8.0   0.0    0.0033       3.5      29      86 ..    1143    1205 ..    1140    1211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                       ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                       ++ +vr++a  pdg+  + a  d ++++ d e g+ +++l  +s++ v
  gi|386002760|ref|YP_005921059.1| 654 HSDSVRAVAVTPDGRRAVSASGDRTLKVWDLERGEELRTLIGHSNS-V 700
                                       6789********************************9999877764.4 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.057
                       ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavt 85 
                                       +++vr++a  pdg   + a +d+++r+ d   g+ +++l+ +s++ v+
  gi|386002760|ref|YP_005921059.1| 697 SNSVRAVAVTPDGLRAVSASDDSTLRVWDLVRGEELRTLEGHSNS-VS 743
                                       6899**********************************9999885.66 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00099
                       ANAPC4_WD40  28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtc 86 
                                       rvw+l       + ++++++v+++a  pdg+  + a  d ++++ d e g+ +++l+ +s++ v+ 
  gi|386002760|ref|YP_005921059.1| 722 RVWDLvrgeelrTLEGHSNSVSAVAVTPDGRRAVSASRDRTLKVWDLERGEELRTLKGHSNS-VSA 786
                                       6777777777766689999*************************************999985.665 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.035
                       ANAPC4_WD40  19 llvfRlngqrvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsls 77 
                                       + ++R    +vw+l       + ++++++v+++a  pdg   + a  d ++++ d e g+ +++l 
  gi|386002760|ref|YP_005921059.1| 755 VSASRDRTLKVWDLergeelrTLKGHSNSVSAVAVTPDGLRAVSASGDLTLKVWDLERGEELRTLI 820
                                       556666667777777777776667778888888888888888888888888888888888777765 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.13
                       ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       ++  v++++  p+g   + a  d ++++ d +sg+++ +l+ +s+
  gi|386002760|ref|YP_005921059.1| 822 HSCWVNAVKVTPNGLRAVSASGDQTLKVWDLKSGEMLLTLKGHSS 866
                                       566788999999**999********************99988776 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0027
                       ANAPC4_WD40  29 vwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       vw+l       + ++++s v+++   pdg+  + a +d ++++ d e g+++ +l+ +s+
  gi|386002760|ref|YP_005921059.1| 849 VWDLksgemllTLKGHSSWVNAVTLTPDGRRAVSASDDQTLKVWDLERGEMLLTLKGHSS 908
                                       4444444444444899999*********************************99987765 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.026
                       ANAPC4_WD40  29 vwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                       vw+l       + ++++s v+++a  pdg   + a +d ++++ d e g+++ +l+ +
  gi|386002760|ref|YP_005921059.1| 891 VWDLergemllTLKGHSSWVNEVAVTPDGLRAVSASDDQTLKVWDLERGEMLLTLKGH 948
                                       4444444444444889999********************************9988765 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.028
                       ANAPC4_WD40  28 rvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       ++ t   +++   v+++a  pdg+  + a  d ++++ d e  + +++l+ +s+
  gi|386002760|ref|YP_005921059.1| 941 MLLT--LKGHYCWVNAVALTPDGRRVVSASRDKTLKVWDLERYEELRTLKGHSN 992
                                       3333..477888899***************************999999988776 PP

  == domain 9  score: 7.7 bits;  conditional E-value: 0.0041
                       ANAPC4_WD40   19 llvfRlngqrvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtc 86  
                                        + ++R +  +vw+l       + +++++ v+++a  pdg+  + a +d ++++ d e  + +++l+ +s++ v+ 
  gi|386002760|ref|YP_005921059.1|  965 VSASRDKTLKVWDLeryeelrTLKGHSNWVSAVAVTPDGRRAVSASDDHTLKVWDLERYEELRTLKGHSDS-VSA 1038
                                        56788888999999999998877899999************************************999995.765 PP

                       ANAPC4_WD40   87 l 87  
                                        +
  gi|386002760|ref|YP_005921059.1| 1039 V 1039
                                        5 PP

  == domain 10  score: 8.8 bits;  conditional E-value: 0.0019
                       ANAPC4_WD40   28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81  
                                        +vw+l       + ++++++vr++a  pdg+  + a  d ++++ d e g+ +++l+ +s+
  gi|386002760|ref|YP_005921059.1| 1058 KVWDLeryeelrTLKGHSNSVRAVAVTPDGRRAVSASRDRTLKVWDLERGEELRTLKGHSN 1118
                                        5666666666666678999**********************************99988776 PP

  == domain 11  score: 8.0 bits;  conditional E-value: 0.0033
                       ANAPC4_WD40   29 vwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtc 86  
                                        vw+l       + ++++  vr++a  pdg+  + +  d ++++ d e+g++v +++++ +  + c
  gi|386002760|ref|YP_005921059.1| 1143 VWDLekgeelrTLKGHSYWVRAVAVTPDGRKAVSSSFDQTLKVWDLETGEIVATFTADGS--IRC 1205
                                        55555555544446677789***********************************98766..555 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.018        19     229     256 ..     666     694 ..     653     709 .. 0.79
   2 ?    1.4   0.1      0.09        95     233     255 ..     712     734 ..     692     738 .. 0.78
   3 !    8.0   0.0   0.00092      0.97     225     255 ..     747     776 ..     734     792 .. 0.78
   4 ?    0.1   0.0      0.23   2.4e+02     233     255 ..     796     818 ..     778     833 .. 0.79
   5 ?    3.3   0.0     0.024        26     234     255 ..     839     860 ..     826     864 .. 0.86
   6 ?    3.1   0.1     0.029        30     230     254 ..     877     901 ..     864     906 .. 0.77
   7 ?    2.4   0.1     0.045        47     233     254 ..     922     943 ..     906     947 .. 0.82
   8 !    6.5   0.1    0.0027       2.8     233     255 ..     964     986 ..     952     992 .. 0.82
   9 !    5.3   0.0    0.0059       6.2     229     255 ..    1002    1028 ..     990    1034 .. 0.78
  10 ?    3.1   0.1     0.028        30     233     255 ..    1048    1070 ..    1032    1081 .. 0.80
  11 !    7.2   0.0    0.0016       1.7     229     255 ..    1086    1112 ..    1072    1126 .. 0.80
  12 ?   -0.3   0.0       0.3   3.1e+02     233     255 ..    1132    1154 ..    1114    1159 .. 0.82
  13 !    9.4   0.0   0.00034      0.36     233     258 ..    1174    1199 ..    1162    1214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                                       TTTEEEEEETT-EEEEEETTTTEEEEE.E CS
                            Nup160 229 gqtylfalsrdgkLrvWnlltgkclat.i 256
                                       +   ++++s d++L+vW+l+ g  l+t i
  gi|386002760|ref|YP_005921059.1| 666 DGRRAVSASGDRTLKVWDLERGEELRTlI 694
                                       5566789999**********999888865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.09
                                       EEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 233 lfalsrdgkLrvWnlltgkclat 255
                                       ++++s d +LrvW+l  g  l+t
  gi|386002760|ref|YP_005921059.1| 712 AVSASDDSTLRVWDLVRGEELRT 734
                                       788999********987776665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00092
                                       ....TTTEEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 225 vveigqtylfalsrdgkLrvWnlltgkclat 255
                                       v+  +   ++++srd++L+vW+l+ g  l+t
  gi|386002760|ref|YP_005921059.1| 747 VTP-DGRRAVSASRDRTLKVWDLERGEELRT 776
                                       333.7777999************99888777 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.23
                                       EEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 233 lfalsrdgkLrvWnlltgkclat 255
                                       ++++s d +L+vW+l+ g  l+t
  gi|386002760|ref|YP_005921059.1| 796 AVSASGDLTLKVWDLERGEELRT 818
                                       67889999*******99888877 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.024
                                       EEEETT-EEEEEETTTTEEEEE CS
                            Nup160 234 falsrdgkLrvWnlltgkclat 255
                                       +++s d++L+vW+l++g  l t
  gi|386002760|ref|YP_005921059.1| 839 VSASGDQTLKVWDLKSGEMLLT 860
                                       67899**********9988766 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.029
                                       TTEEEEEETT-EEEEEETTTTEEEE CS
                            Nup160 230 qtylfalsrdgkLrvWnlltgkcla 254
                                          ++++s d++L+vW+l+ g  l 
  gi|386002760|ref|YP_005921059.1| 877 GRRAVSASDDQTLKVWDLERGEMLL 901
                                       55678999**********9887765 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.045
                                       EEEEETT-EEEEEETTTTEEEE CS
                            Nup160 233 lfalsrdgkLrvWnlltgkcla 254
                                       ++++s d++L+vW+l+ g  l 
  gi|386002760|ref|YP_005921059.1| 922 AVSASDDQTLKVWDLERGEMLL 943
                                       678999*********9887765 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.0027
                                       EEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 233 lfalsrdgkLrvWnlltgkclat 255
                                       ++++srd++L+vW+l+ +  l+t
  gi|386002760|ref|YP_005921059.1| 964 VVSASRDKTLKVWDLERYEELRT 986
                                       7899***********98877766 PP

  == domain 9  score: 5.3 bits;  conditional E-value: 0.0059
                                        TTTEEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160  229 gqtylfalsrdgkLrvWnlltgkclat 255 
                                        +   ++++s d++L+vW+l+ +  l+t
  gi|386002760|ref|YP_005921059.1| 1002 DGRRAVSASDDHTLKVWDLERYEELRT 1028
                                        66668899***********98877666 PP

  == domain 10  score: 3.1 bits;  conditional E-value: 0.028
                                        EEEEETT-EEEEEETTTTEEEEE CS
                            Nup160  233 lfalsrdgkLrvWnlltgkclat 255 
                                        ++++s d++L+vW+l+ +  l+t
  gi|386002760|ref|YP_005921059.1| 1048 AVSASFDQTLKVWDLERYEELRT 1070
                                        78899**********98877776 PP

  == domain 11  score: 7.2 bits;  conditional E-value: 0.0016
                                        TTTEEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160  229 gqtylfalsrdgkLrvWnlltgkclat 255 
                                        +   ++++srd++L+vW+l+ g  l+t
  gi|386002760|ref|YP_005921059.1| 1086 DGRRAVSASRDRTLKVWDLERGEELRT 1112
                                        6666899************98887776 PP

  == domain 12  score: -0.3 bits;  conditional E-value: 0.3
                                        EEEEETT-EEEEEETTTTEEEEE CS
                            Nup160  233 lfalsrdgkLrvWnlltgkclat 255 
                                        ++++s d +L+vW+l+ g  l+t
  gi|386002760|ref|YP_005921059.1| 1132 AVSASGDLTLKVWDLEKGEELRT 1154
                                        56788899*******99887776 PP

  == domain 13  score: 9.4 bits;  conditional E-value: 0.00034
                                        EEEEETT-EEEEEETTTTEEEEEEE- CS
                            Nup160  233 lfalsrdgkLrvWnlltgkclatidl 258 
                                        +++ s d++L+vW+l+tg ++at++ 
  gi|386002760|ref|YP_005921059.1| 1174 AVSSSFDQTLKVWDLETGEIVATFTA 1199
                                        556688****************9765 PP

>> 120_Rick_ant  120 KDa Rickettsia surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00053      0.56      77     114 ..     669     706 ..     656     722 .. 0.85
   2 ?    0.6   0.0      0.26   2.7e+02      79     125 ..     713     759 ..     705     765 .. 0.79
   3 ?    3.5   0.0     0.032        34      77     113 ..     753     789 ..     737     797 .. 0.84
   4 !    6.0   0.0    0.0055       5.8      78     109 ..     796     827 ..     789     838 .. 0.85
   5 ?    0.5   0.0      0.27   2.9e+02      79     111 ..     839     871 ..     836     883 .. 0.85
   6 ?    0.6   0.0      0.25   2.7e+02      78     113 ..     880     915 ..     871     933 .. 0.83
   7 ?   -1.6   0.0       1.2   1.3e+03      79     116 ..     923     960 ..     918     975 .. 0.79
   8 ?   -1.0   0.0       0.8   8.4e+02      78     113 ..    1006    1041 ..     989    1055 .. 0.84
   9 ?    0.5   0.0      0.27   2.9e+02      79     125 ..    1049    1095 ..    1035    1100 .. 0.82
  10 ?    2.8   0.0     0.053        56      78     116 ..    1090    1129 ..    1082    1132 .. 0.85
  11 !    9.1   0.0   0.00065      0.69      79     122 ..    1133    1176 ..    1130    1185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00053
                      120_Rick_ant  77 tqvsavgdlrakvvkndaGeklvdLvetsvktklvakv 114
                                         vsa+gd + kv   + Ge+l +L+ +s +++ va  
  gi|386002760|ref|YP_005921059.1| 669 RAVSASGDRTLKVWDLERGEELRTLIGHSNSVRAVAVT 706
                                       5699*****************************77743 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                      120_Rick_ant  79 vsavgdlrakvvkndaGeklvdLvetsvktklvakvdGttktitkyr 125
                                       vsa+ d + +v     Ge+l +L  +s ++  va     ++ ++  r
  gi|386002760|ref|YP_005921059.1| 713 VSASDDSTLRVWDLVRGEELRTLEGHSNSVSAVAVTPDGRRAVSASR 759
                                       7888888999999999***************8886654455555544 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.032
                      120_Rick_ant  77 tqvsavgdlrakvvkndaGeklvdLvetsvktklvak 113
                                         vsa+ d + kv   + Ge+l +L  +s ++  va 
  gi|386002760|ref|YP_005921059.1| 753 RAVSASRDRTLKVWDLERGEELRTLKGHSNSVSAVAV 789
                                       5689999************************997764 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0055
                      120_Rick_ant  78 qvsavgdlrakvvkndaGeklvdLvetsvktk 109
                                        vsa+gdl+ kv   + Ge+l +L+ +s  ++
  gi|386002760|ref|YP_005921059.1| 796 AVSASGDLTLKVWDLERGEELRTLIGHSCWVN 827
                                       589************************98877 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.27
                      120_Rick_ant  79 vsavgdlrakvvkndaGeklvdLvetsvktklv 111
                                       vsa+gd + kv     Ge l +L  +s  ++ v
  gi|386002760|ref|YP_005921059.1| 839 VSASGDQTLKVWDLKSGEMLLTLKGHSSWVNAV 871
                                       89************************9888743 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.25
                      120_Rick_ant  78 qvsavgdlrakvvkndaGeklvdLvetsvktklvak 113
                                        vsa+ d + kv   + Ge l +L  +s  ++ va 
  gi|386002760|ref|YP_005921059.1| 880 AVSASDDQTLKVWDLERGEMLLTLKGHSSWVNEVAV 915
                                       689999**********************99985553 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 1.2
                      120_Rick_ant  79 vsavgdlrakvvkndaGeklvdLvetsvktklvakvdG 116
                                       vsa+ d + kv   + Ge l +L  +   ++ va    
  gi|386002760|ref|YP_005921059.1| 923 VSASDDQTLKVWDLERGEMLLTLKGHYCWVNAVALTPD 960
                                       7999999*****************99999987775433 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 0.8
                      120_Rick_ant   78 qvsavgdlrakvvkndaGeklvdLvetsvktklvak 113 
                                         vsa+ d + kv   +  e+l +L  +s ++  va 
  gi|386002760|ref|YP_005921059.1| 1006 AVSASDDHTLKVWDLERYEELRTLKGHSDSVSAVAV 1041
                                        68999999*********************9997664 PP

  == domain 9  score: 0.5 bits;  conditional E-value: 0.27
                      120_Rick_ant   79 vsavgdlrakvvkndaGeklvdLvetsvktklvakvdGttktitkyr 125 
                                        vsa+ d + kv   +  e+l +L  +s +++ va     ++ ++  r
  gi|386002760|ref|YP_005921059.1| 1049 VSASFDQTLKVWDLERYEELRTLKGHSNSVRAVAVTPDGRRAVSASR 1095
                                        7899999999999******************8887655555555554 PP

  == domain 10  score: 2.8 bits;  conditional E-value: 0.053
                      120_Rick_ant   78 qvsavgdlrakvvkndaGeklvdLvetsvktk.lvakvdG 116 
                                         vsa+ d + kv   + Ge+l +L  +s  ++ ++a  dG
  gi|386002760|ref|YP_005921059.1| 1090 AVSASRDRTLKVWDLERGEELRTLKGHSNWVNaVAATPDG 1129
                                        58999999*********************99956666666 PP

  == domain 11  score: 9.1 bits;  conditional E-value: 0.00065
                      120_Rick_ant   79 vsavgdlrakvvkndaGeklvdLvetsvktklvakvdGttktit 122 
                                        vsa+gdl+ kv   ++Ge+l +L  +s+ ++ va     +k ++
  gi|386002760|ref|YP_005921059.1| 1133 VSASGDLTLKVWDLEKGEELRTLKGHSYWVRAVAVTPDGRKAVS 1176
                                        89*****************************8887655555555 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1    0.0001      0.11       5      87 ..     709     792 ..     705     814 .. 0.87
   2 ?    0.6   0.0      0.15   1.6e+02       6      72 ..     836     902 ..     831     913 .. 0.80
   3 !   14.1   0.0   1.2e-05     0.013       5      92 ..     919    1007 ..     915    1010 .. 0.89
   4 !    9.2   0.1   0.00036      0.38       9      94 ..    1007    1093 ..    1001    1118 .. 0.79
   5 ?    3.5   0.0      0.02        21       6      94 ..    1130    1218 ..    1125    1221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                       GEEEEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEE CS
                      Cytochrom_D1   5 nlfvvverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnars 81 
                                        l +v  +d+  +++ d  + e+l +le++ +   ++  ++dgR +  ++RD ++++ DL + e ++++k  +n+ s
  gi|386002760|ref|YP_005921059.1| 709 GLRAVSASDDSTLRVWDLVRGEELRTLEGHSNSVSAVAVTPDGRRAVSASRDRTLKVWDLERGEELRTLKGHSNSVS 785
                                       57789999************************999999*******************************99999987 PP

                                       .EEE--T CS
                      Cytochrom_D1  82 .vavSqd 87 
                                        vav  d
  gi|386002760|ref|YP_005921059.1| 786 aVAVTPD 792
                                       2444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                                       EEEEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEE CS
                      Cytochrom_D1   6 lfvvverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivae 72 
                                       l +v  +++  +++ d +s e l +l+++     ++  ++dgR +  ++ D ++++ DL + e++ +
  gi|386002760|ref|YP_005921059.1| 836 LRAVSASGDQTLKVWDLKSGEMLLTLKGHSSWVNAVTLTPDGRRAVSASDDQTLKVWDLERGEMLLT 902
                                       6677788888888888888888888888888888888899999999999999999999887776555 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.2e-05
                                        GEEEEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEE CS
                      Cytochrom_D1    5 nlfvvverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlna 79  
                                         l +v  +d+  +++ d ++ e l +l+++y    ++  ++dgR v  ++RD ++++ DL + e ++++k  +n 
  gi|386002760|ref|YP_005921059.1|  919 GLRAVSASDDQTLKVWDLERGEMLLTLKGHYCWVNAVALTPDGRRVVSASRDKTLKVWDLERYEELRTLKGHSNW 993 
                                        6788999*********************************************************99999998887 PP

                                        EE.EEE--TTSEEE CS
                      Cytochrom_D1   80 rs.vavSqddryvi 92  
                                         s vav  d+r ++
  gi|386002760|ref|YP_005921059.1|  994 VSaVAVTPDGRRAV 1007
                                        65377778888666 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00036
                                        EEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEE.EEE CS
                      Cytochrom_D1    9 vverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlna.rsv 82  
                                        v  +d++ +++ d +++e+l +l+++ +   ++  ++dg  +  ++ D ++++ DL + e ++++k  +n+ r v
  gi|386002760|ref|YP_005921059.1| 1007 VSASDDHTLKVWDLERYEELRTLKGHSDSVSAVAVTPDGLRAVSASFDQTLKVWDLERYEELRTLKGHSNSvRAV 1081
                                        667888999999999999999999999888888888889888889999999999999888888888888765788 PP

                                        EE--TTSEEEEE CS
                      Cytochrom_D1   83 avSqddryvivg 94  
                                        av  d+r ++ +
  gi|386002760|ref|YP_005921059.1| 1082 AVTPDGRRAVSA 1093
                                        888888876654 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.02
                                        EEEEEEGGGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEE CS
                      Cytochrom_D1    6 lfvvverdagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnar 80  
                                        l +v  +++  +++ d ++ e+l +l+++     ++  ++dgR +   + D ++++ DL + eiva+  + +  r
  gi|386002760|ref|YP_005921059.1| 1130 LRAVSASGDLTLKVWDLEKGEELRTLKGHSYWVRAVAVTPDGRKAVSSSFDQTLKVWDLETGEIVATFTADGSIR 1204
                                        66788888889999999999999999999777777888999**************************99999999 PP

                                        EEEE--TTSEEEEE CS
                      Cytochrom_D1   81 svavSqddryvivg 94  
                                           +  d+  +++g
  gi|386002760|ref|YP_005921059.1| 1205 CCTIGPDGVTIVAG 1218
                                        99999988888887 PP

>> Nudix_N  Hydrolase of X-linked nucleoside diphosphate N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.9   4.1e+03      24      36 ..     681     693 ..     680     695 .. 0.87
   2 ?   -3.0   0.0       5.3   5.6e+03      24      36 ..     765     777 ..     764     778 .. 0.87
   3 ?   -2.5   0.0       3.9   4.1e+03      24      36 ..     807     819 ..     806     821 .. 0.87
   4 !    6.2   0.0    0.0072       7.6      24      36 ..     975     987 ..     969     989 .. 0.89
   5 !    6.4   0.0    0.0066       6.9      24      36 ..    1017    1029 ..    1012    1032 .. 0.88
   6 !    6.3   0.0     0.007       7.3      24      36 ..    1059    1071 ..    1055    1074 .. 0.89
   7 ?   -3.0   0.0       5.3   5.6e+03      24      36 ..    1101    1113 ..    1100    1114 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.9
                           Nudix_N  24 vYDreRYeeLrei 36 
                                       v D eR eeLr++
  gi|386002760|ref|YP_005921059.1| 681 VWDLERGEELRTL 693
                                       579********97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                           Nudix_N  24 vYDreRYeeLrei 36 
                                       v D eR eeLr++
  gi|386002760|ref|YP_005921059.1| 765 VWDLERGEELRTL 777
                                       579*******986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                           Nudix_N  24 vYDreRYeeLrei 36 
                                       v D eR eeLr++
  gi|386002760|ref|YP_005921059.1| 807 VWDLERGEELRTL 819
                                       579********97 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0072
                           Nudix_N  24 vYDreRYeeLrei 36 
                                       v D eRYeeLr++
  gi|386002760|ref|YP_005921059.1| 975 VWDLERYEELRTL 987
                                       68*********87 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.0066
                           Nudix_N   24 vYDreRYeeLrei 36  
                                        v D eRYeeLr++
  gi|386002760|ref|YP_005921059.1| 1017 VWDLERYEELRTL 1029
                                        68*********87 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.007
                           Nudix_N   24 vYDreRYeeLrei 36  
                                        v D eRYeeLr++
  gi|386002760|ref|YP_005921059.1| 1059 VWDLERYEELRTL 1071
                                        68*********87 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 5.3
                           Nudix_N   24 vYDreRYeeLrei 36  
                                        v D eR eeLr++
  gi|386002760|ref|YP_005921059.1| 1101 VWDLERGEELRTL 1113
                                        579*******986 PP

>> DUF5570  Family of unknown function (DUF5570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3     0.015        16      15      68 ..     659     709 ..     654     720 .. 0.77
   2 ?    2.6   0.1      0.13   1.3e+02      15      47 ..     701     733 ..     696     747 .. 0.82
   3 ?    5.7   0.2     0.014        14      17      71 ..     745     796 ..     737     814 .. 0.79
   4 ?   -0.7   0.0       1.4   1.4e+03      19      44 ..     831     856 ..     814     865 .. 0.84
   5 ?    3.4   0.0     0.072        76      19      44 ..     873     898 ..     862     908 .. 0.87
   6 ?   -0.7   0.0       1.3   1.4e+03      19      44 ..     915     940 ..     900     945 .. 0.86
   7 ?   -1.9   0.0       3.1   3.3e+03      20      42 ..     958     980 ..     951     992 .. 0.85
   8 ?    2.8   0.1      0.11   1.2e+02      19      66 ..     999    1043 ..     990    1059 .. 0.75
   9 ?    4.5   0.0     0.034        35      14      46 ..    1078    1110 ..    1064    1125 .. 0.87
  10 ?   -1.0   0.0       1.7   1.8e+03      18      46 ..    1124    1152 ..    1115    1167 .. 0.83
  11 ?    4.6   0.1     0.032        34      18      48 ..    1166    1196 ..    1160    1218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                           DUF5570  15 iilldspsgrsasarsegstaslwdvsdgqdvhahaivtrtcesvlssavytqg 68 
                                       + +  +p gr a + s   t  +wd+  g+++    ++    +sv + av  +g
  gi|386002760|ref|YP_005921059.1| 659 RAVAVTPDGRRAVSASGDRTLKVWDLERGEEL---RTLIGHSNSVRAVAVTPDG 709
                                       566779************************99...4445556677777766666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                           DUF5570  15 iilldspsgrsasarsegstaslwdvsdgqdvh 47 
                                       + +  +p g  a + s+ st  +wd+  g++++
  gi|386002760|ref|YP_005921059.1| 701 RAVAVTPDGLRAVSASDDSTLRVWDLVRGEELR 733
                                       566679***999999************999874 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.014
                           DUF5570  17 lldspsgrsasarsegstaslwdvsdgqdvhahaivtrtcesvlssavytqgcgy 71 
                                       +  +p gr a + s   t  +wd+  g+++    ++    +sv + av  +g   
  gi|386002760|ref|YP_005921059.1| 745 VAVTPDGRRAVSASRDRTLKVWDLERGEEL---RTLKGHSNSVSAVAVTPDGLRA 796
                                       4559************************99...5566667777777776666555 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.4
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgq 44 
                                        +p g  a + s  +t  +wd+ +g+
  gi|386002760|ref|YP_005921059.1| 831 VTPNGLRAVSASGDQTLKVWDLKSGE 856
                                       49999999999999*******99986 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.072
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgq 44 
                                        +p gr a + s+ +t  +wd+  g+
  gi|386002760|ref|YP_005921059.1| 873 LTPDGRRAVSASDDQTLKVWDLERGE 898
                                       39*******************99886 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.3
                           DUF5570  19 dspsgrsasarsegstaslwdvsdgq 44 
                                        +p g  a + s+ +t  +wd+  g+
  gi|386002760|ref|YP_005921059.1| 915 VTPDGLRAVSASDDQTLKVWDLERGE 940
                                       48999999999**********99886 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 3.1
                           DUF5570  20 spsgrsasarsegstaslwdvsd 42 
                                       +p gr   + s  +t  +wd+  
  gi|386002760|ref|YP_005921059.1| 958 TPDGRRVVSASRDKTLKVWDLER 980
                                       89*****999*********9865 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.11
                           DUF5570   19 dspsgrsasarsegstaslwdvsdgqdvhahaivtrtcesvlssavyt 66  
                                         +p gr a + s+  t  +wd+   +++    ++    +sv + av  
  gi|386002760|ref|YP_005921059.1|  999 VTPDGRRAVSASDDHTLKVWDLERYEEL---RTLKGHSDSVSAVAVTP 1043
                                        49*******************9887777...44555556665555555 PP

  == domain 9  score: 4.5 bits;  conditional E-value: 0.034
                           DUF5570   14 piilldspsgrsasarsegstaslwdvsdgqdv 46  
                                         + +  +p gr a + s   t  +wd+  g+++
  gi|386002760|ref|YP_005921059.1| 1078 VRAVAVTPDGRRAVSASRDRTLKVWDLERGEEL 1110
                                        5666779*********************99986 PP

  == domain 10  score: -1.0 bits;  conditional E-value: 1.7
                           DUF5570   18 ldspsgrsasarsegstaslwdvsdgqdv 46  
                                          +p g  a + s   t  +wd+ +g+++
  gi|386002760|ref|YP_005921059.1| 1124 AATPDGLRAVSASGDLTLKVWDLEKGEEL 1152
                                        4589999999999999********99986 PP

  == domain 11  score: 4.6 bits;  conditional E-value: 0.032
                           DUF5570   18 ldspsgrsasarsegstaslwdvsdgqdvha 48  
                                          +p gr a + s  +t  +wd+  g+ v +
  gi|386002760|ref|YP_005921059.1| 1166 AVTPDGRKAVSSSFDQTLKVWDLETGEIVAT 1196
                                        459***********************99843 PP

>> HIRA_B  HIRA B motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.37   3.9e+02       4      12 ..     661     669 ..     660     670 .. 0.91
   2 ?    1.5   0.0      0.26   2.8e+02       4      12 ..     745     753 ..     743     755 .. 0.89
   3 ?   -0.1   0.0      0.87   9.2e+02       4      12 ..     871     879 ..     870     879 .. 0.91
   4 ?   -3.2   0.0       7.9   8.3e+03       7      12 ..     958     963 ..     957     963 .. 0.92
   5 ?    1.5   0.0      0.26   2.8e+02       4      12 ..     997    1005 ..     995    1007 .. 0.89
   6 ?    1.0   0.0      0.37   3.9e+02       4      12 ..    1081    1089 ..    1080    1090 .. 0.91
   7 ?    1.4   0.0      0.28   2.9e+02       4      12 ..    1165    1173 ..    1164    1175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.37
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG++
  gi|386002760|ref|YP_005921059.1| 661 VAVTPDGRR 669
                                       789*****9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                            HIRA_B   4 vTitKdGKK 12 
                                       v +t+dG++
  gi|386002760|ref|YP_005921059.1| 745 VAVTPDGRR 753
                                       88******9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.87
                            HIRA_B   4 vTitKdGKK 12 
                                       vT t+dG++
  gi|386002760|ref|YP_005921059.1| 871 VTLTPDGRR 879
                                       899*****9 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 7.9
                            HIRA_B   7 tKdGKK 12 
                                       t+dG++
  gi|386002760|ref|YP_005921059.1| 958 TPDGRR 963
                                       89***9 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.26
                            HIRA_B    4 vTitKdGKK 12  
                                        v +t+dG++
  gi|386002760|ref|YP_005921059.1|  997 VAVTPDGRR 1005
                                        88******9 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.37
                            HIRA_B    4 vTitKdGKK 12  
                                        v +t+dG++
  gi|386002760|ref|YP_005921059.1| 1081 VAVTPDGRR 1089
                                        789*****9 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.28
                            HIRA_B    4 vTitKdGKK 12  
                                        v +t+dG+K
  gi|386002760|ref|YP_005921059.1| 1165 VAVTPDGRK 1173
                                        789*****9 PP

>> TIR  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.018      22      72 ..      20      68 ..       4      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      HHHHTTCCTTSEEEESSTT--SSS-HHHHHHHHHHCSSEEEEEE-TTHHHH CS
                               TIR 22 lkellekqkgiklfiddrdlepGeaiadelksaIkkSrrlivvlSknyass 72
                                        +l  ++ g+++ i+  d+ pG + + e+++a ++  r i vlS+ny++ 
  gi|386002760|ref|YP_005921059.1| 20 AWHL--EETGYSTVIQVWDFRPGSNFVLEMDKASRETERTIAVLSPNYLEA 68
                                      5577..899***************************************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.3e-05     0.066      25     107 ..     201     294 ..     171     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                            AAA_16  25 elvllsGesGvGKsslvrellr...alekd....ggif.lrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                         v + G+ G+GKs l+  ++r       +    +gif l+   d  e++     l+q+    +l r l+de+   +
  gi|386002760|ref|YP_005921059.1| 201 KKVGVQGMGGIGKSVLAAVVARddgV---RlafpDGIFwLSIGRDIREAD-----LLQIQ-S-KLARILGDESVFEN 267
                                       667799***************84440...255554455466666666333.....66666.4.89999999999999 PP

                            AAA_16  94 leawrekleeala.............a 107
                                       l++ +ekl+e la             a
  gi|386002760|ref|YP_005921059.1| 268 LNDGKEKLLELLAdkvcllilddvwkA 294
                                       999999999988866666655544440 PP

>> DUF4597  Domain of unknown function (DUF4597)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.4   5.7e+03      22      49 ..     658     685 ..     651     689 .. 0.77
   2 ?   -2.3   0.0       3.7   3.9e+03      22      46 ..     700     724 ..     693     725 .. 0.84
   3 ?    3.1   0.0     0.073        77      15      51 ..     735     771 ..     728     775 .. 0.83
   4 ?   -2.8   0.0       5.2   5.5e+03      22      49 ..     910     937 ..     907     940 .. 0.78
   5 ?   -2.4   0.0       3.9   4.1e+03      26      46 ..     956     976 ..     952     980 .. 0.77
   6 ?    2.7   0.0       0.1   1.1e+02      15      50 ..    1071    1106 ..    1062    1109 .. 0.82
   7 ?   -0.7   0.0       1.2   1.3e+03      22      52 ..    1162    1192 ..    1149    1203 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.4
                           DUF4597  22 vPdiiitPPtPtgmtlpRDsrravwlDe 49 
                                       v  + +tP    ++  + D   +vw  e
  gi|386002760|ref|YP_005921059.1| 658 VRAVAVTPDGRRAVSASGDRTLKVWDLE 685
                                       6667888888888999999888888666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.7
                           DUF4597  22 vPdiiitPPtPtgmtlpRDsrravw 46 
                                       v  + +tP    ++  + Ds   vw
  gi|386002760|ref|YP_005921059.1| 700 VRAVAVTPDGLRAVSASDDSTLRVW 724
                                       6677899999999999999999998 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.073
                           DUF4597  15 LsdkhLdvPdiiitPPtPtgmtlpRDsrravwlDetg 51 
                                       L+    +v  + +tP    ++  +RD   +vw  e g
  gi|386002760|ref|YP_005921059.1| 735 LEGHSNSVSAVAVTPDGRRAVSASRDRTLKVWDLERG 771
                                       555566899999********************77765 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.2
                           DUF4597  22 vPdiiitPPtPtgmtlpRDsrravwlDe 49 
                                       v ++ +tP    ++  + D   +vw  e
  gi|386002760|ref|YP_005921059.1| 910 VNEVAVTPDGLRAVSASDDQTLKVWDLE 937
                                       5577888888888899999999998655 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 3.9
                           DUF4597  26 iitPPtPtgmtlpRDsrravw 46 
                                        +tP     +  +RD   +vw
  gi|386002760|ref|YP_005921059.1| 956 ALTPDGRRVVSASRDKTLKVW 976
                                       567777778999999999999 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.1
                           DUF4597   15 LsdkhLdvPdiiitPPtPtgmtlpRDsrravwlDet 50  
                                        L     +v  + +tP    ++  +RD   +vw  e 
  gi|386002760|ref|YP_005921059.1| 1071 LKGHSNSVRAVAVTPDGRRAVSASRDRTLKVWDLER 1106
                                        555666888999********************7665 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 1.2
                           DUF4597   22 vPdiiitPPtPtgmtlpRDsrravwlDetgs 52  
                                        v  + +tP    ++  + D   +vw  etg 
  gi|386002760|ref|YP_005921059.1| 1162 VRAVAVTPDGRKAVSSSFDQTLKVWDLETGE 1192
                                        56678999999999***********999985 PP

>> UN_NPL4  Nuclear pore localisation protein NPL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.084        88      48      75 ..     831     858 ..     794     863 .. 0.72
   2 ?    1.9   0.0      0.31   3.3e+02      54      75 ..     879     900 ..     871     905 .. 0.85
   3 ?    1.6   0.0      0.37   3.9e+02      55      75 ..     922     942 ..     917     947 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.084
                                       SSTTCGCCCSSSSSSCCCTCH--TT-EE CS
                           UN_NPL4  48 lernkttelvssssksvkevglkhGdml 75 
                                          n  + + +s+++++k   lk G+ml
  gi|386002760|ref|YP_005921059.1| 831 VTPNGLRAVSASGDQTLKVWDLKSGEML 858
                                       5568888999*****************9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.31
                                       CCCSSSSSSCCCTCH--TT-EE CS
                           UN_NPL4  54 telvssssksvkevglkhGdml 75 
                                       + + +s+++++k   l++G+ml
  gi|386002760|ref|YP_005921059.1| 879 RAVSASDDQTLKVWDLERGEML 900
                                       56889****************9 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.37
                                       CCSSSSSSCCCTCH--TT-EE CS
                           UN_NPL4  55 elvssssksvkevglkhGdml 75 
                                        + +s+++++k   l++G+ml
  gi|386002760|ref|YP_005921059.1| 922 AVSASDDQTLKVWDLERGEML 942
                                       5789****************9 PP

>> RVT_thumb  Reverse transcriptase thumb domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.42   4.4e+02      19      39 ..     547     565 ..     543     578 .. 0.77
   2 ?    5.2   0.0     0.017        18      26      64 ..     632     670 ..     616     672 .. 0.87
   3 ?   -2.5   0.0       4.4   4.6e+03      43      64 ..     733     754 ..     732     755 .. 0.89
   4 ?   -1.3   0.0       1.9     2e+03      43      64 ..     859     880 ..     846     882 .. 0.86
   5 ?   -1.7   0.0       2.5   2.6e+03      43      64 ..     985    1006 ..     984    1008 .. 0.85
   6 ?   -3.5   0.0       9.3   9.8e+03      43      61 ..    1027    1045 ..    1026    1048 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.42
                                       HHHHHHHHHTTTS..TT---H CS
                         RVT_thumb  19 kLlgdiNWirpllklttaelk 39 
                                        +l d NWir  l   t +++
  gi|386002760|ref|YP_005921059.1| 547 NILLDFNWIRAKL--ETTDVS 565
                                       678899****877..555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                                       HHTTTS..TT---HHHHHTTTSSSSTTSBE--SHHHHHH CS
                         RVT_thumb  26 WirpllklttaelkpLfklLrGdsdltspreLTeeAeea 64 
                                       Wirp+    t    pL ++L+G sd  + +  T+ ++ a
  gi|386002760|ref|YP_005921059.1| 632 WIRPMTPNLTPPGGPLLRILKGHSDSVRAVAVTPDGRRA 670
                                       99999866666678********************99887 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.4
                                       HTTTSSSSTTSBE--SHHHHHH CS
                         RVT_thumb  43 klLrGdsdltspreLTeeAeea 64 
                                       ++L+G s+  s +  T+ ++ a
  gi|386002760|ref|YP_005921059.1| 733 RTLEGHSNSVSAVAVTPDGRRA 754
                                       689**************99876 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.9
                                       HTTTSSSSTTSBE--SHHHHHH CS
                         RVT_thumb  43 klLrGdsdltspreLTeeAeea 64 
                                        +L+G s     ++LT+ ++ a
  gi|386002760|ref|YP_005921059.1| 859 LTLKGHSSWVNAVTLTPDGRRA 880
                                       5799*************99987 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 2.5
                                        HTTTSSSSTTSBE--SHHHHHH CS
                         RVT_thumb   43 klLrGdsdltspreLTeeAeea 64  
                                        ++L+G s+  s +  T+ ++ a
  gi|386002760|ref|YP_005921059.1|  985 RTLKGHSNWVSAVAVTPDGRRA 1006
                                        5799999999999999999876 PP

  == domain 6  score: -3.5 bits;  conditional E-value: 9.3
                                        HTTTSSSSTTSBE--SHHH CS
                         RVT_thumb   43 klLrGdsdltspreLTeeA 61  
                                        ++L+G sd  s +  T+ +
  gi|386002760|ref|YP_005921059.1| 1027 RTLKGHSDSVSAVAVTPDG 1045
                                        589*********9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.97u 0.34s 00:00:01.31 Elapsed: 00:00:00.51
# Mc/sec: 7281.01
//
Query:       gi|386002761|ref|YP_005921060.1|  [L=117]
Description: hypothetical protein Mhar_2081 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-05   24.3   0.1      6e-05   23.6   0.1    1.3  1  DUF488    Protein of unknown function, DUF488


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   3.4e-09     6e-05      52     121 ..      48     114 ..      39     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-09
                            DUF488  52 elgpsrelrkwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                        l+p+ +l  ++k+   +++e  +rY+ e++sk    ++   + + + +  +Llc e+    chr+++ae+
  gi|386002761|ref|YP_005921060.1|  48 PLAPPWRLLAAAKSGAiDEDEYIRRYRSEVLSKL---DHAT-VYADLGEDAILLCWERAGAFCHRRLVAEW 114
                                       589999999999988889*************952...3333.3333444589******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 893.25
//
Query:       gi|386002762|ref|YP_005921061.1|  [L=795]
Description: DNA gyrase subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete 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-159  531.3   0.0   2.2e-159  531.0   0.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    3.7e-68  224.8  15.7    7.1e-16   57.4   0.3    6.4  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
      0.057   14.2   2.1        0.2   12.5   1.5    2.3  1  FliT           Flagellar protein FliT


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.0   0.0  3.6e-163  2.2e-159       1     425 [.      27     464 ..      27     465 .. 0.99

  Alignments for each domain:
  == domain 1  score: 531.0 bits;  conditional E-value: 3.6e-163
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       Ra+P+vrDGlKPv+RriLyam+++ +++d+++kK+a++vG+v+gkYhPHGda++y+++vr+aqdf++++pl+d+qGn
  gi|386002762|ref|YP_005921061.1|  27 RALPDVRDGLKPVHRRILYAMYEQgMTHDQPYKKSARVVGDVMGKYHPHGDAAIYETMVRMAQDFSMRYPLIDGQGN 103
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGsi dgd++Aa+RY+e+rLs+ia e+l++i+k+tvd+++nyD+s kEP+vlp+++PnlLvnG++GIavGmat++pp
  gi|386002762|ref|YP_005921061.1| 104 FGSI-DGDPAAAMRYTEVRLSEIAGEMLTDIEKDTVDFVPNYDDSLKEPTVLPSKLPNLLVNGSSGIAVGMATNVPP 179
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie..e.ktivitEl 224
                                       hnl+e+   + +l++++++   +l+e  +gPdfptgg i+g+++i+ ay tgrG ik+rak  ie  +  +iv+tEl
  gi|386002762|ref|YP_005921061.1| 180 HNLSEVAGGITRLIDDPDStleDLMEELPGPDFPTGGYILGSSGIEAAYATGRGIIKLRAKSVIErgDrPKIVVTEL 256
                                       *****************999999**************************************999998669******* PP

                     DNA_topoisoIV 225 Pigvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkk 299
                                       P++vn++k++e i++l+k+++++ isd+rdesdr g+r+v+el++g+++e+v+++l+++t+Le+s+s+ n+vl+d++
  gi|386002762|ref|YP_005921061.1| 257 PYQVNKAKVVETIADLIKADRVDgISDLRDESDReGIRLVVELRSGVNPEVVINQLHRQTQLETSYSIINVVLVDGQ 333
                                       *******************************9999****************************************** PP

                     DNA_topoisoIV 300 pkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lse 374
                                       p +l l++ilk+++++r ev+err++y+l+++e+r++il gll+al kidevi++ir+ ++ ++a+++L e   lse
  gi|386002762|ref|YP_005921061.1| 334 PATLPLRDILKQYVSHRAEVIERRTSYDLDRAEKRAHILAGLLIALGKIDEVIKLIRAAESPSEARAALTEAfgLSE 410
                                       ***************************************************************************** PP

                     DNA_topoisoIV 375 eqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                       eq +++l+mrl+rLt++e+ k+++e  +le  i++++++la+   + ++ik+el
  gi|386002762|ref|YP_005921061.1| 411 EQTKAILDMRLQRLTALEQGKIRSEEMDLEVAIARFREILADpreILNIIKQEL 464
                                       *****************************************9988888888887 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   3.1e-15   1.8e-11       4      46 ..     499     541 ..     497     543 .. 0.96
   2 !   19.0   0.0   1.2e-07   0.00074       1      48 []     546     596 ..     546     596 .. 0.97
   3 !   24.2   0.2   2.7e-09   1.6e-05       3      46 ..     604     644 ..     602     646 .. 0.93
   4 !   51.6   0.2   7.9e-18   4.7e-14       1      47 [.     649     695 ..     649     696 .. 0.97
   5 !   35.9   0.1   6.5e-13   3.9e-09       2      42 ..     700     740 ..     699     741 .. 0.92
   6 !   57.4   0.3   1.2e-19   7.1e-16       1      48 []     748     795 .]     748     795 .] 0.97

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 3.1e-15
                                       EEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                     DNA_gyraseA_C   4 lliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                       ++iTs Gy+kr pls +++q+Rg++Gv+g ++k +d+++++++
  gi|386002762|ref|YP_005921061.1| 499 VTITSDGYIKRQPLSAYRQQRRGGMGVMGADTKSEDFVTDLFI 541
                                       79*************************************9997 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.2e-07
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvlvvs 48 
                                       +++l++T+ G++ ++++ ++p+ gR+a+G+ ++    l+ ++k++ +++v+
  gi|386002762|ref|YP_005921061.1| 546 EYILFFTDMGKAHWLRVFDVPSFGRTARGKSIVnllSLEADEKITEAIPVK 596
                                       69********************************************99985 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 2.7e-09
                                       EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                     DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                       ++++Ts G+v+++p+  +++ ++g  G+k+++l  gd+lv++ +
  gi|386002762|ref|YP_005921061.1| 604 IVMATSLGQVVKTPIRAYSNPRKG--GIKAVNL-RGDRLVAARL 644
                                       89**********************..*******.7899999986 PP

  == domain 4  score: 51.6 bits;  conditional E-value: 7.9e-18
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       ++l+l+T  G+++rf++ ++++++Rg++Gv+gi+l+ +d+++s+ vv
  gi|386002762|ref|YP_005921061.1| 649 QDLILATAGGKAIRFSEGDVRPSNRGSMGVRGITLEGDDEVISMDVV 695
                                       589******************************************99 PP

  == domain 5  score: 35.9 bits;  conditional E-value: 6.5e-13
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklv 42 
                                        ll++T++Gy+kr+ lse+++ +Rg+kG k i+ ++gd + 
  gi|386002762|ref|YP_005921061.1| 700 SLLTVTRQGYGKRTELSEYSPHRRGGKGMKNIDSRKGDVVA 740
                                       59******************************998888775 PP

  == domain 6  score: 57.4 bits;  conditional E-value: 1.2e-19
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       del++ T+ G ++r+p+s+++ qgR+++Gv++++lk gd++ +v+ ++
  gi|386002762|ref|YP_005921061.1| 748 DELMITTKDGVMIRIPASDIRIQGRATQGVRIMRLKAGDEVAAVARIN 795
                                       89******************************************9886 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.5   3.3e-05       0.2      19      79 ..     419     478 ..     411     482 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHCS--ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHH CS
                              FliT  19 erqqlverlreldaaplspaereekrellrrilandaeirallqprldelqkllgalrrqr 79 
                                        r q + +l++    + ++ + e   + +r+ila+ +ei ++++++l+el  ++g++rr++
  gi|386002762|ref|YP_005921061.1| 419 MRLQRLTALEQGK-IRSEEMDLEVAIARFREILADPREILNIIKQELAELVGKYGDGRRTQ 478
                                       4555555555555.7777788888899999****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 4536.81
//
Query:       gi|386002763|ref|YP_005921062.1|  [L=640]
Description: DNA gyrase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-62  208.4   0.2    7.7e-62  207.8   0.2    1.3  1  DNA_gyraseB    DNA gyrase B
    3.4e-32  110.4   0.7    7.6e-32  109.3   0.7    1.6  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    9.4e-22   77.6   0.0    2.2e-21   76.5   0.0    1.7  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    7.6e-19   67.8   0.0    2.2e-18   66.4   0.0    1.8  1  Toprim         Toprim domain
      0.004   17.0   0.0     0.0094   15.8   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.8   0.2   2.2e-65   7.7e-62       1     173 [.     230     398 ..     230     399 .. 0.99

  Alignments for each domain:
  == domain 1  score: 207.8 bits;  conditional E-value: 2.2e-65
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       G+ +fve+lnk+k+ l++ ++++++ek  +    vevalq++++y+en+lsF+Nni+t+eGGtH++gf++altkt n
  gi|386002763|ref|YP_005921062.1| 230 GIVSFVEHLNKNKDILHSPPIYFNREK--DG-TSVEVALQYNNTYNENVLSFANNINTREGGTHLAGFRAALTKTTN 303
                                       89*************************..77.9******************************************** PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       eya+ +kllk++  k++g+d+regl+av+sv++++pqFeGQTK+kLgns+v +iv+++vse l++f+een+ +  ki
  gi|386002763|ref|YP_005921062.1| 304 EYARANKLLKDDT-KLTGDDLREGLVAVISVRLADPQFEGQTKTKLGNSAVGGIVSSLVSEGLSEFFEENPLVTVKI 379
                                       ***********98.*************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       +eka +a++ar aarkare
  gi|386002763|ref|YP_005921062.1| 380 VEKATQAYRARVAARKARE 398
                                       *****************98 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.7   2.1e-35   7.6e-32       2      63 .]     568     629 ..     567     629 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 2.1e-35
                     DNA_gyraseB_C   2 kkveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                       +k+++qR+KGLGEmnpeqLweTTmdpe+R++l+vt+eda+eade+fs+LmG+kvepRrefie
  gi|386002763|ref|YP_005921062.1| 568 GKATVQRYKGLGEMNPEQLWETTMDPERRTMLKVTLEDAMEADEIFSILMGEKVEPRREFIE 629
                                       5889*********************************************************8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0     6e-25   2.2e-21       4     111 ..      44     184 ..      41     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 6e-25
                                       HHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTTCHH CS
                         HATPase_c   4 krLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekfsqd 64 
                                        +L++++ ++vdN++++  a+ ++ei + ++    d + sv+D+G+Gip+++++              + ++kf+  
  gi|386002763|ref|YP_005921062.1|  44 AGLHHLVYEVVDNSIDEamAGRCSEINLVLH--A-DGTASVRDDGRGIPVDIHEhykkpaleivmtklHAGGKFDH- 116
                                       68***************65559999999999..5.99*****************************555555****. PP

                                       CSTCHTSTSSSHHHHHHHHHHHHTTTEEEE..................EEET.....TTEEEEEEEEESS CS
                         HATPase_c  65 dstkrggggtGlGlsivkklvelmgGeiwv..................esep.....grGttftftlple 111
                                       +s+k++gg +G+G+s+v++l+e m+ e+++                  e        + Gtt++f+++ e
  gi|386002763|ref|YP_005921062.1| 117 KSYKVSGGLHGVGVSVVNALSEWMEVEVRRnnlvywqryergrpvsdlE--VhgvsdHTGTTVRFKPDPE 184
                                       **************************99999999999888777665440..14444577*******9986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0     6e-22   2.2e-18       1     102 [.     427     538 ..     427     539 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 6e-22
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       el+ivEg+s+ +++++ +++ fqa+++++G+il++e  +++++++  ei++++++l++     ++  + r+ +++++
  gi|386002763|ref|YP_005921062.1| 427 ELYIVEGESAGGSAKQGRNRHFQAILPLRGKILNVERaRLDKILKnnEIRNIITALGTgigddFQLDRARYRKVVIM 503
                                       69***********************************988888889999999999999******************* PP

                                       CSSSHHHHHHHHHHHHHHTHHHTT..TEEEEEESS CS
                            Toprim  70 tDpDreGeaiawellevlkellen..kigrvefse 102
                                       tD+D++G++i+++ll++++++ ++  + g+v++++
  gi|386002763|ref|YP_005921062.1| 504 TDADVDGSHIRTLLLTFFYRYMRElvEAGYVYIAQ 538
                                       *******************5555544448888876 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 !   15.8   0.0   2.6e-06    0.0094       7      48 ..      50      91 ..      45     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                       HATPase_c_3  7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmsee 48
                                      + e+vdNs+d    +++ +++++++ +    g+ +++DdG G++ +
  gi|386002763|ref|YP_005921062.1| 50 VYEVVDNSIDeamaGRCSEINLVLHAD----GTASVRDDGRGIPVD 91
                                      88********97766677799999986....69**********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3800.92
//
Query:       gi|386002764|ref|YP_005921063.1|  [L=134]
Description: hypothetical protein Mhar_2084 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-19   69.4   0.0    2.7e-19   68.9   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    1.3e-12   47.3   2.2    2.3e-12   46.5   2.2    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.049   13.0   0.8          2    7.8   0.0    2.3  2  zf-TFIIB       Transcription factor zinc-finger
       0.06   13.2   0.1      0.076   12.9   0.1    1.1  1  FdhE           Protein involved in formate dehydrogenase form
       0.12   12.0   0.4       0.17   11.6   0.4    1.2  1  TackOD1        Thaumarchaeal output domain 1
       0.68   10.1   4.7        4.8    7.4   4.0    2.4  3  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   9.2e-23   2.7e-19       5      65 .]      51     110 ..      48     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 9.2e-23
                                       -GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   5 sgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                        grGtv+++t+++ a + f+ ++Py ++++eL+eg+r+++++ +++++ ++iGmrV+ vfr
  gi|386002764|ref|YP_005921063.1|  51 DGRGTVVTYTTIYNATDDFKRQTPYNLAIIELEEGPRLTGQVICAPEE-IEIGMRVKPVFR 110
                                       79*****************************************88765.77********97 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   2.2   7.8e-16   2.3e-12       1      34 [.       9      42 ..       9      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 7.8e-16
                           DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                      ++  +++ Lvg++Cp+C+ +++PPr +Cp+C++ 
  gi|386002764|ref|YP_005921063.1|  9 RHIPQRYNLVGTHCPKCDEYYYPPRTICPNCRRA 42
                                      56789**************************654 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.016        48       1       6 [.      21      26 ..      17      27 .. 0.82
   2 ?    7.8   0.0   0.00066         2       2      16 ..      36      52 ..      35      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                          zf-TFIIB  1 kCPkCq 6 
                                      +CPkC 
  gi|386002764|ref|YP_005921063.1| 21 HCPKCD 26
                                      688885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00066
                          zf-TFIIB  2 CPkCq.d.eleesergg 16
                                      CP+C+ +  +e+++++g
  gi|386002764|ref|YP_005921063.1| 36 CPNCRrAaKMEDYKFDG 52
                                      ****8344699999976 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.5e-05     0.076     195     230 ..      20      55 ..       6      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                       EEETTT--EEE--TTS-TTT---SS-EEE------C CS
                              FdhE 195 lhCslCeteWhvvRvkCsnCeetkelaylsledeka 230
                                        hC  C   +   R++C nC  +++++  +++++  
  gi|386002764|ref|YP_005921063.1|  20 THCPKCDEYYYPPRTICPNCRRAAKMEDYKFDGRGT 55 
                                       59************************9999998765 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   5.6e-05      0.17      75      95 ..      21      41 ..      13      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                           TackOD1 75 lCpsCksghlnvrevCpkCkS 95
                                      +Cp+C+ +    r +Cp+C+ 
  gi|386002764|ref|YP_005921063.1| 21 HCPKCDEYYYPPRTICPNCRR 41
                                      7******************85 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.0    0.0016       4.8       9      39 ..      13      39 ..      11      40 .. 0.79
   2 ?    2.7   0.4     0.047   1.4e+02      16      22 ..      34      41 ..      33      53 .. 0.68
   3 ?   -3.0   0.0         3   8.9e+03      31      36 ..      89      94 ..      85      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0016
                     Auto_anti-p27  9 kGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                      + + + +++Cp+C           +++C++C
  gi|386002764|ref|YP_005921063.1| 13 QRYNLVGTHCPKCDEYYYPP----RTICPNC 39
                                      568899*******8777763....5689888 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.047
                     Auto_anti-p27 16 etCpvC.g 22
                                      + Cp+C  
  gi|386002764|ref|YP_005921063.1| 34 TICPNCrR 41
                                      46888855 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3
                     Auto_anti-p27 31 ggkvyC 36
                                      +g+v+C
  gi|386002764|ref|YP_005921063.1| 89 TGQVIC 94
                                      478888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 874.82
//
Query:       gi|386002765|ref|YP_005921064.1|  [L=387]
Description: Thiolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-27   95.3   0.0    5.9e-27   94.7   0.0    1.3  1  Thiolase_N       Thiolase, N-terminal domain
    5.2e-12   45.5   0.2    1.5e-11   44.0   0.2    1.8  1  Thiolase_C       Thiolase, C-terminal domain
      7e-07   29.1   8.4    5.9e-06   26.0   3.6    3.5  4  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.013   15.5   0.3       0.97    9.5   0.0    2.5  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
      0.056   13.3   2.2        2.7    7.9   0.0    2.6  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   1.6e-30   5.9e-27       1     258 [.       4     224 ..       4     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.6e-30
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-T. CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipe. 74 
                                       v i++a  t +g+      d s ++L  e++ ++le+ +v+ ee+d ++vGn+  + + +q  i   ++  ag+++ 
  gi|386002765|ref|YP_005921064.1|   4 VSIIGAGCTRFGE----RWDDSLRDLVVETGIRALEDGNVSGEEIDGLYVGNMSGGrFVEQEhIGALISDCAGLSRl 76 
                                       6799999999999....88999********************************99988888688888888999865 PP

                                       TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT.TGGSSSSEEEEEHHHHHHTEETT CS
                        Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr.sglklgdekakdllipdgladaf 150
                                       +vp+++v+ +c+Sg  a+ +++ ++a+g +dvv+a GvE+m++++  +++d+  + +  + e   + + p       
  gi|386002765|ref|YP_005921064.1|  77 HVPSTRVEAACASGGLALRQGILAVASGYSDVVIAAGVEKMTDVTGGVAADALaAAADREWECFFGATFPA------ 147
                                       8*********************************************9998876244455556677778777...... PP

                                       TTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHH CS
                        Thiolase_N 151 neehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLa 227
                                            ++ a+   ++y+ +Re+++++Avk+h++++ ++ ++ ++ ei              + d+ ++s+++a++L+
  gi|386002765|ref|YP_005921064.1| 148 ---LYAMIARLHMHRYATTREDLAAVAVKNHHHGSMNPISQ-YQMEI--------------TVDKVLNSPLVADPLR 206
                                       ...889***********************************.*****..............899************* PP

                                       TS-BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                        Thiolase_N 228 klkpaFkkeGtvtAgnasqisDGaaavllms 258
                                        l             ++s+i+DGaaav+l++
  gi|386002765|ref|YP_005921064.1| 207 VL-------------DCSPITDGAAAVVLAP 224
                                       **.............*************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.2   4.1e-15   1.5e-11      23     109 ..     261     365 ..     237     385 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.1e-15
                                       HHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B- CS
                        Thiolase_C  23 gPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHP 81 
                                       + ++a++++   agl+ ed+dl E+++AF+   ++++++l++                      +N  GG  a GHP
  gi|386002765|ref|YP_005921064.1| 261 ASVFAARRAFRMAGLEPEDVDLAEVHDAFTIGEIVAIEDLGFFDkgdggratregltaiggeIPINTSGGLKACGHP 337
                                       56899************************************9878***************9878************* PP

                                       TTTHHHHHHHHHHHHHHHCTTSEEEEEE CS
                        Thiolase_C  82 lGasGaRivvtllselkkeggklgvaal 109
                                       +Ga+G +++  ++ +l+ e g+  v  +
  gi|386002765|ref|YP_005921064.1| 338 VGATGIKQAYEMVLQLRGEAGERQVEGA 365
                                       ****************998877766554 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.029     1e+02      89     129 ..      23      63 ..      14      71 .. 0.82
   2 !   26.0   3.6   1.6e-09   5.9e-06     164     222 ..      76     134 ..      63     143 .. 0.88
   3 ?   -1.3   0.0      0.37   1.3e+03     239     253 .]     214     228 ..     210     228 .. 0.90
   4 ?   -0.6   0.0      0.22     8e+02      95     114 ..     265     284 ..     258     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHH CS
                     ketoacyl-synt  89 qrllleaawealedagltpeeldgsrvgvfiGvgagdyaal 129
                                         l++e+  +aled +++ ee+dg  vg++ G    +++++
  gi|386002765|ref|YP_005921064.1|  23 RDLVVETGIRALEDGNVSGEEIDGLYVGNMSGGRFVEQEHI 63 
                                       568999*****************999999999877666555 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.6e-09
                                       --SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-T CS
                     ketoacyl-synt 164 lrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllsp 222
                                       l+ ps  v++AC+S+  a+ + + ++ sg +dv++a Gve ++   + ++ +a+++ ++
  gi|386002765|ref|YP_005921064.1|  76 LHVPSTRVEAACASGGLALRQGILAVASGYSDVVIAAGVEKMTDVTGGVAADALAAAAD 134
                                       66799****************************************99999999986554 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.37
                                       B-EEEEEEEEECHHH CS
                     ketoacyl-synt 239 GEGvGavvLkrleda 253
                                       ++G++avvL + e+a
  gi|386002765|ref|YP_005921064.1| 214 TDGAAAVVLAPTEEA 228
                                       79********99987 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.22
                                       HHHHHHHHHTS-HHTCTTGG CS
                     ketoacyl-synt  95 aawealedagltpeeldgsr 114
                                       aa++a++ agl+pe++d  +
  gi|386002765|ref|YP_005921064.1| 265 AARRAFRMAGLEPEDVDLAE 284
                                       8999*********9997665 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00027      0.97      24      52 ..     260     288 ..     238     292 .. 0.84
   2 ?    3.4   0.1     0.021        74      87     108 ..     334     355 ..     329     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C  24 eaqaraiekalaeagvdpedvdyveahgt 52 
                                       +a   a ++a+++ag++pedvd+ e h++
  gi|386002765|ref|YP_005921064.1| 260 DASVFAARRAFRMAGLEPEDVDLAEVHDA 288
                                       45566899*******************86 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                                       H-B-GGGHHHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkh 108
                                        GH  +A G+ ++  +vl+l+ 
  gi|386002765|ref|YP_005921064.1| 334 CGHPVGATGIKQAYEMVLQLRG 355
                                       7******************985 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.2     0.016        56       3      40 ..      83     120 ..      82     133 .. 0.89
   2 ?    7.9   0.0   0.00076       2.7      52      68 ..     213     229 ..     198     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.016
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGC CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlski 40 
                                       ++aaC++   al +   +++sg    v+  g e+++++
  gi|386002765|ref|YP_005921064.1|  83 VEAACASGGLALRQGILAVASGYSDVVIAAGVEKMTDV 120
                                       689*******************8888888888998875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00076
                                       B-EEEEEEEEEEESSSS CS
                       ACP_syn_III  52 fGDGAgAvvleaseeeg 68 
                                         DGA+Avvl ++ee +
  gi|386002765|ref|YP_005921064.1| 213 ITDGAAAVVLAPTEEAK 229
                                       67**********95543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2475.64
//
Query:       gi|386002766|ref|YP_005921065.1|  [L=345]
Description: Hydroxymethylglutaryl-CoA synthase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-09   37.8   0.0    2.8e-09   37.0   0.0    1.4  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    0.00013   21.7   0.0     0.0041   16.8   0.0    2.2  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
     0.0022   17.4   0.1     0.0034   16.8   0.1    1.2  1  Thiolase_N      Thiolase, N-terminal domain
  ------ inclusion threshold ------
      0.093   12.6   0.0       0.15   11.9   0.0    1.2  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   6.3e-13   2.8e-09       3      86 ..     220     303 ..     218     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 6.3e-13
                                       HTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB-..-THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEE CS
                     ACP_syn_III_C   3 kagltpedidalvphqanlriidavakklglpeekvv..vnldeyGntsaasiplaLdeaveegklkpgdlvllvgf 77 
                                       k g  ped d+ v+hq n ++   va klg+++e++     +  +Gnt + s+++ L+  ++    +pg+++ l++f
  gi|386002766|ref|YP_005921065.1| 220 KMGTIPEDYDYAVFHQPNGKFPARVASKLGFSAEQIEpgLVVPWIGNTYSGSSLIGLAATLD--VARPGERIFLASF 294
                                       567779****************************875115569*******************..99*********** PP

                                       ETTTEEEEE CS
                     ACP_syn_III_C  78 GaGltwgaa 86 
                                       G G    a 
  gi|386002766|ref|YP_005921065.1| 295 GSGAGSDAF 303
                                       ***876665 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        62      65      87 ..     223     245 ..     204     256 .. 0.67
   2 !   16.8   0.0   9.2e-07    0.0041     141     207 ..     252     313 ..     244     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                       --GGG-SEEEE--SSHHHHHHHH CS
                    HMG_CoA_synt_C  65 ftlddfdyvifhsPfcklvqksl 87 
                                       +  +d+dy +fh P  k+  +  
  gi|386002766|ref|YP_005921065.1| 223 TIPEDYDYAVFHQPNGKFPARVA 245
                                       33479*********999866555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.2e-07
                                       HHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--ST CS
                    HMG_CoA_synt_C 141 kkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvse 207
                                        ++++p l+vp  +Gn Y  s    la+ l    +    g+ri l s+GsG  +  fs+rv++  +e
  gi|386002766|ref|YP_005921065.1| 252 AEQIEPGLVVP-WIGNTYSGSSLIGLAATL----DVARPGERIFLASFGSGAGSDAFSIRVEEGIEE 313
                                       56788888888.59****************....334469*********************998776 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   7.6e-07    0.0034      20     113 ..      47     140 ..      37     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.6e-07
                                       TS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHH CS
                        Thiolase_N  20 dlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaa 96 
                                       d  a+ ++ ea+++++ +a++dp  +  ++ G   +  + +     +  ++g+ ++ +a   + +c  g +av ++ 
  gi|386002766|ref|YP_005921065.1|  47 DEDAVTMAVEAARNAVRRASIDPFRIGAIYAGSESHPYAVKPTGTIVGEALGVDHQLTAADFEFACKAGTAAVQACL 123
                                       556888999****************************999999999******************************* PP

                                       HHHHTTSHSEEEEEEEE CS
                        Thiolase_N  97 qsiaageadvvvagGvE 113
                                       + +a + +d  +a+G+ 
  gi|386002766|ref|YP_005921065.1| 124 GLVAGKLIDLGLAIGTD 140
                                       ***************86 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.3e-05      0.15       6     171 ..       4     165 ..       2     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                    HMG_CoA_synt_N   6 gilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgt 82 
                                       gi++  +y+p   ++  e+ +  g e+   + gl   + +  +  ed  ++++   ++ ++r ++d   ig +  g+
  gi|386002766|ref|YP_005921065.1|   4 GIVSYGVYVPRYRIKAEEIARVWG-EREDMAKGLNVFEKSVPDTDEDAVTMAVEAARNAVRRASIDPFRIGAIYAGS 79 
                                       8999999***99999999999877.5667889********************************************* PP

                    HMG_CoA_synt_N  83 etiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna.rp 158
                                       e+     k   +++ + ++   + ++   d   ac  gtaa+  ++  +  +  d    l +  d +  + g+a   
  gi|386002766|ref|YP_005921065.1|  80 ESHPYAVKPTGTIVGEALGV--DHQLTAADFEFACKAGTAAVQACLGLVAGKLIDLG--LAIGTDTSQGAPGDAlEY 152
                                       *9998888888888888776..788999******************99999999965..556778888888877356 PP

                    HMG_CoA_synt_N 159 tggagavalligp 171
                                       t  aga a +ig 
  gi|386002766|ref|YP_005921065.1| 153 TAAAGAAAYVIGC 165
                                       8889999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 2389.88
//
Query:       gi|386002767|ref|YP_005921066.1|  [L=169]
Description: XRE family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.7   0.0       0.15   12.0   0.0    1.8  2  YAcAr     YspA, cpYpsA-related SLOG family
      0.052   13.9   0.0      0.073   13.4   0.0    1.2  1  DUF5546   Family of unknown function (DUF5546)
      0.091   12.6   0.1        4.4    7.2   0.0    2.3  2  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.62   3.7e+03       4       8 ..      61      65 ..      51      94 .. 0.59
   2 ?   12.0   0.0   2.5e-05      0.15      27      60 ..     122     155 ..     115     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.62
                             YAcAr  4 lvtGg 8 
                                      +v+G 
  gi|386002767|ref|YP_005921066.1| 61 VVCGD 65
                                      34444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.5e-05
                             YAcAr  27 eapidmvlvhGga.kGaDrlAarWAaergvelvrf 60 
                                         p  +v+++G + +G+D  A+r A+ + ++l++ 
  gi|386002767|ref|YP_005921066.1| 122 LKP-GAVILQGIDpSGVDGVARRIAELERIPLLAT 155
                                       557.79**********************9999876 PP

>> DUF5546  Family of unknown function (DUF5546)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.073      84     134 ..      91     144 ..      73     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                           DUF5546  84 hppsaasasqaltvtslshgllpfvgvklta.hpqa..lngrfpsgvgaaarql 134
                                       h     s+++al  t +s g  p+v v+++  +p a  l+g  psgv   ar++
  gi|386002767|ref|YP_005921066.1|  91 HRIYGRSTARALIFTGVSTGRSPMVAVRVSHlKPGAviLQGIDPSGVDGVARRI 144
                                       55566799*******************987435665337999*****9999987 PP

>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        82      25      44 ..       5      24 ..       3      35 .. 0.82
   2 ?    7.2   0.0   0.00073       4.4      38      73 ..     106     141 ..      87     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                      B-TTSEEEES--S--SS-TT CS
                            DUF126 25 siagkiLvlpsgkGStvgsy 44
                                      +i +  L +++ +GS+++ +
  gi|386002767|ref|YP_005921066.1|  5 KIIDALLTIDELRGSCTART 24
                                      5778999*********9764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00073
                                       --SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHH CS
                            DUF126  38 GStvgsyvllelakngtaPaAlilreadpilalGai 73 
                                       G ++g   +++++ ++ +P A+il+ +dp  + G++
  gi|386002767|ref|YP_005921066.1| 106 GVSTGRSPMVAVRVSHLKPGAVILQGIDPSGVDGVA 141
                                       678899999********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1104.40
//
Query:       gi|386002768|ref|YP_005921067.1|  [L=181]
Description: hypothetical protein Mhar_2089 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-51  174.0   3.4      3e-51  173.9   3.4    1.0  1  CarS-like        CDP-archaeol synthase
    4.6e-06   26.6   1.0    4.6e-06   26.6   1.0    1.9  2  CTP_transf_1     Cytidylyltransferase family
  ------ inclusion threshold ------
       0.49   10.2   5.9          2    8.2   2.3    2.3  2  Gly-zipper_YMGG  YMGG-like Gly-zipper


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.9   3.4     5e-55     3e-51       5     175 .]       4     181 .]       1     181 [] 0.92

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 5e-55
                         CarS-like   5 ilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsi.lalds 80 
                                       ++ +i+l+lpay++n++av++GGG+p+d+G+t+ dGrr++GdG+t+rGt+aG+l+Gvl gl+  ++  +   l l  
  gi|386002768|ref|YP_005921067.1|   4 VIIAIWLMLPAYLPNNFAVIFGGGRPLDFGRTFPDGRRILGDGKTFRGTIAGTLAGVLLGLLLHAIAAVRPdLGLPG 80 
                                       5678**************************************************************99988799999 PP

                         CarS-like  81 sgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgallla...yp...vkllpieliiliv 151
                                       +g   e +++ + l++Ga+ Gd+v sf krr+++erG    ++dqldfv+g+ +l+    p      +++e+i +++
  gi|386002768|ref|YP_005921067.1|  81 FGRGFELILVLVGLSLGAMAGDIVASFFKRRMGMERGAALFLVDQLDFVFGSWALTlllAPrwfSESFTAEVIFIVL 157
                                       9999999999999*************************************97665533322433679********** PP

                         CarS-like 152 litlvlhlsaniiayklglkdvwy 175
                                       ++t+vlh  +n++ y++  k+ ++
  gi|386002768|ref|YP_005921067.1| 158 VVTPVLHRVMNVLGYRIKAKKEPW 181
                                       *****************9998877 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   1.0   7.8e-10   4.6e-06     170     231 ..      46     113 ..      39     116 .. 0.92
   2 ?   -0.1   0.3      0.11   6.5e+02      60      85 ..     133     158 ..     118     178 .. 0.45

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.8e-10
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS......---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal......alsllhllllslllslvavfGDLveSglKRafg 231
                                       +KT  G i+G++a v++glll  ++  +           ++l+l+ + lsl a+ GD+v+S +KR++g
  gi|386002768|ref|YP_005921067.1|  46 GKTFRGTIAGTLAGVLLGLLLHAIAAVRPdlglpgFGRGFELILVLVGLSLGAMAGDIVASFFKRRMG 113
                                       6**********************99988889988877778899999999****************998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHTTTSSSHHHHHHHHHH CS
                      CTP_transf_1  60 lvlllllllflylesliallklvlll 85 
                                       ++l+lll   ++ es++a++  ++l+
  gi|386002768|ref|YP_005921067.1| 133 WALTLLLAPRWFSESFTAEVIFIVLV 158
                                       33333333333333332222211111 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.3   0.00033         2       1      20 [.      46      65 ..      46      72 .. 0.88
   2 ?    3.3   0.1     0.012        69       9      28 ..      92     113 ..      89     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00033
                                      ....XXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  1 ggavrGAaiGAaaGAvvGal 20
                                      g++ rG+ +G+ aG ++G l
  gi|386002768|ref|YP_005921067.1| 46 GKTFRGTIAGTLAGVLLGLL 65
                                      5899*************976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXX..XXXXXX CS
                   Gly-zipper_YMGG   9 iGAaaGAvvGaliG..sgggkG 28 
                                       +G  +GA +G+++    +++ G
  gi|386002768|ref|YP_005921067.1|  92 VGLSLGAMAGDIVAsfFKRRMG 113
                                       6778889888888766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1167.77
//
Query:       gi|386002769|ref|YP_005921068.1|  [L=300]
Description: Tetrahydromethanopterin S-methyltransferase, subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete 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-133  443.6  13.6   2.6e-133  443.4  13.6    1.0  1  MtrE      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.061   13.8   0.5      0.061   13.8   0.5    2.0  2  DUF3899   Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> MtrE  Tetrahydromethanopterin S-methyltransferase, subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.4  13.6  2.9e-137  2.6e-133       1     271 []       4     277 ..       4     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 443.4 bits;  conditional E-value: 2.9e-137
                              MtrE   1 lGvlalmgalatiagaaedlesdvgsqsnpnsqvqLapqmgylhrifnkaisGePvaygllaavagavalvllsalk 77 
                                       +G+la+mgalat+aga+edlesdvgsqsnpnsqvqLa+q+g++hri+nkaisGeP++++l+aa+a+++a+vl+s ++
  gi|386002769|ref|YP_005921068.1|   4 MGLLAAMGALATVAGASEDLESDVGSQSNPNSQVQLAAQVGHTHRIYNKAISGEPPSNALYAALAAVTASVLMSGYG 80 
                                       8**************************************************************************** PP

                              MtrE  78 lnvvlaivlgalvaalvhgvyavtaylGriasqakfkqpvyldvlkshlgaivahafiavfaivvlsylmtlvlk.. 152
                                       +n+++ai++g+++aa+++g+++vtay+Gr++sqa+f+q+vyldvl++h++ai+aha+i++f++v++sy+mt+++   
  gi|386002769|ref|YP_005921068.1|  81 MNAFFAIAIGSVMAAIFNGIFSVTAYMGRNTSQARFNQYVYLDVLRTHTTAIMAHAYITAFCVVTISYIMTAPWLpi 157
                                       **********************************************************************9865444 PP

                              MtrE 153 .hpfplpllaliwGitvGaiGsstGdvhyGaereyqkkefGaGvpvaasGdivrkaeaGlrnsidnalfcakfggpl 228
                                        hpfp+pl+a+iwG+++GaiGsstGdvhyG ere+q++ fGaG+++a+sGdiv++aeaGlr+sidn++fca+fggp+
  gi|386002769|ref|YP_005921068.1| 158 qHPFPFPLVAMIWGLAIGAIGSSTGDVHYGGEREFQNYIFGAGLNAANSGDIVTRAEAGLRSSIDNVWFCARFGGPV 234
                                       4**************************************************************************** PP

                              MtrE 229 tGlafglivflelWrtivfekvtagwlavivgliivllliiln 271
                                       tG+afgl+vfl++Wrt++f+++t+gw+av++g++iv+l+i++n
  gi|386002769|ref|YP_005921068.1| 235 TGMAFGLTVFLDNWRTTIFDPATQGWYAVLTGIVIVILFIVYN 277
                                       *****************************************98 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   6.8e-06     0.061       8      43 ..      83     118 ..      79     150 .. 0.86
   2 ?   -2.2   0.4       0.7   6.3e+03      11      21 ..     266     276 ..     260     278 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-06
                           DUF3899   8 glllliigillivlnsGfFdgfsygfrklkklflkk 43 
                                       +++ ++ig ++  + +G+F++++y+ r+  ++++++
  gi|386002769|ref|YP_005921068.1|  83 AFFAIAIGSVMAAIFNGIFSVTAYMGRNTSQARFNQ 118
                                       7899*************************9998876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.7
                           DUF3899  11 lliigillivl 21 
                                        ++i il+iv+
  gi|386002769|ref|YP_005921068.1| 266 GIVIVILFIVY 276
                                       34555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2314.38
//
Query:       gi|386002770|ref|YP_005921069.1|  [L=221]
Description: Tetrahydromethanopterin S-methyltransferase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-96  320.2  22.9    7.9e-96  320.0  22.9    1.1  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.0  22.9  4.4e-100   7.9e-96       4     218 .]       2     207 ..       1     207 [. 0.99

  Alignments for each domain:
  == domain 1  score: 320.0 bits;  conditional E-value: 4.4e-100
                              MtrD   4 lliliviggvligvgvhfvPvGGapaamaqatGvgtGtaqlaaGagltGlltaaalaektdslllillsGavgamlm 80 
                                        +i+ivigg+l+g+gvhfvPvGGapaamaqatGvgtGt+qlaaG+gltGll+a+++++ tds+ll+++sGavgam+m
  gi|386002770|ref|YP_005921069.1|   2 HIIEIVIGGLLVGIGVHFVPVGGAPAAMAQATGVGTGTVQLAAGSGLTGLLSAGLMLNYTDSILLVVISGAVGAMIM 78 
                                       799************************************************************************** PP

                              MtrD  81 laitmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtvsfvsGviGgllgGiGGalvyyallel 157
                                       ++ tm+vgn++y+ygvG++ asak+++dpit+d+q+ yv++Gt G+giPtv+fvsG+iGgllgG+GG+l+yy l+++
  gi|386002770|ref|YP_005921069.1|  79 IDATMIVGNWVYIYGVGTPLASAKANYDPITKDSQAPYVAPGTVGQGIPTVCFVSGTIGGLLGGAGGSLIYYVLYQI 155
                                       ***************************************************************************88 PP

                              MtrD 158 lkaalklaaaaavalaailavglflvnavlasynigGtieGfhdpkfkrlpkavvaslvas 218
                                       ++           +l+a++a+g+f+vnav+asyni+GtieGfhdpkfkr+p+a+  +lvas
  gi|386002770|ref|YP_005921069.1| 156 NR---------DPGLSAFFAIGIFVVNAVIASYNIQGTIEGFHDPKFKRVPRAFQVCLVAS 207
                                       77.........79**********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1585.85
//
Query:       gi|386002771|ref|YP_005921070.1|  [L=267]
Description: Tetrahydromethanopterin S-methyltransferase, subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-99  329.8  29.7      1e-98  329.7  29.7    1.0  1  MtrC      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrC  Tetrahydromethanopterin S-methyltransferase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.7  29.7  5.8e-103     1e-98       1     266 [.       1     264 [.       1     266 [. 0.99

  Alignments for each domain:
  == domain 1  score: 329.7 bits;  conditional E-value: 5.8e-103
                              MtrC   1 msaggggkeaeeaipekkllalgivggligiylasvl....epalgsllaalgaicaivwGadavrrvasYglGTGV 73 
                                       ms+++gg++a+  i+++kl+++g+ gg++giyla+vl    +++++s+la+lg+i+a+v+G+davrrv+sYg+GTGV
  gi|386002771|ref|YP_005921070.1|   1 MSVAAGGGAAK--IDKTKLMMYGLGGGVLGIYLAHVLnevtGTDYFSFLAGLGVIAAVVMGSDAVRRVCSYGIGTGV 75 
                                       89999998886..************************99999999******************************** PP

                              MtrC  74 PSigmlalgmGivaalaglavgsalkllagpiialvvaliiglvvgvlakkvikmkipileksttelaaagalsiig 150
                                       PSig++a+gmG+vaa++gl++g+    +agpii+++v++ +g+vvg+l++k+ikm+ip+le+++++l +aga+++ig
  gi|386002771|ref|YP_005921070.1|  76 PSIGLMAMGMGLVAAMFGLSIGG----VAGPIIGIAVSMGFGYVVGLLTNKIIKMNIPVLEEALMTLGGAGAIVLIG 148
                                       ***********************....99************************************************ PP

                              MtrC 151 lsvaiagsfeikailskviatGliallfilaglailhPfNaclGPdEkqdRTLklalekgalaliivgivsletesa 227
                                       l v+i+g +++++i+++vi+tG+ia++fi+++lailhPfNa+lGPdE+qdRTL++++++gala+++vgi+slet ++
  gi|386002771|ref|YP_005921070.1| 149 LGVMISGVIDYRVIIANVIDTGYIAIVFIIGSLAILHPFNANLGPDETQDRTLVHSVSAGALAMFAVGIASLETIGV 225
                                       ***************************************************************************** PP

                              MtrC 228 aalvviivgliiWlisfkkfvklvkrdaakvkgtgllPk 266
                                       + +v+i+v++++W+++fkkf++lvkrd+a vkgtgllP+
  gi|386002771|ref|YP_005921070.1| 226 EGFVSIFVAAVVWIVFFKKFFDLVKRDSAGVKGTGLLPE 264
                                       **************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1768.52
//
Query:       gi|386002772|ref|YP_005921071.1|  [L=103]
Description: Tetrahydromethanopterin S-methyltransferase, subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-35  119.5   0.0    6.5e-35  119.4   0.0    1.0  1  MtrB      Tetrahydromethanopterin S-methyltransferase subunit
  ------ inclusion threshold ------
      0.031   13.7   1.0       0.19   11.2   1.0    2.0  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   7.3e-39   6.5e-35       7      93 ..      10      96 ..       3      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 7.3e-39
                              MtrB  7 elnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfyGfivg 85
                                      +l+lv+dp  g++ae+r+dv+ + ldp++++id+++k+addlvnsLdp+ +ll+sy+gRe+++++aG++tn++yGfi+g
  gi|386002772|ref|YP_005921071.1| 10 DLHLVFDPLEGMIAEERDDVIQFALDPIMAQIDEINKAADDLVNSLDPRAPLLNSYKGREGASYMAGIYTNIWYGFIIG 88
                                      79***************************************************************************** PP

                              MtrB 86 lviaalla 93
                                      lv+a++ +
  gi|386002772|ref|YP_005921071.1| 89 LVVAFVYL 96
                                      ****9965 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   2.1e-05      0.19      34      55 ..      74      95 ..      29      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                              MtrF 34 dSGvsatgivGfaiGfvlAllL 55
                                       +G+ +   +Gf+iG+v+A++ 
  gi|386002772|ref|YP_005921071.1| 74 MAGIYTNIWYGFIIGLVVAFVY 95
                                      58999999***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 713.97
//
Query:       gi|386002773|ref|YP_005921072.1|  [L=242]
Description: Tetrahydromethanopterin S-methyltransferase, subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-83  279.1   1.5    1.5e-83  278.6   1.5    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.019   14.3   3.5       0.25   10.8   3.5    2.4  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.6   1.5   1.7e-87   1.5e-83       1     173 []       4     176 ..       4     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.6 bits;  conditional E-value: 1.7e-87
                                       -----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE- CS
                              MtrA   1 kkepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGa 77 
                                       kk +++ WP ++G+y vG++espvavvt+gshl++++ ++aG+a+aGp+kten+Giek+van+isnpnirfli+tG+
  gi|386002773|ref|YP_005921072.1|   4 KKPTSDPWPWLTGEYVVGNPESPVAVVTCGSHLNNAPFIDAGSALAGPCKTENIGIEKMVANIISNPNIRFLIITGM 80 
                                       7888999********************************************************************** PP

                                       --TTT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHHHHT--- CS
                              MtrA  78 evkGhitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikelvakdpg 154
                                       evkGhitGqa++a+ +nG+d+e++ivga+GaiPfi+nlt ea+erf++q+ ++++idted+g+i++kike+v+kdpg
  gi|386002773|ref|YP_005921072.1|  81 EVKGHITGQAIEAFAANGIDQEGRIVGATGAIPFIQNLTPEAIERFKQQITTINIIDTEDTGTIVSKIKECVSKDPG 157
                                       ***************************************************************************** PP

                                       --SS-------XXXXXXXX CS
                              MtrA 155 afeeeplvievkeeeeeee 173
                                       a++ ep+ +e++e+e+eee
  gi|386002773|ref|YP_005921072.1| 158 ALDVEPMAVEISEGEAEEE 176
                                       *************999885 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.5   2.8e-05      0.25      30      57 ..     207     234 ..     187     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                              MtrF  30 eqkLdSGvsatgivGfaiGfvlAllLvv 57 
                                       ++k ++G+ a +i G+a+G++++l+L +
  gi|386002773|ref|YP_005921072.1| 207 QNKYSAGIYAGKIEGIAAGLTIVLVLFG 234
                                       6899*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1742.03
//
Query:       gi|386002774|ref|YP_005921073.1|  [L=90]
Description: Tetrahydromethanopterin S-methyltransferase subunit F [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-23   82.3   0.5    1.5e-23   81.9   0.5    1.2  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu
    0.00032   20.5   1.6    0.00046   20.1   1.6    1.2  1  Syndecan  Syndecan domain


Domain annotation for each model (and alignments):
>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.5   1.7e-27   1.5e-23       1      62 []      27      88 ..      27      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.7e-27
                              MtrF  1 gvptvnkpnmkaiksvvedirYraqLiaReqkLdSGvsatgivGfaiGfvlAllLvvlPvll 62
                                      g+ptv +p m++++++++++ YraqL+ R+qkL+SGv+a++ +G ++Gf++A+l+v+lPv++
  gi|386002774|ref|YP_005921073.1| 27 GLPTVLAPFMGPFDQITDSVLYRAQLVVRDQKLSSGVNAAMPIGAVVGFLFAILMVLLPVYI 88
                                      689********************************************************986 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.6   5.1e-08   0.00046       6      34 ..      61      89 ..      58      90 .] 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-08
                          Syndecan  6 pevlaaviggvvvgllfaillvlflvYRm 34
                                      ++v aa+  g+vvg+lfail+vl+ vY m
  gi|386002774|ref|YP_005921073.1| 61 SGVNAAMPIGAVVGFLFAILMVLLPVYIM 89
                                      68999**********************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 618.03
//
Query:       gi|386002775|ref|YP_005921074.1|  [L=74]
Description: Tetrahydromethanopterin S-methyltransferase, subunit G [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-31  106.1   0.9    6.6e-31  106.0   0.9    1.0  1  MtrG      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.9   3.7e-35   6.6e-31       2      64 .]       9      71 ..       8      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 3.7e-35
                              MtrG  2 iPsvvvdpddfnevkkrLdeieekvefvnsEiaqriGkkvGRdiGilYGlviGliillvyill 64
                                      +Psvvvdpd+++ev ++L +i+ek+efv++Eiaqr+Gkk+GRdiG+lYG++ Gli++l+y+ll
  gi|386002775|ref|YP_005921074.1|  9 VPSVVVDPDQYREVLDKLAKIDEKIEFVSAEIAQRQGKKIGRDIGVLYGVCGGLILVLAYYLL 71
                                      8***********************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.32s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 488.77
//
Query:       gi|386002776|ref|YP_005921075.1|  [L=311]
Description: Tetrahydromethanopterin S-methyltransferase, subunit H [Methanosaeta harundinacea 6Ac]
Scores for complete 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-130  434.9   1.8   1.5e-130  434.7   1.8    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.7   1.8  8.4e-135  1.5e-130       1     298 [.       6     300 ..       6     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 434.7 bits;  conditional E-value: 8.4e-135
                              MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGetee 77 
                                       k+q+v+e + +k+GGqpGeyPtv +gt+fy++hkiv++e+kGifd +aae+l+k qee+sd+tGnP ++q+v et+e
  gi|386002776|ref|YP_005921075.1|   6 KKQEVFEFGKIKVGGQPGEYPTVCIGTMFYSRHKIVTNEEKGIFDVAAAEKLWKDQEEMSDTTGNPCFNQIVAETNE 82 
                                       79*************************************************************************** PP

                              MtrH  78 aivkyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmd 154
                                       a+ ky+d+++++ daP+l+ds++  v+  ++kyate+G+adr+i+nsinasi  +e++a+kesd++aaivlafn+ d
  gi|386002776|ref|YP_005921075.1|  83 AMTKYLDWFVEISDAPFLVDSSAPSVRGFGVKYATEIGVADRAIHNSINASITPEEFQAVKESDLDAAIVLAFNALD 159
                                       ***************************************************************************** PP

                              MtrH 155 ptvegklkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdw 231
                                        t++gk+++l++++g+aekg+l+ a+eaGi++plidva++plg+g+ga+++a +avka lGlPvG+g+hn +saWdw
  gi|386002776|ref|YP_005921075.1| 160 STTKGKMDVLTKAAGGAEKGMLDYAAEAGITRPLIDVAAMPLGNGSGATIRAGIAVKALLGLPVGAGYHNGASAWDW 236
                                       ***************************************************************************** PP

                              MtrH 232 lrefkkkekekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgvel 298
                                       ++++kk +k +     + d+g+nlv+ i+g+d+ lyGPiena++vfPa amvdi+ +e akelg+e+
  gi|386002776|ref|YP_005921075.1| 237 MKKYKKVNKAAFP---PVDIGSNLVAGIMGADYYLYGPIENATMVFPAAAMVDIMCAESAKELGLEV 300
                                       *****99988877...99**********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2179.66
//
Query:       gi|386002777|ref|YP_005921076.1|  [L=216]
Description: hypothetical protein Mhar_2098 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.7   0.0    3.5e-12   46.8   0.0    1.5  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.19   11.9   0.0    1.4  1  DUF4287   Domain of unknown function (DUF4287)


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   3.9e-16   3.5e-12       1      74 [.      17     137 ..      17     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 3.9e-16
                          CxxCxxCC   1 eCkeCgaCCk......................elkvklteedlerlkaaevaeeeeeskkiak.............. 41 
                                       +C++Cg CC+                      ++ ++lte+d++ ++++   + +e+  ++++              
  gi|386002777|ref|YP_005921076.1|  17 KCQRCGSCCHhrrprefddlippermaeflekSNLIYLTERDIDAISKKTGLDPQEFVDTLYEdrrgsvmveeggkk 93 
                                       6*****************************999999**********777776666666666666************* PP

                          CxxCxxCC  42 ............adgrCvfldeetklCkiYeeRpkicrlfpasek 74 
                                                    dg Cvf++e  + C+iY  Rp++crlfp++  
  gi|386002777|ref|YP_005921076.1|  94 vildlpvmrsrePDGSCVFFQEG-RGCTIYPVRPTACRLFPFVVV 137
                                       ***********99********99.5*****************833 PP

>> DUF4287  Domain of unknown function (DUF4287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.1e-05      0.19       6      26 ..      59      79 ..      56      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                           DUF4287  6 ldniekkTGktldewlalade 26
                                      +d+i kkTG +++e+++++ e
  gi|386002777|ref|YP_005921076.1| 59 IDAISKKTGLDPQEFVDTLYE 79
                                      799*************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1419.85
//
Query:       gi|386002778|ref|YP_005921077.1|  [L=684]
Description: Putative aminopeptidase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-44  151.3   0.0    3.8e-44  150.7   0.0    1.3  1  Peptidase_S9   Prolyl oligopeptidase family
    4.3e-10   39.6   0.2      8e-09   35.5   0.1    2.4  3  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    5.1e-10   39.3   0.0    3.4e-09   36.6   0.0    2.1  1  DLH            Dienelactone hydrolase family
    2.6e-08   33.4   0.0    2.4e-05   23.7   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    2.3e-05   25.1   5.2    5.6e-05   23.9   4.1    2.2  2  Abhydrolase_6  Alpha/beta hydrolase family
      9e-05   22.2   2.3      0.013   15.1   1.1    2.7  3  Abhydrolase_1  alpha/beta hydrolase fold
    0.00073   19.5   1.3        1.6    8.6   0.2    3.2  3  Abhydrolase_3  alpha/beta hydrolase fold
     0.0023   17.9   0.0     0.0048   16.8   0.0    1.5  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
     0.0028   16.5   0.0      0.083   11.6   0.0    2.6  3  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.026   14.2   0.0    1.5  2  Esterase       Putative esterase
      0.023   13.4   0.4       0.39    9.3   0.4    2.2  1  AXE1           Acetyl xylan esterase (AXE1)
      0.041   13.1   0.0       0.13   11.4   0.0    1.7  1  DUF5050        Domain of unknown function (DUF5050)


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.7   0.0   2.5e-47   3.8e-44       3     211 ..     436     649 ..     434     650 .. 0.90

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 2.5e-47
                                       --HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH CS
                      Peptidase_S9   3 fsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltg 79 
                                       ++   q+la+rGy+v+ +n+rGs+g+G++f ++g+ ++g +  dD+i+a+++++ eg++d++r+ai+GgSyGGy t+
  gi|386002778|ref|YP_005921077.1| 436 YNPAHQWLANRGYAVLSVNFRGSTGFGKDFVNRGNLEWGARMHDDLIDAVDWAVGEGIADPDRVAIMGGSYGGYATL 512
                                       556779*********************************************************************** PP

                                       HHHHH-GGG-SEEEEESE---CCCHHCS......TTS..THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEE CS
                      Peptidase_S9  80 aalnqrpdlFkaavaevpvvdvlrydsd......tdl..lteeymewgnpeeneegykelspyspldnvkaypplLl 148
                                       + l+  p++F+++v  v+ +++++   +      +++  +++++ ++ ++ e +    e+sp++ ++n  +  plL+
  gi|386002778|ref|YP_005921077.1| 513 VGLTFTPEVFACGVDIVGPSNLTSLIETippywqPQIelFATRMGDHRTE-EGRRLLFERSPINRVEN--IARPLLI 586
                                       *********************99976551111114557777777777776.55555569999999999..******* PP

                                       EEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT- CS
                      Peptidase_S9 149 ihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkealgk 211
                                        +G +D rv  +e+ ++v a+q+kg +v ++ +pdegHg+++p+++   +a   aFl e+lg 
  gi|386002778|ref|YP_005921077.1| 587 GQGANDPRVSQNESDQIVGAMQEKGIPVTYVLYPDEGHGFARPENRMSFFAVAEAFLSEHLGG 649
                                       ************************************************************985 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         2   2.9e+03     115     144 ..     260     288 ..     258     347 .. 0.79
   2 !   35.5   0.1   5.4e-12     8e-09      17     138 ..     415     534 ..     392     541 .. 0.80
   3 ?    1.1   0.0      0.17   2.5e+02     217     258 ..     570     612 ..     545     624 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                                       HHHHCTT--TTEEEEEEECE-S-TCCCCSE CS
                     Peptidase_S15 115 qllaaatgvpalkaivpeaaisdlyddyyr 144
                                       + l a+++  ++k++++e + sd+ d ++ 
  gi|386002778|ref|YP_005921077.1| 260 AALFAMNPATGVKTLIAEDPRSDFSD-WMV 288
                                       56778889999999999999988888.654 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 5.4e-12
                                       SSSEEEEE..EEESS-CCT.CCCCHTTCHHCCHGGGHHHHHTT-EEEEEE-TTSTTS-S---TT.....TTTHHHHH CS
                     Peptidase_S15  17 keklPvll..trtPYgkndelasdkalaleelelqdkvfvarGYavVvqdvrGtggSeGeftvg.....dsdeaedg 86 
                                       +e+lP++l  +  P+ ++   ++d   a+++       +++rGYav+ ++ rG+ g   +f+       + +  +d 
  gi|386002778|ref|YP_005921077.1| 415 EEPLPMVLyvHGGPWARD---VWDYNPAHQW-------LANRGYAVLSVNFRGSTGFGKDFVNRgnlewGARMHDDL 481
                                       566776652255677753...5777777765.......8**************8764322222245555999***** PP

                                       HHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-T CS
                     Peptidase_S15  87 advidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdl 138
                                        d++dW++++     ++V+ +G SY+G+  l+ ++  ++  ++ v +++ s+l
  gi|386002778|ref|YP_005921077.1| 482 IDAVDWAVGEgIADPDRVAIMGGSYGGYATLVGLTFTPEVFACGVDIVGPSNL 534
                                       ********************************999999888888877777665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.17
                                       TT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT- CS
                     Peptidase_S15 217 drnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv 258
                                       +r++ ++++++  p+l+ +G nD  v  n++ ++  a++++g+
  gi|386002778|ref|YP_005921077.1| 570 ERSPINRVENIARPLLIGQGANDPRVSqNESDQIVGAMQEKGI 612
                                       7889999****************99998888888888887765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   2.2e-12   3.4e-09      34     196 ..     441     634 ..     414     646 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.2e-12
                               DLH  34 erlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGa 110
                                       ++la+ GY++l  ++    +   +d  ++ ++     +    +++ ddl +av+++   + +++++v+++G   GG 
  gi|386002778|ref|YP_005921077.1| 441 QWLANRGYAVLSVNFRGSTG-FGKDFVNRGNL----EW---GARMHDDLIDAVDWAVGEGIADPDRVAIMGGSYGGY 509
                                       78888888888777655555.23333333333....23...347899999*************************** PP

                               DLH 111 lalllaaev.pevdaavafYG.....................................lspekeleeaakikapila 149
                                        +l+  +   + +++ v   G                                     l+  ++++++++i+ p+l+
  gi|386002778|ref|YP_005921077.1| 510 ATLVGLTFTpEVFACGVDIVGpsnltslietippywqpqielfatrmgdhrteegrrlLFERSPINRVENIARPLLI 586
                                       999998888566788899999************************************99999*************** PP

                               DLH 150 lfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre.s 196
                                         g +D+ + ++e +++  a++++++++  ++Yp+ gH+Fa+++++ s
  gi|386002778|ref|YP_005921077.1| 587 GQGANDPRVSQNESDQIVGAMQEKGIPVTYVLYPDEGHGFARPENRmS 634
                                       ******************************************998853 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.6e-08   2.4e-05       3     109 ..     417     531 ..     415     558 .. 0.83
   2 !    7.4   0.0    0.0015       2.3     186     232 ..     576     624 ..     572     628 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.6e-08
                       Hydrolase_4   3 pkavvvlvHGl..aehsgryaelaeaLaaqGfavyalDhrG...hGrsegkrghvpsfddyvdDlaafvekvkeehp 74 
                                       p   v+ vHG   a  ++ y+   ++La++G+av+ ++ rG   +G+   +rg ++   ++ dDl  +v+ ++ e  
  gi|386002778|ref|YP_005921077.1| 417 PLPMVLYVHGGpwARDVWDYNPAHQWLANRGYAVLSVNFRGstgFGKDFVNRGNLEWGARMHDDLIDAVDWAVGEGI 493
                                       5567999999644778999*******************99544489999************************7766 PP

                       Hydrolase_4  75 el..plfllGhSmGGliallyllrypdkva.glilsaP 109
                                           ++ ++G S GG+ +l  l+  p+ +a g+ +++P
  gi|386002778|ref|YP_005921077.1| 494 ADpdRVAIMGGSYGGYATLVGLTFTPEVFAcGVDIVGP 531
                                       66689**********99988777777766656666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                       Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyH 232
                                       r+++i  Pll+ +G++D+ v++++s +++ +++ k   +t+ lyp   H
  gi|386002778|ref|YP_005921077.1| 576 RVENIARPLLIGQGANDPRVSQNESDQIVGAMQEKgiPVTYVLYPDEGH 624
                                       6788999*************************99988889999998777 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.1   6.1e+03     121     152 ..      98     128 ..      12     181 .. 0.48
   2 !   23.9   4.1   3.7e-08   5.6e-05       1     207 [.     421     624 ..     421     642 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.1
                                       CCCCHCCHS-HS.CCCCHHHCCCCHCHCCCGHH CS
                     Abhydrolase_6 121 llawlsreplpr.lfladedadaawrarlarla 152
                                       ++ w  +    + l++ d d d+ wr +   l+
  gi|386002778|ref|YP_005921077.1|  98 SYSWAHT--NEHiLYIQDKDGDENWRIYSVNLR 128
                                       2333321..111244444444444544444444 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.7e-08
                                       EEEE--GC.....G.CHHHH.HHHHCCTCEEEEE--TTS.TS-GGCS......--HHH..CHHHHHHHCCTT..... CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapL.aallaagvhvlapDlpGh.Grsdppp......ldled..ladlaalldelaa.... 62 
                                       vl +HG++  +++W +  p  + l+++g++vl++ ++G  G   +++      l++ +   +dl +++d  ++    
  gi|386002778|ref|YP_005921077.1| 421 VLYVHGGPWARDVWdY-NPAhQWLANRGYAVLSVNFRGStG--FGKDfvnrgnLEWGArmHDDLIDAVDWAVGegia 494
                                       6889**9977777752.22245578888999******8876..3333222222444444323334444444446666 PP

                                       .TTSEEEEEETCHHHHHHHHHHCC..EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHH CS
                     Abhydrolase_6  63 gggpvvlvGHSlGGalalaaaplalvvgvlldppptalpagllaaalelllallallrllawlsreplprlfladed 139
                                       ++++v ++G S+GG+       ++l vg+   p    + a  ++ + +  l+ l   ++++w       +lf     
  gi|386002778|ref|YP_005921077.1| 495 DPDRVAIMGGSYGGY-------ATL-VGLTFTP---EVFACGVDIVGPSNLTSLIETIPPYWQP---QIELFAT--- 554
                                       **************9.......332.4444444...3333334444444444444444456662...3333333... PP

                                       CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEEC..TT-C.HHHHCHHCCCH.STTEEET...CE...SSS CS
                     Abhydrolase_6 140 adaawrarlarlaallaglgllpaaawadlpvpllvlg..geDp.lvprllerlla.qagarlp...vvlpgaGH 207
                                         +    r  ++++ll  + + +  +++ +  pll+ g  ++Dp + +   +++   ++ +++p   v++p+ GH
  gi|386002778|ref|YP_005921077.1| 555 --RMGDHRTEEGRRLLFERSPIN--RVENIARPLLI-GqgANDPrVSQNESDQIVGaMQEKGIPvtyVLYPDEGH 624
                                       ..333333333333333444333..66666666644.33344444333333344444444444444466666666 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.2   3.3e+03      87     123 ..     259     300 ..     256     314 .. 0.75
   2 !   15.1   1.1     9e-06     0.013       1      85 [.     419     509 ..     419     544 .. 0.83
   3 !    5.3   0.0    0.0089        13     206     250 ..     566     624 ..     542     627 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.2
                                       HHHHHHHH.GGGEEEEEEESE....CSSCCHHHHHHHHHHHH CS
                     Abhydrolase_1  87 alayaaey.perVkalvllga....idpaaslieaqrqqaks 123
                                        +a++a++    Vk l++ ++    +d++ ++ e + q+a+ 
  gi|386002778|ref|YP_005921077.1| 259 TAALFAMNpATGVKTLIAEDPrsdfSDWMVHPTEKNVQAAAF 300
                                       455555555889999999999999999999999988888765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9e-06
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB.....CHHSHHHHHHHHHHH..HHHC CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGv.gySspapacin....ddygtasvaddldri..ldal 70 
                                       p ++++hG+p   dvw  +   + La +g+ v+ ++ rG+ g+++   +  n     +++++ + d +d++      
  gi|386002778|ref|YP_005921077.1| 419 PMVLYVHGGPWARDVWDYNPAHQWLANRGYAVLSVNFRGStGFGKDFVNRGNlewgARMHDD-LIDAVDWAvgEGIA 494
                                       579***************9999****************963334444443347799999985.99999977788888 PP

                                       TTSSEEEEEETHHHH CS
                     Abhydrolase_1  71 gddkltlvGhSmGGm 85 
                                       + d+++++G+S+GG 
  gi|386002778|ref|YP_005921077.1| 495 DPDRVAIMGGSYGGY 509
                                       899999********7 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0089
                                       C..........THHHHSEEEEEEETTCSSSCHHHHHHHHHC.HTS....EEEEEEETCSS CS
                     Abhydrolase_1 206 e..........lknvlaptlvisgtsDplvppkaledlaql.lpk....krlvvisdagH 250
                                       +          + n+  p l+ +g++Dp v+ ++++++ ++   +    +++v ++d+gH
  gi|386002778|ref|YP_005921077.1| 566 RllferspinrVENIARPLLIGQGANDPRVSQNESDQIVGAmQ-EkgipVTYVLYPDEGH 624
                                       34444555666788888************************72.335666*********9 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.26     4e+02       1      38 [.     421     456 ..     421     459 .. 0.64
   2 !    8.6   0.2    0.0011       1.6      49      83 ..     478     509 ..     475     516 .. 0.88
   3 !    6.9   0.0    0.0034         5     166     210 ..     581     627 ..     550     628 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.26
                                       EEEE--STTTS--TTTT..HHHHHHHHHHHTSEEEEEE-- CS
                     Abhydrolase_3   1 lvyfHGGGfvlgsldth..dalcrelakelgavvvsvdYr 38 
                                       ++y+HGG +     d +  ++++   a + g++v+sv++r
  gi|386002778|ref|YP_005921077.1| 421 VLYVHGGPWARDVWDYNpaHQWL---A-NRGYAVLSVNFR 456
                                       79*******85544433224444...3.457777777776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHH CS
                     Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGn 83 
                                       ++d ++a+ w++ +     adp+r++++G S GG 
  gi|386002778|ref|YP_005921077.1| 478 HDDLIDAVDWAVGEG---IADPDRVAIMGGSYGGY 509
                                       7999******99995...59*************95 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0034
                                       ---EEEEEETT-TTHH..HHHHHHHHHHHTT--EEEEEETTEETTGG CS
                     Abhydrolase_3 166 lpptlvvvaefDplrd..egeayaerlraagvevelieyegmvHgfa 210
                                       + p l+  + +Dp  +  e+ +   +++++g +v+++ y+++ Hgfa
  gi|386002778|ref|YP_005921077.1| 581 ARPLLIGQGANDPRVSqnESDQIVGAMQEKGIPVTYVLYPDEGHGFA 627
                                       468888888888865511566899**********************8 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.2e-06    0.0048      19     168 ..     494     631 ..     483     653 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.2e-06
                                       B--SSEEEEEETHHHHHHHHHHHHSSSEEEE.EEES--SB--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT CS
                            BAAT_C  19 vkkdkigllGiSkGgelalllasflkkisav.vlingsavvvegklvykdeskvlpelklsmeklkvnknglldivd 94 
                                          d+++++G S Gg  +l+  +f +++ a+ v i+g++  +   ++ +    ++p+ +  + +l  +  g +++ +
  gi|386002778|ref|YP_005921077.1| 494 ADPDRVAIMGGSYGGYATLVGLTFTPEVFACgVDIVGPSNLT---SLIE----TIPPYWQPQIELFATRMGDHRTEE 563
                                       567899999***999888877777777765548888887666...3444....689999999999888888888888 PP

                                       -B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S---STT- CS
                            BAAT_C  95 vlallkeklaekalipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHliepPyf 168
                                        ++ll e      + +ve++  p+l+ +g +D  +  +es ++++  ++++g +  v+++ Yp+ GH ++ P  
  gi|386002778|ref|YP_005921077.1| 564 GRRLLFER---SPINRVENIARPLLIGQGANDPRVSQNES-DQIVGAMQEKGIP--VTYVLYPDEGHGFARPEN 631
                                       88888544...44679****************99866665.5999*******99..99999******9988854 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 !   11.6   0.0   5.6e-05     0.083     236     329 ..      48     140 ..      39     153 .. 0.88
   2 ?    1.5   0.0     0.069     1e+02     302     342 ..     162     198 ..     159     208 .. 0.76
   3 ?   -2.6   0.0       1.2   1.8e+03     195     260 ..     246     308 ..     223     334 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                                       S-S-EEE-TTTSSEEEEEEETTSSEEEEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEEESSSETTEBEEEE CS
                           DPPIV_N 236 lhdevhflkrdesgflwisekdGfkHLylfdldgkseikqlTsGeweVtsilavdekrdlvyFtatkdsPlerhlYs 312
                                       ++++++ +++d+s++ ++ +kdG   +++ + ++ +   ++T+  +  +  ++++ +++++ ++  kd+  + ++Ys
  gi|386002778|ref|YP_005921077.1|  48 PDKITVRTSPDGSRISYLAPKDGVLNVWVGPIEDPEAAEPVTNDTYRGIRSYSWAHTNEHILYIQDKDGDENWRIYS 124
                                       55666666799999999999****************888************************************** PP

                                       EESSCTTEEEESSTTTS CS
                           DPPIV_N 313 vslesggeltrltdeeg 329
                                       v+l+ +ge++ lt+ e 
  gi|386002778|ref|YP_005921077.1| 125 VNLR-SGEMRDLTPFED 140
                                       ****.*******97655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.069
                                       SSETTEBEEEEEESSCTTEEEESSTTTSEEEEEEE-TTSSE CS
                           DPPIV_N 302 kdsPlerhlYsvslesggeltrltdeegdhysasfspsgky 342
                                       +++P ++ lY+ ++e +g++t ++ +++ + s+ ++++  y
  gi|386002778|ref|YP_005921077.1| 162 DRDPEYHDLYRLNIE-TGKMTLIQENGYFS-SFDIDDD--Y 198
                                       568************.*******9999888.4444433..3 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.2
                                       SCCEEEEEEETTSTEEEEEEEETTTCCEEEEEEEESSS-SSS-S-EEE-TTTSSEEEEEEETTSSE CS
                           DPPIV_N 195 eksllvqwlnRsqnrlkvvlvdaetgravvkleetsdgWvelhdevhflkrdesgflwisekdGfk 260
                                       ++ +l  + +R  n++ +++++++tg ++++ e+ +  + +  + vh+++++ +   +++e+++++
  gi|386002778|ref|YP_005921077.1| 246 GE-ILYFVDSRGRNTAALFAMNPATGVKTLIAEDPRSDFSD--WMVHPTEKNVQAAAFTYERKDWQ 308
                                       44.55556678888888888888888888888666665543..33344444555555555555554 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       5.2   7.8e+03      19      39 ..     413     432 ..     405     447 .. 0.78
   2 ?   14.2   0.0   1.7e-05     0.026     112     200 ..     494     598 ..     462     617 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5.2
                                       GGTTTEEEEEEE--TTHHCCH CS
                          Esterase  19 spgrkypvvylldGltgwdqn 39 
                                       +p++++p v++ +G   w ++
  gi|386002778|ref|YP_005921077.1| 413 RPEEPLPMVLYVHG-GPWARD 432
                                       57788888888888.666654 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.7e-05
                                       EECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC......HCHHHC........TTCCHHHCC-CCCCH CS
                          Esterase 112 tapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps......namWgq........eekeawqendpvlla 174
                                        +pd+ a++G S GG++ L+  +  p+ F++     ++ n++      +++W +          + + +e++ +l +
  gi|386002778|ref|YP_005921077.1| 494 ADPDRVAIMGGSYGGYATLVGLTFTPEVFACGVDIVGPSNLTslietiPPYWQPqielfatrMGDHRTEEGRRLLFE 570
                                       567779***********************876666666566589999888888888888887555555677777777 PP

                                       CHHCHTTSEE..EEEEEECTTBCCCHTS CS
                          Esterase 175 kelsaslkal..riyldvGtseddlgeq 200
                                        + +++ +++    ++ +G +++++ ++
  gi|386002778|ref|YP_005921077.1| 571 RSPINRVENIarPLLIGQGANDPRVSQN 598
                                       6666555543114667777777766655 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4   0.00026      0.39      81     192 ..     416     515 ..     412     528 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                       SSEEEEEEEE-..TT--GGGHHHHHHH.HHTT-EEEEEE-TTTS..SSB-SSCCSS-SSSSTTTTTTSTTT-HHHHH CS
                              AXE1  81 eklPavvefhG..Yegsrgeihdllny.aaaGyavvvmdvRGqggesedkvgskgnkakGfiirGlldkeklyyrrv 154
                                       e+lP+v+  hG  +  + ++ +   ++ a  Gyav++++ RG  g  +d           f+ rG l+       r+
  gi|386002778|ref|YP_005921077.1| 416 EPLPMVLYVHGgpWARDVWDYNPAHQWlANRGYAVLSVNFRGSTGFGKD-----------FVNRGNLEWG----ARM 477
                                       6666666666633333345555556662345777777777776644443...........4445544422....356 PP

                                       HHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHH CS
                              AXE1 155 flDavrlveivaslpevDeeRvavlGasqGGalalava 192
                                       + D + +v+ + +    D++Rva++G+s GG  +l+  
  gi|386002778|ref|YP_005921077.1| 478 HDDLIDAVDWAVGEGIADPDRVAIMGGSYGGYATLVGL 515
                                       77889999999999*****************9888765 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.9e-05      0.13     107     255 ..     108     278 ..      97     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
                                       EEEEEEESSSS-EEEEEEETTS---EEEESS----SEEETTEEEEE-T..........TT--EEEEETTTTEEEEEE CS
                           DUF5050 107 wiYYqhydekdglklykikidgkektklsdeaieplsvkdgwiYytge.........sedhslykldtdgksiskvs 174
                                        +Y q+ d +++ ++y++++   e ++l+  +  ++ +++    + +e          e h ly+l++++++++ + 
  gi|386002778|ref|YP_005921077.1| 108 ILYIQDKDGDENWRIYSVNLRSGEMRDLTPFEDVQARIVKVSRNFPEEiivglndrdPEYHDLYRLNIETGKMTLIQ 184
                                       45566677788888888888888888885544444444433333444444444444456789**************9 PP

                                       -S-EEE.EEEEETTE..EEEEG..GGTT-EEEE-SSS---...EE-S-S-EEE....EEEETTEEEEEE-SSS-E.. CS
                           DUF5050 175 eenlyl.lvvegdyi..Yyidl..sknyaLyrvklsgsek...evltedkvdn....yNvtgnwiYyqkesdeeka. 238
                                       e+ +++ + +++dy   + +++  +   ++ r + +g+ +   e+  ed +++    +N tg+++Y+  + + + a 
  gi|386002778|ref|YP_005921077.1| 185 ENGYFSsFDIDDDYAvrFATNMtcDGGAEIFRPTGEGGWEvftEIPMEDVITTgsigFNKTGEILYFVDSRGRNTAa 261
                                       988777799***99876777777789999***99999877443444666666677789*********9998887777 PP

                                       EEEEETTS---EEEEES CS
                           DUF5050 239 lyrikldGsekeklaeg 255
                                       l  ++  +  k+++ae+
  gi|386002778|ref|YP_005921077.1| 262 LFAMNPATGVKTLIAED 278
                                       ************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 4156.74
//
Query:       gi|386002779|ref|YP_005921078.1|  [L=627]
Description: Oligopeptidase F, Metallo peptidase, MEROPS family M03B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-16   60.1   7.8    2.3e-16   60.1   7.8    2.3  2  Peptidase_M3  Peptidase family M3
     0.0056   17.2   1.8       0.78   10.3   0.1    4.3  3  RPAP3_C       Potential Monad-binding region of RPAP3


Domain annotation for each model (and alignments):
>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2      0.55     5e+03     381     394 ..     110     121 ..      91     158 .. 0.46
   2 !   60.1   7.8   2.5e-20   2.3e-16       2     457 ..     222     607 ..     221     608 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.55
                                       CCHTSS-TTTTCHH CS
                      Peptidase_M3 381 hlfahgYaanYYsy 394
                                       ++    ++a YY+ 
  gi|386002779|ref|YP_005921078.1| 110 EI--QTFYADYYAA 121
                                       33..2333455543 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 2.5e-20
                                       HHC-S-HHHHHHHHHHHCTTTCCSS..THHHHHHHHHHHHHHHHHHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHH CS
                      Peptidase_M3   2 lkespdrelRkeayeashskaaeqrntlensklleellklraelAkllgyesyaelaledkmaknpetvldfleelv 78 
                                       l+ +pdre Rk +y +     +++ +++  ++l+    k+ + l++ l+y+++ + +++d   + +e+  + ++++ 
  gi|386002779|ref|YP_005921078.1| 222 LATDPDRENRKLCYDKRFYHLKDESDKM--AALYLLKAKKDDHLSRELNYSDAYASTIFD--SYLSEEQIEEMNSVF 294
                                       6789******************998888..88888888888889****************..999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHCCT-SSS--CCCHHHHHHHHHCCCCS--CCCCGGG-BHHHHHHCHHHHHHHHHTEEE CS
                      Peptidase_M3  79 kklrpllekelkllkelkkkelglegelqpwDvaYYsekqreekydldqeelkeyfpletvleGllelfeeLfGikf 155
                                       k+ + ++  + ++++e    + g++ +l p+D+       ++   d+dq      +++ ++l               
  gi|386002779|ref|YP_005921078.1| 295 KERKDAFYGYHEFKRE----KMGVD-RLMPYDL------FLQLTDDPDQ-----IYNYTETLA-------------- 341
                                       9999999999999998....999**.*******......3333333555.....555555555.............. PP

                                       EEETTS..--SSTT-EEEEEEET.TT-EEEEEEEEEEC--T..TS-SS-EEEEEE--BTTS-B--EEEEEEEEE--- CS
                      Peptidase_M3 156 veekdakgevwhedVrkleVvdeilsegligeiylDlyerk..gKrggAasfglvksredgtrqlpviylllNftkp 230
                                         e  + g  ++    +  +++ei+  ++  ++ +D+y+++  gK++  ++ +l +       +l   +++lN+++ 
  gi|386002779|ref|YP_005921078.1| 342 --E--I-GASYSG---MDPIFSEIFAYMV-TSNLIDVYPNPdnGKQTSEYCMSLFPL------KL-PGMIFLNYEG- 401
                                       ..1..1.344444...3346666888888.9*******986227************4......33.35899*****. PP

                                       BTTS--B--HHHHHHHHHHHHHHHHHHC--BSSGGGSTT-S-CCCCCHHHHHHHHGGGSHHHHHCC-B-TTT--B-- CS
                      Peptidase_M3 231 sskkPsLLtldevetLfHEfGHsmHsllsrteysnvsgtnvpidfvElpSqlmEnlltepevlkslskhyetgeaip 307
                                                +++ +t+ HE+GH++  +l  + + ++ +   p    E+pS+++E l+ ++ + +s   + et  a++
  gi|386002779|ref|YP_005921078.1| 402 --------LIYDKKTVTHEVGHAINFYLMGNSV-DFIYCGGPEYEMEIPSTFNEELFVDYVLENS---DRETALAVL 466
                                       ........99***************99999997.557788888889*************976665...589999999 PP

                                       HHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHCTT-TCCGHH.....HHHHHHHHHHCTTS...CTTBTTSSGGGC-C CS
                      Peptidase_M3 308 eelleklikaknvnaalellrqlvfaafdqelHeeaeeeqilk.kdlletyaelrkkflg...lpvapdeasqasFg 380
                                       ++++ +            ++ q ++++f+ + H   + ++  +  +l++ +++l+k++       +++d+a  ++  
  gi|386002779|ref|YP_005921078.1| 467 DQHIGEYK--------NYFTFQSMITEFERQAHILCDGKDEISgAELNSLWRDLCKEYEDeniGYYDEDSAEWTYVD 535
                                       99999977........555558899********9877766666699************9955333344444444666 PP

                                       CCHTSS-TTTTC..HHHHHHHHHHHHHHCCHHCCTT-CCHHHHHHHHTTTTTTSS-HHHHHHCCCSS---SHHHHHH CS
                      Peptidase_M3 381 hlfahgYaanYY..sylyaevlaldifekffeedplnretGeryrkeiLsrGgskdplellkkflgrepsadallka 455
                                       h++      nYY  sy  +++++l++f+ ++e +p +    ++++  +Ls+G ++ p e l+kf g e + + +++a
  gi|386002779|ref|YP_005921078.1| 536 HIYL---TNNYYtfSYSLSKAITLSLFKIYKE-NPQEF---NERYVGYLSAGTTMTPPEKLEKFFGIEINRTLFEDA 605
                                       7764...3356611555678999999*99999.65553...589*********************999999999988 PP

                                       CT CS
                      Peptidase_M3 456 lg 457
                                       ++
  gi|386002779|ref|YP_005921078.1| 606 MD 607
                                       85 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.16   1.4e+03      51      79 ..     159     185 ..      98     188 .. 0.59
   2 ?    1.4   0.1     0.054   4.9e+02      14      59 ..     241     299 ..     234     302 .. 0.72
   3 !   10.3   0.1   8.7e-05      0.78      28      61 ..     578     616 ..     500     623 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.16
                           RPAP3_C  51 ldalnerlqeekaedsslvleiLdrLskv 79 
                                       +++ ++r ++e+  + ++++ei d+L k+
  gi|386002779|ref|YP_005921078.1| 159 IRYADHRPRNET--HAAFIAEIADQLMKL 185
                                       334444444433..337888888888775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.054
                           RPAP3_C  14 klkredkdlka.vllqinp............kqlpkiFknsledeilsdildalnerlq 59 
                                       +lk+e+++  a +ll+ ++            +   +iF++ l+ e ++++  +++er+ 
  gi|386002779|ref|YP_005921078.1| 241 HLKDESDKMAAlYLLKAKKddhlsrelnysdAYASTIFDSYLSEEQIEEMNSVFKERKD 299
                                       56555555555666665555666666666657777899999999999999999999875 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 8.7e-05
                           RPAP3_C  28 q.....inpkqlpkiFknsledeilsdildalnerlqee 61 
                                       +     ++p++l+k+F+ +++ ++++d +d+++ r+++ 
  gi|386002779|ref|YP_005921078.1| 578 SagttmTPPEKLEKFFGIEINRTLFEDAMDVVEMRVNQL 616
                                       335555788************************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3684.98
//
Query:       gi|386002780|ref|YP_005921079.1|  [L=379]
Description: Aspartate aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-57  193.8   0.0    5.4e-57  193.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    6.3e-07   29.0   0.0    9.1e-07   28.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.6e-06   27.4   0.0    2.4e-06   26.8   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    3.2e-05   22.6   0.0    6.7e-05   21.6   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.046   14.1   0.2       0.43   10.9   0.0    2.5  3  Radical_SAM      Radical SAM superfamily
      0.061   12.2   0.0      0.081   11.8   0.0    1.1  1  Alliinase_C      Allinase
       0.14   10.8   0.0       0.27    9.9   0.0    1.4  1  EPSP_synthase    EPSP synthase (3-phosphoshikimate 1-carboxyv


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.6   0.0   2.1e-60   5.4e-57       2     363 .]      30     372 ..      29     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 193.6 bits;  conditional E-value: 2.1e-60
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dv+ L ++e+++d     +  v++a +   +  ++ + y+++ g pel+ea+ + + +++ ++++++ ++vv+sG++
  gi|386002780|ref|YP_005921079.1|  30 DVVHLEVGEPDFD----IPAPVREAVAA--ALAEGHTHYTHSCGDPELREAISDHYAERYSVTVDPD-RIVVCSGTS 99 
                                       7999*********....77777777765..66677788999999***********************.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +  +++ +l l++gde +++dp ya y n +r sgg  v++p  ++++f+l+  a+   +++      ktk i+++
  gi|386002780|ref|YP_005921079.1| 100 PAMMLVFSAL-LEAGDEAIISDPGYACYPNFIRFSGGVPVPVPAAEADGFQLNPGAVASRITD------KTKAIVIN 169
                                       **********.9***************************************************......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp+NPtGt+++    e++    +  ++++++De+Y g+v+   +    r+ +e + + ++++++sK ++++G+R+Gy
  gi|386002780|ref|YP_005921079.1| 170 SPSNPTGTLLSARRMEAI---SD-LGVRVISDEIYHGLVYAGRE----RSILEFAEDAIVLNGFSKLYAMTGLRLGY 238
                                       ******************...44.7***************9543....6666666678******************* PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSS CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgm 306
                                       +++ +++++ ++k+++++ +   s++q+a  aal+ a +   ++e mr+++ +rr++++++L++lg+ v  ++ +++
  gi|386002780|ref|YP_005921079.1| 239 LIAPPELIRPIQKMQQNLFIcaNSAVQRAGIAALREASD---DVERMRRTYDERRRFMVKRLRKLGFGVAVEPtGAF 312
                                       ****************988889**************997...9************************9988887*** PP

                                       EEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       +++ d +++  +   l+  +le+  v v pg  f++  +g lR+++ + + e + e ++++
  gi|386002780|ref|YP_005921079.1| 313 YVFADARHLssNSYNLAFDILERARVGVAPGIDFGAegEGYLRFSY-ASSIERIAEGLDRI 372
                                       *********5545555555***************************.88888888888776 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.6e-10   9.1e-07      42     117 ..      92     168 ..      74     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.6e-10
                                       EEESSHHH.HHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE CS
                   DegT_DnrJ_EryC1  42 iavssGta.AlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl 116
                                       i v+sGt+ A++l+ +al +++gde I+   +++   n ++ +g +pv+v    +d ++++p a+++ it +tkaI+
  gi|386002780|ref|YP_005921079.1|  92 IVVCSGTSpAMMLVFSAL-LEAGDEAIISDPGYACYPNFIRFSGGVPVPVPAAeADGFQLNPGAVASRITDKTKAIV 167
                                       78999*985777777775.5558***************************87615679******************9 PP

                                       E CS
                   DegT_DnrJ_EryC1 117 p 117
                                       +
  gi|386002780|ref|YP_005921079.1| 168 I 168
                                       6 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   9.4e-10   2.4e-06      59     160 ..      88     183 ..      46     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 9.4e-10
                                       STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS.CBEGGGHHH CS
                       Aminotran_5  59 eseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg.eldldelek 134
                                       +  ++i+++sGt+ a+ lv  +l   l++gde+++++ ++ +     + ++   g+ v v  ++++g +l++ ++++
  gi|386002780|ref|YP_005921079.1|  88 D-PDRIVVCSGTSPAMMLVFSAL---LEAGDEAIISDPGYACYP---NFIRFSGGVPVPVPAAEADGfQLNPGAVAS 157
                                       3.589******************...****************99...7777788*******9999994577****** PP

                                       H--TTEEEEEEESBETTTTEB--HHH CS
                       Aminotran_5 135 llnektklvaithvsnvtGtiqpvee 160
                                        +++ktk++ i+  sn tGt+    +
  gi|386002780|ref|YP_005921079.1| 158 RITDKTKAIVINSPSNPTGTLLSARR 183
                                       ********************876655 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.6e-08   6.7e-05      71     154 ..      92     179 ..      57     202 .. 0.82
   2 ?   -2.9   0.0      0.74   1.9e+03      74     119 ..     259     304 ..     245     312 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-08
                                       EEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST..TSHHHHHHHCCTTEEEEEE CS
                   Cys_Met_Meta_PP  71 lavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt..sdleelekaikentklvyl 143
                                       ++v sG++ A+++++ all+aGde ++sd  Y +  ++++      + + +   d    ++ ++++ i+++tk++ +
  gi|386002780|ref|YP_005921079.1|  92 IVVCSGTSpAMMLVFSALLEAGDEAIISDPGYACYPNFIRFSGGVpVPVPAAEADGfqLNPGAVASRITDKTKAIVI 168
                                       56788887477788899*****************9999998754436666666665446889*************** PP

                                       ESS-TTTT--- CS
                   Cys_Met_Meta_PP 144 Etptnpllkvv 154
                                        +p+np+  ++
  gi|386002780|ref|YP_005921079.1| 169 NSPSNPTGTLL 179
                                       ******97765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.74
                                       SSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEE CS
                   Cys_Met_Meta_PP  74 ssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgiev 119
                                        +  a + a i al +a d++  ++  Y+  +r++ k l+klg  v
  gi|386002780|ref|YP_005921079.1| 259 CANSAVQRAGIAALREASDDVERMRRTYDERRRFMVKRLRKLGFGV 304
                                       4444555566788888889999999999999999999888877655 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.43      33      92 ..      16      73 ..       4      92 .. 0.80
   2 ?   -2.5   0.0       2.3     6e+03      90     144 ..     180     194 ..     129     203 .. 0.61
   3 ?   -0.6   0.0      0.58   1.5e+03     118     146 ..     280     305 ..     270     315 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM 33 eileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpd.ee 92
                                      ++le ++++ +++g+++v+l  gep+++ +  +  + +a+l  ++ +++++ + + p+ +e
  gi|386002780|ref|YP_005921079.1| 16 DVLERARAM-ERQGIDVVHLEVGEPDFDIPAPVREAVAAAL--AEGHTHYTHSCGDPElRE 73
                                      688889999.9**************************9999..688888888877764433 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                       GHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  90 deeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                       + + +e++ +lg                                        +++
  gi|386002780|ref|YP_005921079.1| 180 SARRMEAISDLG----------------------------------------VRV 194
                                       244444444444........................................443 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.58
                                       HHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 118 lklmnrghtfeevlealeklreagikrvv 146
                                        ++  r    e++   +++lr++g+  v 
  gi|386002780|ref|YP_005921079.1| 280 ERMR-R-TYDERRRFMVKRLRKLGFG-VA 305
                                       4444.4.4455555789999999998.43 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05     0.081     142     207 ..     167     240 ..     146     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                                       EEESS-TTT---....------TT-EEEEEE-TT-STTTS....---S-B--SEEEEEHHHHHS-GGG-EEEEE CS
                       Alliinase_C 142 lvtsPnnPdgll....reavvkgseakviyDlayYWPhyt....pitskadedimLftlskltGhaGsrlGWal 207
                                       ++ sP nP g+l    r + +++  ++vi D +y+   y+     i + a++ i+L  +skl   +G rlG+ +
  gi|386002780|ref|YP_005921079.1| 167 VINSPSNPTGTLlsarRMEAISDLGVRVISDEIYHGLVYAgrerSILEFAEDAIVLNGFSKLYAMTGLRLGYLI 240
                                       689*******996665667899999********9777776333378889999*******************955 PP

>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00011      0.27     318     361 ..     268     311 ..     246     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEE CS
                     EPSP_synthase 318 afaegttviegiaelrvketdrlaamateLrklGaeveeeedgl 361
                                        +a+++   ++++++r +  +r+  m++ LrklG+ v +e+ g 
  gi|386002780|ref|YP_005921079.1| 268 GIAALREASDDVERMRRTYDERRRFMVKRLRKLGFGVAVEPTGA 311
                                       355577777899************************99998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2459.88
//
Query:       gi|386002781|ref|YP_005921080.1|  [L=737]
Description: KAP P-loop domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-58  198.0   2.6    1.7e-57  195.1   2.6    2.1  1  KAP_NTPase      KAP family P-loop domain
    1.7e-08   34.8   0.0    1.4e-07   31.9   0.0    2.2  1  AAA_22          AAA domain
    7.1e-05   22.1   0.0    0.00024   20.4   0.0    1.8  1  NB-ARC          NB-ARC domain
    7.3e-05   22.8   2.1    0.00025   21.0   2.1    1.9  1  ATPase_2        ATPase domain predominantly from Archaea
    9.4e-05   22.9   0.0    0.00027   21.4   0.0    1.8  1  AAA_16          AAA ATPase domain
     0.0024   16.9   0.0     0.0039   16.2   0.0    1.2  1  ORC2            Origin recognition complex subunit 2
      0.004   17.6   1.1      0.046   14.1   1.1    2.5  1  AAA             ATPase family associated with various cellula
     0.0043   16.6   0.2     0.0078   15.8   0.2    1.3  1  Elong_Iki1      Elongator subunit Iki1
     0.0079   16.1   0.8       0.32   10.9   0.8    2.6  1  NACHT           NACHT domain
     0.0098   15.3   0.3      0.036   13.5   0.3    1.9  2  TniB            Bacterial TniB protein
  ------ inclusion threshold ------
      0.023   15.2   0.8      0.023   15.2   0.8    2.5  3  AAA_23          AAA domain
      0.065   12.1   0.1      0.095   11.6   0.1    1.2  1  Phage_min_cap2  Phage minor capsid protein 2
       0.07   13.5   0.1        5.5    7.4   0.0    2.7  2  RNA_helicase    RNA helicase
      0.084   12.0   0.6       0.26   10.4   0.1    2.1  2  PLU-1           PLU-1-like protein
        0.1   13.1   0.0       0.91   10.0   0.0    2.4  2  ABC_tran        ABC transporter
       0.12   11.8   0.1       0.78    9.1   0.0    2.0  2  SMC_N           RecF/RecN/SMC N terminal domain
       0.13   12.1   0.0       0.31   10.8   0.0    1.6  1  AAA_29          P-loop containing region of AAA domain
          1    9.7   3.5        1.3    9.3   0.3    2.4  2  DNA_ligase_A_N  DNA ligase N terminus


Domain annotation for each model (and alignments):
>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.1   2.6   1.7e-60   1.7e-57       1     324 [.      35     314 ..      35     316 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 1.7e-60
                        KAP_NTPase   1 ydlyasaladilseptlatpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaL 77 
                                       y+++a++lad ++++++ +++v+++yg WGsGKs+l+n+++ +l++  + ++ +++ fn+w+f+g++d++ +++ +L
  gi|386002781|ref|YP_005921080.1|  35 YSNFAEHLADSICKMAPLEGFVISVYGSWGSGKSTLINFIKYYLNQLPEDEQPIIVHFNPWWFSGQEDLTIHFFGQL 111
                                       789************************************************************************** PP

                        KAP_NTPase  78 adaleeeygqlatkllrakklkalkikgkiklrkacaiplvlilevalflliegasllavlsraaklkeeaplkklq 154
                                       + +l++e+ + + + l++  l a ++++  k+   ++++l+ +                           ++ +k +
  gi|386002781|ref|YP_005921080.1| 112 QAELGKEKWITDPDKLKH--LIAEFSDLLSKTPEPTINILARV--------------------------INKFTKTH 160
                                       *******99996666666..88888888888666666666522..........................24569*** PP

                        KAP_NTPase 155 teveelladmektLdalqkrlVvviDdLDrceteevlqlleavkllfslkpvvfilavDphviakaieansesllge 231
                                       ++v+e +++++ktL+++qk+++v+iDd+Dr++ +e++ql++++k ++++++v+++la+D+ v++ a+e+++      
  gi|386002781|ref|YP_005921080.1| 161 KSVSEFKDKIAKTLREQQKKILVIIDDIDRLTADEIRQLFRVIKSVADFPNVIYLLAFDKRVVINALEKTQDI---P 234
                                       **********************************************************************984...4 PP

                        KAP_NTPase 232 iaghdYlekiiqlpvyLppsglrevkkvlmeaveaseettesesrdetlgnsasksnlqlaldlskilltedfsdvn 308
                                        ag++Yleki+q p++Lp  ++++++++l e++  +   t++e  d              +++l+ +++++d+++++
  gi|386002781|ref|YP_005921080.1| 235 GAGEEYLEKIVQTPFELPIPDKNSLRSLLFEKLNLILTDTPEELFD-------------KRYWLNVYFQGIDHFITT 298
                                       79*****************************************997.............68**************** PP

                        KAP_NTPase 309 pRemkrlinalsitrr 324
                                       pR++ rl n+l++t+ 
  gi|386002781|ref|YP_005921080.1| 299 PRDVIRLTNTLNVTYP 314
                                       **************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.4e-10   1.4e-07       8     112 ..      57     199 ..      53     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.4e-10
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.............. 70 
                                       + v+G  G+GK+tl++ +++ l+  + +e+e+p +v++++   ++++dl  +++ +l+ el +              
  gi|386002781|ref|YP_005921080.1|  57 ISVYGSWGSGKSTLINFIKYYLN--QLPEDEQPIIVHFNPWWFSGQEDLTIHFFGQLQAELGKekwitdpdklkhli 131
                                       789***********998888874..34556899999***************************************** PP

                            AAA_22  71 ...........................erlsseellealeqalraravielliiDEaqhlrseealeeL 112
                                                                    +s +e+ +++++ lr+++++ l+iiD++++l +++ +++L
  gi|386002781|ref|YP_005921080.1| 132 aefsdllsktpeptinilarvinkftkTHKSVSEFKDKIAKTLREQQKKILVIIDDIDRL-TADEIRQL 199
                                       **************************8888999999************************.75555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.4e-07   0.00024       6     112 ..      40     188 ..      36     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                       HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE........................ CS
                            NB-ARC   6 ekviekLlekdelqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv........................ 57 
                                       e++++   ++  l+ +v++++G  G+GK+tl++ i   ++++ + + ++++                          
  gi|386002781|ref|YP_005921080.1|  40 EHLADSICKMAPLEGFVISVYGSWGSGKSTLINFIKYYLNQLPEdEQPIIVHFnpwwfsgqedltihffgqlqaelg 116
                                       677888889999999******************9999988887757777776688889******************* PP

                                       ....................EEESXXH.HHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCT..TEEEEEEE CS
                            NB-ARC  58 ....................vvsktdk.seeiletilkeLslseddleekeeveslkrklvrlLltk..rfllvlDD 111
                                                            +skt +   +il ++++++ ++++  +e       k+k+ + L+++  + l+++DD
  gi|386002781|ref|YP_005921080.1| 117 kekwitdpdklkhliaefsdLLSKTPEpTINILARVINKFTKTHKSVSE------FKDKIAKTLREQqkKILVIIDD 187
                                       ***9999999999888888888887652447777788888666333333......668888888765559******* PP

                                       E CS
                            NB-ARC 112 V 112
                                       +
  gi|386002781|ref|YP_005921080.1| 188 I 188
                                       9 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 !   21.0   2.1   2.5e-07   0.00025      21     145 ..      55     199 ..      44     224 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                          ATPase_2  21 eiyfiYGpegsGKtaLl...keiienl.edkdkyviyyial....reesiskldefie..........eeeekkkle 79 
                                        ++ +YG+ gsGK++L+   k  +++l ed +  ++ +++     +e+ + ++    +                 ++
  gi|386002781|ref|YP_005921080.1|  55 FVISVYGSWGSGKSTLInfiKYYLNQLpEDEQPIIVHFNPWwfsgQEDLTIHFF---GqlqaelgkekW------IT 122
                                       5788***********982224567777555555666666541100333333333...234464444331......22 PP

                          ATPase_2  80 kal............giavpkaeleeilk......eksklvfkaielllekikkkgkkiiiiiDelqklidlglnga 138
                                       ++             ++++p+ +++ +        ++ k v +  +++ + +++++kki +iiD++ +l        
  gi|386002781|ref|YP_005921080.1| 123 DPDklkhliaefsdlLSKTPEPTINILARvinkftKTHKSVSEFKDKIAKTLREQQKKILVIIDDIDRLTAD----- 194
                                       2225556669999995555555543322243224377777778888888888888999********999822..... PP

                          ATPase_2 139 ellvkeL 145
                                          + +L
  gi|386002781|ref|YP_005921080.1| 195 --EIRQL 199
                                       ..23344 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.7e-07   0.00027      26     154 ..      56     198 ..      40     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.7e-07
                            AAA_16  26 lvllsGesGvGKsslvrellralekd...........ggiflrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                       ++ ++G  G+GKs+l++ ++ +l++            + ++++g+ d              +   +++ ql +e+ +
  gi|386002781|ref|YP_005921080.1|  56 VISVYGSWGSGKSTLINFIKYYLNQLpedeqpiivhfNPWWFSGQEDLT------------I---HFFGQLQAELGK 117
                                       5789************888843333355587776655555566666666............4...778888888888 PP

                            AAA_16  92 aeleawrekleealaavpelagaea.................srllellkrll.allsrderplvlvlDdlqwadea 150
                                        ++  +++kl+  +a+ ++l ++ +                 +    ++k+ + + l+++++++++++Dd++++ ++
  gi|386002781|ref|YP_005921080.1| 118 EKWITDPDKLKHLIAEFSDLLSKTPeptinilarvinkftktHKSVSEFKDKIaKTLREQQKKILVIIDDIDRLTAD 194
                                       899999999999999666666666633333334444455555333333333333444554558*********99886 PP

                            AAA_16 151 slql 154
                                           
  gi|386002781|ref|YP_005921080.1| 195 EIRQ 198
                                       5444 PP

>> ORC2  Origin recognition complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.9e-06    0.0039      50     176 ..      52     217 ..      23     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                                       HTT-EEEE--.SS--HHHHHHHHSSS----...SSS-EEEE----TT-..........................-SH CS
                              ORC2  50 eqGFslllyG.vGSKrklleeFaeellskr...kdgpvvvvnGylpsl..........................tlk 96 
                                        +GF + +yG +GS ++ l +F++ +l++    +++ +v +n +  s                           +lk
  gi|386002781|ref|YP_005921080.1|  52 LEGFVISVYGsWGSGKSTLINFIKYYLNQLpedEQPIIVHFNPWWFSGqedltihffgqlqaelgkekwitdpdKLK 128
                                       48********77****************98875444455555555444899999999999999***********999 PP

                                       HHHHHHHHTT--S.--.............-SSS--HHHHHHHHHHHHHS--S-..S--EEEES-SSSTTTTS.HHHH CS
                              ORC2  97 dilseiasallekkea.............kklsssvaaqlekilslleekeseeksklylvihniDgpsLrk.ekaq 159
                                       ++++e ++ l+++  +             +k+++sv++  +ki ++l+e+    ++k++++i  iD     +  +  
  gi|386002781|ref|YP_005921080.1| 129 HLIAEFSDLLSKT-PEptinilarvinkfTKTHKSVSEFKDKIAKTLREQ----QKKILVIIDDIDRLTADEiRQLF 200
                                       9999999655444.446999999995555555555555555555555555....567*********76555422244 PP

                                       HHHHTTTT-SSSEEEEE CS
                              ORC2 160 alLarLaaipqIhlias 176
                                        +++++a  p++  + +
  gi|386002781|ref|YP_005921080.1| 201 RVIKSVADFPNVIYLLA 217
                                       55777787777655555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.1   4.6e-05     0.046      29     107 ..     153     216 ..      57     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-05
                                       EETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEE CS
                               AAA  29 isgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskviv 105
                                       i+  + + k v+e ++ki+++++e  +k  +  ++iD+id+l+ ++           + qL+++++ v +  + vi 
  gi|386002781|ref|YP_005921080.1| 153 INKFTKTHKSVSEFKDKIAKTLREQ-QK--KILVIIDDIDRLTADE-----------IRQLFRVIKSVADFPN-VIY 214
                                       3333333458999999999999763.33..49**********9999...........9999999999998755.665 PP

                                       EE CS
                               AAA 106 ig 107
                                       ++
  gi|386002781|ref|YP_005921080.1| 215 LL 216
                                       54 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   7.8e-06    0.0078      63     133 ..     155     220 ..     137     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.8e-06
                        Elong_Iki1  63 eaterskklkelakeiksalspkssekkkkalviiDslnplaslikeeslaaflssllsspsvslvavYHt 133
                                       + t+++k+++e++++i+++l+++    +kk lviiD++  l  +++ ++l ++++s+++ p+v  +  + +
  gi|386002781|ref|YP_005921080.1| 155 KFTKTHKSVSEFKDKIAKTLREQ----QKKILVIIDDIDRLT-ADEIRQLFRVIKSVADFPNVIYLLAFDK 220
                                       444557789*********99443....389*********997.56899**********9888776666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.8   0.00032      0.32       5      97 ..      59     195 ..      56     228 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                       EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C......... CS
                             NACHT   5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse......... 71 
                                       + G  GsGK+tL+  +   + +   ++   + + +++   +s +++       + f ql+++ ++ +          
  gi|386002781|ref|YP_005921080.1|  59 VYGSWGSGKSTLINFIKYYLNQLPEDE--QPIIVHFNPWWFSGQEDLtI----HFFGQLQAELGKEKWitdpdklkh 129
                                       566666666666666666665433333..35555555555555554431....222222222222222222233444 PP

                                       ........................................CHHHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  72 ........................................vwavllelperlLlilDglDelvtdl 97 
                                                                               + + l e+++++L i+D++D+l +d 
  gi|386002781|ref|YP_005921080.1| 130 liaefsdllsktpeptinilarvinkftkthksvsefkdkIAKTLREQQKKILVIIDDIDRLTADE 195
                                       44444444444445666666666666666666777788878889999***************9854 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.5   2.5e+03      40      62 ..      59      80 ..      55      93 .. 0.67
   2 !   13.5   0.3   3.6e-05     0.036      89     151 ..     147     208 ..     139     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                              TniB 40 lvGdsnnGKtmivekFarlhppe 62
                                      ++G    GK+++++ F + + ++
  gi|386002781|ref|YP_005921080.1| 59 VYGSWGSGKSTLIN-FIKYYLNQ 80
                                      78899999999986.44444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.6e-05
                              TniB  89 aiLealgaplkar.arvskleqqvlrllrelkvrvLi.iDEihnllagsarkqreflnalksLgn 151
                                       +iL+++  ++ ++ ++vs++++++ ++lre + ++L+ iD i++l    a++ r+++ ++ks  +
  gi|386002781|ref|YP_005921080.1| 147 NILARVINKFTKThKSVSEFKDKIAKTLREQQKKILViIDDIDRLT---ADEIRQLFRVIKSVAD 208
                                       688888887655516899****************996268888887...8889999999998765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.8   2.3e-05     0.023      24     124 ..      59     199 ..      55     247 .. 0.58
   2 ?   -1.6   0.0       3.2   3.2e+03     115     133 ..     353     371 ..     260     509 .. 0.61
   3 ?   -2.9   0.1         8     8e+03     149     161 ..     703     715 ..     630     720 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                            AAA_23  24 ItGpNGaGKTTildAiklaLygetprlsrks.......grgfeksdveiese......................... 68 
                                       ++G  G+GK+T++++ik+ L   ++++ +          +g e+  ++++ +                         
  gi|386002781|ref|YP_005921080.1|  59 VYGSWGSGKSTLINFIKYYLNQLPEDEQPIIvhfnpwwFSGQEDLTIHFFGQlqaelgkekwitdpdklkhliaefs 135
                                       68999***************998877777778888888555555555544444555555555666555555555555 PP

                            AAA_23  69 ....gkvkayvelt......fenkdgrytrsiererelskkkgkttkkaklellei..deleqfisel 124
                                           ++ ++ + +       f+++++    s+++ + ++ k  ++++k++l ++++  + + ++i++l
  gi|386002781|ref|YP_005921080.1| 136 dllsKTPEPTINILarvinkFTKTHK----SVSEFKDKIAKTLREQQKKILVIIDDidRLTADEIRQL 199
                                       56653333334444333333333333....45444444445555555555555555542223334443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                            AAA_23 115 deleqfisellgskkiiln 133
                                       ++++ fi+++++  k+  n
  gi|386002781|ref|YP_005921080.1| 353 NKRDGFIDSKIEGLKKFHN 371
                                       4444444444444444222 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8
                            AAA_23 149 kdkkerleeleke 161
                                       +++ ++l++++ke
  gi|386002781|ref|YP_005921080.1| 703 ENQRNALKQFIKE 715
                                       2233333333333 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   9.5e-05     0.095       2      79 ..     123     201 ..     122     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.5e-05
                    Phage_min_cap2   2 tpeqleelsdkivdlysaleqeiiediarrikktge.ltntaewqieklaelgllnreilkliskltgksekelrkl 77 
                                       +p++l++l+ + +dl s+  +  i+ +ar i+k ++ ++++ e++ + ++ l+  +++il +i+++ + +++e+r+l
  gi|386002781|ref|YP_005921080.1| 123 DPDKLKHLIAEFSDLLSKTPEPTINILARVINKFTKtHKSVSEFKDKIAKTLREQQKKILVIIDDIDRLTADEIRQL 199
                                       58999************998888888888888865548899***********************************9 PP

                    Phage_min_cap2  78 lk 79 
                                       + 
  gi|386002781|ref|YP_005921080.1| 200 FR 201
                                       96 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0055       5.5       2      30 ..      58      85 ..      57     117 .. 0.73
   2 ?    3.0   0.0      0.13   1.3e+02      37      85 ..     167     211 ..     144     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0055
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkk 30
                                       +yG+ g GKStl++  +k  l++l +++
  gi|386002781|ref|YP_005921080.1| 58 SVYGSWGSGKSTLINF-IKYYLNQLPEDE 85
                                      69************99.666666664444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                      RNA_helicase  37 rnpeddfwdgYtgqevvvidDfgqvkdeenpsdlaelirlvsstpypln 85 
                                       + +  + +   +++  v+idD+ + + +    ++ +l+r+++s+   +n
  gi|386002781|ref|YP_005921080.1| 167 KDKIAKTLREQQKKILVIIDDIDRLTAD----EIRQLFRVIKSVADFPN 211
                                       55555555555666789********977....88888888888765555 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00026      0.26     215     299 ..     127     205 ..     123     217 .. 0.87
   2 ?   -2.5   0.1       2.2   2.2e+03      21      48 ..     685     715 ..     683     718 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                             PLU-1 215 aekweekakelLeareklsleeLeallneaqeipvslpslaaleeilkkarewqrkveelikssqdaaerptlsele 291
                                        +++++++++lL+++++++++ L +++n++++   s+  ++  ++i k +re q+k+  +i       +r t++e++
  gi|386002781|ref|YP_005921080.1| 127 LKHLIAEFSDLLSKTPEPTINILARVINKFTKTHKSVSEFK--DKIAKTLREQQKKILVIIDD----IDRLTADEIR 197
                                       689999*************************8776665555..488999***********998....799******* PP

                             PLU-1 292 ellkkges 299
                                       +l + ++s
  gi|386002781|ref|YP_005921080.1| 198 QLFRVIKS 205
                                       **998877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                             PLU-1  21 lrallneaekikfp...lkellekLktfvkd 48 
                                       l ++++ a+ki ++    +++ ++Lk+f+k+
  gi|386002781|ref|YP_005921080.1| 685 LSQIIDRARKIAYDegiTENQRNALKQFIKE 715
                                       6678999999988877766666999999987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00092      0.91      11      32 ..      54      75 ..      49     103 .. 0.88
   2 ?   -0.8   0.0       2.1   2.1e+03      79     112 ..     594     659 ..     532     662 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00092
                                      TSEEEEEESTTSSHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlklla 32
                                      g ++ + G+ G+GKStL++ + 
  gi|386002781|ref|YP_005921080.1| 54 GFVISVYGSWGSGKSTLINFIK 75
                                      6678999************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                       H...............................HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HH CS
                                       x...............................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          ABC_tran  79 n...............................esdeeiekalsklglkelkdtvvkssp.ssLSgG 112
                                                                       ++ ++ie+++++++ + ++d+v+     + LS+G
  gi|386002781|ref|YP_005921080.1| 594 LlekialekvveaaqngtllnisdlvyvlywwNKFDKIEDIRHWVQEVITDDDVLAMFLeKFLSKG 659
                                       033344444444444456666666667777777778899999999988888887755445667776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00078      0.78      22      49 ..      52      79 ..      30      87 .. 0.82
   2 ?   -0.3   0.1      0.61   6.1e+02     178     212 ..     169     203 ..     130     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00078
                                      TTSSEEEEEESTTSSHHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 22 fsksftaivGpNGSGKsnlldAilFvLG 49
                                      ++  + +++G+ GSGKs l++ i+++L 
  gi|386002781|ref|YP_005921080.1| 52 LEGFVISVYGSWGSGKSTLINFIKYYLN 79
                                      45556789*****************996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.61
                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemlekadklvgvt 212
                                       k+a+ l+e++k+  +i+  +++ +  + ++l++v 
  gi|386002781|ref|YP_005921080.1| 169 KIAKTLREQQKKILVIIDDIDRLTADEIRQLFRVI 203
                                       56666666666666666666666666666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.31      22      40 ..      53      72 ..      41      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                            AAA_29 22 kg.atlltGpsGsGKSTllD 40
                                      +g ++ + G  GsGKSTl+ 
  gi|386002781|ref|YP_005921080.1| 53 EGfVISVYGSWGSGKSTLIN 72
                                      46678899**********96 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3    0.0013       1.3     110     156 ..     159     204 ..     114     207 .. 0.82
   2 ?    0.3   0.2      0.79   7.8e+02       6     111 ..     476     600 ..     473     720 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                                       BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHC CS
                    DNA_ligase_A_N 110 tieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriil 156
                                       t + v e+ dk+a++ +  ++++k+ ++ + ++r++++E++ l+r i+
  gi|386002781|ref|YP_005921080.1| 159 THKSVSEFKDKIAKTlR--EQQKKILVIIDDIDRLTADEIRQLFRVIK 204
                                       668999999***98744..59999999******************997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.79
                                       HHHHHHHCC..---HH....HHHHHHHHHH...HTS-........SHHH.........HHHHHHHSS-CCC.S---- CS
                    DNA_ligase_A_N   6 aelfekiee.stkkrl....ekrailanff...rkves......agped.........lypalrLllPdyd.greyg 58 
                                        ++fek+e+ +         ++ +il+ ff       +          d         +  + r ll ++d + +y+
  gi|386002781|ref|YP_005921080.1| 476 RQFFEKLEDyTAE--DvpeeAIPKILKVFFdigD---EllcpedR---DempfgnsirIIRISRQLLLRFDeNERYN 544
                                       6677777773321..2244466777777774331...13333320...12332221123333344777777444788 PP

                                       --HHHHH..HHHHHHHT.--HHHHHHH...HHHHS-HHHHHHHHHCCHHHH------BH CS
                    DNA_ligase_A_N  59 igeslla..kalaealg.lskkkikda...lakvgDlgevaeevlskrstlakksplti 111
                                       i  ++++  +a++ ++  +s   ++ +   ++k g++g+ a e+l ++  l   +++++
  gi|386002781|ref|YP_005921080.1| 545 ILNKSMSegRAISMIVHeVS---VQRQgldKHKEGEVGSGADEILINSDHLDLLEKIAL 600
                                       77666651133333333222...222233344467777777766666555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.97u 0.39s 00:00:01.36 Elapsed: 00:00:00.56
# Mc/sec: 3992.48
//
Query:       gi|386002782|ref|YP_005921081.1|  [L=120]
Description: nucleotidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-14   54.2   0.1    1.7e-14   53.9   0.1    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
    4.2e-12   46.0   0.0    5.4e-12   45.6   0.0    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0069   16.6   0.0      0.009   16.2   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   2.8e-18   1.7e-14       7      93 ..      37     118 ..      24     120 .] 0.91

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.8e-18
                                       HHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                      NTP_transf_2   7 elkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83 
                                       el+++++va++ +fGSy rG+a ++SDiDllv l++  +    + +l++ +  +  l+ llg +vdlv+++ l+ p 
  gi|386002782|ref|YP_005921081.1|  37 ELSRRYKVASIGIFGSYLRGEADEESDIDLLVDLEDGDE----PLTLLEFIALENHLSDLLGAKVDLVEKSALK-PA 108
                                       6888888******************************65....7899***************************.99 PP

                                       EEEEEECEEE CS
                      NTP_transf_2  84 lvksileerp 93 
                                       + + ilee +
  gi|386002782|ref|YP_005921081.1| 109 IGRRILEEVQ 118
                                       9999999876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   9.1e-16   5.4e-12       8      85 ..      40     118 ..      21     120 .] 0.87

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 9.1e-16
                                       HHHHHHHSTTEEEEEE-S------EEEEEEEESS-...--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHH CS
                           Polbeta   8 ekekeielaylFGSrakgkareeSDiDlavllkek...ldleeelelaaelediklgkkvDlvdlneapplllyeil 81 
                                       +++ +++ + +FGS+++g+a eeSDiDl v l++    l+l e + l++ l+d+ lg kvDlv+ ++ +p + ++il
  gi|386002782|ref|YP_005921081.1|  40 RRY-KVASIGIFGSYLRGEADEESDIDLLVDLEDGdepLTLLEFIALENHLSDL-LGAKVDLVEKSALKPAIGRRIL 114
                                       334.9*****************************999999999***********.9********99999*9999999 PP

                                       HS-E CS
                           Polbeta  82 kegk 85 
                                       +e +
  gi|386002782|ref|YP_005921081.1| 115 EEVQ 118
                                       8755 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-06     0.009       7      55 ..      24      76 ..      21     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHHHHHHH-TT-EEE...E-HHHHTT-S.EESSEEEEEEBTTBSTT CS
                    DNA_pol_B_palm  7 vealealvkkaakeldpevevi...vcGSYRRgae.ssGDvDvlitkkdakse 55
                                      +e++++++++++ el+++++v    + GSY Rg++ +  D+D+l+  +d+++ 
  gi|386002782|ref|YP_005921081.1| 24 AEEIAEILRSQMPELSRRYKVAsigIFGSYLRGEAdEESDIDLLVDLEDGDEP 76
                                      5788899999999999886654222889**999761579******99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.35s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 719.22
//
Query:       gi|386002783|ref|YP_005921082.1|  [L=81]
Description: hypothetical protein Mhar_2104 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 612.39
//
Query:       gi|386002784|ref|YP_005921083.1|  [L=306]
Description: hypothetical protein Mhar_2105 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   13.5   1.3      0.091   12.0   0.0    2.1  2  DUF5050   Domain of unknown function (DUF5050)
       0.06   13.9   0.1       0.06   13.9   0.1    4.5  4  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.13   1.1e+03      34      34 ..      87      87 ..      57     111 .. 0.44
   2 ?   12.0   0.0     1e-05     0.091     149     212 ..     193     258 ..     186     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.13
                                      E CS
                           DUF5050 34 n 34
                                       
  gi|386002784|ref|YP_005921083.1| 87 T 87
                                      2 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1e-05
                                       EEEE-T..TT--EEEEETTTTEEEEEE-...S-EEEEEEEETTEEEEEGGGTT-EEEE-SSS---EE- CS
                           DUF5050 149 iYytge.sedhslykldtdgksiskvse...enlyllvvegdyiYyidlsknyaLyrvklsgsekevl 212
                                       +Y ++      s+yk+ t ++ ++k+ e   + +  lv+ g  +Yy d    +++yr++ls+ + ++ 
  gi|386002784|ref|YP_005921083.1| 193 LYLSSGnRVPASIYKVATGTGAVTKIFEsteGSIAGLVYRGGRLYYAD--WRQNIYRLDLSSMTSTLY 258
                                       554443033448999999998888887633245555899999999966..555688888887776654 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4      0.13   1.1e+03      10      25 ..      60      76 ..      51      78 .. 0.57
   2 ?    2.9   0.5     0.018   1.6e+02      27      37 ..     152     162 ..     112     167 .. 0.85
   3 ?   -0.1   0.1      0.16   1.4e+03      21      30 ..     190     199 ..     171     218 .. 0.72
   4 ?   13.9   0.1   6.7e-06      0.06      10      39 ..     223     251 ..     200     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                             PQQ_3 10 pg.pvnsspavdgglvy 25
                                      ++ ++ ++++++++++y
  gi|386002784|ref|YP_005921083.1| 60 GSvYYAGTATAADNIIY 76
                                      33233334466788887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.018
                             PQQ_3  27 gtgdGtlyAlD 37 
                                       ++gdG++y +D
  gi|386002784|ref|YP_005921083.1| 152 AGGDGRIYRVD 162
                                       56799999999 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.16
                             PQQ_3  21 gglvyvgtgd 30 
                                       +g +y ++g+
  gi|386002784|ref|YP_005921083.1| 190 EGNLYLSSGN 199
                                       7888888884 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 6.7e-06
                             PQQ_3  10 pgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                        g + +++++ gg++y +++  ++y lD  
  gi|386002784|ref|YP_005921083.1| 223 EGSI-AGLVYRGGRLYYADWRQNIYRLDLS 251
                                       4455.789********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1847.44
//
Query:       gi|386002785|ref|YP_005921084.1|  [L=269]
Description: Sodium bile acid symporter family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-09   36.1   7.1      5e-09   36.1   7.1    2.1  2  SBF       Sodium Bile acid symporter family
    7.5e-09   35.3  12.2    1.1e-07   31.5   4.3    2.1  2  SBF_like  SBF-like CPA transporter family (DUF4137)


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   7.1   5.6e-13     5e-09      31     144 ..      20     128 ..      16     139 .. 0.93
   2 !    2.7   1.4      0.01        89      60     116 ..     163     222 ..     131     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.6e-13
                               SBF  31 llglvlqwvikPllmfilakillrdlklepelavGlilvglapggamsnvwtylakGdlelsvvlvalstllaillt 107
                                       ++g+++++++  l + il++++  +   ++ l++G ++++++p + +++ +t l+ Gd+ l++   als +++i+l+
  gi|386002785|ref|YP_005921084.1|  20 VAGFLANYLF--LSGLILSIAPAVL--EAEALVLGFVVMAAVPPAVAVIPLTRLLAGDVRLALYSEALSYIASIVLM 92 
                                       689*******..9*******77444..48999********************************************* PP

                               SBF 108 PlllyllaksleqttlkvpieeivksvlivviiPlia 144
                                       P ++y++a++  +    v   e++k vl+++++P++a
  gi|386002785|ref|YP_005921084.1|  93 PSIIYIFARDA-GDGAGVGLGETAKIVLLLILLPILA 128
                                       ***********.88899*****************987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.01
                               SBF  60 pelavGlilvglapg...gamsnvwtylakGdlelsvvlvalstllailltPlllyllak 116
                                       +  a+G++ +++a+    ga++++++ +a+ + +  + l+++ ++  ++l + ++ ll +
  gi|386002785|ref|YP_005921084.1| 163 SGEAAGVLFIAIARTfvsGAAVYAAAAFAGVEAPQRIALTLFASFKNLGLAAAVALLLFG 222
                                       456899999999995444899999999999999***********9999999777776654 PP

>> SBF_like  SBF-like CPA transporter family (DUF4137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   4.3   1.2e-11   1.1e-07      64     173 ..      20     128 ..      11     136 .. 0.88
   2 !    8.8   1.0   9.7e-05      0.87     228     284 ..     169     225 ..     152     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-11
                          SBF_like  64 llvllisflltplivlalvsllkaaldpelliGllllaalPtTvssnvvmtsqAgGnealalceavignllGvfltP 140
                                       +  +l+++l+ + ++l +++++   + ++l++G++++aa+P++v+  + +t+   G++ lal++ +++ ++ ++l P
  gi|386002785|ref|YP_005921084.1|  20 VAGFLANYLFLSGLILSIAPAVL--EAEALVLGFVVMAAVPPAVA-VIPLTRLLAGDVRLALYSEALSYIASIVLMP 93 
                                       55678899999999999988884..5788***************7.699**************************** PP

                          SBF_like 141 alvqlll..sgssvsvdyaevlkklllsvllPlvv 173
                                        ++ ++    g +++v ++e+ k +ll +llP+++
  gi|386002785|ref|YP_005921084.1|  94 SIIYIFArdAGDGAGVGLGETAKIVLLLILLPILA 128
                                       *******6656699999999999999******975 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 9.7e-05
                          SBF_like 228 ifnvallLllvvlvillllarllklskedeiavlfcgsaKslalgvplisvlfgsnp 284
                                       ++++a++  +v  ++++++a + +++++++ia+++ +s K l l+  ++ +lfg   
  gi|386002785|ref|YP_005921084.1| 169 VLFIAIARTFVSGAAVYAAAAFAGVEAPQRIALTLFASFKNLGLAAAVALLLFGPRA 225
                                       45566667777778899999999******************************8754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1436.38
//
Query:       gi|386002786|ref|YP_005921085.1|  [L=76]
Description: Deoxyribonuclease/rho motif-related TRAM [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   50.9   0.5    1.2e-13   50.8   0.5    1.1  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.5   6.9e-18   1.2e-13       3      61 ..      21      75 ..      19      76 .] 0.94

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 6.9e-18
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                      + G+t+eV++e+ s ++g+gi+r++ g+v+fv++++   Gd+V + I++v r+++ ++ 
  gi|386002786|ref|YP_005921085.1| 21 EAGKTYEVEIEDIS-RQGDGIARVE-GFVIFVSDTKV--GDKVSISIDRVMRRFAIAHK 75
                                      67************.**********.*********99..****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 474.78
//
Query:       gi|386002787|ref|YP_005921086.1|  [L=241]
Description: Lipoprotein-releasing system, ABC transporter, ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.6e-34  117.2   0.0    1.1e-33  116.6   0.0    1.2  1  ABC_tran     ABC transporter
    1.4e-08   34.5   0.1    7.6e-05   22.2   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    4.2e-05   23.2   0.2    8.6e-05   22.2   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00027   20.9   0.0      0.021   14.6   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0003   21.2   0.0    0.00059   20.2   0.0    1.6  1  AAA_16       AAA ATPase domain
    0.00071   19.5   0.0     0.0016   18.4   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
     0.0017   18.7   0.1      0.017   15.4   0.0    2.2  2  AAA_22       AAA domain
     0.0028   17.2   0.2       0.22   11.1   0.0    2.7  2  AAA_25       AAA domain
     0.0033   18.0   0.1     0.0069   16.9   0.0    1.6  2  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.011   15.1   0.3          4    6.7   0.1    2.2  2  ATPase       KaiC
      0.014   15.1   0.0      0.031   14.0   0.0    1.6  2  AAA_30       AAA domain
      0.021   15.0   0.3       0.24   11.6   0.0    2.4  2  AAA_33       AAA domain
      0.025   14.2   1.2       0.26   10.9   0.2    2.2  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.029   14.1   0.0      0.095   12.4   0.0    1.7  2  AAA_15       AAA ATPase domain
      0.042   13.4   0.0        1.3    8.5   0.0    2.1  2  AAA_7        P-loop containing dynein motor region
      0.066   13.3   0.1       0.19   11.8   0.1    1.8  2  MMR_HSR1     50S ribosome-binding GTPase
       0.07   12.9   0.0        1.2    8.8   0.0    2.1  2  IstB_IS21    IstB-like ATP binding protein
        0.1   12.5   0.0       0.21   11.5   0.0    1.5  2  Rad17        Rad17 P-loop domain
       0.11   11.1   0.0       0.61    8.7   0.0    1.8  2  AAA_13       AAA domain
       0.12   11.5   0.5       0.21   10.7   0.1    1.5  2  NB-ARC       NB-ARC domain
       0.13   11.0   0.2       0.24   10.1   0.2    1.3  1  ABC_ATPase   Predicted ATPase of the ABC class
       0.15   12.0   0.2       0.53   10.2   0.1    1.9  2  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   1.4e-36   1.1e-33       1     136 [.      23     171 ..      23     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.4e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l++v+l++kege++ ivG++G+GKStLl+++  l +p  Gei+l+g+++++    ++ +  +ke+g+++q ++l pe
  gi|386002787|ref|YP_005921086.1|  23 LDDVDLTIKEGEVLSIVGPSGSGKSTLLNMIGLLDTPSGGEIWLKGQNITRatpkERARLRNKELGFIFQFHHLLPE 99 
                                       799*************************************************997777788899************* PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        ++ en             e+++++ ++l+++gl +   + + ++p++LSgGq qrva+aral+ +p++++ DEpt
  gi|386002787|ref|YP_005921086.1| 100 FNAVENvmmplliagvdrdEARDRAIALLQEVGLAD---RLM-NRPNQLSGGQNQRVAVARALAGHPSIVIGDEPT 171
                                       **9999*********955555555556666666555...555.777*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00034      0.28      25      44 ..      34      53 ..      10      58 .. 0.83
   2 !   22.2   0.0   9.4e-08   7.6e-05     134     212 ..     141     217 ..      66     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      ++ +ivGp GSGKs ll+ i
  gi|386002787|ref|YP_005921086.1| 34 EVLSIVGPSGSGKSTLLNMI 53
                                      4678***********99866 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9.4e-08
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadkl 208
                                       +++LSgG+ + va+a  +A +     ++++ De   +LD k    + ell++ + +    fi ++++ +m ek d++
  gi|386002787|ref|YP_005921086.1| 141 PNQLSGGQNQRVAVARALAGH----PSIVIGDEPTGNLDTKSSDMIYELLRKLNRQmnQTFILVTHDMTMAEKTDRI 213
                                       459***********9998865....468999********************766553256999************** PP

                                       EEEE CS
                                       xxxx RF
                             SMC_N 209 vgvt 212
                                       +++ 
  gi|386002787|ref|YP_005921086.1| 214 LRIV 217
                                       9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   1.1e-07   8.6e-05      13      42 ..      24      53 ..      21      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAi 42
                                      d+ +++i++ ++  ++GpsGsGKSTll  i
  gi|386002787|ref|YP_005921086.1| 24 DDVDLTIKEGEVLSIVGPSGSGKSTLLNMI 53
                                      56778888666999************9655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.6e-05     0.021       4      38 ..      38      60 ..      35      98 .. 0.74
   2 ?    4.6   0.0      0.03        24     259     300 ..     163     205 ..     120     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                            AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsg 38
                                      ++Gp gsGKS+LL  + ll            + ++
  gi|386002787|ref|YP_005921086.1| 38 IVGPSGSGKSTLLNMIGLL------------DTPS 60
                                      9***************888............3333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.03
                            AAA_21 259 sllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSpl 300
                                       s+++ DEp  +L+ k    ++ell++l+r   Q  il+TH+ +
  gi|386002787|ref|YP_005921086.1| 163 SIVIGDEPTGNLDTKSSDMIYELLRKLNRQMNQTfILVTHDMT 205
                                       77777*******************88888555655*****965 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.3e-07   0.00059      22     163 ..      31     190 ..      17     214 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.3e-07
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.........salaqalareellrqllde. 88 
                                        ++e++ ++G+sG+GKs+l++++   l +  g  ++ k +  ++a+p          +    ++ +++ll + ++  
  gi|386002787|ref|YP_005921086.1|  31 KEGEVLSIVGPSGSGKSTLLNMIG-LLDTPSGGEIWLKGQNITRATPKerarlrnkeL--GFIFQFHHLLPEFNAVe 104
                                       455899**************9998.666665566666666666664444444565433..44444457777777766 PP

                            AAA_16  89 ...........aesaeleawrekleeala.............................avpelagaeasrllellkr 125
                                                  +    ++++r++  + l+                             a                  
  gi|386002787|ref|YP_005921086.1| 105 nvmmplliagvD----RDEARDRAIALLQevgladrlmnrpnqlsggqnqrvavaralA------------------ 159
                                       667666544321....2222222222222222444444433333332222222222220.................. PP

                            AAA_16 126 llallsrderplvlvlDdlq.wadeaslqllaaLlrlle 163
                                               ++p +++ D+    +d+ s +++++Llr l+
  gi|386002787|ref|YP_005921086.1| 160 --------GHPSIVIGDEPTgNLDTKSSDMIYELLRKLN 190
                                       ........4444444443333444555555555544444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0016      91     119 ..      24      53 ..      11      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinal 119
                                       +++   +k+ ++  +vG+SG GKStL+n++
  gi|386002787|ref|YP_005921086.1|  24 DDVDLTIKEgEVLSIVGPSGSGKSTLLNMI 53 
                                       55566666669999**************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-05     0.017       4      26 ..      32      54 ..      14      80 .. 0.90
   2 ?    1.1   0.0      0.52   4.3e+02      94     127 ..     164     199 ..     115     215 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      +  +l ++G+sG+GK+tll+++ 
  gi|386002787|ref|YP_005921086.1| 32 EGEVLSIVGPSGSGKSTLLNMIG 54
                                      567899*************9876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.52
                            AAA_22  94 lliiDEaqh.lr..seealeeL.rsllnlsrkgvqliL 127
                                       ++i DE    l+  s +++ eL r+l    + + ++iL
  gi|386002787|ref|YP_005921086.1| 164 IVIGDEPTGnLDtkSSDMIYELlRKLNR--QMNQTFIL 199
                                       4444444433544433333333133333..55555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00027      0.22      29      50 ..      29      50 ..      25      79 .. 0.83
   2 ?    3.5   0.1     0.058        48     163     188 ..     177     202 ..     110     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                       + +ge+  ++G++g+GK+tl+
  gi|386002787|ref|YP_005921086.1| 29 TIKEGEVLSIVGPSGSGKSTLL 50
                                      5789****************98 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.058
                            AAA_25 163 sdvgalvealeriarrtgaavllvhH 188
                                       +  ++++e l+++ r+ + +++lv H
  gi|386002787|ref|YP_005921086.1| 177 KSSDMIYELLRKLNRQMNQTFILVTH 202
                                       23488999999999999999999999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.5e-06    0.0069      19      40 ..      33      54 ..       5      58 .. 0.74
   2 ?   -2.9   0.0       9.8     8e+03     118     138 ..     179     199 ..     167     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.5e-06
                            AAA_23 19 kgltlItGpNGaGKTTildAik 40
                                        +  I+Gp G+GK+T+l+ i 
  gi|386002787|ref|YP_005921086.1| 33 GEVLSIVGPSGSGKSTLLNMIG 54
                                      45678*************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.8
                            AAA_23 118 eqfisellgskkiilnlilfl 138
                                        ++i ell + ++++n+ ++l
  gi|386002787|ref|YP_005921086.1| 179 SDMIYELLRKLNRQMNQTFIL 199
                                       456666666667777666655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0061       4.9      15      35 ..      29      49 ..      18      52 .. 0.85
   2 ?    6.7   0.1    0.0049         4     143     193 ..     181     229 ..     170     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0061
                            ATPase 15 GipegrvvlitGepGtGKtif 35
                                       i eg+v  i+G +G+GK+++
  gi|386002787|ref|YP_005921086.1| 29 TIKEGEVLSIVGPSGSGKSTL 49
                                      5889**************987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0049
                            ATPase 143 ilrqlvrvl.kklgvTailvsekssseeaaggygveefivdgvivLdlkeie 193
                                        + +l+r l +++++T ilv+       a ++ ++   ivdg iv + ++  
  gi|386002787|ref|YP_005921086.1| 181 MIYELLRKLnRQMNQTFILVTHD--MTMAEKTDRILR-IVDGRIVCEMRRDG 229
                                       6778999999999********94..445667788999.9***9998877655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.8e-05     0.031      16      47 ..      31      69 ..      24     140 .. 0.77
   2 ?   -1.9   0.0       2.7   2.2e+03      27      27 ..     171     171 ..     143     216 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaag.......g 47
                                      ++  v  ++Gp G+GK+t+l+ +  + + +g       +
  gi|386002787|ref|YP_005921086.1| 31 KEGEVLSIVGPSGSGKSTLLNMIGLLDTPSGgeiwlkgQ 69
                                      3445999**************999988888734444433 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                            AAA_30  27 A 27 
                                        
  gi|386002787|ref|YP_005921086.1| 171 T 171
                                       2 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00029      0.24       2      16 ..      36      50 ..      35      89 .. 0.91
   2 ?    1.3   0.1      0.42   3.4e+02      41      83 ..     168     210 ..     102     223 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                            AAA_33  2 vllvGlpGsGKstla 16
                                      + +vG++GsGKstl+
  gi|386002787|ref|YP_005921086.1| 36 LSIVGPSGSGKSTLL 50
                                      6689*********97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.42
                            AAA_33  41 dqqsktdytrvldrlyqilnelarkalsagrnvil...datnlsrr 83 
                                       d+++ +  t+ +d +y+ l++l r++ +    +il   d+t++++ 
  gi|386002787|ref|YP_005921086.1| 168 DEPTGNLDTKSSDMIYELLRKLNRQMNQT---FILvthDMTMAEKT 210
                                       33444444555555555555555433333...33333366666554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00032      0.26       2      20 ..      35      53 ..      34      63 .. 0.88
   2 ?    2.0   0.1      0.17   1.4e+02      39      70 ..     200     230 ..     184     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                      EEEEEESTTCCHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhl 20
                                      v+ ++G+ GsGK+tLln +
  gi|386002787|ref|YP_005921086.1| 35 VLSIVGPSGSGKSTLLNMI 53
                                      6789************976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                                       CHCCCCCCHCCCT.EEEETTTTECCHCTT-HH CS
                              cobW  39 vsiDaellretgveivelenGciCctlredll 70 
                                       v +D ++ ++t + i+ + +G i c +r d  
  gi|386002787|ref|YP_005921086.1| 200 VTHDMTMAEKT-DRILRIVDGRIVCEMRRDGD 230
                                       56676666666.67999999999999998865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.095      14      46 ..      23      56 ..      22      97 .. 0.85
   2 ?   -0.9   0.0       1.3     1e+03     326     368 ..     164     206 ..     158     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlF 46
                                      l+dv++ ++e  +  ++G+ +sGKS++l+++ l+
  gi|386002787|ref|YP_005921086.1| 23 LDDVDLTIKEGeVLSIVGPSGSGKSTLLNMIGLL 56
                                      567777777777999***************9776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                       i++ +EP  +L ++   ++++ll++l ++ ++  i+ TH   +
  gi|386002787|ref|YP_005921086.1| 164 IVIGDEPTGNLDTKSSDMIYELLRKLNRQMNQTFILVTHDMTM 206
                                       5566777777777777888888888888888666789997665 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 ?    8.5   0.0    0.0016       1.3      27      52 ..      27      52 ..      18      67 .. 0.87
   2 ?    2.6   0.0       0.1        83      34      82 ..     161     214 ..     152     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                             AAA_7 27 elllknkkpvllvGptGtGKtviikd 52
                                      +l +k++  + +vGp+G+GK+++++ 
  gi|386002787|ref|YP_005921086.1| 27 DLTIKEGEVLSIVGPSGSGKSTLLNM 52
                                      67889999999***********9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                             AAA_7  34 kpvllvGptGtG....K.tviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                                       +p +++G++ tG    K + +i +ll+kl+++  ++ ++  + +t a+++ +i+
  gi|386002787|ref|YP_005921086.1| 161 HPSIVIGDEPTGnldtKsSDMIYELLRKLNRQMNQTFILVTHDMTMAEKTDRIL 214
                                       666667766666444442457778******888888888888999999998887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00023      0.19       3      19 ..      37      53 ..      35      90 .. 0.86
   2 ?   -1.8   0.0         4   3.3e+03      66      66 ..     200     200 ..     157     231 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                      EEEESTTSSHHHHHHHH CS
                          MMR_HSR1  3 aivGrpNvGKStLinal 19
                                       ivG + +GKStL+n +
  gi|386002787|ref|YP_005921086.1| 37 SIVGPSGSGKSTLLNMI 53
                                      69*************86 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                                       H CS
                          MMR_HSR1  66 l 66 
                                       +
  gi|386002787|ref|YP_005921086.1| 200 V 200
                                       1 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0015       1.2      44      68 ..      30      54 ..      16      67 .. 0.83
   2 ?    1.8   0.0      0.22   1.8e+02     107     153 ..     160     208 ..     134     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      i++ e + ++GpsG GKs l   +g
  gi|386002787|ref|YP_005921086.1| 30 IKEGEVLSIVGPSGSGKSTLLNMIG 54
                                      67889999**********9987776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.22
                         IstB_IS21 107 lkvdllilDdlgllpldqaeaellfevi...ekryerrsiiitsnlpfae 153
                                        +++++i D+  + +ld +++ +++e++   +++ +++ i++t ++++ae
  gi|386002787|ref|YP_005921086.1| 160 GHPSIVIGDE-PTGNLDTKSSDMIYELLrklNRQMNQTFILVTHDMTMAE 208
                                       4455555555.456677777777777761115567888899999888876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.21      40      67 ..      28      55 ..       9     111 .. 0.79
   2 ?   -2.8   0.0       6.1   4.9e+03     146     170 ..     176     199 ..     154     210 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLsk 67
                                      L  ++ ++L i GPsG gkst ++++  
  gi|386002787|ref|YP_005921086.1| 28 LTIKEGEVLSIVGPSGSGKSTLLNMIGL 55
                                      55666779*************9998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.1
                             Rad17 146 yrdsdalrevirkylrssealplil 170
                                        ++sd + e++rk  r  +  ++il
  gi|386002787|ref|YP_005921086.1| 176 TKSSDMIYELLRKLNRQMNQ-TFIL 199
                                       44556666666665544443.3343 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.25     2e+02      22      41 ..      39      58 ..      35     130 .. 0.81
   2 ?    8.7   0.0   0.00075      0.61     526     575 ..     161     208 ..     151     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                            AAA_13 22 YGwNGaGKTtLSrllrslel 41
                                       G  G+GK+tL +++  l +
  gi|386002787|ref|YP_005921086.1| 39 VGPSGSGKSTLLNMIGLLDT 58
                                      5888*******999987755 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00075
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiL.THnleffk 575
                                          iv+ D P   LD++s+ +++ l+++      +++Q fiL TH ++   
  gi|386002787|ref|YP_005921086.1| 161 HPSIVIGDEPTGNLDTKSSDMIYELLRKLN---RQMNQTFILvTHDMTMAE 208
                                       5789999**********************7...9999999987**998765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00026      0.21      19      40 ..      34      53 ..      22      55 .. 0.85
   2 ?   -3.2   0.1       4.7   3.8e+03      11     100 ..     188     193 ..     175     216 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                                      CSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqi 40
                                      +  v+++vG  G+GK+tl++ i
  gi|386002787|ref|YP_005921086.1| 34 E--VLSIVGPSGSGKSTLLNMI 53
                                      4..99*************9765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.7
                                       HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS- CS
                            NB-ARC  11 kLlekdelqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleeke 87 
                                       kL                                                                           
  gi|386002787|ref|YP_005921086.1| 188 KLN-------------------------------------------------------------------------- 190
                                       222.......................................................................... PP

                                       STTSHHHHHHHHC CS
                            NB-ARC  88 eveslkrklvrlL 100
                                                 r +
  gi|386002787|ref|YP_005921086.1| 191 ----------RQM 193
                                       ..........111 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0003      0.24     240     264 ..      28      53 ..      26      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                                       EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                                       + i++G v  IvG+   GKsTLL+ +
  gi|386002787|ref|YP_005921086.1|  28 LTIKEGeVLSIVGPSGSGKSTLLNMI 53 
                                       679********************976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00065      0.53       2      20 ..      35      53 ..      34      56 .. 0.87
   2 ?   -1.3   0.0       2.3   1.9e+03     108     127 ..     185     202 ..     168     223 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00065
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      ++ + G++GsGK+tLl  +
  gi|386002787|ref|YP_005921086.1| 35 VLSIVGPSGSGKSTLLNMI 53
                                      67799***********876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                                       .HHHHHCTTTTT--EEEEEE CS
                             NACHT 108 lLselirkkllpeasllltv 127
                                       lL++l r+  + ++ +l+t 
  gi|386002787|ref|YP_005921086.1| 185 LLRKLNRQ--MNQTFILVTH 202
                                       33333333..4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.60
# Mc/sec: 1207.36
//
Query:       gi|386002788|ref|YP_005921087.1|  [L=384]
Description: ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-17   62.9   2.5    7.3e-17   62.4   2.5    1.3  1  MacB_PCD  MacB-like periplasmic core domain
    2.7e-15   56.6   7.0    8.9e-15   54.9   2.1    3.1  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   2.5   8.2e-21   7.3e-17       2     193 ..      19     225 ..      18     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 8.2e-21
                          MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsges.ls.dpdvealrrevp.veavapvv.. 73 
                                       l+tv+++a++v++++++++l+eg ++ + ++  +++  vtv+p++g  e+ +  ++ + a+++e p v+a++p++  
  gi|386002788|ref|YP_005921087.1|  19 LFTVISVALAVGVIVVLIGLTEGYRQDLIDNTVENSPHVTVSPKEG--EDyIYlYRTLAAIATEHPeVVAASPRLvg 93 
                                       68****************************9654444366666543..2212212222255667899******9756 PP

                          MacB_PCD  74 ..tvrgggsgeeevtvvgvdp.dyfkvfgl.kl.aeGrffteadlrggpnvvvigeelaerlf.pvGdtirl..... 139
                                         +++ +++  +++t +gvdp ++  ++ + +  + G   +++dl+ +++++v+g++la++l  +vGd+ r+     
  gi|386002788|ref|YP_005921087.1|  94 gaAAKHRDN-VKGITFIGVDPlQEDLLLRVqEEvVWG---DFYDLQFRRYAAVVGSALADDLElKVGDKFRItrlda 166
                                       542222221.244888999974333366663222336...6699999**************88*************9 PP

                          MacB_PCD 140 .kpftVvGvledppgsgsalgddavylplttlqrrs........itvrlkdgadleaaaaele 193
                                         ++t vG++e+  g  ++l+++ +ylpl t+q+          + +rl++   + a+aa+l+
  gi|386002788|ref|YP_005921087.1| 167 sLQLTAVGIIET--G--TGLDRTLIYLPLGTAQQLLgegdvvteVGIRLSEIYAAPAIAADLN 225
                                       999******944..4..568999*****88884433555556568889988888888888775 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.037   3.3e+02      18      36 ..      19      37 ..       9      62 .. 0.60
   2 ?   -0.0   0.1      0.14   1.2e+03      26      41 ..     255     270 ..     240     279 .. 0.55
   3 !   54.9   2.1     1e-18   8.9e-15       2      96 .]     281     377 ..     280     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.037
                              FtsX 18 lllllteillitlvalviG 36
                                      l  +++ +l+++++  +iG
  gi|386002788|ref|YP_005921087.1| 19 LFTVISVALAVGVIVVLIG 37
                                      3333333333333333333 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.14
                              FtsX  26 llitlvalviGlglgl 41 
                                       +++ l+ +++Glg+ +
  gi|386002788|ref|YP_005921087.1| 255 AFYLLIFFISGLGIVN 270
                                       3333444444444333 PP

  == domain 3  score: 54.9 bits;  conditional E-value: 1e-18
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs..selkisidlitvliiivll 76 
                                       reigil a+G++++++++++++e+++++ +++++G gl+ +aa+l+ +      f   +++++ +dl t+l +++++
  gi|386002788|ref|YP_005921087.1| 281 REIGILMAMGASRGSIIKIFILESVILGPPSALLGGGLAHVAAKLIGTIEVPAEFYmtDRMTVVLDLGTFLYVALFA 357
                                       9********************************************6654333322235******************* PP

                              FtsX  77 lllallagllsiskilkkep 96 
                                       l++  +ag+++++k+++ +p
  gi|386002788|ref|YP_005921087.1| 358 LVVNFIAGIYPAFKASRLDP 377
                                       *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2352.69
//
Query:       gi|386002789|ref|YP_005921088.1|  [L=385]
Description: ABC transporter permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-11   45.5   3.5    1.1e-11   45.5   3.5    1.6  2  MacB_PCD     MacB-like periplasmic core domain
    1.2e-11   44.9   0.6    1.2e-11   44.9   0.6    3.2  3  FtsX         FtsX-like permease family
  ------ inclusion threshold ------
       0.29   11.5   4.5       0.57   10.5   0.0    2.9  3  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   3.5   1.8e-15   1.1e-11       1     194 [.      18     226 ..      18     227 .. 0.73
   2 ?   -2.9   0.8       1.2   7.3e+03       9      37 ..     255     283 ..     254     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.8e-15
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrr...evp.veavapvv 73 
                                       +ll+v ++ ++va +i++ ++++g+ +++ s i +l+  v v p++  ge+    ++++l +    +p v+av+p +
  gi|386002789|ref|YP_005921088.1|  18 TLLAVGAVGLAVAIIIVFRAIMNGSIDTFFSLIFELAPHVLVLPKE--GEE-YIYLYKTLIEfvwTIPgVAAVSPAL 91 
                                       89*****************************988898845555654..333.22233332223456899******98 PP

                          MacB_PCD  74 .....tvrgggsgeeevtvvg.vdpdyfkvfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl.. 139
                                            ++  g+   e+v ++g v +++ kv ++  ++ eG f   + +++g++ vv+g+++ae+l  ++G+ +    
  gi|386002789|ref|YP_005921088.1|  92 sgtaaLAFEGN--VENVEMTGgVPAEMNKVMSIekYMIEGDF---YSIASGRR-VVLGDKVAEKLGvKIGEGVVAsf 162
                                       66442222222..24478888755599999999633477844...55665666.**********99*******9999 PP

                          MacB_PCD 140 .....kpftVvGvledppgsgsalg..ddavylplttlqrrs.........itvrlkdgadleaaaaelek 194
                                             ++ V+G++ +  g        d a++++l t+++ +         i + l+d+ +++a+a+e+ +
  gi|386002789|ref|YP_005921088.1| 163 pdaktMNLVVAGIFRT--G-V---EewDGAAFVSLGTARE-FvgdgdvinyINIHLQDPYQADAVAEEISA 226
                                       9997777******933..2.2...235799****888822.1355555666*****************975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                          MacB_PCD   9 aiGvaaviaivslgeglqasvlsqisdlg 37 
                                       +++   +ia +++ + ++  vl+  +d g
  gi|386002789|ref|YP_005921088.1| 255 ILALVLLIASFGIANVMNMLVLEKTRDVG 283
                                       66666777777777777766666666555 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.0      0.12   7.2e+02      26      85 ..      20      94 ..      16      99 .. 0.47
   2 ?    1.8   0.2     0.056   3.3e+02      16      45 ..     244     273 ..     242     278 .. 0.74
   3 !   44.9   0.6     2e-15   1.2e-11       2      96 .]     280     379 ..     279     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                              FtsX 26 llitlvalviGlglgllaaqllsdvllssvf...............s..selkisidlitvliiivlllllallagl 85
                                      l++++v+l+++  + +++  +++  ++++++               +      + + ++ v++i +++ +   l+g 
  gi|386002789|ref|YP_005921088.1| 20 LAVGAVGLAVA--IIIVFRAIMNGSIDTFFSlifelaphvlvlpkeGeeYIYLYKTLIEFVWTIPGVAAVSPALSGT 94
                                      45556666666..3333333333333333333333333333333321335555556666666666666666666655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.056
                              FtsX  16 qvlllllteillitlvalviGlglgllaaq 45 
                                       +++   l+ +l+++lv l++++g+++++  
  gi|386002789|ref|YP_005921088.1| 244 TLAFETLSNNLILALVLLIASFGIANVMNM 273
                                       566667788899999999999888887755 PP

  == domain 3  score: 44.9 bits;  conditional E-value: 2e-15
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs.....selkisidlitvliii 73 
                                       r +g+l a+G+ +  +++++++e+ +++l + ++G + g+l++ +l ++  ++        +  k+ +d+++++++ 
  gi|386002789|ref|YP_005921088.1| 280 RDVGMLMAMGADSSAIRRIFVIESGILGLAGGIAGSASGYLISAYLHSLQITITAPnapqpIVFKFLVDPFDLIAFP 356
                                       789******************************************9999999977567888**************** PP

                              FtsX  74 vlllllallagllsiskilkkep 96 
                                       +l+l+l ++ag++++ +++  +p
  gi|386002789|ref|YP_005921088.1| 357 LLALVLSMIAGVYPAHRASQLDP 379
                                       *****************998776 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.5e-05      0.57       2      62 ..       9      86 ..       8     107 .. 0.82
   2 ?    1.4   0.4     0.066   3.9e+02      16      38 ..     250     272 ..     243     287 .. 0.52
   3 ?   -2.4   0.1         1     6e+03      20      37 ..     353     370 ..     352     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.5e-05
                       Sigma_reg_N  2 kilkkakrksilrivlislivlllifvilvvtllyl...............aekegnklrevlelave..itsPNvyv 62
                                      k ++ +kr+++l +  + l+v+++i++  +++++++               ++keg+++++ +++++e  +t P v +
  gi|386002789|ref|YP_005921088.1|  9 KHIRTRKRQTLLAVGAVGLAVAIIIVFRAIMNGSIDtffslifelaphvlvLPKEGEEYIYLYKTLIEfvWTIPGVAA 86
                                      56999**********************999999988889999999999999999999999999998873356666665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.066
                       Sigma_reg_N  16 vlislivlllifvilvvtllyla 38 
                                        +  li++l++++ ++ +++ ++
  gi|386002789|ref|YP_005921088.1| 250 LSNNLILALVLLIASFGIANVMN 272
                                       44445555555555555544442 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1
                       Sigma_reg_N  20 livlllifvilvvtllyl 37 
                                       +++ ll +v++++ + y 
  gi|386002789|ref|YP_005921088.1| 353 IAFPLLALVLSMIAGVYP 370
                                       788899999998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2367.28
//
Query:       gi|386002790|ref|YP_005921089.1|  [L=265]
Description: Fructose-bisphosphate aldolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-58  196.9   0.0    4.3e-58  196.7   0.0    1.0  1  DeoC       DeoC/LacD family aldolase
    0.00045   19.9   0.0    0.00064   19.4   0.0    1.2  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
       0.11   11.9   0.0        9.4    5.5   0.0    2.4  2  TMP-TENI   Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.7   0.0   7.2e-62   4.3e-58       1     234 [.      21     236 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 196.7 bits;  conditional E-value: 7.2e-62
                                       EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTT CS
                              DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskq 77 
                                       +vi+++D++   +++++       +dl++ v++++++ga+avl + g+ + ++++y++d++l+v+l+++  l ++++
  gi|386002790|ref|YP_005921089.1|  21 TVIVPMDHGLTVGPIQGL------IDLQEAVDKVAEGGANAVLGHMGLPLFGHRGYGRDVGLIVHLSASSSLGPDPN 91 
                                       69****************......9**************************************************** PP

                                       EEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  78 rdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                       ++v+ v++ve a++ GAdav+++v++   g+e+e+++l++++rv+ +c+ +g+pl++++y+r+ ++k e+ d + v+
  gi|386002790|ref|YP_005921089.1|  92 HKVL-VTEVEDAIRVGADAVSIHVNV---GAEDEATMLQDLGRVARTCDGWGMPLLAMMYPRGTKVKSEH-DVEYVK 163
                                       ****.*********************...*****************************************.****** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvls 228
                                       +Aar++aelG+Di+K++++        ++ e+f++v+k++ vp vv++GG+   +e ++le+v d++ + g+ G+++
  gi|386002790|ref|YP_005921089.1| 164 HAARIGAELGVDIVKTNYT--------GSPETFREVVKGCSVP-VVIAGGPkmdTEHQVLEMVYDSI-KVGGGGLSI 230
                                       *******************........****************.**********9************.********* PP

                                       SHHHHT CS
                              DeoC 229 GRaifq 234
                                       GR+ifq
  gi|386002790|ref|YP_005921089.1| 231 GRNIFQ 236
                                       *****9 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-07   0.00064      82     220 ..     102     242 ..      94     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                                       HHHTTESEEEEEGTGH....HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESE CS
                         OMPdecase  82 rikewadivtvhavaG....kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmG 154
                                       +i  +ad+v +h+ +G      +++ l ++a+ +++ g+ +la+m   g     e   + + v++a++  ae    G
  gi|386002790|ref|YP_005921089.1| 102 AIRVGADAVSIHVNVGaedeATMLQDLGRVARTCDGWGMPLLAMMYPRGTKVKSE--HDVEYVKHAARIGAE---LG 173
                                       5778899999998888433345999999999999999************999999..*************99...67 PP

                                       EECCCHTHHHHHHTTCSCEEEHHHTT......EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHH CS
                         OMPdecase 155 fvaqetlnateedaddfihltpgigl......eqggdgkgqqyntpekligiagadiiivGRgIlkagdpve 220
                                       +   +t   t  + ++f  +++g+ +        + d++ q  +++ + i++     + +GR I++a+dp  
  gi|386002790|ref|YP_005921089.1| 174 VDIVKTNY-T-GSPETFREVVKGCSVpvviagGPKMDTEHQVLEMVYDSIKVG-GGGLSIGRNIFQAKDPTL 242
                                       76666644.2.2246**************888888999999999999999977.567889*********975 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0057        34      12      61 ..      92     143 ..      84     145 .. 0.85
   2 ?    5.5   0.0    0.0016       9.4     139     174 ..     185     220 ..     175     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0057
                          TMP-TENI  12 neellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpli 61 
                                       ++ l+  ve+a++ g+++v +       d++++l+   ++a+ c+  g+pl+
  gi|386002790|ref|YP_005921089.1|  92 HKVLVTEVEDAIRVGADAVSIHVNvgAEDEATMLQDLGRVARTCDGWGMPLL 143
                                       5568999********99999888876789999999999******99999886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0016
                          TMP-TENI 139 leglkelaealeiPvvaiGGitlenvaevleagadg 174
                                        e+++e+++ +++Pvv  GG ++++ ++vle   d+
  gi|386002790|ref|YP_005921089.1| 185 PETFREVVKGCSVPVVIAGGPKMDTEHQVLEMVYDS 220
                                       68899***********************99876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1690.86
//
Query:       gi|386002791|ref|YP_005921090.1|  [L=245]
Description: outer membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-48  165.4   2.7    2.6e-48  165.2   2.7    1.0  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.2   2.7   1.4e-52   2.6e-48       1     200 []      34     235 ..      34     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 1.4e-52
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy.engknk 76 
                                       +tV+G++e+++ +D +t+tl+v++++++aa+a++++a++m+a +eal+++g++e++i+tss+s++p +++ ++++ +
  gi|386002791|ref|YP_005921090.1|  34 LTVSGTGEATADSDSVTITLGVQTRDESAAKAADDNARRMAASIEALQAAGVPEEEIKTSSYSIYPTRDWiDGRQSE 110
                                       69**********************************************99********************7333333 PP

                             SIMPL  77 itgyeasqsltvkfrdldk..lgevldaavka.aneingvsfslsdedelrdeareeAvkdArakAealAkalgvkl 150
                                          +e+s+++t++++ +d   +g ++daav a an+i+gvsf+l+d+ + r+ea+eeAv d + kA ++A+a+gv+l
  gi|386002791|ref|YP_005921090.1| 111 KVIFEVSNRVTFTLNLTDEvdVGGIIDAAVGAgANTIDGVSFGLRDPTPVREEALEEAVLDGMGKAAVIAEAAGVSL 187
                                       3349*********98666578******************************************************** PP

                             SIMPL 151 gkvvsisesgsnpyappapamaaaaaa..aasaatpfepgeievtasVtvvf 200
                                       g+++sise+gs+p +++ ++         +a aatp+ pg+++vta+Vt+++
  gi|386002791|ref|YP_005921090.1| 188 GRILSISEGGSAPIPMAESKVF----FaaDAGAATPIAPGDVKVTATVTITY 235
                                       ********76666555444444....2458********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1910.11
//
Query:       gi|386002792|ref|YP_005921091.1|  [L=131]
Description: hypothetical protein Mhar_2113 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-41  140.4   0.0    2.5e-41  140.2   0.0    1.0  1  DUF473    Protein of unknown function (DUF473)


Domain annotation for each model (and alignments):
>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   0.0   1.4e-45   2.5e-41       1     117 [.       3     119 ..       3     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 1.4e-45
                            DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvv 77 
                                       M++vaLtGis+ vi+eL++n +rt+e+rs+ N+++ll++++gd++FlT++s  D++ Gt G++++v++++++t++vv
  gi|386002792|ref|YP_005921091.1|   3 MECVALTGISRPVIRELLTNGIRTLEIRSPGNFLALLQTNPGDVIFLTEASGPDIVAGTGGMLTRVREIQVVTHKVV 79 
                                       9**************************************************************************** PP

                            DUF473  78 essesfieErEttvarvqlkllglgrvrevkeeellkptk 117
                                       ++ + f+eErE+++arvql ++g+grvr+vk+ ++++pt+
  gi|386002792|ref|YP_005921091.1|  80 QAGADFYEERESQAARVQLVIVGHGRVRRVKSLKIGSPTV 119
                                       ************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 841.33
//
Query:       gi|386002793|ref|YP_005921092.1|  [L=245]
Description: hypothetical protein Mhar_2114 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-49  168.6   0.1    2.1e-49  168.4   0.1    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
      0.039   12.9   0.0      0.052   12.5   0.0    1.2  1  DUF726    Protein of unknown function (DUF726)


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   0.1   2.4e-53   2.1e-49       2     213 .]      20     222 ..      19     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 2.4e-53
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...r 75 
                                       i+GfpgiG++g +a ++++++le++++g+ids++ +p     p+ ++ +g+  +p+r+y k+  +  ++v+ +   +
  gi|386002793|ref|YP_005921092.1|  20 IEGFPGIGLIGNIASQYVVNKLEMDYLGAIDSRF-FP-----PISVLVGGVAHMPVRIYEKP--ELGVVVVSSdipV 88 
                                       9*********************************.**.....*****************996..599******9988 PP

                                       -HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT....-CEEEEHHHH CS
                              PAC2  76 epilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees....eyggivgitg 148
                                       +p + y+ +a+ +++wae++g +e+v+L+g+  +         +++v+gaat++e+le++  +    e g+i+gi+g
  gi|386002793|ref|YP_005921092.1|  89 HPAASYD-LARGIVSWAESIGSREMVCLAGITVMGD-------QQRVFGAATNREMLEKIRGEvevfEFGTISGISG 157
                                       8888888.************************8754.......45***************63336799********* PP

                                       HHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHHH CS
                              PAC2 149 lLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleela 213
                                       + ++++  r++pa++ll+e++   pdP+aa++ ++ l+ l+gl+vdt+dLee+aee+e q+++la
  gi|386002793|ref|YP_005921092.1| 158 SVMNECLLRKMPAICLLGETHSMAPDPRAAVVTVKMLNTLYGLQVDTTDLEERAEEIELQMQKLA 222
                                       **************************************************************985 PP

>> DUF726  Protein of unknown function (DUF726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-06     0.052      37     148 ..     102     215 ..      85     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-06
                            DUF726  37 allaglGltgsaafLasvggsavitallgaagAklsvkkmkkrvkeikdFefiplseqirl........ksltvtvs 105
                                       +   ++G+      +  ++g++v++    ++gA +  + ++k  +e++ Fef ++s+ + +        k   +++ 
  gi|386002793|ref|YP_005921092.1| 102 SWAESIGSR---E-MVCLAGITVMGDQQRVFGAATNREMLEKIRGEVEVFEFGTISGISGSvmnecllrKMPAICLL 174
                                       444444442...2.33467999********************************99988777777776444466776 PP

                            DUF726 106 islelsdeddvtapwralakaekdlYalkwEvelLkelGkale 148
                                       +++  s   d +a+  +++   + lY l+ ++  L e  + +e
  gi|386002793|ref|YP_005921092.1| 175 GET-HSMAPDPRAAVVTVKML-NTLYGLQVDTTDLEERAEEIE 215
                                       666.56666777777777777.888888888888887777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.60
# Mc/sec: 1233.42
//
Query:       gi|386002794|ref|YP_005921093.1|  [L=93]
Description: glutaredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-12   45.2   0.0    1.2e-11   44.6   0.0    1.2  1  Glutaredoxin  Glutaredoxin
    0.00062   20.0   0.0    0.00077   19.7   0.0    1.1  1  GST_N_2       Glutathione S-transferase, N-terminal domain
     0.0012   19.2   0.0     0.0015   18.9   0.0    1.1  1  GST_N_3       Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.016   15.5   0.0    1.1  1  GST_N         Glutathione S-transferase, N-terminal domain
       0.14   12.6   0.0       0.14   12.5   0.0    1.2  1  DUF836        Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   3.3e-15   1.2e-11       1      58 [.      14      76 ..      14      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.3e-15
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.....HHHHHHHHHHTSSSSSEEEETTE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde.....eireelkelsgvrtvPqvfidgk 58
                                      ++l+  +tC++C+k+k+lL++lg+kf+++ vd  e        e++k+ ++ +t+P+ +i+g+
  gi|386002794|ref|YP_005921093.1| 14 ITLYALSTCVWCHKTKKLLERLGAKFRYVYVDLLEgderdRTLEDVKKHNPSVTFPTTVIGGD 76
                                      799********************998888888887767888888999999**********996 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.1e-07   0.00077       2      52 ..      22      74 ..      21      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                                      -HHHHHHHHHHHHCT--EEEEEE..H...-TTSHHHHHHHHCTTTSSSEEE-C CS
                           GST_N_2  2 CPwahRvlialalkglediisvv..vlepkgfekseefprlnprgtVPvLwdk 52
                                      C w+h++  +l+ +g  +++  v  + +++ +++ e+++++np++t P+ ++ 
  gi|386002794|ref|YP_005921093.1| 22 CVWCHKTKKLLERLGAKFRYVYVdlLEGDERDRTLEDVKKHNPSVTFPTTVIG 74
                                      *******************9998655566666778999**********97774 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.2e-07    0.0015       1      55 [.      16      76 ..      16      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.2e-07
                                      EES-TTSHHHHHHHHHHHHHT--EEEE---......TTTTHHHHHHH-TT--SSEEETTS- CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvevt......pgehdeellaknplgkvPvLeddge 55
                                      Ly   +++++ + + +L+ +g ++++v v+       +++ e +++ np  ++P+ +++g+
  gi|386002794|ref|YP_005921093.1| 16 LYALSTCVWCHKTKKLLERLGAKFRYVYVDllegdeRDRTLEDVKKHNPSVTFPTTVIGGD 76
                                      8999*******************9998887666443333477888889*******999865 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   4.5e-06     0.016       3      55 ..      14      69 ..      12      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                                      EEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGC...HHHHHHCTTS-SS CS
                             GST_N  3 ltlysirgsprahrirlllaakgveyevvpldfeageeks...pellklnplgkvP 55
                                      +tly   ++ + h+++ ll+ +g+++++v +d+ +g e++   ++ +k np    P
  gi|386002794|ref|YP_005921093.1| 14 ITLYALSTCVWCHKTKKLLERLGAKFRYVYVDLLEGDERDrtlEDVKKHNPSVTFP 69
                                      89**************************9999988877762133334444445555 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    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       2      41 ..      14      51 ..      13      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CC CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIakdee 41
                                      +tLy    C  C++ k++L+  +l  +++ + +D ++++e
  gi|386002794|ref|YP_005921093.1| 14 ITLYALSTCVWCHKTKKLLE--RLGAKFRYVYVDLLEGDE 51
                                      9*******************..566777888888886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 753.55
//
Query:       gi|386002795|ref|YP_005921094.1|  [L=172]
Description: Rubredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-26   90.9   0.1    6.5e-26   90.4   0.1    1.2  1  FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta ch
     0.0042   16.6   0.6       0.01   15.4   0.6    1.7  1  RecR       RecR protein
     0.0062   16.9   0.0     0.0077   16.6   0.0    1.2  1  zf-C4H2    Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.1   1.1e-29   6.5e-26       3      91 ..      12      98 ..      10     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.1e-29
                                      HHHHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH....---T CS
                         FeThRed_B  3 ektrkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvplreeldeekeCh 81
                                      e++r+ l+++a+++g+ +npd ++t+++++gl+ n+++yG+++CPCrl  ++++e+ +++  CPC++++++l+e+++C+
  gi|386002795|ref|YP_005921094.1| 12 ENLREQLDREAEEMGYHLNPDLDFTTSLVRGLLVNERRYGYPSCPCRLASGDRDEDLDII--CPCDYRDQDLNEYGACY 88
                                      5788999*****************************************************..***************** PP

                                      TSSSB-TTST CS
                         FeThRed_B 82 Cglfvtkdna 91
                                      C l+v++++ 
  gi|386002795|ref|YP_005921094.1| 89 CALYVSEEVL 98
                                      ******9975 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   1.7e-06      0.01      18      35 ..     141     162 ..     130     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-06
                                       E-TTT--EESSS....S-CCCC CS
                              RecR  18 hCsrCgnlteed....lCaICs 35 
                                       +C++Cg l+ +d    +C+IC+
  gi|386002795|ref|YP_005921094.1| 141 RCRVCGYLCARDeppgVCPICK 162
                                       7*******999988888****7 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06    0.0077     130     201 ..      51     164 ..       3     167 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                           zf-C4H2 130 k..........................................aaavelkkesstapappa.pptsllskssqapsa 163
                                                                                  +++v +++++ +a +    +p++++  +++a   
  gi|386002795|ref|YP_005921094.1|  51 GypscpcrlasgdrdedldiicpcdyrdqdlneygacycalyvSEEVLAGERDLSAVPERRpSPEERAR-AAKAL-- 124
                                       256666666666666666666666666666666666666555533333333333333222212222222.11111.. PP

                           zf-C4H2 164 pstatasfrqqpPPMKsClsChqqIHRNAP..iCPlCKaK 201
                                       +  + ++f+  p P   C  C     R  P  +CP+CKaK
  gi|386002795|ref|YP_005921094.1| 125 SAPSGEAFSALPYPVWRCRVCGYLCARDEPpgVCPICKAK 164
                                       22334789999*****************99899******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1381.99
//
Query:       gi|386002796|ref|YP_005921095.1|  [L=818]
Description: Putative cadmium-transporting P-type ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-59  198.6   1.8    1.5e-58  197.3   1.8    1.7  1  E1-E2_ATPase   E1-E2 ATPase
    1.5e-45  156.0   4.3    3.4e-45  154.9   4.3    1.6  1  Hydrolase      haloacid dehalogenase-like hydrolase
    5.8e-32  109.9   3.4    1.4e-16   60.6   0.1    3.0  3  HMA            Heavy-metal-associated domain
     0.0011   18.7   0.2      0.021   14.6   0.1    2.1  2  Hydrolase_3    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.03   14.7   0.0       0.19   12.1   0.0    2.2  1  HAD            haloacid dehalogenase-like hydrolase
      0.039   13.2   0.9      0.095   11.9   0.1    1.9  2  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3   1.8   4.9e-62   1.5e-58       2     180 ..     292     476 ..     291     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 4.9e-62
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+p+ta+v+rdg+e+e++a++l +GD++l+++g++vpaDg+++eg++ vde+++TGE  pv+k++gd v +Gt +++
  gi|386002796|ref|YP_005921095.1| 292 LQPKTATVLRDGQEVEVAAADLLVGDVILVRPGEKVPADGVVLEGESYVDEAMITGEPIPVKKSRGDAVVGGTLNKN 368
                                       79*************************************************************************** PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT......HHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla......eall 149
                                       g +k+++ ++g++t l++i++lveea+ +++++q+++d+ ++ ++p+vl++a+++fl++ ++  +l+      +al+
  gi|386002796|ref|YP_005921095.1| 369 GAIKFEASKVGRETALAQIIALVEEAQGSRPSIQRMADRAVALFIPAVLTVAAATFLLWRFVLADLVpgdpllFALT 445
                                       **************************************************************9999999999***** PP

                                       HHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 150 ralallvaaiPcaLplavplalalgarrlak 180
                                        ++++lv+a+PcaL+la p+a+++g++r+a+
  gi|386002796|ref|YP_005921095.1| 446 ATISVLVVACPCALGLASPTAITVGIGRAAE 476
                                       ****************************985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9   4.3   1.2e-48   3.4e-45       2     210 .]     494     710 ..     493     710 .. 0.95

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 1.2e-48
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakarsgal...tgfatfigrg.. 67 
                                       +tvvfDk+GTLt g+p+v+d+++   +++++ l+++      sehp+++a+v++a  ++++l   t+f+++ g+g  
  gi|386002796|ref|YP_005921095.1| 494 NTVVFDKTGTLTVGRPEVTDILPFG-VDERELLRIAggieanSEHPLAEAVVRKARSEGIDLaeaTSFEALGGKGvl 569
                                       8************************.********************************77774457777777777** PP

                                       ......HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTT CS
                                       ......xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaag 134
                                              +a+g++ +l++l  ++p+  +aa    +++g+t+ l+   +r+++v+ +ad   +k+  +eav +Lka+g
  gi|386002796|ref|YP_005921095.1| 570 aeiegrDAAVGNRILLRELgiEVPEGTEAAALRIEEEGKTALLValAGRIVGVVGVADA--LKKNSVEAVGRLKAMG 644
                                       ********************************************8888***********..**************** PP

                                       EEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 135 ievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +ev ++tgdnp+ta  +a++ G           ie   a+++p+ k + i++Lq ++e va+VGDg+nDa+ala+A+
  gi|386002796|ref|YP_005921095.1| 645 FEVLMITGDNPSTAGIVAKETG-----------IERvLAEVLPSEKAREIKRLQDEGEVVAFVGDGINDAPALAQAD 710
                                       **********************...........8888***************************************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1   4.8e-20   1.4e-16       2      61 ..      13      72 ..      12      73 .. 0.98
   2 !   49.1   0.2   1.9e-16   5.6e-13       2      62 .]      81     141 ..      80     141 .. 0.97
   3 ?   -3.6   0.0       5.6   1.7e+04      18      40 ..     284     308 ..     283     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 4.8e-20
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61
                                      +++sgm+Ca+Caa+ve++L e++gV+++ v+l++ t+ Ve+d++++ l ++ +a+++agy
  gi|386002796|ref|YP_005921095.1| 13 LQISGMTCASCAAAVEEALMEVEGVSEARVNLGKETAMVELDPSKARLADLERAVSDAGY 72
                                      789********************************************************9 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.9e-16
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                       ++v gm Ca+C+++ve+++ e++gV +v v+l+  ++ V++++  +++ + ++aie+agy+
  gi|386002796|ref|YP_005921095.1|  81 LKVGGMICASCVSSVEEAIGEVEGVVEVAVNLGDERARVTYNPRIASVADMRAAIEEAGYQ 141
                                       6899*******************************************************95 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.6
                               HMA  18 kvLselpgV..esvkvdlatktvtV 40 
                                       +++++l g   ++++v  + ++v+V
  gi|386002796|ref|YP_005921095.1| 284 EAIKKLMGLqpKTATVLRDGQEVEV 308
                                       6788888888888999999888887 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.057   1.7e+02      16      56 ..     629     669 ..     626     674 .. 0.89
   2 !   14.6   0.1     7e-06     0.021     199     238 ..     686     725 ..     679     741 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.057
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                       ++++++ea+ +lk+ g++v   TG +++++  v++e g++ 
  gi|386002796|ref|YP_005921095.1| 629 LKKNSVEAVGRLKAMGFEVLMITGDNPSTAGIVAKETGIER 669
                                       568899*****************************999985 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7e-06
                                       CT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHH CS
                       Hydrolase_3 199 lnisleeviafGDgeNDieMLeaaglgvAmgnaseevkka 238
                                       l+ + e v+ +GDg ND + L +a++g+A+g++++ +++ 
  gi|386002796|ref|YP_005921095.1| 686 LQDEGEVVAFVGDGINDAPALAQADVGIAIGSGTDVAIES 725
                                       55566677888***********************988775 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-05      0.19      91     187 ..     634     706 ..     582     707 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                               HAD  91 lellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaege 167
                                       +e++ + +a G++v +++g +   + ++++e g+++vla+      +l              +k++++++       
  gi|386002796|ref|YP_005921095.1| 634 VEAVGRLKAMGFEVLMITGDNPSTAGIVAKETGIERVLAE------VLPS------------EKAREIKR------L 686
                                       44555555999**********************9999999......4444............46778888......4 PP

                               HAD 168 gidleevvayGDspsDlpll 187
                                        ++ e v ++GD+++D p+l
  gi|386002796|ref|YP_005921095.1| 687 QDEGEVVAFVGDGINDAPAL 706
                                       4455667777********98 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.2e-05     0.095     163     236 ..      65     138 ..      58     168 .. 0.84
   2 ?   -1.5   0.1      0.38   1.1e+03      67      91 ..     640     664 ..     591     675 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                     PEP_hydrolase 163 ramaeaGadvivahlGlttggsigaktalsleeavelvqeiadaakevnpdvivlvhGGpiaepedaeyvlert 236
                                       ra+ +aG  v+   + l  gg+i a+ ++s+eea+ +v+ ++++a ++ ++   +++  +ia+  d++  +e+ 
  gi|386002796|ref|YP_005921095.1|  65 RAVSDAGYAVVNERVSLKVGGMICASCVSSVEEAIGEVEGVVEVAVNLGDERARVTYNPRIASVADMRAAIEEA 138
                                       67889**************************************************************9998543 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.38
                     PEP_hydrolase  67 vvemakevlpvvketpvlaGvcatD 91 
                                       +  m+ evl ++ + p  aG++a +
  gi|386002796|ref|YP_005921095.1| 640 LKAMGFEVLMITGDNPSTAGIVAKE 664
                                       4568889999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (818 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 5563.96
//
Query:       gi|386002797|ref|YP_005921096.1|  [L=51]
Description: hypothetical protein Mhar_2118 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-20   72.9   2.9    1.7e-20   72.8   2.9    1.0  1  YHS              YHS domain
     0.0055   17.4   0.1     0.0059   17.3   0.1    1.1  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
  ------ inclusion threshold ------
      0.018   15.4   0.7      0.028   14.7   0.6    1.4  1  Arc_trans_TRASH  Archaeal TRASH domain
        0.2   11.3   0.5       0.42   10.2   0.4    1.7  2  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   2.9   3.8e-24   1.7e-20       2      46 ..       6      50 ..       5      51 .] 0.96

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.8e-24
                               YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYat 46
                                      +dPvc+m+vd ++a++k+eYkG+ YyFc +gCk +Fe++Pe+Y++
  gi|386002797|ref|YP_005921096.1|  6 IDPVCKMTVDEKTAKFKTEYKGTAYYFCAPGCKKAFEKDPERYLK 50
                                      8******************************************96 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.3e-06    0.0059       5      36 ..      10      42 ..       9      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                     ATPase-cat_bd  5 Cglpveesa.klkaeiegeerefCCkGCqavaq 36
                                      C+  v+e++ k+k+e++g+  +fC +GC+  ++
  gi|386002797|ref|YP_005921096.1| 10 CKMTVDEKTaKFKTEYKGTAYYFCAPGCKKAFE 42
                                      88888766549*****************98875 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6   6.3e-06     0.028      17      35 ..      25      43 ..      21      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                   Arc_trans_TRASH 17 lknkvYyvCCktCkselkk 35
                                      +k   Yy+C + Ck+ + k
  gi|386002797|ref|YP_005921096.1| 25 YKGTAYYFCAPGCKKAFEK 43
                                      56678***********998 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.58   2.6e+03      34      43 ..       9      18 ..       8      19 .. 0.81
   2 ?   10.2   0.4   9.4e-05      0.42       2      18 ..      20      36 ..      19      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.58
                                      EEEEEEEEEE CS
                   GalKase_gal_bdg 34 VlpmAieqdi 43
                                      V+ m ++ ++
  gi|386002797|ref|YP_005921096.1|  9 VCKMTVDEKT 18
                                      8899999887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.4e-05
                                      HHHHHHS---EEEEEEE CS
                   GalKase_gal_bdg  2 eFqktFgkepfvasAPG 18
                                      +F+ +++ ++++++APG
  gi|386002797|ref|YP_005921096.1| 20 KFKTEYKGTAYYFCAPG 36
                                      79****9999******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 436.53
//
Query:       gi|386002798|ref|YP_005921097.1|  [L=471]
Description: Dihydrolipoamide dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete 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   0.1    2.9e-47  161.3   0.1    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    6.7e-24   84.3   0.7    2.4e-23   82.5   0.3    2.0  2  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
      8e-15   55.2   0.1    2.1e-14   53.8   0.1    1.8  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    6.4e-09   35.5   0.0    9.4e-09   34.9   0.0    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.18   10.5   3.1        3.4    6.3   0.0    2.5  3  HI0933_like    HI0933-like protein
        1.6    8.6   3.7       0.43   10.4   0.1    1.9  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.3   0.1   9.8e-51   2.9e-47       1     294 []       4     321 ..       4     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 9.8e-51
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +dv+v+G+G++ + +++ ++ ag++++lv+    +gtcln+gc++sk+l   a+  ++++                 
  gi|386002798|ref|YP_005921097.1|   4 YDVIVVGSGAGMIIVSRGIR-AGMRIALVDhgpMGGTCLNNGCIPSKVLIYPADVVRTLEaaravgvearveridfd 79 
                                       69*******76666666665.5*******999*************************999***************** PP

                                       .......HHHHCHHHHCCCCHCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEEC CS
                                       .......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .......evvkklnqgielllgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgkl 126
                                               vv++ + g+e+ +++  +++ ++g+++++   + +   e+i++ ++++A+Gs+p  ++ipG+ae +   
  gi|386002798|ref|YP_005921097.1|  80 limrrmrAVVDEGRRGMERSAERAeGLDWYRGWGEFVGDFLIKIGDETITAPRIFIASGSRPLVPPIPGLAEAG--- 153
                                       **9999999999999999888866699999********888876668***********************6666... PP

                                       CSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 127 vrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklg 203
                                         +ld++  l+l+  p+++++ GgGy ++E+A +++ lg +vt++ ++  ll+  d+e+ ++++++l +  v+v++g
  gi|386002798|ref|YP_005921097.1| 154 --YLDNVSVLSLQRPPESLIILGGGYLASEYAHFFSALGTKVTILGRNRMLLKDEDPEICEIVKRRLSRY-VDVRTG 227
                                       ..68***************************************999999999***************995.888888 PP

                                       CEEEEEEETTE.....EEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE- CS
                                       xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 204 tsvkeidgnge.....klevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyai 274
                                       +++++++ +g       l++  +  +e++a+ v+va G+r ++++l+ ek g+e+d+ g+ivv+++++t  +gi+  
  gi|386002798|ref|YP_005921097.1| 228 HEAVKVEVKGGkkvvsALDLASDAVREFAAEEVMVALGRRSNSDILKpEKTGVEVDRSGWIVVNDRMETRREGIWTF 304
                                       888877666666576555599999999************************************************** PP

                                       GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 275 GDvaggkggpelaqaAvqqG 294
                                       GD +   g+ +  ++A +++
  gi|386002798|ref|YP_005921097.1| 305 GDAI---GKHMFRHTANREA 321
                                       **99...8888888887765 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.67     2e+03      17      42 ..      60      88 ..      59      98 .. 0.73
   2 !   82.5   0.3     8e-27   2.4e-23       1     108 [.     341     449 ..     341     451 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.67
                                      -HHHHHHHHSGEEEEEEEEE...CGHHHC CS
                     Pyr_redox_dim 17 teeeAkaagieikvgkfpfk...angral 42
                                      t e A+a g+e +v +++f+      ra+
  gi|386002798|ref|YP_005921097.1| 60 TLEAARAVGVEARVERIDFDlimRRMRAV 88
                                      67899******999999998544444444 PP

  == domain 2  score: 82.5 bits;  conditional E-value: 8e-27
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p +vft p+v+svG+te+eAkaag+++ vg++++ ++++  a+ae++ +vK+v++a +g++lG++i G ga+el+q
  gi|386002798|ref|YP_005921097.1| 341 VPHAVFTYPQVGSVGMTEAEAKAAGYKVLVGRAEYGDVTKGYAMAEEESLVKVVVNAGDGRILGCSIAGSGAAELVQ 417
                                       799************************************************************************** PP

                                       HHHHHHHTTSBHH.HHHTSBSSSSSTGGGGHC CS
                     Pyr_redox_dim  78 elavaikagltve.dladtihihPtlsealke 108
                                       ++  +++ag   +  + + + ihP  se++  
  gi|386002798|ref|YP_005921097.1| 418 QVVYLMNAGDRDSgPIGRALVIHPATSEVVAR 449
                                       **********99978************99876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.1     7e-18   2.1e-14       2      73 ..     170     241 ..     169     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 7e-18
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.v 73 
                                       ++++GgGy++ E+A ++++lg kVt++ r+ +ll+ +D+e+ +i++++l++  ++v+++++++++e ++ + v
  gi|386002798|ref|YP_005921097.1| 170 LIILGGGYLASEYAHFFSALGTKVTILGRNRMLLKDEDPEICEIVKRRLSRY-VDVRTGHEAVKVEVKGGKkV 241
                                       79*************************************************9.*************7777643 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   3.1e-12   9.4e-09     113     305 .]     118     305 ..     115     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.1e-12
                       Pyr_redox_3 113 gfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvk..efhkyagqkvvViGgknSavDaAlelvrkg 187
                                        f ++   et++A++++iA G   +P ++ ipG  + +    +v+  ++ +   + +++ Gg+  a ++A  + + g
  gi|386002798|ref|YP_005921097.1| 118 DFLIKIGDETITAPRIFIASGS--RPLVPPIPGLAE-AGYLDNVSvlSL-QRPPESLIILGGGYLASEYAHFFSALG 190
                                       58889999*************9..*********995.333334441144.5568999******************** PP

                       Pyr_redox_3 188 aeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla 264
                                        +Vt++ r+  + k+e dp+  +  +++ rl ++v+ ++ + + + evk  k+  +  ++ ++  +++   ++v++a
  gi|386002798|ref|YP_005921097.1| 191 TKVTILGRNRMLLKDE-DPE--ICEIVKRRLSRYVDVRTGHEAVKVEVKGGKKVVSALDLASDAVREFA-AEEVMVA 263
                                       *********9888764.665..79999999999876532233333344444444444455555555544.6899*** PP

                       Pyr_redox_3 265 tGykpdlsflkk..slfeldedgrpvlteeteetnvpglflaG 305
                                       +G +++ ++lk    ++e d++g++v+++  +et  +g++  G
  gi|386002798|ref|YP_005921097.1| 264 LGRRSNSDILKPekTGVEVDRSGWIVVND-RMETRREGIWTFG 305
                                       **********9988999********9996.699*****99877 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9    0.0075        23       1      34 [.       4      36 ..       4      42 .. 0.88
   2 ?    6.3   0.0    0.0011       3.4      80     166 ..     180     268 ..     175     272 .. 0.81
   3 ?   -3.8   0.0       1.3   3.8e+03     167     188 ..     348     369 ..     346     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0075
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      +dviv+G G AG+    +  ++g r++l+++++ 
  gi|386002798|ref|YP_005921097.1|  4 YDVIVVGSG-AGMIIVSRGIRAGMRIALVDHGPM 36
                                      59*******.5999999999**********9975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.....TTEE CS
                       HI0933_like  80 edlialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktk....seee 152
                                        +  +++++lg ++++  + r+  ++ +  +i ++ +++l++  v++r+ +e  +ve + ++k+  +++      +e
  gi|386002798|ref|YP_005921097.1| 180 SEYAHFFSALGTKVTILGRNRMLLKD-EDPEICEIVKRRLSR-YVDVRTGHEAVKVEVKGGKKVVSALDlasdAVRE 254
                                       567789*****************999.8899****9999976.69**********9888777654433322327789 PP

                                       EEESEEEE----SS CS
                       HI0933_like 153 leadklvlAtGGlS 166
                                       ++a+++++A+G  S
  gi|386002798|ref|YP_005921097.1| 255 FAAEEVMVALGRRS 268
                                       ***********888 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.3
                                       -GGGT--SHHHHHHHHTT--EE CS
                       HI0933_like 167 iPklGstgkgyklaeqfghtiv 188
                                       +P++Gs g     a+++g +++
  gi|386002798|ref|YP_005921097.1| 348 YPQVGSVGMTEAEAKAAGYKVL 369
                                       8999999999999999999986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.9       2.2   6.6e+03       2      29 ..       6      32 ..       5      35 .. 0.82
   2 ?   10.4   0.1   0.00015      0.43       4      88 ..     172     258 ..     169     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvd 29
                                      v v+G+G  G  i +  ++ag+++ lvd
  gi|386002798|ref|YP_005921097.1|  6 VIVVGSGA-GMIIVSRGIRAGMRIALVD 32
                                      67899996.8888899999999999998 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH..C CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav..d 78 
                                       ++G G + ++ a+ f + g +V+++ +++  l++   +i + +++  ++    +   ea+  +++  +++ +a    
  gi|386002798|ref|YP_005921097.1| 172 ILGGGYLASEYAHFFSALGTKVTILGRNRMLLKDEDPEICEIVKRRLSRYVDVRTGHEAVKVEVKGGKKVVSALdlA 248
                                       89********************************9999999888876655444444445555555555544444234 PP

                                       -SEEEE-S-S CS
                           3HCDH_N  79 adlviEavvE 88 
                                        d v E ++E
  gi|386002798|ref|YP_005921097.1| 249 SDAVREFAAE 258
                                       4555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3300.68
//
Query:       gi|386002799|ref|YP_005921098.1|  [L=154]
Description: Guanine deaminase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-23   82.5   0.0      2e-23   82.2   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    6.1e-21   74.6   0.0    7.6e-21   74.3   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
       0.15   12.2   0.1       0.26   11.4   0.1    1.4  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
       0.65    9.6   2.7        1.2    8.7   0.7    2.1  2  RecR             RecR protein


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   4.5e-27     2e-23       6     101 .]       3     100 ..       1     100 [. 0.97

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 4.5e-27
                                       HHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHH.TSSCETTEEEEEEE- CS
                   dCMP_cyt_deam_1   6 kllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaakn.ggsklegatlyvtle 80 
                                       ++l lal++a+    +++  ++Gaviv++g +is+++n+  + +++t+HAE++Ai++a  + g+ +l  + +y t e
  gi|386002799|ref|YP_005921098.1|   3 EFLALALEEARAGIeNDDGGPFGAVIVQEGVVISKAHNEVLRRNDPTAHAEILAIREASAIlGSFDLSTCEIYSTSE 79 
                                       79999******9999**********************************************8899************ PP

                                       -BHHHHHHHHHHT-SEEEEEE CS
                   dCMP_cyt_deam_1  81 PCsmCakaiiqsgikkvvvgt 101
                                       PC+mC  ai +++ik++v+gt
  gi|386002799|ref|YP_005921098.1|  80 PCPMCFAAIFWARIKRLVYGT 100
                                       *******************85 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   1.7e-24   7.6e-21       9     107 ..       7     116 ..       2     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.7e-24
                       MafB19-deam   9 kalaevekatkike.dkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepCdm 84 
                                        al+e++++++ ++  + gaviv+++ vi +++ne   ++++taHaEi a++ A+  l+s  l+ + +y t epC+m
  gi|386002799|ref|YP_005921098.1|   7 LALEEARAGIENDDgGPFGAVIVQEGVVISKAHNEVLRRNDPTAHAEILAIREASAILGSFDLSTCEIYSTSEPCPM 83 
                                       67788888887754279************************************************************ PP

                       MafB19-deam  85 Cagaivqaglkklvygagnpks..........l 107
                                       C  ai  a++k+lvyg+  ++            
  gi|386002799|ref|YP_005921098.1|  84 CFAAIFWARIKRLVYGTTREDVaeigfddsliY 116
                                       *****************9888777776666652 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.9e-05      0.26      14      60 ..      40      88 ..      29      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                             SNAD4 14 kgvlkn.kke.haEllflekikseldpsqeyrvtwylswsPCaeCaeki 60
                                      ++vl+  + + haE+l +++ ++ l +    +  +y +  PC+ C ++i
  gi|386002799|ref|YP_005921098.1| 40 NEVLRRnDPTaHAEILAIREASAILGSFDLSTCEIYSTSEPCPMCFAAI 88
                                      34444414447**********88666665666678999*******9988 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.12   5.2e+02       5      16 ..       5      16 ..       3      18 .. 0.86
   2 ?    8.7   0.7   0.00028       1.2      20      34 ..      70      84 ..      70      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      La aL+ea+ ++
  gi|386002799|ref|YP_005921098.1|  5 LALALEEARAGI 16
                                      899******988 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00028
                                      TTT--EESSSS-CCC CS
                              RecR 20 srCgnlteedlCaIC 34
                                      s C  ++++++C+ C
  gi|386002799|ref|YP_005921098.1| 70 STCEIYSTSEPCPMC 84
                                      68************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1041.66
//
Query:       gi|386002800|ref|YP_005921099.1|  [L=965]
Description: hypothetical protein Mhar_2121, partial [Methanosaeta harundinacea 6Ac]
Scores for complete 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-40  134.8  19.3    1.8e-09   38.0   0.8    7.8  7  WD40         WD domain, G-beta repeat
      5e-19   68.6   0.1      9e-19   67.8   0.1    1.4  1  DUF4365      Domain of unknown function (DUF4365)
    1.9e-17   63.3   0.0    3.7e-17   62.4   0.0    1.5  1  Ras          Ras family
    4.6e-16   59.1   0.0    2.4e-15   56.8   0.0    2.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    1.6e-10   41.2   1.1       0.49   10.7   0.0    6.6  7  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    4.2e-07   29.0   3.3     0.0057   15.3   0.1    3.8  4  Nup160       Nucleoporin Nup120/160
    8.1e-07   28.7   0.0    1.7e-06   27.6   0.0    1.5  1  Arf          ADP-ribosylation factor family
      2e-05   24.1   0.0      0.069   12.5   0.0    2.4  2  WD40_like    WD40-like domain
     0.0016   17.5   5.5       0.18   10.7   0.1    4.0  6  PALB2_WD40   Partner and localizer of BRCA2 WD40 domain
  ------ inclusion threshold ------
      0.016   15.1   0.2       0.04   13.9   0.2    1.6  1  zf-DNL       DNL zinc finger
      0.066   13.2   5.8         30    4.7   0.1    4.2  4  PD40         WD40-like Beta Propeller Repeat
       0.18   11.5   0.0       0.37   10.5   0.0    1.6  1  AAA_24       AAA domain
       0.21   11.6   0.4       0.57   10.2   0.4    1.7  1  DZR          Double zinc ribbon
       0.27   11.4   0.9        0.7   10.0   0.9    1.7  1  zf-GRF       GRF zinc finger


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.4   3.7e-08   4.7e-05      17      38 .]       2      23 ..       1      23 [. 0.93
   2 !   17.8   0.1   3.6e-06    0.0046       1      38 []      27      63 ..      27      63 .. 0.81
   3 ?   -0.3   0.0       1.9   2.4e+03       2      31 ..      68      98 ..      67     103 .. 0.70
   4 !   22.4   0.0   1.2e-07   0.00016       1      38 []     109     147 ..     109     147 .. 0.90
   5 !   31.4   0.1   1.7e-10   2.2e-07       1      38 []     151     189 ..     151     189 .. 0.94
   6 !   38.0   0.8   1.4e-12   1.8e-09       1      38 []     193     232 ..     193     232 .. 0.91
   7 !    8.1   0.0     0.004       5.1      13      37 ..     250     274 ..     236     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.7e-08
                                      EEETTSSEEEEEETTSEEEEEE CS
                              WD40 17 afspdgawlasGsdDgtvriWd 38
                                      a spdg+w asGs D+tv+iWd
  gi|386002800|ref|YP_005921099.1|  2 AISPDGKWAASGSGDKTVKIWD 23
                                      67**********99*******9 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.6e-06
                                      TEEEEEEESS.SS...EEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40  1 gqclrtltGH.ss...vtslafspdgawlasGsdDgtvriWd 38
                                      g+cl tltGH +    + ++      ++++s+  Dg++r Wd
  gi|386002800|ref|YP_005921099.1| 27 GECLATLTGHsKAvrfIACQ-----TDYVLSSANDGKIRTWD 63
                                      68********7775555566.....788888888*******9 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.9
                                      EEEEEEESS.SSEEEEE.EETTSSEEEEEETT CS
                              WD40  2 qclrtltGH.ssvtsla.fspdgawlasGsdD 31
                                      ++l +l+   + +++++  s   ++l+++s +
  gi|386002800|ref|YP_005921099.1| 68 KLLSSLDSNlGEIHCVKeLSNREQLLVCSS-N 98
                                      56777777777799**97777777777655.4 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 1.2e-07
                                       TEEEEEEESS.SS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ss.vtslafspdgawlasGsdDgtvriWd 38 
                                       g+ +r++ GH ++ v s+a +  ++ ++sGs D+tvr+W+
  gi|386002800|ref|YP_005921099.1| 109 GKSIRKFQGHtGPaV-SVALDETHNRFVSGSFDRTVRLWN 147
                                       57899*****76677.99999999999************8 PP

  == domain 5  score: 31.4 bits;  conditional E-value: 1.7e-10
                                       TEEEEEEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                              WD40   1 gqclrtltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                       g+c+ tl+GHs+ v+s++   dg++ +sGs+D tv++Wd
  gi|386002800|ref|YP_005921099.1| 151 GECQATLKGHSGiVRSVQITLDGQFAVSGSEDMTVKVWD 189
                                       68********7757************************9 PP

  == domain 6  score: 38.0 bits;  conditional E-value: 1.4e-12
                                       TEEEEEEESS.SSEEEEEEETTSSEEE.EEETTSEEEEEE CS
                              WD40   1 gqclrtltGH.ssvtslafspdgawla.sGsdDgtvriWd 38 
                                       g+c++tl+GH s+v+s++ spdg+++a +G  Dgtvr+Wd
  gi|386002800|ref|YP_005921099.1| 193 GTCVGTLEGHqSDVHSVSISPDGSLIAsTGFIDGTVRLWD 232
                                       68********999*************945668*******9 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.004
                                       EEEEEEETTSSEEEEEETTSEEEEE CS
                              WD40  13 vtslafspdgawlasGsdDgtvriW 37 
                                        ts+afspdg+ ++ G+  g ++i+
  gi|386002800|ref|YP_005921099.1| 250 PTSVAFSPDGSRVVVGTFGGVIYIY 274
                                       49************9*889999887 PP

>> DUF4365  Domain of unknown function (DUF4365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.1     7e-22     9e-19      18     135 ..     830     951 ..     820     955 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 7e-22
                           DUF4365  18 viareqereDyGiDlvielvkkdgkatgrllavQvKstesleikkekdagvsf.eldvknlnyllnlsvpvilvlvd 93 
                                       +++r+ +  DyGiD+++e++++dg+++g+ ++vQ+Ks++s+  ++++d   +f   ++++l+y+  ++  v+lv+  
  gi|386002800|ref|YP_005921099.1| 830 QVFRPVSMFDYGIDGEVEFRDNDGQPSGKKIYVQLKSGNSYLRTRRRDGREVFdVKKDRHLQYWVSQPADVYLVIRQ 906
                                       556666666********************************999999998899556789****************** PP

                           DUF4365  94 lpteka....yWvslkgadktsnekksvtiripksqrlddeslrtl 135
                                       +++ +      W +++++ k++++k+s++i +  +  l+ e++ +l
  gi|386002800|ref|YP_005921099.1| 907 TDERTNggtiRWMNVTQYLKNREDKESRQIIFEGET-LTMEAVWRL 951
                                       ***999************************999884.777766665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   2.9e-20   3.7e-17       1     150 [.     295     450 ..     295     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.9e-20
                                       EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET...TEEEEEEEEEETTSGGGHHHHHHHHTTESE CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd...gkevkleiwDTAGqeefkslrelyyrdaeg 74 
                                       K+vl+G++avGKtsl +r ++d++  + + T g++    e+ +      + +  +wD AGqe+++ +++l++ ++  
  gi|386002800|ref|YP_005921099.1| 295 KVVLLGEGAVGKTSLAYRLIEDEYVVK-DRTHGMNVWPLELPLPpdaTMDSEALLWDLAGQEDYRLIHRLFLDETAL 370
                                       9***********************976.89999**9999999987666677889*********************** PP

                                       EEEEEETTBHHHHHTHHHHHHHHHHHST....TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTT CS
                               Ras  75 illvyditsresfenvkkwveeikrvae....envpivLvGnKvDleekravsteegeelakelg.lkfletSAktn 146
                                       +ll+ + ++ + f ++ +w++ + +  +     + + +L+  +vD+    ++s ++ +++a+e+g +k+l tSAkt 
  gi|386002800|ref|YP_005921099.1| 371 ALLLINPQKDDPFAEAGDWLKALDTASNhkskCEAARLLIFSQVDVGY-MKLSDAKIKRFAQEHGfAKWLATSAKTG 446
                                       *********************99988777767568999*********6.8999************99********** PP

                                       CTHH CS
                               Ras 147 enve 150
                                       en +
  gi|386002800|ref|YP_005921099.1| 447 ENCS 450
                                       9976 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   1.9e-18   2.4e-15       1     109 [.     295     400 ..     295     415 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.9e-18
                                       EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHH CS
                               Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplyl 77 
                                       Kvvl+G+++vGKtsl+ r++ed++  k + t+g+++   e+        d +  + +  +WD+aGqe++r +h+l+l
  gi|386002800|ref|YP_005921099.1| 295 KVVLLGEGAVGKTSLAYRLIEDEYVVK-DRTHGMNVWPLELPLPP----DAT-MDSEALLWDLAGQEDYRLIHRLFL 365
                                       9***********************876.799*****998875322....333.3456789***************** PP

                                       CTSCEEEEEEEGHHH...HCHHHHHHHHHHHCSSS CS
                               Roc  78 reaalailvydsrss...enlkeWlkelkkvagks 109
                                        e ala+l+++ +++   +++ +Wlk l++ ++++
  gi|386002800|ref|YP_005921099.1| 366 DETALALLLINPQKDdpfAEAGDWLKALDTASNHK 400
                                       **********9665422267889****99876654 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00038      0.49      46      86 ..       3      42 ..       1      48 [. 0.87
   2 ?    1.6   0.0      0.26   3.4e+02      55      87 ..      52      83 ..      45      88 .. 0.86
   3 ?    2.3   0.0      0.16   2.1e+02      49      84 ..      88     123 ..      78     132 .. 0.82
   4 !    9.9   0.1   0.00069      0.89      33      84 ..     156     206 ..     141     210 .. 0.83
   5 !   10.1   0.0    0.0006      0.76      36      78 ..     201     244 ..     197     256 .. 0.85
   6 ?   -0.3   0.0       1.1   1.4e+03      42      66 ..     251     275 ..     248     285 .. 0.88
   7 ?   -2.9   0.0         7     9e+03      18      35 ..     870     887 ..     864     904 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                       ANAPC4_WD40 46 WkpdgklLavaysdgevrlldaesgkvvhslsvksekavtc 86
                                       +pdgk  a +  d +v++ d e+g+++ +l+ +s+ av  
  gi|386002800|ref|YP_005921099.1|  3 ISPDGKWAASGSGDKTVKIWDLETGECLATLTGHSK-AVRF 42
                                      579****************************99988.4655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                       ANAPC4_WD40 55 vaysdgevrlldaesgkvvhslsvksekavtcl 87
                                       + +dg++r  d+ + k+++sl+ +  + + c+
  gi|386002800|ref|YP_005921099.1| 52 SSANDGKIRTWDIRERKLLSSLDSNLGE-IHCV 83
                                      5678******************999885.8887 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.16
                       ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                       + + L v  s++ + lld  +gk +++++ ++  av
  gi|386002800|ref|YP_005921099.1|  88 NREQLLVCSSNSVITLLDRGTGKSIRKFQGHTGPAV 123
                                       4556889999******************98887655 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00069
                       ANAPC4_WD40  33 eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                       + +++++ vrs++   dg++ + + +d +v++ d e+g++v +l+ ++++ v
  gi|386002800|ref|YP_005921099.1| 156 TLKGHSGIVRSVQITLDGQFAVSGSEDMTVKVWDLEDGTCVGTLEGHQSD-V 206
                                       456778889********************************999988874.5 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0006
                       ANAPC4_WD40  36 kedsevrsLaWkpdgklLav.aysdgevrlldaesgkvvhslsv 78 
                                       +++s v+s++ +pdg+l+a  ++ dg+vrl d  sg +++ l  
  gi|386002800|ref|YP_005921099.1| 201 GHQSDVHSVSISPDGSLIAStGFIDGTVRLWDWMSGACLQVLAS 244
                                       68999*************96489*************99987765 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1.1
                       ANAPC4_WD40  42 rsLaWkpdgklLavaysdgevrlld 66 
                                       +s+a++pdg+  +v++  g + ++ 
  gi|386002800|ref|YP_005921099.1| 251 TSVAFSPDGSRVVVGTFGGVIYIYR 275
                                       6899***********9999988875 PP

  == domain 7  score: -2.9 bits;  conditional E-value: 7
                       ANAPC4_WD40  18 ellvfRlngqrvwtleed 35 
                                        l+  R +g++v+++++d
  gi|386002800|ref|YP_005921099.1| 870 YLRTRRRDGREVFDVKKD 887
                                       57789999*****99544 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0011       1.4     237     255 ..      14      32 ..       3      41 .. 0.86
   2 !    4.8   0.1     0.007         9     226     259 ..      43      76 ..      36      92 .. 0.79
   3 !   15.3   0.1   4.5e-06    0.0057     156     255 ..      87     198 ..      78     214 .. 0.84
   4 ?   -2.3   0.0         1   1.3e+03     237     254 ..     223     240 ..     205     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                                       ETT-EEEEEETTTTEEEEE CS
                            Nup160 237 srdgkLrvWnlltgkclat 255
                                       s d+++++W+l+tg clat
  gi|386002800|ref|YP_005921099.1|  14 SGDKTVKIWDLETGECLAT 32 
                                       679**************99 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.007
                                       ...TTTEEEEEETT-EEEEEETTTTEEEEEEE-- CS
                            Nup160 226 veigqtylfalsrdgkLrvWnlltgkclatidll 259
                                       +  + +y+++   dgk+r W+++  k+l++ d +
  gi|386002800|ref|YP_005921099.1|  43 IACQTDYVLSSANDGKIRTWDIRERKLLSSLDSN 76 
                                       434889***********************99987 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 4.5e-06
                                       -SSSEEEEEETTS-EEEEEE..........ETTEEEEEEEEE-------B--TTTT.TSS--SS---TT-ECEEEEE CS
                            Nup160 156 vssnellvsladggllklkr..........dedggawkesvfepksfllslsgllglladpsrrksgasvalsldva 222
                                       +++++llv++++  ++ l+r          + +g a+++  ++++++  ++sg + +  + ++ ++g + +++l+  
  gi|386002800|ref|YP_005921099.1|  87 SNREQLLVCSSNSVITLLDRgtgksirkfqGHTGPAVSV-ALDETHN-RFVSGSFDRTVRLWNFETGEC-QATLKGH 160
                                       57899*******************999774333444433.3444444.68888888899**********.9****** PP

                                       T..........TTTEEEEEETT-EEEEEETTTTEEEEE CS
                            Nup160 223 vavvei.....gqtylfalsrdgkLrvWnlltgkclat 255
                                       +++v++     + +++++ s d +++vW+l++g+c+ t
  gi|386002800|ref|YP_005921099.1| 161 SGIVRSvqitlDGQFAVSGSEDMTVKVWDLEDGTCVGT 198
                                       ****99999**************************987 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1
                                       ETT-EEEEEETTTTEEEE CS
                            Nup160 237 srdgkLrvWnlltgkcla 254
                                         dg++r+W+  +g cl 
  gi|386002800|ref|YP_005921099.1| 223 FIDGTVRLWDWMSGACLQ 240
                                       579*******99999986 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.4e-09   1.7e-06      14     127 ..     293     416 ..     286     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.4e-09
                                       EEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEE.......TTEEEEEEEE-SSGGGGGGGGGGCTTES CS
                               Arf  14 elrilllGLDnaGKtTilkklkleelvttvPTigfnveelei.......knlkftvwDvGGqeklRplWknYfektd 83 
                                       +++++llG  + GKt + ++l ++e v    T g+nv  le         + +  +wD+ Gqe  R + + ++++t 
  gi|386002800|ref|YP_005921099.1| 293 NAKVVLLGEGAVGKTSLAYRLIEDEYVVKDRTHGMNVWPLELplppdatMDSEALLWDLAGQEDYRLIHRLFLDETA 369
                                       689*************************************9988988666777889********************* PP

                                       EEEEEEETT-CTTHHHHHHHHHHHCTSGCCT....TSEEEEEEE-TTS CS
                               Arf  84 avifvvDsadreRleeakeeLkalleeeelk....evallvlaNKqDl 127
                                         + ++  ++ + ++ea + Lkal + ++ k     + ll+++ + D+
  gi|386002800|ref|YP_005921099.1| 370 LALLLINPQKDDPFAEAGDWLKALDTASNHKskceAARLLIFS-QVDV 416
                                       *********************9997665544444256666665.4454 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   5.4e-05     0.069       8      91 ..       3      86 ..       1     109 [. 0.84
   2 !    9.2   0.0   0.00052      0.67       5     108 ..     166     275 ..     163     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                         WD40_like  8 iskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeevenekie.edi 85
                                      is++g+  + G+ d+++++ +le++e    +++ +  v f+   + d +l  ++DG+i + ++++ +  ++ + +  +i
  gi|386002800|ref|YP_005921099.1|  3 ISPDGKWAASGSGDKTVKIWDLETGECLATLTGHSKAVRFIAC-QTDYVLSSANDGKIRTWDIRERKLLSSLDSNlGEI 80
                                      799999**********************************975.78899*********999999988777666553567 PP

                         WD40_like 86 stvkvi 91
                                       +vk +
  gi|386002800|ref|YP_005921099.1| 81 HCVKEL 86
                                      777655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00052
                         WD40_like   5 sidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvt..lDGtillsllenee...ev 76 
                                       s++i  +g++ + G++d +++v +le ++ v  +e+ +  v  v +  d  ++  t  +DGt+ l +   +    + 
  gi|386002800|ref|YP_005921099.1| 166 SVQITLDGQFAVSGSEDMTVKVWDLEDGTCVGTLEGHQSDVHSVSISPDGSLIASTgfIDGTVRLWDWMSGAclqVL 242
                                       89999*******************************98887666655555666555779****99998888756455 PP

                         WD40_like  77 enekieedistv.kviddklliGtnkGsiyvfs 108
                                        +e      s++ + ++ ++++Gt  G iy++ 
  gi|386002800|ref|YP_005921099.1| 243 ASEGWPTPTSVAfSPDGSRVVVGTFGGVIYIYR 275
                                       5666666666551446679************97 PP

>> PALB2_WD40  Partner and localizer of BRCA2 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.2    0.0093        12     296     330 ..      11      41 ..       6      63 .. 0.64
   2 ?   -0.7   0.0      0.42   5.4e+02     189     243 ..      46      98 ..      40     116 .. 0.80
   3 ?    1.2   0.0      0.11   1.4e+02     193     320 ..     134     159 ..      65     171 .. 0.60
   4 ?    0.8   0.0      0.14   1.8e+02     303     327 ..     142     166 ..     116     189 .. 0.78
   5 ?   -0.6   0.0      0.37   4.8e+02     303     321 ..     184     202 ..     159     211 .. 0.78
   6 !   10.7   0.1   0.00014      0.18     300     351 .]     224     275 ..     214     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0093
                        PALB2_WD40 296 aavltsGaiavWdlllghctalllpesdesWslvr 330
                                       a+     ++ +Wdl  g+c a l+ +s      vr
  gi|386002800|ref|YP_005921099.1|  11 ASGSGDKTVKIWDLETGECLATLTGHSKA----VR 41 
                                       544455699**********9999877653....34 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.42
                        PALB2_WD40 189 ekdallgttvlnniviWnlktGqllkkieigesyqasvclkaysdsGllfvvlsh 243
                                       + d +l+++ + +i  W+++  +ll+++  ++  ++  c k  s+   l+v  s+
  gi|386002800|ref|YP_005921099.1|  46 QTDYVLSSANDGKIRTWDIRERKLLSSL--DSNLGEIHCVKELSNREQLLVCSSN 98 
                                       5688999999999999999999999976..5667777888888887777766555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.11
                        PALB2_WD40 193 llgttvlnniviWnlktGqllkkieigesyqasvclkaysdsGllfvvlshphakesesakkpvfkliainPktars 269
                                       +++ + +  + +                                                                 
  gi|386002800|ref|YP_005921099.1| 134 FVSGSFDRTVRL----------------------------------------------------------------- 145
                                       445555555555................................................................. PP

                        PALB2_WD40 270 vevllytlPeGqtGryleGdvkdqlaaavltsGaiavWdlllghctalllp 320
                                                                            W++  g+c+a l  
  gi|386002800|ref|YP_005921099.1| 146 -------------------------------------WNFETGECQATLKG 159
                                       .....................................55555555555544 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.14
                        PALB2_WD40 303 aiavWdlllghctalllpesdesWs 327
                                       ++ +W++  g+c+a l  +s+   s
  gi|386002800|ref|YP_005921099.1| 142 TVRLWNFETGECQATLKGHSGIVRS 166
                                       7889999999999999988876554 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.37
                        PALB2_WD40 303 aiavWdlllghctalllpe 321
                                       ++ vWdl  g+c   l  +
  gi|386002800|ref|YP_005921099.1| 184 TVKVWDLEDGTCVGTLEGH 202
                                       899*********9988754 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00014
                        PALB2_WD40 300 tsGaiavWdlllghctalllpesdesWslvrWsgtdsqllaGqkdGsvlvys 351
                                         G++ +Wd + g c  +l++e   + + v +s   s+++ G   G +++y+
  gi|386002800|ref|YP_005921099.1| 224 IDGTVRLWDWMSGACLQVLASEGWPTPTSVAFSPDGSRVVVGTFGGVIYIYR 275
                                       67********************99999************************6 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.1e-05      0.04       4      47 ..     743     787 ..     741     807 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                            zf-DNL   4 ftCkaCetrss.keiskkaYekGvVivqCpgCknrHliaDnLgwf 47 
                                       + C  C+t  +  +i ++  ++G  +++C++C++r l+ D+++  
  gi|386002800|ref|YP_005921099.1| 743 YVCVHCGTPVTnLTIVRNRLDSGKNFITCQNCDERVLLIDHIEQR 787
                                       89****99754279***************************9865 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.023        30      15      24 ..       2      11 ..       2      11 .. 0.88
   2 ?    4.3   0.0     0.032        40      12      24 ..     207     219 ..     202     231 .. 0.78
   3 ?    4.5   0.0     0.027        35      14      23 ..     253     262 ..     251     273 .. 0.88
   4 ?   -2.7   0.2       4.8   6.1e+03      24      38 .]     644     659 ..     644     659 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                                      EE-TTSSEEE CS
                              PD40 15 sfSPDGkrla 24
                                      ++SPDGk+ a
  gi|386002800|ref|YP_005921099.1|  2 AISPDGKWAA 11
                                      68******86 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.032
                                       EEEEE-TTSSEEE CS
                              PD40  12 gaPsfSPDGkrla 24 
                                       ++ s+SPDG+ +a
  gi|386002800|ref|YP_005921099.1| 207 HSVSISPDGSLIA 219
                                       5679******998 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.027
                                       EEE-TTSSEE CS
                              PD40  14 PsfSPDGkrl 23 
                                        +fSPDG+r 
  gi|386002800|ref|YP_005921099.1| 253 VAFSPDGSRV 262
                                       59*****996 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.8
                                       EEEEECT.TCEE.EEE CS
                              PD40  24 aFsSdRgsGkpd.Iyv 38 
                                       +F+S+   G ++ I++
  gi|386002800|ref|YP_005921099.1| 644 VFVSYTFGGEWQtIWT 659
                                       69999559****9995 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00029      0.37       2      36 ..     293     328 ..     292     366 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                            AAA_24   2 klkiliyGpsgiGKTtlakel.gpkplfidtekGlk 36 
                                       ++k+++ G+  +GKT+la++l +++ ++ d  +G++
  gi|386002800|ref|YP_005921099.1| 293 NAKVVLLGEGAVGKTSLAYRLiEDEYVVKDRTHGMN 328
                                       689******************999999999988885 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00045      0.57      10      38 ..     740     778 ..     734     782 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                               DZR  10 pdarfCseCgtklkavaa..........edrCpsCgekv 38 
                                       ++  +C +Cgt++ + +            ++C +C+e v
  gi|386002800|ref|YP_005921099.1| 740 DRRYVCVHCGTPVTNLTIvrnrldsgknFITCQNCDERV 778
                                       56679*******985555999999**999******9875 PP

>> zf-GRF  GRF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00055       0.7       3      33 ..     745     776 ..     743     778 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                            zf-GRF   3 Ck.cgrlavlltvrktgpNkGRkFYkCpkgke 33 
                                       C  cg++ + lt  +++ + G++F +C +++e
  gi|386002800|ref|YP_005921099.1| 745 CVhCGTPVTNLTIVRNRLDSGKNFITCQNCDE 776
                                       877**9988888778**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (965 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 6427.05
//
Query:       gi|386002801|ref|YP_005921100.1|  [L=268]
Description: type 11 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-18   64.6   0.0    2.2e-17   63.5   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      2e-17   63.7   0.0    4.7e-17   62.5   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    5.7e-17   61.9   0.0    8.8e-17   61.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.2e-12   47.0   0.0    5.1e-12   46.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.3e-10   41.0   0.0    2.2e-10   40.3   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
    2.3e-10   40.6   0.0    2.9e-10   40.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    8.5e-10   38.4   0.0    1.3e-09   37.8   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00013   21.6   0.0     0.0002   20.9   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00038   20.3   0.0    0.00053   19.8   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0053   15.8   0.0     0.0074   15.3   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0074   15.6   0.0     0.0094   15.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.018   14.1   0.0      0.023   13.8   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.022   13.7   0.0      0.036   13.0   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.03   14.0   0.0       0.17   11.5   0.0    2.1  2  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.058   13.0   0.0      0.084   12.5   0.0    1.2  1  NodS             Nodulation protein S (NodS)
        0.2   11.3   0.0       0.28   10.8   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0     2e-20   2.2e-17       1      94 [.      41     137 ..      41     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 2e-20
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       L++GcG G+ + +la++   +++v++++s    + a+ +a+ +gl +v+++++d+ +lpf+++sfD  ++ +vl+h+
  gi|386002801|ref|YP_005921100.1|  41 LEAGCGVGAQTLPLAQNSpaSTIVALEISRPSAAEARGRAEAAGLaNVRVLQGDIFSLPFRKASFDHLFVCFVLEHL 117
                                       799************88889************************9******************************** PP

                                       CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGll 94 
                                       ++p +al+ ++   kpgG++
  gi|386002801|ref|YP_005921100.1| 118 PRPVEALSILKEFIKPGGTI 137
                                       ******************87 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   4.2e-20   4.7e-17       1      97 []      40     135 ..      40     135 .. 0.97
   2 ?   -2.8   0.0       9.7   1.1e+04      60      70 ..     234     244 ..     207     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 4.2e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL++GcG G  tl la++ +++++++++is    ++ar rae++gl nv+++qgd+ +lpf ++sfD  +++++l+h
  gi|386002801|ref|YP_005921100.1|  40 VLEAGCGVGAQTLPLAQNSPASTIVALEISRPSAAEARGRAEAAGLaNVRVLQGDIFSLPFRKASFDHLFVCFVLEH 116
                                       8*****************889**************************************************9***** PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       l+++   +al+ +++ +kpgG
  gi|386002801|ref|YP_005921100.1| 117 LPRP--VEALSILKEFIKPGG 135
                                       9965..59************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.7
                                       SSTTTEEEEEE CS
                   Methyltransf_25  60 fedgsfDlvvs 70 
                                        e+++fDl vs
  gi|386002801|ref|YP_005921100.1| 234 MEEEEFDLGVS 244
                                       23444554444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   7.8e-20   8.8e-17       7     151 ..      40     187 ..      36     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 7.8e-20
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                       vl++GCG G+ t+ la +  p +++v ++is  +   Ar +a+  gl nv++ qgdi++l+  + +++fD ++   v
  gi|386002801|ref|YP_005921100.1|  40 VLEAGCGVGAQTLPLA-QNSPASTIVALEISRPSAAEARGRAEAAGLANVRVLQGDIFSLP--FRKASFDHLFVCFV 113
                                       89**************.6678999*************************************..********999889 PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggilliedprllaelp..akveeeskay.evvegak......igt..qkdelyelle 149
                                       l +l+ p ++l  +++ +kpgg + + + ++ + +   ++  + +    +            +g+   + ely+ll 
  gi|386002801|ref|YP_005921100.1| 114 LEHLPRPVEALSILKEFIKPGGTITAIEGDHGSAYFypDSPAARQAIGcQ-----VrlqeraGGNamIGRELYPLLV 185
                                       9**************************99944444433222222221110.....0112233333466666666666 PP

                   Methyltransf_31 150 ea 151
                                       +a
  gi|386002801|ref|YP_005921100.1| 186 RA 187
                                       65 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   4.5e-15   5.1e-12       1      99 []      41     137 ..      41     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4.5e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       Le GcG+G+ + +l+++ p +++++++is+ + + a+ +  + +  n   v++ + d+++l+ + +sfD  ++++vl
  gi|386002801|ref|YP_005921100.1|  41 LEAGCGVGAQTLPLAQNSPASTIVALEISRPSAAEARGRAEAAGLAN---VRVLQGDIFSLPFRkASFDHLFVCFVL 114
                                       89*******************************99999999999755...5555555555555558*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                       +hl+ + e+l+ +++ +kpgG +
  gi|386002801|ref|YP_005921100.1| 115 EHLPRPVEALSILKEFIKPGGTI 137
                                       *********************75 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0     2e-13   2.2e-10       3      80 ..      38     112 ..      36     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2e-13
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEE CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifil 79 
                                       ++vle GcG G  ++ lA++ P  +++++Ei++++ a++  ++ea +l N+r+l+gd    ++  ++++s++ +f++
  gi|386002801|ref|YP_005921100.1|  38 SLVLEAGCGVGAQTLPLAQNSPASTIVALEISRPSAAEARGRAEAAGLANVRVLQGDI---FSLPFRKASFDHLFVC 111
                                       589******************************************************8...7778***********9 PP

                                       S CS
                    Methyltransf_4  80 F 80 
                                       F
  gi|386002801|ref|YP_005921100.1| 112 F 112
                                       9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.5e-13   2.9e-10      21     118 ..      35     140 ..      11     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.5e-13
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlI 86 
                                       ++g+ vL+ GcG+G  +  l++n    ++++ ++s+   ++a+         + +  q d f   + ++ +++fd  
  gi|386002801|ref|YP_005921100.1|  35 PPGSLVLEAGCGVGAQTLPLAQNSPasTIVALEISRPSAAEARgraeaaglaNVRVLQGDIF---SLPFRKASFDHL 108
                                       56678*********66666666644489********9999999***9**8888888888888...9999******** PP

                   Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGyllls 118
                                          +vleh+p p e+l+ +++ +kpgG +   
  gi|386002801|ref|YP_005921100.1| 109 FVCFVLEHLPRPVEALSILKEFIKPGGTITAI 140
                                       ***************************98655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.1e-12   1.3e-09      47     156 ..      36     144 ..      25     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.1e-12
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvs 123
                                       +g+ vl+  +G g  ++ l+++     ++v l+i+     +++ +++  g  n++ lq++   Lpf + sfD + v 
  gi|386002801|ref|YP_005921100.1|  36 PGSLVLEAGCGVGAQTLPLAQNSP-ASTIVALEISRPSAAEARGRAEAAGLANVRVLQGDIFSLPFRKASFDHLFVC 111
                                       578899*************99865.568999********************************************** PP

                                       S-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                   Ubie_methyltran 124 fGlrnvtDklkaLkeayrvlkpGGrlvvlefsk 156
                                       f l  ++   +aL  +   +kpGG+++ +e  +
  gi|386002801|ref|YP_005921100.1| 112 FVLEHLPRPVEALSILKEFIKPGGTITAIEGDH 144
                                       ****************************99655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.8e-07    0.0002      22      99 ..      23     106 ..      14     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                                       HHHHHCHCC....TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTS CS
                               MTS  22 lLletlpke....lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleev 93 
                                        L++ l+++        vl  GcG+G+ ++ la++sp  ++++++++  + + a+  +ea +l+ v+v++ d+++  
  gi|386002801|ref|YP_005921100.1|  23 TLVDLLHSDtsypPGSLVLEAGCGVGAQTLPLAQNSPASTIVALEISRPSAAEARGRAEAAGLAnVRVLQGDIFSLP 99 
                                       566666666555556669********************************************999*******99854 PP

                                       T.TS-EE CS
                               MTS  94 e.ekkfd 99 
                                         +++fd
  gi|386002801|ref|YP_005921100.1| 100 FrKASFD 106
                                       3255565 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.7e-07   0.00053      63     158 ..      22     120 ..      15     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.7e-07
                                       HHHHHHTT....--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG CS
                              PCMT  63 alalelle....lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk 135
                                       a++++ll+      +g+ vLe G+G G +t  la+   +++ +v++e ++  ++ea+ + ++ +l+nv v  gD   
  gi|386002801|ref|YP_005921100.1|  22 ATLVDLLHsdtsYPPGSLVLEAGCGVGAQTLPLAQNSPAST-IVALEISRPSAAEARGRAEAAGLANVRVLQGDIFS 97 
                                       56667776665567999******************977666.********************************999 PP

                                       TTGGG-SEEEEEESSBBSS--HH CS
                              PCMT 136 GyeekaPYdaihvgaaapeiPea 158
                                           ka +d ++v    +++P++
  gi|386002801|ref|YP_005921100.1|  98 LPFRKASFDHLFVCFVLEHLPRP 120
                                       8889999*****99999999876 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.6e-06    0.0074     205     254 ..      40      91 ..      24      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.6e-06
                   tRNA_U5-meth_tr 205 llelycGnGnfslalarn..fekvlateiakssveaaqyniaankidnvqii 254
                                       +le  cG G  +l+la+n   + ++a ei+++s + a+   +a  + nv+++
  gi|386002801|ref|YP_005921100.1|  40 VLEAGCGVGAQTLPLAQNspASTIVALEISRPSAAEARGRAEAAGLANVRVL 91 
                                       68999************944479************************99975 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.4e-06    0.0094      32     116 ..       6      90 ..       2     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.4e-06
                                       S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHT CS
                              CMAS  32 sCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvde 107
                                          y+ r+++ L++   + +dl+    +  pG+ +L+ GcG G+ +   +++  +  +v+l +S+  a+ a+ r ++
  gi|386002801|ref|YP_005921100.1|   6 VHGYHPRESTRLQDQAATLVDLLHSDTSYPPGSLVLEAGCGVGAQTLPLAQNSPAsTIVALEISRPSAAEARGRAEA 82 
                                       55688899999999999999***********************9998888876552689****************** PP

                                       S-SSS-EEE CS
                              CMAS 108 ldlerkvev 116
                                       ++l++ + v
  gi|386002801|ref|YP_005921100.1|  83 AGLANVR-V 90 
                                       9987643.3 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     2e-05     0.023      30      92 ..      36     102 ..      13     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                                       TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  30 ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92 
                                       +   vle g G+G++T +La+ +     v+lE+ +  a++ + + +     ++ v++ D+    + +
  gi|386002801|ref|YP_005921100.1|  36 PGSLVLEAGCGVGAQTLPLAQNSpaSTIVALEISRPSAAEARGRAEaaGLANVRVLQGDIFSLPFRK 102
                                       6677***************9888889******99988888888777667889999999998776665 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.2e-05     0.036     119     226 ..      40     144 ..      29     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                                       EEEET-TTSHHHHHHHHCT.-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-GG CS
                    Methyltransf_9 119 ildvGcgnGyhlwrmvgeg.aklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvly 193
                                       +l+ Gcg G     ++ +  a+++v ++ s+      +   +  g  + + +l   i  lp   ++fd +f   vl 
  gi|386002801|ref|YP_005921100.1|  40 VLEAGCGVGAQTLPLAQNSpASTIVALEISRPSAAEARGRAEAAGLAN-VRVLQGDIFSLPFrKASFDHLFVCFVLE 115
                                       666677777666666655414455666666665555555555555444.34455678889986789*********** PP

                                       G-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-T CS
                    Methyltransf_9 194 hrrsPldhllqlkdqlvkgGelvletlvieGde 226
                                       h   P++ l+ lk+ ++ gG++      ieGd+
  gi|386002801|ref|YP_005921100.1| 116 HLPRPVEALSILKEFIKPGGTIT----AIEGDH 144
                                       ********************974....566665 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.17      19     121 ..      18     109 ..      12     137 .. 0.75
   2 ?   -2.5   0.0       2.9   3.3e+03      59      93 ..     172     206 ..     170     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                       -SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-B..TTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE-- CS
                              TPMT  19 qeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAe..qgrevvGvelselAvekffeeanlepkvkelsgvke 93 
                                       q+++ +l+  + ++++ ++g  vl  +CG +     lA+  +  ++v++e+s    +++      + ++  l+    
  gi|386002801|ref|YP_005921100.1|  18 QDQAATLVDLLHSDTSYPPGSLVLEAGCGVGAQTLPLAQnsPASTIVALEISRPSAAEA----RGRAEAAGLA---- 86 
                                       5667777777777789999999*************9996226789*******8765552....2222333333.... PP

                                       ...........-TTT---SS-..EEEEE CS
                              TPMT  94 ysageiellcgdvFtlraeelgkfdliy 121
                                           ++ +l+gd+F l+ ++  +fd ++
  gi|386002801|ref|YP_005921100.1|  87 ----NVRVLQGDIFSLPFRKA-SFDHLF 109
                                       ....35669999999998887.777766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                       TEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE-- CS
                              TPMT  59 grevvGvelselAvekffeeanlepkvkelsgvke 93 
                                       g+ ++G el +l v++ f+e   +p++ + +g + 
  gi|386002801|ref|YP_005921100.1| 172 GNAMIGRELYPLLVRAGFAEVCVSPRMVYADGSRP 206
                                       66789999999999999999999999988877665 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-05     0.084      46     121 ..      39     119 ..      12     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-05
                              NodS  46 dalevGcaaGalterlapyckrltvv..dvveeaiararerv..kesshiswivsdvqqfst.dekfdlivvaevly 117
                                        +le Gc  Ga t  la  +   t+v  ++   + a ar r      +++  ++ d+  +   ++ fd + v+ vl 
  gi|386002801|ref|YP_005921100.1|  39 LVLEAGCGVGAQTLPLAQNSPASTIValEISRPSAAEARGRAeaAGLANVRVLQGDIFSLPFrKASFDHLFVCFVLE 115
                                       58*****************9999988235555556666655510567889999999999875267899999999987 PP

                              NodS 118 yied 121
                                       ++  
  gi|386002801|ref|YP_005921100.1| 116 HLPR 119
                                       7654 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.28      32     139 ..      28     135 ..      16     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                             GCD14  32 iimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGf.d 107
                                       ++      pGs v+e+G G g+ +  +a+  +P   + ++e  +  a +ar   +  +l+ +v v + D+ +  f +
  gi|386002801|ref|YP_005921100.1|  28 LHSDTSYPPGSLVLEAGCGVGAQTLPLAQN-SPASTIVALEISRPSAAEARGRAEAAGLA-NVRVLQGDIFSLPFrK 102
                                       555566679*************99999876.8********************99999997.69999*********77 PP

                             GCD14 108 eevsgkvDavfL.DlPaPweaiphaakalkkeg 139
                                       +  ++   +  L  lP P ea+  +++ +k  g
  gi|386002801|ref|YP_005921100.1| 103 ASFDHLFVCFVLeHLPRPVEALSILKEFIKPGG 135
                                       77777655544427********99999885444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1705.26
//
Query:       gi|386002802|ref|YP_005921101.1|  [L=213]
Description: Orotidine 5'-phosphate decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-38  133.0   0.1    1.4e-38  132.8   0.1    1.0  1  OMPdecase   Orotidine 5'-phosphate decarboxylase / HUMPS fami
  ------ inclusion threshold ------
      0.075   12.5   3.3        0.8    9.1   0.6    2.2  2  PEP_mutase  Phosphoenolpyruvate phosphomutase
       0.09   10.9   0.1      0.099   10.8   0.1    1.0  1  DUF1633     Protein of unknown function (DUF1633)


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   0.1   2.3e-42   1.4e-38       1     224 [.       5     207 ..       5     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 2.3e-42
                                       SEEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHH CS
                         OMPdecase   1 snLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqat 77 
                                       s+L+lalDv +++++l+la  +++ ++++K++y+l+ + g      +++ ++++  +++++D+K+aDI+nt  ++++
  gi|386002802|ref|YP_005921101.1|   5 SRLILALDVLSRDRALHLATALKDRVDYVKVGYPLILAAG-----LDIVGEIARI-APVIADLKIADIPNTNTLICE 75 
                                       68**************************************.....*******999.6*******************9 PP

                                       STCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESE CS
                         OMPdecase  78 agsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmG 154
                                             +++a  +++ha++G +s++a++eaa++ g   ++++++ms++g+++l        ++e++++++a+++v+G
  gi|386002802|ref|YP_005921101.1|  76 ---EVLDSGAAGIIAHAFVGRDSLSACVEAAREAG-GLVFAVTEMSHPGAEELMG-----PAAERLARMAADCGVDG 143
                                       ...667****************************8.89*****************.....999999999999***** PP

                                       EECCCHTHHHHHHTTCSCEEEHHHTT.EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 155 fvaqetlnateedaddfihltpgigl.eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       +va +t++      + +  ++  +g  +  + g g+q   p ++ + agad +ivGR+I+++++p++ a +
  gi|386002802|ref|YP_005921101.1| 144 VVAPATRP------ERISLVRSIVGErAIISPGVGVQGGSPSAALK-AGADSLIVGRSITESPNPAASADA 207
                                       ******99......45555555555555999999***998887777.99******************9986 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5   0.00028       1.6     145     237 ..      12     105 ..       3     106 .. 0.92
   2 ?    9.1   0.6   0.00013       0.8     125     197 ..      95     167 ..      90     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00028
                        PEP_mutase 145 dalllsagagleeaieRaraYaeAGAdgvfvpglqkdaeiaelvaav.dvplnvvplkgtlsvaelaelGvarislg 220
                                       d+l ++++ +l++a++    Y++ G   +++ gl    eia+++  + d+ +  +p+++tl ++e+ + G+a i+ +
  gi|386002802|ref|YP_005921101.1|  12 DVLSRDRALHLATALKDRVDYVKVGYPLILAAGLDIVGEIARIAPVIaDLKIADIPNTNTLICEEVLDSGAAGIIAH 88 
                                       777778999999***9999****************************8899999998889***************** PP

                        PEP_mutase 221 nhllraalaalreaaee 237
                                        ++ r  l+a  eaa+e
  gi|386002802|ref|YP_005921101.1|  89 AFVGRDSLSACVEAARE 105
                                       *****999999999886 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00013
                        PEP_mutase 125 kiaaaraaaeeagfvinARtdalllsagagleeaieR.araYaeAGAdgvfvpglqkdaeiaelvaav.dvplnv 197
                                        ++a+++aa+eag +++A t++    a++ +  a eR ar+ a+ G dgv++p  + +  i   v+ + + + ++
  gi|386002802|ref|YP_005921101.1|  95 SLSACVEAAREAGGLVFAVTEMSHPGAEELMGPAAERlARMAADCGVDGVVAPATRPE-RISL-VRSIvGERAII 167
                                       68899*****************99999999*******4567788*********66443.3333.33332433444 PP

>> DUF1633  Protein of unknown function (DUF1633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   1.7e-05     0.099     322     412 ..      39     135 ..       3     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.7e-05
                           DUF1633 322 vivlpaaqldpleevprlefrpsadlqkknevtkdssstse.......cgs.....saraddlsavvaaartslavs 386
                                          + aa ld + e+ r+ ++  adl++  ++++  +   e                   d lsa v aar++    
  gi|386002802|ref|YP_005921101.1|  39 L--ILAAGLDIVGEIARIAPV-IADLKI-ADIPNTNTLICEevldsgaA-GiiahaFVGRDSLSACVEAAREAGGLV 110
                                       2..237889999999999987.477777.67777666555555554441.144422445689*************** PP

                           DUF1633 387 nasasashpslpevnarpllrrrarl 412
                                        a +  shp   e    p   r ar+
  gi|386002802|ref|YP_005921101.1| 111 FAVTEMSHPGAEELM-GPAAERLARM 135
                                       *********988876.6666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1363.02
//
Query:       gi|386002803|ref|YP_005921102.1|  [L=96]
Description: hypothetical protein Mhar_2124 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-26   92.2   0.6    1.5e-26   92.1   0.6    1.0  1  Thiamine_BP  Thiamine-binding protein
  ------ inclusion threshold ------
      0.051   12.7   0.3      0.099   11.8   0.3    1.5  1  Sugar-bind   Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.6   1.7e-30   1.5e-26       1      91 [.       4      94 ..       4      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.7e-30
                                      EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEES CS
                       Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrr 78
                                      +e+s+i +gt g+s s+yV +v++vlkesglk+  +pm+T ie+  ++e++evv+ka  +l+ +Ga R++t+ikid+r 
  gi|386002803|ref|YP_005921102.1|  4 AELSMITMGT-GTSASRYVRAVHQVLKESGLKFVPGPMSTSIEAGsMKEIFEVVEKADAVLAGMGAGRIVTTIKIDHRL 81
                                      689******9.********************************988********************************* PP

                                      SS---HHHHHHHH CS
                       Thiamine_BP 79 dkeqtleeKvksv 91
                                      dke ++e K++++
  gi|386002803|ref|YP_005921102.1| 82 DKEISIETKMEAI 94
                                      **********986 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   1.1e-05     0.099      54     143 ..       7      95 ..       1      96 [] 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                                       EEEEE-SSHHHHHHHHHTHH.CCHTCEEEEESBSECSSCHCGSHHHHHHHHHHHCTSEEE--SSBSB-SSHHHHHHH CS
                        Sugar-bind  54 dvvgvgwGrtlsavaealtp.kslrdvkvvqliGglsekvsaevnevvarlAqklggeyellpaPavlssaelreal 129
                                       +++++g+G++ s+ ++a+++  + +++k+v+  G +s   +a +++ + +  +k+ +  + + a  ++++ ++   l
  gi|386002803|ref|YP_005921102.1|   7 SMITMGTGTSASRYVRAVHQvLKESGLKFVP--GPMSTSIEAGSMKEIFEVVEKADAVLAGMGAGRIVTTIKIDHRL 81 
                                       6899****************99999*****9..8999999999999999999******************9999999 PP

                                       HTSHHHHHHHHHHH CS
                        Sugar-bind 130 laersikevlelak 143
                                        +e si++ +e+++
  gi|386002803|ref|YP_005921102.1|  82 DKEISIETKMEAIR 95 
                                       99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 626.92
//
Query:       gi|386002804|ref|YP_005921103.1|  [L=408]
Description: Chaperone protein DnaJ [Methanosaeta harundinacea 6Ac]
Scores for 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-41  139.7   0.0    9.4e-41  139.3   0.0    1.2  1  DnaJ_C          DnaJ C terminal domain
    5.8e-28   96.8   2.7    8.3e-28   96.3   2.7    1.2  1  DnaJ            DnaJ domain
    2.3e-14   53.5  20.6    4.3e-14   52.6  20.6    1.5  1  DnaJ_CXXCXGXG   DnaJ central domain
    0.00038   20.4  15.6     0.0045   16.9   2.8    3.5  3  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
  ------ inclusion threshold ------
       0.17   11.8   7.3       0.45   10.5   1.6    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.92    9.5   9.4        1.6    8.8   0.8    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
          6    7.0  14.3    2.5e+02    1.8  14.4    2.2  1  DZR             Double zinc ribbon
        8.3    6.7  25.5        2.8    8.2   0.5    4.6  4  DUF5351         Family of unknown function (DUF5351)


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.3   0.0   4.2e-44   9.4e-41       2     148 .]     131     350 ..     130     350 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 4.2e-44
                                       EEEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                            DnaJ_C   2 eveleisleelykGktkkikikrnvi................................................... 27 
                                       +++le++lee++kG+++ i++ r +                                                    
  gi|386002804|ref|YP_005921103.1| 131 RYDLEMTLEEVAKGVETSIEVPRMEAcstcggtgakpgtspqtcdqcqgsgqvtrvqktpfgqmmtsstcpkcggrg 207
                                       799********************999*************************************************** PP

                                       ...................TEEEEEE-TT--TT-EEEETT-SSSS.....S---EEEEEEE---SS-EEETTEEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ...............kkekktlevkipaGikdgqkirlegeGdeeg...gepGDlivtikvkphpvFkrkgndlyve 86 
                                                      ++++++++vk+paG+++gq++rl g+G++++   ge+GDl+v ++v+php Fkr ++dl++e
  gi|386002804|ref|YP_005921103.1| 208 qtvsdpcsecrgsgrVRKTRRINVKVPAGVDSGQHLRLGGQGEASPdpgGESGDLYVFVNVRPHPLFKRADDDLLYE 284
                                       **************7666669**********************555558**************************** PP

                                       EEEEHHHHHHTEEEEEE-S.S-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  87 veislaeallGgklevptl.dgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                       +++s+++a+lG+ levptl + ++++k+   tq+g+v+r+kgkG+p+l+  g+ Gd++v+v+v++P
  gi|386002804|ref|YP_005921103.1| 285 ADLSITQAALGADLEVPTLdGMRARIKVppgTQSGSVFRLKGKGIPRLHGFGGTGDMHVRVNVKTP 350
                                       *******************6668899**************************************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   2.7   3.7e-31   8.3e-28       1      63 []       7      68 ..       7      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 3.7e-31
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      dyYe+Lgv k+ +++eIk+aYrklalkyHPD++ ++p+aee+Fkei+eAy vLsdp+kR+qYD
  gi|386002804|ref|YP_005921103.1|  7 DYYEVLGVGKETDQKEIKSAYRKLALKYHPDRS-QEPDAEERFKEISEAYAVLSDPDKRRQYD 68
                                      8********************************.9***************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6  20.6   1.9e-17   4.3e-14       1      67 []     157     221 ..     157     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.9e-17
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C++C G+gak+g+ ++tC++C+GsG+v++ qkt +g+++  ++stCp+C+G+G+++  +d+C++C+G+g
  gi|386002804|ref|YP_005921103.1| 157 CSTCGGTGAKPGTsPQTCDQCQGSGQVTRVQKTpFGQMM--TSSTCPKCGGRGQTV--SDPCSECRGSG 221
                                       **********9777***********98888776798877..679************..899******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   5.5    0.0019       4.4       9      40 ..     154     181 ..     147     182 .. 0.81
   2 !   16.9   2.8     2e-06    0.0045      12      41 ..     173     208 ..     171     212 .. 0.83
   3 !    6.8   0.2     0.003       6.6      11      35 ..     212     235 ..     208     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0019
                                       CEEE-TTTTTTSEETTE......E-TTTTTSS CS
                         Anti-TRAP   9 LEtkCdaCngsGkiepeeprasleCPkCsGkg 40 
                                       + ++C +C g+G  +++   +   C +C+G g
  gi|386002804|ref|YP_005921103.1| 154 M-EACSTCGGTGAKPGT---SPQTCDQCQGSG 181
                                       4.48*************...556899**9987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2e-06
                                       E-TTTTTTSEETTE............E-TTTTTSSE CS
                         Anti-TRAP  12 kCdaCngsGkiepe......eprasleCPkCsGkgl 41 
                                       +Cd+C+gsG++         +  +s  CPkC+G+g 
  gi|386002804|ref|YP_005921103.1| 173 TCDQCQGSGQVTRVqktpfgQMMTSSTCPKCGGRGQ 208
                                       8********998766666777778889******985 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.003
                                       EE-TTTTTTSEETTE......E-TT CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPk 35 
                                        +C +C gsG++  +  r  ++ P+
  gi|386002804|ref|YP_005921103.1| 212 DPCSECRGSGRVRKT-RRINVKVPA 235
                                       58*********9988.666666665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4     0.022        48      30      53 ..     156     178 ..     132     183 .. 0.80
   2 ?   10.5   1.6    0.0002      0.45      26      50 ..     195     218 ..     186     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCg 53 
                                        Cs Cg ++ + + +   +C++C+
  gi|386002804|ref|YP_005921103.1| 156 ACSTCGGTGAK-PGTSPQTCDQCQ 178
                                       6*******999.888888899997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                    OrfB_Zn_ribbon  26 yTSktCseCgsknkealsgrtfkCp 50 
                                        TS+tC++Cg ++++ +s+   +C+
  gi|386002804|ref|YP_005921103.1| 195 MTSSTCPKCGGRGQT-VSDPCSECR 218
                                       6***********999.776666665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.8   0.00069       1.6      53      96 ..     138     181 ..     128     192 .. 0.72
   2 ?    5.2   2.0    0.0089        20      69     104 ..     196     228 ..     181     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00069
                                       CC.TTTT-EEEEEEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA  53 egtvlegaeLeieevpvkvrCreCgkefeleek.alrCpkCgsad 96 
                                        ++v++g e +ie  +++  C++Cg ++ +  +   +C +C++++
  gi|386002804|ref|YP_005921103.1| 138 LEEVAKGVETSIEVPRME-ACSTCGGTGAKPGTsPQTCDQCQGSG 181
                                       455788888888765555.69****999966644668****9873 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0089
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSS CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadveivsGee 104
                                        + +C +Cg ++++ ++   C +C +++ ++ + + 
  gi|386002804|ref|YP_005921103.1| 196 TSSTCPKCGGRGQTVSD--PCSECRGSG-RVRKTRR 228
                                       56789****99997756..799999864.5555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  14.4      0.11   2.5e+02       1      48 [.     157     217 ..     148     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                               DZR   1 CpqCgee...lppdarfCseCgtk..lkavaa........edrCpsCgekvdpearfCpeC 48 
                                       C++Cg        + ++C++C+ +  + +v++        + +Cp+Cg   +  +  C eC
  gi|386002804|ref|YP_005921103.1| 157 CSTCGGTgakPGTSPQTCDQCQGSgqVTRVQKtpfgqmmtSSTCPKCGGRGQTVSDPCSEC 217
                                       6666544322334566888888774433333377788888888888888888888888888 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.3     0.044        98      18      28 ..     155     165 ..     154     166 .. 0.89
   2 ?    8.2   0.5    0.0012       2.8      19      28 ..     173     182 ..     170     183 .. 0.91
   3 ?    5.4   2.9    0.0093        21      17      28 ..     197     208 ..     196     209 .. 0.89
   4 ?    3.3   0.3     0.044        98      18      28 ..     212     222 ..     211     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.044
                           DUF5351  18 ETCesCeGtgk 28 
                                       E C  C Gtg 
  gi|386002804|ref|YP_005921103.1| 155 EACSTCGGTGA 165
                                       89*******96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                           DUF5351  19 TCesCeGtgk 28 
                                       TC++C+G+g+
  gi|386002804|ref|YP_005921103.1| 173 TCDQCQGSGQ 182
                                       ********97 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0093
                           DUF5351  17 SETCesCeGtgk 28 
                                       S TC++C G g+
  gi|386002804|ref|YP_005921103.1| 197 SSTCPKCGGRGQ 208
                                       77********97 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.044
                           DUF5351  18 ETCesCeGtgk 28 
                                         C +C G+g 
  gi|386002804|ref|YP_005921103.1| 212 DPCSECRGSGR 222
                                       66******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 2163.06
//
Query:       gi|386002805|ref|YP_005921104.1|  [L=619]
Description: Chaperone protein DnaK [Methanosaeta harundinacea 6Ac]
Scores for complete 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-223  742.0  12.2   7.5e-204  678.3   8.2    2.0  2  HSP70            Hsp70 protein
    3.5e-17   62.2   6.0    3.5e-17   62.2   6.0    3.0  3  MreB_Mbl         MreB/Mbl protein
     0.0027   17.0   0.5       0.48    9.6   0.1    2.4  2  StbA             StbA protein
  ------ inclusion threshold ------
        0.1   12.3   0.7       0.22   11.2   0.0    1.8  2  FGGY_C           FGGY family of carbohydrate kinases, C-termi
       0.11   12.5   0.2        2.2    8.3   0.0    2.3  2  DUF547           Protein of unknown function, DUF547
       0.16   11.8   4.4       0.33   10.7   4.4    1.4  1  M_domain         M domain of GW182
       0.74   10.0  15.6       0.45   10.6  12.7    2.1  2  DUF1090          Protein of unknown function (DUF1090)
       0.78   10.0  14.1        1.3    9.3  14.1    1.2  1  Vfa1             AAA-ATPase Vps4-associated protein 1
        1.2    9.7   4.6        2.3    8.8   1.2    2.7  2  Phage_connect_1  Phage gp6-like head-tail connector protein
        3.7    7.7   9.4        6.6    6.9   9.4    1.4  1  DUF3347          Protein of unknown function (DUF3347)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   5.1e-22   9.2e-19       1      74 [.       4      84 ..       4      88 .. 0.90
   2 !  678.3   8.2  4.2e-207  7.5e-204     101     599 .]      85     581 ..      83     581 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 5.1e-22
                                      EEEEEEXSSEEEEEEEETTEEEEEXXTTSX......SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXB CS
                             HSP70  1 viGiDLGttnsvvavmeggkievianeegn......rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrk 72
                                      +iGiDLGt ns+ av+ ggk+++i  +eg+      ++ Ps+vaFtk+ +rlvGe+A+rqa+tnp+ t++ +Kr +G++
  gi|386002805|ref|YP_005921104.1|  4 IIGIDLGTSNSAAAVLIGGKPTMIPSAEGTsivaggKAFPSYVAFTKDgQRLVGEPARRQAATNPEGTITGIKRKMGQD 82
                                      69*************************986333333678***************************************9 PP

                                      TT CS
                             HSP70 73 fs 74
                                      + 
  gi|386002805|ref|YP_005921104.1| 83 YR 84
                                      97 PP

  == domain 2  score: 678.3 bits;  conditional E-value: 4.2e-207
                                       EEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHH CS
                             HSP70 101 veaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaY 177
                                       ve+ g+++tp++is+++L+k+k++ ea+lg+kv++avitvPaYfnd+qRqatkdAg+iAGL+v+Ri+NepTAaalaY
  gi|386002805|ref|YP_005921104.1|  85 VEVYGKSYTPQDISSFILRKIKDDSEAFLGEKVEKAVITVPAYFNDNQRQATKDAGTIAGLDVVRIINEPTAAALAY 161
                                       6778************************************************************************* PP

                                       HTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHH CS
                             HSP70 178 GldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalq 254
                                       G+dk+  e +++v+DlGggt dv i+e ++Gvfevk+T+gDt+lGG+d+De l++++ve++++++gidl+ d++a+q
  gi|386002805|ref|YP_005921104.1| 162 GMDKEG-EATLMVFDLGGGTLDVTIMEAGEGVFEVKSTSGDTQLGGRDMDEILTNYVVERYRQESGIDLKGDRMAMQ 237
                                       *****9.********************************************************************** PP

                                       HHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEE CS
                             HSP70 255 rlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedllertlepvekalkdaklkkeeidev 330
                                       rl+ea+e aK+eLSs+ qt+inl+++t+d++g k+l+++++Rak+eel++++ler+ +p+ +a++dakl+k+ id++
  gi|386002805|ref|YP_005921104.1| 238 RLREAVEIAKIELSSVLQTTINLPYITADQTGpKHLEMTITRAKLEELIKEVLERCRNPMIQAIRDAKLDKSGIDKI 314
                                       ***************************************************************************** PP

                                       EEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEE CS
                             HSP70 331 vlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkli 407
                                       vlvGG tR+P+v++ v e++gkep+ +v+p e+vaiGAAvq+gvl g  evkd+lllDvtpLslgietlggv+tkli
  gi|386002805|ref|YP_005921104.1| 315 VLVGGPTRMPAVRKFVTEFMGKEPEGGVDPMECVAIGAAVQGGVLGG--EVKDILLLDVTPLSLGIETLGGVATKLI 389
                                       ***********************************************..**************************** PP

                                       STTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEE CS
                             HSP70 408 ernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsak 484
                                       ernttipt+ksq+f+taadnqt+vei+vlqger l+kdn++lg+f+l+gippaprG pqieV+fdidanGil+vsak
  gi|386002805|ref|YP_005921104.1| 390 ERNTTIPTRKSQIFTTAADNQTTVEIHVLQGERPLAKDNTSLGRFTLSGIPPAPRGIPQIEVAFDIDANGILNVSAK 466
                                       ***************************************************************************** PP

                                       ETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHH CS
                             HSP70 485 dketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekve 561
                                       d +tgke+ iti+a ++ls++eie+ +++ae++a ed ++ke+ieakn+ae+lvy++ek+l++++e v++++kek+e
  gi|386002805|ref|YP_005921104.1| 467 DLATGKEQAITISAPHKLSQNEIERKIREAEQHAYEDTRRKEEIEAKNQAETLVYTAEKTLKDAGEVVTADQKEKIE 543
                                       ***************************************************************************** PP

                                       HHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 562 saieeLkeeleeeekeeieakteelkkvvekiaeklye 599
                                       +ai e ke+l++ ++++i++kte+l+++++++ +++y+
  gi|386002805|ref|YP_005921104.1| 544 RAIGEAKEALAGGDIAKIKEKTEALQNAIYELSTAMYQ 581
                                       ********************************999986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   6.0   1.9e-20   3.5e-17       3     316 ..       4     353 ..       2     356 .. 0.65
   2 ?   -4.0   0.0       2.8     5e+03     220     239 ..     461     480 ..     450     499 .. 0.63
   3 ?   -1.5   0.1      0.49   8.8e+02      11      57 ..     516     561 ..     514     592 .. 0.70

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.9e-20
                                       EEEEEE-SSEEE..EEETTTEEEE...EEES-EEEETTT--EEEESHHHHTTTTS-GTTEEEE-SEETTEES..... CS
                          MreB_Mbl   3 dlgiDLGtantl..vyvkgkgivl...nepsvvAikkktkkvlavGeeAkkmlgktpgnikavrPlkdGvia..... 69 
                                        +giDLGt n    v + gk  ++   +  s+vA  k   + +a  ++ ++++g   ++  a+ P  +G+i+     
  gi|386002805|ref|YP_005921104.1|   4 IIGIDLGTSNSAaaVLIGGKPTMIpsaEGTSIVAGGKAFPSYVAFTKDGQRLVGEPARRQAATNP--EGTITgikrk 78 
                                       68999999886522566777666522234688988888888888888888888887777777777..3444311111 PP

                                       ...SHHH.......HHHHHHH.HHHHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHH CS
                          MreB_Mbl  70 ...dlev.......aeellky.fikkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieepl 131
                                          d++v       + + + + +++k+k+ ++++   + ++ vi+vP   ++ +r+A k+a + aG + v +i+ep 
  gi|386002805|ref|YP_005921104.1|  79 mgqDYRVevygksyTPQDISSfILRKIKDdSEAFlgeKVEKAVITVPAYFNDNQRQATKDAGTIAGLDVVRIINEPT 155
                                       111332211211223344444055666664333334456789*********************************** PP

                                       HHHHHTT--TTSSS-EEEEEE-SS-EEEEEEETTEEE.EEEE....ES-SHHHHHHHHHHHHHHHHSEE--HH.... CS
                          MreB_Mbl 132 aAAiGaglpveepsgnmvvdiGggttevavislggiv.tsks....vrvaGdeldeaiikyirkkynlliGer.... 199
                                       aAA+  g++ e  +  mv d+Gggt +v+++ +g+ v + ks     +++G ++de +++y+ ++y+   G      
  gi|386002805|ref|YP_005921104.1| 156 AAALAYGMDKEGEATLMVFDLGGGTLDVTIMEAGEGVfEVKStsgdTQLGGRDMDEILTNYVVERYRQESGIDlkgd 232
                                       ********************************99755233432233789*****************98766531110 PP

                                       .HH.HHHHHHH-BSS--HHHH.EEEEEEEETT..TTCEE..EEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHH CS
                          MreB_Mbl 200 .ta.ekikieigsavkeeeee.kmeikGrdlv..tglpk..evevsseevrealkepvsaiveavkevLektppeLa 269
                                         a ++++ ++  a+ e ++  +++i+   ++  +  pk  e++++ ++++e +ke++++  + + +++++++ +  
  gi|386002805|ref|YP_005921104.1| 233 rMAmQRLREAVEIAKIELSSVlQTTINLPYITadQTGPKhlEMTITRAKLEELIKEVLERCRNPMIQAIRDAKLD-- 307
                                       032123333333332222222333333222220022233114455555555666666655555555555554433.. PP

                                       HHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHH CS
                          MreB_Mbl 270 adivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtg 316
                                       +  +d+ ivl+GG + +  ++k+++e +g + + + dp++cva G++
  gi|386002805|ref|YP_005921104.1| 308 KSGIDK-IVLVGGPTRMPAVRKFVTEFMGKEPEGGVDPMECVAIGAA 353
                                       333444.8999**********************************86 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.8
                                       EEEEEEETTTTCEEEEEEEH CS
                          MreB_Mbl 220 meikGrdlvtglpkevevss 239
                                       ++++ +dl+tg  + +++s+
  gi|386002805|ref|YP_005921104.1| 461 LNVSAKDLATGKEQAITISA 480
                                       56666777777766666654 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.49
                                       SEEEEEETTTEEEEEEES-EEEETTT--EEEESHHHHTTTTS-GTTE CS
                          MreB_Mbl  11 antlvyvkgkgivlnepsvvAikkktkkvlavGeeAkkmlgktpgni 57 
                                       a+tlvy+ +k  + +   vv  ++k+k   a+Ge  + + g    +i
  gi|386002805|ref|YP_005921104.1| 516 AETLVYTAEKT-LKDAGEVVTADQKEKIERAIGEAKEALAGGDIAKI 561
                                       67778877775.35666777777777777888877666666444444 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00027      0.48     142     198 ..     148     206 ..     130     227 .. 0.69
   2 !    5.5   0.0    0.0049       8.7     203     290 ..     237     327 ..     203     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                              StbA 142 vkvlPeslPagfealkeldeleslLiiDlGGttLDvakvrgklegi...skvkgdskiGv 198
                                       v+++ e   a+     + +    l++ DlGG tLDv+ ++ + eg+     + gd ++G 
  gi|386002805|ref|YP_005921104.1| 148 VRIINEPTAAALAYGMDKEGEATLMVFDLGGGTLDVTIME-AGEGVfevKSTSGDTQLGG 206
                                       66777777777777777777788999**********8654.4444400044556666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0049
                              StbA 203 davkealetaktrtssfladel.....iknrkdeeyLkrrindedkresvlevinekvkkLkerviravsefsgyth 274
                                       + ++ea+e ak++ ss l  ++       ++   ++L+ +i+ ++  e + ev+++  + + + +++a    sg+ +
  gi|386002805|ref|YP_005921104.1| 237 QRLREAVEIAKIELSSVLQTTInlpyiTADQTGPKHLEMTITRAKLEELIKEVLERCRNPMIQAIRDAKLDKSGIDK 313
                                       5555666666666666554443222215667788999999*999999999*************************** PP

                              StbA 275 vmvvGGGaeliaeaik 290
                                       +++vGG + +  +a++
  gi|386002805|ref|YP_005921104.1| 314 IVLVGGPTRM--PAVR 327
                                       ******8875..4455 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.22     145     196 ..     296     358 ..     275     359 .. 0.76
   2 ?   -2.1   0.1       1.5   2.6e+03      78      78 ..     522     522 ..     462     596 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                            FGGY_C 145 d..........sgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                                                  +++ +d+++++GG ++ ++++++  + +g  p   +++ e++a+GaA+ ++v
  gi|386002805|ref|YP_005921104.1| 296 PmiqairdaklDKSGIDKIVLVGGPTRMPAVRKFVTEFMGkEPEGGVDPMECVAIGAAVQGGV 358
                                       044444444546778*************************777667778**********9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                            FGGY_C  78 a 78 
                                        
  gi|386002805|ref|YP_005921104.1| 522 T 522
                                       2 PP

>> DUF547  Protein of unknown function, DUF547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0012       2.2      40      73 ..      79     112 ..      58     139 .. 0.73
   2 ?    1.6   0.1      0.15   2.6e+02      41      94 ..     472     525 ..     449     552 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                            DUF547  40 f.kkaayniggqslslddIehgiLrknlsrlkkka 73 
                                       + ++ ++++ g+s++ +dI + iLrk  +++++ +
  gi|386002805|ref|YP_005921104.1|  79 MgQDYRVEVYGKSYTPQDISSFILRKI-KDDSEAF 112
                                       4478889999***************97.3333333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                            DUF547  41 kkaayniggq.slslddIehgiLrknlsrlkkkarderrkyaleqpdprihfaLv 94 
                                       k++a++i+   +ls ++Ie +i  ++ +++ + +r++++ +a +q++ +++ a +
  gi|386002805|ref|YP_005921104.1| 472 KEQAITISAPhKLSQNEIERKIREAE-QHAYEDTRRKEEIEAKNQAETLVYTAEK 525
                                       677778875449********998887.5666666777777777788887777655 PP

>> M_domain  M domain of GW182
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.4   0.00018      0.33     175     225 ..     551     605 ..     538     613 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                          M_domain 175 vqva...InklkqQIqqlQnQiaa.qQaiylKQqqqqqqsqqqqqqgqppaavgg 225
                                         +a   I+k+k+  + lQn i+    a+y +  +qqq++q++qqq+q +++ +g
  gi|386002805|ref|YP_005921104.1| 551 EALAggdIAKIKEKTEALQNAIYElSTAMYQRAAEQQQREQEKQQQSQGGPTASG 605
                                       4566667***************952568888878888888877777666666665 PP

>> DUF1090  Protein of unknown function (DUF1090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.6   2.9e+03      42      69 ..     280     307 ..     276     310 .. 0.82
   2 ?   10.6  12.7   0.00025      0.45      22     109 ..     486     576 ..     482     577 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                           DUF1090  42 agLekaLkevkanCtdeklkaerqekve 69 
                                       a+Le+  kev + C++  ++a r +k++
  gi|386002805|ref|YP_005921104.1| 280 AKLEELIKEVLERCRNPMIQAIRDAKLD 307
                                       6799999999999999988888887776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                           DUF1090  22 kqaIekqieaAkah..gnqkrvagLekaLkevkanCtdeklkaerqekv.eekeeeVaereaeLaeakekgdkdkia 95 
                                       +++Ie++i++A++h  ++++r ++ e+  ++ +   t ek ++++ e v ++++e++++   e +ea + gd +ki+
  gi|386002805|ref|YP_005921104.1| 486 QNEIERKIREAEQHayEDTRRKEEIEAKNQAETLVYTAEKTLKDAGEVVtADQKEKIERAIGEAKEALAGGDIAKIK 562
                                       689********98844699999999987766666666666666666665599************************* PP

                           DUF1090  96 krqekLaeakeeLk 109
                                       ++ e L++a  eL+
  gi|386002805|ref|YP_005921104.1| 563 EKTEALQNAIYELS 576
                                       ********999986 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  14.1   0.00071       1.3      62     168 ..     483     597 ..     466     603 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00071
                              Vfa1  62 akkkkeleeeiekvkkeyeekqkkkkekekkkkekd....kkdkdkkkekekdkkkekek.........eeekkkel 125
                                       + +++e+e++i++ +++  e +++k+e e+k++  +    + +k+ k+  e  ++++kek         e  +  ++
  gi|386002805|ref|YP_005921104.1| 483 KLSQNEIERKIREAEQHAYEDTRRKEEIEAKNQA-EtlvyTAEKTLKDAGEVVTADQKEKieraigeakEALAGGDI 558
                                       3456668888888877777777777766665533.346764444444444444444554434454432122222233 PP

                              Vfa1 126 kkaeeeleekeeprvkkykLhkefyqsRlerkrqaeaakenee 168
                                       +k +e+   +e+ +++ y+L++ +yq   e+ +q+e++k++++
  gi|386002805|ref|YP_005921104.1| 559 AKIKEK---TEALQNAIYELSTAMYQRAAEQ-QQREQEKQQQS 597
                                       333333...34445555********865555.44444444443 PP

>> Phage_connect_1  Phage gp6-like head-tail connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2       0.4   7.2e+02      22      42 ..     489     513 ..     485     541 .. 0.72
   2 ?    8.8   1.2    0.0013       2.3      19      83 ..     539     597 ..     525     605 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.4
                   Phage_connect_1  22 LesliqaAeeyikdylgrkl....e 42 
                                       +e+ i+ Ae+++ ++++rk     +
  gi|386002805|ref|YP_005921104.1| 489 IERKIREAEQHAYEDTRRKEeieaK 513
                                       89999*******9999999855331 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                   Phage_connect_1  19 DalLesliqaAeeyikdylgrkleadedgielpedlktavlelaahryenregtssdssegksls 83 
                                       ++ +e+ i  A+e++          +++ +e +e l +a++el +++y++   ++++++e +++s
  gi|386002805|ref|YP_005921104.1| 539 KEKIERAIGEAKEALAG------GDIAKIKEKTEALQNAIYELSTAMYQRAAEQQQREQEKQQQS 597
                                       44444444444444422......224455567889****************55554555555555 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.4    0.0037       6.6      19     112 ..     499     601 ..     475     613 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0037
                           DUF3347  19 eekeeeeeeeeeeekekkkekse.........eeee.........kdeklkevlesYlklkdALvaddakeakkaak 77 
                                       +  e  +++++ee ++k     +         e  +         ++++ +++  +  + k+AL+  d +++k++++
  gi|386002805|ref|YP_005921104.1| 499 HAYE--DTRRKEEIEAK-----NqaetlvytaE--KtlkdagevvTADQKEKIERAIGEAKEALAGGDIAKIKEKTE 566
                                       1111..11111111111.....11222344431..145666667777777889999999****************** PP

                           DUF3347  78 kleeklkavdtsklkekekkelkeiseelkekaek 112
                                       +l++++ +++t+ +++ ++++ +e++++ +++   
  gi|386002805|ref|YP_005921104.1| 567 ALQNAIYELSTAMYQRAAEQQQREQEKQQQSQGGP 601
                                       *********99999988888888888877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1748  (0.0974957); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.83u 0.37s 00:00:01.20 Elapsed: 00:00:00.53
# Mc/sec: 3488.48
//
Query:       gi|386002806|ref|YP_005921105.1|  [L=179]
Description: Co-chaperone GrpE [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-40  136.9   3.5    6.8e-40  136.4   3.5    1.3  1  GrpE      GrpE


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   3.5   3.8e-44   6.8e-40      15     166 .]      36     177 ..       4     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 3.8e-44
                                       CCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHH CS
                              GrpE  15 eeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeeksl 91 
                                        el ++l+e+e+ v+el+++llr++ae++n  kr+++e+e+   fa e+++++LLpvlD+l+ a k+          
  gi|386002806|ref|YP_005921105.1|  36 LELARQLAEAERLVEELTDQLLRSRAELDNTVKRAAREREASTLFASERLMTKLLPVLDSLDQAAKH---------- 102
                                       4567789***********************************************************8.......... PP

                                       HHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEEE CS
                              GrpE  92 leGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVsk 166
                                       +eG++ ++kqll++L  +g+ +ie+kge+FDp  hea+++ve+de eegtv e+vq+GY l+++v+R ++V Vsk
  gi|386002806|ref|YP_005921105.1| 103 VEGMDKVRKQLLDVLRTEGLSPIEAKGEKFDPYKHEALMMVESDEDEEGTVTEEVQRGYALNSKVIRFSKVLVSK 177
                                       8************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1155.18
//
Query:       gi|386002807|ref|YP_005921106.1|  [L=548]
Description: Thermosome subunit [Methanosaeta harundinacea 6Ac]
Scores for 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-166  552.3  10.3   9.9e-166  552.2  10.3    1.0  1  Cpn60_TCP1       TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.12   12.3   0.7        5.3    7.0   0.0    3.1  3  DUF2000          Protein of unknown function (DUF2000)
       0.12   11.8   0.3        3.6    7.0   0.0    2.5  2  Inj_translocase  DNA/protein translocase of phage P22 injecto


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  552.2  10.3  1.7e-169  9.9e-166       1     490 [.      35     523 ..      35     524 .. 0.98

  Alignments for each domain:
  == domain 1  score: 552.2 bits;  conditional E-value: 1.7e-169
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a ++kttlGPkGmdKmlv+  g+vv+TnDGatil+e++iehP+ak++ve+a++q++evGDGTtt+v+Lag Lle+a
  gi|386002807|ref|YP_005921106.1|  35 VAAVLKTTLGPKGMDKMLVDGSGDVVITNDGATILREMDIEHPVAKMIVEVARAQEDEVGDGTTTAVVLAGGLLENA 111
                                       5789************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+li+ gvhpt+i++gy+ a +ka e+L+e+  +++++++dre+L+++a+t++++k ++  ++ l++++v A  +ie
  gi|386002807|ref|YP_005921106.1| 112 EELIDIGVHPTVIVQGYKAAQKKAYEFLEEM--AVEVSKEDREILKRIAETAMTGKGIEVFKKDLAEICVVAAAAIE 186
                                       *******************************..5555567*********************************9997 PP

                                       CCSEECSCCC.EECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHH CS
                        Cpn60_TCP1 155 enekeldlgr.ikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeel 230
                                       e+ +++d+++ +  vki ggs++d+ l+eG+vldk+ l+p+mpk++e ak++lld +Le +k  t+++v++s++e l
  gi|386002807|ref|YP_005921106.1| 187 EE-GKFDVEErVSFVKIGGGSVKDTILEEGVVLDKERLNPEMPKRVEGAKIALLDSTLELKKLSTDAKVTISSPESL 262
                                       66.79999887****************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCG CS
                        Cpn60_TCP1 231 eklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpe 307
                                        ++++ e + l+e++e+++k g+nvv+c++gi  +a  +la ngi+a+rrv+ ++++ la atG+++v+++ ++  e
  gi|386002807|ref|YP_005921106.1| 263 SSFREGEDEVLREKVEAMAKVGANVVFCKQGIGAYASRYLANNGIIAARRVSDEEMKFLALATGGRIVTDPLEMRGE 339
                                       ***************************************************************************** PP

                                       C-EEEEEEEECCETT.CCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHH CS
                        Cpn60_TCP1 308 elGtakkveeekigs.ekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelel 383
                                       +lG+a+ v e+k+g  +k++++e++  +k++t+++ g++++  + iera+edAl +v+ ++e++k+vpGGGa e+e+
  gi|386002807|ref|YP_005921106.1| 340 DLGSADLVAERKVGRdKKMIFVEGCHGAKAVTVVIHGSSEQLRENIERALEDALWSVATVLESKKIVPGGGAPEIEV 416
                                       ********9999997367888******************************************************** PP

                                       HHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXE CS
                        Cpn60_TCP1 384 akklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvv 460
                                       a++l++ya++++g++qla++afa+A e+ip  LaeNaG+dpi+vl +lr++h +ge ++g+d+++g++ d++eagvv
  gi|386002807|ref|YP_005921106.1| 417 AERLRQYASTITGRDQLAVKAFADAVEEIPFNLAENAGFDPIDVLVRLRSSHGAGERSYGLDINTGKPADMIEAGVV 493
                                       ***************************************************************************** PP

                                       EEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 461 DplkvkrqalksAteaastiLrideiikak 490
                                       +plkvk+qa+ks t aa+++Lr+d++i ak
  gi|386002807|ref|YP_005921106.1| 494 EPLKVKTQAIKSGTAAATLVLRVDDVIAAK 523
                                       ***************************997 PP

>> DUF2000  Protein of unknown function (DUF2000)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.41   2.4e+03      48      61 ..       2      15 ..       1      42 [. 0.76
   2 ?    7.0   0.0   0.00089       5.3      20      80 ..     100     169 ..      89     181 .. 0.86
   3 ?    1.8   0.0     0.034     2e+02      56      75 ..     372     391 ..     367     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.41
                                      ---BSS-EEEEEE- CS
                           DUF2000 48 agiselPvpvlkas 61
                                      ag++++P+++lk  
  gi|386002807|ref|YP_005921106.1|  2 AGLTNAPILILKEG 15
                                      68999999999973 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHH.........-GGGB-S-EE-TTS-EE---BSS-EEEEEE-HHHHHHHHHHHHHT.T--- CS
                           DUF2000  20 aavlalglgaa.........apelvgedyaDadgeahagiselPvpvlkassekLrelrekaleregltv 80 
                                       a vla gl ++         +p ++ + y+ a+++a++ + e+ v v k ++e L+++ e a++ +g++v
  gi|386002807|ref|YP_005921106.1| 100 AVVLAGGLLENaeelidigvHPTVIVQGYKAAQKKAYEFLEEMAVEVSKEDREILKRIAETAMTGKGIEV 169
                                       55666666666666666666999**************************************999888876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.034
                                       EEEEE-HHHHHHHHHHHHHT CS
                           DUF2000  56 pvlkassekLrelrekaler 75 
                                       +v  +sse+Lre +e+ale+
  gi|386002807|ref|YP_005921106.1| 372 VVIHGSSEQLRENIERALED 391
                                       78999************998 PP

>> Inj_translocase  DNA/protein translocase of phage P22 injectosome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.02   1.2e+02      99     138 ..      17      56 ..       4      63 .. 0.87
   2 ?    7.0   0.0    0.0006       3.6     133     174 ..     106     147 ..      73     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.02
                   Inj_translocase  99 kalsglneqkredlGklamklkvalaqGpeavskfvtkna 138
                                       k  +g ++q+r+ +   a+++ +  + Gp+ ++k++++ +
  gi|386002807|ref|YP_005921106.1|  17 KRETGRDAQRRNIMAAKAVAAVLKTTLGPKGMDKMLVDGS 56 
                                       5567889****************************99876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0006
                   Inj_translocase 133 fvtknadrlkrvGvdPedllqtlkqdPeqlseladlvgLgal 174
                                        + +na++l  +Gv+P  ++q +k   +++ e+++ ++++  
  gi|386002807|ref|YP_005921106.1| 106 GLLENAEELIDIGVHPTVIVQGYKAAQKKAYEFLEEMAVEVS 147
                                       4789***********************999999999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3290.26
//
Query:       gi|386002808|ref|YP_005921107.1|  [L=289]
Description: Phosphate ABC transporter substrate-binding protein, PhoT family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-36  125.1   0.1    1.1e-35  123.7   0.1    1.5  1  PBP_like_2      PBP superfamily domain
    2.3e-13   49.7   0.1    3.5e-13   49.1   0.1    1.3  1  PBP_like        PBP superfamily domain
    4.9e-08   33.0   0.0     0.0073   16.1   0.0    2.2  2  SBP_bac_11      Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.056   12.8   0.0    1.4  1  LysR_substrate  LysR substrate binding domain
       0.17   11.3   0.0       0.41   10.0   0.0    1.6  2  SBP_bac_6       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   0.1     3e-39   1.1e-35      11     277 ..      33     262 ..      27     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 3e-39
                        PBP_like_2  11 eifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggliq 87 
                                       +++++Gstt+ pa++  a+ f++a+  ++v+++s+GSg gi+++++g +d+++++r++++sei  ++ +++   +++
  gi|386002808|ref|YP_005921107.1|  33 NLVITGSTTVLPAVERCAEVFNRAQDEIRVQVSSGGSGRGIQDVASGLADIGMASRDVKDSEI--RIFGDR---FVE 104
                                       489**********************************************************99..666666...*** PP

                        PBP_like_2  88 vpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpw 160
                                       + ++++aia+vv+++   ++++ l+ e+++ I+sg+It Wn+ +g+p ++ I +v+r +gsgt ++f ++++    +
  gi|386002808|ref|YP_005921107.1| 105 HLIGYDAIAVVVSQEvydGGVRgLTSEEVSRIYSGEITRWNE-VGGP-ETMILPVARVPGSGTGETFNEMIMGSTMA 179
                                       *************998988888********************.6666.**************************888 PP

                        PBP_like_2 161 tasgigasg..segvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplaws 234
                                       +++g++++   + ++++ + + + aigy+ ++y++                         + ++  + i++      
  gi|386002808|ref|YP_005921107.1| 180 ETEGVEVNAmeNAEIKTLIvQSDKAIGYLGIGYAK-------------------------TGKIRPLAIDG------ 225
                                       8888875555577777776699999******9999.........................33334444433...... PP

                        PBP_like_2 235 lqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldy 277
                                       + p+ en++   y lsr++y+++ + +      +++  +F+++
  gi|386002808|ref|YP_005921107.1| 226 VSPTAENVKGLQYKLSRPLYLYTWDGT------SEAEAEFINF 262
                                       556666666666**********99987......6666666666 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   9.7e-17   3.5e-13       1     163 [.      50     238 ..      50     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 9.7e-17
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH..HCCCCCEEE..EEEEEEEE........E- CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketee..ynapalrka..ldgievvl........vn 65 
                                       ae +++++ ++rv+v+  Gsg G++ ++ g adi+++++  k++e       +++++  +d+i+vv+        v+
  gi|386002808|ref|YP_005921107.1|  50 AEVFNRAQDEIRVQVSSGGSGRGIQDVASGLADIGMASRDVKDSEIriFGDRFVEHLigYDAIAVVVsqevydggVR 126
                                       678999*********************************87766543322223333311455555555555555566 PP

                                       CC-HCHCCCCHCCHHHS--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCH CS
                          PBP_like  66 larreqglvvakgnpkkitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaV 140
                                       +++ e+   +++g   +it w+++  ++  +  v R  GSGt   f+e++ +     ++ +g++  a ++ ++++ +
  gi|386002808|ref|YP_005921107.1| 127 GLTSEEVSRIYSG---EITRWNEVggPETMILPVARVPGSGTGETFNEMIMGS--TMAETEGVEVNAMENAEIKTLI 198
                                       6666665556666...7*******999999999*****************665..677899999************* PP

                                       CCETTCCE................C.CCGG-HCCCCCCEC CS
                          PBP_like 141 aagradvg................v.gieavaeelkgldf 163
                                        + + ++g                + g++++ae++kgl++
  gi|386002808|ref|YP_005921107.1| 199 VQSDKAIGylgigyaktgkirplaIdGVSPTAENVKGLQY 238
                                       ********77777777777777664466888888888887 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     2e-06    0.0073       1      45 [.      34      79 ..      34      89 .. 0.90
   2 !   15.2   0.0   3.7e-06     0.013     201     229 ..     249     277 ..     141     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                                      .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH CS
                        SBP_bac_11  1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadg 45
                                      l ++ ++++ +a++++a+ F +a+ +++v+vs+ggsg+ ++ +a+g
  gi|386002808|ref|YP_005921107.1| 34 LVITGSTTVLPAVERCAEVFnRAQDEIRVQVSSGGSGRGIQDVASG 79
                                      5688899999**********999**************998888877 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.7e-06
                                       -TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 201 kaakreaAraFlafLrspeaqailrkyGf 229
                                        ++ +ea ++F++f+r+pe+q+i+++ Gf
  gi|386002808|ref|YP_005921107.1| 249 WDGTSEAEAEFINFVRGPEGQRIMEEEGF 277
                                       34568999********************9 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.056      27      71 ..      52      96 ..      12     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                      HHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSSCCTTEE CS
                    LysR_substrate 27 rfraryPevelelvegdseelldllaegelDlairagppedsgle 71
                                       f ++  e+++++++g s + ++ +a+g +D++ ++++  ds+++
  gi|386002808|ref|YP_005921107.1| 52 VFNRAQDEIRVQVSSGGSGRGIQDVASGLADIGMASRDVKDSEIR 96
                                      47888889*******************************999865 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       2.1   7.7e+03       4      21 ..      81     109 ..      80     115 .. 0.67
   2 ?   10.0   0.0   0.00011      0.41     189     223 ..     252     284 ..     242     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.1
                         SBP_bac_6   4 pdlils...........fdkdflekfiee 21 
                                       +d++++           f+++f+e++i  
  gi|386002808|ref|YP_005921107.1|  81 ADIGMAsrdvkdseiriFGDRFVEHLIGY 109
                                       56666566666666677889999988865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                         SBP_bac_6 189 kkelakafidfllspevqailakaggvfPvvtnpa 223
                                       ++e  ++fi+f  +pe+q+i++++g+ f v ++p+
  gi|386002808|ref|YP_005921107.1| 252 TSEAEAEFINFVRGPEGQRIMEEEGF-FSV-AAPE 284
                                       5666689******************9.877.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1631.56
//
Query:       gi|386002809|ref|YP_005921108.1|  [L=244]
Description: Phosphate ABC transporter, ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-32  111.4   0.0    6.1e-32  111.0   0.0    1.2  1  ABC_tran     ABC transporter
    2.9e-14   53.6   0.0    3.4e-07   30.4   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.1e-06   26.4   0.1    0.00011   21.7   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    8.8e-05   23.0   0.0    0.00032   21.1   0.0    2.0  2  AAA_16       AAA ATPase domain
    0.00017   21.4   0.0    0.00029   20.7   0.0    1.4  1  AAA_15       AAA ATPase domain
    0.00022   21.5   0.0    0.00074   19.8   0.0    2.0  1  AAA_22       AAA domain
    0.00027   20.9   0.0    0.00067   19.6   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
     0.0012   18.8   0.0      0.002   18.1   0.0    1.4  1  Rad17        Rad17 P-loop domain
     0.0014   18.3   0.0     0.0025   17.5   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0016   19.0   0.3     0.0034   17.9   0.3    1.7  1  AAA_23       AAA domain
     0.0046   17.4   0.0      0.062   13.7   0.0    2.2  1  AAA          ATPase family associated with various cellular a
     0.0052   17.0   0.0     0.0087   16.2   0.0    1.5  1  AAA_33       AAA domain
  ------ inclusion threshold ------
      0.015   15.8   0.0      0.041   14.4   0.0    1.7  1  AAA_18       AAA domain
      0.019   14.6   0.0      0.053   13.1   0.0    1.7  2  AAA_25       AAA domain
      0.025   14.8   0.0       0.57   10.4   0.0    2.3  2  AAA_28       AAA domain
      0.025   13.9   0.0      0.055   12.8   0.0    1.5  1  ATPase       KaiC
      0.037   12.8   0.0        1.5    7.5   0.0    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.068   12.9   0.0        1.6    8.4   0.0    2.1  2  AAA_30       AAA domain
      0.086   12.6   0.0       0.17   11.6   0.0    1.5  1  PRK          Phosphoribulokinase / Uridine kinase family
       0.12   11.3   0.0       0.17   10.8   0.0    1.3  1  AAA_PrkA     PrkA AAA domain
       0.14   11.8   0.0       0.29   10.8   0.0    1.5  1  AAA_24       AAA domain
       0.18   10.4   0.0       0.29    9.7   0.0    1.3  1  AAA_13       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   7.5e-35   6.1e-32       1     136 [.      16     168 ..      16     169 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 7.5e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepql 70 
                                       lk++s+ + e++++a++G++G+GKSt++++l ++ +       eGeil+d+ ++ +  ++  +lrk+ig+++q+p+ 
  gi|386002809|ref|YP_005921108.1|  16 LKDISMGIPENQITALIGPSGCGKSTFIRCLNRMNDLvdivrIEGEILYDSVNIYDkdTDVVELRKNIGMVFQKPNP 92 
                                       79********************************99999999***********9998889999************** PP

                                       -TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       fp + +r+n           + d+ +e+ l+k  l e   +++++ +  LSgGq+qr+++aral+ kp+++l+DEp+
  gi|386002809|ref|YP_005921108.1|  93 FPMS-IRDNiaygprihgvkNVDKIAEESLKKAALWEEVSDRLDKPAMGLSGGQQQRLCIARALAMKPDVILFDEPC 168
                                       ****.***********998777777******************9999*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.2e-07   0.00018       1      51 [.      28      78 ..      28     102 .. 0.70
   2 !   30.4   0.0   4.2e-10   3.4e-07     208     295 ..     112     196 ..      94     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51
                                      +++liGp g+GKS+++++l  + +l + v+ ++ +l ++++i + +    +
  gi|386002809|ref|YP_005921108.1| 28 ITALIGPSGCGKSTFIRCLNRMNDLVDIVRIEGEILYDSVNIYDKDTDVVE 78
                                      79******************9988755555555555555555544444444 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 4.2e-10
                            AAA_21 208 liasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                       + ++++e ++ +   ++e +d+ + pa  lS G+++ l+++ al+  +   +++l+DEp + L+P  ++++ el++e
  gi|386002809|ref|YP_005921108.1| 112 NVDKIAEESLKKAALWEEVSDRLDKPAMGLSGGQQQRLCIARALAMKP---DVILFDEPCSALDPLSTAKIEELMDE 185
                                       444444444444556667777777799999*******99999999877...************************** PP

                            AAA_21 285 lsrngaQvilt 295
                                       l+   +Qvi+t
  gi|386002809|ref|YP_005921108.1| 186 LRGSYTQVIVT 196
                                       *********98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.3e-07   0.00011      23     200 ..      25     201 ..      15     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeev 97 
                                       ++++ta++Gp G+GKs ++  +  +    +   +  e l d ++   +++     + ++ ++f++++      ++++
  gi|386002809|ref|YP_005921108.1|  25 ENQITALIGPSGCGKSTFIRCLNRMNDLVDIVRIEGEILYDSVNIydKDTDVVELRKNIGMVFQKPNPFPMSIRDNI 101
                                       6789******************877777788888888888877665455666667789999***9999855556666 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTC.S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiskel.LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                           r+   ++   ki +++ +k+ + e +++   ++ + LSgG+++ + +a  +A+   kp  + l+De  +aLD 
  gi|386002809|ref|YP_005921108.1| 102 AYGPRIHGVKN-VDKIAEESLKKAALWEEVSDRLDKPAMgLSGGQQQRLCIARALAM---KPD-VILFDEPCSALDP 173
                                       66665554444.45777777777666666555444433339*****99999988876...454.679********** PP

                                       HHHHHHHHHHHHHCTT.SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkekskn.aQfivislree 200
                                         ++k+ el++e + + +Q+iv+   ++
  gi|386002809|ref|YP_005921108.1| 174 LSTAKIEELMDELRGSyTQVIVTHNMQQ 201
                                       ***********99887588887654444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.9e-07   0.00032      14      46 ..      14      48 ..      13     194 .. 0.62
   2 ?   -1.1   0.0       2.7   2.2e+03      41      83 ..     179     219 ..     175     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.9e-07
                            AAA_16 14 salervrsgrp..elvllsGesGvGKsslvrellr 46
                                      +al+++++g p  +++ l+G+sG+GKs+ +r+l r
  gi|386002809|ref|YP_005921108.1| 14 HALKDISMGIPenQITALIGPSGCGKSTFIRCLNR 48
                                      7899999999999*******************996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                            AAA_16  41 vrellralekdggiflrgkcdqlesaipysalaqalareellr 83 
                                       ++el+++l++++  ++ +++ q   a++ s ++ ++   el++
  gi|386002809|ref|YP_005921108.1| 179 IEELMDELRGSYTQVIVTHNMQQ--AARVSDYTAYFLLGELVE 219
                                       67888888888777766666666..333344555554444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.6e-07   0.00029      14      76 ..      16      74 ..      14     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.6e-07
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskd 76
                                      lkd+++ + e+ +t liG+ ++GKS++++ l+ + +       + + ie e l ++ ni+ + +
  gi|386002809|ref|YP_005921108.1| 16 LKDISMGIPENqITALIGPSGCGKSTFIRCLNRMNDLV-----DIVRIEGEILYDSVNIYDKDT 74
                                      788888888888********************999965.....455555555555555554443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     9e-07   0.00074       5      68 ..      26      91 ..      24     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9e-07
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdllrellralglel 68
                                       +i++++G+sG+GK+t +r l + +d +   + e+  ++ +v++  +  +  +l++++   ++ ++
  gi|386002809|ref|YP_005921108.1| 26 NQITALIGPSGCGKSTFIRCLNRMNDLVDIVRIEGEILYdSVNIYDKDtDVVELRKNIGMVFQKPN 91
                                      5899*******************9987765555444444555554444455555555555555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.2e-07   0.00067      88     122 ..      14      49 ..       5      62 .. 0.80
   2 ?   -2.9   0.0       6.6   5.4e+03      62      81 ..     177     195 ..     167     207 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.2e-07
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++l++++  + + ++++l+G+SG GKSt+i  l+  
  gi|386002809|ref|YP_005921108.1|  14 HALKDISMGIPEnQITALIGPSGCGKSTFIRCLNRM 49 
                                       55666766666659****************999874 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHHTTSEEEE CS
                       RsgA_GTPase  62 eeeleelkeelealgyevll 81 
                                       ++ +eel++el+   ++v++
  gi|386002809|ref|YP_005921108.1| 177 AK-IEELMDELRGSYTQVIV 195
                                       33.45555555555444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.4e-06     0.002      43      69 ..      24      50 ..      13      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLskel 69
                                       +++i  + GPsGCgkst ++ L +  
  gi|386002809|ref|YP_005921108.1| 24 PENQITALIGPSGCGKSTFIRCLNRMN 50
                                      45689999**************98765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.1e-06    0.0025      16      39 ..      20      43 ..       2      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.1e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      ++ i ++++t l+GpsG GKST++
  gi|386002809|ref|YP_005921108.1| 20 SMGIPENQITALIGPSGCGKSTFI 43
                                      445555669*************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   4.2e-06    0.0034      18      40 ..      25      47 ..      13     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                            AAA_23 18 skgltlItGpNGaGKTTildAik 40
                                      ++ +t+++Gp G+GK+T+++++ 
  gi|386002809|ref|YP_005921108.1| 25 ENQITALIGPSGCGKSTFIRCLN 47
                                      6889*****************96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.6e-05     0.062       3      38 ..      31     122 ..      29     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.6e-05
                                       EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS......................................... CS
                               AAA   3 lyGppGtGKTllakavakelg.vefleisgsellsk......................................... 37 
                                       l+Gp G+GK+++++ + +  + v++++i+g  l ++                                         
  gi|386002809|ref|YP_005921108.1|  31 LIGPSGCGKSTFIRCLNRMNDlVDIVRIEGEILYDSvniydkdtdvvelrknigmvfqkpnpfpmsirdniaygpri 107
                                       89************998886578899999888875567777777555555555555555555555555555555555 PP

                                       ..............S CS
                               AAA  38 ..............y 38 
                                                      
  gi|386002809|ref|YP_005921108.1| 108 hgvknvdkiaeeslK 122
                                       555555555555550 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0087       3      44 ..      30      74 ..      28     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg...avllssdtlrrrlfgtdqqs 44
                                       l+G++G+GKst+++ l + ++    v+++  +l++ +   d+++
  gi|386002809|ref|YP_005921108.1| 30 ALIGPSGCGKSTFIRCLNRMNDlvdIVRIEGEILYDSVNIYDKDT 74
                                      589**************9988888999999999998887766654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.1e-05     0.041       3      31 ..      31      62 ..      30      93 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.......gvnlrdv 31
                                      l G++G+GK+t+ + L++++ +       g    ++
  gi|386002809|ref|YP_005921108.1| 31 LIGPSGCGKSTFIRCLNRMNDLvdivrieG----EI 62
                                      89**************99975556633331....32 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.053      24      50 ..      18      43 ..      11      47 .. 0.83
   2 ?   -1.8   0.0       2.4     2e+03     112     147 ..     159     195 ..     129     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                            AAA_25 24 wlvkgllpagelallaGapgtGKttla 50
                                      ++ +g+ p++ +++l+G++g+GK+t+ 
  gi|386002809|ref|YP_005921108.1| 18 DISMGI-PENQITALIGPSGCGKSTFI 43
                                      555666.9*****************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                            AAA_25 112 eslpLfak..drggtlltadvdaleaaieevegvrlvv 147
                                        ++ Lf++   + ++l ta++++l+++++     +++v
  gi|386002809|ref|YP_005921108.1| 159 PDVILFDEpcSALDPLSTAKIEELMDELRGS-YTQVIV 195
                                       4455554422344555677777777777763.366665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0007      0.57       3      22 ..      30      49 ..      28      81 .. 0.81
   2 ?    2.3   0.0      0.22   1.8e+02      98     121 ..     197     220 ..     108     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0007
                            AAA_28  3 vitGgestGKTtlleaLaar 22
                                      +++G++++GK+t ++ L+++
  gi|386002809|ref|YP_005921108.1| 30 ALIGPSGCGKSTFIRCLNRM 49
                                      79*************99976 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                            AAA_28  98 aeleaaarekrydlvfllppapei 121
                                        ++++aar + y+++fll +  e+
  gi|386002809|ref|YP_005921108.1| 197 HNMQQAARVSDYTAYFLLGELVEF 220
                                       234557888888888888776655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.7e-05     0.055      13      35 ..      20      42 ..      14      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                            ATPase 13 kgGipegrvvlitGepGtGKtif 35
                                      + Gipe++++ + G +G+GK++f
  gi|386002809|ref|YP_005921108.1| 20 SMGIPENQITALIGPSGCGKSTF 42
                                      47*******************98 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0018       1.5     240     266 ..      21      48 ..      13      51 .. 0.91
   2 ?    3.2   0.0     0.039        32     324     354 ..     142     172 ..     139     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                       mgip+  +t+++G+   GKsT ++ l++
  gi|386002809|ref|YP_005921108.1|  21 MGIPENqITALIGPSGCGKSTFIRCLNR 48 
                                       9***999****************99975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.039
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HH CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtN 354
                                       SG   q   i++al ++ +++L+DE  sA  
  gi|386002809|ref|YP_005921108.1| 142 SGGQQQRLCIARALAMKPDVILFDEPCSALD 172
                                       888899999****************999965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.002       1.6      18      40 ..      26      48 ..      17      53 .. 0.88
   2 ?    2.4   0.0      0.14   1.1e+02      86     131 ..     155     205 ..     107     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                            AAA_30 18 drvavltGpAGtGKttalkalre 40
                                      +++++l Gp G GK+t ++ l++
  gi|386002809|ref|YP_005921108.1| 26 NQITALIGPSGCGKSTFIRCLNR 48
                                      67999*************98876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                            AAA_30  86 lepg.tllivDEagmv....dtkqlaallkaaekagakvilvGDerQlasV 131
                                       l+ + ++++ DE   +    +t+++++l+++++ + ++vi+    +Q a V
  gi|386002809|ref|YP_005921108.1| 155 LAMKpDVILFDEPCSAldplSTAKIEELMDELRGSYTQVIVTHNMQQAARV 205
                                       333448999999877778889************999999999888888776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.17       3      46 ..      30      71 ..      28      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraek 46
                                      ++ g+SG+Gk+t+ r l+ +     v  + ieg  +   +++++
  gi|386002809|ref|YP_005921108.1| 30 ALIGPSGCGKSTFIRCLNRMND--LVDIVRIEGEILYDSVNIYD 71
                                      788***********99887655..44445666655544444433 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.17      87     147 ..      25      85 ..      14     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                          AAA_PrkA  87 rkqilyllGPvggGksslverlkklleaapiyalegsPvfeePlhli.peelrkkleeeygi 147
                                       + qi  l+GP g Gks+++  l ++ + + i  +eg  ++++ ++++  + +  +l ++ g+
  gi|386002809|ref|YP_005921108.1|  25 ENQITALIGPSGCGKSTFIRCLNRMNDLVDIVRIEGEILYDS-VNIYdKDTDVVELRKNIGM 85 
                                       4699*******************9999999998887766655.3333344555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.29       4      22 ..      28      46 ..      25      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                        +++Gpsg GK+t+++ l
  gi|386002809|ref|YP_005921108.1| 28 ITALIGPSGCGKSTFIRCL 46
                                      5789************987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00036      0.29     526     574 ..     158     202 ..     150     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                       k  ++ +D P S LD  s   +  l+++      ++ Q+++ THn++  
  gi|386002809|ref|YP_005921108.1| 158 KPDVILFDEPCSALDPLSTAKIEELMDELR---GSYTQVIV-THNMQQA 202
                                       899*************************97...9****976.***9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1497.80
//
Query:       gi|386002810|ref|YP_005921109.1|  [L=219]
Description: Phosphate transport system regulatory protein PhoU [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-44  149.1   7.1    7.3e-22   77.6   2.5    2.1  2  PhoU        PhoU domain
     0.0051   17.1   1.2     0.0051   17.1   1.2    1.8  2  TBCA        Tubulin binding cofactor A
  ------ inclusion threshold ------
      0.079   13.3   2.4       0.26   11.6   0.2    2.3  2  Cdh1_DBD_1  Chromodomain helicase DNA-binding domain 1
       0.15   11.6   3.6       0.24   10.9   3.6    1.4  1  DUF5394     Family of unknown function (DUF5394)


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   2.5   1.6e-25   7.3e-22       4      89 .]      22     107 ..      19     107 .. 0.96
   2 !   74.1   0.1   2.1e-24   9.4e-21       1      89 []     122     207 ..     122     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.6e-25
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                                       + ++v  ++ ++++al+++d+e arevi++d+ i++l  +ie++++++la +qp+a+dlr +++ l+i  dlERigD
  gi|386002810|ref|YP_005921109.1|  22 LVDLVGFAVAKSVDALRDYDVEKAREVIRDDQTINDLNLRIEKRCMQLLALQQPMAKDLRLIVTTLKIGIDLERIGD 98 
                                       678888999******************************************************************** PP

                                       HHHHHHHHH CS
                              PhoU  81 havniaerv 89 
                                        av+ia++v
  gi|386002810|ref|YP_005921109.1|  99 LAVDIARIV 107
                                       ******986 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 2.1e-24
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       + rmaei+ eml +a +a++e+d +lare  + d e+d+l++++++ ll++++ + +l   +++++ ll + ++lER
  gi|386002810|ref|YP_005921109.1| 122 IPRMAEIAVEMLAQANRAFKENDSNLARETTKWDYEVDALYQKVRDTLLKIIGGNPEL---IEDATPLLLVNKHLER 195
                                       579*************************************************866666...778999********** PP

                                       HHHHHHHHHHHH CS
                              PhoU  78 igDhavniaerv 89 
                                       i+Dh++ni+e++
  gi|386002810|ref|YP_005921109.1| 196 IADHVCNICESI 207
                                       *********975 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.2   1.1e-06    0.0051      17      72 ..       7      70 ..       5      80 .. 0.88
   2 ?   -1.5   0.1      0.75   3.4e+03      48      61 ..     131     144 ..     109     166 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                              TBCA 17 sYekEleeqearleklka..........dgdedeydlkkqeevleetkamipdlkkrlekavekLe 72
                                       Y+kElee +a  ekl +          d    +yd++k++ev+ + +  i dl+ r+ek + +L 
  gi|386002810|ref|YP_005921109.1|  7 RYHKELEELKADAEKLVDlvgfavaksvDAL-RDYDVEKAREVIRDDQ-TINDLNLRIEKRCMQLL 70
                                      5***********************9877664.4************975.69********9998885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
                              TBCA  48 evleetkamipdlk 61 
                                       e+l ++++ +++ +
  gi|386002810|ref|YP_005921109.1| 131 EMLAQANRAFKEND 144
                                       33333333333333 PP

>> Cdh1_DBD_1  Chromodomain helicase DNA-binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.098   4.4e+02      38      84 ..       6      53 ..       3      76 .. 0.64
   2 ?   11.6   0.2   5.7e-05      0.26      34      82 ..     119     167 ..      93     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.098
                        Cdh1_DBD_1 38 elleelyeelleeakklvkeeeekrakeleelea.daeeykeklkkge 84
                                      e++++  eel + a+klv+    + ak++++l   d+e+ +e ++  +
  gi|386002810|ref|YP_005921109.1|  6 ERYHKELEELKADAEKLVDLVGFAVAKSVDALRDyDVEKAREVIRDDQ 53
                                      566677777777777777777777777777765325555555555544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.7e-05
                        Cdh1_DBD_1  34 eknielleelyeelleeakklvkeeeekrakeleeleadaeeykeklkk 82 
                                        kni ++ e+  e+l++a++ +ke++++ a+e  + + ++++  +k++ 
  gi|386002810|ref|YP_005921109.1| 119 LKNIPRMAEIAVEMLAQANRAFKENDSNLARETTKWDYEVDALYQKVRD 167
                                       49999***************************99999999887777765 PP

>> DUF5394  Family of unknown function (DUF5394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.6   5.4e-05      0.24      25     133 ..      32     155 ..       9     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.4e-05
                           DUF5394  25 tssdnL.syevkeiyeklkkNeefeaE.....................lealistlelnlDvsklqtklillikklL 79 
                                        s d L  y+v+++ e +++ + ++                       l  +++tl++ +D++++    + + + ++
  gi|386002810|ref|YP_005921109.1|  32 KSVDALrDYDVEKAREVIRDDQTINDLnlriekrcmqllalqqpmakdLRLIVTTLKIGIDLERIGDLAVDIARIVV 108
                                       555666556666666666555544443455555566666666666666*****************999999888877 PP

                           DUF5394  80 kskksskkkieltkeleqqitkqiakiskeliykhtrtlaeenkdLekekdkle 133
                                       +sk++ + k    k++ +     +a+i+ e++ +  r  +e++ +L++e  k +
  gi|386002810|ref|YP_005921109.1| 109 HSKNKVHVKSL--KNIPR-----MAEIAVEMLAQANRAFKENDSNLARETTKWD 155
                                       77766666655..55555.....5***********************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1386.43
//
Query:       gi|386002811|ref|YP_005921110.1|  [L=333]
Description: Phosphate regulatory protein-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-24   85.8  10.4    1.2e-19   70.6   3.8    2.5  2  PhoU            PhoU domain
      5e-06   26.3   0.1      7e-05   22.6   0.0    2.5  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.068   13.2   0.2    1.7  1  RTX_C           RTX C-terminal domain
      0.035   14.7   0.2       0.79   10.3   0.0    2.8  3  FliL            Flagellar basal body-associated protein FliL


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   3.8   2.6e-23   1.2e-19       1      88 [.     136     225 ..     136     226 .. 0.89
   2 !   19.0   0.5   3.3e-07    0.0015      10      88 ..     250     319 ..     241     320 .. 0.66

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.6e-23
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH...HHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae...dlrellsllriard 74 
                                       lrr++ +v++m++dal+a +++d+e+a +v++rdd++drl+ +++r+  e+l    +l e   d  +++++ r+a++
  gi|386002811|ref|YP_005921110.1| 136 LRRIKTVVRSMIQDALTAMVTNDREMAADVVQRDDDVDRLYLLVSRQFTEILRS-GSLKEesiDPITAFNYTRAATN 211
                                       7899*******************************************7777754.444444678888899******* PP

                                       HHHHHHHHHHHHHH CS
                              PhoU  75 lERigDhavniaer 88 
                                       lER++Dha +ia+ 
  gi|386002811|ref|YP_005921110.1| 212 LERMADHASRIADM 225
                                       ************85 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  10 emlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavnia 86 
                                       + ++d++++l   +   a+evie+ +++ r         + +++  ++ +e  ++l  l+++a+++ERi D+++ni 
  gi|386002811|ref|YP_005921110.1| 250 SLIEDSISSLLLLNSGKANEVIELSRQLRRE-------MILMVSSASSSGEHEDAL--LRMVASSIERILDYIKNIG 317
                                       5667777777777778888887666665555.......333333333333322233..6679**************9 PP

                                       HH CS
                              PhoU  87 er 88 
                                       e 
  gi|386002811|ref|YP_005921110.1| 318 EL 319
                                       86 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.6e-08     7e-05       2      45 ..       9      53 ..       8      54 .. 0.94
   2 ?    0.7   0.0      0.12   5.3e+02      10      19 ..     232     241 ..     232     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-08
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHHSX CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplkslp 45
                                      ++ ++ +v++Pk ++ +++i++G+ + +++ ++  ++l+p +s++
  gi|386002811|ref|YP_005921110.1|  9 TGKSTFIVSLPKLWAVKNDIQPGSLIYITQSDNgALVLSPDRSER 53
                                      78899***********************************99986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                                       EE-CCCHHHC CS
                    MazE_antitoxin  10 riPkevrfel 19 
                                       ++P+ev++ +
  gi|386002811|ref|YP_005921110.1| 232 TLPAEVAEGM 241
                                       8******976 PP

>> RTX_C  RTX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.5e-05     0.068      82     145 ..     237     299 ..     232     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                             RTX_C  82 iakgngkisaeelskvinnknkleeklsssesynllkqkknlsndieklisstsaftssskals 145
                                       +a+g g+is++ ls +i++   +  +l s+++ ++++ +++l++++  ++ss s+ +  ++al 
  gi|386002811|ref|YP_005921110.1| 237 VAEGMGRISPQLLS-LIEDSISSLLLLNSGKANEVIELSRQLRREMILMVSSASSSGEHEDALL 299
                                       6899******9887.7888677778899**************************9988877764 PP

>> FliL  Flagellar basal body-associated protein FliL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00018      0.79      41     101 ..      64     125 ..      43     126 .. 0.83
   2 ?   -0.7   0.0      0.47   2.1e+03      58      84 ..     127     153 ..     125     177 .. 0.66
   3 ?    0.5   0.0      0.21   9.4e+02      18      75 ..     218     282 ..     206     303 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                              FliL  41 k..epeirdailsllssktaeelstpegkekLkeelleelnkvleegklekgpvedVlFtsfv 101
                                       k  +p ird i  ++s+ +  e++++      k ++ + ++k++++ +  ++ v++Vl+++++
  gi|386002811|ref|YP_005921110.1|  64 KvgDPLIRDIIGCYVSGYRTIEVTGAHMTADQKRDIHQIVQKLIGP-EILEETVNKVLIQDLI 125
                                       1558***********************9999**********98866.46899*******9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                              FliL  58 aeelstpegkekLkeelleelnkvlee 84 
                                       +eel+++    ++k  +++ ++ +l+ 
  gi|386002811|ref|YP_005921110.1| 127 PEELQSERALRRIKTVVRSMIQDALTA 153
                                       677888888878877777777776633 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.21
                              FliL  18 ggerylkveitlev.adaeleekekepeirdailsllssktaeelstpegk........ekLkeell 75 
                                       ++ r++ + +++     ae++e   + +i  ++lsl+ +  ++ l  ++gk         +L+ e++
  gi|386002811|ref|YP_005921110.1| 218 HASRIADMILQCDCtLPAEVAEG--MGRISPQLLSLIEDSISSLLLLNSGKanevielsRQLRREMI 282
                                       44455555444444312233333..444444444444444333333333332222111134444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1934.53
//
Query:       gi|386002812|ref|YP_005921111.1|  [L=241]
Description: Endonuclease V [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-54  183.3   0.0    4.8e-54  183.0   0.0    1.0  1  Endonuclease_5  Endonuclease V


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.0   0.0   2.7e-58   4.8e-54       2     197 .]      21     214 ..      20     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.0 bits;  conditional E-value: 2.7e-58
                                       HHHCC-------SGG-SEEEEEEEEEEECTCEEE..EEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHH CS
                    Endonuclease_5   2 elakkveledklkeklklvaGvDvsfvkeekkea..vaalvvldlpslevvekavavvklsfpYipgfLaFRElpvl 76 
                                       e+a+ v+le++++e+  +++GvD +f++ e+ ++  v+ +v +d +s++ + +++a  +++fpY+pg+L+FRE p++
  gi|386002812|ref|YP_005921111.1|  21 EIASLVVLENRFSEE--VIGGVDQAFISGEDGREmvVSGAVAFD-SSFRPLSRSWALLETTFPYLPGLLSFREGPAA 94 
                                       677889999999996..*************99999888889998.79****************************** PP

                                       HHHHCC-SS--SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEE CS
                    Endonuclease_5  77 lkaleklkqkpdvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaal 153
                                       ++a+++l++kp +l+vDG Gi Hprr+G+As +Gv+ldlpt+Gv+K++l+g+++ p +++g+++pl ++g v+g++l
  gi|386002812|ref|YP_005921111.1|  95 VEAVKRLEAKPTLLFVDGCGINHPRRAGMASAIGVALDLPTVGVTKRVLCGSFDPP-RREGEASPLHHRGLVVGHVL 170
                                       ***************************************************99855.78899*************** PP

                                       ESSTTS--EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHHH CS
                    Endonuclease_5 154 rtkknvkpiyvSvGhrisletalelvlallkkyrlPepirqAdl 197
                                        +kk+++pi v++Ghri+ e+al+l++++l++ +lP p  +A++
  gi|386002812|ref|YP_005921111.1| 171 LSKKECRPIVVAPGHRITPESALDLARRYLRGEKLPLPSLAAHR 214
                                       ****************************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1798.26
//
Query:       gi|386002813|ref|YP_005921112.1|  [L=163]
Description: Methylated-DNA/protein-cysteinemethyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-27   93.6   0.0    8.5e-27   93.1   0.0    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
      0.005   16.3   0.0     0.0086   15.6   0.0    1.3  1  Sigma70_r4     Sigma-70, region 4


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   9.5e-31   8.5e-27       1      80 [.      74     152 ..      74     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 9.5e-31
                                       HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHH CS
                     DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLe 77 
                                       +fq++V+ ++ +I +G+++tYge+A++lg+p+aaraVg+al++np+++++PcHRVvg++  lggy+ g++ kr++Le
  gi|386002813|ref|YP_005921112.1|  74 PFQREVLLATMAIRPGETATYGEVAERLGRPGAARAVGGALRRNPIPVIIPCHRVVGSRD-LGGYNPGVDLKRRILE 149
                                       69********************************************************99.**************** PP

                                       HTT CS
                     DNA_binding_1  78 aEg 80 
                                        E+
  gi|386002813|ref|YP_005921112.1| 150 VER 152
                                       995 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.5e-07    0.0086       2      33 ..      69     104 ..      69     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-07
                                       HHHS-HHHHHHHHHHH....TTT--HHHHHHHHTS- CS
                        Sigma70_r4   2 LasLpererevlelrf....geglTleEIgerlgiS 33 
                                       L+ L++ +revl        ge  T+ E++erlg +
  gi|386002813|ref|YP_005921112.1|  69 LSGLTPFQREVLLATMairpGETATYGEVAERLGRP 104
                                       789******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1079.68
//
Query:       gi|386002814|ref|YP_005921113.1|  [L=175]
Description: Phosphodiesterase, MJ0936 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-23   82.1   0.0    5.6e-23   81.9   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.4e-06   26.4   2.3    0.00058   20.4   0.1    2.2  2  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   6.2e-27   5.6e-23       6     164 ..       1     150 [.       1     151 [. 0.86

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 6.2e-27
                     Metallophos_2   6 iSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnD.eev.veedvlreaaelgt 79 
                                       +SD+H+n+  l +++e++++ gv++i+haGD+  ++p ++++++  a +++ V+GNnD ++  +++d++r    + +
  gi|386002814|ref|YP_005921113.1|   1 MSDSHDNFPGLLEAVEIFRRRGVEMILHAGDV--VAPGMCYAFEGWAgKLKLVYGNNDgDRTgLKRDFGRVGGVFLE 75 
                                       6*******************************..***9999999988***********4333566666666666655 PP

                     Metallophos_2  80 dlpeeaelelagekvlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe 155
                                       d+    e+e++g++++l+Hg+   ++  ++ l+++   g++ vvv GH H  +v    ++l++nPG+v +  +g++ 
  gi|386002814|ref|YP_005921113.1|  76 DF---GEVEADGRRIALLHGT---YEPLVTGLVES---GAFdVVVRGHDHHLRVVPG-KTLMINPGEVWGHFTGRK- 141
                                       55...99999**********9...88888888877...5555*********999765.9************88887. PP

                     Metallophos_2 156 tyaildtde 164
                                       t+aildt++
  gi|386002814|ref|YP_005921113.1| 142 TVAILDTES 150
                                       ******986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   6.4e-08   0.00058       6      75 ..       1      56 [.       1      97 [. 0.73
   2 !    6.2   0.6    0.0015        13     182     203 ..      96     117 ..      72     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.4e-08
                                      EESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS...HHHHHHHHHHHHHHHHTSEEEEEC-TTS CS
                       Metallophos  6 igDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg...dlekellellaalvkypipvylllGNHe 75
                                      ++D H      +++ ll++++ ++r+ ++ ++l+aGD+v  g    +e      +a ++k      l+ GN +
  gi|386002814|ref|YP_005921113.1|  1 MSDSH-----DNFPGLLEAVEIFRRR-GVEMILHAGDVVAPGmcyAFEG-----WAGKLK------LVYGNND 56
                                      59***.....*************999.**************95554333.....233333......4555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 182 ealedllkkygvdlvisGHtHv 203
                                       + +  l + +  d+v++GH+H+
  gi|386002814|ref|YP_005921113.1|  96 PLVTGLVESGAFDVVVRGHDHH 117
                                       455577888889*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1155.70
//
Query:       gi|386002815|ref|YP_005921114.1|  [L=138]
Description: hypothetical protein Mhar_2138 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   15.3   5.4        1.3    9.3   0.2    2.6  3  ABC_tran_CTD  ABC transporter C-terminal domain
       0.09   13.1   3.1       0.65   10.4   0.2    2.4  2  CLZ           C-terminal leucine zipper domain of cyclic nucl
       0.11   13.1   0.0       0.18   12.3   0.0    1.4  1  DUF1474       Protein of unknown function (DUF1474)
       0.12   12.9   1.8       0.31   11.5   1.2    2.0  2  ZapB          Cell division protein ZapB
       0.25   11.8   2.6       0.76   10.2   0.3    2.1  2  DUF4140       N-terminal domain of unknown function (DUF4140)


Domain annotation for each model (and alignments):
>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.8   6.5e+03      42      54 ..      11      23 ..       6      26 .. 0.63
   2 ?    8.0   0.4   0.00096       3.4      14      48 ..      62      96 ..      54     104 .. 0.85
   3 ?    9.3   0.2   0.00036       1.3      11      32 ..     110     131 ..     100     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                      ABC_tran_CTD 42 klaelsaeleele 54
                                      kl+++++ +e le
  gi|386002815|ref|YP_005921114.1| 11 KLQQITKPYEPLE 23
                                      5666666665554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00096
                      ABC_tran_CTD 14 eaeIeaLEeeiaeleaeladpelysdpeklaelsa 48
                                      e+ Ie+ E+ +++le   a+   +s +e  +el +
  gi|386002815|ref|YP_005921114.1| 62 EELIERYEALKEQLEGLSAAHPWFSEDESTQELIR 96
                                      78899999999999999999999999999999865 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00036
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaela 32 
                                       e+ e++I aL  +i+ele++l 
  gi|386002815|ref|YP_005921114.1| 110 EKFEEKIGALRRRIEELEDKLG 131
                                       7899999999999999999986 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.04   1.4e+02      15      44 ..      50      79 ..      45      96 .. 0.79
   2 ?   10.4   0.2   0.00018      0.65      15      47 ..      98     130 ..      94     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.04
                               CLZ 15 LDeeaakagaeqkeleekverLessLeaLq 44
                                      LD   +++++  +el e+ e L+++Le L 
  gi|386002815|ref|YP_005921114.1| 50 LDLLQENRESPGEELIERYEALKEQLEGLS 79
                                      566666778888999999999999999886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                               CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrl 47 
                                       L+  +a ++a+++++eek+  L  ++e L+++l
  gi|386002815|ref|YP_005921114.1|  98 LEVFTARRSADREKFEEKIGALRRRIEELEDKL 130
                                       5555677889*******************9998 PP

>> DUF1474  Protein of unknown function (DUF1474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05      0.18       7      42 ..      63      98 ..      59     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                           DUF1474  7 slieeveiikekledvvstfswfidevfttdsgrlk 42
                                       lie  e +ke+le   +++ wf ++  t++  rl+
  gi|386002815|ref|YP_005921114.1| 63 ELIERYEALKEQLEGLSAAHPWFSEDESTQELIRLL 98
                                      599***********************9999865554 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.2   8.5e-05      0.31      14      71 .]      62     125 ..      44     125 .. 0.87
   2 ?    3.9   0.1      0.02        71      18      33 ..     114     129 ..     110     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                              ZapB  14 qkaidtitlLqmeieeLkeen......eelkeenreleeeneqlkeereawqerlkkLLgklee 71 
                                       +++i+++++L++++e L + +      e+ +e +r le    +  ++re+++e++ +L +++ee
  gi|386002815|ref|YP_005921114.1|  62 EELIERYEALKEQLEGLSAAHpwfsedESTQELIRLLEVFTARRSADREKFEEKIGALRRRIEE 125
                                       578999999999999999988888887888888899999999999**********999888776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                              ZapB  18 dtitlLqmeieeLkee 33 
                                       ++i +L+ +ieeL+ +
  gi|386002815|ref|YP_005921114.1| 114 EKIGALRRRIEELEDK 129
                                       6888999999999876 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.089   3.2e+02      59      78 ..      56      79 ..      50      94 .. 0.61
   2 ?   10.2   0.3   0.00021      0.76      55      82 ..     104     131 ..      90     138 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.089
                           DUF4140 59 nreaeee....elkalraeleele 78
                                      nre++ e    +++al+++le l 
  gi|386002815|ref|YP_005921114.1| 56 NRESPGEelieRYEALKEQLEGLS 79
                                      344444334423566666655554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00021
                           DUF4140  55 ervpnreaeeeelkalraeleeledela 82 
                                       +r++ re++ee++ alr+++eeled+l 
  gi|386002815|ref|YP_005921114.1| 104 RRSADREKFEEKIGALRRRIEELEDKLG 131
                                       567888999999************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1068.74
//
Query:       gi|386002816|ref|YP_005921115.1|  [L=132]
Description: hypothetical protein Mhar_2139 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0063   17.1   0.0      0.016   15.8   0.0    1.7  1  DUF4430   Domain of unknown function (DUF4430)


Domain annotation for each model (and alignments):
>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     9e-07     0.016       1      72 [.      24     101 ..      24     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9e-07
                           DUF4430   1 Gttvfdvleaaakkkedkteaqsge..hyitsIngleqdtakk.syWmye.vNG..epsdvGagsyklkdgdkivfr 71 
                                       G+tv+d+l a a++  ++ e+  g    ++t+I+g+++d   +  +  +e ++    ++ ++a+ ++ +dg++i +r
  gi|386002816|ref|YP_005921115.1|  24 GATVLDALRASAEVVLATDEGACGHrgSMVTAIDGVARDIDRGwIFYIFErGDSgwRIPREMADGVEASDGMRIGWR 100
                                       89********999999999886666789********65554444333333333222346669999999999999998 PP

                           DUF4430  72 y 72 
                                       +
  gi|386002816|ref|YP_005921115.1| 101 L 101
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 978.99
//
Query:       gi|386002817|ref|YP_005921116.1|  [L=599]
Description: Arginine decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-40  139.2   0.0      2e-40  138.7   0.0    1.3  1  Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal b
    9.9e-20   70.6   0.9    9.9e-20   70.6   0.9    1.7  2  Arg_decarb_HB  Arginine decarboxylase helical bundle domain
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.22   10.9   0.0    1.3  1  DUF2181        Uncharacterized conserved protein (DUF2181)


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.0   3.4e-44     2e-40       3     247 .]      74     339 ..      72     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 3.4e-44
                                       HHHHHHHHHHHHCT...CCEEEEEGGG---HHHHHHHHHTT....EEEEESSHHHHHHHHHCTTTGGGEEEEESS-- CS
                     Orn_Arg_deC_N   3 sierklkrwkkalp...rikvfYavKansdlavlellaelG....lgldcaSkaElelvlaagvsperiifanpckq 72 
                                       +i+ ++ +  ++l+    +++++++K+n+ ++v+e + + G    +gl+++ kaEl ++l++g  p+  i++n++k+
  gi|386002817|ref|YP_005921116.1|  74 EINGAFLASMEELEyrgGYRLVFPMKVNQRKEVVEYIVNGGrdlkVGLEVGTKAELLAALSLGLGPDALIICNGYKD 150
                                       56666666666666666899*********************9999******************************** PP

                                       HHHHHHHHHCTHT...EEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHC...HH CS
                     Orn_Arg_deC_N  73 reelryalekgvk...vvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaale...ea 139
                                       r++lr al+ g +   v+++d +ee+  l + ++e    + + lR k+ +s ++ ++  +gge sKFG +++   e+
  gi|386002817|ref|YP_005921116.1| 151 RDYLRLALKFGETnkiVIVIDIFEEIFDLLRCSKElsakPILGLRTKL-FSRGSGRWEESGGELSKFGLSTAeilES 226
                                       *******98766555699*************999999878899****9.*******************998878999 PP

                                       HHHHHHHHHHTTEEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSST... CS
                     Orn_Arg_deC_N 140 vealleaakeenlqlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplk... 213
                                       +e l+e    + l++  ++fH+GS+++d+++++ a+++a++++ +++++  +++ ++vGGG++v+y + + p++   
  gi|386002817|ref|YP_005921116.1| 227 MEILKENGMIDRLKM--LHFHIGSQITDIRKIKVAMNEAARIYAKVRKVA-EVEYFNVGGGLSVDYDGSQTPTPasa 300
                                       9**************..****************************99985.89**************9999998999 PP

                                       ...HHHHHHHHHHHHHHHHH..TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 214 ...leeiaekirealeeafp..gdkevtiiaEpGRalva 247
                                          l+e+ +++   l++ +   + + +ti++E+GRa++a
  gi|386002817|ref|YP_005921116.1| 301 nytLQEYSNDVVYTLQRTCDeeEVPCPTIVSESGRAIAA 339
                                       999****************9888999**********987 PP

>> Arg_decarb_HB  Arginine decarboxylase helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.8   1.6e+04      22      35 ..     303     316 ..     300     318 .. 0.82
   2 !   70.6   0.9   1.7e-23   9.9e-20       1      83 [.     363     444 ..     363     445 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                     Arg_decarb_HB  22 nlqEiyhDavhyld 35 
                                        lqE+ +D+v+ l+
  gi|386002817|ref|YP_005921116.1| 303 TLQEYSNDVVYTLQ 316
                                       58999999999887 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 1.7e-23
                     Arg_decarb_HB   1 sedapellqnLwelleelsqrnlqEiyhDavhyldearelFrlGllsLeerAkaEqlylaicrkirkllkeeerapr 77 
                                       +ed+p  ++++++ le+++ +n+ E yhDa+hy++e+ ++F+lG + Leer+k++ l++++c+k ++ ++++e+  +
  gi|386002817|ref|YP_005921116.1| 363 EEDDPVQIEDMRQALENMDLENYAEFYHDALHYREELFNAFNLGNIGLEERSKGDLLFWKVCQKAASFAEADENDSE 439
                                       589*************************************************************************9 PP

                     Arg_decarb_HB  78 eildeL 83 
                                       e +++L
  gi|386002817|ref|YP_005921116.1| 440 E-FESL 444
                                       9.9888 PP

>> DUF2181  Uncharacterized conserved protein (DUF2181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.7e-05      0.22     154     230 ..     303     383 ..     286     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                           DUF2181 154 anegYteemveemlelvke..lkqe..vtFpvravlaansleqlkwLleqserytLtiwsskedavdvedllklrke 226
                                       + + Y+++ v +++++++e  ++++  v+ + ra  a +s+  ++ + ++ ++  L + ++++d+v++ed+++  ++
  gi|386002817|ref|YP_005921116.1| 303 TLQEYSNDVVYTLQRTCDEeeVPCPtiVSESGRAIAAYHSFLAFRVIGKKNSKDGLEVVAEEDDPVQIEDMRQALEN 379
                                       4567**************989666677***********************************************999 PP

                           DUF2181 227 lgks 230
                                       ++ +
  gi|386002817|ref|YP_005921116.1| 380 MDLE 383
                                       9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4016.43
//
Query:       gi|386002818|ref|YP_005921117.1|  [L=345]
Description: deoxyhypusine synthase [Methanosaeta harundinacea 6Ac]
Scores for 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-92  307.3   0.0    1.1e-91  307.1   0.0    1.0  1  DS        Deoxyhypusine synthase
  ------ inclusion threshold ------
       0.17   11.1   0.0       0.34   10.1   0.0    1.5  1  PRTase_1  Phosphoribosyl transferase (PRTase)


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.1   0.0   1.2e-95   1.1e-91       2     287 ..      30     318 ..      29     319 .. 0.97

  Alignments for each domain:
  == domain 1  score: 307.1 bits;  conditional E-value: 1.2e-95
                                DS   2 llesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikal 78 
                                       l  +++k gfqa +lg++++ +++m ++e++tif+gl+++++++Glr++ia+++ +++vd++v+T++++ +Dl++ l
  gi|386002818|ref|YP_005921117.1|  30 LAMAMAKLGFQAGQLGRSVEAWERMLAEEEITIFFGLAGAMVPAGLRKLIATMISRRMVDCVVSTGANLFHDLCEGL 106
                                       7789************************************************************************* PP

                                DS  79 gkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSilyw 155
                                       g  +y gd  +dd++Lre+gi+Ri++++v++  +++ + +v+e++++l+++ ++ +++el++ lG+++  e+ il +
  gi|386002818|ref|YP_005921117.1| 107 GVVHYRGDPGADDASLREEGIDRIYDVYVSEAGLQRGDLYVAEFVKTLDPR-RTYTSRELMEGLGRRM-PEDTILGS 181
                                       *************************************************95.678*************.69****** PP

                                DS 156 AykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlm.. 230
                                       A ++++p+f+pal+D+s+G++++l+   +e +++++d ++D++e+++i+ k+++tg++++GGGvpK++i++++++  
  gi|386002818|ref|YP_005921117.1| 182 ASRAGVPIFVPALSDSSIGIGMVLAW--REGHRVVVDQIQDVDEISQITEKSTQTGVVFVGGGVPKNFIQQTKVVad 256
                                       ********************999999..79999****************************************988* PP

                                DS 231 .....rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                            r g++ya+++t + ++ G+lsg+t++E+vSwgki +ea+ ++v+ DaTi+lP+ v+a
  gi|386002818|ref|YP_005921117.1| 257 lcgryRGGHNYAIQYTIDPPQFGGLSGCTFSEGVSWGKIAREARMIQVFVDATIALPIAVHA 318
                                       ***9988***************************************************9986 PP

>> PRTase_1  Phosphoribosyl transferase (PRTase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.8e-05      0.34      70     158 ..     161     250 ..     137     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.8e-05
                          PRTase_1  70 avavlaeailaekgkeivlvSLaRAGtpiGvllkralkeklg.levpHysiSiirdrGiDenAleyilarheeasiv 145
                                       + ++l e + +++ ++++l S  RAG+pi v      +  +g + +   +  ++ d+  D   +++i+++++++ +v
  gi|386002818|ref|YP_005921117.1| 161 TSRELMEGLGRRMPEDTILGSASRAGVPIFVPALSDSSIGIGmVLAWREGHRVVVDQIQDVDEISQITEKSTQTGVV 237
                                       455677888899999*************99855554444455234445678899999999999************** PP

                          PRTase_1 146 FvDgWtgKGaitr 158
                                       Fv g + K  i++
  gi|386002818|ref|YP_005921117.1| 238 FVGGGVPKNFIQQ 250
                                       ****999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2195.53
//
Query:       gi|386002819|ref|YP_005921118.1|  [L=175]
Description: Lipoprotein, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1315.06
//
Query:       gi|386002820|ref|YP_005921119.1|  [L=448]
Description: N-6 DNA methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-12   48.6   4.5    5.6e-07   29.9   0.1    2.4  2  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
      0.075   13.2   0.0       0.21   11.8   0.0    1.7  1  LigT_PEase   LigT like Phosphoesterase


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   6.2e-11   5.6e-07       3     132 ..      40     182 ..      38     185 .. 0.80
   2 !   19.5   1.1   9.8e-08   0.00088       3     109 ..     265     380 ..     263     416 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.2e-11
                                       T-EEEEHHHHEEEEE-----TT.GGTTT--EEEE-HH.HCCT........EE-HHHHCCTT---B-TT-EEEE-SSS CS
                       Methylase_S   3 dwevvkLgdvfeikkgktpkkk.elkengkypyirag.ilnn........kvvkdglgykkkyilpkgdilissrat 69 
                                       d+ev+kL  ++++kkg   ++  e+k+ g+ p+ir++ i++           + d  +   k  +  gdi+is+++t
  gi|386002820|ref|YP_005921119.1|  40 DYEVRKLAAFGNLKKGIFSISAsEYKDAGV-PFIRVScIKYLtidinditYLSADLHDSNIKTEVSPGDIVISKSGT 115
                                       89***********77766666625555555.****************94444444445555555569********** PP

                                       TT-EEEESS...-BEE-TTEEEEEESTTT--HHHHHHHHHHCHH..HHHHHCCSSTTT---HHHHCC- CS
                       Methylase_S  70 iGkvayrdk...kyylnqsvivlipknkkkineflylylllklk..klkslsvgstqpkltkenlkki 132
                                       +G++a+ ++   k + +q++  l +++ k+ + fl+ yl+ kl   ++++++ + t+++lt++ l+++
  gi|386002820|ref|YP_005921119.1| 116 VGNIALVPEylgKSNISQDIVGLYVND-KNFSGFLAAYLSSKLGkiQMQRVKTQQTHAHLTLAPLREL 182
                                       *********88888***********53.44489******97766568888899999999999988875 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.8e-08
                                       T-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HHHCCT.........EE-HHHHCCTT---B-TT-EEEE-SSST CS
                       Methylase_S   3 dwevvkLgdvfeikkgktpkkkelkengkypyiragilnn.........kvvkdglgykkkyilpkgdilissrati 70 
                                        +e+ +L  +++i kgk   +k++ + g  p+ir+++l n         k++k++ + +k+ +   +dil++ +++i
  gi|386002820|ref|YP_005921119.1| 265 RFETTNLWKIAKIIKGKEVGSKNYSDHGI-PFIRTSDLVNhgidrdshhKINKKIYDEYKQDLR-PNDILFTNDGKI 339
                                       567778888999*9999999977777776.******66666*****999555555555444333.49********** PP

                                       T-EEEESS..-BEE-TTEEEEEESTTT--HHHHHHHHHHCH CS
                       Methylase_S  71 Gkvayrdk..kyylnqsvivlipknkkkineflylylllkl 109
                                       G  a+  +  +++ ++++++++  ++  + ef++ +l +k 
  gi|386002820|ref|YP_005921119.1| 340 GLSAMCLEgdDCVIQSHIKRIRIVDDYFTPEFIFIFLNTKF 380
                                       *9888666558************996666799999998765 PP

>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05      0.21      19      69 ..     154     206 ..     149     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                                       HHHHCCTTEEET..SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEE CS
                        LigT_PEase  19 eralaklglkpv..rpfnpHiTLaflgevdeekvpellealaeiasgaepfel 69 
                                        ++l+k + + v  +  + H+TLa l+e      +e +++++++ ++a++fe+
  gi|386002820|ref|YP_005921119.1| 154 SSKLGKIQMQRVktQQTHAHLTLAPLRELLVVFNKECVNKVSDLMEKAAKFEV 206
                                       555555555555578899************99999999999999777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3168.03
//
Query:       gi|386002821|ref|YP_005921120.1|  [L=613]
Description: Putative N-6 DNA methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-39  133.8   0.0    1.5e-38  132.9   0.0    1.4  1  N6_Mtase         N-6 DNA Methylase
    9.7e-16   57.7   0.0    2.7e-15   56.3   0.0    1.8  1  HSDR_N_2         Type I restriction enzyme R protein N termin
    5.6e-08   32.7   0.0    3.4e-07   30.2   0.0    2.0  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.044   13.6   0.0       0.41   10.4   0.0    2.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.0   3.3e-42   1.5e-38       2     263 ..     288     587 ..     287     594 .. 0.86

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 3.3e-42
                          N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee....... 71 
                                       ++d+lGd++E +++         +G+ffTPr+v+k++v++l+p +ge v+DpacGsgg+l+ a +++ ++       
  gi|386002821|ref|YP_005921120.1| 288 ERDALGDAFEVFIGPA---LRGGEGQFFTPRNVVKMVVRILDPDPGEYVIDPACGSGGFLIVALEYVWDKieeegkr 361
                                       68***********976...44555*******************************************999999**** PP

                          N6_Mtase  72 ...........dgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe........kdkkfdvv 129
                                                  +++++++ ++G +k++  ++++k  +++ g      ++  +++l +p           +  +fdv 
  gi|386002821|ref|YP_005921120.1| 362 knwsqelivqkKKDISNKYFFGIDKDSFLAKVTKAYMAIIGDGRG--GVFCENSLFSPLDWqnktqdriNFGSFDVL 436
                                       *********9999999999*******************9886555..799*****999765568888888889**** PP

                          N6_Mtase 130 vaNppfnqkew...............kektlekderfrea..vapksnadlafllhiieslkpkGraavvlangvLf 189
                                       ++Nppf++k                 k + ++++++++ +  +a+++  ++ f+  ++e lkp+Gr+++vl++ +  
  gi|386002821|ref|YP_005921120.1| 437 LTNPPFGSK-IsitskevlsqyslsyKWRFNKNEQKWERTqkFADRRPPQILFIERCLELLKPGGRIGIVLPDSIV- 511
                                       ********9.548888888888887656666777788877889999999***********************9875. PP

                          N6_Mtase 190 rggkegkIrkalvekdlveavialpeklFyn.tsiptcilvlkkekae..rkgkvlfidaseefkkkdrkknkltee 263
                                        +  +g Ir+ ++   ++ av+ lp++ F++ ts +t++++l+k+ +   ++ k+++  a++  +   r+k +++++
  gi|386002821|ref|YP_005921120.1| 512 GNQSDGYIREFILSRANLLAVVDLPNETFQPsTSTKTSVVFLQKKDQVmeTDYKIFMAFAEKCGHDR-RAKPIFKKD 587
                                       667899************************88**********9988665445556555555444444.666666655 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0     6e-19   2.7e-15       7     110 .]      44     156 ..      37     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6e-19
                          HSDR_N_2   7 qklikyLveelgypkeliavekelqlg.....skkkraDivvykkd....kkpllivecKapsvkiseevleqlksY 74 
                                       q+++k+Lve++gy k++i+   + + +     ++k  +Di+v+ +d    ++++++vecK+p+ +    +l+ql+ Y
  gi|386002821|ref|YP_005921120.1|  44 QVFAKKLVEDYGYRKHQIQTHPQFRTKtapsgEEKYPVDIAVFYNDkkeyNNMRIVVECKQPNRSD---GLKQLSIY 117
                                       99******************999998888885555559****9888666667**********9855...89****** PP

                          HSDR_N_2  75 leal.kaeylvvtNglehivykvdkkkk..kfeelkdiP 110
                                       l+ + ++e +v+ Ng++h ++++  +++  +++e++diP
  gi|386002821|ref|YP_005921120.1| 118 LNLIpSVEIGVWFNGKDHLYLRKAFDDGriTWKEIPDIP 156
                                       **988*****************9988885679******9 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   7.5e-11   3.4e-07      21     136 ..     322     447 ..     316     463 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 7.5e-11
                                       HHHTT--TTS-EEETT-TTSHHHHHHH.HHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHH CS
                           UPF0020  21 vrlagwkpgepllDPmCGsGtilIEaa.llganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNa 96 
                                       vr+ + +pge  +DP CGsG++lI a   ++ +i     r+++++ +   +++   +  ++g+D+d+ + + ++   
  gi|386002821|ref|YP_005921120.1| 322 VRILDPDPGEYVIDPACGSGGFLIVALeYVWDKIEEEGKRKNWSQELIVQKKKDISNKYFFGIDKDSFLAKVTKAYM 398
                                       7888999*****************98625677777777788888755555544445566*******98877666554 PP

                                       HHTT-G.GGEEEEE--GGG--........STTS---EEEE--------- CS
                           UPF0020  97 ekagvg.dliefsqadaakLr........lkegevdvivtnpPYGerlg 136
                                          g g + +  ++  +  L          + g++dv++tnpP+G +++
  gi|386002821|ref|YP_005921120.1| 399 AIIGDGrGGVFCENSLFSPLDwqnktqdrINFGSFDVLLTNPPFGSKIS 447
                                       444432123333333333333333224455678************9876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   9.2e-05      0.41       2     113 ..     328     508 ..     327     548 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.2e-05
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelae.................elgpkae............vvGiDiseeaielAre... 46 
                                       d g +v+D++CG+G +++++ e                 e                  ++GiD + +  ++ ++   
  gi|386002821|ref|YP_005921120.1| 328 DPGEYVIDPACGSGGFLIVALEyvwdkieeegkrknwsqE-----LivqkkkdisnkyFFGIDKDSFLAKVTKAyma 399
                                       56789****************9777766655555444441.....04444456667779999999988888888555 PP

                   Methyltransf_31  47 ....naqklgldnveFeqgdieelekl.ledekfDlilsn..................................... 81 
                                            +   + +n  F+  d++++ ++ ++  +fD++l+n                                     
  gi|386002821|ref|YP_005921120.1| 400 iigdGRGGVFCENSLFSPLDWQNKTQDrINFGSFDVLLTNppfgskisitskevlsqyslsykwrfnkneqkwertq 476
                                       44332333334466666666666665555558899977776666666666665555544444444444444443332 PP

                   Methyltransf_31  82 evl.naladpdkileeiervlkpggilliedpr 113
                                         + +  + +  ++e+  ++lkpgg++ i  p+
  gi|386002821|ref|YP_005921120.1| 477 K-FaDRRPPQILFIERCLELLKPGGRIGIVLPD 508
                                       2.1355555555566777777777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4696.99
//
Query:       gi|386002822|ref|YP_005921121.1|  [L=47]
Description: hypothetical protein Mhar_2145 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-08   34.4   0.1    1.5e-08   34.3   0.1    1.1  1  DUF2080         Putative transposon-encoded protein (DUF2080)
  ------ inclusion threshold ------
       0.04   13.9   0.0      0.069   13.1   0.0    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.6e-12   1.5e-08      13      48 ..       6      41 ..       2      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.6e-12
                           DUF2080 13 eilpffegkVkpfGnSAkvsiPkeylGkkvylvIld 48
                                      +++ ++e++Vk+ GnS++v +P+e++ k+v ++ ++
  gi|386002822|ref|YP_005921121.1|  6 DAYQVIEKVVKAGGNSGRVYVPREWVDKRVKIILME 41
                                      6899**************************999877 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.7e-06     0.069       3      17 ..      18      32 ..      16      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                                      ETTEEEEEE-CCCHH CS
                    MazE_antitoxin  3 vGnsgavriPkevrf 17
                                      +Gnsg+v  P+e+++
  gi|386002822|ref|YP_005921121.1| 18 GGNSGRVYVPREWVD 32
                                      7************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 321.83
//
Query:       gi|386002823|ref|YP_005921122.1|  [L=409]
Description: Transposase, IS4 family protein/SWIM domain fusion [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-19   69.4   0.3    1.1e-18   67.7   0.3    1.8  1  DDE_Tnp_1       Transposase DDE domain
    1.5e-05   24.6   0.1      3e-05   23.6   0.1    1.4  1  SWIM            SWIM zinc finger
  ------ inclusion threshold ------
      0.038   14.3   0.9       0.15   12.5   0.1    2.3  2  Ribosomal_L27e  Ribosomal L27e protein family
       0.13   11.0   0.0        0.2   10.4   0.0    1.2  1  DUF740          Protein of unknown function (DUF740)
       0.21   10.9   0.0       0.37   10.1   0.0    1.4  1  ThrE            Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.3   2.9e-22   1.1e-18       6     214 .]     209     384 ..     205     384 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 2.9e-22
                         DDE_Tnp_1   6 vlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr.kgklvl 81 
                                        +++D+t +r++++ ++   +++++k+++++k+h+    ++ ++ ++ it+  ++ds+++ +l++  ++  + + v 
  gi|386002823|ref|YP_005921122.1| 209 DFAIDSTGFRTTTFNAYCGTKHGEKKQHRWVKAHLCAGVKTNIVAAISITDEYSNDSPQFGPLVRKTAEGfTIDEVS 285
                                       589************99999*********************************************99988******* PP

                         DDE_Tnp_1  82 aDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntn 158
                                       aD +Y+s+++l+ + + g+   i+++kn+              + k++    ++   k  ++               
  gi|386002823|ref|YP_005921122.1| 286 ADMAYSSRKNLELVGDVGGTAYIPYRKNA--------------TGKAGGSPLWK---KMYHY--------------- 330
                                       *************************7777..............44444444444...44444............... PP

                         DDE_Tnp_1 159 sellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                        ++l   e+++ y++R+ iE + + +krkfg + l++++  + +++ll+++ a+nl
  gi|386002823|ref|YP_005921122.1| 331 -FQLNRDEFMDHYHKRSNIEATNAAIKRKFG-ETLKSKNEVAQVNELLAKIVAYNL 384
                                       .44578889**********************.***********************8 PP

>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   8.3e-09     3e-05      16      34 ..      52      70 ..      46      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.3e-09
                              SWIM 16 tCsCpefqkngipCkHalA 34
                                      tC+Cp+f + g  CkH++A
  gi|386002823|ref|YP_005921122.1| 52 TCTCPDFVYRGGKCKHIMA 70
                                      8****************99 PP

>> Ribosomal_L27e  Ribosomal L27e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.1e-05      0.15      26      54 ..      65      95 ..      61     118 .. 0.67
   2 ?   -1.6   0.1         1   3.7e+03      56      74 ..     348     366 ..     332     376 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                    Ribosomal_L27e 26 ynhlmpTRYtvdv..edlkelvkkealkdpa 54
                                      ++h+m+TRY ++v     k +v++++  + a
  gi|386002823|ref|YP_005921122.1| 65 CKHIMATRYYLEVekDTPKGVVTEKVHLTYA 95
                                      68*******9988524467888876644444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                    Ribosomal_L27e  56 rkeakkevkkkfeeryksg 74 
                                        +++  ++k+kf e  ks+
  gi|386002823|ref|YP_005921122.1| 348 IEATNAAIKRKFGETLKSK 366
                                       3344556667776666665 PP

>> DUF740  Protein of unknown function (DUF740)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.5e-05       0.2     381     489 ..     149     246 ..     144     264 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.5e-05
                            DUF740 381 ysDsssrRrksldRsssvrktaaavvaevdelkavsnakvspatgsylhhaklvlderdfssnslrdDlsasetael 457
                                       ys  ssrR +sl    +  k +++     ++ +++s+  ++p t+  + h   +++        +  D+      + 
  gi|386002823|ref|YP_005921122.1| 149 YSQLSSRRAHSLFQN-ATDKGQISKA---PHFNSTSELFNKPETTA-ILHQ--LVTLSALPVAGIETDF----AIDS 214
                                       666666666666543.3344444422...33333333333444333.3332..2223334666777777....6677 PP

                            DUF740 458 egfrdnaivignGerkgakksrrwrkawsiwG 489
                                       +gfr ++    +G+++g kk +rw ka+   G
  gi|386002823|ref|YP_005921122.1| 215 TGFRTTTFNAYCGTKHGEKKQHRWVKAHLCAG 246
                                       89999999999**************9986666 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0001      0.37       7      53 ..      13      63 ..      10     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                              ThrE  7 GeiLlesGaetyrvedtmkriaralgleevevfvtptsiivsv.d...eee 53
                                      G++    G ++ +v +t  ++ +  g ++ ev  tp+++++++ d   + +
  gi|386002823|ref|YP_005921122.1| 13 GKAIADQGNQIKKVSETSFKVRSQSGNKTYEVKSTPNGMTCTCpDfvyRGG 63
                                      8899999************************************77774333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2698.94
//
Query:       gi|386002824|ref|YP_005921123.1|  [L=217]
Description: hypothetical protein Mhar_2147 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-26   93.8   0.0    1.6e-26   93.4   0.0    1.2  1  DUF2589   Protein of unknown function (DUF2589)


Domain annotation for each model (and alignments):
>> DUF2589  Protein of unknown function (DUF2589)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.0   9.1e-31   1.6e-26       2     151 ..      13     202 ..      12     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 9.1e-31
                           DUF2589   2 lesLIggllkAaieAqeslaqqtidfiqqvfdkdkkk.......trt...lvafklkrkvpdedek........... 57 
                                       +es+Igg+l A+++Aq+ +a +t++fi+ v++k ++        t     +v+fk++ +++ ++             
  gi|386002824|ref|YP_005921123.1|  13 FESMIGGPLIAVVNAQAQAALSTVNFIKSVGFKAGESddpeasdT-GdpiYVTFKYPKEISPYQPAvpasgdtpatp 88 
                                       79*****************************65555545666542.15689*********9999999999999**** PP

                           DUF2589  58 .....eeekevkvPLlalvpipsLaIeevtvdfdlevkssetdkasedaaakleaeas..............sskke 115
                                             ++++++vP+l+++pip+++Iee t+df+ +++s+e +k  ++ +++++ ea+              s++++
  gi|386002824|ref|YP_005921123.1|  89 avpaqIQQMKLEVPILTMLPIPFIRIEETTIDFNAKITSMEYRKVDTNLKVDASLEAKagwffgsaklkvstSYQRS 165
                                       ***9778889**************************************99999888889999999999988755555 PP

                           DUF2589 116 qtre.skdnsakyhvsvkakqseppEGlarlldaltk 151
                                       ++++ + +++ ++++ vka+q+e+p G+ ++l++l++
  gi|386002824|ref|YP_005921123.1| 166 TSEGsNVNRTYSLAIHVKAVQDEMPGGMEKILSILEE 202
                                       55557789999***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1520.57
//
Query:       gi|386002825|ref|YP_005921124.1|  [L=249]
Description: hypothetical protein Mhar_2148 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.031   13.9   0.1       0.07   12.7   0.1    1.5  1  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
       0.14   11.8   0.3        4.4    6.9   0.1    2.2  2  DUF2777        Protein of unknown function (DUF2777)


Domain annotation for each model (and alignments):
>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.8e-06      0.07      80     135 ..      68     124 ..      51     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-06
                     PI3K_P85_iSH2  80 ehEie.klqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqL 135
                                       + E   ++ +n+++   r+  ++++k+++e +  +++  e+el+R+i alk e + L
  gi|386002825|ref|YP_005921124.1|  68 DPEATgRVLTNIRESFPRVLAIQAKKAQIEMKDDEKIRIEKELDRRILALKKEPVIL 124
                                       44555588999999999**********************************998776 PP

>> DUF2777  Protein of unknown function (DUF2777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00049       4.4      65      96 ..      88     119 ..      83     133 .. 0.87
   2 ?    2.7   0.0    0.0096        86      89     112 ..     170     193 ..     159     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00049
                           DUF2777  65 ilksdgevlrlkegekirlekkllkayeelle 96 
                                       +++ ++ ++++k++ekir+ek+l +   +l +
  gi|386002825|ref|YP_005921124.1|  88 AIQAKKAQIEMKDDEKIRIEKELDRRILALKK 119
                                       5678899****************988877766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0096
                           DUF2777  89 kayeelleeledeaflafvqtLns 112
                                       + +++l  +l++ af++f ++L++
  gi|386002825|ref|YP_005921124.1| 170 ERLQKLKTDLKKAAFMEFSKFLHE 193
                                       56899****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1747.98
//
Query:       gi|386002826|ref|YP_005921125.1|  [L=185]
Description: hypothetical protein Mhar_2149 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.8   0.0      0.044   14.0   0.0    1.4  1  TMEM191C  TMEM191C family


Domain annotation for each model (and alignments):
>> TMEM191C  TMEM191C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.5e-06     0.044      17      61 ..      23      67 ..      17      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-06
                          TMEM191C 17 cdsqlrrvqdsagslmeevaradcekrlfGgagaaalrlwalgal 61
                                       ds+  r  d  +s ++++ ra +e+rlf +a  aalr ++++a 
  gi|386002826|ref|YP_005921125.1| 23 LDSKDPRFSDLVKSWLQDLERAFAENRLFQAAEVAALRAMVISAE 67
                                      6899999999******************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1284.33
//
Query:       gi|386002827|ref|YP_005921126.1|  [L=201]
Description: hypothetical protein Mhar_2150 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-06   28.0   0.0      3e-06   27.4   0.0    1.3  1  DcrB      DcrB
    5.6e-06   26.6   0.0    3.5e-05   24.0   0.0    1.9  1  PsbP      PsbP
  ------ inclusion threshold ------
      0.043   13.5   0.2       0.08   12.6   0.2    1.4  1  DUF4946   Domain of unknown function (DUF4946)


Domain annotation for each model (and alignments):
>> DcrB  DcrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     5e-10     3e-06      29     128 .]      99     197 ..      92     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5e-10
                                       EEEEEE---TTS-HHHHHHHHHHHHHHHSTT-EEEEEEEEEET.TEEEEEEEEEEEETTEEEEEEEEEE--S.SSEE CS
                              DcrB  29 lvIsRdeleegetleeylerqlkqlrkrlkgfqlleekpatlgaglpaeelevtyrkkgkpvyqlqvlvevp.rrvL 104
                                       +++ ++ l+ g +l+ey+e  l++lr++  +f++l+e +++++ ++pa  + +  + +g + yq+++++ ++ +r+ 
  gi|386002827|ref|YP_005921126.1|  99 VTVQIEDLPGGTNLPEYTEAVLANLRSSYDDFEVLAEGEMKIS-EEPATVIGYGATVEG-TAYQVLLAYTIKeDRAY 173
                                       7899***************************************.9********999887.5788888888888**** PP

                                       EEEEEE-CCCHHHHHHHHHHHHCT CS
                              DcrB 105 iftltspgefteeqrahweailas 128
                                       ++t+ + +e   e +++++++++s
  gi|386002827|ref|YP_005921126.1| 174 VITYRALAERYSEFEDDAKRMINS 197
                                       ****99999888888888887775 PP

>> PsbP  PsbP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   5.8e-09   3.5e-05       6     155 ..      54     199 ..      50     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.8e-09
                                       EEETTTTEEEEEETTEEEEE-TTTEEE........EEEESS-TTSEEEEEEEE-STT--CHHH--HHHHHHHHHHHC CS
                              PsbP   6 ytdeedgysflyPsgWqevkgaegadv........vFrdeiesdenvsVvispvskdksledlGspeevaerlvkqv 74 
                                       +++ + g++ +yPs W+  + +  +d+          +++i++d+ v+V i++++  ++l ++   e+v  +l +++
  gi|386002827|ref|YP_005921126.1|  54 FESRAYGFAVAYPSAWTAEEAD-PNDLgivagflpPGENLIDPDNYVTVQIEDLPGGTNLPEYT--EAVLANLRSSY 127
                                       788899***********96666.5555566654444477899**************99999985..66777787777 PP

                                       CCHCTSSEEEEEEEEEEEEET.TEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEHHHHCCCHHHHHHHH CS
                              PsbP  75 lassesgreaelidaeereaddgktyYeleytvkspdeqerhqlaavavsngkLYtltlqtpekrwekvekklekvv 151
                                       +       + e+++  e + + +++   + y  + ++    + l a ++++++ Y +t  +  +r+++ e++ ++++
  gi|386002827|ref|YP_005921126.1| 128 D-------DFEVLAEGEMKIS-EEPATVIGYGATVEG-TAYQVLLAYTIKEDRAYVITYRALAERYSEFEDDAKRMI 195
                                       6.......7889888887776.899999999999998.77888889999**************************** PP

                                       HC-E CS
                              PsbP 152 kSFr 155
                                       +SF+
  gi|386002827|ref|YP_005921126.1| 196 NSFS 199
                                       ***8 PP

>> DUF4946  Domain of unknown function (DUF4946)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.3e-05      0.08     115     152 .]     163     200 ..     152     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                           DUF4946 115 lvaalgkeaaysLsYaasaeayaaskdeilavreslrl 152
                                       l+  + ++ ay+++Y a ae y + +d+++++ +s++l
  gi|386002827|ref|YP_005921126.1| 163 LAYTIKEDRAYVITYRALAERYSEFEDDAKRMINSFSL 200
                                       45678899***********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1295.09
//
Query:       gi|386002828|ref|YP_005921127.1|  [L=70]
Description: hypothetical protein Mhar_2151 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.062   13.3   1.1       0.12   12.3   1.1    1.6  1  Ion_trans_2  Ion channel


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.1     7e-06      0.12      26      78 ..      18      69 ..       3      70 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-06
                                      HHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 26 ldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78
                                       +a+Yfs  ++      ++ +++ + r+++i++++lG +++alfl  lg++++
  gi|386002828|ref|YP_005921127.1| 18 GEAIYFSSLVFIAQAPAEYRARGRY-RYLVIFEGILGWLMLALFLVGLGNLMI 69
                                      5677777777777777778888777.*******************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 421.05
//
Query:       gi|386002829|ref|YP_005921128.1|  [L=403]
Description: Peptidase S1 and S6, chymotrypsin/Hap [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-30  106.1   0.1    1.1e-29  104.3   0.1    1.8  1  Trypsin_2      Trypsin-like peptidase domain
    4.4e-14   52.8   0.0    4.6e-10   39.7   0.0    2.1  2  Trypsin        Trypsin
    1.4e-06   27.3   0.1     0.0058   15.3   0.0    3.0  3  Peptidase_S46  Peptidase S46
  ------ inclusion threshold ------
      0.016   15.3   0.1      0.064   13.4   0.0    2.0  2  TPR_2          Tetratricopeptide repeat
      0.021   14.6   0.0      0.051   13.3   0.0    1.5  2  Peptidase_S29  Hepatitis C virus NS3 protease
       0.15   11.6   2.0         28    4.1   0.1    3.1  3  DUF31          Putative peptidase (DUF31)


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.1   3.6e-33   1.1e-29       1     150 []      91     312 ..      91     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 3.6e-33
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadp........................ 53 
                                       GsGf+v+sdg+i+TnaHvv++ +++ +   ++ + + ++  re+p + +a                           
  gi|386002829|ref|YP_005921128.1|  91 GSGFVVNSDGYIVTNAHVVQETEEELK--AEFARQALEWAAREFPPTYIANGKdpypvteedlqwlynlflaeydld 165
                                       9******************99999999..455555555555555555333322334444455566666666666667 PP

                         Trypsin_2  54 .............................................elDlAllkvssderaglpplplgpsealkgge 85 
                                                                                    ++DlA++k+  +++++lp+++lg+s+++++g+
  gi|386002829|ref|YP_005921128.1| 166 ykreimvyfgapsildrspvgypaeirkispqevwysygdykyrsGKDLAIIKI--ETSNDLPTATLGNSKDVEVGD 240
                                       77777777777777777778888888888889999999999998777*******..********************* PP

                         Trypsin_2  86 pvyvvGyp........lggeksg.........svssGivsgvvesesaasgegesfl.qtdaatspGsSGGplfdsd 144
                                       +v+v+Gyp        +     +         sv+sGi+s+ ++       +++s + qtdaa+++G+SGGp f+++
  gi|386002829|ref|YP_005921128.1| 241 KVVVIGYPgvttswqnA-----FlspeteyvpSVTSGIISAEKR------LPDKSEVfQTDAAIYHGNSGGPAFNAE 306
                                       *******8777666551.....1444556678************......55555555******************* PP

                         Trypsin_2 145 GrvvGl 150
                                       G+v+G+
  gi|386002829|ref|YP_005921128.1| 307 GEVIGI 312
                                       *****8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   8.6e-05      0.26      25      47 ..      89     113 ..      77     130 .. 0.79
   2 !   39.7   0.0   1.5e-13   4.6e-10      85     202 ..     206     319 ..     164     344 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.6e-05
                                       EEEEEEEEETT.EEEEEGGGTTT.G CS
                           Trypsin  25 hlCgGslisen.wvlTAaHCvsn.a 47 
                                       +  +G++++++ +++T+aH+v++ +
  gi|386002829|ref|YP_005921128.1|  89 YSGSGFVVNSDgYIVTNAHVVQEtE 113
                                       45579****999*********9853 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.5e-13
                                       T....TTTEEEEEESSSSTSBSSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSS..BSSBEEEEEEEEEEHHHHHHH CS
                           Trypsin  85 l....dnDiallklkepvklgdtvrpiclpaassslpvgttclvsGwgrtkekg..ksdtlqevevpvvsretcksa 155
                                       +     +D+a++k++++    +   ++ l   s++++vg++++v+G++   +++     + ++ +vp v +  ++ +
  gi|386002829|ref|YP_005921128.1| 206 YkyrsGKDLAIIKIETS----NDLPTATLGN-SKDVEVGDKVVVIGYPGVTTSWqnAFLSPETEYVPSVTSGIISAE 277
                                       2334478*********9....7777777887.7789***********996666655344445556666666544444 PP

                                       TTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETTTEEEEEEEEESSS CS
                           Trypsin 156 ykgkvtenmlcagakeggkdacqGDSGGPlvcsdgelvGivswgkgc 202
                                        +   +++ ++++a     ++ +G+SGGP+++ +ge++Gi ++g g 
  gi|386002829|ref|YP_005921128.1| 278 KRLPDKSEVFQTDA-----AIYHGNSGGPAFNAEGEVIGIATFGSGR 319
                                       333367999*****.....9***********************9775 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0041        12      49      70 ..      91     112 ..      82     119 .. 0.85
   2 !    4.0   0.0    0.0053        16     235     256 ..     233     254 ..     230     269 .. 0.86
   3 !   15.3   0.0   1.9e-06    0.0058     625     652 ..     287     315 ..     275     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0041
                                       EE-EE-STT-EEEE-HHHHHHH CS
                     Peptidase_S46  49 CtasfVSpeGLvlTNHHCayga 70 
                                        ++ +V ++G ++TN H+++++
  gi|386002829|ref|YP_005921128.1|  91 GSGFVVNSDGYIVTNAHVVQET 112
                                       68999*************9875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0053
                                       SS---TT-EEEEEE------TT CS
                     Peptidase_S46 235 lkGvkegdlvfvlGyPGstsRy 256
                                        k v+ gd v v+GyPG t  +
  gi|386002829|ref|YP_005921128.1| 233 SKDVEVGDKVVVIGYPGVTTSW 254
                                       567899***********99765 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.9e-06
                                       EEES----TT-TT-EEE-TTS-EEEEE.E CS
                     Peptidase_S46 625 flstnDitGGNSGSPvlngkgelvGla.F 652
                                       f +++ i  GNSG P +n++ge++G+a F
  gi|386002829|ref|YP_005921128.1| 287 FQTDAAIYHGNSGGPAFNAEGEVIGIAtF 315
                                       788999999****************9734 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.5   4.5e+03       2      16 ..     198     212 ..     197     212 .. 0.84
   2 ?   13.4   0.0   2.1e-05     0.064       4      34 .]     360     390 ..     357     390 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                             TPR_2   2 ealynlGlayyklgd 16 
                                       e++y  G+  y++g+
  gi|386002829|ref|YP_005921128.1| 198 EVWYSYGDYKYRSGK 212
                                       789999999999885 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.1e-05
                             TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++++G  +y +g   eA+  f++ l+ldPnn
  gi|386002829|ref|YP_005921128.1| 360 HFERGFELYWNGSRPEARGEFDAILALDPNN 390
                                       89****************************8 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.9   5.8e+03      72      79 ..      97     104 ..      54     117 .. 0.61
   2 ?   13.3   0.0   1.7e-05     0.051      47     125 ..     236     313 ..     227     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.9
                     Peptidase_S29  72 asdlylvt 79 
                                       +sd y+vt
  gi|386002829|ref|YP_005921128.1|  97 NSDGYIVT 104
                                       23333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.7e-05
                     Peptidase_S29  47 tsaddDlvvypaPaGaksltpCtcgasdlylvtrdadliearrrgdkrvellsprelselkGssGsPilCdsGhvvG 123
                                       +++ d +vv   P  ++s ++     +  y+   ++ +i a++r  ++ e+ + ++ +  +G sG+P +  +G v+G
  gi|386002829|ref|YP_005921128.1| 236 VEVGDKVVVIGYPGVTTSWQNAFLSPETEYVPSVTSGIISAEKRLPDKSEVFQ-TDAAIYHGNSGGPAFNAEGEVIG 311
                                       5677888899999999999*999*********99*******999887888776.67899****************** PP

                     Peptidase_S29 124 ll 125
                                       + 
  gi|386002829|ref|YP_005921128.1| 312 IA 313
                                       95 PP

>> DUF31  Putative peptidase (DUF31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.03        89      58      69 ..     101     112 ..      97     133 .. 0.79
   2 ?    2.9   0.0     0.022        66     222     258 ..     220     257 ..     187     289 .. 0.65
   3 ?    4.1   0.1    0.0093        28     347     370 ..     289     312 ..     284     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.03
                             DUF31  58 YlATNlHVaaal 69 
                                       Y+ TN+HV+++ 
  gi|386002829|ref|YP_005921128.1| 101 YIVTNAHVVQET 112
                                       99*******944 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.022
                             DUF31 222 akykkldekldtdkqkttleeakklyilGYPtseed...t 258
                                        ++ +l++   t ++++++e   k++++GYP ++++    
  gi|386002829|ref|YP_005921128.1| 220 ETSNDLPT--ATLGNSKDVEVGDKVVVIGYPGVTTSwqnA 257
                                       33334444..44566777777778********99984441 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0093
                             DUF31 347 kssalagGaSGSlvrnkdnklvGI 370
                                       ++ a+++G SG +++n  ++++GI
  gi|386002829|ref|YP_005921128.1| 289 TDAAIYHGNSGGPAFNAEGEVIGI 312
                                       56789******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2528.19
//
Query:       gi|386002830|ref|YP_005921129.1|  [L=496]
Description: hypothetical protein Mhar_2153 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3280.94
//
Query:       gi|386002831|ref|YP_005921130.1|  [L=53]
Description: hypothetical protein Mhar_2154 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-10   41.0   0.9    1.9e-10   40.9   0.9    1.0  1  CooT      CO dehydrogenase accessory protein CooT


Domain annotation for each model (and alignments):
>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.9     1e-14   1.9e-10      12      61 .]       3      51 ..       1      51 [. 0.94

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1e-14
                              CooT 12 gkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiile 61
                                      g e+e +me V+ +  ++d+v+++di+G++ke +g+I e++++++k +le
  gi|386002831|ref|YP_005921130.1|  3 G-EKESLMEGVVVLVTRGDKVLMEDILGRTKEAKGRIFEVNITSQKAFLE 51
                                      3.669*****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 364.58
//
Query:       gi|386002832|ref|YP_005921131.1|  [L=116]
Description: Prefoldin, beta subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-24   85.5  16.3    2.4e-24   85.3  16.3    1.0  1  Prefoldin_2   Prefoldin subunit
     0.0025   18.1   0.8     0.0032   17.7   0.8    1.1  1  DUF3014       Protein of unknown function (DUF3014)
  ------ inclusion threshold ------
      0.052   13.4   0.1       0.11   12.3   0.1    1.6  1  Tnp_DNA_bind  Transposase DNA-binding
       0.12   12.7   8.3        0.1   12.9   2.0    2.2  2  BLOC1_2       Biogenesis of lysosome-related organelles compl
       0.13   12.4   2.3       0.51   10.5   0.1    2.3  2  CinA_KH       Damage-inducible protein CinA KH domain
       0.17   12.4  10.4       0.19   12.2   1.5    2.3  2  Cep57_MT_bd   Centrosome microtubule-binding domain of Cep57
       0.21   11.1   8.8       0.27   10.7   8.8    1.1  1  LRRFIP        LRRFIP family
       0.26   11.1   7.8        0.3   10.9   7.8    1.1  1  DUF724        Protein of unknown function (DUF724)
       0.34   10.8  10.1        1.7    8.6   1.8    2.3  2  Prefoldin     Prefoldin subunit
       0.42   10.2  15.1       0.89    9.2   6.0    2.1  2  DUF2968       Protein of unknown function (DUF2968)
        1.1    9.6  13.5        2.6    8.4   2.2    2.1  2  YlqD          YlqD protein
          2    7.6  13.1        0.4   10.0   3.2    2.0  2  DUF4763       Domain of unknown function (DUF4763)
        2.7    8.2  10.4        6.3    6.9   1.0    2.1  2  PilO          Pilus assembly protein, PilO
        3.1    7.8  20.3        2.1    8.4   9.6    2.2  2  FlxA          FlxA-like protein
        4.8    7.4  12.1        6.6    7.0   2.6    2.1  2  JIP_LZII      JNK-interacting protein  leucine zipper II
        8.3    6.7   8.9        7.9    6.8   3.3    2.1  2  Spc24         Spc24 subunit of Ndc80
        8.7    6.6  12.9        4.6    7.5   3.2    2.2  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3  16.3   2.3e-27   2.4e-24       1     105 [.       6     110 ..       6     111 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 2.3e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q++i+++qqlqqq q+l  q+ q+e+ ++e e++ +ele  +e + +yk+vG+vl+k d+++++ee +e+ke l+ +
  gi|386002832|ref|YP_005921131.1|   6 QNQIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEASPEGAVIYKSVGEVLFKADRTKLIEEYQEKKEVLDLR 82 
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklqq 105
                                       +ktl kq+e+++k++++l+++l++ l+q
  gi|386002832|ref|YP_005921131.1|  83 LKTLGKQEERIQKRFTQLQDQLKASLGQ 110
                                       ************************9987 PP

>> DUF3014  Protein of unknown function (DUF3014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   3.1e-06    0.0032      15     103 ..      13     106 ..       4     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                           DUF3014  15 gevarkllpvkapeekf.....tveeaeeklviaeanaaRYdayvnllesvdkdklvalYrrlkpllqeayeeLGyp 86 
                                       +++ +++  + ++++++     ++e+a ++l  +++ a  Y+ + ++l + d++kl++ Y++ k +l+   + LG++
  gi|386002832|ref|YP_005921131.1|  13 QQLQQQAQALLGQKSQIemmirETESAVKELEASPEGAVIYKSVGEVLFKADRTKLIEEYQEKKEVLDLRLKTLGKQ 89 
                                       344455555555555553322233345577999999***************************************** PP

                           DUF3014  87 kasFndrlvaaidella 103
                                       +++ ++r+ +  d+l a
  gi|386002832|ref|YP_005921131.1|  90 EERIQKRFTQLQDQLKA 106
                                       *********99999976 PP

>> Tnp_DNA_bind  Transposase DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011      0.11      15      40 ..      91     116 .]      80     116 .] 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                      Tnp_DNA_bind  15 kRltkRlvklaeslaekpgasiPqac 40 
                                       +R +kR+++l ++l ++ g+ +P+a+
  gi|386002832|ref|YP_005921131.1|  91 ERIQKRFTQLQDQLKASLGQKLPEAA 116
                                       799*********************95 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.0   9.7e-05       0.1      46      86 ..       5      45 ..       2      46 .. 0.93
   2 ?    3.5   0.5     0.082        87      42      68 ..      75     101 ..      61     111 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-05
                           BLOC1_2 46 lekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86
                                      +++++ +l++++++ q +l q  qie  ++e e+av+eL++
  gi|386002832|ref|YP_005921131.1|  5 VQNQIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEA 45
                                      688999********************************985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.082
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqid 68 
                                       + + l   l+ l +++e +q+ ++q++
  gi|386002832|ref|YP_005921131.1|  75 KKEVLDLRLKTLGKQEERIQKRFTQLQ 101
                                       333333334444444444444444442 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 ?    2.0   0.3      0.22   2.3e+02      25      64 ..      16      41 ..       3      61 .. 0.58
   2 ?   10.5   0.1   0.00048      0.51      34      70 ..      75     111 ..      50     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                                      SSSEEEEEEETTEEEEEEE...EEHHHHHHHHH....HHH CS
                           CinA_KH 25 enptlAiyakegevtvRltakaaneeeaealiapveeeir 64
                                      +++  A++ ++++++               +i ++e +++
  gi|386002832|ref|YP_005921131.1| 16 QQQAQALLGQKSQIEM--------------MIRETESAVK 41
                                      4444444444444444..............4444444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00048
                                       ETTEEEEEEE...EEHHHHHHHHH....HHHHHTTTT CS
                           CinA_KH  34 kegevtvRltakaaneeeaealiapveeeirerlgdy 70 
                                       k++  ++Rl   +++ee  +++  ++++++++ lg++
  gi|386002832|ref|YP_005921131.1|  75 KKEVLDLRLKTLGKQEERIQKRFTQLQDQLKASLGQK 111
                                       566779****************************986 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.8     0.032        34      29      66 ..      10      45 ..       4      48 .. 0.82
   2 ?   12.2   1.5   0.00018      0.19       4      41 ..      70     107 ..      67     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.032
                       Cep57_MT_bd 29 lelqelaaqynaldpslgkrkRkdLaeeleelvkrlEa 66
                                      ++lq+l++q +al    +k++ + + +e e  vk+lEa
  gi|386002832|ref|YP_005921131.1| 10 AQLQQLQQQAQALL--GQKSQIEMMIRETESAVKELEA 45
                                      67788888888887..7999999999**********97 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00018
                       Cep57_MT_bd   4 rpsqspkeaLaevlkeLedEfehlklelqelaaqynal 41 
                                       ++ q+ ke+L   lk+L ++ e +++++++l++q++a+
  gi|386002832|ref|YP_005921131.1|  70 EEYQEKKEVLDLRLKTLGKQEERIQKRFTQLQDQLKAS 107
                                       677999****************************9975 PP

>> LRRFIP  LRRFIP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   8.8   0.00025      0.27     148     249 ..       6     107 ..       3     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                            LRRFIP 148 erlkrqlealkleldelkeklkqrdeLiedhglvlveeeatdgekeeesssssksalvskeaaellesa..gegtld 222
                                       +++  ql++l+++ + l  +  q + +i +    ++e ea+ +   ++  +s   +l  ++  +l e++   + +ld
  gi|386002832|ref|YP_005921131.1|   6 QNQIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEASPEG--AVIYKSVGEVLFKADRTKLIEEYqeKKEVLD 80 
                                       55667777777777777777777788887665455444443333..35566667778888888988888667899** PP

                            LRRFIP 223 vrLkklaeekeeLleeveklkqqleee 249
                                        rLk l ++ e++++   +l++ql+++
  gi|386002832|ref|YP_005921131.1|  81 LRLKTLGKQEERIQKRFTQLQDQLKAS 107
                                       ************************986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   7.8   0.00028       0.3      90     183 ..       5     106 ..       3     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                            DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeid..elekkilelerqlallk......ekkeaadk 158
                                       +q+++ +L +l+++ + ll +++++e  i+e es+ ++le++ +   + k + e+  +++++k      ekke  d 
  gi|386002832|ref|YP_005921131.1|   5 VQNQIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEASPEgaVIYKSVGEVLFKADRTKlieeyqEKKEVLDL 81 
                                       7899******************************9999998765447888888888888888899999999999999 PP

                            DUF724 159 eiarlkseaekleeeledveqeFea 183
                                       ++++l +++e+++++  + +++ +a
  gi|386002832|ref|YP_005921131.1|  82 RLKTLGKQEERIQKRFTQLQDQLKA 106
                                       9999999*****9999999999876 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.3    0.0044       4.7       2      49 ..      13      60 ..       8      67 .. 0.61
   2 ?    8.6   1.8    0.0016       1.7      75     108 ..      72     105 ..      68     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0044
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTE CS
                         Prefoldin  2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgagl 49
                                      ++ ++  qa l+q ++  + +++t++++k+l++++eg+ +   +g+ l
  gi|386002832|ref|YP_005921131.1| 13 QQLQQQAQALLGQKSQIEMMIRETESAVKELEASPEGAVIYKSVGEVL 60
                                      333344444444444444556788889999999888876655555554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  75 leeAiellkkkleelekqlekleeeleklkdqit 108
                                       ++e +e+l+ +l++l kq e +++  ++l+dq++
  gi|386002832|ref|YP_005921131.1|  72 YQEKKEVLDLRLKTLGKQEERIQKRFTQLQDQLK 105
                                       6777999************************987 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.0   0.00085      0.89     136     177 ..       6      46 ..       2      49 .. 0.82
   2 ?    6.7   1.7    0.0049       5.1     109     152 ..      63     106 ..      61     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00085
                           DUF2968 136 eqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                       ++++a+  +q++++a+aL  q+++++  +r+++  +++L+a 
  gi|386002832|ref|YP_005921131.1|   6 QNQIAQ-LQQLQQQAQALLGQKSQIEMMIRETESAVKELEAS 46 
                                       344444.457999**************************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0049
                           DUF2968 109 aqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaa 152
                                       a   ++i++ +++ e L   l+   +Qe+++++r  q++++ +a
  gi|386002832|ref|YP_005921131.1|  63 ADRTKLIEEYQEKKEVLDLRLKTLGKQEERIQKRFTQLQDQLKA 106
                                       56678899999999999999999999999999999999998876 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.7    0.0073       7.7      32      98 ..       8      41 ..       2      51 .. 0.43
   2 ?    8.4   2.2    0.0025       2.6      15      61 ..      62     108 ..      54     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0073
                              YlqD 32 ldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsevkqg 98
                                         +lqqL++qa+ l                                 l q +q++ +  ++e   +
  gi|386002832|ref|YP_005921131.1|  8 QIAQLQQLQQQAQAL---------------------------------LGQKSQIEMMIRETESAVK 41
                                      223334444444444.................................3333333333333333333 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                              YlqD  15 eklKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieei 61 
                                       ++ +++l++++q+++e ld  l+ L  q++r+ k   + + q ++++
  gi|386002832|ref|YP_005921131.1|  62 KADRTKLIEEYQEKKEVLDLRLKTLGKQEERIQKRFTQLQDQLKASL 108
                                       566899*************************9998877665544444 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.2   0.00038       0.4      98     136 ..       8      46 ..       2      48 .. 0.89
   2 ?    3.4   2.3     0.038        40      43      74 ..      74     106 ..      62     114 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                           DUF4763  98 eqpeileLqrnnhkLrqqlaelqqhlkasrkslkelres 136
                                       +  ++++Lq++ + L  q ++++   +++++++kel++s
  gi|386002832|ref|YP_005921131.1|   8 QIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEAS 46 
                                       55799*******************************976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.038
                           DUF4763  43 e.eeeeeldLdeiydelekiKqrvlelrskLal 74 
                                       e +e  +l L++  ++ e+i +r  +l+ +L+ 
  gi|386002832|ref|YP_005921131.1|  74 EkKEVLDLRLKTLGKQEERIQKRFTQLQDQLKA 106
                                       223444445566666666666666666666654 PP

>> PilO  Pilus assembly protein, PilO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.0     0.006       6.3      11      46 ..       8      43 ..       3      59 .. 0.67
   2 ?    6.3   2.7    0.0098        10       5      46 ..      62     104 ..      60     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
                              PilO 11 LkkefeekkekaanLeklkkqleeleeeleellkqL 46
                                        +++++ +++a++L   k+q+e + +e e+++k+L
  gi|386002832|ref|YP_005921131.1|  8 QIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKEL 43
                                      345566677777777777777777777777777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0098
                              PilO   5 eakekeLkkefeekkekaa.nLeklkkqleeleeeleellkqL 46 
                                       +a++++L +e++ekke    +L++l kq e++++++++l +qL
  gi|386002832|ref|YP_005921131.1|  62 KADRTKLIEEYQEKKEVLDlRLKTLGKQEERIQKRFTQLQDQL 104
                                       577899999999999876439******************9998 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   9.6     0.002       2.1      60      97 ..       4      42 ..       3      46 .. 0.69
   2 ?    5.4   2.9     0.018        18      49      66 ..      88     105 ..      62     115 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                              FlxA 60 qlqaQIaqlqqqqae.kaqekqqsekeekskskqegvnk 97
                                      q+q+QIaqlqq q++ +a   q+s+ e + ++++++v++
  gi|386002832|ref|YP_005921131.1|  4 QVQNQIAQLQQLQQQaQALLGQKSQIEMMIRETESAVKE 42
                                      79*******995555055556666666677777877765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                              FlxA  49 kqqqliqaQIqqlqaQIa 66 
                                       kq++ iq+  +qlq Q++
  gi|386002832|ref|YP_005921131.1|  88 KQEERIQKRFTQLQDQLK 105
                                       666666776666666665 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.1     0.014        15      32      68 ..       9      45 ..       5      46 .. 0.87
   2 ?    7.0   2.6    0.0063       6.6      35      71 .]      69     105 ..      61     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                          JIP_LZII 32 IarvdeLtsereiLreEleslqkakerlesrikelEe 68
                                      Ia++ +L+++ ++L    ++++++ ++ es +kelE+
  gi|386002832|ref|YP_005921131.1|  9 IAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEA 45
                                      8999999999999999999999999999999999986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0063
                          JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikelEeelk 71 
                                       ++e ++ +e+L   l++l k+ er+++r ++l+++lk
  gi|386002832|ref|YP_005921131.1|  69 IEEYQEKKEVLDLRLKTLGKQEERIQKRFTQLQDQLK 105
                                       799999****************************998 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.3    0.0075       7.9      14      79 ..       6      72 ..       3      82 .. 0.69
   2 ?    3.2   1.7     0.099     1e+02      13      42 ..      76     105 ..      62     114 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0075
                             Spc24 14 sdleselesleselaelkeeleeleeeseekeserve.detllklklYrsL.Gielekdvnkvlirnk 79
                                      +++ ++l++l+++ + l  +  ++e++  e es+++e +++   + +Y+s+  + ++ d  + li+++
  gi|386002832|ref|YP_005921131.1|  6 QNQIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKElEASPEGAVIYKSVgEVLFKAD-RTKLIEEY 72
                                      55556788888888888888888888888877777777777788888988844555555.44555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.099
                             Spc24  13 lsdleselesleselaelkeeleeleeese 42 
                                        + l+  l+ l ++ ++ ++++++l+++ +
  gi|386002832|ref|YP_005921131.1|  76 KEVLDLRLKTLGKQEERIQKRFTQLQDQLK 105
                                       344555566666777777777777776655 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.2    0.0043       4.6      54      96 ..       4      46 ..       3      53 .. 0.90
   2 ?    5.0   2.0     0.026        28      63      96 ..      73     103 ..      51     114 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0043
                                      HHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 54 elskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96
                                      +++++I+++ + +++a++l+ + +++   + ++e ++kelea 
  gi|386002832|ref|YP_005921131.1|  4 QVQNQIAQLQQLQQQAQALLGQKSQIEMMIRETESAVKELEAS 46
                                      57899*****999**************************9986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                                       CCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  63 kkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                           e++e l  + k+l+++ ++++++ ++l+++
  gi|386002832|ref|YP_005921131.1|  73 Q---EKKEVLDLRLKTLGKQEERIQKRFTQLQDQ 103
                                       1...222333333444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2065  (0.115177); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 691.80
//
Query:       gi|386002833|ref|YP_005921132.1|  [L=75]
Description: hypothetical protein Mhar_2157 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-08   33.2   0.4    5.1e-08   32.9   0.4    1.1  1  Pcc1      Transcription factor Pcc1
  ------ inclusion threshold ------
      0.092   13.3   0.7         14    6.3   0.0    2.3  2  PKS_DE    Polyketide synthase dimerisation element domain


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.4   5.7e-12   5.1e-08       8      72 ..       9      72 ..       4      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.7e-12
                                      -SSHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  8 fpterlAsialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                      f+ e + +++  +L++++e + + +++ ++  +  + ++++++++ +LR+a+n++++++++++++
  gi|386002833|ref|YP_005921132.1|  9 FEVE-DPEAVAAALAPEAEDQIQRSHVRIEAVEGAVLLKVESEDLVSLRAALNTWIRLVDIAIKM 72
                                      4443.5689999*****999988788888888889999***********************9987 PP

>> PKS_DE  Polyketide synthase dimerisation element domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0031        28       9      26 ..      10      27 ..       8      35 .. 0.82
   2 ?    6.3   0.0    0.0016        14       8      22 ..      47      61 ..      46      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0031
                            PKS_DE  9 ereDlaaLaatLgldada 26
                                      e eD++a+aa+L+ +a++
  gi|386002833|ref|YP_005921132.1| 10 EVEDPEAVAAALAPEAED 27
                                      789*********996555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0016
                            PKS_DE  8 VereDlaaLaatLgl 22
                                      Ve+eDl +L a+L++
  gi|386002833|ref|YP_005921132.1| 47 VESEDLVSLRAALNT 61
                                      9**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.52
# Mc/sec: 434.60
//
Query:       gi|386002834|ref|YP_005921133.1|  [L=136]
Description: hypothetical protein Mhar_2158 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0084   15.3   0.1     0.0096   15.1   0.1    1.1  1  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0092   14.7   0.0      0.011   14.5   0.0    1.0  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.1e-06    0.0096     169     208 ..      60      99 ..      45     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-06
                       K_oxygenase 169 legkervvHsseylerkeellakkriaVvGsGqSaaeife 208
                                         g+er++  s + e  +++l++kr aVvGsG+ aae++e
  gi|386002834|ref|YP_005921133.1|  60 SGGEERILRFSAVQEGGAKRLTRKRAAVVGSGKAAAEVAE 99 
                                       4567889999999999999*******************86 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.3e-06     0.011     203     292 ..      12     102 ..       8     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-06
                                       HCHHHHHHHHHHHH---EEEEE-SSSHHHHHHHHHHHHHHHT..CHHHHHHHHHHH.HHHHHHHHHHHHHHTT-EEE CS
                    Oxidored_nitro 203 rsanyaaelleekfgvpyiklvspiGleatdaflrelakllg..kevaperiaeer.arlldaladyheylagkrva 276
                                       r+++ ++++l+  fg++y++ +   Gle+ d+ ++ + + +g  +  a  +  eer  r+ +  +   ++l  kr+a
  gi|386002834|ref|YP_005921133.1|  12 RARR-FGRVLANYFGARYMT-RGKSGLEDGDEVWMVVVEGSGgpAGLARRSGGEERiLRFSAVQEGGAKRLTRKRAA 86 
                                       5555.99*************.99*******************664455566667776666666666*********** PP

                                       EECSSHHHHHHHHHHH CS
                    Oxidored_nitro 277 iygdpdrvvalarllk 292
                                       ++g ++ +  +a+++ 
  gi|386002834|ref|YP_005921133.1|  87 VVGSGKAAAEVAEFFG 102
                                       ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 893.90
//
Query:       gi|386002835|ref|YP_005921134.1|  [L=45]
Description: DNA-directed RNA polymerase subunit P [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-09   36.6   8.1    3.3e-09   36.3   8.1    1.2  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
    2.3e-05   23.9   0.8       0.14   11.8   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
     0.0002   20.6   0.3     0.0091   15.4   0.1    2.1  2  zf-ribbon_3     zinc-ribbon domain
     0.0011   19.0   0.5     0.0011   19.0   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0015   18.0   1.6     0.0018   17.7   1.6    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0019   18.1   2.9      0.004   17.0   2.9    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0022   17.6   2.1     0.0044   16.7   2.1    1.5  1  zinc_ribbon_2   zinc-ribbon domain
     0.0033   17.5   4.4     0.0059   16.7   4.3    1.5  1  Zn-ribbon_8     Zinc ribbon domain
     0.0063   16.4   1.6      0.052   13.4   0.2    2.0  2  Cys_rich_CPXG   Cysteine-rich CPXCG
     0.0095   15.9   1.1      0.013   15.5   1.1    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.5   4.0       0.19   11.7   0.1    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.016   15.1   3.7       0.39   10.7   3.7    2.1  1  zinc_ribbon_4   zinc-ribbon domain
      0.016   15.3   0.9      0.019   15.1   0.9    1.2  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.018   15.3   1.3      0.028   14.7   1.3    1.3  1  zinc_ribbon_9   zinc-ribbon
      0.021   14.8   1.6      0.031   14.3   1.6    1.2  1  zinc_ribbon_6   Zinc-ribbon
      0.024   14.5   3.8      0.049   13.6   0.3    2.0  2  DUF951          Bacterial protein of unknown function (DUF951
      0.026   14.5   1.7       0.46   10.5   0.1    2.0  2  CpXC            CpXC protein
      0.028   14.1   0.6          2    8.2   0.1    2.0  2  YacG            DNA gyrase inhibitor YacG
      0.036   13.9   2.6        4.5    7.2   0.1    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.041   13.9   0.8      0.041   13.9   0.8    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.053   13.5   0.1      0.055   13.4   0.1    1.1  1  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
      0.056   13.3   1.1      0.096   12.6   1.1    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.061   13.6   0.3      0.061   13.6   0.3    1.1  1  DUF2072         Zn-ribbon containing protein
      0.071   13.4   2.3       0.77   10.1   0.1    2.0  2  DUF3268         zinc-finger-containing domain
       0.11   12.5   2.8        2.6    8.2   0.1    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.14   12.6   3.1        8.2    7.1   0.1    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.22   12.3   4.4       0.46   11.3   4.4    1.4  2  zinc_ribbon_15  zinc-ribbon family
       0.31   10.8   4.0        2.9    7.7   0.2    2.1  2  zf-CCHC_5       GAG-polyprotein viral zinc-finger
       0.33   10.9   9.7        5.7    6.9   9.1    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.35   11.0   2.5        9.9    6.4   0.1    2.0  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
       0.36   10.6   4.7         15    5.4   4.2    2.3  3  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        2.1    8.5   6.3        9.4    6.4   6.3    1.9  1  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   8.1   5.8e-12   3.3e-09       1      32 []       3      35 ..       3      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.8e-12
                                      -B-SSS--B--.--SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhRilYKkR 32
                                      Y C +C++ v+ + +   iRC +CGhRil+K+R
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEvDYEYSGIRCPYCGHRILMKER 35
                                      99*********7777899**************9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00025      0.14       3      15 ..       3      15 ..       2      18 .. 0.87
   2 !   11.1   0.0   0.00039      0.22       3      18 ..      21      36 ..      19      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            zf_UBZ  3 ylCerCgkeipes 15
                                      y C rC+k+++++
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVD 15
                                      89********987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00039
                            zf_UBZ  3 ylCerCgkeipeselq 18
                                      + C+ Cg++i++ e++
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHRILMKERP 36
                                      68**********9997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.07        39       3      11 ..       3      12 ..       1      15 [. 0.75
   2 !   15.4   0.1   1.6e-05    0.0091       3      11 ..      21      30 ..      19      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      +rC +C++ +
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKtV 12
                                      79****9955 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-05
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      +rCP+CG+ +
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHrI 30
                                      7999999977 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   1.9e-06    0.0011      71      95 ..       3      29 ..       1      44 [. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-06
                                      EEETTTS-EEECHHH..HHS-TTTSSS CS
                              HypA 71 vrCreCgkefeleek..alrCpkCgsa 95
                                      +rC++C+k++e++ +   +rCp Cg++
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVDYEysGIRCPYCGHR 29
                                      79*********98744678*****986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.6   3.3e-06    0.0018       1      27 [.       3      28 ..       3      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                                      EEETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                      y+C  C+ t +++D+e   ++C+ CG 
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKT-VEVDYEYSGIRCPYCGH 28
                                      79*****87.9***************6 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.9   7.2e-06     0.004      16      39 ..       8      31 ..       1      43 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.2e-06
                    OrfB_Zn_ribbon 16 GikveevnpayTSktCseCgsknk 39
                                       +k++ev+ +y+  +C+ Cg++  
  gi|386002835|ref|YP_005921134.1|  8 CKKTVEVDYEYSGIRCPYCGHRIL 31
                                      468999***************964 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.1   7.8e-06    0.0044       1      22 [.       4      29 ..       4      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.8e-06
                     zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGtp 22
                                      +C++C ++++ +  +    CpyCG+ 
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVEVDYEYsgirCPYCGHR 29
                                      6********9777777********96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.3   1.1e-05    0.0059       6      34 ..       3      28 ..       2      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                      YrC++C+++ ev  + s    + CP Cg+
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVDYEYS---GIRCPYCGH 28
                                      ***********888666...999*****8 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.23   1.3e+02       1      16 [.       3      18 ..       3      20 .. 0.75
   2 !   13.4   0.2   9.3e-05     0.052       1      11 [.      21      31 ..      21      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.23
                     Cys_rich_CPXG  1 iqCPyCgeeievlvDl 16
                                      + C  C +++ev+ + 
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVDYEY 18
                                      6799999999887655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.3e-05
                     Cys_rich_CPXG  1 iqCPyCgeeie 11
                                      i CPyCg++i 
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHRIL 31
                                      78******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.1   2.3e-05     0.013      14      38 ..       4      30 ..       1      37 [. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                               DZR 14 fCseCgtklkavaa..edrCpsCgekv 38
                                       C +C+++++   +   +rCp Cg+ +
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVEVDYEysGIRCPYCGHRI 30
                                      577777776644446677777777765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.032        18      38      46 .]       3      11 ..       1      11 [. 0.86
   2 ?   11.7   0.1   0.00034      0.19      18      28 ..      20      35 ..      18      44 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.032
                     Zn_Tnp_IS1595 38 fqCkeCrkq 46
                                      ++C +C+k+
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKT 11
                                      9*****985 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00034
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.....k 28
                                      g +CP+Cg+r     +
  gi|386002835|ref|YP_005921134.1| 20 GIRCPYCGHRilmkeR 35
                                      789*****98554433 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.7   0.00069      0.39       1      35 [.       1      30 [.       1      31 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
                     zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                      M  +C +Ck++ e+d e      + +rC+ Cgh +
  gi|386002835|ref|YP_005921134.1|  1 MAYRCTRCKKTVEVDYE-----YSGIRCPYCGHRI 30
                                      7779**********996.....7889*******86 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.9   3.4e-05     0.019       9      38 ..       3      35 ..       1      44 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-05
                      NOB1_Zn_bind  9 lrChaCfkvt...kdmtkkFCpkCGnktLkrva 38
                                      +rC+ C k++    + +   Cp CG++ L +  
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVevdYEYSGIRCPYCGHRILMKER 35
                                      79******995444588899*******999865 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.3   4.9e-05     0.028       5      30 ..       5      29 ..       2      32 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-05
                     zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCggg 30
                                      C +C+++V+v  + + +  CP+Cg  
  gi|386002835|ref|YP_005921134.1|  5 CTRCKKTVEVDYEYSGIR-CPYCGHR 29
                                      779*******98888888.****976 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.6   5.5e-05     0.031      32      54 ..       5      27 ..       2      28 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                     zinc_ribbon_6 32 CnDCekksevkfhvlglkCkeCg 54
                                      C  C+k+ ev++ + g++C  Cg
  gi|386002835|ref|YP_005921134.1|  5 CTRCKKTVEVDYEYSGIRCPYCG 27
                                      999*******************7 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3       0.2   1.1e+02      32      41 ..       4      13 ..       1      18 [. 0.83
   2 ?   13.6   0.3   8.7e-05     0.049      30      54 ..      20      45 .]      18      45 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                            DUF951 32 kClgcgrevm 41
                                      +C++c++ v 
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVE 13
                                      8*****9985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.7e-05
                            DUF951 30 klkClgcgrevml.pRskfekkikkv 54
                                       ++C  cg+ +++ +R +  k++k v
  gi|386002835|ref|YP_005921134.1| 20 GIRCPYCGHRILMkERPTTVKRMKAV 45
                                      59*******99973699999999976 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.039        22      38      52 ..       3      17 ..       1      19 [. 0.82
   2 ?   10.5   0.1   0.00082      0.46      35      51 ..      18      34 ..      14      44 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.039
                              CpXC 38 atCpkCgatakleap 52
                                      ++C +C +t++++++
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVDYE 17
                                      789999999999886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00082
                              CpXC 35 lfeatCpkCgataklea 51
                                      +  ++Cp+Cg+++ ++ 
  gi|386002835|ref|YP_005921134.1| 18 YSGIRCPYCGHRILMKE 34
                                      66789******998764 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.036        20       2      13 ..       4      15 ..       3      20 .. 0.84
   2 ?    8.2   0.1    0.0035         2       1      14 [.      21      34 ..      21      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.036
                              YacG  2 kCPtCkkevews 13
                                      +C  Ckk+ve++
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVEVD 15
                                      799*****9986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0035
                              YacG  1 vkCPtCkkevewse 14
                                      ++CP C++++ ++e
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHRILMKE 34
                                      69******999887 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5      0.01       5.7      29      37 ..       3      11 ..       1      12 [. 0.84
   2 ?    7.2   0.1     0.008       4.5       1       9 [.      21      29 ..      21      33 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                           TFIIS_C 29 ykCtkCghr 37
                                      y+Ct C+++
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKT 11
                                      99****986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.008
                           TFIIS_C  1 akCpkCgsr 9 
                                      ++Cp Cg+r
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHR 29
                                      579999998 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   7.4e-05     0.041      39      66 ..       2      29 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.4e-05
                       Zn_Tnp_IS91 39 ryeCeeCghekivyfsCksrhCpsCqkk 66
                                       y+C+ C+++  v +      Cp C+++
  gi|386002835|ref|YP_005921134.1|  2 AYRCTRCKKTVEVDYEYSGIRCPYCGHR 29
                                      79************************97 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.8e-05     0.055      12      42 ..       4      31 ..       1      39 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                                      E-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkgli 42
                                       C  C+++ +++ e   +++ CP C G+ ++
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVEVDYE--YSGIRCPYC-GHRIL 31
                                      7**********999..99*******.55555 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.1   0.00017     0.096      13      36 ..       4      28 ..       1      31 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                      B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1 13 fCkhCgeflwg.kekqglkCswCkl 36
                                      +C+ C++ ++   e+ g++C  C+ 
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVEVdYEYSGIRCPYCGH 28
                                      8********888***********86 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   0.00011     0.061       2      30 ..       3      31 ..       2      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                           DUF2072  2 HkCtkCekvfedgskeilkGCpsCGgkkF 30
                                       +Ct+C+k+ e   +     Cp CG +  
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVDYEYSGIRCPYCGHRIL 31
                                      59*********999977888*****8754 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3       0.1        58      29      43 ..       1      15 [.       1      20 [. 0.85
   2 ?   10.1   0.1    0.0014      0.77       3      16 ..      21      34 ..      19      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                           DUF3268 29 llylCpkCdayvgvh 43
                                      ++y C++C   v v 
  gi|386002835|ref|YP_005921134.1|  1 MAYRCTRCKKTVEVD 15
                                      68*******999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0014
                           DUF3268  3 trCpyCGekvilvs 16
                                      +rCpyCG+++ +++
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHRILMKE 34
                                      79******998876 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4     0.049        27      17      22 ..       2       7 ..       1      10 [. 0.82
   2 ?    8.2   0.1    0.0046       2.6       1      12 [.      22      33 ..      22      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.049
                    DNA_ligase_ZBD 17 iyRCtn 22
                                      +yRCt+
  gi|386002835|ref|YP_005921134.1|  2 AYRCTR 7 
                                      7****8 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0046
                    DNA_ligase_ZBD  1 hCPvCGsavvRe 12
                                      +CP CG+ +  +
  gi|386002835|ref|YP_005921134.1| 22 RCPYCGHRILMK 33
                                      5*****998755 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5     0.022        12       1       9 [.       3      11 ..       3      17 .. 0.91
   2 ?    7.1   0.1     0.015       8.2       2       8 ..      22      28 ..      21      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      y+C+ C+k+
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKT 11
                                      9******97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +Cp+Cg 
  gi|386002835|ref|YP_005921134.1| 22 RCPYCGH 28
                                      8****95 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.4   0.00083      0.46      66      86 .]       3      27 ..       2      27 .. 0.94
   2 ?    4.2   0.3      0.13        71       1      10 [.      21      30 ..      21      41 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00083
                    zinc_ribbon_15 66 keCknCgkeveeefky....CpkCg 86
                                      ++C +C+k+ve +++y    Cp+Cg
  gi|386002835|ref|YP_005921134.1|  3 YRCTRCKKTVEVDYEYsgirCPYCG 27
                                      68*************99999****9 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.13
                    zinc_ribbon_15  1 ilCpkCgkls 10
                                      i+Cp+Cg++ 
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHRI 30
                                      5677777644 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0051       2.9       4      10 ..       4      10 ..       2      14 .. 0.90
   2 ?    4.7   0.5     0.046        26       4      11 ..      22      29 ..      20      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0051
                                      B-TTT-S CS
                         zf-CCHC_5  4 lCpRCkk 10
                                      +C RCkk
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKK 10
                                      8*****9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.046
                                      B-TTT-SS CS
                         zf-CCHC_5  4 lCpRCkkg 11
                                      +Cp C+ +
  gi|386002835|ref|YP_005921134.1| 22 RCPYCGHR 29
                                      8*****87 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.1      0.01       5.7       4      34 ..       2      30 ..       2      34 .. 0.74
   2 ?    6.0   1.6      0.02        11      26      34 ..      22      30 ..      16      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                    Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhnYrCrrCkgtL 34
                                      +YrCt+C++++++         rC++C+ ++
  gi|386002835|ref|YP_005921134.1|  2 AYRCTRCKKTVEVDYEYSG--IRCPYCGHRI 30
                                      59******76666666666..6699999776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                    Zn_ribbon_SprT 26 rCrrCkgtL 34
                                      rC++C+ ++
  gi|386002835|ref|YP_005921134.1| 22 RCPYCGHRI 30
                                      788887665 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.032        18      54      66 ..       4      16 ..       1      21 [. 0.80
   2 ?    6.4   0.1     0.018       9.9      29      39 ..      22      32 ..      17      36 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                         DiS_P_DiS 54 rCraCkakislry 66
                                      rC +Ck+++++ y
  gi|386002835|ref|YP_005921134.1|  4 RCTRCKKTVEVDY 16
                                      8999999988887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                         DiS_P_DiS 29 rCpkCghklkw 39
                                      rCp Cgh++ +
  gi|386002835|ref|YP_005921134.1| 22 RCPYCGHRILM 32
                                      78888888765 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6     0.039        22      44      52 ..       2      10 ..       1      12 [. 0.83
   2 ?    5.4   4.2     0.027        15      35      53 ..      12      29 ..       5      30 .. 0.72
   3 ?   -1.8   0.0       4.8   2.7e+03       8      22 ..      30      44 ..      29      45 .] 0.69

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.039
                    zinc_ribbon_10 44 kyrCpkCga 52
                                       yrC  C+ 
  gi|386002835|ref|YP_005921134.1|  2 AYRCTRCKK 10
                                      7******97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.027
                    zinc_ribbon_10 35 apkeeleevkyrCpkCgal 53
                                      + + ++e+   rCp+Cg+ 
  gi|386002835|ref|YP_005921134.1| 12 V-EVDYEYSGIRCPYCGHR 29
                                      3.678899999******96 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.8
                    zinc_ribbon_10  8 vLvGddetsaknrya 22
                                      +L+ + +t +k ++a
  gi|386002835|ref|YP_005921134.1| 30 ILMKERPTTVKRMKA 44
                                      577777777777766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.3     0.017       9.4      15      23 ..      21      29 ..       4      29 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                           UPF0547 15 qfCphCGyv 23
                                       +Cp+CG++
  gi|386002835|ref|YP_005921134.1| 21 IRCPYCGHR 29
                                      58*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 303.14
//
Query:       gi|386002836|ref|YP_005921135.1|  [L=93]
Description: 50S ribosomal protein L37Ae [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-32  109.3   4.9    8.6e-32  109.1   4.9    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    0.00011   22.2   0.3       0.31   11.2   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain
    0.00035   20.4   0.6    0.00055   19.8   0.6    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0016   18.3   4.3     0.0029   17.5   3.2    1.9  2  HalOD2           Halobacterial output domain 2
     0.0028   17.1   1.3     0.0045   16.5   1.3    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.004   17.5   1.3        0.2   12.1   0.1    2.3  2  DUF4379          Probable Zinc-ribbon domain
      0.007   16.3   2.4      0.064   13.2   0.5    2.4  2  zinc_ribbon_4    zinc-ribbon domain
     0.0074   16.3   4.2      0.014   15.5   4.2    1.5  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.027   14.5   0.3    1.6  1  Elf1             Transcription elongation factor Elf1 like
      0.015   15.3   4.0      0.024   14.6   4.0    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.015   15.5   0.1      0.021   15.0   0.1    1.2  1  IBR              IBR domain, a half RING-finger domain
      0.025   14.5   5.1      0.075   13.0   5.1    1.7  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.03   14.2   2.5        1.4    8.8   0.4    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.056   13.6   1.8      0.082   13.1   1.8    1.3  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.062   13.0   0.1      0.074   12.8   0.1    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
      0.075   12.7   3.0        1.7    8.3   0.2    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.083   13.4   0.4         17    6.0   0.0    2.4  2  zf-H2C2_2        Zinc-finger double domain
      0.093   13.3   0.0       0.12   13.0   0.0    1.2  1  RPA_interact_C   Replication protein A interacting C-terminal
       0.11   12.6   0.3         16    5.6   0.0    2.2  2  XPA_N            XPA protein N-terminal
       0.17   11.7   0.1       0.36   10.7   0.1    1.5  1  Rad50_zn_hook    Rad50 zinc hook motif
        0.2   12.2   2.9         13    6.5   0.4    2.4  2  zf-C2H2          Zinc finger, C2H2 type
       0.21   11.4   2.8        5.7    6.8   0.3    2.2  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.25   11.1   3.6        9.1    6.1   1.3    2.3  2  zinc_ribbon_2    zinc-ribbon domain
        0.3   11.2   1.6        5.9    7.0   0.0    2.1  2  CpXC             CpXC protein
       0.43   10.9   9.9        1.9    8.8   9.9    2.0  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   4.9   1.2e-34   8.6e-32       2      84 ..       8      90 ..       7      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.2e-34
                                      XXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-X CS
                   Ribosomal_L37ae  2 tkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksai 80
                                       +k+++aG++g+rYG+++rk v++ie+++ +ky Cp cg+ +v+R+++giw+C+kcg+t+aGg+y+p t+ +++v++++
  gi|386002836|ref|YP_005921135.1|  8 GRKTRSAGRFGPRYGRKIRKLVADIEERSTRKYDCPVCGRIRVRREGTGIWRCTKCGHTFAGGTYIPVTSVGQSVARSV 86
                                      689**************************************************************************** PP

                                      XXXX CS
                   Ribosomal_L37ae 81 rrlk 84
                                      +r+ 
  gi|386002836|ref|YP_005921135.1| 87 KRAV 90
                                      9975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00043      0.31      26      38 ..      38      52 ..      22      53 .. 0.77
   2 !    9.5   0.0    0.0015       1.1       7      15 ..      59      67 ..      57      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                       Zn-ribbon_8 26 lta.CPeCgs.evrr 38
                                       +  CP Cg  +vrr
  gi|386002836|ref|YP_005921135.1| 38 RKYdCPVCGRiRVRR 52
                                      4555*********99 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0015
                       Zn-ribbon_8  7 rCeeCghef 15
                                      rC++Cgh+f
  gi|386002836|ref|YP_005921135.1| 59 RCTKCGHTF 67
                                      9*******9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.6   7.7e-07   0.00055      30      56 ..      41      67 ..      20      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.7e-07
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                      +C++Cg++  ++  +  ++C++Cg+++
  gi|386002836|ref|YP_005921135.1| 41 DCPVCGRIRVRREGTGIWRCTKCGHTF 67
                                      7**********99***********985 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.1   8.2e+02      33      40 ..      41      48 ..      15      51 .. 0.77
   2 !   17.5   3.2   4.1e-06    0.0029      24      44 ..      50      70 ..      44      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                            HalOD2 33 kCtrCGev 40
                                       C  CG +
  gi|386002836|ref|YP_005921135.1| 41 DCPVCGRI 48
                                      57777765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.1e-06
                            HalOD2 24 yrqLGayvWkCtrCGevqaaA 44
                                      +r+ G+ +W+Ct+CG++ a+ 
  gi|386002836|ref|YP_005921135.1| 50 VRREGTGIWRCTKCGHTFAGG 70
                                      6778999**********9886 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.3   6.2e-06    0.0045       2      27 ..      41      65 ..      40      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-06
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                       CP+Cg  + v+ + +g  +Ct+CG 
  gi|386002836|ref|YP_005921135.1| 41 DCPVCGRIR-VRREGTGIWRCTKCGH 65
                                      6*****853.***************5 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.065        47      41      56 .]      30      45 ..      26      45 .. 0.80
   2 !   12.1   0.1   0.00028       0.2      29      39 ..      57      67 ..      48      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.065
                           DUF4379 41 asvsnrtkgsskCpkC 56
                                      a +++r  ++ +Cp C
  gi|386002836|ref|YP_005921135.1| 30 ADIEERSTRKYDCPVC 45
                                      678889866666**** PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00028
                           DUF4379 29 wWkCakCgheW 39
                                       W+C kCgh++
  gi|386002836|ref|YP_005921135.1| 57 IWRCTKCGHTF 67
                                      6********98 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.17   1.2e+02      22      33 ..      36      47 ..      31      48 .. 0.78
   2 !   13.2   0.5   8.9e-05     0.064      25      35 ..      57      67 ..      49      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                     zinc_ribbon_4 22 kgvkvrCskCgh 33
                                      +++k  C+ Cg 
  gi|386002836|ref|YP_005921135.1| 36 STRKYDCPVCGR 47
                                      567888999996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.9e-05
                     zinc_ribbon_4 25 kvrCskCghvF 35
                                        rC+kCgh+F
  gi|386002836|ref|YP_005921135.1| 57 IWRCTKCGHTF 67
                                      569*******9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.2   1.9e-05     0.014       2      21 ..      42      61 ..      41      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                    DNA_ligase_ZBD  2 CPvCGsavvReegeaiyRCt 21
                                      CPvCG   vR eg  i+RCt
  gi|386002836|ref|YP_005921135.1| 42 CPVCGRIRVRREGTGIWRCT 61
                                      *******************9 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   3.7e-05     0.027      15      56 ..      33      68 ..      18      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                              Elf1 15 kkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                       ++  +k+dCp+C+     +v   ++e++++ +C++Cg +f 
  gi|386002836|ref|YP_005921135.1| 33 EERSTRKYDCPVCGRI---RV---RREGTGIWRCTKCGHTFA 68
                                      3446799*******98...33...5779**********9876 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 ?   14.6   4.0   3.3e-05     0.024      20      46 .]      41      66 ..      35      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrkq 46
                                       CP Cg  +++r  t g ++C +C+++
  gi|386002836|ref|YP_005921135.1| 41 DCPVCGRIRVRREGT-GIWRCTKCGHT 66
                                      5*****667777777.********996 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1     3e-05     0.021      11      48 ..      31      67 ..      20      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                               IBR 11 sles.dpnlkwCprpdCeaiieksegcksvtCskCgfef 48
                                       +e+ +  +  Cp   C++i    eg++  +C+kCg+ f
  gi|386002836|ref|YP_005921135.1| 31 DIEErSTRKYDCP--VCGRIRVRREGTGIWRCTKCGHTF 67
                                      46663333566**..9*********************98 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.1    0.0001     0.075       4      35 ..      39      68 ..      39      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                    Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhn...YrCrrCkgtLr 35
                                      +Y C+ Cg     + ++rr+    +rC +C+ t+ 
  gi|386002836|ref|YP_005921135.1| 39 KYDCPVCG-----RIRVRREGtgiWRCTKCGHTFA 68
                                      699*****.....56666665678*******9876 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.027        19      22      35 ..      33      46 ..      31      48 .. 0.84
   2 ?    8.8   0.4     0.002       1.4      29      38 ..      58      67 ..      53      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                           TFIIS_C 22 DEpmtvfykCtkCg 35
                                      +E +t+ y C  Cg
  gi|386002836|ref|YP_005921135.1| 33 EERSTRKYDCPVCG 46
                                      58889999999998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                           TFIIS_C 29 ykCtkCghrW 38
                                       +CtkCgh++
  gi|386002836|ref|YP_005921135.1| 58 WRCTKCGHTF 67
                                      68******98 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.8   0.00011     0.082      18      40 .]      42      64 ..      39      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                     Auto_anti-p27 18 CpvCgvPLmrdrkggkvyCvaCd 40
                                      CpvCg + +r  ++g + C  C+
  gi|386002836|ref|YP_005921135.1| 42 CPVCGRIRVRREGTGIWRCTKCG 64
                                      **********7799********6 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1    0.0001     0.074      20      51 ..      41      71 ..      24      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                      B--STT---.B-EEETTTEEEETTTTEEESS-- CS
                       Rep_fac-A_C 20 ACpsedCnk.KvveeedgewrCekCdkeveepk 51
                                       Cp   C + +v +e+ g wrC kC ++++  +
  gi|386002836|ref|YP_005921135.1| 41 DCP--VCGRiRVRREGTGIWRCTKCGHTFAGGT 71
                                      588..888835666699********99987655 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0024       1.7       4      15 ..      37      48 ..      34      56 .. 0.76
   2 ?    5.1   0.4     0.024        17       5      14 ..      56      65 ..      52      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                                      T-EEE-TTT--E CS
                   Desulfoferrod_N  4 levYkCevCGni 15
                                      + +Y C vCG i
  gi|386002836|ref|YP_005921135.1| 37 TRKYDCPVCGRI 48
                                      678*******98 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                                      -EEE-TTT-- CS
                   Desulfoferrod_N  5 evYkCevCGn 14
                                       +++C+ CG 
  gi|386002836|ref|YP_005921135.1| 56 GIWRCTKCGH 65
                                      689******5 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1      0.04        29      13      21 ..      38      46 ..      33      47 .. 0.80
   2 ?    6.0   0.0     0.024        17      13      25 ..      56      68 ..      48      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.04
                         zf-H2C2_2 13 kpyeCplCd 21
                                      ++y Cp+C+
  gi|386002836|ref|YP_005921135.1| 38 RKYDCPVCG 46
                                      5799****7 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                         zf-H2C2_2 13 kpyeCplCdkaFk 25
                                       ++ C +C+ +F+
  gi|386002836|ref|YP_005921135.1| 56 GIWRCTKCGHTFA 68
                                      5789******995 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016      0.12       2      44 ..      42      85 ..      41      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                    RPA_interact_C  2 CPvCkkrklkets.evifCe.Cglrletseesltleelkrrlaet 44
                                      CPvC + +++++   +  C+ Cg +++   + + ++++ +++a++
  gi|386002836|ref|YP_005921135.1| 42 CPVCGRIRVRREGtGIWRCTkCGHTFAG-GTYIPVTSVGQSVARS 85
                                      ***********9966678*99**99988.5666666666666555 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.032        23      18      25 ..      38      45 ..      37      47 .. 0.86
   2 ?    5.6   0.0     0.022        16       3      12 ..      59      68 ..      58      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                             XPA_N 18 dnFdysVC 25
                                      +++d++VC
  gi|386002836|ref|YP_005921135.1| 38 RKYDCPVC 45
                                      589***** PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                             XPA_N  3 kCdeCgkefl 12
                                      +C +Cg++f+
  gi|386002836|ref|YP_005921135.1| 59 RCTKCGHTFA 68
                                      6********7 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0005      0.36      12      27 ..      32      47 ..      23      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                                      HHHHTT-SEE-TTT-- CS
                     Rad50_zn_hook 12 ieelkeakgcCPlCgR 27
                                      iee + +k +CP+CgR
  gi|386002836|ref|YP_005921135.1| 32 IEERSTRKYDCPVCGR 47
                                      5555556669*****9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.026        19       1       9 [.      40      48 ..      40      53 .. 0.81
   2 ?    6.5   0.4     0.018        13       2      10 ..      59      67 ..      58      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      y Cp+Cg+ 
  gi|386002836|ref|YP_005921135.1| 40 YDCPVCGRI 48
                                      89*****85 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                      EETTTTEEE CS
                           zf-C2H2  2 kCpdCgksF 10
                                      +C++Cg +F
  gi|386002836|ref|YP_005921135.1| 59 RCTKCGHTF 67
                                      8*******9 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.023        17      38      52 ..      33      47 ..      28      49 .. 0.78
   2 ?    6.8   0.3    0.0079       5.7      44      53 ..      57      66 ..      48      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.023
                    zinc_ribbon_10 38 eeleevkyrCpkCga 52
                                      ee ++ ky Cp Cg 
  gi|386002836|ref|YP_005921135.1| 33 EERSTRKYDCPVCGR 47
                                      5566679******96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0079
                    zinc_ribbon_10 44 kyrCpkCgal 53
                                       +rC kCg++
  gi|386002836|ref|YP_005921135.1| 57 IWRCTKCGHT 66
                                      7*******95 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.028        20      16      20 ..      42      46 ..      31      48 .. 0.75
   2 ?    6.1   1.3     0.013       9.1       2       7 ..      60      65 ..      59      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.028
                     zinc_ribbon_2 16 CpyCG 20
                                      Cp CG
  gi|386002836|ref|YP_005921135.1| 42 CPVCG 46
                                      78787 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C++CG+
  gi|386002836|ref|YP_005921135.1| 60 CTKCGH 65
                                      777776 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0083       5.9      25      45 ..      27      47 ..      23      55 .. 0.87
   2 ?    3.7   0.3     0.086        62      38      47 ..      58      67 ..      49      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0083
                              CpXC 25 elkeklldgslfeatCpkCga 45
                                      +l++++ + s +++ Cp Cg+
  gi|386002836|ref|YP_005921135.1| 27 KLVADIEERSTRKYDCPVCGR 47
                                      688999999***********7 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.086
                              CpXC 38 atCpkCgata 47
                                      ++C kCg+t+
  gi|386002836|ref|YP_005921135.1| 58 WRCTKCGHTF 67
                                      7899999987 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.9    0.0027       1.9       2      34 ..      38      69 ..      37      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                                      EEE--TTTT-TTTEEETT....S-EEETTTTB....X CS
                    Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgrGtwfCrqCgg....g 34
                                      ++  CPvCG   r r ++ +g+G w C +C g    g
  gi|386002836|ref|YP_005921135.1| 38 RKYDCPVCG---RIRVRR-EGTGIWRCTKC-GhtfaG 69
                                      7789****9...678777.9**********.536644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 624.98
//
Query:       gi|386002837|ref|YP_005921136.1|  [L=259]
Description: Exosome complex exonuclease 2 [Methanosaeta harundinacea 6Ac]
Scores for 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-28   97.7   0.0    1.5e-27   96.7   0.0    1.5  2  RNase_PH    3' exoribonuclease family, domain 1
    4.1e-08   33.2   0.0    6.4e-08   32.5   0.0    1.3  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   1.7e-31   1.5e-27       1     132 []      31     166 ..      31     166 .. 0.95
   2 ?   -2.5   0.0      0.77   6.9e+03      10      19 ..     213     222 ..     206     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 1.7e-31
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeie 77 
                                       e+R+++++tg++++a+GSa ++lG+t vl++v+ +  e p+++  +++g++ ++ e+ p+as++++  g p++  ie
  gi|386002837|ref|YP_005921136.1|  31 EYREITLQTGTIRKADGSADVRLGKTRVLVGVKIQPGE-PFAD-TPNKGVIITNAELVPLASPNFEP-GPPNEVGIE 104
                                       79**********************************99.7777.556799***************77.9******** PP

                                       HHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  78 lsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       l+r+++r +r+s+ +        ++++ + + id++vl++ g +l+da++++a++AL++a +p
  gi|386002837|ref|YP_005921136.1| 105 LARVVDRGVRESGAIdlpslciaPGEKVWIVFIDVHVLDDCG-NLMDASSLGAIAALMTATVP 166
                                       **************99999999999999**************.*****************998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.77
                                       SSSSTTSEEE CS
                          RNase_PH  10 gvlsqanGSa 19 
                                        v++ a+GS+
  gi|386002837|ref|YP_005921136.1| 213 TVITTADGSV 222
                                       5777888886 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   7.1e-12   6.4e-08       2      66 ..     183     247 ..     182     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.1e-12
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       +++a t   ++d ++ Dp+ +Ee++++ +lt+  + +++v+ ++k+g + l+++++ + +++A +
  gi|386002837|ref|YP_005921136.1| 183 VPVATTAVEFGDAIIFDPDTDEESVADTKLTVITTADGSVCGMQKSGPGFLSQDKIYRIVDIACE 247
                                       7999********************************************99*********999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1869.94
//
Query:       gi|386002838|ref|YP_005921137.1|  [L=251]
Description: Exosome complex exonuclease 1 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-34  116.9   0.0    1.2e-33  116.4   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    1.1e-14   54.2   0.0    1.8e-14   53.5   0.0    1.4  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   1.3e-37   1.2e-33       1     132 []      21     150 ..      21     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 1.3e-37
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CC.EEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddae.galdveveyapfasgerrregrpsdeei 76 
                                       elR+++ie gvl++a+GS+y+e+Gd+kv+a+v+gp+e++p+   ++++   +  ++++a+f+ +er+r   p++++ 
  gi|386002838|ref|YP_005921137.1|  21 ELRPIKIEVGVLERADGSCYIEMGDNKVIAAVYGPREVHPRHL-QEVTrAIVRYRYNMASFSVEERKR-PGPDRRSY 95 
                                       79************************************77776.444424499999999*******77.56****** PP

                                       HHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       e+s++  +al ++il++ +p+s +di+++vl++d  ++  a inaas+ALadagip
  gi|386002838|ref|YP_005921137.1|  96 EVSKVSREALASVILTSYFPRSVVDIFVEVLQADA-GTRTAGINAASVALADAGIP 150
                                       ***********************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0     2e-18   1.8e-14       2      65 ..     154     215 ..     153     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2e-18
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAk 65 
                                       ++++++ gkvd+++vlDp k E++ +e+d+++a++  +e+ tl++++g  l+++++ +a+elAk
  gi|386002838|ref|YP_005921137.1| 154 LISSCAAGKVDGEIVLDPMKAEDNFGEADVPIAMTPGGEI-TLLQMDGR-LSRDEFRRALELAK 215
                                       7899**********************************99.********.*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 2095.98
//
Query:       gi|386002839|ref|YP_005921138.1|  [L=232]
Description: Exosome complex RNA-binding protein RRP4 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-09   36.9   0.1      7e-09   35.9   0.1    1.5  1  KH_6      KH domain
    5.8e-07   29.8   0.1    1.5e-06   28.4   0.0    1.7  2  S1        S1 RNA binding domain
    1.5e-06   27.9   0.2    5.4e-06   26.1   0.0    2.0  2  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    1.8e-05   24.4   0.0    4.1e-05   23.3   0.0    1.5  1  KH_1      KH domain
    5.4e-05   22.9   0.0    0.00011   22.0   0.0    1.6  1  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   1.9e-12     7e-09       1      44 [.     148     194 ..     148     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.9e-12
                              KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvkses 44 
                                       G + e+s+  v+Rl+     ++ +L+k++ +++ vG+NGriWv++++
  gi|386002839|ref|YP_005921138.1| 148 GRVAEISPTRVPRLIgkgGSMINMLKKELNCNLFVGQNGRIWVDGND 194
                                       6789***********888444488888899**************876 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4     5e+03      27      49 ..      12      33 ..       7      41 .. 0.60
   2 !   28.4   0.0   4.3e-10   1.5e-06       2      72 ..      66     135 ..      65     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                                      TEEEEEEGGGSSSSCEESCHHHC CS
                                S1 27 gvegfvpaselsrdarvedpdev 49
                                      +  + vp  +ls+d++  +++ +
  gi|386002839|ref|YP_005921138.1| 12 DRNVVVPGDLLSDDPK-ASGEGT 33
                                      5567788888888833.333333 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 4.3e-10
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEE CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriil 72 
                                       p+ g+ v G+V++++  + +V++  + eg++++sel+r+    + ++ l++G  v  +v +vd + + + l
  gi|386002839|ref|YP_005921138.1|  66 PAPGDTVIGTVQDIVFSNWIVNINSPYEGLLHISELPRKIEMNEMSKYLRIGSSVMTRVKDVDSTMK-VEL 135
                                       678************************************88889999****************9977.665 PP

>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.5e-09   5.4e-06       1      33 [.      15      46 ..      15      49 .. 0.89
   2 ?   -1.2   0.1      0.51   1.8e+03       4      12 ..      68      77 ..      67      80 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.5e-09
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaG 33
                                      +V+PG+ l +d++  +G+GTYv++g++++ + G
  gi|386002839|ref|YP_005921138.1| 15 VVVPGDLLSDDPK-ASGEGTYVKDGKVRSLLYG 46
                                      69******66666.89**************999 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.51
                                      TT-EE.EETT CS
                            ECR1_N  4 PGevl.ttde 12
                                      PG+++ +t +
  gi|386002839|ref|YP_005921138.1| 68 PGDTViGTVQ 77
                                      6776655555 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.1e-08   4.1e-05       6      63 ..     153     203 ..     149     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-08
                                       EGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHH CS
                              KH_1   6 vPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkel 63 
                                       +    v+r+IGkgGs+I+ +++e +++  v  +      +  + + G+ ++ + A++ 
  gi|386002839|ref|YP_005921138.1| 153 ISPTRVPRLIGKGGSMINMLKKELNCNLFVG-Q------NGRIWVDGNDDDMDLALKT 203
                                       66667*****************88****975.3......2357777766667777665 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.1e-08   0.00011      31      68 ..     153     190 ..     126     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.1e-08
                                       EEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                              KH_2  31 iresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                       i   +  ++IGkgGs+i++++kel+ ++ + +++++++
  gi|386002839|ref|YP_005921138.1| 153 ISPTRVPRLIGKGGSMINMLKKELNCNLFVGQNGRIWV 190
                                       6678999******************9999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1486.94
//
Query:       gi|386002840|ref|YP_005921139.1|  [L=232]
Description: hypothetical protein Mhar_2164 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-24   84.6   0.0    7.2e-24   83.7   0.0    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    8.6e-20   70.9   0.0    1.4e-19   70.2   0.0    1.4  1  SBDS_C    SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0     8e-28   7.2e-24       3      88 .]       8      93 ..       6      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 8e-28
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiq 81
                                      +++r+k +++ Fe++v+++ +l yr+g + dL+++l++e++F+na +G++ s+++l  af+t+++  i+ +ILkkGeiq
  gi|386002840|ref|YP_005921139.1|  8 VTARLKTHGTVFEVLVDPEGALAYRQGDDLDLEKILAAEDVFENAGRGDRSSEEDLLRAFETTDVLTIAAKILKKGEIQ 86
                                      789**************************************************************************** PP

                                      --HHHHH CS
                              SBDS 82 vsaeerk 88
                                      ++a++rk
  gi|386002840|ref|YP_005921139.1| 87 LTADQRK 93
                                      ****997 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   1.6e-23   1.4e-19       2     113 ..     100     215 ..      99     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 1.6e-23
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       ++++++++a +++npqt++p+++ +Ie+a++e++++v+++ks+++ +  ++ka++ +ipi+++++ +++++p + + 
  gi|386002840|ref|YP_005921139.1| 100 RRQVVHVIATNAINPQTGTPHPPARIERAMEEAHFNVDPTKSVEEMVNLAMKAIRPIIPIRFEEVDVAVKIPPAYAP 176
                                       789*********************************************************************66654 PP

                                       CHHHHHHHH.HH........S.EEEEEEEEGGGHHHHHH CS
                            SBDS_C  79 kilklieqv.esqk..vae.kewevvvliePgaykelee 113
                                       k+   i++  + q   +++ ++w  vv  ++g+++e+  
  gi|386002840|ref|YP_005921139.1| 177 KAYGEIASFgKLQReqWQNdGSWIGVVRLPAGLQNEFYG 215
                                       444444444222222233323355555588888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1540.42
//
Query:       gi|386002841|ref|YP_005921140.1|  [L=250]
Description: Proteasome subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete 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-58  196.4   0.4    4.1e-58  196.0   0.4    1.2  1  Proteasome      Proteasome subunit
    1.1e-14   53.8   0.5    4.1e-14   51.9   0.1    2.1  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.0   0.4   4.5e-62   4.1e-58       1     190 []      32     216 ..      32     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 4.5e-62
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       v++Gtt+vGik+ dgv++ +dkr+t  s l++++++eKif+id+hig+a++Gl+aDar+l++rar+e q  rl y++
  gi|386002841|ref|YP_005921140.1|  32 VRRGTTAVGIKAVDGVAVLVDKRIT--SRLMEPESIEKIFQIDQHIGAATSGLVADARVLIDRARVESQINRLVYDE 106
                                       679**********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        i ve+l++++++ +q ytq++g+rpfg slli+g d+    +L+++dpsG+++e+k a+ iG g+ a+++++e++y
  gi|386002841|ref|YP_005921140.1| 107 SIGVEVLAKKICDFKQTYTQYGGVRPFGTSLLIVGADDAR-VRLFETDPSGALLEYK-ATGIGAGRSAVMEIFEEKY 181
                                       *************************************665.9**************8.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       +ed++ +ea+ l ++al++a+e+ k+  ++ e++vi
  gi|386002841|ref|YP_005921140.1| 182 REDMNCDEAILLGLEALYKAAEG-KFEASTTEIGVI 216
                                       **********************5.599999999987 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1   4.6e-18   4.1e-14       1      23 []       9      31 ..       9      31 .. 0.99
   2 ?   -0.9   0.0      0.15   1.4e+03      13      18 ..      67      72 ..      67      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 4.6e-18
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr++t+FSPdGRLfQVEYA +A
  gi|386002841|ref|YP_005921140.1|  9 YDRAITVFSPDGRLFQVEYAREA 31
                                      *********************99 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
                    Proteasome_A_N 13 RLfQVE 18
                                      ++fQ++
  gi|386002841|ref|YP_005921140.1| 67 KIFQID 72
                                      79**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1568.17
//
Query:       gi|386002842|ref|YP_005921141.1|  [L=178]
Description: ribonuclease P protein component 2 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-14   53.0   0.1    4.7e-14   52.5   0.1    1.2  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.1   2.6e-18   4.7e-14       1     103 []      13     108 ..      13     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.6e-18
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT-- CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlit 77 
                                       RY+++e+  +    +++  +l+ +ir++ ++lfGd+g++k +   +v++f+   + +++R  +  +++++a L++++
  gi|386002842|ref|YP_005921141.1|  13 RYIAFEVEAEG---RVRGGDLVAEIRAAQTSLFGDLGAAKNRL--RVISFDG--RFGLLRSTHTRTEECRALLATVN 82 
                                       9**********...4678*******************998877..8888887..9********************** PP

                                       EETTEEEEEEEEEEESSHHHHHHHTT CS
                     RNase_P_Rpp14  78 kiegrpvvfrvvrvsGTikkaeeeai 103
                                       +++g+++ +rv ++sG+ik+a e++i
  gi|386002842|ref|YP_005921141.1|  83 SVGGMRAAIRVRGISGSIKAATEKYI 108
                                       **********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1272.99
//
Query:       gi|386002843|ref|YP_005921142.1|  [L=228]
Description: ribonuclease P protein component 3 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-37  129.0   0.0      2e-37  128.8   0.0    1.1  1  RNase_P_p30  RNase P subunit p30
     0.0003   21.1   0.0    0.00033   21.0   0.0    1.2  1  PHP          PHP domain


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.0   2.2e-41     2e-37       3     213 ..       6     207 ..       4     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 2.2e-41
                                       EEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H CS
                       RNase_P_p30   3 lnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpsk 79 
                                        n +  +++s++ sr+++ +++lgy g++i++++   +  +p   e           ++ g++++ + ++v+sd+++
  gi|386002843|ref|YP_005921142.1|   6 PNLHSLPEGSASASRLALAAKRLGYAGIIITNHTT--TCGRPIGVE--------AARRVGGIEVVIGAEIVASDQRS 72 
                                       67888899999999*********************..444444444........4589999***************9 PP

                                       ..HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HH CS
                       RNase_P_p30  80 l.qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsgl 155
                                       l  + + +r ++d lav++++ek++raace ++vD++ ++  +  + g+  + ++aA e++va+ +++sp++  +g 
  gi|386002843|ref|YP_005921142.1|  73 LhSKAASLRERVDFLAVHGGDEKINRAACEEPNVDLLAHPHQG--RAGIGVAAAKAAQENQVAIALDLSPMILLRGP 147
                                       88***************************************98..889999************************** PP

                                       HHHHHHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTT CS
                       RNase_P_p30 156 aRrnfisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavs 213
                                       aR+++++ +r+ l l  +   ++ i+ g +s+l+lR+p+++++++++lGL+ dra+ea+s
  gi|386002843|ref|YP_005921142.1| 148 ARIRWMETVRRDLDLFGKfdIPLMITTGGRSHLDLRSPRELTAMAALLGLDRDRASEAFS 207
                                       ******************99*************************************987 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.7e-08   0.00033      11      74 ..      12     100 ..       8     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.7e-08
                                       -.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                               PHP  11 ldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse.............. 73 
                                        +g++s++ l+ +ak+lg+  i iT h    g +  ++aa+  + +gi+++iG+e  va+d++              
  gi|386002843|ref|YP_005921142.1|  12 PEGSASASRLALAAKRLGYAGIIITNHTTTCGRPIGVEAAR--RVGGIEVVIGAE-IVASDQRslhskaaslrervd 85 
                                       5688888999******************************6..5569********.444444446666666665555 PP

                                       ............... CS
                                       ..............x RF
                               PHP  74 ..............k 74 
                                                      
  gi|386002843|ref|YP_005921142.1|  86 flavhggdekinraA 100
                                       555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1627.24
//
Query:       gi|386002844|ref|YP_005921143.1|  [L=138]
Description: hypothetical protein Mhar_2168 [Methanosaeta harundinacea 6Ac]
Scores for 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-38  129.3   0.1    9.9e-38  129.1   0.1    1.0  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.1   5.5e-42   9.9e-38       1     118 [.       4     119 ..       4     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 5.5e-42
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHH CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLl 77 
                                       ++++rafv +TEdeekV+eals ++p+e+  ++++++ Gh+gn+i+il + l+kk+ ++++++l+e l+e ei +L+
  gi|386002844|ref|YP_005921143.1|   4 RVTFRAFVASTEDEEKVREALSLFVPPES--LTRTRVVGHHGNEIIILAIDLRKKEGLRFFDRLREVLSEGEIARLR 78 
                                       699***********************995..99*********************999******************** PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                       +e++ rvd++++l++rldKQaay+g+ +l++++d+I+v ++
  gi|386002844|ref|YP_005921143.1|  79 REVDLRVDDECRLHFRLDKQAAYRGVARLTDSGDSITVSAH 119
                                       **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 882.62
//
Query:       gi|386002845|ref|YP_005921144.1|  [L=208]
Description: 50S ribosomal protein L15e [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-83  278.7   7.3    2.4e-83  278.5   7.3    1.0  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.5   7.3   1.4e-87   2.4e-83       1     191 []      16     203 ..      16     203 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.5 bits;  conditional E-value: 1.4e-87
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y+y+r++wk+++++++ el +erl+ +r+e +v++++rptrldrAr+LGYkakqGi+vvrv+vrrGgr+k  s++
  gi|386002845|ref|YP_005921144.1|  16 SFYAYIRDAWKTPSESYVGELRQERLIGWRREASVQKIDRPTRLDRARALGYKAKQGITVVRVKVRRGGRRK--SRY 90 
                                       68**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       ++gr++k++g nk++  kslq+iaeer+gr++pn++vLnSYwvgeDg++k+yEvilvDp+h+ai +d+++ wi   +
  gi|386002845|ref|YP_005921144.1|  91 IRGRRSKHMGANKITAGKSLQRIAEERAGRRHPNMEVLNSYWVGEDGMQKWYEVILVDPNHPAIASDPDLAWISGGS 167
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsrran 191
                                       h++R+ rG+tsagk++RGlrkkg  gaek+r+s+ran
  gi|386002845|ref|YP_005921144.1| 168 HRGRANRGKTSAGKRGRGLRKKG-IGAEKVRPSIRAN 203
                                       ***********************.99*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1268.18
//
Query:       gi|386002846|ref|YP_005921145.1|  [L=158]
Description: hypothetical protein Mhar_2170 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1034.56
//
Query:       gi|386002847|ref|YP_005921146.1|  [L=479]
Description: hypothetical protein Mhar_2171 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-227  755.1   0.2   2.2e-227  754.9   0.2    1.0  1  DUF2114   Uncharacterized protein conserved in archaea (DUF21
     0.0099   15.8   0.1      0.018   15.0   0.1    1.4  1  Borealin  Cell division cycle-associated protein 8


Domain annotation for each model (and alignments):
>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  754.9   0.2  2.4e-231  2.2e-227       1     448 [.      30     475 ..      30     476 .. 0.99

  Alignments for each domain:
  == domain 1  score: 754.9 bits;  conditional E-value: 2.4e-231
                           DUF2114   1 eyyivasvelGntttkciltatnletgktyllnktvkmtrdvrkpkegeevfgktlagveltresvaelvrdtlles 77 
                                       +yyivasve+Gn+ttkciltatn+++g+t+++nktvkmtrdvrkp++geevf++tl+g++ltresv+elvrdtlles
  gi|386002847|ref|YP_005921146.1|  30 PYYIVASVEVGNSTTKCILTATNMKNGQTRIVNKTVKMTRDVRKPRPGEEVFAHTLCGTPLTRESVSELVRDTLLES 106
                                       7**************************************************************************** PP

                           DUF2114  78 lkkakldieedldfvvrstGvvagfdspeevgelikaladGCleagvppkkmtpamskenlpeklrkyslldkvvfd 154
                                       + +a+l+i++dl+fvvrstGvvagf+sp+evg++i+aladGCl agvpp+ mtpams++n+p+++r ysl++k+vf+
  gi|386002847|ref|YP_005921146.1| 107 HATARLSIKDDLNFVVRSTGVVAGFSSPDEVGTFIQALADGCLIAGVPPRLMTPAMSIQNIPDRFRPYSLMEKIVFN 183
                                       ***************************************************************************** PP

                           DUF2114 155 GavasvvpPkgktgvevvanemegeLvtaGikegakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGla 231
                                       G vasv+pPkg+tgve+vanemegeL+taGikeg+kwtdvdfrnPc+s+dfGttLdGri++ e+Py++t+gnfcGla
  gi|386002847|ref|YP_005921146.1| 184 GPVASVFPPKGSTGVEIVANEMEGELATAGIKEGSKWTDVDFRNPCLSLDFGTTLDGRITSAEMPYSNTIGNFCGLA 260
                                       ***************************************************************************** PP

                           DUF2114 232 GaipdaivrGtglvdkklgaaldlfkekkkkkkkkkkikeyaekihelidiekvPkdrerfGtvPvdakaaeeagvv 308
                                       Gaipda+++Gtglvd ++g++ldlf+ kk   k ++++++ya+ i+e+i+ie+vP +r+r+G+vPvd++aae++gvv
  gi|386002847|ref|YP_005921146.1| 261 GAIPDALIQGTGLVDPQTGTTLDLFSGKK--VKVDRTARDYARVIDEHIRIERVPVGRSRYGSVPVDPAAAEKIGVV 335
                                       **************************777..788899**************************************** PP

                           DUF2114 309 liGcdvgengsdlekleeigaeilekeglkvllavldevsakivkrlievaveeglveektaiGitGragitGkkpe 385
                                       liGcdvgengs+l++l+++g++i++++glk+l+a++d  +a  ++rl++vav+ glv+++taiG+tGragi+G+kpe
  gi|386002847|ref|YP_005921146.1| 336 LIGCDVGENGSELNRLSQLGRKIHQEKGLKTLFAAIDVAAAITARRLVKVAVDAGLVTRDTAIGVTGRAGISGNKPE 412
                                       ***************************************************************************** PP

                           DUF2114 386 lilekieelglyddkeenvvfvddgLarGaavmarCmnslGtpknPlGGvrggkCilkkrikl 448
                                       lile+i +lglyd++e+n+vfvddgLarGaavmarCmns+Gtp++P+GG rgg Cil++ri++
  gi|386002847|ref|YP_005921146.1| 413 LILEEIGTLGLYDQPEKNIVFVDDGLARGAAVMARCMNSMGTPRHPMGGLRGGGCILRQRIEY 475
                                       ************************************************************986 PP

>> Borealin  Cell division cycle-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     2e-06     0.018      28      68 ..      54      97 ..      35     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
                          Borealin 28 tslitpkvdprlpkt.llRtpkagErvlsls..GSPlaegvvte 68
                                          t+ v++ + +t  +R+p++gE v+  +  G+Pl  ++v+e
  gi|386002847|ref|YP_005921146.1| 54 KNGQTRIVNKTVKMTrDVRKPRPGEEVFAHTlcGTPLTRESVSE 97
                                      4456777888999**99***********99999****9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3014.61
//
Query:       gi|386002848|ref|YP_005921147.1|  [L=373]
Description: geranylgeranyl reductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-17   63.0   0.1    1.9e-06   27.4   0.0    3.1  2  FAD_binding_3   FAD binding domain
      3e-11   43.0   0.0    4.9e-05   22.5   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    1.4e-09   38.1   0.7     0.0015   18.2   0.0    2.4  3  DAO             FAD dependent oxidoreductase
    6.3e-08   32.2   0.2    3.3e-07   29.8   0.2    1.8  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.4e-07   29.5   0.0    1.8e-06   28.1   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.1e-05   24.7   0.2    1.8e-05   24.0   0.2    1.3  1  FAD_binding_2   FAD binding domain
    1.3e-05   24.1   0.2    0.00063   18.6   0.1    2.1  2  HI0933_like     HI0933-like protein
    2.8e-05   23.4   0.0     0.0008   18.6   0.2    2.1  2  GIDA            Glucose inhibited division protein A
    4.9e-05   23.8   0.1     0.0014   19.2   0.1    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    9.8e-05   21.4   0.1      0.099   11.5   0.1    3.0  2  Trp_halogenase  Tryptophan halogenase
    0.00033   20.2   0.2    0.00042   19.8   0.2    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0032   16.7   0.0     0.0056   16.0   0.0    1.3  1  Thi4            Thi4 family
       0.01   16.1   0.0       0.02   15.1   0.0    1.5  1  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.019   14.2   0.0       0.07   12.4   0.0    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.057   13.3   0.1      0.091   12.6   0.1    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.059   12.7   0.1        0.1   11.8   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.062   12.6   0.0       0.11   11.9   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
        0.1   13.1   0.0       0.19   12.2   0.0    1.5  1  XdhC_C          XdhC Rossmann domain
        0.1   12.2   0.0       0.19   11.3   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.23   11.0   0.0       0.37   10.3   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   5.2e-09   4.6e-06       4      34 ..       4      34 ..       1      44 [. 0.92
   2 !   27.4   0.0   2.1e-09   1.9e-06     113     326 ..      99     284 ..      82     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.2e-09
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       ++VGaGpaG ++a++Lse G +v+l+++ +
  gi|386002848|ref|YP_005921147.1|  4 AAVVGAGPAGSTAARFLSEMGHKVLLIDRKE 34
                                      68**************************986 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.1e-09
                                       HHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEE CS
                     FAD_binding_3 113 ehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvld 189
                                         ae +g++v  +++ve    + + ++ ++r +  g  et+ra+ +vGaDG  S+v+k++g +    +++       
  gi|386002848|ref|YP_005921147.1|  99 RLAEGAGAEVALERKVE----EIDPESGVLRLR--GG-ETIRAEAIVGADGPASRVAKSIGAR----NRL------- 157
                                       55555555555555555....223333444444..33.48*********************66....444....... PP

                                       EEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEE CS
                     FAD_binding_3 190 vlfdadlsdiveplvlilsaesrgvmviPlentlerfyvqvearaekeersekfteeevkarlreivgektldveie 266
                                        l++a++++++ +  +i++  +r    +P e         + + +++e+ + ++     +  l++ + +++++ ei 
  gi|386002848|ref|YP_005921147.1| 158 -LPAAQVEMTWPEDDAIYAIIDRD---LPSEP------YSCWIFPKNERGTANVGCFGTVPTLEAFISKYRIEGEIV 224
                                       .44444443333323333333333...34455......4445556677888899999999***************** PP

                                       EEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS CS
                     FAD_binding_3 267 evsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeA 326
                                       e++   +   vae++++gr  l+GDA   + P +G Gl  a++ a   a ++  +l+Ge 
  gi|386002848|ref|YP_005921147.1| 225 EKNGGAIPLGVAERLQRGRAVLIGDAGGLTNPFTGGGLYPAARSARIAAEAIDRFLRGET 284
                                       **************************************9999999999999999999875 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.5e-08   4.9e-05       3     145 ..       5     147 ..       4     164 .. 0.81
   2 !   18.4   0.0     1e-06    0.0009     234     298 ..     222     288 ..     212     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.5e-08
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga....leecvehsWsgtivylddgkki 75 
                                       +v+GaGpAg   A  l  +++g kv+li+  + +  p +     + + l +      ++++ + + ++v +++ ++ 
  gi|386002848|ref|YP_005921147.1|   5 AVVGAGPAGSTAARFL--SEMGHKVLLIDRKEVVGVPKQCAEGLFAACLPEfetaVGDFITGKVPYLEVVFPNRASY 79 
                                       69*******9999999..***********999887777765444444444334447899999999***********9 PP

                     Lycopene_cycl  76 llgraYgrvsskrlkeellerlvengv.klleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                        +  +  ++ + r+ ++ll+    +g+   le kve++ +e+    +  l gg++ira ++v a g as+ 
  gi|386002848|ref|YP_005921147.1|  80 RVRGEVLMLDRPRFDQHLLRLAEGAGAeVALERKVEEIDPESG---VLRLRGGETIRAEAIVGADGPASRV 147
                                       9999**************987775555156899*******999...999*****************55444 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1e-06
                     Lycopene_cycl 234 evveeEqgviPvtlggslprl.eqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....s 298
                                       e+ve+  g iP+   g ++rl   + + iG a+gl+ P TG  +  + + a++ a+ai + lr +    +
  gi|386002848|ref|YP_005921147.1| 222 EIVEKNGGAIPL---GVAERLqRGRAVLIGDAGGLTNPFTGGGLYPAARSARIAAEAIDRFLRGEtrtiE 288
                                       899*********...4444440456899*********************************997644441 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0015       3      33 ..       5      37 ..       3      56 .. 0.89
   2 !   18.1   0.0   1.7e-06    0.0015     143     248 ..      88     183 ..      67     225 .. 0.74
   3 ?   -2.7   0.1       3.8   3.4e+03       8      65 ..     229     276 ..     228     313 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                                      EEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      +++G+G +G+++A++L++ g  V+l+++++ +g
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGhkVLLIDRKEVVG 37
                                      8****************99999******97665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.7e-06
                                       EEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTT..TSE CS
                               DAO 143 vdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllkel..dlp 216
                                       +d  ++ + l+r ae +G+e+ ++++v++++  + +v ++    + ge+ +a+a+V a G+ s+ +   k +  + +
  gi|386002848|ref|YP_005921147.1|  88 LDRPRFDQHLLRLAEGAGAEVALERKVEEIDP-ESGVLRL----RgGETIRAEAIVGADGPASRVA---KSIgaRNR 156
                                       5788999***********************54.3344444....2266644588*********977...55544567 PP

                                       EEEEEEEEEEEEECCTHSTGSGCSEEEEE..EEE CS
                               DAO 217 ispvrgqvlvlkplseklvspaailpvpe..tdd 248
                                       + p+    ++  p ++      ai+++ +     
  gi|386002848|ref|YP_005921147.1| 157 LLPAAQVEMTW-PEDD------AIYAIIDrdLPS 183
                                       78877777777.6554......666666533333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.8
                                       SHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHH CS
                               DAO   8 GiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlsleal 65 
                                       G i l++A  L +rg  V++ ++g   g  +   ++g l+++ r        ar ++ea+
  gi|386002848|ref|YP_005921147.1| 229 GAIPLGVAERL-QRGraVLIGDAG---G-LTNPFTGGGLYPAAR-S------ARIAAEAI 276
                                       55555666666.555545544444...2.334444444444332.1......14444444 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.2   3.7e-10   3.3e-07       2     111 ..       3     145 ..       2     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.7e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHC..SHHHHCHHHHHHHHHHHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclng..gcllskallgvaedaeias................... 57 
                                       + +v+G+GpAG +aa++l++ g+kv+l+ ++++++++  +c     ++  +e++  a                    
  gi|386002848|ref|YP_005921147.1|   3 SAAVVGAGPAGSTAARFLSEMGHKVLLI-DRKEVVGVpkQCAEGLFAACLPEFET-AVgdfitgkvpylevvfpnra 77 
                                       569*************************.66666555114444444444444443.335888888999999999999 PP

                                       .................HHHHCHHHH..CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE CS
                                       .................xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .................evvkklnqg..ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssp 111
                                                        +++ +l +g   e+ l+++v +idp+++ + l       +e+i ++++v A G  +
  gi|386002848|ref|YP_005921147.1|  78 syrvrgevlmldrprfdQHLLRLAEGagAEVALERKVEEIDPESGVLRL-----RGGETIRAEAIVGADGPAS 145
                                       999999999999999995555554443488888889999**99999999.....4578999999999988444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0     2e-09   1.8e-06       1      32 [.       6      37 ..       6      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G++aA++L++ g++vll+++ + +G
  gi|386002848|ref|YP_005921147.1|  6 VVGAGPAGSTAARFLSEMGHKVLLIDRKEVVG 37
                                      8**************************99887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2     2e-08   1.8e-05       3      51 ..       5      52 ..       3      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2e-08
                                      EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT.. CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlsp 51
                                       V+G+G AG +AA  ++e G+kv++++ ++++g   ++++G ++a l p
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGHKVLLIDRKEVVGVPKQCAEGLFAACL-P 52
                                      7******************************************9988.4 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1     7e-07   0.00063       3      36 ..       4      37 ..       2      39 .. 0.92
   2 ?    3.4   0.0     0.029        26     115     176 ..      97     157 ..      94     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7e-07
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                       +v+G+G+AG  aA  +++ g++Vll+++++ +g
  gi|386002848|ref|YP_005921147.1|  4 AAVVGAGPAGSTAARFLSEMGHKVLLIDRKEVVG 37
                                      78**************************998776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.029
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS..-GGGT--SHH CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS..iPklGstgkg 176
                                       ll+ ++ ag ++ le++v++++  e+g   ++++++e+++a+++v A G +S  + ++G+ +  
  gi|386002848|ref|YP_005921147.1|  97 LLRLAEGAGAEVALERKVEEIDP-ESG--VLRLRGGETIRAEAIVGADGPASrvAKSIGARNRL 157
                                       777788899************54.444..4556679***********99988323456666555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   8.9e-07    0.0008       3      29 ..       5      33 ..       3      61 .. 0.82
   2 ?    2.5   0.0     0.067        60     114     161 ..     110     154 ..      79     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.9e-07
                                      EEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLi..t 29
                                       V+G+G AG+ AA  ++++G+kvlLi   
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGHKVLLIdrK 33
                                      69***********************9540 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.067
                                       EES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTE CS
                              GIDA 114 ieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigek 161
                                       +e++vee+++   +  +++++ geti+a+a+v a G+ ++    ig +
  gi|386002848|ref|YP_005921147.1| 110 LERKVEEIDP---ESGVLRLRGGETIRAEAIVGADGPASRVAKSIGAR 154
                                       5677888888...444578999***************88888777765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.5e-06    0.0014       2      35 ..       4      37 ..       3      49 .. 0.88
   2 ?    1.9   0.0      0.37   3.3e+02      42      71 ..      93     122 ..      82     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      ++vvG+G  g  +A +l+e+g+kV +++r++ + 
  gi|386002848|ref|YP_005921147.1|  4 AAVVGAGPAGSTAARFLSEMGHKVLLIDRKEVVG 37
                                      79****************************9887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsed 71 
                                       + + l +  e  g ev l++kveei+ ++ 
  gi|386002848|ref|YP_005921147.1|  93 FDQHLLRLAEGAGAEVALERKVEEIDPESG 122
                                       5566777788889************97764 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00011     0.099       3      36 ..       5      35 ..       3      47 .. 0.90
   2 !    5.4   0.0    0.0079         7     151     217 ..      88     151 ..      85     302 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseei 36
                                       +vG+G+aG++aA  l++++   ++v+l++ +e+
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMG---HKVLLIDRKEV 35
                                      69******************...89****98876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0079
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIII CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqa 217
                                       ld+ +++++L r ae +G ++   + ve ++d++  v  lrl  g+++ a+ ++ + G ++++ ++ 
  gi|386002848|ref|YP_005921147.1|  88 LDRPRFDQHLLRLAEGAGAEVALERKVE-EIDPESGV--LRLRGGETIRAEAIVGADGPASRVAKSI 151
                                       7899999999999999999987665543.34443334..6666788999998888888888776653 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   4.7e-07   0.00042       4      35 ..       6      37 ..       4     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.7e-07
                      FAD_oxidored  4 VvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      VvG+gpaG +AA    ++G kvlL+++++v+G
  gi|386002848|ref|YP_005921147.1|  6 VVGAGPAGSTAARFLSEMGHKVLLIDRKEVVG 37
                                      9****************************999 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.2e-06    0.0056      21      54 ..       5      37 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.2e-06
                                      EEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 21 vivGaGssGLtaayylakkpdlkvailersvspG 54
                                      ++vGaG++G taa+ l++  + kv++++r+  +G
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEM-GHKVLLIDRKEVVG 37
                                      69****************9.********997666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.2e-05      0.02       2      31 ..       5      34 ..       4      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkde 31
                                      +++G+G  G++ a+ Lse g+ +v++id++e
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEmGH-KVLLIDRKE 34
                                      79****************777.6*****987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05      0.07       2      33 ..       6      36 ..       5      41 .. 0.93
   2 ?   -1.1   0.0      0.98   8.8e+02      81     133 ..      91     142 ..      64     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnig 33
                                      ++GaGPaG +aa  l ++g  ++l +++++++
  gi|386002848|ref|YP_005921147.1|  6 VVGAGPAGSTAARFLSEMGH-KVLLIDRKEVV 36
                                      8******************9.7******9987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.98
                       Pyr_redox_3  81 kealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtG 133
                                         + ++l ++a+    ++ l+ +Ve++++e++  +++   et++A+ ++ A G
  gi|386002848|ref|YP_005921147.1|  91 PRFDQHLLRLAEGAGAEVALERKVEEIDPESGVLRLRG-GETIRAEAIVGADG 142
                                       55566677777888888889999999998887777653.45777777776655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1    0.0001     0.091       2      32 ..       4      34 ..       3      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdise 32
                                       av+GaG  G+  a  + + g++V l+d++e
  gi|386002848|ref|YP_005921147.1|  4 AAVVGAGPAGSTAARFLSEMGHKVLLIDRKE 34
                                      69**************************986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012       0.1      32      61 ..       5      34 ..       3      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      EEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlDvrp 61
                                       v+G+G aG  A++  +++g kV ++D ++
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGHKVLLIDRKE 34
                                      69*************************875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.11      40      70 ..       5      35 ..       2      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                      EEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 40 GiiGlGrIGqavakrlkafgmkviaydrskk 70
                                      +++G+G  G+++a+ l+++g kv+ +dr++ 
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGHKVLLIDRKEV 35
                                      79**************************976 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.19       2      63 ..       5     100 ..       4     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.................................. CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.................................. 44 
                                       +++Gag+ +   ar+++++g +v ++d +e +  +++ +   e                                  
  gi|386002848|ref|YP_005921147.1|   5 AVVGAGPAGSTAARFLSEMGHKVLLIDRKEVVGVPKQCA---Eglfaaclpefetavgdfitgkvpylevvfpnras 78 
                                       599*************************99877444443...22333444444445555555555555555555555 PP

                                       ...-EEEE--S-HHHHHHHHHH CS
                            XdhC_C  45 ...tavvvlthdhklDaealea 63 
                                             v++   +++D+++l+ 
  gi|386002848|ref|YP_005921147.1|  79 yrvRGEVLMLDRPRFDQHLLRL 100
                                       6666666666677777776665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.19       2      31 ..       5      34 ..       4      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr 31
                                      a++GaG  Gs+ a  L++ g++v li+r++
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGHKVLLIDRKE 34
                                      79**************************86 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00042      0.37       4      33 ..       5      34 ..       2      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                                      EEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                    UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDide 33
                                      +v+G+G  G + a  l+e+gh+v+++D  e
  gi|386002848|ref|YP_005921147.1|  5 AVVGAGPAGSTAARFLSEMGHKVLLIDRKE 34
                                      79*************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2417.48
//
Query:       gi|386002849|ref|YP_005921148.1|  [L=602]
Description: von Willebrand factor, type A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   64.9   0.0    1.9e-17   64.1   0.0    1.3  1  VWA       von Willebrand factor type A domain
      1e-15   58.3   0.0    1.2e-14   54.8   0.1    2.2  2  VWA_2     von Willebrand factor type A domain
      3e-07   30.5   0.0      6e-07   29.5   0.0    1.5  1  VWA_3     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   3.1e-21   1.9e-17       1     172 [.      65     233 ..      65     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3.1e-21
                                       EEEEEEE-STTSCHHHHH.HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGG CS
                               VWA   1 DivfvlDgSgsmgeenfe.kvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgg 76 
                                       D+v+++D+S sm+e + +  +++++ ++v +++  p ++rvg+v+f ++v    + +   + + +l+a+  +  s+g
  gi|386002849|ref|YP_005921148.1|  65 DVVLAIDSSASMTETDPTkMRLDAARSFVVRMD--PARDRVGIVSFDDDVDFSLPPTG--EFARVLEAIGGV-DSDG 136
                                       9***********99998846789**********..***************99999999..5599*******5.6666 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS...HTHHHHHHHHGCTEEEEEEEE..SSSHHHHHH CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndg...dpkeaaneakeqgikvfavGv..gnadekelL 148
                                        t+ ++ +l++a++ l   s g  ++  ++++ll+dG+ + +       +a++ak +g+ ++++G   g+  +++ L
  gi|386002849|ref|YP_005921148.1| 137 RTN-LDRGLAEAIDLLAANSTG-SDERARFLVLLSDGDGDYTpsgRSGSQADRAKGEGVVIYTIGLalGDPAKRS-L 210
                                       666.**********88888888.55789********8886656789999******************99999999.* PP

                                       HHHSSSSCHHCEEEESSHHHHHHH CS
                               VWA 149 nkiasepgeghvftvtdfeeleel 172
                                       +++a+ +g g+ f + + ++le +
  gi|386002849|ref|YP_005921148.1| 211 EEMAGATG-GKHFDACNASALEAI 233
                                       *******9.888888777777665 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 !   54.8   0.1   2.1e-18   1.2e-14       1     106 [.      66     171 ..      66     172 .. 0.90
   2 ?    0.8   0.0      0.13   7.6e+02      48      78 ..     349     379 ..     334     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.1e-18
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtn 77 
                                       +v+ +D+S+Sm+++d ++ rl+aa+++v ++  +  +drvg+v+f+d++   +p+t   a++l+a+ +++ + g tn
  gi|386002849|ref|YP_005921148.1|  66 VVLAIDSSASMTETDPTKMRLDAARSFVVRMDPA--RDRVGIVSFDDDVDFSLPPTGEFARVLEAIGGVDSD-GRTN 139
                                       79************97777777777777665444..9*********************************86.**** PP

                             VWA_2  78 laaaLqlarkalkkrr...kgekrvivlitDg 106
                                       l+ +L  a ++l +++     + r +vl++Dg
  gi|386002849|ref|YP_005921148.1| 140 LDRGLAEAIDLLAANStgsDERARFLVLLSDG 171
                                       ************9999998899999999**98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.13
                             VWA_2  48 gpevliplt.kdkakilnalrnleakgggtnl 78 
                                       +  ++ip++ ++ ++i  a++++e++ ++t++
  gi|386002849|ref|YP_005921148.1| 349 STSLEIPFNfSSAKEIVGAVHEVEEE-DETTI 379
                                       4578999998999**********986.77765 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0     1e-10     6e-07       2     151 ..      65     219 ..      64     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1e-10
                             VWA_3   2 evvivvDvsssmsaen...klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelsl 75 
                                       +vv+++D+s+sm         +++a s+++r +p +d++ +++f++++++  p   +       ++l++i   +  +
  gi|386002849|ref|YP_005921148.1|  65 DVVLAIDSSASMTETDptkMRLDAARSFVVRMDPARDRVGIVSFDDDVDFSLPPTGEFA-----RVLEAIGGVDS-D 135
                                       8**********998778744567788999******************998877766555.....899*****999.* PP

                             VWA_3  76 gasnlegaLkealrqp.....akpgevrsvilltDgss.aqgeervsdlisrarek.irfhalglgs.slsaamlqa 144
                                       g +nl + L+ea++        + +++r+++ll+Dg     ++ r  ++ +ra+++ + + ++gl   +  ++ l++
  gi|386002849|ref|YP_005921148.1| 136 GRTNLDRGLAEAIDLLaanstGSDERARFLVLLSDGDGdYTPSGRSGSQADRAKGEgVVIYTIGLALgDPAKRSLEE 212
                                       *************8444456688899**********98566889999999999966566666555441144699*** PP

                             VWA_3 145 LAeasgG 151
                                       +A a+gG
  gi|386002849|ref|YP_005921148.1| 213 MAGATGG 219
                                       ***9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3781.40
//
Query:       gi|386002850|ref|YP_005921149.1|  [L=310]
Description: Methenyltetrahydromethanopterin cyclohydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-117  392.6   0.0   1.4e-117  392.4   0.0    1.0  1  MCH       Cyclohydrolase (MCH)
  ------ inclusion threshold ------
       0.18   10.9   0.0        0.3   10.2   0.0    1.2  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.4   0.0  1.6e-121  1.4e-117      13     311 .]       1     301 [.       1     301 [. 0.99

  Alignments for each domain:
  == domain 1  score: 392.4 bits;  conditional E-value: 1.6e-121
                                       HHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEEEEESSHHHHHTT CS
                               MCH  13 llekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpavevstdhPvlacLa 89 
                                       +l++a+elr+ v el+ng+ v DaGvea+Ggl AG++la++c+++La+++ ++ e++g+++p v+v+tdhP+++c+a
  gi|386002850|ref|YP_005921149.1|   1 MLDYADELRVGVVELDNGTVVADAGVEAKGGLGAGIYLARLCMADLADIQPTPIEIDGITIPGVQVATDHPAISCMA 77 
                                       7899************************************************************************* PP

                                       TTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHHHTS-GGGEEEEE CS
                               MCH  90 sqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaeecgvepenvtllv 165
                                       sq+A W+++a+++fa+gsGPaR la+k +el+++l++e+ +d++vl lesd+lPde++++k+ae+cg++p+++ l+v
  gi|386002850|ref|YP_005921149.1|  78 SQCAMWQVKAGNYFAMGSGPARILARKtKELYDALEFEEYSDVGVLFLESDTLPDEAAADKIAEACGIDPADLRLAV 154
                                       ***************************************************************************** PP

                                       E-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH-EEEEEES....T CS
                               MCH 166 aptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYggrvhltve.aede 241
                                       apt+S+aG vqv+aRvve++lhkl++lgfd+++i++++g+aPiapv + ++++mg++ndai+Ygg++++tve +  +
  gi|386002850|ref|YP_005921149.1| 155 APTDSVAGLVQVSARVVETGLHKLFTLGFDVRTIRNGWGRAPIAPVVGKATRCMGASNDAIIYGGETYYTVEyEPFD 231
                                       ************************************************************************77889 PP

                                       THHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHHHHHT CS
                               MCH 242 eaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneellaesf 311
                                       e+  ++k++ps++s+dyg pF+++fke ++df+k+d+++F+pA+v+vndl++ +t +aG+ln+++l+esf
  gi|386002850|ref|YP_005921149.1| 232 ELLGYVKAIPSDTSRDYGAPFYKTFKECGFDFFKVDHHVFAPAKVVVNDLRSRRTLVAGRLNPQVLKESF 301
                                       9********************************************************************9 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.4e-05       0.3     248     295 ..     249     298 ..     244     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.4e-05
                                       H.HHHHHHTTS--SEEE--TTS..-HHHHHHSS.....EEE--B-G.GGGG CS
                             URO-D 248 gaeiledlaelgadvlsldwtv..dlkeaarevg.dkvalqGnldPialLl 295
                                       ga+++++++e+g+d + +d++v  + k +++++  +++ + G l+P ++L 
  gi|386002850|ref|YP_005921149.1| 249 GAPFYKTFKECGFDFFKVDHHVfaPAKVVVNDLRsRRTLVAGRLNP-QVLK 298
                                       55899*****************65444445577668999*******.8985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2006.77
//
Query:       gi|386002851|ref|YP_005921150.1|  [L=105]
Description: hypothetical protein Mhar_2175 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 661.38
//
Query:       gi|386002852|ref|YP_005921151.1|  [L=152]
Description: hypothetical protein Mhar_2176 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1016.99
//
Query:       gi|386002853|ref|YP_005921152.1|  [L=143]
Description: Universal stress protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-35  122.9   3.8    1.5e-35  122.7   3.8    1.0  1  Usp         Universal stress protein family
     0.0015   18.8   0.3         17    5.9   0.0    3.3  3  E3_binding  e3 binding domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   3.8   1.7e-39   1.5e-35       1     141 []       1     143 []       1     143 [] 0.98

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.7e-39
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaa 75 
                                       m++rIlVa+Dgs ++  A++++++laka+gae+  ++v+d+ a + +  ++ + +e+ + + +a  e++   +++ a
  gi|386002853|ref|YP_005921152.1|   1 MNDRILVATDGSAAAMVAVKKGVDLAKATGAEVLGVYVVDELAVANAVRLFGADKEDLERKLQAGGEEAVsdLRRIA 77 
                                       89************************************************99999999999999888887999**** PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       e++gv ve+vv++g pa +i+e+a+e+++d+iV+G +g+sg+ ++++GSv ++vl +a++pVlvVr
  gi|386002853|ref|YP_005921152.1|  78 EEAGVPVETVVTFGVPANSIIELAKEKGVDMIVMGGHGQSGVTKFIIGSVVKNVLYRATVPVLVVR 143
                                       *****************************************************************8 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0041        37       7      23 ..      14      30 ..      13      35 .. 0.81
   2 !    5.9   0.0    0.0019        17       8      22 ..      74      88 ..      73      92 .. 0.89
   3 !    4.5   0.0     0.005        45      10      17 ..     100     107 ..      99     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0041
                                      HHHHHHHCT--TTTS-- CS
                        E3_binding  7 aRklAkelGidLsdvkG 23
                                      a + A  +G+dL++ +G
  gi|386002853|ref|YP_005921152.1| 14 AAMVAVKKGVDLAKATG 30
                                      6667889******9866 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0019
                                      HHHHHHCT--TTTS- CS
                        E3_binding  8 RklAkelGidLsdvk 22
                                      R++A+e G+  ++v+
  gi|386002853|ref|YP_005921152.1| 74 RRIAEEAGVPVETVV 88
                                      9********999886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.005
                                       HHHHCT-- CS
                        E3_binding  10 lAkelGid 17 
                                       lAke+G+d
  gi|386002853|ref|YP_005921152.1| 100 LAKEKGVD 107
                                       8******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 983.34
//
Query:       gi|386002854|ref|YP_005921153.1|  [L=88]
Description: hypothetical protein Mhar_2178 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.16   12.0   0.0    1.2  1  DUF1930   Domain of unknown function (DUF1930)


Domain annotation for each model (and alignments):
>> DUF1930  Domain of unknown function (DUF1930)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.7e-06      0.16      42      64 ..      22      44 ..       3      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-06
                                      TT-BTT-EEEEEETTS-EEEEE- CS
                           DUF1930 42 vHlHiGEkAqvfFksrRvvviEv 64
                                      + l iG  A v Fk +Rv+v++ 
  gi|386002854|ref|YP_005921153.1| 22 TSLRIGYVADVLFKKERVIVLDT 44
                                      6799****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 626.18
//
Query:       gi|386002855|ref|YP_005921154.1|  [L=108]
Description: hypothetical protein Mhar_2179 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 636.28
//
Query:       gi|386002856|ref|YP_005921155.1|  [L=64]
Description: hypothetical protein Mhar_2180 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-05   24.6   0.1    3.8e-05   24.3   0.1    1.2  1  DUF2281   Protein of unknown function (DUF2281)


Domain annotation for each model (and alignments):
>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   2.1e-09   3.8e-05       2      29 ..       7      34 ..       6      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.1e-09
                           DUF2281  2 LyekiqeLPedlkqEvldFaefLleKya 29
                                      ++  i+  Pe++ +EvldF++fL+e+++
  gi|386002856|ref|YP_005921155.1|  7 ILREIEVFPEPYLKEVLDFVRFLKERSS 34
                                      67899999*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 416.43
//
Query:       gi|386002857|ref|YP_005921156.1|  [L=100]
Description: hypothetical protein Mhar_2181 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-06   28.4   0.0    1.8e-06   28.3   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   9.9e-11   1.8e-06      16     110 ..      10      97 ..       1      98 [. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.9e-11
                                       TS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCCEEEEEGGGEEEEE CS
                        PemK_toxin  16 seqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhveleseildlngldkdswvkldqirtvdkarlrkki 92 
                                        e +krRp++ v + ++      i +++ts++   k+  + v ++ +  ++ +l+kds v+   ++t d + +  + 
  gi|386002857|ref|YP_005921156.1|  10 AE-AKRRPALLVAELEGD---DRILCQITSRH--FKD-RYAVGINDADFEEGSLKKDSNVRPNRLFTADSRIILYRA 79 
                                       34.89********99888...57*********..545.899***87644446678**************998888** PP

                                       EE--HHHHHHHHHHHHHH CS
                        PemK_toxin  93 gklsredlaevqralakl 110
                                       g+l++e++ ev ++++ +
  gi|386002857|ref|YP_005921156.1|  80 GHLKAERVGEVVERIINI 97 
                                       ************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 649.40
//
Query:       gi|386002858|ref|YP_005921157.1|  [L=66]
Description: hypothetical protein Mhar_2182 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.23s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 590.36
//
Query:       gi|386002859|ref|YP_005921158.1|  [L=1071]
Description: hypothetical protein Mhar_2183 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-21   74.4   1.0    1.7e-20   73.3   0.2    2.1  2  TaqI_C       TaqI-like C-terminal specificity domain
    1.1e-15   58.0   0.0    2.5e-15   56.9   0.0    1.6  1  Eco57I       Eco57I restriction-modification methylase
    4.4e-10   39.3   0.0    2.5e-07   30.3   0.0    2.6  2  N6_Mtase     N-6 DNA Methylase
    3.3e-07   30.5   0.0    0.00015   21.8   0.0    2.5  1  HSDR_N       Type I restriction enzyme R protein N terminus (
     0.0024   17.6   0.1        0.2   11.3   0.0    2.9  3  UPF0020      Putative RNA methylase family UPF0020
     0.0079   16.2   0.0       0.02   14.9   0.0    1.6  1  HSDR_N_2     Type I restriction enzyme R protein N terminus (
  ------ inclusion threshold ------
      0.041   14.1   0.4      0.077   13.2   0.4    1.3  1  Methylase_S  Type I restriction modification DNA specificity 
       0.57   10.2   5.5        1.5    9.0   5.5    1.7  1  AT_hook      AT hook motif


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 ?   -2.5   0.0       2.3   5.2e+03      14      58 ..     191     234 ..     179     238 .. 0.73
   2 !   73.3   0.2   7.7e-24   1.7e-20       1     120 []     836     994 ..     836     994 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                            TaqI_C  14 ieikgnYldlikkklknekakelfeekpKilvrdiskkldaayde 58 
                                       i +++ +l+ i +++++  ak++++++p + +r+++++++ ++d 
  gi|386002859|ref|YP_005921158.1| 191 IAVDEAFLREI-DSWREILAKNVHRNNPDLTIRELNSSVQNTIDR 234
                                       55555566555.556666678888899999999999999998886 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 7.7e-24
                            TaqI_C   1 kpllkGkdikrysieikgnYldlikkklknek.................................akelfe...... 38 
                                       kp+l Gkdikry+   +++Yl++ + +++ e+                                 + +++e      
  gi|386002859|ref|YP_005921158.1| 836 KPFLVGKDIKRYQTPRSDRYLIFTRRGVEIENypaikrhltqfkdrlmpkplnwkgdkwngrkpgKYKWYEiqdita 912
                                       79******************************999****99999999999999999888887766578888888888 PP

                            TaqI_C  39 .....ekpKilvrdiskkld.aaydekayyvlntlylliakdelevslkyllgiLNSklikfyykkiystlrggysr 109
                                            ek Kil++ is ++  +a+d+++yy + +  l+i       ++kyllgiLNS+li  ++k+i  + +gg++r
  gi|386002859|ref|YP_005921158.1| 913 yyaefEKGKILWPGISAQVGaFAFDDNGYYGNDNNQLII------SDDKYLLGILNSSLIRTILKSICDKVQGGFYR 983
                                       889999***********98779********998888888......6789**************************** PP

                            TaqI_C 110 lkrkeleklPi 120
                                       lk+ ++e+lPi
  gi|386002859|ref|YP_005921158.1| 984 LKIIYVERLPI 994
                                       **********9 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   1.1e-18   2.5e-15       3     104 ..     627     734 ..     624     736 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.1e-18
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek.......akdiyqkFvekalkle..dkylaliiparflasgkglkefrekll 70 
                                       fd++iGNPPY ++e+  e k+  +k        +d+y +F+ek+++l    ++ + i+ ++++ ++++++ +r++l 
  gi|386002859|ref|YP_005921158.1| 627 FDAVIGNPPYVRQEELGEFKTYFQKryqvyhgVADLYAYFIEKGVSLLrhGGVFSYIVASKWM-RANYGQPLRAWL- 701
                                       9***************999998888899999999*************976788999*******.9********997. PP

                            Eco57I  71 kdkklkklvefedskevFkdveikggilvflkdk 104
                                       k k+++++v+f d + vF++++++ +i+ ++ ++
  gi|386002859|ref|YP_005921158.1| 702 KGKNIEEIVDFGDLR-VFQKATTYPCIIRISNES 734
                                       6789***********.***********9887765 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.1e-10   2.5e-07       4      67 ..     330     416 ..     328     421 .. 0.79
   2 !    5.9   0.0    0.0028       6.4     122     234 ..     623     734 ..     610     761 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-10
                          N6_Mtase   4 dllGdvYEyllrk.............faeeegksgGeffTPrevsklivell..........epksgesvyDpacGs 57 
                                       ++lG+vYE++l+k             +  e  k gG ++TP  ++  ive +           + s+  ++DpacGs
  gi|386002859|ref|YP_005921158.1| 330 EILGHVYEQFLGKvirlgedggveveYKPEVRKAGGVYYTPTYIVDYIVENTvgkllagqtpTTVSELRILDPACGS 406
                                       6889999999876333333333333366778899***************98889999**9987888889******** PP

                          N6_Mtase  58 ggllvqaekv 67 
                                       g++l+ a + 
  gi|386002859|ref|YP_005921158.1| 407 GSFLIGAYQR 416
                                       *****99875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0028
                          N6_Mtase 122 kdkkfdvvvaNppfnqkewkektlekderfrea.vapksnadla..fllhiieslkpkGraavvlangvLfrggkeg 195
                                           fd+v+ Npp+  +   e+  e   +f+++    ++ adl   f+   ++ l+++G  + ++a+  + r + ++
  gi|386002859|ref|YP_005921158.1| 623 GRGGFDAVIGNPPYVRQ---EELGEFKTYFQKRyQVYHGVADLYayFIEKGVSLLRHGGVFSYIVASKWM-RANYGQ 695
                                       56789*********999...33333344466555444555554337999999999999999999999877.678888 PP

                          N6_Mtase 196 kIrkalvekdlveavialpe.klFyntsiptcilvlkkek 234
                                        +r  l + +++e ++ + + ++F++ +   ci+ ++ e 
  gi|386002859|ref|YP_005921158.1| 696 PLRAWL-KGKNIEEIVDFGDlRVFQKATTYPCIIRISNES 734
                                       888765.667789999887657888877777777666655 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.7e-08   0.00015       2     188 ..      26     133 ..      25     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.7e-08
                                       SSHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH-HHHHHHHHTT--HHHHHH CS
                            HSDR_N   2 lsEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgalnikkltkrlalsdgnkefye 78 
                                       ++E +l++++id+++++lG++v ++ +    +r                                            
  gi|386002859|ref|YP_005921158.1|  26 YNETKLRRDFIDPFFKALGWDVANTAGSSELYR-------------------------------------------- 58 
                                       79999*****************97765543332............................................ PP

                                       HHHTS-EEEETS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTEEEEEEEE--TT.-HHHHHHHH CS
                            HSDR_N  79 llkegkvkfkegrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvnglplvviElKrpg.tieeAinQi 153
                                                                     +vv++ +v+ +++++ pD+   ++g   +++E+K+p+ +        
  gi|386002859|ref|YP_005921158.1|  59 ------------------------------DVVHEDSVKvRGSTKAPDYAFRIGGARKFFVEAKKPSvN-------- 97 
                                       ..............................233444444468899********************9645........ PP

                                       TSS---.---S.SSGGGGG-.....-EEEEE-SS-EEEEE- CS
                            HSDR_N 154 kryrkeksdvs.ipqlfrYl.....qfgvisngketrfyak 188
                                             + dv+   ql+ Y+     ++ ++++++e+ +y+ 
  gi|386002859|ref|YP_005921158.1|  98 -----LENDVRaSFQLRSYAwsaglPISLLTDFEEFSIYDC 133
                                       .....44455668************************9997 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   9.1e-05       0.2      29      46 ..     396     413 ..     386     421 .. 0.86
   2 ?   -1.1   0.0      0.56   1.3e+03      66      98 ..     519     552 ..     489     568 .. 0.71
   3 ?    2.2   0.0     0.056   1.2e+02     118     133 ..     623     638 ..     607     670 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.1e-05
                                       TS-EEETT-TTSHHHHHH CS
                           UPF0020  29 gepllDPmCGsGtilIEa 46 
                                       + ++lDP CGsG++lI a
  gi|386002859|ref|YP_005921158.1| 396 ELRILDPACGSGSFLIGA 413
                                       568*************66 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHH--.EEEEES-HHHHHHHHHHHHH CS
                           UPF0020  66 kaeaeeearaelk.lygsDldrrvvqgareNaek 98 
                                       +    e++r  l+ ++g+D+d ++v+ ++  ++ 
  gi|386002859|ref|YP_005921158.1| 519 RLATAERKRILLNnICGVDIDLAAVEVTKLSLQL 552
                                       3344444443344599********9999987775 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.056
                                       TTS---EEEE------ CS
                           UPF0020 118 kegevdvivtnpPYGe 133
                                        +g +d++++npPY +
  gi|386002859|ref|YP_005921158.1| 623 GRGGFDAVIGNPPYVR 638
                                       56789*********65 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.1e-06      0.02      24      99 ..      60     136 ..      56     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
                          HSDR_N_2  24 iavekelqlgskkkraDivvykkdkkpllivecKapsvki..seevleqlksYlealkaeylvvtNglehivykvdk 98 
                                       +  e ++++ +++k +D+++         +ve+K+psv++  + ++  ql sY+  ++ +  ++t+ +e+ +y+++ 
  gi|386002859|ref|YP_005921158.1|  60 VVHEDSVKVRGSTKAPDYAFRIGG-ARKFFVEAKKPSVNLenDVRASFQLRSYAWSAGLPISLLTDFEEFSIYDCRI 135
                                       677999999**********98877.77889**********54446778*************************9876 PP

                          HSDR_N_2  99 k 99 
                                       +
  gi|386002859|ref|YP_005921158.1| 136 E 136
                                       5 PP

>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   3.4e-05     0.077      27     125 ..     897     985 ..     889     996 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                                       TTT--EEEE-HHHCCTEE-HHHHCCTT---B-TT-EEEE-S.SSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHH CS
                       Methylase_S  27 kengkypyiragilnnkvvkdglgykkkyilpkgdilissr.atiGkvayrdkkyylnqsvivlipknkkkinefly 102
                                       +++gky+++++         d++ y+ ++  +kg il+  + a +G +a+ d+ yy n++ + +i+ +k     +l+
  gi|386002859|ref|YP_005921158.1| 897 RKPGKYKWYEIQ--------DITAYYAEF--EKGKILWPGIsAQVGAFAFDDNGYYGNDNNQLIISDDK-----YLL 958
                                       788999999999........899999775..56888886555***********************9654.....444 PP

                                       HHHH.....HCHHHHHHHCCSSTTT--- CS
                       Methylase_S 103 lyll.....lklkklkslsvgstqpklt 125
                                        +l      ++lk++++ +v++++ +l+
  gi|386002859|ref|YP_005921158.1| 959 GILNsslirTILKSICD-KVQGGFYRLK 985
                                       44433322377777777.7888877766 PP

>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.5   0.00065       1.5       2      11 ..     479     488 ..     478     490 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00065
                           AT_hook   2 RkRGRPrKaa 11 
                                       R+RGRPrK++
  gi|386002859|ref|YP_005921158.1| 479 RGRGRPRKNS 488
                                       9*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1071 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.88u 0.36s 00:00:01.24 Elapsed: 00:00:00.54
# Mc/sec: 5995.22
//
Query:       gi|386002860|ref|YP_005921159.1|  [L=420]
Description: adenylosuccinate synthetase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-159  530.1   0.0   4.3e-159  529.9   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.9   0.0  2.4e-163  4.3e-159       2     419 .]       4     418 ..       3     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: 529.9 bits;  conditional E-value: 2.4e-163
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       ++ G+q+GDEGKGk+vDllae++d+vvRfqGG+nAGHtv+v++++yklhl pSG+l  g++ +iG+gvv++p++l +
  gi|386002860|ref|YP_005921159.1|   4 ILTGSQFGDEGKGKVVDLLAEKYDIVVRFQGGDNAGHTVIVGDRTYKLHLTPSGVLF-GARLLIGPGVVLNPKVLWS 79 
                                       789*****************************************************6.9999*************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeel 155
                                       Eie+l+a+g++    +l i++++ +++pyh+alD+l+e+ + k+kiGtTk+GiG ay dk++r  ++++dl d++ l
  gi|386002860|ref|YP_005921159.1|  80 EIEALRAEGIRP---NLGIDAKTSIIMPYHIALDELRESGR-KEKIGTTKRGIGYAYIDKFSRDEVQMKDLTDPALL 152
                                       **********66...9**********************966.59********************************* PP

                                       HHHHHHHHHHTHHHHHHT...T-----..HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTS CS
                   Adenylsucc_synt 156 eeklekllelknkllekldkeelevee..lleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhG 230
                                       e+kl+++   ++k ++++  ++  v++  ll e+l++ + lk+ v+d+++++n al++gkkvL EGaqg++lD+ hG
  gi|386002860|ref|YP_005921159.1| 153 EAKLAEIGPAREKAIAEMGGDPAVVRDpvLLGEYLEIGRSLKENVADVSYEINVALDAGKKVLAEGAQGAFLDVIHG 229
                                       ********999999999987444444445899********************************************* PP

                                       STTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-E CS
                   Adenylsucc_synt 231 tYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwl 307
                                       t  fvTsS ttag+a++ lg++p ++d+v+g+vKAy+trvGeGp+ptelkdevg +l ++GkEfgtttgrpRrcGw+
  gi|386002860|ref|YP_005921159.1| 230 TQKFVTSSFTTAGSACANLGVGPARVDNVVGIVKAYMTRVGEGPMPTELKDEVGAHLSKIGKEFGTTTGRPRRCGWF 306
                                       ***************************************************************************** PP

                                       EHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT---G CS
                   Adenylsucc_synt 308 DlvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvrsf 384
                                       D+vl+++++ +ng+tela+tklDvl gld ik+c++Y+ldgk+l++ p+s+ e+++++p+yee +gW+edi+g++s+
  gi|386002860|ref|YP_005921159.1| 307 DAVLAKKSMYLNGYTELAITKLDVLGGLDPIKICTSYELDGKTLNYPPESTVEFARCRPIYEEAKGWTEDITGAKSY 383
                                       ***************************************************************************** PP

                                       GGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 385 edlpenakkyvefieellgvpvkiisvGpereqti 419
                                        +lp+++++yve+ieellgv+++i+svGp+reqti
  gi|386002860|ref|YP_005921159.1| 384 GALPKAVRDYVERIEELLGVKITIVSVGPGREQTI 418
                                       *********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2563.64
//
Query:       gi|386002861|ref|YP_005921160.1|  [L=290]
Description: Tetrahydromethanopterin:alpha-L-glutamate ligase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-26   92.7   0.0    2.7e-26   92.3   0.0    1.1  1  RimK            RimK-like ATP-grasp domain
    3.9e-13   49.2   0.0    6.5e-13   48.4   0.0    1.3  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    1.2e-06   28.0   0.0     0.0069   15.7   0.0    2.7  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
    3.7e-06   26.4   0.0     0.0032   16.8   0.0    2.1  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
    1.6e-05   25.0   0.0       0.22   11.6   0.0    2.2  2  ATP-grasp_3     ATP-grasp domain
  ------ inclusion threshold ------
      0.023   15.1   0.0      0.035   14.5   0.0    1.3  1  Rimk_N          RimK PreATP-grasp domain
      0.032   14.1   0.1      0.079   12.8   0.1    1.6  1  DUF2249         Uncharacterized conserved protein (DUF2249)
      0.069   13.1   0.1       0.12   12.4   0.1    1.4  1  R2K_3           ATP-grasp domain, R2K clade family 3


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0   1.2e-29   2.7e-26       1     187 [.      95     281 ..      95     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.2e-29
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEE.E.-SHHHHHHHHHHGGG- CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvl.a.kkeqklkqvlealkea 75 
                                       a +K+ +   L +a+i+ p+t ++ +   a +++   +     v K ++g  G +  l a  ++  l+++le  + a
  gi|386002861|ref|YP_005921160.1|  95 AANKFATSVALQRAGIPHPETLVTTSLSSAAEFVSAHG---GAVYKPLFGFKGRGLRLlApGDPSPLRELLEE-RGA 167
                                       6799999999************************9986...899******99877644132688899***986.678 PP

                                       -EEEEE--SS-S..EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEE CS
                              RimK  76 ilvqeyieeaen..ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvD 150
                                       + +qe++e + +  +diR +vv++ v +a+ rv+  G + snl rGg+ e+  l++e ++lA++aa a+++v++GvD
  gi|386002861|ref|YP_005921160.1| 168 VYLQEFLESTAQrpRDIRAFVVGGRVAGAIFRVAPPGSWISNLARGGAPERCPLTPEIEDLAVRAASAVGAVYCGVD 244
                                       899****98777689************************************************************** PP

                                       EEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                              RimK 151 llrakrgllvlEvnsspglekiektlgidiakkliea 187
                                       l+++  gl vlEvn  p   ++++  gid+ + +++a
  gi|386002861|ref|YP_005921160.1| 245 LIETSSGLRVLEVNGTPSGWGLHQAWGIDVGELIARA 281
                                       *****************************98877765 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   2.9e-16   6.5e-13      12     160 ..     112     258 ..     103     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.9e-16
                                       S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG..-EE CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeike..GDk 86 
                                        p+tlv+++ ++  +f++++g ++ KPl g  G+g+  ++  dp+   + ell e+g   v +q++l+   +   D 
  gi|386002861|ref|YP_005921160.1| 112 HPETLVTTSLSSAAEFVSAHGGAVYKPLFGFKGRGLRLLAPGDPS--PLRELLEERGA--VYLQEFLESTAQrpRDI 184
                                       499**************************************9985..67777777776..899****987652379* PP

                                       EEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT....EEEEE CS
                         GSH-S_ATP  87 RillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd....kltEi 159
                                       R ++v G+  g a+ Rv+  g   snla gg  e  +lt + + +a + a+   + G ++ G+D+i++    ++ E+
  gi|386002861|ref|YP_005921160.1| 185 RAFVVGGRVAG-AIFRVAPPGSWISNLARGGAPERCPLTPEIEDLAVRAAS---AVGAVYCGVDLIETssglRVLEV 257
                                       ***********.*********************************998776...569*********76222256677 PP

                                       E CS
                         GSH-S_ATP 160 n 160
                                       n
  gi|386002861|ref|YP_005921160.1| 258 N 258
                                       6 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00023      0.51      30      65 ..     113     148 ..      93     158 .. 0.88
   2 !   15.7   0.0   3.1e-06    0.0069     110     162 ..     170     215 ..     155     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00023
                    ATPgrasp_YheCD  30 PetellesledleemlekyksvylKpanGskGkgil 65 
                                       Pet   +sl++ +e+++ ++  + Kp  G kG+g+ 
  gi|386002861|ref|YP_005921160.1| 113 PETLVTTSLSSAAEFVSAHGGAVYKPLFGFKGRGLR 148
                                       99*******************************975 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.1e-06
                    ATPgrasp_YheCD 110 vQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGt 162
                                       +Q+ +  ++  +rp D+R++v        +v+g+++R+a++gs ++nl+rGG 
  gi|386002861|ref|YP_005921160.1| 170 LQEFL--ESTAQRPRDIRAFVVGG-----RVAGAIFRVAPPGSWISNLARGGA 215
                                       55554..45669999999999933.....69********************96 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0032       8      80 ..      84     151 ..      79     165 .. 0.91
   2 !    7.5   0.0   0.00097       2.2     225     269 ..     222     264 ..     218     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                       ATPgrasp_ST   8 rkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvit 80 
                                       r +Np a++   ++K+ ++  ++rag++ p++l++     ++s++++fv+ +  g v Kp  g+ G+G++ ++
  gi|386002861|ref|YP_005921160.1|  84 RVVNPPAAIARAANKFATSVALQRAGIPHPETLVT----TSLSSAAEFVSAH-GGAVYKPLFGFKGRGLRLLA 151
                                       678****************************8877....67999********.88*************99875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00097
                       ATPgrasp_ST 225 weevlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                        +e+ +la++aa   +g  y G+D+  + ++ + +lE+N +p+ +
  gi|386002861|ref|YP_005921160.1| 222 TPEIEDLAVRAAS-AVGAVYCGVDLIETSSG-LRVLEVNGTPSGW 264
                                       578889*******.99999*****9666666.*******997644 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   9.8e-05      0.22       1      54 [.      95     154 ..      95     179 .. 0.75
   2 !   11.4   0.0   0.00011      0.24     111     156 ..     216     259 ..     206     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                       HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS-- CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveeke 54 
                                       a++K++t  +L++ag++ P      +  +a+e+ ++    v Kp  G  g + r+   ++
  gi|386002861|ref|YP_005921160.1|  95 AANKFATSVALQRAGIPHPetlvttSLSSAAEFVSAHGGAVYKPLFGFKGRGLRLLAPGD 154
                                       69*****************88877555567778888999***********9999887664 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                                       S----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEES CS
                       ATP-grasp_3 111 pietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNP 156
                                       p +  l+ e+++la ++ +++   a y GvDl+ + +++ v+EvN 
  gi|386002861|ref|YP_005921160.1| 216 PERCPLTPEIEDLAVRAASAV--GAVYCGVDLIETSSGLRVLEVNG 259
                                       55667889999*********9..5679******************6 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.5e-05     0.035      16      94 .]      11      92 ..       1      92 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                            Rimk_N 16 rrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.i...gasitfygtavlrqFemmgvfvlne 90
                                      + +   + ++g ++e ld++++ + + + + +++ +g++l  + a i+R +   g+s + ++ + l  +e++gv v+n 
  gi|386002861|ref|YP_005921160.1| 11 EAIGSGLSRQGAKAEYLDFSELAALVGS-DLRLLGEGRDLLGLSALIVRdLgrrGSSDVAFRFEALSALEESGVRVVNP 88
                                      55556678899**********9999888.899*****************878889999********************* PP

                            Rimk_N 91 seAi 94
                                      ++Ai
  gi|386002861|ref|YP_005921160.1| 89 PAAI 92
                                      **98 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.5e-05     0.079      26      51 ..     144     167 ..     143     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                           DUF2249  26 GetlelvndhdPkpLlyqLearrpgf 51 
                                       G +l+l+++ dP pL++ Le+r  g+
  gi|386002861|ref|YP_005921160.1| 144 GRGLRLLAPGDPSPLRELLEER--GA 167
                                       899*******************..76 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.4e-05      0.12     118     183 ..     183     259 ..     163     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                             R2K_3 118 EwRvFvvdGevvaasrYr..........kanddpdl...epdlaafaeavralvgappfyvlDvavtadGrwkVVEv 181
                                         R Fvv+G+v +a               + ++p+     p+++ +a  ++++v  +  + +D+  t++G ++V Ev
  gi|386002861|ref|YP_005921160.1| 183 DIRAFVVGGRVAGAIFRVappgswisnlARGGAPERcplTPEIEDLAVRAASAV-GAVYCGVDLIETSSG-LRVLEV 257
                                       5799**999877765444555688888777777777988899999998888888.6**************.****** PP

                             R2K_3 182 nd 183
                                       n 
  gi|386002861|ref|YP_005921160.1| 258 NG 259
                                       95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1844.58
//
Query:       gi|386002862|ref|YP_005921161.1|  [L=114]
Description: rhodanese-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-13   51.4   0.0    1.5e-13   51.2   0.0    1.1  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   8.3e-18   1.5e-13       8     106 ..      17     106 ..      10     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 8.3e-18
                         Rhodanese   8 llekgkva....llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraa 80 
                                       l+++g+ +    +lDvR+p+e+e+ +I+g+vn+           +  + + ++e+++l  d+ k   vyc  g r++
  gi|386002862|ref|YP_005921161.1|  17 LIQDGGGDpellILDVRTPQEHERIRIEGSVNL-----------DLHSPAFLAEVSAL--DRRKAYLVYCLVGVRSR 80 
                                       554444445566*********************...........88888888888888..99*************88 PP

                         Rhodanese  81 aaaallkklGyknvsvldGGfkawke 106
                                       aaa ++ +lG+ +v++l GG+++w +
  gi|386002862|ref|YP_005921161.1|  81 AAAEAMARLGFGEVFNLAGGIRSWTK 106
                                       88777777**999***********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.51
# Mc/sec: 670.08
//
Query:       gi|386002863|ref|YP_005921162.1|  [L=163]
Description: hypothetical protein Mhar_2187 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 970.95
//
Query:       gi|386002864|ref|YP_005921163.1|  [L=324]
Description: Thiamine-phosphate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-21   75.4   0.2    9.1e-21   74.3   0.2    1.6  1  AIRS      AIR synthase related protein, N-terminal domain
    1.7e-07   31.5   0.5    3.2e-07   30.6   0.5    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.2     1e-24   9.1e-21       1      94 []      27     137 ..      27     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1e-24
                                       SSSE........EEEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HH CS
                              AIRS   1 dDaa........vvvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wl 55 
                                       dD+a        +v+ttd     +l    +f        iG+ a+avnlsD+aamGA P++ll +  +p       +
  gi|386002864|ref|YP_005921163.1|  27 DDCAmvedgedyLVWTTD-----MLHRRADFpdiatgwqIGWMAAAVNLSDVAAMGAAPTGLLSAAGIPpeteleYV 98 
                                       8***766666666*****.....999999999*****************************9*************** PP

                                       HHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEEE CS
                              AIRS  56 eevvrglaeaaeelgvplvgGdtsfsneptisvtavGlv 94 
                                       ee+++g++++a+++g+ ++gGd+ +s+e+t++ ta+G v
  gi|386002864|ref|YP_005921163.1|  99 EEIFAGMKDCARRFGTRVLGGDLDSSDELTLVGTALGRV 137
                                       *************************************86 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.5   3.6e-11   3.2e-07       1     149 [.     149     299 ..     149     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.6e-11
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSEHHHHHHHH.HHHHHHHHHHHHHTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds....avqlgdvllep.tliyvkralaalkglvkaahDvTgGGL 72 
                                       +pGd+l  tg+lG  gag + +   le+eg           l+  llep  ++++ rala++ g ++++ D ++ GL
  gi|386002864|ref|YP_005921163.1| 149 RPGDLLCTTGTLGAAGAG-LRV--ALEAEGKGIGsdpgLIALTRRLLEPfPRLEEGRALALS-GAATSMMDNSD-GL 220
                                       79*********8888888.333..34444433334566555555555554679999999997.***********.7* PP

                                       HHHHHHHHHTTTEEEEEECGTHHHHHHHH.......HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEE CS
                            AIRS_C  73 lgalaemapasgvgaeidldkvpifdele.......splemllsensGrllvavppeeadavlaileeeglpeaavI 142
                                       + +l e+a+asgvg+ ++++k+pi   ++       ++l+++l++     l++  ++e   + +++++++    avI
  gi|386002864|ref|YP_005921163.1| 221 VLSLYELAEASGVGFLLQEEKIPIDPLVAlvaedrdDALDLALTAGGDFELIFTLRPEM--IGEAARACR---LAVI 292
                                       ********************888776666777777888999999888888888888888..788888765...58** PP

                                       EEEEESS CS
                            AIRS_C 143 Gevtake 149
                                       Gevta++
  gi|386002864|ref|YP_005921163.1| 293 GEVTAEG 299
                                       ****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2141.12
//
Query:       gi|386002865|ref|YP_005921164.1|  [L=320]
Description: putative molybdenum cofactor biosynthesis protein A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-26   91.4   0.0    1.4e-25   90.6   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    4.2e-15   55.8   0.0    8.8e-15   54.8   0.0    1.5  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    1.8e-06   28.3   0.0    2.8e-06   27.6   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    3.4e-05   23.9   0.0    5.8e-05   23.2   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
     0.0013   18.8   1.4     0.0016   18.6   1.4    1.1  1  DUF4192      Domain of unknown function (DUF4192)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0     4e-29   1.4e-25       3     166 ..      37     193 ..      35     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 4e-29
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       vt+ Cnl+C +C+       +grgr++s +ei++ + ++ a+ g++ v l+ggepll+ d++ +ler  +    g++
  gi|386002865|ref|YP_005921164.1|  37 VTPRCNLACLYCHHEGE-LVGGRGREISADEIVKVISAG-ADLGIRRVKLTGGEPLLRGDLESILERTPE----GVE 107
                                       89***********9985.99*******************.8********************999999998....9** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGe 155
                                       ++++tng+l+    ++ l+e+g+ rv+++l+++ + ++  +++    +  +vle+++++  ag+ +v++++v+l+ e
  gi|386002865|ref|YP_005921164.1| 108 VSLTTNGVLL-AARARSLAEAGLARVNVSLDSLRPAVYAGITGgTAADHRRVLEGIDAALGAGLLPVKVNVVVLR-E 182
                                       **********.*************************999999999999***************************.* PP

                                       SHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellel 166
                                       n+ e++e++++
  gi|386002865|ref|YP_005921164.1| 183 NEGEVWEMVDF 193
                                       ********998 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   2.5e-18   8.8e-15      34     101 ..     223     292 ..     212     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.5e-18
                                       HHS-EEEE-..-SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEEE-TTSEEESSSS-SS-.EEHHHH CS
                       Mob_synth_C  34 erlalleak..ketkgpakrykikdgkgeiglIapvsep.FCasCnRlRltadGklktCLfaeee.idlrdl 101
                                       ++l+ +++   ++  + +++y +++++  +++++p++++ FCa+C+RlR+t+dG+lk+CL ++++ +dl+ +
  gi|386002865|ref|YP_005921164.1| 223 AALEARADGvvTRDLHRRRKYFLSGAE--VEVVRPMDNTeFCAHCSRLRVTSDGRLKPCLLRNDNlVDLAGA 292
                                       555555555324448999999998888..9********99*************************9999866 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   7.9e-10   2.8e-06      12      97 ..      38     118 ..      29     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 7.9e-10
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                       + +Cnl+C +C+ +      +g+e++ + + ++i   ++  i+ + l+GGEPll   + +l +++++  e     + 
  gi|386002865|ref|YP_005921164.1|  38 TPRCNLACLYCHHEGELVGGRGREISADEIVKVISAGADLGIRRVKLTGGEPLL---RGDLESILERTPEGVE--VS 109
                                       468***********************99999***9999****************...8899999888777665..56 PP

                           Fer4_12  89 wlytgytle 97 
                                       + ++g+ l 
  gi|386002865|ref|YP_005921164.1| 110 LTTNGVLLA 118
                                       666666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.6e-08   5.8e-05       5      92 ..      38     117 ..      35     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-08
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype. 80 
                                       + +Cnl+C  C ++ +     g + + +++++++      +  i+ + ltGGePL+     +    ++ + e++pe 
  gi|386002865|ref|YP_005921164.1|  38 TPRCNLACLYCHHEGELVGGRGREISADEIVKVI--SAGADLGIRRVKLTGGEPLLR---GD----LESILERTPEg 105
                                       569*********9988888777777777788999..4555555688*********55...34....44444555333 PP

                           Fer4_14  81 kkiwletngtle 92 
                                       +++ l tng+l 
  gi|386002865|ref|YP_005921164.1| 106 VEVSLTTNGVLL 117
                                       699999999875 PP

>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.4   4.4e-07    0.0016      34     146 ..      89     236 ..      68     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.4e-07
                           DUF4192  34 pvlRvDlpraeag...............leavardlae.llarega.....davvavvvddrgqdrvrplvdalrea 89 
                                       p lR Dl+   ++               l+a ar+lae  lar ++     + +v  ++++ +++ +r++++ +++a
  gi|386002865|ref|YP_005921164.1|  89 PLLRGDLESILERtpegvevslttngvlLAARARSLAEaGLARVNVsldslRPAVYAGITGGTAADHRRVLEGIDAA 165
                                       666777665554455567777777666666677777775444422234333444444444444349*********** PP

                           DUF4192  90 laaagvpvaaalvvseiaaggrwwsylc..............ccpeeGtvpdpaasplaaaavlaGrvveg 146
                                       l+a+ +pv  ++vv +  +g+ w +++               + p +G + d+a+   a++a ++G+v++ 
  gi|386002865|ref|YP_005921164.1| 166 LGAGLLPVKVNVVVLRENEGEVWEMVDFardrgvilqliellNLPGRGAAGDIAGIEAALEARADGVVTRD 236
                                       ***************************9***************************************9653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2144.13
//
Query:       gi|386002866|ref|YP_005921165.1|  [L=453]
Description: Na+/solute symporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-33  114.8  28.4    5.2e-31  107.9  28.4    2.3  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9  28.4   2.9e-35   5.2e-31       1     406 []      36     414 ..      36     414 .. 0.85

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 2.9e-35
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       +fla r l++  l ++l+a+ ++a+s +G+aG+++  Gl ++++ l  + ++l+l ++laer r +g +Tlp++l +
  gi|386002866|ref|YP_005921165.1|  36 FFLAERGLGPAILTATLTATILGASSTLGMAGLGFREGLTGAWWLLSGTAGLLILSFFLAERVRATGCFTLPELLGA 112
                                       8**************************************************************************** PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                        ++ +   ++ ++  +l+  +  +++++v+ +kl+  ++G   e+ +++ a++ + Yt++GG +++v td +q +++
  gi|386002866|ref|YP_005921165.1| 113 TYDRRV--RLAASALILVSWVGVIAAQIVASGKLLGILFGPRQEAFMVAAALVFVGYTALGGQRSIVKTDALQLLVL 187
                                       **9877..66666667889999***********************99999999************************ PP

                               SSF 155 lvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvagl..philvRflaak 229
                                       l+g+ +++  +l  +G    + e   + +          +           + +l lv G a l  p i  R+l+a+
  gi|386002866|ref|YP_005921165.1| 188 LLGLALVSWRALQLAGPDLLAGESFPTSEA--------RGW--------PEVAGLVLVVGSAYLagPDIYSRLLSAS 248
                                       ******999998766655444444433333........222........23333455777777777*********** PP

                               SSF 230 dakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaim 306
                                       d  +++++ l + ++l+ + + + ++++ a +l  a           ++ a+p L+ + l +l aG++ a+ l+a++
  gi|386002866|ref|YP_005921165.1| 249 DPGTARRAALAAAVILVPIAFVITALGIAARALYPA---------ILPEEALPVLMAETLSPLGAGIVAAALLSALI 316
                                       *********999988877777755555555444433.........46899*************************** PP

                               SSF 307 stltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavla 383
                                       s+ ++ ll a s+++ Dl+ +++++a  +  e+++vsr   l ++ +a+l a+  ++  +  l  +a  ++a   + 
  gi|386002866|ref|YP_005921165.1| 317 SSADTTLLTATSILALDLFGAAKPDA--SAGEILWVSRAGCLLIGGVALLSALRLPEI-ISNLL-AAYTVFAGGLIV 389
                                       *************************9..556799*********************998.66655.556666666666 PP

                               SSF 384 villalfwk..rvneqGAlagliiG 406
                                        ++ +   +  r++ +GAlagl+ G
  gi|386002866|ref|YP_005921165.1| 390 PLVAGFERErlRLTPSGALAGLLGG 414
                                       666666655226899******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2728.39
//
Query:       gi|386002867|ref|YP_005921166.1|  [L=109]
Description: hypothetical protein Mhar_2191 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-41  139.0   0.0    8.6e-41  138.8   0.0    1.0  1  DHNA      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8   0.0   4.8e-45   8.6e-41       1     107 [.       3     107 ..       3     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 4.8e-45
                                       -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTE CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgeml 77 
                                       t+re A+FEagiklgalyHqfvG+Pvs e+aesle a+eesi+lQPfv++v+v+idr++l +++  fgY eL g+ml
  gi|386002867|ref|YP_005921166.1|   3 TEREAAAFEAGIKLGALYHQFVGSPVSAETAESLEVAMEESISLQPFVRSVSVEIDRQMLGRNV--FGYGELAGKML 77 
                                       79***********************************************************999..*********** PP

                                       EEEEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  78 dveitvkyeeaevkarleyieeldYplmkv 107
                                       ++e++++ ++a+v+arley+ + dYplm++
  gi|386002867|ref|YP_005921166.1|  78 RAEVEIDRHGARVRARLEYDPQADYPLMSL 107
                                       ****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 715.06
//
Query:       gi|386002868|ref|YP_005921167.1|  [L=228]
Description: CDP-diacylglycerol/serine O-phosphatidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-08   34.1   1.5    3.5e-08   34.1   1.5    2.4  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   1.5     2e-12   3.5e-08       2      66 .]      10      72 ..       9      72 .. 0.91
   2 ?   -0.1   1.3      0.09   1.6e+03       3      20 ..     146     163 ..     130     209 .. 0.54

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2e-12
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      lP+++++l+  l+++++l ++++  l l ++l+++a+ +D+lDG lAR+ +    lG ++DslaD
  gi|386002868|ref|YP_005921167.1| 10 LPDLVSILNASLGFSSLL-MAAAGRLELSAALIFLAVAADGLDGLLARKVGD-GPLGTQIDSLAD 72
                                      79************9995.556666899999999****************98.99*********9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHHHHHHHHG CS
                   CDP-OH_P_transf   3 PnaiTllrlllsvlaill 20 
                                       P a+ l+   l +++ ++
  gi|386002868|ref|YP_005921167.1| 146 PTALILFATSLLMISSVP 163
                                       444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1567.41
//
Query:       gi|386002869|ref|YP_005921168.1|  [L=185]
Description: Phosphatidylserine decarboxylase-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-29  103.1   0.4    4.1e-26   91.8   0.1    2.0  2  PS_Dcarbxylase   Phosphatidylserine decarboxylase
    0.00028   21.0   0.1        2.5    8.4   0.0    3.2  3  Peptidase_M23    Peptidase family M23
  ------ inclusion threshold ------
      0.013   15.2   0.0        7.1    6.4   0.0    2.5  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
       0.04   14.0   0.0       0.26   11.3   0.0    2.1  1  Apocytochr_F_C   Apocytochrome F, C-terminal
      0.047   13.5   0.3          6    6.8   0.0    3.1  4  Biotin_lipoyl    Biotin-requiring enzyme
      0.094   12.6   0.0         27    4.7   0.0    3.6  5  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00015      0.43       7      34 ..      32      57 ..      26      62 .. 0.85
   2 !   91.8   0.1   1.4e-29   4.1e-26      74     199 ..      63     180 ..      60     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                    PS_Dcarbxylase  7 rklkdgaRpidddpgaivsPaDgrilqi 34
                                       +++d++R +  ++g +vsPaDgr+++ 
  gi|386002869|ref|YP_005921168.1| 32 LFHRDPERTP-RGEG-VVSPADGRVMEA 57
                                      57899***99.7877.*********986 PP

  == domain 2  score: 91.8 bits;  conditional E-value: 1.4e-29
                    PS_Dcarbxylase  74 viyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlview.kGkvavvpvGatnvgsivl 149
                                        i+++  ++H++++P +g+ve+++h +G     +p++l+++    ++neR+++vi++  G+v ++++ + +v++iv+
  gi|386002869|ref|YP_005921168.1|  63 AIFMNHHNVHVNRSPLAGRVERVEHSDGP---HRPAFLRSS----SENERNLIVIDTpAGEVRLTQITGVLVRRIVC 132
                                       79**************************7...9999***99....9**********658****************** PP

                    PS_Dcarbxylase 150 nvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                       +v++gd +++Ge++G+++fGS+v l ++ g  ++ lv +g++v++Ge+++
  gi|386002869|ref|YP_005921168.1| 133 YVRPGDLVERGERVGMIRFGSRVELSIPSG--YRLLVAEGERVRAGETVV 180
                                       ******************************..****************97 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00082       2.5      10      30 ..      40      60 ..      38      92 .. 0.79
   2 !    6.4   0.0    0.0035        10      32      72 ..     103     149 ..      75     162 .. 0.67
   3 ?    3.3   0.0     0.031        93      54      70 ..     164     180 ..     148     185 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00082
                                      ETTT-EEEESSSEEEEEEEEE CS
                     Peptidase_M23 10 apkgtpVlAaadGtVvfagkk 30
                                      +p+g+ V+++adG+V++a++ 
  gi|386002869|ref|YP_005921168.1| 40 TPRGEGVVSPADGRVMEASPG 60
                                      6899*************9874 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0035
                                       TTEEEEEEEECTC...EEEEEEEESE.ES..S-TTEEE-TTCEEEEE CS
                     Peptidase_M23  32 gyGnvviidhgdg...ystlyahlsk.is..vkegqkVkaGqvIGtv 72 
                                       +  n+++id   g   ++++ + l + i   v++g+ V++G+ +G +
  gi|386002869|ref|YP_005921168.1| 103 NERNLIVIDTPAGevrLTQITGVLVRrIVcyVRPGDLVERGERVGMI 149
                                       447788888855544344444444442336699***********976 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.031
                                       EESS-TTEEE-TTCEEE CS
                     Peptidase_M23  54 kisvkegqkVkaGqvIG 70 
                                       ++ v eg++V+aG+++ 
  gi|386002869|ref|YP_005921168.1| 164 RLLVAEGERVRAGETVV 180
                                       56799********9985 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0031       9.4      35      63 ..      41      69 ..      36      74 .. 0.82
   2 ?    6.4   0.0    0.0024       7.1      82     103 ..     161     182 ..     146     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0031
                                      E-SSEEEES--EEEEE--SSSSEEEEESS CS
                        PTS_EIIA_1 35 psegkvvapvdGkvekvfptkHaigiktd 63
                                      p  + vv+p+dG+v+ + p + ai+++++
  gi|386002869|ref|YP_005921168.1| 41 PRGEGVVSPADGRVMEASPGRLAIFMNHH 69
                                      444579*************9999998765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0024
                                       TTEEES----SEE-SEEEEEEE CS
                        PTS_EIIA_1  82 egFellvkegdkVkagdklvev 103
                                        g++llv+eg++V+ag+++v v
  gi|386002869|ref|YP_005921168.1| 161 SGYRLLVAEGERVRAGETVVAV 182
                                       799***************9976 PP

>> Apocytochr_F_C  Apocytochrome F, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.8e-05      0.26      33      60 ..     152     179 ..      70     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-05
                                       SEEE-EEEESSS-BS--ST-EE-TT-BS CS
                    Apocytochr_F_C  33 geavvetipaGpelivsegqevkageal 60 
                                       g+ v+ +ip G +l+v+eg++v+age++
  gi|386002869|ref|YP_005921168.1| 152 GSRVELSIPSGYRLLVAEGERVRAGETV 179
                                       7788999******************986 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   5.1e+03      45      54 ..      46      55 ..      45      57 .. 0.79
   2 ?   -0.9   0.0      0.49   1.5e+03      47      61 ..      76      90 ..      71      92 .. 0.85
   3 ?    3.0   0.0     0.031        93      11      33 ..     126     146 ..     116     150 .. 0.78
   4 ?    6.8   0.0     0.002         6      17      36 ..     163     182 ..     146     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                                      EEBSSSEEEE CS
                     Biotin_lipoyl 45 ieapkaGvvk 54
                                      + +p++G+v 
  gi|386002869|ref|YP_005921168.1| 46 VVSPADGRVM 55
                                      6799999986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.49
                                      BSSSEEEEEESSTTT CS
                     Biotin_lipoyl 47 apkaGvvkeilvkeG 61
                                      +p aG+v+ + +++G
  gi|386002869|ref|YP_005921168.1| 76 SPLAGRVERVEHSDG 90
                                      788999999999988 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.031
                                       EEEE.ECSESSSTTCEE-TTSEE CS
                     Biotin_lipoyl  11 sveegvvevlvkvGdkVkagqvl 33 
                                       +v+   +  +v +Gd V+ g+ +
  gi|386002869|ref|YP_005921168.1| 126 LVR--RIVCYVRPGDLVERGERV 146
                                       555..466899********9865 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.002
                                       CSESSSTTCEE-TTSEEEEE CS
                     Biotin_lipoyl  17 vevlvkvGdkVkagqvlaev 36 
                                        + lv++G+ V ag++++ v
  gi|386002869|ref|YP_005921168.1| 163 YRLLVAEGERVRAGETVVAV 182
                                       5689************9987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2   6.5e+03       7      14 ..      48      55 ..      46      56 .. 0.79
   2 ?    2.6   0.0      0.04   1.2e+02       7      21 ..      76      90 ..      75      92 .. 0.86
   3 ?   -1.1   0.0      0.57   1.7e+03      30      45 ..     107     122 ..     107     129 .. 0.82
   4 ?   -1.5   0.0      0.75   2.2e+03      17      27 ..     133     143 ..     132     144 .. 0.81
   5 ?    4.7   0.0    0.0089        27      15      29 ..     164     178 ..     163     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                   Biotin_lipoyl_2  7 apvsGrVa 14
                                      +p +GrV 
  gi|386002869|ref|YP_005921168.1| 48 SPADGRVM 55
                                      7899*995 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.04
                   Biotin_lipoyl_2  7 apvsGrVaqlnVkdG 21
                                      +p++GrV+++   dG
  gi|386002869|ref|YP_005921168.1| 76 SPLAGRVERVEHSDG 90
                                      89********98887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.57
                   Biotin_lipoyl_2  30 LaelDsralqlalaqa 45 
                                       L+++D++a +++l q 
  gi|386002869|ref|YP_005921168.1| 107 LIVIDTPAGEVRLTQI 122
                                       7889999999888885 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.75
                   Biotin_lipoyl_2  17 nVkdGqrVkaG 27 
                                       +V+ G+ V+ G
  gi|386002869|ref|YP_005921168.1| 133 YVRPGDLVERG 143
                                       68889999988 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0089
                   Biotin_lipoyl_2  15 qlnVkdGqrVkaGdv 29 
                                       +l+V +G rV aG +
  gi|386002869|ref|YP_005921168.1| 164 RLLVAEGERVRAGET 178
                                       699**********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1218.65
//
Query:       gi|386002870|ref|YP_005921169.1|  [L=270]
Description: hypothetical protein Mhar_2194 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.2  29.3    1.9e-13   50.6  29.3    1.2  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6  29.3     1e-17   1.9e-13      29     254 ..       8     249 ..       6     251 .. 0.66

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1e-17
                   Exosortase_EpsH  29 llvpllalyllw.drwrr.alaasasll.gllll....llglfll.........allgelsrvlllsalslvlillg 89 
                                       +l p+++++l+    w   a   +as+l g + l     + lf +         + +    +vll+ a++l+++ lg
  gi|386002870|ref|YP_005921169.1|   8 FLSPMIIGWLIGnVLWMGlA-LLAASALsG-RRLlaglGWVLFGVhwlkqpahyLEIKDPFNVLLTLAVALFCLYLG 82 
                                       57788888888322233331.333333322.222122233333323344454323333333444444455557778* PP

                   Exosortase_EpsH  90 lvllllGlralrlllfpllll...llalPlpavlvaqlslpLqllvaavagfllsllgipvereG.nviqlptgqve 162
                                       +++l+ G + + +++ + ++    + +  +p + v++l+ +L+  +a+++  ll +lgip++  G  vi+l + +ve
  gi|386002870|ref|YP_005921169.1|  83 WIVLARGSASASSAWAASAVAiggFAY--FPFAEVQPLKEWLISETADLTLLLLGALGIPAASGGgSVIVLADRSVE 157
                                       ***************966666314444..56666799***********************877665899999999** PP

                   Exosortase_EpsH 163 VaeaCsGlrsllallalglllallfrrrlw.krklllllaavpiaflaNlvRilllvllay..hygpeaaegllH.. 234
                                       ++ aC+ ++s+   l++g++l     ++++ +r+++ l+a+vp+++l+Nl+R+++ v++ +  ++g++++  ++H  
  gi|386002870|ref|YP_005921169.1| 158 IVLACTAIESMA--LFAGVVLS----VQAPlRRRAAALVASVPVIYLLNLFRNVFVVVAYGwgWFGADSF-YYAHnv 227
                                       *******77764..44444433....333335569*********************99986226899999.9***55 PP

                   Exosortase_EpsH 235 ...eiaGwllfgvalllllgllp 254
                                           +++++lf++a +++++llp
  gi|386002870|ref|YP_005921169.1| 228 iakAGSAVALFAIA-YVVFLLLP 249
                                       55445556777777.88888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1516.06
//
Query:       gi|386002871|ref|YP_005921170.1|  [L=1128]
Description: Peptidase families S8 and S53 protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-56  191.2   3.0    6.9e-56  189.7   3.0    1.7  1  Peptidase_S8  Subtilase family
    0.00047   20.8   0.0    0.00086   19.9   0.0    1.4  1  Inhibitor_I9  Peptidase inhibitor I9


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.7   3.0   7.6e-60   6.9e-56       1     298 []     144     425 ..     144     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: 189.7 bits;  conditional E-value: 7.6e-60
                                       -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 gv+vavlD+G+d++hpdl  +                 ++g+ +   s++ ++d  g    HGt vAGi+a++ +
  gi|386002871|ref|YP_005921170.1| 144 GTGVVVAVLDSGIDKNHPDLAGK-----------------VVGEVNFVDSERTTDDLLG----HGTTVAGIIAGSgT 199
                                       78*******************44.................5666666666666666555....************** PP

                                       .SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  77 peegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnk 153
                                       ++ ge +gvapga++l v+v+d +g+ +   +++i++i++a+ +++d++ mslg + +l+++   i+ +a+++a+ +
  gi|386002871|ref|YP_005921170.1| 200 ASGGEYVGVAPGASLLNVRVIDSKGSGQ--ISDIIAGIDWAIDNDADILTMSLG-GLNLGESNPPIS-MAADNAM-D 271
                                       *********************9999887..49**********************.********9998.7888888.9 PP

                                       CT-EEEEE--SS-T-HH......EEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-C CS
                                       xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 154 kgvlvviSaGNngktgs......slqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgni 224
                                        g++v+++aGN  +         s  ++  v++p+    vitvga++ ++ ia fS +Gp  dg+ kp++vapG+++
  gi|386002871|ref|YP_005921170.1| 272 AGTVVCVAAGNLDERLLllmlvaSSVSLGGVESPGDGVKVITVGATDCDDRIAAFSGSGPLRDGRYKPSLVAPGVSV 348
                                       *************66669999988888999999**999*************************************** PP

                                       CCCCCCCCHHHTTTHH.EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE........SSSSSSTT CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                      Peptidase_S8 225 vstwsrqsnnsaglss.yqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdl..gkadniesfaqGaG 298
                                       vst++ +   + +  + y   sGTS ++P++ag+aAlll+a p+ltp+ v+aal + A+ l  ++ +++e + qGaG
  gi|386002871|ref|YP_005921170.1| 349 VSTVPLKLDIEGKIDNyYARASGTSLSTPVVAGVAALLLQADPSLTPAGVKAALTRGAKKLsnSQDEEYEAYYQGAG 425
                                       ******99555444449********************************************8877789999999998 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.5e-08   0.00086      41      80 ..      74     112 ..      62     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.5e-08
                                       EEEEESSSSSEEEEEE-GGGHHHHHTSTTEEEEEEEEEEE CS
                      Inhibitor_I9  41 ilysYkilfnGfavklteeqaeklrkrpeVesVepDqsvr 80 
                                       +++sY+  +nG +++ +++++++l+++p V  V+pD +v 
  gi|386002871|ref|YP_005921170.1|  74 VKHSYR-TINGVSGRANASVLQRLAEDPQVLGVYPDGTVA 112
                                       79****.6****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 6662.49
//
Query:       gi|386002872|ref|YP_005921171.1|  [L=183]
Description: hypothetical protein Mhar_2196 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1176.91
//
Query:       gi|386002873|ref|YP_005921172.1|  [L=82]
Description: Transposase IS200-like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-22   78.6   0.0    4.2e-22   78.5   0.0    1.0  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   2.3e-26   4.2e-22      43     121 .]       2      79 ..       1      79 [. 0.95

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.3e-26
                            Y1_Tnp  43 lelelmpDHvHllvelppklsiskivkalkgassrlinkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIe 119
                                       ++ e+mpDHvH++v+++p  ++++i k +kg +++++++++pel+++ ++ ++lW+++Y+v t+g+ ++++++rY+e
  gi|386002873|ref|YP_005921172.1|   2 INQEIMPDHVHIFVTAHPIFAPANIAKIFKGITAKKLFEKHPELRNQLWN-GHLWNPSYYVGTCGDTTKDVIERYVE 77 
                                       5679*****************************************99777.88***********************9 PP

                            Y1_Tnp 120 nq 121
                                        q
  gi|386002873|ref|YP_005921172.1|  78 MQ 79 
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 513.64
//
Query:       gi|386002874|ref|YP_005921173.1|  [L=366]
Description: Transposase, IS605 OrfB family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-24   83.6   0.2    3.1e-23   81.5   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    7.3e-21   74.6   0.0    1.6e-20   73.5   0.0    1.5  1  OrfB_IS605      Probable transposase
    4.5e-16   58.1   1.0    9.2e-16   57.1   1.0    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0012   18.4   1.1     0.0023   17.5   1.1    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0082   16.1   0.3      0.014   15.4   0.3    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.022   14.3   0.2        3.5    7.2   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.075   13.0   0.3       0.14   12.1   0.3    1.3  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type


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 ?   -1.4   0.0      0.93   2.4e+03      54      62 ..     137     145 ..     134     153 .. 0.83
   2 !   81.5   0.1   1.2e-26   3.1e-23       1      68 [.     290     357 ..     290     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.93
                    OrfB_Zn_ribbon  54 feadrDvnA 62 
                                        +++rD+++
  gi|386002874|ref|YP_005921173.1| 137 IKLHRDIVG 145
                                       679****98 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 1.2e-26
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       +++l++  +yka+++G+ ve+vnp+ TS+ Cs Cg+++++ ls+r+++Cp Cg+++drD+nAaiNil+
  gi|386002874|ref|YP_005921173.1| 290 WNQLITATSYKAEWAGKRVELVNPSKTSQICSGCGQVVQKVLSERVHRCPFCGLTLDRDHNAAINILR 357
                                       89999*************************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   6.2e-24   1.6e-20       3     117 ..     165     276 ..     163     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 6.2e-24
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                        v+ve+++p pk++   g+D+G++ ++t++ ++    + ++r++  ++ +la+++++l++  k++  + +a + + r
  gi|386002874|ref|YP_005921173.1| 165 LVKVEPDEPIPKTGLSMGVDVGLKSFITLSSGE---HVDNPRFFVHEENALARAQRKLSKAGKGTPERARALKVVHR 238
                                       699******************************...***************************************** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +h++++++r+++++kl+ +l+k ++ ++ e+Ln+++m+
  gi|386002874|ref|YP_005921173.1| 239 VHERITNKRDDFVQKLSLSLVKSYDLIAFEDLNIKGMV 276
                                       *************************************8 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 !   57.1   1.0   3.6e-19   9.2e-16       1      47 []       1      46 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 3.6e-19
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lk  +yr+yPT+ Q++k+a t++ +R+ YN  La rk+aye+egk
  gi|386002874|ref|YP_005921173.1|  1 M-LKVLRYRIYPTKSQRTKMADTLELCRWTYNEVLAVRKNAYEQEGK 46
                                      8.99*****************************************98 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1     9e-07    0.0023       1      29 [.     315     343 ..     315     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9e-07
                     zf-NADH-PPase   1 rthrFCgrCGaptepaeggwarvCpaCgl 29 
                                       +t++ C+ CG+ ++++  ++  +Cp Cgl
  gi|386002874|ref|YP_005921173.1| 315 KTSQICSGCGQVVQKVLSERVHRCPFCGL 343
                                       5899***********************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   5.6e-06     0.014      10      44 ..     315     351 ..     311     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + ++ Cs Cg+ +++v +   +rCp Cg  +d +++ 
  gi|386002874|ref|YP_005921173.1| 315 KTSQICSGCGQVVQKVLSerVHRCPFCGLTLDRDHNA 351
                                       56899*********9998999********99999986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0014       3.5      12      30 ..     310     328 ..     305     333 .. 0.85
   2 ?    4.7   0.0    0.0084        22      21      30 ..     337     346 ..     335     351 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                                       HEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  12 veDpergelvCtdCGlVle 30 
                                       +++p+ +  +C+ CG V++
  gi|386002874|ref|YP_005921173.1| 310 LVNPSKTSQICSGCGQVVQ 328
                                       578888999********97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0084
                                       EESSSSBEEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVle 30 
                                       +C++CGl l+
  gi|386002874|ref|YP_005921173.1| 337 RCPFCGLTLD 346
                                       5777777665 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   5.6e-05      0.14      16      44 ..     316     345 ..     308     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                          zf-C2HC5  16 aapnClnCGkiiCakegls.kpCsfCgspl 44 
                                       +  +C  CG+++ +      ++C+fCg  l
  gi|386002874|ref|YP_005921173.1| 316 TSQICSGCGQVVQKVLSERvHRCPFCGLTL 345
                                       5679********88766656******9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 2389.51
//
Query:       gi|386002875|ref|YP_005921174.1|  [L=457]
Description: Proton/sodium-glutamate symport protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     2e-116  389.2  39.6   2.3e-116  389.1  39.6    1.0  1  SDF       Sodium:dicarboxylate symporter family


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.1  39.6  1.3e-120  2.3e-116       1     389 [.      31     438 ..      31     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 389.1 bits;  conditional E-value: 1.3e-120
                               SDF   1 LllqiliglvlGlviGll..........elvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgkl 67 
                                       ++l++l+g+vlG+++G+            ++k+l +++s++g +f+ ll+m++vPlvf+sii+gia+ ++++ +++l
  gi|386002875|ref|YP_005921174.1|  31 MWLKVLLGMVLGTALGISigpaagvvdpGVSKALSEWLSLPGYIFLGLLQMIVVPLVFSSIILGIAANQEMEMVKRL 107
                                       689*************99*********999*********************************************** PP

                               SDF  68 glktllyfllttliAaiiglilalllkpg.........selaleassakeaekketdslldlilslipsnifealae 135
                                       g+ + lyf++tt++A++ig+ +all++pg           +a+ + s++ a+  e  +++ +i +l+p+n+++a+a+
  gi|386002875|ref|YP_005921174.1| 108 GVLAGLYFVATTAVAIAIGIGIALLINPGqyiqgeeviLLAAAPQGSQEVADLPEIAEIPGIIGGLFPTNPLDAMAS 184
                                       *****************************88888877644555567777888888999999**************** PP

                               SDF 136 gnvlavivfailfGialaalgekg.epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakfl 211
                                       g++l+v++f++++Gia+ +l+ ++ +p+++++ sl+e++m vv++ m laP++vf+l+a+ +a+ gl++l+ +++++
  gi|386002875|ref|YP_005921174.1| 185 GQMLQVVLFSVIVGIAVLTLSPRSsAPFMDILGSLQEICMTVVRWSMLLAPLAVFGLMAKFTAQLGLETLLGMGVYV 261
                                       ********************99888**************************************************** PP

                               SDF 212 ltvylglaihllivlpllllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGa 288
                                       ++v+lgl+i lli++++++l++ ++ pl+fl  +++a+l+AfsT+SSaAt+Pv+++ ae++lg++  + +f++PlGa
  gi|386002875|ref|YP_005921174.1| 262 AAVLLGLFI-LLILYLAIILAYLRRDPLRFLADSRDAILIAFSTSSSAATMPVSIKVAEEKLGIRPAVGQFIIPLGA 337
                                       *********.677777777778888**************************************************** PP

                               SDF 289 tinmdGtalyeavaaifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglpvegialilaid 365
                                       tinm+Gtaly++va++f+aq+fgvel+++qlll++++a+ asiG+++ Pg g+v+l+++l+++g+p+eg+ali+++d
  gi|386002875|ref|YP_005921174.1| 338 TINMNGTALYQGVATVFLAQVFGVELTMAQLLLVMIIAVGASIGTPSTPGVGIVILATILASVGVPAEGVALIIGVD 414
                                       ***************************************************************************** PP

                               SDF 366 rllDmfrTavNvtGdavaalivak 389
                                       r+lDm rT+vNv Gd+va++++++
  gi|386002875|ref|YP_005921174.1| 415 RILDMSRTSVNVAGDLVASAVMDR 438
                                       *********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2958.50
//
Query:       gi|386002876|ref|YP_005921175.1|  [L=560]
Description: Phosphorylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-27   95.3   0.0    1.2e-15   56.9   0.0    3.9  4  Phosphorylase  Carbohydrate phosphorylase


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   8.8e-11   1.6e-06      22      91 ..      18      85 ..       9     114 .. 0.82
   2 !    0.5   0.0    0.0078   1.4e+02     219     281 ..     163     227 ..     148     231 .. 0.79
   3 !   56.9   0.0   6.9e-20   1.2e-15     320     581 ..     244     478 ..     237     483 .. 0.88
   4 !    5.5   0.0   0.00024       4.4     674     706 ..     521     554 ..     507     559 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8.8e-11
                                      SSHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEEBTTCCG-TT-EE-GGG-EEEEE CS
                     Phosphorylase 22 nGGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepdeWlkkgnpweiereekavevkf 91
                                       GGLG LA   + s+a   +p+  +++ Y+ G F+Q+i +dg+q e++  W  +++  e     +ave   
  gi|386002876|ref|YP_005921175.1| 18 SGGLGVLAGDTIRSAADFRVPMAAVTLLYRKGHFRQEIgDDGWQREVAAAWPVEEHL-EEMGARTAVE--V 85
                                      59************************************889**********986543.3333333333..3 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.0078
                                       EEEEESSTTTTHHHHHHHHHHHCC-..--HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHS CS
                     Phosphorylase 219 aiqlnDtHPalaipelmriLvdeeg..lewdeaweitkktfaytnhtvlpealekwpvellekll 281
                                       ++++n+ H al   e++       g     +e  + +++ + +t ht +p   +k+p+ l +k++
  gi|386002876|ref|YP_005921175.1| 163 SFHMNEGHAALLTLEILDEAARAAGrrEVTEEDKRAVQDRCVFTTHTPVPAGHDKFPIGLARKVI 227
                                       6788888888888887766655544113356677889999******************9998876 PP

  == domain 3  score: 56.9 bits;  conditional E-value: 6.9e-20
                                       CEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGGEEE----B-CHHHCCCTSHHHHHHHHHHCSSGGCC CS
                     Phosphorylase 320 kkvrmanlaivgshsvngvaalhsellkkevlkdfyelypekfnnktnGitprrwlllanpelaelitekigeewvk 396
                                       + ++m +l + +s  +ngva+ h e+  + +++ +       +  +tnG+   rw+    p +ael ++++   w +
  gi|386002876|ref|YP_005921175.1| 244 NLLNMTYLGLNMSRYINGVAKKHGEIS-RLLFAGYC------IDAITNGVHVGRWV---SPPFAELFDRHV-PMWRR 309
                                       6789*********************85.44555543......6889*********8...599999999998.57*** PP

                                       SGGGGGGGGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHH CS
                     Phosphorylase 397 dleeLkkLekladdkefleelaeikqenKerlaelikekegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYnei 473
                                       d  +L+   ++      +ee+ ++++e K+rl  +++e+ gve+++e l     +R   YkR  L +++  ++  +i
  gi|386002876|ref|YP_005921175.1| 310 DNFSLRYALSIP-----REEVWSAHTEAKRRLLGYVREEAGVEMEEEILTIGFARRATPYKRGDL-IFRDGERLARI 380
                                       *99998777665.....55677788999******************9999999***********9.67778888888 PP

                                       HHSTTS----EEEEEE----TT-HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE-- CS
                     Phosphorylase 474 kenpekkvvprtvifggkaapgYalAkkiiklinsvaevvnndpevkdklkvvflenynvslaekiipaadlseqis 550
                                        ++      +  ++++gka p  +  k++i+ i +  +      +++d +k+++le+y+++l  +i+++ dl  +  
  gi|386002876|ref|YP_005921175.1| 381 SRG----AGEIQLVYAGKAHPRDQGGKELIRRIFQAKD------ALRDDIKIAYLEDYSMTLGGMITSGVDLWLNTP 447
                                       887....578899******************9987665......567779*************************** PP

                                       -TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                     Phosphorylase 551 tagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                          +eASGT+ mk +lnG    + lDG  vE
  gi|386002876|ref|YP_005921175.1| 448 EPPMEASGTSGMKAALNGVPSFSVLDGWWVE 478
                                       ***************************8887 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.00024
                                       HHCSHHHHHHHHHHHHHCGG.GGBHHHHHHHHHH CS
                     Phosphorylase 674 aYkdkkewakksilniaksg.kFssDrtikeYae 706
                                        Y+d++ w+  +i+++a  g +F + r ++eY  
  gi|386002876|ref|YP_005921175.1| 521 FYQDREGWTDVMIHSVAINGsFFNTQRMMQEYVL 554
                                       59***************87736799*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3463.67
//
Query:       gi|386002877|ref|YP_005921176.1|  [L=318]
Description: 6-phosphofructokinase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-44  151.9   0.0    2.8e-44  151.6   0.0    1.0  1  PfkB          pfkB family carbohydrate kinase
    7.5e-08   32.0   0.0    1.1e-07   31.5   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.0   3.1e-48   2.8e-44      22     298 ..      30     301 ..       9     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 3.1e-48
                                       TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEET CS
                              PfkB  22 egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvd 98 
                                       +g   ++   +  +GG g Nv +a+ +lg++++++ a G+ n G+ l+e+l+ eg++++++   + tr + a+++ +
  gi|386002877|ref|YP_005921176.1|  30 PGRKLRCTAPTIEPGGGGVNVSRAVRKLGGESTLLYAAGGLN-GDLLEELLAGEGLRSRRLPLAGMTRESFAVLEES 105
                                       344458999999******************************.*******************9999*********** PP

                                       TTSEEEEEEEEGGGGGHHHHHHH.HHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEEEEEECESSSHHHH CS
                              PfkB  99 edgertivfnrgaaadltkeele.ededlleeadllyisgllsselpeavleelaeaaknggtfdpnlldplgaqfk 174
                                        +++  + +  +   +++ +    e+++    + +l+ sg+l++++p + ++++a a k +g    +++d++g+   
  gi|386002877|ref|YP_005921176.1| 106 TGQQYRFGMPGPVLKEEEVQLALeEVAASSPDSGFLVASGSLPPGVPADFYARVARAGKGAG--AKVIVDTSGE--- 177
                                       9977777766666666666554458889999999****************************..9********6... PP

                                       HHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGGGEEEEEETTEEEEEEE.SSSS CS
                              PfkB 175 eallellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGkeGalvvekdgelkvpavpkvk 250
                                       +  ++l +++ l+kpn +E+++l++ +l d++e+ aa+ k++a g  +++v++lG+ Gal+v+++++ ++ + p v 
  gi|386002877|ref|YP_005921176.1| 178 PLKRALQEGVYLIKPNLREFRELVDGDLRDEAEIEAAARKVVAGGGcELLVISLGSAGALFVSREAVAHMRP-PTVR 253
                                       44444559***********************************999**************************.**** PP

                                       -SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                              PfkB 251 vvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                       +v+ +GAGDs+v+g++ +l++g+  ++a+ f+ a++a++v ++g+  +
  gi|386002877|ref|YP_005921176.1| 254 IVSKVGAGDSMVAGITLSLARGMAPRDAALFGIAAGAAAVMTPGSELC 301
                                       ****************************************99998765 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.2e-11   1.1e-07     100     221 ..     167     282 ..     161     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-11
                                       SSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH.TT-SEEEEEEGGS-SSSEEEEE CS
                      Phos_pyr_kin 100 gselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk.lgakaVlikGghlegeeavvtd 175
                                       g++++ ++  e lk+ L + + +i PNl E ++L++ ++++e+++++aa+k+++  g++  +i  g +         
  gi|386002877|ref|YP_005921176.1| 167 GAKVIVDTSGEPLKRALQEGVYLIKPNLREFRELVDGDLRDEAEIEAAARKVVAgGGCELLVISLGSA----G---A 236
                                       7788888999999*****************************************78888888887763....2...4 PP

                                       EEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHH CS
                      Phos_pyr_kin 176 vlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAv 221
                                       +++++e v +++ + +   ++ G+G+++ + i+ +la+g+ +++A 
  gi|386002877|ref|YP_005921176.1| 237 LFVSREAVAHMRPPTVRIVSKVGAGDSMVAGITLSLARGMAPRDAA 282
                                       788**************************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2095.80
//
Query:       gi|386002878|ref|YP_005921177.1|  [L=84]
Description: hypothetical protein Mhar_2202 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 542.35
//
Query:       gi|386002879|ref|YP_005921178.1|  [L=377]
Description: Transposase, OrfB family, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-20   72.6   0.2    5.3e-20   71.1   0.2    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.2e-08   34.3   0.0    4.1e-08   33.5   0.0    1.4  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.035   13.6   0.4      0.085   12.4   0.4    1.6  1  HTH_OrfB_IS605  Helix-turn-helix 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 !   71.1   0.2   8.9e-24   5.3e-20       1      69 []     277     346 ..     277     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 8.9e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++ ++++eyka  +G++v++++p yTS++C+ C ++++  ++++++f C  Cgf+  +D++Aa+Ni+ r
  gi|386002879|ref|YP_005921178.1| 277 FYQHRQFVEYKAAIAGVPVVYIDPDYTSQECPICHHISRSnRPTRDRFACVCCGFSGPADTVAARNIAAR 346
                                       677899**********************************999************************976 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   6.8e-12   4.1e-08       3     106 ..     153     246 ..     149     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.8e-12
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       +vev++ +pk ++  ++g+DlGi n+a+ +t++     ++g  + +   +  + +a lqs+  +s     a+r l++
  gi|386002879|ref|YP_005921178.1| 153 VVEVPE-SPKIEPIGVIGVDLGITNIAVDSTGE----EFSGDGIENVRSKIDNLKADLQSCGTDS-----AKRHLKK 219
                                       566665.89999999*****************9....778888******************7777.....7****** PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkev 106
                                       l+ + +r+r+++ h ++++l+ + k++
  gi|386002879|ref|YP_005921178.1| 220 LSGREARFRRDVNHCISKKLVAKAKDT 246
                                       ********************9877665 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 ?   12.4   0.4   1.4e-05     0.085       3      24 ..       2      23 ..       1      27 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                    HTH_OrfB_IS605  3 lkaykyrlyPTpeQeeklartf 24
                                       ++ k+ l+PTpeQ +++++t+
  gi|386002879|ref|YP_005921178.1|  2 MQTLKVKLEPTPEQVQAIRETM 23
                                      5789***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2443.62
//
Query:       gi|386002880|ref|YP_005921179.1|  [L=93]
Description: hypothetical protein Mhar_2204 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.6e-07   29.7   0.3    9.2e-07   29.4   0.3    1.1  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.017   15.2   0.0    1.1  1  Gp49        Phage derived protein Gp49-like (DUF891)


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 !   29.4   0.3     1e-10   9.2e-07       1      81 [.       5      81 ..       5      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1e-10
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC......CTTEEEEEECTEEEEEEEET CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg......lkglrririgdyriiYridd 73
                                      v++ p+A+k+l k+           +r+ d++ e++e+l +np   rp  +++       + ++r+rig+ r+ Y +d+
  gi|386002880|ref|YP_005921179.1|  5 VIVLPKAEKHLIKL----------DQRAFDKIYEHIEELRNNPYNPRPNADIKklrgfkSPPMYRLRIGKQRLEYFVDE 73
                                      68899*********..........68**********************88877899***779***************99 PP

                                      STTEEEEE CS
                        ParE_toxin 74 eelvvvil 81
                                      ++++++i 
  gi|386002880|ref|YP_005921179.1| 74 SDKTIYIA 81
                                      99999885 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 ?   15.2   0.0   1.9e-06     0.017       3      66 ..      15      79 ..      13      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                              Gp49  3 ldalpkkarakilaaldlleeggpdlgkplvkkle......dglwElrpksaggiiRvlyafdpgrkvil 66
                                      l +l++ a +ki+++++ l+++ p +++p  +  +        ++ lr+    g  R+ y++d+++k i 
  gi|386002880|ref|YP_005921179.1| 15 LIKLDQRAFDKIYEHIEELRNN-PYNPRPNADIKKlrgfksPPMYRLRI----GKQRLEYFVDESDKTIY 79
                                      66899999***********999.56777776655555************....788********997653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 616.02
//
Query:       gi|386002881|ref|YP_005921180.1|  [L=68]
Description: PilT protein domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); 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: 0.40u 0.32s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 422.91
//
Query:       gi|386002882|ref|YP_005921181.1|  [L=637]
Description: hypothetical protein Mhar_2206 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.2   1.4      0.067   13.2   1.4    1.4  1  DUF454    Protein of unknown function (DUF454)
      0.083   13.4   0.3       0.31   11.6   0.1    2.0  2  IMP2_N    Immune Mapped Protein 2 (IMP2) N-terminal domain
       0.12   11.1   5.0      0.044   12.5   2.0    1.7  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF454  Protein of unknown function (DUF454)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   1.1e-05     0.067      52     111 ..     545     606 ..     540     610 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                            DUF454  52 klfgpyirdwrekraitlkaKvialllmllsllislll..veslwvkillalvllvvllyil 111
                                        + g+ ir++ +k+  + k+ ++a+++++++ li+ll+   ++++ +++++++++v+ll++l
  gi|386002882|ref|YP_005921181.1| 545 DRTGKNIRQFVTKGIQKIKRLIFAIATIAIITLIALLIinNSNILYAYIIGIMWIVILLILL 606
                                       5789*******999999999999999999999999888544557778888888888887765 PP

>> IMP2_N  Immune Mapped Protein 2 (IMP2) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2   1.2e+04      53      78 ..     139     165 ..     128     166 .. 0.74
   2 ?   11.6   0.1   5.1e-05      0.31      28      86 ..     276     334 ..     262     338 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                            IMP2_N  53 ellkevekkmesk.knkkyyegwckFl 78 
                                        l k ++++++   k+++ y+ +++F+
  gi|386002882|ref|YP_005921181.1| 139 DLTKYIKYNSDLDaKEEEIYQSLLAFI 165
                                       567777777777755588888888886 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.1e-05
                            IMP2_N  28 dgvlayikP.ekevpkfkyekngGkeellkevekkmeskknkkyyegwckFlklakeyeg 86 
                                       ++++a+ik  + +++ fk++ n++++ llk ++++  + ++    + +c++lk  k++ +
  gi|386002882|ref|YP_005921181.1| 276 QELFALIKQnKFKIKTFKFTVNEARRFLLKCASSPD-IYHKPIKVNSICAYLKKEKDMPS 334
                                       447788988677*****************9999986.44446678999999999999877 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.23   1.4e+03     303     331 ..     134     166 ..      96     187 .. 0.61
   2 ?   12.5   2.0   7.4e-06     0.044     349     427 ..     532     606 ..     477     613 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.23
                           DUF2207 303 d....tltilkkndeeldpyEkalldlLfdkse 331
                                       d     lt+ +k++++ld  E+++ + L   ++
  gi|386002882|ref|YP_005921181.1| 134 DalveDLTKYIKYNSDLDAKEEEIYQSLLAFIG 166
                                       133444455555555555555555555554444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.4e-06
                           DUF2207 349 kakkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaii 425
                                        ++k+k+a k +++   k+ r++ +k  +k++  + a+++++ii +++l+++ +      + +++i+++++++i++i
  gi|386002882|ref|YP_005921181.1| 532 IKEKLKNADKYFTDRTGKNIRQFVTKGIQKIKRLIFAIATIAIITLIALLIINNSN----ILYAYIIGIMWIVILLI 604
                                       34444444444455444566777776666666666666666666666666555444....77777777777777777 PP

                           DUF2207 426 vl 427
                                       +l
  gi|386002882|ref|YP_005921181.1| 605 LL 606
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1537  (0.085727); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3990.64
//
Query:       gi|386002883|ref|YP_005921182.1|  [L=150]
Description: Transposase, IS4 family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-12   45.8   0.2    7.7e-12   45.3   0.2    1.2  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.018   15.2   0.1      0.029   14.5   0.1    1.3  1  MWFE       NADH-ubiquinone oxidoreductase MWFE subunit


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.2   8.6e-16   7.7e-12     142     213 ..      17      95 ..       3      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 8.6e-16
                         DDE_Tnp_1 142 nk.......skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqlllllla 211
                                       ++        k+e+ ++ y+tn++sell++ eva++y  Rw++E  Fk+lk+++ l  + +++++++e  +++ +l+
  gi|386002883|ref|YP_005921182.1|  17 ERfrfvsifNKDEDRYHMYITNISSELLEPDEVARIYAARWVVEILFKELKSRYVLYMVPTYNPQAIEVIIWIAILM 93 
                                       335557777889999**********************************************************9998 PP

                         DDE_Tnp_1 212 ln 213
                                       l 
  gi|386002883|ref|YP_005921182.1|  94 LI 95 
                                       75 PP

>> MWFE  NADH-ubiquinone oxidoreductase MWFE subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.3e-06     0.029      10      44 ..      89     123 ..      85     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                              MWFE  10 ImiamfgitgaglskirklqnggkraRhsvdqWdr 44 
                                       I i m+ i+  +l+++r+l  + k aR s+ +W  
  gi|386002883|ref|YP_005921182.1|  89 IAILMLIISRKILKVVRALNKEVKMARFSTLRWSN 123
                                       8899*****************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1033.47
//
Query:       gi|386002884|ref|YP_005921183.1|  [L=89]
Description: hypothetical protein Mhar_2208 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.1e-08   32.7   0.0    9.7e-08   32.4   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   5.4e-12   9.7e-08      19     107 ..       3      88 ..       2      89 .] 0.86

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.4e-12
                                       -SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HH.HCSS.SSSSSSEEEECCCEEEEEGGGEEEEEE CS
                        PemK_toxin  19 gkrRpvvVvsndafnekntvivvpltskdkdkkklpfhvelese.ildl.ngldkdswvkldqirtvdkarlrkkig 93 
                                        krRp++ + +  +++   viv+ + s+ ++++  p +v ++s+  + + +gl +ds+++l + +tv+k+ +++ +g
  gi|386002884|ref|YP_005921183.1|   3 SKRRPALLLRK--YRD--DVIVAYIYSRVPERLS-PAEVLVSSAsASFKgTGLLTDSVIMLNKPATVEKRLIIRVLG 74 
                                       599*****954..554..9***********9999.*******984444455555*********************** PP

                                       E--HHHHHHHHHHH CS
                        PemK_toxin  94 klsredlaevqral 107
                                       + ++++ ae++ +l
  gi|386002884|ref|YP_005921183.1|  75 EADDDLKAEINFKL 88 
                                       *********99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 636.18
//
Query:       gi|386002885|ref|YP_005921184.1|  [L=668]
Description: N-6 DNA methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-35  122.0   0.1    1.1e-34  120.1   0.0    1.9  2  N6_Mtase     N-6 DNA Methylase
    1.1e-11   44.7   0.0      2e-11   43.9   0.0    1.5  1  HSDR_N_2     Type I restriction enzyme R protein N terminus (
    1.6e-05   24.6   0.0    6.8e-05   22.6   0.0    1.9  1  UPF0020      Putative RNA methylase family UPF0020
    0.00075   19.3   0.0     0.0022   17.7   0.0    1.7  1  N6_N4_Mtase  DNA methylase
     0.0096   15.9   0.2      0.027   14.4   0.0    1.9  2  HSDR_N       Type I restriction enzyme R protein N terminus (
  ------ inclusion threshold ------
      0.051   13.5   0.0       0.17   11.8   0.0    1.9  1  PDDEXK_9     PD-(D/E)XK nuclease superfamily
      0.064   13.1   0.0        6.9    6.5   0.0    2.6  2  BCDHK_Adom3  Mitochondrial branched-chain alpha-ketoacid dehy


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.47   1.2e+03     257     299 ..     244     287 ..     233     290 .. 0.75
   2 !  120.1   0.0   4.4e-38   1.1e-34       4     246 ..     299     585 ..     296     602 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.47
                          N6_Mtase 257 knklteediekildtykek.skevdkfskvveleeiaendynln 299
                                       +n+  e+  ++i d+y ++ +ke d f   +++++i  ++ +l 
  gi|386002885|ref|YP_005921184.1| 244 TNETPERLARRIKDMYSKErEKEPDVFNDDIKIDNITLKNVVLH 287
                                       55555666678999998885667779999999999998887775 PP

  == domain 2  score: 120.1 bits;  conditional E-value: 4.4e-38
                          N6_Mtase   4 dllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee......... 71 
                                       d+ G ++E+++  f    + + G++fTPr+++ + +++l+ k++ +v+DpacGsgg+l++a ++++++         
  gi|386002885|ref|YP_005921184.1| 299 DTKGVAFEQFMDGF---FKGDFGQYFTPRNIIAFAIQMLDIKEDDTVIDPACGSGGFLLHALDHVRHKasdywpeds 372
                                       777899*******9...56777*******************************************9879*****999 PP

                          N6_Mtase  72 ......dgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe..................... 121
                                              ++  e+ ++G e+ne+ +r+akmN+++h+      +i  +d+l+                          
  gi|386002885|ref|YP_005921184.1| 373 kehyeyWHSFAEKRLFGIEINEEIARVAKMNMIVHDDGHT--NIIGQDALQPLAAIakrnqgfakilginpdtgqrd 447
                                       9988887888899999*******************97665..799999987555447788999************99 PP

                          N6_Mtase 122 kdkkfdvvvaNppfnqkew.....kektlekderfreavapksna....dlafllhiieslkpkGraavvlangvLf 189
                                       ++k f  + +Nppf++        +  +  + +r+ + +a k+ a    ++ +   + + lkp+G+aavvl++g L 
  gi|386002885|ref|YP_005921184.1| 448 EQKGFSKIPTNPPFGAV-VkeelhSYLSTYELSRYGKETAVKQRAsvktEIIYCERVWQLLKPGGQAAVVLPDGLLT 523
                                       9999***********87.3122222223333447777766666541111667**********************997 PP

                          N6_Mtase 190 rggkegkIrkalvekdlveavialpeklFyn..tsiptcilvlkkekae....rkgkvlfida 246
                                         +  +++r+ ++e   + av++lp+  F     +++ ++++l+k   +     ++ +++  a
  gi|386002885|ref|YP_005921184.1| 524 T-SSLQRVRNWILERFKILAVVSLPQFAFAHfgAGVKSSVVFLEKRGMDesasDDEAIFMAMA 585
                                       6.56789**********************865589**********876667634444444444 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   7.8e-15     2e-11       1      99 [.      43     147 ..      43     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 7.8e-15
                          HSDR_N_2   1 pEEwvRqklikyLveelgypkeliavekelqlgskkkraDivvykkd..kkpllivecKapsvki..seevleqlks 73 
                                       pEE++R  +  +L+ ++gy+ + i ve+++   +  +raD+v++ +   ++p+ ++ecK+++++    +++++q++ 
  gi|386002885|ref|YP_005921184.1|  43 PEEKIRAAYYAELIYRYGYKPDCIGVEVTVPDRTPADRADLVIFHDAtrTRPFAVIECKRDDISDteFKQAIDQAFG 119
                                       8*******************************************9996677************99555699999986 PP

                          HSDR_N_2  74 Ylea..lkaeylvvtNglehivykvdkk 99 
                                         +a  ++a y+ v  g+   ++++++k
  gi|386002885|ref|YP_005921184.1| 120 NGHAhkFRASYVGVIAGHTRGFFDCSDK 147
                                       5554348999999999999988887664 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.7e-08   6.8e-05      17     133 ..     328     463 ..     324     477 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS............................. CS
                           UPF0020  17 AaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvle............................. 64 
                                       A a+ ++ ++k++++ +DP CGsG++l+ a   +++ a     + + e                             
  gi|386002885|ref|YP_005921184.1| 328 AFAI-QMLDIKEDDTVIDPACGSGGFLLHALDHVRHKAS----DYWPEdskehyeywhsfaekrlfgieineeiarv 399
                                       5554.45599******************99888888884....4455543345666666666666666655554433 PP

                                       HHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
                           UPF0020  65 lkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                                       +k ++  +   + +++g D  + + + a++N   a++ ++    + +     +++  +  i tnpP+G 
  gi|386002885|ref|YP_005921184.1| 400 AKMNMIVHDDGHTNIIGQDALQPLAAIAKRNQGFAKILGIN-PDTGQRD---EQK-GFSKIPTNPPFGA 463
                                       33333333334445666666666666666666666665532.2222222...222.3556666666665 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.6e-07    0.0022     118     230 ..     240     401 ..     216     402 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.6e-07
                                       --GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEE..........E-SCCCTTSTTS-CHH................ CS
                       N6_N4_Mtase 118 fnldaikvpyeekdklekrgaytskkkgkkiediW..........dlseiqsnekkskgdt................ 168
                                       f+++++++p +  ++++  +    +k+ +k+ d++           ++ + + e+ + ++t                
  gi|386002885|ref|YP_005921184.1| 240 FQIKTNETPERLARRIKDMY----SKEREKEPDVFnddikidnitLKNVVLHLEGLNLNATdldtkgvafeqfmdgf 312
                                       44444444444444444444....44444444444444444444422223333333333334444444444444444 PP

                                       .----.SS---HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-E........................EEE CS
                       N6_N4_Mtase 169 .kkkH.paqkPvallerlIklstkk.gdivlDpFaGSGtTavaakelgrk........................fiG 218
                                        k+ + ++  P++++ ++I+++  k +d+v+Dp +GSG  +  a+   r+                          G
  gi|386002885|ref|YP_005921184.1| 313 fKGDFgQYFTPRNIIAFAIQMLDIKeDDTVIDPACGSGGFLLHALDHVRHkasdywpedskehyeywhsfaekrLFG 389
                                       42222355569********9985554*************999999999999************************** PP

                                       EESSHHHHHHHH CS
                       N6_N4_Mtase 219 ieieeeyvelae 230
                                       iei+ee+++ a+
  gi|386002885|ref|YP_005921184.1| 390 IEINEEIARVAK 401
                                       *******99886 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.1e-05     0.027     113     153 ..      69     118 ..       9     131 .. 0.86
   2 ?   -3.8   0.1         4     1e+04      37      55 ..     266     288 ..     241     303 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                       ----S.SSS---EEEEEEET...TEEEEEEEE--T...T.-HHHHHHH.H CS
                            HSDR_N 113 Qvtvt.gnqkrrpDivlfvn...glplvviElKrp...g.tieeAinQ.i 153
                                       +vtv  ++   r+D+v+f++     p +viE+Kr      ++++Ai+Q +
  gi|386002885|ref|YP_005921184.1|  69 EVTVPdRTPADRADLVIFHDatrTRPFAVIECKRDdisDtEFKQAIDQaF 118
                                       44555788899*********9999**********9875257888888744 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                                       ......----SHHHHHHHHHHHH CS
                            HSDR_N  37 e....vrkskaevaleknlreql 55 
                                       e    + ++k +++++kn+  +l
  gi|386002885|ref|YP_005921184.1| 266 EpdvfNDDIKIDNITLKNVVLHL 288
                                       12223334444455555555555 PP

>> PDDEXK_9  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.5e-05      0.17       5      83 ..      51     128 ..      48     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                          PDDEXK_9   5 yyksvfyalla..lslgyevksEdetnkGriDlllkpkektkkkiyifEfKylkekesekekaeealeQikekgyae 79 
                                       yy+ ++y +       g ev++ d+t+  r+Dl++    + ++   ++E+K   ++++++ + ++a++Q  ++g a 
  gi|386002885|ref|YP_005921184.1|  51 YYAELIYRYGYkpDCIGVEVTVPDRTPADRADLVIFHDATRTRPFAVIECK---RDDISDTEFKQAIDQAFGNGHAH 124
                                       78888887776444578999999*************5666678889*****...9999999999*****99999999 PP

                          PDDEXK_9  80 kyke 83 
                                       k+++
  gi|386002885|ref|YP_005921184.1| 125 KFRA 128
                                       8876 PP

>> BCDHK_Adom3  Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.021        55      22      42 ..     239     259 ..     219     280 .. 0.84
   2 ?    6.5   0.0    0.0027       6.9      44      70 ..     517     543 ..     512     571 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.021
                       BCDHK_Adom3  22 saqflreelpirlAhrvkele 42 
                                       ++q+  +e p rlA+r+k++ 
  gi|386002885|ref|YP_005921184.1| 239 AFQIKTNETPERLARRIKDMY 259
                                       6788899***********985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0027
                       BCDHK_Adom3  44 lPdglvenpsvkkvkdwYaqsfeelle 70 
                                       lPdgl++++s ++v++w ++ f+ l  
  gi|386002885|ref|YP_005921184.1| 517 LPDGLLTTSSLQRVRNWILERFKILAV 543
                                       9********************997754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 4317.20
//
Query:       gi|386002886|ref|YP_005921185.1|  [L=459]
Description: Type I restriction-modification system, specificity subunit S [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-15   55.7   0.0    2.6e-08   34.3   0.0    2.2  2  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.4e-12   2.6e-08      59     150 ..      91     189 ..      47     192 .. 0.82
   2 !   19.2   0.0   6.1e-08    0.0011      74     147 ..     347     422 ..     313     433 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.4e-12
                                       TT-EEEE-S.SSTT-EEEESS-...BEE-TTEEEEEEST.TT--HHHHHHHHH..HCHHHHHHHCCSSTTT---HHH CS
                       Methylase_S  59 kgdilissr.atiGkvayrdkk...yylnqsvivlipkn.kkkineflylyll..lklkklkslsvgstqpkltken 128
                                        gdi++s+   + G++a+++k+   +++++++  ++ ++  +  +e+l + l    +l ++ + s g+++p +t e+
  gi|386002886|ref|YP_005921185.1|  91 TGDIIVSLTrPHHGSIALIKKEhhgCIASTGFAIIRNIDeTQISKEYLVHTLRssICLDQMLRRSSGGNYPAITEEE 167
                                       4566666555***********65559**********99855555788888888888889****************** PP

                                       HCC-EEEE--HHHHHHHHHHHH CS
                       Methylase_S 129 lkkikIplPpleeQkkIakiLs 150
                                       l++ikIp+Pp e+Q + +  L+
  gi|386002886|ref|YP_005921185.1| 168 LANIKIPVPPAEIQCRLVAELD 189
                                       **************88776665 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.1e-08
                                       EEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHH...HHHHH.CCSSTTT---HHHHCC-EEEE--HHHHHHHH CS
                       Methylase_S  74 ayrdkkyylnqsvivlipknkkkineflylylllklk...klksl.svgstqpkltkenlkkikIplPpleeQkkIa 146
                                          + ++ +++++ ++++k+ + + +f++ +l  + +   ++++l ++  +q+ +++++l+++ +p+P+   Qk Ia
  gi|386002886|ref|YP_005921185.1| 347 YDLETPCACSNHMTRISLKP-GIDPYFIAALLN-AFRgigYFSALsTFFNNQAGINTATLAELRVPVPSETVQKAIA 421
                                       4555689************8.555466666665.445455444446789999*****************9******9 PP

                                       H CS
                       Methylase_S 147 k 147
                                       k
  gi|386002886|ref|YP_005921185.1| 422 K 422
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2946.99
//
Query:       gi|386002887|ref|YP_005921186.1|  [L=531]
Description: hypothetical protein Mhar_2211 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-06   25.8   0.1    2.3e-05   23.8   0.0    2.0  2  DndB      DNA-sulfur modification-associated
  ------ inclusion threshold ------
       0.13   12.6   1.5       0.75   10.1   1.3    2.3  2  PRD       PRD domain
       0.29   11.0   4.0        1.1    9.1   3.6    2.2  2  DUF919    Nucleopolyhedrovirus protein of unknown function (D


Domain annotation for each model (and alignments):
>> DndB  DNA-sulfur modification-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.9e-09   2.3e-05      19     162 ..      22     202 ..       9     221 .. 0.69
   2 ?   -2.1   0.2      0.28   1.7e+03     190     231 ..     373     414 ..     361     429 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.9e-09
                              DndB  19 plrelpklievdeeevpnspelraqRklnksrvkeIakYllensdeyifsaltas...................... 73 
                                       pl +l++  ++d++          qR l+ ++ +eI+++l++++   +f+ +++s                      
  gi|386002887|ref|YP_005921186.1|  22 PLGDLARCSKFDPD---------FQRNLIDTHCQEIVRFLADQHY-CFFPEVVLSaslqfdfdkfkgrdrrsplari 88 
                                       55556666666666.........8****************99965.8*****************************9 PP

                              DndB  74 .........vd.eeleflpls.......ssqkekvGvlkipmda.eil.....ivDGQHRraAieealkeepelgee 127
                                                v+  ++++ +++       +s++ ++++l +p d  e        +DG HR+ A+++a   +   ++ 
  gi|386002887|ref|YP_005921186.1|  89 yesqsfssnVNgLSIKVVKSKlpklilgGSNAPEIAYLDLPEDRlE-EglrliRIDGNHRLSALNDASPGDA-RNKL 163
                                       99999999944445555444443333324446*********98543.12355479************66333.3444 PP

                              DndB 128 eipvvlfvelgleksqq....lFadlNkyakridkslll 162
                                       + p  +++++  + +q+     F+ +N  + ++++  +l
  gi|386002887|ref|YP_005921186.1| 164 PTPFCIVLHEYADNAQRfekvTFHNINSKQIPLTSEENL 202
                                       445555554444444431111688888666666555554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.28
                              DndB 190 meksslskkseklfTlstlveatkellknqsaskealdekie 231
                                       + +s +  +++++f   +++e tke ++  +++ ++ +ek++
  gi|386002887|ref|YP_005921186.1| 373 VFESIMTARKRQIFISMAFQEETKETYETIKKTVQQINEKYQ 414
                                       445555555555555555555555555555555555555444 PP

>> PRD  PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.33     2e+03      51      71 ..     221     241 ..     203     243 .. 0.79
   2 ?   10.1   1.3   0.00012      0.75      49      80 ..     391     422 ..     373     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                                       HHTHHHHHHHHHHHHHHHHHH CS
                               PRD  51 ekypkefeiakeileeleeel 71 
                                       + +  ++ +a+++l+++e ++
  gi|386002887|ref|YP_005921186.1| 221 QSFGPAYYLARKVLADIEDRY 241
                                       45678999*********9987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00012
                                       HHHHTHHHHHHHHHHHHHHHHHHTST--HHHH CS
                               PRD  49 ikekypkefeiakeileeleeeldielpedEi 80 
                                       ++e+ ++ +e++k+++++++e++++++   Ei
  gi|386002887|ref|YP_005921186.1| 391 FQEETKETYETIKKTVQQINEKYQLDIELREI 422
                                       45666779*****************9998887 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 ?   -3.1   0.0       1.3   7.5e+03      39      54 ..     275     290 ..     272     290 .. 0.81
   2 ?    9.1   3.6   0.00019       1.1      15      59 ..     380     431 ..     368     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                            DUF919  39 ElqdlekklnklRqeF 54 
                                         + l+ ++ +lR+ F
  gi|386002887|ref|YP_005921186.1| 275 DAATLDAQVPRLRNAF 290
                                       4578999999999988 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00019
                            DUF919  15 qaKrkltiksqH.......fErlkkitKnpkElqdlekklnklRqeFLnfgv 59 
                                       + Kr++ i +         +E +kk   + +E  +l+ +l ++R +F+n+g+
  gi|386002887|ref|YP_005921186.1| 380 ARKRQIFISMAFqeetketYETIKKTVQQINEKYQLDIELREIRIDFFNKGH 431
                                       56888888886611111114568888888889999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3280.67
//
Query:       gi|386002888|ref|YP_005921187.1|  [L=279]
Description: hypothetical protein Mhar_2212 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1688.25
//
Query:       gi|386002889|ref|YP_005921188.1|  [L=79]
Description: hypothetical protein Mhar_2213 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 577.86
//
Query:       gi|386002890|ref|YP_005921189.1|  [L=296]
Description: Formylmethanofuran-tetrahydromethanopterin formyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-64  216.9   0.9    1.7e-64  216.3   0.3    1.6  2  FTR_C     FTR, proximal lobe
    2.3e-61  205.9   0.5    5.7e-61  204.6   0.1    1.8  2  FTR       Formylmethanofuran-tetrahydromethanopterin formyltr


Domain annotation for each model (and alignments):
>> FTR_C  FTR, proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.44     4e+03      17      37 ..      20      40 ..       8      47 .. 0.74
   2 !  216.3   0.3   1.9e-68   1.7e-64       1     149 []     147     294 ..     147     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.44
                                      EEEEEEEESSHHHHHHHHHHH CS
                             FTR_C 17 Ggnllilaedqeaaleaaeaa 37
                                       + +li+a +++ a+eaa++a
  gi|386002890|ref|YP_005921189.1| 20 VARVLITAITERWAMEAAREA 40
                                      566788888888888888877 PP

  == domain 2  score: 216.3 bits;  conditional E-value: 1.9e-68
                                       EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-S-TT-SEEE-GGG CS
                             FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgskykflkastNeaf 77 
                                       g+f++eek+g+v+g+aGgn++i+ae+q+aal+aaeaav+ai++ eg+itpFpGg+v+sgSKvgs+ykflkastNe+f
  gi|386002890|ref|YP_005921189.1| 147 GDFIVEEKMGAVDGIAGGNFYIMAENQAAALMAAEAAVDAIREEEGTITPFPGGVVASGSKVGSRYKFLKASTNERF 223
                                       8**************************************************************************** PP

                                       -TTSTT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                             FTR_C  78 cptlkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                       cptl+++   + lp++++a +E+Vi+g+++ea++++m+ gi aa+kv+gv+kisAgN++GkLG++ fkL+e+
  gi|386002890|ref|YP_005921189.1| 224 CPTLQDEG-VCILPPSIRASYEVVINGVSREAIERSMRSGIMAACKVPGVVKISAGNFEGKLGPHLFKLHEI 294
                                       ******99.9************************************************************97 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.6   0.1   6.4e-65   5.7e-61       1     142 []       1     144 [.       1     144 [. 0.98
   2 ?   -1.7   0.0      0.28   2.5e+03      51      73 ..     179     201 ..     168     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 6.4e-65
                                       -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEE CS
                               FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailif 77 
                                       +ei gveiedtfaE+F+ikv+rv+iTa t++wa+eaa+eatgf+tsvi+c+aEagier  ++ etpDgRpGv+i+i+
  gi|386002890|ref|YP_005921189.1|   1 MEISGVEIEDTFAEGFPIKVARVLITAITERWAMEAAREATGFGTSVIMCPAEAGIERLARRAETPDGRPGVYIQIC 77 
                                       89*************************************************************************** PP

                                       ESSHHHHHHHHHHHHHHHTTTSTT-EEEE--..GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                               FTR  78 aaskkklekqlleRigqcvLtapttavfngl..aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                       ++s k+le +ll+RigqcvLtapttavfngl  ae+++++g kl+ffgDg+++e  + +r v++iPv
  gi|386002890|ref|YP_005921189.1|  78 NMSFKNLEASLLARIGQCVLTAPTTAVFNGLpeAEKQFDTGAKLKFFGDGFQKEMAYCDRGVCSIPV 144
                                       *******************************7556*******************************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                                       S-EEEESEEB-GGGSTTSS-EEE CS
                               FTR  51 eaEagiervlspeetpDgRpGva 73 
                                        aEa+++ + ++e t    pG +
  gi|386002890|ref|YP_005921189.1| 179 AAEAAVDAIREEEGTITPFPGGV 201
                                       47788887777777665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1865.06
//
Query:       gi|386002891|ref|YP_005921190.1|  [L=209]
Description: IMP cyclohydrolase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-56  191.1   0.0    1.7e-56  190.8   0.0    1.0  1  IMP_cyclohyd  IMP cyclohydrolase-like protein


Domain annotation for each model (and alignments):
>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.0   9.7e-61   1.7e-56       1     187 [.       2     186 ..       2     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 9.7e-61
                                       ---SEEEEEEETTEE.EEEEEEE-SS---EEEEEETTEEEEEE-TGGGGGT-TTSSEEEEEEETTEEEEESSTHHHH CS
                      IMP_cyclohyd   1 YvGRfivvgksedgkavaaYrvssRSfpnrnrvfredkirveptdeeklednpyiiYncvrvlddkavvtNGsqtdt 77 
                                       YvGR++++g +  g+a++ YrvssRSfpnr++++r d++ v p+d+ +le+npyi+Ync+r+++++avv+NG++ d+
  gi|386002891|ref|YP_005921190.1|   2 YVGRIVIIGGT-GGRAWVGYRVSSRSFPNRKAKVRGDSVLVSPVDPLDLEKNPYIAYNCIRIAGKAAVVANGTHADM 77 
                                       9**********.8889************************************************************* PP

                                       HHHHHHTSB-HHHHHHHHHHHH-S--STT---EEEEEE-SS.EEEEEEETTEEEEEE--..TTS-EEEESSS--S-E CS
                      IMP_cyclohyd  78 iaeklekgltardalalsLlaldyEkDdynTPRiagvvkeeeaalgivksdallvekvelkagegtliatYekgepk 154
                                       i ek++ g+   +a+alsL+a  yE+D+ +TPRiag v   + +lgi ++d+++ ++ +l+   + ++atYek+e++
  gi|386002891|ref|YP_005921190.1|  78 IGEKIADGTRPLEAIALSLIAFGYERDELDTPRIAGAVMGGRGWLGIARKDEIWAKEYDLSGDGAFMVATYEKTEFE 154
                                       ***********************************************************9999999*********** PP

                                       E-----SSHHHHHHHHHHGGGSS-EEEEEEEEE CS
                      IMP_cyclohyd 155 eveleaedaeeaaeelweslefenkVslavavi 187
                                       e++l   +a e+a++++e +++e++V++a+a+ 
  gi|386002891|ref|YP_005921190.1| 155 EISLGGGSAGEIAKAAFE-MDYEKPVCSAAAFD 186
                                       ******************.**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1265.06
//
Query:       gi|386002892|ref|YP_005921191.1|  [L=275]
Description: Pyruvate:ferredoxin oxidoreductase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete 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-24   85.5   0.0      4e-24   85.1   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   2.3e-28     4e-24       2     153 .]      22     184 ..      21     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 2.3e-28
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH.....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla.....kpdrevvaivGDGgflmi.lqelatavrrn 72 
                                       +Gcl+++   +    + +s+  + +++ + +  ++A+G+++a     k d +  +i GDG++++i +  ++ +  r+
  gi|386002892|ref|YP_005921191.1|  22 TGCLEVTSTPF----PESSWRVPWIHSLFENPAAVASGVEVAlkrfkKTDINLLVIGGDGSTFDIgFGSISGMFDRG 94 
                                       68888855555....566788899*****************6556645689************************** PP

                                       -SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHH CS
                      TPP_enzyme_C  73 lpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealk 140
                                       + it+v+++Ne+y++tg q   ++pf +k++++p+gk       +++d+ ++a a+G++ +a+ + a++ +l+++++
  gi|386002892|ref|YP_005921191.1|  95 HRITYVCYDNEAYMNTGVQrsgSTPFCAKTTTTPTGKlslgnPRPKKDLPAIAVAHGVPyVATASIAYPVDLRRKVR 171
                                       ****************************************977999*************999999************ PP

                                       HHHCSSSEEEEEE CS
                      TPP_enzyme_C 141 ealekkgpaliev 153
                                       + l+ +gpa+i+v
  gi|386002892|ref|YP_005921191.1| 172 RSLSADGPAYIQV 184
                                       ***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1888.52
//
Query:       gi|386002893|ref|YP_005921192.1|  [L=392]
Description: Pyruvate:ferredoxin oxidoreductase subunit A [Methanosaeta harundinacea 6Ac]
Scores for 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-68  228.8   0.0    9.2e-68  228.4   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.4e-31  108.8   0.2    2.4e-31  108.1   0.2    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    7.2e-11   42.0   0.1    1.7e-10   40.9   0.1    1.6  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.4   0.0   1.5e-71   9.2e-68       4     229 ..      16     236 ..      13     238 .. 0.97

  Alignments for each domain:
  == domain 1  score: 228.4 bits;  conditional E-value: 1.5e-71
                                       HHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHH CS
                             POR_N   4 iaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlg 80 
                                         +++dvi+ YPITP++ i+e l+e++a+g++ d +++++esE+++ s  iGA+aaGar+ T T +qGl+Lm e l+
  gi|386002893|ref|YP_005921192.1|  16 RCCSPDVISVYPITPQTHIVEHLSEFVADGKL-DCQYINVESEFSSLSSLIGASAAGARTYTSTTSQGLALMFEVLF 91 
                                       56899**************************9.9******************************************* PP

                                       HHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEH CS
                             POR_N  81 laageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDg 155
                                        ++g++lP+v++ v+Ral+++ lsi++dq+D+maar+ g+i++++envqea+dl+ + ++++e+  + +P + ++Dg
  gi|386002893|ref|YP_005921192.1|  92 NVSGMRLPIVMTTVNRALSAP-LSIWNDQQDAMAAREAGWIQIYAENVQEAMDLTPQLYKISEDpkILTPSMACMDG 167
                                       *********************.******************************************99*********** PP

                                       HHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
                             POR_N 156 fllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                                       f+l+h +e+ve++d e     ++e+l++y++++  ldp+ p ++g+ a p ++ e+++ +++a+++a+k ++ v
  gi|386002893|ref|YP_005921192.1| 168 FILTHVYEPVEFLDIE----KVREFLPPYRPED-VLDPKDPKTFGAFADPSWFTEFKYLQYQAMERAKKKIALV 236
                                       ****************....9********9988.**********************************998877 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.2     4e-35   2.4e-31       1     102 []     260     363 ..     260     363 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 4e-35
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Aev++v+mGsv+gt+k+a+d lR eg+kvGl+++r++rPFPeeelke+lk+++ +v++++++s+g+e++l+++ k a
  gi|386002893|ref|YP_005921192.1| 260 AEVALVTMGSVVGTVKEAIDGLRSEGVKVGLVKIRSYRPFPEEELKEALKDAEVIVTIEKDVSMGYESALLTDLKGA 336
                                       9**************************************************************************** PP

                                       TGGG..TSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkks..kvkvvnfvaglgGrditvedi 102
                                        ++s  +v++v f aglgGrdi v++i
  gi|386002893|ref|YP_005921192.1| 337 FYNSpiRVPIVGFAAGLGGRDIGVKQI 363
                                       **********************99986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   2.8e-14   1.7e-10       8      91 ..     258     339 ..     254     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.8e-14
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHH CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaal 84 
                                       e  +v+lv++Gs v ++ eA++ L++eg+++ +v +r+ +p+ +e ++e++k  + +v++e +v  +G +s++++ l
  gi|386002893|ref|YP_005921192.1| 258 EDAEVALVTMGSVVGTVKEAIDGLRSEGVKVGLVKIRSYRPFPEEELKEALKDAEVIVTIEKDVS-MGYESALLTDL 333
                                       6789********************************************************99888.99*99999988 PP

                                       HHCCCTT CS
                   Transketolase_C  85 aeeafdg 91 
                                          af +
  gi|386002893|ref|YP_005921192.1| 334 KG-AFYN 339
                                       87.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2311.86
//
Query:       gi|386002894|ref|YP_005921193.1|  [L=86]
Description: Pyruvate:ferredoxin oxidoreductase subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-11   42.8  15.0    4.1e-06   26.4   2.3    2.3  2  Fer4      4Fe-4S binding domain
    1.8e-08   34.4  14.1    3.2e-08   33.6  14.1    1.4  1  Fer4_21   4Fe-4S dicluster domain
    4.3e-07   29.7  17.4    0.00018   21.5   6.0    2.4  2  Fer4_6    4Fe-4S binding domain
    1.2e-06   28.6  12.3    0.00011   22.3  14.0    2.0  2  Fer4_9    4Fe-4S dicluster domain
    2.6e-05   24.0  12.0       0.01   15.9   1.9    2.6  2  Fer4_2    4Fe-4S binding domain
    3.7e-05   24.2  15.5    0.00018   22.0  15.2    2.0  2  Fer4_7    4Fe-4S dicluster domain
    6.5e-05   23.8  13.4     0.0049   17.8   2.1    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00013   22.4  10.1      0.056   14.0   2.4    2.2  2  Fer4_17   4Fe-4S dicluster domain
     0.0006   19.9  15.0      0.012   15.8  15.7    2.1  2  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.043   14.8  15.5       0.27   12.3   1.3    2.6  2  Fer4_3    4Fe-4S binding domain
      0.083   13.5  12.0        1.2    9.8   2.9    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.11   13.0  16.4        1.7    9.1   5.0    2.2  2  Fer4_8    4Fe-4S dicluster domain
       0.85   10.3  21.0        1.8    9.3   6.7    2.8  2  Fer4_4    4Fe-4S binding domain
       0.98   10.2  15.0        1.2    9.9   2.7    2.9  3  Fer4_15   4Fe-4S single cluster domain
        8.3    7.3  15.6        5.3    8.0   4.0    2.2  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   5.1   8.2e-08   9.8e-05       1      23 [.      28      50 ..      28      51 .. 0.93
   2 !   26.4   2.3   3.4e-09   4.1e-06       2      24 .]      58      80 ..      57      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.2e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +v+d  kCi+C +C+  CP  +I
  gi|386002894|ref|YP_005921193.1| 28 PVFDHAKCIKCSLCEIYCPESCI 50
                                      689****************9998 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 3.4e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v d + C gC  C+  CP gAIt
  gi|386002894|ref|YP_005921193.1| 58 VPDLDYCKGCSVCAHECPRGAIT 80
                                      5699******************7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6  14.1   2.6e-11   3.2e-08       3      59 .]      30      81 ..      28      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.6e-11
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      +d++kCi+C +C i C+++++  i++   + +    d C GC +C++ CP  ++i+m
  gi|386002894|ref|YP_005921193.1| 30 FDHAKCIKCSLCEIYCPESCIHQIDG---N-FVPDLDYCKGCSVCAHECP-RGAITM 81
                                      799**************855555544...3.345679*************.7***99 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   6.0   1.5e-07   0.00018       1      24 []      27      50 ..      27      51 .. 0.93
   2 !   13.9   3.5   3.6e-05     0.043       5      24 .]      60      79 ..      60      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-07
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v+++d  kCi C  C++ CPe  i
  gi|386002894|ref|YP_005921193.1| 27 VPVFDHAKCIKCSLCEIYCPESCI 50
                                      79******************9865 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d d C gC  C+  CP gai
  gi|386002894|ref|YP_005921193.1| 60 DLDYCKGCSVCAHECPRGAI 79
                                      5689**************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.6   2.5e-06     0.003      11      51 .]       3      50 ..       1      50 [. 0.84
   2 !   22.3  14.0   9.4e-08   0.00011       1      51 []      34      79 ..      34      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.5e-06
                            Fer4_9 11 aCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkgai 51
                                       C+  +vve  + ++ +  a++         +Ci+C  C+  Cp+ +i
  gi|386002894|ref|YP_005921193.1|  3 RCEVRMVVEPGSSEITKTGAWRTfvpvfdhAKCIKCSLCEIYCPESCI 50
                                      68888888888888888888888999999999************9876 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 9.4e-08
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC++C  C+  Cp   + + +++    l+      C gC  C++ Cp+gai
  gi|386002894|ref|YP_005921193.1| 34 KCIKCSLCEIYCPESCIHQIDGNFVPDLDY-----CKGCSVCAHECPRGAI 79
                                      7*****************999999999854.....**************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.9   8.4e-06      0.01       2      22 .]      27      47 ..      26      47 .. 0.92
   2 !   13.0   2.7     7e-05     0.084       6      21 ..      60      75 ..      56      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.4e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++v+d ++Ci C+ C   CP+
  gi|386002894|ref|YP_005921193.1| 27 VPVFDHAKCIKCSLCEIYCPE 47
                                      5899***********999**5 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7e-05
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      d d C gC+ C + CP
  gi|386002894|ref|YP_005921193.1| 60 DLDYCKGCSVCAHECP 75
                                      6788************ PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   5.8   0.00029      0.35      32      50 ..      29      47 ..       3      49 .. 0.68
   2 !   22.0  15.2   1.5e-07   0.00018       1      52 []      34      78 ..      34      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                            Fer4_7 32 eidpekClgCgaCvavCPt 50
                                      ++d+ kC+ C  C+  CP 
  gi|386002894|ref|YP_005921193.1| 29 VFDHAKCIKCSLCEIYCPE 47
                                      6666677777777777764 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.5e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +Ci+C  C+ +Cp ++i   +          + d ++C gC +C+ +CP ga
  gi|386002894|ref|YP_005921193.1| 34 KCIKCSLCEIYCPESCIHQIDG-------NFVPDLDYCKGCSVCAHECPRGA 78
                                      7****************98664.......4677999*************997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.8   0.00033       0.4       1      19 [.      34      52 ..      34      60 .. 0.89
   2 !   17.8   2.1   4.1e-06    0.0049       2      20 ..      64      82 ..      63      86 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      +C++C  C   CP+++i++
  gi|386002894|ref|YP_005921193.1| 34 KCIKCSLCEIYCPESCIHQ 52
                                      6***************986 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.1e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C  Ca  CP +ai++ 
  gi|386002894|ref|YP_005921193.1| 64 CKGCSVCAHECPRGAITMV 82
                                      ****************976 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.4   4.7e-05     0.056      44      59 ..      33      48 ..       3      50 .. 0.88
   2 !   13.5   1.0   6.9e-05     0.082       2      16 ..      64      78 ..      58      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                       +Ci+C +Ce +CP++
  gi|386002894|ref|YP_005921193.1| 33 AKCIKCSLCEIYCPES 48
                                      68************85 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.9e-05
                           Fer4_17  2 CiqCgyClpeCpsye 16
                                      C +C+ C+ eCp+++
  gi|386002894|ref|YP_005921193.1| 64 CKGCSVCAHECPRGA 78
                                      888888888888765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  15.7   9.7e-06     0.012       3      56 .]      29      75 ..      27      75 .. 0.87
   2 !   12.8   2.8   8.3e-05       0.1       5      21 ..      60      76 ..      56      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.7e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d  +Ci+C  C   CP        + +  +++    +++ C gc  C+ +CP
  gi|386002894|ref|YP_005921193.1| 29 VFDHAKCIKCSLCEIYCPE-------SCIHQIDGNFVPDLDYCKGCSVCAHECP 75
                                      78999**************.......666666666677889************9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.3e-05
                           Fer4_10  5 dddtCirCgkCvkaCPa 21
                                      d d C +C  C   CP 
  gi|386002894|ref|YP_005921193.1| 60 DLDYCKGCSVCAHECPR 76
                                      7899************8 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   0.00023      0.27       1      13 [.      35      47 ..      35      49 .. 0.93
   2 ?    7.5   6.6    0.0076       9.1       1      15 []      64      78 ..      64      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+ C++C+  CP+
  gi|386002894|ref|YP_005921193.1| 35 CIKCSLCEIYCPE 47
                                      ************6 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0076
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gC+ C   CP gA
  gi|386002894|ref|YP_005921193.1| 64 CKGCSVCAHECPRGA 78
                                      9*************9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.9   0.00098       1.2       2      18 ..      31      47 ..      29      55 .. 0.93
   2 ?    8.8   1.8    0.0019       2.3       2      17 ..      60      75 ..      58      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00098
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D  +Ci c +C   +P+
  gi|386002894|ref|YP_005921193.1| 31 DHAKCIKCSLCEIYCPE 47
                                      7889************8 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D d C +c +C++ +P
  gi|386002894|ref|YP_005921193.1| 60 DLDYCKGCSVCAHECP 75
                                      6789************ PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.2     0.003       3.6       3      16 ..      33      46 ..      31      59 .. 0.75
   2 ?    9.1   5.0    0.0014       1.7      48      63 ..      61      76 ..      47      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.003
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                       kCi+C++C+  Cp
  gi|386002894|ref|YP_005921193.1| 33 AKCIKCSLCEIYCP 46
                                      57888888888787 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                            Fer4_8 48 lwsCttcgaCtevCpv 63
                                      l++C +c  C+ +Cp 
  gi|386002894|ref|YP_005921193.1| 61 LDYCKGCSVCAHECPR 76
                                      6777777777777776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.7    0.0015       1.8       3      15 ..      34      46 ..      32      52 .. 0.93
   2 ?    8.7   3.4    0.0023       2.7       2      16 ..      62      76 ..      61      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +Ci C  C+++CP
  gi|386002894|ref|YP_005921193.1| 34 KCIKCSLCEIYCP 46
                                      8************ PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0023
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C gC +C   CP 
  gi|386002894|ref|YP_005921193.1| 62 DYCKGCSVCAHECPR 76
                                      89************6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.4     0.032        39       2      20 ..      29      47 ..      29      56 .. 0.84
   2 ?    9.9   2.7     0.001       1.2       4      20 ..      60      76 ..      57      78 .. 0.91
   3 ?    5.1   0.0     0.031        37      56      65 ..      71      80 ..      71      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      v+D+ +Ci c lC   +pe
  gi|386002894|ref|YP_005921193.1| 29 VFDHAKCIKCSLCEIYCPE 47
                                      68***********999987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D d C gc +C+ e+p+
  gi|386002894|ref|YP_005921193.1| 60 DLDYCKGCSVCAHECPR 76
                                      8899***********95 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.031
                           Fer4_15 56 araCPvdAIr 65
                                      a++CP +AI+
  gi|386002894|ref|YP_005921193.1| 71 AHECPRGAIT 80
                                      89*******8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.0    0.0044       5.3       1      18 [.      34      50 ..      34      62 .. 0.79
   2 ?    6.8   2.4      0.01        12      79      94 ..      61      76 ..      51      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0044
                           Fer4_22  1 rClsCgaCtlvCptCsCf 18
                                      +C++C+ C + Cp   C+
  gi|386002894|ref|YP_005921193.1| 34 KCIKCSLCEIYCPES-CI 50
                                      7************74.33 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                         C GC  C + cp 
  gi|386002894|ref|YP_005921193.1| 61 LDYCKGCSVCAHECPR 76
                                      5689**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 484.03
//
Query:       gi|386002895|ref|YP_005921194.1|  [L=220]
Description: Pyruvate:ferredoxin oxidoreductase subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete 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-40  138.4   0.2      3e-40  138.1   0.2    1.1  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.1   0.2   1.7e-44     3e-40       1     177 []      51     216 ..      51     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 1.7e-44
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqG+vta++++a aa++  +y qa++ +g e+rG+++++  ri++epi+ + +++e+d++++ d ++l+  ++++g
  gi|386002895|ref|YP_005921194.1|  51 GGQGAVTAAELIAIAAFEDKKYSQAFPAFGVERRGAPVMAFARIASEPIRIRSQIYEPDYVIVQDVTLLEvvDVASG 127
                                       9*************************************************99999**************999***** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       lkp+g ii+n+++ +p++lk +            ++v+++dat+ia e++g ++++Nt mlGa+++++g ++le++ 
  gi|386002895|ref|YP_005921194.1| 128 LKPEGKIIINTDR-DPKDLKLKTG----------AEVVTIDATRIALEKLG-RPIVNTTMLGAFCGATGeVSLESVN 192
                                       ***********65.6666666554..........469**************.************************* PP

                                       HHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafragye 177
                                       +ai  rf +   + ekNl+a++ +ye
  gi|386002895|ref|YP_005921194.1| 193 KAILSRFSG--SLGEKNLAAIKTAYE 216
                                       ********9..5*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1325.73
//
Query:       gi|386002896|ref|YP_005921195.1|  [L=240]
Description: hypothetical protein Mhar_2220 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1785.05
//
Query:       gi|386002897|ref|YP_005921196.1|  [L=603]
Description: PIN domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for 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-14   51.3   0.0    1.4e-13   50.6   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
    9.4e-08   32.6   0.0    2.1e-07   31.5   0.0    1.6  1  PIN           PIN domain
    4.5e-06   26.4   0.1    1.2e-05   25.0   0.1    1.7  1  KH_1          KH domain
    0.00027   20.7   0.6     0.0013   18.6   0.6    2.2  1  KH_2          KH domain
     0.0011   19.1   0.0     0.0052   17.0   0.0    2.0  2  AAA_33        AAA domain
     0.0045   17.5   0.0      0.012   16.1   0.0    1.8  1  AAA_18        AAA domain
     0.0069   16.7   0.0      0.028   14.7   0.0    1.9  2  PIN_4         PIN domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.057   13.3   0.0    2.1  2  NTPase_1      NTPase
      0.016   15.3   1.0      0.055   13.6   0.3    2.3  1  KH_5          NusA-like KH domain
      0.017   14.4   0.0       0.04   13.1   0.0    1.6  1  TIP49         TIP49 P-loop domain
      0.021   14.5   0.0      0.069   12.9   0.0    1.8  2  AAA_29        P-loop containing region of AAA domain
      0.022   15.2   0.0       0.06   13.8   0.0    1.7  1  AAA           ATPase family associated with various cellular 
       0.03   14.1   0.0      0.052   13.3   0.0    1.4  1  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.038   14.4   0.0       0.07   13.5   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.067   12.5   0.0       0.12   11.6   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.075   13.0   0.0       0.14   12.1   0.0    1.4  1  NACHT         NACHT domain
      0.086   12.6   0.0       0.19   11.5   0.0    1.5  1  AAA_11        AAA domain
      0.094   13.0   0.0       0.22   11.8   0.0    1.6  1  NUMOD3        NUMOD3 motif (2 copies)
        0.1   13.0   0.0       0.28   11.6   0.0    1.8  1  RNA_helicase  RNA helicase
       0.11   12.3   0.0       0.19   11.4   0.0    1.4  1  AAA_24        AAA domain
       0.11   12.0   0.1       0.45   10.1   0.0    2.1  3  AAA_25        AAA domain
       0.12   12.1   0.0        0.2   11.4   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.12   11.8   0.0       0.19   11.1   0.0    1.3  1  KTI12         Chromatin associated protein KTI12
       0.13   12.3   0.0       0.56   10.2   0.0    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
       0.14   12.4   0.0       0.71   10.2   0.0    2.1  2  AAA_22        AAA domain
       0.23   10.4   0.0       0.36    9.8   0.0    1.2  1  NO_synthase   Nitric oxide synthase, oxygenase domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0     2e-16   1.4e-13      44     244 ..     186     374 ..     167     397 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2e-16
                             T2SSE  44 kaalerlisriaalakldiseerplqd.arlpekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkeki 118
                                       ++ ++ + +r+++  +++i+ e++    a+l  + +r+ ++ +P + g e  ++R   +++++l+d++ + +    +
  gi|386002897|ref|YP_005921196.1| 186 RDMVREIFERVKSDPGAHIEMEKIGAAvAQL--GPMRIAIARPPFSDGlEITAVR--PVARVDLEDYRHSDE----L 254
                                       5677889999999999999988875441445..59*************999****..456678999988765....5 PP

                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllraa 195
                                       ++ l++a   +  i+++G+ gsGK+t++  + k+++k+d+ + t+E p+ +q+  ++ +q  + ++++++++    +
  gi|386002897|ref|YP_005921196.1| 255 KARLKEA---HRGIMIAGPPGSGKSTFAAGVAKYLQKCDHIVKTLEAPRDLQVP-PEITQYGPLEGSMEASAD--IL 325
                                       5667888...9999************************99999*********95.334444444444555544..46 PP

                             T2SSE 196 LRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLe 244
                                       L  rPD  +  E+R ++ +++   +     g ++ +Han++++al+rL 
  gi|386002897|ref|YP_005921196.1| 326 LLVRPDYTIYDEVRKTNDFQVFADLRMAGVGMIGVVHANKPIDALQRLI 374
                                       7889*****************665555556669**************95 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0     3e-10   2.1e-07       1     120 [.       5     119 ..       5     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3e-10
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidae 76 
                                       iv DTsv+i   +g++ a+ +   + +  ++v++++v+aEl + ++  r+++++ ++el++l +l++a ki     +
  gi|386002897|ref|YP_005921196.1|   5 IVPDTSVVI---DGRVSARVVSGEFMG-KRVVVPEAVVAELEAQANHgRETGIKGLEELRRLSELAKAGKIELEYVG 77 
                                       688******...******999999998.************************************************* PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       ++    +i+l    + +Da+i  +A+e g+  + t D+  +rva
  gi|386002897|ref|YP_005921196.1|  78 VRPDLDQIKLAG-GGEIDAMIRDVALEIGAYFL-TSDSIQSRVA 119
                                       **********86.*****************555.****999998 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.7e-08   1.2e-05       3      38 ..     489     525 ..     487     552 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEES.S CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreet.gakIkvpk.s 38 
                                       +++v  + + riIGk G++I eI++ t g +I+v   +
  gi|386002897|ref|YP_005921196.1| 489 VVKVQENEAARIIGKSGKRIEEIER-TlGIHIDVQTfD 525
                                       68999999*****************.88*****98433 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   1.8e-06    0.0013      15      58 ..     475     519 ..     463     523 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-06
                                       EEEEEEEC.CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  15 vskveIer.tanrviiviresqpgivIGkgGsnikkigkelrkdi 58 
                                       ++ +e+e  +   +++ ++e++ +++IGk G++i++i+ +l+  i
  gi|386002897|ref|YP_005921196.1| 475 KGPFEVEMiSDSSAVVKVQENEAARIIGKSGKRIEEIERTLGIHI 519
                                       555566664458899***********************9998665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         3   2.1e+03      22      70 ..     103     157 ..      96     198 .. 0.62
   2 !   17.0   0.0   7.5e-06    0.0052       2      25 ..     265     289 ..     265     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3
                            AAA_33  22 klgavllssdtlrrrlfg......tdqqsktdytrvldrlyqilnelarkalsag 70 
                                       + ga++l+sd++ +r++g      + ++++++ ++  +  ++++ +++   l++g
  gi|386002897|ref|YP_005921196.1| 103 EIGAYFLTSDSIQSRVAGamglevEYVRPQREEIKQISLEKYFTPDTLSVHLKEG 157
                                       5678899999999999987766653333444444555555566666655555555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.5e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.a 25 
                                       +++ G+pGsGKst+a +++k l+ +
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQkC 289
                                       6899**************9988764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-05     0.012       1      24 [.     265     289 ..     265     324 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf 24 
                                       I+++G+pG+GK+t+a  ++k l ++
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLqKC 289
                                       99************99888877555 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     4e-05     0.028       1     101 [.       5     107 ..       5     129 .. 0.76
   2 ?   -1.2   0.0       3.3   2.3e+03       2      38 ..     385     432 ..     384     473 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                             PIN_4   1 fVlDTnvlLhdpealksf...keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsa 74 
                                       +V DT+v+++   +   +       +vv+P  V+ EL+++ ++ +  e++ +  + +r l el +  + +l    ++
  gi|386002897|ref|YP_005921196.1|   5 IVPDTSVVIDGRVSARVVsgeFMGKRVVVPEAVVAELEAQANHGR--ETGIKGLEELRRLSELAKAGKIELEYVGVR 79 
                                       68999999987655443355568999***************9998..777777788888888888888888888888 PP

                             PIN_4  75 eelpee.eseseknDnrIlavalelkee 101
                                        +l++   + + + D +I +vale+   
  gi|386002897|ref|YP_005921196.1|  80 PDLDQIkLAGGGEIDAMIRDVALEIGAY 107
                                       8888764444789999999999987655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                             PIN_4   2 VlDTnvlLhdpealksf...........keehdvviPitVleELdklK 38 
                                       V+DT v++++ e+ k +             e d+  P++V++  +  K
  gi|386002897|ref|YP_005921196.1| 385 VIDTIVFIEKGEVTKVMdvefmvkvpsgMTEADLARPVIVVKDFETGK 432
                                       899999999988887776666666666656666666666666666555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-05     0.057       2      30 ..     265     293 ..     264     301 .. 0.88
   2 ?   -2.1   0.0       4.6   3.2e+03     125     146 ..     354     375 ..     327     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       ++i GppG+GK+T+   v++ l++ +  v
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQKCDHIV 293
                                       79********************9877666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                                       TSEEEEE--SS--SHHHHHHHT CS
                          NTPase_1 125 ekpvlavihrrkdlalveeire 146
                                       ++ +++v+h +k+ + ++++  
  gi|386002897|ref|YP_005921196.1| 354 GVGMIGVVHANKPIDALQRLIG 375
                                       5567888888887777777655 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   7.9e-05     0.055       3      44 ..     486     521 ..     484     529 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-05
                              KH_5   3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidv 44 
                                       + ++v V++++     ++ i+gk+G+ri+++++ L g  idv
  gi|386002897|ref|YP_005921196.1| 486 SSAVVKVQENE-----AARIIGKSGKRIEEIERTL-GIHIDV 521
                                       56788888888.....*******************.999998 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.7e-05      0.04      49      76 ..     261     288 ..     253     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelge 76 
                                       a r++++aGp+g+Gk+  a +++k l +
  gi|386002897|ref|YP_005921196.1| 261 AHRGIMIAGPPGSGKSTFAAGVAKYLQK 288
                                       679*********************9975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.069      19      38 ..     258     278 ..     241     285 .. 0.77
   2 ?   -3.0   0.0         9   6.2e+03      16      32 ..     489     505 ..     486     506 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            AAA_29  19 idlkg.atlltGpsGsGKSTl 38 
                                       ++++   ++++Gp GsGKST+
  gi|386002897|ref|YP_005921196.1| 258 LKEAHrGIMIAGPPGSGKSTF 278
                                       44444459************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9
                            AAA_29  16 tieidlkgatlltGpsG 32 
                                       ++++++++a  ++G+sG
  gi|386002897|ref|YP_005921196.1| 489 VVKVQENEAARIIGKSG 505
                                       56677777888999988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.6e-05      0.06       1      23 [.     265     287 ..     265     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-05
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       +++ GppG GK+++a  vak l+
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQ 287
                                       5789****************985 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.6e-05     0.052       1      25 [.     267     291 ..     267     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgr 25 
                                       ++Gp+GsGK+tf   ++++l+++  
  gi|386002897|ref|YP_005921196.1| 267 IAGPPGSGKSTFAAGVAKYLQKCDH 291
                                       79******************99855 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001      0.07      16      55 ..     258     293 ..     249     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                       l+ +     + +++ G++G+GKs+ +  ++++l+k + i+
  gi|386002897|ref|YP_005921196.1| 258 LKEA----HRGIMIAGPPGSGKSTFAAGVAKYLQKCDHIV 293
                                       3333....3779***************9999888765444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.12      19      47 ..     265     293 ..     252     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvv 47 
                                       i+++G pG+GKs+ a+ ++++l++ + +v
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQKCDHIV 293
                                       899******************99877776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.14       3      26 ..     265     288 ..     263     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                       EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                       +++ G++GsGK+t+++++a  +++
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQK 288
                                       789***************998875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.19      19      42 ..     264     287 ..     249     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                         +i GPPG+gK+++ +++ ++l 
  gi|386002897|ref|YP_005921196.1| 264 GIMIAGPPGSGKSTFAAGVAKYLQ 287
                                       358******************994 PP

>> NUMOD3  NUMOD3 motif (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00032      0.22       2      26 ..     248     275 ..     248     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                            NUMOD3   2 ykhSeetKaKmsealkG...ennpfyGK 26 
                                       y hS+e Ka+++ea++G     +p  GK
  gi|386002897|ref|YP_005921196.1| 248 YRHSDELKARLKEAHRGimiAGPPGSGK 275
                                       78**************977666665565 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00041      0.28       1      23 [.     265     287 ..     265     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       i++ Gp+g GKSt+a  +ak l+
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQ 287
                                       7899*************998887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.19       5      22 ..     265     282 ..     261     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       i+i Gp+g+GK+t+a+  
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGV 282
                                       89*************866 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00066      0.45      34      54 ..     263     283 ..     238     304 .. 0.87
   2 ?   -3.1   0.0       7.1   4.9e+03     128     157 ..     365     395 ..     339     407 .. 0.70
   3 ?   -3.1   0.0         7   4.8e+03     153     182 ..     488     518 ..     486     519 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00066
                            AAA_25  34 elallaGapgtGKttlaldla 54 
                                         +++aG+pg+GK+t+a  +a
  gi|386002897|ref|YP_005921196.1| 263 RGIMIAGPPGSGKSTFAAGVA 283
                                       55799***********98776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.1
                            AAA_25 128 advdaleaaieevegvrlv..viDplsralgg 157
                                         +dal++ i +v +++++  viD++ ++  g
  gi|386002897|ref|YP_005921196.1| 365 KPIDALQRLIGRV-DLGMIpqVIDTIVFIEKG 395
                                       4467777777774.677777777777766555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 7
                            AAA_25 153 ralggdensnsdv.galvealeriarrtgaa 182
                                       +++  +en+++ + g+  +++e+i+r +g++
  gi|386002897|ref|YP_005921196.1| 488 AVVKVQENEAARIiGKSGKRIEEIERTLGIH 518
                                       5667789999888899999999999999887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029       0.2      45      78 ..     260     293 ..     243     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsv 78 
                                       e++ +i++ Gp+G GKs +a+ +++   + ++ v
  gi|386002897|ref|YP_005921196.1| 260 EAHRGIMIAGPPGSGKSTFAAGVAKYLQKCDHIV 293
                                       67899***************99987666655555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.19       4      30 ..     265     291 ..     264     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                       EEEE--TTSSHHHHHHHHHHHHHHTT- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekr 30 
                                       +++ G P sGKst+a+ +ak+l++ + 
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLQKCDH 291
                                       789*******************99554 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 ?   10.2   0.0   0.00081      0.56       2      24 ..     265     288 ..     264     350 .. 0.85
   2 ?   -2.9   0.0         9   6.2e+03      28      47 ..     405     424 ..     403     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00081
                                       EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.n 24 
                                       +++ GppG+gKs++a  +a+ l +
  gi|386002897|ref|YP_005921196.1| 265 IMIAGPPGSGKSTFAAGVAKYLqK 288
                                       7899************99999943 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9
                                       EEEE--TT--HHHHH--B-- CS
                             AAA_5  28 eyvqltrdtteedlkgrrei 47 
                                       ++v  ++++te+dl  ++ +
  gi|386002897|ref|YP_005921196.1| 405 FMVKVPSGMTEADLARPVIV 424
                                       67889999*****9988766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.2   6.4e+03     107     134 ..      54      83 ..      42      85 .. 0.72
   2 ?   10.2   0.0     0.001      0.71       7      30 ..     264     287 ..     258     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.2
                            AAA_22 107 ealeeLrsllnl.srkgvqliLvGtp.elr 134
                                       + leeLr+l++l +  ++ l +vG + +l+
  gi|386002897|ref|YP_005921196.1|  54 KGLEELRRLSELaKAGKIELEYVGVRpDLD 83 
                                       568889998888778888888888776666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                        +++ G++G+GK+t ++ +++ l+
  gi|386002897|ref|YP_005921196.1| 264 GIMIAGPPGSGKSTFAAGVAKYLQ 287
                                       5899**********9998887765 PP

>> NO_synthase  Nitric oxide synthase, oxygenase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00052      0.36     190     272 ..     122     204 ..     113     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                                       CS-EEEE--SS-CCCGCC-EEEES--EE-SEEEEETTEEES---EE--EECHHHHCTTTTSTTTT--HHHHHHHTT- CS
                       NO_synthase 190 lvlevelehpkyewfkelglkwyavpavsnmlleigGieytaapfngwYmgteigarnladekrynlleevakklgl 266
                                       + leve   p+ e++k+++l  y  p   ++ l+ g i        g +   +ig rnl +++  ++++e+ ++++ 
  gi|386002897|ref|YP_005921196.1| 122 MGLEVEYVRPQREEIKQISLEKYFTPDTLSVHLKEGTIPMAKRGKVGEFSLVKIGNRNLSERDLRDMVREIFERVKS 198
                                       5689*******************************************************************999988 PP

                                       -TT-GG CS
                       NO_synthase 267 dtskes 272
                                       d   + 
  gi|386002897|ref|YP_005921196.1| 199 DPGAHI 204
                                       766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 3693.41
//
Query:       gi|386002898|ref|YP_005921197.1|  [L=115]
Description: hypothetical protein Mhar_2222 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-09   35.1   0.0    1.1e-08   34.6   0.0    1.2  1  Cupin_2         Cupin domain
      7e-06   26.0   0.0      9e-06   25.6   0.0    1.1  1  AraC_binding    AraC-like ligand binding domain
    0.00035   20.4   0.0    0.00039   20.2   0.0    1.2  1  Cupin_6         Cupin
    0.00061   19.4   0.0    0.00094   18.8   0.0    1.4  1  Cupin_3         Protein of unknown function (DUF861)
     0.0034   17.2   0.0     0.0045   16.8   0.0    1.4  1  EutQ            Ethanolamine utilisation protein EutQ
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.14   11.9   0.0    1.2  1  AraC_binding_2  AraC-binding-like domain
       0.15   12.2   0.0       0.18   12.0   0.0    1.2  1  Ectoine_synth   Ectoine synthase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   4.5e-12   1.1e-08       3      67 ..      47     108 ..      45     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.5e-12
                                       EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                           Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                       + ++ G+   +h+ p   +++ V+eGe+e+t+ ge ++l+ G++v+ pag+pH ++     p+++
  gi|386002898|ref|YP_005921197.1|  47 FAFDEGQRLSEHTAPFD-AVVNVIEGEAEITISGEAMRLSGGEMVIMPAGEPHSVAAVK--PFKM 108
                                       56777887888888887.99***********************************9988..5554 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   3.5e-09     9e-06      11      65 ..      50     104 ..      41     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.5e-09
                                       STT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
                      AraC_binding  11 ypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65 
                                       + +++ ++h+ ++  ++ v+eG++ +++ g+  +l++G+++++p gepH+ ++ +
  gi|386002898|ref|YP_005921197.1|  50 DEGQRLSEHTAPFDAVVNVIEGEAEITISGEAMRLSGGEMVIMPAGEPHSVAAVK 104
                                       56788999******************************************99987 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.5e-07   0.00039      35      75 ..      64     102 ..      28     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-07
                           Cupin_6  35 alhvvlrGscwlidpasgepvrLsagdvvllpggephvlad 75 
                                       a++ v +G++ ++  +  e +rLs g++v++p geph +a 
  gi|386002898|ref|YP_005921197.1|  64 AVVNVIEGEAEITISG--EAMRLSGGEMVIMPAGEPHSVAA 102
                                       567799*******777..89*****************9975 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.7e-07   0.00094      24      60 ..      61      96 ..      40     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.7e-07
                                      SSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 24 eedEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                      + d  + ++eGe ++t  +ge+++l+ G +v +p+g 
  gi|386002898|ref|YP_005921197.1| 61 PFDAVVNVIEGEAEITI-SGEAMRLSGGEMVIMPAGE 96
                                      4567789**********.*****************97 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06    0.0045      91     129 ..      58      96 ..      23     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                              EutQ  91 wtlnydeidyvieGrldvlidGrkvvaeaGdviliPkgs 129
                                        t  +d +  vieG+ ++ i G  +    G+++++P g 
  gi|386002898|ref|YP_005921197.1|  58 HTAPFDAVVNVIEGEAEITISGEAMRLSGGEMVIMPAGE 96 
                                       6778999*****************************986 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-05      0.14      57     100 ..      64     107 ..      38     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                    AraC_binding_2  57 lvqlplsGraeveqggrevvlgpgdavvldpgrpyrlrwsadce 100
                                        v   ++G+ae++  g+ ++l+ g++v++ +g+p +++   +++
  gi|386002898|ref|YP_005921197.1|  64 AVVNVIEGEAEITISGEAMRLSGGEMVIMPAGEPHSVAAVKPFK 107
                                       5666789***************************9987766655 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05      0.18      58     104 ..      65     109 ..      35     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                                       EEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS-EEEE CS
                     Ectoine_synth  58 avycieGegeveeledgevyeikpgtlYlldkhdkHllrakkelrlv 104
                                        v +ieGe+e++   +ge  +++ g++ ++   + H + a k ++++
  gi|386002898|ref|YP_005921197.1|  65 VVNVIEGEAEITI--SGEAMRLSGGEMVIMPAGEPHSVAAVKPFKMI 109
                                       4679*******97..5**************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 699.95
//
Query:       gi|386002899|ref|YP_005921198.1|  [L=285]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   25.1   0.2    2.2e-05   24.2   0.2    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00018   21.5   0.2     0.0004   20.4   0.2    1.6  1  HTH_20    Helix-turn-helix domain
     0.0058   16.8   0.3      0.026   14.7   0.2    2.1  2  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.092   12.7   0.2        8.3    6.5   0.0    2.5  2  BLACT_WH  Beta-lactamase associated winged helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   4.9e-09   2.2e-05       3      45 ..     196     238 ..     194     240 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.9e-09
                                       HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       +Rl+I+k+La + ++++ l++ +gl  +++  HL kL ea+++
  gi|386002899|ref|YP_005921198.1| 196 QRLQIMKALALETKSFSALSKLTGLRGGNLLFHLQKLSEARMI 238
                                       7***************************************988 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   8.9e-08    0.0004       9      59 ..     194     243 ..     188     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.9e-08
                                       -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                       +  R+ i++aL   e  ++s+l ++ +l+  +l +HL++L+ea  + ++ e
  gi|386002899|ref|YP_005921198.1| 194 SGQRLQIMKAL-ALETKSFSALSKLTGLRGGNLLFHLQKLSEARMIIQRHE 243
                                       5569*******.*******************************99987766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.51   2.3e+03      62      70 ..      15      23 ..      13      25 .. 0.87
   2 !   14.7   0.2   5.9e-06     0.026       2      46 ..     197     240 ..     196     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.51
                            HTH_34 62 TpeGreafk 70
                                      TpeGr+ f+
  gi|386002899|ref|YP_005921198.1| 15 TPEGRDLFM 23
                                      9*****996 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.9e-06
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46 
                                       Rl+++  La + + +f+ l++ +++  gnL  hl+kL +a+ i  
  gi|386002899|ref|YP_005921198.1| 197 RLQIMKALALETK-SFSALSKLTGLRGGNLLFHLQKLSEARMIIQ 240
                                       99******98655.8*************************98864 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0019       8.3      12      29 ..      40      57 ..      39      65 .. 0.93
   2 ?    3.6   0.1     0.015        65      24      35 ..     224     235 ..     222     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0019
                          BLACT_WH 12 dvpeslhpaAergvlahL 29
                                      +v+e+l+++Aer+ ++hL
  gi|386002899|ref|YP_005921198.1| 40 AVHEELLRFAERSNQQHL 57
                                      689**************9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.015
                          BLACT_WH  24 gvlahLeKLeee 35 
                                       ++l hL+KL+e 
  gi|386002899|ref|YP_005921198.1| 224 NLLFHLQKLSEA 235
                                       8999*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1954.34
//
Query:       gi|386002900|ref|YP_005921199.1|  [L=79]
Description: hypothetical protein Mhar_2224 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-30  102.9   0.3    6.4e-30  102.8   0.3    1.0  1  MTH865    MTH865-like family


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.3   3.5e-34   6.4e-30       1      70 []       6      75 ..       6      75 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 3.5e-34
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdive 70
                                      e+++qi +al++a+FPik+p+eLlaa+P+Ga+t+c+agd+e+ta ++gk lk++dFP+ksa+++ad ive
  gi|386002900|ref|YP_005921199.1|  6 EIHAQIEGALKDAKFPIKTPDELLAAMPQGAATRCKAGDCELTAADAGKVLKETDFPFKSAKEVADVIVE 75
                                      79******************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 561.57
//
Query:       gi|386002901|ref|YP_005921200.1|  [L=376]
Description: Transposase, IS605 OrfB family [Methanosaeta harundinacea 6Ac]
Scores for 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-23   80.1   0.1    2.1e-22   78.8   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.8e-22   79.8   0.0    4.2e-22   78.6   0.0    1.6  1  OrfB_IS605      Probable transposase
    2.3e-16   59.0   3.5    5.1e-16   57.9   3.5    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
    0.00081   19.0   0.3     0.0013   18.3   0.3    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0011   18.5   0.3       0.28   10.7   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0019   18.2   0.4     0.0033   17.4   0.4    1.3  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.027   14.0   0.8          1    9.0   0.1    2.9  3  RecR            RecR protein
      0.028   15.0   0.7        3.7    8.1   0.2    2.7  3  FeoB_Cyto       FeoB cytosolic helical domain
       0.05   13.3   0.5        4.3    7.2   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.099   12.3   0.3        1.1    9.0   0.1    2.5  2  GATA            GATA zinc finger


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 !   78.8   0.1   1.2e-25   2.1e-22       5      68 ..     295     358 ..     291     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.2e-25
                    OrfB_Zn_ribbon   5 keqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                           +yka+ +G kv++v+p++TS+ Cs+Cg k++++ls+r+++Cp+Cg+++drD nAaiNil+
  gi|386002901|ref|YP_005921200.1| 295 VITTSYKAESAGSKVVLVDPRNTSQLCSRCGLKVNKSLSDRVHECPQCGLVMDRDENAAINILR 358
                                       55568*********************************************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   2.4e-25   4.2e-22       3     117 ..     165     277 ..     163     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2.4e-25
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                        ve++++ +p+ k + +agiD+G++ +at+++++   ++ ++r+++s++k+lak++++l++  k++  + ka + ++
  gi|386002901|ref|YP_005921200.1| 165 SVEIDDPpKPPWKDGLMAGIDVGLESFATLSNGE---KIDNPRFFRSEEKALAKAQRRLSKYEKGTPERWKALKVVQ 238
                                       678777746677999*******************...**************************************** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       r h+++++rr +++h+++++l+++   ++ e+L + nm 
  gi|386002901|ref|YP_005921200.1| 239 RTHERIANRRYDFAHQVSHNLVERFGLIAFEDLSITNML 277
                                       *************************************97 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 !   57.9   3.5   2.9e-19   5.1e-16       1      47 []       1      46 [.       1      46 [. 0.98

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.9e-19
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M lka+kyr+yPT+ Q+ k+++t++ +R+ YN  La+rk+  e++gk
  gi|386002901|ref|YP_005921200.1|  1 M-LKAFKYRIYPTKAQRSKMEQTLELCRWTYNETLAYRKNSFEQQGK 46
                                      8.******************************************997 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   7.4e-07    0.0013       2      30 ..     317     345 ..     316     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.4e-07
                     zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                       t++ C+rCG ++ ++  ++   Cp+Cgl 
  gi|386002901|ref|YP_005921200.1| 317 TSQLCSRCGLKVNKSLSDRVHECPQCGLV 345
                                       789************************85 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00016      0.28       8      30 ..     307     329 ..     305     335 .. 0.84
   2 !    5.6   0.1    0.0063        11      22      31 ..     339     348 ..     337     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                       CEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   8 stnlveDpergelvCtdCGlVle 30 
                                       s+ +++Dp ++  +C++CGl + 
  gi|386002901|ref|YP_005921200.1| 307 SKVVLVDPRNTSQLCSRCGLKVN 329
                                       444799**************986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0063
                                       ESSSSBEEEE CS
                      TF_Zn_Ribbon  22 CtdCGlVled 31 
                                       C+ CGlV++ 
  gi|386002901|ref|YP_005921200.1| 339 CPQCGLVMDR 348
                                       *******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   1.8e-06    0.0033      10      44 ..     316     352 ..     312     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                               DZR  10 pdarfCseCgtklkavaa..edrCpsCgekvdpearf 44 
                                       + ++ Cs+Cg k+++  +   + Cp+Cg  +d +++ 
  gi|386002901|ref|YP_005921200.1| 316 NTSQLCSRCGLKVNKSLSdrVHECPQCGLVMDRDENA 352
                                       6789*********9877799********999999875 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.73   1.3e+03       5      16 ..      71      82 ..      69      84 .. 0.87
   2 ?    1.8   0.1     0.099   1.8e+02      13      23 ..     315     325 ..     310     326 .. 0.75
   3 ?    9.0   0.1   0.00058         1      12      29 ..     332     349 ..     330     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.73
                                      HHHHHHHHHHH- CS
                              RecR  5 LaeaLqeakekv 16
                                      ++++Lq++ e+v
  gi|386002901|ref|YP_005921200.1| 71 FSQTLQNVQERV 82
                                      89*******998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.099
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       +++ + CsrCg
  gi|386002901|ref|YP_005921200.1| 315 RNTSQLCSRCG 325
                                       666789****8 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00058
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + ++v+ C++Cg + ++d
  gi|386002901|ref|YP_005921200.1| 332 LSDRVHECPQCGLVMDRD 349
                                       679*********998886 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0        10   1.8e+04      49      65 ..      65      81 ..      56      89 .. 0.59
   2 ?    8.1   0.2    0.0021       3.7       6      35 ..     210     237 ..     209     242 .. 0.93
   3 ?    4.7   0.0     0.025        44      70      90 ..     240     260 ..     237     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 10
                         FeoB_Cyto 49 pelraeveearkeleae 65
                                      pel++   ++ ++++++
  gi|386002901|ref|YP_005921200.1| 65 PELNEVFSQTLQNVQER 81
                                      55555555555555554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                         FeoB_Cyto   6 EkaiekleellkesnlkaklppRwlAlklL 35 
                                       Eka++k ++ l+++  ++  p+Rw Alk+ 
  gi|386002901|ref|YP_005921200.1| 210 EKALAKAQRRLSKY--EKGTPERWKALKVV 237
                                       89***********9..************86 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
                         FeoB_Cyto  70 ledvIvdarykfiegilrevv 90 
                                       + + I++ ry+f+++++   v
  gi|386002901|ref|YP_005921200.1| 240 THERIANRRYDFAHQVSHNLV 260
                                       5678************98766 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.024        44      11      20 ..     316     325 ..     315     328 .. 0.77
   2 ?    7.2   0.1    0.0024       4.3       7      20 ..     330     343 ..     329     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                     zinc_ribbon_2  11 dnakFCpyCG 20 
                                       ++++ C++CG
  gi|386002901|ref|YP_005921200.1| 316 NTSQLCSRCG 325
                                       5678899998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2   7 aelqdnakFCpyCG 20 
                                       + l+d++  Cp+CG
  gi|386002901|ref|YP_005921200.1| 330 KSLSDRVHECPQCG 343
                                       679999*******9 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00059       1.1      16      31 ..     314     329 ..     312     333 .. 0.86
   2 ?   -0.1   0.0      0.41   7.4e+02      21      28 ..     337     344 ..     334     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00059
                              GATA  16 pdgnksLCnaCGlyyk 31 
                                       p+++ +LC  CGl+  
  gi|386002901|ref|YP_005921200.1| 314 PRNTSQLCSRCGLKVN 329
                                       89999********865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                              GATA  21 sLCnaCGl 28 
                                       + C +CGl
  gi|386002901|ref|YP_005921200.1| 337 HECPQCGL 344
                                       57999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2604.73
//
Query:       gi|386002902|ref|YP_005921201.1|  [L=109]
Description: hypothetical protein Mhar_2226 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0002   20.8   0.1    0.00051   19.5   0.0    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00021   21.0   0.1    0.00054   19.7   0.0    1.7  2  HTH_23          Homeodomain-like domain
    0.00025   21.1   0.0    0.00045   20.2   0.0    1.5  1  HTH_3           Helix-turn-helix
     0.0057   16.5   0.0       0.02   14.8   0.0    1.8  2  MarR_2          MarR family
     0.0098   15.8   0.2          4    7.5   0.0    2.6  3  HTH_1           Bacterial regulatory helix-turn-helix protein
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.019   14.9   0.0    1.3  1  HTH_37          Helix-turn-helix domain
      0.013   15.9   0.1       0.02   15.2   0.1    1.3  1  HTH_31          Helix-turn-helix domain
       0.02   14.6   0.0      0.037   13.7   0.0    1.4  1  Sigma70_r4_2    Sigma-70, region 4
      0.025   14.7   0.0      0.042   13.9   0.0    1.3  1  RepB            RepB plasmid partitioning protein
      0.046   13.6   0.1       0.41   10.6   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
      0.046   13.6   0.0      0.068   13.0   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.071   13.2   0.0       0.14   12.3   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.076   13.2   0.0       0.13   12.5   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.14   12.2   0.0       0.19   11.8   0.0    1.4  1  HTH_19          Helix-turn-helix domain
       0.14   11.1   0.0       0.17   10.9   0.0    1.1  1  TnsD            Tn7-like transposition protein D
       0.14   12.0   0.0       0.27   11.1   0.0    1.5  1  P22_Cro         DNA-binding transcriptional regulator Cro
       0.16   11.4   0.0       0.29   10.6   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.8e-07   0.00051      15      39 ..      26      50 ..      22      52 .. 0.92
   2 ?   -2.8   0.0       4.7   4.9e+03      38      43 ..      67      72 ..      63      76 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                            HTH_24 15 nprisqreLAerlglSpstvnrrlk 39
                                      + ++sqre+++ l +Sp++v++++ 
  gi|386002902|ref|YP_005921201.1| 26 DRGLSQREVSRLLKISPPAVSQYVT 50
                                      679********************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                            HTH_24 38 lkrLee 43
                                      ++rL +
  gi|386002902|ref|YP_005921201.1| 67 IRRLAD 72
                                      455543 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.1e-07   0.00054       7      38 ..      17      49 ..      16      56 .. 0.82
   2 ?   -2.0   0.0       3.2   3.4e+03      19      25 ..      85      91 ..      66      93 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.1e-07
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwl 38
                                      R+  ++ l + Gls+re++r+L +s+  v++++
  gi|386002902|ref|YP_005921201.1| 17 RAAFAKELVDrGLSQREVSRLLKISPPAVSQYV 49
                                      67766666666*******************996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                            HTH_23 19 svreIAr 25
                                       + eI+r
  gi|386002902|ref|YP_005921201.1| 85 KICEICR 91
                                      3444554 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.3e-07   0.00045       6      34 ..      25      53 ..      20      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.3e-07
                                      HHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  6 kqlglsqeeLAeklGvsrstisriEnGer 34
                                        +glsq+e++++l +s+ ++s++   +r
  gi|386002902|ref|YP_005921201.1| 25 VDRGLSQREVSRLLKISPPAVSQYVTKKR 53
                                      569*********************87765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05      0.02      14      43 ..      24      50 ..       6      51 .. 0.78
   2 ?   -1.2   0.0       1.8   1.9e+03       4      20 ..      64      80 ..      62      94 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHH CS
                            MarR_2 14 Lgrrpgrdltvgelarrlglsksavsrilk 43
                                      L +r+   l+++e+ r l++s++avs+ + 
  gi|386002902|ref|YP_005921201.1| 24 LVDRG---LSQREVSRLLKISPPAVSQYVT 50
                                      44444...9******************886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                      -HHHHHHHHHHHCTTTS CS
                            MarR_2  4 tpaqarvLaaLgrrpgr 20
                                      ++a++r+  ++  +++ 
  gi|386002902|ref|YP_005921201.1| 64 SLAIRRLADEIILNEEV 80
                                      56667776676666663 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.011        11      28      48 ..       7      27 ..       6      34 .. 0.91
   2 !    7.5   0.0    0.0038         4      18      35 ..      33      50 ..      28      53 .. 0.83
   3 ?   -2.1   0.0       3.7   3.9e+03      30      39 ..      63      72 ..      61      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHHHHHTS-SEEE CS
                             HTH_1 28 pavsrqikrLEeelgvpLfeR 48
                                      +av++ + + ++++  +L++R
  gi|386002902|ref|YP_005921201.1|  7 SAVWDTLPNIRAAFAKELVDR 27
                                      89******************9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0038
                                      HHHHHHTS-HHHHHHHHH CS
                             HTH_1 18 rAAeeLglsqpavsrqik 35
                                      +  + L +s+pavs+ + 
  gi|386002902|ref|YP_005921201.1| 33 EVSRLLKISPPAVSQYVT 50
                                      66799**********985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                                      HHHHHHHHHH CS
                             HTH_1 30 vsrqikrLEe 39
                                      vs +i+rL +
  gi|386002902|ref|YP_005921201.1| 63 VSLAIRRLAD 72
                                      7889999966 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.8e-05     0.019      24      50 ..      21      47 ..      15      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                      HHHHHHCT--HHHHHHHHT--HHHHHH CS
                            HTH_37 24 aeliekrelsqseaaqllgiaqPkvsr 50
                                      a+ + +r+lsq+e+ +ll+i+ P vs+
  gi|386002902|ref|YP_005921201.1| 21 AKELVDRGLSQREVSRLLKISPPAVSQ 47
                                      5667789******************97 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.9e-05      0.02      13      40 ..      27      54 ..      17      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                            HTH_31 13 aGLsqeevAerlgvsestlsrlEqGrrg 40
                                      +GLsq+ev ++l +s+  +s++ + +rg
  gi|386002902|ref|YP_005921201.1| 27 RGLSQREVSRLLKISPPAVSQYVTKKRG 54
                                      7*********************997765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.5e-05     0.037      26      48 ..      28      50 ..      26      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                                      ---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrls 48
                                      gls++E+++ll+is+ +V +++ 
  gi|386002902|ref|YP_005921201.1| 28 GLSQREVSRLLKISPPAVSQYVT 50
                                      9*****************99986 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     4e-05     0.042      10      45 ..      17      53 ..      16      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                              RepB 10 rarfaarleerGvdreeiasalgldkqtvskmva.ra 45
                                      ra+fa  l +rG++++e+++ l +++++vs++v+ ++
  gi|386002902|ref|YP_005921201.1| 17 RAAFAKELVDRGLSQREVSRLLKISPPAVSQYVTkKR 53
                                      689******************************9743 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.41      18      35 ..      31      48 ..      22      50 .. 0.83
   2 ?    0.8   0.0      0.44   4.6e+02      16      24 ..      84      92 ..      75      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                      HHHHHHHHTS-HHHHHHH CS
                             HTH_5 18 vcelaeelglsqstvShH 35
                                        e ++ l++s+++vS++
  gi|386002902|ref|YP_005921201.1| 31 QREVSRLLKISPPAVSQY 48
                                      57899***********96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.44
                                      EEHHHHHHH CS
                             HTH_5 16 lcvcelaee 24
                                       ++ce++++
  gi|386002902|ref|YP_005921201.1| 84 DKICEICRM 92
                                      589****97 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.4e-05     0.068      10      47 ..      30      71 ..      21      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkq....vpaervpeIekat 47
                                      +q+++ ++l +s++aVsq +  k++    ++ e  ++I ++ 
  gi|386002902|ref|YP_005921201.1| 30 SQREVSRLLKISPPAVSQYVTKKRGysivFSEEVSLAIRRLA 71
                                      799999**************9888888877788878887776 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.14       2      31 ..      17      47 ..      17      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            HTH_28  2 Rleiiklla.aGhsvreaArelgisrrtvyr 31
                                      R+   k+l  +G s+re++r+l is+  v++
  gi|386002902|ref|YP_005921201.1| 17 RAAFAKELVdRGLSQREVSRLLKISPPAVSQ 47
                                      5666777772566**************9986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.13      24      45 ..      30      51 ..      21      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                      -HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkk 45
                                      ++ ++++ L++sp+ Vs+ + k
  gi|386002902|ref|YP_005921201.1| 30 SQREVSRLLKISPPAVSQYVTK 51
                                      5789***************997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.19      10      36 ..      26      52 ..      20      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            HTH_19 10 elgltqeelaerlgisrskisaiEngk 36
                                       +gl+q+e+++ l+is+   s++ + k
  gi|386002902|ref|YP_005921201.1| 26 DRGLSQREVSRLLKISPPAVSQYVTKK 52
                                      79**************87777777664 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.17     191     224 ..      21      53 ..      15      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklg 224
                                       +keLv+ +gls++e+++ l++++  V +y  k+ 
  gi|386002902|ref|YP_005921201.1|  21 AKELVD-RGLSQREVSRLLKISPPAVSQYVTKKR 53 
                                       799***.**********************99886 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.27      12      39 ..      31      55 ..      22      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                      HHHHHHHHTS-HHHHHHHHTC--HHHHH CS
                           P22_Cro 12 vekvAkalgvtksAVsqWgeeiPelray 39
                                      ++ v ++l++++ AVsq    + ++r y
  gi|386002902|ref|YP_005921201.1| 31 QREVSRLLKISPPAVSQY---VTKKRGY 55
                                      78999************8...5555555 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.29      17      47 ..      17      48 ..      14      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                      HTH_Tnp_ISL3 17 eayilellles.rsvkavArqlgvSwtTVwri 47
                                      +a+ +++l ++  s ++v+r+l +S+  V  +
  gi|386002902|ref|YP_005921201.1| 17 RAAFAKELVDRgLSQREVSRLLKISPPAVSQY 48
                                      567788889999**************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 731.71
//
Query:       gi|386002903|ref|YP_005921202.1|  [L=291]
Description: hypothetical protein Mhar_2227 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-07   29.5   0.0    8.2e-07   29.0   0.0    1.2  1  Asn_synthase   Asparagine synthase
    0.00021   20.9   0.0     0.0031   17.0   0.0    2.5  3  QueC           Queuosine biosynthesis protein QueC
     0.0004   19.6   0.0     0.0022   17.2   0.0    1.9  2  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.015   14.1   0.0       0.75    8.5   0.0    2.1  2  tRNA_Me_trans  tRNA methyl transferase
       0.12   12.1   0.0        0.2   11.4   0.0    1.4  1  ATP_bind_3     PP-loop family
       0.12   11.9   0.0       0.55    9.8   0.0    2.0  1  ThiI           Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.7e-10   8.2e-07      13      81 ..      27      95 ..      22     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.7e-10
                      Asn_synthase 13 rlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlte 81
                                       lrad ++ + +SGGlDSS +aa+aa  + + +  ++++ ++   +e+  a e+a+ lg++h+ + ++ 
  gi|386002903|ref|YP_005921202.1| 27 ILRADYRILIAFSGGLDSSFLAAVAAGVLGEGVLLVTLDSAAIPRSELLEAVEIARSLGLRHRVVPFEI 95
                                      589*************************************99********************9987765 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-06    0.0031       2      66 ..      34      98 ..      33     103 .. 0.89
   2 ?   -0.8   0.0      0.31   9.2e+02     108     129 ..     123     144 ..     115     146 .. 0.88
   3 ?   -0.3   0.0      0.21   6.3e+02     160     178 ..     164     182 ..     149     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                                      EEEE--SSHHHHHHHHHHHH.H-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGG CS
                              QueC  2 avvllSGGlDSttvlalakk.egkevealtfdYgqrhkkeleaakkiakelgveehkildldllke 66
                                      +++ +SGGlDS+ ++a+a    g+ v ++t+d     ++el  a +ia++lg+ +h+++  ++l++
  gi|386002903|ref|YP_005921202.1| 34 ILIAFSGGLDSSFLAAVAAGvLGEGVLLVTLDSAAIPRSELLEAVEIARSLGL-RHRVVPFEILEA 98
                                      6889********9998877616789****************************.9***99998875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.31
                                       HHHHHT-SEEEE---S-STT-- CS
                              QueC 108 yaealgaeaiiiGvneedfsgY 129
                                        a + g+++++ Gvn +d+  Y
  gi|386002903|ref|YP_005921202.1| 123 IAAEAGITRVADGVNLSDYGEY 144
                                       578899************9988 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.21
                                       T--HHHHHHHHHHTTHHHH CS
                              QueC 160 dlsKaeivklgkelgvple 178
                                        ++K++i  l+ke+g+p++
  gi|386002903|ref|YP_005921202.1| 164 GMTKSDIRLLAKEMGLPFS 182
                                       599************8875 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.2e-07    0.0022      21      81 ..      34      93 ..      23     108 .. 0.90
   2 ?   -0.5   0.0      0.19   5.5e+02     148     181 ..     157     190 ..     151     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-07
                                      EEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                      NAD_synthase 21 vvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidi 81
                                      +++  SGG+DSs+ aa+a  +l  e vl + l s   +++++ +a+++a +lg++  +++ 
  gi|386002903|ref|YP_005921202.1| 34 ILIAFSGGLDSSFLAAVAAGVL-GEGVLLVTLDSAAIPRSELLEAVEIARSLGLRHRVVPF 93
                                      56789*****************.678999*************************9988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                                       BETTT..TS-HHHHHHHHHHTT--HHHHCS--B--S CS
                      NAD_synthase 148 lapia..ellKtevkeLakelnvPervlkkpPsAdL 181
                                       + p+a  +++K++++ Lake++ P +  +kp +A L
  gi|386002903|ref|YP_005921202.1| 157 IHPLAeaGMTKSDIRLLAKEMGLPFS--DKPATACL 190
                                       5666511589************9953..66666665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00025      0.75       2      70 ..      33      93 ..      32     104 .. 0.73
   2 ?    3.5   0.0    0.0085        26     164     191 ..     156     185 ..     149     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00025
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                                      ++++a+SgG DSs+ aa+   +g   +gv l + +++         +++l +a ++a+ lg++++vv f
  gi|386002903|ref|YP_005921202.1| 33 RILIAFSGGLDSSFLAAVA--AGVLGEGVLLVTLDSAA------IPRSELLEAVEIARSLGLRHRVVPF 93
                                      799***********99875..46666677777666622......3346677777788888888777766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0085
                     tRNA_Me_trans 164 llfPlge..ltKeevrkiAkeaglavaekk 191
                                       l+ Pl+e  +tK+++r +Ake+gl+  +k+
  gi|386002903|ref|YP_005921202.1| 156 LIHPLAEagMTKSDIRLLAKEMGLPFSDKP 185
                                       56677643389**************99997 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.7e-05       0.2       2      22 ..      34      54 ..      33     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.7e-05
                                      EEEE--SCHHHHHHHHHHHHH CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllakl 22
                                      +l+A+SgGlDS  L  ++a  
  gi|386002903|ref|YP_005921202.1| 34 ILIAFSGGLDSSFLAAVAAGV 54
                                      89************9988765 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00018      0.55       7     160 ..      35     178 ..      30     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                              ThiI   7 laLlSgGiDSp.VaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilek 82 
                                       l   SgG+DS   aa  +   G  v lv+l+++ +   e  e ve +         sl ++ +vv+f+ +  e +  
  gi|386002903|ref|YP_005921202.1|  35 LIAFSGGLDSSfLAAVAAGVLGEGVLLVTLDSAAIPRSELLEAVEIAR--------SLGLRHRVVPFEILEAEGVAD 103
                                       566788888873466666667778888888776666666666665332........234677899998887777665 PP

                              ThiI  83 vkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLi..gldKeeiiklAk 157
                                        +++ ++ l+kr   r+ +++a e g++ + +G +L+            i a  +  ++ PL   g+ K +i  lAk
  gi|386002903|ref|YP_005921202.1| 104 -NPPHRCALCKRAASRLLKRIAAEAGITRVADGVNLSDYGEY----RPGIGASDEEGLIHPLAeaGMTKSDIRLLAK 175
                                       .45689*****************************9875432....2334444455555565333566666666666 PP

                              ThiI 158 eig 160
                                       e+g
  gi|386002903|ref|YP_005921202.1| 176 EMG 178
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2054.52
//
Query:       gi|386002904|ref|YP_005921203.1|  [L=267]
Description: hypothetical protein Mhar_2228 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-93  312.9   5.0    3.4e-93  312.8   5.0    1.0  1  DUF63     Membrane protein of unknown function DUF63


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.8   5.0   1.9e-97   3.4e-93       3     272 .]       3     267 .]       1     267 [] 0.99

  Alignments for each domain:
  == domain 1  score: 312.8 bits;  conditional E-value: 1.9e-97
                             DUF63   3 eFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllkpp 79 
                                        +iy++Y++pi y+ gYn+vnt+t+a+iL+ +++li++ll++l++++de+f+lat pyv++g+slRvveDa+l+++p
  gi|386002904|ref|YP_005921203.1|   3 PWIYHHYVEPILYDAGYNPVNTVTWALILGGMILLILRLLRRLEVSFDERFFLATAPYVLAGASLRVVEDAELVAAP 79 
                                       59*************************************************************************** PP

                             DUF63  80 lsyllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaavl 156
                                       l+yllitPliyfl+++ t+++ll+++++   l +++   yaavG+++++ +l+lL     v++ ++++++l+l +++
  gi|386002904|ref|YP_005921203.1|  80 LKYLLITPLIYFLAAAGTMTALLLCRQA---LGDRWLLGYAAVGLLWTAGNLALLA-PLGVERSTIPIAILALGVAA 152
                                       ***************************9...**********************999.999***************** PP

                             DUF63 157 talvllllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipvly 233
                                       talv + +r ++ + +s   +ll+l+ah++Da++t+vg+d++gYvE+Hvvps+Li+++Gtalvm+plkll+lipvl 
  gi|386002904|ref|YP_005921203.1| 153 TALVAAGSRLIS-SPISGGQSLLILFAHMFDAASTYVGVDWFGYVEKHVVPSLLIEAAGTALVMFPLKLLILIPVLA 228
                                       **********99.99************************************************************** PP

                             DUF63 234 ildkevkeeeelrnlvklailvlGlaPgiRnllrmvlgv 272
                                       ++d + +++ +l+nl+++a+l+lGlaP++Rn++r++lg+
  gi|386002904|ref|YP_005921203.1| 229 VVDGALRDDPSLKNLTLFALLTLGLAPAVRNTIRLTLGI 267
                                       *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1696.72
//
Query:       gi|386002905|ref|YP_005921204.1|  [L=179]
Description: proteasome subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-42  143.7   0.0    6.2e-42  143.2   0.0    1.2  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   3.5e-46   6.2e-42      29     189 ..       4     158 ..       1     159 [. 0.95

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 3.5e-46
                                       EEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCTTTTTS CS
                        Proteasome  29 kllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsgrrpfg 105
                                        + +++t++Ki++i d++g+++aG ++Da+ lvr++++e +ly+++ g+p++v+     ++++l++ +++++  pf+
  gi|386002905|ref|YP_005921204.1|   4 FI-ASTTAQKIYQIADRVGLTTAGVVGDAQSLVRMIQVESKLYNMQRGEPMTVR----GTTSLLSNVLASRRYFPFM 75 
                                       55.67779**********************************************....99999999999******** PP

                                       EEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSC CS
                        Proteasome 106 vslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsg 182
                                       v+ll++gvd++g p+L+++d  G +i+e+++va+Gsgs  a+++le++y +++t+ee+++l v+a+++a++rd++sg
  gi|386002905|ref|YP_005921204.1|  76 VQLLLGGVDKKG-PQLFSLDALGGSIQEQKVVATGSGSPTAYGVLEALYDPEMTVEEGMKLGVRAIHNAMKRDSASG 151
                                       *********888.********999999989*********************************************** PP

                                       SSEEEEE CS
                        Proteasome 183 knievav 189
                                       + i+ + 
  gi|386002905|ref|YP_005921204.1| 152 DVIQAVK 158
                                       *999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 1036.43
//
Query:       gi|386002906|ref|YP_005921205.1|  [L=635]
Description: RNA-metabolising metallo-beta-lactamase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-29  100.4   2.2    1.1e-26   92.5   0.4    2.8  2  KH_7           KH domain
    1.8e-25   89.4   0.0    3.6e-25   88.4   0.0    1.5  1  Beta-Casp      Beta-Casp domain
      2e-15   57.3   0.7    1.1e-14   54.9   0.7    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.3e-15   55.4   0.0    1.3e-14   53.8   0.0    1.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    4.2e-12   45.9   0.0    7.6e-12   45.1   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
      3e-09   36.7   0.1    6.4e-09   35.6   0.1    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
    6.8e-05   22.6   0.1      0.001   18.8   0.0    3.0  3  KH_2           KH domain
    0.00025   21.0   0.0    0.00067   19.6   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.042   13.7   0.1    1.7  1  KH_4           KH domain
      0.095   12.5   0.0       0.27   11.1   0.0    1.8  1  KH_1           KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.4   6.4e-30   1.1e-26       1      68 []       4      71 ..       4      71 .. 0.97
   2 !    6.6   0.1    0.0041       7.3       8      43 ..      78     116 ..      74     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 6.4e-30
                              KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      eevl elk+++++klP+++++t +eFEGPelViYt++p+ +a++g+++r+lAk+lrkR+v+RpD +vl
  gi|386002906|ref|YP_005921205.1|  4 EEVLLELKRRVQTKLPPNINVTGIEFEGPELVIYTDDPRRLADDGEIVRSLAKDLRKRVVVRPDLKVL 71
                                      57899***********************************************************9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0041
                              KH_7   8 kekieeklPkevkitdveFEG..PelViYtknpklfa.e 43 
                                        +ki++ +P+e+ +t++ F G   e+Vi ++ p l++  
  gi|386002906|ref|YP_005921205.1|  78 VKKIQQVVPPEAGLTNYYFDGetGEVVIEAEKPGLVIgR 116
                                       589****************99445899988887777644 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0     2e-28   3.6e-25       2     110 .]     422     545 ..     421     545 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 2e-28
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....H CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewme 53 
                                       qe+++ Lee++++k+l   ++ +yld+ ++++at+++++y+e                         ve++s     
  gi|386002906|ref|YP_005921205.1| 422 QEVMIALEEAIRKKSL--EEISVYLDG-MIYEATAIHTTYPEylnnelrdlifhkginpflsecfvqVETSS----- 490
                                       9**********99664..458******.********************************999985444333..... PP

                                       HHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  54 skkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                        +++++  + +p+v+la+sgm++gG++ e+lk+l +d+rnt+++vgyqaegTlgr++
  gi|386002906|ref|YP_005921205.1| 491 -QRSKI-VDGDPCVVLATSGMMNGGPILEYLKALGPDERNTLVIVGYQAEGTLGRRI 545
                                       .33234.4579********************************************97 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.7   6.1e-18   1.1e-14       4     163 ..     192     373 ..     190     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 6.1e-18
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       ++ +++l+ ++++ i++D+G+    ++ a   ++  + ++++++dav+lTH+HlDH+G ++ l +     ++++   
  gi|386002906|ref|YP_005921205.1| 192 VGRSCMLLSTPESKIIVDCGVNVGSDDSATpyLYVPEAYPLNQIDAVVLTHAHLDHAGLVPMLYKYGYEGPIYCTPP 268
                                       5679*******************999999999********************************************* PP

                                       HHCCHCHHHHHHHHHCCHH..............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEET CS
                       Lactamase_B  79 apalfmeeaddaasrkgll..............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyg 141
                                       ++ lf     d+    g +              l+     + + ++++ +++ + ++     ++ g++ +h++v++g
  gi|386002906|ref|YP_005921205.1| 269 TRDLFVLLQLDYIDIAGREgkrmpyesamireaLKHTITLNYGDVTDIAPDTKLTMHNA--GHILGSSICHFHVGDG 343
                                       *********99999988889******976555544444455555555555555555443..367788999******* PP

                                       TCCEEEECTTTSSHHCCCCCC......... CS
                       Lactamase_B 142 ggkvlftGDallagetgridl........t 163
                                         +v+ftGD+ ++  ++ ++         t
  gi|386002906|ref|YP_005921205.1| 344 LYNVAFTGDFKFEKTRLFDPAvhtfprleT 373
                                       ***********9777666666555555551 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       5.8     1e+04      41      55 ..     422     436 ..     421     443 .. 0.65
   2 !   53.8   0.0   7.4e-18   1.3e-14       1      62 []     562     626 ..     562     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.8
                             RMMBL  41 eeatsalarllkeee 55 
                                       +e + al +++++++
  gi|386002906|ref|YP_005921205.1| 422 QEVMIALEEAIRKKS 436
                                       678999999996555 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 7.4e-18
                             RMMBL   1 tipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       t+++++++ ++d fSgH+d+n+l++++r++ p++  vi +HG+e  +++la+ + ++  i + +P
  gi|386002906|ref|YP_005921205.1| 562 TVKINLEVVTVDgFSGHSDRNQLMDYVRRVYPKPsrVITNHGDESNCLDLASSIYKKHRIPTMAP 626
                                       699***************************************************99888877665 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   4.2e-15   7.6e-12       1     150 [.     198     339 ..     198     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.2e-15
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekv..iptvdliLLshatlehlGayallyakfksklllnipvyatlpv 75 
                                       lL+  + ki++D+G++  ++++ +   ++ ++  ++++d+++L+ha l+h G  ++ly+     ++ + p+y+t p+
  gi|386002906|ref|YP_005921205.1| 198 LLSTPESKIIVDCGVNVGSDDSATPYLYVPEAypLNQIDAVVLTHAHLDHAGLVPMLYK-----YGYEGPIYCTPPT 269
                                       5677789*********66555555555555542689****************6666664.....67899******** PP

                     Lactamase_B_6  76 vkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkis 150
                                         L  ++ ld++  +g +g+      e   i+ea ++ +tl Y   +++     +  +t +naGh lG +i + +
  gi|386002906|ref|YP_005921205.1| 270 RDLFVLLQLDYIDIAGREGKRM--PYESAMIREALKHTITLNYGDVTDIAP---DTKLTMHNAGHILGSSICHFH 339
                                       ****999999998887777554..3456779***************99995...4557789********996553 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   3.6e-12   6.4e-09       3     146 ..     206     356 ..     204     388 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.6e-12
                                       EEES--TTHHHH..HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH........ CS
                     Lactamase_B_2   3 iLiDagpdlrqq..alral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla........ 68 
                                       i++D+g ++     a+++l  P +    l++idaV+lthaH DH   +++l + ++ + p+y+++ +++        
  gi|386002906|ref|YP_005921205.1| 206 IIVDCGVNVGSDdsATPYLyVPEA--YPLNQIDAVVLTHAHLDHAGLVPMLYK-YGYEGPIYCTPPTRDlfvllqld 279
                                       99******8777889999977765..44567**************55666666.45558********9988887777 PP

                                       .......HCCTTCGHHHCHTT...........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEE CS
                     Lactamase_B_2  69 .......vleanfvylaleee...........pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlG 127
                                              +            +           +  ++ +l+ g+ ++++ ++ ++t++ a h  g         ++ 
  gi|386002906|ref|YP_005921205.1| 280 yidiagrE-G----------KrmpyesamireALKHTITLNYGDVTDIA-PDTKLTMHNAGHILGS-------SICH 337
                                       77544431.1..........12222223444456667788899999998.5789999999999998.......9999 PP

                                       EEEECTTEEEEEESS-S-- CS
                     Lactamase_B_2 128 lriegggkrvyyigDtgyi 146
                                       + +++g  +v+++gD ++ 
  gi|386002906|ref|YP_005921205.1| 338 FHVGDGLYNVAFTGDFKFE 356
                                       9999999999999998843 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   2.1e+03      44      59 ..      48      63 ..      46      89 .. 0.72
   2 !   18.8   0.0   5.8e-07     0.001      28      55 ..     102     129 ..      95     146 .. 0.87
   3 ?   -2.3   0.0       2.3   4.2e+03      37      68 ..     415     444 ..     414     445 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                                      GHHHHHHHHHHHHHHH CS
                              KH_2 44 Gsnikkigkelrkdie 59
                                      G+ ++++ k+lrk++ 
  gi|386002906|ref|YP_005921205.1| 48 GEIVRSLAKDLRKRVV 63
                                      7789999999999984 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 5.8e-07
                                       EEEEEESCHHHHHTGGGHHHHHHHHHHH CS
                              KH_2  28 iiviresqpgivIGkgGsnikkigkelr 55 
                                       ++vi +++pg+vIG+ G+++++i+k ++
  gi|386002906|ref|YP_005921205.1| 102 EVVIEAEKPGLVIGRHGATLREITKLIG 129
                                       69***********************987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                                       HHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                              KH_2  37 givIGkgGsnikkigkelrkdieklegkkVkl 68 
                                       + ++G+  + + ++++++rk+   le+  V+l
  gi|386002906|ref|YP_005921205.1| 415 AFAVGRSQEVMIALEEAIRKKS--LEEISVYL 444
                                       5677777777888999999988..77777776 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.7e-07   0.00067       6      51 ..     193     249 ..     191     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.7e-07
                     Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa............eeaDlvlisqaledHah 51 
                                       g +++ll+t++ +i+vD +  n+g + +a             ++D+v++++a+ dHa 
  gi|386002906|ref|YP_005921205.1| 193 GRSCMLLSTPESKIIVDCGV-NVGSDDSAtpylyvpeayplNQIDAVVLTHAHLDHAG 249
                                       89***************883.44444444445666666776***************86 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.3e-05     0.042      32      52 ..     102     122 ..      92     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                              KH_4  32 elnvegedlGrvIGkrGrtld 52 
                                       e+ +e e+ G+vIG++G tl+
  gi|386002906|ref|YP_005921205.1| 102 EVVIEAEKPGLVIGRHGATLR 122
                                       677899*************97 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.27       4      27 ..     103     126 ..     100     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                       EEEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIre 27 
                                       + + +++ g++IG+ G++++eI +
  gi|386002906|ref|YP_005921205.1| 103 VVIEAEKPGLVIGRHGATLREITK 126
                                       667778889*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3854.14
//
Query:       gi|386002907|ref|YP_005921206.1|  [L=171]
Description: ArsR family transcriptional regulator [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-65  217.2   0.0    9.7e-65  217.0   0.0    1.0  1  ArsR           ArsR transcriptional regulator
     0.0051   16.8   0.1      0.018   15.1   0.0    1.8  2  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.4   0.2        4.6    7.2   0.0    2.6  2  HTH_5          Bacterial regulatory protein, arsR family
      0.041   13.8   0.1         11    6.0   0.0    2.5  2  MarR_2         MarR family
      0.092   12.6   0.2       0.28   11.0   0.2    1.9  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.0   0.0   2.7e-68   9.7e-65       1     158 [.       8     167 ..       8     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 217.0 bits;  conditional E-value: 2.7e-68
                              ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgee..veealklLkkikliEsqWrmpepgekpekeYh 75 
                                       indp++Lvpll +f+se++k+v+eel++eW te el+e + +e  v+++l+lLkk++l+E++W+mp+pge+pekeYh
  gi|386002907|ref|YP_005921206.1|   8 INDPSDLVPLLLAFGSEVHKRVFEELCEEWRTEVELAEIMSDErgVHRSLELLKKSGLVETKWKMPKPGESPEKEYH 84 
                                       8***************************************99999******************************** PP

                              ArsR  76 tsYskvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkG 152
                                       +sYs+vqanf+c+ledls++i+++ msd+el+e +e+i++ v +gnts+++lsr+l+ls+ fir+ akr+e l+v+G
  gi|386002907|ref|YP_005921206.1|  85 SSYSRVQANFVCPLEDLSELIYLTSMSDDELREKTERIQRLVANGNTSLTNLSRELNLSQAFIRGAAKRAEGLAVRG 161
                                       ***************************************************************************** PP

                              ArsR 153 qrlelv 158
                                       qr+el+
  gi|386002907|ref|YP_005921206.1| 162 QRIELS 167
                                       ***986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     5e-06     0.018       6      56 ..      20      68 ..      17      71 .. 0.95
   2 ?   -1.4   0.0      0.73   2.6e+03      21      38 ..     127     144 ..     122     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                                      HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      A++++v  r++ +L  +e +t  elae +  +   +++ L+ L + gLve+
  gi|386002907|ref|YP_005921206.1| 20 AFGSEVHKRVFEEL-CEEWRTEVELAEIM-SDERGVHRSLELLKKSGLVET 68
                                      7889999*******.**************.9*******************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.73
                                       TCTTB-HHHHHHHHTS-H CS
                            HTH_20  21 raegltaselaerldlsk 38 
                                        ++  +++ l ++l ls+
  gi|386002907|ref|YP_005921206.1| 127 ANGNTSLTNLSRELNLSQ 144
                                       555677888888888776 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 ?    4.5   0.1    0.0089        32      33      47 .]      54      68 ..      52      68 .. 0.87
   2 ?    7.2   0.0    0.0013       4.6       9      31 ..     124     146 ..     121     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0089
                                      HHHHHHHHHTTSEEE CS
                             HTH_5 33 ShHLkkLreaGLVek 47
                                       + L  L+++GLVe+
  gi|386002907|ref|YP_005921206.1| 54 HRSLELLKKSGLVET 68
                                      6889*********85 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                                       HHHTTSSEEHHHHHHHHTS-HHH CS
                             HTH_5   9 klLaegelcvcelaeelglsqst 31 
                                       +l+a+g+++ + l++el+lsq+ 
  gi|386002907|ref|YP_005921206.1| 124 RLVANGNTSLTNLSRELNLSQAF 146
                                       68999****************85 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.003        11      38      54 ..      53      69 ..      48      77 .. 0.89
   2 ?    5.1   0.1    0.0058        21      22      46 ..     131     155 ..     114     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.003
                                      HHHHHHHHHHTTSEEEE CS
                            MarR_2 38 vsrilkrLvaaGLverr 54
                                      v+r l+ L + GLve++
  gi|386002907|ref|YP_005921206.1| 53 VHRSLELLKKSGLVETK 69
                                      99*************96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0058
                                       EEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  22 ltvgelarrlglsksavsrilkrLv 46 
                                        + + l r+l+ls++ +  + kr++
  gi|386002907|ref|YP_005921206.1| 131 TSLTNLSRELNLSQAFIRGAAKRAE 155
                                       57889************99999987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   7.9e-05      0.28      10      35 ..     123     148 ..     120     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.9e-05
                     HTH_AsnC-type  10 eaLqedaRisyaeLAervGlSestvl 35 
                                       + L +++ +s + L+++++lS++ ++
  gi|386002907|ref|YP_005921206.1| 123 QRLVANGNTSLTNLSRELNLSQAFIR 148
                                       6799*****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 1205.51
//
Query:       gi|386002908|ref|YP_005921207.1|  [L=262]
Description: helix-turn-helix domain-containing protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-10   38.8   0.0    1.6e-09   37.5   0.0    1.6  1  MarR_2          MarR family
    1.2e-09   37.6   0.0    2.2e-09   36.7   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.7e-07   29.7   0.0    1.5e-06   28.6   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
      7e-06   25.9   0.0    1.7e-05   24.7   0.0    1.7  1  HTH_11          HTH domain
    1.5e-05   24.9   0.2    6.2e-05   22.9   0.1    2.1  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    5.1e-05   23.1   0.0    0.00011   22.1   0.0    1.5  1  MarR            MarR family
    5.9e-05   23.0   0.0    0.00034   20.6   0.0    2.1  2  HTH_3           Helix-turn-helix
     0.0007   19.5   0.0     0.0012   18.8   0.0    1.4  1  HTH_45          Winged helix-turn-helix
      0.001   18.8   0.0     0.0029   17.3   0.0    1.8  1  HTH_23          Homeodomain-like domain
     0.0012   19.0   0.0     0.0027   17.9   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0023   18.3   0.0     0.0055   17.0   0.0    1.6  1  Rrf2            Transcriptional regulator
     0.0047   16.6   0.2      0.045   13.4   0.0    2.4  2  GntR            Bacterial regulatory proteins, gntR family
     0.0067   16.5   0.5       0.03   14.4   0.0    2.4  2  HTH_28          Helix-turn-helix domain
     0.0092   15.8   0.0      0.024   14.5   0.0    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   15.6   0.1      0.042   14.1   0.0    1.8  1  HTH_17          Helix-turn-helix domain
      0.015   15.2   0.0      0.031   14.2   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.017   14.9   0.0      0.025   14.3   0.0    1.2  1  DUF4364         Domain of unknown function (DUF4364)
      0.017   14.9   0.0        4.4    7.2   0.0    2.9  2  DUF1495         Winged helix DNA-binding domain (DUF1495)
      0.019   15.3   0.0       0.19   12.1   0.0    2.4  2  HTH_31          Helix-turn-helix domain
       0.02   15.2   0.1       0.07   13.4   0.0    2.0  1  Mnd1            Mnd1 HTH domain
      0.027   14.4   0.0       0.12   12.3   0.0    2.2  2  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.028   14.2   0.0      0.066   13.0   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
      0.032   14.3   0.0      0.076   13.1   0.0    1.7  1  HTH_13          HTH DNA binding domain
      0.033   14.0   0.0      0.087   12.7   0.0    1.7  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.045   13.9   0.0       0.18   12.0   0.0    1.9  1  Mrr_N           Mrr N-terminal domain
      0.048   14.0   0.0       0.11   12.8   0.0    1.7  1  HTH_Tnp_1       Transposase
       0.05   13.6   0.0       0.13   12.3   0.0    1.8  1  HTH_29          Winged helix-turn helix
      0.052   13.7   0.0       0.19   11.9   0.0    2.0  2  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.061   13.1   0.0       0.17   11.7   0.0    1.7  1  HTH_10          HTH DNA binding domain
      0.071   13.4   0.0       0.17   12.2   0.0    1.6  1  KORA            TrfB plasmid transcriptional repressor


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   2.6e-12   1.6e-09       6      51 ..      12      56 ..      10      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.6e-12
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      + +++L +++++ ++ ++++e+a+rlg++++a+s  +k+Lva GLv
  gi|386002908|ref|YP_005921207.1| 12 SRFQILVEIAANQPN-VRQKEVAERLGVTPQAISEYIKDLVADGLV 56
                                      5799*********97.9****************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   3.7e-12   2.2e-09       1      47 [.       9      56 ..       9      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.7e-12
                            HTH_24  1 ldetdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +d  +++IL ++ + +p+  q+e+Aerlg++p+++++++k L+ +Gl+
  gi|386002908|ref|YP_005921207.1|  9 RDSSRFQILVEIAAnQPNVRQKEVAERLGVTPQAISEYIKDLVADGLV 56
                                      58889****677665888****************************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   2.5e-09   1.5e-06       7      68 .]      15      70 ..      11      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.5e-09
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ++L  i+ ++  ++++++++rl v+ ++is+ +k L++ GLv       +++++r+r+T +G
  gi|386002908|ref|YP_005921207.1| 15 QILVEIAANQPNVRQKEVAERLGVTPQAISEYIKDLVADGLV------ISDGRMRYRITKEG 70
                                      678888889999999***************************......***********998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.8e-08   1.7e-05       2      46 ..      13      57 ..      12      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.8e-08
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      ++qil  + ++++++  +e Ae+L+v+ +++  +Ik+L + g+ I
  gi|386002908|ref|YP_005921207.1| 13 RFQILVEIAANQPNVRQKEVAERLGVTPQAISEYIKDLVADGLVI 57
                                      68999999899999************************9999544 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1     1e-07   6.2e-05      20      60 ..      25      67 ..       5      75 .. 0.80
   2 ?   -2.2   0.0         7   4.2e+03      48      62 ..     152     167 ..     151     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1e-07
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.rgrr.iril 60
                                       ++ q+e A++lG+t++ +s  +++L  +gl+   gr   ri+
  gi|386002908|ref|YP_005921207.1| 25 PNVRQKEVAERLGVTPQAISEYIKDLVADGLVIsDGRMrYRIT 67
                                      4799***************************775554226665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                                       TTSEE.E.TEEEEES-H CS
                         HTH_Crp_2  48 eglis.r.grririldl 62 
                                       +glis + g+ +++  +
  gi|386002908|ref|YP_005921207.1| 152 RGLISlKeGK-VTVCKV 167
                                       6999965245.998766 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.8e-07   0.00011       6      47 ..      14      56 ..      11      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                                      HHHHHHH.HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  6 fviLril.yeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      f iL+ + ++q++ +++e a++lgv++ ++++ ++ L+ +Gl+
  gi|386002908|ref|YP_005921207.1| 14 FQILVEIaANQPNVRQKEVAERLGVTPQAISEYIKDLVADGLV 56
                                      6677666157788*****************************8 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.7e-07   0.00034       8      32 ..      25      49 ..      19      52 .. 0.88
   2 ?   -0.9   0.0       2.9   1.7e+03      32      46 ..     174     188 ..     173     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.7e-07
                                      TTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3  8 lglsqeeLAeklGvsrstisriEnG 32
                                       +  q+e+Ae+lGv++++is ++++
  gi|386002908|ref|YP_005921207.1| 25 PNVRQKEVAERLGVTPQAISEYIKD 49
                                      5778******************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                                       TSSCSBHHHHHHHHH CS
                             HTH_3  32 GernPsletlkklak 46 
                                       G rn +le l ++a+
  gi|386002908|ref|YP_005921207.1| 174 GSRNVDLEALARIAR 188
                                       689999999999997 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     2e-06    0.0012      31      72 ..      38      81 ..       9      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
                            HTH_45 31 LsykllnkYLdmLvekgli.kkskekYvlTekGlell.eklkel 72
                                       + + +++Y++ Lv  gl+ ++    Y++T++G e+l e+  el
  gi|386002908|ref|YP_005921207.1| 38 VTPQAISEYIKDLVADGLViSDGRMRYRITKEGVEMLlESAAEL 81
                                      55577899**********7599999********99751555555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.9e-06    0.0029       7      46 ..      13      55 ..       7      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                            HTH_23  7 Rlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      R++il   a      +++e+A++Lgv+++ ++ ++k  +++Gl
  gi|386002908|ref|YP_005921207.1| 13 RFQILVEIAAnqpNVRQKEVAERLGVTPQAISEYIKDLVADGL 55
                                      999999999778***********************99877775 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.5e-06    0.0027      22      54 ..      26      58 ..      18      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.5e-06
                                      SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                       v++k++aerL+v p  +se +k L  dG+v+ 
  gi|386002908|ref|YP_005921207.1| 26 NVRQKEVAERLGVTPQAISEYIKDLVADGLVIS 58
                                      5899***************************86 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.1e-06    0.0055      11      57 ..      14      58 ..       6      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-06
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +++l+++a+++ +  v+ +e+aer ++ p+ ++  ++ L   glv s
  gi|386002908|ref|YP_005921207.1| 14 FQILVEIAANQPN--VRQKEVAERLGVTPQAISEYIKDLVADGLVIS 58
                                      6899****99995..8*****************************87 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   7.6e-05     0.045      26      59 ..      28      61 ..      21      66 .. 0.90
   2 ?    0.1   0.1         1   6.2e+02      33      52 ..     171     190 ..     169     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      +++e+a+++gV+ + + e ++ L+a+glv++  +
  gi|386002908|ref|YP_005921207.1| 28 RQKEVAERLGVTPQAISEYIKDLVADGLVISDGR 61
                                      5789*************************98765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                                       HHTS-HHHHHHHHHHHHHTT CS
                              GntR  33 efgVsrttvReALrrLeaeg 52 
                                       ++g sr++  eAL r +++g
  gi|386002908|ref|YP_005921207.1| 171 QMGGSRNVDLEALARIARDG 190
                                       8999999999*****99987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.1e-05      0.03       2      44 ..      13      55 ..      12      63 .. 0.78
   2 ?   -1.8   0.0       6.2   3.7e+03      10      25 ..     132     149 ..     132     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-05
                            HTH_28  2 Rleiikllaa...GhsvreaArelgisrrtvyrWikryeegGiagL 44
                                      R++i+ ++aa    ++++e+A++lg++++ ++  ik + +    gL
  gi|386002908|ref|YP_005921207.1| 13 RFQILVEIAAnqpNVRQKEVAERLGVTPQAISEYIKDLVAD---GL 55
                                      7888888886333469999*************999988884...44 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.2
                            HTH_28  10 aaGhsvre..aArelgis 25 
                                       a+G++++e  a + +g+s
  gi|386002908|ref|YP_005921207.1| 132 ASGVTIAEarAGEDVGVS 149
                                       579999997778888776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     4e-05     0.024       3      46 ..      12      57 ..      10      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                                      HHHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       R +IL   a  ++     e ae lg+++ ++S++ k L   GLV 
  gi|386002908|ref|YP_005921207.1| 12 SRFQILVEIAAnQPnVRQKEVAERLGVTPQAISEYIKDLVADGLVI 57
                                      566666666664444445689************************7 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     7e-05     0.042       5      49 ..      30      77 ..      28      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-05
                            HTH_17  5 eEaAelLgvsrstvyrlir...rgelpaa..kiGrrwriprsdleewlek 49
                                      +E+Ae Lgv ++ + ++i+   +  l +   ++  r+ri+++ +e  le+
  gi|386002908|ref|YP_005921207.1| 30 KEVAERLGVTPQAISEYIKdlvADGL-VIsdGR-MRYRITKEGVEMLLES 77
                                      8*****************65664444.443333.45****9999988875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.1e-05     0.031      11      55 ..      11      59 ..       7      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                                      CCHCHHHH....HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 11 akvYlaLl....klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      ++ ++ L+    ++ + + +e+ae+lgv  + + e+++ L+  GlV   
  gi|386002908|ref|YP_005921207.1| 11 SSRFQILVeiaaNQPNVRQKEVAERLGVTPQAISEYIKDLVADGLVISD 59
                                      5556666655567788899***************************876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.2e-05     0.025      36      88 ..      43      92 ..      38      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlelfenripksirekidey 88
                                      +++++++Lv +gl+ +   +++ +y+iT++G e+l +   ++    r  ++e 
  gi|386002908|ref|YP_005921207.1| 43 ISEYIKDLVADGLVIS---DGRMRYRITKEGVEMLLESAAELKRYARYVMEEI 92
                                      789************8...9***************999988888777666665 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0074       4.4      57      86 ..      48      73 ..       6      76 .. 0.91
   2 ?    4.4   0.0     0.053        32      34      54 ..     235     255 ..     222     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0074
                           DUF1495 57 ssLielGLveeeeeseglklYklteeGiei 86
                                      + L++ GLv     s+g   Y++t+eG e+
  gi|386002908|ref|YP_005921207.1| 48 KDLVADGLVI----SDGRMRYRITKEGVEM 73
                                      5699*****7....89999********986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.053
                           DUF1495  34 rvrskpsnvkGaleGmgkryn 54 
                                        v  ++ n+ G leG g +y+
  gi|386002908|ref|YP_005921207.1| 235 CVDEQVPNLMGRLEGEGLKYE 255
                                       678899*************98 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00031      0.19      13      34 ..      25      46 ..      12      52 .. 0.90
   2 ?   -0.3   0.0       2.4   1.4e+03      37      52 ..     174     188 ..     157     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                            HTH_31 13 aGLsqeevAerlgvsestlsrl 34
                                       +++q+evAerlgv++  +s +
  gi|386002908|ref|YP_005921207.1| 25 PNVRQKEVAERLGVTPQAISEY 46
                                      578***************9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.4
                            HTH_31  37 Grrgrpspavlealar 52 
                                       G r ++ +++l+++ar
  gi|386002908|ref|YP_005921207.1| 174 GSR-NVDLEALARIAR 188
                                       555.588888888876 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012      0.07      19      48 ..      30      59 ..      26      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                              Mnd1 19 klapkekgivsqsVkdvlqsLvdDglveve 48
                                      k+++   g+++q + ++++ Lv+Dglv ++
  gi|386002908|ref|YP_005921207.1| 30 KEVAERLGVTPQAISEYIKDLVADGLVISD 59
                                      55666689******************9765 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.12      18      58 ..      31      69 ..      12      71 .. 0.69
   2 ?   -2.2   0.0         7   4.2e+03       3      17 ..     179     193 ..     179     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                      HHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSS.EEEE-HH CS
                             HTH_1 18 rAAeeLglsqpavsrqikrLEeelgvpLfeRtgr.glrLTea 58
                                      + Ae+Lg+++ a+s  ik+L   + + L++ +gr + r T +
  gi|386002908|ref|YP_005921207.1| 31 EVAERLGVTPQAISEYIKDL---VADGLVISDGRmRYRITKE 69
                                      68****************87...5556666655555666655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                                       HHHHHHHHHHHSSHH CS
                             HTH_1   3 qlrlfvavaeegsft 17 
                                       +l+++  +a+ g + 
  gi|386002908|ref|YP_005921207.1| 179 DLEALARIARDGEMV 193
                                       589999999999765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.066       6      51 ..      14      59 ..      14      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++iL  +a+ ++ ++ +e+A+r+g+++ + + +++ Lv  G+v  d
  gi|386002908|ref|YP_005921207.1| 14 FQILVEIAANQPNVRQKEVAERLGVTPQAISEYIKDLVADGLVISD 59
                                      6899999999999*****************************9655 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.076       4      49 ..      17      65 ..      15      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                            HTH_13  4 LvelvlsrPlVsagmvakeLkvtpraalklvkel...glRElTGRgrfr 49
                                      Lve+   +P V  + va+ L vtp+a  + +k+l   gl    GR r+r
  gi|386002908|ref|YP_005921207.1| 17 LVEIAANQPNVRQKEVAERLGVTPQAISEYIKDLvadGLVISDGRMRYR 65
                                      8999999**************************9333344456888887 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.087      11      30 ..      29      48 ..      24      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlk 30
                                      qk++Ae+lgv++qa+s  +k
  gi|386002908|ref|YP_005921207.1| 29 QKEVAERLGVTPQAISEYIK 48
                                      99**************9874 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0003      0.18      32      85 ..      26      74 ..       2      76 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                             Mrr_N 32 glseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTekGrevl 85
                                      ++ ++e+ae l         + ++ ++++L+  gl+ s+ r  ++iT++G e+l
  gi|386002908|ref|YP_005921207.1| 26 NVRQKEVAERLGVTP-----QAISEYIKDLVADGLVISDGRMRYRITKEGVEML 74
                                      555555555553332.....345557899*********************9987 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00019      0.11      21      54 ..      24      57 ..       8      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                         HTH_Tnp_1 21 epgksvsevArrhgvspnqLykWrrqyregeeas 54
                                      +p ++ +evA+r+gv p++ +  ++   ++ ++ 
  gi|386002908|ref|YP_005921207.1| 24 QPNVRQKEVAERLGVTPQAISEYIKDLVADGLVI 57
                                      799999****************999988555554 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022      0.13      14      41 ..      28      55 ..      13      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      + +++A++lg++++ +  ++k+ +++Gl
  gi|386002908|ref|YP_005921207.1| 28 RQKEVAERLGVTPQAISEYIKDLVADGL 55
                                      7899***********************6 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00032      0.19       2      34 ..      16      48 ..      15      57 .. 0.81
   2 ?   -2.2   0.0       8.3     5e+03      13      29 ..     186     204 ..     179     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                           AbiEi_4  2 rlpelasrqvGlfttrelea.aGispsalrrLvr 34
                                       l+e+a+ q + ++ +e+++ +G++p+a++++++
  gi|386002908|ref|YP_005921207.1| 16 ILVEIAANQ-PNVRQKEVAErLGVTPQAISEYIK 48
                                      688999888.79******999*******766654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.3
                           AbiEi_4  13 lfttre.leaaGisp.sal 29 
                                       ++++ e + a+Gi    al
  gi|386002908|ref|YP_005921207.1| 186 IARDGEmVGALGIESlVAL 204
                                       6777774455777665555 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00029      0.17      24      45 ..      27      48 ..      25      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                      v+ ke+A++lG++++++se+++
  gi|386002908|ref|YP_005921207.1| 27 VRQKEVAERLGVTPQAISEYIK 48
                                      6679****************97 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00028      0.17      31      53 ..      26      48 ..      11      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                              KORA 31 gkkqadvatelgltkqavsqavk 53
                                      +++q++va++lg+t qa+s+ +k
  gi|386002908|ref|YP_005921207.1| 26 NVRQKEVAERLGVTPQAISEYIK 48
                                      579****************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1652.25
//
Query:       gi|386002909|ref|YP_005921208.1|  [L=812]
Description: DEAD/DEAH box helicase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-20   73.2   0.0    3.9e-20   72.4   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
    1.3e-13   51.3   0.0    2.7e-13   50.2   0.0    1.5  1  Helicase_C  Helicase conserved C-terminal domain
    1.1e-08   35.3   0.0    1.7e-08   34.7   0.0    1.2  1  ResIII      Type III restriction enzyme, res subunit
    0.00059   19.5   0.1       0.13   12.1   0.0    3.8  4  HTH_38      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.056   13.8   0.1       0.23   11.8   0.1    2.1  1  SOCS_box    SOCS box


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   1.1e-23   3.9e-20       2     170 ..     216     378 ..     215     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.1e-23
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.. CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.. 75 
                                       ++Qa+ai   l +g+++lv  +T++GK+l+  ++ +++++e     + k l+++P+ +La+q +++l+ + + ++  
  gi|386002909|ref|YP_005921208.1| 216 PVQAKAIRMGLlEGKNLLVVSATATGKSLVGEMAGIKNFLE----GRGKLLFLVPLVALANQKYDQLSLYRD-LGar 287
                                       79******9888***************************65....7889******************88877.3311 PP

                                       ..SEEE.EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       ..xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 ..lrvl.liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                         +rv  + i+  +a++  ++l  + +i+vgt + +d+ll+tg+  l +v ++V+DE+++l +++++  ++ ++++l
  gi|386002909|ref|YP_005921208.1| 288 aaIRVGvSRIKLGKAKRMNQDL--NSEIIVGTYEGIDQLLRTGR-GLGRVGTVVIDEVHMLEEKERGHRLSGLIARL 361
                                       2244443334444444555555..69**************9999.9******************************* PP

                                       HHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 150 pqitcdgklqrqvivlSATlp 170
                                       +  +       q+i lSAT+ 
  gi|386002909|ref|YP_005921208.1| 362 RFSYPA----AQFIYLSATVG 378
                                       655544....45*******85 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   7.5e-17   2.7e-13      12     111 .]     430     529 ..     416     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 7.5e-17
                                       HTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEE CS
                        Helicase_C  12 leeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlV 88 
                                       ++  +g+++if+n++++++  +l       ++a++h+ ++ ++r+++ + f +g++d +++t +++ G+d+p  +++
  gi|386002909|ref|YP_005921208.1| 430 STGYRGQTIIFTNSRKNCN--SLA--LAIPNSAAYHAGMQYDQRRKVEALFAEGKVDAVVTTAALAAGVDFPASQVI 502
                                       556799************6..444..334689999*************************************88887 PP

                                       EESSSS....SSHHHHHHHHTTSSSTT CS
                        Helicase_C  89 infdlp....rnvtsyiqriGRtgRag 111
                                       ++  +      +v++++q+ GR+gR g
  gi|386002909|ref|YP_005921208.1| 503 FDSLAMgiewLSVHEFNQMLGRAGRPG 529
                                       7666657776679************75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   4.6e-12   1.7e-08       4     169 ..     214     377 ..     211     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.6e-12
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       l + Q++ai+  l      + k++l++ aT tGK+lv  ++ i+++l+ ++  k lflvp  +l +q +++++ + +
  gi|386002909|ref|YP_005921208.1| 214 LLPVQAKAIRMGL-----LEGKNLLVVSATATGKSLVGeMAGIKNFLEGRG--KLLFLVPLVALANQKYDQLSLYRD 283
                                       6667777777766.....346799************************877..*******************99998 PP

                                       G.........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T... CS
                            ResIII  80 eayke.....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk... 148
                                         + +     ++ ++ g+ k+  ++++ n++i+v t++ +d+ +      ++  + +r   ++iDE+H l +k+   
  gi|386002909|ref|YP_005921208.1| 284 LGARAairvgVSRIKLGKAKR--MNQDLNSEIIVGTYEGIDQLL------RTGRGLGRVGTVVIDEVHMLEEKErgh 352
                                       877666776533333333333..46799****************......8899999999************85444 PP

                                       ....TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 ....swreilekfkeavllglTATp 169
                                            + ++  ++++a  ++l+AT 
  gi|386002909|ref|YP_005921208.1| 353 rlsgLIARLRFSYPAAQFIYLSATV 377
                                       4443444444444779999999996 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.81   2.9e+03       7      21 ..     466     480 ..     464     480 .. 0.88
   2 !   12.1   0.0   3.5e-05      0.13       3      31 ..     636     664 ..     634     665 .. 0.89
   3 ?    2.3   0.1     0.041   1.5e+02      12      26 ..     742     756 ..     740     758 .. 0.90
   4 ?   -1.8   0.0      0.79   2.8e+03      23      34 ..     787     798 ..     784     799 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.81
                            HTH_38   7 leeReeIerllaeGl 21 
                                        ++R++ e+l aeG+
  gi|386002909|ref|YP_005921208.1| 466 YDQRRKVEALFAEGK 480
                                       689**********96 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                            HTH_38   3 khLsleeReeIerllaeGlslreIArrLg 31 
                                       + L++ee ++I ++laeG++  +IA  L 
  gi|386002909|ref|YP_005921208.1| 636 HFLTPEEVVVIRKGLAEGKGALDIAVDLE 664
                                       67**********************97665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.041
                            HTH_38  12 eIerllaeGlslreI 26 
                                       +I  l+aeG+s ++I
  gi|386002909|ref|YP_005921208.1| 742 KILELRAEGMSPSRI 756
                                       6999*******9988 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.79
                            HTH_38  23 lreIArrLgrsp 34 
                                       + e+Ar Lg++ 
  gi|386002909|ref|YP_005921208.1| 787 IEEMARVLGKKE 798
                                       5699*****986 PP

>> SOCS_box  SOCS box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.5e-05      0.23       6      34 ..     150     208 ..     149     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                          SOCS_box   6 hLCRlsIRk.sL....gk.........................kieqLpLPpsLknYLl 34 
                                       h++Rl  R+ +L    g                          ++e L+LPp Lk++Ll
  gi|386002909|ref|YP_005921208.1| 150 HMARLLLRRrDLdevlGLlaldrleadltkfdeipaereenpmAVEALDLPPELKSFLL 208
                                       666666666555544422445555666666676777777777889*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 5134.39
//
Query:       gi|386002910|ref|YP_005921209.1|  [L=409]
Description: Peptidase C1A, papain, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-43  149.0   5.1    3.1e-43  148.4   5.1    1.2  1  Peptidase_C1  Papain family cysteine protease
    2.4e-07   31.4   0.1    5.9e-07   30.2   0.1    1.7  1  DUF4114       Domain of unknown function (DUF4114)


Domain annotation for each model (and alignments):
>> Peptidase_C1  Papain family cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   5.1   3.4e-47   3.1e-43       4     213 ..      74     277 ..      72     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 3.4e-47
                                       CEETTTTTTG..SG---B-TSSBTHHHHHHHHHHHHHHHHHHS..SS---B-HHHHHHHSTTTSTGGGBB-HH.HHH CS
                      Peptidase_C1   4 svDwrekgga..vtpvkdqgsCGsCWafsavgaledrlaiktk..kklvslSeqelvdCskeenegCnGGlme.naf 75 
                                       s++wr+ gg    tpvkdq+ CGsC +f++ +++e+ l i ++    + +lSe +l  C   + + C  G+    a+
  gi|386002910|ref|YP_005921209.1|  74 SWNWRNVGGVdwTTPVKDQKGCGSCVSFATSAVVEANLEIFRRnpYLNPNLSEADLFFCG--CGKCCASGWNFpPAL 148
                                       899***6655589************************9998876677899*********6..689*****98637** PP

                                       HHHHHTEBEBTTTS--SSSCSSS-CGCGGGSE.EBEESEEEEEESSBHHHHHHHHHHHSSEEEEEECCSHHHHTEES CS
                      Peptidase_C1  76 eyikkggivtekdypYkakeggkCkkkkkkek.vakikgygkvkenseealkkalakngPvsvaidaseedfqlYks 151
                                       +y+k++gi ++++ypY++k+ + Ck   +++k + ki+g ++++    ++ k+++ ++gPv   + +++ df +Y++
  gi|386002910|ref|YP_005921209.1| 149 DYAKSKGIPDDACYPYTDKD-QPCKPCADRAKrIIKIQGWRSLSTA--SQAKEWICRHGPVITGMAVYT-DFFSYRG 221
                                       ********************.5899886555558999999999986..899******************.6****** PP

                                       SEESSTSCETSS-EEEEEEEEEEEETTEEEEEEE-SBTTTSTBTTEEEEESSSSTGGGTTSS CS
                      Peptidase_C1 152 GvyketecsktelnhavlivGygvengkkyWivkNsWgtdwgekGYiriargknnecgiese 213
                                       Gvy++    + e +ha+++vGy ++  +++Wi+kNsWgt wge G++ri+ g   ecgi s+
  gi|386002910|ref|YP_005921209.1| 222 GVYRHA-SGRLEGYHAIAVVGYSET--EQCWICKNSWGTGWGEGGWFRIRYG---ECGIGST 277
                                       *****6.445689*********987..89*********************88...8999875 PP

>> DUF4114  Domain of unknown function (DUF4114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   6.6e-11   5.9e-07       1      84 [.     342     408 ..     336     409 .] 0.78

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.6e-11
                           DUF4114   1 fpaGttigffLvangtnqellensssgiffSqeslNpdgedqngdrvhqvalndtkstvvvlgfEDllrgsDkDFnD 77 
                                       f aG+++ f L +++          +++++++ ++N+d  d+       +++++++  ++ l +EDl   +D+D+nD
  gi|386002910|ref|YP_005921209.1| 342 FSAGQKLIFALKTPD----------GNTYYTTHAWNKDACDH------VIKVQTGNY-KWELRWEDLYGLGDQDYND 401
                                       667777777777777..........489*********96655......455444444.588*****8666******* PP

                           DUF4114  78 lvfyves 84 
                                       +v  +e+
  gi|386002910|ref|YP_005921209.1| 402 VVAEIEI 408
                                       **98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2434.98
//
Query:       gi|386002911|ref|YP_005921210.1|  [L=119]
Description: hypothetical protein Mhar_2235 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-19   69.9   0.0    2.2e-19   69.7   0.0    1.0  1  Inhibitor_I42  Chagasin family peptidase inhibitor I42


Domain annotation for each model (and alignments):
>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   1.2e-23   2.2e-19       2      91 .]      32     118 ..      31     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.2e-23
                                       EETT-EEEEEEEE-CCCT-EEEEEE--TTTEEE-TTTCECCECCESTTSSEEEEEEEEESSSEEEEEEEEEE-TTST CS
                     Inhibitor_I42   2 vkvgetieieLpenpttGYsWtvdasdseglkllseeyipdesdelvGaggthvwtfkalkpGettiefkyarpwek 78 
                                       vkv e++ei+L++ pttGY+W+  + d+e ++l + ++ ++++  ++G+gg++++tf  l++Get++ +  +r+we 
  gi|386002911|ref|YP_005921210.1|  32 VKVAEEFEISLESVPTTGYVWE-AKFDGEMMRLKDRSFLASQPG-AIGGGGNEIFTFVPLQTGETEVAMIRKRSWER 106
                                       899*******************.55569***************9.******************************** PP

                                       SS--SC.EEEEEE CS
                     Inhibitor_I42  79 ateaeertftltv 91 
                                       + +aeert+++++
  gi|386002911|ref|YP_005921210.1| 107 E-AAEERTYRIKI 118
                                       *.55777999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 771.73
//
Query:       gi|386002912|ref|YP_005921211.1|  [L=312]
Description: hypothetical protein Mhar_2236 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2018.05
//
Query:       gi|386002913|ref|YP_005921212.1|  [L=338]
Description: hypothetical protein Mhar_2237 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-06   26.5   0.0      1e-05   25.3   0.0    1.6  1  MarR_2           MarR family
    9.3e-06   25.4   0.0    2.2e-05   24.1   0.0    1.7  1  HTH_IclR         IclR helix-turn-helix domain
    2.7e-05   24.0   0.1    5.3e-05   23.0   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.005   16.4   0.3      0.067   12.8   0.2    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.03   13.8   0.0      0.054   13.0   0.0    1.4  1  Sigma70_r4       Sigma-70, region 4
      0.064   13.2   0.1       0.16   11.9   0.1    1.7  2  MarR             MarR family
      0.078   13.5   0.2       0.14   12.6   0.2    1.5  1  HTH_27           Winged helix DNA-binding domain
       0.18   12.2   0.2       0.28   11.5   0.2    1.3  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.6e-09     1e-05       3      54 ..     268     318 ..     267     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.6e-09
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       lt  ++ vL aL  ++g+ +t++++  ++g++ks+++ i+  L+++  v+++
  gi|386002913|ref|YP_005921212.1| 268 LTDRERSVLEALMKNEGK-MTQADIRYETGIPKSSLTGIIVSLERRNIVTKK 318
                                       68899***********97.9****************************9876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     1e-08   2.2e-05       7      50 ..     274     317 ..     269     319 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1e-08
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++L+al +  + +t +++  +tg+pkS+  +++ +L+++ +v++
  gi|386002913|ref|YP_005921212.1| 274 SVLEALMKNEGKMTQADIRYETGIPKSSLTGIIVSLERRNIVTK 317
                                       69*************************************99986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   2.4e-08   5.3e-05       6      58 ..     268     321 ..     267     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.4e-08
                                       HHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB   6 LseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       L++ E +v  aL+ ++g++t  +i  e+g+p+s+   ++ sLe++ +V+++++ 
  gi|386002913|ref|YP_005921212.1| 268 LTDRERSVLEALMkNEGKMTQADIRYETGIPKSSLTGIIVSLERRNIVTKKERG 321
                                       8999*********9999*******************************999854 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2     3e-05     0.067       2      47 ..     269     315 ..     268     316 .. 0.87
   2 ?    1.3   0.0      0.12   2.6e+02      15      28 ..     320     333 ..     318     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                            HTH_24   2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                        + +r +Le+L+kn + ++q+++  ++g+++s ++  +  Le+  ++
  gi|386002913|ref|YP_005921212.1| 269 TDRERSVLEALMKNEGkMTQADIRYETGIPKSSLTGIIVSLERRNIV 315
                                       67899********8888***************999888888888777 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                            HTH_24  15 nprisqreLAerlg 28 
                                        +r++  eL+erl+
  gi|386002913|ref|YP_005921212.1| 320 RGRTNVIELSERLN 333
                                       68999*******98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.054       1      33 [.     264     298 ..     264     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       HHHHS-HHHHHHHHHHH..TTT--HHHHHHHHTS- CS
                        Sigma70_r4   1 aLasLpererevlelrf..geglTleEIgerlgiS 33 
                                       ++++L++rer vle     + ++T+++I  + gi+
  gi|386002913|ref|YP_005921212.1| 264 VMDTLTDRERSVLEALMknEGKMTQADIRYETGIP 298
                                       599***********99999999***9996666666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.3e-05      0.16      13      50 ..     281     318 ..     268     323 .. 0.83
   2 ?   -1.5   0.0       1.1   2.4e+03      14      28 ..     319     333 ..     318     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.3e-05
                                       HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       +++g ++++++    g+ ks++t ++  Le+++ ++++
  gi|386002913|ref|YP_005921212.1| 281 KNEGKMTQADIRYETGIPKSSLTGIIVSLERRNIVTKK 318
                                       56777******************************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                       HSTTEEHHHHHHHHT CS
                              MarR  14 eqgplsvseLakklg 28 
                                       e+g  +v+eL ++l+
  gi|386002913|ref|YP_005921212.1| 319 ERGRTNVIELSERLN 333
                                       78999*******986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.4e-05      0.14       1      59 [.     268     323 ..     268     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                            HTH_27   1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59 
                                       lt  ++ vL+ ++ +++++++ad++  + + +s+   ++  L+++  v++++    +r+
  gi|386002913|ref|YP_005921212.1| 268 LTDRERSVLEALMKNEGKMTQADIRYETGIPKSSLTGIIVSLERRNIVTKKE---RGRT 323
                                       6788999***************************************994433...3344 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00013      0.28       1      60 [.     268     324 ..     268     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       ---S-SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R   1 lgelEaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                       l+++E+ v+e+l +++  +t ++++ e   +    +s+ + ++  L++++++++++ gr+ 
  gi|386002913|ref|YP_005921212.1| 268 LTDRERSVLEALMKNEGkMTQADIRYETGIP----KSSLTGIIVSLERRNIVTKKERGRTN 324
                                       699*********999888******9988888....9**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2334.67
//
Query:       gi|386002914|ref|YP_005921213.1|  [L=373]
Description: hypothetical protein Mhar_2238 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2385.57
//
Query:       gi|386002915|ref|YP_005921214.1|  [L=500]
Description: hypothetical protein Mhar_2239 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-16   59.3   0.8    1.4e-06   28.5   0.2    3.6  3  DUF11        Domain of unknown function DUF11
    1.6e-08   34.8   0.0     0.0023   18.1   0.0    3.4  3  CARDB        CARDB
    0.00013   21.0   0.0     0.0012   17.8   0.0    2.1  2  BatD         Oxygen tolerance
    0.00076   19.7   2.2        6.2    7.2   0.0    4.4  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
     0.0024   17.3   0.0      0.037   13.4   0.0    2.6  3  TRAP_beta    Translocon-associated protein beta (TRAPB)
     0.0081   16.4   0.0       0.54   10.5   0.0    2.9  3  ASH          Abnormal spindle-like microcephaly-assoc'd, ASPM
  ------ inclusion threshold ------
      0.033   14.4   0.1         15    5.8   0.0    3.5  3  Top6b_C      Type 2 DNA topoisomerase 6 subunit B C-terminal 
       0.14   12.0   0.3       0.33   10.8   0.3    1.6  1  DUF824       Salmonella repeat of unknown function (DUF824)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.058   1.3e+02       9      68 ..     128     176 ..     119     211 .. 0.85
   2 !   24.1   0.0   1.5e-08   3.3e-05       7      85 ..     242     310 ..     237     316 .. 0.83
   3 !   28.5   0.2   6.5e-10   1.4e-06       1      51 [.     344     393 ..     344     455 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.058
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeage 68 
                                       + r Gd  +  + v N g a+a++v ++    +g    ++s s           sL++ge
  gi|386002915|ref|YP_005921214.1| 128 AYRGGDRARLEVEVENVGMAAAEEVELEVAFGPGIPSARHSIS-----------SLAPGE 176
                                       567799999999***************9999888888888888...........566665 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.5e-08
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaa 83 
                                       ++evr+G++  + l v+Ntgp++  +vv+tD    g  + ++ +       ++++ ++++ges   s+tv+++r ++
  gi|386002915|ref|YP_005921214.1| 242 EEEVRFGEESYVHLSVSNTGPRPQ-EVVLTD--SVGRDFLTGATL------EWRM-TVPPGESEGASYTVTAKRPGE 308
                                       468*********************.******..445555555544......5664.99***************9998 PP

                             DUF11  84 sg 85 
                                        +
  gi|386002915|ref|YP_005921214.1| 309 GQ 310
                                       76 PP

  == domain 3  score: 28.5 bits;  conditional E-value: 6.5e-10
                             DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                       + K  ++s+v  G++vt+t+t++N g++ a ++ ++ t+P+  ++v + + 
  gi|386002915|ref|YP_005921214.1| 344 VEKRASTSRVGVGEEVTVTVTAKNAGNRRA-KASLQETVPPWATLVGGETE 393
                                       5799999***********************.*********98888887777 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     1e-06    0.0023       2      64 ..     116     179 ..     115     186 .. 0.87
   2 ?    2.2   0.0     0.098   2.2e+02      11      54 ..     241     283 ..     230     325 .. 0.64
   3 !   10.1   0.0   0.00033      0.74       6      38 ..     344     376 ..     340     426 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTEEEE CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaagestt 64 
                                       pDLtv +  ++++   g+  +++v+v+N G aa++++++++        +  +++sLa+ge  +
  gi|386002915|ref|YP_005921214.1| 116 PDLTVRVVPKEEAYRGGDRARLEVEVENVGMAAAEEVELEVAFGPGIPsARHSISSLAPGEVWD 179
                                       9****7777777788899***********************99866555999********9765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.098
                                       C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE CS
                             CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv 54 
                                       +++e+  gee+ ++++v+N+G    + + ++  + ++  + +t+
  gi|386002915|ref|YP_005921214.1| 241 AEEEVRFGEESYVHLSVSNTGPRPQEVVLTD-SVGRDFLTGATL 283
                                       6677888999999*******98765544333.344444444444 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00033
                                       E.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEE CS
                             CARDB   6 vtntlnpseafvgeentitvtvkNqGtaasgat 38 
                                       v++ ++ s + vgee+t+tvt kN G+  ++a+
  gi|386002915|ref|YP_005921214.1| 344 VEKRASTSRVGVGEEVTVTVTAKNAGNRRAKAS 376
                                       56677888999****************997765 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.08   1.8e+02      77     108 ..     297     331 ..     239     338 .. 0.73
   2 !   17.8   0.0   5.4e-07    0.0012      11     118 ..     343     452 ..     337     474 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.08
                              BatD  77 wtytLapkkeGt.ltIpaatiev..dgktyksnpi 108
                                        +yt+ +k++G+   +p+a++++  dgk+y+ +++
  gi|386002915|ref|YP_005921214.1| 297 ASYTVTAKRPGEgQALPPAEATYsvDGKGYRVRSM 331
                                       589999*****945699876654449999998776 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.4e-07
                              BatD  11 eftasvdknevevgetfrLtftvngasgepdfsapslek....dfevlsgsqssstqiinGkssssssktwtytLap 83 
                                       e++ +++ ++v+vge++++t+t+++a g+   +a sl++      ++++g+++ s+ +  G+  +     + y L +
  gi|386002915|ref|YP_005921214.1| 343 EVEKRASTSRVGVGEEVTVTVTAKNA-GNRRAKA-SLQEtvppWATLVGGETELSLLLLPGEEAA-----IVYNLSC 412
                                       66777889******************.5555553.354444457899999******999999888.....89***** PP

                              BatD  84 kkeGtltIpaatievdgk.....tyksnpitikVlkseas 118
                                        ++G++tIpa t+ ++++     t++s+ ++i+V ++e++
  gi|386002915|ref|YP_005921214.1| 413 PEPGSFTIPATTVCYRDDrgtacTLESSRLRITVEEEEEA 452
                                       *************995542334468999999999552222 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 !    7.2   0.0    0.0027       6.2       4      51 ..     132     176 ..     129     189 .. 0.89
   2 ?   -3.5   0.0         6   1.3e+04      66      77 ..     199     210 ..     190     212 .. 0.79
   3 ?    3.6   0.1     0.035        77      49      75 ..     279     304 ..     248     305 .. 0.60
   4 ?    4.8   0.0     0.015        33       4      22 ..     356     374 ..     353     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0027
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGe 51 
                                       G++ +l+++v n g aaa++v+l++ + +G     ++  s++slapGe
  gi|386002915|ref|YP_005921214.1| 132 GDRARLEVEVENVGMAAAEEVELEVAFGPGIP---SARHSISSLAPGE 176
                                       88999********************9988877...8888888888887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6
                       NPCBM_assoc  66 aaGdyevtakar 77 
                                       +aG +e++++ar
  gi|386002915|ref|YP_005921214.1| 199 VAGPQELRVEAR 210
                                       478888888887 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.035
                       NPCBM_assoc  49 pGetveatvkVtppagaaaGd.yevtak 75 
                                       +G+t+e  +++t+p+g   G  y+vtak
  gi|386002915|ref|YP_005921214.1| 279 TGATLE--WRMTVPPGESEGAsYTVTAK 304
                                       455555..55555555444444999885 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.015
                       NPCBM_assoc   4 Getvtltltvtndgtaaat 22 
                                       Ge+vt+t+t++n g++ a+
  gi|386002915|ref|YP_005921214.1| 356 GEEVTVTVTAKNAGNRRAK 374
                                       99************87665 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 ?    0.0   0.0      0.21   4.8e+02      34      56 ..     132     154 ..     124     159 .. 0.85
   2 ?   -2.1   0.0      0.95   2.1e+03      78     109 ..     287     319 ..     276     331 .. 0.73
   3 !   13.4   0.0   1.7e-05     0.037      19     117 ..     341     434 ..     328     462 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.21
                         TRAP_beta  34 gedltveytiyNvGssaAldVsl 56 
                                       g +  +e+++ NvG +aA +V+l
  gi|386002915|ref|YP_005921214.1| 132 GDRARLEVEVENVGMAAAEEVEL 154
                                       66677889999**********98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.95
                         TRAP_beta  78 erlapgenvshsfvvepkksgsfng.taavvtY 109
                                        +++pge+   s++v++k +g  ++  +a+ tY
  gi|386002915|ref|YP_005921214.1| 287 MTVPPGESEGASYTVTAKRPGEGQAlPPAEATY 319
                                       478999999999999999999876514577777 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.7e-05
                         TRAP_beta  19 rvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepk 95 
                                        v v+K++ +  +  ge++tv++t  N+G+  A + sl+++  p    ++v+g+++++   l pge+   ++ +   
  gi|386002915|ref|YP_005921214.1| 341 LVEVEKRASTSRVGVGEEVTVTVTAKNAGNRRA-KASLQETVPPWA--TLVGGETELSLL-LLPGEEAAIVYNLSCP 413
                                       577899999999999****************99.679999766555..69********96.679************* PP

                         TRAP_beta  96 ksgsfngtaavvtYresekgae 117
                                        +gsf + a++v Yr+    ++
  gi|386002915|ref|YP_005921214.1| 414 EPGSFTIPATTVCYRDDRG-TA 434
                                       **************98765.44 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.9   4.2e+03      52      76 ..     136     160 ..     132     161 .. 0.66
   2 !   10.5   0.0   0.00024      0.54      17      67 ..     243     294 ..     243     304 .. 0.90
   3 ?    2.1   0.0       0.1   2.3e+02      18      46 ..     352     380 ..     342     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  52 gfsveetelevqpgesvtltvtwtP 76 
                                       ++ ve +++  ++ e+v l+v + P
  gi|386002915|ref|YP_005921214.1| 136 RLEVEVENVGMAAAEEVELEVAFGP 160
                                       4556666666777777777777766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
                                       -----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXX CS
                               ASH  17 gdvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.levqpges 67 
                                       ++v+ G+     L v+N+++ p+ev +++++++++    + ++ ++v+pges
  gi|386002915|ref|YP_005921214.1| 243 EEVRFGEESYVHLSVSNTGPRPQEVVLTDSVGRDFLTGATLEWrMTVPPGES 294
                                       579999*************************88888777777799****997 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.1
                                       ----EEEEEEE-EEESS-SS--EEEEEEE CS
                               ASH  18 dvkvGssaerlLtveNpseepaevkvskv 46 
                                       +v vG+  + ++t +N ++  a+  ++ +
  gi|386002915|ref|YP_005921214.1| 352 RVGVGEEVTVTVTAKNAGNRRAKASLQET 380
                                       67888888888888888888765555444 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   4.2e+03      26      45 ..     130     149 ..     119     159 .. 0.70
   2 ?    5.8   0.0    0.0069        15      74      97 ..     282     305 ..     231     323 .. 0.75
   3 ?    3.8   0.0     0.028        64      28      54 ..     356     382 ..     334     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                                       -SSS-EEEEEEE-------- CS
                           Top6b_C  26 engdgvevslkvkNfsdkke 45 
                                       ++gd ++ +++v+N +  ++
  gi|386002915|ref|YP_005921214.1| 130 RGGDRARLEVEVENVGMAAA 149
                                       56677899999999886543 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0069
                                       EE-EEE---TT-EEEE----SS-G CS
                           Top6b_C  74 dlkWelsvsageskvleYsvdsea 97 
                                        l+W+++v +ges+  +Y+v+++ 
  gi|386002915|ref|YP_005921214.1| 282 TLEWRMTVPPGESEGASYTVTAKR 305
                                       478***************999876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.028
                                       SS-EEEEEEE---------EEE--EES CS
                           Top6b_C  28 gdgvevslkvkNfsdkkeefelheilp 54 
                                       g++v+v+++ kN +++ ++ +l+e++p
  gi|386002915|ref|YP_005921214.1| 356 GEEVTVTVTAKNAGNRRAKASLQETVP 382
                                       356999******************997 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00015      0.33       9      26 ..     353     370 ..     348     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                            DUF824   9 aKkGEsipltitvkDasG 26 
                                       + +GE++++t+t k+a +
  gi|386002915|ref|YP_005921214.1| 353 VGVGEEVTVTVTAKNAGN 370
                                       779*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3418.57
//
Query:       gi|386002916|ref|YP_005921215.1|  [L=167]
Description: hypothetical protein Mhar_2240 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.7   3.2      0.013   15.7   0.2    2.4  2  DUF5122   Domain of unknown function (DUF5122) beta-propeller
  ------ inclusion threshold ------
       0.11   11.8   0.0          2    7.6   0.0    2.0  2  BNR_2     BNR repeat-like domain


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.5e-06     0.013       2      31 ..      67      97 ..      66      99 .. 0.79
   2 ?    3.4   0.4      0.01        94       3      23 ..     120     140 ..     119     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                           DUF5122  2 pDGKIlVaGsft.syngssdfalvRLnaDGs 31
                                      +DG I+VaG++t + +g++d  lv+ ++ G 
  gi|386002916|ref|YP_005921215.1| 67 ADGGIIVAGYTTsRGGGGRDLWLVKTDSEGE 97
                                      7***********5558888887777777665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                           DUF5122   3 DGKIlVaGsftsy.ngssdfal 23 
                                       DG  +VaG ++s  +g++d  l
  gi|386002916|ref|YP_005921215.1| 120 DGY-VVAGVSSSGeGGGRDLLL 140
                                       676.677777756577777665 PP

>> BNR_2  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00022         2     104     153 ..      48     103 ..      35     111 .. 0.84
   2 ?    2.4   0.0    0.0091        81     117     153 ..     116     154 ..     106     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00022
                                       EEEEEE-SS--..EE--...T--EEEEEE.....SS--EEEEEEEESSTTSS-EE- CS
                             BNR_2 104 pflnisgpvknkpiqla...dGrlilPsshe...lagkwrallelsddggktWkkg 153
                                       ++  + gp++ + i+l+   dG++i++ +++     g++  l++++++g++ W+++
  gi|386002916|ref|YP_005921215.1|  48 WEKAFGGPGEERGISLQetaDGGIIVAGYTTsrgGGGRDLWLVKTDSEGELEWDRT 103
                                       55567889999999888888*******9999776677799999999999999*985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.0091
                                       EE--T--EEEE..EE..SS--EEEEEEEESSTTSS-EE- CS
                             BNR_2 117 iqladGrlilP..sshelagkwrallelsddggktWkkg 153
                                       ++++dG ++ +  ss+e  g++  ll++ +dg  +W+k+
  gi|386002916|ref|YP_005921215.1| 116 LEVEDGYVVAGvsSSGEGGGRDLLLLKTYSDGYERWSKT 154
                                       56778888888778889999999*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 1032.49
//
Query:       gi|386002917|ref|YP_005921216.1|  [L=235]
Description: hypothetical protein Mhar_2241 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   15.5   2.2       0.31   11.0   0.0    3.4  4  SPDY           Domain of unknown function (DUF317)
      0.076   12.6   0.1        5.8    6.5   0.0    2.8  3  Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> SPDY  Domain of unknown function (DUF317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.12   1.1e+03      19      38 ..      19      38 ..       8      43 .. 0.69
   2 ?    1.9   0.0     0.024   2.1e+02      20      42 ..      72      93 ..      56      94 .. 0.75
   3 ?   -3.1   0.1      0.85   7.6e+03      28      38 ..     143     153 ..     132     153 .. 0.55
   4 ?   11.0   0.0   3.5e-05      0.31       5      41 ..     159     192 ..     158     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.12
                              SPDY 19 e.paaWtiearpaadgpaWha 38
                                      + +++W + a p ++ p W++
  gi|386002917|ref|YP_005921216.1| 19 GgSDGWILLADP-DGNPDWEV 38
                                      357888888888.88888875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.024
                              SPDY 20 paaWtiearpaadgpaWhatFta 42
                                      ++ W + + + ++ ++W+ tF++
  gi|386002917|ref|YP_005921216.1| 72 KDVWLVKTDR-EGARIWEKTFGK 93
                                      7889999999.9********985 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.85
                              SPDY  28 rpaadgpaWha 38 
                                       + ++ + +W+a
  gi|386002917|ref|YP_005921216.1| 143 GGPGEDGGWQA 153
                                       33455555554 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 3.5e-05
                              SPDY   5 glarlelrpededaepaaWtiearpaadgpaWhatFt 41 
                                       gl+ ++++ +++d  ++ W ++++  a++ +W+atF+
  gi|386002917|ref|YP_005921216.1| 159 GLVVVGYTRGAAD--QDVWLLSVSS-AGEKVWDATFG 192
                                       6778999999998..**********.**********8 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.021   1.9e+02     110     129 ..      72      91 ..      64      95 .. 0.83
   2 ?    0.3   0.0     0.053   4.7e+02     105     128 ..     118     141 ..     111     145 .. 0.85
   3 ?    6.5   0.0   0.00065       5.8     103     128 ..     165     190 ..     160     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.021
                     Pyrid_ox_like 110 pnltlikvtpeeaeyWdsks 129
                                        ++ l+k + e a++W+ + 
  gi|386002917|ref|YP_005921216.1|  72 KDVWLVKTDREGARIWEKTF 91 
                                       5799************9875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.053
                     Pyrid_ox_like 105 egkddpnltlikvtpeeaeyWdsk 128
                                       eg    +l l+k + +  ++W+ +
  gi|386002917|ref|YP_005921216.1| 118 EGSSGRDLLLLKTDLQGEKVWEET 141
                                       7888899**************986 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.00065
                     Pyrid_ox_like 103 fpegkddpnltlikvtpeeaeyWdsk 128
                                       +++g  d ++ l++v+    ++Wd++
  gi|386002917|ref|YP_005921216.1| 165 YTRGAADQDVWLLSVSSAGEKVWDAT 190
                                       789*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1651.37
//
Query:       gi|386002918|ref|YP_005921217.1|  [L=200]
Description: Putative methylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-09   37.4   0.0      4e-09   36.2   0.0    1.5  2  MTS              Methyltransferase small domain
      5e-06   27.1   0.0    1.5e-05   25.6   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    0.00012   22.0   0.0     0.0003   20.7   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
    0.00019   20.9   0.0    0.00028   20.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00045   20.8   0.0    0.00078   20.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    0.00058   20.5   0.0     0.0013   19.5   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
     0.0012   17.9   0.0     0.0016   17.6   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0087   15.9   0.0      0.016   15.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
       0.02   14.8   0.0       0.03   14.2   0.0    1.2  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.022   14.7   0.0      0.033   14.1   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.062   13.0   0.0      0.088   12.5   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.15   11.6   0.0        0.2   11.2   0.0    1.2  1  NodS             Nodulation protein S (NodS)
       0.23   10.5   0.0       0.28   10.2   0.0    1.1  1  DREV             DREV methyltransferase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   2.9e-12     4e-09      22     108 ..      28     106 ..      22     121 .. 0.84
   2 ?   -3.4   0.0       4.5   6.2e+03     112     133 ..     126     147 ..     123     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.9e-12
                                       HHHHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS- CS
                               MTS  22 lLletlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekk 97 
                                       lL+ +l++   +++vl +GcG G+++ al+ +  +  v+++dv+ +Al s + +       v++v  d+++ +  ++
  gi|386002918|ref|YP_005921217.1|  28 LLAAALEEVtPEDRVLEIGCGSGIISRALLPRARR--VVATDVNPAALGSLRGTG------VDAVRADLFSGIR-QR 95 
                                       44556776688999***************998877..9************99774......67899********.** PP

                                       EEEEEE---ST CS
                               MTS  98 fdlivsNPPfh 108
                                       fdli+ NPP+ 
  gi|386002918|ref|YP_005921217.1|  96 FDLILFNPPYL 106
                                       *********85 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.5
                                       HCHHHHHHHHHHHHHHHEEEEE CS
                               MTS 112 atelavaeeliaeAkeaLkegG 133
                                       +t  +++ ++++  k++L++ G
  gi|386002918|ref|YP_005921217.1| 126 ETGRETICRFLEGLKDHLEPAG 147
                                       5666778889999999999877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.1e-08   1.5e-05       1      41 [.      42      80 ..      42     124 .. 0.82
   2 ?   -2.7   0.0       7.1   9.8e+03       6      18 ..     158     170 ..     156     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-08
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41
                                      vL++GcG+G +++al+ r    +v+++D+++++l   r   
  gi|386002918|ref|YP_005921217.1| 42 VLEIGCGSGIISRALLPRA--RRVVATDVNPAALGSLRGTG 80
                                      9*****************6..9************9988765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
                                       -TTSHHHHHHHCT CS
                   Methyltransf_25   6 cGtGrltlalakr 18 
                                       cG+G++ +++ ++
  gi|386002918|ref|YP_005921217.1| 158 CGPGEVEAKARAE 170
                                       8888877766655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.2e-07    0.0003      16      62 ..      32      80 ..      16     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                   Methyltransf_23 16 llpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..k 62
                                      +l++  +  rvL+iGcG+Gi ++ l ++   v++ D +p+a + ++  +
  gi|386002918|ref|YP_005921217.1| 32 ALEEVTPEDRVLEIGCGSGIISRALLPRARRVVATDVNPAALGSLRgtG 80
                                      223346778****************99999*******999988776663 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     2e-07   0.00028     155     198 ..      33      74 ..      25      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                              PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvk 198
                                       le+ v ++++vl +G+GSGi++ a ++  a++vva+D+++ A+ 
  gi|386002918|ref|YP_005921217.1|  33 LEE-VTPEDRVLEIGCGSGIISRA-LLPRARRVVATDVNPAALG 74 
                                       444.578899**********9965.66789**********9975 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.7e-07   0.00078       1      39 [.      43      81 ..      43     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.7e-07
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekas 39
                                      L++GcG+G++++al  r++rvv++D+++++l   +  ++
  gi|386002918|ref|YP_005921217.1| 43 LEIGCGSGIISRALLPRARRVVATDVNPAALGSLRGTGV 81
                                      89***************************9976655444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.1e-07    0.0013       1      33 [.      43      73 ..      43     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-07
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsai 33
                                      LeiGcG+G ++rall++    +++++D++p+a+
  gi|386002918|ref|YP_005921217.1| 43 LEIGCGSGIISRALLPR--ARRVVATDVNPAAL 73
                                      8****************..*************9 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06    0.0016      27      58 ..      35      66 ..      25      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                      -GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE CS
                            RrnaAD 27 nleekltvleigpGkGilTeeLakrakqvvvl 58
                                      ++++++ vleig G Gi ++ L+ ra+ vv+ 
  gi|386002918|ref|YP_005921217.1| 35 EVTPEDRVLEIGCGSGIISRALLPRARRVVAT 66
                                      5779*************************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.016       4      81 ..      39     102 ..      37     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlil 79 
                                       + rvl++GCG+G ++ +l  +++   +vv  D ++ a+ + r        + v   ++d ++ +      ++fDlil
  gi|386002918|ref|YP_005921217.1|  39 EDRVLEIGCGSGIISRALLPRAR---RVVATDVNPAALGSLRG-------TGVDAVRADLFSgIR-----QRFDLIL 100
                                       569****************6654...4***********99998.......577788889999888.....7899998 PP

                   Methyltransf_31  80 sn 81 
                                        n
  gi|386002918|ref|YP_005921217.1| 101 FN 102
                                       87 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05      0.03      11      62 ..      36      90 ..      28      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                      HS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S........STTEE---SSS CS
                           UPF0146 11 enargkvvEvGiGrkldvaealakrgvdlvatDikek...kak.egvrivrDDvtd 62
                                      ++ + +v E+G G  + +++al  r+  +vatD+++      +  gv +vr D+++
  gi|386002918|ref|YP_005921217.1| 36 VTPEDRVLEIGCGSGI-ISRALLPRARRVVATDVNPAalgSLRgTGVDAVRADLFS 90
                                      44456********976.7888888889*********96654445789999999987 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05     0.033       5      54 ..      29      76 ..      24      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                   Methyltransf_18  5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegpleka 54
                                      L+a  + v++++rv+ iG+  g+++ +l+   +a++v+a+D+n+ +l + 
  gi|386002918|ref|YP_005921217.1| 29 LAAALEEVTPEDRVLEIGCGSGIISRALL--PRARRVVATDVNPAALGSL 76
                                      5667788999*******************..57889********998776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05     0.088      70      88 ..      35      53 ..      23      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                      T--TT-EEEEES-TTSHHH CS
                              PCMT 70 elkkgarvLevGsGsGylt 88
                                      e+++ +rvLe+G+GsG+ +
  gi|386002918|ref|YP_005921217.1| 35 EVTPEDRVLEIGCGSGIIS 53
                                      4899************864 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015       0.2      46      79 ..      41      74 ..      19     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                              NodS 46 dalevGcaaGalterlapyckrltvvdvveeaia 79
                                       +le+Gc +G ++  l p ++r+   dv + a+ 
  gi|386002918|ref|YP_005921217.1| 41 RVLEIGCGSGIISRALLPRARRVVATDVNPAALG 74
                                      59**************************999975 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002      0.28      81     135 ..      28      79 ..      18     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                              DREV  81 llaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                       lla+  e+ ++   + ++l++G G G i++ + p   +v at++       l+  
  gi|386002918|ref|YP_005921217.1|  28 LLAAALEEVTP---EDRVLEIGCGSGIISRALLPRARRVVATDVNPAALGSLRGT 79 
                                       44444444444...789*************************9987666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 1126.87
//
Query:       gi|386002919|ref|YP_005921218.1|  [L=112]
Description: hypothetical protein Mhar_2245 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 683.11
//
Query:       gi|386002920|ref|YP_005921219.1|  [L=78]
Description: hypothetical protein Mhar_2243, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-28   96.5   0.1      1e-27   96.4   0.1    1.0  1  DUF1699   Protein of unknown function (DUF1699)
     0.0045   17.2   0.0     0.0062   16.8   0.0    1.2  1  DUF4777   Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.1   1.1e-31     1e-27      56     130 .]       1      75 [.       1      75 [. 0.98

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 1.1e-31
                           DUF1699  56 lsksakmfleiqgiellegdvwghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       +s++ +mfle+qg+e++egdvwghrkdi+eyy+v+++v+eri++l+seg++ eeia ++s+e+klsp ++++++k
  gi|386002920|ref|YP_005921219.1|   1 MSHAGQMFLEMQGVEIVEGDVWGHRKDIDEYYTVDDKVMERITSLQSEGVNLEEIAGRVSRESKLSPAMVRYMIK 75 
                                       7999********************************************************************996 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.9e-07    0.0062       6      46 ..      35      76 ..      31      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.9e-07
                           DUF4777  6 galvlealkvl.nrPaTldEivervaerydlseeelkkvVkn 46
                                      +++v+e +++l  +++ l+Ei++rv++  +ls+ +++  +k+
  gi|386002920|ref|YP_005921219.1| 35 DDKVMERITSLqSEGVNLEEIAGRVSRESKLSPAMVRYMIKQ 76
                                      799********899**********************988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 592.34
//
Query:       gi|386002921|ref|YP_005921220.1|  [L=134]
Description: hypothetical protein Mhar_2244 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-53  179.7   0.1      2e-53  179.5   0.1    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.1   1.1e-57     2e-53       1     130 []       2     131 ..       2     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.1e-57
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       +kir+vssk+ei++l++ +++vHla+r+s+td+++l++ +p+l+a+qvp+Sy++++ ++a++fle+qg+e++egdvw
  gi|386002921|ref|YP_005921220.1|   2 IKIRIVSSKDEIKDLTRGDHTVHLAYRASSTDMFRLLQYSPRLRAVQVPPSYYRNMPTTARAFLETQGVEIIEGDVW 78 
                                       69*************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdi+ey+++++e+ieri++l+s+gl+ eei++++s e+klsp ++++++k
  gi|386002921|ref|YP_005921220.1|  79 GHRKDIDEYFVIDDEMIERITRLQSDGLKVEEISSRISWESKLSPAMVNYIIK 131
                                       ***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 850.75
//
Query:       gi|386002922|ref|YP_005921221.1|  [L=352]
Description: Nucleolar GTP-binding-1 domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-48  163.6   0.0    4.9e-48  163.1   0.0    1.2  1  NOG1_N     NOG1 N-terminal helical domain
    9.1e-23   79.8   0.0    1.7e-22   78.9   0.0    1.5  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    2.1e-18   66.5   0.0    3.9e-18   65.6   0.0    1.5  1  MMR_HSR1   50S ribosome-binding GTPase
    1.3e-12   47.6   0.0    1.9e-12   47.0   0.0    1.2  1  FeoB_N     Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.067   13.2   0.1          3    7.9   0.1    2.2  2  Dynamin_N  Dynamin family
      0.074   12.4   0.0         11    5.3   0.0    2.2  2  DnaB_C     DnaB-like helicase C terminal domain
       0.17   11.2   0.0       0.26   10.6   0.0    1.3  1  AIG1       AIG1 family


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.1   0.0   1.9e-51   4.9e-48       1     160 []      37     182 ..      37     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 1.9e-51
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrel 77 
                                       Fe++ptvpts+el+d+a+rr+kraa+ +kk++           ++++ta n+l+d+L+++v+k+P++++++pFy++l
  gi|386002922|ref|YP_005921221.1|  37 FERLPTVPTSQELVDRAFRRSKRAATGKKKDE-----------AMLMTAGNILADNLTNLVRKYPSFMNIPPFYHDL 102
                                       9**************************98873...........4689****************************** PP

                            NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       +d++v++de++++L++v+wa ++ir+i++++++++k a+dk     +rr+afgr+asv+k++d++l fL+d+r+kLr
  gi|386002922|ref|YP_005921221.1| 103 ADAAVGVDEMRVHLSRVSWAGSTIRSITRDHLTRMKGAQDKP---LVRRAAFGRMASVMKSIDPDLLFLNDARQKLR 176
                                       ****************************************88...9******************************* PP

                            NOG1_N 155 kLpaiD 160
                                        Lp++D
  gi|386002922|ref|YP_005921221.1| 177 VLPTVD 182
                                       *****9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   6.8e-26   1.7e-22       1      58 []     252     308 ..     252     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 6.8e-26
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       eIE+qA+aAL+hl++avlF+lDpse cg+sleeQl+Ll ++k+ ++  pv+vv+nK+D
  gi|386002922|ref|YP_005921221.1| 252 EIELQAVAALRHLRGAVLFILDPSEYCGFSLEEQLRLLADVKSWLS-LPVLVVANKVD 308
                                       6*********************************************.9*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   1.5e-21   3.9e-18       2     114 .]     188     306 ..     187     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.5e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS...HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie...gaseekglgkaflalee 75 
                                       ++++G+pNvGKS++i+a +g++ +++++p+tTr +  g+++ +++++++vDtpGl++   +a++e  + +a++al+ 
  gi|386002922|ref|YP_005921221.1| 188 IIVAGYPNVGKSSFISAVSGARPEIASYPFTTRGVGVGHFTRGHQRYQVVDTPGLLDrplSAKNEI-ELQAVAALRH 263
                                       899*************************************9777**********986554444444.4444444444 PP

                                       T.SEEEEEEETT.......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  76 a.dlillvvdas.......eeklkpldeeleelleeakkplilvlnk 114
                                          ++l+++d s       ee+l +l  +++++l     p+++v+nk
  gi|386002922|ref|YP_005921221.1| 264 LrGAVLFILDPSeycgfslEEQL-RLLADVKSWL---SLPVLVVANK 306
                                       3289******7777766643334.3447777777...5899999998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   7.3e-16   1.9e-12       2     131 ..     187     323 ..     186     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7.3e-16
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..C CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..e 76 
                                       t++++G pnvGk++++ a++ga+ +++ +p +t     g+++  ++++++vD PG  +  + s  +++  + ++  +
  gi|386002922|ref|YP_005921221.1| 187 TIIVAGYPNVGKSSFISAVSGARPEIASYPFTTRGVGVGHFTRGHQRYQVVDTPGLLDR-PLSAKNEIELQAVAalR 262
                                       6899**************************************999**********9874.44555555444444225 PP

                                       TSSSEEEEEEEGG.....GHHHHHHHHHHHHH.TTSSEEEEEETHHHHHHTTEEE-HHHHH CS
                            FeoB_N  77 eepdvvvnvvdat.....nlernLyLtlqlle.lgvpvvlalnmideaekkgieidlkkLs 131
                                       +   +v+ ++d +     +le +L L++++   l++pv+++ n++d a  +g e+ +++Ls
  gi|386002922|ref|YP_005921221.1| 263 HLRGAVLFILDPSeycgfSLEEQLRLLADVKSwLSLPVLVVANKVDLAGYQGAEMGMSTLS 323
                                       56789999**9762333369**********874789******************9999987 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0012         3       1      32 [.     188     219 ..     188     229 .. 0.78
   2 ?    3.5   0.0     0.026        67     101     119 ..     232     250 ..     224     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32 
                                       i+v G  + GKSS++ a+ g++    +   tT
  gi|386002922|ref|YP_005921221.1| 188 IIVAGYPNVGKSSFISAVSGARPEIASYPFTT 219
                                       7899999*************994444444444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                       -SEEEEE---B-SSSGTTS CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq 119
                                       +++ +vD+PGl +++   +
  gi|386002922|ref|YP_005921221.1| 232 QRYQVVDTPGLLDRPLSAK 250
                                       67789******98876666 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0043        11      77     163 ..      70     160 ..      42     166 .. 0.74
   2 ?    5.0   0.0     0.005        13      22      40 ..     188     206 ..     183     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0043
                                       HHHHHTTSXHHHHHHHHHHHHHHHHSEEEEEE..XSSXCHHHHHHHHHHHHHH.TTEEEEEEEEGGGTBTSCSSS.C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.x RF
                            DnaB_C  77 kklrtgklkeedweklteaieelseaklfidd..tpaltvseirskarrlkke.kglgliviDyLqlmegseeke.n 149
                                         +  g++  +++++l ++  ++ + + f +d   +a+ v e+r ++ r++ + ++++ i  D+L  m+g+++k   
  gi|386002922|ref|YP_005921221.1|  70 MLMTAGNILADNLTNLVRKYPSFMNIPPFYHDlaDAAVGVDEMRVHLSRVSWAgSTIRSITRDHLTRMKGAQDKPlV 146
                                       4456788888999999999999999998888833457899*********9988899*************87543346 PP

                                       CCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                            DnaB_C 150 reqevseisrsLka 163
                                       r+    +++  +k+
  gi|386002922|ref|YP_005921221.1| 147 RRAAFGRMASVMKS 160
                                       66666666666665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.005
                                       EEEEEXTTSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  22 iiiAarpsmGktalalnia 40 
                                       ii+A+ p +Gk+++   + 
  gi|386002922|ref|YP_005921221.1| 188 IIVAGYPNVGKSSFISAVS 206
                                       8*************87765 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0001      0.26       2      67 ..     187     250 ..     186     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEE.EETTEEEEEEE--SCCCTTCCHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksr.twdgkkinViDTPglfdlsvsad 67 
                                       ti++ G   +GkS+ + ++ g +    ++++ + t++   +   t+  ++ +V+DTPgl+d   sa+
  gi|386002922|ref|YP_005921221.1| 187 TIIVAGYPNVGKSSFISAVSGARP---EIASYPFTTRGVGVGHfTRGHQRYQVVDTPGLLDRPLSAK 250
                                       789999999999999999988765...33334555544444444899999**********9876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2212.93
//
Query:       gi|386002923|ref|YP_005921222.1|  [L=91]
Description: putative RNA-binding protein involved in rRNA processing [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-15   55.0   0.2      9e-15   54.8   0.2    1.0  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.2     5e-19     9e-15      21     101 ..       2      81 ..       1      84 [. 0.91

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 5e-19
                                       EEEEEEEEEETTEEEEEE---S--B-..-BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTS CS
                              Gar1  21 leiGtvssivenevviksttsgekkv..ldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgd 95 
                                       + +Gt ++ v++++++++ +sgekk   +++ns++ +++k +iG+V++ifGp   py++Vk+   +++   +++ g+
  gi|386002923|ref|YP_005921222.1|   2 KRLGTTHHSVQKKLIVRVEASGEKKEelPKINSVVVDQKKFKIGRVFDIFGPTDRPYVVVKPY--KNVDP-EVHLGK 75 
                                       579**************99998866555***********************************..99998.9999** PP

                                       EEEEE- CS
                              Gar1  96 kvyiap 101
                                       k+y+  
  gi|386002923|ref|YP_005921222.1|  76 KLYFEE 81 
                                       ***875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 510.92
//
Query:       gi|386002924|ref|YP_005921223.1|  [L=337]
Description: Transcription initiation factor IIB [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-43  147.0   3.3    4.6e-22   77.9   1.0    2.3  2  TFIIB            Transcription factor TFIIB repeat
      3e-18   65.0   0.8      3e-18   65.0   0.8    1.8  2  TF_Zn_Ribbon     TFIIB zinc-binding
    7.5e-05   22.2   0.5      0.053   13.0   0.2    3.4  2  Sigma70_r4       Sigma-70, region 4
     0.0035   17.7   0.4      0.092   13.1   0.2    2.5  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0059   16.4   1.9       0.06   13.2   0.1    3.2  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.2   0.0        9.4    6.3   0.0    2.5  2  Cyclin_C         Cyclin, C-terminal domain
      0.017   15.0   0.3      0.055   13.4   0.3    1.9  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.02   14.8   1.0       0.38   10.6   1.2    2.4  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.028   14.5   0.3        3.9    7.6   0.0    3.9  4  HTH_3            Helix-turn-helix
      0.037   14.0   2.4         10    6.1   0.0    3.6  3  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.037   13.8   0.0       0.95    9.2   0.0    2.3  2  Cyclin_N         Cyclin, N-terminal domain
      0.039   14.3   4.5        5.6    7.4   0.1    3.9  3  HTH_31           Helix-turn-helix domain
      0.041   12.4   0.2      0.061   11.9   0.2    1.2  1  Terminase_GpA    Phage terminase large subunit (GpA)
      0.047   13.7   0.0       0.11   12.5   0.0    1.6  1  RB_B             Retinoblastoma-associated protein B domain
      0.049   14.2   0.2        4.1    8.0   0.1    2.5  2  RPA_interact_C   Replication protein A interacting C-terminal
      0.054   13.2   0.2      0.054   13.2   0.2    1.9  1  Ribosomal_S27e   Ribosomal protein S27
      0.057   12.9   0.5          3    7.4   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain
       0.11   12.3   1.1       0.68    9.7   1.1    2.2  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.13   12.4   0.5         26    5.0   0.1    2.7  2  SR1P             SR1 protein
       0.18   12.1   0.5       0.49   10.7   0.2    1.8  2  IBR              IBR domain, a half RING-finger domain
       0.18   11.6   0.9        5.3    6.9   0.1    2.7  2  zinc_ribbon_2    zinc-ribbon domain
       0.36   10.7   2.4        3.5    7.6   0.2    2.6  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.38   10.8   3.4        1.6    8.8   3.4    2.1  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
          1    9.5   5.5        7.7    6.7   2.7    3.1  3  Zn-ribbon_8      Zinc ribbon domain
        2.6    7.7   4.9         16    5.2   0.1    2.7  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        3.6    7.5   7.5       0.91    9.4   0.1    3.5  3  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   1.0   6.6e-25   4.6e-22       2      71 .]     157     226 ..     156     226 .. 0.98
   2 !   69.4   0.0   2.9e-22     2e-19       1      71 []     250     320 ..     250     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 6.6e-25
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+a+al+L+  V++ A  ++++a++++++ Grs +g+aAA+ly Acr+++v rt+ ei++v++Vs k+i
  gi|386002924|ref|YP_005921223.1| 157 DRMASALGLSRNVRETAAVIYRKAVDKNLIRGRSIEGVAAAALYAACRQCNVPRTLDEIAEVSRVSRKEI 226
                                       69*****************************************************************997 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 2.9e-22
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i+rf++ l L+ +V+ +  e++++a+e+++++Gr p+g+aAA++yiA+ +++ +rtq+e+++v+ V+e+ti
  gi|386002924|ref|YP_005921223.1| 250 IPRFCSGLSLKGEVQAKGIEILRQAAEKELTSGRGPTGVAAAAIYIASILCGDRRTQREVADVAGVTEVTI 320
                                       89*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.8   4.4e-21     3e-18       3      43 .]      41      81 ..      39      81 .. 0.97
   2 ?   -3.2   0.1       8.9   6.2e+03       3      10 ..     203     210 ..     202     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 4.4e-21
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      CP+Cgs  lv D+er+elvC+dCGlV+++n id gpewr+f
  gi|386002924|ref|YP_005921223.1| 41 CPECGSHALVHDYERAELVCSDCGLVIDENFIDQGPEWRAF 81
                                      ******99*******************************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.9
                                       ETTTTCEE CS
                      TF_Zn_Ribbon   3 CPnCgstn 10 
                                       C  C+ ++
  gi|386002924|ref|YP_005921223.1| 203 CRQCNVPR 210
                                       99999876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.02        14      20      35 ..     209     224 ..     202     231 .. 0.86
   2 !   13.0   0.2   7.7e-05     0.053      18      43 ..     301     326 ..     293     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                                       T--HHHHHHHHTS-HH CS
                        Sigma70_r4  20 glTleEIgerlgiSre 35 
                                       ++Tl EI+e+  +Sr 
  gi|386002924|ref|YP_005921223.1| 209 PRTLDEIAEVSRVSRK 224
                                       79*********99996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.7e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekr 43 
                                       g+ +T+ E++++ g+++ ++r + k+
  gi|386002924|ref|YP_005921223.1| 301 GDRRTQREVADVAGVTEVTIRNRYKE 326
                                       5679*******************987 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   0.00013     0.092       5      37 ..      40      67 ..      36      89 .. 0.78
   2 ?    1.9   0.0      0.42   2.9e+02      27      36 ..     193     208 ..     164     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga.s 37
                                       CP Cg+ a ++  +r          C dCg   
  gi|386002924|ref|YP_005921223.1| 40 ECPECGSHALVHDYERAE------LVCSDCGLvI 67
                                      7**********9998885......89*****942 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.42
                   Lar_restr_allev  27 q......cvyCadCga 36 
                                              + +C +C++
  gi|386002924|ref|YP_005921223.1| 193 GvaaaalYAACRQCNV 208
                                       144455599******9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   1.2e+03      23      31 ..     159     167 ..     156     169 .. 0.85
   2 ?   -0.0   0.0       1.2     8e+02      15      36 ..     207     228 ..     205     231 .. 0.73
   3 !   13.2   0.1   8.7e-05      0.06      17      41 ..     303     327 ..     301     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                     HTH_AsnC-type  23 LAervGlSe 31 
                                       +A ++GlS+
  gi|386002924|ref|YP_005921223.1| 159 MASALGLSR 167
                                       799*****8 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.2
                     HTH_AsnC-type  15 daRisyaeLAervGlSestvlr 36 
                                       +  ++  e+Ae   +S+ ++ r
  gi|386002924|ref|YP_005921223.1| 207 NVPRTLDEIAEVSRVSRKEIGR 228
                                       5667888999988888887766 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 8.7e-05
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                       R++ +e+A+  G++e t+++R++ L
  gi|386002924|ref|YP_005921223.1| 303 RRTQREVADVAGVTEVTIRNRYKEL 327
                                       99********************988 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.017        12      47      83 ..     194     230 ..     190     238 .. 0.88
   2 ?    6.3   0.0     0.014       9.4      47      88 ..     288     329 ..     283     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcv 83 
                                       +Aaaal++a+++ n p   +++ +++++s +++   +
  gi|386002924|ref|YP_005921223.1| 194 VAAAALYAACRQCNVPRTLDEIAEVSRVSRKEIGRTY 230
                                       7***************999999999999988886655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                       +Aaaa+++a+   ++   ++++  + g+++  +++ ++ ++e
  gi|386002924|ref|YP_005921223.1| 288 VAAAAIYIASILCGDRRTQREVADVAGVTEVTIRNRYKELAE 329
                                       8***********9**********************9999987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.9e-05     0.055      22      57 ..      31      68 ..      13      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                    OrfB_Zn_ribbon 22 vnpay.TSktCseCgsknke.alsgrtfkCpnCgfead 57
                                      v+++     +C+eCgs     + ++ +++C++Cg+++d
  gi|386002924|ref|YP_005921223.1| 31 VDEFEkFIVECPECGSHALVhDYERAELVCSDCGLVID 68
                                      5555545579*****98777699***********9987 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   0.00056      0.38      57     115 ..       8      64 ..       1      66 [. 0.79
   2 ?    1.3   0.0      0.44     3e+02      53      98 ..     163     211 ..     151     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                       EEESETTEEEESSSSSCCHHHHHHHHHHHHHTSTSSSTSTCEEECC.SSSCEEEEESSST CS
                      eIF-5_eIF-2B  57 gsidengrlilngkfeakkleklldkyieeyVlCkeCkspetelek.eerllvlkCkaCg 115
                                        +i+ +++  ++ k++ ++ ++++d++ +  V C+eC+s+    +   er   l C+ Cg
  gi|386002924|ref|YP_005921223.1|   8 REIERSEKEKIQEKIKLRREKEKVDEFEKFIVECPECGSHAL--VHdYERAE-LVCSDCG 64 
                                       567777788899999999999******9999*******9865..45145555.89****9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.44
                                       HTSEEEESETTEEEESSSSSCCHHHH.HHHHHH..HHHTSTSSSTSTCE CS
                      eIF-5_eIF-2B  53 lgtqgsidengrlilngkfeakklek.lldkyi..eeyVlCkeCkspet 98 
                                       lg + ++ e+  +i++++++++ ++   ++       y  C++C+ p t
  gi|386002924|ref|YP_005921223.1| 163 LGLSRNVRETAAVIYRKAVDKNLIRGrSIEGVAaaALYAACRQCNVPRT 211
                                       6666666666666666666666665413443321135899999999887 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.1   2.1e+03      39      51 ..     154     166 ..     150     168 .. 0.76
   2 ?    0.4   0.0         1   7.2e+02      11      27 ..     211     227 ..     202     228 .. 0.85
   3 ?    7.6   0.0    0.0056       3.9      11      27 ..     305     321 ..     303     323 .. 0.92
   4 ?   -0.1   0.0       1.4   9.7e+02      13      21 ..     325     333 ..     323     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHTSE CS
                             HTH_3  39 etlkklakaLgvs 51 
                                       + l ++a aLg+s
  gi|386002924|ref|YP_005921223.1| 154 SELDRMASALGLS 166
                                       5678888888876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                                       HHHHHHHHHTSSHHHHH CS
                             HTH_3  11 sqeeLAeklGvsrstis 27 
                                       ++ e+Ae++ vsr  i 
  gi|386002924|ref|YP_005921223.1| 211 TLDEIAEVSRVSRKEIG 227
                                       67899999999998876 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHTSSHHHHH CS
                             HTH_3  11 sqeeLAeklGvsrstis 27 
                                       +q+e+A+++Gv+  ti+
  gi|386002924|ref|YP_005921223.1| 305 TQREVADVAGVTEVTIR 321
                                       9*************997 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.4
                                       HHHHHHHTS CS
                             HTH_3  13 eeLAeklGv 21 
                                       +eLAe+lG+
  gi|386002924|ref|YP_005921223.1| 325 KELAEELGI 333
                                       89****997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3      0.21   1.5e+02      26      58 ..     158     192 ..     127     202 .. 0.69
   2 ?    3.2   0.0      0.13        88      12      42 ..     203     230 ..     194     239 .. 0.78
   3 ?    6.1   0.0     0.015        10      23      48 ..     305     330 ..     295     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                                       HHHHHTTSSH...HHHHHHHHHHHHTTSEEETEEEE CS
                         HTH_Crp_2  26 elAsmlGltr...etvsrilseLkreglisrgrrir 58 
                                        +As lGl+r   et   i ++  +++li+ +  i+
  gi|386002924|ref|YP_005921223.1| 158 RMASALGLSRnvrETAAVIYRKAVDKNLIRGRS-IE 192
                                       599999998533388888888888888888654.65 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       CTTTCEEEEEHHHHHHHHHTTSSHHHHHHHH CS
                         HTH_Crp_2  12 eraggeielpltqeelAsmlGltretvsril 42 
                                       +r   ++++p t +e+A+   ++r  + r+ 
  gi|386002924|ref|YP_005921223.1| 203 CR---QCNVPRTLDEIAEVSRVSRKEIGRTY 230
                                       33...4789999************9998875 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.015
                                       HHHHHHHHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkre 48 
                                       tq+e A+  G+t +t+    +eL +e
  gi|386002924|ref|YP_005921223.1| 305 TQREVADVAGVTEVTIRNRYKELAEE 330
                                       99*************99999998876 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0014      0.95      38     112 ..     156     227 ..     122     242 .. 0.81
   2 ?    2.0   0.0      0.24   1.6e+02      34      85 ..     246     297 ..     234     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                       HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHH CS
                          Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeil 112
                                       l ++a+ + l++++  +a++++ + + k+ ++ + ++ v+a++L+ A++  ++ p +l++++ ++   ++++ei 
  gi|386002924|ref|YP_005921223.1| 156 LDRMASALGLSRNVRETAAVIYRKAVDKNLIRGRSIEGVAAAALYAACRQCNV-PRTLDEIAEVS--RVSRKEIG 227
                                       5567788889999999*********************************9888.88888888774..35566655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHH CS
                          Cyclin_N  34 lidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAa 85 
                                        id++ + ++ ++l+ e+ +  +++l +  +k+ ++ +    v+a+++++A+
  gi|386002924|ref|YP_005921223.1| 246 PIDYIPRFCSGLSLKGEVQAKGIEILRQAAEKELTSGRGPTGVAAAAIYIAS 297
                                       589999999999999999999999999999999999999999*********8 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.063        44      44      62 ..     153     171 ..     131     173 .. 0.83
   2 ?    1.5   0.1      0.54   3.7e+02      16      33 ..     211     228 ..     187     231 .. 0.81
   3 ?    7.4   0.1    0.0082       5.6      10      32 ..     272     321 ..     269     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.063
                            HTH_31  44 pavlealaralgldpaera 62 
                                       ++ l+++a algl+++ r+
  gi|386002924|ref|YP_005921223.1| 153 LSELDRMASALGLSRNVRE 171
                                       5799**********99887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.54
                            HTH_31  16 sqeevAerlgvsestlsr 33 
                                       +++e Ae ++vs+  ++r
  gi|386002924|ref|YP_005921223.1| 211 TLDEIAEVSRVSRKEIGR 228
                                       778899999999888877 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0082
                            HTH_31  10 Rera...........................GLsqeevAerlgvsestls 32 
                                       R++a                           + +q+evA+ +gv+e t++
  gi|386002924|ref|YP_005921223.1| 272 RQAAekeltsgrgptgvaaaaiyiasilcgdRRTQREVADVAGVTEVTIR 321
                                       555555566666666666666777777777788************99986 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.9e-05     0.061     188     240 ..      27      70 ..      17     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.9e-05
                     Terminase_GpA 188 lyeesdqr.ryyvpCphCgelqelsferlkwpegeaeekaryvCphcgslieeh 240
                                       + e+ d+  ++ v+Cp+Cg++  +           + e a++vC++cg +i+e+
  gi|386002924|ref|YP_005921223.1|  27 EKEKVDEFeKFIVECPECGSHALVH----------DYERAELVCSDCGLVIDEN 70 
                                       5566666559**********99988..........4578************997 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.11      10      96 ..     149     233 ..     141     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a + l ++ + L ls+++re +  + ++++  +++l++ R ++ +  +a+Y+ ++ ++  +++ ei +  r + 
  gi|386002924|ref|YP_005921223.1| 149 LAFALSELDRMASALGLSRNVRETAAVIYRKAV--DKNLIRGRSIEGVAAAALYAACRQCNVPRTLDEIAEVSRVSR 223
                                       6678889999999******99999988888776..568*********************************999999 PP

                              RB_B  87 qasskvyrsv 96 
                                       ++  ++yr v
  gi|386002924|ref|YP_005921223.1| 224 KEIGRTYRFV 233
                                       9999988877 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0059       4.1       2      27 ..      41      69 ..      40     104 .. 0.81
   2 ?    3.4   0.0      0.16   1.1e+02      65      78 ..     195     208 ..     164     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0059
                    RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                      CP C ++ l ++     ++C+ Cgl ++ 
  gi|386002924|ref|YP_005921223.1| 41 CPECGSHALVHDYerAELVCSdCGLVIDE 69
                                      ********998553477***99***9987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                    RPA_interact_C  65 gveaLlaeCeeCdf 78 
                                         +aL+a C++C++
  gi|386002924|ref|YP_005921223.1| 195 AAAALYAACRQCNV 208
                                       5789********86 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   7.8e-05     0.054       8      36 ..      39      67 ..      35      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                      EE-TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e  8 vkCpdCenetvvFshaatvvkCisCgkvL 36
                                      v Cp+C+    v +       C  Cg v+
  gi|386002924|ref|YP_005921223.1| 39 VECPECGSHALVHDYERAELVCSDCGLVI 67
                                      99************************876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0043         3       3      11 ..      39      47 ..      38      50 .. 0.85
   2 ?    3.0   0.0      0.11        73      18      26 .]      59      67 ..      55      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0043
                       zf-ribbon_3  3 vrCPnCGap 11
                                      v+CP+CG++
  gi|386002924|ref|YP_005921223.1| 39 VECPECGSH 47
                                      68*****85 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                       zf-ribbon_3 18 vCpyCGtkl 26
                                      vC  CG ++
  gi|386002924|ref|YP_005921223.1| 59 VCSDCGLVI 67
                                      799999876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1   0.00099      0.68       4      30 ..      39      66 ..      36      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00099
                     A2L_zn_ribbon  4 kvCsvCggngiln.seqgylvCieCgas 30
                                      ++C  Cg+  ++   e+++lvC +Cg++
  gi|386002924|ref|YP_005921223.1| 39 VECPECGSHALVHdYERAELVCSDCGLV 66
                                      679999999999999***********86 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.038        26       5      14 ..      59      68 ..      58      71 .. 0.92
   2 ?    4.5   0.0     0.054        37      22      32 ..     197     207 ..     190     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                              SR1P  5 vCqtCnatId 14
                                      vC++C+ +Id
  gi|386002924|ref|YP_005921223.1| 59 VCSDCGLVID 68
                                      9********9 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.054
                              SR1P  22 ttLYgtCnqce 32 
                                       + LY+ C qc+
  gi|386002924|ref|YP_005921223.1| 197 AALYAACRQCN 207
                                       579****9775 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2    0.0007      0.49       4      45 ..      23      64 ..      20      67 .. 0.75
   2 ?   -2.3   0.0         8   5.5e+03      40      45 ..     202     207 ..     184     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0007
                               IBR  4 eklklkksles.dpnlkwCprpdCeaiiekseg.cksvtCskCg 45
                                      + +++k+++++ ++ ++ Cp  +C++ +   +   +++ Cs+Cg
  gi|386002924|ref|YP_005921223.1| 23 KLRREKEKVDEfEKFIVECP--ECGSHALVHDYeRAELVCSDCG 64
                                      556777789998999*****..99965555554467789****8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8
                               IBR  40 tCskCg 45 
                                        C++C+
  gi|386002924|ref|YP_005921223.1| 202 ACRQCN 207
                                       355554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0077       5.3       8      21 ..      30      46 ..      29      48 .. 0.78
   2 ?    2.2   0.1      0.24   1.6e+02       2      12 ..      60      70 ..      59      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0077
                     zinc_ribbon_2  8 elqdnakF...CpyCGt 21
                                      ++++ +kF   Cp+CG+
  gi|386002924|ref|YP_005921223.1| 30 KVDEFEKFiveCPECGS 46
                                      66777888888999997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.24
                     zinc_ribbon_2  2 CpnCGaelqdn 12
                                      C+ CG  +++n
  gi|386002924|ref|YP_005921223.1| 60 CSDCGLVIDEN 70
                                      99999777766 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2     0.005       3.5       4      28 ..      41      64 ..      37      66 .. 0.76
   2 ?    2.1   0.2      0.26   1.8e+02      23      28 ..     202     207 ..     195     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.005
                                      ESTTTSBEEEEECSCCCEEEESSSS CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCg 28
                                      Cp+Cg++ l+ + +    + C+ Cg
  gi|386002924|ref|YP_005921223.1| 41 CPECGSHALVHDYERAE-LVCSDCG 64
                                      *******9976544443.4499997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                                       EESSSS CS
                    RNA_POL_M_15KD  23 eCrqCg 28 
                                       +CrqC 
  gi|386002924|ref|YP_005921223.1| 202 ACRQCN 207
                                       8***95 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.4    0.0024       1.6       1      20 [.      40      60 ..      40      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                    DNA_ligase_ZBD  1 hCPvCGsavv.ReegeaiyRC 20
                                      +CP+CGs++  +  + a + C
  gi|386002924|ref|YP_005921223.1| 40 ECPECGSHALvHDYERAELVC 60
                                      5******98656666666666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.7     0.011       7.7      28      35 ..      39      48 ..      26      67 .. 0.61
   2 ?    2.0   0.1      0.34   2.3e+02       5      14 ..      57      66 ..      50      77 .. 0.69
   3 ?   -0.9   0.0       2.8   1.9e+03      28      33 ..     201     207 ..     191     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                       Zn-ribbon_8 28 a.CPeCgs.e 35
                                      + CPeCgs +
  gi|386002924|ref|YP_005921223.1| 39 VeCPECGShA 48
                                      3366666633 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.34
                       Zn-ribbon_8  5 eYrCeeCghe 14
                                      e  C +Cg +
  gi|386002924|ref|YP_005921223.1| 57 ELVCSDCGLV 66
                                      3347777755 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.8
                       Zn-ribbon_8  28 a.CPeCg 33 
                                       a C +C+
  gi|386002924|ref|YP_005921223.1| 201 AaCRQCN 207
                                       4477774 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.024        16       4      16 ..      40      52 ..      39      55 .. 0.83
   2 ?    4.3   0.0     0.046        31       4      14 ..      59      69 ..      56      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                            zf_UBZ  4 lCerCgkeipese 16
                                       C++Cg++ ++++
  gi|386002924|ref|YP_005921223.1| 40 ECPECGSHALVHD 52
                                      6******988887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.046
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C++Cg  i e
  gi|386002924|ref|YP_005921223.1| 59 VCSDCGLVIDE 69
                                      8*****99987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.9       6.4   4.4e+03      30      40 ..     125     135 ..     124     142 .. 0.74
   2 ?   -0.0   0.1       1.2   8.3e+02      17      27 ..     220     230 ..     210     238 .. 0.53
   3 ?    9.4   0.1    0.0013      0.91      17      43 ..     303     329 ..     293     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.4
                            HTH_23  30 srrTvyrwlkr 40 
                                       +r ++yr +k+
  gi|386002924|ref|YP_005921223.1| 125 NRAQLYRLRKW 135
                                       57788888887 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.2
                            HTH_23  17 GlsvreIAreL 27 
                                       + s++eI r +
  gi|386002924|ref|YP_005921223.1| 220 RVSRKEIGRTY 230
                                       55555555555 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0013
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkryre 43 
                                       + ++re+A+  gv++ T+++  k  +e
  gi|386002924|ref|YP_005921223.1| 303 RRTQREVADVAGVTEVTIRNRYKELAE 329
                                       679****************55555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1379  (0.0769145); expected 358.6 (0.02)
Passed bias filter:                      926  (0.0516482); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 1794.86
//
Query:       gi|386002925|ref|YP_005921224.1|  [L=269]
Description: tRNA pseudouridine synthase A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-25   89.4   0.0    2.1e-20   73.2   0.0    2.1  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.3e-06     0.041       5      96 ..       9      92 ..       7     102 .. 0.81
   2 !   73.2   0.0   1.2e-24   2.1e-20       1     108 []     126     225 ..     126     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-06
                   PseudoU_synth_1  5 lvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkelln 83
                                      ++G+ + g f  q q++  tv+ +  +a++ +  +     + +++ +g++d++V a+++v+  + q  ++   v++++n
  gi|386002925|ref|YP_005921224.1|  9 YLGRGYHG-F--QLQPAAPTVQAVVGRALRSLGIN-----DGSFCYAGRTDRGVSALGQVIDFYVQPAKADLAVPRVVN 79
                                      78888888.8..88999999****99999977777.....89*******************555567777779****** PP

                   PseudoU_synth_1 84 akkrkkiavetap 96
                                      +++++++ +    
  gi|386002925|ref|YP_005921224.1| 80 SRLPTDVWAWAWA 92
                                      ***9994444444 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 1.2e-24
                   PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklsped 77 
                                       Aa el+G hdf+++  + ++ + ++r++++ +++    ee + +v++v+++gFl+++VR m  vl +vg g+++  +
  gi|386002925|ref|YP_005921224.1| 126 AAGELLGVHDFRNL--SSEKRGPSIRNLMKLDLT----EERGIVVIDVRADGFLWNMVRKMAKVLELVGSGDRDLAW 196
                                       7899********99..6667799***********....778899********************************* PP

                   PseudoU_synth_1  78 vkellnakkrkkiavetapavglvlfhvrYd 108
                                       v+ ll+ ++++   v  apa+glv ++v Y+
  gi|386002925|ref|YP_005921224.1| 197 VEALLDPRTNRG--VAPAPAEGLVMMDVGYP 225
                                       *********866..9***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1582.76
//
Query:       gi|386002926|ref|YP_005921225.1|  [L=388]
Description: 3-isopropylmalate dehydratase large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-90  303.6   1.4    5.8e-88  295.9   1.4    2.2  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
       0.12   11.1   0.0       0.17   10.6   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.9   1.4   6.4e-92   5.8e-88      22     461 .]       1     380 [.       1     380 [. 0.92

  Alignments for each domain:
  == domain 1  score: 295.9 bits;  conditional E-value: 6.4e-92
                         Aconitase  22 llqdvtgvqalvdl.aaa..reavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaak 95 
                                       +++d+tg+ a++++ + a    +v+++++ +   dh+vp+d     s             + +  +e+  +L+s+a+
  gi|386002926|ref|YP_005921225.1|   1 MVHDITGPLAVKGFyEIAgeDAHVWDPEKIVILFDHQVPAD-----SL------------A-A--AENHIMLRSFAA 57 
                                       68**********9964442244569****************.....33............1.2..245668999*** PP

                         Aconitase  96 afgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvklt 172
                                       + gi  +++ +G++Hqv++E+g +lpg ++vg+DSHT+ +g+lG++ +G+G++++++v+++ +l++ +p++++ + +
  gi|386002926|ref|YP_005921225.1|  58 SQGILNYDVFEGVCHQVMPEKGHVLPGDLIVGSDSHTCAYGALGAFSTGIGSTDMASVFATGKLWFMVPETLRLRAE 134
                                       ***************************************************************************** PP

                         Aconitase 173 GklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgr 249
                                       G+l+  vt+kD++l +ig ++++g++ ++ Ef+G++v+++s+ +r+T++NMa+E+G ++gl+ +de+tl Y++  +r
  gi|386002926|ref|YP_005921225.1| 135 GTLPRLVTSKDVILRMIGDIGADGATYQACEFAGSAVSRMSVPERMTMTNMAIEMGGKAGLVDPDETTLGYIR--ER 209
                                       *************************************************************************..66 PP

                         Aconitase 250 eeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekeaaekaley 326
                                         ++    ++d ++    l+ deda++++    ++s+l p+va p++++++vp  ++                    
  gi|386002926|ref|YP_005921225.1| 210 --VP----DFDGERV---LHGDEDASFTER-GWEVSDLPPQVAVPHNVDHVVPA-GDL------------------- 256
                                       ..33....4455444...7799*****975.78********************9.333................... PP

                         Aconitase 327 klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLeka 403
                                                 +k+d++++gSCTN++ ed+ +aa++++     g  v++gv+++v P+S+    ++ ++Gl e++++a
  gi|386002926|ref|YP_005921225.1| 257 --------AGTKIDQVFLGSCTNGRFEDLALAAEVMR-----GEPVARGVRMVVIPASRTEYMKALRAGLVEKFMEA 320
                                       ........245699***********************.....*********************************** PP

                         Aconitase 404 GfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                       G+ v ++ C++C+g   + l +gea++s+sNRNF+gRqg p++r yL+SP+ ++a A++G
  gi|386002926|ref|YP_005921225.1| 321 GAIVESPCCGPCMGgSFGLLGDGEASLSTSNRNFQGRQGsPKARVYLCSPATAAAGAITG 380
                                       **************8889999*****************8799999*************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   1.9e-05      0.17     289     357 ..     259     329 ..     247     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.9e-05
                            DUF521 289 ekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtC 357
                                       +k+d v+lG c    +e+l+  ae+++g+ ++ +v+++v+ +sr+ + +a r+glvek  +aG+ v s +C
  gi|386002926|ref|YP_005921225.1| 259 TKIDQVFLGsCTNGRFEDLALAAEVMRGEPVARGVRMVVIpASRTEYMKALRAGLVEKFMEAGAIVESPCC 329
                                       6788888885677789999999***********98877653889999****************96655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2387.31
//
Query:       gi|386002927|ref|YP_005921226.1|  [L=450]
Description: Pyridoxal-phosphate dependent TrpB-like enzyme [Methanosaeta harundinacea 6Ac]
Scores for complete 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-41  141.1   0.0    5.8e-41  140.8   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.0   3.2e-45   5.8e-41       4     294 .]      75     413 ..      72     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 3.2e-45
                                       CSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaall 77 
                                         +pTPl r++rl+++l++p  +++K+E+  p gS+K ++a+   +   k g   +  +e+++G++g al++a + +
  gi|386002927|ref|YP_005921226.1|  75 LWRPTPLFRAHRLEEHLKTPakIYYKYEGVSPAGSHKPNTAVAQAYFnMKAG-IERIATETGAGQWGSALSMATSFF 150
                                       579*******************************************955555.7777777888************** PP

                                       T-EEEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHH..STTCEE- CS
                              PALP  78 Glkvtivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaae..gegaylv 131
                                       Gl +++++ + +    p+++  ++ +Gae+v +                  gg+   a + a e aa   ++++ l 
  gi|386002927|ref|YP_005921226.1| 151 GLACRVYMVRASFdqkPYRKSIMQVWGAECVASpseltnagrmilkehpdtGGSLGIAISEAVEDAAThdNTNYALG 227
                                       *******9888777779****************55555555555555444444444444443333333323333333 PP

                                       -TTTSHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT-EEEEEEECTTCGGTTC CS
                              PALP 132 sqfdnptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke....rrpdvrvigvepegsdalars 201
                                       s     +v + ++  g+E++eql    + pd+++ +vGgG+++ G+++++      ++ ++r+++ ep+ +++l+++
  gi|386002927|ref|YP_005921226.1| 228 SVL--NHVLLHQTVEGQELKEQLAivdDYPDVIYGCVGGGSNFPGMCFPFVPdklkEKKEIRMVACEPAACPTLTKG 302
                                       333..4677779999***********9************************987755555***************** PP

                                       C...S..S.SS..B.................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHH CS
                              PALP 202 l...ragrrvtvpvs................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarre 259
                                       +   + g+  +                    +  a gl+ + +++l   l+++ v e+++  ++e+++a++++ar+e
  gi|386002927|ref|YP_005921226.1| 303 IytyDFGDTAK---LtpllkmytlghdfippSIHAGGLRYHGDAPLLCNLVHDGVIEAMSFHQNEVFQAAVTFARTE 376
                                       *5443333333...1556999*****777777777777777************************************ PP

                                       SB-B-HHHHHHHHHH..HHHHHHCCTTCEEEEEEE-B CS
                              PALP 260 givvepssaaalaal..klreagelkegdrvvviltg 294
                                       gi++ p s +a+  +  ++  +++ +e++++v+ l+g
  gi|386002927|ref|YP_005921226.1| 377 GILPAPESSHAIKPAidDAIACKKTGEEKTIVISLSG 413
                                       ******7777776666*****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2662.43
//
Query:       gi|386002928|ref|YP_005921227.1|  [L=378]
Description: ATP-NAD/AcoX kinase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-50  171.9   0.1      2e-50  171.6   0.1    1.0  1  NAD_kinase  ATP-NAD kinase
    1.5e-05   25.0   0.1      3e-05   24.0   0.1    1.5  1  DeoRC       DeoR C terminal sensor domain
    2.2e-05   24.0   1.2    6.8e-05   22.5   0.1    2.3  3  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
        0.1   12.8   2.7       0.11   12.7   0.0    2.5  3  TetR_C_16   Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.6   0.1   4.5e-54     2e-50       1     285 [.       3     356 ..       3     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 4.5e-54
                                       .EEEEESSC....................GGTCSHHHHHHHHHHHCT-....EEEEECCGGCCSSSTT--HHHHTTT CS
                        NAD_kinase   1 kvgivvnpi....................kkeaieraeevarwLldals..rvlevtveeklgeslaeaaefrsevi 55 
                                       kvg++vnp                     +++a+ +a ++a  +l+ l   ++l++t ++++ge+  ++a+ rs+v+
  gi|386002928|ref|YP_005921227.1|   3 KVGFLVNPVagmggavglkgtdglaeearARGAVPVAPQRAAAALAGLAdlDALFLTAAGEMGEESLRRAGLRSRVV 79 
                                       79**************************99999****99999999995569************************** PP

                                       T--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..EGGGHHHHHHH CS
                        NAD_kinase  56 svlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..epeaaaellek 130
                                         +  ++t +dtr a + f+++gvdli++ GGDGTa+dva ++   ++P++g++aGvk+++++f  +p+aa+ell+ 
  gi|386002928|ref|YP_005921227.1|  80 HRPSGPSTAEDTRVACRLFVEEGVDLIVFSGGDGTARDVAGVVGS-RVPIIGIPAGVKMHSGVFavSPRAAGELLRG 155
                                       ********************************************6.******************************* PP

                                       HHHT-SEEEEEEEEE.........................EEEEETTE................EEEEEEESSEEEE CS
                        NAD_kinase 131 llegeirvekrevld.........................avimrskgee..........diadiviensvlnevvi 172
                                       +l+g  r+ + e+ld                         + ++++k+ +          +ia +++e + +++  +
  gi|386002928|ref|YP_005921227.1| 156 YLAGVLRTRETEILDvdeekyragtldtqiygvasvpylpVLVQERKQIYsatdeeeikeEIAAFASEFM-RDGSAY 231
                                       ***************************************9666666665566666699999999998886.****** PP

                                       EESSSSS-EE..EEEEETTEEEEEEEESEE.......................EEE-TGGGGTHHHHTT--EE-TT- CS
                        NAD_kinase 173 irgpgstlie..lelyvdtelleadqldgl.......................ivstPtGstayslsaGgplisPgv 224
                                       i+g g+t ++    l+v+++ll++d+++++                       iv++P+G ++++l++G ++is++v
  gi|386002928|ref|YP_005921227.1| 232 ILGAGTTTAKiaELLGVEKTLLGVDVVQDGrticrdaseedllrtieaagrtkIVVSPIGAQGFVLGRGSQQISSRV 308
                                       **********86669***********99999********************************************** PP

                                       --EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESS CS
                        NAD_kinase 225 lailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdk 285
                                       l+         +  + +i+v+++ kl+     ++  ll+++G++el++  ++   v+ +++
  gi|386002928|ref|YP_005921227.1| 309 LR--------RVGPENLIIVATPHKLK-----ETPRLLVDTGDPELDAVVSGKRLVICGYR 356
                                       **........*****************.....***************99888887777775 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   6.7e-09     3e-05       3      61 ..     211     272 ..     209     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.7e-09
                             DeoRC   3 aeeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk...nltvvTnslnvaeeLseke 61 
                                        e K++IA+ A e+ +dg++ +l+aGtTt+ +a+ L  +k    + vv  + +++   se++
  gi|386002928|ref|YP_005921227.1| 211 EEIKEEIAAFASEFMRDGSAYILGAGTTTAKIAELLGVEKtllGVDVVQDGRTICRDASEED 272
                                       577*********************************99986666666666666666666555 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.82   3.7e+03       2      13 ..       4      15 ..       3      29 .. 0.81
   2 !   22.5   0.1   1.5e-08   6.8e-05      40      91 ..      87     134 ..      63     144 .. 0.84
   3 ?   -1.9   0.0      0.52   2.3e+03      26      56 ..     243     273 ..     233     281 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.82
                                      EEEEE-TTCTTT CS
                          DAGK_cat  2 llvivNpksGkg 13
                                      + ++vNp +G g
  gi|386002928|ref|YP_005921227.1|  4 VGFLVNPVAGMG 15
                                      66899***9965 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.5e-08
                                       STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-S CS
                          DAGK_cat  40 epgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlG 91 
                                        ++d +  ++   eegvdliv  GGDGt++ v++++      ++p+  iP+G
  gi|386002928|ref|YP_005921227.1|  87 TAEDTRVACRLFVEEGVDLIVFSGGDGTARDVAGVVGS----RVPIIGIPAG 134
                                       46677788999999*******************99988....7777778888 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.52
                                       HHHCTCEEEEEE--STTHHHHHHHHHHHCC- CS
                          DAGK_cat  26 leeagvelelieteepgdakelakeakeegv 56 
                                        e  gve +l  ++  +d+++++++a+ee+ 
  gi|386002928|ref|YP_005921227.1| 243 AELLGVEKTLLGVDVVQDGRTICRDASEEDL 273
                                       4455677778888888899999999999865 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3      0.81   3.6e+03      49      70 ..      27      48 ..      23      53 .. 0.69
   2 ?   -2.1   0.2         1   4.6e+03      23      51 ..      53      81 ..      40      98 .. 0.63
   3 ?   12.7   0.0   2.6e-05      0.11      31      81 ..     144     194 ..     133     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.81
                                      HHHCTTTS-STTHHHHHHHHHH CS
                         TetR_C_16 49 laplaarlggpdaelRaalvas 70
                                      +++ +ar   p a +Raa +++
  gi|386002928|ref|YP_005921227.1| 27 AEEARARGAVPVAPQRAAAALA 48
                                      5666777777888888876655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                                      HHHHHHH--------HHHHHHHHHHHHHH CS
                         TetR_C_16 23 llallrsalsseeaaellrefleeqvlap 51
                                      l al+ +a+++  ++ l r  l+ +v+ +
  gi|386002928|ref|YP_005921227.1| 53 LDALFLTAAGEMGEESLRRAGLRSRVVHR 81
                                      55666666666666666666666666655 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 2.6e-05
                                       -------HHHHHHHHHHHHHHCTTTS-STTHHHHHHHHHHHHHHHHHHHHT CS
                         TetR_C_16  31 lsseeaaellrefleeqvlaplaarlggpdaelRaalvasqllGlalaRyv 81 
                                       +s  +a ellr +l+ ++ ++ ++ l+ ++ + Ra+ + +q+ G+a + y+
  gi|386002928|ref|YP_005921227.1| 144 VSPRAAGELLRGYLAGVLRTRETEILDVDEEKYRAGTLDTQIYGVASVPYL 194
                                       4778899***************************************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2422.63
//
Query:       gi|386002929|ref|YP_005921228.1|  [L=234]
Description: V-type ATP synthase subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-53  180.0   7.0    5.7e-53  179.7   7.0    1.1  1  ATP-synt_D  ATP synthase subunit D


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.7   7.0   3.2e-57   5.7e-53       2     195 ..      14     205 ..      13     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 3.2e-57
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-.. CS
                        ATP-synt_D   2 LirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkla 78 
                                       Li+lk+r+k+a+ gh+lLk+Krd L++ef+e+l+++++ r+el e + +a++sl +a+a++g  +i+s++ + +k  
  gi|386002929|ref|YP_005921228.1|  14 LIALKRRIKVAKMGHNLLKMKRDGLMIEFFEVLNQARTIRQELVEDFIKAQQSLNMAKATEGALAIKSVAFALQK-- 88 
                                       89********************************************************************97766.. PP

                                       TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  79 kvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikkt 154
                                        +  v+l+++n++GV vp+++ ++  k+  ++ yg+++t+a +dea+ea+++l+++++ +a++et+l++L e i  t
  gi|386002929|ref|YP_005921228.1|  89 -EPAVQLESRNIMGVVVPKITADSVqKQMFERGYGIIGTSAAIDEAAEAYESLVDKIITAAEVETALIKLVEDIDAT 164
                                       .599****************7766553444567******************************************** PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 155 nrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                       +rRvNaLe +vIP +++t+k+I  +L+E++r + + lk++k
  gi|386002929|ref|YP_005921228.1| 165 KRRVNALEFKVIPDIKDTVKFIGFALEEMDRDNLVKLKMLK 205
                                       ***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1558.34
//
Query:       gi|386002930|ref|YP_005921229.1|  [L=460]
Description: V-type ATP synthase subunit B [Methanosaeta harundinacea 6Ac]
Scores for 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-60  203.5   0.0    4.2e-60  203.0   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    4.7e-10   39.8   2.1    4.7e-10   39.8   2.1    2.0  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
     0.0094   16.1   1.4      0.015   15.5   0.6    1.8  2  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.0   7.1e-64   4.2e-60       1     213 []     130     348 ..     130     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 7.1e-64
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D   ++v+Gq++ i++++g++++ ++ ++++q+++     + a++++++G  ++e+++++ +f+++++++r 
  gi|386002930|ref|YP_005921229.1| 130 GISTIDGTNTLVRGQKLPIFSGAGLPHNDVALQIARQAKALgeaeSfAVVFCAMGITNEEAQHFMADFERTGALERA 206
                                       899**********************************8655888768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v+++n +++p+++r++++++g+t+AEy++   +++vl+i++++++++eA+r+++++ +e+p+++gyp+y++++la  
  gi|386002930|ref|YP_005921229.1| 207 VVFLNLADDPAVERLLTPRLGLTTAEYLAFdLDMHVLVIYTDMTNYCEAMRQMGAAREEVPGRRGYPGYMYTDLAIQ 283
                                       ****************************9879********************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag ++ ++Gs+t++++++++g+D+++p+++   +it+g+++++++l++++++P+i++  S+S
  gi|386002930|ref|YP_005921229.1| 284 YERAGIITGKKGSITQFPILTMPGDDITHPIPDLSGYITEGQLIVSRELHRKGIYPPIDIRPSLS 348
                                       ***************************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   2.1   7.9e-14   4.7e-10       2      69 .]       9      73 ..       8      73 .. 0.95
   2 ?   -3.7   0.0         3   1.8e+04      53      64 ..     134     145 ..     130     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 7.9e-14
                                      EEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  2 vqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                       ++ Gp++ ve+ +   +g ++++e++ +e g+  +g++l  ++++V+v+v+++t Gl + ++Vk+TG
  gi|386002930|ref|YP_005921229.1|  9 NEIKGPLLFVEKTEP--IGFNELVEIR-TETGEMKRGQVLDTSNEVVVVQVFEGTGGLGKESTVKFTG 73
                                      689************..**********.55599**********************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                       SS-STTBBTTSE CS
                     ATP-synt_ab_N  53 mgstdGlsrGte 64 
                                       +++t  l+rG++
  gi|386002930|ref|YP_005921229.1| 134 IDGTNTLVRGQK 145
                                       688999999985 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   2.4e-06     0.015       2      88 ..       2      86 ..       1      90 [. 0.82
   2 ?   -3.8   0.0       2.4   1.5e+04       5      21 ..     129     145 ..     129     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                        HAS-barrel  2 Gevigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalat 79
                                       +++ + +   +++ +ve ++++++ e+Vei++++ge   G+v+d ++                       + +v++++
  gi|386002930|ref|YP_005921229.1|  2 TKEYKTINEiKGPLLFVEKTEPIGFNELVEIRTETGEMKRGQVLDTSN-----------------------EVVVVQVF 57
                                      56777777779999**********************************.......................99999999 PP

                        HAS-barrel 80 edt....................gvkvlG 88
                                      e+t                    + +++G
  gi|386002930|ref|YP_005921229.1| 58 EGTgglgkestvkftgdvikmplSPDIIG 86
                                      99999999995555555555555555555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.4
                        HAS-barrel   5 igestssslifrvegsk 21 
                                       +g st++++ + v+g+k
  gi|386002930|ref|YP_005921229.1| 129 TGISTIDGTNTLVRGQK 145
                                       68899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3063.22
//
Query:       gi|386002931|ref|YP_005921230.1|  [L=553]
Description: V-type ATP synthase subunit A [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-94  314.8   0.0    3.4e-94  314.4   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    5.5e-42  142.5   0.1    9.6e-42  141.7   0.1    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    3.5e-06   27.4   0.2    9.6e-06   26.0   0.2    1.8  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
     0.0012   18.8   0.1     0.0025   17.7   0.1    1.5  1  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.052   13.8   0.0    1.5  1  AAA_22           AAA domain
      0.029   14.2   2.1      0.029   14.2   0.4    1.9  2  Biotin_lipoyl    Biotin-requiring enzyme
      0.063   13.5   0.1       0.33   11.2   0.0    2.2  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.4   0.0   1.3e-97   3.4e-94       1     213 []     185     406 ..     185     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.4 bits;  conditional E-value: 1.3e-97
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+rv+D +f++++G++ +ipg+fg+Gktv++q+lsk+s+ d +++yvg+Gergne+a++l+efpe      ++ +m+
  gi|386002931|ref|YP_005921230.1| 185 GQRVIDGFFSLAKGGTAAIPGGFGTGKTVMQQTLSKWSDVD-IVVYVGCGERGNEMADLLHEFPElvdprtNRpLME 260
                                       9************************************9988.************************99975227*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       r+++ antsn+pvaareasiytgit+AEy+rd+g++v++ ads+srwaeA+re+s rl+emp+++gypaylga+la 
  gi|386002931|ref|YP_005921230.1| 261 RSIVYANTSNMPVAAREASIYTGITTAEYYRDMGYDVMMTADSTSRWAEAMRELSSRLEEMPGEEGYPAYLGARLAD 337
                                       ***************************************************************************** PP

                                       HHTTSEEE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yER+g++   + ++Gs++iv avsp+ggDf++pvt++tl+it++f+ Ld+kl+qr+hfP+in+l S+S
  gi|386002931|ref|YP_005921230.1| 338 FYERSGRVttlEGTEGSISIVGAVSPPGGDFTEPVTQNTLRITKVFWALDSKLTQRRHFPSINWLDSYS 406
                                       ********998888******************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   0.1   3.8e-45   9.6e-42       1     119 [.      61     174 ..      61     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 3.8e-45
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvke 77 
                                       yDGiqrpL ++ e+sg+fi+rG+ v+ +d++kkwef+p vk+gdkv++g+++Gtvqe+ li+hkimvpp+ +g+vke
  gi|386002931|ref|YP_005921230.1|  61 YDGIQRPLPQLVEASGNFISRGLFVDGIDHKKKWEFTPVVKKGDKVEPGQTIGTVQEQLLIKHKIMVPPGKRGTVKE 137
                                       9**************************************************************************** PP

                                       E--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESE CS
                   ATP-synt_ab_Xtn  78 iaeegeytvedtiaeveteegkekeltllqkwPvrkprpvke 119
                                       i+ +g++tve+ti+++e+++    el ++q+wPvr++rp + 
  gi|386002931|ref|YP_005921230.1| 138 IK-SGNFTVEETICVLEDGT----ELPMIQYWPVRRARPSRI 174
                                       *9.**************776....8*************9875 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   3.8e-09   9.6e-06      22      69 .]       2      45 ..       1      45 [. 0.91

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.8e-09
                                      TEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N 22 ynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      y+++ v+  e  ++l+ +++++ +dk +++v+++t G+++G++Vk TG
  gi|386002931|ref|YP_005921230.1|  2 YDLVLVG--E--EGLMSEIIGIAGDKHVIQVYEDTAGVKPGEPVKETG 45
                                      6666677..6..9**********************************8 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   9.9e-07    0.0025      43      86 ..      97     144 ..      90     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.9e-07
                            RnfC_N  43 kplvkvgdkVlkGqkiaeaeg..fvsapvhas..vsGtVkaiekrlva 86 
                                       +p+vk+gdkV+ Gq i++ ++  +++ ++  +    GtVk+i++ + +
  gi|386002931|ref|YP_005921230.1|  97 TPVVKKGDKVEPGQTIGTVQEqlLIKHKIMVPpgKRGTVKEIKSGNFT 144
                                       79***************9987678888888873357999999876655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     2e-05     0.052       6      70 ..     199     256 ..     196     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka 70 
                                       g  ++ G  GtGKT+  ++l ++ d         + vv+v + + + + +dll+e+ + ++ ++++
  gi|386002931|ref|YP_005921230.1| 199 GTAAIPGGFGTGKTVMQQTLSKWSD--------VDIVVYVGCGERGnEMADLLHEFPELVDPRTNR 256
                                       6678999*****************7........88899*******999*********999976665 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.8   7.1e+03      20      29 ..      34      43 ..      19      44 .. 0.72
   2 ?   14.2   0.4   1.1e-05     0.029      18      59 ..      97     141 ..      88     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.8
                                      SSSTTCEE-T CS
                     Biotin_lipoyl 20 lvkvGdkVka 29
                                       vk+G+ Vk+
  gi|386002931|ref|YP_005921230.1| 34 GVKPGEPVKE 43
                                      4788888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       SESSSTTCEE-TTSEEEEEECT...TEEEEEEBSSSEEEEEESST CS
                     Biotin_lipoyl  18 evlvkvGdkVkagqvlaeveam...KmemeieapkaGvvkeilvk 59 
                                       +  vk+GdkV+ gq++ +v+     K ++ ++  k+G+vkei+  
  gi|386002931|ref|YP_005921230.1|  97 TPVVKKGDKVEPGQTIGTVQEQlliKHKIMVPPGKRGTVKEIKSG 141
                                       568****************985555*****************865 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   4.5e+03      34      65 ..      14      43 ..       5      48 .. 0.71
   2 ?   11.2   0.0   0.00013      0.33      57      74 ..     100     117 ..      84     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                      EEEEEEEECTCEEEEEEEESEESS-TTEEE-T CS
                     Peptidase_M23 34 GnvviidhgdgystlyahlskisvkegqkVka 65
                                       +++ i  +++++++y       vk+g+ Vk+
  gi|386002931|ref|YP_005921230.1| 14 SEIIGIAGDKHVIQVYEDTAG--VKPGEPVKE 43
                                      667777777778888877666..888888874 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                       S-TTEEE-TTCEEEEEBS CS
                     Peptidase_M23  57 vkegqkVkaGqvIGtvgs 74 
                                       vk+g+kV+ Gq+IGtv +
  gi|386002931|ref|YP_005921230.1| 100 VKKGDKVEPGQTIGTVQE 117
                                       9**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3506.45
//
Query:       gi|386002932|ref|YP_005921231.1|  [L=99]
Description: V-type ATP synthase subunit F [Methanosaeta harundinacea 6Ac]
Scores for 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-16   58.3   0.5    8.1e-16   58.1   0.5    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.5   4.5e-20   8.1e-16       1      88 [.       3      90 ..       3      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.5e-20
                                      EEEEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSC CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPske 77
                                      iavIG+ d v+gf laGv++ + +t++ee+ ++++++++++++gi+++++  +++++++++ +  e ++P+++ I +++
  gi|386002932|ref|YP_005921231.1|  3 IAVIGSGDAVIGFTLAGVRKAYeATTQEELISKIETVMADPEVGIVVLSQGDFNNLPSRLRGTLTEsVKPTVIAIGTEQ 81
                                      8******************9997899*******************************9999877777********7666 PP

                                      CGGSHHCHHHH CS
                        ATP-synt_F 78 gpydeekdsvr 88
                                      ++    +++++
  gi|386002932|ref|YP_005921231.1| 82 STE--MREKIK 90
                                      633..355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 627.08
//
Query:       gi|386002933|ref|YP_005921232.1|  [L=342]
Description: V-type ATP synthase subunit C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-70  238.8   0.2    1.3e-70  238.6   0.2    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.6   0.2     7e-75   1.3e-70       1     335 [.      13     338 ..      13     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 238.6 bits;  conditional E-value: 7e-75
                                       HHHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H CS
                    vATP-synt_AC39   1 leArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapg 77 
                                       +++rvram+++l+++e y+++l + +++++ ryL+et Y++++   + ++++ + +e a  ++la++++kl++ + +
  gi|386002933|ref|YP_005921232.1|  13 ITGRVRAMKTKLIPHEMYQRMLGM-DIPEITRYLEETQYKEEIDLMAKDHSGAELVEFATFANLAKTYRKLLDVSID 88 
                                       579******************655.*****************8888888************************9999 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHH CS
                    vATP-synt_AC39  78 psrefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakylee 154
                                       +++ ++  +l+r+di+N+k++lrgk+ g ++ ee+ ++l+p+gel+++ l+ l++++ vee+++a+ gt y+++l+ 
  gi|386002933|ref|YP_005921232.1|  89 EPQFLILEYLRRWDIWNIKTILRGKFYG-ASEEEITKYLVPAGELDMEFLEGLVKKERVEEVISAFDGTDYYEALAH 164
                                       977999*********************5.777****************************************88887 PP

                                       HHCC...--SHHHHHHHHHHHHHHHHHHH.HHTSS..-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T... CS
                    vATP-synt_AC39 155 aldeleetgdleiienaLdkayledllkf.ckklg..getaeilreilgfeiDlrniniilrskkygelskedrkkl 228
                                           ++  + l+ +enaLdk y+ ++ ++   +l+  g     l ++++ eiD++n+ +++r+ k+g    + +++ 
  gi|386002933|ref|YP_005921232.1| 165 ----YDG-QMLSSVENALDKLYYFRMERAvGGTLSvgGGL---LLKYVRKEIDVKNLVTLFRMNKAG-IEASVIQDN 232
                                       ....565.789******************64444443667...**********************88.445558888 PP

                                       --SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHH CS
                    vATP-synt_AC39 229 lipggslypeglealaeaedveellaalkyteygelleealeeagslksledaldealvkllkk.afrqqfsvgvfy 304
                                       lipgg+l++ +l+++a + ++ e+++ l+ +++++ ++++++e+gs + +e +l+++lv+++   + ++++s+ +++
  gi|386002933|ref|YP_005921232.1| 233 LIPGGKLHE-ELSRMAGQ-SYNEFVRGLEGYPFWSAISDVAAEGGSVSRIEARLRAYLVRYAWAiSNYHPLSILPVL 307
                                       ********6.56668888.9********999999999999888888******************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 305 aYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       +Y+  k +E+ n+r I++g+++glp+e I+e
  gi|386002933|ref|YP_005921232.1| 308 GYIVSKDTEVSNIRKIVRGKEAGLPAELIEE 338
                                       *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2006.38
//
Query:       gi|386002934|ref|YP_005921233.1|  [L=182]
Description: V-type ATP synthase subunit E [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-16   59.7  14.3      5e-14   52.2  14.3    2.0  1  vATP-synt_E   ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
       0.02   14.8   0.3      0.055   13.3   0.0    1.8  1  DUF4897       Domain of unknown function (DUF4897)
      0.036   13.7   2.1      0.045   13.4   2.1    1.1  1  DUF885        Bacterial protein of unknown function (DUF885)
      0.043   13.8   1.3       0.76    9.8   0.1    2.4  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.25   12.4   2.6       0.23   12.5   0.6    1.8  2  PSK           Phytosulfokine precursor protein (PSK)


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2  14.3   1.4e-17     5e-14       2     199 .]      10     181 ..       9     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.4e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   2 IrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevf 78 
                                       I    + k+ eI+a++e+e++ +++++ +++ e + e+  ++   +e+  ++ +S+a ++ +++ L++r++++ee +
  gi|386002934|ref|YP_005921233.1|  10 ILATSKSKVAEINAETEQEVARILNEARARAAEIKSEKEGEADSAVEALERRVLSSAHLQVKRAELNVRKDLMEETR 86 
                                       6677899********************************************************************** PP

                                       HHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESS CS
                       vATP-synt_E  79 eeaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeed 155
                                       +++ + +++++ ++       ++Li++ + + +   + v++ k+D+  v+++    a +           +ag+   
  gi|386002934|ref|YP_005921233.1|  87 SKLVEAVSKLPAKE------NENLIKEIVKSYNLKGMKVKSSKKDETFVSSL----APN-----------FAGT--- 139
                                       **************......899****************************5....333...........3344... PP

                                       EBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 156 fledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                          d++GGvv+e++dg ++ + T e + + ++ + ++ ++k LF
  gi|386002934|ref|YP_005921233.1| 140 --VDTVGGVVIESEDGSMSYDHTYETLASEAFSKSMKDVSKILF 181
                                       ..488**************************************9 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.055      19      58 ..     139     178 ..     127     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                           DUF4897  19 vlttkaelkfkdekkeeeyieqYqkaseetfekylsqlse 58 
                                       +++t+ ++  ++e+   +y ++Y+  ++e+f+k+++++s+
  gi|386002934|ref|YP_005921233.1| 139 TVDTVGGVVIESEDGSMSYDHTYETLASEAFSKSMKDVSK 178
                                       789999*********************************8 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.1   1.3e-05     0.045     224     304 ..      13     100 ..       8     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                       SSSS-HHHHHHHHHHHHHHHHHHHHHHHHHH.HH-..HHHHHHHHHC....H-GGGEEE.SHHHHHHHHHHHHHHHH CS
                            DUF885 224 ttdltpeeihelglaelariraemeaiakev.gfk.gdlaevlaalr....tdprfyle.etdagreellaaaraai 293
                                       t++  ++ei +  ++e+ari +e +a a+e+  +k g+ + +++al+        ++++  + ++r++l+++ r ++
  gi|386002934|ref|YP_005921233.1|  13 TSKSKVAEINAETEQEVARILNEARARAAEIkSEKeGEADSAVEALErrvlSSAHLQVKrAELNVRKDLMEETRSKL 89 
                                       5677899************************6664589999999999888844444444034466789999999988 PP

                                       HHHCCHHHCCT CS
                            DUF885 294 aeldaklpehf 304
                                        e+  klp++ 
  gi|386002934|ref|YP_005921233.1|  90 VEAVSKLPAKE 100
                                       88888888655 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00021      0.76      14      51 ..      23      60 ..       7      71 .. 0.82
   2 ?    2.7   0.1     0.035   1.2e+02      14      36 ..      99     121 ..      87     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                      MMR_HSR1_Xtn 14 kldeetvkkilkeykihnaevliredvtvDdlidvieg 51
                                        +e++v +il+e +   ae++ +++ ++D  ++++e 
  gi|386002934|ref|YP_005921233.1| 23 AETEQEVARILNEARARAAEIKSEKEGEADSAVEALER 60
                                      33569*************************99999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.035
                      MMR_HSR1_Xtn  14 kldeetvkkilkeykihnaevli 36 
                                       k +e+ +k+i+k+y++   +v+ 
  gi|386002934|ref|YP_005921233.1|  99 KENENLIKEIVKSYNLKGMKVKS 121
                                       467899********998888765 PP

>> PSK  Phytosulfokine precursor protein (PSK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   6.3e-05      0.23      34      80 ..      19      68 ..       5      69 .. 0.53
   2 ?   -1.5   0.1       1.4   5.2e+03      20      23 ..     100     103 ..      75     131 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                               PSK 34 ataegeeaeelekelmgaeeee...aeeaCeegdeeeeClkRRtlveAHl 80
                                      a+++ e ++e+++ l +a   +   ++e+  e d   e l+RR+l  AHl
  gi|386002934|ref|YP_005921233.1| 19 AEINAETEQEVARILNEARARAaeiKSEKEGEADSAVEALERRVLSSAHL 68
                                      3333333333323233322222223333334667788************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                               PSK  20 qeee 23 
                                       ++e+
  gi|386002934|ref|YP_005921233.1| 100 ENEN 103
                                       2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1667  (0.0929779); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1286.38
//
Query:       gi|386002935|ref|YP_005921234.1|  [L=43]
Description: H+-transporting two-sector ATPase subunit C, partial [Methanosaeta harundinacea 6Ac]
Scores for complete 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   22.5   1.7    0.00012   22.4   1.7    1.1  1  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.7   6.5e-09   0.00012      27      60 .]       2      35 ..       1      35 [. 0.95

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.5e-09
                                      HHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C 27 ravarnpklftksliilafaeaialygLivalil 60
                                      + va+ p   +k l ++ ++e++ ++gL v+lil
  gi|386002935|ref|YP_005921234.1|  2 GVVAEEPGFLGKGLFLMLLPETLIIFGLAVSLIL 35
                                      7899****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:01.65
# Mc/sec: 78.79
//
Query:       gi|386002936|ref|YP_005921235.1|  [L=643]
Description: V-type ATP synthase subunit I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-27   96.4   0.6    1.3e-14   53.2   0.0    2.9  2  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.062   13.4   0.0       0.19   11.8   0.0    1.8  1  UPF0242     Uncharacterised protein family (UPF0242) N-termin


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.5e-18   1.3e-14     264     556 ..     184     485 ..     161     496 .. 0.75
   2 !   38.9   1.3   3.1e-14   2.7e-10     717     811 ..     535     634 ..     531     635 .. 0.65

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.5e-18
                        V_ATPase_I 264 qteealkevleeiakeleewklkvkkekaiyht..LnlfnldvtkkvliaegWvpkeeleeiqkalkeateess... 335
                                         e  l++ l++i  + e++ l +    +i ++     +++ +t++ ++ +gWvp+++ e+++  ++++   +    
  gi|386002936|ref|YP_005921235.1| 184 GEEAPLQKKLNDIRAQHEDLILAIDEHLSIKAQkaESPLRFASTDNAFVIDGWVPTDQFEALKGEIESVAGGRVqve 260
                                       5555566666666666666666666666554331034467889999*********************9885554333 PP

                        V_ATPase_I 336 .ssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfal 411
                                         ++++  + +e  e+ PT  +   + + f  i   ++i++Y+E  p+++  + FP +F++  GD++ Gl+++++  
  gi|386002936|ref|YP_005921235.1| 261 rLDASEADKLVEAGEDIPTKLNNPGVVKPFELITRLFAIPEYKEYDPTPLIFVFFPLMFGLILGDVAYGLIVFIV-- 335
                                       32222223333334789*******************************************************985.. PP

                        V_ATPase_I 412 llvlkekklkkkkkdeilemlfsgRYiillmGlfsiYtGliYNdifskslnlfgSswevkeka.........veeee 479
                                        +++  +k+++      ++ l++   i+++ ++++i  G+++ +if+ +l l+   ++  + +         +    
  gi|386002936|ref|YP_005921235.1| 336 -MMMLRRKFRTP----GWQSLIN---IVTISSIWAIIFGIVFGEIFG-PLGLWDYIFSGAHYTgllgtvadpH---- 399
                                       .55666777765....4666655...789999999999999999997.6666666666533335555543330.... PP

                        V_ATPase_I 480 lk..............kekkeekvYpfGlDpaWklaenellflnSlKmKlsvilGviqMlfgvllslvNalyfkkkl 542
                                        +                  e   ++ G+ p+ +la+ ++l+l    + +s  +G+++  +g +l + N l   +k 
  gi|386002936|ref|YP_005921235.1| 400 -HvgvdfgsgfygplgRIGPEIGSFAGGVFPMYRLATASVLVL----IGVSLFIGIVHTGIGSILGVKNELAYGEKR 471
                                       .134666677777776677778889999999999999999887....567999999999999999999999999999 PP

                        V_ATPase_I 543 diilefiPqllfll 556
                                       + ++e +P llf +
  gi|386002936|ref|YP_005921235.1| 472 HAYYERLPVLLFQV 485
                                       99999999988843 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 3.1e-14
                        V_ATPase_I 717 iSnTASYLRLWALSLAHaqLseVlwemvlkkal....lksksvlgvillvilfavfavltvavLllmeglsafLHaL 789
                                       +Sn  SYLRL A+ LA    +    +  +   +       +  +++i++v++++v ++   ++ ll+  ls f+H L
  gi|386002936|ref|YP_005921235.1| 535 VSNLISYLRLLAIGLASVGVAFAANQLGFYVLMpmlsGGAHDGFTTIAIVVGIVVLIM-VHFINLLLGILSPFMHPL 610
                                       9**************9765543332222222112211122233334545555555444.456777899********* PP

                        V_ATPase_I 790 RLhWVEfqsKFyk..gdGykFepf 811
                                       RLh VE+ +KFy+  g G++++pf
  gi|386002936|ref|YP_005921235.1| 611 RLHYVEMFTKFYSahGGGVEYSPF 634
                                       ************822567999999 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 ?   11.8   0.0   2.2e-05      0.19     104     150 ..     153     217 ..      54     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                           UPF0242 104 e..................ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                       +                  ++  e+ ++rl+ e++ Lq+kl++i ++ e+l l+++e+L  k ++
  gi|386002936|ref|YP_005921235.1| 153 HgfseisvprgmtgtiagaISTLESDSKRLEGEEAPLQKKLNDIRAQHEDLILAIDEHLSIKAQK 217
                                       455555555555666666689999***********************************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.53
# Mc/sec: 3625.94
//
Query:       gi|386002937|ref|YP_005921236.1|  [L=66]
Description: H(+)-transporting ATP synthase, subunit H [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.016   15.2   0.6      0.016   15.2   0.6    1.0  1  Phasin        Poly(hydroxyalcanoate) granule associated prote
      0.022   15.2   0.8      0.026   14.9   0.8    1.1  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit


Domain annotation for each model (and alignments):
>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.6   1.8e-06     0.016      28      81 ..       3      57 ..       1      65 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                            Phasin 28 kvqeeGsklfea.LvkeGeklekktkkvaeekleevresvkskveevkekaeeqw 81
                                       +++e++++fe+ L+++ + +++k+++ +++ +++v+   + ++++v++ +e+ +
  gi|386002937|ref|YP_005921236.1|  3 TAEAEAQQYFEKrLADAEKGVQSKKQAIIDDGMKKVNVMKSGASGKVNAAVEHLL 57
                                      5899******9648888888*****************888888888888777655 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.8   2.9e-06     0.026      43     101 ..       1      59 [.       1      62 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHH CS
                      V-ATPase_G_2  43 lreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqAvelilka 101
                                       +r Aea+a++  ++  +  ++ v+  ++ +   + ++++ ++  a+++++ Ave+ lk+
  gi|386002937|ref|YP_005921236.1|   1 MRTAEAEAQQYFEKRLADAEKGVQSKKQAIIDDGMKKVNVMKSGASGKVNAAVEHLLKE 59 
                                       57899999998888888888899999999999*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 428.34
//
Query:       gi|386002938|ref|YP_005921237.1|  [L=389]
Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-89  298.6   0.4      6e-89  298.2   0.4    1.2  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.2e-23   83.6   0.1    3.8e-23   81.9   0.0    1.9  2  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.2   0.4   6.7e-93     6e-89       1     299 []     110     387 ..     110     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 298.2 bits;  conditional E-value: 6.7e-93
                                       .HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHH CS
                     RuBisCO_large   1 giaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqd 77 
                                       gi+++r++l++ +rp++GtiiKPk+GLspk++a+v+ ++++gglD+iKdDE l++q f+++ +r+eav+  +++ +d
  gi|386002938|ref|YP_005921237.1| 110 GIKEARKILGVFDRPLVGTIIKPKVGLSPKDTAEVAGQAVRGGLDLIKDDETLTDQSFCPIDERVEAVMAELSKVED 186
                                       799************************************************************************** PP

                                       HHSS--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--S CS
                     RuBisCO_large  78 etGekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskh 154
                                       etG+k+ ya+n+t    ee+l+rae v+  g+++v+vdvl++Gf+a++ l++     ++ +H+Hr +hga+tr+++h
  gi|386002938|ref|YP_005921237.1| 187 ETGKKAFYAVNVTSG-AEEILERAEEVVGRGANMVMVDVLTTGFSAVEVLARG---VKVPIHVHRTMHGAFTRDRRH 259
                                       *************65.5**********************************99...6689***************** PP

                                       EE-HHHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS-- CS
                     RuBisCO_large 155 GisfrvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGih 231
                                       Gis+  +++l+R++G  +lhtg+  +gk+ gd++              e+d+++  ++++++++l++v+pvasgG+h
  gi|386002938|ref|YP_005921237.1| 260 GISMLPISRLVRMAGGTNLHTGSY-LGKMAGDRE--------------ENDSCR-DALREEWYGLRPVFPVASGGVH 320
                                       ************************.*********..............344444.57899***************** PP

                                       TTTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 232 agqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                        g +   l+  g+ d i+qaGGG++gHp g++aGa+a+ qa+ea+v+G+  eeyA++hkeL++Al+ w
  gi|386002938|ref|YP_005921237.1| 321 PGMVRPNLDGYGT-DCIIQAGGGVHGHPSGTTAGATAMVQAVEAWVAGVTTEEYARSHKELDAALKFW 387
                                       *************.****************************************************99 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   4.3e-27   3.8e-23      13     119 ..       2      99 ..       1     100 [. 0.94
   2 ?   -1.8   0.0      0.36   3.3e+03      20      40 ..     130     149 ..     125     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 4.3e-27
                   RuBisCO_large_N  13 dllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvkiAYplelFeegsi 89 
                                       +++a ++ve  +++ +e+aa+a+Aae Stgtwtev  ++   +++l a+v +      e++++++A+p elFe g+i
  gi|386002938|ref|YP_005921237.1|   2 EVIAKYYVE--TDLPIEKAAEAIAAEQSTGTWTEVERERL--ASDLAARVVRA-----EGNFAYVAFPEELFEAGNI 69 
                                       689999999..799*********************99988..99****99887.....579**************** PP

                   RuBisCO_large_N  90 pqllssiaGnifgmkavkalrleDirlPka 119
                                       pq ls +aGn fg++a+k++rl D+ +P++
  gi|386002938|ref|YP_005921237.1|  70 PQYLSVVAGNLFGLGALKKVRLLDVIFPQR 99 
                                       ****************************86 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.36
                   RuBisCO_large_N  20 vePaegvsveeaaaavAaeSS 40 
                                       ++P+ g+s++++a +vA+++ 
  gi|386002938|ref|YP_005921237.1| 130 IKPKVGLSPKDTA-EVAGQAV 149
                                       6677777777665.4555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2433.47
//
Query:       gi|386002939|ref|YP_005921238.1|  [L=370]
Description: fructose 1,6-bisphosphatase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-182  607.1   0.0   1.2e-182  607.0   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.0   0.0  6.8e-187  1.2e-182       1     360 [.       3     366 ..       3     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 607.0 bits;  conditional E-value: 6.8e-187
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       k+t+s+ikaDvG+++Gh++vh++l e++e+vl+++k kg +idf+v++vGDD++l+mth++gvdn e+h+law+++ 
  gi|386002939|ref|YP_005921238.1|   3 KITISLIKADVGGWPGHATVHPALKETAESVLSQEKAKGEIIDFKVMSVGDDLQLMMTHQRGVDNAEIHGLAWEVMC 79 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       +ate akelklygaGqDlL daf+Gn+kG+GPgvae+efeeR +epvv f++Dktepgafnlp+++ifadpfntaGl
  gi|386002939|ref|YP_005921238.1|  80 KATEKAKELKLYGAGQDLLCDAFCGNIKGMGPGVAEMEFEERAAEPVVAFMMDKTEPGAFNLPIFRIFADPFNTAGL 156
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvysk....kdeeiaavvsterlsliaGkY 227
                                       vidp++h+Gf fev+D++e+kk+++++pee+yd+lal+gak+ryvikrvy k     ++e+aavvste+l ++aG+Y
  gi|386002939|ref|YP_005921238.1| 157 VIDPSIHQGFVFEVWDIMEHKKVMMDSPEEMYDILALIGAKSRYVIKRVYPKagklPEDEPAAVVSTEKLYQTAGTY 233
                                       ****************************************************88877899***************** PP

                          FBPase_3 228 vGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvg 304
                                       vGkDDPva+vRaqsglPa+gevlepf+l hlv+GwmrGshngplmP++++da +trfdgpprv+a gfq+++g+l+g
  gi|386002939|ref|YP_005921238.1| 234 VGKDDPVALVRAQSGLPALGEVLEPFSLGHLVSGWMRGSHNGPLMPCAFEDAVCTRFDGPPRVIAAGFQIAKGMLIG 310
                                       ***************************************************************************** PP

                          FBPase_3 305 pvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                       pvDlf dpafd +R++++ei+d++Rr+Gpfephrlp+e++eYttlp+vl++l erf
  gi|386002939|ref|YP_005921238.1| 311 PVDLFRDPAFDLTRQRVHEITDYMRRHGPFEPHRLPMEDMEYTTLPHVLKNLGERF 366
                                       *******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2426.67
//
Query:       gi|386002940|ref|YP_005921239.1|  [L=121]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-10   39.7  21.0     0.0003   21.3   3.6    3.2  3  Fer4_7    4Fe-4S dicluster domain
    1.2e-09   37.6  29.4      3e-05   23.6   1.5    4.0  4  Fer4      4Fe-4S binding domain
    1.3e-09   38.9  19.7     0.0012   19.7   2.8    3.3  3  Fer4_16   4Fe-4S double cluster binding domain
    3.9e-08   33.3  35.0      3e-05   24.1   9.8    2.4  3  Fer4_9    4Fe-4S dicluster domain
    5.8e-08   32.8  12.5    1.6e-07   31.4  12.5    1.7  1  Fer4_11   4Fe-4S dicluster domain
    1.5e-07   31.2  30.0     0.0022   18.0   2.1    3.6  3  Fer4_6    4Fe-4S binding domain
    1.4e-05   24.9  29.2     0.0081   16.2   2.1    3.5  3  Fer4_2    4Fe-4S binding domain
     0.0001   22.6  25.9     0.0043   17.4   4.0    4.1  3  Fer4_4    4Fe-4S binding domain
    0.00012   22.7  33.6      0.054   14.5   7.2    3.9  3  Fer4_3    4Fe-4S binding domain
    0.00023   21.2  28.2     0.0022   18.1  17.0    2.6  3  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.1   2.7      0.014   16.1   2.7    3.4  3  Fer4_15   4Fe-4S single cluster domain
      0.056   14.0  22.7       0.58   10.7   3.0    3.3  5  Fer4_17   4Fe-4S dicluster domain
      0.061   13.8  23.5        1.2    9.6   4.3    3.2  3  Fer4_8    4Fe-4S dicluster domain
        1.8    8.8  23.7       0.55   10.4  14.4    2.6  3  Fer4_21   4Fe-4S dicluster domain
        5.6    7.2  18.2        5.2    7.3   3.9    2.2  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.7   0.00013      0.16      32      52 .]      30      52 ..       3      52 .. 0.76
   2 !   17.1   1.2   5.4e-06    0.0064       2      22 ..      68      88 ..      66      92 .. 0.87
   3 !   21.3   3.6   2.5e-07    0.0003       1      24 [.      93     116 ..      93     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                            Fer4_7 32 eidpekClgCga..CvavCPtga 52
                                      ++    C  C+   C+++CPtga
  gi|386002940|ref|YP_005921239.1| 30 DFAVVVCRACTDppCARACPTGA 52
                                      555667*****999*******98 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.4e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldee 22
                                      C gCgaC++aC  +ai+ d+e
  gi|386002940|ref|YP_005921239.1| 68 CQGCGACAEACLIRAISQDDE 88
                                      99*********9999998876 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.5e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeen 24 
                                       +C +CgaCva Cp++++e++e+e+
  gi|386002940|ref|YP_005921239.1|  93 CCKHCGACVAFCPHGVLEMEEVEE 116
                                       5******************99865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3       1.1   1.4e+03      11      15 ..      36      40 ..      34      41 .. 0.74
   2 !   11.9   0.5   0.00013      0.16      14      23 ..      44      53 ..      44      54 .. 0.94
   3 !   23.6   1.5   2.5e-08     3e-05       3      18 ..      63      78 ..      61      84 .. 0.89
   4 !   16.2   8.0   5.4e-06    0.0065       8      23 ..      94     109 ..      92     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                                      -THHH CS
                              Fer4 11 CGaCv 15
                                      C aC 
  gi|386002940|ref|YP_005921239.1| 36 CRACT 40
                                      99996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      C+ +CP+gA+
  gi|386002940|ref|YP_005921239.1| 44 CARACPTGAL 53
                                      *********8 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 2.5e-08
                                      EETTTSSS-THHHHHS CS
                              Fer4  3 ideekCigCGaCvevC 18
                                       + e+C gCGaC+e+C
  gi|386002940|ref|YP_005921239.1| 63 LNRELCQGCGACAEAC 78
                                      589************* PP

  == domain 4  score: 16.2 bits;  conditional E-value: 5.4e-06
                                       SSS-THHHHHSTTTEE CS
                              Fer4   8 CigCGaCvevCPvgAI 23 
                                       C +CGaCv  CP+g++
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPHGVL 109
                                       **************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.1   0.00011      0.13       2      20 ..      36      56 ..      35      64 .. 0.89
   2 !   16.7   1.4     9e-06     0.011       2      22 ..      68      88 ..      67      92 .. 0.88
   3 !   19.7   2.8     1e-06    0.0012       2      25 ..      94     117 ..      93     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                           Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                      C  C+   Ca +CPt+a+  +
  gi|386002940|ref|YP_005921239.1| 36 CRACTDppCARACPTGALVRR 56
                                      999**999*********9866 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekke 22
                                      C++Cg+Cae+C  +ai+++ e
  gi|386002940|ref|YP_005921239.1| 68 CQGCGACAEACLIRAISQDDE 88
                                      *****************9955 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 1e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekei 25 
                                       C+ Cg+C+  CP++++++++ +e+
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPHGVLEMEEVEEW 117
                                       *****************9976666 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.3   0.00055      0.66      33      50 ..      26      52 ..       3      53 .. 0.66
   2 !   24.1   9.8   2.5e-08     3e-05       2      47 ..      36      79 ..      35      83 .. 0.90
   3 !   21.4  17.3   1.8e-07   0.00021       2      50 ..      68     108 ..      67     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                            Fer4_9 33 e.......eaCigCga..CveaCpkga 50
                                                C  C +  C+ aCp+ga
  gi|386002940|ref|YP_005921239.1| 26 GlegdfavVVCRACTDppCARACPTGA 52
                                      144666666799999999*****9997 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.5e-08
                            Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47
                                      C  C+   C +aCp+g+ v++++++   +r+     C gCgaC+eaC 
  gi|386002940|ref|YP_005921239.1| 36 CRACTDppCARACPTGALVRREGGGVLLNRE----LCQGCGACAEACL 79
                                      999*9778********************986....6***********5 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 1.8e-07
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C gCgaC eaC   ++++d+ ++++         C +CgaCv+ Cp+g+
  gi|386002940|ref|YP_005921239.1|  68 CQGCGACAEACLIRAISQDDEGQTVC--------CKHCGACVAFCPHGV 108
                                       ***********************976........9***********985 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4  12.5   1.3e-10   1.6e-07       5      87 ..      31     101 ..      27     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.3e-10
                           Fer4_11   5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaG 81 
                                       f    Cr C++ppC++++p++a+v++e  G Vll+++ ++ ++ +++eac  +++ +++e + +  C+ c       
  gi|386002940|ref|YP_005921239.1|  31 FAVVVCRACTDPPCARACPTGALVRRE-GGGVLLNRELCQ-GCGACAEACLIRAISQDDEGQ-TVCCKHCG------ 98 
                                       66678********************99.999********8.*************99998866.34455443...... PP

                           Fer4_11  82 llpacv 87 
                                          acv
  gi|386002940|ref|YP_005921239.1|  99 ---ACV 101
                                       ...333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   5.1   0.00039      0.47       9      24 .]      36      53 ..      34      53 .. 0.90
   2 !   18.0   2.1   1.8e-06    0.0022       5      19 ..      64      78 ..      63      83 .. 0.92
   3 !   14.1   7.2   3.1e-05     0.038       9      24 .]      94     109 ..      91     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                            Fer4_6  9 CigCgd..CvrvCPegai 24
                                      C  C d  C+r+CP+ga+
  gi|386002940|ref|YP_005921239.1| 36 CRACTDppCARACPTGAL 53
                                      88898889********97 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.8e-06
                            Fer4_6  5 dpdkCigCgdCvrvC 19
                                      ++++C gCg+C+ +C
  gi|386002940|ref|YP_005921239.1| 64 NRELCQGCGACAEAC 78
                                      79************* PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.1e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C +Cg+Cv+ CP+g++
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPHGVL 109
                                       9************986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   5.8    0.0059         7      10      22 .]      36      50 ..      30      50 .. 0.89
   2 !   16.2   2.1   6.8e-06    0.0081       3      20 ..      61      78 ..      59      78 .. 0.92
   3 !   13.5   5.7   4.9e-05     0.058      10      22 .]      94     106 ..      85     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0059
                            Fer4_2 10 CigCg..aCvsaCPa 22
                                      C +C   +C  aCP+
  gi|386002940|ref|YP_005921239.1| 36 CRACTdpPCARACPT 50
                                      9999888*******7 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.8e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      v  +++ C gCgaC  aC
  gi|386002940|ref|YP_005921239.1| 61 VLLNRELCQGCGACAEAC 78
                                      5689************** PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.9e-05
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C +CgaCv  CP+
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPH 106
                                       9***********7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.9     0.077        92       7      17 .]      36      51 ..      35      51 .. 0.67
   2 !   11.0   3.4   0.00042       0.5       2      14 ..      66      78 ..      64      79 .. 0.92
   3 !   17.4   4.0   3.6e-06    0.0043       4      15 ..      94     105 ..      87     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.077
                            Fer4_4  7 Cgs.....CvaaCPqg 17
                                      C++     C +aCP+g
  gi|386002940|ref|YP_005921239.1| 36 CRActdppCARACPTG 51
                                      44433466999**986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00042
                            Fer4_4  2 erCigCgsCvaaC 14
                                      e C+gCg+C  aC
  gi|386002940|ref|YP_005921239.1| 66 ELCQGCGACAEAC 78
                                      67*********99 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.6e-06
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       C +Cg+Cva+CP
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCP 105
                                       99*********9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   4.8    0.0046       5.5       1      15 []      36      52 ..      36      52 .. 0.79
   2 !   12.0   5.1   0.00028      0.34       1      13 [.      68      80 ..      68      82 .. 0.88
   3 !   14.5   7.2   4.5e-05     0.054       1      14 [.      94     107 ..      94     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0046
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C  C   +C ++CP+gA
  gi|386002940|ref|YP_005921239.1| 36 CRACTdpPCARACPTGA 52
                                      55575668********9 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00028
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gCgaC e+C  
  gi|386002940|ref|YP_005921239.1| 68 CQGCGACAEACLI 80
                                      ***********65 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 4.5e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C +CgaCv  CP g
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPHG 107
                                       9***********88 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  14.1     4e-05     0.048       8      55 ..      35      78 ..      31      79 .. 0.85
   2 !   18.1  17.0   1.8e-06    0.0022       3      56 .]      62     105 ..      60     105 .. 0.80
   3 !   12.5   5.8    0.0001      0.12       7      21 ..      92     106 ..      86     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                           Fer4_10  8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                       C  C+   C +aCP+      +   + e++ v  + e C+gcgaC+eaC
  gi|386002940|ref|YP_005921239.1| 35 VCRACTdpPCARACPT------GALVRREGGGVLLNRELCQGCGACAEAC 78
                                      6999*9999*******......6666666666677799************ PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.8e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        ++++ C +Cg+C +aC           ++ +++ +++    C +cgaCv+ CP
  gi|386002940|ref|YP_005921239.1|  62 LLNRELCQGCGACAEAC----------LIRAISQDDEGQTVCCKHCGACVAFCP 105
                                       67899************..........455555555555666***********9 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0001
                           Fer4_10   7 dtCirCgkCvkaCPa 21 
                                        +C +Cg+Cv++CP 
  gi|386002940|ref|YP_005921239.1|  92 VCCKHCGACVAFCPH 106
                                       579999999999998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.9      0.17   2.1e+02      56      64 ..      45      53 ..      43      54 .. 0.88
   2 ?   16.1   2.7   1.2e-05     0.014       1      28 [.      61      89 ..      61      96 .. 0.79
   3 ?    4.1   2.8     0.066        78       8      20 ..      94     106 ..      90     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                           Fer4_15 56 araCPvdAI 64
                                      araCP++A+
  gi|386002940|ref|YP_005921239.1| 45 ARACPTGAL 53
                                      89****997 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                           Fer4_15  1 VvvDrdaCigcglCvaea.pevfeldedg 28
                                      V ++r++C+gcg+C++++  + + +d++g
  gi|386002940|ref|YP_005921239.1| 61 VLLNRELCQGCGACAEAClIRAISQDDEG 89
                                      7799*************965666666666 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.066
                           Fer4_15   8 CigcglCvaeape 20 
                                       C  cg+Cva +p 
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPH 106
                                       9**********86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.3     0.067        80       2      14 ..      36      50 ..       3      53 .. 0.71
   2 ?    5.1   1.6     0.028        33       2      17 ..      36      53 ..      35      67 .. 0.77
   3 ?    8.8   3.7    0.0019       2.3       2      20 ..      68      86 ..      67      93 .. 0.75
   4 ?   10.7   3.0   0.00048      0.58      46      60 ..      94     108 ..      83     109 .. 0.73
   5 ?    9.8   3.8   0.00093       1.1       2      59 ..      94     107 ..      93     117 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.067
                           Fer4_17  2 CiqCgy..ClpeCps 14
                                      C+ C    C+++Cp+
  gi|386002940|ref|YP_005921239.1| 36 CRACTDppCARACPT 50
                                      555555556666665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
                           Fer4_17  2 CiqCgy..ClpeCpsyea 17
                                      C+ C    C+++Cp+++ 
  gi|386002940|ref|YP_005921239.1| 36 CRACTDppCARACPTGAL 53
                                      888987789999998766 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0019
                           Fer4_17  2 CiqCgyClpeCpsyeaydn 20
                                      C++Cg+C+++C   ++ ++
  gi|386002940|ref|YP_005921239.1| 68 CQGCGACAEACLIRAISQD 86
                                      9999999999998776554 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00048
                           Fer4_17  46 CieCgeCerkCPqgl 60 
                                       C +Cg C++ CP+g+
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPHGV 108
                                       677777777777765 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00093
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       C +Cg+C++ Cp                                             g
  gi|386002940|ref|YP_005921239.1|  94 CKHCGACVAFCPH--------------------------------------------G 107
                                       5666666666654............................................4 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0051       6.1      33      64 ..      18      51 ..       2      52 .. 0.70
   2 ?    8.8   3.9    0.0019       2.2       5      15 ..      68      78 ..      64      92 .. 0.70
   3 ?    9.6   4.3     0.001       1.2      49      65 .]      92     108 ..      80     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0051
                            Fer4_8 33 aedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                      a +v ++ +le++ a+  C +c    C+++Cp+g
  gi|386002940|ref|YP_005921239.1| 18 AIKVKTQGGLEGDFAVVVCRACTDppCARACPTG 51
                                      333445555555888999****9999******87 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                            Fer4_8  5 CieCgaCqsaC 15
                                      C +CgaC +aC
  gi|386002940|ref|YP_005921239.1| 68 CQGCGACAEAC 78
                                      67777777777 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.001
                            Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                         C +cgaC+  Cp g+
  gi|386002940|ref|YP_005921239.1|  92 VCCKHCGACVAFCPHGV 108
                                       56999999*99999886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.0      0.14   1.7e+02      40      53 ..      35      50 ..      12      56 .. 0.68
   2 ?    5.7  11.3     0.014        16       8      55 ..      36      81 ..      33      85 .. 0.77
   3 ?   10.4  14.4   0.00046      0.55       3      59 .]      63     111 ..      61     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                           Fer4_21 40 eCvGCn..lCssvCPv 53
                                       C +C+   C+  CP+
  gi|386002940|ref|YP_005921239.1| 35 VCRACTdpPCARACPT 50
                                      4666653348888886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                           Fer4_21  8 CigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55
                                      C  C+   C+ aC++    a+   +   + +  + C GC  C++ C +  
  gi|386002940|ref|YP_005921239.1| 36 CRACTDppCARACPT---GALVRREGGGVLLNRELCQGCGACAEACLI-R 81
                                      666764449999994...677777777778899*************76.4 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00046
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       ++++ C gCg C+ aC    + ai+ d++ +    +  C  C  C++ CP ++++em
  gi|386002940|ref|YP_005921239.1|  63 LNRELCQGCGACAEACL---IRAISQDDEGQ----TVCCKHCGACVAFCP-HGVLEM 111
                                       57899************...89**9887665....346999*********.588877 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.5    0.0096        12      57      95 ..      32      78 ..       4      86 .. 0.70
   2 ?    7.3   3.9    0.0044       5.2      57      75 ..      90     108 ..      79     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0096
                           Fer4_18 57 gagdcidces..cvkvcPtgidirk...Glqle...ciscllcidac 95
                                      ++  c +c    c + cPtg  +r    G+ l+   c  c+ c +ac
  gi|386002940|ref|YP_005921239.1| 32 AVVVCRACTDppCARACPTGALVRReggGVLLNrelCQGCGACAEAC 78
                                      44557777634499******99985443555544569********** PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0044
                           Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                       ++  c +c++cv+ cP g+
  gi|386002940|ref|YP_005921239.1|  90 QTVCCKHCGACVAFCPHGV 108
                                       4455889*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 815.57
//
Query:       gi|386002941|ref|YP_005921240.1|  [L=577]
Description: Aldehyde ferredoxin oxidoreductase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-66  225.5   0.0    1.3e-66  225.2   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    4.3e-64  216.0   0.1    6.7e-64  215.4   0.1    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.2   0.0   1.4e-70   1.3e-66       6     366 ..     220     577 .]     215     577 .] 0.91

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 1.4e-70
                                       HHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE CS
                            AFOR_C   6 iqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevk 82 
                                       + k + +++  ++++++ GT+  +n++n+ + lpt+nfq+++fe+aekisge+l+++yl ++ +C+ Cpi C +  +
  gi|386002941|ref|YP_005921240.1| 220 LFKTVVQTD-AMEKYHDIGTPININVLNQLKGLPTRNFQDSSFEGAEKISGEVLADNYLFRRVSCAHCPIGCIHIGM 295
                                       556666677.4459************************************************99************* PP

                                       .......ET.....EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHT CS
                            AFOR_C  83 veegkk.vk.....vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtd 153
                                        +++ +  +        +++e l+alGsnlg+++ e +l+l e c++ GlD is+G ++a+a e+  +Gl++ ++t 
  gi|386002941|ref|YP_005921240.1| 296 LKTSFSrEHefeirKISYDFELLYALGSNLGVSSAEGVLELIEACERQGLDAISTGVVLAWATEALDRGLVTLQETL 372
                                       9988875559999866789********************************************************** PP

                                       S----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS CS
                            AFOR_C 154 glelefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGa 229
                                       g++l+++d    l+++e i + e+ + + lA+Gv  ++e++g+ e+am   + e+p y    a  ++l+  +     
  gi|386002941|ref|YP_005921240.1| 373 GVSLRWNDVPSYLKAIENIVRMENeFYAALAQGVVFASERYGGGEFAMALGKNEVPGYHTGPASVVGLTVGVRHS-- 447
                                       **********************************************************99987777777777777.. PP

                                       -SGGG-THHHH..S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHH CS
                            AFOR_C 230 cHlrayliale..ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeell 304
                                        Hl++  ++++    ++ l++e+ + +++   d + +++sl+ C+f++     +++e++ ++l + +Gi+ te+el 
  gi|386002941|ref|YP_005921240.1| 448 -HLDNAGYSIDqrALKKSLTPEEMVDAIIREDDSRGVYNSLVGCLFAR---GVYTPENILEALGS-VGIEKTEGELE 519
                                       .99966666665466777888***************************...689**********9.9********** PP

                                       HHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT- CS
                            AFOR_C 305 kaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGW 366
                                       + G+Ri+  +  f  reG++ ++ ++p+r++e     g  +     + +eem++ y ++rGW
  gi|386002941|ref|YP_005921240.1| 520 ELGRRIFDEKYRFKRREGFDLAEARIPRRFYETVSAVGMID----PETIEEMMRIYRKRRGW 577
                                       *******************************6655666666....4459************* PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.4   0.1   7.5e-68   6.7e-64       2     198 .]       4     202 ..       3     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 215.4 bits;  conditional E-value: 7.5e-68
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       ++l++dL +g+  vee + +l+e++lGg+g+a++lll+e ppg+dplspe p+vf++Gpl+   +p+ +++v+++ks
  gi|386002941|ref|YP_005921240.1|   4 RVLYIDLGRGESAVEERE-DLFEEWLGGTGVATQLLLEECPPGADPLSPEAPIVFSIGPLNAL-FPAITKTVAAFKS 78 
                                       89**************99.79*****************************************9.************* PP

                                       TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHH...HHTS.. CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealke...elgd.. 150
                                       Pl+g+lges+aGgr+g++l++aG +a+v++G+ae+pvy++ie+d+v+i+da+++wg  +  +   l++         
  gi|386002941|ref|YP_005921240.1|  79 PLSGELGESYAGGRLGMALRFAGHEAVVVRGAAERPVYISIENDEVKIKDATSIWGVPATVVGYILRDvetG--Vgr 153
                                       ********************************************************9998777778886332..266 PP

                                       .EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 151 .kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                        +++ iGp Ge+lvr+A ++vd++r++gr GlGav+gsK+lkaivv+gt
  gi|386002941|ref|YP_005921240.1| 154 rSIIRIGPGGERLVRYAGVVVDTYRHFGRLGLGAVFGSKKLKAIVVSGT 202
                                       7999******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3774.49
//
Query:       gi|386002942|ref|YP_005921241.1|  [L=311]
Description: Fructose-1-phosphate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-49  169.4   0.0    1.3e-49  169.1   0.0    1.0  1  PfkB          pfkB family carbohydrate kinase
    3.2e-07   30.0   0.0    4.4e-07   29.5   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
      0.008   15.7   0.0       0.01   15.3   0.0    1.1  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.0   2.2e-53   1.3e-49      20     297 ..      19     290 ..       5     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 2.2e-53
                                       SH.TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEE CS
                              PfkB  20 kl.egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglali 95 
                                       ++ e+ +++  + e ++GG+g+ v ++l  lg+  +++g++ +   G++l+++l  +g d++++ ++++trt++ + 
  gi|386002942|ref|YP_005921241.1|  19 EIkEDVSNRIIREESYPGGKGIDVSKVLTALGVPNRALGFIAGFA-GRQLEAQLTRDGTDCSFIPVSGETRTNVVIH 94 
                                       44344555999999*****************************99.******************************* PP

                                       EETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEEEEEECESSSHH CS
                              PfkB  96 vvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtfdpnlldplgaq 172
                                       ++ ++ +  ++   ++   ++  e  + + ++ee +++ i+g+l++    +v+++++e ak       ++ld   + 
  gi|386002942|ref|YP_005921241.1|  95 ELGSGRQIILNSAGPEVKPFELLEISDLVRKIEEPEFVSIGGSLPPRAHPEVYRKIIETAKLRR--AKVVLDVDRE- 168
                                       ***97555555555666666665555**************************************..9999999995. PP

                                       HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSS CS
                              PfkB 173 fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkv 249
                                           l  +  ++d++kpn +El+al+g+ le   e+l+a+ +++ +g+  v+v++G +G l+v++++ +++ + p+v
  gi|386002942|ref|YP_005921241.1| 169 --ALLVGIRGKPDVIKPNIHELSALVGKRLEKRGEILEAAREINRRGVGIVLVSMGPRGILLVSEGKAYQAVP-PEV 242
                                       ..4555556****************************************************************.*** PP

                                       S-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSST CS
                              PfkB 250 kvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaia 297
                                       +vv+t+GAGDs v+gf+++l++g +l+eal  a+a++ +++ ++g++ 
  gi|386002942|ref|YP_005921241.1| 243 EVVNTIGAGDSSVAGFIYGLVAGRDLKEALIWATAAGTATTLRQGTAL 290
                                       *********************************************986 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   7.3e-11   4.4e-07     119     226 ..     177     277 ..     157     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.3e-11
                                       G-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S- CS
                      Phos_pyr_kin 119 latvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietkn 195
                                       + +vi PN+ E++aL+g+++++  ++ eaa+++ + g+  Vl+  g     +     +l+++++ ++   + +e  n
  gi|386002942|ref|YP_005921241.1| 177 KPDVIKPNIHELSALVGKRLEKRGEILEAAREINRRGVGIVLVSMGP----RGI---LLVSEGKAYQAVPPEVEVVN 246
                                       5689***************************************9996....345...788***************** PP

                                       -BTHHHHHHHHHHHHHHCTSSHHHHHHHHHH CS
                      Phos_pyr_kin 196 thGtGCtlssaiaaelakgesleeAvkkAke 226
                                       t G+G++  +     l  g++l+eA+ +A++
  gi|386002942|ref|YP_005921241.1| 247 TIGAGDSSVAGFIYGLVAGRDLKEALIWATA 277
                                       *************************999875 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-06      0.01      85     217 ..     149     278 ..      94     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                                       HHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEE CS
                       Carb_kinase  85 klleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllk 161
                                       k++e +  +++ +v+D d  +ll        r ++ ++ P++ E + L++  ++k  + le+are+ ++  ++vl+ 
  gi|386002942|ref|YP_005921241.1| 149 KIIETAKLRRAKVVLDVDREALLVG-----IRGKPDVIKPNIHELSALVGKRLEKRGEILEAAREINRRGVGIVLVS 220
                                       4666666677777777765555544.....478899********************************999998876 PP

                                       .STTS.EEEECTTEEEEE----GGG-STTHHHH.HHHHHHHHHHCTSSHHHHHHHHHHH CS
                       Carb_kinase 162 .gekd.vivspegevlinstgssalakGGsGDv.LaGligalLaqneasyeaaiaaawl 217
                                        g    ++vs++++  +++ +     + G GD   aG i +l a     +ea i a+ +
  gi|386002942|ref|YP_005921241.1| 221 mGPRGiLLVSEGKAYQAVPPEVEVVNTIGAGDSsVAGFIYGLVAGRD-LKEALIWATAA 278
                                       254441457778899999**************648******998665.66666655433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1972.93
//
Query:       gi|386002943|ref|YP_005921242.1|  [L=304]
Description: putative fructose-1,6-bisphosphate aldolase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-49  167.2   0.0    5.2e-49  167.0   0.0    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   2.9e-53   5.2e-49       2     235 .]      35     272 ..      34     272 .. 0.99

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 2.9e-53
                                       EEEEECCSHHHHHHHHCTSS..HHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTST CS
                              DeoC   2 vilavDqrvankddtasaqn..eqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllksk 76 
                                       +++a Dq+v++ + ++s +   +   d+++l++ a ++ +++++ ++g+ia++ ++y  ++++lvkl+++t+l++  
  gi|386002943|ref|YP_005921242.1|  35 MLFAGDQKVEHLNRDFSGPGisPEDGDPEHLFRIADRGRIGVFAAQLGLIARYGMDYP-RVPYLVKLNSKTDLVQAD 110
                                       789**************999**************************************.****************** PP

                                       TEEEE.....TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTC CS
                              DeoC  77 qrdvd.....evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekv 148
                                       qrd++     ev +vee+ ++++ +v  v y+ ++gse+e+++l+e +++  ++h  gl+ +l++y+r+ a+ de+ 
  gi|386002943|ref|YP_005921242.1| 111 QRDPLsrqlvEVSQVEEFAKDSGLEVLGVGYTVYLGSEYEAEMLREASQIVLQAHRRGLVAVLWIYPRGRAVRDER- 186
                                       ****************************************************************************. PP

                                       HHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTH CS
                              DeoC 149 dpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeaga 223
                                       dp+l+a A+ v+a lG+D++Kv++p   + ++  ++ +fk++++aa   +vv++GG+  + + fl+ + d+++ +ga
  gi|386002943|ref|YP_005921242.1| 187 DPHLIAGATGVAAALGSDFVKVNYP---KREGASSELIFKEAVAAAGRTKVVCAGGAsrDPKSFLQELFDQIHVSGA 260
                                       *************************...88*****************999*******9999**************** PP

                                       CEEEESHHHHTT CS
                              DeoC 224 sGvlsGRaifqk 235
                                       +G+++GR+i+qk
  gi|386002943|ref|YP_005921242.1| 261 AGNATGRNIHQK 272
                                       **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1999.80
//
Query:       gi|386002944|ref|YP_005921243.1|  [L=449]
Description: Glucosamine-1-phosphate N-acetyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-21   75.9   0.0    5.1e-21   75.4   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    3.1e-17   63.4   1.4      5e-17   62.7   1.4    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
      1e-14   53.6  21.7      2e-08   33.6   4.7    4.8  5  Hexapep          Bacterial transferase hexapeptide (six repea
    1.9e-06   27.5   6.1    1.9e-06   27.5   6.1    4.5  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    0.00034   20.4   0.0    0.00052   19.8   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
        0.2   11.6   0.0        0.3   11.0   0.0    1.1  1  CTP_transf_3     Cytidylyltransferase


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 !   75.4   0.0   1.7e-24   5.1e-21       1     215 [.       2     201 ..       2     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 1.7e-24
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       ka+ILa G+G R++PLt +l+k ++p++gk +l++++l  + ++g e+ ++v+  ++ + ++  +++gs+++ve+++
  gi|386002944|ref|YP_005921243.1|   2 KAIILAAGEGRRMRPLTANLPKGMLPIGGK-PLLEHVLLMAKEAGAERFVFVVG-HQGEKIAGAFGDGSRLEVEIEY 76 
                                       79****************************.*****************888877.7888999*************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       a+++ g gt +A++ a+ l+ed++     lvL gD+l +    + v++ i+ +a   ++ + v+  ++ e G  e++
  gi|386002944|ref|YP_005921243.1|  77 AFQEGGAGTGPALLAAEALAEDRF-----LVLRGDVLPD---ADSVRRLIALEAP-AMAAARVEGPRPAEEGTLEVS 144
                                       *************99988888666.....9*********...6777777777774.455667777777778*****9 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTT CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleeg 215
                                       e g  ++++   k+++ s+l+s+Gi++ ++ +++ l +   +   +e ++ ++++ +l+eg
  gi|386002944|ref|YP_005921243.1| 145 E-GLLKSISKGGKNPP-SNLVSAGIFLLDKRAFEALRR--VPPGGEERDLLEAVRVLLAEG 201
                                       8.78999998888888.*****************9944..777777777888877777765 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 !   62.7   1.4   1.7e-20     5e-17       1     156 [.       3     193 ..       3     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.7e-20
                                       EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE- CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaalarl.....gvrvved 65 
                                       a+iLA+G+++Rm       +K +lp+ggkplle+vl ++++ag+++ v v+g+  e+++ a+ +      +++++ +
  gi|386002944|ref|YP_005921243.1|   3 AIILAAGEGRRMRPltanlPKGMLPIGGKPLLEHVLLMAKEAGAERFVFVVGHqgEKIAGAFGDGsrlevEIEYAFQ 79 
                                       79**********7333568*************************999999999666777666433222112333444 PP

                                       TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE............... CS
                      NTP_transf_3  66 edpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger............... 127
                                       e  g+g++ +l+aa +    +d++lvl +D+ l +++ v+rl+a       ++++++ eg r               
  gi|386002944|ref|YP_005921243.1|  80 E-GGAGTGPALLAAEAL--AEDRFLVLRGDV-LPDADSVRRLIALE---APAMAAARVEGPRpaeegtlevsegllk 149
                                       3.367777777777654..58**********.78**********73...4456666666666788889999999999 PP

                                       ...............EECCEEEGGGHHHHHHHCTHTTHHHCHHH CS
                      NTP_transf_3 128 ...............ghpllfrarllsalaallgdqgarrllrr 156
                                                          l+ +r+++al+++     +r+ll++
  gi|386002944|ref|YP_005921243.1| 150 siskggknppsnlvsAGIFLLDKRAFEALRRVPPGGEERDLLEA 193
                                       99999988875554322337799999999998777777888775 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.7   8.1e+03      16      23 ..     198     205 ..     196     206 .. 0.66
   2 !   10.6   0.1   0.00013      0.37      10      36 .]     240     266 ..     239     266 .. 0.92
   3 !   33.6   4.7   6.6e-12     2e-08       2      36 .]     268     302 ..     267     302 .. 0.96
   4 !    7.4   0.1    0.0012       3.6      14      36 .]     315     336 ..     303     336 .. 0.79
   5 !   12.5   0.2   3.1e-05     0.094      13      34 ..     361     382 ..     350     385 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.7
                                       EETTEEE- CS
                           Hexapep  16 iggnVkIG 23 
                                       ++++V+IG
  gi|386002944|ref|YP_005921243.1| 198 LAEGVQIG 205
                                       55677776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00013
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + ++a + g V +G+++ I +g++++g
  gi|386002944|ref|YP_005921243.1| 240 VEANASLSGEVAVGRGTAIRSGSYVAG 266
                                       5789********************986 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 6.6e-12
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +vIG+++ Igp++ ++g + IGd+v+Ig+g+vi g
  gi|386002944|ref|YP_005921243.1| 268 VVIGEGCEIGPNCLVRGATSIGDGVRIGSGTVIEG 302
                                       89*******************************76 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0012
                                       EEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  14 aviggnVkIGdnvkIgagvvigg 36 
                                       +++ g+  IG+++++g g+vi++
  gi|386002944|ref|YP_005921243.1| 315 CYV-GDSLIGPGCRLGVGTVITN 336
                                       666.7777999999999999986 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 3.1e-05
                                       TEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  13 faviggnVkIGdnvkIgagvvi 34 
                                       +av+g++Vk G +++I +g+vi
  gi|386002944|ref|YP_005921243.1| 361 GAVLGEGVKTGAGTIIYPGTVI 382
                                       4555555555555555555555 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 ?   -2.7   0.1       1.7   5.1e+03      17      24 ..     201     208 ..     198     209 .. 0.73
   2 ?   -0.7   0.1      0.41   1.2e+03      12      32 ..     242     264 ..     242     265 .. 0.74
   3 !   27.5   6.1   6.2e-10   1.9e-06       1      32 [.     267     300 ..     267     301 .. 0.97
   4 ?    2.3   0.8     0.047   1.4e+02      20      33 ..     322     335 ..     315     336 .. 0.70
   5 ?    3.9   0.5     0.015        45      15      33 ..     365     383 ..     359     384 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                                       SEEE-TT- CS
                         Hexapep_2  17 GvslGdnc 24 
                                       Gv++G ++
  gi|386002944|ref|YP_005921243.1| 201 GVQIGVEV 208
                                       88888665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.41
                                       TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  12 anagi.G.vslGdncvvgaGvvi 32 
                                       ana   G v +G++  + +G+++
  gi|386002944|ref|YP_005921243.1| 242 ANASLsGeVAVGRGTAIRSGSYV 264
                                       56665566889999888888887 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 6.2e-10
                                       .EEE-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   1 pviIGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                       pv IG+ C iG+n+ + G +s+Gd++ +g+G vi
  gi|386002944|ref|YP_005921243.1| 267 PVVIGEGCEIGPNCLVrGaTSIGDGVRIGSGTVI 300
                                       8****************99**************9 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.047
                                       E-TT-EE-TT-EE- CS
                         Hexapep_2  20 lGdncvvgaGvvit 33 
                                       +G +c +g G vit
  gi|386002944|ref|YP_005921243.1| 322 IGPGCRLGVGTVIT 335
                                       66777777777776 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.015
                                       EESEEE-TT-EE-TT-EE- CS
                         Hexapep_2  15 giGvslGdncvvgaGvvit 33 
                                       g Gv+ G + ++++G vi 
  gi|386002944|ref|YP_005921243.1| 365 GEGVKTGAGTIIYPGTVIE 383
                                       3466667777777777765 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 !   19.8   0.0   1.7e-07   0.00052       2      55 ..       2      58 ..       1     126 [. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-07
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                       ++i AAG+G+Rm+   a+lpK  l + g++lleh +  + + +a   + vv ++ +
  gi|386002944|ref|YP_005921243.1|  2 KAIILAAGEGRRMRpltANLPKGMLPIGGKPLLEHVLLMAKEAGAERFVFVVGHQGE 58
                                      69**********9544489****************9988888776666666666655 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001       0.3      16      45 ..      23      52 ..      21      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                      GGGSEETTEEHHHHHHHHHHHTTTTSEEEE CS
                      CTP_transf_3 16 Knlldlggkpliayvleaalkskafekviv 45
                                      K +l++ggkpl+++vl  a++++a   v+v
  gi|386002944|ref|YP_005921243.1| 23 KGMLPIGGKPLLEHVLLMAKEAGAERFVFV 52
                                      889********************9777887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2780.71
//
Query:       gi|386002945|ref|YP_005921244.1|  [L=698]
Description: hypothetical protein Mhar_2269 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-75  253.1   0.0    1.7e-75  252.5   0.0    1.3  1  Thioredox_DsbH  Protein of unknown function, DUF255
    1.2e-09   38.2   0.0    2.7e-09   37.1   0.0    1.7  1  Thioredoxin_7   Thioredoxin-like
     0.0024   17.2   0.5       0.46    9.7   0.0    3.0  3  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
  ------ inclusion threshold ------
      0.024   15.1   0.0      0.054   14.0   0.0    1.5  1  Thioredoxin_2   Thioredoxin-like domain
      0.098   12.3   0.4       0.24   11.0   0.4    1.7  1  RPA_interact_N  Replication protein A interacting N-terminal


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.5   0.0   4.7e-79   1.7e-75       1     162 [.       4     165 ..       4     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 252.5 bits;  conditional E-value: 4.7e-79
                    Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvk 77 
                                       knrla ekspYll+ha+npvdWypwgeea+++a++edkp++lsiGys+chWChvm+ esfedeeva+lln++fv++k
  gi|386002945|ref|YP_005921244.1|   4 KNRLAFEKSPYLLEHAENPVDWYPWGEEAFTRAEREDKPVFLSIGYSTCHWCHVMAAESFEDEEVARLLNATFVPIK 80 
                                       69*************************************************************************** PP

                    Thioredox_DsbH  78 vDreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleee 154
                                       vDreerPdld++ym+++q++tgsggWPl+vfltpd+kpff++tY+pke+r gr g+l+++ +i +lw++er  l ++
  gi|386002945|ref|YP_005921244.1|  81 VDREERPDLDAVYMAVAQMMTGSGGWPLTVFLTPDKKPFFAATYIPKESRFGRIGILDLIPRIGHLWKNERAMLLSS 157
                                       ***************************************************************************** PP

                    Thioredox_DsbH 155 aeelleal 162
                                       aee+++al
  gi|386002945|ref|YP_005921244.1| 158 AEEVASAL 165
                                       ***99987 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   7.4e-13   2.7e-09       1      83 []      24     114 ..      24     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.4e-13
                                       ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG........-T CS
                     Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani.......lel 70 
                                       +w+ + +ea+ +a+++ kpv++ +g s+c+ C++++ +  +deev+++l+  fv  +vd +er + +          
  gi|386002945|ref|YP_005921244.1|  24 DWYPWGEEAFTRAEREDKPVFLSIGYSTCHWCHVMAAESFEDEEVARLLNATFVPIKVDREERPD-LdavymavA-- 97 
                                       7**********************************9999999999999************99987.324454332.. PP

                                       T-.....--SSEEEEE-T CS
                     Thioredoxin_7  71 de.....qgvPvvafldp 83 
                                        +      g P  +fl+p
  gi|386002945|ref|YP_005921244.1|  98 -QmmtgsGGWPLTVFLTP 114
                                       .24445444888888876 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00013      0.46      74     127 ..     263     317 ..     214     327 .. 0.62
   2 ?    2.4   0.0      0.02        73     275     314 ..     425     463 ..     398     476 .. 0.77
   3 ?    1.3   0.0     0.045   1.6e+02      33      84 ..     495     548 ..     485     591 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                       EE--EEHHHHHHHHHHHHHHH.TTT-TTHHHHHHHHHHHHHHHTEETTTTEE--E CS
                     GlcNAc_2-epim  74 ldaskdaYdhaFvllalasal.aageeeakdlldetlavlekhlweekaglvkee 127
                                          +k +Yd+a + la  +a+ a+g+ e++++++e+++ l ++l  ++ g++  e
  gi|386002945|ref|YP_005921244.1| 263 PHFEKMLYDQAMISLACLEAHqATGKAEYATIAREVFDYLLRDLAAPEGGFYSAE 317
                                       3445667777777777766441457777777777788777777777777776555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHTB-T CS
                     GlcNAc_2-epim 275 WpqtEalkaaaalaeltgearylewyarvaeylerhlidp 314
                                       W  + a++a+a++a++ g++r +e ++r+a+++ + ++d+
  gi|386002945|ref|YP_005921244.1| 425 WNGL-AIAALARGAQVLGDRRLEEAADRAADLVLHRMRDE 463
                                       5555.48999999999999999999999999987776664 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.045
                                       HHHTT.-TTHHHHHHHHHHHTTTTTB-TTTSSB-SEEETTE.EEE--EEHHHHH CS
                     GlcNAc_2-epim  33 aaqlg.rpgwldlvehGlkflekvlrdaehggyfsalrdgg.vldaskdaYdha 84 
                                       +++ g rp+ l+++   ++ + +  rd   gg+f++ +dg+ ++  +kd  d a
  gi|386002945|ref|YP_005921244.1| 495 LYEAGfRPERLEAALALARDMVERFRDRDGGGFFFTPEDGEeLIVRRKDGHDGA 548
                                       455565666666666666666666777777777777666653566666666555 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05     0.054       2      99 ..      37     124 ..      36     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                     Thioredoxin_2   2 kgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarky.g 77 
                                       + + kpv++ +  ++C  C+ + +e +e+++v        l++ f+p+ v+    ++        + ++++a+++ g
  gi|386002945|ref|YP_005921244.1|  37 EREDKPVFLSIGYSTCHWCHVMAAESFEDEEVARL-----LNATFVPIKVDREERPDLD------AVYMAVAQMMtG 102
                                       6789*****************************99.....9888666665555555554......688899999559 PP

                     Thioredoxin_2  78 vrgtPtivfldgkeivarlpGy 99 
                                         g P +vfl ++++ +    y
  gi|386002945|ref|YP_005921244.1| 103 SGGWPLTVFLTPDKKPFFAATY 124
                                       9999998888777444444555 PP

>> RPA_interact_N  Replication protein A interacting N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   6.8e-05      0.24      22      39 .]     457     474 ..     456     474 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.8e-05
                    RPA_interact_N  22 leRlresRsqLLwklRqg 39 
                                       l R+r++R +LL ++R g
  gi|386002945|ref|YP_005921244.1| 457 LHRMRDERGRLLHRYRGG 474
                                       67**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 4393.41
//
Query:       gi|386002946|ref|YP_005921245.1|  [L=231]
Description: hypothetical protein Mhar_2270 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1530.01
//
Query:       gi|386002947|ref|YP_005921246.1|  [L=191]
Description: hypothetical protein Mhar_2271 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1250.05
//
Query:       gi|386002948|ref|YP_005921247.1|  [L=307]
Description: Ribose-1,5-bisphosphate isomerase, e2b2 family [Methanosaeta harundinacea 6Ac]
Scores for complete 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-82  277.1   0.6    1.6e-82  276.9   0.6    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.9   0.6   8.8e-87   1.6e-82       1     282 []      15     287 ..      15     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 276.9 bits;  conditional E-value: 8.8e-87
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       ++rG++ i++aa+ +l+e++ +++ s  +e+  ++  a+d L ++rPtavsl+nair++++         +v++a++
  gi|386002948|ref|YP_005921247.1|  15 EIRGAALIGRAAAGALKEFALAIDPSGIEEFNAQVDMAADILLNTRPTAVSLSNAIRMVMR-----YRGDEVESART 86 
                                       589**********************************************************.....67999****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeL 154
                                       sl ++++ ++++ + a e ig+i++ ++ dgd+ilT+cns+++l+++++a +++k++kVi++EsrPr qG+lt+k+L
  gi|386002948|ref|YP_005921247.1|  87 SLAKNADGFVERSLMAVERIGEIGSRRVRDGDVILTHCNSSVALSIIKTAFDAGKDVKVIATESRPRYQGHLTVKTL 163
                                       ***************************************************************************** PP

                                       HHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 155 vqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                          gi++ l++dsav+ v++e vd vivGAd +++ G+++nkiGT+ +A++A+e+++ ++v+ae++kfs+++ ++e 
  gi|386002948|ref|YP_005921247.1| 164 DGWGIETELVVDSAVRSVINE-VDEVIVGADVVTASGSLVNKIGTAAIALAAHEARTSFMVAAETYKFSPETLMGEL 239
                                       *********************.******************************************************* PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       + ieer++ee+++  +e +    ++v+npafDvtP+++I++i TevG++pp
  gi|386002948|ref|YP_005921247.1| 240 VPIEERAAEEVYPGISELK---HVRVRNPAFDVTPHQYIDVICTEVGAIPP 287
                                       ****************998...9**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1956.58
//
Query:       gi|386002949|ref|YP_005921248.1|  [L=164]
Description: Flavodoxin/nitric oxide synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-14   53.9   0.3    4.4e-11   42.8   0.0    2.2  2  FMN_red       NADPH-dependent FMN reductase
    4.3e-12   46.5   0.0    5.9e-12   46.0   0.0    1.2  1  Flavodoxin_5  Flavodoxin domain
    2.3e-07   31.1   0.0    3.2e-07   30.7   0.0    1.3  1  Flavodoxin_1  Flavodoxin
    6.1e-07   29.3   0.0    9.3e-06   25.5   0.0    2.1  1  Flavodoxin_2  Flavodoxin-like fold
      4e-06   26.6   0.0    5.7e-06   26.1   0.0    1.2  1  Flavodoxin_3  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00017      0.61       1      36 [.       5      38 ..       5      46 .. 0.86
   2 !   42.8   0.0   1.2e-14   4.4e-11      64     145 ..      43     123 ..      37     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                                      -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEE CS
                           FMN_red  1 mkilvisGSlrkgsntrklaewaaealkeagaevel 36
                                      +k+lv++ S +  +nt ++a ++ae +ke ga+v +
  gi|386002949|ref|YP_005921248.1|  5 TKVLVVYHSRS--GNTARMAAAVAEGAKEGGADVVM 38
                                      58999998876..****************9999965 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 1.2e-14
                                       HHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT CS
                           FMN_red  64 aellekiaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla.elg 139
                                       +++le ++ ad+++++ P+Y+g+ s+ +K ++D  +  r +  l++K++a+++ +g+  gg +++   +   + ++g
  gi|386002949|ref|YP_005921248.1|  43 EAALEDLTGADGIVLGAPTYFGTLSAEMKGFIDGSV--RVRGRLEDKIGAAFTSSGSPTGGNETTLLSMIQGMlIHG 117
                                       578999*****************************8..6999**********************9999999998899 PP

                                       -EEEEC CS
                           FMN_red 140 aivvpr 145
                                       +++v++
  gi|386002949|ref|YP_005921248.1| 118 MVIVGD 123
                                       999987 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   1.6e-15   5.9e-12       1      89 [.       8     100 ..       8     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.6e-15
                      Flavodoxin_5   1 lilYsSrdGqTkkiaeriaeelreegelvdvedvekese.dlesydavvigasvyygkllpelakFvekh...reaL 73 
                                       l++Y Sr G+T++ a ++ae  +e g++v +++ve+++  dl+ +d +v+ga+ y g l+ e++ F++     r +L
  gi|386002949|ref|YP_005921248.1|   8 LVVYHSRSGNTARMAAAVAEGAKEGGADVVMKKVEEAALeDLTGADGIVLGAPTYFGTLSAEMKGFIDGSvrvRGRL 84 
                                       79*******************************9855444***************************9877779999 PP

                      Flavodoxin_5  74 stkpvalfsvsltark 89 
                                       ++k  a+f+ s   ++
  gi|386002949|ref|YP_005921248.1|  85 EDKIGAAFTSSGSPTG 100
                                       9999999999887654 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   8.8e-11   3.2e-07       1      68 [.       9      73 ..       9     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.8e-11
                                      EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC.GGGGGTHSEEEEEEEEETTTBEEGGGHHH CS
                      Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes.lseieeealllvvtsTfgnGdppengesf 68
                                      ++Y+S  Gnt  +A ++ae+++e g     v +++++e+ l++++  + ++++++T + G ++ +++ f
  gi|386002949|ref|YP_005921248.1|  9 VVYHSRSGNTARMAAAVAEGAKEGGA---DVVMKKVEEAaLEDLTGADGIVLGAPT-YFGTLSAEMKGF 73
                                      89********************7665...455777776669*****9999999995.569999888844 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.6e-09   9.3e-06      65     103 ..      38      77 ..       5     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.6e-09
                                       HHHHHHH.HHHHHCSSEEEEEEE-BTTB--HHHHHHHHHH CS
                      Flavodoxin_2  65 adveseq.iekllaadaivlqfPlwwfgvPailKgwiDrv 103
                                        ++ +e+ +e+l  ad ivl++P ++ +++a +Kg+iD  
  gi|386002949|ref|YP_005921248.1|  38 MKKVEEAaLEDLTGADGIVLGAPTYFGTLSAEMKGFIDGS 77 
                                       445677789*****************************64 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.6e-09   5.7e-06       1      63 [.       8      74 ..       8      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.6e-09
                      Flavodoxin_3  1 lilysSltGNTkkvAeaikealee.ekeivsikeakek....veeadvvfvGfwvdkgtadeealkfl 63
                                      l++y S++GNT  +A a++e ++e + + v +k+++e+    ++ ad +++G+ ++ gt ++e++ f+
  gi|386002949|ref|YP_005921248.1|  8 LVVYHSRSGNTARMAAAVAEGAKEgGAD-VVMKKVEEAaledLTGADGIVLGAPTYFGTLSAEMKGFI 74
                                      69*********************95444.44555554445678889******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 907.49
//
Query:       gi|386002950|ref|YP_005921249.1|  [L=119]
Description: hypothetical protein Mhar_2274 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-32  111.2   0.0    2.7e-32  111.1   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
    1.4e-08   34.7   0.0    1.6e-08   34.5   0.0    1.1  1  Cyclophil_like2  Cyclophilin-like family


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   0.0   3.1e-36   2.7e-32       3     119 .]       4     115 ..       2     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 3.1e-36
                                       EEEEET.TEEEEEEEETT..HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEE CS
                    Cyclophil_like   3 ikidie.sseveveLddt..etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalcl 76 
                                       i+i+++ ++++ +e+d++  +ta +i+e lP e+r+++WgeE+Yfs p +l+ +en++++ eagd+++w+pG a+c+
  gi|386002950|ref|YP_005921249.1|   4 IEIIVDgKGSARAEIDGRnpRTAAEIMERLPQEARAQLWGEEVYFSLPFSLA-DENPSPSSEAGDVSFWTPGSAFCI 79 
                                       78888889999999999888********************************.************************ PP

                                       ESS--TT-TTSB--SSSEEEEEEEEC-GGGGGG--TTEEEEEE CS
                    Cyclophil_like  77 ffGktPisddeirpaspvnviGrivedlellkkvkdgekvrve 119
                                       ffG+t       +p+s+vn+iGriv++ +++ +v++g++++++
  gi|386002950|ref|YP_005921249.1|  80 FFGRT-------QPYSAVNTIGRIVSGIDVFPRVEEGDRIILR 115
                                       *****.......***************************9875 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.8e-12   1.6e-08      16      99 ..      24     101 ..      11     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.8e-12
                   Cyclophil_like2  16 aaaralleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysygltrlGr 92 
                                        +a +++e+lP + + +   g E +++lp +l +++   + s +aGd+ +++p+  +++f++ ++   ++ + ++Gr
  gi|386002950|ref|YP_005921249.1|  24 RTAAEIMERLPQEARAQLW-GEEVYFSLPFSLADENP--SPSSEAGDVSFWTPGSAFCIFFGRTQP--YSAVNTIGR 95 
                                       6999*********998655.5***********99888..668899*******************66..88999**** PP

                   Cyclophil_like2  93 ieedaee 99 
                                       i + + +
  gi|386002950|ref|YP_005921249.1|  96 IVS-GID 101
                                       955.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 737.90
//
Query:       gi|386002951|ref|YP_005921250.1|  [L=145]
Description: hypothetical protein Mhar_2275 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-27   96.4   0.0    2.3e-27   95.5   0.0    1.4  2  DUF4231   Protein of unknown function (DUF4231)
    6.9e-07   29.5   0.0    8.4e-07   29.2   0.0    1.2  1  SLATT_3   SMODS and SLOG-associating 2TM effector domain 3
    9.7e-07   28.7   0.0    1.3e-06   28.4   0.0    1.2  1  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1
  ------ inclusion threshold ------
      0.052   13.0   0.0      0.064   12.7   0.0    1.1  1  ESAG1     ESAG protein
      0.099   12.7   0.0       0.18   11.8   0.0    1.5  1  FlaF      Flagellar protein FlaF


Domain annotation for each model (and alignments):
>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   6.3e-31   2.3e-27       2     103 ..      14     109 ..      13     111 .. 0.98
   2 ?   -3.1   0.0         3   1.1e+04      70      77 ..     127     134 ..     121     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 6.3e-31
                           DUF4231   2 qlswyekkasrakrrfrllrlitivlgallpilvssklgagvsvlkiltallsalvailaaleeffrykerWrryRs 78 
                                       ql+wye+++++++ +fr+l++i+iv++al+p+++        +  ++l+ +l++++++l++++++f+++++W++yRs
  gi|386002951|ref|YP_005921250.1|  14 QLKWYEDHSRQSQICFRGLKVIEIVAAALIPFAAG------LMPDPLLIGGLGVIIVVLESVQGLFQFQQNWTNYRS 84 
                                       99*********************************......99********************************** PP

                           DUF4231  79 taEsLktekwlflakagpYsdnksh 103
                                       taE Lk+ek+l+lakagpY+d++++
  gi|386002951|ref|YP_005921250.1|  85 TAEGLKREKYLWLAKAGPYKDPENP 109
                                       **********************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3
                           DUF4231  70 kerWrryR 77 
                                       + +W+ry 
  gi|386002951|ref|YP_005921250.1| 127 HSKWIRYQ 134
                                       56788885 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.4e-10   8.4e-07      55     132 ..      59     135 ..      18     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.4e-10
                           SLATT_3  55 afllalvievvlarrrperkWyegRavAEsvKtlaWrYavrgepFeeelesaeaeklfrerleevlrelrkvssels 131
                                       + ++ +v+e v    + +++W + R+ AE +K     +  ++ p+ ++ e++++++lf+er+e ++++ +++ ++ +
  gi|386002951|ref|YP_005921250.1|  59 LGVIIVVLESVQGLFQFQQNWTNYRSTAEGLKREKYLWLAKAGPY-KDPENPNPDSLFAERVEALISTEHSKWIRYQ 134
                                       344555667777778899***************************.9999**************9998887666544 PP

                           SLATT_3 132 r 132
                                       +
  gi|386002951|ref|YP_005921250.1| 135 E 135
                                       4 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.5e-10   1.3e-06       4     122 .]       9     130 ..       7     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.5e-10
                           SLATT_1   4 eRveeqldwYrkkaeeneraakrwrlllillellalllaalrafgelsv.dlvgvlaavaaallaWlelkqyeelaa 79 
                                       +R +eql+wY++ ++++    +++++ l ++e++a++l+ + a g ++   l+g l +++  l + + l q+++  +
  gi|386002951|ref|YP_005921250.1|   9 DRFNEQLKWYEDHSRQS----QICFRGLKVIEIVAAALIPFAA-GLMPDpLLIGGLGVIIVVLESVQGLFQFQQNWT 80 
                                       79********9876655....5566666666666666665552.222222567777777777777777888888999 PP

                           SLATT_1  80 aYslaaeeLeiiraalea.......eateeewaklVadaEeaisrehtqW 122
                                       +Y  +ae L+  +  + a       +++++  + + +++E +is eh +W
  gi|386002951|ref|YP_005921250.1|  81 NYRSTAEGLKREKYLWLAkagpykdPENPNPDSLFAERVEALISTEHSKW 130
                                       ***********999888889*9998888889999**************** PP

>> ESAG1  ESAG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05     0.064     147     188 ..      11      55 ..       4      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                             ESAG1 147 ssdvleWreeea...tffqLklkvqeifspLiapfaaGkppsvll 188
                                        ++ l+W+e+++   +  +  lkv ei+++ ++pfaaG  p  ll
  gi|386002951|ref|YP_005921250.1|  11 FNEQLKWYEDHSrqsQICFRGLKVIEIVAAALIPFAAGLMPDPLL 55 
                                       6789******9955433344699***************8776554 PP

>> FlaF  Flagellar protein FlaF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-05      0.18      25      73 ..      67     114 ..      63     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                              FlaF  25 raaakLkaaeeagkeseeelaeAlkfnrrlWtilaedlaspenplpeel 73 
                                       ++++ L + ++++++ +   ae lk+ + lW + a   ++penp p++l
  gi|386002951|ref|YP_005921250.1|  67 ESVQGLFQFQQNWTNYR-STAEGLKREKYLWLAKAGPYKDPENPNPDSL 114
                                       67788999******998.99**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1015.66
//
Query:       gi|386002952|ref|YP_005921251.1|  [L=68]
Description: hypothetical protein Mhar_2276 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-23   79.8   0.0    1.1e-22   79.6   0.0    1.0  1  DUF433    Protein of unknown function (DUF433)
     0.0088   15.5   0.4      0.015   14.7   0.4    1.3  1  SHNi-TPR  SHNi-TPR


Domain annotation for each model (and alignments):
>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   1.2e-26   1.1e-22       1      54 [.       7      60 ..       7      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.2e-26
                                      EEE-TTSGGGS-EETTT--BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHHT CS
                            DUF433  1 ItidpeilgGkPvIrgtRipVetilellaaGesieeiledyPdLtlediqaala 54
                                      I+idp il GkPvI+gtR++Ve+i++lla+G+s+ eil++yP+L  ed+qa+l+
  gi|386002952|ref|YP_005921251.1|  7 IVIDPAILAGKPVIKGTRLAVEFIIDLLAQGWSELEILRNYPGLASEDLQACLN 60
                                      9***************************************************95 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   1.7e-06     0.015      20      33 ..      51      64 ..      50      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                          SHNi-TPR 20 AveDlrkaLeLreq 33
                                      A+eDl+++L+L+ q
  gi|386002952|ref|YP_005921251.1| 51 ASEDLQACLNLQSQ 64
                                      99**********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 434.18
//
Query:       gi|386002953|ref|YP_005921252.1|  [L=292]
Description: Acetylglutamate kinase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-44  152.0   3.2    2.3e-44  151.8   3.2    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   3.2   1.3e-48   2.3e-44       2     241 .]      23     268 ..      22     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 1.3e-48
                                       EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                         AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                       + V+K+GGs+++d e   l+ +++++  l+  g+++vvVhGgg+ + + +a+  g +s +   glr+t+ee++e+a+
  gi|386002953|ref|YP_005921252.1|  23 IMVIKIGGSIMSDREV--LDTFVQDLVLLRYVGIHPVVVHGGGPEISEKMAR-FGKKSVFVG-GLRVTDEETLEIAR 95 
                                       68**************..**********************************.*********.************** PP

                                       HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE...............HHHTTTCEEECCHHHHHHHTT-EEE CS
                         AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagr.............degsdgnvesvdaeaieelleagvvpv 142
                                       +++l+ ++++lv+ + ++g + +gls+++  ++ a++             d g +g+v +v+ e i+    +g++pv
  gi|386002953|ref|YP_005921252.1|  96 MVLLGNINSSLVSLIGKHGGKGIGLSGKDGQLIVARKkapivvageeapiDLGWVGEVVRVNPEIIMITAGKGYIPV 172
                                       *********************************9999**************************************** PP

                                       EESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTH CS
                         AA_kinase 143 ltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgG 218
                                       +++++ +d eg  +++++Dt+a  +A algA+kli +tdV+GV  ++ + +   ++++  ++++++  ++++ +tgG
  gi|386002953|ref|YP_005921252.1| 173 ISPIA-VDGEGNNLNVNADTAAGVIAIALGAKKLISVTDVEGVKLRPEDPN---TVISSFRISDFRRmVDEKVITGG 245
                                       ***76.99999988*****************************99999999...*********************** PP

                                       HHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 219 mkvkhpaalaaarrggipvvItn 241
                                       m++k++a+++a+++g+  ++I++
  gi|386002953|ref|YP_005921252.1| 246 MIPKVEACVRAVEGGVQSAHIVD 268
                                       ********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1862.98
//
Query:       gi|386002954|ref|YP_005921253.1|  [L=541]
Description: Pyruvate carboxylase subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete 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-59  200.4   0.2      4e-59  199.7   0.2    1.3  1  PYC_OADA         Conserved carboxylase domain
    3.5e-39  135.0   0.0    4.6e-39  134.6   0.0    1.2  1  HMGL-like        HMGL-like
    7.9e-20   70.5   4.3      2e-19   69.2   4.3    1.7  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.3e-08   34.5   0.9     0.0019   18.0   0.1    2.6  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0036   18.0   0.5       0.65   10.7   0.1    2.6  2  HlyD_3           HlyD family secretion protein
     0.0043   16.3   0.5       0.22   10.7   0.1    2.2  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0046   16.9   0.7      0.026   14.5   0.5    2.1  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0061   16.4   0.8      0.023   14.6   0.8    2.0  1  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.016   15.2   0.5      0.038   14.0   0.5    1.6  1  DUF2118          Uncharacterized protein conserved in archaea
       0.16   10.7   0.6       0.29    9.8   0.2    1.6  2  HlyD_2           HlyD family secretion protein


Domain annotation for each model (and alignments):
>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.2   2.2e-62     4e-59       1     196 [.     265     454 ..     265     455 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 2.2e-62
                                       HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TT CS
                          PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegry 77 
                                       V+++++PGG+l+nl +q+ eq +ldk++evl+e ++v+++lG++++VTP+S++vg +Av+nvl+        +e ry
  gi|386002954|ref|YP_005921253.1| 265 VLVYQVPGGMLSNLVSQLVEQKALDKYDEVLAEFPRVREDLGYPPLVTPTSQIVGSQAVLNVLT--------GE-RY 332
                                       789*************************************************************........86.** PP

                                       SS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHH CS
                          PYC_OADA  78 kdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypk 152
                                       k +p++v+d++kG +G+ pg++++++++++l++eepit+rpad+++p ++ek+++e+e k   + eedvl+yalyp+
  gi|386002954|ref|YP_005921253.1| 333 KAVPKEVKDYVKGLYGRSPGEINPKIRAEILEDEEPITVRPADLIPP-EYEKMKAEAEGKGlvRREEDVLTYALYPQ 408
                                       ***********************************************.***********9855699*********** PP

                                       HHHHHHHHHHHHHHHH...CTTTS.......-SEEEEEETTEEEE. CS
                          PYC_OADA 153 vaekflkfreeygdvs.vlptkvffeglk.vgeeveveveggkyli 196
                                       vaekflk +++ + ++ +lp +  +     ++  ++vev+g++yl+
  gi|386002954|ref|YP_005921253.1| 409 VAEKFLKGEAKEEVLKkALPADLQTGAIGgKPAAFNVEVDGESYLV 454
                                       *******9999999987888887777777789***********984 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   2.6e-42   4.6e-39      25     263 ..       1     242 [.       1     243 [. 0.96

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 2.6e-42
                                       HHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B...........--EE-SSHHHHHHHHH. CS
                         HMGL-like  25 klaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkka......r...ilalvrarekdikaavea 84 
                                       +l+ia++Lde+g+ ++Ev        +++ + ed++e++ra++ a++++      r   ++++++++++ + ++ve+
  gi|386002954|ref|YP_005921253.1|   1 MLPIAEKLDEVGFFSMEVwggatfdsCIRYLNEDPWERLRALKLAMPNTplqmllRgqnLVGYRHYADDIVVKFVER 77 
                                       579*********************************************97777662557****************** PP

                                       ...TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT-BTTTBS--HHHHHHHHHHHHHHT CS
                         HMGL-like  85 lkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..velsledasrtdleflaevveaaeeaG 159
                                       + ++g++++++f+a+++              +++++ a+kaa+++ ++   ++ +++++ +++e+ ++++ +++++G
  gi|386002954|ref|YP_005921253.1|  78 AAKNGVDVFRIFDAVND--------------IRNMTVAIKAAKDMDAHvqGCVCYTTSPVHSIEQFTKMAVELADLG 140
                                       *****************..............****************9566788999999***************** PP

                                       -SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BH CS
                         HMGL-like 160 atriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaal 236
                                       ++++ i+D+ G++ P++a++l++ +ke+++  +++ +H H + G+A + +l + eaG+d +d++++ lG ++ ++++
  gi|386002954|ref|YP_005921253.1| 141 CDSLCIKDMAGLILPHDAYDLVASMKEETS--IPVDLHSHCTSGMAPMSFLFGCEAGVDILDTAISPLGWGTSHPPT 215
                                       ******************************..********************************************* PP

                                       HHHHHHHHHTT-B----HHHHHHHHHH CS
                         HMGL-like 237 eelvaalealgvdtgldlqklrsiaal 263
                                       e +vaale+++++tgldl+ l++i+++
  gi|386002954|ref|YP_005921253.1| 216 ESIVAALEGTPYETGLDLKLLTEIKRY 242
                                       ***********************9875 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   4.3   1.1e-22     2e-19       3      73 .]     475     540 ..     473     540 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.1e-22
                                       EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                       +++Pm G++++     +l+k+GdkV++g+ +a++eamKme++++a k+Gvv+ei++++G+tv  gd+l+ i
  gi|386002954|ref|YP_005921253.1| 475 VTVPMQGVIIR-----YLIKKGDKVSKGDAVAVLEAMKMENKVSANKDGVVAEIYAEVGATVAPGDILMSI 540
                                       799********.....****************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   4.6e-06    0.0082       6      42 ..     476     512 ..     472     514 .. 0.89
   2 !   18.0   0.1   1.1e-06    0.0019       4      34 ..     511     541 .]     509     541 .] 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-06
                   Biotin_lipoyl_2   6 aapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlal 42 
                                       + p  G++ + ++k G+ V +Gd  a+l+  + ++++
  gi|386002954|ref|YP_005921253.1| 476 TVPMQGVIIRYLIKKGDKVSKGDAVAVLEAMKMENKV 512
                                       56789***********************999988876 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.1e-06
                   Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelD 34 
                                       +++a  +G+Va+++ + G  V  Gd+L+ +D
  gi|386002954|ref|YP_005921253.1| 511 KVSANKDGVVAEIYAEVGATVAPGDILMSID 541
                                       689999************************9 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.014        25       2      32 ..     475     505 ..     474     515 .. 0.86
   2 !   10.7   0.1   0.00036      0.65       2      30 ..     512     540 ..     511     541 .] 0.94

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdelleiip 32 
                                       +++p +Gv+    +++g+ v++gd+++ +  
  gi|386002954|ref|YP_005921253.1| 475 VTVPMQGVIIRYLIKKGDKVSKGDAVAVLEA 505
                                       789***********************98865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00036
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       + A  dGvv+e+ +e+g  v++gd l++i
  gi|386002954|ref|YP_005921253.1| 512 VSANKDGVVAEIYAEVGATVAPGDILMSI 540
                                       67899**********************98 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.016        29     112     139 ..     476     503 ..     463     507 .. 0.69
   2 !   10.7   0.1   0.00012      0.22     108     139 ..     509     540 ..     501     541 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 112 kapisGvVteknvreGqyvqpgdtlfti 139
                                       + p++Gv+++  + +G+ v++gd+++ +
  gi|386002954|ref|YP_005921253.1| 476 TVPMQGVIIRYLIKKGDKVSKGDAVAVL 503
                                       4567777777777777777777766544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                       + +v+a+ +GvV e  +  G +v pgd l++i
  gi|386002954|ref|YP_005921253.1| 509 ENKVSANKDGVVAEIYAEVGATVAPGDILMSI 540
                                       56799************************998 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.84   1.5e+03      30      51 ..     310     331 ..     301     334 .. 0.87
   2 !   14.5   0.5   1.4e-05     0.026      24      82 ..     469     525 ..     461     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.84
                            RnfC_N  30 lvlplsqhiGapakplvkvgdk 51 
                                       lv p sq +G++a + v  g++
  gi|386002954|ref|YP_005921253.1| 310 LVTPTSQIVGSQAVLNVLTGER 331
                                       799**********999988876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-05
                            RnfC_N  24 lplpkelvlplsqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiek 82 
                                        ++++ +++p++   G   + l+k+gdkV kG+ +a  e+  +  +v a   G V +i  
  gi|386002954|ref|YP_005921253.1| 469 KAPKDGVTVPMQ---GVIIRYLIKKGDKVSKGDAVAVLEAmKMENKVSANKDGVVAEIYA 525
                                       556667778876...566899***************9998667999**********9975 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.8   1.3e-05     0.023      37      77 ..     486     526 ..     475     531 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                       E---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GG CS
                             GCV_H  37 elpevgtkvkkgeslaavEsvKaasevyapvsGevvevNek 77 
                                        l ++g+kv+kg+++a++E+ K+  +v a+ +G v e+  +
  gi|386002954|ref|YP_005921253.1| 486 YLIKKGDKVSKGDAVAVLEAMKMENKVSANKDGVVAEIYAE 526
                                       46679******************************998766 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   2.1e-05     0.038      85     135 ..     476     525 ..     472     531 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                           DUF2118  85 lipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfike 135
                                        +p++gv +    + Gd+v +gd++a + + k e   + a ++gvV+ i+ 
  gi|386002954|ref|YP_005921253.1| 476 TVPMQGVIIRYLIKKGDKVSKGDAVAVLEAMKMEN-KVSANKDGVVAEIYA 525
                                       6899******************************6.699*******98876 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   2.2e+03      47      75 ..     381     409 ..     380     418 .. 0.77
   2 ?    9.8   0.2   0.00016      0.29      71     106 ..     480     515 ..     472     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                            HlyD_2  47 ngeieesikkkgliirdekviksnaegiv 75 
                                       +++++++ + kgl+ r+e v+    + +v
  gi|386002954|ref|YP_005921253.1| 381 YEKMKAEAEGKGLVRREEDVLTYALYPQV 409
                                       78999999**********99876665555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                            HlyD_2  71 aegivkyfvkeGdkvkkgkkvaeiqkseadeklkek 106
                                       +++i++y++k+Gdkv+kg+ va  +  ++++k  ++
  gi|386002954|ref|YP_005921253.1| 480 QGVIIRYLIKKGDKVSKGDAVAVLEAMKMENKVSAN 515
                                       57899*****************99999988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3576.13
//
Query:       gi|386002955|ref|YP_005921254.1|  [L=72]
Description: hypothetical protein Mhar_2279 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00027   20.8   0.1    0.00064   19.6   0.0    1.6  2  MarR_2        MarR family
     0.0039   17.6   0.2      0.008   16.7   0.1    1.6  2  HTH_27        Winged helix DNA-binding domain
      0.004   17.1   0.0      0.004   17.1   0.0    1.1  1  HTH_45        Winged helix-turn-helix
     0.0058   16.8   0.0      0.009   16.2   0.0    1.3  1  Rio2_N        Rio2, N-terminal
     0.0058   16.2   0.5      0.014   15.0   0.3    1.6  2  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.013   15.5   0.0    1.0  1  Replic_Relax  Replication-relaxation
      0.021   14.9   0.4      0.076   13.1   0.3    1.8  2  DUF2250       Uncharacterized protein conserved in archaea (D
      0.043   13.6   0.0      0.047   13.4   0.0    1.2  1  DUF4364       Domain of unknown function (DUF4364)
      0.057   13.5   0.5       0.11   12.5   0.0    1.7  2  HTH_20        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.2e-07   0.00064      22      52 ..      11      41 ..       2      48 .. 0.87
   2 ?   -1.2   0.0      0.99     2e+03       9      48 ..      61      69 ..      55      72 .] 0.56

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLve 52
                                      + ++e+ar ++ s +++sr++k+++++ Lve
  gi|386002955|ref|YP_005921254.1| 11 VKASEVARSTDRSIQNISRAIKECEEQKLVE 41
                                      689***************************8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.99
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48
                                      +vL +L                                ++
  gi|386002955|ref|YP_005921254.1| 61 HVLRELE-------------------------------KH 69
                                      4555554...............................44 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     4e-06     0.008      10      58 ..       3      47 ..       1      59 [. 0.76
   2 ?   -0.4   0.0      0.82   1.6e+03      34      44 ..      58      68 ..      50      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                            HTH_27 10 hlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                      ++ir + r +k++++++ ++++ ++is ++k+++e+ Lve   + ++ +
  gi|386002955|ref|YP_005921254.1|  3 RSIR-NSRVVKASEVARSTDRSIQNISRAIKECEEQKLVE---CITPEK 47
                                      6677.7778888***************************4...334444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.82
                            HTH_27 34 hisyslkkLte 44
                                      +++ +l++L++
  gi|386002955|ref|YP_005921254.1| 58 QGHHVLRELEK 68
                                      67788888886 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     2e-06     0.004      28      73 ..      19      70 ..       1      72 [] 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                            HTH_45 28 kanLsykllnkYLdmLvekgli......kkskekYvlTekGlelleklkele 73
                                      + + s +++++ ++   e++l+      k++ +kY+lT++G ++l++l++ +
  gi|386002955|ref|YP_005921254.1| 19 STDRSIQNISRAIKECEEQKLVecitpeKHTWKKYMLTDQGHHVLRELEKHK 70
                                      55567788888999999999999999977899****************9876 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.5e-06     0.009      19      74 ..       5      63 ..       2      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                            Rio2_N 19 mrnhevVptelieeisrlkeeevkkrlsrllkaklisr...ktakydGYkLtyeGyDyL 74
                                       rn++vV  +++++ +  + ++++++++++ ++kl++    ++ +++ Y Lt +G+ +L
  gi|386002955|ref|YP_005921254.1|  5 IRNSRVVKASEVARSTDRSIQNISRAIKECEEQKLVECitpEKHTWKKYMLTDQGHHVL 63
                                      699*********************************988788999**********9887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   6.9e-06     0.014      15      48 .]       7      41 ..       5      41 .. 0.87
   2 ?   -1.6   0.0       1.1   2.1e+03       8      14 ..      62      68 ..      56      70 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.9e-06
                            HTH_24 15 npr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      n+r    +e+A+ ++ S+++++r +k++ee+ l++
  gi|386002955|ref|YP_005921254.1|  7 NSRvVKASEVARSTDRSIQNISRAIKECEEQKLVE 41
                                      55556679**********************98885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                            HTH_24  8 ILelLqk 14
                                      +L++L+k
  gi|386002955|ref|YP_005921254.1| 62 VLRELEK 68
                                      5666655 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   6.7e-06     0.013       1      70 [.       2      64 ..       2      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                      Replic_Relax  1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarlla 70
                                      +r++++ rv  ++ +ar +  s ++ ++r++++ +e++l++ ++++  + +       Y Lt +G+ +l+
  gi|386002955|ref|YP_005921254.1|  2 MRSIRNSRVVKASEVARSTDRSIQN-ISRAIKECEEQKLVECITPEKHTWK------KYMLTDQGHHVLR 64
                                      58999*************9999999.****************999944444......5***********3 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 ?    3.3   0.0     0.045        89      26      53 ..      14      41 ..       3      47 .. 0.80
   2 ?   13.1   0.3   3.8e-05     0.076      58      93 .]      29      66 ..      16      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.045
                           DUF2250 26 ksiakeleipleevrellkkLeelGLle 53
                                        +a+ ++ +++++++++k+ ee  L+e
  gi|386002955|ref|YP_005921254.1| 14 SEVARSTDRSIQNISRAIKECEEQKLVE 41
                                      5678888999999999999988888887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.8e-05
                           DUF2250 58 ktikrteaklKkksevhkhHtY..YrltreGelllrel 93
                                      ++ik+ e ++  +  +  +Ht+  Y lt++G+++lrel
  gi|386002955|ref|YP_005921254.1| 29 RAIKECEEQKLVECITPEKHTWkkYMLTDQGHHVLREL 66
                                      566666666666667778999877************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 ?   13.4   0.0   2.4e-05     0.047      36      75 ..      27      68 ..       7      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                           DUF4364 36 lqqalseLvesglieee..ekenktlykiTekGketlelfen 75
                                      ++ a++e +e++l+e+   ek++ + y +T++G  +l+++e+
  gi|386002955|ref|YP_005921254.1| 27 ISRAIKECEEQKLVECItpEKHTWKKYMLTDQGHHVLRELEK 68
                                      7889***********99666788899************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.7e-05      0.11      27      60 ..      13      46 ..       2      47 .. 0.91
   2 ?   -1.2   0.2       1.1   2.2e+03      45      52 ..      63      70 ..      60      72 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 27 aselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      ase+a+  d s +++s+ +++ ee  Lve  +++
  gi|386002955|ref|YP_005921254.1| 13 ASEVARSTDRSIQNISRAIKECEEQKLVECITPE 46
                                      89***************************99986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                      HHHHHHCT CS
                            HTH_20 45 LrvLeeag 52
                                      Lr+Le++ 
  gi|386002955|ref|YP_005921254.1| 63 LRELEKHK 70
                                      58888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 504.22
//
Query:       gi|386002956|ref|YP_005921255.1|  [L=135]
Description: hypothetical protein Mhar_2280 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-57  191.5   0.0    4.5e-57  191.3   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.3   0.0   2.5e-61   4.5e-57       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 191.3 bits;  conditional E-value: 2.5e-61
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       m++rvvssk+ei +ln+ne+ivHlafr+sn d+l+l+k cp+l+aiqvp+Sy+kt+sk++k+fle+qgi+llegdvw
  gi|386002956|ref|YP_005921255.1|   1 MRVRVVSSKNEIPNLNPNERIVHLAFRASNVDFLNLMKICPRLRAIQVPPSYHKTMSKAIKLFLEMQGIDLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdi+ey+ ++ee+i +i+ ++s g++ ee ae+++k+t+l pdlik+++k
  gi|386002956|ref|YP_005921255.1|  78 GHRKDIDEYFLIEEETIGEIEAMISGGATVEEAAEEITKRTRLAPDLIKYIAK 130
                                       **************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 830.33
//
Query:       gi|386002957|ref|YP_005921256.1|  [L=135]
Description: hypothetical protein Mhar_2281 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-58  194.5   0.0    5.2e-58  194.4   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.0   2.9e-62   5.2e-58       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 2.9e-62
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mk+rvvssk+ei +ln+ne+ivHlafr+sn d+l+l+k+cp+l+aiqvp+Sy++t+s+++++fl++qgi+llegdvw
  gi|386002957|ref|YP_005921256.1|   1 MKLRVVSSKKEIPELNPNERIVHLAFRASNVDFLTLMKRCPRLRAIQVPPSYRRTISQAIQVFLDMQGISLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                       ghrkdi+eyy+vsee+i +i+ ++s+g++ ee ae+++k+t+l pdli++++
  gi|386002957|ref|YP_005921256.1|  78 GHRKDIDEYYVVSEETIGEIEAMISRGATAEEAAEEITKRTRLAPDLIRYIA 129
                                       **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 842.60
//
Query:       gi|386002958|ref|YP_005921257.1|  [L=135]
Description: hypothetical protein Mhar_2282 [Methanosaeta harundinacea 6Ac]
Scores for 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-57  190.3   0.0      1e-56  190.1   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.1   0.0   5.8e-61     1e-56       1     129 [.       1     129 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 5.8e-61
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       mkirvvssk+ei++l +ne+ vHlafrpsn d+l+l++ cp+l++iqvp+Sy+ktls+++++fle+qgi+llegdvw
  gi|386002958|ref|YP_005921257.1|   1 MKIRVVSSKDEITKLGPNERNVHLAFRPSNVDFLELIRVCPRLRTIQVPPSYHKTLSRAIRLFLEMQGITLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfll 129
                                       ghrkdi+eyy v+ee ie+i +l++eg+s ee a+ ++++tkls dlik+++
  gi|386002958|ref|YP_005921257.1|  78 GHRKDIDEYYIVDEEPIEEIGSLIREGESLEEAAAAIQRKTKLSADLIKYIA 129
                                       **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 898.38
//
Query:       gi|386002959|ref|YP_005921258.1|  [L=135]
Description: hypothetical protein Mhar_2283 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-59  198.7   0.0    2.5e-59  198.6   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   0.0   1.4e-63   2.5e-59       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 1.4e-63
                           DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvw 77 
                                       m+irvvssk+ei++ln+ne+ivHlafrpsn d+l+l+++cp+l+a+qvp+Sy+kt+sk++k+fle+qgi+llegdvw
  gi|386002959|ref|YP_005921258.1|   1 MRIRVVSSKDEIAELNPNERIVHLAFRPSNVDFLDLMRSCPRLRAVQVPPSYHKTMSKAIKLFLEMQGIDLLEGDVW 77 
                                       9**************************************************************************** PP

                           DUF1699  78 ghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                       ghrkdi+eyy+v+ee ie+i +l+++g+s e+ ++ ++++t+l pdli++++k
  gi|386002959|ref|YP_005921258.1|  78 GHRKDIDEYYVVDEEAIEEIGNLIKQGESIEDASAAIQRKTRLAPDLIRYIAK 130
                                       **************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 850.53
//
Query:       gi|386002960|ref|YP_005921259.1|  [L=292]
Description: hypothetical protein Mhar_2284 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-21   78.1   0.0    1.6e-21   77.7   0.0    1.1  1  DUF4198          Domain of unknown function (DUF4198)
    0.00059   20.1   0.0     0.0016   18.6   0.0    1.8  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.051   13.6   0.0       0.13   12.3   0.0    1.6  1  Big_1            Bacterial Ig-like domain (group 1)
      0.083   12.9   0.0       0.21   11.6   0.0    1.6  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
       0.16   12.0   0.0       0.32   11.1   0.0    1.4  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   4.4e-25   1.6e-21       1     200 [.      19     234 ..      19     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 4.4e-25
                           DUF4198   1 aqAHelwllpsstvvsggewvtvdlafghdpfeadheplkleklkvlapdge.ktdlgkylstf.dvallkpekegt 75 
                                       a++He ++ p s   s+g+ v + l+ gh   + +  p  + +++v++p +e   d  ++ s f d+ ++ pe++g+
  gi|386002960|ref|YP_005921259.1|  19 ASGHETYIRPISGWASPGDVVYLPLGSGHATANTE-LPEGIVNVTVIGPAEEaVLDGMGEISGFwDIYSFVPEEAGL 94 
                                       789**************************555553.555577********954555556666667************ PP

                           DUF4198  76 yklaaakkpgdwke..ygdpk..................lakevp..aeaae..lk.vvkysqyaktfvtvgkpse. 126
                                       y++ + ++ g+w++  +                      l    +  +   +  +  +   + yak+fv vg++ + 
  gi|386002960|ref|YP_005921259.1|  95 YVVDVYHSEGSWTNivT--NPpngsfwehayaydidfdsL---NKtgWAD-DwyVArSYPKNCYAKAFVAVGEEADl 165
                                       **************641..334566666667777765431...2222222.13444044445567*********777 PP

                           DUF4198 127 .twdkpvglglEivPlthpydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlp 200
                                        +++++vg++lEivPl++ +++ +g+ + +q+l++G+P +g +v++ + g+        ++  tda+G++t++l 
  gi|386002960|ref|YP_005921259.1| 166 sKANEAVGQELEIVPLDDISTVGKGD-FAFQLLFQGEPISGIDVWAMKVGD-----DTPVESVTDAEGKFTLNLN 234
                                       8*********************7676.******************987653.....3334469********9985 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.5e-07    0.0016      10      46 ..     199     234 ..     186     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.5e-07
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglp 46 
                                       +g+pi+g  V++ + +++t  + +tda+G+f+l+ l 
  gi|386002960|ref|YP_005921259.1| 199 QGEPISGIDVWAMKVGDDTPVESVTDAEGKFTLN-LN 234
                                       69******************************95.54 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05      0.13      18      57 ..     200     238 ..     199     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                             Big_1  18 gnpvagatVtfsvsggalsassgtTdanGkatvtltstka 57 
                                       g p++g+ V + +  g+ ++ +++Tda+Gk+t +l +  +
  gi|386002960|ref|YP_005921259.1| 200 GEPISGIDV-WAMKVGDDTPVESVTDAEGKFTLNLNDEAS 238
                                       889999999.666666666**************9987665 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.8e-05      0.21      11      46 ..     200     238 ..     198     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                   CarbopepD_reg_2  11 keplpgatVyvkg....tkkgtvTdenGnFelknlpagky 46 
                                       +ep+ g+ V+  +    t +  vTd++G+F+l+ l+++  
  gi|386002960|ref|YP_005921259.1| 200 GEPISGIDVWAMKvgddTPVESVTDAEGKFTLN-LNDEAS 238
                                       6888998888855333377999**********6.665554 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 ?   11.1   0.0   8.9e-05      0.32      20      81 ..     195     254 ..     186     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                              bMG3  20 tsLdsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsArkdedla 81 
                                       + L +g+P++g++V  ++  +++  e  TDa+G  +++ ++++  ++ +  +v A ++ d  
  gi|386002960|ref|YP_005921259.1| 195 QLLFQGEPISGIDVWAMKVGDDTPVESVTDAEGKFTLNLNDEA--SELTEWIVRADTKMDPR 254
                                       56789*****************************999988554..67777777777666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1973.11
//
Query:       gi|386002961|ref|YP_005921260.1|  [L=287]
Description: hypothetical protein Mhar_2285 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-30  106.1   0.2    3.8e-30  105.9   0.2    1.1  1  DUF4198          Domain of unknown function (DUF4198)
    1.3e-05   25.1   0.0    3.5e-05   23.8   0.0    1.7  2  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
  ------ inclusion threshold ------
      0.015   15.5   0.1        0.8   10.0   0.0    2.5  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.2   6.4e-34   3.8e-30       2     213 .]      19     248 ..      18     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 6.4e-34
                           DUF4198   2 qAHelwllpsstvvsggewvtvdlafghdpfeadheplkleklkvlapdg........ektdlg..kylstfdvall 68 
                                       +AH+ wl+ +s   s+g+   v++  gh+  + + +p ++ +++v++p+g        e+t +    y+++fdv++ 
  gi|386002961|ref|YP_005921260.1|  19 HAHDTWLMTTSGWASEGDLALVQMTEGHSFVPMAPPPGDI-SIRVTGPGGydrsfdldETTATNgpYYRTDFDVES- 93 
                                       8*****555555556666999*******444444455555.68********99999875444445799*****999. PP

                           DUF4198  69 kpekegtyklaaakkpgdwke....ygdpk............lakevpaeaae...........lkvvkysqyaktf 118
                                           +g+y+++ +++ g  ++    +g p+                      e              +  +++ k f
  gi|386002961|ref|YP_005921260.1|  94 ----PGLYVATGEQHEGPLTFvrtkFGAPDeemdgydeiawdE--------VEtsgwdpdwyiaEAYEDLVKFSKLF 158
                                       ....********9997777765577677778899666664331........33333333335555899999999*** PP

                           DUF4198 119 vtvgkpse.twdkpvglglEivPlthpydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGv 194
                                       + +++++   ++ p+g++lEivPl++ ++l +g+ +++ vl+dG+P+ag+ev + +  +     p   k  td+dGv
  gi|386002961|ref|YP_005921260.1| 159 IVAENADFaSASVPIGQRLEIVPLENITALGTGD-FRFLVLFDGEPAAGLEVRLATTAN-----PSVGKGVTDEDGV 229
                                       ******4446777*****************8777.******************876543.....3333449****** PP

                           DUF4198 195 vtftlpkaGlwlleaehed 213
                                       v +++p++Glw++++eh+d
  gi|386002961|ref|YP_005921260.1| 230 VLLAVPEPGLWIVATEHKD 248
                                       *****************96 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 ?   -3.5   0.0       1.8   1.1e+04      76      87 ..      33      44 ..      18      48 .. 0.62
   2 !   23.8   0.0   5.8e-09   3.5e-05      22      83 ..     198     254 ..     192     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                              bMG3 76 kdedlaflkldw 87
                                      +++dla++++++
  gi|386002961|ref|YP_005921260.1| 33 SEGDLALVQMTE 44
                                      478888888864 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 5.8e-09
                              bMG3  22 LdsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsAr..kdedlafl 83 
                                       L +g+P+ag eVrl    +  +++g TD++Gv+ +a +       + +++++A+  kd+++ +l
  gi|386002961|ref|YP_005921260.1| 198 LFDGEPAAGLEVRLATTANPSVGKGVTDEDGVVLLAVP-------EPGLWIVATehKDGEMVLL 254
                                       679***********************************.......6778888884445555444 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.024   1.4e+02      45      64 ..      53      72 ..      45      92 .. 0.78
   2 ?   10.0   0.0   0.00013       0.8      10      39 ..     200     229 ..     196     246 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.024
                   CarboxypepD_reg 45 lppgtysvtvsapGyatatr 64
                                       ppg++s++v+ pG   +++
  gi|386002961|ref|YP_005921260.1| 53 PPPGDISIRVTGPGGYDRSF 72
                                      478**********9988876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGa 39 
                                       +g+p ag +V+++++++ +v   +td+dG 
  gi|386002961|ref|YP_005921260.1| 200 DGEPAAGLEVRLATTANPSVGKGVTDEDGV 229
                                       79***************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2063.09
//
Query:       gi|386002962|ref|YP_005921261.1|  [L=224]
Description: Cobalt ABC transporter, ATP-binding protein, partial [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-15   56.6   0.0    5.3e-15   56.2   0.0    1.2  1  ABC_tran  ABC transporter
      2e-08   34.4   0.0    2.4e-08   34.2   0.0    1.3  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00045   19.7   0.0    0.00055   19.4   0.0    1.1  1  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.11   11.2   0.1       0.14   10.8   0.1    1.1  1  AAA_13    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.2e-18   5.3e-15      39     137 .]       8     116 ..       1     116 [. 0.91

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.2e-18
                                       EEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  39 eGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren.............esdeeiekalsklglkelkdt 100
                                        G++++ g++++e++l+++r+++g+++q+  +qlf    +re              e d+++++al+ +gl++l+ +
  gi|386002962|ref|YP_005921261.1|   8 DGTVRILGRKVEEESLPWVRSRVGMVFQDpdDQLFMPN-LREDvafgprnlgraeaEVDRDVSRALEAVGLQGLEGK 83 
                                       69***************************665555544.677799*********9999999************9999 PP

                                       GESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 101 vvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             ++LS Gqk+r ala +l  +p++l++DEpt+
  gi|386002962|ref|YP_005921261.1|  84 AP----HHLSFGQKKRAALASVLSMRPEVLVMDEPTS 116
                                       98....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   5.4e-12   2.4e-08     234     301 ..      85     149 ..      32     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.4e-12
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                       +++lS G+k+ +al++ l  ++    +l+ DEp ++L+Pk  r+++ l+++l + g+ +i +TH+  +
  gi|386002962|ref|YP_005921261.1|  85 PHHLSFGQKKRAALASVLSMRP---EVLVMDEPTSNLDPKSKRTVVSLIRDLCDSGTTIITATHDVNI 149
                                       6899*******66666666666...9***********************555555*********9877 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-07   0.00055      76     204 ..      27     152 ..       5     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                                       EEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  76 kaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfA 152
                                       + +v ++f+++d++l + + +  +     + g+ e ++++   +  e   l   +g  ++ LS G+k+ +ala +++
  gi|386002962|ref|YP_005921261.1|  27 RSRVGMVFQDPDDQLFMPNLREDVAFGPRNLGRAEAEVDRDVSRALEAVGLQGLEGKAPHHLSFGQKKRAALASVLS 103
                                       567777777777777777777777777777777777788777777777777777788888************98865 PP

                                       HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 153 iqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                          ++p+   ++De  ++LD k  + v++l++   ++ + +i  +++ ++++ 
  gi|386002962|ref|YP_005921261.1| 104 ---MRPEV-LVMDEPTSNLDPKSKRTVVSLIRDLCDSgTTIITATHDVNIVTL 152
                                       ...67775.58*********************999883455555666666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.2e-05      0.14     527     574 ..     106     150 ..      97     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                            AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                        ++ v+D P S LD +s   v+sli++ +   ++   ++  TH ++  
  gi|386002962|ref|YP_005921261.1| 106 PEVLVMDEPTSNLDPKSKRTVVSLIRDLC---DSGTTIITATHDVNIV 150
                                       6899*************************...99999******99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1557.50
//
Query:       gi|386002963|ref|YP_005921262.1|  [L=259]
Description: Cobalt ABC transporter, permease protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-34  117.7   9.8      6e-34  117.6   9.3    1.3  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
        4.8    6.8  12.0        8.4    6.0  11.9    1.5  1  Wzy_C     O-Antigen ligase


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   9.3   6.7e-38     6e-34       3     212 ..      14     220 ..      13     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 6.7e-38
                                       CCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE..... CS
                              CbiQ   3 svlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlitt 78 
                                       s++hr+dpr k++ ++ l++ +v++ ++ ++l+  al +++ll + lp r  a+ +++p +f+l+ + il f   t 
  gi|386002963|ref|YP_005921262.1|  14 SPIHRWDPRAKVASILVLIFSVVMVESVRVALLGLALSMAVLLASRLPlRDVARRARWPVIFILPIFFILPF---TG 87 
                                       789************************9988776666555555555556***********************...45 PP

                                       ..EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHH CS
                              CbiQ  79 egefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLle 155
                                        ge ++a+   +++  +Gll g l++ R +++++l+  l++T p++  +++l+ l+ P+++  i+l +yR++flL e
  gi|386002963|ref|YP_005921262.1|  88 GGERTVAVSA-VDLSLDGLLLGSLILARGVSAVLLAYPLFATSPFNITVQALRGLRFPEVVLQIFLFTYRYLFLLSE 163
                                       5555555555.78*****************99999999*************************************** PP

                                       HHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.. CS
                              CbiQ 156 evqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg.s 212
                                       e+++i ++ ++  + +++ +r  ++ +g+++++lf+r+++r+er++ Am +RGY+g  
  gi|386002963|ref|YP_005921262.1| 164 EMRSIEKSLASKSFAKRTDLRT-AKVIGTALGMLFVRSYERSERIYRAMVSRGYDGaL 220
                                       ****************888887.********************************944 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.9   0.00094       8.4       3      59 ..      29     126 ..      27     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00094
                             Wzy_C   3 lllsllalflstsRsgiigllvalivlliifykrri..pfllllgilvgvilliilfv................... 58 
                                       l+l++ ++++   R++++gl++ + vll+ ++  r   +++++++i+++ i++i++f+                   
  gi|386002963|ref|YP_005921262.1|  29 LVLIFSVVMVESVRVALLGLALSMAVLLASRLPLRDvaRRARWPVIFILPIFFILPFTgggertvavsavdlsldgl 105
                                       799*****************9999999999998888999***************99986666666666666665555 PP

                             Wzy_C  59 ....................l 59 
                                                           +
  gi|386002963|ref|YP_005921262.1| 106 llgslilargvsavllayplF 126
                                       555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2003.05
//
Query:       gi|386002964|ref|YP_005921263.1|  [L=138]
Description: hypothetical protein Mhar_2289 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0019   18.2   0.0     0.0026   17.8   0.0    1.2  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
  ------ inclusion threshold ------
      0.023   14.9   0.7       0.03   14.6   0.7    1.3  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain


Domain annotation for each model (and alignments):
>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.9e-07    0.0026      23      66 ..      40      79 ..      29     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-07
                              bMG3 23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkeg 66
                                      d+g P+ g++V+ +d + ++++egtTDa Gv  f ++  +    
  gi|386002964|ref|YP_005921263.1| 40 DDGTPAGGVAVQAYDGD-DLVGEGTTDAGGVFVFRPEGRK---V 79
                                      89************975.79**************998444...3 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   3.3e-06      0.03       5      43 ..      36      73 ..      32     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                   CarboxypepD_reg  5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlr 43
                                      +V   +g+p  g++V ++ ++++ v + ttda G f +r
  gi|386002964|ref|YP_005921263.1| 36 SVFYDDGTPAGGVAVQAY-DGDDLVGEGTTDAGGVFVFR 73
                                      577789************.48999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1064.91
//
Query:       gi|386002965|ref|YP_005921264.1|  [L=136]
Description: hypothetical protein Mhar_2288 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00063   20.2   0.0    0.00085   19.8   0.0    1.2  1  DUF4198          Domain of unknown function (DUF4198)
     0.0095   16.2   0.1      0.014   15.7   0.1    1.2  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.047   13.7   0.0    1.3  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
      0.064   13.3   0.0      0.097   12.7   0.0    1.2  1  Big_1            Bacterial Ig-like domain (group 1)
      0.084   13.6   0.0       0.11   13.2   0.0    1.2  1  TTR-52           Transthyretin-like family
       0.12   12.8   0.0       0.17   12.3   0.0    1.2  1  Pollen_Ole_e_I   Pollen proteins Ole e I like
       0.13   13.0   0.0       0.17   12.6   0.0    1.1  1  Transthyretin    HIUase/Transthyretin family


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.3e-07   0.00085     158     203 ..      40      85 ..      22      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.3e-07
                           DUF4198 158 lldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtftlpkaG 203
                                       + dG+P+++a++++ + + +  ++ d +++  tda+G+ ++tlp +G
  gi|386002965|ref|YP_005921264.1|  40 YDDGEPAKNADISIYRLN-GTTQDYDLYEAgVTDAQGIYKVTLPGKG 85 
                                       559**********98887.67888888888**************998 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.4e-06     0.014      10      72 ..      42     109 ..      38     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-06
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgt.....vastttdadGafrlrglpp...gtysvtvsapGyatatreevtltag 72 
                                       +g+p ++a +++++ +++t         +tda+G ++++ lp    g+ +  +s +G  +  +  +t++a+
  gi|386002965|ref|YP_005921264.1|  42 DGEPAKNADISIYRLNGTTqdydlYEAGVTDAQGIYKVT-LPGkgtGEWRYAISGAGHSEEGY--LTVSAE 109
                                       89**********9965554233335778*********98.77777788888888888777775..677665 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 ?   13.7   0.0   1.8e-05     0.047      23      78 ..      41      99 ..      28     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                              bMG3 23 dsgkPvagaeVrlldkkgev.....laegtTDaqGvarfaallargkegaapylvsArkde 78
                                      d+g+P+++a+++++  +g +        g TDaqG+++++ + +    g+  y++s  + +
  gi|386002965|ref|YP_005921264.1| 41 DDGEPAKNADISIYRLNGTTqdydlYEAGVTDAQGIYKVTLPGKG--TGEWRYAISGAGHS 99
                                      89************9888643333156789********9999554..33333333333333 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.097      17      53 ..      42      82 ..      33      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                             Big_1 17 ngnpvagatVtfsvsggals....assgtTdanGkatvtlt 53
                                      +g p ++a +++   +g++        g+Tda+G++ vtl 
  gi|386002965|ref|YP_005921264.1| 42 DGEPAKNADISIYRLNGTTQdydlYEAGVTDAQGIYKVTLP 82
                                      79999999999999999999999999*************95 PP

>> TTR-52  Transthyretin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05      0.11       8      44 ..      43      80 ..      41     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                      T-GGSS-EEEEEE.HHHHTS--EEEEEE--TTSEEEEE CS
                            TTR-52  8 gkpaknvkVkLwe.kdtldpddlldetkTdedGnFels 44
                                      g+pakn+ +++++ + t++  dl++   Td++G ++++
  gi|386002965|ref|YP_005921264.1| 43 GEPAKNADISIYRlNGTTQDYDLYEAGVTDAQGIYKVT 80
                                      89***********544558889999**********998 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 ?   12.3   0.0   6.6e-05      0.17      37      65 ..      57      85 ..      40      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                    Pollen_Ole_e_I 37 kkeeeevklsasaktdknGyFkvelpkek 65
                                      + +++++ l+++++td++G +kv+lp++ 
  gi|386002965|ref|YP_005921264.1| 57 NGTTQDYDLYEAGVTDAQGIYKVTLPGKG 85
                                      4688999******************9954 PP

>> Transthyretin  HIUase/Transthyretin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-05      0.17      10      57 ..      42      88 ..      36     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                                      TTEE-TS-EEEEEEECTTSSEEEEEEEEE--TTSCESSSSEEGCGB-S CS
                     Transthyretin 10 aGkpaagvevelekleeseeeaellaesttdadGrvkellaekeelea 57
                                       G+pa++ ++++++l+ ++++ +l + ++tda+G +k +l+ ++ + +
  gi|386002965|ref|YP_005921264.1| 42 DGEPAKNADISIYRLNGTTQDYDLYEAGVTDAQGIYKVTLP-GKGTGE 88
                                      69********************************9999988.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 967.61
//
Query:       gi|386002966|ref|YP_005921265.1|  [L=209]
Description: Cobalamin (Vitamin B12) biosynthesis CbiM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-49  168.0  19.5    2.6e-49  167.9  19.5    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9  19.5   1.5e-53   2.6e-49       1     207 []       3     197 ..       3     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 1.5e-53
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLl 77 
                                       Hi+dg+Lsp+vl+a++a+a++ll + lr +r e    ++p+++l++a++f+a+++++p+ g+ts+Hl++++la+iLl
  gi|386002966|ref|YP_005921265.1|   3 HISDGVLSPPVLAAGFALAGLLLFVTLRDVRAE----EIPKISLITAAVFVASLVHFPV-GPTSVHLVMNGLAGILL 74 
                                       *********************************....**********************.***************** PP

                              CbiM  78 GpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaal 154
                                       G   af++vav+l+lqa+lf++GGi+++G+N++nm+++++l+ + ++   +r+++s +r+++ + la+ ++v+ a+l
  gi|386002966|ref|YP_005921265.1|  75 G-KRAFVSVAVALTLQAVLFQHGGISVIGVNAVNMGLPALLAWK-IFE-GRRRLPSPRREVVFGGLAGGAAVLGATL 148
                                       *.************************************999999.777.56777999******************** PP

                              CbiM 155 lvalelalsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                       ++++el++ g++    +t+ +a++l+vh+p++++E+++ ++++ +l++v+pe+
  gi|386002966|ref|YP_005921265.1| 149 ILSAELLVLGEA----FTEIAALVLAVHIPIILIEAAVVGLAAGFLQAVKPEM 197
                                       *********996....***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1575.62
//
Query:       gi|386002967|ref|YP_005921266.1|  [L=260]
Description: hypothetical protein Mhar_2291 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-11   43.4   0.0    1.1e-10   42.2   0.0    1.5  1  DUF4198   Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   6.3e-15   1.1e-10      12     211 ..      29     218 ..      19     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 6.3e-15
                           DUF4198  12 stvvsggewvtvdlafghdpfeadheplkleklkvlapdgektdlg.kylstfdvallkpekegtyklaaakkpgdw 87 
                                       ++ vs+ + v++ + ++h + e++  + +l++ +v++p g ++ l+ ++++   +   +  ++g y l ++++p+++
  gi|386002967|ref|YP_005921266.1|  29 EE-VSEASDVNIWITYSH-DAEGE-TAPQLARAEVIGPAG-TEGLSlAERDGGLAGTVEVGDPGCYILDFEMEPTFF 101
                                       33.444459*********.99996.8888999********.555554333333333444455***********9966 PP

                           DUF4198  88 keygdpklakevpaeaaelkvvkysqyaktfvtvgkpse.twdkpvglglEivPlthpydlkageelevqvlldGkP 163
                                           dp+      +      +++  +   +++ vg++ + +++   g glEivP  +  +l  g+ ++ + l +G+ 
  gi|386002967|ref|YP_005921266.1| 102 ----DPA------WIGFSGAASFLPKAGRAVIPVGSAGDcAFS--SGEGLEIVPQGDMGALGLGDRFRAEALWNGEG 166
                                       ....556......777777778999999*******99552555..5***************9*************** PP

                           DUF4198 164 lag.aeveveyggt..ryrdapdeikv.ktdadGvvtftlpkaGlwlleaeh 211
                                       l g     v++  +    + ++ + +v  t +dG ++f l+++Glw+l+ e 
  gi|386002967|ref|YP_005921266.1| 167 LGGdYAAMVVKSPQdvLTVLHASDSEVeGTTSDGTIEFDLSSPGLWVLSFEA 218
                                       **854444555444674444444555569*******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1561.61
//
Query:       gi|386002968|ref|YP_005921267.1|  [L=273]
Description: hypothetical protein Mhar_2292 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-16   59.6   2.4    5.3e-16   59.6   2.4    1.4  1  DUF4198   Domain of unknown function (DUF4198)
  ------ inclusion threshold ------
       0.13   12.9   1.1       0.84   10.3   0.5    2.5  3  YtkA      YtkA-like


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   2.4   5.9e-20   5.3e-16       1     210 [.      24     230 ..      24     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 5.9e-20
                           DUF4198   1 aqAHelwllpsstvvsggewvtvdlafghdpfeadheplk.leklkvlapdgektdlg.........kylstfdval 67 
                                       a++H lw++  ++v + g++ +v + +gh    a+   ++ +++ ++l+p ge+ dl              ++ ++ 
  gi|386002968|ref|YP_005921267.1|  24 ASGHALWVES-KDVAEAGATQPVYFFYGHAGSVAG-FSVPlMDAAYLLTPAGERLDLAmetgdwvpgYGWVPYGYND 98 
                                       789****776.55666667**********776664.777767788*******9999985444444432222222222 PP

                           DUF4198  68 lkpekegtyklaaakkpgdwkeygdpklakevpaeaae.lkvvkysqyaktfvtvgkp.setwdkpvglglEivPlt 142
                                        + +++g y++a+a++p ++      +      +  ++       ++ya  ++ +g++ +e w +  g +lEivP +
  gi|386002968|ref|YP_005921267.1|  99 VALSTPGDYVFAVARSPSVYDP----G------WGGTQaSNPRLGYSYATMVIHAGDEgKESWEA--GVPLEIVPEK 163
                                       2334455555555555555544....2......44444445788999*********995557777..********** PP

                           DUF4198 143 hpydlkageelevqvlldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtftlpkaGlwlleae 210
                                        py++   ++++++ l +G+P+  a+ ++ y    + +  d++++ ++++ G +t+ +++aG w + a+
  gi|386002968|ref|YP_005921267.1| 164 APYEIMNKDNVTFTALWNGEPVN-ATFTAYYWTW-DAHGGDAVQTgSAGEGGSFTVSFTQAGPWQVMAS 230
                                       ***********************.****999863.55555555559******************99887 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1     1e+04      73      85 ..      99     111 ..      96     112 .. 0.69
   2 ?   10.3   0.5   9.4e-05      0.84       9      84 ..     157     228 ..     149     230 .. 0.66
   3 ?    0.4   0.0      0.11     1e+03      71      84 ..     229     242 ..     228     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                              YtkA  73 vnfsmeGtWqvql 85 
                                       v +s +G++++ +
  gi|386002968|ref|YP_005921267.1|  99 VALSTPGDYVFAV 111
                                       5677788887655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.4e-05
                              YtkA   9 velvspeep..kagentivvtvtqggkpVedadvkvefwm.pameGmeemttkvelkesedGvYeaevnfsmeGtWq 82 
                                        e+v+++ p    +++ +++t   +g+pV+ a+ ++  w  +a++G++     ++ +  e+G  +++v f+++G Wq
  gi|386002968|ref|YP_005921267.1| 157 LEIVPEKAPyeIMNKDNVTFTALWNGEPVN-ATFTAYYWTwDAHGGDA----VQTGSAGEGG--SFTVSFTQAGPWQ 226
                                       5677777776566666788898899*****.55444444404444444....3333434455..7899********* PP

                              YtkA  83 vq 84 
                                       v 
  gi|386002968|ref|YP_005921267.1| 227 VM 228
                                       97 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.11
                              YtkA  71 aevnfsmeGtWqvq 84 
                                       a ++++++G+W+ +
  gi|386002968|ref|YP_005921267.1| 229 ASIDLNEPGKWTAT 242
                                       568999*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1703.94
//
Query:       gi|386002969|ref|YP_005921268.1|  [L=265]
Description: hypothetical protein Mhar_2293 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-23   83.7   1.3    2.9e-23   83.3   1.3    1.1  1  DUF4198   Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   1.3   1.6e-27   2.9e-23       1     212 [.      20     227 ..      20     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.6e-27
                           DUF4198   1 aqAHelwllpsstvvsggewvtvdlafghdpfeadheplk.leklkvlapdgektdlgkylstfdvallkpekegty 76 
                                       a+AH+lw++++++v  g+   +v   fgh p  +++  ++ ++++++++p ge+ dl  +++t          +g+ 
  gi|386002969|ref|YP_005921268.1|  20 AAAHSLWVEAEDAVEVGE-VKDVYSLFGH-PGSSAGMYVPlMDAFYLVSPAGERLDLATEEGTWL--------PGFG 86 
                                       79**********988887.99********.6655456666789*********9999995555553........4444 PP

                           DUF4198  77 klaaakk......pgdwkeygdpk.lakevpaeaaelkvvkysqyaktfvtvgkpse.twdkpvglglEivPlthpy 145
                                       ++ + ++      pgd++    ++    +  ++  e + + +  yak+++++g++ e +wd   g +lE    + py
  gi|386002969|ref|YP_005921268.1|  87 RIGYLSSkaafrwPGDYVLASVRApGVYDSGWHGGESSPMLVKDYAKAVISAGEGGEkAWDG--GFPLEVQFEAAPY 161
                                       44442222333346666664444422222239999********************5559***..************* PP

                           DUF4198 146 dlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaehe 212
                                       + kag++++ + +++G+P+a a  +++y       +p+++  ++++dG +++ ++kaG w++e+e++
  gi|386002969|ref|YP_005921268.1| 162 EAKAGDSFSAVAVFNGEPVA-ANYTAWYWTVDAHSSPEAQRGTAGDDGSFSVLFEKAGPWVIEVETT 227
                                       ********************.*******98755555554444**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1899.63
//
Query:       gi|386002970|ref|YP_005921269.1|  [L=746]
Description: hypothetical protein Mhar_2294 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-37  128.1   0.2    7.1e-37  127.6   0.2    1.2  1  DUF362    Domain of unknown function (DUF362)
  ------ inclusion threshold ------
      0.015   15.6   2.4      0.015   15.6   2.4    4.2  3  YwiC      YwiC-like protein


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   0.2   7.9e-41   7.1e-37       1     202 [.     168     363 ..     168     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 7.9e-41
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                            DUF362   1 VaiKpNlgeagnpe..gatthpevvravvellkeagagkiivgdspglyvsrgkahrevaeeagydelae..gadia 73 
                                       V+iK+N++  g pe  g +t+pevv +vv++++ ag g+ +++d+ ++++    +   va+++g+ + ae  g+ ++
  gi|386002970|ref|YP_005921269.1| 168 VLIKVNIC-GGVPEvkGTFTSPEVVGEVVDMVRGAG-GEAVICDADMIWN----KFWTVAAASGWAAWAEekGVPLV 238
                                       9*******.6777789999*************8888.99********864....47899********8888788876 PP

                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362  74 dglegedevvvpvkgk.hlkkelkiakavleaDviInlpklKgHalagvtgalKnlfGcisgsgkaeiHskrdsekf 149
                                       +  e++ +   ++ g+ +     +++++++eaDviI++p +K+H l+gvt+++Kn++G++++ +ka++H    + k+
  gi|386002970|ref|YP_005921269.1| 239 NLSETRIVG-FDF-GEgSAIGVDHVSRDLVEADVIISIPTMKTHLLTGVTLGMKNMYGTFPEVDKARYH----KMKI 309
                                       666544222.234.3335566699*********************************************....567* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                            DUF362 150 aekiadlakalkpdlnvvdgikamegegpsggs.kelglvlaStDpvalDaaaa 202
                                       +e i ++++a+ p+l++vdg ++ e  gp ++  ++ ++++aS+D+v+ D++a 
  gi|386002970|ref|YP_005921269.1| 310 EEVIYEVNRAFTPNLVIVDGSIGNEAIGPLSSRpIDFQTIIASNDVVCADSIAS 363
                                       **********99*****************9999*****************9985 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.8      0.33     3e+03      58     120 ..      30      94 ..      11     116 .. 0.62
   2 ?   15.6   2.4   1.7e-06     0.015      51     121 ..     475     551 ..     426     554 .. 0.88
   3 ?   -6.0   9.0         2   1.8e+04      62      98 ..     639     673 ..     571     699 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.33
                              YwiC  58 lkplliYgavallllllalllqpallwwallflplv..avavyeakrkreRsllndlatvaasal 120
                                       +k ++  g++ + +++  ll++  + ++ +lf  +   a  +  ++ k  R+++  +a+v+ + l
  gi|386002970|ref|YP_005921269.1|  30 AKIVVGVGLLLVFIIFSSLLYADVFRAVFPLFPEATgsAFMLHSSWTKVTREMVPTAAVVILFLL 94 
                                       55555555555555555555555555555444333311444455677777777766666655543 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.7e-06
                              YwiC  51 a......rrrarylkplliYgavallllllalllqpallwwallflplvavavyeakrkreRsllndlatvaasall 121
                                       +      r r+r+  +ll+  a a+++++++  +  +  ++ l fl+++ava+++a+r + R+ll+ ++++aa++++
  gi|386002970|ref|YP_005921269.1| 475 QgdteadRSRRRINVFLLLLLAEAAIIGFFLDGYLMSSFLFNLNFLVAIAVAILAAARMKTRHLLALILSTAAVMIV 551
                                       24444447889999999999999999**999999999************************************9987 PP

  == domain 3  score: -6.0 bits;  conditional E-value: 2
                              YwiC  62 liYgavallllllalllqpallwwallflplvavavy 98 
                                        +Y+a+ l  l l+  l++ + w a+l+++ va+  y
  gi|386002970|ref|YP_005921269.1| 639 GLYAALIL--LGLLTSLRATIAWNAALVVVSVALGGY 673
                                       22322222..222333444455666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4762.23
//
Query:       gi|386002971|ref|YP_005921270.1|  [L=272]
Description: Imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-78  261.6   0.4    6.3e-78  261.4   0.4    1.0  1  His_biosynth  Histidine biosynthesis protein
    4.6e-06   25.9   0.1      0.065   12.3   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.5e-05   24.4   4.0       0.02   14.2   0.9    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
    0.00013   21.1   2.5      0.059   12.4   0.1    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0012   18.2   1.2        1.2    8.4   0.0    2.5  2  TMP-TENI      Thiamine monophosphate synthase
     0.0015   18.0   8.3      0.049   13.0   1.9    2.1  2  NMO           Nitronate monooxygenase
     0.0021   17.5   0.5       0.17   11.3   0.2    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
     0.0047   16.2   0.4       0.15   11.2   0.1    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
        1.3    8.5   4.0         11    5.5   0.5    2.7  2  DeoC          DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.4   0.4   3.1e-81   6.3e-78       1     229 []       6     255 ..       6     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 3.1e-81
                                       EEEEEEEE..ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSE CS
                      His_biosynth   1 riipalDl..kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfip 75 
                                       riip+lD+   dG+   +vkG++f +l+ +gdpvela ry+++gadel+++D++a++egr+++ ++ +++a+ev++p
  gi|386002971|ref|YP_005921270.1|   6 RIIPCLDVkvVDGRPS-VVKGVKFVDLKRQGDPVELALRYDADGADELVFLDITASAEGRRTMVEVARRTAREVSVP 81 
                                       8******955589743.46********************************************************** PP

                                       EEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C............. CS
                      His_biosynth  76 vqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......g............. 133
                                       + vGGGI+s+e + e+l+agadkv i+taavk+p+li+++a ++gs++i+vaiDa r      g             
  gi|386002971|ref|YP_005921270.1|  82 FAVGGGINSIEGIVEILDAGADKVGINTAAVKDPDLIRRAAAAVGSDRITVAIDAVRnpvpkeGselfpledgssaw 158
                                       ********************************************************9666655177777888899*9 PP

                                       EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHH CS
                      His_biosynth 134 ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelk 210
                                       ++v+i g+r+  gldav +a+++eelgage+llt++drdGt +G+d++lt+++a+av ipviasGG++++e++ +++
  gi|386002971|ref|YP_005921270.1| 159 FEVVILGGRKAIGLDAVAWARRVEELGAGEVLLTSMDRDGTSDGYDIPLTRAVASAVGIPVIASGGAKNPEHMLQAF 235
                                       ***************************************************************************** PP

                                       .HTTCSEEEESHHHHTTSS- CS
                      His_biosynth 211 .segvdavivgsalyegelt 229
                                        ++g+da++++ +++ ge+t
  gi|386002971|ref|YP_005921270.1| 236 rEAGADAALAAGIFHRGEYT 255
                                       78888************986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   3.3e-05     0.065     180     228 ..      76     124 ..      20     139 .. 0.89
   2 !   11.8   0.0   4.7e-05     0.093     140     212 ..     174     245 ..     169     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                       HH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHH CS
                               Dus 180 qavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.sta 228
                                       ++vs+p+ + G+I ++e + +il+  Gad v i  +a ++P l+++  +a
  gi|386002971|ref|YP_005921270.1|  76 REVSVPFAVGGGINSIEGIVEILDA-GADKVGINTAAVKDPDLIRRaAAA 124
                                       6899********************9.*****************9974444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHCT-SEEEEESSECCCTT-C..G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                               Dus 140 alelakiveaaGaqaltvHgRtraqnyeg..tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                       a+  a++ve+ Ga ++ +   t +++       d+   ++v  av ipvia G+ k++e + ++ +e Gad+ ++
  gi|386002971|ref|YP_005921270.1| 174 AVAWARRVEELGAGEVLL---TSMDRDGTsdGYDIPLTRAVASAVGIPVIASGGAKNPEHMLQAFREAGADAALA 245
                                       566777777777777777...333333222266777789999*****************************9875 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.9     1e-05      0.02     160     219 ..      63     123 ..      54     144 .. 0.80
   2 !   11.2   0.1   8.3e-05      0.17     134     205 ..     175     247 ..     170     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                                       --S-HHHH.HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHH CS
                              ThiG 160 Gllnkeal.kiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamAra 219
                                       G +++  + +   +e++vP  v  Gi s + +++ ++ Gad v +nta  +  d ++ A+a
  gi|386002971|ref|YP_005921270.1|  63 GRRTMVEVaRRTAREVSVPFAVGGGINSIEGIVEILDAGADKVGINTAAVKDPDLIRRAAA 123
                                       5555444414456788********************************9999999888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHTT-SEBE.EBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH.HTT-SEEEESH CS
                              ThiG 134 lvlarrleevGcaavm.PlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqam.elGadavllnt 205
                                       +  arr+ee+G+  v+       G++ G   +   + + + + +Pvi   G  +p++  qa+ e Gada l + 
  gi|386002971|ref|YP_005921270.1| 175 VAWARRVEELGAGEVLlTSMDRDGTSDGYDIPL-TRAVASAVGIPVIASGGAKNPEHMLQAFrEAGADAALAAG 247
                                       55799******9766515556789999988775.58899999******************98699****99875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2   0.00031      0.62     133     179 ..      65     112 ..      37     148 .. 0.57
   2 !   12.4   0.1     3e-05     0.059     200     239 ..     209     249 ..     184     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHTTTSEE...EEEEE-SHHHHHHHHHTT-SEEEE-SS-STT CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 133 leavkeikkkveevev...iaGnvataegakaLieagadavkvGiGpGsi 179
                                        ++v+  +++++ev+v   ++G + + eg+ ++++agad  kvGi + ++
  gi|386002971|ref|YP_005921270.1|  65 RTMVEVARRTAREVSVpfaVGGGINSIEGIVEILDAGAD--KVGINTAAV 112
                                       223333333333222222267777777777777777777..555555555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3e-05
                                       HHHHCTCT-EEEEES---SHHHHHHHHH.TT-SEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             IMPDH 200 aeaakkagvpviaDGGikysgdivkAla.aGadavmlGsll 239
                                        ++a+  g+pvia GG k+ +++ +A+  aGada +   ++
  gi|386002971|ref|YP_005921270.1| 209 RAVASAVGIPVIASGGAKNPEHMLQAFReAGADAALAAGIF 249
                                       5688999*******************954999998876665 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3   0.00077       1.5     135     176 ..      64     106 ..      35     111 .. 0.74
   2 !    8.4   0.0   0.00061       1.2     119     173 ..     183     241 ..     172     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00077
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGitl.envaevleagadgva 176
                                       +   +e ++++a+++++P+ + GGi+  e + e+l+agad v 
  gi|386002971|ref|YP_005921270.1|  64 RRTMVEVARRTAREVSVPFAVGGGINSiEGIVEILDAGADKVG 106
                                       45567889999**************964889********9985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00061
                          TMP-TENI 119 YigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGit..lenvaevleagad 173
                                        +g+G +  T+   d   +  ++ + +++a+a+ iPv+a GG +  ++ +++ +eagad
  gi|386002971|ref|YP_005921270.1| 183 ELGAGEVLLTSMDRDGtsDGYDIPLTRAVASAVGIPVIASGGAKnpEHMLQAFREAGAD 241
                                       578888888888777755667788899***************97323456666788887 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.5    0.0005         1     181     224 ..      67     110 ..      56     117 .. 0.84
   2 !   13.0   1.9   2.5e-05     0.049     145     220 ..     174     244 ..     166     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0005
                               NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                        +++  + +  v++P    GGi+  +g+  +L +GA  v i t+
  gi|386002971|ref|YP_005921270.1|  67 MVEVARRTAREVSVPFAVGGGINSIEGIVEILDAGADKVGINTA 110
                                       4556666677799**************************99997 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.5e-05
                               NMO 145 svkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgv.aaaLalGAsgvq 220
                                       +v  ar ve++Ga  + ++ ++  G      +     + L   v++av iPviA GG  + + + +a   +GA ++ 
  gi|386002971|ref|YP_005921270.1| 174 AVAWARRVEELGAGEVLLTSMDRDGTSD--GY----DIPLTRAVASAVGIPVIASGGAKNPEHMlQAFREAGADAAL 244
                                       6777889999999999999988877665..34....478999***************98877651555567888765 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   8.3e-05      0.17     127     167 ..      67     107 ..      65     112 .. 0.91
   2 ?    4.3   0.0     0.012        24     131     164 ..     208     242 ..     203     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                       + +v++++ +e+++p+  GG i++ e + e+l+aGa+ v  
  gi|386002971|ref|YP_005921270.1|  67 MVEVARRTAREVSVPFAVGGGINSIEGIVEILDAGADKVGI 107
                                       78999*******************************99865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                                       HCTSTTS...EEEEESS--SHHHHHHHC.TT.SSE CS
                      G3P_antiterm 131 ikeikkelkipiiaGGLietkedveeal.kaGaia 164
                                       ++++ +++ ip+ia+G  ++ e++ +a+ +aGa+a
  gi|386002971|ref|YP_005921270.1| 208 TRAVASAVGIPVIASGGAKNPEHMLQAFrEAGADA 242
                                       56788999**********99999887762578776 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   7.6e-05      0.15     232     279 ..      69     114 ..      62     124 .. 0.76
   2 ?    3.2   0.0     0.021        42     235     269 ..     209     242 ..     204     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                       +v r+ +++++  +p    GGi+s e  +e + aGA  v + ta v++
  gi|386002971|ref|YP_005921270.1|  69 EVARRTAREVS--VPFAVGGGINSIEGIVEILDAGADKVGINTAAVKD 114
                                       44444444444..7777889************************9654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.021
                                       HHHHHHTTT.S-EEEESS--SHHHHHHHH.HHTECE CS
                            DHO_dh 235 relykrlkkeipiIgvGGiesgeDaleki.eaGAsl 269
                                       r++++ +   ip+I++GG +  e  l  + eaGA +
  gi|386002971|ref|YP_005921270.1| 209 RAVASAVG--IPVIASGGAKNPEHMLQAFrEAGADA 242
                                       66677777..**********9999998763588865 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.023        46      83     120 ..      35      72 ..      24     148 .. 0.70
   2 ?    5.5   0.5    0.0056        11     188     225 ..     209     247 ..     198     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.023
                                       TCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHH CS
                              DeoC  83 vasveeakalGAdavkvvvyyradgseeeqqklaeikr 120
                                          ve a++++Ad  + +v++++  s e ++ + e++r
  gi|386002971|ref|YP_005921270.1|  35 GDPVELALRYDADGADELVFLDITASAEGRRTMVEVAR 72 
                                       56788899999999998888888777775555555544 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0056
                                       HHHHHCHSSTEEEEETTS.SHHHHHHHHHHHHH.HHTHCE CS
                              DeoC 188 kdvikaapvpgvvlsGGv.seedfletvedAvk.eagasG 225
                                       + v++a+ +p v+ sGG+ + e +l++ ++A + +a a+G
  gi|386002971|ref|YP_005921270.1| 209 RAVASAVGIP-VIASGGAkNPEHMLQAFREAGAdAALAAG 247
                                       567889999*.*******999*********9977666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1676.65
//
Query:       gi|386002972|ref|YP_005921271.1|  [L=1215]
Description: hypothetical protein Mhar_2296 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-28   98.3  16.8      7e-08   32.7   1.8    6.9  6  DUF11       Domain of unknown function DUF11
    0.00071   19.8   0.1        6.9    7.0   0.0    4.3  4  Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
     0.0016   18.6   0.5         13    6.0   0.0    4.8  5  bMG10       Bacterial Alpha-2-macroglobulin MG10 domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.099   5.9e+02      22      56 ..      53      88 ..      38     128 .. 0.73
   2 !    6.4   0.7    0.0018        11      17      46 ..     196     224 ..     181     325 .. 0.77
   3 !    9.3   0.8   0.00023       1.4       9      64 ..     324     388 ..     317     414 .. 0.72
   4 !   23.1   0.0   1.1e-08   6.5e-05       1      81 [.     421     506 ..     421     511 .. 0.84
   5 !   29.3   0.0   1.3e-10   7.8e-07      15      90 ..     947    1024 ..     932    1025 .. 0.87
   6 !   32.7   1.8   1.2e-11     7e-08      16      90 ..    1073    1146 ..    1059    1147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.099
                             DUF11 22 vtNtgpasangvvvtDtlPaglayvsvsas.qgtas 56
                                      + N  pa  ++v ++   P gl y s s s +g+a+
  gi|386002972|ref|YP_005921271.1| 53 ACNLPPAVVKNVSLSAEIPKGLVYKSESLSiSGAAD 88
                                      55778888999999999***********99633332 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                             DUF11  17 tytltvtNtgpasangvvvtDtlPaglayv 46 
                                       ++ +  t +++++a++v + D+lPag + v
  gi|386002972|ref|YP_005921271.1| 196 EVAVFHTSSSTSAAYDVLLADLLPAGAS-V 224
                                       56666688899999*********98866.3 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00023
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtl....P.aglayvsvsasqgtasaltsv....gsL 64 
                                        v+ Gd vty+  ++N+g a+++++ v D      P   +a+ ++ a+ gta+ ++ +    g L
  gi|386002972|ref|YP_005921271.1| 324 GVTVGDLVTYVYRLRNSGFANLTDLAVVDAFlgpiPlDKTALAPGEAALGTAERAVVSddfpGPL 388
                                       5899*************************988866466666677777766666655554444444 PP

  == domain 4  score: 23.1 bits;  conditional E-value: 1.1e-08
                             DUF11   1 ltKtvdksevrpGdtvtytltvtN...tgpasangvvvtDtlPaglayvsvsas..qgtasaltsvgsLeagesatl 72 
                                       ++K  dk+ +  G+ v+yt+t  N    +p+s +++vv+D+    +++v vs +  +   +  + +++L+ag +  +
  gi|386002972|ref|YP_005921271.1| 421 IVKRADKKSAERGELVNYTITIANgavDSPVSPTDLVVEDVFSRPVEIVAVSPKpvSDHPHLVWAFKELKAGDREEI 497
                                       6899********************554477778******************999433333444444*********** PP

                             DUF11  73 sftvrvtrt 81 
                                       ++t+rv+ +
  gi|386002972|ref|YP_005921271.1| 498 KITIRVPDE 506
                                       *****9876 PP

  == domain 5  score: 29.3 bits;  conditional E-value: 1.3e-10
                             DUF11   15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrtaasga 86  
                                          +yt+   N g ++++ + v+D+ P+g +++ +s +   ++++sa+++ + L+ g+ a +s+++ vtr a ++ 
  gi|386002972|ref|YP_005921271.1|  947 VADYTIRIENDGSRALAPILVRDLFPPGATFIDSSLRptaSAAGSANWTLTHLAIGGVAEISLRLDVTRFAGEE- 1020
                                        679**********************************8777777888888******************998877. PP

                             DUF11   87 ltnv 90  
                                        +tn+
  gi|386002972|ref|YP_005921271.1| 1021 MTNR 1024
                                        6665 PP

  == domain 6  score: 32.7 bits;  conditional E-value: 1.2e-11
                             DUF11   16 vtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv...gsLeagesatlsftvrvtrtaasgal 87  
                                        v yt++v Nt +a++  ++vtD lP+g+a+  +s   ++ +  + v   +s+++ge+ t++f++ ++  ++   +
  gi|386002972|ref|YP_005921271.1| 1073 VLYTVVVENTAAATR-AATVTDYLPQGMALLASSLPVASQEDGVVVwvlPSMAPGEKVTIEFSALAPGLGR---Y 1143
                                        67*************.********************6666665555778***************9998888...7 PP

                             DUF11   88 tnv 90  
                                        tnv
  gi|386002972|ref|YP_005921271.1| 1144 TNV 1146
                                        776 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.23   1.3e+03      17      72 ..     223     289 ..     219     294 .. 0.55
   2 ?    1.5   0.0     0.064   3.8e+02      49      88 ..     462     502 ..     437     504 .. 0.65
   3 !    7.0   0.0    0.0012       6.9      27      86 ..     949    1008 ..     941    1012 .. 0.92
   4 !    4.5   0.0    0.0072        43      44      85 ..    1090    1131 ..    1063    1135 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.23
                        Chlam_OMP6  17 avpeyatvgsp.ypieitavgkk...dcvdvvitqqlpcevef....vrsdpa..stpta.dgklvw 72 
                                       +v  + tv  p +   ++++g     dcvd+  t   p+ v +      sd +  s p+a  g l w
  gi|386002972|ref|YP_005921271.1| 223 SVSGFVTVAGPaWKSAVVSTGPTvsfDCVDLAWTAASPVLVRYeaasFASDESgsSGPAAaGGTLAW 289
                                       566667776552455566666433339****999999986554111133443211344431455666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.064
                        Chlam_OMP6  49 lpcevefvrsdpastptad.gklvwkidrlgqg..ekskitvw 88 
                                       +   ve+v   p   p +d  +lvw    l  g  e  kit+ 
  gi|386002972|ref|YP_005921271.1| 462 FSRPVEIVAVSPK--PVSDhPHLVWAFKELKAGdrEEIKITIR 502
                                       5455566655553..4444158****99987661155667765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0012
                        Chlam_OMP6   27 pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskit 86  
                                         y i i   g +    +++ + +p  + f+ s    t +a g   w++  l  g  + i+
  gi|386002972|ref|YP_005921271.1|  949 DYTIRIENDGSRALAPILVRDLFPPGATFIDSSLRPTASAAGSANWTLTHLAIGGVAEIS 1008
                                        699************************************************999887775 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0072
                        Chlam_OMP6   44 vitqqlpcevefvrsdpastptadgklvwkidrlgqgekski 85  
                                         +t+ lp  + ++ s    +   dg +vw +  +  gek  i
  gi|386002972|ref|YP_005921271.1| 1090 TVTDYLPQGMALLASSLPVASQEDGVVVWVLPSMAPGEKVTI 1131
                                        5899999999999999888999*****************987 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.021   1.3e+02      36      56 ..     204     224 ..     190     236 .. 0.80
   2 ?   -3.5   0.0       1.8   1.1e+04      21      36 ..     427     443 ..     419     449 .. 0.75
   3 ?    2.8   0.0     0.022   1.3e+02      21      44 ..     481     510 ..     463     535 .. 0.82
   4 !    6.0   0.0    0.0022        13      28      74 ..     949     995 ..     915    1024 .. 0.81
   5 ?   -0.3   0.1      0.19   1.1e+03      31      68 ..    1075    1113 ..    1060    1152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                             bMG10  36 ttprdleyvaledplPAGlep 56 
                                       ++ ++ ++v+l d lPAG+ +
  gi|386002972|ref|YP_005921271.1| 204 SSTSAAYDVLLADLLPAGASV 224
                                       4566889***********876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                             bMG10  21 a.klkvGdkvrvrltvt 36 
                                       + ++++G++v  ++t+ 
  gi|386002972|ref|YP_005921271.1| 427 KkSAERGELVNYTITIA 443
                                       227999*****999997 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.022
                             bMG10  21 a......klkvGdkvrvrltvttprdleyv 44 
                                              +lk+Gd+ ++++t+++p++ ++ 
  gi|386002972|ref|YP_005921271.1| 481 HlvwafkELKAGDREEIKITIRVPDEQDFA 510
                                       24455658****************998875 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0022
                             bMG10  28 kvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewl 74 
                                        +++r++   +r+l  ++++d +P G++ +++sl+ + + a  ++w+
  gi|386002972|ref|YP_005921271.1| 949 DYTIRIENDGSRALAPILVRDLFPPGATFIDSSLRPTASAAGSANWT 995
                                       6788899999999*********************9888887777643 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.19
                             bMG10   31 vrltvt.tprdleyvaledplPAGlepvnpslgtesesa 68  
                                         ++ v+ t ++ +   + d+lP G+ ++ +sl  +s+++
  gi|386002972|ref|YP_005921271.1| 1075 YTVVVEnTAAATRAATVTDYLPQGMALLASSLPVASQED 1113
                                        445555455566888999999999999988887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.88u 0.33s 00:00:01.21 Elapsed: 00:00:00.65
# Mc/sec: 5652.24
//
Query:       gi|386002973|ref|YP_005921272.1|  [L=268]
Description: hypothetical protein Mhar_2297 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.019   15.6   0.2       0.18   12.5   0.1    2.4  2  Glyco_hydro_2  Glycosyl hydrolases family 2
      0.036   14.0   0.0      0.067   13.2   0.0    1.5  1  DUF3324        Protein of unknown function C-terminal (DUF332
       0.09   13.8   0.2       0.31   12.1   0.1    1.9  2  CopC           CopC domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_2  Glycosyl hydrolases family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.69   4.1e+03      18      45 ..     127     152 ..     110     169 .. 0.72
   2 ?   12.5   0.1   3.1e-05      0.18      11     107 ..     170     266 ..     156     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.69
                                       EEEEEEEEEEEECSSSSCEEEEEEEEET CS
                     Glyco_hydro_2  18 akvevevelendsdksvevtleteikda 45 
                                       a v++++    +++++++v + t i+ +
  gi|386002973|ref|YP_005921272.1| 127 ALVTIKT--APKESEKASVMIITAIQVP 152
                                       6677777..7777777777777777765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.1e-05
                                       EEETC.SEEEEEEEEEEEEECSSSSCEEEEEEEEETTSTEEEE....EEEEEEEESTT-EEEEEEEEEES--BBEC. CS
                     Glyco_hydro_2  11 dlsdd.ksakvevevelendsdksvevtleteikdaegkkvke....essvlslgngetksiklelevknpklWsp. 81 
                                       dls + ++++v+v+v+++n+++   +  + +++ d++g++v++    e++++ l  +++  ++ +++       ++ 
  gi|386002973|ref|YP_005921272.1| 170 DLSASmADGNVSVDVTFDNTGNVHYKPFVGANLLDEDGEVVASvapaETRRMIL--PTNSRLV-KMT----LVPDAv 239
                                       56667899***********************************76432222222..2222222.222....222334 PP

                                       CCB--EEEEEEE.EETTEEEEEEEEEE CS
                     Glyco_hydro_2  82 etPnLYtlkvel.dkdgkvidevstrf 107
                                        +P  Yt+++e+  +dg+v+d+ +t++
  gi|386002973|ref|YP_005921272.1| 240 LEPGTYTVEAEVtLDDGTVLDTAETTI 266
                                       79999*******99********99876 PP

>> DUF3324  Protein of unknown function C-terminal (DUF3324)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.067      11     128 ..     148     266 ..     138     268 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                           DUF3324  11 ayvvgvvlrenekkvkpkLklekvkpkqvngrnviqaklqNpqaailnklkveakvtkkgsk.kvlyksekenlqmA 86 
                                       a++v+++l+ ++++ +   ++ + ++++ +g+ ++ +++ N+ ++  + +     + ++g+    ++ +e+ ++ + 
  gi|386002973|ref|YP_005921272.1| 148 AIQVPILLTIKDSDLEMTGEISDLSASMADGNVSVDVTFDNTGNVHYKPFVGANLLDEDGEVvASVAPAETRRMILP 224
                                       6789999999999999999999********************99999888665555555553123556777888888 PP

                           DUF3324  87 PnSnfnfpislkgeelkaGtYtlkvtakskkkkwefekeFtI 128
                                        nS++     + +  l++GtYt++ +++ ++ +   + e tI
  gi|386002973|ref|YP_005921272.1| 225 TNSRLVKMTLVPDAVLEPGTYTVEAEVTLDDGTVLDTAETTI 266
                                       8***9999999***************9988777666655555 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.9   5.4e+03      37      37 ..      78      78 ..      32     129 .. 0.54
   2 ?   12.1   0.1   5.2e-05      0.31      20      82 ..     180     257 ..     170     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.9
                              CopC 37 v 37
                                      +
  gi|386002973|ref|YP_005921272.1| 78 L 78
                                      2 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.2e-05
                              CopC  20 eevtLtFsepvel.....skvkvtdpdgke...........evetvdaktveaelkvplp............elaaG 68 
                                        +v +tF+++ +        ++++d+dg+                            p +             l++G
  gi|386002973|ref|YP_005921272.1| 180 VSVDVTFDNTGNVhykpfVGANLLDEDGEVvasvapaetrrM-------------ILPTNsrlvkmtlvpdaVLEPG 243
                                       568888877776677888888999999966664433322221.............1111112334445577789*** PP

                              CopC  69 tYtVewrvvsaDGH 82 
                                       tYtVe +v+ +DG 
  gi|386002973|ref|YP_005921272.1| 244 TYTVEAEVTLDDGT 257
                                       ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1861.32
//
Query:       gi|386002974|ref|YP_005921273.1|  [L=301]
Description: Acylphosphatase, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-22   77.5   0.2    1.6e-21   76.5   0.2    1.6  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.043   13.2  18.3       0.02   14.3  11.2    2.3  2  DUF3552          Domain of unknown function (DUF3552)
       0.14   12.7  18.6         49    4.5  18.4    2.6  1  DUF16            Protein of unknown function DUF16
       0.51   10.4  14.2        2.3    8.3   6.2    2.3  2  DUF1664          Protein of unknown function (DUF1664)
        1.4    8.4   8.3        2.4    7.7   7.9    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
        3.2    8.1   8.2        3.2    8.1   0.2    2.7  2  DUF948           Bacterial protein of unknown function (DUF94
        9.6    7.0  19.4          5    7.9   1.4    3.9  2  PMC2NT           PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.2   6.2e-25   1.6e-21       3      84 ..      64     145 ..      62     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 6.2e-25
                   Acylphosphatase   3 llvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeee 79 
                                       +lv+GrVQ+vg+R  v  lA+e+g+ G+v Nl+dg+V++vaeg+ + +++f ++lk ++  ++v  veve  ++++e
  gi|386002974|ref|YP_005921273.1|  64 ILVSGRVQKVGYRSKVIALAQEMGIVGWVGNLPDGRVKVVAEGDAAVLDRFASALKVKNSLIEVAAVEVERHDATGE 140
                                       79*************************************************************************** PP

                   Acylphosphatase  80 fkdFe 84 
                                       f+dF+
  gi|386002974|ref|YP_005921273.1| 141 FDDFS 145
                                       ****7 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.1     0.024        62      91     138 ..     183     226 ..     176     228 .. 0.59
   2 ?   14.3  11.2     8e-06      0.02      70     131 ..     211     272 ..     202     293 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.024
                           DUF3552  91 eetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrq 138
                                       + +Ld++++ l+k++e++ + +       ++++++ ++ + ++ +q+q
  gi|386002974|ref|YP_005921273.1| 183 DRMLDKQDQMLDKQDETIAAIKGI----DSKMDRMLDKQDIMIDKQDQ 226
                                       456777777777777777665544....45555555555555555555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8e-06
                           DUF3552  70 ekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeelee 131
                                       ++ l ++   ++++++ l +++++Ld++++ l+k++  + ++++ l+++ q l++++e+  e
  gi|386002974|ref|YP_005921273.1| 211 DRMLDKQDIMIDKQDQMLDKQDQMLDKQDQMLDKQDMMIDKQDQMLDKQDQMLDKQDETTGE 272
                                       44455555556667777777777777777777777777777777777777777766665544 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  18.4     0.019        49      31      87 ..     216     272 ..     134     293 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                                       .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHH CS
                             DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlel 87 
                                         +  + k ++ +dk+++ ++k+ q  +kq+  i+++ +  ++q++ l+k+det   
  gi|386002974|ref|YP_005921273.1| 216 KQDIMIDKQDQMLDKQDQMLDKQDQMLDKQDMMIDKQDQMLDKQDQMLDKQDETTGE 272
                                       233334445555557777777777777777777777777777777777777777654 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.2    0.0009       2.3      29     102 ..     165     237 ..     162     244 .. 0.80
   2 ?    3.9   5.7      0.02        52      49     107 ..     233     292 ..     223     298 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0009
                           DUF1664  29 sdlmfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                        +l+ vT++++sd  +++ + l++  + + + +++  + i+ +d+k+d + + +  + ++ +++ ++ +++ ++
  gi|386002974|ref|YP_005921273.1| 165 KELIDVTRHGFSDLGQKMDRMLDKQDQ-MLDKQDETIAAIKGIDSKMDRMLDKQDIMIDKQDQMLDKQDQMLDK 237
                                       678889************999998655.5556677778899999999999999999888888888887777655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls.eigedvesvk 107
                                       q+ + ++++ + ++ + ++ d++ +k+d++ + + e++ ev  +r+d++ +++  +e ++
  gi|386002974|ref|YP_005921273.1| 233 QMLDKQDQMLDKQDMMIDKQDQMLDKQDQMLDKQDETTGEVRGLRSDMKgSFDMRLERIE 292
                                       344445666666677777777777788888888888888888888877623444555554 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.9   0.00093       2.4     156     235 ..     178     266 ..     156     298 .. 0.37

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00093
                      Exonuc_VII_L 156 lekaikrlleekkqrleklasrl.......kspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k.. 222
                                       l ++++r+l+++ q+l+k ++++       ++ +++l+++   +d+  + l++ +++ l+k+ + l++    + k  
  gi|386002974|ref|YP_005921273.1| 178 LGQKMDRMLDKQDQMLDKQDETIaaikgidSKMDRMLDKQDIMIDKQDQMLDK-QDQMLDKQDQMLDKQDMMIdKqd 253
                                       33444444444444444443333222222223333333333333333222222.33333333333333332221121 PP

                      Exonuc_VII_L 223 ekleekkerlkkl 235
                                       + l+++++ l+k+
  gi|386002974|ref|YP_005921273.1| 254 QMLDKQDQMLDKQ 266
                                       1122222222111 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2    0.0012       3.2      24      74 ..     164     214 ..     159     218 .. 0.85
   2 ?    1.6   6.0      0.13   3.3e+02      29      75 ..     197     243 ..     195     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplt 74 
                                       lk+++d +++   +l++++d +l++ +++l+k  e+ + +++   k+d++ 
  gi|386002974|ref|YP_005921273.1| 164 LKELIDVTRHGFSDLGQKMDRMLDKQDQMLDKQDETIAAIKGIDSKMDRML 214
                                       5778999999999**********************8888887777766665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                                       de+ a+i+++ +++d +l++ + +++k  ++l+   + l+k d++ +
  gi|386002974|ref|YP_005921273.1| 197 DETIAAIKGIDSKMDRMLDKQDIMIDKQDQMLDKQDQMLDKQDQMLD 243
                                       56777788888888888888888888888877777777777777655 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.4    0.0019         5      56      89 ..     160     195 ..     103     198 .. 0.78
   2 ?    0.2  10.8      0.47   1.2e+03      30      89 ..     207     265 ..     204     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                            PMC2NT  56 s.sklededdvee.kfksvvdvvDsllEkadtcLDe 89 
                                       s + l+++ dv++  f++++  +D +l+k d +LD+
  gi|386002974|ref|YP_005921273.1| 160 SaELLKELIDVTRhGFSDLGQKMDRMLDKQDQMLDK 195
                                       245667777788779********************7 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.47
                            PMC2NT  30 deqserllslinsllklaaskseisassklededdveekfksvvdvvDsllEkadtcLDe 89 
                                       d++ +r+l+  + +++ +++  +++++  l+++d++ +k ++++d  D++l+k d +LD+
  gi|386002974|ref|YP_005921273.1| 207 DSKMDRMLDKQDIMIDKQDQMLDKQDQ-MLDKQDQMLDKQDMMIDKQDQMLDKQDQMLDK 265
                                       555666666666666666666666553.66777777889999999999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1255  (0.0699983); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1865.81
//
Query:       gi|386002975|ref|YP_005921274.1|  [L=310]
Description: hypothetical protein Mhar_2299 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-19   69.1   0.0      5e-19   68.2   0.0    1.4  1  DUF333    Domain of unknown function (DUF333)


Domain annotation for each model (and alignments):
>> DUF333  Domain of unknown function (DUF333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   2.8e-23     5e-19       3      47 ..      57     102 ..      56     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.8e-23
                            DUF333   3 aNPAsvyCvkqGGkleiakdad.GgqvgyCqlpdGkrceEwaLyrg 47 
                                       +NPA+++Cv++G+++ei++d+  G+q+gyC++pd ++ce+wa++rg
  gi|386002975|ref|YP_005921274.1|  57 TNPAATFCVNKGYRHEIRTDPVtGNQIGYCVFPDASECEAWAFFRG 102
                                       7********************99**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1780.88
//
Query:       gi|386002976|ref|YP_005921275.1|  [L=560]
Description: Beta-lactamase domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-10   39.9   2.5    1.1e-08   35.4   2.5    2.5  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   2.5     6e-13   1.1e-08       4     162 ..      13     208 ..      10     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 6e-13
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTG..GGCTTHHCCEETCCEH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGgl..gglveatdvpvgavae 77 
                                       +++nsy++   +   LiD+G++  +++ +   +  l  +  ++  + lTH H+DH + l  g+l e  + + +av+e
  gi|386002976|ref|YP_005921275.1|  13 VSSNSYVLSARDQICLIDPGGDDGQMDRLVeVIGELWEERARPVLIYLTHVHVDHSFELsrGDLLEGLGGAAVAVQE 89 
                                       579******************988877543577888888899999************99443344444444444444 PP

                                       HHHCCHCHHHHHHHHHCCHH......................................TTCHCGCCEEEEETTTEEC CS
                       Lactamase_B  78 eapalfmeeaddaasrkgll......................................lagvsadkpdvdeeeldgn 116
                                       ++++ ++++    a+  + l                                        +   ++++v+++ + ++
  gi|386002976|ref|YP_005921275.1|  90 AGAVSLERGD--PAMTLSCLlgrevaprspevrllssadlaapgrrlielgrgaafeyETASFGIGDGVVLHRQRVE 164
                                       4433333333..333333336679**********************************999**************** PP

                                       CCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 117 aggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                       +gg+ al+v+++pgh+++++++++  g +lf GD+l+a + g  + 
  gi|386002976|ref|YP_005921275.1| 165 LGGGDALEVYHTPGHSPDSVCLRA--GELLFLGDLLFASNPGVAGI 208
                                       ******************998875..679********999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 3441.05
//
Query:       gi|386002977|ref|YP_005921276.1|  [L=120]
Description: Putative anti-sigma factor antagonist [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-16   60.0   0.0    1.9e-16   59.8   0.0    1.0  1  STAS      STAS domain
    5.9e-11   42.6   0.0    7.4e-11   42.2   0.0    1.1  1  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   2.1e-20   1.9e-16       9     117 .]      12     108 ..       6     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.1e-20
                                       TEEEEEEEEEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEE CS
                              STAS   9 gililrldgpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvl 85 
                                       ++ il   g +d+ ++e+++ +++  ++ +         +++++ +ls+v++i+ssG+r++   lk+l++ g++++l
  gi|386002977|ref|YP_005921276.1|  12 DVEILSPGGRLDARSSEEIRVRMEGLIDGG---------CRKMVANLSGVDYISSSGLRVMLASLKRLRKEGGDLLL 79 
                                       56799999*********************9.........8************************************* PP

                                       ES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                              STAS  86 vnikpevreklektgffdeveeeklfltvhdA 117
                                       ++++p+vre++e +gf + +   ++++  ++A
  gi|386002977|ref|YP_005921276.1|  80 AGLQPYVRETFEIAGFTQLF---EIYDREEEA 108
                                       ********************...999988887 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   8.3e-15   7.4e-11       5      79 ..      20      95 ..      16      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 8.3e-15
                            STAS_2  5 Geldldtaaelreqllealaag.aevvvDlsgvervDsaalalLlalartarargrrlvlrglppalrrlldlyGl 79
                                      G+ld+++ +e r + + ++  g +++v  lsgv ++ s++l++ la  +++r++g+ l l gl p +r++++++G+
  gi|386002977|ref|YP_005921276.1| 20 GRLDARSSEEIRVRMEGLIDGGcRKMVANLSGVDYISSSGLRVMLASLKRLRKEGGDLLLAGLQPYVRETFEIAGF 95
                                      9************************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 702.76
//
Query:       gi|386002978|ref|YP_005921277.1|  [L=457]
Description: hypothetical protein Mhar_2302 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-54  183.6   2.1    4.8e-54  183.2   0.7    1.8  2  SpoIIE           Stage II sporulation protein E (SpoIIE)
    4.1e-45  153.3  13.2    6.1e-45  152.8  13.2    1.3  1  5TM-5TMR_LYT     5TMR of 5TMR-LYT
  ------ inclusion threshold ------
        4.3    7.1   5.8        1.7    8.4   1.6    2.4  2  DUF3948          Protein of unknown function (DUF3948)
        6.3    6.8  14.1       0.72    9.8   9.6    1.8  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component


Domain annotation for each model (and alignments):
>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.39   1.7e+03      60     102 ..     151     192 ..     136     197 .. 0.69
   2 !  183.2   0.7   1.1e-57   4.8e-54       1     191 [.     262     452 ..     262     453 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.39
                                       TTCEEEEEEEETTTTEEEEEEESSSSEEEEETTSTEEEEE--S CS
                            SpoIIE  60 rfaTavlavydpstgkleyanaGhpppllvrpdggtklllast 102
                                       ++ T++l+  +p  + +++++a   p+++ ++ g   + l +t
  gi|386002978|ref|YP_005921277.1| 151 HMLTVLLLA-EPRPEAVTVVRAAAAPMIVSNAVGALIFALMTT 192
                                       444555554.888899999999988888887766666655555 PP

  == domain 2  score: 183.2 bits;  conditional E-value: 1.1e-57
                                       TTTEEEEEEEECSSSSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT.TTCEEEEEEEETTTTEEE CS
                            SpoIIE   1 pdgrlalvvgDvvGhGleAalimgllrsalrelataglepaevlkrlnralardleeeerfaTavlavydpstgkle 77 
                                       p+gr++++++Dv+G+G++Aal+m+l r ++r+ a+ + +  ev++r+n+++++d ++  +f+T+++a +d++ ++l+
  gi|386002978|ref|YP_005921277.1| 262 PGGRMGIAIADVSGKGVPAALFMVLSRAMVRASASGEPTAGEVARRANELISADANSG-MFVTLFFALLDEEARTLR 337
                                       689*******************************************************.****************** PP

                                       EEEESSSSEEEEETTSTEEEEE--SS--TTTSSST-EEEEEEE--TTEEEEEESCCCCSSSHHHHHHCCCHHCHHHH CS
                            SpoIIE  78 yanaGhpppllvrpdggtklllastglplGilpeadyetaelelepgdtlllyTDGvtEardsdgelfgkerllall 154
                                       y+naGh+ppll+r+ +g++ ll+++g+++G+l+ea++e+ e+el +gd+++lyTDGvtEa d  ge fg+erll l+
  gi|386002978|ref|YP_005921277.1| 338 YVNAGHNPPLLLRGGTGEVALLKTRGIAMGVLEEAEMEEGEVELSEGDVVVLYTDGVTEATDAAGEQFGVERLLLLA 414
                                       **************99************************************************************* PP

                                       CT.....HCCHHHHHHHHHHH.HTTSSSSS-EEEEEEE CS
                            SpoIIE 155 asaegesleelldalveelle.lgsgeleDDitllvlr 191
                                       +++++ ++++l++++  ++l+  ++++++DDitl+vl+
  gi|386002978|ref|YP_005921277.1| 415 KEHRSLPAAALVEEIAGAVLAfSEGEPQFDDITLVVLK 452
                                       *********************7777899********86 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.8  13.2   1.4e-48   6.1e-45       2     167 ..      30     192 ..      29     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 1.4e-48
                      5TM-5TMR_LYT   2 plfrkllsekrktlksklllglifglfsilgtytgieiegaiantRaigvvvaGllgGplvGliagliaglhRyllg 78 
                                       + f +l+ e r t+k+++++ lifg+fsi+gt +g+e++g++an+R +g v++Gl+gGp+vGl+agli+g +R+l+g
  gi|386002978|ref|YP_005921277.1|  30 ESFTELI-EGRLTRKNQAAMALIFGAFSIFGTVSGVEVAGVVANVRDLGPVMGGLVGGPVVGLGAGLIGGGYRLLQG 105
                                       5788999.9999***************************************************************** PP

                      5TM-5TMR_LYT  79 GftalacgistilagllaGlihrklkrrrkkltvlvalligllveilqmllilllakpfdqalalvktialPmilvn 155
                                       Gft  ac+++t+l+g laGl++   +r  + + v+ a+++++l e+l+ml +llla+p ++a+++v+ +a Pmi+ n
  gi|386002978|ref|YP_005921277.1| 106 GFTGPACSLATVLVGSLAGLVYLANRR--RFVGVGGAVVLTALFEALHMLTVLLLAEPRPEAVTVVRAAAAPMIVSN 180
                                       *********************877777..9*********************************************** PP

                      5TM-5TMR_LYT 156 slgtalflsilr 167
                                       ++g+++f+++++
  gi|386002978|ref|YP_005921277.1| 181 AVGALIFALMTT 192
                                       ********9986 PP

>> DUF3948  Protein of unknown function (DUF3948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.29   1.3e+03      14      24 ..     118     128 ..     115     130 .. 0.82
   2 ?    8.4   1.6   0.00039       1.7      14      27 ..     134     146 ..     129     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
                           DUF3948  14 fiGsasGAvvL 24 
                                       ++Gs+ G v L
  gi|386002978|ref|YP_005921277.1| 118 LVGSLAGLVYL 128
                                       89**9998766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00039
                           DUF3948  14 fiGsasGAvvLTaf 27 
                                       f+G  +GAvvLTa+
  gi|386002978|ref|YP_005921277.1| 134 FVG-VGGAVVLTAL 146
                                       666.59*******8 PP

>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   9.6   0.00016      0.72       5     165 ..      43     190 ..      39     197 .. 0.61
   2 ?   -2.8   0.1       1.2   5.4e+03       8      23 ..     274     289 ..     268     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                                       THHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHH CS
                   ECF-ribofla_trS   5 kkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftli 81 
                                       k+ +a+a++   + +++++  + +  ++    n+ d   ++ +l+ GpvvG+ +G+iG     l  g++  a    +
  gi|386002978|ref|YP_005921277.1|  43 KNQAAMALIFGAFSIFGTVSGVEVA-GV--VANVRDLGPVMGGLVGGPVVGLGAGLIGGGYRLLQGGFTGPACS--L 114
                                       5567777777777788887777775.55..99***************************988776667655544..9 PP

                                       HHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH............S-HHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS  82 ikgliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiy..sepaekvalqsipaniiqa 156
                                       +  l+G ++Gl+   +  + + +v    a+vl a++  +  + + +l+           e+ ++v ++ +p+ +++a
  gi|386002978|ref|YP_005921277.1| 115 ATVLVGSLAGLVYLAN--RRR-FVGVGGAVVLTALFEALHMLTVLLLA-------EprPEAVTVVRAAAAPMIVSNA 181
                                       999*******999888..333.22222223333333333332222222.......2112333344444444444444 PP

                                       HHHHHHHHH CS
                   ECF-ribofla_trS 157 vvgaiialp 165
                                       v  +i al+
  gi|386002978|ref|YP_005921277.1| 182 VGALIFALM 190
                                       433333333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS   8 vatailaAlvvvltlf 23 
                                          ++ aAl++vl++ 
  gi|386002978|ref|YP_005921277.1| 274 SGKGVPAALFMVLSRA 289
                                       5568889999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2841.22
//
Query:       gi|386002979|ref|YP_005921278.1|  [L=138]
Description: hypothetical protein Mhar_2303 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-16   60.1   0.1    2.3e-16   59.9   0.1    1.1  1  HATPase_c_2  Histidine kinase-like ATPase domain


Domain annotation for each model (and alignments):
>> 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 !   59.9   0.1   1.3e-20   2.3e-16       3     124 ..      11     130 ..       9     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.3e-20
                       HATPase_c_2   3 adpehvrtvrevaeavlrraglseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfd 79 
                                       ++ e+++ +re++ + ++ + l+ +++ ++ +av+Ea tN++ +         +++++++  ++ +v  +D+G +f+
  gi|386002979|ref|YP_005921278.1|  11 SRTESLAGIREFILSSTEGSALDRRERFRLMMAVDEAATNIIMYSGS----VGIKIECRIYRDRAVVLLRDRGVAFN 83 
                                       67899999*******9999*************************997....6778888899999************* PP

                       HATPase_c_2  80 petlpdpteeepkeslkegGrGlalikglvDevey..dgegnvvtms 124
                                       p ++p p+++ p e+++ gG+G++++++l+D  ey  +g+ n +t++
  gi|386002979|ref|YP_005921278.1|  84 PLEAPAPEVDRPLEEREVGGLGIFFVRNLTDGAEYrrEGDENLLTLT 130
                                       ***********************************777777888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 933.47
//
Query:       gi|386002980|ref|YP_005921279.1|  [L=568]
Description: Xanthine/uracil permease [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-60  202.8  33.6      1e-59  202.2  33.6    1.2  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
        3.1    7.6   3.9        4.2    7.1   0.2    2.7  2  DUF3464          Photosynthesis affected mutant 68


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.2  33.6   1.2e-63     1e-59       3     387 ..      21     400 ..      19     402 .. 0.94

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 1.2e-63
                                       HHHHHHHHHHHHHHHHHHHHHTTTS-..........H.HHHHHHHHHHHHHHHH.....HTTT-----EEE-GGGHH CS
                   Xan_ur_permease   3 llllglQhllamfaalvvvPllvgdalgl.aeelrqlisatllasGiatllqll.....ifgirlpillgssfafvt 73 
                                       +lllglQh++ +  +l+ + ++v +  g+  ee++ ++s+++la+G++t+l +l       g+  p+l+g+sf   +
  gi|386002980|ref|YP_005921279.1|  21 TLLLGLQHVFLIAISLIFPVVIVRSI-GGsPEEAEFMVSMSMLAAGVGTVLHALnrrgvGSGYLCPALCGPSFLSAS 96 
                                       799********999998766666666.67699999999******************988888999************ PP

                                       HHHGGG-....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..B CS
                   Xan_ur_permease  74 almialGsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaav 150
                                       +l  + G       +l+ l+g + vag + +l+s++++  rl+ l+pP vtg vv ++G+s++++a+ +++g   a 
  gi|386002980|ref|YP_005921279.1|  97 LLAANVG-------GLHLLFGMTAVAGSFEVLLSRFLH--RLRVLFPPEVTGLVVAMVGISVIPTALANFMGRGGA- 163
                                       9999999.......7***********************..9**************************999999755. PP

                                       TT.B---HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHH..HHS-SS---------- CS
                   Xan_ur_permease 151 egltvvslkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspe..vseapwfqlpsplkfg 225
                                       ++   +    l++a+ +l +++ +sv  +g ++++++L+g+++g+l+++ +gi+ ++    + eap++ +p++ +fg
  gi|386002980|ref|YP_005921279.1| 164 DA--ATEIPELAVALLTLGTMVGISVWSRGRLRLYSVLVGMAMGYLASIHLGILTADHLdlFAEAPLAAVPHLDYFG 238
                                       44..689999999999************************************9988887779***********9999 PP

                                       -HH..H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TII..IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHH CS
                   Xan_ur_permease 226 tplfnlgliltvlavalvavvesvGdiravakvvgrslkp..kpdlrralladGlatllsgllGalpvttyaeniGv 300
                                       ++ f+ +l+l +++ +  +++ ++Gdi+ + k+ + + k+  +++++ ++ladGl+ +++gl+G+++ +t ++niG+
  gi|386002980|ref|YP_005921279.1| 239 WS-FDVALLLPFMVAITCSSLKTIGDITTCQKINDADWKRtdMKNVSQGILADGLSAVFGGLVGTMGQSTSSSNIGL 314
                                       99.9***********99******************9999999*********************************** PP

                                       HHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHH CS
                   Xan_ur_permease 301 valtkvasrrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavsl 377
                                          t+ +srr+++ +g il+ll++ pkla  + + Pepv+g+ l+ +++ ++++g++++ +  ld ar +++v++ l
  gi|386002980|ref|YP_005921279.1| 315 SIGTGATSRRIAFAIGGILVLLAFLPKLAMVFVVMPEPVMGATLIYSVSFMIVAGFQIIMSRMLD-ARRTFLVGIPL 390
                                       ****************************************************************9.*********** PP

                                       HHHHH----- CS
                   Xan_ur_permease 378 vlGlgvatvp 387
                                       ++Gl+v ++p
  gi|386002980|ref|YP_005921279.1| 391 IMGLSVDALP 400
                                       ****997765 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.5     0.078     7e+02      75     109 ..      32      66 ..      21      69 .. 0.84
   2 ?    7.1   0.2   0.00047       4.2      53      78 ..     371     397 ..     370     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.078
                           DUF3464  75 latfvvfylivskelvdlptwvvllvslvlFglgv 109
                                       +a+  +f +++++++   p+ + ++vs+ ++++gv
  gi|386002980|ref|YP_005921279.1|  32 IAISLIFPVVIVRSIGGSPEEAEFMVSMSMLAAGV 66 
                                       667778888899999999*************9997 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00047
                           DUF3464  53 evVskRmi.rRvalfsGiPlalGlatf 78 
                                       +++++Rm+  R ++++GiPl++Gl++ 
  gi|386002980|ref|YP_005921279.1| 371 QIIMSRMLdARRTFLVGIPLIMGLSVD 397
                                       5788999845999**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 3510.80
//
Query:       gi|386002981|ref|YP_005921280.1|  [L=281]
Description: hypothetical protein Mhar_2305 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1766.16
//
Query:       gi|386002982|ref|YP_005921281.1|  [L=300]
Description: ornithine carbamoyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-51  172.4   0.0    1.1e-50  171.5   0.0    1.5  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    6.9e-51  172.4   0.0    9.7e-51  171.9   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.5   0.0   1.2e-54   1.1e-50       2     148 .]       2     141 ..       1     141 [. 0.98

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 1.2e-54
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       +l+s++dls+ e+e++ld+a+elk+++ + + +++l+gk+la +Fe+pStRTrvS evA+++lGg++l+ls  +d+q
  gi|386002982|ref|YP_005921281.1|   2 NLISIRDLSPGEVEAILDRADELKARRCDPSARSILAGKSLAAIFEKPSTRTRVSLEVAMADLGGHALYLS-TKDLQ 77 
                                       69************************999******************************************.77*** PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       l+     r+E+++Dtarvlsr+v+ai++R+++++++eel +ya+vpviNa+ +d eHP+Q+LaDl+t+re
  gi|386002982|ref|YP_005921281.1|  78 LG-----RGETIADTARVLSRFVHAIAARVYDHKTVEELGRYAEVPVINAL-SDLEHPCQILADLMTVRE 141
                                       **.....78******************************************.****************97 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.9   0.0   1.1e-54   9.7e-51       2     155 ..     148     296 ..     147     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 1.1e-54
                                       C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       glk+a+vGd+ nnv+ns i ++a++gm++ ++aP+g+epd ++l+ a++     gg+  +  d+ eav ga+vv td
  gi|386002982|ref|YP_005921281.1| 148 GLKVAWVGDG-NNVCNSTILAAAMMGMEMAVAAPPGYEPDRKILDLAESL----GGRTAVLADPLEAVRGAEVVSTD 219
                                       89********.*********************************666655....99999999*************** PP

                                       -SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       +wvsmg+e+e  +rl +++ yqv+++ll++ak+daivlHcLPa+rg E+tdeV+d+p+s++ +q eNrlh  kA+l 
  gi|386002982|ref|YP_005921281.1| 220 TWVSMGDEAEAAKRLGAFRRYQVNSDLLRHAKEDAIVLHCLPAHRGHEITDEVMDGPQSAILDQSENRLHSVKAVLE 296
                                       ***************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1863.15
//
Query:       gi|386002983|ref|YP_005921282.1|  [L=130]
Description: Tungsten formylmethanofuran dehydrogenase, subunit D [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-07   30.9   0.0    2.3e-07   30.8   0.0    1.2  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.3e-11   2.3e-07      30      83 ..      35      92 ..      16     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.3e-11
                                      -EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC..... CS
                   Molydop_binding 30 evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe....a 83
                                      + + +   dA  + i+ +  V +e++ G+v+v akv+e+ +pG  fmp   w+    +
  gi|386002983|ref|YP_005921282.1| 35 ALLFLDRGDALGRKIQADSPVLLETATGKVVVVAKVSEEPHPGIGFMPRSPWSaqllP 92
                                      58899999********************************************965541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 870.85
//
Query:       gi|386002984|ref|YP_005921283.1|  [L=393]
Description: Tungsten formylmethanofuran dehydrogenase, subunit B [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.064   13.0   0.1        4.4    7.0   0.1    3.0  3  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00025       4.4       2      54 ..      52     103 ..      51     106 .. 0.85
   2 ?    0.2   0.0     0.033   5.8e+02       4      25 ..     215     236 ..     213     269 .. 0.88
   3 ?    1.3   0.0     0.014   2.6e+02      74      87 ..     299     312 ..     291     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00025
                                       HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-T CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipe 54 
                                       ++a ell+ a rp++l G g ++ +a++   ela+klg+ + +    +g+i e
  gi|386002984|ref|YP_005921283.1|  52 SAAGELLAGADRPLLL-GFGRSTLEAQRLGIELAKKLGAAIGDPTSRQGLITE 103
                                       56789********876.5555556*****************999999999875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.033
                                       HHHHHHH-SSEEEEE-CHHCHT CS
                      TPP_enzyme_M   4 aaellkaakrpvilvGggvars 25 
                                       +a  l++ak  +i+ G g a++
  gi|386002984|ref|YP_005921283.1| 215 LATKLRKAKFGAIFTGPGLADA 236
                                       68899*************9954 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.014
                                       HHHH-SEEEEES-S CS
                      TPP_enzyme_M  74 aleeaDlvlalGar 87 
                                       +le +D vl++G++
  gi|386002984|ref|YP_005921283.1| 299 LLEGCDAVLVVGSD 312
                                       5899********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2503.93
//
Query:       gi|386002985|ref|YP_005921284.1|  [L=155]
Description: Tungsten formylmethanofuran dehydrogenase, subunit G [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-14   53.4   2.3    1.5e-14   53.4   2.3    2.4  1  FeS       Putative Fe-S cluster
    1.4e-08   34.2  20.4    3.3e-07   29.8   4.6    3.5  3  Fer4      4Fe-4S binding domain
    1.2e-06   29.0  20.5    5.1e-05   23.8   7.8    3.2  3  Fer4_7    4Fe-4S dicluster domain
    2.3e-06   27.6  18.7    1.5e-05   25.0  12.4    3.3  3  Fer4_10   4Fe-4S dicluster domain
    0.00021   21.2   4.5    0.00021   21.2   4.5    3.6  3  Fer4_6    4Fe-4S binding domain
    0.00025   21.0   3.6    0.00025   21.0   3.6    3.5  3  Fer4_2    4Fe-4S binding domain
    0.00025   21.5   3.6    0.00025   21.5   3.6    3.1  3  Fer4_17   4Fe-4S dicluster domain
    0.00026   21.1  10.0    0.00026   21.1  10.0    3.2  2  Fer4_9    4Fe-4S dicluster domain
     0.0019   18.6  16.6      0.024   15.1  10.4    3.2  2  Fer4_8    4Fe-4S dicluster domain
     0.0046   17.7   0.7     0.0046   17.7   0.7    2.6  2  Fer4_15   4Fe-4S single cluster domain
     0.0087   16.2   3.3     0.0087   16.2   3.3    3.4  3  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.8   3.1      0.014   15.8   3.1    4.3  4  Fer4_4    4Fe-4S binding domain
      0.017   16.0   2.7      0.017   16.0   2.7    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
      0.091   13.7   7.5      0.091   13.7   7.5    3.8  4  Fer4_3    4Fe-4S binding domain
       0.31   11.6  14.6        0.2   12.2   7.9    3.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   2.3   1.2e-17   1.5e-14       1      33 []      11      43 ..      11      43 .. 0.99

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.2e-17
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LP+tNC++CG+p+CmafA  l+ + + +edC+p
  gi|386002985|ref|YP_005921284.1| 11 LPKTNCKKCGFPTCMAFAVELLGKRKAIEDCTP 43
                                      9******************************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.52   6.2e+02       7      12 ..      15      20 ..      13      21 .. 0.73
   2 !   29.8   4.6   2.7e-10   3.3e-07       2      22 ..      75      95 ..      74      97 .. 0.93
   3 !   13.0   1.8   5.7e-05     0.068       9      24 .]     138     153 ..     138     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.52
                                      TSSS-T CS
                              Fer4  7 kCigCG 12
                                       C +CG
  gi|386002985|ref|YP_005921284.1| 15 NCKKCG 20
                                      588887 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 2.7e-10
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      vi++e+C gCG+Cv +CPv++
  gi|386002985|ref|YP_005921284.1| 75 VIHPERCYGCGNCVVACPVNV 95
                                      89*****************96 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 5.7e-05
                                       SS-THHHHHSTTTEEE CS
                              Fer4   9 igCGaCvevCPvgAIt 24 
                                       + C+aC+  CP  AI+
  gi|386002985|ref|YP_005921284.1| 138 VLCNACIVTCPSKAIE 153
                                       57************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   7.8   4.2e-08   5.1e-05       4      52 .]      15      95 ..      14      95 .. 0.58
   2 ?    5.3   5.7     0.025        30      40      52 .]     132     151 ..     105     151 .. 0.65
   3 !   12.5   1.0   0.00015      0.17       4      19 ..     139     154 ..     138     155 .] 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.2e-08
                            Fer4_7  4 gCgaCv.aaCpvkaieldeeenek................................gtekveidpekClgCgaCvavCP 49
                                      +C++C  ++C++ a+el  + + +                                +   ++i+pe+C+gCg+Cv +CP
  gi|386002985|ref|YP_005921284.1| 15 NCKKCGfPTCMAFAVELLGKRK-AiedctplveepkyekklaglrelmapllsteaTETGMVIHPERCYGCGNCVVACP 92
                                      6888866889877777653211.112333333333333345555544444444433224469***************** PP

                            Fer4_7 50 tga 52
                                      +++
  gi|386002985|ref|YP_005921284.1| 93 VNV 95
                                      986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.025
                            Fer4_7  40 g.......CgaCvavCPtga 52 
                                               C+aC+ +CP++a
  gi|386002985|ref|YP_005921284.1| 132 RfgpekvlCNACIVTCPSKA 151
                                       24444444677777777654 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00015
                            Fer4_7   4 gCgaCvaaCpvkaiel 19 
                                        C+aC ++Cp+kaie+
  gi|386002985|ref|YP_005921284.1| 139 LCNACIVTCPSKAIEF 154
                                       5************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5      0.13   1.5e+02       7      17 ..      14      26 ..       9      43 .. 0.74
   2 !   25.0  12.4   1.2e-08   1.5e-05       2      56 .]      74     148 ..      73     148 .. 0.84
   3 ?    5.6   1.7     0.015        17      11      21 ..     139     149 ..     138     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                           Fer4_10  7 dtCirCg..kCvk 17
                                        C +Cg  +C++
  gi|386002985|ref|YP_005921284.1| 14 TNCKKCGfpTCMA 26
                                      4566666666654 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.2e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtg.............cgaCveaCP 56 
                                       +vi +++C +Cg+Cv aCP+++          ++    + + +v+++v kC +             c aC+  CP
  gi|386002985|ref|YP_005921284.1|  74 MVIHPERCYGCGNCVVACPVNVasdpkgtAIGRGPVSGKAILMVEDGVVKCVNvdqcrrfgpekvlCNACIVTCP 148
                                       799*****************99******9666666777777777777777777666666999999999******9 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.015
                           Fer4_10  11 rCgkCvkaCPa 21 
                                        C++C   CP+
  gi|386002985|ref|YP_005921284.1| 139 LCNACIVTCPS 149
                                       69********9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.0      0.44   5.3e+02       8      16 ..      15      25 ..      13      26 .. 0.71
   2 !   21.2   4.5   1.8e-07   0.00021       3      23 ..      75      95 ..      74      96 .. 0.92
   3 !    8.5   6.0    0.0019       2.2       8      24 .]     129     152 ..     123     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                            Fer4_6  8 kCigCgd..Cv 16
                                      +C  Cg   C+
  gi|386002985|ref|YP_005921284.1| 15 NCKKCGFptCM 25
                                      79999866665 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.8e-07
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                      +i p++C gCg+Cv++CP ++
  gi|386002985|ref|YP_005921284.1| 75 VIHPERCYGCGNCVVACPVNV 95
                                      799***************975 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0019
                            Fer4_6   8 kCi.......gCgdCvrvCPegai 24 
                                        C         C++C++ CP +ai
  gi|386002985|ref|YP_005921284.1| 129 QCRrfgpekvLCNACIVTCPSKAI 152
                                       45555555557**********998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3      0.17     2e+02       9      16 ..      15      24 ..       9      27 .. 0.70
   2 !   21.0   3.6   2.1e-07   0.00025       4      21 ..      75      92 ..      73      93 .. 0.91
   3 ?    4.9   5.1     0.026        31       5      21 ..     125     148 ..     122     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                            Fer4_2  9 rCigCg..aC 16
                                      +C  Cg  +C
  gi|386002985|ref|YP_005921284.1| 15 NCKKCGfpTC 24
                                      4777776666 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+ ++rC gCg Cv aCP
  gi|386002985|ref|YP_005921284.1| 75 VIHPERCYGCGNCVVACP 92
                                      7889************** PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.026
                            Fer4_2   5 vdtdrCig.......CgaCvsaCP 21 
                                       v+ d C +       C+aC+  CP
  gi|386002985|ref|YP_005921284.1| 125 VNVDQCRRfgpekvlCNACIVTCP 148
                                       678888888888888********* PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   3.6   2.1e-07   0.00025       1      60 [.      15      95 ..      15      96 .. 0.79
   2 ?    1.7   0.1      0.33     4e+02      43      57 ..     121     135 ..     109     139 .. 0.77
   3 ?    3.6   0.8     0.081        97      49      58 ..     140     149 ..     138     152 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.1e-07
                           Fer4_17  1 rCiqCgy..Clp.............eCpsyeaydnepkkllraakl....glleeaekeeka..slCieCgeCerkCPq 58
                                      +C +Cg+  C++              C  + + ++++kkl+   +l     ++e++e+ +++  ++C +Cg+C+ +CP 
  gi|386002985|ref|YP_005921284.1| 15 NCKKCGFptCMAfavellgkrkaieDCTPLVEEPKYEKKLAGLRELmaplLSTEATETGMVIhpERCYGCGNCVVACPV 93
                                      69****878***9999999999999999999999999988777766665533444555554344**************8 PP

                           Fer4_17 59 gl 60
                                      ++
  gi|386002985|ref|YP_005921284.1| 94 NV 95
                                      86 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.33
                           Fer4_17  43 aslCieCgeCerkCP 57 
                                       + +C++  +C+r  P
  gi|386002985|ref|YP_005921284.1| 121 VVKCVNVDQCRRFGP 135
                                       668*******98655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.081
                           Fer4_17  49 CgeCerkCPq 58 
                                       C+ C   CP+
  gi|386002985|ref|YP_005921284.1| 140 CNACIVTCPS 149
                                       6666666665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1  10.2   6.8e-05     0.081       4      49 ..      15      94 ..      14      96 .. 0.68
   2 !   21.1  10.0   2.2e-07   0.00026       1      51 []      80     152 ..      80     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                            Fer4_9  4 gCgaC.veaCpagvvvedaaerkarlraase..................................eaCigCgaCveaCp 47
                                      +C++C  + C a +v+   +++ ++ +++                                    e+C+gCg Cv aCp
  gi|386002985|ref|YP_005921284.1| 15 NCKKCgFPTCMAFAVELLGKRKAIE-DCTPLveepkyekklaglrelmapllsteatetgmvihpERCYGCGNCVVACP 92
                                      6777767777555544433333333.34444556666777777777888888888888999999999************ PP

                            Fer4_9 48 kg 49
                                       +
  gi|386002985|ref|YP_005921284.1| 93 VN 94
                                      87 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.2e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.......................eaCigCgaCveaCpkgai 51 
                                       +C+gCg+Cv aCp +v+++ +++ + r    ++                       e  + C+aC+  Cp++ai
  gi|386002985|ref|YP_005921284.1|  80 RCYGCGNCVVACPVNVASDPKGTAIGRGPVSGKailmvedgvvkcvnvdqcrrfgpE-KVLCNACIVTCPSKAI 152
                                       6************************999988889********999888777767642.356888*******987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   7.4     4e-05     0.048       4      65 .]      15      95 ..      13      95 .. 0.70
   2 !   15.1  10.4     2e-05     0.024       3      63 ..      79     149 ..      77     151 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                            Fer4_8  4 kCieCg..aCq.............saC.pvlrrtk.khlldargeaae.....dvqeeqvlee..eealwsCttcgaCt 58
                                      +C +Cg   C+             + C p++++ k + +l    e ++     +     ++e+      ++C +cg+C+
  gi|386002985|ref|YP_005921284.1| 15 NCKKCGfpTCMafavellgkrkaiEDCtPLVEEPKyEKKLAGLRELMApllstE-----ATETgmVIHPERCYGCGNCV 88
                                      788888777888888888888777778778888885566666666666544331.....33334467789********* PP

                            Fer4_8 59 evCpvgi 65
                                      ++Cpv++
  gi|386002985|ref|YP_005921284.1| 89 VACPVNV 95
                                      ****986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaae.......dvqeeqvleeeealwsC.......ttcgaCtevCpv 63 
                                       e+C +Cg C  aCpv  +++ k     rg +++       d + +       ++++C       + c+aC + Cp 
  gi|386002985|ref|YP_005921284.1|  79 ERCYGCGNCVVACPVNVASDpKGTAIGRGPVSGkailmveDGVVK-----CVNVDQCrrfgpekVLCNACIVTCPS 149
                                       68************9999988888888888888443332222222.....33455556666666677777777776 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.7   3.8e-06    0.0046       3      32 ..      76     104 ..      74     132 .. 0.74
   2 ?    0.7   0.7      0.78   9.3e+02      58      65 ..     146     153 ..     138     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.8e-06
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedglasv 32 
                                       +  ++C gcg+Cv ++p  +  d +g a +
  gi|386002985|ref|YP_005921284.1|  76 IHPERCYGCGNCVVACPVNVASDPKGTA-I 104
                                       5568**********************99.2 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.78
                           Fer4_15  58 aCPvdAIr 65 
                                       +CP +AI+
  gi|386002985|ref|YP_005921284.1| 146 TCPSKAIE 153
                                       58888886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.66   7.9e+02      10      23 ..      15      29 ..      12      47 .. 0.66
   2 !   16.2   3.3   7.3e-06    0.0087      35      53 ..      75      93 ..      65      98 .. 0.64
   3 !    8.1  15.5    0.0024       2.8       2      58 ..      75     153 ..      74     154 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.66
                           Fer4_21 10 gCgkC.liaCedtsh 23
                                      +C+kC + +C   ++
  gi|386002985|ref|YP_005921284.1| 15 NCKKCgFPTCMAFAV 29
                                      677773346665444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.3e-06
                           Fer4_21 35 kvvedeCvGCnlCssvCPv 53
                                       +  ++C GC  C+  CPv
  gi|386002985|ref|YP_005921284.1| 75 VIHPERCYGCGNCVVACPV 93
                                      3345666666666666666 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0024
                           Fer4_21   2 ridedkCigCgkCliaCedtsh.....qai..........eidaktvl.kvvedeC.......vGCnlCssvCPved 55 
                                       +i++++C gCg+C++aC+ +       +ai           + ++ v+  v  d+C       v Cn C+  CP ++
  gi|386002985|ref|YP_005921284.1|  75 VIHPERCYGCGNCVVACPVNVAsdpkgTAIgrgpvsgkaiLMVEDGVVkCVNVDQCrrfgpekVLCNACIVTCP-SK 150
                                       699**************965331121256777755554442233333323335666554444467999999999.47 PP

                           Fer4_21  56 cie 58 
                                       +ie
  gi|386002985|ref|YP_005921284.1| 151 AIE 153
                                       775 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.8      0.24   2.9e+02       3      12 ..      15      26 ..      13      27 .. 0.58
   2 ?   15.8   3.1   1.2e-05     0.014       1      17 []      78      94 ..      78      97 .. 0.93
   3 ?    1.6   0.2      0.44   5.2e+02       4      15 ..     124     135 ..     123     137 .. 0.72
   4 ?    5.9   1.1     0.018        21       7      16 ..     140     149 ..     138     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                            Fer4_4  3 rCigCg..sCva 12
                                      +C  Cg   C+a
  gi|386002985|ref|YP_005921284.1| 15 NCKKCGfpTCMA 26
                                      677777444766 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.2e-05
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      +erC gCg Cv aCP++
  gi|386002985|ref|YP_005921284.1| 78 PERCYGCGNCVVACPVN 94
                                      69*************75 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.44
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       C++ ++C+++ P
  gi|386002985|ref|YP_005921284.1| 124 CVNVDQCRRFGP 135
                                       666689999877 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.018
                            Fer4_4   7 CgsCvaaCPq 16 
                                       C +C+ +CP+
  gi|386002985|ref|YP_005921284.1| 140 CNACIVTCPS 149
                                       *********7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  11.6    0.0088        10      52      67 .]      79      94 ..      12      94 .. 0.73
   2 ?   16.0   2.7   1.5e-05     0.017       1      20 [.      80      99 ..      80     110 .. 0.82
   3 ?    9.7   3.9    0.0013       1.6       5      18 ..     140     153 ..     123     155 .] 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0088
                           Fer4_16 52 eaitgCdiCqdvCPan 67
                                      e+++gC++C+ +CP+n
  gi|386002985|ref|YP_005921284.1| 79 ERCYGCGNCVVACPVN 94
                                      7889999999999987 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      rC +Cg+C+ +CP+n+ + +
  gi|386002985|ref|YP_005921284.1| 80 RCYGCGNCVVACPVNVASDP 99
                                      69999999999999988777 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0013
                           Fer4_16   5 CgkCaevCPtnaik 18 
                                       C++C+ +CP++ai+
  gi|386002985|ref|YP_005921284.1| 140 CNACIVTCPSKAIE 153
                                       ************97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.9      0.93   1.1e+03       1       8 [.      16      25 ..      16      27 .. 0.84
   2 ?   13.7   7.5   7.6e-05     0.091       1      14 [.      81      94 ..      81      95 .. 0.95
   3 ?   -1.8   0.3         7   8.3e+03       7      10 ..     124     127 ..     122     133 .. 0.64
   4 ?   11.6   1.7   0.00037      0.44       3      15 .]     139     151 ..     138     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.93
                            Fer4_3  1 CtgCg..aCv 8 
                                      C  Cg  +C+
  gi|386002985|ref|YP_005921284.1| 16 CKKCGfpTCM 25
                                      9999998998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.6e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C gCg Cv++CPv+
  gi|386002985|ref|YP_005921284.1| 81 CYGCGNCVVACPVN 94
                                      99**********98 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7
                            Fer4_3   7 Cvev 10 
                                       Cv+v
  gi|386002985|ref|YP_005921284.1| 124 CVNV 127
                                       5544 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00037
                            Fer4_3   3 gCgaCvevCPvgA 15 
                                        C+aC + CP++A
  gi|386002985|ref|YP_005921284.1| 139 LCNACIVTCPSKA 151
                                       6**********98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.5       4.1   4.9e+03       6      14 ..      16      26 ..      13      41 .. 0.57
   2 ?   12.2   7.9   0.00017       0.2       4      56 ..      79     152 ..      76     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                           Fer4_13  6 Ciacg..aCve 14
                                      C  cg  +C +
  gi|386002985|ref|YP_005921284.1| 16 CKKCGfpTCMA 26
                                      44443223444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                           Fer4_13   4 dtCiacgaCvelaPdvFeeddeggasvvaeqpts.......................eeekadaeeAadaCPvesI 56 
                                       ++C +cg+Cv ++P   + d++g   ++ ++p+s                         ek ++++ + +CP ++I
  gi|386002985|ref|YP_005921284.1|  79 ERCYGCGNCVVACPVNVASDPKGT--AIGRGPVSgkailmvedgvvkcvnvdqcrrfGPEKVLCNACIVTCPSKAI 152
                                       89*******************976..58999999666666666666666665555553345666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1041.40
//
Query:       gi|386002986|ref|YP_005921285.1|  [L=583]
Description: membrane protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-17   61.3   4.7    8.4e-17   61.3   4.7    2.2  2  BatA      Aerotolerance regulator N-terminal
  ------ inclusion threshold ------
      0.019   15.6   0.1      0.038   14.6   0.1    1.5  1  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   4.7   9.4e-21   8.4e-17       1      77 []       3      78 ..       1      78 [. 0.98
   2 ?    1.3   0.1     0.051   4.5e+02      62      75 ..     563     576 ..     546     583 .] 0.53

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 9.4e-21
                              BatA  1 MlpFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeea.lqrlkknllllLrllalallvlalArP 77
                                      M pF +Pl+Ll+ll +++ +i+ly+++++p+  +f+s++++ e e + +a l+rl  + l++ +ll++++lv+a A+P
  gi|386002986|ref|YP_005921285.1|  3 M-PFSSPLALLGLLSVVP-LIILYMIRPKPRDLPFPSTAFILEGEAKPSAsLSRLVTDPLFWTQLLVIVFLVIAAAGP 78
                                      8.9***************.**********************9999999999**************************9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.051
                              BatA  62 LrllalallvlalA 75 
                                       + l+a+al++l lA
  gi|386002986|ref|YP_005921285.1| 563 MVLIAAALIILELA 576
                                       33333333333332 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 ?   14.6   0.1   4.3e-06     0.038       1     106 [.      90     182 ..      90     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-06
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtn 77 
                                       lv+v+D S+Sm+++      ++ a ++  ++++    dr+++v  +++  +l+  + +  + ++a  +l++++   +
  gi|386002986|ref|YP_005921285.1|  90 LVVVIDLSASMEAS------FDEAEAIFLRYSSG--QDRISIVL-AETIPLLALREGNEVQARSAFSALTPRAVSAD 157
                                       79***********9......*****999999998..89999975.6677778888899999**************** PP

                             VWA_2  78 laaaLqlarkalkkrrkgekrvivlitDg 106
                                       l a++ + r++l ++      +i++i+D 
  gi|386002986|ref|YP_005921285.1| 158 LSAGMVMGRSLLGAE----GGQILVISDF 182
                                       *************77....5999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4114.65
//
Query:       gi|386002987|ref|YP_005921286.1|  [L=794]
Description: hypothetical protein Mhar_2312 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-13   50.0   0.0    9.3e-05   22.0   0.0    3.2  3  GATase1_like  Putative glutamine amidotransferase
    9.6e-11   42.3   0.0    3.7e-10   40.4   0.0    2.0  2  VWA_2         von Willebrand factor type A domain
    2.3e-10   41.0   0.0    0.00012   22.4   0.0    2.3  2  VWA           von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.095   13.1   0.3        4.9    7.7   0.1    2.9  2  DUF4350       Domain of unknown function (DUF4350)
        8.3    6.9  10.5          1    9.8   1.3    2.8  3  BatA          Aerotolerance regulator N-terminal


Domain annotation for each model (and alignments):
>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.018        65     101     175 ..     113     190 ..     101     237 .. 0.69
   2 !   21.0   0.0     5e-08   0.00018      91     143 ..     307     355 ..     297     364 .. 0.86
   3 !   22.0   0.0   2.6e-08   9.3e-05     149     244 ..     553     645 ..     547     647 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.018
                      GATase1_like 101 kdyvaeGggllmvGGylsfqGid..gkarykktpvedvlPvtcldv..ddrvevPeGlaaevvasehpvlkglssew 173
                                        +y ++Gg+ll+v   +s +G d        +++   v+ +++ ++  d  ve+  G+ + v+  e+p +  + s  
  gi|386002987|ref|YP_005921286.1| 113 LQYAQQGGALLLVTDGYSNRGRDleEALALARSANTTVFALEMAPIreDRSVEI-SGTNTAVLGGEYPFTVVVRSSG 188
                                       4799*********99999999773222334455555556666655321555666.6777788888887666555555 PP

                      GATase1_like 174 Pk 175
                                        +
  gi|386002987|ref|YP_005921286.1| 189 GE 190
                                       55 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5e-08
                      GATase1_like  91 ksvPnrlkllkdyvaeGggllmvGGylsfqGidgkarykktpvedvlPvtcld 143
                                       ++    l  lkdyv eGggl++vGG  sf       +y+++++e++lPv+ ++
  gi|386002987|ref|YP_005921286.1| 307 QRYGPELSGLKDYVREGGGLVVVGGRSSFDF----GEYRNSSLEEILPVKSVP 355
                                       5555678889*******************74....68************9877 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 2.6e-08
                      GATase1_like 149 evPe.GlaaevvasehpvlkglssewPkllGyneveakdnaevlatvsedshPllvvGeygkGrtaaftsdisphwl 224
                                       evP+ G+a  + +++h +++ l+    +  G+n+v++k++ + l  +  d++P+l   +yg Gr+aa t+d +  w 
  gi|386002987|ref|YP_005921286.1| 553 EVPAsGYALMIANQNHYITSDLA-LAANATGFNDVTPKPGGQRLVVM-LDGKPILTSWRYGLGRVAALTTDDGTAWA 627
                                       677526777777889*******9.557889*********99988654.5669************************* PP

                      GATase1_like 225 spefldwegyarlwknvldw 244
                                       +  +++   ++rl  ++++w
  gi|386002987|ref|YP_005921286.1| 628 PEVYSAP--SSRLVSRMVNW 645
                                       9888764..45677776666 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 ?   -2.5   0.0       2.3   8.2e+03      73      87 ..     131     145 ..     100     148 .. 0.75
   2 !   40.4   0.0     1e-13   3.7e-10       1     106 [.     364     477 ..     364     478 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                             VWA_2  73 gggtnlaaaLqlark 87 
                                       + g +l++aL lar+
  gi|386002987|ref|YP_005921286.1| 131 NRGRDLEEALALARS 145
                                       567788888888776 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 1e-13
                             VWA_2   1 lvfvlDtSgSmrngdy..gptrleaakdaveallk..slpgdrvglvtfsdgpevliplt...kdkakilnalrnle 70 
                                       +v+++D SgS r++    g t l++ k+++++llk  ++++drv+lv+f++++ v++++t        i++++ +l 
  gi|386002987|ref|YP_005921286.1| 364 TVLIMDISGSTRREMSvgGATFLDYEKALAIELLKapEFRDDRVALVVFGTEAFVVFTPTpivGKEIMIQDRISSLS 440
                                       69*********99944558****************88889*******************9887788899******** PP

                             VWA_2  71 ak...gggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       ++   + +t+l+ +L la ++l++ +   + ++++i+Dg
  gi|386002987|ref|YP_005921286.1| 441 PQpgaQEETQLNVGLALAWDLLNASS--SEGEVIVISDG 477
                                       **999999***************886..9*********9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.9e-06      0.01     107     155 ..     122     170 ..     101     186 .. 0.84
   2 !   22.4   0.0   3.3e-08   0.00012       3     139 ..     365     505 ..     365     527 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                                       EEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSSSS CS
                               VWA 107 iilltdGksndg.dpkeaaneakeqgikvfavGvgnadekelLnkiasep 155
                                       ++l+tdG+sn g d++ea++ a++++ +vfa+ +  + e+    +i++++
  gi|386002987|ref|YP_005921286.1| 122 LLLVTDGYSNRGrDLEEALALARSANTTVFALEMAPIREDR-SVEISGTN 170
                                       78*********88******************9998887777.55665555 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.3e-08
                                       EEEEE-STTS......CHHHHH.HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHC.HHHHHHHHHHTG CS
                               VWA   3 vfvlDgSgsm......geenfe.kvkefikklveklevgpegtrvglvqfssevktefslndys.skeellsalnnl 71 
                                       v+++D Sgs       g+ +f  + k  +++l++  e   +++rv+lv f++e+ ++f  +    +  ++++ +++l
  gi|386002987|ref|YP_005921286.1| 365 VLIMDISGSTrremsvGGATFLdYEKALAIELLKAPE--FRDDRVALVVFGTEAFVVFTPTPIVgKEIMIQDRISSL 439
                                       6889999998666666555555466666677777777..999********************884559999****** PP

                                       ..SGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.HTHHHHHHHHGCTEEEEEEEE CS
                               VWA  72 ..kysgggttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.dpkeaaneakeqgikvfavGv 139
                                         +   +++t+++ +l+ a + l+++s++     +  +i+++dG+  +     +e a+ ++e g +v+ v v
  gi|386002987|ref|YP_005921286.1| 440 spQPGAQEETQLNVGLALAWD-LLNASSS-----EGEVIVISDGRIREyPeVFSESARMIQEMGATVHLVEV 505
                                       544444555556667777767.5555555.....5789*******977444455555555566998888877 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0014       4.9      30      67 ..     114     151 ..     100     152 .. 0.80
   2 ?    2.1   0.0     0.073   2.6e+02      39      68 ..     302     329 ..     271     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                           DUF4350  30 alegedgtllvvapdlrlte.eelaallewvarGntlvl 67 
                                       ++++ +g ll+v+++ + +  ++l++ l+++++ nt v 
  gi|386002987|ref|YP_005921286.1| 114 QYAQQGGALLLVTDG-YSNRgRDLEEALALARSANTTVF 151
                                       456788899999999.45559**************9997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.073
                           DUF4350  39 lvvapdlrlteeelaallewvarGntlvla 68 
                                       +v++++ r+ + el  l ++v+ G+ lv++
  gi|386002987|ref|YP_005921286.1| 302 VVLDDQ-RYGP-ELSGLKDYVREGGGLVVV 329
                                       455555.8887.8999************98 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.69   2.5e+03       9      26 ..      12      25 ..       5      32 .. 0.50
   2 ?    9.8   1.3   0.00029         1      53      77 .]      29      53 ..      23      53 .. 0.89
   3 ?    2.6   0.3     0.051   1.8e+02      40      69 ..     750     781 ..     747     787 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.69
                              BatA  9 lLlallllplpiillyll 26
                                      l   l l+pl i++l l 
  gi|386002987|ref|YP_005921286.1| 12 L---LGLIPL-ILILGLA 25
                                      3...445555.4444333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00029
                              BatA 53 rlkknllllLrllalallvlalArP 77
                                      + +++ll+l r+++++llv+alA+P
  gi|386002987|ref|YP_005921286.1| 29 KGRNRLLVLSRTAIFCLLVVALANP 53
                                      56899******************99 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.051
                              BatA  40 lleevekdeea..lqrlkknllllLrllalal 69 
                                       l+ee++k++e    +r +++l+ll   la++l
  gi|386002987|ref|YP_005921286.1| 750 LVEEARKRSEItvQERVSRRLPLLFLALAIFL 781
                                       66777777777878888999988888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (794 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 5195.73
//
Query:       gi|386002988|ref|YP_005921287.1|  [L=101]
Description: Protein translation factor SUI1 like protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-22   77.9   0.6    8.1e-22   77.5   0.6    1.1  1  SUI1           Translation initiation factor SUI1
    0.00069   19.9   0.5     0.0012   19.1   0.5    1.5  1  Img2           Mitochondrial large subunit ribosomal protein 
  ------ inclusion threshold ------
      0.047   13.4   1.1      0.059   13.1   1.1    1.2  1  DTW            DTW domain
       0.09   12.8   0.3        0.1   12.6   0.3    1.3  1  PP1_inhibitor  PKC-activated protein phosphatase-1 inhibitor


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.6   1.8e-25   8.1e-22       1      76 [.      20      92 ..      20      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 1.8e-25
                              SUI1  1 akpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvk.dggeeiqvQGdqrkkvaelLtekygv 76
                                      ++++i++++ +r+ +K vT+++g+++ +idl++la +lk+++ac+g+v k  g  +i++QG++  +++++L++k g+
  gi|386002988|ref|YP_005921287.1| 20 EQQRITVKINRRRYGKEVTVIQGIDPHEIDLSELATHLKSELACGGTV-KgYG--VIELQGNHTGRIKKILVKK-GF 92
                                      5899*******************************************9.5255..9*****************9.86 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   2.6e-07    0.0012      22      80 .]      32      92 ..      11      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.6e-07
                              Img2 22 ggtkkltvirkieG...DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      +  k++tvi+ i+    D+++l+++L++ l+      +  g ie++G+++ ++kk+L +kgF
  gi|386002988|ref|YP_005921287.1| 32 RYGKEVTVIQGIDPheiDLSELATHLKSELA-CGGTVKGYGVIELQGNHTGRIKKILVKKGF 92
                                      45677888888864444999***********.8899999**********************9 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   1.3e-05     0.059       3      31 ..       1      28 [.       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                               DTW  3 lCerCllpaevclcsslppleklpikvli 31
                                      +C+ C lp+ +c+c+++ + e+++i v i
  gi|386002988|ref|YP_005921287.1|  1 MCPVCGLPKDLCICQEVAK-EQQRITVKI 28
                                      5******************.777677755 PP

>> PP1_inhibitor  PKC-activated protein phosphatase-1 inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   2.3e-05       0.1      25      55 ..      15      45 ..       9      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                      SSS-S-SSSSSSSS-SSSSCHHHHHHHHHHH CS
                     PP1_inhibitor 25 lsiqkrqarvtvkydrkelqkrldvekWide 55
                                      +++ k q r+tvk +r+   k + v + id 
  gi|386002988|ref|YP_005921287.1| 15 QEVAKEQQRITVKINRRRYGKEVTVIQGIDP 45
                                      6799*****************9999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 640.64
//
Query:       gi|386002989|ref|YP_005921288.1|  [L=91]
Description: hypothetical protein Mhar_2314 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 540.04
//
Query:       gi|386002990|ref|YP_005921289.1|  [L=65]
Description: Small nuclear ribonucleoprotein, LSM family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-17   63.4   0.8    1.2e-17   63.3   0.8    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.8   6.9e-22   1.2e-17       7      67 .]       2      63 ..       1      63 [. 0.94

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 6.9e-22
                                      TTSEEEEEETTS..EEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  7 inkkvtvelkng..relrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                      i++++ ve+k+    +l+GtL ++D+++Nl+L++++e+++++ + r+lg v++RGnni+lis+
  gi|386002990|ref|YP_005921289.1|  2 IGSRIKVEMKGSqrNVLEGTLNSVDDYLNLHLQETVEIVDGE-RARSLGSVILRGNNIILISP 63
                                      799********65589***********************999.******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 354.16
//
Query:       gi|386002991|ref|YP_005921290.1|  [L=76]
Description: Nitrogen-fixing NifU domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-25   86.9   0.9    8.7e-25   86.7   0.9    1.0  1  NifU            NifU-like domain
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.041   14.0   0.1    1.8  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.9   9.7e-29   8.7e-25       1      67 []       8      74 ..       8      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 9.7e-29
                                      HHHHHHH.HGGG--GG--EEEEEEEETT.EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                              NifU  1 ieevleeeirPaLasdGGdielvdvdeg.vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                      +e+vle  ir aL++ GGdielvdv e+ vV v+l+G+C+gCp s++tlk+ +e+ Lk++v+ +keV+
  gi|386002991|ref|YP_005921290.1|  8 VESVLEV-IRNALRMEGGDIELVDVAEDgVVSVKLTGSCAGCPFSQMTLKNFVERELKKNVDGIKEVV 74
                                      799****.*****************8888*************************************96 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.6e-06     0.041      29      72 ..      29      73 ..       6      76 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
                                      EEE-T.-EEEEEE--SSTT-T.THHHHHHHHHHHHC..STT--EEEE CS
                    FeS_assembly_P 29 idieg.gkVsvditltypacs.laeairadaeaalr.alpgvevveV 72
                                      +d+ + g+Vsv++t   ++c+ +   +++ +e+ l+  + g++  eV
  gi|386002991|ref|YP_005921290.1| 29 VDVAEdGVVSVKLTGSCAGCPfSQMTLKNFVERELKkNVDGIK--EV 73
                                      555555***************8888999999****99999944..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 421.48
//
Query:       gi|386002992|ref|YP_005921291.1|  [L=107]
Description: hypothetical protein Mhar_2317 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-44  149.8   0.0    2.5e-44  149.7   0.0    1.0  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r


Domain annotation for each model (and alignments):
>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   1.4e-48   2.5e-44       1     106 [.       1     105 [.       1     106 [. 0.99

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 1.4e-48
                     Nit_Regul_Hom   1 mkvllklfvesenlgkvinalseagitGfylieYkGlsPqewkgflleedpesaikiikdlseeavlintvvdeekv 77 
                                       mk+l+k+fv++e+lg+vin+l+e gitGfyl+eYkG++P+ewk+fll+edpe++i+++++++e++vl+ntv+d + +
  gi|386002992|ref|YP_005921291.1|   1 MKTLVKIFVDHEHLGRVINTLTELGITGFYLYEYKGMAPKEWKSFLLKEDPEMTIEAVRHHAEPGVLVNTVIDGD-C 76 
                                       8************************************************************************99.9 PP

                     Nit_Regul_Hom  78 ekikeeleeklkderytiieipvekikvn 106
                                       e i++ le+ lk+ ryti+ ++v+ +kv+
  gi|386002992|ref|YP_005921291.1|  77 EPIVKGLEQGLKGIRYTIMGQKVTVLKVR 105
                                       **************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 608.18
//
Query:       gi|386002993|ref|YP_005921292.1|  [L=155]
Description: hypothetical protein Mhar_2318 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-08   34.5   0.1    1.2e-07   31.8   0.1    1.9  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   6.7e-12   1.2e-07      42     141 ..      52     148 ..       8     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.7e-12
                                       H...HHHHHHHHHHHHHHHHHHT.-S-.......HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHHS- CS
                              PgpA  42 l...llilllflvGiwackktek.elg.......ekDpgeiviDEvvgqwiallllpatllalllafilFrlfDivK 107
                                       +   ++++ll+++G+ ++++ ++  l        e+D + ++ DEv+g+ ia       +++   +++ +  +D++K
  gi|386002993|ref|YP_005921292.1|  52 AlsdPNLCLLIYAGLLLEAEGRRgGLPnmkssdyERDLTYLIADEVIGMTIAK------YIGGYKGTFDYVRYDKAK 122
                                       3467788999999999999998866668899999*******************......456799************ PP

                                       -THHHHTSSS.-S---TTHHHHHHHHHHHHHHHH CS
                              PgpA 108 pgpigwldrklkgglgvmlDDllAgiaaalvlal 141
                                       pg++g l          ++DD++Ag+++++   +
  gi|386002993|ref|YP_005921292.1| 123 PGILGVLGP--------FMDDVIAGLIGGVSANM 148
                                       *******77........9*********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.36s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 887.04
//
Query:       gi|386002994|ref|YP_005921293.1|  [L=237]
Description: cobalamin synthase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-35  121.3  22.0    7.8e-35  120.9  22.0    1.0  1  CobS      Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9  22.0   4.3e-39   7.8e-35      15     204 .]       9     217 ..       4     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 4.3e-39
                              CobS  15 ralaffPlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDglgsgrdrerrleImkDsr 89 
                                       r +++fPlvG+ lGl+  ++al+l ++ +  +aa+l+++a++ l g++H DGlaD++Dg+g++ + ++++++mkD +
  gi|386002994|ref|YP_005921293.1|   9 RHIYLFPLVGAALGLIYaAIALALTAVVPpGIAAALIIVAIFKLCGINHADGLADFGDGVGAHTTVDKKIAAMKDVH 85 
                                       56889***********966666666665577788888767777********************************** PP

                              CobS  90 vGafGvlalvlvlllkvaalaala.......lllapvlsRlaallaiallpyaeeglgalfaeaqkk........lv 151
                                       +G++Gvl++ l +l+ + +l+a++       l++a+v+++ ++++++a++++ ++g+g++ ++++++        + 
  gi|386002994|ref|YP_005921293.1|  86 IGTGGVLFVTLSILAVYGSLTAIPaaalpvsLVVAEVAAKQSMVAFAAFSTPLHQGFGSIAIQNADRadfllglgA- 161
                                       *****************9986665667789999******************9999*****9996666565433221. PP

                              CobS 152 llal...avlllll.alllaallvalllrrlarrklggvtGDvlGavieltellvll 204
                                        +al   a++  l  a+llaa + a+++ +++rr++gg tGD +Ga++e+++++ l+
  gi|386002994|ref|YP_005921293.1| 162 -AALlcgAFAGPLGiAVLLAAQVSAFYMVAVSRRNFGGATGDGFGATNEVARAVSLV 217
                                       .1113332222222235566666888999************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1425.36
//
Query:       gi|386002995|ref|YP_005921294.1|  [L=198]
Description: adenosylcobinamide-phosphate guanylyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-18   65.7   0.3    1.2e-17   64.7   0.2    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    6.2e-07   29.6   0.0    1.2e-06   28.7   0.0    1.5  1  CTP_transf_3     Cytidylyltransferase
    7.1e-05   22.6   0.0    0.00086   19.1   0.0    2.1  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0092   15.6   0.0      0.011   15.4   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.062   12.5   0.0      0.098   11.8   0.0    1.3  1  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.2   3.5e-21   1.2e-17       3     116 ..       2     116 ..       1     126 [. 0.91

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3.5e-21
                                       EEEESS-TTTT.TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHH CS
                      NTP_transf_3   3 iLAGGrSsRmg.gdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplasl 76 
                                       ++AGG ++R++ g+K++++l g+pl+ +v+ alr++ +d+v+v++ +  +  +a +++ g++vve +  g+g +  +
  gi|386002995|ref|YP_005921294.1|   2 VMAGGLGTRLKmGEKPMVRLLGRPLIGWVVSALRESALDRVFVATSPrsPGTAAWAEGEGLEVVETP--GAGYVPDM 76 
                                       89*********66*******************************987556789999**********7..9******* PP

                                       HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTS CS
                      NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaaasga 116
                                        +a++ a+ + +vl++++D+Pll+ e+++++l+ ++  ++
  gi|386002995|ref|YP_005921294.1|  77 ISAVEGAGIEGPVLIVMADLPLLRGEILDEILEVYEGVPE 116
                                       *******99***********************99876555 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.3e-10   1.2e-06      15      51 ..      15      50 ..       7     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.3e-10
                                      TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HH CS
                      CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekvivaTDsee 51
                                      +K++ +l+g+pli +v+ a+++s++ ++v+vaT+  +
  gi|386002995|ref|YP_005921294.1| 15 EKPMVRLLGRPLIGWVVSALRESAL-DRVFVATSPRS 50
                                      7*********************888.*******8554 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 !   19.1   0.0   2.4e-07   0.00086       5     115 ..       2     109 ..       1     126 [. 0.70
   2 ?    1.5   0.0     0.058   2.1e+02     204     220 ..     177     193 ..     168     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.4e-07
                                       EECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE--SSHHHHH CS
                              IspD   5 ipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlvaGGdeRaesV 81 
                                       + A G G+R+k g  K  + l g++l+ + v+al + +a+d++ v+ s+   + +++    + +++v+     a  V
  gi|386002995|ref|YP_005921294.1|   2 VMAGGLGTRLKMGE-KPMVRLLGRPLIGWVVSALRE-SALDRVFVATSPRS-PGTAAWAEGEGLEVVET--PGAGYV 73 
                                       789*********95.8999**************998.89*********998.44444444445666653..223444 PP

                                       HHHHHTTSSTT..SEEEE--TT-TT--HHHHHHHHH CS
                              IspD  82 lnglkalegea..kfVLvHDaARpllkaadiaella 115
                                          + a+eg      VL+  a  pll+ + ++e+l+
  gi|386002995|ref|YP_005921294.1|  74 PDMISAVEGAGieGPVLIVMADLPLLRGEILDEILE 109
                                       444444444433355666666666666666666555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.058
                                       ----SHHHHHHHHHHHH CS
                              IspD 204 lKittpeDlalAeailr 220
                                         +  peDla+ eailr
  gi|386002995|ref|YP_005921294.1| 177 ANVNSPEDLAICEAILR 193
                                       56889**********97 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     3e-06     0.011       3      59 ..       1      51 [.       1      95 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-06
                                      EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHH CS
                   NTP_transferase  3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsf 59
                                      +++aGG GtRL    +   k++v  lg  +li  ++s+l +s  ++ ++v t+ +s+
  gi|386002995|ref|YP_005921294.1|  1 MVMAGGLGTRL----KMGEKPMVRLLGR-PLIGWVVSALRESALDR-VFVATSPRSP 51
                                      69*********....699**********.*****************.7777766655 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05     0.098      74     112 ..      75     110 ..      25     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                              CofC  74 dlntavekafeeieekeviiipsdiPlikkedvkdllel 112
                                       d+ +ave a     e +v+i+++d+Pl++ e ++++le 
  gi|386002995|ref|YP_005921294.1|  75 DMISAVEGAG---IEGPVLIVMADLPLLRGEILDEILEV 110
                                       4555555553...3689*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1340.84
//
Query:       gi|386002996|ref|YP_005921295.1|  [L=116]
Description: hypothetical protein Mhar_2321 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.18   11.5   0.0    1.6  1  DUF3945   Protein of unknown function (DUF3945)


Domain annotation for each model (and alignments):
>> DUF3945  Protein of unknown function (DUF3945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     1e-05      0.18      27      44 ..      46      66 ..      16      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1e-05
                           DUF3945 27 p...deikgvkLteeqkqdLr 44
                                      p   +ei+  kL++e+++dLr
  gi|386002996|ref|YP_005921295.1| 46 PrrlKEICSLKLNDEERRDLR 66
                                      35559***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 854.92
//
Query:       gi|386002997|ref|YP_005921296.1|  [L=474]
Description: Acetyl-CoA decarbonylase/synthase gamma subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.9e-133  443.1   0.0   8.3e-133  442.8   0.0    1.0  1  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
    3.5e-14   52.1   1.7    8.4e-14   50.9   1.7    1.7  1  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.8   0.0  9.3e-137  8.3e-133       2     385 ..      73     465 ..      72     466 .. 0.96

  Alignments for each domain:
  == domain 1  score: 442.8 bits;  conditional E-value: 9.3e-137
                                       EEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE-- CS
                              CdhD   2 vvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairli 78 
                                       v +G+++++ k+Gge+v+yr++ tffn++ +a+dv D ++e     l+er++ +   w+k+++g+   ++++a+r  
  gi|386002997|ref|YP_005921296.1|  73 VYVGVGDQQLKVGGEDVMYRHQMTFFNKPPFAYDVTDGMNEA---DLVERVKLIDG-WKKFYIGKWESVEMVAVRSV 145
                                       789**********************************99985...77888876555.********99********** PP

                                       SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SSH CS
                              CdhD  79 stdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvllsindl 155
                                       ++dP +kfa+ v+kv++++k p++l+++dp+vlka+lev +  rpl+yaAtk+++ke+a+la +ykvpv+l++  dl
  gi|386002997|ref|YP_005921296.1| 146 TGDP-AKFAACVKKVMENTKKPMILCSFDPKVLKAGLEVSAATRPLIYAATKENWKEVAQLAFDYKVPVTLSVPFDL 221
                                       ****.************************************************************************ PP

                                       HHHHHHHHHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS.-TTS-S-BEEE---SSHHHHHHHHH... CS
                              CdhD 156 eelkelarkllkagvkdivldPttaalGegleetidnvvriRraaikg.dkdlafPilslttnawlaresdeve... 228
                                       + lk +a++++++g+kd+vldP+ta+ Ge l+e+++n++++Rra++++  kd+++P+++l++naw++  +d v+   
  gi|386002997|ref|YP_005921296.1| 222 DGLKGMAQTFAEMGLKDLVLDPGTAPNGEKLQESLQNFIKLRRASVEEgQKDFNYPVMALPINAWMTT-KDPVRgay 297
                                       ***********************************************99******************6.88888999 PP

                                       ........HHHTT-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHHH CS
                              CdhD 229 ........lvvrYadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtve 297
                                               +v+r adi+i +s+e ++++P ++lr+niYtDPr+Pv+v+pgly++g++ e sPvflttnf+LtyYtve
  gi|386002997|ref|YP_005921296.1| 298 wesvlaatFVIRGADIMIRHSIEPHSVMPDMHLRFNIYTDPRTPVQVKPGLYKVGNPTESSPVFLTTNFALTYYTVE 374
                                       999999*********************************************************************** PP

                                       HHHHHTTS-EEEEEE-SSS--HHHHHHTTSSSHHHHHHHHHHTTHH.HHSSS-EEEE-GGGGGGHHHHHHHHTSEE. CS
                              CdhD 298 gdlesdkitayLLvldteGlgvevslaggqleaekvkdlieetgie.ekvkhrflilPglvavlkgkiedltgwkv. 372
                                       +dl s++i +yLL+++t+G+gv++s+aggql+ +k+kd++ e+g++ ek+ h+  ilPg++a+ +g+++dl   kv 
  gi|386002997|ref|YP_005921296.1| 375 SDLGSNNIDSYLLAVNTDGIGVQASVAGGQLTPAKIKDAFAEAGMDfEKTTHKAFILPGMAAKFSGELDDLYAYKVk 451
                                       *********************************************9789*********************9987662 PP

                                       .EE--SSGGGHHHH CS
                              CdhD 373 .lvgprdsseivav 385
                                        +vgp+ds++i+++
  gi|386002997|ref|YP_005921296.1| 452 aMVGPEDSGRIPGW 465
                                       269********988 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   1.7   9.3e-18   8.4e-14       1      33 []      13      45 ..      13      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 9.3e-18
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LP+tNCg+CG+++CmafA+ +++   ++e+C+p
  gi|386002997|ref|YP_005921296.1| 13 LPQTNCGECGEQTCMAFAAGIISRTRKIEECKP 45
                                      9******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 3625.91
//
Query:       gi|386002998|ref|YP_005921297.1|  [L=450]
Description: Acetyl-CoA decarbonylase/synthase complex subunit delta [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-78  261.7   3.3    4.3e-74  249.5   0.8    3.1  3  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   0.8   2.4e-78   4.3e-74       1     228 [.     127     378 ..     127     383 .. 0.96
   2 !    5.0   0.0   0.00046       8.2     263     293 ..     379     407 ..     378     412 .. 0.84
   3 !    7.3   0.1   9.2e-05       1.6     350     383 ..     413     447 ..     407     450 .] 0.78

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 2.4e-78
                                       EEEESS.......GCG-EEEE----S.STTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETTE CS
                              CdhD   1 evvlGa.......eekavkiGgeevL.yrfeltffnptaiaidvsDelseellkalaerieevvdd...wakkrvge 66 
                                       ev+lGa       +++ +kiGge+++ + f++ ++n+++++idv+D++  + +ka+++++e+v++d   wakk+v+e
  gi|386002998|ref|YP_005921297.1| 127 EVQLGAtkaeggsRGHVIKIGGEKAMpFFFDAAMPNRPVVTIDVFDMPI-GMAKAVKMHYEDVMNDpadWAKKAVKE 202
                                       5777777777777999**********666*****************888.68************************* PP

                                       EEE--EEEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT. CS
                              CdhD  67 kltldaiairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd. 131
                                        +++d+++ +listdP      ak++ k+ve+v++av+vp+v+ggs     d+evl +a ev+++er l+++A+++ 
  gi|386002998|ref|YP_005921297.1| 203 -FKADLVTTHLISTDPlvkdtpAKEAVKVVEDVLQAVDVPIVIGGSgnpekDVEVLSKASEVAQGERALIASASLNl 278
                                       .**************************************************************************** PP

                                       THHHHHHHHHHTT--EEEE-.SSHHHHHHHHHHHHC.TT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS-T CS
                              CdhD 132 dykeiaelaleykvpvvllsindleelkelarkllk.agv..kdivldPttaalGegleetidnvvriRraaikgdk 205
                                       d+++i ++ + ++   +++++ +++++kel+rkl+k agv  ++iv+dPttaal +g++++++n++riR+ ++kgd+
  gi|386002998|ref|YP_005921297.1| 279 DWEAIGKACVANNNVCLAWTQLEINSQKELNRKLMKvAGVprDSIVMDPTTAALAYGMDFAYTNMERIRLGGLKGDE 355
                                       ************************************9999*9*********************************** PP

                                       TS-S-BEEE---SSHHHHHHHHH CS
                              CdhD 206 dlafPilslttnawlaresdeve 228
                                       +l+fP++s+ttnaw++re+++v+
  gi|386002998|ref|YP_005921297.1| 356 ELNFPMSSGTTNAWGVREAWMVN 378
                                       *********************98 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.00046
                                       S--B--SSEEEESS--TTS-EEEEES.BHHHH CS
                              CdhD 263 kPvavdpglyeigdrdensPvflttn.fsLty 293
                                       +P ++d  +   gdr  ++P++++ + fsL+ 
  gi|386002998|ref|YP_005921297.1| 379 SPNKNDSPW---GDRMLRGPIWEILTgFSLAM 407
                                       79999****...**********9965499876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 9.2e-05
                                       EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGGGHH CS
                              CdhD 350 flil.Pglvavlkgkiedltgwkvlvgprdsseiv 383
                                       f+++ P++va l+++++ l+g   ++ p+++++i 
  gi|386002998|ref|YP_005921297.1| 413 FMMMnPIAVAYLQEITQSLMGLVKAETPDTTKWIS 447
                                       89999**************9986666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2840.36
//
Query:       gi|386002999|ref|YP_005921298.1|  [L=253]
Description: CO dehydrogenase maturation factor [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-18   66.7   0.2    2.6e-18   66.3   0.2    1.1  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    3.8e-16   59.5   0.3    5.3e-16   59.0   0.3    1.2  1  AAA_31         AAA domain
    6.1e-10   38.8   0.2    9.5e-10   38.1   0.2    1.4  1  ArsA_ATPase    Anion-transporting ATPase
    1.3e-08   34.7   1.8    8.7e-08   31.9   1.8    2.2  1  ParA           NUBPL iron-transfer P-loop NTPase
    1.2e-07   31.5   0.2     0.0032   17.0   0.0    2.2  2  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
      2e-06   27.4   0.0     0.0074   15.8   0.0    2.2  2  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
    1.3e-05   24.3   0.9    2.6e-05   23.4   0.9    1.7  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
    9.7e-05   22.6   0.3    0.00052   20.2   0.1    2.0  2  DUF87          Helicase HerA, central domain
    0.00015   21.6   0.1    0.00019   21.2   0.1    1.2  1  AAA_24         AAA domain
    0.00018   20.9   3.0      0.057   12.7   0.2    2.7  3  MipZ           ATPase MipZ
    0.00053   19.7   3.7      0.055   13.1   0.6    2.8  3  SRP54          SRP54-type protein, GTPase domain
    0.00057   20.1   0.5      0.052   13.8   0.0    2.4  2  Toprim         Toprim domain
    0.00066   19.5   0.1     0.0012   18.6   0.0    1.6  1  AAA_30         AAA domain
     0.0038   17.5   0.1       0.01   16.1   0.1    1.9  1  AAA_22         AAA domain
      0.005   16.7   2.3       0.45   10.3   0.0    2.4  2  AAA_26         AAA domain
     0.0094   16.5   0.2      0.025   15.1   0.2    1.9  1  ABC_tran       ABC transporter
  ------ inclusion threshold ------
       0.01   16.2   0.0       0.02   15.3   0.0    1.6  1  AAA_16         AAA ATPase domain
      0.011   16.1   2.9       0.03   14.6   2.9    2.1  1  AAA_19         AAA domain
      0.018   15.3   0.7        1.9    8.8   0.1    2.4  2  TrkA_N         TrkA-N domain
      0.023   14.8   0.1      0.059   13.4   0.1    1.6  1  HTH_3          Helix-turn-helix
      0.023   14.4   0.1      0.067   12.9   0.1    1.7  2  PRK            Phosphoribulokinase / Uridine kinase family
      0.027   13.7   0.2       0.13   11.5   0.2    1.9  2  DUF2075        Uncharacterized conserved protein (DUF2075)
      0.029   14.4   0.1       0.14   12.2   0.0    2.1  2  AAA_14         AAA domain
      0.031   14.2   0.0      0.049   13.5   0.0    1.4  1  APS_kinase     Adenylylsulphate kinase
      0.032   13.8   0.1        1.4    8.5   0.0    2.1  2  Ras            Ras family
      0.037   13.5   0.6        2.1    7.7   0.0    2.4  2  Pox_A32        Poxvirus A32 protein
       0.04   13.3   0.1       0.13   11.6   0.0    1.8  2  ATPase         KaiC
      0.042   14.3   0.2         12    6.4   0.0    2.5  2  Toprim_2       Toprim-like
      0.049   14.1   0.1        0.2   12.2   0.0    2.0  1  Toprim_4       Toprim domain
      0.052   13.5   0.0       0.11   12.4   0.0    1.6  1  ResIII         Type III restriction enzyme, res subunit
      0.071   12.3   0.3       0.12   11.5   0.3    1.4  1  PIF1           PIF1-like helicase
       0.11   12.3   0.0       0.38   10.6   0.0    1.9  2  Helicase_RecD  Helicase
       0.12   11.8   0.0        0.3   10.6   0.0    1.7  1  AAA_7          P-loop containing dynein motor region
       0.18   10.7   0.3       0.27   10.1   0.3    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.32   10.1   1.3       0.46    9.5   0.6    1.5  2  LpxK           Tetraacyldisaccharide-1-P 4'-kinase
       0.38    9.9   1.5       0.64    9.2   1.1    1.7  2  NB-ARC         NB-ARC domain
       0.64    9.9   3.9        2.9    7.8   1.5    2.3  2  NTPase_1       NTPase
        2.9    7.4   5.4        1.1    8.8   1.0    2.5  3  AAA_25         AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.2   5.4e-21   2.6e-18       2     127 ..       5     229 ..       4     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 5.4e-21
                                       EEEESSTTSSHHHHHHHHHHHHHHT..T--EEEEEEEESSCCCCH....HTTEB-HHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx....xxxxxxxxxx.................. RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarr..glrVllvDaDpqannlai....leglendiep.................. 54 
                                       +++ +kGG+GKT ++a ++r+l +r  +  +l++DaDp+an++ +    +e +++di++                  
  gi|386002999|ref|YP_005921298.1|   5 IAITGKGGTGKTAVTAMIIRSLLKRekKTTILAIDADPDANLADVlgddVEMTVGDIREeiqdsrislppdidkkql 81 
                                       6789******************9962256689***********988887777777777799**************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386002999|ref|YP_005921298.1|  82 faakifeallekdgydllvmgrsegsgcycylnsllkgimdetiddydlvivdspaglehlsrktisevdslivvtd 158
                                       ***************************************************************************** PP

                                       ....CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                           +lk   e++++l k++ l+ k + v++n+v+   ++ ++ +  e     +g++v+g+ip+de+va+++  g+p
  gi|386002999|ref|YP_005921298.1| 159 esrrGLKT-AETIRQLAKELDLKYKSLYVIANKVRDL-SKDQILKVAEG----LGLKVIGMIPYDENVARLDLAGDP 229
                                       99987755.778888888877779**********964.33333333333....3****************9998877 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.3   1.1e-18   5.3e-16       2     168 ..       3     178 ..       2     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.1e-18
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkk..vLlvDlDpQanattglgiekneiektlyevlieeknikeaiikt 76 
                                       kvIai+  KGG GKT+ + ++  +l k++kk  +L +D+Dp an++  lg   +++e t+ ++  ee++ + +    
  gi|386002999|ref|YP_005921298.1|   3 KVIAIT-GKGGTGKTAVTAMIIRSLLKREKKttILAIDADPDANLADVLG---DDVEMTVGDI-REEIQDSRISLPP 74 
                                       899986.6*****************9999885579************999...6778888888.3455555555555 PP

                            AAA_31  77 kvenldlipssid...Laeaeielvelekk.........eeilkellekvkdeYDyiiiDcpPsLglltenaLvasd 141
                                       ++++ +l  ++i    L +   +l+ + ++         ++ lk ++++  d+YD++i+D p  L+ l ++ +   d
  gi|386002999|ref|YP_005921298.1|  75 DIDKKQLFAAKIFealLEKDGYDLLVMGRSegsgcycylNSLLKGIMDETIDDYDLVIVDSPAGLEHLSRKTISEVD 151
                                       5777777777764332333334555555554577777766669********************************** PP

                            AAA_31 142 sviipvqaeayaleGleqllktieevk 168
                                       s+i++++ + + l+++e + +  +e++
  gi|386002999|ref|YP_005921298.1| 152 SLIVVTDESRRGLKTAETIRQLAKELD 178
                                       ********9999888766665555554 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.2     2e-12   9.5e-10       2     133 ..       3     136 ..       2     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2e-12
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE..EE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHH CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvll..istDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleea 76 
                                       kvi ++GKGG GKt+v a +   l + +kk+ +  i  DP  +l+D++  +++ ++  ++e ++   i    +++++
  gi|386002999|ref|YP_005921298.1|   3 KVIAITGKGGTGKTAVTAMIIRSLLKREKKTTIlaIDADPDANLADVLGDDVEMTVGDIREEIQDSRISLPPDIDKK 79 
                                       799*****************9999988888755115679************************************** PP

                                       HCCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESB CS
                       ArsA_ATPase  77 kqevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDta 133
                                       +  ++k  eall+ ++ + ++   ++   +   + s+ + +   + ++yd v++D++
  gi|386002999|ref|YP_005921298.1|  80 QLFAAKIFEALLEKDGYDLLVMGRSEGSGCYCYLNSLLKGIMDETIDDYDLVIVDSP 136
                                       *********999977766555444444345444555544444444789*******74 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   1.8   1.9e-10   8.7e-08       6     239 ..       4     244 ..       1     251 [. 0.74

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.9e-10
                              ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgll..D.......aDiyGpsiprllgveeekpeqsekkliPvea..k 71 
                                       ++ + gKGG GK+ v++ +  +L k+++k+ +l  D       aD+ G ++   +g  +e+++ s+   +P +   k
  gi|386002999|ref|YP_005921298.1|   4 VIAITGKGGTGKTAVTAMIIRSLLKREKKTTILaiDadpdanlADVLGDDVEMTVGDIREEIQDSR-ISLPPDIdkK 79 
                                       44568***************************9553223333346899999988887777676666.4456666344 PP

                              ParA  72 gi.kvmSigfllesedeavvwrGpm....kskaikqllkdv...ewgelDyLiiDlPPGtgDeqltvaqklplagav 140
                                       ++  +  ++ lle++   ++  G          ++ llk +   + ++ D++i+D P G   e+l+     +++  +
  gi|386002999|ref|YP_005921298.1|  80 QLfAAKIFEALLEKDGYDLLVMGRSegsgCYCYLNSLLKGImdeTIDDYDLVIVDSPAGL--EHLSRKTISEVDSLI 154
                                       44144445788988877776655441111444667776644111567899*******876..89999999999**** PP

                              ParA 141 iVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeire 217
                                       +Vt   +  l+ ++   +++k++++k  ++      +v     +k++ ++k++  k+ae lg++++g ip d+++++
  gi|386002999|ref|YP_005921298.1| 155 VVTDESRRGLKTAETIRQLAKELDLKYKSL------YVIA---NKVRDLSKDQILKVAEGLGLKVIGMIPYDENVAR 222
                                       **********************99988654......3333...3556689999************************ PP

                              ParA 218 asdegkplvlkepeseaakale 239
                                          +g+plv   ++s+a  ++e
  gi|386002999|ref|YP_005921298.1| 223 LDLAGDPLVGLPDDSPAVMEVE 244
                                       9999999998877777655544 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.7e-06    0.0032       2      55 ..       4      58 ..       3      76 .. 0.76
   2 !   12.7   0.0   0.00014     0.065     157     222 ..     166     228 ..     145     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkk..vlivGCDPkaDstrlllggkaqetv 55
                                       iai GkGG Gk+  ++ +  +l ++ kk  +l +  DP a+ +  +lg  ++ tv
  gi|386002999|ref|YP_005921298.1|  4 VIAITGKGGTGKTAVTAMIIRSLLKREKKttILAIDADPDANLA-DVLGDDVEMTV 58
                                      59*****************9999999988446777777877655.34455555455 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                         Fer4_NifH 157 aanniakgiekyaksggvrlgGl..iinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkk 222
                                       +    a++i++ ak+ +++   l  i n +  d  ++ i k ae lg+kv+ ++P de+v + +l+  
  gi|386002999|ref|YP_005921298.1| 166 T----AETIRQLAKELDLKYKSLyvIAN-KVRDLSKDQILKVAEGLGLKVIGMIPYDENVARLDLAGD 228
                                       3....55677777777777766531555.65677999***********************99888765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05    0.0074       3      57 ..       4      59 ..       2      72 .. 0.77
   2 !    9.7   0.0    0.0011      0.53     108     146 ..     120     158 ..      89     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawal..helgesvlviDlspdnlLrlhFnvdieqreg 57
                                      v+a++G +GG+G+t+++a++ ++l  +e +  +l+iD+ pd  L+     d+e + g
  gi|386002999|ref|YP_005921298.1|  4 VIAITG-KGGTGKTAVTAMIIRSLlkREKKTTILAIDADPDANLADVLGDDVEMTVG 59
                                      788888.8*************999333456689********9888777666666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                          CBP_BcsQ 108 alkelkeqyrwillDlpagasaltrellaladlvllvve 146
                                        ++e   +y+++++D pag ++l r++++  d+ + v+ 
  gi|386002999|ref|YP_005921298.1| 120 IMDETIDDYDLVIVDSPAGLEHLSRKTISEVDSLIVVTD 158
                                       45555689*********************9999998865 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.9   5.4e-08   2.6e-05      30      92 ..       3      65 ..       1     204 [. 0.87

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.4e-08
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTE CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegv 92
                                      +v+ +tG  G+Gk  ++  ++ +l +r k+ ++la+D     +   +lGD + ++  +  e +
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIIRSLLKREKKTTILAIDADPDANLADVLGDDVEMTVGDIREEI 65
                                      6899************************************************99877766655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.1e-06   0.00052      26      61 ..       5      41 ..       2      74 .. 0.94
   2 ?    0.1   0.0       1.5   7.2e+02     118     152 ..     140     186 ..     123     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-06
                             DUF87 26 lAilgsTGsGKSntvavLleelle.kkgatililDpH 61
                                      +Ai g+ G+GK+  +a ++++ll+ +k++til +D++
  gi|386002999|ref|YP_005921298.1|  5 IAITGKGGTGKTAVTAMIIRSLLKrEKKTTILAIDAD 41
                                      79**********************9999******986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                             DUF87 118 rsvleealdqaka.....keekeklssdepveklleelk.......k 152
                                       + + +++++++++     +e++  l+++e + +l++el         
  gi|386002999|ref|YP_005921298.1| 140 EHLSRKTISEVDSlivvtDESRRGLKTAETIRQLAKELDlkykslyV 186
                                       55666777777777777777778888888888888888733332221 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1     4e-07   0.00019       1      85 [.       1     147 [.       1     190 [. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4e-07
                            AAA_24   1 kklkiliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdie.swedfldevvel........ 59 
                                       +++ i+i+G+ g+GKT + +++         + ++l id +   ++l +  ++d+e ++ d+++e++          
  gi|386002999|ref|YP_005921298.1|   1 MGKVIAITGKGGTGKTAVTAMIirsllkrekKTTILAIDADP-DANLADVLGDDVEmTVGDIREEIQDSrislppdi 76 
                                       5789******************9******5555555556665.8899999999999999999999999999****** PP

                            AAA_24  60 .............................................aaeladyktlviDtideleelclaev 85 
                                                                                    ++  +dy+ +++D+   le l ++ +
  gi|386002999|ref|YP_005921298.1|  77 dkkqlfaakifeallekdgydllvmgrsegsgcycylnsllkgimDETIDDYDLVIVDSPAGLEHLSRKTI 147
                                       *********************************************999999*******9887777766655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.2    0.0042         2       7      39 ..       8      40 ..       3      57 .. 0.85
   2 !   12.7   0.2   0.00012     0.057      89     140 ..     117     168 ..     112     201 .. 0.77
   3 ?   -0.3   0.0       1.1   5.2e+02     193     218 ..     186     211 ..     169     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                                      -SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  7 nekGGsGksttavhvavaLlkkGarvaaidldl 39
                                        kGG+Gk++++  ++ +Llk+ ++ + + +d+
  gi|386002999|ref|YP_005921298.1|  8 TGKGGTGKTAVTAMIIRSLLKREKKTTILAIDA 40
                                      56*******************999988777775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHCCCE CS
                              MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfdllg 140
                                       l+ +++++  ++d++++d+P   ++lsr + s+ d+l+   ++s   +    
  gi|386002999|ref|YP_005921298.1| 117 LKGIMDETIDDYDLVIVDSPAGLEHLSRKTISEVDSLIVVTDESRRGLKTAE 168
                                       6678999999***************************988777765555555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHT-EEE---B--GG CS
                              MipZ 193 kveealeeLskrvGfrvasGlservi 218
                                        +++++++Lsk   ++va+Gl  +vi
  gi|386002999|ref|YP_005921298.1| 186 VIANKVRDLSKDQILKVAEGLGLKVI 211
                                       57889999999999999999999998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.6   0.00012     0.055       2      38 ..       3      39 ..       2      45 .. 0.95
   2 ?    5.6   0.1     0.023        11      75     125 ..     119     170 ..     110     181 .. 0.79
   3 ?    1.1   0.0      0.54   2.5e+02      16      62 ..     168     213 ..     161     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +vi++ G  G+GKT  +a + + l k++kk+ + a D
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIIRSLLKREKKTTILAID 39
                                      6899*******************************99 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                                       HHHHHHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTB CS
                             SRP54  75 avekakeekidvvlvDT.aGrlqndkelmeelkkikkvvkpdevllvldatt 125
                                       ++  +  +++d+v+vD+ aG  +  ++ ++e++++  v+++ +  l    t+
  gi|386002999|ref|YP_005921298.1| 119 GIMDETIDDYDLVIVDSpAGLEHLSRKTISEVDSLIVVTDESRRGLKTAETI 170
                                       555666779*******879*************99998887766666555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEES CS
                             SRP54  16 ttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikk 62 
                                        t+ +La+ l  + k++ ++a    R    +Q+  +ae lg +vi++
  gi|386002999|ref|YP_005921298.1| 168 ETIRQLAKELDLKYKSLYVIA-NKVRDLSKDQILKVAEGLGLKVIGM 213
                                       578889988887766666665.6889999*********999999975 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.084        40      56      76 ..      23      44 ..       3      50 .. 0.76
   2 !   13.8   0.0   0.00011     0.052      57      96 ..     143     182 ..      76     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.084
                                      HHHHH.HHHSEEEEECSSSHHH CS
                            Toprim 56 lkela.kradeiilatDpDreG 76
                                      +++l+ ++ +  ila+D+D + 
  gi|386002999|ref|YP_005921298.1| 23 IRSLLkREKKTTILAIDADPDA 44
                                      677775778899*******875 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00011
                                       HHHH.HHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEE CS
                            Toprim  57 kela.kradeiilatDpDreGeaiawellevlkellenkig 96 
                                        +   +++d +i+ tD  r G ++a  +++++kel+ + ++
  gi|386002999|ref|YP_005921298.1| 143 SRKTiSEVDSLIVVTDESRRGLKTAETIRQLAKELDLK-YK 182
                                       4444599**********************999966655.44 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.5e-06    0.0012      19      82 ..       3      81 ..       1     160 [. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                            AAA_30 19 rvavltGpAGtGKttalkal.reaweaaggrviglA....ptgkaAkvLaeelgieastiakllkrlk........... 81
                                      +v ++tG  GtGKt + + + r ++++++ +  +lA    p ++ A+vL+++++++   i + ++  +           
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIiRSLLKREK-KTTILAidadPDANLADVLGDDVEMTVGDIREEIQDSRislppdidkkq 80
                                      4789**************99667777665.4444442334889999999999999988888887766677666555544 PP

                            AAA_30 82 g 82
                                       
  gi|386002999|ref|YP_005921298.1| 81 L 81
                                      0 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.1e-05      0.01       6      57 ..       3      50 ..       2     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.....erpevvfvtlpsstsskdll 57
                                      +++++tG  GtGKT + +++ ++l +++k ++     +           + +++d+l
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIIRSLLKREKKTTilaidA---------DPDANLADVL 50
                                      689*********************98876555555552.........4333333332 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.6     0.022        10      11      32 ..      12      33 ..       3      36 .. 0.81
   2 !   10.3   0.0   0.00095      0.45     134     194 ..     155     220 ..     117     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                            AAA_26 11 gvGKTvvslgLvralkrkgvkv 32
                                      g GKT+v+++++r+l +++ k+
  gi|386002999|ref|YP_005921298.1| 12 GTGKTAVTAMIIRSLLKREKKT 33
                                      79*************9988776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00095
                            AAA_26 134 Vargglgtinqllltiealrqk...nvrvlGvilNkvrnp..envetlekksgipvlGvvPylpdl 194
                                       V++ +++   +++ ti  l ++   + + l vi+Nkvr+   +++ ++ +  g++v+G +Py++++
  gi|386002999|ref|YP_005921298.1| 155 VVTDESRRGLKTAETIRQLAKEldlKYKSLYVIANKVRDLskDQILKVAEGLGLKVIGMIPYDENV 220
                                       5555555545556666555543333566788*****987766899999999***********9976 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   5.4e-05     0.025      11      45 ..       2      36 ..       1     210 [. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-05
                                      TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllkpteGeilld 45
                                      g+++ai+G+ G+GK+ + +++++ l + e + ++ 
  gi|386002999|ref|YP_005921298.1|  2 GKVIAITGKGGTGKTAVTAMIIRSLLKREKKTTIL 36
                                      899******************99887766555433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   4.3e-05      0.02      26      63 ..       4      45 ..       1     104 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekd....ggiflrgkcdql 63
                                      ++ ++G  G+GK+++  ++ r+l k+     ++++ ++ d +
  gi|386002999|ref|YP_005921298.1|  4 VIAITGKGGTGKTAVTAMIIRSLLKRekktTILAIDADPDAN 45
                                      689****************99999995543333355555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.9   6.4e-05      0.03      11      47 ..       3      37 ..       1     209 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.4e-05
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeill 47
                                      kv+++t+  GtGKT v+ +i++ l+++++    +il+
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIIRSLLKREKK--TTILA 37
                                      899*********************999954..44544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.065        31       9      50 ..      18      62 ..       5      65 .. 0.67
   2 ?    8.8   0.1     0.004       1.9      43      90 ..     130     179 ..     119     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.065
                                      HHHHHHHHHHHTT..EEEEEEESSHHH.HHHHHHTTSEEEES-TT CS
                            TrkA_N  9 vGrslaeeLsegg..kdvvvidkdeer.veelreeglevvvgdat 50
                                      v+  +++ L +++    +++id d+++ ++ +  + +e  vgd  
  gi|386002999|ref|YP_005921298.1| 18 VTAMIIRSLLKREkkTTILAIDADPDAnLADVLGDDVEMTVGDIR 62
                                      445566777774357669999999976577777777777777766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.004
                                       EEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSS..S CS
                            TrkA_N  43 evvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpk..k 90 
                                        v+v +++  e L +  i+++d++i++t++    + +++++++l ++  +
  gi|386002999|ref|YP_005921298.1| 130 LVIVDSPAGLEHLSRKTISEVDSLIVVTDESRRGLKTAETIRQLAKEldL 179
                                       4777888888899999***************9999999999999887441 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00012     0.059      11      51 ..     169     209 ..     169     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSE CS
                             HTH_3  11 sqeeLAeklGvsrstisriEnGernPsletlkklakaLgvs 51 
                                       ++++LA++l++++ +++ i n  r  s + ++k+a+ Lg++
  gi|386002999|ref|YP_005921298.1| 169 TIRQLAKELDLKYKSLYVIANKVRDLSKDQILKVAEGLGLK 209
                                       679***********************************975 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00014     0.067       1      31 [.       4      34 ..       4      58 .. 0.74
   2 ?   -1.6   0.0       4.1   1.9e+03      31      78 ..     137     184 ..     129     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaa 31
                                      vI+++g+ G Gkt+v++ +  ++ + ++k++
  gi|386002999|ref|YP_005921298.1|  4 VIAITGKGGTGKTAVTAMIIRSLLKREKKTT 34
                                      8**************9987655554444433 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                               PRK  31 aeiegdsflrldraekdleleerkrakekevsflspeandfdllyevl 78 
                                       a+ e+ s  ++ +++  + + +++r++ k+ +     a+++dl y+ l
  gi|386002999|ref|YP_005921298.1| 137 AGLEHLSRKTISEVDSLIVVTDESRRGLKTAETIRQLAKELDLKYKSL 184
                                       566777777777777778888888888888888888888888888765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00028      0.13       2      37 ..       3      37 ..       2      69 .. 0.80
   2 ?    0.1   0.0      0.78   3.7e+02     197     222 ..     125     150 ..      56     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavyl 37
                                      +v+ +tG+ GtGKt v   ++  l  ++e++t++++
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIIRSL-LKREKKTTILA 37
                                      6999**************999999.45555555554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.78
                           DUF2075 197 qenfdirvfddleelkkalkeknkes 222
                                        +++d+ ++d+++ l++  ++  +e 
  gi|386002999|ref|YP_005921298.1| 125 IDDYDLVIVDSPAGLEHLSRKTISEV 150
                                       46789999999988887766655444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0003      0.14       2      47 ..       2      47 ..       1      94 [. 0.77
   2 ?   -1.2   0.0         4   1.9e+03      81     104 ..     115     139 ..     111     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkla 47
                                      +k+++itG   +GKT +   +i++ll   kk  il i+ d  +d++la
  gi|386002999|ref|YP_005921298.1|  2 GKVIAITGKGGTGKTAVTAMIIRSLLkrEKKTTILAIDAD--PDANLA 47
                                      589***********************55555555555555..444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                            AAA_14  81 kalkslvdeg.knldvivtGSnskl 104
                                       + lk+++de+ +++d+++  S ++l
  gi|386002999|ref|YP_005921298.1| 115 SLLKGIMDETiDDYDLVIVDSPAGL 139
                                       6799999999889999999987765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001     0.049       2      39 ..       2      39 ..       1      66 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                      g v+ +tG  g+GK++++ ++ ++L ++ +++++L  d
  gi|386002999|ref|YP_005921298.1|  2 GKVIAITGKGGTGKTAVTAMIIRSLLKREKKTTILAID 39
                                      7899**********************999999988544 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0029       1.4       3      32 ..       6      35 ..       3      61 .. 0.79
   2 ?    3.5   0.0       0.1        49      64     143 ..     142     221 ..     122     226 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0029
                                      EEEESTTSSHHHHHHHHHHSSCSSSCTTTS CS
                               Ras  3 vlvGdsavGKtslllrfvkdkFkeeyesTi 32
                                       + G++++GKt+++   +++  k+e+++Ti
  gi|386002999|ref|YP_005921298.1|  6 AITGKGGTGKTAVTAMIIRSLLKREKKTTI 35
                                      577**************************9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                                       HHHHHHTTESEEEEEEETTBH..HHHHTHHHHHHHHHHHSTTTSEEEEEEETT.TGGGG-SS-HHHHHHHHHHHTSE CS
                               Ras  64 lrelyyrdaegillvyditsr..esfenvkkwveeikrvaeenvpivLvGnKv.Dleekravsteegeelakelglk 137
                                       l ++ +++++ +++v d ++r  ++ e+++++ +e+  + +   ++++++nKv Dl++++ ++ +eg  l     ++
  gi|386002999|ref|YP_005921298.1| 142 LSRKTISEVDSLIVVTDESRRglKTAETIRQLAKELDLKYK---SLYVIANKVrDLSKDQILKVAEGLGLKVIGMIP 215
                                       55566666777777766443322344555555555555555...689999997699999999999998665544466 PP

                                       EEEEBT CS
                               Ras 138 fletSA 143
                                       + e  A
  gi|386002999|ref|YP_005921298.1| 216 YDENVA 221
                                       666555 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.079        37      16      40 ..       5      29 ..       3      40 .. 0.83
   2 ?    7.7   0.0    0.0045       2.1       8      39 ..      90     122 ..      84     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.079
                           Pox_A32 16 lalvGgsGsGktvyLlsLlrtlvkk 40
                                      +a++G+ G Gkt+    ++r+l k+
  gi|386002999|ref|YP_005921298.1|  5 IAITGKGGTGKTAVTAMIIRSLLKR 29
                                      79**********9988888888776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                           Pox_A32   8 sLlkkpFrlalvGgs.GsGktvyLlsLlrtlvk 39 
                                        L k+ + l ++G s GsG   yL sLl+ +++
  gi|386002999|ref|YP_005921298.1|  90 LLEKDGYDLLVMGRSeGSGCYCYLNSLLKGIMD 122
                                       47788899*****987*************9976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.13      19      61 ..       2      43 ..       1      78 [. 0.83
   2 ?   -0.9   0.0       1.8   8.3e+02     163     194 ..     134     163 ..     116     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                            ATPase 19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveepae 61
                                      g+v+ itG+ GtGKt + +  +i+++ k ++++ + +++ ++ 
  gi|386002999|ref|YP_005921298.1|  2 GKVIAITGKGGTGKTAVTA-MIIRSLLKREKKTTILAIDADPD 43
                                      789************9876.57777777799999999998874 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                            ATPase 163 ekssseeaaggygveefivdgvivLdlkeiee 194
                                       + + + e+ ++  ++e  vd  iv++ ++ ++
  gi|386002999|ref|YP_005921298.1| 134 DSPAGLEHLSRKTISE--VDSLIVVTDESRRG 163
                                       4455555555555555..55555555444433 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.026        12      29      57 ..      13      44 ..       3      73 .. 0.82
   2 ?    5.6   0.0     0.044        21      35      75 ..     138     181 ..     124     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.026
                          Toprim_2 29 t...alteaalkllerypekkvvlalDnDkaG 57
                                      t   a+t   ++ l ++++k+ +la D+D   
  gi|386002999|ref|YP_005921298.1| 13 TgktAVTAMIIRSLLKREKKTTILAIDADPDA 44
                                      344466677788888887999********875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.044
                          Toprim_2  35 alkllery...pekkvvlalDnDkaGrkaakrlaellreagvre 75 
                                        l+ l+r+   + + +++ +D+ + G k a+++++l++e  ++ 
  gi|386002999|ref|YP_005921298.1| 138 GLEHLSRKtisEVDSLIVVTDESRRGLKTAETIRQLAKELDLKY 181
                                       5556666644334789********************99877444 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00042       0.2      36      82 ..     141     178 ..     130     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                          Toprim_4  36 girpeklktenlveaekkvkevilaldgDaeGeataerlaellleeg 82 
                                       +++++ +         ++v+ +i+++d + +G +tae + +l +e +
  gi|386002999|ref|YP_005921298.1| 141 HLSRKTI---------SEVDSLIVVTDESRRGLKTAETIRQLAKELD 178
                                       3333333.........4599******************999554544 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00024      0.11      29      58 ..       7      36 ..       2      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                                      EEESTTSTHHHHHHHHHHHH-S.....-EE CS
                            ResIII 29 ikmaTGtGKTlvaaklierllkkgkeekfl 58
                                      i    GtGKT v a +i++llk +k+  +l
  gi|386002999|ref|YP_005921298.1|  7 ITGKGGTGKTAVTAMIIRSLLKREKKTTIL 36
                                      56667****************986643333 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00026      0.12      22      57 ..       2      37 ..       1      40 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                      TS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEE CS
                              PIF1 22 gklfFvtGsgGtgKtflwkallkklrsegkivlavA 57
                                      gk++ +tG gGtgKt +   ++ +l +++k++   A
  gi|386002999|ref|YP_005921298.1|  2 GKVIAITGKGGTGKTAVTAMIIRSLLKREKKTTILA 37
                                      78999******************9988887766555 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0008      0.38       2      31 ..       7      36 ..       6      90 .. 0.81
   2 ?   -0.8   0.0       2.5   1.2e+03      21      41 ..     146     166 ..     121     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0008
                     Helicase_RecD  2 ltAdRGRGKSaalGlalaaliaegksnilv 31
                                      +t++ G+GK+a+ ++++ +l++++k++ ++
  gi|386002999|ref|YP_005921298.1|  7 ITGKGGTGKTAVTAMIIRSLLKREKKTTIL 36
                                      899******************998833222 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                     Helicase_RecD  21 liaegksnilvtapskenvkt 41 
                                        i+e +s i+vt  s++ +kt
  gi|386002999|ref|YP_005921298.1| 146 TISEVDSLIVVTDESRRGLKT 166
                                       344444555555555555544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00064       0.3      34      72 ..       3      41 ..       1      58 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00064
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                      k + ++G+ GtGKt+++  ++++l k++ +++++ + a 
  gi|386002999|ref|YP_005921298.1|  3 KVIAITGKGGTGKTAVTAMIIRSLLKREKKTTILAIDAD 41
                                      567899*************99999988888777776665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00057      0.27      18      49 ..       5      36 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivl 49
                                      i+i+G  G+GKt ++  ++r++ +r+++  +l
  gi|386002999|ref|YP_005921298.1|  5 IAITGKGGTGKTAVTAMIIRSLLKREKKTTIL 36
                                      78********************9999887765 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.6   0.00097      0.46      46      71 ..      11      36 ..       4      37 .. 0.91
   2 ?   -3.0   0.0       6.4     3e+03     177     207 ..     148     175 ..     136     205 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00097
                                      S-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                      GGtGKT +++++++ l +r+ k  +l
  gi|386002999|ref|YP_005921298.1| 11 GGTGKTAVTAMIIRSLLKREKKTTIL 36
                                      9******************9999887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.4
                                       GG-SEEEE..........-TTTSSSS-EEEE CS
                              LpxK 177 kradlvilngakaeeeeaekaeeksipvlrm 207
                                       +++d +i+  +++++  ++   +++i++l+ 
  gi|386002999|ref|YP_005921298.1| 148 SEVDSLIVVTDESRRGLKT---AETIRQLAK 175
                                       5555555533333333221...122333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1    0.0013      0.64      22      44 ..       4      26 ..       1     102 [. 0.83
   2 ?   -1.4   0.0       2.2   1.1e+03       7      24 ..      85     102 ..      79     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                      EEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnks 44
                                      v+a+ G+gG GKt + + i++++
  gi|386002999|ref|YP_005921298.1|  4 VIAITGKGGTGKTAVTAMIIRSL 26
                                      89**************9999874 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                       HHHHHHHCTTTSCSEEEE CS
                            NB-ARC   7 kviekLlekdelqslvva 24 
                                       k+ e Llekd+ ++lv++
  gi|386002999|ref|YP_005921298.1|  85 KIFEALLEKDGYDLLVMG 102
                                       566777777777755443 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.5    0.0061       2.9       2      27 ..       5      30 ..       4      35 .. 0.86
   2 ?    2.2   0.0      0.33   1.5e+02      89     123 ..     121     155 ..     109     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0061
                                      EEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                      ++iTG+ G+GKt +   +++ l +++
  gi|386002999|ref|YP_005921298.1|  5 IAITGKGGTGKTAVTAMIIRSLLKRE 30
                                      89****************99986665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.33
                                       HHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1  89 lrkalseadviviDEiGkmElkskkfkeaveevLk 123
                                       +++++ + d++++D    +E  s+k +++v+ ++ 
  gi|386002999|ref|YP_005921298.1| 121 MDETIDDYDLVIVDSPAGLEHLSRKTISEVDSLIV 155
                                       55666778888888888888888888888887654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0    0.0023       1.1      33      58 ..       2      27 ..       1     100 [. 0.88
   2 ?   -1.6   0.1       3.6   1.7e+03     140     152 ..     125     137 ..     120     166 .. 0.71
   3 ?   -1.4   0.0       3.1   1.4e+03     110     138 ..     149     178 ..     133     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                            AAA_25 33 gelallaGapgtGKttlaldlalava 58
                                      g++++++G +gtGKt+++  +  +++
  gi|386002999|ref|YP_005921298.1|  2 GKVIAITGKGGTGKTAVTAMIIRSLL 27
                                      899*************9987766665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                            AAA_25 140 vegvrlvviDpls 152
                                       + +++lv++D+ +
  gi|386002999|ref|YP_005921298.1| 125 IDDYDLVIVDSPA 137
                                       4568999999755 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.1
                            AAA_25 110 gveslpLfakdrggtl.ltadvdaleaaie 138
                                       +v+sl +++++++  l +++ +++l+++++
  gi|386002999|ref|YP_005921298.1| 149 EVDSLIVVTDESRRGLkTAETIRQLAKELD 178
                                       334455555544444437888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 1444.74
//
Query:       gi|386003000|ref|YP_005921299.1|  [L=93]
Description: CO dehydrogenase/acetyl-CoA synthase C [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score 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   12.8   5.6        0.2   12.1   5.6    1.3  1  K_channel_TID  Potassium channel Kv1.4 tandem inactivation do
       0.35   11.5  10.5       0.27   11.8   8.8    1.6  2  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> K_channel_TID  Potassium channel Kv1.4 tandem inactivation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.6   2.3e-05       0.2      28      59 ..      39      70 ..      31      78 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                     K_channel_TID 28 rererlahsraaaaaavaaaaaaaeGeGGggG 59
                                      +e e  a + aaaa a+aaa a a   GG+gG
  gi|386003000|ref|YP_005921299.1| 39 KEPEAAAPAAAAAAPAAAAAPAFAMPAGGSGG 70
                                      44444544445555455555577777888877 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.8     3e-05      0.27      20      66 ..       7      59 ..       3      65 .. 0.52
   2 ?   -1.9   0.0      0.57   5.1e+03      32      44 ..      79      91 ..      76      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXX CS
                     Ribosomal_60s 20 aarvkllvkalegkdieellangaakla.........aaaaaaaaaaaaaaaaaaa 66
                                      a+++ ++ + + ++   e++++g+ kla         a  aa+aaaaaa aaaaa 
  gi|386003000|ref|YP_005921299.1|  7 ASSPTVDSERCGKNREGEIVMAGK-KLAlklkkkepeA--AAPAAAAAAPAAAAAP 59
                                      555555555555555566666665.4445888888533..3333333333333332 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.57
                                      XXXXXXXXXXXXX CS
                     Ribosomal_60s 32 gkdieellangaa 44
                                      +++i+e++ ++++
  gi|386003000|ref|YP_005921299.1| 79 NVSIKEVIIKPKS 91
                                      5789999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 546.28
//
Query:       gi|386003001|ref|YP_005921300.1|  [L=460]
Description: Acetyl-CoA decarbonylase/synthase complex subunit beta [Methanosaeta harundinacea 6Ac]
Scores for complete 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-54  183.4   0.3    3.9e-54  182.7   0.3    1.3  1  CdhC           CO dehydrogenase/acetyl-CoA synthase complex b
  ------ inclusion threshold ------
      0.029   15.0   0.0      0.058   14.0   0.0    1.5  1  RPA_C          Replication protein A C terminal
       0.12   11.7   0.0       0.19   11.1   0.0    1.2  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.3   6.6e-58   3.9e-54       5     155 .]       1     151 [.       1     151 [. 0.99

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 6.6e-58
                              CdhC   5 vspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkleedlE 81 
                                       +sp++eGeriRk++++ve+gg k+kafEl  +  +de++dgk++viGpdi+e+e g++++++++++vaG+ +e+dlE
  gi|386003001|ref|YP_005921300.1|   1 MSPMYEGERIRKDEIWVEMGGPKAKAFELSVAGTMDEIQDGKVTVIGPDISELEVGKTIDFGMIFKVAGELIEKDLE 77 
                                       69*******************99****************************************************** PP

                              CdhC  82 pvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdeekv 155
                                       +++ERr+H++l+yi+G mHl+qRd+iw+R + + +++G+ ++++i + +++++k+e+ ++++k+evt++td+++v
  gi|386003001|ref|YP_005921300.1|  78 SIIERRNHALLSYIHGWMHLNQRDAIWMRAGLDLKKAGVtSFEQIFKNVMTLYKAEM-PFIEKMEVTILTDPAAV 151
                                       ***************************************99****************.*************9876 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 ?   14.0   0.0   9.8e-06     0.058      48      97 ..     413     459 ..     393     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.8e-06
                                       XHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  48 talaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97 
                                       ++ ++qv+ +i + + ++  + vd i++kl++s+ +  q++++L+neGi+
  gi|386003001|ref|YP_005921300.1| 413 SEYEEQVIAFIEE-TGGD--IDVDAIKAKLNMSEGQFMQVIEYLQNEGIL 459
                                       5666777777777.3333..89**************************85 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.2e-05      0.19      77     130 ..     405     457 ..     396     459 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                                       CHHHHHTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTT CS
                     RNA_pol_Rpc34  77 eAkkktslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskk 130
                                       e  k++  se e+ V ++Iee+G + I+  +ik+kln+ + +  +++ +L  ++
  gi|386003001|ref|YP_005921300.1| 405 EGWKVEDPSEYEEQVIAFIEETGGD-IDVDAIKAKLNMSEGQFMQVIEYLQNEG 457
                                       55677888899999*********98.***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2708.35
//
Query:       gi|386003002|ref|YP_005921301.1|  [L=181]
Description: Acetyl-CoA decarbonylase/synthase complex subunit epsilon [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-36  125.9   0.1    1.5e-36  125.7   0.1    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    0.00021   21.0   0.0    0.00055   19.7   0.0    1.7  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.1   1.7e-40   1.5e-36       4     167 ..       8     175 ..       5     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.7e-40
                                       XXXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET.....HHHTT CS
                             CO_dh   4 ekiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata.....lkeag 75 
                                       + +Pf+ a+i+++++a++ +   v+  +ikkakrPll+vG ++ ++ +++ k+ +i +  ++++ata     + e+g
  gi|386003002|ref|YP_005921301.1|   8 NAVPFEMAQIPGPEMAKAYNT-AVIGAIIKKAKRPLLVVGAELFEDPVMFDKAIAIGKTGVPIAATAhsikgFVERG 83 
                                       578*****************9.9********************************************9999999999 PP

                                       -G..GGSE-HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEEE-- CS
                             CO_dh  76 lkdyekknklveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvslan 152
                                         +   +  l+ lt+ l  ++++g dg+g+yd+v+f+G+ y  as + s lk+f   i+ ++id+yyh +Ad++++n
  gi|386003002|ref|YP_005921301.1|  84 YTENVTMIGLHPLTNYLRFKDWQGLDGKGQYDVVIFTGIFYKFASAMFSTLKNFNRDIKRVSIDRYYHVNADMTFGN 160
                                       998888889******************************************************************** PP

                                       -GGGHHHHHHHHHHH CS
                             CO_dh 153 lskeeeeylemleel 167
                                       l  + e+y e ++e+
  gi|386003002|ref|YP_005921301.1| 161 LAFDPEKYHEAIDEV 175
                                       ************998 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.1e-08   0.00055       6     110 ..      33     147 ..      29     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.1e-08
                                       HHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGG.TTSS-TTSTTEEEESGGGS........CHHHHH CS
                      TPP_enzyme_M   6 ellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmg.kgvipedhplylgmlglhg........skaane 73 
                                       +++k+akrp+++vG +   + +  + +  + k+g+P++ t +  kg++++    ++ m+glh         + ++ +
  gi|386003002|ref|YP_005921301.1|  33 AIIKKAKRPLLVVGAELFEDPVMFDKAIAIGKTGVPIAATAHSiKGFVERGYTENVTMIGLHPltnylrfkDWQGLD 109
                                       68****************9988888888899******9999998******************654333332222223 PP

                                       HHHH-SEEEEES-SSSTCCCTT.TTT.TTTTT-EEEEEE CS
                      TPP_enzyme_M  74 aleeaDlvlalGarfddirttg.sep.efapeakiihid 110
                                          + D+v++ G  +++  ++  s   +f+++ k + id
  gi|386003002|ref|YP_005921301.1| 110 GKGQYDVVIFTGIFYKF-ASAMfSTLkNFNRDIKRVSID 147
                                       33347777777755544.444433332444443555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1182.07
//
Query:       gi|386003003|ref|YP_005921302.1|  [L=811]
Description: Acetyl-CoA decarbonylase/synthase complex subunit alpha [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-88  297.3   0.5    6.2e-72  242.9   0.0    2.1  2  Prismane  Prismane/CO dehydrogenase family
    4.2e-07   30.0   5.7    4.2e-07   30.0   5.7    3.4  3  Fer4_9    4Fe-4S dicluster domain
      1e-06   29.5   5.8      0.018   16.0   0.5    3.6  3  Fer4_16   4Fe-4S double cluster binding domain
    4.8e-06   26.6  19.3    3.8e-05   23.7  10.6    3.9  4  Fer4_10   4Fe-4S dicluster domain
    4.7e-05   23.7  13.9     0.0053   17.2   1.1    3.9  4  Fer4_8    4Fe-4S dicluster domain
    8.5e-05   23.0  17.3     0.0053   17.3   0.6    3.8  4  Fer4_17   4Fe-4S dicluster domain
    0.00063   19.4  21.4     0.0018   18.0   3.8    3.8  3  Fer4      4Fe-4S binding domain
     0.0092   16.0  28.5      0.021   14.9   3.9    4.4  3  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   15.7   2.6      0.012   15.7   2.6    4.7  4  Fer4_6    4Fe-4S binding domain
      0.014   15.2   7.5      0.014   15.2   7.5    2.5  3  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
      0.017   15.7  14.2      0.017   15.7  14.2    3.8  3  Fer4_7    4Fe-4S dicluster domain
      0.019   15.1  12.3      0.055   13.7   0.4    3.5  3  Fer4_18   4Fe-4S dicluster domain
       0.53   10.5  23.6       0.34   11.1  13.9    3.9  4  Fer4_21   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   4.4   3.8e-16   5.3e-13       3      53 ..      67     117 ..      65     132 .. 0.91
   2 !  242.9   0.0   4.5e-75   6.2e-72     115     510 ..     142     696 ..     132     697 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.8e-16
                                       E-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   3 CrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaaharelad 53 
                                       C +C++gpC++t+nkrG+CG+d+++++ r +liavl+g+ ahaah+r+l++
  gi|386003003|ref|YP_005921302.1|  67 CTLCTYGPCDLTGNKRGACGIDQAAQQGRIVLIAVLMGCTAHAAHGRHLYH 117
                                       ************************************************954 PP

  == domain 2  score: 242.9 bits;  conditional E-value: 4.5e-75
                                       HHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          Prismane 115 rslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGtP. 190
                                       r++ +++pk+lk+     + vl+y++e+v ++la t++g+e++++d++skal++G+ld  g e++d +++++++ P 
  gi|386003003|ref|YP_005921302.1| 142 RTIAGIKPKTLKDF----GPVLSYVEEQVSQLLACTHTGQEGNYVDFESKALHAGMLDSLGKEVSDLIQIVAYDMPr 214
                                       77888999999999....*********************************************************** PP

                                       ...--EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCC......... CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx......... RF
                          Prismane 191 ...eppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrh......... 254
                                           +pl+e+++g+ldk+k  ++  GH+la ++e + ++e+++l ++++   + g+ccta + +++ +         
  gi|386003003|ref|YP_005921302.1| 215 gdeDAPLVECGMGTLDKNKAILITYGHNLAGSAEAMFYAEDNKLWDKVD---IGGVCCTAIDnTRICEgighpdkef 288
                                       **9888************8888888************************...**********6666669******** PP

                                       .........EEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE-.-CTTC.. CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.. RF
                          Prismane 255 .........lvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhie.eeeka.. 319
                                                 ++++G   + +k+++ +++d+i+vd++C+ ++    aekyk++li+t+e+++ g+ +   ++ ++  
  gi|386003003|ref|YP_005921302.1| 289 ndkyrmvgtKAKIAGAIGWWRKMVRGDCMDCIMVDEQCVWTDAIVDAEKYKIPLIATNEKIMLGLPDRTnDPVDEiv 365
                                       *****************************************99888****************888888733333333 PP

                                       H................HHHHHHHHHHHCCHCCTTCGG.-..................................... CS
                                       x................xxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                          Prismane 320 d................kdaseiiekAielakareekkve..................................... 343
                                       d                k+ +  i++Ai+++++r+e +++                                     
  gi|386003003|ref|YP_005921302.1| 366 DdlvnfrmpgvvvldpvKAGEVGIKTAIAVKPKRAEIREAdpfiseeefkkyaesctychscqfvcpphikigdvvr 442
                                       15667778888888898999999***********7744336898999999998888888888888888877777766 PP

                                       .................HHH...................................................HHTTSS CS
                                       .................xxx...................................................xxxxxx RF
                          Prismane 344 .................ida...................................................iksGtI 352
                                                        +                                                     ++ GtI
  gi|386003003|ref|YP_005921302.1| 443 aaaegnleplsstyeicV-GcrrceqvcpqeipilslyayanrdyirnqkfkmragrgpikdteirrvgapLVLGTI 518
                                       666666666555555550.0555555566666666666666667777777777888888888888999999****** PP

                                       -EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHC...CCTTTTEC...GHHHHSTHCEESEEEEESCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                          Prismane 353 kgvvlvvGCdnakkgrdyytelakelikrdvlvltaGCakyal...nklglgti...eaaelagegiPrvLdvGsCv 423
                                       +gv++++GC n+++g++  +++a+e++ r  +v ++GC+++++    +++++ti    +  ++g +   + +vGsCv
  gi|386003003|ref|YP_005921302.1| 519 PGVIAIIGCGNYPNGTKECYDIAREFVDRGFIVAATGCMAMDMslyTDAEGKTIweqFPGGFDGRN---ICNVGSCV 592
                                       ******************************************99999*******877778899988...******** PP

                                       CHHHHHHHHHHHHHHT.......TS.SGGGSSE...EEEECC-..-SHHHHHHHHHHHHTT-CEEECSS-TTTT-HH CS
                                       xxxxxxxxxxxxxxxx.......xx.xxxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 424 dnyrivvialklaeal.......gv.dindLpl...aalalew..yeqKAvailltllalGinihlgptlpafgspn 487
                                       +n++++++ +k+a ++       ++ di+d++l   +a+ ++w  y+qKA++i++++++lG+++++  +  ++++++
  gi|386003003|ref|YP_005921302.1| 593 ANAHLHGAGIKVATIFagrneraNYdDIADYILskvGACGVAWgaYSQKAASIATGFNRLGVPAVVQSHSVMYRRAF 669
                                       **********************9999*********9***************************************** PP

                                       HHHHHHCH....HHHHHCEEEECHCHH CS
                                       xxxxxxxx....xxxxxxxxxxxxxxx RF
                          Prismane 488 vlkvlved....fedriggivtveedp 510
                                       + ++  ++    +++r g++v  e++p
  gi|386003003|ref|YP_005921302.1| 670 LGRTDKKEdweiIDARDGSKVYCEPAP 696
                                       999988888888888888888888877 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.5      0.29     4e+02       2      11 ..      64      73 ..      45      99 .. 0.73
   2 ?   -1.2   0.2       1.7   2.3e+03      35      39 ..     315     319 ..     276     329 .. 0.67
   3 !   30.0   5.7     3e-10   4.2e-07       2      49 ..     421     472 ..     420     484 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                            Fer4_9  2 CtgCgaCvea 11
                                      C +C+ C++ 
  gi|386003003|ref|YP_005921302.1| 64 CDRCTLCTYG 73
                                      5556666554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                            Fer4_9  35 aCigC 39 
                                       +C++C
  gi|386003003|ref|YP_005921302.1| 315 DCMDC 319
                                       45555 PP

  == domain 3  score: 30.0 bits;  conditional E-value: 3e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                       Ct C++C+ +Cp ++ ++d ++  a+ + +      e C+gC++C+++Cp++
  gi|386003003|ref|YP_005921302.1| 421 CTYCHSCQFVCPPHIKIGDVVRAAAEGNLEPLsstyEICVGCRRCEQVCPQE 472
                                       **********************9999988766999*99************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.3   3.2e+03       2       8 ..      64      70 ..      26      72 .. 0.70
   2 !   16.0   0.5   1.3e-05     0.018      35      65 ..     402     432 ..     381     434 .. 0.68
   3 !   13.9   0.1   5.9e-05     0.081       2      15 ..     459     472 ..     452     508 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.3
                           Fer4_16  2 CgtCgkC 8 
                                      C +C+ C
  gi|386003003|ref|YP_005921302.1| 64 CDRCTLC 70
                                      4444444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.3e-05
                           Fer4_16  35 taekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                        +e + ++ +ee +k +e +t+C  Cq vCP
  gi|386003003|ref|YP_005921302.1| 402 IREADPFISEEEFKKYAESCTYCHSCQFVCP 432
                                       3444444444444444899***********9 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5.9e-05
                           Fer4_16   2 CgtCgkCaevCPtn 15 
                                       C++C++C +vCP++
  gi|386003003|ref|YP_005921302.1| 459 CVGCRRCEQVCPQE 472
                                       78888888888875 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.9       0.5   6.9e+02       8      19 ..      63      75 ..      57     109 .. 0.71
   2 ?   -1.0   0.2       1.4     2e+03      36      52 ..     310     327 ..     298     328 .. 0.70
   3 !   23.7  10.6   2.7e-08   3.8e-05       6      56 .]     418     470 ..     414     470 .. 0.80
   4 !   16.9   1.4   3.6e-06    0.0049       6      24 ..     456     483 ..     451     505 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.5
                           Fer4_10  8 tCirCgkCvka.C 19
                                       C rC+ C+   C
  gi|386003003|ref|YP_005921302.1| 63 ICDRCTLCTYGpC 75
                                      6888888876545 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                           Fer4_10  36 eavrkkvekCtgcg.aCv 52 
                                       ++vr+++ +C+++  +Cv
  gi|386003003|ref|YP_005921302.1| 310 KMVRGDCMDCIMVDeQCV 327
                                       556667777776644775 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 2.7e-08
                           Fer4_10   6 ddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++C+ C  C+ +CP ++    v+  +++ + e+ +  +e C gc  C ++CP
  gi|386003003|ref|YP_005921302.1| 418 AESCTYCHSCQFVCPPHIkiGDVVRAAAEGNLEPLSSTYEICVGCRRCEQVCP 470
                                       589*************998444444445555566677***************9 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 3.6e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadl.........t 24 
                                        + C++C++C ++CP+ +         +
  gi|386003003|ref|YP_005921302.1| 456 YEICVGCRRCEQVCPQEIpilslyayaN 483
                                       579*************877666644431 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5       2.1     3e+03       5      12 ..      64      71 ..      41      95 .. 0.81
   2 !   17.2   1.1   3.9e-06    0.0053      44      65 .]     401     435 ..     314     435 .. 0.66
   3 !   13.9   0.1   4.1e-05     0.057      49      65 .]     457     473 ..     440     503 .. 0.83
   4 ?   -3.1   0.1       8.5   1.2e+04      44      55 ..     693     713 ..     664     717 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                            Fer4_8  5 CieCgaCq 12
                                      C +C +C+
  gi|386003003|ref|YP_005921302.1| 64 CDRCTLCT 71
                                      44555554 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.9e-06
                            Fer4_8  44 e.............eealwsCttcgaCtevCpvgi 65 
                                       e             +++++sCt c++C+ vCp +i
  gi|386003003|ref|YP_005921302.1| 401 EireadpfiseeefKKYAESCTYCHSCQFVCPPHI 435
                                       03344455556677899***************886 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 4.1e-05
                            Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                       + C++c++C++vCp++i
  gi|386003003|ref|YP_005921302.1| 457 EICVGCRRCEQVCPQEI 473
                                       56888888888888765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.5
                            Fer4_8  44 e.........eealwsCttcg 55 
                                       e         +e++++C+  +
  gi|386003003|ref|YP_005921302.1| 693 EpapehmlyvAESVEECMLMM 713
                                       144444445577888887766 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.9       2.3   3.2e+03       2       9 ..      64      71 ..      44      86 .. 0.77
   2 ?   -2.6   0.1       6.3   8.7e+03      44      50 ..     314     320 ..     289     328 .. 0.68
   3 !   16.4   0.4   7.2e-06    0.0099      36      60 ..     411     435 ..     390     436 .. 0.77
   4 !   17.3   0.6   3.8e-06    0.0053      41      60 ..     454     473 ..     439     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                           Fer4_17  2 CiqCgyCl 9 
                                      C +C  C+
  gi|386003003|ref|YP_005921302.1| 64 CDRCTLCT 71
                                      55555554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.3
                           Fer4_17  44 slCieCg 50 
                                       ++C+ C 
  gi|386003003|ref|YP_005921302.1| 314 GDCMDCI 320
                                       4555553 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 7.2e-06
                           Fer4_17  36 eaekeekaslCieCgeCerkCPqgl 60 
                                       e+e +++a++C+ C+ C+ +CP ++
  gi|386003003|ref|YP_005921302.1| 411 EEEFKKYAESCTYCHSCQFVCPPHI 435
                                       3445689***************997 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 3.8e-06
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                       ++ + C++C++Ce++CPq++
  gi|386003003|ref|YP_005921302.1| 454 STYEICVGCRRCEQVCPQEI 473
                                       67889*************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   2.2       5.8     8e+03       9      14 ..      65      70 ..      63      71 .. 0.56
   2 !   13.1   1.0   4.8e-05     0.066       5      19 ..     418     432 ..     414     435 .. 0.89
   3 !   18.0   3.8   1.3e-06    0.0018       5      21 ..     456     472 ..     455     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.8
                                      SS-THH CS
                              Fer4  9 igCGaC 14
                                       +C +C
  gi|386003003|ref|YP_005921302.1| 65 DRCTLC 70
                                      555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.8e-05
                                       TTTSSS-THHHHHST CS
                              Fer4   5 eekCigCGaCvevCP 19 
                                        e C++C  C  vCP
  gi|386003003|ref|YP_005921302.1| 418 AESCTYCHSCQFVCP 432
                                       799************ PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.3e-06
                                       TTTSSS-THHHHHSTTT CS
                              Fer4   5 eekCigCGaCvevCPvg 21 
                                       +e C+gC +C++vCP +
  gi|386003003|ref|YP_005921302.1| 456 YEICVGCRRCEQVCPQE 472
                                       689************87 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.4     0.038        52       9      18 ..      63      72 ..      55      77 .. 0.60
   2 !   12.8   1.6   7.1e-05     0.098       7      21 ..     418     432 ..     412     433 .. 0.89
   3 !   14.9   3.9   1.5e-05     0.021       8      22 .]     457     471 ..     455     471 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.038
                            Fer4_2  9 rCigCgaCvs 18
                                      +C +C  C+ 
  gi|386003003|ref|YP_005921302.1| 63 ICDRCTLCTY 72
                                      5666666654 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.1e-05
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +++C+ C +C+ +CP
  gi|386003003|ref|YP_005921302.1| 418 AESCTYCHSCQFVCP 432
                                       689***********9 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 1.5e-05
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       ++C+gC+ C ++CP+
  gi|386003003|ref|YP_005921302.1| 457 EICVGCRRCEQVCPQ 471
                                       89************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   3.7       3.6   4.9e+03       8      16 ..      63      71 ..      61      75 .. 0.78
   2 ?    0.6   1.3       0.5   6.8e+02      11      18 ..     315     322 ..     314     328 .. 0.87
   3 ?   -0.1   2.2      0.83   1.1e+03       7      20 ..     419     432 ..     418     437 .. 0.86
   4 ?   15.7   2.6   8.4e-06     0.012       7      20 ..     457     470 ..     455     476 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                            Fer4_6  8 kCigCgdCv 16
                                       C+ C  C+
  gi|386003003|ref|YP_005921302.1| 63 ICDRCTLCT 71
                                      588888885 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.5
                            Fer4_6  11 gCgdCvrv 18 
                                       +C+dC++v
  gi|386003003|ref|YP_005921302.1| 315 DCMDCIMV 322
                                       7****987 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.83
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                       ++C+ C  C  vCP
  gi|386003003|ref|YP_005921302.1| 419 ESCTYCHSCQFVCP 432
                                       68999999*****9 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 8.4e-06
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                       + C+gC++C+ vCP
  gi|386003003|ref|YP_005921302.1| 457 EICVGCRRCEQVCP 470
                                       78************ PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.9       2.7   3.7e+03      22      33 ..      65      76 ..      62      83 .. 0.87
   2 ?   15.2   7.5   9.9e-06     0.014       4      78 ..     401     472 ..     398     474 .. 0.83
   3 ?    1.2   1.7      0.22     3e+02      24      42 ..     459     475 ..     456     484 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                                      TT----TT-HHH CS
                           Fer4_20 22 sRClqCkkapcv 33
                                      +RC  C+  pc 
  gi|386003003|ref|YP_005921302.1| 65 DRCTLCTYGPCD 76
                                      79****999996 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.9e-06
                                       S-S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GG CS
                           Fer4_20   4 nfkevalglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqe 78 
                                       +++e +  ++eee ++ A+ C +C  + c+  CP +i+i + +++ aegnle   ++  e       c +vCpqe
  gi|386003003|ref|YP_005921302.1| 401 EIREADPFISEEEFKKYAESCTYC--HSCQFVCPPHIKIGDVVRAAAEGNLEPLSST-YEICVGCRRCEQVCPQE 472
                                       567888889999************..89**********************9765444.44445567799999998 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.22
                                       ----TT-HHHHCSTT---H CS
                           Fer4_20  24 ClqCkkapcvkgCPveidi 42 
                                       C+ C  + c++ CP ei i
  gi|386003003|ref|YP_005921302.1| 459 CVGC--RRCEQVCPQEIPI 475
                                       8899..7899999999987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.1     7e+03      37      41 ..     315     319 ..     288     329 .. 0.66
   2 ?   11.4   2.8   0.00027      0.37      29      49 ..     412     432 ..     390     435 .. 0.73
   3 ?   15.7  14.2   1.2e-05     0.017       1      51 [.     420     472 ..     420     473 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.1
                            Fer4_7  37 kClgC 41 
                                       +C++C
  gi|386003003|ref|YP_005921302.1| 315 DCMDC 319
                                       45544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00027
                            Fer4_7  29 ekveidpekClgCgaCvavCP 49 
                                       e+ +  +e+C++C++C+ vCP
  gi|386003003|ref|YP_005921302.1| 412 EEFKKYAESCTYCHSCQFVCP 432
                                       445666899***********9 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.2e-05
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee.enekgt.ekveidpekClgCgaCvavCPtg 51 
                                       +C+ C+ C+ +Cp +    d + + ++g+ e +   +e C+gC++C++vCP +
  gi|386003003|ref|YP_005921302.1| 420 SCTYCHSCQFVCPPHIKIGDVVrAAAEGNlEPLSSTYEICVGCRRCEQVCPQE 472
                                       5************65444433302222333445677899************86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.8   2.5e+03      57      71 ..     312     326 ..     301     338 .. 0.73
   2 ?   13.7   0.4     4e-05     0.055      51      79 ..     411     439 ..     394     450 .. 0.82
   3 ?    6.9   1.9    0.0051       7.1      60      77 ..     458     475 ..     444     479 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.8
                           Fer4_18  57 gagdcidcescvkvc 71 
                                         gdc+dc +  + c
  gi|386003003|ref|YP_005921302.1| 312 VRGDCMDCIMVDEQC 326
                                       568888886544444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4e-05
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgidirk 79 
                                       ee+ +k a  c+ c+sc  vcP +i i +
  gi|386003003|ref|YP_005921302.1| 411 EEEFKKYAESCTYCHSCQFVCPPHIKIGD 439
                                       4555777889***************9976 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0051
                           Fer4_18  60 dcidcescvkvcPtgidi 77 
                                        c+ c+ c +vcP +i i
  gi|386003003|ref|YP_005921302.1| 458 ICVGCRRCEQVCPQEIPI 475
                                       5*************9987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.5       1.3   1.8e+03      39      48 ..      62      71 ..      51      80 .. 0.67
   2 ?   -1.5   0.1       2.1   2.8e+03      40      51 ..     315     326 ..     308     342 .. 0.58
   3 ?   10.3   1.8   0.00042      0.59      31      52 ..     411     432 ..     392     438 .. 0.85
   4 ?   11.1  13.9   0.00025      0.34       7      53 ..     420     471 ..     419     475 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                           Fer4_21 39 deCvGCnlCs 48
                                        C  C+lC+
  gi|386003003|ref|YP_005921302.1| 62 PICDRCTLCT 71
                                      5577777775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                           Fer4_21  40 eCvGCnlCssvC 51 
                                       +C+ C +  + C
  gi|386003003|ref|YP_005921302.1| 315 DCMDCIMVDEQC 326
                                       444444443333 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00042
                           Fer4_21  31 ktvlkvvedeCvGCnlCssvCP 52 
                                       ++ +k  +++C+ C+ C  vCP
  gi|386003003|ref|YP_005921302.1| 411 EEEFKKYAESCTYCHSCQFVCP 432
                                       56678889************** PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00025
                           Fer4_21   7 kCigCgkCliaCedtshqai....eidaktvl...kvvedeCvGCnlCssvCPv 53 
                                       +C  C +C  +C+   h  i    + +a+  l     + + CvGC  C +vCP 
  gi|386003003|ref|YP_005921302.1| 420 SCTYCHSCQFVCPP--HIKIgdvvRAAAEGNLeplSSTYEICVGCRRCEQVCPQ 471
                                       7***********96..4333332255555444222556899************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (811 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.81u 0.32s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 4753.52
//
Query:       gi|386003004|ref|YP_005921303.1|  [L=231]
Description: class I and II aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for 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-27   97.3   0.0    1.1e-27   97.1   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
     0.0017   17.4   0.0     0.0023   17.0   0.0    1.1  1  Aminotran_5    Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   1.3e-31   1.1e-27       7     227 ..      38     231 .]      32     231 .] 0.87

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.3e-31
                                       SSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                     Aminotran_1_2   7 gsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                       ++n ++ +  +p+l++ + +e e       +  y+ +d + e++ a a+f+g      + +e +vv g+G+++l  +
  gi|386003004|ref|YP_005921303.1|  38 SANINPLG--HPPLDDLILKEME------WIGHYPEND-YLEFRAASARFVG------VGPE-NVVPGNGSSELMRL 98 
                                       55666555..6666666666655......8899*****.*************......9***.************** PP

                                       HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TT CS
                     Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNP 160
                                       ++ +l ++ gd++l+ +pt+++y+   rl g+e+v +p +        +++ ++ l++a  g +  k  ++++p+NP
  gi|386003004|ref|YP_005921303.1|  99 FAEAL-IEEGDRVLITTPTFGEYEAQSRLFGAEIVHVP-R----GVREAKSPKDFLDDALLGGA--KAAFICNPNNP 167
                                       *****.9*******************************.3....34455555555566655666..9********** PP

                                       T--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGG CS
                     Aminotran_1_2 161 tGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaG 227
                                       tG ++++ e+ +l++ +++ + +lfvDea+ ++   +    +t+a +++e + l++++sl K+fG  G
  gi|386003004|ref|YP_005921303.1| 168 TGILLPRSEIAELAERCERAETFLFVDEAFIELSDPD----QTVAAMAPEMEhLFVARSLTKSFGFRG 231
                                       *********************************9996....469999999999************987 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.6e-07    0.0023      44     177 ..      67     196 ..      53     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEE CS
                       Aminotran_5  44 aveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvip 120
                                        + e r+  a+++++   e+++   G++e + l+a +l   +++gd++++t+    ++    ++ ++  ga+++++p
  gi|386003004|ref|YP_005921303.1|  67 DYLEFRAASARFVGVGP-ENVVPGNGSSELMRLFAEAL---IEEGDRVLITTP-TFGEY---EAQSRLFGAEIVHVP 135
                                       577889999*******7.********************...9********964.56666...3334568*******9 PP

                                       BETTSCBEGGGH.HHH--TTEEEEEEESBETTTTEB--HHHHHHHHHH...TT-EEEEE-T CS
                       Aminotran_5 121 ldeegeldldel.ekllnektklvaithvsnvtGtiqpveeigklakk...kgalvlvDaa 177
                                          +    ++++ +++l   +k+ +i+  +n tG++ p  ei++la +   ++ +++vD a
  gi|386003004|ref|YP_005921303.1| 136 RGVREAKSPKDFlDDALLGGAKAAFICNPNNPTGILLPRSEIAELAERcerAETFLFVDEA 196
                                       988888888887689999*****************98877766665543216888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1436.06
//
Query:       gi|386003005|ref|YP_005921304.1|  [L=126]
Description: L-threonine O-3-phosphate decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-06   25.7   0.0    6.2e-06   25.6   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.064   13.5   0.1       0.11   12.7   0.1    1.6  1  PaaX           PaaX-like protein


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.9e-10   6.2e-06     252     362 ..      10     117 ..       1     118 [. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.9e-10
                                       SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.CHHHHHHHHHHT CS
                     Aminotran_1_2 252 sssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.takelskkLlee 327
                                       s s+l+ a+ + l ++++   +l e+r+ + ++   l  eL++lgl+ ++s  +++l+ +  a  +  el + + ee
  gi|386003005|ref|YP_005921304.1|  10 SISSLASAAGTYLLAQEE---HLVESRRVIREELGWLSGELKRLGLDPIESSVNFILVGVAAAGlRSPELVERMEEE 83 
                                       334555555555555554...99999999999999999999999*******9999998666655999********** PP

                                       CTEEEEEGGGGTS.TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 328 vgvyvtpgtsftv.pgrlRitvAglteeeleelvea 362
                                       +gv+++ ++sf++ +  +R+ v    +ee+ +l+ a
  gi|386003005|ref|YP_005921304.1|  84 EGVLIRDCSSFGLgEDYVRVAV--RRREENARLIGA 117
                                       **********************..999999998876 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.3e-05      0.11      25      52 ..      86     113 ..      67     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                              PaaX  25 sLirllaelGiseslvRaalsRlakaGw 52 
                                        Lir ++++G++e  vR+a+ R +++  
  gi|386003005|ref|YP_005921304.1|  86 VLIRDCSSFGLGEDYVRVAVRRREENAR 113
                                       59999*****************877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 805.95
//
Query:       gi|386003006|ref|YP_005921305.1|  [L=80]
Description: class I and II aminotransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-18   66.2   3.7      2e-18   66.1   3.7    1.1  1  zf-like   Cysteine-rich small domain


Domain annotation for each model (and alignments):
>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   3.7   1.1e-22     2e-18       7      69 ..       3      61 ..       1      72 [. 0.89

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.1e-22
                           zf-like  7 nkeCeyyPCHktedenClfCyCPlYaledeelGefvetengkvkdCskCllvHkkevadellk 69
                                      + +C+ yPCH+  +++C+fC+CP+Y+++d ++G      +g  ++C +C l+H++eva  ++k
  gi|386003006|ref|YP_005921305.1|  3 RVSCDRYPCHY-PGQDCTFCFCPFYPCGDGRTGGGL--ADG-EWSCGDCHLLHDPEVAAMVMK 61
                                      568********.99*****************99854..688.8***************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 515.28
//
Query:       gi|386003007|ref|YP_005921306.1|  [L=318]
Description: Cobalamin biosynthesis protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-86  288.4   0.5    5.9e-86  288.1   0.5    1.1  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.1   0.5   3.3e-90   5.9e-86       1     275 [.      19     298 ..      19     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 288.1 bits;  conditional E-value: 3.3e-90
                         CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla..laall... 72 
                                       lllA+ +Dl+lg+p++++hPvvl+g++i+ l+++ r    +r++Gv++al++++ +++++ ll+ +a  + + l   
  gi|386003007|ref|YP_005921306.1|  19 LLLAVGIDLILGEPPARVHPVVLMGRMIGGLRRWARP---TRWWGVAIALIVIISSAAAGHLLMGAAdhI-R-Lfgl 90 
                                       689****************************997764...699****************99999977641.2.1355 PP

                         CobD_Cbib  73 ..glvlealllkltlalrsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaP 147
                                         g++++a+llk+t+a+ +Lle++r++ + l++d ++a++ +  +V+R++++l++++ ++A++Es++EN +D++v+P
  gi|386003007|ref|YP_005921306.1|  91 slGTLVSAYLLKSTIAIDCLLETSREIGRLLEEDFDEAKKLLPALVSRNPQDLTRTQATSAVIESLSENYVDAIVSP 167
                                       6678***************************99******************************************** PP

                         CobD_Cbib 148 lfyflll.....glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala......aalri 213
                                       lfy+ll+     g+ +ala+ka nTlDsm+GY++e+++d+Gwa+ArlDD++n+ PARl+  ++ala      +a+r+
  gi|386003007|ref|YP_005921306.1| 168 LFYYLLFsplglGVEAALAFKATNTLDSMLGYRTEELKDLGWASARLDDIANWGPARLSLPIIALAspsragEAVRV 244
                                       *****99888888899*************************************************877777788*** PP

                         CobD_Cbib 214 arrdarkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieralrl 275
                                       a+rd+ ++pSpNsgwp+aa+Agalg rL++p+vY  g+  ++         +++ed++ alrl
  gi|386003007|ref|YP_005921306.1| 245 ALRDHGATPSPNSGWPMAAAAGALGTRLEKPGVYvVGDGGRD---------PSTEDVKPALRL 298
                                       **********************************66644444.........455666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2328.91
//
Query:       gi|386003008|ref|YP_005921307.1|  [L=108]
Description: HesB/YadR/YfhF-family protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-05   24.8   0.1    4.6e-05   23.6   0.1    1.6  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   2.6e-09   4.6e-05       3      97 ..       2      84 ..       1      96 [. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.6e-09
                                      EEE-HHHHHHHHHHHHCTTECEEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS.T CS
                       Fe-S_biosyn  3 itlteaAaeklkkllaedkkelrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvflde 81
                                      i++t+aAaekl + + e+k  + L+ ++ +          g   ++ l   + ++ d v+e+n+++vy+++++ + l  
  gi|386003008|ref|YP_005921307.1|  2 IEITDAAAEKLLESQVEGKV-VKLF-KTSS---------PGEVPRFALGLGPFDDKDLVFETNDVQVYINPSEFEEL-R 68
                                      99************999998.8887.4443.........488888888889999***********************.9 PP

                                      TEEEEEEEETTEEEEE CS
                       Fe-S_biosyn 82 glvldfvedlgtlgLk 97
                                        v+d+v+d  + g+ 
  gi|386003008|ref|YP_005921307.1| 69 VAVIDYVDDSRGRGFV 84
                                      9******998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 677.78
//
Query:       gi|386003009|ref|YP_005921308.1|  [L=210]
Description: hypothetical protein Mhar_2334 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1337.82
//
Query:       gi|386003010|ref|YP_005921309.1|  [L=208]
Description: hypothetical protein Mhar_2335 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1344.43
//
Query:       gi|386003011|ref|YP_005921310.1|  [L=93]
Description: nucleotidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-14   52.8   0.1      4e-14   52.7   0.1    1.0  1  NTP_transf_2  Nucleotidyltransferase domain
    2.8e-10   40.1   0.0    3.2e-10   39.9   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1   4.4e-18     4e-14       1      92 [.       7      89 ..       7      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.4e-18
                                      HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEEC CS
                      NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekl 79
                                      lk++ +e+k++++v+++ +fGS arG+ +++SD+D+lv + e++         ++ +   +fle l+g+ vdlvt   l
  gi|386003011|ref|YP_005921310.1|  7 LKEHENEIKRRFGVKRIGIFGSHARGEGKETSDVDVLVEFVEPSF--------DNFMDLAFFLEDLFGRDVDLVTTRGL 77
                                      68999**************************************54........9********************88887 PP

                                      CCCTEEEEEECEE CS
                      NTP_transf_2 80 edpllvksileer 92
                                        p++  +++ e 
  gi|386003011|ref|YP_005921310.1| 78 S-PYIAPFVEREV 89
                                      7.66666666555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   3.6e-14   3.2e-10       8      77 ..      15      82 ..       5      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.6e-14
                                      HHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHH CS
                           Polbeta  8 ekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplll 77
                                      +++ +++ + +FGS a+g+ +e SD+D+ v + e  ++++ ++la  led+  g++vDlv+ +  +p+++
  gi|386003011|ref|YP_005921310.1| 15 KRRFGVKRIGIFGSHARGEGKETSDVDVLVEFVEP-SFDNFMDLAFFLEDL-FGRDVDLVTTRGLSPYIA 82
                                      45558999**************************9.***************.99******9986666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 629.97
//
Query:       gi|386003012|ref|YP_005921311.1|  [L=127]
Description: putative nucleic acid-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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   27.4   0.2    6.9e-06   26.6   0.2    1.4  1  PIN       PIN domain
     0.0017   19.1   0.0     0.0021   18.8   0.0    1.3  1  PIN_3     PIN domain
  ------ inclusion threshold ------
      0.021   14.7   0.1      0.035   14.0   0.1    1.3  1  SCAB-ABD  Actin-binding domain of plant-specific actin-bindin
       0.19   12.2   0.0       0.23   12.0   0.0    1.1  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   1.5e-09   6.9e-06       2     111 ..       5     126 ..       4     127 .] 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.5e-09
                                       EE-HHHHHHHH.............TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHH CS
                               PIN   2 vlDTsvliall.............rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvel 61 
                                       vlDT v+++               r+   + ++r ll+ l     e++++++ ++E+++vl+r + +r++aa+l + 
  gi|386003012|ref|YP_005921311.1|   5 VLDTTVIVKGAltpykslpeeiysRELGTHQKCRLLLNILdessVEVFIPKVCVIETAAVLKR-LANRDLAAKLSRG 80 
                                       67888888877788877777776644444555555554446669*******************.8888888888888 PP

                                       HHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.E CS
                               PIN  62 llllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliat 111
                                       l ++ +l   p   +i+e a+++al +g + +D + +A+A+  ++ l+ t
  gi|386003012|ref|YP_005921311.1|  81 LMRAYDLVGEP---DIFESAWRVALDRGSTGFDTYFLALARMKDALLF-T 126
                                       88877777766...***************************9999555.6 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.6e-07    0.0021       2      57 ..       4      73 ..       3     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                             PIN_3  2 vvlDtnvlldallfds........p.......aarkildaletgaitlvvsprlldElervlarelaypqf 57
                                       vlDt+v++ + l +         +         r +l+ l +  +++++ + +++E + vl+r   ++  
  gi|386003012|ref|YP_005921311.1|  4 AVLDTTVIVKGALTPYkslpeeiySrelgthqKCRLLLNILDESSVEVFIPKVCVIETAAVLKRLANRD-L 73
                                      7********99998885555555505556667******************************7764333.3 PP

>> SCAB-ABD  Actin-binding domain of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.9e-06     0.035      17      40 ..      66      89 ..      60      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                          SCAB-ABD 17 kRLSVRDLasKFekglaAAakLse 40
                                      kRL  RDLa K  +gl  A  L+ 
  gi|386003012|ref|YP_005921311.1| 66 KRLANRDLAAKLSRGLMRAYDLVG 89
                                      9***************99887765 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     5e-05      0.23       3      56 ..       6      72 ..       5      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                            PIN_12  3 iDTnifld.............effrlseeealkklleliesgkiklivpdivldEflknrekkiees 56
                                      +DT ++ +                +l+ +++++ ll+ +++  +++++p++++ E+   +++  ++ 
  gi|386003012|ref|YP_005921311.1|  6 LDTTVIVKgaltpykslpeeiYSRELGTHQKCRLLLNILDESSVEVFIPKVCVIETAAVLKRLANRD 72
                                      6666666555544444444222233444589*************************99999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 871.71
//
Query:       gi|386003013|ref|YP_005921312.1|  [L=64]
Description: hypothetical protein Mhar_2338 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-13   49.5   3.9    6.1e-13   49.0   3.9    1.3  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   3.9   3.4e-17   6.1e-13       5      56 ..       3      48 ..       1      57 [. 0.78

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.4e-17
                            DUF104  5 IeavYEnGvLKPLekvdLkEGeevkikIee.akeilkklkgilkeadeeelee 56
                                      ++a+YE+ vLKPL+k+dL+++ evki+I+e  +++       l e+ eee +e
  gi|386003013|ref|YP_005921312.1|  3 VRAIYEDEVLKPLKKLDLPDKAEVKIIIREsFSKL-------LDEVGEEEAKE 48
                                      8*****************************43333.......33444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 413.89
//
Query:       gi|386003014|ref|YP_005921313.1|  [L=96]
Description: DNA polymerase beta domain-containing protein region [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-11   43.2   0.0    4.4e-11   42.9   0.0    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
    1.6e-09   37.7   0.0    1.9e-09   37.5   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.091   12.5   0.2       0.22   11.3   0.2    1.6  1  MdcG          Phosphoribosyl-dephospho-CoA transferase MdcG


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   7.4e-15   4.4e-11       4      94 ..      14      95 ..       9      96 .] 0.90

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 7.4e-15
                                      HHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCC CS
                      NTP_transf_2  4 lleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledp 82
                                      +l++  e    + v +fGS+arG+a + SD D+lv ++         ++l++l      l+ llg +vd+vt+  l+ +
  gi|386003014|ref|YP_005921313.1| 14 ILQAAAEHG-AYNVRIFGSVARGEADESSDFDFLVDMEPG-------RSLLDLGGLLMDLQDLLGCPVDVVTERGLR-K 83
                                      555555444.899***************************.......789***************************.9 PP

                                      TEEEEEECEEEH CS
                      NTP_transf_2 83 llvksileerpl 94
                                      ++++++l+e+++
  gi|386003014|ref|YP_005921313.1| 84 RIRDQVLKEAVA 95
                                      999999999876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   3.1e-13   1.9e-09       2      85 ..      13      94 ..      12      96 .] 0.91

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.1e-13
                                      STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHH CS
                           Polbeta  2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyei 80
                                      ki + + ++ +   + +FGS+a+g+a e+SD+D+ v ++  ++l +   l ++l+d+ lg  vD+v+ +  ++ ++ ++
  gi|386003014|ref|YP_005921313.1| 13 KILQAAAEH-GAYNVRIFGSVARGEADESSDFDFLVDMEPGRSLLDLGGLLMDLQDL-LGCPVDVVTERGLRKRIRDQV 89
                                      677777777.788899*****************************************.9********99999******* PP

                                      HHS-E CS
                           Polbeta 81 lkegk 85
                                      lke  
  gi|386003014|ref|YP_005921313.1| 90 LKEAV 94
                                      99865 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   3.6e-05      0.22      99     163 ..      15      75 ..       5      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                              MdcG  99 aallaal.glawgvyGSlgwqlatglpylhesSDLDLlirvasalqlarlldllaaleaaa.vrlDg 163
                                        +++a++   +++++GS++         + esSD D l++++  ++l +l  ll +l+++  + +D+
  gi|386003014|ref|YP_005921313.1|  15 LQAAAEHgAYNVRIFGSVARGE------ADESSDFDFLVDMEPGRSLLDLGGLLMDLQDLLgCPVDV 75 
                                       4444444256788888887543......589****************************966***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 613.88
//
Query:       gi|386003015|ref|YP_005921314.1|  [L=115]
Description: nucleotidyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   88.9   1.8    2.4e-25   88.7   1.8    1.1  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   1.8   1.3e-29   2.4e-25       1     117 [.      11     104 ..      11     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.3e-29
                                       HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHH CS
                             DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepee 77 
                                       i ea+e++++++ ++++e+f+ del ++ +++ lqvigEaa  i+++                      +++e+ e 
  gi|386003015|ref|YP_005921314.1|  11 IAEAIERIEKYA-SKGREAFEDDELIQNWILHHLQVIGEAARAISEE----------------------LKDEHDEM 64 
                                       679********9.**********************************......................******** PP

                                       HHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHH CS
                             DUF86  78 pwrkmiglRNrLvHgYlgidpeivwsiikenlpdleefle 117
                                       pw++++g+R +LvH+Y+++d + +ws++++++p+l++ + 
  gi|386003015|ref|YP_005921314.1|  65 PWQQIVGMRHILVHRYFEVDIDLIWSVVEDDVPVLKQQID 104
                                       ************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 856.91
//
Query:       gi|386003016|ref|YP_005921315.1|  [L=366]
Description: Tungstate/molybdate transport system ATP-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-33  114.4   0.0    8.7e-33  113.7   0.0    1.3  1  ABC_tran      ABC transporter
    4.1e-10   39.8   0.0    2.1e-09   37.5   0.0    2.3  1  TOBE          TOBE domain
    4.1e-08   33.3   0.0      9e-08   32.2   0.0    1.6  1  TOBE_2        TOBE domain
    1.5e-07   31.5   0.1      0.011   15.6   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00012   21.6   0.0     0.0029   17.1   0.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
      0.002   18.6   0.0     0.0049   17.3   0.0    1.7  1  AAA_16        AAA ATPase domain
     0.0074   16.6   0.0      0.021   15.1   0.0    1.7  2  AAA_22        AAA domain
     0.0079   15.6   0.0      0.014   14.8   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.014   14.5   0.0      0.022   13.8   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
      0.015   15.0   0.0      0.029   14.1   0.0    1.4  1  AAA_30        AAA domain
      0.016   15.7   0.0      0.027   14.9   0.0    1.2  1  AAA_23        AAA domain
      0.037   13.8   0.0      0.071   12.9   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.053   14.0   0.0       0.11   13.0   0.0    1.5  1  Arc_PepC_II   Archaeal Peptidase A24 C-terminus Type II
       0.09   12.7   0.0       0.17   11.8   0.0    1.4  1  NACHT         NACHT domain
       0.12   12.8   0.2       0.51   10.8   0.2    2.0  1  AAA           ATPase family associated with various cellular 
       0.13   11.7   0.1       0.96    8.9   0.0    2.1  2  PhoH          PhoH-like protein
       0.17   11.5   0.0       0.57    9.8   0.0    1.8  2  SRP54         SRP54-type protein, GTPase domain
       0.17   11.7   0.0       0.28   10.9   0.0    1.4  1  DEAD          DEAD/DEAH box helicase
       0.17   11.9   0.0       0.47   10.5   0.0    1.7  1  AAA_14        AAA domain
       0.22   11.5   0.0       0.34   10.9   0.0    1.4  1  ResIII        Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   9.7e-36   8.7e-33       1     136 [.      16     158 ..      16     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 9.7e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk+vsl++  ge ++i+G++G+GK+ L++++ag + p+eG+i ldg+d+++  +   ++++ ++ q+  lfp+l+v+
  gi|386003016|ref|YP_005921315.1|  16 LKDVSLEVGDGEYLVIIGPTGSGKTILMETVAGIYAPEEGRIFLDGRDITR--EAPRNRRVCMVYQDYMLFPHLSVE 90 
                                       79*************************************************..8888899***************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e +++++++ + lg+++l+ ++      +LSgG+kqrva+ara++ +p+++llDEp 
  gi|386003016|ref|YP_005921315.1|  91 ENiafglksrkvsagEIEVKVAEVSELLGISHLRPRRP----GTLSGGEKQRVAIARAIVMEPSVMLLDEPL 158
                                       **********9999999999*****************9....*****************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   2.4e-12   2.1e-09       1      64 []     304     365 ..     304     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.4e-12
                              TOBE   1 ssarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       ssarN + g+V+++  +g   +V v ++ g +    +tr   ee++L++G++V++++ka++vh+
  gi|386003016|ref|YP_005921315.1| 304 SSARNSFSGRVEEIANGG--MMVKVWVDVGIPFMTMLTRLGYEEMDLKVGDPVYLTFKATAVHV 365
                                       79****************..666666666777888999999**********************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     1e-10     9e-08       2      76 .]     289     366 .]     288     366 .] 0.90

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1e-10
                            TOBE_2   2 aiRPEklrla....aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddav 74 
                                       ++RPE + ++    + +++n++sG+Ve+++  G  +++ v+++     ++ +   + + +l++Gd V l++++ +++
  gi|386003016|ref|YP_005921315.1| 289 SVRPEEILISkvplKSSARNSFSGRVEEIANGGMMVKVWVDVGIPFMTMLTRLGYE-EMDLKVGDPVYLTFKATAVH 364
                                       8***********99777779**********************99977777777776.5799**************** PP

                            TOBE_2  75 vl 76 
                                       v+
  gi|386003016|ref|YP_005921315.1| 365 VF 366
                                       *9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     4e-05     0.036       3      23 ..      30      50 ..      28      73 .. 0.76
   2 !   15.6   0.1   1.2e-05     0.011     226     298 ..     120     190 ..      82     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      v+iGp gsGK+ L+++  ++ 
  gi|386003016|ref|YP_005921315.1| 30 VIIGPTGSGKTILMETVAGIY 50
                                      9***************98875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                        ++ +++ +  lS G k+  a++ a+   +   s+ l+DEp ++L+    +rl + lk+ ++  ++ +i +THS
  gi|386003016|ref|YP_005921315.1| 120 ISHLRPRRPGTLSGGEKQRVAIARAIVMEP---SVMLLDEPLSSLDGLTRERLRRELKRIHQvYRTTIIHVTHS 190
                                       567788889999999999999999999988...***************************9************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.3e-06    0.0029      26     208 ..      28     201 ..       9     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                         +i+Gp GSGK+ l++ +  +   ++ + +     +d i++ ++ ++   + v   +    + +++e+  + ++ r
  gi|386003016|ref|YP_005921315.1|  28 YLVIIGPTGSGKTILMETVAGIYAPEEGRIFLD--GRD-ITR-EAPRNRRVCMVYQDYMLFPHLSVEENIAFGLKSR 100
                                       5689**************977766666644433..234.444.4666666666665555555544444444444444 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                       +++ ge    i   ev+ +evsell  +++ +    +LSgGek+ va+a    i  v   +++llDe  + LD   +
  gi|386003016|ref|YP_005921315.1| 101 KVSAGE----I---EVKVAEVSELLGISHLRPRrpgTLSGGEKQRVAIARA--I--VMEPSVMLLDEPLSSLDGLTR 166
                                       444444....4...55666777777777776543339*******9998854..3..33456789************* PP

                                       HHHHHHHHHHCTT..SEEEEE-SS.HHHCCC-SCE CS
                                       xxxxxxxxxxxxx..xxxxxxxxx.xxxxxxxxxx RF
                             SMC_N 177 kkvaellkekskn..aQfivislr.eemlekadkl 208
                                       +++ + lk+ ++   + +i ++++ ee+++ ad++
  gi|386003016|ref|YP_005921315.1| 167 ERLRRELKRIHQVyrTTIIHVTHSfEEVFSLADRV 201
                                       ***99999777651144444454424455555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.5e-06    0.0049      22      63 ..      24      66 ..      15     185 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      g++e+++++G+ G+GK+ l+++++  +  + g ifl g+    
  gi|386003016|ref|YP_005921315.1| 24 GDGEYLVIIGPTGSGKTILMETVAGIYAPEeGRIFLDGRDITR 66
                                      6779********************9776662588887776555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-05     0.021       7      27 ..      28      48 ..      23     103 .. 0.86
   2 ?   -1.7   0.0       3.7   3.3e+03      95     113 ..     152     174 ..     105     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlle 27
                                       lv++G++G+GKT l+++++ 
  gi|386003016|ref|YP_005921315.1| 28 YLVIIGPTGSGKTILMETVAG 48
                                      589**************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.7
                            AAA_22  95 liiDEaqh.lr...seealeeLr 113
                                       +++DE    l+   +e++ +eL+
  gi|386003016|ref|YP_005921315.1| 152 MLLDEPLSsLDgltRERLRRELK 174
                                       33333222222221122222222 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-05     0.014      24     102 ..      28     107 ..      17     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvGggs.kpkp 99 
                                        l+++Gp GsGKt+l + ++++ +p + +  l+ + i+  a ++++  ++ +  +  ph s+ +    G  s k+  
  gi|386003016|ref|YP_005921315.1|  28 YLVIIGPTGSGKTILMETVAGIYAPEEGRIFLDGRDITREAPRNRRVCMVYQDYMLFPHLSVEENIAFGLKSrKVSA 104
                                       5899*********************9999999999999888877777777777778888888777666665546667 PP

                      Mg_chelatase 100 Gei 102
                                       Gei
  gi|386003016|ref|YP_005921315.1| 105 GEI 107
                                       766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.022     130     161 ..      27      58 ..       3      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderiv 161
                                         +++ G+TgsGKt+l+ ++  + + ++ ri 
  gi|386003016|ref|YP_005921315.1|  27 EYLVIIGPTGSGKTILMETVAGIYAPEEGRIF 58 
                                       568899************99999888888886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-05     0.029      19      49 ..      27      57 ..      20      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                       + v+ Gp G+GKt ++++++ +++ ++gr+
  gi|386003016|ref|YP_005921315.1| 27 EYLVIIGPTGSGKTILMETVAGIYAPEEGRI 57
                                      4789********************9996565 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.1e-05     0.027       5      38 ..       9      45 ..       8      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                            AAA_23  5 enfrsf..rdqeidFskg.ltlItGpNGaGKTTildA 38
                                      +n++ f  +d++++ ++g   +I+Gp+G+GKT +++ 
  gi|386003016|ref|YP_005921315.1|  9 KNLGDFvlKDVSLEVGDGeYLVIIGPTGSGKTILMET 45
                                      6777787788888886651559************985 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     8e-05     0.071      19      50 ..      21      54 ..       9      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-05
                            AAA_29 19 idlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                      +++ +    +++Gp+GsGK+ l+  ++ +  p++
  gi|386003016|ref|YP_005921315.1| 21 LEVGDgeYLVIIGPTGSGKTILMETVAGIYAPEE 54
                                      4433335889***********9988887777765 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012      0.11      41      80 ..     301     339 ..     287     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                       Arc_PepC_II  41 svekeldeelrkelkkykkkglieetvWvtygvPflipit 80 
                                         +++ ++ ++ ++++  + g +  +vWv  g+Pf+ ++t
  gi|386003016|ref|YP_005921315.1| 301 PLKSSARNSFSGRVEEIANGG-MMVKVWVDVGIPFMTMLT 339
                                       556667788888999999999.6669**********9998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.17       2      21 ..      28      47 ..      27      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      ++++ G+ GsGKT+L++ +a
  gi|386003016|ref|YP_005921315.1| 28 YLVIIGPTGSGKTILMETVA 47
                                      689*************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00057      0.51       2      22 ..      30      50 ..      29     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00057
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                      +++Gp G GKT+l++ va   
  gi|386003016|ref|YP_005921315.1| 30 VIIGPTGSGKTILMETVAGIY 50
                                      689**************9875 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011      0.96      20      39 ..      27      46 ..      17      57 .. 0.75
   2 ?   -0.1   0.0      0.59   5.3e+02      48      91 ..     140     184 ..     134     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                      SEEEEE--TTSSTTHHHHHH CS
                              PhoH 20 divfaiGpaGtGKtylaval 39
                                      + +++iGp+G+GKt l  ++
  gi|386003016|ref|YP_005921315.1| 27 EYLVIIGPTGSGKTILMETV 46
                                      56799*********986443 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.59
                                       S-SEEEEEE-S--T.T----SS---------TTTHHHHHHHTTTS CS
                              PhoH  48 kvkriiltrpavea.geelGflpgdleekvdpylrplydaLkdll 91 
                                        + r i++ p+v+  +e l  l+g ++e+++  l+ +++  ++++
  gi|386003016|ref|YP_005921315.1| 140 AIARAIVMEPSVMLlDEPLSSLDGLTRERLRRELKRIHQVYRTTI 184
                                       567889999999777999999999999999888888877665554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00063      0.57       3      43 ..      28      68 ..      26      72 .. 0.92
   2 ?   -1.8   0.0       2.2     2e+03     150     184 ..     314     350 ..     312     357 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00063
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaa 43
                                      +++++G++G+GKT  +  +a ++  e+ ++ l   D+ R a
  gi|386003016|ref|YP_005921315.1| 28 YLVIIGPTGSGKTILMETVAGIYAPEEGRIFLDGRDITREA 68
                                      6789*****************************99999987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                       TTSSSSTTHHHHHHHHHTS-EEEE..E-SSSTTGEEE CS
                             SRP54 150 lDgdakgGaalsiaaelklPikfi..gvGekiedlee 184
                                       +++ a+gG ++++   +++P + +   +G + +dl++
  gi|386003016|ref|YP_005921315.1| 314 VEEIANGGMMVKVWVDVGIPFMTMltRLGYEEMDLKV 350
                                       678899*******999999976541145666666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031      0.28      13      73 ..      25     167 ..      17     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktg.......................................... 47 
                                       +g+ +++ ++TGsGKT  +   +   +y    ++g                                          
  gi|386003016|ref|YP_005921315.1|  25 DGEYLVIIGPTGSGKTILMETVAG--IYA--PEEGrifldgrditreaprnrrvcmvyqdymlfphlsveeniafgl 97 
                                       56778999********98665554..554..2222355666666778888888899999999999999999999999 PP

                                       ............................................-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       ............................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 ............................................pkalivePtreLaeqtlnnlkkfkky 73 
                                                                                    +a+++eP+  L  + l+ l  ++ +
  gi|386003016|ref|YP_005921315.1|  98 ksrkvsageievkvaevsellgishlrprrpgtlsggekqrvaiARAIVMEPSVMLLDEPLSSLDGLTRE 167
                                       9999999999999999999999999999999999999999999988888888888888777777666664 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00052      0.47       3      47 ..      27      70 ..      25      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00052
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                      + lvi G+  +GKT l+++++  +  ++e  ++++  d + ++ +
  gi|386003016|ref|YP_005921315.1| 27 EYLVIIGPTGSGKTILMETVAGIYA-PEEGRIFLDGRDITREAPR 70
                                      679***************9996655.8888888887777665554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00038      0.34      27      52 ..      29      54 ..       5     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                      EEEEESTTSTHHHHHHHHHHHH-S.. CS
                            ResIII 27 glikmaTGtGKTlvaaklierllkkg 52
                                      ++i  +TG+GKT+++  ++  ++ ++
  gi|386003016|ref|YP_005921315.1| 29 LVIIGPTGSGKTILMETVAGIYAPEE 54
                                      45999*********977777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2234.02
//
Query:       gi|386003017|ref|YP_005921316.1|  [L=235]
Description: NifC-like ABC-type porter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-20   71.5   8.1    9.5e-20   71.1   8.1    1.1  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   8.1   5.3e-24   9.5e-20       2     170 ..      43     223 ..      39     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 5.3e-24
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilpviillllsaapy 67 
                                       +++++ +a ++ ++++++  +li+++l+lP++v ++ l+l+f           +   ++ ++ l+++i+ ++ ++p+
  gi|386003017|ref|YP_005921316.1|  43 VPAAYSLA-RYDFPGKNVANTLIDMPLALPPLVAGVGLLLFFgtslpgrqladA-GLVFVFTPLGIVIAQFFVNVPF 117
                                       67778888.99**********************77777777888******9953.447889**************** PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                       +++++r+ ++ ++  ++ +a++lG+++ q +++v+lP+a   +++g ++++   +g++ ++++++   G +++++e+
  gi|386003017|ref|YP_005921316.1| 118 MLRVMRSTFEGISPRYEHVAKTLGCTDGQALWRVTLPMASNGLVAGSVITWSKGIGEFGAVLMMA---GATRMRTET 191
                                       *****************************************************************...889999999 PP

                      BPD_transp_1 145 ilgydyseis......nggvlalviavlllnl 170
                                       +  + + ++s      +++v++++i++ +++l
  gi|386003017|ref|YP_005921316.1| 192 LPTSLFLNMScgkldeAISVATILILISVVCL 223
                                       99888888888889875555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1656.02
//
Query:       gi|386003018|ref|YP_005921317.1|  [L=257]
Description: Molybdenum ABC transporter, periplasmic molybdate-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-46  157.0   0.0    7.2e-46  156.8   0.0    1.0  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    3.9e-05   23.4   0.0    0.00011   21.9   0.0    1.8  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.083   12.8   0.1        1.8    8.5   0.1    2.3  1  SBP_bac_1       Bacterial extracellular solute-binding protei
       0.16   11.4   0.0        0.3   10.5   0.0    1.4  1  SBP_bac_6       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.8   0.0   1.6e-49   7.2e-46       1     229 [.      29     247 ..      29     248 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.8 bits;  conditional E-value: 1.6e-49
                                       .EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEE CS
                        SBP_bac_11   1 ltvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavpla 77 
                                       l v++++++ ++++e+a+ Fe++ gv+v++++ggs++l++qi+  +  D++ p+    +e+++++g+v+  + ++++
  gi|386003018|ref|YP_005921317.1|  29 LLVYCGAGMSEPMEEIADLFEEREGVEVQYTFGGSAQLLSQIELYKTGDLYMPGARSDIESAIEKGFVD--ETRDVV 103
                                       679******************************************************************..****** PP

                                       EEEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHH CS
                        SBP_bac_11  78 ssplviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltav 154
                                       ++  +i++pkgnp++i++++dL+ pg+++a+ dPt  + G+  +++le +g   +++++e++vv++++++  ll +v
  gi|386003018|ref|YP_005921317.1| 104 YHVPCIVTPKGNPAGIDSLEDLAEPGVRVALGDPTGPAIGKVSKKILESLG---IWDEVEENVVVFSGTVNELLIYV 177
                                       ***************************************************...*********************** PP

                                       HTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                        SBP_bac_11 155 eageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                         g+ada+iv+e + +    +d+ e +++p + n +  +++++ l  + + e A++F++f+ s+e++a++ ++Gf
  gi|386003018|ref|YP_005921317.1| 178 SLGQADAAIVWEDLFY----PDGMEKIEIPREKN-EIKVVSIGTLIFSEDEEVAERFMNFVVSEEGKAVFVDHGF 247
                                       ****************....9*************.689************************************9 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.5e-08   0.00011      16     175 ..      41     199 ..      34     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHHHHHHSSEEEEE--SSHHHHHHHHH.TTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEE.EE CS
                    Phosphonate-bd  16 yqpladyLseelGvevelvvatdyaavvealr.agqvDiaflgplayvqardqagveplatrvrsdGsasyrsv.ii 90 
                                       ++++ad ++e+ Gvev+++++ + a++  +++   + D+ + g+ + ++ + ++g   ++ ++r   +  y+   i+
  gi|386003018|ref|YP_005921317.1|  41 MEEIADLFEEREGVEVQYTFGGS-AQLLSQIElYKTGDLYMPGARSDIESAIEKG---FVDETR---DVVYHVPcIV 110
                                       66777777777777777777766.4444444447777777777777777666666...666666...5667775266 PP

                                       EETTSS..--SHHHH..GG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEE.EE--HHHHHHHHHTTSSSEEE CS
                    Phosphonate-bd  91 vradsd..iqsledL..kgktiafvspsStsGylvpaalLvkeagldpeddfsev.fsgshdaavlavlsgdadaaa 162
                                       ++++++  i+sledL   g ++a+++p+  +   v +  L +  g+  e   + v fsg+ ++ +  v  g+adaa 
  gi|386003018|ref|YP_005921317.1| 111 TPKGNPagIDSLEDLaePGVRVALGDPTGPAIGKVSKKIL-ESLGIWDEVEENVVvFSGTVNELLIYVSLGQADAAI 186
                                       66666456********************************.9***96554445556********************* PP

                                       EEHHHHHHHHHH- CS
                    Phosphonate-bd 163 vsadaledlvaeg 175
                                       v++d ++    e+
  gi|386003018|ref|YP_005921317.1| 187 VWEDLFYPDGMEK 199
                                       **99987765443 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00039       1.8      10     314 ..      41     239 ..      32     240 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTT CS
                         SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgv 86 
                                       +++++ + fe+++ g++V+++++gs +l      +i+  +   D+ +            g+  ++ + +++  ++++
  gi|386003018|ref|YP_005921317.1|  41 MEEIA-DLFEERE-GVEVQYTFGGSAQLLS----QIELYKTG-DLYMP-----------GARSDIESAIEKGFVDET 99 
                                       44444.6698855.9999999999999888....66666644.66666...........666666666666544443 PP

                                       CCTEEEEHHHHTHHHHCEEEES.EEEEEEEEEEEETTTHH....CTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCC CS
                         SBP_bac_1  87 kdaadklsssvlpkildskvly.vPlyaargliYNkdlfe....kagldppwtWdelveaakklkekgkkpiggarg 158
                                        d                  +y vP             +     +ag+d   + ++l+e+++++   ++++      
  gi|386003018|ref|YP_005921317.1| 100 RDV-----------------VYhVPCI-----------VTpkgnPAGID---SLEDLAEPGVRVALGDPTG------ 139
                                       221.................2222222...........11233355555...6666666666666666666...... PP

                                       EEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSC CS
                         SBP_bac_1 159 gsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGea 235
                                                        +                    +   + l+  + +++   ++++ + +++++l  ++ G+a
  gi|386003018|ref|YP_005921317.1| 140 ----------------PAI------------------GKVSKKILESLGIWDEVEENVVVFSGTVNELLIYVSLGQA 182
                                       ................111..................1111123333333445556666666666666666666666 PP

                                       SEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                         SBP_bac_1 236 amaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspe 312
                                       ++aiv+    +      +  + +++ ek++                  + +  ++ +  s ++e A+ F++f+ s+e
  gi|386003018|ref|YP_005921317.1| 183 DAAIVWEDLFY----PDGMEKIEIPREKNE------------------IKVVSIGTLIFSEDEEVAERFMNFVVSEE 237
                                       66666542211....111111111111111..................24444444445555556666666666666 PP

                                       HH CS
                         SBP_bac_1 313 aq 314
                                       ++
  gi|386003018|ref|YP_005921317.1| 238 GK 239
                                       65 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.6e-05       0.3     179     217 ..     213     251 ..     208     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                         SBP_bac_6 179 pifmlvkkgkkkelakafidfllspevqailakagg.vfP 217
                                        i  l+ ++  +e a++f++f +s+e+ a++++ g+  +P
  gi|386003018|ref|YP_005921317.1| 213 SIGTLIFSE-DEEVAERFMNFVVSEEGKAVFVDHGFvAYP 251
                                       667788888.99**********************984454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1617.06
//
Query:       gi|386003019|ref|YP_005921318.1|  [L=128]
Description: 4Fe-4S ferredoxin [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-14   50.9  16.8    3.2e-07   29.9   2.6    2.8  3  Fer4          4Fe-4S binding domain
      2e-10   40.3  16.5    4.2e-06   26.6   2.7    2.8  3  Fer4_6        4Fe-4S binding domain
    2.5e-10   39.8  18.2    9.7e-06   25.4   4.4    3.0  3  Fer4_2        4Fe-4S binding domain
    5.8e-10   39.6  27.4    4.2e-07   30.4  15.7    2.8  2  Fer4_7        4Fe-4S dicluster domain
    6.3e-10   39.0  26.3    1.3e-07   31.6  14.4    2.7  3  Fer4_10       4Fe-4S dicluster domain
    6.7e-10   39.0  22.4    7.6e-07   29.2  13.6    2.2  2  Fer4_9        4Fe-4S dicluster domain
    1.2e-07   31.6  19.6    0.00017   21.9   3.5    2.6  2  Fer4_4        4Fe-4S binding domain
    1.5e-07   32.3  11.7     0.0011   19.9   1.1    2.4  2  Fer4_16       4Fe-4S double cluster binding domain
    2.5e-06   27.5  13.0      0.002   18.2   1.0    2.4  2  Fer4_21       4Fe-4S dicluster domain
    5.4e-05   23.4  12.4    0.00041   20.5  12.6    2.1  1  Fer4_18       4Fe-4S dicluster domain
      9e-05   22.9  11.0      0.016   15.7   1.2    2.4  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
    0.00019   22.1  23.3      0.011   16.6   5.0    2.5  2  Fer4_3        4Fe-4S binding domain
    0.00024   21.6  13.6       0.61   10.7   2.8    2.4  2  Fer4_17       4Fe-4S dicluster domain
     0.0029   18.0  17.4      0.099   13.1   4.4    2.3  2  Fer4_8        4Fe-4S dicluster domain
     0.0084   15.9   0.0      0.012   15.4   0.0    1.2  1  NIL           NIL domain
  ------ inclusion threshold ------
      0.045   13.9   6.1       0.12   12.5   6.1    1.7  1  Furin-like_2  Furin-like repeat, cysteine-rich
      0.084   11.7   0.2       0.11   11.3   0.2    1.1  1  Trp_syntA     Tryptophan synthase alpha chain
       0.35   11.7  17.2        1.6    9.6   4.2    2.2  2  Fer4_22       4Fe-4S dicluster domain
        0.6   10.9  13.2        2.4    8.9   2.3    2.8  3  Fer4_15       4Fe-4S single cluster domain
          6    6.7  12.0        9.7    6.0   1.8    2.3  2  zf-C2H2_11    zinc-finger C2H2-type
        9.8    6.4   8.5        8.2    6.6   1.1    2.2  2  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.2   1.9e+03       3       8 ..      46      51 ..      44      53 .. 0.78
   2 !   29.0   3.0   6.9e-10   5.9e-07       2      21 ..      73      92 ..      72      95 .. 0.91
   3 !   29.9   2.6   3.7e-10   3.2e-07       2      23 ..     102     123 ..     101     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.2
                                      EETTTS CS
                              Fer4  3 ideekC 8 
                                      + +e+C
  gi|386003019|ref|YP_005921318.1| 46 VEPERC 51
                                      789999 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 6.9e-10
                                      EEETTTSSS-THHHHHSTTT CS
                              Fer4  2 videekCigCGaCvevCPvg 21
                                      + d e C++CGaC+++CP+g
  gi|386003019|ref|YP_005921318.1| 73 IKDDEECVHCGACISICPTG 92
                                      789****************9 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 3.7e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       v d  kC+ CG+Cv +CP  A+
  gi|386003019|ref|YP_005921318.1| 102 VADAGKCVQCGTCVTACPQRAL 123
                                       66999**************998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.7   2.3e+03       2       9 ..      44      51 ..      43      53 .. 0.79
   2 !   21.5   2.6     2e-07   0.00017       5      22 ..      75      92 ..      72      94 .. 0.88
   3 !   26.6   2.7   4.9e-09   4.2e-06       2      23 ..     101     122 ..     100     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.7
                            Fer4_6  2 veidpdkC 9 
                                      v + p++C
  gi|386003019|ref|YP_005921318.1| 44 VDVEPERC 51
                                      77889999 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2e-07
                            Fer4_6  5 dpdkCigCgdCvrvCPeg 22
                                      d++ C++Cg+C+++CP+g
  gi|386003019|ref|YP_005921318.1| 75 DDEECVHCGACISICPTG 92
                                      6677************98 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 4.9e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       v+ d+ kC++Cg Cv++CP  a
  gi|386003019|ref|YP_005921318.1| 101 VVADAGKCVQCGTCVTACPQRA 122
                                       899****************665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.97   8.3e+02       5      11 ..      46      52 ..      42      53 .. 0.76
   2 !   20.7   3.2   3.5e-07    0.0003       3      22 .]      73      91 ..      71      91 .. 0.81
   3 !   25.4   4.4   1.1e-08   9.7e-06       3      22 .]     101     120 ..      99     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.97
                            Fer4_2  5 vdtdrCi 11
                                      v+++rC 
  gi|386003019|ref|YP_005921318.1| 46 VEPERCS 52
                                      7899**6 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.5e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      ++ d++ C++CgaC+s CP+
  gi|386003019|ref|YP_005921318.1| 73 IKDDEE-CVHCGACISICPT 91
                                      455666.************7 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 1.1e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       vv+d+ +C++Cg+Cv+aCP+
  gi|386003019|ref|YP_005921318.1| 101 VVADAGKCVQCGTCVTACPQ 120
                                       68999**************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.8   3.8e-07   0.00032      32      51 ..      73      92 ..      24      93 .. 0.75
   2 !   30.4  15.7     5e-10   4.2e-07       2      52 .]      79     122 ..      78     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.8e-07
                            Fer4_7 32 eidpekClgCgaCvavCPtg 51
                                        d e+C++CgaC++ CPtg
  gi|386003019|ref|YP_005921318.1| 73 IKDDEECVHCGACISICPTG 92
                                      558899************98 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 5e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C++CgaC + Cp++++ ++         +v+ d+ kC++Cg Cv++CP  a
  gi|386003019|ref|YP_005921318.1|  79 CVHCGACISICPTGTFHFKGT-------EVVADAGKCVQCGTCVTACPQRA 122
                                       ******************765.......6899****************865 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.74   6.3e+02      33      51 ..      39      57 ..      28      60 .. 0.75
   2 !   31.6  14.4   1.6e-10   1.3e-07       2      56 .]      72     119 ..      71     119 .. 0.95
   3 !   19.5   4.1   8.9e-07   0.00076       2      21 ..     101     120 ..     100     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.74
                           Fer4_10 33 seeeavrkkvekCtgcgaC 51
                                      s+e +v++ +e+C ++ a 
  gi|386003019|ref|YP_005921318.1| 39 SGEIVVDVEPERCSEVKAA 57
                                      5677888899999988775 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.6e-10
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +++dd+ C++Cg+C + CP+         +  ++ +v  + +kC +cg Cv aCP
  gi|386003019|ref|YP_005921318.1|  72 IIKDDEECVHCGACISICPT-------GTFHFKGTEVVADAGKCVQCGTCVTACP 119
                                       67899***************.......999999999999***************9 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 8.9e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                       vv d+ +C++Cg+Cv+aCP+
  gi|386003019|ref|YP_005921318.1| 101 VVADAGKCVQCGTCVTACPQ 120
                                       688999*************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.5   2.6e-07   0.00022      33      49 ..      69      92 ..      31      94 .. 0.73
   2 !   29.2  13.6   8.9e-10   7.6e-07       1      50 [.      78     122 ..      78     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                            Fer4_9 33 e.......eaCigCgaCveaCpkg 49
                                      e       e+C++CgaC+ +Cp+g
  gi|386003019|ref|YP_005921318.1| 69 EnpiikddEECVHCGACISICPTG 92
                                      0445555578************97 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 8.9e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C+ CgaC++ Cp+g++  +  e  a        +C++Cg+Cv aCp+ a
  gi|386003019|ref|YP_005921318.1|  78 ECVHCGACISICPTGTFHFKGTEVVADAG-----KCVQCGTCVTACPQRA 122
                                       5****************999888888874.....5************986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.5   1.9e-07   0.00017       2      17 .]      77      92 ..      76      92 .. 0.92
   2 !   17.9   5.2   3.7e-06    0.0032       3      17 .]     107     121 ..     105     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e C++Cg+C+++CP+g
  gi|386003019|ref|YP_005921318.1| 77 EECVHCGACISICPTG 92
                                      68************86 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.7e-06
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +C++Cg Cv aCPq+
  gi|386003019|ref|YP_005921318.1| 107 KCVQCGTCVTACPQR 121
                                       8************86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.1   1.2e-06    0.0011       2      21 ..      79      98 ..      78     106 .. 0.81
   2 !   16.9   3.6   1.1e-05    0.0094       1      18 [.     107     124 ..     107     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-06
                           Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                      C+ Cg+C+++CPt+ ++ k 
  gi|386003019|ref|YP_005921318.1| 79 CVHCGACISICPTGTFHFKG 98
                                      **************998873 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.1e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       +C++Cg C+ +CP++a++
  gi|386003019|ref|YP_005921318.1| 107 KCVQCGTCVTACPQRALR 124
                                       6**************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   4.8   3.7e-05     0.031      37      53 ..      75      91 ..      45      96 .. 0.77
   2 !   18.2   1.0   2.4e-06     0.002       4      26 ..     104     126 ..     101     128 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                           Fer4_21 37 vedeCvGCnlCssvCPv 53
                                       ++eCv C  C+s+CP+
  gi|386003019|ref|YP_005921318.1| 75 DDEECVHCGACISICPT 91
                                      46778888888888885 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.4e-06
                           Fer4_21   4 dedkCigCgkCliaCedtshqai 26 
                                       d  kC++Cg C++aC++ +   i
  gi|386003019|ref|YP_005921318.1| 104 DAGKCVQCGTCVTACPQRALRLI 126
                                       6679************9887665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  12.6   4.8e-07   0.00041      53      96 ..      71     119 ..      17     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.8e-07
                           Fer4_18  53 rkekgagdcidcescvkvcPtgidirkGlql.....eciscllcidacd 96 
                                          k++ +c++c++c+++cPtg    kG  +     +c++c+ c+ ac 
  gi|386003019|ref|YP_005921318.1|  71 PIIKDDEECVHCGACISICPTGTFHFKGTEVvadagKCVQCGTCVTACP 119
                                       4567889*********************987666668***********6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.2   1.9e-05     0.016       2      18 ..      75      91 ..      73     100 .. 0.89
   2 !   11.8   2.8   0.00031      0.27       2      18 ..     104     120 ..     101     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D ++C+ cgaC +++P 
  gi|386003019|ref|YP_005921318.1| 75 DDEECVHCGACISICPT 91
                                      669*************6 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00031
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D  +C+ cg+Cv ++P+
  gi|386003019|ref|YP_005921318.1| 104 DAGKCVQCGTCVTACPQ 120
                                       6679************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   5.0   1.3e-05     0.011       1      14 [.      79      92 ..      79      93 .. 0.96
   2 !   14.2   7.1   7.4e-05     0.063       1      15 []     108     122 ..     108     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C++CgaC   CP+g
  gi|386003019|ref|YP_005921318.1| 79 CVHCGACISICPTG 92
                                      ************98 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.4e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++Cg+Cv +CP +A
  gi|386003019|ref|YP_005921318.1| 108 CVQCGTCVTACPQRA 122
                                       ************987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   2.8   0.00072      0.61      45      58 ..      78      91 ..      60      94 .. 0.76
   2 !    8.8  13.8    0.0028       2.4       2      58 ..      79     120 ..      78     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C++Cg C + CP 
  gi|386003019|ref|YP_005921318.1| 78 ECVHCGACISICPT 91
                                      56666666666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       C +Cg+C+  Cp++  + +  +                   a++C++Cg C+++CPq
  gi|386003019|ref|YP_005921318.1|  79 CVHCGACISICPTGTFHFKGTEV---------------VADAGKCVQCGTCVTACPQ 120
                                       88999999999988776552222...............345789************8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.3   0.00017      0.15       3      17 ..      77      91 ..      75     104 .. 0.80
   2 !   13.1   4.4   0.00012     0.099      48      63 ..     105     120 ..      92     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      e+C++CgaC s Cp+
  gi|386003019|ref|YP_005921318.1| 77 EECVHCGACISICPT 91
                                      579999999999984 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
                            Fer4_8  48 lwsCttcgaCtevCpv 63 
                                       +++C++cg C+++Cp+
  gi|386003019|ref|YP_005921318.1| 105 AGKCVQCGTCVTACPQ 120
                                       4566666666666665 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05     0.012      12      71 ..      12      65 ..       3      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                      -SS-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT-EE CS
                               NIL 12 avePllshlvrqlglevnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkrnvdv 71
                                      ++ P++s+++ + +  +nI  ++v+     + G +v+ +  ++e+  ++++ ++ r+v+v
  gi|386003019|ref|YP_005921318.1| 12 VRRPIVSSVILETKALINIERAKVD----AVSGEIVVDV--EPERCSEVKAAFEARGVRV 65
                                      679*********************8....56899*****..59***************98 PP

>> Furin-like_2  Furin-like repeat, cysteine-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   6.1   0.00014      0.12      27      66 ..      77     115 ..      47     123 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                      Furin-like_2  27 egirqiGvclascpaGyfgvrnkev....nrctkckaeecescf 66 
                                       e+  + G+c++ cp+G f  +++ev     +c++c +     c 
  gi|386003019|ref|YP_005921318.1|  77 EECVHCGACISICPTGTFHFKGTEVvadaGKCVQCGT-----CV 115
                                       556789***************9987432246666665.....33 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00013      0.11     108     154 ..      30      76 ..      17      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       CHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HH CS
                         Trp_syntA 108 laelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsde 154
                                       ++++k   v g iv+D+ +e  +e+++a ++ g+++v l  p ++d+
  gi|386003019|ref|YP_005921318.1|  30 IERAKVDAVSGEIVVDVEPERCSEVKAAFEARGVRVVLLENPIIKDD 76 
                                       567777789999***************************99988875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.2    0.0019       1.6       1      16 [.      78      93 ..      78     104 .. 0.84
   2 ?    8.0   5.1    0.0059         5      79      94 ..     105     120 ..      93     122 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                           Fer4_22  1 rClsCgaCtlvCptCs 16
                                      +C++CgaC  +Cpt +
  gi|386003019|ref|YP_005921318.1| 78 ECVHCGACISICPTGT 93
                                      5999********9964 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0059
                           Fer4_22  79 esgCvGCgRCieacpv 94 
                                       + +Cv Cg C++acp+
  gi|386003019|ref|YP_005921318.1| 105 AGKCVQCGTCVTACPQ 120
                                       5567777777777765 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         3   2.6e+03      43      55 ..      45      57 ..      23      66 .. 0.62
   2 ?    8.7   0.9    0.0035         3       4      20 ..      75      91 ..      72     100 .. 0.86
   3 ?    8.9   2.3    0.0029       2.4       1      20 [.     101     120 ..     101     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3
                           Fer4_15 43 evpddeeeaaqeA 55
                                      +v++++  +++ A
  gi|386003019|ref|YP_005921318.1| 45 DVEPERCSEVKAA 57
                                      4555554444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0035
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D ++C  cg+C+  +p+
  gi|386003019|ref|YP_005921318.1| 75 DDEECVHCGACISICPT 91
                                      899************85 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0029
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       Vv D  +C  cg Cv+++p+
  gi|386003019|ref|YP_005921318.1| 101 VVADAGKCVQCGTCVTACPQ 120
                                       677999************97 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.8     0.011       9.7       7      15 ..      79      87 ..      77      90 .. 0.86
   2 ?    5.7   2.9     0.015        13       6      15 ..     107     116 ..     104     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                        zf-C2H2_11  7 CleCGlcft 15
                                      C++CG c +
  gi|386003019|ref|YP_005921318.1| 79 CVHCGACIS 87
                                      *******66 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                        zf-C2H2_11   6 qCleCGlcft 15 
                                       +C++CG c t
  gi|386003019|ref|YP_005921318.1| 107 KCVQCGTCVT 116
                                       8*******66 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.7      0.04        34      72      92 ..      76      96 ..      68     101 .. 0.76
   2 ?    6.6   1.1    0.0096       8.2      50      88 ..      89     121 ..      86     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                                      CCC--S--HHHHH-TT--EEE CS
                            ETF_QO 72 aqnCvhCktCdikdpsqniew 92
                                       ++CvhC +C    p+   ++
  gi|386003019|ref|YP_005921318.1| 76 DEECVHCGACISICPTGTFHF 96
                                      578*******77777766655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0096
                                       -TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT- CS
                            ETF_QO  50 CPagvyeivedeeakekklqinaqnCvhCktCdikdpsq 88 
                                       CP g + +       +++++ +a  Cv C tC    p++
  gi|386003019|ref|YP_005921318.1|  89 CPTGTFHFK------GTEVVADAGKCVQCGTCVTACPQR 121
                                       666666654......4457899**********8877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 777.87
//
Query:       gi|386003020|ref|YP_005921319.1|  [L=497]
Description: hypothetical protein Mhar_2345 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.2e-137  456.1   0.0   7.6e-137  455.8   0.0    1.1  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    3.2e-24   85.1   1.1    4.7e-11   43.0   0.1    2.7  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.8   0.0  8.5e-141  7.6e-137       2     347 .]      14     350 ..      13     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 455.8 bits;  conditional E-value: 8.5e-141
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio   2 vVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylgat 78 
                                        V+taee+ +lv+e g++ a++evDVVttgTfg+m+ssg +ln g+++p+iki+++wLn+v+ay g+aavdl+lgat
  gi|386003020|ref|YP_005921319.1|  14 RVVTAEEMPDLVDELGTDGAVREVDVVTTGTFGAMCSSGLFLNTGHSDPPIKISRAWLNNVEAYGGVAAVDLFLGAT 90 
                                       69*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  79 aeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNssee 155
                                       ++sed  +++eyGG+hv+edLv+g+evel+a++  tdcypr+++et+++l+d+n+ai+vnpRn y +Y+aa+Ns+e+
  gi|386003020|ref|YP_005921319.1|  91 QPSED--RGDEYGGAHVMEDLVSGREVELRAQGAVTDCYPRSDLETTLRLEDFNQAIMVNPRNSYERYAAATNSTER 165
                                       ****5..456******************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 156 tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLa 232
                                       t++tymg+l p++gn++ysgaG+lsP+ nDp++++ig+G+ri+LgGa+G +ig+GTq+ p++          ++tL+
  gi|386003020|ref|YP_005921319.1| 166 TLHTYMGTLLPRCGNVSYSGAGSLSPIPNDPDFEYIGVGARIFLGGAQGHIIGSGTQHLPQSG---------FATLM 233
                                       ***********************************************************7666.........9**** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            HcyBio 233 vigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael. 308
                                       v+gdlkeMs+e+lr+a+++ yGp+l+vg+g+piPvl+e ++e++av+d+di+++++D++++rr+r+t+ +v+Y++l 
  gi|386003020|ref|YP_005921319.1| 234 VKGDLKEMSAEFLRAATFQDYGPSLYVGLGVPIPVLNEGIAEKTAVRDRDIVTEIIDYGVPRRDRPTVRRVNYEQLy 310
                                       ***************************************************************************** PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 309 .GkieiegkevktarlsslkrareiaeeLkewiekgeflL 347
                                        G++ei+g ev+ + lss+  ar++a+ L + i++geflL
  gi|386003020|ref|YP_005921319.1| 311 sGAVEIDGAEVRASALSSRHVARKVASALGDSIRRGEFLL 350
                                       **************************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   3.8e-14   3.4e-10       1      55 [.     375     429 ..     375     431 .. 0.92
   2 !   43.0   0.1   5.3e-15   4.7e-11       1      53 [.     437     489 ..     437     492 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3.8e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                       V+d+m+++v t++++ ++ ea  +++  g +++lPVV e+g+l+G+vt  D+ +a+
  gi|386003020|ref|YP_005921319.1| 375 VRDVMSTEVATAREEISIQEASAMIVG-GpFDHLPVVSEEGRLIGMVTAWDVSKAV 429
                                       89**********************955.45*********************98876 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 5.3e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       ++++mtr+v+ ++pd+++e a++++ ++++s+lPVVd+d+++vG+vt  +l r
  gi|386003020|ref|YP_005921319.1| 437 ISEMMTRKVFIASPDEPMELAARKLHHHKISALPVVDKDHRVVGMVTSDHLSR 489
                                       5799*********************5555******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2855.97
//
Query:       gi|386003021|ref|YP_005921320.1|  [L=497]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-09   37.9   0.0    5.7e-09   36.6   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.29   11.2   0.0    1.7  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   6.4e-13   5.7e-09       1     166 [.     214     397 ..     214     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 6.4e-13
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfveller 69 
                                       v+++rgC ++CsfC+ +      +r+r+++v +i+e +  +    g + +il++ + + y        p++  +l+r
  gi|386003021|ref|YP_005921320.1| 214 VEIGRGCWRGCSFCSPT-----MRRPRHRPVSRIIEDASVN-LGAGQRDLILHSEDAFTYgsvgtepnPEKLLDLFR 284
                                       5799*************.....7******************.7999*******999999999999877666777777 PP

                                       HHHTC....CCTEEEEEEECSSCHG..HHHHHHHHHTT....-SEEEEEEBSSSHHHHHHHHTCTSHH........H CS
                                       xxxxx....xxxxxxxxxxxxxxxx..xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx........x RF
                       Radical_SAM  70 lakla....vpgiritvetngtlpd..eeklerllelg....vdrvslgleaaddekvlklmnrghtf........e 128
                                        +k      v+  ++++ + ++        + +++  g         +g+e+++++   k+m +++t         e
  gi|386003021|ref|YP_005921320.1| 285 QVKALgprtVDVSHVSLASAYHS-QslLAEISEIVGIGagqrYMSAWIGIETGSPRLLAKHM-KKKTHpapleawpE 359
                                       77664666433333333333333.13556666666666987788888*********777777.55555579999999 PP

                                       HHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 129 evlealeklreagikrvvdrivglpGendeeleellel 166
                                        v ++  ++ ++ + +v + ++glpGe+ ++++ + el
  gi|386003021|ref|YP_005921320.1| 360 MVRDCYALFQDHSWLPVASLVLGLPGETASDVVLTTEL 397
                                       ************9999**************99877665 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.3e-05      0.29      66     120 ..     128     178 ..      58     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                       B12-binding  66 eavkelvel..lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       +++ el++   +++ rp  kvv+GG +    +e+   +++ +d++ +gege +++ +
  gi|386003021|ref|YP_005921320.1| 128 TKFLELLDHplIREHRP--KVVIGGNG---SWEL-RGEDERVDHIYLGEGERTFPSI 178
                                       56677777776777766..99****87...4444.3344999***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2979.56
//
Query:       gi|386003022|ref|YP_005921321.1|  [L=104]
Description: hypothetical protein Mhar_2347 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-29  102.4   0.2    1.4e-29  102.1   0.2    1.1  1  DUF2551   Protein of unknown function (DUF2551)
     0.0036   17.5   0.1     0.0043   17.2   0.1    1.2  1  FUR       Ferric uptake regulator family


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.2   1.6e-33   1.4e-29       1      83 []      16      97 ..      16      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.6e-33
                           DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkek.fdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkee 78
                                      Lk+yl+rD  GiR++vLklfl+ +++t+ee+y+ l+++ f+vsy+gv++mvGl+++rlGIl++  +++g++nvYsLk +
  gi|386003022|ref|YP_005921321.1| 16 LKNYLKRDGMGIRKAVLKLFLHDRSFTTEEVYTYLDQEgFEVSYRGVSAMVGLMNTRLGILSI--DVSGDHNVYSLKPD 92
                                      89*************************************************************..************** PP

                           DUF2551 79 yadlv 83
                                      ++ +v
  gi|386003022|ref|YP_005921321.1| 93 HKVIV 97
                                      99876 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.8e-07    0.0043      10      76 ..      28      93 ..       8      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-07
                                      HHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSS CS
                               FUR 10 RekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakke 76
                                      R+++l+++ + +  ++ eevy  l++e+ e+s   V  ++ l++ +  + ++++++++++y l+ ++
  gi|386003022|ref|YP_005921321.1| 28 RKAVLKLFLHDRS-FTTEEVYTYLDQEGFEVSYRGVSAMVGLMNTRLGILSIDVSGDHNVYSLKPDH 93
                                      8999999998776.5789***************************99999*************9643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 672.23
//
Query:       gi|386003023|ref|YP_005921322.1|  [L=384]
Description: radical SAM protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-06   28.1   0.0    2.9e-06   27.4   0.0    1.2  1  Fer4_14      4Fe-4S single cluster domain
    2.3e-06   28.1   0.0    9.7e-06   26.1   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    3.8e-06   27.2   0.0      6e-06   26.6   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   4.9e-10   2.9e-06       1      89 [.      53     140 ..      53     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.9e-10
                           Fer4_14   1 lfvrlsgCnlsCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74 
                                       lfv ++ C   C  C    ++   +  + ++   e  ++i+   +++ i + g  +tGGePL   + + +lk ++ l
  gi|386003023|ref|YP_005921322.1|  53 LFV-TGVCDRGCFYCPlseERRGIDIAYANERRAESDSEII--EEAHAIGALGTGITGGEPL--LKMEFVLKSIRAL 124
                                       588.999********96665556777999999999999999..7788888899*********..889********** PP

                           Fer4_14  75 keey.pekkiwletng 89 
                                       k e+ +e++i+l+t+ 
  gi|386003023|ref|YP_005921322.1| 125 KGEFgEEHHIHLYTGS 140
                                       ****899*******96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.6e-09   9.7e-06       3     106 ..      55     159 ..      53     163 .. 0.82
   2 ?   -0.9   0.0      0.32   1.9e+03      74      96 ..     246     276 ..     195     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.6e-09
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       vt  C ++C +C+ +e       +     r  s  ei+ee+ ++     + +  ++ggepll  +fv +  r+ k +
  gi|386003023|ref|YP_005921322.1|  55 VTGVCDRGCFYCPLSEErrgidIAYANERRAESDSEIIEEAHAIG----ALGTGITGGEPLLKMEFVLKSIRALKGE 127
                                       6788*************9977766666666666677777776665....99***********999999998888888 PP

                                       .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrvs 106
                                         ++ +i++ t      +  l+ l+e+g+d + 
  gi|386003023|ref|YP_005921322.1| 128 fGEEHHIHLYTGSKPG-PSSLRDLAEAGLDEIR 159
                                       8888888888876666.9999***999999875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                                       C.....CCTEEEEEEECSSCHG...HHHHHH CS
                                       x.....xxxxxxxxxxxxxxxx...xxxxxx RF
                       Radical_SAM  74 a.....vpgiritvetngtlpd...eekler 96 
                                       a     v+g+r+++ ++++++    +e l+r
  gi|386003023|ref|YP_005921322.1| 246 AaehfrVEGLRVHYCSSAFKDAvqlRERLKR 276
                                       0333446788888888888865666555444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     1e-09     6e-06       4      95 ..      47     141 ..      39     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1e-09
                           Fer4_12   4 eGvrlslfvsg.CnlsCkgCfnketw...sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelv 76 
                                       +G  l+lfv+g C++ C +C   e +   +  + +e   e   eiie+++     g  ++GGEPll  + e +l+ +
  gi|386003023|ref|YP_005921322.1|  47 QGASLVLFVTGvCDRGCFYCPLSEERrgiDIAYANERRAESDSEIIEEAHAIGALGTGITGGEPLL--KMEFVLKSI 121
                                       566679**8777*****999755554444888999999***********99999************..********* PP

                           Fer4_12  77 kevkeekp.ekdiwlytgyt 95 
                                       + +k e+  e  i lytg++
  gi|386003023|ref|YP_005921322.1| 122 RALKGEFGeEHHIHLYTGSK 141
                                       ********899999***985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2388.09
//
Query:       gi|386003024|ref|YP_005921323.1|  [L=446]
Description: Signal sequence recognition 54 kDa protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-70  234.7   2.5      1e-69  234.1   2.5    1.3  1  SRP54            SRP54-type protein, GTPase domain
    5.6e-28   97.5   1.9    5.6e-28   97.5   1.9    2.5  2  SRP_SPB          Signal peptide binding domain
    1.5e-21   76.4   1.1    6.3e-21   74.4   0.1    2.6  3  SRP54_N          SRP54-type protein, helical bundle domain
    7.7e-07   29.2   0.0    4.8e-06   26.6   0.0    2.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    7.4e-06   25.7   1.8    0.00021   21.0   1.8    2.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    9.9e-05   21.4   0.2    0.00026   20.1   0.2    1.7  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00088   19.1   0.0     0.0025   17.6   0.0    1.8  1  AAA_24           AAA domain
     0.0015   18.5   0.0     0.0042   17.0   0.0    1.8  1  APS_kinase       Adenylylsulphate kinase
     0.0027   17.9   0.1     0.0095   16.1   0.0    2.0  2  AAA_33           AAA domain
     0.0031   18.1   0.1     0.0098   16.4   0.0    2.0  1  AAA_18           AAA domain
     0.0037   16.2   0.0     0.0085   15.0   0.0    1.6  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0038   17.6   0.3      0.013   15.9   0.2    2.0  1  AAA_16           AAA ATPase domain
     0.0038   16.5   0.0     0.0078   15.5   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0044   17.1   0.7      0.043   13.9   0.7    2.4  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0047   16.3   0.2       0.12   11.7   0.0    2.3  2  AAA_8            P-loop containing dynein motor region D4
     0.0049   16.6   1.2      0.011   15.4   0.4    2.1  1  AAA_30           AAA domain
     0.0062   16.8   0.0      0.017   15.4   0.0    1.9  1  AAA_22           AAA domain
     0.0079   16.1   0.2      0.023   14.6   0.0    1.9  1  MobB             Molybdopterin guanine dinucleotide synthesis
  ------ inclusion threshold ------
       0.01   15.2   0.2        2.8    7.2   0.0    2.4  2  MipZ             ATPase MipZ
      0.019   14.3   0.0      0.043   13.1   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
      0.019   14.9   0.7       0.16   11.9   0.7    2.5  1  AAA_31           AAA domain
      0.028   13.9   0.0      0.071   12.5   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
      0.028   13.8   0.2       0.45    9.9   0.1    2.3  2  SRPRB            Signal recognition particle receptor beta su
      0.042   13.3   0.0      0.084   12.3   0.0    1.4  1  SPO22            Meiosis protein SPO22/ZIP4 like
      0.051   13.8   0.9       0.21   11.8   0.3    2.4  2  AAA_28           AAA domain
      0.073   12.7   0.1       0.21   11.2   0.1    1.8  1  Thymidylate_kin  Thymidylate kinase
      0.081   12.6   0.0       0.12   12.0   0.0    1.3  1  AAA_15           AAA ATPase domain
      0.084   13.3   0.7        0.9   10.0   0.3    2.9  2  AAA              ATPase family associated with various cellul
      0.085   12.6   0.2       0.23   11.2   0.0    1.8  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.09   12.7   0.1        0.2   11.6   0.1    1.6  1  NACHT            NACHT domain
      0.094   12.7   0.1       0.34   10.9   0.1    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
      0.097   12.4   2.0        3.4    7.4   0.2    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.16   11.1   0.0       0.32   10.1   0.0    1.7  1  G-alpha          G-protein alpha subunit
        0.3   10.9   2.1        5.4    6.8   0.3    2.4  2  AAA_26           AAA domain
        1.5    8.3   5.8        1.4    8.5   2.3    2.7  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.1   2.5     2e-72     1e-69       2     196 .]      98     290 ..      97     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 234.1 bits;  conditional E-value: 2e-72
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                       + i+lvGlqG+GKTtt+aKLa  ++++g + ++v+aDtfRa+A++QLk+l ek gv ++++k + d+ ava++++e+
  gi|386003024|ref|YP_005921323.1|  98 QTIMLVGLQGSGKTTTAAKLATFFQRKGLRSAVVCADTFRAGAFDQLKALCEKQGVFFYGEKGNPDAPAVARRGLEA 174
                                       579***********************************************************999***********9 PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                        ++  +d+v+vDTaGr++ +k+l++e+ +i  vv++d++llv+da++gq+a +qakaF++avgitgvi+tklDg+ak
  gi|386003024|ref|YP_005921323.1| 175 SRK--YDIVIVDTAGRHALEKDLIQEMMDIDAVVAADHKLLVMDAALGQQASEQAKAFNKAVGITGVIITKLDGTAK 249
                                       887..************************************************************************ PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG+a+s++ae+++ ++figvGe+ +dle+f+++r++srllg
  gi|386003024|ref|YP_005921323.1| 250 GGGAMSAVAETNSSVAFIGVGETPNDLERFEADRFISRLLG 290
                                       ***************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   1.9   1.1e-30   5.6e-28       1      98 [.     319     419 ..     319     420 .. 0.90
   2 ?   -1.5   0.6       7.8     4e+03      10      28 ..     422     439 ..     419     445 .. 0.62

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 1.1e-30
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC..........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHH CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae.....akaeeeaekklkrieaiidSMTkeErdspekllkesRkr 72 
                                       +ftl+d+ +q++ i+kmGpl+++++m+P  + +      ++ + ++++l+++ +i++SMT++E+++p+ ++++sR++
  gi|386003024|ref|YP_005921323.1| 319 KFTLKDMCKQMEAINKMGPLKQIMQMLPL-GGMgldlsDQEYQVTKDRLEKYRVIMSSMTEAELEDPK-IITASRIK 393
                                       6***************************3.44445675334488899*********************.8889**** PP

                                       HHHHHTTS-HHHHHHHHHHHHHHHHH CS
                           SRP_SPB  73 RiArGsGtsvqevnellkqfeqmkkm 98 
                                       Ri+rGsGt  + v+ellk+++ m+k 
  gi|386003024|ref|YP_005921323.1| 394 RISRGSGTPPELVRELLKSHKAMQKA 419
                                       ***********************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.8
                                       HHHHHHCCCCCCHHHHCCC CS
                           SRP_SPB  10 qlqqikkmGplskllsmiP 28 
                                        ++ ++kmG ++++++++ 
  gi|386003024|ref|YP_005921323.1| 422 GMRGMNKMG-MKRMMKKFG 439
                                       567788887.666666643 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.1   1.2e-23   6.3e-21       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?   -1.7   0.1       6.8   3.5e+03      45      60 ..     295     309 ..     292     329 .. 0.62
   3 ?   -2.1   0.0       9.2   4.7e+03      57      71 ..     407     420 ..     386     422 .. 0.62

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.2e-23
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      Lg++l++alkk+ ++s+id+++++ea++e+++aLl+aDV+vk+v++l ++++++a+ ek    ++p+++v++iv++eL
  gi|386003024|ref|YP_005921323.1|  6 LGGSLRGALKKIASASRIDKQVVDEAVREIQRALLQADVNVKLVMNLSNRIRDRALSEKPapgMNPREHVINIVYQEL 83
                                      799**************************************************9999666*****************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHHCTTS CS
                           SRP54_N  45 kklienvkkkavgekk 60 
                                       k lie+ ++++v+ ++
  gi|386003024|ref|YP_005921323.1| 295 KTLIERAQETKVE-EE 309
                                       4566666666666.33 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.2
                                       CTTSS-HHHHHHHHH CS
                           SRP54_N  57 gekklkpkqqvkkiv 71 
                                       + + lk++++++k++
  gi|386003024|ref|YP_005921323.1| 407 R-ELLKSHKAMQKAL 420
                                       2.3356666666666 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   9.4e-09   4.8e-06       9     109 ..     107     267 ..     102     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.4e-09
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt+aa+La+ ++r+glr ++v aD+ +  ++  ++l+   e+                               
  gi|386003024|ref|YP_005921323.1| 107 GSGKTTTAAKLATFFQRKGLRSAVVCADTFRAGAF--DQLKALCEKqgvffygekgnpdapavarrgleasrkydiv 181
                                       99***************************977766..33333333377889999999999***************** PP

                                       ..................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHH CS
                                       ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkeal 97 
                                                                         d+   ++ +++  k +++++ i gv++++ dg +     ++a+
  gi|386003024|ref|YP_005921323.1| 182 ivdtagrhalekdliqemmdidavvaadhkllvmDAAL-GQQASEQAKAFNKAVGITGVIITKLDGTAKGGGAMSAV 257
                                       *************************9999999986655.44444444456666999**********99999999999 PP

                                       HHHHHHCTS-EE CS
                                       xxxxxxxxxxxx RF
                              CbiA  98 eelkqrygvpvl 109
                                       +e++    v ++
  gi|386003024|ref|YP_005921323.1| 258 AETNS--SVAFI 267
                                       88876..55555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.8     4e-07   0.00021       2     156 ..      99     250 ..      98     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4e-07
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT...EEEETTTTECCHCTT-HHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve..ivelenGciCctlredllkele 74 
                                       +++l+G  GsGKTt   +l    +r+gl+ av+  +    +   +l + ++++   +  e+G      + d+ ++++
  gi|386003024|ref|YP_005921323.1|  99 TIMLVGLQGSGKTTTAAKLAtfFQRKGLRSAVVCADTFRAGAFDQLKALCEKQgvFFYGEKG------NPDAPAVAR 169
                                       5789*************99989899***********98766555554444333213333444......458888888 PP

                                       HHHHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  75 aleereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKt 150
                                       + +e ++++d++++ t G  a  + ++ +  ++ + + +d+++ v+Da +l ++ +++++ +++ +  +  ++++K 
  gi|386003024|ref|YP_005921323.1| 170 RGLEASRKYDIVIVDTAGrHALEKDLIQEMMDIDAVVAADHKLLVMDA-ALGQQASEQAKAFNKAVGITG-VIITKL 244
                                       8888889***********999999998889******************.666788888888888888876.567899 PP

                                       HHHCHC CS
                              cobW 151 Dlldee 156
                                       D   + 
  gi|386003024|ref|YP_005921323.1| 245 DGTAKG 250
                                       977665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   5.1e-07   0.00026      23     149 ..      91     206 ..      76     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-07
                                       GGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-- CS
                              MeaB  23 lakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslps 99 
                                       ++ + + q + l G+ G+Gk t+  +l++ ++r+G r av+  D   +f  G+   D+  l+ l  ++gvf+     
  gi|386003024|ref|YP_005921323.1|  91 SPVTLEKQTIMLVGLQGSGKTTTAAKLATFFQRKGLRSAVVCAD---TFRAGAF--DQ--LKALCEKQGVFFYGEKG 160
                                       555666788999*****************************988...6888886..55..67889999999998888 PP

                                       ---HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHH.TT-SEEEEE CS
                              MeaB 100 rGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdva.evvdtfvvl 149
                                       +  +  +a++ +e+     +  +D+v+++t G    e d++ e++d+  v+
  gi|386003024|ref|YP_005921323.1| 161 NPDAPAVARRGLEA-----SRKYDIVIVDTAGRHALEKDLIqEMMDIDAVV 206
                                       88888888887765.....56899999999999999998662577776555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.9e-06    0.0025       2      76 ..      97     188 ..      96     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-06
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdieswedfldevvel.................. 59 
                                       k+ i+++G +g+GKTt+a++l   + f++  +  ++ + ad f  + ++++++  +++                   
  gi|386003024|ref|YP_005921323.1|  97 KQTIMLVGLQGSGKTTTAAKL---ATFFQRKGlRSAVVCADTFR-AGAFDQLKALCEKQgvffygekgnpdapavar 169
                                       789******************...55666655466555555554.558888888888889999************** PP

                            AAA_24  60 ..aaeladyktlviDtide 76 
                                          ++ ++y+++++Dt++ 
  gi|386003024|ref|YP_005921323.1| 170 rgLEASRKYDIVIVDTAGR 188
                                       99999999********974 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.2e-06    0.0042       3      48 ..      98     143 ..      96     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.2e-06
                                       EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT CS
                        APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkd 48 
                                        +++l Gl gsGK+t a +l++  ++kg +  ++  d+ R g   +
  gi|386003024|ref|YP_005921323.1|  98 QTIMLVGLQGSGKTTTAAKLATFFQRKGLRSAVVCADTFRAGAFDQ 143
                                       689**********************************999886655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.9e-05    0.0095       2      38 ..     100     141 ..     100     217 .. 0.81
   2 ?   -2.3   0.0       8.6   4.4e+03     116     137 ..     298     319 ..     295     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-05
                            AAA_33   2 vllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlf 38 
                                       ++lvGl+GsGK+t a +l    ++ g    ++  dt+r   f
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLatfFQRKGlrSAVVCADTFRAGAF 141
                                       79***************9444444446666666676665555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.6
                            AAA_33 116 akRaangddrsevpeealdrqk 137
                                        +Ra++++++ ev+ eal+r+k
  gi|386003024|ref|YP_005921323.1| 298 IERAQETKVEEEVDVEALMRGK 319
                                       5788988999999999999987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.9e-05    0.0098       1      92 [.     100     228 ..     100     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-05
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf..............gvnlrdvakenglllevdpe......aldeskrld 53 
                                       I+l G +G+GKtt a  L    ++++ +               ++l+ ++ + g  ++ ++         ++ +++ 
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLatffQRKG-LrsavvcadtfragaFDQLKALCEKQGVFFYGEKGnpdapaVARRGLEAS 175
                                       89****************66664442.24577888878888877777777777777777666667777667777777 PP

                            AAA_18  54 edkldklldaleenss..............aleegknlvidghlaeleseaak 92 
                                       ++++ +++d+  +++                 +++k lv+d  l++  se+ak
  gi|386003024|ref|YP_005921323.1| 176 RKYDIVIVDTAGRHALekdliqemmdidavVAADHKLLVMDAALGQQASEQAK 228
                                       77777777777777777777777777777766777777777777777776665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05    0.0085      10      48 ..      92     130 ..      84     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                     TrwB_AAD_bind  10 pkeretqhilivGttGsGKtqalekllrairargdraiv 48 
                                       p+  e+q i++vG +GsGKt+++ kl +  +++g r  v
  gi|386003024|ref|YP_005921323.1|  92 PVTLEKQTIMLVGLQGSGKTTTAAKLATFFQRKGLRSAV 130
                                       6788***********************999999966433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   2.5e-05     0.013      24      88 ..      92     198 ..      71     235 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-05
                            AAA_16  24 p.....elvllsGesGvGKsslvrellralekd..........................ggiflrgkcdqlesa... 66 
                                       p     + ++l+G +G+GK++ + +l++ ++++                                        +   
  gi|386003024|ref|YP_005921323.1|  92 PvtlekQTIMLVGLQGSGKTTTAAKLATFFQRKglrsavvcadtfragafdqlkalcekQ-------------Gvff 155
                                       444455899******************999999665544444444333333333333331.............0222 PP

                            AAA_16  67 ....................ipysa.laqalareellrqllde 88 
                                                           + y++ +++++ r+ l ++l +e
  gi|386003024|ref|YP_005921323.1| 156 ygekgnpdapavarrgleasRKYDIvIVDTAGRHALEKDLIQE 198
                                       2222222222233333333345544455555555555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05    0.0078      15      56 ..      96     138 ..      86     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                       ++  i+l+G +G+GK+++a++l++ ++ ++ +  ++ +D++R+
  gi|386003024|ref|YP_005921323.1|  96 EKQTIMLVGLQGSGKTTTAAKLATFFQrKGLRSAVVCADTFRA 138
                                       567899********************977889999*****996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.7   8.4e-05     0.043       2      99 ..     100     229 ..      99     243 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.4e-05
                                       EEEEESTTSSHHHHHHHHHT..STEEESSSTTSSSSEEEEEEE....ETTEE......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg..ekaivsdkpgtTrdinegrvk....lkgke......................... 47 
                                       +++vG   +GK+t   +l    ++    +   +  + + g ++    l                             
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLATffQRKGLRSAVVCADTFRAGAFDqlkaL---Cekqgvffygekgnpdapavarrgle 173
                                       788888888888888888763322222333333333334433321121...02223444444444555555555666 PP

                                       ......EEEEECGGCSSHHHHHHHHHHHHHH...HHCTSEEEEEEETTTTCSHHHHHHHHH CS
                          MMR_HSR1  48 ......ielvDtpGliegaseekglgkafla...leeadlillvvdaseeklkpldeelee 99 
                                             i++vDt+G  +    ek+l +++ +   +  ad+ llv+da+ +  ++  e+ ++
  gi|386003024|ref|YP_005921323.1| 174 asrkydIVIVDTAG-RH--ALEKDLIQEMMDidaVVAADHKLLVMDAALG--QQASEQAKA 229
                                       666666********.44..4555555555551115569********8833..333333333 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00024      0.12      23      77 ..      96     151 ..      79     156 .. 0.76
   2 ?    2.2   0.0      0.19        95     101     143 ..     284     326 ..     273     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                             AAA_8  23 prghaLlvGvgGsGrqs.ltkLAafiaelelfqiev.tkkykekefredlkkllkka 77 
                                       ++  ++lvG++GsG+ +  +kLA+f ++  l++  v   ++    f ++lk l++k 
  gi|386003024|ref|YP_005921323.1|  96 EKQTIMLVGLQGSGKTTtAAKLATFFQRKGLRSAVVcADTFRAGAF-DQLKALCEKQ 151
                                       66789**********862689*****99999865551555666666.4577776665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.19
                             AAA_8 101 dinnlLntGevpnLfskeekeeiieelrkeakkqgvedskesl 143
                                        i+ lL  G++ +L ++ ++ ++ ee+  ea ++g+ + k+ +
  gi|386003024|ref|YP_005921323.1| 284 FISRLLGMGDIKTLIERAQETKVEEEVDVEALMRGKFTLKDMC 326
                                       6999**********************99888777655555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   2.2e-05     0.011      17      60 ..      96     140 ..      91     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaag.grviglAptgkaAk 60 
                                       ++++ +l+G  G+GKtt+ ++l+  ++++g ++ +++A t +a +
  gi|386003024|ref|YP_005921323.1|  96 EKQTIMLVGLQGSGKTTTAAKLATFFQRKGlRSAVVCADTFRAGA 140
                                       456889***********************8678889999887753 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.3e-05     0.017       5      43 ..      97     131 ..      94     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       ++ ++++G  G+GKTt++++l+  +++       r+ vv
  gi|386003024|ref|YP_005921323.1|  97 KQTIMLVGLQGSGKTTTAAKLATFFQRKG----LRSAVV 131
                                       67899******************996432....244444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.5e-05     0.023       2      33 ..     100     131 ..      99     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                       + +vg +gsGKTt   kl + ++++glr +++
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLATFFQRKGLRSAVV 131
                                       789*************************9998 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0055       2.8      11      39 ..     107     135 ..     100     151 .. 0.90
   2 ?    5.7   0.0     0.016         8      95     123 ..     173     201 ..     156     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0055
                                       TSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  11 GsGksttavhvavaLlkkGarvaaidldl 39 
                                       GsGk+tta  +a+ + +kG+r a++  d+
  gi|386003024|ref|YP_005921323.1| 107 GSGKTTTAAKLATFFQRKGLRSAVVCADT 135
                                       9**********************998876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                                       HHHHH-SEEEEE--SS--HHHHHHHHT-S CS
                              MipZ  95 dleaeldfividtPGsdsalsrlahslad 123
                                       ++++++d++++dt G++     l +++ d
  gi|386003024|ref|YP_005921323.1| 173 EASRKYDIVIVDTAGRHALEKDLIQEMMD 201
                                       67899************987777776655 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.4e-05     0.043      12      53 ..      96     137 ..      89     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.4e-05
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHH CS
                             6PF2K  12 sklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyr 53 
                                       +k  i+lvGL   gKt+++ kl  + +  g+r+ v  +  +r
  gi|386003024|ref|YP_005921323.1|  96 EKQTIMLVGLQGSGKTTTAAKLATFFQRKGLRSAVVCADTFR 137
                                       6788*********************99888887665555444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   0.00031      0.16      12     102 ..     107     224 ..      98     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt...........................glgie.kneiektly 60 
                                       G GKTTt+ +la ++ ++g +  +v +D+  + ++                           + g+e +++++  ++
  gi|386003024|ref|YP_005921323.1| 107 GSGKTTTAAKLATFFQRKGLRSAVVCADTFRAGAFdqlkalcekqgvffygekgnpdapavaRRGLEaSRKYDIVIV 183
                                       89***********************9999777776666666665555555555555544444222221222333444 PP

                            AAA_31  61 evlieeknikeaiiktkvenldlipssidLaeaeielvelek 102
                                       ++ + +  +++ +i++ ++   ++ ++ +L  ++  l +  +
  gi|386003024|ref|YP_005921323.1| 184 DT-AGRHALEKDLIQEMMDIDAVVAADHKLLVMDAALGQQAS 224
                                       44.355555555554555555777777777777777765554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.071       4      43 ..     100     139 ..      99     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.T CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgie 43 
                                       ++l Gl  sGK+t a++La+ ++ ++ +  v+  ++++  
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLATFFQRKGLRSAVVCADTFRAG 139
                                       7899************************999999888754 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00087      0.45       3      32 ..      97     126 ..      95     142 .. 0.83
   2 ?    1.4   0.0      0.37   1.9e+02      44      77 ..     173     206 ..     163     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                                       --EEEEE-STTSSHHHHHHHHHHSS---B- CS
                             SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktv 32 
                                       k++++lvGl+ sGKT+   +L t   +k  
  gi|386003024|ref|YP_005921323.1|  97 KQTIMLVGLQGSGKTTTAAKLATFFQRKGL 126
                                       789**************9999987666655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.37
                                       ...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEE CS
                             SRPRB  44 ksekgskltliDfPGheklrqklleklkaksslk 77 
                                       +++++  + ++D  G + l ++l++++++ + + 
  gi|386003024|ref|YP_005921323.1| 173 EASRKYDIVIVDTAGRHALEKDLIQEMMDIDAVV 206
                                       5667888999***************998877643 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016     0.084     133     223 ..      18     116 ..       8     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                             SPO22 133 llkreadeeeieealeemidsvelseanfklilslikrla............eksaalavrvldylldrklsferse 197
                                        +++ +d +++ ea++e+ +++ ++++n+kl+++l +r++            + ++ + + v ++l++ ++  ++s+
  gi|386003024|ref|YP_005921323.1|  18 ASASRIDKQVVDEAVREIQRALLQADVNVKLVMNLSNRIRdralsekpapgmNPREHVINIVYQELIN-LVG-KSSP 92 
                                       338889999999********999*********************999999988888888889999998.555.8888 PP

                             SPO22 198 dvvekllvalfflltqskkeedaiea 223
                                       + +ek ++ l+ l+ + k+++  + +
  gi|386003024|ref|YP_005921323.1|  93 VTLEKQTIMLVGLQGSGKTTT--AAK 116
                                       99****999999999944443..333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.3   3.2e+03      23      39 ..      24      40 ..      13      60 .. 0.72
   2 ?   11.8   0.3    0.0004      0.21       2      39 ..     100     144 ..      99     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.3
                            AAA_28 23 gypvvpEaareileekl 39
                                      + +vv Ea+rei + +l
  gi|386003024|ref|YP_005921323.1| 24 DKQVVDEAVREIQRALL 40
                                      55788888888876665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0004
                            AAA_28   2 ivitGgestGKTtlleaLa...ar.gyp..vv.pEaareileekl 39 
                                       i+++G +++GKTt++++La   +r g +  vv ++++r   +++l
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLAtffQRkGLRsaVVcADTFRAGAFDQL 144
                                       899****************77744544433445777777666665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00042      0.21       3      27 ..     104     129 ..     102     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                       ESTTSSHHHHHHHHHHHHHHTTE..E CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.v 27 
                                       Gl G+GKtt a++l+  ++++g++ +
  gi|386003024|ref|YP_005921323.1| 104 GLQGSGKTTTAAKLATFFQRKGLRsA 129
                                       99*******************98753 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.12      19      50 ..      93     124 ..      89     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            AAA_15  19 idlseeltvliGkNnsGKSsilealdlFlnnk 50 
                                       + l++++  l+G ++sGK++ +  l  F+++k
  gi|386003024|ref|YP_005921323.1|  93 VTLEKQTIMLVGLQGSGKTTTAAKLATFFQRK 124
                                       56889899**********************88 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3    0.0018       0.9       1      23 [.     100     122 ..     100     289 .. 0.82
   2 ?   -1.5   0.0       6.2   3.2e+03     100     126 ..     366     394 ..     308     399 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       ++l+G  G GKT++a  +a+ ++
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLATFFQ 122
                                       689***************98765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.2
                                       SSTEEEEEEESS.GGGSTHHHHS.TTSSE CS
                               AAA 100 eskvivigatnr.pdkldpallr.gRfdr 126
                                        +k  vi+ + +  +  dp+++  +R++r
  gi|386003024|ref|YP_005921323.1| 366 LEKYRVIMSSMTeAELEDPKIITaSRIKR 394
                                       55678888887734444566667777766 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00045      0.23       2      33 ..     103     134 ..     102     138 .. 0.92
   2 ?   -2.3   0.0       6.1   3.1e+03     136     136 ..     361     361 ..     301     435 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                       vG  GsGKtt   +l+ +++ +g ++avv  D
  gi|386003024|ref|YP_005921323.1| 103 VGLQGSGKTTTAAKLATFFQRKGLRSAVVCAD 134
                                       899***********************999766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.1
                        ATP_bind_1 136 t 136
                                        
  gi|386003024|ref|YP_005921323.1| 361 V 361
                                       1 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00039       0.2       2      29 ..      99     126 ..      98     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegkl 29 
                                       +++l G +GsGKTt ++kla+  +++ l
  gi|386003024|ref|YP_005921323.1|  99 TIMLVGLQGSGKTTTAAKLATFFQRKGL 126
                                       899*****************98877766 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 ?   10.9   0.1   0.00067      0.34       2      26 ..     100     124 ..      99     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                                       EEEE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnre 26 
                                       ++LvG +G+gK++ a +la +++r+
  gi|386003024|ref|YP_005921323.1| 100 IMLVGLQGSGKTTTAAKLATFFQRK 124
                                       79*****************999775 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0066       3.4       2      21 ..      98     117 ..      97     123 .. 0.88
   2 ?    4.0   0.1     0.076        39      39     102 ..     181     247 ..     174     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0066
                         PduV-EutP   2 kkilliGkvgsGKttLtqal 21 
                                       + i+l+G  gsGKtt + +l
  gi|386003024|ref|YP_005921323.1|  98 QTIMLVGLQGSGKTTTAAKL 117
                                       579************98877 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.076
                         PduV-EutP  39 eviDtPGeylenrklysalivt..saeadvialvqdateeesvfppgfasvfnkev..iG.iitkidla 102
                                        ++Dt G ++ ++ l + ++ +   + ad   lv+da   ++    + a+ fnk v   G iitk+d +
  gi|386003024|ref|YP_005921323.1| 181 VIVDTAGRHALEKDLIQEMMDIdaVVAADHKLLVMDAALGQQA--SEQAKAFNKAVgiTGvIITKLDGT 247
                                       479******9999999988654215678888888888776664..455677777643256457999965 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00062      0.32      24      52 ..      98     126 ..      84     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00062
                                       EEEEEEESTTSSHHHHHHHHHHHCS---- CS
                           G-alpha  24 vkllllGqseSGKsTilkqlkllykkgfs 52 
                                        +++l+G ++SGK+T+  +l ++++ +  
  gi|386003024|ref|YP_005921323.1|  98 QTIMLVGLQGSGKTTTAAKLATFFQRKGL 126
                                       589**************999988866533 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.011       5.4       1      35 [.      98     131 ..      98     133 .. 0.89
   2 ?    3.3   0.1      0.12        63      96     170 ..     175     247 ..     164     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyf 35 
                                       +ti+++g  +g+GKT++++ L+  ++rkg + +++
  gi|386003024|ref|YP_005921323.1|  98 QTIMLVGL-QGSGKTTTAAKLATFFQRKGLRSAVV 131
                                       68999998.69******************998876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                            AAA_26  96 ekdadivvVEGagglg..vpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp 170
                                       + ++div+V+ ag     + +++e++++d + + + + +lV+ + lg  +q+  +++a+ +  v ++Gvi+ k+   
  gi|386003024|ref|YP_005921323.1| 175 SRKYDIVIVDTAGRHAleKDLIQEMMDIDAVVAADHK-LLVMDAALG--QQASEQAKAFNK-AVGITGVIITKLDGT 247
                                       5578888888887654436677777777777777765.566666666..456666676665.7999****9998665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.3    0.0026       1.4      32      58 ..      96     122 ..      91     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                            AAA_25  32 agelallaGapgtGKttlaldlalava 58 
                                       ++ +++l+G +g+GKtt a  la    
  gi|386003024|ref|YP_005921323.1|  96 EKQTIMLVGLQGSGKTTTAAKLATFFQ 122
                                       67899***************9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3085.95
//
Query:       gi|386003025|ref|YP_005921324.1|  [L=269]
Description: Di-trans,poly-cis-decaprenylcistransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-65  219.4   0.0      5e-65  219.2   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.075   13.7   1.5        1.3    9.8   0.3    2.6  2  TPR_16        Tetratricopeptide repeat


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 !  219.2   0.0   5.6e-69     5e-65       1     219 [.      37     259 ..      37     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 5.6e-69
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHH.H CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkee.l 76 
                                       i DGNrR+A+ rg+ ++ eGh++Gae+ + + ++clelg+k+++vY+fSteNf R+++e d+l++l++++ll+    
  gi|386003025|ref|YP_005921324.1|  37 IQDGNRRYARMRGV-PNFEGHSRGAETTEMVADWCLELGIKHLSVYTFSTENFDRDEAEKDYLFRLVERKLLELAgS 112
                                       78***********5.5555*************************************************888876547 PP

                                       HHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHS CS
                      Prenyltransf  77 kellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeid 152
                                       ++++k+++rvr+iG++ llp +++ea++k+eeat+   +++ +n+a++Yg+++ei++a+r+l+ ++ e   + +++d
  gi|386003025|ref|YP_005921324.1| 113 EKVHKNRIRVRAIGRTALLPGRLQEAIRKVEEATR-GYDGMYFNLALAYGGKSEIADAARSLAGAVREGGLDpRDVD 188
                                       799999*****************************.6666**********************766655555446789 PP

                                       HHHHHCTSTT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHC CS
                      Prenyltransf 153 eetlekhlytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkr 219
                                       e+ +++hly   +  lp +Dl+iRt+Ge+R SnFl wq+  s   ++f++ +WP+f++ ++l+a++++q+ 
  gi|386003025|ref|YP_005921324.1| 189 ENVVASHLYPPGEapLPRVDLIIRTGGEMRTSNFLPWQANGSRspVHFCSPYWPEFGRIEFLRAVRTFQAC 259
                                       *********8766789**********************8887799***********************975 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.037   3.3e+02      41      62 ..     126     147 ..     123     152 .. 0.71
   2 ?    9.8   0.3   0.00014       1.3       2      35 ..     155     188 ..     154     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.037
                            TPR_16  41 gdaalrqgrlaeAaalyraalr 62 
                                       g+ al  grl+eA+  +++a r
  gi|386003025|ref|YP_005921324.1| 126 GRTALLPGRLQEAIRKVEEATR 147
                                       6666777899999977777755 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00014
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaae 35 
                                       +la+a+    + +dAa+ l  a++ ++ +P++++
  gi|386003025|ref|YP_005921324.1| 155 NLALAYGGKSEIADAARSLAGAVREGGLDPRDVD 188
                                       799***************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1597.61
//
Query:       gi|386003026|ref|YP_005921325.1|  [L=91]
Description: Translation initiation factor 1A (AeIF-1A) [Methanosaeta harundinacea 6Ac]
Scores for complete 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-24   84.6   0.9    4.1e-24   84.2   0.9    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.9   2.3e-28   4.1e-24       2      64 .]      13      74 ..      12      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 2.3e-28
                                      EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      ev g V+ +lg+n+ rV++ d gke++a+ipgk++++iwi++Gd+V+V +++++++k+++v+r
  gi|386003026|ref|YP_005921325.1| 13 EVFGYVETLLGSNRLRVRCLD-GKERMARIPGKMKKRIWIREGDVVIVVPWDFQDEKADVVWR 74
                                      899****************96.***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 690.01
//
Query:       gi|386003027|ref|YP_005921326.1|  [L=261]
Description: Kinase RIO1 family protein [Methanosaeta harundinacea 6Ac]
Scores for 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-63  211.3   0.0    1.4e-62  210.6   0.0    1.2  1  RIO1      RIO1 family
    4.3e-05   23.0   0.0    8.7e-05   22.0   0.0    1.4  2  Pkinase   Protein kinase domain
    0.00015   21.2   0.0     0.0017   17.8   0.0    2.1  1  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.029   14.3   0.0       0.21   11.5   0.0    2.0  2  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.6   0.0   3.2e-66   1.4e-62       1     180 [.      66     244 ..      66     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 3.2e-66
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       n++ a  edg+++aiKiy+++t++Fk +++y  g++rf +   k  +r++v +w++kEfrnLkr+ee gv+vP+pi+
  gi|386003027|ref|YP_005921326.1|  66 NIFRAKGEDGSDLAIKIYRINTSNFKAMQNYLLGDPRFGSI--KGTKRAVVVAWTKKEFRNLKRAEEVGVRVPHPIA 140
                                       79***********************************9977..9********************************* PP

                                       EETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQav 153
                                       +++++lvme++g+ + +ap++kdv  e eea+ +++e+ e++ +ly++a+lvHaDLSe+N+l+ ++++viID++Q+v
  gi|386003027|ref|YP_005921326.1| 141 MRENILVMEMVGDGDAPAPQIKDVAlEPEEAKLALDEISEYVSVLYNRANLVHADLSEFNILYRRGEPVIIDMGQSV 217
                                       *************************889************************************************* PP

                                       ETTSTTHHHHHHHHHHHHHHHHHTTC- CS
                              RIO1 154 eldhpnalefLerDveniikfFrrkgv 180
                                       +ldhp+a++fL+rD++n+++fF++++ 
  gi|386003027|ref|YP_005921326.1| 218 TLDHPMARSFLDRDISNLARFFKKRYG 244
                                       ***********************9975 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.95   4.2e+03      10      34 ..      62      85 ..      58      96 .. 0.72
   2 !   22.0   0.0   1.9e-08   8.7e-05      73     150 ..     144     221 ..     124     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.95
                                      ESSEEEEEEEETTTTEEEEEEEEEC CS
                           Pkinase 10 GsfGkVykaveketgkivAvKkikk 34
                                      G+ +++++a+  e+g   A+K+ + 
  gi|386003027|ref|YP_005921326.1| 62 GKEANIFRAK-GEDGSDLAIKIYRI 85
                                      7777888888.68888888887654 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.9e-08
                                       EEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTSEES CS
                           Pkinase  73 lylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitDFGlakel 148
                                        +lv+e+v  g+      ++++l++eeak  + +i e ++ l+ +++++H Dl   NiL+  +ge  i+D G +  l
  gi|386003027|ref|YP_005921326.1| 144 NILVMEMVGDGDAPAPQIKDVALEPEEAKLALDEISEYVSVLYnRANLVHADLSEFNILYR-RGEPVIIDMGQSVTL 219
                                       579*****99986555557899*********************6678**************.**********99887 PP

                                       SS CS
                           Pkinase 149 es 150
                                       ++
  gi|386003027|ref|YP_005921326.1| 220 DH 221
                                       66 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.8e-07    0.0017      59     191 ..     119     240 ..     110     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-07
                               Kdo  59 vrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwae.laeelkrallkavgrliakl 134
                                        +Efr+lkr ee+gv+vp p+a++++        +l++e + +    +  +++  + l+ e  +  l ++   ++ l
  gi|386003027|ref|YP_005921326.1| 119 KKEFRNLKRAEEVGVRVPHPIAMREN--------ILVMEMVGDGDAPAPQIKD--VaLEPEEAKLALDEISEYVSVL 185
                                       68********************8764........7888877544443433333..2355888889999******998 PP

                               Kdo 135 .hragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsfl 191
                                        +ra++ Hadl   nil + +e      ++iD+ ++ +     a+   ++d+ +L r f+
  gi|386003027|ref|YP_005921326.1| 186 yNRANLVHADLSEFNILYRRGE-----PVIIDMGQSVTLDHpmARSFLDRDISNLARFFK 240
                                       5799**************9997.....899999988876654566677788888877665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.12   5.3e+02      37      62 ..     118     143 ..      83     152 .. 0.84
   2 ?   11.5   0.0   4.7e-05      0.21     163     196 ..     186     216 ..     152     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHTT-B--B-CTTBS CS
                               APH  37 irrevallrlLakagvpvPevlagdt 62 
                                       + +e++ l+  ++ gv+vP ++a+++
  gi|386003027|ref|YP_005921326.1| 118 TKKEFRNLKRAEEVGVRVPHPIAMRE 143
                                       5678888888888888******9765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.7e-05
                                       SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                               APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                         ++ l+H Dl+  N+l + ++ +v  +iD + +
  gi|386003027|ref|YP_005921326.1| 186 YNRANLVHADLSEFNILYR-RGEPV--IIDMGQS 216
                                       457889*************.99999..***8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1588.15
//
Query:       gi|386003028|ref|YP_005921327.1|  [L=177]
Description: hypothetical protein Mhar_2354 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-12   45.3   5.0    1.7e-06   27.7   0.0    2.3  2  KH_1      KH domain
  ------ inclusion threshold ------
       0.46   10.4   2.5          2    8.4   0.1    2.9  4  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     2e-10   1.7e-06       3      51 ..       2      44 ..       1      57 [. 0.82
   2 !   18.1   2.4     2e-07    0.0018      11      65 ..     101     147 ..      95     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2e-10
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEE CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtis 51
                                       i++P++ +g+++G+ Gs+    +e+tga I+++ se++      v+i+
  gi|386003028|ref|YP_005921327.1|  2 HIKIPADRIGALVGPSGSVKSMFEEKTGATIDID-SENG-----AVEIT 44
                                      589*****************************87.6543.....45544 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2e-07
                                       HHHHHTGGGHHHHHHHHH.HT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                              KH_1  11 vgriIGkgGsnIkeIree.tgakIkvpksedegsderevtisGspeavekAkelie 65 
                                        griIGk G++ +eI e+ tga I v  +       +++ i+G+p+++  A+ +ie
  gi|386003028|ref|YP_005921327.1| 101 KGRIIGKDGRT-REIAEKlTGAGISVY-G-------KTIGIIGNPDQIRVARTAIE 147
                                       69********8.88888736*****87.5.......58*************99986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.78     7e+03      33      48 ..       3      18 ..       2      20 .. 0.78
   2 ?   -0.4   0.0      0.12   1.1e+03       8      29 ..      20      41 ..      17      45 .. 0.67
   3 ?    8.4   0.1   0.00022         2      40      50 ..     101     111 ..      93     113 .. 0.92
   4 ?   -0.9   0.0      0.17   1.5e+03      11      45 ..     132     160 ..     129     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.78
                              KH_4 33 lnvegedlGrvIGkrG 48
                                      +++  + +G ++G  G
  gi|386003028|ref|YP_005921327.1|  3 IKIPADRIGALVGPSG 18
                                      6777889999999887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.12
                              KH_4  8 lkalvddpeevevteeeeeeev 29
                                      +k++++++   +++++ e+  v
  gi|386003028|ref|YP_005921327.1| 20 VKSMFEEKTGATIDIDSENGAV 41
                                      6788888887777777544444 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00022
                              KH_4  40 lGrvIGkrGrt 50 
                                       +Gr+IGk+Grt
  gi|386003028|ref|YP_005921327.1| 101 KGRIIGKDGRT 111
                                       6*********9 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.17
                              KH_4  11 lvddpeevevteeeeeeeveielnvegedlGrvIG 45 
                                       ++ +p++++v  +       ie  ++g   G v+G
  gi|386003028|ref|YP_005921327.1| 132 IIGNPDQIRVART------AIEMLIDGAPHGAVYG 160
                                       5667777777665......5666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1194.19
//
Query:       gi|386003029|ref|YP_005921328.1|  [L=239]
Description: Formate dehydrogenase family accessory protein FdhD [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-48  163.6   0.1    6.7e-46  156.9   0.1    2.0  1  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.9   0.1   3.7e-50   6.7e-46       2     236 ..      25     236 ..      24     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 156.9 bits;  conditional E-value: 3.7e-50
                                       --EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........--------- CS
                         FdhD-NarQ   2 eEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrtakrvv 78 
                                       +E++l+i+ ng  +  +++tp++++e+++G+l+  glie+ ++i +++v+  +  ++ +t+a a +  +r    r +
  gi|386003029|ref|YP_005921328.1|  25 KEVELEIFANGVLIGRATITPSQEKEFVAGHLRYRGLIEDGSEILRLSVEGGR--AEASTGAAAARP-SR----RFL 94 
                                       799***********************************************886..555655544323.23....356 PP

                                       ------.---...--H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHH CS
                         FdhD-NarQ  79 tsgCglcgkesleelletlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnA 155
                                         g g    +++        ++     ++a  +l+ +++   +++l+++tgg+H   l++  +e+la++eD GR n+
  gi|386003029|ref|YP_005921328.1|  95 PGGPGA---AAG--------PV---GAVRAGWILANLESTL-ASQLYEKTGGTHTSSLCS-GEEILATAEDFGRLNT 155
                                       777766...333........22...3678888888887766.478**************9.999************* PP

                                       HHHHHHHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE- CS
                         FdhD-NarQ 156 lDkviGaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtg 232
                                       l k+ G+a+l+g+dl +++ v+sgR++   v Ka r+g+p+++s+ a+t+lave+Ae+ g+tlvgf+r++r+nvYtg
  gi|386003029|ref|YP_005921328.1| 156 LEKIFGWAILAGVDLGRCYAVTSGRITGKTVEKASRFGVPIVASKGAVTTLAVEMAEDWGMTLVGFARQGRMNVYTG 232
                                       ***************************************************************************** PP

                                       GGGE CS
                         FdhD-NarQ 233 aeRi 236
                                       ++R+
  gi|386003029|ref|YP_005921328.1| 233 RDRV 236
                                       ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1611.91
//
Query:       gi|386003030|ref|YP_005921329.1|  [L=538]
Description: Peptidase M50, putative [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-19   70.0   0.0    6.2e-19   68.2   0.0    1.9  1  Peptidase_M50  Peptidase family M50
    2.4e-10   40.6   0.1    2.4e-06   27.8   0.0    2.3  2  PDZ_2          PDZ domain
    4.9e-06   26.3   0.4      0.014   15.3   0.0    2.3  2  PDZ_6          PDZ domain
    4.7e-05   23.6   0.0    0.00027   21.2   0.0    2.0  2  PDZ            PDZ domain
     0.0031   17.5   0.0      0.043   13.8   0.0    2.5  3  PDZ_1          PDZ-like domain
  ------ inclusion threshold ------
      0.064   13.6  12.9       0.33   11.3   0.1    3.8  4  DUF3267        Putative zincin peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   2.1e-22   6.2e-19       3     230 ..     129     497 ..     127     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.1e-22
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                        ++l++ ++vHE++H+++ +++g++v++++i +                    LG+ V  + e +eeel    + + 
  gi|386003030|ref|YP_005921329.1| 129 WIALFVTMAVHEFAHGILCRAEGIRVKSMGIAL--------------------LGAPVAAFVEPDEEELFGS-DGRR 184
                                       689*************************88888....................6666666665555555554.4556 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfvv................................................ 108
                                       +k+s  +r++i+ AG +anf++a +++++                                                
  gi|386003030|ref|YP_005921329.1| 185 AKASRAARVRILSAGVVANFVVAAVALALffgpvigaiaplervvvvdvvpgsdadlagferqmilqevegvriddi 261
                                       889999*******************99999*********************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|386003030|ref|YP_005921329.1| 262 gglvamgtdkkrmsllrgedlvemdlegpfrggvvvsyvfegsaadeagiapgfaiseidgvstpdweafravmnst 338
                                       ***************************************************************************** PP

                                       ................-EEECECTTTSCEE-SEEEC-.........XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                                       ................xxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                     Peptidase_M50 109 ................pkkskeseeekrgviGvspkp.........vkkegllealkegvektlkv.vvltvkalgk 159
                                                        + +++ + +++g+iG+  +p         + +e ++  +   +++++++ +  +++ lg 
  gi|386003030|ref|YP_005921329.1| 339 regqtvtlgtnrgehsVNLTANPDGSGTGFIGIIFSPtravyidgaTLQEFPAGPFLAELKNMPRSgIGGMISLLGL 415
                                       99999999998877663333448999*******99999999999996666666666666666665426778888888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 160 litgklslktlggpisiaqlaseaaeagls...........sflqllalisvnLgilNLlPipvLDGghllfallea 225
                                        + g   + ++g p +++ ++     +g+            ++l+++ li++  g++N lP  +LDGgh+++ ll +
  gi|386003030|ref|YP_005921329.1| 416 PFSGIRGFTEMGFPGFVGWITHLFEPTGWAeplggkifwiaNLLFWVGLINLYAGLFNCLPAVPLDGGHIFRDLLHM 492
                                       88888888999999888888855555555566666677778********************************9987 PP

                                       XXXXX CS
                                       xxxxx RF
                     Peptidase_M50 226 irrkp 230
                                          + 
  gi|386003030|ref|YP_005921329.1| 493 GFAAV 497
                                       55333 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2    0.0002      0.59      14      55 ..     226     267 ..     217     278 .. 0.86
   2 !   27.8   0.0     8e-10   2.4e-06      13      76 ..     292     355 ..     273     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                       .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHH CS
                             PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlisl 55 
                                       ++v+vv+V +g+ a+ ag++ + ++ +v+g+++++   l  +
  gi|386003030|ref|YP_005921329.1| 226 ERVVVVDVVPGSDADLAGFERQMILQEVEGVRIDDIGGLVAM 267
                                       469******************************998887765 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 8e-10
                                       ..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEE CS
                             PDZ_2  13 tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkk 76 
                                        ggv+v  V eg+ a++ag+++g  i ++dg+   + e ++  ++++++G+tV+l   R+    
  gi|386003030|ref|YP_005921329.1| 292 RGGVVVSYVFEGSAADEAGIAPGFAISEIDGVSTPDWEAFRAVMNSTREGQTVTLGTNRGEHSV 355
                                       57999999************************************************99987655 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2   0.00041       1.2       1      34 [.     229     260 ..     229     276 .. 0.83
   2 !   15.3   0.0   4.5e-06     0.014       1      50 [.     296     344 ..     296     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00041
                             PDZ_6   1 vVtaVdpgsPAdrAGlrvGDiilsvNGqpvegls 34 
                                       vV  V+pgs Ad AG++   i+ +v G+ +   +
  gi|386003030|ref|YP_005921329.1| 229 VVVDVVPGSDADLAGFERQMILQEVEGVRI--DD 260
                                       6999************99888888888888..55 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.5e-06
                             PDZ_6   1 vVtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesv 50 
                                       vV+ V +gs Ad+AG+ +G  i +++G+++   + + ++a +  +++g+ v
  gi|386003030|ref|YP_005921329.1| 296 VVSYVFEGSAADEAGIAPGFAISEIDGVST--PDWEAFRAVMNsTREGQTV 344
                                       688999************************..7777777777644444444 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.55   1.6e+03      26      58 ..     226     258 ..     216     267 .. 0.76
   2 !   21.2   0.0   9.2e-08   0.00027      26      80 ..     293     347 ..     274     349 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.55
                                       SSEEEEEECTTSHHHHHTSSTTEEEEEETTEET CS
                               PDZ  26 kgifvsevlpggaaeadglkvGDkIlsvNgvdv 58 
                                       + ++v +v+pg+ a+ +g +   ++ +v gv +
  gi|386003030|ref|YP_005921329.1| 226 ERVVVVDVVPGSDADLAGFERQMILQEVEGVRI 258
                                       578999*****8777776776666666666665 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 9.2e-08
                                       SSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEE CS
                               PDZ  26 kgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLt 80 
                                        g++vs v +g+aa+ +g+ +G  I +++gv++ +++  +av   +  +++vtL 
  gi|386003030|ref|YP_005921329.1| 293 GGVVVSYVFEGSAADEAGIAPGFAISEIDGVSTPDWEAFRAVMNSTREGQTVTLG 347
                                       69*********9999999*************************999999999995 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.4   7.2e+03      32      64 ..     228     260 ..     224     264 .. 0.71
   2 !   13.8   0.0   1.5e-05     0.043      30      74 ..     291     337 ..     284     340 .. 0.80
   3 ?    0.1   0.0      0.28   8.4e+02       3      19 ..     374     390 ..     373     392 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                             PDZ_1  32 gvyvseasgsfklsskekkgviitsinnqptpn 64 
                                       +v+v    gs +   + ++++i++++ ++ + +
  gi|386003030|ref|YP_005921329.1| 228 VVVVDVVPGSDADLAGFERQMILQEVEGVRIDD 260
                                       566666666666655588899999998887765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                             PDZ_1  30 vk.gvyvsea.sgsfklsskekkgviitsinnqptpnLdefievvkk 74 
                                       ++ gv+vs   +gs + + ++  g+ i++i+++ tp+ ++f  v+++
  gi|386003030|ref|YP_005921329.1| 291 FRgGVVVSYVfEGSAADEAGIAPGFAISEIDGVSTPDWEAFRAVMNS 337
                                       55566666542666666777************************986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.28
                             PDZ_1   3 tpsrfvevaGatfhdLs 19 
                                       +p+r v + Gat+++ +
  gi|386003030|ref|YP_005921329.1| 374 SPTRAVYIDGATLQEFP 390
                                       699***********976 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5    0.0045        13      26      73 ..      38      94 ..      14     103 .. 0.66
   2 ?   11.3   0.1   0.00011      0.33       1      23 [.     132     154 ..     132     173 .. 0.71
   3 ?   -4.0   0.2         6   1.8e+04      62      70 ..     204     212 ..     188     222 .. 0.49
   4 ?    3.6   0.2     0.027        82      32      71 ..     491     530 ..     474     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0045
                           DUF3267 26 kvkfgi.k.........lliayatsseallskkqfiiillaPfvllgilllllalllp 73
                                      ++k+g+ +         +l ++  +s++  + ++  i +  P+v+lg+l++l+++l  
  gi|386003030|ref|YP_005921329.1| 38 GLKIGNwGpvimirttrWLSLIDRLSRPE-RLWKLSITAGIPLVVLGMLFFLVLFLRT 94
                                      55555442233333444566666666666.88999*****************999843 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF3267   1 llvlvilHEllHglffklfgkkp 23 
                                       l+v++ +HE++Hg++++  g ++
  gi|386003030|ref|YP_005921329.1| 132 LFVTMAVHEFAHGILCRAEGIRV 154
                                       589**************854432 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 6
                           DUF3267  62 gilllllal 70 
                                        ++ +++++
  gi|386003030|ref|YP_005921329.1| 204 FVVAAVALA 212
                                       222222222 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.027
                           DUF3267  32 klliayatsseallskkqfiiillaPfvllgilllllall 71 
                                       ++++a +  sea +++++  +++++  ++++ ll++++++
  gi|386003030|ref|YP_005921329.1| 491 HMGFAAVFKSEARAERMTRAVVAFMAWLIFSSLLFIILAP 530
                                       37888999999999999999******99999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 3237.60
//
Query:       gi|386003031|ref|YP_005921330.1|  [L=323]
Description: putative H4MPT-linked C1 transfer pathway protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-21   76.1   0.1    2.8e-21   76.1   0.1    1.4  2  Hydantoinase_A  Hydantoinase/oxoprolinase
     0.0022   16.7   0.2      0.035   12.7   0.0    2.1  2  MutL            MutL protein


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2      0.57   5.2e+03      82      97 ..       5      20 ..       4      26 .. 0.77
   2 !   76.1   0.1   3.1e-25   2.8e-21      53     287 ..      99     315 ..      52     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.57
                    Hydantoinase_A 82 ItfDmGGTstDvslik 97
                                      +++D+GG  t+++  +
  gi|386003031|ref|YP_005921330.1|  5 LGLDVGGANTKAASSD 20
                                      689****999998755 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 3.1e-25
                    Hydantoinase_A  53 kpvetilSGPaaGvvgaaatsklagekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGg 129
                                        +++++++++ a+++ +a+   + g+  ++++DmG+T+tD+++ik g +        ++ k+++ +l+  ++ + G 
  gi|386003031|ref|YP_005921330.1|  99 DLADLAAANWSASAALVAE---EVGD--CLFVDMGSTTTDLIPIK-GGP--------RAAKTDFLRLARGELIYMGL 161
                                       4578999***********9...6666..*****************.999........799***************** PP

                    Hydantoinase_A 130 sil.vvdeggklrvgpesagadpgpacyrkGgteltvTDanlvLGrlqpedfls.gpdgdqkldvelarraf.eela 203
                                       +++ +    g+++v++e +  + +         +++ +Da+l+LG + + +++  +pdg +k+++++ rr + + +a
  gi|386003031|ref|YP_005921330.1| 162 LRTnLAALLGAVEVDGERVPLSAEL--------FAIAADAHLLLGDIAEGEYAVeTPDGGGKDRESAERRLArTVCA 230
                                       *************************........9*************************************99**** PP

                    Hydantoinase_A 204 kelnlk...veevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivpp..ya. 274
                                       ++ + +   ve +A ++   + e ++  +r+l     ++++ l+lv+ +G G+ ++ ++a++lg++ +   +  ++ 
  gi|386003031|ref|YP_005921330.1| 231 DPGEIGpegVEAIARQARARQLELLKGGIRRL-----AEEHSLNLVAAAGIGEGLIREAARSLGLEVIRLSEryGSa 302
                                       **9999999***********************.....9**********************99998766544300332 PP

                    Hydantoinase_A 275 gvlsalGmalAdv 287
                                        + +++++a+A++
  gi|386003031|ref|YP_005921330.1| 303 VSEVFPAYAVARL 315
                                       3344566666665 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.5   0.1    0.0098        88     249     266 ..       4      20 ..       2      29 .. 0.83
   2 !   12.7   0.0   3.9e-06     0.035     236     272 ..     113     144 ..     103     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.0098
                              MutL 249 llvvDvGGaTTdvhsvae 266
                                       +l++DvGGa T   s  +
  gi|386003031|ref|YP_005921330.1|   4 ILGLDVGGANTKAASS-D 20 
                                       589*********9997.4 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.9e-06
                              MutL 236 ellaeeeekglgdllvvDvGGaTTdvhsvaegspeke 272
                                        l+ae    ++gd+l vD+G++TTd++ + +g p+ +
  gi|386003031|ref|YP_005921330.1| 113 ALVAE----EVGDCLFVDMGSTTTDLIPI-KGGPRAA 144
                                       44555....79***************998.5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1980.56
//
Query:       gi|386003032|ref|YP_005921331.1|  [L=366]
Description: Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-37  129.1   0.0    1.8e-37  128.5   0.0    1.3  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    9.2e-21   73.8   2.3    1.3e-20   73.3   1.1    1.8  2  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
  ------ inclusion threshold ------
       0.01   16.4   3.6       0.81   10.3   1.0    2.6  2  Fer4_17      4Fe-4S dicluster domain
      0.019   15.9   5.9        6.6    7.7   2.4    3.0  3  Fer4_16      4Fe-4S double cluster binding domain
      0.023   15.3   8.4       0.22   12.2   1.1    2.8  2  Fer4_7       4Fe-4S dicluster domain
      0.055   13.6  12.7       0.37   10.9  11.4    2.6  3  Fer4_10      4Fe-4S dicluster domain
      0.062   13.8   3.6         13    6.3   1.6    2.7  2  Fer4_8       4Fe-4S dicluster domain
       0.08   12.8  20.5       0.11   12.4   7.5    2.9  3  Fer4         4Fe-4S binding domain
       0.88   10.4   8.2        2.7    8.8   0.0    3.1  2  Fer4_15      4Fe-4S single cluster domain
       0.93    9.7  10.3        5.3    7.2  10.3    2.2  1  Fer4_21      4Fe-4S dicluster domain
       0.95   10.1   5.3         12    6.5   2.8    2.6  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        1.2    9.3  13.4        1.8    8.8   4.9    2.7  3  Fer4_9       4Fe-4S dicluster domain
        3.3    8.4  16.0       0.84   10.3   0.3    2.6  2  Fer4_4       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   0.0   1.3e-40   1.8e-37       2     154 ..     179     331 ..     178     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 1.3e-40
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk.....kklkekilltiglfCggnfspealrk..lleelgvdpedvkklefrgkgkfr 71 
                                       kk+++vGtPCqi+alrk+q      +  +eki+l++glfC++nf++e l    ++ + g++ e+v k+e+ +kg fr
  gi|386003032|ref|YP_005921331.1| 179 KKIGFVGTPCQIQALRKVQLleepyQFGQEKIALLVGLFCMENFEHELLFPhlVEGKFGFKAEEVDKFEV-QKGMFR 254
                                       89*****************8889987889******************998888999**************.8***** PP

                       FrhB_FdhB_C  72 velkd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagel 147
                                       v   d +ke++l+e+++++ ++C  C+d+ aelAD+svG+v      g ++ g+stvl+rt+ g++++e+a++ag +
  gi|386003032|ref|YP_005921331.1| 255 VLSGDmVKEVPLEETDDYVWKGCGPCFDFAAELADVSVGSV------G-SKAGWSTVLTRTDLGAKVYESALAAGSI 324
                                       *7777*99*********************************......8.**************************** PP

                       FrhB_FdhB_C 148 eleelde 154
                                       e+ +++e
  gi|386003032|ref|YP_005921331.1| 325 EEAAASE 331
                                       *998876 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   1.1   9.1e-24   1.3e-20       4      73 ..     100     166 ..      97     170 .. 0.91
   2 ?   -2.0   0.0         3   4.2e+03      26      59 ..     316     346 ..     313     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 9.1e-24
                       FrhB_FdhB_N   4 ArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspn 73 
                                       Ar+ +     +aq+GG++tall+ +Le giid+++v++++ d+wr  p +att+ee+ aaaG+kYt++p 
  gi|386003032|ref|YP_005921331.1| 100 ARAVKA--GARAQDGGVATALLIGALEAGIIDCAVVTERD-DKWRGLPKVATTAEEIAAAAGTKYTITPS 166
                                       555555..689*****************************.89************************996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                       FrhB_FdhB_N  26 kylLeegiidgvivvaps.kdpwrpkpviattkee 59 
                                       +++L  g i+ + + +++ +       ++a++kee
  gi|386003032|ref|YP_005921331.1| 316 ESALAAGSIEEAAASEKGlA----LAGRLAKSKEE 346
                                       57888888888887776632....45555555555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   0.00059      0.81       2      15 ..      30      43 ..      12      55 .. 0.69
   2 ?    5.7   0.1     0.016        22       5      15 ..      59      69 ..      58     111 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00059
                           Fer4_17  2 CiqCgyClpeCpsy 15
                                      C+ Cg C++ Cp  
  gi|386003032|ref|YP_005921331.1| 30 CCYCGNCIAFCPKI 43
                                      55566666666555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                           Fer4_17  5 CgyClpeCpsy 15
                                      Cg C + Cp+ 
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCPRT 69
                                      55565555553 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.4    0.0048       6.6       2      13 ..      30      41 ..      17      46 .. 0.74
   2 ?    7.7   0.0    0.0049       6.7       5      21 ..      59      76 ..      57     109 .. 0.76
   3 ?   -1.1   0.0       2.8   3.9e+03      46      61 ..     269     281 ..     242     283 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                           Fer4_16  2 CgtCgkCaevCP 13
                                      C  Cg+C+  CP
  gi|386003032|ref|YP_005921331.1| 30 CCYCGNCIAFCP 41
                                      666666666666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0049
                           Fer4_16  5 CgkCaevCPtnaikek.k 21
                                      Cg C   CP   ++++  
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCPRTMLDMPgM 76
                                      ***********9999842 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.8
                           Fer4_16  46 ekckkqeaitgCdiCq 61 
                                         ++     +gC+ C 
  gi|386003032|ref|YP_005921331.1| 269 TDDY---VWKGCGPCF 281
                                       3333...348999885 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   0.00016      0.22      32      50 ..      24      42 ..       2      43 .. 0.75
   2 ?    7.2   0.1    0.0054       7.4       5      21 ..      59      75 ..      58     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            Fer4_7 32 eidpekClgCgaCvavCPt 50
                                      +i+ e C +Cg+C+a CP+
  gi|386003032|ref|YP_005921331.1| 24 VIKKELCCYCGNCIAFCPK 42
                                      567889************6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                            Fer4_7  5 CgaCvaaCpvkaielde 21
                                      Cg C a+Cp   ++++ 
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCPRTMLDMPG 75
                                      99******988888764 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  11.4   0.00027      0.37       1      56 []      22      67 ..      22      67 .. 0.74
   2 ?    5.7   0.2     0.012        16      12      24 ..      59      76 ..      57     113 .. 0.70
   3 ?   -2.4   0.0       3.9   5.4e+03      11      16 ..     276     281 ..     268     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + vi ++ C  Cg+C ++CP          ++ e+++ +  v+  + cg C++ CP
  gi|386003032|ref|YP_005921331.1| 22 HDVIKKELCCYCGNCIAFCPK---------IDREGNRPEL-VDYDPLCGLCYAYCP 67
                                      57999**************99.........3333333333.333379********9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                           Fer4_10 12 CgkCvkaCPadl.....t 24
                                      Cg C + CP ++      
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCPRTMldmpgM 76
                                      999999999865555551 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.9
                           Fer4_10  11 rCgkCv 16 
                                       +Cg C 
  gi|386003032|ref|YP_005921331.1| 276 GCGPCF 281
                                       677775 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.6    0.0094        13       5      22 ..      30      47 ..      22      56 .. 0.70
   2 ?    6.3   0.0    0.0095        13       8      17 ..      59      81 ..      58     135 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0094
                            Fer4_8  5 CieCgaCqsaCpvlrrtk 22
                                      C  Cg C + Cp + r++
  gi|386003032|ref|YP_005921331.1| 30 CCYCGNCIAFCPKIDREG 47
                                      777777777777666655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0095
                            Fer4_8  8 CgaCqsaCp.............v 17
                                      Cg+C + Cp             +
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCPrtmldmpgmakrvF 81
                                      9*******976665555555541 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.5   7.9e-05      0.11       2      19 ..      24      41 ..      23      42 .. 0.92
   2 ?    8.8   1.0     0.001       1.4      11      19 ..      59      67 ..      58      70 .. 0.92
   3 ?   -1.2   0.2       1.5     2e+03      10      15 ..     276     281 ..     275     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                      vi +e+C +CG+C+  CP
  gi|386003032|ref|YP_005921331.1| 24 VIKKELCCYCGNCIAFCP 41
                                      6789************** PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.001
                                      -THHHHHST CS
                              Fer4 11 CGaCvevCP 19
                                      CG+C+  CP
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCP 67
                                      ********* PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.5
                                       S-THHH CS
                              Fer4  10 gCGaCv 15 
                                       gCG C 
  gi|386003032|ref|YP_005921331.1| 276 GCGPCF 281
                                       9**996 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.0     0.065        90       3      21 ..      25      43 ..      24      49 .. 0.84
   2 ?    8.8   0.0     0.002       2.7      10      58 ..      58     105 ..      57     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.065
                           Fer4_15  3 vDrdaCigcglCvaeapev 21
                                      + +++C  cg+C+a +p++
  gi|386003032|ref|YP_005921331.1| 25 IKKELCCYCGNCIAFCPKI 43
                                      56899***********986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                           Fer4_15  10 gcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAara 58 
                                        cglC+a +p +  ld  g+a+ +  ++++++++++  +++a  +A++a
  gi|386003032|ref|YP_005921331.1|  58 LCGLCYAYCP-RTMLDMPGMAKRVFGRERREDEPLGIYRKAASARAVKA 105
                                       59********.899999*******999999999***9999999999875 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.3    0.0039       5.3       2      52 ..      24      67 ..      23      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0039
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52
                                      +i+++ C  Cg+C+  C++     i+ ++++    + d    C lC++ CP
  gi|386003032|ref|YP_005921331.1| 24 VIKKELCCYCGNCIAFCPK-----IDREGNRP--ELVDYDPLCGLCYAYCP 67
                                      699***************5.....65555554..4445556799******* PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.8    0.0087        12       3      19 ..      27      43 ..      25      48 .. 0.89
   2 ?    3.1   0.0       0.1   1.4e+02       9      19 ..      59      69 ..      58     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0087
                           Fer4_13  3 rdtCiacgaCvelaPdv 19
                                      ++ C  cg+C +++P++
  gi|386003032|ref|YP_005921331.1| 27 KELCCYCGNCIAFCPKI 43
                                      688************86 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                           Fer4_13  9 cgaCvelaPdv 19
                                      cg+C++ +P +
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCPRT 69
                                      9********86 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.9    0.0013       1.8      33      48 ..      27      42 ..       4      45 .. 0.77
   2 ?    5.9  11.5     0.011        15       2      49 ..      30      69 ..      29      71 .. 0.75
   3 ?   -2.7   0.0       4.9   6.8e+03      38      43 ..     276     281 ..     266     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                            Fer4_9 33 eeaCigCgaCveaCpk 48
                                      +e C  Cg C++ Cpk
  gi|386003032|ref|YP_005921331.1| 27 KELCCYCGNCIAFCPK 42
                                      268999********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C+ Cg+C++ Cp+   ++ +  + + ++         Cg C++ Cp++
  gi|386003032|ref|YP_005921331.1| 30 CCYCGNCIAFCPKIDREGNRP-ELVDYDP-------LCGLCYAYCPRT 69
                                      99**********865555544.4445443.......5*********97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.9
                            Fer4_9  38 gCgaCv 43 
                                       gCg C+
  gi|386003032|ref|YP_005921331.1| 276 GCGPCF 281
                                       455554 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.1     0.016        22       2      15 ..      28      41 ..      27      49 .. 0.88
   2 ?   10.3   0.3   0.00061      0.84       7      15 ..      59      67 ..      58      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e C  Cg C+a+CP
  gi|386003032|ref|YP_005921331.1| 28 ELCCYCGNCIAFCP 41
                                      77889********* PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00061
                            Fer4_4  7 CgsCvaaCP 15
                                      Cg C+a+CP
  gi|386003032|ref|YP_005921331.1| 59 CGLCYAYCP 67
                                      ********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2112.51
//
Query:       gi|386003033|ref|YP_005921332.1|  [L=388]
Description: hypothetical protein Mhar_2359 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-31  107.6   0.0      8e-31  106.9   0.0    1.3  1  MMR_HSR1_C    GTPase of unknown function C-terminal
    8.7e-20   70.9   0.0    4.8e-19   68.5   0.0    2.0  2  MMR_HSR1      50S ribosome-binding GTPase
    1.1e-12   47.8   0.0    2.6e-12   46.6   0.0    1.6  1  TGS           TGS domain
    6.5e-08   32.3   0.1    5.8e-07   29.2   0.0    2.2  2  FeoB_N        Ferrous iron transport protein B
  ------ inclusion threshold ------
        0.1   13.3   0.0       0.37   11.5   0.0    1.9  2  ThiS          ThiS family
       0.22   11.5   0.0       0.41   10.7   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   2.7e-34     8e-31       1     112 []     217     319 ..     217     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 2.7e-34
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NK+D+ a+ e +++lk+ ++    vvp+sAaaE+aLr a+k+g+i+Y+pgd dfe+ +d    l+  qk+ Leki
  gi|386003033|ref|YP_005921332.1| 217 AANKVDV-APPEFVARLKALDE---IVVPTSAAAEVALRMADKSGAIRYRPGDPDFEMVKD----LSGPQKAGLEKI 285
                                       89*****.************88...8***********************************....************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       r  +lk  g+TGVqe+l++avfell++i+V+PVed
  gi|386003033|ref|YP_005921332.1| 286 RG-ILKAAGGTGVQECLDRAVFELLEYIPVFPVED 319
                                       **.******************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   1.6e-22   4.8e-19       2      87 ..       4     114 ..       3     147 .. 0.78
   2 ?   -0.5   0.0      0.41   1.2e+03      93     114 .]     199     220 ..     171     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.6e-22
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.....................EEEEECGGCS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.....................ielvDtpGli 57 
                                       v+++G+pN+GKSt+++a t ++++++++p+tT+d n+g   ++  +                     +el+D++Gl+
  gi|386003033|ref|YP_005921332.1|   4 VGLAGKPNAGKSTFFKAATLAEVEIANYPFTTIDANHGVSYVR-VPcpcrelatecgrcrdgvryvpVELIDVAGLV 79 
                                       89************************************77643.11233334444444444555555********99 PP

                                       SHHHHHHHHHHHHHHHHC.TSEEEEEEETT....T CS
                          MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas....e 87 
                                        +a+ +kglg++fl+  + a+++++v+das     
  gi|386003033|ref|YP_005921332.1|  80 PDAHLGKGLGNEFLDSLRvAEAVIHVLDASgsadA 114
                                       99*************99978********9854440 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  93 ldeeleelleeakkplilvlnk 114
                                       + ++++ ll++a kp+i+++nk
  gi|386003033|ref|YP_005921332.1| 199 EMKKFAGLLRDASKPMIIAANK 220
                                       3356666777799******998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   8.7e-16   2.6e-12       3      59 ..     329     385 ..     327     386 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 8.7e-16
                                       EEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   3 vytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       v++Pd+ +  +++g+t +D+Ay+Ih++++++f+ Al     +r g +h+L+ gdv++Iv
  gi|386003033|ref|YP_005921332.1| 329 VVLPDAYL--MKKGSTTKDLAYRIHTDIGESFLFALDGRskRRLGEKHELKAGDVIKIV 385
                                       78888888..9**************************99999****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.9e-10   5.8e-07       2      41 ..       3      42 ..       2      47 .. 0.92
   2 ?    0.2   0.0      0.16   4.7e+02     101     119 ..     207     225 ..     203     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.9e-10
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                      +v l+G+pn+Gk+t+f a t a+ +++N+p +t++ ++g 
  gi|386003033|ref|YP_005921332.1|  3 SVGLAGKPNAGKSTFFKAATLAEVEIANYPFTTIDANHGV 42
                                      5789*******************************99986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                                       HHHTTSSEEEEEETHHHHH CS
                            FeoB_N 101 llelgvpvvlalnmideae 119
                                       l + ++p+++a n++d+a 
  gi|386003033|ref|YP_005921332.1| 207 LRDASKPMIIAANKVDVAP 225
                                       567899**********985 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.8   8.2e+03      40      69 ..     210     239 ..     188     240 .. 0.68
   2 ?   11.5   0.0   0.00012      0.37      41      71 ..     355     385 ..     332     387 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                                       TTTTEEEEETTEEEGCCTTTSB--TTCEEE CS
                              ThiS  40 lerrvavavNgeivprlwldtelkdgDeva 69 
                                       +++ +++a N+ +v + +  ++lk+ De++
  gi|386003033|ref|YP_005921332.1| 210 ASKPMIIAANKVDVAPPEFVARLKALDEIV 239
                                       456677777877777645556667777765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                                       TTTEEEEETTEEEGCCTTTSB--TTCEEEEE CS
                              ThiS  41 errvavavNgeivprlwldtelkdgDevail 71 
                                        + + +a++g+  +rl++++elk+gD++ i+
  gi|386003033|ref|YP_005921332.1| 355 GESFLFALDGRSKRRLGEKHELKAGDVIKIV 385
                                       48899************************98 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.41      56      93 ..     212     250 ..     201     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.pnsvviSaekelnl 93 
                                       +p++++ NK+D +  e + +l+   + +v++Sa+ e+ l
  gi|386003033|ref|YP_005921332.1| 212 KPMIIAANKVDVAPPEFVARLKALdEIVVPTSAAAEVAL 250
                                       699********************7256778999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2565.53
//
Query:       gi|386003034|ref|YP_005921333.1|  [L=1163]
Description: hypothetical protein Mhar_2360 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-19   69.9   0.0    5.3e-19   68.6   0.0    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    2.2e-18   66.3   0.0    4.4e-18   65.4   0.0    1.4  1  Ras          Ras family
    4.6e-15   56.7   1.1    1.1e-14   55.4   1.1    1.7  1  Metallophos  Calcineurin-like phosphoesterase
    2.4e-07   31.3   1.9    5.1e-06   27.1   0.0    3.6  3  WD40         WD domain, G-beta repeat
    5.3e-06   26.0   0.0      1e-05   25.1   0.0    1.4  1  Arf          ADP-ribosylation factor family
    2.1e-05   24.6   0.0    0.00013   22.1   0.0    2.2  2  MMR_HSR1     50S ribosome-binding GTPase
    3.9e-05   23.9   0.0       0.38   11.1   0.0    2.7  2  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   2.1e-22   5.3e-19       1     119 [.     295     418 ..     295     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.1e-22
                                       EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHH CS
                               Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplyl 77 
                                       K+v+vG+s++GK++l  r+ ed+++e  ++t+g  f t   ++++ v  +   kk  + iWD++Gq+++r +h+++l
  gi|386003034|ref|YP_005921333.1| 295 KIVFVGESNAGKSCLSLRLSEDRYEEL-ETTHGTRFWTLLPEQLDPVAVTPPGKKRDVVIWDMGGQNEYRLVHQIFL 370
                                       9********************999765.799*****998777889888888899999******************** PP

                                       CTSCEEEEEEE....GHHHHCHHHHHHHHHHH..CSSS-EEEEEE-TT CS
                               Roc  78 reaalailvyd....srssenlkeWlkelkkv..agkspvilvgnkiD 119
                                       ++  la++++d    ++ +++++eW k l+k+  ++k+  ilvg+k+D
  gi|386003034|ref|YP_005921333.1| 371 HDVTLALILFDptrgQNAFKEVEEWNKRLDKQlsGNKATKILVGTKLD 418
                                       ***********76555567899*******98732345678*******9 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   1.7e-21   4.4e-18       1     160 [.     295     463 ..     295     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.7e-21
                                       EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET........TEEEEEEEEEETTSGGGHHHHHHHH CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd........gkevkleiwDTAGqeefkslrelyy 69 
                                       K+v+vG+s+ GK++l lr  +d+++e  e+T g  f t   e          gk+  + iwD  Gq+e++ +++ ++
  gi|386003034|ref|YP_005921333.1| 295 KIVFVGESNAGKSCLSLRLSEDRYEE-LETTHGTRFWTLLPEQLdpvavtppGKKRDVVIWDMGGQNEYRLVHQIFL 370
                                       89**********************76.5889999865543222124445577************************* PP

                                       TTESEEEEEEETTB.HHHHHTHHHHHHHHHHHST.TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBT CS
                               Ras  70 rdaegillvydits.resfenvkkwveeikrvae.envpivLvGnKvDleekravsteegeelakelg.lkfletSA 143
                                       +d++ +l+++d t+ +++f++v++w + + ++ + ++ + +LvG+K D e+   +++ e e+l k+ +   ++ +S 
  gi|386003034|ref|YP_005921333.1| 371 HDVTLALILFDPTRgQNAFKEVEEWNKRLDKQLSgNKATKILVGTKLDDES-TIIDEVELERLIKSCDfEGYYPISS 446
                                       ***********8874789**************999889**********985.99**************667****** PP

                                       TTTCTHHHHHHHHHHHH CS
                               Ras 144 ktnenveeafeellrei 160
                                       +t  +++e+  ++ ++i
  gi|386003034|ref|YP_005921333.1| 447 RTGRGISELRAAISKNI 463
                                       *****999877777665 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   1.1   4.5e-18   1.1e-14       2     204 .]     828    1079 ..     827    1079 .. 0.67

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 4.5e-18
                                        EEEEEESBTB...TTCCTHHHHHHHHHHHHHHH...TTESEEEEESTSSSSS...HHHHHHHHHHHHHHHH.... CS
                       Metallophos    2 rilvigDlHl...algggqlddllkllddllre...ekpdlvllaGDlvdrg...dlekellellaalvky.... 63  
                                        ++l+++DlH+    +   q++ +++ l++l+++   ek d++++ GDl+++g   ++e+   ++++ l+++    
  gi|386003034|ref|YP_005921333.1|  828 WLLHLSDLHFdfkTDPMSQFQPIATDLNNLKESlgfEKLDYLVVSGDLTNHGkpeEFEN-ARQFISSLIMRfglt 901 
                                        689*********988999999999999999666666999*************6655555.555566666669999 PP

                                        TSEEEEEC-TTS...............................CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEE CS
                       Metallophos   64 pipvylllGNHe...............................gfeeellnkygylgifsepwrsdaevfnnlpl 107 
                                          ++++++GNH+                               g       + +++++++  +rs++e f ++ +
  gi|386003034|ref|YP_005921333.1|  902 AERCIIVPGNHDldwdedvynwinrrlidteklangrwirqgdG------YLIRNEERYPSRFRSFSENFYHPLV 970 
                                        9999**************99999999999999999976555442......4444444555555555555533333 PP

                                        EE....EETTE....EEEEEEESECEEE.......THHHHHHHHHHHSCHHHHCC........HHHHHHHHHHTT CS
                       Metallophos  108 as....lgsgs....lkvlllhGgspel.......lvsldklgslnleleapepg........dewlkdlekrek 159 
                                        +         +    + + + +     +       +  ++  + ++++  + ++         d +++     +k
  gi|386003034|ref|YP_005921333.1|  971 QKeyplE---FkdqcISIPFFD-----DgiqfialNSCWEIDEYFPKRSSINQGTlarglenaDRMIRS-FSSNK 1036
                                        3321110...111132222222.....133334432222222222222222222243444444444444.66679 PP

                                        CSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos  160 adwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHvy 204 
                                           +i+++H+p++  + +   d+a+ + l+++g+ ++++GH+H++
  gi|386003034|ref|YP_005921333.1| 1037 SVLKIAVWHHPVT--GNDKIKDDAFLEQLRENGIRVCLHGHVHED 1079
                                        99***********..99999999999999**************85 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2       0.3   7.7e+02      13      38 .]      21      46 ..      10      46 .. 0.72
   2 !   27.1   0.0     2e-09   5.1e-06       2      38 .]     191     228 ..     190     228 .. 0.87
   3 ?   -2.6   0.0       4.9   1.3e+04      17      38 .]     251     273 ..     250     273 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.3
                                      EEEEEEETTSSEEEEE.ETTSEEEEEE CS
                              WD40 13 vtslafspdgawlasG.sdDgtvriWd 38
                                      +  +++sp+g+ la +  d g+++iWd
  gi|386003034|ref|YP_005921333.1| 21 IDRISWSPHGTQLA-AeLDIGKIKIWD 46
                                      55678888888886.533578888887 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 2e-09
                                       EEEEEEESS.SSEEEEEEETTSSEEEEE.ETTSEEEEEE CS
                              WD40   2 qclrtltGH.ssvtslafspdgawlasG.sdDgtvriWd 38 
                                       +  rtl+GH + + s++fs d+++la + s D+t+r+W+
  gi|386003034|ref|YP_005921333.1| 191 KYFRTLEGHtDAIVSISFSFDSKFLA-SmSLDNTIRLWS 228
                                       6789*****66699**********97.6578*******5 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.9
                                       EEETTSSEEEEE..ETTSEEEEEE CS
                              WD40  17 afspdgawlasG..sdDgtvriWd 38 
                                       af+p  ++la+   +  + + iWd
  gi|386003034|ref|YP_005921333.1| 251 AFNPKFPMLAAVvdG-GKVINIWD 273
                                       567777777654434.88999998 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.9e-09     1e-05      13     140 ..     292     433 ..     282     463 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.9e-09
                                       TEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEE............TTEEEEEEEE-SSGGGGGGGGG CS
                               Arf  13 kelrilllGLDnaGKtTilkklkleelvttvPTigfnveelei............knlkftvwDvGGqeklRplWkn 77 
                                        +++i+++G  naGK+ +  +l++++ ++   T g    +l              k+ ++ +wD+GGq++ R + + 
  gi|386003034|ref|YP_005921333.1| 292 SSAKIVFVGESNAGKSCLSLRLSEDRYEELETTHGTRFWTLLPeqldpvavtppgKKRDVVIWDMGGQNEYRLVHQI 368
                                       579******************************9999888766667778889999999******************* PP

                                       GCTTESEEEEEEETT-CT.THHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTS.S-HHHHHHHT CS
                               Arf  78 YfektdavifvvDsadre.RleeakeeLkalleeeelkevallvlaNKqDlpea.lseeelrell 140
                                       ++++++  + + D +  +  ++e +e  k+l ++   ++++ ++++ K D +++ ++e el++l+
  gi|386003034|ref|YP_005921333.1| 369 FLHDVTLALILFDPTRGQnAFKEVEEWNKRLDKQLSGNKATKILVGTKLDDESTiIDEVELERLI 433
                                       ****9998889997765415666655555555555666777788888887655414555555554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.65   1.7e+03      11      48 ..     133     171 ..     131     226 .. 0.68
   2 !   22.1   0.0   4.9e-08   0.00013       1     105 [.     295     400 ..     295     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.65
                                       SHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEE CS
                          MMR_HSR1  11 GKStLinaltge.kaivsdkpgtTrdinegrvklkgkei 48 
                                       GKS +in    +  +i ++  +   +i  ++ ++k + i
  gi|386003034|ref|YP_005921333.1| 133 GKSMIINYAYSSnSSIFASNLFDSNTIDLFETQIKTNLI 171
                                       9******99888456777777666666555555444444 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4.9e-08
                                       EEEEEESTTSSHHHHHHHHHTS....TEEESSSTTSSSSEEEEE.EE....ETTEEEEEEECGGCSSHHHHHHHHHH CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge....kaivsdkpgtTrdinegr.vk....lkgkeielvDtpGliegaseekglgk 68 
                                       ++++vG +N+GKS L  +l+++       +  + + T+ +++   v+     k+++++++D+ G  +    e +l +
  gi|386003034|ref|YP_005921333.1| 295 KIVFVGESNAGKSCLSLRLSEDryeeLETTHGTRFWTLLPEQLDpVAvtppGKKRDVVIWDMGG-QN----EYRLVH 366
                                       689*****************973332345566778888886664233556434589********.43....456666 PP

                                       HHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTT CS
                          MMR_HSR1  69 aflaleeadlillvvdaseeklkpldeeleelleeak 105
                                       ++  l ++ l+l+++d +++  ++  +e+ee++++ +
  gi|386003034|ref|YP_005921333.1| 367 QIF-LHDVTLALILFDPTRG--QNAFKEVEEWNKRLD 400
                                       666.3457899999995522..334466666665522 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00015      0.38      37      70 ..      17      50 ..       8      66 .. 0.89
   2 !    9.9   0.0   0.00035      0.89      32      76 ..     182     238 ..     156     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                       ANAPC4_WD40 37 edsevrsLaWkpdgklLavaysdgevrlldaesg 70
                                       ++++  ++W+p g+ La   + g++++ d+ ++
  gi|386003034|ref|YP_005921333.1| 17 AGKKIDRISWSPHGTQLAAELDIGKIKIWDVDNE 50
                                      6899**************************9885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00035
                       ANAPC4_WD40  32 l............eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76 
                                                    + +++   + s++++ d k+La    d+++rl +  + ++v  +
  gi|386003034|ref|YP_005921333.1| 182 ReaeevyigkyfrTLEGHTDAIVSISFSFDSKFLASMSLDNTIRLWSCDKWETVAII 238
                                       444444444666656788899**************************9998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.53
# Mc/sec: 6649.44
//
Query:       gi|386003035|ref|YP_005921334.1|  [L=87]
Description: Iron-sulfur flavoprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00025   20.8   0.0    0.00028   20.7   0.0    1.0  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-08   0.00028     114     185 ..      11      69 ..       2      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-08
                                       TCSSCCCCTTT.TSEEEEEEEESS-GGGSSTTSSS-S-HHHHHHHHHHHHHHTT-EEEEEEEEESCTCCCHHH CS
                      Flavodoxin_2 114 eggegrgggLk.gkkalvivttGgpeesyqerglegaamdellpplrgilgfiGikdvepvlvegvagaedee 185
                                        g  +r  +L+ gkka+++++ G p           +a++ +   + gil+++G+++ve++++ g  g + ++
  gi|386003035|ref|YP_005921334.1|  11 SG--FR-SRLApGKKAVIVTSQGHPD-I--------SAFEKAADDFAGILKLLGFEVVEIIRMGG--GGAPDA 69 
                                       44..54.45556*************3.2........37888888888***************998..554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 573.59
//
Query:       gi|386003036|ref|YP_005921335.1|  [L=631]
Description: Acetyl-CoA hydrolase/N-acetyltransferase GNAT family fusion protein [Methanosaeta harundinacea 6Ac]
Scores for complete 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-62  208.7   0.0    6.4e-62  208.1   0.0    1.4  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    1.6e-43  149.0   0.0    5.8e-43  147.2   0.0    1.8  2  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
      1e-09   38.6   0.1    3.1e-09   37.1   0.0    1.9  2  Acetyltransf_1   Acetyltransferase (GNAT) family
      1e-07   32.2   0.0      2e-07   31.3   0.0    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.9e-07   31.8   0.0    3.4e-07   31.0   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.4e-05   24.6   0.0    6.9e-05   23.2   0.0    1.8  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00078   19.4   0.1     0.0022   17.9   0.1    1.8  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0024   17.8   0.0     0.0054   16.7   0.0    1.5  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.014   13.8   0.1        2.7    6.2   0.0    2.1  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.0   3.2e-65   6.4e-62       1     154 []     283     436 ..     283     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 3.2e-65
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHST CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalsk 77 
                                       G+k+ y+fldenp+ie++ ++yvn+p +ia+nk +++insa+e+dltGqv++esl g+++ GvGgq dF+rgaal++
  gi|386003036|ref|YP_005921335.1| 283 GKKESYEFLDENPAIEFKTIDYVNSPLIIAKNKLMTAINSAIEIDLTGQVTAESLAGTFYFGVGGQADFMRGAALAP 359
                                       89999************************************************************************ PP

                                       T-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                   AcetylCoA_hyd_C  78 ggksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                       ggksi+alpSta +++iSrIvpsl+eg++vt tr dv+yvvTEyGia+L+gk++rera+ li+iAhp+fr +L+eea
  gi|386003036|ref|YP_005921335.1| 360 GGKSILALPSTAVNDTISRIVPSLREGTGVTLTRGDVHYVVTEYGIAYLHGKNIRERAMDLIAIAHPKFRSWLVEEA 436
                                       **************************************************************************987 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.2   0.0   2.9e-46   5.8e-43      11     191 ..      13     192 ..       4     198 .. 0.97
   2 ?   -1.4   0.0      0.99     2e+03      25      58 ..     217     249 ..     193     290 .. 0.66

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 2.9e-46
                   AcetylCoA_hydro  11 e.peeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekdavlyrp 86 
                                       + pe++a+  +++shi+ ++ +++gt +++p+ l++  v+ +   +k ++ ++   v+++g  +++++ek+  ++r 
  gi|386003036|ref|YP_005921335.1|  13 SwPEKFAPEEEIFSHIHAGDKIFIGTGCGEPQHLVQALVDFVSRSPKAFFGIELIHVWTLG-TAPYIDEKFRDNFRI 88 
                                       249**********************************************************.*************** PP

                   AcetylCoA_hydro  87 apkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEvaelvviv 163
                                        +++++e++r ain g+++++++ ls vp+++ ++ +piDvali+++++d++Gy+ lG++v+++K++   a l v++
  gi|386003036|ref|YP_005921335.1|  89 DSFFISEGTRNAINRGAADYTPVSLSAVPGLIRREIIPIDVALIQTSPPDKHGYMSLGISVDIVKAATQKASLIVAQ 165
                                       ***************************************************************************** PP

                   AcetylCoA_hydro 164 vkknpPrvngydelialdkvdyivvdpe 191
                                       +++++Pr +g d++i +  v +i+  +e
  gi|386003036|ref|YP_005921335.1| 166 INSHMPRTQG-DGFINIKDVHFIIHRDE 192
                                       **********.************98876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.99
                   AcetylCoA_hydro  25 ielsgftavgtakaipkylakrkvekenvkkkll 58 
                                       +e +  + vg   +ip++++   +ek+++ + + 
  gi|386003036|ref|YP_005921335.1| 217 VEDGSTLQVG-YGIIPNAVVSYLDEKKHLGVHTE 249
                                       3333333333.35789999999999999877664 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.5     9e+03       4      33 ..       6      31 ..       4      43 .. 0.55
   2 !   37.1   0.0   1.5e-12   3.1e-09      38     117 .]     531     609 ..     489     609 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.5
                                      HHHHHHHHTHHHHHHHHHHHHHHHHHSTTC CS
                    Acetyltransf_1  4 lvellvesffppnedaseeefeesfsleae 33
                                      l e+l+es+++ +  ++ee+f ++   +a+
  gi|386003036|ref|YP_005921335.1|  6 LLEFLKESWPE-KFAPEEEIFSHI---HAG 31
                                      56677777654.444444444444...444 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 1.5e-12
                                       EEET...TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHH CS
                    Acetyltransf_1  38 aeed...geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairl 111
                                       +e +   +++++  ++ +++    +++++  l+V+ ey+++G+G  Ll++l + ar +g+    ++v + n+++ +l
  gi|386003036|ref|YP_005921335.1| 531 VE-GdsrETIAAIGQYEINDK--MHNGEV-ALVVKDEYQNMGVGHDLLTYLTRLARGRGLLGFTAEVLVENEPMLNL 603
                                       22.234356666666666666..455666.99****************************66688************ PP

                                       HHHTTE CS
                    Acetyltransf_1 112 YeklGF 117
                                       ++k+GF
  gi|386003036|ref|YP_005921335.1| 604 FKKMGF 609
                                       *88**9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   9.9e-11     2e-07      49     142 ..     525     617 ..     503     625 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.9e-11
                    Acetyltransf_4  49 eyvflvae...sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspn 122
                                        +++ v e    ++i+++ +++ +++  k + +e+   +++   +++g+g +l+++l   ++  +++ ++ae+ ++n
  gi|386003036|ref|YP_005921335.1| 525 MMILAVVEgdsRETIAAIGQYE-IND--KMHNGEVALVVKD-EYQNMGVGHDLLTYLTRLARGRGLLGFTAEVLVEN 597
                                       5666777755456677777776.888..9**********95.7********************************** PP

                    Acetyltransf_4 123 ensiqfhkalGFelvgifkk 142
                                       e+  +++k++GF+ ++++++
  gi|386003036|ref|YP_005921335.1| 598 EPMLNLFKKMGFDTEKRSED 617
                                       *************9988776 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.7e-10   3.4e-07       2     137 ..     472     609 ..     471     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                    Acetyltransf_3   2 LlLrplteeD...leal.felrsdpevmrylpepltleeaeewlera....waeeseeegygwaivlkdtgv.iGsv 69 
                                       +lLrp++  D    +++ + l +d   +r+++     ++ +e+l+++    +    +++ + +a+v+ d+++ i  +
  gi|386003036|ref|YP_005921335.1| 472 VLLRPVKMGDeplMKDFfYDLSNDSMYRRFMSV--RMDMPHERLQEFgivdY----ANRMMILAVVEGDSREtIAAI 542
                                       688999888833334442346677778888655..56888888888854334....457888999996666568888 PP

                    Acetyltransf_3  70 glrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       g ++++++ + +e+ +++++++++ G++++ +  l+++a +  gl  + a++  eNe + ++++k+Gf
  gi|386003036|ref|YP_005921335.1| 543 GQYEINDKMHNGEVALVVKDEYQNMGVGHDLLTYLTRLA-RGRGLLGFTAEVLVENEPMLNLFKKMGF 609
                                       88888898888****************************.7888999********************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.5e-08   6.9e-05       8      75 ..     541     610 ..     523     611 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.5e-08
                                       EEETTEEEEEEEEEEES.TCTEE...EEE-GGGTTSSHHHHHHHH....TT.SEEEEE...EEEETHHHHHHHHHHT CS
                    Acetyltransf_7   8 aeddgkivGfialslld.aeitr...laVdpeyrgkGiGraLlea....ae.kgiile...qlelnaekaikfYekl 72 
                                       a      +G++ +         +   l+V+ ey++ G+G+ Ll++    a+ +g+      ++ +++e+ +++++k+
  gi|386003036|ref|YP_005921335.1| 541 A------IGQYEINDKMhN---GevaLVVKDEYQNMGVGHDLLTYltrlARgRGLL-GftaEVLVENEPMLNLFKKM 607
                                       2......565444433333...145699****************856542154432.222223334458899***** PP

                                       TEE CS
                    Acetyltransf_7  73 GFe 75 
                                       GF 
  gi|386003036|ref|YP_005921335.1| 608 GFD 610
                                       **5 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.6   1.3e+04      13      36 ..      14      38 ..      10      42 .. 0.72
   2 !   17.9   0.1   1.1e-06    0.0022      44     124 ..     543     625 ..     507     627 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.6
                   Acetyltransf_10 13 f.kefispealrerieegealllva 36
                                      + ++f  +e++ ++i++g++++++ 
  gi|386003036|ref|YP_005921335.1| 14 WpEKFAPEEEIFSHIHAGDKIFIGT 38
                                      5567777788888888888888775 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.1e-06
                   Acetyltransf_10  44 Gvielrdgshisll..fVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqeen 116
                                       G  e+ d+ h + +  +V++ey+  G+g+ Ll ++ + a+ +g+   + +v   +    ++++k+GF +   ++ e+
  gi|386003036|ref|YP_005921335.1| 543 GQYEINDKMHNGEValVVKDEYQNMGVGHDLLTYLTRLARGRGLLGfTAEVLVENePMLNLFKKMGFDTE--KRSED 617
                                       44455555565543339**********************9998888988888888899*********875..45667 PP

                   Acetyltransf_10 117 GirfvpMe 124
                                       G+  ++M+
  gi|386003036|ref|YP_005921335.1| 618 GVYEMRMK 625
                                       76666665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-06    0.0054      26      80 ..     557     612 ..     535     616 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                       al v++e +++G g  l   l++  + rg    ++ v  +N+p  +l++k+Gf   
  gi|386003036|ref|YP_005921335.1| 557 ALVVKDEYQNMGVGHDLLTYLTRLARGRGLLgFTAEVLVENEPMLNLFKKMGFDTE 612
                                       899********************9999997526789999**************875 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0024       4.9     137     208 ..     125     194 ..     118     208 .. 0.78
   2 ?    6.2   0.0    0.0013       2.7     449     482 ..     392     424 ..     384     429 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0024
                   Mal_decarbox_Al 137 iP.nvalvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdklpr.vdiPadwvdfvveadkpf 208
                                       iP +val+ ++  d++G +  G + +    iv a++ k ++++aq+n  + +      i  + v+f+++ d+p 
  gi|386003036|ref|YP_005921335.1| 125 IPiDVALIQTSPPDKHGYMSLGISVD----IVKAATQKASLIVAQINSHMPRTQGdGFINIKDVHFIIHRDEPL 194
                                       55469*****************9975....9****************866544321236667788888887775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0013
                   Mal_decarbox_Al 449 ygddvthvvteeGiayllkaesleereqairava 482
                                          dv +vvte Giayl+  +++ er   + a+a
  gi|386003036|ref|YP_005921335.1| 392 TRGDVHYVVTEYGIAYLHG-KNIRERAMDLIAIA 424
                                       5679************985.56666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3969.22
//
Query:       gi|386003037|ref|YP_005921336.1|  [L=494]
Description: Thermosome subunit [Methanosaeta harundinacea 6Ac]
Scores for complete 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-167  558.2  19.2   1.7e-167  558.0  19.2    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.077   13.0   0.3        3.1    7.8   0.0    3.0  3  DUF3924     Protein of unknown function (DUF3924)


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.0  19.2  1.9e-171  1.7e-167      17     490 ..       1     472 [.       1     473 [. 0.98

  Alignments for each domain:
  == domain 1  score: 558.0 bits;  conditional E-value: 1.9e-171
                                       EEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHH CS
                        Cpn60_TCP1  17 mlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiieg 93 
                                       mlv+  g+vv+TnDG+tilke++iehPaak++ve+a++qd+evGDGTtt+v+LageLl++ae l+++++hpt+i  g
  gi|386003037|ref|YP_005921336.1|   1 MLVDTLGDVVITNDGVTILKEMDIEHPAAKMMVEIAKTQDQEVGDGTTTAVVLAGELLKQAEGLLEEEIHPTVIAAG 77 
                                       9**************************************************************************** PP

                                       HHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEECSCCCEECCCC CS
                        Cpn60_TCP1  94 yekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekeldlgrikvvki 170
                                       y+ a+ek +e+Lk    ++  + +d++ L+k+a t++++k +++ ++el+ ++v+Av+++ ++++++d ++i v+k+
  gi|386003037|ref|YP_005921336.1|  78 YRAAAEKSMEILKGL--AVIASAEDEDLLRKIAVTAMTGKGSQSARDELAVMAVEAVRSVVDEDGTVDTDNITVEKK 152
                                       ************999..555556799*******************************77778889************ PP

                                       EECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1 171 eggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellek 247
                                        gg ++ds lv+G+v+dk+ l+p+mpk++++a+++l++  +eiekte++++++++++++l++++++ee+ l+ ++++
  gi|386003037|ref|YP_005921336.1| 153 VGGGITDSVLVRGVVIDKERLQPSMPKSVTDARIALINAAVEIEKTEIDAKIQITSPNQLQAFLDQEETTLKGMVDN 229
                                       ***************************************************************************** PP

                                       HHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETTCC CS
                        Cpn60_TCP1 248 iiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigsek 324
                                       i++sg+nv+++qkgiddla+hfla++gi ++rrvkk+d+e+la+atG+++++s+ d+++++lG a+ vee+k+++ek
  gi|386003037|ref|YP_005921336.1| 230 IVASGANVLFVQKGIDDLAQHFLARAGIYTVRRVKKSDMEKLARATGGKVITSIHDIDKDDLGRAGLVEERKVSDEK 306
                                       ***************************************************************************** PP

                                       EEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHH CS
                        Cpn60_TCP1 325 ttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqla 401
                                       +t++e+++++k+++i+lrg t++v+de+ ra edAl+vv  a+ed+ +vpGGGa e+ la +l+++a++v g+eqla
  gi|386003037|ref|YP_005921336.1| 307 MTFVEGCENPKSVSIILRGGTEHVVDELDRAMEDALRVVGVALEDKLLVPGGGAPEVDLALRLRAFASTVGGREQLA 383
                                       ***************************************************************************** PP

                                       HHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1 402 ieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaas 478
                                       ie fa+A+e+ipktLaeNaGld+i+ l  lr+ah++g k+ g+++e+ge++d++++gv++p++vk+qa++sAteaa 
  gi|386003037|ref|YP_005921336.1| 384 IESFADAMEIIPKTLAENAGLDQIDSLMALRSAHETGMKNSGLNMETGEPVDMLKQGVLEPIRVKTQAINSATEAAV 460
                                       ***************************************************************************** PP

                                       HHHCEEEEEXXX CS
                        Cpn60_TCP1 479 tiLrideiikak 490
                                       +iLrid++i  k
  gi|386003037|ref|YP_005921336.1| 461 MILRIDDVIASK 472
                                       *********977 PP

>> DUF3924  Protein of unknown function (DUF3924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00034       3.1      23      48 ..     149     175 ..     141     182 .. 0.83
   2 ?   -2.2   0.1      0.48   4.3e+03      46      60 ..     204     218 ..     200     220 .. 0.83
   3 ?    1.4   0.0     0.035   3.2e+02       8      22 ..     426     440 ..     424     457 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00034
                           DUF3924  23 yekktGasisestlvqt.liskefiqa 48 
                                        ekk G  i++s lv+  +i ke +q 
  gi|386003037|ref|YP_005921336.1| 149 VEKKVGGGITDSVLVRGvVIDKERLQP 175
                                       69*************962689999886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.48
                           DUF3924  46 iqaitPfdlqqfvtG 60 
                                       iq   P  lq f++ 
  gi|386003037|ref|YP_005921336.1| 204 IQITSPNQLQAFLDQ 218
                                       89999******9875 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.035
                           DUF3924   8 lPketaekldllkqa 22 
                                       l  et e +d+lkq 
  gi|386003037|ref|YP_005921336.1| 426 LNMETGEPVDMLKQG 440
                                       5679*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3514.54
//
Query:       gi|386003038|ref|YP_005921337.1|  [L=82]
Description: hypothetical protein Mhar_2364 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 541.22
//
Query:       gi|386003039|ref|YP_005921338.1|  [L=668]
Description: hypothetical protein Mhar_2365 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-75  254.0   0.0    3.2e-75  253.6   0.0    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    7.2e-24   84.5   0.0    1.2e-23   83.9   0.0    1.3  1  NFACT-R_1  NFACT protein RNA binding domain
    0.00048   20.3   0.0     0.0015   18.7   0.0    1.8  1  NFACT-R_2  NFACT protein RNA binding domain


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.6   0.0   5.3e-79   3.2e-75       2     409 ..       7     443 ..       6     457 .. 0.93

  Alignments for each domain:
  == domain 1  score: 253.6 bits;  conditional E-value: 5.3e-79
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLR 77 
                                       ++++aavv+ELq++l+gg + k yq  +d +v++++    g+ +Lll+a   + rihltekp+e pk+pp+F+ +LR
  gi|386003039|ref|YP_005921338.1|   7 NVDVAAVVEELQEKLVGGFVGKSYQLSPDRVVISFQsPASGKLDLLLEA---GRRIHLTEKPREAPKMPPQFPTMLR 80 
                                       789*********************************88888888*****...************************* PP

                                       HHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBST CS
                              FbpA  78 kyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilp 154
                                        +L+g+r+ +++q+gfdR+ e++ie+      + +ytLi+Ei+ + +N++L+d+ ++I+ +++   ++   +R++l 
  gi|386003039|ref|YP_005921338.1|  81 SRLSGGRVAAVRQHGFDRVAEIEIERG-----DDRYTLIAEIFPK-GNVLLLDSGGRIVLPLRPLAFR---DRKLLA 148
                                       ***************************.....999**********.*********************9...9***** PP

                                       TXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............... CS
                              FbpA 155 gekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerl 231
                                       ge+Y++ +   +++P ++++ +++  +l  ++ +lv++Lv+ + ++++++aee++ rag++k+ +a +l+ e+++rl
  gi|386003039|ref|YP_005921338.1| 149 GETYQYRED--QVDPRTVSR-NDLAFILASSDSELVRTLVRGL-NMGGTYAEEICLRAGINKTVPAFALAGEEIDRL 221
                                       ******999..*********.88888888999***********.********************************* PP

                                       HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHH CS
                              FbpA 232 yealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrv 308
                                       + al e++   e     p+lv + e+ +++ + pl  +++le+++f s+sealde+++ k+ + +  + + +le+r 
  gi|386003039|ref|YP_005921338.1| 222 HWALGEVFGLAE---AYPHLVAEGERIVDVVPAPLAVYDGLERREFGSFSEALDEFFSSKEAEAEEAKPKTALERR- 294
                                       *********999...89****99998888888899999*********************99888888777777765. PP

                                       HHHHHHHHHHHHHHHHHHHCCGGH..HHHHCCHH-----------------------.--................. CS
                              FbpA 309 eneleklekklkklekelekaeka..enyrligelltaylyaikkgmsevelenyydege................. 366
                                       ++ +e+  ++  + e+el++  ++  e+y  ++ +l a+++  ++g +  e+   ++  +                 
  gi|386003039|ref|YP_005921338.1| 295 REMQERSIQEFRERERELARLGEKvyERYGEVEAVLAAISKGFERGFTYSEILAKIKT-Sglpiaekilaldyqgel 370
                                       44455555555666677777777799999999999************99999988884.3579************** PP

                                       ..............................---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 367 ..............................evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkee 409
                                                                     +   +L+ ++++++nAq+y++ +k   +++e++e+++eet + 
  gi|386003039|ref|YP_005921338.1| 371 rlrlddpgdgdggegkggtvgdtggkgearGAVLELNSNLTVPQNAQRYYDLAKEQAKKREGAEKALEETIRL 443
                                       *****************************999*************************************9665 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   1.9e-27   1.2e-23       2     109 .]     470     579 ..     469     579 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1.9e-27
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++wF+ssdg+lvi+G+D+++nee++ kyle++d+ +h d  +++ ++++ + ge   +pe++leeaa +a+++S+  
  gi|386003039|ref|YP_005921338.1| 470 FRWFTSSDGFLVIGGRDATSNEEIYAKYLEKRDLALHTDAPGAPLTVIK-TLGE--AVPESTLEEAASFAVSYSSLw 543
                                       99***********************************************.6667..8******************** PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       ++ l + d++ v a++++kt++    l++G+++++g
  gi|386003039|ref|YP_005921338.1| 544 KAGLFEGDCYLVAADQVTKTPEpgefLKKGAFVVRG 579
                                       **********************9*********9876 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.5e-07    0.0015       2      68 ..     471     541 ..     471     549 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                         NFACT-R_2   2 RhfrlsekaklIvgReeeEnkflkgll.kkdfvslrakshkGplvlid..gels.eedlelaarivarYsk 68 
                                       R f  s+++ +I gR+++ n+++ + + +k+ + l++    +pl++i+  ge+  e++le aa++++ Ys+
  gi|386003039|ref|YP_005921338.1| 471 RWFTSSDGFLVIGGRDATSNEEIYAKYlEKRDLALHTDAPGAPLTVIKtlGEAVpESTLEEAASFAVSYSS 541
                                       7899999***************975555666666*************668755559*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 4402.22
//
Query:       gi|386003040|ref|YP_005921339.1|  [L=150]
Description: hypothetical protein Mhar_2366 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-35  120.9   0.0      5e-35  120.7   0.0    1.0  1  Mut7-C    Mut7-C RNAse domain
    0.00011   21.9   0.0    0.00017   21.3   0.0    1.4  1  DUF5615   Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
       0.07   13.5   0.0       0.11   12.8   0.0    1.4  1  PIN_9     PIN like domain


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   8.4e-39     5e-35       2     145 ..       4     144 ..       3     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 8.4e-39
                            Mut7-C   2 rfllDamlgklakyLRllGydalyas.dvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlre 75 
                                       r+l+D ml +la++LR++G+d+       +d+ ll+ a ke+r+llTrdr L++r  ++ +  +l++s+d+ eqlre
  gi|386003040|ref|YP_005921339.1|   4 RYLADLMLLRLARWLRMAGHDVSNPPeGSDDSGLLEVALKEGRTLLTRDRLLARRCGKAGAscILIRSSDLDEQLRE 80 
                                       89********************98874679999***********************9998887888*********** PP

                            Mut7-C  76 viarlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                       +  ++g++l+++p  +rC+ Cng l++ve++ +     +  +e ad+++rCe C+k++W+G+hw+ ++e+
  gi|386003040|ref|YP_005921339.1|  81 L-LAAGVTLEMNP--ERCTLCNGILRKVEASGA---YGSPGPEDADSLWRCEVCGKIYWRGTHWQGIRER 144
                                       *.66789999998..*************99988...667789999*********************9987 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.9e-08   0.00017       6      56 ..       8      53 ..       3      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.9e-08
                           DUF5615  6 DenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                      D  l  rl+++lr aghdv+       eg +D+  le+A +e+r+++T+D+
  gi|386003040|ref|YP_005921339.1|  8 DLML-LRLARWLRMAGHDVSNP----PEGSDDSGLLEVALKEGRTLLTRDR 53
                                      5544.59**********99888....5689********************6 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      73     115 ..      30      71 ..       3      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                             PIN_9  73 eekaDdailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       e++ D  +le+a + + + l T+Dr L +r  ++g   il+R 
  gi|386003040|ref|YP_005921339.1|  30 EGSDDSGLLEVALKEGRTLL-TRDRLLARRCGKAGASCILIRS 71 
                                       5677888*********8888.*******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 866.62
//
Query:       gi|386003041|ref|YP_005921340.1|  [L=356]
Description: Beta-ketoacyl-acyl-carrier-protein synthase I [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-18   65.7   0.0    3.3e-17   62.4   0.0    2.4  2  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    2.1e-13   49.9   0.1    4.8e-13   48.8   0.1    1.7  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    0.00018   20.9   0.1    0.00059   19.2   0.0    1.8  2  FAE1_CUT1_RppA   FAE1/Type III polyketide synthase-like prote
    0.00065   19.2   0.0     0.0012   18.3   0.0    1.4  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
      0.003   17.0   0.0     0.0068   15.8   0.0    1.5  1  Thiolase_N       Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.25   9.1e+02       2      18 ..      85     101 ..      84     105 .. 0.85
   2 !   62.4   0.0   9.2e-21   3.3e-17       1      89 [.     266     354 ..     266     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.25
                                       HHTT--GGG-SEEEE-S CS
                     ACP_syn_III_C   2 ekagltpedidalvphq 18 
                                       e+ag++p +id+lv   
  gi|386003041|ref|YP_005921340.1|  85 ERAGIDPREIDVLVYCS 101
                                       799*********99765 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 9.2e-21
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEE CS
                     ACP_syn_III_C   1 LekagltpedidalvphqanlriidavakklglpeekvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgf 77 
                                       Lek+g + +d+d+l+ +q+++++++++++ l+l  + ++++++++G++++++ +  L++a+e+g+l pg l++l++ 
  gi|386003041|ref|YP_005921340.1| 266 LEKSGRSLQDVDLLLTNQVKRSLLEEILRGLDLGLDHTITSIRDHGHMGTVDALFNLSRAIESGRLGPGSLAVLASS 342
                                       7999************************************************************************* PP

                                       ETTTEEEEEEEE CS
                     ACP_syn_III_C  78 GaGltwgaallr 89 
                                       GaG+tw+a+ ++
  gi|386003041|ref|YP_005921340.1| 343 GAGFTWAAMPVE 354
                                       ********9765 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.3e-16   4.8e-13       1      80 []     128     209 ..     128     209 .. 0.90
   2 ?   -4.0   0.0       4.1   1.5e+04       9      25 ..     314     330 ..     314     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.3e-16
                                       EEEE-GGGHHHHHHHHHHHHHHTT.S-SEEEEEEEEEGGGCS-TTTHHHHT..TB-EEEEEEEEEEESSSSCEEEEE CS
                       ACP_syn_III   1 fDlnaaCsgfvyalsvAdaliesg.aakrvLvigaetlskilDwkdrstav..lfGDGAgAvvleaseeegarilds 74 
                                       f+++++C+g   ++s+ ++l+  +   +++Lv+++e+ls  +D++dr+     ++GDGA+A++l+++ee++ r+l++
  gi|386003041|ref|YP_005921340.1| 128 FEVKNGCNGGNLGISICKSLLLDDpDKRCALVVCSEKLSISVDYEDRNALSlfMVGDGAAAAILKKGEETN-RLLSY 203
                                       889******************9999999*****************9886651167***********97776.8***9 PP

                                       EEEE-G CS
                       ACP_syn_III  75 elgsdg 80 
                                       + +++g
  gi|386003041|ref|YP_005921340.1| 204 AARTEG 209
                                       999876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHTTS CS
                       ACP_syn_III   9 gfvyalsvAdaliesga 25 
                                       g v al + +++iesg+
  gi|386003041|ref|YP_005921340.1| 314 GTVDALFNLSRAIESGR 330
                                       66889999999999996 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.6e-07   0.00059      54     205 ..      46     193 ..      36     207 .. 0.68
   2 ?   -3.2   0.0       1.1   3.9e+03      90     111 ..     261     282 ..     257     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-07
                    FAE1_CUT1_RppA  54 rsglgeetyvPravlelpekktlaeareEa.eevlfgavdellaktkvspkdidilvvncslfsptPslsamvvnry 129
                                       rsg+  e ++ +    +  ++++ +a++E  +e+ + a +  +++++++p++id+lv  ++ f      s     + 
  gi|386003041|ref|YP_005921340.1|  46 RSGIPVEVFLEK----IGMERKHVAAEDEHpSEMGIRAAEVAVERAGIDPREIDVLVYCSAGFYDYRIWSPAAKVQA 118
                                       455444444433....3333344444444414455677788899**************9999988776665544445 PP

                    FAE1_CUT1_RppA 130 klr.edvksynLsgmGCsAglisidlaknllqvhk.ntlalvvstEnitlnwYvGnersmllanclFRvG..gaavl 202
                                        l  +   ++++   GC  g + i + k+ll   + +  alvv +E+++ ++   + r+ l   +lF vG  +aa++
  gi|386003041|ref|YP_005921340.1| 119 ALGaDGCYAFEVKN-GCNGGNLGISICKSLLLDDPdKRCALVVCSEKLSISVDYED-RNAL---SLFMVGdgAAAAI 190
                                       55405688899887.***************999886789**********9986544.4433...4555542155666 PP

                    FAE1_CUT1_RppA 203 lsn 205
                                       l +
  gi|386003041|ref|YP_005921340.1| 191 LKK 193
                                       654 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                    FAE1_CUT1_RppA  90 avdellaktkvspkdidilvvn 111
                                       +++  l+k++ s +d+d+l++n
  gi|386003041|ref|YP_005921340.1| 261 VINRSLEKSGRSLQDVDLLLTN 282
                                       6777889999999999999998 PP

>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.5e-07    0.0012      99     221 ..      72     191 ..      52     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.5e-07
                   Chal_sti_synt_N  99 vlklgkeaalkalkewGrPkskithlvfvsss..evelPGadlklakklGlrpsvkrvmlyflGcygGatvlrlakd 173
                                         ++g  aa+ a++  G    +i  lv++s+   + ++     k+ + lG +         + Gc gG  ++ + k 
  gi|386003041|ref|YP_005921340.1|  72 PSEMGIRAAEVAVERAGIDPREIDVLVYCSAGfyDYRIWSPAAKVQAALGAD--GCYAFEVKNGCNGGNLGISICKS 146
                                       468***************************9733556666666777778865..455667799************** PP

                   Chal_sti_synt_N 174 iaennkGarv.lvvaseitvlgfrgPskdrlddlvGaalfGdGaaavii 221
                                       +  +++  r  lvv+se   ++     +++    +   + GdGaaa+i+
  gi|386003041|ref|YP_005921340.1| 147 LLLDDPDKRCaLVVCSEKLSISVDYEDRNA----LSLFMVGDGAAAAIL 191
                                       **9999999549*****9888765443333....344688*******97 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.9e-06    0.0068      14     133 ..      63     183 ..      53     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                                       TTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCE.EEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHH CS
                        Thiolase_N  14 fggslkdlsaeeLlaealkallekagvdpeevde.vivGnvlqagegqniarqaalkagipeevpavtvnkvcsSgl 89 
                                       ++ + +d   +e++ +a++ ++e+ag+dp e+d  v+++        + +a +++ ++g  +  +a  v++ c  g+
  gi|386003041|ref|YP_005921340.1|  63 KHVAAEDEHPSEMGIRAAEVAVERAGIDPREIDVlVYCSAGFYDYRIWSPAAKVQAALGA-DGCYAFEVKNGCNGGN 138
                                       5667789999***********************73678888888****************.**************** PP

                                       HHHHHHHHHHHTT.SHSEEEEEEEEESTTS-EEETCTTTTGGSSS CS
                        Thiolase_N  90 kavalaaqsiaag.eadvvvagGvEsmsnaptaestdvrsglklg 133
                                        ++  +   +    +  +++++  E++s +  +e++++ s   +g
  gi|386003041|ref|YP_005921340.1| 139 LGISICKSLLLDDpDKRCALVVCSEKLSISVDYEDRNALSLFMVG 183
                                       ***987766544326778999999999987777777776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2215.66
//
Query:       gi|386003042|ref|YP_005921341.1|  [L=296]
Description: UbiE/COQ5 methyltransferase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-21   74.9   0.0    1.6e-20   73.6   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    8.3e-21   74.5   0.0      2e-20   73.3   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
    6.9e-18   64.9   0.0      1e-17   64.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.3e-13   50.3   0.0    3.9e-13   49.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    2.6e-13   50.6   0.0    5.7e-13   49.4   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    8.9e-13   48.1   0.0    1.3e-12   47.6   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    8.7e-07   28.6   0.0    1.5e-06   27.8   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
      4e-06   26.0   0.0    5.8e-06   25.4   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    7.9e-06   25.5   0.0    1.5e-05   24.6   0.0    1.4  1  MTS              Methyltransferase small domain
    7.5e-05   22.1   0.0    9.8e-05   21.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00053   20.0   0.0    0.00081   19.4   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0026   17.5   0.0     0.0035   17.1   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0062   16.0   0.0     0.0087   15.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.042   13.8   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
       0.19   11.2   0.0       0.28   10.7   0.0    1.2  1  DOT1             Histone methylation protein DOT1


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         9   1.1e+04       4      24 ..      83     103 ..      82     122 .. 0.51
   2 !   73.6   0.0   1.3e-23   1.6e-20       1      97 []     147     242 ..     147     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9
                                       ET-TTSHHHHH.HHCTSTSSEE CS
                   Methyltransf_25   4 lGcGtGrltla.lakrlgkakv 24 
                                       +G+G+G +  + l ++ g +kv
  gi|386003042|ref|YP_005921341.1|  83 IGAGEGAIYVRgLMAQNG-SKV 103
                                       577777654332222222.333 PP

  == domain 2  score: 73.6 bits;  conditional E-value: 1.3e-23
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       +Ld+GcG Grltl++a + ++++v g+D+ + + ++ar +ae+ g+ n+ef+++++ dlpfe gsf  v+s+++lhh
  gi|386003042|ref|YP_005921341.1| 147 ILDVGCGFGRLTLDVASQSPASEVFGIDLFDPLTAQARMNAEALGIkNAEFRTASVYDLPFEGGSFETVYSFFMLHH 223
                                       8*****************889**********************999******************************* PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       l+  d++k l ei+rvL  gG
  gi|386003042|ref|YP_005921341.1| 224 LE--DIPKGLFEIRRVLARGG 242
                                       97..9***************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.4   1.1e+04      12      24 ..      94     106 ..      83     121 .. 0.49
   2 !   73.3   0.0   1.6e-23     2e-20       1      94 [.     148     244 ..     148     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.4
                                       HHHHHTTSEEEEE CS
                   Methyltransf_11  12 ealakrgarvvgv 24 
                                         +a++g++v+ v
  gi|386003042|ref|YP_005921341.1|  94 GLMAQNGSKVYLV 106
                                       2333555555544 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 1.6e-23
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       LdvGcG Grl+ ++a++   ++v+g+Dl + ++++a+++a+  g+ + ef+ a++ +lpfe +sf  v+s+++lhh+
  gi|386003042|ref|YP_005921341.1| 148 LDVGCGFGRLTLDVASQSpaSEVFGIDLFDPLTAQARMNAEALGIkNAEFRTASVYDLPFEGGSFETVYSFFMLHHL 224
                                       8**************88889**************************99***************************** PP

                                       CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGll 94 
                                       ed  k l ei+RvL  gG+ 
  gi|386003042|ref|YP_005921341.1| 225 EDIPKGLFEIRRVLARGGRY 244
                                       ******************86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   8.6e-21     1e-17       3     112 ..     143     249 ..     141     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 8.6e-21
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       kg r+lD+GCG G+lt+  a    p +ev+GiD       +Ar na+ lg++n+eF+ +++ +l+  +e  +f  + 
  gi|386003042|ref|YP_005921341.1| 143 KGERILDVGCGFGRLTLDVA-SQSPASEVFGIDLFDPLTAQARMNAEALGIKNAEFRTASVYDLP--FEGGSFETVY 216
                                       7899****************.66899***************************************..********** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedp 112
                                       s+  l++l d +k l ei rvl  gg++l+ +p
  gi|386003042|ref|YP_005921341.1| 217 SFFMLHHLEDIPKGLFEIRRVLARGGRYLAVEP 249
                                       ****************************98876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   3.3e-16   3.9e-13      20     133 ..     141     270 ..     121     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.3e-16
                   Methyltransf_23  20 lraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                       + +g r+Ld+GcG G  +l+v+++ ++ +v g+Dl + + + a+      ++k+a++  +   + +++ g+f+++++
  gi|386003042|ref|YP_005921341.1| 141 ELKGERILDVGCGFGrLTLDVASQSPAsEVFGIDLFDPLTAQARmnaealGIKNAEFRTASVYDLPFEGGSFETVYS 217
                                       56789**********44788889998889*********999999******8888999888888************** PP

                   Methyltransf_23  89 revlehvpdppellrqiatllkpgGylllseplasl........kedrllldw 133
                                       +++l+h++d p+ l  i++ l+ gG+ l  epl  +         ++r ++d 
  gi|386003042|ref|YP_005921341.1| 218 FFMLHHLEDIPKGLFEIRRVLARGGRYLAVEPLGHHhgpnhsgaDWLRIFEDA 270
                                       *******************************9888855555554455555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   4.8e-16   5.7e-13       1      98 [.     148     243 ..     148     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 4.8e-16
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG G+l+  ++ + p +e+ g+D+     ++a+    + + +n+++ +  + dl    +g+sf +v++++ lh
  gi|386003042|ref|YP_005921341.1| 148 LDVGCGFGRLTLDVASQSPASEVFGIDLFDPLTAQARMNAEALGIKNAEFRTASVYDLPF--EGGSFETVYSFFMLH 222
                                       8********************************999999999999999999999999864..456************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       hl+di + l +ir++L+ gGr
  gi|386003042|ref|YP_005921341.1| 223 HLEDIPKGLFEIRRVLARGGR 243
                                       ********************8 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.1e-15   1.3e-12      44     153 ..     140     248 ..     130     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.1e-15
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                        +++g+++lDv +G g l+++++++     +v ++D+ + +  +++  ++  g +n ef +a+  +Lpfe +sf++v
  gi|386003042|ref|YP_005921341.1| 140 PELKGERILDVGCGFGRLTLDVASQ-SPASEVFGIDLFDPLTAQARMNAEALGIKNAEFRTASVYDLPFEGGSFETV 215
                                       57899****************9976.56679********************************************** PP

                                       EEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 121 tvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                          f l  + D++k+L e++rvl  GGr + +e
  gi|386003042|ref|YP_005921341.1| 216 YSFFMLHHLEDIPKGLFEIRRVLARGGRYLAVE 248
                                       ****************************99887 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.3e-09   1.5e-06       5      55 ..     147     197 ..     143     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-09
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEE CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlri 55 
                                       +l++GcG G+++++ A + P  +++Gi++  +++a++  ++eal++kN + 
  gi|386003042|ref|YP_005921341.1| 147 ILDVGCGFGRLTLDVASQSPASEVFGIDLFDPLTAQARMNAEALGIKNAEF 197
                                       79**********************************************765 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   4.9e-09   5.8e-06     106     214 ..     133     243 ..     126     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.9e-09
                                       HHGGG.S.--TT-EEEEET-TTSHHHHHHHHCT.-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T. CS
                    Methyltransf_9 106 rvlph.lsdlkgrtildvGcgnGyhlwrmvgeg.aklvvGidPselfliqfeavrkllgedqrahllplgieqlpe. 179
                                       rv p  l++lkg +ildvGcg G     ++++  a+ v+Gid       q +   + lg ++ ++    ++ +lp  
  gi|386003042|ref|YP_005921341.1| 133 RVWPEvLPELKGERILDVGCGFGRLTLDVASQSpASEVFGIDLFDPLTAQARMNAEALGIKNAEFRT-ASVYDLPFe 208
                                       5555426889*******************9997356799******999**99999****99999988.89*****86 PP

                                       ---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEE CS
                    Methyltransf_9 180 leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGe 214
                                         +f+tv+s  +l+h +     l +++  l +gG 
  gi|386003042|ref|YP_005921341.1| 209 GGSFETVYSFFMLHHLEDIPKGLFEIRRVLARGGR 243
                                       89*************99998999999999999996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.2e-08   1.5e-05      25      91 ..     137     204 ..     132     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle 91 
                                       e lp+ + +++lD+GcG+G l++ +a++sp  ev  +d      + a+ n+ea +++ +e+++ +v++
  gi|386003042|ref|YP_005921341.1| 137 EVLPELKGERILDVGCGFGRLTLDVASQSPASEVFGIDLFDPLTAQARMNAEALGIKnAEFRTASVYD 204
                                       5688888999*****************************999999**********9999999999887 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   8.2e-08   9.8e-05      62     141 ..     143     225 ..     129     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.2e-08
                                       TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEE CS
                              CMAS  62 pGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsv 134
                                       +G+++Ld+GcG+G l+   +++    +v+g+ l +  +++a+ + ++l++++ +e + +   dl+     ++ v s+
  gi|386003042|ref|YP_005921341.1| 143 KGERILDVGCGFGRLTLDVASQSpASEVFGIDLFDPLTAQARMNAEALGIKN-AEFRTASVYDLPFeggSFETVYSF 218
                                       7*************9998887761568**********************765.566666666665335799*****9 PP

                                       S-GGGTS CS
                              CMAS 135 gafehvg 141
                                        ++ h+ 
  gi|386003042|ref|YP_005921341.1| 219 FMLHHLE 225
                                       9999984 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.8e-07   0.00081      25      88 ..     143     201 ..     132     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.8e-07
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88 
                                       + ++++DvG+G g L+  +a+   +    +v+gid+ + l+++a+  ae+lg  + k+ +f ++s
  gi|386003042|ref|YP_005921341.1| 143 KGERILDVGCGFGRLTLDVAS---QsPASEVFGIDLFDPLTAQARMNAEALG--I-KNAEFRTAS 201
                                       6689*****************...44799***********************..6.666666655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.9e-06    0.0035      68     131 ..     138     200 ..     100     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                        l   kg+r+L+vG+G G lt  +a        v +i+    l+++a+ n ++l+++n  ++++
  gi|386003042|ref|YP_005921341.1| 138 VLPELKGERILDVGCGFGRLTLDVASQSP-ASEVFGIDLFDPLTAQARMNAEALGIKNAEFRTA 200
                                       4444579**************98887654.5569**********************99888765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.3e-06    0.0087     161     213 ..     143     197 ..     137     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.3e-06
                              PrmA 161 egeevlDvGtGSGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkvea.kl 213
                                       +ge++lDvG+G G L++ +a++  a++v+++D+ +     a+ Nae  ++++ ++
  gi|386003042|ref|YP_005921341.1| 143 KGERILDVGCGFGRLTLdVASQSPASEVFGIDLFDPLTAQARMNAEALGIKNaEF 197
                                       6899************95577889********97777888999*99888877555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.042      14      70 ..     143     198 ..     137     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievr 70 
                                       kg+r++D+G+  g l++ +++++ a++v  +D+ +   ++a+ n+e  g+++  e+r
  gi|386003042|ref|YP_005921341.1| 143 KGERILDVGCGFGRLTLDVASQSPASEVFGIDLFDPLTAQARMNAEALGIKN-AEFR 198
                                       5899******************************************999854.5655 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.28      45      89 ..     146     190 ..     141     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                       EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHH CS
                              DOT1  45 vFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeel 89 
                                         +D G G G+++l +a +    + +G+++ d  ++ a+ ++e l
  gi|386003042|ref|YP_005921341.1| 146 RILDVGCGFGRLTLDVASQSPASEVFGIDLFDPLTAQARMNAEAL 190
                                       568*****************************9999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1775.31
//
Query:       gi|386003043|ref|YP_005921342.1|  [L=96]
Description: hypothetical protein Mhar_2369 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-05   24.9   0.0    3.2e-05   24.4   0.0    1.2  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par


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 !   24.4   0.0   1.8e-09   3.2e-05       5      83 ..       9      81 ..       5      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-09
                                      HHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE.CTSTC..CTTEEEEEEC.TEEEEEEEETSTTEEE CS
                        ParE_toxin  5 prAlkdlkkiadyiardgpaakrfldaleealellaenpalgrp.rrelg..lkglrririg.dyriiYriddeelvvv 79
                                      ++Alk l ++           ++    ++e++ +l e+p +g   ++el+    +l+r++ig  + ++Y+i + +  v+
  gi|386003043|ref|YP_005921342.1|  9 RKALKYLSEL----------PEKSQRLIKEKCHALSEDPYPGLGaDKELLhlDFKLYRLHIGrSFTVFYQICEKDGLVK 77
                                      5555555555..........5677889999************99888888995599***************55666666 PP

                                      EEEE CS
                        ParE_toxin 80 ilrv 83
                                      il +
  gi|386003043|ref|YP_005921342.1| 78 ILEI 81
                                      9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 651.17
//
Query:       gi|386003044|ref|YP_005921343.1|  [L=61]
Description: hypothetical protein Mhar_2370 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-07   29.9   0.1    7.9e-07   29.8   0.1    1.1  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.052   13.7   0.1      0.061   13.5   0.1    1.2  1  MatP_C        MatP C-terminal ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   8.9e-11   7.9e-07       1      50 [.       5      52 ..       5      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.9e-11
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgils 50
                                      K + ++++v  +L++lKr+ge Fs ++e+++e++kk +   + +l  i +
  gi|386003044|ref|YP_005921343.1|  5 KRVAVTESVWAELSDLKRPGETFSQLLEEMIEREKKAR--LIAHLKTIAD 52
                                      7799****************************888764..4555555544 PP

>> MatP_C  MatP C-terminal ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.8e-06     0.061      12      46 ..      12      44 ..       4      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-06
                            MatP_C 12 avWqrLsklsqrrgsTLSetivqLieeaerkekye 46
                                      +vW  Ls l +r g T S+ ++++ie +e+k++  
  gi|386003044|ref|YP_005921343.1| 12 SVWAELSDL-KRPGETFSQLLEEMIE-REKKARLI 44
                                      79*****99.67899***99999997.45555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 431.13
//
Query:       gi|386003045|ref|YP_005921344.1|  [L=68]
Description: hypothetical protein Mhar_2371 [Methanosaeta harundinacea 6Ac]
Scores for 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-10   38.9   0.0    9.6e-10   38.6   0.0    1.0  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
    0.00077   19.4   0.0    0.00089   19.2   0.0    1.1  1  DUF1902          Domain of unknown function (DUF1902)
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.13   12.6   0.0    1.1  1  YnfE             Uncharacterized YnfE-like
       0.18   12.5   0.0       0.19   12.4   0.0    1.1  1  DUF3750          Protein of unknown function (DUF3750)


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   2.1e-13   9.6e-10       3      57 ..       4      58 ..       3      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 2.1e-13
                   HicB_lk_antitox  3 iaiekdedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipe 57
                                      ++i ++ed  +    P lpGc+s g + eeai+++keaie++  +l+edg  +pe
  gi|386003045|ref|YP_005921344.1|  4 VIIYPGEDGFWVAECPSLPGCISQGRSKEEAIEKIKEAIEVYTAALAEDGIPVPE 58
                                      6788899999999*************************************99996 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     2e-07   0.00089       6      43 ..       5      42 ..       3      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-07
                                      EEEETTTTEEEEE-SSSTT---EESSHHHHHHHHHHHH CS
                           DUF1902  6 vvwDeeAgVWvaesddipGlvteaetleeLlkkleami 43
                                      + + +e g Wvae+  +pG + +  + ee ++k++ +i
  gi|386003045|ref|YP_005921344.1|  5 IIYPGEDGFWVAECPSLPGCISQGRSKEEAIEKIKEAI 42
                                      578899****************************9988 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.9e-05      0.13      24      48 ..      30      54 ..      25      68 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                              YnfE 24 GkeeDlekqkeqlelYekqLkqess 48
                                       kee +ek ke +e+Y   L ++ +
  gi|386003045|ref|YP_005921344.1| 30 SKEEAIEKIKEAIEVYTAALAEDGI 54
                                      69***************99988754 PP

>> DUF3750  Protein of unknown function (DUF3750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.3e-05      0.19      53      90 ..      10      48 ..       4      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                           DUF3750 53 pdrsWfgnepelllel.rgekaeeliekiekavesYpya 90
                                      +d+ W+ + p+l   + +g++ ee+ieki++a+e Y  a
  gi|386003045|ref|YP_005921344.1| 10 EDGFWVAECPSLPGCIsQGRSKEEAIEKIKEAIEVYTAA 48
                                      6899********99888*******************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 412.23
//
Query:       gi|386003046|ref|YP_005921345.1|  [L=83]
Description: hypothetical protein Mhar_2372 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-05   22.5   0.0    0.00011   22.3   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   6.2e-09   0.00011       8      56 ..      19      67 ..      12      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.2e-09
                   HicB_lk_antitox  8 dedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeip 56
                                      d+++ y   vP+l+G++ +g+t ee  +n k aie ++   +  +  ip
  gi|386003046|ref|YP_005921345.1| 19 DDEQPYYGEVPELKGVWATGKTSEECRKNLKMAIEDWIALSLRFDLPIP 67
                                      788889999*****************************98777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 524.43
//
Query:       gi|386003047|ref|YP_005921346.1|  [L=96]
Description: hypothetical protein Mhar_2373 [Methanosaeta harundinacea 6Ac]
Scores for 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-07   29.5   0.1    1.2e-06   29.0   0.1    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
  ------ inclusion threshold ------
      0.033   14.2   0.2      0.043   13.8   0.2    1.2  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a


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 !   29.0   0.1   1.3e-10   1.2e-06       4      83 ..       8      81 ..       5      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.3e-10
                                      EHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE.CTSTC..CTTEEEEEEC.TEEEEEEEETSTTEE CS
                        ParE_toxin  4 tprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrp.rrelg..lkglrririg.dyriiYriddeelvv 78
                                       ++Alk l ++           ++    ++e++ +l e+p +g+  ++el+   ++l+r++ig  + ++Y+i + ++ v
  gi|386003047|ref|YP_005921346.1|  8 DRKALKYLSEL----------PEKSQRLIKEKCHALSEDPYPGQGaDKELLhlDYKLYRLHIGrSFTVFYQICEKDKLV 76
                                      56666666666..........56778999****************8888889*77*****************6566677 PP

                                      EEEEE CS
                        ParE_toxin 79 vilrv 83
                                      +il +
  gi|386003047|ref|YP_005921346.1| 77 KILEI 81
                                      79987 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 ?   13.8   0.2   4.8e-06     0.043       2      78 ..       6      83 ..       5      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-06
                   ParE-like_toxin  2 lqtrrfkkalkklkeklkadldkavkeiiedPelGeeKkGDLsgvfvykfkln.kqltllaYeldekkrvlvlllvGt 78
                                      +  r++ k+l+ l ek ++ ++++ +++ edP+ G+     L  +    ++l+ ++ + + Y++ ek++++++l + t
  gi|386003047|ref|YP_005921346.1|  6 VIDRKALKYLSELPEKSQRLIKEKCHALSEDPYPGQGADKELLHLDYKLYRLHiGRSFTVFYQICEKDKLVKILEITT 83
                                      6678899*****************************99999999977777765378899*********9*99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 632.90
//
Query:       gi|386003048|ref|YP_005921347.1|  [L=61]
Description: hypothetical protein Mhar_2374 [Methanosaeta harundinacea 6Ac]
Scores for complete 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-05   24.3   0.0    4.4e-05   24.2   0.0    1.1  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.5e-09   4.4e-05       3      49 ..       7      51 ..       5      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.5e-09
                      VAPB_antitox  3 IsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgil 49
                                        +++ v  +L++lKr+ge Fs ++ +++e++kk +   + +l  i 
  gi|386003048|ref|YP_005921347.1|  7 LAVTEPVWAELSDLKRPGETFSQLLAEMIEREKKARL--VVHLKSIA 51
                                      578999************************9987754..55555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 363.86
//
Query:       gi|386003049|ref|YP_005921348.1|  [L=618]
Description: hypothetical protein Mhar_2375 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-10   40.3   0.0    6.6e-10   39.3   0.0    1.5  1  SIR2_2    SIR2-like domain
     0.0085   16.0   0.0       0.19   11.6   0.0    2.6  2  SIR2      Sir2 family
  ------ inclusion threshold ------
      0.023   15.1   0.1      0.071   13.5   0.0    1.9  2  HAD       haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> SIR2_2  SIR2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.1e-13   6.6e-10       2     143 .]     136     269 ..     135     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.1e-13
                            SIR2_2   2 liiTTNYDdllekaleesgkpvsdaavskedlerelseaesgrtllyklhGslsrpesivltesdYeellarktpip 78 
                                       +i+TTN+D+l+ekal + g++   ++ + +d++    + + +r  ++k++G++    +i  t+++ e++    t+++
  gi|386003049|ref|YP_005921348.1| 136 VIVTTNFDHLIEKALDDVGIEPA-VVSNSSDVKG-ALPIPYERCTIIKVNGDYL-DTRIRNTRDELEKYG---TEMN 206
                                       89*********************.6777777777.9999**************5.5899******97776...8899 PP

                            SIR2_2  79 tllkallrskslLflGySfs.Dpnirelleellkesgn.arrhyaflpedekeeeekllekknievi 143
                                       +ll+ ++ +  l+ +G S + D    + l++++++ +n + + y+ +++++ e+ +kl+++++ evi
  gi|386003049|ref|YP_005921348.1| 207 KLLDRVFDEFGLIVCGWSAEwD----TALRKAIERRKNhRFTTYWAARDEPGERAHKLIRHRRAEVI 269
                                       99999999999*******8634....45555555555533334555555555999999999888776 PP

>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.051     3e+02       1      13 [.      33      45 ..      33      71 .. 0.79
   2 !   11.6   0.0   3.2e-05      0.19      43      90 ..     103     149 ..      86     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.051
                                      -GGGGGGGT---S CS
                              SIR2  1 GAGiStesGipdf 13
                                      G GiS esGi++ 
  gi|386003049|ref|YP_005921348.1| 33 GSGISQESGIRTA 45
                                      89********985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEEEEES-SSSHHHHT CS
                              SIR2  43 evfyniarellaeeaepnaaHkalkklekkgkllrliTQNiDgLekka 90 
                                       + f  + +e  +  + p++aHka++kl ++g    ++T N D+L +ka
  gi|386003049|ref|YP_005921348.1| 103 Y-FEPNEEEREQGLKVPTTAHKAIAKLVANGYIRVIVTTNFDHLIEKA 149
                                       3.66666666777889****************************9887 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.2e-05     0.071      85     135 ..     115     167 ..      84     201 .. 0.76
   2 ?   -2.7   0.1       1.1   6.5e+03      37      49 ..     233     245 ..     207     278 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                               HAD  85 lldp.galellaahraaGdrvvvvSgglrplvepllaelg.adevlatelevd 135
                                       l  p  a +++a+  a+G+  v+v+ ++++l+e  l+ +g   +v++++ +v+
  gi|386003049|ref|YP_005921348.1| 115 LKVPtTAHKAIAKLVANGYIRVIVTTNFDHLIEKALDDVGiEPAVVSNSSDVK 167
                                       333557888999888*************************7666777754444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                               HAD  37 klllalfrellrl 49 
                                       k+ + + ++++++
  gi|386003049|ref|YP_005921348.1| 233 KAIERRKNHRFTT 245
                                       3333332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3869.32
//
Query:       gi|386003050|ref|YP_005921349.1|  [L=894]
Description: cation-transporting ATPase [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-51  172.2   4.0    7.4e-51  172.2   4.0    3.1  3  E1-E2_ATPase     E1-E2 ATPase
    6.9e-45  153.0   0.5    6.9e-45  153.0   0.5    2.1  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.6e-20   74.3   4.7    7.5e-20   72.1   4.7    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.9e-19   69.1   0.5    6.3e-19   67.4   0.0    2.2  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    2.4e-15   56.4   0.0    4.4e-15   55.5   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    4.5e-05   23.3   0.4      0.003   17.4   0.3    2.3  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00022   21.7   0.3     0.0013   19.1   0.0    2.6  3  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
          2    8.5   6.4        1.2    9.2   0.3    2.5  3  PIG-F            GPI biosynthesis protein family Pig-F


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.069   1.5e+02     107     153 ..      46      92 ..      38      95 .. 0.75
   2 !  172.2   4.0   3.3e-54   7.4e-51       2     180 ..     112     302 ..     111     303 .. 0.98
   3 ?   -3.1   0.0       2.1   4.8e+03      93     135 ..     667     709 ..     662     721 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.069
                                       ---HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHH CS
                      E1-E2_ATPase 107 kktplqkkldklgkvlvpvvlliallvflialllgkslaeallrala 153
                                       k ++l  +l+++ ++l++v +++a++ +++  +++  ++  ++++++
  gi|386003050|ref|YP_005921349.1|  46 KPSKLRVFLRQFENYLIIVLIFAAAVSWIAGETTNAYAILGIIFFIS 92 
                                       56889999999999999999999999998876666655555555554 PP

  == domain 2  score: 172.2 bits;  conditional E-value: 3.3e-54
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............e 65 
                                       + +p+a+v+r+g+ ++i++++lvpGD+v l+agd+vpaDgr++e+++ +v es+LTGEs+p +k            +
  gi|386003050|ref|YP_005921349.1| 112 MVAPEANVLRSGKMTRIAVRDLVPGDVVYLEAGDKVPADGRVIEETSlQVVESSLTGESVPEDKsaavvaeetplaD 188
                                       7899***********************************************************************99 PP

                                       -TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTS CS
                      E1-E2_ATPase  66 kgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgk 142
                                       ++dmv++Gt+vv g+ +a Vtatg  telg+i  lv++  ++++p++ k + l+k+l++vvl++++++f++ + +g 
  gi|386003050|ref|YP_005921349.1| 189 RTDMVYMGTIVVYGNGRAAVTATGTRTELGRISGLVQRR-PEEPPIKIKFQHLAKQLAVVVLAACAIIFAVEVNRGA 264
                                       **************************************8.************************************* PP

                                       STTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 143 slaeallralallvaaiPcaLplavplalalgarrlak 180
                                       ++ ++l+ a al+vaaiP aLp +++++la+g++ +a 
  gi|386003050|ref|YP_005921349.1| 265 PVLDTLIIAAALAVAAIPTALPFITTITLAYGTQIMAG 302
                                       **********************************9985 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.1
                                       TTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase  93 elgkiarlveeakskktplqkkldklgkvlvpvvlliallvfl 135
                                        +++i+++vee ++  +++ k  + l +  ++ v++i++ v+l
  gi|386003050|ref|YP_005921349.1| 667 NFATIVAAVEEGRRIYSNIRKASSYLLSCNFAEVMTIFIGVML 709
                                       5778888888888888888888877777766666666666555 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   3.4e+03     177     177 ..      77      77 ..      26     100 .. 0.62
   2 ?   -3.4   1.2       2.9   6.5e+03     131     167 ..     246     282 ..     233     295 .. 0.51
   3 !  153.0   0.5   3.1e-48   6.9e-45       1     181 [.     712     883 ..     712     884 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                   Cation_ATPase_C 177 e 177
                                       e
  gi|386003050|ref|YP_005921349.1|  77 E 77 
                                       1 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                   Cation_ATPase_C 131 aillslllqvlivyvpglnavfgtaplsleewliall 167
                                       +++l++  +++ v v  ++ v++t  + +   + a++
  gi|386003050|ref|YP_005921349.1| 246 VVVLAACAIIFAVEVNRGAPVLDTLIIAAALAVAAIP 282
                                       3333334455555555555555555554444444444 PP

  == domain 3  score: 153.0 bits;  conditional E-value: 3.1e-48
                   Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfg 77 
                                       p pl a+qiLwin+vtD +pa+ La+ep+++d+mk++Pr++kep++++++++++l++++++++ tl +++ +l   g
  gi|386003050|ref|YP_005921349.1| 712 PVPLIALQILWINIVTDEFPAIGLAVEPAHSDLMKNKPRDPKEPILTRGLFLYTLGISTVIFIGTLGLYANALR-GG 787
                                       78*******************************************************************55554.55 PP

                   Cation_ATPase_C  78 isekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgt 154
                                       +  +e       a+t++F +lv+++i na+n+rs+++s+fk +  ++n  l+l++++sl+ +++ +y p+++++f+t
  gi|386003050|ref|YP_005921349.1| 788 APLEE-------ARTTVFASLVIFEIYNAYNSRSLHTSFFK-MDPRTNGKLILGLIASLGALLVAIYHPWMQRLFET 856
                                       55555.......*****************************.999******************************** PP

                   Cation_ATPase_C 155 aplsleewlialllalvvllvdelvKl 181
                                       apl++ +w+ +++ a++v++v+e++K+
  gi|386003050|ref|YP_005921349.1| 857 APLDAGSWAAIVVAASAVVVVAEIFKR 883
                                       *************************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   4.7   3.3e-23   7.5e-20       2     210 .]     320     642 ..     319     642 .. 0.73

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 3.3e-23
                                       SEEEEESBTTTBCHHHHHHHHHHHH.....................................CHHHHHHHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxx.... RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.....................................alalaaaletg.... 37 
                                       ++++ Dk+GTLt+ge+ v++++  +                                     al+ +  le g    
  gi|386003050|ref|YP_005921349.1| 320 TVICTDKTGTLTRGEMMVRKIWTGRevevtgtgydpagtfrregddlnpsedghlsallvagALCNNSRLEEGsdgw 396
                                       5899*********************7777777777777777777777777766555555555555555555557777 PP

                                       ..HHCHHHHHH.HHHHHHH......HHHHHHHHHETTTE................HHHHTHHHHHHHH..HCHHHHH CS
                                       ..xxxxxxxxx.xxxxxxx......xxxxxxxxxxxxxx................xxxxxxxxxxxxx..xxxxxxx RF
                         Hydrolase  38 ..sehpigkal.vaaakar......sgaltgfatfigrg................ayaigkpewltal..dippdlg 87 
                                            p   al vaa k++      ++ l+++ +f+                   + ++g pe + a          
  gi|386003050|ref|YP_005921349.1| 397 nvIGDPTEGALiVAASKGEildyveGWYLEEVVEFPFDSemrrmttvhrssdgltVSMKGAPETVLAFstR------ 467
                                       77666666666666666666665554444444444433366667766777777776666666655555331...... PP

                                       HHHHHHHHHCHHHHHH....................................................TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxx....................................................xxxxxxxxx RF
                         Hydrolase  88 aaigsaqsqgrtvall....................................................qaralavft 112
                                                                                                           +   l+++ 
  gi|386003050|ref|YP_005921349.1| 468 ---------------ImrdgseepitsedllraskaademagsglrilalagkvmapgaplgrdaveaDLTFLGLVG 529
                                       ...............022222222222222334444456666666666666***********999988889999999 PP

                                       HHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..............GGGESEEEEHHCES...ST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxx...xx RF
                         Hydrolase 113 iadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..............ddyfdaviasdiet...va 172
                                       + dp  +++ea+ea++   +agi+ v++tgd++ ta ++ ++lG              d+  + ++a  ie+   ++
  gi|386003050|ref|YP_005921349.1| 530 MMDP--PREEAKEAIKVCEKAGIRPVMITGDHKLTASAIGRELGilneggrvlegtelDEMTAEELAEMIEEvsiFS 604
                                       99**..******************************************99999998854444777777777789999 PP

                                       TTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 173 kpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                           e+kv++++ L+ k++ vam GDgvnD +al+ A+
  gi|386003050|ref|YP_005921349.1| 605 RTTAEQKVRIVEALRRKGHIVAMTGDGVNDGPALRSAD 642
                                       99***************999****************98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   2.8e-22   6.3e-19       1      69 []       5      72 ..       5      72 .. 0.99
   2 ?   -1.9   0.1       1.2   2.7e+03      41      68 ..     227     255 ..     224     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.8e-22
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      +h+l+++e+le+L  ++ +GL+++eaa+rl++ GpN+l+e  k+s ++ +l+qf n l+i+L++aa+vs
  gi|386003050|ref|YP_005921349.1|  5 WHTLTADETLERLS-SSRDGLSSEEAARRLSEQGPNQLEEFYKPSKLRVFLRQFENYLIIVLIFAAAVS 72
                                      9************6.9***************************************************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                   Cation_ATPase_N  41 kkkkslwvkllkqf.tnplvilLlvaalv 68 
                                       +++++ +++ ++++ +++ v +L ++a++
  gi|386003050|ref|YP_005921349.1| 227 RPEEPPIKIKFQHLaKQLAVVVLAACAII 255
                                       56777777777777699999999999998 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0     2e-18   4.4e-15       1      90 [.     382     467 ..     382     468 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2e-18
                     Cation_ATPase   1 ilcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyv 77 
                                       +lcN++++  ++  d ++++G++tE AL+v+a+k ++         ++v e+pF+s+ +rm++v++   + ++++ +
  gi|386003050|ref|YP_005921349.1| 382 ALCNNSRL--EEGSDGWNVIGDPTEGALIVAASKGEILDYVEGWYLEEVVEFPFDSEMRRMTTVHRS--SDGLTVSM 454
                                       69******..99999*******************954444444567999*****************5..6******* PP

                     Cation_ATPase  78 KGApeiilkrCth 90 
                                       KGApe +l+ +t+
  gi|386003050|ref|YP_005921349.1| 455 KGAPETVLAFSTR 467
                                       ********98775 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.02        45      18      54 ..     536     572 ..     528     603 .. 0.85
   2 !   17.4   0.3   1.3e-06     0.003     196     248 ..     615     668 ..     608     675 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgl 54 
                                       e++keaik ++++gi  v  TG +  +++ + +elg+
  gi|386003050|ref|YP_005921349.1| 536 EEAKEAIKVCEKAGIRPVMITGDHKLTASAIGRELGI 572
                                       799*******************999999999999885 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGG CS
                       Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnne 248
                                       ++ l+ +   v+  GDg ND + L  a++gvAmg  ++e  k+a+d+v+++ n 
  gi|386003050|ref|YP_005921349.1| 615 VEALRRKGHIVAMTGDGVNDGPALRSADIGVAMGRtGTEVSKEASDMVIADDNF 668
                                       56666666778889*******************972555557788889988775 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       6.8   1.5e+04      58      95 ..      17      55 ..       7      65 .. 0.46
   2 !   19.1   0.0   5.9e-07    0.0013      86     188 .]     531     639 ..     487     639 .. 0.69
   3 ?   -2.9   0.0       3.3   7.4e+03      85     118 ..     845     880 ..     801     883 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.8
                               HAD 58 leallagls.eelaaelerfvaevirpklldp.galella 95
                                      l++   gls ee a++l + +  ++++ +++p +++ +l+
  gi|386003050|ref|YP_005921349.1| 17 LSSSRDGLSsEEAARRLSEQGP-NQLEEFYKPsKLRVFLR 55
                                      4444445554444444444442.22222344444444444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.9e-07
                               HAD  86 ldp...galellaahraaGdrvvvvSgglrplvepllaelgadevlat..elevdd...rltge...lglegkpvrg 151
                                       +dp   +a+e+++ + +aG+r v+++g ++  + ++ +elg   +l++  ++ +      +t+e     +e+ +++ 
  gi|386003050|ref|YP_005921349.1| 531 MDPpreEAKEAIKVCEKAGIRPVMITGDHKLTASAIGRELG---ILNEggRVLEGTeldEMTAEelaEMIEEVSIFS 604
                                       555566*******999*************************...433333222222344344444431133334443 PP

                               HAD 152 ....egkvaalrewlaaegegidleevvay.GDspsDlpllr 188
                                           e+kv+ +++   +++ +     +va  GD+++D p+lr
  gi|386003050|ref|YP_005921349.1| 605 rttaEQKVRIVEA--LRRKGH-----IVAMtGDGVNDGPALR 639
                                       3343577766666..333333.....66666******99997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.3
                               HAD  85 lldpgalella.ahraaGd.rvvvvSgglrplvepl 118
                                       +++p + +l++ a ++aG    +vv ++   +v ++
  gi|386003050|ref|YP_005921349.1| 845 IYHPWMQRLFEtAPLDAGSwAAIVVAASAVVVVAEI 880
                                       578999999998888665558888888877777666 PP

>> PIG-F  GPI biosynthesis protein family Pig-F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.2       7.5   1.7e+04      76     108 ..      62      94 ..      52     102 .. 0.65
   2 ?    9.2   0.3   0.00055       1.2      48     108 ..     229     288 ..     166     323 .. 0.67
   3 ?    2.3   0.1     0.071   1.6e+02       8      95 ..     691     799 ..     685     820 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 7.5
                             PIG-F  76 illvlfGApllthlleTlllalhlslltvlpll 108
                                       i++++f A +   + eT+   + l ++ ++ l+
  gi|386003050|ref|YP_005921349.1|  62 IIVLIFAAAVSWIAGETTNAYAILGIIFFISLV 94 
                                       455566666666666777666666666666555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00055
                             PIG-F  48 kkkskkskivlallsllltlllatlllaillvlfGApllthlleTlllalhlslltvlpll 108
                                       ++  +k k+ ++ ++l +++l+a+ +++++ v  GAp+l+ l   + la+  ++ t+lp +
  gi|386003050|ref|YP_005921349.1| 229 EEPPIKIKFQHLAKQLAVVVLAACAIIFAVEVNRGAPVLDTLIIAAALAVA-AIPTALPFI 288
                                       336778888999999999********************8876655554442.223333333 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.071
                             PIG-F   8 allalrfsalvadpvstLlsslivlallqvlyvvlcl....................ekkkk.....kskkskivla 59 
                                       +ll  +f  +++  + ++l   ++l++lq+l++ +++                    +            ++ ++l 
  gi|386003050|ref|YP_005921349.1| 691 YLLSCNFAEVMTIFIGVMLGLPVPLIALQILWINIVTdefpaiglavepahsdlmknK---PrdpkePILTRGLFLY 764
                                       5666788888888899999999999999999999999888888888877776654321...1223333444455555 PP

                             PIG-F  60 llsllltlllatlllaillvlfGApllthlleTlll 95 
                                        l +  +++++tl l++ ++  GApl +   +T++ 
  gi|386003050|ref|YP_005921349.1| 765 TLGISTVIFIGTLGLYANALRGGAPLEEAR-TTVFA 799
                                       555555666899999999999999986543.34443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 5488.62
//
Query:       gi|386003051|ref|YP_005921350.1|  [L=144]
Description: hypothetical protein Mhar_2377 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-29  101.8   0.0      3e-29  101.5   0.0    1.0  1  UPF0146   Uncharacterised protein family (UPF0146)


Domain annotation for each model (and alignments):
>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   0.0   1.7e-33     3e-29       8     126 ..      13     130 ..       8     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 1.7e-33
                                       HHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HHHHTTEEEEEEES--TTSH CS
                           UPF0146   8 iaeenargkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnleiYkgadliYslRpPaelq 84 
                                       ++   + gkvvEvGiG+ ++va +l  +  ++vatD + + a  g+ iv DD+++P l++Y+ga+liYs+RpP e+q
  gi|386003051|ref|YP_005921350.1|  13 FILARYSGKVVEVGIGAAPEVALLLVPQ-REVVATDKVGR-ALGGMAIVGDDIFSPSLDLYRGASLIYSIRPPLEIQ 87 
                                       44478899***************99988.8******8877.999********************************* PP

                                       HHHHHHHHHHT-EEEEE-BTTB-----T.T-EEEEETTEEEEE CS
                           UPF0146  85 saildvakkvgAaliikpLlgedvvvek.elklvnykgalFyi 126
                                        a+ ++akkvgA+++++pL++e   ++  +  lvn + a Fy+
  gi|386003051|ref|YP_005921350.1|  88 LAMGRLAKKVGAEVMVRPLGDEIASIPGfRRTLVNSGEAWFYL 130
                                       ********************99987765144567888888986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       151  (0.00842211); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 989.93
//
Query:       gi|386003052|ref|YP_005921351.1|  [L=259]
Description: Ribose 1,5-bisphosphate isomerase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-79  266.6   3.6    1.6e-79  266.4   3.6    1.0  1  Thi4           Thi4 family
    1.9e-05   24.2   2.2    2.7e-05   23.7   2.2    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    0.00033   20.0   0.7    0.00056   19.2   0.6    1.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00034   20.8   0.4     0.0015   18.7   0.4    2.1  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0044   15.8   2.0     0.0064   15.2   2.0    1.2  1  HI0933_like    HI0933-like protein
     0.0071   15.5   0.0      0.013   14.7   0.0    1.4  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
       0.01   15.1   0.1      0.014   14.7   0.1    1.4  1  FAD_binding_3  FAD binding domain
      0.012   14.7   1.2      0.012   14.7   1.2    2.7  3  FAD_binding_2  FAD binding domain
      0.094   11.7   2.1       0.11   11.6   0.2    1.9  3  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.4   3.6   8.1e-83   1.6e-79       1     235 []       9     239 ..       9     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 266.4 bits;  conditional E-value: 8.1e-83
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       ++aive+y++ +lky + Dv++vGaG++ L aa+ la++ d k++++er++++GGG+w+GG++f +ivv+k++  +L
  gi|386003052|ref|YP_005921351.1|   9 TKAIVESYMDSFLKYTDVDVALVGAGPANLVAAKKLAEA-DAKTVVFERNLAVGGGIWGGGMMFPRIVVQKEGCRIL 84 
                                       79*************************************.************************************* PP

                                       HHTT---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS.- CS
                              Thi4  78 delgikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqscv 152
                                       de+g+ y ++ ++++++ +++ +++l++ v++ a++ ++n vaveD+++re+e+vaG+vinw +ve++  h     v
  gi|386003052|ref|YP_005921351.1|  85 DEFGVWYREYAEGYYIASSIETVAKLTAGVVD-AGAEIINLVAVEDVMIREDERVAGLVINWEAVERTrlH-----V 155
                                       ********************************.*********************************99777.....* PP

                                       B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTT.TS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT- CS
                              Thi4 153 DPlvirakvvvdatGhdgeivavvvkkikleak.iekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdga 228
                                       DPl +rakvv+d tGhd++i +vv++ki  ++     v+gek+++a+++e+++v+ t+ev+p+l++aGm++++v g+
  gi|386003052|ref|YP_005921351.1| 156 DPLSVRAKVVIDGTGHDANICKVVQRKIPGARVgSLGVPGEKPMWADVGERTVVEVTQEVYPGLIAAGMAATAVAGG 232
                                       ****************************7766415579*************************************** PP

                                       EB--SB- CS
                              Thi4 229 nRmGpif 235
                                       +RmGpif
  gi|386003052|ref|YP_005921351.1| 233 PRMGPIF 239
                                       ******9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.2   1.4e-08   2.7e-05       1     144 [.      27     170 ..      27     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq..rgga.r 74 
                                       Dv  vG+gpa ++AA   a+a+ak+++ e++  +GG   +g+++ +    ++e    +i +ef    r+  +g++  
  gi|386003052|ref|YP_005921351.1|  27 DVALVGAGPANLVAAKKLAEADAKTVVFERNLAVGGGIWGGGMMFPRIVVQKE--GCRILDEFGVWYREyaEGYYiA 101
                                       9**********************************999998876666544333..3446666655555542344431 PP

                      FAD_oxidored  75 lk..krskw.ntfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.grktirAkvfiDATg 144
                                        +  ++ ++ ++  +++ +++++ +  e +v +  ++r+ + + + + +e  ++         +rAkv+iD+Tg
  gi|386003052|ref|YP_005921351.1| 102 -SsiETVAKlTAGVVDAGAEIINLVAVE-DVMIREDERVAGLVINWEAVERTRL---HvDPLSVRAKVVIDGTG 170
                                       .222333333456677777777766666.8888888888888887434444444...43599***********8 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.6   2.8e-07   0.00056       2      48 ..      27      77 ..      26     192 .. 0.71
   2 ?   -1.0   0.0       0.4   7.9e+02     123     167 ..     138     205 ..     108     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.8e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallg 48
                                      dv+ +G+GpA l aa++la+a ak++++e     +g + +gg++ + ++++
  gi|386003052|ref|YP_005921351.1| 27 DVALVGAGPANLVAAKKLAEADAKTVVFErnlaVGGGIWGGGMMFPRIVVQ 77
                                      89**************************76676555555555554444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.4
                                       BEECCSECHHHHHHCCSS-T....SEEEEES-SHHHHHHHHHHHHH.T-..................E CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx.xx..................x RF
                       Pyr_redox_2 123 vgklvrtldsaealklkllp....krivvvGgGyiGvElAaalakl.gk..................e 167
                                       v  lv +++ +e+ +l+  p    +++v+ G G  +  +  +++k+ g+                  e
  gi|386003052|ref|YP_005921351.1| 138 VAGLVINWEAVERTRLHVDPlsvrAKVVIDGTGHDANICKVVQRKIpGArvgslgvpgekpmwadvgE 205
                                       44555555555666666666555555565565555555555554444444444444444444444444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.4   7.6e-07    0.0015       2      33 ..      31      62 ..      30      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      vGaG + lvaA  La+a+++ +++e++  +GG
  gi|386003052|ref|YP_005921351.1| 31 VGAGPANLVAAKKLAEADAKTVVFERNLAVGG 62
                                      9**************************99998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.0   3.2e-06    0.0064       2      38 ..      27      63 ..      26      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      dv+ +G+G+A l aA ++a+++++++++e++ ++g  
  gi|386003052|ref|YP_005921351.1| 27 DVALVGAGPANLVAAKKLAEADAKTVVFERNLAVGGG 63
                                      899***************************9998865 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.4e-06     0.013       3      53 ..      26      77 ..      24      79 .. 0.88
   2 ?   -3.7   0.0       2.6   5.2e+03     145     167 ..     158     180 ..     135     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.4e-06
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpefa...Whpgmllegaelq 53
                                      +D++ +G+Gp+nL  a  l+e++   k++++er+ +++   W  gm+++   +q
  gi|386003052|ref|YP_005921351.1| 26 VDVALVGAGPANLVAAKKLAEAD--AKTVVFERNLAVGggiWGGGMMFPRIVVQ 77
                                      69***********9999999999..9*******99875555******9988777 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.6
                       K_oxygenase 145 eelearnlvlgvGtepkiPevle 167
                                        +++a+ ++ g+G  ++i +v++
  gi|386003052|ref|YP_005921351.1| 158 LSVRAKVVIDGTGHDANICKVVQ 180
                                       46778888888888888877766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   6.9e-06     0.014       1      33 [.      25      57 ..      25     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.9e-06
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      ++dV+ VGaGpa l++a+ L+ea  ++v+ e+ 
  gi|386003052|ref|YP_005921351.1| 25 DVDVALVGAGPANLVAAKKLAEADAKTVVFERN 57
                                      689********************9999999985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.2   6.2e-06     0.012       1      43 [.      27      68 ..      27      80 .. 0.85
   2 ?    3.3   0.1     0.017        35     143     203 ..     106     173 ..      94     196 .. 0.75
   3 ?   -0.8   0.1       0.3   6.1e+02     388     412 ..     212     235 ..     204     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.2e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                      Dv  +G+G A L+AA ++aea +k++v e   ++gg + w +G
  gi|386003052|ref|YP_005921351.1| 27 DVALVGAGPANLVAAKKLAEADAKTVVFERNLAVGGGI-WGGG 68
                                      899**************************998877754.5444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHTCTEEEEESEEEEEEEE.CTTEEEEEEEEETTTTCEE......EEEESEEEE-----G CS
                     FAD_binding_2 143 llarlvesarkagvdfqerteadeLiv.edgrvtGavvenpesgrev......rirakavvlatgGfg 203
                                        +a l +++ +ag ++ +  +++++++ ed+rv G v++ ++ +r++       +rak v++ tg   
  gi|386003052|ref|YP_005921351.1| 106 TVAKLTAGVVDAGAEIINLVAVEDVMIrEDERVAGLVINWEAVERTRlhvdplSVRAKVVIDGTGHDA 173
                                       5788899999999*********998774788******9977444444456776777777777777555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.3
                                       EEESSBTEEE-STCEESSSSTTS-- CS
                     FAD_binding_2 388 dgqpipGLYAaGevaaggvhganrl 412
                                       ++++ pGL AaG +a + v g  r+
  gi|386003052|ref|YP_005921351.1| 212 TQEVYPGLIAAGMAA-TAVAGGPRM 235
                                       678899******999.777776665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   5.4e-05      0.11       1      24 [.      27      50 ..      27      59 .. 0.83
   2 ?   -2.7   0.0       1.1   2.3e+03     273     296 ..      97     120 ..      95     153 .. 0.69
   3 ?   -1.1   0.1      0.38   7.6e+02     125     140 ..     155     170 ..     119     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpg 24
                                      Dv+++GaGpA+l  A++l+ea ++
  gi|386003052|ref|YP_005921351.1| 27 DVALVGAGPANLVAAKKLAEADAK 50
                                      9*****************666544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                     Lycopene_cycl 273 GYsvarslaeapllasaiaaalre 296
                                       GY +a s+    +l++ +++a++e
  gi|386003052|ref|YP_005921351.1|  97 GYYIASSIETVAKLTAGVVDAGAE 120
                                       888888888877788888777764 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.38
                     Lycopene_cycl 125 eggrkirarlvvdarg 140
                                        +   +ra++v+d++g
  gi|386003052|ref|YP_005921351.1| 155 VDPLSVRAKVVIDGTG 170
                                       4445899999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 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:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1554.31
//
Query:       gi|386003053|ref|YP_005921352.1|  [L=335]
Description: cell division protein FtsZ [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-18   65.4   0.5      1e-17   64.2   0.2    1.9  2  FtsZ_C    FtsZ family, C-terminal domain


Domain annotation for each model (and alignments):
>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.62   1.1e+04      46      64 ..     173     191 ..     170     197 .. 0.72
   2 !   64.2   0.2   5.7e-22     1e-17       1      94 [.     221     314 ..     221     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.62
                                       -TT--HHHHHHHHHHHHHH CS
                            FtsZ_C  46 gsdltlkEveevaetiree 64 
                                       ++ l+ +E+++v++++  e
  gi|386003053|ref|YP_005921352.1| 173 APGLSAEEASSVMDQVVAE 191
                                       5667788888888877655 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 5.7e-22
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       G A   vGe+  ed  e+a+++a+++p+L++dl+ Akg ++ itgg+dltl+ + ++a++++  + +ea++++Ga++
  gi|386003053|ref|YP_005921352.1| 221 GLASALVGESGCEDGPEAAVRSALRNPMLEADLQRAKGCILTITGGRDLTLRKAAAIASALKGVLGPEAELVWGARL 297
                                       788999*********************************************************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                       +e  e+++   + + g+
  gi|386003053|ref|YP_005921352.1| 298 KEGHEGKVGLLATIVGV 314
                                       ******99988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2178.43
//
Query:       gi|386003054|ref|YP_005921353.1|  [L=437]
Description: UbiD family decarboxylase [Methanosaeta harundinacea 6Ac]
Scores for 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-99  331.4   0.0    8.1e-99  331.2   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.2   0.0  4.5e-103   8.1e-99       2     405 ..      21     393 ..      20     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 331.2 bits;  conditional E-value: 4.5e-103
                                       HHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHH CS
                              UbiD   2 ealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeilek 78 
                                        al++ag+l +++++v+p lE+a++   +       llF+nv+gk    ++ +nl+gtr+ +a+alg+   e+++++
  gi|386003054|ref|YP_005921353.1|  21 HALQEAGHLEEVDRPVSPSLEAAALSVGAG-----PLLFNNVDGK----KCCMNLLGTRDLLARALGIP-REDMAKA 87 
                                       689***********************9998.....9******544....8*****************85.4888888 PP

                                       HHHHHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEE CS
                              UbiD  79 laellepkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqv 155
                                       lae+         ++v+s   p++e v     ++dL+ LP+lt+++gDgGpyit+g+v++    +gk+n++++Rm+v
  gi|386003054|ref|YP_005921353.1|  88 LAEIDLA--GGWIREVDS--SPFMEAV----GEPDLTALPILTHFRGDGGPYITSGIVVSA--FGGKTNASVHRMMV 154
                                       8887443..367899965..8999777....46**************************97..69************ PP

                                       EETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSS CS
                              UbiD 156 ldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetv 232
                                       l+k++++ +++++++  + l++a+++g e+lpv ++iGvdP++++aA++++P g+ E+++a+al+g+pvelv    +
  gi|386003054|ref|YP_005921353.1| 155 LGKDRVAARLVPGRHTSMLLQEALAAG-ERLPVGIVIGVDPLVLIAASTRVPLGM-EFQYASALSGSPVELVAL-DN 228
                                       ***************************.9***********************886.9***************88.66 PP

                                       SSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHH CS
                              UbiD 233 dlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkale 309
                                       ++ vp +AEi +eG+id  e+a EGPf+d+tG+ + +r+e pv++++++++R+ piy+++++    e+++l+g+++e
  gi|386003054|ref|YP_005921353.1| 229 GVFVP-SAEIAFEGYIDG-ERASEGPFVDITGTRDFPRME-PVIHLSKMMTREVPIYHALLPSGG-EHKMLMGVPYE 301
                                       9****.9**********8.79*************999986.*****************9977777.*********** PP

                                       HHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHH CS
                              UbiD 310 alflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevl 386
                                       +l++++ ++ v evk+v l+e g+++l+a+v+ikkr + +  kv++a++++++  sl K+vivvDedvd+++++e++
  gi|386003054|ref|YP_005921353.1| 302 PLIFRAASE-VAEVKNVLLTEGGCSYLHAAVQIKKRSEAEPGKVIDAAFEAHK--SL-KHVIVVDEDVDIYSPEELE 374
                                       *******55.889**************************************99..99.******************* PP

                                       HHHHHC--CCCCEEEECCC CS
                              UbiD 387 waiatrvdpdrDlviiegt 405
                                       +a+atrv+ d+D+v+++++
  gi|386003054|ref|YP_005921353.1| 375 YAVATRVKGDEDMVLYPNV 393
                                       ***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2959.93
//
Query:       gi|386003055|ref|YP_005921354.1|  [L=235]
Description: hypothetical protein Mhar_2381 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-57  193.9  15.6    2.1e-57  193.9  15.6    1.4  2  DUF1614   Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       0.4   7.1e+03      93     110 ..      11      28 ..       8      40 .. 0.53
   2 !  193.9  15.6   1.2e-61   2.1e-57       1     170 []      56     234 ..      56     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.4
                           DUF1614  93 Givvpllipplvaalaal 110
                                       Gi   ll++ l+ a +al
  gi|386003055|ref|YP_005921354.1|  11 GILAILLLALLLWASVAL 28 
                                       444444555555555543 PP

  == domain 2  score: 193.9 bits;  conditional E-value: 1.2e-61
                           DUF1614   1 llgslinipvaelkskeelve...vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaalla 74 
                                       llg  inip+ +l+sk+++v+   v+ +g+ y+vpv+++ +++t+vavNvGGa++P+l+s+yll++++++++ al++
  gi|386003055|ref|YP_005921354.1|  56 LLGAGINIPLFTLESKVPVVKeafVRSFGMVYRVPVVKTVKNETTVAVNVGGALLPVLVSVYLLISYPAAAAVALAG 132
                                       7899***********998744489********************************************99******* PP

                           DUF1614  75 vlivaavvyllarpvpgvGivvpllipplvaalaalllaeeea......aavaYisgvlGtLiGadllnlkkieklg 145
                                       ++iva+v++++arp++g+Gi++pl+ippl+aa++alll+   +      +++aY++gvlGtLiGadllnl +i++lg
  gi|386003055|ref|YP_005921354.1| 133 TAIVALVTHAVARPIRGLGIATPLFIPPLTAAASALLLTAVLSpipegrFVTAYVGGVLGTLIGADLLNLPRISELG 209
                                       ***********************************77776666688888**************************** PP

                           DUF1614 146 apvvsIGGaGtFdGifltgilavll 170
                                       apv+sIGGaGtFdGifltg++avl+
  gi|386003055|ref|YP_005921354.1| 210 APVASIGGAGTFDGIFLTGVIAVLI 234
                                       ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1567.70
//
Query:       gi|386003056|ref|YP_005921355.1|  [L=269]
Description: Nucleotide-binding protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-92  309.1   0.0    2.4e-92  308.9   0.0    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    3.2e-13   49.9   0.0    7.4e-13   48.7   0.0    1.7  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    8.1e-12   45.4   0.6    6.6e-11   42.4   0.6    2.0  1  AAA_31       AAA domain
    8.6e-07   28.4   0.1      2e-06   27.2   0.2    1.6  2  ArsA_ATPase  Anion-transporting ATPase
    5.8e-05   22.5   0.1     0.0001   21.7   0.1    1.4  1  MipZ         ATPase MipZ
    0.00094   18.8   0.1     0.0015   18.2   0.1    1.3  1  AAA_25       AAA domain
     0.0083   15.6   0.1      0.014   14.8   0.1    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.009   15.3   0.0      0.015   14.6   0.0    1.2  1  VirC1        VirC1 protein
  ------ inclusion threshold ------
       0.02   14.4   0.3       0.14   11.6   0.3    1.9  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      0.022   14.7   0.4      0.034   14.1   0.4    1.3  1  RsgA_GTPase  RsgA GTPase
      0.023   14.3   0.3      0.037   13.7   0.3    1.3  1  SRP54        SRP54-type protein, GTPase domain
      0.044   13.7   0.1      0.063   13.2   0.1    1.2  1  APS_kinase   Adenylylsulphate kinase
      0.051   12.7   0.4      0.072   12.3   0.4    1.2  1  NB-ARC       NB-ARC domain
      0.059   12.8   0.1       0.11   12.0   0.1    1.4  1  PhoH         PhoH-like protein
       0.14   11.9   0.0       0.26   11.1   0.0    1.4  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
        0.4   10.6   0.8       0.61   10.0   0.8    1.2  1  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.9   0.0   2.1e-95   2.4e-92       2     245 ..       9     257 ..       8     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 308.9 bits;  conditional E-value: 2.1e-95
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs..ekkliPvea.....k 71 
                                       +k+ i+v+SgKGGVGK+tvavnlAl La +g++vg+lDaDi+Gp++p++l++e++  + +  +++++P e      +
  gi|386003056|ref|YP_005921355.1|   9 IKHRIMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADITGPNVPKMLKIEDAFLTGEgeDETIHPAEIpigldS 85 
                                       89****************************************************87766665667889998888899 PP

                              ParA  72 gikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqev 148
                                       gikv+S++fl+  ++++vvwrGp+k++++kq+++ v+wg+lDy++iDlPPGtgDe l++aq l+ +g+viVttpq++
  gi|386003056|ref|YP_005921355.1|  86 GIKVVSMAFLIG-RESPVVWRGPLKMQILKQFIEGVAWGDLDYMLIDLPPGTGDEPLSIAQLLRPDGTVIVTTPQDL 161
                                       ***********9.**************************************************************** PP

                              ParA 149 aladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkpl 225
                                       al+d++kai+m +++ v+vlG+veNmsgf+cp+cg ++++f+ ggg ++aeel vp+lg+i +dp+i++++d+g+p+
  gi|386003056|ref|YP_005921355.1| 162 ALIDARKAIDMSRSLGVPVLGIVENMSGFTCPRCGGSIDLFKVGGGMRAAEELAVPFLGRIGIDPAICDSGDRGTPF 238
                                       ****************************************************************************9 PP

                              ParA 226 vlkepeseaakaleeiaekv 245
                                       +l+   s+ a+a++ i++k+
  gi|386003056|ref|YP_005921355.1| 239 ILAV-ASKNAEAFDGIVRKI 257
                                       9986.789999*****9998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   6.6e-16   7.4e-13       1     126 [.      13     236 ..      13     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 6.6e-16
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+++s+kGGvGKTt+a+nLa  la  g++V  +DaD  ++n    + l+++ +                        
  gi|386003056|ref|YP_005921355.1|  13 IMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADITGPNVP--KMLKIEDAFltgegedetihpaeipigldsgi 87 
                                       89***************************************99..444444444556666667899*****999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|386003056|ref|YP_005921355.1|  88 kvvsmafligrespvvwrgplkmqilkqfiegvawgdldymlidlppgtgdeplsiaqllrpdgtvivttpqdlali 164
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 dlkrllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqry.gvpvlgviprdeavaeaparge 126
                                       d+ + + + ++lg +  +l    ++ g+   r +g+  + l k +   + ++  +vp+lg i  d a+ ++  rg 
  gi|386003056|ref|YP_005921355.1| 165 DARKAIDMSRSLGVP--VLgivENMSGFTCPRCGGS--IDLFKVGGGMRAAEElAVPFLGRIGIDPAICDSGDRGT 236
                                       888888888888855..4445667777777777777..66666543333322237777777777777777777665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.6   5.9e-14   6.6e-11       4     158 ..      13     167 ..      10     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.9e-14
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekneiektlyevlieeknikeaiiktkve 79 
                                       I ++  KGGvGKTT +vnla  la +gk v + D+D  + n    l+     ie  +++   e+++i+ a i    +
  gi|386003056|ref|YP_005921355.1|  13 IMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADITGpNVPKMLK-----IEDAFLTGEGEDETIHPAEIPIGLD 84 
                                       889999******************************87735555555.....5667777766778888887766766 PP

                            AAA_31  80 nldlipssidLaeaeielvelekk.eeilkellekvk.deYDyiiiDcpPsLg..lltenaLvasdsviipvqaeay 152
                                       +   ++s   L++ e  +v       +ilk+++e v   + Dy++iD pP  g   l +  L+  d  +i++ ++++
  gi|386003056|ref|YP_005921355.1|  85 SGIKVVSMAFLIGRESPVVWRGPLkMQILKQFIEGVAwGDLDYMLIDLPPGTGdePLSIAQLLRPDGTVIVTTPQDL 161
                                       66667888889999888876665427779*****998468**********99744699999***************9 PP

                            AAA_31 153 aleGle 158
                                       al  ++
  gi|386003056|ref|YP_005921355.1| 162 ALIDAR 167
                                       997665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   1.8e-09     2e-06       1      38 [.      11      48 ..      11      64 .. 0.92
   2 ?   -3.6   0.0       4.2   4.7e+03     210     243 ..     153     186 ..     149     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.8e-09
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +++++++GKGGVGKttv+  +a+ l+ +gk+v ++  D
  gi|386003056|ref|YP_005921355.1| 11 HRIMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDAD 48
                                      5899**************************99888766 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.2
                                       EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                       ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivN 243
                                       ++V++p  l+l + ++ai    ++g+ v  ++ N
  gi|386003056|ref|YP_005921355.1| 153 VIVTTPQDLALIDARKAIDMSRSLGVPVLGIVEN 186
                                       6899999999999999999888888888777655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   9.3e-08    0.0001       1      40 [.      11      50 ..      11      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.3e-08
                                      EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                      h+i++   kGG Gk+t+av +a  L+ +G++v+ +d d+ 
  gi|386003056|ref|YP_005921355.1| 11 HRIMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADIT 50
                                      7899999*****************************9975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.3e-06    0.0015      32      63 ..      10      42 ..       4      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                            AAA_25 32 agelallaGapgtGKttlaldlalava.tGkpw 63
                                      ++ + +  G +g+GKtt+a++lal +a +Gk++
  gi|386003056|ref|YP_005921355.1| 10 KHRIMVMSGKGGVGKTTVAVNLALGLAlSGKEV 42
                                      67788999*******************888764 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.3e-05     0.014       2      36 ..      13      47 ..      12      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGC 36
                                       + + GkGG+Gk+t + nl+  la  gk v i+  
  gi|386003056|ref|YP_005921355.1| 13 IMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDA 47
                                      56788***********************9977655 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.3e-05     0.015       4      41 ..      13      50 ..      11      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                      i + s kGG Gktt  + l   la  gk v++++ad  
  gi|386003056|ref|YP_005921355.1| 13 IMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADIT 50
                                      567899*****************************965 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00013      0.14       5      39 ..      15      48 ..      11     168 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                          CBP_BcsQ  5 alqGvRGGvGttsllaaLawalhelgesvlviDls 39
                                      +++G +GGvG+t++++ La  l   g++v ++D+ 
  gi|386003056|ref|YP_005921355.1| 15 VMSG-KGGVGKTTVAVNLALGLALSGKEVGILDAD 48
                                      5555.8**********9999999999999888863 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4     3e-05     0.034      91     121 ..       3      33 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                       HHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinallp 121
                                       e+l++ +k++++v+ G+ GvGK+t+  +l+ 
  gi|386003056|ref|YP_005921355.1|   3 ESLADTIKHRIMVMSGKGGVGKTTVAVNLAL 33 
                                       68999*******************9877765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   3.3e-05     0.037       3      39 ..      13      49 ..      11      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      ++++ G  G+GKTt +  La  l  +gk+v +  aD+
  gi|386003056|ref|YP_005921355.1| 13 IMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADI 49
                                      78999***************************99997 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.6e-05     0.063       4      40 ..      13      49 ..      10      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      ++ ++G  g GK+t+a++l+  L  +g++v +Ld d 
  gi|386003056|ref|YP_005921355.1| 13 IMVMSGKGGVGKTTVAVNLALGLALSGKEVGILDADI 49
                                      67899*****************************985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   6.5e-05     0.072      16      39 ..       7      30 ..       1      34 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                                      TTSCSEEEEEEESTTSSHHHHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlakq 39
                                      d ++  ++ ++G+gGvGKtt+a +
  gi|386003056|ref|YP_005921355.1|  7 DTIKHRIMVMSGKGGVGKTTVAVN 30
                                      567778**************9865 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.4e-05      0.11      17      46 ..       9      38 ..       2      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.4e-05
                                      HH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 17 kkndivfaiGpaGtGKtylavalavealkk 46
                                       k+ i+++ G+ G GKt +av la+ +  +
  gi|386003056|ref|YP_005921355.1|  9 IKHRIMVMSGKGGVGKTTVAVNLALGLALS 38
                                      4899********************987665 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.26       1      33 [.      18      50 ..      18      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                      G+  +GK+T+a +L+  ++ +g+++ ++D+D+ 
  gi|386003056|ref|YP_005921355.1| 18 GKGGVGKTTVAVNLALGLALSGKEVGILDADIT 50
                                      66789**************************96 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   0.00054      0.61       1      27 [.      12      38 ..      12      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaeg 27
                                      r++++ G+ G+GKTt +  lal +a +
  gi|386003056|ref|YP_005921355.1| 12 RIMVMSGKGGVGKTTVAVNLALGLALS 38
                                      6799*****************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1617.91
//
Query:       gi|386003057|ref|YP_005921356.1|  [L=83]
Description: hypothetical protein Mhar_2383 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 531.88
//
Query:       gi|386003058|ref|YP_005921357.1|  [L=365]
Description: Transporter, small conductance mechanosensitive ion channel (MscS) family [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-43  146.6   0.1    9.7e-43  146.1   0.1    1.2  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
          5    7.2   9.3      0.087   12.8   1.4    2.2  2  TM_helix    Conserved TM helix


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1   0.1   1.1e-46   9.7e-43       5     206 .]     133     332 ..     129     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 1.1e-46
                                       HHHHHHHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                        MS_channel   5 kiliivvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                          i++vg ++v+ ++ v      +lla++G++gla+g+a+kd++sn+++Gi+l + +pf++GD+v++++   +Ved
  gi|386003058|ref|YP_005921357.1| 133 VAAIYIVGSILVIYQIPVLsrvAVTLLAGAGVAGLAIGFAAKDSLSNIISGIFLAVFHPFRVGDYVDFEGEYCQVED 209
                                       5667888888888888877665779**************************************************** PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS- CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdke 155
                                       ++lr t+i+t+dgr +++Pns + +  i+N+s  ++  + +v++g+ y++d   +++++e++ +a+k++p vlkd +
  gi|386003058|ref|YP_005921357.1| 210 LTLRHTTIKTWDGRRIFVPNSIMGNMPIVNWSIVDPIISWRVDFGIGYTAD---IDRAREIIIDAAKRHPLVLKDRD 283
                                       ***************************************************...*********************** PP

                                       EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 156 llvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                        +v+++++gd ++n+++ + +++   +  + +  ei++ +k+ +++egiei
  gi|386003058|ref|YP_005921357.1| 284 ITVMVTDLGDFAVNLRLSMELPK--RDVAFTTGCEIREAVKRRFDAEGIEI 332
                                       *********************99..89**********************97 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.4   9.7e-06     0.087       9      39 ..      72     102 ..      67     110 .. 0.90
   2 ?   -3.9   1.4       1.6   1.5e+04      21      29 ..     134     142 ..     130     145 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-06
                                       HHHTTHSHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix   9 ellsflPnLvgAilILlvGwiiAkfvsrlvt 39 
                                       ++ls l+ L+  ++IL++ w+ A++v r++t
  gi|386003058|ref|YP_005921357.1|  72 DVLSLLGTLLTILAILVLTWLAARVVDRALT 102
                                       6899**********************99876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.6
                                       HHHHHHHHH CS
                          TM_helix  21 ilILlvGwi 29 
                                       ++I +vG i
  gi|386003058|ref|YP_005921357.1| 134 AAIYIVGSI 142
                                       344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2707.38
//
Query:       gi|386003059|ref|YP_005921358.1|  [L=196]
Description: hypothetical protein Mhar_2385 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-60  202.6   0.0    3.8e-60  202.4   0.0    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.4   0.0   2.1e-64   3.8e-60       2     182 ..       9     184 ..       8     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 2.1e-64
                                       GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETT CS
                             DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiag 78 
                                       ++rvlG+++sf++    + +s+l+Gvvmr+d ++dg+ ++++tv+G+Date ++e+++ l r+d++++ll+G ++++
  gi|386003059|ref|YP_005921358.1|   9 GVRVLGVAESFLK---AEPRSALAGVVMRRDLRIDGFGLAEITVGGDDATEGVLEIIEGLGRRDLNLLLLNGSVVSW 82 
                                       79*********77...489********************************************************** PP

                                       TEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHH CS
                             DUF99  79 FNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleea 155
                                       FNv+Dl+ lh+et+lPvi++t++e++ g +e ++r +f+d+ee+++++++lg+r++++ ktg+e+y r+ G+++ee+
  gi|386003059|ref|YP_005921358.1|  83 FNVLDLDLLHQETDLPVISLTYQESE-G-IEGYIRGYFSDPEEKIARYRRLGPRRAVRLKTGYEVYARSLGATAEET 157
                                       **************************.8.************************************************ PP

                                       HHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 156 aklvrkltlegriPEPlRvAhliAsal 182
                                         l++++tlegr+PEPlRvA+l+A+ l
  gi|386003059|ref|YP_005921358.1| 158 TGLLNSFTLEGRVPEPLRVARLLARRL 184
                                       ************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1298.24
//
Query:       gi|386003060|ref|YP_005921359.1|  [L=221]
Description: hypothetical protein Mhar_2386 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1584.35
//
Query:       gi|386003061|ref|YP_005921360.1|  [L=217]
Description: hypothetical protein Mhar_2387 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1469.99
//
Query:       gi|386003062|ref|YP_005921361.1|  [L=159]
Description: hypothetical protein Mhar_2388 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0091   15.1   0.0      0.012   14.7   0.0    1.2  1  S-layer   S-layer protein


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 !   14.7   0.0   6.5e-07     0.012     110     169 ..      21      77 ..       8     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.5e-07
                           S-layer 110 eektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyvyek 169
                                        e  +++ +s++ +e+ ++ + +++     vwleL+ dg  + s+++++    +++ y++
  gi|386003062|ref|YP_005921361.1|  21 AEVLMSTRESITFAENLTVVVMDLEPRTGVVWLELQEDGVPLKSSILRT---GESFDYDE 77 
                                       56778899999999*99999998999999********************...77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1011.03
//
Query:       gi|386003063|ref|YP_005921362.1|  [L=191]
Description: Sirohydrochlorin cobaltochelatase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-25   88.0   0.0    5.9e-25   87.7   0.0    1.1  1  CbiX            CbiX
    0.00034   20.0   0.0    0.00038   19.9   0.0    1.0  1  CbiK            Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
       0.24   10.4   0.0       0.28   10.2   0.0    1.1  1  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   9.9e-29   5.9e-25       1     105 [.      72     182 ..      72     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 9.9e-29
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       HGS +p+ +e vek a+++   ++  pv+++fl++ ep++  +l++++  gvkriv++P+fl++Gvh+ eDIp el 
  gi|386003063|ref|YP_005921362.1|  72 HGSTKPYNKEMVEKCAKMIGDLHE-GPVRIAFLNMDEPNIAAGLESFSGTGVKRIVALPIFLAHGVHTLEDIPTELS 147
                                       *********************999.**************************************************** PP

                                       --SSSS-.......TTEEEEE---CCCSCCHHHHH CS
                              CbiX  78 eaeeahp.......kdveieytepLGthplvaevl 105
                                        ++++          +vei+++epLG ++++a++ 
  gi|386003063|ref|YP_005921362.1| 148 VDPTHRRgkcqlngTEVEIRCAEPLGVDESIAALA 182
                                       988888889999999****************9875 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.4e-08   0.00038     141     255 ..      64     184 ..      49     191 .] 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.4e-08
                                       TEEEEEEE---SCHHHH.HHHHHHHHHHHCT-S.EEEEETTS.SS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHC CS
                              CbiK 141 dealvfvgHGtehesna.vyaeldkvlkekdfkqvvvgtveg.yPeveevieelkkkgikevkliPlmlvAGdHakn 215
                                       d  ++ +gHG++ + n+ + ++  k++ + +   v ++ ++   P++   +e+  ++g+k++  +P++l  G H  +
  gi|386003063|ref|YP_005921362.1|  64 DVGILVLGHGSTKPYNKeMVEKCAKMIGDLHEGPVRIAFLNMdEPNIAAGLESFSGTGVKRIVALPIFLAHGVHTLE 140
                                       4557789****99877516788999****87889****998627********************************* PP

                                       CCCSS...STTSHHHHHHHTT--EEE-.---GGGSHHHHHHHHH CS
                              CbiK 216 Dmasd...eedswkealeaaGikveii.lkgLGeieeirsifik 255
                                       D+ ++   +    + + + +G +vei+  + LG +e+i+++   
  gi|386003063|ref|YP_005921362.1| 141 DIPTElsvDPTHRRGKCQLNGTEVEIRcAEPLGVDESIAALAYR 184
                                       **875333556677889999****99625789999999887555 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   4.6e-05      0.28      64     130 ..      75     138 ..      28     159 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.6e-05
                                       S-SHHHHHHHHHHHHHHHHHHH---EEEEEEESSS.SSBHHHHHHHHHCTT-SEEEEEES-SS--TTT CS
                    Ferrochelatase  64 gSPlneitrkqaealekelaergidvkvylamryw.ePsiedaleelkadgvervvvlplyPqysast 130
                                         P n+   + ++++  +l+    + +v +a+ ++ eP i+  le +  +gv+r+v+lp +  ++  t
  gi|386003063|ref|YP_005921362.1|  75 TKPYNKEMVEKCAKMIGDLH----EGPVRIAFLNMdEPNIAAGLESFSGTGVKRIVALPIFLAHGVHT 138
                                       44444444444444444444....56788887654268888888888888888888888765555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 1233.86
//
Query:       gi|386003064|ref|YP_005921363.1|  [L=406]
Description: Mur ligase, middle domain protein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00012   22.1   0.4    0.00029   20.9   0.2    1.7  2  Mur_ligase_M  Mur ligase middle domain
  ------ inclusion threshold ------
      0.082   13.0   0.8       0.15   12.1   0.8    1.4  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.65   5.9e+03      39      56 ..      12      29 ..       7      39 .. 0.82
   2 !   20.9   0.2   3.2e-08   0.00029       1      61 [.      87     164 ..      87     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.65
                                      HHHHHHHHTT-SEEEEE- CS
                      Mur_ligase_M 39 ktlaemekkeaeyavlEv 56
                                      ++ ++m+  ++e+a+lEv
  gi|386003064|ref|YP_005921363.1| 12 LLAERMRGRGIEAAALEV 29
                                      6778999999******98 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.2e-08
                                       EESSS-HHHHHHHHHHHHHCT..EEEEETTC..................SS-THHHHHHHHHHHHHTT-SEEEEE-- CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg..................ttnneiglpktlaemekkeaeyavlEvs 57 
                                       vTGt GKTTt+ ++a+il++   +  ++t g                  t   + ++ ++ + +++ +a+ +v Evs
  gi|386003064|ref|YP_005921363.1|  87 VTGTVGKTTTALILARILSARgtVLSHTTRGievwrdgrsrllrsklsiT---PANVILAWEAAAEVGADDLVSEVS 160
                                       9********************43334445558888888777777765332...555555555666666677777776 PP

                                       HCHH CS
                      Mur_ligase_M  58 shgl 61 
                                         g 
  gi|386003064|ref|YP_005921363.1| 161 LGGT 164
                                       6555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   1.7e-05      0.15       7      27 ..      88     108 ..      86     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                       STTSSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   7 kGGvGKTtlaanLaralarrg 27 
                                       +G vGKTt+a+ Lar+l+ rg
  gi|386003064|ref|YP_005921363.1|  88 TGTVGKTTTALILARILSARG 108
                                       688***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 2189.20
//
Query:       gi|386003065|ref|YP_005921364.1|  [L=367]
Description: Putative methanogenesis marker 13 metalloprotein [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-20   72.2   0.5    8.1e-20   70.9   0.5    1.6  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.073   12.8   0.3       0.19   11.5   0.3    1.8  1  SHOCT           Short C-terminal domain


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.5     9e-24   8.1e-20      17     151 ..      30     204 ..      16     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 9e-24
                                       EEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSEEEEEE-HHHHHTTTTH CS
                    Oxidored_nitro  17 lplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpkaIgVittClteliGdDi 93 
                                       ++++hGp GC++ + +ll       +  ++t+l+e   vfGg+e+L + ++ + + ++pk+IgV+ tC++ +iG+D+
  gi|386003065|ref|YP_005921364.1|  30 VVIMHGPSGCCFKHARLLEEDG---VRTLTTALDEAGFVFGGQEQLTRLLRRATELFDPKLIGVVGTCSSMIIGEDL 103
                                       78*********99999996554...48************************************************** PP

                                       HHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT................................ CS
                    Oxidored_nitro  94 eavareaeeelgeipvipvstpgfggsqseGydaalealvrklvg................................ 138
                                       ++ +  a+ +    pv+ v++     + ++G  ++lea ++k +                                 
  gi|386003065|ref|YP_005921364.1| 104 HQAVVDADVDV---PVLEVEVHAGYRDNTKGVIITLEAALEKGIIdrveferqrfllkkateverlhgaasseylap 177
                                       ***99999876...9*************************9977667777777777777666666666666666666 PP

                                       ..............-TT---SSEEEEE CS
                    Oxidored_nitro 139 ..............kkgekeprkvnil 151
                                                     +  ++ +r +n+l
  gi|386003065|ref|YP_005921364.1| 178 ergdlkyraaerllDLIKEGKRGINVL 204
                                       666666666666664444555555555 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   2.2e-05      0.19       5      24 ..     135     154 ..     133     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                             SHOCT   5 kLkeLyarGeIteEEFeakK 24 
                                       +L + +++G+I++ EFe+++
  gi|386003065|ref|YP_005921364.1| 135 TLEAALEKGIIDRVEFERQR 154
                                       58899*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2400.23
//
Query:       gi|386003066|ref|YP_005921365.1|  [L=88]
Description: Protein translocase subunit secE/sec61 gamma [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-06   26.9   0.0    4.7e-06   26.4   0.0    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.6e-10   4.7e-06       5      47 ..      39      81 ..      38      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-10
                                      HHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  5 kevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvf 47
                                      k+ ++ lk   +Ptr+E+l ++++ +++++++g ++f++ +++
  gi|386003066|ref|YP_005921365.1| 39 KDYIRVLKLARKPTREEFLMISKISILGIALIGMLGFIIYVFL 81
                                      8999**********************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 510.86
//
Query:       gi|386003067|ref|YP_005921366.1|  [L=552]
Description: Na+/Pi-cotransporter [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-54  184.3  27.3    3.9e-38  130.7   6.8    2.3  2  Na_Pi_cotrans    Na+/Pi-cotransporter


Domain annotation for each model (and alignments):
>> Na_Pi_cotrans  Na+/Pi-cotransporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   6.8   2.2e-42   3.9e-38       1     138 [.      15     148 ..      15     149 .. 0.98
   2 !   59.7  13.5   1.8e-20   3.2e-16       8     109 ..     146     252 ..     145     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 2.2e-42
                     Na_Pi_cotrans   1 LfLfGmkllsegleklageklkkilekltsnrlkgvlvGllvTallqSSsattvmvvglvnaglltlkqaigvilGa 77 
                                       LfL+G++  se+++++age++ ++l+++t+++l+g+++G++v+a++qSS+attv++vglvnag++++  +ig+++Ga
  gi|386003067|ref|YP_005921366.1|  15 LFLYGIERFSEEVRHAAGERFWTLLQNATRTPLRGAVAGAGVSAITQSSTATTVIAVGLVNAGAISFLGSIGLVIGA 91 
                                       8**************************************************************************** PP

                     Na_Pi_cotrans  78 niGttvtaqllslalklsslalllllvgvllllfskkkklkklgeillglgllflglelms 138
                                       niGtt+taql+  a+kl+++a+l+++ g+ll l+    +++ +g+ ++ +gl+f++l+++s
  gi|386003067|ref|YP_005921366.1|  92 NIGTTITAQLV--AFKLTAFAPLFVVGGFLLSLIR--GRYRVFGKPIFYFGLVFFCLNMIS 148
                                       ***********..****************999985..59*******************997 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.8e-20
                     Na_Pi_cotrans   8 llsegleklageklkkilekltsnrlkgvlvGllvTallqSSsattvmvvglvnaglltlkqaigvilGaniGttvt 84 
                                       ++s ++  l g+    +l ++ +n l+g+++G+++T ++qSSs+t+ +vv ++++gllt ++ai++ilGaniGtt+t
  gi|386003067|ref|YP_005921366.1| 146 MISAEIAPLQGDPEIIALLSMAENVLIGIAIGFVITNIFQSSSVTAGLVVVMAQSGLLTPAEAIPIILGANIGTTTT 222
                                       56667777777777777889999****************************************************** PP

                     Na_Pi_cotrans  85 aqllsl.....alklsslalllllvgvlll 109
                                        +++++     a ++++  +l+ l+gvll+
  gi|386003067|ref|YP_005921366.1| 223 GLVVAIrmnaaAKRTAAAQFLFNLLGVLLV 252
                                       ****98888863344444455555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 3083.39
//
Query:       gi|386003068|ref|YP_005921367.1|  [L=325]
Description: Isopropylmalate/isohomocitrate dehydrogenase [Methanosaeta harundinacea 6Ac]
Scores for complete 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-90  303.9   0.0      8e-90  301.5   0.0    1.8  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.5   0.0   4.5e-94     8e-90       2     348 .]      10     319 ..       9     319 .. 0.97

  Alignments for each domain:
  == domain 1  score: 301.5 bits;  conditional E-value: 4.5e-94
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkeke 78 
                                       +al++gdg+Gpev++ al+vl+aa     ++le+  v++G    ++tg ++ +e le ik  + vl+ga++tp + e
  gi|386003068|ref|YP_005921367.1|  10 VALVKGDGVGPEVIDGALSVLEAAG----ADLELVPVELGYGRWKRTGAAMADEDLELIKTCHCVLFGAITTPPDPE 82 
                                       899********************99....5689999**************************************999 PP

                                       SSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEE CS
                            Iso_dh  79 vrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtk 155
                                        r+    laLrk ldl+an+rp                   ++d+vivRe+t+g+Y+g ek +++      +a ++ 
  gi|386003068|ref|YP_005921367.1|  83 YRSVL--LALRKGLDLYANIRPFSAP---------------GLDFVIVRENTEGMYSGVEKLDEE------EATTLR 136
                                       99976..9**************8665...............68******************9998......599*** PP

                                       EEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHHHHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGG CS
                            Iso_dh 156 lyseeeieriaraafelAlkrgkkkvtlvdKanvlksselwrkiveevaeeeypdielehqlvDsaamqlvkspkqf 232
                                       +++ +++ ria+ a+++A kr   ++t+v+K+nvlks  l+ +i+ e+a+    d+ ++++lvD+a ++lv +pk+f
  gi|386003068|ref|YP_005921367.1| 137 VITSRGSLRIAERACAIASKR--GRLTIVHKSNVLKSDTLFLRICRETAR--RWDLPFDDMLVDAAGYNLVMNPKRF 209
                                       ******************999..99************************9..89*********************** PP

                                       SEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HH CS
                            Iso_dh 233 dVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslglee 309
                                       dVivt+NlfGDilSD+aa +vG+lGl pSa+lg ++ a+fE++HGsapdiag+++aNpi++i Saa+mL+  +g+ e
  gi|386003068|ref|YP_005921367.1| 210 DVIVTTNLFGDILSDVAAGVVGGLGLCPSANLG-DRYALFEPIHGSAPDIAGRGIANPIGAIRSAAMMLEW-FGEAE 284
                                       *********************************.79***********************************.***** PP

                                       HHHHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 310 aAdkiekAvekvleagivTkDlageaakevstsefgdav 348
                                       +A++ie+Av  ++++gi T Dl+g +    st+e+++av
  gi|386003068|ref|YP_005921367.1| 285 KARMIEEAVGWAVASGIATPDLGGCS----STEEVTEAV 319
                                       *************************9....9****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1986.88
//
Query:       gi|386003069|ref|YP_005921368.1|  [L=275]
Description: hypothetical protein Mhar_2396 [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1759.89
//
Query:       gi|386003070|ref|YP_005921369.1|  [L=160]
Description: 3-isopropylmalate dehydratase small subunit [Methanosaeta harundinacea 6Ac]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-20   73.0   0.0    3.7e-20   72.6   0.0    1.2  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.036   13.6   0.1      0.052   13.1   0.1    1.2  1  IlvN         Acetohydroxy acid isomeroreductase, NADPH-bindin


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   4.1e-24   3.7e-20      64     123 ..      41      99 ..      17     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 4.1e-24
                                       HHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                       Aconitase_C  64 daaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                       d ++  ++ + +++v++ knfG+GSSRe+A++alr  G+  v+a+SF+rIf++n+i+ gl
  gi|386003070|ref|YP_005921369.1|  41 DPEFAKQVRPGDVIVAG-KNFGCGSSREQAPLALREAGVACVVAKSFARIFYRNAINVGL 99 
                                       55555666677777776.***************************************997 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.8e-06     0.052      11      66 ..      61     116 ..      54     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-06
                                       S-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE CS
                              IlvN  11 GyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmi 66 
                                       G+Gs  +   l lr++g+  vv+    +  +++A + g+ v+++a ++++ +vv +
  gi|386003070|ref|YP_005921369.1|  61 GCGSSREQAPLALREAGVACVVAKSFARIFYRNAINVGLPVVEAAVVARQGEVVEV 116
                                       9****99999******************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1032.38
//
[ok]
